digestion

sbol_utilities/helper_functions.py

@@ -363,4 +363,11 @@ def is_circular(obj: Union[sbol3.Component, sbol3.LocalSubComponent, sbol3.Exter
     :param obj: design to be checked
     :return: true if circular
     """    
-    return any(n==sbol3.SO_CIRCULAR for n in obj.types)
+    return any(n==sbol3.SO_CIRCULAR for n in obj.types)
+
+def is_linear(obj: Union[sbol3.Component, sbol3.LocalSubComponent, sbol3.ExternallyDefined]) -> bool:
+    """Check if an SBOL Component or Feature is linear.
+    :param obj: design to be checked
+    :return: true if linear
+    """    
+    return any(n==sbol3.SO_LINEAR for n in obj.types)    

setup.py

@@ -42,7 +42,8 @@
             'tyto>=1.4',
             'openpyxl',
             'requests',
-            'sbol_factory>=1.1'
+            'sbol_factory>=1.1',
+            'pydna'
             ],
       extras_require={  # requirements for development
           'dev': ['pytest', 'interrogate']

test/test_files/ab_j23100.gb

@@ -0,0 +1,80 @@
+LOCUS       AB_J23100               2095 bp ds-DNA     linear       25-OCT-2023
+DEFINITION  .
+FEATURES             Location/Qualifiers
+     misc_feature    346..365
+                     /label="VF Primer binding site"
+                     /ApEinfo_revcolor="#b7e6d7"
+                     /ApEinfo_fwdcolor="#b7e6d7"
+     misc_feature    complement(422..466)
+                     /label="Terminator"
+                     /ApEinfo_revcolor="#c7b0e3"
+                     /ApEinfo_fwdcolor="#c7b0e3"
+     BioBrick        468..473
+                     /label="BsaI Site"
+                     /ApEinfo_revcolor="#f58a5e"
+                     /ApEinfo_fwdcolor="#f58a5e"
+     misc_feature    475..478
+                     /label="A"
+                     /ApEinfo_revcolor="#ff9ccd"
+                     /ApEinfo_fwdcolor="#ff9ccd"
+     misc_feature    479..513
+                     /label="J23100"
+                     /ApEinfo_revcolor="#b1ff67"
+                     /ApEinfo_fwdcolor="#b1ff67"
+     misc_feature    514..517
+                     /label="B"
+                     /ApEinfo_revcolor="#f8d3a9"
+                     /ApEinfo_fwdcolor="#f8d3a9"
+     misc_feature    531..602
+                     /label="His Terminator"
+                     /ApEinfo_revcolor="#ffef86"
+                     /ApEinfo_fwdcolor="#ffef86"
+     misc_feature    complement(666..685)
+                     /label="VR Primer binding site"
+                     /ApEinfo_revcolor="#b1ff67"
+                     /ApEinfo_fwdcolor="#b1ff67"
+     misc_feature    complement(770..1384)
+                     /label="rep (pMB1)"
+                     /ApEinfo_revcolor="#85dae9"
+                     /ApEinfo_fwdcolor="#85dae9"
+     misc_feature    complement(1551..1656)
+                     /label="Terminator T0"
+                     /ApEinfo_revcolor="#c6c9d1"
+                     /ApEinfo_fwdcolor="#c6c9d1"
+ORIGIN
+        1 tcattgccat acgaaattcc ggatgagcat tcatcaggcg ggcaagaatg tgaataaagg
+       61 ccggataaaa cttgtgctta tttttcttta cggtctttaa aaaggccgta atatccagct
+      121 gaacggtctg gttataggta cattgagcaa ctgactgaaa tgcctcaaaa tgttctttac
+      181 gatgccattg ggatatatca acggtggtat atccagtgat ttttttctcc attttagctt
+      241 ccttagctcc tgaaaatctc gataactcaa aaaatacgcc cggtagtgat cttatttcat
+      301 tatggtgaaa gttggaacct cttacgtgcc cgatcaactc gagtgccacc tgacgtctaa
+      361 gaaaccatta ttatcatgac attaacctat aaaaataggc gtatcacgag gcagaatttc
+      421 agataaaaaa aatccttagc tttcgctaag gatgatttct ggaattcggt ctcgGGAGtt
+      481 gacggctagc tcagtcctag gtacagtgct agcTACTCGA Gaccctgcag tccggcaaaa
+      541 aagggcaagg tgtcaccacc ctgccctttt tctttaaaac cgaaaagatt acttcgcgtt
+      601 atgcaggctt cctcgctcac tgactcgctg cgctcggtcg ttcggctgcg gcgagcggta
+      661 tcagctcact caaaggcggt aatacggtta tccacagaat caggggataa cgcaggaaag
+      721 aacatgtgag caaaaggcca gcaaaaggcc aggaaccgta aaaaggccgc gttgctggcg
+      781 tttttccaca ggctccgccc ccctgacgag catcacaaaa atcgacgctc aagtcagagg
+      841 tggcgaaacc cgacaggact ataaagatac caggcgtttc cccctggaag ctccctcgtg
+      901 cgctctcctg ttccgaccct gccgcttacc ggatacctgt ccgcctttct cccttcggga
+      961 agcgtggcgc tttctcatag ctcacgctgt aggtatctca gttcggtgta ggtcgttcgc
+     1021 tccaagctgg gctgtgtgca cgaacccccc gttcagcccg accgctgcgc cttatccggt
+     1081 aactatcgtc ttgagtccaa cccggtaaga cacgacttat cgccactggc agcagccact
+     1141 ggtaacagga ttagcagagc gaggtatgta ggcggtgcta cagagttctt gaagtggtgg
+     1201 cctaactacg gctacactag aagaacagta tttggtatct gcgctctgct gaagccagtt
+     1261 accttcggaa aaagagttgg tagctcttga tccggcaaac aaaccaccgc tggtagcggt
+     1321 ggtttttttg tttgcaagca gcagattacg cgcagaaaaa aaggatctca agaagatcct
+     1381 ttgatctttt ctacggggtc tgacgctcag tggaacgaaa actcacgtta agggattttg
+     1441 gtcatgagat tatcaaaaag gatcttcacc tagatccttt taaattaaaa atgaagtttt
+     1501 aaatcaatct aaagtatata tgagtaaact tggtctgaca gctcgaggct tggattctca
+     1561 ccaataaaaa acgcccggcg gcaaccgagc gttctgaaca aatccagatg gagttctgag
+     1621 gtcattactg gatctatcaa caggagtcca agcgagctcg atatcaaatt acgccccgcc
+     1681 ctgccactca tcgcagtact gttgtaattc attaagcatt ctgccgacat ggaagccatc
+     1741 acaaacggca tgatgaacct gaatcgccag cggcatcagc accttgtcgc cttgcgtata
+     1801 atatttgccc atggtgaaaa cgggggcgaa gaagttgtcc atattggcca cgtttaaatc
+     1861 aaaactggtg aaactcaccc agggattggc tgagacgaaa aacatattct caataaaccc
+     1921 tttagggaaa taggccaggt tttcaccgta acacgccaca tcttgcgaat atatgtgtag
+     1981 aaactgccgg aaatcgtcgt ggtattcact ccagagcgat gaaaacgttt cagtttgctc
+     2041 atggaaaacg gtgtaacaag ggtgaacact atcccatatc accagctcac cgtct
+//

test/test_files/ab_j23101.gb

@@ -0,0 +1,81 @@
+LOCUS       AB_J23101               2095 bp ds-DNA     circular     25-OCT-2023
+DEFINITION  .
+COMMENT     From pSB1C00 - Loop universal L0 acceptor and J23100_B0034_AC
+FEATURES             Location/Qualifiers
+     misc_feature    346..365
+                     /label="VF Primer binding site"
+                     /ApEinfo_revcolor="#b7e6d7"
+                     /ApEinfo_fwdcolor="#b7e6d7"
+     misc_feature    complement(422..466)
+                     /label="Terminator"
+                     /ApEinfo_revcolor="#c7b0e3"
+                     /ApEinfo_fwdcolor="#c7b0e3"
+     BioBrick        468..473
+                     /label="BsaI Site"
+                     /ApEinfo_revcolor="#f58a5e"
+                     /ApEinfo_fwdcolor="#f58a5e"
+     misc_feature    475..478
+                     /label="A"
+                     /ApEinfo_revcolor="#ff9ccd"
+                     /ApEinfo_fwdcolor="#ff9ccd"
+     misc_feature    479..513
+                     /label="J23101"
+                     /ApEinfo_revcolor="#b1ff67"
+                     /ApEinfo_fwdcolor="#b1ff67"
+     misc_feature    514..517
+                     /label="B"
+                     /ApEinfo_revcolor="#f8d3a9"
+                     /ApEinfo_fwdcolor="#f8d3a9"
+     misc_feature    531..602
+                     /label="His Terminator"
+                     /ApEinfo_revcolor="#ffef86"
+                     /ApEinfo_fwdcolor="#ffef86"
+     misc_feature    complement(666..685)
+                     /label="VR Primer binding site"
+                     /ApEinfo_revcolor="#b1ff67"
+                     /ApEinfo_fwdcolor="#b1ff67"
+     misc_feature    complement(770..1384)
+                     /label="rep (pMB1)"
+                     /ApEinfo_revcolor="#85dae9"
+                     /ApEinfo_fwdcolor="#85dae9"
+     misc_feature    complement(1551..1656)
+                     /label="Terminator T0"
+                     /ApEinfo_revcolor="#c6c9d1"
+                     /ApEinfo_fwdcolor="#c6c9d1"
+ORIGIN
+        1 tcattgccat acgaaattcc ggatgagcat tcatcaggcg ggcaagaatg tgaataaagg
+       61 ccggataaaa cttgtgctta tttttcttta cggtctttaa aaaggccgta atatccagct
+      121 gaacggtctg gttataggta cattgagcaa ctgactgaaa tgcctcaaaa tgttctttac
+      181 gatgccattg ggatatatca acggtggtat atccagtgat ttttttctcc attttagctt
+      241 ccttagctcc tgaaaatctc gataactcaa aaaatacgcc cggtagtgat cttatttcat
+      301 tatggtgaaa gttggaacct cttacgtgcc cgatcaactc gagtgccacc tgacgtctaa
+      361 gaaaccatta ttatcatgac attaacctat aaaaataggc gtatcacgag gcagaatttc
+      421 agataaaaaa aatccttagc tttcgctaag gatgatttct ggaattcggt ctcgGGAGtt
+      481 tacagctagc tcagtcctag gtattatgct agcTACTCGA Gaccctgcag tccggcaaaa
+      541 aagggcaagg tgtcaccacc ctgccctttt tctttaaaac cgaaaagatt acttcgcgtt
+      601 atgcaggctt cctcgctcac tgactcgctg cgctcggtcg ttcggctgcg gcgagcggta
+      661 tcagctcact caaaggcggt aatacggtta tccacagaat caggggataa cgcaggaaag
+      721 aacatgtgag caaaaggcca gcaaaaggcc aggaaccgta aaaaggccgc gttgctggcg
+      781 tttttccaca ggctccgccc ccctgacgag catcacaaaa atcgacgctc aagtcagagg
+      841 tggcgaaacc cgacaggact ataaagatac caggcgtttc cccctggaag ctccctcgtg
+      901 cgctctcctg ttccgaccct gccgcttacc ggatacctgt ccgcctttct cccttcggga
+      961 agcgtggcgc tttctcatag ctcacgctgt aggtatctca gttcggtgta ggtcgttcgc
+     1021 tccaagctgg gctgtgtgca cgaacccccc gttcagcccg accgctgcgc cttatccggt
+     1081 aactatcgtc ttgagtccaa cccggtaaga cacgacttat cgccactggc agcagccact
+     1141 ggtaacagga ttagcagagc gaggtatgta ggcggtgcta cagagttctt gaagtggtgg
+     1201 cctaactacg gctacactag aagaacagta tttggtatct gcgctctgct gaagccagtt
+     1261 accttcggaa aaagagttgg tagctcttga tccggcaaac aaaccaccgc tggtagcggt
+     1321 ggtttttttg tttgcaagca gcagattacg cgcagaaaaa aaggatctca agaagatcct
+     1381 ttgatctttt ctacggggtc tgacgctcag tggaacgaaa actcacgtta agggattttg
+     1441 gtcatgagat tatcaaaaag gatcttcacc tagatccttt taaattaaaa atgaagtttt
+     1501 aaatcaatct aaagtatata tgagtaaact tggtctgaca gctcgaggct tggattctca
+     1561 ccaataaaaa acgcccggcg gcaaccgagc gttctgaaca aatccagatg gagttctgag
+     1621 gtcattactg gatctatcaa caggagtcca agcgagctcg atatcaaatt acgccccgcc
+     1681 ctgccactca tcgcagtact gttgtaattc attaagcatt ctgccgacat ggaagccatc
+     1741 acaaacggca tgatgaacct gaatcgccag cggcatcagc accttgtcgc cttgcgtata
+     1801 atatttgccc atggtgaaaa cgggggcgaa gaagttgtcc atattggcca cgtttaaatc
+     1861 aaaactggtg aaactcaccc agggattggc tgagacgaaa aacatattct caataaaccc
+     1921 tttagggaaa taggccaggt tttcaccgta acacgccaca tcttgcgaat atatgtgtag
+     1981 aaactgccgg aaatcgtcgt ggtattcact ccagagcgat gaaaacgttt cagtttgctc
+     2041 atggaaaacg gtgtaacaag ggtgaacact atcccatatc accagctcac cgtct
+//

test/test_files/b0015.gb

@@ -0,0 +1,87 @@
+LOCUS       Copy_of_B0015_EF:_pSB1C 2190 bp ds-DNA     circular     28-JAN-2023
+DEFINITION  .
+COMMENT     From pSB1C00 - Loop universal L0 acceptor and B0015_EF
+FEATURES             Location/Qualifiers
+     misc_feature    385..404
+                     /label="VF Primer binding site"
+                     /ApEinfo_revcolor="#b7e6d7"
+                     /ApEinfo_fwdcolor="#b7e6d7"
+     misc_feature    complement(461..505)
+                     /label="Terminator"
+                     /ApEinfo_revcolor="#c7b0e3"
+                     /ApEinfo_fwdcolor="#c7b0e3"
+     BioBrick        507..512
+                     /label="BsaI Site"
+                     /ApEinfo_revcolor="#f58a5e"
+                     /ApEinfo_fwdcolor="#f58a5e"
+     terminator      517..646
+                     /label="BBa-B0015 Terminator"
+                     /ApEinfo_revcolor="#ff9ccd"
+                     /ApEinfo_fwdcolor="#ff9ccd"
+     terminator      526..597
+                     /label="rrnB T1 terminator"
+                     /ApEinfo_revcolor="#c7b0e3"
+                     /ApEinfo_fwdcolor="#c7b0e3"
+     terminator      613..640
+                     /label="T7Te terminator"
+                     /ApEinfo_revcolor="#75c6a9"
+                     /ApEinfo_fwdcolor="#75c6a9"
+     misc_feature    664..735
+                     /label="His Terminator"
+                     /ApEinfo_revcolor="#ffef86"
+                     /ApEinfo_fwdcolor="#ffef86"
+     misc_feature    complement(799..818)
+                     /label="VR Primer binding site"
+                     /ApEinfo_revcolor="#b1ff67"
+                     /ApEinfo_fwdcolor="#b1ff67"
+     misc_feature    complement(903..1517)
+                     /label="rep (pMB1)"
+                     /ApEinfo_revcolor="#85dae9"
+                     /ApEinfo_fwdcolor="#85dae9"
+     misc_feature    complement(1684..1789)
+                     /label="Terminator T0"
+                     /ApEinfo_revcolor="#c6c9d1"
+                     /ApEinfo_fwdcolor="#c6c9d1"
+     CDS             complement(1802..271)
+                     /label="Cam Resistance"
+                     /ApEinfo_revcolor="#ff9ccd"
+                     /ApEinfo_fwdcolor="#ff9ccd"
+ORIGIN
+        1 aagggtgaac actatcccat atcaccagct caccgtcttt cattgccata cgaaattccg
+       61 gatgagcatt catcaggcgg gcaagaatgt gaataaaggc cggataaaac ttgtgcttat
+      121 ttttctttac ggtctttaaa aaggccgtaa tatccagctg aacggtctgg ttataggtac
+      181 attgagcaac tgactgaaat gcctcaaaat gttctttacg atgccattgg gatatatcaa
+      241 cggtggtata tccagtgatt tttttctcca ttttagcttc cttagctcct gaaaatctcg
+      301 ataactcaaa aaatacgccc ggtagtgatc ttatttcatt atggtgaaag ttggaacctc
+      361 ttacgtgccc gatcaactcg agtgccacct gacgtctaag aaaccattat tatcatgaca
+      421 ttaacctata aaaataggcg tatcacgagg cagaatttca gataaaaaaa atccttagct
+      481 ttcgctaagg atgatttctg gaattcggtc tcggcttcca ggcatcaaat aaaacgaaag
+      541 gctcagtcga aagactgggc ctttcgtttt atctgttgtt tgtcggtgaa cgctctctac
+      601 tagagtcaca ctggctcacc ttcgggtggg cctttctgcg tttatacgct CGAGaccctg
+      661 cagtccggca aaaaagggca aggtgtcacc accctgccct ttttctttaa aaccgaaaag
+      721 attacttcgc gttatgcagg cttcctcgct cactgactcg ctgcgctcgg tcgttcggct
+      781 gcggcgagcg gtatcagctc actcaaaggc ggtaatacgg ttatccacag aatcagggga
+      841 taacgcagga aagaacatgt gagcaaaagg ccagcaaaag gccaggaacc gtaaaaaggc
+      901 cgcgttgctg gcgtttttcc acaggctccg cccccctgac gagcatcaca aaaatcgacg
+      961 ctcaagtcag aggtggcgaa acccgacagg actataaaga taccaggcgt ttccccctgg
+     1021 aagctccctc gtgcgctctc ctgttccgac cctgccgctt accggatacc tgtccgcctt
+     1081 tctcccttcg ggaagcgtgg cgctttctca tagctcacgc tgtaggtatc tcagttcggt
+     1141 gtaggtcgtt cgctccaagc tgggctgtgt gcacgaaccc cccgttcagc ccgaccgctg
+     1201 cgccttatcc ggtaactatc gtcttgagtc caacccggta agacacgact tatcgccact
+     1261 ggcagcagcc actggtaaca ggattagcag agcgaggtat gtaggcggtg ctacagagtt
+     1321 cttgaagtgg tggcctaact acggctacac tagaagaaca gtatttggta tctgcgctct
+     1381 gctgaagcca gttaccttcg gaaaaagagt tggtagctct tgatccggca aacaaaccac
+     1441 cgctggtagc ggtggttttt ttgtttgcaa gcagcagatt acgcgcagaa aaaaaggatc
+     1501 tcaagaagat cctttgatct tttctacggg gtctgacgct cagtggaacg aaaactcacg
+     1561 ttaagggatt ttggtcatga gattatcaaa aaggatcttc acctagatcc ttttaaatta
+     1621 aaaatgaagt tttaaatcaa tctaaagtat atatgagtaa acttggtctg acagctcgag
+     1681 gcttggattc tcaccaataa aaaacgcccg gcggcaaccg agcgttctga acaaatccag
+     1741 atggagttct gaggtcatta ctggatctat caacaggagt ccaagcgagc tcgatatcaa
+     1801 attacgcccc gccctgccac tcatcgcagt actgttgtaa ttcattaagc attctgccga
+     1861 catggaagcc atcacaaacg gcatgatgaa cctgaatcgc cagcggcatc agcaccttgt
+     1921 cgccttgcgt ataatatttg cccatggtga aaacgggggc gaagaagttg tccatattgg
+     1981 ccacgtttaa atcaaaactg gtgaaactca cccagggatt ggctgagacg aaaaacatat
+     2041 tctcaataaa ccctttaggg aaataggcca ggttttcacc gtaacacgcc acatcttgcg
+     2101 aatatatgtg tagaaactgc cggaaatcgt cgtggtattc actccagagc gatgaaaacg
+     2161 tttcagtttg ctcatggaaa acggtgtaac
+//

test/test_files/bc_b0034.gb

@@ -0,0 +1,81 @@
+LOCUS       BC_B0034                2081 bp ds-DNA     circular     25-OCT-2023
+DEFINITION  .
+COMMENT     From pSB1C00 - Loop universal L0 acceptor and J23100_B0034_AC
+FEATURES             Location/Qualifiers
+     misc_feature    346..365
+                     /label="VF Primer binding site"
+                     /ApEinfo_revcolor="#b7e6d7"
+                     /ApEinfo_fwdcolor="#b7e6d7"
+     misc_feature    complement(422..466)
+                     /label="Terminator"
+                     /ApEinfo_revcolor="#c7b0e3"
+                     /ApEinfo_fwdcolor="#c7b0e3"
+     BioBrick        468..473
+                     /label="BsaI Site"
+                     /ApEinfo_revcolor="#f58a5e"
+                     /ApEinfo_fwdcolor="#f58a5e"
+     misc_feature    475..478
+                     /label="B"
+                     /ApEinfo_revcolor="#f8d3a9"
+                     /ApEinfo_fwdcolor="#f8d3a9"
+     misc_feature    479..499
+                     /label="B0034"
+                     /ApEinfo_revcolor="#f58a5e"
+                     /ApEinfo_fwdcolor="#f58a5e"
+     misc_feature    500..503
+                     /label="C"
+                     /ApEinfo_revcolor="#85dae9"
+                     /ApEinfo_fwdcolor="#85dae9"
+     misc_feature    517..588
+                     /label="His Terminator"
+                     /ApEinfo_revcolor="#ffef86"
+                     /ApEinfo_fwdcolor="#ffef86"
+     misc_feature    complement(652..671)
+                     /label="VR Primer binding site"
+                     /ApEinfo_revcolor="#b1ff67"
+                     /ApEinfo_fwdcolor="#b1ff67"
+     misc_feature    complement(756..1370)
+                     /label="rep (pMB1)"
+                     /ApEinfo_revcolor="#85dae9"
+                     /ApEinfo_fwdcolor="#85dae9"
+     misc_feature    complement(1537..1642)
+                     /label="Terminator T0"
+                     /ApEinfo_revcolor="#c6c9d1"
+                     /ApEinfo_fwdcolor="#c6c9d1"
+ORIGIN
+        1 tcattgccat acgaaattcc ggatgagcat tcatcaggcg ggcaagaatg tgaataaagg
+       61 ccggataaaa cttgtgctta tttttcttta cggtctttaa aaaggccgta atatccagct
+      121 gaacggtctg gttataggta cattgagcaa ctgactgaaa tgcctcaaaa tgttctttac
+      181 gatgccattg ggatatatca acggtggtat atccagtgat ttttttctcc attttagctt
+      241 ccttagctcc tgaaaatctc gataactcaa aaaatacgcc cggtagtgat cttatttcat
+      301 tatggtgaaa gttggaacct cttacgtgcc cgatcaactc gagtgccacc tgacgtctaa
+      361 gaaaccatta ttatcatgac attaacctat aaaaataggc gtatcacgag gcagaatttc
+      421 agataaaaaa aatccttagc tttcgctaag gatgatttct ggaattcggt ctcgTACTag
+      481 agaaagagga gaaatactaa atgCGAGacc ctgcagtccg gcaaaaaagg gcaaggtgtc
+      541 accaccctgc cctttttctt taaaaccgaa aagattactt cgcgttatgc aggcttcctc
+      601 gctcactgac tcgctgcgct cggtcgttcg gctgcggcga gcggtatcag ctcactcaaa
+      661 ggcggtaata cggttatcca cagaatcagg ggataacgca ggaaagaaca tgtgagcaaa
+      721 aggccagcaa aaggccagga accgtaaaaa ggccgcgttg ctggcgtttt tccacaggct
+      781 ccgcccccct gacgagcatc acaaaaatcg acgctcaagt cagaggtggc gaaacccgac
+      841 aggactataa agataccagg cgtttccccc tggaagctcc ctcgtgcgct ctcctgttcc
+      901 gaccctgccg cttaccggat acctgtccgc ctttctccct tcgggaagcg tggcgctttc
+      961 tcatagctca cgctgtaggt atctcagttc ggtgtaggtc gttcgctcca agctgggctg
+     1021 tgtgcacgaa ccccccgttc agcccgaccg ctgcgcctta tccggtaact atcgtcttga
+     1081 gtccaacccg gtaagacacg acttatcgcc actggcagca gccactggta acaggattag
+     1141 cagagcgagg tatgtaggcg gtgctacaga gttcttgaag tggtggccta actacggcta
+     1201 cactagaaga acagtatttg gtatctgcgc tctgctgaag ccagttacct tcggaaaaag
+     1261 agttggtagc tcttgatccg gcaaacaaac caccgctggt agcggtggtt tttttgtttg
+     1321 caagcagcag attacgcgca gaaaaaaagg atctcaagaa gatcctttga tcttttctac
+     1381 ggggtctgac gctcagtgga acgaaaactc acgttaaggg attttggtca tgagattatc
+     1441 aaaaaggatc ttcacctaga tccttttaaa ttaaaaatga agttttaaat caatctaaag
+     1501 tatatatgag taaacttggt ctgacagctc gaggcttgga ttctcaccaa taaaaaacgc
+     1561 ccggcggcaa ccgagcgttc tgaacaaatc cagatggagt tctgaggtca ttactggatc
+     1621 tatcaacagg agtccaagcg agctcgatat caaattacgc cccgccctgc cactcatcgc
+     1681 agtactgttg taattcatta agcattctgc cgacatggaa gccatcacaa acggcatgat
+     1741 gaacctgaat cgccagcggc atcagcacct tgtcgccttg cgtataatat ttgcccatgg
+     1801 tgaaaacggg ggcgaagaag ttgtccatat tggccacgtt taaatcaaaa ctggtgaaac
+     1861 tcacccaggg attggctgag acgaaaaaca tattctcaat aaacccttta gggaaatagg
+     1921 ccaggttttc accgtaacac gccacatctt gcgaatatat gtgtagaaac tgccggaaat
+     1981 cgtcgtggta ttcactccag agcgatgaaa acgtttcagt ttgctcatgg aaaacggtgt
+     2041 aacaagggtg aacactatcc catatcacca gctcaccgtc t
+//