Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_32873
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 824
Length: 1374
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.21
Found at i:1232 original size:228 final size:228
Alignment explanation
Indices: 1--1121 Score: 1749
Period size: 228 Copynumber: 4.9 Consensus size: 228
* * * *
1 ATGCAGATCTTCGTCAAAACCCTT-ACCGGCAAGACCATCACCCTCGAGGTTGAGAGTTCTGACA
1 ATGCAGATCTTCGTCAAAA-CCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACA
65 CCATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTC
65 CCATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTC
* * *
130 ATCTTCGCCGGCAAACAGCTCGAGGACGGCCGTACCTTGGCCGATTACAACATTCAGAAGGAATC
130 ATCTTCGCCGGCAAACAGCTCGAAGATGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATC
195 CACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGT
195 CACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGT
229 ATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
1 ATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
* *
294 CATCGATAATGTGAAGTCTAAAATCCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
66 CATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
*
359 TCTTCGCCGGAAAACAGCTCGAAGATGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATCC
131 TCTTCGCCGGCAAACAGCTCGAAGATGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATCC
*
424 ACCCTCCACCTTGTCCTACGTCTTCGTGGGGGT
196 ACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGT
*
457 ATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCTGACAC
1 ATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
522 CATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
66 CATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
*
587 TCTTCGCCGGCAAACAGCTCGAAGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATCC
131 TCTTCGCCGGCAAACAGCTCGAAGATGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATCC
652 ACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGT
196 ACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGT
*
685 ATGCAGATCTTCGTCAAAACCTTAACCGGTAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
1 ATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
* * *
750 CATCGACAATGTCAAGTCTAAAATCCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
66 CATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
* *
815 TCTTCGCCGGCAAACAGCTCGAAGATGGCCGTACCTTGGCCGATTATAATATCCAGAAGGAATCC
131 TCTTCGCCGGCAAACAGCTCGAAGATGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATCC
* * *
880 ACCCTCCACCTCGTCCTCCGTCTTCGCGGGGGC
196 ACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGT
* * * * * * * * *
913 ATGCAGATCTTCGTGAAAACCTTGACTGGCAAGACCATCACCTTAGAGGTGGAGAGTTCGGACAC
1 ATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
* * * * * * * * *
978 CATCGACAATGTAAAGGCGAAGATTCAAGACAAGGAAGGGATCCCACCAGACCAACAACGTTTGA
66 CATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
* * * * * * ** * * * *
1043 TCTTTGCAGGGAAGCAGCTTGAGGATGGGAGGACCTTGGCTGATTATAACATCCAGAAGGAATCG
131 TCTTCGCCGGCAAACAGCTCGAAGATGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATCC
*
1108 ACCCTTCACCTTGT
196 ACCCTCCACCTTGT
1122 TTTGAGGCTT
Statistics
Matches: 830, Mismatches: 62, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
227 4 0.00
228 826 1.00
ACGTcount: A:0.29, C:0.30, G:0.22, T:0.20
Consensus pattern (228 bp):
ATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
CATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
TCTTCGCCGGCAAACAGCTCGAAGATGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATCC
ACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGT
Found at i:1240 original size:228 final size:228
Alignment explanation
Indices: 1--1352 Score: 961
Period size: 228 Copynumber: 5.9 Consensus size: 228
* * * * * ** * * * *
1 ATGCAGATCTTCGTCAAAACCCTT-ACCGGCAAGACCATCACCCTCGAGGTTGAGAGTTCTGACA
1 ATGCAGATCTTCGTGAAAA-CATTGACTGGCAAAACAATCACATTAGAGGTGGAAAGTTCGGACA
* * * * * *
65 CCATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTC
65 CAATCGACAATGTAAAGGCGAAGATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCTC
* * * * ** * * * *
130 ATCTTCGCCGGCAAA-CAGCTCGAGGACGGCCGTACCTTGGCCGATTACAACATTCAGAAGGAAT
130 ATCTTTGCAGG-AAAGCAGCTTGAGGATGGGAGGACCTTGGCTGATTATAACATCCAGAAGGAAT
* * * * * * *
194 CCACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGT
194 CCACCCTTCACCTTGTTCTCAGGCTTCGCGGAGGC
* * * * * * ** * * * * * *
229 ATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
1 ATGCAGATCTTCGTGAAAACATTGACTGGCAAAACAATCACATTAGAGGTGGAAAGTTCGGACAC
* * * * * * * *
294 CATCGATAATGTGAAGTCTAAAATCCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
66 AATCGACAATGTAAAGGCGAAGATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCTCA
* * * * * ** * * *
359 TCTTCGCCGGAAAACAGCTCGAAGATGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATCC
131 TCTTTGCAGGAAAGCAGCTTGAGGATGGGAGGACCTTGGCTGATTATAACATCCAGAAGGAATCC
* * * * * *
424 ACCCTCCACCTTGTCCT-ACGTCTTCGTGGGGGT
196 ACCCTTCACCTTGTTCTCA-GGCTTCGCGGAGGC
* * * * * * ** * * * * * *
457 ATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCTGACAC
1 ATGCAGATCTTCGTGAAAACATTGACTGGCAAAACAATCACATTAGAGGTGGAAAGTTCGGACAC
* * * * * *
522 CATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
66 AATCGACAATGTAAAGGCGAAGATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCTCA
* * * * * ** * * *
587 TCTTCGCCGGCAAA-CAGCTCGAAGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATC
131 TCTTTGCAGG-AAAGCAGCTTGAGGATGGGAGGACCTTGGCTGATTATAACATCCAGAAGGAATC
* * * * * * *
651 CACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGT
195 CACCCTTCACCTTGTTCTCAGGCTTCGCGGAGGC
* * * * * * * ** * * * * * *
685 ATGCAGATCTTCGTCAAAACCTTAACCGGTAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
1 ATGCAGATCTTCGTGAAAACATTGACTGGCAAAACAATCACATTAGAGGTGGAAAGTTCGGACAC
* * * * * * *
750 CATCGACAATGTCAAGTCTAAAATCCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
66 AATCGACAATGTAAAGGCGAAGATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCTCA
* * * * ** * * *
815 TCTTCGCCGGCAAA-CAGCTCGAAGATGGCCGTACCTTGGCCGATTATAATATCCAGAAGGAATC
131 TCTTTGCAGG-AAAGCAGCTTGAGGATGGGAGGACCTTGGCTGATTATAACATCCAGAAGGAATC
* * * * * *
879 CACCCTCCACCTCGTCCTCCGTCTTCGCGGGGGC
195 CACCCTTCACCTTGTTCTCAGGCTTCGCGGAGGC
* * * * *
913 ATGCAGATCTTCGTGAAAACCTTGACTGGCAAGACCATCACCTTAGAGGTGGAGAGTTCGGACAC
1 ATGCAGATCTTCGTGAAAACATTGACTGGCAAAACAATCACATTAGAGGTGGAAAGTTCGGACAC
* * * * *
978 CATCGACAATGTAAAGGCGAAGATTCAAGACAAGGAAGGGATCCCACCAGACCAACAACGTTTGA
66 AATCGACAATGTAAAGGCGAAGATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCTCA
* *
1043 TCTTTGCAGGGAAGCAGCTTGAGGATGGGAGGACCTTGGCTGATTATAACATCCAGAAGGAATCG
131 TCTTTGCAGGAAAGCAGCTTGAGGATGGGAGGACCTTGGCTGATTATAACATCCAGAAGGAATCC
* * *
1108 ACCCTTCACCTTGTTTTGAGGCTTCGTGGAGGC
196 ACCCTTCACCTTGTTCTCAGGCTTCGCGGAGGC
* * * * * *
1141 ATGCAGATTTTCGTTAAGACATTGACTGGGAAAACAATCACATTGGAGGTGGAAAGTTCGGATAC
1 ATGCAGATCTTCGTGAAAACATTGACTGGCAAAACAATCACATTAGAGGTGGAAAGTTCGGACAC
* * * * * * * * *
1206 AATTGATAATGTGAAGGCGAAGATTCAGGACAAGGAAGGTATCCCTCCAGATCAGCAAAGGCTCA
66 AATCGACAATGTAAAGGCGAAGATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCTCA
* * * * * * *
1271 TCTTTGCTGGAAAGCA-ATTGGAGGATGGGAGGACTTTAGCTGATTATAACATTCAGAAAGAGTC
131 TCTTTGCAGGAAAGCAGCTT-GAGGATGGGAGGACCTTGGCTGATTATAACATCCAGAAGGAATC
1335 CACCCTTCACCTTGTTCT
195 CACCCTTCACCTTGTTCT
1353 TCGTCTCCGT
Statistics
Matches: 1017, Mismatches: 100, Indels: 14
0.90 0.09 0.01
Matches are distributed among these distances:
227 11 0.01
228 1003 0.99
229 3 0.00
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.21
Consensus pattern (228 bp):
ATGCAGATCTTCGTGAAAACATTGACTGGCAAAACAATCACATTAGAGGTGGAAAGTTCGGACAC
AATCGACAATGTAAAGGCGAAGATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCTCA
TCTTTGCAGGAAAGCAGCTTGAGGATGGGAGGACCTTGGCTGATTATAACATCCAGAAGGAATCC
ACCCTTCACCTTGTTCTCAGGCTTCGCGGAGGC
Found at i:1339 original size:684 final size:684
Alignment explanation
Indices: 1--1364 Score: 1726
Period size: 684 Copynumber: 2.0 Consensus size: 684
* * * *
1 ATGCAGATCTTCGTCAAAACCCTTACCGGCAAGACCATCACCCTCGAGGTTGAGAGTTCTGACAC
1 ATGCAGATCTTCGTCAAAACCCTTACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
* *
66 CATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
66 CATCGACAATGTAAAGTCTAAAATCCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
* *
131 TCTTCGCCGGCAAACAGCTCGAGGACGGCCGTACCTTGGCCGATTACAACATTCAGAAGGAATCC
131 TCTTCGCCGGCAAACAGCTCGAAGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATCC
* * *
196 ACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGTATGCAGATCTTCGTCAAAACCTTAACCGGCAA
196 ACCCTCCACCTCGTCCTCCGTCTTCGCGGGGGCATGCAGATCTTCGTCAAAACCTTAACCGGCAA
* * * * *
261 GACCATCACCCTCGAAGTCGAGAGCTCCGACACCATCGATAATGTGAAGTCTAAAATCCAAGACA
261 GACCATCACCCTAGAAGTCGAGAGCTCCGACACCATCGACAATGTAAAGGCGAAAATCCAAGACA
* * * * *
326 AGGAAGGCATCCCACCAGACCAGCAGCGTCTCATCTTCGCCGGAAAACAGCTCGAAGATGGCCGT
326 AGGAAGGCATCCCACCAGACCAACAACGTCTCATCTTCGCAGGAAAACAGCTCGAAGATGGCAGG
* *
391 ACCTTGGCCGATTACAACATCCAGAAGGAATCCACCCTCCACCTTGTCCTACGTCTTCGTGGGGG
391 ACCTTGGCCGATTACAACATCCAGAAGGAATCCACCCTCCACCTTGTCCTACGGCTTCGTGGAGG
* * * * * * *
456 TATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCTGACA
456 CATGCAGATCTTCGTCAAAACATTAACCGGCAAAACAATCACACTCGAAGTCGAAAGCTCGGACA
* * * ** *
521 CCATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTC
521 CAATCGATAATGTAAAGGCGAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAAAGGCTC
* * * * *
586 ATCTTCGCCGGCAAACAGCTCGAAGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATC
586 ATCTTCGCCGGCAAACAACTCGAAGACGGCAGGACCTTAGCCGATTACAACATCCAGAAAGAATC
*
651 CACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGT
651 CACCCTCCACCTTGTCCTCCGTCTCCGTGGGGGT
*
685 ATGCAGATCTTCGTCAAAA-CCTTAACCGGTAAGACCATCACCCTCGAAGTCGAGAGCTCCGACA
1 ATGCAGATCTTCGTCAAAACCCTT-ACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACA
*
749 CCATCGACAATGTCAAGTCTAAAATCCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTC
65 CCATCGACAATGTAAAGTCTAAAATCCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTC
* * *
814 ATCTTCGCCGGCAAACAGCTCGAAGATGGCCGTACCTTGGCCGATTATAATATCCAGAAGGAATC
130 ATCTTCGCCGGCAAACAGCTCGAAGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATC
* * *
879 CACCCTCCACCTCGTCCTCCGTCTTCGCGGGGGCATGCAGATCTTCGTGAAAACCTTGACTGGCA
195 CACCCTCCACCTCGTCCTCCGTCTTCGCGGGGGCATGCAGATCTTCGTCAAAACCTTAACCGGCA
* * * * * * *
944 AGACCATCACCTTAGAGGTGGAGAGTTCGGACACCATCGACAATGTAAAGGCGAAGATTCAAGAC
260 AGACCATCACCCTAGAAGTCGAGAGCTCCGACACCATCGACAATGTAAAGGCGAAAATCCAAGAC
* * * * * * * * *
1009 AAGGAAGGGATCCCACCAGACCAACAACGTTTGATCTTTGCAGGGAAGCAGCTTGAGGATGGGAG
325 AAGGAAGGCATCCCACCAGACCAACAACGTCTCATCTTCGCAGGAAAACAGCTCGAAGATGGCAG
* * * * **
1074 GACCTTGGCTGATTATAACATCCAGAAGGAATCGACCCTTCACCTTGTTTTGA-GGCTTCGTGGA
390 GACCTTGGCCGATTACAACATCCAGAAGGAATCCACCCTCCACCTTGTCCT-ACGGCTTCGTGGA
* * * * * * * * * * *
1138 GGCATGCAGATTTTCGTTAAGACATTGACTGGGAAAACAATCACATTGGAGGTGGAAAGTTCGGA
454 GGCATGCAGATCTTCGTCAAAACATTAACCGGCAAAACAATCACACTCGAAGTCGAAAGCTCGGA
* * * * * * * *
1203 TACAATTGATAATGTGAAGGCGAAGATTCAGGACAAGGAAGGTATCCCTCCAGATCAGCAAAGGC
519 CACAATCGATAATGTAAAGGCGAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAAAGGC
* * * * * * * * * * *
1268 TCATCTTTGCTGG-AAAGCAATTGGAGGATGGGAGGACTTTAGCTGATTATAACATTCAGAAAGA
584 TCATCTTCGCCGGCAAA-CAACTCGAAGACGGCAGGACCTTAGCCGATTACAACATCCAGAAAGA
* * * *
1332 GTCCACCCTTCACCTTGTTCTTCGTCTCCGTGG
648 ATCCACCCTCCACCTTGTCCTCCGTCTCCGTGG
1365 TGGGCAGTGA
Statistics
Matches: 571, Mismatches: 106, Indels: 6
0.84 0.16 0.01
Matches are distributed among these distances:
683 7 0.01
684 563 0.99
685 1 0.00
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.21
Consensus pattern (684 bp):
ATGCAGATCTTCGTCAAAACCCTTACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
CATCGACAATGTAAAGTCTAAAATCCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
TCTTCGCCGGCAAACAGCTCGAAGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATCC
ACCCTCCACCTCGTCCTCCGTCTTCGCGGGGGCATGCAGATCTTCGTCAAAACCTTAACCGGCAA
GACCATCACCCTAGAAGTCGAGAGCTCCGACACCATCGACAATGTAAAGGCGAAAATCCAAGACA
AGGAAGGCATCCCACCAGACCAACAACGTCTCATCTTCGCAGGAAAACAGCTCGAAGATGGCAGG
ACCTTGGCCGATTACAACATCCAGAAGGAATCCACCCTCCACCTTGTCCTACGGCTTCGTGGAGG
CATGCAGATCTTCGTCAAAACATTAACCGGCAAAACAATCACACTCGAAGTCGAAAGCTCGGACA
CAATCGATAATGTAAAGGCGAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAAAGGCTC
ATCTTCGCCGGCAAACAACTCGAAGACGGCAGGACCTTAGCCGATTACAACATCCAGAAAGAATC
CACCCTCCACCTTGTCCTCCGTCTCCGTGGGGGT
Done.