Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_04736
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, 687
Length: 1146
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.24
Found at i:701 original size:228 final size:226
Alignment explanation
Indices: 49--1139 Score: 845
Period size: 228 Copynumber: 4.8 Consensus size: 226
39 CACCCTTGAA
* * * * * * * * *
49 GTGGAAAGCTCCGACACAATTGATAATGTCAAGGCCAAGATCCAAGACAAAGAAGGTATCCCTCC
1 GTGGAGAGCTCTGATACGATTGATAATGT-AAAGCCAAGATCCAGGACAAGGAGGGTATCCCACC
* * * ** * * *
114 TGACCAACAGAGGCTT-ATCTTTGCTGGAAAACAATTGGAGGATGGCCGCACCCTTGCTGACTAC
65 GGACCAACAGAGG-TTGATTTTTGCTGGAAAGCAGCTGGAGGATGGCAGAACCCTTGCTGACTAT
* * * * * *
178 AACATCCAGAAAGAGTCTACCCTCCACCTT-GTCCTTCGTCTTAGGGGTGGCATGCAGATCTTTG
129 AACATTCAGAAAGAGTCTACCCTCCA-CTTGGTCCTTCGCCTTCGTGGTGGAATGCAGATATTTG
* * * * *
242 TAAAAACGCTCACTGGAAAAACCATCACTTTAGAG
193 TGAAAACCCTCACAGG-AAAACCATCACCTTGGAG
* * * * * *
277 GTGGAGAGTTCTGATACAATTGATAACGTTAAGTCCAAGATTCAGGACAAGGAGGGCATCCCACC
1 GTGGAGAGCTCTGATACGATTGATAATGTAAAG-CCAAGATCCAGGACAAGGAGGGTATCCCACC
* * * * * * *
342 AGACCAGCAGAGGTTAATTTTTGCTGGGAAA-CAACTTGAAGATGGCAGAACCCTTGCAGACTAT
65 GGACCAACAGAGGTTGATTTTTGCT-GGAAAGCAGCTGGAGGATGGCAGAACCCTTGCTGACTAT
* * * * * *
406 AACATTCA-AAAGGAATCTACCCTCCATTTGGT-GTTGCGTCTTCGTGGTGGTATGCA-AGTTTT
129 AACATTCAGAAA-GAGTCTACCCTCCACTTGGTCCTT-CGCCTTCGTGGTGGAATGCAGA-TATT
* * * *
468 TGTGAAGACCCTCACAGGAAAGACTATTACCTTGGAA
191 TGTGAAAACCCTCACAGGAAA-ACCATCACCTTGGAG
* * * * * *
505 GTTGAGAGTTCTGATACGATTGACAATGTGAAAGCTAAGATCCAGGACAAGGAAGGTATTCCACC
1 GTGGAGAGCTCTGATACGATTGATAATGT-AAAGCCAAGATCCAGGACAAGGAGGGTATCCCACC
* * * * * *
570 GGATCAACAGAGGCTGATTTTTGCTGGCAAGCAGCTGGAGGATGGGAGGACCCTTGCTGATTATA
65 GGACCAACAGAGGTTGATTTTTGCTGGAAAGCAGCTGGAGGATGGCAGAACCCTTGCTGACTATA
* * * *
635 ATATTCAGAAAGAGTCAACCCTCCACTTGGTGCTTCGCCTGCGTGGTGGAATGCAGATATTTGTG
130 ACATTCAGAAAGAGTCTACCCTCCACTTGGTCCTTCGCCTTCGTGGTGGAATGCAGATATTTGTG
** * * * *
700 AAAACTTTGACCGGTAAAACCATTACGTTGGAG
195 AAAACCCTCACAGG-AAAACCATCACCTTGGAG
* * * * * *
733 GTGGAGAGCTCCGACACGGTTGATAATGTTAAGGCCAAGATCCAAGATAAGGAGGGTATCCCACC
1 GTGGAGAGCTCTGATACGATTGATAATG-TAAAGCCAAGATCCAGGACAAGGAGGGTATCCCACC
* * * * * * *
798 TGACCAACAGAGGTTGATTTTTGCCGGAAAGCAGCTCGAGGACGGGAGGACCCTTGCGGACTATA
65 GGACCAACAGAGGTTGATTTTTGCTGGAAAGCAGCTGGAGGATGGCAGAACCCTTGCTGACTATA
* * * * * * * *
863 ACATTCA-AAAGGAGTCGACCCTGCATTTGGT-TTTGCGCCTTAGAGGAGGGATGCAGATATTTG
130 ACATTCAGAAA-GAGTCTACCCTCCACTTGGTCCTT-CGCCTTCGTGGTGGAATGCAGATATTTG
* * * * * *
926 TCAAGACCTTGACTGGGAAAACCATCACCCTGGAG
193 TGAAAACCCTCAC-AGGAAAACCATCACCTTGGAG
* * * * * *
961 GTTGAGAGCTCGGATACGATTGACAATGTAAAAGCAAAGATTCAGGACAAGGAGGGAATTCCC-C
1 GTGGAGAGCTCTGATACGATTGATAATGT-AAAGCCAAGATCCAGGACAAGGAGGGTA-TCCCAC
* * * * * * *
1025 CGGATCAGCAGAGGTTGATCTTTGCTGGGAAGCAGTTGGAGGACGGTC-GAACCCTAGCTGACTA
64 CGGACCAACAGAGGTTGATTTTTGCTGGAAAGCAGCTGGAGGATGG-CAGAACCCTTGCTGACTA
* * * * * * *
1089 CAATATCCAGAAGGAGTCTACTCTGCATCTT-GTCCTTCGCCTCCGTGGTGG
128 TAACATTCAGAAAGAGTCTACCCTCCA-CTTGGTCCTTCGCCTTCGTGGTGG
1140 TTTCTGA
Statistics
Matches: 686, Mismatches: 153, Indels: 48
0.77 0.17 0.05
Matches are distributed among these distances:
227 25 0.04
228 631 0.92
229 30 0.04
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (226 bp):
GTGGAGAGCTCTGATACGATTGATAATGTAAAGCCAAGATCCAGGACAAGGAGGGTATCCCACCG
GACCAACAGAGGTTGATTTTTGCTGGAAAGCAGCTGGAGGATGGCAGAACCCTTGCTGACTATAA
CATTCAGAAAGAGTCTACCCTCCACTTGGTCCTTCGCCTTCGTGGTGGAATGCAGATATTTGTGA
AAACCCTCACAGGAAAACCATCACCTTGGAG
Found at i:967 original size:456 final size:456
Alignment explanation
Indices: 1--1139 Score: 1197
Period size: 456 Copynumber: 2.5 Consensus size: 456
* * * * * * * * * * * *
1 ATGCAAATATTTGTCAAAACTCTTACTGGCAAGACAATCACCCTTGAAGTGGAAAGCTCCGACAC
1 ATGCAAGTATTTGTCAAGACCCTCACAGGAAAGACCATCACCCTGGAAGTTGAGAGCTCGGATAC
* * * * * * * * * * * *
66 AATTGATAATGTCAAGGCCAAGATCCAAGACAAAGAAGGTATCCCTCCTGACCAACAGAGGCTTA
66 GATTGACAATGTAAAAGCAAAGATCCAGGACAAGGAAGGTATTCCACCGGATCAACAGAGGCTGA
* * * *
131 TCTTTGCTGGAAAACAATTGGAGGATGGCCGCACCCTTGCTGACTACAACATCCAGAAAGAGTCT
131 TCTTTGCTGGAAAGCAGTTGGAGGATGGCCGAACCCTTGCTGACTACAATATCCAGAAAGAGTCT
* ** * * * *
196 ACCCTCCACCTTGTCCTTCGTCTTAGGGGTGGCATGCAGATCTTTGTAAAAACGCTCACTGGAAA
196 ACCCTCCACCTTGTCCTTCGCCTCCGTGGTGGAATGCAGATATTTGTAAAAACGCTCACCGGAAA
* * * * * * *
261 AACCATCACTTTAGAGGTGGAGAGTTCTGATACAATTGATAACGTTAAGTCCAAGATTCAGGACA
261 AACCATCACGTTAGAGGTGGAGAGCTCCGACACAATTGATAACGTTAAGGCCAAGATCCAAGACA
* * * *
326 AGGAGGGCATCCCACCAGACCAGCAGAGGTTAATTTTTGCTGGGAAACAACTTGAAGATGGCAGA
326 AGGAGGGCATCCCACCAGACCAACAGAGGTTAATTTTTGCTCGGAAACAACTCGAAGACGGCAGA
* * * * *
391 ACCCTTGCAGACTATAACATTCAAAAGGAATCTACCCTCCATTTGGTGTTGCGTCTTCGTGGTGG
391 ACCCTTGCAGACTATAACATTCAAAAGGAATCGACCCTCCATTTGGTGTTGCGCCTTAGAGGAGG
*
456 T
456 G
* * * * * * *
457 ATGCAAGTTTTTGTGAAGACCCTCACAGGAAAGACTATTACCTTGGAAGTTGAGAGTTCTGATAC
1 ATGCAAGTATTTGTCAAGACCCTCACAGGAAAGACCATCACCCTGGAAGTTGAGAGCTCGGATAC
* *
522 GATTGACAATGTGAAAGCTAAGATCCAGGACAAGGAAGGTATTCCACCGGATCAACAGAGGCTGA
66 GATTGACAATGTAAAAGCAAAGATCCAGGACAAGGAAGGTATTCCACCGGATCAACAGAGGCTGA
* * * ** * * * * *
587 TTTTTGCTGGCAAGCAGCTGGAGGATGGGAGGACCCTTGCTGATTATAATATTCAGAAAGAGTCA
131 TCTTTGCTGGAAAGCAGTTGGAGGATGGCCGAACCCTTGCTGACTACAATATCCAGAAAGAGTCT
* * * ** * *
652 ACCCTCCA-CTTGGTGCTTCGCCTGCGTGGTGGAATGCAGATATTTGTGAAAACTTTGACCGGTA
196 ACCCTCCACCTT-GTCCTTCGCCTCCGTGGTGGAATGCAGATATTTGTAAAAACGCTCACCGGAA
* * ** * *
716 AAACCATTACGTTGGAGGTGGAGAGCTCCGACACGGTTGATAATGTTAAGGCCAAGATCCAAGAT
260 AAACCATCACGTTAGAGGTGGAGAGCTCCGACACAATTGATAACGTTAAGGCCAAGATCCAAGAC
* * * * * *
781 AAGGAGGGTATCCCACCTGACCAACAGAGGTTGATTTTTGC-CGGAAAGCAGCTCGAGGACGGGA
325 AAGGAGGGCATCCCACCAGACCAACAGAGGTTAATTTTTGCTCGGAAA-CAACTCGAAGACGGCA
* * * * *
845 GGACCCTTGCGGACTATAACATTCAAAAGGAGTCGACCCTGCATTTGGTTTTGCGCCTTAGAGGA
389 GAACCCTTGCAGACTATAACATTCAAAAGGAATCGACCCTCCATTTGGTGTTGCGCCTTAGAGGA
910 GGG
454 GGG
* * * *
913 ATGC-AGATATTTGTCAAGACCTTGACTGGGAAA-ACCATCACCCTGGAGGTTGAGAGCTCGGAT
1 ATGCAAG-TATTTGTCAAGACCCTCAC-AGGAAAGACCATCACCCTGGAAGTTGAGAGCTCGGAT
* * * * * *
976 ACGATTGACAATGTAAAAGCAAAGATTCAGGACAAGGAGGGAATTCCCCCGGATCAGCAGAGGTT
64 ACGATTGACAATGTAAAAGCAAAGATCCAGGACAAGGAAGGTATTCCACCGGATCAACAGAGGCT
* * * * *
1041 GATCTTTGCTGGGAAGCAGTTGGAGGACGGTCGAACCCTAGCTGACTACAATATCCAGAAGGAGT
129 GATCTTTGCTGGAAAGCAGTTGGAGGATGGCCGAACCCTTGCTGACTACAATATCCAGAAAGAGT
* * *
1106 CTACTCTGCATCTTGTCCTTCGCCTCCGTGGTGG
194 CTACCCTCCACCTTGTCCTTCGCCTCCGTGGTGG
1140 TTTCTGA
Statistics
Matches: 553, Mismatches: 125, Indels: 10
0.80 0.18 0.01
Matches are distributed among these distances:
455 10 0.02
456 535 0.97
457 8 0.01
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (456 bp):
ATGCAAGTATTTGTCAAGACCCTCACAGGAAAGACCATCACCCTGGAAGTTGAGAGCTCGGATAC
GATTGACAATGTAAAAGCAAAGATCCAGGACAAGGAAGGTATTCCACCGGATCAACAGAGGCTGA
TCTTTGCTGGAAAGCAGTTGGAGGATGGCCGAACCCTTGCTGACTACAATATCCAGAAAGAGTCT
ACCCTCCACCTTGTCCTTCGCCTCCGTGGTGGAATGCAGATATTTGTAAAAACGCTCACCGGAAA
AACCATCACGTTAGAGGTGGAGAGCTCCGACACAATTGATAACGTTAAGGCCAAGATCCAAGACA
AGGAGGGCATCCCACCAGACCAACAGAGGTTAATTTTTGCTCGGAAACAACTCGAAGACGGCAGA
ACCCTTGCAGACTATAACATTCAAAAGGAATCGACCCTCCATTTGGTGTTGCGCCTTAGAGGAGG
G
Done.