Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_21380
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:0.30, C:0.22, G:0.25, T:0.24
Found at i:398 original size:228 final size:227
Alignment explanation
Indices: 1--1337 Score: 1119
Period size: 228 Copynumber: 5.9 Consensus size: 227
* * * * * * * * *
1 ATGCAGATCTTTGTGAAGACCCTTACTGGTAAGACCATCACCCTTGAGGTAGAAAGTTCTGATAC
1 ATGCAGATTTTTGTGAAAACTCTTACTGGAAAAACCATCACCCTGGAGGTGGAGAGTTCTGACAC
* * * * * * * * *
66 TATCGATAATGTCAAGGCTAAAATCCAAGACAAAGAAGGGATCCCTCCTGACCAACAAAGGCTT-
66 AATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAGAGG-TTG
* * * * * * *
130 ATCTTTGCCGGAAAACAACTCGAGGATGGCCGAACTCTTGCCGACTACAATATCCAAAAGGAGTC
130 ATTTTTGCTGG-AAACAGCTCGAAGATGGCCGAACTCTTGCGGATTACAACATCCAAAAGGAGTC
* * * **
195 CACCCTCCACCTAGTGCTTCGTCTAAGGGGTGGC
194 CACCCTCCACTTGGTGCTTCGACTTCGGGGTGGC
* * * * * * *
229 ATGCAGATATTCGTGAAAACTCTTACTGGCAAGACCATCACCCTCGAGGTGGAAAGTTCTGATAC
1 ATGCAGATTTTTGTGAAAACTCTTACTGGAAAAACCATCACCCTGGAGGTGGAGAGTTCTGACAC
*
294 AATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAACAGAGGCTT-
66 AATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAGAGG-TTG
* * *
358 ATCTTTGCCGGTAAACAGCTTGAAGATGGCCGAACTCTTGCGGATTACAACATCCAGAAA-GAGT
130 ATTTTTGCTGG-AAACAGCTCGAAGATGGCCGAACTCTTGCGGATTACAACATCCA-AAAGGAGT
* * * * *
422 CTACCCTCCACCTT-GTCCTTCGTCTTAGGGGTGGG
193 CCACCCTCCA-CTTGGTGCTTCGACTTCGGGGTGGC
* * * * * ** *
457 ATGCAGATTTTTGTAAAAACCCTCACTGGAAAAACTATTACGTTGGAGGTGGAGAGTTCTGATAC
1 ATGCAGATTTTTGTGAAAACTCTTACTGGAAAAACCATCACCCTGGAGGTGGAGAGTTCTGACAC
* * * * * *
522 GATTGATAATGTTAAGGCCAAGATTCAGGATAAGGAAGGGATCCCACCGGACCAGCAGAGGTTGA
66 AATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAGAGGTTGA
* * * * * * *
587 TTTTTGCTGGAAAGCAGCTTGAAGATGGCCGAACTCTTGCTGATTATAACATTCAGAAGGAATCG
131 TTTTTGCTGGAAA-CAGCTCGAAGATGGCCGAACTCTTGCGGATTACAACATCCAAAAGGAGTCC
* * *
652 ACCCTCCATTTGGTG-TTACGACTCCGTGGTGGC
195 ACCCTCCACTTGGTGCTT-CGACTTCGGGGTGGC
* * * * * * * ** * *
685 ATGCAAATTTTTGTGAAGACTCTCACCGGAAAGACTATTACTTTGGAAGTTGAGAGTTCTGACAC
1 ATGCAGATTTTTGTGAAAACTCTTACTGGAAAAACCATCACCCTGGAGGTGGAGAGTTCTGACAC
* * * * * * * *
750 CATTGACAATGTAAAAGCTAAGATCCAGGACAAGGAAGGGATTCCACCAGATCAGCAGAGGTTGA
66 AATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAGAGGTTGA
** * * *
815 TTTTTGCTGGCAAACAGCTCGAAGATGGTAGGACACTTGCAGATTACAACATCCAGAAA-GAGTC
131 TTTTTGCTGG-AAACAGCTCGAAGATGGCCGAACTCTTGCGGATTACAACATCCA-AAAGGAGTC
* * * * * *
879 TACCCTTCACTTGGTGCTCCGACTGCGTGGTGGA
194 CACCCTCCACTTGGTGCTTCGACTTCGGGGTGGC
* ** * *
913 ATGCAGATTTTTGTGAAAACT-TTGACTGGAAAAACTATCACATTGGAGGTGGAGAGCTCAGACA
1 ATGCAGATTTTTGTGAAAACTCTT-ACTGGAAAAACCATCACCCTGGAGGTGGAGAGTTCTGACA
* * *
977 CAATTGATAATGTGAAGGCCAAGATCCAAGATAAGG-AGGGTATCCCACCTGACCAGCAGAGGTT
65 CAATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGG-ATCCCACCAGACCAGCAGAGGTT
* ** * * * *
1041 GATTTTTGCTGGAAAGCAGCTCGAGGATGGGAGGACCCTTGCGGATTATAACATCCAAAAGGAAT
129 GATTTTTGCTGGAAA-CAGCTCGAAGATGGCCGAACTCTTGCGGATTACAACATCCAAAAGGAGT
* * * * * * *
1106 CGACCCTGCATTTGGT-TTTGCGACTTCGAGGAGGG
193 CCACCCTCCACTTGGTGCTT-CGACTTCGGGGTGGC
* * * * * * * *
1141 ATGCAGATATTCGTGAAGAC-CTTGACCGGTAAAACCATCACCCTGGAGGTCGAGAGCTCGGACA
1 ATGCAGATTTTTGTGAAAACTCTT-ACTGGAAAAACCATCACCCTGGAGGTGGAGAGTTCTGACA
* * * * * * * *
1205 CCATTGACAATGTGAAAGCCAAGATTCAGGACAAGGAGGGGATTCCACCAGACCAGCAGAGGTTG
65 CAATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAGAGGTTG
* * * * * * * * * * *
1270 ATATTTGCTGGGAAGCAGTTGGAGGATGGTCGAACTCTAGCTGACTACAATATCCAGAAGGAGTC
130 ATTTTTGCT-GGAAACAGCTCGAAGATGGCCGAACTCTTGCGGATTACAACATCCAAAAGGAGTC
1335 CAC
194 CAC
1338 ACTGCATCTT
Statistics
Matches: 922, Mismatches: 169, Indels: 36
0.82 0.15 0.03
Matches are distributed among these distances:
227 23 0.02
228 881 0.96
229 18 0.02
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.23
Consensus pattern (227 bp):
ATGCAGATTTTTGTGAAAACTCTTACTGGAAAAACCATCACCCTGGAGGTGGAGAGTTCTGACAC
AATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAGAGGTTGA
TTTTTGCTGGAAACAGCTCGAAGATGGCCGAACTCTTGCGGATTACAACATCCAAAAGGAGTCCA
CCCTCCACTTGGTGCTTCGACTTCGGGGTGGC
Found at i:1366 original size:456 final size:452
Alignment explanation
Indices: 70--1367 Score: 1326
Period size: 456 Copynumber: 2.8 Consensus size: 452
60 TGATACTATC
* * * * * * * * * *
70 GATAATGTCAAGGCTAAAATCCAAGACAAAGAAGGGATCCCTCCTGACCAACAAAGGCTT-ATCT
1 GATAATGTGAAGGCCAAGATCCAAGATAAGGAAGGGATCCCACCGGACCAGCAGAGG-TTGATTT
* * * * * * * * * * * *
134 TTGCCGGAAAACAACTCGAGGATGGCCGAACTCTTGCCGACTACAATATCCAAAAGGAGTCCACC
65 TTGCTGGAAAGCAGCTCGAAGATGGCAGAACCCTTGCGGATTATAACATCCAAAAGGAATCGACC
** * * ** * * * * *
199 CTCCACCTAGTGCTT-CGTCTAAGGGGTGGCATGCAGATATTCGTGAAAACTCTTACTGGCAAGA
130 CTCCATTTGGTG-TTACGACTCCGAGGAGGCATGCAGATATTCGTGAAGAC-CTTACCGG-AAAA
* * * * * * * * *
263 CCATCACCCTCGAGGTGGAAAGTTCTGATACAATTGATAATGTCAAGGCCAAGATCCAAGACAAG
192 CCATCACCCTGGAGGTCGAGAGTTCTGACACCATTGACAATGTAAAAGCCAAGATCCAGGACAAG
* * * * * *
328 GAAGGGATCCCACCAGACCAACAGAGGCTT-ATCTTTGCCGGTAAACAGCTTGAAGATGGCCGAA
257 GAAGGGATTCCACCAGACCAGCAGAGG-TTGATATTTGCTGGCAAACAG-TTGAAGATGGTCGAA
* * ** * *
392 CTCTTGCGGATTACAACATCCAGAAAGAGTCTACCCTCCACCTTGTCCTTCGTCTTAGGGGTGGG
320 CTCTTGCAGATTACAACATCCAGAAAGAGTCTACCCTCCA-CTTGTCCTTCGACTCCGTGGTGGA
* * * * *
457 ATGCAGATTTTTGTAAAAACCCTCACTGGAAAAACTATTACGTTGGAGGTGGAGAGTTCTGATAC
384 ATGCAGATTTTTGTAAAAACCCTCACTGGAAAAACTATCACATTGGAGGTGGAGAGCTCAGACAC
*
522 GATT
449 AATT
* * *
526 GATAATGTTAAGGCCAAGATTCAGGATAAGGAAGGGATCCCACCGGACCAGCAGAGGTTGATTTT
1 GATAATGTGAAGGCCAAGATCCAAGATAAGGAAGGGATCCCACCGGACCAGCAGAGGTTGATTTT
* * * * * *
591 TGCTGGAAAGCAGCTTGAAGATGGCCGAACTCTTGCTGATTATAACATTCAGAAGGAATCGACCC
66 TGCTGGAAAGCAGCTCGAAGATGGCAGAACCCTTGCGGATTATAACATCCAAAAGGAATCGACCC
* * * * * * *
656 TCCATTTGGTGTTACGACTCCGTGGTGGCATGCAAATTTTTGTGAAGACTCTCACCGGAAAGACT
131 TCCATTTGGTGTTACGACTCCGAGGAGGCATGCAGATATTCGTGAAGAC-CTTACCGGAAA-ACC
* ** * * *
721 ATTACTTTGGAAGTTGAGAGTTCTGACACCATTGACAATGTAAAAGCTAAGATCCAGGACAAGGA
194 ATCACCCTGGAGGTCGAGAGTTCTGACACCATTGACAATGTAAAAGCCAAGATCCAGGACAAGGA
* * * * * *
786 AGGGATTCCACCAGATCAGCAGAGGTTGATTTTTGCTGGCAAACAGCTCGAAGATGGTAGGACAC
259 AGGGATTCCACCAGACCAGCAGAGGTTGATATTTGCTGGCAAACAG-TTGAAGATGGTCGAACTC
* * * *
851 TTGCAGATTACAACATCCAGAAAGAGTCTACCCTTCACTTGGTGCTCCGACTGCGTGGTGGAATG
323 TTGCAGATTACAACATCCAGAAAGAGTCTACCCTCCACTT-GTCCTTCGACTCCGTGGTGGAATG
* ** *
916 CAGATTTTTGTGAAAACTTTGACTGGAAAAACTATCACATTGGAGGTGGAGAGCTCAGACACAAT
387 CAGATTTTTGTAAAAACCCTCACTGGAAAAACTATCACATTGGAGGTGGAGAGCTCAGACACAAT
981 T
452 T
*
982 GATAATGTGAAGGCCAAGATCCAAGATAAGG-AGGGTATCCCACCTGACCAGCAGAGGTTGATTT
1 GATAATGTGAAGGCCAAGATCCAAGATAAGGAAGGG-ATCCCACCGGACCAGCAGAGGTTGATTT
* * *
1046 TTGCTGGAAAGCAGCTCGAGGATGGGAGGACCCTTGCGGATTATAACATCCAAAAGGAATCGACC
65 TTGCTGGAAAGCAGCTCGAAGATGGCAGAACCCTTGCGGATTATAACATCCAAAAGGAATCGACC
* * * * *
1111 CTGCATTTGGTTTTGCGACTTCGAGGAGGGATGCAGATATTCGTGAAGACCTTGACCGGTAAAAC
130 CTCCATTTGGTGTTACGACTCCGAGGAGGCATGCAGATATTCGTGAAGACCTT-ACCGG-AAAAC
* * * *
1176 CATCACCCTGGAGGTCGAGAGCTCGGACACCATTGACAATGTGAAAGCCAAGATTCAGGACAAGG
193 CATCACCCTGGAGGTCGAGAGTTCTGACACCATTGACAATGTAAAAGCCAAGATCCAGGACAAGG
* * * *
1241 AGGGGATTCCACCAGACCAGCAGAGGTTGATATTTGCTGGGAAGCAGTTGGAGGATGGTCGAACT
258 AAGGGATTCCACCAGACCAGCAGAGGTTGATATTTGCTGGCAAACAGTT-GAAGATGGTCGAACT
* * * * * * * * *
1306 CTAGCTGACTACAATATCCAGAAGGAGTCCACACTGCATCTTGTCCTTCGCCTCCGTGGTGG
322 CTTGCAGATTACAACATCCAGAAAGAGTCTACCCTCCA-CTTGTCCTTCGACTCCGTGGTGG
1368 TTTCTAA
Statistics
Matches: 691, Mismatches: 141, Indels: 20
0.81 0.17 0.02
Matches are distributed among these distances:
455 18 0.03
456 667 0.97
457 6 0.01
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.23
Consensus pattern (452 bp):
GATAATGTGAAGGCCAAGATCCAAGATAAGGAAGGGATCCCACCGGACCAGCAGAGGTTGATTTT
TGCTGGAAAGCAGCTCGAAGATGGCAGAACCCTTGCGGATTATAACATCCAAAAGGAATCGACCC
TCCATTTGGTGTTACGACTCCGAGGAGGCATGCAGATATTCGTGAAGACCTTACCGGAAAACCAT
CACCCTGGAGGTCGAGAGTTCTGACACCATTGACAATGTAAAAGCCAAGATCCAGGACAAGGAAG
GGATTCCACCAGACCAGCAGAGGTTGATATTTGCTGGCAAACAGTTGAAGATGGTCGAACTCTTG
CAGATTACAACATCCAGAAAGAGTCTACCCTCCACTTGTCCTTCGACTCCGTGGTGGAATGCAGA
TTTTTGTAAAAACCCTCACTGGAAAAACTATCACATTGGAGGTGGAGAGCTCAGACACAATT
Done.