Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_02358
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, 1000
Length: 3393
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Found at i:499 original size:24 final size:24
Alignment explanation
Indices: 466--651 Score: 219
Period size: 24 Copynumber: 7.8 Consensus size: 24
456 TTTTGGTTCC
* * *
466 AGTACTCCTGCCTTCGGTGCCACG
1 AGTACCCCTGCCTTTGGTGCCACA
* *
490 AGCACCCCTGCTTTTGGTGCCACA
1 AGTACCCCTGCCTTTGGTGCCACA
*
514 AGTACCCCTGCCTTTGGTGCCACG
1 AGTACCCCTGCCTTTGGTGCCACA
* *
538 AGTGCCCCTGCTTTTGGTGCCACA
1 AGTACCCCTGCCTTTGGTGCCACA
* * *
562 AGTGCCCCTGCTTTTGGTGGCACA
1 AGTACCCCTGCCTTTGGTGCCACA
* **
586 AGTACCCCTGCCTTTGGTTCCATG
1 AGTACCCCTGCCTTTGGTGCCACA
* *
610 AGTACTCCAGCCTTTGGTGCCACA
1 AGTACCCCTGCCTTTGGTGCCACA
*
634 AGCACCCCTGCCTTTGGT
1 AGTACCCCTGCCTTTGGT
652 TCAACTGGAA
Statistics
Matches: 136, Mismatches: 26, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 136 1.00
ACGTcount: A:0.14, C:0.35, G:0.24, T:0.27
Consensus pattern (24 bp):
AGTACCCCTGCCTTTGGTGCCACA
Found at i:570 original size:72 final size:72
Alignment explanation
Indices: 466--651 Score: 246
Period size: 72 Copynumber: 2.6 Consensus size: 72
456 TTTTGGTTCC
* * * *
466 AGTACTCCTGCCTTCGGTGCCACGAGCACCCCTGCTTTTGGTGCCACAAGTACCCCTGCCTTTGG
1 AGTACCCCAGCCTTTGGTGCCACAAGCACCCCTGCTTTTGGTGCCACAAGTACCCCTGCCTTTGG
531 TGCCACG
66 TGCCACG
* * * ** *
538 AGTGCCCCTGCTTTTGGTGCCACAAGTGCCCCTGCTTTTGGTGGCACAAGTACCCCTGCCTTTGG
1 AGTACCCCAGCCTTTGGTGCCACAAGCACCCCTGCTTTTGGTGCCACAAGTACCCCTGCCTTTGG
* *
603 TTCCATG
66 TGCCACG
* *
610 AGTACTCCAGCCTTTGGTGCCACAAGCACCCCTGCCTTTGGT
1 AGTACCCCAGCCTTTGGTGCCACAAGCACCCCTGCTTTTGGT
652 TCAACTGGAA
Statistics
Matches: 97, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
72 97 1.00
ACGTcount: A:0.14, C:0.35, G:0.24, T:0.27
Consensus pattern (72 bp):
AGTACCCCAGCCTTTGGTGCCACAAGCACCCCTGCTTTTGGTGCCACAAGTACCCCTGCCTTTGG
TGCCACG
Found at i:667 original size:48 final size:48
Alignment explanation
Indices: 574--674 Score: 132
Period size: 48 Copynumber: 2.1 Consensus size: 48
564 TGCCCCTGCT
* * * * *
574 TTTGGTGGCACAAGTACCCCTGCCTTTGGTTCCATGAGTACTCCAGCC
1 TTTGGTGCCACAAGCACCCCTGCCTTTGGTTCAATGAGAACTCCAGCA
*
622 TTTGGTGCCACAAGCACCCCTGCCTTTGGTTCAACTG-GAAGTCCAGCA
1 TTTGGTGCCACAAGCACCCCTGCCTTTGGTTCAA-TGAGAACTCCAGCA
670 TTTGG
1 TTTGG
675 GAGCACTGGA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 44 0.96
49 2 0.04
ACGTcount: A:0.18, C:0.30, G:0.24, T:0.29
Consensus pattern (48 bp):
TTTGGTGCCACAAGCACCCCTGCCTTTGGTTCAATGAGAACTCCAGCA
Found at i:772 original size:24 final size:24
Alignment explanation
Indices: 745--809 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
735 TGGAGCATCA
*
745 AGCACACCTGCTTTTGGCACTTCC
1 AGCACTCCTGCTTTTGGCACTTCC
* *** *
769 AGCACTCCTGCATTTGGGGGTTCG
1 AGCACTCCTGCTTTTGGCACTTCC
793 AGCACTCCTGCTTTTGG
1 AGCACTCCTGCTTTTGG
810 AGCATCTTCA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.14, C:0.31, G:0.25, T:0.31
Consensus pattern (24 bp):
AGCACTCCTGCTTTTGGCACTTCC
Found at i:914 original size:24 final size:24
Alignment explanation
Indices: 876--980 Score: 147
Period size: 24 Copynumber: 4.4 Consensus size: 24
866 CATTTGGTAG
* *
876 CTTTGGTGCCTCAAGCACTCCTGC
1 CTTTGGTTCCACAAGCACTCCTGC
900 CTTTGGTTCCACAAGCACTCCTGC
1 CTTTGGTTCCACAAGCACTCCTGC
*
924 CTTTGGTTCCACAAGCACCCCTGC
1 CTTTGGTTCCACAAGCACTCCTGC
* * * *
948 CTTTGGTGCTACCAGCACTCCGGC
1 CTTTGGTTCCACAAGCACTCCTGC
972 CTTTGGTTC
1 CTTTGGTTC
981 AACTGGAAGT
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 72 1.00
ACGTcount: A:0.13, C:0.37, G:0.20, T:0.30
Consensus pattern (24 bp):
CTTTGGTTCCACAAGCACTCCTGC
Found at i:1063 original size:327 final size:327
Alignment explanation
Indices: 550--1169 Score: 889
Period size: 327 Copynumber: 1.9 Consensus size: 327
540 TGCCCCTGCT
** * * * ** *
550 TTTGGTGCCACAAGTGCCCCTGCTTTTGGTGGCACAAGTACCCCTGCCTTTGGTTCCATGAGTAC
1 TTTGGTGCCACAAGCACCCCTGCCTTTGGTGCCACAAGCACCCCTGCCTTTGGTTCCACAAGCAC
* * *
615 TCCAGCCTTTGGTGCCACAAGCACCCCTGCCTTTGGTTCAACTGGAAGTCCAGCATTTGGGAGCA
66 CCCAGCCTTTGGTGCCACAAGCACCCCGGCCTTTGGTTCAACTGGAAGTCCAGCATTCGGGAGCA
** *
680 CTGGAACTGCATTTGGTGTGTCCAATGCCCCAGTCTTTGGAACAGGTGGCACATTTGGAGCATCA
131 CTGGAACTGCATTTGGCATGTCCAATGCCCCAGTCTTTGGAACAGGAGGCACATTTGGAGCATCA
* * * *** *
745 AGCACACCTGCTTTTGGCACTTCCAGCACTCCTGCATTTGGGGGTTCGAGCACTCCTGCTTTTGG
196 AGCACACCTGCTTTTGGCACATCAAGCACACCTGCATTTGGCACTTCAAGCACTCCTGCTTTTGG
*
810 AGCATCTTCAAGTCCATCATTCAGCTTTGGGTCAGCATTTGGGCAGTCAACACCCGCATTTGGTA
261 AGCATCTTCAACTCCATCATTCAGCTTTGGGTCAGCATTTGGGCAGTCAACACCCGCATTTGGTA
875 GC
326 GC
* * * *
877 TTTGGTGCCTCAAGCACTCCTGCCTTTGGTTCCACAAGCACTCCTGCCTTTGGTTCCACAAGCAC
1 TTTGGTGCCACAAGCACCCCTGCCTTTGGTGCCACAAGCACCCCTGCCTTTGGTTCCACAAGCAC
* * * *
942 CCCTGCCTTTGGTGCTACCAGCACTCCGGCCTTTGGTTCAACTGGAAGTCCAGCATTCGGGAGCA
66 CCCAGCCTTTGGTGCCACAAGCACCCCGGCCTTTGGTTCAACTGGAAGTCCAGCATTCGGGAGCA
* * * *
1007 GTGGAACTGCATTTGGCATGTCTAATGCCTCAGTCTTTGGCACAGGAGGCACATTTGGAGCATCA
131 CTGGAACTGCATTTGGCATGTCCAATGCCCCAGTCTTTGGAACAGGAGGCACATTTGGAGCATCA
* *
1072 AGCACACCTGCTTTTGGCACATCAAGCACACCTGCTTTTGGCACTTCAAGCAGTCCTGCTTTTGG
196 AGCACACCTGCTTTTGGCACATCAAGCACACCTGCATTTGGCACTTCAAGCACTCCTGCTTTTGG
* * *
1137 AGCATCTTCTACTCCTTCCTTCAGCTTTGGGTC
261 AGCATCTTCAACTCCATCATTCAGCTTTGGGTC
1170 TAGCCCAACT
Statistics
Matches: 254, Mismatches: 39, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
327 254 1.00
ACGTcount: A:0.19, C:0.29, G:0.24, T:0.29
Consensus pattern (327 bp):
TTTGGTGCCACAAGCACCCCTGCCTTTGGTGCCACAAGCACCCCTGCCTTTGGTTCCACAAGCAC
CCCAGCCTTTGGTGCCACAAGCACCCCGGCCTTTGGTTCAACTGGAAGTCCAGCATTCGGGAGCA
CTGGAACTGCATTTGGCATGTCCAATGCCCCAGTCTTTGGAACAGGAGGCACATTTGGAGCATCA
AGCACACCTGCTTTTGGCACATCAAGCACACCTGCATTTGGCACTTCAAGCACTCCTGCTTTTGG
AGCATCTTCAACTCCATCATTCAGCTTTGGGTCAGCATTTGGGCAGTCAACACCCGCATTTGGTA
GC
Found at i:1088 original size:24 final size:24
Alignment explanation
Indices: 1067--1136 Score: 113
Period size: 24 Copynumber: 2.9 Consensus size: 24
1057 ACATTTGGAG
1067 CATCAAGCACACCTGCTTTTGGCA
1 CATCAAGCACACCTGCTTTTGGCA
1091 CATCAAGCACACCTGCTTTTGGCA
1 CATCAAGCACACCTGCTTTTGGCA
* **
1115 CTTCAAGCAGTCCTGCTTTTGG
1 CATCAAGCACACCTGCTTTTGG
1137 AGCATCTTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.21, C:0.31, G:0.19, T:0.29
Consensus pattern (24 bp):
CATCAAGCACACCTGCTTTTGGCA
Done.