Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_00323
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, 937
Length: 1563
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Found at i:777 original size:111 final size:111
Alignment explanation
Indices: 577--815 Score: 302
Period size: 111 Copynumber: 2.2 Consensus size: 111
567 TCAAGTATAT
* * * **
577 AGGCAAGAGCCGAATATTCAAAGACCCTTTTATGGAAGAGGTGCTGTAGGTGTACAGCCATTGTT
1 AGGCAAGAGCCGAATATACAAAGACCCTTTTATGCAAGAAGTGCTGTAGGTGTACAGCCATTGAG
** * *
642 TTCCATTAATCAAGTTTACGAAAACATGAGCCGAAGCATGCAGGGA
66 TTCCACAAATCAAGTTTACGAAAACATGAACAGAAGCATGCAGGGA
* * * **
688 TGGCAAGAACCGAATATACAGAGACCCTTTTATGCAAGACAG-GCTGTAGGTGTATGGCCATTGA
1 AGGCAAGAGCCGAATATACAAAGACCCTTTTATGCAAGA-AGTGCTGTAGGTGTACAGCCATTGA
*
752 GTTCCACAAATCAAGTTTATC-AAAACATGAACAGTAGCATGCAGGGA
65 GTTCCACAAATCAAGTTTA-CGAAAACATGAACAGAAGCATGCAGGGA
*
799 AGGCAAGAGCTGAATAT
1 AGGCAAGAGCCGAATAT
816 GATAACATCC
Statistics
Matches: 108, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
111 106 0.98
112 2 0.02
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (111 bp):
AGGCAAGAGCCGAATATACAAAGACCCTTTTATGCAAGAAGTGCTGTAGGTGTACAGCCATTGAG
TTCCACAAATCAAGTTTACGAAAACATGAACAGAAGCATGCAGGGA
Found at i:828 original size:111 final size:111
Alignment explanation
Indices: 662--1461 Score: 685
Period size: 111 Copynumber: 7.4 Consensus size: 111
652 CAAGTTTACG
* * * * * * * * * *
662 AAAACATGAGCCGAAGCATGCAGGGATGGCAAGAACCGAATAT-ACAGAGACCCTTTTATGCAAG
1 AAAACATGAACCGTAGCATGCAAGAAAGGCAAGAGCTGAATATGACA-ACATCCTTTGATGCAAG
* * * * * **
726 ACAGGCTGTAGGTG-TATGGCCATTGAGTTCC-ACAAATCAAGTTTATC
65 AGATGCTGTAGGTGAAAT-GCCATTGAGCTCCGAC-GATCAAGTCCATC
* * * *
773 AAAACATGAACAGTAGCATGCAGGGAAGGCAAGAGCTGAATATGATAACATCCTTTGATGCAAGA
1 AAAACATGAACCGTAGCATGCAAGAAAGGCAAGAGCTGAATATGACAACATCCTTTGATGCAAGA
*
838 GATGCTGCAGGTGAAATGCCATCT-AGCTCCGACGATCAAGTCCATC
66 GATGCTGTAGGTGAAATGCCAT-TGAGCTCCGACGATCAAGTCCATC
* *
884 AAAACATGAATCGTAGCACGCAAGAAAGGCAAGAGCTGAATATGACAACATCCTTTGATGCAAGA
1 AAAACATGAACCGTAGCATGCAAGAAAGGCAAGAGCTGAATATGACAACATCCTTTGATGCAAGA
* *
949 GATGCT-TCAGGTGAAATGCCATCGAGCTCCGACGATCAAGCCCATC
66 GATGCTGT-AGGTGAAATGCCATTGAGCTCCGACGATCAAGTCCATC
* *
995 AAAAAATGAACTGTAGCATGCAAGAAAGGCAAGAGCTGAATATGACAACATCCTTTGATGCAAGA
1 AAAACATGAACCGTAGCATGCAAGAAAGGCAAGAGCTGAATATGACAACATCCTTTGATGCAAGA
* *
1060 GATGCTGCAGGTGAAATGCCATCGAGCTCCGACGATCAAGTCCATC
66 GATGCTGTAGGTGAAATGCCATTGAGCTCCGACGATCAAGTCCATC
** * * ** *
1106 AAAACATGAACCGTAGCATGCAAGAAAGGCAAGAGCTGAATATTCCAGCACCCGATGATGTAAGA
1 AAAACATGAACCGTAGCATGCAAGAAAGGCAAGAGCTGAATATGACAACATCCTTTGATGCAAGA
* * * * *
1171 GATGCTGCAGATGAAATGGCATCGAG-TTC--C-ATC--G---ATC
66 GATGCTGTAGGTGAAATGCCATTGAGCTCCGACGATCAAGTCCATC
* ** * ** *
1208 AAAACACGAACCGTAGCATGCAAGAAAGGCAAGAGCTGAATATTCCAACACCCGATGATGTAAGA
1 AAAACATGAACCGTAGCATGCAAGAAAGGCAAGAGCTGAATATGACAACATCCTTTGATGCAAGA
* * * *
1273 GATGCTGCAGGTGAAATGGCATCGAG-TTC--C-ATC--G---ATC
66 GATGCTGTAGGTGAAATGCCATTGAGCTCCGACGATCAAGTCCATC
* ** * * ** * * *
1310 AAAACACGAACCGTAGCATGCCTGGAACGCAAGAGCCAAATATGCCAACACCCTCTGATGCAAGA
1 AAAACATGAACCGTAGCATGCAAGAAAGGCAAGAGCTGAATATGACAACATCCTTTGATGCAAGA
* ** * * * *
1375 GAT-CTTGCAGGTGAAATGCCATTGAATTCCAAAGACCAAGTCAATC
66 GATGC-TGTAGGTGAAATGCCATTGAGCTCCGACGATCAAGTCCATC
* * ** * *
1421 AAGACATGGACTATGGCATGCAAGGAAGGCAAGAGCCTGAA
1 AAAACATGAACCGTAGCATGCAAGAAAGGCAAGAG-CTGAA
1462 GTGACGATCA
Statistics
Matches: 596, Mismatches: 75, Indels: 35
0.84 0.11 0.05
Matches are distributed among these distances:
101 1 0.00
102 178 0.30
103 2 0.00
105 1 0.00
106 2 0.00
107 3 0.01
108 2 0.00
110 2 0.00
111 395 0.66
112 10 0.02
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (111 bp):
AAAACATGAACCGTAGCATGCAAGAAAGGCAAGAGCTGAATATGACAACATCCTTTGATGCAAGA
GATGCTGTAGGTGAAATGCCATTGAGCTCCGACGATCAAGTCCATC
Found at i:1405 original size:102 final size:102
Alignment explanation
Indices: 1103--1392 Score: 447
Period size: 102 Copynumber: 2.8 Consensus size: 102
1093 GATCAAGTCC
* *
1103 ATCAAAACATGAACCGTAGCATGCAAGAAAGGCAAGAGCTGAATATTCCAGCACCCGATGATGTA
1 ATCAAAACACGAACCGTAGCATGCAAGAAAGGCAAGAGCTGAATATTCCAACACCCGATGATGTA
*
1168 AGAGATGCTGCAGATGAAATGGCATCGAGTTCCATCG
66 AGAGATGCTGCAGGTGAAATGGCATCGAGTTCCATCG
1205 ATCAAAACACGAACCGTAGCATGCAAGAAAGGCAAGAGCTGAATATTCCAACACCCGATGATGTA
1 ATCAAAACACGAACCGTAGCATGCAAGAAAGGCAAGAGCTGAATATTCCAACACCCGATGATGTA
1270 AGAGATGCTGCAGGTGAAATGGCATCGAGTTCCATCG
66 AGAGATGCTGCAGGTGAAATGGCATCGAGTTCCATCG
** * * ** * ** *
1307 ATCAAAACACGAACCGTAGCATGCCTGGAACGCAAGAGCCAAATATGCCAACACCCTCTGATGCA
1 ATCAAAACACGAACCGTAGCATGCAAGAAAGGCAAGAGCTGAATATTCCAACACCCGATGATGTA
1372 AGAGAT-CTTGCAGGTGAAATG
66 AGAGATGC-TGCAGGTGAAATG
1393 CCATTGAATT
Statistics
Matches: 174, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
101 1 0.01
102 173 0.99
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (102 bp):
ATCAAAACACGAACCGTAGCATGCAAGAAAGGCAAGAGCTGAATATTCCAACACCCGATGATGTA
AGAGATGCTGCAGGTGAAATGGCATCGAGTTCCATCG
Done.