Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_22457
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, 540
Length: 900
ACGTcount: A:0.38, C:0.31, G:0.16, T:0.15
Found at i:221 original size:45 final size:44
Alignment explanation
Indices: 144--539 Score: 359
Period size: 45 Copynumber: 8.8 Consensus size: 44
134 CACCACCATA
* * * *
144 TGAACCTAAGCCACCAGTGTATGAACCACCAAAAAAGGAGAAGCC
1 TGAACCAAAACCACCAGTTTATGAACCTCCAAAAAA-GAGAAGCC
* * * *
189 TGAACCTAAGCCACCGGTTTATGCACCTCCAAAGAAAGAGAAGCC
1 TGAACCAAAACCACCAGTTTATGAACCTCCAAA-AAAGAGAAGCC
* * * *
234 TGGACCCAAACCACCAGTGTATGAACCTCCAAAGAAGGAGAAGCC
1 TGAACCAAAACCACCAGTTTATGAACCTCCAAA-AAAGAGAAGCC
* * *
279 TGAGCCAAAGCCACCAGTTTAT-ACACCTCCAAAGAAAGAGGAGCC
1 TGAACCAAAACCACCAGTTTATGA-ACCTCCAAA-AAAGAGAAGCC
* * * * *
324 TAAACCTAAACCACCAGTATATGAACCTCCAAAGAAGGAGAAACC
1 TGAACCAAAACCACCAGTTTATGAACCTCCAAA-AAAGAGAAGCC
* *
369 TGAGCCAAAACCACC-GATTTAT-ACACCTCCAAAGAAAGAGAAACC
1 TGAACCAAAACCACCAG-TTTATGA-ACCTCCAAA-AAAGAGAAGCC
* * * *
414 TGAACCCAAACCACCCGTATATGAACCTCCAAAGAAGGAGAAGCC
1 TGAACCAAAACCACCAGTTTATGAACCTCCAAA-AAAGAGAAGCC
* * * * *
459 CGAGCCAAAGCCACCGGTTTAT-ACACCTCCAAAGAAAGAGAAACC
1 TGAACCAAAACCACCAGTTTATGA-ACCTCCAAA-AAAGAGAAGCC
* *
504 TGAACCCAAACCACCAGTGTATGAACCTCCAAAAAA
1 TGAACCAAAACCACCAGTTTATGAACCTCCAAAAAA
540 ACCTCCAATG
Statistics
Matches: 292, Mismatches: 50, Indels: 19
0.81 0.14 0.05
Matches are distributed among these distances:
44 7 0.02
45 278 0.95
46 7 0.02
ACGTcount: A:0.41, C:0.29, G:0.17, T:0.13
Consensus pattern (44 bp):
TGAACCAAAACCACCAGTTTATGAACCTCCAAAAAAGAGAAGCC
Found at i:307 original size:90 final size:90
Alignment explanation
Indices: 144--737 Score: 643
Period size: 90 Copynumber: 6.3 Consensus size: 90
134 CACCACCATA
* * * * * *
144 TGAACCTAAGCCACCAGTGTATGAACCACCAAAAAAGGAGAAGCCTGAACCTAAGCCACCGGTTT
1 TGAACCCAAACCACCAGTGTATGAACCTCCAAAGAAGGAGAAGCCTGAGCCAAAGCCACCGGTTT
* *
209 ATGCACCTCCAAAGAAAGAGAAGCC
66 ATACACCTCCAAAGAAAGAGAAACC
* *
234 TGGACCCAAACCACCAGTGTATGAACCTCCAAAGAAGGAGAAGCCTGAGCCAAAGCCACCAGTTT
1 TGAACCCAAACCACCAGTGTATGAACCTCCAAAGAAGGAGAAGCCTGAGCCAAAGCCACCGGTTT
* *
299 ATACACCTCCAAAGAAAGAGGAGCC
66 ATACACCTCCAAAGAAAGAGAAACC
* * * * * *
324 TAAACCTAAACCACCAGTATATGAACCTCCAAAGAAGGAGAAACCTGAGCCAAAACCACCGATTT
1 TGAACCCAAACCACCAGTGTATGAACCTCCAAAGAAGGAGAAGCCTGAGCCAAAGCCACCGGTTT
389 ATACACCTCCAAAGAAAGAGAAACC
66 ATACACCTCCAAAGAAAGAGAAACC
* * *
414 TGAACCCAAACCACCCGTATATGAACCTCCAAAGAAGGAGAAGCCCGAGCCAAAGCCACCGGTTT
1 TGAACCCAAACCACCAGTGTATGAACCTCCAAAGAAGGAGAAGCCTGAGCCAAAGCCACCGGTTT
479 ATACACCTCCAAAGAAAGAGAAACC
66 ATACACCTCCAAAGAAAGAGAAACC
* * *
504 TGAACCCAAACCACCAGTGTATGAACCTCCAAAAAAACCTCCAATGTACGAA-CCTAAGCCACCA
1 TGAACCCAAACCACCAGTGTATGAACCTCC----AAA----GAA-GGA-GAAGCCTGAG---CCA
*
568 AAACCACCGGTTTATACACCTCCAAAGAAAGAGAAACC
53 AAGCCACCGGTTTATACACCTCCAAAGAAAGAGAAACC
* * *
606 TGAACCCAAACCACCAATGTATGAACCTCCAAAAAAGCCTCCAATGTATGAA-CCTAAGCCACCA
1 TGAACCCAAACCACCAGTGTATGAACCTCC---AAAG-----AA-GGA-GAAGCCTGAG---CCA
*
670 AAGCCACCGGTTTATACACCTCCAAAGAAAGAAAAACC
53 AAGCCACCGGTTTATACACCTCCAAAGAAAGAGAAACC
* * * *
708 AGAACCCAAGCCACCAATGTATCAACCTCC
1 TGAACCCAAACCACCAGTGTATGAACCTCC
738 CAACAACCCA
Statistics
Matches: 444, Mismatches: 42, Indels: 24
0.87 0.08 0.05
Matches are distributed among these distances:
90 271 0.61
94 3 0.01
98 2 0.00
99 6 0.01
100 3 0.01
101 6 0.01
102 153 0.34
ACGTcount: A:0.41, C:0.30, G:0.15, T:0.13
Consensus pattern (90 bp):
TGAACCCAAACCACCAGTGTATGAACCTCCAAAGAAGGAGAAGCCTGAGCCAAAGCCACCGGTTT
ATACACCTCCAAAGAAAGAGAAACC
Found at i:572 original size:57 final size:56
Alignment explanation
Indices: 511--695 Score: 146
Period size: 57 Copynumber: 3.5 Consensus size: 56
501 ACCTGAACCC
511 AAACCACCAGTGTATGA-ACCTCCAAAAAAACCTCCAATGTACGAACCTAAGCCACCA
1 AAACCACCAGTGTAT-ACACCTCCAAAAAAACCTCCAATGTA-GAACCTAAGCCACCA
* * * *
568 AAACCACCGGTTTATACACCTCCAAAGAAA-----GA-G-A-AACCTGAA--C-CC-
1 AAACCACCAGTGTATACACCTCCAAAAAAACCTCCAATGTAGAACCT-AAGCCACCA
* *
613 AAACCACCAATGTATGA-ACCTCCAAAAAAGCCTCCAATGTATGAACCTAAGCCACCA
1 AAACCACCAGTGTAT-ACACCTCCAAAAAAACCTCCAATGTA-GAACCTAAGCCACCA
* * *
670 AAGCCACCGGTTTATACACCTCCAAA
1 AAACCACCAGTGTATACACCTCCAAA
696 GAAAGAAAAA
Statistics
Matches: 97, Mismatches: 14, Indels: 34
0.67 0.10 0.23
Matches are distributed among these distances:
45 23 0.24
46 3 0.03
47 1 0.01
48 5 0.05
49 2 0.02
50 2 0.02
51 2 0.02
52 2 0.02
53 2 0.02
54 5 0.05
55 1 0.01
56 4 0.04
57 45 0.46
ACGTcount: A:0.41, C:0.32, G:0.11, T:0.15
Consensus pattern (56 bp):
AAACCACCAGTGTATACACCTCCAAAAAAACCTCCAATGTAGAACCTAAGCCACCA
Found at i:839 original size:102 final size:102
Alignment explanation
Indices: 463--822 Score: 488
Period size: 102 Copynumber: 3.5 Consensus size: 102
453 GAAGCCCGAG
* *
463 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTGTATGA
1 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAGAGAAACCAGAACCCAAACCACCAATGTATGA
*
528 ACCTCCAAAAAAACCTCCAATGTACGAACCTAAGCCA
66 ACCTCCAAAAAAACCTCCAATGTATGAACCTAAGCCA
* *
565 CCAAAACCACCGGTTTATACACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCAATGTATGA
1 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAGAGAAACCAGAACCCAAACCACCAATGTATGA
*
630 ACCTCCAAAAAAGCCTCCAATGTATGAACCTAAGCCA
66 ACCTCCAAAAAAACCTCCAATGTATGAACCTAAGCCA
* * *
667 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAGAAAAACCAGAACCCAAGCCACCAATGTATCA
1 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAGAGAAACCAGAACCCAAACCACCAATGTATGA
* * * * * * * *
732 ACCTCCCAACAACCCACCAATATATGAGCCAAAACCA
66 ACCTCCAAAAAAACCTCCAATGTATGAACCTAAGCCA
* * * * * * *
769 CCTAAGCCACCAGTTTATGCACCACCAAAGGAAGA-AAAGCCAAAACCTAAACCA
1 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAGAGAAA-CCAGAACCCAAACCA
823 TCAGTTTATG
Statistics
Matches: 232, Mismatches: 25, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
101 3 0.01
102 229 0.99
ACGTcount: A:0.42, C:0.33, G:0.12, T:0.13
Consensus pattern (102 bp):
CCAAAGCCACCGGTTTATACACCTCCAAAGAAAGAGAAACCAGAACCCAAACCACCAATGTATGA
ACCTCCAAAAAAACCTCCAATGTATGAACCTAAGCCA
Done.