Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CotAD_46959
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, 545
Length: 909
ACGTcount: A:0.39, C:0.31, G:0.14, T:0.16
Found at i:214 original size:45 final size:45
Alignment explanation
Indices: 165--447 Score: 295
Period size: 45 Copynumber: 6.3 Consensus size: 45
155 CGGTTTATAC
* * *
165 ACCTCCAAAAAAAGAGAAGCCTGAACCCAAACCACCAGTGTATGA
1 ACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTATATGA
* * * *
210 ACCTCCTAAGAAGGAGAAGCCTGAACCTAAACCACCAGTATATGA
1 ACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTATATGA
* * * * * * * *
255 ACCTCCAAAGAAGGAGAAACTTGAGCCAAAATCACCGGTTTATGC
1 ACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTATATGA
300 ACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCCA-TATATGA
1 ACCTCCAAAGAAAGAGAAACCTGAACCCAAACCA-CCAGTATATGA
* * * * * *
345 ACCTCCAAAGAAGGAGAAGCCCG-AGCCAAAGCCACCGGTTTAT-A
1 ACCTCCAAAGAAAGAGAAACCTGAACCCAAA-CCACCAGTATATGA
* * *
389 CACCTCCAAAGAAAAAGAAACCTGAACCCAAACCACCAATGTATGA
1 -ACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTATATGA
435 ACCTCCAAA-AAAG
1 ACCTCCAAAGAAAG
448 CCTCCAATGT
Statistics
Matches: 195, Mismatches: 37, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
44 12 0.06
45 174 0.89
46 9 0.05
ACGTcount: A:0.43, C:0.29, G:0.16, T:0.13
Consensus pattern (45 bp):
ACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTATATGA
Found at i:245 original size:90 final size:90
Alignment explanation
Indices: 165--647 Score: 354
Period size: 102 Copynumber: 5.1 Consensus size: 90
155 CGGTTTATAC
* * * * * * *
165 ACCTCCAAAAAAAGAGAAGCCTGAACCCAAACCACCAGTGTATGAACCTCCTAAGAAGGAGAAGC
1 ACCTCCAAAGAAGGAGAAGCCTGAACCCAAACCACCGGTTTATGAACCTCCAAAGAAAGAGAAAC
*
230 CTGAACCTAAACCACCAGTATATGA
66 CTGAACCCAAACCACCAGTATATGA
* * * * * *
255 ACCTCCAAAGAAGGAGAAACTTGAGCCAAAATCACCGGTTTATGCACCTCCAAAGAAAGAGAAAC
1 ACCTCCAAAGAAGGAGAAGCCTGAACCCAAACCACCGGTTTATGAACCTCCAAAGAAAGAGAAAC
320 CTGAACCCAAACCACCCA-TATATGA
66 CTGAACCCAAACCA-CCAGTATATGA
* * *
345 ACCTCCAAAGAAGGAGAAGCCCG-AGCCAAAGCCACCGGTTTAT-ACACCTCCAAAGAAAAAGAA
1 ACCTCCAAAGAAGGAGAAGCCTGAACCCAAA-CCACCGGTTTATGA-ACCTCCAAAGAAAGAGAA
* *
408 ACCTGAACCCAAACCACCAATGTATGA
64 ACCTGAACCCAAACCACCAGTATATGA
* *
435 ACCTCCAAAAAAGCCTCCAATGTACGAA-CCT-AAGCCACCAAAACCATCGGTTTAT-ACACCTC
1 ACCTCC---AAAG-----AA-GGA-GAAGCCTGAA--C-CC-AAACCACCGGTTTATGA-ACCTC
* * *
497 CAAAGAAAAAGAAACCTGAACCCAAACCACCAATGTATGA
51 CAAAGAAAGAGAAACCTGAACCCAAACCACCAGTATATGA
*
537 ACCTCCAAAAAAGCCTCCAATGTACGAA-CCT-AAGCCACCAAAACCACCGGTTTAT-ACACCTC
1 ACCTCC---AAAG-----AA-GGA-GAAGCCTGAA--C-CC-AAACCACCGGTTTATGA-ACCTC
* * *
599 CAAAGAAAAAGAAACCTGAACCCAAACCACCAATGTATGA
51 CAAAGAAAGAGAAACCTGAACCCAAACCACCAGTATATGA
639 ACCTCCAAA
1 ACCTCCAAA
648 AAAGCCTCCA
Statistics
Matches: 345, Mismatches: 29, Indels: 29
0.86 0.07 0.07
Matches are distributed among these distances:
89 7 0.02
90 148 0.43
91 3 0.01
93 4 0.01
98 2 0.01
99 8 0.02
100 3 0.01
102 167 0.48
103 3 0.01
ACGTcount: A:0.43, C:0.30, G:0.14, T:0.13
Consensus pattern (90 bp):
ACCTCCAAAGAAGGAGAAGCCTGAACCCAAACCACCGGTTTATGAACCTCCAAAGAAAGAGAAAC
CTGAACCCAAACCACCAGTATATGA
Found at i:394 original size:135 final size:135
Alignment explanation
Indices: 152--401 Score: 371
Period size: 135 Copynumber: 1.9 Consensus size: 135
142 GAACCTAAGC
* * *
152 CACCGGTTTATACACCTCCAAAAAAAGAGAAGCCTGAACCCAAACCACCAGTGTATGAACCTCCT
1 CACCGGTTTATACACCTCCAAAAAAAGAGAAACCTGAACCCAAACCACCAGTATATGAACCTCCA
*
217 AAGAAGGAGAAGCCTGAACCTAAACCACCAGTATATGAACCTCCAAAGAAGGAGAAACTTGAGCC
66 AAGAAGGAGAAGCCCGAACCTAAACCACCAGTATATGAACCTCCAAAGAAGGAGAAACTTGAGCC
282 AAAAT
131 AAAAT
* *
287 CACCGGTTTATGCACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCCA-TATATGAACCTCC
1 CACCGGTTTATACACCTCCAAAAAAAGAGAAACCTGAACCCAAACCA-CCAGTATATGAACCTCC
* * *
351 AAAGAAGGAGAAGCCCGAGCC-AAAGCCACCGGTTTAT-ACACCTCCAAAGAA
65 AAAGAAGGAGAAGCCCGAACCTAAA-CCACCAGTATATGA-ACCTCCAAAGAA
402 AAAGAAACCT
Statistics
Matches: 103, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
134 4 0.04
135 96 0.93
136 3 0.03
ACGTcount: A:0.40, C:0.29, G:0.17, T:0.14
Consensus pattern (135 bp):
CACCGGTTTATACACCTCCAAAAAAAGAGAAACCTGAACCCAAACCACCAGTATATGAACCTCCA
AAGAAGGAGAAGCCCGAACCTAAACCACCAGTATATGAACCTCCAAAGAAGGAGAAACTTGAGCC
AAAAT
Found at i:439 original size:135 final size:134
Alignment explanation
Indices: 165--447 Score: 347
Period size: 135 Copynumber: 2.1 Consensus size: 134
155 CGGTTTATAC
* * *
165 ACCTCCAAAAAAAGAGAAGCCTGAACCCAAACCACCAGTGTATGAACCTCCTAAGAAGGAGAAGC
1 ACCTCC-AAAAAAGAGAAACCTGAACCCAAACCACCAGTATATGAACCTCCAAAGAAGGAGAAGC
* ** * * * ** *
230 CTGAACCTAAACCACCAGTATATGAACCTCCAAAGAAGGAGAAACTTGAGCCAAAATCACCGGTT
65 CCGAACCTAAACCACCAGTATATGAACCTCCAAAGAAAAAGAAACCTGAACCAAAACCACCAATG
*
295 TATGC
130 TATGA
300 ACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCCA-TATATGAACCTCCAAAGAAGGAGAAG
1 ACCTCCAAA-AAAGAGAAACCTGAACCCAAACCA-CCAGTATATGAACCTCCAAAGAAGGAGAAG
* * * *
364 CCCGAGCC-AAAGCCACCGGTTTAT-ACACCTCCAAAGAAAAAGAAACCTGAACCCAAACCACCA
64 CCCGAACCTAAA-CCACCAGTATATGA-ACCTCCAAAGAAAAAGAAACCTGAACCAAAACCACCA
427 ATGTATGA
127 ATGTATGA
435 ACCTCCAAAAAAG
1 ACCTCCAAAAAAG
448 CCTCCAATGT
Statistics
Matches: 127, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
134 11 0.09
135 113 0.89
136 3 0.02
ACGTcount: A:0.43, C:0.29, G:0.16, T:0.13
Consensus pattern (134 bp):
ACCTCCAAAAAAGAGAAACCTGAACCCAAACCACCAGTATATGAACCTCCAAAGAAGGAGAAGCC
CGAACCTAAACCACCAGTATATGAACCTCCAAAGAAAAAGAAACCTGAACCAAAACCACCAATGT
ATGA
Found at i:513 original size:48 final size:48
Alignment explanation
Indices: 461--716 Score: 133
Period size: 57 Copynumber: 5.1 Consensus size: 48
451 CCAATGTACG
*
461 AACCTAAGCCACCAAAACCATCGGTTTATACACCTCCAAAGAAAAAGA
1 AACCTAAGCCACCAAAACCACCGGTTTATACACCTCCAAAGAAAAAGA
** *
509 AACCTGAA--C-CC-AAACCACCAATGTATGA-ACCTCCAAA-AAAGCCTCCAATGTA
1 AACCT-AAGCCACCAAAACCACCGGTTTAT-ACACCTCCAAAGAAA------AA-G-A
561 CGAACCTAAGCCACCAAAACCACCGGTTTATACACCTCCAAAGAAAAAGA
1 --AACCTAAGCCACCAAAACCACCGGTTTATACACCTCCAAAGAAAAAGA
** *
611 AACCTGAA--C-CC-AAACCACCAATGTATGA-ACCTCCAAA-AAAGCCTCCAATGTA
1 AACCT-AAGCCACCAAAACCACCGGTTTAT-ACACCTCCAAAGAAA------AA-G-A
663 CGAACCTAAGCCACCAAAACCACCGGTTTATACACCTCCAAAGAAAGAA-A
1 --AACCTAAGCCACCAAAACCACCGGTTTATACACCTCCAAAGAAA-AAGA
713 AACC
1 AACC
717 AGAACCCAAG
Statistics
Matches: 158, Mismatches: 14, Indels: 72
0.65 0.06 0.30
Matches are distributed among these distances:
44 6 0.04
45 41 0.26
46 6 0.04
47 2 0.01
48 14 0.09
49 4 0.03
50 6 0.04
51 3 0.02
52 4 0.03
53 6 0.04
54 10 0.06
55 2 0.01
56 6 0.04
57 42 0.27
58 6 0.04
ACGTcount: A:0.44, C:0.32, G:0.11, T:0.14
Consensus pattern (48 bp):
AACCTAAGCCACCAAAACCACCGGTTTATACACCTCCAAAGAAAAAGA
Found at i:524 original size:45 final size:45
Alignment explanation
Indices: 475--629 Score: 118
Period size: 45 Copynumber: 3.2 Consensus size: 45
465 TAAGCCACCA
*
475 AAACCATCGGTTTATACACCTCCAAAGAAAAAGAAACCTGAACCC
1 AAACCACCGGTTTATACACCTCCAAAGAAAAAGAAACCTGAACCC
** *
520 AAACCACCAATGTATGA-ACCTCCAAA-AAAGCCTCCAATGTACGAACCT-AAGCCACC
1 AAACCACCGGTTTAT-ACACCTCCAAAGAAA------AA-G-A--AACCTGAA--C-CC
576 AAAACCACCGGTTTATACACCTCCAAAGAAAAAGAAACCTGAACCC
1 -AAACCACCGGTTTATACACCTCCAAAGAAAAAGAAACCTGAACCC
622 AAACCACC
1 AAACCACC
630 AATGTATGAA
Statistics
Matches: 85, Mismatches: 7, Indels: 36
0.66 0.05 0.28
Matches are distributed among these distances:
44 3 0.04
45 28 0.33
46 3 0.04
47 1 0.01
48 5 0.06
49 2 0.02
50 3 0.04
51 2 0.02
52 3 0.04
53 2 0.02
54 5 0.06
55 1 0.01
56 3 0.04
57 21 0.25
58 3 0.04
ACGTcount: A:0.44, C:0.32, G:0.10, T:0.14
Consensus pattern (45 bp):
AAACCACCGGTTTATACACCTCCAAAGAAAAAGAAACCTGAACCC
Found at i:834 original size:102 final size:102
Alignment explanation
Indices: 370--746 Score: 693
Period size: 102 Copynumber: 3.7 Consensus size: 102
360 GAAGCCCGAG
*
370 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAAAGAAACCTGAACCCAAACCACCAATGTATGA
1 CCAAAACCACCGGTTTATACACCTCCAAAGAAAAAGAAACCTGAACCCAAACCACCAATGTATGA
435 ACCTCCAAAAAAGCCTCCAATGTACGAACCTAAGCCA
66 ACCTCCAAAAAAGCCTCCAATGTACGAACCTAAGCCA
*
472 CCAAAACCATCGGTTTATACACCTCCAAAGAAAAAGAAACCTGAACCCAAACCACCAATGTATGA
1 CCAAAACCACCGGTTTATACACCTCCAAAGAAAAAGAAACCTGAACCCAAACCACCAATGTATGA
537 ACCTCCAAAAAAGCCTCCAATGTACGAACCTAAGCCA
66 ACCTCCAAAAAAGCCTCCAATGTACGAACCTAAGCCA
574 CCAAAACCACCGGTTTATACACCTCCAAAGAAAAAGAAACCTGAACCCAAACCACCAATGTATGA
1 CCAAAACCACCGGTTTATACACCTCCAAAGAAAAAGAAACCTGAACCCAAACCACCAATGTATGA
639 ACCTCCAAAAAAGCCTCCAATGTACGAACCTAAGCCA
66 ACCTCCAAAAAAGCCTCCAATGTACGAACCTAAGCCA
* * *
676 CCAAAACCACCGGTTTATACACCTCCAAAGAAAGAA-AAACCAGAACCCAAGCCACCAATGTATC
1 CCAAAACCACCGGTTTATACACCTCCAAAGAAA-AAGAAACCTGAACCCAAACCACCAATGTATG
740 AACCTCC
65 AACCTCC
747 CAACAACCCA
Statistics
Matches: 268, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
102 266 0.99
103 2 0.01
ACGTcount: A:0.43, C:0.33, G:0.11, T:0.14
Consensus pattern (102 bp):
CCAAAACCACCGGTTTATACACCTCCAAAGAAAAAGAAACCTGAACCCAAACCACCAATGTATGA
ACCTCCAAAAAAGCCTCCAATGTACGAACCTAAGCCA
Found at i:834 original size:204 final size:204
Alignment explanation
Indices: 370--807 Score: 698
Period size: 204 Copynumber: 2.1 Consensus size: 204
360 GAAGCCCGAG
370 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAAAGAAACCTGAACCCAAACCACCAATGTATGA
1 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAAAGAAACCTGAACCCAAACCACCAATGTATGA
*
435 ACCTCCAAAAAAGCCTCCAATGTACGAACCTAAGCCACCAAAACCATCGGTTTATACACCTCCAA
66 ACCTCCAAAAAAGCCTCCAATGTACGAACCTAAGCCACCAAAACCACCGGTTTATACACCTCCAA
* * * * *
500 AGAAAAAGAAACCTGAACCCAAACCACCAATGTATGAACCTCCAAAAAAGCCTCCAATGTACGAA
131 AGAAAAAGAAACCAGAACCCAAACCACCAATGTATCAACCTCCAAAAAACCCACCAATATACGAA
* *
565 CCTAAGCCA
196 CCAAAACCA
*
574 CCAAAACCACCGGTTTATACACCTCCAAAGAAAAAGAAACCTGAACCCAAACCACCAATGTATGA
1 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAAAGAAACCTGAACCCAAACCACCAATGTATGA
639 ACCTCCAAAAAAGCCTCCAATGTACGAACCTAAGCCACCAAAACCACCGGTTTATACACCTCCAA
66 ACCTCCAAAAAAGCCTCCAATGTACGAACCTAAGCCACCAAAACCACCGGTTTATACACCTCCAA
* * * *
704 AGAAAGAA-AAACCAGAACCCAAGCCACCAATGTATCAACCTCCCAACAACCCACCAATATATGA
131 AGAAA-AAGAAACCAGAACCCAAACCACCAATGTATCAACCTCCAAAAAACCCACCAATATACGA
*
768 GCCAAAACCA
195 ACCAAAACCA
* * * *
778 CCTAAGCCACCAGTTTATGCACCACCAAAG
1 CCAAAGCCACCGGTTTATACACCTCCAAAG
808 GAAGAAAAGC
Statistics
Matches: 214, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
204 212 0.99
205 2 0.01
ACGTcount: A:0.42, C:0.33, G:0.11, T:0.14
Consensus pattern (204 bp):
CCAAAGCCACCGGTTTATACACCTCCAAAGAAAAAGAAACCTGAACCCAAACCACCAATGTATGA
ACCTCCAAAAAAGCCTCCAATGTACGAACCTAAGCCACCAAAACCACCGGTTTATACACCTCCAA
AGAAAAAGAAACCAGAACCCAAACCACCAATGTATCAACCTCCAAAAAACCCACCAATATACGAA
CCAAAACCA
Done.