Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CotAD_28621
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: 2889
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Found at i:760 original size:342 final size:342
Alignment explanation
Indices: 135--823 Score: 1166
Period size: 342 Copynumber: 2.0 Consensus size: 342
125 TACAGGCCAT
* * * *
135 TGTTAGAATGAAACATTATGCGCTTGTTGTTTTTCTGGGTAGCCAGATGGAATTACGGGGAGTTT
1 TGTTAGAATGAAACATTATGCGCTTGCTGTTTCTCTGGGCAGCCAGATGGAACTACGGGGAGTTT
*
200 CACATAATGCTTATTCTTTCACTATCTTGATTAATTGCTTTTGTCATTTAGGTAAAGTTGATTTT
66 CACATAATGCTTATTCTTTCACTATCTTGATTAATTGCTTTTGTCAGTTAGGTAAAGTTGATTTT
*
265 GGGTTTTCTGTTTTGGGGAAAATGCTCAAGTTAGGTTTTGAACCTAATGTTGTAACTTTGTCCAC
131 GGGTTTTCTGTTTTAGGGAAAATGCTCAAGTTAGGTTTTGAACCTAATGTTGTAACTTTGTCCAC
* * *
330 CTTGATTAATGGACTTTGTAATCAAAGCAGGGTTTCTCAGGCTGTGAATTTGTTTTATGAAATGA
196 CTTGATTAATGGACTTTGTAATCAAAGCAAGGTTTCTCAGGCTGTCAATTTGTTTGATGAAATGA
* * * *
395 TCGAAAAAGGGTATCGACCTGATTCATTTGCTTGCAATACAGTACTTAATGGGTTGTGCAAGTCT
261 TCAAAAAAGGGTATCGACCTGATTCAGTTGCTTACAATACAGTACTTAATGGGTTGTGCAAGACT
*
460 GGTAACACTGGTCGAGC
326 GGGAACACTGGTCGAGC
*
477 TGTTAGAATGAAACATTATGCGCTTGCTGTTTCTCTGGGCAGCCAGATGGAACTATGGGGAGTTT
1 TGTTAGAATGAAACATTATGCGCTTGCTGTTTCTCTGGGCAGCCAGATGGAACTACGGGGAGTTT
*
542 CACATGATGCTTATTCTTTCAAC-ATCTTGATTAATTGCTTTTGTCAGTTAGGTAAAGTTGATTT
66 CACATAATGCTTATTCTTTC-ACTATCTTGATTAATTGCTTTTGTCAGTTAGGTAAAGTTGATTT
*
606 TGGGTTTTCTGTTTTAGGGAAAATGCTCAAGTTAGGTTTTGAACCTGATGTTGTAACTTTGTCCA
130 TGGGTTTTCTGTTTTAGGGAAAATGCTCAAGTTAGGTTTTGAACCTAATGTTGTAACTTTGTCCA
*
671 CTTTGATTAATGGACTTTGTAATCAAAGCAAGGTTTCTCAGGCTG-CAAGTTTGTTTGATGAAAT
195 CCTTGATTAATGGACTTTGTAATCAAAGCAAGGTTTCTCAGGCTGTCAA-TTTGTTTGATGAAAT
* *
735 GATCAAAAAAGGGTGTCGACCTGATTCAGTTGCTTACAATACAGTACTTAATGGGTTGTGTAAGA
259 GATCAAAAAAGGGTATCGACCTGATTCAGTTGCTTACAATACAGTACTTAATGGGTTGTGCAAGA
800 CTGGGAACACTGGTCGAGC
324 CTGGGAACACTGGTCGAGC
819 TGTTA
1 TGTTA
824 AGTTTCTAAG
Statistics
Matches: 325, Mismatches: 20, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
341 2 0.01
342 321 0.99
343 2 0.01
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (342 bp):
TGTTAGAATGAAACATTATGCGCTTGCTGTTTCTCTGGGCAGCCAGATGGAACTACGGGGAGTTT
CACATAATGCTTATTCTTTCACTATCTTGATTAATTGCTTTTGTCAGTTAGGTAAAGTTGATTTT
GGGTTTTCTGTTTTAGGGAAAATGCTCAAGTTAGGTTTTGAACCTAATGTTGTAACTTTGTCCAC
CTTGATTAATGGACTTTGTAATCAAAGCAAGGTTTCTCAGGCTGTCAATTTGTTTGATGAAATGA
TCAAAAAAGGGTATCGACCTGATTCAGTTGCTTACAATACAGTACTTAATGGGTTGTGCAAGACT
GGGAACACTGGTCGAGC
Found at i:1262 original size:105 final size:104
Alignment explanation
Indices: 1069--1607 Score: 404
Period size: 105 Copynumber: 5.1 Consensus size: 104
1059 CAATGTTTCT
* * * * * * * * *
1069 CCTGATATTTTCACGTATAACATATTGATTGATGCACATTGCAAGGAGGGGACAATTTCGGAAGC
1 CCTGATGTTGTCACCTATAATATATTGGTTGATGCATATTGCAAGGAGAGGA-TATTTCTGAAGC
* * * ** * ** **
1134 TGTAAATATCTTTAATGCGATGAGAAAGCAAGGTGTCAAG
65 TGTAGATATCGTTCACACAATGAGAAAGCAAGGCATTGAG
* ** * *
1174 CCTGATGTTGTCACCTATAATATAGTGGTTGATGCATGGTGCAAGGAGAGGCTAATTTCTGAATC
1 CCTGATGTTGTCACCTATAATATATTGGTTGATGCATATTGCAAGGAGAGGAT-ATTTCTGAAGC
* * *
1239 TTTGGATATGGTTCACACAATGAGAAAGCAAGGCATTGAG
65 TGTAGATATCGTTCACACAATGAGAAAGCAAGGCATTGAG
* * * * * * **
1279 CCTGATGTTGTCACGTATAGTACATTAGTTGATGCACATTGCAAGGAGGGGAGGGTTTCTGAAGC
1 CCTGATGTTGTCACCTATAATATATTGGTTGATGCATATTGCAAGGAGAGGA-TATTTCTGAAGC
* * * * * *
1344 CGAAGATATTGTTGACACGATGAGAAAGGAAGGCATTGAG
65 TGTAGATATCGTTCACACAATGAGAAAGCAAGGCATTGAG
* * * *
1384 CCTGATGTTGTGACGTATAATATATTGGTTGATGCGTATTGCAAGGAGAGGAGTATTTCTAAAGC
1 CCTGATGTTGTCACCTATAATATATTGGTTGATGCATATTGCAAGGAGAGGA-TATTTCTGAAGC
* * ** *
1449 TGTAGATACCATTGC-CACAATGAGAAAGCAAGGTGTGGAG
65 TGTAGATATCGTT-CACACAATGAGAAAGCAAGGCATTGAG
* ** * *
1489 CCTGATGTTGTCACCTATAACATATTTATTGATGCACT-TTGCAAGAATG-GGATGGTTTCTGAA
1 CCTGATGTTGTCACCTATAATATATTGGTTGATGCA-TATTGCAAGGA-GAGGAT-ATTTCTGAA
* * * *
1552 GCTGAATG-TATTG-TCGACACAATGAGAAAACAATGCATTGAG
63 GCTGTA-GATATCGTTC-ACACAATGAGAAAGCAAGGCATTGAG
* *
1594 CCTAATTTTGTCAC
1 CCTGATGTTGTCAC
1608 ATACAGAACT
Statistics
Matches: 336, Mismatches: 89, Indels: 18
0.76 0.20 0.04
Matches are distributed among these distances:
103 1 0.00
104 2 0.01
105 330 0.98
106 3 0.01
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (104 bp):
CCTGATGTTGTCACCTATAATATATTGGTTGATGCATATTGCAAGGAGAGGATATTTCTGAAGCT
GTAGATATCGTTCACACAATGAGAAAGCAAGGCATTGAG
Found at i:1470 original size:210 final size:210
Alignment explanation
Indices: 1069--1607 Score: 541
Period size: 210 Copynumber: 2.6 Consensus size: 210
1059 CAATGTTTCT
* * * * * ** *
1069 CCTGATATTTTCACGTATAACATATTGATTGATGCACATTGCAAGGAGGGGACAATTTCGGAAGC
1 CCTGATGTTGTCACCTATAACACATTTATTGATGCACATTGCAAGGAGGGGACGGTTTCTGAAGC
* ** ** **
1134 TGTAA-ATATCT-TTAATGCGATGAGAAAGCAAGGTGTCAAGCCTGATGTTGTCACCTATAATAT
66 TG-AAGATAT-TGTTGACACGATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCACCTATAATAT
* * * * * ***
1197 AGTGGTTGATGCATGGTGCAAGGAGAGGCTAATTTCTGAATCTTTGGATATGGTTCACACAATGA
129 AGTGGTTGATGCATAGTGCAAGGAGAGGCTAATTTCTAAAGCTGTAGATACCATTCACACAATGA
*
1262 GAAAGCAAGGCATTGAG
194 GAAAGCAAGGCATGGAG
* ** *
1279 CCTGATGTTGTCACGTATAGTACA-TTAGTTGATGCACATTGCAAGGAGGGGAGGGTTTCTGAAG
1 CCTGATGTTGTCACCTATAACACATTTA-TTGATGCACATTGCAAGGAGGGGACGGTTTCTGAAG
* * * *
1343 CCGAAGATATTGTTGACACGATGAGAAAGGAAGGCATTGAGCCTGATGTTGTGACGTATAATATA
65 CTGAAGATATTGTTGACACGATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCACCTATAATATA
* * * *
1408 TTGGTTGATGCGTATTGCAAGGAGAGGAGT-ATTTCTAAAGCTGTAGATACCATTGC-CACAATG
130 GTGGTTGATGCATAGTGCAAGGAGAGG-CTAATTTCTAAAGCTGTAGATACCATT-CACACAATG
**
1471 AGAAAGCAAGGTGTGGAG
193 AGAAAGCAAGGCATGGAG
* * * * *
1489 CCTGATGTTGTCACCTATAACATATTTATTGATGCACTTTGCAAGAATGGGATGGTTTCTGAAGC
1 CCTGATGTTGTCACCTATAACACATTTATTGATGCACATTGCAAGGAGGGGACGGTTTCTGAAGC
* * * * * *
1554 TGAATG-TATTGTCGACACAATGAGAAAACAATGCATTGAGCCTAATTTTGTCAC
66 TGAA-GATATTGTTGACACGATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCAC
1608 ATACAGAACT
Statistics
Matches: 269, Mismatches: 53, Indels: 14
0.80 0.16 0.04
Matches are distributed among these distances:
209 5 0.02
210 258 0.96
211 6 0.02
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (210 bp):
CCTGATGTTGTCACCTATAACACATTTATTGATGCACATTGCAAGGAGGGGACGGTTTCTGAAGC
TGAAGATATTGTTGACACGATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCACCTATAATATAG
TGGTTGATGCATAGTGCAAGGAGAGGCTAATTTCTAAAGCTGTAGATACCATTCACACAATGAGA
AAGCAAGGCATGGAG
Found at i:2191 original size:22 final size:21
Alignment explanation
Indices: 2149--2192 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
2139 ATCCTCAACA
2149 CTTCATTGCAAAAGCTCGAAG
1 CTTCATTGCAAAAGCTCGAAG
2170 CTTCACTTGCTAAAAGCT-GAAG
1 CTTCA-TTGC-AAAAGCTCGAAG
2192 C
1 C
2193 AATCGGCTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.24
22 9 0.43
23 7 0.33
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (21 bp):
CTTCATTGCAAAAGCTCGAAG
Done.