Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3098
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: 38697
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Found at i:339 original size:39 final size:40
Alignment explanation
Indices: 203--382 Score: 177
Period size: 40 Copynumber: 4.3 Consensus size: 40
193 GCTACTCGTT
* * *
203 CAAATGCCTCCGGACATAGCCCGG-TTATAGTAACTCGCCA
1 CAAATGCCTTCGGACTTAACCCGGATTATAGTAACTCG-CA
*
243 CAAATGCACTTCGGAACTTAACCTGGATTAGGTAGTAACGATCGCA
1 CAAATGC-CTTCGG-ACTTAACCCGGATTA--TAGTAAC--TCGCA
289 CATAATGCCTTCGGACTTAACCCGGATT-TAGTAACTCGCA
1 CA-AATGCCTTCGGACTTAACCCGGATTATAGTAACTCGCA
* * * * *
329 CCAGTGCCTTCGGGCTTAGCCCGGAAT-TAGTAATCTCGCA
1 CAAATGCCTTCGGACTTAACCCGGATTATAGTAA-CTCGCA
369 CAAATGCCTTCGGA
1 CAAATGCCTTCGGA
383 TACTTAGTCA
Statistics
Matches: 118, Mismatches: 13, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
39 27 0.23
40 30 0.25
41 5 0.04
42 15 0.13
43 3 0.03
45 20 0.17
46 10 0.08
47 8 0.07
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGACTTAACCCGGATTATAGTAACTCGCA
Found at i:8260 original size:40 final size:40
Alignment explanation
Indices: 8223--8445 Score: 269
Period size: 40 Copynumber: 5.7 Consensus size: 40
8213 GCTACTCGTT
* *
8223 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
8263 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
8303 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCG--
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
8341 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
8380 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
8421 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
8446 CATCATTCAA
Statistics
Matches: 163, Mismatches: 13, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
37 20 0.12
38 16 0.10
39 11 0.07
40 103 0.63
41 13 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:8405 original size:117 final size:118
Alignment explanation
Indices: 8223--8445 Score: 301
Period size: 117 Copynumber: 1.9 Consensus size: 118
8213 GCTACTCGTT
*
8223 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
8288 ATTTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCG
66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCG
* * **
8341 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* * *
8403 GGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 GGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
8446 CATCATTCAA
Statistics
Matches: 92, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
116 4 0.04
117 66 0.72
118 22 0.24
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (118 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCG
Found at i:10361 original size:37 final size:37
Alignment explanation
Indices: 10311--10389 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
10301 TTATTACGAA
* *
10311 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
10348 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
10385 GTCTT
1 GTCTT
10390 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:10586 original size:47 final size:47
Alignment explanation
Indices: 10508--10857 Score: 547
Period size: 47 Copynumber: 7.4 Consensus size: 47
10498 CCCTTCGGGA
* * * * * * *
10508 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
10555 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
10602 CTTATCACATCTATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
10649 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
10696 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
10743 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10790 CTTATCACACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTAT--CACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10839 CTTATCACATATATACACT
1 CTTATCACATATATACACT
10858 GTCTTGGCTG
Statistics
Matches: 282, Mismatches: 19, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
47 236 0.84
49 46 0.16
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:17697 original size:39 final size:39
Alignment explanation
Indices: 17642--17825 Score: 280
Period size: 39 Copynumber: 4.7 Consensus size: 39
17632 TTCCAACCCA
** * *
17642 AATGCCTTCGCAACTTAGCGCGGATATAACATCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
* * *
17681 AATGCCTTCGGGACTTAGCCCGAATATAATATCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
* *
17720 AATGCCTTC-GAACTTAGCCCGGATATAATACCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
17758 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
17797 AATGCCTTCGGGACTTAGCCCGGATATAA
1 AATGCCTTCGGGACTTAGCCCGGATATAA
17826 ATCTCACACA
Statistics
Matches: 134, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
38 35 0.26
39 99 0.74
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
Found at i:17852 original size:77 final size:78
Alignment explanation
Indices: 17642--17857 Score: 289
Period size: 77 Copynumber: 2.8 Consensus size: 78
17632 TTCCAACCCA
* * *
17642 AATGCCTTCGCAACTTAGCGCGGATATAA-CATCAGCACGAATGCCTTCGGGACTTAGCCCGAAT
1 AATGCCTTCGGAACTTAGCCCGGATATAATC-TCAGCACGAATGCCTTCGGGACTTAGCCCGGAT
* *
17706 ATAATATCAGCACG
65 ATAACACCAGCACG
17720 AATGCCTTC-GAACTTAGCCCGGATATAATAC-CAGCACGAATGCCTTCGGGACTTAGCCCGGAT
1 AATGCCTTCGGAACTTAGCCCGGATATAAT-CTCAGCACGAATGCCTTCGGGACTTAGCCCGGAT
17783 ATAACACCAGCACG
65 ATAACACCAGCACG
* * * *
17797 AATGCCTTCGGGACTTAGCCCGGATATAAATCTCA-CAC-AAGGCCTGCGGGTCTTAGCCCGG
1 AATGCCTTCGGAACTTAGCCCGGATAT-AATCTCAGCACGAATGCCTTCGGGACTTAGCCCGG
17858 TTAAAATCCT
Statistics
Matches: 124, Mismatches: 9, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
77 89 0.72
78 29 0.23
79 6 0.05
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (78 bp):
AATGCCTTCGGAACTTAGCCCGGATATAATCTCAGCACGAATGCCTTCGGGACTTAGCCCGGATA
TAACACCAGCACG
Found at i:25161 original size:39 final size:40
Alignment explanation
Indices: 25084--25230 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
25074 TAGCTCCTCG
* * *
25084 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
25124 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
25163 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
25203 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
25231 ATTAATAACT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 27 0.29
40 65 0.71
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:25241 original size:80 final size:80
Alignment explanation
Indices: 25130--25310 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
25120 CTCATTCAAT
* * *
25130 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
25193 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
25209 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
25273 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
25290 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
25311 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:25270 original size:40 final size:40
Alignment explanation
Indices: 25127--25310 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
25117 TAACTCATTC
* *
25127 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
25167 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
25207 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
25247 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
25288 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
25311 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:32456 original size:41 final size:41
Alignment explanation
Indices: 32343--32461 Score: 147
Period size: 39 Copynumber: 3.0 Consensus size: 41
32333 CTCATTCAAT
* * * *
32343 GCCTTCGGGACTTAAC-CCGGATTTTA-AACTCGGCACGAAT
1 GCCTTCGGGACTTAACACCGGAATTAATAACTC-GCACAAAG
* *
32383 GCCTTCGGGACTT-A-ACCGGAATTAGTATCTCGCACAAAG
1 GCCTTCGGGACTTAACACCGGAATTAATAACTCGCACAAAG
32422 GCCTTCGGGACTTAACACCGGAATTAATAACTCGCACAAA
1 GCCTTCGGGACTTAACACCGGAATTAATAACTCGCACAAA
32462 TACCTTGATC
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
39 27 0.40
40 18 0.27
41 22 0.33
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (41 bp):
GCCTTCGGGACTTAACACCGGAATTAATAACTCGCACAAAG
Found at i:37928 original size:38 final size:37
Alignment explanation
Indices: 37885--38015 Score: 118
Period size: 40 Copynumber: 3.3 Consensus size: 37
37875 GGACTAAGAT
* *
37885 CCGAAGGTATTTGTGCGAGTTTATTTCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTTAATTCC-GGTTAAGTC
* * *
37923 GCGAAGGCCTTTGTGCGAGATACTAATTCCGGTTAAGTC
1 CCGAAGGCATTTGTGCGAG-T-TTAATTCCGGTTAAGTC
* *
37962 CCGAAAGGCATTCGTGCGAGTTTTAAAAATCCGGTGTTAAGTC
1 CCG-AAGGCATTTGTGCGAG-TTT--AATTCC-G-GTTAAGTC
38005 CCGAAGGCATT
1 CCGAAGGCATT
38016 GAATGAGTTA
Statistics
Matches: 75, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
38 16 0.21
39 13 0.17
40 21 0.28
41 5 0.07
42 9 0.12
43 11 0.15
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (37 bp):
CCGAAGGCATTTGTGCGAGTTTAATTCCGGTTAAGTC
Found at i:38024 original size:41 final size:40
Alignment explanation
Indices: 37953--38063 Score: 107
Period size: 41 Copynumber: 2.7 Consensus size: 40
37943 TACTAATTCC
** *
37953 GGTTAAGTCCCGAAAGGCATTCGTGCGAGTT-TTAAAAATCCG
1 GGTTAAGTCCCG-AAGGCATT-GAACGAGTTACTAAAAA-CCG
* *
37995 GTGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAAACCG
1 G-GTTAAGTCCCGAAGGCATTGAACGAGTTACTAAAAACCG
* *
38036 GGCTATGTCCCGAAGGCACTTGAACGAG
1 GGTTAAGTCCCGAAGGCA-TTGAACGAG
38064 GAGCTAAATC
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
40 15 0.26
41 18 0.31
42 14 0.24
43 11 0.19
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (40 bp):
GGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAAAACCG
Done.