Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1963
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: 25915
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Found at i:3339 original size:45 final size:46
Alignment explanation
Indices: 3275--3449 Score: 216
Period size: 45 Copynumber: 3.8 Consensus size: 46
3265 TGTAACCCGC
*
3275 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
* *
3320 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C--GTTCGCAT
* *
3370 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
*
3413 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
3450 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 9, Indels: 19
0.80 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 36 0.32
46 29 0.26
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
Found at i:3440 original size:93 final size:92
Alignment explanation
Indices: 3282--3452 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 92
3272 CGCCCATAAG
*
3282 CGAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 CGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
3347 CGAGTTCGGATGCCTAGTTACATCTCA
66 CGAGTTCGGATGCCTAGTTACATCTCA
*
3374 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCA
3439 ACGAGTTCGGATGC
65 ACGAGTTCGGATGC
3453 TCAACCATCC
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
92 28 0.37
93 48 0.63
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (92 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCA
Found at i:10882 original size:46 final size:46
Alignment explanation
Indices: 10815--10941 Score: 227
Period size: 46 Copynumber: 2.8 Consensus size: 46
10805 TAACCCGCCT
* * *
10815 ATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCC
1 ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCC
10861 ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCC
1 ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCC
10907 ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
10942 TGCTCAACCA
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 78 1.00
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.20
Consensus pattern (46 bp):
ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCC
Found at i:11398 original size:30 final size:30
Alignment explanation
Indices: 11363--11419 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
11353 TAACTCAATT
11363 TTTTGCAAAATTACAATTTTACCCCTAAAC
1 TTTTGCAAAATTACAATTTTACCCCTAAAC
* * * *
11393 TTTTGCATATTTACATTTTTGCCCCTA
1 TTTTGCAAAATTACAATTTTACCCCTA
11420 GGCTCGGGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.44
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTACCCCTAAAC
Found at i:19518 original size:119 final size:120
Alignment explanation
Indices: 19334--19558 Score: 305
Period size: 119 Copynumber: 1.9 Consensus size: 120
19324 GCTCCTCGTT
*
19334 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
19399 ATTTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * **
19454 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* * *
19516 GGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 GGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
19559 CATCATTCAA
Statistics
Matches: 92, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
118 4 0.04
119 66 0.72
120 22 0.24
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:19558 original size:40 final size:40
Alignment explanation
Indices: 19334--19558 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
19324 GCTCCTCGTT
* *
19334 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
19374 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
19414 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
19454 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
19493 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
19534 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
19559 CATCATTCAA
Statistics
Matches: 166, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
38 2 0.01
39 32 0.19
40 120 0.72
41 12 0.07
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Done.