Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3489
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: 27794
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Found at i:2082 original size:29 final size:28
Alignment explanation
Indices: 2050--2110 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 28
2040 ATTCATATTC
2050 ATATGGCCCATTACGCCCAAATCACCTTT
1 ATATGGCCCATTACGCCCAAATCACC-TT
* *
2079 ATATGGCCCGTTAGGCCCAAATCACCTT
1 ATATGGCCCATTACGCCCAAATCACCTT
2107 ATAT
1 ATAT
2111 TCATGCTCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 6 0.20
29 24 0.80
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (28 bp):
ATATGGCCCATTACGCCCAAATCACCTT
Found at i:4376 original size:47 final size:47
Alignment explanation
Indices: 4268--4398 Score: 153
Period size: 47 Copynumber: 2.8 Consensus size: 47
4258 GACACATCTC
*
4268 GTAGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAA
1 GTAGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTC-TATCAA
*
4316 -T-GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-TAT-AA
1 GTAGCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCTATCAA
* * *
4361 TGTAGCCGATGCATGTACCAGGCATATCTTACACTAGC
1 -GTAGCCGATGCATGTCCCAGACATGTCTTACACTAGC
4399 CCACAATAAC
Statistics
Matches: 72, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
45 2 0.03
46 20 0.28
47 28 0.39
48 22 0.31
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (47 bp):
GTAGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCTATCAA
Found at i:5313 original size:10 final size:9
Alignment explanation
Indices: 5289--5313 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5279 TTCAAGGATC
5289 TCAAAAACA
1 TCAAAAACA
5298 TCAAAAACA
1 TCAAAAACA
5307 TCAAAAA
1 TCAAAAA
5314 TCAACACCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.20, G:0.00, T:0.12
Consensus pattern (9 bp):
TCAAAAACA
Found at i:10859 original size:48 final size:46
Alignment explanation
Indices: 10729--10899 Score: 202
Period size: 46 Copynumber: 3.7 Consensus size: 46
10719 CACTGACACA
*
10729 GCCGATGCATGTCCCAGACATGTCTTACACTGGCT-TACATCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCT-CATCTCAAG
* * * * *
10775 GCCAATGCATGTCCTAGACATGTCTTACACTAGCTCTCGTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCAAG
* *
10821 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-ATG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCAT-CTCAAG
* *
10869 GCCGATGCATGTCCCAAACATGTCTTGCACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
10900 AGCCCACAAT
Statistics
Matches: 106, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
46 53 0.50
47 27 0.25
48 25 0.24
49 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.27
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCAAG
Found at i:10877 original size:94 final size:91
Alignment explanation
Indices: 10729--10902 Score: 235
Period size: 94 Copynumber: 1.9 Consensus size: 91
10719 CACTGACACA
* * *
10729 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCCAATGCATGTCCTAGAC
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATATC-AGGCCAATGCATGTCCCAAAC
10794 ATGTCTTACACTAGCTCTCGTCTCAAT
65 ATGTCTTACACTAGCTCTCGTCTCAAT
*
10821 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAAT-ATGGCCGATGCATGTCCC
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TACAT-ATCA-GGCCAATGCATGTCCC
*
10884 AAACATGTCTTGCACTAGC
61 AAACATGTCTTACACTAGC
10903 CCACAATAGC
Statistics
Matches: 72, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
92 7 0.10
93 15 0.21
94 48 0.67
95 2 0.03
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (91 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATATCAGGCCAATGCATGTCCCAAACA
TGTCTTACACTAGCTCTCGTCTCAAT
Found at i:11375 original size:30 final size:30
Alignment explanation
Indices: 11339--11396 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
11329 CCCAAATCTC
11339 GATTTTCTTGATCTAACATGATGAAATTAT
1 GATTTTCTTGATCTAACATGATGAAATTAT
11369 GATTTTCTTGATCTAACATGATGAAATT
1 GATTTTCTTGATCTAACATGATGAAATT
11397 CACTCATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (30 bp):
GATTTTCTTGATCTAACATGATGAAATTAT
Found at i:14215 original size:40 final size:40
Alignment explanation
Indices: 14163--14394 Score: 326
Period size: 40 Copynumber: 5.8 Consensus size: 40
14153 CGGATATAGC
*
14163 CACTCGCTCAAATGCCTTCGGGACTTAGCCCGG-ATATAGT
1 CACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT
* *
14203 -AGTTCGCACAAATGCCTTCGAGACTTAGCCCGG-ATATAGT
1 CA-CTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT
* *
14243 AACTTGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGT
1 CACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGT
* *
14283 AACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTTGT
1 CACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGT
*
14323 CACTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGT
1 CACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGT
* *
14363 CACTAGCACAAATGCCTTCGAGACTTAGCCCG
1 CACTCGCACAAATGCCTTCGGGACTTAGCCCG
14395 ATTATCATCC
Statistics
Matches: 177, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
39 1 0.01
40 173 0.98
41 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGT
Found at i:23287 original size:24 final size:23
Alignment explanation
Indices: 23253--23306 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
23243 TATGAATCGG
* *
23253 CAAAAGCCGAAATGCCAAAATGC
1 CAAAAGTCGAAATGCCAAAAAGC
*
23276 CGAAAAGTCGAAATGTCAAAAAGC
1 C-AAAAGTCGAAATGCCAAAAAGC
23300 CAAAAGT
1 CAAAAGT
23307 TTGGCTACGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 7 0.26
24 20 0.74
ACGTcount: A:0.50, C:0.20, G:0.19, T:0.11
Consensus pattern (23 bp):
CAAAAGTCGAAATGCCAAAAAGC
Found at i:23571 original size:29 final size:29
Alignment explanation
Indices: 23529--23613 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
23519 AATGTGACTG
* *
23529 GGCCTAACGAGCCATATAAATGTGATTTA
1 GGCCTAATGGGCCATATAAATGTGATTTA
* * *
23558 GGCCTAATGGGCCATATACAGGTGATTTG
1 GGCCTAATGGGCCATATAAATGTGATTTA
* *
23587 GGCCTAATGGGCCATATGAATATGATT
1 GGCCTAATGGGCCATATAAATGTGATT
23614 GGACTTAATG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.28
Consensus pattern (29 bp):
GGCCTAATGGGCCATATAAATGTGATTTA
Found at i:23601 original size:58 final size:57
Alignment explanation
Indices: 23527--23637 Score: 143
Period size: 58 Copynumber: 1.9 Consensus size: 57
23517 TGAATGTGAC
* *
23527 TGGGCCTAACGAGCCATATAAATGTGATTTAGG-CCTAATGGGCCATATACAGGTGATT
1 TGGGCCTAACGAGCCATATAAATATGA-TT-GGACCTAATGGGCCAGATACAGGTGATT
* * * *
23585 TGGGCCTAATGGGCCATATGAATATGATTGGACTTAATGGGCCAGATACAGGT
1 TGGGCCTAACGAGCCATATAAATATGATTGGACCTAATGGGCCAGATACAGGT
23638 ATGTGAAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
56 2 0.04
57 21 0.46
58 23 0.50
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27
Consensus pattern (57 bp):
TGGGCCTAACGAGCCATATAAATATGATTGGACCTAATGGGCCAGATACAGGTGATT
Done.