Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2962
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: 23850
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Found at i:5234 original size:39 final size:41
Alignment explanation
Indices: 5090--5292 Score: 174
Period size: 40 Copynumber: 5.1 Consensus size: 41
5080 CGAAATTTAA
* * *
5090 CCGG-ATATAGCT-ACTCGCTCAAATGCCTTTGGGACATAGC
1 CCGGAATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
5130 CCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * * * *
5170 CCAG-ATTTAGTAAGTCGCTCCAATGCCTTCGGG-CTTAGC
1 CCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
5209 CCGGAAT-TAGTAACTCGCACAAATGCCTT---AATCTTAGT
1 CCGGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
5247 CCGG-ATATAGTCACTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGAATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
5288 CCGGA
1 CCGGA
5293 TATCATTCGA
Statistics
Matches: 130, Mismatches: 23, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
37 2 0.02
38 15 0.12
39 41 0.32
40 62 0.48
41 9 0.07
42 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (41 bp):
CCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:7430 original size:7 final size:7
Alignment explanation
Indices: 7418--7443 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
7408 TAGTATACTC
7418 ATTTTCT
1 ATTTTCT
7425 ATTTTCT
1 ATTTTCT
7432 ATTTTCT
1 ATTTTCT
7439 ATTTT
1 ATTTT
7444 ACTTATACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (7 bp):
ATTTTCT
Found at i:8726 original size:8 final size:8
Alignment explanation
Indices: 8713--8757 Score: 63
Period size: 8 Copynumber: 5.6 Consensus size: 8
8703 ACAAAAGCTA
8713 AAATGCCG
1 AAATGCCG
*
8721 AAATGCTG
1 AAATGCCG
8729 AAATGCCG
1 AAATGCCG
8737 AAATGCCG
1 AAATGCCG
* *
8745 AAAAGCCA
1 AAATGCCG
8753 AAATG
1 AAATG
8758 TTGAAAAGCT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.13
Consensus pattern (8 bp):
AAATGCCG
Found at i:8734 original size:16 final size:16
Alignment explanation
Indices: 8713--8763 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
8703 ACAAAAGCTA
8713 AAATGCCGAAATGCTG
1 AAATGCCGAAATGCTG
*
8729 AAATGCCGAAATGCCG
1 AAATGCCGAAATGCTG
* * *
8745 AAAAGCCAAAATGTTG
1 AAATGCCGAAATGCTG
8761 AAA
1 AAA
8764 AGCTGAAAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.16
Consensus pattern (16 bp):
AAATGCCGAAATGCTG
Found at i:8764 original size:16 final size:16
Alignment explanation
Indices: 8704--8766 Score: 58
Period size: 16 Copynumber: 4.0 Consensus size: 16
8694 TATGAATCAA
8704 CAAAA-GCT-AAAATGC
1 CAAAATGCTGAAAA-GC
* *
8719 CGAAATGCTGAAATGC
1 CAAAATGCTGAAAAGC
* *
8735 CGAAATGCCGAAAAGC
1 CAAAATGCTGAAAAGC
*
8751 CAAAATGTTGAAAAGC
1 CAAAATGCTGAAAAGC
8767 TGAAAGTTTG
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
15 4 0.10
16 32 0.82
17 3 0.08
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (16 bp):
CAAAATGCTGAAAAGC
Found at i:9036 original size:29 final size:29
Alignment explanation
Indices: 8994--9094 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 29
8984 TGAATGTGGC
*
8994 TGGGCCTAACGGGCCATATAAATGTGATT
1 TGGGCCTAATGGGCCATATAAATGTGATT
** *
9023 TGGGCCTAATGGGCCATATTCAGGTGATT
1 TGGGCCTAATGGGCCATATAAATGTGATT
* *
9052 TGGGCCTAAT-GGCCATATGAATATGA-T
1 TGGGCCTAATGGGCCATATAAATGTGATT
* *
9079 TGGGCTTAATAGGCCA
1 TGGGCCTAATGGGCCA
9095 AATACAGGTA
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
27 10 0.16
28 17 0.27
29 35 0.56
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (29 bp):
TGGGCCTAATGGGCCATATAAATGTGATT
Found at i:12004 original size:16 final size:17
Alignment explanation
Indices: 11983--12014 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
11973 GTTGTAACGC
11983 CCCAAAAATCC-GAAAA
1 CCCAAAAATCCTGAAAA
11999 CCCAAAAATCCTGAAA
1 CCCAAAAATCCTGAAA
12015 TCCCGAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.53, C:0.31, G:0.06, T:0.09
Consensus pattern (17 bp):
CCCAAAAATCCTGAAAA
Found at i:13241 original size:16 final size:16
Alignment explanation
Indices: 13183--13237 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
13173 ATGAATCGAC
**
13183 AAAAGCCAAAATGCCG
1 AAAAGCCAAAATGATG
*
13199 AAATGCCAAAATGATG
1 AAAAGCCAAAATGATG
* *
13215 AAAAGCCGAAATGTTG
1 AAAAGCCAAAATGATG
13231 AAAAGCC
1 AAAAGCC
13238 GAAAGTTTGG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.49, C:0.18, G:0.20, T:0.13
Consensus pattern (16 bp):
AAAAGCCAAAATGATG
Found at i:13498 original size:29 final size:28
Alignment explanation
Indices: 13465--13537 Score: 101
Period size: 29 Copynumber: 2.6 Consensus size: 28
13455 TGAATATGGC
* *
13465 TGGGCCTAACGGGCCATATAAATGTGATT
1 TGGGCCTAATGGGCCATATAAATATGA-T
*
13494 TGGGCCTAATGGGCCATATGAATATGAT
1 TGGGCCTAATGGGCCATATAAATATGAT
*
13522 TGGGCTTAATGGGCCA
1 TGGGCCTAATGGGCCA
13538 GATACAGGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 16 0.40
29 24 0.60
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.27
Consensus pattern (28 bp):
TGGGCCTAATGGGCCATATAAATATGAT
Found at i:13533 original size:28 final size:28
Alignment explanation
Indices: 13452--13537 Score: 109
Period size: 28 Copynumber: 3.0 Consensus size: 28
13442 GTGAGCATGA
** *
13452 ATATGAATATGGCTGGGCCTAACGGGCC
1 ATATGAATATGATTGGGCCTAATGGGCC
* *
13480 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATATGA-TTGGGCCTAATGGGCC
*
13509 ATATGAATATGATTGGGCTTAATGGGCC
1 ATATGAATATGATTGGGCCTAATGGGCC
13537 A
1 A
13538 GATACAGGTA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
28 25 0.51
29 24 0.49
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (28 bp):
ATATGAATATGATTGGGCCTAATGGGCC
Found at i:16447 original size:16 final size:17
Alignment explanation
Indices: 16426--16462 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
16416 TGTAACGCCT
*
16426 CAAAAATCTCGAAA-CC
1 CAAAAATCTCAAAATCC
16442 CAAAAATCTCAAAATCC
1 CAAAAATCTCAAAATCC
16459 CAAA
1 CAAA
16463 CTTTTCTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.54, C:0.30, G:0.03, T:0.14
Consensus pattern (17 bp):
CAAAAATCTCAAAATCC
Done.