Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3700
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: 59520
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1030 original size:20 final size:19
Alignment explanation
Indices: 1005--1042 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
995 GAAACTAGTT
1005 ATTTTTTCGAAGTTTTTTTA
1 ATTTTTTCG-AGTTTTTTTA
*
1025 ATTTTTTTGAGTTTTTTT
1 ATTTTTTCGAGTTTTTTT
1043 TTCGAAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.16, C:0.03, G:0.11, T:0.71
Consensus pattern (19 bp):
ATTTTTTCGAGTTTTTTTA
Found at i:6954 original size:16 final size:17
Alignment explanation
Indices: 6929--6960 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
6919 AAGAAGTATG
6929 GGAAATAAAAAAGAAAT
1 GGAAATAAAAAAGAAAT
6946 GGAAA-AAAAAAGAAA
1 GGAAATAAAAAAGAAA
6961 GGATGGGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (17 bp):
GGAAATAAAAAAGAAAT
Found at i:7816 original size:21 final size:21
Alignment explanation
Indices: 7782--7824 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
7772 ATACATATTG
*
7782 AGTTATAATATGTATG-CATT
1 AGTTATAAAATGTATGTCATT
7802 AGTTAGTAAAATGTATGTCATT
1 AGTTA-TAAAATGTATGTCATT
7824 A
1 A
7825 TATGTGGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 10 0.50
22 5 0.25
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (21 bp):
AGTTATAAAATGTATGTCATT
Found at i:8368 original size:27 final size:27
Alignment explanation
Indices: 8330--8522 Score: 223
Period size: 27 Copynumber: 7.2 Consensus size: 27
8320 AAATTGGTAC
8330 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
8357 AGCACTAAGTGTGCGA-TTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
8383 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
8409 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
8437 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
8465 AGCACTAAGTGTGCGATTTG-TTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
8491 AGCACTAA-TGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
8517 AGCACT
1 AGCACT
8523 GATGAGGCGA
Statistics
Matches: 144, Mismatches: 17, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
25 10 0.07
26 47 0.33
27 64 0.44
28 23 0.16
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:8415 original size:53 final size:53
Alignment explanation
Indices: 8331--8482 Score: 216
Period size: 53 Copynumber: 2.8 Consensus size: 53
8321 AATTGGTACA
* **
8331 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGATTGACTATGTT
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGATTGACCATGCG
** *
8384 GCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGATTTGACTATGTA-GCACTAAGTGTGCG-ATTGACCATGCG
8438 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATT
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGATT
8483 TGTTACGTAG
Statistics
Matches: 86, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
52 1 0.01
53 36 0.42
54 27 0.31
55 21 0.24
56 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.30
Consensus pattern (53 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGATTGACCATGCG
Found at i:8522 original size:80 final size:79
Alignment explanation
Indices: 8330--8522 Score: 228
Period size: 80 Copynumber: 2.4 Consensus size: 79
8320 AAATTGGTAC
* *
8330 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGATTGACTATGTTGCACTAAGTGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGATTGACTATGTAGCACTAAGTGT
*
8395 GCGAAATGAATATG
66 GCGAAATGAATACG
* **
8409 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAG
1 A-GCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGA--TTGACTATGTAGCACTAAG
** *
8474 TGTGCGATTTG-TTACG
63 TGTGCGAAATGAATACG
* * *
8490 TAGCACTAA-TGTGCGAGTTGATTATATAGCACT
1 -AGCACTAAGTGTGCGAATTGACTATGTAGCACT
8523 GATGAGGCGA
Statistics
Matches: 95, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
79 1 0.01
80 56 0.59
81 10 0.11
82 28 0.29
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (79 bp):
AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGATTGACTATGTAGCACTAAGTGT
GCGAAATGAATACG
Found at i:21609 original size:15 final size:16
Alignment explanation
Indices: 21574--21614 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
21564 GCTCGTTTCC
21574 AGCTC-ACTCAGCTCA
1 AGCTCAACTCAGCTCA
21589 AG-TCAACTCA-CTCA
1 AGCTCAACTCAGCTCA
21603 AGCTCAA-TCAGC
1 AGCTCAACTCAGC
21615 AATCTTAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.32, C:0.37, G:0.12, T:0.20
Consensus pattern (16 bp):
AGCTCAACTCAGCTCA
Found at i:26902 original size:16 final size:17
Alignment explanation
Indices: 26876--26907 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
26866 ACTTTTTTTG
26876 AATTTTCTTTTTCAATC
1 AATTTTCTTTTTCAATC
26893 AATTTT-TTTTTCAAT
1 AATTTTCTTTTTCAAT
26908 TTTTTGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.62
Consensus pattern (17 bp):
AATTTTCTTTTTCAATC
Found at i:30308 original size:27 final size:27
Alignment explanation
Indices: 30275--30471 Score: 233
Period size: 27 Copynumber: 7.4 Consensus size: 27
30265 GTAAATTGTC
30275 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
30302 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
30329 TGCACTAAGTGTGCGA-ATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* *
30354 ATGCACTAAGTGTGCGAATTGAC-A-GC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
30380 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
30408 AGCACT-AGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
30434 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
30461 AGCACTGAGTG
1 AGCACTAAGTG
30472 AGCGGACTCA
Statistics
Matches: 147, Mismatches: 16, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
25 16 0.11
26 43 0.29
27 82 0.56
28 6 0.04
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:33088 original size:11 final size:11
Alignment explanation
Indices: 33072--33114 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
33062 TAGTTTCTCG
33072 AAAAAAAACTC
1 AAAAAAAACTC
* *
33083 AAAAAAAATTA
1 AAAAAAAACTC
*
33094 AAAAAAAATTC
1 AAAAAAAACTC
*
33105 GAAAAAAACT
1 AAAAAAAACT
33115 AGTTTCCATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.74, C:0.09, G:0.02, T:0.14
Consensus pattern (11 bp):
AAAAAAAACTC
Found at i:33168 original size:13 final size:13
Alignment explanation
Indices: 33150--33175 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33140 GGATATCAAG
33150 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
33163 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
33176 GAGAGCTAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (13 bp):
TTGTGAAAAAAAA
Found at i:42783 original size:19 final size:18
Alignment explanation
Indices: 42747--42786 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
42737 TTCCCACTCG
*
42747 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
42765 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
42784 TTT
1 TTT
42787 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:43934 original size:20 final size:20
Alignment explanation
Indices: 43888--43934 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
43878 AGCTCGTTTC
*
43888 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
43908 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
43928 CAGCTCA
1 CAGCTCA
43935 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:46109 original size:11 final size:10
Alignment explanation
Indices: 46084--46144 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
46074 ACCAATAAAA
46084 TAAA-TGAGC
1 TAAATTGAGC
*
46093 TGAATTGTAGC
1 TAAATTG-AGC
46104 TAAATTGAGC
1 TAAATTGAGC
**
46114 TCGATTGAGC
1 TAAATTGAGC
46124 TGAAA-TGAGC
1 T-AAATTGAGC
*
46134 TCAATTGAGC
1 TAAATTGAGC
46144 T
1 T
46145 GGTCGAGTTG
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:46145 original size:20 final size:20
Alignment explanation
Indices: 46085--46145 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
46075 CCAATAAAAT
*
46085 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
46105 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
46126 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
46146 GTCGAGTTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:48235 original size:18 final size:18
Alignment explanation
Indices: 48214--48248 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
48204 TTTTTCTTTT
48214 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
48232 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
48249 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:49201 original size:12 final size:12
Alignment explanation
Indices: 49186--49253 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 12
49176 TTTTGCTCAA
*
49186 TTTTTTTTG-AC
1 TTTTTTTTGAAT
49197 TTTTTTTTGAATT
1 TTTTTTTTGAA-T
*
49210 TTTTTTTCAATCAAT
1 TTTTTTT---TGAAT
*
49225 TTTTTTTTCAAT
1 TTTTTTTTGAAT
49237 TTTTTTTTG-AT
1 TTTTTTTTGAAT
49248 TTTTTT
1 TTTTTT
49254 GTTACTCCAA
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
11 17 0.35
12 14 0.29
13 7 0.14
15 8 0.16
16 3 0.06
ACGTcount: A:0.15, C:0.06, G:0.04, T:0.75
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:49244 original size:16 final size:16
Alignment explanation
Indices: 49206--49236 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
49196 CTTTTTTTTG
49206 AATTTTTTTTTCAATC
1 AATTTTTTTTTCAATC
49222 AATTTTTTTTTCAAT
1 AATTTTTTTTTCAAT
49237 TTTTTTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.65
Consensus pattern (16 bp):
AATTTTTTTTTCAATC
Found at i:50625 original size:11 final size:10
Alignment explanation
Indices: 50600--50660 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
50590 ACCAATAAAA
50600 TAAA-TGAGC
1 TAAATTGAGC
*
50609 TGAATTGTAGC
1 TAAATTG-AGC
50620 TAAATTGAGC
1 TAAATTGAGC
**
50630 TCGATTGAGC
1 TAAATTGAGC
50640 TGAAA-TGAGC
1 T-AAATTGAGC
*
50650 TCAATTGAGC
1 TAAATTGAGC
50660 T
1 T
50661 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:50661 original size:20 final size:20
Alignment explanation
Indices: 50601--50661 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
50591 CCAATAAAAT
*
50601 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
50621 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
50642 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
50662 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:52649 original size:48 final size:47
Alignment explanation
Indices: 52570--52675 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
52560 GAGTGTCATG
*
52570 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
52618 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
52666 GAAAAAGAAA
1 GAAAAAGAAA
52676 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:57189 original size:13 final size:13
Alignment explanation
Indices: 57171--57201 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
57161 GAAACAATAG
57171 TTTTTTTCGAATT
1 TTTTTTTCGAATT
*
57184 TTTTTTTTGAATT
1 TTTTTTTCGAATT
57197 TTTTT
1 TTTTT
57202 GAGTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.03, G:0.06, T:0.77
Consensus pattern (13 bp):
TTTTTTTCGAATT
Done.