Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold835
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: 23867
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Found at i:2986 original size:20 final size:21
Alignment explanation
Indices: 2961--3014 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
2951 TATTTCGGGC
2961 ATGTATCAATACATTCACT-T
1 ATGTATCAATACATTCACTGT
*
2981 ATGTATCAATACATTTACTGT
1 ATGTATCAATACATTCACTGT
* *
3002 TTGTATCGATACA
1 ATGTATCAATACA
3015 AATTGTAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (21 bp):
ATGTATCAATACATTCACTGT
Found at i:3639 original size:16 final size:16
Alignment explanation
Indices: 3618--3653 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3608 TATTAAGAAG
*
3618 ATTTAATTATTAAATA
1 ATTTAATTAATAAATA
*
3634 ATTTAATTAATAAGTA
1 ATTTAATTAATAAATA
3650 ATTT
1 ATTT
3654 TCAATCAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
ATTTAATTAATAAATA
Found at i:3713 original size:16 final size:17
Alignment explanation
Indices: 3684--3716 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3674 TAATTTAGTT
*
3684 GTTTCAAGTTATTTTGA
1 GTTTCAAGTAATTTTGA
3701 GTTT-AAGTAATTTTGA
1 GTTTCAAGTAATTTTGA
3717 ATTTGGATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.27, C:0.03, G:0.18, T:0.52
Consensus pattern (17 bp):
GTTTCAAGTAATTTTGA
Found at i:13108 original size:56 final size:56
Alignment explanation
Indices: 13038--13230 Score: 359
Period size: 56 Copynumber: 3.4 Consensus size: 56
13028 GCATTTAATT
* *
13038 CAATATGGTTGTTATGATTTTGATTATTTTTTGATTTAGTTGTTATTTTTTAAATC
1 CAATATGGTTGTTATGATTTTGATTATTTTCTGATTTAGTTGTTATTTGTTAAATC
13094 CAATATGGTTGTTATGATTTTGATTATTTTCTGATTTAGTTGTTATTTGTTAAATC
1 CAATATGGTTGTTATGATTTTGATTATTTTCTGATTTAGTTGTTATTTGTTAAATC
*
13150 CAATATGGTTGTTATGATTTTGATTATTTTCTGATTTAGTTGTTATTTGTCAAATC
1 CAATATGGTTGTTATGATTTTGATTATTTTCTGATTTAGTTGTTATTTGTTAAATC
13206 CAATATGGTTGTTATGATTTTGATT
1 CAATATGGTTGTTATGATTTTGATT
13231 TGTTGTTAGC
Statistics
Matches: 134, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 134 1.00
ACGTcount: A:0.23, C:0.05, G:0.16, T:0.55
Consensus pattern (56 bp):
CAATATGGTTGTTATGATTTTGATTATTTTCTGATTTAGTTGTTATTTGTTAAATC
Found at i:13113 original size:28 final size:28
Alignment explanation
Indices: 13082--13170 Score: 67
Period size: 28 Copynumber: 3.2 Consensus size: 28
13072 TTTAGTTGTT
13082 ATTTTTTAAATCCAATATGGTTGTTATG
1 ATTTTTTAAATCCAATATGGTTGTTATG
** ** * *
13110 ATTTTGATTATTTTCTGATTTAGTTG-T-T-
1 ATTTT--TTA-AATCCAATATGGTTGTTATG
*
13138 ATTTGTTAAATCCAATATGGTTGTTATG
1 ATTTTTTAAATCCAATATGGTTGTTATG
13166 ATTTT
1 ATTTT
13171 GATTATTTTC
Statistics
Matches: 41, Mismatches: 14, Indels: 12
0.61 0.21 0.18
Matches are distributed among these distances:
25 9 0.22
26 4 0.10
27 1 0.02
28 13 0.32
29 1 0.02
30 4 0.10
31 9 0.22
ACGTcount: A:0.25, C:0.06, G:0.15, T:0.55
Consensus pattern (28 bp):
ATTTTTTAAATCCAATATGGTTGTTATG
Found at i:13136 original size:31 final size:31
Alignment explanation
Indices: 13045--13195 Score: 101
Period size: 31 Copynumber: 5.3 Consensus size: 31
13035 ATTCAATATG
*
13045 GTTGTTATGATTTTGATTATTTTTTGATTTA
1 GTTGTTATGATTTTGATTATTTTCTGATTTA
** ** * *
13076 GTTG-T-T-ATTTT--TTA-AATCCAATATG
1 GTTGTTATGATTTTGATTATTTTCTGATTTA
13101 GTTGTTATGATTTTGATTATTTTCTGATTTA
1 GTTGTTATGATTTTGATTATTTTCTGATTTA
** ** * *
13132 GTTG-T-T-A-TTTG-TTA-AATCCAATATG
1 GTTGTTATGATTTTGATTATTTTCTGATTTA
13157 GTTGTTATGATTTTGATTATTTTCTGATTTA
1 GTTGTTATGATTTTGATTATTTTCTGATTTA
13188 GTTGTTAT
1 GTTGTTAT
13196 TTGTCAAATC
Statistics
Matches: 83, Mismatches: 25, Indels: 24
0.63 0.19 0.18
Matches are distributed among these distances:
25 17 0.20
26 8 0.10
27 6 0.07
28 12 0.14
29 6 0.07
30 8 0.10
31 26 0.31
ACGTcount: A:0.22, C:0.04, G:0.16, T:0.58
Consensus pattern (31 bp):
GTTGTTATGATTTTGATTATTTTCTGATTTA
Found at i:15469 original size:63 final size:63
Alignment explanation
Indices: 15366--15491 Score: 216
Period size: 63 Copynumber: 2.0 Consensus size: 63
15356 GCAGCTTACT
*
15366 GTCAGCCATAGGAAGAATATGAAACTAGCTTCCAAATACTTTAGGCTATTTCAGGTTCTGGAA
1 GTCAGCCATAGGAAGAATATGAAACTAGATTCCAAATACTTTAGGCTATTTCAGGTTCTGGAA
* **
15429 GTCAGCCATTGGAAGAATATGAAACTAGATTCCATTTACTTTAGGCTATTTCAGGTTCTGGAA
1 GTCAGCCATAGGAAGAATATGAAACTAGATTCCAAATACTTTAGGCTATTTCAGGTTCTGGAA
15492 AGGGTTGGGA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.31
Consensus pattern (63 bp):
GTCAGCCATAGGAAGAATATGAAACTAGATTCCAAATACTTTAGGCTATTTCAGGTTCTGGAA
Found at i:18088 original size:63 final size:61
Alignment explanation
Indices: 17962--18179 Score: 220
Period size: 63 Copynumber: 3.5 Consensus size: 61
17952 CAATTAGTTT
* * * * * *
17962 CTTGAAAATAGGTTCGACTTGAAAACAAAAAGATCTTAACATTAATTCAGGAATTAATTCATTC
1 CTTGAAAACAAGTTCGACTT-AAAAC-AAAAGATCTAAACATTGACTCAGG-ATTAACTCATTC
* * * *
18026 CTTGAAAACAAGTTCGACTTAAAATAAAATGATCTCAACATTGACTCGAGGCTTGACTCATTC
1 CTTGAAAACAAGTTCGACTTAAAACAAAA-GATCTAAACATTGACTC-AGGATTAACTCATTC
* * * * *
18089 CTTAAAAACAAGTTTGACTTAAAACCAAAAGACCTAAACATTGACTCAAAGTTTAACTCATTC
1 CTTGAAAACAAGTTCGACTTAAAA-CAAAAGATCTAAACATTGACTC-AGGATTAACTCATTC
**
18152 CTTGAAAACAAGTTTAACTTAAAACAAA
1 CTTGAAAACAAGTTCGACTTAAAACAAA
18180 CCAGCTTGGC
Statistics
Matches: 131, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
62 8 0.06
63 98 0.75
64 25 0.19
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.28
Consensus pattern (61 bp):
CTTGAAAACAAGTTCGACTTAAAACAAAAGATCTAAACATTGACTCAGGATTAACTCATTC
Found at i:18281 original size:14 final size:14
Alignment explanation
Indices: 18262--18290 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
18252 GAATCTTTAG
18262 ATATACCATTAAAA
1 ATATACCATTAAAA
18276 ATATACCATTAAAA
1 ATATACCATTAAAA
18290 A
1 A
18291 CTTGACTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.28
Consensus pattern (14 bp):
ATATACCATTAAAA
Found at i:22522 original size:19 final size:21
Alignment explanation
Indices: 22482--22529 Score: 75
Period size: 19 Copynumber: 2.4 Consensus size: 21
22472 ATTATTTTTT
22482 TTAA-AAATTTTTATTAAAAA
1 TTAATAAATTTTTATTAAAAA
22502 TTAATAAATTTTT-TT-AAAA
1 TTAATAAATTTTTATTAAAAA
22521 TTAATAAAT
1 TTAATAAAT
22530 ATAATACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.48
20 6 0.22
21 8 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAATAAATTTTTATTAAAAA
Found at i:23558 original size:19 final size:19
Alignment explanation
Indices: 23534--23575 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
23524 AATGTATTAT
23534 ATTTATTAATTTTAAAAAA
1 ATTTATTAATTTTAAAAAA
*
23553 ATTTATTAATTTTAATAAA
1 ATTTATTAATTTTAAAAAA
23572 ATTT
1 ATTT
23576 TAAAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTTATTAATTTTAAAAAA
Found at i:23634 original size:16 final size:18
Alignment explanation
Indices: 23613--23652 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
23603 AAAAAATTTA
*
23613 ATAAATT-A-TTTAATAT
1 ATAAATTCACTTTAACAT
23629 ATAAATTCACTTTAACAT
1 ATAAATTCACTTTAACAT
23647 ATAAAT
1 ATAAAT
23653 CAATCCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
17 1 0.05
18 13 0.62
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAAATTCACTTTAACAT
Done.