Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1165
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: 19498
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:59 original size:27 final size:27
Alignment explanation
Indices: 29--101 Score: 67
Period size: 27 Copynumber: 2.6 Consensus size: 27
19 TTATAGGGAA
*
29 AATATAATTAATAATT-TTAAAAAAATT
1 AATA-AATTAATAATTAATAAAAAAATT
* *
56 AATAAAAATAATATATTAATAAAAAATTT
1 AAT-AAATTAATA-ATTAATAAAAAAATT
**
85 CTTAAATTAATAATTAA
1 AATAAATTAATAATTAA
102 AATTTAGTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
27 15 0.41
28 12 0.32
29 10 0.27
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (27 bp):
AATAAATTAATAATTAATAAAAAAATT
Found at i:560 original size:17 final size:18
Alignment explanation
Indices: 540--576 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
530 AAAATCTTAA
540 AAAACTTAATTAATT-TT
1 AAAACTTAATTAATTATT
*
557 AAAACTTTATTAATTATT
1 AAAACTTAATTAATTATT
575 AA
1 AA
577 GTTTTTTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (18 bp):
AAAACTTAATTAATTATT
Found at i:5398 original size:6 final size:7
Alignment explanation
Indices: 5374--5407 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
5364 TTTAAACTAC
5374 TTTTTAT
1 TTTTTAT
5381 TATTTTAT
1 T-TTTTAT
5389 TTTTTAT
1 TTTTTAT
5396 TTTTTAT
1 TTTTTAT
5403 TTTTT
1 TTTTT
5408 TATACAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTAT
Found at i:7521 original size:31 final size:28
Alignment explanation
Indices: 7463--7517 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
7453 AAACTGCATT
7463 AATTCTCAAAAAATAAAAAATAAATAAA
1 AATTCTCAAAAAATAAAAAATAAATAAA
*
7491 AATTCTCAAAAAAT-AATAATAAATAAA
1 AATTCTCAAAAAATAAAAAATAAATAAA
7518 TAAATAAGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 12 0.46
28 14 0.54
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (28 bp):
AATTCTCAAAAAATAAAAAATAAATAAA
Found at i:7682 original size:2 final size:2
Alignment explanation
Indices: 7675--7704 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
7665 CATTATGTGT
7675 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7705 ACTCATCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7896 original size:21 final size:22
Alignment explanation
Indices: 7845--7897 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
7835 TCAATATTTA
*
7845 AATAAAGAATAAGAAAAATTCAAG
1 AATAAAG--TAAGAAAAATACAAG
**
7869 AGGAAAGTAAGAAAAA-ACAAG
1 AATAAAGTAAGAAAAATACAAG
7890 AATAAAGT
1 AATAAAGT
7898 CATAAATACC
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
21 10 0.42
22 9 0.38
24 5 0.21
ACGTcount: A:0.66, C:0.04, G:0.17, T:0.13
Consensus pattern (22 bp):
AATAAAGTAAGAAAAATACAAG
Found at i:8622 original size:2 final size:2
Alignment explanation
Indices: 8615--8668 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
8605 TTCTTTACAT
8615 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8656 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
8669 GGACATCTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15579 original size:118 final size:116
Alignment explanation
Indices: 15398--15613 Score: 292
Period size: 118 Copynumber: 1.8 Consensus size: 116
15388 TCTTGTCAAT
* * * * *
15398 ACCAAGAACTGGATTCCATGTGCATGTTAAAGCAAAATAGTTGATTCAGCAGCAATTTAAGCTTA
1 ACCAAGAACGGGAATCCATGTGCATGGTAAAGCAAAATAGGTGATGCAGCAGCAATTTAAGCTTA
* * *
15463 TTTTCTTTTTGTAATAAGTTCTTTCTAGAGCCGGTTTACTGTGTTTAAAACAGG
66 -TGTCTTTTT-TAAT-AGTTCGTTCAAGAGCCGGTTTACTGTGTTTAAAACAGG
*
15517 ACCAAGAACGGGAAT-CATGTGCATGGTAAAGCAAAATGAGGTGATGCAGCAGCAA-TTCAGCTT
1 ACCAAGAACGGGAATCCATGTGCATGGTAAAGCAAAAT-AGGTGATGCAGCAGCAATTTAAGCTT
*
15580 ATGTCTTTTTTAGTAGTTCGTTCAAGAGCCGGTT
65 ATGTCTTTTTTAATAGTTCGTTCAAGAGCCGGTT
15614 ACTTGGGCGC
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
115 18 0.21
116 3 0.03
117 8 0.09
118 29 0.34
119 28 0.33
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (116 bp):
ACCAAGAACGGGAATCCATGTGCATGGTAAAGCAAAATAGGTGATGCAGCAGCAATTTAAGCTTA
TGTCTTTTTTAATAGTTCGTTCAAGAGCCGGTTTACTGTGTTTAAAACAGG
Found at i:16472 original size:17 final size:16
Alignment explanation
Indices: 16450--16491 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
16440 ATTATATAAG
16450 TAGATATATAAAATAT
1 TAGATATATAAAATAT
* *
16466 ATAGATATATGAAGTAT
1 -TAGATATATAAAATAT
16483 TAGATATAT
1 TAGATATAT
16492 TTATGTAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (16 bp):
TAGATATATAAAATAT
Done.