Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1141
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: 8490
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Found at i:2420 original size:13 final size:12
Alignment explanation
Indices: 2388--2436 Score: 62
Period size: 13 Copynumber: 3.9 Consensus size: 12
2378 AATATTCAAA
2388 TATAATAAATAT
1 TATAATAAATAT
*
2400 TATTATAAATAAT
1 TATAATAAAT-AT
*
2413 TATCATAAATAT
1 TATAATAAATAT
2425 TAATAATAAATA
1 T-ATAATAAATA
2437 AATTAATAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
12 12 0.38
13 20 0.62
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (12 bp):
TATAATAAATAT
Found at i:2445 original size:25 final size:25
Alignment explanation
Indices: 2385--2453 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 25
2375 TATAATATTC
*
2385 AAATATAATAAATATT-ATTATAAAT
1 AAAT-TAATAAATATTAATAATAAAT
2410 -AATTATCATAAATATTAATAATAAAT
1 AAATTA--ATAAATATTAATAATAAAT
*
2436 AAATTAATAACTA-TAATA
1 AAATTAATAAATATTAATA
2454 TTATATTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
23 2 0.05
24 8 0.21
25 15 0.39
26 8 0.21
27 5 0.13
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (25 bp):
AAATTAATAAATATTAATAATAAAT
Found at i:2456 original size:15 final size:13
Alignment explanation
Indices: 2389--2456 Score: 59
Period size: 13 Copynumber: 5.0 Consensus size: 13
2379 ATATTCAAAT
2389 ATAATAAATATT-
1 ATAATAAATATTA
*
2401 ATTATAAATAATT-
1 ATAATAAAT-ATTA
*
2414 ATCATAAATATTA
1 ATAATAAATATTA
2427 ATAATAAATAAATTA
1 ATAATAAAT--ATTA
2442 ATAACTATAATATTA
1 ATAA-TA-AATATTA
2457 TATTATAATT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
12 11 0.23
13 19 0.40
15 12 0.26
16 2 0.04
17 3 0.06
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (13 bp):
ATAATAAATATTA
Found at i:3154 original size:13 final size:15
Alignment explanation
Indices: 3136--3168 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
3126 TTCAATTATT
3136 AAATTTATA-AAA-A
1 AAATTTATATAAATA
3149 AAATTTATATAAATA
1 AAATTTATATAAATA
3164 AAATT
1 AAATT
3169 GTTACTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
14 3 0.17
15 6 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AAATTTATATAAATA
Found at i:3759 original size:3 final size:3
Alignment explanation
Indices: 3751--3790 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
3741 TTAAGAGGGA
3751 AAT AAT AAT AAAT AAT -AT AAT AAT AAT AAT -AT AAT AAT AA
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3791 GCTACAATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.12
3 27 0.79
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3774 original size:18 final size:19
Alignment explanation
Indices: 3751--3786 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
3741 TTAAGAGGGA
3751 AATAATAATAA-ATAATAT
1 AATAATAATAATATAATAT
3769 AATAATAATAATATAATA
1 AATAATAATAATATAATA
3787 ATAAGCTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AATAATAATAATATAATAT
Found at i:3777 original size:11 final size:11
Alignment explanation
Indices: 3751--3790 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
3741 TTAAGAGGGA
3751 AATAATAATA-
1 AATAATAATAT
3761 AATAAT-ATAAT
1 AATAATAAT-AT
3772 AATAATAATAT
1 AATAATAATAT
3783 AATAATAA
1 AATAATAA
3791 GCTACAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 2 0.07
10 7 0.26
11 16 0.59
12 2 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AATAATAATAT
Found at i:3780 original size:14 final size:14
Alignment explanation
Indices: 3752--3790 Score: 69
Period size: 14 Copynumber: 2.7 Consensus size: 14
3742 TAAGAGGGAA
3752 ATAATAATAAATAAT
1 ATAATAAT-AATAAT
3767 ATAATAATAATAAT
1 ATAATAATAATAAT
3781 ATAATAATAA
1 ATAATAATAA
3791 GCTACAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:4314 original size:17 final size:17
Alignment explanation
Indices: 4292--4325 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4282 ATATATAAAA
4292 ATATTAAAAATTAATTT
1 ATATTAAAAATTAATTT
* *
4309 ATATTAATATTTAATTT
1 ATATTAAAAATTAATTT
4326 GAATCGAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATTAAAAATTAATTT
Found at i:5170 original size:13 final size:13
Alignment explanation
Indices: 5151--5187 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
5141 CATTAAATCC
5151 ATTATTATTATTA
1 ATTATTATTATTA
*
5164 TTTATTATTATTA
1 ATTATTATTATTA
*
5177 ATTAGTATTAT
1 ATTATTATTAT
5188 ATTGTAATCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (13 bp):
ATTATTATTATTA
Found at i:5895 original size:2 final size:2
Alignment explanation
Indices: 5884--5918 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
5874 CTAAAAATAA
*
5884 AT AT -T AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5919 TTACACATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7584 original size:23 final size:23
Alignment explanation
Indices: 7541--7582 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
7531 AGCGATATAG
7541 TTTTTAAAAAATAATTTTTTTAA
1 TTTTTAAAAAATAATTTTTTTAA
7564 TTTTT--AAAATAATTTTTTT
1 TTTTTAAAAAATAATTTTTTT
7583 TTTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTTAAAAAATAATTTTTTTAA
Found at i:7604 original size:19 final size:18
Alignment explanation
Indices: 7563--7606 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
7553 AATTTTTTTA
*
7563 ATTTTTAAAATAATTTTT
1 ATTTTTAAAATAATTATT
*
7581 TTTTTTAATAATAATTATT
1 ATTTTTAA-AATAATTATT
7600 ATTTTTA
1 ATTTTTA
7607 TTTTTTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTTTAAAATAATTATT
Done.