Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1119
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: 32597
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:3352 original size:2 final size:2
Alignment explanation
Indices: 3345--3376 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3335 CAAACATAAC
*
3345 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3377 GTCCCACAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5034 original size:19 final size:20
Alignment explanation
Indices: 4985--5038 Score: 67
Period size: 19 Copynumber: 2.7 Consensus size: 20
4975 TTTTATATTA
*
4985 AATAATATTTATTTAATTTAT
1 AATAAAATTT-TTTAATTTAT
5006 AAGT-AAATTTTTTAATTT-T
1 AA-TAAAATTTTTTAATTTAT
5025 AATAAAATTTTTTA
1 AATAAAATTTTTTA
5039 TTAAATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
18 1 0.03
19 13 0.43
20 8 0.27
21 7 0.23
22 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
AATAAAATTTTTTAATTTAT
Found at i:5100 original size:20 final size:20
Alignment explanation
Indices: 4968--5105 Score: 53
Period size: 20 Copynumber: 7.0 Consensus size: 20
4958 AATTATTATT
4968 ATAAA-TATTTTATATTAAATA
1 ATAAATTATTTTAT-TT-AATA
* *
4989 AT-ATTTATTTAATTT-ATA
1 ATAAATTATTTTATTTAATA
5007 AGTAAATT-TTTTAATTT--TA
1 A-TAAATTATTTT-ATTTAATA
*
5026 ATAAAATT-TTTTATTAAAT-
1 AT-AAATTATTTTATTTAATA
* * * *
5045 AT-ATTTATCTGATGATAATTA
1 ATAAATTATTTTAT-TTAA-TA
**
5066 A-AAATTATTAAATTTAATA
1 ATAAATTATTTTATTTAATA
*
5085 ATAAATTATTTTATTTTATA
1 ATAAATTATTTTATTTAATA
5105 A
1 A
5106 GTTTAAATTT
Statistics
Matches: 86, Mismatches: 18, Indels: 27
0.66 0.14 0.21
Matches are distributed among these distances:
17 3 0.03
18 12 0.14
19 23 0.27
20 31 0.36
21 17 0.20
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (20 bp):
ATAAATTATTTTATTTAATA
Found at i:5259 original size:25 final size:26
Alignment explanation
Indices: 5216--5265 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
5206 AGATTAAAAT
*
5216 AATAAATTTATATATTTAA-ATATTG
1 AATAAATTTATACATTTAAGATATTG
5241 AATAAATTT-TACATGTTAAGATATT
1 AATAAATTTATACAT-TTAAGATATT
5266 TATTAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 13 0.59
26 5 0.23
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (26 bp):
AATAAATTTATACATTTAAGATATTG
Found at i:10255 original size:2 final size:2
Alignment explanation
Indices: 10248--10293 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
10238 TGCATTACAA
*
10248 AT AT AT AT AT AT AT AT AT AT AT AT AT AC 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 AT AT AT
10290 AT AT
1 AT AT
10294 GTATTAAAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18760 original size:41 final size:41
Alignment explanation
Indices: 18709--18788 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
18699 CACATGCGAA
*
18709 GCAATCGTACATCATGCTTATCATCAATCATTTGTCAAGTG
1 GCAATCGTACATCACGCTTATCATCAATCATTTGTCAAGTG
* * *
18750 GCAATGGTACATGACGCTTATTATCAATCATTTGTCAAG
1 GCAATCGTACATCACGCTTATCATCAATCATTTGTCAAG
18789 ATGGTACATC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (41 bp):
GCAATCGTACATCACGCTTATCATCAATCATTTGTCAAGTG
Found at i:21973 original size:126 final size:131
Alignment explanation
Indices: 21778--22037 Score: 467
Period size: 126 Copynumber: 2.0 Consensus size: 131
21768 TGAGCATGGG
21778 AAAGTTTCTTAAATTACTCCTATATAATATATATATATATATATGCATATATTGTATTTTAGCAT
1 AAAGTTTCTTAAATTACTCC-ATATAATATATATATATATATATGCATATATTGTATTTTAGCAT
21843 CTGCGAAGCAGCGATTAAGT-AAGTAAAATTTGATT-AAAAAAATCTTATATTTACATTGTATTG
65 CTGCGAAGCAGCGATTAAGTCAAGTAAAATTTGATTAAAAAAAATCTTATATTTACATTGTATTG
21906 AA
130 AA
21908 AAAGTTTCTTAAATTACTCC-TAT-ATA-ATATATATATATATGCATATATTGTATTTTAGCATC
1 AAAGTTTCTTAAATTACTCCATATAATATATATATATATATATGCATATATTGTATTTTAGCATC
*
21970 TGCGAAGCAGTGATTAAGTCAAGTAAAATTTGATTAAAAAAAATCTTATATTTACATTGTATTGA
66 TGCGAAGCAGCGATTAAGTCAAGTAAAATTTGATTAAAAAAAATCTTATATTTACATTGTATTGA
22035 A
131 A
22036 AA
1 AA
22038 TATCTTTTGG
Statistics
Matches: 127, Mismatches: 1, Indels: 6
0.95 0.01 0.04
Matches are distributed among these distances:
126 54 0.43
127 18 0.14
128 35 0.28
130 20 0.16
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (131 bp):
AAAGTTTCTTAAATTACTCCATATAATATATATATATATATATGCATATATTGTATTTTAGCATC
TGCGAAGCAGCGATTAAGTCAAGTAAAATTTGATTAAAAAAAATCTTATATTTACATTGTATTGA
A
Found at i:22583 original size:2 final size:2
Alignment explanation
Indices: 22507--22568 Score: 80
Period size: 2 Copynumber: 33.5 Consensus size: 2
22497 TTGAAGTTAT
22507 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
22548 -A TA -A TT TA TA T- TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
22569 TTAATTTTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
1 5 0.09
2 48 0.91
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:22588 original size:21 final size:23
Alignment explanation
Indices: 22506--22588 Score: 75
Period size: 24 Copynumber: 3.6 Consensus size: 23
22496 GTTGAAGTTA
22506 TTATATAT-ATATATA-TATATAT
1 TTATATATAATATATATTA-ATAT
*
22528 ATATATATATATATATATTAATAAT
1 TTATATATA-ATATATATTAAT-AT
*
22553 TTATATTATATTATAT-TTAAT-T
1 TTATA-TATAATATATATTAATAT
*
22575 TTTTATATAATATA
1 TTATATATAATATA
22589 ATCATATTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
21 8 0.16
22 12 0.24
24 14 0.27
25 13 0.25
26 4 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TTATATATAATATATATTAATAT
Found at i:23924 original size:21 final size:21
Alignment explanation
Indices: 23885--23924 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
23875 ATTAATAATA
**
23885 TAAACATAAAATTTTAACACG
1 TAAACATAAAATTAAAACACG
23906 TAAACATAAAATTAAAACA
1 TAAACATAAAATTAAAACA
23925 AATATTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.12, G:0.03, T:0.25
Consensus pattern (21 bp):
TAAACATAAAATTAAAACACG
Found at i:25763 original size:15 final size:15
Alignment explanation
Indices: 25743--25773 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
25733 CTTCCAATAG
25743 GGTGAACGCGCGAAA
1 GGTGAACGCGCGAAA
25758 GGTGAACGCGCGAAA
1 GGTGAACGCGCGAAA
25773 G
1 G
25774 CTATTGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.42, T:0.06
Consensus pattern (15 bp):
GGTGAACGCGCGAAA
Found at i:26390 original size:3 final size:3
Alignment explanation
Indices: 26382--26431 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
26372 CATTCATTCT
26382 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
26430 TT
1 TT
26432 TGCTTTGTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:31163 original size:33 final size:33
Alignment explanation
Indices: 31110--31186 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 33
31100 TATTTAAAAT
* **
31110 ATTTT-TTTTTATAAATTTTTAATATGTTAATAA
1 ATTTTATTTATATAAATTTTTAA-ATAATAATAA
*
31143 ATTTTATTTATATAAA-TTTTAAATAATAATAT
1 ATTTTATTTATATAAATTTTTAAATAATAATAA
31175 ATTTATATTTAT
1 ATTT-TATTTAT
31187 TATTTTCATC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 11 0.29
33 18 0.47
34 9 0.24
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (33 bp):
ATTTTATTTATATAAATTTTTAAATAATAATAA
Found at i:31593 original size:6 final size:6
Alignment explanation
Indices: 31584--31608 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
31574 AATTTAAAGC
31584 TAATAT TAATAT TAATAT TAATAT T
1 TAATAT TAATAT TAATAT TAATAT T
31609 TTATTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAATAT
Done.