Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2390
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: 17228
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.37
Found at i:272 original size:21 final size:21
Alignment explanation
Indices: 237--295 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
227 TATCATTTAT
237 AAATAATATTAAATATGACATAA
1 AAATAATA-T-AATATGACATAA
** *
260 TTATAATATAATATGATATAA
1 AAATAATATAATATGACATAA
281 AAATAAATATAATAT
1 AAAT-AATATAATAT
296 AAATATATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 13 0.43
22 11 0.37
23 6 0.20
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (21 bp):
AAATAATATAATATGACATAA
Found at i:286 original size:27 final size:25
Alignment explanation
Indices: 256--306 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 25
246 TAAATATGAC
*
256 ATAATTATAATATAATATGATATAAAA
1 ATAAATATAATATAA-AT-ATATAAAA
283 ATAAATATAATATAAATATATAAA
1 ATAAATATAATATAAATATATAAA
307 TATTTTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.30
26 2 0.09
27 14 0.61
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (25 bp):
ATAAATATAATATAAATATATAAAA
Found at i:295 original size:17 final size:18
Alignment explanation
Indices: 262--309 Score: 62
Period size: 17 Copynumber: 2.6 Consensus size: 18
252 TGACATAATT
*
262 ATAATATAATATGATATAA
1 ATAATA-AATATAATATAA
281 A-AATAAATATAATATAA
1 ATAATAAATATAATATAA
298 ATATATAAATAT
1 ATA-ATAAATAT
310 TTTATAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 12 0.46
18 5 0.19
19 9 0.35
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
ATAATAAATATAATATAA
Found at i:299 original size:11 final size:11
Alignment explanation
Indices: 239--385 Score: 52
Period size: 11 Copynumber: 12.9 Consensus size: 11
229 TCATTTATAA
239 ATAATATTAAAT
1 ATAATA-TAAAT
* * *
251 ATGACATAATT
1 ATAATATAAAT
262 ATAATAT-AAT
1 ATAATATAAAT
* *
272 ATGATATAAAA
1 ATAATATAAAT
283 ATAAATATAATAT
1 AT-AATATAA-AT
*
296 AAATATATAAAT
1 ATA-ATATAAAT
**
308 ATTTTATAAACTT
1 ATAATATAAA--T
*
321 ATTACA-ATATAT
1 A-TA-ATATAAAT
* *
333 TTAAAATAAA-
1 ATAATATAAAT
* *
343 ATATTTTAAAT
1 ATAATATAAAT
354 ATAAT-TATAAT
1 ATAATATA-AAT
365 ATAATA-AAAT
1 ATAATATAAAT
375 ATATATATAAA
1 ATA-ATATAAA
386 CTAATAGGTG
Statistics
Matches: 97, Mismatches: 24, Indels: 28
0.65 0.16 0.19
Matches are distributed among these distances:
10 23 0.24
11 41 0.42
12 18 0.19
13 10 0.10
14 5 0.05
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.39
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:382 original size:16 final size:16
Alignment explanation
Indices: 326--384 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
316 AACTTATTAC
* *
326 AATATATTTAAAATAA
1 AATATATATATAATAA
* *
342 AATAT-TTTA-AATAT
1 AATATATATATAATAA
356 AAT-TATAATATAATAA
1 AATATAT-ATATAATAA
372 AATATATATATAA
1 AATATATATATAA
385 ACTAATAGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
13 1 0.03
14 8 0.22
15 6 0.17
16 18 0.50
17 3 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATATATATATAATAA
Found at i:591 original size:13 final size:12
Alignment explanation
Indices: 572--634 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
562 ATTTTTTTAA
572 AAAATTAATTAT
1 AAAATTAATTAT
584 ATAAATTAA-TA-
1 A-AAATTAATTAT
* *
595 AAAATAAATTTT
1 AAAATTAATTAT
*
607 AAAATT-TTTATT
1 AAAATTAATTA-T
*
619 AAATTTAATTAT
1 AAAATTAATTAT
631 AAAA
1 AAAA
635 ATTATAAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
10 6 0.16
11 4 0.11
12 18 0.47
13 10 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
AAAATTAATTAT
Found at i:1349 original size:21 final size:20
Alignment explanation
Indices: 1325--1383 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
1315 AAATAACCTA
*
1325 AAATAATTTAAAATTTAATTC
1 AAATAAATTAAAATTTAA-TC
1346 AAATAAATT-AAATTT-ATC
1 AAATAAATTAAAATTTAATC
1364 AAATTAAATTAATAATTTAA
1 AAA-TAAATTAA-AATTTAA
1384 CTCGTAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
18 5 0.15
19 7 0.21
20 7 0.21
21 13 0.39
22 1 0.03
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATAAATTAAAATTTAATC
Found at i:3651 original size:16 final size:16
Alignment explanation
Indices: 3622--3660 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
3612 TTTATATATT
3622 ATTT-ATAAAAATAAA
1 ATTTAATAAAAATAAA
*
3637 ATTTAATAAATATAAA
1 ATTTAATAAAAATAAA
*
3653 TTTTAATA
1 ATTTAATA
3661 TTTATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTTAATAAAAATAAA
Found at i:3903 original size:3 final size:3
Alignment explanation
Indices: 3895--3943 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
3885 TACTGAATGT
*
3895 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3943 T
1 T
3944 CATCATAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:3944 original size:15 final size:15
Alignment explanation
Indices: 3895--3956 Score: 88
Period size: 15 Copynumber: 4.1 Consensus size: 15
3885 TACTGAATGT
*
3895 TTATTATTATTATTA
1 TTATCATTATTATTA
*
3910 TTATTATTATTATTA
1 TTATCATTATTATTA
3925 TTATCATTATTATTA
1 TTATCATTATTATTA
* *
3940 TTATCATCATAATTA
1 TTATCATTATTATTA
3955 TT
1 TT
3957 GTTGTTGTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (15 bp):
TTATCATTATTATTA
Found at i:9604 original size:16 final size:16
Alignment explanation
Indices: 9579--9609 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9569 ATTTGTGTCG
*
9579 GATATGTTTCGGACAC
1 GATATATTTCGGACAC
9595 GATATATTTCGGACA
1 GATATATTTCGGACA
9610 TGAATATGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (16 bp):
GATATATTTCGGACAC
Found at i:11412 original size:22 final size:21
Alignment explanation
Indices: 11358--11412 Score: 51
Period size: 22 Copynumber: 2.5 Consensus size: 21
11348 TAATTTGATT
11358 TAAATTATTAATTTAATAATAA
1 TAAA-TATTAATTTAATAATAA
11380 -AAATAATTTAATTTTAA-AATATA
1 TAAAT-A-TTAA-TTTAATAATA-A
11403 TAAATATTAA
1 TAAATATTAA
11413 AATAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
20 1 0.04
21 4 0.14
22 12 0.43
23 7 0.25
24 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAATATTAATTTAATAATAA
Found at i:11652 original size:13 final size:14
Alignment explanation
Indices: 11634--11667 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
11624 AATATACTGC
11634 AAATAAATA-TTAA
1 AAATAAATATTTAA
11647 AAATAAATATTTAA
1 AAATAAATATTTAA
11661 AAATAAA
1 AAATAAA
11668 AAATTCGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAATAAATATTTAA
Found at i:12844 original size:2 final size:2
Alignment explanation
Indices: 12831--12891 Score: 70
Period size: 2 Copynumber: 31.0 Consensus size: 2
12821 ATCAGTTTTA
* * * *
12831 AT AT AC AT AT AT AT AT AT A- AT AT AT AT TT AT AT CT AT CT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
12872 CT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
12892 TCATAGAAAG
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13026 original size:2 final size:2
Alignment explanation
Indices: 13019--13084 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
13009 CTCACATGTG
13019 TA TA TA TA TA TA 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 TA TA TA TA TA TA
13061 TA TA TA TA TA T- TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
13085 CATAATTGAA
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 62 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.