Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2420
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: 31761
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.36
Found at i:4519 original size:21 final size:20
Alignment explanation
Indices: 4468--4533 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 20
4458 TTTGGTTATT
*
4468 AAAAGTTGCATTCTTTCATCC
1 AAAAATTGCATTCTTTCAT-C
*
4489 AAAAAATGCATTCTTTCATC
1 AAAAATTGCATTCTTTCATC
*
4509 AAACTATTGCA-TCATTTCATC
1 AAA-AATTGCATTC-TTTCATC
4530 AAAA
1 AAAA
4534 TACATATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
20 6 0.16
21 32 0.84
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (20 bp):
AAAAATTGCATTCTTTCATC
Found at i:11450 original size:26 final size:26
Alignment explanation
Indices: 11405--11462 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
11395 AAATTTAATT
11405 ATAAATTATAAAAATCTTAATATTTGA
1 ATAAATTATAAAAATCTTAA-ATTTGA
11432 ATAAA-TATAAAAAAT-TTAAATTT-A
1 ATAAATTAT-AAAAATCTTAAATTTGA
*
11456 TTAAATT
1 ATAAATT
11463 TTTAACTCGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
24 5 0.18
25 5 0.18
26 7 0.25
27 11 0.39
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (26 bp):
ATAAATTATAAAAATCTTAAATTTGA
Found at i:11991 original size:16 final size:15
Alignment explanation
Indices: 11916--12020 Score: 67
Period size: 16 Copynumber: 7.0 Consensus size: 15
11906 AAATTAAATT
**
11916 TATTTAAATTTAATT
1 TATTTAAATTTAAAA
*
11931 TGATTAAAATATTAAAA
1 T-ATTTAAAT-TTAAAA
11948 TA---AAATTTAAAA
1 TATTTAAATTTAAAA
* * *
11960 TAATTAAATATGAAA
1 TATTTAAATTTAAAA
11975 TGATTTAAATTTAAAA
1 T-ATTTAAATTTAAAA
11991 TTATCTT-AATTTAAAA
1 -TAT-TTAAATTTAAAA
*
12007 -ATTTAAATTCAAAA
1 TATTTAAATTTAAAA
12021 CTAATTTGAT
Statistics
Matches: 72, Mismatches: 9, Indels: 19
0.72 0.09 0.19
Matches are distributed among these distances:
12 8 0.11
13 6 0.08
14 10 0.14
15 10 0.14
16 30 0.42
17 8 0.11
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (15 bp):
TATTTAAATTTAAAA
Found at i:23466 original size:49 final size:49
Alignment explanation
Indices: 23394--23491 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
23384 ATGTATTCCC
23394 CTGCTCTTTCATCGGGTTCGAATCCTTCTCACCCAAATTGAAGAAAAAT
1 CTGCTCTTTCATCGGGTTCGAATCCTTCTCACCCAAATTGAAGAAAAAT
*
23443 CTGCTCTTTCATCGGGTTCGAATCCTTCTCCCCCAAATTGAAGAAAAAT
1 CTGCTCTTTCATCGGGTTCGAATCCTTCTCACCCAAATTGAAGAAAAAT
23492 TAAGAGAGAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (49 bp):
CTGCTCTTTCATCGGGTTCGAATCCTTCTCACCCAAATTGAAGAAAAAT
Found at i:24178 original size:30 final size:32
Alignment explanation
Indices: 24142--24202 Score: 92
Period size: 30 Copynumber: 2.0 Consensus size: 32
24132 TTGATTTAAT
24142 TTAAAATTTTAAAAA-TTT-AAT-TAAAAAAAA
1 TTAAAA-TTTAAAAAGTTTAAATCTAAAAAAAA
24172 TTAAAATTTAAAAAGTTTAAATCTAAAAAAA
1 TTAAAATTTAAAAAGTTTAAATCTAAAAAAA
24203 TTTTAAATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 8 0.29
30 9 0.32
31 3 0.11
32 8 0.29
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (32 bp):
TTAAAATTTAAAAAGTTTAAATCTAAAAAAAA
Found at i:24184 original size:15 final size:15
Alignment explanation
Indices: 24142--24201 Score: 50
Period size: 15 Copynumber: 4.0 Consensus size: 15
24132 TTGATTTAAT
*
24142 TTAAAATTTTAAAAA
1 TTAAAATTTAAAAAA
* *
24157 TT-TAATTAAAAAAAA
1 TTAAAATT-TAAAAAA
*
24172 TTAAAATTTAAAAAG
1 TTAAAATTTAAAAAA
* *
24187 TTTAAATCTAAAAAA
1 TTAAAATTTAAAAAA
24202 ATTTTAAATC
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
14 4 0.12
15 26 0.76
16 4 0.12
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (15 bp):
TTAAAATTTAAAAAA
Found at i:24201 original size:17 final size:16
Alignment explanation
Indices: 24181--24215 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
24171 ATTAAAATTT
24181 AAAAAGTTTAAATCTAA
1 AAAAAGTTTAAATC-AA
*
24198 AAAAATTTTAAATCAA
1 AAAAAGTTTAAATCAA
24214 AA
1 AA
24216 TGATATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.63, C:0.06, G:0.03, T:0.29
Consensus pattern (16 bp):
AAAAAGTTTAAATCAA
Found at i:24242 original size:16 final size:16
Alignment explanation
Indices: 24139--24246 Score: 64
Period size: 16 Copynumber: 6.8 Consensus size: 16
24129 AATTTGATTT
24139 AATTTAAAATTT-TAAA
1 AATTT-AAATTTATAAA
* *
24155 AATTT-AATTAAAAAA
1 AATTTAAATTTATAAA
*
24170 AATTAAAATTTA-AAA
1 AATTTAAATTTATAAA
* * *
24185 AGTTTAAATCTAAAAA
1 AATTTAAATTTATAAA
*
24201 AATTTTAAA-TCA-AAA
1 AA-TTTAAATTTATAAA
* *
24216 TGATATAAAATTTATAAA
1 -AAT-TTAAATTTATAAA
24234 AATTTAAATTTAT
1 AATTTAAATTTAT
24247 TACAATTCAA
Statistics
Matches: 69, Mismatches: 15, Indels: 16
0.69 0.15 0.16
Matches are distributed among these distances:
14 4 0.06
15 23 0.33
16 29 0.42
17 10 0.14
18 3 0.04
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (16 bp):
AATTTAAATTTATAAA
Found at i:25491 original size:16 final size:15
Alignment explanation
Indices: 25466--25501 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
25456 TTAATCGCTG
25466 TAAT-ATTAT-TTTT
1 TAATAATTATATTTT
25479 TAATAATTATATTTT
1 TAATAATTATATTTT
25494 TAATAATT
1 TAATAATT
25502 GCATTTCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 4 0.19
14 5 0.24
15 12 0.57
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TAATAATTATATTTT
Found at i:27382 original size:14 final size:14
Alignment explanation
Indices: 27363--27398 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
27353 TGTATTGTAT
27363 TGATACAACACTTA
1 TGATACAACACTTA
27377 TGATACAACACTTA
1 TGATACAACACTTA
27391 TGATACAA
1 TGATACAA
27399 TGTATTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.28
Consensus pattern (14 bp):
TGATACAACACTTA
Found at i:27457 original size:19 final size:19
Alignment explanation
Indices: 27433--27482 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
27423 AGCGATACAT
27433 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
*
27452 TGTATCGATACAATACTTA
1 TGTATCGATACAACACTTA
*
27471 TGTATCAATACA
1 TGTATCGATACA
27483 TTTACTGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Done.