Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold396
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: 37011
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1195 original size:23 final size:23
Alignment explanation
Indices: 1169--1227 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
1159 TTAAAGTACA
1169 GCTAAATTGAGCTGCAAACTGAG
1 GCTAAATTGAGCTGCAAACTGAG
* **
1192 GCTAAATTAAGCT-CAATGTGAG
1 GCTAAATTGAGCTGCAAACTGAG
* *
1214 CCTAAATCGAGCTG
1 GCTAAATTGAGCTG
1228 GAAAAACTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
22 17 0.59
23 12 0.41
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.24
Consensus pattern (23 bp):
GCTAAATTGAGCTGCAAACTGAG
Found at i:3182 original size:15 final size:14
Alignment explanation
Indices: 3148--3188 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
3138 TTCTCAATCT
3148 CATTTTCTTTTTCA
1 CATTTTCTTTTTCA
*
3162 -ATTTTCTTTTCTTA
1 CATTTTCTTTT-TCA
3176 CATTTTCTTTTTC
1 CATTTTCTTTTTC
3189 TCTCATAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 10 0.43
14 3 0.13
15 10 0.43
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.68
Consensus pattern (14 bp):
CATTTTCTTTTTCA
Found at i:3247 original size:13 final size:13
Alignment explanation
Indices: 3221--3259 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
3211 TCTTTTGCAA
3221 TTTC-TTTTCTTTT
1 TTTCGTTTTC-TTT
3234 TTTCGTTTTCTTT
1 TTTCGTTTTCTTT
*
3247 TTTTGTTTTCTTT
1 TTTCGTTTTCTTT
3260 CAATTTCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 19 0.79
14 5 0.21
ACGTcount: A:0.00, C:0.13, G:0.05, T:0.82
Consensus pattern (13 bp):
TTTCGTTTTCTTT
Found at i:5407 original size:30 final size:30
Alignment explanation
Indices: 5322--5418 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
5312 TAAACTAAAA
* *
5322 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
5352 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
5382 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
5411 ATGAGCTA
1 -TGAGCTA
5419 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:13521 original size:19 final size:19
Alignment explanation
Indices: 13476--13521 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
13466 ATTAACACAC
*
13476 AATTAATTAAAATATAACT
1 AATTAATAAAAATATAACT
*
13495 -ATTCATAAAAATCATAA-T
1 AATTAATAAAAAT-ATAACT
13513 AATTAATAA
1 AATTAATAA
13522 TTAAACAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTAATAAAAATATAACT
Found at i:14440 original size:21 final size:20
Alignment explanation
Indices: 14397--14452 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 20
14387 AGTTCCCATC
* *
14397 AGCTCACTTGAGCTCGTTTT
1 AGCTCATTTGAGCTCGATTT
*
14417 AGCTCGTTTGAGCTCGAATTT
1 AGCTCATTTGAGCTCG-ATTT
*
14438 AGCTCATTTCAGCTC
1 AGCTCATTTGAGCTC
14453 ATTCCTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.38
Consensus pattern (20 bp):
AGCTCATTTGAGCTCGATTT
Found at i:14695 original size:13 final size:13
Alignment explanation
Indices: 14677--14701 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14667 AATAGTTGTG
14677 TGTTATTTAATTA
1 TGTTATTTAATTA
14690 TGTTATTTAATT
1 TGTTATTTAATT
14702 TTGTAGGTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:20659 original size:15 final size:14
Alignment explanation
Indices: 20623--20677 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 14
20613 TCTATTGATC
20623 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
20637 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
20651 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
*
20666 GAAAGAAAAGAA
1 GAGA-AAAAGAA
20678 TGAGGAGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 16 0.47
15 18 0.53
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:26684 original size:14 final size:14
Alignment explanation
Indices: 26667--26706 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
26657 CGAATGGAAT
*
26667 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
*
26681 GGTAGGAACAAAAT
1 GGTAGGAACAAAAG
*
26695 GGTATGAACAAA
1 GGTAGGAACAAA
26707 TCGGTCAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.47, C:0.07, G:0.33, T:0.12
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Done.