Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5851.1
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: 16952
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.27
Found at i:307 original size:16 final size:18
Alignment explanation
Indices: 280--315 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
270 TTTAATTTTC
280 AAAATTTCAAAAAA-AAA
1 AAAATTTCAAAAAATAAA
297 AAAATTT-AAAAAATAAA
1 AAAATTTCAAAAAATAAA
314 AA
1 AA
316 TTGCATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (18 bp):
AAAATTTCAAAAAATAAA
Found at i:353 original size:30 final size:29
Alignment explanation
Indices: 313--428 Score: 117
Period size: 30 Copynumber: 3.9 Consensus size: 29
303 TAAAAAATAA
* *
313 AAATTGCATTTTGACACCTAAACTTTTC-CT
1 AAATTTCATTTTGAC-CCTAAAC-TTTCATT
*
343 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCC-TAAACTTTCATT
* *
373 AAATTTCACTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTGA-CCCTAAACTTTCATT
* * *
403 AAATTTCATTTTAATCCTAAATTTTC
1 AAATTTCATTTTGACCCTAAACTTTC
429 TAAAAATTAC
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
29 16 0.22
30 54 0.74
31 3 0.04
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.44
Consensus pattern (29 bp):
AAATTTCATTTTGACCCTAAACTTTCATT
Found at i:694 original size:10 final size:10
Alignment explanation
Indices: 675--724 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
665 TTTTTCGAAG
*
675 GAAAAAAGAA
1 GAAAAGAGAA
685 GAAAAGAGAA
1 GAAAAGAGAA
695 GAAAAGAGAA
1 GAAAAGAGAA
* *
705 -AGAGGAGAA
1 GAAAAGAGAA
714 GAAAAGA-AA
1 GAAAAGAGAA
723 GA
1 GA
725 GTACCGGCGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
GAAAAGAGAA
Found at i:725 original size:17 final size:19
Alignment explanation
Indices: 678--720 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
668 TTCGAAGGAA
678 AAAAGAAGAAA-A-GAGAAG
1 AAAAG-AGAAAGAGGAGAAG
696 AAAAGAGAAAGAGGAGAAG
1 AAAAGAGAAAGAGGAGAAG
715 AAAAGA
1 AAAAGA
721 AAGAGTACCG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.22
18 6 0.26
19 12 0.52
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
AAAAGAGAAAGAGGAGAAG
Found at i:786 original size:3 final size:3
Alignment explanation
Indices: 780--825 Score: 51
Period size: 3 Copynumber: 15.0 Consensus size: 3
770 GCTAGACTTT
780 GAA GAA GAA GAA GGAA GAA GAA GGAA GAA GAA -AA -AA GGAA GAA GAA
1 GAA GAA GAA GAA -GAA GAA GAA -GAA GAA GAA GAA GAA -GAA GAA GAA
826 AGAAAAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 4 0.10
3 27 0.69
4 8 0.21
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:798 original size:10 final size:10
Alignment explanation
Indices: 783--811 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
773 AGACTTTGAA
783 GAAGAAGAAG
1 GAAGAAGAAG
793 GAAGAAGAAG
1 GAAGAAGAAG
803 GAAGAAGAA
1 GAAGAAGAA
812 AAAAGGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAG
Found at i:1105 original size:7 final size:7
Alignment explanation
Indices: 1093--1149 Score: 96
Period size: 7 Copynumber: 7.9 Consensus size: 7
1083 CCAGCAGAAA
1093 AAAAAAG
1 AAAAAAG
1100 AAAAAAG
1 AAAAAAG
1107 AAAAAAG
1 AAAAAAG
1114 AAAAAAGG
1 AAAAAA-G
1122 AAAAAAG
1 AAAAAAG
1129 AAAAAAG
1 AAAAAAG
1136 AAAAAAG
1 AAAAAAG
1143 AAGAAAA
1 AA-AAAA
1150 AGGGGGTTCA
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
7 37 0.77
8 11 0.23
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:1124 original size:22 final size:22
Alignment explanation
Indices: 1092--1151 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
1082 CCCAGCAGAA
*
1092 AAAAAAAGAAAAAAGAAAAAAG
1 AAAAAAGGAAAAAAGAAAAAAG
1114 AAAAAAGGAAAAAAGAAAAAAG
1 AAAAAAGGAAAAAAGAAAAAAG
*
1136 AAAAAAGAAGAAAAAG
1 AAAAAAGGA-AAAAAG
1152 GGGGTTCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 29 0.83
23 6 0.17
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (22 bp):
AAAAAAGGAAAAAAGAAAAAAG
Found at i:1744 original size:16 final size:17
Alignment explanation
Indices: 1700--1760 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
1690 GAATTTTCGC
* *
1700 GTTTTCAAAAGTTTTCGT
1 GTTTT-AAAAATTCTCGT
**
1718 GTTTTTGAAATT-TCCGT
1 GTTTTAAAAATTCT-CGT
1735 G-TTTAAAAATTCTCGT
1 GTTTTAAAAATTCTCGT
1751 GTTTTAAAAA
1 GTTTTAAAAA
1761 AAAAACTTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
16 13 0.37
17 17 0.49
18 5 0.14
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.48
Consensus pattern (17 bp):
GTTTTAAAAATTCTCGT
Found at i:1756 original size:17 final size:16
Alignment explanation
Indices: 1712--1760 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
1702 TTTCAAAAGT
**
1712 TTTCGTGTTTTTGAAA
1 TTTCGTGTTTTAAAAA
1728 TTTCCGTG-TTTAAAAA
1 TTT-CGTGTTTTAAAAA
1744 TTCTCGTGTTTTAAAAA
1 TT-TCGTGTTTTAAAAA
1761 AAAAACTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 15 0.54
17 13 0.46
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.49
Consensus pattern (16 bp):
TTTCGTGTTTTAAAAA
Found at i:1765 original size:22 final size:21
Alignment explanation
Indices: 1739--1793 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
1729 TTCCGTGTTT
1739 AAAAATTCTCGTGTTTTAAAAA
1 AAAAATT-TCGTGTTTTAAAAA
* *
1761 AAAAACTTTCCT-TTTTTAAAA
1 AAAAA-TTTCGTGTTTTAAAAA
1782 AAAAATTTCGTG
1 AAAAATTTCGTG
1794 CTTCAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 5 0.18
21 13 0.46
22 8 0.29
23 2 0.07
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.38
Consensus pattern (21 bp):
AAAAATTTCGTGTTTTAAAAA
Found at i:9715 original size:29 final size:30
Alignment explanation
Indices: 9660--9717 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
9650 TTTTGAACTC
* *
9660 TTAAAAAATTAAATATTTTAATTTAATTTT
1 TTAAAAAATTAAATATTATAAGTTAATTTT
*
9690 TTAAAATATTAAA-ATTATAAGTTAATTT
1 TTAAAAAATTAAATATTATAAGTTAATTT
9718 ATGATAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (30 bp):
TTAAAAAATTAAATATTATAAGTTAATTTT
Done.