Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold686
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: 26827
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Found at i:3087 original size:20 final size:20
Alignment explanation
Indices: 3062--3099 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3052 CATTTTAGAC
*
3062 ATGTATCTATACATTCACCT
1 ATGTATCGATACATTCACCT
*
3082 ATGTATCGATGCATTCAC
1 ATGTATCGATACATTCAC
3100 TTGTTGTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTCACCT
Found at i:9049 original size:26 final size:28
Alignment explanation
Indices: 9020--9090 Score: 85
Period size: 26 Copynumber: 2.6 Consensus size: 28
9010 AGATATTCTG
*
9020 TTTGAATTTTAAAATTAATTA-TT-CAA
1 TTTGAATTTTAAAATTAATTATTTGAAA
*
9046 TTTGAATTTTAAGATT-ATTATTTGAAA
1 TTTGAATTTTAAAATTAATTATTTGAAA
* *
9073 TTTAAATTTTAAATTTAA
1 TTTGAATTTTAAAATTAA
9091 ATTCTAATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 4 0.11
26 17 0.46
27 15 0.41
28 1 0.03
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (28 bp):
TTTGAATTTTAAAATTAATTATTTGAAA
Found at i:9086 original size:13 final size:13
Alignment explanation
Indices: 9024--9151 Score: 59
Period size: 13 Copynumber: 9.8 Consensus size: 13
9014 ATTCTGTTTG
*
9024 AATTTTAAAATT-
1 AATTTTAAATTTA
* *
9036 AATTATTCAATTTG
1 AATT-TTAAATTTA
9050 AATTTTAAGA-TTA
1 AATTTTAA-ATTTA
* *
9063 TTATTTGAAATTTA
1 -AATTTTAAATTTA
9077 AATTTTAAATTTA
1 AATTTTAAATTTA
*
9090 AATTCT-AATATT-
1 AATTTTAAAT-TTA
**
9102 AA-TCAAAATTTCA
1 AATTTTAAATTT-A
* * *
9115 AAATATAAATTCA
1 AATTTTAAATTTA
9128 AATTTTAAATTTTA
1 AATTTTAAA-TTTA
*
9142 AAATTTAAAT
1 AATTTTAAAT
9152 AGGTTTTATT
Statistics
Matches: 88, Mismatches: 17, Indels: 21
0.70 0.13 0.17
Matches are distributed among these distances:
11 4 0.05
12 12 0.14
13 41 0.47
14 31 0.35
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (13 bp):
AATTTTAAATTTA
Found at i:9088 original size:20 final size:21
Alignment explanation
Indices: 9037--9102 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 21
9027 TTTAAAATTA
*
9037 ATTATTCAATTTGAATTTTAAG
1 ATTATT-AATTTGAAATTTAAG
9059 ATTATT-ATTTGAAATTTAA-
1 ATTATTAATTTGAAATTTAAG
*
9078 ATT-TTAAATTT-AAATTCTAAT
1 ATTATT-AATTTGAAATT-TAAG
9099 ATTA
1 ATTA
9103 ATCAAAATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
18 2 0.05
19 8 0.21
20 19 0.50
21 3 0.08
22 6 0.16
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.52
Consensus pattern (21 bp):
ATTATTAATTTGAAATTTAAG
Found at i:10430 original size:20 final size:21
Alignment explanation
Indices: 10402--10446 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
10392 ATCAAAATAA
* * *
10402 AAAATAATAACTATAAAAAT-
1 AAAAGAATAAATAAAAAAATG
10422 AAAAGAATAAATAAAAAAATG
1 AAAAGAATAAATAAAAAAATG
10443 AAAA
1 AAAA
10447 ATCTTAGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (21 bp):
AAAAGAATAAATAAAAAAATG
Found at i:15203 original size:31 final size:31
Alignment explanation
Indices: 15165--15227 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
15155 TTATTATTAG
*
15165 AGTTTCTTAAAGAAGTGTTTCTTTTTGCAAA
1 AGTTTCTTAAAGAAGTGTTTCCTTTTGCAAA
15196 AGTTTCTTAAAGAAGTGTTTCCTTTTGCAAA
1 AGTTTCTTAAAGAAGTGTTTCCTTTTGCAAA
15227 A
1 A
15228 ATCCTAAGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (31 bp):
AGTTTCTTAAAGAAGTGTTTCCTTTTGCAAA
Found at i:15769 original size:13 final size:13
Alignment explanation
Indices: 15751--15777 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
15741 ACATTATGCT
15751 TTGTATCGATACA
1 TTGTATCGATACA
15764 TTGTATCGATACA
1 TTGTATCGATACA
15777 T
1 T
15778 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:15863 original size:13 final size:13
Alignment explanation
Indices: 15842--15894 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
15832 CAATACATGG
*
15842 TACAATGTATCGA
1 TACATTGTATCGA
15855 TACATTGTATCGA
1 TACATTGTATCGA
15868 TACA-TG-AT-G-
1 TACATTGTATCGA
15877 -A-ATTGTATCGA
1 TACATTGTATCGA
15888 TACATTG
1 TACATTG
15895 CTTGTAACGG
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
9 2 0.06
10 2 0.06
11 2 0.06
12 3 0.09
13 20 0.61
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:15871 original size:33 final size:33
Alignment explanation
Indices: 15826--15894 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
15816 CTACCACTAT
*
15826 TTGTATCAATACATGGT-ACAATGTATCGATACA
1 TTGTATCAATACATGATGA-AATGTATCGATACA
* *
15859 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCAATACATGATGAAATGTATCGATACA
15892 TTG
1 TTG
15895 CTTGTAACGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.36
Consensus pattern (33 bp):
TTGTATCAATACATGATGAAATGTATCGATACA
Found at i:17647 original size:17 final size:17
Alignment explanation
Indices: 17625--17658 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
17615 AACAAGTAAG
17625 AAGGACAAGGAACAAAT
1 AAGGACAAGGAACAAAT
17642 AAGGACAAGGAACAAAT
1 AAGGACAAGGAACAAAT
17659 CATATGCTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.12, G:0.24, T:0.06
Consensus pattern (17 bp):
AAGGACAAGGAACAAAT
Found at i:18168 original size:21 final size:20
Alignment explanation
Indices: 18134--18176 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
18124 TATTAAAAAG
*
18134 TTAGCTAATGAAAATAATGAA
1 TTAGCTAATGAAAACAA-GAA
18155 TTAGCTAA-GAAAAACAAGAA
1 TTAGCTAATG-AAAACAAGAA
18175 TT
1 TT
18177 TGCATGATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (20 bp):
TTAGCTAATGAAAACAAGAA
Found at i:18175 original size:20 final size:21
Alignment explanation
Indices: 18134--18176 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
18124 TATTAAAAAG
*
18134 TTAGCTAATGAAAATAATGAA
1 TTAGCTAATGAAAATAAAGAA
18155 TTAGCTAA-GAAAA-ACAAGAA
1 TTAGCTAATGAAAATA-AAGAA
18175 TT
1 TT
18177 TGCATGATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 11 0.55
21 8 0.40
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (21 bp):
TTAGCTAATGAAAATAAAGAA
Found at i:24779 original size:20 final size:20
Alignment explanation
Indices: 24754--24803 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
24744 TTCCTTAATT
24754 TTTC-TTTTTCTCTATTTTTC
1 TTTCTTTTTTCT-TATTTTTC
* *
24774 TTTCTTTTTTCTTTTTTTTT
1 TTTCTTTTTTCTTATTTTTC
24794 TTTCTTTTTT
1 TTTCTTTTTT
24804 TCTCTCTACT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 20 0.74
21 7 0.26
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTCTTTTTTCTTATTTTTC
Found at i:24781 original size:10 final size:10
Alignment explanation
Indices: 24754--24802 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
24744 TTCCTTAATT
24754 TTTCTTTTTC
1 TTTCTTTTTC
* *
24764 TCTATTTTTC
1 TTTCTTTTTC
24774 TTTCTTTTTTC
1 TTTC-TTTTTC
*
24785 TTT-TTTTTT
1 TTTCTTTTTC
24794 TTTCTTTTT
1 TTTCTTTTT
24803 TTCTCTCTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 8 0.25
10 15 0.47
11 9 0.28
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:24791 original size:8 final size:8
Alignment explanation
Indices: 24752--24806 Score: 60
Period size: 8 Copynumber: 6.9 Consensus size: 8
24742 TTTTCCTTAA
24752 TTTTTCTT
1 TTTTTCTT
* *
24760 TTTCTCTA
1 TTTTTCTT
24768 TTTTTCTT
1 TTTTTCTT
24776 TCTTTT-TT
1 T-TTTTCTT
24784 CTTTTT-TT
1 -TTTTTCTT
24792 TTTTTCTT
1 TTTTTCTT
24800 TTTTTCT
1 TTTTTCT
24807 CTCTACTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
7 5 0.12
8 30 0.75
9 5 0.12
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTCTT
Found at i:24804 original size:32 final size:36
Alignment explanation
Indices: 24752--24820 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 36
24742 TTTTCCTTAA
24752 TTTTTCTTTTTCTCTATTTTTCT-T-T-CTTTTTTC
1 TTTTTCTTTTTCTCTATTTTTCTCTCTACTTTTTTC
* *
24785 TTTTT-TTTTTTTCTTTTTTTCTCTCTACTTTTTTC
1 TTTTTCTTTTTCTCTATTTTTCTCTCTACTTTTTTC
24820 T
1 T
24821 AATCAACTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 15 0.48
33 6 0.19
34 1 0.03
35 9 0.29
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (36 bp):
TTTTTCTTTTTCTCTATTTTTCTCTCTACTTTTTTC
Found at i:25532 original size:167 final size:163
Alignment explanation
Indices: 25352--25790 Score: 417
Period size: 165 Copynumber: 2.6 Consensus size: 163
25342 GTTCAACAAC
* * * *
25352 AATATTAGATGAA-TTTAAATAATTTTATACCAAAGAAAATCC-CCCAAAAAATATTTATAGAAT
1 AATATTTGATGAATTTTAAA-AATTTTAAACC-AAGAAAATCCTCTCGAAAAATATTTATAGAAT
* * * * *
25415 AGAAAATTCAGTTTTTTAGGAAA-AG-GAGAATTTCAAGGAAAAAAATCAAAAATGAATGAACAT
64 AGAAAATTC-G-TATTTCGAAAATAGAG-GAATTTCAAAG-AAAAAATCAAAAAT-AATGAAAAT
*
25478 GAATGAATTTTTGAAAACTGAATTAAAATTAAA-TAAATAAT
124 GAATGAATTTTTGAAAAAT-AATTAAAA-TAAATTAAATAAT
** * *
25519 AATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCTCTCTCGAAAAA-ATTTATGGACT
1 AATATTTGATGAATTTTAAAAATTTTAAACCAAG-AAAATC-CTCTCGAAAAATATTTATAGAAT
* * * * *
25583 AGAAAATGTCGTATTTCGAAAATAGAGGATTTTCAAAGAAAAAATGAAAACTCATGAAAATGTAT
64 AGAAAAT-TCGTATTTCGAAAATAGAGGAATTTCAAAGAAAAAATCAAAAATAATGAAAATGAAT
* * *
25648 TAATTTTTGAAAAATATTTAATATAAATTAAATAAT
128 GAATTTTTGAAAAATAATTAAAATAAATTAAATAAT
* * *
25684 AATATTTGATGAATTTTAAAAATTTTAAACCCATGAAAATCCTCTCGAAAAATTTTTACAGAGA-
1 AATATTTGATGAATTTTAAAAATTTTAAA-CCAAGAAAATCCTCTCGAAAAATATTTATAGA-AT
* *
25748 AGAAAATTCTGTAATTT-AAAAATATGAGAAATTTCAAAAGAAA
64 AGAAAATTC-GT-ATTTCGAAAATA-GAGGAATTTC-AAAGAAA
25791 GTCAATAACT
Statistics
Matches: 225, Mismatches: 32, Indels: 30
0.78 0.11 0.10
Matches are distributed among these distances:
164 17 0.08
165 68 0.30
166 42 0.19
167 53 0.24
168 35 0.16
169 10 0.04
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.31
Consensus pattern (163 bp):
AATATTTGATGAATTTTAAAAATTTTAAACCAAGAAAATCCTCTCGAAAAATATTTATAGAATAG
AAAATTCGTATTTCGAAAATAGAGGAATTTCAAAGAAAAAATCAAAAATAATGAAAATGAATGAA
TTTTTGAAAAATAATTAAAATAAATTAAATAAT
Done.