Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold632
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: 33753
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1701 original size:5 final size:5
Alignment explanation
Indices: 1682--1748 Score: 59
Period size: 5 Copynumber: 13.0 Consensus size: 5
1672 ACATTCTTGT
*
1682 AAAGA GAAA-A AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA
1 AAAGA -AAAGA AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA
1728 AAATGA AATA-A AAAGA AAAGA
1 AAA-GA AA-AGA AAAGA AAAGA
1749 GAGGCAAGAG
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
4 7 0.13
5 27 0.52
6 17 0.33
7 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:1709 original size:15 final size:14
Alignment explanation
Indices: 1682--1748 Score: 71
Period size: 16 Copynumber: 4.4 Consensus size: 14
1672 ACATTCTTGT
1682 AAAGAGAAAAAAAGA
1 AAAGA-AAAAAAAGA
1697 AAAGAAAAGAAAAAGCA
1 AAAG-AAA-AAAAAG-A
*
1714 AAAGAAGAAAAAGA
1 AAAGAAAAAAAAGA
1728 AAATGAAATAAAAAGA
1 AAA-GAAA-AAAAAGA
1744 AAAGA
1 AAAGA
1749 GAGGCAAGAG
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
14 4 0.09
15 17 0.38
16 19 0.42
17 5 0.11
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.03
Consensus pattern (14 bp):
AAAGAAAAAAAAGA
Found at i:1728 original size:31 final size:29
Alignment explanation
Indices: 1686--1748 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
1676 TCTTGTAAAG
1686 AGAAAAAAAGAAAA-GAAAAGAAAAAGCAAA
1 AGAAAAAAAGAAAATG-AAAGAAAAAG-AAA
*
1716 AGAAGAAAAAGAAAATGAAATAAAAAGAAA
1 AGAA-AAAAAGAAAATGAAAGAAAAAGAAA
1746 AGA
1 AGA
1749 GAGGCAAGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 10 0.33
31 19 0.63
32 1 0.03
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (29 bp):
AGAAAAAAAGAAAATGAAAGAAAAAGAAA
Found at i:1879 original size:30 final size:31
Alignment explanation
Indices: 1816--1886 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
1806 TTTGAAAAGC
* *
1816 AAAAAGAAA-ATGAGATTGAAAAAGAGAACG
1 AAAAAGAAATTTGAGAGTGAAAAAGAGAACG
*
1846 -AAAAGAAATTTGAGAGTGAAAAAGA-AGATG
1 AAAAAGAAATTTGAGAGTGAAAAAGAGA-ACG
1876 AAAAAGAAATT
1 AAAAAGAAATT
1887 GAAACAAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 9 0.26
30 16 0.46
31 10 0.29
ACGTcount: A:0.62, C:0.01, G:0.23, T:0.14
Consensus pattern (31 bp):
AAAAAGAAATTTGAGAGTGAAAAAGAGAACG
Found at i:4016 original size:30 final size:30
Alignment explanation
Indices: 3982--4078 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
3972 AGCTCACTCC
3982 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
4012 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
4042 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
4072 TAGCTCA
1 TAGCTCA
4079 TTTTAGTTTA
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:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:12960 original size:14 final size:14
Alignment explanation
Indices: 12941--12975 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
12931 AGGAAATTTG
12941 AAAAAAAAATTCAA
1 AAAAAAAAATTCAA
12955 AAAAAAAAATTCAA
1 AAAAAAAAATTCAA
12969 AAAAAAA
1 AAAAAAA
12976 TTCGAAGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.83, C:0.06, G:0.00, T:0.11
Consensus pattern (14 bp):
AAAAAAAAATTCAA
Found at i:12977 original size:39 final size:38
Alignment explanation
Indices: 12900--12977 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 38
12890 CATATTGTAA
* * **
12900 TTGAAAAAAAAATCAAAAAAAAAAAGAGAAGAGGAAAT
1 TTGAAAAAAAAATCAAAAAAAAAAAGACAAAAAAAAAT
**
12938 TTGAAAAAAAAATTCAAAAAAAAAAATTCAAAAAAAAAT
1 TTGAAAAAAAAA-TCAAAAAAAAAAAGACAAAAAAAAAT
12977 T
1 T
12978 CGAAGTATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
38 12 0.36
39 21 0.64
ACGTcount: A:0.72, C:0.04, G:0.09, T:0.15
Consensus pattern (38 bp):
TTGAAAAAAAAATCAAAAAAAAAAAGACAAAAAAAAAT
Found at i:14474 original size:30 final size:30
Alignment explanation
Indices: 14440--14536 Score: 115
Period size: 30 Copynumber: 3.2 Consensus size: 30
14430 AGCTCACTCC
14440 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
14470 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
*
14500 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
14530 TAGCTCA
1 TAGCTCA
14537 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:16272 original size:15 final size:14
Alignment explanation
Indices: 16252--16281 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
16242 AAAAGAGAAG
16252 AAATTCAGAAAAAAA
1 AAATTCA-AAAAAAA
16267 AAATTCAAAAAAAA
1 AAATTCAAAAAAAA
16281 A
1 A
16282 TCGAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.77, C:0.07, G:0.03, T:0.13
Consensus pattern (14 bp):
AAATTCAAAAAAAA
Found at i:17258 original size:15 final size:15
Alignment explanation
Indices: 17229--17294 Score: 62
Period size: 15 Copynumber: 4.4 Consensus size: 15
17219 TCTTGTAAAG
*
17229 AGAAAACAAAG-AAA
1 AGAAAAAAAAGAAAA
17243 AGAAAAAAAAGAAAA
1 AGAAAAAAAAGAAAA
* * *
17258 AGCAAGAGAAGAAAA
1 AGAAAAAAAAGAAAA
* *
17273 AGAAAATGAAATAAAA
1 AGAAAA-AAAAGAAAA
17289 AGAAAA
1 AGAAAA
17295 GAGAGGCAAG
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
14 10 0.24
15 19 0.46
16 12 0.29
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.03
Consensus pattern (15 bp):
AGAAAAAAAAGAAAA
Found at i:17275 original size:35 final size:37
Alignment explanation
Indices: 17226--17294 Score: 108
Period size: 35 Copynumber: 1.9 Consensus size: 37
17216 CATTCTTGTA
17226 AAGAGAAAACAAAGAAAA-GAAA-AAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATGAAATAAAAAGAAAAAGC
17261 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAATAAAAAGAAAA
17295 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
35 15 0.48
36 6 0.19
37 10 0.32
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAATAAAAAGAAAAAGC
Found at i:17376 original size:11 final size:12
Alignment explanation
Indices: 17344--17374 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
17334 TTGAGAGAAC
17344 TTGAAAAAGCCT
1 TTGAAAAAGCCT
17356 TTGAAAAAGCCT
1 TTGAAAAAGCCT
17368 TTGAAAA
1 TTGAAAA
17375 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:19573 original size:30 final size:30
Alignment explanation
Indices: 19539--19635 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
19529 AGCTCACTCC
19539 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
19569 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
19599 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
19629 TAGCTCA
1 TAGCTCA
19636 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:30641 original size:1 final size:1
Alignment explanation
Indices: 30637--30703 Score: 80
Period size: 1 Copynumber: 67.0 Consensus size: 1
30627 TTTTCTTTTT
*** ** *
30637 AAAAAAAAAAAAAAAAAAAAAAAAATTCAAAAAAAAAAAAAAAAAATTAAAAAAAAAATAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
30702 AA
1 AA
30704 TTGCAGACTT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.91, C:0.01, G:0.00, T:0.07
Consensus pattern (1 bp):
A
Found at i:30644 original size:20 final size:20
Alignment explanation
Indices: 30607--30644 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
30597 CAAAAAAATT
* *
30607 TTTTTTTTTTATAAAAAACA
1 TTTTCTTTTTAAAAAAAACA
30627 TTTTCTTTTTAAAAAAAA
1 TTTTCTTTTTAAAAAAAA
30645 AAAAAAAAAA
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:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTTCTTTTTAAAAAAAACA
Found at i:30661 original size:21 final size:21
Alignment explanation
Indices: 30643--30705 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
30633 TTTTAAAAAA
30643 AAAAAAAAAAAAAAAAAAATT
1 AAAAAAAAAAAAAAAAAAATT
*
30664 CAAAAAAAAAAAAAAAAAATT
1 AAAAAAAAAAAAAAAAAAATT
*
30685 AAAAAAAAAATAAAAAAAATT
1 AAAAAAAAAAAAAAAAAAATT
30706 GCAGACTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.87, C:0.02, G:0.00, T:0.11
Consensus pattern (21 bp):
AAAAAAAAAAAAAAAAAAATT
Found at i:32921 original size:13 final size:13
Alignment explanation
Indices: 32903--32927 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
32893 TTTTCTAAGA
32903 ATTCCAGATACAC
1 ATTCCAGATACAC
32916 ATTCCAGATACA
1 ATTCCAGATACA
32928 TTCTAATAGT
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:0.40, C:0.28, G:0.08, T:0.24
Consensus pattern (13 bp):
ATTCCAGATACAC
Done.