Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold482
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: 32430
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:9935 original size:48 final size:47
Alignment explanation
Indices: 9879--9971 Score: 127
Period size: 47 Copynumber: 2.0 Consensus size: 47
9869 TCATTGTCTT
*
9879 TTTCTTTCT-TTTCCTCACA-CTTTTGTTCAATCTCAATTTCTTTTTCGA
1 TTTCTTTCTCTTT-CTCACATCCTTT-TTC-ATCTCAATTTCTTTTTCGA
*
9927 TTTCTTTCTCTTTTTCACATCCTTTTTCATCTCAATTTCTTTTTC
1 TTTCTTTCTCTTTCTCACATCCTTTTTCATCTCAATTTCTTTTTC
9972 CATGACACTC
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
47 17 0.41
48 17 0.41
49 7 0.17
ACGTcount: A:0.13, C:0.26, G:0.02, T:0.59
Consensus pattern (47 bp):
TTTCTTTCTCTTTCTCACATCCTTTTTCATCTCAATTTCTTTTTCGA
Found at i:12641 original size:20 final size:20
Alignment explanation
Indices: 12594--12641 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
12584 AGTAAGCTCG
12594 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
12614 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
12634 GTTGAGCT
1 GTTGAGCT
12642 GGATGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:12960 original size:30 final size:30
Alignment explanation
Indices: 12926--13022 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
12916 AGCTCACTCC
12926 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
12956 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
12986 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
13016 TAGCTCA
1 TAGCTCA
13023 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:14738 original size:13 final size:12
Alignment explanation
Indices: 14720--14757 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
14710 AAAAGAGAAG
14720 AAATTCAGAAAAA
1 AAATTC-GAAAAA
14733 AAATTC-AAAAA
1 AAATTCGAAAAA
14744 AAA-TCGAAAAA
1 AAATTCGAAAAA
14755 AAA
1 AAA
14758 AAAAAAAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 2 0.08
11 16 0.67
13 6 0.25
ACGTcount: A:0.74, C:0.08, G:0.05, T:0.13
Consensus pattern (12 bp):
AAATTCGAAAAA
Found at i:15735 original size:37 final size:37
Alignment explanation
Indices: 15684--15754 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
15674 CATTCTTGTA
15684 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
15721 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
15755 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:15754 original size:6 final size:6
Alignment explanation
Indices: 15694--15743 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
15684 AAGAGAAAAC
*
15694 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
15743 A
1 A
15744 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:15836 original size:11 final size:12
Alignment explanation
Indices: 15804--15834 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
15794 TTGAGAGAAC
15804 TTGAAAAAGCCT
1 TTGAAAAAGCCT
15816 TTGAAAAAGCCT
1 TTGAAAAAGCCT
15828 TTGAAAA
1 TTGAAAA
15835 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:18047 original size:30 final size:30
Alignment explanation
Indices: 18013--18109 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
18003 AGCTCACTCC
18013 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
18043 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
18073 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
18103 TAGCTCA
1 TAGCTCA
18110 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:20611 original size:10 final size:10
Alignment explanation
Indices: 20595--20652 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
20585 CAACTCCGAC
20595 CAGCTCAATT
1 CAGCTCAATT
* *
20605 GAGCTCATTT
1 CAGCTCAATT
20615 CAGCTCAA-T
1 CAGCTCAATT
20624 CGAGCTCAATT
1 C-AGCTCAATT
*
20635 TAGCTACAATT
1 CAGCT-CAATT
20646 CAGCTCA
1 CAGCTCA
20653 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:20618 original size:20 final size:20
Alignment explanation
Indices: 20595--20655 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
20585 CAACTCCGAC
20595 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
20615 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
20636 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
20656 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:22275 original size:12 final size:12
Alignment explanation
Indices: 22254--22291 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
22244 ATAGTAGTTT
22254 CTCAAAAAAAAA
1 CTCAAAAAAAAA
22266 CTCGAAAAAAAAA
1 CTC-AAAAAAAAA
*
22279 -TTAAAAAAAAA
1 CTCAAAAAAAAA
22290 CT
1 CT
22292 AGTTTCCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
11 9 0.39
12 5 0.22
13 9 0.39
ACGTcount: A:0.71, C:0.13, G:0.03, T:0.13
Consensus pattern (12 bp):
CTCAAAAAAAAA
Found at i:22351 original size:14 final size:14
Alignment explanation
Indices: 22327--22377 Score: 81
Period size: 13 Copynumber: 3.9 Consensus size: 14
22317 GGATATCAAG
22327 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
22341 TT-TGAAAAAAAAA
1 TTGTGAAAAAAAAA
22354 TTGTG-AAAAAAAA
1 TTGTGAAAAAAAAA
22367 TTGT-AAAAAAA
1 TTGTGAAAAAAA
22378 GAGCTAGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
13 31 0.89
14 4 0.11
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.24
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:22935 original size:21 final size:21
Alignment explanation
Indices: 22909--22953 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
22899 TTTGGTATTT
*
22909 TGGAATTAGTTCGAAATAGTA
1 TGGAATTAGTACGAAATAGTA
* *
22930 TGGAATTGGTACGAAATGGTA
1 TGGAATTAGTACGAAATAGTA
22951 TGG
1 TGG
22954 TATTTGGTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.31
Consensus pattern (21 bp):
TGGAATTAGTACGAAATAGTA
Found at i:22963 original size:22 final size:22
Alignment explanation
Indices: 22920--22977 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
22910 GGAATTAGTT
*
22920 CGAAATAGTATGG-AATTGGTA
1 CGAAATGGTATGGTAATTGGTA
*
22941 CGAAATGGTATGGTATTTGGTA
1 CGAAATGGTATGGTAATTGGTA
*
22963 CGAATTGGTAATGGT
1 CGAAATGGT-ATGGT
22978 TCAAAGAGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 12 0.38
22 15 0.47
23 5 0.16
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.33
Consensus pattern (22 bp):
CGAAATGGTATGGTAATTGGTA
Found at i:25015 original size:18 final size:17
Alignment explanation
Indices: 24994--25038 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
24984 GAGTGACGAG
24994 AGAAAAAGAAATCGAAAA
1 AGAAAAA-AAATCGAAAA
*
25012 AGAAACAAAAATTGAAAA
1 AGAAA-AAAAATCGAAAA
25030 AGAGAAAAA
1 AGA-AAAAA
25039 GATTGGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.73, C:0.04, G:0.16, T:0.07
Consensus pattern (17 bp):
AGAAAAAAAATCGAAAA
Found at i:25043 original size:18 final size:18
Alignment explanation
Indices: 24992--25043 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
24982 AAGAGTGACG
*
24992 AGAGAAAAAGAAATCGAAAA
1 AGAGAAAAAG--ATTGAAAA
*
25012 AGA-AACAAAAATTGAAAA
1 AGAGAA-AAAGATTGAAAA
25030 AGAGAAAAAGATTG
1 AGAGAAAAAGATTG
25044 GAGAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 17 0.63
19 4 0.15
20 6 0.22
ACGTcount: A:0.67, C:0.04, G:0.19, T:0.10
Consensus pattern (18 bp):
AGAGAAAAAGATTGAAAA
Found at i:31424 original size:21 final size:21
Alignment explanation
Indices: 31398--31460 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
31388 TTGGTATTTG
31398 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
31419 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
31440 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
31461 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Done.