Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold964
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: 34693
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:5604 original size:24 final size:25
Alignment explanation
Indices: 5551--5604 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
5541 AACAAATTCT
* *
5551 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
5576 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
5599 TTTTTT
1 TTTTTT
5605 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:7875 original size:14 final size:14
Alignment explanation
Indices: 7856--7883 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
7846 CTAGACCGTA
7856 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
7870 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
7884 CTTTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.71
Consensus pattern (14 bp):
TGCAATTTTTTTTT
Found at i:7892 original size:23 final size:23
Alignment explanation
Indices: 7861--7907 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
7851 CCGTATGCAA
*
7861 TTTTTTTTTTGCAATTTTTTTTTC
1 TTTTTTTTTCG-AATTTTTTTTTC
*
7885 TTTTTTTTTCGGATTTTTTTTTC
1 TTTTTTTTTCGAATTTTTTTTTC
7908 AAAACTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.06, C:0.09, G:0.06, T:0.79
Consensus pattern (23 bp):
TTTTTTTTTCGAATTTTTTTTTC
Found at i:7901 original size:13 final size:12
Alignment explanation
Indices: 7862--7907 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
7852 CGTATGCAAT
*
7862 TTTTTTTTTGCAA
1 TTTTTTTTT-CGA
7875 TTTTTTTTTC--
1 TTTTTTTTTCGA
7885 TTTTTTTTTCGGA
1 TTTTTTTTTC-GA
7898 TTTTTTTTTC
1 TTTTTTTTTC
7908 AAAACTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 10 0.33
12 1 0.03
13 19 0.63
ACGTcount: A:0.07, C:0.09, G:0.07, T:0.78
Consensus pattern (12 bp):
TTTTTTTTTCGA
Found at i:11236 original size:48 final size:48
Alignment explanation
Indices: 11181--11286 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
11171 TTGTCTTTTC
*
11181 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTGTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
11229 TTTCTTTTTCGATTTGTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTGTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
11277 TTTCTTTTTC
1 TTTCTTTTTC
11287 GATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.24, G:0.03, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTGTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:11305 original size:39 final size:36
Alignment explanation
Indices: 11255--11346 Score: 82
Period size: 39 Copynumber: 2.5 Consensus size: 36
11245 TTTCTCTTTT
*
11255 TCACA-TC-CTTTTTCAATCTCAATTTCTTT-TTCGA
1 TCACACTCTCTTTTTCAATCTC-ATTTCTTTCTTCAA
* * * *
11289 TGACACTCGTTTCTTTTACACTCTCGTTTCTTTCTTCAA
1 TCACACTC---TCTTTTTCAATCTCATTTCTTTCTTCAA
11328 TCACACTCTCTTTTTCAAT
1 TCACACTCTCTTTTTCAAT
11347 TTCTTGTTCC
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
34 4 0.09
35 2 0.05
36 9 0.20
38 7 0.16
39 22 0.50
ACGTcount: A:0.18, C:0.28, G:0.04, T:0.49
Consensus pattern (36 bp):
TCACACTCTCTTTTTCAATCTCATTTCTTTCTTCAA
Found at i:12463 original size:29 final size:28
Alignment explanation
Indices: 12401--12465 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 28
12391 TTAAACTTGA
*
12401 TTTTTTTTTGCTCACCTTTTTTTTCTTT
1 TTTTTTTTTGCTCACCTTTTTTTTCCTT
*
12429 TCTTTTTTTTGCTCGA-TTTTTTTTTCACTT
1 T-TTTTTTTTGCTC-ACCTTTTTTTTC-CTT
12459 TTTTTTT
1 TTTTTTT
12466 GAATTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 1 0.03
29 27 0.84
30 4 0.12
ACGTcount: A:0.05, C:0.15, G:0.05, T:0.75
Consensus pattern (28 bp):
TTTTTTTTTGCTCACCTTTTTTTTCCTT
Found at i:12473 original size:13 final size:13
Alignment explanation
Indices: 12457--12519 Score: 58
Period size: 12 Copynumber: 4.8 Consensus size: 13
12447 TTTTTTTCAC
12457 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
**
12470 TTTTTTTCAATCAAAT
1 TTTTTTT---TTGAAT
*
12486 TTTTTTTTCGAA-
1 TTTTTTTTTGAAT
12498 TTTTTTTTTG-AT
1 TTTTTTTTTGAAT
12510 TTTTTTTTTG
1 TTTTTTTTTG
12520 TTACTCCAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
11 1 0.02
12 19 0.45
13 11 0.26
16 11 0.26
ACGTcount: A:0.16, C:0.05, G:0.06, T:0.73
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:14016 original size:20 final size:20
Alignment explanation
Indices: 13993--14039 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
13983 GGGTTAAGAT
*
13993 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
14013 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
14033 TGAGCTG
1 TGAGCTG
14040 GAAACAAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:14972 original size:21 final size:20
Alignment explanation
Indices: 14935--14984 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
14925 ATCAGCTCAC
14935 TTGAGCTCAATTCAGCTCGT
1 TTGAGCTCAATTCAGCTCGT
* *
14955 TTGAGTTCGAATTTAGCTCGT
1 TTGAGCTC-AATTCAGCTCGT
*
14976 TTCAGCTCA
1 TTGAGCTCA
14985 TTCCTTCTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (20 bp):
TTGAGCTCAATTCAGCTCGT
Found at i:16708 original size:11 final size:11
Alignment explanation
Indices: 16692--16731 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
16682 ATACAAGTTA
16692 AAAAAAATTCG
1 AAAAAAATTCG
*
16703 AAAAAAATTTG
1 AAAAAAATTCG
*
16714 AAAAAAATCCG
1 AAAAAAATTCG
16725 AAAAAAA
1 AAAAAAA
16732 ATTGAAGTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.15
Consensus pattern (11 bp):
AAAAAAATTCG
Found at i:16717 original size:22 final size:22
Alignment explanation
Indices: 16692--16737 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
16682 ATACAAGTTA
* *
16692 AAAAAAATTCGAAAAAAATTTG
1 AAAAAAATCCGAAAAAAAATTG
16714 AAAAAAATCCGAAAAAAAATTG
1 AAAAAAATCCGAAAAAAAATTG
16736 AA
1 AA
16738 GTGAAAACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.67, C:0.07, G:0.09, T:0.17
Consensus pattern (22 bp):
AAAAAAATCCGAAAAAAAATTG
Found at i:19575 original size:23 final size:22
Alignment explanation
Indices: 19523--19575 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
19513 TCCACGTCTT
*
19523 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
19545 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
19568 TTTCTTTT
1 TTTCTTTT
19576 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:19626 original size:21 final size:21
Alignment explanation
Indices: 19532--19626 Score: 60
Period size: 21 Copynumber: 4.7 Consensus size: 21
19522 TTTTCTTTTG
19532 TTTCTTTTTC-T-AAT-TCATT
1 TTTCTTTTTCTTCAATCTC-TT
*
19551 TTCTCTTCTTTCTTCAATTTCTT
1 TT-TCTT-TTTCTTCAATCTCTT
**
19574 TTTC--ACTC-TCAATCTCTT
1 TTTCTTTTTCTTCAATCTCTT
* *
19592 TTTGCTCTTT-TTCATTCTCTT
1 TTT-CTTTTTCTTCAATCTCTT
19613 TTTCTTTTTCTTCA
1 TTTCTTTTTCTTCA
19627 CTTGTTTTAA
Statistics
Matches: 59, Mismatches: 7, Indels: 18
0.70 0.08 0.21
Matches are distributed among these distances:
18 12 0.20
19 5 0.08
20 9 0.15
21 21 0.36
22 3 0.05
23 7 0.12
24 2 0.03
ACGTcount: A:0.11, C:0.24, G:0.01, T:0.64
Consensus pattern (21 bp):
TTTCTTTTTCTTCAATCTCTT
Found at i:20775 original size:30 final size:30
Alignment explanation
Indices: 20741--20837 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
20731 AGCTCACTCC
20741 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
20771 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
20801 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
20831 TAGCTCA
1 TAGCTCA
20838 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:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:22577 original size:10 final size:11
Alignment explanation
Indices: 22561--22616 Score: 55
Period size: 11 Copynumber: 5.1 Consensus size: 11
22551 GAAATTCAGA
22561 AAAAAAAATTC-
1 AAAAAAAA-TCG
22572 AAAAAAAATCG
1 AAAAAAAATCG
*
22583 AAAAAAAA-GG
1 AAAAAAAATCG
22593 AAAAAAAAGT-G
1 AAAAAAAA-TCG
22604 ACAAAAAAATCG
1 A-AAAAAAATCG
22616 A
1 A
22617 GTTAAAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
10 11 0.28
11 19 0.49
12 9 0.23
ACGTcount: A:0.73, C:0.07, G:0.11, T:0.09
Consensus pattern (11 bp):
AAAAAAAATCG
Found at i:23570 original size:37 final size:37
Alignment explanation
Indices: 23519--23589 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
23509 CATTCTTGTA
23519 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
23556 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
23590 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:23589 original size:6 final size:6
Alignment explanation
Indices: 23529--23578 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
23519 AAGAGAAAAC
*
23529 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
23578 A
1 A
23579 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:25829 original size:30 final size:30
Alignment explanation
Indices: 25795--25891 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
25785 AGCTCACTCC
25795 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
25825 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
25855 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
25885 TAGCTCA
1 TAGCTCA
25892 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:27640 original size:13 final size:13
Alignment explanation
Indices: 27624--27679 Score: 53
Period size: 13 Copynumber: 4.3 Consensus size: 13
27614 AAAAAAAAAA
27624 AAAAAAAAAAGTG
1 AAAAAAAAAAGTG
* *
27637 AAAAAAAATCGAGTT
1 AAAAAAAA--AAGTG
*
27652 AAAAAAAGAA--G
1 AAAAAAAAAAGTG
27663 AAAAAAAAAAGTG
1 AAAAAAAAAAGTG
27676 AAAA
1 AAAA
27680 GTCTTGTGAG
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
11 9 0.27
13 14 0.42
15 10 0.30
ACGTcount: A:0.75, C:0.02, G:0.14, T:0.09
Consensus pattern (13 bp):
AAAAAAAAAAGTG
Found at i:27643 original size:39 final size:39
Alignment explanation
Indices: 27599--27679 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 39
27589 AAGAAATTCA
*
27599 GAAAAAAATTC-A-AAAAAAAAAAAAAAAAAAAAAAAGT
1 GAAAAAAAATCGAGAAAAAAAAAAAAAAAAAAAAAAAGT
** * *
27636 GAAAAAAAATCGAGTTAAAAAAAGAAGAAAAAAAAAAGT
1 GAAAAAAAATCGAGAAAAAAAAAAAAAAAAAAAAAAAGT
27675 GAAAA
1 GAAAA
27680 GTCTTGTGAG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 10 0.27
38 1 0.03
39 26 0.70
ACGTcount: A:0.78, C:0.02, G:0.11, T:0.09
Consensus pattern (39 bp):
GAAAAAAAATCGAGAAAAAAAAAAAAAAAAAAAAAAAGT
Found at i:28596 original size:37 final size:37
Alignment explanation
Indices: 28545--28615 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
28535 CATTCTTGTA
28545 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
28582 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
28616 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:28615 original size:6 final size:6
Alignment explanation
Indices: 28555--28604 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
28545 AAGAGAAAAC
*
28555 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
28604 A
1 A
28605 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:30853 original size:30 final size:30
Alignment explanation
Indices: 30819--30915 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
30809 AGCTCACTCC
30819 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
30849 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
30879 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
30909 TAGCTCA
1 TAGCTCA
30916 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
Done.