Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1339
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: 59937
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:13982 original size:20 final size:20
Alignment explanation
Indices: 13936--13982 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
13926 AGCTTGTTTC
*
13936 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
13956 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
13976 CAGCTCA
1 CAGCTCA
13983 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:15406 original size:19 final size:20
Alignment explanation
Indices: 15368--15407 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
15358 AAAAATGAAA
**
15368 AATTTTTTTTGTTGTAATTT
1 AATTTTTTTCCTTGTAATTT
15388 AATTTTTTTCCTTGT-ATTT
1 AATTTTTTTCCTTGTAATTT
15407 A
1 A
15408 GCTTACTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.20, C:0.05, G:0.07, T:0.68
Consensus pattern (20 bp):
AATTTTTTTCCTTGTAATTT
Found at i:15465 original size:11 final size:12
Alignment explanation
Indices: 15442--15466 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15432 AAAAAATTTG
15442 AAATTCAAAAAA
1 AAATTCAAAAAA
15454 AAATTCAAAAAA
1 AAATTCAAAAAA
15466 A
1 A
15467 GTGAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:15490 original size:27 final size:26
Alignment explanation
Indices: 15460--15520 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
15450 AAAAAAATTC
**
15460 AAAAAAAGTGAAAAAAAAATCGAGCAA
1 AAAAAAAAAGAAAAAAAAAT-GAGCAA
*
15487 AAAAAAGAAAGAAAAAAAAGTGAGCAA
1 AAAAAA-AAAGAAAAAAAAATGAGCAA
15514 AAAAAAA
1 AAAAAAA
15521 TCAAGTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 1 0.03
27 18 0.60
28 11 0.37
ACGTcount: A:0.75, C:0.05, G:0.15, T:0.05
Consensus pattern (26 bp):
AAAAAAAAAGAAAAAAAAATGAGCAA
Found at i:15515 original size:13 final size:13
Alignment explanation
Indices: 15459--15518 Score: 52
Period size: 13 Copynumber: 4.6 Consensus size: 13
15449 AAAAAAAATT
15459 CAAAAAAAGTGA-
1 CAAAAAAAGTGAG
*
15471 -AAAAAAAATCGAG
1 CAAAAAAAGT-GAG
**
15484 CAAAAAAAAGAAAG
1 C-AAAAAAAGTGAG
*
15498 AAAAAAAAGTGAG
1 CAAAAAAAGTGAG
15511 CAAAAAAA
1 CAAAAAAA
15519 AATCAAGTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
11 8 0.22
12 2 0.06
13 17 0.47
14 2 0.06
15 7 0.19
ACGTcount: A:0.73, C:0.07, G:0.15, T:0.05
Consensus pattern (13 bp):
CAAAAAAAGTGAG
Found at i:16645 original size:48 final size:47
Alignment explanation
Indices: 16566--16671 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
16556 GAGTGTCATG
*
16566 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
16614 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
16662 GAAAAAGAAA
1 GAAAAAGAAA
16672 GAAAAGACAA
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:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:18386 original size:20 final size:20
Alignment explanation
Indices: 18340--18386 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
18330 AGCTTGTTTC
*
18340 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
18360 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
18380 CAGCTCA
1 CAGCTCA
18387 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:20668 original size:20 final size:20
Alignment explanation
Indices: 20643--20697 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
20633 TGTGGTTCAA
*
20643 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
20663 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
20683 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
20698 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:24029 original size:11 final size:11
Alignment explanation
Indices: 24003--24042 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
23993 TAGTTTCTCG
*
24003 AAAAAAAACTC
1 AAAAAAAATTC
*
24014 GAAAAAAATT-
1 AAAAAAAATTC
24024 AAAAAAAATTC
1 AAAAAAAATTC
24035 AAAAAAAA
1 AAAAAAAA
24043 ACTAGTTTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.78, C:0.07, G:0.03, T:0.12
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:24105 original size:14 final size:14
Alignment explanation
Indices: 24081--24131 Score: 74
Period size: 13 Copynumber: 3.9 Consensus size: 14
24071 GGATATCAAG
24081 TTGTG-AAAAAAAA
1 TTGTGAAAAAAAAA
24094 TT-TGAAAAAAAAA
1 TTGTGAAAAAAAAA
24107 TTGTG-AAAAAAAA
1 TTGTGAAAAAAAAA
24120 TTGT-AAAAAAAA
1 TTGTGAAAAAAAA
24132 GAGCTAGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
12 2 0.06
13 31 0.89
14 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.24
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:24110 original size:26 final size:25
Alignment explanation
Indices: 24081--24131 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 25
24071 GGATATCAAG
24081 TTGTGAAAAAAAATTTGAAAAAAAAA
1 TTGTGAAAAAAAA-TTGAAAAAAAAA
*
24107 TTGTGAAAAAAAATTGTAAAAAAAA
1 TTGTGAAAAAAAATTGAAAAAAAAA
24132 GAGCTAGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.24
Consensus pattern (25 bp):
TTGTGAAAAAAAATTGAAAAAAAAA
Found at i:28598 original size:12 final size:12
Alignment explanation
Indices: 28581--28614 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
28571 AGACCGTATA
28581 CAATTTTTTTTT
1 CAATTTTTTTTT
28593 CAA-TTTTTTTT
1 CAATTTTTTTTT
28604 CGAATTTTTTT
1 C-AATTTTTTT
28615 ACAAACTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 9 0.45
12 5 0.25
13 6 0.30
ACGTcount: A:0.18, C:0.09, G:0.03, T:0.71
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:28601 original size:11 final size:12
Alignment explanation
Indices: 28585--28614 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
28575 CGTATACAAT
28585 TTTTTTTTC-AA
1 TTTTTTTTCGAA
28596 TTTTTTTTCGAA
1 TTTTTTTTCGAA
28608 TTTTTTT
1 TTTTTTT
28615 ACAAACTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.13, C:0.07, G:0.03, T:0.77
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:29829 original size:29 final size:29
Alignment explanation
Indices: 29795--29867 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
29785 ATGTATTAGT
* *
29795 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
29824 TTAGGACATATTTAAAACACCTAAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
29853 TTAGGACATATTTAA
1 TTAGGACATATTTAA
29868 TAATATCTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.32
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACCTAAACTAA
Found at i:31125 original size:22 final size:22
Alignment explanation
Indices: 31082--31125 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
31072 TCCTTTTTCA
*
31082 CACCTTCAAGGCTGTTCACTTT
1 CACCTTCAAGGCTGGTCACTTT
* * *
31104 CACCTTTAATGCTGGTCTCTTT
1 CACCTTCAAGGCTGGTCACTTT
31126 TCAGCCAAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.16, C:0.30, G:0.14, T:0.41
Consensus pattern (22 bp):
CACCTTCAAGGCTGGTCACTTT
Found at i:39398 original size:17 final size:18
Alignment explanation
Indices: 39376--39412 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
39366 TGGAATAAAC
39376 TTAGTTAA-TTAAATAAG
1 TTAGTTAATTTAAATAAG
*
39393 TTAGTTAATTTAATTAAG
1 TTAGTTAATTTAAATAAG
39411 TT
1 TT
39413 CAGCTCAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
TTAGTTAATTTAAATAAG
Found at i:42683 original size:9 final size:10
Alignment explanation
Indices: 42648--42686 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
42638 ATTTGCAAGT
42648 TTTGAGCTAA
1 TTTGAGCTAA
*
42658 TTTGAGCTGA
1 TTTGAGCTAA
*
42668 TTTGAGCTCA
1 TTTGAGCTAA
42678 -TTGAGCTAA
1 TTTGAGCTAA
42687 ATTGGAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (10 bp):
TTTGAGCTAA
Found at i:45039 original size:22 final size:22
Alignment explanation
Indices: 45011--45054 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
45001 TTTTGAACCA
45011 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
45033 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
45055 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:46967 original size:28 final size:28
Alignment explanation
Indices: 46912--46974 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
46902 GCACAAGTAG
*
46912 GAATAAAGAAATAAAAATGAAATAGCAA
1 GAATAAAGAAATAAAAATGAAACAGCAA
*
46940 GAAATAAAGAAA-AGAAATTG-AACAGCAA
1 G-AATAAAGAAATA-AAAATGAAACAGCAA
46968 GAATAAA
1 GAATAAA
46975 AGATAAGTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 6 0.19
28 10 0.32
29 15 0.48
ACGTcount: A:0.67, C:0.05, G:0.16, T:0.13
Consensus pattern (28 bp):
GAATAAAGAAATAAAAATGAAACAGCAA
Found at i:47953 original size:10 final size:10
Alignment explanation
Indices: 47937--47994 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
47927 CAACTCCGAC
47937 CAGCTCAATT
1 CAGCTCAATT
* *
47947 GAGCTCATTT
1 CAGCTCAATT
47957 CAGCTCAA-T
1 CAGCTCAATT
*
47966 CGAGCTTAATT
1 C-AGCTCAATT
*
47977 TAGCTACAATT
1 CAGCT-CAATT
47988 CAGCTCA
1 CAGCTCA
47995 TTTATTTTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
9 2 0.05
10 26 0.70
11 9 0.24
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:47960 original size:20 final size:20
Alignment explanation
Indices: 47937--47997 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
47927 CAACTCCGAC
47937 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
* *
47957 CAGCTCAATCGAGCTTAATTT
1 CAGCTCAATTGAGC-TCATTT
*
47978 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
47998 ATTTTATTGG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 22 0.65
21 12 0.35
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:48590 original size:20 final size:20
Alignment explanation
Indices: 48544--48590 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
48534 AGCTCGTTTC
*
48544 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
48564 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
48584 CAGCTCA
1 CAGCTCA
48591 ATCTTAACCC
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:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:50197 original size:14 final size:15
Alignment explanation
Indices: 50161--50198 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
50151 CCCACAAACA
50161 TGAATAAATTGCGAG
1 TGAATAAATTGCGAG
50176 TGAATAAATTGCGAG
1 TGAATAAATTGCGAG
50191 T-AATAAAT
1 TGAATAAAT
50199 CAAATGGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (15 bp):
TGAATAAATTGCGAG
Found at i:52990 original size:10 final size:10
Alignment explanation
Indices: 52974--53030 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
52964 CAACTCCGAC
52974 CAGCTCAATT
1 CAGCTCAATT
* *
52984 GAGCTCATTT
1 CAGCTCAATT
52994 CAGCTCAA-T
1 CAGCTCAATT
*
53003 CGAGCTTAATT
1 C-AGCTCAATT
53014 -AGCTACAATT
1 CAGCT-CAATT
53024 CAGCTCA
1 CAGCTCA
53031 TTTATTTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
9 6 0.16
10 26 0.70
11 5 0.14
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:52997 original size:20 final size:20
Alignment explanation
Indices: 52974--53033 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
52964 CAACTCCGAC
52974 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
* * *
52994 CAGCTCAATCGAGCTTAATT
1 CAGCTCAATTGAGCTCATTT
*
53014 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
53034 ATTTTATTGG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
19 4 0.12
20 28 0.88
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:53615 original size:20 final size:20
Alignment explanation
Indices: 53570--53615 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
53560 AGCTCGTTTC
*
53570 CAGCT-ACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
53589 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
53609 CAGCTCA
1 CAGCTCA
53616 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.30, C:0.35, G:0.13, T:0.22
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Done.