Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3379
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: 28857
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:1670 original size:20 final size:20
Alignment explanation
Indices: 1647--1693 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1637 GGGTTAAGAT
*
1647 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
1667 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
1687 TGAGCTG
1 TGAGCTG
1694 GAAACAAGCT
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:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:3403 original size:48 final size:48
Alignment explanation
Indices: 3348--3453 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
3338 TTGTCTTTTC
*
3348 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
3396 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
3444 TTTCTTTTTC
1 TTTCTTTTTC
3454 CATGACACTC
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:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:7594 original size:33 final size:33
Alignment explanation
Indices: 7556--7618 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
7546 GATTACTCAC
7556 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
7589 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
7619 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:7645 original size:14 final size:13
Alignment explanation
Indices: 7621--7672 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
7611 TCTCTTTCAA
*
7621 TTTCTTTTTTCGCTT
1 TTTC-TTTTTC-CAT
*
7636 TTTCTTTTTCAAT
1 TTTCTTTTTCCAT
*
7649 TTTCTTTTTTTCAT
1 TTTC-TTTTTCCAT
7663 TTTCTTTTTC
1 TTTCTTTTTC
7673 TCTCACTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
13 10 0.32
14 17 0.55
15 4 0.13
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.75
Consensus pattern (13 bp):
TTTCTTTTTCCAT
Found at i:7645 original size:21 final size:21
Alignment explanation
Indices: 7615--7671 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
7605 TCAAGCTCTC
*
7615 TTTCAATTTCTTTTTTCGCTT
1 TTTCATTTTCTTTTTTCGCTT
* ** **
7636 TTTCTTTTTCAATTTTCTTTT
1 TTTCATTTTCTTTTTTCGCTT
7657 TTTCATTTTCTTTTT
1 TTTCATTTTCTTTTT
7672 CTCTCACTTT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.09, C:0.16, G:0.02, T:0.74
Consensus pattern (21 bp):
TTTCATTTTCTTTTTTCGCTT
Found at i:7645 original size:27 final size:27
Alignment explanation
Indices: 7615--7672 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
7605 TCAAGCTCTC
*
7615 TTTCAA-TTTCTTTTTTCGCTTTTTCTT
1 TTTCAATTTTCTTTTTT-GCATTTTCTT
*
7642 TTTCAATTTTCTTTTTTTCATTTTCTT
1 TTTCAATTTTCTTTTTTGCATTTTCTT
7669 TTTC
1 TTTC
7673 TCTCACTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 18 0.64
28 10 0.36
ACGTcount: A:0.09, C:0.17, G:0.02, T:0.72
Consensus pattern (27 bp):
TTTCAATTTTCTTTTTTGCATTTTCTT
Found at i:7670 original size:12 final size:12
Alignment explanation
Indices: 7635--7754 Score: 63
Period size: 12 Copynumber: 10.0 Consensus size: 12
7625 TTTTTTCGCT
7635 TTTTCTTTTTCAA
1 TTTTCTTTTTC-A
7648 TTTTCTTTTTTTCA
1 TTTTC--TTTTTCA
7662 TTTTCTTTTTC-
1 TTTTCTTTTTCA
**
7673 TCTCACTTTTTCGA
1 T-TTTCTTTTTC-A
7687 -TTTCTTTTTC-
1 TTTTCTTTTTCA
** *
7697 TTTTGCAATTTCT
1 TTTT-CTTTTTCA
* *
7710 TTTTCTTCTTCG
1 TTTTCTTTTTCA
*
7722 TTTTCTTTTT-G
1 TTTTCTTTTTCA
7733 TTTTC--TTTCA
1 TTTTCTTTTTCA
*
7743 ATTTCTTTTTCA
1 TTTTCTTTTTCA
7755 ATCTCTTTCT
Statistics
Matches: 83, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
9 3 0.04
10 4 0.05
11 10 0.12
12 45 0.54
13 9 0.11
14 6 0.07
15 6 0.07
ACGTcount: A:0.08, C:0.18, G:0.03, T:0.70
Consensus pattern (12 bp):
TTTTCTTTTTCA
Found at i:7699 original size:18 final size:18
Alignment explanation
Indices: 7678--7736 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
7668 TTTTCTCTCA
7678 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
7696 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
7714 CTTCTTCGTTTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
7732 GTTTT
1 CTTTT
7737 CTTTCAATTT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.05, C:0.17, G:0.07, T:0.71
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:7753 original size:6 final size:6
Alignment explanation
Indices: 7633--7740 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
7623 TCTTTTTTCG
* * * **
7633 CTTTTT CTTTTT CAATTTTCT TTTTTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C--TTTT-T CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** * *
7684 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTCTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
7732 -GTTTT CTTT
1 CTTTTT CTTT
7741 CAATTTCTTT
Statistics
Matches: 72, Mismatches: 26, Indels: 8
0.68 0.25 0.08
Matches are distributed among these distances:
5 4 0.06
6 59 0.82
7 4 0.06
8 4 0.06
9 1 0.01
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:8615 original size:12 final size:12
Alignment explanation
Indices: 8599--8637 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
8589 TTTTTGCTCG
8599 ATTTTTTTTTCA
1 ATTTTTTTTTCA
* *
8611 CTTTTTTTTTGA
1 ATTTTTTTTTCA
8623 ATTTTTTTTTTCA
1 A-TTTTTTTTTCA
8636 AT
1 AT
8638 CAAAATTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.15, C:0.08, G:0.03, T:0.74
Consensus pattern (12 bp):
ATTTTTTTTTCA
Found at i:8619 original size:30 final size:30
Alignment explanation
Indices: 8556--8620 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
8546 TTAAACTTGA
*
8556 TTTTTTTTGCTCACCTTTTTTTTCTTTTCT
1 TTTTTTTTGCTCACCTTTTTTTTCCTTTCT
*
8586 TTTTTTTTGCTCGA-TTTTTTTTTCACTTT-T
1 TTTTTTTTGCTC-ACCTTTTTTTTC-CTTTCT
8616 TTTTT
1 TTTTT
8621 GAATTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 27 0.87
31 4 0.13
ACGTcount: A:0.05, C:0.15, G:0.05, T:0.75
Consensus pattern (30 bp):
TTTTTTTTGCTCACCTTTTTTTTCCTTTCT
Found at i:8655 original size:15 final size:14
Alignment explanation
Indices: 8600--8664 Score: 53
Period size: 14 Copynumber: 4.5 Consensus size: 14
8590 TTTTGCTCGA
*
8600 TTTTTTTTTC--AC
1 TTTTTTTTTCAAAT
* *
8612 TTTTTTTTTGAATT
1 TTTTTTTTTCAAAT
8626 TTTTTTTTCAATCAAAAT
1 TTTTTTTT---TC-AAAT
8644 TTTTTTTTTCAAAT
1 TTTTTTTTTCAAAT
8658 TTTTTTT
1 TTTTTTT
8665 GATTTTTTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
12 9 0.21
14 19 0.45
15 2 0.05
17 1 0.02
18 11 0.26
ACGTcount: A:0.18, C:0.08, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTTTTTTTCAAAT
Found at i:10002 original size:12 final size:11
Alignment explanation
Indices: 9981--10027 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
9971 CTCACAAGAC
*
9981 TTTTCACTTTT
1 TTTTTACTTTT
*
9992 TTTTGTTC-TTT
1 TTTT-TACTTTT
10003 TTTTTACTTTT
1 TTTTTACTTTT
10014 TTTTTACTTTT
1 TTTTTACTTTT
10025 TTT
1 TTT
10028 GCTCACTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
10 2 0.06
11 28 0.90
12 1 0.03
ACGTcount: A:0.06, C:0.11, G:0.02, T:0.81
Consensus pattern (11 bp):
TTTTTACTTTT
Found at i:10035 original size:24 final size:22
Alignment explanation
Indices: 9981--10043 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 22
9971 CTCACAAGAC
*
9981 TTTTCACTTTTTTTTGTTCTTTT
1 TTTTCACTTTTTTTT-TACTTTT
10004 TTTT-ACTTTTTTTTTACTTTT
1 TTTTCACTTTTTTTTTACTTTT
10025 TTTGCTCACTTCTTTTTTT
1 TTT--TCACTT-TTTTTTT
10044 TTTTGAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
21 9 0.26
22 10 0.29
23 5 0.14
24 4 0.11
25 7 0.20
ACGTcount: A:0.06, C:0.14, G:0.03, T:0.76
Consensus pattern (22 bp):
TTTTCACTTTTTTTTTACTTTT
Found at i:11587 original size:20 final size:20
Alignment explanation
Indices: 11564--11610 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
11554 AGGTTAAGAT
*
11564 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
11584 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
11604 TGAGCTG
1 TGAGCTG
11611 GAAACAAGCT
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:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:13246 original size:10 final size:10
Alignment explanation
Indices: 13233--13267 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
13223 AAGCTCGGTT
13233 GAGCTCAAAC
1 GAGCTCAAAC
*
13243 GAGCTGAAAC
1 GAGCTCAAAC
*
13253 GAGCTTAAAC
1 GAGCTCAAAC
13263 GAGCT
1 GAGCT
13268 GAGTTGAGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:13276 original size:20 final size:20
Alignment explanation
Indices: 13230--13277 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
13220 AGTAAGCTCG
13230 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
*** *
13250 AACGAGCTTAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
13270 GTTGAGCT
1 GTTGAGCT
13278 GGACGGAGCT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:16442 original size:13 final size:13
Alignment explanation
Indices: 16424--16453 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
16414 AAAAATAATA
16424 ATAAGATGTTTTC
1 ATAAGATGTTTTC
16437 ATAAGATGTTTTC
1 ATAAGATGTTTTC
16450 ATAA
1 ATAA
16454 AGGGTGGCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (13 bp):
ATAAGATGTTTTC
Found at i:17993 original size:23 final size:22
Alignment explanation
Indices: 17941--17993 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
17931 TCCACGTCTT
*
17941 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
17963 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
17986 TTTCTTTT
1 TTTCTTTT
17994 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:22785 original size:15 final size:14
Alignment explanation
Indices: 22752--22791 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
22742 ATGGAAATAT
*
22752 CAAAAGAAAAAGAG
1 CAAAAGAAAAAGAA
*
22766 CAAAATAAAAAGAA
1 CAAAAGAAAAAGAA
22780 CGAAAAGAAAAA
1 C-AAAAGAAAAA
22792 TAGTGGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.75, C:0.07, G:0.15, T:0.03
Consensus pattern (14 bp):
CAAAAGAAAAAGAA
Found at i:24536 original size:18 final size:18
Alignment explanation
Indices: 24503--24537 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
24493 TTGCTACTGG
*
24503 TTTTAATGTGCCAATTTT
1 TTTTAATGAGCCAATTTT
*
24521 TTTTAATGAGCTAATTT
1 TTTTAATGAGCCAATTT
24538 AATGTGCTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.54
Consensus pattern (18 bp):
TTTTAATGAGCCAATTTT
Found at i:25387 original size:19 final size:19
Alignment explanation
Indices: 25363--25402 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
25353 AGCTCCCATG
25363 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
25382 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
25401 TA
1 TA
25403 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:28334 original size:30 final size:30
Alignment explanation
Indices: 28239--28335 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
28229 AGCTCACTCC
*
28239 TAGCTCATA-TTCAGCTCACTAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
28269 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
28299 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
28329 TAGCTCA
1 TAGCTCA
28336 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:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Done.