Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1553
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: 35195
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:4613 original size:11 final size:10
Alignment explanation
Indices: 4588--4648 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
4578 ACCAATAAAA
4588 TAAA-TGAGC
1 TAAATTGAGC
*
4597 TGAATTGTAGC
1 TAAATTG-AGC
4608 TAAATTGAGC
1 TAAATTGAGC
**
4618 TCGATTGAGC
1 TAAATTGAGC
4628 TGAAA-TGAGC
1 T-AAATTGAGC
*
4638 TCAATTGAGC
1 TAAATTGAGC
4648 T
1 T
4649 GGTCGAGTTG
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:4649 original size:20 final size:20
Alignment explanation
Indices: 4589--4649 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
4579 CCAATAAAAT
*
4589 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
4609 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
4630 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
4650 GTCGAGTTGA
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:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:6735 original size:18 final size:18
Alignment explanation
Indices: 6714--6748 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
6704 TTTTTCTTTT
6714 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
6732 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
6749 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:7661 original size:15 final size:15
Alignment explanation
Indices: 7643--7692 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
7633 TTTAACTTGA
7643 TTTTTTTTGCTCACT
1 TTTTTTTTGCTCACT
**
7658 TTTTTTTT-CTTTCT
1 TTTTTTTTGCTCACT
7672 TTTTTTTTGCTCGA-T
1 TTTTTTTTGCTC-ACT
7687 TTTTTT
1 TTTTTT
7693 CACTTTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 12 0.41
15 17 0.59
ACGTcount: A:0.04, C:0.14, G:0.06, T:0.76
Consensus pattern (15 bp):
TTTTTTTTGCTCACT
Found at i:7675 original size:29 final size:28
Alignment explanation
Indices: 7629--7705 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 28
7619 ACTTTTCACT
* **
7629 TTTTTTTAACTTGATTTTTTTTGCTC-A
1 TTTTTTTCACTTTTTTTTTTTTGCTCGA
**
7656 CTTTTTTTTTCTTTCTTTTTTTTTGCTCGA
1 -TTTTTTTCACTTT-TTTTTTTTTGCTCGA
7686 TTTTTTTCACTTTTTTTTTT
1 TTTTTTTCACTTTTTTTTTT
7706 GAATTTTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 17 0.41
29 23 0.56
30 1 0.02
ACGTcount: A:0.08, C:0.13, G:0.05, T:0.74
Consensus pattern (28 bp):
TTTTTTTCACTTTTTTTTTTTTGCTCGA
Found at i:7712 original size:12 final size:12
Alignment explanation
Indices: 7697--7723 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
7687 TTTTTTCACT
7697 TTTTTTTTTGAA
1 TTTTTTTTTGAA
7709 TTTTTTTTTGAA
1 TTTTTTTTTGAA
7721 TTT
1 TTT
7724 CGATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:9114 original size:20 final size:20
Alignment explanation
Indices: 9075--9135 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
9065 CCAATAAAAT
*
9075 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
* *
9095 AAATTGTGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
9116 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
9136 GTCGGAGTTG
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:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:11448 original size:21 final size:21
Alignment explanation
Indices: 11422--11484 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
11412 TTGGTATTTG
11422 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
11443 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
11464 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
11485 ACGGTTCAAA
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
Found at i:16875 original size:13 final size:13
Alignment explanation
Indices: 16854--16888 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
16844 ATAAGTTGCT
*
16854 GTTAGTTAAATAA
1 GTTAATTAAATAA
16867 GTTAATTAAATAA
1 GTTAATTAAATAA
16880 GTTAATTAA
1 GTTAATTAA
16889 TTTGCTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (13 bp):
GTTAATTAAATAA
Found at i:17142 original size:23 final size:23
Alignment explanation
Indices: 17112--17174 Score: 101
Period size: 23 Copynumber: 2.7 Consensus size: 23
17102 TTTTCCAGAT
17112 GAATTTAATGTATGTCTT-TGGCC
1 GAATTTAATGTATGT-TTCTGGCC
17135 GAATTTAATGTATGTTTCTGGCC
1 GAATTTAATGTATGTTTCTGGCC
*
17158 GAATTTAATGCATGTTT
1 GAATTTAATGTATGTTT
17175 TAAATGGTGT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
22 2 0.05
23 36 0.95
ACGTcount: A:0.24, C:0.11, G:0.21, T:0.44
Consensus pattern (23 bp):
GAATTTAATGTATGTTTCTGGCC
Found at i:18741 original size:12 final size:11
Alignment explanation
Indices: 18711--18757 Score: 62
Period size: 12 Copynumber: 4.3 Consensus size: 11
18701 TCATTACGAT
18711 ATTGTAAAAAAA
1 ATTG-AAAAAAA
18723 ATT--AAAAAA
1 ATTGAAAAAAA
18732 ATTCGAAAAAAA
1 ATT-GAAAAAAA
18744 ATTGAAAAAAA
1 ATTGAAAAAAA
18755 ATT
1 ATT
18758 ATTTGAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
9 9 0.28
11 11 0.34
12 12 0.38
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.23
Consensus pattern (11 bp):
ATTGAAAAAAA
Found at i:19681 original size:21 final size:21
Alignment explanation
Indices: 19641--19699 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
19631 AATCTTGAAT
*
19641 GAAATTGAGAGAAGAA-AAAAA
1 GAAA-TGAGAGAAAAAGAAAAA
19662 GAAATGAGAGAAAAAGAAAAA
1 GAAATGAGAGAAAAAGAAAAA
* *
19683 GAAATAAAAGAAAAAGA
1 GAAATGAGAGAAAAAGA
19700 TGAAAATGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 10 0.29
21 24 0.71
ACGTcount: A:0.71, C:0.00, G:0.22, T:0.07
Consensus pattern (21 bp):
GAAATGAGAGAAAAAGAAAAA
Found at i:19691 original size:15 final size:14
Alignment explanation
Indices: 19652--19699 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
19642 AAATTGAGAG
19652 AAGAAAAAAAGAAA
1 AAGAAAAAAAGAAA
* *
19666 TGAGAGAAAAAGAAA
1 -AAGAAAAAAAGAAA
19681 AAGAAATAAAAGAAA
1 AAGAAA-AAAAGAAA
19696 AAGA
1 AAGA
19700 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (14 bp):
AAGAAAAAAAGAAA
Found at i:19755 original size:12 final size:12
Alignment explanation
Indices: 19738--19800 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 12
19728 AGTGAAAAGC
*
19738 AAAAAGAGATTG
1 AAAAAGAAATTG
19750 AAAAAGAAATTG
1 AAAAAGAAATTG
19762 AAAAAG-AA--G
1 AAAAAGAAATTG
*
19771 AAAAAGAAAGAGTGG
1 AAAAAG-AA-A-TTG
19786 AAAAAGAAATTG
1 AAAAAGAAATTG
19798 AAA
1 AAA
19801 GCGAGCTTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
9 7 0.16
11 3 0.07
12 23 0.53
13 1 0.02
14 2 0.05
15 7 0.16
ACGTcount: A:0.67, C:0.00, G:0.22, T:0.11
Consensus pattern (12 bp):
AAAAAGAAATTG
Found at i:26957 original size:14 final size:15
Alignment explanation
Indices: 26924--26979 Score: 85
Period size: 15 Copynumber: 3.5 Consensus size: 15
26914 CTTCTTCTTC
26924 TTTTTTCACGAAAATTTT
1 TTTTTTCACG--AA-TTT
26942 TTTTTTCACGAATTT
1 TTTTTTCACGAATTT
26957 TTTTTTCACGAATTT
1 TTTTTTCACGAATTT
26972 TTTTTTCA
1 TTTTTTCA
26980 ACTTGATATC
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
15 26 0.68
16 2 0.05
18 10 0.26
ACGTcount: A:0.21, C:0.12, G:0.05, T:0.61
Consensus pattern (15 bp):
TTTTTTCACGAATTT
Found at i:27034 original size:12 final size:12
Alignment explanation
Indices: 27017--27061 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
27007 ATGGAAACCA
27017 AATTTTTTTTTG
1 AATTTTTTTTTG
27029 AATTTTTTTTT-
1 AATTTTTTTTTG
**
27040 AAAATTTTTTTG
1 AATTTTTTTTTG
27052 AATTTTTTTT
1 AATTTTTTTT
27062 GAAGAAACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 9 0.32
12 19 0.68
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.73
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:27036 original size:11 final size:11
Alignment explanation
Indices: 27020--27064 Score: 63
Period size: 11 Copynumber: 4.0 Consensus size: 11
27010 GAAACCAAAT
27020 TTTTTTTTGAA
1 TTTTTTTTGAA
*
27031 TTTTTTTTTAAA
1 -TTTTTTTTGAA
*
27043 ATTTTTTTGAA
1 TTTTTTTTGAA
27054 TTTTTTTTGAA
1 TTTTTTTTGAA
27065 GAAACTACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:31879 original size:41 final size:41
Alignment explanation
Indices: 31833--31919 Score: 138
Period size: 41 Copynumber: 2.1 Consensus size: 41
31823 AAATTCGGCC
*
31833 AAACATGTAGTAGTAGCATTAAATTCGTCCAGGCATATTTA
1 AAACATGTAGTAGCAGCATTAAATTCGTCCAGGCATATTTA
* * *
31874 TAACATGTAGTGGCGGCATTAAATTCGTCCAGGCATATTTA
1 AAACATGTAGTAGCAGCATTAAATTCGTCCAGGCATATTTA
31915 AAACA
1 AAACA
31920 CCTAATTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (41 bp):
AAACATGTAGTAGCAGCATTAAATTCGTCCAGGCATATTTA
Done.