Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3816
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: 39330
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Found at i:3637 original size:41 final size:39
Alignment explanation
Indices: 3578--3726 Score: 151
Period size: 41 Copynumber: 3.7 Consensus size: 39
3568 CAAGCTTGGT
3578 TTCGAAGGGCCTTTGAGCCAGTGCTAATAACCGAACTTAG
1 TTCGAAGGG-CTTTGAGCCAGTGCTAATAACCGAACTTAG
* *
3618 CTTCGAAGGGCTTTAGAGCCAGTG-TCATAACCAAACTTAG
1 -TTCGAAGGGCTTT-GAGCCAGTGCTAATAACCGAACTTAG
* * *
3658 TTCCGAAGGGCCTTCGAGCCAGTGGTCTAAT--CCGAGCTTGG
1 TT-CGAAGGG-CTTTGAGCCAGT-G-CTAATAACCGAACTTAG
3699 TCTCGAAGGGCTTTTGAGCCAGTGCTAA
1 T-TCGAAGGGC-TTTGAGCCAGTGCTAA
3727 GAATCGGGCT
Statistics
Matches: 92, Mismatches: 8, Indels: 18
0.78 0.07 0.15
Matches are distributed among these distances:
39 6 0.07
40 35 0.38
41 47 0.51
42 1 0.01
43 3 0.03
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (39 bp):
TTCGAAGGGCTTTGAGCCAGTGCTAATAACCGAACTTAG
Found at i:12238 original size:41 final size:41
Alignment explanation
Indices: 12059--12240 Score: 162
Period size: 41 Copynumber: 4.5 Consensus size: 41
12049 GGGTTTAAAT
*
12059 CCGAGCTTGGTTTCGAAGGGCCTTTGAGCCAGTGCTAATAA
1 CCGAGCTTGATTTCGAAGGGCCTTTGAGCCAGTGCTAATAA
* *
12100 CCGAACTT-ATCTTCGAAGGG-CTTTAGAGCCAGTG-TCATAA
1 CCGAGCTTGAT-TTCGAAGGGCCTTT-GAGCCAGTGCTAATAA
* *
12140 CCG-GACTT-AGTTCCGAAGGGCCTTCGAGCCAGTGGTCTAAT--
1 CCGAG-CTTGA-TTTCGAAGGGCCTTTGAGCCAGT-G-CTAATAA
* * * *
12181 CCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGCTAAGAA
1 CCGAGCTTGATTTCGAAGGGCCTTTGAGCCAGTGCTAATAA
* *
12222 TCGGGCTTGATTTCGAAGG
1 CCGAGCTTGATTTCGAAGG
12241 ATGTTTGTGC
Statistics
Matches: 112, Mismatches: 17, Indels: 24
0.73 0.11 0.16
Matches are distributed among these distances:
39 4 0.04
40 34 0.30
41 70 0.62
42 1 0.01
43 3 0.03
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26
Consensus pattern (41 bp):
CCGAGCTTGATTTCGAAGGGCCTTTGAGCCAGTGCTAATAA
Found at i:15093 original size:42 final size:42
Alignment explanation
Indices: 15034--15115 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
15024 CGGGTAGACA
* * * *
15034 CACGGTCGTGTGTCTCAACTGTGTGTGACATACGGCCATATG
1 CACGGACGTGTGTCTCAACTGTCTGTGACACACGACCATATG
15076 CACGGACGTGTGTCTCAACTGTCTGTGACACACGACCATA
1 CACGGACGTGTGTCTCAACTGTCTGTGACACACGACCATA
15116 CGTACAAGCG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.22, C:0.27, G:0.26, T:0.26
Consensus pattern (42 bp):
CACGGACGTGTGTCTCAACTGTCTGTGACACACGACCATATG
Found at i:16088 original size:42 final size:42
Alignment explanation
Indices: 16042--16127 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
16032 GTAATGAGAG
16042 ATTAACTGCAAAAGCTTTGAGCCTAATTGGACTGCCATTAGA
1 ATTAACTGCAAAAGCTTTGAGCCTAATTGGACTGCCATTAGA
* *
16084 ATTAACTGCAAGAGCTTTGAGCCTAATTGGACTGCCATTGGA
1 ATTAACTGCAAAAGCTTTGAGCCTAATTGGACTGCCATTAGA
16126 AT
1 AT
16128 GTTTATTGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (42 bp):
ATTAACTGCAAAAGCTTTGAGCCTAATTGGACTGCCATTAGA
Found at i:25136 original size:21 final size:22
Alignment explanation
Indices: 25112--25152 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
25102 CAAAACAACG
25112 TAATTTT-ACCTTTTAACTTGA
1 TAATTTTGACCTTTTAACTTGA
*
25133 TAATTTTGACTTTTTAACTT
1 TAATTTTGACCTTTTAACTT
25153 TAGATAAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.27, C:0.12, G:0.05, T:0.56
Consensus pattern (22 bp):
TAATTTTGACCTTTTAACTTGA
Found at i:25695 original size:14 final size:17
Alignment explanation
Indices: 25664--25700 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
25654 ATTATAAAGG
25664 ATATTATTAAATTAATT
1 ATATTATTAAATTAATT
25681 ATATTA-TAAA-T-ATT
1 ATATTATTAAATTAATT
25695 ATATTA
1 ATATTA
25701 AGAAATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 9 0.45
15 1 0.05
16 4 0.20
17 6 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATTATTAAATTAATT
Found at i:25876 original size:14 final size:14
Alignment explanation
Indices: 25850--25900 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
25840 GAAAACAAAA
25850 GAAATAAAATAAAG
1 GAAATAAAATAAAG
*
25864 GAAATAAAGTAAAG
1 GAAATAAAATAAAG
* * *
25878 TAAGTTAAAATAAAA
1 GAA-ATAAAATAAAG
25893 G-AATAAAA
1 GAAATAAAA
25901 GAAACAAAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
13 5 0.17
14 16 0.55
15 8 0.28
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.18
Consensus pattern (14 bp):
GAAATAAAATAAAG
Found at i:25911 original size:17 final size:16
Alignment explanation
Indices: 25889--25922 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
25879 AAGTTAAAAT
25889 AAAAGAATAAAAGAAAC
1 AAAAGAA-AAAAGAAAC
*
25906 AAAAGAAGAAAGAAAC
1 AAAAGAAAAAAGAAAC
25922 A
1 A
25923 GAATAGCCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAAGAAAAAAGAAAC
Found at i:26641 original size:3 final size:3
Alignment explanation
Indices: 26620--26657 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
26610 GTAAGTATAA
* *
26620 TAT TAG TAT TAA T-T TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
26658 GAGTGGGAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
2 1 0.03
3 29 0.97
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:33143 original size:14 final size:17
Alignment explanation
Indices: 33112--33148 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
33102 ATTATAAAGG
33112 ATATTATTAAATTAATT
1 ATATTATTAAATTAATT
33129 ATATTA-TAAA-T-ATT
1 ATATTATTAAATTAATT
33143 ATATTA
1 ATATTA
33149 AGAAATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 9 0.45
15 1 0.05
16 4 0.20
17 6 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATTATTAAATTAATT
Found at i:33298 original size:24 final size:24
Alignment explanation
Indices: 33271--33350 Score: 72
Period size: 24 Copynumber: 3.1 Consensus size: 24
33261 TTATTATATT
33271 AAAGTAATTAAATAAAAGAAAACA-
1 AAAGTAATTAAATAAAAGAAAA-AG
* * *
33295 AAAGAAATAAAATAAAGGAAAAAG
1 AAAGTAATTAAATAAAAGAAAAAG
33319 TAAAGTAAGTTAAAATAAAAGAATAAAAG
1 -AAAGTAA-TT-AAATAAAAG-A-AAAAG
33348 AAA
1 AAA
33351 CAAAGAAGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
23 1 0.02
24 19 0.43
25 6 0.14
26 1 0.02
27 8 0.18
28 4 0.09
29 5 0.11
ACGTcount: A:0.71, C:0.01, G:0.12, T:0.15
Consensus pattern (24 bp):
AAAGTAATTAAATAAAAGAAAAAG
Found at i:34076 original size:3 final size:3
Alignment explanation
Indices: 34057--34096 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
34047 GTAAGTATAA
*
34057 TAT TAG TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT
34097 GAGTGGGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:34510 original size:37 final size:39
Alignment explanation
Indices: 34451--34546 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
34441 CGGATAGATT
* * * *
34451 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
34488 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
34527 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
34547 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:35499 original size:3 final size:3
Alignment explanation
Indices: 35491--35521 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
35481 TTTTAAAAGC
35491 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
35522 GATATTTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:35659 original size:16 final size:15
Alignment explanation
Indices: 35628--35662 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
35618 TTTTAGATTT
*
35628 TTTTTAAAAATTAAA
1 TTTTTAAAAATCAAA
35643 TTTTTAAAAATACAAA
1 TTTTTAAAAAT-CAAA
35659 TTTT
1 TTTT
35663 GATTTATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTTTAAAAATCAAA
Found at i:35723 original size:18 final size:17
Alignment explanation
Indices: 35658--35723 Score: 62
Period size: 19 Copynumber: 3.7 Consensus size: 17
35648 AAAAATACAA
*
35658 ATTTTGATTTATAAA-T
1 ATTTTGATTTTTAAATT
*
35674 ATTTTGAATTTTAAAAATT
1 ATTTTG-ATTTT-TAAATT
*
35693 ATTTTCAATTTTTGAAATT
1 ATTTT-GATTTTT-AAATT
35712 ATTTTGATTTTT
1 ATTTTGATTTTT
35724 TTGTAATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
16 6 0.15
17 4 0.10
18 9 0.22
19 21 0.52
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (17 bp):
ATTTTGATTTTTAAATT
Found at i:35724 original size:19 final size:19
Alignment explanation
Indices: 35673--35723 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
35663 GATTTATAAA
*
35673 TATTTTGAATTTTAAAAAT
1 TATTTTGAATTTTTAAAAT
* *
35692 TATTTTCAATTTTTGAAAT
1 TATTTTGAATTTTTAAAAT
35711 TATTTTG-ATTTTT
1 TATTTTGAATTTTT
35724 TTGTAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (19 bp):
TATTTTGAATTTTTAAAAT
Done.