Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2618
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: 30587
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:918 original size:2 final size:2
Alignment explanation
Indices: 911--952 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
901 TGATGTTTTA
*
911 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
953 TCTTCATTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:7570 original size:20 final size:20
Alignment explanation
Indices: 7545--7587 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
7535 ATTTTTTTAC
7545 TTTTAAGAATTGTCTCATGG
1 TTTTAAGAATTGTCTCATGG
7565 TTTTAAGAATTGTCTCATGG
1 TTTTAAGAATTGTCTCATGG
7585 TTT
1 TTT
7588 ATAATTATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.09, G:0.19, T:0.49
Consensus pattern (20 bp):
TTTTAAGAATTGTCTCATGG
Found at i:8383 original size:2 final size:2
Alignment explanation
Indices: 8370--8490 Score: 69
Period size: 2 Copynumber: 63.5 Consensus size: 2
8360 ATAGCATGTG
* * * *
8370 TA TA TG TA TA TA TA TA TA TA TA T- TA TA TT TA TA TT TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
8411 TT TT TA T- TA GCA -A GTA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
8452 -A AA GA -A GA GA TA TA -A TA TA TA TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8490 T
1 T
8491 TTGAGAGGAA
Statistics
Matches: 97, Mismatches: 12, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
1 8 0.08
2 87 0.90
3 2 0.02
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.48
Consensus pattern (2 bp):
TA
Found at i:13357 original size:26 final size:24
Alignment explanation
Indices: 13311--13368 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
13301 AAATTTAATC
13311 AAATTTAATTTAATAATAAAAATTAA
1 AAATTTAATTTAATAATAAAAA-T-A
**
13337 AAATTTAATTTTTTTAA-AAAAATA
1 AAATTTAA-TTTAATAATAAAAATA
13361 AAATTTAA
1 AAATTTAA
13369 AATAATCTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 9 0.31
25 1 0.03
26 13 0.45
27 6 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
AAATTTAATTTAATAATAAAAATA
Found at i:13806 original size:20 final size:21
Alignment explanation
Indices: 13773--13814 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
13763 TCTTAAAGTA
13773 ATAATATAAAAAAATTAATTT
1 ATAATATAAAAAAATTAATTT
13794 ATAATAT-AAAAAATTAATTT
1 ATAATATAAAAAAATTAATTT
13814 A
1 A
13815 CATGTAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAATATAAAAAAATTAATTT
Found at i:21718 original size:74 final size:74
Alignment explanation
Indices: 21628--21820 Score: 226
Period size: 74 Copynumber: 2.6 Consensus size: 74
21618 ATGGGCTGGG
* * * * *
21628 AGCTGCTACTGTTGTTGGTGGATGCTGTCGCTGTTGAAAGCTGCTGGAGTTGCTACCGGTGTTCG
1 AGCTGCTACTGCTGTTGGTGGATGCTGTCGCTGCTGAAAGCTGCTGGAGCTGCTACCGATATTCG
21693 CAGGCTAGA
66 CAGGCTAGA
* * * * * **
21702 AGCTGTTGCTGCTGTTGGTGGATGCTGTCGTTGCTGGAAGTTGCTGGAGCTGCTGTCGATATTCG
1 AGCTGCTACTGCTGTTGGTGGATGCTGTCGCTGCTGAAAGCTGCTGGAGCTGCTACCGATATTCG
*
21767 CGGGCTAGA
66 CAGGCTAGA
* * * *
21776 AGCTGCTACTGCTATTGGTGCACGCTGTCGCTGCTG-GAGCTGCTG
1 AGCTGCTACTGCTGTTGGTGGATGCTGTCGCTGCTGAAAGCTGCTG
21821 CCAGTGTCCG
Statistics
Matches: 98, Mismatches: 21, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
73 7 0.07
74 91 0.93
ACGTcount: A:0.13, C:0.20, G:0.36, T:0.31
Consensus pattern (74 bp):
AGCTGCTACTGCTGTTGGTGGATGCTGTCGCTGCTGAAAGCTGCTGGAGCTGCTACCGATATTCG
CAGGCTAGA
Found at i:22656 original size:8 final size:8
Alignment explanation
Indices: 22645--22701 Score: 62
Period size: 9 Copynumber: 6.8 Consensus size: 8
22635 TTTTTTTGGA
22645 ATTTTTTT
1 ATTTTTTT
22653 ATTTTTTT
1 ATTTTTTT
*
22661 GATTTTTTG
1 -ATTTTTTT
22670 ATTTTTTTT
1 A-TTTTTTT
22679 GATTTTTTT
1 -ATTTTTTT
22688 -TTGTTTTT
1 ATT-TTTTT
22696 ATTTTT
1 ATTTTT
22702 AATTTTCAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
7 2 0.05
8 17 0.40
9 22 0.52
10 1 0.02
ACGTcount: A:0.11, C:0.00, G:0.07, T:0.82
Consensus pattern (8 bp):
ATTTTTTT
Found at i:22659 original size:10 final size:10
Alignment explanation
Indices: 22635--22688 Score: 62
Period size: 10 Copynumber: 5.8 Consensus size: 10
22625 CTTTCCCGGC
*
22635 TTTTTTTGGA
1 TTTTTTTTGA
*
22645 ATTTTTTT-A
1 TTTTTTTTGA
22654 -TTTTTTTGA
1 TTTTTTTTGA
22663 --TTTTTTGA
1 TTTTTTTTGA
22671 TTTTTTTTGA
1 TTTTTTTTGA
22681 TTTTTTTT
1 TTTTTTTT
22689 TGTTTTTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
8 15 0.38
9 2 0.05
10 22 0.56
ACGTcount: A:0.11, C:0.00, G:0.09, T:0.80
Consensus pattern (10 bp):
TTTTTTTTGA
Found at i:22694 original size:18 final size:17
Alignment explanation
Indices: 22635--22701 Score: 73
Period size: 18 Copynumber: 3.9 Consensus size: 17
22625 CTTTCCCGGC
*
22635 TTTTTTTGGAATTTTTTT
1 TTTTTTTTG-ATTTTTTT
* *
22653 ATTTTTTTGATTTTTTGA
1 TTTTTTTTGATTTTTT-T
22671 TTTTTTTTGATTTTTTT
1 TTTTTTTTGATTTTTTT
*
22688 TTGTTTTT-ATTTTT
1 TTTTTTTTGATTTTT
22702 AATTTTCAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
16 6 0.14
17 14 0.33
18 22 0.52
ACGTcount: A:0.10, C:0.00, G:0.09, T:0.81
Consensus pattern (17 bp):
TTTTTTTTGATTTTTTT
Found at i:24742 original size:276 final size:278
Alignment explanation
Indices: 24207--24755 Score: 940
Period size: 276 Copynumber: 2.0 Consensus size: 278
24197 ATTGTCAAAT
*
24207 TGTTATGCTCGCCCTTAGGTATCGTATCACCTATTTTTGGGCAAATTTTTTTGTGTACATTGGTT
1 TGTTATGCTCGCCCTTAGGTATCGTATCACCTATTTTTGGGCAAATTTTGTTGTGTACATTGGTT
*
24272 GATATTCTTCCATTTCTTTATTAAGGTGCTTATTTATTTATTTATTTAGTTTTTTTTTGTTTGTT
66 GATATTCTTCCATTTCTTTATTAAGGTGCTTATTTATTTATTTATTTAG-TTTTTTTTGTTTATT
*
24337 TTGTACAATCATTAATTCATTTTCCTTTTTGTTTTCCTTTATCATGCATTCATTATTTCATCATA
130 TTGTACAATCATTAATTCATTTTCCTTTTTATTTTCCTTTATCATGCATTCATTATTTCATCATA
* * *
24402 ACCACTATCATCATGGGACAATTGGCTAATGGTTTAGTGTTCACCAATGGGTGTCAACCATGGAG
195 ACCACTATCATCATGGGACAATTGGCTAATAGTTCAGTGTTCACCAAGGGGTGTCAACCATGGAG
24467 CAACAATCCACTTTAAACA
260 CAACAATCCACTTTAAACA
* *
24486 TGTTCTGCTCGCCCTTAGGTATCGTATCACCT-TTTTTGGGCAAATTTTGTTGTGTACTTTGGTT
1 TGTTATGCTCGCCCTTAGGTATCGTATCACCTATTTTTGGGCAAATTTTGTTGTGTACATTGGTT
*
24550 GATATTCTTCCATTTCTTTATTGAGGTGCTTATTTATTTATTTATTTAG-TTTTTTTGTTTATTT
66 GATATTCTTCCATTTCTTTATTAAGGTGCTTATTTATTTATTTATTTAGTTTTTTTTGTTTATTT
* *
24614 TGTACAATCATTAATTCATTTTCCTTTTTATTTTCTTTTATCATGCATTCATTATTTCATTATAA
131 TGTACAATCATTAATTCATTTTCCTTTTTATTTTCCTTTATCATGCATTCATTATTTCATCATAA
* * * *
24679 CCACTGTCATCATGGGACAATTGGCTAATAGTTCAGTGTTTACCAAGGGGTGTCGATCATGGAGC
196 CCACTATCATCATGGGACAATTGGCTAATAGTTCAGTGTTCACCAAGGGGTGTCAACCATGGAGC
24744 AACAATCCACTT
261 AACAATCCACTT
24756 CAGACTTGAA
Statistics
Matches: 255, Mismatches: 15, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
276 146 0.57
278 78 0.31
279 31 0.12
ACGTcount: A:0.22, C:0.17, G:0.15, T:0.47
Consensus pattern (278 bp):
TGTTATGCTCGCCCTTAGGTATCGTATCACCTATTTTTGGGCAAATTTTGTTGTGTACATTGGTT
GATATTCTTCCATTTCTTTATTAAGGTGCTTATTTATTTATTTATTTAGTTTTTTTTGTTTATTT
TGTACAATCATTAATTCATTTTCCTTTTTATTTTCCTTTATCATGCATTCATTATTTCATCATAA
CCACTATCATCATGGGACAATTGGCTAATAGTTCAGTGTTCACCAAGGGGTGTCAACCATGGAGC
AACAATCCACTTTAAACA
Found at i:25575 original size:33 final size:33
Alignment explanation
Indices: 25538--25604 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
25528 TTCAACGATT
25538 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
25571 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
25604 T
1 T
25605 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:25576 original size:13 final size:13
Alignment explanation
Indices: 25558--25582 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25548 CATAAAATGT
25558 TGTATCGATACAA
1 TGTATCGATACAA
25571 TGTATCGATACA
1 TGTATCGATACA
25583 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:25663 original size:13 final size:13
Alignment explanation
Indices: 25645--25669 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25635 ATTACTCAAA
25645 TGTATCGATACAT
1 TGTATCGATACAT
25658 TGTATCGATACA
1 TGTATCGATACA
25670 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:25771 original size:52 final size:52
Alignment explanation
Indices: 25678--25805 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
25668 CACTGATCTT
*
25678 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
25729 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
25781 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
25806 TCATATTTCG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 19 0.26
52 52 0.70
53 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Done.