Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold906
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: 17750
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:1704 original size:13 final size:13
Alignment explanation
Indices: 1686--1711 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1676 ACATTTTTCT
1686 TTGTATCGATACA
1 TTGTATCGATACA
1699 TTGTATCGATACA
1 TTGTATCGATACA
1712 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1875 original size:20 final size:20
Alignment explanation
Indices: 1832--1878 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
1822 AAATCTTTTG
1832 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1853 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1873 CAAAAT
1 CAAAAT
1879 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.45
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:4258 original size:13 final size:13
Alignment explanation
Indices: 4240--4265 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4230 TACAGCAAGT
4240 ATGTATCGATACA
1 ATGTATCGATACA
4253 ATGTATCGATACA
1 ATGTATCGATACA
4266 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:7849 original size:19 final size:19
Alignment explanation
Indices: 7825--7925 Score: 124
Period size: 19 Copynumber: 5.6 Consensus size: 19
7815 TAGCTTACAT
*
7825 TGTATCGATACAAAACTTA
1 TGTATCGATACAACACTTA
*
7844 TGTATCGATACAACACTTG
1 TGTATCGATACAACACTTA
7863 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
*
7876 TGTATCGATACAACACTCA
1 TGTATCGATACAACACTTA
7895 TGTATCGATACAACACTTTA
1 TGTATCGATACAACAC-TTA
7915 TGTATCGATAC
1 TGTATCGATAC
7926 GAATCGTTGA
Statistics
Matches: 71, Mismatches: 4, Indels: 13
0.81 0.05 0.15
Matches are distributed among these distances:
13 9 0.13
14 1 0.01
16 6 0.08
19 42 0.59
20 13 0.18
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:7875 original size:51 final size:52
Alignment explanation
Indices: 7820--7925 Score: 178
Period size: 51 Copynumber: 2.1 Consensus size: 52
7810 GGCAGTAGCT
* *
7820 TACATTGTATCGATACAAAACTTATGTATCGATACAACAC-TTGTGTATCGA
1 TACATTGTATCGATACAAAACTCATGTATCGATACAACACTTTATGTATCGA
*
7871 TACATTGTATCGATACAACACTCATGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAAAACTCATGTATCGATACAACACTTTATGTATCGA
7923 TAC
1 TAC
7926 GAATCGTTGA
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
51 38 0.75
52 13 0.25
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (52 bp):
TACATTGTATCGATACAAAACTCATGTATCGATACAACACTTTATGTATCGA
Found at i:7881 original size:13 final size:13
Alignment explanation
Indices: 7863--7887 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7853 ACAACACTTG
7863 TGTATCGATACAT
1 TGTATCGATACAT
7876 TGTATCGATACA
1 TGTATCGATACA
7888 ACACTCATGT
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:7885 original size:32 final size:32
Alignment explanation
Indices: 7844--7906 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
7834 ACAAAACTTA
**
7844 TGTATCGATACAACACTTGTGTATCGATACAT
1 TGTATCGATACAACACTCATGTATCGATACAT
7876 TGTATCGATACAACACTCATGTATCGATACA
1 TGTATCGATACAACACTCATGTATCGATACA
7907 ACACTTTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (32 bp):
TGTATCGATACAACACTCATGTATCGATACAT
Found at i:11839 original size:13 final size:13
Alignment explanation
Indices: 11823--11857 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
11813 AAAGAGAAGG
11823 AAAAAAAAAACAA
1 AAAAAAAAAACAA
*
11836 AAAAAAGAAACAA
1 AAAAAAAAAACAA
11849 AAAGAAAAA
1 AAA-AAAAA
11858 GGAAATTCGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.89, C:0.06, G:0.06, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAACAA
Found at i:12210 original size:17 final size:17
Alignment explanation
Indices: 12182--12228 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
12172 TCTCTAAATA
12182 AGAAAAATAAGAAAAAAG
1 AGAAAAA-AAGAAAAAAG
12200 AGAAAAAAAGAAAAAAG
1 AGAAAAAAAGAAAAAAG
*
12217 A-AAAAGAAGAAA
1 AGAAAAAAAGAAA
12229 GAAAAATCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 10 0.36
17 11 0.39
18 7 0.25
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (17 bp):
AGAAAAAAAGAAAAAAG
Found at i:12222 original size:13 final size:13
Alignment explanation
Indices: 12204--12234 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
12194 AAAAAGAGAA
12204 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
*
12217 AAAAAGAAGAAAG
1 AAAAAGAAAAAAG
12230 AAAAA
1 AAAAA
12235 TCATGAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:12254 original size:9 final size:8
Alignment explanation
Indices: 12181--12233 Score: 63
Period size: 9 Copynumber: 6.2 Consensus size: 8
12171 TTCTCTAAAT
12181 AAGAAAAA
1 AAGAAAAA
12189 TAAGAAAAA
1 -AAGAAAAA
12198 AGAGAAAAA
1 A-AGAAAAA
12207 AAG-AAAA
1 AAGAAAAA
12214 AAGAAAAA
1 AAGAAAAA
12222 GAAGAAAGAA
1 -AAGAAA-AA
12232 AA
1 AA
12234 ATCATGAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
7 7 0.17
8 7 0.17
9 24 0.60
10 2 0.05
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (8 bp):
AAGAAAAA
Found at i:13139 original size:11 final size:12
Alignment explanation
Indices: 13123--13152 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
13113 AGAGGCTTAC
13123 AAAAAAAA-CAA
1 AAAAAAAACCAA
13134 AAAAAAAACCAA
1 AAAAAAAACCAA
13146 AAAAAAA
1 AAAAAAA
13153 GAATACTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAACCAA
Found at i:14535 original size:20 final size:20
Alignment explanation
Indices: 14495--14543 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
14485 GTTGGGATAG
*
14495 GTATTGATACAATTCTTCAT
1 GTATTGATACAATTCTCCAT
14515 GTATTGATACAATGTC-CCAT
1 GTATTGATACAAT-TCTCCAT
*
14535 GTATCGATA
1 GTATTGATA
14544 TATTTCACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (20 bp):
GTATTGATACAATTCTCCAT
Found at i:14622 original size:19 final size:20
Alignment explanation
Indices: 14574--14626 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
14564 CTGCCAGTTT
*
14574 CATGTATCAATACAATTGAG
1 CATGTATCGATACAATTGAG
** *
14594 TGTGTCTCGATACAA-TGAG
1 CATGTATCGATACAATTGAG
14613 CATGTATCGATACA
1 CATGTATCGATACA
14627 TTATATCGAT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAG
Found at i:15344 original size:17 final size:17
Alignment explanation
Indices: 15322--15355 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
15312 GTTTAAAACA
*
15322 ATTTTCTCCCCCTTTGT
1 ATTTTCTCCCCCATTGT
15339 ATTTTCTCCCCCATTGT
1 ATTTTCTCCCCCATTGT
15356 CAAATGTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.09, C:0.35, G:0.06, T:0.50
Consensus pattern (17 bp):
ATTTTCTCCCCCATTGT
Found at i:17557 original size:20 final size:20
Alignment explanation
Indices: 17532--17584 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
17522 ATTGGGCATA
*
17532 ATGTATCGATACAAT-TCTT
1 ATGTATCGATACAATGTCCT
17551 CATGTATCGATACAATGTCCT
1 -ATGTATCGATACAATGTCCT
17572 ATGTATCGATACA
1 ATGTATCGATACA
17585 TTTCACTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 28 0.90
21 3 0.10
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACAATGTCCT
Found at i:17660 original size:19 final size:20
Alignment explanation
Indices: 17621--17667 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
17611 TTCATGTATC
*
17621 TCGATACAATTGAGTAGGTA
1 TCGATACAATTGAGCAGGTA
*
17641 TCGATACAA-TGAGCATGTA
1 TCGATACAATTGAGCAGGTA
17660 TCGATACA
1 TCGATACA
17668 TTGTCATCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (20 bp):
TCGATACAATTGAGCAGGTA
Done.