Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold902
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: 27727
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:2591 original size:20 final size:20
Alignment explanation
Indices: 2568--2614 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2558 GGGTTAAGAT
*
2568 TGAGCTTAATTGAGCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
2588 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
2608 TGAGCTG
1 TGAGCTG
2615 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:3562 original size:15 final size:15
Alignment explanation
Indices: 3542--3651 Score: 53
Period size: 16 Copynumber: 6.9 Consensus size: 15
3532 TTTTCACTCA
3542 CTTTTTCTTTTTCTT
1 CTTTTTCTTTTTCTT
*
3557 CTTTTTCTTTTATCGCT
1 CTTTTTCTTTT-TC-TT
* *
3574 CTCTTTTCATTCTCTT
1 CT-TTTTCTTTTTCTT
**
3590 -TTTTTGAATTTTCTT
1 CTTTTT-CTTTTTCTT
*
3605 TTTTTTCATTTTTCTT
1 CTTTTTC-TTTTTCTT
* * *
3621 TTCTTTTGTATTTTC-G
1 CT-TTTTCT-TTTTCTT
3637 CTCTTTTCTTTTTCT
1 CT-TTTTCTTTTTCT
3652 CTCATTTGAT
Statistics
Matches: 74, Mismatches: 12, Indels: 17
0.72 0.12 0.17
Matches are distributed among these distances:
14 4 0.05
15 24 0.32
16 25 0.34
17 14 0.19
18 7 0.09
ACGTcount: A:0.05, C:0.19, G:0.04, T:0.72
Consensus pattern (15 bp):
CTTTTTCTTTTTCTT
Found at i:3608 original size:17 final size:17
Alignment explanation
Indices: 3583--3635 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
3573 TCTCTTTTCA
*
3583 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
* *
3600 TTC-TTTTTTTTCATTT
1 TTCTTTTTTTTTGAATT
* *
3616 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
3633 TTC
1 TTC
3636 GCTCTTTTCT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
16 13 0.46
17 15 0.54
ACGTcount: A:0.08, C:0.13, G:0.04, T:0.75
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:3609 original size:16 final size:16
Alignment explanation
Indices: 3583--3635 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
3573 TCTCTTTTCA
3583 TTCTCTTTTTTTGAATT
1 TTCT-TTTTTTTGAATT
* *
3600 TTCTTTTTTTTCATTT
1 TTCTTTTTTTTGAATT
*
3616 TTCTTTTCTTTTGTATT
1 TTCTTTT-TTTTGAATT
3633 TTC
1 TTC
3636 GCTCTTTTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 17 0.57
17 13 0.43
ACGTcount: A:0.08, C:0.13, G:0.04, T:0.75
Consensus pattern (16 bp):
TTCTTTTTTTTGAATT
Found at i:6099 original size:14 final size:14
Alignment explanation
Indices: 6080--6113 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
6070 TTTAAGTCAA
6080 AATGGTATGACTAG
1 AATGGTATGACTAG
6094 AATGGTATGACTAG
1 AATGGTATGACTAG
6108 AATGGT
1 AATGGT
6114 CGAGTCCGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.29
Consensus pattern (14 bp):
AATGGTATGACTAG
Found at i:6147 original size:13 final size:13
Alignment explanation
Indices: 6129--6188 Score: 61
Period size: 14 Copynumber: 4.5 Consensus size: 13
6119 CCGTGCAAAC
6129 TTTTTTTTTTGAA
1 TTTTTTTTTTGAA
6142 TTTTTTTTTTCGAA
1 TTTTTTTTTT-GAA
* *
6156 TTCTTTTTTTCAA
1 TTTTTTTTTTGAA
6169 GTTTTTATTTTT--A
1 -TTTTT-TTTTTGAA
6182 TTTTTTT
1 TTTTTTT
6189 ACAATACCGT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
11 2 0.05
12 5 0.12
13 13 0.32
14 16 0.39
15 5 0.12
ACGTcount: A:0.13, C:0.05, G:0.05, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTTGAA
Found at i:6148 original size:14 final size:14
Alignment explanation
Indices: 6129--6180 Score: 63
Period size: 14 Copynumber: 3.7 Consensus size: 14
6119 CCGTGCAAAC
6129 TTTTTTTTTT-GAA
1 TTTTTTTTTTCGAA
6142 TTTTTTTTTTCGAA
1 TTTTTTTTTTCGAA
*
6156 TTCTTTTTTTC-AA
1 TTTTTTTTTTCGAA
6169 GTTTTTATTTTT
1 -TTTTT-TTTTT
6181 ATTTTTTTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.35
14 17 0.50
15 5 0.15
ACGTcount: A:0.13, C:0.06, G:0.06, T:0.75
Consensus pattern (14 bp):
TTTTTTTTTTCGAA
Found at i:14191 original size:30 final size:30
Alignment explanation
Indices: 14157--14253 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
14147 AGCTCACTCC
14157 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
14187 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
14217 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
14247 TAGCTCA
1 TAGCTCA
14254 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:16563 original size:21 final size:21
Alignment explanation
Indices: 16537--16599 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
16527 TTGGTATTTG
16537 GGAATTGGTTCGAAATGGTAT
1 GGAATTGGTTCGAAATGGTAT
*
16558 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTTCGAAATGGTAT
* * *
16579 GGTATTTGTTACGAATTGGTA
1 GGAATTGGTT-CGAAATGGTA
16600 ATGGTTCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 27 0.75
22 9 0.25
ACGTcount: A:0.29, C:0.05, G:0.32, T:0.35
Consensus pattern (21 bp):
GGAATTGGTTCGAAATGGTAT
Found at i:20084 original size:11 final size:10
Alignment explanation
Indices: 20071--20107 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
20061 AAAGAAAATA
20071 AAAAAAATTG
1 AAAAAAATTG
*
20081 AAAAAAATCG
1 AAAAAAATTG
*
20091 AAAAAAATTC
1 AAAAAAATTG
20101 AAAAAAA
1 AAAAAAA
20108 AGTTTGTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.14
Consensus pattern (10 bp):
AAAAAAATTG
Found at i:21987 original size:22 final size:22
Alignment explanation
Indices: 21959--22002 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
21949 TTTTGAACCA
21959 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
21981 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
22003 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:22567 original size:21 final size:21
Alignment explanation
Indices: 22552--22597 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
22542 TGAGAGAATA
22552 AAAAAGAAATGAGAGAAAAAG
1 AAAAAGAAATGAGAGAAAAAG
* *
22573 AAAAAGAAATAAAAGAAAAAG
1 AAAAAGAAATGAGAGAAAAAG
22594 AAAA
1 AAAA
22598 TGAGAGTGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.04
Consensus pattern (21 bp):
AAAAAGAAATGAGAGAAAAAG
Found at i:22586 original size:15 final size:15
Alignment explanation
Indices: 22568--22596 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
22558 AAATGAGAGA
22568 AAAAGAAAAAGAAAT
1 AAAAGAAAAAGAAAT
22583 AAAAGAAAAAGAAA
1 AAAAGAAAAAGAAA
22597 ATGAGAGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (15 bp):
AAAAGAAAAAGAAAT
Found at i:22673 original size:27 final size:30
Alignment explanation
Indices: 22643--22699 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 30
22633 AATTTGAGAT
* *
22643 TGAGA-TTGAAAAAGAAAA-AGA-TGAAAA
1 TGAGATTTCAAAAACAAAAGAGAGTGAAAA
22670 TGAGATTTCAAAAACAAAAGAGAGTGAAAA
1 TGAGATTTCAAAAACAAAAGAGAGTGAAAA
22700 GCAAAAAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.20
28 11 0.44
29 3 0.12
30 6 0.24
ACGTcount: A:0.60, C:0.04, G:0.21, T:0.16
Consensus pattern (30 bp):
TGAGATTTCAAAAACAAAAGAGAGTGAAAA
Found at i:22719 original size:12 final size:12
Alignment explanation
Indices: 22702--22741 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
22692 AGTGAAAAGC
22702 AAAAAGAGATTG
1 AAAAAGAGATTG
*
22714 AAAAAGAAATTG
1 AAAAAGAGATTG
* *
22726 AAAGAGAGCTTG
1 AAAAAGAGATTG
22738 AAAA
1 AAAA
22742 GAAATCGAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.60, C:0.03, G:0.23, T:0.15
Consensus pattern (12 bp):
AAAAAGAGATTG
Done.