Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1159
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: 42521
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:1921 original size:4 final size:4
Alignment explanation
Indices: 1912--1942 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
1902 ATTTTAAACT
1912 AATA AATA AATAA AATA AATA AATA AATA AA
1 AATA AATA AAT-A AATA AATA AATA AATA AA
1943 ACTAATTACC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:12506 original size:12 final size:13
Alignment explanation
Indices: 12491--12557 Score: 52
Period size: 11 Copynumber: 5.2 Consensus size: 13
12481 AAAAAATTTC
12491 AAAAAAAAG-G-A
1 AAAAAAAAGTGAA
12502 AAAAAAAAGTGACA
1 AAAAAAAAGTGA-A
* *
12516 AAAAAATCGAGTTAA
1 AAAAAA--AAGTGAA
12531 AAAAAAAA--GAA
1 AAAAAAAAGTGAA
12542 AGAAAAAAAGTGAA
1 A-AAAAAAAGTGAA
12556 AA
1 AA
12558 GTCTTGCGAG
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
11 12 0.27
12 8 0.18
13 2 0.05
14 11 0.25
15 7 0.16
16 4 0.09
ACGTcount: A:0.75, C:0.03, G:0.15, T:0.07
Consensus pattern (13 bp):
AAAAAAAAGTGAA
Found at i:13654 original size:48 final size:47
Alignment explanation
Indices: 13575--13680 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
13565 GAGTGTCATG
*
13575 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
13623 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
13671 GAAAAAGAAA
1 GAAAAAGAAA
13681 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:15396 original size:20 final size:20
Alignment explanation
Indices: 15350--15396 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
15340 AGCTCGTTTC
*
15350 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
15370 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
15390 CAGCTCA
1 CAGCTCA
15397 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:16974 original size:22 final size:22
Alignment explanation
Indices: 16946--16989 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
16936 TTTTGAACCA
16946 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
16968 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
16990 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:22426 original size:21 final size:21
Alignment explanation
Indices: 22381--22443 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
22371 TTTGAACCAT
* *
22381 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
22403 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
22424 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
22444 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:22801 original size:11 final size:11
Alignment explanation
Indices: 22767--22805 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
22757 AAAAAAAGTC
*
22767 AAAATCGAAAA
1 AAAATTGAAAA
22778 AAAATTGAAAAAA
1 AAAATTG--AAAA
22791 AAAATTGAAAA
1 AAAATTGAAAA
22802 AAAA
1 AAAA
22806 AAATTGCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 14 0.56
13 11 0.44
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.13
Consensus pattern (11 bp):
AAAATTGAAAA
Found at i:22811 original size:14 final size:13
Alignment explanation
Indices: 22774--22807 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
22764 GTCAAAATCG
22774 AAAAAAAATTGAA
1 AAAAAAAATTGAA
22787 AAAAAAAATTGAA
1 AAAAAAAATTGAA
22800 AAAAAAAA
1 AAAAAAAA
22808 ATTGCATACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (13 bp):
AAAAAAAATTGAA
Found at i:25052 original size:17 final size:17
Alignment explanation
Indices: 25007--25060 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
24997 AGAAAAGAGC
* *
25007 GAAAATACAAAAGAAAA
1 GAAAATTCAAAAAAAAA
* *
25024 GAAAAATGAAAAAAAAA
1 GAAAATTCAAAAAAAAA
*
25041 GAAAATTCAAAAAAAGA
1 GAAAATTCAAAAAAAAA
25058 GAA
1 GAA
25061 TGAAAAGAGA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.76, C:0.04, G:0.13, T:0.07
Consensus pattern (17 bp):
GAAAATTCAAAAAAAAA
Found at i:29282 original size:21 final size:21
Alignment explanation
Indices: 29237--29299 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
29227 TTTGAACCAT
* *
29237 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
29259 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
29280 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
29300 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:30270 original size:30 final size:30
Alignment explanation
Indices: 30234--30296 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
30224 GCAAGCTAAT
*
30234 TTCAAC-TCAATTCCAGCTCCCTT-AGCTCAA
1 TTCAACTTCAA-T-CAGCTCACTTGAGCTCAA
*
30264 TTCAACTTTAATCAGCTCACTTGAGCTCAA
1 TTCAACTTCAATCAGCTCACTTGAGCTCAA
30294 TTC
1 TTC
30297 CACCTATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 9 0.31
30 17 0.59
31 3 0.10
ACGTcount: A:0.27, C:0.32, G:0.08, T:0.33
Consensus pattern (30 bp):
TTCAACTTCAATCAGCTCACTTGAGCTCAA
Found at i:31507 original size:18 final size:17
Alignment explanation
Indices: 31484--31587 Score: 52
Period size: 18 Copynumber: 5.8 Consensus size: 17
31474 AACAAGTGAG
31484 GAAAAAGAAAAAGAGAAT
1 GAAAAAGAAAAAGA-AAT
*
31502 GAAAAAGAGCAAAAAGAGATT
1 G-AAAA-AG-AAAAAGA-AAT
* **
31523 GAGAGTGAAAAAGAAATT
1 GAAAAAGAAAAAGAAA-T
*
31541 GAAGAAAG-AAGAGAAAAT
1 GAA-AAAGAAAAAG-AAAT
**
31559 GAATTAGAAAAAGAAAT
1 GAAAAAGAAAAAGAAAT
31576 --AAAAGAAAAAGA
1 GAAAAAGAAAAAGA
31588 CGTGGAAAGG
Statistics
Matches: 65, Mismatches: 14, Indels: 17
0.68 0.15 0.18
Matches are distributed among these distances:
15 10 0.15
17 7 0.11
18 23 0.35
19 10 0.15
20 4 0.06
21 11 0.17
ACGTcount: A:0.66, C:0.01, G:0.23, T:0.10
Consensus pattern (17 bp):
GAAAAAGAAAAAGAAAT
Found at i:35840 original size:33 final size:33
Alignment explanation
Indices: 35802--35864 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
35792 GATTACTCAC
35802 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
35835 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
35865 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:35895 original size:26 final size:25
Alignment explanation
Indices: 35861--35941 Score: 85
Period size: 27 Copynumber: 3.1 Consensus size: 25
35851 TCAAGCTCTC
35861 TTTCAATTTCTTTTTTCACTTTTCTT
1 TTTCAATTTCTTTTTTCA-TTTTCTT
*
35887 TTTCAATTT-TTTCATTCTCAATTTCTT
1 TTTCAATTTCTTT--TT-TCATTTTCTT
35914 TTTCAATTTTCTTTTCTTCATTTT-TT
1 TTTCAA-TTTCTTTT-TTCATTTTCTT
35940 TT
1 TT
35942 CTCTCTTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
25 3 0.06
26 13 0.28
27 21 0.45
28 7 0.15
29 3 0.06
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTCAATTTCTTTTTTCATTTTCTT
Found at i:35919 original size:12 final size:12
Alignment explanation
Indices: 35843--35928 Score: 66
Period size: 13 Copynumber: 6.8 Consensus size: 12
35833 TTTTCACTTG
35843 ATTTC-TTTTCA
1 ATTTCTTTTTCA
** *
35854 AGCTCTCTTTCA
1 ATTTCTTTTTCA
35866 ATTTCTTTTTTCA
1 ATTTC-TTTTTCA
*
35879 CTTTTCTTTTTCA
1 -ATTTCTTTTTCA
*
35892 ATTTTTTCATTCTCA
1 ATTTCTT--TT-TCA
35907 ATTTCTTTTTCA
1 ATTTCTTTTTCA
35919 ATTTTCTTTT
1 A-TTTCTTTT
35929 CTTCATTTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
11 3 0.05
12 17 0.29
13 23 0.40
14 6 0.10
15 9 0.16
ACGTcount: A:0.15, C:0.20, G:0.01, T:0.64
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:35948 original size:22 final size:22
Alignment explanation
Indices: 35923--35971 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 22
35913 TTTTCAATTT
35923 TCTTTTCTTCATTTTTTTTC-TC
1 TCTTTT-TTCATTTTTTTTCATC
*
35945 TC-TTTTTGATTTTTTTTCAATC
1 TCTTTTTTCATTTTTTTTC-ATC
35967 TCTTT
1 TCTTT
35972 CTCCTTTCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 12 0.52
21 3 0.13
22 6 0.26
23 2 0.09
ACGTcount: A:0.08, C:0.18, G:0.02, T:0.71
Consensus pattern (22 bp):
TCTTTTTTCATTTTTTTTCATC
Done.