Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1050
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: 34755
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4798 original size:23 final size:22
Alignment explanation
Indices: 4746--4798 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
4736 TCCACGTCTT
*
4746 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
4768 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
4791 TTTCTTTT
1 TTTCTTTT
4799 TCACTTCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:4805 original size:24 final size:23
Alignment explanation
Indices: 4756--4805 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
4746 TTTCTTTTGT
*
4756 TTCTTTTTCTAATTCATTTTCTC
1 TTCTTTTTCTAATTCATTTTCAC
*
4779 TTCTTTCTTC-AATTTCTTTTTCAC
1 TTCTTT-TTCTAA-TTCATTTTCAC
4803 TTC
1 TTC
4806 AATCTCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.64
Consensus pattern (23 bp):
TTCTTTTTCTAATTCATTTTCAC
Found at i:9077 original size:30 final size:29
Alignment explanation
Indices: 9032--9116 Score: 91
Period size: 30 Copynumber: 2.8 Consensus size: 29
9022 TTCTTTTGTT
* *
9032 TCAATTTCTTTTTCATCTTCTTTTTCACTC
1 TCAATTTCATTTTCAT-TTCTTTTTCAATC
9062 TCAAATTTC-TTTTCATTCTCTTTTTCAATC
1 TC-AATTTCATTTTCATT-TCTTTTTCAATC
* *
9092 TCATTTTCATTTTCTTTTTCTTTTT
1 TCAATTTCATTTTC-ATTTCTTTTT
9117 GCTTTTCAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
29 6 0.12
30 34 0.71
31 8 0.17
ACGTcount: A:0.14, C:0.22, G:0.00, T:0.64
Consensus pattern (29 bp):
TCAATTTCATTTTCATTTCTTTTTCAATC
Found at i:9088 original size:12 final size:12
Alignment explanation
Indices: 9071--9111 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
9061 CTCAAATTTC
9071 TTTTCATTCTCT
1 TTTTCATTCTCT
* *
9083 TTTTCAATCTCA
1 TTTTCATTCTCT
*
9095 TTTTCATTTTCT
1 TTTTCATTCTCT
9107 TTTTC
1 TTTTC
9112 TTTTTGCTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.12, C:0.22, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTTCATTCTCT
Found at i:9134 original size:12 final size:12
Alignment explanation
Indices: 9119--9149 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
9109 TTCTTTTTGC
9119 TTTTCAAAGGCT
1 TTTTCAAAGGCT
9131 TTTTCAAAGGCT
1 TTTTCAAAGGCT
9143 TTTTCAA
1 TTTTCAA
9150 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:9236 original size:15 final size:14
Alignment explanation
Indices: 9214--9252 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
9204 TTTTATTTCA
9214 TTTTCTTTTTCTTC
1 TTTTCTTTTTCTTC
9228 TTTTGCTTTTTCTTTTC
1 TTTT-CTTTTTC--TTC
9245 TTTTCTTT
1 TTTTCTTT
9253 GTTTTCTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 4 0.18
15 7 0.32
16 4 0.18
17 7 0.32
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (14 bp):
TTTTCTTTTTCTTC
Found at i:10204 original size:17 final size:17
Alignment explanation
Indices: 10171--10208 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
10161 CATTAAACAC
*
10171 TTTTTTTTCAGATTTTT
1 TTTTTTTTCAGAATTTT
10188 TTTTCTTTTC-GAATTTT
1 TTTT-TTTTCAGAATTTT
10205 TTTT
1 TTTT
10209 GAATTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.11, C:0.08, G:0.05, T:0.76
Consensus pattern (17 bp):
TTTTTTTTCAGAATTTT
Found at i:10219 original size:11 final size:11
Alignment explanation
Indices: 10188--10231 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 11
10178 TCAGATTTTT
10188 TTTTCTTTTCGAA
1 TTTT-TTTT-GAA
10201 TTTTTTTTGAA
1 TTTTTTTTGAA
10212 TTTTTTTTTTGAA
1 --TTTTTTTTGAA
10225 TTTTTTT
1 TTTTTTT
10232 GACTTCTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 10 0.34
12 4 0.14
13 15 0.52
ACGTcount: A:0.14, C:0.05, G:0.07, T:0.75
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:12027 original size:30 final size:30
Alignment explanation
Indices: 11993--12089 Score: 108
Period size: 30 Copynumber: 3.2 Consensus size: 30
11983 AGCTCACTCC
11993 TAGCTCATA-TTTAGCTCACGAGCTAAAGCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
* * * **
12023 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
*
12053 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
12083 TAGCTCA
1 TAGCTCA
12090 TTTTAGTTTT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
29 4 0.08
30 45 0.87
31 3 0.06
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:14787 original size:5 final size:5
Alignment explanation
Indices: 14768--14840 Score: 53
Period size: 5 Copynumber: 14.0 Consensus size: 5
14758 ACATTCTTGT
* *
14768 AAAGA GAAA-A AAAGA AAAGA AAAGAA AAAGA AAA-A GCAAGA GAAGAA
1 AAAGA -AAAGA AAAGA AAAGA AAAG-A AAAGA AAAGA -AAAGA AAAG-A
14815 AAAGA AAATGA AATA-A AAAGA AAAGA
1 AAAGA AAA-GA AA-AGA AAAGA AAAGA
14841 GAGGCAAGAG
Statistics
Matches: 56, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
4 5 0.09
5 33 0.59
6 17 0.30
7 1 0.02
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:14819 original size:37 final size:36
Alignment explanation
Indices: 14769--14838 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 36
14759 CATTCTTGTA
14769 AAGAGAAAAAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAAAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
14805 AAGAGAAGAAAAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AAAAAGAAAATGAAAGAAAAAGAAAA
14839 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
36 7 0.23
37 23 0.74
38 1 0.03
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.03
Consensus pattern (36 bp):
AAGAGAAAAAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:14838 original size:6 final size:6
Alignment explanation
Indices: 14776--14827 Score: 54
Period size: 6 Copynumber: 8.5 Consensus size: 6
14766 GTAAAGAGAA
*
14776 AAAAAG -AAAAG -AAAAG AAAAAG AAAAAG CAAGAGAAG AAAAAG AAAATG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG -AA-A-AAG AAAAAG AAAAAG
14825 AAA
1 AAA
14828 TAAAAAGAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
5 10 0.24
6 22 0.54
7 3 0.07
8 3 0.07
9 3 0.07
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:14920 original size:11 final size:12
Alignment explanation
Indices: 14888--14918 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
14878 TTGAGAGAAC
14888 TTGAAAAAGCCT
1 TTGAAAAAGCCT
14900 TTGAAAAAGCCT
1 TTGAAAAAGCCT
14912 TTGAAAA
1 TTGAAAA
14919 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:17100 original size:30 final size:30
Alignment explanation
Indices: 17066--17162 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
17056 AGCTCACTCC
17066 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
17096 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
17126 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
17156 TAGCTCA
1 TAGCTCA
17163 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:18848 original size:30 final size:30
Alignment explanation
Indices: 18814--18910 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
18804 TAAACTAAAA
*
18814 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
18844 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
18874 TGAGCTAAGCTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
18904 TGAGCTA
1 TGAGCTA
18911 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 3 0.06
30 42 0.84
31 5 0.10
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:19435 original size:15 final size:14
Alignment explanation
Indices: 19414--19462 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
19404 ACTTTTTCCA
19414 CTCTTTTTCTTTT-
1 CTCTTTTTCTTTTG
*
19427 CATTCTTTTTATTTTG
1 C--TCTTTTTCTTTTG
*
19443 CTCTTTTTCTTTTT
1 CTCTTTTTCTTTTG
19457 CTCTTT
1 CTCTTT
19463 CAATGGATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 1 0.03
14 17 0.57
15 11 0.37
16 1 0.03
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.73
Consensus pattern (14 bp):
CTCTTTTTCTTTTG
Found at i:20296 original size:42 final size:42
Alignment explanation
Indices: 20237--20342 Score: 203
Period size: 42 Copynumber: 2.5 Consensus size: 42
20227 CATTTAAGCC
20237 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
20279 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
20321 TCTTAGTTTAATTAAATGAGTT
1 TCTTAGTTTAA-TAAATGAGTT
20343 TATTTAATGA
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 53 0.84
43 10 0.16
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (42 bp):
TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
Found at i:20344 original size:14 final size:14
Alignment explanation
Indices: 20325--20369 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
20315 AACTCATCTT
*
20325 AGTTTAATTAAATG
1 AGTTTAATTTAATG
20339 AGTTT-ATTTAATG
1 AGTTTAATTTAATG
*
20352 AATTTAATTTAATG
1 AGTTTAATTTAATG
20366 AGTT
1 AGTT
20370 GCTTCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:21554 original size:13 final size:12
Alignment explanation
Indices: 21536--21565 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
21526 AGTAAGTTTC
21536 AAAAAAAATTGAA
1 AAAAAAAATT-AA
21549 AAAAAAAATTAA
1 AAAAAAAATTAA
21561 AAAAA
1 AAAAA
21566 GCAAAATCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.13
Consensus pattern (12 bp):
AAAAAAAATTAA
Found at i:23760 original size:21 final size:21
Alignment explanation
Indices: 23696--23769 Score: 50
Period size: 21 Copynumber: 3.6 Consensus size: 21
23686 AAAAAAATCA
23696 GAAAAAGAAAACAAAAGAG-AG
1 GAAAAAGAAAA-AAAAGAGAAG
**
23717 TG-AAAAG-AAAATCAGTA-AA-
1 -GAAAAAGAAAAAAAAG-AGAAG
23736 GAAAAAGAAAAAAAAGAGAAG
1 GAAAAAGAAAAAAAAGAGAAG
**
23757 GAAATTGAAAAAA
1 GAAAAAGAAAAAA
23770 TGAGTGTCTG
Statistics
Matches: 40, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
18 1 0.03
19 9 0.22
20 13 0.32
21 16 0.40
22 1 0.03
ACGTcount: A:0.70, C:0.03, G:0.20, T:0.07
Consensus pattern (21 bp):
GAAAAAGAAAAAAAAGAGAAG
Found at i:25178 original size:20 final size:20
Alignment explanation
Indices: 25131--25178 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
25121 AGTAAGCTCG
25131 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
25151 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
25171 GTTGAGCT
1 GTTGAGCT
25179 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:26904 original size:48 final size:48
Alignment explanation
Indices: 26849--26954 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
26839 TTGTCTTTTC
*
26849 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
26897 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
26945 TTTCTTTTTC
1 TTTCTTTTTC
26955 CATGACACTC
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:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:28022 original size:13 final size:12
Alignment explanation
Indices: 27982--28015 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
27972 ATATACTTCG
27982 ATTTTTTTTTGA
1 ATTTTTTTTTGA
27994 ATTTTTTTTTGA
1 ATTTTTTTTTGA
28006 ATTTTTTTTT
1 ATTTTTTTTT
28016 CAAATTTCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (12 bp):
ATTTTTTTTTGA
Found at i:30684 original size:14 final size:14
Alignment explanation
Indices: 30665--30709 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
30655 AACTCATCTT
*
30665 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
30679 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
30692 AATTTAATTTAATG
1 AGTTTAATTTAATG
30706 AGTT
1 AGTT
30710 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:33833 original size:12 final size:11
Alignment explanation
Indices: 33809--33867 Score: 70
Period size: 10 Copynumber: 5.5 Consensus size: 11
33799 ATACAAGTTT
*
33809 AAAAAATT-CA
1 AAAAAATTGAA
33819 AAAAAATTGAA
1 AAAAAATTGAA
33830 AAAAAATTTGAA
1 AAAAAA-TTGAA
*
33842 AAAAAATT-TA
1 AAAAAATTGAA
33852 AAAAAA-TGAA
1 AAAAAATTGAA
33862 AAAAAA
1 AAAAAA
33868 AGTGATTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
9 1 0.02
10 22 0.51
11 9 0.21
12 11 0.26
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.19
Consensus pattern (11 bp):
AAAAAATTGAA
Done.