Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3544
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: 34540
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:1387 original size:43 final size:41
Alignment explanation
Indices: 1325--1421 Score: 160
Period size: 43 Copynumber: 2.3 Consensus size: 41
1315 GTGGTTTTCA
*
1325 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGAGCAATAAGTGTTCAC-GTTGTGAG-TTG
1368 GCACTAAGTGTGCGAGCAATAAGTGTTCACGTTGTGAGTTG
1 GCACTAAGTGTGCGAGCAATAAGTGTTCACGTTGTGAGTTG
1409 GCACTAA-TGTGCG
1 GCACTAAGTGTGCG
1422 GCTTAAATGC
Statistics
Matches: 53, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
40 6 0.11
41 10 0.19
42 8 0.15
43 29 0.55
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.28
Consensus pattern (41 bp):
GCACTAAGTGTGCGAGCAATAAGTGTTCACGTTGTGAGTTG
Found at i:1469 original size:28 final size:27
Alignment explanation
Indices: 1407--1476 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 27
1397 CGTTGTGAGT
*
1407 TGGCACTAA-TGTGCGGCTTAAATGCA
1 TGGCACTAAGTGTGCGGCTTAAATACA
1433 TGGCACTAAGTGTGCGAG-TTAAAGTACA
1 TGGCACTAAGTGTGCG-GCTTAAA-TACA
1461 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
1477 TGGTGATTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
26 9 0.22
27 11 0.28
28 20 0.50
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (27 bp):
TGGCACTAAGTGTGCGGCTTAAATACA
Found at i:1866 original size:39 final size:39
Alignment explanation
Indices: 1819--1975 Score: 147
Period size: 41 Copynumber: 3.9 Consensus size: 39
1809 CTAAGACCAT
1819 ATCC-GGCTAAGTCCCGAAGAGCATTCATGCTAGTGATG
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATG
* * * *
1857 ATCCGGGCTAAGTTCTGAAGAGCATTCGTGCTAGTGATAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGAT-G
* ** * *
1897 ATCCGTGCTAAACCCCGAAGAAGCATTCGTGCTGGTGTTATG
1 ATCCGGGCTAAGTCCCGAAG-AGCATTCATGCTAGTG--ATG
* * *
1939 -TCCGGGCTAGGTCTCCGAAGAGCAATCATGCTGGTGA
1 ATCCGGGCTAAGTC-CCGAAGAGCATTCATGCTAGTGA
1976 CGATAGGGTT
Statistics
Matches: 96, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
38 4 0.04
39 31 0.32
40 15 0.16
41 38 0.40
42 6 0.06
43 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATG
Found at i:2816 original size:12 final size:13
Alignment explanation
Indices: 2799--2831 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
2789 TTAAACTAAG
2799 TAAATAAATAA-A
1 TAAATAAATAATA
2811 TAAATAAATAATA
1 TAAATAAATAATA
*
2824 AAAATAAA
1 TAAATAAA
2832 ACTTTACAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAATAAATAATA
Found at i:4229 original size:23 final size:22
Alignment explanation
Indices: 4177--4229 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
4167 TCCACGTCTT
*
4177 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
4199 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
4222 TTTCTTTT
1 TTTCTTTT
4230 TCACTCTCAA
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:8790 original size:13 final size:13
Alignment explanation
Indices: 8772--8796 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8762 TAATGGTATA
8772 TTGAATCCATGAT
1 TTGAATCCATGAT
8785 TTGAATCCATGA
1 TTGAATCCATGA
8797 AAATTTAGTA
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):
TTGAATCCATGAT
Found at i:10236 original size:47 final size:47
Alignment explanation
Indices: 10175--10709 Score: 892
Period size: 47 Copynumber: 11.4 Consensus size: 47
10165 CAGCCAAGAC
10175 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
10222 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
10269 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
10316 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
10363 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * *
10410 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAG
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
10457 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
10504 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
10551 AGTGTATATATGTAATAAGGCCT-ATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
10597 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * * *
10644 AGTGCATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
10691 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
10710 TCCCGAAGGG
Statistics
Matches: 464, Mismatches: 23, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
46 45 0.10
47 419 0.90
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:10884 original size:37 final size:37
Alignment explanation
Indices: 10828--10906 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
10818 CCAAGCTCTA
* *
10828 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
10865 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
10902 AAGAC
1 AAGAC
10907 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:13816 original size:20 final size:20
Alignment explanation
Indices: 13793--13839 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
13783 GGGTTAAGAT
*
13793 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
13813 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
13833 TGAGCTG
1 TGAGCTG
13840 GAAACGAGCT
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:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:15561 original size:48 final size:48
Alignment explanation
Indices: 15509--15614 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
15499 TTGTCTTTTC
*
15509 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
15557 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
15605 TTTCTTTTTC
1 TTTCTTTTTC
15615 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:18240 original size:20 final size:20
Alignment explanation
Indices: 18217--18263 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
18207 GGGTTAAGAT
18217 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTTGAG
* *
18237 TGAGTTGACTTGAGCTTGAG
1 TGAGCTGAATTGAGCTTGAG
18257 TGAGCTG
1 TGAGCTG
18264 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.11, G:0.36, T:0.32
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTTGAG
Found at i:22813 original size:6 final size:6
Alignment explanation
Indices: 22802--22835 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
22792 AATTTTTTTC
* *
22802 TCAATA TCAATA TCAATA TCAATC TCAATC TCAA
1 TCAATA TCAATA TCAATA TCAATA TCAATA TCAA
22836 ATTCTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (6 bp):
TCAATA
Found at i:22887 original size:21 final size:20
Alignment explanation
Indices: 22843--22887 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
22833 CAAATTCTTT
*
22843 TTTCTTTTTCTCACTCTCAT
1 TTTCTTTTTCTCACTCTCAA
* *
22863 TTTCTTTTTTTCTTCTCTCAA
1 TTTCTTTTTCTC-ACTCTCAA
22884 TTTC
1 TTTC
22888 ATTCAAGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.09, C:0.27, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCTTTTTCTCACTCTCAA
Found at i:23847 original size:31 final size:32
Alignment explanation
Indices: 23774--23848 Score: 118
Period size: 31 Copynumber: 2.4 Consensus size: 32
23764 TTTCAATCAC
* *
23774 TCTTTTTTTTTTCAATTTTGATTTTTTTTTCT
1 TCTTTTTTTTTTCAATTTCGAATTTTTTTTCT
23806 TCTTTTTTTTTT-AATTTCGAATTTTTTTT-T
1 TCTTTTTTTTTTCAATTTCGAATTTTTTTTCT
23836 TCTTTTTTTTTTC
1 TCTTTTTTTTTTC
23849 TTCAATACTA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
30 13 0.32
31 15 0.38
32 12 0.30
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.79
Consensus pattern (32 bp):
TCTTTTTTTTTTCAATTTCGAATTTTTTTTCT
Found at i:23913 original size:16 final size:15
Alignment explanation
Indices: 23892--23944 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
23882 GAATACAAAC
*
23892 TTTTTTTTTGAAATT
1 TTTTTTTTTCAAATT
*
23907 TTTTTTTTTCAAAAAT
1 TTTTTTTTTC-AAATT
23923 TTTTTTTTTCAAATT
1 TTTTTTTTTCAAATT
23938 TTTTTTT
1 TTTTTTT
23945 ATATTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
15 20 0.59
16 14 0.41
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (15 bp):
TTTTTTTTTCAAATT
Found at i:23914 original size:17 final size:17
Alignment explanation
Indices: 23902--23944 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
23892 TTTTTTTTTG
23902 AAATTTTTTTTTTTCAA
1 AAATTTTTTTTTTTCAA
23919 AAA-TTTTTTTTTTC--
1 AAATTTTTTTTTTTCAA
23933 AAATTTTTTTTT
1 AAATTTTTTTTT
23945 ATATTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 3 0.12
15 8 0.32
16 11 0.44
17 3 0.12
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (17 bp):
AAATTTTTTTTTTTCAA
Found at i:23954 original size:14 final size:14
Alignment explanation
Indices: 23892--23944 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
23882 GAATACAAAC
*
23892 TTTTTTTTTGAAAT
1 TTTTTTTTTTAAAT
23906 TTTTTTTTTTCAAAAAT
1 TTTTTTTTTT---AAAT
*
23923 TTTTTTTTTCAAAT
1 TTTTTTTTTTAAAT
23937 TTTTTTTT
1 TTTTTTTT
23945 ATATTTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
14 21 0.62
17 13 0.38
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (14 bp):
TTTTTTTTTTAAAT
Done.