Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold749
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: 68331
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1005 original size:18 final size:21
Alignment explanation
Indices: 960--1006 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
950 CCACTCTCAA
960 TCTCTTTTTGCTCTTTTTCAT
1 TCTCTTTTTGCTCTTTTTCAT
*
981 TCTCTTTTT-CT-TTTTTGAT
1 TCTCTTTTTGCTCTTTTTCAT
1000 T-TCTTTT
1 TCTCTTTT
1007 GTGTCTTCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 6 0.24
19 8 0.32
20 2 0.08
21 9 0.36
ACGTcount: A:0.04, C:0.19, G:0.04, T:0.72
Consensus pattern (21 bp):
TCTCTTTTTGCTCTTTTTCAT
Found at i:17019 original size:21 final size:23
Alignment explanation
Indices: 16974--17020 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
16964 TCACCTGCAA
* *
16974 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
16997 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
17018 TAA
1 TAA
17021 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:23989 original size:30 final size:30
Alignment explanation
Indices: 23955--24051 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
23945 AGCTCACTCC
23955 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
23985 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
24015 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
24045 TAGCTCA
1 TAGCTCA
24052 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:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:26736 original size:37 final size:37
Alignment explanation
Indices: 26685--26755 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
26675 CATTCTTGTA
26685 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
26722 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
26756 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:26755 original size:6 final size:6
Alignment explanation
Indices: 26695--26744 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
26685 AAGAGAAAAC
*
26695 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
26744 A
1 A
26745 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:26837 original size:11 final size:12
Alignment explanation
Indices: 26805--26835 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
26795 TTGAGAGAAC
26805 TTGAAAAAGCCT
1 TTGAAAAAGCCT
26817 TTGAAAAAGCCT
1 TTGAAAAAGCCT
26829 TTGAAAA
1 TTGAAAA
26836 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:29046 original size:30 final size:30
Alignment explanation
Indices: 29012--29107 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
29002 AGCTCACTCC
29012 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
29042 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
*
29072 CAGCTCAACTTTAGCTCACGAGCTAAA-CT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
29101 TAGCTCA
1 TAGCTCA
29108 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
29 9 0.18
30 42 0.82
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:32119 original size:23 final size:22
Alignment explanation
Indices: 32068--32119 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
32058 TCTCATCTTT
*
32068 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTATTTCTTTTTCTAAC
32090 -TCATTTTATCTTCTTTCTTC-AAC
1 TTC-TTTTAT-TTCTTT-TTCTAAC
32113 TTCTTTT
1 TTCTTTT
32120 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.12, C:0.21, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTATTTCTTTTTCTAAC
Found at i:39802 original size:11 final size:11
Alignment explanation
Indices: 39782--39843 Score: 56
Period size: 10 Copynumber: 5.4 Consensus size: 11
39772 CTCGCAAGAC
*
39782 TTTTCACTTTT
1 TTTTCTCTTTT
39793 TTTTCTC-TTT
1 TTTTCTCTTTT
39803 TTTTCTCGTTTT
1 TTTTCTC-TTTT
39815 TTTGTCACTTCTTTT
1 TTT-T--C-TCTTTT
39830 TTTT-TCTTTT
1 TTTTCTCTTTT
39840 TTTT
1 TTTT
39844 TGAATTTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
10 20 0.45
11 6 0.14
12 6 0.14
13 1 0.02
14 1 0.02
15 8 0.18
16 2 0.05
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.77
Consensus pattern (11 bp):
TTTTCTCTTTT
Found at i:39851 original size:12 final size:12
Alignment explanation
Indices: 39836--39862 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
39826 TTTTTTTTTC
39836 TTTTTTTTTGAA
1 TTTTTTTTTGAA
39848 TTTTTTTTTGAA
1 TTTTTTTTTGAA
39860 TTT
1 TTT
39863 CTTCTCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:42822 original size:20 final size:20
Alignment explanation
Indices: 42799--42845 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
42789 GGGTTAAGAT
*
42799 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
42819 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
42839 TGAGCTG
1 TGAGCTG
42846 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:43279 original size:20 final size:21
Alignment explanation
Indices: 43244--43282 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
43234 CAGCTCGTTG
43244 AGCTCAATTCAGCTCATTTCC
1 AGCTCAATTCAGCTCATTTCC
*
43265 AGCTC-ATTGAGCTCATTT
1 AGCTCAATTCAGCTCATTT
43283 GCTTGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (21 bp):
AGCTCAATTCAGCTCATTTCC
Found at i:43690 original size:13 final size:13
Alignment explanation
Indices: 43672--43697 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43662 TGTGTCCTAA
43672 TATGAATTAAATT
1 TATGAATTAAATT
43685 TATGAATTAAATT
1 TATGAATTAAATT
43698 GCTTTCAGGT
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:45826 original size:6 final size:6
Alignment explanation
Indices: 45801--45898 Score: 65
Period size: 6 Copynumber: 16.0 Consensus size: 6
45791 TAATGAATTC
** * *
45801 GAAAAA GAAAGT GAAGAA GAAAAA GAAAACA -AAAAA G-AAAA GAAAAC
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAA-A GAAAAA GAAAAA GAAAAA
** * * *
45848 GAAAAA GTGAGA GAAAAA GAAAAT GAAGAAAA GAAAATT GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA G-A-AAAA GAAAA-A GAAAAA GAAAAA
45899 TATGAAAATG
Statistics
Matches: 68, Mismatches: 18, Indels: 12
0.69 0.18 0.12
Matches are distributed among these distances:
5 6 0.09
6 50 0.74
7 8 0.12
8 4 0.06
ACGTcount: A:0.72, C:0.02, G:0.20, T:0.05
Consensus pattern (6 bp):
GAAAAA
Found at i:45841 original size:17 final size:17
Alignment explanation
Indices: 45821--45854 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
45811 GTGAAGAAGA
45821 AAAAGAAAACAAAAAAG
1 AAAAGAAAACAAAAAAG
*
45838 AAAAGAAAACGAAAAAG
1 AAAAGAAAACAAAAAAG
45855 TGAGAGAAAA
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:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAGAAAACAAAAAAG
Found at i:45881 original size:14 final size:13
Alignment explanation
Indices: 45860--45897 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
45850 AAAAGTGAGA
45860 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
45872 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
45887 GAAAAAGAAAA
1 GAAAAAGAAAA
45898 ATATGAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:45941 original size:17 final size:18
Alignment explanation
Indices: 45916--45955 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
45906 ATGAGATTTC
45916 AAAAACAAAA-GAGAGTG
1 AAAAACAAAATGAGAGTG
* *
45933 AAAAGCAAAATGAGATTG
1 AAAAACAAAATGAGAGTG
45951 AAAAA
1 AAAAA
45956 GAAAGAGAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.65, C:0.05, G:0.20, T:0.10
Consensus pattern (18 bp):
AAAAACAAAATGAGAGTG
Found at i:45947 original size:18 final size:17
Alignment explanation
Indices: 45916--45965 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
45906 ATGAGATTTC
45916 AAAAACAAAAGAGAGTG
1 AAAAACAAAAGAGAGTG
* *
45933 AAAAGCAAAATGAGATTG
1 AAAAACAAAA-GAGAGTG
*
45951 AAAAA-GAAAGAGAGT
1 AAAAACAAAAGAGAGT
45966 TTGAAAAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 5 0.19
17 12 0.44
18 10 0.37
ACGTcount: A:0.62, C:0.04, G:0.24, T:0.10
Consensus pattern (17 bp):
AAAAACAAAAGAGAGTG
Found at i:45971 original size:36 final size:34
Alignment explanation
Indices: 45902--45997 Score: 92
Period size: 36 Copynumber: 2.8 Consensus size: 34
45892 AGAAAAATAT
* *
45902 GAAAATGAGATTTCAAAAACAAAAGAGAG-TGAAAA
1 GAAAATGAGA-TTGAAAAA-GAAAGAGAGTTGAAAA
45937 GCAAAATGAGATTGAAAAAGAAAGAGAGTTTGAAAA
1 G-AAAATGAGATTGAAAAAGAAAGAGAG-TTGAAAA
* *
45973 GAAAACGAG--TGAAGAAG-AAGAGAGT
1 GAAAATGAGATTGAAAAAGAAAGAGAGT
45998 GCTCAAACAC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
31 1 0.02
32 7 0.13
33 7 0.13
34 8 0.15
35 15 0.28
36 16 0.30
ACGTcount: A:0.56, C:0.04, G:0.26, T:0.14
Consensus pattern (34 bp):
GAAAATGAGATTGAAAAAGAAAGAGAGTTGAAAA
Found at i:45974 original size:17 final size:16
Alignment explanation
Indices: 45923--45997 Score: 52
Period size: 16 Copynumber: 4.6 Consensus size: 16
45913 TTCAAAAACA
45923 AAAGAGAG-TGAAAAG
1 AAAGAGAGTTGAAAAG
45938 CAAA-ATGAGATTGAAAAAG
1 -AAAGA-GAG-TTG-AAAAG
45957 AAAGAGAGTTTGAAAAG
1 AAAGAGAG-TTGAAAAG
45974 AAA-ACGAG-TGAAGAAG
1 AAAGA-GAGTTGAA-AAG
45990 -AAGAGAGT
1 AAAGAGAGT
45998 GCTCAAACAC
Statistics
Matches: 49, Mismatches: 1, Indels: 18
0.72 0.01 0.26
Matches are distributed among these distances:
15 10 0.20
16 11 0.22
17 11 0.22
18 11 0.22
19 6 0.12
ACGTcount: A:0.56, C:0.03, G:0.29, T:0.12
Consensus pattern (16 bp):
AAAGAGAGTTGAAAAG
Found at i:47265 original size:20 final size:21
Alignment explanation
Indices: 47230--47268 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
47220 CAGCTCGTTG
47230 AGCTCAATTCAGCTCATTTCC
1 AGCTCAATTCAGCTCATTTCC
*
47251 AGCTC-ATTGAGCTCATTT
1 AGCTCAATTCAGCTCATTT
47269 GCTTGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (21 bp):
AGCTCAATTCAGCTCATTTCC
Found at i:47675 original size:13 final size:13
Alignment explanation
Indices: 47657--47682 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
47647 TGTGTCCTAA
47657 TATGAATTAAATT
1 TATGAATTAAATT
47670 TATGAATTAAATT
1 TATGAATTAAATT
47683 GCTTTCAGGT
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:50825 original size:48 final size:47
Alignment explanation
Indices: 50746--50851 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
50736 GAGTGTCATG
*
50746 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
50794 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
50842 GAAAAAGAAA
1 GAAAAAGAAA
50852 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:52567 original size:20 final size:20
Alignment explanation
Indices: 52521--52567 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
52511 AGCTCGTTTC
*
52521 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
52541 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
52561 CAGCTCA
1 CAGCTCA
52568 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:56263 original size:11 final size:11
Alignment explanation
Indices: 56247--56278 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
56237 GGAAATTTGA
56247 AAAAAAAATTC
1 AAAAAAAATTC
56258 AAAAAAAATTC
1 AAAAAAAATTC
56269 AAAAAAAATT
1 AAAAAAAATT
56279 TTGAAGTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (11 bp):
AAAAAAAATTC
Done.