Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3440
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: 33872
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:261 original size:12 final size:13
Alignment explanation
Indices: 233--261 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
223 AAAAAGAGAG
233 AAAATTCAGAAAA
1 AAAATTCAGAAAA
246 AAAATTCA-AAAA
1 AAAATTCAGAAAA
258 AAAA
1 AAAA
262 AGAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.76, C:0.07, G:0.03, T:0.14
Consensus pattern (13 bp):
AAAATTCAGAAAA
Found at i:262 original size:13 final size:13
Alignment explanation
Indices: 233--262 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
223 AAAAAGAGAG
*
233 AAAATTCAGAAAA
1 AAAATTCAAAAAA
246 AAAATTCAAAAAA
1 AAAATTCAAAAAA
259 AAAA
1 AAAA
263 GAAAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.77, C:0.07, G:0.03, T:0.13
Consensus pattern (13 bp):
AAAATTCAAAAAA
Found at i:1417 original size:47 final size:47
Alignment explanation
Indices: 1339--1443 Score: 124
Period size: 47 Copynumber: 2.2 Consensus size: 47
1329 GAGTGTCATG
* *
1339 GAAAAAGAAATTAAGATTGAAAAAGGATGTGA-AAAGAGAAAGAAATC
1 GAAAAAGAAATTAAGATTGAAAAAAGATGTGAGAAAAAGAAA-AAATC
* * *
1386 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTAAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
1434 GAAAAAGAAA
1 GAAAAAGAAA
1444 GAAAGACAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
47 25 0.50
48 18 0.36
49 7 0.14
ACGTcount: A:0.60, C:0.02, G:0.24, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTAAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:3157 original size:20 final size:20
Alignment explanation
Indices: 3111--3157 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
3101 AGCTCGTTTC
*
3111 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
3131 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
3151 CAGCTCA
1 CAGCTCA
3158 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:4930 original size:20 final size:20
Alignment explanation
Indices: 4905--4959 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
4895 TGTGGTTCAA
*
4905 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
4925 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
4945 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
4960 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:6768 original size:12 final size:12
Alignment explanation
Indices: 6753--6799 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
6743 AAAAAAAAAG
6753 GAAAAAAAATTT
1 GAAAAAAAATTT
6765 GAAAAAAAA-TT
1 GAAAAAAAATTT
* *
6776 CAAAAAAAATTC
1 GAAAAAAAATTT
*
6788 AAAAAAAAATTT
1 GAAAAAAAATTT
6800 TGTATTCAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 10 0.33
12 20 0.67
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.21
Consensus pattern (12 bp):
GAAAAAAAATTT
Found at i:6780 original size:10 final size:11
Alignment explanation
Indices: 6754--6795 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
6744 AAAAAAAAGG
*
6754 AAAAAAAATTTG
1 AAAAAAAA-TTC
6766 AAAAAAAATTC
1 AAAAAAAATTC
6777 AAAAAAAATTC
1 AAAAAAAATTC
6788 AAAAAAAA
1 AAAAAAAA
6796 ATTTTGTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 21 0.72
12 8 0.28
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.17
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:6797 original size:23 final size:23
Alignment explanation
Indices: 6754--6798 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
6744 AAAAAAAAGG
**
6754 AAAAAAAATTTGAAAAAAAATTC
1 AAAAAAAATTCAAAAAAAAATTC
6777 AAAAAAAATTCAAAAAAAAATT
1 AAAAAAAATTCAAAAAAAAATT
6799 TTGTATTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.20
Consensus pattern (23 bp):
AAAAAAAATTCAAAAAAAAATTC
Found at i:7816 original size:17 final size:15
Alignment explanation
Indices: 7796--7834 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
7786 GCGAGCGAGA
7796 AAATGAACATGAAAAAG
1 AAATGAA-A-GAAAAAG
7813 AAATGAAAGAAAAAG
1 AAATGAAAGAAAAAG
7828 AAGATGA
1 AA-ATGA
7835 GTGGGAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.67, C:0.03, G:0.21, T:0.10
Consensus pattern (15 bp):
AAATGAAAGAAAAAG
Found at i:9340 original size:20 final size:20
Alignment explanation
Indices: 9315--9358 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
9305 TGTGGTTCAA
*
9315 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
9335 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
9355 CTCA
1 CTCA
9359 ATTTAACTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.30
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:11166 original size:13 final size:13
Alignment explanation
Indices: 11150--11198 Score: 75
Period size: 13 Copynumber: 3.9 Consensus size: 13
11140 AAAAAAAAAG
11150 GAAAAAAAAATTC
1 GAAAAAAAAATTC
11163 GAAAAAAAAATTC
1 GAAAAAAAAATTC
11176 --AAAAAAAATTC
1 GAAAAAAAAATTC
*
11187 AAAAAAAAAATT
1 GAAAAAAAAATT
11199 TGTATTCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.32
13 23 0.68
ACGTcount: A:0.73, C:0.06, G:0.04, T:0.16
Consensus pattern (13 bp):
GAAAAAAAAATTC
Found at i:11172 original size:24 final size:24
Alignment explanation
Indices: 11140--11196 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
11130 TCAGTATTGT
*
11140 AAAAAAAAAGGAAAAAAAAATTCG
1 AAAAAAAAAGGAAAAAAAAATTCA
***
11164 AAAAAAAAATTCAAAAAAAATTCA
1 AAAAAAAAAGGAAAAAAAAATTCA
11188 AAAAAAAAA
1 AAAAAAAAA
11197 TTTGTATTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.11
Consensus pattern (24 bp):
AAAAAAAAAGGAAAAAAAAATTCA
Found at i:11194 original size:11 final size:11
Alignment explanation
Indices: 11152--11194 Score: 68
Period size: 11 Copynumber: 3.7 Consensus size: 11
11142 AAAAAAAGGA
11152 AAAAAAAATTC
1 AAAAAAAATTC
11163 GAAAAAAAAATTC
1 --AAAAAAAATTC
11176 AAAAAAAATTC
1 AAAAAAAATTC
11187 AAAAAAAA
1 AAAAAAAA
11195 AATTTGTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 19 0.63
13 11 0.37
ACGTcount: A:0.77, C:0.07, G:0.02, T:0.14
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:11197 original size:24 final size:24
Alignment explanation
Indices: 11152--11198 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
11142 AAAAAAAGGA
*
11152 AAAAAAAATTCGAAAAAAAAATTC
1 AAAAAAAATTCAAAAAAAAAATTC
11176 AAAAAAAATTCAAAAAAAAAATT
1 AAAAAAAATTCAAAAAAAAAATT
11199 TGTATTCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.74, C:0.06, G:0.02, T:0.17
Consensus pattern (24 bp):
AAAAAAAATTCAAAAAAAAAATTC
Found at i:12214 original size:17 final size:15
Alignment explanation
Indices: 12194--12232 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
12184 GCGAGCGAGA
12194 AAATGAACATGAAAAAG
1 AAATGAA-A-GAAAAAG
12211 AAATGAAAGAAAAAG
1 AAATGAAAGAAAAAG
12226 AAGATGA
1 AA-ATGA
12233 GTGGGAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.67, C:0.03, G:0.21, T:0.10
Consensus pattern (15 bp):
AAATGAAAGAAAAAG
Found at i:13738 original size:20 final size:20
Alignment explanation
Indices: 13713--13756 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
13703 TGTGGTTCAA
*
13713 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
13733 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
13753 CTCA
1 CTCA
13757 ATTTAACTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.30
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Done.