Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2136
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: 58544
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:216 original size:12 final size:11
Alignment explanation
Indices: 182--213 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
172 ATGGAAACCA
182 AATTTTTTTTG
1 AATTTTTTTTG
193 AATTTTTTTTG
1 AATTTTTTTTG
204 AATTTTTTTT
1 AATTTTTTTT
214 TGAGAAACTA
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:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (11 bp):
AATTTTTTTTG
Found at i:1231 original size:21 final size:23
Alignment explanation
Indices: 1186--1232 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1176 TCACCTGCAA
* *
1186 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
1209 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
1230 TAA
1 TAA
1233 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:10567 original size:10 final size:10
Alignment explanation
Indices: 10551--10608 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
10541 CAACTCCGAC
10551 CAGCTCAATT
1 CAGCTCAATT
* *
10561 GAGCTCATTT
1 CAGCTCAATT
10571 CAGCTCAA-T
1 CAGCTCAATT
10580 CGAGCTCAATT
1 C-AGCTCAATT
*
10591 TAGCTACAATT
1 CAGCT-CAATT
10602 CAGCTCA
1 CAGCTCA
10609 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:10574 original size:20 final size:20
Alignment explanation
Indices: 10551--10611 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
10541 CAACTCCGAC
10551 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
10571 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
10592 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
10612 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:15917 original size:22 final size:22
Alignment explanation
Indices: 15887--15930 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
15877 TTTGGTATTT
15887 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
15909 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
15931 TGGTTCAAAA
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:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:18583 original size:22 final size:22
Alignment explanation
Indices: 18555--18598 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
18545 TTTTGAACCA
18555 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
18577 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
18599 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:26881 original size:12 final size:12
Alignment explanation
Indices: 26861--26896 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
26851 AAACCGTATG
26861 CAATTTTTTTTT
1 CAATTTTTTTTT
26873 -AATTTTTTTTT
1 CAATTTTTTTTT
26884 CAATTTTTTTTT
1 CAATTTTTTTTT
26896 C
1 C
26897 GAACTCTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.48
12 12 0.52
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:27242 original size:22 final size:22
Alignment explanation
Indices: 27212--27255 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
27202 TTTGGTATTT
27212 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
27234 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
27256 TGGTTCAAAA
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:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:31496 original size:18 final size:18
Alignment explanation
Indices: 31475--31509 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
31465 TTTTTCTTTT
31475 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
31493 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
31510 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:38253 original size:6 final size:6
Alignment explanation
Indices: 38230--38319 Score: 67
Period size: 6 Copynumber: 14.7 Consensus size: 6
38220 AAAGAAATTG
* * * **
38230 AAAG-A AAACAA AAAGAA AATGAA AAAGAA AAAGAA ATCA-AA AAAGTG
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA A-AAGAA AAAGAA
* *
38277 AAAGAA AAAGAA AATGAAGA AAAGAA AATTGAA AAAGAA AAAG
1 AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA AAAGAA AAAG
38320 CGAAAAAAGA
Statistics
Matches: 65, Mismatches: 14, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
5 4 0.06
6 49 0.75
7 8 0.12
8 4 0.06
ACGTcount: A:0.74, C:0.02, G:0.17, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:38260 original size:18 final size:18
Alignment explanation
Indices: 38234--38319 Score: 75
Period size: 18 Copynumber: 4.6 Consensus size: 18
38224 AAATTGAAAG
*
38234 AAAACAAAAAGAAAATGA
1 AAAAGAAAAAGAAAATGA
*
38252 AAAAGAAAAAG-AAATCAA
1 AAAAGAAAAAGAAAAT-GA
** *
38270 AAAAGTGAAAGAAAAAGA
1 AAAAGAAAAAGAAAATGA
*
38288 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-TGA
38309 AAAAGAAAAAG
1 AAAAGAAAAAG
38320 CGAAAAAAGA
Statistics
Matches: 52, Mismatches: 11, Indels: 9
0.72 0.15 0.12
Matches are distributed among these distances:
17 4 0.08
18 25 0.48
19 8 0.15
20 9 0.17
21 6 0.12
ACGTcount: A:0.74, C:0.02, G:0.16, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:38354 original size:12 final size:12
Alignment explanation
Indices: 38323--38354 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
38313 GAAAAAGCGA
*
38323 AAAAAGAATTTG
1 AAAAAGAGTTTG
38335 AAAAAGAGTTTG
1 AAAAAGAGTTTG
38347 AAAAAGAG
1 AAAAAGAG
38355 AAGAGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (12 bp):
AAAAAGAGTTTG
Found at i:43541 original size:23 final size:23
Alignment explanation
Indices: 43515--43562 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
43505 AATCAGCTTC
43515 TTTAATAC-ACCTATTAAGACACA
1 TTTAA-ACGACCTATTAAGACACA
* *
43538 TTTAAACGACTTATTAGGACACA
1 TTTAAACGACCTATTAAGACACA
43561 TT
1 TT
43563 AATCATACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (23 bp):
TTTAAACGACCTATTAAGACACA
Found at i:50988 original size:19 final size:18
Alignment explanation
Indices: 50952--50991 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
50942 CTTCCACTCG
*
50952 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
50970 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
50989 TTT
1 TTT
50992 GTTTGTGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:52061 original size:14 final size:13
Alignment explanation
Indices: 52042--52087 Score: 83
Period size: 13 Copynumber: 3.5 Consensus size: 13
52032 TAGCTTCTTC
52042 TTTTTTCACGATAT
1 TTTTTTCACGA-AT
52056 TTTTTTCACGAAT
1 TTTTTTCACGAAT
52069 TTTTTTCACGAAT
1 TTTTTTCACGAAT
52082 TTTTTT
1 TTTTTT
52088 TTTCAACTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 21 0.66
14 11 0.34
ACGTcount: A:0.20, C:0.13, G:0.07, T:0.61
Consensus pattern (13 bp):
TTTTTTCACGAAT
Found at i:52088 original size:14 final size:14
Alignment explanation
Indices: 52042--52088 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
52032 TAGCTTCTTC
52042 TTTTTTCACG-ATAT
1 TTTTTTCACGAAT-T
52056 TTTTTTCACGAA-T
1 TTTTTTCACGAATT
52069 TTTTTTCACGAATT
1 TTTTTTCACGAATT
52083 TTTTTT
1 TTTTTT
52089 TTCAACTTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.42
14 17 0.55
15 1 0.03
ACGTcount: A:0.19, C:0.13, G:0.06, T:0.62
Consensus pattern (14 bp):
TTTTTTCACGAATT
Found at i:52152 original size:12 final size:11
Alignment explanation
Indices: 52132--52180 Score: 62
Period size: 12 Copynumber: 4.2 Consensus size: 11
52122 TGGGAAACCA
52132 AATTTTTTTTG
1 AATTTTTTTTG
52143 AATCTTTTTTTG
1 AAT-TTTTTTTG
52155 AATTTTTTTTCG
1 AATTTTTTTT-G
*
52167 AAATTCTTTTTG
1 -AATTTTTTTTG
52179 AA
1 AA
52181 AACTACTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
11 12 0.35
12 13 0.38
13 9 0.26
ACGTcount: A:0.22, C:0.06, G:0.08, T:0.63
Consensus pattern (11 bp):
AATTTTTTTTG
Found at i:52176 original size:24 final size:23
Alignment explanation
Indices: 52132--52180 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
52122 TGGGAAACCA
*
52132 AATTTTTTTTGAATCTTTTTTTG
1 AATTTTTTTTGAATCTCTTTTTG
52155 AATTTTTTTTCGAAAT-TCTTTTTG
1 AATTTTTTTT-G-AATCTCTTTTTG
52179 AA
1 AA
52181 AACTACTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 10 0.43
24 10 0.43
25 3 0.13
ACGTcount: A:0.22, C:0.06, G:0.08, T:0.63
Consensus pattern (23 bp):
AATTTTTTTTGAATCTCTTTTTG
Found at i:56422 original size:14 final size:15
Alignment explanation
Indices: 56403--56431 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
56393 GTTGTAAAAG
56403 TTTA-TTTTTATTTA
1 TTTATTTTTTATTTA
56417 TTTATTTTTTATTTA
1 TTTATTTTTTATTTA
56432 CTTAGTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTATTTTTTATTTA
Done.