Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3692
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: 39283
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:15564 original size:20 final size:20
Alignment explanation
Indices: 15518--15564 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
15508 AGCTCGTTTC
*
15518 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
15538 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
15558 CAGCTCA
1 CAGCTCA
15565 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:16506 original size:370 final size:370
Alignment explanation
Indices: 15825--16541 Score: 1407
Period size: 370 Copynumber: 1.9 Consensus size: 370
15815 GTATGCTGCT
15825 AATTTAATGTGTTTGAAATGCATTTAACTTGCTGATTTAATTTGCTGCAGGTTCATGAACGGATT
1 AATTTAATGTGTTTGAAATGCATTTAACTTGCTGATTTAATTTGCTGCAGGTTCATGAACGGATT
15890 GGTGCAATGTATGGGAGTGTGCATGCACAATTGAGGTTCAATGGATGGCATTTAAAGGAGCACAT
66 GGTGCAATGTATGGGAGTGTGCATGCACAATTGAGGTTCAATGGATGGCATTTAAAGGAGCACAT
* *
15955 GCATTTGGGACGTTCATGCAAGAGGGAGTTTCTGAAAGTTCATGTATTTGAAGATTTATGGATCA
131 GCATTTGGGACGTTCATGCAAGAGGGAGTTGCTGAAAGTTCATGTATTTGAAGATTCATGGATCA
16020 TATTTATGGCGGAAAATACATGGGACGTTTCATGCATGATTCATGCATTTTCAAGATGACCATTC
196 TATTTATGGCGGAAAATACATGGGACGTTTCATGCATGATTCATGCATTTTCAAGATGACCATTC
16085 AAGTATTTTAGGCACATTAATGCCTCATTCAGCCAAGGGAGATGTAGGATCATTAAAGAGCTGCA
261 AAGTATTTTAGGCACATTAATGCCTCATTCAGCCAAGGGAGATGTAGGATCATTAAAGAGCTGCA
16150 CATTCATGGAATTATGGAGATTGAAATTGTTAATATGTATGGCCA
326 CATTCATGGAATTATGGAGATTGAAATTGTTAATATGTATGGCCA
16195 AATTTAATGTGTTTGAAATGCATTTAACTTGCTGATTTAATTTGCTGCAGGTTCATGAACGGATT
1 AATTTAATGTGTTTGAAATGCATTTAACTTGCTGATTTAATTTGCTGCAGGTTCATGAACGGATT
16260 GGTGCAATGTATGGGAGTGTGCATGCACAATTGAGGTTCAATGGATGGCATTTAAAGGAGCACAT
66 GGTGCAATGTATGGGAGTGTGCATGCACAATTGAGGTTCAATGGATGGCATTTAAAGGAGCACAT
16325 GCATTTGGGACGTTCATGCAAGAGGGAGTTGCTGAAAGTTCATGTATTTGAAGATTCATGGATCA
131 GCATTTGGGACGTTCATGCAAGAGGGAGTTGCTGAAAGTTCATGTATTTGAAGATTCATGGATCA
*
16390 TATTTATGGGGGAAAATACATGGGACGTTTCATGCATGATTCATGCATTTTCAAGATGACCATTC
196 TATTTATGGCGGAAAATACATGGGACGTTTCATGCATGATTCATGCATTTTCAAGATGACCATTC
16455 AAGTATTTTAGGCACATTAATGCCTCATTCAGCCAAGGGAGATGTAGGATCATTAAAGAGCTGCA
261 AAGTATTTTAGGCACATTAATGCCTCATTCAGCCAAGGGAGATGTAGGATCATTAAAGAGCTGCA
16520 CATTCATGGAATTATGGAGATT
326 CATTCATGGAATTATGGAGATT
16542 CTTCAAGGCT
Statistics
Matches: 344, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
370 344 1.00
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (370 bp):
AATTTAATGTGTTTGAAATGCATTTAACTTGCTGATTTAATTTGCTGCAGGTTCATGAACGGATT
GGTGCAATGTATGGGAGTGTGCATGCACAATTGAGGTTCAATGGATGGCATTTAAAGGAGCACAT
GCATTTGGGACGTTCATGCAAGAGGGAGTTGCTGAAAGTTCATGTATTTGAAGATTCATGGATCA
TATTTATGGCGGAAAATACATGGGACGTTTCATGCATGATTCATGCATTTTCAAGATGACCATTC
AAGTATTTTAGGCACATTAATGCCTCATTCAGCCAAGGGAGATGTAGGATCATTAAAGAGCTGCA
CATTCATGGAATTATGGAGATTGAAATTGTTAATATGTATGGCCA
Found at i:17466 original size:10 final size:11
Alignment explanation
Indices: 17427--17466 Score: 55
Period size: 10 Copynumber: 3.6 Consensus size: 11
17417 TTGGAGTAAC
17427 AAAAAAATCAA
1 AAAAAAATCAA
*
17438 AAAAAATTCGAA
1 AAAAAAATC-AA
17450 AAAAAAAT-AA
1 AAAAAAATCAA
17460 AAAAAAA
1 AAAAAAA
17467 GAAGTGACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 9 0.35
11 8 0.31
12 9 0.35
ACGTcount: A:0.82, C:0.05, G:0.03, T:0.10
Consensus pattern (11 bp):
AAAAAAATCAA
Found at i:18599 original size:48 final size:47
Alignment explanation
Indices: 18520--18625 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
18510 GAGTGTCATG
*
18520 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
18568 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
18616 GAAAAAGAAA
1 GAAAAAGAAA
18626 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:22058 original size:12 final size:12
Alignment explanation
Indices: 22037--22199 Score: 52
Period size: 12 Copynumber: 13.4 Consensus size: 12
22027 AGAAAAGGAG
*
22037 AAAGAGATTGAA
1 AAAGAAATTGAA
22049 AAAGAAATTG--
1 AAAGAAATTGAA
**
22059 AAAGAAA-ACAA
1 AAAGAAATTGAA
*
22070 AAAGAAAATGAA
1 AAAGAAATTGAA
*
22082 AAAGAAA-AGAA
1 AAAGAAATTGAA
** *
22093 ATTGCAAA-AGAA
1 AAAG-AAATTGAA
**
22105 AAAGAAATCAAA
1 AAAGAAATTGAA
22117 AAAGTGAAA--GAA
1 AAA--GAAATTGAA
*
22129 AAAGAAAATGAAGA
1 AAAGAAATTG-A-A
22143 AAAGAAAATTGAA
1 AAAG-AAATTGAA
**
22156 AAAGAAAAAGCGAAA
1 AAAG--AAATTG-AA
*
22171 AAAGAATTTGAA
1 AAAGAAATTGAA
**
22183 AAAGAGTTTGAA
1 AAAGAAATTGAA
22195 AAAGA
1 AAAGA
22200 GAAGAGTGAA
Statistics
Matches: 117, Mismatches: 20, Indels: 28
0.71 0.12 0.17
Matches are distributed among these distances:
10 11 0.09
11 15 0.13
12 56 0.48
13 9 0.08
14 15 0.13
15 11 0.09
ACGTcount: A:0.68, C:0.02, G:0.18, T:0.11
Consensus pattern (12 bp):
AAAGAAATTGAA
Found at i:22082 original size:6 final size:6
Alignment explanation
Indices: 22059--22165 Score: 67
Period size: 6 Copynumber: 17.7 Consensus size: 6
22049 AAAGAAATTG
* * ** *
22059 AAAG-A AAACAA AAAGAA AATGAA AAAG-A AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * *
22105 AAAGAA ATCA-AA AAAGTG AAAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
22156 AAAGAA AAAG
1 AAAGAA AAAG
22166 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 20, Indels: 13
0.69 0.19 0.12
Matches are distributed among these distances:
5 9 0.12
6 54 0.72
7 8 0.11
8 4 0.05
ACGTcount: A:0.73, C:0.03, G:0.17, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:22089 original size:18 final size:18
Alignment explanation
Indices: 22063--22165 Score: 84
Period size: 18 Copynumber: 5.6 Consensus size: 18
22053 AAATTGAAAG
*
22063 AAAACAAAAAGAAAATGA
1 AAAAGAAAAAGAAAATGA
* *
22081 AAAAG-AAAAGAAATTGC
1 AAAAGAAAAAGAAAATGA
*
22098 AAAAGAAAAAG-AAATCAA
1 AAAAGAAAAAGAAAAT-GA
** *
22116 AAAAGTGAAAGAAAAAGA
1 AAAAGAAAAAGAAAATGA
*
22134 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-TGA
22155 AAAAGAAAAAG
1 AAAAGAAAAAG
22166 CGAAAAAAGA
Statistics
Matches: 64, Mismatches: 15, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
17 18 0.28
18 23 0.36
19 8 0.12
20 9 0.14
21 6 0.09
ACGTcount: A:0.73, C:0.03, G:0.17, T:0.08
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:22145 original size:14 final size:13
Alignment explanation
Indices: 22126--22163 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
22116 AAAAGTGAAA
22126 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
22138 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
22153 GAAAAAGAAAA
1 GAAAAAGAAAA
22164 AGCGAAAAAA
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:22200 original size:12 final size:12
Alignment explanation
Indices: 22169--22200 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
22159 GAAAAAGCGA
*
22169 AAAAAGAATTTG
1 AAAAAGAGTTTG
22181 AAAAAGAGTTTG
1 AAAAAGAGTTTG
22193 AAAAAGAG
1 AAAAAGAG
22201 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:26351 original size:19 final size:20
Alignment explanation
Indices: 26306--26351 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
26296 AGCTCGTTTC
*
26306 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
26326 CAACTCA-TCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
26345 CAGCTCA
1 CAGCTCA
26352 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.30, C:0.35, G:0.13, T:0.22
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:27888 original size:11 final size:11
Alignment explanation
Indices: 27872--27926 Score: 69
Period size: 11 Copynumber: 5.2 Consensus size: 11
27862 AGTAGATTCG
27872 TGAAAAAAAAT
1 TGAAAAAAAAT
27883 TGAAAAAAAA-
1 TGAAAAAAAAT
*
27893 T-CAAAAAAAT
1 TGAAAAAAAAT
**
27903 CAAAAAAAAAT
1 TGAAAAAAAAT
27914 TGAAAAAAAAT
1 TGAAAAAAAAT
27925 TG
1 TG
27927 TATACGGTCT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 7 0.19
10 1 0.03
11 29 0.78
ACGTcount: A:0.73, C:0.04, G:0.07, T:0.16
Consensus pattern (11 bp):
TGAAAAAAAAT
Found at i:27898 original size:9 final size:9
Alignment explanation
Indices: 27886--27910 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
27876 AAAAAATTGA
27886 AAAAAAATC
1 AAAAAAATC
27895 AAAAAAATC
1 AAAAAAATC
27904 AAAAAAA
1 AAAAAAA
27911 AATTGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAATC
Found at i:27900 original size:20 final size:20
Alignment explanation
Indices: 27875--27913 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
27865 AGATTCGTGA
**
27875 AAAAAAATTGAAAAAAAATC
1 AAAAAAATCAAAAAAAAATC
27895 AAAAAAATCAAAAAAAAAT
1 AAAAAAATCAAAAAAAAAT
27914 TGAAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.79, C:0.05, G:0.03, T:0.13
Consensus pattern (20 bp):
AAAAAAATCAAAAAAAAATC
Found at i:30156 original size:17 final size:17
Alignment explanation
Indices: 30136--30191 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
30126 GCGAAAATAC
*
30136 AAAAGAAAAGAAAAATG
1 AAAAAAAAAGAAAAATG
* *
30153 AAAAAAAGAAAGAAAATTC
1 -AAAAAA-AAAGAAAAATG
30172 AAAAAAAAAG-AAAATG
1 AAAAAAAAAGAAAAATG
30188 AAAA
1 AAAA
30192 GAAAGCGAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
16 8 0.25
17 4 0.12
18 11 0.34
19 9 0.28
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (17 bp):
AAAAAAAAAGAAAAATG
Found at i:30161 original size:20 final size:19
Alignment explanation
Indices: 30136--30178 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
30126 GCGAAAATAC
*
30136 AAAAGAAAAGAAAAATGAAA
1 AAAAG-AAAGAAAAATCAAA
*
30156 AAAAGAAAGAAAATTCAAA
1 AAAAGAAAGAAAAATCAAA
30175 AAAA
1 AAAA
30179 AAGAAAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (19 bp):
AAAAGAAAGAAAAATCAAA
Found at i:30204 original size:36 final size:36
Alignment explanation
Indices: 30128--30196 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
30118 AGAAAAGAGC
*
30128 GAAAATACAAAAGAAAAGAAAAATGAAAAAAAGAAA
1 GAAAATACAAAAAAAAAGAAAAATGAAAAAAAGAAA
*
30164 GAAAATTCAAAAAAAAAG-AAAATGAAAAGAAAG
1 GAAAATACAAAAAAAAAGAAAAATGAAAA-AAAG
30197 CGAGAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 10 0.33
36 20 0.67
ACGTcount: A:0.75, C:0.03, G:0.14, T:0.07
Consensus pattern (36 bp):
GAAAATACAAAAAAAAAGAAAAATGAAAAAAAGAAA
Found at i:31529 original size:18 final size:20
Alignment explanation
Indices: 31498--31539 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
31488 AAAATCAGTC
*
31498 AAAAAAGTCAAAA-T-AATA
1 AAAAAAGACAAAATTCAATA
*
31516 AAAAAAGACGAAATTCAATA
1 AAAAAAGACAAAATTCAATA
31536 AAAA
1 AAAA
31540 TTTAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 11 0.55
19 1 0.05
20 8 0.40
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.14
Consensus pattern (20 bp):
AAAAAAGACAAAATTCAATA
Done.