Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3279
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: 65670
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:2451 original size:11 final size:11
Alignment explanation
Indices: 2435--2466 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
2425 AAACCAAATT
2435 TTTTTTTTTGA
1 TTTTTTTTTGA
2446 TTTTTTTTTGA
1 TTTTTTTTTGA
2457 TTTTCTTTTT
1 TTTT-TTTTT
2467 CGAAGGAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.84
Consensus pattern (11 bp):
TTTTTTTTTGA
Found at i:11461 original size:10 final size:11
Alignment explanation
Indices: 11445--11477 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
11435 TAGTAGTTTC
11445 TTCAAAAAAAA
1 TTCAAAAAAAA
11456 -TCAAAAAAAAA
1 TTC-AAAAAAAA
11467 TTCAAAAAAAA
1 TTCAAAAAAAA
11478 AATTTGGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.10
11 16 0.80
12 2 0.10
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:11465 original size:12 final size:12
Alignment explanation
Indices: 11448--11480 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
11438 TAGTTTCTTC
11448 AAAAAAAATCAA
1 AAAAAAAATCAA
*
11460 AAAAAAATTCAA
1 AAAAAAAATCAA
11472 AAAAAAAAT
1 AAAAAAAAT
11481 TTGGTTTCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (12 bp):
AAAAAAAATCAA
Found at i:15824 original size:27 final size:27
Alignment explanation
Indices: 15792--15843 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
15782 ACAAGTGAGG
15792 AAAAAGAAAAAGAGAATGAAAAAGAGC
1 AAAAAGAAAAAGAGAATGAAAAAGAGC
* ** *
15819 AAAAAGAGATTGAGAGTGAAAAAGA
1 AAAAAGAAAAAGAGAATGAAAAAGA
15844 AATTGAAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.25, T:0.08
Consensus pattern (27 bp):
AAAAAGAAAAAGAGAATGAAAAAGAGC
Found at i:19927 original size:13 final size:13
Alignment explanation
Indices: 19909--19940 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
19899 AAAATTTGAA
19909 TTTTTTTGAATTT
1 TTTTTTTGAATTT
19922 TTTTTTTGAATTT
1 TTTTTTTGAATTT
19935 TTTTTT
1 TTTTTT
19941 CAAATTTCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.81
Consensus pattern (13 bp):
TTTTTTTGAATTT
Found at i:28391 original size:12 final size:11
Alignment explanation
Indices: 28366--28390 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28356 AAAAGAGAAG
28366 AAATTCAAAAA
1 AAATTCAAAAA
28377 AAATTCAAAAA
1 AAATTCAAAAA
28388 AAA
1 AAA
28391 AAAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:28427 original size:1 final size:1
Alignment explanation
Indices: 28383--28413 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
28373 AAAAAAATTC
*
28383 AAAAAAAAAAAAAAAAAAAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
28414 GGTGAGCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:28434 original size:24 final size:23
Alignment explanation
Indices: 28398--28442 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
28388 AAAAAAAAAA
*
28398 AAAAAAAGAAAAAAAAGGTGAGC
1 AAAAAAAGAAAAAAAAAGTGAGC
*
28421 AAAAAAAGTTAAAAAAAAGTGA
1 AAAAAAAG-AAAAAAAAAGTGA
28443 AAAGTCTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.71, C:0.02, G:0.18, T:0.09
Consensus pattern (23 bp):
AAAAAAAGAAAAAAAAAGTGAGC
Found at i:29476 original size:6 final size:6
Alignment explanation
Indices: 29444--29550 Score: 67
Period size: 6 Copynumber: 17.7 Consensus size: 6
29434 AAAGAAATTG
* * ** *
29444 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* * * * *
29491 AAAGAA ATCA-AA AAAG-T GAAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
29541 AAAGAA AAAG
1 AAAGAA AAAG
29551 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 20, Indels: 13
0.69 0.19 0.12
Matches are distributed among these distances:
5 7 0.09
6 56 0.75
7 8 0.11
8 4 0.05
ACGTcount: A:0.73, C:0.04, G:0.17, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:29527 original size:15 final size:15
Alignment explanation
Indices: 29502--29548 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
29492 AAGAAATCAA
29502 AAAAGTGAAGAAAAAG
1 AAAA-TGAAGAAAAAG
29518 AAAATGAAG-AAAAG
1 AAAATGAAGAAAAAG
*
29532 AAAAT--TGAAAAAG
1 AAAATGAAGAAAAAG
29545 AAAA
1 AAAA
29549 AGCGAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 1 0.03
13 9 0.31
14 10 0.34
15 5 0.17
16 4 0.14
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (15 bp):
AAAATGAAGAAAAAG
Found at i:29549 original size:14 final size:13
Alignment explanation
Indices: 29430--29549 Score: 52
Period size: 13 Copynumber: 9.0 Consensus size: 13
29420 AGAAAGAGAT
*
29430 TGAAAAAG-AAAT
1 TGAAAAAGAAAAA
*
29442 TGAAAGAAAACAAAA
1 TGAAA-AAGA-AAAA
* *
29457 AGAAAACGAAAAA
1 TGAAAAAGAAAAA
*
29470 -GAAAAAG-AAAT
1 TGAAAAAGAAAAA
*
29481 TGCAAAAGAAAAA
1 TGAAAAAGAAAAA
*
29494 -GAAATCAA-AAAAG
1 TGAAA--AAGAAAAA
*
29507 TGAAGAAAAAGAAAA
1 TGAA-AAAGA-AAAA
*
29522 TGAAGAAAAGAAAAT
1 TG-A-AAAAGAAAAA
29537 TGAAAAAGAAAAA
1 TGAAAAAGAAAAA
29550 GCGAAAAAAG
Statistics
Matches: 80, Mismatches: 15, Indels: 25
0.67 0.12 0.21
Matches are distributed among these distances:
11 3 0.04
12 20 0.25
13 24 0.30
14 9 0.11
15 18 0.22
16 5 0.06
17 1 0.01
ACGTcount: A:0.72, C:0.03, G:0.17, T:0.08
Consensus pattern (13 bp):
TGAAAAAGAAAAA
Found at i:29569 original size:27 final size:27
Alignment explanation
Indices: 29428--29550 Score: 78
Period size: 27 Copynumber: 4.6 Consensus size: 27
29418 GGAGAAAGAG
** *
29428 ATTGAAAAAGAAATTGAAAGAAAACAAA
1 ATTGAAAAAGAAAAAG-AAGAAAAGAAA
* *
29456 A-AGAAAACGAAAAAG-A-AAAAG-AA
1 ATTGAAAAAGAAAAAGAAGAAAAGAAA
*
29479 ATTGCAAAAGAAAAAGAA-ATCAAA-AAA
1 ATTGAAAAAGAAAAAGAAGA--AAAGAAA
* * *
29506 GTGAAGAAAAAGAAAATGAAGAAAAGAAA
1 AT--TGAAAAAGAAAAAGAAGAAAAGAAA
29535 ATTGAAAAAGAAAAAG
1 ATTGAAAAAGAAAAAG
29551 CGAAAAAAGA
Statistics
Matches: 71, Mismatches: 15, Indels: 19
0.68 0.14 0.18
Matches are distributed among these distances:
23 3 0.04
24 15 0.21
25 3 0.04
27 28 0.39
28 4 0.06
29 17 0.24
30 1 0.01
ACGTcount: A:0.71, C:0.03, G:0.17, T:0.09
Consensus pattern (27 bp):
ATTGAAAAAGAAAAAGAAGAAAAGAAA
Found at i:33022 original size:20 final size:20
Alignment explanation
Indices: 32999--33052 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
32989 AGTTTTTCCC
32999 AGCTCTATTTAGCTCACATG
1 AGCTCTATTTAGCTCACATG
***
33019 AGCT-TAATTTAGCTCGTTTG
1 AGCTCT-ATTTAGCTCACATG
*
33039 AGCTCAATTTAGCT
1 AGCTCTATTTAGCT
33053 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
AGCTCTATTTAGCTCACATG
Found at i:33043 original size:30 final size:30
Alignment explanation
Indices: 33009--33072 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 30
32999 AGCTCTATTT
33009 AGCTCACA-TGAGCTTAATTTAGCTCGTTTG
1 AGCTCA-ATTGAGCTTAATTTAGCTCGTTTG
* *
33039 AGCTCAATTTAGCTTACTTTAGCTCGTTTG
1 AGCTCAATTGAGCTTAATTTAGCTCGTTTG
33069 AGCT
1 AGCT
33073 TGGCTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 1 0.03
30 30 0.97
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCAATTGAGCTTAATTTAGCTCGTTTG
Found at i:33062 original size:20 final size:20
Alignment explanation
Indices: 32999--33063 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
32989 AGTTTTTCCC
* * * *
32999 AGCTCTATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
33019 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
33038 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
33059 AGCTC
1 AGCTC
33064 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.40
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:34793 original size:21 final size:21
Alignment explanation
Indices: 34769--34809 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
34759 TTAAAACAAG
34769 TGAAGAAAAAG-AAAAAGAGAA
1 TGAA-AAAAAGCAAAAAGAGAA
34790 TGAAAAAAAGCAAAAAGAGA
1 TGAAAAAAAGCAAAAAGAGA
34810 TTGAGAGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.71, C:0.02, G:0.22, T:0.05
Consensus pattern (21 bp):
TGAAAAAAAGCAAAAAGAGAA
Found at i:44056 original size:12 final size:11
Alignment explanation
Indices: 44039--44081 Score: 77
Period size: 11 Copynumber: 3.8 Consensus size: 11
44029 TAGTTTCTTC
44039 AAAAAAATTCGA
1 AAAAAAATTC-A
44051 AAAAAAATTCA
1 AAAAAAATTCA
44062 AAAAAAATTCA
1 AAAAAAATTCA
44073 AAAAAAATT
1 AAAAAAATT
44082 GGTTTCCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 21 0.68
12 10 0.32
ACGTcount: A:0.72, C:0.07, G:0.02, T:0.19
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:44142 original size:17 final size:15
Alignment explanation
Indices: 44118--44158 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
44108 GATATCAAGT
*
44118 TGAAAAAAAATTTTCG
1 TGAAAAAAAA-ATTCG
44134 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
44149 TGAAAAAAAA
1 TGAAAAAAAA
44159 GAAGAAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.61, C:0.05, G:0.12, T:0.22
Consensus pattern (15 bp):
TGAAAAAAAAATTCG
Found at i:49082 original size:20 final size:20
Alignment explanation
Indices: 49059--49112 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
49049 AGTTTTTCCC
*
49059 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
49079 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
49099 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
49113 TACTTTAACT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:55536 original size:15 final size:14
Alignment explanation
Indices: 55500--55554 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 14
55490 TCTATTGATC
55500 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
55514 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
55528 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
*
55543 GAAAGAAAAGAA
1 GAGA-AAAAGAA
55555 TGAGGAGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 16 0.47
15 18 0.53
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:65505 original size:21 final size:23
Alignment explanation
Indices: 65460--65506 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
65450 TCACCTGCAA
* *
65460 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
65483 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
65504 TAA
1 TAA
65507 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
Done.