Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1480
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: 22953
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:289 original size:20 final size:19
Alignment explanation
Indices: 266--319 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
256 GTTCATTCAA
266 CTCAATTTTAGCTCATCGAG
1 CTCAATTTTAGCTCATC-AG
* *
286 CTCACTCTTAGCTCATCAG
1 CTCAATTTTAGCTCATCAG
*
305 CTC-ATTTAAGCTCAT
1 CTCAATTTTAGCTCAT
320 TTGCGTTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
18 9 0.31
19 5 0.17
20 15 0.52
ACGTcount: A:0.24, C:0.30, G:0.11, T:0.35
Consensus pattern (19 bp):
CTCAATTTTAGCTCATCAG
Found at i:2366 original size:27 final size:27
Alignment explanation
Indices: 2335--2512 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
2325 TAAATTGTAC
2335 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
2362 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
2388 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
2416 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
2444 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
2471 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
2498 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
2513 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:2449 original size:82 final size:81
Alignment explanation
Indices: 2336--2491 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
2326 AAATTGTACA
* *
2336 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
2400 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
2417 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
2482 TGCGAGTTGA
65 TGCGAATTGA
2492 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:2503 original size:82 final size:81
Alignment explanation
Indices: 2332--2512 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
2322 GATTAAATTG
* *
2332 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
2397 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
2413 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
2477 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
2495 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
2513 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:10427 original size:14 final size:12
Alignment explanation
Indices: 10407--10469 Score: 65
Period size: 13 Copynumber: 4.9 Consensus size: 12
10397 AGACCGTATG
10407 CAATTTTTTTTT
1 CAATTTTTTTTT
10419 CAAAATTTTTTTTTT
1 C--AA-TTTTTTTTT
10434 CAATTTTTTTTTCT
1 CAA-TTTTTTTT-T
10448 CAATTTTTTTTT
1 CAATTTTTTTTT
*
10460 -GATTTTTTTT
1 CAATTTTTTTT
10470 GAATCTACAA
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
11 9 0.20
12 2 0.04
13 19 0.41
14 6 0.13
15 10 0.22
ACGTcount: A:0.17, C:0.08, G:0.02, T:0.73
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:10430 original size:15 final size:13
Alignment explanation
Indices: 10410--10459 Score: 73
Period size: 14 Copynumber: 3.6 Consensus size: 13
10400 CCGTATGCAA
10410 TTTTTTTTTCAAAAT
1 TTTTTTTTTC--AAT
10425 TTTTTTTTTCAAT
1 TTTTTTTTTCAAT
10438 TTTTTTTTCTCAAT
1 TTTTTTTT-TCAAT
10452 TTTTTTTT
1 TTTTTTTT
10460 GATTTTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
13 11 0.32
14 13 0.38
15 10 0.29
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTCAAT
Found at i:10469 original size:27 final size:27
Alignment explanation
Indices: 10407--10459 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
10397 AGACCGTATG
10407 CAATTTTTTTTTCAAAATTTTTTTTTT
1 CAATTTTTTTTTCAAAATTTTTTTTTT
**
10434 CAATTTTTTTTTCTCAATTTTTTTTT
1 CAATTTTTTTTTCAAAATTTTTTTTT
10460 GATTTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (27 bp):
CAATTTTTTTTTCAAAATTTTTTTTTT
Found at i:13803 original size:20 final size:20
Alignment explanation
Indices: 13757--13803 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
13747 AGCTCGTTTC
*
13757 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
13777 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
13797 CAGCTCA
1 CAGCTCA
13804 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:15236 original size:21 final size:20
Alignment explanation
Indices: 15204--15248 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
15194 GTAATGTAAA
15204 AAAAGTCAAAAAAAAAAATC
1 AAAAGTCAAAAAAAAAAATC
* *
15224 AAAATTCAGAAAAAAAAATTC
1 AAAAGTCA-AAAAAAAAAATC
15245 AAAA
1 AAAA
15249 AAAAAGGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.73, C:0.09, G:0.04, T:0.13
Consensus pattern (20 bp):
AAAAGTCAAAAAAAAAAATC
Found at i:15243 original size:14 final size:13
Alignment explanation
Indices: 15224--15253 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
15214 AAAAAAAATC
15224 AAAATTCAGAAAAA
1 AAAATTCA-AAAAA
15238 AAAATTCAAAAAA
1 AAAATTCAAAAAA
15251 AAA
1 AAA
15254 GGAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.77, C:0.07, G:0.03, T:0.13
Consensus pattern (13 bp):
AAAATTCAAAAAA
Found at i:15279 original size:42 final size:42
Alignment explanation
Indices: 15233--15313 Score: 94
Period size: 42 Copynumber: 1.9 Consensus size: 42
15223 CAAAATTCAG
*
15233 AAAAA-AAAATTCAAAAAAAAAGGAAA-AAAAAAGAAGTGACAA
1 AAAAATAAAATT-AAAAAAAAA-GAAAGAAAAAAAAAGTGACAA
** *
15275 AAAAATCGAGTTAAAAAAAAAGAAAGAAAAAAAAAGTGA
1 AAAAATAAAATTAAAAAAAAAGAAAGAAAAAAAAAGTGA
15314 AAAGTCTTGC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
41 4 0.12
42 26 0.79
43 3 0.09
ACGTcount: A:0.74, C:0.04, G:0.14, T:0.09
Consensus pattern (42 bp):
AAAAATAAAATTAAAAAAAAAGAAAGAAAAAAAAAGTGACAA
Found at i:16350 original size:21 final size:21
Alignment explanation
Indices: 16315--16355 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16305 AAAGAGATTG
** *
16315 AAAAAGAAATTGAAAGAAAAC
1 AAAAAGAAAACGAAAAAAAAC
16336 AAAAAGAAAACGAAAAAAAA
1 AAAAAGAAAACGAAAAAAAA
16356 AAGAAATAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.78, C:0.05, G:0.12, T:0.05
Consensus pattern (21 bp):
AAAAAGAAAACGAAAAAAAAC
Found at i:16602 original size:48 final size:47
Alignment explanation
Indices: 16523--16628 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
16513 GAGTGTCATG
*
16523 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
16571 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
16619 GAAAAAGAAA
1 GAAAAAGAAA
16629 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:18342 original size:20 final size:20
Alignment explanation
Indices: 18296--18342 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
18286 AGCTCGTTTC
*
18296 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
18316 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
18336 CAGCTCA
1 CAGCTCA
18343 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
Done.