Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold606
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: 26085
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Found at i:3359 original size:14 final size:14
Alignment explanation
Indices: 3337--3381 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
3327 TTAAAGAAGC
3337 AACTCATTAAATTA
1 AACTCATTAAATTA
*
3351 AATTCATTAAA-TA
1 AACTCATTAAATTA
*
3364 AACTCATTTAATTA
1 AACTCATTAAATTA
3378 AACT
1 AACT
3382 AAGATGAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:4620 original size:30 final size:30
Alignment explanation
Indices: 4525--4621 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
4515 AGCTCACTCC
* * *
4525 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGGTAAAGCT
* * * **
4555 TAGCTCAACTTCAGCTTAGGA-GTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGGTAAAG-CT
*
4585 CAGCTCAACTTTAGCTCACGAGGTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGGTAAAGCT
4615 TAGCTCA
1 TAGCTCA
4622 TTTTAGTTTA
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 39 0.80
31 8 0.16
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGGTAAAGCT
Found at i:6353 original size:10 final size:10
Alignment explanation
Indices: 6335--6364 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
6325 GTTATACAAG
6335 TCAAAAAAAT
1 TCAAAAAAAT
*
6345 TCGAAAAAAT
1 TCAAAAAAAT
6355 TCAAAAAAAT
1 TCAAAAAAAT
6365 AATTCGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.67, C:0.10, G:0.03, T:0.20
Consensus pattern (10 bp):
TCAAAAAAAT
Found at i:7314 original size:9 final size:10
Alignment explanation
Indices: 7307--7363 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
7297 AAGAGAAAAC
7307 AAAGAAAAGA
1 AAAGAAAAGA
7317 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
7329 AAAGAAGA-A
1 AAAGAAAAGA
7338 AAAGAAAATGA
1 AAAGAAAA-GA
7349 AATA-AAAAGA
1 AA-AGAAAAGA
7359 AAAGA
1 AAAGA
7364 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:7330 original size:21 final size:20
Alignment explanation
Indices: 7296--7363 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
7286 ACATTCTTAT
7296 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
7317 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
7338 AAAGAAAATGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
7359 AAAGA
1 AAAGA
7364 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:7331 original size:6 final size:5
Alignment explanation
Indices: 7307--7363 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
7297 AAGAGAAAAC
*
7307 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
7354 AAAGA AAAGA
1 AAAGA AAAGA
7364 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:7338 original size:15 final size:14
Alignment explanation
Indices: 7307--7363 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
7297 AAGAGAAAAC
7307 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
7323 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
7338 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
7354 AAAGAAAAGA
1 AAAGAAAAGA
7364 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:7428 original size:12 final size:12
Alignment explanation
Indices: 7411--7440 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
7401 TTGAGAGAAC
7411 TTGAAAAAGCCT
1 TTGAAAAAGCCT
7423 TTG-AAAAGCCT
1 TTGAAAAAGCCT
7434 TTGAAAA
1 TTGAAAA
7441 GCAAAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:7431 original size:11 final size:11
Alignment explanation
Indices: 7415--7442 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
7405 GAGAACTTGA
7415 AAAAGCCTTTG
1 AAAAGCCTTTG
7426 AAAAGCCTTTG
1 AAAAGCCTTTG
7437 AAAAGC
1 AAAAGC
7443 AAAAAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (11 bp):
AAAAGCCTTTG
Found at i:7458 original size:12 final size:12
Alignment explanation
Indices: 7443--7467 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7433 TTTGAAAAGC
7443 AAAAAGAAAATG
1 AAAAAGAAAATG
7455 AAAAAGAAAATG
1 AAAAAGAAAATG
7467 A
1 A
7468 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:7464 original size:18 final size:18
Alignment explanation
Indices: 7437--7492 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
7427 AAAGCCTTTG
7437 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
7456 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
7474 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
7491 AA
1 AA
7493 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:7477 original size:30 final size:31
Alignment explanation
Indices: 7443--7524 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
7433 TTTGAAAAGC
*
7443 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
7473 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
7503 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
7525 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:10172 original size:9 final size:9
Alignment explanation
Indices: 10158--10191 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
10148 CAAAAAAATC
10158 AGTCAAAAA
1 AGTCAAAAA
10167 AGTCAAAAA
1 AGTCAAAAA
*
10176 AATCAAAAA
1 AGTCAAAAA
*
10185 AGACAAA
1 AGTCAAA
10192 TTCAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.71, C:0.12, G:0.09, T:0.09
Consensus pattern (9 bp):
AGTCAAAAA
Found at i:21719 original size:24 final size:25
Alignment explanation
Indices: 21666--21719 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
21656 AACAAATTCT
* *
21666 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
21691 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
21714 TTTTTT
1 TTTTTT
21720 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:23206 original size:13 final size:13
Alignment explanation
Indices: 23188--23238 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 13
23178 CTAGACCGTA
23188 TGCAATTTTTTTT
1 TGCAATTTTTTTT
23201 TGCAA-TTTTTTT
1 TGCAATTTTTTTT
*
23213 T-C-CTTTTTTTT
1 TGCAATTTTTTTT
*
23224 TTCAGATTTTTTTT
1 TGCA-ATTTTTTTT
23238 T
1 T
23239 TCAAAACTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
11 9 0.28
12 9 0.28
13 5 0.16
14 9 0.28
ACGTcount: A:0.12, C:0.10, G:0.06, T:0.73
Consensus pattern (13 bp):
TGCAATTTTTTTT
Found at i:23233 original size:14 final size:13
Alignment explanation
Indices: 23193--23267 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 13
23183 CCGTATGCAA
23193 TTTTTTTTTGCAA-
1 TTTTTTTTT-CAAC
23206 -TTTTTTTTC--C
1 TTTTTTTTTCAAC
*
23216 TTTTTTTTTTCAGAT
1 -TTTTTTTTTCA-AC
23231 TTTTTTTTTCAAAAC
1 TTTTTTTTTC--AAC
23246 TTTTTTTTT-AAC
1 TTTTTTTTTCAAC
23258 TTTTTTTTTC
1 TTTTTTTTTC
23268 GAAGCTACGA
Statistics
Matches: 51, Mismatches: 2, Indels: 18
0.72 0.03 0.25
Matches are distributed among these distances:
11 1 0.02
12 29 0.57
14 10 0.20
15 10 0.20
16 1 0.02
ACGTcount: A:0.13, C:0.11, G:0.03, T:0.73
Consensus pattern (13 bp):
TTTTTTTTTCAAC
Done.