Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_660 ID=scaffold_660-JGI_221_v2.0
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: 4831
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Found at i:147 original size:87 final size:87
Alignment explanation
Indices: 1--251 Score: 324
Period size: 87 Copynumber: 2.9 Consensus size: 87
*
1 CAACTCCACTACAACCGATGGATACAAGGCTTTGTTTTCAATCTGCTTCGCTGTTAACGCAGGAA
1 CAACTCCACTACAACCGATGGAGACAAGGCTTTGTTTTCAATCTGCTTCGCTGTTAACGCAGGAA
* *
66 TGCCAGATCTGCTATCTTCAAT
66 GGCCAGATCTGCTATCTTCAAC
88 CAACTCCACTACAACCGATGGAGACAAGGCTTTGTTTTCAATCTGCTTCGCTGTTAACGCAGGAA
1 CAACTCCACTACAACCGATGGAGACAAGGCTTTGTTTTCAATCTGCTTCGCTGTTAACGCAGGAA
*
153 GGCCAGATCTGCTATCTTTAAC
66 GGCCAGATCTGCTATCTTCAAC
** ** * * * * * * *
175 CAGTTCCACCGCAACCGATGAAGACAAAGC-TTGTATCTTCGATCTGCTTCACTATCAAGGCAGG
1 CAACTCCACTACAACCGATGGAGACAAGGCTTTGT-T-TTCAATCTGCTTCGCTGTTAACGCAGG
* *
239 ACGGCAAGATCTG
64 AAGGCCAGATCTG
252 TTGTCTTTGA
Statistics
Matches: 145, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
86 4 0.03
87 108 0.74
88 33 0.23
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (87 bp):
CAACTCCACTACAACCGATGGAGACAAGGCTTTGTTTTCAATCTGCTTCGCTGTTAACGCAGGAA
GGCCAGATCTGCTATCTTCAAC
Found at i:2363 original size:6 final size:6
Alignment explanation
Indices: 2352--2395 Score: 70
Period size: 6 Copynumber: 7.0 Consensus size: 6
2342 TGACCTCTCC
2352 TTTTCT TTTTCT TTTTCT TTTTCTT TTTTCT TCTTTCT TTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTC-T TTTTCT T-TTTCT TTTTCT
2396 CCTATTTTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
6 24 0.67
7 12 0.33
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:2394 original size:13 final size:12
Alignment explanation
Indices: 2352--2395 Score: 70
Period size: 13 Copynumber: 3.5 Consensus size: 12
2342 TGACCTCTCC
2352 TTTTCTTTTTCT
1 TTTTCTTTTTCT
2364 TTTTCTTTTTCTT
1 TTTTCTTTTTC-T
2377 TTTTCTTCTTTCT
1 TTTTCTT-TTTCT
2390 TTTTCT
1 TTTTCT
2396 CCTATTTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 11 0.37
13 15 0.50
14 4 0.13
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTCTTTTTCT
Found at i:2436 original size:7 final size:8
Alignment explanation
Indices: 2420--2464 Score: 54
Period size: 9 Copynumber: 5.2 Consensus size: 8
2410 ATTTTTTTGA
2420 TTATTTTT
1 TTATTTTT
2428 TTATTTTT
1 TTATTTTT
2436 TTATTTTTT
1 TTA-TTTTT
2445 TTGATTTTT
1 TT-ATTTTT
*
2454 TGAATTTTT
1 T-TATTTTT
2463 TT
1 TT
2465 TTGAGTCTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
8 11 0.34
9 20 0.62
10 1 0.03
ACGTcount: A:0.13, C:0.00, G:0.04, T:0.82
Consensus pattern (8 bp):
TTATTTTT
Found at i:2436 original size:19 final size:18
Alignment explanation
Indices: 2412--2466 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 18
2402 TTTCTTTAAT
2412 TTTTTTGATTATTTTTTTA
1 TTTTTTGATT-TTTTTTTA
* *
2431 TTTTTTTATTTTTTTTGA
1 TTTTTTGATTTTTTTTTA
2449 TTTTTTGAATTTTTTTTT
1 TTTTTTG-ATTTTTTTTT
2467 GAGTCTGAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 13 0.42
19 18 0.58
ACGTcount: A:0.13, C:0.00, G:0.05, T:0.82
Consensus pattern (18 bp):
TTTTTTGATTTTTTTTTA
Found at i:3244 original size:24 final size:25
Alignment explanation
Indices: 3217--3280 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 25
3207 CAAAAGAATG
*
3217 AAAGAATCAAA-AATAATTA-TTCAA
1 AAAGAATCAAAGAAT-ATTAGCTCAA
*
3241 AAAGAATGAAAGAATATTAGCTCAA
1 AAAGAATCAAAGAATATTAGCTCAA
3266 AAAGGAATACAAAGA
1 AAA-GAAT-CAAAGA
3281 TGTATTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
24 14 0.42
25 10 0.30
26 4 0.12
27 5 0.15
ACGTcount: A:0.61, C:0.08, G:0.12, T:0.19
Consensus pattern (25 bp):
AAAGAATCAAAGAATATTAGCTCAA
Found at i:4524 original size:19 final size:17
Alignment explanation
Indices: 4502--4544 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 17
4492 GTGAAATTTG
4502 ATGCATGCAATGAAATGCA
1 ATGCATGC-ATGAAATG-A
4521 ATGCAGATGCATGAAATGA
1 ATGC--ATGCATGAAATGA
4540 ATGCA
1 ATGCA
4545 AAAAAAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 1 0.05
19 9 0.41
20 8 0.36
21 4 0.18
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (17 bp):
ATGCATGCATGAAATGA
Done.