Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018101.1 Corchorus olitorius cultivar O-4 contig18134, whole genome shotgun sequence
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: 13907
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Found at i:403 original size:21 final size:21
Alignment explanation
Indices: 379--492 Score: 167
Period size: 21 Copynumber: 5.4 Consensus size: 21
369 CTTAGGCAAT
*
379 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
400 TCCAATGATCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
421 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
442 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
*
463 TCCAATGAGCTTGGAACTTGTC
1 TCCAATGAGCTTGGAACCT-TC
485 TCCAATGA
1 TCCAATGA
493 ACTTCTAGCA
Statistics
Matches: 85, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
20 3 0.04
21 71 0.84
22 10 0.12
23 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:2369 original size:33 final size:31
Alignment explanation
Indices: 2296--2400 Score: 120
Period size: 33 Copynumber: 3.2 Consensus size: 31
2286 GCTATGATCA
** *
2296 ACCAAAACAGATTTGTTTTCATCACAATTAGC
1 ACCAAAACAGATTTG-TTTCATCACAAACAAC
2328 ATCCAAAACAGAATTTGTTTCATCACAAACAAC
1 A-CCAAAACAG-ATTTGTTTCATCACAAACAAC
*
2361 ACCTAAAACAGATTTAGTGTCATCACAAACAAC
1 ACC-AAAACAGATTT-GTTTCATCACAAACAAC
2394 ACTCAAA
1 AC-CAAA
2401 TTAGGTTTAG
Statistics
Matches: 64, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
32 7 0.11
33 51 0.80
34 6 0.09
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.25
Consensus pattern (31 bp):
ACCAAAACAGATTTGTTTCATCACAAACAAC
Found at i:2410 original size:33 final size:34
Alignment explanation
Indices: 2332--2445 Score: 117
Period size: 33 Copynumber: 3.4 Consensus size: 34
2322 ATTAGCATCC
*
2332 AAAACAGAATTT-GTTTCATCACAAACAACAC-CT
1 AAAACAG-ATTTAGTATCATCACAAACAACACTCT
*
2365 AAAACAGATTTAGTGTCATCACAAACAACACTC-
1 AAAACAGATTTAGTATCATCACAAACAACACTCT
** * * *
2398 AAATTAGGTTTAGTATTATCGCAAACAACACTCT
1 AAAACAGATTTAGTATCATCACAAACAACACTCT
*
2432 AAAAATAGATTTAG
1 -AAAACAGATTTAG
2446 AATTACTCTT
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
32 4 0.06
33 52 0.76
34 1 0.01
35 11 0.16
ACGTcount: A:0.45, C:0.19, G:0.10, T:0.26
Consensus pattern (34 bp):
AAAACAGATTTAGTATCATCACAAACAACACTCT
Found at i:4942 original size:21 final size:21
Alignment explanation
Indices: 4918--5009 Score: 141
Period size: 21 Copynumber: 4.4 Consensus size: 21
4908 CTTAGGCAAT
*
4918 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
4939 TCCAATGATCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
4960 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
4981 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
5002 TCCAATGA
1 TCCAATGA
5010 ACTTCTAGCA
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
20 3 0.05
21 63 0.95
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.29
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:12439 original size:17 final size:17
Alignment explanation
Indices: 12417--12450 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
12407 CTAGGAAAAG
12417 GAAATAAAGACATAATT
1 GAAATAAAGACATAATT
12434 GAAATAAAGACATAATT
1 GAAATAAAGACATAATT
12451 AAACAAGGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.24
Consensus pattern (17 bp):
GAAATAAAGACATAATT
Done.