Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012020.1 Corchorus olitorius cultivar O-4 contig12053, 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: 21474
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1493 original size:17 final size:17
Alignment explanation
Indices: 1467--1500 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1457 TACAACCATT
1467 CAAAGCTATTATGGTTA
1 CAAAGCTATTATGGTTA
*
1484 CAAAGTTATTATGGTTA
1 CAAAGCTATTATGGTTA
1501 GTAACGTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (17 bp):
CAAAGCTATTATGGTTA
Found at i:4743 original size:22 final size:23
Alignment explanation
Indices: 4718--4820 Score: 117
Period size: 22 Copynumber: 4.7 Consensus size: 23
4708 TATAATTAGG
* *
4718 TTATCAAAATTTCTTATGG-AGT
1 TTATCAAAATTTCATATGGTAGA
* *
4740 TTATCATAATTTTATA-GGTA-A
1 TTATCAAAATTTCATATGGTAGA
4761 TTATCAAAATTTCATATGGT-GA
1 TTATCAAAATTTCATATGGTAGA
* *
4783 TTATCAAAATTTAATAAGGTAG-
1 TTATCAAAATTTCATATGGTAGA
4805 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
4821 AAAATATTCA
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
21 16 0.24
22 51 0.75
23 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.43
Consensus pattern (23 bp):
TTATCAAAATTTCATATGGTAGA
Found at i:4772 original size:43 final size:44
Alignment explanation
Indices: 4718--4820 Score: 145
Period size: 43 Copynumber: 2.4 Consensus size: 44
4708 TATAATTAGG
* * * *
4718 TTATCAAAATTTCTTATGGAGTTTATCATAATTTTAT-AGGTAA
1 TTATCAAAATTTCATATGGAGATTATCAAAATTTAATAAGGTAA
* *
4761 TTATCAAAATTTCATATGGTGATTATCAAAATTTAATAAGGTAG
1 TTATCAAAATTTCATATGGAGATTATCAAAATTTAATAAGGTAA
4805 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
4821 AAAATATTCA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 32 0.60
44 21 0.40
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.43
Consensus pattern (44 bp):
TTATCAAAATTTCATATGGAGATTATCAAAATTTAATAAGGTAA
Found at i:7853 original size:2 final size:2
Alignment explanation
Indices: 7846--7870 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7836 CATTGATGTG
7846 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
7871 CTATTGAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8291 original size:32 final size:30
Alignment explanation
Indices: 8247--8310 Score: 74
Period size: 32 Copynumber: 2.1 Consensus size: 30
8237 GAACTCACTC
* * * *
8247 GACCTGAGACCCGCAGCCCAGATGACCCGA
1 GACCTGAGACCCGAAACCCAAATAACCCGA
8277 GACCTGTATGACCCGAAACCCAAATAACCCGA
1 GACCTG-A-GACCCGAAACCCAAATAACCCGA
8309 GA
1 GA
8311 AGTTAACCCG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 6 0.21
31 1 0.04
32 21 0.75
ACGTcount: A:0.33, C:0.36, G:0.22, T:0.09
Consensus pattern (30 bp):
GACCTGAGACCCGAAACCCAAATAACCCGA
Found at i:9109 original size:16 final size:16
Alignment explanation
Indices: 9090--9179 Score: 69
Period size: 16 Copynumber: 5.7 Consensus size: 16
9080 ACCTGAGTCC
9090 CGAATGACCCGGAACT
1 CGAATGACCCGGAACT
*
9106 CGAATGACCCGAAACT
1 CGAATGACCCGGAACT
* * *
9122 CGTATGACCCAAGACCT
1 CGAATGACCC-GGAACT
*
9139 -GAATGACCC-GAAAT
1 CGAATGACCCGGAACT
* *
9153 CCGAATAACCC-GAACC
1 -CGAATGACCCGGAACT
*
9169 CGGATGACCCG
1 CGAATGACCCG
9180 AGAAAACTAT
Statistics
Matches: 57, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
14 3 0.05
15 8 0.14
16 43 0.75
17 3 0.05
ACGTcount: A:0.33, C:0.33, G:0.21, T:0.12
Consensus pattern (16 bp):
CGAATGACCCGGAACT
Found at i:12328 original size:30 final size:29
Alignment explanation
Indices: 12287--12345 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
12277 TCTTTTTCTG
*
12287 TTCTGAGGTTTGGTTTTGTGTGTTCTGTTT
1 TTCTGAGGTTTGGTTTTGTGAGTTC-GTTT
*
12317 TTCTTAGGTTTGGTTTTGTGAGTTCGTTT
1 TTCTGAGGTTTGGTTTTGTGAGTTCGTTT
12346 GAATTTGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.05, C:0.07, G:0.29, T:0.59
Consensus pattern (29 bp):
TTCTGAGGTTTGGTTTTGTGAGTTCGTTT
Done.