Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010412.1 Corchorus capsularis cultivar CVL-1 contig10433, 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: 15665
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:323 original size:52 final size:52
Alignment explanation
Indices: 253--425 Score: 262
Period size: 52 Copynumber: 3.3 Consensus size: 52
243 AGATTATATA
*
253 TTTTTAT-A-TTAT-ATTACAAATTATTATACGATTTATTATATTTATTTAT
1 TTTTTATGATTTATGATTACAAATTAATATACGATTTATTATATTTATTTAT
*
302 TTTTTATGATTTATGATTACAAATTAATATGCGATTTATTATATTTATTTAT
1 TTTTTATGATTTATGATTACAAATTAATATACGATTTATTATATTTATTTAT
*
354 TTTTTATGATTTATGATTACAAATTAATATATGATTTATTATATTTATTTATTTGT
1 TTTTTATGATTTATGATTACAAATTAATATACGATTTATTATATTTATTTA----T
410 TTTTTATGATTTATGA
1 TTTTTATGATTTATGA
426 ACTATTAACA
Statistics
Matches: 113, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
49 7 0.06
50 1 0.01
51 4 0.04
52 84 0.74
56 17 0.15
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.58
Consensus pattern (52 bp):
TTTTTATGATTTATGATTACAAATTAATATACGATTTATTATATTTATTTAT
Found at i:6619 original size:29 final size:30
Alignment explanation
Indices: 6587--6649 Score: 110
Period size: 29 Copynumber: 2.1 Consensus size: 30
6577 TGGTAATTTA
*
6587 GAAATATATTTTAAAAAA-GGGTATAATCG
1 GAAATATATTTTAAAAAAGGGGTACAATCG
6616 GAAATATATTTTAAAAAAGGGGTACAATCG
1 GAAATATATTTTAAAAAAGGGGTACAATCG
6646 GAAA
1 GAAA
6650 GCATAAAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 18 0.56
30 14 0.44
ACGTcount: A:0.49, C:0.05, G:0.19, T:0.27
Consensus pattern (30 bp):
GAAATATATTTTAAAAAAGGGGTACAATCG
Found at i:7038 original size:21 final size:21
Alignment explanation
Indices: 7014--7075 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 21
7004 TATTTGATAG
7014 TTTAATGTATTATGATTAAAA
1 TTTAATGTATTATGATTAAAA
*** *
7035 TTT-AT-TATT-TCCCT-AGA
1 TTTAATGTATTATGATTAAAA
7052 -TTAATGTATTATGATTAAAA
1 TTTAATGTATTATGATTAAAA
7072 TTTA
1 TTTA
7076 TTATTTCCCT
Statistics
Matches: 28, Mismatches: 8, Indels: 10
0.61 0.17 0.22
Matches are distributed among these distances:
16 2 0.07
17 4 0.14
18 6 0.21
19 6 0.21
20 4 0.14
21 6 0.21
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (21 bp):
TTTAATGTATTATGATTAAAA
Found at i:7061 original size:37 final size:37
Alignment explanation
Indices: 7015--7088 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
7005 ATTTGATAGT
7015 TTAATGTATTATGATTAAAATTTATTATTTCCCTAGA
1 TTAATGTATTATGATTAAAATTTATTATTTCCCTAGA
7052 TTAATGTATTATGATTAAAATTTATTATTTCCCTAGA
1 TTAATGTATTATGATTAAAATTTATTATTTCCCTAGA
7089 GTGCAATTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.49
Consensus pattern (37 bp):
TTAATGTATTATGATTAAAATTTATTATTTCCCTAGA
Found at i:7395 original size:15 final size:16
Alignment explanation
Indices: 7375--7408 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
7365 CTCAAATGTC
7375 GGGTC-ATTTGGGTTT
1 GGGTCAATTTGGGTTT
*
7390 GGGTCAATTTTGGTTT
1 GGGTCAATTTGGGTTT
7406 GGG
1 GGG
7409 ACTTTTTCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.09, C:0.06, G:0.41, T:0.44
Consensus pattern (16 bp):
GGGTCAATTTGGGTTT
Found at i:8299 original size:22 final size:23
Alignment explanation
Indices: 8274--8332 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
8264 TATATTTATA
8274 TTATTAGTAAATTA-ATAAATAT
1 TTATTAGTAAATTATATAAATAT
* * *
8296 TTATTACT--ATGTATATTATTAT
1 TTATTAGTAAAT-TATATAAATAT
8318 TTATTAGTAAATTAT
1 TTATTAGTAAATTAT
8333 CAAAACATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
20 2 0.07
21 2 0.07
22 20 0.69
23 3 0.10
24 2 0.07
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (23 bp):
TTATTAGTAAATTATATAAATAT
Found at i:11424 original size:64 final size:64
Alignment explanation
Indices: 11345--11472 Score: 229
Period size: 64 Copynumber: 2.0 Consensus size: 64
11335 ATTACAACAA
*
11345 GTTCCTCTACTTCATGTTTAGCTAATCAGGAGTAAATTCTGTCTTCTCTTCTACTTTTTTTTTT
1 GTTCCTCTACTTCATGTTTAGCTAATCAGGAGTAAATTCTGCCTTCTCTTCTACTTTTTTTTTT
* *
11409 GTTCCTCTACTTCATGTTTAGCTAATTAGGAGTAAATTCTGCCTTCTCTTCTATTTTTTTTTTT
1 GTTCCTCTACTTCATGTTTAGCTAATCAGGAGTAAATTCTGCCTTCTCTTCTACTTTTTTTTTT
11473 TTGGCATCTT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.17, C:0.20, G:0.11, T:0.52
Consensus pattern (64 bp):
GTTCCTCTACTTCATGTTTAGCTAATCAGGAGTAAATTCTGCCTTCTCTTCTACTTTTTTTTTT
Done.