Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005139.1 Corchorus capsularis cultivar CVL-1 contig05157, 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: 7536
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Found at i:536 original size:19 final size:18
Alignment explanation
Indices: 497--540 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
487 ATTTTCCTAA
*
497 TTTCCTTTTTCCTTTTCC
1 TTTCTTTTTTCCTTTTCC
515 TTTTCTTTTTTCC-TTTCTC
1 -TTTCTTTTTTCCTTTTC-C
534 TTTCTTT
1 TTTCTTT
541 GGATTGGGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTCTTTTTTCCTTTTCC
Found at i:2469 original size:21 final size:22
Alignment explanation
Indices: 2421--2469 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
2411 ATTTTTAATT
*
2421 TTTTTAGAACTTCAACATACAA
1 TTTTTATAACTTCAACATACAA
* *
2443 -TATTATAACTTCAATAT-CAA
1 TTTTTATAACTTCAACATACAA
2463 TTTTTAT
1 TTTTTAT
2470 GGTTCGAACC
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.39, C:0.14, G:0.02, T:0.45
Consensus pattern (22 bp):
TTTTTATAACTTCAACATACAA
Found at i:2949 original size:24 final size:24
Alignment explanation
Indices: 2922--2983 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
2912 ATGGATACTA
* * *
2922 TTATATTCATCTTATATAGATTTC
1 TTATATTCATCTAAGATAGATTAC
2946 TTATATTCATCTAAGATAGATTAC
1 TTATATTCATCTAAGATAGATTAC
*
2970 TTATATTAATCTAA
1 TTATATTCATCTAA
2984 AATTATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.48
Consensus pattern (24 bp):
TTATATTCATCTAAGATAGATTAC
Found at i:3754 original size:22 final size:23
Alignment explanation
Indices: 3704--3755 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
3694 CTGAATCAAT
3704 TTAAAAAATATATATTTTGGATAA
1 TTAAAAAATATATATTTT-GATAA
*
3728 ATAAAAAATATATATTATT-AT-A
1 TTAAAAAATATATATT-TTGATAA
3750 TTAAAA
1 TTAAAA
3756 TTTTTTTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 6 0.24
23 2 0.08
24 15 0.60
25 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (23 bp):
TTAAAAAATATATATTTTGATAA
Found at i:4128 original size:47 final size:46
Alignment explanation
Indices: 4014--4143 Score: 131
Period size: 46 Copynumber: 2.8 Consensus size: 46
4004 ATTGATAAAA
* ** *
4014 TTTTACTAATAAAGTTATTGAATTTGTTGATAGCACTAATTTTTTT
1 TTTTACTAATAAAGTTATTGAATTTGTCGATAGCACTAACGTATTT
* * * *
4060 TTTTGCTACAT--ATTTGTTGAATTTGTCGATTATCA-TATACGTATTT
1 TTTTACTA-ATAAAGTTATTGAATTTGTCGA-TAGCACTA-ACGTATTT
*
4106 TTTTACTAATAAAGTTATTGAATTTGTTGATAGCACTA
1 TTTTACTAATAAAGTTATTGAATTTGTCGATAGCACTA
4144 TAATTGCTTT
Statistics
Matches: 65, Mismatches: 13, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
45 19 0.29
46 27 0.42
47 19 0.29
ACGTcount: A:0.29, C:0.08, G:0.12, T:0.50
Consensus pattern (46 bp):
TTTTACTAATAAAGTTATTGAATTTGTCGATAGCACTAACGTATTT
Found at i:4537 original size:21 final size:21
Alignment explanation
Indices: 4511--4556 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
4501 ACTGAATATG
4511 ATTTCTTATCATTACACTATA
1 ATTTCTTATCATTACACTATA
4532 ATTTCTTATCATTACACTATA
1 ATTTCTTATCATTACACTATA
4553 ATTT
1 ATTT
4557 TGTGCATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTTCTTATCATTACACTATA
Found at i:5263 original size:2 final size:2
Alignment explanation
Indices: 5256--5290 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5246 TAATTACTAG
5256 TA TA TA TA TA 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 TA TA TA TA TA T
5291 GTTTAAAAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5366 original size:2 final size:2
Alignment explanation
Indices: 5359--5383 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5349 TAAAACCACT
5359 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
5384 ATATATATAT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:6550 original size:165 final size:167
Alignment explanation
Indices: 6330--6632 Score: 386
Period size: 166 Copynumber: 1.8 Consensus size: 167
6320 CTCAAATGCG
6330 CAAAATCGTGAAGTTGAGGTTTTAGTCTTTGAAGAAATCTTTATATGGCGAGCCCACTTT-TCAA
1 CAAAATCGTGAAGTTGAGGTTTTAGTCTTTGAAGAAATCTTTATATGGCGAGCCCACTTTAT-AA
* * ** *
6394 TAAACTCTAGT-AACTCTTAGACACGA-AATTGAGCGTTGGTGTCGCAAAAAGTGCATTCGAAAT
65 TAAACTCTAGTCAA-TCTAAGACACGACAATTGAGCGTTAGTGTCGCAAAAAACGCATTCAAAAT
6457 GATCGTTTTCTCAATAACAATGTTTTGCATACAAACACA
129 GATCGTTTTCTCAATAACAATGTTTTGCATACAAACACA
* *
6496 CAAAATCGTGAAGTTGA-GTTTTAGAATTCTTT-AA-AAA-CTTTATTTGGCGAGCCCAGTTTAT
1 CAAAATCGTGAAGTTGAGGTTTTAG---TCTTTGAAGAAATCTTTATATGGCGAGCCCACTTTAT
* * * * * *
6557 AGTAAGCTCTATTCAATCTAAGACATGACATTTGAGCGTTAGTTTCGCAAAAAACGCATTCAAAA
63 AATAAACTCTAGTCAATCTAAGACACGACAATTGAGCGTTAGTGTCGCAAAAAACGCATTCAAAA
*
6622 TTATCGTTTTC
128 TGATCGTTTTC
6633 CAAAGAATAA
Statistics
Matches: 117, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
165 47 0.40
166 63 0.54
167 2 0.02
168 5 0.04
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (167 bp):
CAAAATCGTGAAGTTGAGGTTTTAGTCTTTGAAGAAATCTTTATATGGCGAGCCCACTTTATAAT
AAACTCTAGTCAATCTAAGACACGACAATTGAGCGTTAGTGTCGCAAAAAACGCATTCAAAATGA
TCGTTTTCTCAATAACAATGTTTTGCATACAAACACA
Done.