Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015954.1 Corchorus capsularis cultivar CVL-1 contig15975, 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: 19533
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Found at i:2318 original size:25 final size:25
Alignment explanation
Indices: 2273--2321 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2263 TTTTGAACTC
*
2273 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
2298 ATTATTTATTGA-ATAATATATATT
1 ATTATTTATT-ATATAAAATATATT
2322 GTATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:9657 original size:21 final size:21
Alignment explanation
Indices: 9614--9657 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
9604 GTAAACTGGA
*
9614 TTGCTAAATACTGCCCCCCTT
1 TTGCTAAATACCGCCCCCCTT
* *
9635 TTGCTAAATACCGCTCCCTTT
1 TTGCTAAATACCGCCCCCCTT
9656 TT
1 TT
9658 ACAGTTTTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.34, G:0.09, T:0.39
Consensus pattern (21 bp):
TTGCTAAATACCGCCCCCCTT
Found at i:9795 original size:24 final size:25
Alignment explanation
Indices: 9735--9793 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
9725 TTCAAACCCT
*
9735 AAACTTCATTTCTAACAACTTCTCC
1 AAACTTCATTTCTAACAACATCTCC
*
9760 AAACTTCATTTCTAACAA-ATCTTC
1 AAACTTCATTTCTAACAACATCTCC
9784 AAAC-TCATTT
1 AAACTTCATTT
9794 TCCTTCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 6 0.19
24 8 0.25
25 18 0.56
ACGTcount: A:0.36, C:0.27, G:0.00, T:0.37
Consensus pattern (25 bp):
AAACTTCATTTCTAACAACATCTCC
Found at i:10318 original size:26 final size:24
Alignment explanation
Indices: 10247--10319 Score: 67
Period size: 26 Copynumber: 2.9 Consensus size: 24
10237 GATGATTAAT
*
10247 TTTAATTAGTTTATTAAAATTAATTTG
1 TTTAATTAGTTTA-T--AATTAATTTA
**
10274 TTT-ATTAGTTTATGTTTAATTAGTA
1 TTTAATTAGTTTATAATTAATT--TA
10299 TTTAATTAGTTTATAATTAAT
1 TTTAATTAGTTTATAATTAAT
10320 AAGTTCATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
23 6 0.16
25 5 0.13
26 24 0.63
27 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (24 bp):
TTTAATTAGTTTATAATTAATTTA
Found at i:10376 original size:18 final size:18
Alignment explanation
Indices: 10241--10376 Score: 76
Period size: 18 Copynumber: 7.9 Consensus size: 18
10231 AATTTTGATG
10241 ATTAATTTTAATTAGTTT
1 ATTAATTTTAATTAGTTT
** *
10259 ATTAAAATTAATTTGTTT
1 ATTAATTTTAATTAGTTT
*
10277 ATT-AGTTT-A-T-GTTT
1 ATTAATTTTAATTAGTTT
*
10291 AATTAGTATTTAATTAGTTT
1 -ATTAAT-TTTAATTAGTTT
* *
10311 A-TAA--TTAATAAGTTC
1 ATTAATTTTAATTAGTTT
**
10326 ATT-ATTTTTGTT--TTT
1 ATTAATTTTAATTAGTTT
*
10341 ATTAATTATTACTTAGTTT
1 ATTAATT-TTAATTAGTTT
*
10360 ATTAGTTTTAATTAGTT
1 ATTAATTTTAATTAGTT
10377 AATTTATGAT
Statistics
Matches: 87, Mismatches: 18, Indels: 26
0.66 0.14 0.20
Matches are distributed among these distances:
14 4 0.05
15 20 0.23
16 5 0.06
17 13 0.15
18 30 0.34
19 11 0.13
20 4 0.05
ACGTcount: A:0.32, C:0.01, G:0.08, T:0.59
Consensus pattern (18 bp):
ATTAATTTTAATTAGTTT
Found at i:13656 original size:34 final size:33
Alignment explanation
Indices: 13618--13686 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
13608 TTAATTAATC
*
13618 ATAAACTAACTAAATACTAATTAAACATAACCTA
1 ATAAACTAACT-AATACTAATTAAACATAAACTA
* ** *
13652 ATAAACTAAGTAATTTTAATTAATCATAAACTA
1 ATAAACTAACTAATACTAATTAAACATAAACTA
13685 AT
1 AT
13687 TAATATTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
33 20 0.67
34 10 0.33
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (33 bp):
ATAAACTAACTAATACTAATTAAACATAAACTA
Found at i:14738 original size:13 final size:13
Alignment explanation
Indices: 14720--14745 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
14710 TAATATAACT
14720 CAAAAAATAAAAG
1 CAAAAAATAAAAG
14733 CAAAAAATAAAAG
1 CAAAAAATAAAAG
14746 GTCAATAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.08, T:0.08
Consensus pattern (13 bp):
CAAAAAATAAAAG
Found at i:15063 original size:23 final size:23
Alignment explanation
Indices: 15037--15084 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
15027 CATTCTGCCA
15037 TACCTTCACCAATATTCAATATT
1 TACCTTCACCAATATTCAATATT
15060 TACCTTCACCAATATTCAATATT
1 TACCTTCACCAATATTCAATATT
15083 TA
1 TA
15085 TTTGTTCTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.25, G:0.00, T:0.40
Consensus pattern (23 bp):
TACCTTCACCAATATTCAATATT
Found at i:19509 original size:2 final size:2
Alignment explanation
Indices: 19502--19533 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
19492 TGTAAGTCAT
19502 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.