Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005499.1 Corchorus capsularis cultivar CVL-1 contig05517, 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: 30994
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:18712 original size:303 final size:303
Alignment explanation
Indices: 18165--18769 Score: 1095
Period size: 303 Copynumber: 2.0 Consensus size: 303
18155 TTGGGTAAAC
* *
18165 TTAAAATTCATATAAAACGTTTTGCCCTCGATTGATAGCCTTGAAACGTTTCATGTGAATTTTAA
1 TTAAAATTCACATAAAACATTTTGCCCTCGATTGATAGCCTTGAAACGTTTCATGTGAATTTTAA
18230 GTTTACCCATATAGTATTTTAAATGAATGTTAGTTTGGAATGTGAAATTTTTAAAAATTTTGTAT
66 GTTTACCCATATAGTATTTTAAATGAATGTTAGTTTGGAATGTGAAATTTTTAAAAATTTTGTAT
*
18295 TTAATTGAGGTAGAAGTTTAACATAAAGTTTCGTACCAAATAAATTTTTCTTTTGTTCAATTAAG
131 TTAATTGAGGTAGAAGTTCAACATAAAGTTTCGTACCAAATAAATTTTTCTTTTGTTCAATTAAG
* * *
18360 GACCTTAATAATTAAGATACAATTTGAATATGAAATTTAGCTCCAAATAAATTTTTTATTTATGT
196 GACCTTAATAATTAAAATACAATTCGAACATGAAATTTAGCTCCAAATAAATTTTTTATTTATGT
*
18425 TATGGGTAGATATGGATTTCTAAACATTGGGTAAACTTAAAAG
261 TATGGGTAGATATGGACTTCTAAACATTGGGTAAACTTAAAAG
*
18468 TTAAAATTCACATGAAACATTTTGCCCTCGATTGATAGCCTTGAAACGTTTCATGTGAATTTTAA
1 TTAAAATTCACATAAAACATTTTGCCCTCGATTGATAGCCTTGAAACGTTTCATGTGAATTTTAA
*
18533 GTTTACCCATATAGTATTTTAAATGAATTTTAGTTTGGAATGTGAAAATTTTT-AAAATTTTGTA
66 GTTTACCCATATAGTATTTTAAATGAATGTTAGTTTGGAATGTG-AAATTTTTAAAAATTTTGTA
18597 TTTAATTGAGGTAGAAGTTCAACATAAAGTTTCGTACCAAATAAATTTTTCTTTTGTTCAATTAA
130 TTTAATTGAGGTAGAAGTTCAACATAAAGTTTCGTACCAAATAAATTTTTCTTTTGTTCAATTAA
*
18662 GGACCTTAATAATTAAAATACGATTCGAACATGAAATTTAGCTCCAAATAAATTTTTTATTTATG
195 GGACCTTAATAATTAAAATACAATTCGAACATGAAATTTAGCTCCAAATAAATTTTTTATTTATG
*
18727 TTATGGGTAGATATGGACTTCTAAACATTGGTTAAACTTAAAA
260 TTATGGGTAGATATGGACTTCTAAACATTGGGTAAACTTAAAA
18770 TTCACATGAA
Statistics
Matches: 290, Mismatches: 11, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
303 282 0.97
304 8 0.03
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (303 bp):
TTAAAATTCACATAAAACATTTTGCCCTCGATTGATAGCCTTGAAACGTTTCATGTGAATTTTAA
GTTTACCCATATAGTATTTTAAATGAATGTTAGTTTGGAATGTGAAATTTTTAAAAATTTTGTAT
TTAATTGAGGTAGAAGTTCAACATAAAGTTTCGTACCAAATAAATTTTTCTTTTGTTCAATTAAG
GACCTTAATAATTAAAATACAATTCGAACATGAAATTTAGCTCCAAATAAATTTTTTATTTATGT
TATGGGTAGATATGGACTTCTAAACATTGGGTAAACTTAAAAG
Found at i:25088 original size:2 final size:2
Alignment explanation
Indices: 25037--25074 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
25027 TTAGTGGCGG
25037 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25075 TATTCCATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27037 original size:3 final size:3
Alignment explanation
Indices: 27029--27095 Score: 63
Period size: 3 Copynumber: 23.3 Consensus size: 3
27019 TTACTAATTT
*
27029 TTA TTA TTA TTA -TA TTA TATA TATA TTA -TA TAA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA T-TA TTA TTA TTA TTA TTA TTA TTA
*
27073 TTA TTA TTT TTA -TA TTA -TA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
27096 CTTTTCTTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
2 10 0.19
3 37 0.69
4 7 0.13
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:27046 original size:11 final size:11
Alignment explanation
Indices: 27030--27095 Score: 68
Period size: 11 Copynumber: 6.1 Consensus size: 11
27020 TACTAATTTT
27030 TATTATTATTA
1 TATTATTATTA
27041 TATTA-TATATA
1 TATTATTAT-TA
27052 TATTATATAATTA
1 TATTAT-T-ATTA
27065 TATTATTA-T-
1 TATTATTATTA
*
27074 TATTATTTTTA
1 TATTATTATTA
27085 TATTA-TATTA
1 TATTATTATTA
27095 T
1 T
27096 CTTTTCTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
9 7 0.15
10 10 0.21
11 18 0.38
12 1 0.02
13 9 0.19
14 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATTATTATTA
Found at i:27057 original size:19 final size:19
Alignment explanation
Indices: 27033--27095 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
27023 TAATTTTTAT
27033 TATTATTATATTATATATA
1 TATTATTATATTATATATA
27052 TATTA-TATAATTATAT-TA
1 TATTATTAT-ATTATATATA
*
27070 TTATTATTAT-TTTTATATTA
1 -TATTATTATATTATATA-TA
27090 TATTAT
1 TATTAT
27096 CTTTTCTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
18 10 0.26
19 23 0.61
20 5 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTATTATATTATATATA
Found at i:27442 original size:40 final size:40
Alignment explanation
Indices: 27380--27460 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
27370 ATTTGTCCCA
*
27380 CCTAATAATTAAGAAAACAAATTAAATCCAGGTTTAGCCC
1 CCTAATAATTAAGAAAACAAATTAAATCCAGGTTTAACCC
** *
27420 CCTAATAATTAAGGTAAGAAATTAAATCCAGGTTTAACCC
1 CCTAATAATTAAGAAAACAAATTAAATCCAGGTTTAACCC
27460 C
1 C
27461 TAGTTATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (40 bp):
CCTAATAATTAAGAAAACAAATTAAATCCAGGTTTAACCC
Found at i:30175 original size:2 final size:2
Alignment explanation
Indices: 30170--30199 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
30160 ACACACACAC
30170 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30200 CTAAATCCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.