Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010999.1 Corchorus capsularis cultivar CVL-1 contig11020, 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: 35114
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:8 original size:2 final size:2
Alignment explanation
Indices: 2--46 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1 G
*
2 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
44 TC T
1 TC T
47 ATAGTCGAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:1972 original size:3 final size:3
Alignment explanation
Indices: 1964--1999 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1954 CTTGATTTTA
1964 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2000 GACAACTAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4242 original size:3 final size:3
Alignment explanation
Indices: 4234--4282 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
4224 TAAATATTAT
4234 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4282 A
1 A
4283 CTAGACTAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:13712 original size:32 final size:32
Alignment explanation
Indices: 13671--13732 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
13661 GGGGCATTTC
*
13671 TTTATCTCACTTAGGGTTTATATATCATGTAT
1 TTTATCTCACTTAGGGTTTAGATATCATGTAT
*
13703 TTTATCTCACTTAGGGTTTAGATTTCATGT
1 TTTATCTCACTTAGGGTTTAGATATCATGT
13733 CATGTCTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.50
Consensus pattern (32 bp):
TTTATCTCACTTAGGGTTTAGATATCATGTAT
Found at i:20021 original size:19 final size:18
Alignment explanation
Indices: 19997--20032 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
19987 TGAAGATTTA
19997 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
20016 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
20033 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:20656 original size:18 final size:17
Alignment explanation
Indices: 20629--20664 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
20619 TTTCTCTTCA
20629 TCTATTTTTCTTCTAGT
1 TCTATTTTTCTTCTAGT
20646 TCTAGTTTTTCTTCTAGT
1 TCTA-TTTTTCTTCTAGT
20664 T
1 T
20665 TTAGGTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (17 bp):
TCTATTTTTCTTCTAGT
Found at i:25284 original size:19 final size:18
Alignment explanation
Indices: 25260--25295 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
25250 TGAAGATTTA
25260 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
25279 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
25296 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:32383 original size:15 final size:15
Alignment explanation
Indices: 32365--32395 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
32355 TTACTTTTGC
*
32365 TACTTTTATCATTTT
1 TACTTTTACCATTTT
32380 TACTTTTACCATTTT
1 TACTTTTACCATTTT
32395 T
1 T
32396 CTTACTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.16, G:0.00, T:0.65
Consensus pattern (15 bp):
TACTTTTACCATTTT
Found at i:32395 original size:24 final size:24
Alignment explanation
Indices: 32350--32422 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 24
32340 TATTGATTAC
* * *
32350 CATTTTTACTTTTGCTACTTTTAT
1 CATTTTTACTTTTACCATTTTTAT
*
32374 CATTTTTACTTTTACCATTTTTCT
1 CATTTTTACTTTTACCATTTTTAT
* *
32398 TACTCTTTTACTTAATACCATTTTT
1 CA-T-TTTTACTT-TTACCATTTTT
32423 TTTAAATTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
24 21 0.52
25 1 0.03
26 8 0.20
27 10 0.25
ACGTcount: A:0.19, C:0.19, G:0.01, T:0.60
Consensus pattern (24 bp):
CATTTTTACTTTTACCATTTTTAT
Found at i:32484 original size:42 final size:42
Alignment explanation
Indices: 32397--32529 Score: 128
Period size: 42 Copynumber: 3.1 Consensus size: 42
32387 ACCATTTTTC
* * **
32397 TTACTCTTTTACTTAATACCATTTTTTTTAAATTAATACCATTT
1 TTACTCTTTTACTTAATACCA--TCTTTGACCTTAATACCATTT
32441 TTGAC-CTTCTTACTTAATACCATACTTT-A-CTTAATACCATTT
1 TT-ACTCTT-TTACTTAATACCAT-CTTTGACCTTAATACCATTT
** * *
32483 TTACTCTTTTGTTTAATACCATTTTTGACCTTAATACCATCT
1 TTACTCTTTTACTTAATACCATCTTTGACCTTAATACCATTT
32525 TTACT
1 TTACT
32530 TGATACCACT
Statistics
Matches: 77, Mismatches: 6, Indels: 14
0.79 0.06 0.14
Matches are distributed among these distances:
40 3 0.04
41 15 0.19
42 34 0.44
43 2 0.03
44 8 0.10
45 15 0.19
ACGTcount: A:0.27, C:0.20, G:0.02, T:0.50
Consensus pattern (42 bp):
TTACTCTTTTACTTAATACCATCTTTGACCTTAATACCATTT
Found at i:32543 original size:58 final size:59
Alignment explanation
Indices: 32453--32566 Score: 194
Period size: 58 Copynumber: 1.9 Consensus size: 59
32443 GACCTTCTTA
* *
32453 CTTAATACCATACTTTACTTAATACCATTTTTACTCTTTTGTTTAATACCATTTTTGAC
1 CTTAATACCATACTTTACTTAATACCACTTTTACTCTCTTGTTTAATACCATTTTTGAC
*
32512 CTTAATACCAT-CTTTACTTGATACCACTTTTACTCTCTTGTTTAATACCATTTTT
1 CTTAATACCATACTTTACTTAATACCACTTTTACTCTCTTGTTTAATACCATTTTT
32567 TTTACTCTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
58 41 0.79
59 11 0.21
ACGTcount: A:0.25, C:0.22, G:0.04, T:0.49
Consensus pattern (59 bp):
CTTAATACCATACTTTACTTAATACCACTTTTACTCTCTTGTTTAATACCATTTTTGAC
Found at i:33077 original size:40 final size:41
Alignment explanation
Indices: 33033--33175 Score: 179
Period size: 40 Copynumber: 3.5 Consensus size: 41
33023 CTTAATTACT
*
33033 GATTTTCTGATTACTAT-TTTTACCTTGACTCTTTATTATC
1 GATTTACTGATTACTATCTTTTACCTTGACTCTTTATTATC
33073 GATTTACTGATTACTAT-TTTTACCTTGACTCTTTAATTA-C
1 GATTTACTGATTACTATCTTTTACCTTGACTCTTT-ATTATC
* * *
33113 TGACTTTACTGATTA--ATCTCTTACCTTGATTCTTGATTATC
1 -GA-TTTACTGATTACTATCTTTTACCTTGACTCTTTATTATC
*
33154 AATTTACTGATTACTATCTTTT
1 GATTTACTGATTACTATCTTTT
33176 TACTTGATTA
Statistics
Matches: 90, Mismatches: 6, Indels: 13
0.83 0.06 0.12
Matches are distributed among these distances:
39 11 0.12
40 41 0.46
41 27 0.30
42 11 0.12
ACGTcount: A:0.23, C:0.17, G:0.08, T:0.52
Consensus pattern (41 bp):
GATTTACTGATTACTATCTTTTACCTTGACTCTTTATTATC
Found at i:33109 original size:81 final size:82
Alignment explanation
Indices: 33024--33175 Score: 220
Period size: 81 Copynumber: 1.9 Consensus size: 82
33014 CTCTTTTTAC
* * * *
33024 TTAATTACTGA-TTTTCTGATTACTAT-TTTTACCTTGACTCTTTATTATCGATTTACTGATTAC
1 TTAATTACTGACTTTACTGATTA--ATCTCTTACCTTGACTCTTGATTATCAATTTACTGATTAC
33087 TAT-TTTTACCTTGACTCT
64 TATCTTTTACCTTGACTCT
*
33105 TTAATTACTGACTTTACTGATTAATCTCTTACCTTGATTCTTGATTATCAATTTACTGATTACTA
1 TTAATTACTGACTTTACTGATTAATCTCTTACCTTGACTCTTGATTATCAATTTACTGATTACTA
33170 TCTTTT
66 TCTTTT
33176 TACTTGATTA
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
80 2 0.03
81 47 0.75
82 14 0.22
ACGTcount: A:0.24, C:0.17, G:0.07, T:0.52
Consensus pattern (82 bp):
TTAATTACTGACTTTACTGATTAATCTCTTACCTTGACTCTTGATTATCAATTTACTGATTACTA
TCTTTTACCTTGACTCT
Done.