Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000138.1 Corchorus capsularis cultivar CVL-1 contig00138, 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, 800
Length: 1334
ACGTcount: A:0.21, C:0.22, G:0.05, T:0.52
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:241 original size:14 final size:14
Alignment explanation
Indices: 224--393 Score: 65
Period size: 14 Copynumber: 12.4 Consensus size: 14
214 TGATCACCTT
224 TTACTCTTTACTGA
1 TTACTCTTTACTGA
* *
238 TTACTCCTTACTAA
1 TTACTCTTTACTGA
*
252 TTAC-CATTTAGCT-C
1 TTACTC-TTTA-CTGA
**
266 TTACTGATTACT-A
1 TTACTCTTTACTGA
*
279 TTTTACTC-TGACTGA
1 --TTACTCTTTACTGA
294 TTAC-CTTTTACTGA
1 TTACTC-TTTACTGA
*
308 TTACT-ATTACCTGA
1 TTACTCTTTA-CTGA
322 TTACT-TTT--T-A
1 TTACTCTTTACTGA
* * **
332 CTACTCTTTGCCATTT
1 TTACTCTTT-AC-TGA
348 TTACT-TTTACTGA
1 TTACTCTTTACTGA
**
361 TTACTCTTTACTTT
1 TTACTCTTTACTGA
*
375 TTCCTCTTTACTGA
1 TTACTCTTTACTGA
389 TTACT
1 TTACT
394 ATTTTACCCT
Statistics
Matches: 115, Mismatches: 24, Indels: 34
0.66 0.14 0.20
Matches are distributed among these distances:
10 5 0.04
11 4 0.03
12 1 0.01
13 16 0.14
14 73 0.63
15 12 0.10
16 4 0.03
ACGTcount: A:0.21, C:0.22, G:0.06, T:0.51
Consensus pattern (14 bp):
TTACTCTTTACTGA
Found at i:268 original size:21 final size:20
Alignment explanation
Indices: 238--318 Score: 74
Period size: 21 Copynumber: 3.9 Consensus size: 20
228 TCTTTACTGA
*
238 TTACTCCTTACTAATTACCAT
1 TTACT-CTTACTGATTACCAT
*
259 TTAGCTCTTACTGATTACTATT
1 TTA-CTCTTACTGATTACCA-T
* *
281 TTACTCTGACTGATTACCTT
1 TTACTCTTACTGATTACCAT
*
301 TTACTGATTACT-ATTACC
1 TTACT-CTTACTGATTACC
319 TGATTACTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
20 12 0.24
21 32 0.64
22 6 0.12
ACGTcount: A:0.25, C:0.23, G:0.06, T:0.46
Consensus pattern (20 bp):
TTACTCTTACTGATTACCAT
Found at i:434 original size:26 final size:27
Alignment explanation
Indices: 388--455 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 27
378 CTCTTTACTG
**
388 ATTACTATTTT-ACCCTCTTGAACTTA
1 ATTACTATTTTCATTCTCTTGAACTTA
*
414 ATTACTATTTTCATTCT-TTGAATTTA
1 ATTACTATTTTCATTCTCTTGAACTTA
* *
440 ATCACCATTTGTCATT
1 ATTACTATTT-TCATT
456 TTACTCTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 27 0.77
27 8 0.23
ACGTcount: A:0.26, C:0.19, G:0.04, T:0.50
Consensus pattern (27 bp):
ATTACTATTTTCATTCTCTTGAACTTA
Found at i:489 original size:33 final size:32
Alignment explanation
Indices: 428--497 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
418 CTATTTTCAT
428 TCTTTGAATTTAATCACCATTTGTCATTTTAC
1 TCTTTGAATTTAATCACCATTTGTCATTTTAC
* *
460 TCTTTGGATTTAATTACCATTT-TACCATTTTAC
1 TCTTTGAATTTAATCACCATTTGT--CATTTTAC
493 TCTTT
1 TCTTT
498 ACCGATTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 1 0.03
32 20 0.59
33 13 0.38
ACGTcount: A:0.23, C:0.19, G:0.06, T:0.53
Consensus pattern (32 bp):
TCTTTGAATTTAATCACCATTTGTCATTTTAC
Found at i:535 original size:16 final size:17
Alignment explanation
Indices: 487--542 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 17
477 CATTTTACCA
487 TTTTACTCTTTACCGAT
1 TTTTACTCTTTACCGAT
*
504 TATTCCCTACTTTTTACC-AT
1 T-TT---TACTCTTTACCGAT
524 TTTTACTCTTTACCGAT
1 TTTTACTCTTTACCGAT
541 TT
1 TT
543 ACTGATTACT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
16 10 0.31
17 5 0.16
18 2 0.06
19 2 0.06
20 3 0.09
21 10 0.31
ACGTcount: A:0.18, C:0.25, G:0.04, T:0.54
Consensus pattern (17 bp):
TTTTACTCTTTACCGAT
Found at i:577 original size:40 final size:40
Alignment explanation
Indices: 533--688 Score: 285
Period size: 40 Copynumber: 3.9 Consensus size: 40
523 TTTTTACTCT
*
533 TTACCGATTTACTGATTACTTCTTTTACTTTTACTCTTAA
1 TTACCGACTTACTGATTACTTCTTTTACTTTTACTCTTAA
573 TTACCGACTTACTGATTACTTCTTTTACTTTTACTCTTAA
1 TTACCGACTTACTGATTACTTCTTTTACTTTTACTCTTAA
*
613 TTATCGACTTACTGATTACTTCTTTTACTTTTACTCTTAA
1 TTACCGACTTACTGATTACTTCTTTTACTTTTACTCTTAA
*
653 TTACCGACTTACTGATTACTTCTTTTACTTTCACTC
1 TTACCGACTTACTGATTACTTCTTTTACTTTTACTC
689 CATTTTACTG
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 112 1.00
ACGTcount: A:0.22, C:0.22, G:0.05, T:0.51
Consensus pattern (40 bp):
TTACCGACTTACTGATTACTTCTTTTACTTTTACTCTTAA
Found at i:767 original size:14 final size:14
Alignment explanation
Indices: 748--774 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
738 TTCTGATTAC
748 TTCTTTTACTTTTG
1 TTCTTTTACTTTTG
762 TTCTTTTACTTTT
1 TTCTTTTACTTTT
775 ACTAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.04, T:0.74
Consensus pattern (14 bp):
TTCTTTTACTTTTG
Found at i:791 original size:16 final size:16
Alignment explanation
Indices: 770--833 Score: 69
Period size: 16 Copynumber: 4.1 Consensus size: 16
760 TGTTCTTTTA
*
770 CTTTTACTAATTACTT
1 CTTTTACTGATTACTT
**
786 CTTTTACT--TTTGTT
1 CTTTTACTGATTACTT
800 CTTTTACTGATTACTT
1 CTTTTACTGATTACTT
* *
816 CCTCTACTGATTACTT
1 CTTTTACTGATTACTT
832 CT
1 CT
834 CTTGATTACC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
14 12 0.31
16 27 0.69
ACGTcount: A:0.17, C:0.22, G:0.05, T:0.56
Consensus pattern (16 bp):
CTTTTACTGATTACTT
Found at i:804 original size:30 final size:32
Alignment explanation
Indices: 743--816 Score: 89
Period size: 36 Copynumber: 2.2 Consensus size: 32
733 CATTTTTCTG
743 ATTACTTCTTTTACTTTTGTTCTTTTACTTTTACTA
1 ATTACTTCTTTTACTTTTG----TTTACTTTTACTA
*
779 ATTACTTCTTTTACTTTTG-TT-CTTTTACTG
1 ATTACTTCTTTTACTTTTGTTTACTTTTACTA
809 ATTACTTC
1 ATTACTTC
817 CTCTACTGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
30 16 0.43
31 2 0.05
36 19 0.51
ACGTcount: A:0.16, C:0.18, G:0.04, T:0.62
Consensus pattern (32 bp):
ATTACTTCTTTTACTTTTGTTTACTTTTACTA
Found at i:830 original size:110 final size:115
Alignment explanation
Indices: 624--877 Score: 329
Period size: 110 Copynumber: 2.2 Consensus size: 115
614 TATCGACTTA
*
624 CTGATTACTTCTTTTACTTTTACTCTTAATTACCGACTTACTGATTACTTCTTTTACTTTCACTC
1 CTGATTACTTCTTTTACTTTTACTCTT-ATTACCGACTTACTAATTACTTCTTTTACTTTCACTC
* * *
689 CATTTTACTGATTACTTCTTCTACGGGTTACTTCTCTTGATTATCATTTTT
65 CATTTTACTGATTACTTCCTCTACGGATTACTTCTCTTGATTACCATTTTT
** ** ** *
740 CTGATTACTTCTTTTACTTTTGTTCTT-TTA-C-TTTTACTAATTACTTCTTTTACTTT-TGTTC
1 CTGATTACTTCTTTTACTTTTACTCTTATTACCGACTTACTAATTACTTCTTTTACTTTCACTCC
*
801 -TTTTACTGATTACTTCCTCTACTGATTACTTCTCTTGATTACCATTTTT
66 ATTTTACTGATTACTTCCTCTACGGATTACTTCTCTTGATTACCATTTTT
* *
850 CTGATTACTTTTTTTTACTTTGACTCTT
1 CTGATTAC-TTCTTTTACTTTTACTCTT
878 TGATTACTGA
Statistics
Matches: 121, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
110 53 0.44
111 17 0.14
112 22 0.18
113 1 0.01
114 3 0.02
116 25 0.21
ACGTcount: A:0.17, C:0.21, G:0.06, T:0.56
Consensus pattern (115 bp):
CTGATTACTTCTTTTACTTTTACTCTTATTACCGACTTACTAATTACTTCTTTTACTTTCACTCC
ATTTTACTGATTACTTCCTCTACGGATTACTTCTCTTGATTACCATTTTT
Found at i:1047 original size:37 final size:38
Alignment explanation
Indices: 934--1079 Score: 148
Period size: 37 Copynumber: 3.9 Consensus size: 38
924 TCAAATTACT
* *
934 AATTAACTGATTACTAT-TACCTTGACTCTTGATTATC
1 AATTTACTGATTACTATCTACCTTGACTCTTAATTATC
*
971 AATTTACTGATTA--ATCT-CCTT--TTACTTAATTA-C
1 AATTTACTGATTACTATCTACCTTGACT-CTTAATTATC
*
1004 TGATTTACTGATTACTAT-TACCTTGACTCTTAATTATC
1 -AATTTACTGATTACTATCTACCTTGACTCTTAATTATC
1042 AATTTACTGATTAATCCT-TCTACCTTGACTCTTAATTA
1 AATTTACTGATT-A--CTATCTACCTTGACTCTTAATTA
1080 CTGACTTACC
Statistics
Matches: 90, Mismatches: 6, Indels: 23
0.76 0.05 0.19
Matches are distributed among these distances:
33 2 0.02
34 19 0.21
35 7 0.08
36 7 0.08
37 31 0.34
38 3 0.03
39 1 0.01
40 20 0.22
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.46
Consensus pattern (38 bp):
AATTTACTGATTACTATCTACCTTGACTCTTAATTATC
Found at i:1204 original size:38 final size:39
Alignment explanation
Indices: 1111--1204 Score: 109
Period size: 38 Copynumber: 2.4 Consensus size: 39
1101 ACCCTTACTT
* * * *
1111 ACTGATTGCTACTTTTACTTCTTCTCTTAGTTATCAATTT
1 ACTGATTACTACTTTTACTTC-TCTCTTAATTACCAATTG
* *
1151 ACTGATTAATCCTTTTACTTC-CTCTTAATTACCAATTG
1 ACTGATTACTACTTTTACTTCTCTCTTAATTACCAATTG
*
1189 ACTGATTACTTCTTTT
1 ACTGATTACTACTTTT
1205 TCTTTTCACT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
38 28 0.61
40 18 0.39
ACGTcount: A:0.22, C:0.21, G:0.06, T:0.50
Consensus pattern (39 bp):
ACTGATTACTACTTTTACTTCTCTCTTAATTACCAATTG
Done.