Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009588.1 Corchorus capsularis cultivar CVL-1 contig09609, 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: 9377
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Found at i:588 original size:22 final size:21
Alignment explanation
Indices: 539--617 Score: 97
Period size: 21 Copynumber: 3.8 Consensus size: 21
529 GCCCAACATT
*
539 TATGAAA-CTTGATAACTACC
1 TATGAAATTTTGATAACTACC
* *
559 TATTAAATTTTGATAACCATCC
1 TATGAAATTTTGATAACTA-CC
*
581 TATGAAATTTTGATAATTACC
1 TATGAAATTTTGATAACTACC
*
602 TATGAAATTATGATAA
1 TATGAAATTTTGATAA
618 AACTGATATG
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
20 6 0.12
21 26 0.52
22 18 0.36
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.38
Consensus pattern (21 bp):
TATGAAATTTTGATAACTACC
Found at i:639 original size:22 final size:23
Alignment explanation
Indices: 602--664 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 23
592 GATAATTACC
* * *
602 TATGAAATTATGATAAAACTGA-
1 TATGAAATTCTAATAAAACTAAG
*
624 TATGAAACTT-TAAT-AACCTAAG
1 TATGAAA-TTCTAATAAAACTAAG
646 TATGAAATTCTAATAAAAC
1 TATGAAATTCTAATAAAAC
665 CTTCCTATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
21 7 0.21
22 21 0.64
23 5 0.15
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.32
Consensus pattern (23 bp):
TATGAAATTCTAATAAAACTAAG
Found at i:3203 original size:16 final size:16
Alignment explanation
Indices: 3182--3221 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
3172 ATCGATTTGG
3182 GTGTATGTGAGTGTGT
1 GTGTATGTGAGTGTGT
*
3198 GTGTATGTGTGTGTGT
1 GTGTATGTGAGTGTGT
*
3214 GTATATGT
1 GTGTATGT
3222 ATATATACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.12, C:0.00, G:0.40, T:0.47
Consensus pattern (16 bp):
GTGTATGTGAGTGTGT
Found at i:3333 original size:22 final size:20
Alignment explanation
Indices: 3288--3359 Score: 83
Period size: 22 Copynumber: 3.5 Consensus size: 20
3278 AAATATTTTT
3288 TAAAA-TTTGATAATCACTA
1 TAAAATTTTGATAATCACTA
*
3307 TAAAATTTTGATAATCTCCATA
1 TAAAATTTTGATAATC-AC-TA
3329 TAAAATTTTGATAATAACACTA
1 TAAAATTTTGATAAT--CACTA
*
3351 TAAAGTTTT
1 TAAAATTTT
3360 TATGATGATA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
19 5 0.11
20 10 0.22
21 1 0.02
22 27 0.60
23 1 0.02
24 1 0.02
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (20 bp):
TAAAATTTTGATAATCACTA
Found at i:3434 original size:22 final size:22
Alignment explanation
Indices: 3397--3740 Score: 195
Period size: 22 Copynumber: 15.7 Consensus size: 22
3387 CCTCCATATG
* * *
3397 ATGATATTTTGTTAACTTCCCT
1 ATGAAATTTTGATAACCTCCCT
* * *
3419 ATAAAATTTTAATAACC-ACCT
1 ATGAAATTTTGATAACCTCCCT
*
3440 AATGAAATTTTGATAACCACCCT
1 -ATGAAATTTTGATAACCTCCCT
*
3463 ATGAAATTTTGATAACCTCCCA
1 ATGAAATTTTGATAACCTCCCT
* * * **
3485 ATGAAATGTTGGTAAGCGCACATT
1 ATGAAATTTTGATAA-C-CTCCCT
* * *
3509 ATGAAATTTTAATAAACATACCAT
1 ATGAAATTTTGAT-AACCT-CCCT
* *
3533 CATGAAATTGTGAT-ACCTCCAT
1 -ATGAAATTTTGATAACCTCCCT
* *
3555 TTGAAATTTTGATAACCTCCAT
1 ATGAAATTTTGATAACCTCCCT
*
3577 TTGAAATTTTGATAACCT--C-
1 ATGAAATTTTGATAACCTCCCT
*
3596 ATGAAATTTTGATAACCAT-CTT
1 ATGAAATTTTGATAACC-TCCCT
* *
3618 TTGAAATTTTGATAACATCCCT
1 ATGAAATTTTGATAACCTCCCT
* *
3640 ATAAACATTTT-ATAACCT-TCT
1 ATGAA-ATTTTGATAACCTCCCT
* *
3661 CATAAAATTTTGTTAACCT-CCT
1 -ATGAAATTTTGATAACCTCCCT
* * *** *
3683 ACGAATTTTTGATAAGAACACT
1 ATGAAATTTTGATAACCTCCCT
* * * *
3705 ATTAAAGTTTGATAACC-ACCA
1 ATGAAATTTTGATAACCTCCCT
3726 ATGAAATTTTGATAA
1 ATGAAATTTTGATAA
3741 TTAACTACAC
Statistics
Matches: 246, Mismatches: 60, Indels: 33
0.73 0.18 0.10
Matches are distributed among these distances:
19 16 0.07
20 1 0.00
21 47 0.19
22 142 0.58
23 12 0.05
24 15 0.06
25 13 0.05
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTCCCT
Found at i:3608 original size:41 final size:41
Alignment explanation
Indices: 3556--3633 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
3546 TACCTCCATT
3556 TGAAATTTTGATAACC-TCCATTTGAAATTTTGATAACCTCA
1 TGAAATTTTGATAACCAT-CATTTGAAATTTTGATAACCTCA
*
3597 TGAAATTTTGATAACCATCTTTTGAAATTTTGATAAC
1 TGAAATTTTGATAACCATCATTTGAAATTTTGATAAC
3634 ATCCCTATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
41 34 0.97
42 1 0.03
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (41 bp):
TGAAATTTTGATAACCATCATTTGAAATTTTGATAACCTCA
Found at i:3655 original size:63 final size:62
Alignment explanation
Indices: 3532--3657 Score: 157
Period size: 63 Copynumber: 2.0 Consensus size: 62
3522 AAACATACCA
* * *
3532 TCATGAAATTGTGATACCTCCATTTGAAATTTTGATAACCTCCATTTGAAATTTTGATAACC
1 TCATGAAATTGTGATACCTCCATTTGAAATTTTGATAACATCCATATAAAATTTTGATAACC
* * *
3594 TCATGAAATTTTGATAACCAT-CTTTTGAAATTTTGATAACATCCCTATAAACATTTT-ATAACC
1 TCATGAAATTGTGAT-ACC-TCCATTTGAAATTTTGATAACATCCATATAAA-ATTTTGATAACC
3657 T
1 T
3658 TCTCATAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
62 14 0.25
63 35 0.64
64 6 0.11
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (62 bp):
TCATGAAATTGTGATACCTCCATTTGAAATTTTGATAACATCCATATAAAATTTTGATAACC
Found at i:3844 original size:21 final size:22
Alignment explanation
Indices: 3772--3857 Score: 61
Period size: 21 Copynumber: 4.0 Consensus size: 22
3762 AATAACTTGC
* *
3772 CTATGAAATTTTGTTAATCTCC
1 CTATAAAATTTTGTTAATCTCA
* * * *
3794 CTATAAAATATTAG--AACCACT
1 CTATAAAAT-TTTGTTAATCTCA
*
3815 CTATCAAATTTTGTTAATCTCA
1 CTATAAAATTTTGTTAATCTCA
* *
3837 CTAT-AAATTTTGATAAACTCA
1 CTATAAAATTTTGTTAATCTCA
3858 TTACGAAATT
Statistics
Matches: 49, Mismatches: 12, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
20 3 0.06
21 27 0.55
22 16 0.33
23 3 0.06
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (22 bp):
CTATAAAATTTTGTTAATCTCA
Found at i:3949 original size:22 final size:22
Alignment explanation
Indices: 3924--4063 Score: 67
Period size: 22 Copynumber: 6.5 Consensus size: 22
3914 CCATATTATA
3924 AAATTTTGATAACCACACTATG
1 AAATTTTGATAACCACACTATG
* *
3946 AAATTGTGATAATCTC-CCCTA--
1 AAATTTTGATAA-C-CACACTATG
* * * * *
3967 AAATTTCGATAATCTCCCCATG
1 AAATTTTGATAACCACACTATG
* *
3989 AAATTTTGTTAA-C-CTCTATG
1 AAATTTTGATAACCACACTATG
* * **
4009 AAATTGTGATTATTACACTATG
1 AAATTTTGATAACCACACTATG
* * * *
4031 AAATTTTGGTAACGACAGT-TA
1 AAATTTTGATAACCACACTATG
4052 AAATTTTGATAA
1 AAATTTTGATAA
4064 GCTCACTCTA
Statistics
Matches: 88, Mismatches: 23, Indels: 15
0.70 0.18 0.12
Matches are distributed among these distances:
19 1 0.01
20 18 0.20
21 23 0.26
22 40 0.45
23 5 0.06
24 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (22 bp):
AAATTTTGATAACCACACTATG
Found at i:3977 original size:21 final size:22
Alignment explanation
Indices: 3953--3994 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
3943 ATGAAATTGT
3953 GATAATCTCCCC-TAAAATTTC
1 GATAATCTCCCCATAAAATTTC
*
3974 GATAATCTCCCCATGAAATTT
1 GATAATCTCCCCATAAAATTT
3995 TGTTAACCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.33
Consensus pattern (22 bp):
GATAATCTCCCCATAAAATTTC
Found at i:4493 original size:22 final size:23
Alignment explanation
Indices: 4468--4527 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 23
4458 AATCTCCAAG
4468 TGAAATTCTAATAACCTTCC-CA
1 TGAAATTCTAATAACCTTCCGCA
* * *
4490 TGAATTTC-GATAACC-TCCGTA
1 TGAAATTCTAATAACCTTCCGCA
4511 TGAAATT-TATATAACCT
1 TGAAATTCTA-ATAACCT
4528 CCATATGGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
20 3 0.10
21 13 0.45
22 13 0.45
ACGTcount: A:0.35, C:0.22, G:0.08, T:0.35
Consensus pattern (23 bp):
TGAAATTCTAATAACCTTCCGCA
Found at i:4516 original size:43 final size:44
Alignment explanation
Indices: 4468--4562 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
4458 AATCTCCAAG
*
4468 TGAAATTCTA-ATAACCTTCC-CAT-GAATTTCGATAACCTCCGTA
1 TGAAATT-TATATAACC-TCCACATGGAATTTCGATAACATCCGTA
* *
4511 TGAAATTTATATAACCTCCATATGGAATTTCGATAACATCCTTA
1 TGAAATTTATATAACCTCCACATGGAATTTCGATAACATCCGTA
4555 TGAAATTT
1 TGAAATTT
4563 TGATAACACC
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
42 5 0.11
43 15 0.33
44 26 0.57
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.36
Consensus pattern (44 bp):
TGAAATTTATATAACCTCCACATGGAATTTCGATAACATCCGTA
Found at i:4528 original size:22 final size:22
Alignment explanation
Indices: 4356--4569 Score: 104
Period size: 22 Copynumber: 9.8 Consensus size: 22
4346 ATAAGCACAG
* **
4356 TATGAAATTTTGATAATTTTCC-
1 TATGAAATTTAGATAA-CCTCCA
* *
4378 TATGAAATTTTGATAAACTCCA
1 TATGAAATTTAGATAACCTCCA
* *
4400 TATAAAATTTCGATAATCGC-CCA
1 TATGAAATTTAGATAA-C-CTCCA
* * **
4423 -ATGAAATTTTGTTAACC-AGA
1 TATGAAATTTAGATAACCTCCA
*
4443 GTATGAAATTTTAG-TAATCTCCA
1 -TATGAAA-TTTAGATAACCTCCA
4466 -AGTGAAATTCTA-ATAACCTTCC-
1 TA-TGAAATT-TAGATAACC-TCCA
* * *
4488 CATG-AATTTCGATAACCTCCG
1 TATGAAATTTAGATAACCTCCA
*
4509 TATGAAATTTATATAACCTCCA
1 TATGAAATTTAGATAACCTCCA
* * * *
4531 TATGGAATTTCGATAACATCCT
1 TATGAAATTTAGATAACCTCCA
*
4553 TATGAAATTTTGATAAC
1 TATGAAATTTAGATAAC
4570 ACCCATGAAC
Statistics
Matches: 150, Mismatches: 27, Indels: 30
0.72 0.13 0.14
Matches are distributed among these distances:
20 6 0.04
21 20 0.13
22 111 0.74
23 12 0.08
24 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (22 bp):
TATGAAATTTAGATAACCTCCA
Found at i:4641 original size:22 final size:22
Alignment explanation
Indices: 4622--4720 Score: 114
Period size: 22 Copynumber: 4.6 Consensus size: 22
4612 TTACCTATTG
* *
4622 AATTTTGGTAACCTCACTATAA
1 AATTTTGATAACCACACTATAA
4644 AATTTTGATAACCACACTATAA
1 AATTTTGATAACCACACTATAA
* *
4666 AATTTTGAAAACTACACTATAA
1 AATTTTGATAACCACACTATAA
* *
4688 AATTTT-AGTAACCAC-CAAT-G
1 AATTTTGA-TAACCACACTATAA
4708 AATTTTGATAACC
1 AATTTTGATAACC
4721 GCCAAAATTA
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
20 11 0.16
21 5 0.07
22 51 0.76
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (22 bp):
AATTTTGATAACCACACTATAA
Found at i:5756 original size:2 final size:2
Alignment explanation
Indices: 5749--5778 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5739 GAGGATAATC
*
5749 TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5779 ATACATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:6847 original size:75 final size:75
Alignment explanation
Indices: 6678--6903 Score: 302
Period size: 75 Copynumber: 3.1 Consensus size: 75
6668 TTTTTATAGC
* * * * *
6678 TTTACTTAACT-AAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAG-CTA-TTT-T-
1 TTTACTCAACTAAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAGTATATTTTATC
6738 ATTTTACTAT
66 ATTTTACTAT
*
6748 TTTACTCAACTAAAAAACTCTATTTTTATATAATTAAATCTAATGTCCTTATAGTATATTTTATC
1 TTTACTCAACTAAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAGTATATTTTATC
6813 ATTTTACTAT
66 ATTTTACTAT
* *
6823 TTTACTCAAC-ACAAAAATTCTATTTTTATATAATTAAATCTAATATCCTTATTAATTATATTTT
1 TTTACTCAACTA-AAAAACTCTATTTTTATATAATTAAATCTAATATCCTTA-T-AGTATATTTT
*
6887 ACCATTTTACTAT
63 ATCATTTTACTAT
6900 TTTA
1 TTTA
6904 ATTAAAAATT
Statistics
Matches: 138, Mismatches: 10, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
70 10 0.07
71 38 0.28
72 2 0.01
73 3 0.02
74 2 0.01
75 57 0.41
76 1 0.01
77 25 0.18
ACGTcount: A:0.36, C:0.12, G:0.01, T:0.50
Consensus pattern (75 bp):
TTTACTCAACTAAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAGTATATTTTATC
ATTTTACTAT
Found at i:8533 original size:13 final size:12
Alignment explanation
Indices: 8515--8553 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
8505 TATTATTGAG
8515 TAAATAAAATAAA
1 TAAATAAAA-AAA
*
8528 TAAATAAAAATTA
1 TAAATAAAAA-AA
8541 TAAATAAAAAAA
1 TAAATAAAAAAA
8553 T
1 T
8554 TTATGAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 3 0.13
13 20 0.87
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
TAAATAAAAAAA
Found at i:8543 original size:17 final size:16
Alignment explanation
Indices: 8523--8557 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
8513 AGTAAATAAA
8523 ATAAATAAATAAAAATT
1 ATAAATAAA-AAAAATT
*
8540 ATAAATAAAAAAATTT
1 ATAAATAAAAAAAATT
8556 AT
1 AT
8558 GAGAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAAATAAAAAAAATT
Done.