Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010208.1 Corchorus capsularis cultivar CVL-1 contig10229, 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: 32570
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2635 original size:42 final size:42
Alignment explanation
Indices: 2570--2654 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
2560 CATGAAGTCT
2570 TGGGTTCTAGTCTCACAAAATGTGAGTTTAGTTTGTAATTTA
1 TGGGTTCTAGTCTCACAAAATGTGAGTTTAGTTTGTAATTTA
* ***
2612 TGGGTTTTAGTCTCACGGTATGTGAGTTTAGTTTGTAATTTA
1 TGGGTTCTAGTCTCACAAAATGTGAGTTTAGTTTGTAATTTA
2654 T
1 T
2655 TGTTTTTTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.22, C:0.08, G:0.24, T:0.46
Consensus pattern (42 bp):
TGGGTTCTAGTCTCACAAAATGTGAGTTTAGTTTGTAATTTA
Found at i:3468 original size:30 final size:30
Alignment explanation
Indices: 3432--3517 Score: 100
Period size: 33 Copynumber: 2.7 Consensus size: 30
3422 AACGTAGCAT
*
3432 GCCACGTGTACAAAAAGTGACATGTGACAC
1 GCCACGTGTACAAAAAGTGACATATGACAC
* *
3462 GCCACGTGTATAAAAAAAAGTGACATATGGCAC
1 GCCACGTG--T-ACAAAAAGTGACATATGACAC
*
3495 GCCATGTGTACCAAAAAGTGACA
1 GCCACGTGTA-CAAAAAGTGACA
3518 CATTTCATGC
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
30 9 0.19
31 12 0.26
32 1 0.02
33 25 0.53
ACGTcount: A:0.40, C:0.21, G:0.22, T:0.17
Consensus pattern (30 bp):
GCCACGTGTACAAAAAGTGACATATGACAC
Found at i:5354 original size:28 final size:28
Alignment explanation
Indices: 5322--5379 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
5312 AAAAAAAAAC
5322 GATATTTTATAGTATAAGATTAAGAAGT
1 GATATTTTATAGTATAAGATTAAGAAGT
*
5350 GATATTTTATAGTATATGATTAAGAAGT
1 GATATTTTATAGTATAAGATTAAGAAGT
5378 GA
1 GA
5380 CTATATTACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.40
Consensus pattern (28 bp):
GATATTTTATAGTATAAGATTAAGAAGT
Found at i:9507 original size:2 final size:2
Alignment explanation
Indices: 9500--9530 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9490 TTAATTGGTG
9500 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9531 GTTGGCATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18689 original size:33 final size:34
Alignment explanation
Indices: 18629--18695 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 34
18619 AGGAAACTTG
*
18629 TATTGGAATACAGTAGGAAATACTTGTATTTTAA
1 TATTGGAATACAATAGGAAATACTTGTATTTTAA
*
18663 TATTGGAATACAAT-GGGAATACTTGTATTTTAA
1 TATTGGAATACAATAGGAAATACTTGTATTTTAA
18696 GCTTTGATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 18 0.58
34 13 0.42
ACGTcount: A:0.37, C:0.06, G:0.18, T:0.39
Consensus pattern (34 bp):
TATTGGAATACAATAGGAAATACTTGTATTTTAA
Found at i:19846 original size:31 final size:31
Alignment explanation
Indices: 19806--19942 Score: 148
Period size: 31 Copynumber: 4.4 Consensus size: 31
19796 ACGGTGTCCG
19806 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* *
19837 ATGTGGCACGCCACATGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* * * * *
19868 ACATGTCATGCCACGTATACCGAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* * ** * *
19899 ACGTGGCATGCCACATGTTTCAAAAAATGGC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
*
19930 ACGTGGCATGCCA
1 ACGTGGCACGCCA
19943 TGTGCACAAA
Statistics
Matches: 88, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 88 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.18
Consensus pattern (31 bp):
ACGTGGCACGCCACGTGTACCAAAAAGTGAC
Found at i:19923 original size:62 final size:62
Alignment explanation
Indices: 19809--19942 Score: 169
Period size: 62 Copynumber: 2.2 Consensus size: 62
19799 GTGTCCGACG
* * * *
19809 TGGCACGCCACGTGTACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAGTGACACA
1 TGGCATGCCACGTATACCAAAAAGTGACACGTGGCACGCCACATGTACCAAAAAATGACACA
* * * ** * *
19871 TGTCATGCCACGTATACCGAAAAGTGACACGTGGCATGCCACATGTTTCAAAAAATGGCACG
1 TGGCATGCCACGTATACCAAAAAGTGACACGTGGCACGCCACATGTACCAAAAAATGACACA
19933 TGGCATGCCA
1 TGGCATGCCA
19943 TGTGCACAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.18
Consensus pattern (62 bp):
TGGCATGCCACGTATACCAAAAAGTGACACGTGGCACGCCACATGTACCAAAAAATGACACA
Found at i:22769 original size:34 final size:34
Alignment explanation
Indices: 22726--22790 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
22716 ATTTTAATCA
* **
22726 TTTTTAAAAACAATTACATAATACATATGAGTTC
1 TTTTTAAAAAAAAAAACATAATACATATGAGTTC
22760 TTTTTAAAAAAAAAAACATAATACATATGAG
1 TTTTTAAAAAAAAAAACATAATACATATGAG
22791 ATGACATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (34 bp):
TTTTTAAAAAAAAAAACATAATACATATGAGTTC
Found at i:22836 original size:5 final size:6
Alignment explanation
Indices: 22818--22842 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
22808 CTAAAATTAG
22818 AAGAAA AAGAAA AAGAAA AAGAAA A
1 AAGAAA AAGAAA AAGAAA AAGAAA A
22843 TCCCATGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:29566 original size:21 final size:21
Alignment explanation
Indices: 29556--30098 Score: 199
Period size: 22 Copynumber: 25.0 Consensus size: 21
29546 ATGATCCCCT
29556 TATGAAATTTTGATAACCTCC
1 TATGAAATTTTGATAACCTCC
* *
29577 TATGAAATTTTGATAACGGTAC
1 TATGAAATTTTGATAAC-CTCC
* ** * **
29599 TATGGAATTTCAAGAATCCTTT
1 TATGAAATTTTGATAA-CCTCC
* * *
29621 TAT-AAATTTT-TTAAACTTTCT
1 TATGAAATTTTGAT-AAC-CTCC
*
29642 TATGAAATTTTGTTAACCTCC
1 TATGAAATTTTGATAACCTCC
* * *
29663 TTAAGGAATTTTGA-AGACCTCAA
1 -TATGAAATTTTGATA-ACCTC-C
* *
29686 TATGAAATTTTAATAACTTCTC
1 TATGAAATTTTGATAACCTC-C
* *
29708 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TC-C
* * * *
29731 TATGAGATGTTGATAACCACTT
1 TATGAAATTTTGATAACCTC-C
* * * *
29753 TATAAAAATTTAAAAACCTCC
1 TATGAAATTTTGATAACCTCC
* * *
29774 -ATGTGAATTGTT-AGTAATCACAC
1 TATG-AAATT-TTGA-TAACCTC-C
* * * *
29797 TTTAAAATTTTGATAATCACAC
1 TATGAAATTTTGATAACCTC-C
*
29819 TATGAAATTGTGATAACCTCAC
1 TATGAAATTTTGATAACCTC-C
* * *
29841 TATGTAATTTTGATAAATCTTTC
1 TATGAAATTTTGAT-AA-CCTCC
* *
29864 TATAAAATTTTAATAAACCTCCC
1 TATGAAATTTTGAT-AACCT-CC
* * *
29887 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAAC-CTCC
*
29909 TATGAAATCTTGATAA----C
1 TATGAAATTTTGATAACCTCC
* *
29926 TA-CAAATTTTGATAAGCTCC
1 TATGAAATTTTGATAACCTCC
** *
29946 TTATGATTTTTTGATAACCTCAT
1 -TATGAAATTTTGATAACCTC-C
* *
29969 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCT-CC
* * *
29991 TATGAAATTTTGATCTACATGC
1 TATGAAATTTTGAT-AACCTCC
*
30013 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAA-CCTCC
* *
30035 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT--CC
* *
30057 TATGAAAATTTGATAACCTTCA
1 TATGAAATTTTGATAACC-TCC
*
30079 TATGAAATTTTGATATCCTC
1 TATGAAATTTTGATAACCTC
30099 ACTGAATTTT
Statistics
Matches: 383, Mismatches: 104, Indels: 70
0.69 0.19 0.13
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
20 6 0.02
21 43 0.11
22 252 0.66
23 65 0.17
24 4 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.40
Consensus pattern (21 bp):
TATGAAATTTTGATAACCTCC
Found at i:29872 original size:23 final size:22
Alignment explanation
Indices: 29846--29924 Score: 79
Period size: 23 Copynumber: 3.5 Consensus size: 22
29836 CTCACTATGT
29846 AATTTTGATAAATCTTTCTATAA
1 AATTTTGATAAA-CTTTCTATAA
* **
29869 AATTTTAATAAACCTCCCTATAA
1 AATTTTGATAAA-CTTTCTATAA
*
29892 AATTTTGAT-AACTTTCTTATGA
1 AATTTTGATAAACTTTC-TATAA
*
29914 AATCTTGATAA
1 AATTTTGATAA
29925 CTACAAATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
21 3 0.07
22 14 0.31
23 28 0.62
ACGTcount: A:0.39, C:0.13, G:0.05, T:0.43
Consensus pattern (22 bp):
AATTTTGATAAACTTTCTATAA
Found at i:30147 original size:20 final size:19
Alignment explanation
Indices: 30083--30150 Score: 82
Period size: 19 Copynumber: 3.5 Consensus size: 19
30073 CCTTCATATG
*
30083 AAATTTTGATATCCTCACT
1 AAATTTTGATATCCTCCCT
* *
30102 GAATTTTGATATCCTTCCT
1 AAATTTTGATATCCTCCCT
* *
30121 GAATTTTGGTATCCTCCCT
1 AAATTTTGATATCCTCCCT
30140 AAAATTTTGAT
1 -AAATTTTGAT
30151 TACTCCATCA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 33 0.80
20 8 0.20
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.44
Consensus pattern (19 bp):
AAATTTTGATATCCTCCCT
Found at i:30345 original size:22 final size:23
Alignment explanation
Indices: 30320--30450 Score: 103
Period size: 22 Copynumber: 5.8 Consensus size: 23
30310 TTGACCCCTC
*
30320 TATGATATTTTGATAATC-ACAT
1 TATGAAATTTTGATAATCAACAT
* * *
30342 TATGTAATTTTGATAATC-TCGCT
1 TATGAAATTTTGATAATCAAC-AT
*
30365 T-TGAAATTTTGATAA-CAACAC
1 TATGAAATTTTGATAATCAACAT
* **
30386 TATGAAATTGTGATAATCTTCA-
1 TATGAAATTTTGATAATCAACAT
*
30408 TAT-AAATTTTGATAATCATATCTT
1 TATGAAATTTTGATAATCA-A-CAT
*
30432 TATGAAATTTCGATAATCA
1 TATGAAATTTTGATAATCA
30451 CTCTATGAGA
Statistics
Matches: 85, Mismatches: 16, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
21 15 0.18
22 47 0.55
23 6 0.07
24 3 0.04
25 14 0.16
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.43
Consensus pattern (23 bp):
TATGAAATTTTGATAATCAACAT
Found at i:30374 original size:44 final size:43
Alignment explanation
Indices: 30326--30425 Score: 114
Period size: 44 Copynumber: 2.3 Consensus size: 43
30316 CCTCTATGAT
* * * * *
30326 ATTTTGATAATCACATTATGTAATTTTGATAATC-TCGCTTTGAA
1 ATTTTGATAATCACACTATGAAATTGTGATAATCTTC-ATAT-AA
30370 ATTTTGATAA-CAACACTATGAAATTGTGATAATCTTCATATAA
1 ATTTTGATAATC-ACACTATGAAATTGTGATAATCTTCATATAA
30413 ATTTTGATAATCA
1 ATTTTGATAATCA
30426 TATCTTTATG
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
43 14 0.29
44 32 0.67
45 2 0.04
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.42
Consensus pattern (43 bp):
ATTTTGATAATCACACTATGAAATTGTGATAATCTTCATATAA
Found at i:30537 original size:22 final size:22
Alignment explanation
Indices: 30256--30618 Score: 89
Period size: 22 Copynumber: 16.3 Consensus size: 22
30246 AATCAGATTT
* *
30256 TGAAAATTTGATAACC-TCTTTA
1 TGAAATTTTGATAACCTTC-ATA
30278 TGAAATTTTGATAACATCTT--TA
1 TGAAATTTTGATAAC--CTTCATA
* * * *
30300 TAAAATTTTGTTGACCCCTC-TA
1 TGAAATTTTGAT-AACCTTCATA
* * *
30322 TGATATTTTGATAATC-ACATTA
1 TGAAATTTTGATAACCTTCA-TA
* * * *
30344 TGTAATTTTGATAATC-TCGCTT
1 TGAAATTTTGATAACCTTC-ATA
**
30366 TGAAATTTTGATAA-CAACACTA
1 TGAAATTTTGATAACCTTCA-TA
* *
30388 TGAAATTGTGATAATCTTCATA
1 TGAAATTTTGATAACCTTCATA
* *
30410 T-AAATTTTGATAATCATATCTTTA
1 TGAAATTTTGATAA-CCT-TC-ATA
*
30434 TGAAATTTCGATAATCAC-TC-TA
1 TGAAATTTTGATAA-C-CTTCATA
*
30456 TGAGA-TTTGATAACCTTC-TA
1 TGAAATTTTGATAACCTTCATA
* *
30476 TCAAATTTTTG-TACTCCTT-ATGGAA
1 TGAAA-TTTTGATA-ACCTTCAT---A
*
30501 TTGAGACTTTT-ATAACCTTCATA
1 -TGA-AATTTTGATAACCTTCATA
*
30524 TGAAATTTTGATAACC-ACACTA
1 TGAAATTTTGATAACCTTCA-TA
* * **
30546 TAAAATTTTGATAACCTCCCGA
1 TGAAATTTTGATAACCTTCATA
* *
30568 TGAAGTATT-AGTAACCTTC-TAA
1 TGAAATTTTGA-TAACCTTCAT-A
* *
30590 TGAAATTTTGTTAACC-ACACTA
1 TGAAATTTTGATAACCTTCA-TA
30612 TGAAATT
1 TGAAATT
30619 CGTATAACCT
Statistics
Matches: 253, Mismatches: 52, Indels: 72
0.67 0.14 0.19
Matches are distributed among these distances:
19 1 0.00
20 9 0.04
21 34 0.13
22 163 0.64
23 10 0.04
24 6 0.02
25 19 0.08
26 10 0.04
27 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTCATA
Found at i:30743 original size:24 final size:22
Alignment explanation
Indices: 30682--30822 Score: 74
Period size: 22 Copynumber: 6.3 Consensus size: 22
30672 TTGTGATAAT
*
30682 TAACC-ACTCTATGAAATTTCAA
1 TAACCAAC-CTATGAAATTTTAA
*
30704 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
* * **
30726 TAACTTGATCCTATGAAATTTTGG
1 TAAC--CAACCTATGAAATTTTAA
* **
30750 TAA-CTACACTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
* *
30772 TAACC-ACACTATGGAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
* * *
30794 TAACC-TCCTCATGGAATTATAA
1 TAACCAACCT-ATGAAATTTTAA
30816 TAACCAA
1 TAACCAA
30823 AGTAAAATTT
Statistics
Matches: 96, Mismatches: 16, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
21 3 0.03
22 74 0.77
23 3 0.03
24 16 0.17
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:30764 original size:22 final size:22
Alignment explanation
Indices: 30736--30798 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
30726 TAACTTGATC
*
30736 CTATGAAATTTTGGTAACTACA
1 CTATGAAATTTTGGTAACCACA
30758 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
* *
30780 CTATGGAATTTTGATAACC
1 CTATGAAATTTTGGTAACC
30799 TCCTCATGGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACA
Found at i:30807 original size:22 final size:22
Alignment explanation
Indices: 30736--30821 Score: 84
Period size: 22 Copynumber: 3.9 Consensus size: 22
30726 TAACTTGATC
* * *
30736 CTATGAAATTTTGGTAACTACA
1 CTATGGAATTTTGATAACCACA
* *
30758 CTATGAAATTTTGGTAACCACA
1 CTATGGAATTTTGATAACCACA
*
30780 CTATGGAATTTTGATAACCTC-
1 CTATGGAATTTTGATAACCACA
* *
30801 CTCATGGAATTATAATAACCA
1 CT-ATGGAATTTTGATAACCA
30822 AAGTAAAATT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
21 2 0.04
22 54 0.96
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (22 bp):
CTATGGAATTTTGATAACCACA
Found at i:31096 original size:14 final size:14
Alignment explanation
Indices: 31067--31107 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
31057 CCTTATTTAT
31067 TTATAATATT-GAA
1 TTATAATATTAGAA
*
31080 TTATTATATTAGAA
1 TTATAATATTAGAA
*
31094 TTAGAATATTAGAA
1 TTATAATATTAGAA
31108 AAACTGTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (14 bp):
TTATAATATTAGAA
Done.