Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011854.1 Corchorus capsularis cultivar CVL-1 contig11875, 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: 30103
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:4547 original size:11 final size:11
Alignment explanation
Indices: 4531--4556 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4521 CTGTGGGTAC
4531 ACTGAAATTTA
1 ACTGAAATTTA
4542 ACTGAAATTTA
1 ACTGAAATTTA
4553 ACTG
1 ACTG
4557 CTCTTTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (11 bp):
ACTGAAATTTA
Found at i:11929 original size:19 final size:19
Alignment explanation
Indices: 11905--11946 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
11895 CATGTTAAGT
11905 GATTAGTTTAATTATGAAA
1 GATTAGTTTAATTATGAAA
11924 GATTAGTTTAATTATGAAA
1 GATTAGTTTAATTATGAAA
11943 GATT
1 GATT
11947 GATGCTTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (19 bp):
GATTAGTTTAATTATGAAA
Found at i:17993 original size:7 final size:7
Alignment explanation
Indices: 17983--18023 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
17973 TAAAAACTTA
17983 TATAAAT
1 TATAAAT
*
17990 TATATAT
1 TATAAAT
*
17997 TA-AACT
1 TATAAAT
18003 TA-AAAT
1 TATAAAT
18009 TATAAAT
1 TATAAAT
18016 TATAAAT
1 TATAAAT
18023 T
1 T
18024 TTAGATACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 9 0.31
7 20 0.69
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (7 bp):
TATAAAT
Found at i:18572 original size:48 final size:48
Alignment explanation
Indices: 18518--18618 Score: 175
Period size: 48 Copynumber: 2.1 Consensus size: 48
18508 ATAACTATAC
18518 TAAAAAATAACACTTTGTACAAATATAAGAGGTATTTAGAGGTTTAGA
1 TAAAAAATAACACTTTGTACAAATATAAGAGGTATTTAGAGGTTTAGA
* * *
18566 TAAAAAATAATACTTTGTATAAATATAAGAGGTATTTAGATGTTTAGA
1 TAAAAAATAACACTTTGTACAAATATAAGAGGTATTTAGAGGTTTAGA
18614 TAAAA
1 TAAAA
18619 TGATATATAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.48, C:0.04, G:0.15, T:0.34
Consensus pattern (48 bp):
TAAAAAATAACACTTTGTACAAATATAAGAGGTATTTAGAGGTTTAGA
Found at i:19110 original size:22 final size:22
Alignment explanation
Indices: 19006--19340 Score: 141
Period size: 22 Copynumber: 15.7 Consensus size: 22
18996 TTGAAGATCT
**
19006 CACTATGAAATTTTGATAACTT
1 CACTATGAAATTTTGATAACCA
* *
19028 CCCAATGAAATTTTGATAACCAA
1 CACTATGAAATTTTGATAACC-A
*
19051 CACTATGAAATTTTGATAACCT
1 CACTATGAAATTTTGATAACCA
* * ** *
19073 CCCTGTGAAACGTTGATAAGCA
1 CACTATGAAATTTTGATAACCA
* * *
19095 CATTATGAAATTTTGAAAACCT
1 CACTATGAAATTTTGATAACCA
* *
19117 C-CATATGAAATGTT-AGTAATCA
1 CAC-TATGAAATTTTGA-TAACCA
**
19139 CACTATGAAA-TTTGATAAATCTT
1 CACTATGAAATTTTGAT-AA-CCA
* *
19162 C-CTATAAAATTCTGATAA--A
1 CACTATGAAATTTTGATAACCA
*
19181 C-CTCATGAAATTTTAATAA--A
1 CACT-ATGAAATTTTGATAACCA
* *
19201 CAC----AAGTTTTGATAACCT
1 CACTATGAAATTTTGATAACCA
* ** *
19219 CCCTATGATTTTTTGATAACCT
1 CACTATGAAATTTTGATAACCA
* * *
19241 CATTATGAAATTTTGTTAACCT
1 CACTATGAAATTTTGATAACCA
*
19263 C-CATATGAAATTTTGAT--CTA
1 CAC-TATGAAATTTTGATAACCA
*
19283 CACTATGAAAATTTG--AACCA
1 CACTATGAAATTTTGATAACCA
* * *
19303 CATTATAAAACTTTGATAACC-
1 CACTATGAAATTTTGATAACCA
* *
19324 CTCCTATGAAAATTTGA
1 C-ACTATGAAATTTTGA
19341 AAACTAAGGG
Statistics
Matches: 230, Mismatches: 60, Indels: 46
0.68 0.18 0.14
Matches are distributed among these distances:
16 10 0.04
18 2 0.01
19 3 0.01
20 41 0.18
21 7 0.03
22 141 0.61
23 26 0.11
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (22 bp):
CACTATGAAATTTTGATAACCA
Found at i:19116 original size:44 final size:44
Alignment explanation
Indices: 18980--19156 Score: 180
Period size: 44 Copynumber: 4.0 Consensus size: 44
18970 AGTTTTGTTT
* * * *
18980 ACCTCCCTATGGAATTTTGA-AGATCTCACTATGAAATTTTGATA
1 ACCTCCCTATGAAATGTTGATA-ACCACACTATGAAATTTTGATA
* * *
19024 ACTTCCCAATGAAATTTTGATAACCAACACTATGAAATTTTGATA
1 ACCTCCCTATGAAATGTTGATAACC-ACACTATGAAATTTTGATA
* * * * *
19069 ACCTCCCTGTGAAACGTTGATAAGCACATTATGAAATTTTGAAA
1 ACCTCCCTATGAAATGTTGATAACCACACTATGAAATTTTGATA
* *
19113 ACCTCCATATGAAATGTT-AGTAATCACACTATGAAA-TTTGATA
1 ACCTCCCTATGAAATGTTGA-TAACCACACTATGAAATTTTGATA
19156 A
1 A
19157 ATCTTCCTAT
Statistics
Matches: 111, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
43 8 0.07
44 65 0.59
45 38 0.34
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (44 bp):
ACCTCCCTATGAAATGTTGATAACCACACTATGAAATTTTGATA
Found at i:21227 original size:28 final size:28
Alignment explanation
Indices: 21151--21286 Score: 202
Period size: 28 Copynumber: 4.8 Consensus size: 28
21141 GAGGCTAAAT
* *
21151 GCTCAATTTGGTCCTAAACCTTTCA-CG
1 GCTCAATTTGGTCCTAAACCTCTGACCG
*
21178 GTCTGCTTGATTTGGTCCTAAACCTCTGACCG
1 G-CT-C--AATTTGGTCCTAAACCTCTGACCG
21210 GCTCAATTTGGTCCTAAACCTCTGACCG
1 GCTCAATTTGGTCCTAAACCTCTGACCG
21238 GCTCAATTTGGTCCTAAACCTCTGACCG
1 GCTCAATTTGGTCCTAAACCTCTGACCG
21266 GCTCAATTTGGTCCTAAACCT
1 GCTCAATTTGGTCCTAAACCT
21287 TTCAATTTCT
Statistics
Matches: 100, Mismatches: 4, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
27 1 0.01
28 74 0.74
29 1 0.01
30 1 0.01
31 20 0.20
32 3 0.03
ACGTcount: A:0.21, C:0.30, G:0.18, T:0.32
Consensus pattern (28 bp):
GCTCAATTTGGTCCTAAACCTCTGACCG
Found at i:25055 original size:31 final size:29
Alignment explanation
Indices: 24985--25070 Score: 111
Period size: 29 Copynumber: 2.9 Consensus size: 29
24975 GTTAAGAAAT
*
24985 TGAAAGGTTTAGGACCAAATTGAGC-CGG
1 TGAAAGGTTTAGGACCAAATTGAGCACCG
* *
25013 TTAGAAGGTTTAGGACCAAATCGAGCAGACCG
1 TGA-AAGGTTTAGGACCAAATTGAGC--ACCG
25045 TGAAAGGTTTAGGACCAAATTGAGCA
1 TGAAAGGTTTAGGACCAAATTGAGCA
25071 TTTAGCCCTG
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
28 2 0.04
29 22 0.45
31 21 0.43
32 4 0.08
ACGTcount: A:0.35, C:0.15, G:0.29, T:0.21
Consensus pattern (29 bp):
TGAAAGGTTTAGGACCAAATTGAGCACCG
Found at i:25417 original size:22 final size:22
Alignment explanation
Indices: 25368--25443 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
25358 CTAAACTATG
25368 AAATTTTGATAAGTTCCTT-AT-TA
1 AAATTTTGATAA---CCTTCATATA
25391 AAATTTTGATAACCTTCATATA
1 AAATTTTGATAACCTTCATATA
* *
25413 AAATTTTAATATCCTTCATAT-
1 AAATTTTGATAACCTTCATATA
*
25434 GAATTTTGAT
1 AAATTTTGAT
25444 TACTCTATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.09
21 10 0.21
22 21 0.45
23 12 0.26
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.46
Consensus pattern (22 bp):
AAATTTTGATAACCTTCATATA
Found at i:25440 original size:21 final size:22
Alignment explanation
Indices: 25389--25472 Score: 75
Period size: 22 Copynumber: 3.9 Consensus size: 22
25379 AGTTCCTTAT
*
25389 TAAAATTTTGATAACCTTCATA
1 TAAAATTTTAATAACCTTCATA
*
25411 TAAAATTTTAATATCCTTCATA
1 TAAAATTTTAATAACCTTCATA
* * *
25433 T-GAATTTTGATTA-C-TCTATAA
1 TAAAATTTTAATAACCTTC-AT-A
*
25454 TAATATTTTAATAACCTTC
1 TAAAATTTTAATAACCTTC
25473 CTAATTTGTT
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
19 2 0.04
20 3 0.06
21 10 0.21
22 29 0.62
23 1 0.02
24 2 0.04
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.45
Consensus pattern (22 bp):
TAAAATTTTAATAACCTTCATA
Found at i:25576 original size:21 final size:22
Alignment explanation
Indices: 25550--25644 Score: 113
Period size: 22 Copynumber: 4.4 Consensus size: 22
25540 GATCATACTT
25550 TGAAATTTTGATAACCTC-CTA
1 TGAAATTTTGATAACCTCTCTA
*
25571 TGAAATCTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* *
25593 CGAAATTTT-ATTGACCTCTCTA
1 TGAAATTTTGA-TAACCTCTCTA
* * *
25615 TGAAATTTTGATAATCACACTA
1 TGAAATTTTGATAACCTCTCTA
25637 TGAAATTT
1 TGAAATTT
25645 CCATATGAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
21 18 0.29
22 43 0.69
23 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:25637 original size:22 final size:22
Alignment explanation
Indices: 25522--25644 Score: 108
Period size: 22 Copynumber: 5.6 Consensus size: 22
25512 CTCAAAACTA
* * *
25522 TCACTATGAAATTTTGGTGATCA
1 TCACTATGAAATTTTGAT-AACC
*
25545 T-ACTTTGAAATTTTGATAACC
1 TCACTATGAAATTTTGATAACC
*
25566 TC-CTATGAAATCTTGATAACC
1 TCACTATGAAATTTTGATAACC
* * *
25587 TCTCTACGAAATTTT-ATTGACC
1 TCACTATGAAATTTTGA-TAACC
* *
25609 TCTCTATGAAATTTTGATAATC
1 TCACTATGAAATTTTGATAACC
*
25631 ACACTATGAAATTT
1 TCACTATGAAATTT
25645 CCATATGAAA
Statistics
Matches: 82, Mismatches: 14, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
21 23 0.28
22 57 0.70
23 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.40
Consensus pattern (22 bp):
TCACTATGAAATTTTGATAACC
Found at i:25642 original size:44 final size:42
Alignment explanation
Indices: 25525--26135 Score: 179
Period size: 44 Copynumber: 14.2 Consensus size: 42
25515 AAAACTATCA
* * * *
25525 CTATGAAATTTTGGTGATCATACTTTGAAATTTTGATAACCTC
1 CTATGAAATTTTGATAATCACACTATGAAATTTT-ATAACCTC
* * * * * *
25568 CTATGAAATCTTGATAACCTCTCTACGAAATTTTATTGACCTC
1 CTATGAAATTTTGATAATCACACTATGAAATTTTA-TAACCTC
25611 TCTATGAAATTTTGATAATCACACTATGAAA--TT-T---C-C
1 -CTATGAAATTTTGATAATCACACTATGAAATTTTATAACCTC
* * * * * *
25647 ATATGAAATTTTGATAAACACTCTATAAAATCTTGATAATCTC
1 CTATGAAATTTTGATAATCACACTATGAAAT-TTTATAACCTC
** * *
25690 ACTATGAAATTTTGATAATCAGTCTATGTGAATTTGATAACCTC
1 -CTATGAAATTTTGATAATCACACTATG-AAATTTTATAACCTC
* * * * *
25734 TTTATGAAATTTCGATAACCACACTATAAAATTTTGATAAACTCC
1 -CTATGAAATTTTGATAATCACACTATGAAATTTT-ATAACCT-C
* * * * * * *
25779 CTGTCATATTTTGATAATCTC-CTTATGAAATTGAGATTTTTATATCTTTT
1 CTATGAAATTTTGATAATCACAC-TATG--A---A-A-TTTTATAAC-CTC
* * * *
25829 CTATAAAATTTCGGTAACCACACTATGAAATTTTGATAACCTC
1 CTATGAAATTTTGATAATCACACTATGAAATTTT-ATAACCTC
* * * * * *
25872 CTTTTGAAATTTTGTTGACCAAACTATGAAATTCTGATAACCTC
1 C-TATGAAATTTTGATAATCACACTATGAAATT-TTATAACCTC
* * * * * * *
25916 GTTATGAATTTTTGATAACCTCCCTAT-AAATTTTTGACAACCAC
1 -CTATGAAATTTTGATAATCACACTATGAAA-TTTT-ATAACCTC
* **
25960 AT-TGAAATTTTGATAA-CATTTCTATGAAATTATTATAACCTGATC
1 CTATGAAATTTTGATAATCA-CACTATGAAATT-TTATAACC---TC
*
26005 CTATGAAA---T--T--T--CA-TAGGAAATTATTATAACCTTC
1 CTATGAAATTTTGATAATCACACTATGAAATT-TTATAACC-TC
* * * * *
26039 CTGTCAAATTTTGGTAACCACAATATGAAATTTTGATAACC-C
1 CTATGAAATTTTGATAATCACACTATGAAATTTT-ATAACCTC
* * * *
26081 CATATGAAATTTTGGTAA-CTAAACTAAGAAATTTTGATAACCTT
1 C-TATGAAATTTTGATAATC-ACACTATGAAATTTT-ATAACCTC
26125 CTCATGAAATT
1 CT-ATGAAATT
26136 ATAATAACCT
Statistics
Matches: 417, Mismatches: 98, Indels: 105
0.67 0.16 0.17
Matches are distributed among these distances:
34 8 0.02
35 26 0.06
36 18 0.04
37 2 0.00
38 1 0.00
39 2 0.00
40 1 0.00
41 2 0.00
42 31 0.07
43 93 0.22
44 189 0.45
45 8 0.02
46 6 0.01
48 1 0.00
49 1 0.00
50 22 0.05
51 6 0.01
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (42 bp):
CTATGAAATTTTGATAATCACACTATGAAATTTTATAACCTC
Found at i:25682 original size:22 final size:22
Alignment explanation
Indices: 25652--25775 Score: 88
Period size: 22 Copynumber: 5.6 Consensus size: 22
25642 TTTCCATATG
25652 AAATTTTGATAAACACTCTATA
1 AAATTTTGATAAACACTCTATA
* * * * *
25674 AAATCTTGATAATCTCACTATG
1 AAATTTTGATAAACACTCTATA
* * *
25696 AAATTTTGATAATCAGTCTATGT
1 AAATTTTGATAAACACTCTAT-A
* * * * *
25719 GAA-TTTGATAACCTCTTTATG
1 AAATTTTGATAAACACTCTATA
* * *
25740 AAATTTCGATAACCACACTATA
1 AAATTTTGATAAACACTCTATA
25762 AAATTTTGATAAAC
1 AAATTTTGATAAAC
25776 TCCCTGTCAT
Statistics
Matches: 76, Mismatches: 24, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
21 2 0.03
22 72 0.95
23 2 0.03
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.37
Consensus pattern (22 bp):
AAATTTTGATAAACACTCTATA
Found at i:25868 original size:22 final size:22
Alignment explanation
Indices: 25829--25976 Score: 106
Period size: 22 Copynumber: 6.8 Consensus size: 22
25819 TATATCTTTT
* * *
25829 CTATAAAATTTCGGTAACCACA
1 CTATGAAATTTTGATAACCACA
*
25851 CTATGAAATTTTGATAACCTC-
1 CTATGAAATTTTGATAACCACA
* * * *
25872 CTTTTGAAATTTTGTTGACCAAA
1 C-TATGAAATTTTGATAACCACA
* * *
25895 CTATGAAATTCTGATAACCTCG
1 CTATGAAATTTTGATAACCACA
* * * *
25917 TTATGAATTTTTGATAACCTCC
1 CTATGAAATTTTGATAACCACA
*
25939 CTAT-AAATTTTTGACAACCACA
1 CTATGAAA-TTTTGATAACCACA
25961 -T-TGAAATTTTGATAAC
1 CTATGAAATTTTGATAAC
25977 ATTTCTATGA
Statistics
Matches: 96, Mismatches: 26, Indels: 10
0.73 0.20 0.08
Matches are distributed among these distances:
20 10 0.10
21 7 0.07
22 78 0.81
23 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.37
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:26069 original size:22 final size:22
Alignment explanation
Indices: 26044--26122 Score: 90
Period size: 22 Copynumber: 3.6 Consensus size: 22
26034 CCTTCCTGTC
*
26044 AAATTTTGGTAACCACAATATG
1 AAATTTTGATAACCACAATATG
*
26066 AAATTTTGATAACC-CCATATG
1 AAATTTTGATAACCACAATATG
* * *
26087 AAATTTTGGTAACTA-AACTAAG
1 AAATTTTGATAACCACAA-TATG
26109 AAATTTTGATAACC
1 AAATTTTGATAACC
26123 TTCTCATGAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
21 19 0.40
22 28 0.60
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (22 bp):
AAATTTTGATAACCACAATATG
Found at i:26133 original size:22 final size:22
Alignment explanation
Indices: 26108--26163 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
26098 ACTAAACTAA
26108 GAAATTTTGATAACCTTCTCAT
1 GAAATTTTGATAACCTTCTCAT
* * *
26130 GAAATTATAATAACCTTCTTAT
1 GAAATTTTGATAACCTTCTCAT
* *
26152 AAAATCTTGATA
1 GAAATTTTGATA
26164 GTATCCCTTA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.39
Consensus pattern (22 bp):
GAAATTTTGATAACCTTCTCAT
Found at i:26392 original size:29 final size:25
Alignment explanation
Indices: 26356--26408 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
26346 AATCCGGTCA
26356 AAATTAAAATTTTATAATTAATTTTTAT
1 AAATTAAAA--TTAT-ATTAATTTTTAT
26384 AAATATAAAATTATATTAATTTTTA
1 AAAT-TAAAATTATATTAATTTTTA
26409 ATAATGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 11 0.46
27 4 0.17
28 4 0.17
29 5 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
AAATTAAAATTATATTAATTTTTAT
Done.