Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015019.1 Corchorus capsularis cultivar CVL-1 contig15040, 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: 54446
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Found at i:17441 original size:18 final size:20
Alignment explanation
Indices: 17389--17439 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
17379 AACACGAAGC
17389 TAAAAAAAAAAATGAGTAAAA
1 TAAAAAAAAAAATGAG-AAAA
*
17410 TAAAAACAAAAATGA-AAAA
1 TAAAAAAAAAAATGAGAAAA
17429 TAAAATAAAAA
1 TAAAA-AAAAA
17440 TGTAGCAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 9 0.33
20 4 0.15
21 14 0.52
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (20 bp):
TAAAAAAAAAAATGAGAAAA
Found at i:25564 original size:18 final size:18
Alignment explanation
Indices: 25538--25615 Score: 120
Period size: 18 Copynumber: 4.3 Consensus size: 18
25528 CTTGGCAACC
*
25538 AATGCAGAGAACAGGGTT
1 AATGAAGAGAACAGGGTT
*
25556 AATGAAGAGCACAGGGTT
1 AATGAAGAGAACAGGGTT
*
25574 AATGAAGACAACAGGGTT
1 AATGAAGAGAACAGGGTT
*
25592 GATGAAGAGAACAGGGTT
1 AATGAAGAGAACAGGGTT
25610 AATGAA
1 AATGAA
25616 CTTCTGGATC
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 53 1.00
ACGTcount: A:0.42, C:0.09, G:0.32, T:0.17
Consensus pattern (18 bp):
AATGAAGAGAACAGGGTT
Found at i:31332 original size:2 final size:2
Alignment explanation
Indices: 31325--31355 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
31315 TAAATCAGGC
31325 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31356 CTTTAATGAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33791 original size:2 final size:2
Alignment explanation
Indices: 33786--33814 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
33776 AAAGGGTGTG
33786 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 T
33815 TAGATTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48279 original size:30 final size:30
Alignment explanation
Indices: 48243--48302 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
48233 AGTCTTTTCC
48243 AGAGTGTATAAAATTAATATGTAGTATATA
1 AGAGTGTATAAAATTAATATGTAGTATATA
48273 AGAGTGTATAAAATTAATATGTAGTATATA
1 AGAGTGTATAAAATTAATATGTAGTATATA
48303 TGAGAATGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.17, T:0.37
Consensus pattern (30 bp):
AGAGTGTATAAAATTAATATGTAGTATATA
Found at i:48858 original size:23 final size:23
Alignment explanation
Indices: 48813--49052 Score: 215
Period size: 23 Copynumber: 10.7 Consensus size: 23
48803 CTTCCAAAAT
* * * *
48813 TAACGCCCAACCACTTGCGAGCC
1 TAACGACCGACCACTTACAAGCC
*
48836 TAACGACCGACCACTTATAAGCC
1 TAACGACCGACCACTTACAAGCC
*
48859 TAGCGACCGACCACTTACAAGCC
1 TAACGACCGACCACTTACAAGCC
*** *
48882 T-A-G--CGA-CA--TAATGGCT
1 TAACGACCGACCACTTACAAGCC
* * * **
48898 TAGCGCCCGACCACTTCCAAGAT
1 TAACGACCGACCACTTACAAGCC
* *
48921 TAACGCCCGACCACTTACAAGTC
1 TAACGACCGACCACTTACAAGCC
48944 TAACGACCGACCACTTACAAGCC
1 TAACGACCGACCACTTACAAGCC
48967 TAACGACCGACCACTTACAAGCC
1 TAACGACCGACCACTTACAAGCC
** *
48990 TGGCGCCCGACCACTTACAAGCC
1 TAACGACCGACCACTTACAAGCC
*
49013 TAGCGACCGACCACTTACAAGCC
1 TAACGACCGACCACTTACAAGCC
** *
49036 TGGCGCCCGACCACTTA
1 TAACGACCGACCACTTA
49053 TGACCACAAG
Statistics
Matches: 179, Mismatches: 31, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
16 5 0.03
18 3 0.02
19 3 0.02
20 3 0.02
21 3 0.02
23 162 0.91
ACGTcount: A:0.29, C:0.38, G:0.17, T:0.15
Consensus pattern (23 bp):
TAACGACCGACCACTTACAAGCC
Found at i:48872 original size:46 final size:46
Alignment explanation
Indices: 48816--49052 Score: 256
Period size: 46 Copynumber: 5.3 Consensus size: 46
48806 CCAAAATTAA
* * * *
48816 CGCCCAACCACTTGCGAGCCTAACGACCGACCACTTATAAGCCTAG
1 CGCCCGACCACTTACAAGCCTAACGACCGACCACTTACAAGCCTAG
* * *
48862 CGACCGACCACTTACAAGCCT-A-G--CGA-CA--TA-ATGGCTTAG
1 CGCCCGACCACTTACAAGCCTAACGACCGACCACTTACA-AGCCTAG
* ** * * *
48901 CGCCCGACCACTTCCAAGATTAACGCCCGACCACTTACAAGTCTAA
1 CGCCCGACCACTTACAAGCCTAACGACCGACCACTTACAAGCCTAG
* *
48947 CGACCGACCACTTACAAGCCTAACGACCGACCACTTACAAGCCTGG
1 CGCCCGACCACTTACAAGCCTAACGACCGACCACTTACAAGCCTAG
* *
48993 CGCCCGACCACTTACAAGCCTAGCGACCGACCACTTACAAGCCTGG
1 CGCCCGACCACTTACAAGCCTAACGACCGACCACTTACAAGCCTAG
49039 CGCCCGACCACTTA
1 CGCCCGACCACTTA
49053 TGACCACAAG
Statistics
Matches: 158, Mismatches: 24, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
38 1 0.01
39 24 0.15
40 1 0.01
41 3 0.02
42 3 0.02
43 3 0.02
44 3 0.02
45 1 0.01
46 118 0.75
47 1 0.01
ACGTcount: A:0.29, C:0.39, G:0.17, T:0.15
Consensus pattern (46 bp):
CGCCCGACCACTTACAAGCCTAACGACCGACCACTTACAAGCCTAG
Found at i:48974 original size:108 final size:108
Alignment explanation
Indices: 48778--48990 Score: 354
Period size: 108 Copynumber: 2.0 Consensus size: 108
48768 TGTTGAGCAT
* *
48778 GACACAATGGCTTAGCGCCCGACCACTTCCAAAATTAACGCCCAACCACTTGCGAGCCTAACGAC
1 GACACAATGGCTTAGCGCCCGACCACTTCCAAAATTAACGCCCAACCACTTACAAGCCTAACGAC
* *
48843 CGACCACTTATAAGCCTAGCGACCGACCACTTACAAGCCTAGC
66 CGACCACTTACAAGCCTAACGACCGACCACTTACAAGCCTAGC
* * * *
48886 GACATAATGGCTTAGCGCCCGACCACTTCCAAGATTAACGCCCGACCACTTACAAGTCTAACGAC
1 GACACAATGGCTTAGCGCCCGACCACTTCCAAAATTAACGCCCAACCACTTACAAGCCTAACGAC
48951 CGACCACTTACAAGCCTAACGACCGACCACTTACAAGCCT
66 CGACCACTTACAAGCCTAACGACCGACCACTTACAAGCCT
48991 GGCGCCCGAC
Statistics
Matches: 97, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
108 97 1.00
ACGTcount: A:0.31, C:0.37, G:0.16, T:0.16
Consensus pattern (108 bp):
GACACAATGGCTTAGCGCCCGACCACTTCCAAAATTAACGCCCAACCACTTACAAGCCTAACGAC
CGACCACTTACAAGCCTAACGACCGACCACTTACAAGCCTAGC
Found at i:49128 original size:26 final size:26
Alignment explanation
Indices: 49092--49187 Score: 131
Period size: 26 Copynumber: 3.7 Consensus size: 26
49082 GCCAACTGGC
49092 ACTCCACACGTGACCTCCGAAGTACA
1 ACTCCACACGTGACCTCCGAAGTACA
* *
49118 ACTCCGCACGTGACCTCC-AACGGACA
1 ACTCCACACGTGACCTCCGAA-GTACA
* *
49144 CCTTCAACACGTGACCTCCGAAGTACA
1 AC-TCCACACGTGACCTCCGAAGTACA
49171 ACTCCACACGTGACCTC
1 ACTCCACACGTGACCTC
49188 ACGCGTGCGA
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
25 2 0.03
26 36 0.61
27 19 0.32
28 2 0.03
ACGTcount: A:0.28, C:0.41, G:0.16, T:0.16
Consensus pattern (26 bp):
ACTCCACACGTGACCTCCGAAGTACA
Found at i:51048 original size:90 final size:90
Alignment explanation
Indices: 50894--51065 Score: 281
Period size: 90 Copynumber: 1.9 Consensus size: 90
50884 AAATTATACT
* * * *
50894 TGACGGACGCCCCCAAGGGGCTCAACGCCAGCAGGCGGGGCGATCGACAAGATTTGACCCTGACC
1 TGACGAACGCCCCCAAGGGGCTCAACGCCAGCAGGCGAGGCGATCGACAAGAATCGACCCTGACC
50959 TAGCATGGCCCCCAACTTATGGGAA
66 TAGCATGGCCCCCAACTTATGGGAA
* * *
50984 TGACGAACGCCCCCAATGGGCTCAATGCCAGCAGGCGAGGCGATCGACAAGAATCGACCTTGACC
1 TGACGAACGCCCCCAAGGGGCTCAACGCCAGCAGGCGAGGCGATCGACAAGAATCGACCCTGACC
51049 TAGCATGGCCCCCAACT
66 TAGCATGGCCCCCAACT
51066 GACAGGAGAT
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 75 1.00
ACGTcount: A:0.26, C:0.33, G:0.28, T:0.13
Consensus pattern (90 bp):
TGACGAACGCCCCCAAGGGGCTCAACGCCAGCAGGCGAGGCGATCGACAAGAATCGACCCTGACC
TAGCATGGCCCCCAACTTATGGGAA
Found at i:51407 original size:58 final size:58
Alignment explanation
Indices: 51313--51619 Score: 436
Period size: 58 Copynumber: 5.3 Consensus size: 58
51303 GGCCATCGAC
* * * * *
51313 AAAGTGGCAAGCGACAACACAGAAAGGGAAGGAGACAAGTGAAAAATTCTCATTTGCA
1 AAAGTGGCGAGCGACAACATAGAAAGGGAAGAAGACAAGTAAAAAATTCTCAATTGCA
* * *
51371 AAAGTGGCGAGCGACAACATAGAATGGGAAGAAGACAAGTCAAAAATTCTTAATTGCA
1 AAAGTGGCGAGCGACAACATAGAAAGGGAAGAAGACAAGTAAAAAATTCTCAATTGCA
** ** * *
51429 AAAGTGGTTAGCGACAGTATAGAAAGGGAAGAAGACAAGTAAAAAATTCTCATTTGTA
1 AAAGTGGCGAGCGACAACATAGAAAGGGAAGAAGACAAGTAAAAAATTCTCAATTGCA
*
51487 AAAGTGGCGAGCGACAACATAGAAAGGGAAGGAGACAAGTAAAAAATTCTCAATTGCA
1 AAAGTGGCGAGCGACAACATAGAAAGGGAAGAAGACAAGTAAAAAATTCTCAATTGCA
* *
51545 AAAGTGGCGAGCGACATCATAGAAAGGGAATG-AGACAAGTCAAAAATTCTCAATTGCA
1 AAAGTGGCGAGCGACAACATAGAAAGGGAA-GAAGACAAGTAAAAAATTCTCAATTGCA
*
51603 AAAGTGGCGTGCGACAA
1 AAAGTGGCGAGCGACAA
51620 GAAAAACAAA
Statistics
Matches: 221, Mismatches: 27, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
58 220 1.00
59 1 0.00
ACGTcount: A:0.44, C:0.14, G:0.25, T:0.17
Consensus pattern (58 bp):
AAAGTGGCGAGCGACAACATAGAAAGGGAAGAAGACAAGTAAAAAATTCTCAATTGCA
Found at i:52407 original size:43 final size:44
Alignment explanation
Indices: 51940--52399 Score: 728
Period size: 44 Copynumber: 10.7 Consensus size: 44
51930 CCCCTCGGAA
*
51940 ACATCACATTCAAACCAAGAAGAAAAGTAACTAGTCGATCGACC
1 ACATCACATTCAAACCAAGAAGAGAAGTAACTAGTCGATCGACC
*
51984 ACATCACATTCAAACCAAGAAGAGAAGTAACTAGTCGACCGACC
1 ACATCACATTCAAACCAAGAAGAGAAGTAACTAGTCGATCGACC
*
52028 ACATCACATTCAAACCAAGAAGAGAAGTAACTAGTCGACCGACC
1 ACATCACATTCAAACCAAGAAGAGAAGTAACTAGTCGATCGACC
52072 ACATCACATTCAAACCAAGAAGAGAAGTAACTAGTCGATCGACC
1 ACATCACATTCAAACCAAGAAGAGAAGTAACTAGTCGATCGACC
52116 ACATCACATTCAAACCAAGAAGAGAAGTAACTAGTCGATCGACC
1 ACATCACATTCAAACCAAGAAGAGAAGTAACTAGTCGATCGACC
52160 ACATCACATTCAAACCAAGAAGAGAAGTAACTAGTCGATCGACC
1 ACATCACATTCAAACCAAGAAGAGAAGTAACTAGTCGATCGACC
* **
52204 ACAT--CA-T------AAGAAGAAAAG-AACCGGTCGATCGACC
1 ACATCACATTCAAACCAAGAAGAGAAGTAACTAGTCGATCGACC
52238 ACATCACATTCAAACCAAGAAGAGAAGTAACTAGTCGATCGACC
1 ACATCACATTCAAACCAAGAAGAGAAGTAACTAGTCGATCGACC
52282 ACATCACATTCAAACCAAGAAGAGAAGTAACTAGTCGATCGACC
1 ACATCACATTCAAACCAAGAAGAGAAGTAACTAGTCGATCGACC
* *
52326 ACATCACATTAAAACCAAGAAGAGAAG-AACTAGTCGATCGATC
1 ACATCACATTCAAACCAAGAAGAGAAGTAACTAGTCGATCGACC
* * * *
52369 ACACCACACTCAAACCAAAAAGATAAG-AACT
1 ACATCACATTCAAACCAAGAAGAGAAGTAACT
52400 TGGCGATCAG
Statistics
Matches: 390, Mismatches: 16, Indels: 21
0.91 0.04 0.05
Matches are distributed among these distances:
34 18 0.05
35 10 0.03
36 2 0.01
37 1 0.00
41 1 0.00
42 2 0.01
43 51 0.13
44 305 0.78
ACGTcount: A:0.45, C:0.25, G:0.15, T:0.15
Consensus pattern (44 bp):
ACATCACATTCAAACCAAGAAGAGAAGTAACTAGTCGATCGACC
Found at i:54243 original size:38 final size:37
Alignment explanation
Indices: 54192--54331 Score: 208
Period size: 38 Copynumber: 3.7 Consensus size: 37
54182 AAAAAACTGG
* *
54192 CGACAAGCTGACAAAATGTGTCGACCGCCATGTTGCT
1 CGACAAGCTGACAAAATGTGTCGACCGCCACGTCGCT
*
54229 CGACAAAGTTGACAAAATGTGTCGACCGCCACGTCGCT
1 CGAC-AAGCTGACAAAATGTGTCGACCGCCACGTCGCT
* * *
54267 CGACAAAGCTGACCAAATGTGTCGACCACCACGTCGTT
1 CGAC-AAGCTGACAAAATGTGTCGACCGCCACGTCGCT
54305 CGACAAGCTGACAAAATGTGTCGACCG
1 CGACAAGCTGACAAAATGTGTCGACCG
54332 TCATAGACCA
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
37 25 0.27
38 68 0.73
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.19
Consensus pattern (37 bp):
CGACAAGCTGACAAAATGTGTCGACCGCCACGTCGCT
Done.