Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013741.1 Corchorus capsularis cultivar CVL-1 contig13762, 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: 49461
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:714 original size:18 final size:18
Alignment explanation
Indices: 691--725 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
681 CGGCAACTTT
691 AATATATAGTTATAGATA
1 AATATATAGTTATAGATA
709 AATATATAGTTATAGAT
1 AATATATAGTTATAGAT
726 TATAGATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (18 bp):
AATATATAGTTATAGATA
Found at i:7251 original size:11 final size:11
Alignment explanation
Indices: 7235--7259 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
7225 GAAGTGGACC
7235 AAAAACTCTAA
1 AAAAACTCTAA
7246 AAAAACTCTAA
1 AAAAACTCTAA
7257 AAA
1 AAA
7260 TTTCGTCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAACTCTAA
Found at i:10324 original size:38 final size:38
Alignment explanation
Indices: 10267--10341 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
10257 ATTGACAGTT
10267 TTTATAAATCACATAGACATAGTTCGTTTTTATAAATA
1 TTTATAAATCACATAGACATAGTTCGTTTTTATAAATA
* * *
10305 TTTATAAATCACTTCGACATAGTTTGTTTTTATAAAT
1 TTTATAAATCACATAGACATAGTTCGTTTTTATAAAT
10342 CACTTCGACA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45
Consensus pattern (38 bp):
TTTATAAATCACATAGACATAGTTCGTTTTTATAAATA
Found at i:21958 original size:31 final size:31
Alignment explanation
Indices: 21888--21947 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
21878 AAATTATAAT
*
21888 GGGGTCAATACTATAAAACTTTCATTTTAAA
1 GGGGTCAATACAATAAAACTTTCATTTTAAA
21919 GGGGTCAATACAATAAATA-TTTCATTTTA
1 GGGGTCAATACAATAAA-ACTTTCATTTTA
21948 GTTGGGTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (31 bp):
GGGGTCAATACAATAAAACTTTCATTTTAAA
Found at i:31951 original size:36 final size:36
Alignment explanation
Indices: 31904--32162 Score: 378
Period size: 36 Copynumber: 7.2 Consensus size: 36
31894 CATCCATGCG
* *
31904 TTAAGTAAGCTCAGTCGAAGACATAATAT-AAGGTAA
1 TTAAGTAAGCTCAGTCAAAGACTTAAT-TCAAGGTAA
31940 TTAAGTAAGCTCAGTCAAAGACTTAATTCAAGGTAA
1 TTAAGTAAGCTCAGTCAAAGACTTAATTCAAGGTAA
* * *
31976 TTAAGTAAGCTCAGTAAAATACTTAATTCAAGATAA
1 TTAAGTAAGCTCAGTCAAAGACTTAATTCAAGGTAA
*
32012 TTAAGTAAGCTCAGTCAAATACTTAATTCAAGGTAA
1 TTAAGTAAGCTCAGTCAAAGACTTAATTCAAGGTAA
*
32048 TTAAGTAAGCTCAGTCAAAGACTGAATTCAAGGTAA
1 TTAAGTAAGCTCAGTCAAAGACTTAATTCAAGGTAA
* *
32084 TTAAGTAAGCTCGGCCAAAGA-TTGAATTCAAGGTAA
1 TTAAGTAAGCTCAGTCAAAGACTT-AATTCAAGGTAA
* * *
32120 TTAAGTAAGCTCGGTAAAAGACTTAATTCAAGTTAA
1 TTAAGTAAGCTCAGTCAAAGACTTAATTCAAGGTAA
32156 TTAAGTA
1 TTAAGTA
32163 CGCTTCTCGG
Statistics
Matches: 205, Mismatches: 15, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
35 2 0.01
36 201 0.98
37 2 0.01
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.28
Consensus pattern (36 bp):
TTAAGTAAGCTCAGTCAAAGACTTAATTCAAGGTAA
Found at i:32254 original size:29 final size:29
Alignment explanation
Indices: 32219--32319 Score: 98
Period size: 29 Copynumber: 3.4 Consensus size: 29
32209 CCAAAATGCT
32219 CAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCCGATCTTTTAATTTGGC
* * * **
32248 CAAATAAGGG-CCTAACGTTATCAAAAAT-GC
1 CAAATAAGGGCCCGATC-TT-T-TAATTTGGC
*
32278 TCAAATAAGGGCACGATCTTTTAATTTGGC
1 -CAAATAAGGGCCCGATCTTTTAATTTGGC
32308 CAAATAAGGGCC
1 CAAATAAGGGCC
32320 TAACATTATC
Statistics
Matches: 54, Mismatches: 12, Indels: 12
0.69 0.15 0.15
Matches are distributed among these distances:
28 4 0.07
29 26 0.48
30 6 0.11
31 15 0.28
32 3 0.06
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.26
Consensus pattern (29 bp):
CAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:32283 original size:60 final size:60
Alignment explanation
Indices: 32190--32350 Score: 261
Period size: 60 Copynumber: 2.7 Consensus size: 60
32180 GTTTAGGTCT
* *
32190 AATAAGGCCCTAACGTT-TGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCA
1 AATAAGGGCCTAACGTTAT-CAAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCA
*
32250 AATAAGGGCCTAACGTTATCAAAAATGCTCAAATAAGGGCACGATCTTTTAATTTGGCCA
1 AATAAGGGCCTAACGTTATCAAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCA
* *
32310 AATAAGGGCCTAACATTATCGAAAATGCTCAAATAAGGGCC
1 AATAAGGGCCTAACGTTATCAAAAATGCTCAAATAAGGGCC
32351 TGGTGTCAGT
Statistics
Matches: 94, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
60 93 0.99
61 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (60 bp):
AATAAGGGCCTAACGTTATCAAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCA
Found at i:32286 original size:31 final size:30
Alignment explanation
Indices: 32248--32351 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 30
32238 TTAATTTGGC
32248 CAAATAAGGGCCTAACGTTATCAAAAATGCT
1 CAAATAAGGGCCTAAC-TTATCAAAAATGCT
* * * **
32279 CAAATAAGGGCACGATCTT-T-TAATTTGGC-
1 CAAATAAGGGC-CTAACTTATCAAAAAT-GCT
*
32308 CAAATAAGGGCCTAACATTATCGAAAATGCT
1 CAAATAAGGGCCTAAC-TTATCAAAAATGCT
32339 CAAATAAGGGCCT
1 CAAATAAGGGCCT
32352 GGTGTCAGTT
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
28 3 0.05
29 16 0.28
30 6 0.11
31 29 0.51
32 3 0.05
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.24
Consensus pattern (30 bp):
CAAATAAGGGCCTAACTTATCAAAAATGCT
Found at i:32476 original size:31 final size:31
Alignment explanation
Indices: 32383--32512 Score: 171
Period size: 31 Copynumber: 4.3 Consensus size: 31
32373 TGAGACAGGT
*
32383 CCTTATTTGAGCATTTTGAC-AACGTTAGGC
1 CCTTATTTGAGCATTTTGGCAAACGTTAGGC
** *
32413 CCTTATTTG-GCCAAATT--CAAA-GATGAGGC
1 CCTTATTTGAG-CATTTTGGCAAACG-TTAGGC
32442 CCTTATTTGAGCATTTTGGCAAACGTTAGGC
1 CCTTATTTGAGCATTTTGGCAAACGTTAGGC
32473 CCTTATTTGAGCATTTTGGCAAACGTTAGGC
1 CCTTATTTGAGCATTTTGGCAAACGTTAGGC
32504 CCTTATTTG
1 CCTTATTTG
32513 GCCAAATTAA
Statistics
Matches: 87, Mismatches: 6, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
28 2 0.02
29 21 0.24
30 14 0.16
31 49 0.56
32 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (31 bp):
CCTTATTTGAGCATTTTGGCAAACGTTAGGC
Found at i:32556 original size:91 final size:90
Alignment explanation
Indices: 32383--32556 Score: 269
Period size: 91 Copynumber: 1.9 Consensus size: 90
32373 TGAGACAGGT
* *
32383 CCTTATTTGAGCATTTTGACAACGTTAGGCCCTTATTTGGCCAAATTCAAAGATGAGGCCCTTAT
1 CCTTATTTGAGCATTTTGACAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATGAGACCCTTAT
* * *
32448 TTGAGCATTTTGGCAAACGTTAGGC
66 TTGAGCAATTAGCCAAACGTTAGGC
*
32473 CCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG-GACCCTT
1 CCTTATTTGAGCATTTTGAC-AACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT-GAGACCCTT
32537 ATTTGAGCAATTAGCCAAAC
64 ATTTGAGCAATTAGCCAAAC
32557 AATTTATACA
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
90 19 0.25
91 56 0.74
92 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Consensus pattern (90 bp):
CCTTATTTGAGCATTTTGACAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATGAGACCCTTAT
TTGAGCAATTAGCCAAACGTTAGGC
Found at i:38030 original size:163 final size:163
Alignment explanation
Indices: 37756--38055 Score: 514
Period size: 163 Copynumber: 1.8 Consensus size: 163
37746 GTGTTTTGGT
37756 CGAAAATGCCCCTGAAGCCAGTGGACAGAAACTGTCCTGGGCCTTTTATGCGGGATTGACCTAAT
1 CGAAAATGCCCCTGAAGCCAGTGGACAGAAACTGTCCTGGGCCTTTTATGCGGGATTGACCTAAT
* *
37821 TAAGCCCAAATTCTTAATTGGATTAGCTTGAAGACTTGGTGAGCAGCCCAGCACGTCCTTAGGGT
66 TAAGCCCAAAATCTTAATTGGATTAGCTTGAAGACTTGGAGAGCAGCCCAGCACGTCCTTAGGGT
37886 TTGTTTAAGCCCAAGTTTGGACGTTTCCATGGA
131 TTGTTTAAGCCCAAGTTTGGACGTTTCCATGGA
*
37919 CGAAAATGCCCCTGAAGTCAGTGGACAGAAACTGTCCTGGGCCTGTTT-TGCGGGATTGATCC-A
1 CGAAAATGCCCCTGAAGCCAGTGGACAGAAACTGTCCTGGGCCT-TTTATGCGGGATTGA-CCTA
* * *
37982 ATTGAGCCCAAAATCTTATTTGGATTAGCTTGAAGACTTGGAGAGCAGCCCAGCACGTTCTTAGG
64 ATTAAGCCCAAAATCTTAATTGGATTAGCTTGAAGACTTGGAGAGCAGCCCAGCACGTCCTTAGG
38047 GTTTGTTTA
129 GTTTGTTTA
38056 GCTCTAAATT
Statistics
Matches: 129, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
163 124 0.96
164 5 0.04
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (163 bp):
CGAAAATGCCCCTGAAGCCAGTGGACAGAAACTGTCCTGGGCCTTTTATGCGGGATTGACCTAAT
TAAGCCCAAAATCTTAATTGGATTAGCTTGAAGACTTGGAGAGCAGCCCAGCACGTCCTTAGGGT
TTGTTTAAGCCCAAGTTTGGACGTTTCCATGGA
Found at i:43117 original size:16 final size:16
Alignment explanation
Indices: 43097--43140 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
43087 TAAAAAACCC
*
43097 GAACCCGAAAAAGCTCA
1 GAACCCGAAAAA-ATCA
43114 -AACCCGAAAAAATCA
1 GAACCCGAAAAAATCA
43129 GAACCCGAAAAA
1 GAACCCGAAAAA
43141 TCTGGAACCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 3 0.12
16 22 0.88
ACGTcount: A:0.55, C:0.27, G:0.14, T:0.05
Consensus pattern (16 bp):
GAACCCGAAAAAATCA
Found at i:43148 original size:16 final size:16
Alignment explanation
Indices: 43097--43149 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
43087 TAAAAAACCC
*
43097 GAACCCGAAAAAGCTCA
1 GAACCCGAAAAATCT-A
43114 -AACCCGAAAAAATC-A
1 GAACCCG-AAAAATCTA
*
43129 GAACCCGAAAAATCTG
1 GAACCCGAAAAATCTA
43145 GAACC
1 GAACC
43150 TGATAAAACC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 8 0.26
16 17 0.55
17 6 0.19
ACGTcount: A:0.49, C:0.28, G:0.15, T:0.08
Consensus pattern (16 bp):
GAACCCGAAAAATCTA
Found at i:43398 original size:32 final size:32
Alignment explanation
Indices: 43360--43468 Score: 175
Period size: 32 Copynumber: 3.4 Consensus size: 32
43350 GCCAAAACCC
*
43360 AACCCGAACCCGAATTAACCTGACCCAAAATTT
1 AACCCGAACCCGAATCAACCTGACCC-AAATTT
43393 -ACCCGAACCCGAATCAACCTGACCCAAATTT
1 AACCCGAACCCGAATCAACCTGACCCAAATTT
* *
43424 AAACCGAACCCGAATCAACCAGACCCAAATTT
1 AACCCGAACCCGAATCAACCTGACCCAAATTT
43456 AACCCGAACCCGA
1 AACCCGAACCCGA
43469 CTTAAGCCCG
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
31 6 0.08
32 65 0.92
ACGTcount: A:0.39, C:0.37, G:0.10, T:0.14
Consensus pattern (32 bp):
AACCCGAACCCGAATCAACCTGACCCAAATTT
Found at i:43478 original size:17 final size:16
Alignment explanation
Indices: 43454--43485 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
43444 AGACCCAAAT
43454 TTAACCCGAACCCGAC
1 TTAACCCGAACCCGAC
43470 TTAAGCCCGAACCCGA
1 TTAA-CCCGAACCCGA
43486 AACGACCTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.31, C:0.41, G:0.16, T:0.12
Consensus pattern (16 bp):
TTAACCCGAACCCGAC
Found at i:43529 original size:30 final size:30
Alignment explanation
Indices: 43474--43530 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
43464 CCCGACTTAA
* *
43474 GCCCGAACCCGAAACGACCTGAACCCGATG
1 GCCCGAACCCGAAACCAACTGAACCCGATG
* *
43504 GCCCGAACCCGAACCCAACTTAACCCG
1 GCCCGAACCCGAAACCAACTGAACCCG
43531 CCCGATTGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.30, C:0.44, G:0.19, T:0.07
Consensus pattern (30 bp):
GCCCGAACCCGAAACCAACTGAACCCGATG
Done.