Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018326.1 Corchorus olitorius cultivar O-4 contig18359, 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: 62173
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:17433 original size:19 final size:20
Alignment explanation
Indices: 17382--17433 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 20
17372 CATGTGGAAT
17382 TTTAATAA-TAATTATTCAA
1 TTTAATAATTAATTATTCAA
** *
17401 TAAAATAATT-ATTATT-TA
1 TTTAATAATTAATTATTCAA
17419 TTTAATAATTAATTA
1 TTTAATAATTAATTA
17434 ATTTCAGCCC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 9 0.35
19 16 0.62
20 1 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTAATAATTAATTATTCAA
Found at i:32877 original size:13 final size:13
Alignment explanation
Indices: 32859--32884 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
32849 CTTGGCATGA
32859 GTGATGATTTTTG
1 GTGATGATTTTTG
32872 GTGATGATTTTTG
1 GTGATGATTTTTG
32885 TTGTTACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
GTGATGATTTTTG
Found at i:33264 original size:19 final size:19
Alignment explanation
Indices: 33242--33292 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
33232 GGGATGAAAT
33242 TAATTAATTATTAATTAAA
1 TAATTAATTATTAATTAAA
* *
33261 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAATTAAA
33280 TAATT-ATTATTAA
1 TAATTAATTATTAA
33293 AAATCCCACA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 9 0.33
19 17 0.63
20 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TAATTAATTATTAATTAAA
Found at i:34744 original size:51 final size:50
Alignment explanation
Indices: 34643--34744 Score: 111
Period size: 51 Copynumber: 2.0 Consensus size: 50
34633 GTTCTTCATA
* **
34643 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAATAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAATAAACACTCGTACAGTGT
*
34693 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATAA-AAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCAGGACA-AATAAACACTCGTACA-GTGT
34744 T
1 T
34745 CTTCATTCAG
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
50 7 0.16
51 34 0.77
52 3 0.07
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.42
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCAGGACAAATAAACACTCGTACAGTGT
Found at i:37409 original size:12 final size:12
Alignment explanation
Indices: 37392--37423 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
37382 TATTAAAGGT
37392 TCGGTTTCTCGG
1 TCGGTTTCTCGG
37404 TCGGTTTCTCGG
1 TCGGTTTCTCGG
37416 TCGGTTTC
1 TCGGTTTC
37424 GGTTCCATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.25, G:0.31, T:0.44
Consensus pattern (12 bp):
TCGGTTTCTCGG
Found at i:38367 original size:12 final size:12
Alignment explanation
Indices: 38350--38379 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
38340 AAATTAATAA
38350 TTAAAATGAAAT
1 TTAAAATGAAAT
38362 TTAAAATGAAAT
1 TTAAAATGAAAT
38374 TTAAAA
1 TTAAAA
38380 ATTAAAGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (12 bp):
TTAAAATGAAAT
Found at i:39086 original size:33 final size:33
Alignment explanation
Indices: 39049--39139 Score: 125
Period size: 32 Copynumber: 2.8 Consensus size: 33
39039 AAATTTTTTT
**
39049 TTTTTTTTTACGAAAGGTCCATTCTAGAATTTC
1 TTTTTTTGAACGAAAGGTCCATTCTAGAATTTC
*
39082 -TTTTTTGAAGGAAAGGTCCATTCTAGAATTTC
1 TTTTTTTGAACGAAAGGTCCATTCTAGAATTTC
39114 -TTTTTTGAA-GAAAAGGTCCATTCTAG
1 TTTTTTTGAACG-AAAGGTCCATTCTAG
39140 TTATACTTTA
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
31 1 0.02
32 53 0.98
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.43
Consensus pattern (33 bp):
TTTTTTTGAACGAAAGGTCCATTCTAGAATTTC
Found at i:39970 original size:33 final size:33
Alignment explanation
Indices: 39933--40005 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
39923 CCATGGCCTA
* *
39933 GTCGCG-CGCGGGTCGCGTCCGGGCCATGGTCAG
1 GTCGCGACGC-GGTCGCGACCGGACCATGGTCAG
** *
39966 GTCGCGATTCGGTCGCGACCGGACCATGGTTAG
1 GTCGCGACGCGGTCGCGACCGGACCATGGTCAG
39999 GTCGCGA
1 GTCGCGA
40006 TTCGTCGCGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 33 0.97
34 1 0.03
ACGTcount: A:0.11, C:0.30, G:0.41, T:0.18
Consensus pattern (33 bp):
GTCGCGACGCGGTCGCGACCGGACCATGGTCAG
Found at i:40006 original size:33 final size:33
Alignment explanation
Indices: 39943--40017 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
39933 GTCGCGCGCG
* *
39943 GGTCGCGTCCGGGCCATGGTCAGGTCGCGATTC
1 GGTCGCGACCGGACCATGGTCAGGTCGCGATTC
*
39976 GGTCGCGACCGGACCATGGTTAGGTCGCGATTC
1 GGTCGCGACCGGACCATGGTCAGGTCGCGATTC
40009 -GTCGCGACC
1 GGTCGCGACC
40018 CGTCTATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
32 9 0.23
33 30 0.77
ACGTcount: A:0.12, C:0.31, G:0.37, T:0.20
Consensus pattern (33 bp):
GGTCGCGACCGGACCATGGTCAGGTCGCGATTC
Found at i:45194 original size:15 final size:15
Alignment explanation
Indices: 45174--45208 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
45164 TATACTATAT
*
45174 AAAATATATTTAGAA
1 AAAATATAGTTAGAA
*
45189 AAAATATGGTTAGAA
1 AAAATATAGTTAGAA
45204 AAAAT
1 AAAAT
45209 TTACCATGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (15 bp):
AAAATATAGTTAGAA
Found at i:45974 original size:2 final size:2
Alignment explanation
Indices: 45967--46002 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
45957 ATCAACATGA
45967 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46003 CACGCCCCGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46678 original size:31 final size:33
Alignment explanation
Indices: 46632--46773 Score: 166
Period size: 34 Copynumber: 4.4 Consensus size: 33
46622 ATAAAATCAT
* * *
46632 CACTGGGCAGAGTCTTCCTGTTATTA-T-ATCC
1 CACTGGGCAGGGTCTTCCAGTTATTATTAAACC
*
46663 CACTGGGTAGGGTCTTCCAGTTATTATTACAACC
1 CACTGGGCAGGGTCTTCCAGTTATTATTA-AACC
*
46697 CACTGGGTAGGGTCTTCCAGTTATTATTACAACC
1 CACTGGGCAGGGTCTTCCAGTTATTATTA-AACC
* *
46731 CACTGGACAGGGTCTTCCAGTTATCA-T-AACC
1 CACTGGGCAGGGTCTTCCAGTTATTATTAAACC
*
46762 CACTGGTCAGGG
1 CACTGGGCAGGG
46774 CCGATAAAAC
Statistics
Matches: 100, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
31 38 0.38
32 1 0.01
33 1 0.01
34 60 0.60
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (33 bp):
CACTGGGCAGGGTCTTCCAGTTATTATTAAACC
Found at i:46699 original size:34 final size:34
Alignment explanation
Indices: 46632--46754 Score: 171
Period size: 34 Copynumber: 3.7 Consensus size: 34
46622 ATAAAATCAT
* * *
46632 CACTGGGCAGAGTCTTCCTGTTATTA-T--ATCC
1 CACTGGGCAGGGTCTTCCAGTTATTATTACAACC
*
46663 CACTGGGTAGGGTCTTCCAGTTATTATTACAACC
1 CACTGGGCAGGGTCTTCCAGTTATTATTACAACC
*
46697 CACTGGGTAGGGTCTTCCAGTTATTATTACAACC
1 CACTGGGCAGGGTCTTCCAGTTATTATTACAACC
*
46731 CACTGGACAGGGTCTTCCAGTTAT
1 CACTGGGCAGGGTCTTCCAGTTAT
46755 CATAACCCAC
Statistics
Matches: 83, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
31 23 0.28
32 1 0.01
34 59 0.71
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (34 bp):
CACTGGGCAGGGTCTTCCAGTTATTATTACAACC
Found at i:46762 original size:65 final size:64
Alignment explanation
Indices: 46632--46767 Score: 159
Period size: 65 Copynumber: 2.1 Consensus size: 64
46622 ATAAAATCAT
* * ** *
46632 CACTGGGCAGAGTCTTCCTGTTATTATATCCCACTGGGTAGGGTCTTCCAGTTATTATTACAACC
1 CACTGGGCAGAGTCTTCCAGTTATTATAACCCACTGGACAGGGTCTTCCAGTTATCATTA-AACC
* *
46697 CACTGGGTAGGGTCTTCCAGTTATTATTACAACCCACTGGACAGGGTCTTCCAGTTATCA-T-AA
1 CACTGGGCAGAGTCTTCCAGTTATTA-T--AACCCACTGGACAGGGTCTTCCAGTTATCATTAAA
46760 CC
63 CC
46762 CACTGG
1 CACTGG
46768 TCAGGGCCGA
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
65 33 0.54
66 1 0.02
67 1 0.02
68 26 0.43
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.31
Consensus pattern (64 bp):
CACTGGGCAGAGTCTTCCAGTTATTATAACCCACTGGACAGGGTCTTCCAGTTATCATTAAACC
Found at i:48294 original size:12 final size:12
Alignment explanation
Indices: 48277--48301 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48267 ATAGAGAATA
48277 TATTTTTGATTT
1 TATTTTTGATTT
48289 TATTTTTGATTT
1 TATTTTTGATTT
48301 T
1 T
48302 CTATCTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TATTTTTGATTT
Found at i:55142 original size:21 final size:21
Alignment explanation
Indices: 55118--55165 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
55108 CCTAATGACC
*
55118 TTTTGCAAC-TACATTATGAAA
1 TTTTGAAACTTACA-TATGAAA
*
55139 TTTTGAAACTTCCATATGAAA
1 TTTTGAAACTTACATATGAAA
55160 TTTTGA
1 TTTTGA
55166 TAACCACACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.42
Consensus pattern (21 bp):
TTTTGAAACTTACATATGAAA
Found at i:59168 original size:12 final size:13
Alignment explanation
Indices: 59151--59181 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
59141 CAAATGACCT
59151 AAAAAACAAAAA-
1 AAAAAACAAAAAC
59163 AAAAAACAAAAAC
1 AAAAAACAAAAAC
59176 AAAAAA
1 AAAAAA
59182 GCAAGTTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAACAAAAAC
Done.