Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015258.1 Corchorus olitorius cultivar O-4 contig15291, 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: 6470
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:5406 original size:30 final size:30
Alignment explanation
Indices: 5322--5685 Score: 471
Period size: 30 Copynumber: 12.1 Consensus size: 30
5312 AAATAAACTG
5322 AAGCAATGATCCT-AAACTAGGATTAAAATA
1 AAGCAATGATCCTCAAAC-AGGATTAAAATA
* * * * * * *
5352 AAACAACGACCCTCAACCAAGATTGAAATG
1 AAGCAATGATCCTCAAACAGGATTAAAATA
* *
5382 AAGCAATGATCCTCAAACAGGATTGAAATG
1 AAGCAATGATCCTCAAACAGGATTAAAATA
*
5412 AAGCAATGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
* * * * * *
5442 AAACAATGACCCTCAACCAAGATTGAAATG
1 AAGCAATGATCCTCAAACAGGATTAAAATA
*
5472 AAGCAATGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
* *
5502 AAGCAATGATCCTCAAACAGGATTGAAATG
1 AAGCAATGATCCTCAAACAGGATTAAAATA
*
5532 AAGCAATGATCCTCAAACAGGATTAAAATG
1 AAGCAATGATCCTCAAACAGGATTAAAATA
** * *
5562 AAGTGATGATCCTCAACCAGGATTAGAATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
*
5592 AAGCAATGATCCTCAAACAGGATTAACATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
5622 AAGCAATGATCCTCAAACAGGATTAAAATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
5652 AAGCAATGATCCTC-AACTAGGATTAAAATA
1 AAGCAATGATCCTCAAAC-AGGATTAAAATA
5682 AAGC
1 AAGC
5686 TGATAAAGCA
Statistics
Matches: 292, Mismatches: 40, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
29 3 0.01
30 286 0.98
31 3 0.01
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.20
Consensus pattern (30 bp):
AAGCAATGATCCTCAAACAGGATTAAAATA
Found at i:6072 original size:31 final size:31
Alignment explanation
Indices: 5993--6093 Score: 103
Period size: 31 Copynumber: 3.1 Consensus size: 31
5983 TAAACTGAAG
5993 AAACTGAAGAAAAGATCGCCCTGGATCAATTGAAAT
1 AAACTGAAGAAAAGATCGCCCTGGATC-----AAAT
* *
6029 GAACTGAAGAAAATATCGCCCTGGATCAAAT
1 AAACTGAAGAAAAGATCGCCCTGGATCAAAT
* * * *
6060 AAACCGAAGAAAAGATCTCCCTCGATCAACT
1 AAACTGAAGAAAAGATCGCCCTGGATCAAAT
6091 AAA
1 AAA
6094 ATAACTTGAA
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
31 32 0.56
36 25 0.44
ACGTcount: A:0.45, C:0.21, G:0.17, T:0.18
Consensus pattern (31 bp):
AAACTGAAGAAAAGATCGCCCTGGATCAAAT
Found at i:6104 original size:67 final size:66
Alignment explanation
Indices: 5993--6123 Score: 165
Period size: 67 Copynumber: 2.0 Consensus size: 66
5983 TAAACTGAAG
* * * * * *
5993 AAACTGAAGAAAAGATCGCCCTGGATCAATTGAAATGAACTGAAGAAAATATCGCCCTGGATCAA
1 AAACCGAAGAAAAGATCGCCCTCGATCAACTAAAATGAACTGAAG-AAAGATCACCCTGGATCAA
6058 AT
65 AT
* *
6060 AAACCGAAGAAAAGATCTCCCTCGATCAACTAAAAT-AACTTGAAGTAAGATCACCCTGGATCAA
1 AAACCGAAGAAAAGATCGCCCTCGATCAACTAAAATGAAC-TGAAGAAAGATCACCCTGGATCAA
6124 TTGAAATGAA
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
66 19 0.35
67 36 0.65
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.19
Consensus pattern (66 bp):
AAACCGAAGAAAAGATCGCCCTCGATCAACTAAAATGAACTGAAGAAAGATCACCCTGGATCAAA
T
Found at i:6111 original size:35 final size:35
Alignment explanation
Indices: 5950--6464 Score: 326
Period size: 35 Copynumber: 14.5 Consensus size: 35
5940 TTTGCGGTCT
* * * * *
5950 ACTGAAATAAACTGCAGAAAAGATCACCATGGATAA
1 ACTGAAATAAATTGAAG-AAAGATCGCCCTGGATCA
* *
5986 ACTG-AAGAAACTGAAGAAAAGATCGCCCTGGATCA
1 ACTGAAATAAATTGAAG-AAAGATCGCCCTGGATCA
* * * *
6021 ATTGAAATGAACTGAAGAAAATATCGCCCTGGAT--
1 ACTGAAATAAATTGAAG-AAAGATCGCCCTGGATCA
** * *
6055 -C--AAATAAACCGAAGAAAAGATCTCCCTCGATCA
1 ACTGAAATAAATTGAAG-AAAGATCGCCCTGGATCA
* * * *
6088 ACTAAAATAACTTGAAGTAAGATCACCCTGGATCA
1 ACTGAAATAAATTGAAGAAAGATCGCCCTGGATCA
* * * *
6123 ATTGAAATGAATTGAAGAAAGACCGCCCTGGGTCA
1 ACTGAAATAAATTGAAGAAAGATCGCCCTGGATCA
* * * *
6158 ACTGAAATAACTTGAAGAATGACCGCCCTGGGTCA
1 ACTGAAATAAATTGAAGAAAGATCGCCCTGGATCA
* * * *
6193 GCTAAAATAAATTGAAGGAAAGATCACCCTGGATCG
1 ACTGAAATAAATTGAA-GAAAGATCGCCCTGGATCA
*
6229 ACTGAAATAAATTGAATAAAAGATCGCCCTGGATCA
1 ACTGAAATAAATTGAA-GAAAGATCGCCCTGGATCA
* * * * * * *
6265 ACTGGAGTAAATTGAGGAGAGATCAACCC-AGATAA
1 ACTGAAATAAATTGAAGAAAGATC-GCCCTGGATCA
* * * * *
6300 ACTGACATAAACTGAATGAAAAGACCACCCTGGGTCA
1 ACTGAAATAAATTGAA-G-AAAGATCGCCCTGGATCA
* * *
6337 ACTTGAAATAAACTGAAGAACGGGTCGCCCTGGATCA
1 AC-TGAAATAAATTGAAGAA-AGATCGCCCTGGATCA
** * * ** *
6374 ACTGAGGTAAAATGAATAAAAGATCATCCTAGATCAA
1 ACTGAAATAAATTGAA-GAAAGATCGCCCTGGATC-A
* * *
6411 ACTGAAATGAATTGAAGAAAGACCACCCTAGG-TCA
1 ACTGAAATAAATTGAAGAAAGATCGCCCT-GGATCA
*
6446 ATTGAAATAAATTGAAGAA
1 ACTGAAATAAATTGAAGAA
6465 GGACCG
Statistics
Matches: 373, Mismatches: 90, Indels: 33
0.75 0.18 0.07
Matches are distributed among these distances:
31 25 0.07
34 1 0.00
35 154 0.41
36 140 0.38
37 40 0.11
38 13 0.03
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.19
Consensus pattern (35 bp):
ACTGAAATAAATTGAAGAAAGATCGCCCTGGATCA
Found at i:6288 original size:71 final size:71
Alignment explanation
Indices: 5950--6461 Score: 281
Period size: 71 Copynumber: 7.2 Consensus size: 71
5940 TTTGCGGTCT
* * * * * * * * * *
5950 ACTGAAATAAACTGCAGAAAAGATCACCATGGATAAACTG-AAGAAACTGAAGAAAAGATCGCCC
1 ACTGAAATAAATTGAATAAAAGACCACCCTGGATCAACTGAAATAAATTG-AGGAAAGATCACCC
6014 TGGATCA
65 TGGATCA
* * * * * * * ** * *
6021 ATTGAAATGAACTGAAGAAAATATCGCCCTGGAT---C--AAATAAACCGAAGAAAAGATCTCCC
1 ACTGAAATAAATTGAATAAAAGACCACCCTGGATCAACTGAAATAAATTG-AGGAAAGATCACCC
*
6081 TCGATCA
65 TGGATCA
* * * * * * * *
6088 ACTAAAATAACTTGAAGT--AAGATCACCCTGGATCAATTGAAATGAATTGAAGAAAGACCGCCC
1 ACTGAAATAAATTGAA-TAAAAGACCACCCTGGATCAACTGAAATAAATTGAGGAAAGATCACCC
*
6151 TGGGTCA
65 TGGATCA
* * * * * * *
6158 ACTGAAATAACTTGAA-GAATGACCGCCCTGGGTCAGCTAAAATAAATTGAAGGAAAGATCACCC
1 ACTGAAATAAATTGAATAAAAGACCACCCTGGATCAACTGAAATAAATTG-AGGAAAGATCACCC
*
6222 TGGATCG
65 TGGATCA
* * * * *
6229 ACTGAAATAAATTGAATAAAAGATCGCCCTGGATCAACTGGAGTAAATTGAGGAGAGATCAACCC
1 ACTGAAATAAATTGAATAAAAGACCACCCTGGATCAACTGAAATAAATTGAGGAAAGATC-ACCC
* *
6294 -AGATAA
65 TGGATCA
* * * * * * * *
6300 ACTGACATAAACTGAATGAAAAGACCACCCTGGGTCAACTTGAAATAAACTGAAGAACGGGTCGC
1 ACTGAAATAAATTGAAT-AAAAGACCACCCTGGATCAAC-TGAAATAAATTGAGGAA-AGATCAC
6365 CCTGGATCA
63 CCTGGATCA
** * * * * * * *
6374 ACTGAGGTAAAATGAATAAAAGATCATCCTAGATCAAACTGAAATGAATTGAAGAAAGACCACCC
1 ACTGAAATAAATTGAATAAAAGACCACCCTGGATC-AACTGAAATAAATTGAGGAAAGATCACCC
6439 TAGG-TCA
65 T-GGATCA
*
6446 ATTGAAATAAATTGAA
1 ACTGAAATAAATTGAA
6462 GAAGGACCG
Statistics
Matches: 336, Mismatches: 87, Indels: 35
0.73 0.19 0.08
Matches are distributed among these distances:
66 13 0.04
67 38 0.11
68 1 0.00
70 53 0.16
71 93 0.28
72 68 0.20
73 46 0.14
74 24 0.07
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.19
Consensus pattern (71 bp):
ACTGAAATAAATTGAATAAAAGACCACCCTGGATCAACTGAAATAAATTGAGGAAAGATCACCCT
GGATCA
Found at i:6369 original size:109 final size:109
Alignment explanation
Indices: 5984--6464 Score: 318
Period size: 109 Copynumber: 4.5 Consensus size: 109
5974 CACCATGGAT
* * * * * * *
5984 AAACTG-AAGAAACTGAAGAAAAGATCGCCCTGGATCAA-TTGAAATGAACTGAAGAAAATATCG
1 AAACTGAAATAAACTGAAG-AAAGACCACCCTGGGTCAACTTGAAATAAATTGAAGAAAAGATCG
** * *
6047 CCCTGGATCAA---A--TAAACCGAAGAAAAGATC-TCCCTCGATC
65 CCCTGGATCAACTGAGGTAAAATGAAGAAAAGATCAACCC-AGATC
* * * * * *
6087 -AACTAAAAT-AACTTGAAGTAAGATCACCCTGGATCAA-TTGAAATGAATTGAAG-AAAGACCG
1 AAACTGAAATAAAC-TGAAGAAAGACCACCCTGGGTCAACTTGAAATAAATTGAAGAAAAGATCG
* ** ** * ** * *
6148 CCCTGGGTCAACTGAAATAACTTGAAG-AATGA-CCGCCCTGGGTC
65 CCCTGGATCAACTGAGGTAAAATGAAGAAAAGATCAACCC-AGATC
* * * * * * *
6192 -AGCTAAAATAAATTGAAGGAAAGATCACCCTGGATCGAC-TGAAATAAATTGAATAAAAGATCG
1 AAACTGAAATAAACTGAA-GAAAGACCACCCTGGGTCAACTTGAAATAAATTGAAGAAAAGATCG
* * *
6255 CCCTGGATCAACTG-GAGTAAATTG-AGGAGAGATCAACCCAGAT-
65 CCCTGGATCAACTGAG-GTAAAATGAAGAAAAGATCAACCCAGATC
* * ** *
6298 AAACTGACATAAACTGAATGAAAAGACCACCCTGGGTCAACTTGAAATAAACTGAAGAACGGGTC
1 AAACTGAAATAAACTGAA-G-AAAGACCACCCTGGGTCAACTTGAAATAAATTGAAGAAAAGATC
* * *
6363 GCCCTGGATCAACTGAGGTAAAATGAATAAAAGATCATCCTAGATC
64 GCCCTGGATCAACTGAGGTAAAATGAAGAAAAGATCAACCCAGATC
* * *
6409 AAACTGAAATGAATTGAAGAAAGACCACCCTAGGTCAA-TTGAAATAAATTGAAGAA
1 AAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTTGAAATAAATTGAAGAA
6465 GGACCG
Statistics
Matches: 301, Mismatches: 56, Indels: 37
0.76 0.14 0.09
Matches are distributed among these distances:
101 16 0.05
102 39 0.13
103 7 0.02
104 2 0.01
105 23 0.08
106 42 0.14
107 45 0.15
108 38 0.13
109 58 0.19
110 16 0.05
111 15 0.05
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.19
Consensus pattern (109 bp):
AAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTTGAAATAAATTGAAGAAAAGATCGC
CCTGGATCAACTGAGGTAAAATGAAGAAAAGATCAACCCAGATC
Done.