Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012532.1 Corchorus olitorius cultivar O-4 contig12565, 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: 49027
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:13953 original size:34 final size:34
Alignment explanation
Indices: 13844--13973 Score: 143
Period size: 34 Copynumber: 3.7 Consensus size: 34
13834 TGAAAACGGC
* *
13844 GGGAACTTTCCCTAAATTGAAAACTAAAGCCTGAT
1 GGGAACTTTCCC-AATTTGAAAACTAAAACCTGAT
* * * *
13879 GAGAACTTTCCCAATTTAAAAAACTTAAAAACTTGTT
1 GGGAACTTTCCCAATTT-GAAAAC-T-AAAACCTGAT
* * *
13916 GGGATCTTTCTCAATTTGAAAACTAAAACCTGGT
1 GGGAACTTTCCCAATTTGAAAACTAAAACCTGAT
13950 GGGAACTTTCCCAATTTGAAAACT
1 GGGAACTTTCCCAATTTGAAAACT
13974 TCGAAGACTG
Statistics
Matches: 78, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
34 34 0.44
35 17 0.22
36 6 0.08
37 21 0.27
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (34 bp):
GGGAACTTTCCCAATTTGAAAACTAAAACCTGAT
Found at i:17226 original size:16 final size:16
Alignment explanation
Indices: 17207--17245 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
17197 AAATTGAGGC
*
17207 ATTGAATAATTGAATA
1 ATTGAAGAATTGAATA
**
17223 ATTGAAGCCTTGAATA
1 ATTGAAGAATTGAATA
17239 ATTGAAG
1 ATTGAAG
17246 TTGAAGAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.18, T:0.33
Consensus pattern (16 bp):
ATTGAAGAATTGAATA
Found at i:17226 original size:24 final size:24
Alignment explanation
Indices: 17198--17244 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
17188 CTTTGAAGTA
*
17198 AATTGAGGCATTGAATAATTGAAT
1 AATTGAAGCATTGAATAATTGAAT
*
17222 AATTGAAGCCTTGAATAATTGAA
1 AATTGAAGCATTGAATAATTGAA
17245 GTTGAAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.06, G:0.19, T:0.32
Consensus pattern (24 bp):
AATTGAAGCATTGAATAATTGAAT
Found at i:17253 original size:80 final size:81
Alignment explanation
Indices: 17156--17309 Score: 256
Period size: 80 Copynumber: 1.9 Consensus size: 81
17146 ATCGAGACTG
* *
17156 AATTGAAGAATTGAAGAAAGATCACCCTGGATCTTTGAAGTAAATTGAGGCATTGAATAATTGAA
1 AATTGAAG-ATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAGGCATTGAATAATTGAA
*
17221 TAATTGAAGCCTTGAAT
65 GAATTGAAGCCTTGAAT
*
17238 AATTGAAG-TTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGATGCATTGAATAATTGAAG
1 AATTGAAGATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAGGCATTGAATAATTGAAG
17302 AATTGAAG
66 AATTGAAG
17310 GAAGATGATT
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
80 60 0.88
82 8 0.12
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (81 bp):
AATTGAAGATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAGGCATTGAATAATTGAAG
AATTGAAGCCTTGAAT
Found at i:17578 original size:30 final size:30
Alignment explanation
Indices: 17543--17601 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
17533 AAGTTCGTGT
17543 TTGAAGACCATTTGAAG-ATAATTTCAAGAC
1 TTGAAGA-CATTTGAAGAATAATTTCAAGAC
* *
17573 TTGAAGACTTTTGAAGAATTATTTCAAGA
1 TTGAAGACATTTGAAGAATAATTTCAAGA
17602 GCAAGAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (30 bp):
TTGAAGACATTTGAAGAATAATTTCAAGAC
Found at i:19296 original size:35 final size:35
Alignment explanation
Indices: 19148--19793 Score: 532
Period size: 35 Copynumber: 18.2 Consensus size: 35
19138 GACCGATCAG
* * * ** *
19148 AAGACCACCCTCGATCATTCTGAAATAAGTTGAAGG
1 AAGACCACCCTGGGTCA-ACTGAAATAAACTGAAGA
* * *
19184 AAGACCACCCTGGGTCAAATGAAATGAATTGAA-A
1 AAGACCACCCTGGGTCAACTGAAATAAACTGAAGA
* * *** * *
19218 AGCGGCCACCCTTAATCATCCTG-ACTCAAACTGAAGA
1 A-AGACCACCCTGGGTCA-ACTGAAAT-AAACTGAAGA
* * * *
19255 AAGACCGCCTTGGGTCAACTGAAATAAATTAAAGA
1 AAGACCACCCTGGGTCAACTGAAATAAACTGAAGA
*
19290 AAGACCGCCCTGGGTCAACTGAAATAAACTGAAGA
1 AAGACCACCCTGGGTCAACTGAAATAAACTGAAGA
* * * * *
19325 ACGACCACCCTCGATCATTCTGACATAAACTGAAGAA
1 AAGACCACCCTGGGTCA-ACTGAAATAAACTGAAG-A
* *
19362 AAGACCACCTTGGGTCAACTGCAATAAACTGAAGA
1 AAGACCACCCTGGGTCAACTGAAATAAACTGAAGA
* * *
19397 AAGACCGCCCTGGGTCAACTGAAATGAATTGAAGA
1 AAGACCACCCTGGGTCAACTGAAATAAACTGAAGA
* * *
19432 AAGATCGCCCTGGGCCAACTGAAATAAACTGAAGA
1 AAGACCACCCTGGGTCAACTGAAATAAACTGAAGA
* * * * *
19467 ACGACCACCCTCGATCATTCTGACATAAACTGAAGAA
1 AAGACCACCCTGGGTCA-ACTGAAATAAACTGAAG-A
*
19504 AAGACCACCCTGGGTCAACTGCAATAAACTGAAGA
1 AAGACCACCCTGGGTCAACTGAAATAAACTGAAGA
* * *
19539 AAGACCGCCCTGGGTCAACTGAAATGAATTGAAGA
1 AAGACCACCCTGGGTCAACTGAAATAAACTGAAGA
* * * * *
19574 ACGA-CACCCCTCGATCATTCTGACATAAACTGAAGAA
1 AAGACCA-CCCTGGGTCA-ACTGAAATAAACTGAAG-A
* *
19611 AAGACCACCCTAGGTTAACT-ACAATAAACTGAAGA
1 AAGACCACCCTGGGTCAACTGA-AATAAACTGAAGA
* * *
19646 AAGACCGCCCTGGGTCAA-TCGAAATGAACTAAAGA
1 AAGACCACCCTGGGTCAACT-GAAATAAACTGAAGA
* * * * *
19681 AAGACCACCCTCGATCATTCTTACATAAACTGAAGAA
1 AAGACCACCCTGGGTCA-ACTGAAATAAACTGAAG-A
*
19718 AAGGACCACCCTGGGTTAA-TAGAAATAAACTGAAGA
1 AA-GACCACCCTGGGTCAACT-GAAATAAACTGAAGA
* * *
19754 AAGACCGCCCTAGGTCAACTGAAAT-AACTGACGA
1 AAGACCACCCTGGGTCAACTGAAATAAACTGAAGA
19788 AAGACC
1 AAGACC
19794 TAGGTCAATA
Statistics
Matches: 480, Mismatches: 108, Indels: 46
0.76 0.17 0.07
Matches are distributed among these distances:
34 17 0.04
35 257 0.54
36 134 0.28
37 58 0.12
38 14 0.03
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.17
Consensus pattern (35 bp):
AAGACCACCCTGGGTCAACTGAAATAAACTGAAGA
Found at i:19404 original size:142 final size:142
Alignment explanation
Indices: 19245--19764 Score: 629
Period size: 142 Copynumber: 3.6 Consensus size: 142
19235 ATCCTGACTC
* * *
19245 AAACTGAAGAAAGACCGCCTTGGGTCAACTGAAATAAATTAAAGAAAGACCGCCCTGGGTCAACT
1 AAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATGAATTGAAGAAAGACCGCCCTGGGTCAACT
*
19310 GAAATAAACTGAAGAACGACCACCCTCGATCATTCTGACATAAACTGAAGAAAAGACCACCTTGG
66 GAAATAAACTGAAGAACGACCACCCTCGATCATTCTGACATAAACTGAAGAAAAGACCACCCTGG
19375 GTCAACTGCAAT
131 GTCAACTGCAAT
* *
19387 AAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATGAATTGAAGAAAGATCGCCCTGGGCCAACT
1 AAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATGAATTGAAGAAAGACCGCCCTGGGTCAACT
19452 GAAATAAACTGAAGAACGACCACCCTCGATCATTCTGACATAAACTGAAGAAAAGACCACCCTGG
66 GAAATAAACTGAAGAACGACCACCCTCGATCATTCTGACATAAACTGAAGAAAAGACCACCCTGG
19517 GTCAACTGCAAT
131 GTCAACTGCAAT
* * * *
19529 AAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATGAATTGAAGAACGACAC-CCCTCGATCATT
1 AAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATGAATTGAAGAAAGAC-CGCCCTGGGTCA-A
* * * * * * *
19593 CTGACATAAACTGAAGAAAAGACCACCCTAGGTTA-ACT-ACAATAAACTGAAG-AAAGACCGCC
64 CTGAAATAAACTGAAG-AACGACCACCCTCGATCATTCTGAC-ATAAACTGAAGAAAAGACCACC
*
19655 CTGGGTCAA-TCGAAAT
127 CTGGGTCAACT-GCAAT
* * * * * * * * * * * *
19671 GAACTAAAGAAAGACCACCCTCGATCATTCTTACATAAACTGAAGAAAAGGACCACCCTGGGTTA
1 AAACTGAAGAAAGACCGCCCTGGGTCA-ACTGAAATGAATTGAAG-AAA-GACCGCCCTGGGTCA
* *
19736 A-TAGAAATAAACTGAAGAAAGACCGCCCT
63 ACT-GAAATAAACTGAAGAACGACCACCCT
19765 AGGTCAACTG
Statistics
Matches: 331, Mismatches: 37, Indels: 19
0.86 0.10 0.05
Matches are distributed among these distances:
141 1 0.00
142 237 0.72
143 53 0.16
144 30 0.09
145 10 0.03
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.17
Consensus pattern (142 bp):
AAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATGAATTGAAGAAAGACCGCCCTGGGTCAACT
GAAATAAACTGAAGAACGACCACCCTCGATCATTCTGACATAAACTGAAGAAAAGACCACCCTGG
GTCAACTGCAAT
Found at i:19411 original size:107 final size:105
Alignment explanation
Indices: 19178--19793 Score: 444
Period size: 107 Copynumber: 5.8 Consensus size: 105
19168 TGAAATAAGT
* * * * * * ** *
19178 TGAAGGAAGACCACCCTGGGTCAAATGAAATGAATTGAA-AAGCGGCCACCCTTAATCATCCTGA
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAA-AGACCACCCTCGATCATACTGA
* *
19242 C-TCAAACTGAAGAAAGACCGCCTTGGGTCAACTGAAATAAAT
65 CAT-AAACTGAAGAAAGACCACCTTGGGTCAACTG-AATAAAC
* * * *
19284 TAAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATTCTGAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCACCCTCGATCATACTGAC
19349 ATAAACTGAAGAAAAGACCACCTTGGGTCAACTGCAATAAAC
66 ATAAACTGAAG-AAAGACCACCTTGGGTCAACTG-AATAAAC
* * * * * * ** *
19391 TGAAGAAAGACCGCCCTGGGTCAACTGAAATGAATTGAAGAAAGATCGCCCTGGGCCA-ACTGAA
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCACCCTCGATCATACTGAC
* * * * *
19455 ATAAACTGAAGAACGACCACCCTCGATCATTCTGACATAAAC
66 ATAAACTGAAGAAAGACCACCTTGGGTCA-ACTGA-ATAAAC
* * * *
19497 TGAAGAAAAGACCACCCTGGGTCAACTGCAATAAACTGAAGAAAGACCGCCCTGGGTCA-ACTGA
1 TGAAG-AAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCACCCTCGATCATACTGA
* * * * * * * *
19561 AATGAATTGAAGAACGA-CACCCCTCGATCATTCTGACATAAAC
65 CATAAACTGAAGAAAGACCA-CCTTGGGTCA-ACTGA-ATAAAC
* * * * *
19604 TGAAGAAAAGACCACCCTAGGTTAACT-ACAATAAACTGAAGAAAGACCGCCCTGGGTCA-A-TC
1 TGAAG-AAAGACCACCCTGGGTCAACTGA-AATAAACTGAAGAAAGACCACCCTCGATCATACT-
* * * * * * * *
19666 GAAATGAACTAAAGAAAGACCACCCTCGATCATTCTTACATAAAC
63 GACATAAACTGAAGAAAGACCACCTTGGGTCA-ACTGA-ATAAAC
* * * *
19711 TGAAGAAAAGGACCACCCTGGGTTAA-TAGAAATAAACTGAAGAAAGACCGCCCTAGGTCA-ACT
1 TGAAG-AAA-GACCACCCTGGGTCAACT-GAAATAAACTGAAGAAAGACCACCCTCGATCATACT
* *
19774 GAAAT-AACTGACGAAAGACC
63 GACATAAACTGAAGAAAGACC
19794 TAGGTCAATA
Statistics
Matches: 448, Mismatches: 48, Indels: 27
0.86 0.09 0.05
Matches are distributed among these distances:
105 15 0.03
106 93 0.21
107 286 0.64
108 52 0.12
109 2 0.00
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.17
Consensus pattern (105 bp):
TGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCACCCTCGATCATACTGAC
ATAAACTGAAGAAAGACCACCTTGGGTCAACTGAATAAAC
Found at i:21052 original size:23 final size:23
Alignment explanation
Indices: 21026--21069 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
21016 TCTTCATCAA
21026 TTTTCCCCTT-TTTTTTCTTTTTC
1 TTTT-CCCTTCTTTTTTCTTTTTC
*
21049 TTTTTCCTTCTTTTTTCTTTT
1 TTTTCCCTTCTTTTTTCTTTT
21070 AATGCACTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTCCCTTCTTTTTTCTTTTTC
Found at i:27579 original size:15 final size:15
Alignment explanation
Indices: 27559--27590 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
27549 TGATATCTAT
27559 TGATTATGAAAACAA
1 TGATTATGAAAACAA
27574 TGATTATGAAAACAA
1 TGATTATGAAAACAA
27589 TG
1 TG
27591 GATAGCTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.28
Consensus pattern (15 bp):
TGATTATGAAAACAA
Found at i:28739 original size:19 final size:18
Alignment explanation
Indices: 28706--28741 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
28696 TTGAAATTAT
28706 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
28724 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
28742 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:40260 original size:30 final size:29
Alignment explanation
Indices: 40221--40277 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 29
40211 GTTTATTAAT
40221 GAAACTTGAAAATTAAAGACATAAGATAAAG
1 GAAACTTGAAAATTAAAG-CATAA-ATAAAG
40252 GAAA-TTGAAAATTAAAGCATAAATAA
1 GAAACTTGAAAATTAAAGCATAAATAA
40278 CTAATCCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 4 0.15
29 5 0.19
30 13 0.50
31 4 0.15
ACGTcount: A:0.60, C:0.05, G:0.14, T:0.21
Consensus pattern (29 bp):
GAAACTTGAAAATTAAAGCATAAATAAAG
Done.