Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012580.1 Corchorus capsularis cultivar CVL-1 contig12601, 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: 46826
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2860 original size:156 final size:155
Alignment explanation
Indices: 2622--2985 Score: 425
Period size: 156 Copynumber: 2.3 Consensus size: 155
2612 GAGCTTCTCA
* *
2622 CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGCTGAAA
1 CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACGAGCTG-AA
* * * * *
2687 TTTTTCCAAGGAGCTTAGAATATC-CACATAAGGTTATGGGAAAAATTCTATGTAAAACCGAGCT
65 TTTTTCCAAGGAGCTTAGAATATCAC-CATAAAGCTATGGGAAAAAATCTAAGTAAAACCGAACT
* * * *
2751 CCCCT-TGATGGTGAACTAGGTTTCTCT
129 -CCCTAGGATAGAGAACTAGGTTTCACT
* **
2778 CC-CTGAGTTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAACGAAGCTG-
1 CCTC-AAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACG-AGCTGA
*
2840 A-TTTTCCACTAGTAGACTTAGAATATCACCATAAAGCTATGGGAAAAAATCTAAGTAAAACCGA
64 ATTTTTCCA--AGGAG-CTTAGAATATCACCATAAAGCTATGGGAAAAAATCTAAGTAAAACCGA
* * * *
2904 ACTCTCTAGGATAGAGAAGTTGGTTTGACT
126 ACTCCCTAGGATAGAGAACTAGGTTTCACT
* *
2934 CCTCAAACTGTCCTTAACTGAAAAACTAGCATAAGTTTTTCATACTAAGTCT
1 CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCT
2986 ATTTGAGATG
Statistics
Matches: 175, Mismatches: 24, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
153 7 0.04
154 1 0.01
155 11 0.06
156 154 0.88
157 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Consensus pattern (155 bp):
CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACGAGCTGAAT
TTTTCCAAGGAGCTTAGAATATCACCATAAAGCTATGGGAAAAAATCTAAGTAAAACCGAACTCC
CTAGGATAGAGAACTAGGTTTCACT
Found at i:11229 original size:25 final size:25
Alignment explanation
Indices: 11183--11231 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
11173 CAATATCAAG
* *
11183 TAAATATCAATTATTAAGAATTTAT
1 TAAATATAAATGATTAAGAATTTAT
11208 TAAATATAAATGATTGAA-AATTTA
1 TAAATATAAATGATT-AAGAATTTA
11232 GGAAAAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (25 bp):
TAAATATAAATGATTAAGAATTTAT
Found at i:19975 original size:2 final size:2
Alignment explanation
Indices: 19968--19994 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19958 TAGATGTTAT
19968 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 T
19995 GCTGCCTGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24342 original size:63 final size:63
Alignment explanation
Indices: 24264--24392 Score: 249
Period size: 63 Copynumber: 2.0 Consensus size: 63
24254 CTGATACGAA
*
24264 TCTAGTTGTGTTAGATTCAAATCTACCCTTTGAATAGCCACCAAAGTCGACTTGAAACACAAC
1 TCTAGTTGTGTTAGATTCAAATCTACCCTTTGAATAACCACCAAAGTCGACTTGAAACACAAC
24327 TCTAGTTGTGTTAGATTCAAATCTACCCTTTGAATAACCACCAAAGTCGACTTGAAACACAAC
1 TCTAGTTGTGTTAGATTCAAATCTACCCTTTGAATAACCACCAAAGTCGACTTGAAACACAAC
24390 TCT
1 TCT
24393 TCTAGATGAG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.29
Consensus pattern (63 bp):
TCTAGTTGTGTTAGATTCAAATCTACCCTTTGAATAACCACCAAAGTCGACTTGAAACACAAC
Found at i:28779 original size:2 final size:2
Alignment explanation
Indices: 28772--28797 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28762 TTCCTCACAA
28772 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
28798 ATACCTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:29060 original size:21 final size:21
Alignment explanation
Indices: 29034--29074 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
29024 TTCTGGTGTA
*
29034 ACCCGCACCTGATCAAGGTTG
1 ACCCGCACCTGAGCAAGGTTG
* *
29055 ACCCGCGCCTGGGCAAGGTT
1 ACCCGCACCTGAGCAAGGTT
29075 TCGGAACAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.34, G:0.29, T:0.17
Consensus pattern (21 bp):
ACCCGCACCTGAGCAAGGTTG
Found at i:29146 original size:21 final size:21
Alignment explanation
Indices: 29100--29147 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
29090 TTAAACCTCC
*
29100 TGAGG-TAGCCCGCGCCTAGG
1 TGAGGTTAACCCGCGCCTAGG
** *
29120 CAAGGTTAACCCGCGCCTGGG
1 TGAGGTTAACCCGCGCCTAGG
29141 TGAGGTT
1 TGAGGTT
29148 TCAAGACCCT
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.17, C:0.27, G:0.38, T:0.19
Consensus pattern (21 bp):
TGAGGTTAACCCGCGCCTAGG
Found at i:33126 original size:101 final size:103
Alignment explanation
Indices: 33012--33214 Score: 313
Period size: 101 Copynumber: 2.0 Consensus size: 103
33002 ATACTATTAA
* * *
33012 TGTGTTATTATTTGCTTTAG-GAATGAGTGGAGTTAATTATCTATTAATGAGAAA-TGACTAAAG
1 TGTGTTATTATTTGATTT-GCCAAGGAGTGGAGTTAATTATCTATTAATGAGAAATTGACTAAAG
33075 GAATTAATGAATGCATTTGGCAAAA-CGGAGAAAGAGAT
65 GAATTAATGAATGCATTTGGCAAAATCGGAGAAAGAGAT
* *
33113 TGTGTTATTATTTGATTTGCCAAGGGGTGGAGTTAATTCTCTATTAATGAGAAATTGACTAAAGG
1 TGTGTTATTATTTGATTTGCCAAGGAGTGGAGTTAATTATCTATTAATGAGAAATTGACTAAAGG
* *
33178 AATTAATGAATGCATTTGGTAAAATGGGAGAAAGAGA
66 AATTAATGAATGCATTTGGCAAAATCGGAGAAAGAGA
33215 AGTATCATAA
Statistics
Matches: 92, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
100 1 0.01
101 47 0.51
102 33 0.36
103 11 0.12
ACGTcount: A:0.36, C:0.06, G:0.25, T:0.33
Consensus pattern (103 bp):
TGTGTTATTATTTGATTTGCCAAGGAGTGGAGTTAATTATCTATTAATGAGAAATTGACTAAAGG
AATTAATGAATGCATTTGGCAAAATCGGAGAAAGAGAT
Found at i:36447 original size:2 final size:2
Alignment explanation
Indices: 36440--36489 Score: 61
Period size: 2 Copynumber: 26.5 Consensus size: 2
36430 ATTATTAATA
* *
36440 AT AT AT AT AT AT AT AT A- AT AT AA AT AT AT TT AT -T A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36479 AT AT AT AT AT A
1 AT AT AT AT AT A
36490 GTCGGTCGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36780 original size:31 final size:32
Alignment explanation
Indices: 36740--36805 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 32
36730 TAATTTGGTT
* *
36740 AATTAAGTCCCTAACATTGTAAAATCGGCTTA
1 AATTAAGTCCCTAACATTGCAAAATCGGCTCA
36772 AATT-AGTCCCTAACATTGCAAAATCGGCTCA
1 AATTAAGTCCCTAACATTGCAAAATCGGCTCA
36803 AAT
1 AAT
36806 CAGACCTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 28 0.88
32 4 0.12
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (32 bp):
AATTAAGTCCCTAACATTGCAAAATCGGCTCA
Found at i:38088 original size:2 final size:2
Alignment explanation
Indices: 38081--38112 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
38071 ATTAATAAGT
38081 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38113 GAAAATTGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43248 original size:20 final size:18
Alignment explanation
Indices: 43223--43267 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
43213 ACACATGTTT
43223 TACTAATAAATAATAATATA
1 TACTAATAAAT-A-AATATA
* *
43243 TACTAACAAATAAATATT
1 TACTAATAAATAAATATA
43261 TACTAAT
1 TACTAAT
43268 TTTGCTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 11 0.50
19 1 0.05
20 10 0.45
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.36
Consensus pattern (18 bp):
TACTAATAAATAAATATA
Found at i:45997 original size:20 final size:20
Alignment explanation
Indices: 45972--46013 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
45962 ATGTCGTCCG
45972 TGATTCCGCTGTCCGTTGTC
1 TGATTCCGCTGTCCGTTGTC
* *
45992 TGATTCCGTTGTTCGTTGTC
1 TGATTCCGCTGTCCGTTGTC
46012 TG
1 TG
46014 CTATCTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.05, C:0.24, G:0.26, T:0.45
Consensus pattern (20 bp):
TGATTCCGCTGTCCGTTGTC
Done.