Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018722.1 Corchorus olitorius cultivar O-4 contig18755, 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: 18902
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Found at i:90 original size:31 final size:31
Alignment explanation
Indices: 1--558 Score: 596
Period size: 31 Copynumber: 17.2 Consensus size: 31
1 CGGAATTGAAAGATAAAAGACCTGTCTGAGGT
1 CGGAATTGAAAGAT-AAAGACCTGTCTGAGGT
* * *
33 CGAAAATTAAAAGCTGAGAAAAGACCTGTCTGAGGT
1 CG-GAATTGAAA---GA-TAAAGACCTGTCTGAGGT
69 CGGAATTGAAAGATAAAGACCTGTCTGAGGT
1 CGGAATTGAAAGATAAAGACCTGTCTGAGGT
100 CGGAATTGAAAGATTAAAGACCTGTCTGAGGT
1 CGGAATTGAAAGA-TAAAGACCTGTCTGAGGT
* * * *
132 CGAAATTAAAAGCTGAGAAAAAGACCTGTCTGAGGC
1 CGGAATT-GAA----AGATAAAGACCTGTCTGAGGT
* *
168 CGGAATTGAAAGATAAAGACTTGTCTGAAGT
1 CGGAATTGAAAGATAAAGACCTGTCTGAGGT
* * *
199 CGAAATTAAAAGCTGAGAAAGACCTGTCTGAGGT
1 CGGAATTGAAA---GATAAAGACCTGTCTGAGGT
*
233 CGGAATTGAAAGATAAAGACATGTCTGAGGT
1 CGGAATTGAAAGATAAAGACCTGTCTGAGGT
264 CGGAATTGAAAGATAAAGACCTGTCTGAGGT
1 CGGAATTGAAAGATAAAGACCTGTCTGAGGT
* * *
295 CGAAATTGAAACTGAGAAGGACCTGTCTGAGGT
1 CGGAATTGAAA--GATAAAGACCTGTCTGAGGT
328 CGGAATTGAAAGATAAAGACCTGTCTGAGGT
1 CGGAATTGAAAGATAAAGACCTGTCTGAGGT
* * *
359 CGAAATTAAAAGCTGAGAAAGACCTGTCTGAGGT
1 CGGAATTGAAA---GATAAAGACCTGTCTGAGGT
393 CGGAATTGAAAGATAAAGACCTGTCTGAGGT
1 CGGAATTGAAAGATAAAGACCTGTCTGAGGT
*
424 CGGAATGGAAAGATAAAGACCTGTCTGAGGT
1 CGGAATTGAAAGATAAAGACCTGTCTGAGGT
* * *
455 CGAAATTGAAACTGAGAAGGACCTGTCTGAGGT
1 CGGAATTGAAA--GATAAAGACCTGTCTGAGGT
* * *
488 CGAAATTGAAACTGAAAAAGACATGTCTGAGGT
1 CGGAATTGAAA--GATAAAGACCTGTCTGAGGT
* ** *
521 CGAAATT-AAACTGAGGAAGACTTGTCTGAGGT
1 CGGAATTGAAA--GATAAAGACCTGTCTGAGGT
553 CTGGAA
1 C-GGAA
559 CTTCGAAATC
Statistics
Matches: 454, Mismatches: 50, Indels: 43
0.83 0.09 0.08
Matches are distributed among these distances:
31 199 0.44
32 51 0.11
33 95 0.21
34 54 0.12
35 9 0.02
36 43 0.09
37 3 0.01
ACGTcount: A:0.37, C:0.13, G:0.28, T:0.22
Consensus pattern (31 bp):
CGGAATTGAAAGATAAAGACCTGTCTGAGGT
Found at i:252 original size:65 final size:64
Alignment explanation
Indices: 16--558 Score: 591
Period size: 65 Copynumber: 8.3 Consensus size: 64
6 TTGAAAGATA
* * * *
16 AAAGACCTGTCTGAGGTCGAAAATTAAAAGCTGAGAAAAGACCTGTCTGAGGTCGGAATTGAAA-
1 AAAGACCTGTCTGAGGTCG-GAATTGAAA---GA-TAAAGACCTGTCTGAGGTCGAAATTGAAAC
*
80 -GAT
61 TGAG
*
83 AAAGACCTGTCTGAGGTCGGAATTGAAAGATTAAAGACCTGTCTGAGGTCGAAATTAAAAGCTGA
1 AAAGACCTGTCTGAGGTCGGAATTGAAAGA-TAAAGACCTGTCTGAGGTCGAAATTGAAA-CTGA
148 G
64 G
* * * *
149 AAAAAGACCTGTCTGAGGCCGGAATTGAAAGATAAAGACTTGTCTGAAGTCGAAATTAAAAGCTG
1 --AAAGACCTGTCTGAGGTCGGAATTGAAAGATAAAGACCTGTCTGAGGTCGAAATTGAAA-CTG
214 AG
63 AG
* * *
216 AAAGACCTGTCTGAGGTCGGAATTGAAAGATAAAGACATGTCTGAGGTCGGAATTGAAA--GAT
1 AAAGACCTGTCTGAGGTCGGAATTGAAAGATAAAGACCTGTCTGAGGTCGAAATTGAAACTGAG
* * * *
278 AAAGACCTGTCTGAGGTCGAAATTGAAACTGAGAAGGACCTGTCTGAGGTCGGAATTGAAA--GA
1 AAAGACCTGTCTGAGGTCGGAATTGAAA--GATAAAGACCTGTCTGAGGTCGAAATTGAAACTGA
*
341 T
64 G
* * * *
342 AAAGACCTGTCTGAGGTCGAAATTAAAAGCTGAGAAAGACCTGTCTGAGGTCGGAATTGAAA--G
1 AAAGACCTGTCTGAGGTCGGAATTGAAA---GATAAAGACCTGTCTGAGGTCGAAATTGAAACTG
*
405 AT
63 AG
*
407 AAAGACCTGTCTGAGGTCGGAATGGAAAGATAAAGACCTGTCTGAGGTCGAAATTGAAACTGAG
1 AAAGACCTGTCTGAGGTCGGAATTGAAAGATAAAGACCTGTCTGAGGTCGAAATTGAAACTGAG
* * * *
471 AAGGACCTGTCTGAGGTCGAAATTGAAACTGAAAAAGACATGTCTGAGGTCGAAATT-AAACTGA
1 AAAGACCTGTCTGAGGTCGGAATTGAAA--GATAAAGACCTGTCTGAGGTCGAAATTGAAACTGA
535 G
64 G
* *
536 GAAGACTTGTCTGAGGTCTGGAA
1 AAAGACCTGTCTGAGGTC-GGAA
559 CTTCGAAATC
Statistics
Matches: 426, Mismatches: 37, Indels: 27
0.87 0.08 0.06
Matches are distributed among these distances:
62 58 0.14
63 28 0.07
64 85 0.20
65 137 0.32
66 37 0.09
67 52 0.12
68 29 0.07
ACGTcount: A:0.37, C:0.13, G:0.28, T:0.22
Consensus pattern (64 bp):
AAAGACCTGTCTGAGGTCGGAATTGAAAGATAAAGACCTGTCTGAGGTCGAAATTGAAACTGAG
Found at i:377 original size:160 final size:160
Alignment explanation
Indices: 1--558 Score: 904
Period size: 160 Copynumber: 3.4 Consensus size: 160
1 CGGAATTGAAAGATAAAAGACCTGTCTGAGGTCGAAAATTAAAAGCTGAGAAAAGACCTGTCTGA
1 CGGAATTGAAAGAT-AAAGACCTGTCTGAGGTCG-AAATTAAAAGCTGAG-AAAGACCTGTCTGA
66 GGTCGGAATTGAAAGATAAAGACCTGTCTGAGGTCGGAATTGAAAGATTAAAGACCTGTCTGAGG
63 GGTCGGAATTGAAAGATAAAGACCTGTCTGAGGTCGGAATTGAAAGA-TAAAGACCTGTCTGAGG
* * *
131 TCGAAATTAAAAGCTGAGAAAAAGACCTGTCTGAGGC
127 TCGAAATTGAAA-CTGAG--AAGGACCTGTCTGAGGT
* *
168 CGGAATTGAAAGATAAAGACTTGTCTGAAGTCGAAATTAAAAGCTGAGAAAGACCTGTCTGAGGT
1 CGGAATTGAAAGATAAAGACCTGTCTGAGGTCGAAATTAAAAGCTGAGAAAGACCTGTCTGAGGT
*
233 CGGAATTGAAAGATAAAGACATGTCTGAGGTCGGAATTGAAAGATAAAGACCTGTCTGAGGTCGA
66 CGGAATTGAAAGATAAAGACCTGTCTGAGGTCGGAATTGAAAGATAAAGACCTGTCTGAGGTCGA
298 AATTGAAACTGAGAAGGACCTGTCTGAGGT
131 AATTGAAACTGAGAAGGACCTGTCTGAGGT
328 CGGAATTGAAAGATAAAGACCTGTCTGAGGTCGAAATTAAAAGCTGAGAAAGACCTGTCTGAGGT
1 CGGAATTGAAAGATAAAGACCTGTCTGAGGTCGAAATTAAAAGCTGAGAAAGACCTGTCTGAGGT
*
393 CGGAATTGAAAGATAAAGACCTGTCTGAGGTCGGAATGGAAAGATAAAGACCTGTCTGAGGTCGA
66 CGGAATTGAAAGATAAAGACCTGTCTGAGGTCGGAATTGAAAGATAAAGACCTGTCTGAGGTCGA
458 AATTGAAACTGAGAAGGACCTGTCTGAGGT
131 AATTGAAACTGAGAAGGACCTGTCTGAGGT
* * * * *
488 CGAAATTGAAACTGAAAAAGACATGTCTGAGGTCGAAATT-AAA-CTGAGGAAGACTTGTCTGAG
1 CGGAATTGAAA--GATAAAGACCTGTCTGAGGTCGAAATTAAAAGCTGAGAAAGACCTGTCTGAG
551 GTCTGGAA
64 GTC-GGAA
559 CTTCGAAATC
Statistics
Matches: 373, Mismatches: 15, Indels: 12
0.93 0.04 0.03
Matches are distributed among these distances:
160 202 0.54
161 7 0.02
162 30 0.08
163 28 0.08
164 60 0.16
165 15 0.04
166 17 0.05
167 14 0.04
ACGTcount: A:0.37, C:0.13, G:0.28, T:0.22
Consensus pattern (160 bp):
CGGAATTGAAAGATAAAGACCTGTCTGAGGTCGAAATTAAAAGCTGAGAAAGACCTGTCTGAGGT
CGGAATTGAAAGATAAAGACCTGTCTGAGGTCGGAATTGAAAGATAAAGACCTGTCTGAGGTCGA
AATTGAAACTGAGAAGGACCTGTCTGAGGT
Found at i:393 original size:129 final size:127
Alignment explanation
Indices: 1--553 Score: 607
Period size: 129 Copynumber: 4.3 Consensus size: 127
*
1 CGGAATTGAAAGATAAAAGACCTGTCTGAGGTCGAAAATTAAAAGCTGAGAAAAGACCTGTCTGA
1 CGGAATTGAAAGAT-AAAGACCTGTCTGAGGTCG-AAATTGAAA---GAG-AAAGACCTGTCTGA
* * * *
66 GGTCGGAATTGAAA-GATAAAGACCTGTCTGAGGTCGGAATTGAAA--GATTAAAGACCTGTCTG
60 GGTCGAAATTGAAACGAGAAAGACCTGTCTGAGGTCGAAATTGAAACTGA-TAAAGACATGTCTG
128 AGGT
124 AGGT
* * * * * * * *
132 CGAAATTAAAAGCTGAGAAAAAGACCTGTCTGAGGCCGGAATTGAAAGATAAAGACTTGTCTGAA
1 CGGAATT-GAA----AGATAAAGACCTGTCTGAGGTCGAAATTGAAAGAGAAAGACCTGTCTGAG
* *
197 GTCGAAATTAAAAGCTGAGAAAGACCTGTCTGAGGTCGGAATTGAAA--GATAAAGACATGTCTG
61 GTCGAAATTGAAA-C-GAGAAAGACCTGTCTGAGGTCGAAATTGAAACTGATAAAGACATGTCTG
260 AGGT
124 AGGT
*
264 CGGAATTGAAAGATAAAGACCTGTCTGAGGTCGAAATTGAAACTGAGAAGGACCTGTCTGAGGTC
1 CGGAATTGAAAGATAAAGACCTGTCTGAGGTCGAAATTGAAA--GAGAAAGACCTGTCTGAGGTC
* * * * *
329 GGAATTGAAA-GATAAAGACCTGTCTGAGGTCGAAATTAAAAGCTGAGAAAGACCTGTCTGAGGT
64 GAAATTGAAACGAGAAAGACCTGTCTGAGGTCGAAATTGAAA-CTGATAAAGACATGTCTGAGGT
* * *
393 CGGAATTGAAAGATAAAGACCTGTCTGAGGTCGGAATGGAAAGATAAAGACCTGTCTGAGGTCGA
1 CGGAATTGAAAGATAAAGACCTGTCTGAGGTCGAAATTGAAAGAGAAAGACCTGTCTGAGGTCGA
* *
458 AATTGAAACTGAGAAGGACCTGTCTGAGGTCGAAATTGAAACTGAAAAAGACATGTCTGAGGT
66 AATTGAAAC-GAGAAAGACCTGTCTGAGGTCGAAATTGAAACTGATAAAGACATGTCTGAGGT
* ** *
521 CGAAATT-AAACTGAGGAAGACTTGTCTGAGGTC
1 CGGAATTGAAA--GATAAAGACCTGTCTGAGGTC
554 TGGAACTTCG
Statistics
Matches: 362, Mismatches: 43, Indels: 36
0.82 0.10 0.08
Matches are distributed among these distances:
126 28 0.08
127 60 0.17
128 26 0.07
129 129 0.36
130 24 0.07
131 10 0.03
132 25 0.07
133 32 0.09
134 7 0.02
135 18 0.05
136 3 0.01
ACGTcount: A:0.37, C:0.13, G:0.28, T:0.22
Consensus pattern (127 bp):
CGGAATTGAAAGATAAAGACCTGTCTGAGGTCGAAATTGAAAGAGAAAGACCTGTCTGAGGTCGA
AATTGAAACGAGAAAGACCTGTCTGAGGTCGAAATTGAAACTGATAAAGACATGTCTGAGGT
Found at i:5032 original size:2 final size:2
Alignment explanation
Indices: 5027--5061 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5017 AAGAGAGAGA
*
5027 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5062 GAAGAAGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:11098 original size:2 final size:2
Alignment explanation
Indices: 11091--11120 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11081 TTTAGAGTCC
11091 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
11121 CATACATGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13375 original size:21 final size:21
Alignment explanation
Indices: 13336--13375 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
13326 CCCAGTGAGG
*
13336 CCTGAGCTTGCCCCTGTCAGC
1 CCTGAGCTTGCCCCGGTCAGC
* *
13357 CCTGAGTTTGCTCCGGTCA
1 CCTGAGCTTGCCCCGGTCA
13376 AATTCAAGCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.10, C:0.38, G:0.25, T:0.28
Consensus pattern (21 bp):
CCTGAGCTTGCCCCGGTCAGC
Found at i:13526 original size:21 final size:21
Alignment explanation
Indices: 13502--13554 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
13492 GCATTTGTGG
13502 CTTCTTCTCGGCGCTTT-GCCT
1 CTTCTTCTCGGCG-TTTCGCCT
13523 CTTCTTCTCGGCGTTTCGCCT
1 CTTCTTCTCGGCGTTTCGCCT
*
13544 CTTCATCTCGG
1 CTTCTTCTCGG
13555 TGCACTAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 3 0.10
21 27 0.90
ACGTcount: A:0.02, C:0.38, G:0.19, T:0.42
Consensus pattern (21 bp):
CTTCTTCTCGGCGTTTCGCCT
Done.