Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015164.1 Corchorus capsularis cultivar CVL-1 contig15185, 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: 80339
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:2252 original size:6 final size:6
Alignment explanation
Indices: 2241--2269 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2231 ATAAGCAATC
2241 TTCAAG TTCAAG TTCAAG TTCAAG TTCAA
1 TTCAAG TTCAAG TTCAAG TTCAAG TTCAA
2270 CCTTGAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (6 bp):
TTCAAG
Found at i:3491 original size:3 final size:3
Alignment explanation
Indices: 3483--3525 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
3473 TTTATAGTTT
* * * *
3483 ATC ATC ATC ACC ATC AAC ATC ACC ATC ACC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
3526 CCGAATCAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.37, C:0.40, G:0.00, T:0.23
Consensus pattern (3 bp):
ATC
Found at i:4049 original size:1 final size:1
Alignment explanation
Indices: 4008--4032 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
3998 CCAGGGTTGG
4008 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
4033 GGGGTCTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:7963 original size:75 final size:75
Alignment explanation
Indices: 7839--7992 Score: 177
Period size: 75 Copynumber: 2.1 Consensus size: 75
7829 TCCTAGAGCC
* * * * * *
7839 AAAATGCCTTTGGTTGGATCATCCTCAGTGCCTGTGAAAGTTCGCGATTTCAAAGA-AAAGTTGG
1 AAAATGCCTTCGGTTGGATCATCATCAGTCCCTGTGAAAGTTAGAGATTTCAAAGAGAAAG-TAG
*
7903 AGGCTGCACAG
65 AAGCTGCACAG
* * *
7914 AAAATGCCTTCGGTTGGATCTTCATCTGTTCCCT-TGAAAGTTAGAGATTTGAAAGAGAAAGTAG
1 AAAATGCCTTCGGTTGGATCATCATCAG-TCCCTGTGAAAGTTAGAGATTTCAAAGAGAAAGTAG
*
7978 AAGCTGCACAT
65 AAGCTGCACAG
7989 AAAA
1 AAAA
7993 GTTCTAGGTT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
75 58 0.88
76 8 0.12
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (75 bp):
AAAATGCCTTCGGTTGGATCATCATCAGTCCCTGTGAAAGTTAGAGATTTCAAAGAGAAAGTAGA
AGCTGCACAG
Found at i:14982 original size:2 final size:2
Alignment explanation
Indices: 14975--15013 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
14965 CCCTTGAATT
*
14975 GA GA GA GA TA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
15014 GAGGCTTGGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.03
Consensus pattern (2 bp):
GA
Found at i:17115 original size:89 final size:89
Alignment explanation
Indices: 16959--17137 Score: 268
Period size: 89 Copynumber: 2.0 Consensus size: 89
16949 CGCACACTCA
** *
16959 GTTTTGGTGAGTGAGTCTACCAACGGACAAACTGGGTAGGCGAAGGTCTCGAACAAGTCACTCAA
1 GTTTTGGTGAGTGAGTCTACCAACGGACAAACTGCATAGGCAAAGGTCTCGAACAAGTCACTCAA
*
17024 GTTGGAATAAGTCGCTTACCACTG
66 GTTGGAACAAGTCGCTTACCACTG
* * * * * *
17048 GTTTTGGTTAGTGAGTCTACCAACGGGCCAACTGCATAGGCAAAGGTCTCGAATAAGTCATTTAA
1 GTTTTGGTGAGTGAGTCTACCAACGGACAAACTGCATAGGCAAAGGTCTCGAACAAGTCACTCAA
17113 GTTGGAACAAGTCGCTTACCACTG
66 GTTGGAACAAGTCGCTTACCACTG
17137 G
1 G
17138 GTAGGGATAT
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
89 80 1.00
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (89 bp):
GTTTTGGTGAGTGAGTCTACCAACGGACAAACTGCATAGGCAAAGGTCTCGAACAAGTCACTCAA
GTTGGAACAAGTCGCTTACCACTG
Found at i:28789 original size:6 final size:6
Alignment explanation
Indices: 28778--28802 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
28768 GTTACCTCTT
28778 GGAGAA GGAGAA GGAGAA GGAGAA G
1 GGAGAA GGAGAA GGAGAA GGAGAA G
28803 CAGCTGGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (6 bp):
GGAGAA
Found at i:29518 original size:30 final size:29
Alignment explanation
Indices: 29482--29548 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
29472 GTTTGATAGA
* *
29482 GACAAAACGTCTAAAATTGAGAAG-TTATGG
1 GACAAAACATCCAAAATT-A-AAGTTTATGG
*
29512 GACAAAATATCCAAAATTAAAGTTTATGG
1 GACAAAACATCCAAAATTAAAGTTTATGG
29541 GACAAAAC
1 GACAAAAC
29549 TTACAAGTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 3 0.09
29 14 0.44
30 15 0.47
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.22
Consensus pattern (29 bp):
GACAAAACATCCAAAATTAAAGTTTATGG
Found at i:29557 original size:22 final size:21
Alignment explanation
Indices: 29523--29570 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
29513 ACAAAATATC
* *
29523 CAAAA-TTAAAGTTTATGGGA
1 CAAAACTTAAAGTTCAAGGGA
29543 CAAAACTTACAAGTTCAAGGGA
1 CAAAACTTA-AAGTTCAAGGGA
29565 CAAAAC
1 CAAAAC
29571 AAGGCATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 5 0.21
21 3 0.12
22 16 0.67
ACGTcount: A:0.48, C:0.15, G:0.17, T:0.21
Consensus pattern (21 bp):
CAAAACTTAAAGTTCAAGGGA
Found at i:32423 original size:22 final size:22
Alignment explanation
Indices: 32389--32434 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
32379 TTCTTAAACT
*
32389 TTGTAATATAGAGGGAGTATTA
1 TTGTAATAGAGAGGGAGTATTA
*
32411 TTGTGATAGAGAGGGAGTATTA
1 TTGTAATAGAGAGGGAGTATTA
32433 TT
1 TT
32435 TACAAGTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.37
Consensus pattern (22 bp):
TTGTAATAGAGAGGGAGTATTA
Found at i:35717 original size:14 final size:14
Alignment explanation
Indices: 35698--35726 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
35688 AAAAGTGTTT
35698 TATTCAATTTAGAA
1 TATTCAATTTAGAA
35712 TATTCAATTTAGAA
1 TATTCAATTTAGAA
35726 T
1 T
35727 TCAACACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (14 bp):
TATTCAATTTAGAA
Found at i:37916 original size:32 final size:32
Alignment explanation
Indices: 37875--37948 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
37865 CAGAAAGGGA
*
37875 AAAAACAGAGTGCTATCGTTAAGAAACAGAGG
1 AAAAACAGAGTGCTATCGGTAAGAAACAGAGG
* *
37907 AAAAACAGAGTGTTATTGGTAAGAAACAGAGG
1 AAAAACAGAGTGCTATCGGTAAGAAACAGAGG
37939 AAAAACAGAG
1 AAAAACAGAG
37949 GAGGTGGGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.50, C:0.09, G:0.26, T:0.15
Consensus pattern (32 bp):
AAAAACAGAGTGCTATCGGTAAGAAACAGAGG
Found at i:38014 original size:6 final size:6
Alignment explanation
Indices: 37998--38027 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
37988 AAGAGATGGA
37998 AGAAGAG AGAAAG AGAAAG AGAAAG AGAAA
1 AGAA-AG AGAAAG AGAAAG AGAAAG AGAAA
38028 AGGGGGAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (6 bp):
AGAAAG
Found at i:38023 original size:23 final size:23
Alignment explanation
Indices: 37975--38023 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
37965 TTTACCTTGG
*
37975 AGAAGAGAAAAGGAAGAGATGGA
1 AGAAGAGAAAAGGAAGAGATGAA
37998 AGAAGAGAGAAAGAGAA-AGA-GAA
1 AGAAGAGA-AAAG-GAAGAGATGAA
38021 AGA
1 AGA
38024 GAAAAGGGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 13 0.57
24 7 0.30
25 3 0.13
ACGTcount: A:0.61, C:0.00, G:0.37, T:0.02
Consensus pattern (23 bp):
AGAAGAGAAAAGGAAGAGATGAA
Found at i:44280 original size:7 final size:7
Alignment explanation
Indices: 44268--44293 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
44258 TAATAAAAAA
44268 AATTAAT
1 AATTAAT
44275 AATTAAT
1 AATTAAT
44282 AATTAAT
1 AATTAAT
44289 AATTA
1 AATTA
44294 CCCGTCCGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AATTAAT
Found at i:60327 original size:21 final size:21
Alignment explanation
Indices: 60298--60337 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
60288 AAATAACTAT
*
60298 ATATTATAAATATTTTTTAGA
1 ATATAATAAATATTTTTTAGA
*
60319 ATATAATAATTATTTTTTA
1 ATATAATAAATATTTTTTA
60338 TATAAGGGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (21 bp):
ATATAATAAATATTTTTTAGA
Found at i:60878 original size:2 final size:2
Alignment explanation
Indices: 60866--60899 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
60856 TGCCATAAAC
*
60866 TA TA TA CA 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 TA
60900 ACACAAACAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:65412 original size:19 final size:18
Alignment explanation
Indices: 65388--65426 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
65378 CTCGTGAGAA
*
65388 ATTAGTCCACGTCTAAAAG
1 ATTAGTCCACAT-TAAAAG
*
65407 ATTAGTCGACATTAAAAG
1 ATTAGTCCACATTAAAAG
65425 AT
1 AT
65427 GGACAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (18 bp):
ATTAGTCCACATTAAAAG
Found at i:66834 original size:17 final size:16
Alignment explanation
Indices: 66794--66844 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
66784 TATGTAATCT
*
66794 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
66810 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
66827 TTAGATCACTAGTGATC
1 TT-GATCACTGGTGATC
66844 T
1 T
66845 GGGGGGTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:76280 original size:12 final size:12
Alignment explanation
Indices: 76263--76288 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
76253 TAATTCCGGA
76263 TCCTTGGTCGTT
1 TCCTTGGTCGTT
76275 TCCTTGGTCGTT
1 TCCTTGGTCGTT
76287 TC
1 TC
76289 GTTTGCAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.27, G:0.23, T:0.50
Consensus pattern (12 bp):
TCCTTGGTCGTT
Done.