Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016097.1 Corchorus olitorius cultivar O-4 contig16130, 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: 57096
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:1894 original size:2 final size:2
Alignment explanation
Indices: 1887--1912 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1877 ATTAATCAAC
1887 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
1913 GTACAACAAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7097 original size:2 final size:2
Alignment explanation
Indices: 7090--7125 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
7080 TAATTTGCAG
7090 TA TA 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 TA TA
7126 ACTTTTTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15677 original size:21 final size:21
Alignment explanation
Indices: 15653--15721 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
15643 GGCCAGGATT
15653 GGCCACAACCATGCCAAGACC
1 GGCCACAACCATGCCAAGACC
** *
15674 GGCCACCGTCGC-T-CCAGGACC
1 GGCCA-CAAC-CATGCCAAGACC
*
15695 AGCCACAACCATGCCAAGACC
1 GGCCACAACCATGCCAAGACC
15716 GGCCAC
1 GGCCAC
15722 CACCGGCCAT
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
19 1 0.03
20 3 0.08
21 28 0.78
22 3 0.08
23 1 0.03
ACGTcount: A:0.28, C:0.45, G:0.22, T:0.06
Consensus pattern (21 bp):
GGCCACAACCATGCCAAGACC
Found at i:28231 original size:16 final size:16
Alignment explanation
Indices: 28193--28230 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
28183 TTACTTTATT
28193 TTGTTTTCTATTATAA
1 TTGTTTTCTATTATAA
*
28209 TTGTTTTCTGTT-TAA
1 TTGTTTTCTATTATAA
28224 TTGTTTT
1 TTGTTTT
28231 TTTTCAACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.16, C:0.05, G:0.11, T:0.68
Consensus pattern (16 bp):
TTGTTTTCTATTATAA
Found at i:29421 original size:18 final size:18
Alignment explanation
Indices: 29398--29432 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
29388 GCATTACTTC
29398 ATTAAAAGCCCACTATTA
1 ATTAAAAGCCCACTATTA
*
29416 ATTAAAAGCCCATTATT
1 ATTAAAAGCCCACTATT
29433 CACAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.31
Consensus pattern (18 bp):
ATTAAAAGCCCACTATTA
Found at i:29984 original size:161 final size:161
Alignment explanation
Indices: 29718--30365 Score: 1053
Period size: 161 Copynumber: 4.0 Consensus size: 161
29708 TTTTGGTTTG
*
29718 TACAAAAGTCCACTATGTGGCAAGGCATTGGTGATTGAGAAACCACTATAGCTCACACCTAGTCT
1 TACAAAAGCCCACTATGTGGCAAGGCATTGGTGATTGAGAAACCACTATAGCTCACACCTAGTCT
* *
29783 TCCTTATATGATGCATTGTTTACCATCATCAAGGCATGGCAAGGCATTATGCCGCTGGTGATTGA
66 TCCTTGTATGATGCATTGTTTACCATCATCAAGGCATGGCAAGGCATTATGCCGCCGGTGATTGA
29848 GACAACCTATAGTTCTCACCGTGTCATTATT
131 GACAACCTATAGTTCTCACCGTGTCATTATT
*
29879 TACAAAAGCCCACTATGTGGCAAGGTATTGGTGATTGAGAAACCACTATAGCTCACACCTAGTCT
1 TACAAAAGCCCACTATGTGGCAAGGCATTGGTGATTGAGAAACCACTATAGCTCACACCTAGTCT
* * * *
29944 TCCTTGTATGGTGCATTGTTTACCATCATAAAGACATGGCAAGGCATTATGCTGCCGGTGATTGA
66 TCCTTGTATGATGCATTGTTTACCATCATCAAGGCATGGCAAGGCATTATGCCGCCGGTGATTGA
* *
30009 GACAACCTATAGTTCTCACCTTGTCTTTATTATG
131 GACAACCTATAGTTCTCACCGTGTC---ATTATT
* * * *
30043 TACAAAAGTCCACAATATGGCAAGGCATTGGTGATTGAGAAAACCACTATAGCTCACACCCAGTC
1 TACAAAAGCCCACTATGTGGCAAGGCATTGGTGATTGAG-AAACCACTATAGCTCACACCTAGTC
* *
30108 TTCCTTGTATGATGCATTGTTTACCATCATCAAGGCATGGCAAGGCATTATGCTGCCGGTGGTTG
65 TTCCTTGTATGATGCATTGTTTACCATCATCAAGGCATGGCAAGGCATTATGCCGCCGGTGATTG
*
30173 AGACAACCTATAGTTCTCACCGTGTCTTTATT
130 AGACAACCTATAGTTCTCACCGTGTCATTATT
* *
30205 TACAAAAGCCCACTATGTGGCAAGGTATTGGTGATTGGGAAACCACTATAGCTCACACCTAGTCT
1 TACAAAAGCCCACTATGTGGCAAGGCATTGGTGATTGAGAAACCACTATAGCTCACACCTAGTCT
* *
30270 TCCTTGTATGATGCATTGTTTACCATCATCAAGGCATGGCAAGGCATTATGCCACCGATGATTGA
66 TCCTTGTATGATGCATTGTTTACCATCATCAAGGCATGGCAAGGCATTATGCCGCCGGTGATTGA
* *
30335 GACAACCTATAGTTCTCACCTTGTCTTTATT
131 GACAACCTATAGTTCTCACCGTGTCATTATT
30366 ATTATGATAC
Statistics
Matches: 450, Mismatches: 33, Indels: 8
0.92 0.07 0.02
Matches are distributed among these distances:
161 262 0.58
162 38 0.08
164 40 0.09
165 110 0.24
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (161 bp):
TACAAAAGCCCACTATGTGGCAAGGCATTGGTGATTGAGAAACCACTATAGCTCACACCTAGTCT
TCCTTGTATGATGCATTGTTTACCATCATCAAGGCATGGCAAGGCATTATGCCGCCGGTGATTGA
GACAACCTATAGTTCTCACCGTGTCATTATT
Found at i:30310 original size:326 final size:325
Alignment explanation
Indices: 29716--30367 Score: 1160
Period size: 326 Copynumber: 2.0 Consensus size: 325
29706 CTTTTTGGTT
* * *
29716 TGTACAAAAGTCCACTATGTGGCAAGGCATTGGTGATTGAGAAACCACTATAGCTCACACCTAGT
1 TGTACAAAAGTCCACAATATGGCAAGGCATTGGTGATTGAGAAACCACTATAGCTCACACCCAGT
*
29781 CTTCCTTATATGATGCATTGTTTACCATCATCAAGGCATGGCAAGGCATTATGCCGCTGGTGATT
66 CTTCCTTATATGATGCATTGTTTACCATCATCAAGGCATGGCAAGGCATTATGCCGCCGGTGATT
29846 GAGACAACCTATAGTTCTCACCGTGTCATTATTTACAAAAGCCCACTATGTGGCAAGGTATTGGT
131 GAGACAACCTATAGTTCTCACCGTGTCATTATTTACAAAAGCCCACTATGTGGCAAGGTATTGGT
*
29911 GATTGAGAAACCACTATAGCTCACACCTAGTCTTCCTTGTATGGTGCATTGTTTACCATCATAAA
196 GATTGAGAAACCACTATAGCTCACACCTAGTCTTCCTTGTATGATGCATTGTTTACCATCATAAA
** *
29976 GACATGGCAAGGCATTATGCTGCCGGTGATTGAGACAACCTATAGTTCTCACCTTGTCTTTATTA
261 GACATGGCAAGGCATTATGCCACCGATGATTGAGACAACCTATAGTTCTCACCTTGTCTTTATTA
30041 TGTACAAAAGTCCACAATATGGCAAGGCATTGGTGATTGAGAAAACCACTATAGCTCACACCCAG
1 TGTACAAAAGTCCACAATATGGCAAGGCATTGGTGATTGAG-AAACCACTATAGCTCACACCCAG
* * *
30106 TCTTCCTTGTATGATGCATTGTTTACCATCATCAAGGCATGGCAAGGCATTATGCTGCCGGTGGT
65 TCTTCCTTATATGATGCATTGTTTACCATCATCAAGGCATGGCAAGGCATTATGCCGCCGGTGAT
*
30171 TGAGACAACCTATAGTTCTCACCGTGTCTTTATTTACAAAAGCCCACTATGTGGCAAGGTATTGG
130 TGAGACAACCTATAGTTCTCACCGTGTCATTATTTACAAAAGCCCACTATGTGGCAAGGTATTGG
* *
30236 TGATTGGGAAACCACTATAGCTCACACCTAGTCTTCCTTGTATGATGCATTGTTTACCATCATCA
195 TGATTGAGAAACCACTATAGCTCACACCTAGTCTTCCTTGTATGATGCATTGTTTACCATCATAA
*
30301 AGGCATGGCAAGGCATTATGCCACCGATGATTGAGACAACCTATAGTTCTCACCTTGTCTTTATT
260 AGACATGGCAAGGCATTATGCCACCGATGATTGAGACAACCTATAGTTCTCACCTTGTCTTTATT
30366 A
325 A
30367 T
1 T
30368 TATGATACAT
Statistics
Matches: 311, Mismatches: 15, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
325 39 0.13
326 272 0.87
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (325 bp):
TGTACAAAAGTCCACAATATGGCAAGGCATTGGTGATTGAGAAACCACTATAGCTCACACCCAGT
CTTCCTTATATGATGCATTGTTTACCATCATCAAGGCATGGCAAGGCATTATGCCGCCGGTGATT
GAGACAACCTATAGTTCTCACCGTGTCATTATTTACAAAAGCCCACTATGTGGCAAGGTATTGGT
GATTGAGAAACCACTATAGCTCACACCTAGTCTTCCTTGTATGATGCATTGTTTACCATCATAAA
GACATGGCAAGGCATTATGCCACCGATGATTGAGACAACCTATAGTTCTCACCTTGTCTTTATTA
Found at i:31077 original size:20 final size:21
Alignment explanation
Indices: 31052--31092 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
31042 TGAAGGGAAT
31052 CTTGT-CATAAGCATTAAATG
1 CTTGTCCATAAGCATTAAATG
* *
31072 CTTGTCCTTGAGCATTAAATG
1 CTTGTCCATAAGCATTAAATG
31093 TTGATGGAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (21 bp):
CTTGTCCATAAGCATTAAATG
Found at i:31586 original size:3 final size:3
Alignment explanation
Indices: 31578--31608 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
31568 CAAGCTCTTT
*
31578 GAA GAA GAA GAA GAA GAA GAA GAA GAT GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
31609 TTTTGAGGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.35, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:33985 original size:12 final size:13
Alignment explanation
Indices: 33962--33991 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
33952 ACTAGTAATT
33962 AAAATCAATCAAG
1 AAAATCAATCAAG
33975 AAAAT-AATCAAG
1 AAAATCAATCAAG
33987 AAAAT
1 AAAAT
33992 TAAAGAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.67, C:0.10, G:0.07, T:0.17
Consensus pattern (13 bp):
AAAATCAATCAAG
Found at i:37054 original size:41 final size:42
Alignment explanation
Indices: 36948--37226 Score: 277
Period size: 41 Copynumber: 6.6 Consensus size: 42
36938 CTCCCTCCCC
* *
36948 AAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTCTCT-CT
1 AAAGTCCCCAAACACATTTATAACACAGAGGC-A--CTCTATACT
* * * *
36992 GAAGTCCTCAAACACATTTATAACACAAAGGCA-TCTAAACT
1 AAAGTCCCCAAACACATTTATAACACAGAGGCACTCTATACT
* * * *
37033 AAAGTCCCCAAACACAATTATAACATAGGGGCAATTCTCT-TTCT
1 AAAGTCCCCAAACACATTTATAACACAGAGGC-A--CTCTATACT
*
37077 AAAGTCCTCAAACACATTTATAACACAGAGGCA-TCTATA-T
1 AAAGTCCCCAAACACATTTATAACACAGAGGCACTCTATACT
* *
37117 CAAAGTCCCCAAACACATTTATAACACATG-GGCACCTCTATTCC
1 -AAAGTCCCCAAACACATTTATAACACA-GAGGCA-CTCTATACT
*
37161 AAAGTCCTCAAACACATTTATAACACAGAGGCA-TCTATA-T
1 AAAGTCCCCAAACACATTTATAACACAGAGGCACTCTATACT
*
37201 CAAAGTCCCCAAACACAATTATAACA
1 -AAAGTCCCCAAACACATTTATAACA
37227 TAAGGGCAAT
Statistics
Matches: 195, Mismatches: 27, Indels: 29
0.78 0.11 0.12
Matches are distributed among these distances:
40 7 0.04
41 87 0.45
42 3 0.02
43 37 0.19
44 58 0.30
45 3 0.02
ACGTcount: A:0.40, C:0.27, G:0.10, T:0.24
Consensus pattern (42 bp):
AAAGTCCCCAAACACATTTATAACACAGAGGCACTCTATACT
Found at i:37067 original size:85 final size:85
Alignment explanation
Indices: 36947--37243 Score: 445
Period size: 85 Copynumber: 3.5 Consensus size: 85
36937 TCTCCCTCCC
* *
36947 CAAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTCTCTCTGAAGTCCTCAAACACATTTA
1 CAAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTCTCTCTAAAGTCCTCAAACACATTTA
* *
37012 TAACACAAAGGCATCTA-AA
66 TAACACAGAGGCATCTATAT
* *
37031 CTAAAGTCCCCAAACACAATTATAACATAGGGGCAATTCTCTTTCTAAAGTCCTCAAACACATTT
1 C-AAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTCTCTCTAAAGTCCTCAAACACATTT
37096 ATAACACAGAGGCATCTATAT
65 ATAACACAGAGGCATCTATAT
* * ** * *
37117 CAAAGTCCCCAAACACATTTATAACACATGGGCACCTCTAT-TCCAAAGTCCTCAAACACATTTA
1 CAAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTCTCTCTAAAGTCCTCAAACACATTTA
37181 TAACACAGAGGCATCTATAT
66 TAACACAGAGGCATCTATAT
* *
37201 CAAAGTCCCCAAACACAATTATAACATAAGGGCAATTCTCTCT
1 CAAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTCTCT
37244 ATATGGCAAA
Statistics
Matches: 191, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
84 78 0.41
85 111 0.58
86 2 0.01
ACGTcount: A:0.39, C:0.27, G:0.10, T:0.24
Consensus pattern (85 bp):
CAAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTCTCTCTAAAGTCCTCAAACACATTTA
TAACACAGAGGCATCTATAT
Found at i:44619 original size:3 final size:3
Alignment explanation
Indices: 44611--44641 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
44601 AAGAGTAACC
44611 AGA AGA AGA AGA AGA AGA AGA AGA AGGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA A-GA AGA
44642 TGTTGCTAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:45046 original size:2 final size:2
Alignment explanation
Indices: 45037--45068 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
45027 TTACTATATG
45037 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
45069 TTTTCTTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:50011 original size:2 final size:2
Alignment explanation
Indices: 50004--50037 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
49994 AAATACTATT
50004 TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
50038 TCTATGTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:50025 original size:15 final size:15
Alignment explanation
Indices: 50005--50034 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
49995 AATACTATTT
50005 ATATATATATATATA
1 ATATATATATATATA
50020 ATATATATATATATA
1 ATATATATATATATA
50035 TATTCTATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:50026 original size:17 final size:17
Alignment explanation
Indices: 50004--50036 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
49994 AAATACTATT
50004 TATATATATATATATAA
1 TATATATATATATATAA
50021 TATATATATATATATA
1 TATATATATATATATA
50037 TTCTATGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATATATATATATAA
Found at i:50705 original size:2 final size:2
Alignment explanation
Indices: 50698--50735 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
50688 CCTGCATGTG
50698 TA TA TA 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 TA TA TA
50736 ATTAATTAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:51741 original size:21 final size:21
Alignment explanation
Indices: 51701--51741 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
51691 TGGTTTCTGC
*
51701 ATAAACTATATATAACATTAT
1 ATAAACTAAATATAACATTAT
51722 ATAAACTAAAATATAA-ATTA
1 ATAAACT-AAATATAACATTA
51742 ATTTTTAGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (21 bp):
ATAAACTAAATATAACATTAT
Found at i:52446 original size:14 final size:14
Alignment explanation
Indices: 52427--52454 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52417 CTCCCCTAAA
52427 ACTATTATCTTAAG
1 ACTATTATCTTAAG
52441 ACTATTATCTTAAG
1 ACTATTATCTTAAG
52455 CAGTCGTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
ACTATTATCTTAAG
Done.