Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018532.1 Corchorus olitorius cultivar O-4 contig18565, 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: 104147
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3276 original size:103 final size:104
Alignment explanation
Indices: 3097--3307 Score: 388
Period size: 103 Copynumber: 2.0 Consensus size: 104
3087 TAACATAATT
*
3097 AAATTACTGGAACAAAACATAATTTTGTTTAAGGAATATAATATTCAAATCTCATTACAATCAAA
1 AAATTACTGGAACAAAACATAATTTTATTTAAGGAATATAATATTCAAATCTCATTACAATCAAA
3162 TAATTCCTTATAAGTTAT-AAAAAAATCCTTATATGACC
66 TAATTCCTTATAAGTTATAAAAAAAATCCTTATATGACC
* *
3200 AAATTGCTGGAACAAAACATAATTTTATTTAAGGAATATAATATTCAAATCTCATTATAATCAAA
1 AAATTACTGGAACAAAACATAATTTTATTTAAGGAATATAATATTCAAATCTCATTACAATCAAA
3265 TAATTCCTTATAAGTTATAAAAAAAATCCTTATATGACC
66 TAATTCCTTATAAGTTATAAAAAAAATCCTTATATGACC
3304 AAAT
1 AAAT
3308 ATTCATTGAG
Statistics
Matches: 104, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
103 80 0.77
104 24 0.23
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.34
Consensus pattern (104 bp):
AAATTACTGGAACAAAACATAATTTTATTTAAGGAATATAATATTCAAATCTCATTACAATCAAA
TAATTCCTTATAAGTTATAAAAAAAATCCTTATATGACC
Found at i:6185 original size:26 final size:26
Alignment explanation
Indices: 6135--6192 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 26
6125 AAATTTTCAC
6135 TATTTTAATAATGAAATAATTAAAATA
1 TATTTTAATAATGAAAT-ATTAAAATA
6162 -ATTTTAATAATGACAAT-TTAAAAATA
1 TATTTTAATAATGA-AATATT-AAAATA
6188 TATTT
1 TATTT
6193 GAAAAAAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
25 2 0.07
26 19 0.68
27 7 0.25
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (26 bp):
TATTTTAATAATGAAATATTAAAATA
Found at i:19878 original size:12 final size:12
Alignment explanation
Indices: 19861--19891 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
19851 ACTCCTCTTC
19861 TCTGTGTGTGTG
1 TCTGTGTGTGTG
19873 TCTGTGTGTGTG
1 TCTGTGTGTGTG
*
19885 TGTGTGT
1 TCTGTGT
19892 CTCTCTCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.06, G:0.42, T:0.52
Consensus pattern (12 bp):
TCTGTGTGTGTG
Found at i:20749 original size:4 final size:4
Alignment explanation
Indices: 20742--20782 Score: 73
Period size: 4 Copynumber: 10.2 Consensus size: 4
20732 TATATATATA
*
20742 TATG TATG TATG TATG TATG TATG TATG TATG TATT TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T
20783 CTAAGCAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (4 bp):
TATG
Found at i:23102 original size:23 final size:24
Alignment explanation
Indices: 23076--23126 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 24
23066 AAACAATATT
23076 TCAG-ATATCAGAAGGAATTGAAA
1 TCAGAATATCAGAAGGAATTGAAA
23099 TCAGAATTATATCAGAAGGAATTGAAA
1 TCAG-A--ATATCAGAAGGAATTGAAA
23126 T
1 T
23127 TCTTACAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 4 0.17
27 20 0.83
ACGTcount: A:0.47, C:0.08, G:0.20, T:0.25
Consensus pattern (24 bp):
TCAGAATATCAGAAGGAATTGAAA
Found at i:51833 original size:20 final size:20
Alignment explanation
Indices: 51795--51835 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
51785 TTGTTTGGCA
**
51795 TTGTTGCCATTTTTGTTTTT
1 TTGTTGCCATTTTCATTTTT
*
51815 TTGTTGTCATTTTCATTTTT
1 TTGTTGCCATTTTCATTTTT
51835 T
1 T
51836 GAAAACAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.07, C:0.10, G:0.12, T:0.71
Consensus pattern (20 bp):
TTGTTGCCATTTTCATTTTT
Found at i:52918 original size:22 final size:22
Alignment explanation
Indices: 52874--52919 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
52864 AAAAATCGAC
* *
52874 AACGTAATAAAACCAAAATAAA
1 AACGAAATAAAACAAAAATAAA
52896 AACGAAATAAAA-AAAAATGAAA
1 AACGAAATAAAACAAAAAT-AAA
52918 AA
1 AA
52920 ACAGAAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.74, C:0.09, G:0.07, T:0.11
Consensus pattern (22 bp):
AACGAAATAAAACAAAAATAAA
Found at i:53133 original size:20 final size:21
Alignment explanation
Indices: 53100--53138 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
53090 AATTAGTACA
* *
53100 AAAAAGTTTAATAAGGTTATT
1 AAAAACTTTAATAAAGTTATT
53121 AAAAACTTT-ATAAAGTTA
1 AAAAACTTTAATAAAGTTA
53139 CTAGAAGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (21 bp):
AAAAACTTTAATAAAGTTATT
Found at i:53586 original size:21 final size:21
Alignment explanation
Indices: 53539--53592 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
53529 ATAAACTTAC
53539 AAGGTTAAC-AAAAAGTTTAAT
1 AAGGTT-ACTAAAAAGTTTAAT
* *
53560 AA-GTTACTAAAATGTTTTAT
1 AAGGTTACTAAAAAGTTTAAT
*
53580 AAGGTTATTAAAA
1 AAGGTTACTAAAA
53593 CTAAAACCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 2 0.07
20 15 0.54
21 11 0.39
ACGTcount: A:0.48, C:0.04, G:0.13, T:0.35
Consensus pattern (21 bp):
AAGGTTACTAAAAAGTTTAAT
Found at i:54932 original size:4 final size:4
Alignment explanation
Indices: 54923--54961 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
54913 CATCATCTAT
54923 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
54962 TTTACCAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:66760 original size:30 final size:30
Alignment explanation
Indices: 66690--66749 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
66680 TTGAACTAGT
66690 AACAGATTTGATAAGGCTTAGGTTCAAACC
1 AACAGATTTGATAAGGCTTAGGTTCAAACC
66720 AACAGATTTGATAAGGCTTAGGTTCAAACC
1 AACAGATTTGATAAGGCTTAGGTTCAAACC
66750 GAAGGATTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (30 bp):
AACAGATTTGATAAGGCTTAGGTTCAAACC
Found at i:76819 original size:4 final size:5
Alignment explanation
Indices: 76794--76822 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
76784 AAACAAAAAA
76794 AAACT AAACT AAACT AAACT -AACT AAACT
1 AAACT AAACT AAACT AAACT AAACT AAACT
76823 TCCGTATTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.59, C:0.21, G:0.00, T:0.21
Consensus pattern (5 bp):
AAACT
Found at i:81383 original size:17 final size:17
Alignment explanation
Indices: 81361--81395 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
81351 AAATCATTAA
81361 TTTAGTGCATACTGTTT
1 TTTAGTGCATACTGTTT
81378 TTTAGTGCATACTGTTT
1 TTTAGTGCATACTGTTT
81395 T
1 T
81396 GCTATTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.54
Consensus pattern (17 bp):
TTTAGTGCATACTGTTT
Found at i:81912 original size:6 final size:6
Alignment explanation
Indices: 81901--81926 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
81891 AAAACCATTT
81901 TCGAGC TCGAGC TCGAGC TCGAGC TC
1 TCGAGC TCGAGC TCGAGC TCGAGC TC
81927 CAACGAGTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.35, G:0.31, T:0.19
Consensus pattern (6 bp):
TCGAGC
Found at i:86678 original size:78 final size:79
Alignment explanation
Indices: 86527--86764 Score: 370
Period size: 78 Copynumber: 3.0 Consensus size: 79
86517 GAACCAAAAT
* * *
86527 CCCTCTTCCGTCAAAACCCTAATTTCAGAAACTTTTCATCGAAAGAAAATCCAATTTCTTCGTCG
1 CCCTCTTCCGCCAAAACCCTAATTTCAAAAACTTTTCATC-AAAGAAAATCCAATTTCTTCTTCG
*
86592 ATTACTATCTTTAAA
65 ATTCCTATCTTTAAA
* * *
86607 CCCTCTTCCGCCAGAACCCTGATCTCAAAAACTTTTCATC-AAGAAAATCCAATTTCTTCTTCGA
1 CCCTCTTCCGCCAAAACCCTAATTTCAAAAACTTTTCATCAAAGAAAATCCAATTTCTTCTTCGA
*
86671 TTCCTATCGTTAAA
66 TTCCTATCTTTAAA
86685 CCCTCTTCCGCCAAAACCCTAATTTCAAAAACTTTTCATCAAACGAAAATCCAATTTCTTCTTCG
1 CCCTCTTCCGCCAAAACCCTAATTTCAAAAACTTTTCATCAAA-GAAAATCCAATTTCTTCTTCG
*
86750 ATCCCTATCTTTAAA
65 ATTCCTATCTTTAAA
86765 GGTTTGATTT
Statistics
Matches: 143, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
78 72 0.50
79 2 0.01
80 69 0.48
ACGTcount: A:0.32, C:0.29, G:0.06, T:0.33
Consensus pattern (79 bp):
CCCTCTTCCGCCAAAACCCTAATTTCAAAAACTTTTCATCAAAGAAAATCCAATTTCTTCTTCGA
TTCCTATCTTTAAA
Found at i:97481 original size:12 final size:12
Alignment explanation
Indices: 97451--97486 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
97441 TAATTTGTTA
* *
97451 TTCTTTCTTTCT
1 TTCTTTTTTTTT
97463 TTCTTTTTTTTT
1 TTCTTTTTTTTT
97475 TTCTTTTTTTTT
1 TTCTTTTTTTTT
97487 GAGAAAAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (12 bp):
TTCTTTTTTTTT
Found at i:97815 original size:11 final size:11
Alignment explanation
Indices: 97795--97841 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
97785 TACTATTAAA
97795 TAAAATATATT
1 TAAAATATATT
** *
97806 TATGATATATA
1 TAAAATATATT
*
97817 TAAAATATATA
1 TAAAATATATT
97828 TAAAATATATT
1 TAAAATATATT
97839 TAA
1 TAA
97842 TTATTTATGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (11 bp):
TAAAATATATT
Found at i:99149 original size:31 final size:31
Alignment explanation
Indices: 99113--99303 Score: 382
Period size: 31 Copynumber: 6.2 Consensus size: 31
99103 GCCCTGCTTG
99113 TATAAATTATATTTATGATATATATAAAATA
1 TATAAATTATATTTATGATATATATAAAATA
99144 TATAAATTATATTTATGATATATATAAAATA
1 TATAAATTATATTTATGATATATATAAAATA
99175 TATAAATTATATTTATGATATATATAAAATA
1 TATAAATTATATTTATGATATATATAAAATA
99206 TATAAATTATATTTATGATATATATAAAATA
1 TATAAATTATATTTATGATATATATAAAATA
99237 TATAAATTATATTTATGATATATATAAAATA
1 TATAAATTATATTTATGATATATATAAAATA
99268 TATAAATTATATTTATGATATATATAAAATA
1 TATAAATTATATTTATGATATATATAAAATA
99299 TATAA
1 TATAA
99304 TAAATTATTT
Statistics
Matches: 160, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 160 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (31 bp):
TATAAATTATATTTATGATATATATAAAATA
Found at i:99308 original size:11 final size:11
Alignment explanation
Indices: 99130--99307 Score: 97
Period size: 11 Copynumber: 17.0 Consensus size: 11
99120 TATATTTATG
99130 ATATATAT-AA
1 ATATATATAAA
99140 A-ATATATAAA
1 ATATATATAAA
* * **
99150 TTATATTTATG
1 ATATATATAAA
99161 ATATATAT-AA
1 ATATATATAAA
99171 A-ATATATAAA
1 ATATATATAAA
* * **
99181 TTATATTTATG
1 ATATATATAAA
99192 ATATATAT-AA
1 ATATATATAAA
99202 A-ATATATAAA
1 ATATATATAAA
* * **
99212 TTATATTTATG
1 ATATATATAAA
99223 ATATATAT-AA
1 ATATATATAAA
99233 A-ATATATAAA
1 ATATATATAAA
* * **
99243 TTATATTTATG
1 ATATATATAAA
99254 ATATATAT-AA
1 ATATATATAAA
99264 A-ATATATAAA
1 ATATATATAAA
* * **
99274 TTATATTTATG
1 ATATATATAAA
99285 ATATATATAAA
1 ATATATATAAA
99296 ATATATAATAAA
1 ATATAT-ATAAA
99308 TTATTTTTAA
Statistics
Matches: 117, Mismatches: 40, Indels: 20
0.66 0.23 0.11
Matches are distributed among these distances:
9 30 0.26
10 15 0.13
11 67 0.57
12 5 0.04
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (11 bp):
ATATATATAAA
Done.