Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012438.1 Corchorus olitorius cultivar O-4 contig12471, 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: 17701
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:783 original size:58 final size:58
Alignment explanation
Indices: 687--796 Score: 168
Period size: 58 Copynumber: 1.9 Consensus size: 58
677 ATTAATCAAA
*
687 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCGGACCAAGACT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGACT
* * *
745 TATCGAGTGACATGTTTTTTTATTAGATGCCT-AAAAAAGACGTTTTAGGACC
1 TATCAAGTGACATG-TTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACC
797 GAGGCATGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
58 32 0.68
59 15 0.32
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGACT
Found at i:1837 original size:36 final size:36
Alignment explanation
Indices: 1790--1859 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
1780 TTCAATAACC
* *
1790 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
1826 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
1860 CTAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:2732 original size:205 final size:203
Alignment explanation
Indices: 2374--2786 Score: 706
Period size: 205 Copynumber: 2.0 Consensus size: 203
2364 GCTTAATAAC
2374 TTTATCAATGGTGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAA
1 TTTATCAATGGTGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAA
*
2439 ATACAACACATCATTATTATATATAAAACTATACCAAAAAAAAGTAAGTTAGAACATTAGTGGTT
66 ATACAACACATCACTATTATATATAAAACTATACCAAAAAAAAGTAAGTTAGAACATTAGTGGTT
2504 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGAT
131 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGA-
2569 TCC-AATTTA
194 TCCGAATTTA
* *
2578 TTTATCGATGGTGAATGTTATTAATTTTTTAAGTTTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAA-TTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* * *
2643 GATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAA-TTAGTT-GAACATTAGTG
65 AATACAACACATCACTATTATATATA-A-AACTATACCAAAAAAAAGTAAGTTAGAACATTAGTG
2706 GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAG
128 GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAG
2771 ATCCGAATTTA
193 ATCCGAATTTA
2782 TTTAT
1 TTTAT
2787 TATTAAGAAA
Statistics
Matches: 199, Mismatches: 6, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
203 3 0.02
204 38 0.19
205 135 0.68
206 6 0.03
207 17 0.09
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (203 bp):
TTTATCAATGGTGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAA
ATACAACACATCACTATTATATATAAAACTATACCAAAAAAAAGTAAGTTAGAACATTAGTGGTT
GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATC
CGAATTTA
Found at i:6919 original size:41 final size:40
Alignment explanation
Indices: 6866--6945 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 40
6856 TTTATAACTA
*
6866 GGGGCTAAACCTGGATTTAATTT-TTTACCTTAATTATTAG
1 GGGGCTAAACCTGAATTTAATTTATTT-CCTTAATTATTAG
6906 GGGGACTAAACCTGAATTTAATTTATTTCCTTAATTATTA
1 GGGG-CTAAACCTGAATTTAATTTATTTCCTTAATTATTA
6946 TGAGGGTCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
40 4 0.11
41 30 0.81
42 3 0.08
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.42
Consensus pattern (40 bp):
GGGGCTAAACCTGAATTTAATTTATTTCCTTAATTATTAG
Found at i:6973 original size:13 final size:13
Alignment explanation
Indices: 6947--6982 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
6937 TAATTATTAT
*
6947 GAGGGTCAAGTTG
1 GAGGGTCAAATTG
*
6960 GAGGGACAAATTG
1 GAGGGTCAAATTG
6973 GAGGGTCAAA
1 GAGGGTCAAA
6983 AAGAATTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.33, C:0.08, G:0.42, T:0.17
Consensus pattern (13 bp):
GAGGGTCAAATTG
Found at i:9796 original size:21 final size:22
Alignment explanation
Indices: 9751--9796 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
9741 CTTCTTCTAA
* *
9751 GTTATGGAGTTGTATTTATAGT
1 GTTAGGGAGTTGTATTTAGAGT
*
9773 GTTAGGGAGTTGTCTTT-GAGT
1 GTTAGGGAGTTGTATTTAGAGT
9794 GTT
1 GTT
9797 TGCAGTAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.17, C:0.02, G:0.33, T:0.48
Consensus pattern (22 bp):
GTTAGGGAGTTGTATTTAGAGT
Found at i:13624 original size:12 final size:12
Alignment explanation
Indices: 13607--13632 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
13597 TTTAAGTTAC
13607 ATGTTGTGTAAT
1 ATGTTGTGTAAT
13619 ATGTTGTGTAAT
1 ATGTTGTGTAAT
13631 AT
1 AT
13633 AATGTTTTTG
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:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (12 bp):
ATGTTGTGTAAT
Found at i:15019 original size:22 final size:22
Alignment explanation
Indices: 14986--15158 Score: 118
Period size: 22 Copynumber: 7.8 Consensus size: 22
14976 ATGACTTCCC
* *
14986 TATGAAAGTTTGATAACCACAT
1 TATGAAATTTTGATAACCACAA
* *
15008 TGTGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCACAA
* *
15030 TATGAAATTTTGATAATCTCAA
1 TATGAAATTTTGATAACCACAA
* * *
15052 TATGAAATTTTAATAATCACAC
1 TATGAAATTTTGATAACCACAA
* * * *
15074 TAT-AAA-ATTGGTAACCGCAC
1 TATGAAATTTTGATAACCACAA
* *
15094 TATGAAAATTTTGATAACCTC-C
1 TATG-AAATTTTGATAACCACAA
* *
15116 TCATAAAAATTTTGATAACCACAC
1 T-AT-GAAATTTTGATAACCACAA
* *
15140 CATGAAAATTTCGATAACC
1 TATG-AAATTTTGATAACC
15159 TCCCTATGAG
Statistics
Matches: 121, Mismatches: 23, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
20 12 0.10
21 3 0.02
22 64 0.53
23 41 0.34
24 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAA
Found at i:15033 original size:44 final size:44
Alignment explanation
Indices: 14931--15479 Score: 170
Period size: 44 Copynumber: 12.2 Consensus size: 44
14921 CTTAGAAGTA
* * *
14931 TTGATAACCACAC--TGAAAATTTGATAACCTCATTATGAAGTT
1 TTGATAACCACACTATGAAATTTTGATAACCACATTATGAAATT
** * ** * * *
14973 TCAATGACTTCCCTATGAAAGTTTGATAACCACATTGTGAAATT
1 TTGATAACCACACTATGAAATTTTGATAACCACATTATGAAATT
* * *
15017 TTGATAACCACACTATGAAATTTTGATAATCTCAATATGAAATT
1 TTGATAACCACACTATGAAATTTTGATAACCACATTATGAAATT
* * * * * *
15061 TTAATAATCACACTAT-AAA-ATTGGTAACCGCACTATGAAAATT
1 TTGATAACCACACTATGAAATTTTGATAACCACATTATG-AAATT
* * **
15104 TTGATAACCTC-CTCATAAAAATTTTGATAACCACACCATGAAAATT
1 TTGATAACCACACT-AT-GAAATTTTGATAACCACATTATG-AAATT
* * * * * ** *
15150 TCGATAACCTCCCTATGAGAATGAAACTGTGATATCTTC-TCTATGTAATT
1 TTGATAACCACACTATGA-AAT-----TTTGATAACCACAT-TATGAAATT
* * * **
15200 TTGATAACCTGATATCCATTAAATTTCCATAAGATCC-C-TTATGAAATT
1 TTGATAACC--ACA-CTATGAAATTTTGAT-A-A-CCACATTATGAAATT
* * * * * *
15248 TTGTTAACCTC-CTTAGGAAATTTTGGTAACCTCCCTCCCTATGAAATT
1 TTGATAACCACAC-TATGAAATTTTGATAACC-ACAT---TATGAAATT
* * * * * * *
15296 TTGTTAACCATAATATAAAATTTCGATAACCTTC-GTATGAAATT
1 TTGATAACCACACTATGAAATTTTGATAACC-ACATTATGAAATT
* * * ***
15340 TTGTTAACCTCCCTA-GAAATTTTGATAACCTTTTTATGAAATT
1 TTGATAACCACACTATGAAATTTTGATAACCACATTATGAAATT
* * ** * *
15383 TTGGTAACCTCTGTATGAAATTTTGATAACTACACTATG-AATT
1 TTGATAACCACACTATGAAATTTTGATAACCACATTATGAAATT
* * * * * *
15426 GTCGATAACCTC-CATATAAAATTTTGGTAACAACACTATGAAATT
1 -TTGATAACCACAC-TATGAAATTTTGATAACCACATTATGAAATT
15471 TTGATAACC
1 TTGATAACC
15480 TTCTATGTAA
Statistics
Matches: 376, Mismatches: 97, Indels: 66
0.70 0.18 0.12
Matches are distributed among these distances:
42 25 0.07
43 57 0.15
44 153 0.41
45 17 0.05
46 35 0.09
47 5 0.01
48 51 0.14
49 2 0.01
50 13 0.03
51 11 0.03
52 3 0.01
53 4 0.01
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (44 bp):
TTGATAACCACACTATGAAATTTTGATAACCACATTATGAAATT
Found at i:15056 original size:66 final size:65
Alignment explanation
Indices: 14986--15110 Score: 153
Period size: 66 Copynumber: 1.9 Consensus size: 65
14976 ATGACTTCCC
* * * *
14986 TATGAAAGTTTGATAACCACATTGTGAAATTTTGATAACCACACTATG-AAATTTTGATAATCTC
1 TATGAAAGTTTAATAACCACACTAT-AAA-ATTGATAACCACACTATGAAAATTTTGATAATCTC
15050 AA
64 AA
* * * *
15052 TATGAAATTTTAATAATCACACTATAAAATTGGTAACCGCACTATGAAAATTTTGATAA
1 TATGAAAGTTTAATAACCACACTATAAAATTGATAACCACACTATGAAAATTTTGATAA
15111 CCTCCTCATA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
64 15 0.30
65 15 0.30
66 20 0.40
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (65 bp):
TATGAAAGTTTAATAACCACACTATAAAATTGATAACCACACTATGAAAATTTTGATAATCTCAA
Found at i:15124 original size:23 final size:22
Alignment explanation
Indices: 15098--15162 Score: 85
Period size: 23 Copynumber: 2.9 Consensus size: 22
15088 CCGCACTATG
15098 AAAATTTTGATAACCTCCTCATA
1 AAAATTTTGATAACCTCC-CATA
* *
15121 AAAATTTTGATAACCACACCATG
1 AAAATTTTGATAACCTC-CCATA
*
15144 AAAATTTCGATAACCTCCC
1 AAAATTTTGATAACCTCCC
15163 TATGAGAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 2 0.05
23 34 0.92
24 1 0.03
ACGTcount: A:0.40, C:0.25, G:0.06, T:0.29
Consensus pattern (22 bp):
AAAATTTTGATAACCTCCCATA
Found at i:15267 original size:22 final size:22
Alignment explanation
Indices: 15236--15494 Score: 165
Period size: 22 Copynumber: 11.7 Consensus size: 22
15226 CCATAAGATC
*
15236 CCTTATGAAATTTTGTTAACCT
1 CCTTATGAAATTTTGATAACCT
* *
15258 CCTTAGGAAATTTTGGTAACCT
1 CCTTATGAAATTTTGATAACCT
*
15280 CCCTCCCTATGAAATTTTGTTAACCAT
1 -CCT---TATGAAATTTTGATAACC-T
** * *
15307 -AATATAAAATTTCGATAACCT
1 CCTTATGAAATTTTGATAACCT
* * *
15328 TCGTATGAAATTTTGTTAACCT
1 CCTTATGAAATTTTGATAACCT
*
15350 CCCTA-GAAATTTTGATAACCT
1 CCTTATGAAATTTTGATAACCT
** *
15371 TTTTATGAAATTTTGGTAACCT
1 CCTTATGAAATTTTGATAACCT
15393 -CTGTATGAAATTTTGATAA-CT
1 CCT-TATGAAATTTTGATAACCT
*
15414 ACAC-TATG-AATTGTCGATAACCT
1 -C-CTTATGAAATT-TTGATAACCT
* * * **
15437 CCATATAAAATTTTGGTAACAA
1 CCTTATGAAATTTTGATAACCT
15459 CAC-TATGAAATTTTGATAACCT
1 C-CTTATGAAATTTTGATAACCT
* *
15481 TC-TATGTAATTTTG
1 CCTTATGAAATTTTG
15495 GTTTGATTGT
Statistics
Matches: 186, Mismatches: 35, Indels: 33
0.73 0.14 0.13
Matches are distributed among these distances:
21 38 0.20
22 120 0.65
23 10 0.05
24 1 0.01
26 16 0.09
27 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.39
Consensus pattern (22 bp):
CCTTATGAAATTTTGATAACCT
Found at i:15391 original size:65 final size:66
Alignment explanation
Indices: 15238--15412 Score: 174
Period size: 65 Copynumber: 2.6 Consensus size: 66
15228 ATAAGATCCC
* * * * * *
15238 TTATGAAATTTTGTTAACCTCCTTAGGAAATTTTGGTAACCTCCCTCCCTATGAAATTTTGTTAA
1 TTATGAAATTTTGATAACCTTCGTATGAAATTTTGATAA----CCTCCCTATGAAATTTTGATAA
15303 CCATA
62 CCATA
* * * * *
15308 ATATAAAATTTCGATAACCTTCGTATGAAATTTTGTTAACCTCCCTA-GAAATTTTGATAACCTT
1 TTATGAAATTTTGATAACCTTCGTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCAT
*
15372 T
66 A
*
15373 TTATGAAATTTTGGTAACC-TCTGTATGAAATTTTGATAAC
1 TTATGAAATTTTGATAACCTTC-GTATGAAATTTTGATAAC
15413 TACACTATGA
Statistics
Matches: 88, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
64 2 0.02
65 47 0.53
66 8 0.09
70 31 0.35
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (66 bp):
TTATGAAATTTTGATAACCTTCGTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCAT
A
Found at i:15492 original size:109 final size:111
Alignment explanation
Indices: 15239--15496 Score: 281
Period size: 109 Copynumber: 2.3 Consensus size: 111
15229 TAAGATCCCT
* * * *
15239 TATGAAATTTTGTTAACCTCCTTAGGAAATTTTGGTAACCTCCCTCCCTATGAAATTTTGTTAAC
1 TATGAAATTTTGATAACCTTC-TATGAAATTTTGGTAACCT-CCT-CCTATGAAATTTTGATAAC
* * * * * ** *
15304 CATAATATAAAATTTCGATAACCTTCGTATGAAATTTTGTTAACCTCCC
63 CACAATATAAAATTTCGATAACCTCCATATAAAATTTTGGTAACAACAC
* * *
15353 TA-GAAATTTTGATAACCTTTTTATGAAATTTTGGTAACCT-CT-GTATGAAATTTTGATAACTA
1 TATGAAATTTTGATAACC-TTCTATGAAATTTTGGTAACCTCCTCCTATGAAATTTTGATAACCA
* *
15415 CACTAT-GAATTGTCGATAACCTCCATATAAAATTTTGGTAACAACAC
65 CAATATAAAATT-TCGATAACCTCCATATAAAATTTTGGTAACAACAC
*
15462 TATGAAATTTTGATAACCTTCTATGTAATTTTGGT
1 TATGAAATTTTGATAACCTTCTATGAAATTTTGGT
15497 TTGATTGTCA
Statistics
Matches: 122, Mismatches: 19, Indels: 11
0.80 0.12 0.07
Matches are distributed among these distances:
108 4 0.03
109 66 0.54
110 15 0.12
111 2 0.02
113 32 0.26
114 3 0.02
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.40
Consensus pattern (111 bp):
TATGAAATTTTGATAACCTTCTATGAAATTTTGGTAACCTCCTCCTATGAAATTTTGATAACCAC
AATATAAAATTTCGATAACCTCCATATAAAATTTTGGTAACAACAC
Done.