Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016575.1 Corchorus olitorius cultivar O-4 contig16608, 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: 75785
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:159 original size:25 final size:24
Alignment explanation
Indices: 109--160 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
99 TTGAAGTTTT
*
109 TTTAATGTTTAATTCTTAAATTTA
1 TTTAATGTTTAATTATTAAATTTA
* *
133 TTTAATGTCTTTATTATTCAATTTA
1 TTTAATGT-TTAATTATTAAATTTA
158 TTT
1 TTT
161 TACAATCCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.62
Consensus pattern (24 bp):
TTTAATGTTTAATTATTAAATTTA
Found at i:441 original size:17 final size:17
Alignment explanation
Indices: 415--448 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
405 TAATCTTATT
*
415 TAATATTTATTCATATA
1 TAATAATTATTCATATA
432 TAATAATTATTCATATA
1 TAATAATTATTCATATA
449 ATGAAGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATAATTATTCATATA
Found at i:4991 original size:25 final size:24
Alignment explanation
Indices: 4951--4998 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
4941 GTAATGAACA
*
4951 AGAGAAAAAGCGCGGAG-CTTTTG
1 AGAGAAAAAGCACGGAGCCTTTTG
4974 AGAGAAAATAAGCACGGAGCCTTTT
1 AGAG-AAA-AAGCACGGAGCCTTTT
4999 TTTTTCTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 3 0.14
25 9 0.43
26 5 0.24
ACGTcount: A:0.38, C:0.15, G:0.29, T:0.19
Consensus pattern (24 bp):
AGAGAAAAAGCACGGAGCCTTTTG
Found at i:9687 original size:78 final size:78
Alignment explanation
Indices: 9605--9759 Score: 265
Period size: 78 Copynumber: 2.0 Consensus size: 78
9595 TTTATAGTTT
* *
9605 TACTCAACTAAAAATTCTATATTTATTTAATTAAATCTAATATCTTTATAACTATTTTATTTTAC
1 TACTCAACTAAAAATTCTATATTTATTTAATTAAATCTAATATCCTTATAACTATTTTAGTTTAC
*
9670 CATTTTACTATTC
66 CATTTGACTATTC
* *
9683 TACTCAACTAAAAATTCTATTTTTATTTAGTTAAATCTAATATCCTTATAACTATTTTAGTTTAC
1 TACTCAACTAAAAATTCTATATTTATTTAATTAAATCTAATATCCTTATAACTATTTTAGTTTAC
9748 CATTTGACTATT
66 CATTTGACTATT
9760 TAAATTTTAA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 72 1.00
ACGTcount: A:0.35, C:0.14, G:0.02, T:0.49
Consensus pattern (78 bp):
TACTCAACTAAAAATTCTATATTTATTTAATTAAATCTAATATCCTTATAACTATTTTAGTTTAC
CATTTGACTATTC
Found at i:10685 original size:17 final size:17
Alignment explanation
Indices: 10663--10695 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
10653 TCATTACATG
10663 AATTAA-AATTATAAATT
1 AATTAATAA-TATAAATT
10680 AATTAATAATATAAAT
1 AATTAATAATATAAAT
10696 ATCCATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATTAATAATATAAATT
Found at i:12542 original size:15 final size:15
Alignment explanation
Indices: 12491--12555 Score: 62
Period size: 15 Copynumber: 4.3 Consensus size: 15
12481 TTTTAGTTTG
*
12491 AAAATAATTTTTCAAA
1 AAAAT-ATTTTTTAAA
*
12507 ACAA-A-TTTTTAAA
1 AAAATATTTTTTAAA
*
12520 AAATTATTTTTTAAA
1 AAAATATTTTTTAAA
12535 AAAATATTCTTTTAATA
1 AAAATATT-TTTTAA-A
12552 AAAA
1 AAAA
12556 AGTGACGTGG
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
13 9 0.22
14 2 0.05
15 15 0.38
16 9 0.22
17 5 0.12
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.42
Consensus pattern (15 bp):
AAAATATTTTTTAAA
Found at i:18234 original size:29 final size:31
Alignment explanation
Indices: 18177--18247 Score: 96
Period size: 29 Copynumber: 2.4 Consensus size: 31
18167 TACCGTACAT
18177 GTCCCTCTACTTACAAAAAGGGATCAATTTG
1 GTCCCTCTACTTACAAAAAGGGATCAATTTG
**
18208 GTCCCTCTAC-TACAAAAATTG-TCAATTTG
1 GTCCCTCTACTTACAAAAAGGGATCAATTTG
18237 GT--CTCTACTTA
1 GTCCCTCTACTTA
18248 TAATTTGGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
27 6 0.16
28 2 0.05
29 10 0.27
30 9 0.24
31 10 0.27
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.34
Consensus pattern (31 bp):
GTCCCTCTACTTACAAAAAGGGATCAATTTG
Found at i:18897 original size:22 final size:22
Alignment explanation
Indices: 18872--19165 Score: 119
Period size: 22 Copynumber: 13.5 Consensus size: 22
18862 TCTTCAAAAC
*
18872 AAATTTCATAGGGAGGTTCTCA
1 AAATTTCATAGGGAGGTTATCA
**
18894 AAATTTC-TTTGGATGGTTATCA
1 AAATTTCATAGGGA-GGTTATCA
* *
18916 AAATCTCATGGGGAGGTTATCA
1 AAATTTCATAGGGAGGTTATCA
* *
18938 AAATTTCATAGTGAGGTTTTCA
1 AAATTTCATAGGGAGGTTATCA
* * ** *
18960 AAATTACATA-AGAAATTAACA
1 AAATTTCATAGGGAGGTTATCA
* *** ** *
18981 AATTTTCATATAAAGGTTCGCG
1 AAATTTCATAGGGAGGTTATCA
** * * *
19003 AAA-TTCTATAGACAGATTCTCG
1 AAATTTC-ATAGGGAGGTTATCA
* * **
19025 AAATTTGATAGTGTCGTTATCA
1 AAATTTCATAGGGAGGTTATCA
*** *
19047 AAATTTCATAAAAATGTTAT-A
1 AAATTTCATAGGGAGGTTATCA
* *
19068 AAATTTAATATGGAGGTTATCA
1 AAATTTCATAGGGAGGTTATCA
* * *
19090 AAATTTCATAGTGTGATTATCA
1 AAATTTCATAGGGAGGTTATCA
* *** * *
19112 TAATTTCATACAAATGTCATCA
1 AAATTTCATAGGGAGGTTATCA
* * * *
19134 CAATTTCATAGTGTGATTATCA
1 AAATTTCATAGGGAGGTTATCA
19156 AAATTTCATA
1 AAATTTCATA
19166 TGAATATTTG
Statistics
Matches: 196, Mismatches: 70, Indels: 12
0.71 0.25 0.04
Matches are distributed among these distances:
21 37 0.19
22 153 0.78
23 6 0.03
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (22 bp):
AAATTTCATAGGGAGGTTATCA
Found at i:19072 original size:65 final size:65
Alignment explanation
Indices: 19015--19165 Score: 162
Period size: 65 Copynumber: 2.3 Consensus size: 65
19005 ATTCTATAGA
* * *
19015 CAGATTCTCGAAATTTGATAGTGTCG-TTATCAAAATTTCATAAAAATGTTATAAAATTTAATAT
1 CAGATTATCAAAATTTCATAGTGT-GATTATCAAAATTTCATAAAAATGTTATAAAATTTAATAT
19079 G
65 G
* * * * * * *
19080 GAGGTTATCAAAATTTCATAGTGTGATTATCATAATTTCATACAAATGTCATCACAATTTCATAG
1 CAGATTATCAAAATTTCATAGTGTGATTATCAAAATTTCATAAAAATGTTAT-AAAATTTAATA-
19145 TG
64 TG
*
19147 -TGATTATCAAAATTTCATA
1 CAGATTATCAAAATTTCATA
19166 TGAATATTTG
Statistics
Matches: 71, Mismatches: 12, Indels: 5
0.81 0.14 0.06
Matches are distributed among these distances:
64 1 0.01
65 42 0.59
66 26 0.37
67 2 0.03
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.38
Consensus pattern (65 bp):
CAGATTATCAAAATTTCATAGTGTGATTATCAAAATTTCATAAAAATGTTATAAAATTTAATATG
Found at i:24335 original size:21 final size:22
Alignment explanation
Indices: 24306--24353 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
24296 CCCAATACAA
* *
24306 ATATATATACATAATTAT-TAT
1 ATATATATAAAAAATTATCTAT
*
24327 ATATTTATAAAAAATTATCTAT
1 ATATATATAAAAAATTATCTAT
24349 ATATA
1 ATATA
24354 CCTGTCGAGC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (22 bp):
ATATATATAAAAAATTATCTAT
Found at i:27751 original size:2 final size:2
Alignment explanation
Indices: 27705--27734 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
27695 ACAAATTTAT
*
27705 TA TA AA 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
27735 ATTAGCTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:60620 original size:42 final size:42
Alignment explanation
Indices: 60561--60643 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
60551 GCTAAGTCTT
* *
60561 GAAAATTTTCTGTAAATTCAGAAATACTCAACTCAATTCATA
1 GAAAATTTTCTGTAAATTAAGAAATACTCAACTCAAATCATA
60603 GAAAATTCTT-TGTAAATTAAGAAATACTCAACTCAAATCAT
1 GAAAATT-TTCTGTAAATTAAGAAATACTCAACTCAAATCAT
60644 GATCCTTAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 36 0.95
43 2 0.05
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.33
Consensus pattern (42 bp):
GAAAATTTTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:71562 original size:2 final size:2
Alignment explanation
Indices: 71549--71611 Score: 72
Period size: 2 Copynumber: 29.5 Consensus size: 2
71539 TTCTGTAAAA
*
71549 AT AT AT AC AT AT AT AT AT GAT AT CAT AT AT AT AT AT AT AT AT GAT
1 AT AT AT AT AT AT AT AT AT -AT AT -AT AT AT AT AT AT AT AT AT -AT
*
71594 AT CAT AT AT AT AT GT AT A
1 AT -AT AT AT AT AT AT AT A
71612 ATAATAATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 45 0.85
3 8 0.15
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (2 bp):
AT
Found at i:71584 original size:24 final size:24
Alignment explanation
Indices: 71549--71611 Score: 108
Period size: 24 Copynumber: 2.6 Consensus size: 24
71539 TTCTGTAAAA
*
71549 ATATATACATATATATATGATATC
1 ATATATATATATATATATGATATC
71573 ATATATATATATATATATGATATC
1 ATATATATATATATATATGATATC
*
71597 ATATATATATGTATA
1 ATATATATATATATA
71612 ATAATAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (24 bp):
ATATATATATATATATATGATATC
Done.