Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018255.1 Corchorus olitorius cultivar O-4 contig18288, 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: 30655
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:2219 original size:17 final size:17
Alignment explanation
Indices: 2194--2299 Score: 51
Period size: 20 Copynumber: 6.1 Consensus size: 17
2184 ATTTCTACCT
* *
2194 TTCTTCATATTTTATTC
1 TTCTCCATATTCTATTC
2211 TTCTCCATATTCTATTGTC
1 TTCTCCATATTCTA-T-TC
*
2230 TCTCTCCATACTTC-A--A
1 T-TCTCCATA-TTCTATTC
* *
2246 TTCT-C-TACTCCATTC
1 TTCTCCATATTCTATTC
2261 TTCTCCATATTCTATTGTC
1 TTCTCCATATTCTA-T-TC
*
2280 TCTCTCCATACTTCAATTC
1 T-TCTCCATA-TTCTATTC
2299 T
1 T
2300 CTACTCCCTT
Statistics
Matches: 68, Mismatches: 8, Indels: 24
0.68 0.08 0.24
Matches are distributed among these distances:
12 2 0.03
13 3 0.04
14 1 0.01
15 7 0.10
16 2 0.03
17 17 0.25
18 2 0.03
19 9 0.13
20 18 0.26
21 7 0.10
ACGTcount: A:0.18, C:0.30, G:0.02, T:0.50
Consensus pattern (17 bp):
TTCTCCATATTCTATTC
Found at i:2282 original size:50 final size:50
Alignment explanation
Indices: 2207--2306 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
2197 TTCATATTTT
2207 ATTCTTCTCCATATTCTATTGTCTCTCTCCATACTTCAATTCTCTACTCC
1 ATTCTTCTCCATATTCTATTGTCTCTCTCCATACTTCAATTCTCTACTCC
2257 ATTCTTCTCCATATTCTATTGTCTCTCTCCATACTTCAATTCTCTACTCC
1 ATTCTTCTCCATATTCTATTGTCTCTCTCCATACTTCAATTCTCTACTCC
2307 CTTGCTTTTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.18, C:0.34, G:0.02, T:0.46
Consensus pattern (50 bp):
ATTCTTCTCCATATTCTATTGTCTCTCTCCATACTTCAATTCTCTACTCC
Found at i:2843 original size:64 final size:64
Alignment explanation
Indices: 2742--2870 Score: 204
Period size: 64 Copynumber: 2.0 Consensus size: 64
2732 CGGCTCTATC
*
2742 ACGGCATCCAACGTGACATGCCATGCGTAAAATAAAATGACAAGTGACACACCACATGTAAAAA
1 ACGGCATCCAACGTAACATGCCATGCGTAAAATAAAATGACAAGTGACACACCACATGTAAAAA
* * * * *
2806 ACGGCGTCCAACGTAATATGTCATGCGTAAAATAAAATGATAAGTGGCACACCACATGTAAAAA
1 ACGGCATCCAACGTAACATGCCATGCGTAAAATAAAATGACAAGTGACACACCACATGTAAAAA
2870 A
1 A
2871 GGACACATGG
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.43, C:0.21, G:0.18, T:0.18
Consensus pattern (64 bp):
ACGGCATCCAACGTAACATGCCATGCGTAAAATAAAATGACAAGTGACACACCACATGTAAAAA
Found at i:2905 original size:45 final size:45
Alignment explanation
Indices: 2841--2931 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
2831 CGTAAAATAA
*
2841 AATGATAAGTGGCACACCACATGTAAAAAAGGACACATGGCATGC
1 AATGACAAGTGGCACACCACATGTAAAAAAGGACACATGGCATGC
* *
2886 AATGACAAGTGGCACACCACATGTAAAAAAGGACACGTGTCATGC
1 AATGACAAGTGGCACACCACATGTAAAAAAGGACACATGGCATGC
2931 A
1 A
2932 TGCCACGTCG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.42, C:0.21, G:0.22, T:0.15
Consensus pattern (45 bp):
AATGACAAGTGGCACACCACATGTAAAAAAGGACACATGGCATGC
Found at i:3374 original size:12 final size:12
Alignment explanation
Indices: 3357--3395 Score: 78
Period size: 12 Copynumber: 3.2 Consensus size: 12
3347 AACAACCAAA
3357 CATCACCAATAT
1 CATCACCAATAT
3369 CATCACCAATAT
1 CATCACCAATAT
3381 CATCACCAATAT
1 CATCACCAATAT
3393 CAT
1 CAT
3396 ATGTGCTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.41, C:0.33, G:0.00, T:0.26
Consensus pattern (12 bp):
CATCACCAATAT
Found at i:4435 original size:56 final size:53
Alignment explanation
Indices: 4321--4481 Score: 272
Period size: 56 Copynumber: 3.0 Consensus size: 53
4311 CTATCTTAAG
*
4321 AAAATAAAGCAAATCCAATGGGGATAGAATTATTATACCTTTAAAATTGAGAT
1 AAAATAAAGCAAATCCAATGGGGATAGAATTATTATACCTTTAAGATTGAGAT
4374 AAAATAAAGCAAATCCAATGGGGATAGAATTATTATTATACCTTTAAGATTGAGAT
1 AAAATAAAGCAAATCCAATGGGGATAG-A--ATTATTATACCTTTAAGATTGAGAT
4430 AAAATAAAGCAAATCCAATGGGGATAGAA-T-TTATACCTTTAAGATTGAGAT
1 AAAATAAAGCAAATCCAATGGGGATAGAATTATTATACCTTTAAGATTGAGAT
4481 A
1 A
4482 CTGTCGAACC
Statistics
Matches: 104, Mismatches: 1, Indels: 8
0.92 0.01 0.07
Matches are distributed among these distances:
51 22 0.21
52 1 0.01
53 28 0.27
54 1 0.01
55 1 0.01
56 51 0.49
ACGTcount: A:0.46, C:0.09, G:0.16, T:0.29
Consensus pattern (53 bp):
AAAATAAAGCAAATCCAATGGGGATAGAATTATTATACCTTTAAGATTGAGAT
Found at i:8822 original size:93 final size:93
Alignment explanation
Indices: 8719--8897 Score: 295
Period size: 93 Copynumber: 1.9 Consensus size: 93
8709 ATTTTTTAAT
* * *
8719 TAAATTAGTAATATCGTAAAAATAAAATAGTTATAAGGATATTAGATTTAACTAAATAAAAATAT
1 TAAAATAGTAAAATCGTAAAAATAAAATAGTTATAAGGATATTAGATTTAACTAAATAAAAATAG
*
8784 AGTTTTTAGTTGAGTAAAACTATAAGAG
66 AGTTTTTAGTTGACTAAAACTATAAGAG
* * *
8812 TAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAGGATATTAGATTTAATTAATTAAAAATAG
1 TAAAATAGTAAAATCGTAAAAATAAAATAGTTATAAGGATATTAGATTTAACTAAATAAAAATAG
8877 AGTTTTTAGTTGACTAAAACT
66 AGTTTTTAGTTGACTAAAACT
8898 GTAAAAATTT
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 79 1.00
ACGTcount: A:0.50, C:0.03, G:0.13, T:0.35
Consensus pattern (93 bp):
TAAAATAGTAAAATCGTAAAAATAAAATAGTTATAAGGATATTAGATTTAACTAAATAAAAATAG
AGTTTTTAGTTGACTAAAACTATAAGAG
Found at i:8983 original size:31 final size:32
Alignment explanation
Indices: 8939--9002 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 32
8929 ATATTCAAAA
*
8939 AATAAGGGCATAATAGGCGATTCAAAAG-TTT
1 AATAAGGACATAATAGGCGATTCAAAAGCTTT
* *
8970 AATAAGGATATAATATGCGATTCAAAAGCTTT
1 AATAAGGACATAATAGGCGATTCAAAAGCTTT
9002 A
1 A
9003 CAAAACTCGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 25 0.86
32 4 0.14
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (32 bp):
AATAAGGACATAATAGGCGATTCAAAAGCTTT
Found at i:9571 original size:17 final size:18
Alignment explanation
Indices: 9549--9586 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
9539 TTTTTCTAAT
*
9549 AATTATTTTAA-GAATTA
1 AATTATATTAATGAATTA
*
9566 AATTATATTAATTAATTA
1 AATTATATTAATGAATTA
9584 AAT
1 AAT
9587 AAATATAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
AATTATATTAATGAATTA
Found at i:11892 original size:40 final size:40
Alignment explanation
Indices: 11848--11927 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
11838 TTTCACATAA
* *
11848 ATGTTATAATAAATCATATCCCCCTTAATTATTTAGAATT
1 ATGTTATAATAAATCATATCCCACTTAATTATCTAGAATT
*
11888 ATGTTATAATAAATCTTATCCCACTTAATTATCTAGAATT
1 ATGTTATAATAAATCATATCCCACTTAATTATCTAGAATT
11928 GTGACCTCTC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (40 bp):
ATGTTATAATAAATCATATCCCACTTAATTATCTAGAATT
Found at i:19689 original size:12 final size:12
Alignment explanation
Indices: 19672--19696 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19662 CAATCTGATT
19672 GTATGATAGTGA
1 GTATGATAGTGA
19684 GTATGATAGTGA
1 GTATGATAGTGA
19696 G
1 G
19697 GAACATATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (12 bp):
GTATGATAGTGA
Found at i:23997 original size:26 final size:26
Alignment explanation
Indices: 23968--24017 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
23958 AAGAAGATTC
23968 GAAGTTTCAAATCAATATATAACACT
1 GAAGTTTCAAATCAATATATAACACT
*
23994 GAAGTTTCGAATCAATATATAACA
1 GAAGTTTCAAATCAATATATAACA
24018 GCAGGTGGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.30
Consensus pattern (26 bp):
GAAGTTTCAAATCAATATATAACACT
Found at i:29906 original size:19 final size:19
Alignment explanation
Indices: 29882--29921 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
29872 TTAGGGATCC
29882 AGTAGATAATTATTTGAAT
1 AGTAGATAATTATTTGAAT
29901 AGTAGATAATTATTTGAAT
1 AGTAGATAATTATTTGAAT
29920 AG
1 AG
29922 ACATTAGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.40
Consensus pattern (19 bp):
AGTAGATAATTATTTGAAT
Done.