Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018849.1 Corchorus olitorius cultivar O-4 contig18882, 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: 20632
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--33 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA 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 T
34 TCATATTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:499 original size:11 final size:11
Alignment explanation
Indices: 483--511 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
473 CTGGTTTCGC
483 CGTGTCCATGT
1 CGTGTCCATGT
494 CGTGTCCATGT
1 CGTGTCCATGT
505 CGTGTCC
1 CGTGTCC
512 CTCCCGTGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.31, G:0.28, T:0.34
Consensus pattern (11 bp):
CGTGTCCATGT
Found at i:3677 original size:25 final size:26
Alignment explanation
Indices: 3625--3680 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
3615 AGTACGTTAA
** * *
3625 TGAATGATCAAATGTTTTTTTTTTTT
1 TGAATGATCAAATGTTTTGATATATT
3651 TGAA-GATCAAATGTTTTGATATATT
1 TGAATGATCAAATGTTTTGATATATT
3676 TGAAT
1 TGAAT
3681 TATCTCCCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.30, C:0.04, G:0.14, T:0.52
Consensus pattern (26 bp):
TGAATGATCAAATGTTTTGATATATT
Found at i:4373 original size:30 final size:31
Alignment explanation
Indices: 4321--4391 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 31
4311 GACGCGAAAT
*
4321 TCAATTCAGGATATACAATTATC-ACTTATG
1 TCAATTCAGGATATACAATTATCTACTTAAG
* **
4351 TCAATTCAGGATATA-ACGTTATCTGGTTAAG
1 TCAATTCAGGATATACA-ATTATCTACTTAAG
4382 TCAATTCAGG
1 TCAATTCAGG
4392 CAAATTATAG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.03
30 20 0.57
31 14 0.40
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Consensus pattern (31 bp):
TCAATTCAGGATATACAATTATCTACTTAAG
Found at i:6899 original size:21 final size:21
Alignment explanation
Indices: 6873--6914 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
6863 TCTATTTTAA
6873 TTAGTACCCTTTTTAGACATT
1 TTAGTACCCTTTTTAGACATT
6894 TTAGTACCCTTTTTAGACATT
1 TTAGTACCCTTTTTAGACATT
6915 AAATGACTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.10, T:0.48
Consensus pattern (21 bp):
TTAGTACCCTTTTTAGACATT
Found at i:6963 original size:86 final size:86
Alignment explanation
Indices: 6818--6982 Score: 312
Period size: 86 Copynumber: 1.9 Consensus size: 86
6808 CTTTTAGACA
*
6818 TTTTAGACATTAAATGGCTAAAATCTCTTAAATATTTTTTCTATTTCTATTTTAATTAGTACCCT
1 TTTTAGACATTAAATGACTAAAATCTCTTAAATATTTTTTCTATTTCTATTTTAATTAGTACCCT
6883 TTTTAGACATTTTAGTACCCT
66 TTTTAGACATTTTAGTACCCT
*
6904 TTTTAGACATTAAATGACTAAACTCTCTTAAATATTTTTTCTATTTCTATTTTAATTAGTACCCT
1 TTTTAGACATTAAATGACTAAAATCTCTTAAATATTTTTTCTATTTCTATTTTAATTAGTACCCT
6969 TTTTAGACATTTTA
66 TTTTAGACATTTTA
6983 TCTCTCAACC
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
86 77 1.00
ACGTcount: A:0.30, C:0.15, G:0.06, T:0.50
Consensus pattern (86 bp):
TTTTAGACATTAAATGACTAAAATCTCTTAAATATTTTTTCTATTTCTATTTTAATTAGTACCCT
TTTTAGACATTTTAGTACCCT
Found at i:8891 original size:6 final size:6
Alignment explanation
Indices: 8880--8916 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
8870 AATTACGATT
8880 GAGTGG GAGTGG GAGTGG GAGTGG GAGTGG GAGTGG G
1 GAGTGG GAGTGG GAGTGG GAGTGG GAGTGG GAGTGG G
8917 GAGGGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.16, C:0.00, G:0.68, T:0.16
Consensus pattern (6 bp):
GAGTGG
Found at i:14269 original size:72 final size:72
Alignment explanation
Indices: 14183--14326 Score: 263
Period size: 72 Copynumber: 2.0 Consensus size: 72
14173 CTTTGGTTTC
*
14183 GGCTTTGATTTGTTAGGAGATTTTGTAGAACTAGTTTTCTTTTCTGGCTTTTGT-ATGGCTTTTT
1 GGCTTTGATCTGTTAGGAGATTTTGTAGAACTAGTTTTCTTTTCTGGCTTTT-TAATGGCTTTTT
14247 TCCTGTCT
65 TCCTGTCT
14255 GGCTTTGATCTGTTAGGAGATTTTGTAGAACTAGTTTTCTTTTCTGGCTTTTTAATGGCTTTTTT
1 GGCTTTGATCTGTTAGGAGATTTTGTAGAACTAGTTTTCTTTTCTGGCTTTTTAATGGCTTTTTT
14320 CCTGTCT
66 CCTGTCT
14327 TTGACAACGA
Statistics
Matches: 70, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
71 1 0.01
72 69 0.99
ACGTcount: A:0.13, C:0.13, G:0.22, T:0.52
Consensus pattern (72 bp):
GGCTTTGATCTGTTAGGAGATTTTGTAGAACTAGTTTTCTTTTCTGGCTTTTTAATGGCTTTTTT
CCTGTCT
Found at i:14842 original size:123 final size:124
Alignment explanation
Indices: 14701--14938 Score: 390
Period size: 124 Copynumber: 1.9 Consensus size: 124
14691 TAAAAACTCT
* *
14701 ATTAAAATCTTAGATATATTAAAA-TTTTTAATATAGAATTTTATTCTACTAAAAACTCTATTTT
1 ATTAAAAACTTAGATATATTAAAATTTTTTAATATACAATTTTATTCTACTAAAAACTCTATTTT
**
14765 CATTTAATTAAATTCAATATTTTTATAAAT-ATTTTATTTTTACCATTTTACTATTTTTC
66 CATGGAATTAAATTCAATATTTTTAT-AATCATTTTATTTTTACCATTTTACTATTTTTC
* * *
14824 ATTAAAAACTTGGATATATTAAAATTTTTTAATATACAGTTTTATTCTACTAATAACTCTATTTT
1 ATTAAAAACTTAGATATATTAAAATTTTTTAATATACAATTTTATTCTACTAAAAACTCTATTTT
14889 CATGGAATTAAATTCAATATTTTTATAATCATTTTATTTTTACCATTTTA
66 CATGGAATTAAATTCAATATTTTTATAATCATTTTATTTTTACCATTTTA
14939 ATTTAAAAGA
Statistics
Matches: 106, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
123 25 0.24
124 81 0.76
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (124 bp):
ATTAAAAACTTAGATATATTAAAATTTTTTAATATACAATTTTATTCTACTAAAAACTCTATTTT
CATGGAATTAAATTCAATATTTTTATAATCATTTTATTTTTACCATTTTACTATTTTTC
Found at i:15178 original size:16 final size:18
Alignment explanation
Indices: 15157--15193 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
15147 GATTATGGTT
*
15157 CCGGT-CGA-CGGTTTAA
1 CCGGTCCGACCGGTTCAA
15173 CCGGTCCGACCGGTTCAA
1 CCGGTCCGACCGGTTCAA
15191 CCG
1 CCG
15194 CCGATCCGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 5 0.28
17 3 0.17
18 10 0.56
ACGTcount: A:0.16, C:0.35, G:0.30, T:0.19
Consensus pattern (18 bp):
CCGGTCCGACCGGTTCAA
Found at i:19631 original size:80 final size:79
Alignment explanation
Indices: 19538--19693 Score: 249
Period size: 80 Copynumber: 2.0 Consensus size: 79
19528 TCGTTATGCA
19538 AACTCCCCTCGTTTTCATTTCCCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTCAAAAGTCG
1 AACTCCCCTCGTTTTCATTTCCCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTCAAAAGTCG
19603 TCTAAGATCCGTGC
66 TCTAAGATCCGTGC
* * * * **
19617 AACTCCCCCTCGTTTTTATTTCTCTTCCTAAAATAGGTTTTCCAGCCGACTTATCTTCAAAAGTC
1 AACT-CCCCTCGTTTTCATTTCCCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTCAAAAGTC
19682 GTCTAAGATCCG
65 GTCTAAGATCCG
19694 AAACCACTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
79 4 0.06
80 66 0.94
ACGTcount: A:0.24, C:0.31, G:0.12, T:0.33
Consensus pattern (79 bp):
AACTCCCCTCGTTTTCATTTCCCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTCAAAAGTCG
TCTAAGATCCGTGC
Done.