Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015177.1 Corchorus olitorius cultivar O-4 contig15210, 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: 38369
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:108 original size:18 final size:18
Alignment explanation
Indices: 85--123 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
75 TGTATTCGTT
85 TACTAGTGCAATGAAATC
1 TACTAGTGCAATGAAATC
103 TACTAGTGCAATGAAATC
1 TACTAGTGCAATGAAATC
121 TAC
1 TAC
124 AAGAGTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (18 bp):
TACTAGTGCAATGAAATC
Found at i:606 original size:14 final size:14
Alignment explanation
Indices: 587--620 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
577 TTTTATAATT
587 ATTTTATTTTTACC
1 ATTTTATTTTTACC
*
601 ATTTTATTTTTACT
1 ATTTTATTTTTACC
615 ATTTTA
1 ATTTTA
621 ATTAAAAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTATTTTTACC
Found at i:667 original size:15 final size:15
Alignment explanation
Indices: 647--677 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
637 GATTAACATG
647 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
662 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
677 T
1 T
678 AATGTATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (15 bp):
TTTCTATTTGATAGT
Found at i:8471 original size:3 final size:3
Alignment explanation
Indices: 8465--8492 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
8455 ATTGATAATA
8465 AAC AAC AAC AAC AAC AAC AAC AAC AAC A
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC A
8493 CATTGCATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:9941 original size:21 final size:19
Alignment explanation
Indices: 9915--9969 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 19
9905 CAATGCCATC
9915 TTAATTAATGGGTAATTAA
1 TTAATTAATGGGTAATTAA
***
9934 TTAA--AATTATTAATTAA
1 TTAATTAATGGGTAATTAA
9951 TTAATTAATGGGATAATTA
1 TTAATTAATGGG-TAATTA
9970 CAACTTCAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
17 14 0.52
19 7 0.26
20 6 0.22
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.44
Consensus pattern (19 bp):
TTAATTAATGGGTAATTAA
Found at i:10611 original size:21 final size:20
Alignment explanation
Indices: 10562--10613 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
10552 TTAGTGATCT
*
10562 AGTAAAAAATAAAAAAAAATT
1 AGTAAAAAA-AAAAAAAAATA
*
10583 AG-AGAAAAAAAAAATAAATCA
1 AGTA-AAAAAAAAAAAAAAT-A
10604 AGTAAAAAAA
1 AGTAAAAAAA
10614 GTAATTGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 10 0.38
21 15 0.58
22 1 0.04
ACGTcount: A:0.77, C:0.02, G:0.08, T:0.13
Consensus pattern (20 bp):
AGTAAAAAAAAAAAAAAATA
Found at i:21656 original size:14 final size:14
Alignment explanation
Indices: 21637--21667 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
21627 AGGTTATGTG
*
21637 CCAGATCAAAGGTT
1 CCAGATCAAAGATT
21651 CCAGATCAAAGATT
1 CCAGATCAAAGATT
21665 CCA
1 CCA
21668 AGATGTAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.26, G:0.16, T:0.19
Consensus pattern (14 bp):
CCAGATCAAAGATT
Found at i:24900 original size:25 final size:24
Alignment explanation
Indices: 24845--24901 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
24835 GTCAGCCTTG
*
24845 AATTT-TTTAATGTTTAATTCTTA
1 AATTTATTTAATGTTTAATTATTA
* *
24868 AATTTATTTAATGTCTTTATTATTC
1 AATTTATTTAATGT-TTAATTATTA
24893 AATTTATTT
1 AATTTATTT
24902 TACAATCCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.28
25 16 0.55
ACGTcount: A:0.30, C:0.05, G:0.04, T:0.61
Consensus pattern (24 bp):
AATTTATTTAATGTTTAATTATTA
Found at i:25182 original size:17 final size:17
Alignment explanation
Indices: 25156--25189 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
25146 TAATCTTATT
*
25156 TAATATTTATTCATATA
1 TAATAATTATTCATATA
25173 TAATAATTATTCATATA
1 TAATAATTATTCATATA
25190 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:26376 original size:24 final size:23
Alignment explanation
Indices: 26296--26377 Score: 56
Period size: 24 Copynumber: 3.3 Consensus size: 23
26286 GATTGAAGGC
** *
26296 ATTATTTTAATCAAATTATTATATT
1 ATTATTTTAATTGAACT-TTATA-T
* * *
26321 ATATATTATAATTGAACTTTTTTT
1 AT-TATTTTAATTGAACTTTATAT
*
26345 AATCATTTTAATTGAACATTTATAT
1 -ATTATTTTAATTGAAC-TTTATAT
26370 ATTATTTT
1 ATTATTTT
26378 GAGACTTATG
Statistics
Matches: 43, Mismatches: 11, Indels: 7
0.70 0.18 0.11
Matches are distributed among these distances:
24 20 0.47
25 12 0.28
26 11 0.26
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (23 bp):
ATTATTTTAATTGAACTTTATAT
Found at i:30586 original size:14 final size:14
Alignment explanation
Indices: 30567--30624 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
30557 TCAAAAATTA
30567 TTAAAAACATATTT
1 TTAAAAACATATTT
*
30581 TTAAAAAACA-ATAT
1 TT-AAAAACATATTT
**
30595 CAAAAAACATATTT
1 TTAAAAACATATTT
30609 TTAAAAA-ATTATTT
1 TTAAAAACA-TATTT
30623 TT
1 TT
30625 TAATTAAAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
13 8 0.23
14 20 0.57
15 7 0.20
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (14 bp):
TTAAAAACATATTT
Found at i:31409 original size:51 final size:52
Alignment explanation
Indices: 31307--31413 Score: 171
Period size: 51 Copynumber: 2.0 Consensus size: 52
31297 GGGCAAAATG
31307 CAATTTTACCAATTTTTTGAACATAGATAGAAATGTATAGCATAATAATTGAACC
1 CAATTTTACCAATTTTTTGAAC--A-ATAGAAATGTATAGCATAATAATTGAACC
*
31362 CAATTTTACCAATTTTTTGGAC-ATAGAAATGTATAGCATAATAATTGAACC
1 CAATTTTACCAATTTTTTGAACAATAGAAATGTATAGCATAATAATTGAACC
31413 C
1 C
31414 CCCCCCCCCA
Statistics
Matches: 51, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
51 30 0.59
55 21 0.41
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (52 bp):
CAATTTTACCAATTTTTTGAACAATAGAAATGTATAGCATAATAATTGAACC
Found at i:34118 original size:13 final size:13
Alignment explanation
Indices: 34100--34134 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
34090 GTGCCGTCAA
34100 ATCTGTCCATGTC
1 ATCTGTCCATGTC
34113 ATCTGTCCATGTC
1 ATCTGTCCATGTC
34126 ATCTGTCCA
1 ATCTGTCCA
34135 CGTGGCTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.17, C:0.31, G:0.14, T:0.37
Consensus pattern (13 bp):
ATCTGTCCATGTC
Found at i:34202 original size:41 final size:42
Alignment explanation
Indices: 34123--34202 Score: 119
Period size: 41 Copynumber: 1.9 Consensus size: 42
34113 ATCTGTCCAT
*
34123 GTCATCTGTCCACGTGGCTCAAAAAGCCACGTGGCCAAACCAC
1 GTCATCTGTCCACGTGGC-CAAAAAGCCACGTGACCAAACCAC
34166 GTCATCT-TCCCACGTGG-CAAAAAGCCACGTGACCAAA
1 GTCATCTGT-CCACGTGGCCAAAAAGCCACGTGACCAAA
34203 ATATTGTGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
41 19 0.54
42 1 0.03
43 15 0.43
ACGTcount: A:0.30, C:0.34, G:0.20, T:0.16
Consensus pattern (42 bp):
GTCATCTGTCCACGTGGCCAAAAAGCCACGTGACCAAACCAC
Found at i:37152 original size:12 final size:12
Alignment explanation
Indices: 37135--37164 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
37125 TGTGCGTGGG
37135 TTTCATGTGCAT
1 TTTCATGTGCAT
*
37147 TTTCATGTGCCT
1 TTTCATGTGCAT
37159 TTTCAT
1 TTTCAT
37165 TGTAGGGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.20, G:0.13, T:0.53
Consensus pattern (12 bp):
TTTCATGTGCAT
Done.