Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016697.1 Corchorus olitorius cultivar O-4 contig16730, 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: 28783
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:8650 original size:19 final size:18
Alignment explanation
Indices: 8617--8652 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
8607 TTGAATTAAT
8617 TCTTCAATAGCCTTCAAG
1 TCTTCAATAGCCTTCAAG
*
8635 TCTTCAAATAGTCTTCAA
1 TCTTC-AATAGCCTTCAA
8653 ACACGAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (18 bp):
TCTTCAATAGCCTTCAAG
Found at i:14248 original size:29 final size:29
Alignment explanation
Indices: 14212--14269 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
14202 TTCAATTTTA
14212 ATTCTGCTATTTAATTACTTATGTTTTGG
1 ATTCTGCTATTTAATTACTTATGTTTTGG
* *
14241 ATTCTGCTATTTATTTAGTTATGTTTTGG
1 ATTCTGCTATTTAATTACTTATGTTTTGG
14270 GCCTTACTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.19, C:0.09, G:0.16, T:0.57
Consensus pattern (29 bp):
ATTCTGCTATTTAATTACTTATGTTTTGG
Found at i:16521 original size:29 final size:29
Alignment explanation
Indices: 16466--16528 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
16456 TGATAAATCT
**
16466 TTATA-TATATATTGATAATAATGTTATA
1 TTATATTATATATTGATAATAAACTTATA
16494 TTATATTATATATT-ATCAATAAACTTATA
1 TTATATTATATATTGAT-AATAAACTTATA
*
16523 TAATAT
1 TTATAT
16529 AAAAGATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 7 0.23
29 23 0.77
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (29 bp):
TTATATTATATATTGATAATAAACTTATA
Found at i:16734 original size:16 final size:16
Alignment explanation
Indices: 16715--16759 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 16
16705 AACTTGACTT
*
16715 AACCCGAGCCCGAAAA
1 AACCCGAACCCGAAAA
16731 AACCCGAACCCG-AAA
1 AACCCGAACCCGAAAA
*
16746 TACCCGAACCCGAA
1 AACCCGAACCCGAA
16760 CCCACCCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.42, C:0.40, G:0.16, T:0.02
Consensus pattern (16 bp):
AACCCGAACCCGAAAA
Found at i:18020 original size:274 final size:273
Alignment explanation
Indices: 17484--18247 Score: 1218
Period size: 274 Copynumber: 2.8 Consensus size: 273
17474 AAATTTACCA
* *
17484 AAGGCCCCTTTTGAGGATCGATAAGAAGGCTCCATTTGAACTTTCTTTGTCCTTTTCTGTCTTTT
1 AAGGCCCCTTTTGAGGATCGATGAGGAGGCTCCATTTGAACTTTCTTTGTCCTTTTCTGTCTTTT
* * * *
17549 CTCACTTGCCAAATTACTAAGAAGCCCCTAGATTAGTTTCTAGCCAGTTCTTGCCCTTGAGCCAT
66 CTCACTTGCCAAATTACTAAGAAGACCCTAGGTTAGTTTCTAGCTAGTTCTTGCCCTTGAGCCCT
*
17614 TTTTTTGTAATTATCCTTTCC-TTTCACATAAATGTTATAATAAATCATATCCCCCTTAATTATC
131 TTTTTTGTAATTATCCTTTCCTTTTCACATAAATGTTATAATAAATCCTATCCCCCTTAATTATC
*
17678 TAGAACTGTAACCTCTCTTCAGGCCTTTCATGTCCATATGAAGAAGAGACTAAACTTAGTTTTGT
196 TAGAATTGTAACCTCTCTTCAGGCCTTTCATGTCCATAT--AGAAGAGACTAAACTTAGTTTTGT
*
17743 TTAAGTGCTACACAT
259 TTAAGTGCTACACAC
*
17758 AAGGCCCCTTTTGAGGATCGATGAGGAGGCTCCATTTGAACTTTCTTTGTCCTTTTCTATCTTTT
1 AAGGCCCCTTTTGAGGATCGATGAGGAGGCTCCATTTGAACTTTCTTTGTCCTTTTCTGTCTTTT
* *
17823 CTCACTTGCCAAATTACTAAGAAGACCCTAGGTTAGTTTCCAGGTAGTTCTTGCCCTTGAGCCCT
66 CTCACTTGCCAAATTACTAAGAAGACCCTAGGTTAGTTTCTAGCTAGTTCTTGCCCTTGAGCCCT
**
17888 TTTTTTAAAAAAATTATCCTTTCCTTTTCACATAAATGTTATAATAAATCCTATCCCCCTTAATT
131 TTTTTT---GTAATTATCCTTTCCTTTTCACATAAATGTTATAATAAATCCTATCCCCCTTAATT
**
17953 ATCTAGAATTGTAACCTCTCTTCAGGGTTTTCATGTCCATAT-GAAGA-A-TAAACTTAGTTTCT
193 ATCTAGAATTGTAACCTCTCTTCAGGCCTTTCATGTCCATATAGAAGAGACTAAACTTAGTTT-T
*
18015 GTTTAATTGCTACACAC
257 GTTTAAGTGCTACACAC
* *
18032 AAGACCCCTTTTGAGGATCGATGAGGAGGCTCCATTTGAACTTTCTTTGTGCTTTTCTGTCTTTT
1 AAGGCCCCTTTTGAGGATCGATGAGGAGGCTCCATTTGAACTTTCTTTGTCCTTTTCTGTCTTTT
* *
18097 TTCACTTGCCAAATTACTAAGAAGACCCTAGGTTAGTTTCTAGCCT-GTTCTTGCCCTTGAG-CT
66 CTCACTTGCCAAATTACTAAGAAGACCCTAGGTTAGTTTCTAG-CTAGTTCTTGCCCTTGAGCCC
*
18160 TTTTTTTGTAATTATCTTTTCCTTTT-ACATAAATGTTATAATAAATCCTATCCCCCTTAATTAT
130 TTTTTTTGTAATTATCCTTTCCTTTTCACATAAATGTTATAATAAATCCTATCCCCCTTAATTAT
18224 CTAGAATTGTAACCTCTCTTCAGG
195 CTAGAATTGTAACCTCTCTTCAGG
18248 AAACTTAGTT
Statistics
Matches: 457, Mismatches: 27, Indels: 17
0.91 0.05 0.03
Matches are distributed among these distances:
269 62 0.14
270 16 0.04
273 20 0.04
274 262 0.57
275 6 0.01
277 13 0.03
278 78 0.17
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (273 bp):
AAGGCCCCTTTTGAGGATCGATGAGGAGGCTCCATTTGAACTTTCTTTGTCCTTTTCTGTCTTTT
CTCACTTGCCAAATTACTAAGAAGACCCTAGGTTAGTTTCTAGCTAGTTCTTGCCCTTGAGCCCT
TTTTTTGTAATTATCCTTTCCTTTTCACATAAATGTTATAATAAATCCTATCCCCCTTAATTATC
TAGAATTGTAACCTCTCTTCAGGCCTTTCATGTCCATATAGAAGAGACTAAACTTAGTTTTGTTT
AAGTGCTACACAC
Found at i:20741 original size:70 final size:70
Alignment explanation
Indices: 20628--20773 Score: 283
Period size: 70 Copynumber: 2.1 Consensus size: 70
20618 TCCATGAAGT
20628 CCAAATTGCCAAGCCAGATGTCTTGAAACCTAAATATGATATTCTTAGACCCAATTCATTAATAT
1 CCAAATTGCCAAGCCAGATGTCTTGAAACCTAAATATGATATTCTTAGACCCAATTCATTAATAT
20693 GTAAC
66 GTAAC
20698 CCAAATTGCCAAGCCAGATGTCTTGAAACCTAAATATGATATTCTTAGACCCAATTCATTAATAT
1 CCAAATTGCCAAGCCAGATGTCTTGAAACCTAAATATGATATTCTTAGACCCAATTCATTAATAT
20763 GTAAC
66 GTAAC
20768 CTCAAA
1 C-CAAA
20774 GAAGGAGTTC
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
70 71 0.95
71 4 0.05
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (70 bp):
CCAAATTGCCAAGCCAGATGTCTTGAAACCTAAATATGATATTCTTAGACCCAATTCATTAATAT
GTAAC
Found at i:24789 original size:12 final size:12
Alignment explanation
Indices: 24772--24800 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
24762 AGGATCTCTT
24772 ATATAAACAAAC
1 ATATAAACAAAC
24784 ATATAAACAAAC
1 ATATAAACAAAC
24796 A-ATAA
1 ATATAA
24801 TAATTGAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.69, C:0.14, G:0.00, T:0.17
Consensus pattern (12 bp):
ATATAAACAAAC
Done.