Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014050.1 Corchorus olitorius cultivar O-4 contig14083, 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: 4342
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Found at i:170 original size:29 final size:29
Alignment explanation
Indices: 118--313 Score: 180
Period size: 29 Copynumber: 6.7 Consensus size: 29
108 CCTGGAGTGC
* * * *
118 AAATGACCAAAATACCCTTGAATGTGCGA
1 AAATGACCAAAATGCCCCTAAATATGCGA
* *
147 AAATGACCATAATGCCCCTAAATGTGC-A
1 AAATGACCAAAATGCCCCTAAATATGCGA
*
175 AAAGTGACCAAAATGCCCCTGAATATGC-A
1 AAA-TGACCAAAATGCCCCTAAATATGCGA
* *
204 AAAGTGACCAAAATGCCCCCTGAATATGCAA
1 AAA-TGACCAAAATG-CCCCTAAATATGCGA
* * **
235 AAATGACCAAAATGCCCCCTAGATTTTTGA
1 AAATGACCAAAATG-CCCCTAAATATGCGA
* * **
265 AAATGACCAAAATGCCCCTAGATTTTTGA
1 AAATGACCAAAATGCCCCTAAATATGCGA
*
294 AAATGACCAAAATTCCCCTA
1 AAATGACCAAAATGCCCCTA
314 GATGATCCTA
Statistics
Matches: 150, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
28 4 0.03
29 94 0.63
30 48 0.32
31 4 0.03
ACGTcount: A:0.40, C:0.24, G:0.14, T:0.21
Consensus pattern (29 bp):
AAATGACCAAAATGCCCCTAAATATGCGA
Found at i:184 original size:58 final size:58
Alignment explanation
Indices: 114--312 Score: 169
Period size: 59 Copynumber: 3.4 Consensus size: 58
104 TACCCCTGGA
* * *
114 GTGC-AAATGACCAAAATACCCTTGAATGTGCGAAAA-TGACCATAATG-CCCCTAAAT
1 GTGCAAAATGACCAAAATACCCCTGAATATGC-AAAAGTGACCAAAATGCCCCCTAAAT
* *
170 GTGCAAAAGTGACCAAAATGCCCCTGAATATGCAAAAGTGACCAAAATGCCCCCTGAAT
1 GTGCAAAA-TGACCAAAATACCCCTGAATATGCAAAAGTGACCAAAATGCCCCCTAAAT
* * * * *
229 ATGCAAAAATGACCAAAATGCCCCCTAGATTTTTG-AAAA-TGACCAAAATG-CCCCTAGATTT
1 GTGC-AAAATGACCAAAAT-ACCCCT-GA-ATATGCAAAAGTGACCAAAATGCCCCCTA-A-AT
* *
290 TTG-AAAATGACCAAAATTCCCCT
1 GTGCAAAATGACCAAAATACCCCT
313 AGATGATCCT
Statistics
Matches: 120, Mismatches: 13, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
56 4 0.03
57 7 0.06
58 36 0.30
59 40 0.33
60 21 0.17
61 9 0.08
62 3 0.03
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.22
Consensus pattern (58 bp):
GTGCAAAATGACCAAAATACCCCTGAATATGCAAAAGTGACCAAAATGCCCCCTAAAT
Found at i:226 original size:30 final size:29
Alignment explanation
Indices: 94--282 Score: 176
Period size: 29 Copynumber: 6.6 Consensus size: 29
84 TGAACTAAAC
* * *
94 ATGACCAAAAT-ACCCCTGGA-GTGC-AA
1 ATGACCAAAATGCCCCCTGAATATGCAAA
* * *
120 ATGACCAAAAT-ACCCTTGAATGTGCGAAA
1 ATGACCAAAATGCCCCCTGAATATGC-AAA
* * *
149 ATGACCATAATG-CCCCTAAATGTGCAAA
1 ATGACCAAAATGCCCCCTGAATATGCAAA
177 AGTGACCAAAATG-CCCCTGAATATGCAAA
1 A-TGACCAAAATGCCCCCTGAATATGCAAA
206 AGTGACCAAAATGCCCCCTGAATATGCAAAA
1 A-TGACCAAAATGCCCCCTGAATATGC-AAA
* *
237 ATGACCAAAATGCCCCCTAGATTTTTG-AAA
1 ATGACCAAAATGCCCCCT-GA-ATATGCAAA
267 ATGACCAAAATGCCCC
1 ATGACCAAAATGCCCC
283 TAGATTTTTG
Statistics
Matches: 144, Mismatches: 10, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
26 18 0.12
27 4 0.03
28 4 0.03
29 60 0.42
30 49 0.34
31 6 0.04
32 3 0.02
ACGTcount: A:0.40, C:0.25, G:0.16, T:0.19
Consensus pattern (29 bp):
ATGACCAAAATGCCCCCTGAATATGCAAA
Found at i:283 original size:59 final size:58
Alignment explanation
Indices: 145--316 Score: 181
Period size: 59 Copynumber: 2.9 Consensus size: 58
135 TTGAATGTGC
* * * *
145 GAAAATGACCATAATGCCCCTAAATGTGCAAAAGTGACCAAAATGCCCCT-GA-ATAT
1 GAAAATGACCAAAATGCCCCTGAATATGCAAAAATGACCAAAATGCCCCTAGATATAT
* *
201 GCAAAAGTGACCAAAATGCCCCCTGAATATGCAAAAATGACCAAAATGCCCCCTAGATTTTT
1 G-AAAA-TGACCAAAATG-CCCCTGAATATGCAAAAATGACCAAAATG-CCCCTAGATATAT
* * *
263 GAAAATGACCAAAATGCCCCTAGATTTTTG--AAAATGACCAAAATTCCCCTAGAT
1 GAAAATGACCAAAATGCCCCT-GA-ATATGCAAAAATGACCAAAATGCCCCTAGAT
317 GATCCTAGTG
Statistics
Matches: 99, Mismatches: 9, Indels: 14
0.81 0.07 0.11
Matches are distributed among these distances:
56 1 0.01
57 4 0.04
58 19 0.19
59 45 0.45
60 18 0.18
61 9 0.09
62 3 0.03
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.22
Consensus pattern (58 bp):
GAAAATGACCAAAATGCCCCTGAATATGCAAAAATGACCAAAATGCCCCTAGATATAT
Found at i:559 original size:30 final size:30
Alignment explanation
Indices: 489--563 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 30
479 ACTTGTAGCA
* * *
489 TTTG-GACGTTTTGCCCCCTGAATTTCAAT
1 TTTGAGACATTTTGCCCCCTAAACTTCAAT
*
518 TTT-AAACATTTTGCCCCCTAAACTTCAAT
1 TTTGAGACATTTTGCCCCCTAAACTTCAAT
547 TTTGAGACATTTTGCCC
1 TTTGAGACATTTTGCCC
564 TCTCAGGCTA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 27 0.69
30 12 0.31
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (30 bp):
TTTGAGACATTTTGCCCCCTAAACTTCAAT
Found at i:1119 original size:14 final size:14
Alignment explanation
Indices: 1100--1128 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1090 TGAGTAAATC
1100 TAGCTTTGGGCTTT
1 TAGCTTTGGGCTTT
1114 TAGCTTTGGGCTTT
1 TAGCTTTGGGCTTT
1128 T
1 T
1129 GAGCCATAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.14, G:0.28, T:0.52
Consensus pattern (14 bp):
TAGCTTTGGGCTTT
Found at i:1773 original size:21 final size:21
Alignment explanation
Indices: 1749--1807 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
1739 ATTAGAGCAA
1749 GTTCCAAGCTCATTGGAGAAG
1 GTTCCAAGCTCATTGGAGAAG
1770 GTTCCAAGCTCATTGGAGAAG
1 GTTCCAAGCTCATTGGAGAAG
*
1791 GTTTCAAGCTCATTGGA
1 GTTCCAAGCTCATTGGA
1808 ATTGCCTAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (21 bp):
GTTCCAAGCTCATTGGAGAAG
Found at i:2680 original size:25 final size:24
Alignment explanation
Indices: 2644--2690 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
2634 TCCTTCTATT
2644 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
2667 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
2691 AATTTTTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Done.