Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020335.1 Corchorus olitorius cultivar O-4 contig20368, 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: 24270
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:3349 original size:16 final size:15
Alignment explanation
Indices: 3308--3338 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3298 ACAGATGTTG
3308 AAAA-AAAACAATTA
1 AAAAGAAAACAATTA
3322 AAAAGAAAACAATTA
1 AAAAGAAAACAATTA
3337 AA
1 AA
3339 CTGGAAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.77, C:0.06, G:0.03, T:0.13
Consensus pattern (15 bp):
AAAAGAAAACAATTA
Found at i:10934 original size:106 final size:106
Alignment explanation
Indices: 10749--10959 Score: 386
Period size: 106 Copynumber: 2.0 Consensus size: 106
10739 CAACCTATTA
* *
10749 CAAGACAACTATTTTATTAGATACATATATGCAGTATATATAAGAAAAAGAGAATAAATATTTAT
1 CAAGACAACTATTTCATCAGATACATATATGCAGTATATATAAGAAAAAGAGAATAAATATTTAT
10814 GAGAATCAAATTAGTGAAATTTTCTAGCTATGAATTTAAAG
66 GAGAATCAAATTAGTGAAATTTTCTAGCTATGAATTTAAAG
*
10855 CAAGACAACTATTTCATCAGATACATATATGCAGTATATATAAGAACAAGAGAATAAATATTTAT
1 CAAGACAACTATTTCATCAGATACATATATGCAGTATATATAAGAAAAAGAGAATAAATATTTAT
*
10920 GATAATCAAATTAGTGAAATTTTCTAGCTATGAATTTAAA
66 GAGAATCAAATTAGTGAAATTTTCTAGCTATGAATTTAAA
10960 AGCATGAGTT
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
106 101 1.00
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.33
Consensus pattern (106 bp):
CAAGACAACTATTTCATCAGATACATATATGCAGTATATATAAGAAAAAGAGAATAAATATTTAT
GAGAATCAAATTAGTGAAATTTTCTAGCTATGAATTTAAAG
Found at i:14280 original size:151 final size:149
Alignment explanation
Indices: 14006--14382 Score: 556
Period size: 151 Copynumber: 2.5 Consensus size: 149
13996 ATTGGAATCA
* * * * *
14006 GAATTTGACACGGAAATTATATTTTCATTTCTAAGGATGTTGCTAGTTAATTATAAAATGAACAT
1 GAATTTCACACGGAAATTATATTTCCATTTCTAAGAACGTTGCTAGCTAATTATAAAATGAACAT
14071 TAGTTTTATTTGGATTATTATAAAGAAAAGGAGTAGAAATATTTAAAGAAATAATTTCATCTATA
66 TAGTTTTATTTGGATTATTATAAAGAAAAGGAGTAGAAATATTTAAAGAAATAATTTCATCTATA
* *
14136 AATGTTTTTCACTTTGAAATG
131 AATG--TTTCACTTAGAAACG
*
14157 GAATTTCACACAGAAATTATATTTCCATTTCTAAGAACGTTGCTAGCTAATTATAAAATGAACAT
1 GAATTTCACACGGAAATTATATTTCCATTTCTAAGAACGTTGCTAGCTAATTATAAAATGAACAT
* * * * *
14222 TAGTTTTATTTGGATTCTTATAAAGACAAGGAGTGGAAATATTTACAGAATTAATTTCATCTATA
66 TAGTTTTATTTGGATTATTATAAAGAAAAGGAGTAGAAATATTTAAAGAAATAATTTCATCTATA
14287 AATGTTTCACTTAGAAACG
131 AATGTTTCACTTAGAAACG
* * * * *
14306 AAATTTCACACGGAAATTACACTTCCGTTTCTAAGAACGTTGCTAACTAATTATAAAATGAACAT
1 GAATTTCACACGGAAATTATATTTCCATTTCTAAGAACGTTGCTAGCTAATTATAAAATGAACAT
14371 TAGAATTTTATT
66 TAG--TTTTATT
14383 CAAATTATTA
Statistics
Matches: 205, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
149 75 0.37
151 130 0.63
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (149 bp):
GAATTTCACACGGAAATTATATTTCCATTTCTAAGAACGTTGCTAGCTAATTATAAAATGAACAT
TAGTTTTATTTGGATTATTATAAAGAAAAGGAGTAGAAATATTTAAAGAAATAATTTCATCTATA
AATGTTTCACTTAGAAACG
Found at i:15022 original size:18 final size:18
Alignment explanation
Indices: 14999--15045 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
14989 CGGGTTACGA
14999 GTCAACCAGGTCAAGCAT
1 GTCAACCAGGTCAAGCAT
15017 GTCAACCAGGTCAAGCAT
1 GTCAACCAGGTCAAGCAT
15035 GTCAACC-GGTC
1 GTCAACCAGGTC
15046 GGGTTTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 4 0.14
18 25 0.86
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.17
Consensus pattern (18 bp):
GTCAACCAGGTCAAGCAT
Found at i:17259 original size:36 final size:36
Alignment explanation
Indices: 17206--17281 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
17196 TTCAACTATT
*
17206 CAGCTCTTAAATAAGTGGCCATTTGATGATCAAATG
1 CAGCTCTTAAATAAGTGGCCATTTGATCATCAAATG
* *
17242 CAGCTCTTACATTAGTGGCCATTTGATCATCAAATG
1 CAGCTCTTAAATAAGTGGCCATTTGATCATCAAATG
17278 CAGC
1 CAGC
17282 AAAATCATCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (36 bp):
CAGCTCTTAAATAAGTGGCCATTTGATCATCAAATG
Found at i:17377 original size:72 final size:72
Alignment explanation
Indices: 17243--17417 Score: 228
Period size: 72 Copynumber: 2.4 Consensus size: 72
17233 GATCAAATGC
* * * * *
17243 AGCTCTTACATTAGTGGCCATTTGATCATCAAATGCAGCAAAATCATCATAACAAAATATAAGTC
1 AGCTCCTAAATTAGTGGCCATTTGATCATCAAAT-CAGCAAAATCATCACAACAAAACATAAGTA
17308 CACTAGTT
65 CACTAGTT
* * *
17316 AGCTTCTAGATTAGTGGCCATTTGAT-ATCAACAAT-AGCAAAATCATCACAATAAAACATAAGT
1 AGCTCCTAAATTAGTGGCCATTTGATCATC-A-AATCAGCAAAATCATCACAACAAAACATAAGT
17379 ACACTAGTT
64 ACACTAGTT
*
17388 AGCTCCTAAATTAGAGGCCATTTGATCATC
1 AGCTCCTAAATTAGTGGCCATTTGATCATC
17418 TAGTAGTATA
Statistics
Matches: 89, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
72 59 0.66
73 27 0.30
74 3 0.03
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (72 bp):
AGCTCCTAAATTAGTGGCCATTTGATCATCAAATCAGCAAAATCATCACAACAAAACATAAGTAC
ACTAGTT
Found at i:23410 original size:20 final size:22
Alignment explanation
Indices: 23362--23406 Score: 72
Period size: 24 Copynumber: 2.0 Consensus size: 22
23352 CACCATCTGT
23362 TGTGCTCATAATCACCCCAATTCA
1 TGTGCTCATAATCACCCCAA-T-A
23386 TGTGCTCATAATCACCCCAAT
1 TGTGCTCATAATCACCCCAAT
23407 GTGCCATCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.29, C:0.33, G:0.09, T:0.29
Consensus pattern (22 bp):
TGTGCTCATAATCACCCCAATA
Done.