Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018371.1 Corchorus olitorius cultivar O-4 contig18404, 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: 27519
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--81 Score: 65
Period size: 2 Copynumber: 40.5 Consensus size: 2
* * * * *
1 CT CT CT CT CT CT CT GT CT C- CGT GT CT CT CT CT CA CT CT AT GT
1 CT CT CT CT CT CT CT CT CT CT C-T CT CT CT CT CT CT CT CT CT CT
* * * *
43 CT CT CT CT CT CT CT CT CT TT TT GT CT CT CT CT CA CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
82 AAACCCTAAA
Statistics
Matches: 63, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
1 1 0.02
2 62 0.98
ACGTcount: A:0.04, C:0.42, G:0.06, T:0.48
Consensus pattern (2 bp):
CT
Found at i:67 original size:24 final size:24
Alignment explanation
Indices: 1--81 Score: 90
Period size: 24 Copynumber: 3.3 Consensus size: 24
* *
1 CTCTCTCTCTCTCTGTCTCCGTGTCT
1 CTCTCTCTCTCTATGTCT-C-TCTCT
*
27 CTCTCTCACTCTATGTCTCTCTCT
1 CTCTCTCTCTCTATGTCTCTCTCT
* *
51 CTCTCTCTCTTTTTGTCTCTCTCT
1 CTCTCTCTCTCTATGTCTCTCTCT
*
75 CACTCTC
1 CTCTCTC
82 AAACCCTAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
24 31 0.65
25 1 0.02
26 16 0.33
ACGTcount: A:0.04, C:0.42, G:0.06, T:0.48
Consensus pattern (24 bp):
CTCTCTCTCTCTATGTCTCTCTCT
Found at i:68 original size:42 final size:42
Alignment explanation
Indices: 1--80 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
*
1 CTCTCTCTCTCTCTGTCTCCGTGTCTCTCTCTCACTCTATGT
1 CTCTCTCTCTCTCTCTCTCCGTGTCTCTCTCTCACTCTATGT
***
43 CTCTCTCTCTCTCTCTCTTTTTGTCTCTCTCTCACTCT
1 CTCTCTCTCTCTCTCTCTCCGTGTCTCTCTCTCACTCT
81 CAAACCCTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.04, C:0.41, G:0.06, T:0.49
Consensus pattern (42 bp):
CTCTCTCTCTCTCTCTCTCCGTGTCTCTCTCTCACTCTATGT
Found at i:81 original size:22 final size:22
Alignment explanation
Indices: 2--81 Score: 74
Period size: 22 Copynumber: 3.7 Consensus size: 22
1 C
* * **
2 TCTCTCTCTCTCTGTCTCCGTG
1 TCTCTCTCTCACTCTCTATGTG
*
24 TCTCTCTCTCA--CTCTATGTC
1 TCTCTCTCTCACTCTCTATGTG
* * *
44 TCTCTCTCTCTCTCTCTTTTTG
1 TCTCTCTCTCACTCTCTATGTG
66 TCTCTCTCTCACTCTC
1 TCTCTCTCTCACTCTC
82 AAACCCTAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
20 15 0.33
22 31 0.67
ACGTcount: A:0.04, C:0.41, G:0.06, T:0.49
Consensus pattern (22 bp):
TCTCTCTCTCACTCTCTATGTG
Found at i:113 original size:13 final size:13
Alignment explanation
Indices: 91--129 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
81 CAAACCCTAA
*
91 AACCCAAAACCCT
1 AACCCTAAACCCT
*
104 AACCCTAAACCAT
1 AACCCTAAACCCT
*
117 TACCCTAAACCCT
1 AACCCTAAACCCT
130 CTATCTATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.41, C:0.44, G:0.00, T:0.15
Consensus pattern (13 bp):
AACCCTAAACCCT
Found at i:148 original size:12 final size:12
Alignment explanation
Indices: 128--183 Score: 67
Period size: 12 Copynumber: 4.7 Consensus size: 12
118 ACCCTAAACC
*
128 CTCTATCTATGT
1 CTCTCTCTATGT
140 CTCTCTCTATGT
1 CTCTCTCTATGT
* *
152 CTCTCTCTGTAT
1 CTCTCTCTATGT
* *
164 CTTTCTCTCTGT
1 CTCTCTCTATGT
176 CTCTCTCT
1 CTCTCTCT
184 CCCTCTCTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.07, C:0.34, G:0.07, T:0.52
Consensus pattern (12 bp):
CTCTCTCTATGT
Found at i:156 original size:14 final size:14
Alignment explanation
Indices: 139--219 Score: 72
Period size: 14 Copynumber: 5.6 Consensus size: 14
129 TCTATCTATG
*
139 TCTCTCTCTATGTC
1 TCTCTCTCTATCTC
*
153 TCTCTCTGTATCTTTC
1 TCTCTCTCTATC--TC
* *
169 TCTCTGTCTCTCTC
1 TCTCTCTCTATCTC
*
183 TCCCTCTCTATCTC
1 TCTCTCTCTATCTC
* *
197 TCTCTCTCTTTCTT
1 TCTCTCTCTATCTC
*
211 TGTCTCTCT
1 TCTCTCTCT
220 CTCACTCTCA
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
14 42 0.79
16 11 0.21
ACGTcount: A:0.04, C:0.38, G:0.05, T:0.53
Consensus pattern (14 bp):
TCTCTCTCTATCTC
Found at i:184 original size:12 final size:12
Alignment explanation
Indices: 137--222 Score: 73
Period size: 12 Copynumber: 7.0 Consensus size: 12
127 CCTCTATCTA
*
137 TGTCTCTCTCTA
1 TGTCTCTCTCTC
*
149 TGTCTCTCTCTG
1 TGTCTCTCTCTC
* *
161 TATCTTTCTCTC
1 TGTCTCTCTCTC
173 TGTCTCTCTCTCCC
1 TGTCTCTCTCT--C
* *
187 TCTCTATCTCTC
1 TGTCTCTCTCTC
* * *
199 TCTCTCTTTCTT
1 TGTCTCTCTCTC
211 TGTCTCTCTCTC
1 TGTCTCTCTCTC
223 ACTCTCAAAC
Statistics
Matches: 58, Mismatches: 14, Indels: 4
0.76 0.18 0.05
Matches are distributed among these distances:
12 48 0.83
14 10 0.17
ACGTcount: A:0.03, C:0.38, G:0.06, T:0.52
Consensus pattern (12 bp):
TGTCTCTCTCTC
Found at i:189 original size:18 final size:18
Alignment explanation
Indices: 168--228 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
158 CTGTATCTTT
168 CTCTCTGTCTCTCTCTCC
1 CTCTCTGTCTCTCTCTCC
*
186 CTCTCTATCTCTCTCTCTC
1 CTCTCTGTCTCTCTCTC-C
* * *
205 TTTCTTTGTCTCTCTCTCA
1 -CTCTCTGTCTCTCTCTCC
224 CTCTC
1 CTCTC
229 AAACCCTAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
18 19 0.56
19 1 0.03
20 14 0.41
ACGTcount: A:0.03, C:0.44, G:0.03, T:0.49
Consensus pattern (18 bp):
CTCTCTGTCTCTCTCTCC
Found at i:260 original size:147 final size:148
Alignment explanation
Indices: 12--369 Score: 495
Period size: 147 Copynumber: 2.4 Consensus size: 148
2 TCTCTCTCTC
* *
12 TCTGTCTC-CGTGTCTCTCTCTCACTCTATGTCTCTCTCTCTCTCTCTCTTTTTGTCTCTCTCTC
1 TCTGTCTCTC-TGTCTCTCTCTCACTCTCTATCTCTCTCTCTCT-T-TC--TTTGTCTCTCTCTC
76 ACTCTCAAACCCTAAAACCCAAAACCCTAACCCTAAACCATTACCCTAAACCCTCTATCTATGTC
61 ACTCTCAAACCCTAAAACCCAAAACCCTAACCCTAAACCATTACCCTAAACCCTCTATCTATGTC
*
141 TCTCTCTATGTCTC-TCTCTGTA
126 TCTCTCTATCTCTCGTCTCTGTA
* *
163 TCTTTCTCTCTGTCTCTCTCTCCCTCTCTATCTCTCTCTCTCTTTCTTTGTCTCTCTCTCACTCT
1 TCTGTCTCTCTGTCTCTCTCTCACTCTCTATCTCTCTCTCTCTTTCTTTGTCTCTCTCTCACTCT
*
228 CAAACCCTAAACCCCAAAACCCTAACCCTAAACCATTACCCTAAACCCTCTATCTATGTCTCTCT
66 CAAACCCTAAAACCCAAAACCCTAACCCTAAACCATTACCCTAAACCCTCTATCTATGTCTCTCT
* * *
293 CTCTCTCTCTGTCTTTGTC
131 CTATCTCTC-GTCTCTGTA
* * * * * * * *
312 TCTGTCTCTCTCTATCTCTGTCTCTCTCTATCTCTGTCTCTCTCTCTGTATCTCTCTC
1 TCTGTCTCTCTGTCTCTCTCTCACTCTCTATCTCTCTCTCTCTTTCTTTGTCTCTCTC
370 CCTGTCTCTC
Statistics
Matches: 186, Mismatches: 18, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
147 90 0.48
149 57 0.31
150 1 0.01
151 37 0.20
152 1 0.01
ACGTcount: A:0.15, C:0.39, G:0.05, T:0.41
Consensus pattern (148 bp):
TCTGTCTCTCTGTCTCTCTCTCACTCTCTATCTCTCTCTCTCTTTCTTTGTCTCTCTCTCACTCT
CAAACCCTAAAACCCAAAACCCTAACCCTAAACCATTACCCTAAACCCTCTATCTATGTCTCTCT
CTATCTCTCGTCTCTGTA
Found at i:293 original size:2 final size:2
Alignment explanation
Indices: 286--406 Score: 91
Period size: 2 Copynumber: 60.5 Consensus size: 2
276 TCTATCTATG
* * * * *
286 TC TC TC TC TC TC TC TC TG TC TT TG TC TC TG TC TC TC TC TA TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * *
328 TC TG TC TC TC TC TA TC TC TG TC TC TC TC TC TG TA TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * *
370 CC TG TC TC TC TG TC CC TC -C ATG TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC -TC TC TC TC TC TC TC TC T
407 TAAACCCAAA
Statistics
Matches: 89, Mismatches: 28, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
1 1 0.01
2 88 0.99
ACGTcount: A:0.03, C:0.40, G:0.07, T:0.49
Consensus pattern (2 bp):
TC
Found at i:313 original size:16 final size:16
Alignment explanation
Indices: 275--356 Score: 105
Period size: 16 Copynumber: 5.2 Consensus size: 16
265 ACCCTAAACC
*
275 CTCTATCTATGTCTCT
1 CTCTATCTCTGTCTCT
* *
291 CTC--TCTCTCTCTGT
1 CTCTATCTCTGTCTCT
* *
305 CTTTGTCTCTGTCTCT
1 CTCTATCTCTGTCTCT
321 CTCTATCTCTGTCTCT
1 CTCTATCTCTGTCTCT
337 CTCTATCTCTGTCTCT
1 CTCTATCTCTGTCTCT
353 CTCT
1 CTCT
357 CTGTATCTCT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
14 10 0.18
16 46 0.82
ACGTcount: A:0.05, C:0.37, G:0.07, T:0.51
Consensus pattern (16 bp):
CTCTATCTCTGTCTCT
Found at i:313 original size:22 final size:22
Alignment explanation
Indices: 288--406 Score: 107
Period size: 22 Copynumber: 5.4 Consensus size: 22
278 TATCTATGTC
*
288 TCTCTCTCTCTCTCTGTCTTTG
1 TCTCTCTCTCTCTCTGTCTCTG
* *
310 TCTCTGTCTCTCTCTATCTCTG
1 TCTCTCTCTCTCTCTGTCTCTG
*
332 TCTCTCTCTATCTCTGTCTC--
1 TCTCTCTCTCTCTCTGTCTCTG
* * * *
352 TCTCTCTGTATCTCTCTCCCTG
1 TCTCTCTCTCTCTCTGTCTCTG
* * *
374 TCTCTCTGTCCCTCCATGTCTCTC
1 TCTCTCTCTCTCT-C-TGTCTCTG
398 TCTCTCTCT
1 TCTCTCTCT
407 TAAACCCAAA
Statistics
Matches: 78, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
20 17 0.22
22 47 0.60
23 1 0.01
24 13 0.17
ACGTcount: A:0.03, C:0.40, G:0.08, T:0.49
Consensus pattern (22 bp):
TCTCTCTCTCTCTCTGTCTCTG
Found at i:437 original size:21 final size:21
Alignment explanation
Indices: 407--454 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
397 CTCTCTCTCT
407 TAAA-CCCAAAACCCTAACCC
1 TAAACCCCAAAACCCTAACCC
427 TAAACCCCAAAACCCTAACCC
1 TAAACCCCAAAACCCTAACCC
448 TAAACCC
1 TAAACCC
455 TCTATCAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.44, C:0.46, G:0.00, T:0.10
Consensus pattern (21 bp):
TAAACCCCAAAACCCTAACCC
Found at i:454 original size:179 final size:174
Alignment explanation
Indices: 211--582 Score: 426
Period size: 179 Copynumber: 2.1 Consensus size: 174
201 TCTCTTTCTT
* * * *
211 TGTCTCTCTCTCACTCTCAAACCCTAAACCCCAAAACCCTAACCCTAAACCATTACCCTAAACCC
1 TGTCTCTCTCTCTCTCTCAAACCCTAAAACCCAAAACCCTAACCCAAAACCATAACCCTAAACCC
* * * * * *
276 TCTATCTATGTCTCTCTCTCTCTCTCTGTCTTTGTCTCTGTCTCTCTCTATCTCTGTCTCTCTCT
66 TCTATCAATGTCTCTATATCTCTCTC--TCTCTGT-T-TCTCTCTCTCTATCTCTCTCTCTCTCT
* *
341 ATCTCTGTCTCTCTCTCTGTATCTCTCTCCCTGTCTCTCTGTCCCTC-CA
127 ATCTCTGTCTCTCTCTCTCTATCT-T-TCCCTGTCTCTCTCTCCCTCGCA
* * *
390 TGTCTCTCTCTCTCTCTTAAACCC-AAAACCC-TAACCCTAAACCCCAAAACCCTAACCCTAAAC
1 TGTCTCTCTCTCTCTCTCAAACCCTAAAACCCAAAACCCT-AA-CCCAAAACCATAACCCTAAAC
* * * *
453 CCTCTATCAATGTCTCTATATGTCTCTCTCTCTGTTTCTCTCTCTGTATCTCTCTCTCTGTCTTT
64 CCTCTATCAATGTCTCTATATCTCTCTCTCTCTGTTTCTCTCTCTCTATCTCTCTCTCTCTCTAT
* * * *
518 CTCTGTCTCTCTCTCTCTGTCTTTCTCTGTCTCTCTCTCTCTCGTCG
129 CTCTGTCTCTCTCTCTCTATCTTTCCCTGTCTCTCTCTCCCTCG-CA
*
565 TATCTCTCTCTCTCTCTC
1 TGTCTCTCTCTCTCTCTC
583 TCTCTCTCTC
Statistics
Matches: 164, Mismatches: 25, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
173 17 0.10
174 1 0.01
175 61 0.37
176 1 0.01
177 12 0.07
178 8 0.05
179 64 0.39
ACGTcount: A:0.15, C:0.40, G:0.06, T:0.40
Consensus pattern (174 bp):
TGTCTCTCTCTCTCTCTCAAACCCTAAAACCCAAAACCCTAACCCAAAACCATAACCCTAAACCC
TCTATCAATGTCTCTATATCTCTCTCTCTCTGTTTCTCTCTCTCTATCTCTCTCTCTCTCTATCT
CTGTCTCTCTCTCTCTATCTTTCCCTGTCTCTCTCTCCCTCGCA
Found at i:455 original size:7 final size:7
Alignment explanation
Indices: 407--455 Score: 57
Period size: 7 Copynumber: 7.1 Consensus size: 7
397 CTCTCTCTCT
407 TAAACCC
1 TAAACCC
*
414 AAAACCC
1 TAAACCC
421 T-AACCC
1 TAAACCC
427 TAAACCCC
1 TAAA-CCC
*
435 AAAACCC
1 TAAACCC
442 T-AACCC
1 TAAACCC
448 TAAACCC
1 TAAACCC
455 T
1 T
456 CTATCAATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
6 12 0.34
7 17 0.49
8 6 0.17
ACGTcount: A:0.43, C:0.45, G:0.00, T:0.12
Consensus pattern (7 bp):
TAAACCC
Found at i:482 original size:2 final size:2
Alignment explanation
Indices: 475--647 Score: 186
Period size: 2 Copynumber: 85.5 Consensus size: 2
465 TCTCTATATG
* * * * * *
475 TC TC TC TC TC TG TT TC TC TC TC TG TA TC TC TC TC TC TG TC TT
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * *
517 TC TC TG TC TC TC TC TC TC TG TC TT TC TC TG TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * *
559 TC GTC GTA TC TC TC TC TC TC TC TC TC TC TC TC TC TC TG TA TC TC
1 TC -TC -TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
603 TC TC TC -C TAA TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC T-C TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
645 TC T
1 TC T
648 AGTGTGTGTG
Statistics
Matches: 143, Mismatches: 25, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
1 1 0.01
2 137 0.96
3 5 0.03
ACGTcount: A:0.03, C:0.41, G:0.05, T:0.51
Consensus pattern (2 bp):
TC
Found at i:760 original size:66 final size:66
Alignment explanation
Indices: 630--829 Score: 339
Period size: 66 Copynumber: 3.0 Consensus size: 66
620 CTCTCTCTCT
*
630 CTCTCTCTCTCTCTCTCTAGTGTGTGTGGTATGTATATAAATCTATATGTTTTTGCGTTACTTAG
1 CTCTCTCTCTCT-TCTTTAGTGTGTGTGGTATGTATATAAATCTATATGTTTTTGCGTTACTTAG
695 CA
65 CA
*
697 CTCTCTCCCATCTTCTTTAGTGTGTGTGGTATGTATA-AAATCTATATGTTTTTGCGTTACTTAG
1 CTCTCTCTC-TCTTCTTTAGTGTGTGTGGTATGTATATAAATCTATATGTTTTTGCGTTACTTAG
761 CA
65 CA
*
763 CTCTCTCTCGTCTTCTTCAGTGTGTGTGGTATGTATATAAATCTATATGTTTTTGCGTTACTTAG
1 CTCTCTCTC-TCTTCTTTAGTGTGTGTGGTATGTATATAAATCTATATGTTTTTGCGTTACTTAG
828 CA
65 CA
830 TCATATGAAA
Statistics
Matches: 126, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
66 63 0.50
67 60 0.48
68 3 0.02
ACGTcount: A:0.18, C:0.18, G:0.17, T:0.46
Consensus pattern (66 bp):
CTCTCTCTCTCTTCTTTAGTGTGTGTGGTATGTATATAAATCTATATGTTTTTGCGTTACTTAGC
A
Found at i:4735 original size:41 final size:42
Alignment explanation
Indices: 4655--4785 Score: 115
Period size: 42 Copynumber: 3.1 Consensus size: 42
4645 ATTATTACTG
* * * * ** *
4655 TTTTTTCTTAAGTAAAGAAGAAAAACTAGCAACTCGTTACCC
1 TTTTTTCTCAAGTCATGAAGAAAAAATATTAACTTGTTACCC
* * *
4697 TTTTTTCTTAAGTCATGAAG-GAAAAT-TGTAA-TATGTTACCA
1 TTTTTTCTCAAGTCATGAAGAAAAAATAT-TAACT-TGTTACCC
**
4738 TTTTTTCTCAAGTTTTGAAGAAAAAATATTAACTTGTTACCC
1 TTTTTTCTCAAGTCATGAAGAAAAAATATTAACTTGTTACCC
4780 TTTTTT
1 TTTTTT
4786 AAGTAACGAG
Statistics
Matches: 71, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
40 1 0.01
41 29 0.41
42 39 0.55
43 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (42 bp):
TTTTTTCTCAAGTCATGAAGAAAAAATATTAACTTGTTACCC
Found at i:5123 original size:29 final size:29
Alignment explanation
Indices: 5082--5145 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
5072 GCCAACGGTT
* *
5082 AAATAA-CCATG-AATTTCAATTTTGACC
1 AAATAAGCCATGAAAATTCAATTTTAACC
*
5109 AAATAAGCTCATGAAAATTCAATTTTAATC
1 AAATAAGC-CATGAAAATTCAATTTTAACC
5139 AAATAAG
1 AAATAAG
5146 TCCCATTTCG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 6 0.19
28 1 0.03
29 4 0.13
30 20 0.65
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (29 bp):
AAATAAGCCATGAAAATTCAATTTTAACC
Found at i:5595 original size:42 final size:42
Alignment explanation
Indices: 5536--5618 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
5526 TAAGGATCAG
*
5536 GATTTGAGTCGAGTATTTCTT-ATTATACAAATAATTTTCAAT
1 GATTTGAGTCGAGTATTTCTTAATT-TACAAAGAATTTTCAAT
5578 GATTTGAGTCGAGTATTTCTTAATTTACAAAGAATTTTCAA
1 GATTTGAGTCGAGTATTTCTTAATTTACAAAGAATTTTCAA
5619 GACTTAGCTA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
42 36 0.92
43 3 0.08
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (42 bp):
GATTTGAGTCGAGTATTTCTTAATTTACAAAGAATTTTCAAT
Found at i:7842 original size:7 final size:7
Alignment explanation
Indices: 7830--7859 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
7820 AAAGGTCTGG
7830 CCTCAGC
1 CCTCAGC
7837 CCTCAGC
1 CCTCAGC
7844 CCTCAGC
1 CCTCAGC
*
7851 CCTCGGC
1 CCTCAGC
7858 CC
1 CC
7860 ATGGCCGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.10, C:0.60, G:0.17, T:0.13
Consensus pattern (7 bp):
CCTCAGC
Found at i:10043 original size:2 final size:2
Alignment explanation
Indices: 10036--10065 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10026 ATTCTCCTAC
10036 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10066 ATTGATGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10841 original size:11 final size:11
Alignment explanation
Indices: 10825--10849 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
10815 GCATCAACCT
10825 GATTAGAGAGA
1 GATTAGAGAGA
10836 GATTAGAGAGA
1 GATTAGAGAGA
10847 GAT
1 GAT
10850 CAAAATTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.36, T:0.20
Consensus pattern (11 bp):
GATTAGAGAGA
Found at i:17417 original size:1 final size:1
Alignment explanation
Indices: 17413--17442 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
17403 AATAAGAAAG
17413 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17443 CCCTTCTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:19760 original size:17 final size:17
Alignment explanation
Indices: 19738--19771 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
19728 TTAGAGTTGC
19738 CAATGTTACGCTTATTA
1 CAATGTTACGCTTATTA
19755 CAATGTTACGCTTATTA
1 CAATGTTACGCTTATTA
19772 ATTCAGTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (17 bp):
CAATGTTACGCTTATTA
Found at i:23366 original size:18 final size:18
Alignment explanation
Indices: 23343--23380 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
23333 AATACCAATC
23343 AAATCTTTGTACCTAACT
1 AAATCTTTGTACCTAACT
23361 AAATCTTTGTACCTAACT
1 AAATCTTTGTACCTAACT
23379 AA
1 AA
23381 TTGGTTCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (18 bp):
AAATCTTTGTACCTAACT
Found at i:24185 original size:15 final size:15
Alignment explanation
Indices: 24163--24199 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
24153 AAATCACTGA
*
24163 CCCCATCAAGTGCTT
1 CCCCATCAAGAGCTT
*
24178 CTCCATCAAGAGCTT
1 CCCCATCAAGAGCTT
24193 CCCCATC
1 CCCCATC
24200 TTCACTCTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.22, C:0.43, G:0.11, T:0.24
Consensus pattern (15 bp):
CCCCATCAAGAGCTT
Done.