Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000048.1 Hibiscus syriacus cultivar Beakdansim tig00000074_pilon, 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: 62163
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:3329 original size:24 final size:25
Alignment explanation
Indices: 3266--3329 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 25
3256 GAAAAATATT
* * *
3266 AATAATAATAATAAAATAGATAACA
1 AATAATAAAAATAAATTAGATAAAA
*
3291 AA-GATAAATAA-AAATTAG-TAAAA
1 AATAATAAA-AATAAATTAGATAAAA
3314 AATAATAAAAATAAAT
1 AATAATAAAAATAAAT
3330 AAAAAGGACC
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
23 8 0.26
24 19 0.61
25 4 0.13
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (25 bp):
AATAATAAAAATAAATTAGATAAAA
Found at i:3448 original size:20 final size:19
Alignment explanation
Indices: 3419--3459 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
3409 ATTTGCACAA
3419 ACAAATTTAAAAGGAAAAC
1 ACAAATTTAAAAGGAAAAC
*
3438 ACAATATTTAAAGGGAAAAC
1 ACAA-ATTTAAAAGGAAAAC
3458 AC
1 AC
3460 GTCAATTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.59, C:0.12, G:0.12, T:0.17
Consensus pattern (19 bp):
ACAAATTTAAAAGGAAAAC
Found at i:5226 original size:84 final size:84
Alignment explanation
Indices: 4893--5777 Score: 432
Period size: 84 Copynumber: 10.5 Consensus size: 84
4883 ACAAATAGCT
* * * * * * *
4893 CTTCTTACATTGAGCTATGCTGC-AACTGATGTGCCTTTGAGCTAAATGGAATCGAACTCGAAGG
1 CTTCTTGCCTTGAGCTATGCTGCAAATTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAA-G
* *
4957 GTCTTTGATGACAGATAACC
65 GTCTTTGTTGGCAGATAACC
* * * * *
4977 CCTCTAG-CTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTATAATCAAACTCGAAG
1 CTTCTTGCCTTGAGCTATGCTGCAAA-TTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
* * *
5041 GTCTTGGTTGACATA-AACC
65 GTCTTTGTTGGCAGATAACC
* * * *
5060 CTTCTCGCCTTGAGTTATGCTGTAAATTGGACATGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
1 CTTCTTGCCTTGAGCTATGCTGCAAATT-GATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
*
5125 GTCTTTTGTTGGCAGATAGCC
65 GTC-TTTGTTGGCAGATAACC
* * *
5146 CTTCTTGCCTTGAGCTATCCTGCAAA-TGATGTGCCTTTGAGTTGAGTGTAATCGAACTCGAAGG
1 CTTCTTGCCTTGAGCTATGCTGCAAATTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
* *
5210 TCTTTCCTTGGTAGATAACTC
66 TCTTT-GTTGGCAGATAAC-C
** *** * * * * *
5231 GAAGGTCTTTTGTTGCAGATA-GC--C--CTT-CT-CGCC-TTGAGCT-ATGCTGCAAAT-G-A-
1 ---CTTCTTGCCTTG-AGCTATGCTGCAAATTGATATGCCTTTGAGCTGA-G-TG-TAATCGAAC
* * *
5284 T-GTA--TCTTTGAGCTGAG-TGTAATCGAACTC
59 TCGAAGGTCTTT--GTTG-GCAG--AT--AAC-C
* *** * * **
5314 GAAGTTCTTTTGTTGGCAGATAACCCTTCTCGC--ATTGAGCTATGCTGCAAATGA--TGAGTGT
1 ---CTTCTTGCCTT-G-AGCT-A---TGCT-GCAAATTGA--TATGC--C-TTTGAGCTGAGTGT
*
5375 AATCGAACTCGAAGGTCTTTTGTTGGCAGATATCC
51 AATCGAACTCGAAGGTC-TTTGTTGGCAGATAACC
* * * * *
5410 CTTCTCGCCTTGAGCTATACTACAAA-TGATGTGCCTTTGAGATGAGTGTAATCGAACTCGAAGG
1 CTTCTTGCCTTGAGCTATGCTGCAAATTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
* *
5474 TTTTTGTTGGCAAATAGA-C
66 TCTTTGTTGGCAGATA-ACC
* * * * * *
5493 TTTCTTGCCCTGAGTTATGCTACAAA-TGATGTGCCTTTGAGCTGAGTGTAATCGAACTTGAAGG
1 CTTCTTGCCTTGAGCTATGCTGCAAATTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
* *
5557 TC--T-TTGGCATATAGCC
66 TCTTTGTTGGCAGATAACC
* * * * * * * * *
5573 TTTCTTTCCTTGAGCTATGCTGCAAA-TAATGTGCTTTTAAGCTAACTTTAATCGAACTCGAAGG
1 CTTCTTGCCTTGAGCTATGCTGCAAATTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
*
5637 TCTTTGTTGACAGATAACC
66 TCTTTGTTGGCAGATAACC
* * * * *
5656 CTTCTAGCCTTGAGTTATGATGTAAA-TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
1 CTTCTTGCCTTGAGCTATGCTGCAAATTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
* *
5720 TCTTTTGTTGGCATATAGCC
66 TC-TTTGTTGGCAGATAACC
* * *
5740 CTTCTTGCCTTGAGTTATGTTGCAAA-TGATGTGCCTTT
1 CTTCTTGCCTTGAGCTATGCTGCAAATTGATATGCCTTT
5778 CGAAGGTCTT
Statistics
Matches: 624, Mismatches: 119, Indels: 116
0.73 0.14 0.14
Matches are distributed among these distances:
78 5 0.01
79 3 0.00
80 68 0.11
81 5 0.01
82 12 0.02
83 188 0.30
84 200 0.32
85 47 0.08
86 27 0.04
87 6 0.01
88 9 0.01
89 5 0.01
90 1 0.00
91 3 0.00
92 4 0.01
93 6 0.01
95 1 0.00
96 6 0.01
97 5 0.01
98 4 0.01
99 4 0.01
100 6 0.01
101 4 0.01
102 2 0.00
103 3 0.00
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (84 bp):
CTTCTTGCCTTGAGCTATGCTGCAAATTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
TCTTTGTTGGCAGATAACC
Found at i:5265 original size:109 final size:110
Alignment explanation
Indices: 5116--5337 Score: 356
Period size: 109 Copynumber: 2.0 Consensus size: 110
5106 AGTGTAATCG
* *
5116 AACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATCCTGCAAATGATGTGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGCTATCCTGCAAATGATGTACC
* *
5181 TTTGAGTTGAGTGTAATCGAACTCGAAGGTCTTTCCTTGGTAGAT
66 TTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTCCTTGGCAGAT
* *
5226 AACTCGAAGGTCTTTTGTT-GCAGATAGCCCTTCTCGCCTTGAGCTATGCTGCAAATGATGTATC
1 AACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGCTATCCTGCAAATGATGTACC
* **
5290 TTTGAGCTGAGTGTAATCGAACTCGAAGTTCTTTTGTTGGCAGAT
66 TTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTCCTTGGCAGAT
5335 AAC
1 AAC
5338 CCTTCTCGCA
Statistics
Matches: 103, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
109 84 0.82
110 19 0.18
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (110 bp):
AACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGCTATCCTGCAAATGATGTACC
TTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTCCTTGGCAGAT
Found at i:5317 original size:83 final size:83
Alignment explanation
Indices: 5226--5777 Score: 530
Period size: 83 Copynumber: 6.8 Consensus size: 83
5216 CTTGGTAGAT
**
5226 AACTCGAAGGTCTTTTGTTGCAGATAGCCCTTCTCGCCTTGAGCTATGCTGCAAATGATGTATCT
1 AACTCGAAGGTCTTTTGTTGCAGATAGCCCTTCTCGCCTTGAGCTATGCTGCAAATGATGTGCCT
5291 TTGAGCTGAGTGTAATCG
66 TTGAGCTGAGTGTAATCG
* * * *
5309 AACTCGAAGTTCTTTTGTTGGCAGATAACCCTTCTCGCATTGAGCTATGCTGCAAATGATGAG--
1 AACTCGAAGGTCTTTTGTT-GCAGATAGCCCTTCTCGCCTTGAGCTATGCTGCAAATGATGTGCC
* * * *
5372 TGTAATC-GA----ACTCG
65 TTTGAGCTGAGTGTAATCG
* * * * *
5386 AA---G--GTCT-TTTGT-TGGCAGATATCCCTTCTCGCCTTGAGCTATACTACAAATGATGTGC
1 AACTCGAAG-GTCTTT-TGTTGCAGATAGCCCTTCTCGCCTTGAGCTATGCTGCAAATGATGTGC
*
5444 CTTTGAGATGAGTGTAATCG
64 CTTTGAGCTGAGTGTAATCG
* * * * * * *
5464 AACTCGAAGGT-TTTTGTTGGCAAATAGACTTTCTTGCCCTGAGTTATGCTACAAATGATGTGCC
1 AACTCGAAGGTCTTTTGTT-GCAGATAGCCCTTCTCGCCTTGAGCTATGCTGCAAATGATGTGCC
5528 TTTGAGCTGAGTGTAATCG
65 TTTGAGCTGAGTGTAATCG
* * * ** * *
5547 AACTTGAAGGTC-TTTG--GCATATAGCCTTTCTTTCCTTGAGCTATGCTGCAAATAATGTGCTT
1 AACTCGAAGGTCTTTTGTTGCAGATAGCCCTTCTCGCCTTGAGCTATGCTGCAAATGATGTGCCT
* * * *
5609 TTAAGCTAACTTTAATCG
66 TTGAGCTGAGTGTAATCG
* * * * *
5627 AACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGATGTAAATGATGTGCC
1 AACTCGAAGGTCTTTTGTTG-CAGATAGCCCTTCTCGCCTTGAGCTATGCTGCAAATGATGTGCC
5691 TTTGAGCTGAGTGTAATCG
65 TTTGAGCTGAGTGTAATCG
* * * *
5710 AACTCGAAGGTCTTTTGTTGGCATATAGCCCTTCTTGCCTTGAGTTATGTTGCAAATGATGTGCC
1 AACTCGAAGGTCTTTTGTT-GCAGATAGCCCTTCTCGCCTTGAGCTATGCTGCAAATGATGTGCC
5775 TTT
65 TTT
5778 CGAAGGTCTT
Statistics
Matches: 381, Mismatches: 65, Indels: 45
0.78 0.13 0.09
Matches are distributed among these distances:
71 38 0.10
72 5 0.01
73 5 0.01
74 3 0.01
77 6 0.02
78 6 0.02
80 67 0.18
81 4 0.01
82 10 0.03
83 149 0.39
84 87 0.23
85 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (83 bp):
AACTCGAAGGTCTTTTGTTGCAGATAGCCCTTCTCGCCTTGAGCTATGCTGCAAATGATGTGCCT
TTGAGCTGAGTGTAATCG
Found at i:5413 original size:71 final size:71
Alignment explanation
Indices: 5297--5440 Score: 243
Period size: 71 Copynumber: 2.0 Consensus size: 71
5287 ATCTTTGAGC
* * *
5297 TGAGTGTAATCGAACTCGAAGTTCTTTTGTTGGCAGATAACCCTTCTCGCATTGAGCTATGCTGC
1 TGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCATTGAGCTATACTAC
5362 AAATGA
66 AAATGA
* *
5368 TGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATATCCCTTCTCGCCTTGAGCTATACTAC
1 TGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCATTGAGCTATACTAC
5433 AAATGA
66 AAATGA
5439 TG
1 TG
5441 TGCCTTTGAG
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (71 bp):
TGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCATTGAGCTATACTAC
AAATGA
Found at i:5645 original size:163 final size:165
Alignment explanation
Indices: 5368--5777 Score: 520
Period size: 163 Copynumber: 2.5 Consensus size: 165
5358 CTGCAAATGA
* * * * *
5368 TGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATATCCCTTCTCGCCTTGAGCTATACTAC
1 TGAGTGTAATCGAACTCGAAGGTC--TTGTTGGCATATAGCCCTTCTTGCCTTGAGCTATGCTGC
* * * * * *
5433 AAATGATGTGCCTTTGAGATGAGTGTAATCGAACTCGAAGGTTTTTGTTGGCAAATAGA-CTTTC
64 AAATGATGTGCCTTTAAGATAACTGTAATCGAACTCGAAGGTCTTTGTTGACAAATA-ACCCTTC
* *
5497 TTGCCCTGAGTTATGCTACAAATGATGTGCCTTTGAGC
128 TAGCCCTGAGTTATGATACAAATGATGTGCCTTTGAGC
* * *
5535 TGAGTGTAATCGAACTTGAAGGTC-T-TTGGCATATAGCCTTTCTTTCCTTGAGCTATGCTGCAA
1 TGAGTGTAATCGAACTCGAAGGTCTTGTTGGCATATAGCCCTTCTTGCCTTGAGCTATGCTGCAA
* * * * *
5598 ATAATGTGCTTTTAAGCTAACTTTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAG
66 ATGATGTGCCTTTAAGATAACTGTAATCGAACTCGAAGGTCTTTGTTGACAAATAACCCTTCTAG
* **
5663 CCTTGAGTTATGATGTAAATGATGTGCCTTTGAGC
131 CCCTGAGTTATGATACAAATGATGTGCCTTTGAGC
* *
5698 TGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCATATAGCCCTTCTTGCCTTGAGTTATGTTGC
1 TGAGTGTAATCGAACTCGAAGGTC--TTGTTGGCATATAGCCCTTCTTGCCTTGAGCTATGCTGC
5763 AAATGATGTGCCTTT
64 AAATGATGTGCCTTT
5778 CGAAGGTCTT
Statistics
Matches: 207, Mismatches: 31, Indels: 10
0.83 0.12 0.04
Matches are distributed among these distances:
162 1 0.00
163 136 0.66
164 1 0.00
166 1 0.00
167 68 0.33
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (165 bp):
TGAGTGTAATCGAACTCGAAGGTCTTGTTGGCATATAGCCCTTCTTGCCTTGAGCTATGCTGCAA
ATGATGTGCCTTTAAGATAACTGTAATCGAACTCGAAGGTCTTTGTTGACAAATAACCCTTCTAG
CCCTGAGTTATGATACAAATGATGTGCCTTTGAGC
Found at i:5865 original size:306 final size:299
Alignment explanation
Indices: 5494--6263 Score: 840
Period size: 320 Copynumber: 2.5 Consensus size: 299
5484 CAAATAGACT
* * **
5494 TTCTTGCCCTGAGTTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTTGAAGGTC
1 TTCTTGCCCTGAGCTATGCTACAAATAATGTGCCTTTGAGCTGAGTGTAATCGAACTCAAAGGTC
* * * * * * *
5559 TTTGGCATATAGCCTTTCTTTCCTTGAGCTATGCTGCAAATAATGTGCTTTTAAGCTAACTTTAA
66 TTTGGCAGATAACCCTTCTTGCCTTAAGCTATACTGCAAATAATGTGCTTTTAAGCTAACTGTAA
* *
5624 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTC-TAGCCTTGAGTTATGATGTAAATGATGT
131 TCGAACTCGAAGGTCTTTG--G-CAGATAACCCTTCTTA-CCTTGAGCTATGATGCAAATGATGT
*
5688 GCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCATATAGCCCTTCTTGCCTTGA
192 GCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC---T-TTGGCAGATAGCCCTTCTTGCCTTGA
* *
5753 GTTATGTTGCAAATGATGTGCCTTTCGAAGGTCTTTAGCAATATCCC
253 GCTATGCTGCAAATGATGTGCCTTTCGAAGGTCTTTAGCAATATCCC
* * *
5800 TTCTTTCCTTGAGCTATGCTGCAAATAATGTGCCTTTGAGCTGAGTGTAATCGAACTCAAAGGTC
1 TTCTTGCCCTGAGCTATGCTACAAATAATGTGCCTTTGAGCTGAGTGTAATCGAACTCAAAGGTC
* * * * * *
5865 TTTGGTAGATAACCCTTCTTGCCTTAAGTTATACTGCAAATGATGTGCTTTTGAGCTGAGTGTAA
66 TTTGGCAGATAACCCTTCTTGCCTTAAGCTATACTGCAAATAATGTGCTTTTAAGCTAACTGTAA
* *
5930 TCGAACTCGAAGGTCTTTGGCAGGTAACCCTTCTTACCTTGAGCTATGCTGCAAATGATGTGCCT
131 TCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTACCTTGAGCTATGATGCAAATGATGTGCCT
* *
5995 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGGTAGCCCTTGTTGCCTTGAGCTATGCT
196 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCT
* * *
6060 GCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCAAATGTCTTTGGCAGCTAGCCC
261 GCAAATGATGTGCCTTT---C-----G-AA--G---------GTCTTTAGCA-ATATCCC
* * * * * *
6120 TTCTTGCCTTGAGCTATACTACAAATGATGTGCCTTTAAGCTGAGTGTAATTGAACTCGAAGGTC
1 TTCTTGCCCTGAGCTATGCTACAAATAATGTGCCTTTGAGCTGAGTGTAATCGAACTCAAAGGTC
* * * * * * * *
6185 TTTGGCAGGTAGCCCTTCTTGCCTTGAGCTATGCTGCAAATAATGTGCCTTTGAGCTGAGTGTAA
66 TTTGGCAGATAACCCTTCTTGCCTTAAGCTATACTGCAAATAATGTGCTTTTAAGCTAACTGTAA
* *
6250 TTGAACTTGAAGGT
131 TCGAACTCGAAGGT
6264 TTTTTGTTAA
Statistics
Matches: 393, Mismatches: 49, Indels: 30
0.83 0.10 0.06
Matches are distributed among these distances:
299 46 0.12
300 1 0.00
302 1 0.00
303 68 0.17
304 3 0.01
306 129 0.33
307 1 0.00
308 2 0.01
310 1 0.00
319 9 0.02
320 132 0.34
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.34
Consensus pattern (299 bp):
TTCTTGCCCTGAGCTATGCTACAAATAATGTGCCTTTGAGCTGAGTGTAATCGAACTCAAAGGTC
TTTGGCAGATAACCCTTCTTGCCTTAAGCTATACTGCAAATAATGTGCTTTTAAGCTAACTGTAA
TCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTACCTTGAGCTATGATGCAAATGATGTGCCT
TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCT
GCAAATGATGTGCCTTTCGAAGGTCTTTAGCAATATCCC
Found at i:5903 original size:80 final size:80
Alignment explanation
Indices: 5777--6263 Score: 733
Period size: 80 Copynumber: 6.1 Consensus size: 80
5767 GATGTGCCTT
* * * * *
5777 TCGAAGGTCTTTAGCA-ATATCCCTTCTTTCCTTGAGCTATGCTGCAAATAATGTGCCTTTGAGC
1 TCGAAGGTCTTTGGCAGGTAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGC
5841 TGAGTGTAATCGAAC
66 TGAGTGTAATCGAAC
* * * * * * * *
5856 TCAAAGGTCTTTGGTAGATAACCCTTCTTGCCTTAAGTTATACTGCAAATGATGTGCTTTTGAGC
1 TCGAAGGTCTTTGGCAGGTAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGC
5921 TGAGTGTAATCGAAC
66 TGAGTGTAATCGAAC
* *
5936 TCGAAGGTCTTTGGCAGGTAACCCTTCTTACCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGC
1 TCGAAGGTCTTTGGCAGGTAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGC
6001 TGAGTGTAATCGAAC
66 TGAGTGTAATCGAAC
*
6016 TCGAAGGTCTTTGGCAGGTAGCCCTTGTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGC
1 TCGAAGGTCTTTGGCAGGTAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGC
6081 TGAGTGTAATCGAAC
66 TGAGTGTAATCGAAC
* * * * * *
6096 TCAAATGTCTTTGGCAGCTAGCCCTTCTTGCCTTGAGCTATACTACAAATGATGTGCCTTTAAGC
1 TCGAAGGTCTTTGGCAGGTAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGC
*
6161 TGAGTGTAATTGAAC
66 TGAGTGTAATCGAAC
*
6176 TCGAAGGTCTTTGGCAGGTAGCCCTTCTTGCCTTGAGCTATGCTGCAAATAATGTGCCTTTGAGC
1 TCGAAGGTCTTTGGCAGGTAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGC
*
6241 TGAGTGTAATTGAAC
66 TGAGTGTAATCGAAC
*
6256 TTGAAGGT
1 TCGAAGGT
6264 TTTTTGTTAA
Statistics
Matches: 370, Mismatches: 37, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
79 13 0.04
80 357 0.96
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (80 bp):
TCGAAGGTCTTTGGCAGGTAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGC
TGAGTGTAATCGAAC
Found at i:7280 original size:98 final size:98
Alignment explanation
Indices: 7098--7306 Score: 303
Period size: 98 Copynumber: 2.1 Consensus size: 98
7088 ACAACTCAAT
* *
7098 GATATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAACTGGGGCGTTTAACCAATT
1 GATATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAACCGGGACGTTTAACCAATT
* *
7163 GCTCTACAGGGACAACTCAAGCTTTATTGTATA
66 GCTCTACAGGAACAACTCAAGCTTTAATGTATA
* * *
7196 GATATTATAATCACCTTTATCAGGTTAGTTGAATCTTATCCATAAAGCCGGGACGTTTAACCAAT
1 GATATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAA-CCGGGACGTTTAACCAAT
* *
7261 TGCTCTAGA-GAACAGCTCAAGCTTTAATGTATA
65 TGCTCTACAGGAACAACTCAAGCTTTAATGTATA
*
7294 TATATATATAATC
1 GATAT-TATAATC
7307 TGGGTATACG
Statistics
Matches: 99, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
98 68 0.69
99 31 0.31
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (98 bp):
GATATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAACCGGGACGTTTAACCAATT
GCTCTACAGGAACAACTCAAGCTTTAATGTATA
Found at i:9923 original size:14 final size:14
Alignment explanation
Indices: 9901--9985 Score: 50
Period size: 14 Copynumber: 5.9 Consensus size: 14
9891 AAAAAGAGAA
* *
9901 AATATTAATATAAT
1 AATAATAATAAAAT
9915 AATAATAATAAAAT
1 AATAATAATAAAAT
*
9929 AAATAGATAACAAAGAT
1 -AATA-ATAATAAA-AT
*
9946 AAATAA-AAGT-TAAT
1 -AATAATAA-TAAAAT
*
9960 AAAAATAATAAAAT
1 AATAATAATAAAAT
9974 AAATAA-AATAAA
1 -AATAATAATAAA
9986 TAAATAAATA
Statistics
Matches: 56, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
13 5 0.09
14 25 0.45
15 11 0.20
16 8 0.14
17 7 0.12
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.26
Consensus pattern (14 bp):
AATAATAATAAAAT
Found at i:9990 original size:17 final size:18
Alignment explanation
Indices: 9907--9998 Score: 77
Period size: 17 Copynumber: 5.1 Consensus size: 18
9897 AGAAAATATT
9907 AATATAATAATAAT-AATAA
1 AATA-AATAA-AATAAATAA
*
9926 AATAAAT-AGATAACA-AA
1 AATAAATAAAATAA-ATAA
* *
9943 GATAAATAAAAGTTAATAA
1 AATAAATAAAA-TAAATAA
9962 AA-ATAATAAAATAAATAA
1 AATA-AATAAAATAAATAA
9980 AATAAAT-AAATAAATAA
1 AATAAATAAAATAAATAA
9997 AA
1 AA
9999 AGGACCAAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
16 2 0.03
17 22 0.37
18 19 0.32
19 17 0.28
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (18 bp):
AATAAATAAAATAAATAA
Found at i:9993 original size:45 final size:45
Alignment explanation
Indices: 9911--9998 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
9901 AATATTAATA
* *
9911 TAATAATAATAATAAAATAAATAGATAACAAAGATAAATAAAAGT
1 TAATAAAAATAATAAAATAAATAAATAACAAAGATAAATAAAAGT
9956 TAATAAAAATAATAAAATAAATAAAATAA-ATAA-ATAAATAAAA
1 TAATAAAAATAATAAAATAAAT-AAATAACA-AAGATAAATAAAA
9999 AGGACCAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
45 32 0.82
46 7 0.18
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (45 bp):
TAATAAAAATAATAAAATAAATAAATAACAAAGATAAATAAAAGT
Found at i:10110 original size:20 final size:20
Alignment explanation
Indices: 10085--10123 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
10075 TTACACAAAC
10085 ATATTTAAAAGGAAAACACA
1 ATATTTAAAAGGAAAACACA
*
10105 ATATTTAAAGGGAAAACAC
1 ATATTTAAAAGGAAAACAC
10124 GTCAATTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.10, G:0.13, T:0.21
Consensus pattern (20 bp):
ATATTTAAAAGGAAAACACA
Found at i:12271 original size:81 final size:81
Alignment explanation
Indices: 12136--12293 Score: 255
Period size: 81 Copynumber: 2.0 Consensus size: 81
12126 TTAAATAGTC
*
12136 GGAGACTCAACAAAGCAACTCCCTATAATAAGAGGATCATTTTGTAACTTTTAATAGTTGAAGAA
1 GGAGACTCAACAAAGCAACTCCCTATAATAAGAGGATCATTTTGTAACTTTTAATAGTTAAAGAA
*
12201 CTCAACAAAGCAACTT
66 CCCAACAAAGCAACTT
* * *
12217 GGAGACTCAACAAAGTAACTCCCTATAATCAA-ATGATCATTTTGTAATTTTTAATAGTTAAAGA
1 GGAGACTCAACAAAGCAACTCCCTATAAT-AAGAGGATCATTTTGTAACTTTTAATAGTTAAAGA
12281 ACCCAACAAAGCA
65 ACCCAACAAAGCA
12294 GCGTCCTATA
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
81 69 0.97
82 2 0.03
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (81 bp):
GGAGACTCAACAAAGCAACTCCCTATAATAAGAGGATCATTTTGTAACTTTTAATAGTTAAAGAA
CCCAACAAAGCAACTT
Found at i:12421 original size:14 final size:11
Alignment explanation
Indices: 12388--12417 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
12378 AGATGTTTCC
12388 CTTTCTTCCAT
1 CTTTCTTCCAT
12399 CTTTCTTCCAT
1 CTTTCTTCCAT
12410 CTTTCTTC
1 CTTTCTTC
12418 TTCCTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.07, C:0.37, G:0.00, T:0.57
Consensus pattern (11 bp):
CTTTCTTCCAT
Found at i:12657 original size:43 final size:42
Alignment explanation
Indices: 12572--12657 Score: 111
Period size: 45 Copynumber: 2.0 Consensus size: 42
12562 GAGTTAAAAG
* *
12572 AAAAATAAAATAACTTCGTTGAATCAAAGGGAGTCCAAAGAAA
1 AAAAATAAAATAACTTAGTTGAATCAAAGAGAGTCC-AAGAAA
*
12615 AAAAATATATAATAACTTATTTGAATCAAAGAGAGTCC-AGAAA
1 AAAAATA-A-AATAACTTAGTTGAATCAAAGAGAGTCCAAGAAA
12658 TTTGAGTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 12 0.32
44 1 0.03
45 25 0.66
ACGTcount: A:0.53, C:0.10, G:0.14, T:0.22
Consensus pattern (42 bp):
AAAAATAAAATAACTTAGTTGAATCAAAGAGAGTCCAAGAAA
Found at i:13157 original size:29 final size:29
Alignment explanation
Indices: 13102--13157 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
13092 TTTTAGGAGG
* **
13102 AAATAAATTTATAAAATTTTAAGAAATGA
1 AAATAAATTAATAAAATAGTAAGAAATGA
13131 AAATAAATTAATAAAAATAGTAA-AAAT
1 AAATAAATTAAT-AAAATAGTAAGAAAT
13158 ATATGATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 15 0.65
30 8 0.35
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.30
Consensus pattern (29 bp):
AAATAAATTAATAAAATAGTAAGAAATGA
Found at i:16333 original size:2 final size:2
Alignment explanation
Indices: 16326--16350 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16316 AACAGTTTTC
16326 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
16351 CATACAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24714 original size:20 final size:19
Alignment explanation
Indices: 24652--24714 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
24642 ATAAATTTAA
24652 AAATTCTAAATTATACCTTT
1 AAATTCTAAATTATACC-TT
* * *
24672 AAATTTTAAATCTAAACCCT
1 AAATTCTAAAT-TATACCTT
*
24692 AAATTCTCAAATTATATCTT
1 AAATTCT-AAATTATACCTT
24712 AAA
1 AAA
24715 CCTTAATCCC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
20 25 0.74
21 9 0.26
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATTCTAAATTATACCTT
Found at i:24929 original size:28 final size:28
Alignment explanation
Indices: 24893--24946 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
24883 AGAAGAAGGT
*
24893 GTTGCCGTTGAGAGAATAAGGTGATATC
1 GTTGCCGTTGAGAGAAGAAGGTGATATC
* *
24921 GTTGTCGTTGAGAGAAGAAGTTGATA
1 GTTGCCGTTGAGAGAAGAAGGTGATA
24947 CAAGAAGGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.30, C:0.07, G:0.33, T:0.30
Consensus pattern (28 bp):
GTTGCCGTTGAGAGAAGAAGGTGATATC
Found at i:27126 original size:30 final size:30
Alignment explanation
Indices: 27087--27153 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
27077 TCGAGAGATA
* *
27087 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAAGATCTTTATGACCTC
27117 TGGATAGTTACCGAAGATCTTTATGACCTC
1 TGGATAGTTACCGAAGATCTTTATGACCTC
27147 TGGATAG
1 TGGATAG
27154 GTCCTTCGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (30 bp):
TGGATAGTTACCGAAGATCTTTATGACCTC
Found at i:28298 original size:43 final size:43
Alignment explanation
Indices: 28245--28330 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
28235 TAAACCAATT
*
28245 TTTTTTTAATAAAACTCGCACATATATTTAACATAGGTTAAAG
1 TTTTTTTAATAAAACTCGCACATATATTTAACACAGGTTAAAG
28288 TTTTTTTAATAAAACTCGCACATATATTTAACACAGGTTAAAG
1 TTTTTTTAATAAAACTCGCACATATATTTAACACAGGTTAAAG
28331 GTAATGTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (43 bp):
TTTTTTTAATAAAACTCGCACATATATTTAACACAGGTTAAAG
Found at i:28730 original size:10 final size:10
Alignment explanation
Indices: 28691--28740 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
28681 TTCATCACAC
28691 CAAATTCTCT
1 CAAATTCTCT
*
28701 CAATTTCTCT
1 CAAATTCTCT
*
28711 CAACTTCTCT
1 CAAATTCTCT
*
28721 CAAATACTCT
1 CAAATTCTCT
* *
28731 TATATTCTCT
1 CAAATTCTCT
28741 GTTTAAGGTA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.26, C:0.30, G:0.00, T:0.44
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:28789 original size:16 final size:17
Alignment explanation
Indices: 28770--28816 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
28760 ACATTTTTAA
*
28770 TATTTTGTA-TTTAATT
1 TATTTAGTATTTTAATT
*
28786 TATTAAGTATTTTAATT
1 TATTTAGTATTTTAATT
*
28803 TATTTAATATTTTA
1 TATTTAGTATTTTA
28817 CTTATATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 7 0.27
17 19 0.73
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (17 bp):
TATTTAGTATTTTAATT
Found at i:28803 original size:22 final size:21
Alignment explanation
Indices: 28762--28808 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
28752 ATTTTATTAC
*
28762 ATTT-TTAATATTTTGTATTT
1 ATTTATTAATATTTTGAATTT
28782 AATTTATTAAGTATTTT-AATTT
1 -ATTTATTAA-TATTTTGAATTT
28804 ATTTA
1 ATTTA
28809 ATATTTTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 9 0.39
22 8 0.35
23 6 0.26
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (21 bp):
ATTTATTAATATTTTGAATTT
Found at i:32626 original size:32 final size:31
Alignment explanation
Indices: 32590--32688 Score: 80
Period size: 31 Copynumber: 3.2 Consensus size: 31
32580 CACCAATTTT
32590 AATTTGATACATGAACTTTAGACAAAAATATC
1 AATTTGATACATGAACTTTAGAC-AAAATATC
* * *
32622 AATTTGACA-ATTAAACTTT-GATTAAAATATC
1 AATTTGATACA-TGAACTTTAGA-CAAAATATC
* *
32653 AATTTAACT-CTTGAACTTTAGATC-AAATATC
1 AATTTGA-TACATGAACTTTAGA-CAAAATATC
32684 AATTT
1 AATTT
32689 AACCCCTTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
31 36 0.67
32 18 0.33
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.37
Consensus pattern (31 bp):
AATTTGATACATGAACTTTAGACAAAATATC
Found at i:32652 original size:31 final size:31
Alignment explanation
Indices: 32603--32691 Score: 99
Period size: 31 Copynumber: 2.8 Consensus size: 31
32593 TTGATACATG
* *
32603 AACTTTAGACAAAAATATCAATTTGACAATTA
1 AACTTTAGA-TAAAATATCAATTTAACAATTA
** *
32635 AACTTT-GATTAAAATATCAATTTAACTCTTG
1 AACTTTAGA-TAAAATATCAATTTAACAATTA
*
32666 AACTTTAGATCAAATATCAATTTAAC
1 AACTTTAGATAAAATATCAATTTAAC
32692 CCCTTAATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
31 41 0.84
32 8 0.16
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.36
Consensus pattern (31 bp):
AACTTTAGATAAAATATCAATTTAACAATTA
Found at i:43264 original size:31 final size:31
Alignment explanation
Indices: 43223--43287 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
43213 TTAATTGCTG
* *
43223 AGGGACTAAAATCGAAT-GAATCAGTAATGTT
1 AGGGACTAAAATCGAATAG-ATCAATAACGTT
*
43254 AGGGATTAAAATCGAATAGATCAATAACGTT
1 AGGGACTAAAATCGAATAGATCAATAACGTT
43285 AGG
1 AGG
43288 ATCATGTATC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 29 0.97
32 1 0.03
ACGTcount: A:0.43, C:0.09, G:0.23, T:0.25
Consensus pattern (31 bp):
AGGGACTAAAATCGAATAGATCAATAACGTT
Found at i:43684 original size:16 final size:16
Alignment explanation
Indices: 43663--43695 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
43653 TAATAAATAA
43663 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
43679 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
43695 A
1 A
43696 AATTTTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:43780 original size:16 final size:16
Alignment explanation
Indices: 43759--43813 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
43749 CATTTAATAA
*
43759 ATAAACGAATACGAAC
1 ATAAACGAACACGAAC
43775 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
*
43791 ATAAATGAACACGAAC
1 ATAAACGAACACGAAC
43807 ATAAACG
1 ATAAACG
43814 TTGGAGACCC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.56, C:0.20, G:0.13, T:0.11
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:44928 original size:24 final size:24
Alignment explanation
Indices: 44901--44949 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
44891 ATAAATGAAT
44901 GAACATAAACGAACATAACCAAAC
1 GAACATAAACGAACATAACCAAAC
*
44925 GAACATAAACGAACATAACCTAAC
1 GAACATAAACGAACATAACCAAAC
44949 G
1 G
44950 TTCACGAACG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.55, C:0.24, G:0.10, T:0.10
Consensus pattern (24 bp):
GAACATAAACGAACATAACCAAAC
Found at i:46736 original size:20 final size:20
Alignment explanation
Indices: 46711--46751 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
46701 AGGAAGAGTT
46711 CATCAGCCTGCCCACCCCAC
1 CATCAGCCTGCCCACCCCAC
*
46731 CATCAGCCTGCCTACCCCAC
1 CATCAGCCTGCCCACCCCAC
46751 C
1 C
46752 TGCAGAGCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.59, G:0.10, T:0.12
Consensus pattern (20 bp):
CATCAGCCTGCCCACCCCAC
Found at i:47328 original size:2 final size:2
Alignment explanation
Indices: 47321--47358 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
47311 TTGTACCAAC
47321 TA TA TA TA 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 TA TA TA TA
47359 GGAGAATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:48637 original size:19 final size:19
Alignment explanation
Indices: 48613--48654 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
48603 CAGACCGATG
48613 CGGGTGACCCGATCCAATC
1 CGGGTGACCCGATCCAATC
48632 CGGGTGACCCGATCCAATC
1 CGGGTGACCCGATCCAATC
48651 CGGG
1 CGGG
48655 GTGTCACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.19, C:0.36, G:0.31, T:0.14
Consensus pattern (19 bp):
CGGGTGACCCGATCCAATC
Found at i:49482 original size:66 final size:66
Alignment explanation
Indices: 49376--49505 Score: 174
Period size: 66 Copynumber: 2.0 Consensus size: 66
49366 TAGGTCCATA
*
49376 AGGAATTACCAGTCGATGTTGAACCTATAAAATGAATTACCAACAGCGACTGAACCTACCAGAGA
1 AGGAATTACCAGTCGATGATGAACCTATAAAATGAATTACCAACAGCGACTGAACCTACCAGAGA
49441 T
66 T
* * ** *
49442 AGGAATTACCGGTCGATGCAT-AACCTATACAA-GTAATTACCCGCAGCGACTGAACCTGCCAGA
1 AGGAATTACCAGTCGATG-ATGAACCTATAAAATG-AATTACCAACAGCGACTGAACCTACCAGA
49505 G
64 G
49506 TCTTCATACC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
65 1 0.02
66 54 0.96
67 1 0.02
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (66 bp):
AGGAATTACCAGTCGATGATGAACCTATAAAATGAATTACCAACAGCGACTGAACCTACCAGAGA
T
Found at i:52801 original size:21 final size:21
Alignment explanation
Indices: 52771--52820 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
52761 TAAAATAAAA
*
52771 TAAAATATAAATAATAATGTTAT
1 TAAAATA-AAAAAATAAT-TTAT
*
52794 TAAAATAAAAAAATAATTTTT
1 TAAAATAAAAAAATAATTTAT
52815 TAAAAT
1 TAAAAT
52821 TCGGACAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 9 0.36
22 9 0.36
23 7 0.28
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
TAAAATAAAAAAATAATTTAT
Found at i:61831 original size:15 final size:15
Alignment explanation
Indices: 61807--61842 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
61797 CCGTAGGACC
* *
61807 ACTACGTCCCGAAGG
1 ACTACATCCCGAAGA
61822 ACTACATCCCGAAGA
1 ACTACATCCCGAAGA
61837 ACTACA
1 ACTACA
61843 ATACCCTCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.36, C:0.33, G:0.17, T:0.14
Consensus pattern (15 bp):
ACTACATCCCGAAGA
Done.