Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002384.1 Hibiscus syriacus cultivar Beakdansim tig00004875_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: 72106
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:12066 original size:36 final size:34
Alignment explanation
Indices: 11985--12123 Score: 170
Period size: 35 Copynumber: 3.9 Consensus size: 34
11975 AGATGAACAA
* *
11985 TTGAATCGAAAGTGCTTATGCTTCCTCCCGTTCAC
1 TTGAATCGAAAGTGC-GATGCTTCCTTCCGTTCAC
* *
12020 TTGAATCGAAAGTGACGATGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTG-CGATGCTTCCTTCCGTTC-AC
*
12056 TTGAATCGAAAGTGCCGATGTTTCCTTCCGTTCAC
1 TTGAATCGAAAGTG-CGATGCTTCCTTCCGTTCAC
* *
12091 TTGAATCGAAAGTGTCGATGATTCCTTTCGTTC
1 TTGAATCGAAAGTG-CGATGCTTCCTTCCGTTC
12124 TTCTTATTCA
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
35 59 0.65
36 32 0.35
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.37
Consensus pattern (34 bp):
TTGAATCGAAAGTGCGATGCTTCCTTCCGTTCAC
Found at i:12101 original size:71 final size:71
Alignment explanation
Indices: 11985--12128 Score: 234
Period size: 71 Copynumber: 2.0 Consensus size: 71
11975 AGATGAACAA
** *
11985 TTGAATCGAAAGTGCTTATGCTTCCTCCCGTTCACTTGAATCGAAAGTGACGATGCTTCCTTTCG
1 TTGAATCGAAAGTGCCGATGCTTCCTCCCGTTCACTTGAATCGAAAGTGACGATGATTCCTTTCG
12050 TTCTTC
66 TTCTTC
* * *
12056 TTGAATCGAAAGTGCCGATGTTTCCTTCCGTTCACTTGAATCGAAAGTGTCGATGATTCCTTTCG
1 TTGAATCGAAAGTGCCGATGCTTCCTCCCGTTCACTTGAATCGAAAGTGACGATGATTCCTTTCG
12121 TTCTTC
66 TTCTTC
12127 TT
1 TT
12129 ATTCACCTTC
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (71 bp):
TTGAATCGAAAGTGCCGATGCTTCCTCCCGTTCACTTGAATCGAAAGTGACGATGATTCCTTTCG
TTCTTC
Found at i:12154 original size:21 final size:21
Alignment explanation
Indices: 12124--12163 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
12114 CCTTTCGTTC
12124 TTCTTATTCA-CCTTCTTTTCT
1 TTCTTATTCATCC-TCTTTTCT
*
12145 TTCTTCTTCATCCTCTTTT
1 TTCTTATTCATCCTCTTTT
12164 ACAAGGTTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.07, C:0.30, G:0.00, T:0.62
Consensus pattern (21 bp):
TTCTTATTCATCCTCTTTTCT
Found at i:18595 original size:137 final size:138
Alignment explanation
Indices: 18341--19321 Score: 976
Period size: 149 Copynumber: 6.9 Consensus size: 138
18331 TAAGGAATTT
* * * * *
18341 CGCCGAGCGCTTCAACATTAAGAGTTGGAAGGGGGACAGAGTTCATGCCGAGCGCTTCCAGTGGG
1 CGCCGAGCGCTTCAACGTT-AGAGTAGGCAGGGAGACAGAGTTCATGCCGAGCGCTTCCAGAGGG
* * * * *
18406 GAGTAGGCCGGATGACCTGATCTTACGCCGGGCGCTCTAATGTATGGGGTAGGCAGGGTAT-T-C
65 GAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCTCTAACGTGTGGAGTAGGCAGGGTATATGC
*
18469 CTATTTTCA
130 CTAATTTCA
* * * * * *
18478 CGCCGAGCGCTTCACCGTTAAGAGTTGGAAGGGGGATAGAGTTCATGCCGAGCGCTTCCAGTGGG
1 CGCCGAGCGCTTCAACGTT-AGAGTAGGCAGGGAGACAGAGTTCATGCCGAGCGCTTCCAGAGGG
* * *
18543 GAGTAGGCAGGATGACTTGATCTTACGCCGGGCGCTCTAACGTGTGGAGTAGGCAGGGTGT-T--
65 GAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCTCTAACGTGTGGAGTAGGCAGGGTATATGC
* *
18605 ATAATATCA
130 CTAATTTCA
* * *
18614 CGCCGAGCACTTCAACGTTGAGAGTAGGCAGGGGGACAGAGTACATGCCGAGCGCTTCCAGAGGG
1 CGCCGAGCGCTTCAACGTT-AGAGTAGGCAGGGAGACAGAGTTCATGCCGAGCGCTTCCAGAGGG
* *
18679 GAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGCTCTAACGTGTGGAGTAGGCCGGGTGAAACA
65 GAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCTCTAACGTGTGGAGTAGGCAGGGT------
* *
18744 AGATGTGCCTTAATGTCA
124 --ATATGCC-TAATTTCA
* *
18762 CGCCGAGCGCTTCAACGTTTAGAGTAGGCAGAGGAGACAGAGTACATGCTGAGCGCTTCCAGAGG
1 CGCCGAGCGCTTCAACG-TTAGAGTAGGCAG-GGAGACAGAGTTCATGCCGAGCGCTTCCAGAGG
* * * *
18827 GAAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGGTCTAACGTGTGGAGTAGGCCGGGTGAAAT
64 GGAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCTCTAACGTGTGGAGTAGGCAGGGT---AT
*
18892 AAGATGTGCCTTAATGTCA
126 ---A--TGCC-TAATTTCA
* *
18911 CGCCGAGCGCTTCAACGTTGAGAGTAGGCAGAGGAGACAGAGTGCATGCCGAGCGCTTCCAAAGG
1 CGCCGAGCGCTTCAACGTT-AGAGTAGGCAG-GGAGACAGAGTTCATGCCGAGCGCTTCCAGAGG
* * *
18976 GGAGTAGGCAGGATGACCTGATCTTACGTCGAGCGCTCTAACGTATGGAGTAGGCAGGG--TGT-
64 GGAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCTCTAACGTGTGGAGTAGGCAGGGTATATG
*
19038 CCCAGA-TTCA
129 CCTA-ATTTCA
* * * * * *
19048 CGCCGAGC-ATCTCAACGTGTAGGGTAAGCAGGGTAGATAGAGTTCATGCCTAGCGCTTCTAGAG
1 CGCCGAGCGCT-TCAACGT-TAGAGTAGGCAGGG-AGACAGAGTTCATGCCGAGCGCTTCCAGAG
* * *
19112 GGGAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGCCCTAACGTGTGGAGTAGGTCGGGTGAAA
63 GGGAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCTCTAACGTGTGGAGTAGG-CAGG-G---
*
19177 TATAATGCGCTTTAATATCA
123 TAT-ATGC-C--TAATTTCA
* * * * * *
19197 GGTCGAGCGCCTCAACGTGTGGGGTAGGCAGGGTAGACAGAGTTCATGCCGAGTGCTTCCAGAGG
1 CGCCGAGCGCTTCAACGT-TAGAGTAGGCAGGG-AGACAGAGTTCATGCCGAGCGCTTCCAGAGG
* *
19262 GGAGTAGGCTGGATGACCTGATCTTACGCCGAGCGC-CTTAACGTGTGGAGTAGGCCGGGT
64 GGAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCTC-TAACGTGTGGAGTAGGCAGGGT
19322 GAAATAAAAT
Statistics
Matches: 729, Mismatches: 76, Indels: 71
0.83 0.09 0.08
Matches are distributed among these distances:
136 121 0.17
137 222 0.30
138 7 0.01
139 2 0.00
144 7 0.01
145 2 0.00
146 1 0.00
147 2 0.00
148 41 0.06
149 324 0.44
ACGTcount: A:0.23, C:0.21, G:0.35, T:0.21
Consensus pattern (138 bp):
CGCCGAGCGCTTCAACGTTAGAGTAGGCAGGGAGACAGAGTTCATGCCGAGCGCTTCCAGAGGGG
AGTAGGCAGGATGACCTGATCTTACGCCGAGCGCTCTAACGTGTGGAGTAGGCAGGGTATATGCC
TAATTTCA
Found at i:19174 original size:286 final size:280
Alignment explanation
Indices: 18341--19322 Score: 1103
Period size: 286 Copynumber: 3.4 Consensus size: 280
18331 TAAGGAATTT
* * * * * *
18341 CGCCGAGCGCTTCAACATTAAGAGTTGGAAGGGGGACAGAGTTCATGCCGAGCGCTTCCAGTGGG
1 CGCCGAGCGCTTCAACGTTGAGAGTAGGCAGGGAGACAGAGTTCATGCCGAGCGCTTCCAGAGGG
* * * * *
18406 GAGTAGGCCGGATGACCTGATCTTACGCCGGGCGCTCTAATGTATGGGGTAGGCAGGGTATTCCT
66 GAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCTCTAACGTATGGAGTAGGCAGGGT-GTCCT
* * * * * *
18471 ATTTTCACGCCGAGCGCTTCACCGTTAAGAGTTGGAAGGGGGATAGAGTTCATGCCGAGCGCTTC
130 A-ATTCACGCCGAGCGCTTCAACGTT-AGAGTAGGCAGGGAGATAGAGTTCATGCCTAGCGCTTC
* * * * *
18536 CAGTGGGGAGTAGGCAGGATGACTTGATCTTACGCCGGGCGCTCTAACGTGTGGAGTAGGCAGG-
193 CAGAGGGGAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGCTCTAACGTGTGGAGTAGGCGGGT
*
18600 G---T--G-T-T--ATAATATCA
258 GAAATAAGATGTGCTTAATATCA
* * *
18614 CGCCGAGCACTTCAACGTTGAGAGTAGGCAGGGGGACAGAGTACATGCCGAGCGCTTCCAGAGGG
1 CGCCGAGCGCTTCAACGTTGAGAGTAGGCAGGGAGACAGAGTTCATGCCGAGCGCTTCCAGAGGG
* * *
18679 GAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGCTCTAACGTGTGGAGTAGGCCGGGTGAAACA
66 GAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCTCTAACGTATGGAGTAGG-C-AG-G-----
* *
18744 AGATGTGCCTTAATGTCACGCCGAGCGCTTCAACGTTTAGAGTAGGCAGAGGAGACAGAGTACAT
123 -G-TGT-CC-TAAT-TCACGCCGAGCGCTTCAACG-TTAGAGTAGGCAG-GGAGATAGAGTTCAT
* *
18809 G-CTGAGCGCTTCCAGAGGGAAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGGTCTAACGTGT
181 GCCT-AGCGCTTCCAGAGGGGAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGCTCTAACGTGT
*
18873 GGAGTAGGCCGGGTGAAATAAGATGTGCCTTAATGTCA
245 GGAGTAGG-CGGGTGAAATAAGATGTG-CTTAATATCA
* *
18911 CGCCGAGCGCTTCAACGTTGAGAGTAGGCAGAGGAGACAGAGTGCATGCCGAGCGCTTCCAAAGG
1 CGCCGAGCGCTTCAACGTTGAGAGTAGGCAG-GGAGACAGAGTTCATGCCGAGCGCTTCCAGAGG
* *
18976 GGAGTAGGCAGGATGACCTGATCTTACGTCGAGCGCTCTAACGTATGGAGTAGGCAGGGTGTCCC
65 GGAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCTCTAACGTATGGAGTAGGCAGGGTGTCCT
* * *
19041 AGATTCACGCCGAGC-ATCTCAACGTGTAGGGTAAGCAGGGTAGATAGAGTTCATGCCTAGCGCT
130 A-ATTCACGCCGAGCGCT-TCAACGT-TAGAGTAGGCAGGG-AGATAGAGTTCATGCCTAGCGCT
* *
19105 TCTAGAGGGGAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGCCCTAACGTGTGGAGTAGGTCG
191 TCCAGAGGGGAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGCTCTAACGTGTGGAGTAGG-CG
*
19170 GGTGAAATATA-ATGCGCTTTAATATCA
255 GGTGAAATA-AGATGTGC-TTAATATCA
* * * * *
19197 GGTCGAGCGCCTCAACGTGTG-GGGTAGGCAGGGTAGACAGAGTTCATGCCGAGTGCTTCCAGAG
1 CGCCGAGCGCTTCAACGT-TGAGAGTAGGCAGGG-AGACAGAGTTCATGCCGAGCGCTTCCAGAG
* * *
19261 GGGAGTAGGCTGGATGACCTGATCTTACGCCGAGCGC-CTTAACGTGTGGAGTAGGCCGGGTG
64 GGGAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCTC-TAACGTATGGAGTAGGCAGGGTG
19323 AAATAAAATG
Statistics
Matches: 606, Mismatches: 64, Indels: 65
0.82 0.09 0.09
Matches are distributed among these distances:
273 105 0.17
274 1 0.00
275 1 0.00
276 1 0.00
282 2 0.00
283 4 0.01
284 31 0.05
285 85 0.14
286 237 0.39
287 10 0.02
288 3 0.00
289 1 0.00
290 1 0.00
292 1 0.00
293 1 0.00
294 1 0.00
295 1 0.00
296 1 0.00
297 38 0.06
298 81 0.13
ACGTcount: A:0.23, C:0.21, G:0.35, T:0.21
Consensus pattern (280 bp):
CGCCGAGCGCTTCAACGTTGAGAGTAGGCAGGGAGACAGAGTTCATGCCGAGCGCTTCCAGAGGG
GAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCTCTAACGTATGGAGTAGGCAGGGTGTCCTA
ATTCACGCCGAGCGCTTCAACGTTAGAGTAGGCAGGGAGATAGAGTTCATGCCTAGCGCTTCCAG
AGGGGAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGCTCTAACGTGTGGAGTAGGCGGGTGAA
ATAAGATGTGCTTAATATCA
Found at i:19226 original size:435 final size:433
Alignment explanation
Indices: 18341--19328 Score: 1224
Period size: 435 Copynumber: 2.3 Consensus size: 433
18331 TAAGGAATTT
* * * * * * *
18341 CGCCGAGCGCTTCAACAT-TAAGAGTTGGAAGGG-GGACAGAGTTCATGCCGAGCGCTTCCAGTG
1 CGCCGAGCGCCTCAACGTGT-AGAGTAGGCAGGGTAGACAGAGTACATGCCGAGCGCTTCCAGAG
* * * * * * *
18404 GGGAGTAGGCCGGATGACCTGATCTTACGCCGGGCG-CTCTAATGTATGGGGTAGG-CAGG-G--
65 GGAAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCCT-TAACGTGTGGAGTAGGCCGGGTGAA
* * * * * * *
18464 -T---AT-T-CC-TATTTTCACGCCGAGCGCTTCACCGTTAAGAGTTGGAAGGGGGATAGAGTTC
129 ATAAGATGTGCCTTAATGTCACGCCGAGCGCTTCAACGTTAAGAGTAGGAAGGGAGACAGAGTGC
** * * *
18522 ATGCCGAGCGCTTCCAGTGGGGAGTAGGCAGGATGACTTGATCTTACGCCGGGCGCTCTAACGTG
194 ATGCCGAGCGCTTCCAAAGGGGAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCTCTAACGTA
* * * *
18587 TGGAGTAGGCAGGGTGTTATAATATCACGCCGAGCACTTCAACGTTGAGAGTAGGCAGGGGGACA
259 TGGAGTAGGCAGGGTGTCACAATATCACGCCGAGCACTTCAACGTTGAGAGTAAGCAGGGAGACA
*
18652 GAGTACATGCCGAGCGCTTCCAGAGGGGAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGCTCT
324 GAGTACATGCCGAGCGCTTCCAGAGGGGAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGCCCT
* *
18717 AACGTGTGGAGTAGGCCGGGTGAAACAAGATGTGCCTTAATGTCA
389 AACGTGTGGAGTAGGCCGGGTGAAACAAGATGCGCCTTAATATCA
* * *
18762 CGCCGAGCGCTTCAACGTTTAGAGTAGGCAGAGG-AGACAGAGTACATGCTGAGCGCTTCCAGAG
1 CGCCGAGCGCCTCAACGTGTAGAGTAGGCAG-GGTAGACAGAGTACATGCCGAGCGCTTCCAGAG
* *
18826 GGAAGTAGGCAGGATGACCTGGTCTTACGCCGAGCG-GTCTAACGTGTGGAGTAGGCCGGGTGAA
65 GGAAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCCT-TAACGTGTGGAGTAGGCCGGGTGAA
* *
18890 ATAAGATGTGCCTTAATGTCACGCCGAGCGCTTCAACGTTGAGAGTAGGCAGAGGAGACAGAGTG
129 ATAAGATGTGCCTTAATGTCACGCCGAGCGCTTCAACGTTAAGAGTAGGAAG-GGAGACAGAGTG
*
18955 CATGCCGAGCGCTTCCAAAGGGGAGTAGGCAGGATGACCTGATCTTACGTCGAGCGCTCTAACGT
193 CATGCCGAGCGCTTCCAAAGGGGAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCTCTAACGT
* *
19020 ATGGAGTAGGCAGGGTGTCCCAGAT-TCACGCCGAGCA-TCTCAACG-TGTAGGGTAAGCAGGGT
258 ATGGAGTAGGCAGGGTGTCACA-ATATCACGCCGAGCACT-TCAACGTTG-AGAGTAAGCAGGG-
* * * *
19082 AGATAGAGTTCATGCCTAGCGCTTCTAGAGGGGAGTAGGCAGGATGACCTGGTCTTACGCCGAGC
319 AGACAGAGTACATGCCGAGCGCTTCCAGAGGGGAGTAGGCAGGATGACCTGGTCTTACGCCGAGC
* * *
19147 GCCCTAACGTGTGGAGTAGGTCGGGTGAAATATA-ATGCGCTTTAATATCA
384 GCCCTAACGTGTGGAGTAGGCCGGGTGAAACA-AGATGCGCCTTAATATCA
* * * * * *
19197 GGTCGAGCGCCTCAACGTGTGGGGTAGGCAGGGTAGACAGAGTTCATGCCGAGTGCTTCCAGAGG
1 CGCCGAGCGCCTCAACGTGTAGAGTAGGCAGGGTAGACAGAGTACATGCCGAGCGCTTCCAGAGG
* *
19262 GGAGTAGGCTGGATGACCTGATCTTACGCCGAGCGCCTTAACGTGTGGAGTAGGCCGGGTGAAAT
66 GAAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCCTTAACGTGTGGAGTAGGCCGGGTGAAAT
19327 AA
131 AA
19329 AATGATTTAG
Statistics
Matches: 486, Mismatches: 60, Indels: 28
0.85 0.10 0.05
Matches are distributed among these distances:
421 26 0.05
422 76 0.16
423 3 0.01
424 1 0.00
427 1 0.00
430 2 0.00
431 1 0.00
432 2 0.00
433 36 0.07
434 118 0.24
435 218 0.45
436 2 0.00
ACGTcount: A:0.24, C:0.21, G:0.35, T:0.21
Consensus pattern (433 bp):
CGCCGAGCGCCTCAACGTGTAGAGTAGGCAGGGTAGACAGAGTACATGCCGAGCGCTTCCAGAGG
GAAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCCTTAACGTGTGGAGTAGGCCGGGTGAAAT
AAGATGTGCCTTAATGTCACGCCGAGCGCTTCAACGTTAAGAGTAGGAAGGGAGACAGAGTGCAT
GCCGAGCGCTTCCAAAGGGGAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCTCTAACGTATG
GAGTAGGCAGGGTGTCACAATATCACGCCGAGCACTTCAACGTTGAGAGTAAGCAGGGAGACAGA
GTACATGCCGAGCGCTTCCAGAGGGGAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGCCCTAA
CGTGTGGAGTAGGCCGGGTGAAACAAGATGCGCCTTAATATCA
Found at i:23309 original size:18 final size:18
Alignment explanation
Indices: 23288--23329 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
23278 CCGTCGTCCA
23288 ATTTG-GAAGGTTTATACT
1 ATTTGTGAAGG-TTATACT
* *
23306 ATTTGTTAAGGTTATATT
1 ATTTGTGAAGGTTATACT
23324 ATTTGT
1 ATTTGT
23330 AATCTTACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.26, C:0.02, G:0.19, T:0.52
Consensus pattern (18 bp):
ATTTGTGAAGGTTATACT
Found at i:23318 original size:19 final size:18
Alignment explanation
Indices: 23294--23329 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
23284 TCCAATTTGG
23294 AAGGTTTATACTATTTGTT
1 AAGG-TTATACTATTTGTT
*
23313 AAGGTTATATTATTTGT
1 AAGGTTATACTATTTGT
23330 AATCTTACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.28, C:0.03, G:0.17, T:0.53
Consensus pattern (18 bp):
AAGGTTATACTATTTGTT
Found at i:23399 original size:5 final size:5
Alignment explanation
Indices: 23389--23431 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
23379 AAATTCTATG
*
23389 ATTTT ATTTT ATTTT ATTTT ATTAGT A-TTT ATTTT AATTTT AT
1 ATTTT ATTTT ATTTT ATTTT ATT-TT ATTTT ATTTT -ATTTT AT
23432 AAAGAGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 2 0.06
5 24 0.73
6 7 0.21
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (5 bp):
ATTTT
Found at i:23932 original size:40 final size:40
Alignment explanation
Indices: 23886--23967 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
23876 ATTTTGATAA
*
23886 ATTAAAATGACATTTTGAAGATGAGAATAAAATAAACTAC
1 ATTAAAATGACATTTTGAAGATAAGAATAAAATAAACTAC
23926 ATTAAAATGACATTTTGAAGATAAGAATAAAATAAACTAC
1 ATTAAAATGACATTTTGAAGATAAGAATAAAATAAACTAC
23966 AT
1 AT
23968 AATACGAACG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.54, C:0.07, G:0.11, T:0.28
Consensus pattern (40 bp):
ATTAAAATGACATTTTGAAGATAAGAATAAAATAAACTAC
Found at i:26773 original size:17 final size:17
Alignment explanation
Indices: 26747--26779 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
26737 TAAAATAATG
*
26747 GTAAATTTTTAATTTGA
1 GTAAAATTTTAATTTGA
26764 GTAAAATTTTAATTTG
1 GTAAAATTTTAATTTG
26780 GTTATTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (17 bp):
GTAAAATTTTAATTTGA
Found at i:28089 original size:19 final size:19
Alignment explanation
Indices: 28065--28104 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
28055 ATAAAGATTC
* * *
28065 TTGTAGAGAATGACGTTTA
1 TTGTAGAAAATAACATTTA
28084 TTGTAGAAAATAACATTTA
1 TTGTAGAAAATAACATTTA
28103 TT
1 TT
28105 TTACAGATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (19 bp):
TTGTAGAAAATAACATTTA
Found at i:31146 original size:21 final size:21
Alignment explanation
Indices: 31095--31147 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
31085 ATTCTGACTA
31095 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* * *
31116 TTGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
31137 TCGCAATGCGA
1 TCGCATTGCGA
31148 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:31298 original size:40 final size:40
Alignment explanation
Indices: 31137--31310 Score: 199
Period size: 40 Copynumber: 4.3 Consensus size: 40
31127 TTTTCCTAAT
**
31137 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGA-AAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAA--TACATAAA
* * *
31178 TCGCAATGCGATTACGTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATACATAAA
* *
31218 TCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATACATAAA
* * *
31258 TCGTAATACAAATACGTAAATCGCAACGCGAAT-CTATAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATAC-ATAAA
* *
31298 TCACAACGCGAAT
1 TCGCAATGCGAAT
31311 CTGACTATCG
Statistics
Matches: 115, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
39 2 0.02
40 83 0.72
41 30 0.26
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAACGCGAATACATAAA
Found at i:31298 original size:60 final size:60
Alignment explanation
Indices: 31137--31310 Score: 208
Period size: 60 Copynumber: 2.9 Consensus size: 60
31127 TTTTCCTAAT
* * * *
31137 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGA-AAATCGCAATGCGATTACGTAAA
1 TCGCAATACAAATACGTAAATCGCAACGCGAATCT--ATAAATCGCAATGCGAATACGTAAA
* * * *
31198 TCGCAATGCGAATACGTAAATCGCAATGCGAATAC-GTAAATCGCAATGCGAATACGTAAA
1 TCGCAATACAAATACGTAAATCGCAACGCGAAT-CTATAAATCGCAATGCGAATACGTAAA
* * *
31258 TCGTAATACAAATACGTAAATCGCAACGCGAATCTATAAATCACAACGCGAAT
1 TCGCAATACAAATACGTAAATCGCAACGCGAATCTATAAATCGCAATGCGAAT
31311 CTGACTATCG
Statistics
Matches: 99, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
59 1 0.01
60 66 0.67
61 32 0.32
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (60 bp):
TCGCAATACAAATACGTAAATCGCAACGCGAATCTATAAATCGCAATGCGAATACGTAAA
Found at i:31299 original size:20 final size:20
Alignment explanation
Indices: 31137--31290 Score: 218
Period size: 20 Copynumber: 7.7 Consensus size: 20
31127 TTTTCCTAAT
31137 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
31157 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
31178 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
31198 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
31218 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
31238 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
31258 TCGTAATACAAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
31278 TCGCAACGCGAAT
1 TCGCAATGCGAAT
31291 CTATAAATCA
Statistics
Matches: 116, Mismatches: 17, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
20 101 0.87
21 15 0.13
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:31324 original size:20 final size:20
Alignment explanation
Indices: 31277--31343 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
31267 AAATACGTAA
31277 ATCGCAACGCGAATCT-A-T
1 ATCGCAACGCGAATCTGACT
*
31295 AAATCACAACGCGAATCTGACT
1 --ATCGCAACGCGAATCTGACT
* *
31317 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGAATCTGACT
31337 ATCGCAA
1 ATCGCAA
31344 TACTGAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
20 39 0.95
21 1 0.02
22 1 0.02
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAATCTGACT
Found at i:34381 original size:20 final size:19
Alignment explanation
Indices: 34356--34463 Score: 117
Period size: 20 Copynumber: 5.5 Consensus size: 19
34346 CAACGCGGAA
*
34356 ATCGCAACGCGAATATGACC
1 ATCGCAACGCGAA-ATGACT
*
34376 ATCGCAACACGAAAATGACT
1 ATCGCAACGCG-AAATGACT
* *
34396 ATCGCAATGCGGAATTGACT
1 ATCGCAACGC-GAAATGACT
34416 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
* **
34436 ATCGCAACGAGAAATGAAA
1 ATCGCAACGCGAAATGACT
34455 ATCGCAACG
1 ATCGCAACG
34464 AGTGAATCGC
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
19 16 0.21
20 57 0.75
21 3 0.04
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:34553 original size:14 final size:14
Alignment explanation
Indices: 34534--34587 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
34524 CATTTTCGCA
34534 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
34548 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
34565 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
34581 TTGCGAT
1 TTGCGAT
34588 AGTCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 13 0.39
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:34569 original size:33 final size:33
Alignment explanation
Indices: 34512--34596 Score: 143
Period size: 33 Copynumber: 2.5 Consensus size: 33
34502 TTTAGTTTCG
34512 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
34546 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
**
34579 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
34597 CGCGTTGTGG
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
33 35 0.71
34 14 0.29
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:34732 original size:14 final size:14
Alignment explanation
Indices: 34713--34749 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
34703 CATCAATTAA
34713 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
34727 ACAAATCATCTTTT
1 ACAAATCAACATTT
34741 ACAAATCAA
1 ACAAATCAA
34750 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:36189 original size:42 final size:42
Alignment explanation
Indices: 36122--36213 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
36112 GTGAATCGGG
* * *
36122 CTCTAGAATGTTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
* ** *
36164 CTCTTGAATGGTGGGAGGGGA-CTCTTGAGGGATGATAGGGGC
1 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGGGGC
36206 CTCTTGAA
1 CTCTTGAA
36214 CGATAGGGGA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 38 0.90
43 4 0.10
ACGTcount: A:0.22, C:0.17, G:0.36, T:0.25
Consensus pattern (42 bp):
CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
Found at i:36240 original size:42 final size:42
Alignment explanation
Indices: 36133--36240 Score: 103
Period size: 42 Copynumber: 2.6 Consensus size: 42
36123 TCTAGAATGT
* * * *
36133 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAATGG
1 TGGGAGAGGA-CTCTTGAACGATGACAGGGGCCTCTTGAACGA
* ** *
36175 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGA
*
36217 TAGGG-GAGGTCTCTTGAACGATGA
1 T-GGGAGAGGACTCTTGAACGATGA
36241 AAGGTGAGTC
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
42 47 0.89
43 6 0.11
ACGTcount: A:0.22, C:0.17, G:0.38, T:0.23
Consensus pattern (42 bp):
TGGGAGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGA
Found at i:36747 original size:20 final size:20
Alignment explanation
Indices: 36724--36830 Score: 151
Period size: 20 Copynumber: 5.3 Consensus size: 20
36714 GAAACTTAAA
*
36724 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
36744 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
36764 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
* **
36784 ATCGCAATGTGAATTTGACT
1 ATCGCAATGCGAAAATGACT
* **
36804 ATCGCAATACGAATTTGACT
1 ATCGCAATGCGAAAATGACT
36824 ATCGCAA
1 ATCGCAA
36831 CGAGAGAATC
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 81 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:36929 original size:20 final size:20
Alignment explanation
Indices: 36878--36935 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
36868 ATTCTTTCGT
** *
36878 TGCGATAGTCAAATTCGCAT
1 TGCGATAGTCATTTTCGCAA
*
36898 TGCGATAGTCATTTTTGCAA
1 TGCGATAGTCATTTTCGCAA
36918 TGCGATAGTCATTTTCGC
1 TGCGATAGTCATTTTCGC
36936 GTTGTGATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (20 bp):
TGCGATAGTCATTTTCGCAA
Found at i:37009 original size:20 final size:20
Alignment explanation
Indices: 36982--37033 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
36972 GCGATTCTCT
36982 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
37002 CGTTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
37022 TATTGCGATAGT
1 CATTGCGATAGT
37034 AAACTATTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.40
Consensus pattern (20 bp):
CATTGCGATAGTCATTTTCG
Found at i:38928 original size:20 final size:20
Alignment explanation
Indices: 38903--39013 Score: 89
Period size: 20 Copynumber: 5.6 Consensus size: 20
38893 TCTTAAACTT
38903 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
38923 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
38943 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** * **
38963 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
*** *
38983 ACTTTCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
39002 AAAATCGCAACA
1 AAAATCGCAACA
39014 ACAGAATCGC
Statistics
Matches: 79, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
19 11 0.14
20 68 0.86
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:39414 original size:22 final size:22
Alignment explanation
Indices: 39350--39415 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
39340 TGACCGTGAA
* *
39350 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
* *
39372 TGATATCGTCGGAGATAGGGAC
1 TGATTTCGTCGGAGATGGGGAC
*
39394 TGATTTCGTCGGATATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
39416 AGATGTCGCT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.23, C:0.15, G:0.36, T:0.26
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:39634 original size:20 final size:20
Alignment explanation
Indices: 39611--39683 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
39601 CGATAGTCAG
*
39611 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
39631 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
39651 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
39671 AATCGCATTGCGA
1 ATTCGCATTGCGA
39684 ATCTGGAAAC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:44298 original size:18 final size:18
Alignment explanation
Indices: 44274--44320 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
44264 GTCACAACCC
44274 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
* * *
44292 TACCCGACCCAACCTGTT
1 GACCCGACCCGACCCGTT
*
44310 GACCCAACCCG
1 GACCCGACCCG
44321 TTGACCCGAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.49, G:0.17, T:0.13
Consensus pattern (18 bp):
GACCCGACCCGACCCGTT
Found at i:44313 original size:13 final size:13
Alignment explanation
Indices: 44297--44339 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
44287 CCGTTTACCC
*
44297 GACCCAACCTGTT
1 GACCCAACCCGTT
44310 GACCCAACCCGTT
1 GACCCAACCCGTT
*
44323 GACCCGACCCGTT
1 GACCCAACCCGTT
44336 GACC
1 GACC
44340 GTTGACCGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.21, C:0.44, G:0.19, T:0.16
Consensus pattern (13 bp):
GACCCAACCCGTT
Found at i:46814 original size:24 final size:23
Alignment explanation
Indices: 46787--46873 Score: 111
Period size: 24 Copynumber: 3.7 Consensus size: 23
46777 ATTTCCGAAT
46787 TGAATTCTGTTCTGATACGTTATC
1 TGAATTCTGTTCTGATAC-TTATC
* *
46811 TGAATTCTGTTCTGATTCTGATC
1 TGAATTCTGTTCTGATACTTATC
* *
46834 TGGATTCTGTTCTGATATCTTATA
1 TGAATTCTGTTCTGATA-CTTATC
*
46858 TGAATTCTGTTTTGAT
1 TGAATTCTGTTCTGAT
46874 TTCTGATATC
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
23 19 0.35
24 35 0.65
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.49
Consensus pattern (23 bp):
TGAATTCTGTTCTGATACTTATC
Found at i:46824 original size:12 final size:12
Alignment explanation
Indices: 46787--46878 Score: 59
Period size: 12 Copynumber: 7.8 Consensus size: 12
46777 ATTTCCGAAT
46787 TGAATTCTGTTC
1 TGAATTCTGTTC
*
46799 TG-ATAC-GTTATC
1 TGAATTCTG-T-TC
46811 TGAATTCTGTTC
1 TGAATTCTGTTC
*
46823 TG-ATTCTGATC
1 TGAATTCTGTTC
*
46834 TGGATTCTGTTC
1 TGAATTCTGTTC
*
46846 TG-ATATCT-TATA
1 TGAAT-TCTGT-TC
*
46858 TGAATTCTGTTT
1 TGAATTCTGTTC
*
46870 TGATTTCTG
1 TGAATTCTG
46879 ATATCTCCGT
Statistics
Matches: 64, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
10 1 0.02
11 17 0.27
12 38 0.59
13 7 0.11
14 1 0.02
ACGTcount: A:0.18, C:0.14, G:0.17, T:0.50
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:46841 original size:47 final size:48
Alignment explanation
Indices: 46790--46880 Score: 141
Period size: 47 Copynumber: 1.9 Consensus size: 48
46780 TCCGAATTGA
*
46790 ATTCTGTTCTGATA-CGTTATCTGAATTCTGTTCTGA-TTCTGATCTGG
1 ATTCTGTTCTGATATC-TTATATGAATTCTGTTCTGATTTCTGATCTGG
*
46837 ATTCTGTTCTGATATCTTATATGAATTCTGTTTTGATTTCTGAT
1 ATTCTGTTCTGATATCTTATATGAATTCTGTTCTGATTTCTGAT
46881 ATCTCCGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
47 32 0.80
48 8 0.20
ACGTcount: A:0.19, C:0.14, G:0.16, T:0.51
Consensus pattern (48 bp):
ATTCTGTTCTGATATCTTATATGAATTCTGTTCTGATTTCTGATCTGG
Found at i:49809 original size:31 final size:31
Alignment explanation
Indices: 49774--50088 Score: 567
Period size: 31 Copynumber: 10.2 Consensus size: 31
49764 GGTCACAATA
*
49774 TAAACTATTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* * *
49805 TAAACTGTTCATATATGTCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
49836 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
49867 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
49898 TAAACTGTTCATATATGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
49929 TAAACTGTTCATATGTGTCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
49960 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
49991 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
50022 TAAATTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
50053 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
50084 TAAAC
1 TAAAC
50089 CCTCGACTCT
Statistics
Matches: 271, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 271 1.00
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.39
Consensus pattern (31 bp):
TAAACTGTTCATATGTGCCTTTAAACATATG
Found at i:49943 original size:15 final size:15
Alignment explanation
Indices: 49923--50006 Score: 50
Period size: 15 Copynumber: 5.5 Consensus size: 15
49913 TGCCTTTAAA
49923 CATATGTAAACTGTT
1 CATATGTAAACTGTT
**
49938 CATATGT-GTCT-TT
1 CATATGTAAACTGTT
49951 AAACATATGTAAACTGTT
1 ---CATATGTAAACTGTT
**
49969 CATATGT-GCCT-TT
1 CATATGTAAACTGTT
49982 AAACATATGTAAACTGTT
1 ---CATATGTAAACTGTT
50000 CATATGT
1 CATATGT
50007 GCCTTTAAAC
Statistics
Matches: 51, Mismatches: 8, Indels: 20
0.65 0.10 0.25
Matches are distributed among these distances:
13 4 0.08
14 4 0.08
15 21 0.41
16 14 0.27
17 4 0.08
18 4 0.08
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.40
Consensus pattern (15 bp):
CATATGTAAACTGTT
Found at i:50706 original size:64 final size:64
Alignment explanation
Indices: 50598--50774 Score: 223
Period size: 64 Copynumber: 2.8 Consensus size: 64
50588 TAATGAAGGT
* * ** ** * *
50598 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGT-AATATTGATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT-GTCAATATTAATGGG
* * *
50662 ATGCATCGATGCACTCCTTATGCATCGATGCACCG-ATTGCATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGAATTGCATTCGATGTGTCAATATTAATGGG
50726 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT
50775 CTTTATTTTA
Statistics
Matches: 98, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
63 3 0.03
64 95 0.97
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.31
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTGTCAATATTAATGGG
Found at i:50795 original size:64 final size:63
Alignment explanation
Indices: 50661--50822 Score: 202
Period size: 64 Copynumber: 2.5 Consensus size: 63
50651 ATATTGATGG
* * *
50661 GATGCATCGATGCACTCCTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAATGG
1 GATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCGATGTTTCACTATTAAAGA
* *
50725 GATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTCTTTA-TTTTAAA-A
1 GATGCATCGATGCACTACTTATGCATCGATGCACG-ATTGCATTCGATGT-TTCACTATTAAAGA
** *
50788 GAGTGCATCGATGCACTACCAATGCATCGGTGCAC
1 GA-TGCATCGATGCACTACTTATGCATCGATGCAC
50823 ATTCAAACAA
Statistics
Matches: 87, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
63 4 0.05
64 80 0.92
65 3 0.03
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (63 bp):
GATGCATCGATGCACTACTTATGCATCGATGCACGATTGCATTCGATGTTTCACTATTAAAGA
Found at i:53597 original size:23 final size:23
Alignment explanation
Indices: 53571--53631 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
53561 CTCATATAAA
*
53571 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* * *
53594 TGCACCGTAGTGCCGCGTAGAGT
1 TGCACCGTAGTGCCACATAGAAT
53617 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
53632 TATAATAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:53773 original size:103 final size:103
Alignment explanation
Indices: 53647--53967 Score: 633
Period size: 103 Copynumber: 3.1 Consensus size: 103
53637 TAATGTCCAT
53647 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
53712 GACTTCACACATGTTCCAAAGAATACATATATGTCTCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
53750 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
53815 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
53853 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
53918 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
53956 AAGGACCACATA
1 AAGGACCACATA
53968 GACCCTCGAC
Statistics
Matches: 217, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 217 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:55439 original size:21 final size:21
Alignment explanation
Indices: 55415--55459 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
55405 TTTTGTTCGT
*
55415 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
55436 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
55457 TTG
1 TTG
55460 CCCAGAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:56990 original size:3 final size:3
Alignment explanation
Indices: 56982--57018 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
56972 TTAATATTAG
*
56982 TAA TAA TAA TAA TAA TAA TAA TAC TAA -AA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
57019 AAAAAGACCC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:59879 original size:28 final size:31
Alignment explanation
Indices: 59823--59880 Score: 77
Period size: 29 Copynumber: 1.9 Consensus size: 31
59813 CGATGGAGAC
*
59823 ATGGAGATTACACGAAAAAGATTGAAGAATGG
1 ATGGAGATTACAC-AAAAAGAGTGAAGAATGG
59855 ATGGAGATT-CA-AAAAAGAGTG-AGAAT
1 ATGGAGATTACACAAAAAGAGTGAAGAAT
59881 ATACGAGTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 5 0.20
29 9 0.36
31 2 0.08
32 9 0.36
ACGTcount: A:0.48, C:0.05, G:0.28, T:0.19
Consensus pattern (31 bp):
ATGGAGATTACACAAAAAGAGTGAAGAATGG
Found at i:61384 original size:107 final size:108
Alignment explanation
Indices: 61244--61526 Score: 379
Period size: 107 Copynumber: 2.6 Consensus size: 108
61234 AAACGGTAAG
* * *
61244 AAAATAAGTTAATTACTTATTTTGTTATTAATATTATGAACATATTATGTTACACCTAAAATGTT
1 AAAATAAGTTAATTACTTATTTTGTTATAAATATTATCAACATATTAGGTTACACCTAAAATGTT
* *
61309 ACCAAAATTTAAGTTGATGAGGCCTTAGAAATCACACGATAAA
66 ACCAAAATTTAAGCTGATGAGGCCTTAGAAATCACACGACAAA
* *
61352 AAAATAAGTTAATTA-TTATTTTGTTATCAATATTATCAACATATTAGGTTGCACCTAAAATGTT
1 AAAATAAGTTAATTACTTATTTTGTTATAAATATTATCAACATATTAGGTTACACCTAAAATGTT
* ** *
61416 ACCAAAGTTTAAGCTGATGAGGCCTTAGAAATTTCACGACAAC
66 ACCAAAATTTAAGCTGATGAGGCCTTAGAAATCACACGACAAA
* * * ** * *
61459 AAAATATGTTAAATACGTATTTTGTTATAAATAAAGATTAACATATTAGGTTACGCCTAATAATG
1 AAAATAAGTTAATTACTTATTTTGTTATAAAT-ATTATCAACATATTAGGTTACACCTAA-AATG
61524 TTA
64 TTA
61527 TTGTGAATAA
Statistics
Matches: 153, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
107 95 0.62
108 29 0.19
109 22 0.14
110 7 0.05
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (108 bp):
AAAATAAGTTAATTACTTATTTTGTTATAAATATTATCAACATATTAGGTTACACCTAAAATGTT
ACCAAAATTTAAGCTGATGAGGCCTTAGAAATCACACGACAAA
Found at i:62302 original size:20 final size:20
Alignment explanation
Indices: 62279--62322 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
62269 CGAAAGTGTC
62279 GATATTTATACGAAAATATT
1 GATATTTATACGAAAATATT
* * *
62299 GATATTTGTAGGAAAGTATT
1 GATATTTATACGAAAATATT
62319 GATA
1 GATA
62323 CTTACAACCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.02, G:0.18, T:0.39
Consensus pattern (20 bp):
GATATTTATACGAAAATATT
Found at i:66227 original size:64 final size:63
Alignment explanation
Indices: 66159--66314 Score: 163
Period size: 63 Copynumber: 2.5 Consensus size: 63
66149 TTGAAGGTGT
** ***
66159 ATCGATGCATTGGTAATGCATCGATGCACTCTTTTAA-AATAGAAACATCGAATGCA-ATTAGTG
1 ATCGATGCATAAGTAATGCATCGATGCA-TCCAGTAATAATA-AAACATCGAATGCATATTA-TG
66222 C
63 C
* * * *
66223 ATCGATGCAGAAGTCATGCATCGATGCATCCAGTAATAATACAACATCGAATGCATTTTATGC
1 ATCGATGCATAAGTAATGCATCGATGCATCCAGTAATAATAAAACATCGAATGCATATTATGC
* * *
66286 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAATGCATCGATGCAT
66315 ACCCTCATTA
Statistics
Matches: 76, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
63 45 0.59
64 31 0.41
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (63 bp):
ATCGATGCATAAGTAATGCATCGATGCATCCAGTAATAATAAAACATCGAATGCATATTATGC
Found at i:66962 original size:149 final size:149
Alignment explanation
Indices: 66769--67083 Score: 560
Period size: 149 Copynumber: 2.1 Consensus size: 149
66759 GGGTAGAGGG
* *
66769 TCTATGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
* *
66834 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATCCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
66899 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
66918 TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
66983 ACTTGATCCCTAGTATATGTATATGATCCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATCCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
*
67048 TATGGTACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
67067 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
67084 TGCATTTATA
Statistics
Matches: 159, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
148 1 0.01
149 158 0.99
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATCCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:69790 original size:19 final size:19
Alignment explanation
Indices: 69766--69804 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
69756 TCGAATGCAT
69766 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
69785 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
69804 T
1 T
69805 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:69821 original size:65 final size:64
Alignment explanation
Indices: 69703--69912 Score: 212
Period size: 65 Copynumber: 3.2 Consensus size: 64
69693 TATTCAAAGG
** *
69703 CATGCATCGATGCATC-AGTCCATGCATCGATGCATCGATGAAT-TAATT-GAACATCGAATGCA
1 CATGCATCGATGCA-CAAG-CCATGCATCGATGCATC-A-GAATATTTTTCAAACATCGAATGCA
*
69765 TTC
62 TTT
* *** *
69768 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATA-TTTTCAAAACATCGAATGCATT
1 CATGCATCGATGCACAAGCCATGCATCGATGCA-TCAGAATATTTTTC-AAACATCGAATGCATT
69832 T
64 T
* * ** *
69833 GATGCATCGATACACAAGCCATGCATCGATGCATCAGGCTATTTTTCAAACATTGAATGCATTT
1 CATGCATCGATGCACAAGCCATGCATCGATGCATCAGAATATTTTTCAAACATCGAATGCATTT
69897 CATGCATCGATGCACA
1 CATGCATCGATGCACA
69913 CTTGGTGCAC
Statistics
Matches: 119, Mismatches: 20, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
63 6 0.05
64 51 0.43
65 62 0.52
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (64 bp):
CATGCATCGATGCACAAGCCATGCATCGATGCATCAGAATATTTTTCAAACATCGAATGCATTT
Found at i:69927 original size:64 final size:64
Alignment explanation
Indices: 69703--69932 Score: 216
Period size: 64 Copynumber: 3.6 Consensus size: 64
69693 TATTCAAAGG
* * *
69703 CATGCATCGATGCATCAGTCCATGCATCGATGCATCGATGAAT-TAATT--GAACATCGAATGCA
1 CATGCATCGATGCA-CACTCCATGCATCGATGCATC-A-GAATAT-TTTCAAAACATCGAATGCA
*
69765 TTC
62 TTT
* * *
69768 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAAAACATCGAATGCATTT
* * ** ** *
69833 GATGCATCGATACACAAGCCATGCATCGATGCATCAGGCTATTTTTC-AAACATTGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAAAACATCGAATGCATTT
*** *
69897 CATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 CATGCATCGATGCACACTCCATGCATCGATGCATCA
69933 AGTGTTCCAA
Statistics
Matches: 135, Mismatches: 25, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
63 6 0.04
64 67 0.50
65 62 0.46
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (64 bp):
CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAAAACATCGAATGCATTT
Done.