Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009596.1 Hibiscus syriacus cultivar Beakdansim tig00116975_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: 1846166
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 8
Found at i:392874 original size:21 final size:21
Alignment explanation
Indices: 392848--392925 Score: 129
Period size: 21 Copynumber: 3.7 Consensus size: 21
392838 CGATAGTCGA
* *
392848 AAAATCGTAACGCGAATTTAG
1 AAAATCGCAACGCGAATTTGG
392869 AAAATCGCAACGCGAATTTGG
1 AAAATCGCAACGCGAATTTGG
392890 AAAATCGCAACGCGAATTTGG
1 AAAATCGCAACGCGAATTTGG
*
392911 AAAATCGCAATGCGA
1 AAAATCGCAACGCGA
392926 TAGTCAGAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.19
Consensus pattern (21 bp):
AAAATCGCAACGCGAATTTGG
Found at i:413035 original size:20 final size:21
Alignment explanation
Indices: 412985--413035 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
412975 ATATACATAT
412985 TATATATA-TTATATATGTAA
1 TATATATATTTATATATGTAA
413005 TAT-TATTATTTAT-TACTG-AA
1 TATATA-TATTTATATA-TGTAA
413025 TATATATATTT
1 TATATATATTT
413036 TGACATTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
19 2 0.07
20 17 0.63
21 8 0.30
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (21 bp):
TATATATATTTATATATGTAA
Found at i:414635 original size:2 final size:2
Alignment explanation
Indices: 414623--414656 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
414613 ATTTATGTGT
*
414623 TA TA T- TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
414657 GTACACATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:414705 original size:211 final size:202
Alignment explanation
Indices: 414304--414716 Score: 598
Period size: 211 Copynumber: 2.0 Consensus size: 202
414294 TGGATTTTAA
* *
414304 TTTTAATTATCTTTCTATATTACATTATAATATTTGTATATATTTTATATCCTTATTAGTTTTTT
1 TTTTAATTATCTTTCTATATTACATTATAATATTTATATATATTTTATA-CCTTATTAGTTGTTT
* *
414369 TTTATACACTCGTATATATGTATTATTAGAATAGTATTATTTCACTTATATGTTATATTATATAT
65 TTTATACACTCGTATACATGTATTATTAGAATAGTATTATTTCACTTATATATTATATTATATAT
414434 ATATGTATATATGTACACATTTTGTATTTTACCCTATTTGTTTACTTCTTTATTATTATATTTAT
130 ATATGTATATATGTACACATTTTGTATTTTACCCTATTTGTTTACTTCTTTATTATTATA-TTAT
414499 TTACATTAG
194 TTACATTAG
*
414508 TTTTAATTATCTTTTTATATTACATTATAATATTTATATATATTTTATA-C-TATTA-TTAGTTT
1 TTTTAATTATCTTTCTATATTACATTATAATATTTATATATATTTTATACCTTATTAGTT-GTTT
* * * *
414570 TTTATACATTCGTATACATTTATTATTAGTATAGTATTATTTCATTTATGTGTTATATTATATAT
65 TTTATACACTCGTATACATGTATTATTAGAATAGTATTATTTC----A---CTTATA-TAT-TAT
*
414635 ATATATATATATATGTATATATGTACACATTTTGTATTTTACCCTATTTTTTTACTTCTTTATTA
121 AT-TATATATATATGTATATATGTACACATTTTGTATTTTACCCTATTTGTTTACTTCTTTATTA
414700 TTATATTATTTACATTA
185 TTATATTATTTACATTA
414717 TTTATTTTTT
Statistics
Matches: 188, Mismatches: 10, Indels: 16
0.88 0.05 0.07
Matches are distributed among these distances:
200 2 0.01
201 47 0.25
202 1 0.01
204 47 0.25
205 1 0.01
208 5 0.03
209 2 0.01
210 17 0.09
211 66 0.35
ACGTcount: A:0.30, C:0.08, G:0.05, T:0.57
Consensus pattern (202 bp):
TTTTAATTATCTTTCTATATTACATTATAATATTTATATATATTTTATACCTTATTAGTTGTTTT
TTATACACTCGTATACATGTATTATTAGAATAGTATTATTTCACTTATATATTATATTATATATA
TATGTATATATGTACACATTTTGTATTTTACCCTATTTGTTTACTTCTTTATTATTATATTATTT
ACATTAG
Found at i:414718 original size:17 final size:18
Alignment explanation
Indices: 414695--414737 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
414685 TTTACTTCTT
414695 TATTATTATATTATTTAC
1 TATTATTATATTATTTAC
* *
414713 -ATTATT-TATTTTTTTC
1 TATTATTATATTATTTAC
414729 TATTATTAT
1 TATTATTAT
414738 TATATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 8 0.38
17 12 0.57
18 1 0.05
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTATTATATTATTTAC
Found at i:414901 original size:14 final size:14
Alignment explanation
Indices: 414875--414917 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
414865 TATATATATA
414875 TATTTTC-TTATTT
1 TATTTTCATTATTT
414888 TATTTTCATTATTT
1 TATTTTCATTATTT
*
414902 T-TTTATTATTATTT
1 TATTT-TCATTATTT
414916 TA
1 TA
414918 CATGTACATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (14 bp):
TATTTTCATTATTT
Found at i:416040 original size:10 final size:10
Alignment explanation
Indices: 416025--416058 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
416015 TTCATTTACC
416025 ATTTATTTTT
1 ATTTATTTTT
416035 ATTTATTTTT
1 ATTTATTTTT
* *
416045 ATCTATTTCT
1 ATTTATTTTT
416055 ATTT
1 ATTT
416059 TACTAACGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:426477 original size:106 final size:105
Alignment explanation
Indices: 426292--427087 Score: 1006
Period size: 106 Copynumber: 7.4 Consensus size: 105
426282 CAGGTTTTAC
*
426292 CAAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTCCAC
1 CAAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
426357 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATCT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAT-T
426398 CAAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
1 CAAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
426463 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATCT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAT-T
426504 CAAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
1 CAAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
426569 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAA-TT
*
426610 C-AGAGCCAATTTCAACTTCACAACGGAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
1 CAAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
* *
426674 GACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAGTT
66 GACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATT
* * ** * * * * *
426715 CCAGAACCAATTTCAACTTCACGGCGGAGGATATTGGACTCGGAACAATACTACTCACTTGGATT
1 CAAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC----C-AGAC-A---ACGT-AAGT
* * * ** * * * ** * **
426780 TCAACTTCACGACGAAGGATATC-C-AGTTCCCAGGCTCAACCTCACGACGAAGGGG
56 TCAACTTCACGACGAAGG-GACCGCTGGTTGTCA-AC-AAACATTTC-TC-AA--TT
* * **
426835 CCATATACAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
1 CAAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
426900 GACGAAGGGACCGCTGGTTGTCAACAAACATCTTCTCAATTT
66 GACGAAGGGACCGCTGGTTGTCAACAAACAT-TTCTCAA-TT
* *
426942 C-AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 CAAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
* *
427006 GACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAGTT
66 GACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATT
* * * *
427047 CCAGAACCAATTTCAACTTCACGACGGAGGATATTGGACTC
1 CAAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
427088 GGAACAATAC
Statistics
Matches: 605, Mismatches: 60, Indels: 50
0.85 0.08 0.07
Matches are distributed among these distances:
105 97 0.16
106 380 0.63
107 4 0.01
108 2 0.00
109 7 0.01
110 24 0.04
111 11 0.02
112 1 0.00
114 1 0.00
115 11 0.02
116 25 0.04
117 6 0.01
118 1 0.00
120 35 0.06
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (105 bp):
CAAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
Found at i:427116 original size:332 final size:331
Alignment explanation
Indices: 426294--427190 Score: 1333
Period size: 332 Copynumber: 2.7 Consensus size: 331
426284 GGTTTTACCA
*
426294 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTCCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
* * * * *
426359 CGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATCTCAAGAGCCAATTTCAACTTCACAAC
66 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAGT-TCCAGAACCAATTTCAACTTCACGAC
* * * * * * *
426423 GAAGGATATTGGACTC----C-AGAC-A---ACGT-AAGTTCAACTTCACGACGAAGG-GACCGC
130 GGAGGATATTGGACTCGGAACAATACTACTCACTTGGATTTCAACTTCACGACGAAGGATATC-C
* ** * * * ** * *** * * **
426477 TGGTTGTCA-AC-AAACATTTC-TC-AA-TCTCAAGAGCCAATTTCAACTTCACAACGAAGGATA
194 -AGTTCCCAGGCTCAACCTCACGACGAAGGGGCCATATACAATTTCAACTTCACAACGAAGGATA
426537 TTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTT
258 TTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTT
426602 CTCAATTTC
323 CTCAATTTC
*
426611 AGAGCCAATTTCAACTTCACAACGGAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
*
426676 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAGTTCCAGAACCAATTTCAACTTCACGGCG
66 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAGTTCCAGAACCAATTTCAACTTCACGACG
426741 GAGGATATTGGACTCGGAACAATACTACTCACTTGGATTTCAACTTCACGACGAAGGATATCCAG
131 GAGGATATTGGACTCGGAACAATACTACTCACTTGGATTTCAACTTCACGACGAAGGATATCCAG
426806 TTCCCAGGCTCAACCTCACGACGAAGGGGCCATATACAATTTCAACTTCACAACGAAGGATATTG
196 TTCCCAGGCTCAACCTCACGACGAAGGGGCCATATACAATTTCAACTTCACAACGAAGGATATTG
426871 GACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATCTTCT
261 GACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAT-TTCT
426936 CAATTTC
325 CAATTTC
* *
426943 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
427008 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAGTTCCAGAACCAATTTCAACTTCACGACG
66 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAGTTCCAGAACCAATTTCAACTTCACGACG
427073 GAGGATATTGGACTCGGAACAATACTACTCACTTGGATTTCAACTTCACGACGAAGGATATCCAG
131 GAGGATATTGGACTCGGAACAATACTACTCACTTGGATTTCAACTTCACGACGAAGGATATCCAG
*
427138 TTCCCAGGCTCAACCTCACGACGAAGGGGCCATATACAATTCCAACTTCACAA
196 TTCCCAGGCTCAACCTCACGACGAAGGGGCCATATACAATTTCAACTTCACAA
427191 ACAGATTGAC
Statistics
Matches: 526, Mismatches: 36, Indels: 21
0.90 0.06 0.04
Matches are distributed among these distances:
317 127 0.24
318 8 0.02
321 1 0.00
322 3 0.01
323 1 0.00
326 8 0.02
327 22 0.04
328 7 0.01
329 1 0.00
330 2 0.00
331 92 0.17
332 254 0.48
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (331 bp):
AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAGTTCCAGAACCAATTTCAACTTCACGACG
GAGGATATTGGACTCGGAACAATACTACTCACTTGGATTTCAACTTCACGACGAAGGATATCCAG
TTCCCAGGCTCAACCTCACGACGAAGGGGCCATATACAATTTCAACTTCACAACGAAGGATATTG
GACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTC
AATTTC
Found at i:427628 original size:20 final size:21
Alignment explanation
Indices: 427578--427628 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
427568 ATATACATAT
427578 TATATATA-TTATATATGTAA
1 TATATATATTTATATATGTAA
427598 TAT-TATTATTTAT-TACTG-AA
1 TATATA-TATTTATATA-TGTAA
427618 TATATATATTT
1 TATATATATTT
427629 TGACATTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
19 2 0.07
20 17 0.63
21 8 0.30
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (21 bp):
TATATATATTTATATATGTAA
Found at i:429015 original size:12 final size:13
Alignment explanation
Indices: 428998--429037 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
428988 ATTATTTCAC
428998 TTATATGT-TATA
1 TTATATGTATATA
*
429010 TTATATATATATA
1 TTATATGTATATA
429023 TATATATGTATATA
1 T-TATATGTATATA
429037 T
1 T
429038 GTACACATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 7 0.29
13 5 0.21
14 12 0.50
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (13 bp):
TTATATGTATATA
Found at i:429277 original size:201 final size:208
Alignment explanation
Indices: 428888--429298 Score: 642
Period size: 201 Copynumber: 2.0 Consensus size: 208
428878 TGGATTTTAA
*
428888 TTTTAATTATCTTTCTATATTACATTATAATATTTGTATATATTTTATATCCTTATTAGTTTTTT
1 TTTTAATTATCTTTCTATATTACATTATAATA-TTGTATATATTTTATA-CCTTATTAGTTGTTT
*
428953 TTTATACACTCGTATATATGTATTATTAGAATAGTATTATTTCACTTATATGTTATATTATATAT
64 TTTATACACTCGTATACATGTATTATTAGAATAGTATTATTTCACTTATATGTTATATTATATAT
429018 ATATATATATATGTATATATGTACACATTTTGTATTTTACCCTATTTGTTTACTTCTTTATTATT
129 ATATATATATATG-ATATATGTACACATTTTGTATTTTACCCTATTTGTTTACTTCTTTATTATT
429083 ATATTTATTTACATTAG
193 -TATTTATTTACATTAG
*
429100 TTTTAATTATCTTTTTATATTACATTATAATA-T-TATATATTTTATA-C-TATTA-TTAGTTTT
1 TTTTAATTATCTTTCTATATTACATTATAATATTGTATATATTTTATACCTTATTAGTT-GTTTT
* * * *
429160 TTATACA-TCGTATACATTTATTATTAGTATAGTATTATTTCATTTATGTGTTATA-T-TATATA
65 TTATACACTCGTATACATGTATTATTAGAATAGTATTATTTCACTTATATGTTATATTATATATA
*
429222 TATATATATATG-TATATGTACACATTTTGTATTTTACCCTATTTTTTTACTTCTTTATTATTTA
130 TATATATATATGATATATGTACACATTTTGTATTTTACCCTATTTGTTTACTTCTTTATTATTTA
429286 TTTATTTACATTA
195 TTTATTTACATTA
429299 TTTATTTTTT
Statistics
Matches: 190, Mismatches: 8, Indels: 14
0.90 0.04 0.07
Matches are distributed among these distances:
200 15 0.08
201 49 0.26
203 18 0.09
204 1 0.01
205 45 0.24
206 16 0.08
207 1 0.01
209 13 0.07
210 1 0.01
212 31 0.16
ACGTcount: A:0.30, C:0.08, G:0.05, T:0.57
Consensus pattern (208 bp):
TTTTAATTATCTTTCTATATTACATTATAATATTGTATATATTTTATACCTTATTAGTTGTTTTT
TATACACTCGTATACATGTATTATTAGAATAGTATTATTTCACTTATATGTTATATTATATATAT
ATATATATATGATATATGTACACATTTTGTATTTTACCCTATTTGTTTACTTCTTTATTATTTAT
TTATTTACATTAG
Found at i:429318 original size:18 final size:18
Alignment explanation
Indices: 429277--429327 Score: 68
Period size: 17 Copynumber: 2.8 Consensus size: 18
429267 TTTACTTCTT
*
429277 TATTATTTATTTATTTAC
1 TATTATTTATTTTTTTAC
*
429295 -ATTATTTATTTTTTTTC
1 TATTATTTATTTTTTTAC
429312 TATTATTATATTTTTT
1 TATTATT-TATTTTTT
429328 CCTCCCTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 15 0.52
18 6 0.21
19 8 0.28
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.73
Consensus pattern (18 bp):
TATTATTTATTTTTTTAC
Found at i:429502 original size:15 final size:14
Alignment explanation
Indices: 429460--429497 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
429450 TATATATATA
429460 TATTTTC-TTATTT
1 TATTTTCATTATTT
429473 TATTTTCATTATTT
1 TATTTTCATTATTT
429487 T-TTTT-ATTATT
1 TATTTTCATTATT
429498 ATTTTACATG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 6 0.25
13 11 0.46
14 7 0.29
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (14 bp):
TATTTTCATTATTT
Found at i:430606 original size:33 final size:33
Alignment explanation
Indices: 430569--430699 Score: 208
Period size: 33 Copynumber: 4.0 Consensus size: 33
430559 TCCCCTAAAT
* *
430569 CCTACAATTTAAAGCTAAGTTTATATTCTTAAG
1 CCTACAATTTAAAGCTAAGCTTATCTTCTTAAG
*
430602 CCTACAAATTAAAGCTAAGCTTATCTTCTTAAG
1 CCTACAATTTAAAGCTAAGCTTATCTTCTTAAG
*
430635 CCTACAATTTAAAGCTAAGCTTATCTTCTTAAA
1 CCTACAATTTAAAGCTAAGCTTATCTTCTTAAG
* *
430668 CCTACAATTTAAGGCTAAGTTTATCTTCTTAA
1 CCTACAATTTAAAGCTAAGCTTATCTTCTTAA
430700 TAAAAAATAT
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 91 1.00
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.37
Consensus pattern (33 bp):
CCTACAATTTAAAGCTAAGCTTATCTTCTTAAG
Found at i:435123 original size:2 final size:2
Alignment explanation
Indices: 435116--435147 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
435106 GTAATTTAAC
435116 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
435148 TATTTTGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:439238 original size:61 final size:61
Alignment explanation
Indices: 439139--439257 Score: 161
Period size: 61 Copynumber: 2.0 Consensus size: 61
439129 AAATTTTGCG
*
439139 TTGCGATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAATGCGA-TTACGTAAATCACA
1 TTGCGATCTTCCTAATTCGCAATGCGAATACGTAAATCGCAATGCGATTTA-GTAAATCACA
* * * *
439200 TTGCGATCTTCCTAATTCGCACTTCGATTTACGT-AATCGCATTGCGATTTAGTAAATC
1 TTGCGATCTTCCTAATTCGCAATGCGA-ATACGTAAATCGCAATGCGATTTAGTAAATC
439258 GCAACGAGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
61 43 0.84
62 8 0.16
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.34
Consensus pattern (61 bp):
TTGCGATCTTCCTAATTCGCAATGCGAATACGTAAATCGCAATGCGATTTAGTAAATCACA
Found at i:439247 original size:20 final size:21
Alignment explanation
Indices: 439139--439260 Score: 103
Period size: 20 Copynumber: 6.0 Consensus size: 21
439129 AAATTTTGCG
* * *
439139 TTGCGATTTTCCTAATTCGCA
1 TTGCGATTTACGTAAATCGCA
* *
439160 ATGCGA-ATACGTAAATCGCA
1 TTGCGATTTACGTAAATCGCA
* *
439180 ATGCGA-TTACGTAAATCACA
1 TTGCGATTTACGTAAATCGCA
* *
439200 TTGCGATCTT-CCTAATTCGCA
1 TTGCGAT-TTACGTAAATCGCA
439221 CTT-CGATTTACGT-AATCGCA
1 -TTGCGATTTACGTAAATCGCA
439241 TTGCGATTTA-GTAAATCGCA
1 TTGCGATTTACGTAAATCGCA
439261 ACGAGATTCT
Statistics
Matches: 82, Mismatches: 13, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
19 4 0.05
20 55 0.67
21 19 0.23
22 4 0.05
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (21 bp):
TTGCGATTTACGTAAATCGCA
Found at i:440149 original size:24 final size:24
Alignment explanation
Indices: 440122--440175 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
440112 GTATTCGAAA
440122 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
440146 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
440170 TTTGAT
1 TTTGAT
440176 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:442713 original size:20 final size:20
Alignment explanation
Indices: 442646--442718 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
442636 GGCATTCATT
442646 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACACGGAAA
* **
442666 TGACGT-TCGTAATCATC-TTAA
1 TGAC-TATCGCAA-CA-CGGAAA
*
442687 TGTCTATCGCAACACGGAAA
1 TGACTATCGCAACACGGAAA
442707 TGACTATCGCAA
1 TGACTATCGCAA
442719 TGCAAAATGA
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 1 0.03
20 25 0.62
21 13 0.32
22 1 0.03
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (20 bp):
TGACTATCGCAACACGGAAA
Found at i:442734 original size:19 final size:19
Alignment explanation
Indices: 442712--442842 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
442702 GGAAATGACT
*
442712 ATCGCAATGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
442731 ATCGTAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
442745 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
442764 ATCGCAA--CGAAA-G--A
1 ATCGCAATGCGAAATGAAA
442778 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
442797 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
442811 ATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
442830 ATCGCAACGCGAA
1 ATCGCAATGCGAA
442843 TTTAGTTTCA
Statistics
Matches: 87, Mismatches: 10, Indels: 30
0.69 0.08 0.24
Matches are distributed among these distances:
14 26 0.30
15 2 0.02
16 10 0.11
17 9 0.10
18 2 0.02
19 38 0.44
ACGTcount: A:0.47, C:0.18, G:0.23, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:442754 original size:33 final size:33
Alignment explanation
Indices: 442712--442838 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
442702 GGAAATGACT
* *
442712 ATCGCAATGCAAAATGAAAATCGTAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
442745 ATCGCAATGCGAAATGAAAATCGCAACGAAAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
442778 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
442811 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
442839 CGAATTTAGT
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:442782 original size:14 final size:14
Alignment explanation
Indices: 442730--442817 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
442720 GCAAAATGAA
* *
442730 AATCGTAACGAGAG
1 AATCGCAACGAAAG
442744 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
442761 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
442777 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
**
442794 AAAATCGCAACGAGGG
1 --AATCGCAACGAAAG
442810 AATCGCAA
1 AATCGCAA
442818 AGCGAAATGA
Statistics
Matches: 60, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 23 0.38
16 11 0.18
17 10 0.17
19 16 0.27
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:442870 original size:19 final size:19
Alignment explanation
Indices: 442848--442913 Score: 52
Period size: 19 Copynumber: 3.7 Consensus size: 19
442838 GCGAATTTAG
442848 TTTCACGTTGCGATTTTCA
1 TTTCACGTTGCGATTTTCA
**
442867 TTTCGTGTTGCGA--TTC-
1 TTTCACGTTGCGATTTTCA
*
442883 TCTCA--TTGCGATTTTCA
1 TTTCACGTTGCGATTTTCA
* *
442900 TTTCGCATTGCGAT
1 TTTCACGTTGCGAT
442914 AGTCATTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
14 6 0.17
16 6 0.17
17 6 0.17
19 18 0.50
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTTCACGTTGCGATTTTCA
Found at i:443039 original size:14 final size:14
Alignment explanation
Indices: 443020--443056 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
443010 CATCAATTAA
443020 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
443034 ACAAATCATCTTTT
1 ACAAATCAACTTTT
443048 ACAAATCAA
1 ACAAATCAA
443057 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:444488 original size:42 final size:42
Alignment explanation
Indices: 444442--444521 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
444432 CGATGACACT
* * * *
444442 GGCCTCTTGAACGGTGGGAGGGGACTCTTGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTATTGAGGAATGATAGG
* *
444484 GGCCTCTTCAACGATAGGAGTGGACTATTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTATTGAGGAATGA
444522 CAGGCGATTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.24, C:0.15, G:0.39, T:0.23
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTATTGAGGAATGATAGG
Found at i:445414 original size:17 final size:17
Alignment explanation
Indices: 445392--445451 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
445382 AAACCGGTTT
445392 GACCCGACCGACCGA-CC
1 GACCCGACCG-CCGACCC
**
445409 GACCCGACCGTTGACCC
1 GACCCGACCGCCGACCC
**
445426 GACCCGACCGTTGACCC
1 GACCCGACCGCCGACCC
445443 GACCCGACC
1 GACCCGACC
445452 CGACCGTTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
16 2 0.05
17 38 0.95
ACGTcount: A:0.20, C:0.50, G:0.23, T:0.07
Consensus pattern (17 bp):
GACCCGACCGCCGACCC
Found at i:445415 original size:5 final size:5
Alignment explanation
Indices: 445392--445456 Score: 55
Period size: 5 Copynumber: 12.8 Consensus size: 5
445382 AAACCGGTTT
* *
445392 GACCC GA-CC GA-CC GA-CC GACCC GACCGTT GACCC GACCC GACCGTT
1 GACCC GACCC GACCC GACCC GACCC GACC--C GACCC GACCC GACC--C
445438 GACCC GACCC GACCC GACC
1 GACCC GACCC GACCC GACC
445457 GTTGACCGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
4 12 0.24
5 31 0.61
7 8 0.16
ACGTcount: A:0.20, C:0.51, G:0.23, T:0.06
Consensus pattern (5 bp):
GACCC
Found at i:445432 original size:22 final size:22
Alignment explanation
Indices: 445421--445463 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
445411 CCCGACCGTT
445421 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
445443 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
445464 GTTGACTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:445463 original size:17 final size:17
Alignment explanation
Indices: 445407--445451 Score: 90
Period size: 17 Copynumber: 2.6 Consensus size: 17
445397 GACCGACCGA
445407 CCGACCCGACCGTTGAC
1 CCGACCCGACCGTTGAC
445424 CCGACCCGACCGTTGAC
1 CCGACCCGACCGTTGAC
445441 CCGACCCGACC
1 CCGACCCGACC
445452 CGACCGTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.18, C:0.51, G:0.22, T:0.09
Consensus pattern (17 bp):
CCGACCCGACCGTTGAC
Found at i:447181 original size:19 final size:19
Alignment explanation
Indices: 447135--447256 Score: 57
Period size: 19 Copynumber: 6.8 Consensus size: 19
447125 ACTGGAACTT
*
447135 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
**
447156 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
447175 AAAATCGTAA--CG--A-G
1 AAAATCGCAACGCGAAATG
* *
447189 AGAATCGCAACGCAAAATG
1 AAAATCGCAACGCGAAATG
* *
447208 AAAATTGCAA--CG--A-C
1 AAAATCGCAACGCGAAATG
**
447222 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAA-TG
447242 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
447257 TTATAGTTTC
Statistics
Matches: 75, Mismatches: 15, Indels: 23
0.66 0.13 0.20
Matches are distributed among these distances:
14 18 0.24
15 2 0.03
16 3 0.04
17 3 0.04
18 2 0.03
19 21 0.28
20 15 0.20
21 11 0.15
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:447201 original size:33 final size:33
Alignment explanation
Indices: 447159--447253 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 33
447149 AAAAATGACT
* * *
447159 ATCGCAACGCGAAATGAAAATCGTAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
* *
447192 ATCGCAACGCAAAATGAAAATTGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
**
447225 ATCGCAACGCGAAACCAAAAATCGCAACG
1 ATCGCAACGCGAAA-TGAAAATCGCAACG
447254 CGATTATAGT
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
33 41 0.79
34 11 0.21
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:447346 original size:20 final size:19
Alignment explanation
Indices: 447284--447357 Score: 112
Period size: 19 Copynumber: 3.8 Consensus size: 19
447274 GATTTTGTCA
447284 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
447303 TTGCGATTTTCGTTTCGCG
1 TTGCGATTTTCATTTCGCG
**
447322 TTGCGATTTTCATTCTCTTG
1 TTGCGATTTTCATT-TCGCG
447342 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
447358 AACCAAAAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 33 0.66
20 17 0.34
ACGTcount: A:0.09, C:0.20, G:0.19, T:0.51
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:447558 original size:94 final size:93
Alignment explanation
Indices: 447446--447723 Score: 374
Period size: 94 Copynumber: 3.1 Consensus size: 93
447436 ATGGATTGCA
* *
447446 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
447511 TAGCAGAATTGGCAGCAAACGAACAAAT
66 TAGCAGAATTGGCAGCAAACGAACAAAT
* *
447539 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACATTGTTAAAGAATACTCAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
447604 TTAGCAAAATTGGCAGC-AAC---CGAAT
65 TTAGCAGAATTGGCAGCAAACGAACAAAT
* * *
447629 ATACTTCAATCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAGT
1 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* * *
447690 TTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAAACGAACAAAT
447719 TTACT
1 TTACT
447724 AAGCAATCTA
Statistics
Matches: 162, Mismatches: 17, Indels: 15
0.84 0.09 0.08
Matches are distributed among these distances:
86 23 0.14
87 2 0.01
89 18 0.11
90 40 0.25
93 7 0.04
94 72 0.44
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (93 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAAACGAACAAAT
Found at i:449426 original size:20 final size:20
Alignment explanation
Indices: 449401--449496 Score: 84
Period size: 20 Copynumber: 5.2 Consensus size: 20
449391 AATTGGTTGA
449401 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
449421 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
**
449440 AAATGACTATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
449459 -A-G--AATCGCAAC-ACGA-
1 AATGAAAATCGCAACGA-GAG
449474 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
449494 AAT
1 AAT
449497 CGCAATACGA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 8 0.13
16 4 0.06
17 2 0.03
18 1 0.02
19 13 0.21
20 34 0.55
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:449467 original size:14 final size:14
Alignment explanation
Indices: 449448--449501 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
449438 GGAAATGACT
449448 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
449462 ATCGCAACACGAAATGAAA
1 ATCGC-A-ACG--A-GAGA
449481 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
449495 ATCGCAA
1 ATCGCAA
449502 TACGATTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 15 0.45
15 2 0.06
16 3 0.09
17 3 0.09
18 2 0.06
19 8 0.24
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:449485 original size:33 final size:33
Alignment explanation
Indices: 449399--449506 Score: 117
Period size: 33 Copynumber: 3.1 Consensus size: 33
449389 GCAATTGGTT
*
449399 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAAC--GAG-A-G--AATCGCAACAC
**
449438 GGAAATGACTATCGCAACGAGAGAATCGCAACAC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACAC
*
449472 GAAATGAAAATCGCAACGAGAGAATCGCAATAC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACAC
449505 GA
1 GA
449507 TTTTGGTTTC
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
33 32 0.52
34 10 0.16
36 1 0.02
37 1 0.02
38 3 0.05
40 15 0.24
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACAC
Found at i:449550 original size:33 final size:33
Alignment explanation
Indices: 449504--449594 Score: 128
Period size: 33 Copynumber: 2.7 Consensus size: 33
449494 AATCGCAATA
**
449504 CGATTTTGGTTTCGCGTTGCGATTATCTCGTTG
1 CGATTTTCATTTCGCGTTGCGATTATCTCGTTG
*
449537 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
1 CGATTTTCATTTCGCGTTGCGATTATCTCGTTG
**
449570 CGATAGTCATTTCCGCGTTGCGATT
1 CGATTTTCATTT-CGCGTTGCGATT
449595 TTCATTCTCG
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
33 40 0.77
34 12 0.23
ACGTcount: A:0.11, C:0.22, G:0.24, T:0.43
Consensus pattern (33 bp):
CGATTTTCATTTCGCGTTGCGATTATCTCGTTG
Found at i:449599 original size:20 final size:19
Alignment explanation
Indices: 449532--449600 Score: 67
Period size: 20 Copynumber: 3.8 Consensus size: 19
449522 GCGATTATCT
449532 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
449551 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
**
449565 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTT-CG
449585 CGTTGCGATTTTCATT
1 CGTTGCGATTTTCATT
449601 CTCGAAACTA
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
14 10 0.26
16 2 0.05
17 3 0.08
19 9 0.23
20 15 0.38
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:450167 original size:20 final size:20
Alignment explanation
Indices: 450144--450237 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
450134 CGATAGTCAG
450144 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
450164 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
*
450184 AATTCGCATTGCGATTTACTT
1 -ATTCGCATTGCGATTTACGT
* * *
450205 AATCACGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
450225 ATTCGCATTGCGA
1 ATTCGCATTGCGA
450238 ATTAGGAAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
20 44 0.71
21 18 0.29
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:450196 original size:41 final size:40
Alignment explanation
Indices: 450144--450237 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 40
450134 CGATAGTCAG
* * *
450144 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGTAATCACATTGCGATTTACCT
* * *
450184 AATTCGCATTGCGATTTACTTAATCACGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATCACATTGCGATTTACCT
450225 ATTCGCATTGCGA
1 ATTCGCATTGCGA
450238 ATTAGGAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 13 0.28
41 34 0.72
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.39
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCACATTGCGATTTACCT
Found at i:450275 original size:61 final size:61
Alignment explanation
Indices: 450123--450278 Score: 179
Period size: 61 Copynumber: 2.6 Consensus size: 61
450113 GGCGCTATGT
* * * * *
450123 AAATCGCATTGCGATAGTCAGATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCT
1 AAATCGCATTGCGATAGTCAGAATCGCGTTGCGATTTACGTATTCGCATTGCGAATTACCA
* * ** * **
450184 AATTCGCATTGCGAT-TTACTTAATCACGTTGCGATTTACGTATTCGCATTGCGAATTAGGA
1 AAATCGCATTGCGATAGT-CAGAATCGCGTTGCGATTTACGTATTCGCATTGCGAATTACCA
*
450245 AAATCGCAATGCGATAGTCAGAATCGCGTTGCGA
1 AAATCGCATTGCGATAGTCAGAATCGCGTTGCGA
450279 ATCTGGAAAC
Statistics
Matches: 75, Mismatches: 18, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
60 1 0.01
61 73 0.97
62 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (61 bp):
AAATCGCATTGCGATAGTCAGAATCGCGTTGCGATTTACGTATTCGCATTGCGAATTACCA
Found at i:451208 original size:41 final size:41
Alignment explanation
Indices: 451161--451278 Score: 193
Period size: 40 Copynumber: 2.9 Consensus size: 41
451151 ATTCGCGCTG
*
451161 CATTTCGCGTTGCGATAGTCTACAATGTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
* *
451202 CATTTCGCGTTGCAATAGTCTGCAGTGTCGTTGCGA-TTTC
1 CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
*
451242 CATTTCGCGTTGCGATAGTGTACAGTGTCGTTGCGAT
1 CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGAT
451279 AGTCTACAGT
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
40 37 0.53
41 33 0.47
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
Found at i:451287 original size:21 final size:21
Alignment explanation
Indices: 451168--451288 Score: 76
Period size: 21 Copynumber: 5.9 Consensus size: 21
451158 CTGCATTTCG
*
451168 CGTTGCGATAGTCTACAATGT
1 CGTTGCGATAGTCTACAGTGT
* * *
451189 CGTTGCGAT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
* *
451207 CGCGTTGCAATAGTCTGCAGTGT
1 --CGTTGCGATAGTCTACAGTGT
* *
451230 CGTTGCGAT--T-TCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
*
451247 CGCGTTGCGATAGTGTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
451270 CGTTGCGATAGTCTACAGT
1 CGTTGCGATAGTCTACAGT
451289 AAATTAAAAA
Statistics
Matches: 76, Mismatches: 13, Indels: 22
0.68 0.12 0.20
Matches are distributed among these distances:
17 2 0.03
18 5 0.07
19 14 0.18
20 8 0.11
21 36 0.47
22 7 0.09
23 4 0.05
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTGT
Found at i:451379 original size:6 final size:6
Alignment explanation
Indices: 451368--451399 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
451358 GACACGTATT
451368 ACCACG ACCACG ACCACG ACCACG A-CACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
451400 CGAGACGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.34, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:451913 original size:6 final size:6
Alignment explanation
Indices: 451892--451945 Score: 94
Period size: 6 Copynumber: 9.3 Consensus size: 6
451882 CGCCGTCTCG
451892 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
451938 GGTCGT GG
1 GGTCGT GG
451946 GAAACAAAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.21
6 38 0.79
ACGTcount: A:0.00, C:0.17, G:0.54, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:452030 original size:34 final size:34
Alignment explanation
Indices: 451984--452053 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
451974 AAACTATCGC
* *
451984 AACGACATTGTAGACTATCGCAACGCGAAATGGA
1 AACGACACTGTAGACTATCGCAACGCGAAAAGGA
*
452018 AACGACACTGTAGACTATCGCAATGCGAAAAGGA
1 AACGACACTGTAGACTATCGCAACGCGAAAAGGA
452052 AA
1 AA
452054 ATCGCGTTGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (34 bp):
AACGACACTGTAGACTATCGCAACGCGAAAAGGA
Found at i:452079 original size:21 final size:21
Alignment explanation
Indices: 452054--452120 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
452044 GAAAAGGAAA
452054 ATCGCGTTGCGATTTTCAACT
1 ATCGCGTTGCGATTTTCAACT
*** ** ** *
452075 ATCGCAACGCGAAATGGAA-A
1 ATCGCGTTGCGATTTTCAACT
452095 ATCGCGTTGCGATTTTCAACT
1 ATCGCGTTGCGATTTTCAACT
452116 ATCGC
1 ATCGC
452121 AACGCGAAAT
Statistics
Matches: 29, Mismatches: 16, Indels: 2
0.62 0.34 0.04
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (21 bp):
ATCGCGTTGCGATTTTCAACT
Found at i:452088 original size:41 final size:41
Alignment explanation
Indices: 452031--452140 Score: 202
Period size: 41 Copynumber: 2.7 Consensus size: 41
452021 GACACTGTAG
* *
452031 ACTATCGCAATGCGAAAAGGAAAATCGCGTTGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCGTTGCGATTTTCA
452072 ACTATCGCAACGCGAAATGGAAAATCGCGTTGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCGTTGCGATTTTCA
452113 ACTATCGCAACGCGAAATGGAAAATCGC
1 ACTATCGCAACGCGAAATGGAAAATCGC
452141 AACGACATTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 67 1.00
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCGTTGCGATTTTCA
Found at i:452127 original size:21 final size:21
Alignment explanation
Indices: 452062--452189 Score: 75
Period size: 21 Copynumber: 6.2 Consensus size: 21
452052 AAATCGCGTT
452062 GCGATTTTCAACTATCGCAAC
1 GCGATTTTCAACTATCGCAAC
** ** * ***
452083 GCGAAATGGAA-AATCGCGTT
1 GCGATTTTCAACTATCGCAAC
452103 GCGATTTTCAACTATCGCAAC
1 GCGATTTTCAACTATCGCAAC
** ** *
452124 GCGAAATGGAA-AATCGCAAC
1 GCGATTTTCAACTATCGCAAC
*
452144 GAC-ATTGT-AGACTATCGCAAC
1 G-CGATTTTCA-ACTATCGCAAC
*
452165 GAGATTTTCAACTATCGCAAC
1 GCGATTTTCAACTATCGCAAC
452186 GCGA
1 GCGA
452190 AATGCAGCGC
Statistics
Matches: 72, Mismatches: 29, Indels: 12
0.64 0.26 0.11
Matches are distributed among these distances:
19 1 0.01
20 23 0.32
21 47 0.65
22 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (21 bp):
GCGATTTTCAACTATCGCAAC
Found at i:452141 original size:20 final size:20
Alignment explanation
Indices: 452075--452144 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 20
452065 ATTTTCAACT
452075 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*** ** ** *
452095 ATCGCGTTGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
452116 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
452136 ATCGCAACG
1 ATCGCAACG
452145 ACATTGTAGA
Statistics
Matches: 33, Mismatches: 16, Indels: 2
0.65 0.31 0.04
Matches are distributed among these distances:
20 21 0.64
21 12 0.36
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:452158 original size:41 final size:41
Alignment explanation
Indices: 452031--452165 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
452021 GACACTGTAG
* * *** *
452031 ACTATCGCAATGCGAAAAGGAAAATCGCGTTGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTGTCA
*** *
452072 ACTATCGCAACGCGAAATGGAAAATCGCGTTGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTGTCA
452113 ACTATCGCAACGCGAAATGGAAAATCGCAACGAC-ATTGT-A
1 ACTATCGCAACGCGAAATGGAAAATCGCAACG-CGATTGTCA
452153 GACTATCGCAACG
1 -ACTATCGCAACG
452166 AGATTTTCAA
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
40 1 0.01
41 84 0.98
42 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.21
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTGTCA
Found at i:454729 original size:15 final size:13
Alignment explanation
Indices: 454682--454739 Score: 53
Period size: 15 Copynumber: 4.2 Consensus size: 13
454672 AAATGAAAAG
*
454682 TAATAAAAAATTA
1 TAATAAAAAAATA
*
454695 CAATTAAACAAAATA
1 TAA-TAAA-AAAATA
*
454710 AAATAAATACAAATA
1 TAATAAA-A-AAATA
454725 TAATAAAAAAATA
1 TAATAAAAAAATA
454738 TA
1 TA
454740 TCGATGTCTG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
13 9 0.24
14 10 0.27
15 18 0.49
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (13 bp):
TAATAAAAAAATA
Found at i:454862 original size:21 final size:21
Alignment explanation
Indices: 454838--454877 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
454828 CTGTCATCAT
*
454838 CATCGCCGTCGTCGTCGTCAC
1 CATCGCCATCGTCGTCGTCAC
*
454859 CATCGTCATCGTCGTCGTC
1 CATCGCCATCGTCGTCGTC
454878 GTCATCCTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.40, G:0.23, T:0.28
Consensus pattern (21 bp):
CATCGCCATCGTCGTCGTCAC
Found at i:455251 original size:18 final size:18
Alignment explanation
Indices: 455228--455262 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
455218 GCGATGGCGG
455228 CATCATATATGGCTGCGA
1 CATCATATATGGCTGCGA
455246 CATCATATATGGCTGCG
1 CATCATATATGGCTGCG
455263 GTGGCTGCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (18 bp):
CATCATATATGGCTGCGA
Found at i:456967 original size:111 final size:111
Alignment explanation
Indices: 456769--456990 Score: 381
Period size: 111 Copynumber: 2.0 Consensus size: 111
456759 ATTACAAAAA
* *
456769 TTAATTCTTACTCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* * *
456834 AATTAAAACGTTAAAATATTACCGTATCATCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATATTACCATATCAGCAAAGTGTAGAGATAT
*
456880 TTAATTCTTAATCTAATAATCATGTATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
456945 AATTAAAACGTTAAAATGTTACCATATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATATTACCATATCAGCAAAGTGTAGAGATAT
456991 ATGATTTCTA
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
111 104 1.00
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATATTACCATATCAGCAAAGTGTAGAGATAT
Found at i:457384 original size:50 final size:50
Alignment explanation
Indices: 457279--457385 Score: 117
Period size: 50 Copynumber: 2.1 Consensus size: 50
457269 ATAGTGCGGA
* * * * *
457279 TCAGGGGGTGCGCTATACTCACGTAGTGTCAGATCACCGTATATCGCATG
1 TCAGGGGGCGCGCTATACCCACGTAGCGTCAAATCACCGTATAACGCATG
* * * *
457329 GCAGGGGGCGCGTTATACCCACGTGGCGTCAAATCAGCGTATAACGCGAT-
1 TCAGGGGGCGCGCTATACCCACGTAGCGTCAAATCACCGTATAACGC-ATG
457379 TCAGGGG
1 TCAGGGG
457386 CACACTTTAC
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
50 44 0.96
51 2 0.04
ACGTcount: A:0.22, C:0.24, G:0.32, T:0.21
Consensus pattern (50 bp):
TCAGGGGGCGCGCTATACCCACGTAGCGTCAAATCACCGTATAACGCATG
Found at i:458875 original size:15 final size:15
Alignment explanation
Indices: 458840--458875 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
458830 CTAATATATA
458840 AATTTTTTAAAATGT
1 AATTTTTTAAAATGT
*
458855 CATTTTTTAAAAT-T
1 AATTTTTTAAAATGT
458869 AATTTTT
1 AATTTTT
458876 ATATTATGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (15 bp):
AATTTTTTAAAATGT
Found at i:461201 original size:6 final size:6
Alignment explanation
Indices: 461190--461215 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
461180 AGTGTACAGT
461190 GTCGTG GTCGTG GTCGTG GTCGTG GT
1 GTCGTG GTCGTG GTCGTG GTCGTG GT
461216 AATACGTGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.50, T:0.35
Consensus pattern (6 bp):
GTCGTG
Found at i:461321 original size:21 final size:21
Alignment explanation
Indices: 461295--461415 Score: 76
Period size: 21 Copynumber: 5.9 Consensus size: 21
461285 TTTTTAATTT
461295 ACTGTAGACTATCGCAACGAC
1 ACTGTAGACTATCGCAACGAC
*
461316 ACTGTACACTATCGCAACG-C
1 ACTGTAGACTATCGCAACGAC
* *
461336 GAAATG--GA-AATCGCAACGAC
1 --ACTGTAGACTATCGCAACGAC
* *
461356 ACTGCAGACTATTGCAACG-C
1 ACTGTAGACTATCGCAACGAC
* **
461376 GAAATG--GAAAATCGCAACGAC
1 --ACTGTAGACTATCGCAACGAC
*
461397 ATTGTAGACTATCGCAACG
1 ACTGTAGACTATCGCAACG
461416 CGAAATGCAG
Statistics
Matches: 75, Mismatches: 14, Indels: 22
0.68 0.13 0.20
Matches are distributed among these distances:
18 3 0.04
19 12 0.16
20 16 0.21
21 38 0.51
22 6 0.08
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (21 bp):
ACTGTAGACTATCGCAACGAC
Found at i:461367 original size:40 final size:41
Alignment explanation
Indices: 461305--461422 Score: 193
Period size: 41 Copynumber: 2.9 Consensus size: 41
461295 ACTGTAGACT
*
461305 ATCGCAACGACACTGTACACTATCGCAACGCGAAATGG-AA
1 ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
* *
461345 ATCGCAACGACACTGCAGACTATTGCAACGCGAAATGGAAA
1 ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
*
461386 ATCGCAACGACATTGTAGACTATCGCAACGCGAAATG
1 ATCGCAACGACACTGTAGACTATCGCAACGCGAAATG
461423 CAGCGCGAAT
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 35 0.49
41 36 0.51
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.16
Consensus pattern (41 bp):
ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
Found at i:463472 original size:31 final size:31
Alignment explanation
Indices: 463434--463572 Score: 251
Period size: 31 Copynumber: 4.5 Consensus size: 31
463424 GGGTCGAGGG
463434 TTACCTATGTTCTTCGGGACATACGGACTGT
1 TTACCTATGTTCTTCGGGACATACGGACTGT
463465 TTACCTATGTTCTTCGGGACATACGGACTGT
1 TTACCTATGTTCTTCGGGACATACGGACTGT
463496 TTACCTATGTTCTTCGGGACATACGGACTGT
1 TTACCTATGTTCTTCGGGACATACGGACTGT
* *
463527 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATACGGACTGT
*
463558 TTACCTAGGTTCTTC
1 TTACCTATGTTCTTC
463573 AGAATCTATG
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 105 1.00
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATACGGACTGT
Found at i:467842 original size:31 final size:31
Alignment explanation
Indices: 467804--467942 Score: 251
Period size: 31 Copynumber: 4.5 Consensus size: 31
467794 GGGTCGAGGG
467804 TTACCTATGTTCTTCGGGACATACGGACTGT
1 TTACCTATGTTCTTCGGGACATACGGACTGT
467835 TTACCTATGTTCTTCGGGACATACGGACTGT
1 TTACCTATGTTCTTCGGGACATACGGACTGT
467866 TTACCTATGTTCTTCGGGACATACGGACTGT
1 TTACCTATGTTCTTCGGGACATACGGACTGT
* *
467897 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATACGGACTGT
*
467928 TTACCTAGGTTCTTC
1 TTACCTATGTTCTTC
467943 AGAATCTATG
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 105 1.00
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATACGGACTGT
Found at i:468825 original size:4 final size:4
Alignment explanation
Indices: 468816--471399 Score: 5094
Period size: 4 Copynumber: 648.0 Consensus size: 4
468806 GGGGTGTTAC
468816 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
468864 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
468912 ACAT ACAT ATAC ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
468960 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
469008 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
469056 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
469104 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
469152 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
469200 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
469248 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
469296 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
469344 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
469392 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
469440 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
469488 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
469536 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
469584 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
469632 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
469680 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
469728 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
469776 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-T ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
469823 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
469871 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
469919 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
469967 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
470015 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
470063 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
470111 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
470159 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
470207 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
470255 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
470303 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
470351 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
470399 ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
470445 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
470493 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
470541 ACAT ACAT ACAT ACAT AC-T ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
470588 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
470636 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
470684 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
470732 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
470780 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
470828 ACAT ACAT AC-- ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
470874 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
470922 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
470970 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
471018 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
471066 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
471114 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
471162 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
471210 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
471258 ACAT ACAT AC-- ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
471304 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
471352 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
471400 GTGTAAGAGG
Statistics
Matches: 2568, Mismatches: 4, Indels: 16
0.99 0.00 0.01
Matches are distributed among these distances:
2 6 0.00
3 6 0.00
4 2556 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:485949 original size:31 final size:31
Alignment explanation
Indices: 485914--485972 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
485904 CATTATAAGT
* *
485914 TTATAACATGGATTATCAGT-TAACAGTCAAA
1 TTATAACAT-CATAATCAGTGTAACAGTCAAA
*
485945 TTATATCATCATAATCAGTGTAACAGTC
1 TTATAACATCATAATCAGTGTAACAGTC
485973 TAACTACTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 8 0.33
31 16 0.67
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (31 bp):
TTATAACATCATAATCAGTGTAACAGTCAAA
Found at i:485986 original size:31 final size:30
Alignment explanation
Indices: 485928--485986 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
485918 AACATGGATT
*
485928 ATCAGTTAACAGTCAAATTATATCATCATA
1 ATCAGTTAACAGTCAAACTATATCATCATA
*
485958 ATCAGTGTAACAGTCTAACTACTA-CATCA
1 ATCAGT-TAACAGTCAAACTA-TATCATCA
485987 GTTGAATAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 6 0.24
31 17 0.68
32 2 0.08
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (30 bp):
ATCAGTTAACAGTCAAACTATATCATCATA
Found at i:486771 original size:31 final size:30
Alignment explanation
Indices: 486732--486794 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 30
486722 ACTATATCTA
* *
486732 ATTACTAATTATTAGTAAGATTATAAATAG
1 ATTACTAATTATTAATAAGATTACAAATAG
*
486762 ATTATCTAATTATTAATAAGATTACCAATAG
1 ATTA-CTAATTATTAATAAGATTACAAATAG
486793 AT
1 AT
486795 CATTCAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 4 0.14
31 25 0.86
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (30 bp):
ATTACTAATTATTAATAAGATTACAAATAG
Found at i:486845 original size:29 final size:28
Alignment explanation
Indices: 486788--486846 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 28
486778 TAAGATTACC
* *
486788 AATAGATCATTCAATTTTAAAAAGTTATA
1 AATAAATCACTCAATTTTAAAAAG-TATA
486817 AATAAATCACTCAATTAATTAAAAA-TATA
1 AATAAATCACTCAATT--TTAAAAAGTATA
486846 A
1 A
486847 TCTAAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
29 19 0.73
31 7 0.27
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.34
Consensus pattern (28 bp):
AATAAATCACTCAATTTTAAAAAGTATA
Found at i:496345 original size:29 final size:30
Alignment explanation
Indices: 496312--496374 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
496302 CAAATAAAAG
496312 CTAT-ATCGGACATCCCTTGATAATTTGTA
1 CTATAATCGGACATCCCTTGATAATTTGTA
496341 CTATAATCGGACATCCCTTGATAATTTGTA
1 CTATAATCGGACATCCCTTGATAATTTGTA
496371 CTAT
1 CTAT
496375 TATCCAACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 4 0.12
30 29 0.88
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.38
Consensus pattern (30 bp):
CTATAATCGGACATCCCTTGATAATTTGTA
Found at i:504139 original size:23 final size:24
Alignment explanation
Indices: 504095--504143 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
504085 AATCGACCAT
**
504095 ATCATTAATTTTTTATTCGATTAA
1 ATCATTAATTTTACATTCGATTAA
*
504119 ATCATTAATTTTACGTT-GATTAA
1 ATCATTAATTTTACATTCGATTAA
504142 AT
1 AT
504144 AAAAAAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (24 bp):
ATCATTAATTTTACATTCGATTAA
Found at i:505602 original size:21 final size:21
Alignment explanation
Indices: 505573--505614 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
505563 TGGGATTATC
505573 GGTGATGGTATCAGCGACATA
1 GGTGATGGTATCAGCGACATA
* *
505594 GGTGCTGGTATCAGCGGCATA
1 GGTGATGGTATCAGCGACATA
505615 AACTGCTGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.17, G:0.36, T:0.24
Consensus pattern (21 bp):
GGTGATGGTATCAGCGACATA
Found at i:513391 original size:28 final size:28
Alignment explanation
Indices: 513359--513417 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
513349 GCGTGCATGC
*
513359 TGCTACATACATTTTTGACATGAATGAG
1 TGCTACATACATTGTTGACATGAATGAG
* *
513387 TGCTACATACATTGTTGGCATGCATGAG
1 TGCTACATACATTGTTGACATGAATGAG
513415 TGC
1 TGC
513418 ATGCTGCTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (28 bp):
TGCTACATACATTGTTGACATGAATGAG
Found at i:516134 original size:21 final size:21
Alignment explanation
Indices: 516090--516134 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
516080 GAACAGCATT
* * *
516090 TTCAGCACCTTTTCTCTCTTC
1 TTCAGCACCTTTTCCCGCTCC
*
516111 TTCAGCCCCTTTTCCCGCTCC
1 TTCAGCACCTTTTCCCGCTCC
516132 TTC
1 TTC
516135 CAGCTCTCAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.07, C:0.44, G:0.07, T:0.42
Consensus pattern (21 bp):
TTCAGCACCTTTTCCCGCTCC
Found at i:519338 original size:16 final size:19
Alignment explanation
Indices: 519295--519342 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 19
519285 TTCTTTCCTC
519295 TTTGATTTATTTATTATG-
1 TTTGATTTATTTATTATGT
*
519313 TTT-A-TTATTTATTTATTT
1 TTTGATTTATTTA-TTATGT
519331 TTTGATTTATTT
1 TTTGATTTATTT
519343 TCTTTTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 7 0.28
17 5 0.20
18 6 0.24
19 1 0.04
20 6 0.24
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (19 bp):
TTTGATTTATTTATTATGT
Found at i:519349 original size:16 final size:16
Alignment explanation
Indices: 519295--519342 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 16
519285 TTCTTTCCTC
519295 TTTGATTTATTTATTATGT
1 TTTGATTTATTTA-T-T-T
*
519314 TTATTATTTATTTATTT
1 TT-TGATTTATTTATTT
519331 TTTGATTTATTT
1 TTTGATTTATTT
519343 TCTTTTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 9 0.35
17 3 0.12
18 1 0.04
19 3 0.12
20 10 0.38
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (16 bp):
TTTGATTTATTTATTT
Found at i:519359 original size:27 final size:26
Alignment explanation
Indices: 519329--519417 Score: 71
Period size: 26 Copynumber: 3.4 Consensus size: 26
519319 ATTTATTTAT
519329 TTTTTGATTTATTTTCT-T-TTTTCTCTC
1 TTTTTGATTTATTTT-TATCTTTT-T-TC
519356 TTTTT-ATTTATTCTTTATCTTTTTTC
1 TTTTTGATTTATT-TTTATCTTTTTTC
* *
519382 CTTTTGATTTA-TTTTATCATTTTATC
1 TTTTTGATTTATTTTTATC-TTTTTTC
519408 ATTTTT-ATTT
1 -TTTTTGATTT
519418 TTTATTTTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
25 6 0.11
26 25 0.47
27 18 0.34
28 4 0.08
ACGTcount: A:0.13, C:0.11, G:0.02, T:0.73
Consensus pattern (26 bp):
TTTTTGATTTATTTTTATCTTTTTTC
Found at i:519417 original size:22 final size:22
Alignment explanation
Indices: 519389--519435 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
519379 TTCCTTTTGA
519389 TTTATTTTATCATTTTAT-CATT
1 TTTATTTT-TCATTTTATACATT
* *
519411 TTTATTTTTTATTTTTTACATT
1 TTTATTTTTCATTTTATACATT
519433 TTT
1 TTT
519436 TCTTCTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTATTTTTCATTTTATACATT
Found at i:519500 original size:17 final size:17
Alignment explanation
Indices: 519480--519532 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 17
519470 CCCTTTTGAT
519480 TTATT-TTTTTTGATTTA
1 TTATTATTTTTT-ATTTA
519497 TTATTATTTTTTATTTTCA
1 TTATTATTTTTTA-TTT-A
519516 TTATTATGTTTTT-TTTA
1 TTATTAT-TTTTTATTTA
519533 AATATTTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
17 7 0.22
18 12 0.38
19 8 0.25
20 5 0.16
ACGTcount: A:0.19, C:0.02, G:0.04, T:0.75
Consensus pattern (17 bp):
TTATTATTTTTTATTTA
Found at i:519508 original size:19 final size:20
Alignment explanation
Indices: 519480--519529 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 20
519470 CCCTTTTGAT
*
519480 TTATT-TTTTTTGA-TTT-A
1 TTATTATTTTTTTATTTTCA
519497 TTATTA-TTTTTTATTTTCA
1 TTATTATTTTTTTATTTTCA
519516 TTATTATGTTTTTT
1 TTATTAT-TTTTTT
519530 TTAAATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 11 0.41
18 3 0.11
19 7 0.26
21 6 0.22
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (20 bp):
TTATTATTTTTTTATTTTCA
Found at i:519508 original size:22 final size:20
Alignment explanation
Indices: 519483--519531 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 20
519473 TTTTGATTTA
*
519483 TTTTTTTTGATTTATTATTATT
1 TTTTTTTTCA-TTATTA-TATT
*
519505 TTTTATTTTCATTATTATGTT
1 TTTT-TTTTCATTATTATATT
519526 TTTTTT
1 TTTTTT
519532 AAATATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 2 0.08
21 7 0.29
22 10 0.42
23 5 0.21
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (20 bp):
TTTTTTTTCATTATTATATT
Found at i:519634 original size:13 final size:13
Alignment explanation
Indices: 519616--519645 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
519606 CTAATCGAGT
519616 TTTTAAATTTTAA
1 TTTTAAATTTTAA
*
519629 TTTTAATTTTTAA
1 TTTTAAATTTTAA
519642 TTTT
1 TTTT
519646 CACAATTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:520457 original size:25 final size:24
Alignment explanation
Indices: 520421--520471 Score: 93
Period size: 25 Copynumber: 2.1 Consensus size: 24
520411 TTTCCTGCTT
520421 TACTTTTGTTCAAAGCATGCGAAC
1 TACTTTTGTTCAAAGCATGCGAAC
520445 TACTTTCTGTTCAAAGCATGCGAAC
1 TACTTT-TGTTCAAAGCATGCGAAC
520470 TA
1 TA
520472 GACAAATATG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.23
25 20 0.77
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (24 bp):
TACTTTTGTTCAAAGCATGCGAAC
Found at i:520996 original size:22 final size:23
Alignment explanation
Indices: 520947--520996 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 23
520937 AGTAACCTTA
520947 CAATTCACTCAAGAATTATACCC
1 CAATTCACTCAAGAATTATACCC
*
520970 C-ATTCCCTCAAGAATTA-ACCC
1 CAATTCACTCAAGAATTATACCC
520991 CAATTC
1 CAATTC
520997 TTAAACAGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 5 0.20
22 19 0.76
23 1 0.04
ACGTcount: A:0.36, C:0.34, G:0.04, T:0.26
Consensus pattern (23 bp):
CAATTCACTCAAGAATTATACCC
Found at i:521516 original size:64 final size:63
Alignment explanation
Indices: 521448--521655 Score: 226
Period size: 65 Copynumber: 3.2 Consensus size: 63
521438 TGGACTAAGA
* *
521448 GTGCATCTATGCATAAAATGCACTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGTTG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATA-CCAGAGTGCATCGATGCATGGTTG
* * *
521512 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAATACCTTA-ACTGCATCGATGCATGGTA
1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCAAAATACC--AGAGTGCATCGATGCATGGT-
521576 T-
62 TG
* * *
521577 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAA--AATACCA-GAGTGCATCGATGCATGG-T
521640 TG
62 TG
*
521642 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
521656 CACTTTGAAA
Statistics
Matches: 123, Mismatches: 11, Indels: 19
0.80 0.07 0.12
Matches are distributed among these distances:
63 5 0.04
64 44 0.36
65 72 0.59
66 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATACCAGAGTGCATCGATGCATGGTTG
Found at i:523031 original size:13 final size:13
Alignment explanation
Indices: 523013--523037 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
523003 AAATCCATCA
523013 AAGTTTGAAATCC
1 AAGTTTGAAATCC
523026 AAGTTTGAAATC
1 AAGTTTGAAATC
523038 TAAGAAAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (13 bp):
AAGTTTGAAATCC
Found at i:523783 original size:15 final size:15
Alignment explanation
Indices: 523760--523789 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
523750 ATTTTCATTC
*
523760 TCATTATATAACCCA
1 TCATCATATAACCCA
523775 TCATCATATAACCCA
1 TCATCATATAACCCA
523790 AAATGGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.30, G:0.00, T:0.30
Consensus pattern (15 bp):
TCATCATATAACCCA
Found at i:524890 original size:23 final size:22
Alignment explanation
Indices: 524858--524934 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
524848 TGGCCTTGTA
524858 CATCGATGCACATTCAAGGCGTG
1 CATCGATGCACATTCAAGG-GTG
* * *
524881 CATCGGTGCACCTTC-ATGGTG
1 CATCGATGCACATTCAAGGGTG
* * *
524902 TATCGATGCACTTTCAAGGATG
1 CATCGATGCACATTCAAGGGTG
524924 CATCGATGCAC
1 CATCGATGCAC
524935 TGTTAGGTGT
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
21 15 0.34
22 16 0.36
23 13 0.30
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (22 bp):
CATCGATGCACATTCAAGGGTG
Found at i:524909 original size:44 final size:42
Alignment explanation
Indices: 524859--524953 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 42
524849 GGCCTTGTAC
* *
524859 ATCGATGCACATTCAAGGCGTGCATCGGTGCACCT-TCATGGTGT
1 ATCGATGCACATTCAAGG-ATGCATCGATGCA-CTGTCA-GGTGT
* *
524903 ATCGATGCACTTTCAAGGATGCATCGATGCACTGTTAGGTGT
1 ATCGATGCACATTCAAGGATGCATCGATGCACTGTCAGGTGT
524945 ATCGATGCA
1 ATCGATGCA
524954 TTAAGCACAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 16 0.35
43 13 0.28
44 17 0.37
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.28
Consensus pattern (42 bp):
ATCGATGCACATTCAAGGATGCATCGATGCACTGTCAGGTGT
Found at i:524911 original size:21 final size:20
Alignment explanation
Indices: 524858--524953 Score: 68
Period size: 21 Copynumber: 4.5 Consensus size: 20
524848 TGGCCTTGTA
*
524858 CATCGATGCACATTCAAGGCGTG
1 CATCGATGCACCTTC-A-G-GTG
*
524881 CATCGGTGCACCTTCATGGTG
1 CATCGATGCACCTTCA-GGTG
* *
524902 TATCGATGCACTTTCAAGGATG
1 CATCGATGCACCTTC-AGG-TG
*
524924 CATCGATGCA-CTGTTAGGTG
1 CATCGATGCACCT-TCAGGTG
*
524944 TATCGATGCA
1 CATCGATGCA
524954 TTAAGCACAA
Statistics
Matches: 60, Mismatches: 10, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
20 11 0.18
21 21 0.35
22 15 0.25
23 13 0.22
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (20 bp):
CATCGATGCACCTTCAGGTG
Found at i:524950 original size:20 final size:20
Alignment explanation
Indices: 524898--524953 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 20
524888 GCACCTTCAT
524898 GGTGTATCGATGCACTTTCAA
1 GGTGTATCGATGCACTTT-AA
*
524919 GGATGCATCGATGCACTGTT-A
1 GG-TGTATCGATGCACT-TTAA
524940 GGTGTATCGATGCA
1 GGTGTATCGATGCA
524954 TTAAGCACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 11 0.35
21 5 0.16
22 13 0.42
23 2 0.06
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (20 bp):
GGTGTATCGATGCACTTTAA
Found at i:532912 original size:16 final size:16
Alignment explanation
Indices: 532879--532910 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
532869 ATATAATTAA
532879 TTATTAATTAAATATT
1 TTATTAATTAAATATT
532895 TTATT-ATT-AATATT
1 TTATTAATTAAATATT
532909 TT
1 TT
532911 TTCTCTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATTAATTAAATATT
Found at i:562097 original size:30 final size:30
Alignment explanation
Indices: 562061--562124 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
562051 GAAGGACCTG
* *
562061 TCCAGAGGTTACAAAGAACCCCGGTAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
* * *
562091 TCCAGAGGTCATAAAGATCCTCGGCAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
562121 TCCA
1 TCCA
562125 TATGTTCCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCCCGGCAACTA
Found at i:562306 original size:14 final size:16
Alignment explanation
Indices: 562279--562310 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
562269 CATATATCTC
562279 ATATCATATCACATGT
1 ATATCATATCACATGT
562295 ATAT-ATAT-ACATGT
1 ATATCATATCACATGT
562309 AT
1 AT
562311 TCACGTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 4 0.25
16 4 0.25
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (16 bp):
ATATCATATCACATGT
Found at i:562907 original size:64 final size:64
Alignment explanation
Indices: 562799--562959 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 64
562789 CAATGAATGT
* * ** *
562799 ATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTTT-TATTTAATGGGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTAA-AAGC
* * *
562863 ATGCATCGATGCACTCCTTATGCATCGATGCAT-AAATCCTATTCGATGTTTTCTATTTAAAATC
1 ATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCC-ATTCGATGTTTTCTATTTAAAAGC
* *
562927 ATGCATCGATGCACTGCATGTGCATCGATGCAT
1 ATGCATCGATGCACTACTTGTGCATCGATGCAT
562960 CTTAAACAAT
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
63 5 0.06
64 72 0.86
65 7 0.08
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTAAAAGC
Found at i:565179 original size:61 final size:61
Alignment explanation
Indices: 565110--565239 Score: 188
Period size: 61 Copynumber: 2.1 Consensus size: 61
565100 GAGCACCATT
* * * * *
565110 CGCGCCTTCGCGGGGTTTTATCCGATATGGCGCTACGTAAAGGAAGGCGCGGATCGACATC
1 CGCGCCTTCACGGGGTTTTATCCGAAATGGCACCACGTAAAAGAAGGCGCGGATCGACATC
* **
565171 CGCGCCTTCACGGGGTTTTGTCCGAAATGGCACCACGTAAAAGAAGGCGCGGATCGTTATC
1 CGCGCCTTCACGGGGTTTTATCCGAAATGGCACCACGTAAAAGAAGGCGCGGATCGACATC
565232 CGCGCCTT
1 CGCGCCTT
565240 AGTTGAACCT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.20, C:0.28, G:0.31, T:0.22
Consensus pattern (61 bp):
CGCGCCTTCACGGGGTTTTATCCGAAATGGCACCACGTAAAAGAAGGCGCGGATCGACATC
Found at i:597699 original size:31 final size:31
Alignment explanation
Indices: 597641--597700 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
597631 TGCCAAAGCT
*
597641 TAATATAAATTTAGATGAATTTGATTTGAAA
1 TAATATAAATTTAGATGAATTTAATTTGAAA
* ** *
597672 TAATATTAATTTATTTGATTTTAATTTGA
1 TAATATAAATTTAGATGAATTTAATTTGA
597701 CAAAGTTTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (31 bp):
TAATATAAATTTAGATGAATTTAATTTGAAA
Found at i:597715 original size:2 final size:2
Alignment explanation
Indices: 597708--597754 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
597698 TGACAAAGTT
597708 TA TA 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 TA TA
597750 TA TA T
1 TA TA T
597755 GTGTTTGAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:598058 original size:32 final size:33
Alignment explanation
Indices: 598017--598098 Score: 148
Period size: 34 Copynumber: 2.5 Consensus size: 33
598007 GCCCCGATTA
598017 TATATATATAATATTTATA-TTTTTATATTAAT
1 TATATATATAATATTTATATTTTTTATATTAAT
598049 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATA-TTTATATTTTTTATATTAAT
598083 TATATATATAATATTT
1 TATATATATAATATTT
598099 TCGGGTTCGG
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.27
33 9 0.19
34 26 0.54
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (33 bp):
TATATATATAATATTTATATTTTTTATATTAAT
Found at i:598087 original size:25 final size:24
Alignment explanation
Indices: 598013--598099 Score: 53
Period size: 23 Copynumber: 3.8 Consensus size: 24
598003 CCCCGCCCCG
598013 ATTATATATATATAATATTTATATT-
1 ATTATATATATA-AAT-TTTATATTA
*
598038 -TT-TATAT-T-AATTATATATATA
1 ATTATATATATAAATTTTATAT-TA
* **
598059 A-TAT-TTTATATTTTTTATATTA
1 ATTATATATATAAATTTTATATTA
598081 ATTATATATATAATATTTT
1 ATTATATATATAA-ATTTT
598100 CGGGTTCGGG
Statistics
Matches: 45, Mismatches: 8, Indels: 18
0.63 0.11 0.25
Matches are distributed among these distances:
19 6 0.13
20 4 0.09
21 3 0.07
22 6 0.13
23 15 0.33
24 7 0.16
25 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
ATTATATATATAAATTTTATATTA
Found at i:608684 original size:60 final size:60
Alignment explanation
Indices: 608604--608790 Score: 195
Period size: 60 Copynumber: 3.1 Consensus size: 60
608594 TCATCATATG
* * *
608604 TCCTC-AACTATAAC-CGTCATTTTAAATTGGTCCTTAAACTTTTGAATATTCCAGTTTCA
1 TCCTCAAACTATGACTC-TCATTTTAAATTGGTCCCTAAACTTTTGAATATTCCAATTTCA
* * * * *
608663 TCCTCAAACTATGACTCTCATTCTAAATTAGTCCCTAAACTTTTAAACAATT-TAATTTCA
1 TCCTCAAACTATGACTCTCATTTTAAATTGGTCCCTAAACTTTTGAA-TATTCCAATTTCA
* * *
608723 TCC-CTAAACTATGACTCTC-TTTCTAAATTGGTCCCCACACTTTTGAATCTTCCAATTTCA
1 TCCTC-AAACTATGACTCTCATTT-TAAATTGGTCCCTAAACTTTTGAATATTCCAATTTCA
*
608783 TCCCCAAA
1 TCCTCAAA
608791 TTCATCCAAA
Statistics
Matches: 105, Mismatches: 16, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
59 10 0.10
60 90 0.86
61 5 0.05
ACGTcount: A:0.30, C:0.26, G:0.06, T:0.38
Consensus pattern (60 bp):
TCCTCAAACTATGACTCTCATTTTAAATTGGTCCCTAAACTTTTGAATATTCCAATTTCA
Found at i:609071 original size:60 final size:60
Alignment explanation
Indices: 608959--609071 Score: 131
Period size: 60 Copynumber: 1.9 Consensus size: 60
608949 TGGAGACCAA
* * * *
608959 TTTAGAATGAAGGTCATAGTTTGAGAATAAAATTGAAATGTTCAAAATTTTAAATACTAG
1 TTTAGAATGAAGATCATAGTTTGAGAATAAAATTAAAATATTCAAAAGTTTAAATACTAG
* * *
609019 TTTAGAATGATA-ATCATAGTTT-AGAGATGAAATTAAAATATTTACAAGTTTAA
1 TTTAGAATGA-AGATCATAGTTTGAGA-ATAAAATTAAAATATTCAAAAGTTTAA
609072 GGATCAATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
59 3 0.07
60 40 0.91
61 1 0.02
ACGTcount: A:0.44, C:0.04, G:0.15, T:0.36
Consensus pattern (60 bp):
TTTAGAATGAAGATCATAGTTTGAGAATAAAATTAAAATATTCAAAAGTTTAAATACTAG
Found at i:613493 original size:83 final size:84
Alignment explanation
Indices: 613353--613517 Score: 296
Period size: 83 Copynumber: 2.0 Consensus size: 84
613343 GTGAAACTGC
* *
613353 CACTCATTGAAGTTGGTTAGTTTTTTTTACTCATTCTATGCAGATGGACAGTAAGTACCAACATC
1 CACTCATTGAAGTTGATTAGTTTTTCTTACTCATTCTATGCAGATGGACAGTAAGTACCAACATC
613418 CGAGTATTCAACCCTTCGT
66 CGAGTATTCAACCCTTCGT
613437 CACTCATTGAAGTTGATTAG-TTTTCTTACTCATTCTATGCAGATGGACAGTAAGTACCAACATC
1 CACTCATTGAAGTTGATTAGTTTTTCTTACTCATTCTATGCAGATGGACAGTAAGTACCAACATC
*
613501 CGAGTATTCAACTCTTC
66 CGAGTATTCAACCCTTC
613518 ATTATGGGGC
Statistics
Matches: 78, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
83 59 0.76
84 19 0.24
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (84 bp):
CACTCATTGAAGTTGATTAGTTTTTCTTACTCATTCTATGCAGATGGACAGTAAGTACCAACATC
CGAGTATTCAACCCTTCGT
Found at i:621962 original size:23 final size:23
Alignment explanation
Indices: 621932--621981 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
621922 AAGCATAGAA
*
621932 AGCCATGGAGTAATAAAATGGAG
1 AGCCATGGAGTAATAAAAAGGAG
621955 AGCCATGGAGTAATAAAAAGGAG
1 AGCCATGGAGTAATAAAAAGGAG
621978 AGCC
1 AGCC
621982 CTTTTTAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.44, C:0.12, G:0.30, T:0.14
Consensus pattern (23 bp):
AGCCATGGAGTAATAAAAAGGAG
Found at i:624535 original size:20 final size:20
Alignment explanation
Indices: 624510--624556 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
624500 GCTAAATTAA
624510 CATGAAATTAACCAAAATTT
1 CATGAAATTAACCAAAATTT
624530 CATGAAATTAACCAAAATTT
1 CATGAAATTAACCAAAATTT
624550 CATGAAA
1 CATGAAA
624557 CTAAGCCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (20 bp):
CATGAAATTAACCAAAATTT
Found at i:626516 original size:17 final size:17
Alignment explanation
Indices: 626494--626560 Score: 73
Period size: 17 Copynumber: 3.9 Consensus size: 17
626484 AATTCTAAAC
*
626494 ATTTACAGTTATCAAAT
1 ATTTACAGATATCAAAT
* *
626511 ATTTACAGACATCAGAT
1 ATTTACAGATATCAAAT
*
626528 ATTTACAGATA-CATAT
1 ATTTACAGATATCAAAT
*
626544 ATTTTACAGTTATCAAA
1 A-TTTACAGATATCAAA
626561 CACATATTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
16 5 0.12
17 33 0.80
18 3 0.07
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.37
Consensus pattern (17 bp):
ATTTACAGATATCAAAT
Found at i:631181 original size:29 final size:29
Alignment explanation
Indices: 631119--631206 Score: 124
Period size: 29 Copynumber: 3.1 Consensus size: 29
631109 AAGCATTTAA
*
631119 GTTCAGCTTTGGTACATTAG-GTACTAAT
1 GTTCAACTTTGGTACATTAGTGTACTAAT
* *
631147 ATTCAACTTTAGTACATTAGTGTACTAAT
1 GTTCAACTTTGGTACATTAGTGTACTAAT
* *
631176 GTTCAACTTTGGTACATTCGTGTACCAAT
1 GTTCAACTTTGGTACATTAGTGTACTAAT
631205 GT
1 GT
631207 CACATCGCTG
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
28 17 0.33
29 35 0.67
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (29 bp):
GTTCAACTTTGGTACATTAGTGTACTAAT
Found at i:651627 original size:2 final size:2
Alignment explanation
Indices: 651620--651650 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
651610 CCTTTTAATC
651620 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
651651 ATAACTGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:660922 original size:30 final size:30
Alignment explanation
Indices: 660887--660952 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
660877 AGAACCGGAA
*
660887 GAACCGGCTGAAAATCGGAAAAACCGGGGT
1 GAACCGGCTGAAAACCGGAAAAACCGGGGT
* **
660917 GAACCGGCTGAAAACCGGCAAAACCGGTTT
1 GAACCGGCTGAAAACCGGAAAAACCGGGGT
660947 GAACCG
1 GAACCG
660953 CCGGTTCACT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.35, C:0.24, G:0.30, T:0.11
Consensus pattern (30 bp):
GAACCGGCTGAAAACCGGAAAAACCGGGGT
Found at i:661202 original size:24 final size:24
Alignment explanation
Indices: 661172--661230 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
661162 ATTTAGAAGT
661172 TCAATTGAAGCCTAAAATTTGAAC
1 TCAATTGAAGCCTAAAATTTGAAC
*
661196 TCAATTGAAGCCTAAAATTTGAGC
1 TCAATTGAAGCCTAAAATTTGAAC
661220 TCAATTGAAGC
1 TCAATTGAAGC
661231 GAAAGATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (24 bp):
TCAATTGAAGCCTAAAATTTGAAC
Found at i:663572 original size:21 final size:21
Alignment explanation
Indices: 663548--663590 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
663538 CATAGAGAAA
*
663548 CACTAGAATCACAATTAAACC
1 CACTAAAATCACAATTAAACC
663569 CACTAAAATCACAATTAAACC
1 CACTAAAATCACAATTAAACC
663590 C
1 C
663591 TCTTTCACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.30, G:0.02, T:0.19
Consensus pattern (21 bp):
CACTAAAATCACAATTAAACC
Found at i:664364 original size:3 final size:3
Alignment explanation
Indices: 664358--664412 Score: 87
Period size: 3 Copynumber: 18.7 Consensus size: 3
664348 CCTCCTTATT
664358 ATA ATA ATA ATA AT- ATA ATA A-A ATA ATA TATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
664402 ATA ATA ATA AT
1 ATA ATA ATA AT
664413 TTTGGTTATG
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.08
3 42 0.86
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:668936 original size:34 final size:34
Alignment explanation
Indices: 668883--668949 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
668873 TGAGTACGAG
* *
668883 ACTCGAATCTAATAGATTTTGATTTGATCTGATA
1 ACTCAAATCTAATAGATTTTAATTTGATCTGATA
*
668917 ACTCAAATCTAAT-GAATTTTAATTTGATTTGAT
1 ACTCAAATCTAATAG-ATTTTAATTTGATCTGAT
668950 TTGATTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 1 0.03
34 28 0.97
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.43
Consensus pattern (34 bp):
ACTCAAATCTAATAGATTTTAATTTGATCTGATA
Found at i:670048 original size:30 final size:30
Alignment explanation
Indices: 670012--670076 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
670002 AGAACTGACA
* * *
670012 GTTCACACTGGTTTTGCC-GTTTTTCAACCG
1 GTTCACACCGATTTTACCGGTTTTT-AACCG
670042 GTTCACACCGATTTTACCGGTTTTTAACCG
1 GTTCACACCGATTTTACCGGTTTTTAACCG
670072 GTTCA
1 GTTCA
670077 TTGCAAAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 25 0.81
31 6 0.19
ACGTcount: A:0.17, C:0.26, G:0.18, T:0.38
Consensus pattern (30 bp):
GTTCACACCGATTTTACCGGTTTTTAACCG
Found at i:672179 original size:23 final size:23
Alignment explanation
Indices: 672146--672205 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
672136 AATGATTCAG
*
672146 TGCTGACTGATTCAACAAAACAA
1 TGCTGAATGATTCAACAAAACAA
*
672169 TGCTGAATGATTCAGCAAAACAA
1 TGCTGAATGATTCAACAAAACAA
*
672192 TGCCGAATGATTCA
1 TGCTGAATGATTCA
672206 GCACAGAAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (23 bp):
TGCTGAATGATTCAACAAAACAA
Found at i:672206 original size:23 final size:23
Alignment explanation
Indices: 672153--672208 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
672143 CAGTGCTGAC
* *
672153 TGATTCAACAAAACAATGCTGAA
1 TGATTCAGCAAAACAATGCCGAA
672176 TGATTCAGCAAAACAATGCCGAA
1 TGATTCAGCAAAACAATGCCGAA
672199 TGATTCAGCA
1 TGATTCAGCA
672209 CAGAAGTACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.21
Consensus pattern (23 bp):
TGATTCAGCAAAACAATGCCGAA
Found at i:673237 original size:20 final size:16
Alignment explanation
Indices: 673192--673227 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
673182 AATAACAAAA
673192 AGAGAAATCCACAACC
1 AGAGAAATCCACAACC
673208 AGAGAAATCCACAACC
1 AGAGAAATCCACAACC
673224 AGAG
1 AGAG
673228 TCTAAAATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.28, G:0.17, T:0.06
Consensus pattern (16 bp):
AGAGAAATCCACAACC
Found at i:682851 original size:8 final size:8
Alignment explanation
Indices: 682838--682865 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
682828 AGATTCTCCC
682838 ATATGTAT
1 ATATGTAT
682846 ATATGTAT
1 ATATGTAT
682854 ATATGTAT
1 ATATGTAT
682862 ATAT
1 ATAT
682866 CTTCTTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (8 bp):
ATATGTAT
Found at i:686411 original size:9 final size:9
Alignment explanation
Indices: 686376--686422 Score: 55
Period size: 8 Copynumber: 5.3 Consensus size: 9
686366 AAAATGAGTG
686376 AAAATGAAAA
1 AAAATG-AAA
686386 AAAAT-AAA
1 AAAATGAAA
686394 AAAAT-AAA
1 AAAATGAAA
686402 AAAATG-AA
1 AAAATGAAA
686410 AAAATGGAAA
1 AAAAT-GAAA
686420 AAA
1 AAA
686423 GAAGGGTTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
8 23 0.68
9 1 0.03
10 10 0.29
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.11
Consensus pattern (9 bp):
AAAATGAAA
Found at i:687484 original size:55 final size:53
Alignment explanation
Indices: 687415--687622 Score: 228
Period size: 53 Copynumber: 3.9 Consensus size: 53
687405 AGGTTTCCCA
*
687415 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTG-T-GAGTCTCATACTCTCTAAAGAAATAGGGAGCAGAC
* * *
687470 ACGATTGTTGAAGATTGTGGGTCTTATACTCTCTGAAGAAATA-GGAGGCAGAC
1 ACGATTGTTGAAGATTGTGAGTCTCATACTCTCTAAAGAAATAGGGA-GCAGAC
* * * * *
687523 GCGATCGTTGAAGATTGTGGGTCTTATACTCTCTAAAGAAATAGGGAGCATAC
1 ACGATTGTTGAAGATTGTGAGTCTCATACTCTCTAAAGAAATAGGGAGCAGAC
* * *
687576 ACG--T-TTGAAGATTTTCGAGT-TCTATACTCCCTAAAGAAAGAGGGAGC
1 ACGATTGTTGAAGATTGT-GAGTCTC-ATACTCTCTAAAGAAATAGGGAGC
687623 GAACCTGTTA
Statistics
Matches: 136, Mismatches: 13, Indels: 12
0.84 0.08 0.07
Matches are distributed among these distances:
50 11 0.08
51 25 0.18
52 3 0.02
53 76 0.56
54 4 0.03
55 17 0.12
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (53 bp):
ACGATTGTTGAAGATTGTGAGTCTCATACTCTCTAAAGAAATAGGGAGCAGAC
Found at i:687512 original size:53 final size:53
Alignment explanation
Indices: 687415--687578 Score: 240
Period size: 53 Copynumber: 3.1 Consensus size: 53
687405 AGGTTTCCCA
* *
687415 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
687470 ACGATTGTTGAAGATTGTGGGTCTTATACTCTCTGAAGAAATA-GGAGGCAGAC
1 ACGATTGTTGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGA-GCAGAC
* * * *
687523 GCGATCGTTGAAGATTGTGGGTCTTATACTCTCTAAAGAAATAGGGAGCATAC
1 ACGATTGTTGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
687576 ACG
1 ACG
687579 TTTGAAGATT
Statistics
Matches: 100, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
52 3 0.03
53 76 0.76
54 4 0.04
55 17 0.17
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.27
Consensus pattern (53 bp):
ACGATTGTTGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
Done.