Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009021.1 Hibiscus syriacus cultivar Beakdansim tig00112411_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: 1242735
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:163289 original size:35 final size:33
Alignment explanation
Indices: 163250--163316 Score: 82
Period size: 35 Copynumber: 2.0 Consensus size: 33
163240 TGGTAAAAGA
163250 GTATAAAAAGAAATAA-AATATATACATATATATAC
1 GTATAAAAA-AAATAACAATA-ATA-ATATATATAC
* *
163285 GTATAATAATAATAACAATAATAATATATATA
1 GTATAAAAAAAATAACAATAATAATATATATA
163317 TATATATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 9 0.31
34 8 0.28
35 12 0.41
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (33 bp):
GTATAAAAAAAATAACAATAATAATATATATAC
Found at i:164486 original size:18 final size:18
Alignment explanation
Indices: 164461--164508 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
164451 AGTTTACTAA
*
164461 AACA-ATAATATTTATAC
1 AACATATAATATATATAC
* *
164478 AATATATAATATATATAT
1 AACATATAATATATATAC
164496 AACATATAA-ATAT
1 AACATATAATATAT
164509 GTGTGATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 7 0.27
18 19 0.73
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (18 bp):
AACATATAATATATATAC
Found at i:190908 original size:210 final size:213
Alignment explanation
Indices: 190628--191039 Score: 746
Period size: 210 Copynumber: 1.9 Consensus size: 213
190618 AGGATCATTG
190628 ATTACCTACCCTCCCATTAACTCAGTTAGCTTAGTAGAATATTCTTCTGATGCTTCTACATTACA
1 ATTACCTACCCTCCCATTAACTCAGTTAGCTTAGTAGAATATTCTTCTGAT-CTTCTACATTACA
190693 ACAGAAAAGAGTTATCTAGGGATG-ATTACATCCTACTCCAGTGTGGTTGGT-AAACGAGACAAA
65 ACAGAAAAGAGTTATCTAGGGATGAATTACATCCTACTCCAGTGTGGTTGGTAAAACGAGACAAA
190756 GATAAAAGC-ATGTCGTGCCTACCGA-TTGTGATATTGGCAGTAAGCACCCTGAAGTCTGAAAAA
130 GATAAAAGCAATGTCGTGCCTACCGATTTGTGATATTGGCAGTAAGCACCCTGAAGTCTG-AAAA
190819 ACATAACATTACTCAGTAAC
194 ACATAACATTACTCAGTAAC
190839 ATTA-CTACCCTCCCATTAACTCAGTTAGCTTAGTAGAATATTCTTCTGAT-TTCTACATTACAT
1 ATTACCTACCCTCCCATTAACTCAGTTAGCTTAGTAGAATATTCTTCTGATCTTCTACATTAC--
190902 AACAGAAAAGAGTTATCTAGGGATGAATTACATCCTACTCCAGTGTGGTTGGTAAAACGAGACAA
64 AACAGAAAAGAGTTATCTAGGGATGAATTACATCCTACTCCAGTGTGGTTGGTAAAACGAGACAA
190967 AGATAAAAGCAATGTCGTGCCTACCGATTTGTGATATTGGCAGTAAGCACCCTGAAGTCTGAAAA
129 AGATAAAAGCAATGTCGTGCCTACCGATTTGTGATATTGGCAGTAAGCACCCTGAAGTCTGAAAA
191032 ACATAACA
194 ACATAACA
191040 CATTAAAAGT
Statistics
Matches: 195, Mismatches: 0, Indels: 10
0.95 0.00 0.05
Matches are distributed among these distances:
208 11 0.06
210 71 0.36
211 31 0.16
212 21 0.11
213 28 0.14
214 33 0.17
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.28
Consensus pattern (213 bp):
ATTACCTACCCTCCCATTAACTCAGTTAGCTTAGTAGAATATTCTTCTGATCTTCTACATTACAA
CAGAAAAGAGTTATCTAGGGATGAATTACATCCTACTCCAGTGTGGTTGGTAAAACGAGACAAAG
ATAAAAGCAATGTCGTGCCTACCGATTTGTGATATTGGCAGTAAGCACCCTGAAGTCTGAAAAAC
ATAACATTACTCAGTAAC
Found at i:203270 original size:1 final size:1
Alignment explanation
Indices: 203264--203290 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
203254 ATTTCACTTC
203264 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
203291 CGTAAGTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:206883 original size:24 final size:24
Alignment explanation
Indices: 206830--206884 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
206820 CATCTTCATG
* *
206830 ATCATCATCTTCATCATCAGAAAT
1 ATCATCATCTTCATCACCAGAAAC
* *
206854 ACCATCATCTTCAATCACCA-AAGC
1 ATCATCATCTTC-ATCACCAGAAAC
206878 ATCATCA
1 ATCATCA
206885 ATCTCCACAG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.38, C:0.31, G:0.04, T:0.27
Consensus pattern (24 bp):
ATCATCATCTTCATCACCAGAAAC
Found at i:214017 original size:33 final size:31
Alignment explanation
Indices: 213979--214056 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
213969 TTCGACTCTG
*
213979 AATAAAATATTAATCT-AATCCTTAAATATTTTA
1 AATAAAATATTAAT-TGAA-CCCT-AATATTTTA
**
214012 AATAAAATACCAATTGAACCCTAATATTTTA
1 AATAAAATATTAATTGAACCCTAATATTTTA
214043 AATAAAATATTAAT
1 AATAAAATATTAAT
214057 AATTCTTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
31 21 0.54
32 4 0.10
33 14 0.36
ACGTcount: A:0.51, C:0.10, G:0.01, T:0.37
Consensus pattern (31 bp):
AATAAAATATTAATTGAACCCTAATATTTTA
Found at i:219691 original size:23 final size:23
Alignment explanation
Indices: 219665--219709 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
219655 CACCACAGCT
*
219665 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
219688 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
219710 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:220372 original size:18 final size:19
Alignment explanation
Indices: 220335--220371 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
220325 TATATATATA
*
220335 TGGGGGAATCGGTTCCCCC
1 TGGGGGAATCGATTCCCCC
*
220354 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
220372 TCTAGCATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.30, G:0.35, T:0.24
Consensus pattern (19 bp):
TGGGGGAATCGATTCCCCC
Found at i:220422 original size:21 final size:21
Alignment explanation
Indices: 220398--220440 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
220388 TTCATATTCG
* * *
220398 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATACCCC
*
220419 TTGAATGGGTACCGATACCCC
1 TTGAAGGGGTACCGATACCCC
220440 T
1 T
220441 AGCCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.28
Consensus pattern (21 bp):
TTGAAGGGGTACCGATACCCC
Found at i:227968 original size:2 final size:2
Alignment explanation
Indices: 227961--228010 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
227951 TAAAATAGTC
227961 AT AT AT AT AT 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 AT AT AT AT AT
228003 AT AT AT AT
1 AT AT AT AT
228011 GTTATAAACT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:230086 original size:21 final size:22
Alignment explanation
Indices: 230062--230129 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 22
230052 ACAACCAAAC
230062 GATAAAAAAATGTATCATAAA-
1 GATAAAAAAATGTATCATAAAT
* *
230083 GATAAAGGAAGATGTAACATAAAT
1 GATAAA--AAAATGTATCATAAAT
* *
230107 GCAGGAAAAAAACGTATCATAAA
1 G-A-TAAAAAAATGTATCATAAA
230130 AAATTATTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
21 6 0.17
23 13 0.36
24 13 0.36
25 1 0.03
26 3 0.08
ACGTcount: A:0.57, C:0.07, G:0.16, T:0.19
Consensus pattern (22 bp):
GATAAAAAAATGTATCATAAAT
Found at i:234717 original size:225 final size:221
Alignment explanation
Indices: 234320--234783 Score: 716
Period size: 225 Copynumber: 2.1 Consensus size: 221
234310 AAACCTCCAT
*
234320 CCGAGACCCGACCCGACCGAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACC
1 CCGA-ACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACC
* * * * *
234385 CGACTTGACTCGGAATAATAAAAAAATTATTTTTATTAAATAAAAACAGTGACTTAATTGGGAAA
65 CGACTCGACCCGAAATAATAAAAAAATTATTTTTATTAAATAAAAACAATGACTTAATTGGAAAA
* *
234450 AAATATATAGAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTTT
130 AAATATATAGAGAAGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATA--TAT
234515 TTGGGTCGGGTCGGGTATTTTTCACCCTAAAC
193 TT---TCGGGTCGGGTATTTTTCACCCTAAAC
*
234547 CCGAACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAATCC
1 CCGAACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCC
* *
234612 GAC-CGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAATAATGACTTAATT-GAAAAA
66 GACTCGACCCGAAATAATAAAAAAATTATTTTTATTAAATAAAAACAATGACTTAATTGGAAAAA
* *
234675 AATTATATATAGAAGGGTATTGTTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTT
131 AA-TATATAGAGAAGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTT
*
234740 TCGGGTCGGGTATTTTTCACCCTAAAT
195 TCGGGTCGGGTATTTTTCACCCTAAAC
*
234767 CCGAACTCGACCCGACC
1 CCGAACCCGACCCGACC
234784 CGAATATCAC
Statistics
Matches: 221, Mismatches: 15, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
220 42 0.19
223 4 0.02
224 7 0.03
225 102 0.46
226 62 0.28
227 4 0.02
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (221 bp):
CCGAACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCC
GACTCGACCCGAAATAATAAAAAAATTATTTTTATTAAATAAAAACAATGACTTAATTGGAAAAA
AATATATAGAGAAGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTT
CGGGTCGGGTATTTTTCACCCTAAAC
Found at i:235353 original size:18 final size:18
Alignment explanation
Indices: 235309--235369 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
235299 TGATTCACGA
* *
235309 AATGTAAGATTATCAGTAGA
1 AATGTAAGATTACCAG--GG
235329 AATGTAAGATTACCAGGG
1 AATGTAAGATTACCAGGG
*
235347 GATGTAAGATTACCAGGG
1 AATGTAAGATTACCAGGG
235365 AATGT
1 AATGT
235370 TGTATTTTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
18 22 0.59
20 15 0.41
ACGTcount: A:0.39, C:0.08, G:0.26, T:0.26
Consensus pattern (18 bp):
AATGTAAGATTACCAGGG
Found at i:235576 original size:37 final size:37
Alignment explanation
Indices: 235503--235577 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
235493 GTTAGAAAAT
* **
235503 ATTTATATATTTTCTTTAAAAAATTTAATTTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
235540 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
235577 A
1 A
235578 AGGTTTAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 14 0.44
38 18 0.56
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:239888 original size:2 final size:2
Alignment explanation
Indices: 239881--239907 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
239871 GGCAATTGTT
239881 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
239908 GCATTCCCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:244109 original size:20 final size:20
Alignment explanation
Indices: 244072--244123 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
244062 GTTGAAAATT
244072 TAAA-AATAATATTATGAAAA
1 TAAATAATAA-ATTATGAAAA
* *
244092 TAAATAATAAATTTTGAATA
1 TAAATAATAAATTATGAAAA
* *
244112 CAAATTATAAAT
1 TAAATAATAAAT
244124 AAATATAGTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (20 bp):
TAAATAATAAATTATGAAAA
Found at i:245325 original size:15 final size:15
Alignment explanation
Indices: 245305--245355 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
245295 ATATTTAGTT
*
245305 GGGCGGGTGGATGTG
1 GGGCGGGTGGATGCG
*
245320 GGGCGGGTGGATACG
1 GGGCGGGTGGATGCG
*
245335 AGGCGGGTGGATGCG
1 GGGCGGGTGGATGCG
*
245350 GTGCGG
1 GGGCGG
245356 ATGCGGGGCG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.10, C:0.12, G:0.63, T:0.16
Consensus pattern (15 bp):
GGGCGGGTGGATGCG
Found at i:258826 original size:34 final size:34
Alignment explanation
Indices: 258788--258856 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
258778 GTTTTATTAA
* *
258788 AAATAAAAAT-ATTTAAATTACAATGATGATATAC
1 AAATAAAAATCATTCAAA-TACAATAATGATATAC
*
258822 AAATAAAAATCATTCAAATACAATAATGATTTAC
1 AAATAAAAATCATTCAAATACAATAATGATATAC
258856 A
1 A
258857 TCACAACCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 25 0.81
35 6 0.19
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (34 bp):
AAATAAAAATCATTCAAATACAATAATGATATAC
Found at i:270218 original size:16 final size:17
Alignment explanation
Indices: 270199--270234 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
270189 ATATTCCAAA
270199 TTATTTAAATTA-AATT
1 TTATTTAAATTATAATT
*
270215 TTATTTGAATTATAATT
1 TTATTTAAATTATAATT
270232 TTA
1 TTA
270235 AGTTATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TTATTTAAATTATAATT
Found at i:278858 original size:18 final size:18
Alignment explanation
Indices: 278835--278870 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
278825 ACATTTATTA
278835 TTAAATA-ATTATTATTTT
1 TTAAATATA-TATTATTTT
278853 TTAAATATATATTATTTT
1 TTAAATATATATTATTTT
278871 ATAATCACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 16 0.94
19 1 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTAAATATATATTATTTT
Found at i:279446 original size:37 final size:37
Alignment explanation
Indices: 279393--279463 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
279383 TTCATTTATA
*
279393 TTTATTTATTTATTAAATGAATAAATATAAATAATTT
1 TTTATTTATTTATTAAATGAATAAACATAAATAATTT
*
279430 TTTATTT-TTTATTTAAATGAATGAACATAAATAA
1 TTTATTTATTTA-TTAAATGAATAAACATAAATAA
279464 ATAAATAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 4 0.13
37 27 0.87
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (37 bp):
TTTATTTATTTATTAAATGAATAAACATAAATAATTT
Found at i:280948 original size:9 final size:10
Alignment explanation
Indices: 280929--280969 Score: 59
Period size: 9 Copynumber: 4.3 Consensus size: 10
280919 CTATTTTTTG
280929 TTTGTAATTT
1 TTTGTAATTT
280939 TTTG-AATTT
1 TTTGTAATTT
280948 TTTGTAATTT
1 TTTGTAATTT
*
280958 TTT-TGATTT
1 TTTGTAATTT
280967 TTT
1 TTT
280970 ATATTTATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 17 0.59
10 12 0.41
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.73
Consensus pattern (10 bp):
TTTGTAATTT
Found at i:280953 original size:19 final size:19
Alignment explanation
Indices: 280929--280969 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
280919 CTATTTTTTG
280929 TTTGTAA-TTTTTTGAATTT
1 TTTGTAATTTTTTTG-ATTT
280948 TTTGTAATTTTTTTGATTT
1 TTTGTAATTTTTTTGATTT
280967 TTT
1 TTT
280970 ATATTTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.73
Consensus pattern (19 bp):
TTTGTAATTTTTTTGATTT
Found at i:281005 original size:16 final size:14
Alignment explanation
Indices: 280974--281010 Score: 56
Period size: 16 Copynumber: 2.5 Consensus size: 14
280964 TTTTTTATAT
280974 TTATAAAATTAATA
1 TTATAAAATTAATA
280988 TTATAATAATTAAATA
1 TTATAA-AATT-AATA
281004 TTATAAA
1 TTATAAA
281011 TAAAGTAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.29
15 5 0.24
16 10 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTATAAAATTAATA
Found at i:293290 original size:21 final size:19
Alignment explanation
Indices: 293264--293307 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
293254 TAATCTTGGT
293264 TTTCTTTAATAATTATCTCCG
1 TTTCTTTAATAA-TATC-CCG
**
293285 TTTCTTTTCTAATATCCCG
1 TTTCTTTAATAATATCCCG
293304 TTTC
1 TTTC
293308 CGTCCCCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.33
20 4 0.19
21 10 0.48
ACGTcount: A:0.18, C:0.23, G:0.05, T:0.55
Consensus pattern (19 bp):
TTTCTTTAATAATATCCCG
Found at i:299024 original size:20 final size:20
Alignment explanation
Indices: 298999--299044 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
298989 AGCTCGACTC
298999 AAGCTCGAAATCAAAAAATA
1 AAGCTCGAAATCAAAAAATA
299019 AAGCTCGAAATCAAAAAATA
1 AAGCTCGAAATCAAAAAATA
299039 AAGCTC
1 AAGCTC
299045 AACATAAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.57, C:0.17, G:0.11, T:0.15
Consensus pattern (20 bp):
AAGCTCGAAATCAAAAAATA
Found at i:303186 original size:2 final size:2
Alignment explanation
Indices: 303179--303236 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
303169 AAATTATCTC
303179 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
303221 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
303237 GAGAGAGAGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:307412 original size:305 final size:305
Alignment explanation
Indices: 306861--307471 Score: 1177
Period size: 305 Copynumber: 2.0 Consensus size: 305
306851 TATATAATAG
*
306861 AGGAGAGACACTTCGTCTCTCCCTCTTATAGGCTCTCTTCAATTTGTCATTCTTATAATCCTATT
1 AGGAGAGACACTTCGTCTCTCCCTCTTATAGGCTCTCTTCAATTTATCATTCTTATAATCCTATT
* * *
306926 TATCTCTTAACTTAGATGACACTTCATCTAAATCAAAAAAGATAATCACAAATCACGATTTAACT
66 TATCTCTTAACTTAGATAACACTTCATCTAAATAAAAAAAGATAATCACAAATCACGACTTAACT
306991 GTCTCATTTTCATCATAGATCACCATTAATGAGAATTAATGAGAGGCACGAAGGGAAGTTTCAAA
131 GTCTCATTTTCATCATAGATCACCATTAATGAGAATTAATGAGAGGCACGAAGGGAAGTTTCAAA
*
307056 ACCAGACCATTATCTATTTCAAATTTCAGTAGCGTATTTAGATTTTAAAACCAGAATCGAGGTTT
196 ACCACACCATTATCTATTTCAAATTTCAGTAGCGTATTTAGATTTTAAAACCAGAATCGAGGTTT
307121 CGAAATTGGGATACCCGGTTTTGATACCAACTTGCTAGTTTCCAA
261 CGAAATTGGGATACCCGGTTTTGATACCAACTTGCTAGTTTCCAA
307166 AGGAGAGACACTTCGTCTCTCCCTCTTATAGGCTCTCTTCAATTTATCATTCTTATAATCCTATT
1 AGGAGAGACACTTCGTCTCTCCCTCTTATAGGCTCTCTTCAATTTATCATTCTTATAATCCTATT
307231 TATCTCTTAACTTAGATAACACTTCATCTAAATAAAAAAAGATAATCACAAATCACGACTTAACT
66 TATCTCTTAACTTAGATAACACTTCATCTAAATAAAAAAAGATAATCACAAATCACGACTTAACT
307296 GTCTCATTTTCATCATAGATCACCATTAATGAGAATTAATGAGAGGCACGAAGGGAAGTTTCAAA
131 GTCTCATTTTCATCATAGATCACCATTAATGAGAATTAATGAGAGGCACGAAGGGAAGTTTCAAA
307361 ACCACACCATTATCTATTTCAAATTTCAGTAGCGTATTTAGATTTTAAAACCAGAATCGAGGTTT
196 ACCACACCATTATCTATTTCAAATTTCAGTAGCGTATTTAGATTTTAAAACCAGAATCGAGGTTT
307426 CGAAATTGGGATACCCGGTTTTGATACCAACTTGCTAGTTTCCAA
261 CGAAATTGGGATACCCGGTTTTGATACCAACTTGCTAGTTTCCAA
307471 A
1 A
307472 CTACTGTAGC
Statistics
Matches: 301, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
305 301 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (305 bp):
AGGAGAGACACTTCGTCTCTCCCTCTTATAGGCTCTCTTCAATTTATCATTCTTATAATCCTATT
TATCTCTTAACTTAGATAACACTTCATCTAAATAAAAAAAGATAATCACAAATCACGACTTAACT
GTCTCATTTTCATCATAGATCACCATTAATGAGAATTAATGAGAGGCACGAAGGGAAGTTTCAAA
ACCACACCATTATCTATTTCAAATTTCAGTAGCGTATTTAGATTTTAAAACCAGAATCGAGGTTT
CGAAATTGGGATACCCGGTTTTGATACCAACTTGCTAGTTTCCAA
Found at i:308573 original size:2 final size:2
Alignment explanation
Indices: 308566--308654 Score: 53
Period size: 2 Copynumber: 47.0 Consensus size: 2
308556 AAATAATTAT
* * * * * *
308566 TA TA TA TA TA TA TA T- TA -A TA AA TT TA AA T- TA AA TT TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
308605 TA TA TA TA TA TA TA TA TA TA -A TA TT TA TA TA TT TA -A TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
308645 AA TA TA TA TA
1 TA TA TA TA TA
308655 CCTGGCCCGA
Statistics
Matches: 62, Mismatches: 20, Indels: 10
0.67 0.22 0.11
Matches are distributed among these distances:
1 5 0.08
2 57 0.92
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:308587 original size:37 final size:38
Alignment explanation
Indices: 308546--308654 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 38
308536 ATCCGGCCTG
* *
308546 ATAAATATTAAAATAATTATTATATATATATATAT-TA-
1 ATAAATATTAAAATAAAT-TTAAATATATATATATATAT
*
308583 ATAAAT-TTAAATTAAATTTAAATATATATATATATAT
1 ATAAATATTAAAATAAATTTAAATATATATATATATAT
* *
308620 ATATAATATTTATATATTTAATTTAAATATATATA
1 ATA-AATA-TTA-A-AATAAATTTAAATATATATA
308655 CCTGGCCCGA
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
35 15 0.25
36 11 0.18
37 9 0.15
38 3 0.05
40 3 0.05
41 1 0.02
42 19 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (38 bp):
ATAAATATTAAAATAAATTTAAATATATATATATATAT
Found at i:310593 original size:214 final size:214
Alignment explanation
Indices: 310224--310653 Score: 851
Period size: 214 Copynumber: 2.0 Consensus size: 214
310214 AACCGACTAA
310224 AACCATAGCAGTAGGCAGGACTAAACCATTTAATGAAACCTTATAAACAGAGTAAAGGGTTTAAA
1 AACCATAGCAGTAGGCAGGACTAAACCATTTAATGAAACCTTATAAACAGAGTAAAGGGTTTAAA
310289 AACAAAGGACCACTGGCAATTAAAAATAGCAAATAACCCTATAATCAGGAGACTTTATGTTGCAT
66 AACAAAGGACCACTGGCAATTAAAAATAGCAAATAACCCTATAATCAGGAGACTTTATGTTGCAT
310354 TATTCACACTTTACTCACCAACCCCTTTCACCATCTAGTATAAAGAATCAAACAAGAACACACTT
131 TATTCACACTTTACTCACCAACCCCTTTCACCATCTAGTATAAAGAATCAAACAAGAACACACTT
310419 CCTGCACATCTAACAAAAG
196 CCTGCACATCTAACAAAAG
310438 AACCATAGCAGTAGGCAGGACTAAACCATTTAATGAAACCTTATAAACAGAGTAAAGGGTTTAAA
1 AACCATAGCAGTAGGCAGGACTAAACCATTTAATGAAACCTTATAAACAGAGTAAAGGGTTTAAA
310503 AACAAAGGACCACTGGCAATTAAAAATAGCAAATAACCCTATAATCAGGAGACTTTATGTTGCAT
66 AACAAAGGACCACTGGCAATTAAAAATAGCAAATAACCCTATAATCAGGAGACTTTATGTTGCAT
*
310568 TATTCACACTTTACTCACCAACCCCTTTCACCATCTAGTATAAAGAATCAAACAAGAACACTCTT
131 TATTCACACTTTACTCACCAACCCCTTTCACCATCTAGTATAAAGAATCAAACAAGAACACACTT
310633 CCTGCACATCTAACAAAAG
196 CCTGCACATCTAACAAAAG
310652 AA
1 AA
310654 ACCCAAAAAA
Statistics
Matches: 215, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
214 215 1.00
ACGTcount: A:0.42, C:0.22, G:0.13, T:0.23
Consensus pattern (214 bp):
AACCATAGCAGTAGGCAGGACTAAACCATTTAATGAAACCTTATAAACAGAGTAAAGGGTTTAAA
AACAAAGGACCACTGGCAATTAAAAATAGCAAATAACCCTATAATCAGGAGACTTTATGTTGCAT
TATTCACACTTTACTCACCAACCCCTTTCACCATCTAGTATAAAGAATCAAACAAGAACACACTT
CCTGCACATCTAACAAAAG
Found at i:311278 original size:21 final size:21
Alignment explanation
Indices: 311254--311303 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
311244 AGCACCACCG
*
311254 CCGCCTCCACCGCCACCATAA
1 CCGCCGCCACCGCCACCATAA
* *
311275 CCGCCGCCGCCTCCACCATAA
1 CCGCCGCCACCGCCACCATAA
*
311296 CCACCGCC
1 CCGCCGCC
311304 GCCTCCATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.20, C:0.60, G:0.12, T:0.08
Consensus pattern (21 bp):
CCGCCGCCACCGCCACCATAA
Found at i:311304 original size:21 final size:21
Alignment explanation
Indices: 311266--311310 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
311256 GCCTCCACCG
*
311266 CCACCATAACCGCCGCCGCCT
1 CCACCATAACCACCGCCGCCT
311287 CCACCATAACCACCGCCGCCT
1 CCACCATAACCACCGCCGCCT
311308 CCA
1 CCA
311311 TATCTGCCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.22, C:0.58, G:0.11, T:0.09
Consensus pattern (21 bp):
CCACCATAACCACCGCCGCCT
Found at i:312400 original size:6 final size:6
Alignment explanation
Indices: 312383--312412 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
312373 CAACAATTAG
312383 TTAAAA -TAAAA TTAAAA TTAAAA TTAAAA T
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA T
312413 GTAATGCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
TTAAAA
Found at i:316817 original size:28 final size:24
Alignment explanation
Indices: 316747--316800 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
316737 ATATGAACAT
316747 GAACACATAAAAAAATAAACAAAC
1 GAACACATAAAAAAATAAACAAAC
316771 GAACACATAAAAAAATAAACAAAC
1 GAACACATAAAAAAATAAACAAAC
316795 GAACAC
1 GAACAC
316801 GATATTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.69, C:0.19, G:0.06, T:0.07
Consensus pattern (24 bp):
GAACACATAAAAAAATAAACAAAC
Found at i:326883 original size:27 final size:26
Alignment explanation
Indices: 326839--326898 Score: 61
Period size: 27 Copynumber: 2.3 Consensus size: 26
326829 ATGGATAAAC
* *
326839 TACTTATTTGGTCCCTC-ATCTATTAAT
1 TACTTTTTTGGTCACTCAAT-TATT-AT
*
326866 TACTTTTTTGGTTACTCAATTATTAT
1 TACTTTTTTGGTCACTCAATTATTAT
326892 TA-TTTTT
1 TACTTTTT
326899 CAAAATCATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 5 0.17
26 4 0.14
27 18 0.62
28 2 0.07
ACGTcount: A:0.22, C:0.15, G:0.07, T:0.57
Consensus pattern (26 bp):
TACTTTTTTGGTCACTCAATTATTAT
Found at i:328337 original size:26 final size:26
Alignment explanation
Indices: 328285--328336 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
328275 ATATACATAT
***
328285 ATGTTGAAGGTACTTGCTCTTGCAAA
1 ATGTTGAAGGTACTTGCTCAACCAAA
328311 ATGTTGAAGGTACTTGC-CAACCAAA
1 ATGTTGAAGGTACTTGCTCAACCAAA
328336 A
1 A
328337 ACAACAGAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (26 bp):
ATGTTGAAGGTACTTGCTCAACCAAA
Found at i:331703 original size:2 final size:2
Alignment explanation
Indices: 331696--331720 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
331686 AAATGATTAT
331696 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
331721 CACAAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:339850 original size:22 final size:22
Alignment explanation
Indices: 339825--339873 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
339815 ATTTATTAAG
339825 AAAAT-AACAATAAACAGA-ATAT
1 AAAATGAA-AATAAA-AGATATAT
*
339847 AAAATGAAAATAAAATATATAT
1 AAAATGAAAATAAAAGATATAT
339869 AAAAT
1 AAAAT
339874 TAAAGTGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 2 0.08
22 20 0.83
23 2 0.08
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.22
Consensus pattern (22 bp):
AAAATGAAAATAAAAGATATAT
Found at i:347104 original size:36 final size:36
Alignment explanation
Indices: 347005--347291 Score: 350
Period size: 36 Copynumber: 8.1 Consensus size: 36
346995 TTCGTTCTAG
* * *
347005 TTGAATCGGAAGTG-CAATGCTTCTTTCCGTTCAAC
1 TTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGAC
* * *
347040 TTGAATCGGAAGTG-TGATGCTTCTTTCCGTTCGAT
1 TTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGAC
*
347075 TTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGAT
1 TTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGAC
* *
347111 TTGAATCGGAAGTGCTGATGCTTCCTTCCGTTCGAT
1 TTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGAC
* *
347147 TTGAATCGGAAGTGCCGATGCTTTCTTCCGTTCAAC
1 TTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGAC
* * *
347183 TTGAATCGGAAGTGTCGATTCCTT-CTTCCATTCGAC
1 TTGAATCGGAAGTGCCGA-TGCTTCCTTCCGTTCGAC
* *
347219 TTGAATCGGAAGTGTCGATGCCTT-CTTCCGTTCGAA
1 TTGAATCGGAAGTGCCGATG-CTTCCTTCCGTTCGAC
* * *
347255 TTGAATCGGAAGTGCCAATCCTTCCTTCTGTTC-AC
1 TTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGAC
347290 TT
1 TT
347292 CCATTCTGTC
Statistics
Matches: 225, Mismatches: 23, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
35 52 0.23
36 169 0.75
37 4 0.02
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (36 bp):
TTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGAC
Found at i:350866 original size:18 final size:18
Alignment explanation
Indices: 350839--350887 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
350829 TTCGGAGAAG
*
350839 GGCAACGGTGGCA-TCGGA
1 GGCAATGGTGGCAGT-GGA
350857 GGCAATGGTGGCAGTGGA
1 GGCAATGGTGGCAGTGGA
*
350875 GGCAATCGTGGCA
1 GGCAATGGTGGCA
350888 AAGGCGGCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 27 0.96
19 1 0.04
ACGTcount: A:0.22, C:0.18, G:0.45, T:0.14
Consensus pattern (18 bp):
GGCAATGGTGGCAGTGGA
Found at i:352247 original size:2 final size:2
Alignment explanation
Indices: 352240--352287 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
352230 TGAATTATTG
352240 AT AT AT AT AT 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 AT AT AT AT AT
352282 AT AT AT
1 AT AT AT
352288 GTCCACTGTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:358514 original size:57 final size:57
Alignment explanation
Indices: 358442--358557 Score: 137
Period size: 57 Copynumber: 2.0 Consensus size: 57
358432 TGGAGTCGGA
*
358442 GGTTTGTACACTGGAACT-GATGGAGGTAA-TGGTTTCTTGTATACAGGAACTGGAGGG
1 GGTTTGTACACTGGAACTGGA-GGAGG-AAGTGGTTTCTTATATACAGGAACTGGAGGG
* * * * * *
358499 GGTTTGTAGATTGGAATTGGAGGAGGAAGTGGTTTCTTATATACCGGATCTGGTGGG
1 GGTTTGTACACTGGAACTGGAGGAGGAAGTGGTTTCTTATATACAGGAACTGGAGGG
358556 GG
1 GG
358558 AAGCGGTTTC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
56 2 0.04
57 46 0.92
58 2 0.04
ACGTcount: A:0.22, C:0.09, G:0.38, T:0.31
Consensus pattern (57 bp):
GGTTTGTACACTGGAACTGGAGGAGGAAGTGGTTTCTTATATACAGGAACTGGAGGG
Found at i:358746 original size:33 final size:33
Alignment explanation
Indices: 358510--358734 Score: 261
Period size: 33 Copynumber: 6.8 Consensus size: 33
358500 GTTTGTAGAT
* *
358510 TGGAATTGGAGGAGGAAGTGGTTTCTTATATAC
1 TGGAACTGGAGGAGGAAGTGGCTTCTTATATAC
* * * * * *
358543 CGGATCTGGTGGGGGAAGCGGTTTCTTATATAC
1 TGGAACTGGAGGAGGAAGTGGCTTCTTATATAC
* * * * *
358576 TGGAACTGGAGGAGGATGTGGTTTCCTATAGAT
1 TGGAACTGGAGGAGGAAGTGGCTTCTTATATAC
358609 TGGAACTGGAGGAGGAAGTGGCTTCTTATATAC
1 TGGAACTGGAGGAGGAAGTGGCTTCTTATATAC
* * * *
358642 TGGAAATGGCGGAGGATGTGGCTTCTTGTATAC
1 TGGAACTGGAGGAGGAAGTGGCTTCTTATATAC
* * *
358675 TGGTACTGGCGGAGGAAGTGGCTTCTTGTATAC
1 TGGAACTGGAGGAGGAAGTGGCTTCTTATATAC
*
358708 TGGAACTGGTGGAGGAAGTGGCTTCTT
1 TGGAACTGGAGGAGGAAGTGGCTTCTT
358735 GTATTTTGGA
Statistics
Matches: 163, Mismatches: 29, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 163 1.00
ACGTcount: A:0.22, C:0.12, G:0.36, T:0.30
Consensus pattern (33 bp):
TGGAACTGGAGGAGGAAGTGGCTTCTTATATAC
Found at i:358815 original size:57 final size:57
Alignment explanation
Indices: 358708--358816 Score: 130
Period size: 57 Copynumber: 1.9 Consensus size: 57
358698 TCTTGTATAC
* * ** *
358708 TGGAACTGGTGGAGGAAGTGGCTTCTTGTATTTTGGAACCGGTGGAGGTTTATAGAT
1 TGGAACAGGTGGAGGAAGTGGCTTCTTATATACTGGAACCGGCGGAGGTTTATAGAT
* * *
358765 TGGAACAGGTGGAGGAAGTGG-TTTTTCATATACTGGAACTGGCGGTGGTTTA
1 TGGAACAGGTGGAGGAAGTGGCTTCTT-ATATACTGGAACCGGCGGAGGTTTA
358817 GACACCGGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
56 4 0.09
57 39 0.91
ACGTcount: A:0.22, C:0.09, G:0.37, T:0.32
Consensus pattern (57 bp):
TGGAACAGGTGGAGGAAGTGGCTTCTTATATACTGGAACCGGCGGAGGTTTATAGAT
Found at i:363582 original size:33 final size:33
Alignment explanation
Indices: 363475--363766 Score: 205
Period size: 33 Copynumber: 8.7 Consensus size: 33
363465 CGGAGGTTGT
* *
363475 TTGTACACTGGAACTGGTGGAGGTAA-TGGTTTC
1 TTGTATACTGGAACTGGAGGAGG-AAGTGGTTTC
* * *
363508 CTGTATACAGGAACTGGAGGAGGAAATGGTTTC
1 TTGTATACTGGAACTGGAGGAGGAAGTGGTTTC
* * *
363541 TTATATACCGGAACTGGTGGAGGAAGTGGTTTC
1 TTGTATACTGGAACTGGAGGAGGAAGTGGTTTC
* * * * * ***
363574 TTGTATACCGGGACCGGAGGAGATTTATAGACCGGAGGC
1 TTGTATACTGGAACTGGAGGAG---GA-AG--TGGTTTC
* * *
363613 TTGTAAACTGGGACTGGA-GATGGATGTGGTTTC
1 TTGTATACTGGAACTGGAGGA-GGAAGTGGTTTC
* * *
363646 TTATAGACTGGAACTGGA-GAGGGATGTGGTTTC
1 TTGTATACTGGAACTGGAGGA-GGAAGTGGTTTC
* * * *
363679 TTATGTACTGGAACTGGAGGAAGAAGTGGCTTC
1 TTGTATACTGGAACTGGAGGAGGAAGTGGTTTC
*
363712 TTGTATACTGGAACTGGTGGAGGAAGTGGTTT-
1 TTGTATACTGGAACTGGAGGAGGAAGTGGTTTC
** *
363744 TCATATACTGGAACTGGCGGAGG
1 TTGTATACTGGAACTGGAGGAGG
363767 TTTAGACACC
Statistics
Matches: 206, Mismatches: 44, Indels: 19
0.77 0.16 0.07
Matches are distributed among these distances:
32 22 0.11
33 156 0.76
34 2 0.01
35 1 0.00
36 2 0.01
37 2 0.01
38 2 0.01
39 19 0.09
ACGTcount: A:0.25, C:0.12, G:0.35, T:0.28
Consensus pattern (33 bp):
TTGTATACTGGAACTGGAGGAGGAAGTGGTTTC
Found at i:366484 original size:28 final size:28
Alignment explanation
Indices: 366453--366526 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 28
366443 AAGAGACATA
* ** *
366453 ATGAAAATTTTAAAAATTTTGGGGCTTG
1 ATGAAAATTTTAAAAAATGAGGGGCCTG
* *
366481 ATGATAATATCTAAAAAATGAGGGGCCTG
1 ATGAAAAT-TTTAAAAAATGAGGGGCCTG
*
366510 ATTAAAATTTTAAAAAA
1 ATGAAAATTTTAAAAAA
366527 AACATCATGT
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
28 15 0.42
29 21 0.58
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32
Consensus pattern (28 bp):
ATGAAAATTTTAAAAAATGAGGGGCCTG
Found at i:372440 original size:32 final size:31
Alignment explanation
Indices: 372387--372446 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
372377 AATGTTTGGG
*
372387 GAAATTTAAATTACACCCCTCAATTTTGTTA
1 GAAATTTAAATTACACCCCTCAAATTTGTTA
* **
372418 GAAATTTTAATTAGGCCTCCTCAAATTTG
1 GAAATTTAAATTACACC-CCTCAAATTTG
372447 CTAAAAATAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 14 0.58
32 10 0.42
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.38
Consensus pattern (31 bp):
GAAATTTAAATTACACCCCTCAAATTTGTTA
Found at i:375753 original size:23 final size:22
Alignment explanation
Indices: 375727--375771 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
375717 TTATTATATT
375727 TTTAA-TATTTTATATTTAATTTA
1 TTTAAGTATTTTA-ATTT-ATTTA
375750 TTTAAGTATTTTAATTTATTTA
1 TTTAAGTATTTTAATTTATTTA
375772 ATATTTTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.24
23 9 0.43
24 7 0.33
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTAAGTATTTTAATTTATTTA
Found at i:375776 original size:17 final size:17
Alignment explanation
Indices: 375732--375779 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
375722 ATATTTTTAA
*
375732 TATTTTATA-TTTAATT
1 TATTTAATATTTTAATT
375748 TATTTAAGTATTTTAATT
1 TATTTAA-TATTTTAATT
375766 TATTTAATATTTTA
1 TATTTAATATTTTA
375780 CTTATATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 6 0.21
17 9 0.31
18 14 0.48
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
TATTTAATATTTTAATT
Found at i:382842 original size:23 final size:23
Alignment explanation
Indices: 382814--382865 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
382804 TTGAATGATT
* *
382814 AAAAATAT-ATCATAAAGACAGAA
1 AAAAATATGA-CATAAAAACAAAA
382837 AAAAATATGACATAAAAACAAAA
1 AAAAATATGACATAAAAACAAAA
382860 AAAAAT
1 AAAAAT
382866 CATAAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 25 0.96
24 1 0.04
ACGTcount: A:0.71, C:0.08, G:0.06, T:0.15
Consensus pattern (23 bp):
AAAAATATGACATAAAAACAAAA
Found at i:382914 original size:16 final size:16
Alignment explanation
Indices: 382893--382924 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
382883 TATAAATTAA
382893 ATATAAAAAAATAAAT
1 ATATAAAAAAATAAAT
382909 ATATAAAAAAATAAAT
1 ATATAAAAAAATAAAT
382925 GAAAAATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
ATATAAAAAAATAAAT
Found at i:383674 original size:14 final size:14
Alignment explanation
Indices: 383657--383715 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
383647 ATATTAAATA
383657 ATAAATATAATTAT
1 ATAAATATAATTAT
* *
383671 ATAACTATAATTAAAAA
1 ATAAATATAATT---AT
383688 ATAAAATATAATTAT
1 AT-AAATATAATTAT
*
383703 ATAACTATAATTA
1 ATAAATATAATTA
383716 AAAAATAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
14 21 0.58
15 3 0.08
17 3 0.08
18 9 0.25
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.37
Consensus pattern (14 bp):
ATAAATATAATTAT
Found at i:383700 original size:32 final size:32
Alignment explanation
Indices: 383649--383724 Score: 136
Period size: 32 Copynumber: 2.4 Consensus size: 32
383639 GGTAAAACAT
*
383649 ATTAAATAAT-AAATATAATTATATAACTATA
1 ATTAAAAAATAAAATATAATTATATAACTATA
383680 ATTAAAAAATAAAATATAATTATATAACTATA
1 ATTAAAAAATAAAATATAATTATATAACTATA
383712 ATTAAAAAATAAA
1 ATTAAAAAATAAA
383725 TTTGGGGCTA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 9 0.21
32 34 0.79
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (32 bp):
ATTAAAAAATAAAATATAATTATATAACTATA
Found at i:395910 original size:29 final size:31
Alignment explanation
Indices: 395863--395929 Score: 77
Period size: 29 Copynumber: 2.2 Consensus size: 31
395853 TTAAAATTTA
395863 ATATTTTTATATATGTTAAATAATTT-TAAAT
1 ATATTTTTATATATGTTAAA-AATTTATAAAT
* *
395894 ATATTTTTA-ATCT-TTAAAATTTTATAAAT
1 ATATTTTTATATATGTTAAAAATTTATAAAT
*
395923 TTATTTT
1 ATATTTT
395930 ACTAAAATAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 4 0.12
29 16 0.50
30 3 0.09
31 9 0.28
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (31 bp):
ATATTTTTATATATGTTAAAAATTTATAAAT
Found at i:407097 original size:18 final size:17
Alignment explanation
Indices: 407074--407116 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
407064 ATATATACAT
407074 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
407092 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
407109 ATAA-AATA
1 ATAATAATA
407117 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:407550 original size:37 final size:36
Alignment explanation
Indices: 407507--407608 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
407497 ATAGTAGAAC
407507 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
407544 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
407578 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
407609 TAGGACGAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
34 33 0.54
37 28 0.46
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:408455 original size:105 final size:105
Alignment explanation
Indices: 408156--408882 Score: 1106
Period size: 105 Copynumber: 7.0 Consensus size: 105
408146 CATTGTTCCA
* * * ** * *
408156 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGTTCTG-GAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGAGAAGTTG-TTGTTGACAA
* * * * *
408220 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
408262 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGA-A-TGA-AA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAAGC
408322 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
408362 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTTAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAAGC
*
408427 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
408467 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAAGC
**
408532 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
408572 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAAGC
408637 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
408677 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAAGC
408742 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
408782 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTG-TTGTTGACAAG
* * * *
408847 CAGCCGTCCCTTTGTTGTGAAGTTGAACTTGTGTTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
408883 CCTCGAGTGC
Statistics
Matches: 580, Mismatches: 34, Indels: 14
0.92 0.05 0.02
Matches are distributed among these distances:
100 84 0.14
101 1 0.00
102 4 0.01
103 4 0.01
104 3 0.01
105 408 0.70
106 76 0.13
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:409699 original size:65 final size:67
Alignment explanation
Indices: 409526--409681 Score: 199
Period size: 68 Copynumber: 2.3 Consensus size: 67
409516 AGATATCTGT
* * * * ** *
409526 TGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGAGT
409591 TTG
65 TTG
* *
409594 TGTTTCAAGAGTAACTGTCTCAAAGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAG-GTT
1 TGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
409658 T-
66 TG
*
409659 TGTTTCAAGGGAAACTGTCTCAA
1 TGTTTCAAGAGAAACTGTCTCAA
409682 GATAGACGAA
Statistics
Matches: 77, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
65 21 0.27
66 3 0.04
67 22 0.29
68 31 0.40
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.32
Consensus pattern (67 bp):
TGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
TG
Found at i:409709 original size:36 final size:35
Alignment explanation
Indices: 409658--409990 Score: 254
Period size: 36 Copynumber: 9.5 Consensus size: 35
409648 TTCAAAGGTT
* *
409658 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
409694 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
409729 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
409767 TTGTTTCAA-AGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
* *
409796 TTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
409831 TTTATTTCAAGGGAAACTGTCTCAGGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
409868 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
409903 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
409939 CT-CTTCTAATGA-AAACGGTCTCAAGCGAGACAAATC
1 TTGTTTC-AA-GAGAAACTGTCTCAAGAGAGACAAA-A
* *
409975 TTGTTTTAAGAAAAAC
1 TTGTTTCAAGAGAAAC
409991 AATCATGAGT
Statistics
Matches: 238, Mismatches: 38, Indels: 42
0.75 0.12 0.13
Matches are distributed among these distances:
28 2 0.01
29 16 0.07
30 1 0.00
31 1 0.00
32 2 0.01
33 1 0.00
34 4 0.02
35 35 0.15
36 139 0.58
37 35 0.15
38 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:409768 original size:138 final size:137
Alignment explanation
Indices: 409606--409919 Score: 405
Period size: 138 Copynumber: 2.3 Consensus size: 137
409596 TTTCAAGAGT
* * * * *
409606 AACTGTCTCAAAGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGGTTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
* *
409671 AACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGT
66 AACTGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGT
409735 TCCAAAAGA
129 TCCAAAAGA
** * * * * *
409744 AACTGTCTCAAGGGAGACGGAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTTAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
* * * * * *
409809 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAGGATAGACGAAATTTGTTT
66 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
*
409874 CAAGAGA
131 CAAAAGA
*
409881 AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC
409920 TGTCTCAAGA
Statistics
Matches: 149, Mismatches: 26, Indels: 3
0.84 0.15 0.02
Matches are distributed among these distances:
137 49 0.33
138 100 0.67
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.27
Consensus pattern (137 bp):
AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
CAAAAGA
Found at i:409826 original size:102 final size:102
Alignment explanation
Indices: 409694--409882 Score: 274
Period size: 102 Copynumber: 1.9 Consensus size: 102
409684 TAGACGAAAA
409694 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGG-G
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA-TTCCAAAAGAAACTGTCTC-AGGAG
*
409758 AGACGGAATTTGTTTCAA-AGAAAACATATTCAAATATT
64 AGACGAAATTTGTTTCAAGAGAAAACATATTCAAATATT
* * * * ** *
409796 TTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAGGATAG
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAGGAGAG
409861 ACGAAATTTGTTTCAAGAGAAA
66 ACGAAATTTGTTTCAAGAGAAA
409883 CTGTCTCAAG
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
100 3 0.04
101 33 0.43
102 41 0.53
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.28
Consensus pattern (102 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAGGAGAG
ACGAAATTTGTTTCAAGAGAAAACATATTCAAATATT
Found at i:410445 original size:18 final size:18
Alignment explanation
Indices: 410418--410453 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
410408 TGTTGAATCC
* *
410418 CCAAATATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
410436 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
410454 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.06, T:0.22
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:410894 original size:22 final size:22
Alignment explanation
Indices: 410868--410916 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
410858 TTGTGTTTGG
* *
410868 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
410890 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
410912 TCAAA
1 TCAAA
410917 AGATTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:410923 original size:22 final size:22
Alignment explanation
Indices: 410880--410923 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
410870 AAAGGTTTGG
* * *
410880 CATTTGATGCTCAAAGGTTTGA
1 CATTGGATGCTCAAAAGATTGA
410902 CATTGGATGCTCAAAAGATTGA
1 CATTGGATGCTCAAAAGATTGA
410924 TGGGGTAGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
CATTGGATGCTCAAAAGATTGA
Found at i:411622 original size:35 final size:34
Alignment explanation
Indices: 411566--411639 Score: 80
Period size: 35 Copynumber: 2.1 Consensus size: 34
411556 TTCTTTTTGA
*
411566 TTTTTGCTTTTTTTTCCTTTTTGTT-CTTGTTTCTC
1 TTTTTGCTTTTTTTTCCTTTTT-TTGCTTCTTT-TC
**
411601 TTTTT-CTTTGTTTTTTGTTTTTTTGCTTCTTTTC
1 TTTTTGCTTT-TTTTTCCTTTTTTTGCTTCTTTTC
411635 TTTTT
1 TTTTT
411640 TGTTCTTGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
34 13 0.38
35 21 0.62
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (34 bp):
TTTTTGCTTTTTTTTCCTTTTTTTGCTTCTTTTC
Found at i:411631 original size:29 final size:28
Alignment explanation
Indices: 411583--411637 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 28
411573 TTTTTTTTCC
411583 TTTTTGTTCTTGTTTCTCTTTTTCTTTGT
1 TTTTTGTTCTTGTTTCTC-TTTTCTTTGT
411612 TTTTTGTT-TT-TTTGCTTCTTTTCTTT
1 TTTTTGTTCTTGTTT-C-TCTTTTCTTT
411638 TTTGTTCTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 3 0.12
28 11 0.46
29 10 0.42
ACGTcount: A:0.00, C:0.13, G:0.09, T:0.78
Consensus pattern (28 bp):
TTTTTGTTCTTGTTTCTCTTTTCTTTGT
Found at i:412819 original size:8 final size:8
Alignment explanation
Indices: 412803--412841 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
412793 AATGTAGATG
412803 AAAATGCA
1 AAAATGCA
*
412811 AAAAGGCA
1 AAAATGCA
412819 AAAATGC-
1 AAAATGCA
412826 AAAATGCA
1 AAAATGCA
*
412834 AGAATGCA
1 AAAATGCA
412842 CGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:412829 original size:15 final size:15
Alignment explanation
Indices: 412803--412841 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
412793 AATGTAGATG
412803 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
412819 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
412834 AGAATGCA
1 AAAATGCA
412842 CGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:413387 original size:18 final size:18
Alignment explanation
Indices: 413364--413403 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
413354 ATTAGTCTTT
413364 CAGAAGTGGATGTGAATC
1 CAGAAGTGGATGTGAATC
413382 CAGAAGTGGATGTGAATC
1 CAGAAGTGGATGTGAATC
413400 CAGA
1 CAGA
413404 CTTGAAGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.33, T:0.20
Consensus pattern (18 bp):
CAGAAGTGGATGTGAATC
Found at i:415974 original size:18 final size:17
Alignment explanation
Indices: 415951--415993 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
415941 ATATATACAT
415951 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
415969 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
415986 ATAA-AATA
1 ATAATAATA
415994 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:416427 original size:37 final size:36
Alignment explanation
Indices: 416384--416485 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
416374 ATAGTAGAAC
416384 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
416421 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
416455 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
416486 TAGGACGAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
34 33 0.54
37 28 0.46
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:417985 original size:24 final size:24
Alignment explanation
Indices: 417957--418005 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
417947 TAAATTATTG
*
417957 ATATATTATATATCATGTTATTTA
1 ATATATTATATATCACGTTATTTA
417981 ATATATTATATATCACGTTATTTA
1 ATATATTATATATCACGTTATTTA
418005 A
1 A
418006 GATAATGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (24 bp):
ATATATTATATATCACGTTATTTA
Found at i:419158 original size:13 final size:13
Alignment explanation
Indices: 419140--419164 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
419130 CGTACTGAGT
419140 TTTTTTTTTTTGA
1 TTTTTTTTTTTGA
419153 TTTTTTTTTTTG
1 TTTTTTTTTTTG
419165 TGTTGGGGGA
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:0.04, C:0.00, G:0.08, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTTTGA
Found at i:428304 original size:29 final size:29
Alignment explanation
Indices: 428262--428395 Score: 259
Period size: 29 Copynumber: 4.6 Consensus size: 29
428252 TACCGGGGGT
428262 AGGTCGCCATGCACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
*
428291 AGGTCGCCATGCACGCCCGGCGCCCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
428320 AGGTCGCCATGCACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
428349 AGGTCGCCATGCACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
428378 AGGTCGCCATGCACGCCC
1 AGGTCGCCATGCACGCCC
428396 CTGCGACCTA
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 103 1.00
ACGTcount: A:0.19, C:0.46, G:0.28, T:0.07
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAACC
Found at i:428446 original size:30 final size:30
Alignment explanation
Indices: 428410--428519 Score: 175
Period size: 30 Copynumber: 3.7 Consensus size: 30
428400 GACCTACCCC
428410 ACGACCTCCATGCACGCCCATGCACGCCCA
1 ACGACCTCCATGCACGCCCATGCACGCCCA
* * *
428440 ACGACCTCCATGCATGCCCAGGCACGTCCA
1 ACGACCTCCATGCACGCCCATGCACGCCCA
* *
428470 ACGACCTCCGTGCACGGCCATGCACGCCCA
1 ACGACCTCCATGCACGCCCATGCACGCCCA
428500 ACGACCTCCATGCACGCCCA
1 ACGACCTCCATGCACGCCCA
428520 GCTCGCCAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 70 1.00
ACGTcount: A:0.23, C:0.47, G:0.19, T:0.11
Consensus pattern (30 bp):
ACGACCTCCATGCACGCCCATGCACGCCCA
Found at i:429192 original size:21 final size:21
Alignment explanation
Indices: 429167--429210 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
429157 AATTTAGTTA
429167 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
429188 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
429209 AT
1 AT
429211 ATTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:429224 original size:28 final size:28
Alignment explanation
Indices: 429187--429240 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
429177 TAGTATAAAT
*
429187 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAATTTGTTAGTTTAAGTTATATTA
429215 TATTAATTTGTTAGTTTAAGTTATAT
1 TATTAATTTGTTAGTTTAAGTTATAT
429241 ATTAGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (28 bp):
TATTAATTTGTTAGTTTAAGTTATATTA
Found at i:429320 original size:41 final size:45
Alignment explanation
Indices: 429209--429320 Score: 115
Period size: 50 Copynumber: 2.4 Consensus size: 45
429199 AGTTTAAGTT
429209 ATATTATATTAATTTGTTAGTTTAAGTTATATATTAGATTATATAAAAA
1 ATATTA-ATTAATTTGTTAGTTTAAG-T-TATATTAGA-TATATAAAAA
* * *
429258 ATTAGTTAATTAGTTTCTTAGTTTAAG-T-TATTA-A-ATGTAAAAA
1 A-TA-TTAATTAATTTGTTAGTTTAAGTTATATTAGATATATAAAAA
429301 ATATTAATTAATTTGTTAGT
1 ATATTAATTAATTTGTTAGT
429321 GTGTTTAAAC
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
41 15 0.27
42 2 0.04
43 9 0.16
45 1 0.02
46 5 0.09
47 1 0.02
49 1 0.02
50 19 0.34
51 3 0.05
ACGTcount: A:0.40, C:0.01, G:0.10, T:0.49
Consensus pattern (45 bp):
ATATTAATTAATTTGTTAGTTTAAGTTATATTAGATATATAAAAA
Found at i:431609 original size:28 final size:28
Alignment explanation
Indices: 431578--431631 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
431568 ATAATCTAAT
*
431578 ATATAACTTAAACTAACAAATTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
431606 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
431632 ATTTATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:431638 original size:28 final size:28
Alignment explanation
Indices: 431574--431638 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
431564 TTATATAATC
*
431574 TAATATATAACTTAAACTAACAAATTAA
1 TAATATATAACTTAAACTAACAAACTAA
431602 T-ATAATATAACTTAAACTAACAAACTAA
1 TAAT-ATATAACTTAAACTAACAAACTAA
*
431630 TAATTTATA
1 TAATATATA
431639 CTAACAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (28 bp):
TAATATATAACTTAAACTAACAAACTAA
Found at i:431641 original size:21 final size:21
Alignment explanation
Indices: 431608--431656 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
431598 TTAATATAAT
431608 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
431629 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
431650 ATTAACT
1 A-TAACT
431657 AAATTTCTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:432344 original size:30 final size:30
Alignment explanation
Indices: 432299--432408 Score: 175
Period size: 30 Copynumber: 3.7 Consensus size: 30
432289 TTTGGCGAGC
432299 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
* * * *
432329 TGGCCGTGCACGGAGGTCGTTGGACGTGCC
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
*
432359 TGGGCATGCATGGAGGTCGTTGGGCGTGCA
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
432389 TGGGCGTGCATGGAGGTCGT
1 TGGGCGTGCATGGAGGTCGT
432409 GGGGTAGGTC
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 70 1.00
ACGTcount: A:0.11, C:0.19, G:0.47, T:0.23
Consensus pattern (30 bp):
TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
Found at i:432458 original size:29 final size:29
Alignment explanation
Indices: 432423--432556 Score: 259
Period size: 29 Copynumber: 4.6 Consensus size: 29
432413 TAGGTCGCAG
432423 GGGCGTGCATGGCGACCTGGTTGGTCGCC
1 GGGCGTGCATGGCGACCTGGTTGGTCGCC
432452 GGGCGTGCATGGCGACCTGGTTGGTCGCC
1 GGGCGTGCATGGCGACCTGGTTGGTCGCC
*
432481 GGGCGTGCATGGCGACCTGGTTGGGCGCC
1 GGGCGTGCATGGCGACCTGGTTGGTCGCC
432510 GGGCGTGCATGGCGACCTGGTTGGTCGCC
1 GGGCGTGCATGGCGACCTGGTTGGTCGCC
432539 GGGCGTGCATGGCGACCT
1 GGGCGTGCATGGCGACCT
432557 ACCCCCGGTA
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 103 1.00
ACGTcount: A:0.07, C:0.28, G:0.46, T:0.19
Consensus pattern (29 bp):
GGGCGTGCATGGCGACCTGGTTGGTCGCC
Found at i:436173 original size:20 final size:19
Alignment explanation
Indices: 436150--436206 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
436140 CACGGAATGT
436150 AAGATTATAAGTGGGAATAA
1 AAGATTATAA-TGGGAATAA
*
436170 AAGATTACCAATGGGAATAA
1 AAGATTA-TAATGGGAATAA
*
436190 AAGATTATTA-GGGAATA
1 AAGATTATAATGGGAATA
436207 GGATTACTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 7 0.21
19 1 0.03
20 23 0.70
21 2 0.06
ACGTcount: A:0.49, C:0.04, G:0.23, T:0.25
Consensus pattern (19 bp):
AAGATTATAATGGGAATAA
Found at i:441311 original size:23 final size:23
Alignment explanation
Indices: 441229--441302 Score: 103
Period size: 23 Copynumber: 3.2 Consensus size: 23
441219 CTAGTAATTA
** *
441229 ACCTATTTTATTAAATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
* *
441252 ACCTATTACATTATATAAGCACA
1 ACCTATTACATTATATAAGCGCT
441275 ACCTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
441298 ACCTA
1 ACCTA
441303 ATATGTTATT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.38, C:0.22, G:0.07, T:0.34
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:442541 original size:22 final size:23
Alignment explanation
Indices: 442504--442613 Score: 163
Period size: 22 Copynumber: 4.9 Consensus size: 23
442494 CCAGTAATTA
**
442504 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
442527 ACCTATTA-ATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
*
442549 ACATATTACATTATATAA-CGCT
1 ACCTATTACATTATATAAGCGCT
*
442571 ACCTATTACATTATATAAACGCT
1 ACCTATTACATTATATAAGCGCT
442594 ACCTATTACATTATA-AAGCG
1 ACCTATTACATTATATAAGCG
442614 GTATCTATGT
Statistics
Matches: 81, Mismatches: 4, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
22 46 0.57
23 35 0.43
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.36
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:442584 original size:45 final size:45
Alignment explanation
Indices: 442513--442613 Score: 161
Period size: 45 Copynumber: 2.3 Consensus size: 45
442503 AACCTATTTT
*
442513 ATTATATAAGCGCTACCTATTAATTATATAAGCGCTACATATTAC
1 ATTATATAAGCGCTACCTATTAATTATATAAACGCTACATATTAC
*
442558 ATTATATAA-CGCTACCTATTACATTATATAAACGCTACCTATTAC
1 ATTATATAAGCGCTACCTATTA-ATTATATAAACGCTACATATTAC
442603 ATTATA-AAGCG
1 ATTATATAAGCG
442614 GTATCTATGT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
44 14 0.27
45 38 0.73
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.35
Consensus pattern (45 bp):
ATTATATAAGCGCTACCTATTAATTATATAAACGCTACATATTAC
Found at i:442689 original size:23 final size:23
Alignment explanation
Indices: 442654--442727 Score: 112
Period size: 23 Copynumber: 3.2 Consensus size: 23
442644 CTAGTAATTA
**
442654 ACCTATTTTATTATATAAGCGTT
1 ACCTATTACATTATATAAGCGTT
*
442677 ACCTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGTT
*
442700 ACCTATTACATTATATAAGTGTT
1 ACCTATTACATTATATAAGCGTT
442723 ACCTA
1 ACCTA
442728 ATATAACATG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.41
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGTT
Found at i:460708 original size:6 final size:6
Alignment explanation
Indices: 460697--460723 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
460687 TGATCGAATT
460697 TTTAAA TTTAAA TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT
460724 TTGTAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:463590 original size:2 final size:2
Alignment explanation
Indices: 463583--463613 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
463573 CAGAGAAATA
463583 AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
463614 TCCTCTCAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:463602 original size:13 final size:13
Alignment explanation
Indices: 463586--463611 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
463576 AGAAATAATA
463586 TATATATATATAT
1 TATATATATATAT
463599 TATATATATATAT
1 TATATATATATAT
463612 ATTCCTCTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATATAT
Found at i:463604 original size:15 final size:15
Alignment explanation
Indices: 463584--463614 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
463574 AGAGAAATAA
463584 TATATATATATATAT
1 TATATATATATATAT
463599 TATATATATATATAT
1 TATATATATATATAT
463614 T
1 T
463615 CCTCTCAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:464199 original size:44 final size:44
Alignment explanation
Indices: 464136--464223 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
464126 TTTTCATTTT
464136 GCTGATGAAATATGGATAAACTGAATTGACATACTGACCATGCA
1 GCTGATGAAATATGGATAAACTGAATTGACATACTGACCATGCA
464180 GCTGATGAAATATGGATAAACTGAATTGACATACTGACCATGCA
1 GCTGATGAAATATGGATAAACTGAATTGACATACTGACCATGCA
464224 ACTCTATGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (44 bp):
GCTGATGAAATATGGATAAACTGAATTGACATACTGACCATGCA
Found at i:464782 original size:61 final size:61
Alignment explanation
Indices: 464674--464806 Score: 221
Period size: 61 Copynumber: 2.2 Consensus size: 61
464664 AAGGTAAAAT
* *
464674 ATGTCACATCAGTCGGTCAAGTGAGATCGAGCGTAATTTTGACCAAATAAGTTAGCCTAAC
1 ATGTCACATCAGTCGATCAAGTGAGATCGAGCGTAATTTTGACCAAATAAGCTAGCCTAAC
* * *
464735 ATGTTACATTAGTCGATCAAGTGAGATCGAGCGTAATTTTGATCAAATAAGCTAGCCTAAC
1 ATGTCACATCAGTCGATCAAGTGAGATCGAGCGTAATTTTGACCAAATAAGCTAGCCTAAC
464796 ATGTCACATCA
1 ATGTCACATCA
464807 ATTTTTTGTT
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.28
Consensus pattern (61 bp):
ATGTCACATCAGTCGATCAAGTGAGATCGAGCGTAATTTTGACCAAATAAGCTAGCCTAAC
Found at i:470167 original size:12 final size:12
Alignment explanation
Indices: 470145--470189 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
470135 AAAAGGATAA
470145 TCGAGTAAATGAG
1 TCGA-TAAATGAG
**
470158 TTTATAAATGAG
1 TCGATAAATGAG
470170 TCGATAAATGAG
1 TCGATAAATGAG
*
470182 TCAATAAA
1 TCGATAAA
470190 CAAGGTTACT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 25 0.93
13 2 0.07
ACGTcount: A:0.44, C:0.07, G:0.20, T:0.29
Consensus pattern (12 bp):
TCGATAAATGAG
Found at i:470834 original size:17 final size:19
Alignment explanation
Indices: 470794--470836 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
470784 AAATTTCAAC
*
470794 TATAATTATTTTAAATATT
1 TATAATTATCTTAAATATT
470813 T-TAATTA-CTTAAA-ATT
1 TATAATTATCTTAAATATT
470829 TATAATTA
1 TATAATTA
470837 ATAAATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 4 0.18
17 11 0.50
18 6 0.27
19 1 0.05
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
TATAATTATCTTAAATATT
Found at i:473031 original size:14 final size:12
Alignment explanation
Indices: 472998--473073 Score: 65
Period size: 12 Copynumber: 6.8 Consensus size: 12
472988 AGCTCAACAT
472998 AATTTTTT-TTA
1 AATTTTTTATTA
473009 AATTTTTTATTA
1 AATTTTTTATTA
**
473021 AATGCTTT-TT-
1 AATTTTTTATTA
473031 -ATTTTTTATTA
1 AATTTTTTATTA
473042 AATGTTTTT-TTA
1 AAT-TTTTTATTA
* *
473054 TA-TTTTTATTT
1 AATTTTTTATTA
473065 AATTTTTTA
1 AATTTTTTA
473074 AATAATTATG
Statistics
Matches: 51, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
9 5 0.10
10 7 0.14
11 13 0.25
12 21 0.41
13 5 0.10
ACGTcount: A:0.26, C:0.01, G:0.03, T:0.70
Consensus pattern (12 bp):
AATTTTTTATTA
Found at i:473036 original size:22 final size:22
Alignment explanation
Indices: 473010--473063 Score: 83
Period size: 21 Copynumber: 2.5 Consensus size: 22
473000 TTTTTTTTAA
473010 ATTTTTTATTAAATG-CTTTTT
1 ATTTTTTATTAAATGTCTTTTT
*
473031 ATTTTTTATTAAATGTTTTTTT
1 ATTTTTTATTAAATGTCTTTTT
473053 ATATTTTTATT
1 AT-TTTTTATT
473064 TAATTTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 15 0.50
22 7 0.23
23 8 0.27
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (22 bp):
ATTTTTTATTAAATGTCTTTTT
Found at i:473070 original size:21 final size:21
Alignment explanation
Indices: 473001--473072 Score: 74
Period size: 21 Copynumber: 3.3 Consensus size: 21
472991 TCAACATAAT
*
473001 TTTTTTTAAATTTTTTATTAAA
1 TTTTTTTATA-TTTTTATTAAA
*
473023 TGCTTTTTAT-TTTTTATTAAA
1 T-TTTTTTATATTTTTATTAAA
*
473044 TGTTTTTTTATATTTTTATTTAA
1 --TTTTTTTATATTTTTATTAAA
473067 TTTTTT
1 TTTTTT
473073 AAATAATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
21 17 0.40
22 8 0.19
23 17 0.40
ACGTcount: A:0.24, C:0.01, G:0.03, T:0.72
Consensus pattern (21 bp):
TTTTTTTATATTTTTATTAAA
Found at i:475891 original size:22 final size:22
Alignment explanation
Indices: 475851--475911 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
475841 GGGTCTACGC
* * *
475851 GGTCCTTCGAGACATATACAGA
1 GGTCCTTCGGGATAAATACAGA
*
475873 GGTCCTTCGGGATAAATACATA
1 GGTCCTTCGGGATAAATACAGA
* *
475895 GGTCATTTGGGATAAAT
1 GGTCCTTCGGGATAAAT
475912 TTCACATGCC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (22 bp):
GGTCCTTCGGGATAAATACAGA
Found at i:476594 original size:21 final size:21
Alignment explanation
Indices: 476570--476613 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
476560 TGCTGAAAGT
*
476570 ACTGTAGCAGTGCATCGGTAC
1 ACTGTAGCAGTGCATCGATAC
476591 ACTGTAGCAGTGCATCGATAC
1 ACTGTAGCAGTGCATCGATAC
476612 AC
1 AC
476614 ATTTTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGATAC
Found at i:479005 original size:2 final size:2
Alignment explanation
Indices: 478998--479024 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
478988 GAAGTTATTC
478998 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 A
479025 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:479029 original size:2 final size:2
Alignment explanation
Indices: 479024--479059 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
479014 ATATATATAT
*
479024 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
479060 GGGGAGGGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:479064 original size:8 final size:8
Alignment explanation
Indices: 479024--479079 Score: 58
Period size: 8 Copynumber: 7.0 Consensus size: 8
479014 ATATATATAT
*
479024 AGAGAGAG
1 AGAGAGGG
*
479032 AGAGAGAG
1 AGAGAGGG
*
479040 AGAGAGAG
1 AGAGAGGG
479048 AGAGAGGG
1 AGAGAGGG
*
479056 AGAGGGGG
1 AGAGAGGG
*
479064 AGGGAGGG
1 AGAGAGGG
*
479072 AGGGAGGG
1 AGAGAGGG
479080 TTATCCTAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 44 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (8 bp):
AGAGAGGG
Found at i:480754 original size:2 final size:2
Alignment explanation
Indices: 480747--480776 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
480737 CAACATCCTA
480747 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
480777 CACCATTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:485117 original size:31 final size:31
Alignment explanation
Indices: 485082--485144 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
485072 GTCTTGTTAG
*
485082 ATCCTATTAAATTAATGACGTGTCACCTTAA
1 ATCCTATTAAATTAATGACGTGCCACCTTAA
485113 ATCCTATTAAATTAATGACGTGCCACCTTAA
1 ATCCTATTAAATTAATGACGTGCCACCTTAA
485144 A
1 A
485145 ATAAAATGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.33
Consensus pattern (31 bp):
ATCCTATTAAATTAATGACGTGCCACCTTAA
Found at i:485345 original size:16 final size:16
Alignment explanation
Indices: 485308--485346 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
485298 CATTTGGAGA
* *
485308 ATATTTTTTAATATTT
1 ATATTTATTAAGATTT
485324 -TATTTATTAAGATTT
1 ATATTTATTAAGATTT
485339 ATATTTAT
1 ATATTTAT
485347 CAAATAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (16 bp):
ATATTTATTAAGATTT
Found at i:485525 original size:43 final size:43
Alignment explanation
Indices: 485477--485560 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
485467 AACTGCGATT
* *
485477 GCATTAGATTTAATCACATAAAATAAAA-TTAAAATTGGAATAA
1 GCATTAGATTTAACCACATAAAATAAAAGAT-AAATTGGAATAA
*
485520 GCATTAGATTTAACCACATTAAATAAAAGATAAATTGGAAT
1 GCATTAGATTTAACCACATAAAATAAAAGATAAATTGGAAT
485561 TTGGAAGTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 36 0.97
44 1 0.03
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (43 bp):
GCATTAGATTTAACCACATAAAATAAAAGATAAATTGGAATAA
Found at i:488107 original size:30 final size:30
Alignment explanation
Indices: 488073--488133 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
488063 TTCTGAAACT
*
488073 AAAGTTTTCAATCAATAATTGCATGAAAGA
1 AAAGTTTTCAATCAAAAATTGCATGAAAGA
488103 AAAGTTTTCAATCAAAAATTGCATGAAAGA
1 AAAGTTTTCAATCAAAAATTGCATGAAAGA
488133 A
1 A
488134 GAAGGCTTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.28
Consensus pattern (30 bp):
AAAGTTTTCAATCAAAAATTGCATGAAAGA
Found at i:492777 original size:2 final size:2
Alignment explanation
Indices: 492770--492802 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
492760 TAACTTATTA
492770 AT 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 AT A
492803 ATAAAGATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:501047 original size:11 final size:12
Alignment explanation
Indices: 501009--501050 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
500999 CACAAACAAT
*
501009 TATTGGGCCAGG
1 TATTGGGTCAGG
*
501021 TATTGGGTCGGG
1 TATTGGGTCAGG
501033 TATTGGGTC-GG
1 TATTGGGTCAGG
501044 TATTGGG
1 TATTGGG
501051 CTGGGAATCG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
11 9 0.32
12 19 0.68
ACGTcount: A:0.12, C:0.10, G:0.45, T:0.33
Consensus pattern (12 bp):
TATTGGGTCAGG
Found at i:501130 original size:24 final size:25
Alignment explanation
Indices: 501068--501130 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
501058 TCGGGCCGAG
501068 TATATA-TATATATATTTAAATTAAA
1 TATATATTATAT-TATTTAAATTAAA
*
501093 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
501117 T-T-TATTAATATTAT
1 TATATATT-ATATTAT
501131 ATATATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 1 0.03
24 19 0.58
25 8 0.24
26 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:501192 original size:13 final size:12
Alignment explanation
Indices: 501161--501197 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
501151 TTTTAATATT
*
501161 TATCGGGTCGGG
1 TATCGGGGCGGG
501173 TATCGGGGCGGG
1 TATCGGGGCGGG
501185 TAATCGGGGCGGG
1 T-ATCGGGGCGGG
501198 GATTACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.11, C:0.16, G:0.54, T:0.19
Consensus pattern (12 bp):
TATCGGGGCGGG
Found at i:502733 original size:68 final size:68
Alignment explanation
Indices: 502624--502760 Score: 220
Period size: 68 Copynumber: 2.0 Consensus size: 68
502614 AAAATTTATA
* * * *
502624 TTCATTTAATAAACGAACGAACACGAACATACGTGTGTTTTGTTCGTTTATGTTCTCAAATAGGT
1 TTCATTTAATAAACGAACGAACACGAACATACATGTGTTTTGTTCGTTTATGTTCACAAACAAGT
502689 TTG
66 TTG
* *
502692 TTCATTTAATAAACGAACGAACACGAACATATATGTGTTTTGTTGGTTTATGTTCACAAACAAGT
1 TTCATTTAATAAACGAACGAACACGAACATACATGTGTTTTGTTCGTTTATGTTCACAAACAAGT
502757 TTG
66 TTG
502760 T
1 T
502761 AATTAGATTA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (68 bp):
TTCATTTAATAAACGAACGAACACGAACATACATGTGTTTTGTTCGTTTATGTTCACAAACAAGT
TTG
Found at i:504891 original size:133 final size:133
Alignment explanation
Indices: 504653--504918 Score: 478
Period size: 133 Copynumber: 2.0 Consensus size: 133
504643 GTGATGCTGG
*
504653 TGTCAGGTATGCTGCTTTTAGTGACATGTTTGAAACTTACAAATGACACTGTTATTATTGATTGA
1 TGTCAGGTATGCTGCTTTAAGTGACATGTTTGAAACTTACAAATGACACTGTTATTATTGATTGA
* *
504718 TACCAGAAGCATATGACCTGTGAAAATGTGGATTTATAACTTTTATAAAGTGAAAACATGTCTCA
66 TACCAGAAGCATATGACCTGTGAAAATGTGGATTTATAACTTTCATAAAGCGAAAACATGTCTCA
504783 AGA
131 AGA
* *
504786 TGTCAGGTATGCTGCTTTAAGTGCCATGTTTGAAACTTACATATGACACTGTTATTATTGATTGA
1 TGTCAGGTATGCTGCTTTAAGTGACATGTTTGAAACTTACAAATGACACTGTTATTATTGATTGA
*
504851 TACCAGAAGCATATGACCTGTGAAAATGTTGATTTATAACTTTCATAAAGCGAAAACATGTCTCA
66 TACCAGAAGCATATGACCTGTGAAAATGTGGATTTATAACTTTCATAAAGCGAAAACATGTCTCA
504916 AGA
131 AGA
504919 AAATTTTCGT
Statistics
Matches: 127, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
133 127 1.00
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.34
Consensus pattern (133 bp):
TGTCAGGTATGCTGCTTTAAGTGACATGTTTGAAACTTACAAATGACACTGTTATTATTGATTGA
TACCAGAAGCATATGACCTGTGAAAATGTGGATTTATAACTTTCATAAAGCGAAAACATGTCTCA
AGA
Found at i:506011 original size:21 final size:21
Alignment explanation
Indices: 505986--506042 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
505976 TAATGAAAAT
*
505986 TCTTTGTATTAACATCACAAC
1 TCTTTATATTAACATCACAAC
* * *
506007 TCTTTATGTTAACATCATATC
1 TCTTTATATTAACATCACAAC
*
506028 TTTTTATATTAACAT
1 TCTTTATATTAACAT
506043 TAAATAAGTC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.32, C:0.18, G:0.04, T:0.47
Consensus pattern (21 bp):
TCTTTATATTAACATCACAAC
Found at i:506788 original size:15 final size:16
Alignment explanation
Indices: 506750--506789 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
506740 ACAGAGCCTC
*
506750 TGAATCATTCAGCATT
1 TGAATCATTCAACATT
*
506766 TGAATCATTCAACGTT
1 TGAATCATTCAACATT
506782 T-AATCATT
1 TGAATCATT
506790 TTGAAGTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (16 bp):
TGAATCATTCAACATT
Found at i:506984 original size:2 final size:2
Alignment explanation
Indices: 506979--507006 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
506969 TTAAAGGTGA
506979 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
507007 TAATAATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:512878 original size:32 final size:32
Alignment explanation
Indices: 512824--512884 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
512814 ATAATTTTTT
**
512824 TTTGTTCATGTTCGTTTTTTTAAGAAATATAG
1 TTTGTTCATGTTCGTTCATTTAAGAAATATAG
*
512856 TTTGTTCATGTTCGTTCATTTAATAAATA
1 TTTGTTCATGTTCGTTCATTTAAGAAATA
512885 AACGAACATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.52
Consensus pattern (32 bp):
TTTGTTCATGTTCGTTCATTTAAGAAATATAG
Done.