Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002890.1 Hibiscus syriacus cultivar Beakdansim tig00005974_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: 5046466
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 21
Found at i:2373601 original size:183 final size:184
Alignment explanation
Indices: 2373261--2373692 Score: 595
Period size: 183 Copynumber: 2.3 Consensus size: 184
2373251 AAATGAATCG
* * *
2373261 AAAAAACAAGAAAGAGGGAAAAAATTTGTGTTTATTTGGATCGAGGAAAGAAATAGGTGAAGAAC
1 AAAAAAC-ACAAAGAGAGAAAAAATTTGTGTTTATTTGGATCGAGGAAAGAGAT-GGTGAAGAAC
* * *
2373326 AATAGATGAAAGTTAGGGTTTGATAAAAAAAAAAGAATAGTTTTTTTAATTTTTTTGGATAGAAG
64 AATAGATAAAAGTTAGGGTTTGATAAAAAAAAAAGAAGAGTTTTTATAATTTTTTTGGATAGAAG
2373391 AAATAAAATGTTGAAGAACTGATGAAAAAACTTTTAGGGTTTTTTGGGTTTGATCC
129 AAATAAAATGTTGAAGAACTGATGAAAAAACTTTTAGGGTTTTTTGGGTTTGATCC
* *
2373447 AAAAAA-ACATAAGAGAGAAAAAGTTTATGTTTATTTGGATCGAGGAAAGAGATGGATGAAGAAC
1 AAAAAACACA-AAGAGAGAAAAAATTTGTGTTTATTTGGATCGAGGAAAGAGATGG-TGAAGAAC
* * * *
2373511 AATGGATAAAAGTTA-GGTTTGAT-TAAAAAAATGAAGAGTTTTTGAT-ATTTTTTTGGATCGAA
64 AATAGATAAAAGTTAGGGTTTGATAAAAAAAAAAGAAGAGTTTTT-ATAATTTTTTTGGATAGAA
* * *
2373573 GAGATAAAATGTTGAAGAATTGATGAAAAAACTTTTAGGGTTTTTTGGGTTTGATCG
128 GAAATAAAATGTTGAAGAACTGATGAAAAAACTTTTAGGGTTTTTTGGGTTTGATCC
* * * *
2373630 AAAAAACACAAA-AAATGAGAAATTTTGTGTTTATTTAGATCGAGGAAAGAGATTGGTGAAGAA
1 AAAAAACACAAAGAGA-GAAAAAATTTGTGTTTATTTGGATCGAGGAAAGAGA-TGGTGAAGAA
2373693 AAAAATGAAA
Statistics
Matches: 220, Mismatches: 20, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
182 2 0.01
183 133 0.60
184 19 0.09
185 60 0.27
186 6 0.03
ACGTcount: A:0.43, C:0.04, G:0.23, T:0.31
Consensus pattern (184 bp):
AAAAAACACAAAGAGAGAAAAAATTTGTGTTTATTTGGATCGAGGAAAGAGATGGTGAAGAACAA
TAGATAAAAGTTAGGGTTTGATAAAAAAAAAAGAAGAGTTTTTATAATTTTTTTGGATAGAAGAA
ATAAAATGTTGAAGAACTGATGAAAAAACTTTTAGGGTTTTTTGGGTTTGATCC
Found at i:2374167 original size:13 final size:13
Alignment explanation
Indices: 2374149--2374217 Score: 61
Period size: 13 Copynumber: 5.3 Consensus size: 13
2374139 ATATATACAC
*
2374149 ACTTTATTCTTAT
1 ACTTTATACTTAT
2374162 ACTTTATACTTAT
1 ACTTTATACTTAT
*
2374175 ACTATATA-TATAT
1 ACTTTATACT-TAT
*
2374188 A-TATATACTTTAT
1 ACTTTATAC-TTAT
* *
2374201 ACATTATACATAT
1 ACTTTATACTTAT
2374214 ACTT
1 ACTT
2374218 CATATATATA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
12 7 0.15
13 33 0.72
14 6 0.13
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (13 bp):
ACTTTATACTTAT
Found at i:2374201 original size:39 final size:39
Alignment explanation
Indices: 2374158--2374234 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
2374148 CACTTTATTC
* *
2374158 TTATACTTTATACTTATACTAT-ATATATATATATATACT
1 TTATACATTATACATATACT-TCATATATATATATATACT
2374197 TTATACATTATACATATACTTCATATATATATATATAC
1 TTATACATTATACATATACTTCATATATATATATATAC
2374235 ATACATACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 1 0.03
39 34 0.97
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (39 bp):
TTATACATTATACATATACTTCATATATATATATATACT
Found at i:2374396 original size:26 final size:24
Alignment explanation
Indices: 2374357--2374406 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
2374347 ATATATGAAG
2374357 TATATATATAAAGTATAAAGTATA
1 TATATATATAAAGTATAAAGTATA
*
2374381 TATATATAATATAAGTATAAATTATA
1 TATATAT-ATA-AAGTATAAAGTATA
2374407 AGAATAAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (24 bp):
TATATATATAAAGTATAAAGTATA
Found at i:2374406 original size:13 final size:12
Alignment explanation
Indices: 2374349--2374414 Score: 53
Period size: 13 Copynumber: 5.1 Consensus size: 12
2374339 ATGTATGTAT
*
2374349 ATATGAAGTATAT
1 ATAT-AAGTATAA
2374362 ATATAAAGTATAA
1 ATAT-AAGTATAA
2374375 AGTATATA-TATATA
1 A-TATA-AGTATA-A
2374389 ATATAAGTATAA
1 ATATAAGTATAA
*
2374401 ATTATAAGAATAA
1 A-TATAAGTATAA
2374414 A
1 A
2374415 GTGTATATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
12 3 0.07
13 36 0.80
14 6 0.13
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (12 bp):
ATATAAGTATAA
Found at i:2374414 original size:39 final size:39
Alignment explanation
Indices: 2374332--2374425 Score: 102
Period size: 39 Copynumber: 2.4 Consensus size: 39
2374322 TGATGCATGT
* * * * *
2374332 ATAATGTATGTATGTATATATGAAGTATATATATAAAGT
1 ATAAAGTATATATATATATATGAAGTATAAATATAAAGA
2374371 ATAAAGTATATATATATAATAT-AAGTATAAAT-TATAAGA
1 ATAAAGTATATATATAT-ATATGAAGTATAAATATA-AAGA
*
2374410 ATAAAGTGTATATATA
1 ATAAAGTATATATATA
2374426 AAGTATAGTG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
38 2 0.04
39 41 0.87
40 4 0.09
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (39 bp):
ATAAAGTATATATATATATATGAAGTATAAATATAAAGA
Found at i:2374832 original size:2 final size:2
Alignment explanation
Indices: 2374821--2374888 Score: 129
Period size: 2 Copynumber: 34.5 Consensus size: 2
2374811 AATACTCATC
2374821 AT AT -T 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
2374862 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
2374889 CAATTGTTTT
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 64 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2376554 original size:45 final size:44
Alignment explanation
Indices: 2376424--2376571 Score: 140
Period size: 44 Copynumber: 3.3 Consensus size: 44
2376414 GACCAGAACC
* ** *
2376424 GGGTAAGATCTTACCGTTTCTATAGGCTCCTCTAG-TATGTGCAA
1 GGGTAAGACCTTACCGTTTCTGCAGGCT-CTCTGGCTATGTGCAA
* * * *
2376468 GGGTATGACTTTACCGTTTCTGCAGGCTCTTTTGCTATGTGCAA
1 GGGTAAGACCTTACCGTTTCTGCAGGCTCTCTGGCTATGTGCAA
*
2376512 GGGTAAGACCTTACCGCTTTGC-GCAGGCTC-CTGGACTTTGTGCACA
1 GGGTAAGACCTTACCG-TTT-CTGCAGGCTCTCTGG-CTATGTGCA-A
*
2376558 GGGTAAGCCCTTAC
1 GGGTAAGACCTTAC
2376572 TGAGTGTACA
Statistics
Matches: 86, Mismatches: 13, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
43 4 0.05
44 48 0.56
45 19 0.22
46 15 0.17
ACGTcount: A:0.19, C:0.24, G:0.26, T:0.32
Consensus pattern (44 bp):
GGGTAAGACCTTACCGTTTCTGCAGGCTCTCTGGCTATGTGCAA
Found at i:2382027 original size:29 final size:30
Alignment explanation
Indices: 2381995--2382051 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
2381985 TACAAATTTA
* *
2381995 TCGAGGACTAAATTG-AATTTTGATTAATT
1 TCGAGGACCAAAGTGAAATTTTGATTAATT
2382024 TCGAGGACCAAAGTGAAATTTTGATTAA
1 TCGAGGACCAAAGTGAAATTTTGATTAA
2382052 ATTCATATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (30 bp):
TCGAGGACCAAAGTGAAATTTTGATTAATT
Found at i:2384925 original size:17 final size:15
Alignment explanation
Indices: 2384892--2384937 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 15
2384882 GGTCCTCCTA
2384892 TTTTTTTATTTTATG
1 TTTTTTTATTTTATG
2384907 TTGTTTTTATTTTACTG
1 TT-TTTTTATTTTA-TG
*
2384924 TTTTTTAATTTTAT
1 TTTTTTTATTTTAT
2384938 TATTTGATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 3 0.11
16 21 0.75
17 4 0.14
ACGTcount: A:0.15, C:0.02, G:0.07, T:0.76
Consensus pattern (15 bp):
TTTTTTTATTTTATG
Found at i:2387963 original size:13 final size:13
Alignment explanation
Indices: 2387945--2387978 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
2387935 ATGGGTCGAG
2387945 TCTTCATCTCAGA
1 TCTTCATCTCAGA
2387958 TCTTCATCTCAGA
1 TCTTCATCTCAGA
2387971 TCTTCATC
1 TCTTCATC
2387979 CTTGACAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.21, C:0.32, G:0.06, T:0.41
Consensus pattern (13 bp):
TCTTCATCTCAGA
Found at i:2390440 original size:15 final size:16
Alignment explanation
Indices: 2390420--2390450 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2390410 AACAATGTAT
2390420 CAAAAT-TAAAATAAA
1 CAAAATATAAAATAAA
2390435 CAAAATATAAAATAAA
1 CAAAATATAAAATAAA
2390451 AGGGTCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.19
Consensus pattern (16 bp):
CAAAATATAAAATAAA
Found at i:2391693 original size:17 final size:17
Alignment explanation
Indices: 2391671--2391729 Score: 118
Period size: 17 Copynumber: 3.5 Consensus size: 17
2391661 TACTCTTAAC
2391671 AAGCGAAAATAACAGCT
1 AAGCGAAAATAACAGCT
2391688 AAGCGAAAATAACAGCT
1 AAGCGAAAATAACAGCT
2391705 AAGCGAAAATAACAGCT
1 AAGCGAAAATAACAGCT
2391722 AAGCGAAA
1 AAGCGAAA
2391730 TTAAGATTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.54, C:0.17, G:0.19, T:0.10
Consensus pattern (17 bp):
AAGCGAAAATAACAGCT
Found at i:2392380 original size:3 final size:3
Alignment explanation
Indices: 2392372--2392459 Score: 176
Period size: 3 Copynumber: 29.3 Consensus size: 3
2392362 TCAATGAAGC
2392372 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2392420 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2392460 AATTAAGCTG
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 85 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2394673 original size:7 final size:7
Alignment explanation
Indices: 2394517--2394775 Score: 196
Period size: 7 Copynumber: 36.3 Consensus size: 7
2394507 ATTAAAAACA
2394517 ATATAAT
1 ATATAAT
2394524 ATAATAAAT
1 AT-AT-AAT
2394533 ATATAAT
1 ATATAAT
2394540 A-ATAAAT
1 ATAT-AAT
2394547 AATGATAAT
1 -AT-ATAAT
2394556 ATATAAT
1 ATATAAT
*
2394563 ATAAATAT
1 ATATA-AT
2394571 ACTATAAT
1 A-TATAAT
2394579 ATATAAT
1 ATATAAT
*
2394586 AAATATAT
1 ATATA-AT
*
2394594 GCTATAAT
1 -ATATAAT
2394602 ATATAAT
1 ATATAAT
*
2394609 ATATATT
1 ATATAAT
2394616 ATATAAT
1 ATATAAT
2394623 ATAT-AT
1 ATATAAT
2394629 AATATAAT
1 -ATATAAT
*
2394637 A-ATACT
1 ATATAAT
2394643 ATTATAAT
1 A-TATAAT
*
2394651 ATA-CAT
1 ATATAAT
2394657 AATATAAT
1 -ATATAAT
2394665 ATATAAT
1 ATATAAT
2394672 ATAT-AT
1 ATATAAT
*
2394678 ATGTAAT
1 ATATAAT
2394685 ATA-ATAT
1 ATATA-AT
2394692 ATATAAT
1 ATATAAT
**
2394699 ACTACCAT
1 A-TATAAT
2394707 A-A-AAT
1 ATATAAT
2394712 ATATAAT
1 ATATAAT
2394719 ATAT-AT
1 ATATAAT
2394725 AATATAAT
1 -ATATAAT
2394733 ATATAAT
1 ATATAAT
*
2394740 ATATATT
1 ATATAAT
*
2394747 ATATACT
1 ATATAAT
*
2394754 ATATACT
1 ATATAAT
*
2394761 -TATACT
1 ATATAAT
2394767 ATATAAT
1 ATATAAT
2394774 AT
1 AT
2394776 GTACTATCCC
Statistics
Matches: 207, Mismatches: 20, Indels: 50
0.75 0.07 0.18
Matches are distributed among these distances:
5 3 0.01
6 27 0.13
7 127 0.61
8 34 0.16
9 14 0.07
10 2 0.01
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (7 bp):
ATATAAT
Found at i:2395697 original size:15 final size:16
Alignment explanation
Indices: 2395662--2395703 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
2395652 TTTCTAATGT
2395662 TTCTTGATTTTTTCCA
1 TTCTTGATTTTTTCCA
* *
2395678 ATCTTGATTTTTT-GA
1 TTCTTGATTTTTTCCA
*
2395693 TTCTTGGTTTT
1 TTCTTGATTTT
2395704 GGATTCTTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.64
Consensus pattern (16 bp):
TTCTTGATTTTTTCCA
Found at i:2397357 original size:15 final size:15
Alignment explanation
Indices: 2397337--2397368 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2397327 GGACTAAAAC
*
2397337 ATAAGAAATAATTCA
1 ATAAGAAACAATTCA
2397352 ATAAGAAACAATTCA
1 ATAAGAAACAATTCA
2397367 AT
1 AT
2397369 GAAAAGAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.09, G:0.06, T:0.25
Consensus pattern (15 bp):
ATAAGAAACAATTCA
Found at i:2401470 original size:24 final size:23
Alignment explanation
Indices: 2401443--2401554 Score: 113
Period size: 24 Copynumber: 4.8 Consensus size: 23
2401433 AACTACCGCG
2401443 TAGAATTTG-CACCGAAGTGCCACA
1 TAGAATTTGTC-CCGAAG-GCCACA
* * *
2401467 TAGAATATATACCGAAGTGCCACA
1 TAGAATTTGTCCCGAAG-GCCACA
* *
2401491 TAG-ATTTGTCCCGAAAGACCGCA
1 TAGAATTTGTCCCG-AAGGCCACA
2401514 TAGAATTTGTCCCGAAGGACCACA
1 TAGAATTTGTCCCGAAGG-CCACA
2401538 TAGAA-TTGTCCCGAAGG
1 TAGAATTTGTCCCGAAGG
2401555 ACCGCGTAGA
Statistics
Matches: 74, Mismatches: 10, Indels: 9
0.80 0.11 0.10
Matches are distributed among these distances:
23 29 0.39
24 45 0.61
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.21
Consensus pattern (23 bp):
TAGAATTTGTCCCGAAGGCCACA
Found at i:2401516 original size:47 final size:47
Alignment explanation
Indices: 2401465--2401565 Score: 132
Period size: 47 Copynumber: 2.1 Consensus size: 47
2401455 CGAAGTGCCA
*
2401465 CATAGAATATATACCGAAGTG-CCACATAGATTTGTCCCGAAAGACCG
1 CATAGAATATATACCGAAG-GACCACATAGAATTGTCCCGAAAGACCG
* * * *
2401512 CATAGAATTTGTCCCGAAGGACCACATAGAATTGTCCCGAAGGACCG
1 CATAGAATATATACCGAAGGACCACATAGAATTGTCCCGAAAGACCG
*
2401559 CGTAGAA
1 CATAGAA
2401566 CCCTTAACTC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
46 1 0.02
47 46 0.98
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.20
Consensus pattern (47 bp):
CATAGAATATATACCGAAGGACCACATAGAATTGTCCCGAAAGACCG
Found at i:2401565 original size:23 final size:23
Alignment explanation
Indices: 2401489--2401565 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
2401479 CGAAGTGCCA
* *
2401489 CATAGATTTGTCCCGAAAGACCG
1 CATAGAATTGTCCCGAAGGACCG
*
2401512 CATAGAATTTGTCCCGAAGGACCA
1 CATAGAA-TTGTCCCGAAGGACCG
2401536 CATAGAATTGTCCCGAAGGACCG
1 CATAGAATTGTCCCGAAGGACCG
*
2401559 CGTAGAA
1 CATAGAA
2401566 CCCTTAACTC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 27 0.56
24 21 0.44
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.19
Consensus pattern (23 bp):
CATAGAATTGTCCCGAAGGACCG
Found at i:2413624 original size:23 final size:24
Alignment explanation
Indices: 2413554--2413625 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
2413544 TGCCACATAT
* *
2413554 ATTTGTCCTGAAAGACCGTATAGA
1 ATTTGTCCCGAAAGACCGCATAGA
* * *
2413578 ATTTGTCCCGAATGATCACATAGA
1 ATTTGTCCCGAAAGACCGCATAGA
*
2413602 A-TTGTCCCGAAAGACCGCGTAGA
1 ATTTGTCCCGAAAGACCGCATAGA
2413625 A
1 A
2413626 CCCTCGACTT
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 19 0.49
24 20 0.51
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (24 bp):
ATTTGTCCCGAAAGACCGCATAGA
Found at i:2413868 original size:57 final size:57
Alignment explanation
Indices: 2413715--2413908 Score: 182
Period size: 57 Copynumber: 3.4 Consensus size: 57
2413705 ATAATTTTAT
* * ** *
2413715 TCAAATTATTATTTGTTCACATA-AAACATATACTCATAATATTTCACATAGCATTAC
1 TCAAATTATCATTTATTCACATAGAAA-ATATACTCATAGCATTTCATATAGCATTAC
* * * * * *
2413772 CCAAATTTATTATTTATTCCCCTAGGATAAT-TACTCATAGCATTTCATAT-GATATTAC
1 TCAAA-TTATCATTTATTCACATA-GAAAATATACTCATAGCATTTCATATAG-CATTAC
* * *
2413830 TCAACTTATCATTTATTCACATAGAAAATATACTCATAGTGA-TTCATATAGCATTAT
1 TCAAATTATCATTTATTCACATAGAAAATATACTCATAG-CATTTCATATAGCATTAC
2413887 TCAAATTATCATTTATTC-CATA
1 TCAAATTATCATTTATTCACATA
2413909 CAACATATTC
Statistics
Matches: 111, Mismatches: 19, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
56 9 0.08
57 57 0.51
58 41 0.37
59 2 0.02
60 2 0.02
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (57 bp):
TCAAATTATCATTTATTCACATAGAAAATATACTCATAGCATTTCATATAGCATTAC
Found at i:2432198 original size:22 final size:22
Alignment explanation
Indices: 2432173--2432219 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2432163 TTATGAATAT
*
2432173 TGATAAACAATACCGTGAACAG
1 TGATAAACAATACCGTGAAAAG
* *
2432195 TGATGAACAATACTGTGAAAAG
1 TGATAAACAATACCGTGAAAAG
2432217 TGA
1 TGA
2432220 ATAGTGTACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.21
Consensus pattern (22 bp):
TGATAAACAATACCGTGAAAAG
Found at i:2435121 original size:2 final size:2
Alignment explanation
Indices: 2435073--2435422 Score: 160
Period size: 2 Copynumber: 184.5 Consensus size: 2
2435063 TAATAATACA
* *
2435073 AT AT A- AT AA AT AT AT A- AT AT AA AT AT ACT AT A- AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * * *
2435112 AT AA AT AT AT GCT AT A- AT AT AT AC AT AT A- AT AT AT AA AT AT
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2435153 AT AT AA AT -T AT ACT AT A- AT A- AT A- AT AT AT ACT AT AT A- AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
2435192 AT AT A- AT AT AT AT AT AT AT AT AT AT A- AT A- AT ACT ACT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T A-T AT AT
* *
2435232 AA AT AT AT CAT AT AC AT A- AT AT A- AT AT AT A- AT AT A- AT A-
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
2435270 AT ACT ACT AT A- AT AT AC AC A- AT AT ACT ACC AT A- AA AT AT AT
1 AT A-T A-T AT AT AT AT AT AT AT AT AT A-T A-T AT AT AT AT AT AT
* *
2435311 A- AT A- AT ACT ACC AT A- AA AT AT AT A- AT AT AT AT A- AT AT A-
1 AT AT AT AT A-T A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2435349 AT AT AT A- AT AT AT AT ACT AT AT ACT -T AT ACT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT A-T AT AT AT AT AT
2435389 AT A- AT AT AT A- AT AT AT A- AT AT CAT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT A
2435423 CTATCGTGGA
Statistics
Matches: 275, Mismatches: 24, Indels: 98
0.69 0.06 0.25
Matches are distributed among these distances:
1 36 0.13
2 205 0.75
3 34 0.12
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (2 bp):
AT
Found at i:2435422 original size:7 final size:7
Alignment explanation
Indices: 2435062--2435409 Score: 232
Period size: 7 Copynumber: 48.0 Consensus size: 7
2435052 AATAATATTA
2435062 ATAATAAT
1 ATAAT-AT
*
2435070 ACAATAT
1 ATAATAT
2435077 AATAAATAT
1 -AT-AATAT
2435086 ATAATAT
1 ATAATAT
*
2435093 AAATATACT
1 ATA-ATA-T
2435102 ATAATAT
1 ATAATAT
*
2435109 ATAATAA
1 ATAATAT
*
2435116 ATATATGCT
1 ATA-AT-AT
2435125 ATAATAT
1 ATAATAT
*
2435132 AT-ACAT
1 ATAATAT
2435138 ATAATAT
1 ATAATAT
2435145 ATAA-AT
1 ATAATAT
*
2435151 ATATATAA
1 ATA-ATAT
*
2435159 ATTATACT
1 ATAATA-T
2435167 ATAATA-
1 ATAATAT
2435173 ATAATAT
1 ATAATAT
*
2435180 ATACTAT
1 ATAATAT
2435187 ATAATAT
1 ATAATAT
2435194 ATAATAT
1 ATAATAT
2435201 AT-ATAT
1 ATAATAT
2435207 ATATATAT
1 ATA-ATAT
2435215 ATAATA-
1 ATAATAT
*
2435221 ATACTACT
1 ATAATA-T
*
2435229 ATAAAAT
1 ATAATAT
2435236 AT-ATCAT
1 ATAAT-AT
2435243 ATACATAAT
1 ATA-AT-AT
2435252 ATAATAT
1 ATAATAT
2435259 ATAATAT
1 ATAATAT
2435266 AATAATACT
1 -ATAATA-T
2435275 ACT-ATA-
1 A-TAATAT
*
2435281 AT-ATAC
1 ATAATAT
*
2435287 ACAATAT
1 ATAATAT
**
2435294 ACTACCAT
1 A-TAATAT
*
2435302 AAAATAT
1 ATAATAT
2435309 ATAATAAT
1 ATAAT-AT
**
2435317 ACTACCAT
1 A-TAATAT
*
2435325 AAAATAT
1 ATAATAT
2435332 ATAATAT
1 ATAATAT
2435339 AT-ATAAT
1 ATAAT-AT
2435346 ATAATAT
1 ATAATAT
2435353 ATAATAT
1 ATAATAT
2435360 ATATACTAT
1 ATA-A-TAT
*
2435369 ATACT-T
1 ATAATAT
*
2435375 ATACTAT
1 ATAATAT
2435382 ATAATAT
1 ATAATAT
2435389 ATAATAT
1 ATAATAT
2435396 ATAATAT
1 ATAATAT
2435403 ATAATAT
1 ATAATAT
2435410 CATATAATAT
Statistics
Matches: 271, Mismatches: 38, Indels: 63
0.73 0.10 0.17
Matches are distributed among these distances:
5 4 0.01
6 38 0.14
7 140 0.52
8 61 0.23
9 28 0.10
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.39
Consensus pattern (7 bp):
ATAATAT
Found at i:2442600 original size:20 final size:20
Alignment explanation
Indices: 2442575--2442621 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
2442565 CTTTCTCTAC
2442575 GCTACGCCTTAACCTATTAT
1 GCTACGCCTTAACCTATTAT
2442595 GCTACGCCTTAACCTATTAT
1 GCTACGCCTTAACCTATTAT
2442615 GCTACGC
1 GCTACGC
2442622 TAGGATGATG
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:0.23, C:0.32, G:0.13, T:0.32
Consensus pattern (20 bp):
GCTACGCCTTAACCTATTAT
Found at i:2442623 original size:25 final size:23
Alignment explanation
Indices: 2442571--2442623 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 23
2442561 GCAGCTTTCT
2442571 CTACGCTACGCCTTAACCTATTA
1 CTACGCTACGCCTTAACCTATTA
2442594 -T--GCTACGCCTTAACCTATTA
1 CTACGCTACGCCTTAACCTATTA
2442614 TGCTACGCTA
1 --CTACGCTA
2442624 GGATGATGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
20 19 0.76
22 1 0.04
23 1 0.04
25 4 0.16
ACGTcount: A:0.25, C:0.32, G:0.11, T:0.32
Consensus pattern (23 bp):
CTACGCTACGCCTTAACCTATTA
Found at i:2447738 original size:3 final size:3
Alignment explanation
Indices: 2447730--2447765 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
2447720 AAAAACAATA
2447730 TAT TAT TAT TAT TATT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TA
2447766 ATTTATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2448071 original size:3 final size:3
Alignment explanation
Indices: 2448063--2448103 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2448053 AAAAACAATA
2448063 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2448104 ATTTATATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2452212 original size:21 final size:21
Alignment explanation
Indices: 2452186--2452239 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
2452176 TCTTTGAGTA
2452186 TTATATAAGCTTAAGGAAAGC
1 TTATATAAGCTTAAGGAAAGC
2452207 TTATATAAGCTTAAGGAAAGC
1 TTATATAAGCTTAAGGAAAGC
2452228 TTATATAAGCTT
1 TTATATAAGCTT
2452240 TAAACATCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (21 bp):
TTATATAAGCTTAAGGAAAGC
Found at i:2452755 original size:24 final size:20
Alignment explanation
Indices: 2452728--2452785 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
2452718 GCATGGGTAG
2452728 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
2452752 TGCATCGATACACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
2452772 TGTATCGATGCACT
1 TGCATCGATGCACT
2452786 TCAAGGGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 16 0.52
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:2453320 original size:2 final size:2
Alignment explanation
Indices: 2453251--2453302 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
2453241 TGTATTTGCG
2453251 TA TA TA T- 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
2453292 TA TA TA TA TA T
1 TA TA TA TA TA T
2453303 GAATAAGATA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2453910 original size:31 final size:32
Alignment explanation
Indices: 2453839--2453915 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 32
2453829 AGTCGAGGGT
2453839 TTACCTATGTTCTACGAAACATATGGACAGAA
1 TTACCTATGTTCTACGAAACATATGGACAGAA
* * *
2453871 TTACCTATG-TCTTTCGAGACATATGGACAGTA
1 TTACCTATGTTC-TACGAAACATATGGACAGAA
2453903 -TACCTATGTTCTA
1 TTACCTATGTTCTA
2453916 AGGAATATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
31 11 0.28
32 28 0.72
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (32 bp):
TTACCTATGTTCTACGAAACATATGGACAGAA
Found at i:2453926 original size:31 final size:32
Alignment explanation
Indices: 2453839--2453928 Score: 94
Period size: 32 Copynumber: 2.8 Consensus size: 32
2453829 AGTCGAGGGT
* *
2453839 TTACCTATGTTCTACGAAACATATGGACAGAA
1 TTACCTATGTTCTAAGGAACATATGGACAGAA
*** *
2453871 TTACCTATG-TCTTTCGAGACATATGGACAGTA
1 TTACCTATGTTCTAAGGA-ACATATGGACAGAA
*
2453903 -TACCTATGTTCTAAGGAATATATGGA
1 TTACCTATGTTCTAAGGAACATATGGA
2453929 TAGTTTGCCT
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
31 20 0.43
32 27 0.57
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (32 bp):
TTACCTATGTTCTAAGGAACATATGGACAGAA
Found at i:2453958 original size:31 final size:30
Alignment explanation
Indices: 2453923--2453992 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
2453913 CTAAGGAATA
*
2453923 TATGGATAGTTTGCCTAGGTTCTTCAGGACC
1 TATGGATAG-TTGCCGAGGTTCTTCAGGACC
* * * *
2453954 TATGGACAGTTGTCGAGGTTCTTTATGACC
1 TATGGATAGTTGCCGAGGTTCTTCAGGACC
*
2453984 TCTGGATAG
1 TATGGATAG
2453993 GTCCTTCGGG
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
30 24 0.75
31 8 0.25
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.36
Consensus pattern (30 bp):
TATGGATAGTTGCCGAGGTTCTTCAGGACC
Found at i:2456468 original size:20 final size:20
Alignment explanation
Indices: 2456443--2456480 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2456433 CACATGTTAA
2456443 AGAATGCATCGATACACTAT
1 AGAATGCATCGATACACTAT
* *
2456463 AGAATGTATCGATGCACT
1 AGAATGCATCGATACACT
2456481 TCAAGGGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATACACTAT
Found at i:2458057 original size:17 final size:17
Alignment explanation
Indices: 2458032--2458076 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
2458022 TTATTTTCAG
*
2458032 TTATCAGATGTTTACAA
1 TTATTAGATGTTTACAA
* *
2458049 TTATTAGATTTTTACAG
1 TTATTAGATGTTTACAA
2458066 TTATTAGATGT
1 TTATTAGATGT
2458077 ACATTAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.49
Consensus pattern (17 bp):
TTATTAGATGTTTACAA
Found at i:2466677 original size:18 final size:18
Alignment explanation
Indices: 2466646--2466737 Score: 71
Period size: 18 Copynumber: 5.1 Consensus size: 18
2466636 CTTCCCAAGT
*
2466646 ATGATATTTACAGTTATCGG
1 ATGAT-TTT-CAGTTATCAG
*
2466666 ATGATTTTCAGTTACCAG
1 ATGATTTTCAGTTATCAG
* *
2466684 ATAATTTTCAATTATCAG
1 ATGATTTTCAGTTATCAG
* * *
2466702 ATG-TTTACAATTATAAG
1 ATGATTTTCAGTTATCAG
*
2466719 ATG-TTTTACATTTATCAG
1 ATGATTTT-CAGTTATCAG
2466737 A
1 A
2466738 GGTAGATTAA
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
17 18 0.30
18 34 0.57
19 3 0.05
20 5 0.08
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (18 bp):
ATGATTTTCAGTTATCAG
Found at i:2469362 original size:17 final size:17
Alignment explanation
Indices: 2469340--2469392 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
2469330 ATGATTTTTT
2469340 ATGTTAGATTACATGTC
1 ATGTTAGATTACATGTC
* *
2469357 ATGTTA-TTTAC---TA
1 ATGTTAGATTACATGTC
2469370 ATGTTAGATTACATGTC
1 ATGTTAGATTACATGTC
2469387 ATGTTA
1 ATGTTA
2469393 TTTACTAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
13 7 0.25
14 4 0.14
16 4 0.14
17 13 0.46
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.45
Consensus pattern (17 bp):
ATGTTAGATTACATGTC
Found at i:2469374 original size:30 final size:30
Alignment explanation
Indices: 2469340--2469400 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
2469330 ATGATTTTTT
2469340 ATGTTAGATTACATGTCATGTTATTTACTA
1 ATGTTAGATTACATGTCATGTTATTTACTA
2469370 ATGTTAGATTACATGTCATGTTATTTACTA
1 ATGTTAGATTACATGTCATGTTATTTACTA
2469400 A
1 A
2469401 GTATGCCTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (30 bp):
ATGTTAGATTACATGTCATGTTATTTACTA
Found at i:2469547 original size:14 final size:14
Alignment explanation
Indices: 2469528--2469554 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2469518 ACAAAAAATG
2469528 TTAATTTTTTATGT
1 TTAATTTTTTATGT
2469542 TTAATTTTTTATG
1 TTAATTTTTTATG
2469555 CAAATCTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.70
Consensus pattern (14 bp):
TTAATTTTTTATGT
Found at i:2471907 original size:20 final size:20
Alignment explanation
Indices: 2471879--2471916 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2471869 TTTGGAAAAA
2471879 AAAAAGGATCAATCCCTTGG
1 AAAAAGGATCAATCCCTTGG
* *
2471899 AAAAGGGATCCATCCCTT
1 AAAAAGGATCAATCCCTT
2471917 TTCAAAGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (20 bp):
AAAAAGGATCAATCCCTTGG
Found at i:2478073 original size:19 final size:19
Alignment explanation
Indices: 2478049--2478086 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2478039 AGTTACTTAA
2478049 ATGATTTCTAAATATAACC
1 ATGATTTCTAAATATAACC
2478068 ATGATTTCTAAATATAACC
1 ATGATTTCTAAATATAACC
2478087 GTGTTTAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.37
Consensus pattern (19 bp):
ATGATTTCTAAATATAACC
Found at i:2478595 original size:46 final size:46
Alignment explanation
Indices: 2478528--2478619 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
2478518 TCTATATGAA
2478528 TCTTATCTTAGTTCTCCATCTGATACACATTGGTAGGGGTCAATTC
1 TCTTATCTTAGTTCTCCATCTGATACACATTGGTAGGGGTCAATTC
2478574 TCTTATCTTAGTTCTCCATCTGATACACATTGGTAGGGGTCAATTC
1 TCTTATCTTAGTTCTCCATCTGATACACATTGGTAGGGGTCAATTC
2478620 CAATCGAAGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (46 bp):
TCTTATCTTAGTTCTCCATCTGATACACATTGGTAGGGGTCAATTC
Found at i:2490576 original size:18 final size:20
Alignment explanation
Indices: 2490543--2490590 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
2490533 GACCATTTTG
2490543 GTATCGATA-CTCATGG-GA
1 GTATCGATACCTCATGGAGA
*
2490561 TTATCGATACCT-ATGGTAGA
1 GTATCGATACCTCATGG-AGA
2490581 GTATCGATAC
1 GTATCGATAC
2490591 TGCCTATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 12 0.48
19 2 0.08
20 11 0.44
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (20 bp):
GTATCGATACCTCATGGAGA
Found at i:2490799 original size:20 final size:20
Alignment explanation
Indices: 2490776--2490815 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2490766 GGTGGGTATT
*
2490776 AATACCCAAGGTTCAATATC
1 AATACCCAAGGGTCAATATC
**
2490796 AATACTGAAGGGTCAATATC
1 AATACCCAAGGGTCAATATC
2490816 GGTATCAGCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (20 bp):
AATACCCAAGGGTCAATATC
Found at i:2495638 original size:78 final size:78
Alignment explanation
Indices: 2495509--2495656 Score: 251
Period size: 78 Copynumber: 1.9 Consensus size: 78
2495499 ACATTCCATA
**
2495509 TTTTTGATGAACCTGTGATTATTTTGGTTGACCCTGGTTCTTCACACTCTTACATTAGTACGAAA
1 TTTTTGATGAACCTGTGATTATTTTGGTTGACCCTGGTTCTTCACACTCTTACATTAGTAAAAAA
2495574 CTGATGTTTTATC
66 CTGATGTTTTATC
* * *
2495587 TTTTTGATGAACCTGTGTTTATTTTGGTTGACCCTGGTTCTTCGCATTCTTACATTAGTAAAAAA
1 TTTTTGATGAACCTGTGATTATTTTGGTTGACCCTGGTTCTTCACACTCTTACATTAGTAAAAAA
2495652 CTGAT
66 CTGAT
2495657 TAGAGAGCTG
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 65 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (78 bp):
TTTTTGATGAACCTGTGATTATTTTGGTTGACCCTGGTTCTTCACACTCTTACATTAGTAAAAAA
CTGATGTTTTATC
Found at i:2498379 original size:14 final size:14
Alignment explanation
Indices: 2498357--2498386 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2498347 AATATATAAA
*
2498357 ATTATGTTTTCTTC
1 ATTAAGTTTTCTTC
2498371 ATTAAGTTTTCTTC
1 ATTAAGTTTTCTTC
2498385 AT
1 AT
2498387 GTGTGTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.07, T:0.60
Consensus pattern (14 bp):
ATTAAGTTTTCTTC
Found at i:2501316 original size:36 final size:35
Alignment explanation
Indices: 2501272--2501372 Score: 141
Period size: 36 Copynumber: 2.8 Consensus size: 35
2501262 GAAAGAAAGA
*
2501272 ATCGCACTTCCGATTCAAATCGAATGGAA-GAAGGC
1 ATCGCACTTCCGATTCAAATCGAACGGAATGAA-GC
*
2501307 ATCGACACTTCTGATTCAAATCGAACGGAATGAAGC
1 ATCG-CACTTCCGATTCAAATCGAACGGAATGAAGC
*
2501343 ATCGGCACTTCCGATTCAAATTGAACGGAA
1 ATC-GCACTTCCGATTCAAATCGAACGGAA
2501373 AGATGTATTG
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
35 4 0.07
36 51 0.86
37 4 0.07
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.22
Consensus pattern (35 bp):
ATCGCACTTCCGATTCAAATCGAACGGAATGAAGC
Found at i:2504262 original size:20 final size:19
Alignment explanation
Indices: 2504223--2504274 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
2504213 TTTCTTTGAT
2504223 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
2504242 ATTAAAATAATTAATATATA
1 ATTAAAA-AATAAATAAATA
*
2504262 ATTTATAAAATAA
1 A-TTAAAAAATAA
2504275 GATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:2504375 original size:120 final size:120
Alignment explanation
Indices: 2504136--2504368 Score: 294
Period size: 120 Copynumber: 2.0 Consensus size: 120
2504126 TATATTAATT
* * *
2504136 TATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGGTGCCT
1 TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTGCCT
* * *
2504201 TAAGACAGCTATTTTCTTTGATATTAAAAAATAAATAAATAATTAAAATAATTAA
66 TAAGACAGCTACTTTCTTTAATATTAAAAAATAAATAAATAATTAAAACAATTAA
* **
2504256 TATATA-ATTTATAAAATAAGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAGGTTT
1 TATATATATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GGACATCCAGGTGC
* ** * *
2504320 TTTAAGATTGC-CCTTTC-TTAATATTGAAAAATAAATAAAT-ATTAAAACA
64 CTTAAGACAGCTACTTTCTTTAATATTAAAAAATAAATAAATAATTAAAACA
2504369 GGATTAAAAT
Statistics
Matches: 97, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
118 8 0.08
119 27 0.28
120 44 0.45
121 18 0.19
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.38
Consensus pattern (120 bp):
TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTGCCT
TAAGACAGCTACTTTCTTTAATATTAAAAAATAAATAAATAATTAAAACAATTAA
Found at i:2504459 original size:22 final size:18
Alignment explanation
Indices: 2504414--2504449 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2504404 TTAATAAATA
2504414 AAATAAATATTATTTATT
1 AAATAAATATTATTTATT
*
2504432 AGATAAATATATATTTAT
1 AAATAAATAT-TATTTAT
2504450 GACTAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
AAATAAATATTATTTATT
Found at i:2504463 original size:3 final size:3
Alignment explanation
Indices: 2504455--2504505 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
2504445 TTTATGACTA
*
2504455 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2504503 AAT
1 AAT
2504506 TAAGAGTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2505441 original size:18 final size:20
Alignment explanation
Indices: 2505418--2505456 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
2505408 TTCGTTTCTA
2505418 TCTCTGTTCT-T-TTTTTTT
1 TCTCTGTTCTCTATTTTTTT
2505436 TCTCTGTTCTCTATTTTTTT
1 TCTCTGTTCTCTATTTTTTT
2505456 T
1 T
2505457 TTGTTTTGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.53
19 1 0.05
20 8 0.42
ACGTcount: A:0.03, C:0.18, G:0.05, T:0.74
Consensus pattern (20 bp):
TCTCTGTTCTCTATTTTTTT
Found at i:2505964 original size:3 final size:3
Alignment explanation
Indices: 2505956--2506027 Score: 89
Period size: 3 Copynumber: 24.7 Consensus size: 3
2505946 GGCATGTTTG
*
2505956 TAA TAA TAA TAA TAA TAAA TAA -AA TAA TGA TAA TAA TAA -AA T-A
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2505999 TAA -AA TAA TAA TAA TAA TAAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TA
2506028 GAAAATGGAG
Statistics
Matches: 61, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
2 8 0.13
3 47 0.77
4 6 0.10
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:2505988 original size:24 final size:24
Alignment explanation
Indices: 2505956--2506019 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
2505946 GGCATGTTTG
2505956 TAATAATAATAATAATAA-ATAAAA
1 TAATAATAATAATAA-AATATAAAA
*
2505980 TAATGATAATAATAAAATATAAAA
1 TAATAATAATAATAAAATATAAAA
2506004 TAATAATAATAATAAA
1 TAATAATAATAATAAA
2506020 TAATAATAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 2 0.05
24 35 0.95
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (24 bp):
TAATAATAATAATAAAATATAAAA
Found at i:2506003 original size:7 final size:8
Alignment explanation
Indices: 2505956--2506025 Score: 74
Period size: 7 Copynumber: 8.8 Consensus size: 8
2505946 GGCATGTTTG
2505956 TAATAATAA
1 TAATAA-AA
*
2505965 TAATAATA
1 TAATAAAA
2505973 -AATAAAA
1 TAATAAAA
*
2505980 TAATGATAA
1 TAAT-AAAA
2505989 TAATAAAA
1 TAATAAAA
2505997 T-ATAAAA
1 TAATAAAA
2506004 TAATAATAA
1 TAATAA-AA
2506013 TAAT-AAA
1 TAATAAAA
2506020 TAATAA
1 TAATAA
2506026 TAGAAAATGG
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
7 19 0.37
8 14 0.27
9 19 0.37
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (8 bp):
TAATAAAA
Found at i:2506521 original size:124 final size:122
Alignment explanation
Indices: 2506227--2506561 Score: 496
Period size: 124 Copynumber: 2.7 Consensus size: 122
2506217 GGGATGATAA
* * * *
2506227 TATCTCATTCTATGAT-GTAATT-TGGAAAAGGGTTAAACAAGTTCTTCTCATTATGAACTTCTT
1 TATCTCCTTCTATGATAG-AATTAT-GAAAAAGGTTGAACAAGATCTTCTCATTATGAACTTCTT
2506290 CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAATTTCTGGAAAAGTTGATGCTGATC
64 CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAATTTCTGGAAAAGTTGATGCTGATC
* * * *
2506349 TATCTCCTTCTATGATAGAGTCATGAAAAAGGTTGAACAAAATTTTCTCATTATGAACTTCTTCT
1 TATCTCCTTCTATGATAGAATTATGAAAAAGGTTGAACAAGATCTTCTCATTATGAACTTCTTCT
*
2506414 T-CTTCCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATC
66 TCCTT-CTTCAGATGAGTTCTTCTCATTATGAA-ATT-TCTGGAAAAGTTGATGCTGATC
* * *
2506473 TATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCT
1 TATCTCCTTCTATGATAGAATTATGAAAAAGGTTGAACAAGATCTTCTCATTATGAACTTCTTCT
2506538 TCCTTCTTCAGATGAGTTCTTCTC
66 TCCTTCTTCAGATGAGTTCTTCTC
2506562 TATCTGGCAA
Statistics
Matches: 191, Mismatches: 16, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
121 3 0.02
122 81 0.42
123 4 0.02
124 100 0.52
125 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (122 bp):
TATCTCCTTCTATGATAGAATTATGAAAAAGGTTGAACAAGATCTTCTCATTATGAACTTCTTCT
TCCTTCTTCAGATGAGTTCTTCTCATTATGAAATTTCTGGAAAAGTTGATGCTGATC
Found at i:2506577 original size:113 final size:106
Alignment explanation
Indices: 2506458--2507004 Score: 402
Period size: 113 Copynumber: 5.0 Consensus size: 106
2506448 TTCTCTGGAA
* * *
2506458 AAGTTGATGCTGATCTATCTCCTTCTGTGATAGAATT-ATGCAAAAGGTTGAACAAGCTCTTCTC
1 AAGTTGATGC--ATCTA-C-CCTTC-GTGATAGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTC
2506522 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCTATCTGG
61 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC-ATCTGG
* *** *
2506569 CAATGTTGATCCA--TA----GAATGAT-GAATTCAAGCAAAAAGTTGAACAAATTCTTCTCATT
1 -AA-GTTGATGCATCTACCCTTCGTGATAGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATT
*
2506627 ATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT-TATG
64 ATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATCT-GG
* * *
2506670 AACTTGACCTGGCAATGCTGACCCATCGAATGATA-AATTCAAGCAAAAATTTGAACAAGTTCTT
1 AAGTTGA--T-GC-AT-CT-ACCCTTCG--TGATAGAATTCAAGCAAAAAGTTGAACAAGTTCTT
* *
2506734 CTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTTCTCAT-TATG
58 CTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATCT-GG
* * * * * * *
2506783 AACTCGACCTGGTAATGCTGATCCATCGAATGAT-GAATTCAAACGAAAAGTTGAACAAGTTCTT
1 AAGTTGA--T-G-CAT-CT-ACCCTTCG--TGATAGAATTCAAGCAAAAAGTTGAACAAGTTCTT
* * *
2506847 CTCATTATGAACTTCTTATTCCTTCTTTAGATGAGTTCTTCTCAT-TATG
58 CTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATCT-GG
* * * * * *
2506896 AACTCGACCTGGTAATGCTGATCCATCGAATGAT-GAATTCAAGCGAAAAGTTGAACAAGTTCTT
1 AAGTTGA--T-G-CAT-CT-ACCCTTCG--TGATAGAATTCAAGCAAAAAGTTGAACAAGTTCTT
*
2506960 CTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCAT
58 CTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
2507005 TATGAACTCG
Statistics
Matches: 385, Mismatches: 30, Indels: 39
0.85 0.07 0.09
Matches are distributed among these distances:
99 4 0.01
100 3 0.01
101 9 0.02
102 68 0.18
103 1 0.00
106 1 0.00
107 1 0.00
109 2 0.01
111 1 0.00
112 2 0.01
113 293 0.76
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (106 bp):
AAGTTGATGCATCTACCCTTCGTGATAGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTAT
GAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATCTGG
Found at i:2507005 original size:113 final size:113
Alignment explanation
Indices: 2506565--2507043 Score: 805
Period size: 113 Copynumber: 4.2 Consensus size: 113
2506555 TCTTCTCTAT
* * * *
2506565 CTGGCAATGTTGATCCATAGAATGATGAATTCAAGCAAAAAGTTGAACAAATTCTTCTCATTATG
1 CTGGTAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATG
*
2506630 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTGAC
66 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC
* * * *
2506678 CTGGCAATGCTGACCCATCGAATGATAAATTCAAGCAAAAATTTGAACAAGTTCTTCTCATTATG
1 CTGGTAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATG
*
2506743 AACTTCTTCTTCCTTCTTCAGATGAGTTTTTCTCATTATGAACTCGAC
66 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC
* *
2506791 CTGGTAATGCTGATCCATCGAATGATGAATTCAAACGAAAAGTTGAACAAGTTCTTCTCATTATG
1 CTGGTAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATG
* *
2506856 AACTTCTTATTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTCGAC
66 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC
*
2506904 CTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATG
1 CTGGTAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATG
*
2506969 AACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC
66 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC
*
2507017 CTGGTAATGCTGATCCATTGAATGATG
1 CTGGTAATGCTGATCCATCGAATGATG
2507044 GATTTGAATT
Statistics
Matches: 344, Mismatches: 22, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
113 344 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (113 bp):
CTGGTAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATG
AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC
Found at i:2507960 original size:115 final size:114
Alignment explanation
Indices: 2507759--2507982 Score: 385
Period size: 115 Copynumber: 2.0 Consensus size: 114
2507749 AATCATGCAG
* * *
2507759 TTCATCTTTCAATTCTAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCTAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
2507824 ACACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGAGCAAA
* *
2507873 TTCATCTTTCAAATCTAATGATTGGTTTTGGGGTTTATACCAAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCTAATGATTGGTTCTGGGGTTCATACC-AAACCAGATCAGATAACTCAAAG
2507938 AACACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGA
65 AACACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGA
2507983 TAACGTGGCA
Statistics
Matches: 103, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
114 37 0.36
115 66 0.64
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (114 bp):
TTCATCTTTCAAATCTAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGAGCAAA
Found at i:2516089 original size:15 final size:15
Alignment explanation
Indices: 2516066--2516097 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2516056 TGCAATGAAT
2516066 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
2516081 AATGCATGTATGCAA
1 AATGAATGTATGCAA
2516096 AA
1 AA
2516098 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:2520067 original size:20 final size:19
Alignment explanation
Indices: 2520028--2520079 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
2520018 TTTCTTTGAT
2520028 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
2520047 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
*
2520067 ATTTATAAAATAA
1 A-TTAAAAAATAA
2520080 GATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:2520180 original size:120 final size:120
Alignment explanation
Indices: 2519935--2520174 Score: 319
Period size: 120 Copynumber: 2.0 Consensus size: 120
2519925 AATATATATT
* * * *
2519935 AATTTATATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAG
1 AATTAATATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAG
* *
2520000 GTGCCTTAAGACAGCTATTTTCTTTGATATTAAAAAATAAATAAATAATTAAAAC
66 GTGCCTTAAGACAGCCATTTTCTTTAATATTAAAAAATAAATAAATAATTAAAAC
*
2520055 AATTAATATATA-ATTTATAAAATAAGATATTTATTTATTTAAAAATATCAGAAAATGGACATCC
1 AATTAATATATATATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GGACATCC
* ** *
2520119 AGTTGTTTTAAGACTA-CCA-TTTC-TTAATATTGAAAAATAAATAAAT-ATTAAAAC
64 AGGTGCCTTAAGAC-AGCCATTTTCTTTAATATTAAAAAATAAATAAATAATTAAAAC
2520173 AA
1 AA
2520175 GATTAAAATA
Statistics
Matches: 106, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
118 10 0.09
119 27 0.25
120 49 0.46
121 19 0.18
122 1 0.01
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.38
Consensus pattern (120 bp):
AATTAATATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAG
GTGCCTTAAGACAGCCATTTTCTTTAATATTAAAAAATAAATAAATAATTAAAAC
Found at i:2520264 original size:22 final size:18
Alignment explanation
Indices: 2520219--2520254 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2520209 TTAATAAATA
2520219 AAATAAATATTATTTATT
1 AAATAAATATTATTTATT
*
2520237 AGATAAATATATATTTAT
1 AAATAAATAT-TATTTAT
2520255 GACTAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
AAATAAATATTATTTATT
Found at i:2520284 original size:16 final size:16
Alignment explanation
Indices: 2520260--2520313 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
2520250 TTTATGACTA
*
2520260 AATAATAATAATAAAT
1 AATAGTAATAATAAAT
*
2520276 AATAGTAATAATAATT
1 AATAGTAATAATAAAT
* *
2520292 AAGAGTAAACATATAAAT
1 AATAGT-AATA-ATAAAT
2520310 AATA
1 AATA
2520314 AATAAAATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
16 19 0.63
17 3 0.10
18 8 0.27
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.30
Consensus pattern (16 bp):
AATAGTAATAATAAAT
Found at i:2521221 original size:18 final size:20
Alignment explanation
Indices: 2521198--2521236 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
2521188 TTCGTGTCTA
2521198 TCTCTGTTCT-T-TTTTTTT
1 TCTCTGTTCTCTCTTTTTTT
2521216 TCTCTGTTCTCTCTTTTTTT
1 TCTCTGTTCTCTCTTTTTTT
2521236 T
1 T
2521237 TTGTTTTGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.53
19 1 0.05
20 8 0.42
ACGTcount: A:0.00, C:0.21, G:0.05, T:0.74
Consensus pattern (20 bp):
TCTCTGTTCTCTCTTTTTTT
Found at i:2521575 original size:3 final size:3
Alignment explanation
Indices: 2521567--2521646 Score: 128
Period size: 3 Copynumber: 26.7 Consensus size: 3
2521557 GGCCTGTTTG
2521567 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2521614 TATA TAA -AA TAA TAA TAA TAA TAAA TAA TAA TA
1 TA-A TAA TAA TAA TAA TAA TAA T-AA TAA TAA TA
2521647 GAAAATAGAG
Statistics
Matches: 73, Mismatches: 0, Indels: 8
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.05
3 63 0.86
4 6 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2521664 original size:41 final size:41
Alignment explanation
Indices: 2521580--2521665 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 41
2521570 TAATAATAAT
* * *
2521580 AATAATAATAATAATAAAATAATAATAATAATAATATATAA
1 AATAATAATAATAATAAAATAATAATAAAAATAAGATAAAA
2521621 AATAATAATAATAAT-AAATAATAATAGAAAATAGAGA-AAAA
1 AATAATAATAATAATAAAATAATAATA-AAAATA-AGATAAAA
2521662 AATA
1 AATA
2521666 GTATCTTCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
40 11 0.28
41 27 0.68
42 2 0.05
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (41 bp):
AATAATAATAATAATAAAATAATAATAAAAATAAGATAAAA
Found at i:2533334 original size:2 final size:2
Alignment explanation
Indices: 2533327--2533365 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2533317 AGCAATTTTA
*
2533327 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2533366 ATAAAGTTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2534959 original size:133 final size:133
Alignment explanation
Indices: 2534811--2535324 Score: 725
Period size: 133 Copynumber: 3.9 Consensus size: 133
2534801 TCTTTAAGAC
*
2534811 TGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAACCTTTGAGA
1 TGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAAAACCTTTGAGA
* *
2534876 TCGTTTCCCTTAAAACAAAGTTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATGAACCTGTGA
66 TCGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATGAACCTGTGA
2534941 GAT
131 GAT
* * * * *
2534944 TGTTTCTCTTGAAACAAATTTTGTGTATCTTGAGACAATTTCTCTTGAAATAGAAACCTTTGAGA
1 TGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAAAACCTTTGAGA
*
2535009 TCATTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATGAACCTGTGA
66 TCGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATGAACCTGTGA
*
2535074 TAT
131 GAT
* * * *
2535077 TATTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAGAAATCTTTGAGA
1 TGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAAAACCTTTGAGA
* * * * * * * *
2535142 TTGTTTCCTTTGAAAC-AACTTTT-T-TCTCTT-AAAAATGTTTCTCTTGAAATA-GAAATCTTT
66 TCGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA-GTTTCTCTTGAAACATG-AACCTGT
2535202 GAGAT
129 GAGAT
*
2535207 TGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAAAACTTTTGAGA
1 TGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAAAACCTTTGAGA
* * * *
2535272 TCGTTTCCCTTGAAATAAA-TTTTGTCTCGCTTAAGATAGTTTCTCTTGAAACA
66 TCGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
2535325 AATTATCCCT
Statistics
Matches: 338, Mismatches: 37, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
129 4 0.01
130 106 0.31
131 4 0.01
132 25 0.07
133 199 0.59
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (133 bp):
TGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAAAACCTTTGAGA
TCGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATGAACCTGTGA
GAT
Found at i:2535002 original size:66 final size:66
Alignment explanation
Indices: 2534802--2535322 Score: 665
Period size: 66 Copynumber: 7.9 Consensus size: 66
2534792 CAAAATTAAT
* * * *
2534802 CTTTAAGACTGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAA
1 CTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAGAAA
2534867 C
66 C
* * * *
2534868 CTTTGAGATCGTTTCCCTTAAAACAAAGTTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATG-
1 CTTTGAGATTGTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATA-GA
2534932 AAC
64 AAC
* * * * *
2534935 CTGTGAGATTGTTTCTCTTGAAACAAATTTTGTGTATCTTGAGACAATTTCTCTTGAAATAGAAA
1 CTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAGAAA
2535000 C
66 C
** *
2535001 CTTTGAGATCATTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATG-
1 CTTTGAGATTGTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATA-GA
2535065 AAC
64 AAC
* * * *
2535068 CTGTGATATTATTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAGAAA
1 CTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAGAAA
*
2535133 T
66 C
* * * *
2535134 CTTTGAGATTGTTTCCTTTGAAACAACTTTT-T-TCTCTT-AAAAATGTTTCTCTTGAAATAGAA
1 CTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA-GTTTCTCTTGAAATAGAA
*
2535196 AT
65 AC
*
2535198 CTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAAAA
1 CTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAGAAA
2535263 C
66 C
* * * * * *
2535264 TTTTGAGATCGTTTCCCTTGAAATAAATTTTGTCTCGCTTAAGATAGTTTCTCTTGAAA
1 CTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
2535323 CAAATTATCC
Statistics
Matches: 396, Mismatches: 49, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
63 3 0.01
64 55 0.14
65 4 0.01
66 215 0.54
67 118 0.30
68 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (66 bp):
CTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAGAAA
C
Found at i:2535148 original size:30 final size:30
Alignment explanation
Indices: 2535114--2535220 Score: 83
Period size: 30 Copynumber: 3.4 Consensus size: 30
2535104 TCTTGAGACA
2535114 GTTTCTCTTGAAATAGAAATCTTTGAGATT
1 GTTTCTCTTGAAATAGAAATCTTTGAGATT
* ** * * *
2535144 GTTTC-CTTTGAAACA-ACTTTTTTCTCTTAAAAAT
1 GTTTCTC-TTGAAATAGA----AATCT-TTGAGATT
2535178 GTTTCTCTTGAAATAGAAATCTTTGAGATT
1 GTTTCTCTTGAAATAGAAATCTTTGAGATT
*
2535208 GTTTCCCTTGAAA
1 GTTTCTCTTGAAA
2535221 CAAATTTTGT
Statistics
Matches: 56, Mismatches: 13, Indels: 16
0.66 0.15 0.19
Matches are distributed among these distances:
29 2 0.04
30 29 0.52
31 3 0.05
33 3 0.05
34 17 0.30
35 2 0.04
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (30 bp):
GTTTCTCTTGAAATAGAAATCTTTGAGATT
Found at i:2535248 original size:36 final size:36
Alignment explanation
Indices: 2535208--2535328 Score: 103
Period size: 36 Copynumber: 3.5 Consensus size: 36
2535198 CTTTGAGATT
2535208 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * **
2535244 GTTTCTCTTGAAATAAA----AACT-T-TTGAGATC-
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGA-CA
* * * *
2535274 GTTTCCCTTGAAATAAATTTTGTCTCGCTTAAGATA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
*
2535310 GTTTCTCTTGAAACAAATT
1 GTTTCCCTTGAAACAAATT
2535329 ATCCCTAAGG
Statistics
Matches: 65, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
30 22 0.34
31 2 0.03
32 2 0.03
34 2 0.03
36 37 0.57
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.40
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:2535592 original size:139 final size:139
Alignment explanation
Indices: 2535323--2536372 Score: 1248
Period size: 139 Copynumber: 7.6 Consensus size: 139
2535313 TCTCTTGAAA
* * *
2535323 CAAATTATCCCTAAGGATGGCTAGACGTCCTTATCACGTAAGAACAATGTCATCCACCGACC--A
1 CAAATTATCCCTAAGTATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGA
* * * * *
2535386 TAT-CTCATCACATAGGAGCAGCGTCATCCTTAGATAACCAAACTTCCTTATCACGTAGTAACCG
66 TCTCCTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCG
2535450 TGTTATCTC
131 TGTTATCTC
* ** * * ** *
2535459 CAAATTATCCCTAAGTATGACTAGATTTCCTCATAATGTAGGAACAATGTCATCCACTAACCATA
1 CAAATTATCCCTAAGTATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGA
* * * * *
2535524 TCTCCTCATCACGCAGGAGCAACGTCATCCTTATATAACCAGACTTCCTCATCACATAGGAACTG
66 TCTCCTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCG
2535589 TGTTATCTC
131 TGTTATCTC
* ** ** * * *
2535598 TAAATTATCTTTAAAAATGGTTAGACGTCCTCATCACGTAAGAACAACGTCATCCACCGACCAGA
1 CAAATTATCCCTAAGTATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGA
* *
2535663 TCTCCTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGTAATCG
66 TCTCCTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCG
*
2535728 TGTTATCTA
131 TGTTATCTC
* * * * *
2535737 CAAATTATCCCTAAGTATGACTAGATGTCCTCATCATGTAGGAACAATGTCATGCACCGACCATA
1 CAAATTATCCCTAAGTATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGA
* * *
2535802 TCTCCTCATCATGTAGGAGCAGCGTCATCCTTATATAACCAGACTTCCTCATCACATAGGAACCG
66 TCTCCTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCG
2535867 TGTTATCTC
131 TGTTATCTC
* ** ** * * *
2535876 TAAATTATCTTTAAAAATGGCTAGACGTCCTCATCACGTAAGAACAACGTCATCCACTGACCAGA
1 CAAATTATCCCTAAGTATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGA
* *
2535941 TCTCCTAATCACGTAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGAAACCG
66 TCTCCTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCG
*
2536006 TGTTTTCTC
131 TGTTATCTC
* * * * * ** *
2536015 CAAATTATCCCTAAGAATGGCTAAATGTCCTCATCAAGTAGGAATAATGTCATCCACAAACCATA
1 CAAATTATCCCTAAGTATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGA
* * * * * * * *
2536080 TCTCATAATCACGTAGAAGCAACGTCATCCTTCGATAACCAGACTACCTCATCACATAGGGACCG
66 TCTCCTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCG
2536145 TGTTATCTC
131 TGTTATCTC
* ** * * **
2536154 TAAATTATCTTTAAAGCTA--ACTAGGCGTCCTCATCACGTAAGG-ACAACATCATCCACCGACC
1 CAAATTATCCCT-AAG-TATGGCTAGACGTCCTCATCACGT-AGGAACAATGTCATCCACCGACC
* * * * * *
2536216 AGACCTCTTCATCACGTAGTAGCAGCATCATCCTTAGATAACCAGACTTTCTCATCACGTAAGAA
63 AGATCTCCTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAA
*
2536281 CCATGTTATCTC
128 CCGTGTTATCTC
* ** * *
2536293 CAAATTATCCCTAAATATGGCTAGATATCCTCATCACATAGGAACAATGTCATCCACCAACCAGA
1 CAAATTATCCCTAAGTATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGA
*
2536358 CCTCCTCATCACGTA
66 TCTCCTCATCACGTA
2536373 AGAGTAGTGT
Statistics
Matches: 760, Mismatches: 145, Indels: 15
0.83 0.16 0.02
Matches are distributed among these distances:
136 52 0.07
137 2 0.00
138 8 0.01
139 691 0.91
140 6 0.01
141 1 0.00
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.27
Consensus pattern (139 bp):
CAAATTATCCCTAAGTATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGA
TCTCCTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCG
TGTTATCTC
Found at i:2535822 original size:278 final size:278
Alignment explanation
Indices: 2535339--2536372 Score: 1536
Period size: 278 Copynumber: 3.7 Consensus size: 278
2535329 ATCCCTAAGG
* * * *
2535339 ATGGCTAGACGTCCTTATCACGTAAGAACAATGTCATCCACCGACC--ATAT-CTCATCACATAG
1 ATGGCTAGACGTCCTCATCACGTAAGAACAACGTCATCCACCGACCAGATCTCCTCATCACGTAG
* *
2535401 GAGCAGCGTCATCCTTAGATAACCAAACTTCCTTATCACGTAGTAACCGTGTTATCTCCAAATTA
66 GAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGTAACCGTGTTATCTCCAAATTA
* * *
2535466 TCCCTAAGTATGACTAGATTTCCTCATAATGTAGGAACAATGTCATCCACTAACCATATCTCCTC
131 TCCCTAAGTATGACTAGATGTCCTCATCATGTAGGAACAATGTCATCCACCAACCATATCTCCTC
* *
2535531 ATCACGCAGGAGCAACGTCATCCTTATATAACCAGACTTCCTCATCACATAGGAACTGTGTTATC
196 ATCACGTAGGAGCAACGTCATCCTTATATAACCAGACTTCCTCATCACATAGGAACCGTGTTATC
2535596 TCTAAATTATCTTTAAAA
261 TCTAAATTATCTTTAAAA
*
2535614 ATGGTTAGACGTCCTCATCACGTAAGAACAACGTCATCCACCGACCAGATCTCCTCATCACGTAG
1 ATGGCTAGACGTCCTCATCACGTAAGAACAACGTCATCCACCGACCAGATCTCCTCATCACGTAG
* *
2535679 GAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGTAATCGTGTTATCTACAAATTA
66 GAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGTAACCGTGTTATCTCCAAATTA
* *
2535744 TCCCTAAGTATGACTAGATGTCCTCATCATGTAGGAACAATGTCATGCACCGACCATATCTCCTC
131 TCCCTAAGTATGACTAGATGTCCTCATCATGTAGGAACAATGTCATCCACCAACCATATCTCCTC
* *
2535809 ATCATGTAGGAGCAGCGTCATCCTTATATAACCAGACTTCCTCATCACATAGGAACCGTGTTATC
196 ATCACGTAGGAGCAACGTCATCCTTATATAACCAGACTTCCTCATCACATAGGAACCGTGTTATC
2535874 TCTAAATTATCTTTAAAA
261 TCTAAATTATCTTTAAAA
* *
2535892 ATGGCTAGACGTCCTCATCACGTAAGAACAACGTCATCCACTGACCAGATCTCCTAATCACGTAG
1 ATGGCTAGACGTCCTCATCACGTAAGAACAACGTCATCCACCGACCAGATCTCCTCATCACGTAG
* *
2535957 GAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGAAACCGTGTTTTCTCCAAATTA
66 GAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGTAACCGTGTTATCTCCAAATTA
* * * * * * * *
2536022 TCCCTAAGAATGGCTAAATGTCCTCATCAAGTAGGAATAATGTCATCCACAAACCATATCTCATA
131 TCCCTAAGTATGACTAGATGTCCTCATCATGTAGGAACAATGTCATCCACCAACCATATCTCCTC
* ** * *
2536087 ATCACGTAGAAGCAACGTCATCCTTCGATAACCAGACTACCTCATCACATAGGGACCGTGTTATC
196 ATCACGTAGGAGCAACGTCATCCTTATATAACCAGACTTCCTCATCACATAGGAACCGTGTTATC
*
2536152 TCTAAATTATCTTTAAAG
261 TCTAAATTATCTTTAAAA
* ** * * * * *
2536170 CTAACTAGGCGTCCTCATCACGTAAGGACAACATCATCCACCGACCAGACCTCTTCATCACGTAG
1 ATGGCTAGACGTCCTCATCACGTAAGAACAACGTCATCCACCGACCAGATCTCCTCATCACGTAG
* * * *
2536235 TAGCAGCATCATCCTTAGATAACCAGACTTTCTCATCACGTAAG-AACCATGTTATCTCCAAATT
66 GAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGT-AGTAACCGTGTTATCTCCAAATT
* * * ** * *
2536299 ATCCCTAAATATGGCTAGATATCCTCATCACATAGGAACAATGTCATCCACCAACCAGACCTCCT
130 ATCCCTAAGTATGACTAGATGTCCTCATCATGTAGGAACAATGTCATCCACCAACCATATCTCCT
2536364 CATCACGTA
195 CATCACGTA
2536373 AGAGTAGTGT
Statistics
Matches: 685, Mismatches: 70, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
275 43 0.06
277 3 0.00
278 637 0.93
279 2 0.00
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.27
Consensus pattern (278 bp):
ATGGCTAGACGTCCTCATCACGTAAGAACAACGTCATCCACCGACCAGATCTCCTCATCACGTAG
GAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGTAACCGTGTTATCTCCAAATTA
TCCCTAAGTATGACTAGATGTCCTCATCATGTAGGAACAATGTCATCCACCAACCATATCTCCTC
ATCACGTAGGAGCAACGTCATCCTTATATAACCAGACTTCCTCATCACATAGGAACCGTGTTATC
TCTAAATTATCTTTAAAA
Found at i:2544358 original size:200 final size:200
Alignment explanation
Indices: 2544015--2544400 Score: 709
Period size: 200 Copynumber: 1.9 Consensus size: 200
2544005 CTAAAAAAAG
* *
2544015 TTCAAGCTTTTTCATCTTTTCTTTGTCTTGTCAACTAATCATGGTGCGCTCACATCCCTCCAGCA
1 TTCAAGCTTTTTCATATTTTCTTTGTCTTGTCAACTAATCATGGTGCGATCACATCCCTCCAGCA
* *
2544080 CGACTCCATCATCTCCATTACGTTTCGTTGATGAAGCAGCACAAGAAAGATTTCAAATCCTTAAA
66 CGACTCCATCATCTCCATCACATTTCGTTGATGAAGCAGCACAAGAAAGATTTCAAATCCTTAAA
*
2544145 AACTGTCGGGTGTTCTTTGAGTTAGGCTTTGTTTTCTCCGACGAGGAAGATGCATACCTTTGCAG
131 AACTGTCGGGTGTTCTTTGAGTTAGGCTTTGTTTTCTCCGACGAGGAAGATACATACCTTTGCAG
2544210 TGATC
196 TGATC
*
2544215 TTCAAGCTTTTTCATATTTTCTTTGTCTTTTCAACTAATCATGGTGCGATCACATCCCTCCAGCA
1 TTCAAGCTTTTTCATATTTTCTTTGTCTTGTCAACTAATCATGGTGCGATCACATCCCTCCAGCA
*
2544280 CGACTCCATCATCTCCATCACATTTCGTTGATGAAGTAGCACAAGAAAGATTTCAAATCCTTAAA
66 CGACTCCATCATCTCCATCACATTTCGTTGATGAAGCAGCACAAGAAAGATTTCAAATCCTTAAA
2544345 AACTGTCGGGTGTTCTTTGAGTTAGGCTTTGTTTTCTCCGACGAGGAAGATACATA
131 AACTGTCGGGTGTTCTTTGAGTTAGGCTTTGTTTTCTCCGACGAGGAAGATACATA
2544401 GTGATGTCAT
Statistics
Matches: 179, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
200 179 1.00
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (200 bp):
TTCAAGCTTTTTCATATTTTCTTTGTCTTGTCAACTAATCATGGTGCGATCACATCCCTCCAGCA
CGACTCCATCATCTCCATCACATTTCGTTGATGAAGCAGCACAAGAAAGATTTCAAATCCTTAAA
AACTGTCGGGTGTTCTTTGAGTTAGGCTTTGTTTTCTCCGACGAGGAAGATACATACCTTTGCAG
TGATC
Found at i:2548840 original size:17 final size:17
Alignment explanation
Indices: 2548808--2548846 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2548798 GGGTTCTCAT
*
2548808 TTATTATTAATCTATTA
1 TTATTATTAATATATTA
*
2548825 TTATTATTATTATATTA
1 TTATTATTAATATATTA
*
2548842 ATATT
1 TTATT
2548847 TATTTACATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATTATTAATATATTA
Found at i:2552715 original size:2 final size:2
Alignment explanation
Indices: 2552708--2552766 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
2552698 ATAACCTACT
2552708 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
2552750 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
2552767 GTGTGTGTGT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2552771 original size:2 final size:2
Alignment explanation
Indices: 2552766--2552851 Score: 165
Period size: 2 Copynumber: 43.5 Consensus size: 2
2552756 TATATATATA
2552766 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2552808 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T- TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2552849 TG T
1 TG T
2552852 TTACTTTAGA
Statistics
Matches: 83, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 82 0.99
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:2558392 original size:36 final size:41
Alignment explanation
Indices: 2558307--2558426 Score: 150
Period size: 46 Copynumber: 2.7 Consensus size: 41
2558297 ACCATTTATC
*
2558307 CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATA
1 CCATAAGCTCGTAAGCTTATTTTACCAATATAC-CACCA--T--TA
*
2558353 CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTA
1 CCATAAGCTCGTAAGCTTATTTTACCAATATAC-CACCA-TTA
2558396 TCCATAAGCTCGTAAGCTTATTTTACCAATA
1 -CCATAAGCTCGTAAGCTTATTTTACCAATA
2558427 CACTTACCAT
Statistics
Matches: 73, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
43 2 0.03
44 30 0.41
45 2 0.03
46 39 0.53
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (41 bp):
CCATAAGCTCGTAAGCTTATTTTACCAATATACCACCATTA
Found at i:2558416 original size:44 final size:45
Alignment explanation
Indices: 2558294--2558446 Score: 256
Period size: 44 Copynumber: 3.4 Consensus size: 45
2558284 TATAAAATCT
*
2558294 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAATATA
2558339 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTT-ATACCATAAGCTCGTAAGCTTATTTTACCAATATA
*
2558385 CTTACCATTTAT-CCATAAGCTCGTAAGCTTATTTTACCAATACA
1 CTTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAATATA
*
2558429 CTTACCA-TTATTCCATAA
1 CTTACCATTTATACCATAA
2558447 CCATATACCA
Statistics
Matches: 104, Mismatches: 2, Indels: 5
0.94 0.02 0.05
Matches are distributed among these distances:
43 4 0.04
44 44 0.42
45 12 0.12
46 44 0.42
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.37
Consensus pattern (45 bp):
CTTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:2562337 original size:259 final size:255
Alignment explanation
Indices: 2561701--2562314 Score: 838
Period size: 255 Copynumber: 2.4 Consensus size: 255
2561691 AGTAAACTAA
* *
2561701 TTCTTGAATTTATAAGTCCATCGGGCCATCTGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCG
1 TTCTTG-ATTCATAAGTCCATC-GGCCATCTGTAAGTCTTTCGAGCTTGATGTTTAAATCCTTCG
* * * * * *
2561766 GATTATCTGTAAGTCTTTCGAGCAGGATGATAAAGCTTTCAGGTCAACCATAAGATCTTCAGTGT
64 GGTTATCTGTAAGTCTTTCGAGCAAGATGATAAAACTTTCAGGTCATCCATAAGACCTTCAGTGC
* *
2561831 TGGATGCTTTCAAATGAGATTTTAGAAACTAAGCCTTTCATTCCTAATTATCTCAAAAGAATTGT
129 TGGATGCTTTAAAATGAGATTTTAGAAACTAAACCTTTCATTCCTAATTATCTCAAAAGAATTGT
* *
2561896 TAAAGGAATCTAAGCCTAACAAAGAGGTTCCTTGACAACTAAGAAACTAAGATTTCTAGGGT
194 TAAAGGAAGCTAAGCCTAACAAAGAGGTTCCTTGACAACTAAGAAACTAAGATTTCGAGGGT
** * * * *
2561958 TTCTTGATTTGTAAGT-CATTCGGACCAT-TTTAAGTGTTTCGCG-TATGATATTTAAATCCTTC
1 TTCTTGATTCATAAGTCCA-TCGG-CCATCTGTAAGTCTTTCGAGCT-TGATGTTTAAATCCTTC
* *
2562020 GGGTCATCTGTAAGTCTTTCGAGCAAGATTATAAAACTTTCAGGTCATCCATAAGACCTTCAGTG
63 GGGTTATCTGTAAGTCTTTCGAGCAAGATGATAAAACTTTCAGGTCATCCATAAGACCTTCAGTG
* *
2562085 CTGGATGTTTTAAAATGAGATTTTAGAAACTAAACCTTTCAGGGTTTCCTAATTATCTCAAAATA
128 CTGGATGCTTTAAAATGAGATTTTAGAAACTAAACCTTTCA----TTCCTAATTATCTCAAAAGA
* * *
2562150 GTTGTTAAAGGAAGCTAAGCCTAACAAAGAGGTTCCTTTACAACTAAGAAACTAAGCTTTCGAGG
189 ATTGTTAAAGGAAGCTAAGCCTAACAAAGAGGTTCCTTGACAACTAAGAAACTAAGATTTCGAGG
2562215 GT
254 GT
* * * *
2562217 TTTTTGATTCATAAGTCCGTCGAGCCATCTGTAAGTCTTTCGAGCTTGATGTGTAAATCCTCCGG
1 TTCTTGATTCATAAGTCCATCG-GCCATCTGTAAGTCTTTCGAGCTTGATGTTTAAATCCTTCGG
* *
2562282 GTTATTTGTAAGCCTTTCGAGCAAGATGATAAA
65 GTTATCTGTAAGTCTTTCGAGCAAGATGATAAA
2562315 CCTCTGAGCC
Statistics
Matches: 309, Mismatches: 37, Indels: 19
0.85 0.10 0.05
Matches are distributed among these distances:
255 127 0.41
256 15 0.05
257 6 0.02
259 101 0.33
260 59 0.19
261 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (255 bp):
TTCTTGATTCATAAGTCCATCGGCCATCTGTAAGTCTTTCGAGCTTGATGTTTAAATCCTTCGGG
TTATCTGTAAGTCTTTCGAGCAAGATGATAAAACTTTCAGGTCATCCATAAGACCTTCAGTGCTG
GATGCTTTAAAATGAGATTTTAGAAACTAAACCTTTCATTCCTAATTATCTCAAAAGAATTGTTA
AAGGAAGCTAAGCCTAACAAAGAGGTTCCTTGACAACTAAGAAACTAAGATTTCGAGGGT
Found at i:2565341 original size:20 final size:20
Alignment explanation
Indices: 2565313--2565355 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2565303 TATATTGGGC
* *
2565313 TATTGTCTATTGTTTATGGT
1 TATTGTCTATGGTATATGGT
*
2565333 TATTTTCTATGGTATATGGT
1 TATTGTCTATGGTATATGGT
2565353 TAT
1 TAT
2565356 GGAATAATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.05, G:0.19, T:0.58
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGT
Found at i:2565418 original size:47 final size:46
Alignment explanation
Indices: 2565352--2565463 Score: 131
Period size: 49 Copynumber: 2.4 Consensus size: 46
2565342 TGGTATATGG
* * *
2565352 TTATGGAAT-AATGGCAAGTA-TATTG-ATAAAATAATCTTACGAGC
1 TTATGGGATAAATGGTAAGTAGTATTGTA-AAAATAAACTTACGAGC
*
2565396 TTATGGGATTTAAATGGTAAGTATGTTTTGTAAAAATAAACTTACGAGC
1 TTATGGGA--TAAATGGTAAGTA-GTATTGTAAAAATAAACTTACGAGC
2565445 TTATGGGATAAATGGTAAG
1 TTATGGGATAAATGGTAAG
2565464 GGATTTTATA
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
44 7 0.12
46 1 0.02
47 21 0.36
49 28 0.48
50 1 0.02
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.34
Consensus pattern (46 bp):
TTATGGGATAAATGGTAAGTAGTATTGTAAAAATAAACTTACGAGC
Found at i:2565835 original size:11 final size:10
Alignment explanation
Indices: 2565810--2565835 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2565800 TGAAAGGTTA
2565810 ATTTTTATGT
1 ATTTTTATGT
2565820 ATTTTTATGT
1 ATTTTTATGT
2565830 ATTTTT
1 ATTTTT
2565836 GGAAGTTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.73
Consensus pattern (10 bp):
ATTTTTATGT
Found at i:2567632 original size:42 final size:41
Alignment explanation
Indices: 2567565--2567671 Score: 124
Period size: 42 Copynumber: 2.6 Consensus size: 41
2567555 TCTTGATTTG
* ** * *
2567565 TAAATCCTTCAGGTCATCTGCAAGTCTTTCGACCATGATGTT
1 TAAATCCTTCGGGTCATCTATAAGTCTTTCGACCAAGATG-A
* *
2567607 TAAATCCTTCGGGTAATCTATAAGTCTTTCGAGCAAGATGA
1 TAAATCCTTCGGGTCATCTATAAGTCTTTCGACCAAGATGA
* *
2567648 TAAAACCTTCGGGTCATCCATAAG
1 TAAATCCTTCGGGTCATCTATAAG
2567672 ACCTTCAGTG
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 21 0.38
42 34 0.62
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (41 bp):
TAAATCCTTCGGGTCATCTATAAGTCTTTCGACCAAGATGA
Found at i:2567671 original size:41 final size:42
Alignment explanation
Indices: 2567586--2567671 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 42
2567576 GGTCATCTGC
* * * *
2567586 AAGTCTTTCGACCATGATGTTTAAATCCTTCGGGTAATCTAT
1 AAGTCTTTCGACCAAGATGTATAAAACCTTCGGGTAATCCAT
* *
2567628 AAGTCTTTCGAGCAAGATG-ATAAAACCTTCGGGTCATCCAT
1 AAGTCTTTCGACCAAGATGTATAAAACCTTCGGGTAATCCAT
2567669 AAG
1 AAG
2567672 ACCTTCAGTG
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
41 21 0.55
42 17 0.45
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (42 bp):
AAGTCTTTCGACCAAGATGTATAAAACCTTCGGGTAATCCAT
Found at i:2567952 original size:260 final size:261
Alignment explanation
Indices: 2567304--2567955 Score: 873
Period size: 260 Copynumber: 2.5 Consensus size: 261
2567294 TCCCGAATTT
* * *
2567304 ATAAGTCCTTCGAGCCATCTGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTA
1 ATAAGTCCTTCGGGCCATCTGTAAGTCTTTCGACCATGATGTTTAAATCCTTCGGGTCATCTATA
* * * * *
2567369 AGTCTTTCAAGCAAGAAGATAAG-CCTTTGGGTCATCCATAAG-TCCTTTAGTGATGAATGCTTT
66 AGTCTTTCGAGCAAGATGATAAGACCTTCGGGTCATCCATAAGAT-CTTCAGTGATGAATGTTTT
* * *
2567432 AAAATGAGATTTTAGAAACTAAGCCTTTTAGGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAAG
130 CAAATGAGATTTTAGAAACTAAACCTTTTAGGGGTTTCCTAATTATCTCAAAAGAGTTGGTAAAG
*
2567497 GAAGCTAAGCCTAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGATTTCGAGGGTTTCTTGAT
195 AAAGCTAAGCCTAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGATTTCGAGGGTTTCTTGAT
*
2567562 TT
260 TA
* * * * * *
2567564 GTAAATCCTTCAGGTCATCTGCAAGTCTTTCGACCATGATGTTTAAATCCTTCGGGTAATCTATA
1 ATAAGTCCTTCGGGCCATCTGTAAGTCTTTCGACCATGATGTTTAAATCCTTCGGGTCATCTATA
* * * *
2567629 AGTCTTTCGAGCAAGATGATAAAACCTTCGGGTCATCCATAAGACCTTCAGTGCTGGATGTTTTC
66 AGTCTTTCGAGCAAGATGATAAGACCTTCGGGTCATCCATAAGATCTTCAGTGATGAATGTTTTC
* * *
2567694 AAATGAGATTTTAGAAACTAAACC-TTTCGGGGTTTCTTAATTATCTCAAAATAGTTGGTAAAGA
131 AAATGAGATTTTAGAAACTAAACCTTTTAGGGGTTTCCTAATTATCTCAAAAGAGTTGGTAAAGA
* * *
2567758 AAGCTAAGCCTAATAAAGGGGTTCCTTGACAACTAAGAAACTAAGGTTTTGAGGGTTTCTTGATT
196 AAGCTAAGCCTAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGATTTCGAGGGTTTCTTGATT
2567823 A
261 A
* * * * * *
2567824 ATAAGTCATTCGGGCCATCTGTAAGTCTTTCGATCTTGATGTGTAAATCATCTGGGGTCATCTAT
1 ATAAGTCCTTCGGGCCATCTGTAAGTCTTTCGACCATGATGTTTAAATCCT-TCGGGTCATCTAT
* * * * * *
2567889 AAG-CCTTCTGAGCAAGATGATAAGACCTTCGGGCCATTCATAAGATC-TCGGGGAAGAATGTTT
65 AAGTCTTTC-GAGCAAGATGATAAGACCTTCGGGTCATCCATAAGATCTTCAGTGATGAATGTTT
2567952 TCAA
129 TCAA
2567956 CATTTCCATT
Statistics
Matches: 337, Mismatches: 51, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
260 233 0.69
261 104 0.31
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (261 bp):
ATAAGTCCTTCGGGCCATCTGTAAGTCTTTCGACCATGATGTTTAAATCCTTCGGGTCATCTATA
AGTCTTTCGAGCAAGATGATAAGACCTTCGGGTCATCCATAAGATCTTCAGTGATGAATGTTTTC
AAATGAGATTTTAGAAACTAAACCTTTTAGGGGTTTCCTAATTATCTCAAAAGAGTTGGTAAAGA
AAGCTAAGCCTAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGATTTCGAGGGTTTCTTGATT
A
Found at i:2568423 original size:123 final size:121
Alignment explanation
Indices: 2568140--2568517 Score: 454
Period size: 121 Copynumber: 3.1 Consensus size: 121
2568130 CACTCAATGG
* * * *
2568140 ATCAACATTTCCATAAGAAGTTCATAATAAGAAGAACTCATCTGAATAGGAAGAAGAAGTTCATG
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT-
* * *
2568205 AA-CTAAAGAACTTGTTCAACCTTAGGTCGACTTTATCACAGAAAGAGTAGAGCAAC
65 AATCTAAAGAACTTGTTCAACCTTAGCTCGACTCTATCACAGAAAGAGTAAAGCAAC
* * *
2568261 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTAAAGAAGATGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * * * * *** * *
2568326 ATCTGAAGAACTTATTCAACTTTTTGCTTGACTCTATTGTAGTAGGAGATAAAGCAAC
66 ATCTAAAGAACTTGTTCAAC-CTTAGCTCGACTCTATCACAGAAAGAG-TAAAGCAAC
* *
2568384 ATCAATATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGGAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * * * * *
2568449 ATCTAAAGAACTTGTTCAACCTTAGCTCGATTC-ATCGCAGAAGGAGATAGATCATC
66 ATCTAAAGAACTTGTTCAACCTTAGCTCGACTCTATCACAGAAAGAG-TAAAGCAAC
2568505 ATCAACATTTCCA
1 ATCAACATTTCCA
2568518 TCTTAATCAA
Statistics
Matches: 216, Mismatches: 38, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
120 2 0.01
121 102 0.47
122 26 0.12
123 86 0.40
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (121 bp):
ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
ATCTAAAGAACTTGTTCAACCTTAGCTCGACTCTATCACAGAAAGAGTAAAGCAAC
Found at i:2568657 original size:3 final size:3
Alignment explanation
Indices: 2568651--2568705 Score: 76
Period size: 3 Copynumber: 18.7 Consensus size: 3
2568641 TTAATAATAA
* * *
2568651 TAT TAT TAT TAT TAT TAA TAT T-T TAT TAA TAT TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2568698 TAT TAT TA
1 TAT TAT TA
2568706 AATAAAAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2568681 original size:32 final size:32
Alignment explanation
Indices: 2568637--2568704 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
2568627 TCCGCCATTT
*
2568637 TATTTTAATAATAATATTATTATTATTATTAA
1 TATTTTAATAATAATATTATTATTATCATTAA
* * *
2568669 TATTTTATTAATATTATTATTATTATCATTAT
1 TATTTTAATAATAATATTATTATTATCATTAA
2568701 TATT
1 TATT
2568705 AAATAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (32 bp):
TATTTTAATAATAATATTATTATTATCATTAA
Found at i:2570002 original size:19 final size:19
Alignment explanation
Indices: 2569975--2570072 Score: 63
Period size: 19 Copynumber: 4.8 Consensus size: 19
2569965 CATTGTTTAA
*
2569975 TTATAATTTTATTTTATTT
1 TTATTATTTTATTTTATTT
**
2569994 TTATTATTTTCCTTTATTT
1 TTATTATTTTATTTTATTT
*
2570013 TTCAATATTTTAATTTACTATTT
1 TT-ATTATTTT-ATTT--TATTT
* *
2570036 TAATTATTATT-CTTTATTT
1 TTATTATT-TTATTTTATTT
*
2570055 TATATTTATTTAATTTTA
1 T-TA-TTATTTTATTTTA
2570073 GTCATATTAA
Statistics
Matches: 59, Mismatches: 12, Indels: 14
0.69 0.14 0.16
Matches are distributed among these distances:
19 24 0.41
20 9 0.15
21 13 0.22
22 5 0.08
23 8 0.14
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTATTTTATTTTATTT
Found at i:2570401 original size:2 final size:2
Alignment explanation
Indices: 2570390--2570420 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2570380 ATAACCTACT
2570390 TA TA -A 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
2570421 CTTTAGTTCT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2579839 original size:19 final size:19
Alignment explanation
Indices: 2579804--2579840 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2579794 TTTTAAAAAT
* *
2579804 ATATTTTAAATATTAATTA
1 ATATTTTAAAAAATAATTA
2579823 ATATTTTAAAAAATAATT
1 ATATTTTAAAAAATAATT
2579841 GGTGGGATCA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTTTAAAAAATAATTA
Found at i:2604650 original size:81 final size:81
Alignment explanation
Indices: 2604515--2604862 Score: 583
Period size: 81 Copynumber: 4.3 Consensus size: 81
2604505 TTTTAAAATG
*
2604515 AAAGACTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTACATGAAAGGT
1 AAAGACTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGT
*
2604580 TAAATACCTTTGAATA
66 TAAATACCTTTGAGTA
* *
2604596 AAAGACTAATTGCCTAGTTGTACATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGT
1 AAAGACTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGT
2604661 TAAATACCTTTGAGTA
66 TAAATACCTTTGAGTA
*
2604677 AAAGAATAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGT
1 AAAGACTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGT
2604742 TAAATACCTTTGAGTA
66 TAAATACCTTTGAGTA
* * * *
2604758 AAAGACT-ATTGCCTAGATGTGCATTTGAGAGAAATGTGTCAATCACGCCAGTTAGATG-AAGGT
1 AAAGACTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGT
2604821 TAAATACCTTTGAGTA
66 TAAATACCTTTGAGTA
**
2604837 AAAGACTAATTGCCTATTTGTGCATT
1 AAAGACTAATTGCCTAGCTGTGCATT
2604863 GAATCATGCC
Statistics
Matches: 252, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
79 28 0.11
80 63 0.25
81 161 0.64
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (81 bp):
AAAGACTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGT
TAAATACCTTTGAGTA
Found at i:2604905 original size:67 final size:66
Alignment explanation
Indices: 2604798--2604929 Score: 219
Period size: 67 Copynumber: 2.0 Consensus size: 66
2604788 GAAATGTGTC
* **
2604798 AATCACGCCAGTTAGATGAAGGTTAAATACCTTTGAGTAAAAGACTAATTGCCTATTTGTGCATT
1 AATCACGCCAGTTAGATGAAGGTTAAATACCTTTGAGTAAAAGAATAATTGCCTAGCTGTGCATT
2604863 G
66 G
*
2604864 AATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGAATAATTGCCTAGCTGTGCAT
1 AATCACGCCAGTTAGATG-AAGGTTAAATACCTTTGAGTAAAAGAATAATTGCCTAGCTGTGCAT
2604929 T
65 T
2604930 TGACAGAAAG
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
66 17 0.28
67 44 0.72
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (66 bp):
AATCACGCCAGTTAGATGAAGGTTAAATACCTTTGAGTAAAAGAATAATTGCCTAGCTGTGCATT
G
Found at i:2604999 original size:81 final size:81
Alignment explanation
Indices: 2604864--2605317 Score: 710
Period size: 81 Copynumber: 5.6 Consensus size: 81
2604854 TTGTGCATTG
*
2604864 AATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGAATAATTGCCTAGCTGTGCAT
1 AATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGACTAATTGCCTAGCTGTGCAT
2604929 TTGACAGAAAGGTGTC
66 TTGACAGAAAGGTGTC
* *
2604945 AATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGACTATTTGCCTAGATGTGCAT
1 AATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGACTAATTGCCTAGCTGTGCAT
* *
2605010 TTGAGAGAAATGTGTC
66 TTGACAGAAAGGTGTC
* **
2605026 AATCACGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGACTAATTGCCTATTTGTGCAT
1 AATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGACTAATTGCCTAGCTGTGCAT
2605091 TTGACAGAAAGGTGTC
66 TTGACAGAAAGGTGTC
* * * *
2605107 AATCGTGTCAGTTAGATGTAAGGTTAAATACCTTTGAGTAAAAGACTAATTGCCTAGTTGTGCAT
1 AATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGACTAATTGCCTAGCTGTGCAT
2605172 TTGACAGAAAGGTGTC
66 TTGACAGAAAGGTGTC
* * ** *
2605188 AATCATGCCAGTTGGATGAAAGGTCAAGCACCTTTGAGTAAAATACTAATTGCCTAGCTGTGCAT
1 AATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGACTAATTGCCTAGCTGTGCAT
*
2605253 TTGACAGAACGGTGTC
66 TTGACAGAAAGGTGTC
* * * *
2605269 AATCATTCCGGTTAGATGAAACGTTAAATACCTTTGAGTAAAAGGCTAA
1 AATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGACTAA
2605318 ATACTTAATA
Statistics
Matches: 338, Mismatches: 35, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 338 1.00
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (81 bp):
AATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGACTAATTGCCTAGCTGTGCAT
TTGACAGAAAGGTGTC
Found at i:2605334 original size:162 final size:161
Alignment explanation
Indices: 2604515--2605335 Score: 1134
Period size: 162 Copynumber: 5.2 Consensus size: 161
2604505 TTTTAAAATG
* *
2604515 AAAGACTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTACATGAAAGGT
1 AAAGACTAATTGCCTA-ATGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGT
* * * *
2604580 TAAATACCTTTGAATAAAAGACTAATTGCCTAGTTGTACATTTGACAGAAAGGTGTCAATCATGC
65 TAAATACCTTTGAGTAAAAGACTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATTC
2604645 CAGTTAGATGAAAGGTTAAATACCTTTGAGTA
130 CAGTTAGATGAAAGGTTAAATACCTTTGAGTA
* *
2604677 AAAGAATAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGT
1 AAAGACTAATTGCCTA-ATGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGT
* * * **
2604742 TAAATACCTTTGAGTAAAAGACT-ATTGCCTAGATGTGCATTTGAGAGAAATGTGTCAATCACGC
65 TAAATACCTTTGAGTAAAAGACTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATTC
2604806 CAGTTAGATG-AAGGTTAAATACCTTTGAGTA
130 CAGTTAGATGAAAGGTTAAATACCTTTGAGTA
* *
2604837 AAAGACTAATTGCCT-AT-T---TGTG-C----A--T-TGAATCATGCCAGTTAGATGAAAGGTT
1 AAAGACTAATTGCCTAATGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTT
* *
2604889 AAATACCTTTGAGTAAAAGAATAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCC
66 AAATACCTTTGAGTAAAAGACTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATTCC
2604954 AGTTAGATGAAAGGTTAAATACCTTTGAGTA
131 AGTTAGATGAAAGGTTAAATACCTTTGAGTA
* * * *
2604985 AAAGACTATTTGCCTAGATGTGCATTTGAGAGAAATGTGTCAATCACGCCAGTTAGATGAAAGGT
1 AAAGACTAATTGCCTA-ATGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGT
** *
2605050 TAAATACCTTTGAGTAAAAGACTAATTGCCTATTTGTGCATTTGACAGAAAGGTGTCAATCGTGT
65 TAAATACCTTTGAGTAAAAGACTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCAT-T
*
2605115 -CAGTTAGATGTAAGGTTAAATACCTTTGAGTA
129 CCAGTTAGATGAAAGGTTAAATACCTTTGAGTA
* *
2605147 AAAGACTAATTGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTGGATGAAAGGT
1 AAAGACTAATTGCCTA-ATGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGT
* ** * *
2605212 CAAGCACCTTTGAGTAAAATACTAATTGCCTAGCTGTGCATTTGACAGAACGGTGTCAATCATTC
65 TAAATACCTTTGAGTAAAAGACTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATTC
* *
2605277 CGGTTAGATGAAACGTTAAATACCTTTGAGTA
130 CAGTTAGATGAAAGGTTAAATACCTTTGAGTA
* * * *
2605309 AAAGGCTAAATACTTAATAGTGCATTT
1 AAAGACTAATTGCCTAAT-GTGCATTT
2605336 TTACATAAAT
Statistics
Matches: 590, Mismatches: 50, Indels: 38
0.87 0.07 0.06
Matches are distributed among these distances:
146 47 0.08
147 48 0.08
148 35 0.06
149 1 0.00
150 2 0.00
151 1 0.00
153 1 0.00
154 6 0.01
157 1 0.00
158 1 0.00
159 1 0.00
160 35 0.06
161 49 0.08
162 362 0.61
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.30
Consensus pattern (161 bp):
AAAGACTAATTGCCTAATGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTT
AAATACCTTTGAGTAAAAGACTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATTCC
AGTTAGATGAAAGGTTAAATACCTTTGAGTA
Found at i:2608408 original size:20 final size:17
Alignment explanation
Indices: 2608367--2608400 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2608357 TCCTACCTCA
2608367 TTCTTCTTCTCTTTCTT
1 TTCTTCTTCTCTTTCTT
*
2608384 TTCTTCTTCTTTTTCTT
1 TTCTTCTTCTCTTTCTT
2608401 GCTTTCTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (17 bp):
TTCTTCTTCTCTTTCTT
Found at i:2609410 original size:15 final size:15
Alignment explanation
Indices: 2609390--2609419 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2609380 AAATAGGTGC
2609390 CTAAACACATCAAGG
1 CTAAACACATCAAGG
2609405 CTAAACACATCAAGG
1 CTAAACACATCAAGG
2609420 GATGCAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.27, G:0.13, T:0.13
Consensus pattern (15 bp):
CTAAACACATCAAGG
Found at i:2612010 original size:25 final size:25
Alignment explanation
Indices: 2611988--2612036 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
2611978 ATCTAATGTA
2611988 ACATGAATTAAAAACATGCAATGAC
1 ACATGAATTAAAAACATGCAATGAC
* *
2612013 ACATGAATTGATAACATGCAATGA
1 ACATGAATTAAAAACATGCAATGA
2612037 ATTATTAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.22
Consensus pattern (25 bp):
ACATGAATTAAAAACATGCAATGAC
Found at i:2613266 original size:29 final size:27
Alignment explanation
Indices: 2613207--2613276 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 27
2613197 TAGTTTTTTC
2613207 TTCTATTTTCCTTTTTCTTCTCTTATCT
1 TTCTATTTT-CTTTTTCTTCTCTTATCT
*
2613235 TTCCTATTTTCTTTTTCTTTTCATT-TCAT
1 TT-CTATTTTCTTTTTCTTCTC-TTATC-T
*
2613264 TTCTTTTTTCTTT
1 TTCTATTTTCTTT
2613277 GCTTTTTTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
28 25 0.68
29 12 0.32
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.71
Consensus pattern (27 bp):
TTCTATTTTCTTTTTCTTCTCTTATCT
Found at i:2613313 original size:22 final size:22
Alignment explanation
Indices: 2613274--2613315 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2613264 TTCTTTTTTC
*
2613274 TTTGCTTTTTTCATTCTTCAGT
1 TTTGCTTTTTTCACTCTTCAGT
2613296 TTTGCTCTTTTTC-CTCTTCA
1 TTTGCT-TTTTTCACTCTTCA
2613316 TCGGCAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.07, C:0.24, G:0.07, T:0.62
Consensus pattern (22 bp):
TTTGCTTTTTTCACTCTTCAGT
Found at i:2613996 original size:12 final size:11
Alignment explanation
Indices: 2613979--2614080 Score: 95
Period size: 11 Copynumber: 9.4 Consensus size: 11
2613969 CTTGAACACC
2613979 TCTTTTTTATTT
1 TCTTTTTT-TTT
*
2613991 TC-TTTTATTT
1 TCTTTTTTTTT
*
2614001 TC--TCTTTTT
1 TCTTTTTTTTT
*
2614010 TC-TTTTCTTT
1 TCTTTTTTTTT
2614020 TCTTTTTTTTT
1 TCTTTTTTTTT
2614031 TCTTTTTCTTTT
1 TCTTTTT-TTTT
*
2614043 TCTTCTTTTTT
1 TCTTTTTTTTT
*
2614054 TCTTTTCTTTT
1 TCTTTTTTTTT
*
2614065 TCTTCTTTTTCT
1 TCTT-TTTTTTT
2614077 TCTT
1 TCTT
2614081 CTTCAAGCAT
Statistics
Matches: 75, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
9 7 0.09
10 12 0.16
11 35 0.47
12 21 0.28
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (11 bp):
TCTTTTTTTTT
Found at i:2614037 original size:22 final size:22
Alignment explanation
Indices: 2613981--2614080 Score: 114
Period size: 23 Copynumber: 4.4 Consensus size: 22
2613971 TGAACACCTC
*
2613981 TTTTTTATTTTCTTTTAT-TTTCT
1 TTTTTTCTTTTCTTTT-TCTTT-T
2614004 CTTTTTTCTTTTC-TTTTCTTTT
1 -TTTTTTCTTTTCTTTTTCTTTT
*
2614026 TTTTTTCTTTTTCTTTTTCTTCT
1 TTTTTTC-TTTTCTTTTTCTTTT
2614049 TTTTTTCTTTTCTTTTTCTTCTT
1 TTTTTTCTTTTCTTTTTCTT-TT
*
2614072 TTTCTTCTT
1 TTTTTTCTT
2614081 CTTCAAGCAT
Statistics
Matches: 68, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
21 7 0.10
22 20 0.29
23 30 0.44
24 11 0.16
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (22 bp):
TTTTTTCTTTTCTTTTTCTTTT
Found at i:2614043 original size:28 final size:28
Alignment explanation
Indices: 2613982--2614068 Score: 106
Period size: 28 Copynumber: 3.1 Consensus size: 28
2613972 GAACACCTCT
* *
2613982 TTTTTATTTTCTTTTATTTTCTCTTTTT-
1 TTTTTCTTTTCTTTT-TTTTTTCTTTTTC
2614010 TCTTTTCTTTTCTTTTTTTTTTCTTTTTC
1 T-TTTTCTTTTCTTTTTTTTTTCTTTTTC
*
2614039 TTTTTCTTCTT-TTTTTCTTTTCTTTTTC
1 TTTTTCTT-TTCTTTTTTTTTTCTTTTTC
2614067 TT
1 TT
2614069 CTTTTTCTTC
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
28 37 0.70
29 16 0.30
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (28 bp):
TTTTTCTTTTCTTTTTTTTTTCTTTTTC
Found at i:2614055 original size:34 final size:35
Alignment explanation
Indices: 2613979--2614084 Score: 110
Period size: 37 Copynumber: 3.0 Consensus size: 35
2613969 CTTGAACACC
* *
2613979 TCTTTT-TTATTTTCTTTTATTTTCTCTTTTTTCTT-T
1 TCTTTTCTT-TTTTTTTTTCTTTT-TC-TTTTTCTTCT
2614015 TCTTTTC-TTTTTTTTTTCTTTTTCTTTTTCTTCT
1 TCTTTTCTTTTTTTTTTTCTTTTTCTTTTTCTTCT
* *
2614049 TTTTTTCTTTTCTTTTTCTTCTTTTTCTTCTTCTTC
1 TCTTTTCTTTT-TTTTT-TTCTTTTTCTTTTTCTTC
2614085 AAGCATAATA
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
33 8 0.13
34 9 0.15
35 15 0.25
36 12 0.20
37 17 0.28
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (35 bp):
TCTTTTCTTTTTTTTTTTCTTTTTCTTTTTCTTCT
Found at i:2614084 original size:6 final size:6
Alignment explanation
Indices: 2613979--2614083 Score: 87
Period size: 6 Copynumber: 17.7 Consensus size: 6
2613969 CTTGAACACC
*
2613979 TCTTTT T-TATTT TCTTTT AT-TTTC TCTTTT T-TCTTT TC-TTT TCTTTT
1 TCTTTT TCT-TTT TCTTTT -TCTTTT TCTTTT TCT-TTT TCTTTT TCTTTT
* *
2614026 T-TTTT TCTTTT TCTTTT TCTTCT T-TTTT TCTTTT CTTTTTCT TCTTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT -TCTTT-T TCTTTT
*
2614074 TCTTCT TCTT
1 TCTTTT TCTT
2614084 CAAGCATAAT
Statistics
Matches: 81, Mismatches: 7, Indels: 22
0.74 0.06 0.20
Matches are distributed among these distances:
5 17 0.21
6 53 0.65
7 10 0.12
8 1 0.01
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (6 bp):
TCTTTT
Found at i:2623216 original size:47 final size:49
Alignment explanation
Indices: 2623137--2623238 Score: 138
Period size: 47 Copynumber: 2.1 Consensus size: 49
2623127 ACTAAAATAC
*
2623137 TAATATGCAATGTAAAATGCTAATTACATAACAT-CTAATGGAACATGAAT
1 TAATATGCAATGCAAAATGC-AATTACATAACATGC-AATGGAACATGAAT
* *
2623187 TAATATGCAATGCAACATG-AATTA-ATAACATGCAATGGCACATGAAT
1 TAATATGCAATGCAAAATGCAATTACATAACATGCAATGGAACATGAAT
2623234 TAATA
1 TAATA
2623239 ACATGTAATA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
47 25 0.52
48 6 0.12
50 17 0.35
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (49 bp):
TAATATGCAATGCAAAATGCAATTACATAACATGCAATGGAACATGAAT
Found at i:2623229 original size:25 final size:25
Alignment explanation
Indices: 2623158--2623243 Score: 101
Period size: 25 Copynumber: 3.5 Consensus size: 25
2623148 GTAAAATGCT
*
2623158 AATTACATAACAT-CTAATGGAACATG
1 AATTA-ATAACATGC-AATGGCACATG
2623184 AATTAAT---ATGCAAT-GCAACATG
1 AATTAATAACATGCAATGGC-ACATG
2623206 AATTAATAACATGCAATGGCACATG
1 AATTAATAACATGCAATGGCACATG
2623231 AATTAATAACATG
1 AATTAATAACATG
2623244 TAATAAATTA
Statistics
Matches: 53, Mismatches: 1, Indels: 13
0.79 0.01 0.19
Matches are distributed among these distances:
21 1 0.02
22 17 0.32
23 1 0.02
25 27 0.51
26 7 0.13
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.27
Consensus pattern (25 bp):
AATTAATAACATGCAATGGCACATG
Found at i:2623258 original size:18 final size:18
Alignment explanation
Indices: 2623231--2623265 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2623221 ATGGCACATG
2623231 AATTAATAACATGTAATA
1 AATTAATAACATGTAATA
*
2623249 AATTACTAACATGTAAT
1 AATTAATAACATGTAAT
2623266 TATTATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (18 bp):
AATTAATAACATGTAATA
Found at i:2626575 original size:22 final size:21
Alignment explanation
Indices: 2626534--2626588 Score: 51
Period size: 22 Copynumber: 2.6 Consensus size: 21
2626524 CAAGGACATA
*
2626534 GTAGCT-GAGCTGGAGACTAATT
1 GTAGCTGGAG-TGGAGACTAA-G
2626556 GTAGCTGGAGTGTGAG-CTAAG
1 GTAGCTGGAGTG-GAGACTAAG
*
2626577 GCAGCTGGAGTG
1 GTAGCTGGAGTG
2626589 ACACTAGGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 11 0.38
22 12 0.41
23 6 0.21
ACGTcount: A:0.24, C:0.13, G:0.40, T:0.24
Consensus pattern (21 bp):
GTAGCTGGAGTGGAGACTAAG
Found at i:2626968 original size:20 final size:19
Alignment explanation
Indices: 2626931--2626973 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
2626921 CAGTCTAAGG
* **
2626931 CATGATTCTTCATTAAAAA
1 CATGAATCTTCACCAAAAA
2626950 TCATGAATCTTCACCAAAAA
1 -CATGAATCTTCACCAAAAA
2626970 CATG
1 CATG
2626974 TATTTTCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (19 bp):
CATGAATCTTCACCAAAAA
Found at i:2628875 original size:29 final size:29
Alignment explanation
Indices: 2628850--2629001 Score: 112
Period size: 29 Copynumber: 5.3 Consensus size: 29
2628840 CTATTTCTGT
2628850 ATGGGATCATATCCTCATCTTGTTTCTAC
1 ATGGGATCATATCCTCATCTTGTTTCTAC
** * *
2628879 ATTAGATCATATCC-CTGTCTTATTTCTGA-
1 ATGGGATCATATCCTC-ATCTTGTTTCT-AC
* * * *
2628908 ATAGGATCATATCCACATTTTGTTCCTAC
1 ATGGGATCATATCCTCATCTTGTTTCTAC
* * * * *
2628937 ATGGGATCATACCCTCATCCTATTTTTGC
1 ATGGGATCATATCCTCATCTTGTTTCTAC
* * *
2628966 ATGGGA-CATATCCCCATATTGTTTCTAT
1 ATGGGATCATATCCTCATCTTGTTTCTAC
*
2628994 TTGGGATC
1 ATGGGATC
2629002 CTCTTCGAAG
Statistics
Matches: 90, Mismatches: 28, Indels: 10
0.70 0.22 0.08
Matches are distributed among these distances:
28 21 0.23
29 67 0.74
30 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (29 bp):
ATGGGATCATATCCTCATCTTGTTTCTAC
Found at i:2628915 original size:58 final size:58
Alignment explanation
Indices: 2628820--2628992 Score: 172
Period size: 58 Copynumber: 3.0 Consensus size: 58
2628810 ATAACATATG
* * * * *
2628820 CATGAGATCAAATCCTTGT-TCTATTTCTGTATGGGATCATATCCTCATCTTGTTTCTA
1 CATGAGATCATATCCCTGTCT-TATTTCTGAATGGGATCATATCCACATATTGTTTCTA
* * * *
2628878 CATTAGATCATATCCCTGTCTTATTTCTGAATAGGATCATATCCACATTTTGTTCCTA
1 CATGAGATCATATCCCTGTCTTATTTCTGAATGGGATCATATCCACATATTGTTTCTA
* * * * * *
2628936 CATGGGATCATA-CCCTCATCCTATTTTTGCATGGGA-CATATCCCCATATTGTTTCTA
1 CATGAGATCATATCCCT-GTCTTATTTCTGAATGGGATCATATCCACATATTGTTTCTA
2628993 TTTGGGATCC
Statistics
Matches: 95, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
57 22 0.23
58 72 0.76
59 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.40
Consensus pattern (58 bp):
CATGAGATCATATCCCTGTCTTATTTCTGAATGGGATCATATCCACATATTGTTTCTA
Found at i:2640892 original size:20 final size:20
Alignment explanation
Indices: 2640859--2640900 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2640849 CCAGCCATAA
*
2640859 ACTTTGTATGCTGATCCTCC
1 ACTTTGTATACTGATCCTCC
*
2640879 ACTTTTTATACTGATCCTCC
1 ACTTTGTATACTGATCCTCC
2640899 AC
1 AC
2640901 ATCCATCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.31, G:0.10, T:0.40
Consensus pattern (20 bp):
ACTTTGTATACTGATCCTCC
Found at i:2655324 original size:13 final size:13
Alignment explanation
Indices: 2655290--2655324 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
2655280 CCATTGAATG
* *
2655290 TTGACTTTGACCA
1 TTGACTTTTACAA
2655303 TTGACTTTTACAA
1 TTGACTTTTACAA
2655316 TTGACTTTT
1 TTGACTTTT
2655325 TTGTTGGTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.23, C:0.17, G:0.11, T:0.49
Consensus pattern (13 bp):
TTGACTTTTACAA
Found at i:2657844 original size:35 final size:34
Alignment explanation
Indices: 2657746--2657845 Score: 110
Period size: 34 Copynumber: 2.9 Consensus size: 34
2657736 TTAATTTTAC
* * **
2657746 TCTAAACCCCAAATTCCAAAGTAATTCAATTTCAT
1 TCTAAACCCCAAATT-CAAAATAATTTAATTAAAT
* *
2657781 TCTAAACCCTAAATTCTAAATAATTTAATTAAAT
1 TCTAAACCCCAAATTCAAAATAATTTAATTAAAT
* *
2657815 TTTAAACCCCAAATTCAAAAATACTTTAATT
1 TCTAAACCCCAAATTC-AAAATAATTTAATT
2657846 TAAGGTTTAG
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
34 28 0.52
35 26 0.48
ACGTcount: A:0.44, C:0.20, G:0.01, T:0.35
Consensus pattern (34 bp):
TCTAAACCCCAAATTCAAAATAATTTAATTAAAT
Found at i:2657908 original size:35 final size:35
Alignment explanation
Indices: 2657842--2657916 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
2657832 AAAATACTTT
** * *
2657842 AATTTAAGGTTTAGAATGTAATTGAATTATTTTGG
1 AATTTAAGGTTTAGAATAAAATTGAAGTATTTTGA
*
2657877 AATTTAGGGTTTAGAATAAAATT-AAGGTATTTTGA
1 AATTTAAGGTTTAGAATAAAATTGAA-GTATTTTGA
2657912 AATTT
1 AATTT
2657917 TGAGCATGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 2 0.06
35 32 0.94
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (35 bp):
AATTTAAGGTTTAGAATAAAATTGAAGTATTTTGA
Done.