Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397263.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_86.0, 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: 8461613
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 85630 characters in sequence are not A, C, G, or T
File 10 of 18
Found at i:4655006 original size:4 final size:4
Alignment explanation
Indices: 4654981--4655052 Score: 90
Period size: 4 Copynumber: 18.0 Consensus size: 4
4654971 AGTTTATAAC
* * * *
4654981 ACAT ACAA ACAT ACAA ACAT ACAT ACAA ACAT ACAT ATAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
4655029 ATAG ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT
4655053 GATGTTAAGT
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 56 1.00
ACGTcount: A:0.54, C:0.22, G:0.01, T:0.22
Consensus pattern (4 bp):
ACAT
Found at i:4656968 original size:81 final size:81
Alignment explanation
Indices: 4656830--4656980 Score: 230
Period size: 81 Copynumber: 1.9 Consensus size: 81
4656820 TATAAGAATA
* * * * *
4656830 GCTACATTGTTTCAATAACAATGTTTATAACCCTTTATTAGTTTAGTGAACTGATGATCTAAATA
1 GCTACATTGTTACAATAACAATGTTTATAACCCTTGATTAGTTTAATAAACTAATGATCTAAATA
4656895 TCTTCAAATTAAAATG
66 TCTTCAAATTAAAATG
* * *
4656911 GCTACATTGTTACATTAACGATGTTTATAACCCTTGATTATTTTAATAAACTAATGATCTAAATA
1 GCTACATTGTTACAATAACAATGTTTATAACCCTTGATTAGTTTAATAAACTAATGATCTAAATA
4656976 TCTTC
66 TCTTC
4656981 CTATTGAAAC
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 62 1.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (81 bp):
GCTACATTGTTACAATAACAATGTTTATAACCCTTGATTAGTTTAATAAACTAATGATCTAAATA
TCTTCAAATTAAAATG
Found at i:4678276 original size:22 final size:22
Alignment explanation
Indices: 4678251--4678295 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
4678241 CTAGAAGAGA
*
4678251 TAGTTGTTGGTGATGGCATAGG
1 TAGTTGTTGGTGATGGCACAGG
4678273 TAGTTGTTGGTGATGGCACAGG
1 TAGTTGTTGGTGATGGCACAGG
4678295 T
1 T
4678296 TTGTCAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.07, G:0.40, T:0.36
Consensus pattern (22 bp):
TAGTTGTTGGTGATGGCACAGG
Found at i:4682413 original size:28 final size:28
Alignment explanation
Indices: 4682380--4682446 Score: 134
Period size: 28 Copynumber: 2.4 Consensus size: 28
4682370 GAAGAACAAA
4682380 TATCAATACTTGAAACCCAAAACAAAAG
1 TATCAATACTTGAAACCCAAAACAAAAG
4682408 TATCAATACTTGAAACCCAAAACAAAAG
1 TATCAATACTTGAAACCCAAAACAAAAG
4682436 TATCAATACTT
1 TATCAATACTT
4682447 CTACCCTAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.51, C:0.21, G:0.06, T:0.22
Consensus pattern (28 bp):
TATCAATACTTGAAACCCAAAACAAAAG
Found at i:4683416 original size:37 final size:37
Alignment explanation
Indices: 4683332--4683426 Score: 104
Period size: 37 Copynumber: 2.6 Consensus size: 37
4683322 ATATAAGCAT
4683332 AAGGGCCATGATGTGGGGCATTGTACCACACAACCATA
1 AAGGGCCATGATGTGGGGCATTGTACCACAC-ACCATA
* ** *
4683370 AA-AGCCATGATGTGGGGGGTTGTACCACAC-GCATA
1 AAGGGCCATGATGTGGGGCATTGTACCACACACCATA
* *
4683405 GAAGGGTCATGATATGGGGCAT
1 -AAGGGCCATGATGTGGGGCAT
4683427 CATAACACAC
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
35 4 0.09
36 2 0.04
37 38 0.83
38 2 0.04
ACGTcount: A:0.29, C:0.19, G:0.32, T:0.20
Consensus pattern (37 bp):
AAGGGCCATGATGTGGGGCATTGTACCACACACCATA
Found at i:4688388 original size:21 final size:21
Alignment explanation
Indices: 4688342--4688388 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
4688332 TGTTAAGTGA
4688342 TTAA-TTTAAGTTATTTTAGT
1 TTAATTTTAAGTTATTTTAGT
* * *
4688362 TAAATTTTAGGTTATTTTATT
1 TTAATTTTAAGTTATTTTAGT
4688383 TTAATT
1 TTAATT
4688389 ACTTTAAGAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.62
Consensus pattern (21 bp):
TTAATTTTAAGTTATTTTAGT
Found at i:4692036 original size:80 final size:79
Alignment explanation
Indices: 4691944--4692189 Score: 323
Period size: 80 Copynumber: 3.1 Consensus size: 79
4691934 TATGTGCTCC
* * * * * **
4691944 ATTTATGGGATTATAACATGCATGCTATGAGATGTATGTGTTGGGATAGTTATATACACTATAAG
1 ATTTATGAGATTATAA-ATGCATGCCATGAGATATATGTGTTGAGATAGTCATATACACTATGGG
4692009 CTAAGCATGTGAGTG
65 CTAAGCATGTGAGTG
*
4692024 ATTTATGAGATTATGAAATGCATGCCATGAGATATATGTGTTGAGATAGTCATATACATTATGGG
1 ATTTATGAGATTAT-AAATGCATGCCATGAGATATATGTGTTGAGATAGTCATATACACTATGGG
4692089 CTAAGCATGTGAGTG
65 CTAAGCATGTGAGTG
* * * * *
4692104 ATTTATGAGGTTATAAATTGCATGCCATGAGATATGTGTGTTAAGATAGTCACATACACTGTGGG
1 ATTTATGAGATTATAAA-TGCATGCCATGAGATATATGTGTTGAGATAGTCATATACACTATGGG
*
4692169 CTAAGCAAGATGA-TG
65 CTAAGCATG-TGAGTG
4692184 ATTTAT
1 ATTTAT
4692190 AAAAATGTTA
Statistics
Matches: 148, Mismatches: 15, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
79 3 0.02
80 140 0.95
81 5 0.03
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.34
Consensus pattern (79 bp):
ATTTATGAGATTATAAATGCATGCCATGAGATATATGTGTTGAGATAGTCATATACACTATGGGC
TAAGCATGTGAGTG
Found at i:4697546 original size:6 final size:7
Alignment explanation
Indices: 4697530--4697555 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4697520 CTAAATCAAG
4697530 AAAAATA
1 AAAAATA
4697537 AAAAATA
1 AAAAATA
4697544 AAAAATA
1 AAAAATA
4697551 AAAAA
1 AAAAA
4697556 ACTCCAGGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:4699111 original size:20 final size:21
Alignment explanation
Indices: 4699075--4699113 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
4699065 GATAATTTGG
4699075 AAATTCATAAAAAAAAATTTA
1 AAATTCATAAAAAAAAATTTA
*
4699096 AAATTC-TAATAAAAAATT
1 AAATTCATAAAAAAAAATT
4699114 GTAGTAGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATTCATAAAAAAAAATTTA
Found at i:4701552 original size:2 final size:2
Alignment explanation
Indices: 4701545--4701569 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4701535 TTTGTGAATC
4701545 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4701570 GTAAATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4704111 original size:18 final size:18
Alignment explanation
Indices: 4704072--4704105 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4704062 ATGATGGCCC
*
4704072 AAGGACAAAGTTAAGCCG
1 AAGGACAAAGTTAAGCAG
4704090 AAGG-CAAAGTTAAGCA
1 AAGGACAAAGTTAAGCA
4704106 ATAAGGTGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.47, C:0.15, G:0.26, T:0.12
Consensus pattern (18 bp):
AAGGACAAAGTTAAGCAG
Found at i:4717533 original size:20 final size:21
Alignment explanation
Indices: 4717505--4717546 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
4717495 AATTGAGTTG
4717505 TTTTAG-TTTAATTTTACTTTA
1 TTTTAGTTTTAA-TTTACTTTA
4717526 TTTT-GTTTTAATTTACTTTA
1 TTTTAGTTTTAATTTACTTTA
4717546 T
1 T
4717547 GAAGAGTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTAGTTTTAATTTACTTTA
Found at i:4724844 original size:343 final size:346
Alignment explanation
Indices: 4724214--4725176 Score: 1202
Period size: 351 Copynumber: 2.8 Consensus size: 346
4724204 TGGAATCTAA
* * * *
4724214 CTATTGTTTTTAATTTCATGTAATTAAAGACGAACTCAT-TAGTTAATTAAATTAATTTATTAAA
1 CTATTGTTTTTAATTTCATGTAATTAAAGACAAACTCATATAATTAATTAAATTAATTAATAAAA
* * * * *
4724278 TTATAATAATTAATTAACTTGGAAAGATTTTTTAATA--TATAC-AT-TATATTATTGGGTTCAT
66 TTATGATTATTAATTAACTTGTAATG-TCTTTTAATATCTATACTATATATA-TATTGGGTTCAT
* * *
4724339 TTAT-AAGAA-ATAGTATTACTATATTATACATATACT--AATACTTTTAGTATATATATAATTT
129 TTATAAAGAATATA--ATTACTATA-TATATATACACTAAAATACTTTTAATATATATATAATTT
* * * *
4724400 AAATATAAATATATTTACTTTCTATTTTCTATTAACATTACAAAAATTATAACTTGTAAAATTAT
191 AAATATAAATATATTTACTTTTTATTTTGTATTAACATTA-TAAAATTATAACTTAT-AAATTAT
* * *
4724465 TAATTATAA-TATATACACCTTTGCTTATAAAAACTTAT-A-ATAT-AC-AA-ACCTTAAGAGAA
254 TAATTATAATTATATACACATTTGCTTATAAAAACTTATAATATATAACTAATACCTAAAAAGAA
* * *
4724524 GCT-TGATTAAAATAGTTTTTAGACTTAG
319 G-TGAGATTAAAATAGTTTTGAAACTTAG
* * * * * *
4724552 TTATTTTTTTTAATTTCATATAATTAAGGACAAACTCATAAAATTAATTAAATTAATTCATAAAA
1 CTATTGTTTTTAATTTCATGTAATTAAAGACAAACTCATATAATTAATTAAATTAATTAATAAAA
*
4724617 TTATGATTATTAATTACCTTGTAATGTCTTTTAATATCTATACTATATATATATTGGGTTCATTT
66 TTATGATTATTAATTAACTTGTAATGTCTTTTAATATCTATACTATATATATATTGGGTTCATTT
*
4724682 ATAAAGAATATAATTACTATCATATATATACACTAAAATGCTTTTAATATATATATAATTTAAAT
131 ATAAAGAATATAATTACTAT-ATATATATACACTAAAATACTTTTAATATATATATAATTTAAAT
* * *
4724747 ATAAATATATTTACTTTTTATTCTGTGTTAGCATTATAAAATTATAACTTATAAAGTTATTAATT
195 ATAAATATATTTACTTTTTATTTTGTATTAACATTATAAAATTATAACTTATAAA-TTATTAATT
* ** * *
4724812 ATAATTATATATACATTTTTTTATATAAACTTATAATATATAAACTTAATTATCTAAAAAGAAGT
259 ATAATTATATACACATTTGCTTATAAAAACTTATAATATAT-AAC-TAA-TACCTAAAAAGAAGT
*
4724877 GAGATTAGAATAGTTTTGAAACTTAG
321 GAGATTAAAATAGTTTTGAAACTTAG
**
4724903 CTATTGTTTTTAATTTCATGTAATTAAAGACAAACTCATATAATTAATTAAATTAATTAATGTAA
1 CTATTGTTTTTAATTTCATGTAATTAAAGACAAACTCATATAATTAATTAAATTAATTAATAAAA
* * * * * *
4724968 CTATGATTATTAAATAACTTATAATGTCTTTTAATATCTATTCTTTATACATATTGGGTTCATTT
66 TTATGATTATTAATTAACTTGTAATGTCTTTTAATATCTATACTATATATATATTGGGTTCATTT
* * *
4725033 ATAAGGAATATAATTACTATTATATATATACACTAAAATACTTTTAATACATATATACTTTAAAT
131 ATAAAGAATATAATTACTA-TATATATATACACTAAAATACTTTTAATATATATATAATTTAAAT
*
4725098 ATAAATATATTTACTTTTTATTTTGTATTAACATTATAAAAATTATAACTTATAGAATTAATAAT
195 ATAAATATATTTACTTTTTATTTTGTATTAACATTAT-AAAATTATAACTTATA-AATTATTAAT
4725163 TATAATGTATATAC
258 TATAAT-TATATAC
4725177 GCACACTTTA
Statistics
Matches: 538, Mismatches: 62, Indels: 35
0.85 0.10 0.06
Matches are distributed among these distances:
338 43 0.08
339 42 0.08
340 5 0.01
341 39 0.07
342 37 0.07
343 85 0.16
344 1 0.00
345 4 0.01
347 2 0.00
349 2 0.00
350 1 0.00
351 239 0.44
352 30 0.06
353 8 0.01
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (346 bp):
CTATTGTTTTTAATTTCATGTAATTAAAGACAAACTCATATAATTAATTAAATTAATTAATAAAA
TTATGATTATTAATTAACTTGTAATGTCTTTTAATATCTATACTATATATATATTGGGTTCATTT
ATAAAGAATATAATTACTATATATATATACACTAAAATACTTTTAATATATATATAATTTAAATA
TAAATATATTTACTTTTTATTTTGTATTAACATTATAAAATTATAACTTATAAATTATTAATTAT
AATTATATACACATTTGCTTATAAAAACTTATAATATATAACTAATACCTAAAAAGAAGTGAGAT
TAAAATAGTTTTGAAACTTAG
Found at i:4726338 original size:15 final size:15
Alignment explanation
Indices: 4726299--4726339 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
4726289 TTAGGTCTAC
*
4726299 TACATTATAAAATAT
1 TACATTATATAATAT
* *
4726314 TATATTATATTATAT
1 TACATTATATAATAT
4726329 TACATTATATA
1 TACATTATATA
4726340 TCAGTTTTAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (15 bp):
TACATTATATAATAT
Found at i:4727211 original size:23 final size:23
Alignment explanation
Indices: 4727184--4727228 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
4727174 TAATTTCAAC
*
4727184 TTTTTCTACA-TAATATCTTATGA
1 TTTTT-TACATTAATATCCTATGA
*
4727207 TTTTTTAGATTAATATCCTATG
1 TTTTTTACATTAATATCCTATG
4727229 CTTAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.29, C:0.11, G:0.07, T:0.53
Consensus pattern (23 bp):
TTTTTTACATTAATATCCTATGA
Found at i:4727836 original size:20 final size:20
Alignment explanation
Indices: 4727813--4727851 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4727803 AACAATAATA
4727813 AAATATTTT-AAAAAAATTTT
1 AAAT-TTTTGAAAAAAATTTT
*
4727833 AAATTTTTGAACAAAATTT
1 AAATTTTTGAAAAAAATTT
4727852 ATGTAAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (20 bp):
AAATTTTTGAAAAAAATTTT
Found at i:4733019 original size:2 final size:2
Alignment explanation
Indices: 4733012--4733040 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4733002 ATATTTATTG
4733012 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4733041 AAATGTATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4741209 original size:2 final size:2
Alignment explanation
Indices: 4741197--4741250 Score: 92
Period size: 2 Copynumber: 27.0 Consensus size: 2
4741187 ATACATAGGA
4741197 TC TC TC T- TC TC TC TC TC TC TC TC TC TC TC GTC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC -TC TC TC TC TC TC
4741239 TC TC TC TC TC TC
1 TC TC TC TC TC TC
4741251 ATATATACAC
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.02
2 47 0.94
3 2 0.04
ACGTcount: A:0.00, C:0.48, G:0.02, T:0.50
Consensus pattern (2 bp):
TC
Found at i:4741230 original size:23 final size:23
Alignment explanation
Indices: 4741197--4741248 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
4741187 ATACATAGGA
*
4741197 TCTCTCTTCTCTCTCTCTCTCTC
1 TCTCTCGTCTCTCTCTCTCTCTC
4741220 TCTCTCGTCTCTCTCTCTCTCTC
1 TCTCTCGTCTCTCTCTCTCTCTC
4741243 TCTCTC
1 TCTCTC
4741249 TCATATATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.00, C:0.48, G:0.02, T:0.50
Consensus pattern (23 bp):
TCTCTCGTCTCTCTCTCTCTCTC
Found at i:4747241 original size:17 final size:16
Alignment explanation
Indices: 4747203--4747252 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
4747193 ATATAAAATT
*
4747203 AAAATAACTCATT-TA
1 AAAATAACTAATTATA
*
4747218 AAGATAAACTAATTATA
1 AAAAT-AACTAATTATA
4747235 AAAATAACTAAATTATA
1 AAAATAACT-AATTATA
4747252 A
1 A
4747253 TTAAAAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 4 0.14
16 11 0.38
17 14 0.48
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (16 bp):
AAAATAACTAATTATA
Found at i:4761647 original size:20 final size:20
Alignment explanation
Indices: 4761614--4761651 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4761604 TTCTTACTCT
* *
4761614 AACTTTAACTAATTAAAATA
1 AACTTCAACCAATTAAAATA
4761634 AACTTCAACCAATTAAAA
1 AACTTCAACCAATTAAAA
4761652 ATTCTTCAAA
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:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (20 bp):
AACTTCAACCAATTAAAATA
Found at i:4785516 original size:26 final size:26
Alignment explanation
Indices: 4785487--4785544 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
4785477 AGGTGTTCCT
*
4785487 AAGAGTATTATTAGTGACAAGGATCC
1 AAGAGTATTATCAGTGACAAGGATCC
4785513 AAGAGTATTATCAGTGACAAGGATCC
1 AAGAGTATTATCAGTGACAAGGATCC
4785539 AAGAGT
1 AAGAGT
4785545 CAGAACTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (26 bp):
AAGAGTATTATCAGTGACAAGGATCC
Found at i:4789932 original size:18 final size:19
Alignment explanation
Indices: 4789909--4789951 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
4789899 GAAAATCATG
*
4789909 ATTTTTTTATTT-TTTATC
1 ATTTTTTTATTTATATATC
*
4789927 A-TTTTTTATTTATATATT
1 ATTTTTTTATTTATATATC
4789945 ATTTTTT
1 ATTTTTT
4789952 CAAAATGAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 10 0.48
18 6 0.29
19 5 0.24
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (19 bp):
ATTTTTTTATTTATATATC
Found at i:4789933 original size:17 final size:18
Alignment explanation
Indices: 4789911--4789951 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
4789901 AAATCATGAT
*
4789911 TTTTTTATTT-TTTATCA
1 TTTTTTATTTATATATCA
*
4789928 TTTTTTATTTATATATTA
1 TTTTTTATTTATATATCA
4789946 TTTTTT
1 TTTTTT
4789952 CAAAATGAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTTATTTATATATCA
Found at i:4801250 original size:65 final size:65
Alignment explanation
Indices: 4801174--4801367 Score: 370
Period size: 65 Copynumber: 3.0 Consensus size: 65
4801164 CTTTAGTTAG
*
4801174 TTTATTTCTTATTTATCATGCTTTTGTCTAAGCATTCATGTATATAAGTATGAGCTAATACGTAA
1 TTTATTTCTTATTTATCATGCATTTGTCTAAGCATTCATGTATATAAGTATGAGCTAATACGTAA
4801239 TTTATTTCTTATTTATCATGCATTTGTCTAAGCATTCATGTATATAAGTATGAGCTAATACGTAA
1 TTTATTTCTTATTTATCATGCATTTGTCTAAGCATTCATGTATATAAGTATGAGCTAATACGTAA
*
4801304 TTTATTTCTTATTTATCAGGCATTTGTCTAAGCATTCATGTATATAAGTATGAGCTAATACGTA
1 TTTATTTCTTATTTATCATGCATTTGTCTAAGCATTCATGTATATAAGTATGAGCTAATACGTA
4801368 GTGCAAAACT
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 127 1.00
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (65 bp):
TTTATTTCTTATTTATCATGCATTTGTCTAAGCATTCATGTATATAAGTATGAGCTAATACGTAA
Found at i:4806835 original size:14 final size:15
Alignment explanation
Indices: 4806818--4806846 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4806808 ACTTTAGTGC
4806818 ATTGGA-AAATAAGA
1 ATTGGACAAATAAGA
4806832 ATTGGACAAATAAGA
1 ATTGGACAAATAAGA
4806847 CTGCTAGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.55, C:0.03, G:0.21, T:0.21
Consensus pattern (15 bp):
ATTGGACAAATAAGA
Found at i:4818902 original size:60 final size:59
Alignment explanation
Indices: 4818830--4818963 Score: 169
Period size: 60 Copynumber: 2.2 Consensus size: 59
4818820 TAATTGATAA
* * * *
4818830 TAAAGGGAGACCTGAAGCCCCGACTTATATTTGATGGCGTGGGGAGTTCCCACGAGTAAG
1 TAAAGGG-GACCTGAAGCCCCGACTCATATTAGATGGCGGGGGGAGTTCCCACAAGTAAG
* * *
4818890 TAAAGAGGGACCTGAAGCCTCGACTCATATTAGGTGGCGGGGGGAGTTCCCACAAGTAGG
1 TAAAG-GGGACCTGAAGCCCCGACTCATATTAGATGGCGGGGGGAGTTCCCACAAGTAAG
4818950 TAAAAGGGGGACCT
1 T-AAA-GGGGACCT
4818964 CTCCTCACGA
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
60 51 0.80
61 12 0.19
62 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.34, T:0.19
Consensus pattern (59 bp):
TAAAGGGGACCTGAAGCCCCGACTCATATTAGATGGCGGGGGGAGTTCCCACAAGTAAG
Found at i:4831900 original size:24 final size:24
Alignment explanation
Indices: 4831873--4831935 Score: 117
Period size: 24 Copynumber: 2.6 Consensus size: 24
4831863 ACACGTTATG
4831873 ATGTTACACGTTATGTACAAAAAC
1 ATGTTACACGTTATGTACAAAAAC
4831897 ATGTTACACGTTATGTACAAAAAC
1 ATGTTACACGTTATGTACAAAAAC
*
4831921 ATGTGACACGTTATG
1 ATGTTACACGTTATG
4831936 GTTAGTTCGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (24 bp):
ATGTTACACGTTATGTACAAAAAC
Found at i:4832020 original size:32 final size:32
Alignment explanation
Indices: 4831983--4832051 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 32
4831973 TCAGGTTGAA
* * *
4831983 AAAAAATAAATATTGTTGTTACATGTCATGTT
1 AAAAAATAAATATTATTGTTACATATCATATT
*
4832015 --GAAA-AAATATTATTGTTACATATCATATT
1 AAAAAATAAATATTATTGTTACATATCATATT
4832044 AAAAAATA
1 AAAAAATA
4832052 TTTTGTTACA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
29 22 0.76
30 3 0.10
31 3 0.10
32 1 0.03
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.38
Consensus pattern (32 bp):
AAAAAATAAATATTATTGTTACATATCATATT
Found at i:4832057 original size:27 final size:29
Alignment explanation
Indices: 4831990--4832061 Score: 103
Period size: 29 Copynumber: 2.6 Consensus size: 29
4831980 GAAAAAAAAT
* * *
4831990 AAATATTGTTGTTACATGTCATGTTGAAA
1 AAATATTATTGTTACATATCATATTGAAA
4832019 AAATATTATTGTTACATATCATATT-AAA
1 AAATATTATTGTTACATATCATATTGAAA
4832047 AAATATT-TTGTTACA
1 AAATATTATTGTTACA
4832062 CTTTAATGCG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
27 8 0.20
28 10 0.25
29 22 0.55
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (29 bp):
AAATATTATTGTTACATATCATATTGAAA
Found at i:4833853 original size:18 final size:19
Alignment explanation
Indices: 4833830--4833872 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
4833820 AGTTTCAAAC
*
4833830 AATATTAAGATAATT-TAT
1 AATATTAAAATAATTATAT
4833848 AATATTAAAATAATTATAT
1 AATATTAAAATAATTATAT
4833867 AA-ATTA
1 AATATTA
4833873 TTTAATTAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
AATATTAAAATAATTATAT
Found at i:4833880 original size:26 final size:27
Alignment explanation
Indices: 4833851--4833901 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
4833841 AATTTATAAT
**
4833851 ATTAAAATAATTATATAA-ATTATTTA
1 ATTAAAATAAGAATATAATATTATTTA
*
4833877 ATTAGAATAAGAATATAATATTATT
1 ATTAAAATAAGAATATAATATTATT
4833902 ACCTAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (27 bp):
ATTAAAATAAGAATATAATATTATTTA
Found at i:4835471 original size:213 final size:214
Alignment explanation
Indices: 4835133--4835517 Score: 598
Period size: 213 Copynumber: 1.8 Consensus size: 214
4835123 AGGCTGAACC
* *
4835133 TTTATAAAAACCATTATGTTGATTTCTGTCTCTCACTCATTCTATCTTGTTTGTGTTTCTAACTT
1 TTTATAAAAACCATTATGTTGATTTCTGTCTCTCACTCATTCAATCTTGTTTGTGTTTCTAACAT
* *
4835198 CTTTTATTAGATAAGAATTCAATTATCTTTGTTCATTTACAAAAAAAGGATTTGACTTG-AAGAA
66 CTTTTATTAGATAAGAAATCAATTATCTTTGTTCATTCACAAAAAAAGGATTTGACTTGAAAG-A
*
4835262 ACCTCATTCTCTT-G-AATTGAAAAGAAATTTTTCAAAATATTTTAGCAAATCTAAAGGAGAAGA
130 ACCTCATT-TCTTAGAAATTGAAAAGAAAATTTTCAAAATATTTTAGCAAATCTAAAGGAGAAGA
4835325 TGTAAGTAAGGAGGTCAAACT
194 TGTAAGTAAGGAGGTCAAACT
* * * *
4835346 TTTATAAAAACCATTGTGTTGATTTTTTTCTCTCACTCGTTCAATCTTGTTTGTGTTTCTAACAT
1 TTTATAAAAACCATTATGTTGATTTCTGTCTCTCACTCATTCAATCTTGTTTGTGTTTCTAACAT
*
4835411 CTTTTATTAGATAAGAAATCAATTATC-TTGTTTATTCACAAAAAAAGAGATTTGACTTGAAAGA
66 CTTTTATTAGATAAGAAATCAATTATCTTTGTTCATTCACAAAAAAAG-GATTTGACTTGAAAGA
* * *
4835475 ACCTCATTTTTTAGAAATTGAAAAGAAAATTTTCTAGATATTT
130 ACCTCATTTCTTAGAAATTGAAAAGAAAATTTTCAAAATATTT
4835518 AAAATATTCC
Statistics
Matches: 155, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
212 21 0.14
213 106 0.68
214 28 0.18
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (214 bp):
TTTATAAAAACCATTATGTTGATTTCTGTCTCTCACTCATTCAATCTTGTTTGTGTTTCTAACAT
CTTTTATTAGATAAGAAATCAATTATCTTTGTTCATTCACAAAAAAAGGATTTGACTTGAAAGAA
CCTCATTTCTTAGAAATTGAAAAGAAAATTTTCAAAATATTTTAGCAAATCTAAAGGAGAAGATG
TAAGTAAGGAGGTCAAACT
Found at i:4840240 original size:15 final size:15
Alignment explanation
Indices: 4840222--4840256 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
4840212 TTCGTCGTTC
4840222 TCATTTTTAGGATCA
1 TCATTTTTAGGATCA
**
4840237 TCATTTTTATTATCA
1 TCATTTTTAGGATCA
4840252 TCATT
1 TCATT
4840257 GTTGTCTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.14, G:0.06, T:0.54
Consensus pattern (15 bp):
TCATTTTTAGGATCA
Found at i:4844077 original size:17 final size:17
Alignment explanation
Indices: 4844051--4844083 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4844041 ATTTATCATT
4844051 ATATAAATAATATTATA
1 ATATAAATAATATTATA
*
4844068 ATATATATAATATTAT
1 ATATAAATAATATTAT
4844084 CATTTTTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATAAATAATATTATA
Found at i:4844247 original size:16 final size:16
Alignment explanation
Indices: 4844226--4844258 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
4844216 TATTGTACAT
*
4844226 TATTATATATTTAATA
1 TATTATATATATAATA
4844242 TATTATATATATAATA
1 TATTATATATATAATA
4844258 T
1 T
4844259 CCATATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTATATATATAATA
Found at i:4844341 original size:5 final size:5
Alignment explanation
Indices: 4844316--4844361 Score: 62
Period size: 5 Copynumber: 9.6 Consensus size: 5
4844306 TTCATCAAAT
4844316 TTATCA TTA-A TTATA -TATA TTATA TTATA TTATA TTATA -TATA TTA
1 TTAT-A TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTA
4844362 CTTTTGTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
4 12 0.32
5 22 0.59
6 3 0.08
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (5 bp):
TTATA
Found at i:4844343 original size:24 final size:24
Alignment explanation
Indices: 4844316--4844361 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
4844306 TTCATCAAAT
4844316 TTATCATTA-ATTATATATATTATA
1 TTAT-ATTATATTATATATATTATA
4844340 TTATATTATATTATATATATTA
1 TTATATTATATTATATATATTA
4844362 CTTTTGTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
TTATATTATATTATATATATTATA
Found at i:4844399 original size:97 final size:99
Alignment explanation
Indices: 4844224--4844421 Score: 237
Period size: 97 Copynumber: 2.0 Consensus size: 99
4844214 CTTATTGTAC
*
4844224 ATTATTATATATTTAATATATTATATATATAATATCCATATAATTTTTTTTTGTAAATCAATAAA
1 ATTATTATATATTTAATATATTATATATATAATAT-CATATAATTTTTTATTGTAAATCAATAAA
**
4844289 AAATAATGGATATATAGTTCATCAAATTTATCATTA
65 AAATAAT-GATATATAGGACATCAAATTTATCATTA
* * *
4844325 ATTA-TATATATTATATTATATTATAT-TAT-ATAT-AT-TACTTTTGTTATTGTAATTCAATAA
1 ATTATTATATATT-TAATATATTATATATATAATATCATATAATTTT-TTATTGTAAATCAATAA
*
4844385 AATTATATAT-ATATATAGGACATCAAATTTATCATTA
64 AA-AATA-ATGATATATAGGACATCAAATTTATCATTA
4844422 TATATAATTT
Statistics
Matches: 86, Mismatches: 7, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
96 6 0.07
97 44 0.51
98 3 0.03
99 6 0.07
100 11 0.13
101 16 0.19
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (99 bp):
ATTATTATATATTTAATATATTATATATATAATATCATATAATTTTTTATTGTAAATCAATAAAA
AATAATGATATATAGGACATCAAATTTATCATTA
Found at i:4844607 original size:191 final size:185
Alignment explanation
Indices: 4844410--4844760 Score: 567
Period size: 185 Copynumber: 1.9 Consensus size: 185
4844400 TAGGACATCA
*
4844410 AATTTATCATTATATATAATTTATATGCATACATATATATATGTATGTATATAATTTTTCTTATT
1 AATTTATCATTATATATAATTTATATACATAC--ATATATA--TATGTATATAATTTTTCTTATT
* * *
4844475 GTACATTATTATATGTTTAATATATTATCTATATAATTTTCATATAATTTTTGTTTTTGTAAATC
62 GTACATCATTATATATTTAATATATTA--TATATAATTTTCATATAATTTTTGCTTTTGTAAATC
* * *
4844540 AATAAAAATAATTGATATATATTTTATCAAATTTATCATTATTTTTTTTTGAAAAGCTTCT
125 AATAAAAATAATGGATACATATTTCATCAAATTTATCATTATTTTTTTTTGAAAAGCTTCT
4844601 AATTTATCATTATATATAATTTATATACATACATATATATATGTATATAATTTTTCTTATTGTAC
1 AATTTATCATTATATATAATTTATATACATACATATATATATGTATATAATTTTTCTTATTGTAC
*
4844666 ATCATTATATATTTAATATATTATATATAATTTTCATATAATTTTTGCTTTTGTAAATCAATAAC
66 ATCATTATATATTTAATATATTATATATAATTTTCATATAATTTTTGCTTTTGTAAATCAATAAA
*
4844731 ACTAATGGATACATATTTCATCAAATTTAT
131 AATAATGGATACATATTTCATCAAATTTAT
4844761 TAGTAATTAT
Statistics
Matches: 151, Mismatches: 9, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
185 66 0.44
187 47 0.31
189 7 0.05
191 31 0.21
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (185 bp):
AATTTATCATTATATATAATTTATATACATACATATATATATGTATATAATTTTTCTTATTGTAC
ATCATTATATATTTAATATATTATATATAATTTTCATATAATTTTTGCTTTTGTAAATCAATAAA
AATAATGGATACATATTTCATCAAATTTATCATTATTTTTTTTTGAAAAGCTTCT
Found at i:4845734 original size:222 final size:222
Alignment explanation
Indices: 4845322--4845855 Score: 563
Period size: 222 Copynumber: 2.4 Consensus size: 222
4845312 TACAGCTCAA
* * *
4845322 AGTCAATTAACAAGCAACATCATTC-AAAAAATTAT-ATGCTCAGGGATTTCACACAACAACAAA
1 AGTCAATTAACAAGCAACTTCA-TCAAAAAAATT-TCATGCTCAAGGATTTCACAAAACAACAAA
* * * * *
4845385 TATAACAGCATCCACAATCC-AAAAAAAAAAATGGCAACATCTTCCATCTTCTAATCAAGCAACA
64 AATAACAGCAACCACAATCCAAAAAAAAAAAATGGCAACAGCTTCCAGCTTCCAATCAAGCAACA
* * *
4845449 CACTTAATAACAACGACAACAACTTCTAGTCACTAAACAAGAAAAAGAAAACAAGCGTCAATTAA
129 CACTTAAT-ACAACGACAACAACTTCCAATCAATAAACAAGAAAAAGAAAACAAGCGTCAATTAA
*
4845514 ATTCAACAATCGCAATCCCCC-TCACT-TCAC
193 ATTCAACAATCACAATCCCCCAT-ACTCT-AC
* * *
4845544 AGTCAATTAACAAACAACTTCATCAAAAAAACTTTCATGCTCAAGGATTTTACAGAACAACAAAA
1 AGTCAATTAACAAGCAACTTCATCAAAAAAA-TTTCATGCTCAAGGATTTCACAAAACAACAAAA
* * *
4845609 ATAATAGCAACCACAATCCAAAAAAAAAAAACTTGGCAATAGCTTCCAGCTTCCACTCAAGC-A-
65 ATAACAGCAACCACAATCCAAAAAAAAAAAA--TGGCAACAGCTTCCAGCTTCCAATCAAGCAAC
* * * *
4845672 AC-C-TACT-CAACGACAACAATTTCCAATCAATAAACAAGCACAAAA-AACAACATGCTTCAAT
128 ACACTTAATACAACGACAACAACTTCCAATCAATAAACAAG-A-AAAAGAA-AACAAGCGTCAAT
* * * *
4845733 TAAATTTAGCAATCATAATCCCCCATACTCTAT
190 TAAATTCAACAATCACAATCCCCCATACTCTAC
* * * * * * *
4845766 AATCAATTAACAAGCAACTCCATCAAGAAAAATTACATGCTCAAGTATTTCACAAAATAATATAA
1 AGTCAATTAACAAGCAACTTCATCAA-AAAAATTTCATGCTCAAGGATTTCACAAAACAACAAAA
*
4845831 ATAACAGCAACCATAAT--AAAAAAAA
65 ATAACAGCAACCACAATCCAAAAAAAA
4845856 TGACAACAAC
Statistics
Matches: 263, Mismatches: 37, Indels: 26
0.81 0.11 0.08
Matches are distributed among these distances:
220 35 0.13
221 5 0.02
222 133 0.51
223 52 0.20
224 13 0.05
225 1 0.00
226 24 0.09
ACGTcount: A:0.48, C:0.24, G:0.07, T:0.21
Consensus pattern (222 bp):
AGTCAATTAACAAGCAACTTCATCAAAAAAATTTCATGCTCAAGGATTTCACAAAACAACAAAAA
TAACAGCAACCACAATCCAAAAAAAAAAAATGGCAACAGCTTCCAGCTTCCAATCAAGCAACACA
CTTAATACAACGACAACAACTTCCAATCAATAAACAAGAAAAAGAAAACAAGCGTCAATTAAATT
CAACAATCACAATCCCCCATACTCTAC
Found at i:4848646 original size:29 final size:29
Alignment explanation
Indices: 4848611--4848706 Score: 111
Period size: 29 Copynumber: 3.3 Consensus size: 29
4848601 AACACTTGGT
*
4848611 ATCTTGATCACGAACTTCATTGCCGTTTG
1 ATCTTGATCACGAACTTCATTGCCGCTTG
* * *
4848640 ATCTTGATCACAAACATCATTGCCGCATG
1 ATCTTGATCACGAACTTCATTGCCGCTTG
* * * * *
4848669 ATCTTGATTATGAGCTTCGTTGCCACTTG
1 ATCTTGATCACGAACTTCATTGCCGCTTG
4848698 ATCTTGATC
1 ATCTTGATC
4848707 GTGAACCTCA
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (29 bp):
ATCTTGATCACGAACTTCATTGCCGCTTG
Found at i:4852927 original size:16 final size:16
Alignment explanation
Indices: 4852906--4852980 Score: 50
Period size: 16 Copynumber: 4.7 Consensus size: 16
4852896 GTTCAGTATT
4852906 TTATAATATAAT-ATAA
1 TTATAATATAATAAT-A
* *
4852922 TTATAAAAAAATAATA
1 TTATAATATAATAATA
*
4852938 TTATAATAT-TTAATA
1 TTATAATATAATAATA
4852953 -TATAA-ATAAATTAATAA
1 TTATAATAT-AA-TAAT-A
*
4852970 TTAAAATATAA
1 TTATAATATAA
4852981 AAGATATAAC
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
13 2 0.04
14 5 0.11
15 5 0.11
16 22 0.49
17 3 0.07
18 6 0.13
19 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TTATAATATAATAATA
Found at i:4852942 original size:32 final size:34
Alignment explanation
Indices: 4852906--4852980 Score: 88
Period size: 32 Copynumber: 2.3 Consensus size: 34
4852896 GTTCAGTATT
4852906 TTATAATATAATATAAT-TATAAA-AAAATAAT-A
1 TTATAATATAAT-TAATATATAAATAAAATAATAA
*
4852938 TTATAATAT--TTAATATATAAATAAATTAATAA
1 TTATAATATAATTAATATATAAATAAAATAATAA
*
4852970 TTAAAATATAA
1 TTATAATATAA
4852981 AAGATATAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
29 4 0.11
30 7 0.19
31 7 0.19
32 18 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
TTATAATATAATTAATATATAAATAAAATAATAA
Found at i:4853164 original size:13 final size:13
Alignment explanation
Indices: 4853146--4853189 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
4853136 ATATCATATA
4853146 TTTTATTTTTATT
1 TTTTATTTTTATT
* *
4853159 TTTTATTATAATT
1 TTTTATTTTTATT
4853172 TTTTATTTTTATT
1 TTTTATTTTTATT
4853185 TTTTA
1 TTTTA
4853190 ATATAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTATTTTTATT
Found at i:4853175 original size:26 final size:26
Alignment explanation
Indices: 4853146--4853228 Score: 105
Period size: 26 Copynumber: 3.1 Consensus size: 26
4853136 ATATCATATA
4853146 TTTTATTTTTATTTTTTATTATAATT
1 TTTTATTTTTATTTTTTATTATAATT
*
4853172 TTTTATTTTTATTTTTTAATATAATTT
1 TTTTATTTTTATTTTTTATTATAA-TT
* *
4853199 TTTTATATTATATATTTTAATT-TAATT
1 TTTTAT-TTTTAT-TTTTTATTATAATT
4853226 TTT
1 TTT
4853229 AAAAAAATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
26 23 0.46
27 13 0.26
28 8 0.16
29 6 0.12
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (26 bp):
TTTTATTTTTATTTTTTATTATAATT
Found at i:4853198 original size:13 final size:13
Alignment explanation
Indices: 4853156--4853228 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
4853146 TTTTATTTTT
*
4853156 ATTTTTTATTATA
1 ATTTTTTAATATA
* * *
4853169 ATTTTTTATTTTT
1 ATTTTTTAATATA
4853182 ATTTTTTAATATA
1 ATTTTTTAATATA
*
4853195 ATTTTTTTATATTA
1 ATTTTTTAATA-TA
* *
4853209 TATATTTTAATTTA
1 -ATTTTTTAATATA
4853223 ATTTTT
1 ATTTTT
4853229 AAAAAAATTT
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
13 36 0.75
14 4 0.08
15 8 0.17
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
ATTTTTTAATATA
Found at i:4853238 original size:40 final size:41
Alignment explanation
Indices: 4853157--4853247 Score: 96
Period size: 40 Copynumber: 2.2 Consensus size: 41
4853147 TTTATTTTTA
* * * * *
4853157 TTTTTTATTATAATTTTTTATTTTTATTTTTTAATATAATT
1 TTTTTTATTATAATATTTTATATTTAATTTTTAAAAAAATT
4853198 TTTTTATATTAT-ATATTTTA-ATTTAATTTTTAAAAAAATT
1 TTTTT-TATTATAATATTTTATATTTAATTTTTAAAAAAATT
*
4853238 TGATTTTATT
1 T-TTTTTATT
4853248 GATAGTCATC
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
40 21 0.50
41 15 0.36
42 6 0.14
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (41 bp):
TTTTTTATTATAATATTTTATATTTAATTTTTAAAAAAATT
Found at i:4854695 original size:15 final size:14
Alignment explanation
Indices: 4854671--4854700 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
4854661 TATGTTATAT
4854671 TTCTAATAATTACA
1 TTCTAATAATTACA
4854685 TTCTCAATAATTACA
1 TTCT-AATAATTACA
4854700 T
1 T
4854701 ATTTAGCGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (14 bp):
TTCTAATAATTACA
Found at i:4856000 original size:19 final size:19
Alignment explanation
Indices: 4855973--4856011 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
4855963 TTTAAATTTA
*
4855973 ATTTTTTAAATAAAAAATT
1 ATTTATTAAATAAAAAATT
* *
4855992 ATTTATTAATTAATAAATT
1 ATTTATTAAATAAAAAATT
4856011 A
1 A
4856012 AATGATCGGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTATTAAATAAAAAATT
Found at i:4859185 original size:17 final size:16
Alignment explanation
Indices: 4859163--4859203 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 16
4859153 TAAGAGATAG
4859163 TATTTAGAGAAAAATAA
1 TATTTAGAGAAAAA-AA
4859180 TATTTAAAGAGAAAAAAA
1 TATTT--AGAGAAAAAAA
4859198 TATTTA
1 TATTTA
4859204 AAGGGAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 1 0.05
17 5 0.23
18 7 0.32
19 9 0.41
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.32
Consensus pattern (16 bp):
TATTTAGAGAAAAAAA
Found at i:4859199 original size:18 final size:19
Alignment explanation
Indices: 4859168--4859206 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
4859158 GATAGTATTT
4859168 AGAGAAAAATAATATTTAA
1 AGAGAAAAATAATATTTAA
4859187 AGAGAAAAA-AATATTTAA
1 AGAGAAAAATAATATTTAA
4859205 AG
1 AG
4859207 GGAGAAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.23
Consensus pattern (19 bp):
AGAGAAAAATAATATTTAA
Found at i:4866904 original size:24 final size:23
Alignment explanation
Indices: 4866877--4866934 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
4866867 AACAATAAAT
4866877 ACATAATTAAAACACATAATAAGA
1 ACATAATTAAAA-ACATAATAAGA
* *
4866901 ACATATCATT-TAAATATAATAAGA
1 ACATA--ATTAAAAACATAATAAGA
4866925 ACAT-ATTAAA
1 ACATAATTAAA
4866935 GCATCTTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
21 3 0.11
22 1 0.04
24 19 0.68
25 2 0.07
26 3 0.11
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.28
Consensus pattern (23 bp):
ACATAATTAAAAACATAATAAGA
Found at i:4875524 original size:2 final size:2
Alignment explanation
Indices: 4875517--4875543 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4875507 TCTATCATTT
4875517 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4875544 TCATTCATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4883784 original size:2 final size:2
Alignment explanation
Indices: 4883777--4883803 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4883767 AAATAAATAA
4883777 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
4883804 ATTTGTTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4885589 original size:35 final size:35
Alignment explanation
Indices: 4885425--4885615 Score: 133
Period size: 35 Copynumber: 5.5 Consensus size: 35
4885415 CATTTGATTA
*
4885425 AAATTGTTTAATTAAGTTA-T--GCCTAATTAATT
1 AAATTGTTTAATTAAGTTATTAGGCTTAATTAATT
*** *
4885457 -AATTGTTTAATTAACCCATT-GGGTCTAATTAATT
1 AAATTGTTTAATTAAGTTATTAGGCT-TAATTAATT
* * * * *
4885491 AAATTACTTT-ATTAAGTCATTAGGCCTAGTTGATT
1 AAATT-GTTTAATTAAGTTATTAGGCTTAATTAATT
* * * *
4885526 AAAATTGTTTAATTAAATTGTTAAGCTTAATCAATT
1 -AAATTGTTTAATTAAGTTATTAGGCTTAATTAATT
* * *
4885562 AAATTGTTTAATTAATTTATTGGGCTTAATTGATT
1 AAATTGTTTAATTAAGTTATTAGGCTTAATTAATT
***
4885597 AAATTAAATAATTAAGTTA
1 AAATTGTTTAATTAAGTTA
4885616 ACTAAGCTTC
Statistics
Matches: 120, Mismatches: 31, Indels: 13
0.73 0.19 0.08
Matches are distributed among these distances:
31 15 0.12
32 1 0.01
33 1 0.01
34 9 0.08
35 67 0.56
36 27 0.22
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.45
Consensus pattern (35 bp):
AAATTGTTTAATTAAGTTATTAGGCTTAATTAATT
Found at i:4885611 original size:106 final size:102
Alignment explanation
Indices: 4885418--4885613 Score: 250
Period size: 106 Copynumber: 1.9 Consensus size: 102
4885408 TGTCAAGCAT
* *
4885418 TTGATTAAAATTGTTTAATTAAGTTATGCCTAATTAATTAATTGTTTAATTAACCCATTGGGTCT
1 TTGATTAAAATTGTTTAATTAAGTTAAGCCTAATCAATTAATTGTTTAATTAACCCATTGGGTCT
** *
4885483 AATTAATTAAATTACTTTATTAAGTCATTAGGCCTAG
66 AATTAATTAAATTAAATAATTAAGTCATTAGGCCTAG
* ***
4885520 TTGATTAAAATTGTTTAATTAAATTGTTAAGCTTAATCAATTAAATTGTTTAATTAATTTATTGG
1 TTGATTAAAATTGTTTAATT-AA--GTTAAGCCTAATCAATT-AATTGTTTAATTAACCCATTGG
*
4885585 G-CTTAATTGATTAAATTAAATAATTAAGT
62 GTC-TAATTAATTAAATTAAATAATTAAGT
4885614 TAACTAAGCT
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
102 20 0.25
103 2 0.03
105 15 0.19
106 42 0.53
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.45
Consensus pattern (102 bp):
TTGATTAAAATTGTTTAATTAAGTTAAGCCTAATCAATTAATTGTTTAATTAACCCATTGGGTCT
AATTAATTAAATTAAATAATTAAGTCATTAGGCCTAG
Found at i:4896889 original size:2 final size:2
Alignment explanation
Indices: 4896884--4896916 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4896874 TATATATATA
4896884 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
4896917 ATAAACAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:4910214 original size:2 final size:2
Alignment explanation
Indices: 4910202--4910233 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
4910192 CGCATTTCTC
4910202 AT AT AT CAT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT A
4910234 CTGCAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4921818 original size:2 final size:2
Alignment explanation
Indices: 4921806--4921839 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
4921796 ATGGACATTC
* *
4921806 GA GA GA CA GA GA GA GA GA GA GA GA TA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4921840 AAGATGGCTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.44, T:0.03
Consensus pattern (2 bp):
GA
Found at i:4928456 original size:8 final size:8
Alignment explanation
Indices: 4928443--4928472 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
4928433 TCTTTGGTTC
4928443 CTCTTTGG
1 CTCTTTGG
4928451 CTCTTTGG
1 CTCTTTGG
*
4928459 CTCTTTGC
1 CTCTTTGG
4928467 CTCTTT
1 CTCTTT
4928473 CTGCCGTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.00, C:0.30, G:0.17, T:0.53
Consensus pattern (8 bp):
CTCTTTGG
Found at i:4949436 original size:2 final size:2
Alignment explanation
Indices: 4949429--4949459 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4949419 TTATGTTCTG
4949429 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4949460 AAGGTGATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4950560 original size:2 final size:2
Alignment explanation
Indices: 4950553--4950582 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4950543 AATGTGTCTA
4950553 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
4950583 CTTGATTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4951629 original size:2 final size:2
Alignment explanation
Indices: 4951624--4951666 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
4951614 TGTGTGTGTG
4951624 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4951665 TA
1 TA
4951667 GACTAAATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4952481 original size:23 final size:23
Alignment explanation
Indices: 4952455--4952498 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
4952445 ATCCAAAAAC
4952455 TGATTTTAAGAAGAGGACTAAAT
1 TGATTTTAAGAAGAGGACTAAAT
*
4952478 TGATTTTTAGAAGAGGACTAA
1 TGATTTTAAGAAGAGGACTAA
4952499 GAATGGCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.32
Consensus pattern (23 bp):
TGATTTTAAGAAGAGGACTAAAT
Found at i:4959884 original size:2 final size:2
Alignment explanation
Indices: 4959877--4959902 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4959867 CCCTTTTATT
4959877 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
4959903 GTTGTACCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:4969713 original size:23 final size:23
Alignment explanation
Indices: 4969686--4969740 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
4969676 GAAATGCCAC
*
4969686 GGTGGGAATGTATGACATGGCAT
1 GGTGGGAATGTATGACACGGCAT
* * *
4969709 GGTGGGATTGTGTGACACGTCAT
1 GGTGGGAATGTATGACACGGCAT
*
4969732 GGTGAGAAT
1 GGTGGGAAT
4969741 ATGTGACAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.24, C:0.09, G:0.40, T:0.27
Consensus pattern (23 bp):
GGTGGGAATGTATGACACGGCAT
Found at i:4969875 original size:23 final size:23
Alignment explanation
Indices: 4969845--4969925 Score: 87
Period size: 23 Copynumber: 3.6 Consensus size: 23
4969835 TGTAAGATGA
*
4969845 CATGGTGAGAATATGTGACACAT
1 CATGGTGAGAATATGTGACACAC
*
4969868 CA-GTGTGAG-A-ATGTGACACGC
1 CATG-GTGAGAATATGTGACACAC
* *
4969889 CATGGTGAGAATATGTGAGACAA
1 CATGGTGAGAATATGTGACACAC
*
4969912 CATGGTGAGCATAT
1 CATGGTGAGAATAT
4969926 ATACATGACT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
21 16 0.33
22 4 0.08
23 28 0.58
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.23
Consensus pattern (23 bp):
CATGGTGAGAATATGTGACACAC
Found at i:4970090 original size:23 final size:23
Alignment explanation
Indices: 4970063--4970173 Score: 91
Period size: 23 Copynumber: 4.8 Consensus size: 23
4970053 GTTCAGAGTT
* *
4970063 TGTGACAT-GCCATGGTGGGAATG
1 TGTGACATAG-CATGGTGAGAATC
4970086 TGTGACATAGCATGGTGAGAATC
1 TGTGACATAGCATGGTGAGAATC
* * *
4970109 TGTGACACAACATGTTGA-AATC
1 TGTGACATAGCATGGTGAGAATC
* * * *
4970131 GTGTGAGATGGCATGGTGAGTACC
1 -TGTGACATAGCATGGTGAGAATC
**
4970155 TGTGACACGGCATGGTGAG
1 TGTGACATAGCATGGTGAG
4970174 CATATATGTG
Statistics
Matches: 71, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
22 4 0.06
23 64 0.90
24 3 0.04
ACGTcount: A:0.26, C:0.14, G:0.34, T:0.25
Consensus pattern (23 bp):
TGTGACATAGCATGGTGAGAATC
Found at i:4970136 original size:104 final size:104
Alignment explanation
Indices: 4969892--4970122 Score: 239
Period size: 104 Copynumber: 2.2 Consensus size: 104
4969882 GACACGCCAT
* * * ** * * * * * * *
4969892 GGTGAGAATATGTGAGACAACATGGTGAGCATATAT-ACATGACTGTGACATGGTAAGGTTTAGA
1 GGTGAGAATCTGTGACACAACATGGTAAAAATATGTGACACGACTATGACACGGCAGGGTTCAGA
*
4969956 GTTTGTGACACGCCATGGAGGGAATCTATGACATAGTAG
66 GTTTGTGACACGCCATGGAGGGAATCTATGACATAGCAG
* * ****
4969995 GGTGAGAATGTGTGAGATGGTATGGTAAAAATATGTGACACGACTATGACACGGCAGGGTTCAGA
1 GGTGAGAATCTGTGACACAACATGGTAAAAATATGTGACACGACTATGACACGGCAGGGTTCAGA
* * * * *
4970060 GTTTGTGACATGCCATGGTGGGAATGTGTGACATAGCAT
66 GTTTGTGACACGCCATGGAGGGAATCTATGACATAGCAG
4970099 GGTGAGAATCTGTGACACAACATG
1 GGTGAGAATCTGTGACACAACATG
4970123 TTGAAATCGT
Statistics
Matches: 100, Mismatches: 27, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
103 27 0.27
104 73 0.73
ACGTcount: A:0.31, C:0.12, G:0.32, T:0.26
Consensus pattern (104 bp):
GGTGAGAATCTGTGACACAACATGGTAAAAATATGTGACACGACTATGACACGGCAGGGTTCAGA
GTTTGTGACACGCCATGGAGGGAATCTATGACATAGCAG
Found at i:4970628 original size:32 final size:32
Alignment explanation
Indices: 4970591--4970654 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
4970581 TTTTACTAAC
*
4970591 ATGGTTTATCGTCATATCAAAGTTTTGAAGGG
1 ATGGTTTAACGTCATATCAAAGTTTTGAAGGG
*
4970623 ATGGTTTAAGGTCATATCAAAGTTTTGAAGGG
1 ATGGTTTAACGTCATATCAAAGTTTTGAAGGG
4970655 GGTCTGTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.30, C:0.08, G:0.27, T:0.36
Consensus pattern (32 bp):
ATGGTTTAACGTCATATCAAAGTTTTGAAGGG
Found at i:4970858 original size:31 final size:31
Alignment explanation
Indices: 4970820--4971010 Score: 148
Period size: 31 Copynumber: 6.5 Consensus size: 31
4970810 AATGATTGAT
**
4970820 GTGTAACAGTATTTGACTTGGTATGCTTAGC
1 GTGTAACAACATTTGACTTGGTATGCTTAGC
*
4970851 GTGTAACAATATTTGAC-T--TA-GC--A--
1 GTGTAACAACATTTGACTTGGTATGCTTAGC
* * **
4970874 -TGTAACAACATTTGACTTGGCATACTTAAT
1 GTGTAACAACATTTGACTTGGTATGCTTAGC
* * *
4970904 GTGTAACAACATTTGACTTGGCATACTTAAC
1 GTGTAACAACATTTGACTTGGTATGCTTAGC
* * *
4970935 GTGTAACAACATTTTACCTGGTATGCATAGC
1 GTGTAACAACATTTGACTTGGTATGCTTAGC
* * * * *
4970966 ATGCAATAACATTTTACTTGGTATGCATAGC
1 GTGTAACAACATTTGACTTGGTATGCTTAGC
*
4970997 GTGTAACAATATTT
1 GTGTAACAACATTT
4971011 ATATCTTTCT
Statistics
Matches: 132, Mismatches: 19, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
22 15 0.11
23 1 0.01
25 2 0.02
26 1 0.01
27 2 0.02
28 3 0.02
30 1 0.01
31 107 0.81
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36
Consensus pattern (31 bp):
GTGTAACAACATTTGACTTGGTATGCTTAGC
Found at i:4970877 original size:22 final size:22
Alignment explanation
Indices: 4970845--4970896 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
4970835 ACTTGGTATG
* *
4970845 CTTAGCGTGTAACAATATTTGA
1 CTTAGCATGTAACAACATTTGA
4970867 CTTAGCATGTAACAACATTTGA
1 CTTAGCATGTAACAACATTTGA
*
4970889 CTTGGCAT
1 CTTAGCAT
4970897 ACTTAATGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (22 bp):
CTTAGCATGTAACAACATTTGA
Found at i:4970887 original size:53 final size:53
Alignment explanation
Indices: 4970821--4970927 Score: 142
Period size: 53 Copynumber: 2.0 Consensus size: 53
4970811 ATGATTGATG
** * * * *
4970821 TGTAACAGTATTTGACTTGGTATGCTTAGCGTGTAACAATATTTGACTTAGCA
1 TGTAACAACATTTGACTTGGCATACTTAACGTGTAACAACATTTGACTTAGCA
* *
4970874 TGTAACAACATTTGACTTGGCATACTTAATGTGTAACAACATTTGACTTGGCA
1 TGTAACAACATTTGACTTGGCATACTTAACGTGTAACAACATTTGACTTAGCA
4970927 T
1 T
4970928 ACTTAACGTG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (53 bp):
TGTAACAACATTTGACTTGGCATACTTAACGTGTAACAACATTTGACTTAGCA
Found at i:4972662 original size:151 final size:151
Alignment explanation
Indices: 4972506--4972778 Score: 341
Period size: 151 Copynumber: 1.8 Consensus size: 151
4972496 TGTTCAATAG
* * * * * * *
4972506 CATAGTGCCAATGAGTTACC-AGTAAGAGCAATTTTAATGGTTTGTGTTTAACATTTCCACATAT
1 CATAGTGCCAATGAGCTACCGA-TAAGAACAATTCTAACGATTTATGTTGAACATTTCCACATAT
* * *
4972570 GTTTATCAAATAACACAATAATTTTTGTTATTACAGTTGACAGAGGTGACGATAGCTCCTCAACC
65 GTTTATCAAATAACACAATAATTTATGTTATTACAGTTGACAGAGGAGAAGATAGCTCCTCAACC
4972635 ATTGACCGGTCTGACTCAGCCT
130 ATTGACCGGTCTGACTCAGCCT
** * * **
4972657 CATAGTGTTAATGAGCTACCGATAATAACAGTTCTAACGATTTATGTTGAACATTTTTACATATG
1 CATAGTGCCAATGAGCTACCGATAAGAACAATTCTAACGATTTATGTTGAACATTTCCACATATG
* * * * *
4972722 TTTATCGAATTACATAGTAATTTATGTTATTACAGTTGATAGAGGAGAAGATAGCTC
66 TTTATCAAATAACACAATAATTTATGTTATTACAGTTGACAGAGGAGAAGATAGCTC
4972779 TTTAGCCACC
Statistics
Matches: 100, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
151 99 0.99
152 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (151 bp):
CATAGTGCCAATGAGCTACCGATAAGAACAATTCTAACGATTTATGTTGAACATTTCCACATATG
TTTATCAAATAACACAATAATTTATGTTATTACAGTTGACAGAGGAGAAGATAGCTCCTCAACCA
TTGACCGGTCTGACTCAGCCT
Found at i:4975517 original size:152 final size:151
Alignment explanation
Indices: 4975009--4975765 Score: 781
Period size: 152 Copynumber: 5.0 Consensus size: 151
4974999 ACATCTAACA
** * *
4975009 AGCATGGCGTGTCA--CCATAATACTGCAATGACTCAACGTGTCACCGTAAGATGTCAATGATAT
1 AGCATGGCGTGTCACCCCATAATACTGCAATGACTCAACGTGTCACCACAAGATGTCAACGACAT
* * * * *
4975072 CTAACAATTGGAGTGTGGCTTGTCACCTCATAATACTGCAACCACTCAGCGTGTCATCACAAGAT
66 CTAACAATTGGAGCGTGGCATGTCACC-CATAATATTGCAACCACTCAACGTGTCACCACAAGAT
* *
4975137 GTCAACAACATTTAACAATTGT
130 GTCAACAACATCTAACAATTGG
* * * * ** *
4975159 AGCATGTCATGTCACTCCATAGTACTGCAACCACTCAACGTGTCACCATAAGATGTCAACGACAT
1 AGCATGGCGTGTCACCCCATAATACTGCAATGACTCAACGTGTCACCACAAGATGTCAACGACAT
* * * * * *
4975224 CTAACAATTGAAGCATGGCATGCCACCCCACAATATTGCAACGACTCAACGTGTTACCACAAGAT
66 CTAACAATTGGAGCGTGGCATGTCA-CCCATAATATTGCAACCACTCAACGTGTCACCACAAGAT
4975289 GT---CAACATCTAACAATTGG
130 GTCAACAACATCTAACAATTGG
* * * * * * * * *
4975308 AGCGTGGCGTGTCACCCTATAATATTGCAACT-ATTTAATGTGTCACCAAAAAATGTCAACAACA
1 AGCATGGCGTGTCACCCCATAATACTGCAA-TGACTCAACGTGTCACCACAAGATGTCAACGACA
* * * * * *
4975372 TCTAACATTTGGAGCGTGGCATGTCACCTCATCATATTGCAACGACTTAGCATGTCACCACAAGA
65 TCTAACAATTGGAGCGTGGCATGTCACC-CATAATATTGCAACCACTCAACGTGTCACCACAAGA
4975437 TGTCAACAACATCTAACAATTGG
129 TGTCAACAACATCTAACAATTGG
* * *
4975460 AGCATGGCATGTCACCCCATCATACTGCAATGACTCAACGTGTCACCACAAGATGTCAATGACAT
1 AGCATGGCGTGTCACCCCATAATACTGCAATGACTCAACGTGTCACCACAAGATGTCAACGACAT
* * ** ** *
4975525 TTGACAATTATAGCGTGGTGTGTCACCCTATAATATTGCAACCACTCAATGTGTCACCACAAGAT
66 CTAACAATTGGAGCGTGGCATGTCACCC-ATAATATTGCAACCACTCAACGTGTCACCACAAGAT
* *
4975590 GTCAACATCATCTAATAATTGG
130 GTCAACAACATCTAACAATTGG
* * * * * * ** *
4975612 AGCATGGCGTGTCACCTCATAATA-TGACAACGACTTAGCGTGTCACCACAATATATTGACGATA
1 AGCATGGCGTGTCACCCCATAATACTG-CAATGACTCAACGTGTCACCACAAGATGTCAACGACA
* * * * *
4975676 TCTAATAATTGGAGTGTGGCGTGTCACCCTATAATATTTCAACCACTCAACATGTCACCACAAGA
65 TCTAACAATTGGAGCGTGGCATGTCACCC-ATAATATTGCAACCACTCAACGTGTCACCACAAGA
* ***
4975741 AGTCAATGGCATCTAACAATTGG
129 TGTCAACAACATCTAACAATTGG
4975764 AG
1 AG
4975766 TGCAACATGT
Statistics
Matches: 497, Mismatches: 99, Indels: 20
0.81 0.16 0.03
Matches are distributed among these distances:
148 2 0.00
149 119 0.24
150 12 0.02
151 4 0.01
152 358 0.72
153 2 0.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (151 bp):
AGCATGGCGTGTCACCCCATAATACTGCAATGACTCAACGTGTCACCACAAGATGTCAACGACAT
CTAACAATTGGAGCGTGGCATGTCACCCATAATATTGCAACCACTCAACGTGTCACCACAAGATG
TCAACAACATCTAACAATTGG
Found at i:4975767 original size:76 final size:76
Alignment explanation
Indices: 4975013--4975765 Score: 709
Period size: 76 Copynumber: 10.0 Consensus size: 76
4975003 CTAACAAGCA
* * ** * *
4975013 TGGCGTGTCA-CC-ATAATACTGCAATGACTCAACGTGTCACCGTAAGATGTCAATGATATCTAA
1 TGGCGTGTCACCCTATAATATTGCAACGACTCAACGTGTCACCACAAGATGTCAACGACATCTAA
*
4975076 CAATTGGAGTG
66 CAATTGGAGCG
* * * * * * *
4975087 TGGCTTGTCA-CCTCATAATACTGCAACCACTCAGCGTGTCATCACAAGATGTCAACAACATTTA
1 TGGCGTGTCACCCT-ATAATATTGCAACGACTCAACGTGTCACCACAAGATGTCAACGACATCTA
* *
4975151 ACAATTGTAGCA
65 ACAATTGGAGCG
* * * * * *
4975163 TGTCATGTCACTCC-ATAGTACTGCAACCACTCAACGTGTCACCATAAGATGTCAACGACATCTA
1 TGGCGTGTCAC-CCTATAATATTGCAACGACTCAACGTGTCACCACAAGATGTCAACGACATCTA
* *
4975227 ACAATTGAAGCA
65 ACAATTGGAGCG
* * * * *
4975239 TGGCATGCCACCCCACAATATTGCAACGACTCAACGTGTTACCACAAGATGTC-A--ACATCTAA
1 TGGCGTGTCACCCTATAATATTGCAACGACTCAACGTGTCACCACAAGATGTCAACGACATCTAA
4975301 CAATTGGAGCG
66 CAATTGGAGCG
* * * * * * *
4975312 TGGCGTGTCACCCTATAATATTGCAACTATTTAATGTGTCACCAAAAAATGTCAACAACATCTAA
1 TGGCGTGTCACCCTATAATATTGCAACGACTCAACGTGTCACCACAAGATGTCAACGACATCTAA
*
4975377 CATTTGGAGCG
66 CAATTGGAGCG
* * * * * *
4975388 TGGCATGTCA-CCTCATCATATTGCAACGACTTAGCATGTCACCACAAGATGTCAACAACATCTA
1 TGGCGTGTCACCCT-ATAATATTGCAACGACTCAACGTGTCACCACAAGATGTCAACGACATCTA
*
4975452 ACAATTGGAGCA
65 ACAATTGGAGCG
* * * * * * * *
4975464 TGGCATGTCACCCCATCATACTGCAATGACTCAACGTGTCACCACAAGATGTCAATGACATTTGA
1 TGGCGTGTCACCCTATAATATTGCAACGACTCAACGTGTCACCACAAGATGTCAACGACATCTAA
**
4975529 CAATTATAGCG
66 CAATTGGAGCG
* * *
4975540 TGGTGTGTCACCCTATAATATTGCAACCACTCAATGTGTCACCACAAGATGTCAAC-ATCATCTA
1 TGGCGTGTCACCCTATAATATTGCAACGACTCAACGTGTCACCACAAGATGTCAACGA-CATCTA
* *
4975604 ATAATTGGAGCA
65 ACAATTGGAGCG
* * * * ** *
4975616 TGGCGTGTCA-CCTCATAATA-TGACAACGACTTAGCGTGTCACCACAATATATTGACGATATCT
1 TGGCGTGTCACCCT-ATAATATTG-CAACGACTCAACGTGTCACCACAAGATGTCAACGACATCT
* *
4975679 AATAATTGGAGTG
64 AACAATTGGAGCG
* * * * * *
4975692 TGGCGTGTCACCCTATAATATTTCAACCACTCAACATGTCACCACAAGAAGTCAATGGCATCTAA
1 TGGCGTGTCACCCTATAATATTGCAACGACTCAACGTGTCACCACAAGATGTCAACGACATCTAA
4975757 CAATTGGAG
66 CAATTGGAG
4975766 TGCAACATGT
Statistics
Matches: 553, Mismatches: 110, Indels: 30
0.80 0.16 0.04
Matches are distributed among these distances:
73 59 0.11
74 12 0.02
75 12 0.02
76 461 0.83
77 7 0.01
78 2 0.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.26
Consensus pattern (76 bp):
TGGCGTGTCACCCTATAATATTGCAACGACTCAACGTGTCACCACAAGATGTCAACGACATCTAA
CAATTGGAGCG
Found at i:4989237 original size:69 final size:69
Alignment explanation
Indices: 4989146--4989310 Score: 242
Period size: 69 Copynumber: 2.4 Consensus size: 69
4989136 TATAAAAGAA
* * *
4989146 TCACGCGATTCCAAATCAACTAGTCATG-TGATTCCATAACAACTAGTAACGCAATTCCATGTTT
1 TCACGCGATTCCATATCAACTAGTCACGAT-ATTCCATAACAACTAGTAACGCAAGTCCATGTTT
4989210 ACTAC
65 ACTAC
* *
4989215 TCACACGATTCCATATCAACTAGTCACGATATTCCATAATAACTAGTAACGCAAGTCCATGTTTA
1 TCACGCGATTCCATATCAACTAGTCACGATATTCCATAACAACTAGTAACGCAAGTCCATGTTTA
4989280 CTAC
66 CTAC
* * *
4989284 TCATGCGATTCAATATCAACTAATCAC
1 TCACGCGATTCCATATCAACTAGTCAC
4989311 ACGATTCTAA
Statistics
Matches: 86, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
69 85 0.99
70 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.10, T:0.29
Consensus pattern (69 bp):
TCACGCGATTCCATATCAACTAGTCACGATATTCCATAACAACTAGTAACGCAAGTCCATGTTTA
CTAC
Found at i:4989312 original size:92 final size:89
Alignment explanation
Indices: 4989210--4989445 Score: 240
Period size: 92 Copynumber: 2.6 Consensus size: 89
4989200 TTCCATGTTT
* *
4989210 ACTACTCACACGATTCCATATCAACTAGTCACGATATTCCATAATAACTAGTAACGCAAGTCCAT
1 ACTAATCACACGATTCCA-ATC-ACTAGTCACG-TATTCCATATTAACTAGTAACGCAAGTCCAT
* *
4989275 GTTTACTACTCATGCGATTCAATATCA
63 ATTTACTACTCACGCGATTCAATATCA
* * * * * *
4989302 ACTAATCACACGATTCTAAATCACATAGTCACGCGATTCCATTTTAAC-GGTTCACGCAATTCCA
1 ACTAATCACACGATTC-CAATCAC-TAGTCACG-TATTCCATATTAACTAG-TAACGCAAGTCCA
4989366 TATTTACTACTCACGCGATTCAATATCA
62 TATTTACTACTCACGCGATTCAATATCA
* * * * *
4989394 ACTAGTAACATGATTCCAATTCGATTAGTCATGTAATTCCATATTAACTAGT
1 ACTAATCACACGATTCCAA-TC-ACTAGTCACGT-ATTCCATATTAACTAGT
4989446 CATGTGATTC
Statistics
Matches: 117, Mismatches: 20, Indels: 14
0.77 0.13 0.09
Matches are distributed among these distances:
91 5 0.04
92 109 0.93
93 3 0.03
ACGTcount: A:0.34, C:0.25, G:0.10, T:0.31
Consensus pattern (89 bp):
ACTAATCACACGATTCCAATCACTAGTCACGTATTCCATATTAACTAGTAACGCAAGTCCATATT
TACTACTCACGCGATTCAATATCA
Found at i:4989397 original size:23 final size:23
Alignment explanation
Indices: 4989146--4989528 Score: 173
Period size: 23 Copynumber: 16.7 Consensus size: 23
4989136 TATAAAAGAA
*
4989146 TCACGCGATTCCAAATCAACTAG
1 TCACGCGATTCCATATCAACTAG
* * *
4989169 TCATGTGATTCCATAACAACTAG
1 TCACGCGATTCCATATCAACTAG
* * * ** *
4989192 TAACGCAATTCCATGTTTACTAC
1 TCACGCGATTCCATATCAACTAG
*
4989215 TCACACGATTCCATATCAACTAG
1 TCACGCGATTCCATATCAACTAG
**
4989238 TCACGATATTCCATAAT-AACTAG
1 TCACGCGATTCCAT-ATCAACTAG
* * * * ** *
4989261 TAACGCAAGTCCATGTTTACTAC
1 TCACGCGATTCCATATCAACTAG
* * *
4989284 TCATGCGATTCAATATCAACTAA
1 TCACGCGATTCCATATCAACTAG
* * *
4989307 TCACACGATTCTAAATC-ACATAG
1 TCACGCGATTCCATATCAAC-TAG
* * *
4989330 TCACGCGATTCCATTTTAAC-GG
1 TCACGCGATTCCATATCAACTAG
* ** *
4989352 TTCACGCAATTCCATATTTACTAC
1 -TCACGCGATTCCATATCAACTAG
*
4989376 TCACGCGATTCAATATCAACTAG
1 TCACGCGATTCCATATCAACTAG
* ** * *
4989399 TAACATGATTCCA-ATTCGATTAG
1 TCACGCGATTCCATA-TCAACTAG
* ** *
4989422 TCATGTAATTCCATATTAACTAG
1 TCACGCGATTCCATATCAACTAG
* * * * ***
4989445 TCATGTGATTCTAAATTTGCTAG
1 TCACGCGATTCCATATCAACTAG
* * *
4989468 TCACGCTATTCCATATCAAATAC
1 TCACGCGATTCCATATCAACTAG
* * *
4989491 TCACGGGATTCAATATAAACT-G
1 TCACGCGATTCCATATCAACTAG
*
4989513 CTCATGCGATTCCATA
1 -TCACGCGATTCCATA
4989529 CACACCATTC
Statistics
Matches: 254, Mismatches: 97, Indels: 18
0.69 0.26 0.05
Matches are distributed among these distances:
22 5 0.02
23 244 0.96
24 5 0.02
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.31
Consensus pattern (23 bp):
TCACGCGATTCCATATCAACTAG
Found at i:4989867 original size:26 final size:27
Alignment explanation
Indices: 4989826--4989881 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
4989816 TGCACTTCTC
*
4989826 TTTGTTAAATGGTACAA-AAAGGAAAAA
1 TTTGTTAAATGATACAACAAA-GAAAAA
*
4989853 TTTG-TAAATGATACAACAAAGAATAA
1 TTTGTTAAATGATACAACAAAGAAAAA
4989879 TTT
1 TTT
4989882 AGAGATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 19 0.73
27 7 0.27
ACGTcount: A:0.50, C:0.05, G:0.14, T:0.30
Consensus pattern (27 bp):
TTTGTTAAATGATACAACAAAGAAAAA
Found at i:4993505 original size:23 final size:23
Alignment explanation
Indices: 4993450--4993505 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
4993440 TGAACAATTT
* *
4993450 TCACGCAATGACTTATCTACCAC
1 TCACGCAATGACCTATCAACCAC
** * *
4993473 TTGCGTAATGACCTATCAACCAG
1 TCACGCAATGACCTATCAACCAC
4993496 TCACGCAATG
1 TCACGCAATG
4993506 TTAAACCTTA
Statistics
Matches: 24, Mismatches: 9, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (23 bp):
TCACGCAATGACCTATCAACCAC
Found at i:4993571 original size:110 final size:110
Alignment explanation
Indices: 4993361--4993724 Score: 414
Period size: 110 Copynumber: 3.3 Consensus size: 110
4993351 CATGAACCAT
* * * * *
4993361 ATTCACGCAATGACCTATCAACCACTCATGTAATGTTAAACCCTAATGCAATCACGCACACCTTA
1 ATTCACGTAATGACCTATCAACCAGTCACGCAATGTTAAACCCTAATGCAATCACGCACACCCTA
* *
4993426 AGTGGCA-CCATGCCTGAACAAT-TTTCACGCAATGACTTATCTACC
66 AGT-G-ATCCATGCCTGAACAATATTTCACGCAATGACCTATCAACC
* * *
4993471 ACTT-GCGTAATGACCTATCAACCAGTCACGCAATGTTAAACCTTAATGCAATCACACACACCCT
1 A-TTCACGTAATGACCTATCAACCAGTCACGCAATGTTAAACCCTAATGCAATCACGCACACCCT
* *
4993535 AAGTGATGCCATGCCTGAACAATATTT-ACGCGATGACCTATCAACT
65 AAGTGAT-CCATGCCTGAACAATATTTCACGCAATGACCTATCAACC
* * *
4993581 ATTCACGTACTGACCTATCAACCAGTCACACAATGTTAAACCCTAATGCAATCACGCACACCCTC
1 ATTCACGTAATGACCTATCAACCAGTCACGCAATGTTAAACCCTAATGCAATCACGCACACCCTA
* ** * *
4993646 AGTGACTCCATGCTTGAACAATA-TTCACAAAATAACCTATCAATC
66 AGTGA-TCCATGCCTGAACAATATTTCACGCAATGACCTATCAACC
* ** * * *
4993691 ACTCACACAATTACTTATCAACCAGTCATGCAAT
1 ATTCACGTAATGACCTATCAACCAGTCACGCAAT
4993725 AACCTATCAA
Statistics
Matches: 214, Mismatches: 33, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
108 1 0.00
109 5 0.02
110 202 0.94
111 6 0.03
ACGTcount: A:0.35, C:0.30, G:0.11, T:0.25
Consensus pattern (110 bp):
ATTCACGTAATGACCTATCAACCAGTCACGCAATGTTAAACCCTAATGCAATCACGCACACCCTA
AGTGATCCATGCCTGAACAATATTTCACGCAATGACCTATCAACC
Found at i:4993696 original size:23 final size:23
Alignment explanation
Indices: 4993670--4993742 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
4993660 TGAACAATAT
* *
4993670 TCACAAAATAACCTATCAATCAC
1 TCACACAATAACCTATCAATCAG
* * *
4993693 TCACACAATTACTTATCAACCAG
1 TCACACAATAACCTATCAATCAG
**
4993716 TCATGCAATAACCTATCAATCAG
1 TCACACAATAACCTATCAATCAG
4993739 TCAC
1 TCAC
4993743 CTAATGACAC
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.41, C:0.30, G:0.04, T:0.25
Consensus pattern (23 bp):
TCACACAATAACCTATCAATCAG
Found at i:4993770 original size:46 final size:46
Alignment explanation
Indices: 4993676--4993770 Score: 102
Period size: 46 Copynumber: 2.1 Consensus size: 46
4993666 ATATTCACAA
* ** *
4993676 AATAACCTATCAATCACTCACACAATTACTTATCAACCAGTCATGC
1 AATAACCTATCAATCACTCACACAATGACACATCAACCAGTCACGC
* * * *
4993722 AATAACCTATCAATCAGTCAC-CTAATGACACATCAGCTAGTTACGC
1 AATAACCTATCAATCACTCACAC-AATGACACATCAACCAGTCACGC
4993768 AAT
1 AAT
4993771 GTTGAACCCT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
45 1 0.03
46 39 0.98
ACGTcount: A:0.39, C:0.28, G:0.07, T:0.25
Consensus pattern (46 bp):
AATAACCTATCAATCACTCACACAATGACACATCAACCAGTCACGC
Found at i:5002515 original size:16 final size:17
Alignment explanation
Indices: 5002487--5002518 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5002477 AAGTAAAAGG
5002487 AAGTAAGAGAGAAAAAA
1 AAGTAAGAGAGAAAAAA
5002504 AAGTAA-AGAGAAAAA
1 AAGTAAGAGAGAAAAA
5002519 CTAATAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (17 bp):
AAGTAAGAGAGAAAAAA
Found at i:5016961 original size:18 final size:17
Alignment explanation
Indices: 5016939--5016980 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
5016929 AATTAATTTA
5016939 ATTAATA-AAATACAAAT
1 ATTAATATAAAT-CAAAT
5016956 ACTTAATATTAAATCAAAT
1 A-TTAATA-TAAATCAAAT
5016975 ATTAAT
1 ATTAAT
5016981 GCATCTGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.05
18 11 0.50
19 6 0.27
20 4 0.18
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (17 bp):
ATTAATATAAATCAAAT
Found at i:5023640 original size:68 final size:68
Alignment explanation
Indices: 5023513--5023640 Score: 150
Period size: 68 Copynumber: 1.9 Consensus size: 68
5023503 ATTCTGTTGG
** * * ** * *
5023513 AAATTTTCAACGGAATTTTCCGTTGGGAATGTTTTTTCATTGAAAATTTTCATTTGAAATTTTTA
1 AAATTTTCAACAAAATTTTCCGTTGGGAATGCTTTTCCATACAAAATTTCCATTGGAAATTTTTA
5023578 GTA
66 GTA
* *
5023581 AAATTTTCAACAAAATTTTCTGTTGGGAATGCTTTTCCA-ACAAAATTTCCCGTTGGAAAT
1 AAATTTTCAACAAAATTTTCCGTTGGGAATGCTTTTCCATACAAAATTT-CCATTGGAAAT
5023641 AGAGCAACGG
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
67 7 0.14
68 42 0.86
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.42
Consensus pattern (68 bp):
AAATTTTCAACAAAATTTTCCGTTGGGAATGCTTTTCCATACAAAATTTCCATTGGAAATTTTTA
GTA
Found at i:5024218 original size:12 final size:12
Alignment explanation
Indices: 5024197--5024231 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
5024187 TGTATTCTTA
*
5024197 ATTTCTTCACGT
1 ATTTCCTCACGT
5024209 ATTTCCTCACGT
1 ATTTCCTCACGT
*
5024221 GTTTCCTCACG
1 ATTTCCTCACG
5024232 AATCTTATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.14, C:0.31, G:0.11, T:0.43
Consensus pattern (12 bp):
ATTTCCTCACGT
Found at i:5029561 original size:13 final size:14
Alignment explanation
Indices: 5029537--5029565 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5029527 TAATTTTTAG
5029537 ATGTATATGATAAA
1 ATGTATATGATAAA
5029551 ATGTA-ATGATAAA
1 ATGTATATGATAAA
5029564 AT
1 AT
5029566 TGCATATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (14 bp):
ATGTATATGATAAA
Found at i:5045169 original size:39 final size:39
Alignment explanation
Indices: 5045115--5045191 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
5045105 ATTTCCATAG
*
5045115 GAAATATCATTATCTATTAGTTTTGAATCTTGCATGTTT
1 GAAATATCATTATCTATTAGTTTTGAATCTTGAATGTTT
5045154 GAAATATCATTATCTATTAGTTTTGAATCTTGAATGTT
1 GAAATATCATTATCTATTAGTTTTGAATCTTGAATGTT
5045192 CAAACGATCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.48
Consensus pattern (39 bp):
GAAATATCATTATCTATTAGTTTTGAATCTTGAATGTTT
Found at i:5062168 original size:80 final size:78
Alignment explanation
Indices: 5062062--5062208 Score: 179
Period size: 80 Copynumber: 1.9 Consensus size: 78
5062052 GGTACGATGC
* * * * *
5062062 CTAACTTAACCTTATTGTATTCTTACCC-CTACACCAGGACTAGAGCTAACACATAAAAAGGGAA
1 CTAACTTAACCCTATGGTATTCTTACCCTC-ACACCAGGACTAAAGCCAACACACAAAAA-GGAA
5062126 AAAGTGACACATTAG
64 AAAGTGACACATTAG
* ** *
5062141 CTAAGCTTAACCCTATGGTATTGTTACCCTCACAGTAGGACTAAAGCCAACATACAAAAAGGAAA
1 CTAA-CTTAACCCTATGGTATTCTTACCCTCACACCAGGACTAAAGCCAACACACAAAAAGGAAA
5062206 AAG
65 AAG
5062209 GTGGCATGTT
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
79 12 0.21
80 44 0.77
81 1 0.02
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.22
Consensus pattern (78 bp):
CTAACTTAACCCTATGGTATTCTTACCCTCACACCAGGACTAAAGCCAACACACAAAAAGGAAAA
AGTGACACATTAG
Found at i:5089157 original size:15 final size:15
Alignment explanation
Indices: 5089137--5089166 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5089127 CAAAAGCTCT
5089137 CTATAAGTATATATA
1 CTATAAGTATATATA
*
5089152 CTATAAGTTTATATA
1 CTATAAGTATATATA
5089167 AACAATGGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (15 bp):
CTATAAGTATATATA
Found at i:5089163 original size:342 final size:345
Alignment explanation
Indices: 5088492--5089269 Score: 975
Period size: 342 Copynumber: 2.2 Consensus size: 345
5088482 TATCTTAAAA
*
5088492 ATAATTAATAATTTTATAAGTTATTAGTTTTGTAATGTTAACACAAAATAGAAAGTAAATATGTT
1 ATAATTAATAATTTTATAAGTTA-TAATTTTGTAATGTTAACACAAAATAGAAAGTAAATATGTT
* * * *
5088557 TATATTTAAAGTATATATATATATTTAGAAAAAAATTATTTTAATATATATAATAGTAATTATAT
65 TATATTTAAAG--TATATATATATCTA-AAAAAAATTATTTCAACATATATAATACTAATTATAT
* * *
5088622 TCCTTATAAATGAACCTAATATATATAAAGTATATATATTAAAAGACATTACAAGTTAATTAAAT
127 TCCTTATAAATGAACC-AATATATATAAACTATATATAGTAAAAAACATTACAAGTTAATTAAAT
* * *
5088687 AATTATAATTTTATGAATTAATTTAATTAACTATATGGGTTAGTCCATAATTACATAAAATTAAA
191 AATCATAATTTCATGAATTAATTTAATTAACTATATGGATTAGTCCATAATTACATAAAATTAAA
* * * *
5088752 AAAAATAACTAAGTTTCAAAACTATTCTAATCTCACAACTTCTCTTGAGGTTTATAAATTATAAG
256 AAAAATAACTAAGTTTCAAAACTATTCTAATCTCAAAACTTCTCTTGAAGTATATAAACTATAAG
* *
5088817 TTTATGTAAACAAAGGTCTATATATT
321 TTTATATAAACAAAGGTAT-TATATT
* * * *
5088843 ATAATTAATAA-TTTATAGGTTAAAATTTTTATAATGTTAACATAAAATAGAAAGTAAATATGTT
1 ATAATTAATAATTTTATAAGTTATAA-TTTTGTAATGTTAACACAAAATAGAAAGTAAATATGTT
* *
5088907 TATATTTAAAGGATATATATA-CT-AAAAATATT-TTATCATACATATATAATACTAATTATATT
65 TATATTTAAAGTATATATATATCTAAAAAAAATTATT-TCA-ACATATATAATACTAATTATATT
* * *
5088969 TCTTATAAATTAA-CACA-ATATATAAACTATATATAGTAAAAAACATTATAAGTTAATT-AATA
128 CCTTATAAATGAACCA-ATATATATAAACTATATATAGTAAAAAACATTACAAGTTAATTAAATA
* * * * *
5089031 ATCATAGTTTCATGAATTAATTTAATTAACTATATGGATTTGTCCTTAATTTCATGAAATT-AAA
192 ATCATAATTTCATGAATTAATTTAATTAACTATATGGATTAGTCCATAATTACATAAAATTAAAA
** * *
5089095 AAAATAGTTATG-TTCTAAAACTATTCTAATCTCAAAAGC-TCTCTAT-AAGTATATATACTATA
257 AAAATAACTAAGTTTC-AAAACTATTCTAATCTCAAAA-CTTCTCT-TGAAGTATATAAACTATA
*
5089157 AGTTTATATAAACAATGGTATTATATT
319 AGTTTATATAAACAAAGGTATTATATT
* * * * *
5089184 ATGATCAATAATTTTCTAAGTTATAATTTTGTAATGTTAACACAAAATAGAATGTAAATATATTT
1 ATAATTAATAATTTTATAAGTTATAATTTTGTAATGTTAACACAAAATAGAAAGTAAATATGTTT
* *
5089249 ATATTGAGAGTATATATATAT
66 ATATTTAAAGTATATATATAT
5089270 ATAATAGTAA
Statistics
Matches: 370, Mismatches: 48, Indels: 27
0.83 0.11 0.06
Matches are distributed among these distances:
341 70 0.19
342 78 0.21
343 59 0.16
344 40 0.11
345 12 0.03
346 32 0.09
347 1 0.00
348 9 0.02
349 1 0.00
350 57 0.15
351 11 0.03
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.40
Consensus pattern (345 bp):
ATAATTAATAATTTTATAAGTTATAATTTTGTAATGTTAACACAAAATAGAAAGTAAATATGTTT
ATATTTAAAGTATATATATATCTAAAAAAAATTATTTCAACATATATAATACTAATTATATTCCT
TATAAATGAACCAATATATATAAACTATATATAGTAAAAAACATTACAAGTTAATTAAATAATCA
TAATTTCATGAATTAATTTAATTAACTATATGGATTAGTCCATAATTACATAAAATTAAAAAAAA
TAACTAAGTTTCAAAACTATTCTAATCTCAAAACTTCTCTTGAAGTATATAAACTATAAGTTTAT
ATAAACAAAGGTATTATATT
Found at i:5098583 original size:16 final size:17
Alignment explanation
Indices: 5098550--5098584 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5098540 AGTTTATCTC
*
5098550 ATAATATCTAATAGAAA
1 ATAATATCCAATAGAAA
5098567 ATAATATCCAA-AGAAA
1 ATAATATCCAATAGAAA
5098583 AT
1 AT
5098585 TAGCCATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.60, C:0.09, G:0.06, T:0.26
Consensus pattern (17 bp):
ATAATATCCAATAGAAA
Found at i:5099232 original size:11 final size:10
Alignment explanation
Indices: 5099212--5099245 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
5099202 AATTTAAAAC
5099212 AAAATAAGAT
1 AAAATAAGAT
5099222 AAAACTAAGAT
1 AAAA-TAAGAT
*
5099233 AAAATAACAT
1 AAAATAAGAT
5099243 AAA
1 AAA
5099246 CTAACTAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (10 bp):
AAAATAAGAT
Found at i:5109036 original size:41 final size:41
Alignment explanation
Indices: 5108979--5109068 Score: 180
Period size: 41 Copynumber: 2.2 Consensus size: 41
5108969 ATGAGTTGGG
5108979 GCAAAAATGGAGAAATTTTGCATCTTAAAGCTCCTTTGTAT
1 GCAAAAATGGAGAAATTTTGCATCTTAAAGCTCCTTTGTAT
5109020 GCAAAAATGGAGAAATTTTGCATCTTAAAGCTCCTTTGTAT
1 GCAAAAATGGAGAAATTTTGCATCTTAAAGCTCCTTTGTAT
5109061 GCAAAAAT
1 GCAAAAAT
5109069 TATGAACCAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (41 bp):
GCAAAAATGGAGAAATTTTGCATCTTAAAGCTCCTTTGTAT
Found at i:5116609 original size:14 final size:14
Alignment explanation
Indices: 5116590--5116616 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5116580 CAAAATTTAT
5116590 TAATTAACTAAAAC
1 TAATTAACTAAAAC
5116604 TAATTAACTAAAA
1 TAATTAACTAAAA
5116617 TTTAAACTAA
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:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (14 bp):
TAATTAACTAAAAC
Found at i:5117466 original size:22 final size:22
Alignment explanation
Indices: 5117441--5117490 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
5117431 AGTGTCGCAG
* *
5117441 CTCTTATTTCCTAGAGTCACAA
1 CTCTTATTTCCCAGAGCCACAA
*
5117463 CTCTTATTTCCCAGAGCCACGA
1 CTCTTATTTCCCAGAGCCACAA
5117485 CTCTTA
1 CTCTTA
5117491 AAGGTTCTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.24, C:0.32, G:0.10, T:0.34
Consensus pattern (22 bp):
CTCTTATTTCCCAGAGCCACAA
Found at i:5134125 original size:113 final size:113
Alignment explanation
Indices: 5133937--5134148 Score: 352
Period size: 113 Copynumber: 1.9 Consensus size: 113
5133927 CCTTTGCTTC
* *
5133937 TGTGATGTGAAACGTGCACAAAGTTAAATGTAAATTACATGCAAAGATTACGTACAAGCATACAT
1 TGTGATGTGAAACGTGCACAAAATTAAATGTAAATTACAAGCAAAGATTACGTACAAGCATACAT
* *
5134002 GATCGTAACAAGTAATAAAGTGGTAAATAAAGTGATGTCCTTCGTTTG
66 GATCGCAACAAGAAATAAAGTGGTAAATAAAGTGATGTCCTTCGTTTG
* * *
5134050 TGTGATGTGAAATGTGCTCAAAATTAAATGTAAATTACAAGCAAAGATTACGTGCAAGCATACAT
1 TGTGATGTGAAACGTGCACAAAATTAAATGTAAATTACAAGCAAAGATTACGTACAAGCATACAT
*
5134115 GATCGCAACAAGAAATAAAGTGGTAAATAGAGTG
66 GATCGCAACAAGAAATAAAGTGGTAAATAAAGTG
5134149 CCGGTCCCTC
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
113 91 1.00
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (113 bp):
TGTGATGTGAAACGTGCACAAAATTAAATGTAAATTACAAGCAAAGATTACGTACAAGCATACAT
GATCGCAACAAGAAATAAAGTGGTAAATAAAGTGATGTCCTTCGTTTG
Found at i:5138436 original size:22 final size:21
Alignment explanation
Indices: 5138376--5138436 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 21
5138366 TAATCTTATT
5138376 TATTTTATTTTCATTTCTTTA-A
1 TATTTTATTTT-ATTT-TTTACA
*
5138398 TATTTT-TTTTA--TATTACA
1 TATTTTATTTTATTTTTTACA
5138416 TATTTTATTTTGATTTTTTAC
1 TATTTTATTTT-ATTTTTTAC
5138437 CTATAATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
17 3 0.09
18 8 0.25
19 4 0.12
20 2 0.06
21 4 0.12
22 11 0.34
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.69
Consensus pattern (21 bp):
TATTTTATTTTATTTTTTACA
Found at i:5139049 original size:39 final size:40
Alignment explanation
Indices: 5138980--5139056 Score: 115
Period size: 39 Copynumber: 1.9 Consensus size: 40
5138970 CTAATACTAC
5138980 AATAGTAATTATTATTATTATAATAGTTTTT-TAATTGAA
1 AATAGTAATTATTATTATTATAATAGTTTTTGTAATTGAA
5139019 AATAGTAATTATTATTA-TA-AATAGTTTTTTTGTAATTG
1 AATAGTAATTATTATTATTATAATAG--TTTTTGTAATTG
5139057 GGCAAAGGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
37 5 0.14
38 2 0.06
39 22 0.63
40 6 0.17
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (40 bp):
AATAGTAATTATTATTATTATAATAGTTTTTGTAATTGAA
Found at i:5143995 original size:97 final size:97
Alignment explanation
Indices: 5143815--5143997 Score: 217
Period size: 97 Copynumber: 1.9 Consensus size: 97
5143805 TTTCGATTAC
* * * *
5143815 GTGTTAAGTATAAAATAAAGATATTTTTTAACAATTATTTCATACTGAGATTTGATATCTTTAAT
1 GTGTTAAGTATAAAATAAAGACATTTTTTAACAACTATTACATACTAAGATTTGATATCTTTAAT
* * * *
5143880 CGAGTTCGATGATTTTTCATAACTCCAACTAT
66 CGACTTCAACGATCTTTCATAACTCCAACTAT
* * *
5143912 GTGTTAAGTATTAAGTAAAGACATTTTTTAACAACTATTACATGCTAAGATTATG-TATCTTTAA
1 GTGTTAAGTATAAAATAAAGACATTTTTTAACAACTATTACATACTAAGATT-TGATATCTTTAA
* *
5143976 TTGAACTT-AACGGTCTTTCATA
65 TCG-ACTTCAACGATCTTTCATA
5143998 GAGTAGAAGG
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
97 66 0.93
98 5 0.07
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (97 bp):
GTGTTAAGTATAAAATAAAGACATTTTTTAACAACTATTACATACTAAGATTTGATATCTTTAAT
CGACTTCAACGATCTTTCATAACTCCAACTAT
Found at i:5150267 original size:52 final size:52
Alignment explanation
Indices: 5150204--5150307 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
5150194 AATACATAGG
5150204 AGTGATATTTACATACATATATAGATTCTAAAACTCTTTGAAAACATTTGGA
1 AGTGATATTTACATACATATATAGATTCTAAAACTCTTTGAAAACATTTGGA
5150256 AGTGATATTTACATACATATATAGATTCTAAAACTCTTTGAAAACATTTGGA
1 AGTGATATTTACATACATATATAGATTCTAAAACTCTTTGAAAACATTTGGA
5150308 TCAAAATCAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (52 bp):
AGTGATATTTACATACATATATAGATTCTAAAACTCTTTGAAAACATTTGGA
Found at i:5152736 original size:34 final size:34
Alignment explanation
Indices: 5152698--5152764 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
5152688 TTACCGAGCT
* *
5152698 CAAGCATAACCCTCACAATGCTTTTTAATGGGAA
1 CAAGCACAACCCTCACAATGCCTTTTAATGGGAA
* * *
5152732 CAAGCACAAGCCTTATAATGCCTTTTAATGGGA
1 CAAGCACAACCCTCACAATGCCTTTTAATGGGA
5152765 GGCACAATGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.27
Consensus pattern (34 bp):
CAAGCACAACCCTCACAATGCCTTTTAATGGGAA
Found at i:5164877 original size:19 final size:19
Alignment explanation
Indices: 5164845--5164891 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
5164835 AAGATAAACA
* *
5164845 AGAAATAAAGGAAACAAAAG
1 AGAAAAAAAAGAAA-AAAAG
*
5164865 -GAAAAAAAAGAAAATAAG
1 AGAAAAAAAAGAAAAAAAG
5164883 AGAAAAAAA
1 AGAAAAAAA
5164892 TTTAGAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (19 bp):
AGAAAAAAAAGAAAAAAAG
Found at i:5177667 original size:34 final size:35
Alignment explanation
Indices: 5177612--5177757 Score: 118
Period size: 38 Copynumber: 4.0 Consensus size: 35
5177602 AAAAGGTTGA
* * *
5177612 GAGGTCGTGCATGATTC-TTAAAAGGCATTTGGTT
1 GAGGTTGTGCTTGATCCTTTAAAAGGCATTTGGTT
* *
5177646 GAGGTTGTGCTTGAT-GTTTAAAAGTCATTTTGGTT
1 GAGGTTGTGCTTGATCCTTTAAAAGGCA-TTTGGTT
* **
5177681 GTAAAGGTTGTACTTGATCCTAAAAAGTAGTGTC-TTTGGTT
1 G---AGGTTGTGCTTGATCCTTTAAA--AG-G-CATTTGGTT
*
5177722 GAGGTTGTGCTTGATCCTTTAAAAGGCATTTTGTT
1 GAGGTTGTGCTTGATCCTTTAAAAGGCATTTGGTT
5177757 G
1 G
5177758 TAAAGGTTAC
Statistics
Matches: 88, Mismatches: 13, Indels: 21
0.72 0.11 0.17
Matches are distributed among these distances:
34 23 0.26
35 16 0.18
36 2 0.02
38 32 0.36
39 4 0.05
41 10 0.11
43 1 0.01
ACGTcount: A:0.23, C:0.10, G:0.27, T:0.40
Consensus pattern (35 bp):
GAGGTTGTGCTTGATCCTTTAAAAGGCATTTGGTT
Found at i:5177697 original size:38 final size:38
Alignment explanation
Indices: 5177647--5177776 Score: 117
Period size: 38 Copynumber: 3.4 Consensus size: 38
5177637 CATTTGGTTG
*
5177647 AGGTTGTGCTTGATGTTTAAAAGTCATTTTGGTTGTAA
1 AGGTTGTGCTTGATCTTTAAAAGTCATTTTGGTTGTAA
* * *
5177685 AGGTTGTACTTGATCCTAAAAAGT-AGTGTCTTTGGTTG---
1 AGGTTGTGCTTGATCTTTAAAAGTCA---T-TTTGGTTGTAA
*
5177723 AGGTTGTGCTTGATCCTTTAAAAGGCATTTT-GTTGTAA
1 AGGTTGTGCTTGAT-CTTTAAAAGTCATTTTGGTTGTAA
**
5177761 AGGTTACGCTTGATCT
1 AGGTTGTGCTTGATCT
5177777 AGTGTTAAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 19
0.72 0.10 0.19
Matches are distributed among these distances:
35 4 0.05
36 3 0.04
37 4 0.05
38 45 0.62
39 7 0.10
40 2 0.03
41 8 0.11
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.42
Consensus pattern (38 bp):
AGGTTGTGCTTGATCTTTAAAAGTCATTTTGGTTGTAA
Found at i:5184064 original size:36 final size:36
Alignment explanation
Indices: 5184017--5184109 Score: 145
Period size: 36 Copynumber: 2.6 Consensus size: 36
5184007 TTTTAATTAT
5184017 GTGCTATTATAAAGAGCA-CCTCCCAAGGATCAACAA
1 GTGCTATTATAAAGAGCACCCT-CCAAGGATCAACAA
*
5184053 GTGCTATTATAAAGAGCACCCTCCAAGGATCGACAA
1 GTGCTATTATAAAGAGCACCCTCCAAGGATCAACAA
*
5184089 GTGCTACTATAAAGAG-ACCCT
1 GTGCTATTATAAAGAGCACCCT
5184110 TCAAATTGTA
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
35 5 0.09
36 46 0.85
37 3 0.06
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (36 bp):
GTGCTATTATAAAGAGCACCCTCCAAGGATCAACAA
Found at i:5185145 original size:33 final size:33
Alignment explanation
Indices: 5185098--5185232 Score: 155
Period size: 33 Copynumber: 4.1 Consensus size: 33
5185088 ATTTCTTCAA
* *
5185098 ATAGTTTTAGTGCAATATACTTCTTCTAAGATT
1 ATAGTTTTATTGCAATATACTTCTTCCAAGATT
* * *
5185131 ATTGTTTTATTGCAAAATAAC-TCTTCCAAGAGT
1 ATAGTTTTATTGCAATAT-ACTTCTTCCAAGATT
* *
5185164 ATAGTTTTATTGCAATATATTTCTTCCAAGGTT
1 ATAGTTTTATTGCAATATACTTCTTCCAAGATT
** * *
5185197 ATAGTTTTAAGGCAATACACATCTTCCAAGATT
1 ATAGTTTTATTGCAATATACTTCTTCCAAGATT
5185230 ATA
1 ATA
5185233 ATTCTCTTAC
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.96
34 2 0.02
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (33 bp):
ATAGTTTTATTGCAATATACTTCTTCCAAGATT
Found at i:5186024 original size:18 final size:18
Alignment explanation
Indices: 5185984--5186017 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5185974 AAAGGATTCA
*
5185984 AAGATTGTGAGGTATTTG
1 AAGATTGAGAGGTATTTG
5186002 AAGATTGAGA-GTATTT
1 AAGATTGAGAGGTATTT
5186018 TAGAGATCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.00, G:0.29, T:0.38
Consensus pattern (18 bp):
AAGATTGAGAGGTATTTG
Found at i:5186234 original size:25 final size:26
Alignment explanation
Indices: 5186142--5186264 Score: 69
Period size: 25 Copynumber: 4.9 Consensus size: 26
5186132 AAAGTTCATG
** *
5186142 ATCAAGC-GAAGTTTGTGGTCAAGTC
1 ATCAAGCAGAAGTTCATGATCAAGTC
* * * * *
5186167 TTTAAGCA-AAGCTCGTGACCAAGTC
1 ATCAAGCAGAAGTTCATGATCAAGTC
* *
5186192 ATCAAG-AGATGTTTATGATCAAGTC
1 ATCAAGCAGAAGTTCATGATCAAGTC
* *
5186217 ATCAAGCA-AAGGTCATGAACAAGAT-
1 ATCAAGCAGAAGTTCATGATCAAG-TC
* *
5186242 ATCAAGTATAA-TTCATGATCAAG
1 ATCAAGCAGAAGTTCATGATCAAG
5186265 ATTAAGTCAT
Statistics
Matches: 73, Mismatches: 20, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
24 1 0.01
25 68 0.93
26 4 0.05
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.26
Consensus pattern (26 bp):
ATCAAGCAGAAGTTCATGATCAAGTC
Found at i:5186246 original size:50 final size:50
Alignment explanation
Indices: 5186142--5186264 Score: 115
Period size: 50 Copynumber: 2.5 Consensus size: 50
5186132 AAAGTTCATG
* * * * * * *
5186142 ATCAAGCGAAGTTTGTGGTCAAGTCTTTAAGCAAAGCTCGTGACCAAGTC
1 ATCAAGAGAAGTTTATGATCAAGTCATCAAGCAAAGCTCATGAACAAGTC
* *
5186192 ATCAAGAGATGTTTATGATCAAGTCATCAAGCAAAGGTCATGAACAAGAT-
1 ATCAAGAGAAGTTTATGATCAAGTCATCAAGCAAAGCTCATGAACAAG-TC
* *
5186242 ATCAAGTATAA-TTCATGATCAAG
1 ATCAAG-AGAAGTTTATGATCAAG
5186265 ATTAAGTCAT
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
50 56 0.95
51 3 0.05
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.26
Consensus pattern (50 bp):
ATCAAGAGAAGTTTATGATCAAGTCATCAAGCAAAGCTCATGAACAAGTC
Found at i:5186322 original size:44 final size:44
Alignment explanation
Indices: 5186250--5186337 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
5186240 ATATCAAGTA
* * *
5186250 TAATTCATGATCAAGATTAAGTCATGAAGACCCTTGAAGTGAAG
1 TAATTCATGATCAAGATCAAGTCATGAAGACCCTTAAAGCGAAG
* * **
5186294 TAATTCATGATTATGATCAAGTTGTGAAGACCCTTAAAGCGAAG
1 TAATTCATGATCAAGATCAAGTCATGAAGACCCTTAAAGCGAAG
5186338 ATATCAAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (44 bp):
TAATTCATGATCAAGATCAAGTCATGAAGACCCTTAAAGCGAAG
Found at i:5189126 original size:14 final size:15
Alignment explanation
Indices: 5189107--5189135 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5189097 TATGGATAGA
5189107 TTGAG-TTTGACTTT
1 TTGAGTTTTGACTTT
5189121 TTGAGTTTTGACTTT
1 TTGAGTTTTGACTTT
5189136 CTTCAAGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.14, C:0.07, G:0.21, T:0.59
Consensus pattern (15 bp):
TTGAGTTTTGACTTT
Found at i:5192108 original size:67 final size:67
Alignment explanation
Indices: 5191957--5192129 Score: 159
Period size: 67 Copynumber: 2.6 Consensus size: 67
5191947 CATCCCTGTG
* * * *
5191957 GTATTCTTACCCCCAAACCAAGCTTAAGGAGGAAAAAAATGGTTCATTTGTCCAACTTAACCCTA
1 GTATACTTACCCCCACATCAAGCTTAAGAAGGAAAAAAATGGTTCATTTGTCCAACTTAACCCTA
*
5192022 TG
66 TA
** * * * * * *
5192024 GTATTTTTAACCTCACATCAAGCTTAAGAACGG-GAAAAGTGGTTTATTTGTCTAACTTAACCCT
1 GTATACTTACCCCCACATCAAGCTTAAGAA-GGAAAAAAATGGTTCATTTGTCCAACTTAACCCT
*
5192088 GTA
65 ATA
* **
5192091 GTGTACTTACCCCCACATCGGGCTTAAGTAAAGGAAAAA
1 GTATACTTACCCCCACATCAAGCTTAAG--AAGGAAAAA
5192130 TGGCACACTT
Statistics
Matches: 82, Mismatches: 20, Indels: 6
0.76 0.19 0.06
Matches are distributed among these distances:
67 73 0.89
68 4 0.05
69 5 0.06
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (67 bp):
GTATACTTACCCCCACATCAAGCTTAAGAAGGAAAAAAATGGTTCATTTGTCCAACTTAACCCTA
TA
Found at i:5201259 original size:6 final size:6
Alignment explanation
Indices: 5201243--5201276 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
5201233 TAGCATTTAT
* *
5201243 AAAATA GAAATA AAAATA AAAATA AAAACA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
5201277 AAATTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (6 bp):
AAAATA
Found at i:5208849 original size:28 final size:28
Alignment explanation
Indices: 5208817--5208871 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
5208807 GCCTTTAAAG
*
5208817 ATTATGCCTGATCCTTGAAAAGGCAATT
1 ATTATGCCTGATCCTTCAAAAGGCAATT
* * *
5208845 ATTATGCTTTATCCTTCAAAATGCAAT
1 ATTATGCCTGATCCTTCAAAAGGCAAT
5208872 GGTTATTCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (28 bp):
ATTATGCCTGATCCTTCAAAAGGCAATT
Found at i:5208877 original size:28 final size:28
Alignment explanation
Indices: 5208816--5208900 Score: 71
Period size: 28 Copynumber: 3.0 Consensus size: 28
5208806 AGCCTTTAAA
*
5208816 GATTATGCCTGATCCTTGAAAAGGCAAT
1 GATTATGCCTGATCCTTCAAAAGGCAAT
* * * *
5208844 TATTATGCTTTATCCTTCAAAATGCAAT
1 GATTATGCCTGATCCTTCAAAAGGCAAT
* * * * * *
5208872 GGTTATTCTTGAACCTTTAAAAGACAAT
1 GATTATGCCTGATCCTTCAAAAGGCAAT
5208900 G
1 G
5208901 TATTGATTTT
Statistics
Matches: 44, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Consensus pattern (28 bp):
GATTATGCCTGATCCTTCAAAAGGCAAT
Found at i:5219090 original size:13 final size:13
Alignment explanation
Indices: 5219067--5219098 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
5219057 TTCAAGTAAG
5219067 TTTCA-ATTTTTC
1 TTTCATATTTTTC
5219079 TTTCATATTTTTC
1 TTTCATATTTTTC
5219092 TTTCATA
1 TTTCATA
5219099 GATATGTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.19, C:0.16, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTCATATTTTTC
Done.