Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397259.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_147.0, 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: 10737078
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 75620 characters in sequence are not A, C, G, or T
File 10 of 22
Found at i:3989717 original size:29 final size:29
Alignment explanation
Indices: 3989557--3989862 Score: 126
Period size: 28 Copynumber: 10.6 Consensus size: 29
3989547 AATAAAAATA
* *
3989557 AAATATATTGACATTAAAAATATATTTAA-
1 AAATATATT-ATATTAAAAATATAATTAAG
3989586 AATATGATATTATA-TAAAAAT-TAATAATATA-
1 AA-AT-ATATTATATTAAAAATATAAT--TA-AG
* *
3989617 AAATATAAATATATTAAAAA-ATAA--AAT
1 AAATAT-ATTATATTAAAAATATAATTAAG
* * *
3989644 ATAA-ATATTATAATAATAAATAAAAAT-A-
1 A-AATATATTATATTAA-AAATATAATTAAG
* *
3989672 AAATATATGATATTAAAAATATATTTAAG
1 AAATATATTATATTAAAAATATAATTAAG
* *
3989701 AAATGATATTATA-TAAAAAT-TAATAATAT
1 AAAT-ATATTATATTAAAAATATAATTA-AG
* * *
3989730 AAATATAAATATATTAAAAATA-AAAT-AT
1 AAATAT-ATTATATTAAAAATATAATTAAG
* * *
3989758 AAA-ATATTATAATAATAAATAAAAAT-A-
1 AAATATATTATATTAA-AAATATAATTAAG
* * *
3989785 AAATATATGACATTAAAAATATATTTAAG
1 AAATATATTATATTAAAAATATAATTAAG
* *
3989814 AAATGATATTATA-TAAAAATTAATAATAAAA
1 AAAT-ATATTATATTAAAAA-T-ATAATTAAG
*
3989845 AAATATAAATATATTAAA
1 AAATAT-ATTATATTAAA
3989863 CTTATATTTT
Statistics
Matches: 213, Mismatches: 32, Indels: 61
0.70 0.10 0.20
Matches are distributed among these distances:
26 17 0.08
27 33 0.15
28 46 0.22
29 43 0.20
30 38 0.18
31 32 0.15
32 4 0.02
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (29 bp):
AAATATATTATATTAAAAATATAATTAAG
Found at i:3989735 original size:21 final size:22
Alignment explanation
Indices: 3989597--3989784 Score: 119
Period size: 21 Copynumber: 8.5 Consensus size: 22
3989587 ATATGATATT
3989597 ATATAAAA-ATTAATAATATAAA
1 ATATAAAATATTAATAATAT-AA
*
3989619 ATATAAATATATTAA-AAAATAA
1 ATATAAA-ATATTAATAATATAA
3989641 A-ATATAAATATT-ATAATAATAA
1 ATATA-AAATATTAATAAT-ATAA
*
3989663 ATA-AAAATA-AAAT-ATATGATA
1 ATATAAAATATTAATAATAT-A-A
* * * *
3989684 TTAAAAATATATTTAAGAAATGATATT
1 ATATAAA-ATA-TTAA-TAAT-ATA-A
3989711 ATATAAAA-ATTAATAATATAA
1 ATATAAAATATTAATAATATAA
*
3989732 ATATAAATATATTAAAAATA-AA
1 ATATAAA-ATATTAATAATATAA
3989754 ATATAAAATATT-ATAATAATAA
1 ATATAAAATATTAATAAT-ATAA
3989776 ATA-AAAATA
1 ATATAAAATA
3989785 AAATATATGA
Statistics
Matches: 133, Mismatches: 13, Indels: 41
0.71 0.07 0.22
Matches are distributed among these distances:
19 2 0.02
20 8 0.06
21 39 0.29
22 39 0.29
23 21 0.16
24 9 0.07
25 3 0.02
26 1 0.01
27 9 0.07
28 2 0.02
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (22 bp):
ATATAAAATATTAATAATATAA
Found at i:3989787 original size:26 final size:26
Alignment explanation
Indices: 3989725--3989790 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
3989715 AAAAATTAAT
* *
3989725 AATATAAATATAAATATATTAAAAATAA
1 AATATAAA-AT-ATTATAATAAAAATAA
3989753 AATATAAAATATTATAATAATAAATAA
1 AATATAAAATATTATAATAA-AAATAA
3989780 AA-ATAAAATAT
1 AATATAAAATAT
3989791 ATGACATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 17 0.49
27 10 0.29
28 8 0.23
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (26 bp):
AATATAAAATATTATAATAAAAATAA
Found at i:3990045 original size:15 final size:15
Alignment explanation
Indices: 3990027--3990065 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
3990017 CATTGCTATT
3990027 AATCACATTA-CTTGC
1 AATCACATTATC-TGC
*
3990042 AATCACATTATCTGT
1 AATCACATTATCTGC
3990057 AATCACATT
1 AATCACATT
3990066 GCATTGTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 21 0.95
16 1 0.05
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.36
Consensus pattern (15 bp):
AATCACATTATCTGC
Found at i:4002282 original size:30 final size:29
Alignment explanation
Indices: 4002248--4002321 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
4002238 CACTATTAAT
* *
4002248 TATAATAATTTATTTT-ATTTAAGATAAAAA
1 TATAAAAATTTATTTTAATAT-A-ATAAAAA
*
4002278 TATAAAAATTTAATTTAATATAATAAAAA
1 TATAAAAATTTATTTTAATATAATAAAAA
*
4002307 AATAAAAATTTATTT
1 TATAAAAATTTATTT
4002322 AAAAATTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 20 0.53
30 15 0.39
31 3 0.08
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (29 bp):
TATAAAAATTTATTTTAATATAATAAAAA
Found at i:4017905 original size:20 final size:20
Alignment explanation
Indices: 4017864--4017902 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
4017854 AGGTTCGACC
* *
4017864 AAACACCTCTAAAGATACCA
1 AAACACCTATAAACATACCA
4017884 AAACTACCTATAAACATAC
1 AAAC-ACCTATAAACATAC
4017903 AAATTTAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.51, C:0.28, G:0.03, T:0.18
Consensus pattern (20 bp):
AAACACCTATAAACATACCA
Found at i:4024678 original size:17 final size:17
Alignment explanation
Indices: 4024652--4024687 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
4024642 AGAGACACAC
4024652 AGAGACAGAGAGAAAAG
1 AGAGACAGAGAGAAAAG
* *
4024669 AGAGAGAGAGAGACAAG
1 AGAGACAGAGAGAAAAG
4024686 AG
1 AG
4024688 TTGGCTGATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.56, C:0.06, G:0.39, T:0.00
Consensus pattern (17 bp):
AGAGACAGAGAGAAAAG
Found at i:4024991 original size:23 final size:23
Alignment explanation
Indices: 4024948--4024991 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
4024938 GAGTTTAAAC
*
4024948 GAATTAGATATGTTATGTAATAT
1 GAATTAGATATGTTATATAATAT
*
4024971 GAATTAG-TTTGTTAATATAAT
1 GAATTAGATATGTT-ATATAAT
4024992 TAATTATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (23 bp):
GAATTAGATATGTTATATAATAT
Found at i:4029902 original size:20 final size:19
Alignment explanation
Indices: 4029875--4029916 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
4029865 ATAATACTTA
4029875 TTAAAATTTATTA-ATTATT
1 TTAAAATTTATTATA-TATT
4029894 TTAATAATTTATTATATATT
1 TTAA-AATTTATTATATATT
4029914 TTA
1 TTA
4029917 TTTTAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 16 0.76
21 1 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTAAAATTTATTATATATT
Found at i:4031365 original size:2 final size:2
Alignment explanation
Indices: 4031358--4031387 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4031348 TGTGGAGATA
4031358 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
4031388 CAACTCACTT
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:4034671 original size:20 final size:21
Alignment explanation
Indices: 4034613--4034672 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
4034603 AAAAGAATCA
*
4034613 AAAATGAAAAACGAAAAAACAG
1 AAAATGAAAAAC-AAATAACAG
* * *
4034635 AAAACGAATAACGAATAAC-G
1 AAAATGAAAAACAAATAACAG
4034655 AAAATGAAAAACAAATAA
1 AAAATGAAAAACAAATAA
4034673 TTAATTATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
20 16 0.52
21 5 0.16
22 10 0.32
ACGTcount: A:0.70, C:0.10, G:0.12, T:0.08
Consensus pattern (21 bp):
AAAATGAAAAACAAATAACAG
Found at i:4035076 original size:287 final size:290
Alignment explanation
Indices: 4034327--4035146 Score: 1173
Period size: 299 Copynumber: 2.8 Consensus size: 290
4034317 AATTAAAAAT
* *
4034327 AAAACCAAAAAACAAAAAATGAACAACGAAAAAAGAAAAATAGACAAATTAATTATTTAAAAAAA
1 AAAACGAAAAAACAAAAAATGAATAACG-AAAAAGAAAAATAGACAAATTAATTATTTAAAAAAA
* * * * * *
4034392 TCTCAACTTAATTATTGCTAGAGCCAAAAAAGGGTGAATAGACTATCAGTATGATAGTTCAAATA
65 TCTCAAATTAATTATTGCAAGAGCCAAAAAAGGGTGAATAGATTATCAATATGGTAGTACAAATA
* *
4034457 ACCATTTATCCACTTGCCTAAATAAAATTACAAAATAGAAAAGAACAATCATTCTTTGTCTTTCA
130 ACCATTTATCCACTTGTCTAAATAAAATTACAAAATAGGAAAGAACAATCATTCTTTGTCTTTCA
*
4034522 TAATTAATTTTAAAAAATGGAAACCTTGTTTTTGATAACAACAACATGTTTCCAAACTTACCTTT
195 TAATTAATTTTAAAAAATGGAAACCTTGTTTTTGGTAACAACAACATGTTTCCAAACTTACCTTT
* *
4034587 TCTAATTGTTATTTCCAAAAGAATCAAAAATGA
260 TCTAATTGTTATTT-CAAAAAAATC-AAAACGA
* * * * *
4034620 AAAACGAAAAAACAGAAAACGAATAACGAATAACGAAAATGAAAAACAAATAATTAATTATTTAA
1 AAAACGAAAAAACAAAAAATGAATAACGAA-AAAGAAAA--ATAGAC--A-AATTAATTATTT-A
* *
4034685 AAAAAATCTCAAATTAATTATTGCAAGAACCAAAAAAGAGT-ACATAGATTATCAATATGGTAGT
59 AAAAAATCTCAAATTAATTATTGCAAGAGCCAAAAAAGGGTGA-ATAGATTATCAATATGGTAGT
* * * * * *
4034749 ACAAATAACCATTTATCTACTTATCTGAATAAACTTACAAAATAGGAAAGAATAATCATTCTTTA
123 ACAAATAACCATTTATCCACTTGTCTAAATAAAATTACAAAATAGGAAAGAACAATCATTCTTTG
* * *
4034814 TCTTTCATAATTAAGTTTAAGAAATGGAAACCTTGTTTTTGGTAACAACAACATGTTTCCAGACT
188 TCTTTCATAATTAATTTTAAAAAATGGAAACCTTGTTTTTGGTAACAACAACATGTTTCCAAACT
* *
4034879 TACTTTTTTTAATTGTTATTT-AAAAAAAGTC-AAACG-
253 TACCTTTTCTAATTGTTATTTCAAAAAAA-TCAAAACGA
* *
4034915 AACAC-AATAAACAAAAAATGAATAACGAAAAAGAAAAATAGACAAATTAATTATTTAAAAAAAT
1 AAAACGAAAAAACAAAAAATGAATAACGAAAAAGAAAAATAGACAAATTAATTATTTAAAAAAAT
*
4034979 CTCAAATTAATTATTGCAAGAGTCAAAAAAGGGTGAATAGATTATCAATATGGTAGTACAAATAA
66 CTCAAATTAATTATTGCAAGAGCCAAAAAAGGGTGAATAGATTATCAATATGGTAGTACAAATAA
* *
4035044 CCATTTATCCACTTGTCTAAATAAAATTACAAAATAAGAAAGAACAATGATTCTTTGTCTTTCAT
131 CCATTTATCCACTTGTCTAAATAAAATTACAAAATAGGAAAGAACAATCATTCTTTGTCTTTCAT
4035109 AATTAATTTTAAAAAATGGAAACCTTGTTTTTGGTAAC
196 AATTAATTTTAAAAAATGGAAACCTTGTTTTTGGTAAC
4035147 NNNNNNNNNN
Statistics
Matches: 466, Mismatches: 51, Indels: 26
0.86 0.09 0.05
Matches are distributed among these distances:
287 161 0.35
288 13 0.03
289 1 0.00
291 4 0.01
292 2 0.00
293 38 0.08
294 21 0.05
295 8 0.02
296 4 0.01
297 7 0.02
298 15 0.03
299 192 0.41
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.30
Consensus pattern (290 bp):
AAAACGAAAAAACAAAAAATGAATAACGAAAAAGAAAAATAGACAAATTAATTATTTAAAAAAAT
CTCAAATTAATTATTGCAAGAGCCAAAAAAGGGTGAATAGATTATCAATATGGTAGTACAAATAA
CCATTTATCCACTTGTCTAAATAAAATTACAAAATAGGAAAGAACAATCATTCTTTGTCTTTCAT
AATTAATTTTAAAAAATGGAAACCTTGTTTTTGGTAACAACAACATGTTTCCAAACTTACCTTTT
CTAATTGTTATTTCAAAAAAATCAAAACGA
Found at i:4036789 original size:14 final size:14
Alignment explanation
Indices: 4036759--4036803 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
4036749 CTGTTATTTT
*
4036759 AAACAAGAAAC-AA
1 AAACAAAAAACGAA
4036772 AAACAAAAAACGAA
1 AAACAAAAAACGAA
* *
4036786 AAACGAAAAATGAA
1 AAACAAAAAACGAA
4036800 AAAC
1 AAAC
4036804 CGAAAACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 10 0.36
14 18 0.64
ACGTcount: A:0.76, C:0.13, G:0.09, T:0.02
Consensus pattern (14 bp):
AAACAAAAAACGAA
Found at i:4036800 original size:7 final size:7
Alignment explanation
Indices: 4036766--4036809 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
4036756 TTTAAACAAG
4036766 AAAC-AA
1 AAACGAA
*
4036772 AAACAAA
1 AAACGAA
4036779 AAACGAA
1 AAACGAA
4036786 AAACGAA
1 AAACGAA
*
4036793 AAATGAA
1 AAACGAA
4036800 AAACCGAA
1 AAA-CGAA
4036808 AA
1 AA
4036810 CTATTAAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
6 4 0.12
7 24 0.73
8 5 0.15
ACGTcount: A:0.75, C:0.14, G:0.09, T:0.02
Consensus pattern (7 bp):
AAACGAA
Found at i:4043657 original size:42 final size:42
Alignment explanation
Indices: 4043596--4043698 Score: 111
Period size: 42 Copynumber: 2.4 Consensus size: 42
4043586 TCATACCCAT
* * * *
4043596 ATTAATATTTGTAAATAAAATATTAATATTTTAATAT-ATTAATA
1 ATTAATA-TTATAAATAAAATAATAACA-TTTAA-ATGATCAATA
*
4043640 ATTAA-ATTATAAATAAAATAATAACATTTAAATGATCAATT
1 ATTAATATTATAAATAAAATAATAACATTTAAATGATCAATA
*
4043681 ATTAATATTTTAAATAAA
1 ATTAATATTATAAATAAA
4043699 TGATAAATTA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
40 2 0.04
41 15 0.29
42 28 0.55
43 1 0.02
44 5 0.10
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (42 bp):
ATTAATATTATAAATAAAATAATAACATTTAAATGATCAATA
Found at i:4044114 original size:26 final size:26
Alignment explanation
Indices: 4044085--4044134 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
4044075 TATTAATATT
* *
4044085 TAAATGATCAGTTATTAATATTTATA
1 TAAATGATAAATTATTAATATTTATA
* *
4044111 TAAATTATAAATTATTAATCTTTA
1 TAAATGATAAATTATTAATATTTA
4044135 AAAAATAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (26 bp):
TAAATGATAAATTATTAATATTTATA
Found at i:4044172 original size:159 final size:157
Alignment explanation
Indices: 4043904--4044403 Score: 632
Period size: 159 Copynumber: 3.1 Consensus size: 157
4043894 CCAAAAAAAA
* * *
4043904 TATAAATAAAATATTAATATTTAAATGATCAATTATTAAAATTTTAAAAAAAATTATAAATGATT
1 TATAAATAAAATATTAATATTTAAATGATCAGTTATTAAAA-TTT-AAATAAATTATAAATTATT
* * *
4043969 CATATTTAAAAATAAAATAAATTAAAAATAAATAATCATAATAACATTTAAATTATAAACAAAAT
64 AATATTTAAAAATAAAATAAAATAAAAATAATTAATCATAATAACATTTAAATTATAAACAAAAT
4044034 ATTAATATTTTCAAATATTAATTATTAAAT
129 ATTAATATTTT-AAATATTAATTATTAAAT
* * *
4044064 TATAAACAAAATATTAATATTTAAATGATCAGTTATTAATATTTATATAAATTATAAATTATTAA
1 TATAAATAAAATATTAATATTTAAATGATCAGTTATTAAAATTTAAATAAATTATAAATTATTAA
* * *
4044129 TCTTTAAAAAATAAAATAAAATAAAAATAATTAATGATAATAACATTTGAATTATAAACAAAATA
66 TATTT-AAAAATAAAATAAAATAAAAATAATTAATCATAATAACATTTAAATTATAAACAAAATA
* * *
4044194 TTAATATTTTAAAAATTTAATGATTACAT
130 TTAATATTTTAAATA-TTAATTATTAAAT
*
4044223 TATAAATTAAAA-ATTAATATTTAAATGATCAGTTATTAACATTATAAATAAATTATAAATTATT
1 TATAAA-TAAAATATTAATATTTAAATGATCAGTTATTAAAATT-TAAATAAATTATAAATTATT
* ** * * *
4044287 AATATTTAAGAAGGAAATAATAT-AAAATAAATT-ATTATAATAACA-TTAAATTATAAATAAAA
64 AATATTTAAAAATAAAATAAAATAAAAAT-AATTAATCATAATAACATTTAAATTATAAACAAAA
*
4044349 TATTAATA-TTTAAATTATCAATTATTAATAT
128 TATTAATATTTTAAA-TATTAATTATTAA-AT
* * *
4044380 TTTAAATAAATTATAAATTATTTA
1 TATAAATAAAATATTAA-TATTTA
4044404 TTACATTCGT
Statistics
Matches: 298, Mismatches: 33, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
156 18 0.06
157 35 0.12
158 47 0.16
159 131 0.44
160 67 0.22
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (157 bp):
TATAAATAAAATATTAATATTTAAATGATCAGTTATTAAAATTTAAATAAATTATAAATTATTAA
TATTTAAAAATAAAATAAAATAAAAATAATTAATCATAATAACATTTAAATTATAAACAAAATAT
TAATATTTTAAATATTAATTATTAAAT
Found at i:4044913 original size:28 final size:28
Alignment explanation
Indices: 4044869--4044923 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
4044859 TGTTACAAAT
4044869 AAATAAGTTACACCAAACATAAATAAAC
1 AAATAAGTTACACCAAACATAAATAAAC
* *
4044897 AAATAAGTTACATCAAATATAAATAAA
1 AAATAAGTTACACCAAACATAAATAAA
4044924 GTTTCAATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.62, C:0.13, G:0.04, T:0.22
Consensus pattern (28 bp):
AAATAAGTTACACCAAACATAAATAAAC
Found at i:4051753 original size:19 final size:19
Alignment explanation
Indices: 4051724--4051778 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
4051714 ATATTTTTTA
4051724 AAAAATCAATATATTAATAT
1 AAAAAT-AATATATTAATAT
* *
4051744 AAAAATAATATTTTACTAT
1 AAAAATAATATATTAATAT
**
4051763 ATTAATAATATTATTA
1 AAAAATAATA-TATTA
4051779 TTGTTATGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 19 0.66
20 10 0.34
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAAATAATATATTAATAT
Found at i:4055169 original size:30 final size:31
Alignment explanation
Indices: 4055135--4055192 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
4055125 TGGAGCCAAA
*
4055135 TAAAAAA-ATTAAATTTTCAATATAAATAAG
1 TAAAAAATAATAAATTTTCAATATAAATAAG
*
4055165 TAAAAAATAATAATTTTTCAATATAAAT
1 TAAAAAATAATAAATTTTCAATATAAAT
4055193 TTTTGAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (31 bp):
TAAAAAATAATAAATTTTCAATATAAATAAG
Found at i:4055365 original size:2 final size:2
Alignment explanation
Indices: 4055358--4055382 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4055348 TAATACATAC
4055358 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 A
4055383 CTTGTTAAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4064622 original size:22 final size:24
Alignment explanation
Indices: 4064576--4064623 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
4064566 TTTTAATTTA
*
4064576 TTTTTATTTTATAATTTATATTAT
1 TTTTTATTTTATAATTTATACTAT
*
4064600 TTTTTA-TTTAT-ATTTATCCTAT
1 TTTTTATTTTATAATTTATACTAT
4064622 TT
1 TT
4064624 GCTCAAATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 11 0.50
23 5 0.23
24 6 0.27
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTTTATTTTATAATTTATACTAT
Found at i:4065046 original size:14 final size:14
Alignment explanation
Indices: 4065013--4065054 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
4065003 TAATTCTCTT
*
4065013 TATTATATTTAACTA
1 TATTATATTTTA-TA
4065028 T-TTATATTTTATA
1 TATTATATTTTATA
4065041 TATTATAGTTTTAT
1 TATTATA-TTTTAT
4065055 CTTTAGTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 3 0.12
14 14 0.58
15 7 0.29
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (14 bp):
TATTATATTTTATA
Found at i:4068831 original size:22 final size:22
Alignment explanation
Indices: 4068806--4068847 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
4068796 GTGAGTTGTT
*
4068806 CATTGTGTGACTAGTTTGTAGG
1 CATTGCGTGACTAGTTTGTAGG
* *
4068828 CATTGCGTGATTGGTTTGTA
1 CATTGCGTGACTAGTTTGTA
4068848 AGTATTACGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.17, C:0.10, G:0.31, T:0.43
Consensus pattern (22 bp):
CATTGCGTGACTAGTTTGTAGG
Found at i:4068858 original size:22 final size:22
Alignment explanation
Indices: 4068819--4068862 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
4068809 TGTGTGACTA
* *
4068819 GTTTGTAGGCATTGCGTGATTG
1 GTTTGTAAGCATTACGTGATTG
*
4068841 GTTTGTAAGTATTACGTGATTG
1 GTTTGTAAGCATTACGTGATTG
4068863 ATTTTAGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.18, C:0.07, G:0.32, T:0.43
Consensus pattern (22 bp):
GTTTGTAAGCATTACGTGATTG
Found at i:4069697 original size:22 final size:22
Alignment explanation
Indices: 4069672--4069720 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
4069662 TTATTTATAG
4069672 GCATTAAGTGAATGGATATTAT
1 GCATTAAGTGAATGGATATTAT
**
4069694 GCATTGTGTGAATGGATATTAT
1 GCATTAAGTGAATGGATATTAT
4069716 GCATT
1 GCATT
4069721 GTTTGAATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.31, C:0.06, G:0.24, T:0.39
Consensus pattern (22 bp):
GCATTAAGTGAATGGATATTAT
Found at i:4069721 original size:22 final size:22
Alignment explanation
Indices: 4069679--4069736 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
4069669 TAGGCATTAA
4069679 GTGAATGGATATTATGCATTGT
1 GTGAATGGATATTATGCATTGT
4069701 GTGAATGGATATTATGCATTGT
1 GTGAATGGATATTATGCATTGT
* *
4069723 TTGAATGAATATTA
1 GTGAATGGATATTA
4069737 GGCCTTGCGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.31, C:0.03, G:0.24, T:0.41
Consensus pattern (22 bp):
GTGAATGGATATTATGCATTGT
Found at i:4074149 original size:21 final size:21
Alignment explanation
Indices: 4074123--4074180 Score: 107
Period size: 21 Copynumber: 2.7 Consensus size: 21
4074113 ATTTGCAACT
4074123 AGCCTTAGATCATGACTTCTA
1 AGCCTTAGATCATGACTTCTA
4074144 AGCCTTAGATCATGACTTCTA
1 AGCCTTAGATCATGACTTCTA
4074165 AGCCTTAGATGCATGA
1 AGCCTTAGAT-CATGA
4074181 ATTTGCAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 31 0.86
22 5 0.14
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.31
Consensus pattern (21 bp):
AGCCTTAGATCATGACTTCTA
Found at i:4074475 original size:27 final size:28
Alignment explanation
Indices: 4074423--4074480 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
4074413 AACATGTTAC
4074423 AAACAAATAGTTTATACCAAACATAAAT
1 AAACAAATAGTTTATACCAAACATAAAT
*
4074451 AAACAAATAAG-TTA-ATCAAACATAAAT
1 AAACAAAT-AGTTTATACCAAACATAAAT
4074478 AAA
1 AAA
4074481 GTTTCAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 15 0.54
28 11 0.39
29 2 0.07
ACGTcount: A:0.62, C:0.12, G:0.03, T:0.22
Consensus pattern (28 bp):
AAACAAATAGTTTATACCAAACATAAAT
Found at i:4077284 original size:29 final size:30
Alignment explanation
Indices: 4077261--4077319 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
4077251 TAAGTTTTTA
4077261 TATTTT-ATTTTAAATCAAATAAGTCTTAT
1 TATTTTCATTTTAAATCAAATAAGTCTTAT
*
4077290 TATTTTCATTTTTAATCAAATAAGTCTTAT
1 TATTTTCATTTTAAATCAAATAAGTCTTAT
4077320 AATTAATGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 6 0.21
30 22 0.79
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.53
Consensus pattern (30 bp):
TATTTTCATTTTAAATCAAATAAGTCTTAT
Found at i:4078256 original size:28 final size:31
Alignment explanation
Indices: 4078224--4078291 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 31
4078214 GAAATAAATC
*
4078224 ATTATTTTTTAT-TAT-ATTCAAATAAG-TTT
1 ATTATTTTTTATCT-TGAATCAAATAAGTTTT
*
4078253 -TTATATTTTATCTTGAATCAAATAAGTTTT
1 ATTATTTTTTATCTTGAATCAAATAAGTTTT
4078283 ATTATTTTT
1 ATTATTTTT
4078292 ATTTTTAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
28 11 0.34
29 11 0.34
30 3 0.09
31 7 0.22
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.59
Consensus pattern (31 bp):
ATTATTTTTTATCTTGAATCAAATAAGTTTT
Found at i:4078302 original size:30 final size:29
Alignment explanation
Indices: 4078224--4078302 Score: 81
Period size: 30 Copynumber: 2.7 Consensus size: 29
4078214 GAAATAAATC
* *
4078224 ATTATTTTT-TATTATATTCAAATAAGTTT
1 ATTATTTTTAT-TTTTAATCAAATAAGTTT
* *
4078253 -TTATATTTTATCTTGAATCAAATAAGTTTT
1 ATTAT-TTTTATTTTTAATCAAATAAG-TTT
4078283 ATTATTTTTATTTTTAATCA
1 ATTATTTTTATTTTTAATCA
4078303 NNNNNNNNNN
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
28 4 0.10
29 15 0.38
30 17 0.43
31 4 0.10
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.58
Consensus pattern (29 bp):
ATTATTTTTATTTTTAATCAAATAAGTTT
Found at i:4080601 original size:2 final size:2
Alignment explanation
Indices: 4080594--4080637 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
4080584 TTTTGTAAGC
4080594 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
4080636 TA
1 TA
4080638 AAATATTTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4084216 original size:2 final size:2
Alignment explanation
Indices: 4084205--4084250 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
4084195 TGCCTTGAAA
4084205 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
4084246 AT AT A
1 AT AT A
4084251 GCCTACAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4086302 original size:93 final size:94
Alignment explanation
Indices: 4086142--4086328 Score: 279
Period size: 93 Copynumber: 2.0 Consensus size: 94
4086132 ATTATCAATA
* * *
4086142 TACGAAATGATTGATCTATTCAAATTAACAAATATATAAAATAAGAGTAATAAATAATATTATTA
1 TACGAAATGATTGATCTATTCAAACTAACAAATATATAAAAAAAAAGTAATAAATAATATTATTA
*
4086207 CCTTCCGAACATTC-TAAGTGTGGCTTGAG
66 CCTTCCGAACA-TCATAAGTGTAGCTTGAG
** *
4086236 TACGAAATGATTGATCTATTTGAACTAACGAATAT-TAAAAAAAAAGTAATAAATAATATTATTA
1 TACGAAATGATTGATCTATTCAAACTAACAAATATATAAAAAAAAAGTAATAAATAATATTATTA
*
4086300 CCTTCCGAGCATCATAAGTGTAGCTTGAG
66 CCTTCCGAACATCATAAGTGTAGCTTGAG
4086329 GATTANNNNN
Statistics
Matches: 84, Mismatches: 8, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
92 2 0.02
93 51 0.61
94 31 0.37
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (94 bp):
TACGAAATGATTGATCTATTCAAACTAACAAATATATAAAAAAAAAGTAATAAATAATATTATTA
CCTTCCGAACATCATAAGTGTAGCTTGAG
Found at i:4088286 original size:28 final size:28
Alignment explanation
Indices: 4088246--4088334 Score: 160
Period size: 28 Copynumber: 3.2 Consensus size: 28
4088236 ATCTACTTTT
*
4088246 GTTTCACACAAGCATGCATAATAATTTC
1 GTTTTACACAAGCATGCATAATAATTTC
4088274 GTTTTACACAAGCATGCATAATAATTTC
1 GTTTTACACAAGCATGCATAATAATTTC
*
4088302 ATTTTACACAAGCATGCATAATAATTTC
1 GTTTTACACAAGCATGCATAATAATTTC
4088330 GTTTT
1 GTTTT
4088335 GGAAAAAAAG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 58 1.00
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (28 bp):
GTTTTACACAAGCATGCATAATAATTTC
Found at i:4090979 original size:29 final size:29
Alignment explanation
Indices: 4090937--4091096 Score: 120
Period size: 29 Copynumber: 5.6 Consensus size: 29
4090927 TCATAACTAG
4090937 GGATTACCACCTAATTAATGTAAGTAATA
1 GGATTACCACCTAATTAATGTAAGTAATA
**
4090966 GGATTACCACCTAATTTTTGCT-AG-AGA-A
1 GGATTACCACCTAATTAATG-TAAGTA-ATA
* *
4090994 GGAATTACCACCTAATTAAGGTAAGTTAT-
1 GG-ATTACCACCTAATTAATGTAAGTAATA
* * *
4091023 GGTATTATCACCTAATT-TTGCT-AG-AAAA
1 GG-ATTACCACCTAATTAATG-TAAGTAATA
* *
4091051 GGGATTACCACCTAATTAATGTAAGTTATG
1 -GGATTACCACCTAATTAATGTAAGTAATA
4091081 GGATTA-CACTCTAATT
1 GGATTACCAC-CTAATT
4091097 TTTGCTAGAA
Statistics
Matches: 101, Mismatches: 17, Indels: 26
0.70 0.12 0.18
Matches are distributed among these distances:
27 1 0.01
28 25 0.25
29 73 0.72
30 2 0.02
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (29 bp):
GGATTACCACCTAATTAATGTAAGTAATA
Found at i:4091035 original size:58 final size:56
Alignment explanation
Indices: 4090939--4091110 Score: 247
Period size: 58 Copynumber: 3.0 Consensus size: 56
4090929 ATAACTAGGG
* *
4090939 ATTACCACCTAATTAATGTAAGTAATAGGATTACCACCTAATTTTTGCTAGAGAAGGA
1 ATTACCACCTAATTAATGTAAGTTAT-GGATTA-CACCTAATTTTTGCTAGAAAAGGA
* *
4090997 ATTACCACCTAATTAAGGTAAGTTATGGTATTATCACCTAA-TTTTGCTAGAAAAGGG
1 ATTACCACCTAATTAATGTAAGTTATGG-ATTA-CACCTAATTTTTGCTAGAAAAGGA
4091054 ATTACCACCTAATTAATGTAAGTTATGGGATTACACTCTAATTTTTGCTAGAAAAGG
1 ATTACCACCTAATTAATGTAAGTTAT-GGATTACAC-CTAATTTTTGCTAGAAAAGG
4091111 GGCCTCAAGT
Statistics
Matches: 104, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
56 3 0.03
57 49 0.47
58 52 0.50
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (56 bp):
ATTACCACCTAATTAATGTAAGTTATGGATTACACCTAATTTTTGCTAGAAAAGGA
Found at i:4091885 original size:19 final size:20
Alignment explanation
Indices: 4091857--4091906 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
4091847 TACATAAATA
*
4091857 TAATTTTTTTCTAAAAGATT
1 TAATTTTTTTCAAAAAGATT
4091877 TAATTTTTTTCAAAAAGATT
1 TAATTTTTTTCAAAAAGATT
4091897 TAATTTTTTT
1 TAATTTTTTT
4091907 ATAACATGTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (20 bp):
TAATTTTTTTCAAAAAGATT
Found at i:4094719 original size:17 final size:17
Alignment explanation
Indices: 4094697--4094733 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
4094687 AATCTGCATT
4094697 ACATTGATCCACAAGTA
1 ACATTGATCCACAAGTA
4094714 ACATTGATCCACAAGTA
1 ACATTGATCCACAAGTA
4094731 ACA
1 ACA
4094734 ATCATAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.43, C:0.24, G:0.11, T:0.22
Consensus pattern (17 bp):
ACATTGATCCACAAGTA
Found at i:4110908 original size:19 final size:19
Alignment explanation
Indices: 4110884--4110926 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
4110874 GTCAAATTTT
4110884 AATGACAACAGTTGCAACA
1 AATGACAACAGTTGCAACA
* *
4110903 AATGACAATAGTTGTAACA
1 AATGACAACAGTTGCAACA
4110922 AATGA
1 AATGA
4110927 ATTTAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.49, C:0.14, G:0.16, T:0.21
Consensus pattern (19 bp):
AATGACAACAGTTGCAACA
Found at i:4119799 original size:2 final size:2
Alignment explanation
Indices: 4119792--4119832 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
4119782 TTATTTATTT
* * *
4119792 TA TA TA TA TA CA TA CA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4119833 GAGTGTGAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:4121789 original size:115 final size:113
Alignment explanation
Indices: 4121544--4121789 Score: 280
Period size: 114 Copynumber: 2.1 Consensus size: 113
4121534 TTCATCAACA
* * * *
4121544 ATTTAAGATAGAATATGCATTTTAGTTATAAGTTTTTCAATTTCCAGTTGTGTATAACAATAATG
1 ATTTAAGATA-AATATGCATTTTAGTTATAAGTTTTACAAATTCAAGATGTGTATAACAATAATG
* * * * * *
4121609 ATTTAGATTAAATATGCATATTACAACAGGGCTATATAGTTTACTAATG
65 ATTTAGACTAAATATGCATATAAAAACAAGGCTACATAGTTCACTAATG
*
4121658 ATTTAAGATTAAATATGCATATTTA-TTATAAGTTTTACAAATTCAAGATGTGTATATTATAATA
1 ATTTAAGA-TAAATATGCAT-TTTAGTTATAAGTTTTACAAATTCAAGATGTGTATA--ACAATA
* ** * *
4121722 ATGATTTAGACTAAATATGCCTATAAAAACAATTC-GCGTAGTTCACTAATG
62 ATGATTTAGACTAAATATGCATATAAAAACAAGGCTACATAGTTCACTAATG
4121773 ATTTAAGATCAAATATG
1 ATTTAAGAT-AAATATG
4121790 TTTGTTGGCT
Statistics
Matches: 111, Mismatches: 16, Indels: 9
0.82 0.12 0.07
Matches are distributed among these distances:
114 45 0.41
115 33 0.30
116 33 0.30
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (113 bp):
ATTTAAGATAAATATGCATTTTAGTTATAAGTTTTACAAATTCAAGATGTGTATAACAATAATGA
TTTAGACTAAATATGCATATAAAAACAAGGCTACATAGTTCACTAATG
Found at i:4129090 original size:25 final size:26
Alignment explanation
Indices: 4129062--4129112 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
4129052 GGTGCAATGT
*
4129062 ATCTAATCTTG-TAAATAATATGTTC
1 ATCTAATCTTGATAAACAATATGTTC
* *
4129087 ATCTAATTTTGATAAGCAATATGTTC
1 ATCTAATCTTGATAAACAATATGTTC
4129113 GAGTCTATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (26 bp):
ATCTAATCTTGATAAACAATATGTTC
Found at i:4130627 original size:22 final size:22
Alignment explanation
Indices: 4130562--4130635 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 22
4130552 TATAAAAAAA
4130562 TATTAATATTTTAATTATAAAT
1 TATTAATATTTTAATTATAAAT
* **
4130584 TA-TAA-AATTTAAAAAGTAAAT
1 TATTAATATTTTAATTA-TAAAT
* *
4130605 TATTAATATTTTAATTCTCAAT
1 TATTAATATTTTAATTATAAAT
4130627 TATTAATAT
1 TATTAATAT
4130636 CGTATATAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
20 7 0.17
21 10 0.24
22 18 0.44
23 6 0.15
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (22 bp):
TATTAATATTTTAATTATAAAT
Found at i:4130696 original size:92 final size:93
Alignment explanation
Indices: 4130557--4130727 Score: 231
Period size: 92 Copynumber: 1.8 Consensus size: 93
4130547 TGACTTATAA
* * ** *
4130557 AAAAATATTAATATTTTAATTATAAATTATAAAATTTAAAAAGTAAATTATTAATATTTTAATTC
1 AAAAATATTAATATTTTAATTAGAAACTATAAAATTTAAAAAGTAAATTATTAATAGATTAATTA
*
4130622 TCAATTATTAATATCGTATATAAATTTT
66 TAAATTATTAATATCGTATATAAATTTT
* *
4130650 AAAAA-ATTAATATTTTAATTGGAAACTA-AATAATTATAGAAA-TAAATTATTAATAGATTAAT
1 AAAAATATTAATATTTTAATTAGAAACTATAA-AATT-TAAAAAGTAAATTATTAATAGATTAAT
4130712 TATAAATTATTAATAT
64 TATAAATTATTAATAT
4130728 TTTTAAAAGG
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
91 2 0.03
92 56 0.82
93 10 0.15
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (93 bp):
AAAAATATTAATATTTTAATTAGAAACTATAAAATTTAAAAAGTAAATTATTAATAGATTAATTA
TAAATTATTAATATCGTATATAAATTTT
Found at i:4130811 original size:6 final size:6
Alignment explanation
Indices: 4130800--4130839 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
4130790 ACATATTAAC
*
4130800 AAATAA AAAT-- AAAGAA AAAT-A AAATAA AAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA A
4130840 TAAAAAGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
4 3 0.10
5 5 0.17
6 21 0.72
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:4130825 original size:21 final size:21
Alignment explanation
Indices: 4130800--4130844 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 21
4130790 ACATATTAAC
4130800 AAATAAAAATAAAGAA-AAATA
1 AAATAAAAATAAA-AATAAATA
4130821 AAATAAAAATAAAAATAAATA
1 AAATAAAAATAAAAATAAATA
4130842 AAA
1 AAA
4130845 AGTGTTAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (21 bp):
AAATAAAAATAAAAATAAATA
Found at i:4135626 original size:197 final size:197
Alignment explanation
Indices: 4135284--4135675 Score: 642
Period size: 197 Copynumber: 2.0 Consensus size: 197
4135274 AGCTATCCCT
*
4135284 TCCCCCCCTTTCTTCCCTTTTTAATTGGATTTCTAGTCTAGATGAAACGGTGTGGAAAGAAACGC
1 TCCCCCCCTTTCTTCCCTTTTTAATTGGATTCCTAGTCTAGATGAAACGGTGTGGAAAGAAACGC
* * * * *
4135349 AAGTGGATGATATGATCGCACCTGACTTAGCACTATTACTGTCCTTAAACAAGATACCTACGTTA
66 AAGTAGATGACATGATCGCACCTCACTTAGCACCATCACTGTCCTTAAACAAGATACCTACGTTA
* **
4135414 ATTGTTGTATTATCATAACTTTCTTCTTCT-TTTTGTTGGTTGGTTTTGCTGCCCTTGAATGATA
131 ATTGTTGTATTATCATAACTTTCTCCTTCTATTTTGTCAGTTGGTTTTGCTGCCCTTGAATGATA
4135478 CC
196 CC
* *
4135480 TCCCCCCACTTTCTTCCCTTTTTAATTGGATTCCTAGTCTAGATGAAATGGTGTGGAAAGAAATG
1 TCCCCCC-CTTTCTTCCCTTTTTAATTGGATTCCTAGTCTAGATGAAACGGTGTGGAAAGAAACG
* * *
4135545 CAAGTAGATGACCTGATCGCACCTCACTTATCACCATCACTGTCCTTAAACAAGATACCTATGTT
65 CAAGTAGATGACATGATCGCACCTCACTTAGCACCATCACTGTCCTTAAACAAGATACCTACGTT
4135610 AATTGTTGTATTATCATAACTTTCTCCTTCTATTTTGTCAGTTGGTTTTGCTGCCCTTGAATGAT
130 AATTGTTGTATTATCATAACTTTCTCCTTCTATTTTGTCAGTTGGTTTTGCTGCCCTTGAATGAT
4135675 A
195 A
4135676 TAACTGACTC
Statistics
Matches: 180, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
196 7 0.04
197 141 0.78
198 32 0.18
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (197 bp):
TCCCCCCCTTTCTTCCCTTTTTAATTGGATTCCTAGTCTAGATGAAACGGTGTGGAAAGAAACGC
AAGTAGATGACATGATCGCACCTCACTTAGCACCATCACTGTCCTTAAACAAGATACCTACGTTA
ATTGTTGTATTATCATAACTTTCTCCTTCTATTTTGTCAGTTGGTTTTGCTGCCCTTGAATGATA
CC
Found at i:4136306 original size:38 final size:37
Alignment explanation
Indices: 4136241--4136313 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 37
4136231 TGATAAAAGG
4136241 TATGTTCATTAATTCTACTAAACAATATGTTCAAGTC
1 TATGTTCATTAATTCTACTAAACAATATGTTCAAGTC
* * * *
4136278 TATGTTCATCTAATTTTCCTACATAATATGTTCAAG
1 TATGTTCAT-TAATTCTACTAAACAATATGTTCAAG
4136314 CATTAGTTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 9 0.29
38 22 0.71
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.42
Consensus pattern (37 bp):
TATGTTCATTAATTCTACTAAACAATATGTTCAAGTC
Found at i:4138048 original size:19 final size:19
Alignment explanation
Indices: 4138009--4138048 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4137999 TATATATTGG
*
4138009 TTTAGGATATTTTAGATTA
1 TTTAGGATATTTTAGAGTA
* *
4138028 TTTAGGTTATTTTATAGTA
1 TTTAGGATATTTTAGAGTA
4138047 TT
1 TT
4138049 AATTAGTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (19 bp):
TTTAGGATATTTTAGAGTA
Found at i:4143166 original size:15 final size:15
Alignment explanation
Indices: 4143143--4143172 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4143133 TTAGCTAGTA
*
4143143 TTAATTTATTTATAT
1 TTAAATTATTTATAT
4143158 TTAAATTATTTATAT
1 TTAAATTATTTATAT
4143173 ATTTAATAAT
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTAAATTATTTATAT
Found at i:4151540 original size:30 final size:31
Alignment explanation
Indices: 4151505--4151564 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 31
4151495 AACTTTGGAA
4151505 AAGACTAAATTGAAAA-GAAAAAAATATTGG
1 AAGACTAAATTGAAAAGGAAAAAAATATTGG
*
4151535 AAGACTAAATTGAAAAGGAAGAAAATATTG
1 AAGACTAAATTGAAAAGGAAAAAAATATTG
4151565 AGGGACTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 16 0.57
31 12 0.43
ACGTcount: A:0.58, C:0.03, G:0.18, T:0.20
Consensus pattern (31 bp):
AAGACTAAATTGAAAAGGAAAAAAATATTGG
Found at i:4153152 original size:59 final size:58
Alignment explanation
Indices: 4152956--4153155 Score: 150
Period size: 59 Copynumber: 3.3 Consensus size: 58
4152946 AATGGTTTTA
* * * *
4152956 GTGGGGCAAAGCAATACCATTGGAGTAAAGGGTCGGAGAACTTGAAATGTATTGCCTTG
1 GTGGGGCAAAGGAATACCACTGG-GTAAAGGGTCGGAGTACTCGAAATGTATTGCCTTG
* ** * * * * * * **
4153015 ATAAGGCGAAGGAATACCACTAGAGATATTAAGGGTCAGAGTACTC-AAATTGCATGGCGTCA
1 GTGGGGCAAAGGAATACCACT-G-GGTA--AAGGGTCGGAGTACTCGAAA-TGTATTGCCTTG
* * * *
4153077 GTGGAGCAAAGTAATACCACTGCGGTAAAAGGTCGGAGTACCCGAAATGTATTGCCTTG
1 GTGGGGCAAAGGAATACCACTG-GGTAAAGGGTCGGAGTACTCGAAATGTATTGCCTTG
*
4153136 GTGGGGCGAAGGAATACCAC
1 GTGGGGCAAAGGAATACCAC
4153156 AAGAGATATT
Statistics
Matches: 101, Mismatches: 34, Indels: 12
0.69 0.23 0.08
Matches are distributed among these distances:
59 52 0.51
60 6 0.06
61 8 0.08
62 35 0.35
ACGTcount: A:0.33, C:0.17, G:0.30, T:0.21
Consensus pattern (58 bp):
GTGGGGCAAAGGAATACCACTGGGTAAAGGGTCGGAGTACTCGAAATGTATTGCCTTG
Found at i:4154793 original size:30 final size:30
Alignment explanation
Indices: 4154758--4154824 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
4154748 TATAAAAGTC
4154758 TATTTGATTCAAAATAAAAGTAAAAGAAAT
1 TATTTGATTCAAAATAAAAGTAAAAGAAAT
* * *
4154788 TATTTGGTTCAAAATAAAAGTATAAGAGAT
1 TATTTGATTCAAAATAAAAGTAAAAGAAAT
*
4154818 TAATTGA
1 TATTTGA
4154825 ACGTAATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.51, C:0.03, G:0.13, T:0.33
Consensus pattern (30 bp):
TATTTGATTCAAAATAAAAGTAAAAGAAAT
Found at i:4154862 original size:59 final size:59
Alignment explanation
Indices: 4154789--4154900 Score: 161
Period size: 59 Copynumber: 1.9 Consensus size: 59
4154779 AAAAGAAATT
* * *
4154789 ATTTGGTTCAAAATAAAAGTATAAGAGATTAATTGAACGTAATAAAAATATAAGAGCTC
1 ATTTGGCTCAAAATAAAAATATAAGAGATTAATTGAACGTAATAAAAAAATAAGAGCTC
* ** *
4154848 ATTTGGCTCAAAATAAAAATATAAGAGTTTGGTTGAAGGTAATAAAAAAATAA
1 ATTTGGCTCAAAATAAAAATATAAGAGATTAATTGAACGTAATAAAAAAATAA
4154901 AAGTTTATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 46 1.00
ACGTcount: A:0.50, C:0.05, G:0.16, T:0.29
Consensus pattern (59 bp):
ATTTGGCTCAAAATAAAAATATAAGAGATTAATTGAACGTAATAAAAAAATAAGAGCTC
Found at i:4154911 original size:59 final size:59
Alignment explanation
Indices: 4154787--4154911 Score: 160
Period size: 59 Copynumber: 2.1 Consensus size: 59
4154777 GTAAAAGAAA
* * * *
4154787 TTATTTGGTTCAAAATAAAAGTATAAGAGATTAATTGAACGTAATAAAAATATAAGAGC
1 TTATTTGGCTCAAAATAAAAATATAAGAGATTAATTGAACGTAATAAAAAAATAAAAGC
* * ** * *
4154846 TCATTTGGCTCAAAATAAAAATATAAGAGTTTGGTTGAAGGTAATAAAAAAATAAAAGT
1 TTATTTGGCTCAAAATAAAAATATAAGAGATTAATTGAACGTAATAAAAAAATAAAAGC
4154905 TTATTTG
1 TTATTTG
4154912 AATTTTTTAA
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.47, C:0.05, G:0.16, T:0.32
Consensus pattern (59 bp):
TTATTTGGCTCAAAATAAAAATATAAGAGATTAATTGAACGTAATAAAAAAATAAAAGC
Found at i:4161960 original size:103 final size:103
Alignment explanation
Indices: 4161781--4161969 Score: 288
Period size: 103 Copynumber: 1.8 Consensus size: 103
4161771 CAAGTTTCTT
* *
4161781 TGACTTTTCTCAATCTATACAGTTTGTCAATTTAATGAGATCTTGGTTAGATGATAGTAGACACA
1 TGACTTTTCTCAATCTATACAGTTTGTCAATTCAATGAGATCCTGGTTAGATGATAGTAGACACA
4161846 CAAACATTACAGTAAGCCATATCTTTGTCAATTTAATG
66 CAAACATTACAGTAAGCCATATCTTTGTCAATTTAATG
** * * * * *
4161884 TGACTTTTCTCTGTCTATGCATTTTGTCAATTCAATGAGATCCTGGTTATATGATAGTTGACATA
1 TGACTTTTCTCAATCTATACAGTTTGTCAATTCAATGAGATCCTGGTTAGATGATAGTAGACACA
*
4161949 CAGACATTACAGTAAGCCATA
66 CAAACATTACAGTAAGCCATA
4161970 CCTTGAGCAC
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
103 76 1.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37
Consensus pattern (103 bp):
TGACTTTTCTCAATCTATACAGTTTGTCAATTCAATGAGATCCTGGTTAGATGATAGTAGACACA
CAAACATTACAGTAAGCCATATCTTTGTCAATTTAATG
Found at i:4174796 original size:34 final size:34
Alignment explanation
Indices: 4174741--4174810 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 34
4174731 TTTATTAAAA
* * *
4174741 TAAAATATTAATTTTTAAAATTT-TTTTTATTTAT
1 TAAAATATAAATTTATAAAATTTATATTT-TTTAT
4174775 TAAAATATAAATTTA-ATAAATTTATATTTTTTAT
1 TAAAATATAAATTTATA-AAATTTATATTTTTTAT
4174809 TA
1 TA
4174811 TTAATTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
33 1 0.03
34 26 0.84
35 4 0.13
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (34 bp):
TAAAATATAAATTTATAAAATTTATATTTTTTAT
Found at i:4174892 original size:33 final size:32
Alignment explanation
Indices: 4174855--4174941 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 32
4174845 TTTTAATTAC
*
4174855 ATATATTTTATTTTTATTTTTTATTATAATCTT
1 ATATATTTTATTTTTATTTTTTAATATAAT-TT
*
4174888 ATATATTTTATTTTTATATATTTAATATAATTT
1 ATATATTTTATTTTTAT-TTTTTAATATAATTT
* *
4174921 TTATATTATATATTTTATTTT
1 ATATATTTTAT-TTTTATTTT
4174942 AAATTTTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
33 30 0.64
34 17 0.36
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (32 bp):
ATATATTTTATTTTTATTTTTTAATATAATTT
Found at i:4174920 original size:25 final size:23
Alignment explanation
Indices: 4174855--4174935 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 23
4174845 TTTTAATTAC
4174855 ATATATTT-TAT-TTTTATTTTTT
1 ATATATTTATATATTTTA-TTTTT
4174877 ATTATAATCTTATATATTTTATTTTT
1 A-TAT-AT-TTATATATTTTATTTTT
*
4174903 ATATATTTAATATAATTTT-TATATT
1 ATATATTT-ATAT-ATTTTAT-TTTT
4174928 ATATATTT
1 ATATATTT
4174936 TATTTTAAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 13
0.78 0.02 0.20
Matches are distributed among these distances:
22 1 0.02
23 5 0.10
24 9 0.18
25 21 0.42
26 9 0.18
27 5 0.10
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (23 bp):
ATATATTTATATATTTTATTTTT
Found at i:4174951 original size:82 final size:81
Alignment explanation
Indices: 4174865--4175051 Score: 222
Period size: 82 Copynumber: 2.3 Consensus size: 81
4174855 ATATATTTTA
*
4174865 TTTTTATTTTTTATTATAATCTTATATATTTTAT-TTTTA-TATATTTAATATAATTTTTATATT
1 TTTTTATTTTTTATTATAATATTA-ATATTTTATATTTTATTATATTT--TATAATTTTTATATT
4174928 ATATATTTTATTTTAA-AT
63 ATATATTTTATTTTAATAT
* * * * *
4174946 TTTTT-TCTTGTATTGTATAAATATTAATTTTTTATATTTTATTTTATTTTTTAATTTTTATATT
1 TTTTTATTTTTTA-T-TAT-AATATTAATATTTTATATTTTATTATATTTTATAATTTTTATATT
4175010 ATATATTTTATTTTAATAT
63 ATATATTTTATTTTAATAT
*
4175029 TTTTTA-TTTTAATTATAATATTA
1 TTTTTATTTTTTATTATAATATTA
4175052 CAAAATATTT
Statistics
Matches: 90, Mismatches: 9, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
80 12 0.13
81 9 0.10
82 42 0.47
83 21 0.23
84 6 0.07
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (81 bp):
TTTTTATTTTTTATTATAATATTAATATTTTATATTTTATTATATTTTATAATTTTTATATTATA
TATTTTATTTTAATAT
Found at i:4174987 original size:7 final size:7
Alignment explanation
Indices: 4174975--4175039 Score: 57
Period size: 7 Copynumber: 9.7 Consensus size: 7
4174965 AATATTAATT
4174975 TTTTATA
1 TTTTATA
4174982 -TTT-TA
1 TTTTATA
*
4174987 TTTTATT
1 TTTTATA
4174994 TTTTA-A
1 TTTTATA
4175000 TTTTTATA
1 -TTTTATA
*
4175008 TTATATA
1 TTTTATA
4175015 TTTTAT-
1 TTTTATA
*
4175021 TTTAATA
1 TTTTATA
*
4175028 TTTTTTA
1 TTTTATA
4175035 TTTTA
1 TTTTA
4175040 ATTATAATAT
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
5 2 0.04
6 11 0.24
7 31 0.69
8 1 0.02
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTATA
Found at i:4175016 original size:33 final size:33
Alignment explanation
Indices: 4174978--4175050 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 33
4174968 ATTAATTTTT
4174978 TATATTTTATTTT-AT-TTTTTAATTTTTATATTA
1 TATATTTTATTTTAATATTTTTAA-TTTTA-ATTA
*
4175011 TATATTTTATTTTAATATTTTTTATTTTAATTA
1 TATATTTTATTTTAATATTTTTAATTTTAATTA
4175044 TAATATT
1 T-ATATT
4175051 ACAAAATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
33 18 0.50
34 12 0.33
35 6 0.17
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (33 bp):
TATATTTTATTTTAATATTTTTAATTTTAATTA
Found at i:4175028 original size:15 final size:15
Alignment explanation
Indices: 4175001--4175041 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
4174991 ATTTTTTAAT
*
4175001 TTTTATATT-ATATA
1 TTTTATTTTAATATA
*
4175015 TTTTATTTTAATATT
1 TTTTATTTTAATATA
4175030 TTTTATTTTAAT
1 TTTTATTTTAAT
4175042 TATAATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 8 0.33
15 16 0.67
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTATTTTAATATA
Found at i:4175049 original size:21 final size:21
Alignment explanation
Indices: 4174985--4175050 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
4174975 TTTTATATTT
*
4174985 TATTTTATT-TTTTAATTTTTA
1 TATTTT-TTATTTTAATTTTAA
* *
4175006 TATTATATATTTT-ATTTTAA
1 TATTTTTTATTTTAATTTTAA
*
4175026 TATTTTTTATTTTAATTATAA
1 TATTTTTTATTTTAATTTTAA
4175047 TATT
1 TATT
4175051 ACAAAATATT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
20 18 0.49
21 19 0.51
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TATTTTTTATTTTAATTTTAA
Found at i:4175564 original size:2 final size:2
Alignment explanation
Indices: 4175557--4175586 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4175547 TCTAGTTTTA
4175557 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
4175587 TACGGGCCAG
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:4178919 original size:98 final size:98
Alignment explanation
Indices: 4178748--4178945 Score: 288
Period size: 98 Copynumber: 2.0 Consensus size: 98
4178738 AGTTTCCTCT
* * * * * *
4178748 CATCTCTTCATCGGTCTATCCTTCCCCCGTTTGGACTGAATATTCTCCATTAAATCACATAATCA
1 CATCTCTTCATCAGACTACCCTTCCCCCGTTTCGAATGAACATTCTCCATTAAATCACATAATCA
*
4178813 AAAAGGAGCATTTAGGCCTTTGTCCCACAGGAC
66 AAAAGGAGCATTTAGCCCTTTGTCCCACAGGAC
* **
4178846 CATCTCTTCATCAGACTACCCTTCCCCCTTTTCGAATGAACATTCTCCATTAAATTGCATAATCA
1 CATCTCTTCATCAGACTACCCTTCCCCCGTTTCGAATGAACATTCTCCATTAAATCACATAATCA
* *
4178911 AAATGGAGCATTTAGCCCTTTGTCCCACATGAC
66 AAAAGGAGCATTTAGCCCTTTGTCCCACAGGAC
4178944 CA
1 CA
4178946 AACCAACTTA
Statistics
Matches: 88, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
98 88 1.00
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.31
Consensus pattern (98 bp):
CATCTCTTCATCAGACTACCCTTCCCCCGTTTCGAATGAACATTCTCCATTAAATCACATAATCA
AAAAGGAGCATTTAGCCCTTTGTCCCACAGGAC
Found at i:4182109 original size:30 final size:30
Alignment explanation
Indices: 4182073--4182131 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
4182063 GGCAAAATTT
* *
4182073 CTCTAAATGATTAAGAATATCTCCTAAATA
1 CTCTAAATAATTAACAATATCTCCTAAATA
4182103 CTCTAAATAATTAACAATATCTCCTAAAT
1 CTCTAAATAATTAACAATATCTCCTAAAT
4182132 TATAACAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.34
Consensus pattern (30 bp):
CTCTAAATAATTAACAATATCTCCTAAATA
Found at i:4196389 original size:17 final size:16
Alignment explanation
Indices: 4196361--4196395 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
4196351 GACATCTCGG
4196361 CTTCCTTCATCTCCTT
1 CTTCCTTCATCTCCTT
*
4196377 CTTCCTGTCATCTTCTT
1 CTTCCT-TCATCTCCTT
4196394 CT
1 CT
4196396 GGGTTGAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.06, C:0.40, G:0.03, T:0.51
Consensus pattern (16 bp):
CTTCCTTCATCTCCTT
Found at i:4198253 original size:34 final size:36
Alignment explanation
Indices: 4198194--4198299 Score: 108
Period size: 34 Copynumber: 2.9 Consensus size: 36
4198184 AGATATTCTT
* * * * *
4198194 TAAAAATCAATCACATAATATCTAAAAATTAATCATG
1 TAAAAAT-TATCACGTAATACCTAAAAATCAATCACG
*
4198231 T-AATATT-TCACGTAATACCTAAAAATCAATCACG
1 TAAAAATTATCACGTAATACCTAAAAATCAATCACG
*
4198265 TAAAAATTAAGTCACGTAATACTTAAAAATCAATC
1 TAAAAATT-A-TCACGTAATACCTAAAAATCAATC
4198300 TCCTAATCAA
Statistics
Matches: 57, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
34 24 0.42
35 5 0.09
36 4 0.07
37 1 0.02
38 23 0.40
ACGTcount: A:0.50, C:0.16, G:0.05, T:0.29
Consensus pattern (36 bp):
TAAAAATTATCACGTAATACCTAAAAATCAATCACG
Found at i:4198290 original size:16 final size:16
Alignment explanation
Indices: 4198250--4198283 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
4198240 ACGTAATACC
*
4198250 TAAAAATCAA-TCACG
1 TAAAAATTAAGTCACG
4198265 TAAAAATTAAGTCACG
1 TAAAAATTAAGTCACG
4198281 TAA
1 TAA
4198284 TACTTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.53, C:0.15, G:0.09, T:0.24
Consensus pattern (16 bp):
TAAAAATTAAGTCACG
Found at i:4201597 original size:15 final size:15
Alignment explanation
Indices: 4201577--4201609 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
4201567 TTCCGTAGCC
*
4201577 TTAAAAAATGAATTT
1 TTAAAAAATAAATTT
4201592 TTAAAAAATAAATTT
1 TTAAAAAATAAATTT
4201607 TTA
1 TTA
4201610 TTTCGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
TTAAAAAATAAATTT
Found at i:4225739 original size:27 final size:27
Alignment explanation
Indices: 4225685--4225739 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
4225675 CATAATATAT
* *
4225685 AAAAATAAAAAACTTATATAATATAAA
1 AAAAATAAAAAACTTATATAAGACAAA
* * *
4225712 AAAAATAAACATCTTCTATAAGACAAA
1 AAAAATAAAAAACTTATATAAGACAAA
4225739 A
1 A
4225740 CATATCTAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.65, C:0.09, G:0.02, T:0.24
Consensus pattern (27 bp):
AAAAATAAAAAACTTATATAAGACAAA
Found at i:4228259 original size:3 final size:3
Alignment explanation
Indices: 4228251--4228276 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4228241 CGTCTATTGT
4228251 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
4228277 TTAACTGTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:4229661 original size:14 final size:15
Alignment explanation
Indices: 4229636--4229664 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4229626 AGCAAGTTTT
4229636 TATTTTTAAATTAAC
1 TATTTTTAAATTAAC
4229651 TATTTTT-AATTAAC
1 TATTTTTAAATTAAC
4229665 CAAAAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTTTTAAATTAAC
Found at i:4244392 original size:15 final size:15
Alignment explanation
Indices: 4244354--4244393 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
4244344 TGTTATTTTT
4244354 CCTGTAATCACATTA
1 CCTGTAATCACATTA
* *
4244369 CTTGCAATCACATTA
1 CCTGTAATCACATTA
4244384 CCTGTAATCA
1 CCTGTAATCA
4244394 AATTGCATTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.33, C:0.28, G:0.07, T:0.33
Consensus pattern (15 bp):
CCTGTAATCACATTA
Found at i:4245395 original size:10 final size:10
Alignment explanation
Indices: 4245353--4245407 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
4245343 AGAATTTATT
*
4245353 TAATTAAATA
1 TAATAAAATA
4245363 TAATAAAA-A
1 TAATAAAATA
*
4245372 T-ATAAAAATT
1 TAAT-AAAATA
*
4245382 TAATTAAATA
1 TAATAAAATA
*
4245392 TAATAAAAAA
1 TAATAAAATA
4245402 TAATAA
1 TAATAA
4245408 TTTATTTAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
8 2 0.06
9 6 0.17
10 26 0.72
11 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
TAATAAAATA
Found at i:4245409 original size:28 final size:29
Alignment explanation
Indices: 4245350--4245416 Score: 109
Period size: 29 Copynumber: 2.3 Consensus size: 29
4245340 ACAAGAATTT
4245350 ATTTAATTAAATATAATAAAAATATAAAA
1 ATTTAATTAAATATAATAAAAATATAAAA
*
4245379 ATTTAATTAAATATAATAAAAA-ATAATA
1 ATTTAATTAAATATAATAAAAATATAAAA
*
4245407 ATTTATTTAA
1 ATTTAATTAA
4245417 TTTTTTTTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
28 14 0.39
29 22 0.61
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (29 bp):
ATTTAATTAAATATAATAAAAATATAAAA
Found at i:4253393 original size:28 final size:28
Alignment explanation
Indices: 4253353--4253412 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
4253343 AAAATTACTG
4253353 ACAAATTTACTAGGGATCCTATATGCTA
1 ACAAATTTACTAGGGATCCTATATGCTA
4253381 ACAAATTTACTAGGGATCCTATATGCTA
1 ACAAATTTACTAGGGATCCTATATGCTA
4253409 ACAA
1 ACAA
4253413 GACATTAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.30
Consensus pattern (28 bp):
ACAAATTTACTAGGGATCCTATATGCTA
Found at i:4260983 original size:65 final size:67
Alignment explanation
Indices: 4260902--4261034 Score: 252
Period size: 67 Copynumber: 2.0 Consensus size: 67
4260892 ATGACTCCAT
4260902 GACAAGTGGTATCAGAGC-AAC-GGACCTCATCTGACTCACGCCAAGCGCTTCAACGGATCGAGG
1 GACAAGTGGTATCAGAGCAAACTGGACCTCATCTGACTCACGCCAAGCGCTTCAACGGATCGAGG
4260965 TA
66 TA
4260967 GACAAGTGGTATCAGAGCAAACTGGACCTCATCTGACTCACGCCAAGCGCTTCAACGGATCGAGG
1 GACAAGTGGTATCAGAGCAAACTGGACCTCATCTGACTCACGCCAAGCGCTTCAACGGATCGAGG
4261032 TA
66 TA
4261034 G
1 G
4261035 GCAGGGTGGT
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
65 18 0.27
66 3 0.05
67 45 0.68
ACGTcount: A:0.29, C:0.27, G:0.26, T:0.17
Consensus pattern (67 bp):
GACAAGTGGTATCAGAGCAAACTGGACCTCATCTGACTCACGCCAAGCGCTTCAACGGATCGAGG
TA
Found at i:4261680 original size:206 final size:206
Alignment explanation
Indices: 4261326--4261738 Score: 808
Period size: 206 Copynumber: 2.0 Consensus size: 206
4261316 TTAAAACTAG
4261326 TAGTTTATTGTATCGTGGGGATATGAATGAGACATTTTCCAGTTTTAATTTGGCTATGAGGTCTC
1 TAGTTTATTGTATCGTGGGGATATGAATGAGACATTTTCCAGTTTTAATTTGGCTATGAGGTCTC
4261391 CTTCTTCTTCTTTTTCTTTGGCTTTACTCACTATTGTTGTTTTTTCAAGATTTATTGTTCTTAAA
66 CTTCTTCTTCTTTTTCTTTGGCTTTACTCACTATTGTTGTTTTTTCAAGATTTATTGTTCTTAAA
4261456 GTTAAAATGGTATCAAAGCGTTTTCTAAATCTTGTGGGACTATGAAAAAGGGTTTTTTTTAGTAT
131 GTTAAAATGGTATCAAAGCGTTTTCTAAATCTTGTGGGACTATGAAAAAGGGTTTTTTTTAGTAT
4261521 TGATTTTCGGT
196 TGATTTTCGGT
*
4261532 TAGTTTATTGTATCGTGGGGATATGAATGAGACATTTTTCAGTTTTAATTTGGCTATGAGGTCTC
1 TAGTTTATTGTATCGTGGGGATATGAATGAGACATTTTCCAGTTTTAATTTGGCTATGAGGTCTC
4261597 CTTCTTCTTCTTTTTCTTTGGCTTTACTCACTATTGTTGTTTTTTCAAGATTTATTGTTCTTAAA
66 CTTCTTCTTCTTTTTCTTTGGCTTTACTCACTATTGTTGTTTTTTCAAGATTTATTGTTCTTAAA
*
4261662 GTTAAAATGGTATCAAAGCGTTTTCTAAATCTTGTGGGATTATGAAAAAGGGTTTTTTTTAGTAT
131 GTTAAAATGGTATCAAAGCGTTTTCTAAATCTTGTGGGACTATGAAAAAGGGTTTTTTTTAGTAT
4261727 TGATTTTCGGT
196 TGATTTTCGGT
4261738 T
1 T
4261739 TGATAAGCTT
Statistics
Matches: 205, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
206 205 1.00
ACGTcount: A:0.22, C:0.11, G:0.19, T:0.48
Consensus pattern (206 bp):
TAGTTTATTGTATCGTGGGGATATGAATGAGACATTTTCCAGTTTTAATTTGGCTATGAGGTCTC
CTTCTTCTTCTTTTTCTTTGGCTTTACTCACTATTGTTGTTTTTTCAAGATTTATTGTTCTTAAA
GTTAAAATGGTATCAAAGCGTTTTCTAAATCTTGTGGGACTATGAAAAAGGGTTTTTTTTAGTAT
TGATTTTCGGT
Found at i:4274248 original size:62 final size:62
Alignment explanation
Indices: 4274174--4274300 Score: 168
Period size: 62 Copynumber: 2.0 Consensus size: 62
4274164 TATTATTTTT
* * *
4274174 TATTCATATTAATAATTTAATATAAAATTATTTTAAAGGC-CTATTTAAAATATATATATAATA
1 TATTCATATTAATAAATTAATAAAAAATTATTTTAAAGGCTC-A-TTAAAAAATATATATAATA
** *
4274237 TATT-ATATTAATAAATTAATAAAAAATTATTTTGGAGGCTCATTAAAAAATATATGTAATA
1 TATTCATATTAATAAATTAATAAAAAATTATTTTAAAGGCTCATTAAAAAATATATATAATA
4274298 TAT
1 TAT
4274301 AGAAATTTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
61 20 0.35
62 32 0.56
63 5 0.09
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.43
Consensus pattern (62 bp):
TATTCATATTAATAAATTAATAAAAAATTATTTTAAAGGCTCATTAAAAAATATATATAATA
Found at i:4276689 original size:11 final size:11
Alignment explanation
Indices: 4276675--4276703 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4276665 TTATTTTTAA
4276675 ATTTTTTTCTT
1 ATTTTTTTCTT
4276686 ATTTTTTTCTT
1 ATTTTTTTCTT
4276697 -TTTTTTT
1 ATTTTTTT
4276704 ATAAAATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (11 bp):
ATTTTTTTCTT
Found at i:4283796 original size:2 final size:2
Alignment explanation
Indices: 4283789--4283824 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4283779 CTTAATTGTC
4283789 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
4283825 TTTCTCCTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4284826 original size:21 final size:23
Alignment explanation
Indices: 4284781--4284828 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
4284771 TTCTCTCTCT
*
4284781 AATTTTTAATTATATATCATAAA
1 AATTTTTAATTATAAATCATAAA
*
4284804 AATTTTT-ATTATAAAT-TTAAA
1 AATTTTTAATTATAAATCATAAA
4284825 AATT
1 AATT
4284829 AATTAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 8 0.35
22 8 0.35
23 7 0.30
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
AATTTTTAATTATAAATCATAAA
Found at i:4284897 original size:23 final size:23
Alignment explanation
Indices: 4284871--4284919 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
4284861 TATTTAACTT
*
4284871 ATAAATAAAAAATTAAAATATTA
1 ATAAATAAAAAATAAAAATATTA
* *
4284894 ATAATTAAATAATAAAAATATTA
1 ATAAATAAAAAATAAAAATATTA
4284917 ATA
1 ATA
4284920 TTATCAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
ATAAATAAAAAATAAAAATATTA
Found at i:4285167 original size:26 final size:26
Alignment explanation
Indices: 4285115--4285170 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
4285105 TTAAATTATC
** * *
4285115 AATTATTAATATTTTGAATTAATATA
1 AATTATTAATATTTAAAAATAAAATA
*
4285141 AATTGTTAATATTTAAAAATAAAATA
1 AATTATTAATATTTAAAAATAAAATA
4285167 AATT
1 AATT
4285171 TTTTTTTGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.45
Consensus pattern (26 bp):
AATTATTAATATTTAAAAATAAAATA
Found at i:4285283 original size:162 final size:162
Alignment explanation
Indices: 4285103--4285429 Score: 403
Period size: 162 Copynumber: 2.0 Consensus size: 162
4285093 AAATATTAAT
* * * *
4285103 ATTTAAATTATCAATTATTAATATTTTGAATTAATATAAATTGTTAATA-TT-T-A-AAAATAAA
1 ATTTAAATTATCAATTATTAATATTTTAAATTAATAAAAATTATTAATATTTATAAGAAAACAAA
***** ** * *
4285164 ATAAATTTTTTTTTGTTTATATATTATAAAAAATAATATTTTAAATT-TGAAAATTAATTTAAAT
66 ATAAAAAAAGTTTTAATTATATATTAT-AAAAATAATATTTTAAATTAAG-AAATTAA-TTAAAA
4285228 TTATTAATATTTTAATCATAACGACATTTAAATTATA
128 TTATTAATATTTTAATCATAA-GA-ATTTAAATTATA
*
4285265 ATTTAAATTATCAATTATTAATATTTTAAATTGATAAAAATTATTAATATTTATAAAGTAAAACA
1 ATTTAAATTATCAATTATTAATATTTTAAATTAATAAAAATTATTAATATTTAT-AAG-AAAACA
*
4285330 AAATAAAAAAAGTTTTAATTATATATTATTAAAATAATATTTTAAATTAAGAAATTAATTAAAAT
64 AAATAAAAAAAGTTTTAATTATATATTATAAAAATAATATTTTAAATTAAGAAATTAATTAAAAT
* *
4285395 TGTTAATATTTTAATCATAATAATTTAAATTATA
129 TATTAATATTTTAATCATAAGAATTTAAATTATA
4285429 A
1 A
4285430 ATAAATATTA
Statistics
Matches: 141, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
162 45 0.32
163 2 0.01
164 14 0.10
165 1 0.01
166 26 0.18
167 25 0.18
168 28 0.20
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (162 bp):
ATTTAAATTATCAATTATTAATATTTTAAATTAATAAAAATTATTAATATTTATAAGAAAACAAA
ATAAAAAAAGTTTTAATTATATATTATAAAAATAATATTTTAAATTAAGAAATTAATTAAAATTA
TTAATATTTTAATCATAAGAATTTAAATTATA
Found at i:4285463 original size:15 final size:15
Alignment explanation
Indices: 4285432--4285504 Score: 59
Period size: 16 Copynumber: 5.1 Consensus size: 15
4285422 AATTATAAAT
4285432 AAATATTAAT-ATTTTA
1 AAATATTAATGA--TTA
4285448 AAATATTAATGATT-
1 AAATATTAATGATTA
4285462 -AA-ATT-ATGATTA
1 AAATATTAATGATTA
*
4285474 AAATATTAAT-ATTT
1 AAATATTAATGATTA
*
4285488 AAATGATCAATGATTA
1 AAAT-ATTAATGATTA
4285504 A
1 A
4285505 CGTTTTAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
11 6 0.13
12 3 0.06
13 4 0.09
14 10 0.21
15 9 0.19
16 14 0.30
17 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.05, T:0.42
Consensus pattern (15 bp):
AAATATTAATGATTA
Found at i:4285489 original size:41 final size:41
Alignment explanation
Indices: 4285397--4285504 Score: 116
Period size: 41 Copynumber: 2.7 Consensus size: 41
4285387 ATTAAAATTG
* *
4285397 TTAATATTTT-AATCAT-AATAATTTAAATTATAAATAAATA
1 TTAATATTTTAAATGATCAATGA-TTAAATTATAAATAAATA
* * *
4285437 TTAATATTTTAAAAT-ATTAATGATTAAATTATGATTAAAATA
1 TTAATATTTT-AAATGATCAATGATTAAATTATAAAT-AAATA
4285479 TTAATA-TTTAAATGATCAATGATTAA
1 TTAATATTTTAAATGATCAATGATTAA
4285505 CGTTTTAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
40 14 0.24
41 27 0.46
42 18 0.31
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (41 bp):
TTAATATTTTAAATGATCAATGATTAAATTATAAATAAATA
Found at i:4308412 original size:42 final size:41
Alignment explanation
Indices: 4308360--4308443 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 41
4308350 ATTCAATATG
*
4308360 CATCCTGAATTGAAAGAGTTAGATCCAAATTCCGTATTTTTT
1 CATCCTGAATTGAAAAAGTTAGATCCAAATTCCGT-TTTTTT
* * * * *
4308402 CATCTTGAATTGAAAAAGTTGGATTCGAATTCGGTTTTTTT
1 CATCCTGAATTGAAAAAGTTAGATCCAAATTCCGTTTTTTT
4308443 C
1 C
4308444 TAAAAATAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 7 0.19
42 29 0.81
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (41 bp):
CATCCTGAATTGAAAAAGTTAGATCCAAATTCCGTTTTTTT
Found at i:4308532 original size:21 final size:21
Alignment explanation
Indices: 4308508--4308548 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4308498 GTTTTAATGG
* * *
4308508 GAAATAAAATTTGGAGGAGAA
1 GAAAGAAAAATTGAAGGAGAA
4308529 GAAAGAAAAATTGAAGGAGA
1 GAAAGAAAAATTGAAGGAGA
4308549 GATATTAATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.29, T:0.15
Consensus pattern (21 bp):
GAAAGAAAAATTGAAGGAGAA
Found at i:4309416 original size:35 final size:35
Alignment explanation
Indices: 4309370--4309440 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
4309360 ATTTCCTTCC
4309370 TGGGATTGTCAATCATTTCATGATTATGTATAAAT
1 TGGGATTGTCAATCATTTCATGATTATGTATAAAT
*
4309405 TGGGATTGTCAATCATTTTATGATTATGTATAAAT
1 TGGGATTGTCAATCATTTCATGATTATGTATAAAT
4309440 T
1 T
4309441 CTTGTTTGGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.07, G:0.17, T:0.45
Consensus pattern (35 bp):
TGGGATTGTCAATCATTTCATGATTATGTATAAAT
Found at i:4322595 original size:24 final size:23
Alignment explanation
Indices: 4322544--4322599 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
4322534 TCCCAACTCT
* *
4322544 TCTTTTTCCTTCTTGCCTTATTC
1 TCTTTTTCTTTCTTGCCTTATCC
4322567 TCTTTCTTCTTTCTTGCCTT-TCC
1 TCTTT-TTCTTTCTTGCCTTATCC
4322590 TCCTTTTTCT
1 T-CTTTTTCT
4322600 CACTGTCCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 12 0.41
24 17 0.59
ACGTcount: A:0.02, C:0.32, G:0.04, T:0.62
Consensus pattern (23 bp):
TCTTTTTCTTTCTTGCCTTATCC
Found at i:4322921 original size:20 final size:20
Alignment explanation
Indices: 4322896--4322942 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
4322886 TAAAATAATA
*
4322896 TATCTATTAATAGATGTTCT
1 TATCTATCAATAGATGTTCT
*
4322916 TATCTATCAATAGATGTTTT
1 TATCTATCAATAGATGTTCT
4322936 TATCTAT
1 TATCTAT
4322943 GATAGATTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.51
Consensus pattern (20 bp):
TATCTATCAATAGATGTTCT
Found at i:4323137 original size:20 final size:20
Alignment explanation
Indices: 4323112--4323153 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
4323102 AATTAATATA
*
4323112 AAAATATTGTGTTATT-TTTT
1 AAAATATTAT-TTATTATTTT
4323132 AAAATATTATTTATTATTTT
1 AAAATATTATTTATTATTTT
4323152 AA
1 AA
4323154 TTGCTTAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (20 bp):
AAAATATTATTTATTATTTT
Found at i:4323791 original size:33 final size:33
Alignment explanation
Indices: 4323754--4323826 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
4323744 TTTTAATGTC
*
4323754 ATATATTTTATTTTCATTTCTTATTATAATCTT
1 ATATATTTTATTTTCATTTCTTAATATAATCTT
* *
4323787 ATATATTTTATTTTCATTTTTTAATATAATTTT
1 ATATATTTTATTTTCATTTCTTAATATAATCTT
*
4323820 TTATATT
1 ATATATT
4323827 ATATATGTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (33 bp):
ATATATTTTATTTTCATTTCTTAATATAATCTT
Found at i:4323811 original size:28 final size:30
Alignment explanation
Indices: 4323743--4323808 Score: 80
Period size: 33 Copynumber: 2.1 Consensus size: 30
4323733 CGTAAATATA
*
4323743 TTTTTAATGTCATATATTTTATTTTCATTTC
1 TTTTTAATCTCATATATTTTATTTTCA-TTC
*
4323774 TTATTATAATCTTATATATTTTATTTTCATT-
1 TT-TT-TAATCTCATATATTTTATTTTCATTC
4323805 TTTT
1 TTTT
4323809 AATATAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
30 2 0.06
31 4 0.13
32 4 0.13
33 21 0.68
ACGTcount: A:0.24, C:0.08, G:0.02, T:0.67
Consensus pattern (30 bp):
TTTTTAATCTCATATATTTTATTTTCATTC
Found at i:4325592 original size:119 final size:119
Alignment explanation
Indices: 4325371--4325589 Score: 318
Period size: 119 Copynumber: 1.8 Consensus size: 119
4325361 TTTGTAGATA
* * *
4325371 AAAAATAAATTAAAATAAAAATTATATTAGTAATTTAATAATAAATTATTAATATTTAAATTTTT
1 AAAAAGAAATTAAAATAAAAATCATATTAGTAATTTAATAATAAATTAATAATATTTAAATTTTT
* *
4325436 AATGAAAATAAAAATTAAAAGATTAAAAAATGAAAATACAAACACAGAAAAAAT
66 AATAAAAATAAAAATTAAAAGATTAAAAAAAGAAAATACAAACACAGAAAAAAT
* * *
4325490 AAAAAGAAATTGAAATAAAAATCATATT-GATAATTTATTATTAAATTAATAATATTTTAAA-TT
1 AAAAAGAAATTAAAATAAAAATCATATTAG-TAATTTAATAATAAATTAATAATA-TTTAAATTT
*
4325553 TTAATAAAAAT-AAAATTAAAAGGTTAAAAAAAGAAAA
64 TTAATAAAAATAAAAATTAAAAGATTAAAAAAAGAAAA
4325590 ATATTATTTA
Statistics
Matches: 89, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
118 25 0.28
119 58 0.65
120 6 0.07
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (119 bp):
AAAAAGAAATTAAAATAAAAATCATATTAGTAATTTAATAATAAATTAATAATATTTAAATTTTT
AATAAAAATAAAAATTAAAAGATTAAAAAAAGAAAATACAAACACAGAAAAAAT
Found at i:4326059 original size:21 final size:21
Alignment explanation
Indices: 4326034--4326075 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
4326024 AAAATAAAAA
*
4326034 TTATACCAATACTTTAATAAT
1 TTATACAAATACTTTAATAAT
*
4326055 TTATACAAATGCTTTAATAAT
1 TTATACAAATACTTTAATAAT
4326076 AAATTATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.12, G:0.02, T:0.43
Consensus pattern (21 bp):
TTATACAAATACTTTAATAAT
Found at i:4333414 original size:6 final size:6
Alignment explanation
Indices: 4333403--4333436 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
4333393 TTTCTATCCT
4333403 CCACTG CCACTG CCACTG CCACTG CCACTG CCAC
1 CCACTG CCACTG CCACTG CCACTG CCACTG CCAC
4333437 CAAACTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.53, G:0.15, T:0.15
Consensus pattern (6 bp):
CCACTG
Found at i:4335285 original size:2 final size:2
Alignment explanation
Indices: 4335278--4335308 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4335268 TGTGTATTTA
4335278 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
4335309 CACTTCATTG
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:4335705 original size:17 final size:16
Alignment explanation
Indices: 4335668--4335711 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
4335658 AAATTTGATT
*
4335668 TATTTAT-TTAAATTA
1 TATTTATATTAAAATA
4335683 TATTTATTATTAAAATA
1 TATTTA-TATTAAAATA
*
4335700 TTTTTATATTAA
1 TATTTATATTAA
4335712 TATACTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.24
16 7 0.28
17 12 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTTATATTAAAATA
Found at i:4339130 original size:24 final size:24
Alignment explanation
Indices: 4339098--4339146 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
4339088 TGTTTTGGGA
4339098 AAGGGGAAAGGAAGGAGAAAGAAT
1 AAGGGGAAAGGAAGGAGAAAGAAT
*
4339122 AAGGGGAAAGGAAGGAGAGAGAAT
1 AAGGGGAAAGGAAGGAGAAAGAAT
4339146 A
1 A
4339147 TGTGGAGGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.43, T:0.04
Consensus pattern (24 bp):
AAGGGGAAAGGAAGGAGAAAGAAT
Found at i:4344183 original size:16 final size:16
Alignment explanation
Indices: 4344150--4344183 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4344140 AAGTCCAATC
*
4344150 TTTTGACTGGATTTTT
1 TTTTGACTGGATTATT
*
4344166 TTTTGACTGGGTTATT
1 TTTTGACTGGATTATT
4344182 TT
1 TT
4344184 AGCAAAGAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.06, G:0.21, T:0.62
Consensus pattern (16 bp):
TTTTGACTGGATTATT
Found at i:4349975 original size:1 final size:1
Alignment explanation
Indices: 4349969--4350035 Score: 134
Period size: 1 Copynumber: 67.0 Consensus size: 1
4349959 AAAGAAGGGA
4349969 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
4350034 GG
1 GG
4350036 TCAGTCGGAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:4351732 original size:33 final size:33
Alignment explanation
Indices: 4351685--4351767 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 33
4351675 TTTGTAATGG
4351685 TATAAT-TAA-AATTAAAAAGTAAAATAAAATA
1 TATAATATAAGAATTAAAAAGTAAAATAAAATA
* *
4351716 TATAATATAAGAATTAAAAATTAAAATAGAATA
1 TATAATATAAGAATTAAAAAGTAAAATAAAATA
*
4351749 -A-AATATATGAAATTAAAAA
1 TATAATATAAG-AATTAAAAA
4351768 TTTATATAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
31 13 0.28
32 13 0.28
33 20 0.43
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (33 bp):
TATAATATAAGAATTAAAAAGTAAAATAAAATA
Found at i:4352111 original size:15 final size:15
Alignment explanation
Indices: 4352071--4352112 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
4352061 AATTTCTTTG
*
4352071 TAATCACATTACTTA
1 TAATCACATTATTTA
* *
4352086 TAATTATATTATTTA
1 TAATCACATTATTTA
4352101 TAATCACATTAT
1 TAATCACATTAT
4352113 ATTGTAAAGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (15 bp):
TAATCACATTATTTA
Found at i:4353570 original size:2 final size:2
Alignment explanation
Indices: 4353551--4353590 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
4353541 TATTCTATGC
* *
4353551 AT AT AC AT AT AC 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
4353591 GTAATCTCAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:4361658 original size:15 final size:15
Alignment explanation
Indices: 4361635--4361884 Score: 53
Period size: 16 Copynumber: 15.5 Consensus size: 15
4361625 GTAAAATATT
4361635 ATAATAATAAATAAAA
1 ATAA-AATAAATAAAA
* *
4361651 ATAAAATATATAACA
1 ATAAAATAAATAAAA
* *
4361666 TTAAAAATATATTTAAAAA
1 AT-AAAATA-A-AT-AAAA
* * *
4361685 ATGATATTATATAAAA
1 AT-AAAATAAATAAAA
* *
4361701 AT-TAAT-AATATAA
1 ATAAAATAAATAAAA
*
4361714 ATATAAATATATTAAAA
1 ATA-AAATA-AATAAAA
*
4361731 ATAAAATATAA-AATATT
1 ATAAAATA-AATAA-A-A
4361748 ATAATAATAAATAAAA
1 ATAA-AATAAATAAAA
* * *
4361764 ATAAAATATATGATA
1 ATAAAATAAATAAAA
* *
4361779 TTAAAAATATATTTAAGAA
1 AT-AAAATA-A-ATAA-AA
* * *
4361798 ATGATATTATATAAAA
1 AT-AAAATAAATAAAA
*
4361814 AT-TAAT-AATAAAA
1 ATAAAATAAATAAAA
*
4361827 ATATAAATATATTAAAA
1 ATA-AAATA-AATAAAA
*
4361844 ATAAAATATAA-AATATT
1 ATAAAATA-AATAA-A-A
4361861 ATAATAATAAATAAAA
1 ATAA-AATAAATAAAA
4361877 ATAAAATA
1 ATAAAATA
4361885 TGTGATATTA
Statistics
Matches: 168, Mismatches: 42, Indels: 49
0.65 0.16 0.19
Matches are distributed among these distances:
13 15 0.09
14 6 0.04
15 33 0.20
16 50 0.30
17 35 0.21
18 15 0.09
19 14 0.08
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (15 bp):
ATAAAATAAATAAAA
Found at i:4361691 original size:14 final size:15
Alignment explanation
Indices: 4361653--4361846 Score: 80
Period size: 16 Copynumber: 13.4 Consensus size: 15
4361643 AAATAAAAAT
* *
4361653 AAAATATATAACATTA
1 AAAATATATTATA-TA
4361669 AAAATATATT-TA-A
1 AAAATATATTATATA
4361682 AAAATGATATTATATA
1 AAAAT-ATATTATATA
*
4361698 AAAAT-TAATA-ATA
1 AAAATATATTATATA
* *
4361711 TAAATATAAATATATTA
1 AAAATAT-ATTATA-TA
4361728 AAAATA-A--A-ATA
1 AAAATATATTATATA
*
4361739 TAAA-ATATTATAATA
1 AAAATATATTAT-ATA
*
4361754 ATAAATA-A--AAAT-
1 A-AAATATATTATATA
*
4361766 AAAATATATGATATTA
1 AAAATATATTATA-TA
4361782 AAAATATATT-TA-A
1 AAAATATATTATATA
*
4361795 GAAATGATATTATATA
1 AAAAT-ATATTATATA
*
4361811 AAAAT-TAATA-ATA
1 AAAATATATTATATA
*
4361824 AAAATATAAATATATTA
1 AAAATAT-ATTATA-TA
4361841 AAAATA
1 AAAATA
4361847 AAATATAAAA
Statistics
Matches: 139, Mismatches: 13, Indels: 51
0.68 0.06 0.25
Matches are distributed among these distances:
10 1 0.01
11 11 0.08
12 3 0.02
13 30 0.22
14 23 0.17
15 20 0.14
16 35 0.25
17 16 0.12
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (15 bp):
AAAATATATTATATA
Found at i:4361699 original size:29 final size:27
Alignment explanation
Indices: 4361630--4361943 Score: 150
Period size: 27 Copynumber: 11.1 Consensus size: 27
4361620 TCCCTGTAAA
4361630 ATATTATAATAATAAATA-AA-AATAAAAT
1 ATATTAT-ATAA-AAATATAATAA-AAAAT
* * *
4361658 ATATAACATTAAAAATATATTTAAAAAAT
1 ATATTATA-TAAAAATATA-ATAAAAAAT
4361687 GATATTATATAAAAAT-TAATAATATAAAT
1 -ATATTATATAAAAATATAATAA-A-AAAT
* * *
4361716 ATAAATATATTAAAAATAAAAT-ATAAA-
1 AT-ATTATA-TAAAAATATAATAAAAAAT
4361743 ATATTATAATAATAAATA-AA-AATAAAAT
1 ATATTAT-ATAA-AAATATAATAA-AAAAT
* * *
4361771 ATATGATATTAAAAATATATTTAAGAAAT
1 ATATTATA-TAAAAATATA-ATAAAAAAT
4361800 GATATTATATAAAAAT-TAATAATAAAAAT
1 -ATATTATATAAAAATATAAT-A-AAAAAT
* * *
4361829 ATAAATATATTAAAAATAAAAT-ATAAA-
1 AT-ATTATA-TAAAAATATAATAAAAAAT
4361856 ATATTATAATAATAAATA-AA-AATAAAAT
1 ATATTAT-ATAA-AAATATAATAA-AAAAT
* * * *
4361884 ATGTGATATTAAAAATAT-TTAAGAAAT
1 ATATTATA-TAAAAATATAATAAAAAAT
4361911 GATATTATATAAAAATTAATAATAAAAAAT
1 -ATATTATATAAAAA-T-ATAATAAAAAAT
4361941 ATA
1 ATA
4361944 AATATATTAA
Statistics
Matches: 219, Mismatches: 30, Indels: 73
0.68 0.09 0.23
Matches are distributed among these distances:
26 20 0.09
27 54 0.25
28 53 0.24
29 47 0.21
30 39 0.18
31 6 0.03
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (27 bp):
ATATTATATAAAAATATAATAAAAAAT
Found at i:4361718 original size:6 final size:6
Alignment explanation
Indices: 4361707--4361773 Score: 50
Period size: 6 Copynumber: 11.0 Consensus size: 6
4361697 AAAAATTAAT
* *
4361707 AATATA AATATA AATAT- ATTAAA AATA-A AATATAA AATATTA TAATAATA
1 AATATA AATATA AATATA AATATA AATATA AATAT-A AATA-TA -AAT-ATA
*
4361757 AATAAA AATA-A AATATA
1 AATATA AATATA AATATA
4361774 TGATATTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
5 13 0.26
6 21 0.42
7 9 0.18
8 6 0.12
9 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AATATA
Found at i:4361931 original size:111 final size:113
Alignment explanation
Indices: 4361626--4361954 Score: 590
Period size: 113 Copynumber: 2.9 Consensus size: 113
4361616 ACATTCCCTG
* * *
4361626 TAAAATATTATAATAATAAATAAAAATAAAATATATAACATTAAAAATATATTTAAAAAATGATA
1 TAAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAGAAATGATA
*
4361691 TTATATAAAAATTAATAATATAAATATAAATATATTAAAAATAAAATA
66 TTATATAAAAATTAATAATAAAAATATAAATATATTAAAAATAAAATA
4361739 TAAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAGAAATGATA
1 TAAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAGAAATGATA
4361804 TTATATAAAAATTAATAATAAAAATATAAATATATTAAAAATAAAATA
66 TTATATAAAAATTAATAATAAAAATATAAATATATTAAAAATAAAATA
*
4361852 TAAAATATTATAATAATAAATAAAAATAAAATATGTGATATT-AAAA-ATATTTAAGAAATGATA
1 TAAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAGAAATGATA
4361915 TTATATAAAAATTAATAATAAAAAATATAAATATATTAAA
66 TTATATAAAAATTAATAAT-AAAAATATAAATATATTAAA
4361955 CTTATATTTT
Statistics
Matches: 210, Mismatches: 5, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
111 36 0.17
112 24 0.11
113 150 0.71
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (113 bp):
TAAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAGAAATGATA
TTATATAAAAATTAATAATAAAAATATAAATATATTAAAAATAAAATA
Found at i:4367492 original size:23 final size:23
Alignment explanation
Indices: 4367452--4367514 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
4367442 AATAAATGAT
* *
4367452 ATAAAACATTATTCTTTAGAATATA
1 ATAAAATATTATT-TTTA-AATAAA
* *
4367477 A-AAATTATTATTTTTAATTAAA
1 ATAAAATATTATTTTTAAATAAA
4367499 ATAAAATATTATTTTT
1 ATAAAATATTATTTTT
4367515 TAAACTAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
22 5 0.16
23 17 0.53
24 9 0.28
25 1 0.03
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (23 bp):
ATAAAATATTATTTTTAAATAAA
Found at i:4375494 original size:2 final size:2
Alignment explanation
Indices: 4375487--4375523 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4375477 CCTTAATCAT
4375487 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4375524 TATGTCAAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:4376057 original size:2 final size:2
Alignment explanation
Indices: 4376050--4376079 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4376040 AAGCTAATGC
*
4376050 AG AG AG AG AG AG AG AG AG AG AG GG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4376080 TATTTCTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4379045 original size:69 final size:68
Alignment explanation
Indices: 4378952--4379089 Score: 186
Period size: 69 Copynumber: 2.0 Consensus size: 68
4378942 CTTGATTTTA
* * *
4378952 CTACAACATATACATGACTAAGTATATATGCTGACCAAGTTTTCTCTCTAACTCCTTAAGGCTTT
1 CTACAACATAGACATGACTAAGTATACATACTGACCAAGTTTT-TCTCTAACTCCTTAAGGCTTT
4379017 TTCT
65 TTCT
* * * * * *
4379021 CTACAACATAGACCTGATTAAGTATACATACTGACCAGGTTTTTTTTTAACTCCTTGAGGCTTTT
1 CTACAACATAGACATGACTAAGTATACATACTGACCAAGTTTTTCTCTAACTCCTTAAGGCTTTT
4379086 TCT
66 TCT
4379089 C
1 C
4379090 AACTCCTTGA
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
68 23 0.38
69 37 0.62
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (68 bp):
CTACAACATAGACATGACTAAGTATACATACTGACCAAGTTTTTCTCTAACTCCTTAAGGCTTTT
TCT
Found at i:4379156 original size:284 final size:284
Alignment explanation
Indices: 4378641--4379172 Score: 843
Period size: 284 Copynumber: 1.9 Consensus size: 284
4378631 TACCATGTCA
* * * *
4378641 ACCATGCTAATGACTCTCTTGATTTTACTACAATATATACCTGACTATGTATATATGCTGACCAG
1 ACCATGCTAATGACTCTCTTGATTTTACTACAACATATACATGACTAAGTATATATGCTGACCAA
* * * * * * **
4378706 GTTTTTTCTCTAACTCCTTGAGATTTTTTCTCTATAACGTATACTAGACTAAGTATACATGTTGA
66 GTTTTCTCTCTAACTCCTTAAGACTTTTTCTCTACAACATAGACTAGACTAAGTATACATACTGA
*
4378771 CCAGGTTTTTTTTTAACTCCTTGAGGCTTTTTCTCAACTCCTTGGTTTGGTGTAATATTCATTTC
131 CCAGGTTTTTTTTTAACTCCTTGAGGCTTTTTCTCAACTCCTTGATTTGGTGTAATATTCATTTC
*
4378836 ATTTCCTGTTTATAAATACAACTTCTCTACCTCACTCACAACACACCAAAAGCTTGATGACTCTC
196 ATTTCCTGTTTATAAATACAACTTCCCTACCTCACTCACAACACACCAAAAGCTTGATGACTCTC
4378901 AACATCTATCTAACCAAGTCCTCT
261 AACATCTATCTAACCAAGTCCTCT
4378925 ACCATGCTAATGACTCTCTTGATTTTACTACAACATATACATGACTAAGTATATATGCTGACCAA
1 ACCATGCTAATGACTCTCTTGATTTTACTACAACATATACATGACTAAGTATATATGCTGACCAA
* *
4378990 GTTTTCTCTCTAACTCCTTAAGGCTTTTTCTCTACAACATAGACCT-GATTAAGTATACATACTG
66 GTTTTCTCTCTAACTCCTTAAGACTTTTTCTCTACAACATAGA-CTAGACTAAGTATACATACTG
* *
4379054 ACCAGGTTTTTTTTTAACTCCTTGAGGCTTTTTCTCAACTCCTTGATTTGGTGTAATGTTTATTT
130 ACCAGGTTTTTTTTTAACTCCTTGAGGCTTTTTCTCAACTCCTTGATTTGGTGTAATATTCATTT
* * *
4379119 CA-TTCTCTGTTTATAAATACAGCTTCCCTATCTCACTCACAACATACCAAAAGC
195 CATTTC-CTGTTTATAAATACAACTTCCCTACCTCACTCACAACACACCAAAAGC
4379173 CTCTCATCTT
Statistics
Matches: 225, Mismatches: 21, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
283 3 0.01
284 220 0.98
285 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (284 bp):
ACCATGCTAATGACTCTCTTGATTTTACTACAACATATACATGACTAAGTATATATGCTGACCAA
GTTTTCTCTCTAACTCCTTAAGACTTTTTCTCTACAACATAGACTAGACTAAGTATACATACTGA
CCAGGTTTTTTTTTAACTCCTTGAGGCTTTTTCTCAACTCCTTGATTTGGTGTAATATTCATTTC
ATTTCCTGTTTATAAATACAACTTCCCTACCTCACTCACAACACACCAAAAGCTTGATGACTCTC
AACATCTATCTAACCAAGTCCTCT
Done.