Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167838.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_11, 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: 23775123
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 69000 characters in sequence are not A, C, G, or T
File 26 of 129
Found at i:5267051 original size:356 final size:354
Alignment explanation
Indices: 5266042--5267228 Score: 1511
Period size: 356 Copynumber: 3.3 Consensus size: 354
5266032 ATTGCTACAT
* * * *
5266042 AAATTTTAACA-CAGTTATTGAAGGTGTATATCCAAGAAAGACGCCTTTAATAATTTCTATCACA
1 AAATTTTAACATGA-TTATTGAAGGCGTATATCCAAGAAAGATGCCTTTAATAATTTCTATAACA
* * *
5266106 GTTTGTAGATAATTAGTGAAGGCAGTTGTAGATAATAACACC-TCTAATAATTTTTTAAAAAAAA
65 GTTTGTAGATAATTAGTGAAGGCAGTTGCAGATAACAACGCCTTC-AATAATTTTTTAAAAAAAA
* * *
5266170 TTTTTTTGGATTATTAAA-GCGTCTTTTATTATAAAACGCCTTCAATATATCACGATGGTTATGA
129 --TTTTTGGATTATTAAATGCGTCTTTTATTATGAAACGCCTTCAATATACCATGATGGTTATGA
* * * *
5266234 AAGGCGTTTATTCAAAAAAGCTCTTTCAATATACCTTTAAACTTAGTAATCCATTACTGAAGGTG
192 AAGGCGTTTATTCAAAAAAGCACCTTCAATATACCTTTAAACTTAGTAAT-TATTACTGAAGGCG
* * * *
5266299 TTTGTTAATAACAGATGCCTTCAAAATTTTCTCACTAAAAATTTTGAGAATTATTAAAGGGGTCT
256 TTTGTTAATAACAGACGCTTTCAAAATTTTCTCACTAAAAATTTTAAGAATTATTAAAGGCGTCT
* * * * * * *
5266364 ACTATTATAAAATGCCTTCTATATGCTACCACAT
321 TCTACTATAAAATACCTTCTATATACCATCACAC
* * *
5266398 AAATTTTAACATGATTTTTGAAGGCGTATATCCAAGAAAGATGCCTTTAATAATTTTTATCACAA
1 AAATTTTAACATGATTATTGAAGGCGTATATCCAAGAAAGATGCCTTTAATAATTTCTATAAC-A
* * *
5266463 TTTTGTAGATAATTAATGAAGGCAGTTGCAGATAACAACGCCTTTAATAATTTTCTTAAAAAAAA
65 GTTTGTAGATAATTAGTGAAGGCAGTTGCAGATAACAACGCCTTCAATAATTTT-TTAAAAAAAA
* * *
5266528 TTCTTTGGATTGTTAAATGCGTCTTTTATTATGAAACGCCTTCAATATACTATGATAGTTATGAA
129 TT-TTTGGATTATTAAATGCGTCTTTTATTATGAAACGCCTTCAATATACCATGATGGTTATGAA
* ** * *
5266593 AGGCGTTTATTTAAAAAAATATCTTCAATATACCTTTAAACTTAGTAATCTATTATTGAAGGCGT
193 AGGCGTTTATTCAAAAAAGCACCTTCAATATACCTTTAAACTTAGTAAT-TATTACTGAAGGCGT
* * * * *
5266658 TTGTTAATAACATACGCTTTTAAAATTTT-TCCACTAAACATTTTAAAAATCATTAAAGGCGTCT
257 TTGTTAATAACAGACGCTTTCAAAATTTTCT-CACTAAAAATTTTAAGAATTATTAAAGGCGTCT
*
5266722 TTTACTATAAAATACCTTCTATATACCATCACAC
321 TCTACTATAAAATACCTTCTATATACCATCACAC
* * * * *
5266756 AAATTTTAACATGATTATTGAATGTGTATATCTAAGAAAGATGCCTTTAATAATTTTTATAATAG
1 AAATTTTAACATGATTATTGAAGGCGTATATCCAAGAAAGATGCCTTTAATAATTTCTATAACAG
* * * * *
5266821 TTTGTAGATAATTAGTAAAGGCGGTTACAGATAACAATGCCTTCAATAACTTTTTTTAAAAAAAT
66 TTTGTAGATAATTAGTGAAGGCAGTTGCAGATAACAACGCCTTCAATAA-TTTTTTAAAAAAAAT
* * * * *
5266886 TTTTGGATTACTAAATGTGTCTTTTATTATGAAATGCCTTGAATATACCATGATGGTTATAAAAG
130 TTTTGGATTATTAAATGCGTCTTTTATTATGAAACGCCTTCAATATACCATGATGGTTATGAAAG
* * *
5266951 GTGTTTATTCAAAAAAGCACCTTCAATATACCTTTAAATTTAGTAATTAATTACTAAAGGCGTTT
195 GCGTTTATTCAAAAAAGCACCTTCAATATACCTTTAAACTTAGTAATT-ATTACTGAAGGCGTTT
* * *
5267016 GTTAATAATAGACACTTTCAAAATTTTCTCACTAAAAATTTTAAGAATTATTAAAGGTGTCTTCT
259 GTTAATAACAGACGCTTTCAAAATTTTCTCACTAAAAATTTTAAGAATTATTAAAGGCGTCTTCT
* * * * * *
5267081 ACTGTAAAATATCTTTTATATATCGTCATAC
324 ACTATAAAATACCTTCTATATACCATCACAC
* *
5267112 AAATTTTAACATGGTTATTGAAGGCGTATATCCAAGAAAGATGCCTTTAATAATTTCTATCACAG
1 AAATTTTAACATGATTATTGAAGGCGTATATCCAAGAAAGATGCCTTTAATAATTTCTATAACAG
** * * *
5267177 TTTGTAGATAATTAGTGAAGGTGGTTGTAAATAATAACGCCATT-AATAATTT
66 TTTGTAGATAATTAGTGAAGGCAGTTGCAGATAACAACGCC-TTCAATAATTT
5267229 GTTATAAATT
Statistics
Matches: 718, Mismatches: 102, Indels: 23
0.85 0.12 0.03
Matches are distributed among these distances:
355 4 0.01
356 345 0.48
357 120 0.17
358 249 0.35
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.38
Consensus pattern (354 bp):
AAATTTTAACATGATTATTGAAGGCGTATATCCAAGAAAGATGCCTTTAATAATTTCTATAACAG
TTTGTAGATAATTAGTGAAGGCAGTTGCAGATAACAACGCCTTCAATAATTTTTTAAAAAAAATT
TTTGGATTATTAAATGCGTCTTTTATTATGAAACGCCTTCAATATACCATGATGGTTATGAAAGG
CGTTTATTCAAAAAAGCACCTTCAATATACCTTTAAACTTAGTAATTATTACTGAAGGCGTTTGT
TAATAACAGACGCTTTCAAAATTTTCTCACTAAAAATTTTAAGAATTATTAAAGGCGTCTTCTAC
TATAAAATACCTTCTATATACCATCACAC
Found at i:5268018 original size:11 final size:11
Alignment explanation
Indices: 5268002--5268030 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
5267992 AAATTGGGGG
5268002 GCTGAATCTAT
1 GCTGAATCTAT
5268013 GCTGAATCTAT
1 GCTGAATCTAT
5268024 GCTGAAT
1 GCTGAAT
5268031 GATGTTTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (11 bp):
GCTGAATCTAT
Found at i:5272972 original size:14 final size:14
Alignment explanation
Indices: 5272955--5273004 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
5272945 ATTCAATTAA
5272955 TTTATATAATTATT
1 TTTATATAATTATT
* * *
5272969 TTTAAAAAATAATAT
1 TTTATATAATTAT-T
*
5272984 TTAATATAATTATT
1 TTTATATAATTATT
5272998 TTTATAT
1 TTTATAT
5273005 TTTACATTTG
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 17 0.63
15 10 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTATATAATTATT
Found at i:5273281 original size:34 final size:34
Alignment explanation
Indices: 5273243--5273310 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
5273233 ATTGATTTCC
*
5273243 TTAAATTTAGTTAAATAATAAATTAAGAGTGTAT
1 TTAAATTTAGTTAAATAACAAATTAAGAGTGTAT
5273277 TTAAATTTAGTTAAATAACAAATTAAGAGTGTAT
1 TTAAATTTAGTTAAATAACAAATTAAGAGTGTAT
5273311 CTGATAAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.47, C:0.01, G:0.12, T:0.40
Consensus pattern (34 bp):
TTAAATTTAGTTAAATAACAAATTAAGAGTGTAT
Found at i:5273547 original size:21 final size:21
Alignment explanation
Indices: 5273522--5273565 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5273512 ATTTGTTTCA
5273522 TATTCTTT-CATTTTAACTGTT
1 TATTCTTTCCATTTTAACT-TT
*
5273543 TATTCTTTCCTTTTTAACTTT
1 TATTCTTTCCATTTTAACTTT
5273564 TA
1 TA
5273566 CTAATTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.18, C:0.16, G:0.02, T:0.64
Consensus pattern (21 bp):
TATTCTTTCCATTTTAACTTT
Found at i:5278479 original size:2 final size:2
Alignment explanation
Indices: 5278472--5278497 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5278462 ATATGAACAA
5278472 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
5278498 GAAAGCAGGT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5279279 original size:15 final size:15
Alignment explanation
Indices: 5279259--5279287 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5279249 AAATATTTTT
5279259 TATTTTAACTATTAA
1 TATTTTAACTATTAA
5279274 TATTTTAACTATTA
1 TATTTTAACTATTA
5279288 CTTGGGAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTTTAACTATTAA
Found at i:5280386 original size:198 final size:198
Alignment explanation
Indices: 5280048--5280444 Score: 731
Period size: 198 Copynumber: 2.0 Consensus size: 198
5280038 TTAATATATA
* * *
5280048 TTGTAATAGAAAAATATATATTTTAAAAGGTAAAATAAATATGAACGTTCTTTTAATACATTTTA
1 TTGTAATAGAAAAATATATATTTTAAAAGGTAAAATAAATATGAACATTATTTTAACACATTTTA
*
5280113 GATATCTCATAGATTTTAAAAGTGAAAAAATCATAAGGATAGAAATAAAAAAAGGTCATATTTTT
66 GATATCTCATAAATTTTAAAAGTGAAAAAATCATAAGGATAGAAATAAAAAAAGGTCATATTTTT
* *
5280178 CACAATTAAAAAGGTAAATGAATTTTATTAAATAATAAAATGATAAACTGTAGCAATGCGTAAGT
131 CACAATTAAAAAGATAAATGAATTTTATTAAATAATAAAATGATAAACTGTAGCAACGCGTAAGT
5280243 TAT
196 TAT
5280246 TTGTAATAGAAAAATATATATTTTAAAAGGTAAAATAAATATGAACATTATTTTAACACATTTTA
1 TTGTAATAGAAAAATATATATTTTAAAAGGTAAAATAAATATGAACATTATTTTAACACATTTTA
5280311 GATATCTCATAAATTTTAAAAGTGAAAAAATCATAAGGATAGAAATAAAAAAAGGTCATATTTTT
66 GATATCTCATAAATTTTAAAAGTGAAAAAATCATAAGGATAGAAATAAAAAAAGGTCATATTTTT
*
5280376 CACAATTAAAAAGATAACTGAATTTTATTAAATAATAAAATGATAAACTGTAGCAACGCGTAAGT
131 CACAATTAAAAAGATAAATGAATTTTATTAAATAATAAAATGATAAACTGTAGCAACGCGTAAGT
5280441 TAT
196 TAT
5280444 T
1 T
5280445 ATCTTATACA
Statistics
Matches: 192, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
198 192 1.00
ACGTcount: A:0.49, C:0.07, G:0.11, T:0.34
Consensus pattern (198 bp):
TTGTAATAGAAAAATATATATTTTAAAAGGTAAAATAAATATGAACATTATTTTAACACATTTTA
GATATCTCATAAATTTTAAAAGTGAAAAAATCATAAGGATAGAAATAAAAAAAGGTCATATTTTT
CACAATTAAAAAGATAAATGAATTTTATTAAATAATAAAATGATAAACTGTAGCAACGCGTAAGT
TAT
Found at i:5282274 original size:2 final size:2
Alignment explanation
Indices: 5282267--5282303 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
5282257 TAATTTTGTT
*
5282267 TA TA TA TA TA TA T- TA -A CA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5282304 TGACGTGGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5282837 original size:17 final size:19
Alignment explanation
Indices: 5282800--5282842 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 19
5282790 TAAAGTTAAA
5282800 AAAAAAAAGTTGAAAGTAG
1 AAAAAAAAGTTGAAAGTAG
*
5282819 AAAAAAAA-TTGATAG-AG
1 AAAAAAAAGTTGAAAGTAG
5282836 AAAAAAA
1 AAAAAAA
5282843 TATGTGCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.39
18 6 0.26
19 8 0.35
ACGTcount: A:0.70, C:0.00, G:0.16, T:0.14
Consensus pattern (19 bp):
AAAAAAAAGTTGAAAGTAG
Found at i:5283319 original size:29 final size:30
Alignment explanation
Indices: 5283270--5283344 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 30
5283260 TATTAATGTA
*
5283270 ATTTTTATTAA-ATTAAAATAT-TAA-ATAAT
1 ATTTTT-TTAATA-TAAAATATATAATAAAAT
*
5283299 ATTTTTGTTAATATAATATATATAATAAAAT
1 ATTTTT-TTAATATAAAATATATAATAAAAT
5283330 ATATTTTTTAATATA
1 AT-TTTTTTAATATA
5283345 TCCCAAGACA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
29 17 0.44
30 4 0.10
31 14 0.36
32 4 0.10
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (30 bp):
ATTTTTTTAATATAAAATATATAATAAAAT
Found at i:5284170 original size:7 final size:7
Alignment explanation
Indices: 5284152--5284197 Score: 60
Period size: 7 Copynumber: 6.9 Consensus size: 7
5284142 ATTTATCTAA
5284152 TAAAAAT
1 TAAAAAT
5284159 T--AAAT
1 TAAAAAT
5284164 TAAAAAT
1 TAAAAAT
5284171 TAAAAAT
1 TAAAAAT
*
5284178 AAAAAAT
1 TAAAAAT
*
5284185 TAAAAAA
1 TAAAAAT
5284192 TAAAAA
1 TAAAAA
5284198 GATTTAAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
5 5 0.15
7 29 0.85
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
TAAAAAT
Found at i:5284494 original size:16 final size:17
Alignment explanation
Indices: 5284460--5284496 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
5284450 TACCTTTTAA
5284460 AAATTATATAAATAATTT
1 AAATTATATAAAT-ATTT
5284478 AAATTATATAAAT-TTT
1 AAATTATATAAATATTT
5284494 AAA
1 AAA
5284497 AAAGCATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.32
18 13 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATTATATAAATATTT
Found at i:5284595 original size:27 final size:26
Alignment explanation
Indices: 5284565--5284622 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
5284555 AGATAAAATG
5284565 ATATTATTTAATCTAATCATATTCATA
1 ATATTATTTAATCTAATCATATT-ATA
* * * *
5284592 ATATTATTTTATTTTATCTTATTATA
1 ATATTATTTAATCTAATCATATTATA
5284618 ATATT
1 ATATT
5284623 TATACTAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 8 0.30
27 19 0.70
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (26 bp):
ATATTATTTAATCTAATCATATTATA
Found at i:5292732 original size:52 final size:52
Alignment explanation
Indices: 5292654--5292758 Score: 158
Period size: 52 Copynumber: 2.0 Consensus size: 52
5292644 TGGATAAAAA
*
5292654 GACTTACAGAAGAAAAATTCTAAGAGAAAA-GAGATTTTTAATAGGTAAGTTT
1 GACTTACAAAAGAAAAATTCTAAGAGAAAATGA-ATTTTTAATAGGTAAGTTT
* * *
5292706 GACTTACAAAAGAAGAATTTTAAGAGAAAATTAATTTTTAATAGGTAAGTTT
1 GACTTACAAAAGAAAAATTCTAAGAGAAAATGAATTTTTAATAGGTAAGTTT
5292758 G
1 G
5292759 TATGCTTATA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
52 47 0.98
53 1 0.02
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.31
Consensus pattern (52 bp):
GACTTACAAAAGAAAAATTCTAAGAGAAAATGAATTTTTAATAGGTAAGTTT
Found at i:5293979 original size:31 final size:30
Alignment explanation
Indices: 5293936--5293999 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
5293926 AATTAAAATA
*
5293936 ATTTATTTATTAATGAGA-TATTATCATTTG
1 ATTTATTTATTAATGA-ATTATCATCATTTG
*
5293966 ATTTATTTTATTAATGAATTATCATTATTTG
1 ATTTA-TTTATTAATGAATTATCATCATTTG
5293997 ATT
1 ATT
5294000 CACTGATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 6 0.20
31 24 0.80
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (30 bp):
ATTTATTTATTAATGAATTATCATCATTTG
Found at i:5296006 original size:24 final size:24
Alignment explanation
Indices: 5295974--5296019 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
5295964 AATTCTTTTA
5295974 TTATTAAAATGAATTATATGTTGG
1 TTATTAAAATGAATTATATGTTGG
*
5295998 TTATTAAAATGAATTATCTGTT
1 TTATTAAAATGAATTATATGTT
5296020 AGGAATATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.02, G:0.13, T:0.48
Consensus pattern (24 bp):
TTATTAAAATGAATTATATGTTGG
Found at i:5297789 original size:20 final size:20
Alignment explanation
Indices: 5297753--5297791 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
5297743 AATAGACAAA
*
5297753 TAAATAAATGAATAAATAAG
1 TAAATAAATGAACAAATAAG
5297773 TAAATAAAAT-AACAAATAA
1 TAAAT-AAATGAACAAATAA
5297792 AGAAAAGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (20 bp):
TAAATAAATGAACAAATAAG
Found at i:5297870 original size:25 final size:26
Alignment explanation
Indices: 5297842--5297890 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
5297832 TGAAGAGGTC
*
5297842 GGCTAC-GACATAAATCAACTTGAGT
1 GGCTACAGACACAAATCAACTTGAGT
* *
5297867 GGCTACAGGCACAAATCAATTTGA
1 GGCTACAGACACAAATCAACTTGA
5297891 ACGGCTTGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 6 0.30
26 14 0.70
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.22
Consensus pattern (26 bp):
GGCTACAGACACAAATCAACTTGAGT
Found at i:5298647 original size:107 final size:107
Alignment explanation
Indices: 5298461--5298653 Score: 298
Period size: 107 Copynumber: 1.8 Consensus size: 107
5298451 AAAAAACACA
* * * *
5298461 TTGAATAATCTTTACAAAAAATTGAATTGGGTTATTCAAGACGTTTGTGGCTGAAAATGCCTTGA
1 TTGAATAATCCTTACAAAAAATTGAATAGGGTTATTCAAGACGTTTGTGGCTAAAAATGCCTTAA
*
5298526 ATAATCTCTTTTAATTTTTATAAGGGAATTATTCAAGGTGTT
66 ATAATCTCCTTTAATTTTTATAAGGGAATTATTCAAGGTGTT
* **
5298568 TTGAATAATCCTTATAAAAAATTGAATAGGGTTATTCAAGGTGTTTGTGG-TAAAAAATGCCTTA
1 TTGAATAATCCTTACAAAAAATTGAATAGGGTTATTCAAGACGTTTGTGGCT-AAAAATGCCTTA
5298632 AATAATCTCCTTTAATTTTTAT
65 AATAATCTCCTTTAATTTTTAT
5298654 GATAGGATTA
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
106 1 0.01
107 76 0.99
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.40
Consensus pattern (107 bp):
TTGAATAATCCTTACAAAAAATTGAATAGGGTTATTCAAGACGTTTGTGGCTAAAAATGCCTTAA
ATAATCTCCTTTAATTTTTATAAGGGAATTATTCAAGGTGTT
Found at i:5298664 original size:107 final size:107
Alignment explanation
Indices: 5298461--5298676 Score: 294
Period size: 107 Copynumber: 2.0 Consensus size: 107
5298451 AAAAAACACA
* * * *
5298461 TTGAATAATCTTTACAAAAAATTGAATTGGGTTATTCAAGACGTTTGTGGCTGAAAATGCCTTGA
1 TTGAATAATCCTTACAAAAAATTGAATAGGGTTATTCAAGACGTTTGTGGCTAAAAATGCCTTAA
* *
5298526 ATAATCTCTTTTAATTTTTATAAGGGAATTATTCAAGGTGTT
66 ATAATCTCCTTTAATTTTTATAAGGGAATTATTCAAGGTATT
* **
5298568 TTGAATAATCCTTATAAAAAATTGAATAGGGTTATTCAAGGTGTTTGTGG-TAAAAAATGCCTTA
1 TTGAATAATCCTTACAAAAAATTGAATAGGGTTATTCAAGACGTTTGTGGCT-AAAAATGCCTTA
*
5298632 AATAATCTCCTTTAATTTTTATGATA-GG-ATTATTCGAGGTATT
65 AATAATCTCCTTTAATTTTTAT-A-AGGGAATTATTCAAGGTATT
5298675 TT
1 TT
5298677 TGGTCAAAAA
Statistics
Matches: 96, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
106 1 0.01
107 91 0.95
108 3 0.03
109 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (107 bp):
TTGAATAATCCTTACAAAAAATTGAATAGGGTTATTCAAGACGTTTGTGGCTAAAAATGCCTTAA
ATAATCTCCTTTAATTTTTATAAGGGAATTATTCAAGGTATT
Found at i:5298686 original size:62 final size:62
Alignment explanation
Indices: 5298593--5298713 Score: 163
Period size: 62 Copynumber: 2.0 Consensus size: 62
5298583 AAAAAATTGA
* *
5298593 ATAGGGTTATTCAAGGTGTTTGTGGTAAAAAATGCC-TTAAATAATCTCCTTTAATTTTTATG
1 ATAGGATTATTCAAGGTATTTGTGGTAAAAAATGCCATT-AATAATCTCCTTTAATTTTTATG
* * * **
5298655 ATAGGATTATTCGAGGTATTTTTGGTCAAAAATGCCATTAATAATCTTTTTTAATTTTT
1 ATAGGATTATTCAAGGTATTTGTGGTAAAAAATGCCATTAATAATCTCCTTTAATTTTT
5298714 TATAAGAAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
62 49 0.96
63 2 0.04
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.45
Consensus pattern (62 bp):
ATAGGATTATTCAAGGTATTTGTGGTAAAAAATGCCATTAATAATCTCCTTTAATTTTTATG
Found at i:5298726 original size:62 final size:62
Alignment explanation
Indices: 5298599--5298738 Score: 160
Period size: 62 Copynumber: 2.3 Consensus size: 62
5298589 TTGAATAGGG
* * *
5298599 TTATTCAAGGTGTTTGTGGTAAAAAATGCCTTAAATAATCTCCTTTAATTTTTATGATAGGA
1 TTATTCAAGGTATTTTTGGTAAAAAATGCCTTAAATAATCTCCTTTAATTTTTATGATAGAA
* * **
5298661 TTATTCGAGGTATTTTTGGTCAAAAATGCCATT-AATAATCTTTTTTAATTTTT-T-ATAAGAAA
1 TTATTCAAGGTATTTTTGGTAAAAAATGCC-TTAAATAATCTCCTTTAATTTTTATGAT-AG-AA
*
5298723 TTATTCAAAGTATTTT
1 TTATTCAAGGTATTTT
5298739 CTATAAAAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
60 2 0.03
61 3 0.05
62 59 0.89
63 2 0.03
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.46
Consensus pattern (62 bp):
TTATTCAAGGTATTTTTGGTAAAAAATGCCTTAAATAATCTCCTTTAATTTTTATGATAGAA
Found at i:5299222 original size:125 final size:124
Alignment explanation
Indices: 5299064--5299295 Score: 276
Period size: 125 Copynumber: 1.9 Consensus size: 124
5299054 AATTAAAGTA
* * *
5299064 GATTATTAAAGGATTTTTGGCCATAAACACCTTAAATAA-CCCCAT-CAAATTTTTTGTAAGGGA
1 GATTATTAAAGGATTTTTGGCCAAAAACACCTTAAATAATCCCCATAAAAATTTTTT-T--GAGA
*
5299127 TTATTCAAGGCTTTTTTGGCC-AAAAATA-CCTTGAATAATCCCCTTTAATTTTTTTATGAAGG
63 TTATTCAAGGCATTTTT-GCCTAAAAA-ACCCTTGAATAATCCCCTTTAATTTTTTTATGAAGG
* * * **
5299189 GATTATTCAAGGCA-TTTTGGTCAAAAACGCCTTAAATAATCCCTTTAAAAATTTTTTTGAGATT
1 GATTATTAAAGG-ATTTTTGGCCAAAAACACCTTAAATAATCCCCATAAAAATTTTTTTGAGATT
*
5299253 ATTCAATGCATTTTTGCCTAAAAAACTCCTTGAATAATCCCCT
65 ATTCAAGGCATTTTTGCCTAAAAAAC-CCTTGAATAATCCCCT
5299296 CCTTTTTTTT
Statistics
Matches: 91, Mismatches: 10, Indels: 12
0.81 0.09 0.11
Matches are distributed among these distances:
123 4 0.04
124 23 0.25
125 49 0.54
126 6 0.07
127 9 0.10
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (124 bp):
GATTATTAAAGGATTTTTGGCCAAAAACACCTTAAATAATCCCCATAAAAATTTTTTTGAGATTA
TTCAAGGCATTTTTGCCTAAAAAACCCTTGAATAATCCCCTTTAATTTTTTTATGAAGG
Found at i:5299227 original size:63 final size:63
Alignment explanation
Indices: 5299064--5299295 Score: 230
Period size: 62 Copynumber: 3.7 Consensus size: 63
5299054 AATTAAAGTA
* * * *
5299064 GATTATTAAAGG-ATTTTTGGCCATAAACACCTTAAATAA-CCCCATCAAA-TTTTTTGTAAGG
1 GATTATTCAAGGCATTTTTGGCCAAAAACACCTTAAATAATCCCCTTTAAATTTTTTTG-AAGG
* * * *
5299125 GATTATTCAAGGCTTTTTTGGCCAAAAATACCTTGAATAATCCCCTTTAATTTTTTTATGAAGG
1 GATTATTCAAGGCATTTTTGGCCAAAAACACCTTAAATAATCCCCTTTAAATTTTTT-TGAAGG
* *
5299189 GATTATTCAAGGCA-TTTTGGTCAAAAACGCCTTAAATAAT-CCCTTTAAAAATTTTTTTG-A--
1 GATTATTCAAGGCATTTTTGGCCAAAAACACCTTAAATAATCCCCTTT--AAATTTTTTTGAAGG
* * *
5299249 GATTATTCAATGCATTTTT-GCCTAAAAAACTCCTTGAATAATCCCCT
1 GATTATTCAAGGCATTTTTGGCC--AAAAACACCTTAAATAATCCCCT
5299296 CCTTTTTTTT
Statistics
Matches: 143, Mismatches: 18, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
60 15 0.10
61 15 0.10
62 46 0.32
63 35 0.24
64 30 0.21
65 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (63 bp):
GATTATTCAAGGCATTTTTGGCCAAAAACACCTTAAATAATCCCCTTTAAATTTTTTTGAAGG
Found at i:5299327 original size:60 final size:59
Alignment explanation
Indices: 5299240--5299352 Score: 133
Period size: 60 Copynumber: 1.9 Consensus size: 59
5299230 CCTTTAAAAA
5299240 TTTTTTTGAGATTATTCAATGCATTTTT-GCCTAAAAAACT-CCTTGAATAATCCCCTCCT
1 TTTTTTTGAGATTATTCAATGCATTTTTAGCC-AAAAAA-TGCCTTGAATAATCCCCTCCT
** * *
5299299 TTTTTTTGAGGATTATTC-ATGGTGTTTTTAGTCAAAAAATGCTTTGAATAATCC
1 TTTTTTTGA-GATTATTCAAT-GCATTTTTAGCCAAAAAATGCCTTGAATAATCC
5299353 ATTAAACCCT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
59 12 0.26
60 32 0.70
61 2 0.04
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.44
Consensus pattern (59 bp):
TTTTTTTGAGATTATTCAATGCATTTTTAGCCAAAAAATGCCTTGAATAATCCCCTCCT
Found at i:5299706 original size:62 final size:63
Alignment explanation
Indices: 5299574--5299715 Score: 162
Period size: 62 Copynumber: 2.3 Consensus size: 63
5299564 TTCTCAAACA
* * * * * *
5299574 AAAAATGTCTTGAATAATCCCTTACAAAAAATTTAATGAAGGTTATTTAATGCATTTCTGGCT
1 AAAAATGCCTTCAATAATCCCTTACAAAAAATTTAATGAAGATTATTTAAGGCATTTCTAGCC
* * ** *
5299637 AAAAATGCTTTTAATAATCCCTT-CATAAAAATTTTTTG-AGATTATTTAAGGCATTTTTAGCC
1 AAAAATGCCTTCAATAATCCCTTACA-AAAAATTTAATGAAGATTATTTAAGGCATTTCTAGCC
5299699 AAAAATGCCTTCAATAA
1 AAAAATGCCTTCAATAA
5299716 GCCCATTTAA
Statistics
Matches: 66, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
62 36 0.55
63 30 0.45
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (63 bp):
AAAAATGCCTTCAATAATCCCTTACAAAAAATTTAATGAAGATTATTTAAGGCATTTCTAGCC
Found at i:5300156 original size:22 final size:20
Alignment explanation
Indices: 5300108--5300147 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
5300098 CATATAGTTC
5300108 ATAAACACAAGCTTCATAAA
1 ATAAACACAAGCTTCATAAA
5300128 ATTTAAACACAAGCTTCATA
1 A--TAAACACAAGCTTCATA
5300148 CACAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
22 17 0.94
ACGTcount: A:0.50, C:0.20, G:0.05, T:0.25
Consensus pattern (20 bp):
ATAAACACAAGCTTCATAAA
Found at i:5303023 original size:24 final size:24
Alignment explanation
Indices: 5302996--5303051 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
5302986 TTACATGTTA
* * * *
5302996 AAAATAAATGTCTAATCAAATAAT
1 AAAATAAATATCCAATAAAATAAC
5303020 AAAATAAATATCCAATAAAATAAC
1 AAAATAAATATCCAATAAAATAAC
5303044 AAAA-AAAT
1 AAAATAAAT
5303052 CTTTATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.66, C:0.09, G:0.02, T:0.23
Consensus pattern (24 bp):
AAAATAAATATCCAATAAAATAAC
Found at i:5306725 original size:20 final size:19
Alignment explanation
Indices: 5306688--5306736 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
5306678 TTAAAACTAG
*
5306688 ATAAAT-AAAAGACTAAAA
1 ATAAATAAAAAGACAAAAA
5306706 ATAAATAAATAAGACAAAAA
1 ATAAATAAA-AAGACAAAAA
5306726 A-AATATAAAAA
1 ATAA-ATAAAAA
5306737 AGAAATGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 6 0.22
19 6 0.22
20 15 0.56
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (19 bp):
ATAAATAAAAAGACAAAAA
Found at i:5306739 original size:20 final size:20
Alignment explanation
Indices: 5306694--5306739 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
5306684 CTAGATAAAT
*
5306694 AAAAGACTAAAAATAAATAA
1 AAAAGACTAAAAAAAAATAA
*
5306714 ATAAGAC-AAAAAAAATATAA
1 AAAAGACTAAAAAAAA-ATAA
5306734 AAAAGA
1 AAAAGA
5306740 AATGTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.76, C:0.04, G:0.07, T:0.13
Consensus pattern (20 bp):
AAAAGACTAAAAAAAAATAA
Found at i:5307162 original size:22 final size:22
Alignment explanation
Indices: 5307137--5307185 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
5307127 TTAAAAGATC
5307137 ATGCTTGGAGGACTTAGAGACT
1 ATGCTTGGAGGACTTAGAGACT
* ** *
5307159 ATGCCTGGAGGTGTTAGAGATT
1 ATGCTTGGAGGACTTAGAGACT
5307181 ATGCT
1 ATGCT
5307186 CGAAGGTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.12, G:0.33, T:0.31
Consensus pattern (22 bp):
ATGCTTGGAGGACTTAGAGACT
Found at i:5307192 original size:22 final size:22
Alignment explanation
Indices: 5307150--5307192 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
5307140 CTTGGAGGAC
*
5307150 TTAGAGACTATGCCTGGAGGTG
1 TTAGAGACTATGCCTGAAGGTG
*
5307172 TTAGAGATTATG-CTCGAAGGT
1 TTAGAGACTATGCCT-GAAGGT
5307193 TTTACAAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.26, C:0.12, G:0.33, T:0.30
Consensus pattern (22 bp):
TTAGAGACTATGCCTGAAGGTG
Found at i:5307298 original size:84 final size:84
Alignment explanation
Indices: 5307172--5307452 Score: 286
Period size: 84 Copynumber: 3.3 Consensus size: 84
5307162 CCTGGAGGTG
* * **
5307172 TTAGAGATTATGCTCGAAGGTTTTACAAATCTTAACTCTAAAATAGATTCAGCTCAGAAGACTTA
1 TTAGAGATTACGCTCGAAGGTCTTACAAATCTCGACTCTAAAATAGATTCAGCTCAGAAGACTTA
5307237 TGAATCTTGCCAGGAAGAC
66 TGAATCTTGCCAGGAAGAC
* * * *
5307256 TTAGAGATTACGCTTGGAGGTCTTACAAATCTCGACTTTAAAATAGATTTAGCTCCA-AAGACTT
1 TTAGAGATTACGCTCGAAGGTCTTACAAATCTCGACTCTAAAATAGATTCAGCT-CAGAAGACTT
* *
5307320 ATGAATCTTACCTA-AAAGAC
65 ATGAATCTTGCC-AGGAAGAC
* * * * * * *
5307340 TTAAAGATTATGCCCGAAAG-CTTTACATATCTCGACTCTAAAATGGATTCAGCTC-GAAAGAGT
1 TTAGAGATTACGCTCGAAGGTC-TTACAAATCTCGACTCTAAAATAGATTCAGCTCAG-AAGACT
*
5307403 TATGAATCTTGCCTGG-AGAAC
64 TATGAATCTTGCCAGGAAG-AC
* *
5307424 TTAGAGATTAC-ATCTAGAGGTCTTACAAA
1 TTAGAGATTACGCTCGA-AGGTCTTACAAA
5307453 CTAAACTTCG
Statistics
Matches: 157, Mismatches: 31, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
83 6 0.04
84 147 0.94
85 4 0.03
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (84 bp):
TTAGAGATTACGCTCGAAGGTCTTACAAATCTCGACTCTAAAATAGATTCAGCTCAGAAGACTTA
TGAATCTTGCCAGGAAGAC
Found at i:5307794 original size:14 final size:14
Alignment explanation
Indices: 5307775--5307812 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
5307765 GGCATGATGC
*
5307775 ATGCAATGCATAAA
1 ATGCAATGAATAAA
*
5307789 ATGCAATGAATATA
1 ATGCAATGAATAAA
5307803 ATGC-ATGAAT
1 ATGCAATGAAT
5307813 TCTATACCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.26
Consensus pattern (14 bp):
ATGCAATGAATAAA
Found at i:5311483 original size:65 final size:66
Alignment explanation
Indices: 5311400--5311549 Score: 232
Period size: 65 Copynumber: 2.3 Consensus size: 66
5311390 TTTATGCAAA
* * * *
5311400 AAGAAAGAAAAAAA-TTTATTTACGAATGAATAGATGCATGCATGCATTGAGTGTCATCACATAA
1 AAGAAAGAAAAAAATTTTATATACAAATGAATAGATGCATACATGCATTGAATGTCATCACATAA
5311464 T
66 T
*
5311465 AAGAAA-AAAAAAATTTTATATACAAATGAATGGATGCATACATGCATTGAATGTCATCACATAA
1 AAGAAAGAAAAAAATTTTATATACAAATGAATAGATGCATACATGCATTGAATGTCATCACATAA
5311529 T
66 T
5311530 AAGAAAGAAAAAAATCTTTA
1 AAGAAAGAAAAAAAT-TTTA
5311550 ATTAAAAATA
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
64 7 0.09
65 58 0.75
66 8 0.10
67 4 0.05
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (66 bp):
AAGAAAGAAAAAAATTTTATATACAAATGAATAGATGCATACATGCATTGAATGTCATCACATAA
T
Found at i:5314251 original size:68 final size:68
Alignment explanation
Indices: 5314116--5314309 Score: 298
Period size: 68 Copynumber: 2.8 Consensus size: 68
5314106 ATAATAGACA
* *
5314116 AATAAGATGTTTATAAAATTATTTTCTACTAGTATATATGAATGGATGATTATCTTTTGTATATA
1 AATAAGATGTTTATAAAATTA-TTTCTACTAG--TATATGAATGGATGATTACCTTCTGTATATA
5314181 TGAATG
63 TGAATG
* *
5314187 AATAAGATGTTTATAAAATTATTTATACTAGTATATGAATGGATTATTACCTTCTGTATATATGA
1 AATAAGATGTTTATAAAATTATTTCTACTAGTATATGAATGGATGATTACCTTCTGTATATATGA
5314252 ATG
66 ATG
* * *
5314255 AATAAGATATTTATAAAATTATTTCTACTGGTATATGAATGAATGATTACCTTCT
1 AATAAGATGTTTATAAAATTATTTCTACTAGTATATGAATGGATGATTACCTTCT
5314310 TACCTTCATA
Statistics
Matches: 114, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
68 84 0.74
70 9 0.08
71 21 0.18
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43
Consensus pattern (68 bp):
AATAAGATGTTTATAAAATTATTTCTACTAGTATATGAATGGATGATTACCTTCTGTATATATGA
ATG
Found at i:5315199 original size:55 final size:54
Alignment explanation
Indices: 5315115--5315250 Score: 157
Period size: 55 Copynumber: 2.5 Consensus size: 54
5315105 AAATATAATA
* *
5315115 AAAAAATTAAAACATATAAATT-TATATTGACAATCTCTAACCGTCGGTAAAGGT
1 AAAAAATTAAAACATA-CAATTCTATATTGACAATCTCTAACCATCGGTAAAGGT
* * * * *
5315169 GAAAAAATTAAAGCATACAATTCTATATTGATAGTCTCTAACCATTGGTATAGGT
1 -AAAAAATTAAAACATACAATTCTATATTGACAATCTCTAACCATCGGTAAAGGT
* *
5315224 AACAAAATTAAAAAATACAAGTCTATA
1 AA-AAAATTAAAACATACAATTCTATA
5315251 CTGATGAATG
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
54 6 0.09
55 63 0.91
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.29
Consensus pattern (54 bp):
AAAAAATTAAAACATACAATTCTATATTGACAATCTCTAACCATCGGTAAAGGT
Found at i:5315393 original size:160 final size:158
Alignment explanation
Indices: 5315227--5315520 Score: 376
Period size: 159 Copynumber: 1.8 Consensus size: 158
5315217 TATAGGTAAC
* * ** **
5315227 AAAATTAAAAAATACAAGTCTATACTGATGAATGC-TAAGTGTTGGTATAGGTAAAAAAAATTAC
1 AAAATTAAAAAATACAAATCTATACTGACG-A-GCTTAAGCATCAGTATAGGT-AAAAAAATTAC
* * * * *
5315291 AAGTTTATACTAACAAGCATTAATAGTCAGTATAGGTCAA-AAAAATTAAAACATATAAGTTTAT
63 AAGTCTATACTAACAACCATTAATAGTCAGTATAAG-CAAGAAAAATTAAAACATACAAGTCTAT
5315355 ACTAACGGGCGCTAGCTGTCTATACAGATGAG
127 ACTAACGGGCGCTAGCTGTCTATACAGATGAG
*
5315387 AAAATTAAAACATACAAATCTATACTGACGAGCTTTAAGCATCAGTATAGGTAAAAAAATTACAA
1 AAAATTAAAAAATACAAATCTATACTGACGAGC-TTAAGCATCAGTATAGGTAAAAAAATTACAA
* * ** *
5315452 GTCTATACTAACGACCATTAATTGTTTGTATAAGCAAGAAAAATTAAAATATACAAGTCTATACT
65 GTCTATACTAACAACCATTAATAGTCAGTATAAGCAAGAAAAATTAAAACATACAAGTCTATACT
5315517 AACG
130 AACG
5315521 AATGTTAACT
Statistics
Matches: 114, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
158 5 0.04
159 69 0.61
160 40 0.35
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.28
Consensus pattern (158 bp):
AAAATTAAAAAATACAAATCTATACTGACGAGCTTAAGCATCAGTATAGGTAAAAAAATTACAAG
TCTATACTAACAACCATTAATAGTCAGTATAAGCAAGAAAAATTAAAACATACAAGTCTATACTA
ACGGGCGCTAGCTGTCTATACAGATGAG
Found at i:5318452 original size:14 final size:14
Alignment explanation
Indices: 5318435--5318484 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
5318425 TTTTTTACTA
5318435 AAAATAAATAAATT
1 AAAATAAATAAATT
5318449 AAAATAAAATTAAAATT
1 AAAAT-AAA-T-AAATT
**
5318466 AAAATTGATAAATT
1 AAAATAAATAAATT
5318480 AAAAT
1 AAAAT
5318485 TTTTATCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 15 0.48
15 4 0.13
16 2 0.06
17 10 0.32
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (14 bp):
AAAATAAATAAATT
Found at i:5318453 original size:6 final size:6
Alignment explanation
Indices: 5318444--5318485 Score: 59
Period size: 6 Copynumber: 6.8 Consensus size: 6
5318434 AAAAATAAAT
5318444 AAATTA AAA-TA AAATTA AAATTA AAATTGA TAAATTA AAATT
1 AAATTA AAATTA AAATTA AAATTA AAATT-A -AAATTA AAATT
5318486 TTTATCAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 5 0.15
6 21 0.64
7 2 0.06
8 5 0.15
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (6 bp):
AAATTA
Found at i:5318569 original size:15 final size:16
Alignment explanation
Indices: 5318540--5318570 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5318530 AATTTTGATA
5318540 TTTAATAACAAATATT
1 TTTAATAACAAATATT
5318556 TTTAATAA-AAATATT
1 TTTAATAACAAATATT
5318571 AACAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTAATAACAAATATT
Found at i:5318696 original size:35 final size:31
Alignment explanation
Indices: 5318628--5318706 Score: 81
Period size: 36 Copynumber: 2.4 Consensus size: 31
5318618 AATAGTATTT
*
5318628 TTAAATTTTTTATATATTATTAATTTTTATA
1 TTAAATTTATTATATATTATTAATTTTTATA
5318659 TTAAATTCTATTAGTATATTGATTTAGATTTTT-TA
1 TTAAATT-TATTA-TATATT-A-TTA-ATTTTTATA
5318694 TTAAAATTT-TTAT
1 TT-AAATTTATTAT
5318707 TAAATCATTA
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
31 7 0.17
32 4 0.10
33 7 0.17
34 4 0.10
35 8 0.20
36 11 0.27
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (31 bp):
TTAAATTTATTATATATTATTAATTTTTATA
Found at i:5322830 original size:10 final size:10
Alignment explanation
Indices: 5322816--5322868 Score: 74
Period size: 10 Copynumber: 5.5 Consensus size: 10
5322806 CTATGGAGGT
5322816 AAAAAA-AAA
1 AAAAAATAAA
* *
5322825 TAAAAA-ACA
1 AAAAAATAAA
5322834 AAAAAATAAA
1 AAAAAATAAA
5322844 AAAAAATAAA
1 AAAAAATAAA
5322854 AAAAAATAAA
1 AAAAAATAAA
5322864 AAAAA
1 AAAAA
5322869 GGGAAAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
9 12 0.31
10 27 0.69
ACGTcount: A:0.91, C:0.02, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:5322849 original size:25 final size:24
Alignment explanation
Indices: 5322815--5322868 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 24
5322805 GCTATGGAGG
5322815 TAAAAAAAAATAAAAAACAAAAAAA
1 TAAAAAAAAATAAAAAA-AAAAAAA
*
5322840 TAAAAAAAAATAAAAAAAAATAAA
1 TAAAAAAAAATAAAAAAAAAAAAA
5322864 -AAAAA
1 TAAAAA
5322869 GGGAAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 5 0.18
24 6 0.21
25 17 0.61
ACGTcount: A:0.89, C:0.02, G:0.00, T:0.09
Consensus pattern (24 bp):
TAAAAAAAAATAAAAAAAAAAAAA
Found at i:5322877 original size:1 final size:1
Alignment explanation
Indices: 5322816--5322868 Score: 61
Period size: 1 Copynumber: 53.0 Consensus size: 1
5322806 CTATGGAGGT
* * * * *
5322816 AAAAAAAAATAAAAAACAAAAAAATAAAAAAAAATAAAAAAAAATAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5322869 GGGAAAAAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.91, C:0.02, G:0.00, T:0.08
Consensus pattern (1 bp):
A
Found at i:5324244 original size:33 final size:33
Alignment explanation
Indices: 5324168--5324725 Score: 551
Period size: 33 Copynumber: 16.7 Consensus size: 33
5324158 AAAATGAAAT
*
5324168 TTTAAGCCCAATTTATCTGGCCATCAATG-AGC
1 TTTAAGCCCAGTTTATCTGGCCATCAATGAAGC
* * *
5324200 TTTAGGTCCAGTTTATCTGGTCATCAATGAAGC
1 TTTAAGCCCAGTTTATCTGGCCATCAATGAAGC
*
5324233 TTTAAGCCCAGTTTATCTGGCCAACAATG-A-C
1 TTTAAGCCCAGTTTATCTGGCCATCAATGAAGC
* * **
5324264 ATTTAAGCCTAGTTTATCTGGCCATCAATAAAAT
1 -TTTAAGCCCAGTTTATCTGGCCATCAATGAAGC
* * * *
5324298 TTTAAGCCTAGTTTATCTAGCCATTAATGAAGT
1 TTTAAGCCCAGTTTATCTGGCCATCAATGAAGC
* * * *
5324331 TTTAAGCTCATTTTATCTGACCATCAATAAAGC
1 TTTAAGCCCAGTTTATCTGGCCATCAATGAAGC
* *
5324364 TTTAAGCCTAGTTTATCTGGCC-TCAAATGAAGT
1 TTTAAGCCCAGTTTATCTGGCCATC-AATGAAGC
* *
5324397 TTTAAGCCCAGTTTATCTGACCATCAATGAAAC
1 TTTAAGCCCAGTTTATCTGGCCATCAATGAAGC
* ** *
5324430 TTTAAGTCCAGTTTATCTGATCATCAATGAA-A
1 TTTAAGCCCAGTTTATCTGGCCATCAATGAAGC
*
5324462 TTTAAGCCCAGTTTATCTGGCC-TCAAATGAAGT
1 TTTAAGCCCAGTTTATCTGGCCATC-AATGAAGC
* *
5324495 TTTAAGCCTAGTTTATCTGGCCATCAATGAAAC
1 TTTAAGCCCAGTTTATCTGGCCATCAATGAAGC
5324528 TTTAAGCCTAACTTTAAGTCCAGTTTATCTGGCCATCAATG-A-C
1 TTTAAG-----C-------CCAGTTTATCTGGCCATCAATGAAGC
* * *
5324571 ATTTAAGTCCAGTTTATCTGGCCATCAATAAAGT
1 -TTTAAGCCCAGTTTATCTGGCCATCAATGAAGC
*
5324605 TTTAAGCCCAGTTTATCTGGCCATTAATGAAGC
1 TTTAAGCCCAGTTTATCTGGCCATCAATGAAGC
* * *
5324638 TTTAAGCTCATTTTATCTGACCATCAATGAAGC
1 TTTAAGCCCAGTTTATCTGGCCATCAATGAAGC
*
5324671 TTTAAGCCCAGTTTATTTGGCCATCAATG-A-C
1 TTTAAGCCCAGTTTATCTGGCCATCAATGAAGC
* *
5324702 ATTTAAGCCTAGTTTATCTAGCCA
1 -TTTAAGCCCAGTTTATCTGGCCA
5324726 AATGAGATTT
Statistics
Matches: 438, Mismatches: 63, Indels: 50
0.79 0.11 0.09
Matches are distributed among these distances:
31 4 0.01
32 121 0.28
33 279 0.64
34 4 0.01
38 1 0.00
43 1 0.00
44 7 0.02
45 21 0.05
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.35
Consensus pattern (33 bp):
TTTAAGCCCAGTTTATCTGGCCATCAATGAAGC
Found at i:5324357 original size:66 final size:66
Alignment explanation
Indices: 5324160--5324778 Score: 570
Period size: 65 Copynumber: 9.3 Consensus size: 66
5324150 CTAAAAAAAA
* * * * * * *
5324160 AATGAAATTTTAAGCCCAATTTATCTGGCCATCAATG-AGCTTTAGGTCCAGTTTATCTGGTCAT
1 AATGAAACTTTAAGCCTAGTTTATCTGGCCATCAATGAAGTTTTAAGCCCAGTTTATCTGGCCAT
5324224 C
66 C
* * * *
5324225 AATGAAGCTTTAAGCCCAGTTTATCTGGCCAACAATGACA--TTTAAGCCTAGTTTATCTGGCCA
1 AATGAAACTTTAAGCCTAGTTTATCTGGCCATCAATGA-AGTTTTAAGCCCAGTTTATCTGGCCA
5324288 TC
65 TC
* * * * * * *
5324290 AATAAAATTTTAAGCCTAGTTTATCTAGCCATTAATGAAGTTTTAAGCTCATTTTATCTGACCAT
1 AATGAAACTTTAAGCCTAGTTTATCTGGCCATCAATGAAGTTTTAAGCCCAGTTTATCTGGCCAT
5324355 C
66 C
*
5324356 AAT-AAAGCTTTAAGCCTAGTTTATCTGGCC-TCAAATGAAGTTTTAAGCCCAGTTTATCTGACC
1 AATGAAA-CTTTAAGCCTAGTTTATCTGGCCATC-AATGAAGTTTTAAGCCCAGTTTATCTGGCC
5324419 ATC
64 ATC
** *
5324422 AATGAAACTTTAAGTCC-AGTTTATCTGATCATCAATGAA-ATTTAAGCCCAGTTTATCTGGCC-
1 AATGAAACTTTAAG-CCTAGTTTATCTGGCCATCAATGAAGTTTTAAGCCCAGTTTATCTGGCCA
5324484 TC
65 TC
** *
5324486 AAATGAAGTTTTAAGCCTAGTTTATCTGGCCATCAATGAAACTTTAAGCCTAACTTTAAGTCCAG
1 -AATGAAACTTTAAGCCTAGTTTATCTGGCCATCAATG-------AAG--T---TTTAAGCCCAG
5324551 TTTATCTGGCCATC
53 TTTATCTGGCCATC
* *
5324565 AATGACA-TTTAAGTCC-AGTTTATCTGGCCATCAATAAAGTTTTAAGCCCAGTTTATCTGGCCA
1 AATGAAACTTTAAG-CCTAGTTTATCTGGCCATCAATGAAGTTTTAAGCCCAGTTTATCTGGCCA
*
5324628 TT
65 TC
* * * * *
5324630 AATGAAGCTTTAAG-CTCATTTTATCTGACCATCAATGAAGCTTTAAGCCCAGTTTATTTGGCCA
1 AATGAAACTTTAAGCCT-AGTTTATCTGGCCATCAATGAAGTTTTAAGCCCAGTTTATCTGGCCA
5324694 TC
65 TC
* * * *
5324696 AATGACA-TTTAAGCCTAGTTTATCTAGCCA--AATG-AGATTTTAAGCCCAAG-TTAGCTAGCC
1 AATGAAACTTTAAGCCTAGTTTATCTGGCCATCAATGAAG-TTTTAAGCCC-AGTTTATCTGGCC
*
5324756 TTC
64 ATC
* *
5324759 AAT-AAAATTTAAGCCCAGTT
1 AATGAAACTTTAAGCCTAGTT
5324779 CCCAAAAAAA
Statistics
Matches: 462, Mismatches: 59, Indels: 68
0.78 0.10 0.12
Matches are distributed among these distances:
62 4 0.01
63 37 0.08
64 8 0.02
65 185 0.40
66 159 0.34
67 8 0.02
68 1 0.00
70 3 0.01
72 2 0.00
77 25 0.05
78 28 0.06
79 2 0.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (66 bp):
AATGAAACTTTAAGCCTAGTTTATCTGGCCATCAATGAAGTTTTAAGCCCAGTTTATCTGGCCAT
C
Found at i:5324587 original size:110 final size:110
Alignment explanation
Indices: 5324427--5324741 Score: 349
Period size: 110 Copynumber: 3.0 Consensus size: 110
5324417 CCATCAATGA
* *
5324427 AACTTTAAGTCCAGTTTATCTGATCATCAATGAAATTTAAGCCCAGTTTATCTGGCC-TCAAATG
1 AACTTTAAGTCCAGTTTATCTGACCATCAATGAAATTTAAGCCCAGTTTATCTGGCCATC-AATA
*
5324491 AAGTTTTAAGCCTAGTTTATCTGGCCATCAATGAAACTTTAAGCCT
65 AAGTTTTAAGCCCAGTTTATCTGGCCATCAATGAAACTTTAAGCCT
* * *
5324537 AACTTTAAGTCCAGTTTATCTGGCCATCAATGACATTTAAGTCCAGTTTATCTGGCCATCAATAA
1 AACTTTAAGTCCAGTTTATCTGACCATCAATGAAATTTAAGCCCAGTTTATCTGGCCATCAATAA
* *
5324602 AGTTTTAAGCCCAGTTTATCTGGCCATTAATGAAGCTTTAAG-CT
66 AGTTTTAAGCCCAGTTTATCTGGCCATCAATGAAACTTTAAGCCT
* *
5324646 --C----A-T----TTTATCTGACCATCAATGAAGCTTTAAGCCCAGTTTATTTGGCCATCAATG
1 AACTTTAAGTCCAGTTTATCTGACCATCAATGAA-ATTTAAGCCCAGTTTATCTGGCCATCAAT-
* * * * *
5324700 ACA--TTTAAGCCTAGTTTATCTAGCCA--AATGAGATTTTAAGCC
64 AAAGTTTTAAGCCCAGTTTATCTGGCCATCAATGAAACTTTAAGCC
5324742 CAAGTTAGCT
Statistics
Matches: 182, Mismatches: 19, Indels: 21
0.82 0.09 0.09
Matches are distributed among these distances:
96 11 0.06
97 1 0.01
98 39 0.21
99 26 0.14
100 2 0.01
102 1 0.01
103 1 0.01
107 1 0.01
109 2 0.01
110 96 0.53
111 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (110 bp):
AACTTTAAGTCCAGTTTATCTGACCATCAATGAAATTTAAGCCCAGTTTATCTGGCCATCAATAA
AGTTTTAAGCCCAGTTTATCTGGCCATCAATGAAACTTTAAGCCT
Found at i:5324609 original size:143 final size:143
Alignment explanation
Indices: 5324397--5324678 Score: 410
Period size: 143 Copynumber: 2.0 Consensus size: 143
5324387 CAAATGAAGT
*
5324397 TTTAAGCCCAGTTTATCTGACCATCAATGAAACTTTAAGTCCAGTTTATCTGATCATCAATGAAA
1 TTTAAGCCCAGTTTATCTGACCATCAATGAAACTTTAAGTCCAGTTTATCTGACCATCAATGAAA
* *
5324462 TTTAAGCCCAGTTTATCTGGCC-TCAAATGAAGTTTTAAGC-CTAGTTTATCTGGCCATCAATGA
66 TTTAAGCCCAGTTTATCTGGCCAT-AAATGAAGCTTTAAGCTC-AGTTTATCTGACCATCAATGA
5324525 AACTTTAAGCCTAAC
129 AACTTTAAGCCTAAC
* * * *
5324540 TTTAAGTCCAGTTTATCTGGCCATCAATGACA-TTTAAGTCCAGTTTATCTGGCCATCAAT-AAA
1 TTTAAGCCCAGTTTATCTGACCATCAATGAAACTTTAAGTCCAGTTTATCTGACCATCAATGAAA
* *
5324603 GTTTTAAGCCCAGTTTATCTGGCCATTAATGAAGCTTTAAGCTCATTTTATCTGACCATCAATGA
66 --TTTAAGCCCAGTTTATCTGGCCATAAATGAAGCTTTAAGCTCAGTTTATCTGACCATCAATGA
*
5324668 AGCTTTAAGCC
129 AACTTTAAGCC
5324679 CAGTTTATTT
Statistics
Matches: 125, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
141 3 0.02
142 26 0.21
143 94 0.75
144 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (143 bp):
TTTAAGCCCAGTTTATCTGACCATCAATGAAACTTTAAGTCCAGTTTATCTGACCATCAATGAAA
TTTAAGCCCAGTTTATCTGGCCATAAATGAAGCTTTAAGCTCAGTTTATCTGACCATCAATGAAA
CTTTAAGCCTAAC
Found at i:5324656 original size:241 final size:239
Alignment explanation
Indices: 5324298--5324741 Score: 619
Period size: 241 Copynumber: 1.8 Consensus size: 239
5324288 TCAATAAAAT
* *
5324298 TTTAAGCCTAGTTTATCTAGCCATTAATGAAGTTTTAAGCTCATTTTATCTGACCATCAATAAAG
1 TTTAAGCCTAGTTTATCTAGCCATCAATGAAG-TTTAAGCTCAGTTTATCTGACCATCAATAAAG
* *
5324363 CTTTAAGCCTAGTTTATCTGGCCTCAAATGAAGTTTTAAGCCCAGTTTATCTGACCATCAATGAA
65 CTTTAAGCCCAGTTTATCTGGCCTCAAATGAAGCTTTAAGCCCAGTTTATCTGACCATCAATGAA
* * *
5324428 ACTTTAAGTCCAGTTTATCTGATCATCAATGAAATTTAAGCCCAGTTTATCTGGCCTCAAATGA-
130 ACTTTAAGCCCAGTTTATCTGACCATCAATGAAATTTAAGCCCAGTTTATCTAG-C-CAAATGAG
5324492 AGTTTTAAGCCTAGTTTATCTGGCCATCAATGAAACTTTAAGCCTAAC
193 A-TTTTAAGCCTAGTTTATCTGGCCATCAATGAAACTTTAAGCCTAAC
* *
5324540 TTTAAGTCC-AGTTTATCTGGCCATCAATGACA-TTTAAG-TCCAGTTTATCTGGCCATCAATAA
1 TTTAAG-CCTAGTTTATCTAGCCATCAATGA-AGTTTAAGCT-CAGTTTATCTGACCATCAATAA
* * * *
5324602 AGTTTTAAGCCCAGTTTATCTGGCCAT-TAATGAAGCTTTAAGCTCATTTTATCTGACCATCAAT
63 AGCTTTAAGCCCAGTTTATCTGGCC-TCAAATGAAGCTTTAAGCCCAGTTTATCTGACCATCAAT
* * * * *
5324666 GAAGCTTTAAGCCCAGTTTATTTGGCCATCAATGACATTTAAGCCTAGTTTATCTAGCCAAATGA
127 GAAACTTTAAGCCCAGTTTATCTGACCATCAATGAAATTTAAGCCCAGTTTATCTAGCCAAATGA
5324731 GATTTTAAGCC
192 GATTTTAAGCC
5324742 CAAGTTAGCT
Statistics
Matches: 179, Mismatches: 18, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
239 16 0.09
240 3 0.02
241 131 0.73
242 26 0.15
243 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (239 bp):
TTTAAGCCTAGTTTATCTAGCCATCAATGAAGTTTAAGCTCAGTTTATCTGACCATCAATAAAGC
TTTAAGCCCAGTTTATCTGGCCTCAAATGAAGCTTTAAGCCCAGTTTATCTGACCATCAATGAAA
CTTTAAGCCCAGTTTATCTGACCATCAATGAAATTTAAGCCCAGTTTATCTAGCCAAATGAGATT
TTAAGCCTAGTTTATCTGGCCATCAATGAAACTTTAAGCCTAAC
Found at i:5324741 original size:31 final size:31
Alignment explanation
Indices: 5324540--5324778 Score: 148
Period size: 33 Copynumber: 7.4 Consensus size: 31
5324530 TAAGCCTAAC
* *
5324540 TTTAAGTCCAGTTTATCTGGCCATCAATGACA
1 TTTAAGCCCAGTTTATCTAGCCA-CAATGACA
* * *
5324572 TTTAAGTCCAGTTTATCTGGCCATCAAT-AAA
1 TTTAAGCCCAGTTTATCTAGCCA-CAATGACA
* *
5324603 GTTTTAAGCCCAGTTTATCTGGCCATTAATGA-A
1 --TTTAAGCCCAGTTTATCTAGCCA-CAATGACA
* *
5324636 GCTTTAAGCTCATTTTATCT-GACCATCAATGA-A
1 --TTTAAGCCCAGTTTATCTAG-CCA-CAATGACA
* *
5324669 GCTTTAAGCCCAGTTTATTTGGCCATCAATGACA
1 --TTTAAGCCCAGTTTATCTAGCCA-CAATGACA
* *
5324703 TTTAAGCCTAGTTTATCTAGCCA-AATGAGA
1 TTTAAGCCCAGTTTATCTAGCCACAATGACA
* * * *
5324733 TTTTAAGCCCAAG-TTAGCTAGCCTTCAATAAAA
1 -TTTAAGCCC-AGTTTATCTAGCC-ACAATGACA
5324766 TTTAAGCCCAGTT
1 TTTAAGCCCAGTT
5324779 CCCAAAAAAA
Statistics
Matches: 177, Mismatches: 19, Indels: 22
0.81 0.09 0.10
Matches are distributed among these distances:
30 6 0.03
31 21 0.12
32 61 0.34
33 86 0.49
34 3 0.02
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (31 bp):
TTTAAGCCCAGTTTATCTAGCCACAATGACA
Found at i:5325505 original size:86 final size:87
Alignment explanation
Indices: 5325349--5325639 Score: 304
Period size: 86 Copynumber: 3.4 Consensus size: 87
5325339 TTTAAAGATT
* *
5325349 TTGATT-TTTAAGACCTCCGAGCATGATTTTGATTCGCGGTGTTATCCCAATCGATTCTTTAATT
1 TTGATTCTGTAAGACCTCCGGGCATGATTTTGATTCGCGGTGTTATCCCAATCGATTCTTTAATT
*
5325413 TTGACTT--G-TAGTGTATCCCAG
66 TCGACTTACGAT-GT-TATCCCAG
* * **
5325434 TTGATTCTGTAAGACTTCCGGGCATGATTTCGATTAACGGTGTTATCCCAATCGATTCTTTAATT
1 TTGATTCTGTAAGACCTCCGGGCATGATTTTGATTCGCGGTGTTATCCCAATCGATTCTTTAATT
5325499 TCGACTTACGATGTTATCCCAG
66 TCGACTTACGATGTTATCCCAG
* * * ** * ** *
5325521 TTGATTCTGTAAAACCTCCAGGCATAATTTTGATTCGCGGTGTTATCCTGATTGATTCCATATTT
1 TTGATTCTGTAAGACCTCCGGGCATGATTTTGATTCGCGGTGTTATCCCAATCGATTCTTTA-AT
* * *
5325586 TTTGACTTGCGATATTATCCCAG
65 TTCGACTTACGATGTTATCCCAG
* * * *
5325609 TAGAATT-TTTAAGACCTTCGGGCATAATTTT
1 TTG-ATTCTGTAAGACCTCCGGGCATGATTTT
5325640 TTTACTTACA
Statistics
Matches: 172, Mismatches: 28, Indels: 9
0.82 0.13 0.04
Matches are distributed among these distances:
85 6 0.03
86 58 0.34
87 58 0.34
88 46 0.27
89 4 0.02
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (87 bp):
TTGATTCTGTAAGACCTCCGGGCATGATTTTGATTCGCGGTGTTATCCCAATCGATTCTTTAATT
TCGACTTACGATGTTATCCCAG
Found at i:5325514 original size:36 final size:36
Alignment explanation
Indices: 5325460--5325528 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
5325450 TCCGGGCATG
*
5325460 ATTTCGATTAACGGTGTTATCCCAATCGATTCTTTA
1 ATTTCGATTAACGATGTTATCCCAATCGATTCTTTA
* *
5325496 ATTTCGACTT-ACGATGTTATCCCAGTTGATTCT
1 ATTTCGA-TTAACGATGTTATCCCAATCGATTCT
5325529 GTAAAACCTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
36 27 0.93
37 2 0.07
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.42
Consensus pattern (36 bp):
ATTTCGATTAACGATGTTATCCCAATCGATTCTTTA
Found at i:5325937 original size:20 final size:19
Alignment explanation
Indices: 5325908--5325945 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
5325898 CAGGTCTACA
5325908 TTTTAAAATAATAATAATT
1 TTTTAAAATAATAATAATT
5325927 TTTTAAAAATAATAATAAT
1 TTTT-AAAATAATAATAAT
5325946 AATAATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTTTAAAATAATAATAATT
Found at i:5325940 original size:3 final size:3
Alignment explanation
Indices: 5325934--5325973 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
5325924 ATTTTTTAAA
5325934 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5325974 TTGGTTTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5327382 original size:45 final size:44
Alignment explanation
Indices: 5327336--5327566 Score: 238
Period size: 43 Copynumber: 5.2 Consensus size: 44
5327326 AACTCCCCTA
5327336 AAATAGAGGCTTCACAACTTTTGAAAAATAAATAAGGCTTATCT
1 AAATAGAGGCTTCACAACTTTTGAAAAATAAATAAGGCTTATCT
* * * * * *
5327380 AAATAGAGGTTTAACAAC-TTTGGAAAACAAATAAGACTT-TTT
1 AAATAGAGGCTTCACAACTTTTGAAAAATAAATAAGGCTTATCT
* * *
5327422 AAAATAGAAGC-TCAACAACTTTTGAAAAACTAAATAAGGCTCATTT
1 -AAATAGAGGCTTC-ACAACTTTTGAAAAA-TAAATAAGGCTTATCT
* * **
5327468 AAATAGAGGCTTAACGAC-TTTGAAAAATAAATAAGGCTCCTCT
1 AAATAGAGGCTTCACAACTTTTGAAAAATAAATAAGGCTTATCT
* *
5327511 AAACAGAGG-TTCAACAACTTTTGAAAAACTAAATAAGGCTTCTCT
1 AAATAGAGGCTTC-ACAACTTTTGAAAAA-TAAATAAGGCTTATCT
*
5327556 AAATAAAGGCT
1 AAATAGAGGCT
5327567 CAATGACTTA
Statistics
Matches: 153, Mismatches: 24, Indels: 18
0.78 0.12 0.09
Matches are distributed among these distances:
42 5 0.03
43 57 0.37
44 42 0.27
45 44 0.29
46 5 0.03
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (44 bp):
AAATAGAGGCTTCACAACTTTTGAAAAATAAATAAGGCTTATCT
Found at i:5327482 original size:88 final size:89
Alignment explanation
Indices: 5327327--5327566 Score: 301
Period size: 88 Copynumber: 2.7 Consensus size: 89
5327317 TAACATAAAA
* * *
5327327 ACTCCCCTAAAATAGAGGCTTC-ACAACTTTTGAAAAA-TAAATAAGGCTTATCTAAATAGAGGT
1 ACTCCTCTAAAATAGAGGC-TCAACAACTTTTGAAAAACTAAATAAGGCTCATCTAAATAGAGGC
*
5327390 TTAACAACTTTGGAAAACAAATAAG
65 TTAACAACTTTGAAAAACAAATAAG
* * * *
5327415 ACT-TTTTAAAATAGAAGCTCAACAACTTTTGAAAAACTAAATAAGGCTCATTTAAATAGAGGCT
1 ACTCCTCTAAAATAGAGGCTCAACAACTTTTGAAAAACTAAATAAGGCTCATCTAAATAGAGGCT
* *
5327479 TAACGACTTTGAAAAATAAATAAG
66 TAACAACTTTGAAAAACAAATAAG
* * * *
5327503 GCTCCTCT-AAACAGAGGTTCAACAACTTTTGAAAAACTAAATAAGGCTTC-TCTAAATAAAGGC
1 ACTCCTCTAAAATAGAGGCTCAACAACTTTTGAAAAACTAAATAAGGC-TCATCTAAATAGAGGC
5327566 T
65 T
5327567 CAATGACTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
86 2 0.02
87 26 0.20
88 98 0.75
89 4 0.03
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (89 bp):
ACTCCTCTAAAATAGAGGCTCAACAACTTTTGAAAAACTAAATAAGGCTCATCTAAATAGAGGCT
TAACAACTTTGAAAAACAAATAAG
Found at i:5327608 original size:60 final size:64
Alignment explanation
Indices: 5327530--5327650 Score: 162
Period size: 60 Copynumber: 2.0 Consensus size: 64
5327520 TTCAACAACT
*
5327530 TTTGAAAAACTAAATAAGGCTT-CTCTAAATAAAGGCTCAATGAC-TT-AAAAA-AAATAAATAC
1 TTTGAAAAACTAAATAAGG-TTACTCTAAACAAAGGCTCAATGACTTTGAAAAATAAATAAATAC
* * *
5327591 TTTGAAAAA-TAAATAAGGTTATTCTAAACAGAGTCTCAATGACTTTGAAAAATAAATAAA
1 TTTGAAAAACTAAATAAGGTTACTCTAAACAAAGGCTCAATGACTTTGAAAAATAAATAAA
5327651 GCTCCTCTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
59 2 0.04
60 27 0.52
61 11 0.21
62 5 0.10
63 7 0.13
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.28
Consensus pattern (64 bp):
TTTGAAAAACTAAATAAGGTTACTCTAAACAAAGGCTCAATGACTTTGAAAAATAAATAAATAC
Found at i:5327638 original size:43 final size:42
Alignment explanation
Indices: 5327589--5327736 Score: 197
Period size: 43 Copynumber: 3.5 Consensus size: 42
5327579 AAAAATAAAT
* *
5327589 ACTTTGAAAAATAAATAAGGTTATTCTAAACAGAGTCTCAATG
1 ACTTTGAAAAATAAATAAGGCTCTTCTAAACAGAG-CTCAATG
* * * *
5327632 ACTTTGAAAAATAAATAAAGCTCCTCTAAACAGAAGCTTAACG
1 ACTTTGAAAAATAAATAAGGCTCTTCTAAACAG-AGCTCAATG
5327675 ACTTTGAAAAATAAATAAGGCTCTTCTAAACAGAGGCTCAATG
1 ACTTTGAAAAATAAATAAGGCTCTTCTAAACAGA-GCTCAATG
* *
5327718 GCTTTAAAAAATAAATAAG
1 ACTTTGAAAAATAAATAAG
5327737 CTTTTCGATA
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
42 1 0.01
43 88 0.97
44 2 0.02
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.26
Consensus pattern (42 bp):
ACTTTGAAAAATAAATAAGGCTCTTCTAAACAGAGCTCAATG
Found at i:5327679 original size:148 final size:146
Alignment explanation
Indices: 5327442--5327734 Score: 396
Period size: 148 Copynumber: 2.0 Consensus size: 146
5327432 CTCAACAACT
* * *
5327442 TTTGAAAAACTAAATAAGGCTCATTTAAATAGAGGCTTAACGACTTTGAAAAATAAATAAGGCTC
1 TTTGAAAAACTAAATAAGGCTCATTTAAACAGAGGCTCAACGACTTTGAAAAATAAATAAAGCTC
* *
5327507 CTCTAAACAGAGGTTCAACAACTTTTGAAAAACTAAATAAGGCT-TCTCTAAATAAAGGCTCAAT
66 CTCTAAACAGAGCTTCAACAAC-TTTGAAAAA-TAAATAAGGCTCT-TCTAAACAAAGGCTCAAT
5327571 GACTTAAAAAAAATAAATAC
128 GACTT-AAAAAAATAAATAC
* * *
5327591 TTTGAAAAA-TAAATAAGG-TTATTCTAAACAGAGTCTCAATGACTTTGAAAAATAAATAAAGCT
1 TTTGAAAAACTAAATAAGGCTCATT-TAAACAGAGGCTCAACGACTTTGAAAAATAAATAAAGCT
* *
5327654 CCTCTAAACAGAAGCTT-AACGACTTTGAAAAATAAATAAGGCTCTTCTAAACAGAGGCTCAATG
65 CCTCTAAACAG-AGCTTCAACAACTTTGAAAAATAAATAAGGCTCTTCTAAACAAAGGCTCAATG
* *
5327718 GCTTTAAAAAATAAATA
129 ACTTAAAAAAATAAATA
5327735 AGCTTTTCGA
Statistics
Matches: 129, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
145 12 0.09
146 31 0.24
147 14 0.11
148 59 0.46
149 13 0.10
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.27
Consensus pattern (146 bp):
TTTGAAAAACTAAATAAGGCTCATTTAAACAGAGGCTCAACGACTTTGAAAAATAAATAAAGCTC
CTCTAAACAGAGCTTCAACAACTTTGAAAAATAAATAAGGCTCTTCTAAACAAAGGCTCAATGAC
TTAAAAAAATAAATAC
Found at i:5327685 original size:105 final size:106
Alignment explanation
Indices: 5327484--5327692 Score: 257
Period size: 105 Copynumber: 2.0 Consensus size: 106
5327474 AGGCTTAACG
* *
5327484 ACTTTGAAAAATAAATAAGGCTCCTCTAAACAGAGGTTCAACAACTTTTGAAAAACTAAATAAGG
1 ACTTTGAAAAATAAATAAGGCTACTCTAAACAGAGGTTCAACAACTTTTGAAAAACTAAATAAAG
* * *
5327549 CTTCTCTAAATAAAGGCTCAATGACTTAAAAA-AAATAAAT
66 CTCCTCTAAACAAAGGCTCAACGACTTAAAAATAAATAAAT
* * **
5327589 ACTTTGAAAAATAAATAAGGTTATTCTAAACAGA-GTCTCAATGAC-TTTGAAAAA-TAAATAAA
1 ACTTTGAAAAATAAATAAGGCTACTCTAAACAGAGGT-TCAACAACTTTTGAAAAACTAAATAAA
*
5327651 GCTCCTCTAAACAGAA-GCTTAACGACTTTGAAAAATAAATAA
65 GCTCCTCTAAACA-AAGGCTCAACGAC-TT-AAAAATAAATAA
5327693 GGCTCTTCTA
Statistics
Matches: 89, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
103 26 0.29
104 15 0.17
105 42 0.47
106 6 0.07
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.26
Consensus pattern (106 bp):
ACTTTGAAAAATAAATAAGGCTACTCTAAACAGAGGTTCAACAACTTTTGAAAAACTAAATAAAG
CTCCTCTAAACAAAGGCTCAACGACTTAAAAATAAATAAAT
Found at i:5329144 original size:17 final size:16
Alignment explanation
Indices: 5329097--5329148 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
5329087 AATTTGAGTA
5329097 TTCATTTTCTCTTATTTT
1 TTCATTTTC-CTT-TTTT
**
5329115 TT-ATTTTTATTTTTT
1 TTCATTTTCCTTTTTT
5329130 TATCATTTTCCTTTTTT
1 T-TCATTTTCCTTTTTT
5329147 TT
1 TT
5329149 ATTGATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 5 0.18
16 4 0.14
17 17 0.61
18 2 0.07
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (16 bp):
TTCATTTTCCTTTTTT
Found at i:5329156 original size:19 final size:19
Alignment explanation
Indices: 5329124--5329168 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
5329114 TTTATTTTTA
5329124 TTTTTTTATCA-TTTTCCT
1 TTTTTTTATCATTTTTCCT
* *
5329142 TTTTTTTATTGATTTTTTCT
1 TTTTTTTA-TCATTTTTCCT
5329162 TTTTTTT
1 TTTTTTT
5329169 CAATTTTCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
19 2 0.09
20 13 0.57
ACGTcount: A:0.09, C:0.09, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTTTTATCATTTTTCCT
Found at i:5336340 original size:15 final size:14
Alignment explanation
Indices: 5336318--5336352 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 14
5336308 TTCCAAAATT
5336318 TTTATTAAAATTTA
1 TTTATTAAAATTTA
5336332 TTTACTTAAAATTTA
1 TTTA-TTAAAATTTA
5336347 TTTATT
1 TTTATT
5336353 TTTTTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTATTAAAATTTA
Found at i:5337427 original size:14 final size:15
Alignment explanation
Indices: 5337395--5337432 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
5337385 CCAACTACTG
5337395 ATTTTTC-TTTTTGT
1 ATTTTTCATTTTTGT
*
5337409 TTTTTTCATTTTT-T
1 ATTTTTCATTTTTGT
5337423 ATTTTTCATT
1 ATTTTTCATT
5337433 GTTATTAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.11, C:0.08, G:0.03, T:0.79
Consensus pattern (15 bp):
ATTTTTCATTTTTGT
Found at i:5345248 original size:14 final size:14
Alignment explanation
Indices: 5345170--5345312 Score: 90
Period size: 14 Copynumber: 9.9 Consensus size: 14
5345160 GTACGAAAGG
*
5345170 TTTAGGATTTTGAT
1 TTTAGGGTTTTGAT
* *
5345184 TTTAGAGTTTGGAGAT
1 TTTAGGGTTT--TGAT
*
5345200 TTTAGGGTTTTGGT
1 TTTAGGGTTTTGAT
*** *
5345214 TTTA-AAATTTGAGG
1 TTTAGGGTTTTGA-T
5345228 TTTAGGGTTTTGAT
1 TTTAGGGTTTTGAT
* *
5345242 TTAAGGGTTTAGAT
1 TTTAGGGTTTTGAT
5345256 TTTAGGGATTTTGGAT
1 TTTAGGG-TTTT-GAT
* *
5345272 TTTGGGGTTTGGAT
1 TTTAGGGTTTTGAT
* * **
5345286 TTAAAGGTTGGGAT
1 TTTAGGGTTTTGAT
5345300 TTTAGGGTTTTGA
1 TTTAGGGTTTTGA
5345313 AACTTAAGAA
Statistics
Matches: 94, Mismatches: 29, Indels: 12
0.70 0.21 0.09
Matches are distributed among these distances:
13 4 0.04
14 58 0.62
15 11 0.12
16 21 0.22
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (14 bp):
TTTAGGGTTTTGAT
Found at i:5345287 original size:30 final size:28
Alignment explanation
Indices: 5345231--5345312 Score: 56
Period size: 30 Copynumber: 2.9 Consensus size: 28
5345221 TTTGAGGTTT
* * * *
5345231 AGGGTTTTGATTTAAGGGTTTAGATTTT
1 AGGGTTTAGATTTTAGGGTTTTGATTTA
* * *
5345259 AGGGATTTTGGATTTTGGGGTTTGGATTTA
1 AGGG--TTTAGATTTTAGGGTTTTGATTTA
* **
5345289 AAGGTTGGGATTTTAGGGTTTTGA
1 AGGGTTTAGATTTTAGGGTTTTGA
5345313 AACTTAAGAA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
28 21 0.49
30 22 0.51
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.46
Consensus pattern (28 bp):
AGGGTTTAGATTTTAGGGTTTTGATTTA
Found at i:5345554 original size:3 final size:3
Alignment explanation
Indices: 5345548--5345587 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
5345538 AATAAAAAAA
*
5345548 TAT TAT TAT TAT TAT TAT T-T AGAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT T
5345588 TTAAGCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 1 0.03
3 31 0.94
4 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:5346818 original size:25 final size:23
Alignment explanation
Indices: 5346781--5346828 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 23
5346771 TTAAAAATAT
5346781 TTATTATTATTATTATTACTAAAAA
1 TTATTATTATTATTA-TA-TAAAAA
*
5346806 TTATTATTGTTATTATATAAAAA
1 TTATTATTATTATTATATAAAAA
5346829 AGAGAGACCG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.27
24 2 0.09
25 14 0.64
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTATTATTATTATTATATAAAAA
Found at i:5346829 original size:25 final size:24
Alignment explanation
Indices: 5346771--5346829 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 24
5346761 TCAATTTTTT
*
5346771 TTAAAAATATTTATTATTATTATTA
1 TTAAAAA-AATTATTATTATTATTA
* *
5346796 TTACTAAAAATTATTATTGTTATTA
1 TTA-AAAAAATTATTATTATTATTA
5346821 TATAAAAAA
1 T-TAAAAAA
5346830 GAGAGACCGA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
25 23 0.82
26 5 0.18
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (24 bp):
TTAAAAAAATTATTATTATTATTA
Found at i:5347245 original size:88 final size:87
Alignment explanation
Indices: 5347044--5347300 Score: 293
Period size: 88 Copynumber: 2.9 Consensus size: 87
5347034 AGTTGATCGA
** * * *
5347044 GATAACATCGTGAGTCAAAATTAAAGAATCAATCAAGACAACATCGCGAATCAAAATTATGCCCA
1 GATAACATCGCAAGTCAAAAGTAAAGAATCAATCAAGACAACACCACGAATCAAAATTATGCCCA
*
5347109 GAGATTTTACAGAATCGACTGG
66 GAGATCTTACAGAATCGACTGG
** * ** *
5347131 GATAACATCGCAAGTTGAAAGATAAAGAATCGATCGGGATAACACCACGAATCAAAATTATGCCC
1 GATAACATCGCAAGTCAAAAG-TAAAGAATCAATCAAGACAACACCACGAATCAAAATTATGCCC
*
5347196 AGAGGTCTTACAGAATCGACTGG
65 AGAGATCTTACAGAATCGACTGG
* * * **
5347219 GATAACATCGCAAGTCAAAAAGTAAAGAATCAATTGAA-AAAATATTACGAATCAAAAATTATGC
1 GATAACATCGCAAGTC-AAAAGTAAAGAATCAA-TCAAGACAACACCACGAATC-AAAATTATGC
*
5347283 CCGGAGATCTTACA-AATC
63 CCAGAGATCTTACAGAATC
5347301 TCAAAATCTT
Statistics
Matches: 141, Mismatches: 25, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
87 16 0.11
88 98 0.70
89 27 0.19
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.21
Consensus pattern (87 bp):
GATAACATCGCAAGTCAAAAGTAAAGAATCAATCAAGACAACACCACGAATCAAAATTATGCCCA
GAGATCTTACAGAATCGACTGG
Found at i:5347469 original size:41 final size:42
Alignment explanation
Indices: 5347424--5347513 Score: 114
Period size: 41 Copynumber: 2.2 Consensus size: 42
5347414 ATATGAAGAA
*
5347424 GGTTCCTTC-TAAACAGAAGCTTTGAAATCTTAATT-GAAAT
1 GGTTCCTTCTTAAACAGAAGCTTTGAAATCTTAATTAAAAAT
* * *
5347464 CGGTTCC-TCTTAAATAGAGGCTTTGAAATCTTGATTAAAAAT
1 -GGTTCCTTCTTAAACAGAAGCTTTGAAATCTTAATTAAAAAT
5347506 GGTTCCTT
1 GGTTCCTT
5347514 TTATACAAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
40 2 0.05
41 35 0.83
42 5 0.12
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.37
Consensus pattern (42 bp):
GGTTCCTTCTTAAACAGAAGCTTTGAAATCTTAATTAAAAAT
Found at i:5349772 original size:8 final size:9
Alignment explanation
Indices: 5349760--5349784 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5349750 TTTTTCTTTT
5349760 TTTTTTTGA
1 TTTTTTTGA
5349769 TTTTTTTGA
1 TTTTTTTGA
5349778 TTTTTTT
1 TTTTTTT
5349785 TTTAAATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (9 bp):
TTTTTTTGA
Found at i:5355187 original size:20 final size:20
Alignment explanation
Indices: 5355163--5355202 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
5355153 TAATATTACA
*
5355163 ATTTTTT-TTA-AAAGTATT
1 ATTTTTTATTATAAAATATT
5355181 ATTTTTTATTATAAAATATT
1 ATTTTTTATTATAAAATATT
5355201 AT
1 AT
5355203 ATCACCAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 3 0.16
20 9 0.47
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (20 bp):
ATTTTTTATTATAAAATATT
Found at i:5355678 original size:29 final size:28
Alignment explanation
Indices: 5355644--5355720 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 28
5355634 AAGGTACGAA
* *
5355644 AGATTTAGAGTTTTGATTTTAGAATTTGG
1 AGATTTAGGGTTTTGATTTTAAAATTT-G
*
5355673 AGATTTTAGGGTTTTGGTTTTAAAATTTG
1 AGA-TTTAGGGTTTTGATTTTAAAATTTG
* *
5355702 AGGTTTGGGGTTTTGATTT
1 AGATTTAGGGTTTTGATTT
5355721 AAGGGTTTAG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
28 14 0.34
29 6 0.15
30 21 0.51
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (28 bp):
AGATTTAGGGTTTTGATTTTAAAATTTG
Found at i:5355728 original size:14 final size:14
Alignment explanation
Indices: 5355709--5355771 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
5355699 TTGAGGTTTG
5355709 GGGTTTTGATTTAA
1 GGGTTTTGATTTAA
* *
5355723 GGGTTTAGATTTTA
1 GGGTTTTGATTTAA
**
5355737 GGGATTTTGGATTTTG
1 GGG-TTTT-GATTTAA
*
5355753 GGGTTTGGATTTAA
1 GGGTTTTGATTTAA
*
5355767 AGGTT
1 GGGTT
5355772 GGGTTTCAGG
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
14 24 0.62
15 6 0.15
16 9 0.23
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.48
Consensus pattern (14 bp):
GGGTTTTGATTTAA
Found at i:5357143 original size:21 final size:21
Alignment explanation
Indices: 5357102--5357144 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
5357092 TTGGGTGGAG
*
5357102 TAGGGTGGCTGCAGGGATGGC
1 TAGGGTGGCTGCAGAGATGGC
*
5357123 TAGGGTAGGCTGTAGAG-TGGC
1 TAGGGT-GGCTGCAGAGATGGC
5357144 T
1 T
5357145 GTAGGGGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.16, C:0.12, G:0.49, T:0.23
Consensus pattern (21 bp):
TAGGGTGGCTGCAGAGATGGC
Found at i:5361915 original size:43 final size:43
Alignment explanation
Indices: 5361841--5362019 Score: 207
Period size: 43 Copynumber: 4.2 Consensus size: 43
5361831 AAGTAGAATA
* * *
5361841 TTTTAAAATTTCAAAACTCGTTGAACTTCTACTTAGAGGAGTC
1 TTTTAAATTTTCAAAAGTCGTTGAACCTCTACTTAGAGGAGTC
* * * *
5361884 TTTTAAATTTTCAAAAGTCATTGAGCCTCTACTTATAGAAGTC
1 TTTTAAATTTTCAAAAGTCGTTGAACCTCTACTTAGAGGAGTC
* * * *
5361927 TTTTAAGTTTTCAAAAATTGTTGAACCTCTACTTAAAGGAG-C
1 TTTTAAATTTTCAAAAGTCGTTGAACCTCTACTTAGAGGAGTC
* * * *
5361969 TTTTTAAATTTTCAAAAGTTGTTGAGCCTTTACTTAGAGGAGTT
1 -TTTTAAATTTTCAAAAGTCGTTGAACCTCTACTTAGAGGAGTC
5362013 TTTTAAA
1 TTTTAAA
5362020 GTTGTCGAGC
Statistics
Matches: 114, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
42 1 0.01
43 113 0.99
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (43 bp):
TTTTAAATTTTCAAAAGTCGTTGAACCTCTACTTAGAGGAGTC
Found at i:5361986 original size:86 final size:86
Alignment explanation
Indices: 5361849--5362018 Score: 234
Period size: 86 Copynumber: 2.0 Consensus size: 86
5361839 TATTTTAAAA
* * *
5361849 TTTCAAAACTCGTTGAACTTCTACTTAGAGGAGTCTTTTAAATTTTCAAAAGTCATTGAGCCTCT
1 TTTCAAAAATCGTTGAACCTCTACTTAAAGGAGTCTTTTAAATTTTCAAAAGTCATTGAGCCTCT
*
5361914 ACTTATAGAAGTCTTTTAAGT
66 ACTTAGAGAAGTCTTTTAAGT
* ** *
5361935 TTTCAAAAATTGTTGAACCTCTACTTAAAGGAG-CTTTTTAAATTTTCAAAAGTTGTTGAGCCTT
1 TTTCAAAAATCGTTGAACCTCTACTTAAAGGAGTC-TTTTAAATTTTCAAAAGTCATTGAGCCTC
* *
5361999 TACTTAGAGGAGTTTTTTAA
65 TACTTAGAGAAGTCTTTTAA
5362019 AGTTGTCGAG
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
85 1 0.01
86 72 0.99
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.41
Consensus pattern (86 bp):
TTTCAAAAATCGTTGAACCTCTACTTAAAGGAGTCTTTTAAATTTTCAAAAGTCATTGAGCCTCT
ACTTAGAGAAGTCTTTTAAGT
Found at i:5362075 original size:36 final size:36
Alignment explanation
Indices: 5361977--5362076 Score: 105
Period size: 36 Copynumber: 2.8 Consensus size: 36
5361967 GCTTTTTAAA
* ** *
5361977 TTTTCAAAAGTTGTTGAGCCTTTACTTAG-AGGAGT
1 TTTTCAAAAGTTGTTGAGCCTTTATTTAGAAAAACT
* * **
5362012 TTTT-TAAAGTTGTCGAGCCTTCGTTTAGAAAAACT
1 TTTTCAAAAGTTGTTGAGCCTTTATTTAGAAAAACT
*
5362047 TTTTCAAAAGATGTTGAGCCTTTATTTAGA
1 TTTTCAAAAGTTGTTGAGCCTTTATTTAGA
5362077 TGAGCCTTTT
Statistics
Matches: 50, Mismatches: 13, Indels: 3
0.76 0.20 0.05
Matches are distributed among these distances:
34 19 0.38
35 11 0.22
36 20 0.40
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (36 bp):
TTTTCAAAAGTTGTTGAGCCTTTATTTAGAAAAACT
Found at i:5363299 original size:34 final size:34
Alignment explanation
Indices: 5363235--5363299 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
5363225 ATTAGCATTT
*
5363235 TTTTCTTTATTATTTTATTATTTATTATTTACTA
1 TTTTCTTTATTATTTTAGTATTTATTATTTACTA
*
5363269 TTTT-TTTGTTATTTCTAGTATTT-TTAATTTA
1 TTTTCTTTATTATTT-TAGTATTTATT-ATTTA
5363300 TAAGTTAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 11 0.41
34 16 0.59
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.71
Consensus pattern (34 bp):
TTTTCTTTATTATTTTAGTATTTATTATTTACTA
Found at i:5363394 original size:18 final size:18
Alignment explanation
Indices: 5363371--5363406 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
5363361 TGAATGAATA
5363371 AAATAAATACTGA-AAAAT
1 AAATAAATA-TGATAAAAT
5363389 AAATAAATATGATAAAAT
1 AAATAAATATGATAAAAT
5363407 TAAAGAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.18
18 14 0.82
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
AAATAAATATGATAAAAT
Found at i:5363548 original size:122 final size:122
Alignment explanation
Indices: 5363421--5363743 Score: 397
Period size: 122 Copynumber: 2.7 Consensus size: 122
5363411 GAAATTACAT
* *
5363421 GTGGTGATTTTATTAAAAATATTTATTTAAGGAAATTTTCTAAAATATTCTAAAAGTGTAAGAAA
1 GTGGTGATTTTATTAAAAATATTTATATAAAGAAATTTTCTAAAATATTCTAAAAGTGTAAGAAA
* * *
5363486 TATTTTAGATTTTTTTTAAACAT-TAAAAAAATTATTAATAA-AAAATAAAATTCAC-A
66 TATTTTAGAATTTTTTTAAA-ATATAAAAAAAATATTAATAATAAAAT-AAAGTCACAA
* * * * *
5363542 GATGGTGATTTTACTAAAAATATTTATACAAAGAGATTTTCTATAATATTCTAAAAGTGTCAGAG
1 G-TGGTGATTTTATTAAAAATATTTATATAAAGAAATTTTCTAAAATATTCTAAAAGTGTAAGA-
* *
5363607 AATATTTTAGAATTTTTTTCAAATATAAAAAAAATATTATTAATAAAATAAAGTCACAA
64 AATATTTTAGAATTTTTTTAAAATATAAAAAAAATATTAATAATAAAATAAAGTCACAA
* * * * * *
5363666 GTGGTGATTTTATT-GAAA-ATTTATATAAAGAAATTTTTTTAAAGTATTATAAAAGTATTAGAA
1 GTGGTGATTTTATTAAAAATATTTATATAAAGAAA-TTTTCTAAAATATTCTAAAAGTGTAAGAA
5363729 ATA-TTTAGAATTTTT
65 ATATTTTAGAATTTTT
5363744 CAAACACAAA
Statistics
Matches: 174, Mismatches: 22, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
120 12 0.07
121 18 0.10
122 82 0.47
123 55 0.32
124 7 0.04
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.41
Consensus pattern (122 bp):
GTGGTGATTTTATTAAAAATATTTATATAAAGAAATTTTCTAAAATATTCTAAAAGTGTAAGAAA
TATTTTAGAATTTTTTTAAAATATAAAAAAAATATTAATAATAAAATAAAGTCACAA
Found at i:5363800 original size:17 final size:16
Alignment explanation
Indices: 5363751--5363804 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
5363741 TTTCAAACAC
5363751 AAAAATT-AAATAAAT
1 AAAAATTAAAATAAAT
*
5363766 ACATAAA-TAAAATTAAT
1 A-A-AAATTAAAATAAAT
5363783 AAAAATTAAAATAAAAT
1 AAAAATTAAAAT-AAAT
5363800 AAAAA
1 AAAAA
5363805 ATGATGATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
15 4 0.12
16 9 0.28
17 19 0.59
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAATTAAAATAAAT
Found at i:5364135 original size:17 final size:17
Alignment explanation
Indices: 5364109--5364153 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
5364099 AAAATATTAA
5364109 AATAAATCCAAAAGCAC
1 AATAAATCCAAAAGCAC
* *
5364126 AATAAGTCCAAAATCAC
1 AATAAATCCAAAAGCAC
5364143 AATAAATCCAA
1 AATAAATCCAA
5364154 GTGATTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.58, C:0.22, G:0.04, T:0.16
Consensus pattern (17 bp):
AATAAATCCAAAAGCAC
Found at i:5365753 original size:23 final size:21
Alignment explanation
Indices: 5365727--5365778 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 21
5365717 AGAAAAGATG
5365727 TTTTGAAACAAAAAATGAAAAA
1 TTTTGAAACAAAAAATG-AAAA
** *
5365749 CTTTTGAAATGAAAAGTGAAAA
1 -TTTTGAAACAAAAAATGAAAA
5365771 TTTTGAAA
1 TTTTGAAA
5365779 TGAAAAGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 8 0.31
22 4 0.15
23 14 0.54
ACGTcount: A:0.54, C:0.04, G:0.13, T:0.29
Consensus pattern (21 bp):
TTTTGAAACAAAAAATGAAAA
Found at i:5365776 original size:21 final size:23
Alignment explanation
Indices: 5365727--5365785 Score: 77
Period size: 21 Copynumber: 2.7 Consensus size: 23
5365717 AGAAAAGATG
** *
5365727 TTTTGAAACAAAAAATGAAAAAC
1 TTTTGAAATGAAAAGTGAAAAAC
5365750 TTTTGAAATGAAAAGTG-AAAA-
1 TTTTGAAATGAAAAGTGAAAAAC
5365771 TTTTGAAATGAAAAG
1 TTTTGAAATGAAAAG
5365786 ATTTCAAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 15 0.45
22 4 0.12
23 14 0.42
ACGTcount: A:0.54, C:0.03, G:0.15, T:0.27
Consensus pattern (23 bp):
TTTTGAAATGAAAAGTGAAAAAC
Found at i:5365933 original size:41 final size:40
Alignment explanation
Indices: 5365825--5365958 Score: 144
Period size: 41 Copynumber: 3.3 Consensus size: 40
5365815 GGAGAATGAC
* *
5365825 TAAATGATTTCCAAAGACCTCCGGGCAAAATCTTAAATTC
1 TAAATGATTTCCAAAGACCTCCGGGCAAAATCTTAATTTT
** *
5365865 TAAATGATTT-TTAAGACCTCCGGGCAAAATTTTAGATTTT
1 TAAATGATTTCCAAAGACCTCCGGGCAAAATCTTA-ATTTT
* ** *
5365905 TGAATGATTTCCAAAGACCTTAGAGCAAAATCTTAAATTTT
1 TAAATGATTTCCAAAGACCTCCGGGCAAAATCTT-AATTTT
* *
5365946 TCAATAATTTCCA
1 TAAATGATTTCCA
5365959 TGATCTTCGG
Statistics
Matches: 77, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
39 21 0.27
40 22 0.29
41 33 0.43
42 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (40 bp):
TAAATGATTTCCAAAGACCTCCGGGCAAAATCTTAATTTT
Found at i:5366909 original size:103 final size:104
Alignment explanation
Indices: 5366061--5366915 Score: 621
Period size: 104 Copynumber: 8.2 Consensus size: 104
5366051 GCATAATCTC
* * * * * * * * *
5366061 TAAGACCTTTAGACATCATCACTAAAACCTTCGA-CAAAATATTTTAAAGTTTTAATGTTTCAAT
1 TAAGACCTCTGGACATAATCTCTAAGACCTTTGAGCAAAACATTTTAAATTTTTAAAGTTTCAAT
* * * * * *
5366125 GCCT-TTAATTA-AATGAGCTTTCATAAATATCAAGATTTC
66 ACCTCTT-ATTAGAA-GAGCTTTAATAGATGTTAAGATTTG
* * * *** * * *
5366164 TAAGACCTCTGGGCACAACCTCTATA-ACCTCCAAGCAAAATATTTTAAATTTTTGAAGTTTTAA
1 TAAGACCTCTGGACATAATCTCTA-AGACCTTTGAGCAAAACATTTTAAATTTTTAAAGTTTCAA
* * * * ** * * *
5366228 TGCCTCTAATAAGATA-AGTTTTTTTAAATATCAAGATTTG
65 TACCTCTTATTAGA-AGAGCTTTAATAGATGTTAAGATTTG
* * * *
5366268 TAAGA-CTTTCGAGCATAATCTCTAAGACC-TTCAGGCAAAATATTTTAAATTTTTAAAGTTTCA
1 TAAGACCTCTGGA-CATAATCTCTAAGACCTTTGA-GCAAAACATTTTAAATTTTTAAAGTTTCA
** *
5366331 ATGTCT-TTGATTAGAAGAGCTTTCATAGATGTTAAGATTTG
64 ATACCTCTT-ATTAGAAGAGCTTTAATAGATGTTAAGATTTG
* *
5366372 TAAGACCTCCAGG-CATAATCTCTAAGACCTCTTG-GCAAAGCATTTTAAATTTTTAAAGCTTT-
1 TAAGACCT-CTGGACATAATCTCTAAGACCT-TTGAGCAAAACATTTTAAATTTTTAAAG-TTTC
** * * * *
5366434 AATACCGGTGATTAAAAGAGTTTTCATAGATGTTAAGATTTG
63 AATACCTCTTATTAGAAGAGCTTTAATAGATGTTAAGATTTG
* * * * *
5366476 TAAGACCTTTGAACATAATCTCTAAGA-CTTTCGGGCAAAGCATTTTAAATTTTTAAAGCTTCAA
1 TAAGACCTCTGGACATAATCTCTAAGACCTTT-GAGCAAAACATTTTAAATTTTTAAAGTTTCAA
* * * * * * * **
5366540 T-GCTGATGATTA-AAGGTGTTTTCATATATGTCGAGATTTG
65 TACCT-CTTATTAGAA-GAGCTTTAATAGATGTTAAGATTTG
** * * * * *
5366580 TAAGATTTCTGGGCATAATCTCTAA-AACTTCAGGGCAAAATATTTTAAATTTTTAAAGTTTCAA
1 TAAGACCTCTGGACATAATCTCTAAGACCTT-TGAGCAAAACATTTTAAATTTTTAAAGTTTCAA
* * * *
5366644 TATCTCTAATTAGAATAGCTTTAATAGATGTTGAGATTTG
65 TACCTCTTATTAGAAGAGCTTTAATAGATGTTAAGATTTG
* * * * * *
5366684 TAAGACTTC-GGGCATAATCTCTAAGTCCTTTGAGCAAAACATTTTAAATGTTTAAAGTTTTAAC
1 TAAGACCTCTGGACATAATCTCTAAGACCTTTGAGCAAAACATTTTAAATTTTTAAAGTTTCAAT
* *
5366748 AACTCTTATTAGATGAGCTTTAATAGATGTTAAGATTTG
66 ACCTCTTATTAGAAGAGCTTTAATAGATGTTAAGATTTG
** * *
5366787 TAAGACCTC-CAAAAGTAATCTCTAAGTCCTTTGAG-AAAACATTTTAAATTTTTAAAGTTTCAA
1 TAAGACCTCTGGACA-TAATCTCTAAGACCTTTGAGCAAAACATTTTAAATTTTTAAAGTTTCAA
* * **
5366850 TGCCTCTTATTAGAGGAGCTTTAATAGATGGCAAGATTTG
65 TACCTCTTATTAGAAGAGCTTTAATAGATGTTAAGATTTG
* * *
5366890 TAAAACCTCTGGATATAATCTTTAAG
1 TAAGACCTCTGGACATAATCTCTAAG
5366916 TCCTCAAGGC
Statistics
Matches: 612, Mismatches: 111, Indels: 58
0.78 0.14 0.07
Matches are distributed among these distances:
102 2 0.00
103 205 0.33
104 389 0.64
105 12 0.02
106 4 0.01
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (104 bp):
TAAGACCTCTGGACATAATCTCTAAGACCTTTGAGCAAAACATTTTAAATTTTTAAAGTTTCAAT
ACCTCTTATTAGAAGAGCTTTAATAGATGTTAAGATTTG
Found at i:5367686 original size:25 final size:25
Alignment explanation
Indices: 5367641--5367690 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
5367631 TTATATACAG
* *
5367641 AAAAAACACACACACAAAAATTAAA
1 AAAAAAAACAAACACAAAAATTAAA
5367666 AAAAAAAACAAACA-AACAAATTAAA
1 AAAAAAAACAAACACAA-AAATTAAA
5367691 GGTGACCAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.76, C:0.16, G:0.00, T:0.08
Consensus pattern (25 bp):
AAAAAAAACAAACACAAAAATTAAA
Found at i:5369752 original size:3 final size:3
Alignment explanation
Indices: 5369744--5369803 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
5369734 AGAAAATATG
5369744 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5369792 TAA TAA TAA TAA
1 TAA TAA TAA TAA
5369804 ATTTTCATAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5378903 original size:30 final size:29
Alignment explanation
Indices: 5378863--5378966 Score: 118
Period size: 30 Copynumber: 3.5 Consensus size: 29
5378853 TATATTTTTA
*
5378863 TTATATTTAAATAAACTCTTAAATTTTAAT
1 TTATATTTAAATAAA-TCCTAAATTTTAAT
* ** *
5378893 TTACATTTAAATATGTCACTAATTTTTAAT
1 TTATATTTAAATAAATC-CTAAATTTTAAT
*
5378923 TTTTATTTAAATAAATCCTAAATCTTTAAT
1 TTATATTTAAATAAATCCTAAAT-TTTAAT
*
5378953 TTATACTTAAATAA
1 TTATATTTAAATAA
5378967 GTTTTTAATT
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
29 7 0.12
30 53 0.88
ACGTcount: A:0.41, C:0.09, G:0.01, T:0.49
Consensus pattern (29 bp):
TTATATTTAAATAAATCCTAAATTTTAAT
Found at i:5378976 original size:60 final size:60
Alignment explanation
Indices: 5378844--5379000 Score: 149
Period size: 60 Copynumber: 2.6 Consensus size: 60
5378834 TTTTAGTTAG
* * * *
5378844 ATAAATTTTTATATTTTT-A-TTATATTTAAATAAACTCTTAAATTTTAATTTACATTTAA
1 ATAAGTTTTTA-ATTTTTAATTTTTATTTAAATAAACTCCTAAATTTTAATTTACACTTAA
* *** *
5378903 ATATGTCACTAATTTTTAATTTTTATTTAAATAAA-TCCTAAATCTTTAATTTATACTTAA
1 ATAAGTTTTTAATTTTTAATTTTTATTTAAATAAACTCCTAAAT-TTTAATTTACACTTAA
*
5378963 ATAAGTTTTTAATTAAATTAATATTTTATTTGAAATAA
1 ATAAGTTTTTAATT--TTTAAT-TTTTATTT-AAATAA
5379001 GAGTTTATTT
Statistics
Matches: 77, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
58 6 0.08
59 14 0.18
60 38 0.49
62 5 0.06
63 8 0.10
64 6 0.08
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.52
Consensus pattern (60 bp):
ATAAGTTTTTAATTTTTAATTTTTATTTAAATAAACTCCTAAATTTTAATTTACACTTAA
Found at i:5388703 original size:20 final size:23
Alignment explanation
Indices: 5388668--5388709 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 23
5388658 GGAAAGAAAG
5388668 ATTATACAAGTAAAATT-TTAAA
1 ATTATACAAGTAAAATTATTAAA
5388690 ATTATA-AA-TAAAATTATTAA
1 ATTATACAAGTAAAATTATTAA
5388710 TTTAAGTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
21 6 0.32
22 6 0.32
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (23 bp):
ATTATACAAGTAAAATTATTAAA
Found at i:5392183 original size:16 final size:16
Alignment explanation
Indices: 5392142--5392184 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
5392132 AATTTTTAAA
*
5392142 TTATATTACTTACATAT
1 TTATATTA-TAACATAT
* *
5392159 TTTTTTTATAACATAT
1 TTATATTATAACATAT
5392175 TTATATTATA
1 TTATATTATA
5392185 TTATCATATT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATATTATAACATAT
Found at i:5392209 original size:20 final size:19
Alignment explanation
Indices: 5392170--5392210 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
5392160 TTTTTTATAA
*
5392170 CATATTTATATTATATTAT
1 CATATTTATATTAAATTAT
*
5392189 CATATTATATTTTAAATTAT
1 CATATT-TATATTAAATTAT
5392209 CA
1 CA
5392211 ATGTCTTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (19 bp):
CATATTTATATTAAATTAT
Found at i:5393218 original size:24 final size:26
Alignment explanation
Indices: 5393178--5393236 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
5393168 AGTTTGTATA
5393178 ATTTTAAATTAACAT-A-ATATTATG
1 ATTTTAAATTAACATAAGATATTATG
* *
5393202 ATTTTAAATTGAA-ATAAGATATTTTT
1 ATTTTAAATT-AACATAAGATATTATG
5393228 ATTTTAAAT
1 ATTTTAAAT
5393237 AAATCATAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 12 0.40
25 3 0.10
26 15 0.50
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (26 bp):
ATTTTAAATTAACATAAGATATTATG
Found at i:5393285 original size:17 final size:17
Alignment explanation
Indices: 5393260--5393292 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5393250 AGAGAGGTAA
5393260 AAATAGAATGGTAAACC
1 AAATAGAATGGTAAACC
*
5393277 AAATGGAATGGTAAAC
1 AAATAGAATGGTAAAC
5393293 AATAGTTACT
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:0.52, C:0.09, G:0.21, T:0.18
Consensus pattern (17 bp):
AAATAGAATGGTAAACC
Found at i:5395152 original size:4 final size:4
Alignment explanation
Indices: 5395128--5395174 Score: 51
Period size: 4 Copynumber: 11.2 Consensus size: 4
5395118 TCCTATTTGA
*
5395128 TATT T-TT TATTT TATTT TATT TATT TATTT TATT TGTT TATT TATT T
1 TATT TATT TA-TT TA-TT TATT TATT TA-TT TATT TATT TATT TATT T
5395175 TTAAAGTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
3 3 0.08
4 22 0.58
5 13 0.34
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (4 bp):
TATT
Found at i:5395156 original size:13 final size:13
Alignment explanation
Indices: 5395133--5395174 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
5395123 TTTGATATTT
5395133 TTTATTTTATTTTA
1 TTTA-TTTATTTTA
5395147 TTTATTTATTTTA
1 TTTATTTATTTTA
*
5395160 TTTGTTTA-TTTA
1 TTTATTTATTTTA
5395172 TTT
1 TTT
5395175 TTAAAGTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 7 0.26
13 16 0.59
14 4 0.15
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:5397556 original size:22 final size:22
Alignment explanation
Indices: 5397501--5397560 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
5397491 AAATTTTCCT
*
5397501 TTTTTCTTATTTT-TT-ATTAC
1 TTTTTCTTATTTTATTAATTAA
* *
5397521 TTATTCTTAATTTATTAATTAA
1 TTTTTCTTATTTTATTAATTAA
*
5397543 TTTTTATTATTTTATTAA
1 TTTTTCTTATTTTATTAA
5397561 AGAAAAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 11 0.34
21 2 0.06
22 19 0.59
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTTCTTATTTTATTAATTAA
Found at i:5397726 original size:21 final size:21
Alignment explanation
Indices: 5397701--5397746 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
5397691 GATAAAAAAA
* *
5397701 AATTTTTTCTTATTTTTCA-TT
1 AATTTTGTATTATTTTT-ATTT
5397722 AATTTTGTATTATTTTTATTT
1 AATTTTGTATTATTTTTATTT
5397743 AATT
1 AATT
5397747 ATACTTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (21 bp):
AATTTTGTATTATTTTTATTT
Found at i:5397799 original size:13 final size:13
Alignment explanation
Indices: 5397730--5397805 Score: 55
Period size: 13 Copynumber: 5.8 Consensus size: 13
5397720 TTAATTTTGT
5397730 ATTATTTTTATTTA
1 ATTATTTTTA-TTA
** *
5397744 ATTATACTTATAA
1 ATTATTTTTATTA
**
5397757 AAAATTTTTATT-
1 ATTATTTTTATTA
* *
5397769 ATAAATTTTATTA
1 ATTATTTTTATTA
*
5397782 TTTATTTTTATTA
1 ATTATTTTTATTA
*
5397795 ATTATTATTAT
1 ATTATTTTTAT
5397806 AAAATAATAA
Statistics
Matches: 46, Mismatches: 15, Indels: 3
0.72 0.23 0.05
Matches are distributed among these distances:
12 10 0.22
13 28 0.61
14 8 0.17
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTATTTTTATTA
Found at i:5399295 original size:142 final size:140
Alignment explanation
Indices: 5399059--5399551 Score: 475
Period size: 142 Copynumber: 3.5 Consensus size: 140
5399049 TCTCTAATCT
* * * * *
5399059 GGTTAAACAACTTTAAAAATTCATATTGAAAAAGACTCATCTAAGTAGAGGCTCAATAACTTTAA
1 GGTTCAACAACTTT-AAAATTCATTTTGAAAAAAACTCCTCTAAGTAGAGGCTCAACAACTTTAA
* * * *
5399124 AATTCATCTTGAGAAAAAGCTCTTATAAGTAGAGGCTCAACAACTTTAAAAAAATTT-AAAAAGC
65 AATTCATCTTGA-AAAAAGTTC-TCTAAGTAGAGACTCAATAACTTTAAAAAAATTTAAAAAAGC
*
5399188 TCCTCTAAGTAGC
128 TCCTCTAAGTAGA
*
5399201 GGTTCAACAACTTTAAAATTCATTTTGAAAAAAAGCTCCTCTAAGTAGAGGCTCAATAACTTTAA
1 GGTTCAACAACTTTAAAATTCATTTTGAAAAAAA-CTCCTCTAAGTAGAGGCTCAACAACTTTAA
* *
5399266 AATTCATCTTGAAAAAAAGTTCATCTAAGTAGAGACTCAATAACTTTAAAATTCATTTTGAAAAA
65 AATTCATCTTG-AAAAAAGTTC-TCTAAGTAGAGACTCAATAACTTTAAAA--AAATTT-AAAAA
* * * *
5399331 AACTCCTCTTATTATA
125 AGCTCCTCTAAGTAGA
* * * * * * *
5399347 GGCTCAATAACTTTAAAATTAATCTTGAAAAAAACTTCTTTCAGTAGAGGCTCAACAACTTTAAA
1 GGTTCAACAACTTTAAAATTCATTTTGAAAAAAACTCCTCTAAGTAGAGGCTCAACAACTTTAAA
* * * **
5399412 A-T--TCTTG-AAAATGCTTCTCTCAGCAGAGACTCAATAACTTTAAAAATTTTTAAAAAAATGC
66 ATTCATCTTGAAAAAAG-TTCTCTAAGTAGAGACTCAATAACTTTAAAAAAATTT-AAAAAA-GC
*
5399473 TCCTCTCAGTAGA
128 TCCTCTAAGTAGA
** * * *
5399486 GGCTTC-ACAACTTTAAAA---ATTCTT-AAAAATGCTGCTCTCAGCAGAGGCTCAACAACTTTA
1 GG-TTCAACAACTTTAAAATTCATT-TTGAAAAAAACTCCTCTAAGTAGAGGCTCAACAACTTTA
5399546 AAATTC
64 AAATTC
5399552 CACTTTTCTC
Statistics
Matches: 297, Mismatches: 42, Indels: 28
0.81 0.11 0.08
Matches are distributed among these distances:
136 36 0.12
137 3 0.01
138 10 0.03
139 24 0.08
140 33 0.11
141 21 0.07
142 91 0.31
143 1 0.00
144 5 0.02
145 28 0.09
146 45 0.15
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (140 bp):
GGTTCAACAACTTTAAAATTCATTTTGAAAAAAACTCCTCTAAGTAGAGGCTCAACAACTTTAAA
ATTCATCTTGAAAAAAGTTCTCTAAGTAGAGACTCAATAACTTTAAAAAAATTTAAAAAAGCTCC
TCTAAGTAGA
Found at i:5399356 original size:48 final size:48
Alignment explanation
Indices: 5399067--5399551 Score: 417
Period size: 49 Copynumber: 10.3 Consensus size: 48
5399057 CTGGTTAAAC
* * *
5399067 AACTTTAAAAATTCATATTGAAAAAGACTCATCTAAGTAGAGGCTCAAT
1 AACTTT-AAAATTCATCTTGAAAAAAACTCCTCTAAGTAGAGGCTCAAT
* * * *
5399116 AACTTTAAAATTCATCTTGAGAAAAAGCTCTTATAAGTAGAGGCTCAAC
1 AACTTTAAAATTCATCTTGA-AAAAAACTCCTCTAAGTAGAGGCTCAAT
** * * * *
5399165 AACTTTAAAA-AAAT-TT--AAAAAGCTCCTCTAAGTAGCGGTTCAAC
1 AACTTTAAAATTCATCTTGAAAAAAACTCCTCTAAGTAGAGGCTCAAT
*
5399209 AACTTTAAAATTCATTTTGAAAAAAAGCTCCTCTAAGTAGAGGCTCAAT
1 AACTTTAAAATTCATCTTGAAAAAAA-CTCCTCTAAGTAGAGGCTCAAT
* * *
5399258 AACTTTAAAATTCATCTTGAAAAAAAGTTCATCTAAGTAGAGACTCAAT
1 AACTTTAAAATTCATCTTGAAAAAAA-CTCCTCTAAGTAGAGGCTCAAT
* * * *
5399307 AACTTTAAAATTCATTTTGAAAAAAACTCCTCTTATTATAGGCTCAAT
1 AACTTTAAAATTCATCTTGAAAAAAACTCCTCTAAGTAGAGGCTCAAT
* * * * *
5399355 AACTTTAAAATTAATCTTGAAAAAAACTTCTTTCAGTAGAGGCTCAAC
1 AACTTTAAAATTCATCTTGAAAAAAACTCCTCTAAGTAGAGGCTCAAT
** * * * *
5399403 AACTTTAAAA-T--TCTTG-AAAATGCTTCTCTCAGCAGAGACTCAAT
1 AACTTTAAAATTCATCTTGAAAAAAACTCCTCTAAGTAGAGGCTCAAT
* *
5399447 AACTTTAAAAATT--T-TT-AAAAAAATGCTCCTCTCAGTAGAGGCTTC-AC
1 AACTTT-AAAATTCATCTTGAAAAAAA--CTCCTCTAAGTAGAGGC-TCAAT
* ** * * * *
5399494 AACTTTAAAAAT--TCTT-AAAAATGCTGCTCTCAGCAGAGGCTCAAC
1 AACTTTAAAATTCATCTTGAAAAAAACTCCTCTAAGTAGAGGCTCAAT
5399539 AACTTTAAAATTC
1 AACTTTAAAATTC
5399552 CACTTTTCTC
Statistics
Matches: 366, Mismatches: 55, Indels: 33
0.81 0.12 0.07
Matches are distributed among these distances:
44 64 0.17
45 45 0.12
46 10 0.03
47 31 0.08
48 88 0.24
49 128 0.35
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (48 bp):
AACTTTAAAATTCATCTTGAAAAAAACTCCTCTAAGTAGAGGCTCAAT
Found at i:5399458 original size:45 final size:45
Alignment explanation
Indices: 5399346--5399548 Score: 221
Period size: 45 Copynumber: 4.4 Consensus size: 45
5399336 CTCTTATTAT
* * ** * *
5399346 AGGCTCAATAACTTTAAAATTAATCTTGAAAAAAACTTCTTTCAGTAG
1 AGGCTCAACAACTTTAAAA--ATTCTT-AAAAATGCTTCTCTCAGCAG
*
5399394 AGGCTCAACAACTTT-AAAATTCTTGAAAATGCTTCTCTCAGCAG
1 AGGCTCAACAACTTTAAAAATTCTTAAAAATGCTTCTCTCAGCAG
* * * * *
5399438 AGACTCAATAACTTTAAAAATTTTTAAAAAAATGCTCCTCTCAGTAG
1 AGGCTCAACAACTTTAAAAATTCTT--AAAAATGCTTCTCTCAGCAG
*
5399485 AGGCTTC-ACAACTTTAAAAATTCTTAAAAATGCTGCTCTCAGCAG
1 AGGC-TCAACAACTTTAAAAATTCTTAAAAATGCTTCTCTCAGCAG
5399530 AGGCTCAACAACTTTAAAA
1 AGGCTCAACAACTTTAAAA
5399549 TTCCACTTTT
Statistics
Matches: 132, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
44 30 0.23
45 47 0.36
47 39 0.30
48 16 0.12
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.30
Consensus pattern (45 bp):
AGGCTCAACAACTTTAAAAATTCTTAAAAATGCTTCTCTCAGCAG
Found at i:5399515 original size:92 final size:92
Alignment explanation
Indices: 5399067--5399548 Score: 320
Period size: 92 Copynumber: 5.1 Consensus size: 92
5399057 CTGGTTAAAC
* * * * *
5399067 AACTTTAAAAATTCATATTGAAAAAGACTCATCTAAGTAGAGGCTCAATAACTTTAAAATTCATC
1 AACTTTAAAAATT-ATCTTGAAAAAAACTCCTCTCAGTAGAGGCTCAACAACTTTAAAA-T--TC
* * * * * *
5399132 TTGAGAAAAAGCT-CTTATAAGTAGAGGCTCAAC
62 TT-A-AAAATGCTGC-TCTCAGCAGAGACTCAAT
* * * * *
5399165 AACTTTAAAAA-AAT-TT--AAAAAGCTCCTCTAAGTAGCGGTTCAACAACTTTAAAATTCATTT
1 AACTTTAAAAATTATCTTGAAAAAAACTCCTCTCAGTAGAGGCTCAACAACTTTAAAATTC---T
* * * * *
5399226 TGAAAAAAAGCTCCTCTAAGTAGAGGCTCAAT
63 T--AAAAATGCTGCTCTCAGCAGAGACTCAAT
* * * * *
5399258 AACTTT-AAAATTCATCTTGAAAAAAAGTTCATCTAAGTAGAGACTCAATAACTTTAAAATTCAT
1 AACTTTAAAAATT-ATCTTGAAAAAAA-CTCCTCTCAGTAGAGGCTCAACAACTTTAAAATTC--
** * * ** * *
5399322 TTTGAAAAAAACTCCTCTTATTATAGGCTCAAT
62 -TT-AAAAATGCTGCTCTCAGCAGAGACTCAAT
* * *
5399355 AACTTT-AAAATTAATCTTGAAAAAAACTTCTTTCAGTAGAGGCTCAACAACTTTAAAATTCTTG
1 AACTTTAAAAATT-ATCTTGAAAAAAACTCCTCTCAGTAGAGGCTCAACAACTTTAAAATTCTTA
*
5399419 AAAATGCTTCTCTCAGCAGAGACTCAAT
65 AAAATGCTGCTCTCAGCAGAGACTCAAT
5399447 AACTTTAAAAATT-T-TT-AAAAAAATGCTCCTCTCAGTAGAGGCTTC-ACAACTTTAAAAATTC
1 AACTTTAAAAATTATCTTGAAAAAAA--CTCCTCTCAGTAGAGGC-TCAACAACTTT-AAAATTC
* *
5399508 TTAAAAATGCTGCTCTCAGCAGAGGCTCAAC
62 TTAAAAATGCTGCTCTCAGCAGAGACTCAAT
5399539 AACTTTAAAA
1 AACTTTAAAA
5399549 TTCCACTTTT
Statistics
Matches: 322, Mismatches: 46, Indels: 38
0.79 0.11 0.09
Matches are distributed among these distances:
89 7 0.02
90 4 0.01
91 24 0.07
92 77 0.24
93 72 0.22
94 4 0.01
95 4 0.01
96 30 0.09
97 55 0.17
98 45 0.14
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.30
Consensus pattern (92 bp):
AACTTTAAAAATTATCTTGAAAAAAACTCCTCTCAGTAGAGGCTCAACAACTTTAAAATTCTTAA
AAATGCTGCTCTCAGCAGAGACTCAAT
Found at i:5408994 original size:15 final size:16
Alignment explanation
Indices: 5408974--5409006 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5408964 GTGACAGGAA
*
5408974 CAAATTG-CTATGCAC
1 CAAATTGCCTAAGCAC
5408989 CAAATTGCCTAAGCAC
1 CAAATTGCCTAAGCAC
5409005 CA
1 CA
5409007 TTAACGAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.36, C:0.30, G:0.12, T:0.21
Consensus pattern (16 bp):
CAAATTGCCTAAGCAC
Found at i:5411668 original size:22 final size:22
Alignment explanation
Indices: 5411643--5411687 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
5411633 CTCATTTTTT
* *
5411643 ATTACTTATTCTTAATTTATTA
1 ATTAATTATTATTAATTTATTA
* *
5411665 ATTAATTTTTATTATTTTATTA
1 ATTAATTATTATTAATTTATTA
5411687 A
1 A
5411688 GGAAAAGAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTAATTATTATTAATTTATTA
Found at i:5419259 original size:470 final size:469
Alignment explanation
Indices: 5417969--5419386 Score: 2194
Period size: 471 Copynumber: 3.0 Consensus size: 469
5417959 CCCCTAACTT
*
5417969 TCATCTATAAATACAAACATCCAAGCACCACCAAAGCAAGTTCCATCTAATCCTAATCCTAATCC
1 TCATTTATAAATACAAACATCCAAGCACCACCAAAGCAAGTTCCATCTAAT-C----CC-AATCC
* * * *
5418034 TTTACATTTTTTTCCTTCCGACCTTTCTTATTCTAATTTATGCGTCGAAGTGTAAACTCAGGGAA
60 -TTACATTTCTCTCCTTCCGACCTTTCTTATTTTAATTTGTGCGTCGAAGTGTAAACTCAGGGAA
* *
5418099 CACTCTCTGCCTTTGCGTCTAATCGTTCTCTTCCAATCTCTTATTCTTTTAGGAATACCCTTACT
124 CACTCTCTGCCTTTGCGTCTAACCGTTCTCTTCCAATCTCTTATTCTTTTAGGAATACCTTTACT
*
5418164 TCGAAGCTAGGCACAAACACTTGACACGCTAGGTAAAGGGCCTTTTTTATTCATTAGCTGAGCGT
189 TCGAAGCTAGGCACAAACACTTGACGCGCTAGGTAAAGGGCCTTTTTTATTCATTAGCTGAGCGT
*
5418229 GGAGCAATGCAACCCAAGAAAATAACATTGAAGGAAGGAGAGACAACTGT-CCAAGCCGAAATAG
254 GGAGCAATGCAACCCAAGAAAATAACATTGAAGGAAGGAGAGACAACTGTCCCAA-CTGAAATAG
*
5418293 AAATAAATAACAACCAACACTCAGATCGACCTGCCCTACAACAAGCCAGTCCAACCATGAAACAA
318 AAATAAATAACAACCAACACTCAGACCGACCTGCCCTACAACAAGCCAGTCCAACCATGAAACAA
* *
5418358 TTTCAAGCCTTAACCAAGCAAACACAATCCCTTAAATAGATGTTGTAAATTATAACCCCCACCAT
383 TTTCAAGCCTTAACCAAGCAAACACAAGCCCTTAAACAGATGTTGTAAATTATAA-CCCCACCAT
5418423 AGGCTTAGAAAGTGCCCGACCTA
447 AGGCTTAGAAAGTGCCCGACCTA
* *
5418446 TCATTTATAAATACAAACATCCAAGCACCACCAAAGTAAGTTCCATCTAATCCCAATCTTTTACA
1 TCATTTATAAATACAAACATCCAAGCACCACCAAAGCAAGTTCCATCTAATCCCAATC-CTTACA
* *
5418511 TTTCTCTTCTTCCGACCTTTCTTATTTTAATTTGTGCGTCGAAGTGTAAACTCAGGGAACATTCT
65 TTTCTCTCCTTCCGACCTTTCTTATTTTAATTTGTGCGTCGAAGTGTAAACTCAGGGAACACTCT
*
5418576 CTGCCTTTGCGTCTAGCCGTTCTCTTCCAATCTCTTATTCTTTTAGGAATACCTTTACTTCGAAG
130 CTGCCTTTGCGTCTAACCGTTCTCTTCCAATCTCTTATTCTTTTAGGAATACCTTTACTTCGAAG
*
5418641 CTAGGCACAAACACTTGACGCGTTAGGTAAAGGGCCTTTTTTATTCATTAGCTGAGCGTGGAGCA
195 CTAGGCACAAACACTTGACGCGCTAGGTAAAGGGCCTTTTTTATTCATTAGCTGAGCGTGGAGCA
*
5418706 ATGCAACCCAAGAAAATAACATTGAAGGAAGGAGAGACAACTGTCCC-AGTCGAAATAGAAATAA
260 ATGCAACCCAAGAAAATAACATTGAAGGAAGGAGAGACAACTGTCCCAACT-GAAATAGAAATAA
*
5418770 ATAACAACCAACACTCAGACCGACTTGCCCTACAACAAGCCAGTCCAACCATGAAACAATTTCAA
324 ATAACAACCAACACTCAGACCGACCTGCCCTACAACAAGCCAGTCCAACCATGAAACAATTTCAA
*
5418835 GCCTTAACTAAGCAAACACAAGCCCTTAAACAGATGTTGTAAATTATAACCCACACCATAGGCTT
389 GCCTTAACCAAGCAAACACAAGCCCTTAAACAGATGTTGTAAATTATAACCC-CACCATAGGCTT
* *
5418900 AGAAAGTGCTCGACCTC
453 AGAAAGTGCCCGACCTA
5418917 TCATTTATAAATACAAACATCCAAGCACCACCAAAGCAAGTTCCATCTAATCCCAATCCTTACAT
1 TCATTTATAAATACAAACATCCAAGCACCACCAAAGCAAGTTCCATCTAATCCCAATCCTTACAT
* * ** *
5418982 ATCTCTCCTTCCGACCTTTCTTATTTTGATTTGTAAGTCGAAGTGTAAACTCAAGGAACACTCTC
66 TTCTCTCCTTCCGACCTTTCTTATTTTAATTTGTGCGTCGAAGTGTAAACTCAGGGAACACTCTC
* *
5419047 TGCCTTTGCATCTAACCATTCTCTTCCAATCTCTTATTCTTTTAGGAATACCTTTACTTCGAAGC
131 TGCCTTTGCGTCTAACCGTTCTCTTCCAATCTCTTATTCTTTTAGGAATACCTTTACTTCGAAGC
* * * * * *
5419112 TAGGCACAAACACTTAACGCGCCAGGT-AAGAGGCCTTTTTTATTCGTTAGCTAAGTGTAGAGCA
196 TAGGCACAAACACTTGACGCGCTAGGTAAAG-GGCCTTTTTTATTCATTAGCTGAGCGTGGAGCA
** * *
5419176 ATGCAACCCAAGAAAATAACATTGAAGGAAAAAGAGACAACTATCCCAACTGGAATAGAAATAAA
260 ATGCAACCCAAGAAAATAACATTGAAGGAAGGAGAGACAACTGTCCCAACTGAAATAGAAATAAA
* * ** * * * * * *
5419241 CAGCAACCAACACTCAGACTAACCTACCCCACAACAAGCCAATCTAACCATGAAACAATTTTAGG
325 TAACAACCAACACTCAGACCGACCTGCCCTACAACAAGCCAGTCCAACCATGAAACAATTTCAAG
* * * * *
5419306 CCTTAACCAAGCAAACACAAGCCCTTAAACAGATGTTGTAGACTATAACCTCTACCATAAGCTTC
390 CCTTAACCAAGCAAACACAAGCCCTTAAACAGATGTTGTAAATTATAACC-CCACCATAGGCTTA
5419371 GAAAGTGCCCGACCTA
454 GAAAGTGCCCGACCTA
5419387 GTCACTCATG
Statistics
Matches: 868, Mismatches: 66, Indels: 21
0.91 0.07 0.02
Matches are distributed among these distances:
469 3 0.00
470 364 0.42
471 447 0.51
472 4 0.00
476 1 0.00
477 49 0.06
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (469 bp):
TCATTTATAAATACAAACATCCAAGCACCACCAAAGCAAGTTCCATCTAATCCCAATCCTTACAT
TTCTCTCCTTCCGACCTTTCTTATTTTAATTTGTGCGTCGAAGTGTAAACTCAGGGAACACTCTC
TGCCTTTGCGTCTAACCGTTCTCTTCCAATCTCTTATTCTTTTAGGAATACCTTTACTTCGAAGC
TAGGCACAAACACTTGACGCGCTAGGTAAAGGGCCTTTTTTATTCATTAGCTGAGCGTGGAGCAA
TGCAACCCAAGAAAATAACATTGAAGGAAGGAGAGACAACTGTCCCAACTGAAATAGAAATAAAT
AACAACCAACACTCAGACCGACCTGCCCTACAACAAGCCAGTCCAACCATGAAACAATTTCAAGC
CTTAACCAAGCAAACACAAGCCCTTAAACAGATGTTGTAAATTATAACCCCACCATAGGCTTAGA
AAGTGCCCGACCTA
Found at i:5437632 original size:25 final size:26
Alignment explanation
Indices: 5437573--5437632 Score: 61
Period size: 25 Copynumber: 2.3 Consensus size: 26
5437563 TATATTTATA
* **
5437573 TTATATTTAATGTAAAAATTATATTAT
1 TTAT-TTTAATATAAAAATTATAAAAT
*
5437600 TT-TATTAATATAAAAA-TATAAAAT
1 TTATTTTAATATAAAAATTATAAAAT
5437624 TTATTTTAA
1 TTATTTTAA
5437633 ATTTATTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
24 8 0.30
25 16 0.59
26 1 0.04
27 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
TTATTTTAATATAAAAATTATAAAAT
Found at i:5438662 original size:21 final size:21
Alignment explanation
Indices: 5438629--5438668 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
5438619 GAGTTAAAAT
5438629 TTTAATAAAAATTATAAATAGA
1 TTTAATAAAAATTA-AAATAGA
5438651 TTTAAT-AAAATTAAAATA
1 TTTAATAAAAATTAAAATA
5438669 TATATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 7 0.39
22 6 0.33
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (21 bp):
TTTAATAAAAATTAAAATAGA
Found at i:5438675 original size:22 final size:22
Alignment explanation
Indices: 5438629--5438675 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
5438619 GAGTTAAAAT
*
5438629 TTTAATAAAAATTATAAATAGA
1 TTTAATAAAAATTAAAAATAGA
*
5438651 TTTAAT-AAAATTAAAATATATA
1 TTTAATAAAAATTAAAA-ATAGA
5438673 TTT
1 TTT
5438676 TATATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TTTAATAAAAATTAAAAATAGA
Found at i:5445240 original size:4 final size:4
Alignment explanation
Indices: 5445231--5445269 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
5445221 TATTATATAA
5445231 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
5445270 TATATATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:5455643 original size:11 final size:10
Alignment explanation
Indices: 5455625--5455657 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 10
5455615 TGAAACCCCC
5455625 TTTTTCTTTT
1 TTTTTCTTTT
5455635 TTCTTTCTTTT
1 TT-TTTCTTTT
5455646 TTTTT-TTTT
1 TTTTTCTTTT
5455655 TTT
1 TTT
5455658 GCCCAGAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 7 0.32
10 5 0.23
11 10 0.45
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:5460769 original size:16 final size:16
Alignment explanation
Indices: 5460745--5460778 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
5460735 AATTCTATAA
*
5460745 TTGTTAATTTTTTACT
1 TTGTAAATTTTTTACT
5460761 TTGTAAATTTTTTACT
1 TTGTAAATTTTTTACT
5460777 TT
1 TT
5460779 AAGGTCAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.68
Consensus pattern (16 bp):
TTGTAAATTTTTTACT
Found at i:5463050 original size:18 final size:21
Alignment explanation
Indices: 5463018--5463066 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 21
5463008 AAAAATTTAT
*
5463018 TAATGTTTT-ATTTTATT-T-
1 TAATTTTTTAATTTTATTCTC
5463036 T-ATTTTTTAATTTTATTCTC
1 TAATTTTTTAATTTTATTCTC
5463056 TAATTTTTTAA
1 TAATTTTTTAA
5463067 AAAAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 6 0.23
18 9 0.35
19 1 0.04
20 1 0.04
21 9 0.35
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.69
Consensus pattern (21 bp):
TAATTTTTTAATTTTATTCTC
Found at i:5463114 original size:9 final size:10
Alignment explanation
Indices: 5463093--5463132 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
5463083 AAAATAATTT
5463093 TAAAAAAGTAA
1 TAAAAAA-TAA
*
5463104 TAAAATA-AA
1 TAAAAAATAA
5463113 TAAAAAATAA
1 TAAAAAATAA
5463123 TAAAAAATAA
1 TAAAAAATAA
5463133 ATACCAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
9 8 0.31
10 12 0.46
11 6 0.23
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.20
Consensus pattern (10 bp):
TAAAAAATAA
Found at i:5463129 original size:21 final size:21
Alignment explanation
Indices: 5463093--5463148 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
5463083 AAAATAATTT
5463093 TAAAAAAGTAAT--AAAATAAA
1 TAAAAAA-TAATAAAAAATAAA
5463113 TAAAAAATAATAAAAAATAAA
1 TAAAAAATAATAAAAAATAAA
*
5463134 TACCAAAATAA-AAAA
1 TA-AAAAATAATAAAA
5463149 CTAACTCGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 4 0.12
20 7 0.22
21 14 0.44
22 7 0.22
ACGTcount: A:0.77, C:0.04, G:0.02, T:0.18
Consensus pattern (21 bp):
TAAAAAATAATAAAAAATAAA
Done.