Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397275.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_34.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2955990
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 53928 characters in sequence are not A, C, G, or T
File 2 of 8
Found at i:438607 original size:17 final size:17
Alignment explanation
Indices: 438573--438645 Score: 53
Period size: 17 Copynumber: 4.4 Consensus size: 17
438563 TAGTAATGTT
438573 TATGTATAAATCAA-ATA
1 TATGTATAAAT-AATATA
*
438590 TATGTATATATAATATA
1 TATGTATAAATAATATA
* * *
438607 TTTATACAAAT-ATATA
1 TATGTATAAATAATATA
* *
438623 TATTTATAACATATTA-A
1 TATGTATAA-ATAATATA
438640 TATGTA
1 TATGTA
438646 GGATGTTTAC
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
16 13 0.30
17 28 0.65
18 2 0.05
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (17 bp):
TATGTATAAATAATATA
Found at i:439498 original size:24 final size:24
Alignment explanation
Indices: 439453--439499 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
439443 TATATTTTAA
*
439453 ATATATTATCTTAATAAGTTTATT
1 ATATATTATCTTAATAAATTTATT
*
439477 ATATATCTATCTT-TTAAATTTAT
1 ATATAT-TATCTTAATAAATTTAT
439500 ATTAACTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.55
Consensus pattern (24 bp):
ATATATTATCTTAATAAATTTATT
Found at i:450276 original size:9 final size:9
Alignment explanation
Indices: 450262--450296 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
450252 CAAAATCTTC
*
450262 TAACCAATT
1 TAACCAAAT
450271 TAACCAAAT
1 TAACCAAAT
*
450280 TAATCAAAT
1 TAACCAAAT
450289 TAACCAAA
1 TAACCAAA
450297 CCGAATTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.54, C:0.20, G:0.00, T:0.26
Consensus pattern (9 bp):
TAACCAAAT
Found at i:465143 original size:53 final size:54
Alignment explanation
Indices: 465053--465160 Score: 139
Period size: 53 Copynumber: 2.0 Consensus size: 54
465043 AAGGAATTTT
* *
465053 CAATCTATTAAAAGGATTATTGCTTTTTAACAGGATCAAGTGATAA-CCTTTACA
1 CAATCCATTAAAAGGATTATTGCTTTTTAACAGGATCAAGCGATAAGCC-TTACA
* * **
465107 CAATCCATTAAAA-GATTCTTGTTTTTTAATGGGATCAAGCGATAAGCCTTACA
1 CAATCCATTAAAAGGATTATTGCTTTTTAACAGGATCAAGCGATAAGCCTTACA
465160 C
1 C
465161 TAGCTTTTTC
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
53 33 0.70
54 14 0.30
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (54 bp):
CAATCCATTAAAAGGATTATTGCTTTTTAACAGGATCAAGCGATAAGCCTTACA
Found at i:465230 original size:89 final size:89
Alignment explanation
Indices: 465086--465257 Score: 231
Period size: 89 Copynumber: 1.9 Consensus size: 89
465076 TTTTTAACAG
* * * *
465086 GATCAAGTGATAACCTTTACACAATCCATTAAAAGATTCTTGTTTTTTAATGGGATCAAGCGATA
1 GATCAAGCGATAACCTTTACACAATCCATTAAAAGATTCTTGCTTTTAAACGGGATCAAGCGATA
*
465151 AGC-CTTACACTAGCTTTTTCATAA
66 A-CACTTACACTAACTTTTTCATAA
* * * *
465175 GATCAAGCGATAACCTTTATACAATTCA-TAAAGAGATTCTTGCTTTTAAACGGGATCAAGTGGT
1 GATCAAGCGATAACCTTTACACAATCCATTAAA-AGATTCTTGCTTTTAAACGGGATCAAGCGAT
465239 AACACTTACACTAACTTTT
65 AACACTTACACTAACTTTT
465258 CATGGTTAAG
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
88 5 0.07
89 67 0.93
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (89 bp):
GATCAAGCGATAACCTTTACACAATCCATTAAAAGATTCTTGCTTTTAAACGGGATCAAGCGATA
ACACTTACACTAACTTTTTCATAA
Found at i:466392 original size:69 final size:69
Alignment explanation
Indices: 466314--466452 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 69
466304 AGATCAAAAT
466314 CAAAATATCATATAATTTTGTCGAATCAAAACATAAAATATTTAATGCTAACAAGATGCTCCCAA
1 CAAAATATCATATAATTTTGTCGAATCAAAACATAAAATATTTAATGCTAACAAGATGCTCCCAA
466379 GCAA
66 GCAA
*
466383 CAAAATATCATATAATTTTGTCGAATCAAAACATAAAATATTTAATGCTAACAAGATGCTCCTAA
1 CAAAATATCATATAATTTTGTCGAATCAAAACATAAAATATTTAATGCTAACAAGATGCTCCCAA
466448 GCAA
66 GCAA
466452 C
1 C
466453 TCTACCTCGC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.28
Consensus pattern (69 bp):
CAAAATATCATATAATTTTGTCGAATCAAAACATAAAATATTTAATGCTAACAAGATGCTCCCAA
GCAA
Found at i:471310 original size:30 final size:31
Alignment explanation
Indices: 471248--471318 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 31
471238 ATGTTTGCTC
* * *
471248 AAATCTTTACATTTTTATTTTAAATTATAT-
1 AAATCTTTATATTTTTATTTTAAATCAAATA
*
471278 AAATCTTTATATTTTTATTTTGAATCAAATA
1 AAATCTTTATATTTTTATTTTAAATCAAATA
471309 AAAT-TTTATA
1 AAATCTTTATA
471319 ACTAATAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
30 32 0.89
31 4 0.11
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (31 bp):
AAATCTTTATATTTTTATTTTAAATCAAATA
Found at i:488979 original size:7 final size:7
Alignment explanation
Indices: 488967--488996 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
488957 GTCCCTCTAG
488967 TTTATAT
1 TTTATAT
488974 TTTATAT
1 TTTATAT
488981 TTTATAT
1 TTTATAT
*
488988 TTTAAAT
1 TTTATAT
488995 TT
1 TT
488997 AAATTATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTATAT
Found at i:489850 original size:15 final size:16
Alignment explanation
Indices: 489822--489851 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
489812 ATTTTATGAT
489822 AATAAAATAAAATAAA
1 AATAAAATAAAATAAA
489838 AATAAAA-AAAATAA
1 AATAAAATAAAATAA
489852 TTATTACGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (16 bp):
AATAAAATAAAATAAA
Found at i:490192 original size:26 final size:26
Alignment explanation
Indices: 490161--490210 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
490151 AATATTAGAA
490161 ATTCATACAATAAAT-ATTAATATTTT
1 ATTCATA-AATAAATCATTAATATTTT
* *
490187 ATTCATAATTTAATCATTAATATT
1 ATTCATAAATAAATCATTAATATT
490211 ATAAAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (26 bp):
ATTCATAAATAAATCATTAATATTTT
Found at i:490356 original size:154 final size:152
Alignment explanation
Indices: 490012--490507 Score: 653
Period size: 154 Copynumber: 3.2 Consensus size: 152
490002 GAATTTTATT
*
490012 TTTAAATATTAATATTTTATTTATAATCTAATCATTAACATTATAAAATACTAATATTTTATTTA
1 TTTAAATATTAATATTTTATTTATAATTTAATCATTAACATTATAAAATACTAATATTTTATTTA
* * *
490077 TAATTTAAATGTTGA-TACT-ATTATTTATTTTCAACTTCTTTATTTTTCAATATTAATAATTTA
66 TAATTTAAATGTT-ATTA-TGATTATTTATTTT-TA--T-TTTATTTTTAAATACTAATAATTTA
*
490140 TAATTTA-TTAAAATATTAGA-AATTCATAC
125 T-ATTTATTTAAAATATTA-ATAATTGA-AC
** * * *
490169 AATAAATATTAATATTTTATTCATAATTTAATCATTAATATTATAAAATATTAATATTTTATTTA
1 TTTAAATATTAATATTTTATTTATAATTTAATCATTAACATTATAAAATACTAATATTTTATTTA
490234 T-ATTTAAATGTTATTATGATTATTTATTTTTATTTTATTTTTAAATACTAATAATTTATATTTT
66 TAATTTAAATGTTATTATGATTATTTATTTTTATTTTATTTTTAAATACTAATAATTTATA--TT
*
490298 TATTTAAAATATTAATAATTGAGC
129 TATTTAAAATATTAATAATTGAAC
*
490322 GTTTAAATATTAATATTTTATTTATAATTTAATCATTAACATTATAAAATACTAAAATTTTATTT
1 -TTTAAATATTAATATTTTATTTATAATTTAATCATTAACATTATAAAATACTAATATTTTATTT
* * *
490387 ATAATTTAAATGTTATTATGATTATTTGTTTTTATTTTA-TTTTAAAAAGTGAATAATTTATCAT
65 ATAATTTAAATGTTATTATGATTATTTATTTTTATTTTATTTTTAAATACT-AATAATTTAT-AT
* * *
490451 TGATTTAAAATATTCATAATTGATAT
128 TTATTTAAAATATTAATAATTGA-AC
490477 TTTAAATATTAATATTTTATTTATAATTTAA
1 TTTAAATATTAATATTTTATTTATAATTTAA
490508 ATGTTACTAT
Statistics
Matches: 304, Mismatches: 24, Indels: 25
0.86 0.07 0.07
Matches are distributed among these distances:
151 1 0.00
152 24 0.08
153 7 0.02
154 138 0.45
155 48 0.16
156 26 0.09
157 60 0.20
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.53
Consensus pattern (152 bp):
TTTAAATATTAATATTTTATTTATAATTTAATCATTAACATTATAAAATACTAATATTTTATTTA
TAATTTAAATGTTATTATGATTATTTATTTTTATTTTATTTTTAAATACTAATAATTTATATTTA
TTTAAAATATTAATAATTGAAC
Found at i:490613 original size:311 final size:310
Alignment explanation
Indices: 490012--490588 Score: 674
Period size: 311 Copynumber: 1.9 Consensus size: 310
490002 GAATTTTATT
*
490012 TTTAAATATTAATATTTTATTTATAATCTAATCATTAACATTATAAAATACTAATATTTTATTTA
1 TTTAAATATTAATATTTTATTTATAATCTAATCATTAACATTATAAAATACTAAAATTTTATTTA
* * *
490077 TAATTTAAATGTTGATACTATTATTTATTTTCAACTTCTTTATTTTTCAATATTAATAATTTATA
66 TAATTTAAATGTTGATACTATTATTTATTTTCAAC-TCTTTATTTTTAAAAATGAATAATTTATA
*
490142 ATTTATTAAAATATTAGAAATTCATACAATAAATATTAATATTTTATTCATAATTTAATCATTAA
130 ATTGATTAAAATATTAGAAATTCATACAATAAATATTAATATTTTATTCATAATTTAATCATTAA
* * * * * * * ** *
490207 TATTATAAAATATTAATATTTTATTTATATTTAAATGTTATTATGATTATTTATTTTTATTTTAT
195 TATGATAAAATATAAATATTTTAATTATATTTAAATGTCAATATGATTATTTATTATAATTAAAA
** **
490272 TTTTAAATACTAATAATTTATATTTTTATTTAAAATATTAATAATTGAGCG
260 ACTTAAATACTAATAATTTATAGATTTATTTAAAATATTAATAATTGAGCG
*
490323 TTTAAATATTAATATTTTATTTATAATTTAATCATTAACATTATAAAATACTAAAATTTTATTTA
1 TTTAAATATTAATATTTTATTTATAATCTAATCATTAACATTATAAAATACTAAAATTTTATTTA
* *
490388 TAATTTAAATGTT-ATTA-TGATTATTTGTTTT-TA-T-TTTA-TTTTAAAAAGTGAATAATTTA
66 TAATTTAAATGTTGA-TACT-ATTATTTATTTTCAACTCTTTATTTTTAAAAA-TGAATAATTTA
* * * *** *
490447 TCATTGATTTAAAATATTCA-TAATTGATATTTTAAATATTAATATTTTATTTATAATTTAAAT-
128 TAATTGA-TTAAAATATT-AGAAATTCATACAATAAATATTAATATTTTATTCATAATTT-AATC
* *
490510 GTTACTATGATTAAAATATAAATACTTTTAATTA-AGTTTAAAT-TCAATAT-ATTTCATATTA-
190 ATTAATATGA-TAAAATATAAATA-TTTTAATTATA-TTTAAATGTCAATATGA-TT-AT-TTAT
490571 TATAATTAAAAACTTAAA
249 TATAATTAAAAACTTAAA
490589 CTTTTTATTA
Statistics
Matches: 225, Mismatches: 29, Indels: 25
0.81 0.10 0.09
Matches are distributed among these distances:
306 7 0.03
307 19 0.08
308 52 0.23
309 24 0.11
310 31 0.14
311 92 0.41
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.51
Consensus pattern (310 bp):
TTTAAATATTAATATTTTATTTATAATCTAATCATTAACATTATAAAATACTAAAATTTTATTTA
TAATTTAAATGTTGATACTATTATTTATTTTCAACTCTTTATTTTTAAAAATGAATAATTTATAA
TTGATTAAAATATTAGAAATTCATACAATAAATATTAATATTTTATTCATAATTTAATCATTAAT
ATGATAAAATATAAATATTTTAATTATATTTAAATGTCAATATGATTATTTATTATAATTAAAAA
CTTAAATACTAATAATTTATAGATTTATTTAAAATATTAATAATTGAGCG
Found at i:490684 original size:16 final size:16
Alignment explanation
Indices: 490658--490699 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
490648 ATTTTCACTC
* *
490658 AATAATTTAAAATTTTT
1 AATATTTTAAAA-TATT
490675 AAT-TTTTAAAATATT
1 AATATTTTAAAATATT
490690 AATATTTTAA
1 AATATTTTAA
490700 TTATAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 6 0.27
16 13 0.59
17 3 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATATTTTAAAATATT
Found at i:490713 original size:22 final size:23
Alignment explanation
Indices: 490671--490714 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
490661 AATTTAAAAT
*
490671 TTTTAATTTTTAAAATATTAATA
1 TTTTAATTTATAAAATATTAATA
*
490694 TTTTAA-TTATAATATATTAAT
1 TTTTAATTTATAAAATATTAAT
490715 GTTATCAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTAATTTATAAAATATTAATA
Found at i:491432 original size:26 final size:25
Alignment explanation
Indices: 491403--491454 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
491393 TTAATATTTG
* * *
491403 AATTATCAATTATTAATATGTTAAAA
1 AATTATAAAGTATCAATAT-TTAAAA
491429 AATTATAAAGTATCAATATTTAAAA
1 AATTATAAAGTATCAATATTTAAAA
491454 A
1 A
491455 TAAAATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (25 bp):
AATTATAAAGTATCAATATTTAAAA
Found at i:497165 original size:23 final size:23
Alignment explanation
Indices: 497131--497177 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
497121 GTTATGGAAA
497131 ATAACTTAAAAGAACAAATAAAG
1 ATAACTTAAAAGAACAAATAAAG
* * *
497154 ATAACTTGAAAGAATAATTAAAG
1 ATAACTTAAAAGAACAAATAAAG
497177 A
1 A
497178 GAAGAAAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.62, C:0.06, G:0.11, T:0.21
Consensus pattern (23 bp):
ATAACTTAAAAGAACAAATAAAG
Found at i:497935 original size:23 final size:22
Alignment explanation
Indices: 497918--497992 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 22
497908 AATTATCTTG
497918 TAATACAAAATATTATTAAATTA
1 TAATA-AAAATATTATTAAATTA
497941 TAATAAAAATATT-TTAATATT-
1 TAATAAAAATATTATTAA-ATTA
** * *
497962 TGGGTGAAAATATTATTTAATTA
1 T-AATAAAAATATTATTAAATTA
*
497985 TAGTAAAA
1 TAATAAAA
497993 GGTATTTTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
21 5 0.12
22 28 0.67
23 9 0.21
ACGTcount: A:0.51, C:0.01, G:0.07, T:0.41
Consensus pattern (22 bp):
TAATAAAAATATTATTAAATTA
Found at i:498387 original size:24 final size:22
Alignment explanation
Indices: 498344--498389 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
498334 TACAAAAATA
*
498344 ACAAAAAAATAAAATAAAAAAC
1 ACAAAAAAATAAAAGAAAAAAC
498366 ACAAACAAATATAAAAGGAAAAAA
1 ACAAA-AAA-ATAAAA-GAAAAAA
498390 ATCTCTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 3 0.15
24 6 0.30
25 6 0.30
ACGTcount: A:0.78, C:0.09, G:0.04, T:0.09
Consensus pattern (22 bp):
ACAAAAAAATAAAAGAAAAAAC
Found at i:498482 original size:19 final size:18
Alignment explanation
Indices: 498429--498485 Score: 51
Period size: 19 Copynumber: 3.1 Consensus size: 18
498419 AGAATCAAAT
*
498429 AAAATAAAATTGAATCAA
1 AAAATTAAATTGAATCAA
* * **
498447 ACATTTCAAATCCAATCAA
1 AAAATT-AAATTGAATCAA
498466 AAAATTAAAGTTGAATCAA
1 AAAATTAAA-TTGAATCAA
498485 A
1 A
498486 CACACAAGCA
Statistics
Matches: 28, Mismatches: 9, Indels: 3
0.70 0.22 0.08
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.58, C:0.12, G:0.05, T:0.25
Consensus pattern (18 bp):
AAAATTAAATTGAATCAA
Found at i:499700 original size:15 final size:15
Alignment explanation
Indices: 499680--499721 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
499670 AATATTACAC
499680 AATTATAACTTATAA
1 AATTATAACTTATAA
499695 AATTATTAA-TTATAA
1 AATTA-TAACTTATAA
*
499710 TATATATAACTT
1 AAT-TATAACTT
499722 TGTTTATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTATAACTTATAA
Found at i:499815 original size:336 final size:330
Alignment explanation
Indices: 499326--500376 Score: 977
Period size: 331 Copynumber: 3.1 Consensus size: 330
499316 ATTTTGTGTT
* * * * * *
499326 TTAAAATTACAAAAATTATGACTTATAAAATTATTAATTATAATATATATATATCATTATTTATA
1 TTAACATTACAAAAATTATAACTCATAAAATTATTAATTACAATATATATA-A-CTTTGTTTATA
* * * ** * * * * * * * * * *
499391 TAAACTTATGACATATATATTTAAAGAGAGCTTTTGATATTATAATAGCTTTGGAACT-TAACTA
64 TAAACTCATAACA-ATAAACCTAAAGA-AG-TTATGAGATTAGAACAG-TCTAGAAATAGAAGTT
499455 TTTTTTTTAATTTCATGA-AATTAAGGATAAATCCTTATAGTTAATTAAATTAATTCATGAAACT
125 TTTTTTTTAATTTCAT-ATAATTAAGGATAAA-CCTTATAGTTAATTAAATTAATTCATGAAACT
* * *
499519 ATTATTATTAATTAACTAGTAATGTCTTTCAATATATATAGTTTATATATTGTGTTAATTTATAA
188 ATAATTATTAATTAACT-GTAATGTCTTTTAATATATATA-TTTATATATT-TGTTCATTTATAA
*
499584 -AAACTATAATTACTATTATATATATACTAAAATATTTTTAGTATATATATTTTAAATATAAACA
250 GAAA-TATAATTACTATTATATATATA-TAAAATA-TTTTAGTATATATACTTTAAATATAAACA
** * *
499648 TATTTATTTTTTATTTTATG
312 TATTT-GCTTCTACTTTATG
* * * *
499668 TTAATATTAC-ACAATTATAACTTATAAAATTATTAATTATAATATATATAACTTTGTTTATATA
1 TTAACATTACAAAAATTATAACTCATAAAATTATTAATTACAATATATATAACTTTGTTTATATA
* * * *
499732 AACTTATAATATATCAACCTAGAA-AAGTTATGAGATTAGAATAGT-TCA-AAA-ACGAAGTTTT
66 AACTCATAACA-ATAAACCTA-AAGAAGTTATGAGATTAGAACAGTCT-AGAAATA-GAAGTTTT
* * *
499793 TTTTTTAATTTCATATAATTAAGAACAAACTCATATAGTTAATTAAATTAATTCATGAAACTATA
127 TTTTTTAATTTCATATAATTAAGGATAAAC-CTTATAGTTAATTAAATTAATTCATGAAACTATA
*
499858 ATTATTAATTAACCTGTAATGTCTTTTAATATATATACTTTATATATATTAAAG-TCATTTAGAA
191 ATTATTAATTAA-CTGTAATGTCTTTTAATATATATA-TTTATATAT-TT---GTTCATTTATAA
* * * * *
499922 GGAAA-ATAATTACTATTATATATATAT----GAGTGT-GTGTATGTACTTTAAATATAAACATA
250 -GAAATATAATTACTATTATATATATATAAAATATTTTAGTATATATACTTTAAATATAAACATA
499981 TTTGCTTCTACTTTATG
314 TTTGCTTCTACTTTATG
* *
499998 TTAACATTACAAAAATTATTACTCATAAAATTATTAATTACAATATATATACCTTTGTTTATATA
1 TTAACATTACAAAAATTATAACTCATAAAATTATTAATTACAATATATATAACTTTGTTTATATA
* * **
500063 AACTCATAACAATAAATCTAAATGGAAGTTGTGAGATTAGAACAGTCTAGAAATATTAGTTTTTT
66 AACTCATAACAATAAACCTAAA--GAAGTTATGAGATTAGAACAGTCTAGAAATAGAAGTTTTTT
** * * *
500128 TTTTAATTTTTTGTAATTAAGGATAAACCTCTATAGTTAATTAAATTAATTTATGAAACTATGAT
129 TTTTAATTTCATATAATTAAGGATAAACCT-TATAGTTAATTAAATTAATTCATGAAACTATAAT
* * * *
500193 TATTAATTGACTTCTAATTTCTTTTAATATATAT-TTTATATACATTTGATTCATTTTTAAGAAA
193 TATTAATTAAC-TGTAATGTCTTTTAATATATATATTTATAT--ATTTG-TTCATTTATAAGAAA
* * **
500257 TATAATTACTATTATATATAT-TAAAATACTTTTAGTATATATACACTTTCAATATGATTATATT
254 TATAATTACTATTATATATATATAAAATA-TTTTAGTATATAT--ACTTTAAATATAAACATATT
* *
500321 TACTTTCTA-TTTCGTG
316 TGC-TTCTACTTT-ATG
* * * * *
500337 TTAACATTATAAAAATCATAAGTAATAAATTTATTAATTA
1 TTAACATTACAAAAATTATAACTCATAAAATTATTAATTA
500377 TGTTTGAGAT
Statistics
Matches: 591, Mismatches: 81, Indels: 77
0.79 0.11 0.10
Matches are distributed among these distances:
329 3 0.01
330 31 0.05
331 119 0.20
332 26 0.04
333 99 0.17
334 2 0.00
335 7 0.01
336 112 0.19
337 18 0.03
338 52 0.09
339 69 0.12
340 6 0.01
341 38 0.06
342 9 0.02
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.45
Consensus pattern (330 bp):
TTAACATTACAAAAATTATAACTCATAAAATTATTAATTACAATATATATAACTTTGTTTATATA
AACTCATAACAATAAACCTAAAGAAGTTATGAGATTAGAACAGTCTAGAAATAGAAGTTTTTTTT
TTAATTTCATATAATTAAGGATAAACCTTATAGTTAATTAAATTAATTCATGAAACTATAATTAT
TAATTAACTGTAATGTCTTTTAATATATATATTTATATATTTGTTCATTTATAAGAAATATAATT
ACTATTATATATATATAAAATATTTTAGTATATATACTTTAAATATAAACATATTTGCTTCTACT
TTATG
Found at i:503752 original size:115 final size:115
Alignment explanation
Indices: 503513--503736 Score: 279
Period size: 115 Copynumber: 1.9 Consensus size: 115
503503 TACCAAGAAT
* * * ** *
503513 AGTAGAAAAATTAATACTAAGAAAAAACCCAGCAAAATGGAATAGTAGAAAAATTAATAACCAGA
1 AGTAAAAAAATTAATAATAAGAAAAAACCCAGCAAAATGGAACACCAGAAAAATTAATAACAAGA
* * * * *
503578 AAGAACCCAATAGGAAGTGAAGGAAGCAAAGAAGAGGGTGGCAAAGGAAC
66 AAGAACACAACAAGAAGTGAAGAAAGCAAAGAAGAGGATGGCAAAGGAAC
* *
503628 AGTAAAAAAATTAATAATAAGAAAAAATCTAGCAAAATGGAACACCAGAAAAATTAATAACAAGA
1 AGTAAAAAAATTAATAATAAGAAAAAACCCAGCAAAATGGAACACCAGAAAAATTAATAACAAGA
* * * *
503693 AAGAACATAGCAAGAAGTGACA-AAAGTAGAGAAGAGGATGGCAA
66 AAGAACACAACAAGAAGTGA-AGAAAGCAAAGAAGAGGATGGCAA
503737 GAAAGTTGAG
Statistics
Matches: 91, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
115 90 0.99
116 1 0.01
ACGTcount: A:0.56, C:0.10, G:0.21, T:0.13
Consensus pattern (115 bp):
AGTAAAAAAATTAATAATAAGAAAAAACCCAGCAAAATGGAACACCAGAAAAATTAATAACAAGA
AAGAACACAACAAGAAGTGAAGAAAGCAAAGAAGAGGATGGCAAAGGAAC
Found at i:508173 original size:20 final size:20
Alignment explanation
Indices: 508148--508191 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
508138 CTCTTAAAGT
508148 AATTTAAA-ATAAATAACTTA
1 AATTTAAATA-AAATAACTTA
*
508168 AATTTAACTAAAATAACTTA
1 AATTTAAATAAAATAACTTA
508188 AATT
1 AATT
508192 AATCACTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (20 bp):
AATTTAAATAAAATAACTTA
Found at i:511678 original size:20 final size:19
Alignment explanation
Indices: 511625--511685 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
511615 TGTTTTGTAA
*
511625 TATAAAATGTTATAAATAT
1 TATAAAATTTTATAAATAT
* * *
511644 ATGTATAATTGTATAAATAT
1 -TATAAAATTTTATAAATAT
*
511664 TATAAAATATTTATATATAT
1 TATAAAAT-TTTATAAATAT
511684 TA
1 TA
511686 AATTTATACA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
19 6 0.19
20 26 0.81
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (19 bp):
TATAAAATTTTATAAATAT
Found at i:519855 original size:19 final size:19
Alignment explanation
Indices: 519828--519873 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
519818 TCTTTAATTT
519828 TTATT-TTTAAAATTAAAAA
1 TTATTATTT-AAATTAAAAA
* *
519847 TT-TTATTTAGATTAAAAC
1 TTATTATTTAAATTAAAAA
519865 TTATTATTT
1 TTATTATTT
519874 TTTTATAGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (19 bp):
TTATTATTTAAATTAAAAA
Found at i:520183 original size:15 final size:18
Alignment explanation
Indices: 520153--520192 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
520143 AAATTAAATT
520153 ATAAAATAATTTTATT-A
1 ATAAAATAATTTTATTAA
520170 ATAAAA-AA-TTTATTAA
1 ATAAAATAATTTTATTAA
520186 ATAAAAT
1 ATAAAAT
520193 TATAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 6 0.29
16 9 0.43
17 6 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAAAATAATTTTATTAA
Found at i:520221 original size:24 final size:24
Alignment explanation
Indices: 520194--520276 Score: 148
Period size: 24 Copynumber: 3.5 Consensus size: 24
520184 AAATAAAATT
520194 ATAAAAATAAATTTTTTTTAAAAA
1 ATAAAAATAAATTTTTTTTAAAAA
*
520218 ATAAAAATAATTTTTTTTTAAAAA
1 ATAAAAATAAATTTTTTTTAAAAA
*
520242 ATAAAAATAAATTTTTTTAAAAAA
1 ATAAAAATAAATTTTTTTTAAAAA
520266 ATAAAAATAAA
1 ATAAAAATAAA
520277 CTAGTTCAAC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
ATAAAAATAAATTTTTTTTAAAAA
Found at i:539761 original size:39 final size:39
Alignment explanation
Indices: 539702--539806 Score: 174
Period size: 39 Copynumber: 2.7 Consensus size: 39
539692 TTTCAGAAGG
* * * *
539702 AAGTGAGGTAAAGAAGCCAGAGGGAAACCAAATAGCAGA
1 AAGTGAGCTAAACAAACCAGAGGCAAACCAAATAGCAGA
539741 AAGTGAGCTAAACAAACCAGAGGCAAACCAAATAGCAGA
1 AAGTGAGCTAAACAAACCAGAGGCAAACCAAATAGCAGA
539780 AAGTGAGCTAAACAAACCAGAGGCAAA
1 AAGTGAGCTAAACAAACCAGAGGCAAA
539807 GGAAAAGCCA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 62 1.00
ACGTcount: A:0.50, C:0.17, G:0.25, T:0.08
Consensus pattern (39 bp):
AAGTGAGCTAAACAAACCAGAGGCAAACCAAATAGCAGA
Found at i:540338 original size:67 final size:67
Alignment explanation
Indices: 540258--540392 Score: 261
Period size: 67 Copynumber: 2.0 Consensus size: 67
540248 AAAATTATTG
540258 TCTCTCCCACCCACTCCCCAAAACCCCTAGTCCCCTCCCTACTCCCCTACCTCCTACCAAGAAAT
1 TCTCTCCCACCCACTCCCCAAAACCCCTAGTCCCCTCCCTACTCCCCTACCTCCTACCAAGAAAT
540323 CT
66 CT
*
540325 TCTCTCCCACCCACTCCCCAAAACCCCTAGTCTCCTCCCTACTCCCCTACCTCCTACCAAGAAAT
1 TCTCTCCCACCCACTCCCCAAAACCCCTAGTCCCCTCCCTACTCCCCTACCTCCTACCAAGAAAT
540390 CT
66 CT
540392 T
1 T
540393 TCTTCCAAAA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.22, C:0.53, G:0.03, T:0.22
Consensus pattern (67 bp):
TCTCTCCCACCCACTCCCCAAAACCCCTAGTCCCCTCCCTACTCCCCTACCTCCTACCAAGAAAT
CT
Found at i:552834 original size:22 final size:19
Alignment explanation
Indices: 552782--552835 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
552772 ATACCTTATT
*
552782 TTTTAAAATTAAATTAAAA
1 TTTTAAAAATAAATTAAAA
**
552801 TTTTAATTATAAATTATTAATA
1 TTTTAAAAATAAATTA--AA-A
552823 TTTTAAAAATAAA
1 TTTTAAAAATAAA
552836 AATAAAATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 13 0.48
21 2 0.07
22 12 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTTAAAAATAAATTAAAA
Found at i:555231 original size:44 final size:43
Alignment explanation
Indices: 555168--555256 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 43
555158 GTGGGGGGGT
555168 GGAATCAGGTCAGGAGTCGGGACTCGTGGGAAGAGGGGCCGAGG
1 GGAATCAGGTCAGGAGTCGGGACTCGT-GGAAGAGGGGCCGAGG
* *
555212 GGAATCAGGTTC-GGAGTCGGGACTCGTGGAGGGGGGGCCGAGG
1 GGAATCAGG-TCAGGAGTCGGGACTCGTGGAAGAGGGGCCGAGG
555255 GG
1 GG
555257 CCGAGGGAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
43 16 0.38
44 24 0.57
45 2 0.05
ACGTcount: A:0.19, C:0.16, G:0.53, T:0.12
Consensus pattern (43 bp):
GGAATCAGGTCAGGAGTCGGGACTCGTGGAAGAGGGGCCGAGG
Found at i:555278 original size:50 final size:52
Alignment explanation
Indices: 555200--555306 Score: 148
Period size: 50 Copynumber: 2.1 Consensus size: 52
555190 CTCGTGGGAA
* * * *
555200 GAGGGGCCGAGGGGAATCAGGTTCGGAGTCGGGACTCGT-GGAGGGGGGGCC
1 GAGGGGCCGAGGGGAATCAAGTGCGGAGTCGGGACACATGGGAGGGGGGGCC
*
555251 GAGGGGCCGA-GGGAATCAAGTGGGGAGTCGGGACACATGGGAGGGGGGGCC
1 GAGGGGCCGAGGGGAATCAAGTGCGGAGTCGGGACACATGGGAGGGGGGGCC
555302 G-GGGG
1 GAGGGG
555307 AATTAGGTTG
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
50 27 0.54
51 23 0.46
ACGTcount: A:0.18, C:0.16, G:0.57, T:0.09
Consensus pattern (52 bp):
GAGGGGCCGAGGGGAATCAAGTGCGGAGTCGGGACACATGGGAGGGGGGGCC
Found at i:555309 original size:43 final size:43
Alignment explanation
Indices: 555253--555339 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
555243 GGGGGGCCGA
555253 GGGGCCGAGGGAATCAAGTGGGGAGTCGGGACACATGGGAGGG
1 GGGGCCGAGGGAATCAAGTGGGGAGTCGGGACACATGGGAGGG
* * * * *
555296 GGGGCCGGGGGAATTAGGTTGGGAGTCGGGACTCATGGGAGGG
1 GGGGCCGAGGGAATCAAGTGGGGAGTCGGGACACATGGGAGGG
555339 G
1 G
555340 ATTTCGTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.20, C:0.13, G:0.55, T:0.13
Consensus pattern (43 bp):
GGGGCCGAGGGAATCAAGTGGGGAGTCGGGACACATGGGAGGG
Found at i:567819 original size:13 final size:13
Alignment explanation
Indices: 567801--567825 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
567791 TAAAAGCAAA
567801 ATTAAACTAATAG
1 ATTAAACTAATAG
567814 ATTAAACTAATA
1 ATTAAACTAATA
567826 ATTGAAAGGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.32
Consensus pattern (13 bp):
ATTAAACTAATAG
Found at i:569362 original size:38 final size:38
Alignment explanation
Indices: 569259--569439 Score: 127
Period size: 38 Copynumber: 4.8 Consensus size: 38
569249 CTTAATATCA
* * * **
569259 TCCAAGATAGT-GGAGACTATACCATTATTAA-AATTCA
1 TCCAAGATAGTGGGA-ATTATACCATTATCAACACTTTG
** * *
569296 TCCAAGATAGTGGAGAA-GGTACCGTTATCAACATTTTG
1 TCCAAGATAGTGG-GAATTATACCATTATCAACACTTTG
* * * **
569334 TCGAAGATAGTGGGGATTATACCCTTATCAATGCTTTG
1 TCCAAGATAGTGGGAATTATACCATTATCAACACTTTG
* ** **
569372 TCCAAGATAGTGGGAATTGTACCATTATCAATGCTTCA
1 TCCAAGATAGTGGGAATTATACCATTATCAACACTTTG
*
569410 TCCAAGATAGT-GGAGACTATACCATTATCA
1 TCCAAGATAGTGGGA-ATTATACCATTATCA
569440 TTGTTTTATC
Statistics
Matches: 116, Mismatches: 23, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
37 26 0.22
38 88 0.76
39 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30
Consensus pattern (38 bp):
TCCAAGATAGTGGGAATTATACCATTATCAACACTTTG
Found at i:574249 original size:25 final size:25
Alignment explanation
Indices: 574220--574267 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
574210 TTTTACATTT
*
574220 TTTAAAGAACTAATAGTATGTTTTG
1 TTTAAAAAACTAATAGTATGTTTTG
574245 TTTAAAAAACTAATAGTATGTTT
1 TTTAAAAAACTAATAGTATGTTT
574268 GGTTAAGGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (25 bp):
TTTAAAAAACTAATAGTATGTTTTG
Found at i:574273 original size:24 final size:25
Alignment explanation
Indices: 574221--574273 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
574211 TTTACATTTT
* *
574221 TTAAAGAACTAATAGTATGTTTTGT
1 TTAAAAAACTAATAGTATGTTTTGG
574246 TTAAAAAACTAATAGTATG-TTTGG
1 TTAAAAAACTAATAGTATGTTTTGG
574270 TTAA
1 TTAA
574274 GGGGAATGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.40, C:0.04, G:0.15, T:0.42
Consensus pattern (25 bp):
TTAAAAAACTAATAGTATGTTTTGG
Found at i:574590 original size:16 final size:16
Alignment explanation
Indices: 574566--574625 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
574556 CTTCTCTCAC
*
574566 TAAATTAAAAAGAATT
1 TAAAATAAAAAGAATT
*
574582 TAAAATAAAAAGAA-A
1 TAAAATAAAAAGAATT
* *
574597 AAAAATTAAAATGAATT
1 TAAAA-TAAAAAGAATT
*
574614 TAAAACAAAAAG
1 TAAAATAAAAAG
574626 GTTTAAGTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
15 4 0.12
16 26 0.76
17 4 0.12
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.22
Consensus pattern (16 bp):
TAAAATAAAAAGAATT
Found at i:575341 original size:54 final size:56
Alignment explanation
Indices: 575219--575369 Score: 141
Period size: 59 Copynumber: 2.7 Consensus size: 56
575209 ACTTAAAAAT
* * *
575219 TAAATTAAAATTTTAATTATAAATT-TTTATATTTTAGAAATAAATAAAAAATAAAATAA
1 TAAATTAATATTTTAATTATTAATTATTAATATTTTA-AAAT--AT-AAAAATAAAATAA
*
575278 TAAAGTAATATTTTAATTATTAATTATTAATATTTTAAAAT-T-AAAAT-AAATAA
1 TAAATTAATATTTTAATTATTAATTATTAATATTTTAAAATATAAAAATAAAATAA
* * * *
575331 TCATATTAATAATTTACATAATTATTTATTAAT-TTTTAA
1 T-AAATTAATATTTTA-ATTATTAATTATTAATATTTTAA
575370 TAAATTGTTA
Statistics
Matches: 80, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
53 7 0.09
54 22 0.28
55 14 0.17
56 1 0.01
59 26 0.32
60 10 0.12
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (56 bp):
TAAATTAATATTTTAATTATTAATTATTAATATTTTAAAATATAAAAATAAAATAA
Found at i:578935 original size:26 final size:25
Alignment explanation
Indices: 578899--578950 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 25
578889 TTTTGAATTC
578899 TTTGAAGTTCAAAAGCCACCCTAACA
1 TTTGAAGTTCAAAAGCCA-CCTAACA
578925 TTTGAAGTTCAAAAGCCACCTAACA
1 TTTGAAGTTCAAAAGCCACCTAACA
578950 T
1 T
578951 CCTCAAAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 8 0.31
26 18 0.69
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (25 bp):
TTTGAAGTTCAAAAGCCACCTAACA
Found at i:586981 original size:12 final size:13
Alignment explanation
Indices: 586959--586987 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
586949 AAAATTAAGT
586959 TAAAGTTGTTTGG
1 TAAAGTTGTTTGG
586972 TAAA-TTGTTTGG
1 TAAAGTTGTTTGG
586984 TAAA
1 TAAA
586988 ATAAATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.31, C:0.00, G:0.24, T:0.45
Consensus pattern (13 bp):
TAAAGTTGTTTGG
Found at i:589498 original size:23 final size:23
Alignment explanation
Indices: 589464--589510 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
589454 TGCAAGGAGG
*
589464 AAAGAAAGAGAAAAAAGAAAAAA
1 AAAGAAAAAGAAAAAAGAAAAAA
*
589487 AAAGAAAAAGAAAAAGGAAAAAA
1 AAAGAAAAAGAAAAAAGAAAAAA
589510 A
1 A
589511 GGAAAGTGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (23 bp):
AAAGAAAAAGAAAAAAGAAAAAA
Found at i:591457 original size:4 final size:4
Alignment explanation
Indices: 591429--591504 Score: 57
Period size: 4 Copynumber: 18.8 Consensus size: 4
591419 CTAATGTAAT
* * * *
591429 ATTA ATTG ATTA ATTA TTTTAA ATTA ATTAA ATTA ATTA ATTA ATTT ATCA
1 ATTA ATTA ATTA ATTA -ATT-A ATTA ATT-A ATTA ATTA ATTA ATTA ATTA
* *
591480 AATA ATTA A-T- ATTA ATGA ATTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATT
591505 CTTTGTAAAA
Statistics
Matches: 55, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
2 1 0.02
3 2 0.04
4 43 0.78
5 8 0.15
6 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (4 bp):
ATTA
Found at i:604242 original size:2 final size:2
Alignment explanation
Indices: 604235--604264 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
604225 ACTCTTTGGA
604235 TC TC TC TC TC -C TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
604265 GTGTCACTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:608401 original size:3 final size:3
Alignment explanation
Indices: 608393--608424 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
608383 GCTATGCACC
608393 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
608425 CCACTACATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:611955 original size:26 final size:26
Alignment explanation
Indices: 611926--611976 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
611916 AAATATTTTA
611926 TTAAT-TATATTAATTTATAT-ATATAT
1 TTAATATA-ATTAA-TTATATCATATAT
611952 TTAATATAATTAATTATATCATATA
1 TTAATATAATTAATTATATCATATA
611977 AAATTATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 6 0.26
26 15 0.65
27 2 0.09
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (26 bp):
TTAATATAATTAATTATATCATATAT
Found at i:612693 original size:43 final size:44
Alignment explanation
Indices: 612606--612702 Score: 124
Period size: 43 Copynumber: 2.2 Consensus size: 44
612596 ATGAATGTAT
* * * *
612606 TGAATTTAAACTTTCTTTAGTTTAATGTTAAAACGTTTAGTTTA
1 TGAATTTTAACTTTCTTTAATATAATGTTAAAACGTTTAATTTA
**
612650 TGAATTTTAACTTT-TTTAATATAATGTTAAAATTTTTAATTTA
1 TGAATTTTAACTTTCTTTAATATAATGTTAAAACGTTTAATTTA
*
612693 TAAATTTTAA
1 TGAATTTTAA
612703 TATATTTTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
43 33 0.72
44 13 0.28
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.53
Consensus pattern (44 bp):
TGAATTTTAACTTTCTTTAATATAATGTTAAAACGTTTAATTTA
Found at i:612694 original size:22 final size:22
Alignment explanation
Indices: 612628--612695 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 22
612618 TTCTTTAGTT
** *
612628 TAATGTTAAAACGTTTAGTTTA
1 TAATGTTAAAATTTTTAATTTA
* **
612650 TGAATTTTAACTTTTTTAA--TA
1 T-AATGTTAAAATTTTTAATTTA
612671 TAATGTTAAAATTTTTAATTTA
1 TAATGTTAAAATTTTTAATTTA
612693 TAA
1 TAA
612696 ATTTTAATAT
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
20 14 0.41
21 3 0.09
22 6 0.18
23 11 0.32
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.51
Consensus pattern (22 bp):
TAATGTTAAAATTTTTAATTTA
Found at i:612718 original size:18 final size:18
Alignment explanation
Indices: 612696--612739 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
612686 TAATTTATAA
*
612696 ATTTTAATATATTTTTATT
1 ATTTTAATA-ATTATTATT
612715 -TTTTAATAATTATTATT
1 ATTTTAATAATTATTATT
612732 ATTTTAAT
1 ATTTTAAT
612740 TATGATAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTTTAATAATTATTATT
Found at i:615770 original size:18 final size:18
Alignment explanation
Indices: 615735--615777 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
615725 CTTGAAGCTC
**
615735 TTCTTTT-AAAAATTTTA
1 TTCTTTTAAAAAAAGTTA
615752 TTCTTTTAAAAAAAGTTA
1 TTCTTTTAAAAAAAGTTA
615770 TT-TTTTAA
1 TTCTTTTAA
615778 TAGCTTTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (18 bp):
TTCTTTTAAAAAAAGTTA
Found at i:624037 original size:20 final size:21
Alignment explanation
Indices: 623987--624026 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
623977 TCATGCAATT
*
623987 CATAGCAAAGAATGATGCCTA
1 CATATCAAAGAATGATGCCTA
624008 CATATCAAAGAATGATGCC
1 CATATCAAAGAATGATGCC
624027 ATCATTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.20
Consensus pattern (21 bp):
CATATCAAAGAATGATGCCTA
Found at i:626737 original size:18 final size:18
Alignment explanation
Indices: 626695--626737 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
626685 TCTATTTATT
626695 TGTTTTTCATCAATTAAA
1 TGTTTTTCATCAATTAAA
*
626713 T-TATTTTCATCAATTACA
1 TGT-TTTTCATCAATTAAA
626731 TGTTTTT
1 TGTTTTT
626738 GTTTTGCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 20 0.91
19 1 0.05
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.56
Consensus pattern (18 bp):
TGTTTTTCATCAATTAAA
Found at i:634684 original size:74 final size:72
Alignment explanation
Indices: 634569--634764 Score: 189
Period size: 73 Copynumber: 2.7 Consensus size: 72
634559 AATTTTTGGA
* * * * * * * *
634569 CAGTGTGCTCTTAGTTGACTAAAATACTTCTTAGTCAACTAAGTCTTTTATGTTTT-TTACTCCT
1 CAGTGAGCACTTAGTCGACTAACATACTTCTTGGTCGACTAAGCCTTTTATGTTTTCTGA-T--T
**
634633 -AATTTTTAG
63 GAAGCTTTAG
* *
634642 CGGTGAGCACTTAGTCGACTAACCATACTTCTTGGTCGACTAAGCCTTTTTTGTTTTCTGATTGA
1 CAGTGAGCACTTAGTCGACTAA-CATACTTCTTGGTCGACTAAGCCTTTTATGTTTTCTGATTGA
*
634707 AGCTTTGG
65 AGCTTTAG
* * *
634715 CAGTGAGCACTTAGTCGACTAATCGTGCTTCTTGGTTGACTAAGCCTTTT
1 CAGTGAGCACTTAGTCGACTAA-CATACTTCTTGGTCGACTAAGCCTTTT
634765 CTATTTTTGG
Statistics
Matches: 102, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
72 1 0.01
73 69 0.68
74 30 0.29
75 2 0.02
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.41
Consensus pattern (72 bp):
CAGTGAGCACTTAGTCGACTAACATACTTCTTGGTCGACTAAGCCTTTTATGTTTTCTGATTGAA
GCTTTAG
Found at i:648600 original size:3 final size:3
Alignment explanation
Indices: 648592--648626 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
648582 TCATAACTAA
648592 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
648627 CTTATAGTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:648923 original size:29 final size:29
Alignment explanation
Indices: 648897--648956 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
648887 ATGACAACTT
*
648897 AAACATACTT-GTCTTAATTTATACAACA
1 AAACATACTTAGTCTTAATTTAAACAACA
** *
648925 AAACATGTTTAGTCTTAATTTAAACAAGA
1 AAACATACTTAGTCTTAATTTAAACAACA
648954 AAA
1 AAA
648957 TATGCTTGTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 8 0.30
29 19 0.70
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (29 bp):
AAACATACTTAGTCTTAATTTAAACAACA
Found at i:649274 original size:13 final size:13
Alignment explanation
Indices: 649256--649280 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
649246 TCTAAATAAT
649256 AATTAAAAAATTA
1 AATTAAAAAATTA
649269 AATTAAAAAATT
1 AATTAAAAAATT
649281 CTTTAATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AATTAAAAAATTA
Found at i:653930 original size:109 final size:104
Alignment explanation
Indices: 653734--653930 Score: 234
Period size: 104 Copynumber: 1.8 Consensus size: 104
653724 ACCCAACATC
* * * * *
653734 CTTTAGGTTGGGTAGAAAATATTTTAAACTTTAATAGAATATAATTATAAGGAGGGAGAATGATG
1 CTTTAGGTTGGGTAGAAAACATTTAAAACTTTAATAGAATATAATTATAAAGAGAGAGAATGATA
**
653799 TGAAAAAAATCTTATCTTTAGATTATTTAGTTTAAAAAT
66 TGAAAAAAATCTTATAGTTAGATTATTTAGTTTAAAAAT
* * * *
653838 CTTTAGGTTGGGTAGAAAACCTTTAAAATTTTAATATAATAAATTATACTTATAAAGAGAGAGAC
1 CTTTAGGTTGGGTAGAAAACATTTAAAACTTTAATAGAAT--A-TA-A-TTATAAAGAGAGAGAA
653903 TGATATGAAAAAAAATCTTA-AGTTAGAT
61 TGATATG-AAAAAAATCTTATAGTTAGAT
653931 AATTAATTGG
Statistics
Matches: 76, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
104 35 0.46
106 1 0.01
107 2 0.03
108 1 0.01
109 25 0.33
110 12 0.16
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.36
Consensus pattern (104 bp):
CTTTAGGTTGGGTAGAAAACATTTAAAACTTTAATAGAATATAATTATAAAGAGAGAGAATGATA
TGAAAAAAATCTTATAGTTAGATTATTTAGTTTAAAAAT
Found at i:657320 original size:4 final size:4
Alignment explanation
Indices: 657306--657356 Score: 50
Period size: 4 Copynumber: 12.8 Consensus size: 4
657296 GCTAGGAAGC
* * * *
657306 AAAG GAAG AAAG AAAG AAA- AGAG AAAG GAAG CAAAG AAAG AAAG GAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG -AAAG AAAG AAAG AAAG
657354 AAA
1 AAA
657357 TGAGGAAGAA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
3 2 0.05
4 32 0.86
5 3 0.08
ACGTcount: A:0.69, C:0.02, G:0.29, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:658196 original size:2 final size:2
Alignment explanation
Indices: 658191--658215 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
658181 GATCATATAT
658191 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
658216 AGTTATGTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:672008 original size:307 final size:307
Alignment explanation
Indices: 671416--672008 Score: 717
Period size: 307 Copynumber: 1.9 Consensus size: 307
671406 CAAATGATTT
* * *
671416 AAAGGAAAAATCTCAAAAAACTTGATTTGATTTTGAAAAACAGTTTTGACAAACCTAGAGCATTG
1 AAAGGAAAAACCTCAAAAAACTTGATTTGATTTTGAAAAACAGTTTTGACAAACCAAGAGCACTG
* *** * * * *
671481 AGAGTTGGTTGAATGTCACGTTGAGATAGTGTGACCCTTGTGCACCAGTGAGCTCTAGCTAGAGA
66 AGAGTAGGCCAAATGTCACATCGAGATAGTGTGACCCTTATGCACAAGTGAGCTCTAGCTAGAGA
* ** *
671546 ACCTTTAGGTTGTGGACAGACTGTTAGATGTAGCTGGGGCCATGGTCTGTGATTATACGTAACAA
131 ACCTTTAGGTTATGGACAGACTGTTAGACATAGCTGGGGCCATGGTCTGTGATTATACATAACAA
* * * * * *
671611 GGCCACGGGTTATTATATGTGACTAGGCCACATGTTGTGATACGCGATTGCGATCGCTTGTTTTC
196 GGCCACGGATTATTATATATGACTAGGCCACAAGTTGTGATACGCGATTACGATCACTTATTTTC
** *
671676 TGTAATGTCGGCCAACATCGTCAAGACTGTCATGATTGATTTGGTTA
261 TCCAATGTCAGCCAACATCGTCAAGACTGTCATGATTGATTTGGTTA
* * * * * *
671723 AAAGGAAAAACCTTAGAAAACTTGATTTGGTTTTGAAAAA-TGATTTTGACAAATCAAGAGCGCC
1 AAAGGAAAAACCTCAAAAAACTTGATTTGATTTTGAAAAACAG-TTTTGACAAACCAAGAGC-AC
* * *
671787 T-AGAGTAGGCCAAATGTCACATCGGGATATTGTTACCCTTATGCACAAGTGAGCTCTAGCTAGA
64 TGAGAGTAGGCCAAATGTCACATCGAGATAGTGTGACCCTTATGCACAAGTGAGCTCTAGCTAGA
* ** * ***
671851 GAACCTTTGGGTTATGGATGGACTGTTAGACATGGCTGGGGCCATGGTCTGTGATTATACATGGT
129 GAACCTTTAGGTTATGGACAGACTGTTAGACATAGCTGGGGCCATGGTCTGTGATTATACATAAC
* *
671916 AAGGCCACGGATTATTATATATGGCTAGGCCACAAGTTGTGATACGC-AGTTACGA-CTATTTAT
194 AAGGCCACGGATTATTATATATGACTAGGCCACAAGTTGTGATACGCGA-TTACGATC-ACTTAT
* * *
671979 TTTCTCCGATGTCAGCGAACATTGTCAAGA
257 TTTCTCCAATGTCAGCCAACATCGTCAAGA
672009 TTGCCATGGC
Statistics
Matches: 237, Mismatches: 45, Indels: 8
0.82 0.16 0.03
Matches are distributed among these distances:
306 3 0.01
307 233 0.98
308 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (307 bp):
AAAGGAAAAACCTCAAAAAACTTGATTTGATTTTGAAAAACAGTTTTGACAAACCAAGAGCACTG
AGAGTAGGCCAAATGTCACATCGAGATAGTGTGACCCTTATGCACAAGTGAGCTCTAGCTAGAGA
ACCTTTAGGTTATGGACAGACTGTTAGACATAGCTGGGGCCATGGTCTGTGATTATACATAACAA
GGCCACGGATTATTATATATGACTAGGCCACAAGTTGTGATACGCGATTACGATCACTTATTTTC
TCCAATGTCAGCCAACATCGTCAAGACTGTCATGATTGATTTGGTTA
Found at i:673260 original size:49 final size:50
Alignment explanation
Indices: 673203--673334 Score: 169
Period size: 49 Copynumber: 2.7 Consensus size: 50
673193 AGCTTGATGA
* *
673203 ACGATGATATGATGTGAGATATCTATGTTCCATCT-GTGGATGATTTCGG
1 ACGATGATATGATGTGAGATATGTATGTTCCATCTAGTGCATGATTTCGG
** *
673252 ACGATGATATGATGTGAGATATGTATGTTCTGT-TAGTGCATGATTTTGG
1 ACGATGATATGATGTGAGATATGTATGTTCCATCTAGTGCATGATTTCGG
* ** *
673301 ACGATAATATGACATGAGATATGTTTGTTCCATC
1 ACGATGATATGATGTGAGATATGTATGTTCCATC
673335 CGATGATGAT
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
48 1 0.01
49 69 0.99
ACGTcount: A:0.27, C:0.11, G:0.25, T:0.38
Consensus pattern (50 bp):
ACGATGATATGATGTGAGATATGTATGTTCCATCTAGTGCATGATTTCGG
Found at i:687683 original size:13 final size:13
Alignment explanation
Indices: 687665--687695 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
687655 TCCAGTGATT
687665 ACTTTAGGCAATG
1 ACTTTAGGCAATG
687678 ACTTTAGGCAATG
1 ACTTTAGGCAATG
687691 ACTTT
1 ACTTT
687696 GTTTCTCCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.35
Consensus pattern (13 bp):
ACTTTAGGCAATG
Found at i:693917 original size:16 final size:16
Alignment explanation
Indices: 693886--693919 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
693876 TTGGGGAGTT
* *
693886 AAGTTTGGATTTTTGA
1 AAGTTTGGAATGTTGA
693902 AAGTTTGGAATGTTGA
1 AAGTTTGGAATGTTGA
693918 AA
1 AA
693920 AACTGAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.41
Consensus pattern (16 bp):
AAGTTTGGAATGTTGA
Found at i:694876 original size:20 final size:20
Alignment explanation
Indices: 694851--694895 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
694841 AATAAATTTT
*
694851 TATATGAATGTGTATATGTA
1 TATATGAATGTGTATATATA
* * *
694871 TATATGCATTTTTATATATA
1 TATATGAATGTGTATATATA
694891 TATAT
1 TATAT
694896 ACGTATATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.51
Consensus pattern (20 bp):
TATATGAATGTGTATATATA
Found at i:697934 original size:81 final size:80
Alignment explanation
Indices: 697792--697951 Score: 268
Period size: 81 Copynumber: 2.0 Consensus size: 80
697782 AGTAGGCAAT
*
697792 TCATTGCTCAATTTGTTCCACTCTATTTAATTTAGCATTTTTTTCTATGTCAATATGATGATATC
1 TCATTGCTCAATTTGTTCCACTCTATTGAATTTAGCATTTTTTTCTATGTCAATATGATGATATC
697857 TTGTCTTATATTCAC
66 TTGTCTTATATTCAC
*
697872 TCATTGCTCAATTTGTT-CACTTTATTGAATTTAGCATTTTTTTTTCTATGTCAATATGATGATA
1 TCATTGCTCAATTTGTTCCACTCTATTGAATTTAGCA--TTTTTTTCTATGTCAATATGATGATA
*
697936 TGTTGTCTTATATTCA
64 TCTTGTCTTATATTCA
697952 AGAATTTTAG
Statistics
Matches: 75, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
79 17 0.23
80 17 0.23
81 41 0.55
ACGTcount: A:0.24, C:0.15, G:0.10, T:0.51
Consensus pattern (80 bp):
TCATTGCTCAATTTGTTCCACTCTATTGAATTTAGCATTTTTTTCTATGTCAATATGATGATATC
TTGTCTTATATTCAC
Found at i:698040 original size:2 final size:2
Alignment explanation
Indices: 698033--698062 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
698023 CTTCAATGAC
698033 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
698063 GTCTTCACGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:700418 original size:17 final size:18
Alignment explanation
Indices: 700386--700423 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
700376 GGGTCGAGCC
700386 AAGGCAAAATTTTGATGG
1 AAGGCAAAATTTTGATGG
*
700404 AAGGCAAGA-TTTGATGG
1 AAGGCAAAATTTTGATGG
700421 AAG
1 AAG
700424 TAACTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.39, C:0.05, G:0.32, T:0.24
Consensus pattern (18 bp):
AAGGCAAAATTTTGATGG
Found at i:710010 original size:36 final size:36
Alignment explanation
Indices: 709968--710067 Score: 103
Period size: 36 Copynumber: 2.8 Consensus size: 36
709958 AAAGTTAGTG
* *
709968 AGGGTTATCGCTTGATCTTGTG-AAAAGGTCATTAAA
1 AGGGTTATCGCTTGATCTCGTGAAAAAGCT-ATTAAA
* * * * *
710004 AGGGTTACCACTTAATCCCGTGAAAAAGCTATTATA
1 AGGGTTATCGCTTGATCTCGTGAAAAAGCTATTAAA
* *
710040 AGGGTTATTGCTTGATCTCGTCAAAAAG
1 AGGGTTATCGCTTGATCTCGTGAAAAAG
710068 TTGTTGTGAA
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
36 44 0.88
37 6 0.12
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (36 bp):
AGGGTTATCGCTTGATCTCGTGAAAAAGCTATTAAA
Found at i:713502 original size:21 final size:21
Alignment explanation
Indices: 713470--713534 Score: 103
Period size: 21 Copynumber: 3.0 Consensus size: 21
713460 CTCTTAAAGT
*
713470 AATTTAAAATAAAATAACATAA
1 AATTT-AAATAAAATAACTTAA
713492 AATTTAAATAAAATAACTTAA
1 AATTTAAATAAAATAACTTAA
*
713513 AATTTAACTAAAATAACTTAA
1 AATTTAAATAAAATAACTTAA
713534 A
1 A
713535 CTAACTACTT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 36 0.88
22 5 0.12
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (21 bp):
AATTTAAATAAAATAACTTAA
Found at i:717168 original size:10 final size:10
Alignment explanation
Indices: 717153--717182 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
717143 CTTGATAAAG
717153 TTGAAACTTT
1 TTGAAACTTT
717163 TTGAAAACTTT
1 TTG-AAACTTT
717174 TTGAAACTT
1 TTGAAACTT
717183 CATGCATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (10 bp):
TTGAAACTTT
Found at i:720939 original size:17 final size:17
Alignment explanation
Indices: 720917--720949 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
720907 TTGTAAAGGT
720917 TGAAAA-TCTTGTAGAAG
1 TGAAAAGTCTTG-AGAAG
720934 TGAAAAGTCTTGAGAA
1 TGAAAAGTCTTGAGAA
720950 AATAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.42, C:0.06, G:0.24, T:0.27
Consensus pattern (17 bp):
TGAAAAGTCTTGAGAAG
Found at i:723459 original size:28 final size:28
Alignment explanation
Indices: 723427--723541 Score: 88
Period size: 28 Copynumber: 4.0 Consensus size: 28
723417 ATTAAGATAA
* * *
723427 AAATATGTTATTTTGTCTAAATTGAGAC
1 AAATATATTATTTTATCTAAATTAAGAC
*
723455 AAATATATTTTTTTATCTAAATTAAGAC
1 AAATATATTATTTTATCTAAATTAAGAC
* * * *
723483 AAAATATATTTTTCTTTTCTTAAATTACGAT
1 -AAATATATTATT-TTATC-TAAATTAAGAC
** *
723514 AAGCATATT-TTCTTGTCTAAATTAAGAC
1 AAATATATTATT-TTATCTAAATTAAGAC
723542 TAAACATGTT
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
28 33 0.46
29 19 0.26
30 11 0.15
31 9 0.12
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (28 bp):
AAATATATTATTTTATCTAAATTAAGAC
Found at i:723522 original size:59 final size:57
Alignment explanation
Indices: 723459--723576 Score: 146
Period size: 59 Copynumber: 2.0 Consensus size: 57
723449 TGAGACAAAT
* * * * * *
723459 ATATTTTTTTATCTAAATTAAGACAAAATATATTTTTCTTTTCTTAAATTACGATAAGC
1 ATATTTTCTTATCTAAATTAAGACAAAACAT-GTTTTCTTGT-ATAAATTAAGATAAGC
* *
723518 ATATTTTCTTGTCTAAATTAAGACTAAACATGTTTTCTTGTATAAATTAAGATAAGC
1 ATATTTTCTTATCTAAATTAAGACAAAACATGTTTTCTTGTATAAATTAAGATAAGC
723575 AT
1 AT
723577 GTTTAAACTG
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
57 16 0.31
58 8 0.16
59 27 0.53
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (57 bp):
ATATTTTCTTATCTAAATTAAGACAAAACATGTTTTCTTGTATAAATTAAGATAAGC
Found at i:723527 original size:29 final size:28
Alignment explanation
Indices: 723439--723576 Score: 114
Period size: 29 Copynumber: 4.8 Consensus size: 28
723429 ATATGTTATT
* * ** *
723439 TTGTCTAAATTGAGACAAATATATTTTT
1 TTGTCTAAATTAAGATAAGCATATTTTC
* * **
723467 TTATCTAAATTAAGACAAAATATATTTTTC
1 TTGTCTAAATTAAGA-TAAGCATA-TTTTC
* *
723497 TTTTCTTAAATTACGATAAGCATATTTTC
1 TTGTC-TAAATTAAGATAAGCATATTTTC
* *
723526 TTGTCTAAATTAAGACTAAACATGTTTTC
1 TTGTCTAAATTAAGA-TAAGCATATTTTC
*
723555 TTGTATAAATTAAGATAAGCAT
1 TTGTCTAAATTAAGATAAGCAT
723577 GTTTAAACTG
Statistics
Matches: 91, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
28 28 0.31
29 41 0.45
30 13 0.14
31 9 0.10
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (28 bp):
TTGTCTAAATTAAGATAAGCATATTTTC
Found at i:724328 original size:27 final size:27
Alignment explanation
Indices: 724297--724381 Score: 70
Period size: 27 Copynumber: 3.2 Consensus size: 27
724287 TGTCTTATTG
724297 ATGAAGAAAAACCTCTAATCATTCAAT
1 ATGAAGAAAAACCTCTAATCATTCAAT
* * * * *
724324 ATGAATG-ATATCAT-TATGTC-TT-ATT
1 ATGAA-GAAAAACCTCTA-ATCATTCAAT
724349 GATGAAGAAAAACCTCTAATCATTCAAT
1 -ATGAAGAAAAACCTCTAATCATTCAAT
724377 ATGAA
1 ATGAA
724382 TGATATCATT
Statistics
Matches: 41, Mismatches: 10, Indels: 14
0.63 0.15 0.22
Matches are distributed among these distances:
25 3 0.07
26 15 0.37
27 20 0.49
28 3 0.07
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.32
Consensus pattern (27 bp):
ATGAAGAAAAACCTCTAATCATTCAAT
Found at i:724348 original size:53 final size:53
Alignment explanation
Indices: 724286--724391 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
724276 ATTATAACTA
724286 ATGTCTTATTGATGAAGAAAAACCTCTAATCATTCAATATGAATGATATCATT
1 ATGTCTTATTGATGAAGAAAAACCTCTAATCATTCAATATGAATGATATCATT
724339 ATGTCTTATTGATGAAGAAAAACCTCTAATCATTCAATATGAATGATATCATT
1 ATGTCTTATTGATGAAGAAAAACCTCTAATCATTCAATATGAATGATATCATT
724392 GCATGATTAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (53 bp):
ATGTCTTATTGATGAAGAAAAACCTCTAATCATTCAATATGAATGATATCATT
Found at i:726683 original size:100 final size:99
Alignment explanation
Indices: 726491--726684 Score: 230
Period size: 100 Copynumber: 1.9 Consensus size: 99
726481 AGAAGATACA
** * *
726491 TGTTTTCCATTTAATAGATAGAAAATACCAAAAAGTACATGTTAAAAGATATAAAATTGCTATAA
1 TGTTTTCCATTTAATAGATAGAAAATACCAAAAAACACATATTAAAAGATATAAAAATGCTATAA
* * *
726556 TACCTTCTGGAGGTGAGGATCATTATAGTTTAGT
66 TACCTTCTGGAAGTGAGAATCACTATAGTTTAGT
* * **
726590 TGTTTTCTATTTAATATATAGCAAAATATTAAAAAACACATATTAAAAGATA-AAAAATGACTAT
1 TGTTTTCCATTTAATAGATAG-AAAATACCAAAAAACACATATTAAAAGATATAAAAATG-CTAT
* *
726654 AATACTCTT-TGTAAGTGATAATCACTATAGT
64 AATAC-CTTCTGGAAGTGAGAATCACTATAGT
726685 ATAGATTGCA
Statistics
Matches: 79, Mismatches: 13, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
99 25 0.32
100 51 0.65
101 3 0.04
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (99 bp):
TGTTTTCCATTTAATAGATAGAAAATACCAAAAAACACATATTAAAAGATATAAAAATGCTATAA
TACCTTCTGGAAGTGAGAATCACTATAGTTTAGT
Found at i:727133 original size:2 final size:2
Alignment explanation
Indices: 727128--727174 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
727118 TATATCTATA
*
727128 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG AG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
727170 TG TG T
1 TG TG T
727175 AAAGATATGC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.02, C:0.00, G:0.49, T:0.49
Consensus pattern (2 bp):
TG
Found at i:733106 original size:31 final size:31
Alignment explanation
Indices: 733068--733142 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
733058 GTATAAGGGT
*
733068 TAAATTGAATAAAAATGTAAAATACACGA-AC
1 TAAATTGAACAAAAATGTAAAATACA-GAGAC
* * *
733099 TAAATTGAACAAAATTGTAAAGTACATAGAC
1 TAAATTGAACAAAAATGTAAAATACAGAGAC
733130 TAAATTGAACAAA
1 TAAATTGAACAAA
733143 GATCTATCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 1 0.03
31 38 0.97
ACGTcount: A:0.56, C:0.09, G:0.11, T:0.24
Consensus pattern (31 bp):
TAAATTGAACAAAAATGTAAAATACAGAGAC
Found at i:734411 original size:31 final size:30
Alignment explanation
Indices: 734373--734472 Score: 87
Period size: 31 Copynumber: 3.2 Consensus size: 30
734363 AAAAGTACCT
*
734373 AATTTAGTCC-ATATATC-ATAGATCTTTGTTC
1 AATTTAGTCCTATAT-TCTATA-AT-TTTATTC
*
734404 AATTTAGTTTCTATATTCTATAATTTTATTC
1 AATTTAG-TCCTATATTCTATAATTTTATTC
* **
734435 AATTTAGTCCTTATAGTCTACTTTTTTTATTC
1 AATTTAGTCC-TATATTCTA-TAATTTTATTC
734467 AATTTA
1 AATTTA
734473 AGTTCTTATG
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
30 2 0.03
31 28 0.48
32 21 0.36
33 7 0.12
ACGTcount: A:0.28, C:0.13, G:0.06, T:0.53
Consensus pattern (30 bp):
AATTTAGTCCTATATTCTATAATTTTATTC
Found at i:753618 original size:21 final size:21
Alignment explanation
Indices: 753594--753649 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
753584 TTGAATGGAG
753594 GCATCAGTCTTTGTTATAAAT
1 GCATCAGTCTTTGTTATAAAT
** * *
753615 GCATTGGTCGTTGTTATGAAT
1 GCATCAGTCTTTGTTATAAAT
*
753636 GCACCAGTCTTTGT
1 GCATCAGTCTTTGT
753650 CATGAACTAC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.41
Consensus pattern (21 bp):
GCATCAGTCTTTGTTATAAAT
Found at i:753654 original size:21 final size:21
Alignment explanation
Indices: 753598--753655 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
753588 ATGGAGGCAT
* *
753598 CAGTCTTTGTTATAAATGCAT
1 CAGTCTTTGTTATGAATGCAC
** *
753619 TGGTCGTTGTTATGAATGCAC
1 CAGTCTTTGTTATGAATGCAC
*
753640 CAGTCTTTGTCATGAA
1 CAGTCTTTGTTATGAA
753656 CTACGTGAAC
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (21 bp):
CAGTCTTTGTTATGAATGCAC
Found at i:757930 original size:23 final size:23
Alignment explanation
Indices: 757899--757948 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
757889 TAGGGTTTAA
* *
757899 CATTGCATGACTGGTTGATATGT
1 CATTACATGACTGGTTGATAGGT
757922 CATTACATGACTGGTTGATAGGT
1 CATTACATGACTGGTTGATAGGT
757945 CATT
1 CATT
757949 GCGTGAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (23 bp):
CATTACATGACTGGTTGATAGGT
Found at i:758050 original size:110 final size:110
Alignment explanation
Indices: 757856--758060 Score: 320
Period size: 110 Copynumber: 1.9 Consensus size: 110
757846 CTAGATTTTG
* * * *
757856 GCATGGCGTCACTTAGGGTGTGCGTGATTGCATTAGGGTTTAACATTGCATGACTGGTTGATATG
1 GCATGGCATCACTTAGGGTGTGCGTGATTGCATTAAGGTTTAACAGTACATGACTGGTTGATATG
* *
757921 TCATTACATGACTGGTTGATAGGTCATTGCGTGAATATTGTTTAA
66 TCATTACATAACTGATTGATAGGTCATTGCGTGAATATTGTTTAA
* *
757966 GCATGGCATTACTTAGGGTGTGCGTGATTGCATTAAGGTTTAACAGTACGTGACTGGTTGATATG
1 GCATGGCATCACTTAGGGTGTGCGTGATTGCATTAAGGTTTAACAGTACATGACTGGTTGATATG
* *
758031 TCATTGCATAAGTGATTGATAGGTCATTGC
66 TCATTACATAACTGATTGATAGGTCATTGC
758061 CTGAGTGGTT
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
110 85 1.00
ACGTcount: A:0.23, C:0.13, G:0.28, T:0.36
Consensus pattern (110 bp):
GCATGGCATCACTTAGGGTGTGCGTGATTGCATTAAGGTTTAACAGTACATGACTGGTTGATATG
TCATTACATAACTGATTGATAGGTCATTGCGTGAATATTGTTTAA
Found at i:758056 original size:23 final size:23
Alignment explanation
Indices: 758023--758085 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
758013 ACGTGACTGG
*
758023 TTGATATGTCATTGCATAAGTGA
1 TTGATAGGTCATTGCATAAGTGA
* * *
758046 TTGATAGGTCATTGCCTGAGTGG
1 TTGATAGGTCATTGCATAAGTGA
*
758069 TTGATAGGTTATTGCAT
1 TTGATAGGTCATTGCAT
758086 GAATATTCCT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.24, C:0.10, G:0.27, T:0.40
Consensus pattern (23 bp):
TTGATAGGTCATTGCATAAGTGA
Found at i:759558 original size:5 final size:5
Alignment explanation
Indices: 759548--759575 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
759538 AGACACCATA
759548 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
759576 TTTATCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:762155 original size:20 final size:20
Alignment explanation
Indices: 762117--762156 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
762107 AGGTTATGAT
* *
762117 TCCTAATGTCTAGTCACATA
1 TCCTAATATCCAGTCACATA
*
762137 TCCTAATATCCAGTGACATA
1 TCCTAATATCCAGTCACATA
762157 ATGCCTAACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.33
Consensus pattern (20 bp):
TCCTAATATCCAGTCACATA
Found at i:762538 original size:25 final size:24
Alignment explanation
Indices: 762491--762541 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
762481 GTTGGAAAAG
762491 AATTTCCAACCAAATTCCATTGGA
1 AATTTCCAACCAAATTCCATTGGA
* *
762515 AATTTCCAACAGAAATTCCCTTGGA
1 AATTTCCAAC-CAAATTCCATTGGA
762540 AA
1 AA
762542 AGAATTTCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (24 bp):
AATTTCCAACCAAATTCCATTGGA
Found at i:762601 original size:14 final size:15
Alignment explanation
Indices: 762584--762616 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
762574 CATTTCTCAT
*
762584 GAAA-AATTTCGTTG
1 GAAATAATTTCGTAG
762598 GAAATAATTTCGTAG
1 GAAATAATTTCGTAG
762613 GAAA
1 GAAA
762617 GGAATTTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.30
Consensus pattern (15 bp):
GAAATAATTTCGTAG
Found at i:762677 original size:99 final size:101
Alignment explanation
Indices: 762515--762723 Score: 221
Period size: 99 Copynumber: 2.1 Consensus size: 101
762505 TTCCATTGGA
* * *
762515 AATTTCCAACAGAAATTCCCTTGGAAAAGAATTTCCAACGGAATTATGCATTGGTAAAGCA-TTT
1 AATTTCCAACAGAAATTCCCTTGG--AAGAATTTCCAACAGAATTATGCATTGGAAAAACATTTT
* *
762579 CTCATGAAAAATTTCGTTGGAAATAATT-TCGTAGGAAAGG
64 C-CATGAAAAATTCCGTGGGAAA-AATTCT-GTAGGAAAGG
* * * * *
762619 AATTTCCAACAG-AATTCCGTTGG-A-AATTTCCAACAGACTTTTTCGTTGGAAAAACATTTTCC
1 AATTTCCAACAGAAATTCCCTTGGAAGAATTTCCAACAGAATTATGCATTGGAAAAACATTTTCC
* **
762681 ATGGAAAATTCCGTGGGAAAAATTCTGTAGGAAATT
66 ATGAAAAATTCCGTGGGAAAAATTCTGTAGGAAAGG
762717 AATTTCC
1 AATTTCC
762724 CACGAAAAAT
Statistics
Matches: 90, Mismatches: 13, Indels: 10
0.80 0.12 0.09
Matches are distributed among these distances:
98 19 0.21
99 44 0.49
100 5 0.06
103 10 0.11
104 12 0.13
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (101 bp):
AATTTCCAACAGAAATTCCCTTGGAAGAATTTCCAACAGAATTATGCATTGGAAAAACATTTTCC
ATGAAAAATTCCGTGGGAAAAATTCTGTAGGAAAGG
Found at i:768171 original size:13 final size:14
Alignment explanation
Indices: 768143--768171 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
768133 AATCCGTTGG
768143 AAATTTCCAACAGA
1 AAATTTCCAACAGA
768157 AAATTTCCAAC-GA
1 AAATTTCCAACAGA
768170 AA
1 AA
768172 TTTTTTCCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.52, C:0.21, G:0.07, T:0.21
Consensus pattern (14 bp):
AAATTTCCAACAGA
Found at i:770975 original size:13 final size:13
Alignment explanation
Indices: 770957--770983 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
770947 ATCATAAGAG
770957 AATCTCCATTTTC
1 AATCTCCATTTTC
770970 AATCTCCATTTTC
1 AATCTCCATTTTC
770983 A
1 A
770984 TTCTAAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.30, G:0.00, T:0.44
Consensus pattern (13 bp):
AATCTCCATTTTC
Found at i:773451 original size:41 final size:40
Alignment explanation
Indices: 773365--773451 Score: 131
Period size: 41 Copynumber: 2.1 Consensus size: 40
773355 AGCCGCTGTA
*
773365 AAATTATTCTCATAACTTTGTTCATGTGGACTTCCTCTGCC
1 AAATTATTCTCATAACTTTGTTCATGTGGACTTCATCTG-C
773406 AAATTATTCTCATAACTTTGTTCATGTGGACTCTGCATCTG-
1 AAATTATTCTCATAACTTTGTTCATGTGGACT-T-CATCTGC
773447 AAATT
1 AAATT
773452 CAGTCTTCAG
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
41 37 0.86
42 1 0.02
43 5 0.12
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (40 bp):
AAATTATTCTCATAACTTTGTTCATGTGGACTTCATCTGC
Found at i:776841 original size:12 final size:12
Alignment explanation
Indices: 776824--776858 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
776814 TTGCATGCCC
776824 CAATTTTTTTTA
1 CAATTTTTTTTA
776836 CAATTTTTTTTA
1 CAATTTTTTTTA
*
776848 AAATTTTTTTT
1 CAATTTTTTTT
776859 CACATCAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (12 bp):
CAATTTTTTTTA
Found at i:776959 original size:31 final size:31
Alignment explanation
Indices: 776888--776966 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
776878 CACGCCATGA
* * *
776888 GGACTAAATTGAATAAAAATGTAAAGTACAC
1 GGACTAAATTGAACAAAAATATAAAATACAC
* * *
776919 GAACTAAATTGAACAAAATTATAAAATACAT
1 GGACTAAATTGAACAAAAATATAAAATACAC
* *
776950 GGACCAAATTAAACAAA
1 GGACTAAATTGAACAAA
776967 GATCTATCAT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22
Consensus pattern (31 bp):
GGACTAAATTGAACAAAAATATAAAATACAC
Found at i:778940 original size:3 final size:3
Alignment explanation
Indices: 778932--778959 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
778922 TAGATTAGAC
778932 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
778960 TTGAGAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:784925 original size:15 final size:15
Alignment explanation
Indices: 784905--784938 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
784895 AAATATTGAA
784905 AAAAGGCAAGAAAAC
1 AAAAGGCAAGAAAAC
* *
784920 AAAAGGGAAGAAAAG
1 AAAAGGCAAGAAAAC
784935 AAAA
1 AAAA
784939 AGATGCAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.71, C:0.06, G:0.24, T:0.00
Consensus pattern (15 bp):
AAAAGGCAAGAAAAC
Found at i:789620 original size:32 final size:32
Alignment explanation
Indices: 789578--789639 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
789568 TTTTAGGTTA
789578 AGAACATGAGCCCTAACCATAATTAGGTGATG
1 AGAACATGAGCCCTAACCATAATTAGGTGATG
* *
789610 AGAACGTGAGCCCTAACCTTAATTAGGTGA
1 AGAACATGAGCCCTAACCATAATTAGGTGA
789640 GGTAAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (32 bp):
AGAACATGAGCCCTAACCATAATTAGGTGATG
Found at i:790511 original size:20 final size:20
Alignment explanation
Indices: 790488--790539 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 20
790478 TCTATTTGAT
790488 TTTTTAAAAATAAAAATTTA
1 TTTTTAAAAATAAAAATTTA
*
790508 -TTTTAAAAATTAAATATTTA
1 TTTTTAAAAA-TAAAAATTTA
790528 TTTTTCAAAAAT
1 TTTTT-AAAAAT
790540 CAATTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 9 0.32
20 9 0.32
21 5 0.18
22 5 0.18
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTTTAAAAATAAAAATTTA
Found at i:790513 original size:19 final size:20
Alignment explanation
Indices: 790489--790531 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
790479 CTATTTGATT
790489 TTTTAAAAA-TAAAAATTTA
1 TTTTAAAAATTAAAAATTTA
*
790508 TTTTAAAAATTAAATATTTA
1 TTTTAAAAATTAAAAATTTA
790528 TTTT
1 TTTT
790532 TCAAAAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTTAAAAATTAAAAATTTA
Found at i:790631 original size:17 final size:17
Alignment explanation
Indices: 790611--790654 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
790601 AAATATAAAG
790611 AAAAA-TAAATTCTT-TA
1 AAAAATTAAATT-TTATA
*
790627 AAAAATTATATTTTATA
1 AAAAATTAAATTTTATA
790644 AAAAATTAAAT
1 AAAAATTAAAT
790655 AAAATTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 7 0.29
17 17 0.71
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAAATTAAATTTTATA
Found at i:798421 original size:21 final size:21
Alignment explanation
Indices: 798397--798436 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
798387 TATTTATTTA
798397 ATTATTTTTATCAAA-TAAACT
1 ATTATTTTTAT-AAAGTAAACT
798418 ATTATTTTTATAAAGTAAA
1 ATTATTTTTATAAAGTAAA
798437 AATAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (21 bp):
ATTATTTTTATAAAGTAAACT
Found at i:801234 original size:170 final size:170
Alignment explanation
Indices: 800962--801269 Score: 519
Period size: 170 Copynumber: 1.8 Consensus size: 170
800952 TATTCATCTA
* * *
800962 TGCCTGGGCTTACACTAGCCCAATACCAACTGTTAATGAACCTATTAGGGCGACAGTCAAATAAA
1 TGCCTGGGCTTACACTAGCCCAATACCAACTGCTAATGAACCTACTAGGGCAACAGTCAAATAAA
*
801027 TCCAATTCTAATATTGGACCAACAATCAACATGGCCTCAAATGCTTTTAATGCAAACATTTCTGG
66 TCCAATTCTAATATTGGACCAACAATCAACATGGCCTCAAATGCTTTTAATGCAAACATTTCTAG
801092 TAATTCCTTTGATAAGGAGAACACAAGCTCTATTCATTCG
131 TAATTCCTTTGATAAGGAGAACACAAGCTCTATTCATTCG
*
801132 TGCCTGGGCTTACAC-AGACCCAATACCAACTGCTAATGAACCTACTAGGGCAACAGTCAAATGA
1 TGCCTGGGCTTACACTAG-CCCAATACCAACTGCTAATGAACCTACTAGGGCAACAGTCAAATAA
* * * *
801196 CTCTAATTCTAGTATTGGACCAACAATCAACATGGCCTCAAATGCTTTTAATGCAAACTTTTCTA
65 ATCCAATTCTAATATTGGACCAACAATCAACATGGCCTCAAATGCTTTTAATGCAAACATTTCTA
801261 GTAATTCCT
130 GTAATTCCT
801270 ATGGTAAGAA
Statistics
Matches: 128, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
169 2 0.02
170 126 0.98
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (170 bp):
TGCCTGGGCTTACACTAGCCCAATACCAACTGCTAATGAACCTACTAGGGCAACAGTCAAATAAA
TCCAATTCTAATATTGGACCAACAATCAACATGGCCTCAAATGCTTTTAATGCAAACATTTCTAG
TAATTCCTTTGATAAGGAGAACACAAGCTCTATTCATTCG
Found at i:803811 original size:2 final size:2
Alignment explanation
Indices: 803806--803838 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
803796 CCTCCTTTTT
803806 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
803839 AAAGATGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:805266 original size:3 final size:3
Alignment explanation
Indices: 805260--805298 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
805250 TTGTTAATGG
* * *
805260 TAA TAA TAA TAA CAA TTA TAA TAA TCA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
805299 CAATCATGTG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:822256 original size:128 final size:134
Alignment explanation
Indices: 822133--822371 Score: 318
Period size: 128 Copynumber: 1.8 Consensus size: 134
822123 TTATTATACC
822133 TTATAGTAACACTTATGAATAAA-TAAATATATGTATA-ATAAATTATAAT-AC-TT-TATTATA
1 TTATAGTAACACTTATGAATAAATTAAATATATGTATATAT-AA-TAT-ATGACTTTATATTATA
822193 TA-AT-A-AAATTAATGTACA-AA-TTATATGTTAAAATGTTTTATATACATATAAATTAAGTCT
63 TATATAAGAAATTAATG-ACATAACTTATATGTTAAAATGTTTTATATACATATAAATTAAGTCT
822253 ATTAGAAA
127 ATTAGAAA
* * *
822261 TTATAGTAATATTTATGTATAAATTAAATATATGTATATATAATATATGACTTTATATTATATAT
1 TTATAGTAACACTTATGAATAAATTAAATATATGTATATATAATATATGACTTTATATTATATAT
*
822326 ATAGATGAAATTAATGACATAACTTATATGTTATAATGTTTTATAT
66 ATA-A-GAAATTAATGACATAACTTATATGTTAAAATGTTTTATAT
822372 CAAAGTTTGT
Statistics
Matches: 95, Mismatches: 4, Indels: 16
0.83 0.03 0.14
Matches are distributed among these distances:
127 2 0.02
128 25 0.26
129 18 0.19
130 11 0.12
131 2 0.02
133 1 0.01
134 3 0.03
135 11 0.12
136 22 0.23
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.44
Consensus pattern (134 bp):
TTATAGTAACACTTATGAATAAATTAAATATATGTATATATAATATATGACTTTATATTATATAT
ATAAGAAATTAATGACATAACTTATATGTTAAAATGTTTTATATACATATAAATTAAGTCTATTA
GAAA
Found at i:822308 original size:17 final size:18
Alignment explanation
Indices: 822262--822308 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
822252 TATTAGAAAT
*
822262 TATAGTAATATTTATGTA
1 TATAGTAATATATATGTA
* *
822280 TAAATTAA-ATATATGTA
1 TATAGTAATATATATGTA
822297 TATA-TAATATAT
1 TATAGTAATATAT
822309 GACTTTATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 3 0.12
17 15 0.62
18 6 0.25
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (18 bp):
TATAGTAATATATATGTA
Found at i:822508 original size:22 final size:22
Alignment explanation
Indices: 822467--822508 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
822457 TAAATAAAGT
*
822467 TTATTATAAATTATAGTAATAC
1 TTATTATAAATAATAGTAATAC
822489 TTATGTATAAATAATA-TAAT
1 TTAT-TATAAATAATAGTAAT
822509 GTATATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (22 bp):
TTATTATAAATAATAGTAATAC
Found at i:827745 original size:85 final size:84
Alignment explanation
Indices: 827642--827811 Score: 200
Period size: 84 Copynumber: 2.0 Consensus size: 84
827632 TTGTTGGAAT
* * * * * *
827642 CAACTAGAAGTCCATAAAATGTACATAAAAAATAAACGAAAGAAGAAA-ACATTTTTATTCAGCC
1 CAACTAGAAGTCAATAAAA-ATACATAAAAAACAAACAAAAGAAGAAACA-AATTTTATACAGCC
***
827706 AATAAATTGTCTATATAACAA
64 AATAAAACATCTATATAACAA
* *
827727 CAACTA-ATAGTCAATAAAAATACATAAAAAACAAATAAAAGAAGAAACAAATTTTATACAGCTA
1 CAACTAGA-AGTCAATAAAAATACATAAAAAACAAACAAAAGAAGAAACAAATTTTATACAGCCA
827791 ATAAAACATCTATATAACAA
65 ATAAAACATCTATATAACAA
827811 C
1 C
827812 TTGAGACCAC
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
84 55 0.76
85 17 0.24
ACGTcount: A:0.56, C:0.14, G:0.07, T:0.23
Consensus pattern (84 bp):
CAACTAGAAGTCAATAAAAATACATAAAAAACAAACAAAAGAAGAAACAAATTTTATACAGCCAA
TAAAACATCTATATAACAA
Found at i:831454 original size:11 final size:11
Alignment explanation
Indices: 831438--831463 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
831428 AATGTTTATG
831438 TATAAATTAAA
1 TATAAATTAAA
831449 TATAAATTAAA
1 TATAAATTAAA
831460 TATA
1 TATA
831464 TGCATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TATAAATTAAA
Found at i:831611 original size:17 final size:18
Alignment explanation
Indices: 831570--831611 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
831560 TAAATTGTAG
*
831570 TAATATTTATGTATAAAT
1 TAATATATATGTATAAAT
*
831588 TAA-ATATATGTATATA-
1 TAATATATATGTATAAAT
831604 TAATATAT
1 TAATATAT
831612 GACTTTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 3 0.14
17 15 0.71
18 3 0.14
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (18 bp):
TAATATATATGTATAAAT
Found at i:831936 original size:20 final size:20
Alignment explanation
Indices: 831907--831947 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
831897 TATATGTATA
*
831907 TATAATATATTTAT-ACAAT
1 TATAATATATTCATAACAAT
831926 TATACATATATTCATAACAAT
1 TATA-ATATATTCATAACAAT
831947 T
1 T
831948 TATATTACGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 9 0.47
21 6 0.32
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (20 bp):
TATAATATATTCATAACAAT
Found at i:838562 original size:37 final size:36
Alignment explanation
Indices: 838506--838581 Score: 107
Period size: 37 Copynumber: 2.1 Consensus size: 36
838496 TAATGTTAAA
*
838506 TTACATTATCATGTTTAAAAAGAAAATCAATTAATT
1 TTACATTATCATGTTTAAAAAGAAAATCAATCAATT
* * *
838542 TTACTTTATCATATTTTAAAAAGAAAATCAGTCAATT
1 TTACATTATCAT-GTTTAAAAAGAAAATCAATCAATT
838579 TTA
1 TTA
838582 AGTAATCAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
36 11 0.31
37 24 0.69
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (36 bp):
TTACATTATCATGTTTAAAAAGAAAATCAATCAATT
Found at i:839108 original size:80 final size:81
Alignment explanation
Indices: 838988--839153 Score: 203
Period size: 81 Copynumber: 2.1 Consensus size: 81
838978 GTTGGTCTCA
** * * *
838988 AGTTGTTATTAGATGTCTTATTAGCTGTATAAAATTTG-TTTCTTCTTT-TATTTTTTTTTATGT
1 AGTTGTTATTAGACATCTTATTAGCTGAATAAAATATGTTTTCTTCTTTGT-TTATTTTTTATGT
* *
839051 ACTTTTTATTGACTACT
65 ACATTTTACTGACTACT
* *
839068 AGTTGTTATATAGACATTTTATTGGCTGAATAAAA-ATGTTTTCTTCTTTGTTTATTTTTTATGT
1 AGTTGTTAT-TAGACATCTTATTAGCTGAATAAAATATGTTTTCTTCTTTGTTTATTTTTTATGT
*
839132 ACATTTTACTGACTTCT
65 ACATTTTACTGACTACT
839149 AGTTG
1 AGTTG
839154 ATTCAACAAC
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
80 11 0.15
81 61 0.84
82 1 0.01
ACGTcount: A:0.23, C:0.09, G:0.13, T:0.55
Consensus pattern (81 bp):
AGTTGTTATTAGACATCTTATTAGCTGAATAAAATATGTTTTCTTCTTTGTTTATTTTTTATGTA
CATTTTACTGACTACT
Found at i:844051 original size:22 final size:22
Alignment explanation
Indices: 844003--844051 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
843993 ATGTTTCGTA
*
844003 ATATAAATTGTTAAGATATAAT
1 ATATAAATTGATAAGATATAAT
* *
844025 GTATAAATTGATATA-ATATATT
1 ATATAAATTGATA-AGATATAAT
844047 ATATA
1 ATATA
844052 TCATATATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (22 bp):
ATATAAATTGATAAGATATAAT
Found at i:848654 original size:63 final size:63
Alignment explanation
Indices: 848555--848682 Score: 247
Period size: 63 Copynumber: 2.0 Consensus size: 63
848545 AGTCATCATA
*
848555 TGGTTGGAATTAAAACATGTTTCATTTTAGGAATGGAGATGAAGACTTCTAAAACCCTATGTT
1 TGGTTGGAATTAAAACATGTTTCATTTTAAGAATGGAGATGAAGACTTCTAAAACCCTATGTT
848618 TGGTTGGAATTAAAACATGTTTCATTTTAAGAATGGAGATGAAGACTTCTAAAACCCTATGTT
1 TGGTTGGAATTAAAACATGTTTCATTTTAAGAATGGAGATGAAGACTTCTAAAACCCTATGTT
848681 TG
1 TG
848683 CATCCAGCCA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (63 bp):
TGGTTGGAATTAAAACATGTTTCATTTTAAGAATGGAGATGAAGACTTCTAAAACCCTATGTT
Found at i:849798 original size:83 final size:82
Alignment explanation
Indices: 849693--849862 Score: 216
Period size: 83 Copynumber: 2.1 Consensus size: 82
849683 TGTGGTCTCA
* ** * *
849693 AGTTGTTATGTAGATGTCTTATTAGCTGTAT-AAAATTTGTTTCTTCTTTTATTTATTTTTTTAT
1 AGTTGTTATATAGACATCTTATTAGCTGAATAAAAATGT-TTTCTTCTTTTATTTA-TTTTTTAT
* *
849757 GTACTTTTTATTGACTACT
64 GTACATTTTACTGACTACT
* * *
849776 AGTTGTTATATAGACATTTTATTGGCTGAATAAAAATGTTTTCTTCTTTTGTTTATTTTTTATGT
1 AGTTGTTATATAGACATCTTATTAGCTGAATAAAAATGTTTTCTTCTTTTATTTATTTTTTATGT
*
849841 ACATTTTACTGACTTCT
66 ACATTTTACTGACTACT
849858 AGTTG
1 AGTTG
849863 ATTCCAACAA
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
82 29 0.39
83 40 0.53
84 6 0.08
ACGTcount: A:0.23, C:0.09, G:0.13, T:0.55
Consensus pattern (82 bp):
AGTTGTTATATAGACATCTTATTAGCTGAATAAAAATGTTTTCTTCTTTTATTTATTTTTTATGT
ACATTTTACTGACTACT
Found at i:850655 original size:20 final size:22
Alignment explanation
Indices: 850627--850669 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
850617 GCATCCCTTT
*
850627 TTTATTATTTT-TAAA-TAATA
1 TTTAATATTTTATAAAGTAATA
850647 TTTAATATTTTATAAAGTAATA
1 TTTAATATTTTATAAAGTAATA
850669 T
1 T
850670 ATTTATAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 4 0.20
22 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTAATATTTTATAAAGTAATA
Found at i:850671 original size:17 final size:15
Alignment explanation
Indices: 850649--850712 Score: 62
Period size: 15 Copynumber: 4.3 Consensus size: 15
850639 AAATAATATT
850649 TAATAT-TTTATAAAG
1 TAATATATTTAT-AAG
850664 TAATATATTTATAAG
1 TAATATATTTATAAG
* *
850679 TAATGTGA-TTATAAT
1 TAATAT-ATTTATAAG
850694 TAATATAATTT-TAAG
1 TAATAT-ATTTATAAG
850709 TAAT
1 TAAT
850713 GTGATTACAG
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
15 33 0.80
16 8 0.20
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (15 bp):
TAATATATTTATAAG
Found at i:850732 original size:30 final size:31
Alignment explanation
Indices: 850665--850732 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
850655 TTTATAAAGT
* *
850665 AATATATTTATAAGTAATGTGATTATAATTAA
1 AATA-ATTTATAAGTAATGTGATTACAATGAA
* *
850697 TATAATTT-TAAGTAATGTGATTACAGTGAA
1 AATAATTTATAAGTAATGTGATTACAATGAA
850727 AATAAT
1 AATAAT
850733 ATTACATTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 24 0.77
31 4 0.13
32 3 0.10
ACGTcount: A:0.46, C:0.01, G:0.12, T:0.41
Consensus pattern (31 bp):
AATAATTTATAAGTAATGTGATTACAATGAA
Done.