Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397258.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4.1, 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: 11097736
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 71999 characters in sequence are not A, C, G, or T
File 19 of 22
Found at i:9367868 original size:63 final size:64
Alignment explanation
Indices: 9367756--9367879 Score: 169
Period size: 64 Copynumber: 2.0 Consensus size: 64
9367746 TTATAATGTT
* * * *
9367756 TAAATAATGTGAATTGACAATTTAAAGGTTCTGAAATTCAAGTATTTTTGAAATCACATGAGTC
1 TAAATAATGTGAATTGACAATTCAAAGATTCAGAAATTCAAGTACTTTTGAAATCACATGAGTC
* * * *
9367820 TAAATCATGTTAATTGGCAATTCAAAGATTCAG-AATTCAAGTACTTTTGAAATCCCATGA
1 TAAATAATGTGAATTGACAATTCAAAGATTCAGAAATTCAAGTACTTTTGAAATCACATGA
9367880 TTCATAACCA
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
63 25 0.48
64 27 0.52
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.35
Consensus pattern (64 bp):
TAAATAATGTGAATTGACAATTCAAAGATTCAGAAATTCAAGTACTTTTGAAATCACATGAGTC
Found at i:9369035 original size:8 final size:7
Alignment explanation
Indices: 9369009--9369033 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
9368999 AGATTTTGGC
9369009 TTTTGTT
1 TTTTGTT
9369016 TTTTGTT
1 TTTTGTT
9369023 TTTTGTT
1 TTTTGTT
9369030 TTTT
1 TTTT
9369034 TGGCTGCAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTGTT
Found at i:9375511 original size:2 final size:2
Alignment explanation
Indices: 9375504--9375539 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
9375494 AAAGAAATGA
9375504 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
9375540 ATATCTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:9379516 original size:20 final size:19
Alignment explanation
Indices: 9379471--9379521 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
9379461 AAATTTGGAT
*
9379471 ATAATGTTTTAAAAAATAA
1 ATAAAGTTTTAAAAAATAA
*
9379490 TTAAAGTATTTAAAAAATTAA
1 ATAAAGT-TTTAAAAAA-TAA
9379511 AT-AAGTTTTAA
1 ATAAAGTTTTAA
9379522 TTTTTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.37
20 13 0.48
21 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (19 bp):
ATAAAGTTTTAAAAAATAA
Found at i:9379871 original size:20 final size:19
Alignment explanation
Indices: 9379848--9379886 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
9379838 TAAAAGTATA
9379848 AAAAAAATTTTAAATTTTTT
1 AAAAAAA-TTTAAATTTTTT
*
9379868 AAAATAATTTAAATTTTTT
1 AAAAAAATTTAAATTTTTT
9379887 TAATTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAAAAAATTTAAATTTTTT
Found at i:9381288 original size:2 final size:2
Alignment explanation
Indices: 9381281--9381305 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9381271 ATTATGCGAA
9381281 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
9381306 GTTTGGAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9382104 original size:37 final size:37
Alignment explanation
Indices: 9382063--9382148 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 37
9382053 TGAAGCGTCC
*
9382063 AATCATGCACGATGCCA-AAGCAACTAATAGAGGTTCA
1 AATCATGCACGATG-CATAAACAACTAATAGAGGTTCA
* * *
9382100 AATCATACACGATGCATAAACAATTAATAGAGGTTCC
1 AATCATGCACGATGCATAAACAACTAATAGAGGTTCA
*
9382137 AATCAAGCACGA
1 AATCATGCACGA
9382149 CACTGAAGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
36 2 0.05
37 40 0.95
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.20
Consensus pattern (37 bp):
AATCATGCACGATGCATAAACAACTAATAGAGGTTCA
Found at i:9384085 original size:21 final size:21
Alignment explanation
Indices: 9384059--9384098 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
9384049 CTACTAATTT
9384059 TTACTA-TAATTATTTTTATCC
1 TTACTACT-ATTATTTTTATCC
*
9384080 TTACTACTATTCTTTTTAT
1 TTACTACTATTATTTTTAT
9384099 AAATTGTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.25, C:0.15, G:0.00, T:0.60
Consensus pattern (21 bp):
TTACTACTATTATTTTTATCC
Found at i:9384695 original size:226 final size:226
Alignment explanation
Indices: 9384302--9384740 Score: 580
Period size: 226 Copynumber: 1.9 Consensus size: 226
9384292 ATTTTTCACT
* * * *
9384302 ATAATTATTTTTATCCTTACTATTATTCATTTATAGTTTAAATTTATAAATCCTTCAATACTGTA
1 ATAATTATTTTTATCCTAACTATTATTCATTTATAATTAAAATTTATAAATCCTTAAATACTGTA
* *
9384367 AACTCGAGAATAGAAATTTAAATATGTAATTTTTTAAAAAATTATGTTTATTTATCATAATTGAC
66 AACTCGAGAATAGAAATTTAAATATGTAATTTTTAAAAAAATTATGTTTATTTATCATAATTAAC
* * * * * * * * *
9384432 TTGTTACGTTAAACTCTATATGTTTATGTCAATATTTTGATAATATTTGTTCCACCTTTATAA-T
131 TTATTACATTAAACTCTATACGTTTACGTCAATATTTTAACAATATCTGTTACACCTTTACAATT
**
9384496 TTTTATGTTAATTCTTACAAGTTTACATCAA
196 TTTTACATTAATTCTTACAAGTTTACATCAA
* *
9384527 ATAATTATTTTTATCCTAACTATTGTTCATTTATAAATTAAAATTTATAAA-CCGTTAAATACTT
1 ATAATTATTTTTATCCTAACTATTATTCATTTAT-AATTAAAATTTATAAATCC-TTAAATACTG
* * * *
9384591 TAAACTCGAGAATATAAATTTAAATGTTTAATTTTTAAAAAAATTATGTTTATTTGA-CATATTT
64 TAAACTCGAGAATAGAAATTTAAATATGTAATTTTTAAAAAAATTATGTTTATTT-ATCATAATT
* * *
9384655 AACTTATTGCATTAAAACTC-ATACGTTTACGTTAATATTTTAACAATATCTGTTACACTTTTAC
128 AACTTATTACATT-AAACTCTATACGTTTACGTCAATATTTTAACAATATCTGTTACACCTTTAC
9384719 AATTTTTTACATTAATTCTTAC
192 AATTTTTTACATTAATTCTTAC
9384741 TATTTTATGT
Statistics
Matches: 183, Mismatches: 26, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
225 34 0.19
226 125 0.68
227 24 0.13
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (226 bp):
ATAATTATTTTTATCCTAACTATTATTCATTTATAATTAAAATTTATAAATCCTTAAATACTGTA
AACTCGAGAATAGAAATTTAAATATGTAATTTTTAAAAAAATTATGTTTATTTATCATAATTAAC
TTATTACATTAAACTCTATACGTTTACGTCAATATTTTAACAATATCTGTTACACCTTTACAATT
TTTTACATTAATTCTTACAAGTTTACATCAA
Found at i:9384856 original size:231 final size:232
Alignment explanation
Indices: 9384593--9385056 Score: 587
Period size: 231 Copynumber: 2.0 Consensus size: 232
9384583 AAATACTTTA
* *
9384593 AACTCGAGAATATAAATTTAAATGTTTAATTTTTAAAAAAATTATGTTTATTTGACATATTTAAC
1 AACTCGAGAATATAAATTTAAATGTTTAATTTTTAAAAAAATTATGTTTATTTAACATAATTAAC
* * * * * * *
9384658 TTATTGCATTAAAACTCATACGTTTACGTTAATATTTTAACAAT-ATCTG-TTACACTTTTACAA
66 TTATTACATTAAAACTCACACATATACGTCAATATTTTAACAATGCT-TGTTTAC-CCTTTACAA
* * * * * * *
9384721 TTTTTTACATTAATTCTTACTATTTTATGTCAAGGTTTTTTAACAACTAATTTTT-GCTATAATT
129 TATTTTACATTAATTCTTACAAATTTACGTCAAGATTTTTCAACAACT-ATTTTTCACTATAATT
*
9384785 ATTTTTATCTTTACTATTATTTATTGTA-A-ATTAAAATTT
193 ATTTTTATCTTTACTATTATTCATT-TATAGATTAAAATTT
* * *
9384824 AACTCGAGAATATAAATTTAAATGTTTAATTTTTAAAAAACTTATGTTTATTTAACATAATTGAT
1 AACTCGAGAATATAAATTTAAATGTTTAATTTTTAAAAAAATTATGTTTATTTAACATAATTAAC
* * * * * *
9384889 TTGTTACGTTAAATCTCACACATATACGTCAATATTTTTACAATGCTTGTTTTCCCTTTATAATA
66 TTATTACATTAAAACTCACACATATACGTCAATATTTTAACAATGCTTGTTTACCCTTTACAATA
* **
9384954 TTTTACATTAATTTTTACAAATTTACGTCAAGATTTTTCAATTACTATTTTTCACTATAATTATT
131 TTTTACATTAATTCTTACAAATTTACGTCAAGATTTTTCAACAACTATTTTTCACTATAATTATT
*
9385019 TTTATCTTTATTATTATTCATTTATAGATTAAAATTT
196 TTTATCTTTACTATTATTCATTTATAGATTAAAATTT
9385056 A
1 A
9385057 TAAACCCTTA
Statistics
Matches: 198, Mismatches: 30, Indels: 9
0.84 0.13 0.04
Matches are distributed among these distances:
230 8 0.04
231 175 0.88
232 15 0.08
ACGTcount: A:0.35, C:0.11, G:0.06, T:0.49
Consensus pattern (232 bp):
AACTCGAGAATATAAATTTAAATGTTTAATTTTTAAAAAAATTATGTTTATTTAACATAATTAAC
TTATTACATTAAAACTCACACATATACGTCAATATTTTAACAATGCTTGTTTACCCTTTACAATA
TTTTACATTAATTCTTACAAATTTACGTCAAGATTTTTCAACAACTATTTTTCACTATAATTATT
TTTATCTTTACTATTATTCATTTATAGATTAAAATTT
Found at i:9385652 original size:250 final size:250
Alignment explanation
Indices: 9384824--9386018 Score: 1302
Period size: 250 Copynumber: 4.8 Consensus size: 250
9384814 ATTAAAATTT
* * * * *
9384824 AACTCGAGAATATAAATTTAAATGTTTAATTTTTAAAAAACTTATGTTTATTTAACATAATTGAT
1 AACTCAAGAATATAAATTTAAATGTTTAATTTTTCAAAAA-TTATATTTATTTGACATAATTGAC
* *
9384889 TTGTTACGTTAAATCTCACACATATACGTCAATATTTTTACAATGCTTGTTTTC-CCTTTATAAT
65 TTGTTACGTTAAATCTCACACATATACGTCAATATTTTGACAAT-ATT-TTTTCACCTTTATAAT
* * * *
9384953 ATTTTACATTAATTTTTACAAATTTACGTCAAGATTTTTCAATTACTATTTTTCACTATAATTAT
128 TTTTTACATTAATTCTTACAAGTTTATGTCAAGATTTTTCAATTACTATTTTTCACTATAATTAT
*
9385018 TTTTATCTTTATTATTATTCATTTATAGATTAAAATTTATAAACCCTTAAATACTTTA
193 TTTTATCTTTATTATTATTCATTTATAGATTAAAATTTATAAACCGTTAAATACTTTA
* * * * *
9385076 AACTCAAGAGTAGAAATTTAAATGTTT-ATTTTTAAAAAAATTATATTTATTAGATATAATTGAC
1 AACTCAAGAATATAAATTTAAATGTTTAATTTTT-CAAAAATTATATTTATTTGACATAATTGAC
* * * * * * * *
9385140 TTGTTA-TTTAAATTTTACACATTTACGTTAATATTTTGACAATACTTATTCCACTTTTATAATT
65 TTGTTACGTTAAATCTCACACATATACGTCAATATTTTGACAATA-TTTTTTCACCTTTATAATT
* * * * * * * * *
9385204 TTTTACGTTCATCCTTACTACTTTA-GTCAATG-TTTGTCAATTATTAATTTTCACTATAATTAG
129 TTTTACATTAATTCTTACAAGTTTATGTCAA-GATTTTTCAATTACTATTTTTCACTATAATTAT
* * *
9385267 TTTTATCTTTATTATTATTTATTTATTA-ATTAAAATTTATAAATCGTTAAATAATTTA
193 TTTTATCTTTATTATTATTCATTTA-TAGATTAAAATTTATAAACCGTTAAATACTTTA
* * *
9385325 AACTCAAGAATTTAAATTTAAATGTTTAATTTTTCAAAAAATATATTTATTTGATATAATTGACT
1 AACTCAAGAATATAAATTTAAATGTTTAATTTTTCAAAAATTATATTTATTTGACATAATTGACT
* * * *
9385390 TGTTACGTTAAATCTCACACGTTTATGTCAATATTTTGACAATGTTTTTTCTACCTTTATAATTT
66 TGTTACGTTAAATCTCACACATATACGTCAATATTTTGACAATATTTTTTC-ACCTTTATAATTT
** * * *
9385455 TTTATGTTAATTCTTATAAGTTTATGTCAAGGTTTTTCAATTGCTATTTTTCACTATAATTATTT
130 TTTACATTAATTCTTACAAGTTTATGTCAAGATTTTTCAATTACTATTTTTCACTATAATTATTT
* * * *
9385520 TTATCTTTATTGTTAATCATTTATAGATTAAAATTTTTAAACCGTTACATACTTTA
195 TTATCTTTATTATTATTCATTTATAGATTAAAATTTATAAACCGTTAAATACTTTA
* * *
9385576 AACTCGAGAATATAAATTTAAATGTTT-TTTTTTCAAAAATTATGTTTATTTGACATAATT-AGC
1 AACTCAAGAATATAAATTTAAATGTTTAATTTTTCAAAAATTATATTTATTTGACATAATTGA-C
* * * * * **
9385639 TTGTTAGGTTAAATCTCATACATATACATCAATATTTTAACGATATTTGTTAAACCTTTATAATT
65 TTGTTACGTTAAATCTCACACATATACGTCAATATTTTGACAATATTT-TTTCACCTTTATAATT
* * * * *
9385704 TTTTATATTAATTCTTACAGGTTTATGTCAA-ATTGTTTCAACTATTGA-TTTTCATTATAATTA
129 TTTTACATTAATTCTTACAAGTTTATGTCAAGATT-TTTCAATTACT-ATTTTTCACTATAATTA
* * * * * *
9385767 TTTTTATCCTTATTATCATTCCTTTATAAATTAAAATTTGTAAACCGTTAAATACTTTC
192 TTTTTATCTTTATTATTATTCATTTATAGATTAAAATTTATAAACCGTTAAATACTTTA
* *
9385826 AACTCAAGAAAATAAATTTAAATGTTTAATTTTTCAAGAAATTATATTTATTTGTCATAATTGAC
1 AACTCAAGAATATAAATTTAAATGTTTAATTTTTCAA-AAATTATATTTATTTGACATAATTGAC
* * * * *
9385891 ATGTTACATTAAAT-T------T-TA---C-ATATTTTGATAATATTTGTTCCACTTTTATAATT
65 TTGTTACGTTAAATCTCACACATATACGTCAATATTTTGACAATATTT-TTTCACCTTTATAATT
* ** * * *
9385944 TTTTACGTTAATTCTTA-GTGTTTTAAGTCAAGATTTTTCAATTATTAGTTTTCACTATAATTAT
129 TTTTACATTAATTCTTACAAG-TTTATGTCAAGATTTTTCAATTACTATTTTTCACTATAATTA-
9386008 TTTTTATCTTT
192 TTTTTATCTTT
9386019 TCCTTTAAAA
Statistics
Matches: 798, Mismatches: 123, Indels: 55
0.82 0.13 0.06
Matches are distributed among these distances:
239 2 0.00
240 76 0.10
241 14 0.02
244 2 0.00
245 1 0.00
249 151 0.19
250 340 0.43
251 147 0.18
252 64 0.08
253 1 0.00
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.49
Consensus pattern (250 bp):
AACTCAAGAATATAAATTTAAATGTTTAATTTTTCAAAAATTATATTTATTTGACATAATTGACT
TGTTACGTTAAATCTCACACATATACGTCAATATTTTGACAATATTTTTTCACCTTTATAATTTT
TTACATTAATTCTTACAAGTTTATGTCAAGATTTTTCAATTACTATTTTTCACTATAATTATTTT
TATCTTTATTATTATTCATTTATAGATTAAAATTTATAAACCGTTAAATACTTTA
Found at i:9386982 original size:7 final size:7
Alignment explanation
Indices: 9386945--9387029 Score: 70
Period size: 7 Copynumber: 12.4 Consensus size: 7
9386935 NNNNATATCA
9386945 TATATTT
1 TATATTT
9386952 TAT-TTT
1 TATATTT
9386958 TAT-TTAT
1 TATATT-T
*
9386965 TAT-TAT
1 TATATTT
*
9386971 AATATTT
1 TATATTT
9386978 TATATTT
1 TATATTT
9386985 TATATTTT
1 TATA-TTT
9386993 TATATTT
1 TATATTT
* *
9387000 T-TAATA
1 TATATTT
*
9387006 TATTTTT
1 TATATTT
*
9387013 TATATTA
1 TATATTT
9387020 TATATTT
1 TATATTT
9387027 TAT
1 TAT
9387030 TTTAATTTGT
Statistics
Matches: 62, Mismatches: 12, Indels: 8
0.76 0.15 0.10
Matches are distributed among these distances:
6 15 0.24
7 40 0.65
8 7 0.11
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TATATTT
Found at i:9386987 original size:33 final size:36
Alignment explanation
Indices: 9386945--9387031 Score: 110
Period size: 35 Copynumber: 2.5 Consensus size: 36
9386935 NNNNATATCA
9386945 TATATTTTAT-TTTTATTTATTATT-ATA-ATATTT
1 TATATTTTATATTTTATTTATTATTAATATATATTT
* * *
9386978 TATATTTTATATTTT-TATATTTTTAATATATTTTT
1 TATATTTTATATTTTATTTATTATTAATATATATTT
*
9387013 TATATTATATATTTTATTT
1 TATATTTTATATTTTATTT
9387032 TAATTTGTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
33 17 0.38
34 7 0.16
35 19 0.42
36 2 0.04
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (36 bp):
TATATTTTATATTTTATTTATTATTAATATATATTT
Found at i:9386990 original size:22 final size:21
Alignment explanation
Indices: 9386952--9387002 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
9386942 TCATATATTT
9386952 TATTTTTATTTATTATTATAA
1 TATTTTTATTTATTATTATAA
* *
9386973 TATTTTATATTT-TATATTTTTA
1 TATTTT-TATTTAT-TATTATAA
9386995 TATTTTTA
1 TATTTTTA
9387003 ATATATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
TATTTTTATTTATTATTATAA
Found at i:9393997 original size:251 final size:247
Alignment explanation
Indices: 9393291--9394004 Score: 751
Period size: 254 Copynumber: 2.8 Consensus size: 247
9393281 AAAGATAAGC
* * * *
9393291 ATAATTTTTTAGAAAATTAAAAATTTAAATTTCTATTTTT-GAGTTTAAAATATTTAACGGTTTA
1 ATAATTTTTTAAAAAATTAAAAATTTAAATTTAT-TTTTTCAAGTTTAAAGTATTTAACGGTTTA
* * * ** *
9393355 CAAATTTTAATTTATAGATG-AATAATAATAAAGATAAAAATAATTATATTAAAAAATACTAATT
65 CAAATTTT-ATTTA-AAAAGAAATAATAATAAAGATAAAAATAATTATAATAAAATCTAATAATT
* *
9393419 AAAAAAATTTGATGTAAAACAATAAGAATTAACGTAAAAAACTTATAAAGATAGAATAAGTATTG
128 --AAAAATTTGACGTAAAAC-ATAAGAATTAACATAAAAAA-TTATAAAG-TAGAATAAGTATTG
* * * * * *
9393484 TTAAAATATTAACGTAAACGTGTGAGGTTTAACATAATAAGTCAACTATATTAAATAAAT
188 TTAAAATATTGACGTAAACATATGAGATTTAACATAACAAGTCAACTATATCAAATAAAT
* * * ** *
9393544 ATAATTTTTTTAAAAAATTAAACATTTAAATTTATATTCTCAAGTTTAAAGTATTTAACAATTTT
1 ATAA-TTTTTTAAAAAATTAAAAATTTAAATTTATTTTTTCAAGTTTAAAGTATTTAACGGTTTA
* * * * *
9393609 TAAATTTTAATT-AATAGATGAATAATAATAAGGATAAAAATAATTATAATGAAAATC-AATATT
65 CAAATTTTATTTAAAAAGA--AATAATAATAAAGATAAAAATAATTATAAT-AAAATCTAATAAT
* * *
9393672 TCAAAAGTTTTGACGTAAAACAGTAAGAATTAATAT-AAAAATTATAAAAGTAAAAT-AGATATT
127 T-AAAA-ATTTGACGTAAAACA-TAAGAATTAACATAAAAAATTAT-AAAGTAGAATAAG-TATT
* * * *
9393735 ATCAAAATATTGACGTAAACATATGAGATTTAATC-TAACAAGTCAATTATGTCAAATAAAT
187 GTTAAAATATTGACGTAAACATATGAGATTTAA-CATAACAAGTCAACTATATCAAATAAAT
* *
9393796 ATAATTTTTTAAAAAATTAAATATTTAAATTTATTTTTTCTAGTTTAAAGTATTTAACGGTTTAC
1 ATAATTTTTTAAAAAATTAAAAATTTAAATTTATTTTTTCAAGTTTAAAGTATTTAACGGTTTAC
* * *
9393861 AAA-TTTACTTTAAAAAGAAATAATAATAAAGATAAAAATAATTATAGTAAAATCTAGTACTTGA
66 AAATTTTA-TTTAAAAAGAAATAATAATAAAGATAAAAATAATTATAATAAAATCTAATAATT-A
* * * *
9393925 AATATCTTGACATAAATCTATAAGAATTAACATAAAAAATTATAAAGTTGGAATAAGTATTGTTA
129 AAAAT-TTGACGTAAAAC-ATAAGAATTAACATAAAAAATTATAAAG-TAGAATAAGTATTGTTA
*
9393990 AAATATTGATGTAAA
191 AAATATTGACGTAAA
9394005 TGTGTGAAAT
Statistics
Matches: 380, Mismatches: 62, Indels: 40
0.79 0.13 0.08
Matches are distributed among these distances:
249 7 0.02
250 66 0.17
251 96 0.25
252 73 0.19
253 25 0.07
254 109 0.29
255 4 0.01
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.37
Consensus pattern (247 bp):
ATAATTTTTTAAAAAATTAAAAATTTAAATTTATTTTTTCAAGTTTAAAGTATTTAACGGTTTAC
AAATTTTATTTAAAAAGAAATAATAATAAAGATAAAAATAATTATAATAAAATCTAATAATTAAA
AATTTGACGTAAAACATAAGAATTAACATAAAAAATTATAAAGTAGAATAAGTATTGTTAAAATA
TTGACGTAAACATATGAGATTTAACATAACAAGTCAACTATATCAAATAAAT
Found at i:9394019 original size:251 final size:247
Alignment explanation
Indices: 9393291--9394026 Score: 768
Period size: 251 Copynumber: 2.9 Consensus size: 247
9393281 AAAGATAAGC
* * * *
9393291 ATAATTTTTTAGAAAATTAAAAATTTAAATTTCTATTTTT-GAGTTTAAAATATTTAACGGTTTA
1 ATAATTTTTTAAAAAATTAAAAATTTAAATTTAT-TTTTTCAAGTTTAAAGTATTTAACGGTTTA
* * * ** *
9393355 CAAATTTTAATTTATAGATG-AATAATAATAAAGATAAAAATAATTATATTAAAAAATACTAATT
65 CAAATTTT-ATTTA-AAAAGAAATAATAATAAAGATAAAAATAATTATAATAAAATCTAATAATT
* *
9393419 AAAAAAATTTGATGTAAAACAATAAGAATTAACGTAAAAAACTTATAAAGATAGAATAAGTATTG
128 --AAAAATTTGACGTAAAAC-ATAAGAATTAACATAAAAAA-TTATAAAG-TAGAATAAGTATTG
* * * *
9393484 TTAAAATATTAACGTAAACGTGTGAGGTTTAA-CATAATAAGTCAACTATATTAAATAAAT
188 TTAAAATATTGACGTAAACGTGTGAGATTTAATC-TAACAAGTCAACTATATCAAATAAAT
* * * ** *
9393544 ATAATTTTTTTAAAAAATTAAACATTTAAATTTATATTCTCAAGTTTAAAGTATTTAACAATTTT
1 ATAA-TTTTTTAAAAAATTAAAAATTTAAATTTATTTTTTCAAGTTTAAAGTATTTAACGGTTTA
* * * * *
9393609 TAAATTTTAATT-AATAGATGAATAATAATAAGGATAAAAATAATTATAATGAAAATC-AATATT
65 CAAATTTTATTTAAAAAGA--AATAATAATAAAGATAAAAATAATTATAAT-AAAATCTAATAAT
* * *
9393672 TCAAAAGTTTTGACGTAAAACAGTAAGAATTAATAT-AAAAATTATAAAAGTAAAAT-AGATATT
127 T-AAAA-ATTTGACGTAAAACA-TAAGAATTAACATAAAAAATTAT-AAAGTAGAATAAG-TATT
* * * * * *
9393735 ATCAAAATATTGACGTAAACATATGAGATTTAATCTAACAAGTCAATTATGTCAAATAAAT
187 GTTAAAATATTGACGTAAACGTGTGAGATTTAATCTAACAAGTCAACTATATCAAATAAAT
* *
9393796 ATAATTTTTTAAAAAATTAAATATTTAAATTTATTTTTTCTAGTTTAAAGTATTTAACGGTTTAC
1 ATAATTTTTTAAAAAATTAAAAATTTAAATTTATTTTTTCAAGTTTAAAGTATTTAACGGTTTAC
* * *
9393861 AAA-TTTACTTTAAAAAGAAATAATAATAAAGATAAAAATAATTATAGTAAAATCTAGTACTTGA
66 AAATTTTA-TTTAAAAAGAAATAATAATAAAGATAAAAATAATTATAATAAAATCTAATAATT-A
* * * *
9393925 AATATCTTGACATAAATCTATAAGAATTAACATAAAAAATTATAAAGTTGGAATAAGTATTGTTA
129 AAAAT-TTGACGTAAAAC-ATAAGAATTAACATAAAAAATTATAAAG-TAGAATAAGTATTGTTA
* * * *
9393990 AAATATTGATGTAAATGTGTGAAATTTAATGTAACAA
191 AAATATTGACGTAAACGTGTGAGATTTAATCTAACAA
9394027 ATCATAATAA
Statistics
Matches: 397, Mismatches: 67, Indels: 40
0.79 0.13 0.08
Matches are distributed among these distances:
249 7 0.02
250 66 0.17
251 113 0.28
252 73 0.18
253 25 0.06
254 109 0.27
255 4 0.01
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (247 bp):
ATAATTTTTTAAAAAATTAAAAATTTAAATTTATTTTTTCAAGTTTAAAGTATTTAACGGTTTAC
AAATTTTATTTAAAAAGAAATAATAATAAAGATAAAAATAATTATAATAAAATCTAATAATTAAA
AATTTGACGTAAAACATAAGAATTAACATAAAAAATTATAAAGTAGAATAAGTATTGTTAAAATA
TTGACGTAAACGTGTGAGATTTAATCTAACAAGTCAACTATATCAAATAAAT
Found at i:9394121 original size:22 final size:20
Alignment explanation
Indices: 9394093--9394133 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 20
9394083 TTTTAGGGTA
9394093 AAAATAAAATAATATTTAAAAT
1 AAAAT-AAATAA-ATTTAAAAT
9394115 AAAATAAATAAATTTAAAA
1 AAAATAAATAAATTTAAAA
9394134 ATTAACTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
21 6 0.32
22 5 0.26
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAATAAATAAATTTAAAAT
Found at i:9394134 original size:21 final size:18
Alignment explanation
Indices: 9394091--9394135 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 18
9394081 TATTTTAGGG
9394091 TAAAAATAAAATAATATT
1 TAAAAATAAAATAATATT
9394109 T-AAAATAAAATAAATAAATT
1 TAAAAATAAAAT-AAT--ATT
9394129 TAAAAAT
1 TAAAAAT
9394136 TAACTTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 10 0.43
18 4 0.17
20 4 0.17
21 5 0.22
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAAATAAAATAATATT
Found at i:9407974 original size:44 final size:44
Alignment explanation
Indices: 9407909--9408296 Score: 297
Period size: 44 Copynumber: 8.9 Consensus size: 44
9407899 TTGTTTTTTC
* * * * *
9407909 TTTTAAAGTTATGTAGTCTCATTTTAGGTGAAAAGCTTATTCCT
1 TTTTAAAGTTATATAGCCTCATTCTAGATGAAAAGCTTATTCAT
* ** *
9407953 TTTTAAAGTTATGTAGCCTCATTCTAGAT-AAGGGGCTTGTTCAT
1 TTTTAAAGTTATATAGCCTCATTCTAGATGAA-AAGCTTATTCAT
* * * * ** * *
9407997 TTTTAAAGTTACATAACCTTATT-TCAAATGAAGGGCGTATTCCT
1 TTTTAAAGTTATATAGCCTCATTCT-AGATGAAAAGCTTATTCAT
* *
9408041 TTTTAAAGTTATATAGCCTTATTTCCA-ATGAGAAAG-TTATTCAT
1 TTTTAAAGTTATATAGCCTCA-TTCTAGATGA-AAAGCTTATTCAT
* * * * * *
9408085 TTTTTAAGTTACATAGCCTCATTCTACAT-AAGGAGTTTATTTAT
1 TTTTAAAGTTATATAGCCTCATTCTAGATGAA-AAGCTTATTCAT
* * * *
9408129 TTTTAAAGTTACATTGCTTCATTCTAGATGAAAAGCTAATTCA-
1 TTTTAAAGTTATATAGCCTCATTCTAGATGAAAAGCTTATTCAT
* * * * *
9408172 TTTAAAAGTTACATAGGCTCATCCTAGATGAAAAGCTAATTCAT
1 TTTTAAAGTTATATAGCCTCATTCTAGATGAAAAGCTTATTCAT
* * *
9408216 TTTTAAAGTTATGTAGCCTTATT-TCAGATGAAGAGCTTATTCA-
1 TTTTAAAGTTATATAGCCTCATTCT-AGATGAAAAGCTTATTCAT
* * * *
9408259 TTTTAAAGTTATGTAGCTTTATTCTAAATGAAAAGCTT
1 TTTTAAAGTTATATAGCCTCATTCTAGATGAAAAGCTT
9408297 TTTCTTTGGC
Statistics
Matches: 279, Mismatches: 52, Indels: 27
0.78 0.15 0.08
Matches are distributed among these distances:
42 1 0.00
43 82 0.29
44 187 0.67
45 9 0.03
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (44 bp):
TTTTAAAGTTATATAGCCTCATTCTAGATGAAAAGCTTATTCAT
Found at i:9408199 original size:43 final size:44
Alignment explanation
Indices: 9408127--9408226 Score: 141
Period size: 43 Copynumber: 2.3 Consensus size: 44
9408117 GAGTTTATTT
* * *
9408127 ATTTTTAAAGTTACATTGCTTCATTCTAGATGAAAAGCTAATTC
1 ATTTTAAAAGTTACATGGCTTCATCCTAGATGAAAAGCTAATTC
9408171 A-TTTAAAAGTTACATAGGC-TCATCCTAGATGAAAAGCTAATTC
1 ATTTTAAAAGTTACAT-GGCTTCATCCTAGATGAAAAGCTAATTC
*
9408214 ATTTTTAAAGTTA
1 ATTTTAAAAGTTA
9408227 TGTAGCCTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
43 37 0.74
44 13 0.26
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (44 bp):
ATTTTAAAAGTTACATGGCTTCATCCTAGATGAAAAGCTAATTC
Found at i:9412509 original size:21 final size:21
Alignment explanation
Indices: 9412455--9412496 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
9412445 AATTAGATTG
*
9412455 CAAGTATTAATACCCAATTAA
1 CAAGTATTGATACCCAATTAA
*
9412476 CAAGTATTGATACCTAATTAA
1 CAAGTATTGATACCCAATTAA
9412497 TAGGTTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.31
Consensus pattern (21 bp):
CAAGTATTGATACCCAATTAA
Found at i:9423029 original size:16 final size:16
Alignment explanation
Indices: 9423008--9423038 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9422998 GGATAATGTA
*
9423008 TTATATTGGATTATTT
1 TTATATTAGATTATTT
9423024 TTATATTAGATTATT
1 TTATATTAGATTATT
9423039 GAATCCCTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (16 bp):
TTATATTAGATTATTT
Found at i:9426137 original size:36 final size:36
Alignment explanation
Indices: 9426097--9426259 Score: 170
Period size: 36 Copynumber: 4.5 Consensus size: 36
9426087 ACTTTTAAAT
* * *
9426097 GAGATGAAGTGATAACTCTCATAATGGCT-TTTTCAC
1 GAGATCAAGTGATAACTCTCATAACGACTATTTT-AC
* * * *
9426133 GAGATCAAATGATAACCCTCACAACGGCTATTTTAC
1 GAGATCAAGTGATAACTCTCATAACGACTATTTTAC
* *
9426169 GAGATCAAGTGATAACCCTCATAACGACTATTTTAT
1 GAGATCAAGTGATAACTCTCATAACGACTATTTTAC
* * *
9426205 GAGATCAAGTGATAACTTTTATAATGACT-TTTTAAC
1 GAGATCAAGTGATAACTCTCATAACGACTATTTT-AC
9426241 GAGATCAAGCT-ATAACTCT
1 GAGATCAAG-TGATAACTCT
9426260 TGATTTTTTT
Statistics
Matches: 109, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
35 4 0.04
36 100 0.92
37 5 0.05
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.31
Consensus pattern (36 bp):
GAGATCAAGTGATAACTCTCATAACGACTATTTTAC
Found at i:9432343 original size:21 final size:20
Alignment explanation
Indices: 9432315--9432362 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
9432305 ATTTTTTTTT
9432315 AAATTAATAAAAATAATAAA
1 AAATTAATAAAAATAATAAA
* *
9432335 AAATATAATAATAATTAT-AA
1 AAAT-TAATAAAAATAATAAA
9432355 AAATTAAT
1 AAATTAAT
9432363 TAAAGATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.16
20 10 0.40
21 11 0.44
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATTAATAAAAATAATAAA
Found at i:9441532 original size:271 final size:269
Alignment explanation
Indices: 9441049--9441566 Score: 686
Period size: 269 Copynumber: 1.9 Consensus size: 269
9441039 TTTTGAAATT
* * *
9441049 TTTTTTCTTTTTTTTTTAGCCACCAACTAAGTATAATAAATTTTTTAACTTGTAAAAATTTGAAA
1 TTTTTTCTATTTTTTTTAGCCACCAAATAAGTATAATAAACTTTTTAACTTGTAAAAATTTGAAA
* * * * *
9441114 TCCCTTTCTCCTCTCCAAACCAAATAACTTTTTTTTTTTGAATTCGCAAGTAATGTTTCTTTACA
66 T-CCTCTCTCCTCTACAAACCAAATAAATTCTTTTTTTTGAATTCACAAGTAATGTTTCTTTACA
* *
9441179 TCCTAAATCATAATTCAATTTTAATTTTAAATTTACTTCATTAGTAATATTTGAATTTATAAAGA
130 TCCTAAATCATAATTCAATTTTAATTTTAAACTTACTTCATTAGTAATAGTTGAATTTATAAAGA
* * * * * * *
9441244 TATTGTAATTTAATTATTGTTTTGTGTTTTTAATTGACACGGATTTAGTAATCGATATATTTTGA
195 TATTGTAATTCAATTATTATTATATATGTTTAATTGACACGAATTTAGTAATCGATATATTTTGA
9441309 AATTATTTTA
260 AATTATTTTA
* * *
9441319 TTTTTTC-ATTTTTTTTAGCCTCCAAATAAGTATACTAAACTTTTTAACTTGTACAAATTTGAAA
1 TTTTTTCTATTTTTTTTAGCCACCAAATAAGTATAATAAACTTTTTAACTTGTAAAAATTTGAAA
*
9441383 T-CTCTCTCCTCTACAAATCAAATAAAAATTCTTTTTTTT-AATTCAC-AGATAATGTTTCTTTA
66 TCCTCTCTCCTCTACAAACCAAAT--AAATTCTTTTTTTTGAATTCACAAG-TAATGTTTCTTTA
* * * *
9441445 CTTCCTAAATC-TCAATTCAATTTTAATTTTTACACTTGCTTTATATTAGTAATAGTTGAATTTA
128 CATCCTAAATCAT-AATTCAATTTTAA-TTTTAAACTTAC-TT-CATTAGTAATAGTTGAATTTA
* *
9441509 TAAAGATATTGTAGTTCAATTATTATTATATATGTTTAATTGACATGAATTTAGTAAT
189 TAAAGATATTGTAATTCAATTATTATTATATATGTTTAATTGACACGAATTTAGTAAT
9441567 TGATGAATTT
Statistics
Matches: 214, Mismatches: 27, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
267 22 0.10
268 42 0.20
269 73 0.34
270 9 0.04
271 68 0.32
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.48
Consensus pattern (269 bp):
TTTTTTCTATTTTTTTTAGCCACCAAATAAGTATAATAAACTTTTTAACTTGTAAAAATTTGAAA
TCCTCTCTCCTCTACAAACCAAATAAATTCTTTTTTTTGAATTCACAAGTAATGTTTCTTTACAT
CCTAAATCATAATTCAATTTTAATTTTAAACTTACTTCATTAGTAATAGTTGAATTTATAAAGAT
ATTGTAATTCAATTATTATTATATATGTTTAATTGACACGAATTTAGTAATCGATATATTTTGAA
ATTATTTTA
Found at i:9441913 original size:2 final size:2
Alignment explanation
Indices: 9441906--9441934 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9441896 CTATCAAATG
9441906 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9441935 GAAAAGGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9444734 original size:7 final size:7
Alignment explanation
Indices: 9444719--9444759 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
9444709 CATATATATG
9444719 AAAAA-A
1 AAAAAGA
9444725 AAAAAGA
1 AAAAAGA
9444732 AAAAAGA
1 AAAAAGA
*
9444739 AAAAGGA
1 AAAAAGA
*
9444746 AAAAGGA
1 AAAAAGA
9444753 AAAAAGA
1 AAAAAGA
9444760 GCTCTTATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 5 0.16
7 27 0.84
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:9456151 original size:14 final size:15
Alignment explanation
Indices: 9456114--9456151 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
9456104 ATACATTTGT
9456114 TTATATAAACTTATA
1 TTATATAAACTTATA
9456129 TTATATAAACTTA-A
1 TTATATAAACTTATA
*
9456143 TTATCTAAA
1 TTATATAAA
9456152 ATGAAGTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (15 bp):
TTATATAAACTTATA
Found at i:9456591 original size:11 final size:11
Alignment explanation
Indices: 9456575--9456599 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9456565 CGCGGGGGGC
9456575 CGCGGCCGCCG
1 CGCGGCCGCCG
9456586 CGCGGCCGCCG
1 CGCGGCCGCCG
9456597 CGC
1 CGC
9456600 CGGGGCGCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.56, G:0.44, T:0.00
Consensus pattern (11 bp):
CGCGGCCGCCG
Found at i:9456601 original size:19 final size:18
Alignment explanation
Indices: 9456558--9456601 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
9456548 GGCGCCGGCG
**
9456558 GCGCCGCCGCGGGGGGCC
1 GCGCCGCCGCGGGCCGCC
9456576 GCGGCCGCCGCGCGGCCGCC
1 GC-GCCGCCGCG-GGCCGCC
9456596 GCGCCG
1 GCGCCG
9456602 GGGCGCGGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 13 0.59
20 7 0.32
ACGTcount: A:0.00, C:0.50, G:0.50, T:0.00
Consensus pattern (18 bp):
GCGCCGCCGCGGGCCGCC
Found at i:9456607 original size:19 final size:19
Alignment explanation
Indices: 9456585--9456624 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
9456575 CGCGGCCGCC
9456585 GCGCGGCCGCCGCGCCGGG
1 GCGCGGCCGCCGCGCCGGG
* * *
9456604 GCGCGGGCGGCGCGGCGGG
1 GCGCGGCCGCCGCGCCGGG
9456623 GC
1 GC
9456625 CGCCGGGGCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.00, C:0.40, G:0.60, T:0.00
Consensus pattern (19 bp):
GCGCGGCCGCCGCGCCGGG
Found at i:9456634 original size:19 final size:18
Alignment explanation
Indices: 9456595--9456663 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 18
9456585 GCGCGGCCGC
* *
9456595 CGCGCCGGGGCGCGGGCGG
1 CGCGGCGGGGCGCCGG-GG
9456614 CGCGGCGGGGCCGCCGGGG
1 CGCGGCGGGG-CGCCGGGG
*
9456633 CG-GGCGGGGGGCCGGGG
1 CGCGGCGGGGCGCCGGGG
*
9456650 CGCGCGCGGCGCGC
1 CGCG-GCGGGGCGC
9456664 TCGCGCGGCG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
17 9 0.21
18 8 0.19
19 20 0.48
20 5 0.12
ACGTcount: A:0.00, C:0.36, G:0.64, T:0.00
Consensus pattern (18 bp):
CGCGGCGGGGCGCCGGGG
Found at i:9457099 original size:15 final size:16
Alignment explanation
Indices: 9457068--9457112 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 16
9457058 TTTTATTTTG
9457068 TATTAACATTATAAAAAT
1 TATTAAC-TTAT-AAAAT
9457086 TA-TAACTTATAAAAT
1 TATTAACTTATAAAAT
9457101 TATTAA-TTATAA
1 TATTAACTTATAA
9457113 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 13 0.50
16 7 0.27
17 4 0.15
18 2 0.08
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (16 bp):
TATTAACTTATAAAAT
Found at i:9457568 original size:15 final size:17
Alignment explanation
Indices: 9457535--9457577 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 17
9457525 TAATTTTATG
9457535 TTAACATTATAAGAATTA
1 TTAAC-TTATAAGAATTA
9457553 -TAACTTATAA-AATTA
1 TTAACTTATAAGAATTA
9457568 TTAA-TTATAA
1 TTAACTTATAA
9457578 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 11 0.46
16 9 0.38
17 4 0.17
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (17 bp):
TTAACTTATAAGAATTA
Found at i:9461248 original size:41 final size:41
Alignment explanation
Indices: 9461143--9461305 Score: 197
Period size: 41 Copynumber: 4.0 Consensus size: 41
9461133 GTTTAAGTAG
* * *
9461143 TTGTTTGGATATTTATTTTTAGTTATTTAAGTTTATGTTGCT
1 TTGTTGGGATATTTGTGTTTAGTTATTTAAGTTTATGTTG-T
9461185 GTTGTTTGGG-TATTTGTGTTTAGTTATTTAAGTTTATGTTGT
1 -TTG-TTGGGATATTTGTGTTTAGTTATTTAAGTTTATGTTGT
* ** *
9461227 TTGTTGGGATCTTTGAATTTAGTTATTTAAGTTTATATTGT
1 TTGTTGGGATATTTGTGTTTAGTTATTTAAGTTTATGTTGT
*
9461268 TAT-TT-GGATATTTGTGTATAGTTATTTAAGTTTATGTT
1 T-TGTTGGGATATTTGTGTTTAGTTATTTAAGTTTATGTT
9461306 TAAGATATTT
Statistics
Matches: 105, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
40 33 0.31
41 34 0.32
42 2 0.02
43 32 0.30
44 4 0.04
ACGTcount: A:0.20, C:0.01, G:0.20, T:0.59
Consensus pattern (41 bp):
TTGTTGGGATATTTGTGTTTAGTTATTTAAGTTTATGTTGT
Found at i:9461777 original size:22 final size:23
Alignment explanation
Indices: 9461740--9461786 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
9461730 ATATAAAGTT
9461740 ATTTAGGCTTAA-TTTTGATAGTA
1 ATTTAGGCTTAATTTTTG-TAGTA
*
9461763 ATTTA-GCTTAGTTTTTGTAGTA
1 ATTTAGGCTTAATTTTTGTAGTA
9461785 AT
1 AT
9461787 ATATAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.28, C:0.04, G:0.17, T:0.51
Consensus pattern (23 bp):
ATTTAGGCTTAATTTTTGTAGTA
Found at i:9463194 original size:21 final size:22
Alignment explanation
Indices: 9463170--9463212 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
9463160 AATATTCTTT
*
9463170 ATTATAATATTTAAT-TTTTAA
1 ATTAAAATATTTAATATTTTAA
*
9463191 ATTAAAATATTTATTATTTTAA
1 ATTAAAATATTTAATATTTTAA
9463213 TAATTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTAAAATATTTAATATTTTAA
Found at i:9463433 original size:16 final size:17
Alignment explanation
Indices: 9463394--9463433 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
9463384 TTTGTTTTTT
9463394 ATTTTAAAAATATTAAA
1 ATTTTAAAAATATTAAA
* *
9463411 ATATTAAAAAT-TTATA
1 ATTTTAAAAATATTAAA
9463427 ATTTTAA
1 ATTTTAA
9463434 TTTAATTTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTTTAAAAATATTAAA
Found at i:9464620 original size:60 final size:60
Alignment explanation
Indices: 9464552--9464664 Score: 154
Period size: 60 Copynumber: 1.9 Consensus size: 60
9464542 AGTTGTTTAA
* * *
9464552 TTGGTGAATGAGAAGAAATTTATTTAATTGTTATGTTTATTGTTAATCTTGTTGGTAATG
1 TTGGTGAATGAGAAGAAATATATTTAATTGTTATATTTAGTGTTAATCTTGTTGGTAATG
* * * * *
9464612 TTGGTGAATGGGAAGTAATATATTTAGTTGTTGTATTTAGTGTTAATTTTGTT
1 TTGGTGAATGAGAAGAAATATATTTAATTGTTATATTTAGTGTTAATCTTGTT
9464665 ATTAATATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.27, C:0.01, G:0.23, T:0.50
Consensus pattern (60 bp):
TTGGTGAATGAGAAGAAATATATTTAATTGTTATATTTAGTGTTAATCTTGTTGGTAATG
Found at i:9473718 original size:33 final size:33
Alignment explanation
Indices: 9473676--9473738 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
9473666 ACACCCTCAC
9473676 ATAAGGACTTGACCATGAATGTGTTCAACGCCA
1 ATAAGGACTTGACCATGAATGTGTTCAACGCCA
9473709 ATAAGGACTTGACCATGAATGTGTTCAACG
1 ATAAGGACTTGACCATGAATGTGTTCAACG
9473739 ACATTGGCGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (33 bp):
ATAAGGACTTGACCATGAATGTGTTCAACGCCA
Found at i:9490109 original size:33 final size:34
Alignment explanation
Indices: 9490071--9490142 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 34
9490061 GAAAAGTTAG
* * *
9490071 TTGTTG-GGTTTTGGTTGATCCTCGGAAAAACCA
1 TTGTTGAGGTTGTGGTTGAGCCTAGGAAAAACCA
*
9490104 TTGTTGAAGGTTGTGGTTGAGCCTATGAAAAACCA
1 TTGTTG-AGGTTGTGGTTGAGCCTAGGAAAAACCA
9490139 TTGT
1 TTGT
9490143 AAAAGCTTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 6 0.18
35 27 0.82
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.36
Consensus pattern (34 bp):
TTGTTGAGGTTGTGGTTGAGCCTAGGAAAAACCA
Found at i:9500268 original size:25 final size:25
Alignment explanation
Indices: 9500234--9500282 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
9500224 CGAAATCCTC
9500234 GGTGAACTTTGCTGGTATTATCATG
1 GGTGAACTTTGCTGGTATTATCATG
9500259 GGTGAACTTTGCTGGTATTATCAT
1 GGTGAACTTTGCTGGTATTATCAT
9500283 TGAATTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.20, C:0.12, G:0.27, T:0.41
Consensus pattern (25 bp):
GGTGAACTTTGCTGGTATTATCATG
Found at i:9516128 original size:21 final size:22
Alignment explanation
Indices: 9516103--9516147 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
9516093 ATGGCCCTAT
*
9516103 GTCACGCAAT-ACTTAAAACTA
1 GTCACGCAATGACTAAAAACTA
*
9516124 GTCACGCAATGTCTAAAAACTA
1 GTCACGCAATGACTAAAAACTA
9516146 GT
1 GT
9516148 TAATAAATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.24
Consensus pattern (22 bp):
GTCACGCAATGACTAAAAACTA
Found at i:9516262 original size:188 final size:188
Alignment explanation
Indices: 9515937--9516294 Score: 529
Period size: 188 Copynumber: 1.9 Consensus size: 188
9515927 TAATACACAT
*
9515937 TCACGCAATGCTTAAAAACTAGTTAAGAAATGCCTTAAAACAAGAGATACATTGCACAACTCACG
1 TCACGCAATGCTTAAAAACTAGTTAAGAAATGCCTCAAAACAAGAGATACATTGCACAACTCACG
* * * * *
9516002 CAACGCCTATAAGCTAGTATCGTAATAGCTAATACTAAGTCACACAATGCCCAATATCCACTCAC
66 CAACACCTATAAGCTAGTATCATAATACCTAATAATAAGTCACACAATGCCCAATATCCACTAAC
* *
9516067 ATTATGCCAAGTTAACTAGTCAAGCAATGGCCCTATGTCACGCAATACTTAAAACTAG
131 ATTATGCCAACTTAACTAGTCAAGCAATGGCCCTAAGTCACGCAATACTTAAAACTAG
* * * * *
9516125 TCACGCAATG-TCTAAAAACTAGTTAATAAATGCCTCAAAACAAGAGATGCATTGCATAATTCAT
1 TCACGCAATGCT-TAAAAACTAGTTAAGAAATGCCTCAAAACAAGAGATACATTGCACAACTCAC
* * * *
9516189 GCAGCACCTATAAGCTAGTCTCATAATACCTAATAATAAGTCACATAATGCCTAATATCCACTAA
65 GCAACACCTATAAGCTAGTATCATAATACCTAATAATAAGTCACACAATGCCCAATATCCACTAA
* *
9516254 CGTTATGCCAACTTAACTAGTCATGCAATGGCCCTAAGTCA
130 CATTATGCCAACTTAACTAGTCAAGCAATGGCCCTAAGTCA
9516295 TATAATACAT
Statistics
Matches: 150, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
187 1 0.01
188 149 0.99
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.25
Consensus pattern (188 bp):
TCACGCAATGCTTAAAAACTAGTTAAGAAATGCCTCAAAACAAGAGATACATTGCACAACTCACG
CAACACCTATAAGCTAGTATCATAATACCTAATAATAAGTCACACAATGCCCAATATCCACTAAC
ATTATGCCAACTTAACTAGTCAAGCAATGGCCCTAAGTCACGCAATACTTAAAACTAG
Found at i:9516364 original size:22 final size:22
Alignment explanation
Indices: 9516336--9516413 Score: 97
Period size: 22 Copynumber: 3.6 Consensus size: 22
9516326 TAACAATCAA
*
9516336 TCACACAATCCCTAATATCCAT
1 TCACACAATGCCTAATATCCAT
*
9516358 TCACACAATACC--ATATCCAT
1 TCACACAATGCCTAATATCCAT
* *
9516378 TCACACAAAGCCAAATATCCAT
1 TCACACAATGCCTAATATCCAT
*
9516400 TCACATAATGCCTA
1 TCACACAATGCCTA
9516414 TAAACAAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 18 0.38
22 30 0.62
ACGTcount: A:0.40, C:0.33, G:0.03, T:0.24
Consensus pattern (22 bp):
TCACACAATGCCTAATATCCAT
Found at i:9521780 original size:40 final size:40
Alignment explanation
Indices: 9521722--9521797 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
9521712 TGTGATCATG
*
9521722 AAAGATTTTACGTCAGGTAGTTATGACTATTTTTTTATTT
1 AAAGATTTTACGTAAGGTAGTTATGACTATTTTTTTATTT
* *
9521762 AAAGATTTTACTTAAGGTAGTTATTACTATTTTTTT
1 AAAGATTTTACGTAAGGTAGTTATGACTATTTTTTT
9521798 TTTGTTCTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.29, C:0.07, G:0.13, T:0.51
Consensus pattern (40 bp):
AAAGATTTTACGTAAGGTAGTTATGACTATTTTTTTATTT
Found at i:9530068 original size:26 final size:26
Alignment explanation
Indices: 9529996--9530070 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 26
9529986 TGGATGGATG
* *
9529996 ATTTTATCATCAAAATTTA-AGAATA
1 ATTTTACCATCAAAATTGATAGAATA
* *
9530021 ATTTTACCATTTAAAATGGATA-AATA
1 ATTTTACCA-TCAAAATTGATAGAATA
9530047 ATTTTACCATCAAAAGTTGATAGA
1 ATTTTACCATCAAAA-TTGATAGA
9530071 TTCTTTAACC
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
25 13 0.32
26 25 0.62
27 2 0.05
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.37
Consensus pattern (26 bp):
ATTTTACCATCAAAATTGATAGAATA
Found at i:9530134 original size:18 final size:18
Alignment explanation
Indices: 9530084--9530138 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
9530074 TTTAACCCAT
* * *
9530084 TAATCCATTAAAAATGGA
1 TAATCCATCATAAGTGGA
*
9530102 TAATCCA-CCTAAAGTGGA
1 TAATCCATCAT-AAGTGGA
9530120 TAATCCATCATAAGTGGA
1 TAATCCATCATAAGTGGA
9530138 T
1 T
9530139 TACCTACAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 28 0.93
19 2 0.07
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (18 bp):
TAATCCATCATAAGTGGA
Found at i:9530246 original size:115 final size:115
Alignment explanation
Indices: 9530039--9530255 Score: 303
Period size: 115 Copynumber: 1.9 Consensus size: 115
9530029 ATTTAAAATG
* * * * *
9530039 GATAAATAATTTTACCATCAAAAGTTGATAGATTCTTTAACCCATTAATCCATTAAAAATGGATA
1 GATAAATAATTTTACCATCAAAAGTTGATAGATGCCTTAACCCACTAATCCACTAAAAATAGATA
9530104 ATCCACCTAAAGTGGATAATCCATCATAAGTGGATTACCTACAAAAACTA
66 ATCCACCTAAAGTGGATAATCCATCATAAGTGGATTACCTACAAAAACTA
* * * * *
9530154 GATAGATAATTTTACCATCAGAA-TTGAATAGATGCCTTAACCCACTAATCTACTAAGAGTAGAT
1 GATAAATAATTTTACCATCAAAAGTTG-ATAGATGCCTTAACCCACTAATCCACTAAAAATAGAT
*
9530218 AATCCA-GTAGAAGTGGATAATCCATCATAAGTGGATTA
65 AATCCACCTA-AAGTGGATAATCCATCATAAGTGGATTA
9530256 TTCATCAAAA
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
114 5 0.06
115 84 0.94
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.29
Consensus pattern (115 bp):
GATAAATAATTTTACCATCAAAAGTTGATAGATGCCTTAACCCACTAATCCACTAAAAATAGATA
ATCCACCTAAAGTGGATAATCCATCATAAGTGGATTACCTACAAAAACTA
Found at i:9530249 original size:18 final size:18
Alignment explanation
Indices: 9530215--9530271 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
9530205 ACTAAGAGTA
*
9530215 GATAATCCAGT-AGAAGTG
1 GATAATCCA-TCAAAAGTG
*
9530233 GATAATCCATCATAAGTG
1 GATAATCCATCAAAAGTG
* *
9530251 GATTATTCATCAAAAGTG
1 GATAATCCATCAAAAGTG
9530269 GAT
1 GAT
9530272 GAATACTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 1 0.03
18 33 0.97
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (18 bp):
GATAATCCATCAAAAGTG
Found at i:9530282 original size:115 final size:113
Alignment explanation
Indices: 9530033--9530282 Score: 281
Period size: 115 Copynumber: 2.2 Consensus size: 113
9530023 TTTACCATTT
* * * *
9530033 AAAATGGATAAATAATTTTACCATCAAAAGTTGATAGATTCTTTAACCCATTAATCCATTAAAAA
1 AAAATGGAT-AATAATTTTACCATCAAAAGTTGATAGATGCCTTAACCCACTAATCCACTAAAAA
* *
9530098 TGGATAATCCACCTAAAGTGGATAATCCATCATAAGTGGATTACCTACA
65 TAGATAATCCACCTAAAGTGGATAATCCATCATAAGTGGATTACATACA
* * * *
9530147 AAAACTAGATAGATAATTTTACCATCAGAA-TTGAATAGATGCCTTAACCCACTAATCTACTAAG
1 AAAA-TGGATA-ATAATTTTACCATCAAAAGTTG-ATAGATGCCTTAACCCACTAATCCACTAAA
* *
9530211 AGTAGATAATCCA-GTAGAAGTGGATAATCCATCATAAGTGGATTATTCAT-CA
63 AATAGATAATCCACCTA-AAGTGGATAATCCATCATAAGTGGATTA--CATACA
* *
9530263 AAAGTGGATGAATACTTTTA
1 AAAATGGAT-AATAATTTTA
9530283 ATCTTTTAAA
Statistics
Matches: 114, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
114 10 0.09
115 96 0.84
116 6 0.05
117 2 0.02
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (113 bp):
AAAATGGATAATAATTTTACCATCAAAAGTTGATAGATGCCTTAACCCACTAATCCACTAAAAAT
AGATAATCCACCTAAAGTGGATAATCCATCATAAGTGGATTACATACA
Found at i:9532597 original size:12 final size:12
Alignment explanation
Indices: 9532563--9532610 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
9532553 CCTTTTTCTT
9532563 TTTCTTCCTTTC
1 TTTCTTCCTTTC
* *
9532575 TTTATTTCTTTC
1 TTTCTTCCTTTC
*
9532587 TTTCTCCCTTTC
1 TTTCTTCCTTTC
*
9532599 TCTTCTTACTTT
1 T-TTCTTCCTTT
9532611 GTTATGGGCG
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
12 20 0.71
13 8 0.29
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTCTTCCTTTC
Found at i:9549486 original size:36 final size:36
Alignment explanation
Indices: 9549446--9549543 Score: 110
Period size: 36 Copynumber: 2.7 Consensus size: 36
9549436 TTTCAAACAT
*
9549446 TTTTTTACAAGATCAAGCAATAACCCTTATAAATGC
1 TTTTTTACAAGATCAAGCAATAACCCTCATAAATGC
* *
9549482 -TTTTTA-AAGGGATAAAGCAACAACCCTCATAAATGC
1 TTTTTTACAA--GATCAAGCAATAACCCTCATAAATGC
* **
9549518 TTTTTAACGGGATCAAGCAATAACCC
1 TTTTTTACAAGATCAAGCAATAACCC
9549544 ATGTAATGAT
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
34 2 0.04
35 6 0.12
36 37 0.74
37 5 0.10
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (36 bp):
TTTTTTACAAGATCAAGCAATAACCCTCATAAATGC
Found at i:9562675 original size:21 final size:19
Alignment explanation
Indices: 9562649--9562689 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
9562639 AATTTAAAAC
9562649 AAAATAACATAACATTTAACT
1 AAAATAACATAA-A-TTAACT
*
9562670 AAAATAACTTAAATTAACT
1 AAAATAACATAAATTAACT
9562689 A
1 A
9562690 TTCAATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 1 0.05
21 11 0.58
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATAACATAAATTAACT
Found at i:9565615 original size:11 final size:11
Alignment explanation
Indices: 9565599--9565623 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9565589 CCTTACCTTC
9565599 TCACCTTTATA
1 TCACCTTTATA
9565610 TCACCTTTATA
1 TCACCTTTATA
9565621 TCA
1 TCA
9565624 TTAGACAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (11 bp):
TCACCTTTATA
Found at i:9570425 original size:291 final size:290
Alignment explanation
Indices: 9569896--9570477 Score: 769
Period size: 291 Copynumber: 2.0 Consensus size: 290
9569886 ATACCAAAAC
* * ** *
9569896 ATATACGAATGAAGCCATCACCATACTTACATTGATTTTCATCAAATAAGCCTTTTTCATCAATT
1 ATATACGAATGAAACCATCAACATACTTACACGGATTTTCATCAAATAAGCCTTTTGCATCAATT
** * *
9569961 TCCTACAAAAGTCATAAGAAAAATTAGCAATAACTACTCTTAAAGTAATTTAAAACAAAACAACA
66 TCCTACAAAAGTCATAAGAAAAACCAACAATAACTACTATTAAAGTAATTTAAAACAAAACAACA
* *
9570026 TAAAATTCAACTAAAACAACTTAAATTAATCACTTAACAAGTAGTCAAACTTAAACTAAGAAAAC
131 AAAAATTCAACTAAAACAACTTAAATTAATCACTTAACAAGTAATCAAACTTAAACTAAGAAAAC
*
9570091 ACCTAAAATGCTAAAATCTGAACCTAAAATCTCAAAGATCTAGCAACTTAAGCCCCCAAAATGTG
196 ACCTAAAATGCTAAAATCCGAACCTAAAATCTCAAAGATCTAGCAACTTAAGCCCCCAAAATGTG
*
9570156 TCAAAATAACTCTATATAATAGAGTTATCA
261 TCAAAATAACTCTATATAATAAAGTTATCA
* * * *
9570186 ATATATGAATGAAACCATCAATATACTTGCACGGATTTTCATCAAATGAGCCTTTTGCATCAAAT
1 ATATACGAATGAAACCATCAACATACTTACACGGATTTTCATCAAATAAGCCTTTTGCATC-AAT
* * *
9570251 TTCTTACAATAG-CAGTAA-AAGAAACCAACAATAACTACTATTAAAGTAATTTAAAACAAAATA
65 TTCCTACAAAAGTCA-TAAGAA-AAACCAACAATAACTACTATTAAAGTAATTTAAAACAAAACA
* * * * * *
9570314 ATAAAAAATTTAACTATAATAACTTAAATTAA-CTA-TTCAACATGTAATCAAATTTAAACT-AG
128 ACAAAAAATTCAACTAAAACAACTTAAATTAATC-ACTT-AACAAGTAATCAAACTTAAACTAAG
* * * * * * *
9570376 AAAAACACCTAAAATGCTACAATCCGAACTTAAAATTTCAACGATCTAGCTACTTAAGCCTCTAA
191 -AAAACACCTAAAATGCTAAAATCCGAACCTAAAATCTCAAAGATCTAGCAACTTAAGCCCCCAA
*
9570441 AATGTGTCAAAATAACTCTATATCATAAAGTTATCA
255 AATGTGTCAAAATAACTCTATATAATAAAGTTATCA
9570477 A
1 A
9570478 AGTTCAATTT
Statistics
Matches: 252, Mismatches: 34, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
290 61 0.24
291 191 0.76
ACGTcount: A:0.46, C:0.18, G:0.07, T:0.28
Consensus pattern (290 bp):
ATATACGAATGAAACCATCAACATACTTACACGGATTTTCATCAAATAAGCCTTTTGCATCAATT
TCCTACAAAAGTCATAAGAAAAACCAACAATAACTACTATTAAAGTAATTTAAAACAAAACAACA
AAAAATTCAACTAAAACAACTTAAATTAATCACTTAACAAGTAATCAAACTTAAACTAAGAAAAC
ACCTAAAATGCTAAAATCCGAACCTAAAATCTCAAAGATCTAGCAACTTAAGCCCCCAAAATGTG
TCAAAATAACTCTATATAATAAAGTTATCA
Found at i:9578156 original size:1 final size:1
Alignment explanation
Indices: 9578150--9578175 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
9578140 CAATTTCACT
9578150 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
9578176 AAACTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:9578853 original size:12 final size:14
Alignment explanation
Indices: 9578835--9578866 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
9578825 TAAACTAATC
9578835 TAAAATA-TCACAA
1 TAAAATACTCACAA
9578848 -AAAATACTCACAA
1 TAAAATACTCACAA
9578861 TAAAAT
1 TAAAAT
9578867 CTTCCCCCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.35
13 6 0.35
14 5 0.29
ACGTcount: A:0.62, C:0.16, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAAATACTCACAA
Found at i:9587680 original size:20 final size:20
Alignment explanation
Indices: 9587652--9587709 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
9587642 TTCATAGTTA
*
9587652 AGTTAGATTATATGTTA-ATT
1 AGTTTGATT-TATGTTATATT
* *
9587672 AGTTTGATTTAAGTTATTTT
1 AGTTTGATTTATGTTATATT
*
9587692 AGTTTAATTTTATGTTAT
1 AGTTTGA-TTTATGTTAT
9587710 TGTTTATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 6 0.19
20 16 0.52
21 9 0.29
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (20 bp):
AGTTTGATTTATGTTATATT
Found at i:9607898 original size:13 final size:12
Alignment explanation
Indices: 9607882--9607914 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
9607872 AATTTTTATA
9607882 TAATATCATTTCT
1 TAATATCATTT-T
9607895 TAATAT-ATTTT
1 TAATATCATTTT
9607906 TAATATCAT
1 TAATATCAT
9607915 ATATTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 7 0.37
12 6 0.32
13 6 0.32
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (12 bp):
TAATATCATTTT
Found at i:9607969 original size:59 final size:58
Alignment explanation
Indices: 9607877--9608175 Score: 253
Period size: 56 Copynumber: 5.2 Consensus size: 58
9607867 TTATTAATTT
* *
9607877 TTATATAATATCATTTCTT-AATATATTTTTAATATCATATATTTTATTTTATTTATA
1 TTATATATTTTCATTTCTTAAATATATTTTTAATATCATATATTTTATTTTATTTATA
* * *
9607934 TTATAATATTTTACA-TT-TTATATTTATTTTTTAATAT--TTTATTTATATTATTATTT-T-
1 TTAT-ATATTTT-CATTTCTTAAATATA-TTTTTAATATCATATATTT-TATT-TTATTTATA
* * *
9607991 TTATATAATATCATTTCTTAAATATATTTTTAATATCGTATATTTTATTTTATTTATTA
1 TTATATATTTTCATTTCTTAAATATATTTTTAATATCATATATTTTATTTTATTTA-TA
* * * * * *
9608050 TTATATATTTT-A-TT-TTATAT-TTTATTTTAATAT-ATTTATATTTATATTATTAATTT
1 TTATATATTTTCATTTCTTAAATATAT-TTTTAATATCATATAT-TTTATTTTATTTA-TA
* * * *
9608106 TTATATAATATCATTTCTTAAATATATTTTTAATGTCATATATTTTATTTTTATTTTTA
1 TTATATATTTTCATTTCTTAAATATATTTTTAATATCATATATTTTA-TTTTATTTATA
9608165 TTATAATATTT
1 TTAT-ATATTT
9608176 ATTTTTTACA
Statistics
Matches: 189, Mismatches: 31, Indels: 41
0.72 0.12 0.16
Matches are distributed among these distances:
55 8 0.04
56 59 0.31
57 30 0.16
58 26 0.14
59 49 0.26
60 17 0.09
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (58 bp):
TTATATATTTTCATTTCTTAAATATATTTTTAATATCATATATTTTATTTTATTTATA
Found at i:9608042 original size:115 final size:115
Alignment explanation
Indices: 9607846--9608180 Score: 529
Period size: 115 Copynumber: 2.9 Consensus size: 115
9607836 AAAATATAAG
*
9607846 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTT-AATATATTTTTAAT
1 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
9607910 ATCATATATTTTATTTTATTTATATTATAATATTTTACATTTTATA-TTTAT
66 ATCATATATTTTATTTTATTTATATTATAATATTTT--ATTTTATATTTTAT
* *
9607961 TTT-TTAATATTT-TATTTATATTATTATTTTTTATATAATATCATTTCTTAAATATATTTTTAA
1 TTTAAT-ATATTTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
*
9608024 TATCGTATATTTTATTTTATTTATTATTAT-ATATTTTATTTTATATTTTAT
65 TATCATATATTTTATTTTATTTA-TATTATAATATTTTATTTTATATTTTAT
9608075 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
1 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
* *
9608140 GTCATATATTTTATTTTTATTTTTATTATAATA-TTTATTTT
66 ATCATATATTTTA-TTTTATTTATATTATAATATTTTATTTT
9608181 TTACAATTTA
Statistics
Matches: 203, Mismatches: 9, Indels: 16
0.89 0.04 0.07
Matches are distributed among these distances:
113 8 0.04
114 50 0.25
115 128 0.63
116 17 0.08
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.64
Consensus pattern (115 bp):
TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
ATCATATATTTTATTTTATTTATATTATAATATTTTATTTTATATTTTAT
Found at i:9608062 original size:12 final size:12
Alignment explanation
Indices: 9608029--9608112 Score: 63
Period size: 12 Copynumber: 7.3 Consensus size: 12
9608019 TTTAATATCG
*
9608029 TATATTTTATTT
1 TATATTTTATTA
9608041 TAT-TTATTATTA
1 TATATT-TTATTA
*
9608053 TATATTTTATTT
1 TATATTTTATTA
9608065 TATATTTTATT-
1 TATATTTTATTA
* *
9608076 T-TAATATATT-
1 TATATTTTATTA
9608086 TATATTTATATTA
1 TATATTT-TATTA
*
9608099 T-TAATTT-TTA
1 TATATTTTATTA
9608109 TATA
1 TATA
9608113 ATATCATTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
10 12 0.20
11 9 0.15
12 35 0.59
13 3 0.05
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATATTTTATTA
Found at i:9608087 original size:21 final size:21
Alignment explanation
Indices: 9608062--9608111 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
9608052 ATATATTTTA
9608062 TTTTATATTT-TATT-TTAAT
1 TTTTATATTTATATTATTAAT
9608081 ATATTTATATTTATATTATTAAT
1 -T-TTTATATTTATATTATTAAT
9608104 TTTTATAT
1 TTTTATAT
9608112 AATATCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 1 0.04
21 16 0.59
22 5 0.19
23 5 0.19
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTATATTTATATTATTAAT
Found at i:9608219 original size:102 final size:105
Alignment explanation
Indices: 9608083--9608275 Score: 349
Period size: 102 Copynumber: 1.9 Consensus size: 105
9608073 ATTTTAATAT
9608083 ATTTATATTTATATTATTAATTTTTATATAATATCAT-TTCTTAAATATATTTTTAATGTCATAT
1 ATTTATATTTATATTATTAATTTTTATATAATATCATATT-TTAAATATATTTTTAATGTCATAT
9608147 A-TTTTATTTTTATTT-TTATTATAATATTTATTTTTTACA
65 ATTTTTATTTTTATTTATTATTATAATATTTATTTTTTACA
9608186 ATTTATATTT-TATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTAATGTCATATA
1 ATTTATATTTATATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTAATGTCATATA
9608250 TTTTTATTTTTATTTATTATTATAAT
66 TTTTTATTTTTATTTATTATTATAAT
9608276 TTATATATTT
Statistics
Matches: 87, Mismatches: 0, Indels: 5
0.95 0.00 0.05
Matches are distributed among these distances:
102 51 0.59
103 26 0.30
104 10 0.11
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (105 bp):
ATTTATATTTATATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTAATGTCATATA
TTTTTATTTTTATTTATTATTATAATATTTATTTTTTACA
Found at i:9608278 original size:102 final size:102
Alignment explanation
Indices: 9608058--9608279 Score: 337
Period size: 102 Copynumber: 2.2 Consensus size: 102
9608048 TATTATATAT
* *
9608058 TTTATT-TTATATTTTATTTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATTT
1 TTTATTATTATAATTTATTTTAATAAATTTATATTTATATTATTAATTTTTATATAATATCATTT
9608122 CTTAAATATATTTTTAATGTCATATATTTTATTTTTA
66 CTTAAATATATTTTTAATGTCATATATTTTATTTTTA
*
9608159 TTT-TTATTATAATATTTATTTT-TTACAATTTATATTT-TATTATTAATTTTTATATAATATCA
1 TTTATTATTAT-A-ATTTATTTTAATA-AATTTATATTTATATTATTAATTTTTATATAATATCA
9608221 TATT-TTAAATATATTTTTAATGTCATATATTTTTATTTTTA
63 T-TTCTTAAATATATTTTTAATGTCATATA-TTTTATTTTTA
9608262 TTTATTATTATAATTTAT
1 TTTATTATTATAATTTAT
9608280 ATATTTTATT
Statistics
Matches: 111, Mismatches: 3, Indels: 13
0.87 0.02 0.10
Matches are distributed among these distances:
100 2 0.02
101 7 0.06
102 60 0.54
103 35 0.32
104 7 0.06
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.64
Consensus pattern (102 bp):
TTTATTATTATAATTTATTTTAATAAATTTATATTTATATTATTAATTTTTATATAATATCATTT
CTTAAATATATTTTTAATGTCATATATTTTATTTTTA
Found at i:9608310 original size:102 final size:100
Alignment explanation
Indices: 9608083--9608326 Score: 313
Period size: 102 Copynumber: 2.4 Consensus size: 100
9608073 ATTTTAATAT
*
9608083 ATTTATATTTATATTATTAATTTTTATATAATATCAT-TTCTTAAATATATTTTTAATGTCATAT
1 ATTTATATTT-TATTAATAATTTTTATATAATATCATATT-TTAAATATATTTTTAATGTCATAT
*
9608147 ATTTTATTTTTATTTTTATTATAATATTTATTTTTTACA
64 ATTTTATTTTTATTTTTATTATAATATTTATATTTT--A
*
9608186 ATTTATATTTTATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTAATGTCATATAT
1 ATTTATATTTTATTAATAATTTTTATATAATATCATATTTTAAATATATTTTTAATGTCATATA-
9608251 TTTTATTTTTATTTATTATTATAAT-TTATATATTTT-
65 TTTTATTTTTATTT-TTATTATAATATT-TATATTTTA
*
9608287 ATTT-TCATTTCT-TTAATATATTTTT-TATATTAT-ATATTTT
1 ATTTAT-ATTT-TATTAATA-ATTTTTATATAATATCATATTTT
9608327 TTTAATTGTT
Statistics
Matches: 131, Mismatches: 3, Indels: 17
0.87 0.02 0.11
Matches are distributed among these distances:
100 8 0.06
101 20 0.15
102 58 0.44
103 28 0.21
104 17 0.13
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (100 bp):
ATTTATATTTTATTAATAATTTTTATATAATATCATATTTTAAATATATTTTTAATGTCATATAT
TTTATTTTTATTTTTATTATAATATTTATATTTTA
Found at i:9608316 original size:33 final size:32
Alignment explanation
Indices: 9608245--9608326 Score: 83
Period size: 33 Copynumber: 2.4 Consensus size: 32
9608235 TTTTAATGTC
* *
9608245 ATATATTTTTATTTTTATTTATTATTATAATTT
1 ATATA-TTTTATTTTCATTTATTAATATAATTT
* *
9608278 ATATATTTTATTTTCATTTCTTTAATATATTTT
1 ATATATTTTATTTTCATTT-ATTAATATAATTT
*
9608311 TTATATTATATATTTT
1 ATATATT-T-TATTTT
9608327 TTTAATTGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 13 0.32
33 21 0.51
34 1 0.02
35 6 0.15
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (32 bp):
ATATATTTTATTTTCATTTATTAATATAATTT
Found at i:9608320 original size:14 final size:14
Alignment explanation
Indices: 9607851--9608379 Score: 103
Period size: 14 Copynumber: 36.9 Consensus size: 14
9607841 ATAAGTTTAA
9607851 TATATT-TATATTTT
1 TATATTATAT-TTTT
9607865 TATTATTA-ATTTTT
1 TA-TATTATATTTTT
* *
9607879 ATATAATATCATTTCT
1 -TATATTAT-ATTTTT
9607895 TA-A-TATATTTTT
1 TATATTATATTTTT
* * *
9607907 AATATCATATATTT
1 TATATTATATTTTT
9607921 TAT-TT-TATTTATAT
1 TATATTATATTT-T-T
* *
9607935 TATAATATTTTACATTT
1 TATATTATATT---TTT
9607952 TATATT-TATTTTT
1 TATATTATATTTTT
9607965 TA-A-TAT-TTTATT
1 TATATTATATTT-TT
9607977 TATATTATTATTTTT
1 TATATTA-TATTTTT
*
9607992 TATATAATATCATTTCT
1 TATAT--TAT-ATTTTT
*
9608009 TA-AATATATTTTT
1 TATATTATATTTTT
*
9608022 AATATCGTATATTTTAT
1 TATAT--TATATTTT-T
* *
9608039 TTTATT-TATTATTA
1 TATATTATATT-TTT
*
9608053 TATATT-T-TATTT
1 TATATTATATTTTT
* *
9608065 TATATTTTATTTTAA
1 TATATTATATTTT-T
*
9608080 TATATT-TA-TATT
1 TATATTATATTTTT
9608092 TATATTATTAATTTTT
1 TATATTA-T-ATTTTT
* *
9608108 ATATAATATCATTTCT
1 -TATATTAT-ATTTTT
*
9608124 TA-AATATATTTTT
1 TATATTATATTTTT
* * * *
9608137 AATGTCATATATTT
1 TATATTATATTTTT
*
9608151 TAT-TTTTATTTTTAT
1 TATATTATA-TTTT-T
*
9608166 TATAATATTTATTTTT
1 TAT-AT-TATATTTTT
* *
9608182 TACAATT-TATATTT
1 TA-TATTATATTTTT
9608196 TATTATTA-ATTTTT
1 TA-TATTATATTTTT
* *
9608210 ATATAATATCATATTT
1 -TATATTAT-ATTTTT
*
9608226 TA-AATATATTTTT
1 TATATTATATTTTT
* * *
9608239 AATGTCATATATTTT
1 TATATTATAT-TTTT
*
9608254 TAT-TTTTATTTATTAT
1 TATATTATA-TT-TT-T
*
9608270 TATAATTTATATATTT
1 TAT-A-TTATATTTTT
9608286 TAT-TT-TCATTTCTT
1 TATATTAT-ATTT-TT
9608300 TA-A-TATATTTTT
1 TATATTATATTTTT
*
9608312 TATATTATATATTT
1 TATATTATATTTTT
9608326 T-T-TTA-ATTGTTT
1 TATATTATATT-TTT
*
9608338 T-TATCTATATTATATA
1 TATAT-TATATT-T-TT
*
9608354 AATATTA-ATTTTT
1 TATATTATATTTTT
*
9608367 TATATTTTATTTT
1 TATATTATATTTT
9608380 ATTTTAATTT
Statistics
Matches: 379, Mismatches: 68, Indels: 136
0.65 0.12 0.23
Matches are distributed among these distances:
11 6 0.02
12 43 0.11
13 56 0.15
14 118 0.31
15 56 0.15
16 54 0.14
17 35 0.09
18 6 0.02
19 5 0.01
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (14 bp):
TATATTATATTTTT
Found at i:9608377 original size:217 final size:216
Alignment explanation
Indices: 9607953--9608394 Score: 527
Period size: 217 Copynumber: 2.0 Consensus size: 216
9607943 TTTACATTTT
*
9607953 ATATTTATTTTTTAATATTTTATTTATATTATTATTTTTTATATAATATCATTTCTTAAATATAT
1 ATATTTATTTTTTAATATTTTATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATAT
*
9608018 TTTTAATATCGTATATTTTATTTTATTTATTATTATATATTTTATTTTATATTTTATTTTAATAT
66 TTTTAATATCATATATTTTATTTTATTTATTATTATATATTTTATTTTATATTTTATTTTAATAT
* *
9608083 ATTTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATGTCATATA
131 ATTTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTAAATATCATATA
9608148 TTTTATTTTTATTTTTATTATA
196 TTTTATTTTTA-TTTTATTATA
9608170 ATATTTATTTTTTACA-ATTTATATTT-TATTATTAATTTTTATATAATATCATATT-TTAAATA
1 ATATTTATTTTTTA-ATATTT-TATTTATATTATTAATTTTTATATAATATCAT-TTCTTAAATA
*
9608232 TATTTTTAATGTCATATATTTTTATTTTTATTTATTATTATA-ATTTATATATTT-TATTTTCAT
63 TATTTTTAATATCATATA-TTTTA-TTTTATTTATTATTATATATTT-TAT-TTTATATTTT-A-
* **
9608295 TTCTTTAATATA-TT-T-TTTATATTA-TATATTTTT-T-TAAT-T-GTTT-TTATCTATATTAT
122 -T-TTTAATATATTTATATTTATATTATTA-ATTTTTATATAATATCATTTCTTAAATATATT-T
* * *
9608351 ATAAATATTA-ATTTTTTATATTTTATTTTATTTTA
183 -TAAATATCATATATTTTAT-TTTTATTTTATTATA
*
9608386 ATTTTTATT
1 ATATTTATT
9608395 CTTATATTAT
Statistics
Matches: 198, Mismatches: 12, Indels: 31
0.82 0.05 0.13
Matches are distributed among these distances:
215 9 0.05
216 29 0.15
217 78 0.39
218 21 0.11
219 29 0.15
220 19 0.10
221 1 0.01
222 3 0.02
223 9 0.05
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.65
Consensus pattern (216 bp):
ATATTTATTTTTTAATATTTTATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATAT
TTTTAATATCATATATTTTATTTTATTTATTATTATATATTTTATTTTATATTTTATTTTAATAT
ATTTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTAAATATCATATA
TTTTATTTTTATTTTATTATA
Found at i:9608430 original size:30 final size:30
Alignment explanation
Indices: 9608366--9608439 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
9608356 TATTAATTTT
* * * *
9608366 TTATATTTTATTTTATTTTAATTTTTATTC
1 TTATATTATATTTTATTTTAATTTATAATA
9608396 TTATATTATATATTTATTTTAA-TTATAATA
1 TTATATTATAT-TTTATTTTAATTTATAATA
**
9608426 TTATAAAATATTTT
1 TTATATTATATTTT
9608440 TAATAAGTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 3 0.08
30 24 0.65
31 10 0.27
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (30 bp):
TTATATTATATTTTATTTTAATTTATAATA
Found at i:9609679 original size:25 final size:26
Alignment explanation
Indices: 9609643--9609699 Score: 91
Period size: 25 Copynumber: 2.3 Consensus size: 26
9609633 CCTTTCCCTA
9609643 TCTCT-TTCTTTTCCTTTTCATTCCT
1 TCTCTCTTCTTTTCCTTTTCATTCCT
*
9609668 TCTCTCTT-TTTTCCTTTTCTTTCCT
1 TCTCTCTTCTTTTCCTTTTCATTCCT
9609693 TCTCTCT
1 TCTCTCT
9609700 CTTCTATGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 28 0.93
26 2 0.07
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (26 bp):
TCTCTCTTCTTTTCCTTTTCATTCCT
Found at i:9610476 original size:40 final size:39
Alignment explanation
Indices: 9610429--9610505 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 39
9610419 TCTTTTTTTT
* *
9610429 TTTTTATTAT-TTAAATTTATTTCTTATTTCTTCTTTTTAG
1 TTTTTATTATATTAAA-TTATTACTTATTT-TTATTTTTAG
*
9610469 TTTTTATTATATTACATTATTACTTATTTTTATTTTT
1 TTTTTATTATATTAAATTATTACTTATTTTTATTTTT
9610506 GGTGAATAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 7 0.21
40 22 0.67
41 4 0.12
ACGTcount: A:0.22, C:0.06, G:0.01, T:0.70
Consensus pattern (39 bp):
TTTTTATTATATTAAATTATTACTTATTTTTATTTTTAG
Found at i:9610993 original size:24 final size:24
Alignment explanation
Indices: 9610964--9611021 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
9610954 AGTTTGTGAT
9610964 TATACGTGGTAAGGCCACGGTTGA
1 TATACGTGGTAAGGCCACGGTTGA
*
9610988 TATACGTGGCAAGGCCACGGTTGA
1 TATACGTGGTAAGGCCACGGTTGA
9611012 TATACGTGGT
1 TATACGTGGT
9611022 TGTGATCACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (24 bp):
TATACGTGGTAAGGCCACGGTTGA
Found at i:9612013 original size:16 final size:16
Alignment explanation
Indices: 9611992--9612022 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9611982 TCGACTGTTA
9611992 TTGTAGATTATAACTC
1 TTGTAGATTATAACTC
*
9612008 TTGTAGTTTATAACT
1 TTGTAGATTATAACT
9612023 ATCATGGTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.48
Consensus pattern (16 bp):
TTGTAGATTATAACTC
Found at i:9613437 original size:10 final size:10
Alignment explanation
Indices: 9613422--9613446 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
9613412 AAGGGATGTA
9613422 TCTCACTTGT
1 TCTCACTTGT
9613432 TCTCACTTGT
1 TCTCACTTGT
9613442 TCTCA
1 TCTCA
9613447 ATTCTTGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.32, G:0.08, T:0.48
Consensus pattern (10 bp):
TCTCACTTGT
Found at i:9617920 original size:38 final size:38
Alignment explanation
Indices: 9617878--9617956 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
9617868 TTTTAAAACC
* *
9617878 TAACCACACTAACTTAAATGTGAT-AATAAAATTGACTT
1 TAACCACACTAACATAAATGTGATAAAT-AAACTGACTT
*
9617916 TAACCCCACTAACATAAATGTGATAAATAAACTGACTT
1 TAACCACACTAACATAAATGTGATAAATAAACTGACTT
9617954 TAA
1 TAA
9617957 TTAAACTTCT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 34 0.92
39 3 0.08
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.29
Consensus pattern (38 bp):
TAACCACACTAACATAAATGTGATAAATAAACTGACTT
Found at i:9625871 original size:38 final size:38
Alignment explanation
Indices: 9625820--9625898 Score: 124
Period size: 38 Copynumber: 2.1 Consensus size: 38
9625810 TTTTAAAACC
9625820 TAACCCCACTAACTTAAACATGAT-AATAAAACTGACTT
1 TAACCCCACTAACTTAAACATGATAAAT-AAACTGACTT
* *
9625858 TAACCCTACTAACTTAAACTTGATAAATAAACTGACTT
1 TAACCCCACTAACTTAAACATGATAAATAAACTGACTT
9625896 TAA
1 TAA
9625899 TTAAACTTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 35 0.92
39 3 0.08
ACGTcount: A:0.44, C:0.22, G:0.05, T:0.29
Consensus pattern (38 bp):
TAACCCCACTAACTTAAACATGATAAATAAACTGACTT
Found at i:9632711 original size:57 final size:57
Alignment explanation
Indices: 9632621--9632731 Score: 177
Period size: 57 Copynumber: 1.9 Consensus size: 57
9632611 TCGAATCCCC
*
9632621 TCTCCCCAAATTATAAAAAAAAAAACTACATACATATACTATATGTGTTTGAAAAGT
1 TCTCCCCAAATTATAAAAAAAAAAACTACATACATATACTATATGTATTTGAAAAGT
* * * *
9632678 TCTCCCCTAATTTTAAAAAGAAAAACTATATACATATACTATATGTATTTGAAA
1 TCTCCCCAAATTATAAAAAAAAAAACTACATACATATACTATATGTATTTGAAA
9632732 GTGCATGGGA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.32
Consensus pattern (57 bp):
TCTCCCCAAATTATAAAAAAAAAAACTACATACATATACTATATGTATTTGAAAAGT
Found at i:9633608 original size:17 final size:17
Alignment explanation
Indices: 9633586--9633618 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
9633576 AATAGGTCCT
9633586 TAATATTATAA-CAATAA
1 TAATATT-TAACCAATAA
9633603 TAATATTTAACCAATA
1 TAATATTTAACCAATA
9633619 CCTAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (17 bp):
TAATATTTAACCAATAA
Found at i:9638800 original size:18 final size:18
Alignment explanation
Indices: 9638777--9638813 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
9638767 TTAAACTTGT
9638777 AATGTATGACTAGGGTTA
1 AATGTATGACTAGGGTTA
9638795 AATGTATGACTAGGGTTA
1 AATGTATGACTAGGGTTA
9638813 A
1 A
9638814 GGTAGAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.32
Consensus pattern (18 bp):
AATGTATGACTAGGGTTA
Found at i:9643205 original size:20 final size:20
Alignment explanation
Indices: 9643180--9643252 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
9643170 GCAACAATTC
9643180 TATCGATACATTCTGGAATG
1 TATCGATACATTCTGGAATG
* * *
9643200 TATCGATACATGCAAGGAATC
1 TATCGATACATTC-TGGAATG
**
9643221 TATCGATACCCT-TGGTAATG
1 TATCGATACATTCTGG-AATG
*
9643241 TATCAATACATT
1 TATCGATACATT
9643253 TCACACAGAA
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
19 2 0.05
20 24 0.60
21 14 0.35
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (20 bp):
TATCGATACATTCTGGAATG
Found at i:9643224 original size:21 final size:20
Alignment explanation
Indices: 9643178--9643229 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
9643168 TTGCAACAAT
* *
9643178 TCTATCGATACATTCTGGAA
1 TCTATCGATACATGCAGGAA
*
9643198 TGTATCGATACATGCAAGGAA
1 TCTATCGATACATGC-AGGAA
9643219 TCTATCGATAC
1 TCTATCGATAC
9643230 CCTTGGTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (20 bp):
TCTATCGATACATGCAGGAA
Found at i:9644563 original size:73 final size:73
Alignment explanation
Indices: 9644482--9644622 Score: 219
Period size: 73 Copynumber: 1.9 Consensus size: 73
9644472 AGCACTTATC
* * * * *
9644482 GACTAAGAAGTTTTGTTAGTCGACTAAGAGCTTATTGTCAGAAACTGGGTTCAGAGATAGAAACG
1 GACTAAGAAGTTTAGTTAATCGACTAAGAGCCTATTGTCAAAAACTGAGTTCAGAGATAGAAACG
9644547 ACTTAATT
66 ACTTAATT
* *
9644555 GACTAAGAAGTTTAGTTAATCGACTAAGAGCCTATTGTCAAAAATTGAGTTCAGAGATAGAGACG
1 GACTAAGAAGTTTAGTTAATCGACTAAGAGCCTATTGTCAAAAACTGAGTTCAGAGATAGAAACG
9644620 ACT
66 ACT
9644623 AGGTAACAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 61 1.00
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (73 bp):
GACTAAGAAGTTTAGTTAATCGACTAAGAGCCTATTGTCAAAAACTGAGTTCAGAGATAGAAACG
ACTTAATT
Found at i:9650542 original size:13 final size:14
Alignment explanation
Indices: 9650524--9650559 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
9650514 CATTATTAAA
9650524 AAATAATAAT-TTC
1 AAATAATAATGTTC
9650537 AAATAA-AATGTTC
1 AAATAATAATGTTC
9650550 AAATAATAAT
1 AAATAATAAT
9650560 AAATTAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 3 0.14
13 15 0.71
14 3 0.14
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (14 bp):
AAATAATAATGTTC
Found at i:9657546 original size:18 final size:20
Alignment explanation
Indices: 9657517--9657566 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 20
9657507 TACTGAACAG
* *
9657517 ATATAAAAAATAACAAA-A-
1 ATATATAAAATAAAAAATAT
*
9657535 ATGTATAAAATAAAAAATAT
1 ATATATAAAATAAAAAATAT
9657555 ATATATAAAATA
1 ATATATAAAATA
9657567 TCTTGTCATC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 14 0.54
19 1 0.04
20 11 0.42
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (20 bp):
ATATATAAAATAAAAAATAT
Found at i:9657795 original size:63 final size:64
Alignment explanation
Indices: 9657683--9657809 Score: 213
Period size: 63 Copynumber: 2.0 Consensus size: 64
9657673 CATCAAGATG
9657683 TTGTTGATTTTCTTGTCCACCTTGAAAAAGGAATTGATCATATAATTAGTAATAG-AAATATCCA
1 TTGTTGATTTTCTTGTCCACCTTGAAAAAGGAATTGATCATATAATTAGTAAT-GTAAATATCCA
* *
9657747 TTGTTGATTTTCTTGTCCACCTT-AAAAAGGAATTGATCATTTGATTAGTAATGTAAATATCCA
1 TTGTTGATTTTCTTGTCCACCTTGAAAAAGGAATTGATCATATAATTAGTAATGTAAATATCCA
9657810 AGAATGAAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
62 1 0.02
63 36 0.60
64 23 0.38
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (64 bp):
TTGTTGATTTTCTTGTCCACCTTGAAAAAGGAATTGATCATATAATTAGTAATGTAAATATCCA
Found at i:9657823 original size:64 final size:64
Alignment explanation
Indices: 9657691--9657824 Score: 175
Period size: 63 Copynumber: 2.1 Consensus size: 64
9657681 TGTTGTTGAT
* * *
9657691 TTTCTTGTCCACCTTGAAAAAGGAATTGATCATATAATTAGTAATAGAAATATCCATTGTTGAT
1 TTTCTTGTCCACCTTGAAAAAGGAATTGATCATATAATTAGTAATAGAAATATCCATAGATGAA
* *
9657755 TTTCTTGTCCACCTT-AAAAAGGAATTGATCATTTGATTAGTAAT-GTAAATATCCA-AGAATGA
1 TTTCTTGTCCACCTTGAAAAAGGAATTGATCATATAATTAGTAATAG-AAATATCCATAG-ATG-
9657817 AA
63 AA
9657819 TTTCTT
1 TTTCTT
9657825 AATAGTTTGT
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
62 2 0.03
63 38 0.61
64 22 0.35
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (64 bp):
TTTCTTGTCCACCTTGAAAAAGGAATTGATCATATAATTAGTAATAGAAATATCCATAGATGAA
Found at i:9659604 original size:19 final size:19
Alignment explanation
Indices: 9659582--9659622 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
9659572 GGCCAATGCA
*
9659582 GAAATACACAATCAAGGTG
1 GAAAGACACAATCAAGGTG
**
9659601 GAAAGACGTAATCAAGGTG
1 GAAAGACACAATCAAGGTG
9659620 GAA
1 GAA
9659623 TTGATTTCAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.27, T:0.15
Consensus pattern (19 bp):
GAAAGACACAATCAAGGTG
Found at i:9665074 original size:16 final size:16
Alignment explanation
Indices: 9665049--9665082 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
9665039 TAACAAAGTG
* *
9665049 AGAAAGAAAGGGAGAA
1 AGAAACAAAGGAAGAA
9665065 AGAAACAAAGGAAGAA
1 AGAAACAAAGGAAGAA
9665081 AG
1 AG
9665083 GAGGAAGAAG
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:0.65, C:0.03, G:0.32, T:0.00
Consensus pattern (16 bp):
AGAAACAAAGGAAGAA
Found at i:9665098 original size:24 final size:24
Alignment explanation
Indices: 9665052--9665101 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
9665042 CAAAGTGAGA
*
9665052 AAGAAAGGGAGAAAGAAACAAAGG
1 AAGAAAGGGAGAAAGAAAAAAAGG
*
9665076 AAGAAA-GGAGGAAGAAGAAAAAGG
1 AAGAAAGGGAGAAAGAA-AAAAAGG
9665100 AA
1 AA
9665102 AGGAAAGATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.00
Consensus pattern (24 bp):
AAGAAAGGGAGAAAGAAAAAAAGG
Found at i:9668423 original size:20 final size:20
Alignment explanation
Indices: 9668388--9668425 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
9668378 GCCATTTTGC
**
9668388 ATGCATTTATTGATAGATGA
1 ATGCATTTATCAATAGATGA
9668408 ATGCATTTATCAATAGAT
1 ATGCATTTATCAATAGAT
9668426 TTGTTGTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (20 bp):
ATGCATTTATCAATAGATGA
Found at i:9670491 original size:19 final size:18
Alignment explanation
Indices: 9670466--9670507 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
9670456 TAAAATTAGT
9670466 AAAAAATAAAATAACTTA
1 AAAAAATAAAATAACTTA
* *
9670484 ATAAAAATAAACTAATTTA
1 A-AAAAATAAAATAACTTA
9670503 AAAAA
1 AAAAA
9670508 TGACTAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAAAATAAAATAACTTA
Found at i:9672075 original size:22 final size:22
Alignment explanation
Indices: 9672047--9672093 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
9672037 GAAAGTCACA
*
9672047 CAGCGCTGCGGCGCTACTTCTC
1 CAGCGCTGCAGCGCTACTTCTC
*
9672069 CAGCGCTGCAGTGCTACTTCTC
1 CAGCGCTGCAGCGCTACTTCTC
9672091 CAG
1 CAG
9672094 AGCTTTCTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.13, C:0.38, G:0.26, T:0.23
Consensus pattern (22 bp):
CAGCGCTGCAGCGCTACTTCTC
Found at i:9672612 original size:21 final size:22
Alignment explanation
Indices: 9672577--9672620 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
9672567 CTCTTAAAGT
9672577 AATTTAAAATAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
*
9672599 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
9672620 A
1 A
9672621 TTGATCACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (22 bp):
AATTTAAAATAAAATAACTTAA
Found at i:9677568 original size:11 final size:11
Alignment explanation
Indices: 9677552--9677580 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
9677542 AGATTTGGAG
9677552 GCAGCAAGAGA
1 GCAGCAAGAGA
9677563 GCAGCAAGAGA
1 GCAGCAAGAGA
9677574 GCAGCAA
1 GCAGCAA
9677581 AGGAGGCAGC
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:0.45, C:0.21, G:0.34, T:0.00
Consensus pattern (11 bp):
GCAGCAAGAGA
Found at i:9683733 original size:25 final size:25
Alignment explanation
Indices: 9683657--9683733 Score: 70
Period size: 25 Copynumber: 3.1 Consensus size: 25
9683647 AATTTAAATG
*
9683657 AATTTAAA-AATATAAAATATTATTT
1 AATTTAAATAA-ATAAAATATTATAT
* * **
9683682 AA-TTAATTTAATAAAACCTTA-ATT
1 AATTTAAATAAATAAAATATTATA-T
9683706 AATTTAAATAAATAAAATATTATAT
1 AATTTAAATAAATAAAATATTATAT
9683731 AAT
1 AAT
9683734 ATTACTTATT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
24 16 0.41
25 22 0.56
26 1 0.03
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (25 bp):
AATTTAAATAAATAAAATATTATAT
Found at i:9683801 original size:116 final size:115
Alignment explanation
Indices: 9683675--9684178 Score: 466
Period size: 116 Copynumber: 4.4 Consensus size: 115
9683665 AATATAAAAT
*
9683675 ATTATTTAATTAATTTAATAAAACCTTAATTAATTTAAATAAATAAAATATTATATAATATTACT
1 ATTATCTAATTAATTTAATAAAACCTTAATTAATTTAAATAAATAAAATATTATATAATATTACT
* * * * **
9683740 TATTTAGTTAATTGCTTAATTACTAGCACAT-TACTTTACTTAATTAACTAA
66 AATTTAATTAATTACTTAATTACTA-CA-ATATACTTTATTTAATTAGTTAA
* * * ** ** *
9683791 ATTATCTAATTAACTTATTAACACCTTAATTAATTTAAATATTTTTTAA-ATTAAATAATATTAC
1 ATTATCTAATTAATTTAATAAAACCTTAATTAATTTAAATA-AATAAAATATTATATAATATTAC
* * * * * * * *
9683855 TAAGTTAATTAATTGCTTAATTTC-AAAAAAAAATTTAATTTGATTAGTTAA
65 TAATTTAATTAATTACTTAATTACTACAATATACTTT-ATTTAATTAGTTAA
* * * * *
9683906 ATTATCTCATTAATTTGATAGAACCTTAATTAATTTAAATAATTATAAATTTTACTA-AAT-TTA
1 ATTATCTAATTAATTTAATAAAACCTTAATTAATTTAAATAAATA-AAATATTA-TATAATATTA
*
9683969 CTAATTTAATTAATTACTTAATTACTA-ATATATGA-TTCTTTTTAATTAGTTAA
64 CTAATTTAATTAATTACTTAATTACTACA-ATAT-ACTT-TATTTAATTAGTTAA
** * * * *
9684022 ATTAGGTAATTAATTCT-CTTAAACCTTAATTAATTTAAACAAACAAAATATTATATAATATTAC
1 ATTATCTAATTAATT-TAATAAAACCTTAATTAATTTAAATAAATAAAATATTATATAATATTAC
* * ** * *
9684086 TTATTTAATGAATTACTTAATTACTACAATATTTTTTATTTGATTGGTTAA
65 TAATTTAATTAATTACTTAATTACTACAATATACTTTATTTAATTAGTTAA
* * *
9684137 ATTATTTCATTAATTTAACAAAACCTTAATTAATTTAAATAA
1 ATTATCTAATTAATTTAATAAAACCTTAATTAATTTAAATAA
9684179 TTATAATTTT
Statistics
Matches: 310, Mismatches: 62, Indels: 33
0.77 0.15 0.08
Matches are distributed among these distances:
113 1 0.00
114 10 0.03
115 129 0.42
116 162 0.52
117 8 0.03
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (115 bp):
ATTATCTAATTAATTTAATAAAACCTTAATTAATTTAAATAAATAAAATATTATATAATATTACT
AATTTAATTAATTACTTAATTACTACAATATACTTTATTTAATTAGTTAA
Found at i:9684086 original size:231 final size:230
Alignment explanation
Indices: 9683683--9684203 Score: 568
Period size: 231 Copynumber: 2.3 Consensus size: 230
9683673 ATATTATTTA
* * *
9683683 ATTAATTTAATAAAACCTTAATTAATTTAAATAAATA-AAATATTA-TATAATATTACTTATTTA
1 ATTAATTTAATAAAACCTTAATTAATTTAAATAATTATAAATTTTACTA-AAT-TTACTAATTTA
* * * *
9683746 GTTAATTGCTTAATTACTAGCACATTACTTTACTTAATTAACTAAATTATCTAATTAACTTATTA
64 ATTAATTACTTAATTACTAACACATTACTTTA-TTAATTAACTAAATTAGCTAATTAACTTATTA
* ***** * *
9683811 ACACCTTAATTAATTTAAATATTTTTTAAATTAAATAATATTACTAAGTTAATTAATTGCTTAAT
128 ACACCTTAATTAATTTAAACATAACAAAAATTAAATAATATTACTAAGTTAATGAATTACTTAAT
*
9683876 TTCAAAAAAAAATTTAATTTGATTAGTTAAATTATCTC
193 TACAAAAAAAAATTTAATTTGATTAGTTAAATTATCTC
* *
9683914 ATTAATTTGATAGAACCTTAATTAATTTAAATAATTATAAATTTTACTAAATTTACTAATTTAAT
1 ATTAATTTAATAAAACCTTAATTAATTTAAATAATTATAAATTTTACTAAATTTACTAATTTAAT
* * * ** * * *
9683979 TAATTACTTAATTACTAATATATGATTCTTT-TTAATTAGTTAAATTAGGTAATTAATTCTCTTA
66 TAATTACTTAATTACTAACACAT--TACTTTATTAATTAACTAAATTAGCTAATTAACT-TATTA
* * *
9684043 A-ACCTTAATTAATTTAAACA-AACAAAATATTATATAATATTACTTATTTAATGAATTACTTAA
128 ACACCTTAATTAATTTAAACATAACAAAA-ATTAAATAATATTACTAAGTTAATGAATTACTTAA
* * * ** * * *
9684106 TTACTACAATATTTTTTATTTGATTGGTTAAATTATTTC
192 TTACAAAAAAAAATTTAATTTGATTAGTTAAATTATCTC
* * * *
9684145 ATTAATTTAACAAAACCTTAATTAATTTAAATAATTATAATTTTTGCTTAA-TTACTAAT
1 ATTAATTTAATAAAACCTTAATTAATTTAAATAATTATAAATTTTACTAAATTTACTAAT
9684204 CTTGTAGTCT
Statistics
Matches: 241, Mismatches: 43, Indels: 13
0.81 0.14 0.04
Matches are distributed among these distances:
230 10 0.04
231 209 0.87
232 15 0.06
233 7 0.03
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.46
Consensus pattern (230 bp):
ATTAATTTAATAAAACCTTAATTAATTTAAATAATTATAAATTTTACTAAATTTACTAATTTAAT
TAATTACTTAATTACTAACACATTACTTTATTAATTAACTAAATTAGCTAATTAACTTATTAACA
CCTTAATTAATTTAAACATAACAAAAATTAAATAATATTACTAAGTTAATGAATTACTTAATTAC
AAAAAAAAATTTAATTTGATTAGTTAAATTATCTC
Found at i:9689662 original size:21 final size:21
Alignment explanation
Indices: 9689637--9689778 Score: 81
Period size: 21 Copynumber: 6.8 Consensus size: 21
9689627 CTCCATCATT
*
9689637 TCCAACAGCTTTAGATGGGCC
1 TCCAACAGCTTTAAATGGGCC
* * *
9689658 TCCAATAGCTTCAGAA-AGGCC
1 TCCAACAGCTTTA-AATGGGCC
* *
9689679 ACC-ACTAGCTTTAAATTGGCC
1 TCCAAC-AGCTTTAAATGGGCC
* * * *
9689700 TTCAGCAACTTCAAATGGGCC
1 TCCAACAGCTTTAAATGGGCC
* *
9689721 TCTAGCAGCTTTAAATGGGCC
1 TCCAACAGCTTTAAATGGGCC
* * * * *
9689742 TTCAACAACTTCAGATGAGCC
1 TCCAACAGCTTTAAATGGGCC
* *
9689763 ACCAGCAGCTTTAAAT
1 TCCAACAGCTTTAAAT
9689779 TGGCTTTTTA
Statistics
Matches: 86, Mismatches: 31, Indels: 8
0.69 0.25 0.06
Matches are distributed among these distances:
20 3 0.03
21 81 0.94
22 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (21 bp):
TCCAACAGCTTTAAATGGGCC
Found at i:9689712 original size:42 final size:42
Alignment explanation
Indices: 9689642--9689782 Score: 135
Period size: 42 Copynumber: 3.4 Consensus size: 42
9689632 TCATTTCCAA
* * * * *
9689642 CAGCTTTAGATGGGCCTCCAATAGCTTCAGAAAGGCCACCA-
1 CAGCTTTAAATTGGCCTTCAACAACTTCAGAAAGGCCACCAG
* * * *
9689683 CTAGCTTTAAATTGGCCTTCAGCAACTTCA-AATGGGCCTCTAG
1 C-AGCTTTAAATTGGCCTTCAACAACTTCAGAA-AGGCCACCAG
* *
9689726 CAGCTTTAAATGGGCCTTCAACAACTTCAG-ATGAGCCACCAG
1 CAGCTTTAAATTGGCCTTCAACAACTTCAGAAAG-GCCACCAG
9689768 CAGCTTTAAATTGGC
1 CAGCTTTAAATTGGC
9689783 TTTTTATAGT
Statistics
Matches: 80, Mismatches: 15, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
41 4 0.05
42 75 0.94
43 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (42 bp):
CAGCTTTAAATTGGCCTTCAACAACTTCAGAAAGGCCACCAG
Found at i:9691174 original size:80 final size:81
Alignment explanation
Indices: 9691053--9691208 Score: 178
Period size: 80 Copynumber: 1.9 Consensus size: 81
9691043 TGTGATATCT
* * * * * *
9691053 AATACATCAACAACAATAACATATTAAAAAAACAATGCCAAT-TTAG-C-ATACATTAAAAATTC
1 AATACATCAACAACAATAAAAAATGAAAAAAACAATCCCAATCTCAGTCAATA-A-TAAAAATAC
9691115 AACCTAATACTATAAACA
64 AACCTAATACTATAAACA
*
9691133 AATACATCAACAACAATAAAAAATGAAACAACAA-AA-CCCAATCTCAGTCAATAATAAAAATAG
1 AATACATCAACAACAATAAAAAATGAAA-AA-AACAATCCCAATCTCAGTCAATAATAAAAATAC
9691196 AACCTAATACTAT
64 AACCTAATACTAT
9691209 TCATCATCAA
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
80 30 0.47
81 27 0.42
82 4 0.06
83 3 0.05
ACGTcount: A:0.56, C:0.19, G:0.03, T:0.21
Consensus pattern (81 bp):
AATACATCAACAACAATAAAAAATGAAAAAAACAATCCCAATCTCAGTCAATAATAAAAATACAA
CCTAATACTATAAACA
Found at i:9691275 original size:11 final size:11
Alignment explanation
Indices: 9691259--9691283 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9691249 CTAATAGCTT
9691259 TTTCCTTTTCC
1 TTTCCTTTTCC
9691270 TTTCCTTTTCC
1 TTTCCTTTTCC
9691281 TTT
1 TTT
9691284 TCTCGATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTCCTTTTCC
Found at i:9691954 original size:18 final size:18
Alignment explanation
Indices: 9691928--9691962 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9691918 TTATCTTCAA
*
9691928 AATTTTCTTCTTCCTCCC
1 AATTGTCTTCTTCCTCCC
*
9691946 AATTGTCTTCTTTCTCC
1 AATTGTCTTCTTCCTCC
9691963 TTTATTCATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.34, G:0.03, T:0.51
Consensus pattern (18 bp):
AATTGTCTTCTTCCTCCC
Found at i:9695961 original size:5 final size:5
Alignment explanation
Indices: 9695951--9696003 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
9695941 ATTAAAGGAG
* *
9695951 ATGAA ATGAA ATGTAA ATTAA GATGAA ATGAA ATGTAA ATTGAG ATGAA
1 ATGAA ATGAA ATG-AA ATGAA -ATGAA ATGAA ATG-AA A-TGAA ATGAA
9696000 ATGA
1 ATGA
9696004 TAGGAAATGT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 25 0.62
6 13 0.32
7 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.21, T:0.26
Consensus pattern (5 bp):
ATGAA
Found at i:9695974 original size:22 final size:22
Alignment explanation
Indices: 9695949--9696003 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
9695939 ACATTAAAGG
9695949 AGATGAAATGAAATGTAAATTA
1 AGATGAAATGAAATGTAAATTA
*
9695971 AGATGAAATGAAATGTAAATTG
1 AGATGAAATGAAATGTAAATTA
9695993 AGATGAAATGA
1 AGATGAAATGA
9696004 TAGGAAATGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.25
Consensus pattern (22 bp):
AGATGAAATGAAATGTAAATTA
Found at i:9705336 original size:10 final size:10
Alignment explanation
Indices: 9705321--9705346 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
9705311 CCAATTTTTA
9705321 TTATAAAGTC
1 TTATAAAGTC
9705331 TTATAAAGTC
1 TTATAAAGTC
9705341 TTATAA
1 TTATAA
9705347 GGGATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (10 bp):
TTATAAAGTC
Found at i:9710775 original size:20 final size:23
Alignment explanation
Indices: 9710735--9710775 Score: 61
Period size: 20 Copynumber: 1.9 Consensus size: 23
9710725 TAGTTTGTTA
9710735 AGTAAATAAATCAATCAATAACC
1 AGTAAATAAATCAATCAATAACC
9710758 AGTAAA-AAA-CAA-CAATAA
1 AGTAAATAAATCAATCAATAA
9710776 AAAAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 3 0.17
22 3 0.17
23 6 0.33
ACGTcount: A:0.63, C:0.15, G:0.05, T:0.17
Consensus pattern (23 bp):
AGTAAATAAATCAATCAATAACC
Found at i:9717343 original size:30 final size:31
Alignment explanation
Indices: 9717273--9717345 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 31
9717263 TTGTTTTGCT
* *
9717273 TTAAATA-TTTATAATTTTATTCTTAATTTT
1 TTAAATATTTTATAATTTTATTCTTAATATA
*
9717303 TTAAAAATTTTATAATTTTA-TCTGTAA-ATA
1 TTAAATATTTTATAATTTTATTCT-TAATATA
9717333 TTAAATATTTTAT
1 TTAAATATTTTAT
9717346 TTTAATTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
30 22 0.59
31 15 0.41
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (31 bp):
TTAAATATTTTATAATTTTATTCTTAATATA
Found at i:9721509 original size:49 final size:49
Alignment explanation
Indices: 9721437--9721532 Score: 147
Period size: 49 Copynumber: 2.0 Consensus size: 49
9721427 ATGAACAATG
* *
9721437 AACAATTTATGTACTTCGCTTCAAGGGTCTTATGACTTAATCTTGAATA
1 AACAATTTAGGTACTTCCCTTCAAGGGTCTTATGACTTAATCTTGAATA
* * *
9721486 AACAATTTGGGTATTTCCCTTCAAGGGTCTTATGACTTGATCTTGAA
1 AACAATTTAGGTACTTCCCTTCAAGGGTCTTATGACTTAATCTTGAA
9721533 AGATTAACAC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (49 bp):
AACAATTTAGGTACTTCCCTTCAAGGGTCTTATGACTTAATCTTGAATA
Found at i:9723054 original size:117 final size:115
Alignment explanation
Indices: 9722748--9723089 Score: 397
Period size: 113 Copynumber: 3.0 Consensus size: 115
9722738 GGCACCTTAG
* * * *
9722748 GCATAACTGGATTTTGGCATGGGATCACTTAGAGGGTGCATGATTGCATTAAGGTTTAACATTGA
1 GCATGACTGGATTTAGGCAT-GGATCACTTAGA-TGTGCATGATTGCATTAGGGTTTAACATTGA
* * * *
9722813 GTGACTGGTTGATAGGTCTTTGCAAGAATGGTTGATAGGTCATTGCATGACA
64 GTGACTGGTTGATAGGTCTTTGCATGATTGATTGATAGGTCATTGCATAACA
* * *
9722865 GCATGACTGGATGTAGGCATAGG----GTTAGGATGTGCATGATTGCATTAGGGTTTAACATTGC
1 GCATGACTGGATTTAGGCAT-GGATCACTTA-GATGTGCATGATTGCATTAGGGTTTAACATTGA
* * * * *
9722926 GTGATTGGTTGATAAGTCATTCCATGATTGATTGATAGGTCATTGCGTAACA
64 GTGACTGGTTGATAGGTCTTTGCATGATTGATTGATAGGTCATTGCATAACA
* * *
9722978 GCATGACTAGATTTAGGCATGGCATCACTTATGCTGTGCATGATTGCATTAGGGTTTAACATTGT
1 GCATGACTGGATTTAGGCATGG-ATCACTTA-GATGTGCATGATTGCATTAGGGTTTAACATTGA
* *
9723043 GTGACTAGTTGATAGGTCTTTGCGTGACTT-ATTGATAGGTCATTGCA
64 GTGACTGGTTGATAGGTCTTTGCATGA-TTGATTGATAGGTCATTGCA
9723090 AGAATATTGT
Statistics
Matches: 188, Mismatches: 30, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
112 2 0.01
113 92 0.49
114 2 0.01
117 90 0.48
118 2 0.01
ACGTcount: A:0.25, C:0.13, G:0.28, T:0.34
Consensus pattern (115 bp):
GCATGACTGGATTTAGGCATGGATCACTTAGATGTGCATGATTGCATTAGGGTTTAACATTGAGT
GACTGGTTGATAGGTCTTTGCATGATTGATTGATAGGTCATTGCATAACA
Found at i:9723077 original size:23 final size:23
Alignment explanation
Indices: 9723037--9723088 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
9723027 TAGGGTTTAA
*
9723037 CATTGTGTGACTAGTTGATAGGT
1 CATTGCGTGACTAGTTGATAGGT
*
9723060 CTTTGCGTGACTTA-TTGATAGGT
1 CATTGCGTGAC-TAGTTGATAGGT
9723083 CATTGC
1 CATTGC
9723089 AAGAATATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 23 0.92
24 2 0.08
ACGTcount: A:0.19, C:0.13, G:0.27, T:0.40
Consensus pattern (23 bp):
CATTGCGTGACTAGTTGATAGGT
Found at i:9726916 original size:26 final size:26
Alignment explanation
Indices: 9726887--9726955 Score: 104
Period size: 26 Copynumber: 2.6 Consensus size: 26
9726877 TAACATTGTT
9726887 TTGTATCATCTT-CAAATTATTCTTTG
1 TTGTATCAT-TTACAAATTATTCTTTG
*
9726913 TTGTATCATTTACAAATTATTCTTTT
1 TTGTATCATTTACAAATTATTCTTTG
9726939 TTGTATCATTTAACAAA
1 TTGTATCATTT-ACAAA
9726956 GAAAAGGGCA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
25 2 0.05
26 33 0.82
27 5 0.12
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.52
Consensus pattern (26 bp):
TTGTATCATTTACAAATTATTCTTTG
Found at i:9727198 original size:23 final size:23
Alignment explanation
Indices: 9727157--9727227 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
9727147 AGTGACATAG
* *
9727157 GCATGTAATCAGTTGATATTGAATT
1 GCATG-AAT-AGTGGATATTGAATC
* *
9727182 GCATGAATGGTGGATATGGAATC
1 GCATGAATAGTGGATATTGAATC
* * *
9727205 GCTTGACTAGTTGATATTGAATC
1 GCATGAATAGTGGATATTGAATC
9727228 ATGCCAGTAT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
23 29 0.78
24 3 0.08
25 5 0.14
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.35
Consensus pattern (23 bp):
GCATGAATAGTGGATATTGAATC
Found at i:9727295 original size:23 final size:23
Alignment explanation
Indices: 9727241--9727341 Score: 69
Period size: 23 Copynumber: 4.4 Consensus size: 23
9727231 CCAGTATTTG
*
9727241 ATATGGAATCACA-GAACTACTAA
1 ATATGGAATCACATG-ACTAGTAA
* * *
9727264 ATTTAGAATCACATGACTAGTTA
1 ATATGGAATCACATGACTAGTAA
* * * **
9727287 ATATGGAATCGCGTGACTAATCG
1 ATATGGAATCACATGACTAGTAA
* * *
9727310 ATTTGGAATCGCATAACTAGTAA
1 ATATGGAATCACATGACTAGTAA
*
9727333 ATATAGAAT
1 ATATGGAAT
9727342 TATGTGAACC
Statistics
Matches: 58, Mismatches: 19, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
23 57 0.98
24 1 0.02
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.29
Consensus pattern (23 bp):
ATATGGAATCACATGACTAGTAA
Found at i:9727514 original size:23 final size:23
Alignment explanation
Indices: 9727363--9727718 Score: 118
Period size: 23 Copynumber: 15.6 Consensus size: 23
9727353 TTAAGATTTA
* *
9727363 GAATCGCGTGACTAGCTGA-TATT
1 GAATCGCGTGACTAG-TTATTATG
* * * *
9727386 GAATCGCGTGAGTCGTAACTAT-
1 GAATCGCGTGACTAGTTATTATG
* *
9727408 GAATTG-GTGTTACTAGTTATCATG
1 GAATCGCGTG--ACTAGTTATTATG
* * *
9727432 GAATTGTGTGACTAGTCATTAT-
1 GAATCGCGTGACTAGTTATTATG
* * * * *
9727454 AAATCGCGTGAGTAATAAATAT-
1 GAATCGCGTGACTAGTTATTATG
* * * *
9727476 GAGTCGCATTATTAGTTATTATG
1 GAATCGCGTGACTAGTTATTATG
*
9727499 GAATCGCGTGACTAGTTGA-TATT
1 GAATCGCGTGACTAGTT-ATTATG
* * * *
9727522 GAGTCGCGTGAGTAGTAAATATG
1 GAATCGCGTGACTAGTTATTATG
* *
9727545 GAGT-GTCGTTACTAGTTATTATG
1 GAATCG-CGTGACTAGTTATTATG
***
9727568 GAATTATGTGACTAGTTATTAT-
1 GAATCGCGTGACTAGTTATTATG
* * * * * *
9727590 AACATAGCATGAGTAGTAAATATG
1 GA-ATCGCGTGACTAGTTATTATG
* * * *
9727614 GAGTCACGTTACAAGTTATTATG
1 GAATCGCGTGACTAGTTATTATG
* * *
9727637 GAAACACGTGAATAGTTATTATG
1 GAATCGCGTGACTAGTTATTATG
* ** *
9727660 CAATCATGTGAGTAGTTATTATG
1 GAATCGCGTGACTAGTTATTATG
* * *
9727683 GAGTCGCATTACTAGTTGA-TATG
1 GAATCGCGTGACTAGTT-ATTATG
* *
9727706 TAATTGCGTGACT
1 GAATCGCGTGACT
9727719 CTTTGATATG
Statistics
Matches: 238, Mismatches: 82, Indels: 26
0.69 0.24 0.08
Matches are distributed among these distances:
21 3 0.01
22 39 0.16
23 184 0.77
24 9 0.04
25 3 0.01
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (23 bp):
GAATCGCGTGACTAGTTATTATG
Found at i:9727529 original size:136 final size:138
Alignment explanation
Indices: 9727363--9727653 Score: 381
Period size: 136 Copynumber: 2.1 Consensus size: 138
9727353 TTAAGATTTA
* * * *
9727363 GAATCGCGTGACTAGCTGATATTGAATCGCGTGAGTCGTAACTATGAATTGGT-GTTACTAGTTA
1 GAATCGCGTGACTAGTTGATATTGAATCGCGTGAGTAGTAAATATGAAGT-GTCGTTACTAGTTA
* * * * **
9727427 TCATGGAATTGTGTGACTAGTCATTATAA-ATCGCGTGAGTAATAAATAT-GAGTCGCATTATTA
65 TCATGGAATTATGTGACTAGTCATTATAACATAGCATGAGTAATAAATATGGAGTCACATTACAA
9727490 GTTATTATG
130 GTTATTATG
* *
9727499 GAATCGCGTGACTAGTTGATATTGAGTCGCGTGAGTAGTAAATATGGAGTGTCGTTACTAGTTAT
1 GAATCGCGTGACTAGTTGATATTGAATCGCGTGAGTAGTAAATATGAAGTGTCGTTACTAGTTAT
* * * *
9727564 TATGGAATTATGTGACTAGTTATTATAACATAGCATGAGTAGTAAATATGGAGTCACGTTACAAG
66 CATGGAATTATGTGACTAGTCATTATAACATAGCATGAGTAATAAATATGGAGTCACATTACAAG
9727629 TTATTATG
131 TTATTATG
* * *
9727637 GAAACACGTGAATAGTT
1 GAATCGCGTGACTAGTT
9727654 ATTATGCAAT
Statistics
Matches: 133, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
135 2 0.02
136 81 0.61
137 17 0.13
138 33 0.25
ACGTcount: A:0.31, C:0.11, G:0.24, T:0.34
Consensus pattern (138 bp):
GAATCGCGTGACTAGTTGATATTGAATCGCGTGAGTAGTAAATATGAAGTGTCGTTACTAGTTAT
CATGGAATTATGTGACTAGTCATTATAACATAGCATGAGTAATAAATATGGAGTCACATTACAAG
TTATTATG
Found at i:9727579 original size:69 final size:70
Alignment explanation
Indices: 9727370--9727718 Score: 263
Period size: 69 Copynumber: 5.1 Consensus size: 70
9727360 TTAGAATCGC
* * * * * * * *
9727370 GTGACTAGCTGA-TATTGAATCGCGTGAGTCGTAACTATGAATTGGT-GTTACTAGTTATCATGG
1 GTGACTAGTTGATTA-TAAATCGCGTGAGTAGTAAATATGGAGTCGTCGTTACTAGTTATTATGG
9727433 AATTGT
65 AATTGT
* * * *
9727439 GTGACTAG-TCATTATAAATCGCGTGAGTAATAAATAT-GAGTCG-CATTATTAGTTATTATGGA
1 GTGACTAGTTGATTATAAATCGCGTGAGTAGTAAATATGGAGTCGTCGTTACTAGTTATTATGGA
* *
9727501 ATCGC
66 ATTGT
* *
9727506 GTGACTAGTTGA-TATTGAGTCGCGTGAGTAGTAAATATGGAGT-GTCGTTACTAGTTATTATGG
1 GTGACTAGTTGATTA-TAAATCGCGTGAGTAGTAAATATGGAGTCGTCGTTACTAGTTATTATGG
*
9727569 AATTAT
65 AATTGT
* * * *
9727575 GTGACTAGTT-ATTATAACATAGCATGAGTAGTAAATATGGAGTC-ACGTTACAAGTTATTATGG
1 GTGACTAGTTGATTATAA-ATCGCGTGAGTAGTAAATATGGAGTCGTCGTTACTAGTTATTATGG
****
9727638 AAACAC
65 AATTGT
* * ** * * *
9727644 GTGAATAGTT-ATTATGCAATCATGTGAGTAGTTATTATGGAGTCG-CATTACTAGTTGA-TATG
1 GTGACTAGTTGATTAT-AAATCGCGTGAGTAGTAAATATGGAGTCGTCGTTACTAGTT-ATTATG
* *
9727706 TAATTGC
64 GAATTGT
9727713 GTGACT
1 GTGACT
9727719 CTTTGATATG
Statistics
Matches: 222, Mismatches: 46, Indels: 24
0.76 0.16 0.08
Matches are distributed among these distances:
67 31 0.14
68 47 0.21
69 142 0.64
70 2 0.01
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.36
Consensus pattern (70 bp):
GTGACTAGTTGATTATAAATCGCGTGAGTAGTAAATATGGAGTCGTCGTTACTAGTTATTATGGA
ATTGT
Found at i:9727724 original size:23 final size:23
Alignment explanation
Indices: 9727698--9727742 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
9727688 GCATTACTAG
*
9727698 TTGATATGTAATTGCGTGACTCT
1 TTGATATGGAATTGCGTGACTCT
* *
9727721 TTGATATGGGATTGTGTGACTC
1 TTGATATGGAATTGCGTGACTC
9727743 ACTTATTGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.11, G:0.27, T:0.42
Consensus pattern (23 bp):
TTGATATGGAATTGCGTGACTCT
Found at i:9731740 original size:203 final size:202
Alignment explanation
Indices: 9731378--9731760 Score: 563
Period size: 203 Copynumber: 1.9 Consensus size: 202
9731368 CACATTCATG
* *
9731378 CAATGCCTAAACACTAGTGAACAAAAGCCTCAAAACAAGAGATGAATTGCACAAGTCACGTAGCA
1 CAATGCCTAAAAACTAGTGAACAAAAGCCCCAAAACAAGAGATGAATTGCACAAGTCAC-TAGCA
* *
9731443 CTAGTCTCGCAATACCTAATAATAAGTCACTCAATGCCTAATATCCACTCACATTATACCAATAT
65 CTAGTCTCGCAATACCTAATAATAACTCACTCAATGCCTAATATCCACTCACATTATACCAACAT
* * * * *
9731508 AACTAGTCACGTACTGGCCCAATGTCACGCAATATATAACAACAGGTCACTCAATACATAAAAAC
130 AACCAGTCACGTACTGACCCAACGTCACGCAATACATAACAACAAGTCACTCAATACATAAAAAC
9731573 CAATCGCA
195 CAATCGCA
*
9731581 CAATGCCTAAAAACTAGTGAACAAAAGCCCCAAAATAAGAGATGAATTGCACAAGTCA-T-GCAT
1 CAATGCCTAAAAACTAGTGAACAAAAGCCCCAAAACAAGAGATGAATTGCACAAGTCACTAGCA-
* ** * ** *
9731644 TGTCAGTCTCGCAATACCTAATAATAACTCACTTGATGCCTAATATCCATTCATGTTATGCCAAC
65 -CT-AGTCTCGCAATACCTAATAATAACTCACTCAATGCCTAATATCCACTCACATTATACCAAC
9731709 ATAACCAGTCACGTACTGACCCAACGTCACGCAATACATAACAACAAGTCAC
128 ATAACCAGTCACGTACTGACCCAACGTCACGCAATACATAACAACAAGTCAC
9731761 AATATAGATA
Statistics
Matches: 160, Mismatches: 17, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
200 3 0.02
201 1 0.01
202 1 0.01
203 155 0.97
ACGTcount: A:0.40, C:0.26, G:0.12, T:0.22
Consensus pattern (202 bp):
CAATGCCTAAAAACTAGTGAACAAAAGCCCCAAAACAAGAGATGAATTGCACAAGTCACTAGCAC
TAGTCTCGCAATACCTAATAATAACTCACTCAATGCCTAATATCCACTCACATTATACCAACATA
ACCAGTCACGTACTGACCCAACGTCACGCAATACATAACAACAAGTCACTCAATACATAAAAACC
AATCGCA
Done.