Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397279.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_239.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2022356
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6073 characters in sequence are not A, C, G, or T
File 3 of 5
Found at i:1067662 original size:28 final size:28
Alignment explanation
Indices: 1067622--1067675 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
1067612 AAGGTGCTTT
*
1067622 TTGTGAGACAAAATCATGAGACCAACTA
1 TTGTGAAACAAAATCATGAGACCAACTA
* *
1067650 TTGTGAAATAAAATCATGAGATCAAC
1 TTGTGAAACAAAATCATGAGACCAAC
1067676 GAGTCAAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.24
Consensus pattern (28 bp):
TTGTGAAACAAAATCATGAGACCAACTA
Found at i:1082567 original size:15 final size:17
Alignment explanation
Indices: 1082532--1082570 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
1082522 AATACTTATA
1082532 ATTATTAATTAATTAATT
1 ATTATTAATTAA-TAATT
1082550 ATTATTAATTAA-AA-T
1 ATTATTAATTAATAATT
1082565 ATTATT
1 ATTATT
1082571 TATCATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 2 0.10
18 12 0.57
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTATTAATTAATAATT
Found at i:1090026 original size:30 final size:30
Alignment explanation
Indices: 1089992--1090057 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
1089982 AGCAAATCAA
*
1089992 CAGCAATCCTGGTGC-AATTCAGCCACATAT
1 CAGCAATCCAGGTGCTAA-TCAGCCACATAT
* * **
1090022 CAGCACTTCAGGTGCTAATCAGCCATTTAT
1 CAGCAATCCAGGTGCTAATCAGCCACATAT
1090052 CAGCAA
1 CAGCAA
1090058 ACCCAGTGCT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
30 27 0.93
31 2 0.07
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (30 bp):
CAGCAATCCAGGTGCTAATCAGCCACATAT
Found at i:1099404 original size:10 final size:11
Alignment explanation
Indices: 1099378--1099407 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1099368 TAAAAAACTG
1099378 AAAGCAGAGCA
1 AAAGCAGAGCA
1099389 AAAGCAGAGC-
1 AAAGCAGAGCA
1099399 AAAGCAGAG
1 AAAGCAGAG
1099408 GGAACAACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.53, C:0.17, G:0.30, T:0.00
Consensus pattern (11 bp):
AAAGCAGAGCA
Found at i:1103395 original size:30 final size:30
Alignment explanation
Indices: 1103361--1103420 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1103351 ATTAAATCTG
1103361 CTTCCTGTTTTAAAACCAAATAAAAATATA
1 CTTCCTGTTTTAAAACCAAATAAAAATATA
1103391 CTTCCTGTTTTAAAACCAAATAAAAATATA
1 CTTCCTGTTTTAAAACCAAATAAAAATATA
1103421 TATGTAAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (30 bp):
CTTCCTGTTTTAAAACCAAATAAAAATATA
Found at i:1107065 original size:16 final size:17
Alignment explanation
Indices: 1107028--1107065 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1107018 GAAGGAATAA
*
1107028 GGAGAGGAAGAGAAGTT
1 GGAGAGGAAGAGAAGAT
*
1107045 AGAGA-GAAGAGAAGAT
1 GGAGAGGAAGAGAAGAT
1107061 GGAGA
1 GGAGA
1107066 ATAATATAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.47, C:0.00, G:0.45, T:0.08
Consensus pattern (17 bp):
GGAGAGGAAGAGAAGAT
Found at i:1138516 original size:19 final size:19
Alignment explanation
Indices: 1138492--1138539 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1138482 GACATAAGAT
* *
1138492 TAAAATAATACTTTTATAA
1 TAAAATAATACTATAATAA
**
1138511 TAAAATAATGGTATAATAA
1 TAAAATAATACTATAATAA
1138530 TAAAATAATA
1 TAAAATAATA
1138540 ATATTTTATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.35
Consensus pattern (19 bp):
TAAAATAATACTATAATAA
Found at i:1144755 original size:20 final size:20
Alignment explanation
Indices: 1144730--1144771 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1144720 TTTCATATAT
1144730 ATATATATATTATGTAAATA
1 ATATATATATTATGTAAATA
1144750 ATATATATATTATGTAAATA
1 ATATATATATTATGTAAATA
1144770 AT
1 AT
1144772 TTTATTAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
ATATATATATTATGTAAATA
Found at i:1150709 original size:24 final size:22
Alignment explanation
Indices: 1150638--1150713 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 22
1150628 AATAAATATT
*
1150638 AATATTTATTATTAAAAATTAAA
1 AATATTTATTATT-AAAAGTAAA
*
1150661 AATATTTATATATTTAAAGCATAAA
1 AATATTTAT-TATTAAAAG--TAAA
*
1150686 ACTTATTTATTATTAAATAGTAAA
1 A-ATATTTATTATTAAA-AGTAAA
1150710 AATA
1 AATA
1150714 GCAATATAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
23 14 0.33
24 9 0.21
25 11 0.26
26 9 0.21
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (22 bp):
AATATTTATTATTAAAAGTAAA
Found at i:1160168 original size:14 final size:13
Alignment explanation
Indices: 1160149--1160333 Score: 63
Period size: 13 Copynumber: 14.3 Consensus size: 13
1160139 GTTATAATTA
1160149 AAATTAAAAATATT
1 AAATTAAAAATA-T
*
1160163 AAATTAAATATAT
1 AAATTAAAAATAT
*
1160176 -AATATAAAAATAC
1 AAAT-TAAAAATAT
*
1160189 AAATTTAAAATA-
1 AAATTAAAAATAT
1160201 AAA-T-AAAATA-
1 AAATTAAAAATAT
1160211 AAATATAAAAA-ATT
1 AAAT-TAAAAATA-T
* *
1160225 AAAATTTATATATTAT
1 -AAA-TTA-AAAATAT
** *
1160241 AGGTAAAAAATA-
1 AAATTAAAAATAT
*
1160253 AAAAT-AAAATAT
1 AAATTAAAAATAT
1160265 ATAATATAAAAA-AT
1 A-AAT-TAAAAATAT
*
1160279 ATATTAAAAA-AT
1 AAATTAAAAATAT
*
1160291 AAAAATAAAATATAT
1 -AAATTAAAA-ATAT
1160306 AAGATT-AAAATA-
1 AA-ATTAAAAATAT
*
1160318 AAAATAAAAATA-
1 AAATTAAAAATAT
1160330 AAAT
1 AAAT
1160334 ATATGACATT
Statistics
Matches: 129, Mismatches: 22, Indels: 42
0.67 0.11 0.22
Matches are distributed among these distances:
10 9 0.07
11 9 0.07
12 29 0.22
13 37 0.29
14 26 0.20
15 14 0.11
16 4 0.03
17 1 0.01
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.29
Consensus pattern (13 bp):
AAATTAAAAATAT
Found at i:1160218 original size:7 final size:7
Alignment explanation
Indices: 1160155--1160336 Score: 80
Period size: 7 Copynumber: 27.1 Consensus size: 7
1160145 ATTAAAATTA
1160155 AAAATAT
1 AAAATAT
*
1160162 TAAAT-T
1 AAAATAT
1160168 -AAATAT
1 AAAATAT
*
1160174 ATAATAT
1 AAAATAT
1160181 AAAA-AT
1 AAAATAT
*
1160187 ACAAATTT
1 A-AAATAT
*
1160195 AAAATAA
1 AAAATAT
*
1160202 AATAAAAT
1 AA-AATAT
1160210 AAAATAT
1 AAAATAT
*
1160217 AAAAAATT
1 AAAATA-T
1160225 AAAAT-T
1 AAAATAT
* *
1160231 TATATAT
1 AAAATAT
* * **
1160238 TATAGGT
1 AAAATAT
*
1160245 AAAAAAT
1 AAAATAT
1160252 AAAA-AT
1 AAAATAT
1160258 AAAATAT
1 AAAATAT
*
1160265 ATAATAT
1 AAAATAT
*
1160272 AAAAAAT
1 AAAATAT
*
1160279 -ATAT-T
1 AAAATAT
*
1160284 AAAAAAT
1 AAAATAT
1160291 AAAA-AT
1 AAAATAT
1160297 AAAATAT
1 AAAATAT
* *
1160304 ATAAGAT
1 AAAATAT
*
1160311 TAAA-AT
1 AAAATAT
1160317 AAAA-AT
1 AAAATAT
1160323 AAAA-AT
1 AAAATAT
1160329 AAAATAT
1 AAAATAT
1160336 A
1 A
1160337 TGACATTCAA
Statistics
Matches: 132, Mismatches: 31, Indels: 24
0.71 0.17 0.13
Matches are distributed among these distances:
5 5 0.04
6 42 0.32
7 73 0.55
8 12 0.09
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.29
Consensus pattern (7 bp):
AAAATAT
Found at i:1160257 original size:6 final size:6
Alignment explanation
Indices: 1160246--1160332 Score: 68
Period size: 6 Copynumber: 13.7 Consensus size: 6
1160236 ATTATAGGTA
* * *
1160246 AAAAAT AAAAAT AAAATAT ATAATAT AAAAA- ATATATT AAAAAAT AAAAAT
1 AAAAAT AAAAAT AAAA-AT A-AAAAT AAAAAT A-AAAAT -AAAAAT AAAAAT
* *
1160297 AAAATAT ATAAGAT TAAAAT AAAAAT AAAAAT AAAA
1 AAAA-AT A-AAAAT AAAAAT AAAAAT AAAAAT AAAA
1160333 TATATGACAT
Statistics
Matches: 64, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
5 1 0.02
6 44 0.69
7 14 0.22
8 5 0.08
ACGTcount: A:0.75, C:0.00, G:0.01, T:0.24
Consensus pattern (6 bp):
AAAAAT
Found at i:1160274 original size:91 final size:88
Alignment explanation
Indices: 1160154--1160316 Score: 220
Period size: 87 Copynumber: 1.8 Consensus size: 88
1160144 AATTAAAATT
* *
1160154 AAAAATATTAAATTAAATATATAATATAAAAATACAAATTTAAAATAAAATAAAATAAAATATAA
1 AAAAATATAAAATAAAATATATAATATAAAAA-ACAAA-TTAAAA-AAAA-AAAATAAAATATAA
1160219 AAAATTAAAATTTATATATTATAGGTA
62 AAAATTAAAATTTATATATTATAGGTA
* * * * *
1160246 AAAAATA-AAAATAAAATATATAATATAAAAAATATATTAAAAAATAAAAATAAAATATATAAGA
1 AAAAATATAAAATAAAATATATAATATAAAAAACAAATTAAAAAAAAAAAATAAAATATAAAAAA
1160310 TTAAAAT
66 TTAAAAT
1160317 AAAAATAAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
87 23 0.36
88 3 0.05
89 6 0.09
90 3 0.05
91 22 0.34
92 7 0.11
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (88 bp):
AAAAATATAAAATAAAATATATAATATAAAAAACAAATTAAAAAAAAAAAATAAAATATAAAAAA
TTAAAATTTATATATTATAGGTA
Found at i:1160298 original size:25 final size:26
Alignment explanation
Indices: 1160244--1160327 Score: 82
Period size: 26 Copynumber: 3.2 Consensus size: 26
1160234 ATATTATAGG
* *
1160244 TAAAAAATA-AAAATAAAATATATAATA
1 TAAAAAATATAAGATAAAA-ATA-AAAA
**
1160271 TAAAAAATATATTA-AAAAATAAAAA
1 TAAAAAATATAAGATAAAAATAAAAA
* *
1160296 TAAAATATATAAGATTAAAATAAAAA
1 TAAAAAATATAAGATAAAAATAAAAA
1160322 TAAAAA
1 TAAAAA
1160328 TAAAATATAT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
25 14 0.30
26 18 0.38
27 13 0.28
28 2 0.04
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.25
Consensus pattern (26 bp):
TAAAAAATATAAGATAAAAATAAAAA
Found at i:1160326 original size:39 final size:39
Alignment explanation
Indices: 1160244--1160332 Score: 121
Period size: 39 Copynumber: 2.3 Consensus size: 39
1160234 ATATTATAGG
* *
1160244 TAAAAAATAAAAATAAAATATATAATATAAAAAATATAT
1 TAAAAAATAAAAATAAAATATATAAGATAAAAAATATAA
1160283 TAAAAAATAAAAATAAAATATATAAGATTAAAATAA-A-AA
1 TAAAAAATAAAAATAAAATATATAAGA-TAAAA-AATATAA
1160322 T-AAAAATAAAA
1 TAAAAAATAAAA
1160333 TATATGACAT
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
38 10 0.22
39 28 0.61
40 6 0.13
41 2 0.04
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.25
Consensus pattern (39 bp):
TAAAAAATAAAAATAAAATATATAAGATAAAAAATATAA
Found at i:1160337 original size:32 final size:32
Alignment explanation
Indices: 1160247--1160337 Score: 112
Period size: 32 Copynumber: 2.8 Consensus size: 32
1160237 TTATAGGTAA
*
1160247 AAAATAAAAATAAAATATATAATATA-AAAAAT
1 AAAATAAAAATAAAA-ATAAAATATATAAAAAT
* * * *
1160279 ATATTAAAAAATAAAAATAAAATATATAAGATT
1 AAAAT-AAAAATAAAAATAAAATATATAAAAAT
1160312 AAAATAAAAATAAAAATAAAATATAT
1 AAAATAAAAATAAAAATAAAATATAT
1160338 GACATTCAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
32 33 0.66
33 17 0.34
ACGTcount: A:0.73, C:0.00, G:0.01, T:0.26
Consensus pattern (32 bp):
AAAATAAAAATAAAAATAAAATATATAAAAAT
Found at i:1161016 original size:3 final size:3
Alignment explanation
Indices: 1161010--1161097 Score: 83
Period size: 3 Copynumber: 29.3 Consensus size: 3
1161000 TTGTTTGTTG
* * * *
1161010 TTA TTA TTA TTA TTA TTA TTA TTA TTA GTCA -TA ATA CGTA TGA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA -TTA TTA TTA
*
1161055 TGT- TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1161098 CTTACGCTTA
Statistics
Matches: 73, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
2 3 0.04
3 66 0.90
4 4 0.05
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1161038 original size:54 final size:54
Alignment explanation
Indices: 1160973--1161090 Score: 209
Period size: 54 Copynumber: 2.2 Consensus size: 54
1160963 TTTCCTGTTA
* *
1160973 ATTATTGTTAGTCACAATACGTATGATTTGTTTGTTGTTATTATTATTATTATT
1 ATTATTATTAGTCACAATACGTATGATTTGTTTGTTATTATTATTATTATTATT
*
1161027 ATTATTATTAGTCATAATACGTATGATTTGTTTGTTATTATTATTATTATTATT
1 ATTATTATTAGTCACAATACGTATGATTTGTTTGTTATTATTATTATTATTATT
1161081 ATTATTATTA
1 ATTATTATTA
1161091 TTATTATCTT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 61 1.00
ACGTcount: A:0.29, C:0.04, G:0.10, T:0.57
Consensus pattern (54 bp):
ATTATTATTAGTCACAATACGTATGATTTGTTTGTTATTATTATTATTATTATT
Found at i:1161213 original size:3 final size:3
Alignment explanation
Indices: 1161205--1161235 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1161195 GATTTGTTTG
1161205 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1161236 CTTACGCTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1161280 original size:138 final size:139
Alignment explanation
Indices: 1161026--1161295 Score: 479
Period size: 138 Copynumber: 1.9 Consensus size: 139
1161016 TTATTATTAT
1161026 TATTATTATTAGTCATAATACGTATGATTTGTTTGTTATTATTATTATTATTATTATTATTATTA
1 TATTATTATTAGTCATAATACGTATGATTTGTTTG----T-TTATTATTATTATTATTATTATTA
1161091 TTATTATCTTACGCTTAACCAATTTGCCCAAAAGATTGATCTTTACTTCATAAGTGTATAAATTA
61 TTATTATCTTACGCTTAACCAATTTGCCCAAAAGATTGATCTTTACTTCATAAGTGTATAAATTA
1161156 TTATCCTTCAACTC
126 TTATCCTTCAACTC
*
1161170 TATTATTTTTAGTCATAATACGTATGATTTGTTTG-TTATTATTATTATTATTATTATTATTATT
1 TATTATTATTAGTCATAATACGTATGATTTGTTTGTTTATTATTATTATTATTATTATTATTATT
1161234 ATCTTACGCTTAACCAATTTGCCCAAAAGATTGATCTTTACTTCATAAGTGTATAAATTATT
66 ATCTTACGCTTAACCAATTTGCCCAAAAGATTGATCTTTACTTCATAAGTGTATAAATTATT
1161296 TAATTAGAAT
Statistics
Matches: 125, Mismatches: 1, Indels: 6
0.95 0.01 0.05
Matches are distributed among these distances:
138 91 0.73
144 34 0.27
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.49
Consensus pattern (139 bp):
TATTATTATTAGTCATAATACGTATGATTTGTTTGTTTATTATTATTATTATTATTATTATTATT
ATCTTACGCTTAACCAATTTGCCCAAAAGATTGATCTTTACTTCATAAGTGTATAAATTATTATC
CTTCAACTC
Found at i:1162123 original size:29 final size:29
Alignment explanation
Indices: 1162057--1162116 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
1162047 TTATTCTATT
** *
1162057 TATAATAAAAAAATATAAATTTAATTAAA
1 TATAATAAATGAATAAAAATTTAATTAAA
*
1162086 TATAATAAATGAATAAAAATTTATTTAAA
1 TATAATAAATGAATAAAAATTTAATTAAA
1162115 TA
1 TA
1162117 ATTTAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (29 bp):
TATAATAAATGAATAAAAATTTAATTAAA
Found at i:1163055 original size:3 final size:3
Alignment explanation
Indices: 1163047--1163072 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1163037 AAACGACGGC
1163047 CGA CGA CGA CGA CGA CGA CGA CGA CG
1 CGA CGA CGA CGA CGA CGA CGA CGA CG
1163073 TCTGATGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.35, G:0.35, T:0.00
Consensus pattern (3 bp):
CGA
Found at i:1170637 original size:30 final size:30
Alignment explanation
Indices: 1170603--1170667 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
1170593 GGTGATTCCA
*
1170603 GGTGATGATGTGGTTCCCCCTCCATTCCCT
1 GGTGATGATGTGGTTCCCCCTCCAATCCCT
*
1170633 GGTGATGATGTGGTTCCCCCTCTAATCCCT
1 GGTGATGATGTGGTTCCCCCTCCAATCCCT
1170663 GGTGA
1 GGTGA
1170668 AGGTATTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.12, C:0.29, G:0.26, T:0.32
Consensus pattern (30 bp):
GGTGATGATGTGGTTCCCCCTCCAATCCCT
Found at i:1176612 original size:2 final size:2
Alignment explanation
Indices: 1176605--1176629 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1176595 CTCATATTTC
1176605 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
1176630 GAGAGAGAGA
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:1176634 original size:2 final size:2
Alignment explanation
Indices: 1176629--1176655 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1176619 ATATATATAT
1176629 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1176656 TCAAATCAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1187917 original size:20 final size:22
Alignment explanation
Indices: 1187889--1187931 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1187879 AATAATATAA
1187889 TTATATAA-TATT-TTTACTTT
1 TTATATAATTATTATTTACTTT
* *
1187909 TTATGTAATTATTATTTTCTTT
1 TTATATAATTATTATTTACTTT
1187931 T
1 T
1187932 CTCACATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 4 0.21
22 8 0.42
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (22 bp):
TTATATAATTATTATTTACTTT
Found at i:1189335 original size:17 final size:17
Alignment explanation
Indices: 1189313--1189346 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1189303 CGTTCATTTA
1189313 ACAAAAAATATTAACTT
1 ACAAAAAATATTAACTT
1189330 ACAAAAAATATTAACTT
1 ACAAAAAATATTAACTT
1189347 CATGCTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (17 bp):
ACAAAAAATATTAACTT
Found at i:1197485 original size:28 final size:29
Alignment explanation
Indices: 1197446--1197504 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
1197436 CATATGAGAT
1197446 AATGGTTCAATTAAGTA-AAATAAA-AAA
1 AATGGTTCAATTAAGTATAAATAAATAAA
**
1197473 AATGAGTTCAATTGGGTATAAATAAATAAA
1 AATG-GTTCAATTAAGTATAAATAAATAAA
1197503 AA
1 AA
1197505 GAAACTTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 4 0.15
28 11 0.41
29 7 0.26
30 5 0.19
ACGTcount: A:0.56, C:0.03, G:0.14, T:0.27
Consensus pattern (29 bp):
AATGGTTCAATTAAGTATAAATAAATAAA
Found at i:1202314 original size:66 final size:66
Alignment explanation
Indices: 1202202--1202385 Score: 264
Period size: 66 Copynumber: 2.8 Consensus size: 66
1202192 CGGTAGCTGA
* * * *
1202202 AACTGAAATCCTGGAGCAACAATATGAGAATATCCTTCCACTTCAAATTGAAATTCCAGCAGC-C
1 AACTGAAATCCTGGAGCAGCAATATGGGAATATCCTTCCACCTCAAACTGAAATTCCAGCAGCTC
1202266 C
66 C
* * *
1202267 ACGCTGAAATCCTGGAGCAGCAATATGGGAATATCCTTCCACCTCAAACTGAAATTCCCGCTGCT
1 A-ACTGAAATCCTGGAGCAGCAATATGGGAATATCCTTCCACCTCAAACTGAAATTCCAGCAGCT
1202332 CC
65 CC
*
1202334 AACTGAAATCCTGAAGCAAG-AATATGGGAATATCCTTCCACCTCAAACTGAA
1 AACTGAAATCCTGGAGC-AGCAATATGGGAATATCCTTCCACCTCAAACTGAA
1202386 CAGGTTCAAC
Statistics
Matches: 107, Mismatches: 9, Indels: 5
0.88 0.07 0.04
Matches are distributed among these distances:
65 1 0.01
66 101 0.94
67 5 0.05
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (66 bp):
AACTGAAATCCTGGAGCAGCAATATGGGAATATCCTTCCACCTCAAACTGAAATTCCAGCAGCTC
C
Found at i:1202764 original size:57 final size:54
Alignment explanation
Indices: 1202625--1203055 Score: 529
Period size: 57 Copynumber: 7.9 Consensus size: 54
1202615 ATTCGGTGGG
* *
1202625 CCATGATCCTTTGAACATGCATCAGCAGCAGCTATTTTCAGGTGCCCCAAGCAT
1 CCATGATCCTTTGAACATGCATCAGCAGCAGCAATTTTCAGGTGCCCCAAACAT
* * *
1202679 CCATAATCCTTTGAACATGCATCAGCAGCAGCAATTTTCAAGTGTCCCAAACAT
1 CCATGATCCTTTGAACATGCATCAGCAGCAGCAATTTTCAGGTGCCCCAAACAT
*
1202733 CCATGATCCTTTGAATATGCTTCATCAGCAGCAGCAATTTTCAGGTGCCCCAAACAT
1 CCATGATCCTTTGAACATG---CATCAGCAGCAGCAATTTTCAGGTGCCCCAAACAT
* * * *
1202790 CCATAATCCTTTGAACATGCATCAGCAGCAGCAATTTTTAAGTGTCCCAAACAT
1 CCATGATCCTTTGAACATGCATCAGCAGCAGCAATTTTCAGGTGCCCCAAACAT
*
1202844 CCATGATCCTTTGAACATGTATCAGCAGCAGCAGCAATTTTCAGGTGCCCCAAACAT
1 CCATGATCCTTTGAACATG---CATCAGCAGCAGCAATTTTCAGGTGCCCCAAACAT
*
1202901 CCATGATCCTTTG-A-A--CAT-----GCAGCAATTTTCAGGCGCCCCAAACAT
1 CCATGATCCTTTGAACATGCATCAGCAGCAGCAATTTTCAGGTGCCCCAAACAT
* *
1202946 CCATGATCCTTTGAGCATGGATCAGCAGCAGCAGCAATTTTCAGGTGCCCCAAACAT
1 CCATGATCCTTTGAACAT-G--CATCAGCAGCAGCAATTTTCAGGTGCCCCAAACAT
* * * *
1203003 CAAGGCTCCTTTGAACATGCATCAGCAGGAGCAGCAATTTTCAGATGCCCCAA
1 CCATGATCCTTTGAACATGCATCAGC---AGCAGCAATTTTCAGGTGCCCCAA
1203056 GCATTACCGA
Statistics
Matches: 326, Mismatches: 30, Indels: 39
0.83 0.08 0.10
Matches are distributed among these distances:
45 39 0.12
47 1 0.00
50 2 0.01
52 2 0.01
54 122 0.37
55 1 0.00
56 2 0.01
57 157 0.48
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (54 bp):
CCATGATCCTTTGAACATGCATCAGCAGCAGCAATTTTCAGGTGCCCCAAACAT
Found at i:1202816 original size:111 final size:110
Alignment explanation
Indices: 1202625--1203045 Score: 567
Period size: 111 Copynumber: 3.9 Consensus size: 110
1202615 ATTCGGTGGG
* * *
1202625 CCATGATCCTTTGAACATG--CATCAGCAGCAGCTATTTTCAGGTGCCCCAAGCATCCATAATCC
1 CCATGATCCTTTGAACATGTTCAGCAGCAGCAGCAATTTTCAGGTGCCCCAAACATCCATAATCC
1202688 TTTGAACATGCATCAGCAGCAGCAATTTTCAAGTGTCCCAAACAT
66 TTTGAACATGCATCAGCAGCAGCAATTTTCAAGTGTCCCAAACAT
* *
1202733 CCATGATCCTTTGAATATGCTTCATCAGCAGCAGCAATTTTCAGGTGCCCCAAACATCCATAATC
1 CCATGATCCTTTGAACATG-TTCAGCAGCAGCAGCAATTTTCAGGTGCCCCAAACATCCATAATC
*
1202798 CTTTGAACATGCATCAGCAGCAGCAATTTTTAAGTGTCCCAAACAT
65 CTTTGAACATGCATCAGCAGCAGCAATTTTCAAGTGTCCCAAACAT
*
1202844 CCATGATCCTTTGAACATGTATCAGCAGCAGCAGCAATTTTCAGGTGCCCCAAACATCCATGATC
1 CCATGATCCTTTGAACATGT-TCAGCAGCAGCAGCAATTTTCAGGTGCCCCAAACATCCATAATC
* * *
1202909 CTTTG-A-A--CAT-----GCAGCAATTTTCAGGCGCCCCAAACAT
65 CTTTGAACATGCATCAGCAGCAGCAATTTTCAAGTGTCCCAAACAT
* * * ***
1202946 CCATGATCCTTTGAGCATGGATCAGCAGCAGCAGCAATTTTCAGGTGCCCCAAACATCAAGGCTC
1 CCATGATCCTTTGAACAT-GTTCAGCAGCAGCAGCAATTTTCAGGTGCCCCAAACATCCATAATC
1203011 CTTTGAACATGCATCAGCAGGAGCAGCAATTTTCA
65 CTTTGAACATGCATCAGC---AGCAGCAATTTTCA
1203046 GATGCCCCAA
Statistics
Matches: 280, Mismatches: 16, Indels: 28
0.86 0.05 0.09
Matches are distributed among these distances:
102 86 0.31
103 2 0.01
104 1 0.00
106 3 0.01
107 3 0.01
108 18 0.06
109 1 0.00
110 2 0.01
111 151 0.54
114 13 0.05
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (110 bp):
CCATGATCCTTTGAACATGTTCAGCAGCAGCAGCAATTTTCAGGTGCCCCAAACATCCATAATCC
TTTGAACATGCATCAGCAGCAGCAATTTTCAAGTGTCCCAAACAT
Found at i:1202939 original size:45 final size:45
Alignment explanation
Indices: 1202874--1202964 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
1202864 ATCAGCAGCA
*
1202874 GCAGCAATTTTCAGGTGCCCCAAACATCCATGATCCTTTGAACAT
1 GCAGCAATTTTCAGGCGCCCCAAACATCCATGATCCTTTGAACAT
*
1202919 GCAGCAATTTTCAGGCGCCCCAAACATCCATGATCCTTTGAGCAT
1 GCAGCAATTTTCAGGCGCCCCAAACATCCATGATCCTTTGAACAT
1202964 G
1 G
1202965 GATCAGCAGC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (45 bp):
GCAGCAATTTTCAGGCGCCCCAAACATCCATGATCCTTTGAACAT
Found at i:1202941 original size:102 final size:102
Alignment explanation
Indices: 1202706--1203023 Score: 431
Period size: 102 Copynumber: 3.0 Consensus size: 102
1202696 TGCATCAGCA
* *
1202706 GCAGCAATTTTCAAGTGTCCCAAACATCCATGATCCTTTGAATATGCT-TCATCAGCAGCAGCAA
1 GCAGCAATTTTCAAGTGTCCCAAACATCCATGATCCTTTGAACATG-TATCAGCAGCAGCAGCAA
*
1202770 TTTTCAGGTGCCCCAAACATCCATAATCCTTTGAACATGCAT
65 TTTTCAGGTGCCCCAAACATCCATGATCCTTTG-A-A--CAT
*
1202812 CAGCAGCAGCAATTTTTAAGTGTCCCAAACATCCATGATCCTTTGAACATGTATCAGCAGCAGCA
1 -----GCAGCAATTTTCAAGTGTCCCAAACATCCATGATCCTTTGAACATGTATCAGCAGCAGCA
1202877 GCAATTTTCAGGTGCCCCAAACATCCATGATCCTTTGAACAT
61 GCAATTTTCAGGTGCCCCAAACATCCATGATCCTTTGAACAT
* * * * *
1202919 GCAGCAATTTTCAGGCGCCCCAAACATCCATGATCCTTTGAGCATGGATCAGCAGCAGCAGCAAT
1 GCAGCAATTTTCAAGTGTCCCAAACATCCATGATCCTTTGAACATGTATCAGCAGCAGCAGCAAT
* * *
1202984 TTTCAGGTGCCCCAAACATCAAGGCTCCTTTGAACAT
66 TTTCAGGTGCCCCAAACATCCATGATCCTTTGAACAT
1203021 GCA
1 GCA
1203024 TCAGCAGGAG
Statistics
Matches: 193, Mismatches: 13, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
102 96 0.50
107 3 0.02
109 1 0.01
110 2 0.01
111 91 0.47
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (102 bp):
GCAGCAATTTTCAAGTGTCCCAAACATCCATGATCCTTTGAACATGTATCAGCAGCAGCAGCAAT
TTTCAGGTGCCCCAAACATCCATGATCCTTTGAACAT
Found at i:1203027 original size:159 final size:156
Alignment explanation
Indices: 1202763--1203055 Score: 442
Period size: 159 Copynumber: 1.9 Consensus size: 156
1202753 TTCATCAGCA
* *
1202763 GCAGCAATTTTCAGGTGCCCCAAACATCCATAATCCTTTGAACATGCATCAGCAGCAGCAATTTT
1 GCAGCAATTTTCAGGCGCCCCAAACATCCATAATCCTTTGAACATGCAGCAGCAGCAGCAATTTT
* * * * * *
1202828 TAAGTGTCCCAAACATCCATGATCCTTTGAACATGTATCAGCAGCAGCAGCAATTTTCAGGTGCC
66 CAAGTGCCCCAAACATCAAGGATCCTTTGAACATGCATCAGCAGCAGCAGCAATTTTCAGATGCC
1202893 CCAAACATCCATGATCCTTTGAACAT
131 CCAAACATCCATGATCCTTTGAACAT
* *
1202919 GCAGCAATTTTCAGGCGCCCCAAACATCCATGATCCTTTGAGCATGGATCAGCAGCAGCAGCAAT
1 GCAGCAATTTTCAGGCGCCCCAAACATCCATAATCCTTTGAACAT-G--CAGCAGCAGCAGCAAT
* * *
1202984 TTTCAGGTGCCCCAAACATCAAGGCTCCTTTGAACATGCATCAGCAGGAGCAGCAATTTTCAGAT
63 TTTCAAGTGCCCCAAACATCAAGGATCCTTTGAACATGCATCAGCAGCAGCAGCAATTTTCAGAT
1203049 GCCCCAA
128 GCCCCAA
1203056 GCATTACCGA
Statistics
Matches: 121, Mismatches: 13, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
156 42 0.35
157 1 0.01
159 78 0.64
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (156 bp):
GCAGCAATTTTCAGGCGCCCCAAACATCCATAATCCTTTGAACATGCAGCAGCAGCAGCAATTTT
CAAGTGCCCCAAACATCAAGGATCCTTTGAACATGCATCAGCAGCAGCAGCAATTTTCAGATGCC
CCAAACATCCATGATCCTTTGAACAT
Found at i:1227519 original size:16 final size:16
Alignment explanation
Indices: 1227494--1227530 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
1227484 CTTTTAAATG
1227494 ATTTTAAAGAAT-ATT
1 ATTTTAAAGAATAATT
1227509 ATTTCTAAAGAATAATT
1 ATTT-TAAAGAATAATT
1227526 ATTTT
1 ATTTT
1227531 TTGATACAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
16 9 0.45
17 7 0.35
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (16 bp):
ATTTTAAAGAATAATT
Found at i:1239132 original size:7 final size:7
Alignment explanation
Indices: 1239120--1239150 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
1239110 TCTTCTCTCC
1239120 CTCCTCT
1 CTCCTCT
1239127 CTCCTCT
1 CTCCTCT
1239134 CTCCTCT
1 CTCCTCT
1239141 CT-CTCT
1 CTCCTCT
1239147 CTCC
1 CTCC
1239151 ACACGTGCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (7 bp):
CTCCTCT
Found at i:1239136 original size:18 final size:20
Alignment explanation
Indices: 1239113--1239150 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1239103 CTCTTTGTCT
1239113 TCTCTCC-CTC-CTCTCTCC
1 TCTCTCCTCTCTCTCTCTCC
1239131 TCTCTCCTCTCTCTCTCTCC
1 TCTCTCCTCTCTCTCTCTCC
1239151 ACACGTGCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 3 0.17
20 8 0.44
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (20 bp):
TCTCTCCTCTCTCTCTCTCC
Found at i:1241470 original size:2 final size:2
Alignment explanation
Indices: 1241463--1241492 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1241453 TATGTTGATT
1241463 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1241493 ATGTTGCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1249085 original size:2 final size:2
Alignment explanation
Indices: 1249078--1249105 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1249068 GGATACATAG
1249078 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1249106 GAGAAAGCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1266563 original size:24 final size:24
Alignment explanation
Indices: 1266536--1266583 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1266526 TTATTTAAAA
*
1266536 ATGTTTAAATAAAATTTTTTTATT
1 ATGTTTAAATAAAATTTTTATATT
* * *
1266560 ATGTTTTAATTAAGTTTTTATATT
1 ATGTTTAAATAAAATTTTTATATT
1266584 TTTATTTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.60
Consensus pattern (24 bp):
ATGTTTAAATAAAATTTTTATATT
Found at i:1269644 original size:14 final size:14
Alignment explanation
Indices: 1269625--1269654 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1269615 GTTTGGTAAA
1269625 TTTTTTTTTATAAG
1 TTTTTTTTTATAAG
1269639 TTTTTTTTTATAAG
1 TTTTTTTTTATAAG
1269653 TT
1 TT
1269655 ATAGTTTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (14 bp):
TTTTTTTTTATAAG
Found at i:1269833 original size:15 final size:15
Alignment explanation
Indices: 1269815--1269866 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
1269805 CAAAGTTCTT
1269815 TTTTTAAAAATTTTA
1 TTTTTAAAAATTTTA
**
1269830 TTTTTAAAAAAATTA
1 TTTTTAAAAATTTTA
1269845 TTTTT-AAAATTTT-
1 TTTTTAAAAATTTTA
*
1269858 TTTTCAAAA
1 TTTTTAAAA
1269867 TTTATGTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
13 4 0.13
14 9 0.29
15 18 0.58
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTTTAAAAATTTTA
Found at i:1269861 original size:13 final size:13
Alignment explanation
Indices: 1269813--1269869 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
1269803 ACCAAAGTTC
*
1269813 TTTTTTTAAAAAT
1 TTTTTTTTAAAAT
*
1269826 TTTATTTTTAAAAAAA
1 TTT-TTTTT--AAAAT
*
1269842 TTATTTTTAAAAT
1 TTTTTTTTAAAAT
*
1269855 TTTTTTTCAAAAT
1 TTTTTTTTAAAAT
1269868 TT
1 TT
1269870 ATGTTTAACT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
13 20 0.57
14 4 0.11
15 5 0.14
16 6 0.17
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTTTTTAAAAT
Found at i:1269886 original size:26 final size:28
Alignment explanation
Indices: 1269821--1269888 Score: 70
Period size: 26 Copynumber: 2.5 Consensus size: 28
1269811 TCTTTTTTTA
*
1269821 AAAATTTTATTTTTAAAAAAATTATTTTT
1 AAAA-TTTATTTTTAAAAAAATTATGTTT
* *
1269850 AAAATTT-TTTTT-CAAAATTTATGTTT
1 AAAATTTATTTTTAAAAAAATTATGTTT
*
1269876 -AACTTTATTTTTA
1 AAAATTTATTTTTA
1269889 TTTTTAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
25 5 0.15
26 16 0.48
27 5 0.15
28 3 0.09
29 4 0.12
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.57
Consensus pattern (28 bp):
AAAATTTATTTTTAAAAAAATTATGTTT
Found at i:1285063 original size:18 final size:19
Alignment explanation
Indices: 1285040--1285079 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1285030 AACTCCTCAA
1285040 ACACACC-A-CCCACCAAAC
1 ACACACCTATCCC-CCAAAC
1285058 ACACACCTATCCCCCAAAC
1 ACACACCTATCCCCCAAAC
1285077 ACA
1 ACA
1285080 GAGAGCGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 10 0.50
20 3 0.15
ACGTcount: A:0.42, C:0.53, G:0.00, T:0.05
Consensus pattern (19 bp):
ACACACCTATCCCCCAAAC
Found at i:1287567 original size:13 final size:13
Alignment explanation
Indices: 1287549--1287574 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1287539 ACATTAGAAA
1287549 TAGAGATAACAGG
1 TAGAGATAACAGG
1287562 TAGAGATAACAGG
1 TAGAGATAACAGG
1287575 GCATGAACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.31, T:0.15
Consensus pattern (13 bp):
TAGAGATAACAGG
Found at i:1292786 original size:106 final size:108
Alignment explanation
Indices: 1292434--1292819 Score: 467
Period size: 106 Copynumber: 3.5 Consensus size: 108
1292424 GAACTCATTA
* * * * * *
1292434 ATGTTTGGGGCATCTGAAAATTGCTGCTCCTGCTTATGCATGTTCAAAGGAGCCTGGATGTTTGG
1 ATGTTTGGGACACCAGAAAATTGCTG---CTGCTGATGCATGTTCAAAGGATCATGGATGTTTGG
* *
1292499 GGCACCTGAAAATTGCTGCTGCTGCTGATCCATGTTCAAAGGATCATGG
63 GGCACTTGAAAA-T--TGCTGCTGCTGATGCATGTTCAAAGGATCATGG
* *
1292548 ATGTTTGGGACACTTA-AAAATTGCTGCTGCTGATGCTATCGCGTCAAAGGATCATGGATGTTTG
1 ATGTTTGGGACAC-CAGAAAATTGCTGCTGCTGATGC-AT-G-TTCAAAGGATCATGGATGTTTG
1292612 GGGCACTTG-AAATTGCTGCTGCTGATG-ATGCATTTCAAAGGATCATGG
62 GGGCACTTGAAAATTGCTGCTGCTGATGCATG---TTCAAAGGATCATGG
** *
1292660 ATGTTTGGGACACTTGAAAATTGCTGCTGCTGATGCATGTTCAAAGGATTATGGATG-TT-GGGC
1 ATGTTTGGGACACCAGAAAATTGCTGCTGCTGATGCATGTTCAAAGGATCATGGATGTTTGGGGC
*
1292723 ACTTGAAAATTGCTGCTGCTGATGCATGTTCAAAGGATTATGG
66 ACTTGAAAATTGCTGCTGCTGATGCATGTTCAAAGGATCATGG
* * *
1292766 ATGCTTGGGGCACCAGAAAATAGCTGCTGCTGATGCATGTTCAAAGGATCATGG
1 ATGTTTGGGACACCAGAAAATTGCTGCTGCTGATGCATGTTCAAAGGATCATGG
1292820 CCCACCGAAT
Statistics
Matches: 242, Mismatches: 20, Indels: 28
0.83 0.07 0.10
Matches are distributed among these distances:
106 62 0.26
107 9 0.04
108 20 0.08
109 22 0.09
110 14 0.06
111 12 0.05
112 51 0.21
113 4 0.02
114 48 0.20
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.31
Consensus pattern (108 bp):
ATGTTTGGGACACCAGAAAATTGCTGCTGCTGATGCATGTTCAAAGGATCATGGATGTTTGGGGC
ACTTGAAAATTGCTGCTGCTGATGCATGTTCAAAGGATCATGG
Found at i:1292801 original size:54 final size:54
Alignment explanation
Indices: 1292434--1292819 Score: 485
Period size: 57 Copynumber: 7.0 Consensus size: 54
1292424 GAACTCATTA
* * *
1292434 ATGTTTGGGGCA-TCTGAAAATTGCTGCTCCTGCTTATGCATGTTCAAAGGAGCCTGG
1 ATGTTTGGGGCACT-TGAAAATTGCTG---CTGCTGATGCATGTTCAAAGGATCATGG
* *
1292491 ATGTTTGGGGCACCTGAAAATTGCTGCTGCTGCTGATCCATGTTCAAAGGATCATGG
1 ATGTTTGGGGCACTTGAAAA-T--TGCTGCTGCTGATGCATGTTCAAAGGATCATGG
* * *
1292548 ATGTTTGGGACACTTAAAAATTGCTGCTGCTGATGCTATCGCGTCAAAGGATCATGG
1 ATGTTTGGGGCACTTGAAAATTGCTGCTGCTGATGC-AT-G-TTCAAAGGATCATGG
1292605 ATGTTTGGGGCACTTG-AAATTGCTGCTGCTGATG-ATGCATTTCAAAGGATCATGG
1 ATGTTTGGGGCACTTGAAAATTGCTGCTGCTGATGCATG---TTCAAAGGATCATGG
* *
1292660 ATGTTTGGGACACTTGAAAATTGCTGCTGCTGATGCATGTTCAAAGGATTATGG
1 ATGTTTGGGGCACTTGAAAATTGCTGCTGCTGATGCATGTTCAAAGGATCATGG
*
1292714 ATG-TT-GGGCACTTGAAAATTGCTGCTGCTGATGCATGTTCAAAGGATTATGG
1 ATGTTTGGGGCACTTGAAAATTGCTGCTGCTGATGCATGTTCAAAGGATCATGG
* ** *
1292766 ATGCTTGGGGCACCAGAAAATAGCTGCTGCTGATGCATGTTCAAAGGATCATGG
1 ATGTTTGGGGCACTTGAAAATTGCTGCTGCTGATGCATGTTCAAAGGATCATGG
1292820 CCCACCGAAT
Statistics
Matches: 295, Mismatches: 21, Indels: 29
0.86 0.06 0.08
Matches are distributed among these distances:
52 49 0.17
53 5 0.02
54 76 0.26
55 31 0.11
56 38 0.13
57 90 0.31
58 1 0.00
60 5 0.02
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.31
Consensus pattern (54 bp):
ATGTTTGGGGCACTTGAAAATTGCTGCTGCTGATGCATGTTCAAAGGATCATGG
Found at i:1293194 original size:62 final size:64
Alignment explanation
Indices: 1293054--1293199 Score: 169
Period size: 62 Copynumber: 2.3 Consensus size: 64
1293044 GTTGAACCTG
* *
1293054 TTCAGTTTG-AGTGGAAGGATATTCCCATATCTGCTTCAGGATTTCAGTTGGAGCAGCGGGAAT
1 TTCAGTTTGAAGTGGAAGGATATTCCCATATCTGCTCCAGGATTTCAGGTGGAGCAGCGGGAAT
* * *
1293117 TTCAGTTTGAGGTGGAAGGATA-T-CCATATTGCTGCTCCAGGATTTCAGCGT-G-GCTGC-TGA
1 TTCAGTTTGAAGTGGAAGGATATTCCCATA-T-CTGCTCCAGGATTTCAG-GTGGAGCAGCGGGA
1293177 AT
63 AT
*
1293179 TTCAATTTGAAGTGGAAGGAT
1 TTCAGTTTGAAGTGGAAGGAT
1293200 TTCTCATTCA
Statistics
Matches: 72, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
62 28 0.39
63 15 0.21
64 28 0.39
65 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.32
Consensus pattern (64 bp):
TTCAGTTTGAAGTGGAAGGATATTCCCATATCTGCTCCAGGATTTCAGGTGGAGCAGCGGGAAT
Found at i:1300296 original size:23 final size:25
Alignment explanation
Indices: 1300270--1300316 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
1300260 AAATAATATA
*
1300270 AAAAGAAA-ATTTTTAAT-TTTTAC
1 AAAAGAAATATTTTAAATATTTTAC
*
1300293 AAAATAAATATTTTAAATATTTTA
1 AAAAGAAATATTTTAAATATTTTA
1300317 ATTTATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.35
24 8 0.40
25 5 0.25
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
AAAAGAAATATTTTAAATATTTTAC
Found at i:1306589 original size:17 final size:18
Alignment explanation
Indices: 1306567--1306608 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
1306557 ATTGAAGATG
*
1306567 ATTAAATTTTCA-TTAAA
1 ATTAAATATTCATTTAAA
*
1306584 ATTAAAAATTCATTTAAA
1 ATTAAATATTCATTTAAA
*
1306602 TTTAAAT
1 ATTAAAT
1306609 CAAAATTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTAAATATTCATTTAAA
Found at i:1306716 original size:2 final size:2
Alignment explanation
Indices: 1306709--1306734 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1306699 TTATCAATTC
1306709 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1306735 CATTTATGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1307295 original size:21 final size:21
Alignment explanation
Indices: 1307271--1307319 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
1307261 ACCGTATAAC
* *
1307271 ATAAAAATGACAAATAATATT
1 ATAAAAATAACAAATAAAATT
* *
1307292 ATAATAATAACAATTAAAATT
1 ATAAAAATAACAAATAAAATT
1307313 A-AAAAAT
1 ATAAAAAT
1307320 TAAATTATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (21 bp):
ATAAAAATAACAAATAAAATT
Found at i:1326986 original size:50 final size:50
Alignment explanation
Indices: 1326924--1327036 Score: 208
Period size: 50 Copynumber: 2.3 Consensus size: 50
1326914 CTCCTCCAGA
* *
1326924 AGGTTCTTCAATCCATTTCTCTAGTATATGCTGATTACTATATAAAATCC
1 AGGTTCTTCAATCCATTTCTCTAGTATATACTGATTACTATATAAAAGCC
1326974 AGGTTCTTCAATCCATTTCTCTAGTATATACTGATTACTATATAAAAGCC
1 AGGTTCTTCAATCCATTTCTCTAGTATATACTGATTACTATATAAAAGCC
1327024 AGGTTCTTCAATC
1 AGGTTCTTCAATC
1327037 AGTACTTCCA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 61 1.00
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (50 bp):
AGGTTCTTCAATCCATTTCTCTAGTATATACTGATTACTATATAAAAGCC
Found at i:1331306 original size:2 final size:2
Alignment explanation
Indices: 1331299--1331349 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
1331289 TTCTTCACTA
* *
1331299 CT CT CT CT GT CT TT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1331341 CT CT CT CT C
1 CT CT CT CT C
1331350 CATTCTTTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.47, G:0.02, T:0.51
Consensus pattern (2 bp):
CT
Found at i:1331309 original size:22 final size:22
Alignment explanation
Indices: 1331284--1331349 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
1331274 TCATATACCT
1331284 TGTCCTTCT-TCACTACTCTCTC
1 TGTCCTTCTCTCACT-CTCTCTC
* *
1331306 TGTCTTTCTCTCTCTCTCTCTC
1 TGTCCTTCTCTCACTCTCTCTC
* *
1331328 TCT-CTCTCTCTCTCTCTCTCTC
1 TGTCCT-TCTCTCACTCTCTCTC
1331350 CATTCTTTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.03
22 33 0.87
23 4 0.11
ACGTcount: A:0.03, C:0.44, G:0.03, T:0.50
Consensus pattern (22 bp):
TGTCCTTCTCTCACTCTCTCTC
Found at i:1332075 original size:24 final size:24
Alignment explanation
Indices: 1332043--1332095 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
1332033 GGAACTCTAG
1332043 TGTTGGTGAATTTGGTTCAGAAGA
1 TGTTGGTGAATTTGGTTCAGAAGA
1332067 TGTTGGTGAATTTGGTTCAGAAGA
1 TGTTGGTGAATTTGGTTCAGAAGA
1332091 TGTTG
1 TGTTG
1332096 ATAAAAAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.23, C:0.04, G:0.34, T:0.40
Consensus pattern (24 bp):
TGTTGGTGAATTTGGTTCAGAAGA
Found at i:1334260 original size:7 final size:6
Alignment explanation
Indices: 1334238--1334315 Score: 54
Period size: 6 Copynumber: 12.8 Consensus size: 6
1334228 ATACGCTACT
*
1334238 GAAAAA -AAAAGA GAAAAA TGAAAAA GAAAAA -AAAAA GCAGAAA GAAAAA
1 GAAAAA GAAAA-A GAAAAA -GAAAAA GAAAAA GAAAAA G-AAAAA GAAAAA
* * * *
1334287 -AAAAA GTCAAAA CAAAAG GAAAAA TAAAA
1 GAAAAA G-AAAAA GAAAAA GAAAAA GAAAA
1334316 GAATGAGTAT
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
5 14 0.25
6 23 0.41
7 19 0.34
ACGTcount: A:0.78, C:0.04, G:0.14, T:0.04
Consensus pattern (6 bp):
GAAAAA
Found at i:1334272 original size:18 final size:18
Alignment explanation
Indices: 1334237--1334291 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
1334227 GATACGCTAC
1334237 TGAAAAA-AAAAGAGAAAAA
1 TGAAAAAGAAAA-A-AAAAA
1334256 TGAAAAAGAAAAAAAAAA
1 TGAAAAAGAAAAAAAAAA
*
1334274 -GCAGAAAGAAAAAAAAAA
1 TG-AAAAAGAAAAAAAAAA
1334292 GTCAAAACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
17 1 0.03
18 20 0.61
19 8 0.24
20 4 0.12
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.04
Consensus pattern (18 bp):
TGAAAAAGAAAAAAAAAA
Found at i:1334273 original size:19 final size:19
Alignment explanation
Indices: 1334237--1334291 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
1334227 GATACGCTAC
*
1334237 TGAAAAA-AAAAGAGAAAAA
1 TGAAAAAGAAAA-AAAAAAA
1334256 TGAAAAAG-AAAAAAAAAA
1 TGAAAAAGAAAAAAAAAAA
*
1334274 -GCAGAAAGAAAAAAAAAA
1 TG-AAAAAGAAAAAAAAAA
1334292 GTCAAAACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
17 1 0.03
18 11 0.35
19 19 0.61
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.04
Consensus pattern (19 bp):
TGAAAAAGAAAAAAAAAAA
Found at i:1334288 original size:27 final size:26
Alignment explanation
Indices: 1334239--1334315 Score: 75
Period size: 26 Copynumber: 2.8 Consensus size: 26
1334229 TACGCTACTG
*
1334239 AAAAAAAAAGAGAAAAATGAAAAAGA
1 AAAAAAAAAGAGAAAAATAAAAAAGA
* *
1334265 AAAAAAAAAGCAGAAAGAAAAAAAAAAGTC
1 AAAAAAAAAG-AG-AA-AAATAAAAAAG-A
*
1334295 AAAACAAAAG-GAAAAATAAAA
1 AAAAAAAAAGAGAAAAATAAAA
1334316 GAATGAGTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
26 17 0.40
27 4 0.10
28 3 0.07
29 9 0.21
30 9 0.21
ACGTcount: A:0.79, C:0.04, G:0.13, T:0.04
Consensus pattern (26 bp):
AAAAAAAAAGAGAAAAATAAAAAAGA
Found at i:1334303 original size:18 final size:17
Alignment explanation
Indices: 1334259--1334303 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
1334249 AGAAAAATGA
1334259 AAAAGAAAAAAAAAAGC
1 AAAAGAAAAAAAAAAGC
1334276 AGAAAGAAAAAAAAAAGTC
1 A-AAAGAAAAAAAAAAG-C
*
1334295 AAAACAAAA
1 AAAAGAAAA
1334304 GGAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 1 0.04
18 22 0.88
19 2 0.08
ACGTcount: A:0.80, C:0.07, G:0.11, T:0.02
Consensus pattern (17 bp):
AAAAGAAAAAAAAAAGC
Found at i:1335161 original size:14 final size:14
Alignment explanation
Indices: 1335142--1335175 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1335132 TGCTATTTTC
1335142 ATTAAAAATTTAAT
1 ATTAAAAATTTAAT
*
1335156 ATTAAAAATTTATT
1 ATTAAAAATTTAAT
1335170 ATTAAA
1 ATTAAA
1335176 TTATTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTAAAAATTTAAT
Found at i:1335858 original size:24 final size:24
Alignment explanation
Indices: 1335826--1335894 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
1335816 ACAAATTTAT
* *
1335826 TTTAAATTATATAAGAATTAAACA
1 TTTAAATTATAAAAAAATTAAACA
*
1335850 TTTATATTATAAAAAAATTAAA-A
1 TTTAAATTATAAAAAAATTAAACA
* *
1335873 -TTAAAATATAAAATATATTAAA
1 TTTAAATTATAAAA-AAATTAAA
1335895 ATTAAAGTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
22 11 0.29
23 8 0.21
24 19 0.50
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (24 bp):
TTTAAATTATAAAAAAATTAAACA
Found at i:1335895 original size:23 final size:22
Alignment explanation
Indices: 1335857--1335900 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
1335847 ACATTTATAT
1335857 TATAAAAAAATTAAAATTAAAA
1 TATAAAAAAATTAAAATTAAAA
*
1335879 TATAAAATATATTAAAATTAAA
1 TATAAAA-AAATTAAAATTAAA
1335901 GTTTTTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
TATAAAAAAATTAAAATTAAAA
Found at i:1346627 original size:2 final size:2
Alignment explanation
Indices: 1346620--1346657 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1346610 CTAAAGGATT
1346620 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1346658 ATGTCATGGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1349345 original size:22 final size:24
Alignment explanation
Indices: 1349305--1349368 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 24
1349295 TGTAATGAAT
*
1349305 TAAATTTTTAT-TTTAAATT-A-AA
1 TAAATTTTTATAATT-AATTAATAA
1349327 TAAATTTTTATAATTAATTAATAA
1 TAAATTTTTATAATTAATTAATAA
*
1349351 TTAATTTTTATTAATTAA
1 TAAATTTTTA-TAATTAA
1349369 AATATTATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
22 15 0.42
23 3 0.08
24 11 0.31
25 7 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TAAATTTTTATAATTAATTAATAA
Found at i:1349380 original size:22 final size:21
Alignment explanation
Indices: 1349330--1349384 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
1349320 AATTAAATAA
*
1349330 ATTTTTATAATTAATTAATAATT
1 ATTTTT-T-ATTAATTAAAAATT
*
1349353 AATTTTTATTAATTAAAATATT
1 ATTTTTTATTAATTAAAA-ATT
1349375 ATTTTTTATT
1 ATTTTTTATT
1349385 TTGTACTCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 10 0.36
22 13 0.46
23 5 0.18
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTTATTAATTAAAAATT
Found at i:1349761 original size:18 final size:18
Alignment explanation
Indices: 1349738--1349772 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1349728 AAAGAAATAG
1349738 AAAAAATAGAAA-ATTTTA
1 AAAAAATA-AAAGATTTTA
1349756 AAAAAATAAAAGATTTT
1 AAAAAATAAAAGATTTT
1349773 GAGTGTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (18 bp):
AAAAAATAAAAGATTTTA
Found at i:1351194 original size:2 final size:2
Alignment explanation
Indices: 1351189--1351225 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1351179 TGTGACTGGA
1351189 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1351226 GTTTTAGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1353707 original size:17 final size:18
Alignment explanation
Indices: 1353676--1353718 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1353666 ACTTGTTTAT
1353676 TTATTTCTTTAATATATTA
1 TTATTT-TTTAATATATTA
* *
1353695 TTATTTTTT-ATATTTTT
1 TTATTTTTTAATATATTA
1353712 TTATTTT
1 TTATTTT
1353719 GAATTAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 13 0.59
18 3 0.14
19 6 0.27
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (18 bp):
TTATTTTTTAATATATTA
Found at i:1354861 original size:15 final size:15
Alignment explanation
Indices: 1354841--1354897 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
1354831 TTTACAATGC
* *
1354841 AATGTGATTACAGGT
1 AATGTGATTGCAAGT
*
1354856 AATGTGATTGTAAGT
1 AATGTGATTGCAAGT
* *
1354871 AATGTGATTCCAAGC
1 AATGTGATTGCAAGT
1354886 AATGTGATTGCA
1 AATGTGATTGCA
1354898 GGAAAAATAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.33, C:0.09, G:0.25, T:0.33
Consensus pattern (15 bp):
AATGTGATTGCAAGT
Found at i:1355266 original size:33 final size:35
Alignment explanation
Indices: 1355228--1355304 Score: 99
Period size: 33 Copynumber: 2.3 Consensus size: 35
1355218 TATTATATAA
* *
1355228 ATTTTAATTTTTTATATT-T-TATTTTATTTTAAT
1 ATTTTTATTTTTTAAATTATATATTTTATTTTAAT
*
1355261 -TTTTTA-TTCTTAAATTATATATTTTATTTTAAT
1 ATTTTTATTTTTTAAATTATATATTTTATTTTAAT
1355294 ATTTTTATTTT
1 ATTTTTATTTT
1355305 AATTATAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
31 8 0.22
32 6 0.17
33 14 0.39
34 6 0.17
35 2 0.06
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.71
Consensus pattern (35 bp):
ATTTTTATTTTTTAAATTATATATTTTATTTTAAT
Found at i:1355301 original size:14 final size:14
Alignment explanation
Indices: 1355228--1355307 Score: 62
Period size: 14 Copynumber: 5.6 Consensus size: 14
1355218 TATTATATAA
1355228 ATTTTAAT-TTTTT
1 ATTTTAATATTTTT
1355241 ATATTT--TA-TTTT
1 AT-TTTAATATTTTT
1355253 ATTTTAAT-TTTTT
1 ATTTTAATATTTTT
1355266 ATTCTTAAATTATATATTTT
1 ATT-TT--A--ATAT-TTTT
1355286 ATTTTAATATTTTT
1 ATTTTAATATTTTT
1355300 ATTTTAAT
1 ATTTTAAT
1355308 TATAACATTA
Statistics
Matches: 55, Mismatches: 0, Indels: 23
0.71 0.00 0.29
Matches are distributed among these distances:
11 3 0.05
12 7 0.13
13 10 0.18
14 17 0.31
15 4 0.07
16 1 0.02
17 1 0.02
18 2 0.04
19 3 0.05
20 7 0.13
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (14 bp):
ATTTTAATATTTTT
Found at i:1371851 original size:71 final size:69
Alignment explanation
Indices: 1371659--1371864 Score: 234
Period size: 71 Copynumber: 2.9 Consensus size: 69
1371649 GAAGCAAATG
* * *
1371659 AAATCTCCATGAATTGAGCTAATTAATTTGATGTTGAAATGG-GTTGGAAAGTAAAGAAGAGGAA
1 AAATCTCCATGACTTGAGCTAATAAATTTGATATTGAAATGGAG--GGAAAGTAAAGAAGAGGAA
*
1371723 GCTCCC
64 CCTCCC
* * **
1371729 AAATCTCCATGACTTGAGCTAGTACATTTGATATTGAAATTAAGGGAGAAAGTAAAGAAGAGGAA
1 AAATCTCCATGACTTGAGCTAATAAATTTGATATTGAAATGGA-GG-GAAAGTAAAGAAGAGGAA
1371794 CCTCCC
64 CCTCCC
* * * * *
1371800 AAAAATCTCGATGACTTGACCTAATAAATTGGATATTAAAATGGAGGGAAAGGAAAGAAGAGGAA
1 --AAATCTCCATGACTTGAGCTAATAAATTTGATATTGAAATGGAGGGAAAGTAAAGAAGAGGAA
1371865 GAAGCTCCCA
Statistics
Matches: 114, Mismatches: 17, Indels: 9
0.81 0.12 0.06
Matches are distributed among these distances:
70 36 0.32
71 40 0.35
72 3 0.03
73 35 0.31
ACGTcount: A:0.41, C:0.12, G:0.23, T:0.24
Consensus pattern (69 bp):
AAATCTCCATGACTTGAGCTAATAAATTTGATATTGAAATGGAGGGAAAGTAAAGAAGAGGAACC
TCCC
Found at i:1375960 original size:8 final size:8
Alignment explanation
Indices: 1375947--1375978 Score: 50
Period size: 7 Copynumber: 4.2 Consensus size: 8
1375937 ATAAGCAACC
1375947 ATTTTTTT
1 ATTTTTTT
1375955 A-TTTTTT
1 ATTTTTTT
1375962 A-TTTTTT
1 ATTTTTTT
1375969 ATTTTTTT
1 ATTTTTTT
1375977 AT
1 AT
1375979 GTTGGGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 14 0.61
8 9 0.39
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (8 bp):
ATTTTTTT
Found at i:1375966 original size:6 final size:7
Alignment explanation
Indices: 1375949--1375975 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1375939 AAGCAACCAT
1375949 TTTTTTA
1 TTTTTTA
1375956 TTTTTTA
1 TTTTTTA
1375963 TTTTTTA
1 TTTTTTA
1375970 TTTTTT
1 TTTTTT
1375976 TATGTTGGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTA
Found at i:1378973 original size:2 final size:2
Alignment explanation
Indices: 1378966--1378993 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1378956 ATATACTGTA
1378966 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1378994 TGCTGTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1383510 original size:15 final size:15
Alignment explanation
Indices: 1383460--1383511 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
1383450 ACATTACAAT
* *
1383460 GCAATGTGATTACAG
1 GCAATGTGATTGCAA
* *
1383475 GTAATATGATTGCAA
1 GCAATGTGATTGCAA
*
1383490 GTAATGTGATTGCAA
1 GCAATGTGATTGCAA
1383505 GCAATGT
1 GCAATGT
1383512 AATTACAGGG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.31
Consensus pattern (15 bp):
GCAATGTGATTGCAA
Found at i:1383719 original size:13 final size:12
Alignment explanation
Indices: 1383702--1383734 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1383692 AATTTTTATA
1383702 TAATATCATTTT
1 TAATATCATTTT
1383714 TAAATAT-ATTTT
1 T-AATATCATTTT
1383726 TAATATCAT
1 TAATATCAT
1383735 ATATTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 5 0.26
12 9 0.47
13 5 0.26
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (12 bp):
TAATATCATTTT
Found at i:1383763 original size:33 final size:34
Alignment explanation
Indices: 1383709--1383790 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 34
1383699 ATATAATATC
1383709 ATTTTTAAATATATT-TT-TAATATCATATATTTT
1 ATTTTT-AATATATTATTATAATATCATATATTTT
* **
1383742 ATTTTT-ATTTATTATTATAATATTTTATATTTT
1 ATTTTTAATATATTATTATAATATCATATATTTT
1383775 ATTTTTAATATATTAT
1 ATTTTTAATATATTAT
1383791 ATTTTTTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
31 6 0.14
32 2 0.05
33 26 0.62
34 8 0.19
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (34 bp):
ATTTTTAATATATTATTATAATATCATATATTTT
Found at i:1383804 original size:24 final size:25
Alignment explanation
Indices: 1383690--1383819 Score: 68
Period size: 26 Copynumber: 4.9 Consensus size: 25
1383680 TTTGTTATTA
*
1383690 TTAATTTTTATATAATATCATTTTT
1 TTAATTTTAATATAATATCATTTTT
* *
1383715 AAATATATTTTTAATATCATATAT-TTTATTT
1 ---T-TAATTTTAATAT-A-ATATCATT-TTT
* * *
1383746 TTATTTATTATTATAATAT-TTTATATT
1 TTAATT-TTAATATAATATCATT-T-TT
* *
1383773 TTATTTTTAATATATTAT-ATTTTT
1 TTAATTTTAATATAATATCATTTTT
*
1383797 TTAATTTTTATATAATATCATTT
1 TTAATTTTAATATAATATCATTT
1383820 CTTAAATATA
Statistics
Matches: 85, Mismatches: 10, Indels: 17
0.76 0.09 0.15
Matches are distributed among these distances:
24 17 0.20
25 5 0.06
26 21 0.25
27 14 0.16
28 8 0.09
29 10 0.12
30 3 0.04
31 7 0.08
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (25 bp):
TTAATTTTAATATAATATCATTTTT
Found at i:1383809 original size:17 final size:18
Alignment explanation
Indices: 1383717--1383801 Score: 54
Period size: 18 Copynumber: 4.7 Consensus size: 18
1383707 TCATTTTTAA
*
1383717 ATATATTTTTAATATCA-T
1 ATATTTTTTTAATAT-ATT
1383735 ATATTTTATTT--T-TATT
1 ATATTTT-TTTAATATATT
* * *
1383751 -TATTATTATAATATTTT
1 ATATTTTTTTAATATATT
1383768 ATATTTTATTTTTAATATATT
1 ATA--TT-TTTTTAATATATT
1383789 ATATTTTTTTAAT
1 ATATTTTTTTAAT
1383802 TTTTATATAA
Statistics
Matches: 51, Mismatches: 7, Indels: 18
0.67 0.09 0.24
Matches are distributed among these distances:
14 2 0.04
15 6 0.12
16 3 0.06
17 4 0.08
18 16 0.31
19 5 0.10
20 2 0.04
21 13 0.25
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (18 bp):
ATATTTTTTTAATATATT
Found at i:1383824 original size:24 final size:25
Alignment explanation
Indices: 1383690--1383824 Score: 64
Period size: 28 Copynumber: 5.2 Consensus size: 25
1383680 TTTGTTATTA
1383690 TTAATTTTT-ATATAATATCATTTT-
1 TTAATTTTTAATATAATAT-ATTTTC
* *
1383714 TAAATATATTTTTAATATCATATATTTTATT
1 T---TA-ATTTTTAATATAATATA-TTT-TC
* * *
1383745 TTTATTTATTATTATAATAT-TTTATAT
1 TTAATTT-TTAATATAATATATTT-T-C
* * *
1383772 TTTATTTTTAATATATTATATTTTT
1 TTAATTTTTAATATAATATATTTTC
1383797 TTAATTTTT-ATATAATATCA-TTTC
1 TTAATTTTTAATATAATAT-ATTTTC
1383821 TTAA
1 TTAA
1383825 ATATATTTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 24
0.73 0.07 0.20
Matches are distributed among these distances:
24 16 0.18
25 10 0.11
26 16 0.18
27 17 0.19
28 18 0.20
29 11 0.12
30 1 0.01
31 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (25 bp):
TTAATTTTTAATATAATATATTTTC
Found at i:1383879 original size:32 final size:29
Alignment explanation
Indices: 1383842--1384028 Score: 96
Period size: 26 Copynumber: 6.6 Consensus size: 29
1383832 TTTAATATCA
1383842 TATATTTTATTTTTATTTATTATTATAATATT
1 TATATTTTATTTTTATTTA-TATT-T-ATATT
1383874 TATATTTTA--TTT-TTTATATTTATATT
1 TATATTTTATTTTTATTTATATTTATATT
* * *
1383900 TATATTATTAATTTTTATATA-ATATCATTTCT
1 TATATT-TT-ATTTTTATTTATAT-TTATAT-T
* * * *
1383932 TA-AATATATTTTTA---ATGTCATATATT
1 TATATTTTATTTTTATTTATAT-TTATATT
*
1383958 TAT-TTTTATTTATTA-TTATA-ATAT-TT
1 TATATTTTATTT-TTATTTATATTTATATT
*
1383984 TATATTTTA-TTTTA-ATATATTTATATT
1 TATATTTTATTTTTATTTATATTTATATT
1384011 TATATTATTAATTTTTAT
1 TATATT-TT-ATTTTTAT
1384029 ATAATATCAT
Statistics
Matches: 121, Mismatches: 15, Indels: 39
0.69 0.09 0.22
Matches are distributed among these distances:
25 7 0.06
26 31 0.26
27 27 0.22
28 7 0.06
29 14 0.12
30 14 0.12
31 9 0.07
32 12 0.10
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.65
Consensus pattern (29 bp):
TATATTTTATTTTTATTTATATTTATATT
Found at i:1383894 original size:20 final size:21
Alignment explanation
Indices: 1383849--1384030 Score: 108
Period size: 21 Copynumber: 8.4 Consensus size: 21
1383839 TCATATATTT
*
1383849 TATTTTTATTTATTATTA-TAA
1 TATTTATATTTA-TATTATTAA
* *
1383870 TATTTATATTT-TATTTTTTA
1 TATTTATATTTATATTATTAA
1383890 TATTTATATTTATATTATTAA
1 TATTTATATTTATATTATTAA
* * *
1383911 TTTTTATATAATATCATTTCTTAA
1 TATTTATAT-TTAT-A-TTATTAA
* * *
1383935 -ATATATTTTTA-ATGTCATATATT
1 TATTTATATTTATAT-T-AT-TA-A
*
1383958 TATTTTTATTTATTATTA-TAA
1 TATTTATATTTA-TATTATTAA
1383979 TATTTTATATTT-TATT-TTAATA
1 TA-TTTATATTTATATTATT-A-A
1384001 TATTTATATTTATATTATTAA
1 TATTTATATTTATATTATTAA
*
1384022 TTTTTATAT
1 TATTTATAT
1384031 AATATCATAT
Statistics
Matches: 123, Mismatches: 20, Indels: 36
0.69 0.11 0.20
Matches are distributed among these distances:
19 5 0.04
20 20 0.16
21 47 0.38
22 25 0.20
23 8 0.07
24 15 0.12
25 1 0.01
26 2 0.02
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.65
Consensus pattern (21 bp):
TATTTATATTTATATTATTAA
Found at i:1384060 original size:111 final size:112
Alignment explanation
Indices: 1383665--1384090 Score: 703
Period size: 111 Copynumber: 3.9 Consensus size: 112
1383655 AAAATATAAG
*
1383665 TTTAATATATTTATATTTGTTATTATTAATTTTTATATAATATCATTT-TTAAATATATTTTTAA
1 TTTAATATATTTATATTT-ATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
1383729 TATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
65 TATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTA-T
1383778 TTTAATATA-TTATA-TT-T-TT-TTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
1 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
1383838 ATCATATATTTTATTTTTATTTATTATTATAATA-TTTATATTTTAT
66 ATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTAT
*
1383884 TTT-TTATATTTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
1 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
*
1383948 GTCATATA-TTTATTTTTATTTATTATTATAATATTTTATATTTTAT
66 ATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTAT
*
1383994 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATT-TTAAATATATTTTAAA
1 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCAT-TTCTTAAATATATTTTTAA
*
1384058 TGTCATATATTTTATTTTTATTTATTA-TATAAT
65 TATCATATATTTTATTTTTATTTATTATTATAAT
1384091 TTATATTTTT
Statistics
Matches: 299, Mismatches: 4, Indels: 22
0.92 0.01 0.07
Matches are distributed among these distances:
105 4 0.01
106 9 0.03
107 36 0.12
108 54 0.18
109 28 0.09
110 63 0.21
111 72 0.24
112 24 0.08
113 9 0.03
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (112 bp):
TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
ATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTAT
Found at i:1384079 original size:27 final size:26
Alignment explanation
Indices: 1383720--1384100 Score: 138
Period size: 27 Copynumber: 14.0 Consensus size: 26
1383710 TTTTTAAATA
*
1383720 TATTTTTAATATCATATATTTTATTTT
1 TATTTTAAATAT-ATATATTTTATTTT
* *
1383747 TATTTATTATTATA-ATATTTTATATTT
1 TATTT-TAAATATATATATTTTAT-TTT
*
1383774 TATTTTTAATATAT-TATATTT-TTTT
1 TATTTTAAATATATATAT-TTTATTTT
* * ** *
1383799 AATTTT-TATATAATATCATTTCTTAAATA
1 TATTTTAAATAT-ATAT-A-TT-TTATTTT
*
1383828 TATTTTTAATATCATATATTTTATTTT
1 TATTTTAAATAT-ATATATTTTATTTT
* *
1383855 TATTTATTATTATA-ATA-TTTATATTT
1 TATTT-TAAATATATATATTTTAT-TTT
** *
1383881 TATTTTTTATATTTATATTTATATTATT
1 TATTTTAAATATATATATTT-TATT-TT
* * ** *
1383909 AATTTT-TATATAATATCATTTCTTAAATA
1 TATTTTAAATAT-ATAT-A-TT-TTATTTT
* *
1383938 TATTTTTAATGTCATATA-TTTATTTT
1 TATTTTAAATAT-ATATATTTTATTTT
* *
1383964 TATTTATTATTATA-ATATTTTATATTT
1 TATTT-TAAATATATATATTTTAT-TTT
*
1383991 TATTTTAATATATTTATATTTATATTATT
1 TATTTTAA-ATATATATATTT-TATT-TT
* * ** *
1384020 AATTTTTATATAATATCATATTTTAAATA
1 TA-TTTTAAAT-ATAT-ATATTTTATTTT
*
1384049 TATTTTAAATGTCATATATTTTATTTT
1 TATTTTAAATAT-ATATATTTTATTTT
*
1384076 TA-TTT-ATTATATA-ATTTATATTTT
1 TATTTTAAATATATATATTT-TATTTT
1384100 T
1 T
1384101 TTCATTTCTT
Statistics
Matches: 272, Mismatches: 48, Indels: 71
0.70 0.12 0.18
Matches are distributed among these distances:
23 4 0.01
24 14 0.05
25 26 0.10
26 55 0.20
27 66 0.24
28 46 0.17
29 25 0.09
30 29 0.11
31 7 0.03
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.64
Consensus pattern (26 bp):
TATTTTAAATATATATATTTTATTTT
Found at i:1384139 original size:20 final size:20
Alignment explanation
Indices: 1383828--1384141 Score: 102
Period size: 20 Copynumber: 15.3 Consensus size: 20
1383818 TTCTTAAATA
*
1383828 TATTTTTAATATCATATATTT
1 TATTTTT-ATATTATATATTT
1383849 TATTTTTAT-TTAT-TATTAT
1 TATTTTTATATTATATATT-T
* * * *
1383868 AATATTTATATTTTATTTTT
1 TATTTTTATATTATATATTT
*
1383888 TATATTTATATT-TATATTAT
1 TATTTTTATATTATATATT-T
1383908 TAATTTTTATA-TA-ATA--T
1 T-ATTTTTATATTATATATTT
* *
1383925 CATTTCTTA-AATATAT-TTT
1 TATTT-TTATATTATATATTT
**
1383944 TAATGTCATATATT-TAT-TTT
1 T-AT-TTTTATATTATATATTT
*
1383964 TATTTAT-TATTATAATATTT
1 TATTTTTATATTAT-ATATTT
*
1383984 TATATTTTATTTTA-ATATATT
1 TAT-TTTTATATTATATAT-TT
* *
1384005 TATATTTATATTAT-TA-AT
1 TATTTTTATATTATATATTT
* *
1384023 T-TTTATATAATATCATATTTT
1 TATTTTTATATTAT-ATA-TTT
*
1384044 AAATATATTTTAAATGTCATATATTT
1 ---TAT-TTTTATAT-T-ATATATTT
1384070 TATTTTTATTTATTATATAATTT
1 TATTTTTA--TATTATAT-ATTT
* * * * *
1384093 ATATTTTTTTCATTTCTTTAATA
1 -TATTTTTAT-A-TTATATATTT
1384116 TATTTTTATATTATATATTT
1 TATTTTTATATTATATATTT
1384136 TATTTT
1 TATTTT
1384142 AATTTGTTTT
Statistics
Matches: 218, Mismatches: 37, Indels: 77
0.66 0.11 0.23
Matches are distributed among these distances:
16 5 0.02
17 19 0.09
18 12 0.06
19 23 0.11
20 66 0.30
21 31 0.14
22 22 0.10
23 11 0.05
24 14 0.06
25 1 0.00
26 8 0.04
27 4 0.02
28 2 0.01
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.64
Consensus pattern (20 bp):
TATTTTTATATTATATATTT
Found at i:1384153 original size:24 final size:26
Alignment explanation
Indices: 1384126--1384192 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 26
1384116 TATTTTTATA
*
1384126 TTATATATTTTATTTTAAT-TT-GTT
1 TTATATATTTTATTTTAATATTAATT
* * * *
1384150 TTATCTATATTATATAAATATTAATT
1 TTATATATTTTATTTTAATATTAATT
*
1384176 TTTTATATTTTATTTTA
1 TTATATATTTTATTTTA
1384193 TTCTAATTTT
Statistics
Matches: 31, Mismatches: 10, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
24 15 0.48
25 2 0.06
26 14 0.45
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (26 bp):
TTATATATTTTATTTTAATATTAATT
Found at i:1386006 original size:8 final size:8
Alignment explanation
Indices: 1385995--1386032 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
1385985 TTTGTTATTT
1385995 AAAAATTA
1 AAAAATTA
1386003 AAAAATT-
1 AAAAATTA
*
1386010 TAAAATTA
1 AAAAATTA
*
1386018 AAAAATAA
1 AAAAATTA
1386026 AAAAATT
1 AAAAATT
1386033 TTAAAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
7 6 0.24
8 19 0.76
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
AAAAATTA
Found at i:1386016 original size:15 final size:16
Alignment explanation
Indices: 1385991--1386023 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
1385981 AGATTTTGTT
1385991 ATTTAAAAATTAAAAA
1 ATTTAAAAATTAAAAA
1386007 ATTT-AAAATTAAAAA
1 ATTTAAAAATTAAAAA
1386022 AT
1 AT
1386024 AAAAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTTAAAAATTAAAAA
Found at i:1386029 original size:15 final size:15
Alignment explanation
Indices: 1385995--1386029 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1385985 TTTGTTATTT
*
1385995 AAAAATTAAAAAATT
1 AAAAATTAAAAAATA
*
1386010 TAAAATTAAAAAATA
1 AAAAATTAAAAAATA
1386025 AAAAA
1 AAAAA
1386030 ATTTTAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAAATTAAAAAATA
Found at i:1399026 original size:15 final size:15
Alignment explanation
Indices: 1399006--1399053 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
1398996 CATTAATAAA
1399006 TAAATTTAAAAATTT
1 TAAATTTAAAAATTT
*
1399021 TAAATTTAAAAA--A
1 TAAATTTAAAAATTT
*
1399034 TAAATATTAATAATTT
1 TAAAT-TTAAAAATTT
1399050 TAAA
1 TAAA
1399054 ATATATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
13 5 0.19
14 6 0.22
15 12 0.44
16 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAATTTAAAAATTT
Found at i:1399052 original size:29 final size:28
Alignment explanation
Indices: 1398998--1399053 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
1398988 TATCATCTCA
*
1398998 TTAATAAATAAATTTAAAAATTTTAAAT
1 TTAAAAAATAAATTTAAAAATTTTAAAT
*
1399026 TTAAAAAATAAATATTAATAATTTTAAA
1 TTAAAAAATAAAT-TTAAAAATTTTAAA
1399054 ATATATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 12 0.48
29 13 0.52
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
TTAAAAAATAAATTTAAAAATTTTAAAT
Found at i:1399077 original size:22 final size:23
Alignment explanation
Indices: 1399021--1399094 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
1399011 TTAAAAATTT
* * *
1399021 TAAATTTAAAAAATAAATATTAA
1 TAAATTTAAAATATATATTTTAA
*
1399044 TAATTTTAAAATATATATTTTAA
1 TAAATTTAAAATATATATTTTAA
* *
1399067 -AAATTTAAAAT-TTTATTTTTA
1 TAAATTTAAAATATATATTTTAA
*
1399088 TATATTT
1 TAAATTT
1399095 TATTTAATAA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
21 8 0.19
22 15 0.36
23 19 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TAAATTTAAAATATATATTTTAA
Found at i:1399123 original size:18 final size:16
Alignment explanation
Indices: 1399076--1399132 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
1399066 AAAATTTAAA
* *
1399076 ATTTTATTTTTAT-AT
1 ATTTTATATTAATAAT
1399091 ATTTTAT-TTAATAAT
1 ATTTTATATTAATAAT
1399106 ATTTTATAATTAAATAAT
1 ATTTTAT-ATT-AATAAT
*
1399124 AATTTATAT
1 ATTTTATAT
1399133 ATCGCATATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
14 4 0.11
15 16 0.44
17 4 0.11
18 12 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTTTATATTAATAAT
Found at i:1399338 original size:16 final size:16
Alignment explanation
Indices: 1399313--1399344 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1399303 TGAAATATTA
*
1399313 AAATCGAAATAGGTTC
1 AAATCAAAATAGGTTC
1399329 AAATCAAAATAGGTTC
1 AAATCAAAATAGGTTC
1399345 TTCTCTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (16 bp):
AAATCAAAATAGGTTC
Found at i:1400068 original size:14 final size:14
Alignment explanation
Indices: 1400009--1400069 Score: 63
Period size: 13 Copynumber: 4.5 Consensus size: 14
1399999 AAAGAAAAAA
1400009 ATAAAATAAAATAT
1 ATAAAATAAAATAT
*
1400023 ATAATATAAAA-AT
1 ATAAAATAAAATAT
* * * *
1400036 TTATATTAAAAAAT
1 ATAAAATAAAATAT
1400050 A-AAAATAAAATAT
1 ATAAAATAAAATAT
1400063 ATAAAAT
1 ATAAAAT
1400070 TGTAATAAAA
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
13 19 0.53
14 17 0.47
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
ATAAAATAAAATAT
Found at i:1400079 original size:33 final size:33
Alignment explanation
Indices: 1400011--1400087 Score: 104
Period size: 33 Copynumber: 2.3 Consensus size: 33
1400001 AGAAAAAAAT
*
1400011 AAAATAAAATATATAATATAAAAATTTATATTAA
1 AAAATAAAA-ATAAAATATAAAAATTTATATTAA
1400045 AAAATAAAAATAAAATATATAAAATTGTA-A-TAA
1 AAAATAAAAATAAAATATA-AAAATT-TATATTAA
1400078 AAAATAAAAA
1 AAAATAAAAA
1400088 ATGCATGACA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
33 22 0.55
34 16 0.40
35 2 0.05
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (33 bp):
AAAATAAAAATAAAATATAAAAATTTATATTAA
Found at i:1400716 original size:15 final size:15
Alignment explanation
Indices: 1400698--1400728 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1400688 TTAAATATTT
*
1400698 TAAATTTTTTTAAAA
1 TAAATATTTTTAAAA
1400713 TAAATATTTTTAAAA
1 TAAATATTTTTAAAA
1400728 T
1 T
1400729 TATAACTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TAAATATTTTTAAAA
Found at i:1408280 original size:6 final size:6
Alignment explanation
Indices: 1408261--1408301 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
1408251 AATGAAAACT
* * *
1408261 ACCCAT ACCCAA ACCGAA ACACAA ACCCAA ACCCAA ACCCA
1 ACCCAA ACCCAA ACCCAA ACCCAA ACCCAA ACCCAA ACCCA
1408302 TGCACATAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.49, C:0.46, G:0.02, T:0.02
Consensus pattern (6 bp):
ACCCAA
Found at i:1409008 original size:21 final size:22
Alignment explanation
Indices: 1408979--1409024 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
1408969 ACTAGGTCAT
1408979 TCATAG-CTCTGTTAAACTCTA
1 TCATAGCCTCTGTTAAACTCTA
*
1409000 TCATGGCTCTCTGTTAAACTCTA
1 TCATAGC-CTCTGTTAAACTCTA
1409023 TC
1 TC
1409025 TTCAAAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.23
23 17 0.77
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (22 bp):
TCATAGCCTCTGTTAAACTCTA
Found at i:1409137 original size:16 final size:16
Alignment explanation
Indices: 1409116--1409146 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1409106 GTACTTTGTT
1409116 CATATATATATATATG
1 CATATATATATATATG
1409132 CATATATATATATAT
1 CATATATATATATAT
1409147 AAATAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (16 bp):
CATATATATATATATG
Found at i:1411627 original size:24 final size:23
Alignment explanation
Indices: 1411600--1411658 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
1411590 TTTTCAAGAG
* * *
1411600 TCACGAACTTGGACTTTGTCTTGA
1 TCACGAACTTCGACGTCGT-TTGA
*
1411624 TCACGAACTTCGCCGTCGTTTGA
1 TCACGAACTTCGACGTCGTTTGA
1411647 TCACGAACTTCG
1 TCACGAACTTCG
1411659 CCGTTGCTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 16 0.52
24 15 0.48
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.32
Consensus pattern (23 bp):
TCACGAACTTCGACGTCGTTTGA
Found at i:1411650 original size:23 final size:23
Alignment explanation
Indices: 1411619--1411671 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
1411609 TGGACTTTGT
1411619 CTTGATCACGAACTTCGCCGTCG
1 CTTGATCACGAACTTCGCCGTCG
* *
1411642 TTTGATCACGAACTTCGCCGTTG
1 CTTGATCACGAACTTCGCCGTCG
1411665 CTTGATC
1 CTTGATC
1411672 TTCACCCCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.17, C:0.30, G:0.21, T:0.32
Consensus pattern (23 bp):
CTTGATCACGAACTTCGCCGTCG
Found at i:1412159 original size:80 final size:80
Alignment explanation
Indices: 1412006--1412318 Score: 486
Period size: 80 Copynumber: 3.9 Consensus size: 80
1411996 AATATAATTA
* * * * * *
1412006 TTAGAGATAATTTAAATGACCAATAACTAA-ATTTTAATTGGTCAAAAATATGAAGATTATCTCT
1 TTAGAGATAAATTAGATGACCAATAGCTAATA-TTTGATTGGTC-AAAATATAAATATTATCTCT
*
1412070 AAATTATTTAGATTTAT
64 AAATAATTTAGATTTAT
*
1412087 TTAGAGATAAATTAGATAACCAATAGCTAATATTTGATTGGTCAAAATATAAATATTATCTCTAA
1 TTAGAGATAAATTAGATGACCAATAGCTAATATTTGATTGGTCAAAATATAAATATTATCTCTAA
1412152 ATAATTTAGATTTAT
66 ATAATTTAGATTTAT
1412167 TTAGAGATAAATT-GAATGACCAATAGCTAATATTTGATTGGTCAAAATATAAATATTATCTCTA
1 TTAGAGATAAATTAG-ATGACCAATAGCTAATATTTGATTGGTCAAAATATAAATATTATCTCTA
1412231 AATAATTTAGATTTAT
65 AATAATTTAGATTTAT
* *
1412247 TTAGAGATAAATTGGATGACCAATAGCTAATATTTGATTGGTCAAAATATGAATATTATCTCTAA
1 TTAGAGATAAATTAGATGACCAATAGCTAATATTTGATTGGTCAAAATATAAATATTATCTCTAA
*
1412312 ATTATTT
66 ATAATTT
1412319 TGGGAGATAA
Statistics
Matches: 218, Mismatches: 11, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
79 1 0.00
80 179 0.82
81 37 0.17
82 1 0.00
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (80 bp):
TTAGAGATAAATTAGATGACCAATAGCTAATATTTGATTGGTCAAAATATAAATATTATCTCTAA
ATAATTTAGATTTAT
Found at i:1412178 original size:38 final size:38
Alignment explanation
Indices: 1412135--1412258 Score: 97
Period size: 38 Copynumber: 3.2 Consensus size: 38
1412125 TGGTCAAAAT
1412135 ATAAATATTATCTCTAAATAATTTAGATTTATTTAGAG
1 ATAAATATTATCTCTAAATAATTTAGATTTATTTAGAG
* ** * * ** ** * *
1412173 ATAAAT-TGAATGACCAATAGCTAATATTTGATTGGTCAAAAT
1 ATAAATAT-TATCTCTAA-A--TAAT-TTAGATTTATTTAGAG
1412215 ATAAATATTATCTCTAAATAATTTAGATTTATTTAGAG
1 ATAAATATTATCTCTAAATAATTTAGATTTATTTAGAG
1412253 ATAAAT
1 ATAAAT
1412259 TGGATGACCA
Statistics
Matches: 58, Mismatches: 22, Indels: 12
0.63 0.24 0.13
Matches are distributed among these distances:
37 1 0.02
38 26 0.45
39 5 0.09
41 5 0.09
42 20 0.34
43 1 0.02
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (38 bp):
ATAAATATTATCTCTAAATAATTTAGATTTATTTAGAG
Found at i:1415965 original size:2 final size:2
Alignment explanation
Indices: 1415958--1415995 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1415948 TGTGTTTGTC
1415958 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1415996 CCAACAATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1445590 original size:18 final size:19
Alignment explanation
Indices: 1445552--1445591 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
1445542 CGGTTAAATG
* *
1445552 ATTTTCTTTTAATATTTAA
1 ATTTTATTTTAATATTAAA
1445571 ATTTTATTTT-ATATTAAA
1 ATTTTATTTTAATATTAAA
1445589 ATT
1 ATT
1445592 AGAAAGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTATTTTAATATTAAA
Found at i:1452297 original size:39 final size:41
Alignment explanation
Indices: 1452231--1452358 Score: 99
Period size: 39 Copynumber: 3.2 Consensus size: 41
1452221 TAAATTGACA
* * * * *
1452231 TTCATCATAAGAATCAACCAAAACATTCATAAAAT-AATATT
1 TTCATCATATGAGTAAATCAAATCATTCATAAAATCAAT-TT
* *
1452272 TGTCAT-ATAT-A-TAAATCAAATCATTCGT-AAATCCATTT
1 T-TCATCATATGAGTAAATCAAATCATTCATAAAATCAATTT
* *
1452310 TTCATCATATGAGTAAATCAAATAATTCAT-AAATC-ATTG
1 TTCATCATATGAGTAAATCAAATCATTCATAAAATCAATTT
*
1452349 TTAATCATAT
1 TTCATCATAT
1452359 TATTAAGTTC
Statistics
Matches: 72, Mismatches: 10, Indels: 12
0.77 0.11 0.13
Matches are distributed among these distances:
37 4 0.06
38 11 0.15
39 28 0.39
40 21 0.29
41 4 0.06
42 4 0.06
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.36
Consensus pattern (41 bp):
TTCATCATATGAGTAAATCAAATCATTCATAAAATCAATTT
Found at i:1452319 original size:40 final size:39
Alignment explanation
Indices: 1452274--1452358 Score: 100
Period size: 40 Copynumber: 2.2 Consensus size: 39
1452264 ATAATATTTG
* * * *
1452274 TCATAT-ATATAAATCAAATCATTCGTAAATCCATTTTTCA
1 TCATATGA-ATAAATCAAATAATTCATAAAT-CATTGTTAA
*
1452314 TCATATGAGTAAATCAAATAATTCATAAATCATTGTTAA
1 TCATATGAATAAATCAAATAATTCATAAATCATTGTTAA
1452353 TCATAT
1 TCATAT
1452359 TATTAAGTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
39 13 0.33
40 25 0.64
41 1 0.03
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.39
Consensus pattern (39 bp):
TCATATGAATAAATCAAATAATTCATAAATCATTGTTAA
Found at i:1452371 original size:40 final size:40
Alignment explanation
Indices: 1452283--1452358 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
1452273 GTCATATATA
* * * *
1452283 TAAATCAAATCATTCGTAAATCCATTTTTCATCATATGAG
1 TAAATCAAATAATTCATAAATCCATTGTTAATCATATGAG
1452323 TAAATCAAATAATTCATAAAT-CATTGTTAATCATAT
1 TAAATCAAATAATTCATAAATCCATTGTTAATCATAT
1452359 TATTAAGTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
39 13 0.41
40 19 0.59
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.38
Consensus pattern (40 bp):
TAAATCAAATAATTCATAAATCCATTGTTAATCATATGAG
Found at i:1463533 original size:60 final size:60
Alignment explanation
Indices: 1463441--1463563 Score: 149
Period size: 60 Copynumber: 2.0 Consensus size: 60
1463431 TTCAGAGTAC
* * * * *
1463441 GATGTCATTGTCTCAAAAGAGGCTTTAAGAGTAAAATTAAGCATTGTTAGAGTGGGAGAA
1 GATGTCATGGTCCCAAAAGAGGCTTTAAGAGTAAAATTAAGCATTGTTAAAGTAGGAAAA
* * * *
1463501 GATGTCATGGTCCCAAATG-GGTCTTTGAGAGTAAGATTGAGCATTGTTAAAGTAGGAAAA
1 GATGTCATGGTCCCAAAAGAGG-CTTTAAGAGTAAAATTAAGCATTGTTAAAGTAGGAAAA
1463561 GAT
1 GAT
1463564 AAGGGCTCCG
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 2 0.04
60 51 0.96
ACGTcount: A:0.35, C:0.09, G:0.28, T:0.28
Consensus pattern (60 bp):
GATGTCATGGTCCCAAAAGAGGCTTTAAGAGTAAAATTAAGCATTGTTAAAGTAGGAAAA
Found at i:1463774 original size:111 final size:111
Alignment explanation
Indices: 1463476--1463836 Score: 351
Period size: 111 Copynumber: 3.3 Consensus size: 111
1463466 TAAGAGTAAA
* * *
1463476 ATTAAGCATTGTTAGAGTGGGAG-AAGATGTCATGGTCCC-AAATGGGTCTTTGAGAGTAAGATT
1 ATTAAACATTGTTAGAGTGGGGGAAAGATGTCATGGTCCCAAAAAGGG-CTTTGAGAGTAAGATT
* *
1463539 GAGCATTGTTAAAGTAGGAAAAGATAAGGGCTCCGAGCTTAAGAAAG
65 GAGCATTGTTAAAGTAGGAAAAGATAAGAGCTCCGAGCATAAGAAAG
* * * * *
1463586 ATTAAACATTATTAGAGTGGGGAAAAGATGTCATGGTCCCAAAAAAGGTTTTGATAGTAAGATTG
1 ATTAAACATTGTTAGAGTGGGGGAAAGATGTCATGGTCCCAAAAAGGGCTTTGAGAGTAAGATTG
** * * * * *
1463651 AGCATTAATAAAGTAAGG-GAAGATGAGAG-TTCTATCAATAAGAAAG
66 AGCATTGTTAAAGT-AGGAAAAGATAAGAGCTCCGAGC-ATAAGAAAG
* *
1463697 ATTAAACATTGTTAGAGTGGGGGAAAGGA-GTCATGGTCCCAAAAAGGGCTCTGAGAATAAGATT
1 ATTAAACATTGTTAGAGTGGGGGAAA-GATGTCATGGTCCCAAAAAGGGCTTTGAGAGTAAGATT
* * * * * ***
1463761 GCGCATTGTTAAAGTGGGGCAAA-ATAGGGGCTTTTAG-AGTAAGAAAG
65 GAGCATTGTTAAAGT-AGGAAAAGATAAGAGCTCCGAGCA-TAAGAAAG
* *
1463808 ATTAAGCATTGTTAGAGTGCGGG-AAGATG
1 ATTAAACATTGTTAGAGTGGGGGAAAGATG
1463837 AGGACTCTAA
Statistics
Matches: 205, Mismatches: 37, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
109 2 0.01
110 27 0.13
111 160 0.78
112 16 0.08
ACGTcount: A:0.37, C:0.09, G:0.29, T:0.25
Consensus pattern (111 bp):
ATTAAACATTGTTAGAGTGGGGGAAAGATGTCATGGTCCCAAAAAGGGCTTTGAGAGTAAGATTG
AGCATTGTTAAAGTAGGAAAAGATAAGAGCTCCGAGCATAAGAAAG
Found at i:1463817 original size:50 final size:50
Alignment explanation
Indices: 1463763--1463871 Score: 123
Period size: 50 Copynumber: 2.2 Consensus size: 50
1463753 ATAAGATTGC
* * *
1463763 GCATTGTTAAAGTG-GGGCAAAAT-AGGGGCTTTTAGAGTAAGAAAGATTAA
1 GCATTGTTAAAGTGCGGG-AAAATGA-GGACTCTAAGAGTAAGAAAGATTAA
* * *
1463813 GCATTGTTAGAGTGCGGGAAGATGAGGACTCTAAGAGTAAGAACGATTAA
1 GCATTGTTAAAGTGCGGGAAAATGAGGACTCTAAGAGTAAGAAAGATTAA
*
1463863 GCGTTGTTA
1 GCATTGTTA
1463872 GAGTAGAGGG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
50 46 0.92
51 4 0.08
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.26
Consensus pattern (50 bp):
GCATTGTTAAAGTGCGGGAAAATGAGGACTCTAAGAGTAAGAAAGATTAA
Found at i:1464289 original size:44 final size:45
Alignment explanation
Indices: 1464235--1464320 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
1464225 CTAGATTGAG
*
1464235 CATTGTTAGAG-TCGAGGAAGCCCTTTGAGAGTAAAATTGAGTAT
1 CATTGTTAGAGTTAGAGGAAGCCCTTTGAGAGTAAAATTGAGTAT
* *
1464279 CATTGTTAGAGTTAGGGGAAGCTCTTTGAGAGTAAAATTGAG
1 CATTGTTAGAGTTAGAGGAAGCCCTTTGAGAGTAAAATTGAG
1464321 CATTGTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
44 11 0.29
45 27 0.71
ACGTcount: A:0.31, C:0.09, G:0.29, T:0.30
Consensus pattern (45 bp):
CATTGTTAGAGTTAGAGGAAGCCCTTTGAGAGTAAAATTGAGTAT
Found at i:1464463 original size:46 final size:46
Alignment explanation
Indices: 1464386--1464481 Score: 133
Period size: 46 Copynumber: 2.1 Consensus size: 46
1464376 AAGATTAAGC
* *
1464386 AAGATTGAGCATTATTAGAGTGAAGGAAAATGGAGG-CTTTGAGAGT
1 AAGATTGAGCATTATTAGAATGAAGGAAAAT-GAGGACTCTGAGAGT
*
1464432 AAGATTGAGCCATTATTAGAATG-AGGGAAATGAGGACTCTGAGAGT
1 AAGATTGAG-CATTATTAGAATGAAGGAAAATGAGGACTCTGAGAGT
1464478 AAGA
1 AAGA
1464482 AAGATTAAGC
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
45 4 0.09
46 29 0.64
47 12 0.27
ACGTcount: A:0.39, C:0.06, G:0.31, T:0.24
Consensus pattern (46 bp):
AAGATTGAGCATTATTAGAATGAAGGAAAATGAGGACTCTGAGAGT
Found at i:1464676 original size:105 final size:107
Alignment explanation
Indices: 1464464--1464717 Score: 250
Period size: 105 Copynumber: 2.4 Consensus size: 107
1464454 GAGGGAAATG
* * *
1464464 AGGACTCTGAGAGTAAGAAAGATTAAGCATTTTGTTAGAGTGAGGGAAGCTCTCTAAGAGTAAGA
1 AGGACTCTAAGAGTAAGAAAGATTAAG--TATTGTTAGAGTGAGAGAAGCTCTCTAAGAGTAAGA
* * ** * * **
1464529 TTAAGCATCATTGCTAGAGTTGGGAAAGATGTCATTTTCCCAAAA
64 TT-AGCAGCATTGCTAAAGTAAGAAAAGAAGTCATGGTCCCAAAA
*
1464574 AGGACTCTAAGAGTAAGAAAGATTAAGTATTGTTAGAGTG-GAAGAAG-TACTTTAAGAGTAAGA
1 AGGACTCTAAGAGTAAGAAAGATTAAGTATTGTTAGAGTGAG-AGAAGCT-CTCTAAGAGTAAGA
* *
1464637 TT-G-GGCATTGTTAAAGTAAGAAAAGAAGTCATGGTCCCAAAA
64 TTAGCAGCATTGCTAAAGTAAGAAAAGAAGTCATGGTCCCAAAA
* * *
1464679 AGGGCTATAA-AGGTTAA-AAAGATTAAGCATTGTTAGAGT
1 AGGACTCTAAGA-G-TAAGAAAGATTAAGTATTGTTAGAGT
1464718 TGGGGGAAAA
Statistics
Matches: 123, Mismatches: 17, Indels: 13
0.80 0.11 0.08
Matches are distributed among these distances:
104 1 0.01
105 59 0.48
106 4 0.03
107 2 0.02
108 31 0.25
110 26 0.21
ACGTcount: A:0.39, C:0.09, G:0.26, T:0.26
Consensus pattern (107 bp):
AGGACTCTAAGAGTAAGAAAGATTAAGTATTGTTAGAGTGAGAGAAGCTCTCTAAGAGTAAGATT
AGCAGCATTGCTAAAGTAAGAAAAGAAGTCATGGTCCCAAAA
Found at i:1465210 original size:105 final size:105
Alignment explanation
Indices: 1464952--1465211 Score: 261
Period size: 105 Copynumber: 2.4 Consensus size: 105
1464942 GGAAGATGGG
* * **
1464952 GACTCTAATAGTAAGAAAGATTAAGTATTTTGTTAAAGTGGGAGAAGCCCATTAAGAGTAAGATT
1 GACTCTAAAAGTAAGAAAAATTAA--ACATTGTTAAAGTGGG-GAAGCCCATTAAGAGTAAGATT
* * * * * *
1465017 GAGCATCATTGTTAGAGTGAGGGAAGATGTCATTGTCTAAAAGAA
63 GAG-A-CATTGTTAAAGTAAAGGAAAATGTCATAGTCCAAAAGAA
* * * *
1465062 GACTCTAAAAGTAAGAAAGATTAAGCATTGTTAGAGTGGGGGAAGCCCTTTAAGAGTAAGATTGA
1 GACTCTAAAAGTAAGAAAAATTAAACATTGTTAAAGT-GGGGAAGCCCATTAAGAGTAAGATTGA
* **
1465127 G-CATTGTTAAAGTAAAGGAAAATGTCATAGTCCCAAAGGG
65 GACATTGTTAAAGTAAAGGAAAATGTCATAGTCCAAAAGAA
* * * *
1465167 GGCTTTAAGAGTAAGAAAAATTAAACATTGTTAAAGCGAGGGAAG
1 GACTCTAAAAGTAAGAAAAATTAAACATTGTTAAAGTG-GGGAAG
1465212 ATAAGGGCTC
Statistics
Matches: 126, Mismatches: 22, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
104 1 0.01
105 66 0.52
108 33 0.26
109 3 0.02
110 23 0.18
ACGTcount: A:0.40, C:0.09, G:0.26, T:0.25
Consensus pattern (105 bp):
GACTCTAAAAGTAAGAAAAATTAAACATTGTTAAAGTGGGGAAGCCCATTAAGAGTAAGATTGAG
ACATTGTTAAAGTAAAGGAAAATGTCATAGTCCAAAAGAA
Done.