Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167915.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_18, 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: 20765110
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 90000 characters in sequence are not A, C, G, or T
File 2 of 117
Found at i:125790 original size:63 final size:62
Alignment explanation
Indices: 125718--125849 Score: 165
Period size: 63 Copynumber: 2.1 Consensus size: 62
125708 TTTCAAGTTA
* * * *
125718 ATATTTTTATAAAAAGATTATTTAAGACGTTTCTGTACAGAAAATATCTTAAATAATTTTTTT
1 ATATTTTTATAAAAAGATTATTTAAGACGTTTCTGAACAGAAAAGATATTAAATAA-TCTTTT
* * * * * *
125781 ATATTTTTATAAATAGATTATTTAGGGCGTTTGTGAATAGAAAAGGTATTAAATAATCTTTT
1 ATATTTTTATAAAAAGATTATTTAAGACGTTTCTGAACAGAAAAGATATTAAATAATCTTTT
125843 ATATTTT
1 ATATTTT
125850 ATGGTTTAGG
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
62 12 0.20
63 47 0.80
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.46
Consensus pattern (62 bp):
ATATTTTTATAAAAAGATTATTTAAGACGTTTCTGAACAGAAAAGATATTAAATAATCTTTT
Found at i:125976 original size:153 final size:154
Alignment explanation
Indices: 125675--125968 Score: 414
Period size: 153 Copynumber: 1.9 Consensus size: 154
125665 AAAAAACGCC
125675 TTAAATAATCTTTTTATATTTTAAGATTTAGAGTTTCAAGTTAATATTTTTATAAAAAGATTATT
1 TTAAATAATCTTTTTATATTTTAAGATTTAGAGTTTCAAGTTAATATTTTTATAAAAAGATTATT
* * * *
125740 TAAGACGTTTCTGTACAGAAAATATCTTAAATAATTTTTTTATATTTTTATAAATAGATTATTTA
66 TAAGACGTTTCTATACAGAAAATATCTTAAATAATTATTTTATATTTTTACAAACAGATTATTTA
* * * * *
125805 GGGCGTTTGTGAATAGAAAAGGTA
131 AGACATTTCTGAACAGAAAAGGTA
* * * *
125829 TTAAATAATC-TTTTATATTTTATGGTTTAGGGTTT-ATGGTTAATATTTTTATAAAAAGATTAT
1 TTAAATAATCTTTTTATATTTTAAGATTTAGAGTTTCA-AGTTAATATTTTTATAAAAAGATTAT
**
125892 TTAAGGTGTTTCTATACAGAAAATGA-CTTAAATAATTATTTTATATTTTTACAAACAGATTATT
65 TTAAGACGTTTCTATACAGAAAAT-ATCTTAAATAATTATTTTATATTTTTACAAACAGATTATT
125956 TAAGACATTTCTG
129 TAAGACATTTCTG
125969 TGCAGAAATG
Statistics
Matches: 124, Mismatches: 14, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
152 1 0.01
153 112 0.90
154 11 0.09
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (154 bp):
TTAAATAATCTTTTTATATTTTAAGATTTAGAGTTTCAAGTTAATATTTTTATAAAAAGATTATT
TAAGACGTTTCTATACAGAAAATATCTTAAATAATTATTTTATATTTTTACAAACAGATTATTTA
AGACATTTCTGAACAGAAAAGGTA
Found at i:135395 original size:17 final size:18
Alignment explanation
Indices: 135352--135397 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
135342 TTTATTATAC
135352 AAATATTATATTAATAAA
1 AAATATTATATTAATAAA
135370 AAATA-TATATTAA-AAA
1 AAATATTATATTAATAAA
* *
135386 TATTATTATATT
1 AAATATTATATT
135398 TATTATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 6 0.24
17 14 0.56
18 5 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATATTATATTAATAAA
Found at i:135419 original size:23 final size:21
Alignment explanation
Indices: 135360--135428 Score: 67
Period size: 23 Copynumber: 3.4 Consensus size: 21
135350 ACAAATATTA
135360 TATTAATAAA-AA-AT-ATA-
1 TATTAATAAATAATATCATAT
* *
135377 TATTAA-AAATATTATTATATT
1 TATTAATAAATAATATCATA-T
135398 TATTATATAAATAATATCATAT
1 TATTA-ATAAATAATATCATAT
135420 TATTAATAA
1 TATTAATAA
135429 TAAATTGAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
16 3 0.07
17 7 0.17
18 2 0.05
19 3 0.07
21 9 0.21
22 7 0.17
23 11 0.26
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (21 bp):
TATTAATAAATAATATCATAT
Found at i:137390 original size:13 final size:13
Alignment explanation
Indices: 137372--137397 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
137362 ATTTACTAAA
137372 ATATTATTAAAAT
1 ATATTATTAAAAT
137385 ATATTATTAAAAT
1 ATATTATTAAAAT
137398 TGCACCAAAA
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATTATTAAAAT
Found at i:137806 original size:2 final size:2
Alignment explanation
Indices: 137799--137910 Score: 89
Period size: 2 Copynumber: 60.0 Consensus size: 2
137789 AATTTTAATG
* * *
137799 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA AA T- TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
137840 TA T- TA T- TT TA T- TA -A GA -A TA CT- TA TT TG TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
137876 TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
137911 ATAACCATCA
Statistics
Matches: 92, Mismatches: 8, Indels: 20
0.77 0.07 0.17
Matches are distributed among these distances:
1 9 0.10
2 82 0.89
3 1 0.01
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:141515 original size:2 final size:2
Alignment explanation
Indices: 141510--141542 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
141500 TATGTGTGTG
141510 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
141543 TATTACAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:142293 original size:53 final size:53
Alignment explanation
Indices: 142185--142293 Score: 146
Period size: 53 Copynumber: 2.1 Consensus size: 53
142175 ATATCAATTT
* *
142185 TTTATTTTTTTTATTTACAACTTTTTTCAAAATATATTCTATTACAATTATAA
1 TTTATTTTTTTGATTTACAACTTTTTTCAAAATATATTCTATTACAATTACAA
* * * * * *
142238 TTTATTTTTTTGGTTTACAACTTTTTTTAATATATATTTTATTACTATTGCAA
1 TTTATTTTTTTGATTTACAACTTTTTTCAAAATATATTCTATTACAATTACAA
142291 TTT
1 TTT
142294 CATTCTTATA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.60
Consensus pattern (53 bp):
TTTATTTTTTTGATTTACAACTTTTTTCAAAATATATTCTATTACAATTACAA
Found at i:143187 original size:9 final size:9
Alignment explanation
Indices: 143173--143197 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
143163 AATATGATAA
143173 ATTATTTTC
1 ATTATTTTC
143182 ATTATTTTC
1 ATTATTTTC
143191 ATTATTT
1 ATTATTT
143198 ATCCAAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (9 bp):
ATTATTTTC
Found at i:147122 original size:14 final size:14
Alignment explanation
Indices: 147099--147129 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
147089 TTTCTTTCTT
*
147099 AAATATATTTTATA
1 AAATACATTTTATA
147113 AAATACATTTTATA
1 AAATACATTTTATA
147127 AAA
1 AAA
147130 AATAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (14 bp):
AAATACATTTTATA
Found at i:149241 original size:2 final size:2
Alignment explanation
Indices: 149234--149265 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
149224 TTATTTAATA
149234 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
149266 CAGGTTAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:153117 original size:11 final size:11
Alignment explanation
Indices: 153101--153136 Score: 72
Period size: 11 Copynumber: 3.3 Consensus size: 11
153091 ATTAAAATTA
153101 AAATAATTTTT
1 AAATAATTTTT
153112 AAATAATTTTT
1 AAATAATTTTT
153123 AAATAATTTTT
1 AAATAATTTTT
153134 AAA
1 AAA
153137 AAGTATTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AAATAATTTTT
Found at i:153125 original size:45 final size:45
Alignment explanation
Indices: 153040--153129 Score: 103
Period size: 45 Copynumber: 2.0 Consensus size: 45
153030 AATTCACGTC
*
153040 AAAATAATAAAAATTAAAATAAATTGTAAATTCATATTAAAATAAT
1 AAAATAATAAAAATTAAAATAAATTGTAAATTAATATT-AAATAAT
* * * *
153086 AAAA-AATTAAAATTAAAATAATTTTTAAA-TAATTTTTAAATAAT
1 AAAATAATAAAAATTAAAATAAATTGTAAATTAA-TATTAAATAAT
153130 TTTTAAAAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
44 9 0.24
45 25 0.66
46 4 0.11
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (45 bp):
AAAATAATAAAAATTAAAATAAATTGTAAATTAATATTAAATAAT
Found at i:161565 original size:28 final size:28
Alignment explanation
Indices: 161534--161592 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
161524 ATTATAATAA
* *
161534 AAAATATTCAATGTGATTAT-TAAATTTT
1 AAAATATTCAATATGA-CATCTAAATTTT
*
161562 AAAATATTTAATATGACATCTAAATTTT
1 AAAATATTCAATATGACATCTAAATTTT
161590 AAA
1 AAA
161593 TCTTAAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 2 0.07
28 25 0.93
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (28 bp):
AAAATATTCAATATGACATCTAAATTTT
Found at i:162118 original size:13 final size:13
Alignment explanation
Indices: 162089--162126 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
162079 ATTTTACTAA
162089 AAAATATA-TATT
1 AAAATATATTATT
*
162101 TAAATATATTATT
1 AAAATATATTATT
*
162114 AAAATAAATTATT
1 AAAATATATTATT
162127 TATTAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 7 0.32
13 15 0.68
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AAAATATATTATT
Found at i:162143 original size:17 final size:16
Alignment explanation
Indices: 162104--162145 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
162094 ATATATTTAA
162104 ATATA-TTATTAAAAT
1 ATATATTTATTAAAAT
*
162119 AAATTATTTATTAAAAAT
1 ATA-TATTTATT-AAAAT
162137 ATATATTTA
1 ATATATTTA
162146 ATATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 2 0.09
16 2 0.09
17 11 0.50
18 7 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATATTTATTAAAAT
Found at i:163026 original size:6 final size:6
Alignment explanation
Indices: 163015--163045 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
163005 CTAGACTAGT
*
163015 AATTGA AATTGA AATTGA AATTGA AACTGA A
1 AATTGA AATTGA AATTGA AATTGA AATTGA A
163046 TTGCAGATCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.52, C:0.03, G:0.16, T:0.29
Consensus pattern (6 bp):
AATTGA
Found at i:171285 original size:20 final size:19
Alignment explanation
Indices: 171256--171294 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
171246 AAATAGCCCA
*
171256 TATTAATTTTTTTAAAAAT
1 TATTAATTTTTTAAAAAAT
171275 TATTGAATTTTTTAAAAAAT
1 TATT-AATTTTTTAAAAAAT
171295 AAAATAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
TATTAATTTTTTAAAAAAT
Found at i:172258 original size:17 final size:18
Alignment explanation
Indices: 172236--172274 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
172226 GTAGAGCTTT
172236 TTTATTTTTATA-TTATA
1 TTTATTTTTATATTTATA
*
172253 TTTATTTTTGTATTTATA
1 TTTATTTTTATATTTATA
172271 TTTA
1 TTTA
172275 ATAAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTATTTTTATATTTATA
Found at i:172434 original size:19 final size:17
Alignment explanation
Indices: 172385--172425 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
172375 ACTATTTTTT
*
172385 AATA-ATTTTTTATTAA
1 AATATATTTTTTAATAA
*
172401 CATATATTTTTTAATAA
1 AATATATTTTTTAATAA
172418 AATATATT
1 AATATATT
172426 AATTTTAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
AATATATTTTTTAATAA
Found at i:172469 original size:20 final size:20
Alignment explanation
Indices: 172405--172470 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 20
172395 TATTAACATA
* *
172405 TATTTTTTAATAAAATATATT
1 TATTTATTAA-AAAATTTATT
* * *
172426 AATTTTAATTAATAATTTTA-T
1 TA-TTT-ATTAAAAAATTTATT
172447 TATTTATTAAAAAATTTATT
1 TATTTATTAAAAAATTTATT
172467 TATT
1 TATT
172471 AAATATATAT
Statistics
Matches: 34, Mismatches: 8, Indels: 7
0.69 0.16 0.14
Matches are distributed among these distances:
19 11 0.32
20 8 0.24
21 3 0.09
22 8 0.24
23 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TATTTATTAAAAAATTTATT
Found at i:173092 original size:17 final size:17
Alignment explanation
Indices: 173066--173098 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
173056 TTAAATAACT
*
173066 TTAAATTTATTTAAATA
1 TTAAAATTATTTAAATA
173083 TTAAAATTATTTAAAT
1 TTAAAATTATTTAAAT
173099 TATAATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAAAATTATTTAAATA
Found at i:173186 original size:21 final size:19
Alignment explanation
Indices: 173161--173209 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
173151 TGAAATATGG
*
173161 ATTTTATGTTCATAATAAATA
1 ATTTTATGTT--TAACAAATA
173182 ATTTTAATTGTTTAACAAATA
1 ATTTT-A-TGTTTAACAAATA
173203 ATTTTAT
1 ATTTTAT
173210 TTAAAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 1 0.04
20 1 0.04
21 18 0.72
22 1 0.04
23 4 0.16
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (19 bp):
ATTTTATGTTTAACAAATA
Found at i:176297 original size:8 final size:8
Alignment explanation
Indices: 176284--176321 Score: 62
Period size: 8 Copynumber: 5.0 Consensus size: 8
176274 ACTTTTCTTT
176284 TAAATATA
1 TAAATATA
176292 TAAATATA
1 TAAATATA
176300 T-AA-ATA
1 TAAATATA
176306 TAAATATA
1 TAAATATA
176314 TAAATATA
1 TAAATATA
176322 ATGAAATAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 4 0.14
7 4 0.14
8 20 0.71
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
TAAATATA
Found at i:176308 original size:14 final size:14
Alignment explanation
Indices: 176289--176322 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
176279 TCTTTTAAAT
176289 ATATAAATATATAA
1 ATATAAATATATAA
176303 ATATAAATATATAA
1 ATATAAATATATAA
176317 ATATAA
1 ATATAA
176323 TGAAATAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATATAAATATATAA
Found at i:177179 original size:23 final size:25
Alignment explanation
Indices: 177131--177188 Score: 68
Period size: 23 Copynumber: 2.4 Consensus size: 25
177121 TGCAAATATA
*
177131 TATATATATATATATATAACTCAAT
1 TATATATATATATATATAACTAAAT
177156 TATATATA-ATATA-ACTAA-TAAAT
1 TATATATATATATATA-TAACTAAAT
*
177179 TTTATATATA
1 TATATATATA
177189 AAAAAAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
23 12 0.41
24 9 0.31
25 8 0.28
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (25 bp):
TATATATATATATATATAACTAAAT
Found at i:179582 original size:2 final size:2
Alignment explanation
Indices: 179575--179610 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
179565 GAGGAATCCA
179575 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
179611 TGAGGTACGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:179921 original size:2 final size:2
Alignment explanation
Indices: 179914--179940 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
179904 AATCCAACTA
179914 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
179941 ATTTTTTTTT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:184869 original size:2 final size:2
Alignment explanation
Indices: 184864--184888 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
184854 AGTGTGTGTG
184864 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
184889 TATGGGCTTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:199413 original size:16 final size:16
Alignment explanation
Indices: 199383--199430 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
199373 TCACTAGCCT
199383 TCAAGTCTA-TTTATG
1 TCAAGTCTACTTTATG
199398 TCTAA-TCTACTTTATG
1 TC-AAGTCTACTTTATG
*
199414 TCAAGTATACTTTATG
1 TCAAGTCTACTTTATG
199430 T
1 T
199431 TGTTGATAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (16 bp):
TCAAGTCTACTTTATG
Found at i:209475 original size:141 final size:136
Alignment explanation
Indices: 209259--209536 Score: 450
Period size: 141 Copynumber: 2.0 Consensus size: 136
209249 TGATAAATTT
*
209259 TTATTTATTTTATTAATATCACATAAAATTTTATTTTAATTGATAAAAAATTAATAATTTTAATT
1 TTATTTATTTTATTAATATCACATAAAATTTAATTTTAATTGATAAAAAATTAATAATTTTAATT
*
209324 TTTTATTCTAAATAAGGGTTTAATTGAATACAAATAAATATTAAAAGGTTTTGATATATTTCAAT
66 TTTTATTCTAAATAAGGGTTTAATTGAATACAAATAAATATTAAAAGGTTTTGATAGATTTCAAT
209389 AAAAAA
131 AAAAAA
209395 TTATTTATTTTATTAATATCACATAAAAAATTAATAATTTTAATTGATAAAAAAATTAATAATTT
1 TTATTTATTTTATTAATATCACAT--AAAATT--TAATTTTAATTGAT-AAAAAATTAATAATTT
* * *
209460 T-ATTTTTTTTATCTAAATAAGGGTTTAATTGCATATAAATAAATATTAAAAGGTTTTGATAGAT
61 TAATTTTTTAT-TCTAAATAAGGGTTTAATTGAATACAAATAAATATTAAAAGGTTTTGATAGAT
209524 TTCAATAAAAAA
125 TTCAATAAAAAA
209536 T
1 T
209537 AAAATTTTGA
Statistics
Matches: 131, Mismatches: 5, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
136 24 0.18
138 6 0.05
140 21 0.16
141 80 0.61
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (136 bp):
TTATTTATTTTATTAATATCACATAAAATTTAATTTTAATTGATAAAAAATTAATAATTTTAATT
TTTTATTCTAAATAAGGGTTTAATTGAATACAAATAAATATTAAAAGGTTTTGATAGATTTCAAT
AAAAAA
Found at i:209875 original size:13 final size:12
Alignment explanation
Indices: 209843--209876 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
209833 ATTAAAAAAA
209843 TTAATAAATATT
1 TTAATAAATATT
209855 TTAGATAAATATTT
1 TTA-ATAAATA-TT
209869 TTAATAAA
1 TTAATAAA
209877 AATGTAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 3 0.15
13 12 0.60
14 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (12 bp):
TTAATAAATATT
Found at i:218962 original size:3 final size:3
Alignment explanation
Indices: 218954--218979 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
218944 AAGCTCTTTT
218954 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
218980 GTTTTGGTGT
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:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:220813 original size:2 final size:2
Alignment explanation
Indices: 220806--220852 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
220796 AAGTAATCCT
220806 TC TC TC 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 TC TC TC
220848 TC TC T
1 TC TC T
220853 GTGTATGCAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:239897 original size:12 final size:13
Alignment explanation
Indices: 239883--239925 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
239873 TTATTAACAT
239883 TTTTTATTAATT-
1 TTTTTATTAATTA
239895 TTTTATATT-ATTA
1 TTTT-TATTAATTA
239908 TTTTTA-TAATTA
1 TTTTTATTAATTA
239920 TTTTTA
1 TTTTTA
239926 ATTATGGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 1 0.04
12 19 0.68
13 8 0.29
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTATTAATTA
Found at i:240201 original size:17 final size:17
Alignment explanation
Indices: 240181--240214 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
240171 TATTTTACTT
240181 AAACTTATTAGTTTGTA
1 AAACTTATTAGTTTGTA
240198 AAACTTATTAGTTTGTA
1 AAACTTATTAGTTTGTA
240215 TTGAATTAGT
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:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (17 bp):
AAACTTATTAGTTTGTA
Found at i:240667 original size:23 final size:25
Alignment explanation
Indices: 240641--240690 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
240631 AAGGATTTAT
*
240641 ATTTAATACACTGTCAGT-AAT-AA
1 ATTTAATACACTATCAGTGAATCAA
*
240664 ATTTTATACACTATCAGTGAATCAA
1 ATTTAATACACTATCAGTGAATCAA
240689 AT
1 AT
240691 GATGATAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 16 0.70
24 3 0.13
25 4 0.17
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (25 bp):
ATTTAATACACTATCAGTGAATCAA
Found at i:240718 original size:31 final size:30
Alignment explanation
Indices: 240683--240746 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
240673 ACTATCAGTG
* *
240683 AATCAAATGATGATAATTTATTAATGAAATA
1 AATCAAATGATAATAATTCATTAATG-AATA
* *
240714 AATCATATGATAATACTTCATTAATGAATA
1 AATCAAATGATAATAATTCATTAATGAATA
240744 AAT
1 AAT
240747 TTTTAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 7 0.24
31 22 0.76
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (30 bp):
AATCAAATGATAATAATTCATTAATGAATA
Found at i:241681 original size:2 final size:2
Alignment explanation
Indices: 241674--241699 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
241664 GCAGAGGTGA
241674 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
241700 GGAGGGTTGG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:245936 original size:2 final size:2
Alignment explanation
Indices: 245929--245984 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
245919 AGGAGATGAC
245929 CT CT CT CT CT CT CT 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
245971 CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT
245985 ATTTTTCCTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:246677 original size:25 final size:25
Alignment explanation
Indices: 246617--246669 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
246607 ATCATCTCTA
246617 GCCACTTAGAGCTGACTTCATTTTG
1 GCCACTTAGAGCTGACTTCATTTTG
246642 GCCACTTAGAGCTGACTTCATTTTG
1 GCCACTTAGAGCTGACTTCATTTTG
246667 GCC
1 GCC
246670 TTATAGAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.34
Consensus pattern (25 bp):
GCCACTTAGAGCTGACTTCATTTTG
Found at i:256539 original size:2 final size:2
Alignment explanation
Indices: 256532--256562 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
256522 AAATTTTTCT
256532 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
256563 AGTGCAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:258415 original size:17 final size:19
Alignment explanation
Indices: 258361--258418 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 19
258351 TTCAATTTAT
*
258361 ATTTATTATTAAAATATTAA
1 ATTTATT-TTACAATATTAA
258381 A---ATTTTACAATATTAA
1 ATTTATTTTACAATATTAA
258397 ATTTATTTTA-AAT-TTAA
1 ATTTATTTTACAATATTAA
258414 ATTTA
1 ATTTA
258419 AATAATTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
16 12 0.35
17 12 0.35
18 3 0.09
19 6 0.18
20 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTTATTTTACAATATTAA
Found at i:259595 original size:15 final size:15
Alignment explanation
Indices: 259575--259603 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
259565 TTCAATTACA
259575 ATTAAAAAATAATTG
1 ATTAAAAAATAATTG
259590 ATTAAAAAATAATT
1 ATTAAAAAATAATT
259604 AATAATGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
ATTAAAAAATAATTG
Found at i:263449 original size:12 final size:12
Alignment explanation
Indices: 263432--263468 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
263422 AACATTTCTA
*
263432 ATATATATATAT
1 ATATATGTATAT
263444 ATATATGTATAT
1 ATATATGTATAT
*
263456 GTATATGTATAT
1 ATATATGTATAT
263468 A
1 A
263469 GTAGTGCTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (12 bp):
ATATATGTATAT
Found at i:266626 original size:2 final size:2
Alignment explanation
Indices: 266619--266652 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
266609 CTATTACATG
266619 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
266653 TTGACCTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:270141 original size:20 final size:20
Alignment explanation
Indices: 270116--270156 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
270106 TAGTTCCACA
*
270116 TAGATCCAAGTTGAAAGCTT
1 TAGATCCAAATTGAAAGCTT
270136 TAGATCCAAATTGAAAGCTT
1 TAGATCCAAATTGAAAGCTT
270156 T
1 T
270157 TGGTTGCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.32
Consensus pattern (20 bp):
TAGATCCAAATTGAAAGCTT
Found at i:275863 original size:30 final size:30
Alignment explanation
Indices: 275827--275930 Score: 181
Period size: 30 Copynumber: 3.5 Consensus size: 30
275817 ATTTGTGATA
*
275827 CTAATTCTTATGGTCAAGTTAGAAGTAATG
1 CTAATTCTTATGGTCAAGTTACAAGTAATG
*
275857 CTAATTCTTATGGTCAAGTTACAAGTAACG
1 CTAATTCTTATGGTCAAGTTACAAGTAATG
*
275887 CTAATTCTTATGGTCAAGTAACAAGTAATG
1 CTAATTCTTATGGTCAAGTTACAAGTAATG
275917 CTAATTCTTATGGT
1 CTAATTCTTATGGT
275931 TACGTATCAG
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 70 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (30 bp):
CTAATTCTTATGGTCAAGTTACAAGTAATG
Found at i:282830 original size:4 final size:4
Alignment explanation
Indices: 282821--282846 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
282811 TTAGTGGACT
282821 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
282847 GGGACGGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:287821 original size:15 final size:15
Alignment explanation
Indices: 287797--287834 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
287787 ATCAACATCT
*
287797 TTATTGTTGTTATTA
1 TTATTATTGTTATTA
*
287812 TTATTATTGTTATTG
1 TTATTATTGTTATTA
287827 TTATTATT
1 TTATTATT
287835 TCATTTTGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.11, T:0.68
Consensus pattern (15 bp):
TTATTATTGTTATTA
Found at i:290098 original size:8 final size:8
Alignment explanation
Indices: 290085--290123 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
290075 TTTGCTGTAG
290085 ATATATAC
1 ATATATAC
290093 ATATATAC
1 ATATATAC
*
290101 AAAATATAC
1 -ATATATAC
*
290110 ATATATAT
1 ATATATAC
290118 ATATAT
1 ATATAT
290124 TCTTTATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
8 20 0.74
9 7 0.26
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATATAC
Found at i:293244 original size:14 final size:14
Alignment explanation
Indices: 293225--293251 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
293215 TGCAATTAGC
293225 TTTTTTTTTTATTA
1 TTTTTTTTTTATTA
293239 TTTTTTTTTTATT
1 TTTTTTTTTTATT
293252 TAATTTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (14 bp):
TTTTTTTTTTATTA
Found at i:293258 original size:15 final size:14
Alignment explanation
Indices: 293226--293259 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
293216 GCAATTAGCT
*
293226 TTTTTTTTTATTAT
1 TTTTTTTTTATTAA
293240 TTTTTTTTTATTTAA
1 TTTTTTTTTA-TTAA
293255 TTTTT
1 TTTTT
293260 AACTAACCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTTTTTATTAA
Found at i:293574 original size:20 final size:21
Alignment explanation
Indices: 293551--293600 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
293541 ATAATTATTT
*
293551 TATATATAAA-TTTATTTAAA
1 TATATATAAATTTTATTAAAA
293571 TATAT-TAAAATTTTATTAAAA
1 TATATAT-AAATTTTATTAAAA
293592 TAATATATA
1 T-ATATATA
293601 TAAATTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 1 0.04
20 8 0.32
21 10 0.40
22 5 0.20
23 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TATATATAAATTTTATTAAAA
Found at i:295559 original size:3 final size:3
Alignment explanation
Indices: 295551--295600 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
295541 TATAGACGAA
295551 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
295599 AA
1 AA
295601 AAGTGTTGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:296534 original size:2 final size:2
Alignment explanation
Indices: 296527--296591 Score: 51
Period size: 2 Copynumber: 31.5 Consensus size: 2
296517 TCACTCTTGT
* * * *
296527 TA TA TA TA TA GTA TG TA -A CTA TA TA AA TG TA TA TA TA TT TA TA
1 TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
*
296570 CA TA TA TA TA TA TA TGA TA TA T
1 TA TA TA TA TA TA TA T-A TA TA T
296592 TGCCTCCAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
1 1 0.02
2 43 0.88
3 5 0.10
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (2 bp):
TA
Found at i:305708 original size:2 final size:2
Alignment explanation
Indices: 305701--305730 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
305691 AATTGATTTA
*
305701 AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
305731 TGGTGAAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:312651 original size:21 final size:21
Alignment explanation
Indices: 312625--312664 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
312615 ACCATATCAC
312625 ACTCAGATGTGAAACTTTGCA
1 ACTCAGATGTGAAACTTTGCA
312646 ACTCAGATGTGAAACTTTG
1 ACTCAGATGTGAAACTTTG
312665 TCCCCAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (21 bp):
ACTCAGATGTGAAACTTTGCA
Found at i:314503 original size:16 final size:16
Alignment explanation
Indices: 314482--314525 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
314472 CTATGATATA
314482 ATAATATAATAAAAAT
1 ATAATATAATAAAAAT
*
314498 ATAATATAATTTAAAAT
1 ATAATATAA-TAAAAAT
*
314515 TTAA-ATAATAA
1 ATAATATAATAA
314526 TTATATATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 2 0.08
16 13 0.54
17 9 0.38
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAATATAATAAAAAT
Found at i:314920 original size:2 final size:2
Alignment explanation
Indices: 314913--314943 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
314903 CAACATCTTC
*
314913 TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
314944 CTATTTCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 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):
TA
Found at i:319298 original size:29 final size:30
Alignment explanation
Indices: 319257--319335 Score: 99
Period size: 29 Copynumber: 2.6 Consensus size: 30
319247 TATAATTAAA
319257 ATTTTAATATAATATTTAAATT-TAAAATTT
1 ATTTTAATATAATATTTAAATTAT-AAATTT
* *
319287 -TTTTAATGTAATATATAAATTATAAATTT
1 ATTTTAATATAATATTTAAATTATAAATTT
319316 ATTAATTAATATAATATTTA
1 ATT--TTAATATAATATTTA
319336 TTTTTAATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 25 0.61
30 3 0.07
32 13 0.32
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (30 bp):
ATTTTAATATAATATTTAAATTATAAATTT
Found at i:319342 original size:18 final size:18
Alignment explanation
Indices: 319307--319348 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
319297 ATATATAAAT
319307 TATAAATTTATTAATTAA
1 TATAAATTTATTAATTAA
*
319325 TATAATATTTATT-TTTAA
1 TATAA-ATTTATTAATTAA
319343 TATAAA
1 TATAAA
319349 AAATTTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 14 0.64
19 7 0.32
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TATAAATTTATTAATTAA
Found at i:322265 original size:5 final size:5
Alignment explanation
Indices: 322255--322293 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
322245 TGCTCATCTT
* * *
322255 AAATA AAATA AAATA AAATA AAAAA AAAAA AAACA AAAT
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAAT
322294 GTAGTGCGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.13
Consensus pattern (5 bp):
AAATA
Found at i:323254 original size:31 final size:31
Alignment explanation
Indices: 323219--323277 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
323209 ATCCTCTTAT
*
323219 ATATATTTATTAATA-AAAAAATTTATATTTA
1 ATATA-TTATCAATATAAAAAATTTATATTTA
*
323250 ATATATTATCAATATATAAAATTTATAT
1 ATATATTATCAATATAAAAAATTTATAT
323278 ACTGTTAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (31 bp):
ATATATTATCAATATAAAAAATTTATATTTA
Found at i:326899 original size:3 final size:3
Alignment explanation
Indices: 326893--326932 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
326883 ATTTCCATTC
326893 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
326933 AACAGTAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:328751 original size:3 final size:3
Alignment explanation
Indices: 328745--328785 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
328735 ATAATAATAA
328745 TAT TAT TAT TAT TAT TATT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT T
328786 GAGATTTGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:328769 original size:19 final size:19
Alignment explanation
Indices: 328745--328782 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
328735 ATAATAATAA
328745 TATTATTATTATTATTATT
1 TATTATTATTATTATTATT
328764 TATTATTATTATTATTATT
1 TATTATTATTATTATTATT
328783 ATTGAGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TATTATTATTATTATTATT
Found at i:330402 original size:3 final size:3
Alignment explanation
Indices: 330394--330442 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
330384 TAACTTCACC
330394 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
330442 T
1 T
330443 CTAAAGGGCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:362351 original size:21 final size:21
Alignment explanation
Indices: 362325--362365 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
362315 ATAAAAATAT
362325 TAAATTATTA-ATTTTAATAAA
1 TAAATT-TTATATTTTAATAAA
*
362346 TAAATTTTATTTTTTAATAA
1 TAAATTTTATATTTTAATAA
362366 TTTTAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TAAATTTTATATTTTAATAAA
Found at i:364514 original size:1 final size:1
Alignment explanation
Indices: 364510--364540 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
364500 TTTTTTTTTT
*
364510 GGGGGGGGGGGGGGGGGGGGGGGGGAGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
364541 ATCAAAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.03, C:0.00, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:366295 original size:30 final size:30
Alignment explanation
Indices: 366259--366379 Score: 170
Period size: 30 Copynumber: 4.0 Consensus size: 30
366249 TTGACAGCCA
* * *
366259 ATGCACCTTTATCAGCTGTCCAATCTTCTC
1 ATGCACCTTCACCAGCAGTCCAATCTTCTC
366289 ATGCACCTTCACCAGCAGTCCAATCTTCTC
1 ATGCACCTTCACCAGCAGTCCAATCTTCTC
* *
366319 ATGCACCTTCACCAACAGCCCAATCTTCTC
1 ATGCACCTTCACCAGCAGTCCAATCTTCTC
* **
366349 ATGCACCTTCACCAACCCTCCAATCTTCTC
1 ATGCACCTTCACCAGCAGTCCAATCTTCTC
366379 A
1 A
366380 ACCAGTATGG
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 83 1.00
ACGTcount: A:0.24, C:0.40, G:0.07, T:0.28
Consensus pattern (30 bp):
ATGCACCTTCACCAGCAGTCCAATCTTCTC
Found at i:378110 original size:16 final size:16
Alignment explanation
Indices: 378086--378116 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
378076 GTCACTCGTA
378086 AAAAATAAAAAAAAAC
1 AAAAATAAAAAAAAAC
*
378102 AAAATTAAAAAAAAA
1 AAAAATAAAAAAAAA
378117 AAAGTCATCT
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:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (16 bp):
AAAAATAAAAAAAAAC
Found at i:378111 original size:15 final size:14
Alignment explanation
Indices: 378085--378119 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 14
378075 CGTCACTCGT
378085 AAAAAATAAAAAAA
1 AAAAAATAAAAAAA
378099 AACAAAATTAAAAAAA
1 AA-AAAA-TAAAAAAA
378115 AAAAA
1 AAAAA
378120 GTCATCTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 2 0.11
15 7 0.37
16 10 0.53
ACGTcount: A:0.89, C:0.03, G:0.00, T:0.09
Consensus pattern (14 bp):
AAAAAATAAAAAAA
Found at i:380373 original size:2 final size:2
Alignment explanation
Indices: 380366--380397 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
380356 CTTTTCATTA
*
380366 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
380398 GATCTCATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:381260 original size:2 final size:2
Alignment explanation
Indices: 381253--381288 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
381243 TTCAAGCAAC
381253 CT CT CT CT 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
381289 ATATATATAT
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):
CT
Found at i:381293 original size:2 final size:2
Alignment explanation
Indices: 381288--381315 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
381278 TCTCTCTCTC
381288 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
381316 CACACACACA
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):
TA
Found at i:385549 original size:171 final size:171
Alignment explanation
Indices: 385264--385608 Score: 663
Period size: 171 Copynumber: 2.0 Consensus size: 171
385254 TAGAGGTTGC
*
385264 CAAGTATTAAGACCTGATCACTAGAACTAGGTTCCCAAGTTTGTTAAATCTTTACTTTTTATTCT
1 CAAGTATTAAGACCTGATCACTAGAACTAGGTTCCCAAGTTTGTTAAATCTTTACTTTTCATTCT
385329 TTTGATTGGGTTTCAGTTTTCATTTGCTCTGTTTCCACCAGGCAGCTGTTGATAGCATTACCAGA
66 TTTGATTGGGTTTCAGTTTTCATTTGCTCTGTTTCCACCAGGCAGCTGTTGATAGCATTACCAGA
*
385394 AGCTTGGCATTGGAGTGGGGGACAGATCATGGCATTCGAGT
131 AGCTTGGCATTGAAGTGGGGGACAGATCATGGCATTCGAGT
*
385435 CAAGTATTAAGACCTGATCACTAGAACTAGGTTGCCAAGTTTGTTAAATCTTTACTTTTCATTCT
1 CAAGTATTAAGACCTGATCACTAGAACTAGGTTCCCAAGTTTGTTAAATCTTTACTTTTCATTCT
385500 TTTGATTGGGTTTCAGTTTTCATTTGCTCTGTTTCCACCAGGCAGCTGTTGATAGCATTACCAGA
66 TTTGATTGGGTTTCAGTTTTCATTTGCTCTGTTTCCACCAGGCAGCTGTTGATAGCATTACCAGA
385565 AGCTTGGCATTGAAGTGGGGGACAGATCATGGCATTCGAGT
131 AGCTTGGCATTGAAGTGGGGGACAGATCATGGCATTCGAGT
385606 CAA
1 CAA
385609 TTGGATTGCA
Statistics
Matches: 171, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
171 171 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (171 bp):
CAAGTATTAAGACCTGATCACTAGAACTAGGTTCCCAAGTTTGTTAAATCTTTACTTTTCATTCT
TTTGATTGGGTTTCAGTTTTCATTTGCTCTGTTTCCACCAGGCAGCTGTTGATAGCATTACCAGA
AGCTTGGCATTGAAGTGGGGGACAGATCATGGCATTCGAGT
Found at i:388241 original size:111 final size:111
Alignment explanation
Indices: 388109--388332 Score: 394
Period size: 111 Copynumber: 2.0 Consensus size: 111
388099 ATCAAAAAAT
388109 TATTCTCTAATATGTTGGTAGGATTGAAAAATTATTTGTCCAATAAAATTTATTAAGCCCCCAAT
1 TATTCTCTAATATGTTGGTAGGATTGAAAAATTATTTGTCCAATAAAATTTATTAAGCCCCCAAT
*
388174 AGTTTGGTAAGACTTAATTCAAAATTTAAATCTTCTAATTGTTTGA
66 AGTTTGATAAGACTTAATTCAAAATTTAAATCTTCTAATTGTTTGA
* *
388220 TATTCTCTAATATGTTGGTAGGATTGAAAAATTATTTGTGCAATAAAATTTATTAAGCCCCTAAT
1 TATTCTCTAATATGTTGGTAGGATTGAAAAATTATTTGTCCAATAAAATTTATTAAGCCCCCAAT
* * *
388285 AGTTTGATAAGACTTAATTCAAGATTTAAATTTTTTAATTGTTTGA
66 AGTTTGATAAGACTTAATTCAAAATTTAAATCTTCTAATTGTTTGA
388331 TA
1 TA
388333 GGAATGAAAA
Statistics
Matches: 107, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 107 1.00
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (111 bp):
TATTCTCTAATATGTTGGTAGGATTGAAAAATTATTTGTCCAATAAAATTTATTAAGCCCCCAAT
AGTTTGATAAGACTTAATTCAAAATTTAAATCTTCTAATTGTTTGA
Found at i:388483 original size:20 final size:21
Alignment explanation
Indices: 388450--388489 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
388440 ATGCAAAAAT
* *
388450 AATATTATCGTGTAATAATAC
1 AATATTATCATGTAAGAATAC
388471 AATA-TATCATGTAAGAATA
1 AATATTATCATGTAAGAATA
388490 TAATTAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.35
Consensus pattern (21 bp):
AATATTATCATGTAAGAATAC
Found at i:391251 original size:91 final size:90
Alignment explanation
Indices: 391079--391261 Score: 303
Period size: 91 Copynumber: 2.0 Consensus size: 90
391069 GCTATGGCAG
*
391079 CTCTTTATCTTGCATCTGATGCAGGTTTGTAATTTTGTCTGACCTTTTAGTTCTATGACCATCAT
1 CTCTTTATCTTGCATCTGATGCAGGTTTGTAATTTTGTCTGACCTTTTAGTTATATGACCATCAT
391144 TCAACTACACCAGGCTAGAATTCCT
66 TCAACTACACCAGGCTAGAATTCCT
* * * *
391169 CTCTTTATCTTGCATCTGATGCAGGTTTTTAGTTTTGTCTTACTTTTTTAGTTATATGACCATCA
1 CTCTTTATCTTGCATCTGATGCAGGTTTGTAATTTTGTCTGAC-CTTTTAGTTATATGACCATCA
*
391234 TTCAACTATACCAGGCTAGAATTCCT
65 TTCAACTACACCAGGCTAGAATTCCT
391260 CT
1 CT
391262 ATCTTAACCT
Statistics
Matches: 86, Mismatches: 6, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
90 40 0.47
91 46 0.53
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.43
Consensus pattern (90 bp):
CTCTTTATCTTGCATCTGATGCAGGTTTGTAATTTTGTCTGACCTTTTAGTTATATGACCATCAT
TCAACTACACCAGGCTAGAATTCCT
Found at i:397174 original size:32 final size:33
Alignment explanation
Indices: 397138--397203 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 33
397128 TAAATGGGAT
* *
397138 ATTTAAGATTTTAACTAATGTTTT-TGAGATTA
1 ATTTAAGATATTAACTAATATTTTGTGAGATTA
* *
397170 ATTTAAGATATTAACTTATATTTTGTGAGTTTA
1 ATTTAAGATATTAACTAATATTTTGTGAGATTA
397203 A
1 A
397204 GTTAGTAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 21 0.72
33 8 0.28
ACGTcount: A:0.35, C:0.03, G:0.12, T:0.50
Consensus pattern (33 bp):
ATTTAAGATATTAACTAATATTTTGTGAGATTA
Found at i:397298 original size:17 final size:19
Alignment explanation
Indices: 397262--397298 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
397252 TCAATTAAAA
397262 AATCAAATAGTTAGGCCTTT
1 AATCAAATA-TTAGGCCTTT
397282 AATCAAAT-TTA-GCCTTT
1 AATCAAATATTAGGCCTTT
397299 TTTTTTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.35
18 3 0.18
20 8 0.47
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (19 bp):
AATCAAATATTAGGCCTTT
Found at i:397539 original size:94 final size:94
Alignment explanation
Indices: 397378--397548 Score: 252
Period size: 94 Copynumber: 1.8 Consensus size: 94
397368 TATGGTAAAA
* ** * **
397378 TGAAGCTTAATTTTTAACCACCTAAGTTGTGTTACAAATAATTTTTTGATGGATGAATTCGACTT
1 TGAAGCTTAATTTTTAACCACCTAAATCATGTCACAAATAATAATTTGATGGATGAATTCGACTT
397443 TTAACTTAAGAAGTTATTTTAAGGGAAAT
66 TTAACTTAAGAAGTTATTTTAAGGGAAAT
* * * *
397472 TGAAGGTTAATTTTTAATCACCTAAATCATGTCATAAATAATAATTTGATGGATGAATTTGACTT
1 TGAAGCTTAATTTTTAACCACCTAAATCATGTCACAAATAATAATTTGATGGATGAATTCGACTT
397537 TTAACTTAAGAA
66 TTAACTTAAGAA
397549 TTTGAATTAA
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
94 67 1.00
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (94 bp):
TGAAGCTTAATTTTTAACCACCTAAATCATGTCACAAATAATAATTTGATGGATGAATTCGACTT
TTAACTTAAGAAGTTATTTTAAGGGAAAT
Found at i:404815 original size:13 final size:13
Alignment explanation
Indices: 404799--404841 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
404789 ATTTAAATTC
*
404799 AAAAAATACATTT
1 AAAAAATATATTT
* *
404812 AAAAATTATA-CT
1 AAAAAATATATTT
404824 AAAAAATATATTT
1 AAAAAATATATTT
404837 AAAAA
1 AAAAA
404842 TTTTAAATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAAAATATATTT
Found at i:404817 original size:12 final size:12
Alignment explanation
Indices: 404800--404842 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
404790 TTTAAATTCA
*
404800 AAAAATACATTT
1 AAAAATATATTT
* *
404812 AAAAATTATACTA
1 AAAAA-TATATTT
404825 AAAAATATATTT
1 AAAAATATATTT
404837 AAAAAT
1 AAAAAT
404843 TTTAAATATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
12 16 0.64
13 9 0.36
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAAATATATTT
Found at i:413471 original size:2 final size:2
Alignment explanation
Indices: 413466--413496 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
413456 TGTGAAGTTC
413466 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
413497 TGACCATACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:417299 original size:167 final size:165
Alignment explanation
Indices: 416995--417364 Score: 499
Period size: 167 Copynumber: 2.2 Consensus size: 165
416985 TATATTTTTC
* ** * * * * *
416995 TCTGACTAATTTTATCGTGATCAGAAAAAGAAGGTAAATAACAACGGAGGTCATCAGCCACCTAA
1 TCTGACTAATTTTATCATGATCAGGGAAAGGAGGTAAACAACAACGCAGGTCATCAACCACCCAA
* **
417060 AAATTTCGCTAATAGTCATCCAAGATTGAATACTAATTCTCTTAAGGTGAGGAAAATATGTATAA
66 AAATTTCGCTAATAGTCATCCAAGATTGAATACTAATTCTCTTAAGGCGAGGAAAATACATATAA
*
417125 TAAAGAGTAAGACTAAATTTTTCTCCATTTTCGATTA
131 CAAAGAGTAAGACT--ATTTTTCTCCATTTTCGATTA
* * * * * *
417162 TTTGACTACTTTTATCTTGATCAGGGAAAGGAGGTAAACAACAGCGCTGGTCATCAACTACCCAA
1 TCTGACTAATTTTATCATGATCAGGGAAAGGAGGTAAACAACAACGCAGGTCATCAACCACCCAA
*
417227 AAATTTCGCTAATAGTCATCCAAGATTGAATACTAATTCTCTTACGGCGA-GAAAAGTACATATA
66 AAATTTCGCTAATAGTCATCCAAGATTGAATACTAATTCTCTTAAGGCGAGGAAAA-TACATATA
*
417291 ACAAAGAGTAAGACTATTTTTCTCCATTTTTGATTA
130 ACAAAGAGTAAGACTATTTTTCTCCATTTTCGATTA
* **
417327 TCTGACTATTTTTATCATGATCAGGGATGGGAGGTAAA
1 TCTGACTAATTTTATCATGATCAGGGAAAGGAGGTAAA
417365 TAAGGACGTA
Statistics
Matches: 178, Mismatches: 24, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
165 53 0.30
166 5 0.03
167 120 0.67
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (165 bp):
TCTGACTAATTTTATCATGATCAGGGAAAGGAGGTAAACAACAACGCAGGTCATCAACCACCCAA
AAATTTCGCTAATAGTCATCCAAGATTGAATACTAATTCTCTTAAGGCGAGGAAAATACATATAA
CAAAGAGTAAGACTATTTTTCTCCATTTTCGATTA
Found at i:422224 original size:12 final size:11
Alignment explanation
Indices: 422189--422251 Score: 54
Period size: 12 Copynumber: 5.4 Consensus size: 11
422179 ATAAACCAGT
*
422189 AAAATAACACAA
1 AAAATAA-ATAA
*
422201 AAAATAACTAA
1 AAAATAAATAA
422212 AAAATAAATTAA
1 AAAATAAA-TAA
*
422224 AACATAAATAA
1 AAAATAAATAA
*
422235 AGAAAGAAAATAA
1 A-AAA-TAAATAA
422248 AAAA
1 AAAA
422252 AATGAAATGA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
11 13 0.31
12 22 0.52
13 7 0.17
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.14
Consensus pattern (11 bp):
AAAATAAATAA
Found at i:422252 original size:27 final size:28
Alignment explanation
Indices: 422212--422271 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 28
422202 AAATAACTAA
422212 AAAATAAATTAAAACAT-AAAT-AAAGAAAG
1 AAAATAAA-TAAAA-ATGAAATGAAA-AAAG
422241 AAAATAAA-AAAAATGAAATGAAAAAAG
1 AAAATAAATAAAAATGAAATGAAAAAAG
422268 AAAA
1 AAAA
422272 ACCTGCGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
26 2 0.07
27 16 0.55
28 3 0.10
29 8 0.28
ACGTcount: A:0.77, C:0.02, G:0.08, T:0.13
Consensus pattern (28 bp):
AAAATAAATAAAAATGAAATGAAAAAAG
Found at i:422734 original size:20 final size:20
Alignment explanation
Indices: 422709--422747 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
422699 AACACCTCCA
*
422709 GAAACCTAAATCTAAACCCC
1 GAAACCCAAATCTAAACCCC
422729 GAAACCCAAATCTAAACCC
1 GAAACCCAAATCTAAACCC
422748 AAAAATTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.36, G:0.05, T:0.13
Consensus pattern (20 bp):
GAAACCCAAATCTAAACCCC
Found at i:423154 original size:3 final size:3
Alignment explanation
Indices: 423121--423226 Score: 75
Period size: 3 Copynumber: 37.3 Consensus size: 3
423111 AAAGAAAAAA
* * *
423121 AAT AAA AAT AAA AAT AAAT AAT AA- AAT -AT AAT AAT AAT GAT AAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
423165 AAT AAT AA- AAT -AT AAT AAT AAT GAT GAT -AT AAT -AT AAT -AT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
423207 ACT ATAT TAT AAT AAT AAT A
1 AAT A-AT AAT AAT AAT AAT A
423227 TAGTATACCA
Statistics
Matches: 82, Mismatches: 11, Indels: 20
0.73 0.10 0.18
Matches are distributed among these distances:
2 15 0.18
3 63 0.77
4 4 0.05
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:423166 original size:22 final size:21
Alignment explanation
Indices: 423128--423233 Score: 83
Period size: 22 Copynumber: 4.9 Consensus size: 21
423118 AAAAATAAAA
* *
423128 ATAAAAATAA-ATAATAAAAT
1 ATAATAATAATATAATATAAT
423148 ATAATAATAATGATAATAATAAT
1 ATAATAATAAT-ATAAT-ATAAT
* *
423171 AAAAT-ATAATAATAATGATGAT
1 ATAATAATAAT-ATAAT-ATAAT
*
423193 ATAAT-ATAATATAAACTATATT
1 ATAATAATAATAT-AA-TATAAT
*
423215 ATAATAATAATATAGTATA
1 ATAATAATAATATAATATA
423234 CCATGCTATA
Statistics
Matches: 70, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
20 9 0.13
21 6 0.09
22 39 0.56
23 16 0.23
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (21 bp):
ATAATAATAATATAATATAAT
Found at i:423228 original size:28 final size:28
Alignment explanation
Indices: 423137--423226 Score: 121
Period size: 28 Copynumber: 3.2 Consensus size: 28
423127 AATAAAAATA
423137 AATAATAAAATATAATAATAATGATAAT
1 AATAATAAAATATAATAATAATGATAAT
*
423165 AATAATAAAATATAATAATAATGATGAT
1 AATAATAAAATATAATAATAATGATAAT
* * *
423193 -ATAATATAATATAA-ACTATATTATAAT
1 AATAATAAAATATAATAATA-ATGATAAT
423220 AATAATA
1 AATAATA
423227 TAGTATACCA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
26 3 0.05
27 19 0.35
28 33 0.60
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.34
Consensus pattern (28 bp):
AATAATAAAATATAATAATAATGATAAT
Found at i:424102 original size:11 final size:11
Alignment explanation
Indices: 424061--424111 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
424051 GGTTTACATA
*
424061 TATATTTTTAA
1 TATATTTTTAT
424072 TATAATTTTT-T
1 TAT-ATTTTTAT
**
424083 TATCCTTTTAT
1 TATATTTTTAT
424094 TATATTTTTAT
1 TATATTTTTAT
424105 TATATTT
1 TATATTT
424112 ATTTGTATAC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
10 4 0.12
11 23 0.70
12 6 0.18
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (11 bp):
TATATTTTTAT
Found at i:426941 original size:23 final size:24
Alignment explanation
Indices: 426915--426960 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
426905 AGAAACTAGA
*
426915 AAGAGAAAGA-AAGGAAAGAGAAT
1 AAGAAAAAGATAAGGAAAGAGAAT
*
426938 AAGAAAAAGATAGGGAAAGAGAA
1 AAGAAAAAGATAAGGAAAGAGAA
426961 ATTTGAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.65, C:0.00, G:0.30, T:0.04
Consensus pattern (24 bp):
AAGAAAAAGATAAGGAAAGAGAAT
Found at i:427389 original size:24 final size:25
Alignment explanation
Indices: 427345--427391 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
427335 ATAATTATCC
*
427345 AATGATAAAATTTTTAGAAATTTCA
1 AATGATAAAATTTCTAGAAATTTCA
*
427370 AATGAT-AAATTTCTATAAATTT
1 AATGATAAAATTTCTAGAAATTT
427392 TTTAGGTGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (25 bp):
AATGATAAAATTTCTAGAAATTTCA
Found at i:427737 original size:22 final size:21
Alignment explanation
Indices: 427712--427766 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
427702 CCAAATGGTG
* *
427712 AAAATTTTAAAAATTAAAAAAA
1 AAAAATTTAAAAA-TCAAAAAA
**
427734 AAAAATTTCTAAATCAAAAAA
1 AAAAATTTAAAAATCAAAAAA
427755 AAAAATTTAAAA
1 AAAAATTTAAAA
427767 GAGTACTCAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (21 bp):
AAAAATTTAAAAATCAAAAAA
Found at i:430501 original size:49 final size:49
Alignment explanation
Indices: 430447--430775 Score: 294
Period size: 48 Copynumber: 6.8 Consensus size: 49
430437 AAAAAAGTTA
* * * *
430447 CTATGAAGATAGGTAACAAATTTTAAAAATCTCATTTTAAAAATGGCTC
1 CTATGAAAATAGGCAACAAACTTTAAAAATCTCATTTTGAAAATGGCTC
* * ** * *
430496 GTATGAAAATAGGTAATGAACTTTAAAAATCTCATTTAGAAAA-GGCTT
1 CTATGAAAATAGGCAACAAACTTTAAAAATCTCATTTTGAAAATGGCTC
* * * *
430544 TTATAAAAATAGGCAACAAACTTTAAAAAT-TCATTTTGAAAACGACTC
1 CTATGAAAATAGGCAACAAACTTTAAAAATCTCATTTTGAAAATGGCTC
* * * *
430592 ATAT-AAAGATAGGCAACGAAA-TTTAAAAAT-TCATTTTGAAATTGACTA
1 CTATGAAA-ATAGGCAAC-AAACTTTAAAAATCTCATTTTGAAAATGGCTC
* * * * * * *
430640 TTATGAAGATCGACAATAAATTTTAAAAATCTCATTTTGGAAA-GAG-TC
1 CTATGAAAATAGGCAACAAACTTTAAAAATCTCATTTTGAAAATG-GCTC
* * * * * *
430688 CTATGAAAATAAGCAACGAATTTTAAAAATCTCATTTTGAATATAGCAC
1 CTATGAAAATAGGCAACAAACTTTAAAAATCTCATTTTGAAAATGGCTC
*
430737 CTATGAAAATAGGCAACATACTTTAAAAATCTCATTTTG
1 CTATGAAAATAGGCAACAAACTTTAAAAATCTCATTTTG
430776 GAAAGGTTTT
Statistics
Matches: 227, Mismatches: 44, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
47 17 0.07
48 123 0.54
49 87 0.38
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (49 bp):
CTATGAAAATAGGCAACAAACTTTAAAAATCTCATTTTGAAAATGGCTC
Found at i:430617 original size:96 final size:97
Alignment explanation
Indices: 430448--430780 Score: 336
Period size: 96 Copynumber: 3.4 Consensus size: 97
430438 AAAAAGTTAC
* * * * * * * *
430448 TATGAAGATAGGTAACAAATTTTAAAAATCTCATTTTAAAAATGGCTCGTATGAAAATAGGTAAT
1 TATGAAAATAGGCAACAAACTTTAAAAATCTCATTTTGAAAA-GACTCATATGAAAATAGGCAAC
* * *
430513 GAACTTTAAAAATCTCATTTAGAAA-AGGCTTT
65 GAAATTTAAAAATCTCATTTTGAAATAGGCTAT
*
430545 TATAAAAATAGGCAACAAACTTTAAAAAT-TCATTTTGAAAACGACTCATAT-AAAGATAGGCAA
1 TATGAAAATAGGCAACAAACTTTAAAAATCTCATTTTGAAAA-GACTCATATGAAA-ATAGGCAA
* *
430608 CGAAATTTAAAAAT-TCATTTTGAAATTGACTAT
64 CGAAATTTAAAAATCTCATTTTGAAATAGGCTAT
* * * * * * * * *
430641 TATGAAGATCGACAATAAATTTTAAAAATCTCATTTTGGAAAGAGTCCTATGAAAATAAGCAACG
1 TATGAAAATAGGCAACAAACTTTAAAAATCTCATTTTGAAAAGACTCATATGAAAATAGGCAACG
* *
430706 AATTTTAAAAATCTCATTTTGAATATA-GC-ACC
66 AAATTTAAAAATCTCATTTTGAA-ATAGGCTA-T
* *
430738 TATGAAAATAGGCAACATACTTTAAAAATCTCATTTTGGAAAG
1 TATGAAAATAGGCAACAAACTTTAAAAATCTCATTTTGAAAAG
430781 GTTTTTGAAA
Statistics
Matches: 194, Mismatches: 35, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
95 13 0.07
96 92 0.47
97 87 0.45
98 2 0.01
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (97 bp):
TATGAAAATAGGCAACAAACTTTAAAAATCTCATTTTGAAAAGACTCATATGAAAATAGGCAACG
AAATTTAAAAATCTCATTTTGAAATAGGCTAT
Found at i:430825 original size:26 final size:26
Alignment explanation
Indices: 430762--430831 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
430752 ACATACTTTA
* * *
430762 AAAATCTCATTTTGGAAAGGTTTTTG
1 AAAATCTTATTTTGAAAAAGTTTTTG
*
430788 -AAATTTTGATTTTGAAAAAG-TTTTG
1 AAAATCTT-ATTTTGAAAAAGTTTTTG
430813 CAAAATCTTATTTTGAAAA
1 -AAAATCTTATTTTGAAAA
430832 GTTGGGTTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
25 10 0.28
26 20 0.56
27 6 0.17
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (26 bp):
AAAATCTTATTTTGAAAAAGTTTTTG
Found at i:430832 original size:25 final size:24
Alignment explanation
Indices: 430762--430834 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 24
430752 ACATACTTTA
* *
430762 AAAATCTCATTTTGGAAAGGTTTTTG
1 AAAATCTTATTTT-GAAAAG-TTTTG
*
430788 -AAATTTTGATTTTGAAAAAGTTTTG
1 AAAATCTT-ATTTTG-AAAAGTTTTG
430813 CAAAATCTTATTTTGAAAAGTT
1 -AAAATCTTATTTTGAAAAGTT
430835 GGGTTTCATC
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
25 18 0.46
26 15 0.38
27 6 0.15
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.44
Consensus pattern (24 bp):
AAAATCTTATTTTGAAAAGTTTTG
Found at i:432722 original size:38 final size:38
Alignment explanation
Indices: 432680--432755 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
432670 ACTAGTACTT
*
432680 TAATAACAAAATAAAAATAATATTATACCTATCTAAAA
1 TAATAACAAAATAAAAATAATATTATACCTATCCAAAA
432718 TAATAACAAAATAAAAATAATATTATACCTATCCAAAA
1 TAATAACAAAATAAAAATAATATTATACCTATCCAAAA
432756 AATTTGGGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.28
Consensus pattern (38 bp):
TAATAACAAAATAAAAATAATATTATACCTATCCAAAA
Found at i:432755 original size:21 final size:21
Alignment explanation
Indices: 432692--432756 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 21
432682 ATAACAAAAT
432692 AAAAATAATATTATACCTATC
1 AAAAATAATATTATACCTATC
* * **
432713 TAAAATAATA--ACA-AAAT-
1 AAAAATAATATTATACCTATC
432730 AAAAATAATATTATACCTATCC
1 AAAAATAATATTATACCTAT-C
432752 AAAAA
1 AAAAA
432757 ATTTGGGATT
Statistics
Matches: 31, Mismatches: 8, Indels: 9
0.65 0.17 0.19
Matches are distributed among these distances:
17 9 0.29
18 2 0.06
19 4 0.13
20 2 0.06
21 9 0.29
22 5 0.16
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAAATAATATTATACCTATC
Found at i:443247 original size:151 final size:147
Alignment explanation
Indices: 443040--443333 Score: 457
Period size: 151 Copynumber: 2.0 Consensus size: 147
443030 CAACTAGGAA
*
443040 CCTATCAGTGGAATTGCAAATGAAATAAAAACATATTCTAGGAAACCAACAAGCCAGGCTCACAT
1 CCTATCAGTGGAATTGCAAATGAAATAAAAACATATTCCAGGAAACCAACAAGCCAGGCTCACAT
* *
443105 CTAACTGCTGCTACAA-AAATGGACCAGAGACAGATTTAGCAAGACTGACCTCCTTCAGAACAAA
66 CTAACTGCTGCTA-AATAAAAGGACCAGAGAC--A--TAGCAAGACTGACCTCCCTCAGAACAAA
* *
443169 GACATGATTTAGAACACACATG
126 GAAATGATTCAGAACACACATG
*
443191 CCTATCAGTGGAATTGCAAATGAAATGAAAAA-ATATTCCAGGAAACCAACAGGCCAGGCTCACA
1 CCTATCAGTGGAATTGCAAATGAAAT-AAAAACATATTCCAGGAAACCAACAAGCCAGGCTCACA
*
443255 TCTAACTGCTGCTAAATAAAAGGGCCAGAGACATAGCAAGACTGACCTCCCTCAGAACAAAGAAA
65 TCTAACTGCTGCTAAATAAAAGGACCAGAGACATAGCAAGACTGACCTCCCTCAGAACAAAGAAA
443320 TGATTCAGAACACA
130 TGATTCAGAACACA
443334 TATAGGCTCC
Statistics
Matches: 134, Mismatches: 7, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
147 43 0.32
149 1 0.01
150 2 0.01
151 83 0.62
152 5 0.04
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.18
Consensus pattern (147 bp):
CCTATCAGTGGAATTGCAAATGAAATAAAAACATATTCCAGGAAACCAACAAGCCAGGCTCACAT
CTAACTGCTGCTAAATAAAAGGACCAGAGACATAGCAAGACTGACCTCCCTCAGAACAAAGAAAT
GATTCAGAACACACATG
Found at i:445433 original size:2 final size:2
Alignment explanation
Indices: 445417--445468 Score: 58
Period size: 2 Copynumber: 27.5 Consensus size: 2
445407 ACACAAATAA
*
445417 AT AT A- AT AGT AT AT AT AT AT AT AT AT AT AT AT GT AT AT -T AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
445458 A- AT -T AT AT AT A
1 AT AT AT AT AT AT A
445469 AACTATTCCC
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
1 4 0.09
2 37 0.86
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:463163 original size:21 final size:21
Alignment explanation
Indices: 463131--463188 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 21
463121 GAATTATTTC
*
463131 AAATT-TA-TAAAAGTTATGA
1 AAATTATATTAAAAGTTATCA
* *
463150 TAATTATATTAAAAATTATCA
1 AAATTATATTAAAAGTTATCA
* *
463171 AAATTATCTTAAAGGTTA
1 AAATTATATTAAAAGTTA
463189 GAGAGAAAAG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
19 4 0.13
20 2 0.07
21 24 0.80
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (21 bp):
AAATTATATTAAAAGTTATCA
Found at i:473531 original size:22 final size:23
Alignment explanation
Indices: 473506--473555 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 23
473496 TATATTAATA
*
473506 TAAAATATATTTTTAA-TTTTAT
1 TAAAATATATTTATAATTTTTAT
*
473528 T-AAATTTATTTATAATTTTTAT
1 TAAAATATATTTATAATTTTTAT
473550 TAAAAT
1 TAAAAT
473556 TTTAAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 12 0.50
22 8 0.33
23 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TAAAATATATTTATAATTTTTAT
Found at i:473576 original size:11 final size:11
Alignment explanation
Indices: 473562--473603 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
473552 AAATTTTAAA
473562 TTATATTATTT
1 TTATATTATTT
473573 TTATATT-TTT
1 TTATATTATTT
473583 TGGTCATATTATTT
1 T--T-ATATTATTT
473597 TTATATT
1 TTATATT
473604 GATTCATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
10 4 0.15
11 12 0.44
12 2 0.07
13 5 0.19
14 4 0.15
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.69
Consensus pattern (11 bp):
TTATATTATTT
Found at i:473582 original size:24 final size:24
Alignment explanation
Indices: 473555--473603 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
473545 TTTATTAAAA
*
473555 TTTTAAATTATATTATTTTTATAT
1 TTTTAAATCATATTATTTTTATAT
***
473579 TTTTTGGTCATATTATTTTTATAT
1 TTTTAAATCATATTATTTTTATAT
473603 T
1 T
473604 GATTCATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (24 bp):
TTTTAAATCATATTATTTTTATAT
Found at i:487284 original size:12 final size:12
Alignment explanation
Indices: 487267--487292 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
487257 GTAGCGTGAA
487267 GGAAAAGCCGTG
1 GGAAAAGCCGTG
487279 GGAAAAGCCGTG
1 GGAAAAGCCGTG
487291 GG
1 GG
487293 CTTCAATGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.15, G:0.46, T:0.08
Consensus pattern (12 bp):
GGAAAAGCCGTG
Found at i:491017 original size:24 final size:25
Alignment explanation
Indices: 490985--491032 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
490975 ATTCGATGCG
* * *
490985 TTTAGTTCATTTTGAATTGATTTTT
1 TTTAGTTCAGTTTAAATTAATTTTT
491010 TTTA-TTCAGTTTAAATTAATTTT
1 TTTAGTTCAGTTTAAATTAATTTT
491033 AGAAATTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.25, C:0.04, G:0.08, T:0.62
Consensus pattern (25 bp):
TTTAGTTCAGTTTAAATTAATTTTT
Found at i:492688 original size:21 final size:21
Alignment explanation
Indices: 492658--492698 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
492648 CTTCCTTGAA
*
492658 ATGATAATTTTTTTTTATTTT
1 ATGATAATTTTTTCTTATTTT
*
492679 ATGATTATTTTTTCTTATTT
1 ATGATAATTTTTTCTTATTT
492699 CCTTAATCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (21 bp):
ATGATAATTTTTTCTTATTTT
Found at i:494422 original size:5 final size:5
Alignment explanation
Indices: 494414--494473 Score: 54
Period size: 5 Copynumber: 12.6 Consensus size: 5
494404 TCGATTAATT
* * * **
494414 TTAAA TTAAA TTAAA GT-AA TTAAA TTAAA TT-AT TTTAA TTTTA TT-AA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA
494461 TTAAA TTAAA TTA
1 TTAAA TTAAA TTA
494474 TTTTAATTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
4 9 0.20
5 37 0.80
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (5 bp):
TTAAA
Found at i:494436 original size:14 final size:14
Alignment explanation
Indices: 494417--494492 Score: 71
Period size: 14 Copynumber: 5.4 Consensus size: 14
494407 ATTAATTTTA
*
494417 AATTAAATTAAAGT
1 AATTAAATTAAATT
494431 AATTAAATTAAATT
1 AATTAAATTAAATT
* * **
494445 ATTTTAATTTTATT
1 AATTAAATTAAATT
494459 AATTAAATTAAATT
1 AATTAAATTAAATT
* * **
494473 ATTTTAATTTTATT
1 AATTAAATTAAATT
494487 AATTAA
1 AATTAA
494493 TTTAGTTGAT
Statistics
Matches: 47, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 47 1.00
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (14 bp):
AATTAAATTAAATT
Found at i:494452 original size:19 final size:19
Alignment explanation
Indices: 494411--494481 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 19
494401 GATTCGATTA
*
494411 ATTTTAAATTAAATTAAAGT
1 ATTTT-AATTAAATTAAATT
* *
494431 AATTAAATTAAATTATTTTAATT
1 ATTTTAATTAAATTA----AATT
494454 -TTATTAATTAAATTAAATT
1 ATT-TTAATTAAATTAAATT
494473 ATTTTAATT
1 ATTTTAATT
494482 TTATTAATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 13
0.69 0.09 0.22
Matches are distributed among these distances:
19 20 0.50
20 5 0.12
22 1 0.03
23 14 0.35
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (19 bp):
ATTTTAATTAAATTAAATT
Found at i:494504 original size:28 final size:28
Alignment explanation
Indices: 494430--494492 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
494420 TAAATTAAAG
494430 TAATTAAATTAAATTATTTTAATTTTAT
1 TAATTAAATTAAATTATTTTAATTTTAT
494458 TAATTAAATTAAATTATTTTAATTTTAT
1 TAATTAAATTAAATTATTTTAATTTTAT
494486 TAATTAA
1 TAATTAA
494493 TTTAGTTGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
TAATTAAATTAAATTATTTTAATTTTAT
Found at i:494864 original size:13 final size:13
Alignment explanation
Indices: 494834--494858 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
494824 AATTAACAAA
494834 ATTAATTAATTTG
1 ATTAATTAATTTG
494847 ATTAATTAATTT
1 ATTAATTAATTT
494859 AGTTAAAATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
ATTAATTAATTTG
Found at i:497039 original size:20 final size:20
Alignment explanation
Indices: 497002--497040 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
496992 TCTCTGTTTT
* **
497002 TTTCTCTTTTTTTTTTGCAG
1 TTTCCCTTTTTTGCTTGCAG
497022 TTTCCCTTTTTTGCTTGCA
1 TTTCCCTTTTTTGCTTGCA
497041 CACAAATCTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.05, C:0.21, G:0.10, T:0.64
Consensus pattern (20 bp):
TTTCCCTTTTTTGCTTGCAG
Found at i:501928 original size:21 final size:22
Alignment explanation
Indices: 501880--501936 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
501870 GATTATATAT
*
501880 ATAATTATTTTATTTTTACATTA
1 ATAA-TATTTTATTTTTACATAA
501903 ATAATATTTTATATTTTA-A-AA
1 ATAATATTTTAT-TTTTACATAA
501924 ATAATATTTTATT
1 ATAATATTTTATT
501937 AATTTTGAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 1 0.03
21 13 0.41
22 9 0.28
23 9 0.28
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
ATAATATTTTATTTTTACATAA
Found at i:505950 original size:123 final size:122
Alignment explanation
Indices: 505729--505979 Score: 412
Period size: 123 Copynumber: 2.0 Consensus size: 122
505719 ATAGCACAAT
*
505729 ACAAGTCGAAGACGTTTAAGATGACCAGACCTGAGACAAGCATCATTTGAAGAATAAAAAAAGGG
1 ACAAGTCAAAGACGTTTAAGATGACCAGACCTGAGACAAGCATCATTTGAAGAATAAAAAAAGGG
** * *
505794 CAGCGTCAGCAGTTTTACACAAATGAATAACCATTTCAGTACAGTAGTACAGTGAAA
66 CAGCGTCAGCAGTTGCACACAAATGAATAACCATTTCAGTACAGTAATACAGCGAAA
* * *
505851 ACAAGTCAAAGACGTTTAAGATGAGCAGACCTGTGACAAGCATCATTTTGAAGAATAAAAAATGG
1 ACAAGTCAAAGACGTTTAAGATGACCAGACCTGAGACAAGCATCA-TTTGAAGAATAAAAAAAGG
*
505916 GCAGCGTCAGCAGTTGCACACAAATGAATAACCATTTCAGTACAGTAATATAGCGAAA
65 GCAGCGTCAGCAGTTGCACACAAATGAATAACCATTTCAGTACAGTAATACAGCGAAA
505974 ACAAGT
1 ACAAGT
505980 GATGTATGAA
Statistics
Matches: 119, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
122 42 0.35
123 77 0.65
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.21
Consensus pattern (122 bp):
ACAAGTCAAAGACGTTTAAGATGACCAGACCTGAGACAAGCATCATTTGAAGAATAAAAAAAGGG
CAGCGTCAGCAGTTGCACACAAATGAATAACCATTTCAGTACAGTAATACAGCGAAA
Done.