Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008428.1 Hibiscus syriacus cultivar Beakdansim tig00111213_pilon, 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: 6915314
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 30
Found at i:2324103 original size:80 final size:80
Alignment explanation
Indices: 2323846--2324345 Score: 552
Period size: 80 Copynumber: 6.2 Consensus size: 80
2323836 TTTTAAAATA
* *
2323846 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTAATTTATTTTAA
1 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT--
*
2323911 ATAATTTA-TTAGTATGGATTG
62 AT--TGTAGTT-GTATGGATTG
* * * ** * * * *
2323932 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA--TT--AGTATAGATTGATTTA-T
1 ATTTATTTT-AAATA---ATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
*** *
2323992 -TT-TA-AAATATAGATTG
62 ATTGTAGTTGTATGGATTG
2324008 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
*
2324073 TAGTTTTATGGATTG
66 TAGTTGTATGGATTG
**
2324088 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATAAATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
2324153 TAGTTGTATGGATTG
66 TAGTTGTATGGATTG
* *
2324168 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT--
* *
2324233 ATAATTTA-TTAGTATGAATTG
62 AT--TGTAGTT-GTATGGATTG
*
2324254 ATTTAATTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
2324319 TAGTTGTATGGATTG
66 TAGTTGTATGGATTG
2324334 ATTTATTTTAAA
1 ATTTATTTTAAA
2324346 ATATGAATTG
Statistics
Matches: 351, Mismatches: 43, Indels: 46
0.80 0.10 0.10
Matches are distributed among these distances:
72 16 0.05
74 2 0.01
75 5 0.01
76 31 0.09
77 3 0.01
78 3 0.01
79 2 0.01
80 164 0.47
81 2 0.01
82 4 0.01
83 1 0.00
84 4 0.01
85 2 0.01
86 90 0.26
87 5 0.01
88 2 0.01
90 15 0.04
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (80 bp):
ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
TAGTTGTATGGATTG
Found at i:2324119 original size:134 final size:131
Alignment explanation
Indices: 2323891--2324662 Score: 539
Period size: 134 Copynumber: 5.9 Consensus size: 131
2323881 TATTTTAAAA
* ** * *
2323891 TATGGATTAATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATGGATTAGTATAGATTGATTTAGTTT---ATATGGATTGAT
* *
2323956 TTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGATTTATTTTAAAT
63 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAAATTGATTTA--TT--AT
* *
2324021 AATTTATTTG
124 --TGTAGTTG
**
2324031 TATGGATTGATTTATTTTAAA-ATATGGATT-G-ATTTATT-ATTGTAGTTT-TATGGATTGATT
1 TATGGATTGATTTATTTTAAATA-ATGGATTAGTATAGATTGATT-TAGTTTATATGGATTGATT
*
2324091 TATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATAAATTGATTTATTATTGTAG
64 TATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAAATTGATTTATTATTGTAG
2324156 TTG
129 TTG
** *
2324159 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATGGATTAGTATAGATTGATTTAGTTT---ATATGGATTGAT
* * * *
2324224 TTATTTTAAATAATTTATTAGTATGAATTGATTTAATTT-AAATAATTTATTTGTATGGATTGAT
63 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAT-A-TAAATTG-AT---TT-A-
* ***
2324288 TTATTTTA-AAA
120 TTATTGTAGTTG
* * * *
2324299 TATGGATTGATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAAATATGAATTGA
1 TATGGATTGATTTATTTTAAATAATGGA-TTAGTATAGATTGATTTAGTTT---ATATGGATTGA
2324357 TTTATTTTAAATAATTTATTAGTATGGATTGATTTA--TT----T-TAAA-T-A---A-T-TTGT
62 TTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAAATTGATTTATTATTGT
2324408 --TTG
127 AGTTG
** *
2324411 TATGGATTGATTTATTTTAAA-ATATGGATT-G-ATTTATT-ATTGTAG-TTGTATGGATTGATT
1 TATGGATTGATTTATTTTAAATA-ATGGATTAGTATAGATTGATT-TAGTTTATATGGATTGATT
* **
2324471 TATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATA
64 TATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAAATTGATTTA--TT--AT-
*
2324536 ATTTA-TTAG
124 -TGTAGTT-G
** *
2324545 TATGGATTGATTTATTTTAAA-ATATGGATT-G-ATTTATT-ATTGTAGTTGTATA--AATTGAT
1 TATGGATTGATTTATTTTAAATA-ATGGATTAGTATAGATTGATT-TAGTT-TATATGGATTGAT
* ** *
2324604 TTATTTTAAATAATTTATTAGAATAAATTGATTTATTTTAAAATATAGATTGATTTATT
63 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAAATTGATTTATT
2324663 TTAAATAATT
Statistics
Matches: 531, Mismatches: 50, Indels: 110
0.77 0.07 0.16
Matches are distributed among these distances:
112 58 0.11
113 3 0.01
114 5 0.01
115 5 0.01
116 9 0.02
117 3 0.01
118 4 0.01
119 2 0.00
120 1 0.00
121 1 0.00
123 1 0.00
124 1 0.00
125 1 0.00
126 2 0.00
127 1 0.00
128 32 0.06
129 3 0.01
130 13 0.02
131 3 0.01
132 8 0.02
133 6 0.01
134 288 0.54
135 8 0.02
136 7 0.01
137 3 0.01
138 12 0.02
139 4 0.01
140 40 0.08
141 7 0.01
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (131 bp):
TATGGATTGATTTATTTTAAATAATGGATTAGTATAGATTGATTTAGTTTATATGGATTGATTTA
TTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAAATTGATTTATTATTGTAGTT
G
Found at i:2324287 original size:300 final size:302
Alignment explanation
Indices: 2323945--2324662 Score: 1011
Period size: 300 Copynumber: 2.4 Consensus size: 302
2323935 TATTTTAAAA
* *
2323945 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGAT
1 TATGGATTGATTTAATTTAAATAATTTATTTGTATAGATTGATTTATTTTAAAATATAGATTGAT
2324010 TTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT-AT-TG
66 TTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTAATATG
*
2324073 TAGTT-TTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATA
131 TA-TTAGTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATA
2324137 AATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTAT-AGATTGA
195 AATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGA-ATTGA
2324201 TTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
259 TTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
* * *
2324245 TATGAATTGATTTAATTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTAATTTAAATAATTTATTTGTATAGATTGATTTATTTTAAAATATAGATTGAT
* * *
2324310 TTA--TT--AT--TGTAGTTGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTTTAAAT
66 TTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT-AAT
* *
2324369 AATTTATTAGTATGGATTGATTTATTTTAAATAATTTGTTTGTATGGATTGATTTATTTTAAAAT
128 -ATGTATTAGTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAAT
**
2324434 ATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATT
192 ATAAATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATT
2324499 GATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
257 GATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
* * * * * *** *
2324545 TATGGATTGATTT-ATTTTAA-AA--TA--TGGATTGATTTA-TTATTGTAGTTGTATAAATTGA
1 TATGGATTGATTTAATTTAAATAATTTATTTGTATAGATTGATTTATTTTA-AAATATAGATTGA
* * ** *
2324603 TTTATTTTAAATAATTTATTAGAATAAATTGATTTATTTTAAAATATAGATTGATTTATT
65 TTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
2324663 TTAAATAATT
Statistics
Matches: 371, Mismatches: 32, Indels: 32
0.85 0.07 0.07
Matches are distributed among these distances:
293 7 0.02
294 62 0.17
296 8 0.02
298 10 0.03
299 8 0.02
300 275 0.74
301 1 0.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (302 bp):
TATGGATTGATTTAATTTAAATAATTTATTTGTATAGATTGATTTATTTTAAAATATAGATTGAT
TTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTAATATG
TATTAGTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATAA
ATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATT
TATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:2324302 original size:22 final size:22
Alignment explanation
Indices: 2324277--2324367 Score: 110
Period size: 22 Copynumber: 4.0 Consensus size: 22
2324267 AATTTATTTG
2324277 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
***
2324299 TATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTA-T-TT-TA-AAA
2324325 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
2324347 TATGAATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
2324368 TAATTTATTA
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
22 34 0.59
23 3 0.05
24 4 0.07
25 3 0.05
26 14 0.24
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:2324368 original size:268 final size:270
Alignment explanation
Indices: 2323846--2324613 Score: 771
Period size: 268 Copynumber: 2.8 Consensus size: 270
2323836 TTTTAAAATA
* * *
2323846 ATTTATTTTAAAT-AATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTAATTTATTTTA
1 ATTTATTTTAAATAAATTGATT-GTATGGATTG--TTATGTT--AATATGGATTGATTTATTTTA
2323910 AATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATT
61 AATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATT
* * * ** * * *
2323975 AGTAT-AGATTGATTTATTTTAAAATATAGATTGATTTATTTTAAATAATTTA-TTT---GTATG
126 AGTATGA-ATTGATTTATTTT--AA-ATA-ATTTATTTGTATGGATTGATTTATTTTAAAATATG
*** *** *
2324035 GATTGATTTA-T-TT-TA-AAATATGGATTGATTTATTATTGTAGTTTTATGGATTGATTTATTT
186 GATTGATTTATTATTGTAGTTGTATGGATTGATTTA-T-TT-TA-AAATATGAATTGATTTATTT
*
2324096 TAAATAATTTATTTGTATGGATTG
247 TAAATAATTTATTAGTATGGATTG
* *
2324120 ATTTATTTTAAAATATAAATTGATT-TAT-TATTG-TA-GTT-GTATGGATTGATTTATTTTAAA
1 ATTTATTTT--AA-ATAAATTGATTGTATGGATTGTTATGTTAATATGGATTGATTTATTTTAAA
*
2324180 TAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
63 TAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
*
2324245 TATGAATTGATTTAATTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGAT
128 TATGAATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGAT
2324310 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTTTAAATAATTTA
193 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTTTAAATAATTTA
2324375 TTAGTATGGATTG
258 TTAGTATGGATTG
* * *
2324388 ATTTATTTTAAATAATTTGTTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT--
1 ATTTATTTTAAATAAATTGATTGTATGGATTG--TTATGTT--AATATGGATTGATTTATTTTAA
* * * * * *
2324449 AT--TGTAGTT-GTATGGATTGATTTATTTT-AAATA---ATTTA-TTAGTATGAATTGATTTAT
62 ATAATTTA-TTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTA-TTTTAAATAATTTA-
* * *
2324506 TTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
124 -TT--AGTATGAATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATG
**
2324571 GATTGATTTATTATTGTAGTTGTATAAATTGATTTATTTTAAA
186 GATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAA
2324614 TAATTTATTA
Statistics
Matches: 425, Mismatches: 41, Indels: 62
0.80 0.08 0.12
Matches are distributed among these distances:
263 3 0.01
264 30 0.07
265 15 0.04
266 9 0.02
267 9 0.02
268 279 0.66
269 6 0.01
270 8 0.02
271 7 0.02
272 18 0.04
274 23 0.05
275 4 0.01
276 5 0.01
277 2 0.00
278 7 0.02
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (270 bp):
ATTTATTTTAAATAAATTGATTGTATGGATTGTTATGTTAATATGGATTGATTTATTTTAAATAA
TTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTAT
GAATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTA
TTATTGTAGTTGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTTTAAATAATTTATTA
GTATGGATTG
Found at i:2324387 original size:80 final size:77
Alignment explanation
Indices: 2323914--2324669 Score: 284
Period size: 80 Copynumber: 9.4 Consensus size: 77
2323904 ATTTTAAATA
*
2323914 ATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA-TTAGT
1 ATTTATT-GTATGGATTGATTTATTTT-AAATAT-AATTGATTTATTTTAAATAATTTATTTAGT
*
2323978 ATAGATTGATTTA-T
63 ATGGATTGATTTATT
*** * * * * ** * * *
2323992 -TTTAAAATATAGATTGATTTATTTT-AA-ATAATTTATTTGTATGGATTGATTTATTTTAAAAT
1 ATTTATTGTATGGATTGATTTATTTTAAATATAATTGATTTATTTTAAATAATTTA-TTT--AGT
2324054 ATGGATTGATTTATT
63 ATGGATTGATTTATT
* * * * ** * *
2324069 ATTGTAGTTTTATGGATTGATTTATTTT-AA-ATAATTTATTTGTATGGATTGATTTATTTTAAA
1 ATT-TA-TTGTATGGATTGATTTATTTTAAATATAATTGATTTATTTTAAATAATTTA-TTT--A
* **
2324132 ATATAAATTGATTTATT
61 GTATGGATTGATTTATT
* * * * *
2324149 ATTGTAGTTGTATGGATTGATTTATTTT-AA-ATAATTTA-TTAGTATAGATTGATTTATTTTAA
1 ATT-TA-TTGTATGGATTGATTTATTTTAAATATAATTGATTTATTTTA-AATAATTTA-TTT--
*
2324211 AATATGGATTGATTTATTTTAAAT
60 AGTATGGATTGATTTA---T---T
* * * * * ** * *
2324235 AATTTATTAGTATGAATTGATTTAATTT-AA-ATAATTTATTTGTATGGATTGATTTATTTTAAA
1 -ATTTATT-GTATGGATTGATTTATTTTAAATATAATTGATTTATTTTAAATAATTTA-TTT--A
*
2324298 ATATGGATTGATTTATT
61 GTATGGATTGATTTATT
2324315 ATTGTAGTTGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTTTAAATAATTTA-TTAG
1 ATT-TA-TTGTATGGATTGATTTATTTT-AAATAT-AATTGATTTATTTTAAATAATTTATTTAG
2324379 TATGGATTGATTTATTTTAAAT
62 TATGGATTGATTTA---T---T
* * * * *
2324401 AATTTGTTTGTATGGATTGATTTATTTTAAA-AT-ATGGATTGA-TTT--ATTATTGTAGTT-GT
1 -ATTT-ATTGTATGGATTGATTTATTTTAAATATAATTGATTTATTTTAAATAATT-TATTTAGT
2324460 ATGGATTGATTTATTTTAAAT
63 ATGGATTGATTTA---T---T
* *
2324481 AATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA-TTAG
1 -ATTTATT-GTATGGATTGATTTATTTT-AAATAT-AATTGATTTATTTTAAATAATTTATTTAG
2324545 TATGGATTGATTTA-T
62 TATGGATTGATTTATT
*** **
2324560 -TTTAAAATATGGATTGATTTATTATTGTAGTTGTATAAATTGATTTATTTTAAATAATTTA-TT
1 ATTTATTGTATGGATTGATTTA-T-TT-TA--AATAT-AATTGATTTATTTTAAATAATTTATTT
* **
2324623 AGAATAAATTGATTTA-T
60 AGTATGGATTGATTTATT
*** *
2324640 -TTTAAAATATAGATTGATTTATTTTAAATA
1 ATTTATTGTATGGATTGATTTATTTTAAATA
2324670 ATTTATTATT
Statistics
Matches: 560, Mismatches: 70, Indels: 99
0.77 0.10 0.14
Matches are distributed among these distances:
72 16 0.03
73 2 0.00
74 4 0.01
75 2 0.00
76 44 0.08
77 12 0.02
78 7 0.01
79 17 0.03
80 278 0.50
81 10 0.02
82 13 0.02
83 5 0.01
84 26 0.05
85 10 0.02
86 101 0.18
87 13 0.02
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (77 bp):
ATTTATTGTATGGATTGATTTATTTTAAATATAATTGATTTATTTTAAATAATTTATTTAGTATG
GATTGATTTATT
Found at i:2324390 original size:246 final size:241
Alignment explanation
Indices: 2324004--2324511 Score: 634
Period size: 246 Copynumber: 2.1 Consensus size: 241
2323994 TAAAATATAG
2324004 ATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
1 ATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
* * * * * *
2324069 ATTGTAGTTTTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAAT
66 ATTGTAGTTGTATGGATTGATTTATTTTAAATAATTGATTTATATGAAATAATTTA-TTT-AAAT
*
2324134 ATAAATTGATTTA-TT-AT-TGTAG-TTGTATGGATTGATTTATTTTAAATAATTTATTAGTATA
129 ATAAATTGATTTATTTAATAT-TAGTTTGTATGGATTGATTTATTTT-AA-AA--TA-T-GGATA
*
2324195 GATTGATTTATTTTA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGA
187 GATTGA-TTATTGTAGAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGA
*
2324250 ATTGATTTAATTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
1 ATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
* *
2324315 ATTGTAGTTGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTTTAAATAATTTA-TT-A
66 ATTGTAGTTGTATGGATTGATTTATTTT--AA-AT-AATTGATTTATATGAAATAATTTATTTAA
* ** * *
2324378 GTATGGATTGATTTATTTTAAATAATTTGTTTGTATGGATTGATTTATTTTAAAATATGGATTGA
127 ATATAAATTGATTTA-TTT-AAT-ATTAGTTTGTATGGATTGATTTATTTTAAAATATGGATAGA
* ***
2324443 TTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGA
189 TTGATTATTGTAGAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGA
2324496 ATTGATTTATTTTAAA
1 ATTGATTTATTTTAAA
2324512 ATATGGATTG
Statistics
Matches: 229, Mismatches: 21, Indels: 24
0.84 0.08 0.09
Matches are distributed among these distances:
245 7 0.03
246 164 0.72
247 1 0.00
248 8 0.03
249 2 0.01
250 21 0.09
251 4 0.02
252 22 0.10
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (241 bp):
ATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
ATTGTAGTTGTATGGATTGATTTATTTTAAATAATTGATTTATATGAAATAATTTATTTAAATAT
AAATTGATTTATTTAATATTAGTTTGTATGGATTGATTTATTTTAAAATATGGATAGATTGATTA
TTGTAGAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGA
Found at i:2324500 original size:32 final size:32
Alignment explanation
Indices: 2324458--2324565 Score: 137
Period size: 32 Copynumber: 3.7 Consensus size: 32
2324448 TATTGTAGTT
2324458 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
2324490 GTATGAATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
2324513 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
2324544 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
2324566 ATATGGATTG
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
22 13 0.20
23 4 0.06
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
31 4 0.06
32 35 0.55
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:2324516 original size:22 final size:22
Alignment explanation
Indices: 2324491--2324533 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2324481 AATTTATTAG
2324491 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
2324513 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
2324534 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:2324559 original size:18 final size:18
Alignment explanation
Indices: 2324536--2324583 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
2324526 ATTTTAAATA
*
2324536 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
2324554 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
2324576 ATTTATTA
1 ATTTATTA
2324584 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:2324663 original size:134 final size:134
Alignment explanation
Indices: 2324245--2324677 Score: 645
Period size: 134 Copynumber: 3.2 Consensus size: 134
2324235 AATTTATTAG
* * *
2324245 TATGAATTGATTTAATTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
** * * * * ** *
2324310 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAA-ATATGAATT-GATTTATTTTAAATAATT
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATA-ATTTATTAGAATAAATTGATTTATTT
* *
2324373 TATTAG
130 TA-AAA
* *
2324379 TATGGATTGATTTATTTTAAATAATTTGTTTGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
* *
2324444 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGAATAAATTGATTTATTTT
2324509 AAAA
131 AAAA
2324513 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
**
2324578 TTATTATTGTAGTTGTATAAATTGATTTATTTTAAATAATTTATTAGAATAAATTGATTTATTTT
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGAATAAATTGATTTATTTT
2324643 AAAA
131 AAAA
*
2324647 TATAGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTA
2324678 TTGTAGTTGT
Statistics
Matches: 275, Mismatches: 22, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
134 262 0.95
135 13 0.05
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (134 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGAATAAATTGATTTATTTT
AAAA
Found at i:2324727 original size:30 final size:30
Alignment explanation
Indices: 2324691--2324747 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
2324681 TAGTTGTATG
*
2324691 AATTATTTAAAT-TCCAGTATTGTAAAATAA
1 AATTATTTAAATCT-CAGTATTGCAAAATAA
2324721 AATTATTTAAATCTCAGTATTGCAAAA
1 AATTATTTAAATCTCAGTATTGCAAAA
2324748 CTCTTTTAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.39
Consensus pattern (30 bp):
AATTATTTAAATCTCAGTATTGCAAAATAA
Found at i:2334291 original size:18 final size:18
Alignment explanation
Indices: 2334265--2334302 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2334255 CAGCAGCCAC
*
2334265 CGCAACCATTTATGATGT
1 CGCAACCATATATGATGT
*
2334283 CGCAGCCATATATGATGT
1 CGCAACCATATATGATGT
2334301 CG
1 CG
2334303 TCGCCTTTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (18 bp):
CGCAACCATATATGATGT
Found at i:2334858 original size:26 final size:24
Alignment explanation
Indices: 2334787--2334858 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
2334777 TTATATTTGT
2334787 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
*
2334812 ATTT--TTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
2334834 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
2334859 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 5 0.14
25 7 0.19
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:2337159 original size:23 final size:23
Alignment explanation
Indices: 2337133--2337196 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
2337123 CAGCTCATAT
*
2337133 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
2337156 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
2337179 AATTGCATCGAAGTGCCA
1 AATTGCACCGAAGTGCCA
2337197 TATAATAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.28, C:0.25, G:0.27, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:2337389 original size:103 final size:103
Alignment explanation
Indices: 2337212--2337429 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
2337202 TAATGTCCAT
* *
2337212 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
**
2337277 GACTTCACACATATTCCAAAGAATACATATATGTCCCG
66 GACCACACACATATTCCAAAGAATACATATATGTCCCG
*
2337315 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
2337380 GACCACACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCACACACATATTCCAAAGAATACATATATGTCCCG
2337418 AAGGACCACATA
1 AAGGACCACATA
2337430 GACCCTCTAC
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACCACACACATATTCCAAAGAATACATATATGTCCCG
Found at i:2338041 original size:64 final size:63
Alignment explanation
Indices: 2337889--2338048 Score: 171
Period size: 64 Copynumber: 2.5 Consensus size: 63
2337879 TAATGGAGGT
* * *
2337889 ATGCATCGATGCACTACACCA-GCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACTACA-TATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGA
* * * * * *
2337953 ATGCATCGATGCAATCCTTATGCATAGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT-TA
1 ATGCATCGATGCACTACATATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGA
* *
2338017 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACTACATATGCATCGATGCA
2338049 CCTTAAACAA
Statistics
Matches: 79, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
63 1 0.01
64 68 0.86
65 7 0.09
66 3 0.04
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTACATATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGA
Found at i:2344181 original size:23 final size:22
Alignment explanation
Indices: 2344155--2344223 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 22
2344145 CACCACAACT
*
2344155 CATATAATTGCACCTAAGTGCCA
1 CATAGAATTGCACCT-AGTGCCA
* *
2344178 CATAGAATTGCACCGGAGTGCCG
1 CATAGAATTGCACC-TAGTGCCA
2344201 CATAGAATTGCACCGTAGTGCCA
1 CATAGAATTGCACC-TAGTGCCA
2344224 TATAATAATG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (22 bp):
CATAGAATTGCACCTAGTGCCA
Found at i:2344912 original size:64 final size:67
Alignment explanation
Indices: 2344802--2344929 Score: 210
Period size: 64 Copynumber: 2.0 Consensus size: 67
2344792 ATTTTCATGT
2344802 TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTTGATGTTTG
1 TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTTGATGTTTG
2344867 TA
66 TA
*
2344869 TTTAATGG-GG-ATGCATCGATGCACT-C-CTTATGCATCGATGCATAAATCCTATTTGATGTTT
1 TTTAATGGAGGTATGCATCGATGCACTACAC-CATGCATCGATGCATAAATCCTATTTGATGTTT
2344930 TCTTTTTAAA
Statistics
Matches: 59, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
63 1 0.02
64 33 0.56
65 15 0.25
66 2 0.03
67 8 0.14
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.36
Consensus pattern (67 bp):
TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTTGATGTTTG
TA
Found at i:2344947 original size:64 final size:62
Alignment explanation
Indices: 2344814--2344974 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 62
2344804 TAATGGAGGT
* * *
2344814 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTTGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTTGATGTTTCTATTTAAT-GGA
* *
2344879 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTTGATGTTTTCTTTTTAAAT-TA
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTTGATG-TTTCTATTT-AATGGA
* * *
2344943 ATGCATCGGTGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
2344975 CCTTAAACAA
Statistics
Matches: 84, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
63 1 0.01
64 57 0.68
65 23 0.27
66 3 0.04
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (62 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTTGATGTTTCTATTTAATGGA
Found at i:2347502 original size:13 final size:12
Alignment explanation
Indices: 2347469--2347502 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2347459 AATAAGTATA
*
2347469 ATAAAAAAATTT
1 ATAACAAAATTT
2347481 ATAACAAAATTT
1 ATAACAAAATTT
2347493 ATAACGAAAA
1 ATAAC-AAAA
2347503 ATCGTACGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (12 bp):
ATAACAAAATTT
Found at i:2349676 original size:31 final size:31
Alignment explanation
Indices: 2349631--2349690 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
2349621 TTTGGCTCGA
2349631 TTAATTTTAAAATATTATTT-AATATAAAAT
1 TTAATTTTAAAATATTATTTGAATATAAAAT
* *
2349661 TTAATTTTTATAATATTATTTGAGTATAAA
1 TTAA-TTTTAAAATATTATTTGAATATAAA
2349691 CTTTTTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 4 0.15
31 15 0.58
32 7 0.27
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (31 bp):
TTAATTTTAAAATATTATTTGAATATAAAAT
Found at i:2349770 original size:27 final size:27
Alignment explanation
Indices: 2349740--2349802 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
2349730 TCACTTTTTG
2349740 TTTAAATTTAAAAA-TATTTTTATATA
1 TTTAAATTTAAAAATTATTTTTATATA
* **
2349766 TTT-TATCAAAAAAATTATTTTTATATA
1 TTTAAAT-TTAAAAATTATTTTTATATA
2349793 TTTAAATTTA
1 TTTAAATTTA
2349803 TATTTTAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
25 2 0.07
26 8 0.29
27 16 0.57
28 2 0.07
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (27 bp):
TTTAAATTTAAAAATTATTTTTATATA
Found at i:2349807 original size:22 final size:25
Alignment explanation
Indices: 2349781--2349829 Score: 68
Period size: 22 Copynumber: 2.1 Consensus size: 25
2349771 TCAAAAAAAT
*
2349781 TATTTTTATATAT-T-T-AAATTTA
1 TATTTTAATATATCTATCAAATTTA
2349803 TATTTTAATATATCTATCAAATTTA
1 TATTTTAATATATCTATCAAATTTA
2349828 TA
1 TA
2349830 AGAGATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 12 0.52
23 1 0.04
24 1 0.04
25 9 0.39
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (25 bp):
TATTTTAATATATCTATCAAATTTA
Found at i:2355888 original size:21 final size:20
Alignment explanation
Indices: 2355864--2355902 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2355854 ATCATATACT
2355864 CATATATTCATTCTTTTAAAC
1 CATATA-TCATTCTTTTAAAC
*
2355885 CATATATGATTCTTTTAA
1 CATATATCATTCTTTTAA
2355903 TCACGTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.49
Consensus pattern (20 bp):
CATATATCATTCTTTTAAAC
Found at i:2356329 original size:31 final size:30
Alignment explanation
Indices: 2356264--2356365 Score: 91
Period size: 30 Copynumber: 3.3 Consensus size: 30
2356254 CCGAAGAACC
* *
2356264 TAGGTAAACTTTCCATATGTTCTTAAAACA
1 TAGGTAAACTATCCATATGTTCTGAAAACA
*
2356294 TAGGTATACTATCCATATG-TCTCGAAAGACA
1 TAGGTAAACTATCCATATGTTCT-GAAA-ACA
* * *
2356325 TAGGTAATTA-TGTCCATATGTTCCGTAGAACA
1 TAGGTAA--ACTATCCATATGTTCTG-AAAACA
2356357 TAGGTAAAC
1 TAGGTAAAC
2356366 CCTCGACTCT
Statistics
Matches: 58, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
29 3 0.05
30 21 0.36
31 9 0.16
32 20 0.34
33 5 0.09
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (30 bp):
TAGGTAAACTATCCATATGTTCTGAAAACA
Found at i:2360726 original size:4 final size:4
Alignment explanation
Indices: 2360717--2360753 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
2360707 AAAAACAATA
2360717 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
2360754 CAAGATACCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:2367230 original size:5 final size:5
Alignment explanation
Indices: 2367210--2367389 Score: 54
Period size: 5 Copynumber: 35.0 Consensus size: 5
2367200 AAAAAATAGT
*
2367210 TAAAA TATAAA CTAAAA TAAAAA TAAAAA TAAACA AATAAA TAAAA T-AAA
1 TAAAA TA-AAA -TAAAA T-AAAA T-AAAA TAAA-A TA-AAA TAAAA TAAAA
* * * *
2367260 CAAAA T-AAA T-AAA TAAACA TAAAA TTAAAT TAAAAA TAAGGA -AAAG
1 TAAAA TAAAA TAAAA TAAA-A TAAAA -TAAAA T-AAAA TAA-AA TAAAA
* * * *
2367306 GAAAA -CAAA TAAAAA TAAAA TAATGGAA TTAAA TAGAA TAAAA TAAAA
1 TAAAA TAAAA T-AAAA TAAAA TAA---AA TAAAA TAAAA TAAAA TAAAA
* * * *
2367354 -GAAA CAAAA -AAAA -AAAA GAAAA AAAAA T-AAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
2367390 ATAATTAAAT
Statistics
Matches: 135, Mismatches: 20, Indels: 40
0.69 0.10 0.21
Matches are distributed among these distances:
4 29 0.21
5 59 0.44
6 39 0.29
7 4 0.03
8 4 0.03
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.17
Consensus pattern (5 bp):
TAAAA
Found at i:2367232 original size:18 final size:19
Alignment explanation
Indices: 2367213--2367289 Score: 63
Period size: 18 Copynumber: 4.0 Consensus size: 19
2367203 AAATAGTTAA
2367213 AATATAAACTAAAATAAA-
1 AATATAAACTAAAATAAAT
*
2367231 AATA-AAAATAAACAAATAAAT
1 AATATAAACT--A-AAATAAAT
*
2367252 AAAATAAAC-AAAATAAAT
1 AATATAAACTAAAATAAAT
2367270 AA-ATAAACATAAAATTAAAT
1 AATATAAAC-TAAAA-TAAAT
2367290 TAAAAATAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
17 10 0.21
18 14 0.29
19 6 0.12
20 12 0.25
21 3 0.06
22 3 0.06
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (19 bp):
AATATAAACTAAAATAAAT
Found at i:2367242 original size:17 final size:17
Alignment explanation
Indices: 2367210--2367328 Score: 61
Period size: 17 Copynumber: 6.8 Consensus size: 17
2367200 AAAAAATAGT
*
2367210 TAAAATATAAACT-AAAA
1 TAAAA-ATAAAATAAAAA
2367227 TAAAAATAAAAATAAACAA
1 TAAAAAT-AAAATAAA-AA
*
2367246 -ATAAATAAAATAAACAA
1 TAAAAATAAAATAAA-AA
*
2367263 -AATAAAT-AAATAAACA
1 TAA-AAATAAAATAAAAA
* *
2367279 TAAAATTAAATTAAAAA
1 TAAAAATAAAATAAAAA
*
2367296 TAAGGAAA-AGGAAA-ACAAA
1 TAA--AAATA--AAATAAAAA
2367315 TAAAAATAAAATAA
1 TAAAAATAAAATAA
2367329 TGGAATTAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
16 9 0.11
17 44 0.56
18 13 0.16
19 11 0.14
20 2 0.03
ACGTcount: A:0.74, C:0.04, G:0.03, T:0.18
Consensus pattern (17 bp):
TAAAAATAAAATAAAAA
Found at i:2367370 original size:17 final size:16
Alignment explanation
Indices: 2367345--2367380 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
2367335 TAAATAGAAT
*
2367345 AAAATAAAAGAAACAAA
1 AAAAAAAAAGAAA-AAA
2367362 AAAAAAAAAGAAAAAA
1 AAAAAAAAAGAAAAAA
2367378 AAA
1 AAA
2367381 TAAATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.89, C:0.03, G:0.06, T:0.03
Consensus pattern (16 bp):
AAAAAAAAAGAAAAAA
Found at i:2375765 original size:2 final size:2
Alignment explanation
Indices: 2375758--2375786 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2375748 CTAACAATCC
2375758 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2375787 AAATAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2375827 original size:17 final size:17
Alignment explanation
Indices: 2375807--2375846 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
2375797 CATAAACCTT
2375807 AAAAAATAGATAAAATAA
1 AAAAAATA-ATAAAATAA
2375825 AAAAAATAATAAAATAA
1 AAAAAATAATAAAATAA
*
2375842 TAAAA
1 AAAAA
2375847 GACTAATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (17 bp):
AAAAAATAATAAAATAA
Found at i:2375899 original size:36 final size:36
Alignment explanation
Indices: 2375859--2375928 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
2375849 CTAATTTCCA
* *
2375859 AAAAAAAGCAATAAAATAAATAAA-GTAAAATAAAGT
1 AAAAAAA-CAAAAAAATAAATAAACATAAAATAAAGT
*
2375895 AAAAAAATAAAAAAATAAATAAACATAAAATAAA
1 AAAAAAACAAAAAAATAAATAAACATAAAATAAA
2375929 AATAAAACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 14 0.47
36 16 0.53
ACGTcount: A:0.77, C:0.03, G:0.04, T:0.16
Consensus pattern (36 bp):
AAAAAAACAAAAAAATAAATAAACATAAAATAAAGT
Found at i:2375922 original size:6 final size:5
Alignment explanation
Indices: 2375868--2375993 Score: 71
Period size: 5 Copynumber: 24.4 Consensus size: 5
2375858 AAAAAAAAGC
* * * *
2375868 AATAA AAT-A AATAA AGTAA AATAA AGTAA AAAAA TAAAAA AAT-A AATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA -AATAA AATAA AATAA
* **
2375917 ACATAA AATAAA AATAA AA-CA AGGAA AATAAA AATAA AA-ATA AATAA
1 A-ATAA AAT-AA AATAA AATAA AATAA AAT-AA AATAA AATA-A AATAA
* *
2375964 AATAA TGGAATTA AATAG AATAA AATAA AA
1 AATAA ---AATAA AATAA AATAA AATAA AA
2375994 GAAACAAAAA
Statistics
Matches: 94, Mismatches: 15, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
4 11 0.12
5 58 0.62
6 21 0.22
8 4 0.04
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.18
Consensus pattern (5 bp):
AATAA
Found at i:2375923 original size:31 final size:32
Alignment explanation
Indices: 2375868--2376042 Score: 96
Period size: 31 Copynumber: 5.3 Consensus size: 32
2375858 AAAAAAAAGC
*
2375868 AATAAAATAAATAAAGTAAAATAAAGTAAAAA
1 AATAAAATAAATAAAGTAAAATAAAATAAAAA
2375900 AATAAAA-AAATAAA-TAAACATAAAAT--AAA
1 AATAAAATAAATAAAGTAAA-ATAAAATAAAAA
* ** *
2375929 AATAAAACAAGGAAAATAAAAATAAAAATAAATAA
1 AATAAAATAAATAAAGT-AAAAT-AAAATAAA-AA
* *
2375964 AATAATGGAATTAAATAGAA-TAAAATAAAAGAAACA
1 AATAA---AA-TAAATA-AAGTAAAATAAAATAAAAA
** *
2376000 AA-AAACCAAAAAATAG-AAAATAGAAAATAAAAA
1 AATAAAATAAATAA-AGTAAAAT--AAAATAAAAA
2376033 AAT-AAATAAA
1 AATAAAATAAA
2376043 AATAATTAAA
Statistics
Matches: 110, Mismatches: 15, Indels: 35
0.69 0.09 0.22
Matches are distributed among these distances:
29 10 0.09
30 10 0.09
31 26 0.24
32 16 0.15
33 15 0.14
34 1 0.01
35 9 0.08
36 3 0.03
37 7 0.06
38 7 0.06
39 4 0.04
40 2 0.02
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.16
Consensus pattern (32 bp):
AATAAAATAAATAAAGTAAAATAAAATAAAAA
Found at i:2375935 original size:26 final size:25
Alignment explanation
Indices: 2375868--2375964 Score: 76
Period size: 26 Copynumber: 3.9 Consensus size: 25
2375858 AAAAAAAAGC
*
2375868 AATAAAAT--AAATAAAGTAAAATAA
1 AATAAAATAAAAATAAAAT-AAATAA
* *
2375892 AGTAAAA-AAATAAAAAAATAAATAA
1 AATAAAATAAA-AATAAAATAAATAA
* **
2375917 ACATAAAATAAAAATAAAACAAGGAA
1 A-ATAAAATAAAAATAAAATAAATAA
2375943 AATAAAAATAAAAAT-AAATAAA
1 AAT-AAAATAAAAATAAAATAAA
2375965 ATAATGGAAT
Statistics
Matches: 57, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
24 6 0.11
25 15 0.26
26 33 0.58
27 3 0.05
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.16
Consensus pattern (25 bp):
AATAAAATAAAAATAAAATAAATAA
Found at i:2377085 original size:31 final size:32
Alignment explanation
Indices: 2377031--2377100 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 32
2377021 AGAAACATAA
2377031 ATAT-AATATATAACTATACAATGTATATAT-
1 ATATAAATATATAACTATACAATGTATATATG
* * *
2377061 ATTATAAATATGTAA-TATATAATGTGTATATG
1 A-TATAAATATATAACTATACAATGTATATATG
2377093 ATATAAAT
1 ATATAAAT
2377101 CACATAACAC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
30 1 0.03
31 24 0.71
32 9 0.26
ACGTcount: A:0.49, C:0.03, G:0.07, T:0.41
Consensus pattern (32 bp):
ATATAAATATATAACTATACAATGTATATATG
Found at i:2377290 original size:16 final size:16
Alignment explanation
Indices: 2377247--2377304 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
2377237 AACATTATAT
2377247 TAATTTAAAC-AAAAA
1 TAATTTAAACTAAAAA
* *
2377262 TAATTTAATCTAAAAG
1 TAATTTAAACTAAAAA
* *
2377278 TAATATAAACTAACTAAT
1 TAATTTAAACTAA--AAA
2377296 TAATTTAAA
1 TAATTTAAA
2377305 AAATCAATCG
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
15 9 0.26
16 15 0.44
18 10 0.29
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (16 bp):
TAATTTAAACTAAAAA
Found at i:2377354 original size:7 final size:7
Alignment explanation
Indices: 2377347--2377496 Score: 228
Period size: 7 Copynumber: 21.4 Consensus size: 7
2377337 TTCTTTTTTC
*
2377347 TTCCTTC
1 TTCCTTG
*
2377354 TTCCTTC
1 TTCCTTG
*
2377361 TTCCTTC
1 TTCCTTG
*
2377368 TTCCTTC
1 TTCCTTG
*
2377375 TTCCTTC
1 TTCCTTG
*
2377382 TTCCTTC
1 TTCCTTG
2377389 TTCCTTG
1 TTCCTTG
2377396 TTCCTTG
1 TTCCTTG
2377403 TTCCTTG
1 TTCCTTG
2377410 TTCCTTG
1 TTCCTTG
2377417 TTCCTTG
1 TTCCTTG
2377424 TTCCTTG
1 TTCCTTG
2377431 TTCCTTG
1 TTCCTTG
2377438 TTCCTTG
1 TTCCTTG
2377445 TTCCTTG
1 TTCCTTG
2377452 TTCCTTG
1 TTCCTTG
2377459 TTCCTTG
1 TTCCTTG
*
2377466 TTCCTTC
1 TTCCTTG
2377473 TTCCTTG
1 TTCCTTG
*
2377480 TTCCTTC
1 TTCCTTG
2377487 TTCCTTG
1 TTCCTTG
2377494 TTC
1 TTC
2377497 TCTTCAGAGT
Statistics
Matches: 138, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 138 1.00
ACGTcount: A:0.00, C:0.34, G:0.09, T:0.57
Consensus pattern (7 bp):
TTCCTTG
Found at i:2377704 original size:35 final size:35
Alignment explanation
Indices: 2377607--2377691 Score: 161
Period size: 35 Copynumber: 2.4 Consensus size: 35
2377597 TTTATTACTA
*
2377607 CCATATGCAGCTTCAAACAAGCAAAATTATTGTTG
1 CCATATGCAGCTTTAAACAAGCAAAATTATTGTTG
2377642 CCATATGCAGCTTTAAACAAGCAAAATTATTGTTG
1 CCATATGCAGCTTTAAACAAGCAAAATTATTGTTG
2377677 CCATATGCAGCTTTA
1 CCATATGCAGCTTTA
2377692 GTCATACAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 49 1.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (35 bp):
CCATATGCAGCTTTAAACAAGCAAAATTATTGTTG
Found at i:2385441 original size:18 final size:18
Alignment explanation
Indices: 2385415--2385449 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2385405 TCGAAAGGAC
*
2385415 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
2385433 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
2385450 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:2388584 original size:29 final size:29
Alignment explanation
Indices: 2388552--2388607 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
2388542 TTTATGTATA
*
2388552 TATTTTGATCAAAAAATACTTTAGATATT
1 TATTTTGACCAAAAAATACTTTAGATATT
2388581 TATTTTGACCAAAAAATACTTTAGATA
1 TATTTTGACCAAAAAATACTTTAGATA
2388608 CTTAAATGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (29 bp):
TATTTTGACCAAAAAATACTTTAGATATT
Found at i:2390771 original size:16 final size:15
Alignment explanation
Indices: 2390750--2390785 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
2390740 TCTTATCATC
2390750 TTCTTATTCTCTTTAT
1 TTCTTATT-TCTTTAT
*
2390766 TTCTTATTTCTTTTT
1 TTCTTATTTCTTTAT
2390781 TTCTT
1 TTCTT
2390786 TCTCATTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (15 bp):
TTCTTATTTCTTTAT
Found at i:2402059 original size:3 final size:3
Alignment explanation
Indices: 2402051--2402079 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2402041 CCCTTTATAT
2402051 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2402080 TTTACTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2403324 original size:24 final size:24
Alignment explanation
Indices: 2403296--2403353 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
2403286 TTCGGGATAC
2403296 TTCTACGTGGTCC-TTATGGACAAA
1 TTCTACGTGGTCCTTTA-GGACAAA
*
2403320 TTCTACGCGGTCCTTTAGGACAAA
1 TTCTACGTGGTCCTTTAGGACAAA
*
2403344 TTTTACGTGG
1 TTCTACGTGG
2403354 CACTTCGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 27 0.90
25 3 0.10
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.34
Consensus pattern (24 bp):
TTCTACGTGGTCCTTTAGGACAAA
Found at i:2406478 original size:42 final size:42
Alignment explanation
Indices: 2406431--2406528 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
2406421 GTCCTTCGTG
* *
2406431 ACATATATGCGGTCATTCAAGACAAATATTTGGTCCTTTGGA
1 ACATATATGCGGTCATTCAAGACAAATATTTGGTCATTCGGA
* * * *
2406473 ACATATATACAGTCATTCGAGACAAATATTTGGTTATTCGGA
1 ACATATATGCGGTCATTCAAGACAAATATTTGGTCATTCGGA
*
2406515 ACATATATGTGGTC
1 ACATATATGCGGTC
2406529 CTTAGGGACA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (42 bp):
ACATATATGCGGTCATTCAAGACAAATATTTGGTCATTCGGA
Found at i:2406539 original size:21 final size:21
Alignment explanation
Indices: 2406415--2406583 Score: 95
Period size: 21 Copynumber: 8.0 Consensus size: 21
2406405 TCGAGGGTTC
* *
2406415 TATGTGGTCCTTCGTGACATA
1 TATGTGGTCCTTTGGGACATA
* * *** *
2406436 TATGCGGTCATTCAAGACAAA
1 TATGTGGTCCTTTGGGACATA
* *
2406457 TATTTGGTCCTTTGGAACATA
1 TATGTGGTCCTTTGGGACATA
*** * * * *
2406478 TATACAGTCATTCGAGACAAA
1 TATGTGGTCCTTTGGGACATA
* ** * *
2406499 TATTTGGTTATTCGGAACATA
1 TATGTGGTCCTTTGGGACATA
*
2406520 TATGTGGTCCTTAGGGACATTTA
1 TATGTGGTCCTTTGGGACA--TA
*
2406543 TATGTGGTCATTTGGGACATA
1 TATGTGGTCCTTTGGGACATA
*
2406564 TATGTAGTCCTTTGGGACAT
1 TATGTGGTCCTTTGGGACAT
2406584 TTCTATTAGG
Statistics
Matches: 109, Mismatches: 37, Indels: 4
0.73 0.25 0.03
Matches are distributed among these distances:
21 90 0.83
23 19 0.17
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (21 bp):
TATGTGGTCCTTTGGGACATA
Found at i:2406548 original size:23 final size:23
Alignment explanation
Indices: 2406518--2406585 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
2406508 ATTCGGAACA
*
2406518 TATATGTGGTCCTTAGGGACATT
1 TATATGTGGTCCTTTGGGACATT
*
2406541 TATATGTGGTCATTTGGGACA--
1 TATATGTGGTCCTTTGGGACATT
*
2406562 TATATGTAGTCCTTTGGGACATT
1 TATATGTGGTCCTTTGGGACATT
2406585 T
1 T
2406586 CTATTAGGTC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 19 0.49
23 20 0.51
ACGTcount: A:0.22, C:0.12, G:0.25, T:0.41
Consensus pattern (23 bp):
TATATGTGGTCCTTTGGGACATT
Found at i:2406581 original size:44 final size:44
Alignment explanation
Indices: 2406498--2406605 Score: 137
Period size: 44 Copynumber: 2.5 Consensus size: 44
2406488 TTCGAGACAA
* * * *
2406498 ATATTTGGTTATTCGGAACATATATGTGGTCCTTAGGGACATTT
1 ATATTAGGTCATTCGGGACATATATGTAGTCCTTAGGGACATTT
* *
2406542 ATATGT-GGTCATTTGGGACATATATGTAGTCCTTTGGGACATTT
1 ATAT-TAGGTCATTCGGGACATATATGTAGTCCTTAGGGACATTT
*
2406586 CTATTAGGTCATTCGGGACA
1 ATATTAGGTCATTCGGGACA
2406606 ATCTTATATG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
43 1 0.02
44 53 0.96
45 1 0.02
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.39
Consensus pattern (44 bp):
ATATTAGGTCATTCGGGACATATATGTAGTCCTTAGGGACATTT
Found at i:2410872 original size:21 final size:21
Alignment explanation
Indices: 2410847--2410926 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
2410837 TTAATTCAGG
2410847 ACATATATGTGATCCTTTGGA
1 ACATATATGTGATCCTTTGGA
* **
2410868 ACATATATGCGATCC-TTCAA
1 ACATATATGTGATCCTTTGGA
* * *
2410888 GACAAATATTTGGTCCTTTGGA
1 -ACATATATGTGATCCTTTGGA
*
2410910 ACATATATGTGGTCCTT
1 ACATATATGTGATCCTT
2410927 ACGGACATTT
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 3 0.07
21 40 0.87
22 3 0.07
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.36
Consensus pattern (21 bp):
ACATATATGTGATCCTTTGGA
Found at i:2410934 original size:21 final size:20
Alignment explanation
Indices: 2410845--2410934 Score: 72
Period size: 21 Copynumber: 4.3 Consensus size: 20
2410835 TTTTAATTCA
*
2410845 GGACATATATGTGATCCTTT
1 GGACATATATGTGATCCTTC
*
2410865 GGAACATATATGCGATCCTTC
1 GG-ACATATATGTGATCCTTC
* * * * *
2410886 AAGACAAATATTTGGTCCTTT
1 -GGACATATATGTGATCCTTC
*
2410907 GGAACATATATGTGGTCCTTAC
1 GG-ACATATATGTGATCCTT-C
2410929 GGACAT
1 GGACAT
2410935 TTAAAATAAA
Statistics
Matches: 54, Mismatches: 12, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
20 3 0.06
21 48 0.89
22 3 0.06
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (20 bp):
GGACATATATGTGATCCTTC
Found at i:2419256 original size:19 final size:19
Alignment explanation
Indices: 2419232--2419268 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2419222 TTTATTTATC
2419232 TTTCAA-GCACAATACTAAG
1 TTTCAATGC-CAATACTAAG
2419251 TTTCAATGCCAATACTAA
1 TTTCAATGCCAATACTAA
2419269 CTAGAGTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.30
Consensus pattern (19 bp):
TTTCAATGCCAATACTAAG
Found at i:2428739 original size:23 final size:23
Alignment explanation
Indices: 2428711--2428785 Score: 132
Period size: 23 Copynumber: 3.3 Consensus size: 23
2428701 TGGAGGATTA
* *
2428711 CGATTCGCAACGTTCATGATCAC
1 CGATTCGCAGCGTTCGTGATCAC
2428734 CGATTCGCAGCGTTCGTGATCAC
1 CGATTCGCAGCGTTCGTGATCAC
2428757 CGATTCGCAGCGTTCGTGATCAC
1 CGATTCGCAGCGTTCGTGATCAC
2428780 CGATTC
1 CGATTC
2428786 TCGTTGATGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.27
Consensus pattern (23 bp):
CGATTCGCAGCGTTCGTGATCAC
Found at i:2430457 original size:30 final size:30
Alignment explanation
Indices: 2430408--2430480 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
2430398 AATGGATTTA
** *
2430408 TTTAGTGACCAAATTATAAAT-TTGGTAAAG
1 TTTAGTGACCAAAGCATAAATATT-GAAAAG
*
2430438 TTTGGTGACCAAAGCATAAATATTGAAAAG
1 TTTAGTGACCAAAGCATAAATATTGAAAAG
*
2430468 TTTAGAGACCAAA
1 TTTAGTGACCAAA
2430481 ATGTAATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
30 34 0.94
31 2 0.06
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.30
Consensus pattern (30 bp):
TTTAGTGACCAAAGCATAAATATTGAAAAG
Found at i:2434780 original size:55 final size:55
Alignment explanation
Indices: 2434728--2434875 Score: 199
Period size: 55 Copynumber: 2.7 Consensus size: 55
2434718 CTATACGGAA
* * ** * **
2434728 ATTCGTCAACTCATGATGAATTCCGTGGATTTGCACACAAGGTGCTTGTACGGTG
1 ATTCATCAACTCATGATGAATTACGTAAATATGCACACAAAATGCTTGTACGGTG
*
2434783 ATTCATCAACTCATGATGAATTACGTAAATATGTACACAAAATGCTTGTACGGTG
1 ATTCATCAACTCATGATGAATTACGTAAATATGCACACAAAATGCTTGTACGGTG
*
2434838 ATTTATCAACTCATGATGAATTACG-AGAATATGCACAC
1 ATTCATCAACTCATGATGAATTACGTA-AATATGCACAC
2434876 GAAGTGACTT
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
54 1 0.01
55 81 0.99
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (55 bp):
ATTCATCAACTCATGATGAATTACGTAAATATGCACACAAAATGCTTGTACGGTG
Found at i:2435357 original size:22 final size:23
Alignment explanation
Indices: 2435314--2435358 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
2435304 CTGGTATCAA
**
2435314 TACCCTTACCATGGTATTGATAC
1 TACCCTTACCATGGTACCGATAC
*
2435337 TACCC-TACTATGGTACCGATAC
1 TACCCTTACCATGGTACCGATAC
2435359 CCCCTATCGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.27, C:0.29, G:0.13, T:0.31
Consensus pattern (23 bp):
TACCCTTACCATGGTACCGATAC
Found at i:2435423 original size:21 final size:21
Alignment explanation
Indices: 2435397--2435453 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
2435387 ATTCGATGTT
2435397 TCATGGTATCGATACCCCTTA
1 TCATGGTATCGATACCCCTTA
*
2435418 TCATGGTATCAATACCCCTTA
1 TCATGGTATCGATACCCCTTA
2435439 TCATGGTATCGATAC
1 TCATGGTATCGATAC
2435454 TATCTCATCG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.33
Consensus pattern (21 bp):
TCATGGTATCGATACCCCTTA
Found at i:2435445 original size:95 final size:93
Alignment explanation
Indices: 2435250--2435473 Score: 229
Period size: 95 Copynumber: 2.4 Consensus size: 93
2435240 ACTTCTTTAC
* * *
2435250 CATGGTAATGATACCCCCT-TCGAGTATCGATACCAAGAATAGGTTCGATGTAGCCTGGTATCAA
1 CATGGTAACGATACCCCCTATCG-GTATCGATACCAAGAATAGATTCGATGTAGCATGGTATCAA
**
2435314 TACCCTTACCATGGTATTGATACTACCCTA
65 TACCCTTACCATGGTATCAATAC-ACCCTA
* ** *
2435344 CTATGGTACCGATACCCCCTATCGGTATCGATACCAA-AATTAGATTCGATGTTTCATGGTATCG
1 C-ATGGTAACGATACCCCCTATCGGTATCGATACCAAGAA-TAGATTCGATGTAGCATGGTATCA
*
2435408 ATACCCCTTATCATGGTATCAATAC-CCCTTA
64 ATA-CCCTTACCATGGTATCAATACACCC-TA
* ***
2435439 TCATGGTATCGATACTATCTCATCGGTATCGATAC
1 -CATGGTAACGATACCCCCT-ATCGGTATCGATAC
2435474 TGATTGAATC
Statistics
Matches: 109, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
94 6 0.06
95 67 0.61
96 36 0.33
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.31
Consensus pattern (93 bp):
CATGGTAACGATACCCCCTATCGGTATCGATACCAAGAATAGATTCGATGTAGCATGGTATCAAT
ACCCTTACCATGGTATCAATACACCCTA
Found at i:2435486 original size:21 final size:20
Alignment explanation
Indices: 2435443--2435489 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
2435433 CCCTTATCAT
*
2435443 GGTATCGATACTATCTCATC
1 GGTATCGATACTATCTAATC
2435463 GGTATCGATACTGAT-TGAATC
1 GGTATCGATACT-ATCT-AATC
2435484 GGTATC
1 GGTATC
2435490 AGTACTACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (20 bp):
GGTATCGATACTATCTAATC
Found at i:2451594 original size:3 final size:3
Alignment explanation
Indices: 2451586--2451638 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
2451576 TTTTTATTGA
* *
2451586 TAT TAT TAT TAT TAT T-T TATT TAT TAT TAT TAT TAT TAA AAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
2451631 TAT TAT TA
1 TAT TAT TA
2451639 CAAATAGGCC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2451629 original size:15 final size:16
Alignment explanation
Indices: 2451611--2451643 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
2451601 TTTATTTATT
2451611 ATTATTATTATTA-AA
1 ATTATTATTATTACAA
2451626 ATTATTATTATTACAA
1 ATTATTATTATTACAA
2451642 AT
1 AT
2451644 AGGCCAAAAT
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:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTATTATTATTACAA
Found at i:2453011 original size:2 final size:2
Alignment explanation
Indices: 2452995--2453042 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
2452985 CTTTCATTAT
*
2452995 TA TA TT 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 TA TA TA
2453036 TA TA TA T
1 TA TA TA T
2453043 GGTTTAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:2453446 original size:22 final size:20
Alignment explanation
Indices: 2453412--2453451 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
2453402 CTGATATTTC
2453412 TAAATAAATAAATATTTTTA
1 TAAATAAATAAATATTTTTA
2453432 TAAATATATATAAATATTTT
1 TAAATA-A-ATAAATATTTT
2453452 CTTAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 1 0.06
22 11 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAATAAATAAATATTTTTA
Found at i:2453457 original size:22 final size:20
Alignment explanation
Indices: 2453408--2453457 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
2453398 TTTTCTGATA
2453408 TTTC-TAAATAAATAAATAT
1 TTTCTTAAATAAATAAATAT
2453427 TTT-TATAAATATATATAAATAT
1 TTTCT-TAAATA-A-ATAAATAT
2453449 TTTCTTAAA
1 TTTCTTAAA
2453458 AATTATAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 3 0.12
20 6 0.23
21 1 0.04
22 15 0.58
23 1 0.04
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTCTTAAATAAATAAATAT
Found at i:2453978 original size:28 final size:27
Alignment explanation
Indices: 2453947--2454000 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
2453937 TAATTCTTTC
*
2453947 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATA-TTATTA
* *
2453975 TTTTCATAGTATTTATATATATTATT
1 TTTTCAAAATATTTATATATATTATT
2454001 TTATTAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATATTATTA
Found at i:2454021 original size:24 final size:24
Alignment explanation
Indices: 2453964--2454045 Score: 59
Period size: 24 Copynumber: 3.6 Consensus size: 24
2453954 AATTTTTATA
* *
2453964 TATACTTATTATTTTCATAGTATT
1 TATATTTATTATTTTCATAATATT
*
2453988 TATATATATTATTTT-ATTAATATT
1 TATATTTATTATTTTCA-TAATATT
* *
2454012 T-CA-TT-TTATTTTCA-AGTATT
1 TATATTTATTATTTTCATAATATT
2454032 T-TATTTCATTATTT
1 TATATTT-ATTATTT
2454046 ATTTTTTTGT
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
20 7 0.15
21 9 0.20
22 2 0.04
23 8 0.17
24 20 0.43
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.62
Consensus pattern (24 bp):
TATATTTATTATTTTCATAATATT
Found at i:2455631 original size:12 final size:12
Alignment explanation
Indices: 2455614--2455668 Score: 65
Period size: 12 Copynumber: 4.3 Consensus size: 12
2455604 ACATTCACAT
2455614 ATTTACATTTGC
1 ATTTACATTTGC
2455626 ATTTACATTTGC
1 ATTTACATTTGC
* *
2455638 ATTTTTTACGTTTGT
1 A---TTTACATTTGC
2455653 ATTTACATTTGC
1 ATTTACATTTGC
2455665 ATTT
1 ATTT
2455669 TTTACGTTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 26 0.72
15 10 0.28
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:2455651 original size:15 final size:15
Alignment explanation
Indices: 2455615--2455683 Score: 60
Period size: 15 Copynumber: 5.0 Consensus size: 15
2455605 CATTCACATA
2455615 TTTACATTTGCA---
1 TTTACATTTGCATTT
2455627 TTTACATTTGCATTT
1 TTTACATTTGCATTT
* *
2455642 TTTACGTTTG---TA
1 TTTACATTTGCATTT
2455654 TTTACATTTGCATTT
1 TTTACATTTGCATTT
* *
2455669 TTTACGTTTGTATTT
1 TTTACATTTGCATTT
2455684 ACATTTTCAT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
12 22 0.49
15 23 0.51
ACGTcount: A:0.19, C:0.12, G:0.10, T:0.59
Consensus pattern (15 bp):
TTTACATTTGCATTT
Found at i:2455651 original size:27 final size:27
Alignment explanation
Indices: 2455615--2455697 Score: 139
Period size: 27 Copynumber: 3.1 Consensus size: 27
2455605 CATTCACATA
* *
2455615 TTTACATTTGCATTTACATTTGCATTT
1 TTTACGTTTGTATTTACATTTGCATTT
2455642 TTTACGTTTGTATTTACATTTGCATTT
1 TTTACGTTTGTATTTACATTTGCATTT
*
2455669 TTTACGTTTGTATTTACATTTTCATTT
1 TTTACGTTTGTATTTACATTTGCATTT
2455696 TT
1 TT
2455698 ACATAATTAC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.19, C:0.12, G:0.08, T:0.60
Consensus pattern (27 bp):
TTTACGTTTGTATTTACATTTGCATTT
Found at i:2463518 original size:113 final size:113
Alignment explanation
Indices: 2462717--2463505 Score: 1217
Period size: 113 Copynumber: 7.0 Consensus size: 113
2462707 TAGAAAAGAT
* * *
2462717 TCAAATCCATCA--TAATGGATCAACATTTCCAGA-AAGAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTG
2462779 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
2462828 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
2462893 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
*
2462941 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
2463006 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
2463054 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
2463119 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
* *
2463167 TCAAATCCATCACTCGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAAAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* ** *
2463232 AGAAGGAAGAAGAAGTTCATAATGAGAAAATTTTGTTCAACCTTTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
** * * * * * * * *
2463280 TTGAATTCAACATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCTG
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTG
* * ** * *
2463344 AAGAAGGAAGACGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGT
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
** * * *
2463393 TTGAATTCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * *
2463458 AGAATGAAGAAGAAGTTCATAATAAGAAGAGCTTGTTCGACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
2463506 ATGACTCTAT
Statistics
Matches: 628, Mismatches: 45, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
111 12 0.02
112 1 0.00
113 612 0.97
114 3 0.00
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (113 bp):
TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
Found at i:2463859 original size:3 final size:3
Alignment explanation
Indices: 2463851--2463900 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
2463841 TTTTTATTGA
* *
2463851 TAT TAT TAT TAT TAT T-T TATT TAT TAT TAT TAT TAA AAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
2463896 TAT TA
1 TAT TA
2463901 CAAACAGGCC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2465667 original size:22 final size:20
Alignment explanation
Indices: 2465633--2465672 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
2465623 CTGATATTTC
2465633 TAAATAAATAAATATTTTTA
1 TAAATAAATAAATATTTTTA
2465653 TAAATATATATAAATATTTT
1 TAAATA-A-ATAAATATTTT
2465673 CTTAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 1 0.06
22 11 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAATAAATAAATATTTTTA
Found at i:2465678 original size:22 final size:20
Alignment explanation
Indices: 2465629--2465678 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
2465619 TTTTCTGATA
2465629 TTTC-TAAATAAATAAATAT
1 TTTCTTAAATAAATAAATAT
2465648 TTT-TATAAATATATATAAATAT
1 TTTCT-TAAATA-A-ATAAATAT
2465670 TTTCTTAAA
1 TTTCTTAAA
2465679 AATTATAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 3 0.12
20 6 0.23
21 1 0.04
22 15 0.58
23 1 0.04
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTCTTAAATAAATAAATAT
Found at i:2468194 original size:21 final size:21
Alignment explanation
Indices: 2468157--2468196 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2468147 ATAGATGTCC
*
2468157 ATAAGGAAAACACTGAGAAAT
1 ATAAGGAAAACAATGAGAAAT
2468178 ATAA-GAAAGACAATGAGAA
1 ATAAGGAAA-ACAATGAGAA
2468197 GCTTGACGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.60, C:0.07, G:0.20, T:0.12
Consensus pattern (21 bp):
ATAAGGAAAACAATGAGAAAT
Found at i:2473194 original size:49 final size:49
Alignment explanation
Indices: 2473091--2473248 Score: 210
Period size: 49 Copynumber: 3.2 Consensus size: 49
2473081 TATTAGTTGT
* * *
2473091 GAATATTAATTGGGTAATTAATTAT-CTAGTGAATTATGTTAGTAATTG
1 GAATATTAATTGGGTAATTAATTATGATGGTTAATTATGTTAGTAATTG
*
2473139 GAATATTAATTGGGTTATTAATTATGATGGTTAATTATGTTAGTAATTG
1 GAATATTAATTGGGTAATTAATTATGATGGTTAATTATGTTAGTAATTG
* * * * *
2473188 GAATATTAATTGGGTCATTAATTATGTTGATTAATTATGTTATTAGTTG
1 GAATATTAATTGGGTAATTAATTATGATGGTTAATTATGTTAGTAATTG
*
2473237 TGGATATTAATT
1 -GAATATTAATT
2473249 TTGAATATTA
Statistics
Matches: 98, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
48 24 0.24
49 64 0.65
50 10 0.10
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.47
Consensus pattern (49 bp):
GAATATTAATTGGGTAATTAATTATGATGGTTAATTATGTTAGTAATTG
Found at i:2473222 original size:13 final size:12
Alignment explanation
Indices: 2473142--2473232 Score: 58
Period size: 12 Copynumber: 7.4 Consensus size: 12
2473132 GTAATTGGAA
**
2473142 TATTAATTGGGT
1 TATTAATTATGT
2473154 TATTAATTATGAT
1 TATTAATTATG-T
**
2473167 GGTTAATTATGT
1 TATTAATTATGT
* * *
2473179 TAGTAATT-GGAA
1 TATTAATTATG-T
**
2473191 TATTAATTGGGT
1 TATTAATTATGT
*
2473203 CATTAATTATGT
1 TATTAATTATGT
2473215 TGATTAATTATGT
1 T-ATTAATTATGT
2473228 TATTA
1 TATTA
2473233 GTTGTGGATA
Statistics
Matches: 60, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
11 1 0.02
12 35 0.58
13 24 0.40
ACGTcount: A:0.32, C:0.01, G:0.18, T:0.49
Consensus pattern (12 bp):
TATTAATTATGT
Found at i:2473301 original size:19 final size:20
Alignment explanation
Indices: 2473269--2473307 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
2473259 AATGTGCCAT
2473269 TAATTGTGGGAATTA-ATTG
1 TAATTGTGGGAATTATATTG
**
2473288 TAATTGTGTTAATTATATTG
1 TAATTGTGGGAATTATATTG
2473308 ATTTTAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.49
Consensus pattern (20 bp):
TAATTGTGGGAATTATATTG
Found at i:2473475 original size:33 final size:33
Alignment explanation
Indices: 2473431--2473494 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
2473421 GAAGGTCCAC
*
2473431 AACTCATCCCAATAAGCAGACCCAAAATGACAT
1 AACTCAGCCCAATAAGCAGACCCAAAATGACAT
*
2473464 AACTCAGCCCAATAAGCAGACCCATAATGAC
1 AACTCAGCCCAATAAGCAGACCCAAAATGAC
2473495 CCGAGGGCCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.44, C:0.31, G:0.11, T:0.14
Consensus pattern (33 bp):
AACTCAGCCCAATAAGCAGACCCAAAATGACAT
Found at i:2475114 original size:18 final size:17
Alignment explanation
Indices: 2475060--2475108 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
2475050 TTGGACCCTT
* *
2475060 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
2475078 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
2475096 AGTGCATTCGATG
1 AGTGCA-TCGATG
2475109 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:2475148 original size:64 final size:65
Alignment explanation
Indices: 2475080--2475237 Score: 196
Period size: 65 Copynumber: 2.4 Consensus size: 65
2475070 TGCACTAAGA
* *
2475080 GTGCATCGATGCATCAAGTGCATTCGATG-TTTCA-AAATAGCCAGAGTGCATCGATGCATGGCT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-AGCCACAGTGCATCGATGCATGG-T
2475143 -G
64 AG
* * * *
2475144 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCACAGTGCATCGATGCATGGTAG
* * *
2475209 GTTCATTGATGCATGAAATGCATTCGATG
1 GTGCATCGATGCATCAAATGCATTCGATG
2475238 CTCAATTTAA
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
64 29 0.35
65 50 0.61
66 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCACAGTGCATCGATGCATGGTAG
Found at i:2475766 original size:2 final size:2
Alignment explanation
Indices: 2475759--2475793 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2475749 AATTGATTAA
2475759 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 A
2475794 GCTTAAACTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2483748 original size:19 final size:19
Alignment explanation
Indices: 2483724--2483780 Score: 89
Period size: 19 Copynumber: 3.0 Consensus size: 19
2483714 TTGGACCCTT
*
2483724 AGTGCATCGGTGCA-CTAAG
1 AGTGCATCGATGCATC-AAG
2483743 AGTGCATCGATGCATCAAG
1 AGTGCATCGATGCATCAAG
2483762 AGTGCATCGATGCATCAAG
1 AGTGCATCGATGCATCAAG
2483781 TGTATTCGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 35 0.97
20 1 0.03
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (19 bp):
AGTGCATCGATGCATCAAG
Found at i:2485027 original size:5 final size:5
Alignment explanation
Indices: 2484996--2485063 Score: 59
Period size: 5 Copynumber: 13.0 Consensus size: 5
2484986 TTATCTTCAC
*
2484996 TTTAT CTTTA- TTTAT TATT-T ATTTAT TTTAT TTTTT TTAATAT TTTAT
1 TTTAT -TTTAT TTTAT T-TTAT -TTTAT TTTAT TTTAT TT--TAT TTTAT
*
2485044 TTTAT TTTAT TTTAT GTTAT
1 TTTAT TTTAT TTTAT TTTAT
2485064 CATTTTATTC
Statistics
Matches: 53, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
4 4 0.08
5 37 0.70
6 8 0.15
7 4 0.08
ACGTcount: A:0.22, C:0.01, G:0.01, T:0.75
Consensus pattern (5 bp):
TTTAT
Found at i:2485041 original size:17 final size:18
Alignment explanation
Indices: 2485019--2485052 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2485009 ATTATTTATT
2485019 TATTTTATTTT-TTTTAA
1 TATTTTATTTTATTTTAA
2485036 TATTTTATTTTATTTTA
1 TATTTTATTTTATTTTA
2485053 TTTTATGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
TATTTTATTTTATTTTAA
Found at i:2487216 original size:109 final size:109
Alignment explanation
Indices: 2487025--2487243 Score: 420
Period size: 109 Copynumber: 2.0 Consensus size: 109
2487015 TAGCATTGAA
*
2487025 CTGAACAAAAGAGAATAGTAAAAGTGTCTAAAATTGGCTCTAGTGAAAAAACTGCATATTTCCAA
1 CTGAACAAAAGAGAATAGTAAAAGTGTCTAAAATTGGCTCTAGTGAAAAAACTGCATATTTACAA
2487090 TCTGATAGAGGTGGCTAAACCTAGCTCTAGTAATGAAATAGAAG
66 TCTGATAGAGGTGGCTAAACCTAGCTCTAGTAATGAAATAGAAG
2487134 CTGAACAAAAGAGAATAGTAAAAGTGTCTAAAATTGGCTCTAGTGAAAAAACTGCATATTTACAA
1 CTGAACAAAAGAGAATAGTAAAAGTGTCTAAAATTGGCTCTAGTGAAAAAACTGCATATTTACAA
*
2487199 TCTGATAGAGGTGGCTAAACCTAGGTCTAGTAATGAAATAGAAG
66 TCTGATAGAGGTGGCTAAACCTAGCTCTAGTAATGAAATAGAAG
2487243 C
1 C
2487244 AAAAGAATGC
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
109 108 1.00
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.25
Consensus pattern (109 bp):
CTGAACAAAAGAGAATAGTAAAAGTGTCTAAAATTGGCTCTAGTGAAAAAACTGCATATTTACAA
TCTGATAGAGGTGGCTAAACCTAGCTCTAGTAATGAAATAGAAG
Found at i:2487228 original size:52 final size:52
Alignment explanation
Indices: 2487063--2487229 Score: 117
Period size: 52 Copynumber: 3.1 Consensus size: 52
2487053 TAAAATTGGC
* *
2487063 TCTAGTGAAAAAACTGCATATTTCCAATCTGATAGAGGTGGCTAAACCTAGC
1 TCTAGTGAAAAAACTGCATATTTACAATCTGATAGAGGTGGCTAAACCTAGG
*** * * * * * * *
2487115 TCTAGTAATGAAATAGAAGCTGAACA-AAAGAGAAT-AG-TAAAAGTGTCTAAA-ATTGG
1 TCTAG---TGAAA-A-AA-CTG--CATATTTACAATCTGATAGAGGTGGCTAAACCTAGG
2487171 CTCTAGTGAAAAAACTGCATATTTACAATCTGATAGAGGTGGCTAAACCTAGG
1 -TCTAGTGAAAAAACTGCATATTTACAATCTGATAGAGGTGGCTAAACCTAGG
2487224 TCTAGT
1 TCTAGT
2487230 AATGAAATAG
Statistics
Matches: 80, Mismatches: 22, Indels: 26
0.62 0.17 0.20
Matches are distributed among these distances:
49 2 0.03
50 5 0.06
51 4 0.05
52 24 0.30
53 4 0.05
54 5 0.06
55 5 0.06
56 3 0.04
57 18 0.22
58 4 0.05
59 4 0.05
60 2 0.03
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.26
Consensus pattern (52 bp):
TCTAGTGAAAAAACTGCATATTTACAATCTGATAGAGGTGGCTAAACCTAGG
Found at i:2489430 original size:68 final size:68
Alignment explanation
Indices: 2489321--2489457 Score: 265
Period size: 68 Copynumber: 2.0 Consensus size: 68
2489311 AATCTATTAG
2489321 GTAAGAACCTTTTGAGATCATTTTCTTACTTTCCAAAAAGTTGTTTTCTCATTAAAACATCATAC
1 GTAAGAACCTTTTGAGATCATTTTCTTACTTTCCAAAAAGTTGTTTTCTCATTAAAACATCATAC
2489386 CCT
66 CCT
*
2489389 GTAAGAACCTTTTGAGATCATTTTCTTACTTTTCAAAAAGTTGTTTTCTCATTAAAACATCATAC
1 GTAAGAACCTTTTGAGATCATTTTCTTACTTTCCAAAAAGTTGTTTTCTCATTAAAACATCATAC
2489454 CCT
66 CCT
2489457 G
1 G
2489458 AAGGTCTCGT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (68 bp):
GTAAGAACCTTTTGAGATCATTTTCTTACTTTCCAAAAAGTTGTTTTCTCATTAAAACATCATAC
CCT
Found at i:2495114 original size:66 final size:66
Alignment explanation
Indices: 2495040--2495169 Score: 251
Period size: 66 Copynumber: 2.0 Consensus size: 66
2495030 TCCCTCCCAA
2495040 AATATATATGTGATTTTTGCAACAATAAGACTCAAACTATAGGCAAATTTGGTAGAATAATCCCC
1 AATATATATGTGATTTTTGCAACAATAAGACTCAAACTATAGGCAAATTTGGTAGAATAATCCCC
2495105 T
66 T
*
2495106 AATATATATGTGATTTTTGCAACAATAAGACTCAAACTATAGGTAAATTTGGTAGAATAATCCC
1 AATATATATGTGATTTTTGCAACAATAAGACTCAAACTATAGGCAAATTTGGTAGAATAATCCC
2495170 TGTGCCAAAA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (66 bp):
AATATATATGTGATTTTTGCAACAATAAGACTCAAACTATAGGCAAATTTGGTAGAATAATCCCC
T
Found at i:2495165 original size:32 final size:32
Alignment explanation
Indices: 2495063--2495165 Score: 82
Period size: 32 Copynumber: 3.2 Consensus size: 32
2495053 TTTTTGCAAC
*
2495063 AATAAGACTCAAACTATAGGCAAATTTGGTAG
1 AATAAGACTCAAACTATAGGTAAATTTGGTAG
** * * ** ** *
2495095 AATAATCCCCTAATA-TATATGTGATTTTTGCAAC
1 AATAAGACTC-AA-ACTATAGGT-AAATTTGGTAG
2495129 AATAAGACTCAAACTATAGGTAAATTTGGTAG
1 AATAAGACTCAAACTATAGGTAAATTTGGTAG
2495161 AATAA
1 AATAA
2495166 TCCCTGTGCC
Statistics
Matches: 48, Mismatches: 19, Indels: 8
0.64 0.25 0.11
Matches are distributed among these distances:
32 19 0.40
33 15 0.31
34 14 0.29
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (32 bp):
AATAAGACTCAAACTATAGGTAAATTTGGTAG
Found at i:2498762 original size:2 final size:2
Alignment explanation
Indices: 2498755--2498788 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2498745 GAATAAAATA
2498755 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
2498789 TAAACAATTC
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:2498933 original size:6 final size:6
Alignment explanation
Indices: 2498924--2498999 Score: 52
Period size: 6 Copynumber: 13.0 Consensus size: 6
2498914 TTTAAAAAAG
* * * *
2498924 AAAATA AAAATA ATATTA TATAATA ATAATA AAAA-A AAAA-A AATAA-A
1 AAAATA AAAATA AAAATA -AAAATA AAAATA AAAATA AAAATA AA-AATA
* *
2498971 AAAAAA AAAATA AAAATA TAAA-A AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA
2499000 TGTATAATAA
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
5 14 0.24
6 40 0.68
7 5 0.08
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
AAAATA
Found at i:2498960 original size:1 final size:1
Alignment explanation
Indices: 2498954--2498997 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
2498944 TAATAATAAT
* * * *
2498954 AAAAAAAAAAAAATAAAAAAAAAAAAATAAAAATATAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2498998 TATGTATAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (1 bp):
A
Found at i:2498973 original size:13 final size:14
Alignment explanation
Indices: 2498951--2498996 Score: 74
Period size: 14 Copynumber: 3.1 Consensus size: 14
2498941 ATATAATAAT
2498951 AATAAAAAAAAAAA
1 AATAAAAAAAAAAA
2498965 AATAAAAAAAAAAA
1 AATAAAAAAAAAAA
2498979 AATAAAAATATAAAAA
1 AATAAAAA-A-AAAAA
2498995 AA
1 AA
2498997 ATATGTATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
14 22 0.73
15 1 0.03
16 7 0.23
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (14 bp):
AATAAAAAAAAAAA
Found at i:2499070 original size:11 final size:10
Alignment explanation
Indices: 2499041--2499079 Score: 51
Period size: 11 Copynumber: 3.6 Consensus size: 10
2499031 TAAAGAACAA
2499041 AAATATATACAT
1 AAATA-ATA-AT
2499053 AAATAATAAT
1 AAATAATAAT
2499063 ATAATAATAAT
1 A-AATAATAAT
2499074 AAATAA
1 AAATAA
2499080 CATCAATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 8 0.31
11 13 0.50
12 5 0.19
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (10 bp):
AAATAATAAT
Found at i:2499292 original size:39 final size:39
Alignment explanation
Indices: 2499196--2499278 Score: 109
Period size: 37 Copynumber: 2.2 Consensus size: 39
2499186 GTAATAAAGC
* * *
2499196 AAGTAAAAA-ACAATAAAAATATAATCATATAAAAAATT
1 AAGTAAAAACAAAATAATAATATAATCATATAAAAAATA
*
2499234 AGGTAAAAACAAAATAATAATATAAT-A-ATAAAAAATA
1 AAGTAAAAACAAAATAATAATATAATCATATAAAAAATA
2499271 AAGTAAAA
1 AAGTAAAA
2499279 TATATACATA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
37 16 0.41
38 9 0.23
39 14 0.36
ACGTcount: A:0.70, C:0.04, G:0.05, T:0.22
Consensus pattern (39 bp):
AAGTAAAAACAAAATAATAATATAATCATATAAAAAATA
Found at i:2499403 original size:64 final size:65
Alignment explanation
Indices: 2499311--2499446 Score: 156
Period size: 64 Copynumber: 2.1 Consensus size: 65
2499301 AAGCAAGAAG
* **
2499311 AAAATAAAAATAGATAAATAAGTAAAATATGTATTAAAAA-ATAA-T-AATATA-ATATAATATA
1 AAAATAAAAATAGAGAAATAAGTAAAATAAATA-TAAAAATATAATTAAATATATATAT-ATATA
2499372 AA
64 AA
2499374 AAAATCAAAAATAGAGAAATAATGT-AAATAAATATAAAAATATAATTAAATATATATATATATA
1 AAAAT-AAAAATAGAGAAATAA-GTAAAATAAATATAAAAATATAATTAAATATATATATATATA
*
2499438 CA
64 AA
*
2499440 CAAATAA
1 AAAATAA
2499447 TAAGGGTTAA
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
63 11 0.18
64 26 0.42
65 5 0.08
66 16 0.26
67 4 0.06
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.28
Consensus pattern (65 bp):
AAAATAAAAATAGAGAAATAAGTAAAATAAATATAAAAATATAATTAAATATATATATATATAAA
Found at i:2511825 original size:212 final size:212
Alignment explanation
Indices: 2511415--2511839 Score: 825
Period size: 212 Copynumber: 2.0 Consensus size: 212
2511405 TTTCTGAGTC
2511415 TTCTCGGACTATTGTCGTACCTCAACTTTTTTTATCTATTGTATTACAACACCTTTGTCCATTAA
1 TTCTCGGACTATTGTCGTACCTCAACTTTTTTTATCTATTGTATTACAACACCTTTGTCCATTAA
2511480 TTTATATTATTTTGTGCGTAACAAATATCTTTTTTAGGGATCAATGGCCTCTTGTTATGAGGTAA
66 TTTATATTATTTTGTGCGTAACAAATATCTTTTTTAGGGATCAATGGCCTCTTGTTATGAGGTAA
2511545 ATGCTAAAAAAAAACAACACAAAGGCAAAAAGTTAGTAAAATAAATAAATGACGGAAGAAAGAAA
131 ATGCTAAAAAAAAACAACACAAAGGCAAAAAGTTAGTAAAATAAATAAATGACGGAAGAAAGAAA
2511610 GTAAAAATACAAAAAAA
196 GTAAAAATACAAAAAAA
2511627 TTCTCGGACTATTGTCGTACCTCAACTTTTTTTATCTATTGTATTACAACACCTTTGTCCATTAA
1 TTCTCGGACTATTGTCGTACCTCAACTTTTTTTATCTATTGTATTACAACACCTTTGTCCATTAA
2511692 TTTATATTATTTTGTGCGTAACAAATATCTTTTTTAGGGATCAATGGCCTCTTGTTATGAGGTAA
66 TTTATATTATTTTGTGCGTAACAAATATCTTTTTTAGGGATCAATGGCCTCTTGTTATGAGGTAA
*
2511757 ATGCTAAAAAAACA-AACACAAAGGCAAAAAGTTAGTAAAATAAATAAATGACGGAAGAAAGAAA
131 ATGCTAAAAAAAAACAACACAAAGGCAAAAAGTTAGTAAAATAAATAAATGACGGAAGAAAG-AA
2511821 AGTAAAAATACAAAAAAA
195 AGTAAAAATACAAAAAAA
2511839 T
1 T
2511840 AGTATGATTA
Statistics
Matches: 211, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
211 47 0.22
212 164 0.78
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (212 bp):
TTCTCGGACTATTGTCGTACCTCAACTTTTTTTATCTATTGTATTACAACACCTTTGTCCATTAA
TTTATATTATTTTGTGCGTAACAAATATCTTTTTTAGGGATCAATGGCCTCTTGTTATGAGGTAA
ATGCTAAAAAAAAACAACACAAAGGCAAAAAGTTAGTAAAATAAATAAATGACGGAAGAAAGAAA
GTAAAAATACAAAAAAA
Found at i:2512769 original size:12 final size:12
Alignment explanation
Indices: 2512752--2512776 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2512742 TAAAAAGTCT
2512752 ATGATAATAATA
1 ATGATAATAATA
2512764 ATGATAATAATA
1 ATGATAATAATA
2512776 A
1 A
2512777 GGAGGAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
ATGATAATAATA
Found at i:2512949 original size:33 final size:33
Alignment explanation
Indices: 2512903--2512982 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
2512893 AGTAATAAAT
*
2512903 AATACATATATATAGTAACGTTTAAAAAAAAGA
1 AATATATATATATAGTAACGTTTAAAAAAAAGA
*
2512936 AATATATATATATAGTAATGTTTAAAAAAAAGA
1 AATATATATATATAGTAACGTTTAAAAAAAAGA
*
2512969 AATATATGTATATA
1 AATATATATATATA
2512983 TACCCCACAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.56, C:0.03, G:0.09, T:0.33
Consensus pattern (33 bp):
AATATATATATATAGTAACGTTTAAAAAAAAGA
Found at i:2513130 original size:3 final size:3
Alignment explanation
Indices: 2513122--2513163 Score: 57
Period size: 3 Copynumber: 13.3 Consensus size: 3
2513112 TGTAGGTAGT
*
2513122 ATA ATA ATA ATA AAA ATA TATA TATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA -ATA -ATA ATA ATA ATA ATA ATA A
2513164 AGACAAAAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 29 0.81
4 7 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2513237 original size:56 final size:56
Alignment explanation
Indices: 2513130--2513239 Score: 136
Period size: 56 Copynumber: 1.9 Consensus size: 56
2513120 GTATAATAAT
* **
2513130 AATAAAAATATATATATAATAATAATAATAATAAAGACAAAAGGTTTTAAAAAAGAA
1 AATAAAAATATATATATAATAATAATAATAATAAAAACAAAA-GTAATAAAAAAGAA
2513187 AATAAAAATA-ATAT-TATATAATAATAATGAATAAAAACGAAAA-TAATAAAAAA
1 AATAAAAATATATATATA-ATAATAATAAT-AATAAAAAC-AAAAGTAATAAAAAA
2513240 ATATAGAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
55 2 0.04
56 23 0.49
57 18 0.38
58 4 0.09
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.25
Consensus pattern (56 bp):
AATAAAAATATATATATAATAATAATAATAATAAAAACAAAAGTAATAAAAAAGAA
Found at i:2513239 original size:57 final size:56
Alignment explanation
Indices: 2513130--2513240 Score: 129
Period size: 57 Copynumber: 1.9 Consensus size: 56
2513120 GTATAATAAT
* * *
2513130 AATAAAAATATATATATAATAATAATAATAATAAAGACAAAAGGTTTTAAAAAAGAA
1 AATAAAAATATATATATAATAATAATAATAATAAAAACAAAA-GTATAAAAAAAGAA
2513187 AATAAAAATA-ATAT-TATATAATAATAATGAATAAAAACGAAAA-TAATAAAAAAA
1 AATAAAAATATATATATA-ATAATAATAAT-AATAAAAAC-AAAAGT-ATAAAAAAA
2513241 TATAGAAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
55 2 0.04
56 16 0.34
57 25 0.53
58 4 0.09
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (56 bp):
AATAAAAATATATATATAATAATAATAATAATAAAAACAAAAGTATAAAAAAAGAA
Found at i:2513303 original size:24 final size:24
Alignment explanation
Indices: 2513227--2513303 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
2513217 ATAAAAACGA
* *
2513227 AAATAATAAAAAAATATAGAAAAT
1 AAATAATTAAAAAATATAGTAAAT
*
2513251 AAATAGA-TAAAAAATATA-TATAT
1 AAATA-ATTAAAAAATATAGTAAAT
* * *
2513274 ATATAATTATAAAATATAGTACAT
1 AAATAATTAAAAAATATAGTAAAT
2513298 AAATAA
1 AAATAA
2513304 AAACTCAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
22 1 0.02
23 17 0.40
24 24 0.56
25 1 0.02
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (24 bp):
AAATAATTAAAAAATATAGTAAAT
Found at i:2513581 original size:39 final size:39
Alignment explanation
Indices: 2513485--2513567 Score: 109
Period size: 37 Copynumber: 2.2 Consensus size: 39
2513475 GTAATAAAGC
* * *
2513485 AAGTAAAAA-ACAATAAAAATATAATCATATAAAAAATT
1 AAGTAAAAACAAAATAATAATATAATCATATAAAAAATA
*
2513523 AGGTAAAAACAAAATAATAATATAAT-A-ATAAAAAATA
1 AAGTAAAAACAAAATAATAATATAATCATATAAAAAATA
2513560 AAGTAAAA
1 AAGTAAAA
2513568 TATATACATA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
37 16 0.41
38 9 0.23
39 14 0.36
ACGTcount: A:0.70, C:0.04, G:0.05, T:0.22
Consensus pattern (39 bp):
AAGTAAAAACAAAATAATAATATAATCATATAAAAAATA
Found at i:2513692 original size:64 final size:67
Alignment explanation
Indices: 2513600--2513728 Score: 162
Period size: 64 Copynumber: 2.0 Consensus size: 67
2513590 AAGCAAGAAG
* **
2513600 AAAATAAAAATAGATAAATAAGTAAAATATGTATTAAAAA-ATAA-T-AATATA-ATATA-ATAT
1 AAAATAAAAATAGAGAAATAAGTAAAATAAATA-TAAAAATATAATTAAATATATATATATATAT
2513660 AAA
65 AAA
2513663 AAAATCAAAAATAGAGAAATAATGT-AAATAAATATAAAAATATAATTAAATATATATATATATA
1 AAAAT-AAAAATAGAGAAATAA-GTAAAATAAATATAAAAATATAATTAAATATATATATATATA
2513727 TA
64 TA
2513729 TATACAAATA
Statistics
Matches: 56, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
63 11 0.20
64 26 0.46
65 3 0.05
66 6 0.11
67 5 0.09
68 5 0.09
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.29
Consensus pattern (67 bp):
AAAATAAAAATAGAGAAATAAGTAAAATAAATATAAAAATATAATTAAATATATATATATATATA
AA
Found at i:2515618 original size:26 final size:26
Alignment explanation
Indices: 2515578--2515631 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
2515568 GTTGAGGAAG
*
2515578 CAGTTATGCTTTGTTAGGGCTAACAA
1 CAGTTATGCTCTGTTAGGGCTAACAA
*
2515604 CAGTTATGCTCTGTTAGGGTTAACAA
1 CAGTTATGCTCTGTTAGGGCTAACAA
2515630 CA
1 CA
2515632 TTTGTTAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (26 bp):
CAGTTATGCTCTGTTAGGGCTAACAA
Found at i:2519214 original size:44 final size:43
Alignment explanation
Indices: 2519166--2519292 Score: 125
Period size: 44 Copynumber: 3.2 Consensus size: 43
2519156 AAATCCTAAT
2519166 TAAAATACTAAAACCTATTTAATCTAAAATACCTAAAACAAAGA
1 TAAAATACTAAAACCTATTTAA-CTAAAATACCTAAAACAAAGA
* *
2519210 TAAAATA-TAAAA---A--TAA-T---ATA-CTAAAACTTAA-T
1 TAAAATACTAAAACCTATTTAACTAAAATACCTAAAAC-AAAGA
2519242 TAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGA
1 TAAAATACTAAAACCTATTT-AACTAAAATACCTAAAACAAAGA
2519286 TAAAATA
1 TAAAATA
2519293 TAATGTTTAA
Statistics
Matches: 65, Mismatches: 4, Indels: 28
0.67 0.04 0.29
Matches are distributed among these distances:
32 14 0.22
33 10 0.15
36 2 0.03
38 4 0.06
39 2 0.03
40 2 0.03
43 10 0.15
44 21 0.32
ACGTcount: A:0.60, C:0.13, G:0.02, T:0.26
Consensus pattern (43 bp):
TAAAATACTAAAACCTATTTAACTAAAATACCTAAAACAAAGA
Found at i:2519242 original size:76 final size:76
Alignment explanation
Indices: 2519085--2519295 Score: 274
Period size: 76 Copynumber: 2.9 Consensus size: 76
2519075 TAAAACATCT
* * * * * *
2519085 TAAATCCTAATTAAAACACTTAAAA-ATATTTAAACTAAAATACCT----GAAA-ATAATAT-TT
1 TAAAACCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
*
2519143 AAAATAATATTC
65 AAAATAATATAC
* *
2519155 TAAATCCTAATTAAAATACTAAAACCTATTTAATCTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
2519220 AAATAATATAC
66 AAATAATATAC
*
2519231 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
2519296 TGTTTAAAAT
Statistics
Matches: 124, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
69 5 0.04
70 36 0.29
74 3 0.02
75 6 0.05
76 74 0.60
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.29
Consensus pattern (76 bp):
TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
AAATAATATAC
Found at i:2519263 original size:19 final size:19
Alignment explanation
Indices: 2519227--2519264 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2519217 TAAAAATAAT
*
2519227 ATACTAAAACTTAATTAAA
1 ATACTAAAACCTAATTAAA
*
2519246 ATACTAAAACCTATTTAAA
1 ATACTAAAACCTAATTAAA
2519265 CTAAAATACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
ATACTAAAACCTAATTAAA
Found at i:2523789 original size:22 final size:22
Alignment explanation
Indices: 2523764--2523815 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
2523754 GATGAAATTG
2523764 AAAAAATAGAATAA-AATAAAAT
1 AAAAAATAGAA-AATAATAAAAT
* *
2523786 AAAAATTGGAAAATAATAAAAT
1 AAAAAATAGAAAATAATAAAAT
*
2523808 AATAAATA
1 AAAAAATA
2523816 ATGATTTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (22 bp):
AAAAAATAGAAAATAATAAAAT
Found at i:2524625 original size:24 final size:24
Alignment explanation
Indices: 2524598--2524712 Score: 72
Period size: 25 Copynumber: 4.6 Consensus size: 24
2524588 AAATCCTAAT
2524598 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACCTATTTAAAC
** ** *
2524622 TAAAATACCTAAAACAAAGATAAAA
1 TAAAATA-CTAAAACCTATTTAAAC
* * * *
2524647 TATAAA-AATAATATCCTAAAACTT-AAT
1 TA-AAATACTAA-AACCT---ATTTAAAC
2524674 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACCTATTTAAAC
2524698 TAAAATACCTAAAAC
1 TAAAATA-CTAAAAC
2524713 AAAGATAGAA
Statistics
Matches: 66, Mismatches: 16, Indels: 17
0.67 0.16 0.17
Matches are distributed among these distances:
23 3 0.05
24 19 0.29
25 24 0.36
26 10 0.15
27 8 0.12
28 2 0.03
ACGTcount: A:0.58, C:0.15, G:0.01, T:0.26
Consensus pattern (24 bp):
TAAAATACTAAAACCTATTTAAAC
Found at i:2524646 original size:44 final size:44
Alignment explanation
Indices: 2524598--2524724 Score: 127
Period size: 44 Copynumber: 3.2 Consensus size: 44
2524588 AAATCCTAAT
2524598 TAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGA
1 TAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGA
* *
2524642 TAAAATA-TAAAA---A--T-AA-T---AT-CCTAAAACTTAA-T
1 TAAAATACTAAAACCTATTTAAACTAAAATACCTAAAAC-AAAGA
2524674 TAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGA
1 TAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGA
*
2524718 TAGAATA
1 TAAAATA
2524725 TAATGTTTAA
Statistics
Matches: 64, Mismatches: 5, Indels: 28
0.66 0.05 0.29
Matches are distributed among these distances:
32 15 0.23
33 9 0.14
36 2 0.03
37 2 0.03
38 2 0.03
39 2 0.03
40 2 0.03
43 9 0.14
44 21 0.33
ACGTcount: A:0.59, C:0.13, G:0.02, T:0.25
Consensus pattern (44 bp):
TAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGA
Found at i:2524655 original size:76 final size:76
Alignment explanation
Indices: 2524575--2524727 Score: 270
Period size: 76 Copynumber: 2.0 Consensus size: 76
2524565 AATAATATTT
* *
2524575 AAAATAATATTCTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAA
1 AAAATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAA
2524640 GATAAAATATA
66 GATAAAATATA
*
2524651 AAAATAATATCCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAA
1 AAAATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAA
*
2524716 GATAGAATATA
66 GATAAAATATA
2524727 A
1 A
2524728 TGTTTAAAAT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.58, C:0.13, G:0.02, T:0.27
Consensus pattern (76 bp):
AAAATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAA
GATAAAATATA
Found at i:2536017 original size:6 final size:6
Alignment explanation
Indices: 2536006--2536036 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
2535996 CATGCTTAAT
2536006 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA T
2536037 GTAACGGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:2544092 original size:27 final size:26
Alignment explanation
Indices: 2544053--2544106 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 26
2544043 TTCCAGAAGG
2544053 CGCTGACTAGATCTTCTAGAAAACTGC
1 CGCTGACTAGATCTTCTAG-AAACTGC
*
2544080 CGCTGACTGGATCTTCTAGAAACTGC
1 CGCTGACTAGATCTTCTAGAAACTGC
2544106 C
1 C
2544107 ACATCAGACT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (26 bp):
CGCTGACTAGATCTTCTAGAAACTGC
Found at i:2552576 original size:13 final size:13
Alignment explanation
Indices: 2552558--2552608 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
2552548 CTTAGCATAT
2552558 TTAAAAATAAAAC
1 TTAAAAATAAAAC
2552571 TT-AAAATAAAA-
1 TTAAAAATAAAAC
**
2552582 GAAAAAATGAAAAC
1 TTAAAAAT-AAAAC
2552596 TTGAAAAATAAAA
1 TT-AAAAATAAAA
2552609 GAGAGAACCT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
12 14 0.47
13 6 0.20
14 4 0.13
15 6 0.20
ACGTcount: A:0.71, C:0.04, G:0.06, T:0.20
Consensus pattern (13 bp):
TTAAAAATAAAAC
Found at i:2552610 original size:27 final size:24
Alignment explanation
Indices: 2552560--2552610 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 24
2552550 TAGCATATTT
2552560 AAAAATAAAACTTAAAATAAAAGA
1 AAAAATAAAACTTAAAATAAAAGA
2552584 AAAAATGAAAACTTGAAAAATAAAAGA
1 AAAAAT-AAAACTT--AAAATAAAAGA
2552611 GAGAACCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 6 0.25
25 7 0.29
27 11 0.46
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.16
Consensus pattern (24 bp):
AAAAATAAAACTTAAAATAAAAGA
Found at i:2552868 original size:27 final size:27
Alignment explanation
Indices: 2552837--2552908 Score: 110
Period size: 26 Copynumber: 2.7 Consensus size: 27
2552827 CCAAAAGGCG
* *
2552837 CTGACTAGATCTTCTAGAAAACTGTCA
1 CTGACTGGATCTTCTAGAAAACTGCCA
*
2552864 TTGACTGGATCTTCTAG-AAACTGCCA
1 CTGACTGGATCTTCTAGAAAACTGCCA
2552890 CTGACTGGATCTTCTAGAA
1 CTGACTGGATCTTCTAGAA
2552909 CGTGCTACAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 24 0.60
27 16 0.40
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (27 bp):
CTGACTGGATCTTCTAGAAAACTGCCA
Found at i:2559510 original size:18 final size:18
Alignment explanation
Indices: 2559475--2559516 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
2559465 TCCAAGGAGT
*
2559475 GATGAGCTAGGCGTCTGA
1 GATGAGCTAGGCGGCTGA
2559493 GATGAGCTA-GCGAGCTGA
1 GATGAGCTAGGCG-GCTGA
*
2559511 GGTGAG
1 GATGAG
2559517 TCGTGGTGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.24, C:0.14, G:0.43, T:0.19
Consensus pattern (18 bp):
GATGAGCTAGGCGGCTGA
Done.