Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, 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: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 21 of 109
Found at i:3537412 original size:15 final size:16
Alignment explanation
Indices: 3537392--3537422 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3537382 ATTTTGAATC
3537392 AATTTTT-GATTTTTT
1 AATTTTTCGATTTTTT
3537407 AATTTTTCGATTTTTT
1 AATTTTTCGATTTTTT
3537423 TTCTTACCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.19, C:0.03, G:0.06, T:0.71
Consensus pattern (16 bp):
AATTTTTCGATTTTTT
Found at i:3540263 original size:19 final size:21
Alignment explanation
Indices: 3540241--3540283 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
3540231 TTTTTAGAAC
*
3540241 TTTTATAAAATTT-TA-ATTT
1 TTTTAGAAAATTTCTATATTT
*
3540260 TTTTAGAAATTTTCTATATTT
1 TTTTAGAAAATTTCTATATTT
3540281 TTT
1 TTT
3540284 AATATTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 11 0.55
20 2 0.10
21 7 0.35
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTTAGAAAATTTCTATATTT
Found at i:3540282 original size:28 final size:27
Alignment explanation
Indices: 3540223--3540282 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 27
3540213 TAATTTTTTG
*
3540223 TTTTTAACTTTTTAGAACTTTTATAAA
1 TTTTTAACTTTTTAGAAATTTTATAAA
* * * *
3540250 ATTTTAATTTTTTTAGAAATTTTCTATA
1 TTTTTAA-CTTTTTAGAAATTTTATAAA
3540278 TTTTT
1 TTTTT
3540283 TAATATTTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (27 bp):
TTTTTAACTTTTTAGAAATTTTATAAA
Found at i:3541103 original size:268 final size:269
Alignment explanation
Indices: 3540618--3541127 Score: 756
Period size: 268 Copynumber: 1.9 Consensus size: 269
3540608 CTATTAAATT
*
3540618 AAAAAAATACAAAACGTTCAAAAAAATGAAATTAAGAAAATTAAAATATTGAAAAAAAGAAATTT
1 AAAAAAATACAAAACGTTCAAAAAAATGAAATTAAAAAAATTAAAATATTGAAAAAAAGAAATTT
**
3540683 AATATTTTTAAAAACTAAAAAATATATAAAAAAATTCAAAATATATTTTATATTAGAGTGACTAA
66 AATATTTTTAAAAACTAAAAAATATATAAAAAAATTCAAAATATATTTTATATTAGAAAGACTAA
* * * * *
3540748 ATTTTAAATTTCTTACGAGCATAAGAATTAAGTTCTAAATTTCATATGAATATACAGACCATTTA
131 ATTTTAAATTTCTCACGAACATAAGAATAAAGTTCTAAATTTCATATGAATACACAGACAATTTA
* * *
3540813 TCTAATTTAACAACTTATTTCATTCATCCAAATTACCATGTTAGCAATTTTAAAAATGAAAATGT
196 TATAATTGAACAACTGATTTCATTCATCCAAATTACCATGTTAGCAATTTTAAAAATGAAAATGT
3540878 TAAATTTAA
261 TAAATTTAA
*
3540887 AAAAAAATACAAAACGTTC-AAAAAATGAAATTAAAAAAATTAAAATATTGAAAAAAATAAATTT
1 AAAAAAATACAAAACGTTCAAAAAAATGAAATTAAAAAAATTAAAATATTGAAAAAAAGAAATTT
* * * *
3540951 AATATTTTTAAAAATTAGAAAATTTAT-AAAAAATTCAAAATATATATTTATATTAGAAAGATTA
66 AATATTTTTAAAAACTAAAAAATATATAAAAAAATTCAAAATATAT-TTTATATTAGAAAGACTA
* * * *
3541015 AATTTTAAATTTCTCACTAATATAAGAAGTAAATTTC-AAATTTCATATGAATACAGAGACAATT
130 AATTTTAAATTTCTCACGAACATAAGAA-TAAAGTTCTAAATTTCATATGAATACACAGACAATT
* * * **
3541079 TATATAATTGAACAAGTGATTTCATTTATCCAAGTTGTCATGTTAGCAA
194 TATATAATTGAACAACTGATTTCATTCATCCAAATTACCATGTTAGCAA
3541128 GCCATCGTTA
Statistics
Matches: 214, Mismatches: 25, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
267 18 0.08
268 171 0.80
269 25 0.12
ACGTcount: A:0.51, C:0.08, G:0.07, T:0.34
Consensus pattern (269 bp):
AAAAAAATACAAAACGTTCAAAAAAATGAAATTAAAAAAATTAAAATATTGAAAAAAAGAAATTT
AATATTTTTAAAAACTAAAAAATATATAAAAAAATTCAAAATATATTTTATATTAGAAAGACTAA
ATTTTAAATTTCTCACGAACATAAGAATAAAGTTCTAAATTTCATATGAATACACAGACAATTTA
TATAATTGAACAACTGATTTCATTCATCCAAATTACCATGTTAGCAATTTTAAAAATGAAAATGT
TAAATTTAA
Found at i:3542592 original size:13 final size:12
Alignment explanation
Indices: 3542576--3542627 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 12
3542566 TAATATATTT
3542576 TATTAAGTTAATA
1 TATTAA-TTAATA
*
3542589 TATTGAATTAAAA
1 TATT-AATTAATA
*
3542602 TATTAAATAATA
1 TATTAATTAATA
3542614 -ATTATATTAATA
1 TATTA-ATTAATA
3542626 TA
1 TA
3542628 ATACAGATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
11 4 0.12
12 12 0.38
13 14 0.44
14 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (12 bp):
TATTAATTAATA
Found at i:3543247 original size:11 final size:11
Alignment explanation
Indices: 3543233--3543277 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
3543223 TTATTTTTTA
3543233 ATTTTATATTT
1 ATTTTATATTT
*
3543244 A-TTTATATAT
1 ATTTTATATTT
*
3543254 ATTATATATTT
1 ATTTTATATTT
*
3543265 AATTTATATTT
1 ATTTTATATTT
3543276 AT
1 AT
3543278 ATTAAAAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTTTATATTT
Found at i:3543302 original size:32 final size:31
Alignment explanation
Indices: 3543215--3543302 Score: 97
Period size: 32 Copynumber: 2.7 Consensus size: 31
3543205 ACCTGATATA
*
3543215 TATAAAAATTATTTTTTAATTTTATATTTATT
1 TATAAAAATTATATTTTAA-TTTATATTTATT
* *
3543247 TATATATATTATATATTTAATTTATATTTATAT
1 TATAAAAATTATAT-TTTAATTTATATTTAT-T
*
3543280 TA-AAAAATAATATTTTATATTTA
1 TATAAAAATTATATTTTA-ATTTA
3543303 AAAATATTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
31 4 0.09
32 35 0.74
33 8 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (31 bp):
TATAAAAATTATATTTTAATTTATATTTATT
Found at i:3543429 original size:39 final size:41
Alignment explanation
Indices: 3543348--3543443 Score: 101
Period size: 39 Copynumber: 2.4 Consensus size: 41
3543338 GATACGATTT
*
3543348 TATATAAT--ATTAAATCGAATCAAATTCAAATATAAAAAA
1 TATATAATAAATTAAATCAAATCAAATTCAAATATAAAAAA
* * * * *
3543387 TATA-AA-AAATTAAATCAAATCAAATTTAAATTTTATATA
1 TATATAATAAATTAAATCAAATCAAATTCAAATATAAAAAA
3543426 TATATAATTAAATTAAAT
1 TATATAA-TAAATTAAAT
3543444 TTGAAATGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
38 2 0.04
39 33 0.72
40 2 0.04
42 9 0.20
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.36
Consensus pattern (41 bp):
TATATAATAAATTAAATCAAATCAAATTCAAATATAAAAAA
Found at i:3548521 original size:15 final size:15
Alignment explanation
Indices: 3548501--3548533 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3548491 CTTGTGCATG
3548501 TGAGGAGATAGAGAA
1 TGAGGAGATAGAGAA
3548516 TGAGGAGATAGAGAA
1 TGAGGAGATAGAGAA
3548531 TGA
1 TGA
3548534 CACCTTTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.39, T:0.15
Consensus pattern (15 bp):
TGAGGAGATAGAGAA
Found at i:3551304 original size:3 final size:3
Alignment explanation
Indices: 3551296--3551329 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
3551286 ATCCCCTCCA
*
3551296 TTC TTC TTC TTC TTC TTC TTC TTC TTA TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
3551330 CCCAGAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:3559943 original size:34 final size:38
Alignment explanation
Indices: 3559905--3559989 Score: 133
Period size: 34 Copynumber: 2.3 Consensus size: 38
3559895 ATTAAAATGA
*
3559905 AAAAAAAAAAACTTATTT-GGAA-AA-TTTTTT-AGAC
1 AAAAATAAAAACTTATTTAGGAATAATTTTTTTGAGAC
3559939 AAAAATAAAAACTTATTTAGGAATAATTTTTTTGAGAC
1 AAAAATAAAAACTTATTTAGGAATAATTTTTTTGAGAC
3559977 AAAAATAAAAACT
1 AAAAATAAAAACT
3559990 CTTTTTACTT
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
34 17 0.37
35 4 0.09
36 2 0.04
37 6 0.13
38 17 0.37
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.32
Consensus pattern (38 bp):
AAAAATAAAAACTTATTTAGGAATAATTTTTTTGAGAC
Found at i:3560073 original size:21 final size:21
Alignment explanation
Indices: 3560049--3560090 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
3560039 TATTGATAAA
3560049 TATTAAAATTTTAATT-TTAAT
1 TATT-AAATTTTAATTCTTAAT
3560070 TATTAAATTTTAATTCTTAAT
1 TATTAAATTTTAATTCTTAAT
3560091 AATCTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTAAATTTTAATTCTTAAT
Found at i:3562061 original size:29 final size:29
Alignment explanation
Indices: 3561999--3562100 Score: 88
Period size: 29 Copynumber: 3.6 Consensus size: 29
3561989 AATTTTTTTT
** *
3561999 AATTATAATAAATATTTAATATAATGTTTT
1 AATTATAA-AAATATTTAATATAATAATTA
* *
3562029 AATTTTAAAAATATTTAATATGATAATTA
1 AATTATAAAAATATTTAATATAATAATTA
*
3562058 AATTATAAATATA-TTAAT-TAA-AA-TA
1 AATTATAAAAATATTTAATATAATAATTA
3562083 ATATT-TAAAAATTATTTA
1 A-ATTATAAAAA-TATTTA
3562101 TCAATTACAT
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
25 8 0.13
26 7 0.12
27 5 0.08
28 5 0.08
29 28 0.47
30 7 0.12
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (29 bp):
AATTATAAAAATATTTAATATAATAATTA
Found at i:3564215 original size:3 final size:3
Alignment explanation
Indices: 3564207--3564239 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3564197 TCAATTGATC
3564207 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
3564240 ACATCTTCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:3565744 original size:14 final size:14
Alignment explanation
Indices: 3565709--3565744 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3565699 AAATGAGAAA
3565709 ATTTTTTTTTATAG
1 ATTTTTTTTTATAG
3565723 -TTTCTTTTTTATAG
1 ATTT-TTTTTTATAG
3565737 ATTTTTTT
1 ATTTTTTT
3565745 ATTGATTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.15
14 14 0.70
15 3 0.15
ACGTcount: A:0.17, C:0.03, G:0.06, T:0.75
Consensus pattern (14 bp):
ATTTTTTTTTATAG
Found at i:3570129 original size:15 final size:15
Alignment explanation
Indices: 3570111--3570302 Score: 117
Period size: 16 Copynumber: 12.5 Consensus size: 15
3570101 TTGAAGATTC
3570111 GGATTTTAGGGTTTT
1 GGATTTTAGGGTTTT
3570126 GGATTTTAGGGGTTTT
1 GGATTTTA-GGGTTTT
* * *
3570142 GAATTTT-GGGGTAT
1 GGATTTTAGGGTTTT
* *
3570156 GGATTTAAAGG--TT
1 GGATTTTAGGGTTTT
3570169 GGAATTTTAGGGTTTT
1 GG-ATTTTAGGGTTTT
*
3570185 GGATTTTATGGGGTTT
1 GGATTTTA-GGGTTTT
* * *
3570201 GGATTTAAAGGTTTAAA
1 GGATTTTAGGGTTT--T
3570218 GG-TTTTAGGGTTTT
1 GGATTTTAGGGTTTT
*
3570232 AGATTTTAGAGAG-TTT
1 GGATTTTAG-G-GTTTT
* *
3570248 AGATTTAAGGGATTTT
1 GGATTTTAGGG-TTTT
3570264 GGATTTTAGGGGTTTT
1 GGATTTTA-GGGTTTT
* **
3570280 AGAATCCTAGGGTTTT
1 -GGATTTTAGGGTTTT
3570296 GG-TTTTA
1 GGATTTTA
3570303 AAAAATTGAG
Statistics
Matches: 135, Mismatches: 27, Indels: 31
0.70 0.14 0.16
Matches are distributed among these distances:
13 3 0.02
14 22 0.16
15 28 0.21
16 71 0.53
17 11 0.08
ACGTcount: A:0.21, C:0.01, G:0.31, T:0.46
Consensus pattern (15 bp):
GGATTTTAGGGTTTT
Found at i:3570271 original size:47 final size:46
Alignment explanation
Indices: 3570120--3570282 Score: 140
Period size: 47 Copynumber: 3.5 Consensus size: 46
3570110 CGGATTTTAG
* * * *
3570120 GGTTTTGGATTTTAGGGGTTTT-GAATTT-TGGGGTATGGATTTAAA
1 GGTTTTGGATTTTA-GGGTTTTAGATTTTATGGAGTTTAGATTTAAA
* * *
3570165 GG--TTGGAATTTTAGGGTTTTGGATTTTATGGGGTTTGGATTTAAA
1 GGTTTTGG-ATTTTAGGGTTTTAGATTTTATGGAGTTTAGATTTAAA
* *
3570210 GGTTTAAAGG-TTTTAGGGTTTTAGATTTTA-GAGAGTTTAGATTTAAG
1 GGTTT--TGGATTTTAGGGTTTTAGATTTTATG-GAGTTTAGATTTAAA
3570257 GGATTTTGGATTTTAGGGGTTTTAGA
1 GG-TTTTGGATTTTA-GGGTTTTAGA
3570283 ATCCTAGGGT
Statistics
Matches: 99, Mismatches: 8, Indels: 19
0.79 0.06 0.15
Matches are distributed among these distances:
43 11 0.11
44 11 0.11
45 20 0.20
46 3 0.03
47 39 0.39
48 13 0.13
49 2 0.02
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.46
Consensus pattern (46 bp):
GGTTTTGGATTTTAGGGTTTTAGATTTTATGGAGTTTAGATTTAAA
Found at i:3570499 original size:14 final size:16
Alignment explanation
Indices: 3570470--3570501 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
3570460 TCCCAACATC
3570470 TAGGCAAAATTATTTT
1 TAGGCAAAATTATTTT
3570486 TAGG-AAAA-TATTTT
1 TAGGCAAAATTATTTT
3570500 TA
1 TA
3570502 TTCTCTCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 4 0.25
16 4 0.25
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (16 bp):
TAGGCAAAATTATTTT
Found at i:3571003 original size:16 final size:16
Alignment explanation
Indices: 3570984--3571018 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3570974 TTTTAGGAAG
3570984 TTTGGATTTAAGGGAT
1 TTTGGATTTAAGGGAT
* *
3571000 TTTGGATTTTAGGGGT
1 TTTGGATTTAAGGGAT
3571016 TTT
1 TTT
3571019 AGAATCCTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.51
Consensus pattern (16 bp):
TTTGGATTTAAGGGAT
Found at i:3572368 original size:12 final size:12
Alignment explanation
Indices: 3572351--3572375 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3572341 GATGGCTATA
3572351 GACAGGGGGCTG
1 GACAGGGGGCTG
3572363 GACAGGGGGCTG
1 GACAGGGGGCTG
3572375 G
1 G
3572376 TTGGGGGCGG
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:0.16, C:0.16, G:0.60, T:0.08
Consensus pattern (12 bp):
GACAGGGGGCTG
Found at i:3573170 original size:147 final size:147
Alignment explanation
Indices: 3572901--3573185 Score: 376
Period size: 147 Copynumber: 1.9 Consensus size: 147
3572891 AAATGACTTT
* * * * * *
3572901 AACTTGGATTGAATCACAAGTCAGAAAATAAGAAGATTGAGAATAAACCACGAGTCAGAGGTTAA
1 AACTTAGATTGAATCACAAGTCAAAAAACAAGAAGATCGAGAATAAACCACGAGTCAAAGGATAA
* * * *
3572966 CAACAATTAAGATTAAACTACGATTTTAAATTAAAGAGATCGAGATTGAACCGTGAATTAG-AGA
66 CAACAATCAAGATTAAACTACGATTTTAAATTAAAAAGATCGAGATTAAACCATGAA-TAGAAGA
3573030 ATAAAGAGATAAGTATTG
130 ATAAAGAGATAAGTATTG
* * *
3573048 AACTTAGATTGAATCACAAGTCAAAAAACAAGGAGATCGAGATTAGACCACGAGTCAAAGGATAA
1 AACTTAGATTGAATCACAAGTCAAAAAACAAGAAGATCGAGAATAAACCACGAGTCAAAGGATAA
* * * * *
3573113 CAACAATCGATATTAAACTATGATTTTGAATTAAAAAGATC-AGGATTAAACTATGAATAGAAGA
66 CAACAATCAAGATTAAACTACGATTTTAAATTAAAAAGATCGA-GATTAAACCATGAATAGAAGA
3573177 ATAAAGAGA
130 ATAAAGAGA
3573186 CCGAGATTAA
Statistics
Matches: 118, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
146 4 0.03
147 114 0.97
ACGTcount: A:0.48, C:0.11, G:0.19, T:0.23
Consensus pattern (147 bp):
AACTTAGATTGAATCACAAGTCAAAAAACAAGAAGATCGAGAATAAACCACGAGTCAAAGGATAA
CAACAATCAAGATTAAACTACGATTTTAAATTAAAAAGATCGAGATTAAACCATGAATAGAAGAA
TAAAGAGATAAGTATTG
Found at i:3573350 original size:171 final size:170
Alignment explanation
Indices: 3573048--3574085 Score: 1095
Period size: 171 Copynumber: 6.1 Consensus size: 170
3573038 ATAAGTATTG
* * * *
3573048 AACTTAGATTGAATCACAAGTCAAAAAACAAGGAGATCGAGATTAGACCACGAGTCAAAGGATAA
1 AACTTGGATTGAATCACAAGTAAAAAAATAAGGAGATCGAGATTAAACCACGAGTCAAAGGATAA
* * * * ** *
3573113 CAACAATCGATATTAAACTATGATTTTGAATTAAAAAGATCAGGATTAAACTATGAAT-AGAAGA
66 CAACAATCGAGATTAAACTATGATTTTGAATTAAAGAGATCAAGATTGAACCGTAAATCA-AAGA
* * * *
3573177 ATAAAGAGACCGAGATT-AATCCGTGAATCAGAGAATAATGTT
130 ATAAAGAGATCGAGATTAAATCC--GAATCAAAAAATAACGTT
* *
3573219 AACTTGGATTGAATCACAAGTAAAAAAATAAGGAGATCGAGATTAAACAACGAGTCAGAGGATAA
1 AACTTGGATTGAATCACAAGTAAAAAAATAAGGAGATCGAGATTAAACCACGAGTCAAAGGATAA
* * * **
3573284 CAACAATCGATATTAAACTGTGACTTTGAATTAAAGAGATCGGGATTGAACCGTAAATCAAAGAA
66 CAACAATCGAGATTAAACTATGATTTTGAATTAAAGAGATCAAGATTGAACCGTAAATCAAAGAA
* *
3573349 TAAA-AGATCGAGATTAAATCACGAGTCAAAAAATGACGTT
131 TAAAGAGATCGAGATTAAATC-CGAATCAAAAAATAACGTT
** * * * * *
3573389 AACTTGGATTGAATCACAAGTCCAAAAATAAGGAGACCGGGATTAGACCATGAGTCAAAAGATAA
1 AACTTGGATTGAATCACAAGTAAAAAAATAAGGAGATCGAGATTAAACCACGAGTCAAAGGATAA
* * * * **
3573454 CAACAACCGAGATTAAACTTTGATTTTGAATTAAAGAGATC-GGAATTGAATCGCGAATCGAAA-
66 CAACAATCGAGATTAAACTATGATTTTGAATTAAAGAGATCAAG-ATTGAACCGTAAATC-AAAG
* *
3573517 AATAAAGAGATCGAGATTAAATCGCGAATTAAAAAATAATGTT
129 AATAAAGAGATCGAGATTAAATC-CGAATCAAAAAATAACGTT
* * *
3573560 AACTTGGATTGAATCACAAGTAAGAAAATAAGGAGA-CTGAGATTAAACCATGAGTTC-GAGGAT
1 AACTTGGATTGAATCACAAGTAAAAAAATAAGGAGATC-GAGATTAAACCACGAG-TCAAAGGAT
* * * * * *
3573623 AACAACAATCGAGATTAAATTACGACTTTGAATTAAAGAGATCAAGATTAAACCGTAAATTAGAG
64 AACAACAATCGAGATTAAACTATGATTTTGAATTAAAGAGATCAAGATTGAACCGTAAATCAAAG
* * * * *
3573688 AATAAAAAGACTGGA-ATTAAATTACGAGTCAAAAAATGACGTT
129 AATAAAGAGA-TCGAGATTAAA-TCCGAATCAAAAAATAACGTT
*** * * * * ** *
3573731 AACTTGGATTGAATCACAAGTTCGAAAATAAAGAGACCGGGATTAGACCACGAGTCAAAAAAAAA
1 AACTTGGATTGAATCACAAGTAAAAAAATAAGGAGATCGAGATTAAACCACGAGTCAAAGGATAA
* * * * * * **
3573796 TAACAGTCGAGATTAAACCATGATTTTAAATTAAAGAGATCGAGATTGAATCACAAATCGAAA-A
66 CAACAATCGAGATTAAACTATGATTTTGAATTAAAGAGATCAAGATTGAACCGTAAATC-AAAGA
* * *
3573860 ATAAAGAGATCGAGATTAAATCACGAATCAGAGAATAATGTT
130 ATAAAGAGATCGAGATTAAATC-CGAATCAAAAAATAACGTT
* * * *
3573902 AACTTGGATTGAATCACAAATAAGAAAATAAAGAGATCGAGATTAAACCACGAGTCAGAGGATAA
1 AACTTGGATTGAATCACAAGTAAAAAAATAAGGAGATCGAGATTAAACCACGAGTCAAAGGATAA
* * * * * * *
3573967 CAACAATCAAGATCAAATTGTGATTTTTAATTAAAGAGATCAAGATTGAACCGTGAATCAGAGAA
66 CAACAATCGAGATTAAACTATGATTTTGAATTAAAGAGATCAAGATTGAACCGTAAATCAAAGAA
* * *
3574032 TAAAAAGATCGAGATTAAATCGCGAGTCAAAAAATAACATT
131 TAAAGAGATCGAGATTAAATC-CGAATCAAAAAATAACGTT
3574073 AACTTGGATTGAA
1 AACTTGGATTGAA
3574086 CTGCAAGTTA
Statistics
Matches: 719, Mismatches: 130, Indels: 36
0.81 0.15 0.04
Matches are distributed among these distances:
169 2 0.00
170 145 0.20
171 560 0.78
172 12 0.02
ACGTcount: A:0.47, C:0.12, G:0.19, T:0.23
Consensus pattern (170 bp):
AACTTGGATTGAATCACAAGTAAAAAAATAAGGAGATCGAGATTAAACCACGAGTCAAAGGATAA
CAACAATCGAGATTAAACTATGATTTTGAATTAAAGAGATCAAGATTGAACCGTAAATCAAAGAA
TAAAGAGATCGAGATTAAATCCGAATCAAAAAATAACGTT
Found at i:3573471 original size:341 final size:341
Alignment explanation
Indices: 3573048--3574085 Score: 1444
Period size: 342 Copynumber: 3.0 Consensus size: 341
3573038 ATAAGTATTG
* * * * * *
3573048 AACTTAGATTGAATCACAAGTCAAAAAACAAGGAGATCGAGATTAGACCACGAGTCAAAGGATAA
1 AACTTGGATTGAATCACAAGTCCAAAAATAAGGAGACCGGGATTAGACCACGAGTCAAAAGATAA
* * * * * *
3573113 CAACAATCGATATTAAACTATGATTTTGAATTAAAAAGATCAGGATT-AAACTATGAATAGAAGA
66 CAACAATCGAGATTAAACTATGATTTTGAATTAAAGAGATC-GGATTGAATC-ACGAATCGAAAA
*
3573177 ATAAAGAGACCGAGATT-AATCCGTGAATCAGAGAATAATGTTAACTTGGATTGAATCACAAGTA
129 ATAAAGAGATCGAGATTAAATCCG-GAATCAGAGAATAATGTTAACTTGGATTGAATCACAAGTA
* * * *
3573241 AAAAAATAAGGAGATCGAGATTAAACAACGAGTCAGAGGATAACAACAATCGATATTAAACTGTG
193 AGAAAATAAGGAGATCGAGATTAAACCACGAGTCAGAGGATAACAACAATCGAGATTAAATTGTG
** *
3573306 ACTTTGAATTAAAGAGATCGGGATTGAACCGTAAATCAAAGAAT-AAAAGATCGAGATTAAATCA
258 ACTTTGAATTAAAGAGATCAAGATTGAACCGTAAATCAGAGAATAAAAAGATCGAGATTAAATCA
3573370 CGAGTCAAAAAATGACGTT
323 CGAGTCAAAAAATGACGTT
*
3573389 AACTTGGATTGAATCACAAGTCCAAAAATAAGGAGACCGGGATTAGACCATGAGTCAAAAGATAA
1 AACTTGGATTGAATCACAAGTCCAAAAATAAGGAGACCGGGATTAGACCACGAGTCAAAAGATAA
* * *
3573454 CAACAACCGAGATTAAACTTTGATTTTGAATTAAAGAGATCGGAATTGAATCGCGAATCGAAAAA
66 CAACAATCGAGATTAAACTATGATTTTGAATTAAAGAGATCGG-ATTGAATCACGAATCGAAAAA
* * *
3573519 TAAAGAGATCGAGATTAAAT-CGCGAATTAAAAAATAATGTTAACTTGGATTGAATCACAAGTAA
130 TAAAGAGATCGAGATTAAATCCG-GAATCAGAGAATAATGTTAACTTGGATTGAATCACAAGTAA
* **
3573583 GAAAATAAGGAGA-CTGAGATTAAACCATGAGTTC-GAGGATAACAACAATCGAGATTAAATTAC
194 GAAAATAAGGAGATC-GAGATTAAACCACGAG-TCAGAGGATAACAACAATCGAGATTAAATTGT
* * *
3573646 GACTTTGAATTAAAGAGATCAAGATTAAACCGTAAATTAGAGAATAAAAAGACTGGA-ATTAAAT
257 GACTTTGAATTAAAGAGATCAAGATTGAACCGTAAATCAGAGAATAAAAAGA-TCGAGATTAAAT
*
3573710 TACGAGTCAAAAAATGACGTT
321 CACGAGTCAAAAAATGACGTT
* * * * *
3573731 AACTTGGATTGAATCACAAGTTCGAAAATAAAGAGACCGGGATTAGACCACGAGTCAAAAAAAAA
1 AACTTGGATTGAATCACAAGTCCAAAAATAAGGAGACCGGGATTAGACCACGAGTCAAAAGATAA
* * * * *
3573796 TAACAGTCGAGATTAAACCATGATTTTAAATTAAAGAGATCGAGATTGAATCACAAATCGAAAAA
66 CAACAATCGAGATTAAACTATGATTTTGAATTAAAGAGATCG-GATTGAATCACGAATCGAAAAA
*
3573861 TAAAGAGATCGAGATTAAATCAC-GAATCAGAGAATAATGTTAACTTGGATTGAATCACAAATAA
130 TAAAGAGATCGAGATTAAATC-CGGAATCAGAGAATAATGTTAACTTGGATTGAATCACAAGTAA
* * *
3573925 GAAAATAAAGAGATCGAGATTAAACCACGAGTCAGAGGATAACAACAATCAAGATCAAATTGTGA
194 GAAAATAAGGAGATCGAGATTAAACCACGAGTCAGAGGATAACAACAATCGAGATTAAATTGTGA
* * * *
3573990 TTTTTAATTAAAGAGATCAAGATTGAACCGTGAATCAGAGAATAAAAAGATCGAGATTAAATCGC
259 CTTTGAATTAAAGAGATCAAGATTGAACCGTAAATCAGAGAATAAAAAGATCGAGATTAAATCAC
* *
3574055 GAGTCAAAAAATAACATT
324 GAGTCAAAAAATGACGTT
3574073 AACTTGGATTGAA
1 AACTTGGATTGAA
3574086 CTGCAAGTTA
Statistics
Matches: 615, Mismatches: 69, Indels: 25
0.87 0.10 0.04
Matches are distributed among these distances:
340 3 0.00
341 258 0.42
342 348 0.57
343 5 0.01
344 1 0.00
ACGTcount: A:0.47, C:0.12, G:0.19, T:0.23
Consensus pattern (341 bp):
AACTTGGATTGAATCACAAGTCCAAAAATAAGGAGACCGGGATTAGACCACGAGTCAAAAGATAA
CAACAATCGAGATTAAACTATGATTTTGAATTAAAGAGATCGGATTGAATCACGAATCGAAAAAT
AAAGAGATCGAGATTAAATCCGGAATCAGAGAATAATGTTAACTTGGATTGAATCACAAGTAAGA
AAATAAGGAGATCGAGATTAAACCACGAGTCAGAGGATAACAACAATCGAGATTAAATTGTGACT
TTGAATTAAAGAGATCAAGATTGAACCGTAAATCAGAGAATAAAAAGATCGAGATTAAATCACGA
GTCAAAAAATGACGTT
Found at i:3573528 original size:34 final size:34
Alignment explanation
Indices: 3573485--3573555 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
3573475 GATTTTGAAT
* *
3573485 TAAAGAGATCG-GAATTGAATCGCGAATCGAAAAA
1 TAAAGAGATCGAG-ATTAAATCGCGAATCAAAAAA
*
3573519 TAAAGAGATCGAGATTAAATCGCGAATTAAAAAA
1 TAAAGAGATCGAGATTAAATCGCGAATCAAAAAA
3573553 TAA
1 TAA
3573556 TGTTAACTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 32 0.97
35 1 0.03
ACGTcount: A:0.51, C:0.10, G:0.20, T:0.20
Consensus pattern (34 bp):
TAAAGAGATCGAGATTAAATCGCGAATCAAAAAA
Found at i:3573868 original size:34 final size:34
Alignment explanation
Indices: 3573827--3573945 Score: 127
Period size: 34 Copynumber: 3.5 Consensus size: 34
3573817 GATTTTAAAT
3573827 TAAAGAGATCGAGATTGAATCACAAATC-GAAAAA
1 TAAAGAGATCGAGATTGAATCACAAATCAG-AAAA
* * *
3573861 TAAAGAGATCGAGATTAAATCACGAATCAGAGAA
1 TAAAGAGATCGAGATTGAATCACAAATCAGAAAA
* * *
3573895 TAATGTTA-ACTTG-GATTGAATCACAAATAAGAAAA
1 TAAAG--AGA-TCGAGATTGAATCACAAATCAGAAAA
3573930 TAAAGAGATCGAGATT
1 TAAAGAGATCGAGATT
3573946 AAACCACGAG
Statistics
Matches: 68, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
33 3 0.04
34 38 0.56
35 24 0.35
36 3 0.04
ACGTcount: A:0.50, C:0.10, G:0.18, T:0.22
Consensus pattern (34 bp):
TAAAGAGATCGAGATTGAATCACAAATCAGAAAA
Found at i:3574528 original size:88 final size:88
Alignment explanation
Indices: 3574374--3574665 Score: 333
Period size: 88 Copynumber: 3.3 Consensus size: 88
3574364 GGAGGTCTTA
* * * * * * *
3574374 AAAATCATGTCCGGAGGTCTTATAGAATCGATTGAGATAACATCGCCAGTCAAAAAATAATA-AA
1 AAAATTATGCCCGAAGGTCTTACAGAATCGATCGGGATAACATCGCAAGTCAAAAAATAA-AGAA
*
3574438 TCGATCAGGATAACACCGCT-AATC
65 TCGATCAGGATAACATCG-TGAATC
* * * * *
3574462 AAAATTATGCTCGGAGGTCTTACAGAATTGATCGGGATAACA-CTGCAAGTCGAAAGATAAAGAA
1 AAAATTATGCCCGAAGGTCTTACAGAATCGATCGGGATAACATC-GCAAGTCAAAAAATAAAGAA
* *
3574526 TCGATCGGGATAACATCATGAATC
65 TCGATCAGGATAACATCGTGAATC
* *
3574550 AAAATTATGCCCGAAGGTCTTACAGAATCGA-CTAGAATAACATCGCAAGTCAAAAAATAAAGAA
1 AAAATTATGCCCGAAGGTCTTACAGAATCGATC-GGGATAACATCGCAAGTCAAAAAATAAAGAA
* *
3574614 TCAATCAGGATAATATCGTGAATC
65 TCGATCAGGATAACATCGTGAATC
*
3574638 AAAATTATGCCCGAAAGTCTTA-AGAATC
1 AAAATTATGCCCGAAGGTCTTACAGAATC
3574666 ATACCCAAAG
Statistics
Matches: 174, Mismatches: 25, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
87 10 0.06
88 163 0.94
89 1 0.01
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (88 bp):
AAAATTATGCCCGAAGGTCTTACAGAATCGATCGGGATAACATCGCAAGTCAAAAAATAAAGAAT
CGATCAGGATAACATCGTGAATC
Found at i:3574725 original size:110 final size:110
Alignment explanation
Indices: 3574563--3574878 Score: 334
Period size: 110 Copynumber: 2.9 Consensus size: 110
3574553 ATTATGCCCG
* * * * *
3574563 AAGGTCTTACAGAATCGACTAGAATAACATCGCAAGTCAAAAAATAAAGAATCAATCAGGATAAT
1 AAGGTCTTACAGAATCGACTGGGATAACACCGCAAGTCAAAAGAT-AAGAATCAATCAGGATAAC
*
3574628 ATCGTGAATCAAAATTATGCCCGAAAGTCTTAAG-AATCATACCCA
65 ATCGTGAATCGAAATTATGCCCGAAAGTCTTAAGAAATCATACCCA
* * * *
3574673 AAGGTCTTGCAGAATCGACTGGGATAACACCGTAAGTCAAAAGATAATGAATCGATCGGGATAAC
1 AAGGTCTTACAGAATCGACTGGGATAACACCGCAAGTCAAAAGATAA-GAATCAATCAGGATAAC
* * * ** * * * *
3574738 ACCATAAATCGAAATTATGTTCG-GAGATCTT-AGAAATTATGCCCG
65 ATCGTGAATCGAAATTATGCCCGAAAG-TCTTAAGAAATCATACCCA
* ** *
3574783 AAGGTCTTACAGAATCAACTGGGATAACACCGCAAGTTGAAAGATAAGAAATCAATGA-GATAAC
1 AAGGTCTTACAGAATCGACTGGGATAACACCGCAAGTCAAAAGATAAG-AATCAATCAGGATAAC
* * *
3574847 ATCGCGAATCGAGATTATGCCCGAAAATCTTA
65 ATCGTGAATCGAAATTATGCCCGAAAGTCTTA
3574879 CAAAATCGAC
Statistics
Matches: 164, Mismatches: 36, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
109 33 0.20
110 131 0.80
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22
Consensus pattern (110 bp):
AAGGTCTTACAGAATCGACTGGGATAACACCGCAAGTCAAAAGATAAGAATCAATCAGGATAACA
TCGTGAATCGAAATTATGCCCGAAAGTCTTAAGAAATCATACCCA
Found at i:3574966 original size:88 final size:87
Alignment explanation
Indices: 3574773--3574970 Score: 263
Period size: 87 Copynumber: 2.3 Consensus size: 87
3574763 GATCTTAGAA
* * *
3574773 ATTATGCCCGAAGGTCTTACAGAATCAACTGGGATAACACCGCAAGTTGAAAGATAAGAAATCAA
1 ATTATGCCCGAAGGTCTTACAAAATCAACTGAGATAACACCGCAAGTCGAAAGATAAGAAATCAA
*
3574838 TGAGATAACATCGCGAATCGAG
66 TGAGATAACACCGCGAATCGAG
** * *
3574860 ATTATGCCCGAAAATCTTACAAAATCGACTGAGATAACACCGCAAGTCGAAAGATAA-AGAATCG
1 ATTATGCCCGAAGGTCTTACAAAATCAACTGAGATAACACCGCAAGTCGAAAGATAAGA-AATCA
* *
3574924 ATCGAGATAATACCGTGAATCGAG
65 AT-GAGATAACACCGCGAATCGAG
* *
3574948 ATTATGTCCGGAGGTCTTACAAA
1 ATTATGCCCGAAGGTCTTACAAA
3574971 TCTCAAAATT
Statistics
Matches: 95, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
86 1 0.01
87 57 0.60
88 37 0.39
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.21
Consensus pattern (87 bp):
ATTATGCCCGAAGGTCTTACAAAATCAACTGAGATAACACCGCAAGTCGAAAGATAAGAAATCAA
TGAGATAACACCGCGAATCGAG
Found at i:3575280 original size:41 final size:41
Alignment explanation
Indices: 3575223--3575321 Score: 155
Period size: 41 Copynumber: 2.4 Consensus size: 41
3575213 ATCTGAAGAA
* *
3575223 GGTTCCTCCTAAACAGA-GCTTTTGAAATCTTGATTGAAAAT
1 GGTTCCTCTTAAACAGAGGC-TTTAAAATCTTGATTGAAAAT
*
3575264 GGTTCCTCTTAAACAGAGGCTTTAAAATCTTGATTGGAAAT
1 GGTTCCTCTTAAACAGAGGCTTTAAAATCTTGATTGAAAAT
3575305 GGTTCCTCTTAAACAGA
1 GGTTCCTCTTAAACAGA
3575322 AAGTTAAAAC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
41 52 0.96
42 2 0.04
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (41 bp):
GGTTCCTCTTAAACAGAGGCTTTAAAATCTTGATTGAAAAT
Found at i:3575445 original size:18 final size:18
Alignment explanation
Indices: 3575419--3575462 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3575409 TCATCAAATG
*
3575419 ATGCTAATGGAAATGTCA
1 ATGCAAATGGAAATGTCA
* **
3575437 ATGCAAATGTAAATGTTG
1 ATGCAAATGGAAATGTCA
3575455 ATGCAAAT
1 ATGCAAAT
3575463 ACAAGAATGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (18 bp):
ATGCAAATGGAAATGTCA
Found at i:3577112 original size:13 final size:13
Alignment explanation
Indices: 3577094--3577141 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
3577084 TTGAAGATGT
3577094 CTTTTTTTTTTTA
1 CTTTTTTTTTTTA
3577107 C---TTTTTTTTA
1 CTTTTTTTTTTTA
*
3577117 TTTTTTTTTTTTA
1 CTTTTTTTTTTTA
3577130 -TTTTTATTTTTT
1 CTTTTT-TTTTTT
3577142 GTGATGCCCC
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
10 9 0.30
12 5 0.17
13 16 0.53
ACGTcount: A:0.08, C:0.04, G:0.00, T:0.88
Consensus pattern (13 bp):
CTTTTTTTTTTTA
Found at i:3577113 original size:9 final size:9
Alignment explanation
Indices: 3577098--3577141 Score: 61
Period size: 10 Copynumber: 4.7 Consensus size: 9
3577088 AGATGTCTTT
3577098 TTTTTTTTA
1 TTTTTTTTA
3577107 CTTTTTTTTA
1 -TTTTTTTTA
*
3577117 TTTTTTTTT
1 TTTTTTTTA
3577126 TTTATTTTTA
1 TTT-TTTTTA
3577136 TTTTTT
1 TTTTTT
3577142 GTGATGCCCC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
9 14 0.45
10 17 0.55
ACGTcount: A:0.09, C:0.02, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:3577122 original size:19 final size:19
Alignment explanation
Indices: 3577098--3577141 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
3577088 AGATGTCTTT
3577098 TTTTTTTTACTTT-TTTTTA
1 TTTTTTTT-CTTTATTTTTA
*
3577117 TTTTTTTTTTTTATTTTTA
1 TTTTTTTTCTTTATTTTTA
3577136 TTTTTT
1 TTTTTT
3577142 GTGATGCCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 3 0.13
19 20 0.87
ACGTcount: A:0.09, C:0.02, G:0.00, T:0.89
Consensus pattern (19 bp):
TTTTTTTTCTTTATTTTTA
Found at i:3577731 original size:8 final size:8
Alignment explanation
Indices: 3577713--3577762 Score: 55
Period size: 8 Copynumber: 5.9 Consensus size: 8
3577703 AAAATAAAAT
3577713 TTTTTTCTC
1 TTTTTT-TC
3577722 TTTTTTTC
1 TTTTTTTC
3577730 TTTTTTCTC
1 TTTTTT-TC
*
3577739 TTTTTTTTG
1 -TTTTTTTC
*
3577748 TTTTTTTA
1 TTTTTTTC
3577756 TTTTTTT
1 TTTTTTT
3577763 GAAATCTTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
8 22 0.59
9 9 0.24
10 6 0.16
ACGTcount: A:0.02, C:0.10, G:0.02, T:0.86
Consensus pattern (8 bp):
TTTTTTTC
Found at i:3577752 original size:17 final size:17
Alignment explanation
Indices: 3577713--3577745 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3577703 AAAATAAAAT
3577713 TTTTTTCTCTTTTTTTC
1 TTTTTTCTCTTTTTTTC
3577730 TTTTTTCTCTTTTTTT
1 TTTTTTCTCTTTTTTT
3577746 TGTTTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTTCTCTTTTTTTC
Found at i:3577759 original size:17 final size:17
Alignment explanation
Indices: 3577712--3577762 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
3577702 CAAAATAAAA
3577712 TTTTTTTCTCTTTTTTTC
1 TTTTTTTCT-TTTTTTTC
*
3577730 TTTTTTCTCTTTTTTTTG
1 TTTTTT-TCTTTTTTTTC
*
3577748 TTTTTTTATTTTTTT
1 TTTTTTTCTTTTTTT
3577763 GAAATCTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 8 0.27
18 19 0.63
19 3 0.10
ACGTcount: A:0.02, C:0.10, G:0.02, T:0.86
Consensus pattern (17 bp):
TTTTTTTCTTTTTTTTC
Found at i:3577762 original size:9 final size:9
Alignment explanation
Indices: 3577712--3577754 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
3577702 CAAAATAAAA
3577712 TTTTTTTCT
1 TTTTTTTCT
3577721 CTTTTTTTCT
1 -TTTTTTTCT
*
3577731 TTTTTCTCT
1 TTTTTTTCT
*
3577740 TTTTTTTGT
1 TTTTTTTCT
3577749 TTTTTT
1 TTTTTT
3577755 ATTTTTTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
9 21 0.70
10 9 0.30
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.86
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:3583231 original size:15 final size:15
Alignment explanation
Indices: 3583213--3583388 Score: 110
Period size: 16 Copynumber: 11.5 Consensus size: 15
3583203 TGAAGATTCA
3583213 GATTTTAGGGTTTTG
1 GATTTTAGGGTTTTG
3583228 GATTTTAGGGGTTTTG
1 GATTTTA-GGGTTTTG
* * *
3583244 AATTTT-GGGGTATG
1 GATTTTAGGGTTTTG
* *
3583258 GATTTAAAGG--TTG
1 GATTTTAGGGTTTTG
3583271 GAATTTTAGGGTTTTG
1 G-ATTTTAGGGTTTTG
*
3583287 GATTTTATGGGGTTTG
1 GATTTTA-GGGTTTTG
* * *
3583303 GATTTAAAGGTTTAAAG
1 GATTTTAGGGTTT--TG
*
3583320 G-TTTTAGGGAGTTTG
1 GATTTTAGGG-TTTTG
*
3583335 GATTTAAGGGATTTTG
1 GATTTTAGGG-TTTTG
3583351 GATTTTAGGAGTTTTAG
1 GATTTTAGG-GTTTT-G
* **
3583368 AATCCTAGGGTTTTG
1 GATTTTAGGGTTTTG
3583383 G-TTTTA
1 GATTTTA
3583389 AAAAATTGAG
Statistics
Matches: 122, Mismatches: 27, Indels: 25
0.70 0.16 0.14
Matches are distributed among these distances:
13 3 0.02
14 20 0.16
15 22 0.18
16 65 0.53
17 12 0.10
ACGTcount: A:0.21, C:0.01, G:0.32, T:0.46
Consensus pattern (15 bp):
GATTTTAGGGTTTTG
Found at i:3583305 original size:45 final size:43
Alignment explanation
Indices: 3583225--3583314 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 43
3583215 TTTTAGGGTT
3583225 TTGGATTTTAGGGGTTTTGAATTTTGGGGTATGGATTTAAAGG
1 TTGGATTTTAGGGGTTTTGAATTTTGGGGTATGGATTTAAAGG
* *
3583268 TTGGAATTTTA-GGGTTTTGGATTTTATGGGGTTTGGATTTAAAGG
1 TTGG-ATTTTAGGGGTTTT-GAATTT-TGGGGTATGGATTTAAAGG
3583313 TT
1 TT
3583315 TAAAGGTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
43 11 0.26
44 11 0.26
45 20 0.48
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (43 bp):
TTGGATTTTAGGGGTTTTGAATTTTGGGGTATGGATTTAAAGG
Found at i:3585877 original size:120 final size:117
Alignment explanation
Indices: 3585732--3586051 Score: 432
Period size: 120 Copynumber: 2.7 Consensus size: 117
3585722 TATATATAAT
* *
3585732 TTTTTCACAATTTGGGCGAAATTAGAAAATTTTCTCTTTTTGAATTTCTAAATTTTTTCACCATT
1 TTTTTCACCATTTGGGCCAAATTAGAAAATTTTCTCTTTTTGAATTTCTAAA-TTTTTCACCATT
*
3585797 TTAGCATATTTAGAAATTCTCTATTTCTTATTTTCTTTTTGTTAGATTTTTAAA
65 TTAGCCTATTTAGAAATTCTCTATTTCTTATTTT-TTTTTGTTAGATTTTTAAA
* *
3585851 TATTTTCACCATTTGGGCCAAATTAGAAAATTTTTCTCTTTTTGAATTTTTAAAATTTTCACCAT
1 T-TTTTCACCATTTGGGCCAAATTAGAAAA-TTTTCTCTTTTTGAATTTCTAAATTTTTCACCAT
*
3585916 TTTAGCCTATTTAGAAATTCTCTATTTCTTCTTTTTTTTTGTTAGATTTTTAAA
64 TTTAGCCTATTTAGAAATTCTCTATTTCTTATTTTTTTTTGTTAGATTTTTAAA
* * * * ** *
3585970 TTTTTCATCATTTGAGTCAATTTA-AAAATAAT-T-TTTTTGAAATTTCTAAATTTTTCA-CAAT
1 TTTTTCACCATTTGGGCCAAATTAGAAAATTTTCTCTTTTTG-AATTTCTAAATTTTTCACCATT
*
3586031 TTGGACCTATTTAGAAATTCT
65 TTAG-CCTATTTAGAAATTCT
3586052 TTTTTTTTTG
Statistics
Matches: 181, Mismatches: 16, Indels: 12
0.87 0.08 0.06
Matches are distributed among these distances:
114 12 0.07
115 32 0.18
116 2 0.01
117 4 0.02
118 19 0.10
119 21 0.12
120 69 0.38
121 22 0.12
ACGTcount: A:0.28, C:0.12, G:0.08, T:0.52
Consensus pattern (117 bp):
TTTTTCACCATTTGGGCCAAATTAGAAAATTTTCTCTTTTTGAATTTCTAAATTTTTCACCATTT
TAGCCTATTTAGAAATTCTCTATTTCTTATTTTTTTTTGTTAGATTTTTAAA
Found at i:3586681 original size:10 final size:10
Alignment explanation
Indices: 3586666--3586698 Score: 52
Period size: 9 Copynumber: 3.5 Consensus size: 10
3586656 AAATAATACC
3586666 AAAAATATCA
1 AAAAATATCA
3586676 AAAAATAT-A
1 AAAAATATCA
3586685 AAAAATA-CA
1 AAAAATATCA
3586694 AAAAA
1 AAAAA
3586699 AATGGCTCGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAATATCA
Found at i:3586699 original size:10 final size:9
Alignment explanation
Indices: 3586660--3586698 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
3586650 ATAAATAAAT
*
3586660 AATACCAAA
1 AATACAAAA
3586669 AATATCAAAA
1 AATA-CAAAA
*
3586679 AATATAAAA
1 AATACAAAA
3586688 AATACAAAA
1 AATACAAAA
3586697 AA
1 AA
3586699 AATGGCTCGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.15
Consensus pattern (9 bp):
AATACAAAA
Found at i:3590178 original size:10 final size:9
Alignment explanation
Indices: 3590172--3590212 Score: 55
Period size: 10 Copynumber: 4.2 Consensus size: 9
3590162 AAAATTTTTA
3590172 TTTATTTATT
1 TTTA-TTATT
3590182 TTTATTTATT
1 TTTA-TTATT
3590192 TTTATTATT
1 TTTATTATT
3590201 ATTTATTATT
1 -TTTATTATT
3590211 TT
1 TT
3590213 ATAGTGTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
9 7 0.23
10 23 0.77
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTATTATT
Found at i:3590193 original size:23 final size:23
Alignment explanation
Indices: 3590165--3590211 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
3590155 AATTATCAAA
3590165 ATTTTTATTTATTTATTT-TTATTT
1 ATTTTTA-TTA-TTATTTATTATTT
3590189 ATTTTTATTATTATTTATTATTT
1 ATTTTTATTATTATTTATTATTT
3590212 TATAGTGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.27
23 9 0.41
24 7 0.32
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (23 bp):
ATTTTTATTATTATTTATTATTT
Found at i:3590209 original size:19 final size:20
Alignment explanation
Indices: 3590172--3590212 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
3590162 AAAATTTTTA
3590172 TTTATTTATTTTTATTTATT
1 TTTATTTATTTTTATTTATT
3590192 TTTA-TTATTATTTA-TTATT
1 TTTATTTATT-TTTATTTATT
3590211 TT
1 TT
3590213 ATAGTGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTATTTATTTTTATTTATT
Found at i:3590336 original size:16 final size:13
Alignment explanation
Indices: 3590317--3590385 Score: 65
Period size: 11 Copynumber: 5.4 Consensus size: 13
3590307 ACGTATGCTA
3590317 AAAAAGTAATAATAAT
1 AAAAA-TAA-AAT-AT
3590333 AAAAATAAAATAT
1 AAAAATAAAATAT
3590346 AAAAAT-AAAT-T
1 AAAAATAAAATAT
*
3590357 ACAAATAAAA-A-
1 AAAAATAAAATAT
*
3590368 AAATATAAAATAT
1 AAAAATAAAATAT
3590381 AAAAA
1 AAAAA
3590386 AATACTTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
11 14 0.31
12 8 0.18
13 12 0.27
14 3 0.07
15 3 0.07
16 5 0.11
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.22
Consensus pattern (13 bp):
AAAAATAAAATAT
Found at i:3590344 original size:17 final size:15
Alignment explanation
Indices: 3590315--3590389 Score: 62
Period size: 16 Copynumber: 4.7 Consensus size: 15
3590305 AAACGTATGC
*
3590315 TAAAAAAGTAATAATA
1 TAAAAAAATAA-AATA
*
3590331 -ATAAAAATAAAATA
1 TAAAAAAATAAAATA
3590345 TAAAAATAAATTACAAATA
1 T-AAAA-AAA-TA-AAATA
*
3590364 AAAAAAATATAAAATA
1 TAAAAAA-ATAAAATA
3590380 TAAAAAAATA
1 TAAAAAAATA
3590390 CTTAAATAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
14 4 0.08
15 11 0.23
16 14 0.29
17 7 0.15
18 7 0.15
19 5 0.10
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.23
Consensus pattern (15 bp):
TAAAAAAATAAAATA
Found at i:3590354 original size:6 final size:6
Alignment explanation
Indices: 3590324--3590385 Score: 56
Period size: 6 Copynumber: 10.3 Consensus size: 6
3590314 CTAAAAAAGT
* * *
3590324 AATAAT AATAAA AATAAA ATATAAA AAT-AA ATTACA AATAAA AA-AAA
1 AATAAA AATAAA AATAAA A-ATAAA AATAAA AATAAA AATAAA AATAAA
*
3590371 TATAAA ATATAAA AA
1 AATAAA A-ATAAA AA
3590386 AATACTTAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
5 8 0.18
6 25 0.56
7 12 0.27
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.23
Consensus pattern (6 bp):
AATAAA
Found at i:3590397 original size:18 final size:16
Alignment explanation
Indices: 3590327--3590389 Score: 67
Period size: 17 Copynumber: 3.8 Consensus size: 16
3590317 AAAAAGTAAT
*
3590327 AATAATAAAAATA-AA
1 AATAAAAAAAATATAA
3590342 ATATAAAAATAAAT-TACA
1 A-ATAAAAA-AAATATA-A
3590360 AATAAAAAAAATATAA
1 AATAAAAAAAATATAA
3590376 AATATAAAAAAATA
1 AATA-AAAAAAATA
3590390 CTTAAATAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
15 1 0.02
16 15 0.37
17 23 0.56
18 2 0.05
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (16 bp):
AATAAAAAAAATATAA
Found at i:3595118 original size:18 final size:20
Alignment explanation
Indices: 3595097--3595133 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
3595087 GATTTTTCAT
3595097 TTATTATTT-TT-TTTTATA
1 TTATTATTTATTGTTTTATA
3595115 TTATTATTTATTGTTTTAT
1 TTATTATTTATTGTTTTAT
3595134 TTTTTTATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 2 0.12
20 6 0.35
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.76
Consensus pattern (20 bp):
TTATTATTTATTGTTTTATA
Found at i:3595134 original size:18 final size:19
Alignment explanation
Indices: 3595097--3595142 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
3595087 GATTTTTCAT
*
3595097 TTATTATTT-TTTTTTATA
1 TTATTATTTATTGTTTATA
3595115 TTATTATTTATTGTTT-TA
1 TTATTATTTATTGTTTATA
3595133 TT-TT-TTTATT
1 TTATTATTTATT
3595143 CGAGAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 6 0.23
17 2 0.08
18 13 0.50
19 5 0.19
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (19 bp):
TTATTATTTATTGTTTATA
Found at i:3599685 original size:30 final size:30
Alignment explanation
Indices: 3599649--3599707 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
3599639 TGGTGGTTTG
* *
3599649 CCTCACATTGAAGGTCCAATATATAAACTT
1 CCTCACATTAAAGGTCCAATATAAAAACTT
*
3599679 CCTCACATTAAAGGTTCAATATAAAAACT
1 CCTCACATTAAAGGTCCAATATAAAAACT
3599708 CATTCAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.29
Consensus pattern (30 bp):
CCTCACATTAAAGGTCCAATATAAAAACTT
Found at i:3614526 original size:5 final size:5
Alignment explanation
Indices: 3614516--3614550 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
3614506 TAATAATAGA
3614516 AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT
3614551 TTTTTAAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:3618326 original size:2 final size:2
Alignment explanation
Indices: 3618319--3618349 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3618309 AACAAACAAC
3618319 AG AG AG AG AG AG AG AG AG A- AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3618350 GGGTAGCTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3620139 original size:2 final size:2
Alignment explanation
Indices: 3620134--3620165 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3620124 CAACACACAC
*
3620134 AT AT AT AT GT 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
3620166 GTGTGTGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3620170 original size:2 final size:2
Alignment explanation
Indices: 3620165--3620195 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3620155 TATATATATA
3620165 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
3620196 TAATAATTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3621703 original size:26 final size:27
Alignment explanation
Indices: 3621640--3621703 Score: 64
Period size: 26 Copynumber: 2.4 Consensus size: 27
3621630 CATTAATGAG
3621640 GTGATA-TATATTATTGATTTACCTCA
1 GTGATAGTATATTATTGATTTACCTCA
* *
3621666 TTGATTAG-ATATTATT-ATTTGA-TTCA
1 GTGA-TAGTATATTATTGATTT-ACCTCA
3621692 GTGATAGTATAT
1 GTGATAGTATAT
3621704 AGAATTTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
25 3 0.10
26 17 0.55
27 11 0.35
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.48
Consensus pattern (27 bp):
GTGATAGTATATTATTGATTTACCTCA
Found at i:3622023 original size:2 final size:2
Alignment explanation
Indices: 3622018--3622046 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3622008 TATACATTGG
3622018 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3622047 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3622901 original size:2 final size:2
Alignment explanation
Indices: 3622889--3622926 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
3622879 TTTGGGATTG
3622889 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3622927 TGTGTGTACA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3623922 original size:23 final size:23
Alignment explanation
Indices: 3623892--3623938 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
3623882 AAAAAAGATA
3623892 AGAGAGAAATTTGGCACCATTTT
1 AGAGAGAAATTTGGCACCATTTT
3623915 AGAGAGAAATTTGGCACCATTTT
1 AGAGAGAAATTTGGCACCATTTT
3623938 A
1 A
3623939 TTGGGGAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (23 bp):
AGAGAGAAATTTGGCACCATTTT
Found at i:3624395 original size:16 final size:17
Alignment explanation
Indices: 3624374--3624405 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3624364 TTATAAAAAT
3624374 ATTA-TTTTTAATATAA
1 ATTATTTTTTAATATAA
3624390 ATTATTTTTTAATATA
1 ATTATTTTTTAATATA
3624406 TATAAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTATTTTTTAATATAA
Found at i:3624410 original size:41 final size:41
Alignment explanation
Indices: 3624358--3624559 Score: 137
Period size: 41 Copynumber: 4.8 Consensus size: 41
3624348 ATTAATTTAA
* * *
3624358 TAATATTTATAAAAATATTATTTTTAATATAAATTATTTTT
1 TAATATATATAAAAATAATATTTTTAATATAAATTATTTCT
* * * *
3624399 TAATATATATAAATATAATATTTTTATTCACAAAATGATTT-T
1 TAATATATATAAAAATAATATTTTTAAT-A-TAAATTATTTCT
* * *
3624441 TCGA-AT-TATAAAAATATTACTTGTTTAATATAAATTATGTCT
1 T-AATATATATAAAAATAATA-TT-TTTAATATAAATTATTTCT
**
3624483 TAATTATATATAAATGTAATATTTTT-AT-TAAATTAATTTCT
1 TAA-TATATATAAAAATAATATTTTTAATATAAATT-ATTTCT
3624524 TAAATTAATATATTAAATAATAAT-TTTATTAATATA
1 T-AA-T-ATATA-TAAA-AATAATATTT-TTAATATA
3624560 TATACATATA
Statistics
Matches: 124, Mismatches: 20, Indels: 28
0.72 0.12 0.16
Matches are distributed among these distances:
40 6 0.05
41 51 0.41
42 17 0.14
43 23 0.19
44 17 0.14
45 6 0.05
46 2 0.02
47 2 0.02
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (41 bp):
TAATATATATAAAAATAATATTTTTAATATAAATTATTTCT
Found at i:3624539 original size:13 final size:13
Alignment explanation
Indices: 3624508--3624560 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
3624498 GTAATATTTT
*
3624508 TATTAAATTAATT
1 TATTAAATTAATA
*
3624521 TCTTAAATTAATA
1 TATTAAATTAATA
3624534 TATTAAA-TAATA
1 TATTAAATTAATA
**
3624546 -ATTTTATTAATA
1 TATTAAATTAATA
3624558 TAT
1 TAT
3624561 ATACATATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
11 4 0.12
12 10 0.30
13 19 0.58
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (13 bp):
TATTAAATTAATA
Found at i:3624551 original size:42 final size:39
Alignment explanation
Indices: 3624471--3624555 Score: 100
Period size: 42 Copynumber: 2.1 Consensus size: 39
3624461 TTGTTTAATA
*
3624471 TAAATTATGTCTTAATTATATATAAATGTAATATTTTTAT
1 TAAATTATGTCTTAATTATATATAAA-GTAATAATTTTAT
*
3624511 TAAATTAATTTCTTAAATTAATATATTAAA-TAATAATTTTAT
1 TAAATT-ATGTCTT-AATT-ATATA-TAAAGTAATAATTTTAT
3624553 TAA
1 TAA
3624556 TATATATACA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
40 6 0.15
41 6 0.15
42 18 0.46
43 5 0.13
44 4 0.10
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (39 bp):
TAAATTATGTCTTAATTATATATAAAGTAATAATTTTAT
Found at i:3624562 original size:2 final size:2
Alignment explanation
Indices: 3624555--3624585 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3624545 AATTTTATTA
*
3624555 AT AT AT AT AC 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 A
3624586 ATTGAAGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3626775 original size:24 final size:24
Alignment explanation
Indices: 3626748--3626795 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
3626738 TAAATTTATT
*
3626748 TTGAATTTTTGAAAGCTTTGATTG
1 TTGAATTTTTGAAAACTTTGATTG
3626772 TTGAATTTTTGAAAACTTTGATTG
1 TTGAATTTTTGAAAACTTTGATTG
3626796 AAATAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.04, G:0.19, T:0.50
Consensus pattern (24 bp):
TTGAATTTTTGAAAACTTTGATTG
Found at i:3627879 original size:17 final size:17
Alignment explanation
Indices: 3627859--3627896 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
3627849 GAGAGAGAGG
3627859 GAGAGA-AAAGAGAAGAA
1 GAGAGAGAAA-AGAAGAA
*
3627876 GAGAGAGAAAAGAATAA
1 GAGAGAGAAAAGAAGAA
3627893 GAGA
1 GAGA
3627897 AATATGAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.63, C:0.00, G:0.34, T:0.03
Consensus pattern (17 bp):
GAGAGAGAAAAGAAGAA
Found at i:3628161 original size:17 final size:16
Alignment explanation
Indices: 3628139--3628175 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
3628129 AGCCAAGCCA
3628139 TTTTTTATTTTGATATT
1 TTTTTTATTTT-ATATT
*
3628156 TTTTTTATTTTTTATT
1 TTTTTTATTTTATATT
3628172 TTTT
1 TTTT
3628176 AAAAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.84
Consensus pattern (16 bp):
TTTTTTATTTTATATT
Found at i:3628880 original size:44 final size:45
Alignment explanation
Indices: 3628823--3628917 Score: 122
Period size: 44 Copynumber: 2.1 Consensus size: 45
3628813 AAAAGAAAAG
* *
3628823 AAAAATTTTTAAATAGACCCAAATTGTGAAAAATTTTA-AAATAA-
1 AAAAATTTCTAAATAGACCCAAATGGTGAAAAA-TTTAGAAATAAT
* **
3628867 AAAAATTTCTAAATTGGTCCAAATGGTGAAAAATTTAGAAATAAT
1 AAAAATTTCTAAATAGACCCAAATGGTGAAAAATTTAGAAATAAT
3628912 AAAAAT
1 AAAAAT
3628918 AAAAATAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
43 4 0.09
44 34 0.77
45 6 0.14
ACGTcount: A:0.54, C:0.06, G:0.09, T:0.31
Consensus pattern (45 bp):
AAAAATTTCTAAATAGACCCAAATGGTGAAAAATTTAGAAATAAT
Found at i:3631092 original size:31 final size:32
Alignment explanation
Indices: 3631047--3631110 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
3631037 TATATTTTTT
3631047 ATTTTTTTAATATTTTATATAT-AATATAATATA
1 ATTTTTTT-ATATTTTAT-TATGAATATAATATA
*
3631080 ATTTTTTT-TATTTTATTATGAATTTAATATA
1 ATTTTTTTATATTTTATTATGAATATAATATA
3631111 TTGGCTTCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 3 0.10
31 18 0.62
33 8 0.28
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (32 bp):
ATTTTTTTATATTTTATTATGAATATAATATA
Found at i:3633060 original size:21 final size:21
Alignment explanation
Indices: 3633036--3633077 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3633026 TCATACGAAT
3633036 AAATATAAA-ATATATTTTTTA
1 AAATATAAATATA-ATTTTTTA
3633057 AAATATAAATATAATTTTTTA
1 AAATATAAATATAATTTTTTA
3633078 TGTTATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AAATATAAATATAATTTTTTA
Found at i:3633518 original size:15 final size:12
Alignment explanation
Indices: 3633484--3633512 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3633474 GCAACATCAA
3633484 ATTTAGTAAAAT
1 ATTTAGTAAAAT
3633496 ATTTAGTAAAAT
1 ATTTAGTAAAAT
3633508 ATTTA
1 ATTTA
3633513 TTAGTAGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (12 bp):
ATTTAGTAAAAT
Found at i:3635415 original size:16 final size:17
Alignment explanation
Indices: 3635380--3635416 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3635370 CAAATATCAT
3635380 AATAAAAATCATGCCAA
1 AATAAAAATCATGCCAA
*
3635397 AATAAACATCATG-CAA
1 AATAAAAATCATGCCAA
3635413 AATA
1 AATA
3635417 CTACAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.59, C:0.16, G:0.05, T:0.19
Consensus pattern (17 bp):
AATAAAAATCATGCCAA
Found at i:3636195 original size:20 final size:18
Alignment explanation
Indices: 3636153--3636202 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
3636143 TAAAATTCAA
* *
3636153 CCAAAATTTCAAAAAATC
1 CCAAAAATTCAAAAAAAC
3636171 CCAAAAATTCAAAACAAGAC
1 CCAAAAATTCAAAA-AA-AC
*
3636191 CCAAATATTCAA
1 CCAAAAATTCAA
3636203 GAATGATCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 13 0.48
19 2 0.07
20 12 0.44
ACGTcount: A:0.56, C:0.24, G:0.02, T:0.18
Consensus pattern (18 bp):
CCAAAAATTCAAAAAAAC
Found at i:3636773 original size:19 final size:19
Alignment explanation
Indices: 3636745--3636783 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3636735 CCCATTGACC
* *
3636745 AAAAATAAAAATAACAAAT
1 AAAAAGAAAAATAAAAAAT
*
3636764 AAAAAGAAAATTAAAAAAT
1 AAAAAGAAAAATAAAAAAT
3636783 A
1 A
3636784 TATATTTTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (19 bp):
AAAAAGAAAAATAAAAAAT
Found at i:3637153 original size:43 final size:43
Alignment explanation
Indices: 3637106--3637344 Score: 236
Period size: 43 Copynumber: 5.6 Consensus size: 43
3637096 CAACAAAGGT
*
3637106 TTTGAAACTTATT-AAAAATAAAATGA-TCCCCCCCATCAGAGGC
1 TTTGAAACTT-TTGAAAAATAAAATGATTCCCCCCAAT-AGAGGC
* * * *
3637149 TTTGAAGCTTTTGAAAAATAAAAT-ATTCTTCCTCAATATAGGC
1 TTTGAAACTTTTGAAAAATAAAATGATTC-CCCCCAATAGAGGC
* * ***
3637192 ATTGAAACTTTTGAAAAATAAAATGCTTCCTTTCAATAGAGGC
1 TTTGAAACTTTTGAAAAATAAAATGATTCCCCCCAATAGAGGC
* * *
3637235 TTTGAAGCTTTTGAAAAATAAAAT-ATTCCTCCTCAACAGAGGC
1 TTTGAAACTTTTGAAAAATAAAATGATTCC-CCCCAATAGAGGC
* * * **
3637278 TTTAAAACTTTTGAAAAATAAAATGCTTCTCTTCAATAGAGGC
1 TTTGAAACTTTTGAAAAATAAAATGATTCCCCCCAATAGAGGC
*
3637321 TTTGAAAC-TTTGAAAAATATAATG
1 TTTGAAACTTTTGAAAAATAAAATG
3637345 TTTTTTTTTC
Statistics
Matches: 164, Mismatches: 26, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
42 22 0.13
43 131 0.80
44 11 0.07
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (43 bp):
TTTGAAACTTTTGAAAAATAAAATGATTCCCCCCAATAGAGGC
Found at i:3637197 original size:86 final size:86
Alignment explanation
Indices: 3637107--3637383 Score: 330
Period size: 86 Copynumber: 3.2 Consensus size: 86
3637097 AACAAAGGTT
* ** *
3637107 TTGAAACTTATT-AAAAATAAAATG-ATCCCCCCCATCAGAGGCTTTGAAGCTTTTGAAAAATAA
1 TTGAAACTT-TTGAAAAATAAAATGCTTCCCTTCAAT-AGAGGCTTTGAAGCTTTTGAAAAATAA
*
3637170 AATATTCTTCCTCAATATAGGCA
64 AATATTCTTCCTCAATAAAGGCA
*
3637193 TTGAAACTTTTGAAAAATAAAATGCTTCCTTTCAATAGAGGCTTTGAAGCTTTTGAAAAATAAAA
1 TTGAAACTTTTGAAAAATAAAATGCTTCCCTTCAATAGAGGCTTTGAAGCTTTTGAAAAATAAAA
* * * *
3637258 TATTCCTCCTCAACAGAGGCT
66 TATTCTTCCTCAATAAAGGCA
* * * *
3637279 TTAAAACTTTTGAAAAATAAAATGCTTCTCTTCAATAGAGGCTTTGAAAC-TTTGAAAAATATAA
1 TTGAAACTTTTGAAAAATAAAATGCTTCCCTTCAATAGAGGCTTTGAAGCTTTTGAAAAATAAAA
* * **
3637343 TGTTTTTTTTTCAATAAAGGCA
66 T-ATTCTTCCTCAATAAAGGCA
3637365 TTGAAAC-TTT-AAAAATAAA
1 TTGAAACTTTTGAAAAATAAA
3637384 GGGTATTCGA
Statistics
Matches: 165, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
84 9 0.05
85 19 0.12
86 131 0.79
87 6 0.04
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (86 bp):
TTGAAACTTTTGAAAAATAAAATGCTTCCCTTCAATAGAGGCTTTGAAGCTTTTGAAAAATAAAA
TATTCTTCCTCAATAAAGGCA
Found at i:3637254 original size:129 final size:128
Alignment explanation
Indices: 3637095--3637383 Score: 343
Period size: 129 Copynumber: 2.2 Consensus size: 128
3637085 ATGCTCTCAC
* * * * *
3637095 TCAACAAAGGTTTTGAAACTTATTAAAAATAAAATGA-TCCCCCCCATCAGAGGCTTTGAAGCTT
1 TCAATAAAGGCTTTGAAACTT-TTAAAAATAAAAT-ATTCCCCCCCAACAGAGGCTTTAAAACTT
*
3637159 TTGAAAAATAAAAT-ATTCTTCCTCAATATAGGCATTGAAACTTTTGAAAAATAAAATG-CTTCC
64 TTGAAAAATAAAATGATTC-TCCTCAATAGAGGCATTGAAAC-TTTGAAAAATAAAATGTCTTCC
3637222 TT
127 TT
* * * *
3637224 TCAATAGAGGCTTTGAAGCTTTTGAAAAATAAAATATTCCTCCTCAACAGAGGCTTTAAAACTTT
1 TCAATAAAGGCTTTGAAACTTTT-AAAAATAAAATATTCCCCCCCAACAGAGGCTTTAAAACTTT
* * * * * **
3637289 TGAAAAATAAAATGCTTCTCTTCAATAGAGGCTTTGAAACTTTGAAAAATATAATGTTTTTTTT
65 TGAAAAATAAAATGATTCTCCTCAATAGAGGCATTGAAACTTTGAAAAATAAAATGTCTTCCTT
*
3637353 TCAATAAAGGCATTGAAAC-TTTAAAAATAAA
1 TCAATAAAGGCTTTGAAACTTTTAAAAATAAA
3637384 GGGTATTCGA
Statistics
Matches: 136, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
127 9 0.07
128 21 0.15
129 103 0.76
130 3 0.02
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (128 bp):
TCAATAAAGGCTTTGAAACTTTTAAAAATAAAATATTCCCCCCCAACAGAGGCTTTAAAACTTTT
GAAAAATAAAATGATTCTCCTCAATAGAGGCATTGAAACTTTGAAAAATAAAATGTCTTCCTT
Found at i:3637356 original size:43 final size:43
Alignment explanation
Indices: 3637143--3637383 Score: 258
Period size: 43 Copynumber: 5.7 Consensus size: 43
3637133 CCCCCCCATC
* * *
3637143 AGAGGCTTTGAAGCTTTTGAAAAATAAAAT-ATTCTTCCTCAAT
1 AGAGGCTTTGAAACTTTTGAAAAATAAAATGTTTC-TCTTCAAT
* * *
3637186 ATAGGCATTGAAACTTTTGAAAAATAAAATGCTTC-CTTTCAAT
1 AGAGGCTTTGAAACTTTTGAAAAATAAAATGTTTCTC-TTCAAT
* * * * *
3637229 AGAGGCTTTGAAGCTTTTGAAAAATAAAATATTCCTCCTCAAC
1 AGAGGCTTTGAAACTTTTGAAAAATAAAATGTTTCTCTTCAAT
* *
3637272 AGAGGCTTTAAAACTTTTGAAAAATAAAATGCTTCTCTTCAAT
1 AGAGGCTTTGAAACTTTTGAAAAATAAAATGTTTCTCTTCAAT
* * *
3637315 AGAGGCTTTGAAAC-TTTGAAAAATATAATGTTTTTTTTTCAAT
1 AGAGGCTTTGAAACTTTTGAAAAATAAAATG-TTTCTCTTCAAT
* *
3637358 AAAGGCATTGAAAC-TTT-AAAAATAAA
1 AGAGGCTTTGAAACTTTTGAAAAATAAA
3637384 GGGTATTCGA
Statistics
Matches: 166, Mismatches: 28, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
42 24 0.14
43 138 0.83
44 4 0.02
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (43 bp):
AGAGGCTTTGAAACTTTTGAAAAATAAAATGTTTCTCTTCAAT
Found at i:3638344 original size:3 final size:3
Alignment explanation
Indices: 3638336--3638366 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3638326 AGTTCTTGTT
3638336 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3638367 GGTTTAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3639957 original size:30 final size:29
Alignment explanation
Indices: 3639923--3640163 Score: 116
Period size: 29 Copynumber: 8.5 Consensus size: 29
3639913 TAAAAAAAAT
3639923 TAAAATCAAAACCCAAAATTTCTAAACCCC
1 TAAAATCAAAACCCAAAATTTCTAAA-CCC
**
3639953 TAAAATCTAAAAACTTAAAA--TCTAAACCC
1 TAAAATC--AAAACCCAAAATTTCTAAACCC
* * *
3639982 T-AAATCCAAACCCCTAAAA-TCCAAAACCC
1 TAAAAT-CAAAACCC-AAAATTTCTAAACCC
* *** *
3640011 TAAAATCCAAATCTTTAAA-TTCCAAACCC
1 TAAAAT-CAAAACCCAAAATTTCTAAACCC
* * *
3640040 TAATATCCAAACCCCAAAATTTTCGAAA-CC
1 TAAAAT-CAAAACCCAAAA-TTTCTAAACCC
3640070 -----T--AAACCCAAAATTTCTAAACCC
1 TAAAATCAAAACCCAAAATTTCTAAACCC
* ** **
3640092 TAAAATCAAAACCCCAAACCTC-AAACTT
1 TAAAATCAAAACCCAAAATTTCTAAACCC
*
3640120 TAAAACCAAAACCCTAAAATCTTC-AAACCC
1 TAAAATCAAAACCC-AAAAT-TTCTAAACCC
3640150 TAAAATCAAAACCC
1 TAAAATCAAAACCC
3640164 TAAACCTTCC
Statistics
Matches: 160, Mismatches: 33, Indels: 36
0.70 0.14 0.16
Matches are distributed among these distances:
21 7 0.04
22 11 0.07
25 1 0.01
27 5 0.03
28 25 0.16
29 52 0.32
30 44 0.28
31 6 0.04
32 9 0.06
ACGTcount: A:0.49, C:0.30, G:0.00, T:0.20
Consensus pattern (29 bp):
TAAAATCAAAACCCAAAATTTCTAAACCC
Found at i:3640012 original size:58 final size:58
Alignment explanation
Indices: 3639950--3640059 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 58
3639940 ATTTCTAAAC
*
3639950 CCCTAAAATCTAAAAAC-TTAAAATCTAAACCCTAA-ATCCAAACCCCTAAAATCCAAAA
1 CCCTAAAATC-AAAAACTTTAAAATCCAAACCCTAATATCCAAACCCC-AAAATCCAAAA
* * *
3640008 CCCTAAAATCCAAATCTTTAAATTCCAAACCCTAATATCCAAACCCCAAAAT
1 CCCTAAAATCAAAAACTTTAAAATCCAAACCCTAATATCCAAACCCCAAAAT
3640060 TTTCGAAACC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
57 4 0.09
58 31 0.67
59 11 0.24
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.21
Consensus pattern (58 bp):
CCCTAAAATCAAAAACTTTAAAATCCAAACCCTAATATCCAAACCCCAAAATCCAAAA
Found at i:3640018 original size:15 final size:15
Alignment explanation
Indices: 3639923--3640059 Score: 97
Period size: 15 Copynumber: 9.4 Consensus size: 15
3639913 TAAAAAAAAT
3639923 TAAAAT-CAAAACCC
1 TAAAATCCAAAACCC
* *
3639937 -AAAATTTCTAAACCCC
1 TAAAA--TCCAAAACCC
* * *
3639953 TAAAATCTAAAAACT
1 TAAAATCCAAAACCC
*
3639968 TAAAAT-CTAAACCC
1 TAAAATCCAAAACCC
*
3639982 T-AAATCCAAACCCC
1 TAAAATCCAAAACCC
3639996 TAAAATCCAAAACCC
1 TAAAATCCAAAACCC
* **
3640011 TAAAATCCAAATCTT
1 TAAAATCCAAAACCC
*
3640026 TAAATTCC-AAACCC
1 TAAAATCCAAAACCC
*
3640040 TAATATCC-AAACCC
1 TAAAATCCAAAACCC
*
3640054 CAAAAT
1 TAAAAT
3640060 TTTCGAAACC
Statistics
Matches: 94, Mismatches: 23, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
13 8 0.09
14 31 0.33
15 45 0.48
16 6 0.06
17 4 0.04
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (15 bp):
TAAAATCCAAAACCC
Found at i:3640101 original size:22 final size:22
Alignment explanation
Indices: 3640053--3640102 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
3640043 TATCCAAACC
*
3640053 CCAAAATTTTCGAAACCTAAAC
1 CCAAAATTTTCGAAACCTAAAA
*
3640075 CCAAAA-TTTCTAAACCCTAAAA
1 CCAAAATTTTCGAAA-CCTAAAA
*
3640097 TCAAAA
1 CCAAAA
3640103 CCCCAAACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.50, C:0.26, G:0.02, T:0.22
Consensus pattern (22 bp):
CCAAAATTTTCGAAACCTAAAA
Found at i:3640105 original size:14 final size:14
Alignment explanation
Indices: 3640086--3640167 Score: 76
Period size: 14 Copynumber: 5.7 Consensus size: 14
3640076 CAAAATTTCT
3640086 AAACCCTAAAATCA
1 AAACCCTAAAATCA
* *
3640100 AAACCCCAAACCTC-
1 AAACCCTAAA-ATCA
** *
3640114 AAACTTTAAAACCA
1 AAACCCTAAAATCA
*
3640128 AAACCCTAAAATCTTC
1 AAACCCTAAAATC--A
3640144 AAACCCTAAAATCA
1 AAACCCTAAAATCA
3640158 AAACCCTAAA
1 AAACCCTAAA
3640168 CCTTCCATAC
Statistics
Matches: 52, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
13 1 0.02
14 36 0.69
15 2 0.04
16 13 0.25
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (14 bp):
AAACCCTAAAATCA
Found at i:3640184 original size:30 final size:29
Alignment explanation
Indices: 3640086--3640229 Score: 105
Period size: 30 Copynumber: 4.9 Consensus size: 29
3640076 CAAAATTTCT
* *
3640086 AAACCCTAAAATCAAAACCCCAAACC-TC
1 AAACCATAAAATCAAAACCCTAAACCTTC
** * *
3640114 AAACTTTAAAACCAAAACCCTAAAATCTTC
1 AAACCATAAAATCAAAACCCT-AAACCTTC
*
3640144 AAACCCTAAAATCAAAACCCTAAACCTTCC
1 AAACCATAAAATCAAAACCCTAAACCTT-C
* * * *
3640174 ATACCATAAAATTC-AAGCCTTAAGACCTTAT
1 AAACCATAAAA-TCAAAACCCTAA-ACCTT-C
* *
3640205 AAACCCTAAAATC-AAACCTTAAACC
1 AAACCATAAAATCAAAACCCTAAACC
3640230 CTTAAAACTC
Statistics
Matches: 93, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
28 17 0.18
29 13 0.14
30 47 0.51
31 16 0.17
ACGTcount: A:0.48, C:0.31, G:0.01, T:0.19
Consensus pattern (29 bp):
AAACCATAAAATCAAAACCCTAAACCTTC
Found at i:3640229 original size:20 final size:22
Alignment explanation
Indices: 3640204--3640243 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
3640194 TAAGACCTTA
3640204 TAAACCC-TAAAA-TCAAACCT
1 TAAACCCTTAAAACTCAAACCT
3640224 TAAACCCTTAAAACTCAAAC
1 TAAACCCTTAAAACTCAAAC
3640244 TAAAATTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (22 bp):
TAAACCCTTAAAACTCAAACCT
Found at i:3648817 original size:128 final size:128
Alignment explanation
Indices: 3648672--3648983 Score: 393
Period size: 128 Copynumber: 2.5 Consensus size: 128
3648662 AAATTTCATT
3648672 ACCTCTGATTA-AGAGGAGCACTT-AAAGATTTTAAGATTTATAAGACCTTCGGACGTAATATCT
1 ACCTCTGATTAGA-AGGAGCA-TTCAAAGATTTTAAGATTTATAAGACCTTCGGACGTAATATCT
* * * *
3648735 AAAGCCTCCGAGCACAACTTTCAAGATTTTT-GGATAAAAGGTTTTAAAATTTTTAAAGTTCACA
64 AAAACCTCCGAGCACAACTTTCAAGATTTTTAGG-TAAAAGATTTTAAAATTTTCAAAGATCACA
3648799 G
128 G
* * *
3648800 ACCTCTGATTAGAAGGAGCATTCAAAGATTTTGAGATTTGTAAGACCTTCGGACGTAATCTCTAA
1 ACCTCTGATTAGAAGGAGCATTCAAAGATTTTAAGATTTATAAGACCTTCGGACGTAATATCTAA
** * * * *
3648865 AACCTGTGGGCATAACTTTCAAGATTTTTAGGTAAAAGATTTTTAAATTTTCAAAGATCACAT
66 AACCTCCGAGCACAACTTTCAAGATTTTTAGGTAAAAGATTTTAAAATTTTCAAAGATCACAG
* * * * *
3648928 ACCTCTGATTAGAA-GAGCATTCAAAAATGTT--GATTTCTAAGACCTCCGGACATAAT
1 ACCTCTGATTAGAAGGAGCATTCAAAGATTTTAAGATTTATAAGACCTTCGGACGTAAT
3648984 TTTGATTCAC
Statistics
Matches: 163, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
125 22 0.13
127 17 0.10
128 121 0.74
129 3 0.02
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (128 bp):
ACCTCTGATTAGAAGGAGCATTCAAAGATTTTAAGATTTATAAGACCTTCGGACGTAATATCTAA
AACCTCCGAGCACAACTTTCAAGATTTTTAGGTAAAAGATTTTAAAATTTTCAAAGATCACAG
Found at i:3649123 original size:110 final size:110
Alignment explanation
Indices: 3648958--3649199 Score: 306
Period size: 110 Copynumber: 2.2 Consensus size: 110
3648948 TCAAAAATGT
* * * * *
3648958 TGATTTCTAAGACCTCCGGACATAATTTTGATTCACAGTGTTATCTCGATTGATTCTTTATTTTT
1 TGATTTCTAAGACCTTCGGGCATAATTTTGATTCACAATGTTATCCCGATCGATTCTTTATTTTT
* * * * *
3649023 TGACTTG-CAGTGTTGTTTCGGTCGATTCTGTAAGACTTTTAGGCA
66 TGA-TTGACAGTGTTGTCTCGATCGATTCTGTAAGACCTTCAAGCA
*** *
3649068 TGATTTCTAAGACCTTCGGGCATAATTTTGATTTGTAATGTTGTCCCGATCGATTCTTTATTTTT
1 TGATTTCTAAGACCTTCGGGCATAATTTTGATTCACAATGTTATCCCGATCGATTCTTTATTTTT
*
3649133 TGATTGACGGTGTTGTCTCGATCGATTCTGTAAGACCTTCAAGCA
66 TGATTGACAGTGTTGTCTCGATCGATTCTGTAAGACCTTCAAGCA
* * *
3649178 TGATTTTTAAAACCTTCAGGCA
1 TGATTTCTAAGACCTTCGGGCA
3649200 CAATCTTTAA
Statistics
Matches: 113, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
109 3 0.03
110 110 0.97
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (110 bp):
TGATTTCTAAGACCTTCGGGCATAATTTTGATTCACAATGTTATCCCGATCGATTCTTTATTTTT
TGATTGACAGTGTTGTCTCGATCGATTCTGTAAGACCTTCAAGCA
Found at i:3649208 original size:22 final size:22
Alignment explanation
Indices: 3649183--3649237 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
3649173 AAGCATGATT
* * *
3649183 TTTAAAACCTTCAGGCACAATC
1 TTTAAGACCTCCAGGCACAATA
*
3649205 TTTAAGACCTCCGGGCACAATA
1 TTTAAGACCTCCAGGCACAATA
3649227 TTTAAGACCTC
1 TTTAAGACCTC
3649238 TGAGCATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (22 bp):
TTTAAGACCTCCAGGCACAATA
Found at i:3649343 original size:22 final size:22
Alignment explanation
Indices: 3649317--3649360 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3649307 GTCGATTTTG
* * *
3649317 TAAGACCTTCAGGCATGATTTC
1 TAAGACCTCCAGACATAATTTC
3649339 TAAGACCTCCAGACATAATTTC
1 TAAGACCTCCAGACATAATTTC
3649361 GATTCACGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.30
Consensus pattern (22 bp):
TAAGACCTCCAGACATAATTTC
Found at i:3649445 original size:264 final size:263
Alignment explanation
Indices: 3648965--3649454 Score: 601
Period size: 264 Copynumber: 1.9 Consensus size: 263
3648955 TGTTGATTTC
* * * * *
3648965 TAAGACCTCCGGACATAATTTTGATTCACAGTGTTATCTCGATTGATTCTTTATTTTTTGACTTG
1 TAAGACCTCCGGACATAATTTTAATTCACAGTGTTATCCCGATAGATTCTTTATTTTTTAACTTA
* * * * *
3649030 CAGTGTTGTTTCGGTCGATTCTGTAAGACTTTTAGGCATGATTTCTAAGACCTTCGGGCATAATT
66 CAGTGTTGTTTC-GTCGATTCTGTAAGACCTTCAGGCATGATTTCTAAGACCTCCAGACATAATT
* *** * * *
3649095 TTGATTTGTAATGTTGTCCCGATCGATTCTTTATTTTTTGATTGACGGTGTTGTCTCGATCGATT
130 TCGATTCACAATGTTATCCCGATCGATTCTTTATTTTTTGATTGACGGTATTATCTCGATCGATT
* *
3649160 CTGTAAGACCTTCAAGCATGATTTTTAAAACCTTCAGGCACAATCTTTAAGACCTCCGGGCACAA
195 CTGTAAGACCTCCAAGCATGATTTGTAAAACCTTCAGGCACAATCTTTAAGACCTCCGGGCACAA
3649225 TATT
260 TATT
*
3649229 TAAGACCT-CTGAGCATAATTTTAATTCACAG-GATTATCCCGATAGATTCTTTATTTTTTAACT
1 TAAGACCTCCGGA-CATAATTTTAATTCACAGTG-TTATCCCGATAGATTCTTTATTTTTTAACT
* *
3649292 TACGGTGTTGTCCTT-GTCGATTTTGTAAGACCTTCAGGCATGATTTCTAAGACCTCCAGACATA
64 TACAGTGTTGT--TTCGTCGATTCTGTAAGACCTTCAGGCATGATTTCTAAGACCTCCAGACATA
** ** ** * *
3649356 ATTTCGATTCACGGTGTTATCTTGATTTATTCTTTATTTTTTGACTT-ACGGTATTATCTCGGTT
127 ATTTCGATTCACAATGTTATCCCGATCGATTCTTTATTTTTTGA-TTGACGGTATTATCTCGATC
* **
3649420 GATTTTGTAAGACCTCCGGGCATGATTTGTAAAAC
191 GATTCTGTAAGACCTCCAAGCATGATTTGTAAAAC
3649455 TTTTGGGCAC
Statistics
Matches: 188, Mismatches: 33, Indels: 10
0.81 0.14 0.04
Matches are distributed among these distances:
263 4 0.02
264 180 0.96
265 2 0.01
266 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41
Consensus pattern (263 bp):
TAAGACCTCCGGACATAATTTTAATTCACAGTGTTATCCCGATAGATTCTTTATTTTTTAACTTA
CAGTGTTGTTTCGTCGATTCTGTAAGACCTTCAGGCATGATTTCTAAGACCTCCAGACATAATTT
CGATTCACAATGTTATCCCGATCGATTCTTTATTTTTTGATTGACGGTATTATCTCGATCGATTC
TGTAAGACCTCCAAGCATGATTTGTAAAACCTTCAGGCACAATCTTTAAGACCTCCGGGCACAAT
ATT
Found at i:3650970 original size:15 final size:14
Alignment explanation
Indices: 3650959--3651092 Score: 92
Period size: 14 Copynumber: 9.3 Consensus size: 14
3650949 TCTAAACCTT
3650959 TAAAATCCAAACCCC
1 TAAAATCCAAA-CCC
*
3650974 AAAAATCCAAAACCC
1 TAAAATCC-AAACCC
**
3650989 TAAAATCCAAATCTT
1 TAAAATCCAAA-CCC
* *
3651004 TAAATTCAAAACCC
1 TAAAATCCAAACCC
3651018 TAAAATCCAAACCC
1 TAAAATCCAAACCC
* * **
3651032 CAAACT-CAAACTT
1 TAAAATCCAAACCC
3651045 TAAAA-CCAAAACCC
1 TAAAATCC-AAACCC
*
3651059 CAAAATCTTCAAACCC
1 TAAAATC--CAAACCC
* *
3651075 TAAAATCAAAATCC
1 TAAAATCCAAACCC
3651089 TAAA
1 TAAA
3651093 CCTTCCATAC
Statistics
Matches: 90, Mismatches: 22, Indels: 15
0.71 0.17 0.12
Matches are distributed among these distances:
13 9 0.10
14 37 0.41
15 28 0.31
16 15 0.17
17 1 0.01
ACGTcount: A:0.51, C:0.31, G:0.00, T:0.18
Consensus pattern (14 bp):
TAAAATCCAAACCC
Found at i:3651092 original size:14 final size:14
Alignment explanation
Indices: 3650929--3651092 Score: 89
Period size: 14 Copynumber: 11.3 Consensus size: 14
3650919 TAAAAAAAAT
3650929 TAAAATCAAAACCC
1 TAAAATCAAAACCC
* *
3650943 -AAAATTTCTAAACCTT
1 TAAAA--TCAAAACC-C
*
3650959 TAAAATCCAAACCCC
1 TAAAAT-CAAAACCC
*
3650974 AAAAATCCAAAACCC
1 TAAAAT-CAAAACCC
* **
3650989 TAAAATCCAAATCTT
1 TAAAAT-CAAAACCC
*
3651004 TAAATTCAAAACCC
1 TAAAATCAAAACCC
*
3651018 TAAAATCCAAACCC
1 TAAAATCAAAACCC
* * **
3651032 CAAACTC-AAACTT
1 TAAAATCAAAACCC
*
3651045 TAAAACCAAAACCC
1 TAAAATCAAAACCC
* *
3651059 CAAAATCTTCAAACCC
1 TAAAATC--AAAACCC
*
3651075 TAAAATCAAAATCC
1 TAAAATCAAAACCC
3651089 TAAA
1 TAAA
3651093 CCTTCCATAC
Statistics
Matches: 110, Mismatches: 32, Indels: 16
0.70 0.20 0.10
Matches are distributed among these distances:
13 12 0.11
14 40 0.36
15 37 0.34
16 17 0.15
17 4 0.04
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (14 bp):
TAAAATCAAAACCC
Found at i:3651155 original size:21 final size:19
Alignment explanation
Indices: 3651130--3651183 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 19
3651120 AAGACCTTCT
3651130 AAACCCTAAAATCAAACCCTA
1 AAACCCTAAAATCAAA-CC-A
3651151 AAACCCTTAAAACTCAAACCA
1 AAACCC-TAAAA-TCAAACCA
*
3651172 AAATCCTAAAAT
1 AAACCCTAAAAT
3651184 TTGAATATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 1 0.03
20 5 0.17
21 12 0.40
22 7 0.23
23 5 0.17
ACGTcount: A:0.54, C:0.30, G:0.00, T:0.17
Consensus pattern (19 bp):
AAACCCTAAAATCAAACCA
Found at i:3655064 original size:15 final size:16
Alignment explanation
Indices: 3655044--3655088 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
3655034 TTACAATTGC
3655044 TTCACATATATA-TAT
1 TTCACATATATATTAT
3655059 TTCACATATATATTAT
1 TTCACATATATATTAT
*
3655075 TT-ATAT-TATATTAT
1 TTCACATATATATTAT
3655089 AAAATGTATG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 8 0.29
15 15 0.54
16 5 0.18
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (16 bp):
TTCACATATATATTAT
Found at i:3656802 original size:42 final size:43
Alignment explanation
Indices: 3656743--3656828 Score: 138
Period size: 42 Copynumber: 2.0 Consensus size: 43
3656733 TGACATGGGT
*
3656743 AACAACTTCAGACTTGATTTTGGTTGAGTTCC-TTACTTTTCA
1 AACAACTTCAGACTTGATTTTGGTTAAGTTCCATTACTTTTCA
* *
3656785 AACAACTTCAGGCTTGATTTTGTTTAAGTTCCATTACTTTTCA
1 AACAACTTCAGACTTGATTTTGGTTAAGTTCCATTACTTTTCA
3656828 A
1 A
3656829 TTCAGTTTGT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 29 0.73
43 11 0.28
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.43
Consensus pattern (43 bp):
AACAACTTCAGACTTGATTTTGGTTAAGTTCCATTACTTTTCA
Found at i:3661947 original size:2 final size:2
Alignment explanation
Indices: 3661940--3661971 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3661930 TAGCAGTAAA
3661940 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
3661972 CTGTAGGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3663861 original size:2 final size:2
Alignment explanation
Indices: 3663856--3663882 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3663846 GTGTGTCTAC
3663856 GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT G
3663883 CATGTACTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:3672089 original size:36 final size:36
Alignment explanation
Indices: 3672005--3672090 Score: 118
Period size: 36 Copynumber: 2.4 Consensus size: 36
3671995 ACCAGAGCTC
3672005 CTACTTATGCTTCTCCGAGAAGATCTTACAGGACTT
1 CTACTTATGCTTCTCCGAGAAGATCTTACAGGACTT
* * * * * *
3672041 CTGCTAAAGCTTCTCCTAGAAGATCTTGCTGGACTT
1 CTACTTATGCTTCTCCGAGAAGATCTTACAGGACTT
3672077 CTACTTATGCTTCT
1 CTACTTATGCTTCT
3672091 TTTCAAAAGT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (36 bp):
CTACTTATGCTTCTCCGAGAAGATCTTACAGGACTT
Found at i:3672288 original size:24 final size:24
Alignment explanation
Indices: 3672259--3672304 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3672249 TACCCCTCAA
*
3672259 AGGGCTTCTGCTGATGCCTCTAGC
1 AGGGCTCCTGCTGATGCCTCTAGC
*
3672283 AGGGCTCCTGCTGATGCTTCTA
1 AGGGCTCCTGCTGATGCCTCTA
3672305 CTCTTTCTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.13, C:0.28, G:0.28, T:0.30
Consensus pattern (24 bp):
AGGGCTCCTGCTGATGCCTCTAGC
Found at i:3672312 original size:63 final size:63
Alignment explanation
Indices: 3672221--3672364 Score: 243
Period size: 63 Copynumber: 2.3 Consensus size: 63
3672211 TGCTCTAACT
** *
3672221 GGGCTCCTGCTGATGCTTCTACTCTTTCTACCCCTCAAAGGGCTTCTGCTGATGCCTCTAGCA
1 GGGCTCCTGCTGATGCTTCTACTCTTTCTACCCCTCAAAGGGCTTCCACTGATGCCTCTAGAA
* *
3672284 GGGCTCCTGCTGATGCTTCTACTCTTTCTACCCTTCAAAGGGCTTCCACTGATGCTTCTAGAA
1 GGGCTCCTGCTGATGCTTCTACTCTTTCTACCCCTCAAAGGGCTTCCACTGATGCCTCTAGAA
3672347 GGGCTCCTGCTGATGCTT
1 GGGCTCCTGCTGATGCTT
3672365 TTAGCAGGGC
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 76 1.00
ACGTcount: A:0.15, C:0.31, G:0.22, T:0.33
Consensus pattern (63 bp):
GGGCTCCTGCTGATGCTTCTACTCTTTCTACCCCTCAAAGGGCTTCCACTGATGCCTCTAGAA
Found at i:3672349 original size:24 final size:24
Alignment explanation
Indices: 3672332--3672403 Score: 117
Period size: 24 Copynumber: 3.0 Consensus size: 24
3672322 AGGGCTTCCA
*
3672332 CTGATGCTTCTAGAAGGGCTCCTG
1 CTGATGCTTTTAGAAGGGCTCCTG
*
3672356 CTGATGCTTTTAGCAGGGCTCCTG
1 CTGATGCTTTTAGAAGGGCTCCTG
*
3672380 CTGATGCTTTTAGCAGGGCTCCTG
1 CTGATGCTTTTAGAAGGGCTCCTG
3672404 TTCCTACTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.14, C:0.25, G:0.29, T:0.32
Consensus pattern (24 bp):
CTGATGCTTTTAGAAGGGCTCCTG
Found at i:3672426 original size:48 final size:48
Alignment explanation
Indices: 3672332--3672429 Score: 115
Period size: 48 Copynumber: 2.0 Consensus size: 48
3672322 AGGGCTTCCA
* * * * *
3672332 CTGATGCTTCTAGAAGGGCTCCTGCTGATGCTTTTAGCAGGGCTCCTG
1 CTGATGCTTCTAGAAGGGCTCCTGCTCATACTTCTAACAGGACTCCTG
* * * *
3672380 CTGATGCTTTTAGCAGGGCTCCTGTTCCTACTTCTAACAGGACTCCTG
1 CTGATGCTTCTAGAAGGGCTCCTGCTCATACTTCTAACAGGACTCCTG
3672428 CT
1 CT
3672430 TACACTTCTT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.15, C:0.28, G:0.24, T:0.33
Consensus pattern (48 bp):
CTGATGCTTCTAGAAGGGCTCCTGCTCATACTTCTAACAGGACTCCTG
Found at i:3681799 original size:37 final size:37
Alignment explanation
Indices: 3681749--3681824 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
3681739 TCAGATTCTT
* *
3681749 GGCCATATCCGACTTGTTTCATCAACAACCCGGAACA
1 GGCCATATCCGACTTGCTTCATCAACAACCCCGAACA
3681786 GGCCATATCCGACTTGCTTCATCAACAACCCCGAACA
1 GGCCATATCCGACTTGCTTCATCAACAACCCCGAACA
3681823 GG
1 GG
3681825 TCAACAACCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.29, C:0.34, G:0.17, T:0.20
Consensus pattern (37 bp):
GGCCATATCCGACTTGCTTCATCAACAACCCCGAACA
Found at i:3695179 original size:133 final size:133
Alignment explanation
Indices: 3694916--3695178 Score: 287
Period size: 133 Copynumber: 2.0 Consensus size: 133
3694906 TAAAAAAAAA
* * * **
3694916 TCACTAAATTAGCGGCGTTTCAAAGATACAAACGTCACTAATATAGAAGCATTTTCATTTACAAA
1 TCACTAAATTAGCGACGTCTCAAAGATACAAACGCCACTAATATAGAAGCATTTTCAAATACAAA
* * ***
3694981 CGCTTCTAAAGTAACGGCAATATAAGTTACAAACATCACCAAAGCAATGGTATTTTCTCATAAAA
66 CGCCTCTAAAGTAACAGCAATATAAGTTACAAACATCACCAAAGCAACAATATTTTCTCATAAAA
3695046 ATG
131 ATG
* * ** * *
3695049 TCACTAAATTAGTGACGTCTGAAAGATACAAACGCCGTTAATATAGATGTATTTTCAAATACAAA
1 TCACTAAATTAGCGACGTCTCAAAGATACAAACGCCACTAATATAGAAGCATTTTCAAATAC-AA
* * * * * ** *
3695114 ATGCCTCTAAAGTAGCAGCATTTTCAGTTGTAAACGTCACCAAAGCAACAATATTTT-TC-TAAA
65 ACGCCTCTAAAGTAACAGCAATATAAGTTACAAACATCACCAAAGCAACAATATTTTCTCATAAA
3695177 AA
130 AA
3695179 AAACACAACT
Statistics
Matches: 105, Mismatches: 24, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
132 6 0.06
133 53 0.50
134 46 0.44
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (133 bp):
TCACTAAATTAGCGACGTCTCAAAGATACAAACGCCACTAATATAGAAGCATTTTCAAATACAAA
CGCCTCTAAAGTAACAGCAATATAAGTTACAAACATCACCAAAGCAACAATATTTTCTCATAAAA
ATG
Found at i:3695527 original size:17 final size:17
Alignment explanation
Indices: 3695470--3695528 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
3695460 TGAAATATTC
*
3695470 TAAAAATTATAAAAAAAT
1 TAAAATTTA-AAAAAAAT
*
3695488 T-AAATTTAAAAAAAAA
1 TAAAATTTAAAAAAAAT
* *
3695504 CATAATTTAAAAAAAAT
1 TAAAATTTAAAAAAAAT
3695521 TAAAATTT
1 TAAAATTT
3695529 TAATTAAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
16 7 0.21
17 25 0.76
18 1 0.03
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAATTTAAAAAAAAT
Found at i:3695611 original size:24 final size:24
Alignment explanation
Indices: 3695579--3695628 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
3695569 GTAAGATTCA
3695579 AAAAAAAATGTT-C-ATTATTTTTTT
1 AAAAAAAAT-TTACAATT-TTTTTTT
3695603 AAAAAAAATTTACAATTTTTTTTT
1 AAAAAAAATTTACAATTTTTTTTT
3695627 AA
1 AA
3695629 TTTTTAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 2 0.08
24 19 0.79
25 3 0.12
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (24 bp):
AAAAAAAATTTACAATTTTTTTTT
Found at i:3696154 original size:15 final size:15
Alignment explanation
Indices: 3696134--3696164 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3696124 TAATTAAGTT
3696134 AATTATTTATTGATA
1 AATTATTTATTGATA
3696149 AATTATTTATTGATA
1 AATTATTTATTGATA
3696164 A
1 A
3696165 TATTGTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (15 bp):
AATTATTTATTGATA
Found at i:3696957 original size:16 final size:14
Alignment explanation
Indices: 3696921--3696968 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 14
3696911 TTCAGTAATT
3696921 TTAAAAAATAAAAA
1 TTAAAAAATAAAAA
3696935 TAATAAAATAATAAAACA
1 T--TAAAA-AATAAAA-A
*
3696953 TTAAAAAATTAAAA
1 TTAAAAAATAAAAA
3696967 TT
1 TT
3696969 TAAGAAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
14 4 0.14
15 6 0.21
16 10 0.34
17 7 0.24
18 2 0.07
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (14 bp):
TTAAAAAATAAAAA
Found at i:3696958 original size:24 final size:24
Alignment explanation
Indices: 3696922--3696967 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
3696912 TCAGTAATTT
3696922 TAAAAAATAAAAATAA-TAAAATAA
1 TAAAAAATAAAAA-AATTAAAATAA
* *
3696946 TAAAACATTAAAAAATTAAAAT
1 TAAAAAATAAAAAAATTAAAAT
3696968 TTAAGAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (24 bp):
TAAAAAATAAAAAAATTAAAATAA
Found at i:3702067 original size:20 final size:20
Alignment explanation
Indices: 3702039--3702161 Score: 192
Period size: 20 Copynumber: 6.2 Consensus size: 20
3702029 ATGGCATTGC
*
3702039 CACGTCAACACACCGTTAGA
1 CACGTCAACACACTGTTAGA
* *
3702059 CATGTCAACACATTGTTAGA
1 CACGTCAACACACTGTTAGA
*
3702079 CACGTCAACACATTGTTAGA
1 CACGTCAACACACTGTTAGA
* *
3702099 CACGTCAACTCATTGTTAGA
1 CACGTCAACACACTGTTAGA
3702119 CACGTCAACACACTGTTAGA
1 CACGTCAACACACTGTTAGA
3702139 CACGTCAACACACTGTTAGA
1 CACGTCAACACACTGTTAGA
3702159 CAC
1 CAC
3702162 TAACGGCTGA
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 96 1.00
ACGTcount: A:0.34, C:0.28, G:0.15, T:0.23
Consensus pattern (20 bp):
CACGTCAACACACTGTTAGA
Found at i:3704412 original size:17 final size:18
Alignment explanation
Indices: 3704380--3704415 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
3704370 AGCTATGATA
3704380 TTTTAAAAATCAAATTATT
1 TTTTAAAAAT-AAATTATT
3704399 TTTTAAAAAT-AATTATT
1 TTTTAAAAATAAATTATT
3704416 ATTATAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
19 10 0.59
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTAAAAATAAATTATT
Found at i:3707955 original size:12 final size:12
Alignment explanation
Indices: 3707946--3707987 Score: 56
Period size: 10 Copynumber: 3.8 Consensus size: 12
3707936 TTAGTTTTGA
3707946 TTATTATTTTAT
1 TTATTATTTTAT
3707958 TTATTA--TTAT
1 TTATTATTTTAT
3707968 TTA-TATTTT-T
1 TTATTATTTTAT
3707978 TTATTATTTT
1 TTATTATTTT
3707988 TTATGAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
9 2 0.07
10 11 0.41
11 8 0.30
12 6 0.22
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTATTATTTTAT
Found at i:3707969 original size:10 final size:10
Alignment explanation
Indices: 3707945--3707991 Score: 50
Period size: 9 Copynumber: 5.2 Consensus size: 10
3707935 TTTAGTTTTG
3707945 ATTA-TTATT
1 ATTATTTATT
3707954 -TTATTTATT
1 ATTATTTATT
3707963 ATTATTTA-T
1 ATTATTTATT
3707972 ATT-TTT-TT
1 ATTATTTATT
*
3707980 ATTATTTTTT
1 ATTATTTATT
3707990 AT
1 AT
3707992 GAATTAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
8 10 0.30
9 12 0.36
10 11 0.33
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTATTTATT
Found at i:3707982 original size:20 final size:21
Alignment explanation
Indices: 3707950--3707991 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
3707940 TTTTGATTAT
3707950 TATTTTATTTATTATTATTTA
1 TATTTTATTTATTATTATTTA
*
3707971 TATTTT-TTTATTATTTTTTA
1 TATTTTATTTATTATTATTTA
3707991 T
1 T
3707992 GAATTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (21 bp):
TATTTTATTTATTATTATTTA
Found at i:3708002 original size:27 final size:27
Alignment explanation
Indices: 3707954--3708005 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
3707944 GATTATTATT
* * *
3707954 TTATTTATTATTATTTATATTTTTTTA
1 TTATTTATTATGAATTAAATTTTTTTA
*
3707981 TTATTTTTTATGAATTAAATTTTTT
1 TTATTTATTATGAATTAAATTTTTT
3708006 GAAAGGTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (27 bp):
TTATTTATTATGAATTAAATTTTTTTA
Found at i:3708266 original size:3 final size:3
Alignment explanation
Indices: 3708258--3708303 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
3708248 GAGATTTTCG
3708258 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3708304 CATTCCTTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3710219 original size:22 final size:22
Alignment explanation
Indices: 3710181--3710231 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
3710171 TCTGTTATGG
3710181 TATTTTTCGTTTATCTTTTCAT
1 TATTTTTCGTTTATCTTTTCAT
* * * *
3710203 TCTTTTTCTTTTCTCTTTTCCT
1 TATTTTTCGTTTATCTTTTCAT
3710225 TATTTTT
1 TATTTTT
3710232 TCCTTTGCTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.08, C:0.18, G:0.02, T:0.73
Consensus pattern (22 bp):
TATTTTTCGTTTATCTTTTCAT
Found at i:3718643 original size:16 final size:18
Alignment explanation
Indices: 3718622--3718664 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
3718612 AGTTTTGTTT
3718622 ATTAATATTAAA-AT-TA
1 ATTAATATTAAATATATA
3718638 ATTAATAATTAAATATAATA
1 ATTAAT-ATTAAATAT-ATA
3718658 ATTAATA
1 ATTAATA
3718665 AAAACAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 6 0.26
17 6 0.26
18 2 0.09
19 1 0.04
20 8 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTAATATTAAATATATA
Done.