Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008527.1 Hibiscus syriacus cultivar Beakdansim tig00111402_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: 9057482
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 37
Found at i:1010308 original size:60 final size:58
Alignment explanation
Indices: 1010180--1010313 Score: 144
Period size: 60 Copynumber: 2.3 Consensus size: 58
1010170 GCGAAAAAGA
* * * *
1010180 AATTCGCGTTGCGAAAAAGAAATTGAGTTGCTAATTGAAATTCCGTGTTGCGAATTTGG
1 AATTCGCGTTGCGAAAAAGAAATTGAGTTGCGAATTGAAA-TCCGAGTTACGAATTTAG
* * * *
1010239 AAATCGCGTTGCGAGAAAGAAATTCGCGTTGCGAATTTGGAAA-CTGAGTTACGAATTTAG
1 AATTCGCGTTGCGAAAAAGAAATT-GAGTTGCGAA-TT-GAAATCCGAGTTACGAATTTAG
*
1010299 AGTTCGCGTTGCGAA
1 AATTCGCGTTGCGAA
1010314 TTCGAGATCA
Statistics
Matches: 61, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
59 22 0.36
60 33 0.54
61 2 0.03
62 4 0.07
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (58 bp):
AATTCGCGTTGCGAAAAAGAAATTGAGTTGCGAATTGAAATCCGAGTTACGAATTTAG
Found at i:1010328 original size:79 final size:79
Alignment explanation
Indices: 1010167--1010328 Score: 175
Period size: 79 Copynumber: 2.1 Consensus size: 79
1010157 GGAAACTTGT
* * * *
1010167 GTTGCGAAAAAGAAATTCGCGTTGCGAAAAAGAAATTGAGTTGCTAATTGAAATTCCGTGTTGCG
1 GTTGCGAAAAAGAAATTCGCGTTGCGAAAAAGAAACTGAGTTACGAATTGAAATTCCGCGTTGCG
* *
1010232 AATTTGGAAATCGC
66 AATTTCGAAATCAC
* *** * *
1010246 GTTGCGAGAAAGAAATTCGCGTTGCGAATTTGGAAACTGAGTTACGAATTTAGAGTT-CGCGTTG
1 GTTGCGAAAAAGAAATTCGCGTTGCGAA-AAAGAAACTGAGTTACGAATTGA-AATTCCGCGTTG
*
1010310 CGAA-TTCGAGATCAC
64 CGAATTTCGAAATCAC
1010325 GTTG
1 GTTG
1010329 AGAATTTGTT
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
79 39 0.57
80 26 0.38
81 3 0.04
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (79 bp):
GTTGCGAAAAAGAAATTCGCGTTGCGAAAAAGAAACTGAGTTACGAATTGAAATTCCGCGTTGCG
AATTTCGAAATCAC
Found at i:1018204 original size:6 final size:6
Alignment explanation
Indices: 1018193--1018219 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1018183 CGTGTATATT
1018193 TCCCAG TCCCAG TCCCAG TCCCAG TCC
1 TCCCAG TCCCAG TCCCAG TCCCAG TCC
1018220 TATCTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.52, G:0.15, T:0.19
Consensus pattern (6 bp):
TCCCAG
Found at i:1020137 original size:15 final size:17
Alignment explanation
Indices: 1020106--1020138 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1020096 CAAATCAACA
1020106 TCAAACTATTAAATAAT
1 TCAAACTATTAAATAAT
1020123 TCAAA-TATT-AATAAT
1 TCAAACTATTAAATAAT
1020138 T
1 T
1020139 TAAAGATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 4 0.25
17 5 0.31
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (17 bp):
TCAAACTATTAAATAAT
Found at i:1027680 original size:8 final size:8
Alignment explanation
Indices: 1027667--1027699 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
1027657 TAAAACTTGA
1027667 ATACAAAT
1 ATACAAAT
1027675 ATACAAAT
1 ATACAAAT
1027683 ATACAAAT
1 ATACAAAT
1027691 ATACAAAT
1 ATACAAAT
1027699 A
1 A
1027700 ACTAACATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (8 bp):
ATACAAAT
Found at i:1029548 original size:20 final size:20
Alignment explanation
Indices: 1029519--1029564 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1029509 ATTGATTTTT
*
1029519 TAAAAATTATAAAATAATTA
1 TAAAATTTATAAAATAATTA
* *
1029539 TAAAATTTATTAAATTATTA
1 TAAAATTTATAAAATAATTA
*
1029559 TGAAAT
1 TAAAAT
1029565 GGAAATTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
TAAAATTTATAAAATAATTA
Found at i:1030982 original size:21 final size:21
Alignment explanation
Indices: 1030956--1030998 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1030946 TACCTGTTGC
1030956 ATGCTTTAAAACGCTATCGGA
1 ATGCTTTAAAACGCTATCGGA
1030977 ATGCTTTAAAACGCTATCGGA
1 ATGCTTTAAAACGCTATCGGA
1030998 A
1 A
1030999 CTATGCCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (21 bp):
ATGCTTTAAAACGCTATCGGA
Found at i:1032801 original size:18 final size:19
Alignment explanation
Indices: 1032759--1032803 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
1032749 TTTGGTTTAC
1032759 GGAATATAAGATTACCACTG
1 GGAATATAAGATTACCAC-G
* *
1032779 GGAATGTAAGATTATCA-G
1 GGAATATAAGATTACCACG
1032797 GGAATAT
1 GGAATAT
1032804 GATTACTAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.40, C:0.09, G:0.24, T:0.27
Consensus pattern (19 bp):
GGAATATAAGATTACCACG
Found at i:1032987 original size:39 final size:36
Alignment explanation
Indices: 1032944--1033029 Score: 91
Period size: 38 Copynumber: 2.2 Consensus size: 36
1032934 AACAAGTTGA
* * *
1032944 AAAATATTTATATATTTTCTTTAAAAAATTTAAATTCAT
1 AAAAT-TTTATATATATT-TTTAAAAAATTAAAAAT-AT
*
1032983 AAAATTTATATATATATTTTTACAAAATTAAAAATAT
1 AAAATTT-TATATATATTTTTAAAAAATTAAAAATAT
1033020 AAAATGTTTA
1 AAAAT-TTTA
1033030 ATGAAAGGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
37 9 0.22
38 18 0.44
39 14 0.34
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.45
Consensus pattern (36 bp):
AAAATTTTATATATATTTTTAAAAAATTAAAAATAT
Found at i:1033022 original size:37 final size:37
Alignment explanation
Indices: 1032949--1033024 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
1032939 GTTGAAAAAT
* *
1032949 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
*
1032986 ATTTATATATATATT-TTTACAAAATTAAAAAT-ATAAA
1 ATTTATATAT-T-TTCTTTAAAAAATTAAAAATCATAAA
1033023 AT
1 AT
1033025 GTTTAATGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 17 0.50
38 15 0.44
39 2 0.06
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
Found at i:1039410 original size:42 final size:39
Alignment explanation
Indices: 1039316--1039410 Score: 93
Period size: 39 Copynumber: 2.4 Consensus size: 39
1039306 ACTTTTCTAA
* * * *
1039316 TTTATATAAAAATTAAATATTTTATAATTAAAAAAACAG
1 TTTATATAAAATTTAAATAATATATAATTAAAAAAAAAG
* *
1039355 TTTATA-ATTAATTTAAATAATATATAATTATAAAATAAAAAT
1 TTTATATA-AAATTTAAATAATATATAA-T-TAAAA-AAAAAG
1039397 TTTATATAAAATTT
1 TTTATATAAAATTT
1039411 TTAATTAATT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
38 1 0.02
39 21 0.48
40 1 0.02
41 5 0.11
42 15 0.34
43 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (39 bp):
TTTATATAAAATTTAAATAATATATAATTAAAAAAAAAG
Found at i:1039664 original size:187 final size:185
Alignment explanation
Indices: 1039318--1039709 Score: 635
Period size: 187 Copynumber: 2.1 Consensus size: 185
1039308 TTTTCTAATT
* * * *
1039318 TATATAA-AAATTAAATATTTTATAATTAAAAAAACAGTTTATAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTATAATTAAAAAAACAATTTACAATTAATTTAAATAATATATAA
*
1039382 TTATAAAATAAAAATTTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
66 TTATAAAATAAAAATTTTATATAAAATTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTAT
1039447 TAGATCTTAAATTATTAATTGGGGTTTAAATAGTTTGGATTAAGCTCATATGTTA
131 TAGATCTTAAATTATTAATTGGGGTTTAAATAGTTTGGATTAAGCTCATATGTTA
*
1039502 TATATAATATATTTAATATTTTTTAATTCAGAAAAAACAATTTACAATTAATTTAAATAATATAT
1 TATATAATATATTTAATATTTTATAATT-A-AAAAAACAATTTACAATTAATTTAAATAATATAT
*
1039567 AATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTT
64 AATTATAAAATAAAAATTTTATATAAAATTTTTAATTAATTAATATTGATTTAGATTTAAAAGTT
* * * *
1039632 ATT-GAATCTTAAATTATTAATTGTGTTTTAAATGGTTTGGGTTAAGCTCATATGTTA
129 ATTAG-ATCTTAAATTATTAATTGGGGTTTAAATAGTTTGGATTAAGCTCATATGTTA
*
1039689 TATAAAATATATTTAATATTT
1 TATATAATATATTTAATATTT
1039710 AAAATTTTAT
Statistics
Matches: 192, Mismatches: 12, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
184 7 0.04
185 17 0.09
186 2 0.01
187 166 0.86
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (185 bp):
TATATAATATATTTAATATTTTATAATTAAAAAAACAATTTACAATTAATTTAAATAATATATAA
TTATAAAATAAAAATTTTATATAAAATTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTAT
TAGATCTTAAATTATTAATTGGGGTTTAAATAGTTTGGATTAAGCTCATATGTTA
Found at i:1044699 original size:8 final size:8
Alignment explanation
Indices: 1044679--1044711 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
1044669 GGAGATTAAA
1044679 TTGAAACAT
1 TTGAAA-AT
1044688 TTGAAAAT
1 TTGAAAAT
1044696 TTGAAAAT
1 TTGAAAAT
1044704 TTGAAAAT
1 TTGAAAAT
1044712 GAGAATCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.75
9 6 0.25
ACGTcount: A:0.48, C:0.03, G:0.12, T:0.36
Consensus pattern (8 bp):
TTGAAAAT
Found at i:1061847 original size:60 final size:59
Alignment explanation
Indices: 1061716--1061862 Score: 163
Period size: 60 Copynumber: 2.4 Consensus size: 59
1061706 GAATATATGA
** *
1061716 ATAGTCA-GGGATCCATTTTGTAACTTTTAATAGTCGGGGGACTCATCAAAGTATTGTCCT
1 ATAGTCAGGGGAT-CA-TTTGTAACTTTTAATAGTCAAGGGACTCAACAAAGTATTGTCCT
* *
1061776 ATGGTCAGGGGATCATTCTGTAACTTTTAATAGTCAAGGGACTCAACAAAGTAATT-TCTT
1 ATAGTCAGGGGATCATT-TGTAACTTTTAATAGTCAAGGGACTCAACAAAGT-ATTGTCCT
** *
1061836 ATAGTTGGGGGATTATTTGTATACTTT
1 ATAGTCAGGGGATCATTTGTA-ACTTT
1061863 ACCCATTCTA
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
59 6 0.08
60 60 0.81
61 8 0.11
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.37
Consensus pattern (59 bp):
ATAGTCAGGGGATCATTTGTAACTTTTAATAGTCAAGGGACTCAACAAAGTATTGTCCT
Found at i:1087139 original size:60 final size:60
Alignment explanation
Indices: 1087043--1087159 Score: 198
Period size: 60 Copynumber: 1.9 Consensus size: 60
1087033 GTTAAAAGAA
* *
1087043 TATTTACTTGACTTGAGCATAGATGCTTAGCCAGCATGAAATTTTTAACTATCATGGTTT
1 TATTTACTTGACTTGAGCATAGATGCTTAGCAAGCATGAAATTTTGAACTATCATGGTTT
* *
1087103 TATTTACTTGACTTGAGCGTAGATGCTTAGCAAGCATGATATTTTGAACTATCATGG
1 TATTTACTTGACTTGAGCATAGATGCTTAGCAAGCATGAAATTTTGAACTATCATGG
1087160 GTTTGCAGGA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (60 bp):
TATTTACTTGACTTGAGCATAGATGCTTAGCAAGCATGAAATTTTGAACTATCATGGTTT
Found at i:1109393 original size:29 final size:28
Alignment explanation
Indices: 1109361--1109425 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 28
1109351 ACCTTTTTAT
1109361 ATTTTTAATTTTGTTAAAAAATTATATAA
1 ATTTTTAATTTTGTTAAAAAA-TATATAA
* * * *
1109390 ATTTTATGATTTTTTTTAAATATATATAA
1 ATTTT-TAATTTTGTTAAAAAATATATAA
1109419 ATATTTT
1 AT-TTTT
1109426 TCAACTTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (28 bp):
ATTTTTAATTTTGTTAAAAAATATATAA
Found at i:1112042 original size:14 final size:14
Alignment explanation
Indices: 1112010--1112040 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
1112000 TATATCATTT
1112010 AAAATTATATTTTA
1 AAAATTATATTTTA
1112024 AAAATTAT-TTTTA
1 AAAATTATATTTTA
1112037 AAAA
1 AAAA
1112041 ATAAAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AAAATTATATTTTA
Found at i:1112078 original size:6 final size:6
Alignment explanation
Indices: 1112063--1112100 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
1112053 AAACAACTCG
1112063 CCCT-C CCCTCC CCCTCC CCCTCC CCCTCC CCCTCC CCC
1 CCCTCC CCCTCC CCCTCC CCCTCC CCCTCC CCCTCC CCC
1112101 AACCTTTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.00, C:0.84, G:0.00, T:0.16
Consensus pattern (6 bp):
CCCTCC
Found at i:1123371 original size:15 final size:16
Alignment explanation
Indices: 1123351--1123416 Score: 50
Period size: 15 Copynumber: 4.3 Consensus size: 16
1123341 ATAATTCTAA
1123351 ATAAATAATAATT-AT
1 ATAAATAATAATTAAT
* *
1123366 ATAAATATTATTTTAAT
1 ATAAATAATA-ATTAAT
* * *
1123383 AAAAATAAT-ATTTAC
1 ATAAATAATAATTAAT
1123398 ATAAAT-AT-ATTAAT
1 ATAAATAATAATTAAT
1123412 ATAAA
1 ATAAA
1123417 ATATAATAAC
Statistics
Matches: 39, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
14 11 0.28
15 17 0.44
16 2 0.05
17 9 0.23
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
ATAAATAATAATTAAT
Found at i:1123423 original size:32 final size:32
Alignment explanation
Indices: 1123353--1123425 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
1123343 AATTCTAAAT
* *
1123353 AAATAATAATTATATAAATATTATTTTAATAA
1 AAATAATAATTACATAAATATTATTATAATAA
*
1123385 AAATAATATTTACATAAATA-TATTA-ATATAA
1 AAATAATAATTACATAAATATTATTATA-ATAA
1123416 AATATAATAA
1 AA-ATAATAA
1123426 CTATTTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
30 1 0.03
31 10 0.29
32 24 0.69
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (32 bp):
AAATAATAATTACATAAATATTATTATAATAA
Found at i:1125295 original size:18 final size:17
Alignment explanation
Indices: 1125265--1125298 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1125255 ATATTTAATT
*
1125265 ATATAAAATATAATATA
1 ATATAAAACATAATATA
1125282 ATATGAAAACATAATAT
1 ATAT-AAAACATAATAT
1125299 TGTGATCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (17 bp):
ATATAAAACATAATATA
Found at i:1125402 original size:17 final size:18
Alignment explanation
Indices: 1125380--1125414 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
1125370 TATAATTCTA
1125380 AATAATTATAT-TTTTAC
1 AATAATTATATATTTTAC
1125397 AATAATTATATATTTTAC
1 AATAATTATATATTTTAC
1125415 CTCATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (18 bp):
AATAATTATATATTTTAC
Found at i:1127428 original size:17 final size:17
Alignment explanation
Indices: 1127385--1127436 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
1127375 TTTACAGTAG
*
1127385 AAACTCTTTAAATTAAT
1 AAACTCTCTAAATTAAT
**
1127402 --ACTCAGTAAATTAAT
1 AAACTCTCTAAATTAAT
*
1127417 AAACTCTCTAAAATAAT
1 AAACTCTCTAAATTAAT
1127434 AAA
1 AAA
1127437 TTTGTCCGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (17 bp):
AAACTCTCTAAATTAAT
Found at i:1132538 original size:19 final size:19
Alignment explanation
Indices: 1132514--1132599 Score: 73
Period size: 19 Copynumber: 4.2 Consensus size: 19
1132504 GCGATTTTGA
*
1132514 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTG
* * *
1132533 AAAATGTATTGTGAGAGTTTG
1 AAAATGTGTTGCGATAG--TG
1132554 AAAAACGTGTTGTTGCGATAGTG
1 -AAAA--TG-TGTTGCGATAGTG
*
1132577 AAAAAGTGTTGCGATAGTG
1 AAAATGTGTTGCGATAGTG
1132596 AAAA
1 AAAA
1132600 ATTCAAAATA
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
19 31 0.58
20 1 0.02
21 1 0.02
22 8 0.15
23 2 0.04
24 2 0.04
25 8 0.15
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.31
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTG
Found at i:1132600 original size:19 final size:19
Alignment explanation
Indices: 1132564--1132600 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1132554 AAAAACGTGT
1132564 TGTTGCGATAGTGAAAAAG
1 TGTTGCGATAGTGAAAAAG
1132583 TGTTGCGATAGTGAAAAA
1 TGTTGCGATAGTGAAAAA
1132601 TTCAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.30, T:0.27
Consensus pattern (19 bp):
TGTTGCGATAGTGAAAAAG
Found at i:1133050 original size:19 final size:20
Alignment explanation
Indices: 1132999--1133053 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
1132989 TCGTTGCGAT
1132999 TTTGGAAAATCGCAACGCGAA
1 TTTGGAAAATCGCAAC-CGAA
* **
1133020 CTTGGACTATCGCAA-CGAA
1 TTTGGAAAATCGCAACCGAA
1133039 TTTGGAAAATCGCAA
1 TTTGGAAAATCGCAA
1133054 TGCGATAGTC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
19 16 0.57
21 12 0.43
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (20 bp):
TTTGGAAAATCGCAACCGAA
Found at i:1133116 original size:20 final size:19
Alignment explanation
Indices: 1133093--1133138 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1133083 GGAAACTGAT
* *
1133093 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
1133113 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
1133132 TTGCGAT
1 TTGCGAT
1133139 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:1133128 original size:19 final size:19
Alignment explanation
Indices: 1133104--1133140 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1133094 TGCGATACTG
*
1133104 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
1133123 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
1133141 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:1133666 original size:21 final size:21
Alignment explanation
Indices: 1133640--1133721 Score: 103
Period size: 21 Copynumber: 4.0 Consensus size: 21
1133630 CACGTTGTGA
*
1133640 TATCGCAATGCGAATTTGGAC
1 TATCGCAACGCGAATTTGGAC
* *
1133661 TATCGCAACGCGAA-ATGGAA
1 TATCGCAACGCGAATTTGGAC
* * *
1133681 AATCACAACACGAATTTGGAC
1 TATCGCAACGCGAATTTGGAC
1133702 TATCGCAACGCGAATTTGGA
1 TATCGCAACGCGAATTTGGA
1133722 TACTGAGTTG
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 15 0.31
21 34 0.69
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (21 bp):
TATCGCAACGCGAATTTGGAC
Found at i:1137941 original size:34 final size:34
Alignment explanation
Indices: 1137898--1137962 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
1137888 CAAACAACGT
1137898 AATTGGTTTTCTGGAATTGATTTTCCAGAAATGC
1 AATTGGTTTTCTGGAATTGATTTTCCAGAAATGC
1137932 AATTGGTTTTCTGGAATTGATTTTCCAGAAA
1 AATTGGTTTTCTGGAATTGATTTTCCAGAAA
1137963 ACCAATTACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.42
Consensus pattern (34 bp):
AATTGGTTTTCTGGAATTGATTTTCCAGAAATGC
Found at i:1140535 original size:136 final size:136
Alignment explanation
Indices: 1140291--1140555 Score: 342
Period size: 136 Copynumber: 1.9 Consensus size: 136
1140281 CCCAATTAAC
* * *
1140291 ATGGAAAATAGAAGAACACAACAATGCGCCAAAGAGAATTGAACTTGTGTATTTGGGGAGAATAA
1 ATGGAAAATAGAAGAACACAACAATGCGCCAAAGAGAATCGAACTTGTGTATTAGGAGAGAATAA
* *
1140356 TCAGGCGCCCAAACCATTGGGATAAGGGTCTCATATGATTCTAACTTACAACAATTTGTATTTTA
66 CCAGGCGCCCAAACCATTGGGATAAGGGTCCCATATGATTCTAACTTACAACAATTTGTATTTTA
1140421 CTTGAA
131 CTTGAA
* * * * *
1140427 ATGGAAAATTGAAGAACA-AA-TATGCGCCCAAGGAGAATCGAA-TCTGTGTCTGTAGGAGAGAG
1 ATGGAAAATAGAAGAACACAACAATGCG-CCAAAGAGAATCGAACT-TGTGTAT-TAGGAGAGAA
* *
1140489 TAACCAGGCGCCCAAACCATTGGGCTAAGGGTCCCGA-AT-AGTTCTAATTTACAACAATTTGTA
63 TAACCAGGCGCCCAAACCATTGGGATAAGGGTCCC-ATATGA-TTCTAACTTACAACAATTTGTA
1140552 TTTT
126 TTTT
1140556 TCTTTCAAAA
Statistics
Matches: 112, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
134 6 0.05
135 22 0.20
136 83 0.74
137 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.26
Consensus pattern (136 bp):
ATGGAAAATAGAAGAACACAACAATGCGCCAAAGAGAATCGAACTTGTGTATTAGGAGAGAATAA
CCAGGCGCCCAAACCATTGGGATAAGGGTCCCATATGATTCTAACTTACAACAATTTGTATTTTA
CTTGAA
Found at i:1140679 original size:61 final size:63
Alignment explanation
Indices: 1140582--1140725 Score: 168
Period size: 64 Copynumber: 2.3 Consensus size: 63
1140572 TAATGATAAA
**
1140582 AAATTTCGGTTCGATTAATGGTTAAAGAAAAAAATTT-GGTTAAT-G-TAAATAATTTTCAAAT
1 AAATTTCGGTTCGATTAA-CATTAAAGAAAAAAATTTAGGTTAATCGATAAATAATTTTCAAAT
* ** * *
1140643 AAATTTCGGTTCGATTAACATTAAGGAAAAATAATTTATTTTATTCGATTAATAATTTTCAAAT
1 AAATTTCGGTTCGATTAACATTAAAGAAAAA-AATTTAGGTTAATCGATAAATAATTTTCAAAT
* *
1140707 AAATTTTGATTCGATTAAC
1 AAATTTCGGTTCGATTAAC
1140726 GATCAAATAA
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
60 10 0.14
61 23 0.33
62 4 0.06
63 1 0.01
64 32 0.46
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.40
Consensus pattern (63 bp):
AAATTTCGGTTCGATTAACATTAAAGAAAAAAATTTAGGTTAATCGATAAATAATTTTCAAAT
Found at i:1140795 original size:94 final size:91
Alignment explanation
Indices: 1140637--1140818 Score: 242
Period size: 94 Copynumber: 2.0 Consensus size: 91
1140627 TAAATAATTT
* *
1140637 TCAAATAAATTTCGGTTCGATTAACATTAAGGAAAAATAATTTATTTTATTCGATTAATAATTTT
1 TCAAATAAATTTCGGTTCGATTAACATTAAAGAAAAATAATTTATTTGATTCGATTAATAATTTT
1140702 CAAATAAATTTTGATTCGATTAACGA
66 CAAATAAATTTTGATTCGATTAACGA
** * *
1140728 TCAAAT-AATTTCGGTTCGATTAATGGTTAAAGAAAAA-AATCGGTTGATTTGGTTCGGTTAATA
1 TCAAATAAATTTCGGTTCGATTAA-CATTAAAGAAAAATAAT---TT-ATTTGATTCGATTAATA
*
1140791 ATTTTCAAATAAATTTTGGTTCGATTAA
61 ATTTTCAAATAAATTTTGATTCGATTAA
1140819 TGGTTAAGGA
Statistics
Matches: 79, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
90 20 0.25
91 16 0.20
93 2 0.03
94 41 0.52
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (91 bp):
TCAAATAAATTTCGGTTCGATTAACATTAAAGAAAAATAATTTATTTGATTCGATTAATAATTTT
CAAATAAATTTTGATTCGATTAACGA
Found at i:1140868 original size:66 final size:68
Alignment explanation
Indices: 1140728--1140884 Score: 205
Period size: 66 Copynumber: 2.4 Consensus size: 68
1140718 CGATTAACGA
** *
1140728 TCAAAT-AATTTCGGTTCGATTAATGGTTAAAGAAAAAAATCGGTTGATTTGGTTCGGTTAATAA
1 TCAAATAAATTTCGGTTCGATTAATGGTTAAAGAAAAAAATCAATTGATTTGATTCGGTTAATAA
1140792 TTT
66 TTT
* * *
1140795 TCAAATAAATTTTGGTTCGATTAATGGTT-AAGGAAAAAAT-AATAT-ATTTTATTCGGTTAATA
1 TCAAATAAATTTCGGTTCGATTAATGGTTAAAGAAAAAAATCAAT-TGATTTGATTCGGTTAATA
1140857 ATTT
65 ATTT
* *
1140861 TTAAATAAATTTCGATTCGATTAA
1 TCAAATAAATTTCGGTTCGATTAA
1140885 CGATCAAATA
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
66 41 0.52
67 17 0.22
68 21 0.27
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.41
Consensus pattern (68 bp):
TCAAATAAATTTCGGTTCGATTAATGGTTAAAGAAAAAAATCAATTGATTTGATTCGGTTAATAA
TTT
Found at i:1140869 original size:160 final size:158
Alignment explanation
Indices: 1140583--1141078 Score: 667
Period size: 160 Copynumber: 3.2 Consensus size: 158
1140573 AATGATAAAA
* ** *
1140583 AATTTCGGTTCGATTAATGGTTAAAGAAAAAAAT---TTG-GTT-AAT--GTAAATAATTTTCAA
1 AATTTCGGTTCGATTAATGGTTAAAGAAAAAAATCGGTTGATTTGGTTCGGTTAATAATTTTCAA
* ** *
1140641 ATAAATTTCGGTTCGATTAACATTAAGGAAAAATAATTTATTTTATTCGATTAATAATTTTCAAA
66 ATAAATTTTGGTTCGATTAAGGTTAAGGAAAAATAATTTATTTTATTCGGTTAATAATTTTCAAA
*
1140706 TAAATTTTGATTCGATTAACGATCAAAT
131 TAAATTTCGATTCGATTAACGATCAAAT
1140734 AATTTCGGTTCGATTAATGGTTAAAGAAAAAAATCGGTTGATTTGGTTCGGTTAATAATTTTCAA
1 AATTTCGGTTCGATTAATGGTTAAAGAAAAAAATCGGTTGATTTGGTTCGGTTAATAATTTTCAA
* *
1140799 ATAAATTTTGGTTCGATTAATGGTTAAGGAAAAAATAATATATTTTATTCGGTTAATAATTTTTA
66 ATAAATTTTGGTTCGATTAA-GGTTAAGG-AAAAATAATTTATTTTATTCGGTTAATAATTTTCA
1140864 AATAAATTTCGATTCGATTAACGATCAAAT
129 AATAAATTTCGATTCGATTAACGATCAAAT
* * * *
1140894 AATTTCGGTTCGATCAATGATTAAAGAAAAAAATCGGTTAATTTGGTTCGATTAATAATTTTCAA
1 AATTTCGGTTCGATTAATGGTTAAAGAAAAAAATCGGTTGATTTGGTTCGGTTAATAATTTTCAA
* *
1140959 ATAAATTTTGTTTTGATTAACGGTT------AAATAATTTATTTTATTCGGTTAATAATTTTCAA
66 ATAAATTTTGGTTCGATTAA-GGTTAAGGAAAAATAATTTATTTTATTCGGTTAATAATTTTCAA
* * * *
1141018 ATAAATTTGGGTTCAATTAACGGTCAAAT
130 ATAAATTTCGATTCGATTAACGATCAAAT
* *
1141047 AATTTTGGTTCCATTAATGGTTAAAGAAAAAA
1 AATTTCGGTTCGATTAATGGTTAAAGAAAAAA
1141079 TTTGGTTAAT
Statistics
Matches: 308, Mismatches: 28, Indels: 16
0.88 0.08 0.05
Matches are distributed among these distances:
151 34 0.11
153 85 0.28
154 3 0.01
155 2 0.01
156 1 0.00
158 33 0.11
159 6 0.02
160 144 0.47
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (158 bp):
AATTTCGGTTCGATTAATGGTTAAAGAAAAAAATCGGTTGATTTGGTTCGGTTAATAATTTTCAA
ATAAATTTTGGTTCGATTAAGGTTAAGGAAAAATAATTTATTTTATTCGGTTAATAATTTTCAAA
TAAATTTCGATTCGATTAACGATCAAAT
Found at i:1141015 original size:59 final size:59
Alignment explanation
Indices: 1140940--1141051 Score: 170
Period size: 59 Copynumber: 1.9 Consensus size: 59
1140930 GTTAATTTGG
* * ** *
1140940 TTCGATTAATAATTTTCAAATAAATTTTGTTTTGATTAACGGTTAAATAATTTATTTTA
1 TTCGATTAATAATTTTCAAATAAATTTGGGTTCAATTAACGGTCAAATAATTTATTTTA
*
1140999 TTCGGTTAATAATTTTCAAATAAATTTGGGTTCAATTAACGGTCAAATAATTT
1 TTCGATTAATAATTTTCAAATAAATTTGGGTTCAATTAACGGTCAAATAATTT
1141052 TGGTTCCATT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 47 1.00
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.46
Consensus pattern (59 bp):
TTCGATTAATAATTTTCAAATAAATTTGGGTTCAATTAACGGTCAAATAATTTATTTTA
Found at i:1141095 original size:80 final size:81
Alignment explanation
Indices: 1140998--1141169 Score: 258
Period size: 80 Copynumber: 2.1 Consensus size: 81
1140988 AATTTATTTT
* * * *
1140998 ATTCGGTTAATAATTTTCAAATAAATTTGGGTTCAATTAACGGTCAAATAATTTTGGTTCCATTA
1 ATTCGGTTAATAATTTTCAAATAAATTTAGATTCAATTAACGGACAAATAATTTCGGTTCCATTA
1141063 ATGGTTAAAG-AAA-AA
66 AT-GTTAAAGAAAACAA
* * *
1141078 ATTTGGTTAATAATTTTCAAATAAATTTAGATTCGATTAACGGACAAATAATTTCGGTTCGATTA
1 ATTCGGTTAATAATTTTCAAATAAATTTAGATTCAATTAACGGACAAATAATTTCGGTTCCATTA
1141143 ATGTTAAAGAAAACAA
66 ATGTTAAAGAAAACAA
1141159 ATTCGGTTAAT
1 ATTCGGTTAAT
1141170 TTGTTTCGAT
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
79 7 0.09
80 63 0.77
81 12 0.15
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.37
Consensus pattern (81 bp):
ATTCGGTTAATAATTTTCAAATAAATTTAGATTCAATTAACGGACAAATAATTTCGGTTCCATTA
ATGTTAAAGAAAACAA
Found at i:1141247 original size:95 final size:95
Alignment explanation
Indices: 1141084--1141311 Score: 384
Period size: 95 Copynumber: 2.4 Consensus size: 95
1141074 AAAAATTTGG
* * *
1141084 TTAATAATTTTCAAATAAATTTAGATTCGATTAACGGACAAATAATTTCGGTTCGATTAATGTTA
1 TTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGTTA
* * *
1141149 AAGAAAACAAATTCGGTTAATTTGTTTCGA
66 AAGAAAAAAAATTCGGTTAATTTGGTTCAA
*
1141179 TTAATAATTTTCAAATAAATTTCGGTTTGATTAACGGTCAAATAATTTCGGTTCGATTAATGTTA
1 TTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGTTA
1141244 AAGAAAAAAAATTCGGTTAATTTGGTTCAA
66 AAGAAAAAAAATTCGGTTAATTTGGTTCAA
*
1141274 TTCATAATTTTCAAATAAATTTCGGTTCGATTAACGGT
1 TTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGT
1141312 TAAAAAAAAT
Statistics
Matches: 124, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
95 124 1.00
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (95 bp):
TTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGTTA
AAGAAAAAAAATTCGGTTAATTTGGTTCAA
Found at i:1144631 original size:28 final size:28
Alignment explanation
Indices: 1144599--1144652 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
1144589 ATATTTTCTT
1144599 GTATTAGTAATCTAGTACTGTGTTGCAA
1 GTATTAGTAATCTAGTACTGTGTTGCAA
* *
1144627 GTATTAGTAATTTAGTATTGTGTTGC
1 GTATTAGTAATCTAGTACTGTGTTGC
1144653 GAATGCACCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.26, C:0.07, G:0.22, T:0.44
Consensus pattern (28 bp):
GTATTAGTAATCTAGTACTGTGTTGCAA
Found at i:1161549 original size:13 final size:13
Alignment explanation
Indices: 1161519--1161543 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1161509 TATAATTAAA
1161519 ATTAAATTTTATT
1 ATTAAATTTTATT
1161532 ATTAAATTTTAT
1 ATTAAATTTTAT
1161544 AGTTAATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTAAATTTTATT
Found at i:1162074 original size:96 final size:96
Alignment explanation
Indices: 1161910--1162088 Score: 245
Period size: 96 Copynumber: 1.9 Consensus size: 96
1161900 GGAATAACAA
* * * * *
1161910 GTGATTGATACGTGATCGTCGCTGGTAGTTCGAGGAATACACTCCGCGTGATTGAGAATTCACAT
1 GTGATTGACACGTGATCGTCACTGATAGTTCGAGGAATACACTCCGCGTGATTGAAAATCCACAT
*
1161975 AAATCTTACATTCGCATCTTTGGAGATTTAG
66 AAATCTTACATTCACATCTTTGGAGATTTAG
* * *
1162006 GTGATTGACACGTGATCGTCACTGATAGTTCGCGGAATACGCTCCGCGTG-TCT-AAAAGTCCGC
1 GTGATTGACACGTGATCGTCACTGATAGTTCGAGGAATACACTCCGCGTGAT-TGAAAA-TCCAC
1162069 ATAAATCTTACATTCACATC
64 ATAAATCTTACATTCACATC
1162089 CCTGGAGGTT
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
95 4 0.06
96 68 0.94
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.30
Consensus pattern (96 bp):
GTGATTGACACGTGATCGTCACTGATAGTTCGAGGAATACACTCCGCGTGATTGAAAATCCACAT
AAATCTTACATTCACATCTTTGGAGATTTAG
Found at i:1166946 original size:26 final size:26
Alignment explanation
Indices: 1166892--1166958 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 26
1166882 TATATTTTTA
1166892 TTAAAATTTTATTTTTGCTTCTAAAATT
1 TTAAAA-TTTA-TTTTGCTTCTAAAATT
*
1166920 TTATAAATTTATTTT-CTTTTAAAATT
1 TTA-AAATTTATTTTGCTTCTAAAATT
*
1166946 TTAAAATTCATTT
1 TTAAAATTTATTT
1166959 CCTAAAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
25 9 0.25
26 13 0.36
27 4 0.11
28 7 0.19
29 3 0.08
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.58
Consensus pattern (26 bp):
TTAAAATTTATTTTGCTTCTAAAATT
Found at i:1171954 original size:2 final size:2
Alignment explanation
Indices: 1171949--1171976 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1171939 GTTTTTTAAA
1171949 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
1171977 TATTTTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1172286 original size:2 final size:2
Alignment explanation
Indices: 1172279--1172329 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1172269 GTATCTAAAC
1172279 TA TA TA TA TA 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
1172321 TA TA TA TA T
1 TA TA TA TA T
1172330 CATTTATGTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1173796 original size:2 final size:2
Alignment explanation
Indices: 1173789--1173813 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1173779 ATTATATGAT
1173789 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1173814 GTGATGGGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1174328 original size:32 final size:31
Alignment explanation
Indices: 1174287--1174378 Score: 89
Period size: 32 Copynumber: 2.9 Consensus size: 31
1174277 AGTCGAGGGT
*
1174287 TTACCTATGTTCTACGGAACATATGGACATAA
1 TTACCTATGTTCTACGGAACATAT-GACACAA
* *
1174319 TTACCTATG-TCTTTCGGGACATATGA-ACAA
1 TTACCTATGTTC-TACGGAACATATGACACAA
* *
1174349 TATACCTATGTTATAAGGAACATATAGACA
1 T-TACCTATGTTCTACGGAACATAT-GACA
1174379 GTTTACCTAG
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
30 4 0.08
31 21 0.44
32 22 0.46
33 1 0.02
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (31 bp):
TTACCTATGTTCTACGGAACATATGACACAA
Found at i:1174386 original size:31 final size:29
Alignment explanation
Indices: 1174285--1174387 Score: 82
Period size: 31 Copynumber: 3.3 Consensus size: 29
1174275 AGAGTCGAGG
1174285 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTT-TACGGAACATAT-GACA
* *
1174316 -TAATTACCTATGTCTTTCGGGACATATGAACA
1 GT--TTACCTATGT-TTACGGAACATATG-ACA
* * *
1174348 ATATACCTATGTTATAAGGAACATATAGACA
1 GTTTACCTATGTT-TACGGAACATAT-GACA
1174379 GTTTACCTA
1 GTTTACCTA
1174388 GGTTCTTCGG
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
30 2 0.04
31 29 0.51
32 24 0.42
33 2 0.04
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (29 bp):
GTTTACCTATGTTTACGGAACATATGACA
Found at i:1178392 original size:17 final size:17
Alignment explanation
Indices: 1178351--1178395 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1178341 CCATACTTGA
1178351 TTAAATATTTAATAAAT
1 TTAAATATTTAATAAAT
** **
1178368 TTCTATATTTTTTAAAT
1 TTAAATATTTAATAAAT
1178385 TTAAATATTTA
1 TTAAATATTTA
1178396 TTTTTACGTG
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAAATATTTAATAAAT
Found at i:1181315 original size:29 final size:31
Alignment explanation
Indices: 1181273--1181334 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
1181263 TGATGATTGA
1181273 TACTTGTATCAA-T-TATATACTTTTTTATT
1 TACTTGTATCAATTATATATACTTTTTTATT
* *
1181302 TACTTGTATTAATTATATATATTTTTTTATT
1 TACTTGTATCAATTATATATACTTTTTTATT
1181333 TA
1 TA
1181335 GTTTTCTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 11 0.38
30 1 0.03
31 17 0.59
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.61
Consensus pattern (31 bp):
TACTTGTATCAATTATATATACTTTTTTATT
Found at i:1206355 original size:52 final size:52
Alignment explanation
Indices: 1206277--1206387 Score: 222
Period size: 52 Copynumber: 2.1 Consensus size: 52
1206267 ACGCCTCCCA
1206277 TTCCAAATTCAACAAGCTTCTCATTTGGTTCTGTTATGCAATCTAGGAAGAG
1 TTCCAAATTCAACAAGCTTCTCATTTGGTTCTGTTATGCAATCTAGGAAGAG
1206329 TTCCAAATTCAACAAGCTTCTCATTTGGTTCTGTTATGCAATCTAGGAAGAG
1 TTCCAAATTCAACAAGCTTCTCATTTGGTTCTGTTATGCAATCTAGGAAGAG
1206381 TTCCAAA
1 TTCCAAA
1206388 ACATTAAGCT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 59 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (52 bp):
TTCCAAATTCAACAAGCTTCTCATTTGGTTCTGTTATGCAATCTAGGAAGAG
Found at i:1218076 original size:29 final size:25
Alignment explanation
Indices: 1218017--1218077 Score: 68
Period size: 29 Copynumber: 2.2 Consensus size: 25
1218007 TTCTAATATA
*
1218017 ATATAATTAAAAATTAAAATTTAAT
1 ATATAATTAAAAATGAAAATTTAAT
1218042 ACTATAATTGAAATAATGGAAAATTTAAT
1 A-TATAATT-AAA-AAT-GAAAATTTAAT
1218071 GATATAA
1 -ATATAA
1218078 AGTTGAATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 1 0.03
26 7 0.23
27 3 0.10
28 3 0.10
29 15 0.50
30 1 0.03
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (25 bp):
ATATAATTAAAAATGAAAATTTAAT
Found at i:1224244 original size:20 final size:20
Alignment explanation
Indices: 1224150--1224518 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
1224140 GATTTTCCAT
* ** *
1224150 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1224170 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1224190 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1224210 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
1224230 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
1224250 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1224270 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1224290 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1224310 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1224330 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1224350 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1224370 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1224390 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
1224410 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1224430 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1224450 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1224470 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1224490 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1224510 AATCACAAC
1 AATCGCAAC
1224519 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1225240 original size:24 final size:24
Alignment explanation
Indices: 1225201--1225247 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1225191 AAATTTGGTC
1225201 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1225225 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1225248 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1225439 original size:12 final size:12
Alignment explanation
Indices: 1225422--1225446 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1225412 ATATAATCCT
1225422 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1225434 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1225446 G
1 G
1225447 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1227751 original size:19 final size:19
Alignment explanation
Indices: 1227729--1228035 Score: 376
Period size: 19 Copynumber: 17.4 Consensus size: 19
1227719 CGGAAAATAC
*
1227729 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1227748 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1227762 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1227782 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1227796 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1227815 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1227834 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1227848 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1227867 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1227886 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
1227900 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
1227919 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1227938 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1227957 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1227976 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
1227990 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1228009 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1228028 AATCGCAA
1 AATCGCAA
1228036 CGAGATAATC
Statistics
Matches: 252, Mismatches: 10, Indels: 52
0.80 0.03 0.17
Matches are distributed among these distances:
14 48 0.19
15 2 0.01
16 16 0.06
17 14 0.06
18 3 0.01
19 156 0.62
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1227844 original size:52 final size:52
Alignment explanation
Indices: 1227757--1228035 Score: 388
Period size: 52 Copynumber: 5.2 Consensus size: 52
1227747 AAATCCCAAC
1227757 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1227810 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
1227862 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
1227914 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
1227971 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
1228023 ATGAAAATCGCAA
1 ATGAAAATCGCAA
1228036 CGAGATAATC
Statistics
Matches: 216, Mismatches: 5, Indels: 11
0.93 0.02 0.05
Matches are distributed among these distances:
52 164 0.76
53 16 0.07
54 3 0.01
55 5 0.02
56 1 0.00
57 27 0.12
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:1227880 original size:71 final size:71
Alignment explanation
Indices: 1227796--1228035 Score: 373
Period size: 71 Copynumber: 3.4 Consensus size: 71
1227786 GCAACGAGAG
*
1227796 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1227861 AATGAA
66 AATGAA
* *
1227867 AATCGCAATGCGAAATGAAAATCGCAA--CGACA-G--AATCGCAATGCGAAATTAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG-AA--AGAATCGCAA
1227927 TGCGAAATGAA
61 TGCGAAATGAA
1227938 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1228003 AATGAA
66 AATGAA
1228009 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
1228036 CGAGATAATC
Statistics
Matches: 154, Mismatches: 5, Indels: 20
0.86 0.03 0.11
Matches are distributed among these distances:
66 8 0.05
68 3 0.02
69 5 0.03
71 121 0.79
73 6 0.04
74 3 0.02
76 8 0.05
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAA
Found at i:1227981 original size:142 final size:138
Alignment explanation
Indices: 1227729--1228073 Score: 518
Period size: 142 Copynumber: 2.5 Consensus size: 138
1227719 CGGAAAATAC
* * *
1227729 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAA--CG
1 AATCGCAATGCGAAATGAAAATCGCAAC--GAAAATCGCAATGC-GAAATTAAAATCGCAATGCG
* *
1227792 -AGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAA
63 AAGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAA
1227856 TGCGAAATGAA
128 TGCGAAATGAA
1227867 AATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATTAAAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-A-AATCGCAATGCGAAATTAAAATCGCAATGCG-
1227932 AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
63 AA-GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
1227997 ATGCGAAATGAA
127 ATGCGAAATGAA
*
1228009 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATTATAAA-CGCATTGCG
1 AATCGCAATGCGAAATGAAAATCGCAACGA-A-AATCGCAATGCGAAATTA-AAATCGCAATGCG
1228073 A
63 A
1228074 TTTTCATTTC
Statistics
Matches: 191, Mismatches: 8, Indels: 13
0.90 0.04 0.06
Matches are distributed among these distances:
136 2 0.01
137 16 0.08
138 37 0.19
139 2 0.01
141 2 0.01
142 129 0.68
143 3 0.02
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (138 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAATCGCAATGCGAAATTAAAATCGCAATGCGAAG
AAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGC
GAAATGAA
Found at i:1228036 original size:52 final size:55
Alignment explanation
Indices: 1227729--1228057 Score: 332
Period size: 52 Copynumber: 6.3 Consensus size: 55
1227719 CGGAAAATAC
* *
1227729 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GC-GAAATG-A
*
1227782 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
*
1227834 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
* *
1227886 AATCGCAA--CGACA-G--AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
1227938 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAAA-G-
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
*
1227990 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAT--
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
1228042 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
1228058 TATAAACGCA
Statistics
Matches: 257, Mismatches: 6, Indels: 27
0.89 0.02 0.09
Matches are distributed among these distances:
48 9 0.04
49 1 0.00
50 1 0.00
51 2 0.01
52 181 0.70
53 24 0.09
54 7 0.03
55 6 0.02
57 26 0.10
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (55 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
Found at i:1228173 original size:19 final size:19
Alignment explanation
Indices: 1228064--1228165 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1228054 AAATTATAAA
1228064 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1228083 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
1228103 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
1228119 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1228136 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1228155 CGCATTGCGAT
1 CGCATTGCGAT
1228166 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:1228291 original size:14 final size:14
Alignment explanation
Indices: 1228272--1228308 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1228262 CATCAATTAC
1228272 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1228286 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1228300 ACAAATCAA
1 ACAAATCAA
1228309 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1230283 original size:14 final size:14
Alignment explanation
Indices: 1230264--1230320 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1230254 GCGAAATGAA
*
1230264 AATCGCAACGACAG
1 AATCGCAACGAAAG
1230278 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1230295 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1230311 AATCGCAACG
1 AATCGCAACG
1230321 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1230291 original size:33 final size:33
Alignment explanation
Indices: 1230245--1230337 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1230235 GCGAAACCAA
*
1230245 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1230278 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1230311 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1230338 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1230302 original size:19 final size:19
Alignment explanation
Indices: 1230208--1230342 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1230198 TAGTTTACTT
* *
1230208 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1230228 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1230247 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1230266 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1230280 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1230299 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1230313 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1230332 TCGCAATGCGA
1 TCGCAACGCGA
1230343 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1230360 original size:19 final size:19
Alignment explanation
Indices: 1230338--1230466 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1230328 AAAATCGCAA
1230338 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1230357 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1230371 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1230390 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1230404 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1230423 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1230442 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1230462 TGCGA
1 TGCGA
1230467 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1230380 original size:33 final size:33
Alignment explanation
Indices: 1230338--1230429 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1230328 AAAATCGCAA
1230338 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1230371 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1230404 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1230430 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1230669 original size:93 final size:93
Alignment explanation
Indices: 1230510--1231167 Score: 1293
Period size: 93 Copynumber: 7.1 Consensus size: 93
1230500 TTGAATGGAT
1230510 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1230575 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1230603 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1230668 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1230696 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1230760 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1230788 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1230853 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1230881 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1230946 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1230974 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1231038 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1231066 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1231131 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1231159 AAATTTACT
1 AAATTTACT
1231168 AAGCAATCTA
Statistics
Matches: 562, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
92 184 0.33
93 378 0.67
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1230823 original size:185 final size:186
Alignment explanation
Indices: 1230510--1231167 Score: 1293
Period size: 185 Copynumber: 3.5 Consensus size: 186
1230500 TTGAATGGAT
1230510 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1230575 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1230640 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1230696 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1230760 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1230825 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1230881 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1230946 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1231011 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1231066 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1231131 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
1231168 AAGCAATCTA
Statistics
Matches: 470, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
185 339 0.72
186 131 0.28
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1231007 original size:278 final size:278
Alignment explanation
Indices: 1230510--1231167 Score: 1307
Period size: 278 Copynumber: 2.4 Consensus size: 278
1230500 TTGAATGGAT
1230510 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1230575 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1230640 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
1230705 TTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
196 TTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
1230770 AATTGGCAGCAACCGAAC
261 AATTGGCAGCAACCGAAC
1230788 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1230853 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1230918 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
1230983 TTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
196 TTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
1231048 AATTGGCAGCAACCGAAC
261 AATTGGCAGCAACCGAAC
1231066 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1231131 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
1231168 AAGCAATCTA
Statistics
Matches: 379, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
278 379 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (278 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
TTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
AATTGGCAGCAACCGAAC
Found at i:1232890 original size:14 final size:14
Alignment explanation
Indices: 1232871--1232960 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1232861 TTGAAATGAA
1232871 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1232885 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1232902 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1232918 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1232937 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1232951 AATCGCAACG
1 AATCGCAACG
1232961 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1232908 original size:33 final size:33
Alignment explanation
Indices: 1232863--1232977 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1232853 TCTTTTGGTT
1232863 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1232896 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1232929 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1232962 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1232978 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1232909 original size:19 final size:18
Alignment explanation
Indices: 1232870--1232982 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
1232860 GTTGAAATGA
1232870 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1232885 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1232902 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1232918 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1232935 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
1232951 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1232968 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1232983 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1233013 original size:14 final size:14
Alignment explanation
Indices: 1232994--1233048 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1232984 TTTGGTTTCG
1232994 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1233008 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1233027 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1233041 CGTTGCGA
1 CGTTGCGA
1233049 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1233026 original size:33 final size:33
Alignment explanation
Indices: 1232978--1233048 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1232968 AAAATCGCAA
**
1232978 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1233011 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1233044 TGCGA
1 TGCGA
1233049 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1233056 original size:33 final size:33
Alignment explanation
Indices: 1232989--1233070 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
1232979 GCGATTTTGG
***
1232989 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1233022 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
1233055 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
1233071 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:1233075 original size:20 final size:20
Alignment explanation
Indices: 1233001--1233089 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
1232991 TCGCGTTGCG
1233001 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1233021 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
1233034 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
1233054 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1233074 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
1233090 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1233211 original size:33 final size:33
Alignment explanation
Indices: 1233169--1233239 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1233159 AATACTAACT
*
1233169 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1233202 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1233235 TGAAA
1 TGAAA
1233240 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1233472 original size:22 final size:22
Alignment explanation
Indices: 1233420--1233474 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1233410 TGGTTGTGAG
**
1233420 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1233442 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1233464 GGATTTCTTCG
1 GGATTTCTTCG
1233475 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1233641 original size:20 final size:20
Alignment explanation
Indices: 1233616--1233808 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
1233606 CTTTAAATAT
1233616 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1233636 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1233658 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1233677 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1233697 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1233717 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1233737 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1233757 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1233777 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1233797 CGCGTTGCGATT
1 CGCGTTGCGATT
1233809 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1233803 original size:60 final size:60
Alignment explanation
Indices: 1233616--1233808 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
1233606 CTTTAAATAT
**
1233616 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1233677 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1233737 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1233797 CGCGTTGCGATT
1 CGCGTTGCGATT
1233809 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1233889 original size:20 final size:20
Alignment explanation
Indices: 1233864--1233915 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1233854 AAGAATCGCG
*
1233864 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1233884 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1233904 TTGCGATTCTGG
1 TTGCGATTCTGG
1233916 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:1239622 original size:19 final size:19
Alignment explanation
Indices: 1239594--1239631 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1239584 TTAATTGTTG
*
1239594 ACCGGTTTGACCGATCTGA
1 ACCGGGTTGACCGATCTGA
*
1239613 ACCGGGTTGACCGGTCTGA
1 ACCGGGTTGACCGATCTGA
1239632 CCCGACCCGT
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:0.18, C:0.26, G:0.32, T:0.24
Consensus pattern (19 bp):
ACCGGGTTGACCGATCTGA
Found at i:1239647 original size:13 final size:13
Alignment explanation
Indices: 1239629--1239653 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1239619 TTGACCGGTC
1239629 TGACCCGACCCGT
1 TGACCCGACCCGT
1239642 TGACCCGACCCG
1 TGACCCGACCCG
1239654 ACCCGGTGAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.48, G:0.24, T:0.12
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:1254657 original size:2 final size:2
Alignment explanation
Indices: 1254650--1254675 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1254640 TTATGCATAC
1254650 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
1254676 GAACATCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1258643 original size:29 final size:29
Alignment explanation
Indices: 1258612--1258673 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
1258602 TTAAATAAAT
* *
1258612 AAATAAATATTATTTAAATAAGTAATTTTA
1 AAAT-AATATTATGTAAATAAATAATTTTA
**
1258642 AAATAATATTATGTCTATAAATAATTTTA
1 AAATAATATTATGTAAATAAATAATTTTA
1258671 AAA
1 AAA
1258674 ACAAATATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (29 bp):
AAATAATATTATGTAAATAAATAATTTTA
Found at i:1260697 original size:21 final size:21
Alignment explanation
Indices: 1260671--1260711 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1260661 CTATAAACAG
*
1260671 TGCTACAGTGCATCGATGCAT
1 TGCTACAGTGCACCGATGCAT
1260692 TGCTACAGTGCACCGATGCA
1 TGCTACAGTGCACCGATGCA
1260712 CTAAAATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (21 bp):
TGCTACAGTGCACCGATGCAT
Found at i:1261506 original size:31 final size:31
Alignment explanation
Indices: 1261471--1261572 Score: 177
Period size: 31 Copynumber: 3.3 Consensus size: 31
1261461 CTGAATAACC
* *
1261471 TAGGTAATCGGTCCATATGTCCCGAAGAACA
1 TAGGTAAACAGTCCATATGTCCCGAAGAACA
*
1261502 TAGGTAAACAGCCCATATGTCCCGAAGAACA
1 TAGGTAAACAGTCCATATGTCCCGAAGAACA
1261533 TAGGTAAACAGTCCATATGTCCCGAAGAACA
1 TAGGTAAACAGTCCATATGTCCCGAAGAACA
1261564 TAGGTAAAC
1 TAGGTAAAC
1261573 TCTCGACCCT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 67 1.00
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.20
Consensus pattern (31 bp):
TAGGTAAACAGTCCATATGTCCCGAAGAACA
Found at i:1261869 original size:26 final size:25
Alignment explanation
Indices: 1261822--1261874 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
1261812 ACATAGCTCA
*
1261822 TCACATAGACATGTATTCTCATATAT
1 TCACATAGACATATATTCTCAT-TAT
*
1261848 TCACATATACATATCATT-TCATTAT
1 TCACATAGACATAT-ATTCTCATTAT
1261873 TC
1 TC
1261875 TTATTATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.21
26 16 0.67
27 3 0.12
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.42
Consensus pattern (25 bp):
TCACATAGACATATATTCTCATTAT
Found at i:1262858 original size:3 final size:3
Alignment explanation
Indices: 1262850--1262882 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1262840 CTCGTACATT
*
1262850 AAG AAG AAG AAG AAG AAG AAG AAG AAG ATG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1262883 TGGAGAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:1263673 original size:2 final size:2
Alignment explanation
Indices: 1263666--1263707 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1263656 TTATTTCATA
1263666 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1263708 TAATTACATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1264021 original size:21 final size:21
Alignment explanation
Indices: 1263978--1264022 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1263968 TATCGCATTA
* **
1263978 CGATTTTTCAAATTCGCGTTG
1 CGATTTTCCAAATTCGCAATG
*
1263999 CGATTTTCCTAATTCGCAATG
1 CGATTTTCCAAATTCGCAATG
1264020 CGA
1 CGA
1264023 ATACGTAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (21 bp):
CGATTTTCCAAATTCGCAATG
Found at i:1264037 original size:20 final size:20
Alignment explanation
Indices: 1264012--1264124 Score: 190
Period size: 20 Copynumber: 5.7 Consensus size: 20
1264002 TTTTCCTAAT
1264012 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1264032 TCGCAATGGGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1264052 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1264072 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
**
1264092 TCGCAATGCGAATATATAAA
1 TCGCAATGCGAATACGTAAA
*
1264112 TCGCAACGCGAAT
1 TCGCAATGCGAAT
1264125 CTGACTATCG
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 88 1.00
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1264373 original size:22 final size:22
Alignment explanation
Indices: 1264323--1264366 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1264313 GACATCCGTA
1264323 CCCATCTCCGACGAAATCAGTC
1 CCCATCTCCGACGAAATCAGTC
*
1264345 CCCATCTCCGACGATATCAGTC
1 CCCATCTCCGACGAAATCAGTC
1264367 TTCATCTTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.41, G:0.14, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCAGTC
Found at i:1264793 original size:20 final size:20
Alignment explanation
Indices: 1264773--1264895 Score: 98
Period size: 20 Copynumber: 6.5 Consensus size: 20
1264763 ATTCAAATTT
*
1264773 GCGTTGCGATAGTCATTTTT
1 GCGTTGCGATAGTCATTTTC
* **
1264793 GTGTTGCGATTTTCA-TTTC
1 GCGTTGCGATAGTCATTTTC
1264812 GCGTTGCGAT--TC---TT-
1 GCGTTGCGATAGTCATTTTC
* **
1264826 ACGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCATTTTC
1264846 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCATTTTC
* **
1264866 GTGTTGCGATTTTCATTTTC
1 GCGTTGCGATAGTCATTTTC
*
1264886 GTGTTGCGAT
1 GCGTTGCGAT
1264896 TTTAAGTTTC
Statistics
Matches: 85, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
14 9 0.11
15 2 0.02
16 2 0.02
17 2 0.02
19 14 0.16
20 56 0.66
ACGTcount: A:0.15, C:0.17, G:0.24, T:0.44
Consensus pattern (20 bp):
GCGTTGCGATAGTCATTTTC
Found at i:1264831 original size:53 final size:54
Alignment explanation
Indices: 1264774--1264876 Score: 136
Period size: 53 Copynumber: 1.9 Consensus size: 54
1264764 TTCAAATTTG
** * * **
1264774 CGTTGCGATAGTCATTTTTGTGTTGCGATTTTCA-TTTCGCGTTGCGATTCTTA
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCGTTGCGATTCTTA
*
1264827 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCGTTGCGATT
1264877 TTCATTTTCG
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
53 28 0.67
54 14 0.33
ACGTcount: A:0.16, C:0.17, G:0.24, T:0.43
Consensus pattern (54 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCGTTGCGATTCTTA
Found at i:1264842 original size:73 final size:73
Alignment explanation
Indices: 1264722--1264896 Score: 287
Period size: 73 Copynumber: 2.4 Consensus size: 73
1264712 CGATTCTGTC
* * *
1264722 GTTGCGATTTTCATTTCGCGTTGCGATTCTTGCGTTACGATATTCAAATTTGCGTTGCGATAGTC
1 GTTGCGATTTTCATTTCGCGTTGCGATTCTTACGTTACGATAGTCAAATTCGCGTTGCGATAGTC
*
1264787 ATTTTTGT
66 ATTTTCGT
*
1264795 GTTGCGATTTTCATTTCGCGTTGCGATTCTTACGTTGCGATAGTCAAATTCGCGTTGCGATAGTC
1 GTTGCGATTTTCATTTCGCGTTGCGATTCTTACGTTACGATAGTCAAATTCGCGTTGCGATAGTC
1264860 ATTTTCGT
66 ATTTTCGT
*
1264868 GTTGCGATTTTCATTTTCGTGTTGCGATT
1 GTTGCGATTTTCA-TTTCGCGTTGCGATT
1264897 TTAAGTTTCA
Statistics
Matches: 95, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
73 81 0.85
74 14 0.15
ACGTcount: A:0.15, C:0.17, G:0.23, T:0.45
Consensus pattern (73 bp):
GTTGCGATTTTCATTTCGCGTTGCGATTCTTACGTTACGATAGTCAAATTCGCGTTGCGATAGTC
ATTTTCGT
Found at i:1264905 original size:20 final size:20
Alignment explanation
Indices: 1264862--1264905 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1264852 CGATAGTCAT
* *
1264862 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
1264882 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
1264902 TTTC
1 TTTC
1264906 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:1266914 original size:20 final size:20
Alignment explanation
Indices: 1266851--1266917 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
1266841 CAACAACAAA
*
1266851 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
*
1266871 ATCACAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
1266891 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
1266911 ATCGCAA
1 ATCGCAA
1266918 CGAAAGAATC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:1266979 original size:20 final size:20
Alignment explanation
Indices: 1266954--1267016 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
1266944 ATCGCATTGT
** *
1266954 GATAGTCAAATTCGTGTTGC
1 GATAGTCATTTTCGCGTTGC
*
1266974 GATAGTCATTTTTGCGTTGC
1 GATAGTCATTTTCGCGTTGC
1266994 GATAGTCATTTTCGCGTTGC
1 GATAGTCATTTTCGCGTTGC
1267014 GAT
1 GAT
1267017 TTTAAGTTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.40
Consensus pattern (20 bp):
GATAGTCATTTTCGCGTTGC
Found at i:1267528 original size:21 final size:21
Alignment explanation
Indices: 1267501--1267586 Score: 84
Period size: 21 Copynumber: 4.1 Consensus size: 21
1267491 ACTCACCTGT
1267501 CATCGTTCAAGAGGCCTCC-CC
1 CATCGTTCAAGAGGCC-CCTCC
* *
1267522 TATCGTTCAAGAGTCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
* * **
1267543 CACCGTTCAAGAGGCCACTGT
1 CATCGTTCAAGAGGCCCCTCC
* *
1267564 CATCGTTGAAGAGGTCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
1267585 CA
1 CA
1267587 ACATTCTAGA
Statistics
Matches: 50, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
20 2 0.04
21 48 0.96
ACGTcount: A:0.21, C:0.37, G:0.20, T:0.22
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:1268998 original size:14 final size:14
Alignment explanation
Indices: 1268964--1269002 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1268954 TTGATTGTTT
1268964 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
1268978 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
1268992 TGTTGATTTGT
1 AATTGATTTGT
1269003 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1269147 original size:14 final size:14
Alignment explanation
Indices: 1269128--1269180 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
1269118 GGAAATGACT
1269128 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
* *
1269142 ATCGCAATGCGAAAATAA
1 ATCGCAA--CG-AGA-GA
1269160 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
1269174 ATCGCAA
1 ATCGCAA
1269181 TGCAAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 15 0.48
15 2 0.06
16 4 0.13
17 2 0.06
18 8 0.26
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:1269166 original size:32 final size:32
Alignment explanation
Indices: 1269128--1269192 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
1269118 GGAAATGACT
*
1269128 ATCGCAACGAGAGAATCGCAATGCGAAAATAA
1 ATCGCAACGAGAGAATCGCAATGCAAAAATAA
1269160 ATCGCAACGAGAGAATCGCAATGCAAAAATAA
1 ATCGCAACGAGAGAATCGCAATGCAAAAATAA
1269192 A
1 A
1269193 AATCGCAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.49, C:0.18, G:0.20, T:0.12
Consensus pattern (32 bp):
ATCGCAACGAGAGAATCGCAATGCAAAAATAA
Found at i:1269226 original size:20 final size:20
Alignment explanation
Indices: 1269173--1269232 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
1269163 GCAACGAGAG
*
1269173 AATCGCAATGCAAAAATAAA
1 AATCGCAATGCGAAAATAAA
* *
1269193 AATCGCAATACGAAAATGAA
1 AATCGCAATGCGAAAATAAA
*
1269213 AATCGCAATGCGAAACTAAA
1 AATCGCAATGCGAAAATAAA
1269233 TTCGCGTTGC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.55, C:0.17, G:0.13, T:0.15
Consensus pattern (20 bp):
AATCGCAATGCGAAAATAAA
Found at i:1269294 original size:33 final size:34
Alignment explanation
Indices: 1269237--1269309 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 34
1269227 ACTAAATTCG
1269237 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
* *
1269271 CGTTGCGATTTTCA-TTTCGCATTGTGATTCTTT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1269304 CGTTGC
1 CGTTGC
1269310 AATAGTCATT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
33 23 0.62
34 14 0.38
ACGTcount: A:0.11, C:0.22, G:0.19, T:0.48
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
Found at i:1269319 original size:33 final size:33
Alignment explanation
Indices: 1269252--1269321 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
1269242 CGATTTTCAT
* **
1269252 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTCTCTCGTTGCAATAGTCA
* *
1269285 TTTCGCATTGTGATTCTTTCGTTGCAATAGTCA
1 TTTCGCATTGCGATTCTCTCGTTGCAATAGTCA
1269318 TTTC
1 TTTC
1269322 CACGTTGCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTCTCTCGTTGCAATAGTCA
Found at i:1269329 original size:20 final size:19
Alignment explanation
Indices: 1269304--1269397 Score: 109
Period size: 20 Copynumber: 4.7 Consensus size: 19
1269294 GTGATTCTTT
* *
1269304 CGTTGCAATAGTCATTTCCA
1 CGTTGCGATAGTCATTT-CG
1269324 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
1269344 CGTTGCGATAGTCATTTC-
1 CGTTGCGATAGTCATTTCG
1269362 CGTACTGCGATAGTCATATTCG
1 CGT--TGCGATAGTCAT-TTCG
*
1269384 CGTTGCAATAGTCA
1 CGTTGCGATAGTCA
1269398 AATGAATGTC
Statistics
Matches: 67, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
18 3 0.04
19 1 0.01
20 57 0.85
21 3 0.04
22 3 0.04
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.34
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:1269359 original size:40 final size:39
Alignment explanation
Indices: 1269304--1269397 Score: 129
Period size: 40 Copynumber: 2.4 Consensus size: 39
1269294 GTGATTCTTT
1269304 CGTTGCAATAGTCATTTCCACGT-TGCGATAGTCAT-TTCCG
1 CGTTGCAATAGTCATTT-C-CGTATGCGATAGTCATATT-CG
*
1269344 CGTTGCGATAGTCATTTCCGTACTGCGATAGTCATATTCG
1 CGTTGCAATAGTCATTTCCGTA-TGCGATAGTCATATTCG
1269384 CGTTGCAATAGTCA
1 CGTTGCAATAGTCA
1269398 AATGAATGTC
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
38 3 0.06
39 1 0.02
40 43 0.88
41 2 0.04
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.34
Consensus pattern (39 bp):
CGTTGCAATAGTCATTTCCGTATGCGATAGTCATATTCG
Found at i:1271847 original size:24 final size:24
Alignment explanation
Indices: 1271813--1271866 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1271803 CTGAAAAATC
1271813 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1271837 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1271861 ATCAAA
1 ATCAAA
1271867 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1272737 original size:20 final size:20
Alignment explanation
Indices: 1272707--1272754 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1272697 GAAATTCAGT
* *
1272707 ATTGTGATAGTCATAATCGC
1 ATTGCGATAGTCAGAATCGC
* *
1272727 GTTGCGATAGTCAGATTCGC
1 ATTGCGATAGTCAGAATCGC
1272747 ATTGCGAT
1 ATTGCGAT
1272755 TTACGTATTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (20 bp):
ATTGCGATAGTCAGAATCGC
Found at i:1272764 original size:20 final size:20
Alignment explanation
Indices: 1272741--1272813 Score: 137
Period size: 20 Copynumber: 3.6 Consensus size: 20
1272731 CGATAGTCAG
1272741 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1272761 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
1272781 ATTCGCATTGCGATTCACGT
1 ATTCGCATTGCGATTTACGT
1272801 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1272814 ATTAGGAAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1272835 original size:21 final size:21
Alignment explanation
Indices: 1272811--1272850 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1272801 ATTCGCATTG
1272811 CGAATTAGGAAAATCGCAACA
1 CGAATTAGGAAAATCGCAACA
*
1272832 CGAATTTGGAAAATCGCAA
1 CGAATTAGGAAAATCGCAA
1272851 TGCGATAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.17
Consensus pattern (21 bp):
CGAATTAGGAAAATCGCAACA
Found at i:1274155 original size:5 final size:5
Alignment explanation
Indices: 1274145--1274177 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
1274135 ATATGTTTAA
1274145 TTATT TTATT TTATT TTATT TTATT TTATT TTA
1 TTATT TTATT TTATT TTATT TTATT TTATT TTA
1274178 ATGAAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:1281395 original size:12 final size:12
Alignment explanation
Indices: 1281378--1281421 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
1281368 TACGGATTGA
1281378 GTTTATATTTAT
1 GTTTATATTTAT
*
1281390 GTTTATGTTTAT
1 GTTTATATTTAT
1281402 GTTTATATTTAT
1 GTTTATATTTAT
*
1281414 ATTTATAT
1 GTTTATAT
1281422 ATAAATTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (12 bp):
GTTTATATTTAT
Found at i:1281420 original size:6 final size:6
Alignment explanation
Indices: 1281379--1281421 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
1281369 ACGGATTGAG
* * *
1281379 TTTATA TTTATG TTTATG TTTATG TTTATA TTTATA TTTATA T
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA T
1281422 ATAAATTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (6 bp):
TTTATA
Found at i:1281424 original size:2 final size:2
Alignment explanation
Indices: 1281405--1281587 Score: 50
Period size: 2 Copynumber: 94.5 Consensus size: 2
1281395 TGTTTATGTT
* * * * * *
1281405 TA TA TT TA TA TT TA TA TA TA AA T- TA TA TA TGC TA CA TA GTT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA -TA TA
* * * *
1281448 TA TA TA AA T- TA TA TA TGA -A T- TA TA TA TA AA CTA TA CA -A TT
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA -TA TA TA TA TA
* * *
1281488 TA TA TT TA TA TA T- TA TG TA TA -A T- TA TA AA TA -A 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
* * * * *
1281526 T- TG TA TA AA T- TA TA TA GTT TA T- TA -A TA TA AA CTA TA TA GTT
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA -TA
1281567 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
1281588 GGTTTAGGGG
Statistics
Matches: 127, Mismatches: 34, Indels: 40
0.63 0.17 0.20
Matches are distributed among these distances:
1 13 0.10
2 107 0.84
3 7 0.06
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1281461 original size:11 final size:11
Alignment explanation
Indices: 1281445--1281482 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
1281435 GCTACATAGT
1281445 TTATATATAAA
1 TTATATATAAA
*
1281456 TTATATATGAA
1 TTATATATAAA
1281467 TTATATATAAA
1 TTATATATAAA
*
1281478 CTATA
1 TTATA
1281483 CAATTTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (11 bp):
TTATATATAAA
Found at i:1281508 original size:17 final size:17
Alignment explanation
Indices: 1281488--1281541 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
1281478 CTATACAATT
* *
1281488 TATATTTATATATTATG
1 TATATTTATAAATTATA
* *
1281505 TATAATTATAAATAATA
1 TATATTTATAAATTATA
1281522 TATATTGTATAAATTATA
1 TATATT-TATAAATTATA
1281540 TA
1 TA
1281542 GTTTATTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 18 0.60
18 12 0.40
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
TATATTTATAAATTATA
Found at i:1281561 original size:22 final size:23
Alignment explanation
Indices: 1281520--1281586 Score: 75
Period size: 22 Copynumber: 2.9 Consensus size: 23
1281510 TTATAAATAA
*
1281520 TATATATTGTATAAATTATATAGTT
1 TATATA-TATATAAA-TATATAGTT
1281545 TAT-TA-ATATAAACTATATAGTT
1 TATATATATATAAA-TATATAGTT
*
1281567 TATATATATATATATATATA
1 TATATATATATAAATATATA
1281587 TGGTTTAGGG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
22 18 0.49
23 8 0.22
24 8 0.22
25 3 0.08
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (23 bp):
TATATATATATAAATATATAGTT
Found at i:1281704 original size:20 final size:20
Alignment explanation
Indices: 1281679--1281751 Score: 65
Period size: 20 Copynumber: 3.4 Consensus size: 20
1281669 TATAAACTAC
1281679 ATACTATAATTTATATTTAT
1 ATACTATAATTTATATTTAT
**
1281699 ATACTATGTTTTATACTATTTCTAT
1 ATACTAT-AATT-TA-TA-TT-TAT
* *
1281724 AAACTATAGTTTATATTTAT
1 ATACTATAATTTATATTTAT
1281744 ATACTATA
1 ATACTATA
1281752 TATATGAACT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
20 17 0.40
21 4 0.10
22 4 0.10
23 4 0.10
24 4 0.10
25 9 0.21
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.52
Consensus pattern (20 bp):
ATACTATAATTTATATTTAT
Done.