Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007761.1 Hibiscus syriacus cultivar Beakdansim tig00110030_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: 1497221
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:545260 original size:25 final size:22
Alignment explanation
Indices: 545232--545284 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 22
545222 ATAGATATAA
545232 CATATATAAATAAATATATGCATAT
1 CATATATAAATAAA-ATATG-A-AT
* *
545257 CATA-ACAAATGAAATATGAAT
1 CATATATAAATAAAATATGAAT
545278 CATATAT
1 CATATAT
545285 TATGAATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
21 6 0.25
22 2 0.08
23 5 0.21
24 7 0.29
25 4 0.17
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32
Consensus pattern (22 bp):
CATATATAAATAAAATATGAAT
Found at i:549106 original size:16 final size:16
Alignment explanation
Indices: 549076--549121 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
549066 TATAATGTTA
549076 ATAAGAAATAT-TTTAT
1 ATAA-AAATATATTTAT
549092 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
*
549108 AAAAAAAT-TATTTA
1 ATAAAAATATATTTA
549122 ACAAATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:549121 original size:15 final size:16
Alignment explanation
Indices: 549081--549121 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
549071 TGTTAATAAG
*
549081 AAATAT-TTTATATAA
1 AAATATATTTATAAAA
549096 AAATATATTTATAAAA
1 AAATATATTTATAAAA
549112 AAAT-TATTTA
1 AAATATATTTA
549122 ACAAATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATATATTTATAAAA
Found at i:549948 original size:233 final size:237
Alignment explanation
Indices: 549505--549965 Score: 858
Period size: 237 Copynumber: 2.0 Consensus size: 237
549495 GATTTCTAAT
549505 TATATATATATAACTTGTTATTCTTTTGCACACCCACCATGTGGGAAGGTAAATGTAAATGAATT
1 TATATATATATAACTTGTTATTCTTTTGCACACCCACCATGTGGGAAGGTAAATGTAAATGAATT
* * *
549570 GAAACAATAGAAATAAAATATATACCTAAAAGTAGTGGGTAATTCATAAAAAAAATAGTTGAGTA
66 GAAAAAATAGAAATAAAATATATAACTAAAACTAGTGGGTAATTCATAAAAAAAATAGTTGAGTA
*
549635 ATTTTTAATCAGGCGTAGTGTCCAAAAAATATTCTTAATATTTGAATAAATATTTATTTTGGGTA
131 ATTTTTAATCAGGCGTAGTGTCCAAAAAATATTCTTAATATTTGAATAAATAATTATTTTGGGTA
549700 TGCTTAATATATAGGAATTTTTATAAGTTATACGAGTGTATA
196 TGCTTAATATATAGGAATTTTTATAAGTTATACGAGTGTATA
549742 TATATATATATAACTTGTTATTCTTTTGCACACCCACCATGTGGGAAGGTAAATGTAAATGAATT
1 TATATATATATAACTTGTTATTCTTTTGCACACCCACCATGTGGGAAGGTAAATGTAAATGAATT
549807 GAAAAAATAGAAATAAAATATATAACTAAAACTAGTGGGTAATTCATAAAAAAAA-A-TTGAGTA
66 GAAAAAATAGAAATAAAATATATAACTAAAACTAGTGGGTAATTCATAAAAAAAATAGTTGAGTA
549870 A-TTTTAATCAGGCGTAGTGT-CAAAAAATATTCTTAATATTTGAATAAATAATTATTTTGGGTA
131 ATTTTTAATCAGGCGTAGTGTCCAAAAAATATTCTTAATATTTGAATAAATAATTATTTTGGGTA
549933 TGCTTAATATATAGGAATTTTTATAAGTTATAC
196 TGCTTAATATATAGGAATTTTTATAAGTTATAC
549966 AAGTATTGAA
Statistics
Matches: 220, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
233 75 0.34
234 19 0.09
235 8 0.04
236 1 0.00
237 117 0.53
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (237 bp):
TATATATATATAACTTGTTATTCTTTTGCACACCCACCATGTGGGAAGGTAAATGTAAATGAATT
GAAAAAATAGAAATAAAATATATAACTAAAACTAGTGGGTAATTCATAAAAAAAATAGTTGAGTA
ATTTTTAATCAGGCGTAGTGTCCAAAAAATATTCTTAATATTTGAATAAATAATTATTTTGGGTA
TGCTTAATATATAGGAATTTTTATAAGTTATACGAGTGTATA
Found at i:551126 original size:14 final size:14
Alignment explanation
Indices: 551107--551145 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
551097 AAAATCAGAC
551107 AGCAGATTCTGCAA
1 AGCAGATTCTGCAA
*
551121 AGCAGATTCTACAA
1 AGCAGATTCTGCAA
* *
551135 AACAGAATCTG
1 AGCAGATTCTG
551146 TTGATCAACT
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:0.41, C:0.21, G:0.18, T:0.21
Consensus pattern (14 bp):
AGCAGATTCTGCAA
Found at i:552403 original size:20 final size:21
Alignment explanation
Indices: 552378--552422 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
552368 ATATTGGGCG
* *
552378 ATTGTCTATTGTTTATGG-TT
1 ATTGTCTATGGTATATGGTTT
552398 ATTGTCTATGGTATATGGTTT
1 ATTGTCTATGGTATATGGTTT
552419 ATTG
1 ATTG
552423 CTTGATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.18, C:0.04, G:0.22, T:0.56
Consensus pattern (21 bp):
ATTGTCTATGGTATATGGTTT
Found at i:552619 original size:46 final size:45
Alignment explanation
Indices: 552444--552608 Score: 228
Period size: 44 Copynumber: 3.7 Consensus size: 45
552434 GTAAGCATGC
552444 AAATAAGCTTACGAGCTTAT-GGA-ACAATGGCAAGTATATGGGTA
1 AAATAAGCTTACGAGCTTATGGGATA-AATGGCAAGTATATGGGTA
* *
552488 AAATAAGCTTGCGAGCTTATGGAAT-AATGGCAAGTATATGGGTA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGCAAGTATATGGGTA
* * * * *
552532 AAATAAGCTTACGAGCTTATGTGATTAAATGGTAAGTATTTTGGTT
1 AAATAAGCTTACGAGCTTATGGGA-TAAATGGCAAGTATATGGGTA
552578 AAATAAGCTTACGAGCTTATGGGATAAATGG
1 AAATAAGCTTACGAGCTTATGGGATAAATGG
552609 TAAGAGATTT
Statistics
Matches: 107, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
44 59 0.55
45 10 0.09
46 38 0.36
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGGATAAATGGCAAGTATATGGGTA
Found at i:553024 original size:12 final size:12
Alignment explanation
Indices: 553003--553037 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
552993 TTTTTGGAAG
*
553003 TTACTATAGCAA
1 TTACTGTAGCAA
553015 TTACTGTAGCAA
1 TTACTGTAGCAA
*
553027 TTATTGTAGCA
1 TTACTGTAGCA
553038 GTGAACAGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (12 bp):
TTACTGTAGCAA
Found at i:561707 original size:17 final size:17
Alignment explanation
Indices: 561677--561716 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
561667 ATGCTGGATC
*
561677 CGGGTTGGGCTTGTAAA
1 CGGGTCGGGCTTGTAAA
*
561694 CGGGTCGGGTTTGTAAA
1 CGGGTCGGGCTTGTAAA
*
561711 TGGGTC
1 CGGGTC
561717 ATCTGGACTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.12, G:0.42, T:0.30
Consensus pattern (17 bp):
CGGGTCGGGCTTGTAAA
Found at i:561804 original size:15 final size:14
Alignment explanation
Indices: 561784--561828 Score: 67
Period size: 15 Copynumber: 3.3 Consensus size: 14
561774 TAATATAATA
561784 AAATAAATAAAAAT
1 AAATAAATAAAAAT
561798 AACATAAATAAAAAT
1 AA-ATAAATAAAAAT
561813 -AA-AAATAAAAAT
1 AAATAAATAAAAAT
561825 AAAT
1 AAAT
561829 GGATGAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 10 0.36
13 3 0.11
14 3 0.11
15 12 0.43
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (14 bp):
AAATAAATAAAAAT
Found at i:561827 original size:6 final size:6
Alignment explanation
Indices: 561788--561827 Score: 53
Period size: 6 Copynumber: 6.2 Consensus size: 6
561778 ATAATAAAAT
561788 AAATAA AAATAACA TAAATAA AAATAA AAATAA AAATAA A
1 AAATAA AAAT-A-A -AAATAA AAATAA AAATAA AAATAA A
561828 TGGATGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
6 23 0.74
7 2 0.06
8 2 0.06
9 4 0.13
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:562468 original size:113 final size:113
Alignment explanation
Indices: 562259--562786 Score: 846
Period size: 113 Copynumber: 4.7 Consensus size: 113
562249 CGATAGAGTC
* * * *
562259 GAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTATT-ATC-CTCTTCAGATGAGTTCTTC
1 GAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTC
* **** * *
562322 TCATTATGAATTTTTTCTGGAAATGTTGATCCATCGAATGATGAA-TT
66 TCATTATGAACTCGACCTGGCAATGTTGATCCATCGAGTGATGAATTT
* *
562369 CACGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTTCTTTCTTCAGATGAGTTCTT
1 GA-GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTT
* *
562434 CTCATTATGACCTCGACCTGGCAATGCTGATCCATCGAGTGATGAATTT
65 CTCATTATGAACTCGACCTGGCAATGTTGATCCATCGAGTGATGAATTT
*
562483 GAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTC
1 GAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTC
562548 TCATTATGAACTCGACCTGGCAATGTTGATCCATCGAGTGATGAATTT
66 TCATTATGAACTCGACCTGGCAATGTTGATCCATCGAGTGATGAATTT
*
562596 GAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTC
1 GAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTC
562661 TCATTATGAACTCGACCTGGCAATGTTGATCCATCGAGTGATGAATTT
66 TCATTATGAACTCGACCTGGCAATGTTGATCCATCGAGTGATGAATTT
* * *
562709 GAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 GAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTC
562774 TCATTATGAACTC
66 TCATTATGAACTC
562787 TTCCAGAAAT
Statistics
Matches: 391, Mismatches: 23, Indels: 5
0.93 0.05 0.01
Matches are distributed among these distances:
110 1 0.00
111 37 0.09
112 2 0.01
113 348 0.89
114 3 0.01
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38
Consensus pattern (113 bp):
GAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTC
TCATTATGAACTCGACCTGGCAATGTTGATCCATCGAGTGATGAATTT
Found at i:563248 original size:22 final size:22
Alignment explanation
Indices: 563223--563277 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
563213 CATAAAGCTT
563223 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
563245 TCATCTTTAAAAATAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
563267 TCATCTTTGAA
1 TCATCTTTGAA
563278 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:565925 original size:115 final size:114
Alignment explanation
Indices: 565724--565947 Score: 376
Period size: 115 Copynumber: 2.0 Consensus size: 114
565714 CATGCAGTTC
* * * *
565724 ATCTTTTAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGAACA
1 ATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
*
565789 CTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAATTT
66 CTTCCAGAAGATACTATTGGGTCTCCTTATTTCTACTATGAGCAAATTT
*
565838 ATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAAC
1 ATCTTTCAAATCCAATGATTGG-TTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAAC
*
565903 ACTTCCAGAAGATACTATTGGGTCTTCTTATTTCTACTATGAGCA
65 ACTTCCAGAAGATACTATTGGGTCTCCTTATTTCTACTATGAGCA
565948 CATGGCACTT
Statistics
Matches: 102, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
114 20 0.20
115 82 0.80
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (114 bp):
ATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
CTTCCAGAAGATACTATTGGGTCTCCTTATTTCTACTATGAGCAAATTT
Found at i:570191 original size:27 final size:27
Alignment explanation
Indices: 570161--570216 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
570151 GTAATTATGT
570161 AAAAATGAAAATGTAAATACAAACGTA
1 AAAAATGAAAATGTAAATACAAACGTA
* * *
570188 AAAAATGCAAATGTAAATGCAAATGTA
1 AAAAATGAAAATGTAAATACAAACGTA
570215 AA
1 AA
570217 TATGTGAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.61, C:0.07, G:0.12, T:0.20
Consensus pattern (27 bp):
AAAAATGAAAATGTAAATACAAACGTA
Found at i:570205 original size:12 final size:12
Alignment explanation
Indices: 570190--570217 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
570180 CAAACGTAAA
570190 AAATGCAAATGT
1 AAATGCAAATGT
570202 AAATGCAAATGT
1 AAATGCAAATGT
570214 AAAT
1 AAAT
570218 ATGTGAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.07, G:0.14, T:0.25
Consensus pattern (12 bp):
AAATGCAAATGT
Found at i:570310 original size:7 final size:7
Alignment explanation
Indices: 570276--570317 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
570266 ATAAAAGTAT
570276 AAATGCA
1 AAATGCA
* *
570283 CAATGAA
1 AAATGCA
570290 AAATGCA
1 AAATGCA
570297 AAGATGCA
1 AA-ATGCA
570305 AAATGC-
1 AAATGCA
570311 AAATGCA
1 AAATGCA
570318 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:572764 original size:25 final size:25
Alignment explanation
Indices: 572731--572790 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
572721 ATAAATAAAT
*
572731 AATATTAATATAAA-ATA-ATCATGAA
1 AATAATAATATAAACATATATCA--AA
*
572756 AATAATAATTTAAACATATATCAAA
1 AATAATAATATAAACATATATCAAA
*
572781 AGTAATAATA
1 AATAATAATA
572791 AAATAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
25 22 0.76
26 3 0.10
27 4 0.14
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (25 bp):
AATAATAATATAAACATATATCAAA
Found at i:574257 original size:15 final size:14
Alignment explanation
Indices: 574237--574281 Score: 67
Period size: 12 Copynumber: 3.3 Consensus size: 14
574227 TAATATAATA
574237 AAATAAATAAAAAT
1 AAATAAATAAAAAT
574251 AACATAAATAAAAAT
1 AA-ATAAATAAAAAT
574266 --ATAAATAAAAAT
1 AAATAAATAAAAAT
574278 AAAT
1 AAAT
574282 GGATGAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 12 0.43
14 4 0.14
15 12 0.43
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (14 bp):
AAATAAATAAAAAT
Found at i:574261 original size:27 final size:28
Alignment explanation
Indices: 574226--574279 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
574216 TTTATTAATA
574226 ATAATATAATAAA-ATAAATAAAAATAAC
1 ATAATATAA-AAATATAAATAAAAATAAC
574254 ATAA-ATAAAAATATAAATAAAAATAA
1 ATAATATAAAAATATAAATAAAAATAA
574280 ATGGATGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 3 0.12
27 18 0.72
28 4 0.16
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (28 bp):
ATAATATAAAAATATAAATAAAAATAAC
Found at i:574271 original size:12 final size:12
Alignment explanation
Indices: 574222--574278 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
574212 CATATTTATT
*
574222 AATAATAATAT-
1 AATAAAAATATA
*
574233 AATAAAATAAATA
1 AATAAAA-ATATA
* *
574246 AA-AATAACATA
1 AATAAAAATATA
574257 AATAAAAATATA
1 AATAAAAATATA
574269 AATAAAAATA
1 AATAAAAATA
574279 AATGGATGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
11 12 0.32
12 23 0.62
13 2 0.05
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.25
Consensus pattern (12 bp):
AATAAAAATATA
Found at i:577797 original size:21 final size:19
Alignment explanation
Indices: 577765--577808 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
577755 TGAAGAACTA
*
577765 TGATGAATAGTACCTATAC
1 TGATGAATAGTACCGATAC
*
577784 TGATGCAATTAGTATCGATAC
1 TGATG-AA-TAGTACCGATAC
577805 TGAT
1 TGAT
577809 ATAGGTATCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 2 0.10
21 14 0.67
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (19 bp):
TGATGAATAGTACCGATAC
Found at i:578922 original size:18 final size:18
Alignment explanation
Indices: 578899--578933 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
578889 ACCGGTCACA
578899 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
578917 ACCCGACCCGACCCGTT
1 ACCCGACCCGACCCGTT
578934 AACCGTTGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.51, G:0.20, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:581393 original size:23 final size:23
Alignment explanation
Indices: 581346--581436 Score: 112
Period size: 23 Copynumber: 3.9 Consensus size: 23
581336 TCAAATTTGA
* * *
581346 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATCTGATACTTGA-CTGG
581370 ATTCTGATCTGATA-TTGACATGG
1 ATTCTGATCTGATACTTGAC-TGG
*
581393 ATTCTGATCTGATACATGACTGG
1 ATTCTGATCTGATACTTGACTGG
*
581416 ATTCTGATATGATACTTGACT
1 ATTCTGATCTGATACTTGACT
581437 TGAATTATGT
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
22 1 0.02
23 42 0.71
24 16 0.27
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.38
Consensus pattern (23 bp):
ATTCTGATCTGATACTTGACTGG
Found at i:581565 original size:35 final size:35
Alignment explanation
Indices: 581514--581588 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
581504 TGGAGGAAGA
* * *
581514 TTACTTGGAGGTTCCTCGGCTTTGTGATCAGGGCC
1 TTACTTGCAGGCTCCTCGGATTTGTGATCAGGGCC
*
581549 TTACTTGCAGGCTCCTCGGATTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGATTTGTGATCAGGGCC
581584 TTACT
1 TTACT
581589 GTTCGTGACG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.12, C:0.25, G:0.28, T:0.35
Consensus pattern (35 bp):
TTACTTGCAGGCTCCTCGGATTTGTGATCAGGGCC
Found at i:583659 original size:15 final size:15
Alignment explanation
Indices: 583625--583669 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
583615 CAACCCGACC
583625 CGACCCGTTGA-C-T
1 CGACCCGTTGACCGT
583638 CGACCCGTTGACCGT
1 CGACCCGTTGACCGT
*
583653 TGACCCGTTGACCGT
1 CGACCCGTTGACCGT
583668 CG
1 CG
583670 TTGACCACTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 11 0.39
14 1 0.04
15 16 0.57
ACGTcount: A:0.13, C:0.38, G:0.27, T:0.22
Consensus pattern (15 bp):
CGACCCGTTGACCGT
Found at i:583673 original size:10 final size:8
Alignment explanation
Indices: 583639--583685 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 8
583629 CCGTTGACTC
583639 GACCCGTT
1 GACCCGTT
583647 GA-CCGTT
1 GACCCGTT
583654 GACCCGTT
1 GACCCGTT
583662 GACCGTCGTT
1 GACC--CGTT
583672 GACCACTGTT
1 GACC-C-GTT
583682 GACC
1 GACC
583686 AAAACTTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
7 7 0.21
8 11 0.32
9 1 0.03
10 15 0.44
ACGTcount: A:0.15, C:0.34, G:0.26, T:0.26
Consensus pattern (8 bp):
GACCCGTT
Found at i:585058 original size:51 final size:51
Alignment explanation
Indices: 584982--585086 Score: 201
Period size: 51 Copynumber: 2.1 Consensus size: 51
584972 GATGAGATTG
584982 AATTAAATAATAAGAGTGGATGGAGGAAAAAGATATAAATTGGAATTAAAT
1 AATTAAATAATAAGAGTGGATGGAGGAAAAAGATATAAATTGGAATTAAAT
*
585033 AATTAAATAATAAGATTGGATGGAGGAAAAAGATATAAATTGGAATTAAAT
1 AATTAAATAATAAGAGTGGATGGAGGAAAAAGATATAAATTGGAATTAAAT
585084 AAT
1 AAT
585087 AAGACCGAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.27
Consensus pattern (51 bp):
AATTAAATAATAAGAGTGGATGGAGGAAAAAGATATAAATTGGAATTAAAT
Found at i:586263 original size:47 final size:48
Alignment explanation
Indices: 586191--586281 Score: 121
Period size: 47 Copynumber: 1.9 Consensus size: 48
586181 TCAAATTTGA
* * * *
586191 ATTCTGTTATGATACCTGACCTGGATTCTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACATGACCTGGATTCTAATATGATACTTGACATGG
* *
586238 ATTCTGATCTGATACATGACTTGGATTCTAATATGATACTTGAC
1 ATTCTGATATGATACATGACCTGGATTCTAATATGATACTTGAC
586282 TTGAATTATG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
47 32 0.86
48 5 0.14
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.38
Consensus pattern (48 bp):
ATTCTGATATGATACATGACCTGGATTCTAATATGATACTTGACATGG
Found at i:586282 original size:24 final size:24
Alignment explanation
Indices: 586191--586284 Score: 109
Period size: 24 Copynumber: 4.0 Consensus size: 24
586181 TCAAATTTGA
* * *
586191 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATATGATACTTGACTTGG
* *
586215 ATTCTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACTTGACTTGG
* *
586238 ATTCTGATCTGATACATGACTTGG
1 ATTCTGATATGATACTTGACTTGG
*
586262 ATTCTAATATGATACTTGACTTG
1 ATTCTGATATGATACTTGACTTG
586285 AATTATGTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
23 21 0.35
24 39 0.65
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACTTGG
Found at i:586405 original size:33 final size:35
Alignment explanation
Indices: 586360--586432 Score: 114
Period size: 33 Copynumber: 2.1 Consensus size: 35
586350 TGGAGGAAGA
*
586360 TTACTTGGAGGCTCCTCAGC-TT-TGCTCAGGGCC
1 TTACTTGCAGGCTCCTCAGCTTTGTGCTCAGGGCC
*
586393 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCAGCTTTGTGCTCAGGGCC
586428 TTACT
1 TTACT
586433 GTTCGTGACG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 18 0.50
34 2 0.06
35 16 0.44
ACGTcount: A:0.11, C:0.30, G:0.26, T:0.33
Consensus pattern (35 bp):
TTACTTGCAGGCTCCTCAGCTTTGTGCTCAGGGCC
Found at i:587293 original size:44 final size:44
Alignment explanation
Indices: 587244--587531 Score: 405
Period size: 44 Copynumber: 6.5 Consensus size: 44
587234 TTGCTCTAAA
* * *
587244 ATAAATGAAAATGCATAACGGTGCATTATTGGTAGAAATGTTCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* *
587288 ATAAATGAAAATGCATAACAGTGCATTATTGGCAGAAAGGTGTC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
** * * **
587332 ATAAATGAAAATGCATAACAATGCATTATTGGTAGAAAGATTTC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* * *
587376 ATAAATGAAAATGCATAACGGTGCATTATCGTCAGAAAGGTGAC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
**
587420 ATAAATGAAAATGCATAACGGTATATTATTGGCAGAAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAG-AAAGGTGCC
*
587465 ATAAATGAAAATGCATAACAGTGCATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
*
587509 ATAAATGAAAATGCATAGCGGTG
1 ATAAATGAAAATGCATAACGGTG
587532 GAAAAAAGGT
Statistics
Matches: 216, Mismatches: 27, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
44 176 0.81
45 40 0.19
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.25
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
Found at i:593739 original size:266 final size:265
Alignment explanation
Indices: 593258--593761 Score: 712
Period size: 266 Copynumber: 1.9 Consensus size: 265
593248 CTCCTCTAAA
* *
593258 AAATGAAAATGCATAACGGTGCATTATTGGCCGAAAGGTGCTATAAATGAAAATGCATAACAGCT
1 AAATGAAAATGCATAACGGTGAATTATTGGCAGAAAGGTGCTATAAATGAAAATGCATAACAGCT
* * * **
593323 TATTATTGGCATAAAGATGTCATAAATGAAAATGCATAATGATGCATTATTGGTAGAAAAGTTCC
66 CATTATTGGCAGAAAGATGTCATAAATGAAAATGCATAACGATGCATTATTGACAGAAAAGTTCC
* * * *
593388 ATAAATGAAAATGCATAATGGTGCATTATTGGCAGAAAAGTGTCATAAATGAAAATGTATAACGG
131 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAAGTGCCATAAATGAAAATGCATAACGA
*
593453 TGCATTATTGGAAAAAAGGTGCCATAAATGAAAATGTATAATGATGCATTTTTTAACATAAAGGT
196 TGCATTATTGGAAAAAAGGTGCCATAAATGAAAATGCATAATGATGCATTTTTTAACATAAAGGT
593518 GCCAT
261 GCCAT
* *
593523 AAATGAAAAATGCATAATGGTGAATTATTGGCAGAAAGGTG-TCATAAATGAAAATGTATAAC-G
1 AAATG-AAAATGCATAACGGTGAATTATTGGCAGAAAGGTGCT-ATAAATGAAAATGCATAACAG
* * * *
593586 GTGCATTATTGGCAGAAAGGTG-CTATAAATGAAAATGCATAACGGTGCATTATTGACATAAAGG
64 CT-CATTATTGGCAGAAAGATGTC-ATAAATGAAAATGCATAACGATGCATTATTGACAGAAA--
*
593650 AG-T-CATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTGCCATAAATGAAAATGCA
125 AGTTCCATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAAGTGCCATAAATGAAAATGCA
** * *
593713 TAGTGATGCATTATTGGCAGAAAGGTGCCATAAATGAAAATGCATAATG
190 TAACGATGCATTATTGGAAAAAAGGTGCCATAAATGAAAATGCATAATG
593762 GTACATTATT
Statistics
Matches: 210, Mismatches: 23, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
265 9 0.04
266 198 0.94
267 1 0.00
268 2 0.01
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.27
Consensus pattern (265 bp):
AAATGAAAATGCATAACGGTGAATTATTGGCAGAAAGGTGCTATAAATGAAAATGCATAACAGCT
CATTATTGGCAGAAAGATGTCATAAATGAAAATGCATAACGATGCATTATTGACAGAAAAGTTCC
ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAAGTGCCATAAATGAAAATGCATAACGA
TGCATTATTGGAAAAAAGGTGCCATAAATGAAAATGCATAATGATGCATTTTTTAACATAAAGGT
GCCAT
Found at i:593785 original size:44 final size:44
Alignment explanation
Indices: 593258--593786 Score: 655
Period size: 44 Copynumber: 12.0 Consensus size: 44
593248 CTCCTCTAAA
* * *
593258 AAATGAAAATGCATAACGGTGCATTATTGGCCGAAAGGTGCTAT
1 AAATGAAAATGCATAATGGTGCATTATTGGCAGAAAGGTGCCAT
* * * * * *
593302 AAATGAAAATGCATAACAGCT-TATTATTGGCATAAAGATGTCAT
1 AAATGAAAATGCATAA-TGGTGCATTATTGGCAGAAAGGTGCCAT
* * * *
593346 AAATGAAAATGCATAATGATGCATTATTGGTAGAAAAGTTCCAT
1 AAATGAAAATGCATAATGGTGCATTATTGGCAGAAAGGTGCCAT
* *
593390 AAATGAAAATGCATAATGGTGCATTATTGGCAGAAAAGTGTCAT
1 AAATGAAAATGCATAATGGTGCATTATTGGCAGAAAGGTGCCAT
* * * *
593434 AAATGAAAATGTATAACGGTGCATTATTGGAAAAAAGGTGCCAT
1 AAATGAAAATGCATAATGGTGCATTATTGGCAGAAAGGTGCCAT
* * * ** *
593478 AAATGAAAATGTATAATGATGCATTTTTTAACATAAAGGTGCCAT
1 AAATGAAAATGCATAATGGTGCA-TTATTGGCAGAAAGGTGCCAT
* *
593523 AAATGAAAAATGCATAATGGTGAATTATTGGCAGAAAGGTGTCAT
1 AAATG-AAAATGCATAATGGTGCATTATTGGCAGAAAGGTGCCAT
* * *
593568 AAATGAAAATGTATAACGGTGCATTATTGGCAGAAAGGTGCTAT
1 AAATGAAAATGCATAATGGTGCATTATTGGCAGAAAGGTGCCAT
* * * * *
593612 AAATGAAAATGCATAACGGTGCATTATTGACATAAAGGAGTCAT
1 AAATGAAAATGCATAATGGTGCATTATTGGCAGAAAGGTGCCAT
* *
593656 AAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTGCCAT
1 AAATGAAAATGCATAATGGTGCATTATTGGCAGAAAGGTGCCAT
* *
593700 AAATGAAAATGCATAGTGATGCATTATTGGCAGAAAGGTGCCAT
1 AAATGAAAATGCATAATGGTGCATTATTGGCAGAAAGGTGCCAT
* *
593744 AAATGAAAATGCATAATGGTACATTATTGGCAGAATGGTGCCA
1 AAATGAAAATGCATAATGGTGCATTATTGGCAGAAAGGTGCCA
593787 CTCATGGTAT
Statistics
Matches: 415, Mismatches: 66, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
43 2 0.00
44 354 0.85
45 44 0.11
46 15 0.04
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.27
Consensus pattern (44 bp):
AAATGAAAATGCATAATGGTGCATTATTGGCAGAAAGGTGCCAT
Found at i:596762 original size:138 final size:138
Alignment explanation
Indices: 596507--596770 Score: 334
Period size: 138 Copynumber: 1.9 Consensus size: 138
596497 GACATACTTC
* * * *
596507 GTGTATGATAGTTATCGATCGATTTTGATTAAGGCATAACAGTGCATTTTCGTATCAGTACTATT
1 GTGTATAAAAGTTATCGATCGATTTTGATTAAGGCATAACAGTGCATTTTCGTATCAGTACCATG
* * * * *
596572 TGTACTATCGGCACTAGATGTGCAATCATGGTATTCATAATGATTTTATGAATTACCATTTTGAT
66 TATACTATCAGCACTAGAAGTACAATCATGGAATTCATAATGATTTTATGAATTACCATTTTGAT
596637 ATACAATT
131 ATACAATT
* * **
596645 GTGTATAAAAGTTATCGATCGATTTTGTTTAATGCATAATGGTGCATTTTCGTATCAGTACCATG
1 GTGTATAAAAGTTATCGATCGATTTTGATTAAGGCATAACAGTGCATTTTCGTATCAGTACCATG
* * * * *
596710 TATACTTTTAGCACTATAAGTAC-ATCCATGGAATTCATAATG-TGTTTGTGAATTTCCATTT
66 TATACTATCAGCACTAGAAGTACAAT-CATGGAATTCATAATGAT-TTTATGAATTACCATTT
596771 CGGCACTTCA
Statistics
Matches: 106, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
137 3 0.03
138 103 0.97
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (138 bp):
GTGTATAAAAGTTATCGATCGATTTTGATTAAGGCATAACAGTGCATTTTCGTATCAGTACCATG
TATACTATCAGCACTAGAAGTACAATCATGGAATTCATAATGATTTTATGAATTACCATTTTGAT
ATACAATT
Found at i:597955 original size:17 final size:17
Alignment explanation
Indices: 597933--597972 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
597923 TGGTCGACTG
597933 TTGACCGTTAACCT-GCA
1 TTGACCGTTAA-CTGGCA
*
597950 TTGACCGTTGACTGGCA
1 TTGACCGTTAACTGGCA
597967 TTGACC
1 TTGACC
597973 ATAACTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 2 0.10
17 19 0.90
ACGTcount: A:0.20, C:0.28, G:0.23, T:0.30
Consensus pattern (17 bp):
TTGACCGTTAACTGGCA
Found at i:606598 original size:9 final size:9
Alignment explanation
Indices: 606584--606610 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
606574 GATTAAGAGT
606584 TTAATTTTA
1 TTAATTTTA
606593 TTAATTTTA
1 TTAATTTTA
606602 TTAATTTTA
1 TTAATTTTA
606611 AAATTCAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTAATTTTA
Found at i:609700 original size:91 final size:88
Alignment explanation
Indices: 609542--609704 Score: 272
Period size: 91 Copynumber: 1.8 Consensus size: 88
609532 CATTGGATTG
*
609542 AACAAGTTCTTCTCATTATGAACTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAAATCTTCA
1 AACAAGTTCTTCTCATTATGAACTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAAATCTCCA
609607 TTGGAAATACTGATGCGAGATCA
66 TTGGAAATACTGATGCGAGATCA
* *
609630 AACAAGTTCTTCTCATTATGAACTTCTTTTCTCTTGTTGGATGAGTTCTTCTCATTATGAACTCT
1 AACAAGTTCTTCTCATTATGAACTTC--TTC-CTCGTTGGATGAGTTCTTCTCATTATGAAATCT
609695 CCATTGGAAA
63 CCATTGGAAA
609705 CATTGATCCA
Statistics
Matches: 69, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
88 26 0.38
90 3 0.04
91 40 0.58
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.40
Consensus pattern (88 bp):
AACAAGTTCTTCTCATTATGAACTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAAATCTCCA
TTGGAAATACTGATGCGAGATCA
Found at i:609796 original size:19 final size:17
Alignment explanation
Indices: 609744--609797 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
609734 TGAAAGGAAC
609744 AAGTTCTTCTCATTATG
1 AAGTTCTTCTCATTATG
* * *
609761 AACTTTTTC-CTTTATG
1 AAGTTCTTCTCATTATG
609777 ACGAGTTCTTCTCATTATG
1 A--AGTTCTTCTCATTATG
609796 AA
1 AA
609798 CTCTTCTGGA
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
16 7 0.25
17 8 0.29
18 6 0.21
19 7 0.25
ACGTcount: A:0.24, C:0.19, G:0.11, T:0.46
Consensus pattern (17 bp):
AAGTTCTTCTCATTATG
Found at i:609804 original size:19 final size:18
Alignment explanation
Indices: 609747--609804 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 18
609737 AAGGAACAAG
609747 TTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACT
* *
609765 TT-TTC-CTTTATG-ACGAG
1 TTCTTCTCATTATGAAC--T
609782 TTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACT
609800 CTTCT
1 -TTCT
609805 GGAAATATCA
Statistics
Matches: 30, Mismatches: 4, Indels: 11
0.67 0.09 0.24
Matches are distributed among these distances:
15 2 0.07
16 6 0.20
17 5 0.17
18 5 0.17
19 10 0.33
20 2 0.07
ACGTcount: A:0.19, C:0.22, G:0.09, T:0.50
Consensus pattern (18 bp):
TTCTTCTCATTATGAACT
Found at i:610026 original size:91 final size:92
Alignment explanation
Indices: 609867--610043 Score: 302
Period size: 91 Copynumber: 1.9 Consensus size: 92
609857 GAGTGATAGG
*
609867 TCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAA
1 TCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTCGGATGAGTTCTTCTCATTATGAA
609932 CTCTCCATTGGAAACACTGATGTGAGA
66 CTCTCCATTGGAAACACTGATGTGAGA
* * * *
609959 TCGAACAAGTTCTTCTCATTATGAACTTTTTTTCTCTCGTT-GGATGAGTTCTTCTCATTATGAA
1 TCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTCGGATGAGTTCTTCTCATTATGAA
610023 CTCTCCATTGGAAACACTGAT
66 CTCTCCATTGGAAACACTGAT
610044 CCATCTCCTT
Statistics
Matches: 80, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
91 44 0.55
92 36 0.45
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38
Consensus pattern (92 bp):
TCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTCGGATGAGTTCTTCTCATTATGAA
CTCTCCATTGGAAACACTGATGTGAGA
Found at i:610624 original size:76 final size:76
Alignment explanation
Indices: 610526--610668 Score: 189
Period size: 76 Copynumber: 1.9 Consensus size: 76
610516 GAGATAAATT
* * * *
610526 TTGTTTCGAAGGAAAATTGTCTCAAGCAAGACGAAGTAAGTTTTAAGAAAAACCATCTTAAGTGA
1 TTGTTTCGAAGGAAAATTGTCTCAAGCAAGACAAAATAAGTTTCAAGAAAAACCATCTTAAGAGA
610591 GATTCAATTTC
66 GATTCAATTTC
* ** **
610602 TTGTTTC-AAGGGAAATCTGTCTCAAGGGAGACAAAATTTGTTTCAAGAAAAACCATCTTAAGAG
1 TTGTTTCGAAGGAAAAT-TGTCTCAAGCAAGACAAAATAAGTTTCAAGAAAAACCATCTTAAGAG
610666 AGA
65 AGA
610669 CAAAACATTT
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
75 8 0.14
76 49 0.86
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (76 bp):
TTGTTTCGAAGGAAAATTGTCTCAAGCAAGACAAAATAAGTTTCAAGAAAAACCATCTTAAGAGA
GATTCAATTTC
Found at i:610760 original size:62 final size:65
Alignment explanation
Indices: 610656--610827 Score: 172
Period size: 66 Copynumber: 2.7 Consensus size: 65
610646 AAGAAAAACC
* * * *
610656 ATCTTAAGAGAGACAAAACATTTTTTCAAGAGAAACTATCTCAAAA-ACT-TGTTTCAAAAGAAA
1 ATCTCAAGGGAGACAAAA-ATTATTTCAAGGGAAACTATCTCAAAATACTGTGTTTCAAAAGAAA
610719 -
65 T
* * * ** *
610719 CTGTCAAGGGAGACAAAAATCATTTCAAGGGAAACGT-TCTCAAAATTTTGTGTTTCAAGAGAAA
1 ATCTCAAGGGAGACAAAAATTATTTCAAGGGAAAC-TATCTCAAAATACTGTGTTTCAAAAGAAA
610783 TT
65 -T
* * *
610785 ATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAA
1 ATCTCAAGGGAGACAAAAATTATTTCAAGGGAAACTATCTCAA
610828 GAGAGACAAA
Statistics
Matches: 88, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
62 22 0.25
63 16 0.18
64 13 0.15
65 1 0.01
66 36 0.41
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (65 bp):
ATCTCAAGGGAGACAAAAATTATTTCAAGGGAAACTATCTCAAAATACTGTGTTTCAAAAGAAAT
Found at i:610812 original size:36 final size:36
Alignment explanation
Indices: 610769--611053 Score: 408
Period size: 36 Copynumber: 7.8 Consensus size: 36
610759 CAAAATTTTG
* * *
610769 TGTTTCAAGAGAAATTATCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
*
610805 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
* * *
610841 TGTTTCAACGGAAACTGTCTCAAGAGAGATAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
**
610877 TGTTTCAAGGGAAACTGTCTCAAGAAAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
* **
610913 TGTTTCATGGGAAACAATCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
610949 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
* * *
610985 TGTTTCAAGGGAAACTATCTCAAGTGAGATAAAATATTT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGA-CAAA-A-TT
611024 TGTTTCAAGGGAAACTGTCTCAAGGGAGAC
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGAC
611054 TCAAGGGAAA
Statistics
Matches: 223, Mismatches: 23, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
36 190 0.85
37 3 0.01
38 1 0.00
39 29 0.13
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
Found at i:610958 original size:21 final size:21
Alignment explanation
Indices: 610932--610996 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
610922 GGAAACAATC
610932 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
* *
610953 TCAA-GG-G---AAA-CTGTC
1 TCAAGGGAGACAAAATTTGTT
610968 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
610989 TCAAGGGA
1 TCAAGGGA
610997 AACTATCTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 7 0.21
16 5 0.15
17 1 0.03
19 1 0.03
20 5 0.15
21 15 0.44
ACGTcount: A:0.37, C:0.12, G:0.26, T:0.25
Consensus pattern (21 bp):
TCAAGGGAGACAAAATTTGTT
Found at i:611070 original size:26 final size:26
Alignment explanation
Indices: 611028--611078 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
611018 ATATTTTGTT
*
611028 TCAAGGGAAACTGTCTCAAGGGAGAC
1 TCAAGGGAAACTATCTCAAGGGAGAC
* *
611054 TCAAGGGAAATTATCTCAAGTGAGA
1 TCAAGGGAAACTATCTCAAGGGAGA
611079 TAAAATCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.20
Consensus pattern (26 bp):
TCAAGGGAAACTATCTCAAGGGAGAC
Found at i:611116 original size:40 final size:40
Alignment explanation
Indices: 611072--611351 Score: 416
Period size: 40 Copynumber: 7.0 Consensus size: 40
611062 AATTATCTCA
* *
611072 AGTGAGATAAAATCTTTTGTTTCAAGAAAAAACAATCTTG
1 AGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
*
611112 AGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATATTG
1 AGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
* *
611152 AGTGAGATAAAATCTTATGTTTCAAGAAAAAACAATCTTG
1 AGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
* *
611192 AGTGAGATTAAATCTTCTGTTTCAAAGAAAAACAATCTTG
1 AGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
* *
611232 AATGAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTG
1 AGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
* *
611272 AATGAGATTAAATCTTCTGTTTCAAGGAAAAACAATCTTG
1 AGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
** * * *
611312 AGCAAAATAAAATATTATGTTTCAAGGAAAAACAATCTTG
1 AGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
611352 TAAAATGAAA
Statistics
Matches: 217, Mismatches: 23, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 217 1.00
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (40 bp):
AGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
Found at i:611694 original size:34 final size:34
Alignment explanation
Indices: 611651--611770 Score: 168
Period size: 34 Copynumber: 3.5 Consensus size: 34
611641 TCTCAGAGAA
*
611651 AAATTGTCTCAAACGAGACGAAATTTGTTTTGAG
1 AAATTGTCTCAAGCGAGACGAAATTTGTTTTGAG
* * *
611685 AAATTGTCTCAAGCGAGACGGAATTTGCTTTGAT
1 AAATTGTCTCAAGCGAGACGAAATTTGTTTTGAG
* *
611719 AAATTGTCTCAAGTGAGACAAAATTTGTTTTGAG
1 AAATTGTCTCAAGCGAGACGAAATTTGTTTTGAG
* *
611753 AAATTATCTCAAGTGAGA
1 AAATTGTCTCAAGCGAGA
611771 ATTTTTTTAA
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 76 1.00
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.33
Consensus pattern (34 bp):
AAATTGTCTCAAGCGAGACGAAATTTGTTTTGAG
Found at i:611934 original size:33 final size:32
Alignment explanation
Indices: 611875--612008 Score: 205
Period size: 32 Copynumber: 4.2 Consensus size: 32
611865 AAGATATTGA
* * * *
611875 ATGCCCCAATATTCGATCTTGAATCTCCAAGG
1 ATGCCCCAACATTTGATGTTGAATCTCCAAAG
611907 ATGCCCCAACATTTTGATGTTGAATCTCCAAAG
1 ATGCCCCAACA-TTTGATGTTGAATCTCCAAAG
*
611940 ATGCCCCAACATTTGATGTTGAATTTCCAAAG
1 ATGCCCCAACATTTGATGTTGAATCTCCAAAG
*
611972 ATGCCCCAACATTTGATGTTGAATCTTCAAAG
1 ATGCCCCAACATTTGATGTTGAATCTCCAAAG
612004 ATGCC
1 ATGCC
612009 TTCTATTGCT
Statistics
Matches: 94, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
32 65 0.69
33 29 0.31
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.30
Consensus pattern (32 bp):
ATGCCCCAACATTTGATGTTGAATCTCCAAAG
Found at i:611979 original size:65 final size:64
Alignment explanation
Indices: 611875--612008 Score: 205
Period size: 65 Copynumber: 2.1 Consensus size: 64
611865 AAGATATTGA
* *
611875 ATGCCCCAATATTCGATCTTGAATCTCCAAGGATGCCCCAACATTTTGATGTTGAATCTCCAAAG
1 ATGCCCCAACATTCGATCTTGAATCTCCAAAGATGCCCCAACA-TTTGATGTTGAATCTCCAAAG
* * * *
611940 ATGCCCCAACATTTGATGTTGAATTTCCAAAGATGCCCCAACATTTGATGTTGAATCTTCAAAG
1 ATGCCCCAACATTCGATCTTGAATCTCCAAAGATGCCCCAACATTTGATGTTGAATCTCCAAAG
612004 ATGCC
1 ATGCC
612009 TTCTATTGCT
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
64 25 0.40
65 38 0.60
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.30
Consensus pattern (64 bp):
ATGCCCCAACATTCGATCTTGAATCTCCAAAGATGCCCCAACATTTGATGTTGAATCTCCAAAG
Found at i:613069 original size:6 final size:6
Alignment explanation
Indices: 613049--613199 Score: 98
Period size: 7 Copynumber: 24.0 Consensus size: 6
613039 ATTATCGTCC
*
613049 CTTTTT C-TTTA CTTTTT CTTTTT -TCTTTT -TTTTT CTTTGTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CT-TTTT CTTTTT C-TT-TTT CTTTTT
* * *
613097 C-TTTT CATTTTT GCTCTTTT TTTATTT GC-TTTA ATTTTT C-TTTT CTTTTCT
1 CTTTTT C-TTTTT -CT-TTTT CTT-TTT -CTTTTT CTTTTT CTTTTT CTTTT-T
*
613148 CTTTTCT CTTTTCT CTTTTCT CTTTTCT CTGTTT CTTTTT CTTTTT CTTTTT
1 CTTTT-T CTTTT-T CTTTT-T CTTTT-T CTTTTT CTTTTT CTTTTT CTTTTT
613200 TTATTTTGTT
Statistics
Matches: 121, Mismatches: 10, Indels: 28
0.76 0.06 0.18
Matches are distributed among these distances:
5 19 0.16
6 46 0.38
7 47 0.39
8 9 0.07
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (6 bp):
CTTTTT
Found at i:613193 original size:58 final size:58
Alignment explanation
Indices: 613063--613198 Score: 147
Period size: 58 Copynumber: 2.3 Consensus size: 58
613053 TTCTTTACTT
* *
613063 TTTCTTTTTTCTTTTT-TTTTCTTTGTTTCTTTTTCTTTTCATTTTTGCTCTTTTTTTA
1 TTTC-TTTTTCTTTTTCTTTTCTTTGTCTCTTTTTCTTTTCATTTTTGCTCTTTTTCTA
** *
613121 TTTGC-TTTAATTTTTCTTTTCTTT-TCTCTTTTCTCTTTTC-TCTTTT-CTCTTTTCTCTG
1 TTT-CTTTTTCTTTTTCTTTTCTTTGTCTCTTTT-TCTTTTCAT-TTTTGCTCTTTT-TCTA
613179 TTTCTTTTTCTTTTTCTTTT
1 TTTCTTTTTCTTTTTCTTTT
613199 TTTATTTTGT
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
57 24 0.37
58 40 0.62
59 1 0.02
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (58 bp):
TTTCTTTTTCTTTTTCTTTTCTTTGTCTCTTTTTCTTTTCATTTTTGCTCTTTTTCTA
Found at i:613200 original size:14 final size:14
Alignment explanation
Indices: 613061--613206 Score: 53
Period size: 12 Copynumber: 10.7 Consensus size: 14
613051 TTTTCTTTAC
613061 TTTTTC-TTTT-TT
1 TTTTTCTTTTTCTT
*
613073 CTTTT-TTTTTCTT
1 TTTTTCTTTTTCTT
*
613086 TGTTTCTTTTTCTT
1 TTTTTCTTTTTCTT
**
613100 TTCATTT-TTGCTCTT
1 TT--TTTCTTTTTCTT
* *
613115 TTTTT-ATTTGCTT
1 TTTTTCTTTTTCTT
613128 TAATTTT-TCTTTTC-T
1 T--TTTTCT-TTTTCTT
*
613143 TTTCTC-TTTTC-T
1 TTTTTCTTTTTCTT
*
613155 CTTTTCTCTTTTCTCT
1 TTTTTCT-TTTTCT-T
* *
613171 TTTCTCTGTTTC--
1 TTTTTCTTTTTCTT
613183 TTTTTCTTTTTCTT
1 TTTTTCTTTTTCTT
*
613197 TTTTTATTTT
1 TTTTTCTTTT
613207 GTTTGATTGG
Statistics
Matches: 98, Mismatches: 21, Indels: 28
0.67 0.14 0.19
Matches are distributed among these distances:
12 28 0.29
13 16 0.16
14 23 0.23
15 18 0.18
16 13 0.13
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.77
Consensus pattern (14 bp):
TTTTTCTTTTTCTT
Found at i:613206 original size:20 final size:21
Alignment explanation
Indices: 613142--613206 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
613132 TTTTCTTTTC
*
613142 TTTTCTCTTTTCTCT-TTTCT
1 TTTTCTCTTTTCTCTGTTTAT
*
613162 CTTTTCTCTTTTCTCTGTTTCT
1 -TTTTCTCTTTTCTCTGTTTAT
* *
613184 TTTTCT-TTTTCTTTTTTTAT
1 TTTTCTCTTTTCTCTGTTTAT
613204 TTT
1 TTT
613207 GTTTGATTGG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
20 14 0.35
21 21 0.52
22 5 0.12
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.77
Consensus pattern (21 bp):
TTTTCTCTTTTCTCTGTTTAT
Found at i:614399 original size:27 final size:27
Alignment explanation
Indices: 614369--614469 Score: 184
Period size: 27 Copynumber: 3.7 Consensus size: 27
614359 AATGAAATGC
*
614369 AAATGCAAATGCAAAATGCAAAGATGT
1 AAATGCAGATGCAAAATGCAAAGATGT
614396 AAATGCAGATGCAAAATGCAAAGATGT
1 AAATGCAGATGCAAAATGCAAAGATGT
614423 AAATGCAGATGCAAAATGCAAAGATGT
1 AAATGCAGATGCAAAATGCAAAGATGT
*
614450 AAATACAGATGCAAAATGCA
1 AAATGCAGATGCAAAATGCA
614470 GATGCAAAAT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 72 1.00
ACGTcount: A:0.50, C:0.12, G:0.20, T:0.18
Consensus pattern (27 bp):
AAATGCAGATGCAAAATGCAAAGATGT
Found at i:614467 original size:67 final size:67
Alignment explanation
Indices: 614396--614550 Score: 258
Period size: 67 Copynumber: 2.3 Consensus size: 67
614386 GCAAAGATGT
* *
614396 AAATGCAGATGCAAAATGCAAAGATGTAAATGCAGATGCAAAATGCAAAGATGTAAATACAGATG
1 AAATGCAGATGCAAAATGCAAAGATGCAAATGCAGATGCAAAATGCAAAGATGCAAATACAGATG
614461 CA
66 CA
*
614463 AAATGCAGATGCAAAATGCAAAGATGCAAATGCAGATGCAAAATGCAAAGATGCAAATGCAGATG
1 AAATGCAGATGCAAAATGCAAAGATGCAAATGCAGATGCAAAATGCAAAGATGCAAATACAGATG
614528 CA
66 CA
614530 AAATGCAAAGATGC-AAATGCA
1 AAATGC--AGATGCAAAATGCA
614551 TATGCAAAAA
Statistics
Matches: 83, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
67 70 0.84
68 7 0.08
69 6 0.07
ACGTcount: A:0.49, C:0.14, G:0.21, T:0.16
Consensus pattern (67 bp):
AAATGCAGATGCAAAATGCAAAGATGCAAATGCAGATGCAAAATGCAAAGATGCAAATACAGATG
CA
Found at i:614493 original size:27 final size:27
Alignment explanation
Indices: 614456--614559 Score: 190
Period size: 27 Copynumber: 3.8 Consensus size: 27
614446 ATGTAAATAC
614456 AGATGCAAAATGCAGATGCAAAATGCAA
1 AGATGC-AAATGCAGATGCAAAATGCAA
614484 AGATGCAAATGCAGATGCAAAATGCAA
1 AGATGCAAATGCAGATGCAAAATGCAA
614511 AGATGCAAATGCAGATGCAAAATGCAA
1 AGATGCAAATGCAGATGCAAAATGCAA
*
614538 AGATGCAAATGCATATGCAAAA
1 AGATGCAAATGCAGATGCAAAA
614560 ATGTTGATCC
Statistics
Matches: 75, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
27 69 0.92
28 6 0.08
ACGTcount: A:0.49, C:0.14, G:0.21, T:0.15
Consensus pattern (27 bp):
AGATGCAAATGCAGATGCAAAATGCAA
Found at i:614494 original size:54 final size:54
Alignment explanation
Indices: 614365--614550 Score: 201
Period size: 54 Copynumber: 3.5 Consensus size: 54
614355 TAAAAATGAA
*
614365 ATGC-AAATGC-AAATGCAAAATGCAAAGATGTAAATGC-AGATGCAAAATGCAAAG
1 ATGCAAAATGCAAGATGCA-AATGCAAAGATGTAAATGCAAGATGCAAAATGC--AG
* *
614419 ATG-TAAATGC-AGATGCAAAATGCAAAGATGTAAATAC-AGATGCAAAATGCAG
1 ATGCAAAATGCAAGATGC-AAATGCAAAGATGTAAATGCAAGATGCAAAATGCAG
*
614471 ATGCAAAATGCAAAGATGCAAATGC--AGATGCAAAATGCAAAGATGC-AAATGCAG
1 ATGCAAAATGC-AAGATGCAAATGCAAAGATG-TAAATGC-AAGATGCAAAATGCAG
614525 ATGCAAAATGCAAAGATGCAAATGCA
1 ATGCAAAATGC-AAGATGCAAATGCA
614551 TATGCAAAAA
Statistics
Matches: 118, Mismatches: 5, Indels: 17
0.84 0.04 0.12
Matches are distributed among these distances:
52 10 0.08
53 11 0.09
54 84 0.71
55 13 0.11
ACGTcount: A:0.49, C:0.13, G:0.21, T:0.17
Consensus pattern (54 bp):
ATGCAAAATGCAAGATGCAAATGCAAAGATGTAAATGCAAGATGCAAAATGCAG
Found at i:614502 original size:94 final size:94
Alignment explanation
Indices: 614365--614559 Score: 329
Period size: 94 Copynumber: 2.1 Consensus size: 94
614355 TAAAAATGAA
* *
614365 ATGC-AAATGCAAATGCAAAATGCAAAGATGTAAATGCAGATGCAAAATGCAAAGATGTAAATGC
1 ATGCAAAATGCAAATGCAAAATGCAAAGATGCAAATGCAGATGCAAAATGCAAAGATGCAAATGC
*
614429 AGATGCAAAATGCAAAGATGTAAATACAG
66 AGATGCAAAATGCAAAGATGCAAATACAG
*
614458 ATGCAAAATGCAGATGCAAAATGCAAAGATGCAAATGCAGATGCAAAATGCAAAGATGCAAATGC
1 ATGCAAAATGCAAATGCAAAATGCAAAGATGCAAATGCAGATGCAAAATGCAAAGATGCAAATGC
* *
614523 AGATGCAAAATGCAAAGATGCAAATGCAT
66 AGATGCAAAATGCAAAGATGCAAATACAG
614552 ATGCAAAA
1 ATGCAAAA
614560 ATGTTGATCC
Statistics
Matches: 95, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
93 4 0.04
94 91 0.96
ACGTcount: A:0.49, C:0.13, G:0.21, T:0.17
Consensus pattern (94 bp):
ATGCAAAATGCAAATGCAAAATGCAAAGATGCAAATGCAGATGCAAAATGCAAAGATGCAAATGC
AGATGCAAAATGCAAAGATGCAAATACAG
Found at i:614543 original size:21 final size:20
Alignment explanation
Indices: 614363--614559 Score: 115
Period size: 20 Copynumber: 9.8 Consensus size: 20
614353 TTTAAAAATG
*
614363 AAATGCAAATGC-AAATGCA
1 AAATGCAGATGCAAAATGCA
*
614382 AAATGCAAAGATG-TAAATGC-
1 AAATGC--AGATGCAAAATGCA
* * *
614402 AGATGCAAAATGCAAAGATG-T
1 AAATGC-AGATGCAAA-ATGCA
614423 AAATGCAGATGCAAAATGCA
1 AAATGCAGATGCAAAATGCA
* * * *
614443 AAGATGTAAATAC-AGATGCA
1 AA-ATGCAGATGCAAAATGCA
614463 AAATGCAGATGCAAAATGCA
1 AAATGCAGATGCAAAATGCA
* *
614483 AAGATGCAAATGC-AGATGCA
1 AA-ATGCAGATGCAAAATGCA
614503 AAATGCAAAGATGC-AAATGC-
1 AAATGC--AGATGCAAAATGCA
* *
614523 AGATGCAAAATGCAAAGATGC-
1 AAATGC-AGATGCAAA-ATGCA
*
614544 AAATGCATATGCAAAA
1 AAATGCAGATGCAAAA
614560 ATGTTGATCC
Statistics
Matches: 141, Mismatches: 23, Indels: 28
0.73 0.12 0.15
Matches are distributed among these distances:
19 32 0.23
20 56 0.40
21 53 0.38
ACGTcount: A:0.50, C:0.13, G:0.20, T:0.17
Consensus pattern (20 bp):
AAATGCAGATGCAAAATGCA
Found at i:617353 original size:55 final size:53
Alignment explanation
Indices: 617276--617425 Score: 149
Period size: 55 Copynumber: 2.7 Consensus size: 53
617266 TTTAAAGGAA
* * * *
617276 GTCTTCAATCGGCTTCAAATTTCTTCCTTCATTGGATGTCATTCTTCACAG-ATCT
1 GTCTTCAATCAG-TTTAAATTTCTTCATTCATCGGATGTCATTCTTCA-AGAAT-T
* * * ** *
617331 GTCTTCAATCTGTTTAAGATTTCTTCAATCATCGAATGTTTTTCTTCATGAATT
1 GTCTTCAATCAGTTTAA-ATTTCTTCATTCATCGGATGTCATTCTTCAAGAATT
617385 GATCTTCAATCAGTTTCAAATTTCTTCATTCATCGGATGTC
1 G-TCTTCAATCAGTTT-AAATTTCTTCATTCATCGGATGTC
617426 CAATTCATGA
Statistics
Matches: 78, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
54 7 0.09
55 69 0.88
56 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.44
Consensus pattern (53 bp):
GTCTTCAATCAGTTTAAATTTCTTCATTCATCGGATGTCATTCTTCAAGAATT
Found at i:619223 original size:29 final size:28
Alignment explanation
Indices: 619170--619230 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
619160 ATTATAACAG
* *
619170 TGACCTAAATAGAAAAACTATAAATTAA
1 TGACCAAAATAGAAAAACTAAAAATTAA
619198 TGACCAAAATAAGAAAAA-TCAAAAATTAA
1 TGACCAAAAT-AGAAAAACT-AAAAATTAA
619227 -GACC
1 TGACC
619231 CCAAGCATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 14 0.48
29 15 0.52
ACGTcount: A:0.59, C:0.13, G:0.08, T:0.20
Consensus pattern (28 bp):
TGACCAAAATAGAAAAACTAAAAATTAA
Found at i:623002 original size:30 final size:30
Alignment explanation
Indices: 622945--623002 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
622935 TGAAAAATAA
*
622945 AAAAAAACATAAAATAGAAGACCATAAATT
1 AAAAAAACATAAAATACAAGACCATAAATT
* * *
622975 AAAATAACATAAAATACAATACGATAAA
1 AAAAAAACATAAAATACAAGACCATAAA
623003 CATATAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.67, C:0.10, G:0.05, T:0.17
Consensus pattern (30 bp):
AAAAAAACATAAAATACAAGACCATAAATT
Found at i:626171 original size:21 final size:21
Alignment explanation
Indices: 626145--626203 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
626135 TGCTTCCAAG
626145 TCTCCATCATCTATCTCTATT
1 TCTCCATCATCTATCTCTATT
* * *
626166 TCTCCATCATCTAGCTTTGTT
1 TCTCCATCATCTATCTCTATT
*
626187 TCTCCATCATTTATCTC
1 TCTCCATCATCTATCTC
626204 CACATTAGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.17, C:0.32, G:0.03, T:0.47
Consensus pattern (21 bp):
TCTCCATCATCTATCTCTATT
Found at i:627327 original size:50 final size:50
Alignment explanation
Indices: 627230--627327 Score: 115
Period size: 50 Copynumber: 2.0 Consensus size: 50
627220 AGGCATGTTC
** * *
627230 TTCTATATGTGCTGCCAAATCAGCATAAAATGCGTTCTGTTGAACACACA
1 TTCTATATGTGCTGCCAAATCAGCATAAAACACATTCTGTAGAACACACA
* * * * *
627280 TTCTATGTGTGTTGTCAAATCAGCATAAGACACATTCTGTAGCACACA
1 TTCTATATGTGCTGCCAAATCAGCATAAAACACATTCTGTAGAACACA
627328 TTTGTCATGT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 39 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (50 bp):
TTCTATATGTGCTGCCAAATCAGCATAAAACACATTCTGTAGAACACACA
Found at i:627605 original size:14 final size:14
Alignment explanation
Indices: 627586--627620 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
627576 AAAATTAGTT
627586 ATATTTTTTGAAAA
1 ATATTTTTTGAAAA
627600 ATATTTTTTGAAAA
1 ATATTTTTTGAAAA
627614 ATATTTT
1 ATATTTT
627621 ACGGTGTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (14 bp):
ATATTTTTTGAAAA
Found at i:627913 original size:30 final size:31
Alignment explanation
Indices: 627845--627913 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
627835 TTCTATTGAA
*
627845 ATAAAAATATTATATATTATATTAGTTATTT
1 ATAAAAATATGATATATTATATTAGTTATTT
*
627876 ATTAAAATATGA-ATATTATATATA-TTATATT
1 ATAAAAATATGATATATTATAT-TAGTTAT-TT
627907 -TAAAAAT
1 ATAAAAAT
627914 TATTGATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
30 19 0.58
31 14 0.42
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (31 bp):
ATAAAAATATGATATATTATATTAGTTATTT
Found at i:635708 original size:30 final size:30
Alignment explanation
Indices: 635612--635709 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 30
635602 ATTCAGGGGA
* **
635612 CAAATTAATATTTTATATAAATTTTAAAGG-T
1 CAAATTAGTATTTTATATAAAAATT--AGGAT
* * *
635643 TAAATTAGTGTTTTATATAAAAATTATGAT
1 CAAATTAGTATTTTATATAAAAATTAGGAT
* *
635673 TAAATTAGTATTTTATCT-AAAATTCAGGAT
1 CAAATTAGTATTTTATATAAAAATT-AGGAT
635703 CAAATTA
1 CAAATTA
635710 AAATTTAAAC
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
29 8 0.15
30 27 0.49
31 20 0.36
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (30 bp):
CAAATTAGTATTTTATATAAAAATTAGGAT
Found at i:636446 original size:86 final size:86
Alignment explanation
Indices: 636301--636472 Score: 299
Period size: 86 Copynumber: 2.0 Consensus size: 86
636291 ATTGCTACCC
636301 AAAGGAGGGATATGGTGATGGCCATAAGGCCTGAACATACAAAAACAATGGTAGGTGTCCTCCCT
1 AAAGGAGGGATATGGTGATGGCCATAAGGCCTGAACATACAAAAACAATGGTAGGTGTCCTCCCT
*
636366 CTTCTTCCCATAAACCCTTTT
66 CTTATTCCCATAAACCCTTTT
* * *
636387 AAAGGAGGGATATGGTGATGGCCATAAGGCCTGACCATACGAAAATAATGGTAGGTGTCCTCCCT
1 AAAGGAGGGATATGGTGATGGCCATAAGGCCTGAACATACAAAAACAATGGTAGGTGTCCTCCCT
*
636452 CTTATTCCCATAAGCCCTTTT
66 CTTATTCCCATAAACCCTTTT
636473 GCGAGAGCAT
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 81 1.00
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (86 bp):
AAAGGAGGGATATGGTGATGGCCATAAGGCCTGAACATACAAAAACAATGGTAGGTGTCCTCCCT
CTTATTCCCATAAACCCTTTT
Found at i:638879 original size:29 final size:29
Alignment explanation
Indices: 638845--638903 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
638835 CCTAAATTAA
638845 TTTGATGTCATTGATTACATCAATTTAGT
1 TTTGATGTCATTGATTACATCAATTTAGT
*
638874 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGATTACATCAATTTAGT
638903 T
1 T
638904 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGATTACATCAATTTAGT
Found at i:641772 original size:43 final size:42
Alignment explanation
Indices: 641724--641851 Score: 166
Period size: 43 Copynumber: 3.0 Consensus size: 42
641714 TCAAGAATGT
*
641724 TTTTAATATGCTAGTTTGATGTATTTGTGGATTGTTACTTTGG
1 TTTTAATATGTTAGTTTG-TGTATTTGTGGATTGTTACTTTGG
* *
641767 TTTTAATATGTTAGTTTTGTGAAATTGTGGATTGTTACTTTGG
1 TTTTAATATGTTAG-TTTGTGTATTTGTGGATTGTTACTTTGG
* * * *
641810 TTTAAACATGTTAGTTTGGTGTATTTGTGGATTATTAGTTTG
1 TTTTAATATGTTAGTTT-GTGTATTTGTGGATTGTTACTTTG
641852 TAATTTAGAC
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
42 3 0.04
43 67 0.91
44 4 0.05
ACGTcount: A:0.20, C:0.03, G:0.23, T:0.53
Consensus pattern (42 bp):
TTTTAATATGTTAGTTTGTGTATTTGTGGATTGTTACTTTGG
Found at i:642017 original size:21 final size:20
Alignment explanation
Indices: 641991--642034 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
641981 AATTTCTAGT
641991 GAGCTTAACAAGCAACGAGTC
1 GAGCTTAACAAGC-ACGAGTC
*
642012 GAGCTTAACGAGCACGAGTC
1 GAGCTTAACAAGCACGAGTC
642032 GAG
1 GAG
642035 TAACAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.34, C:0.23, G:0.30, T:0.14
Consensus pattern (20 bp):
GAGCTTAACAAGCACGAGTC
Found at i:642373 original size:25 final size:25
Alignment explanation
Indices: 642339--642388 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
642329 CTCGGCCATT
642339 GGAATTGAATCAATGAGAAATGTCG
1 GGAATTGAATCAATGAGAAATGTCG
642364 GGAATTGAATCAATGAGAAATGTCG
1 GGAATTGAATCAATGAGAAATGTCG
642389 AGTTCCCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.28, T:0.24
Consensus pattern (25 bp):
GGAATTGAATCAATGAGAAATGTCG
Found at i:644435 original size:19 final size:17
Alignment explanation
Indices: 644389--644424 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
644379 AATTAGAATT
644389 AAGAATCAAAATTTTAG
1 AAGAATCAAAATTTTAG
644406 AAGAATCAAAATTTTAG
1 AAGAATCAAAATTTTAG
644423 AA
1 AA
644425 AAGATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.56, C:0.06, G:0.11, T:0.28
Consensus pattern (17 bp):
AAGAATCAAAATTTTAG
Found at i:649140 original size:56 final size:57
Alignment explanation
Indices: 649054--649166 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 57
649044 TTGTACCAAT
649054 GCATCTATCGTCATCAGTAAGGGAGTTCTTCCTGTGCTGTTTGCA-ATTACGATACA
1 GCATCTATCGTCATCAGTAAGGGAGTTCTTCCTGTGCTGTTTGCAGATTACGATACA
649110 GCATCTATCGTCATCAGTAAGGGAGTTCTTCCTGTGCTGTTTGCAGATTACGATACA
1 GCATCTATCGTCATCAGTAAGGGAGTTCTTCCTGTGCTGTTTGCAGATTACGATACA
649167 TACGATTAGG
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 45 0.80
57 11 0.20
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (57 bp):
GCATCTATCGTCATCAGTAAGGGAGTTCTTCCTGTGCTGTTTGCAGATTACGATACA
Found at i:651203 original size:19 final size:19
Alignment explanation
Indices: 651179--651220 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
651169 ATGGGTTGTA
651179 CTAATATGGACTATTTATT
1 CTAATATGGACTATTTATT
651198 CTAATATGGACTATTTATT
1 CTAATATGGACTATTTATT
651217 CTAA
1 CTAA
651221 CATGCAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (19 bp):
CTAATATGGACTATTTATT
Found at i:651250 original size:18 final size:18
Alignment explanation
Indices: 651227--651263 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
651217 CTAACATGCA
* *
651227 AACTATATAGTATATACT
1 AACTATATAATATAAACT
651245 AACTATATAATATAAACT
1 AACTATATAATATAAACT
651263 A
1 A
651264 TGTAATATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.03, T:0.35
Consensus pattern (18 bp):
AACTATATAATATAAACT
Found at i:651476 original size:17 final size:17
Alignment explanation
Indices: 651454--651487 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
651444 ATTATCTAAA
*
651454 CTATATACTATATACAT
1 CTATATACTATAAACAT
*
651471 CTATATATTATAAACAT
1 CTATATACTATAAACAT
651488 GTCCACCCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (17 bp):
CTATATACTATAAACAT
Found at i:653661 original size:25 final size:27
Alignment explanation
Indices: 653621--653670 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
653611 GTTTTCCCCT
*
653621 TTTTTTCCTTTCCTTTAC-TCTTTTTA
1 TTTTTCCCTTTCCTTTACTTCTTTTTA
*
653647 TTTTTCCCTTT-CTTTTCTTCTTTT
1 TTTTTCCCTTTCCTTTACTTCTTTT
653671 CTTCTCCAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.72
Consensus pattern (27 bp):
TTTTTCCCTTTCCTTTACTTCTTTTTA
Found at i:659783 original size:30 final size:30
Alignment explanation
Indices: 659749--659828 Score: 144
Period size: 30 Copynumber: 2.7 Consensus size: 30
659739 CAAAATGGTT
659749 TTTGGACTTGAATTGAATTTACAAAACGTA
1 TTTGGACTTGAATTGAATTTACAAAACGTA
*
659779 TTTGGACTTGAATTGAATTTACAAAATGTA
1 TTTGGACTTGAATTGAATTTACAAAACGTA
659809 TTTGGACTT-AATTGAATTTA
1 TTTGGACTTGAATTGAATTTA
659829 TTCAAAATTT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 11 0.22
30 38 0.78
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.41
Consensus pattern (30 bp):
TTTGGACTTGAATTGAATTTACAAAACGTA
Found at i:660066 original size:21 final size:21
Alignment explanation
Indices: 660040--660081 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
660030 ATTTGAATAT
*
660040 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
660061 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
660082 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:661317 original size:19 final size:20
Alignment explanation
Indices: 661293--661340 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
661283 AACGATTTTC
*
661293 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
661312 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
661332 TTTTGAAAA
1 TTTTGAAAA
661341 AAGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:662634 original size:30 final size:30
Alignment explanation
Indices: 662600--662679 Score: 135
Period size: 30 Copynumber: 2.7 Consensus size: 30
662590 CAAAATGGTT
662600 TTTGGACTTGAATTGAATTTACAAAACGTA
1 TTTGGACTTGAATTGAATTTACAAAACGTA
* *
662630 TTTGGATTTGAATTGAATTTACAAAATGTA
1 TTTGGACTTGAATTGAATTTACAAAACGTA
662660 TTTGGACTT-AATTGAATTTA
1 TTTGGACTTGAATTGAATTTA
662680 TTCAAAATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 11 0.23
30 36 0.77
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.42
Consensus pattern (30 bp):
TTTGGACTTGAATTGAATTTACAAAACGTA
Found at i:662922 original size:21 final size:21
Alignment explanation
Indices: 662892--662931 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
662882 ATTTGAATAT
* *
662892 TATGATGGGGTATCGATTCTC
1 TATGAAGGGGTACCGATTCTC
662913 TATGAAGGGGTACCGATTC
1 TATGAAGGGGTACCGATTC
662932 CCCCCATTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCTC
Found at i:668948 original size:18 final size:18
Alignment explanation
Indices: 668914--668950 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
668904 ATTTATTTCT
**
668914 AATTAATATTATTAAATA
1 AATTAATATTAAAAAATA
668932 AATTAATATTAAAAAATA
1 AATTAATATTAAAAAATA
668950 A
1 A
668951 TTCTAAACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTAATATTAAAAAATA
Found at i:671634 original size:40 final size:40
Alignment explanation
Indices: 671528--671635 Score: 155
Period size: 40 Copynumber: 2.7 Consensus size: 40
671518 AAGGACAGTA
* **
671528 AGTGTATATGGTGGGCACGACCTTATATGTAATACATTTC
1 AGTGTATATGGTGGGCACGACCTTATGTGTAATACACATC
* *
671568 AGTGTATATGGAGGACACGACCTTATGTGTAATACACATC
1 AGTGTATATGGTGGGCACGACCTTATGTGTAATACACATC
671608 -GATGTATATGGTGGGCACGACCTTATGT
1 AG-TGTATATGGTGGGCACGACCTTATGT
671636 AGCACTACAG
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
39 1 0.02
40 59 0.98
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (40 bp):
AGTGTATATGGTGGGCACGACCTTATGTGTAATACACATC
Found at i:684397 original size:18 final size:19
Alignment explanation
Indices: 684365--684401 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
684355 CATGTGGTTT
*
684365 AAAATTTTAGACCTCAACA
1 AAAAGTTTAGACCTCAACA
684384 AAAAGTTTAG-CCTCAACA
1 AAAAGTTTAGACCTCAACA
684402 TGCTAGACTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.46, C:0.22, G:0.08, T:0.24
Consensus pattern (19 bp):
AAAAGTTTAGACCTCAACA
Found at i:714129 original size:3 final size:3
Alignment explanation
Indices: 714121--714150 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
714111 AGTTAATCCC
714121 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
714151 TGAAAAGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:719137 original size:24 final size:26
Alignment explanation
Indices: 719105--719158 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 26
719095 GAAATTTGTG
* *
719105 TTTTCTTTTTTAAA-A-TATATAGAA
1 TTTTATTTTTTAAATATTATATAAAA
719129 TTTTATTTTTTAAATATTATATAAAA
1 TTTTATTTTTTAAATATTATATAAAA
719155 TTTT
1 TTTT
719159 TAAAATTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 13 0.50
25 1 0.04
26 12 0.46
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (26 bp):
TTTTATTTTTTAAATATTATATAAAA
Found at i:723044 original size:4 final size:4
Alignment explanation
Indices: 723035--723061 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
723025 ACCTGACTAG
723035 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
723062 TTAGAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:723413 original size:16 final size:16
Alignment explanation
Indices: 723392--723423 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
723382 GCATATTTTA
*
723392 GCATGTTATTTTGTTT
1 GCATGTCATTTTGTTT
723408 GCATGTCATTTTGTTT
1 GCATGTCATTTTGTTT
723424 TTGTTAGCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.09, G:0.19, T:0.59
Consensus pattern (16 bp):
GCATGTCATTTTGTTT
Found at i:725808 original size:15 final size:15
Alignment explanation
Indices: 725788--725821 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
725778 ATTCATTAAT
725788 TATTTTAAGAT-AAAA
1 TATTTTAA-ATCAAAA
725803 TATTTTAAATCAAAA
1 TATTTTAAATCAAAA
725818 TATT
1 TATT
725822 ACCGTCTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 16 0.89
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (15 bp):
TATTTTAAATCAAAA
Found at i:727963 original size:17 final size:17
Alignment explanation
Indices: 727929--728000 Score: 56
Period size: 17 Copynumber: 4.3 Consensus size: 17
727919 TTTATTTCAT
** *
727929 TTAATAAAGTTAGTTCA
1 TTAATAAAACTAGCTCA
727946 TTAATAAAACTAGCTCA
1 TTAATAAAACTAGCTCA
* * *
727963 TAAATCAAACTAGTTCA
1 TTAATAAAACTAGCTCA
* * *
727980 TTTATTAAACTAACTC-
1 TTAATAAAACTAGCTCA
727996 TTAAT
1 TTAAT
728001 TGTTTCATCC
Statistics
Matches: 43, Mismatches: 12, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
16 4 0.09
17 39 0.91
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.38
Consensus pattern (17 bp):
TTAATAAAACTAGCTCA
Found at i:728421 original size:25 final size:25
Alignment explanation
Indices: 728393--728444 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
728383 AAGCATTCAA
728393 GGCTGATTTAATCATCCAAACCAAG
1 GGCTGATTTAATCATCCAAACCAAG
* *
728418 GGCTGATTTAATCATTCAAACCCAG
1 GGCTGATTTAATCATCCAAACCAAG
728443 GG
1 GG
728445 TTGTTCATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (25 bp):
GGCTGATTTAATCATCCAAACCAAG
Found at i:728783 original size:13 final size:13
Alignment explanation
Indices: 728765--728790 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
728755 ACTTCAAATT
728765 ATCTAGATTCATC
1 ATCTAGATTCATC
728778 ATCTAGATTCATC
1 ATCTAGATTCATC
728791 CCAAAATGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
ATCTAGATTCATC
Found at i:734653 original size:20 final size:20
Alignment explanation
Indices: 734624--734682 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
734614 TGCTAACTAT
*
734624 CTCACACATACATTCACACC
1 CTCACGCATACATTCACACC
734644 CTCACGCATACATTCACACC
1 CTCACGCATACATTCACACC
734664 CTCACGCATACATTCACAC
1 CTCACGCATACATTCACAC
734683 TTAACATTCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.32, C:0.44, G:0.03, T:0.20
Consensus pattern (20 bp):
CTCACGCATACATTCACACC
Found at i:736033 original size:99 final size:99
Alignment explanation
Indices: 735916--736114 Score: 274
Period size: 99 Copynumber: 2.0 Consensus size: 99
735906 AGATTAAATT
* * * * *
735916 ATTGCTTTCTAGATTTTCGCAAATGATATTATTATCCATGGTTTAAAA-AATAATATATTTTTCT
1 ATTGCTTTCTAGACTTTCGCAAATGAAATTATTATCAATGG-TTAAAACAACAATATATTCTTCT
* * *
735980 GATTAATAATAATCATTAATTTTATTAAATATAAA
65 AACTAATAATAATCATTAATTTTATTAAATACAAA
* * *
736015 ATTGCTTTTTCGACTTTCGCTAATGAAATTATTATCAATGGTTAAAACAACAATATATTCTTCTA
1 ATTGCTTTCTAGACTTTCGCAAATGAAATTATTATCAATGGTTAAAACAACAATATATTCTTCTA
*
736080 ACTAATAATAATTATTAATTTTATTAAATACAAA
66 ACTAATAATAATCATTAATTTTATTAAATACAAA
736114 A
1 A
736115 CTACTAATTT
Statistics
Matches: 87, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
98 6 0.07
99 81 0.93
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (99 bp):
ATTGCTTTCTAGACTTTCGCAAATGAAATTATTATCAATGGTTAAAACAACAATATATTCTTCTA
ACTAATAATAATCATTAATTTTATTAAATACAAA
Found at i:736353 original size:38 final size:36
Alignment explanation
Indices: 736311--736451 Score: 165
Period size: 38 Copynumber: 3.8 Consensus size: 36
736301 CACATATAAT
*
736311 ATATATAATATATATTTTTGAAAACATGTTTCGAAAAC
1 ATATATAATATATAGTTTTGAAAACAT-TTT-GAAAAC
* *
736349 ATATATAGTATATAGTTTTGAAAACCTTATTGAAAAC
1 ATATATAATATATAGTTTTGAAAACATT-TTGAAAAC
* * *
736386 ATATATGATATATAGTTTTAAAAAGATATTTTGAAAAC
1 ATATATAATATATAGTTTT-GAAA-ACATTTTGAAAAC
*
736424 ATATATAATATATAATTTTGGAAAACAT
1 ATATATAATATATAGTTTT-GAAAACAT
736452 ATTATATAGT
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
37 27 0.31
38 57 0.66
39 3 0.03
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.39
Consensus pattern (36 bp):
ATATATAATATATAGTTTTGAAAACATTTTGAAAAC
Found at i:736436 original size:22 final size:21
Alignment explanation
Indices: 736411--736484 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 21
736401 TTTTAAAAAG
736411 ATATTTTGAAAACATATATAATAT
1 ATATTTTGAAAAC--ATAT-ATAT
736435 ATAATTTTGGAAAACATAT-TAT
1 AT-ATTTT-GAAAACATATATAT
* *
736457 ATAGTTTTTGAATATATATATAT
1 ATA--TTTTGAAAACATATATAT
736480 ATATT
1 ATATT
736485 ATGTGTATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
21 3 0.07
22 13 0.30
23 10 0.23
24 6 0.14
25 5 0.12
26 6 0.14
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.46
Consensus pattern (21 bp):
ATATTTTGAAAACATATATAT
Found at i:736473 original size:2 final size:2
Alignment explanation
Indices: 736468--736561 Score: 64
Period size: 2 Copynumber: 51.0 Consensus size: 2
736458 TAGTTTTTGA
* *
736468 AT AT AT AT AT AT AT AT -T AT GT GT AT AT -T 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 AT
* *
736507 -T GT AC AT AT AT -T AT AT -T AT AGT AT AT AGT AT -T AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT
736546 AT AT -T AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT
736562 TACGTTATGG
Statistics
Matches: 75, Mismatches: 5, Indels: 24
0.72 0.05 0.23
Matches are distributed among these distances:
1 10 0.13
2 61 0.81
3 4 0.05
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.53
Consensus pattern (2 bp):
AT
Found at i:736502 original size:7 final size:7
Alignment explanation
Indices: 736468--736561 Score: 68
Period size: 7 Copynumber: 12.6 Consensus size: 7
736458 TAGTTTTTGA
736468 ATATA-T
1 ATATATT
736474 ATATA-T
1 ATATATT
736480 ATATTATGT
1 ATA-TAT-T
*
736489 GTATATT
1 ATATATT
736496 ATATATT
1 ATATATT
736503 ATAT-TGT
1 ATATAT-T
736510 ACATATATT
1 --ATATATT
736519 ATATTATAGT
1 ATA-TAT--T
*
736529 ATATAGT
1 ATATATT
736536 ATTATATT
1 A-TATATT
736544 ATATATT
1 ATATATT
736551 ATATATT
1 ATATATT
736558 ATAT
1 ATAT
736562 TACGTTATGG
Statistics
Matches: 73, Mismatches: 4, Indels: 21
0.74 0.04 0.21
Matches are distributed among these distances:
6 10 0.14
7 36 0.49
8 12 0.16
9 10 0.14
10 5 0.07
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.53
Consensus pattern (7 bp):
ATATATT
Found at i:736505 original size:5 final size:5
Alignment explanation
Indices: 736468--736563 Score: 63
Period size: 5 Copynumber: 18.2 Consensus size: 5
736458 TAGTTTTTGA
* * *
736468 ATATAT ATATAT ATATT ATGTGT ATATTAT ATATT ATATT GTACAT ATATT
1 ATAT-T ATAT-T ATATT ATAT-T ATA-T-T ATATT ATATT ATA-TT ATATT
*
736519 ATATT ATAGT ATA-T AGTATT ATATT ATA-T AT-TAT ATATT ATATT A
1 ATATT ATATT ATATT A-TATT ATATT ATATT ATAT-T ATATT ATATT A
736564 CGTTATGGTA
Statistics
Matches: 74, Mismatches: 8, Indels: 17
0.75 0.08 0.17
Matches are distributed among these distances:
4 5 0.07
5 44 0.59
6 20 0.27
7 5 0.07
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (5 bp):
ATATT
Found at i:736555 original size:39 final size:37
Alignment explanation
Indices: 736468--736593 Score: 116
Period size: 39 Copynumber: 3.3 Consensus size: 37
736458 TAGTTTTTGA
*
736468 ATATA-TATATA-TATATTATGTGTATATTA-TATATT
1 ATATATTATATATTATATTATGT-TATAGTATTATATT
736503 ATAT-TGTACATATATTATATTATAGTATATAGTATTATATT
1 ATATAT-T--ATATATTATATTAT-GT-TATAGTATTATATT
* *
736544 ATATATTATATATTATATTACGTTATGGTATAGTATATT
1 ATATATTATATATTATATTATGTTATAGTAT--TATATT
*
736583 ATTTATTATAT
1 ATATATTATAT
736594 TTTTATTTTC
Statistics
Matches: 76, Mismatches: 5, Indels: 16
0.78 0.05 0.16
Matches are distributed among these distances:
35 4 0.05
36 1 0.01
37 7 0.09
38 7 0.09
39 37 0.49
40 8 0.11
41 11 0.14
42 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (37 bp):
ATATATTATATATTATATTATGTTATAGTATTATATT
Found at i:736712 original size:13 final size:13
Alignment explanation
Indices: 736694--736727 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
736684 AGGCAAGCCT
736694 GACCCAGCAAACC
1 GACCCAGCAAACC
*
736707 GACCCAACAAACC
1 GACCCAGCAAACC
736720 GACCCAGC
1 GACCCAGC
736728 TAAGAGTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.38, C:0.47, G:0.15, T:0.00
Consensus pattern (13 bp):
GACCCAGCAAACC
Found at i:745681 original size:15 final size:15
Alignment explanation
Indices: 745647--745683 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
745637 AGTATATGTC
745647 AAATCAA-AGATCAG
1 AAATCAAGAGATCAG
745661 AAATCAAGA-ATCAG
1 AAATCAAGAGATCAG
745675 AAAATCAAG
1 -AAATCAAG
745684 TTTGTCAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (15 bp):
AAATCAAGAGATCAG
Found at i:746616 original size:14 final size:13
Alignment explanation
Indices: 746597--746646 Score: 55
Period size: 14 Copynumber: 3.7 Consensus size: 13
746587 TAATATATAG
746597 TTTTGAAAACTTTT
1 TTTTGAAAAC-TTT
**
746611 TTTTGAAAACATAG
1 TTTTGAAAAC-TTT
*
746625 TTTTGAAAACGTT
1 TTTTGAAAACTTT
746638 TTTTGAAAA
1 TTTTGAAAA
746647 TATATATAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 9 0.30
14 21 0.70
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.46
Consensus pattern (13 bp):
TTTTGAAAACTTT
Found at i:746625 original size:28 final size:27
Alignment explanation
Indices: 746593--746646 Score: 90
Period size: 28 Copynumber: 2.0 Consensus size: 27
746583 TATATAATAT
*
746593 ATAGTTTTGAAAACTTTTTTTTGAAAAC
1 ATAGTTTTGAAAAC-GTTTTTTGAAAAC
746621 ATAGTTTTGAAAACGTTTTTTGAAAA
1 ATAGTTTTGAAAACGTTTTTTGAAAA
746647 TATATATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (27 bp):
ATAGTTTTGAAAACGTTTTTTGAAAAC
Found at i:746672 original size:38 final size:38
Alignment explanation
Indices: 746621--746775 Score: 204
Period size: 38 Copynumber: 4.1 Consensus size: 38
746611 TTTTGAAAAC
* * *
746621 ATAGTTTTGAAAACGTTTTTTGAAAATATATATAATAT
1 ATAGTTTTAAAAACATTTTTTGAAAACATATATAATAT
* *
746659 ATAGTTTTAAAAACATTTTTCGAAAACATATATAGTAT
1 ATAGTTTTAAAAACATTTTTTGAAAACATATATAATAT
* * *
746697 ATAGTTTTGAAAAC-CTTTTTGAAAACATATATGATAT
1 ATAGTTTTAAAAACATTTTTTGAAAACATATATAATAT
**
746734 ATAGTTTTAAAAACATAATTTGAAAACATATATATATAT
1 ATAGTTTTAAAAACATTTTTTGAAAACATATATA-ATAT
746773 ATA
1 ATA
746776 TATATATATT
Statistics
Matches: 100, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
37 32 0.32
38 61 0.61
39 7 0.07
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (38 bp):
ATAGTTTTAAAAACATTTTTTGAAAACATATATAATAT
Found at i:746716 original size:75 final size:75
Alignment explanation
Indices: 746621--746773 Score: 238
Period size: 75 Copynumber: 2.0 Consensus size: 75
746611 TTTTGAAAAC
* * *
746621 ATAGTTTTGAAAACGTTTTTTGAAAATATATATAATATATAGTTTTAAAAACAT-TTTTCGAAAA
1 ATAGTTTTGAAAACGCTTTTTGAAAACATATATAATATATAGTTTTAAAAACATAATTT-GAAAA
746685 CATATATAGTAT
65 CATATATA-TAT
*
746697 ATAGTTTTGAAAAC-CTTTTTGAAAACATATATGATATATAGTTTTAAAAACATAATTTGAAAAC
1 ATAGTTTTGAAAACGCTTTTTGAAAACATATATAATATATAGTTTTAAAAACATAATTTGAAAAC
746761 ATATATATAT
66 ATATATATAT
746771 ATA
1 ATA
746774 TATATATATA
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
74 6 0.08
75 49 0.68
76 17 0.24
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (75 bp):
ATAGTTTTGAAAACGCTTTTTGAAAACATATATAATATATAGTTTTAAAAACATAATTTGAAAAC
ATATATATAT
Found at i:746776 original size:10 final size:10
Alignment explanation
Indices: 746761--747282 Score: 290
Period size: 8 Copynumber: 59.0 Consensus size: 10
746751 ATTTGAAAAC
746761 ATATATATAT
1 ATATATATAT
746771 ATATATATAT
1 ATATATATAT
746781 ATAT-TATA-
1 ATATATATAT
746789 ATATATATAT
1 ATATATATAT
746799 ATATATATAT
1 ATATATATAT
746809 ATATATATAT
1 ATATATATAT
* * *
746819 ATAGAGTTTTT
1 ATATA-TATAT
* * *
746830 A-AAATGGTTT
1 ATATAT-ATAT
* * *
746840 TTGA-AAACAT
1 AT-ATATATAT
746850 ATATA-ATAT
1 ATATATATAT
* *
746859 ATACT-TTTAG
1 ATA-TATATAT
* *
746869 A-AAACAT-T
1 ATATATATAT
* *
746877 ATATATTTTT
1 ATATATATAT
*
746887 GA-AAATAT-T
1 -ATATATATAT
746896 AT-TATAT-T
1 ATATATATAT
746904 ATATATATAT
1 ATATATATAT
746914 -TATAT-TAT
1 ATATATATAT
746922 AT-TATATAT
1 ATATATATAT
*
746931 AT-TATATTT
1 ATATATATAT
746940 ATAT-TATAT
1 ATATATATAT
746949 -TATAT-TAT
1 ATATATATAT
746957 AT-TATATAT
1 ATATATATAT
746966 ATATATAT-T
1 ATATATATAT
746975 ATAT-TATAT
1 ATATATATAT
746984 -TATAT-TAT
1 ATATATATAT
746992 ATATATATAT
1 ATATATATAT
747002 -TATAT-TAT
1 ATATATATAT
747010 AT-TATAT-T
1 ATATATATAT
747018 ATAT-TATAT
1 ATATATATAT
747027 -TATAT-TAT
1 ATATATATAT
747035 AT-TATATAT
1 ATATATATAT
747044 AT-TATAT-T
1 ATATATATAT
747052 ATAT-TATAT
1 ATATATATAT
747061 -TATAT-TAT
1 ATATATATAT
747069 AT-TATAT-T
1 ATATATATAT
747077 ATAT-TATAT
1 ATATATATAT
747086 -TATATATAT
1 ATATATATAT
747095 ATAT-TATAT
1 ATATATATAT
747104 -TATAT-TAT
1 ATATATATAT
747112 AT-TATAT-T
1 ATATATATAT
747120 ATAT-TATAT
1 ATATATATAT
747129 -TATAT-TAT
1 ATATATATAT
747137 AT-TATAT-T
1 ATATATATAT
747145 ATAT-TATAT
1 ATATATATAT
747154 -TATAT-TAT
1 ATATATATAT
747162 AT-TATAT-T
1 ATATATATAT
*
747170 ATAT-TATTT
1 ATATATATAT
747179 AT-TATAT-T
1 ATATATATAT
747187 ATAT-TATAT
1 ATATATATAT
747196 -TATAT-TAT
1 ATATATATAT
*
747204 ATATATTTAT
1 ATATATATAT
*
747214 ATATTTAT-T
1 ATATATATAT
747223 ATAT-TATAT
1 ATATATATAT
747232 -TATAT-TAT
1 ATATATATAT
747240 AT-TATAT-T
1 ATATATATAT
747248 ATAT-TATAT
1 ATATATATAT
*
747257 -TATTTAT-T
1 ATATATATAT
747265 ATAT-TATAT
1 ATATATATAT
*
747274 TTAT-TATAT
1 ATATATATAT
747283 TTTTATTATA
Statistics
Matches: 410, Mismatches: 29, Indels: 147
0.70 0.05 0.25
Matches are distributed among these distances:
8 165 0.40
9 161 0.39
10 77 0.19
11 6 0.01
12 1 0.00
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (10 bp):
ATATATATAT
Found at i:746790 original size:38 final size:38
Alignment explanation
Indices: 746714--746821 Score: 105
Period size: 38 Copynumber: 2.8 Consensus size: 38
746704 TGAAAACCTT
* *
746714 TTTGAAAACATATATGATATATAGT-TTTA-AAAACATAA
1 TTTGAAAACATATAT-ATATATA-TATATATATAACATAA
**
746752 TTTGAAAACATATATATATATATATATATATATTATAA
1 TTTGAAAACATATATATATATATATATATATAACATAA
* * *
746790 TAT-ATATATATATATATATATATATATATATA
1 TTTGA-AAACATATATATATATATATATATATA
746822 GAGTTTTTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
36 1 0.02
37 11 0.18
38 48 0.80
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.44
Consensus pattern (38 bp):
TTTGAAAACATATATATATATATATATATATAACATAA
Found at i:746792 original size:20 final size:19
Alignment explanation
Indices: 746761--746820 Score: 69
Period size: 18 Copynumber: 3.4 Consensus size: 19
746751 ATTTGAAAAC
746761 ATATATA-TAT-ATATA-T
1 ATATATATTATAATATATT
746777 ATATATATTATAATATA-T
1 ATATATATTATAATATATT
746795 ATATATA-TAT-ATATATAT
1 ATATATATTATAATATAT-T
746813 ATATATAT
1 ATATATAT
746821 AGAGTTTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
16 12 0.31
17 6 0.15
18 21 0.54
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATATATTATAATATATT
Found at i:746821 original size:20 final size:20
Alignment explanation
Indices: 746761--747282 Score: 290
Period size: 17 Copynumber: 29.5 Consensus size: 20
746751 ATTTGAAAAC
746761 ATATATATATATATATATAT
1 ATATATATATATATATATAT
746781 ATAT-TATA-ATATATATAT
1 ATATATATATATATATATAT
746799 ATATATATATATATATATAT
1 ATATATATATATATATATAT
* * * * * *
746819 ATAGAGTTTTTA-AAATGGTTT
1 ATATA-TATATATATAT-ATAT
* * *
746840 TTGA-AAACATATATA-ATAT
1 AT-ATATATATATATATATAT
* * * *
746859 ATACT-TTTAGA-AAACAT-T
1 ATA-TATATATATATATATAT
* * *
746877 ATATATTTTTGA-AAATAT-T
1 ATATATATAT-ATATATATAT
746896 AT-TATAT-TATATATATAT
1 ATATATATATATATATATAT
746914 -TATAT-TATAT-TATATAT
1 ATATATATATATATATATAT
*
746931 AT-TATATTTATAT-TATAT
1 ATATATATATATATATATAT
746949 -TATAT-TATAT-TATATAT
1 ATATATATATATATATATAT
746966 ATATATAT-TATAT-TATAT
1 ATATATATATATATATATAT
746984 -TATAT-TATATATATATAT
1 ATATATATATATATATATAT
747002 -TATAT-TATAT-TATAT-T
1 ATATATATATATATATATAT
747018 ATAT-TATAT-TATAT-TAT
1 ATATATATATATATATATAT
747035 AT-TATATATAT-TATAT-T
1 ATATATATATATATATATAT
747052 ATAT-TATAT-TATAT-TAT
1 ATATATATATATATATATAT
747069 AT-TATAT-TATAT-TATAT
1 ATATATATATATATATATAT
747086 -TATATATATATAT-TATAT
1 ATATATATATATATATATAT
747104 -TATAT-TATAT-TATAT-T
1 ATATATATATATATATATAT
747120 ATAT-TATAT-TATAT-TAT
1 ATATATATATATATATATAT
747137 AT-TATAT-TATAT-TATAT
1 ATATATATATATATATATAT
747154 -TATAT-TATAT-TATAT-T
1 ATATATATATATATATATAT
*
747170 ATAT-TATTTAT-TATAT-T
1 ATATATATATATATATATAT
747187 ATAT-TATAT-TATAT-TAT
1 ATATATATATATATATATAT
* *
747204 ATATATTTATATATTTAT-T
1 ATATATATATATATATATAT
747223 ATAT-TATAT-TATAT-TAT
1 ATATATATATATATATATAT
747240 AT-TATAT-TATAT-TATAT
1 ATATATATATATATATATAT
*
747257 -TATTTAT-TATAT-TATAT
1 ATATATATATATATATATAT
*
747274 TTAT-TATAT
1 ATATATATAT
747283 TTTTATTATA
Statistics
Matches: 403, Mismatches: 34, Indels: 132
0.71 0.06 0.23
Matches are distributed among these distances:
16 34 0.08
17 192 0.48
18 106 0.26
19 36 0.09
20 24 0.06
21 10 0.02
22 1 0.00
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (20 bp):
ATATATATATATATATATAT
Found at i:746844 original size:125 final size:123
Alignment explanation
Indices: 746686--746948 Score: 318
Period size: 125 Copynumber: 2.1 Consensus size: 123
746676 TTTCGAAAAC
* * *
746686 ATATATAGTATATAGTTTTGAAAACCTTTTTGAAAACATATATGATATATAGTTTTA-AAAAC-A
1 ATATATA-TATAGAGTTTTGAAAACCTTTTTGAAAACATATATAATATATACTTTTAGAAAACTA
746749 TA-A-TTTGAAAACATATATATATATATATATATATATTATAATATATATATATATATATATAT
65 TATATTTTGAAAACAT-TAT-TATAT-TATATATATATTATAATATAT-TATATATAT-TATAT
* **
746811 ATATATATATAGAGTTTTTAAAATGGTTTTTGAAAACATATATAATATATACTTTTAGAAAACAT
1 ATATATATATAGAGTTTTGAAAA-CCTTTTTGAAAACATATATAATATATACTTTTAGAAAAC--
* *
746876 TATATATTTTTGAAAATATTATTATATTATATATATATTATATTATATTATATATATTATAT
63 TATATA-TTTTGAAAACATTATTATATTATATATATATTATAATATATTATATATATTATAT
*
746938 TTATATTATAT
1 ATATA-TATAT
746949 TATATTATAT
Statistics
Matches: 120, Mismatches: 9, Indels: 15
0.83 0.06 0.10
Matches are distributed among these distances:
124 14 0.12
125 36 0.30
126 5 0.04
127 9 0.08
128 14 0.12
129 23 0.19
130 6 0.05
131 3 0.03
132 10 0.08
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (123 bp):
ATATATATATAGAGTTTTGAAAACCTTTTTGAAAACATATATAATATATACTTTTAGAAAACTAT
ATATTTTGAAAACATTATTATATTATATATATATTATAATATATTATATATATTATAT
Found at i:746905 original size:5 final size:5
Alignment explanation
Indices: 746895--747294 Score: 635
Period size: 5 Copynumber: 80.8 Consensus size: 5
746885 TTGAAAATAT
746895 TATTA TATTA TATATA TATTA TATTA TATTA TA-TA TATTA TATTTA TATTA
1 TATTA TATTA TAT-TA TATTA TATTA TATTA TATTA TATTA TA-TTA TATTA
746946 TATTA TATTA TATTA TA-TA TATATA TATTA TATTA TATTA TATTA TA-TA
1 TATTA TATTA TATTA TATTA TAT-TA TATTA TATTA TATTA TATTA TATTA
746995 TA-TA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TA-TA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
747043 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TA-TA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
747092 TA-TA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
747141 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TTTATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA --TATTA TATTA TATTA
747193 TATTA TATTA TA-TA TATT- TA-TA TATT- TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
*
747239 TATTA TATTA TATTA TATTA TTTATTA TATTA TATT- TATTA TATTTT
1 TATTA TATTA TATTA TATTA --TATTA TATTA TATTA TATTA TA-TTA
747286 TATTA TATT
1 TATTA TATT
747295 TTGTTTTATT
Statistics
Matches: 375, Mismatches: 2, Indels: 36
0.91 0.00 0.09
Matches are distributed among these distances:
3 1 0.00
4 44 0.12
5 301 0.80
6 19 0.05
7 10 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:748520 original size:21 final size:21
Alignment explanation
Indices: 748496--748543 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
748486 TTTTTTCTTA
*
748496 AATTCACCACTCACTTTATTT
1 AATTCAACACTCACTTTATTT
* * **
748517 AATTTAATACTTTCTTTATTT
1 AATTCAACACTCACTTTATTT
748538 AATTCA
1 AATTCA
748544 TGTTTTCATT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (21 bp):
AATTCAACACTCACTTTATTT
Found at i:748843 original size:2 final size:2
Alignment explanation
Indices: 748836--748871 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
748826 ATTTCTCGAC
* *
748836 AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
748872 TTCTTTTCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:752410 original size:31 final size:31
Alignment explanation
Indices: 752373--752436 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
752363 CAATGACGTT
*
752373 CACATGCCACGTGTCGAAAGTGATAATGTGA
1 CACATGCCACGTGTCGAAAGTGATAACGTGA
* *
752404 CACATGCCACGTGTTGAAAGTGATGACGTGA
1 CACATGCCACGTGTCGAAAGTGATAACGTGA
752435 CA
1 CA
752437 TTATGTCTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (31 bp):
CACATGCCACGTGTCGAAAGTGATAACGTGA
Found at i:755207 original size:37 final size:39
Alignment explanation
Indices: 755160--755269 Score: 149
Period size: 37 Copynumber: 2.9 Consensus size: 39
755150 TATAGTATAG
755160 TTTTGAAAAACGTATAATATATAGTTTTTAGAAAACA-AT
1 TTTTG-AAAACGTATAATATATAGTTTTTAGAAAACATAT
*
755199 TTTT-AAAACATATAATATATAG-TTTT-GAAAACATAT
1 TTTTGAAAACGTATAATATATAGTTTTTAGAAAACATAT
755235 TTTTGAAAACGTATATAATATATAGTTTTTA-AAAA
1 TTTTGAAAACG--TATAATATATAGTTTTTAGAAAA
755270 TCGGTTGCTG
Statistics
Matches: 63, Mismatches: 2, Indels: 11
0.83 0.03 0.14
Matches are distributed among these distances:
35 7 0.11
36 10 0.16
37 22 0.35
39 16 0.25
40 8 0.13
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (39 bp):
TTTTGAAAACGTATAATATATAGTTTTTAGAAAACATAT
Found at i:755313 original size:13 final size:14
Alignment explanation
Indices: 755295--755332 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
755285 ATATAATATA
755295 GTTTTTT-AAAAAT
1 GTTTTTTGAAAAAT
*
755308 GTTTTTTGAAACAT
1 GTTTTTTGAAAAAT
*
755322 ATTTTTTGAAA
1 GTTTTTTGAAA
755333 TATATAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (14 bp):
GTTTTTTGAAAAAT
Done.