Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397257.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_95.0, 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: 12062019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 103452 characters in sequence are not A, C, G, or T
File 20 of 26
Found at i:8157988 original size:2 final size:2
Alignment explanation
Indices: 8157981--8158018 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
8157971 TAAACATGTG
* *
8157981 AT AT AT AT AA AT AC 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
8158019 TCTCTCAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:8159255 original size:35 final size:33
Alignment explanation
Indices: 8159204--8159285 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 33
8159194 ACCTTTTTTA
* *
8159204 AAAAATAATA-ATATAAGAAAAGTATATTAAAAAT
1 AAAAATAAAATATATAAGAAAA-TA-ATAAAAAAT
* **
8159238 AAATATAAAATATATAAGATTATAATAAAAAAT
1 AAAAATAAAATATATAAGAAAATAATAAAAAAT
8159271 AAAAATAAAATATAT
1 AAAAATAAAATATAT
8159286 GACATTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
33 22 0.54
34 10 0.24
35 9 0.22
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (33 bp):
AAAAATAAAATATATAAGAAAATAATAAAAAAT
Found at i:8159295 original size:27 final size:29
Alignment explanation
Indices: 8159229--8159298 Score: 72
Period size: 33 Copynumber: 2.3 Consensus size: 29
8159219 AGAAAAGTAT
* *
8159229 ATTAAAAATAAATATAAAATATATAAGATT
1 ATTAAAAATAAAAATAAAATATAT-AGATC
8159259 ATAATAAAAAATAAAAATAAAATATAT-GA-C
1 AT--T-AAAAATAAAAATAAAATATATAGATC
8159289 ATTAAAAATA
1 ATTAAAAATA
8159299 TTTAAAAGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
27 7 0.20
28 1 0.03
30 4 0.11
31 2 0.06
32 1 0.03
33 20 0.57
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (29 bp):
ATTAAAAATAAAAATAAAATATATAGATC
Found at i:8164946 original size:27 final size:29
Alignment explanation
Indices: 8164916--8164976 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
8164906 GGCATTAAAA
*
8164916 TGTAACAA-AAT-GTTTTTGAATATGACG
1 TGTAACAATAATAGTTTTTCAATATGACG
*
8164943 TGTAACAATAATATTTTTTCAATATGACG
1 TGTAACAATAATAGTTTTTCAATATGACG
8164972 TGTAA
1 TGTAA
8164977 TAACAGTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 8 0.27
28 3 0.10
29 19 0.63
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (29 bp):
TGTAACAATAATAGTTTTTCAATATGACG
Found at i:8164969 original size:29 final size:27
Alignment explanation
Indices: 8164916--8165086 Score: 102
Period size: 26 Copynumber: 6.1 Consensus size: 27
8164906 GGCATTAAAA
*
8164916 TGTAACAA-AATGTTTTTGAATATGACG
1 TGTAACAATAAT-TTTTTTAATATGACG
8164943 TGTAACAATAATATTTTTTCAATATGACG
1 TGTAACAATAAT-TTTTTT-AATATGACG
* * *
8164972 TGTAATAACAGTATTTTTTTTCAACATGACG
1 TG---TAACAATAATTTTTTT-AATATGACG
* * *
8165003 TATAAC-A-ACTTTTTTTAACTATAACG
1 TGTAACAATAATTTTTTTAA-TATGACG
* * * *
8165029 TGTAA-TAT-GTTTTTGT-ACATGACG
1 TGTAACAATAATTTTTTTAATATGACG
8165053 TGTAACAATAGTATTTTTTTTAATATGACG
1 TGTAACAATA--A-TTTTTTTAATATGACG
8165083 TGTA
1 TGTA
8165087 GCAACCTAAT
Statistics
Matches: 111, Mismatches: 19, Indels: 25
0.72 0.12 0.16
Matches are distributed among these distances:
24 10 0.09
25 5 0.05
26 24 0.22
27 8 0.07
28 12 0.11
29 17 0.15
30 11 0.10
31 16 0.14
32 8 0.07
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (27 bp):
TGTAACAATAATTTTTTTAATATGACG
Found at i:8164994 original size:31 final size:29
Alignment explanation
Indices: 8164916--8165011 Score: 97
Period size: 31 Copynumber: 3.3 Consensus size: 29
8164906 GGCATTAAAA
* *
8164916 TGTAACAA-AAT-GTTTTTGAATATGACG
1 TGTAACAACAATATTTTTTCAATATGACG
*
8164943 TGTAACAATAATATTTTTTCAATATGACG
1 TGTAACAACAATATTTTTTCAATATGACG
* * *
8164972 TGTAATAACAGTATTTTTTTTCAACATGACG
1 TGTAACAACA--ATATTTTTTCAATATGACG
*
8165003 TATAACAAC
1 TGTAACAAC
8165012 TTTTTTTAAC
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
27 8 0.14
28 3 0.05
29 22 0.39
31 24 0.42
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (29 bp):
TGTAACAACAATATTTTTTCAATATGACG
Found at i:8165231 original size:45 final size:45
Alignment explanation
Indices: 8165128--8165231 Score: 127
Period size: 45 Copynumber: 2.3 Consensus size: 45
8165118 GTAAATAACT
* **
8165128 TGTAACATATTTTTGGACATGGAGTGTAACAACCTAACCATGATG
1 TGTAACATATTTTTGCACATGGAGTGTAACAACCTAACCATGACA
* * * * * *
8165173 TGTTACATGTTTTTGCATATGGCGTGTAATAATCTAACCATGACA
1 TGTAACATATTTTTGCACATGGAGTGTAACAACCTAACCATGACA
8165218 TGTAACATATTTTT
1 TGTAACATATTTTT
8165232 ATACATAATA
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (45 bp):
TGTAACATATTTTTGCACATGGAGTGTAACAACCTAACCATGACA
Found at i:8165372 original size:2 final size:2
Alignment explanation
Indices: 8165367--8165400 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
8165357 AAAATGTTCT
8165367 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
8165401 GTGTTGATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8179762 original size:2 final size:2
Alignment explanation
Indices: 8179755--8179783 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
8179745 CTTACTGCAA
8179755 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8179784 ATCTCTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8185566 original size:12 final size:12
Alignment explanation
Indices: 8185538--8185566 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
8185528 ACTTTTGCTG
8185538 TTTTT-TTTTTT
1 TTTTTGTTTTTT
8185549 TTTTTGTTTTTT
1 TTTTTGTTTTTT
8185561 TTTTTG
1 TTTTTG
8185567 CTTAGCAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (12 bp):
TTTTTGTTTTTT
Found at i:8198236 original size:47 final size:45
Alignment explanation
Indices: 8198183--8198282 Score: 132
Period size: 45 Copynumber: 2.2 Consensus size: 45
8198173 AATGACAATG
8198183 TCTTATTA-TTTAAA-AAAATAAAAAATTAATAAAAAGACACAGCA
1 TCTTATTATTTTAAAGAAAATAAAAAATTAAT-AAAAGACACAGCA
* * * *
8198227 TCTTATTATTTTAAAGAAAATAAAAACTTTATTAATGACACAGCA
1 TCTTATTATTTTAAAGAAAATAAAAAATTAATAAAAGACACAGCA
*
8198272 TCTTATGATTT
1 TCTTATTATTT
8198283 GATAGTATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
44 8 0.16
45 27 0.55
46 14 0.29
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.35
Consensus pattern (45 bp):
TCTTATTATTTTAAAGAAAATAAAAAATTAATAAAAGACACAGCA
Found at i:8203927 original size:2 final size:2
Alignment explanation
Indices: 8203920--8203966 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
8203910 TTTTCTCCTT
8203920 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
8203962 TA TA T
1 TA TA T
8203967 TGCCCCCTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8204627 original size:3 final size:3
Alignment explanation
Indices: 8204621--8204656 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
8204611 ATCATCTTTA
* *
8204621 TCT TCT TCT TCT TCT TCT TCC TCT TCT TCC TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
8204657 GTGACTAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (3 bp):
TCT
Found at i:8223228 original size:108 final size:104
Alignment explanation
Indices: 8223069--8223272 Score: 270
Period size: 108 Copynumber: 1.9 Consensus size: 104
8223059 AATAGAAAAT
* *
8223069 AAAAATTAAAAAAAAAAGTAAAAATGAAGTTAAAGTAAAAAACTATATTAATAATTTAATAATAA
1 AAAAATTAAAAAAAAAAGTAAAAAAGAAATTAAAGTAAAAAACTATATTAATAATTTAATAATAA
8223134 ATAATT-A-ATATTAAAATTTTTAATGAAAATGGAAATTA
66 ATAATTAACATATTAAAA-TTTTAATGAAAATGGAAATTA
* *
8223172 AAAAATTAAAATACAAATAGAGATAAAAAAGAAATTGAAA-TAAAAAATTGTATTAATAATTTAA
1 AAAAATTAAAA-A-AAA-A-AG-TAAAAAAGAAATT-AAAGTAAAAAACTATATTAATAATTTAA
* *
8223236 TAATAAATTATTAACATTTTAAAATTTTAATGAAAAT
60 TAATAAATAATTAACATATTAAAATTTTAATGAAAAT
8223273 ACAAATCAAA
Statistics
Matches: 87, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
103 11 0.13
104 1 0.01
105 3 0.03
106 1 0.01
107 2 0.02
108 44 0.51
109 17 0.20
110 8 0.09
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.32
Consensus pattern (104 bp):
AAAAATTAAAAAAAAAAGTAAAAAAGAAATTAAAGTAAAAAACTATATTAATAATTTAATAATAA
ATAATTAACATATTAAAATTTTAATGAAAATGGAAATTA
Found at i:8227727 original size:27 final size:27
Alignment explanation
Indices: 8227681--8227734 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
8227671 TTTTATCATA
* * * *
8227681 TTTAATAAATTTTTATATATTTTTTAT
1 TTTAATAAATATTAAAATATTTCTTAT
8227708 TTTAATAAATATTAAAATATTTCTTAT
1 TTTAATAAATATTAAAATATTTCTTAT
8227735 GTAACATTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTAATAAATATTAAAATATTTCTTAT
Found at i:8227880 original size:29 final size:29
Alignment explanation
Indices: 8227848--8227942 Score: 70
Period size: 30 Copynumber: 3.3 Consensus size: 29
8227838 GATAAAAAAA
*
8227848 ATTTCAATTAATAATAATTAAAATTTTTT
1 ATTTAAATTAATAATAATTAAAATTTTTT
* * **
8227877 ATTTTAGTTAA-AATAAAATTAAAAAGTTTT
1 ATTTAAATTAATAAT--AATTAAAATTTTTT
* * *
8227907 AATTAAATGTAATAAAAATTAAAA--ATTT
1 ATTTAAAT-TAATAATAATTAAAATTTTTT
8227935 ATTTAAAT
1 ATTTAAAT
8227943 AGTTTTAAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
28 13 0.25
29 9 0.17
30 25 0.48
31 3 0.06
32 2 0.04
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (29 bp):
ATTTAAATTAATAATAATTAAAATTTTTT
Found at i:8253298 original size:1 final size:1
Alignment explanation
Indices: 8253292--8253321 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
8253282 AGAGAGAAAA
8253292 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
8253322 TGTTACAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:8258126 original size:23 final size:21
Alignment explanation
Indices: 8258100--8258156 Score: 51
Period size: 23 Copynumber: 2.5 Consensus size: 21
8258090 TATTCTTGAC
**
8258100 ATAATATTTTAAAAAGTTTTTAA
1 ATAA-ATTTTAAAAA-AATTTAA
8258123 ATAAATTATTTAAAAAAATTTAA
1 ATAAA-T-TTTAAAAAAATTTAA
8258146 ATAAAATTTTA
1 AT-AAATTTTA
8258157 TTTTTTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
22 5 0.17
23 13 0.45
24 11 0.38
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
ATAAATTTTAAAAAAATTTAA
Found at i:8258214 original size:31 final size:29
Alignment explanation
Indices: 8258152--8258217 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 29
8258142 TTAAATAAAA
*
8258152 TTTTATTTTTTTATTACATTCAATTAAGT
1 TTTTATTTTTTTATTACATTCAAATAAGT
** *
8258181 TTTTATATTTTTTATTTTATGTCAAATAGGT
1 TTTTAT-TTTTTTATTACAT-TCAAATAAGT
8258212 TTTTAT
1 TTTTAT
8258218 GAGTAATGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 6 0.19
30 11 0.35
31 14 0.45
ACGTcount: A:0.26, C:0.05, G:0.06, T:0.64
Consensus pattern (29 bp):
TTTTATTTTTTTATTACATTCAAATAAGT
Found at i:8258923 original size:15 final size:15
Alignment explanation
Indices: 8258873--8258928 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
8258863 AAAATTAAAA
*
8258873 TTTATATAAA-TTAT
1 TTTATAAAAATTTAT
*
8258887 TTTACCAAACAATTTA-
1 TTTA-TAAA-AATTTAT
8258903 TTTATAAAAATTTAT
1 TTTATAAAAATTTAT
8258918 TTTATAAAAAT
1 TTTATAAAAAT
8258929 AAGTTTATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
14 10 0.29
15 16 0.46
16 6 0.17
17 3 0.09
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTATAAAAATTTAT
Found at i:8262768 original size:17 final size:17
Alignment explanation
Indices: 8262726--8262759 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
8262716 TATGAAATTG
*
8262726 ACTTTGTATGATATCTA
1 ACTTTGTAAGATATCTA
8262743 ACTTTGTAAGATATCTA
1 ACTTTGTAAGATATCTA
8262760 TTTTTGTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (17 bp):
ACTTTGTAAGATATCTA
Found at i:8263027 original size:27 final size:27
Alignment explanation
Indices: 8262997--8263060 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
8262987 TTTACCTACC
*
8262997 AGAAGTGGATGGAT-ACTTTTATTCACA
1 AGAAGTGGATGGATAAC-TTTACTCACA
* *
8263024 AGAAGTGAATGGATAACTTTACTCACC
1 AGAAGTGGATGGATAACTTTACTCACA
8263051 AGAAGTGGAT
1 AGAAGTGGAT
8263061 AGCTTTTACC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 30 0.94
28 2 0.06
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.28
Consensus pattern (27 bp):
AGAAGTGGATGGATAACTTTACTCACA
Found at i:8263066 original size:23 final size:24
Alignment explanation
Indices: 8263033--8263078 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
8263023 AAGAAGTGAA
*
8263033 TGGATAAC-TTTACTCACCAGAAG
1 TGGATAACTTTTACCCACCAGAAG
*
8263056 TGGATAGCTTTTACCCACCAGAA
1 TGGATAACTTTTACCCACCAGAA
8263079 ATAGATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (24 bp):
TGGATAACTTTTACCCACCAGAAG
Found at i:8277792 original size:2 final size:2
Alignment explanation
Indices: 8277787--8277858 Score: 135
Period size: 2 Copynumber: 36.0 Consensus size: 2
8277777 AAAATATATG
8277787 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
8277829 GA GA GA GA GA GA GA GA GA TA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
8277859 AGGGAGGGGG
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.49, T:0.01
Consensus pattern (2 bp):
GA
Found at i:8279114 original size:8 final size:8
Alignment explanation
Indices: 8279101--8279130 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
8279091 TATTATAGGA
8279101 ATAAAATT
1 ATAAAATT
8279109 ATAAAATT
1 ATAAAATT
*
8279117 ATAAAAAT
1 ATAAAATT
8279125 ATAAAA
1 ATAAAA
8279131 ATATGTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (8 bp):
ATAAAATT
Found at i:8279131 original size:8 final size:8
Alignment explanation
Indices: 8279101--8279134 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
8279091 TATTATAGGA
*
8279101 ATAAAATT
1 ATAAAAAT
*
8279109 ATAAAATT
1 ATAAAAAT
8279117 ATAAAAAT
1 ATAAAAAT
8279125 ATAAAAAT
1 ATAAAAAT
8279133 AT
1 AT
8279135 GTTAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (8 bp):
ATAAAAAT
Found at i:8279191 original size:27 final size:29
Alignment explanation
Indices: 8279155--8279209 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
8279145 TAAAAACTTT
*
8279155 ATAAGAATAAATTAT-AAAATTTTAAAAA
1 ATAAGAATAAAGTATAAAAATTTTAAAAA
8279183 ATAA-AATAAAGTATAAAAATTTTAAAA
1 ATAAGAATAAAGTATAAAAATTTTAAAA
8279210 TTGTTGAGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 9 0.36
28 16 0.64
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (29 bp):
ATAAGAATAAAGTATAAAAATTTTAAAAA
Found at i:8282072 original size:45 final size:45
Alignment explanation
Indices: 8281999--8282088 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 45
8281989 GTAGTTGCGA
* * *
8281999 CTATAATTGTGAAATCTCTTACATAGATTCATGGT-ATTATATAGC
1 CTATAATTGTGAAATCTCTGACAAAGATTCAAGGTAATT-TATAGC
* * *
8282044 CTATAGTTGTGAACTCTCTGAGAAAGATTCAAGGTAATTTATAGC
1 CTATAATTGTGAAATCTCTGACAAAGATTCAAGGTAATTTATAGC
8282089 TAGGCTATCT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 35 0.92
46 3 0.08
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (45 bp):
CTATAATTGTGAAATCTCTGACAAAGATTCAAGGTAATTTATAGC
Found at i:8286978 original size:7 final size:8
Alignment explanation
Indices: 8286960--8286986 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
8286950 AAGGTATGTG
8286960 TTTTGGGT
1 TTTTGGGT
8286968 TTTTGGGT
1 TTTTGGGT
8286976 TTTTGGGT
1 TTTTGGGT
8286984 TTT
1 TTT
8286987 ATCAGTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (8 bp):
TTTTGGGT
Found at i:8290987 original size:23 final size:20
Alignment explanation
Indices: 8290957--8291007 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
8290947 TTTACCTTTG
8290957 ATTAATTTTTATAATTATTATT
1 ATTAATTTTTATAATT-TT-TT
*
8290979 ATATAA-TTTTATTATTTTTT
1 AT-TAATTTTTATAATTTTTT
8290999 ATTAATTTT
1 ATTAATTTT
8291008 AAAAAAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 3 0.12
20 7 0.27
21 2 0.08
22 11 0.42
23 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTAATTTTTATAATTTTTT
Found at i:8290992 original size:19 final size:19
Alignment explanation
Indices: 8290970--8291008 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
8290960 AATTTTTATA
8290970 ATTATTATTATA-TAATTTT
1 ATTATT-TTATATTAATTTT
*
8290989 ATTATTTTTTATTAATTTT
1 ATTATTTTATATTAATTTT
8291008 A
1 A
8291009 AAAAAAAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTATTTTATATTAATTTT
Found at i:8299433 original size:27 final size:27
Alignment explanation
Indices: 8299398--8299454 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
8299388 CCGTGTACGT
8299398 TATGTATGCCTTGGGACAGGCTGTTTA
1 TATGTATGCCTTGGGACAGGCTGTTTA
8299425 TATGTATGCCTTGGGACAGGCTGTTTA
1 TATGTATGCCTTGGGACAGGCTGTTTA
8299452 TAT
1 TAT
8299455 ATATCCGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.19, C:0.14, G:0.28, T:0.39
Consensus pattern (27 bp):
TATGTATGCCTTGGGACAGGCTGTTTA
Found at i:8301767 original size:2 final size:2
Alignment explanation
Indices: 8301760--8301804 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
8301750 TGCTTGCAGC
8301760 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8301801 AT AT
1 AT AT
8301805 TCCAAATTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:8310351 original size:46 final size:46
Alignment explanation
Indices: 8310284--8310376 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
8310274 AGCTAATATA
8310284 TTCCCTCCAATGCTAGATTTTGTAGTGCAAGCATGTGAAAACAGTT
1 TTCCCTCCAATGCTAGATTTTGTAGTGCAAGCATGTGAAAACAGTT
8310330 TTCCCTCCAATGCTAGATTTTGTAGTGCAAGCATGTGAAAACAGTT
1 TTCCCTCCAATGCTAGATTTTGTAGTGCAAGCATGTGAAAACAGTT
8310376 T
1 T
8310377 AGTTAAAACC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (46 bp):
TTCCCTCCAATGCTAGATTTTGTAGTGCAAGCATGTGAAAACAGTT
Found at i:8313450 original size:11 final size:10
Alignment explanation
Indices: 8313436--8313479 Score: 54
Period size: 11 Copynumber: 4.3 Consensus size: 10
8313426 GTTTATTTTA
8313436 TTTTTATAATT
1 TTTTTAT-ATT
8313447 TTTTT-TATT
1 TTTTTATATT
8313456 TTTTTATCATT
1 TTTTTAT-ATT
*
8313467 TATTTATATT
1 TTTTTATATT
8313477 TTT
1 TTT
8313480 AATTTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 8 0.28
10 7 0.24
11 14 0.48
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTATATT
Found at i:8313458 original size:19 final size:20
Alignment explanation
Indices: 8313427--8313479 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
8313417 ATTTTACAAG
8313427 TTTA-TTTTA-TTTTTATAA
1 TTTATTTTTATTTTTTATAA
*
8313445 TTT-TTTTTATTTTTTTATCA
1 TTTATTTTTA-TTTTTTATAA
*
8313465 TTTATTTATATTTTT
1 TTTATTTTTATTTTT
8313480 AATTTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 8 0.28
20 16 0.55
21 5 0.17
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTATTTTTATTTTTTATAA
Found at i:8313461 original size:20 final size:21
Alignment explanation
Indices: 8313427--8313479 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
8313417 ATTTTACAAG
*
8313427 TTTATTTTATTTTTATAATTT-
1 TTTATATT-TTTTTATAATTTA
* *
8313448 TTTTTATTTTTTTATCATTTA
1 TTTATATTTTTTTATAATTTA
8313469 TTTATATTTTT
1 TTTATATTTTT
8313480 AATTTAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTATATTTTTTTATAATTTA
Found at i:8313480 original size:19 final size:20
Alignment explanation
Indices: 8313427--8313480 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
8313417 ATTTTACAAG
8313427 TTTATTT-TATTTTTATAAT
1 TTTATTTATATTTTTATAAT
* * *
8313446 TTTTTTTATTTTTTTATCA-
1 TTTATTTATATTTTTATAAT
8313465 TTTATTTATATTTTTA
1 TTTATTTATATTTTTA
8313481 ATTTAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 20 0.69
20 9 0.31
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTATTTATATTTTTATAAT
Found at i:8326626 original size:51 final size:51
Alignment explanation
Indices: 8326560--8326659 Score: 191
Period size: 51 Copynumber: 2.0 Consensus size: 51
8326550 ATTTATATAC
*
8326560 ATATATATATGGAAAAAGAAAGAAGAGAGAATTTATTTAGTTACTTGTTAT
1 ATATATATATAGAAAAAGAAAGAAGAGAGAATTTATTTAGTTACTTGTTAT
8326611 ATATATATATAGAAAAAGAAAGAAGAGAGAATTTATTTAGTTACTTGTT
1 ATATATATATAGAAAAAGAAAGAAGAGAGAATTTATTTAGTTACTTGTT
8326660 GCAGCCGGTA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.46, C:0.02, G:0.17, T:0.35
Consensus pattern (51 bp):
ATATATATATAGAAAAAGAAAGAAGAGAGAATTTATTTAGTTACTTGTTAT
Found at i:8345058 original size:18 final size:18
Alignment explanation
Indices: 8345031--8345076 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
8345021 ATAATAATTA
*
8345031 CTTAACATTAAAACTCTT
1 CTTAATATTAAAACTCTT
*
8345049 TTTAATATTAAAACTCTT
1 CTTAATATTAAAACTCTT
8345067 CTTAATATTA
1 CTTAATATTA
8345077 TTCATTACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.46
Consensus pattern (18 bp):
CTTAATATTAAAACTCTT
Found at i:8349261 original size:2 final size:2
Alignment explanation
Indices: 8349254--8349283 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
8349244 ACTCATAACG
8349254 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
8349284 CAAATTTTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:8379526 original size:2 final size:2
Alignment explanation
Indices: 8379519--8379545 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8379509 CAGAGGAAAG
8379519 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
8379546 GTTTTCTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:8394815 original size:2 final size:2
Alignment explanation
Indices: 8394808--8394833 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8394798 AGATTATGAT
8394808 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
8394834 ATTGAAATAA
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):
TA
Found at i:8409872 original size:3 final size:3
Alignment explanation
Indices: 8409864--8409899 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
8409854 TTCGCTTTTC
* *
8409864 TTG TTG TTG ATG TTG TTG TTG TTG TTG TTG CTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
8409900 CCGTTGTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.03, C:0.03, G:0.33, T:0.61
Consensus pattern (3 bp):
TTG
Found at i:8413594 original size:3 final size:3
Alignment explanation
Indices: 8413588--8413617 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
8413578 TGTTGTTGTT
*
8413588 GTG GTG GTG GTG GTG GTA GTG GTG GTG GTG
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG
8413618 TTATCATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.03, C:0.00, G:0.63, T:0.33
Consensus pattern (3 bp):
GTG
Found at i:8434889 original size:15 final size:16
Alignment explanation
Indices: 8434866--8434907 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
8434856 GTGCAGGAAG
8434866 AAATAAAAGAAA-AAA
1 AAATAAAAGAAAGAAA
*
8434881 AAATGAAAGAAAG-AA
1 AAATAAAAGAAAGAAA
8434896 AAA-AAAAGAAAG
1 AAATAAAAGAAAG
8434908 TAATGGATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 8 0.33
15 16 0.67
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (16 bp):
AAATAAAAGAAAGAAA
Found at i:8434895 original size:19 final size:18
Alignment explanation
Indices: 8434871--8434907 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
8434861 GGAAGAAATA
8434871 AAAGAAAAAAAAATGAAAG
1 AAAGAAAAAAAAA-GAAAG
8434890 AAAGAAAAAAAAAGAAAG
1 AAAGAAAAAAAAAGAAAG
8434908 TAATGGATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (18 bp):
AAAGAAAAAAAAAGAAAG
Found at i:8434899 original size:18 final size:19
Alignment explanation
Indices: 8434871--8434907 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
8434861 GGAAGAAATA
*
8434871 AAAGAAAAAAAAATGAAAG
1 AAAGAAAAAAAAAAGAAAG
8434890 AAAG-AAAAAAAAAGAAAG
1 AAAGAAAAAAAAAAGAAAG
8434908 TAATGGATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (19 bp):
AAAGAAAAAAAAAAGAAAG
Found at i:8434994 original size:34 final size:33
Alignment explanation
Indices: 8434924--8434988 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 33
8434914 ATTGTGTGGG
*
8434924 AATTTAATTAATTAATTAATATTTTTATAAAAT
1 AATTTAATTAACTAATTAATATTTTTATAAAAT
*
8434957 AATTTAAATTAACTAATTTA-ATTTTT-TAAAAT
1 AATTT-AATTAACTAATTAATATTTTTATAAAAT
8434989 TTAATTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 6 0.21
33 11 0.38
34 12 0.41
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (33 bp):
AATTTAATTAACTAATTAATATTTTTATAAAAT
Found at i:8435570 original size:18 final size:19
Alignment explanation
Indices: 8435531--8435571 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
8435521 TAATAGATAT
*
8435531 AATATTTAAAAAATATTGA
1 AATATTTAAAAAATATTCA
8435550 AATA-TTAAGAAAA-ATTCA
1 AATATTTAA-AAAATATTCA
8435568 AATA
1 AATA
8435572 AATTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (19 bp):
AATATTTAAAAAATATTCA
Found at i:8444279 original size:52 final size:52
Alignment explanation
Indices: 8444201--8444301 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 52
8444191 AAGCAGTTCT
*
8444201 CTTAACTGAACGCCTAACTGCCTATTGTAACAAACACTAGAGAAAACTATTG
1 CTTAACTGAACGCCTAACTGCCTATTGCAACAAACACTAGAGAAAACTATTG
* *
8444253 CTTAACTGAATGCCTAACTGCCTATTGCAACAAAGACTAGAGAAAACTA
1 CTTAACTGAACGCCTAACTGCCTATTGCAACAAACACTAGAGAAAACTA
8444302 CGTCTACCTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.24
Consensus pattern (52 bp):
CTTAACTGAACGCCTAACTGCCTATTGCAACAAACACTAGAGAAAACTATTG
Found at i:8450645 original size:2 final size:2
Alignment explanation
Indices: 8450638--8450680 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
8450628 TTGTGAATAT
* * *
8450638 GA GA GA GA AA GA GA GA AA TA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
8450680 G
1 G
8450681 GATGGTACCG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.44, T:0.02
Consensus pattern (2 bp):
GA
Found at i:8466564 original size:29 final size:29
Alignment explanation
Indices: 8466532--8466587 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
8466522 CATTTCCTAG
* *
8466532 AACAGACCCTACCCTCTTAGTGGTGAACA
1 AACAGACCCTAACCTCTTAGTGATGAACA
8466561 AACAGACCCTAACCTCTTAGTGATGAA
1 AACAGACCCTAACCTCTTAGTGATGAA
8466588 ACTGGAGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (29 bp):
AACAGACCCTAACCTCTTAGTGATGAACA
Found at i:8468950 original size:63 final size:63
Alignment explanation
Indices: 8468877--8468995 Score: 186
Period size: 63 Copynumber: 1.9 Consensus size: 63
8468867 ATAATTTGGG
* *
8468877 TTATGAACATGACAAGGCGGTCCCAAACGCTGCTTTATACGTT-TCCTAGTAGAAGGATATGGA
1 TTATGAACATGACAAGGCGGCCCCAAACGCTGCTTTACAC-TTGTCCTAGTAGAAGGATATGGA
* *
8468940 TTATGAACATGAGAAGGCGGCCCCAAACGCTGCTTTACACTTGTCCTATTAGAAGG
1 TTATGAACATGACAAGGCGGCCCCAAACGCTGCTTTACACTTGTCCTAGTAGAAGG
8468996 TTGTGCAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (63 bp):
TTATGAACATGACAAGGCGGCCCCAAACGCTGCTTTACACTTGTCCTAGTAGAAGGATATGGA
Found at i:8479852 original size:30 final size:29
Alignment explanation
Indices: 8479802--8479861 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 29
8479792 TTCCATAAGG
*
8479802 AATCGTAAACGGATCGAAATTGAAAGCGAA
1 AATCGTAAACGGATCGAAATTAAAAG-GAA
8479832 AATCGTAAA-GGAAT-GAAAATTAAAAGGAA
1 AATCGTAAACGG-ATCG-AAATTAAAAGGAA
8479861 A
1 A
8479862 CAAAAGAACG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.53, C:0.08, G:0.22, T:0.17
Consensus pattern (29 bp):
AATCGTAAACGGATCGAAATTAAAAGGAA
Found at i:8487482 original size:89 final size:89
Alignment explanation
Indices: 8487334--8487503 Score: 268
Period size: 89 Copynumber: 1.9 Consensus size: 89
8487324 CCCACCACAA
*
8487334 AGCTGGCTTCTTTTCTAACCCAGCAAAGATTCAGCGACAGAGTCACGAAACAGACACCCAGGAGA
1 AGCTAGCTTCTTTTCTAACCCAGCAAAGATTCAGCGACAGAGTCACGAAACAGACACCCAGGAGA
* *
8487399 GGGATGGAGGAAAGCCCACGATAT
66 GAGATGGAAGAAAGCCCACGATAT
* * * * *
8487423 AGCTAGCTTCTTTTCTAACCCAGCAAAGATTCAGGGACTGAGTCACGAGACATATACCCAGGAGA
1 AGCTAGCTTCTTTTCTAACCCAGCAAAGATTCAGCGACAGAGTCACGAAACAGACACCCAGGAGA
8487488 GAGATGGAAGAAAGCC
66 GAGATGGAAGAAAGCC
8487504 GTGAGTCACC
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
89 73 1.00
ACGTcount: A:0.34, C:0.24, G:0.25, T:0.17
Consensus pattern (89 bp):
AGCTAGCTTCTTTTCTAACCCAGCAAAGATTCAGCGACAGAGTCACGAAACAGACACCCAGGAGA
GAGATGGAAGAAAGCCCACGATAT
Found at i:8488428 original size:2 final size:2
Alignment explanation
Indices: 8488421--8488466 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
8488411 TCTGGGGGAA
* *
8488421 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CG CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
8488463 CT CT
1 CT CT
8488467 TTACGTCTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.48, G:0.02, T:0.50
Consensus pattern (2 bp):
CT
Found at i:8492484 original size:31 final size:32
Alignment explanation
Indices: 8492415--8492484 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 32
8492405 TTTTAAGTAT
8492415 AATATTT-AATAAAATATTTAAATTATTAAAA
1 AATATTTAAATAAAATATTTAAATTATTAAAA
** *
8492446 AAT-TTTAAAT-AAATATTTATTTTTTTAAAA
1 AATATTTAAATAAAATATTTAAATTATTAAAA
*
8492476 GATATTTAA
1 AATATTTAA
8492485 TTAAGTTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 22 0.67
31 11 0.33
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (32 bp):
AATATTTAAATAAAATATTTAAATTATTAAAA
Found at i:8494148 original size:22 final size:22
Alignment explanation
Indices: 8494108--8494150 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
8494098 TATTTAATTT
*
8494108 TTTTAAAATTTTATCTTTTTCA
1 TTTTAAAATTTGATCTTTTTCA
*
8494130 TTTTAAAATTATGATTTTTTT
1 TTTTAAAATT-TGATCTTTTT
8494151 GAATTGTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTTAAAATTTGATCTTTTTCA
Found at i:8496039 original size:2 final size:2
Alignment explanation
Indices: 8496027--8496070 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
8496017 TAGTCGGTCC
8496027 TA TA T- 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
8496068 TA T
1 TA T
8496071 GCATCAGCCT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8498669 original size:4 final size:4
Alignment explanation
Indices: 8498662--8498696 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
8498652 TATATATATA
8498662 TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
8498697 AAAGTGGTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:8502544 original size:30 final size:30
Alignment explanation
Indices: 8502473--8502553 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
8502463 TTTCTCCCAC
* * *
8502473 CTTCCTCTGAAGAAGCATCAAGAAATAGTA
1 CTTCCACTGAAGAAACATCAAGAAAGAGTA
*
8502503 CTTCCATTGAAGAAACATCAAGAAAGAGTA
1 CTTCCACTGAAGAAACATCAAGAAAGAGTA
* *
8502533 GC-TCGACTGAAGAAACGTCAA
1 -CTTCCACTGAAGAAACATCAA
8502554 CATTCCTTCA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 42 0.98
31 1 0.02
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.20
Consensus pattern (30 bp):
CTTCCACTGAAGAAACATCAAGAAAGAGTA
Found at i:8512660 original size:22 final size:22
Alignment explanation
Indices: 8512635--8512678 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
8512625 GATTAAAAAT
* * *
8512635 AAAATAAACAAATAAACAAACA
1 AAAAGAAACAAAGAAAAAAACA
*
8512657 AAAAGAAAGAAAGAAAAAAACA
1 AAAAGAAACAAAGAAAAAAACA
8512679 GATTGAACAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.80, C:0.09, G:0.07, T:0.05
Consensus pattern (22 bp):
AAAAGAAACAAAGAAAAAAACA
Found at i:8523593 original size:15 final size:14
Alignment explanation
Indices: 8523575--8523604 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
8523565 AAAAATAATG
8523575 AAAGAAAAGAAGAGA
1 AAAGAAAAGAA-AGA
8523590 AAAGAAAAGAAAGA
1 AAAGAAAAGAAAGA
8523604 A
1 A
8523605 GCTGTTCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
AAAGAAAAGAAAGA
Found at i:8548159 original size:26 final size:26
Alignment explanation
Indices: 8548080--8548160 Score: 83
Period size: 26 Copynumber: 3.1 Consensus size: 26
8548070 TTTTATTTTT
** *
8548080 AAATATTAATAATTAAGAATTTATTTA
1 AAATATTAATAATT-TTAATTAATTTA
* * *
8548107 AAGTATTAAT-ATTTTATTTATAATTA
1 AAATATTAATAATTTTAATTA-ATTTA
8548133 AAATATTAATAATTTTAATTAATTTA
1 AAATATTAATAATTTTAATTAATTTA
8548159 AA
1 AA
8548161 TTTAAAATAT
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
25 3 0.07
26 22 0.51
27 18 0.42
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
AAATATTAATAATTTTAATTAATTTA
Found at i:8548170 original size:52 final size:51
Alignment explanation
Indices: 8548079--8548199 Score: 122
Period size: 52 Copynumber: 2.3 Consensus size: 51
8548069 ATTTTATTTT
* *
8548079 TAAATATTAATAATTAAGAATTTATTTAAAGTATTAATATT-TTATTTATAA
1 TAAATATTAATAATT-TGAATTAATTTAAAGTATTAATATTATTATTTATAA
* *
8548130 TTAAAATATTAATAATTTTAATTAATTTAAA-T-TTAAAATATTATTTTTTATAA
1 -T-AAATATTAATAATTTGAATTAATTTAAAGTATT--AATATTATTATTTATAA
*
8548183 TATATAATTAATAATTT
1 TAAAT-ATTAATAATTT
8548200 AATCTTTTTA
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
50 2 0.03
51 4 0.07
52 30 0.51
53 23 0.39
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (51 bp):
TAAATATTAATAATTTGAATTAATTTAAAGTATTAATATTATTATTTATAA
Found at i:8551018 original size:15 final size:16
Alignment explanation
Indices: 8550998--8551035 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
8550988 TTAAAGATTT
8550998 TTTTTAAATAATA-TA
1 TTTTTAAATAATAGTA
8551013 TTTTT-AA-AATAGTA
1 TTTTTAAATAATAGTA
8551027 TTTTTAAAT
1 TTTTTAAAT
8551036 TTAGAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
13 4 0.20
14 9 0.45
15 7 0.35
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TTTTTAAATAATAGTA
Found at i:8552602 original size:10 final size:9
Alignment explanation
Indices: 8552584--8552617 Score: 52
Period size: 10 Copynumber: 3.8 Consensus size: 9
8552574 TTTTATTTAT
8552584 AAAATAATA
1 AAAATAATA
8552593 AAACATAATA
1 AAA-ATAATA
8552603 AAAATAA-A
1 AAAATAATA
8552611 AAAATAA
1 AAAATAA
8552618 GAAATAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.33
9 7 0.29
10 9 0.38
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (9 bp):
AAAATAATA
Found at i:8556568 original size:32 final size:31
Alignment explanation
Indices: 8556486--8556560 Score: 111
Period size: 29 Copynumber: 2.5 Consensus size: 31
8556476 TTTTAAAAAT
8556486 TTAAATAAATTTTTATTTTTATTATATGTAA
1 TTAAATAAATTTTTATTTTTATTATATGTAA
* *
8556517 TTAAAT--ATTTTTATTTTTATT-TTTTTAA
1 TTAAATAAATTTTTATTTTTATTATATGTAA
8556545 TTAAATAAATTTTTAT
1 TTAAATAAATTTTTAT
8556561 CATTTTATGT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
28 11 0.28
29 15 0.38
30 8 0.20
31 6 0.15
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (31 bp):
TTAAATAAATTTTTATTTTTATTATATGTAA
Found at i:8558804 original size:190 final size:190
Alignment explanation
Indices: 8558430--8559044 Score: 704
Period size: 190 Copynumber: 3.2 Consensus size: 190
8558420 TATTAACTCG
* * ** * *
8558430 TGACGTTAATTTAGTTATTCATTATATAATAATATAAATATAGGTAGTAT-AATAATTAGTTCGT
1 TGACGTTAATTCAGTTATTCATTATATAATAATATAGATATAGGTAACATCAATAGTTAATTCGT
* * * ** * * **
8558494 AACGTTAATTCAATTATTTATTATATAATGATAT-ATATGGATAGTATCAATAAATAACTCGTGA
66 GATGTTAATTCAGTTATTCGTTATATAATAATATAATATGAATAGTATCAATAGTTAACTCGTGA
*
8558558 CGTTAATTCAATTATTCATTATATAAT-ATAATAGATATGAGTAGCATCAATAGTTAACTTA
131 CGTTAATTCAGTTATTCATTATATAATAAT-ATAGATATGA-TAGCATCAATAGTTAACTTA
* * * * *
8558619 TGAGGTTAATTCAGTTATTCGTTATATAATCATATAGATATGGGTAACATCAATAGTTAATTTGT
1 TGACGTTAATTCAGTTATTCATTATATAATAATATAGATATAGGTAACATCAATAGTTAATTCGT
* * **
8558684 GATGCTAATTCAGTTATTCGTTATATAATAATATAGATATAAATAACATCAATAGTTAACTCGTG
66 GATGTTAATTCAGTTATTCGTTATATAATAATATA-ATATGAATAGTATCAATAGTTAACTCGTG
* * * * * * *
8558749 ACGCTAATTCAGTTATTCGTTATGTAATAATATA-A-ATGGAAAGTAGCAATAGTTAACTTT
130 ACGTTAATTCAGTTATTCATTATATAATAATATAGATAT-GATAGCATCAATAGTTAACTTA
* * * *
8558809 TGATGTTAATTCAGTTATTCGTTATATAATAATATAGATATAGATAACATCAATAGTTAACTCGT
1 TGACGTTAATTCAGTTATTCATTATATAATAATATAGATATAGGTAACATCAATAGTTAATTCGT
* * * **
8558874 GATGTTATTTCAGTTATTCGTTATGTAATAATATAA-ATGGAA-AGTAGCAATAGTTAACTTTTG
66 GATGTTAATTCAGTTATTCGTTATATAATAATATAATAT-GAATAGTATCAATAGTTAACTCGTG
* *
8558937 ATGTTAATTCAGTTATTCATTATATAATAATATAGATATAGATAGCATCAATAGTTAACTTG
130 ACGTTAATTCAGTTATTCATTATATAATAATATAGATAT-GATAGCATCAATAGTTAACTTA
* * * *
8558999 TGACGCTAATTCAATTATTCATTACATAATAATATGGATATAGGTA
1 TGACGTTAATTCAGTTATTCATTATATAATAATATAGATATAGGTA
8559045 GTAGTATAGT
Statistics
Matches: 355, Mismatches: 63, Indels: 15
0.82 0.15 0.03
Matches are distributed among these distances:
188 48 0.14
189 46 0.13
190 206 0.58
191 3 0.01
192 50 0.14
193 2 0.01
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.40
Consensus pattern (190 bp):
TGACGTTAATTCAGTTATTCATTATATAATAATATAGATATAGGTAACATCAATAGTTAATTCGT
GATGTTAATTCAGTTATTCGTTATATAATAATATAATATGAATAGTATCAATAGTTAACTCGTGA
CGTTAATTCAGTTATTCATTATATAATAATATAGATATGATAGCATCAATAGTTAACTTA
Found at i:8558841 original size:126 final size:126
Alignment explanation
Indices: 8558434--8559033 Score: 715
Period size: 126 Copynumber: 4.8 Consensus size: 126
8558424 AACTCGTGAC
* * * * * ** *
8558434 GTTAATTTAGTTATTCATTATATAATAATATAAATATAGGTAGTAT-AATAATTAGTTCGTAACG
1 GTTAATTCAGTTATTCATTATATAATAATATAGATATAGATAGCATCAATAGTTAACTCGTGACG
* ** * * * * ** ** *
8558498 TTAATTCAATTATTTATTATATAATGATATATATGGATAGTATCAATAAATAACTCGTGAC
66 TTAATTCAGTTATTCGTTATATAATAATATAAATGGAAAGTAGCAATAGTTAACTTTTGAT
* **
8558559 GTTAATTCAATTATTCATTATATAAT-ATAATAGATAT-GAGTAGCATCAATAGTTAACTTATGA
1 GTTAATTCAGTTATTCATTATATAATAAT-ATAGATATAGA-TAGCATCAATAGTTAACTCGTGA
* * * * *
8558622 GGTTAATTCAGTTATTCGTTATATAATCATATAGATATGGGTAA-CATCAATAGTTAA-TTTGTG
64 CGTTAATTCAGTTATTCGTTATATAATAATATA-A-AT-GGAAAGTAGCAATAGTTAACTTT-TG
8558685 AT
125 AT
* * * *
8558687 GCTAATTCAGTTATTCGTTATATAATAATATAGATATAAATAACATCAATAGTTAACTCGTGACG
1 GTTAATTCAGTTATTCATTATATAATAATATAGATATAGATAGCATCAATAGTTAACTCGTGACG
* *
8558752 CTAATTCAGTTATTCGTTATGTAATAATATAAATGGAAAGTAGCAATAGTTAACTTTTGAT
66 TTAATTCAGTTATTCGTTATATAATAATATAAATGGAAAGTAGCAATAGTTAACTTTTGAT
* * *
8558813 GTTAATTCAGTTATTCGTTATATAATAATATAGATATAGATAACATCAATAGTTAACTCGTGATG
1 GTTAATTCAGTTATTCATTATATAATAATATAGATATAGATAGCATCAATAGTTAACTCGTGACG
* *
8558878 TTATTTCAGTTATTCGTTATGTAATAATATAAATGGAAAGTAGCAATAGTTAACTTTTGAT
66 TTAATTCAGTTATTCGTTATATAATAATATAAATGGAAAGTAGCAATAGTTAACTTTTGAT
*
8558939 GTTAATTCAGTTATTCATTATATAATAATATAGATATAGATAGCATCAATAGTTAACTTGTGACG
1 GTTAATTCAGTTATTCATTATATAATAATATAGATATAGATAGCATCAATAGTTAACTCGTGACG
* * * *
8559004 CTAATTCAATTATTCATTACATAATAATAT
66 TTAATTCAGTTATTCGTTATATAATAATAT
8559034 GGATATAGGT
Statistics
Matches: 410, Mismatches: 54, Indels: 21
0.85 0.11 0.04
Matches are distributed among these distances:
124 3 0.01
125 40 0.10
126 261 0.64
127 5 0.01
128 95 0.23
129 6 0.01
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.40
Consensus pattern (126 bp):
GTTAATTCAGTTATTCATTATATAATAATATAGATATAGATAGCATCAATAGTTAACTCGTGACG
TTAATTCAGTTATTCGTTATATAATAATATAAATGGAAAGTAGCAATAGTTAACTTTTGAT
Found at i:8559040 original size:64 final size:64
Alignment explanation
Indices: 8558422--8559163 Score: 639
Period size: 64 Copynumber: 11.7 Consensus size: 64
8558412 ATTTGATATA
* * * * * *
8558422 TTAACTCGTGACGTTAATTTAGTTATTCATTATATAATAATATAAATATAGGTAGTAT-AATAA
1 TTAACTTGTGACGTTAATTCAGTTATTCATTATATAATAATATAGATATAGATAGCATCAATAG
* * * * * * * *
8558485 TT-AGTTCGTAACGTTAATTCAATTATTTATTATATAATGATAT--ATATGGATAGTATCAATAA
1 TTAACTT-GTGACGTTAATTCAGTTATTCATTATATAATAATATAGATATAGATAGCATCAATAG
* * *
8558547 ATAACTCGTGACGTTAATTCAATTATTCATTATATAAT-ATAATAGATAT-GAGTAGCATCAATA
1 TTAACTTGTGACGTTAATTCAGTTATTCATTATATAATAAT-ATAGATATAGA-TAGCATCAATA
8558610 G
64 G
* * * * * * *
8558611 TTAACTTATGAGGTTAATTCAGTTATTCGTTATATAATCATATAGATATGGGTAACATCAATAG
1 TTAACTTGTGACGTTAATTCAGTTATTCATTATATAATAATATAGATATAGATAGCATCAATAG
* * * * * *
8558675 TTAATTTGTGATGCTAATTCAGTTATTCGTTATATAATAATATAGATATAAATAACATCAATAG
1 TTAACTTGTGACGTTAATTCAGTTATTCATTATATAATAATATAGATATAGATAGCATCAATAG
* * * * * * * *
8558739 TTAACTCGTGACGCTAATTCAGTTATTCGTTATGTAATAATATA-A-ATGGAAAGTAGCAATAG
1 TTAACTTGTGACGTTAATTCAGTTATTCATTATATAATAATATAGATATAGATAGCATCAATAG
* * * *
8558801 TTAACTTTTGATGTTAATTCAGTTATTCGTTATATAATAATATAGATATAGATAACATCAATAG
1 TTAACTTGTGACGTTAATTCAGTTATTCATTATATAATAATATAGATATAGATAGCATCAATAG
* * * * * * * * *
8558865 TTAACTCGTGATGTTATTTCAGTTATTCGTTATGTAATAATATA-A-ATGGAAAGTAGCAATAG
1 TTAACTTGTGACGTTAATTCAGTTATTCATTATATAATAATATAGATATAGATAGCATCAATAG
* *
8558927 TTAACTTTTGATGTTAATTCAGTTATTCATTATATAATAATATAGATATAGATAGCATCAATAG
1 TTAACTTGTGACGTTAATTCAGTTATTCATTATATAATAATATAGATATAGATAGCATCAATAG
* * * * * *
8558991 TTAACTTGTGACGCTAATTCAATTATTCATTACATAATAATATGGATATAGGTAGTAGT--ATAG
1 TTAACTTGTGACGTTAATTCAGTTATTCATTATATAATAATATAGATATAGATAGCA-TCAATAG
* ** * * * * * * * *
8559054 TTACCTCATGACGTTACTTCAATTTTTTATTATATAATAATAATACATATATGGGTAGTATTAAT
1 TTAACTTGTGACGTTAATTCAGTTATTCATTATATAATAAT-ATAGATATA--GATAGCATCAAT
*
8559119 AA
63 AG
* * * *
8559121 TTAACTT-TGATGTTAATTTAGTTACTT-GTTGTATAATAATATA
1 TTAACTTGTGACGTTAATTCAGTTA-TTCATTATATAATAATATA
8559164 AATGTATTAT
Statistics
Matches: 561, Mismatches: 98, Indels: 38
0.80 0.14 0.05
Matches are distributed among these distances:
61 13 0.02
62 140 0.25
63 78 0.14
64 282 0.50
65 8 0.01
66 30 0.05
67 10 0.02
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (64 bp):
TTAACTTGTGACGTTAATTCAGTTATTCATTATATAATAATATAGATATAGATAGCATCAATAG
Found at i:8559617 original size:23 final size:25
Alignment explanation
Indices: 8559591--8559644 Score: 78
Period size: 23 Copynumber: 2.2 Consensus size: 25
8559581 ATTTTTTTTT
8559591 ATTTTTTAAATT-A-TATAAAAA-TA
1 ATTTTTTAAATTAATTA-AAAAATTA
8559614 ATTTTTTAAATTAATTAAAAAATTA
1 ATTTTTTAAATTAATTAAAAAATTA
8559639 ATTTTT
1 ATTTTT
8559645 ATTATTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 12 0.43
24 6 0.21
25 10 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTTTTTAAATTAATTAAAAAATTA
Found at i:8565590 original size:20 final size:20
Alignment explanation
Indices: 8565565--8565603 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
8565555 ATATTTTTAT
**
8565565 TATTAATAATTAATTAATTA
1 TATTAATAAAAAATTAATTA
8565585 TATTAATAAAAAATTAATT
1 TATTAATAAAAAATTAATT
8565604 TTTATTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TATTAATAAAAAATTAATTA
Found at i:8565651 original size:21 final size:20
Alignment explanation
Indices: 8565627--8565667 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
8565617 GAGAATTAAA
8565627 AATATTACATGATTATGTTAT
1 AATATTACATGATTAT-TTAT
* *
8565648 AATATTATATTATTATTTAT
1 AATATTACATGATTATTTAT
8565668 TGTAATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (20 bp):
AATATTACATGATTATTTAT
Found at i:8569706 original size:27 final size:26
Alignment explanation
Indices: 8569676--8569746 Score: 92
Period size: 26 Copynumber: 2.7 Consensus size: 26
8569666 ACAATATTTT
*
8569676 TTTTTTCAAA-ATAATGTGTAATAATA
1 TTTTTT-AAACATAATGTGTAACAATA
8569702 CTTTTTTAAACATAACT-TGTAACAATA
1 -TTTTTTAAACATAA-TGTGTAACAATA
8569729 TTTTTTAAACATAATGTG
1 TTTTTTAAACATAATGTG
8569747 GAACTTACTC
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
25 1 0.03
26 19 0.47
27 19 0.47
28 1 0.03
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.45
Consensus pattern (26 bp):
TTTTTTAAACATAATGTGTAACAATA
Found at i:8570760 original size:6 final size:6
Alignment explanation
Indices: 8570749--8570775 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
8570739 ACCTTACTAG
8570749 AAGCTC AAGCTC AAGCTC AAGCTC AAG
1 AAGCTC AAGCTC AAGCTC AAGCTC AAG
8570776 ACTTTTTGAG
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:0.37, C:0.30, G:0.19, T:0.15
Consensus pattern (6 bp):
AAGCTC
Found at i:8577810 original size:2 final size:2
Alignment explanation
Indices: 8577803--8577828 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8577793 AAAGCTTTAC
8577803 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
8577829 TCATAATATT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:8580060 original size:21 final size:21
Alignment explanation
Indices: 8580034--8580093 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
8580024 GTAATACTTA
*
8580034 AAAACTAATCACGTAATGTCT
1 AAAACTAATCACGCAATGTCT
* * *
8580055 AAAACTAGTTATGCAATGTCT
1 AAAACTAATCACGCAATGTCT
*
8580076 AAAA-TCAATCACACAATG
1 AAAACT-AATCACGCAATG
8580094 GTTAAATCAT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.45, C:0.18, G:0.10, T:0.27
Consensus pattern (21 bp):
AAAACTAATCACGCAATGTCT
Found at i:8580152 original size:22 final size:22
Alignment explanation
Indices: 8580127--8580176 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
8580117 CTCGGTCTAG
*
8580127 CAATACTTAAAAATCAGTGATA
1 CAATACTTAAAAATCAGTAATA
* *
8580149 CAATATTTAAAAATCAGTAATG
1 CAATACTTAAAAATCAGTAATA
8580171 CAATAC
1 CAATAC
8580177 CTAATAACTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.50, C:0.14, G:0.08, T:0.28
Consensus pattern (22 bp):
CAATACTTAAAAATCAGTAATA
Found at i:8581409 original size:2 final size:2
Alignment explanation
Indices: 8581402--8581426 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8581392 ACCAAAACTC
8581402 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
8581427 CCTCAAATTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8585171 original size:31 final size:31
Alignment explanation
Indices: 8585133--8585192 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
8585123 ATATTAGTAA
* *
8585133 AATTTTAAGCAACAATCAATCATGCAATGTT
1 AATTTTAAACAACAATCAATAATGCAATGTT
*
8585164 AATTTTAAACAACAATCAATAATGTAATG
1 AATTTTAAACAACAATCAATAATGCAATG
8585193 CTACAATGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (31 bp):
AATTTTAAACAACAATCAATAATGCAATGTT
Found at i:8585425 original size:23 final size:24
Alignment explanation
Indices: 8585394--8585450 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
8585384 ACATATATCA
*
8585394 AATAGAATA-AAATTGA-AAAAAAT
1 AATAAAATATAAA-TGATAAAAAAT
*
8585417 AATAAAATATAAATGATAACAAAT
1 AATAAAATATAAATGATAAAAAAT
8585441 AATATAAATA
1 AATA-AAATA
8585451 GAAAAAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 11 0.38
24 13 0.45
25 5 0.17
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (24 bp):
AATAAAATATAAATGATAAAAAAT
Found at i:8588438 original size:22 final size:21
Alignment explanation
Indices: 8588393--8588431 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
8588383 GACAGAGATG
8588393 TTTTTTTTTTCTTTCTTGTCT
1 TTTTTTTTTTCTTTCTTGTCT
*
8588414 TTTTTTTTTTGTTT-TTGT
1 TTTTTTTTTTCTTTCTTGT
8588432 AGCTTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (21 bp):
TTTTTTTTTTCTTTCTTGTCT
Found at i:8598564 original size:39 final size:39
Alignment explanation
Indices: 8598519--8598606 Score: 106
Period size: 39 Copynumber: 2.3 Consensus size: 39
8598509 GTTTCCTTAA
8598519 CTTGCTTTGGAGCTGAAACCCTTGGTTTCTTTT-CCTTGG
1 CTTGCTTTGGAGCTGAAACCCTTGGTTTCTTTTCCCTT-G
* * ** * *
8598558 TTTGCTTTGGAGTTGCGAGCTTTGGTTTCTTTTCCCTTG
1 CTTGCTTTGGAGCTGAAACCCTTGGTTTCTTTTCCCTTG
8598597 CTTGCTTTGG
1 CTTGCTTTGG
8598607 GGTTGCAGGC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 37 0.90
40 4 0.10
ACGTcount: A:0.07, C:0.20, G:0.25, T:0.48
Consensus pattern (39 bp):
CTTGCTTTGGAGCTGAAACCCTTGGTTTCTTTTCCCTTG
Found at i:8598612 original size:39 final size:39
Alignment explanation
Indices: 8598540--8598624 Score: 120
Period size: 39 Copynumber: 2.2 Consensus size: 39
8598530 GCTGAAACCC
*
8598540 TTGGTTTCTTTTCCTTGGTTTGCTTTGGAGTTGC-GAGCT
1 TTGGTTTCTTTTCCTTGGCTTGCTTTGGAGTTGCAG-GCT
*
8598579 TTGGTTTCTTTTCCCTT-GCTTGCTTTGGGGTTGCAGGCT
1 TTGGTTTCTTTT-CCTTGGCTTGCTTTGGAGTTGCAGGCT
8598618 TTGGTTT
1 TTGGTTT
8598625 GGTTGGCTCG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
39 37 0.88
40 5 0.12
ACGTcount: A:0.04, C:0.16, G:0.28, T:0.52
Consensus pattern (39 bp):
TTGGTTTCTTTTCCTTGGCTTGCTTTGGAGTTGCAGGCT
Found at i:8601158 original size:19 final size:21
Alignment explanation
Indices: 8601134--8601174 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
8601124 TATATATTTG
8601134 ATTTAA-TAAAAAT-ATAAAA
1 ATTTAATTAAAAATAATAAAA
*
8601153 ATTTAATTAAATATAATAAAA
1 ATTTAATTAAAAATAATAAAA
8601174 A
1 A
8601175 AATAATTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 6 0.32
21 7 0.37
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
ATTTAATTAAAAATAATAAAA
Found at i:8614173 original size:15 final size:15
Alignment explanation
Indices: 8614153--8614182 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
8614143 TGACTCAGAT
8614153 TTTAATTGAAAATCA
1 TTTAATTGAAAATCA
*
8614168 TTTAATTGATAATCA
1 TTTAATTGAAAATCA
8614183 ATTTGAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (15 bp):
TTTAATTGAAAATCA
Found at i:8618749 original size:2 final size:2
Alignment explanation
Indices: 8618742--8618773 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
8618732 TGGGCAAATC
8618742 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
8618774 AATTTATTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8620107 original size:28 final size:28
Alignment explanation
Indices: 8620075--8620135 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
8620065 TAACAAAATG
*
8620075 TTTTTAAATATAACGTGTAATAATAATA
1 TTTTTAAACATAACGTGTAATAATAATA
* **
8620103 TTTTTCAACATAGTGTGTAATAATAATA
1 TTTTTAAACATAACGTGTAATAATAATA
8620131 TTTTT
1 TTTTT
8620136 TTTAACATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (28 bp):
TTTTTAAACATAACGTGTAATAATAATA
Found at i:8620152 original size:24 final size:25
Alignment explanation
Indices: 8620133--8620180 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
8620123 TAATAATATT
*
8620133 TTTTTTAAC-ATGGTGTATAATAAC
1 TTTTTTAACTATGATGTATAATAAC
8620157 TTTTTTAACTATGATGTAT-ATAAC
1 TTTTTTAACTATGATGTATAATAAC
8620181 GCATAATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.48
Consensus pattern (25 bp):
TTTTTTAACTATGATGTATAATAAC
Found at i:8620162 original size:27 final size:30
Alignment explanation
Indices: 8620089--8620155 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
8620079 TAAATATAAC
8620089 GTGTAATAATAATA--TTTTTCAACATAGT
1 GTGTAATAATAATATTTTTTTCAACATAGT
* *
8620117 GTGTAATAATAATATTTTTTTTAACATGGT
1 GTGTAATAATAATATTTTTTTCAACATAGT
*
8620147 GTATAATAA
1 GTGTAATAA
8620156 CTTTTTTAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 14 0.41
30 20 0.59
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (30 bp):
GTGTAATAATAATATTTTTTTCAACATAGT
Found at i:8620376 original size:15 final size:14
Alignment explanation
Indices: 8620356--8620406 Score: 61
Period size: 15 Copynumber: 3.6 Consensus size: 14
8620346 ATTAAAATAA
8620356 TTAAAAAGTTATTTT
1 TTAAAAA-TTATTTT
8620371 TTAAAATATCT-TTTT
1 TTAAAA-AT-TATTTT
8620386 TTAAAAATTA-TTT
1 TTAAAAATTATTTT
8620399 TTAAAAAT
1 TTAAAAAT
8620407 ATTCTCTCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
13 12 0.36
14 2 0.06
15 17 0.52
16 2 0.06
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (14 bp):
TTAAAAATTATTTT
Found at i:8621802 original size:2 final size:2
Alignment explanation
Indices: 8621795--8621823 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
8621785 TCTCTGTCTT
8621795 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8621824 TTAAAAAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8624552 original size:18 final size:18
Alignment explanation
Indices: 8624525--8624584 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
8624515 TGAGGATGAT
*
8624525 GATGAGAGTGATTCTGAG
1 GATGAAAGTGATTCTGAG
* *
8624543 GATGAAAGTGGTTCTGAT
1 GATGAAAGTGATTCTGAG
*
8624561 GA-GGAAGATGATTCTGAG
1 GATGAAAG-TGATTCTGAG
8624579 GATGAA
1 GATGAA
8624585 GATGAGTCTG
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
17 4 0.12
18 27 0.82
19 2 0.06
ACGTcount: A:0.32, C:0.05, G:0.37, T:0.27
Consensus pattern (18 bp):
GATGAAAGTGATTCTGAG
Found at i:8624585 original size:18 final size:18
Alignment explanation
Indices: 8624533--8624595 Score: 74
Period size: 18 Copynumber: 3.5 Consensus size: 18
8624523 ATGATGAGAG
8624533 TGATTCTGAGGATGAA-A
1 TGATTCTGAGGATGAAGA
* * *
8624550 GTGGTTCTGATGAGGAAGA
1 -TGATTCTGAGGATGAAGA
8624569 TGATTCTGAGGATGAAGA
1 TGATTCTGAGGATGAAGA
*
8624587 TGAGTCTGA
1 TGATTCTGA
8624596 TGAGGTCTCT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
18 36 0.97
19 1 0.03
ACGTcount: A:0.30, C:0.06, G:0.35, T:0.29
Consensus pattern (18 bp):
TGATTCTGAGGATGAAGA
Found at i:8626316 original size:27 final size:26
Alignment explanation
Indices: 8626277--8626452 Score: 107
Period size: 27 Copynumber: 6.7 Consensus size: 26
8626267 AATGTATATA
8626277 TTTTAT-TTTTATTTATTATTATAAT
1 TTTTATATTTTATTTATTATTATAAT
**
8626302 TTTATATATTTTATTTATTAAAATAAT
1 TTT-TATATTTTATTTATTATTATAAT
* *
8626329 TTTTATATTATA-TTA-TATTTTAAT
1 TTTTATATTTTATTTATTATTATAAT
**
8626353 TTATT-TATTTATATTATAGAAATTATAATT
1 TT-TTATATTT-TATT-TA-TTATTATAA-T
*
8626383 TTTTATATTATATTTTAATT-TT-TAAT
1 TTTTATATTTTA-TTT-ATTATTATAAT
*
8626409 TTTTATATTGTATATT-TTAGTT-TAAT
1 TTTTATATTTTAT-TTATTA-TTATAAT
* *
8626435 ATTTTTTATTTTAATTAT
1 -TTTTATATTTTATTTAT
8626453 AATATTGTAA
Statistics
Matches: 118, Mismatches: 16, Indels: 32
0.71 0.10 0.19
Matches are distributed among these distances:
24 14 0.12
25 11 0.09
26 34 0.29
27 36 0.31
28 2 0.02
29 11 0.09
30 10 0.08
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTTATATTTTATTTATTATTATAAT
Found at i:8626340 original size:33 final size:33
Alignment explanation
Indices: 8626246--8626341 Score: 81
Period size: 33 Copynumber: 2.9 Consensus size: 33
8626236 TTTTATGAAA
8626246 TATTATTT-TAAATATATTTTTA-ATGTATATATTT
1 TATT-TTTATAAATA-ATTTTTATAT-TATATATTT
** * * * *
8626280 TATTTTTATTTATTATTATAATTTTATATATTT
1 TATTTTTATAAATAATTTTTATATTATATATTT
8626313 TATTTATTA-AAATAATTTTTATATTATAT
1 TATTT-TTATAAATAATTTTTATATTATAT
8626342 TATATTTTAA
Statistics
Matches: 47, Mismatches: 12, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
33 36 0.77
34 11 0.23
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (33 bp):
TATTTTTATAAATAATTTTTATATTATATATTT
Found at i:8626341 original size:64 final size:67
Alignment explanation
Indices: 8626212--8626357 Score: 162
Period size: 64 Copynumber: 2.2 Consensus size: 67
8626202 ATAAGTTTAA
* *
8626212 TATATTTATATTT-TTATTATTAATTTTTATGAAATATTATTTTAAATATATTTTTAATGTATAT
1 TATATTTTTATTTATTATTATTAATTTTTATGAAATATTATTTTAAATATATTTTTAATATATAT
8626276 AT
66 AT
* * *
8626278 TTTATTTTTATTTATTATTA-TAA-TTTTAT-ATATTTTATTTATTAAA-ATAATTTTT-ATAT-
1 TATATTTTTATTTATTATTATTAATTTTTATGAAATATTA-TT-TTAAATAT-ATTTTTAATATA
8626337 TATAT
63 TATAT
*
8626342 TATATTTTAATTTATT
1 TATATTTTTATTTATT
8626358 TATTTATATT
Statistics
Matches: 69, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
64 25 0.36
65 13 0.19
66 25 0.36
67 6 0.09
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (67 bp):
TATATTTTTATTTATTATTATTAATTTTTATGAAATATTATTTTAAATATATTTTTAATATATAT
AT
Found at i:8626357 original size:20 final size:19
Alignment explanation
Indices: 8626273--8626367 Score: 62
Period size: 17 Copynumber: 5.3 Consensus size: 19
8626263 TTTTAATGTA
8626273 TATATTTTATTT-TTAT-T
1 TATATTTTATTTATTATAT
* * *
8626290 TAT-TATTA-TAATTTTA-
1 TATATTTTATTTATTATAT
* *
8626306 TATATTTTATTTATTAAAA
1 TATATTTTATTTATTATAT
*
8626325 TA-ATTTT-TATATTATAT
1 TATATTTTATTTATTATAT
8626342 TATATTTTAATTTATT-TATT
1 TATATTTT-ATTTATTATA-T
8626362 TATATT
1 TATATT
8626368 ATAGAAATTA
Statistics
Matches: 58, Mismatches: 11, Indels: 15
0.69 0.13 0.18
Matches are distributed among these distances:
15 1 0.02
16 10 0.17
17 16 0.28
18 15 0.26
19 4 0.07
20 12 0.21
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TATATTTTATTTATTATAT
Found at i:8626440 original size:54 final size:53
Alignment explanation
Indices: 8626318--8626453 Score: 129
Period size: 54 Copynumber: 2.5 Consensus size: 53
8626308 TATTTTATTT
*
8626318 ATTAAAATAATTTTTATATTATATTATATTTTAATTTATTTATTTATATTATAG
1 ATTATAAT-ATTTTTATATTATATTATATTTTAATTTATTTATTTATATTATAG
* *
8626372 AAATTATAAT-TTTTTATATTATATTTTAATTTTTAATTT-TTATATTGTATATTTTAG
1 --ATTATAATATTTTTATATTATATTAT-A-TTTTAATTTATT-TATT-TATATTATAG
*
8626429 -TT-TAATATTTTT-TATTTTAATTATA
1 ATTATAATATTTTTATATTAT-ATTATA
8626454 ATATTGTAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 15
0.78 0.06 0.17
Matches are distributed among these distances:
53 10 0.14
54 27 0.39
55 3 0.04
56 20 0.29
57 9 0.13
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (53 bp):
ATTATAATATTTTTATATTATATTATATTTTAATTTATTTATTTATATTATAG
Found at i:8636199 original size:14 final size:14
Alignment explanation
Indices: 8636182--8636208 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
8636172 TGATAAAATT
8636182 TTTTTTATAAGTTC
1 TTTTTTATAAGTTC
8636196 TTTTTTATAAGTT
1 TTTTTTATAAGTT
8636209 ATAATTTTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.04, G:0.07, T:0.67
Consensus pattern (14 bp):
TTTTTTATAAGTTC
Found at i:8636400 original size:16 final size:16
Alignment explanation
Indices: 8636381--8636411 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
8636371 TTAAAATTTT
8636381 TATTTTTTAAAAAAAG
1 TATTTTTTAAAAAAAG
8636397 TATTTTTTAAAAAAA
1 TATTTTTTAAAAAAA
8636412 AATTTCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
TATTTTTTAAAAAAAG
Found at i:8656051 original size:86 final size:86
Alignment explanation
Indices: 8655906--8656078 Score: 292
Period size: 86 Copynumber: 2.0 Consensus size: 86
8655896 CAAACTTGTC
* * *
8655906 TTACCAAAAAGATTTAGATTTGTTGGAAGGGTAAACATTTATTTTGTTACGAAATATAACTTGAA
1 TTACCAAAAAGATTTAGACTCGCTGGAAGGGTAAACATTTATTTTGTTACGAAATATAACTTGAA
*
8655971 AAATCAATTATGAAAGAAAAA
66 AAACCAATTATGAAAGAAAAA
* *
8655992 TTACCAAAAAGATTTAGACTCGCTGGAAGGGTAAACGTTTATTTTGTTATGAAATATAACTTGAA
1 TTACCAAAAAGATTTAGACTCGCTGGAAGGGTAAACATTTATTTTGTTACGAAATATAACTTGAA
8656057 AAACCAATTATGAAAGAAAAA
66 AAACCAATTATGAAAGAAAAA
8656078 T
1 T
8656079 ATTAATAGAA
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
86 81 1.00
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.31
Consensus pattern (86 bp):
TTACCAAAAAGATTTAGACTCGCTGGAAGGGTAAACATTTATTTTGTTACGAAATATAACTTGAA
AAACCAATTATGAAAGAAAAA
Found at i:8660189 original size:5 final size:5
Alignment explanation
Indices: 8660166--8660243 Score: 54
Period size: 5 Copynumber: 15.2 Consensus size: 5
8660156 CTGTTATAAT
* * *
8660166 TAAAA TAAAA -AATAT TAAAA TAAAA T-ATA TAATA TAAGAA TCAAAAA
1 TAAAA TAAAA TAA-AA TAAAA TAAAA TAAAA TAAAA TAA-AA T--AAAA
*
8660213 TAAAA TAAAA TAAAA TATAAA -AAAT TAAAA T
1 TAAAA TAAAA TAAAA TA-AAA TAAAA TAAAA T
8660244 TTATATAATA
Statistics
Matches: 59, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
4 7 0.12
5 40 0.68
6 7 0.12
7 3 0.05
8 2 0.03
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.26
Consensus pattern (5 bp):
TAAAA
Found at i:8660243 original size:30 final size:30
Alignment explanation
Indices: 8660181--8660351 Score: 79
Period size: 30 Copynumber: 5.6 Consensus size: 30
8660171 TAAAAAATAT
* *
8660181 TAAAATAAAATATATAATAT-AAGAATCAAAAA
1 TAAAATAAAATA-A-AATATAAAAAAT-TAAAA
8660213 TAAAATAAAATAAAATATAAAAAATTAAAA
1 TAAAATAAAATAAAATATAAAAAATTAAAA
** * ** *
8660243 T-TTATATAATATAGGTA-AACCAAATTAAAA
1 TAAAATAAAATA-AAATATAA-AAAATTAAAA
*
8660273 TAAAAT---ATATAATATAAAAAATATATTAAA
1 TAAAATAAAATAAAATATAAAAAAT-TA--AAA
* * * *
8660303 -GAAATAAAAATAAAATATATAAGATTATAA
1 TAAAAT-AAAATAAAATATAAAAAATTAAAA
8660333 T-AAATGAAAATAAAATATA
1 TAAAAT-AAAATAAAATATA
8660352 TGACATTAAA
Statistics
Matches: 106, Mismatches: 20, Indels: 28
0.69 0.13 0.18
Matches are distributed among these distances:
27 6 0.06
28 7 0.07
29 13 0.12
30 45 0.42
31 8 0.08
32 14 0.13
33 13 0.12
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.28
Consensus pattern (30 bp):
TAAAATAAAATAAAATATAAAAAATTAAAA
Found at i:8660348 original size:35 final size:36
Alignment explanation
Indices: 8660264--8660367 Score: 106
Period size: 34 Copynumber: 2.9 Consensus size: 36
8660254 TAGGTAAACC
* *
8660264 AAATTAAAATAAAATATATAATATAAAAAATATATT
1 AAATGAAAATAAAATATATAATATAAAAAATATAAT
* * *
8660300 AAA-G-AAATAAAA-ATAAAATATATAAGATTATAAT
1 AAATGAAAATAAAATATATAATATA-AAAAATATAAT
* * *
8660334 AAATGAAAATAAAATATATGACATTAAAAATATA
1 AAATGAAAATAAAATATATAATATAAAAAATATA
8660368 TTTAAGAGAC
Statistics
Matches: 53, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
33 9 0.17
34 19 0.36
35 1 0.02
36 18 0.34
37 6 0.11
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (36 bp):
AAATGAAAATAAAATATATAATATAAAAAATATAAT
Found at i:8660389 original size:57 final size:56
Alignment explanation
Indices: 8660328--8660519 Score: 193
Period size: 57 Copynumber: 3.4 Consensus size: 56
8660318 TATATAAGAT
*
8660328 TATAATAAATGAA-AATAAAATATATGACATTAAAAATATATTTAAGAGACGATATTA
1 TATAA-AAATTAATAATAAAATATATGACATTAAAAATATATTTAAGAGA-GATATTA
* * ** *
8660385 TAT-AAAATTAATAATAAAAATAAAT-ATATTAAAAATA-AAATATATA-AG--ATTA
1 TATAAAAATTAATAAT-AAAATATATGACATTAAAAATATATTTA-AGAGAGATATTA
*
8660437 TAATAATAAA-TAAAAATAAAATATATGACATTAAAAATATATTTAAGAGATGATATTA
1 T-ATAA-AAATTAATAATAAAATATATGACATTAAAAATATATTTAAGAGA-GATATTA
*
8660495 TATAAAAATTAATAATAAAAAATAT
1 TATAAAAATTAATAATAAAATATAT
8660520 AAATATATTA
Statistics
Matches: 108, Mismatches: 14, Indels: 26
0.73 0.09 0.18
Matches are distributed among these distances:
52 5 0.05
53 10 0.09
54 21 0.19
55 17 0.16
56 21 0.19
57 29 0.27
58 5 0.05
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (56 bp):
TATAAAAATTAATAATAAAATATATGACATTAAAAATATATTTAAGAGAGATATTA
Found at i:8660419 original size:15 final size:16
Alignment explanation
Indices: 8660399--8660462 Score: 62
Period size: 15 Copynumber: 4.0 Consensus size: 16
8660389 AAATTAATAA
8660399 TAAAAAT-AAATATAT
1 TAAAAATAAAATATAT
8660414 TAAAAATAAAATATA-
1 TAAAAATAAAATATAT
* *
8660429 TAAGATTATAATAATA-AA
1 TAA-A-AATAA-AATATAT
8660447 TAAAAATAAAATATAT
1 TAAAAATAAAATATAT
8660463 GACATTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
15 14 0.35
16 13 0.32
17 6 0.15
18 7 0.17
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (16 bp):
TAAAAATAAAATATAT
Found at i:8660426 original size:107 final size:113
Alignment explanation
Indices: 8660307--8660531 Score: 381
Period size: 110 Copynumber: 2.0 Consensus size: 113
8660297 ATTAAAGAAA
*
8660307 TAAAAATAAAATATATAAGA-T-T-ATAATAAATGAAAATAAAATATATGACATTAAAAATATAT
1 TAAAAATAAAATATATAAGATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATAT
8660369 TTAAGAGACGATATTATAT-AAAATTAATAAT-AAAA-ATAAATATAT
66 TTAAGAGACGATATTATATAAAAATTAATAATAAAAATATAAATATAT
8660414 TAAAAATAAAATATATAAGATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATAT
1 TAAAAATAAAATATATAAGATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATAT
*
8660479 TTAAGAGATGATATTATATAAAAATTAATAATAAAAAATATAAATATAT
66 TTAAGAGACGATATTATATAAAAATTAATAAT-AAAAATATAAATATAT
8660528 TAAA
1 TAAA
8660532 CTTGTATTTT
Statistics
Matches: 109, Mismatches: 2, Indels: 7
0.92 0.02 0.06
Matches are distributed among these distances:
107 20 0.18
108 1 0.01
109 1 0.01
110 57 0.52
111 12 0.11
113 4 0.04
114 14 0.13
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (113 bp):
TAAAAATAAAATATATAAGATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATAT
TTAAGAGACGATATTATATAAAAATTAATAATAAAAATATAAATATAT
Found at i:8660701 original size:15 final size:15
Alignment explanation
Indices: 8660681--8660734 Score: 99
Period size: 15 Copynumber: 3.6 Consensus size: 15
8660671 TTTTCTCTGT
*
8660681 AATCACATTGCTTGC
1 AATCACATTACTTGC
8660696 AATCACATTACTTGC
1 AATCACATTACTTGC
8660711 AATCACATTACTTGC
1 AATCACATTACTTGC
8660726 AATCACATT
1 AATCACATT
8660735 GCATTGTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.33
Consensus pattern (15 bp):
AATCACATTACTTGC
Found at i:8661255 original size:22 final size:22
Alignment explanation
Indices: 8661213--8661256 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
8661203 TTTTTATATT
*
8661213 TCTTTTATTTTATCTATTTTTA
1 TCTTTTATTTTATCTACTTTTA
*
8661235 TCTTTTTTTTATATCT-CTTTTA
1 TCTTTTATTT-TATCTACTTTTA
8661257 ATAGTTAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (22 bp):
TCTTTTATTTTATCTACTTTTA
Found at i:8661296 original size:27 final size:27
Alignment explanation
Indices: 8661263--8661413 Score: 122
Period size: 27 Copynumber: 5.4 Consensus size: 27
8661253 TTTAATAGTT
* * * *
8661263 AAGTATCTATCTACTTCTAGTAGTTAA
1 AAGTATCCATCTATTTTTAGTGGTTAA
*
8661290 AAGTATCTATCCATCATTTTTAGTGGTTAA
1 AAGTATCCAT-C-T-ATTTTTAGTGGTTAA
* *
8661320 AAGTATCCATCAATTTTTGGTGGTTAA
1 AAGTATCCATCTATTTTTAGTGGTTAA
* * *
8661347 AAGTGTCCATCTTCAACTTTTAGTAGTTAA
1 AAGTATCCATC-T--ATTTTTAGTGGTTAA
* * * *
8661377 AAGTATCCATATGTTTCTGGTGGTTAA
1 AAGTATCCATCTATTTTTAGTGGTTAA
8661404 AAGTATCCAT
1 AAGTATCCAT
8661414 GCATCTTTTC
Statistics
Matches: 100, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
27 54 0.54
28 1 0.01
29 3 0.03
30 42 0.42
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.40
Consensus pattern (27 bp):
AAGTATCCATCTATTTTTAGTGGTTAA
Found at i:8661321 original size:30 final size:29
Alignment explanation
Indices: 8661280--8661422 Score: 125
Period size: 27 Copynumber: 5.0 Consensus size: 29
8661270 TATCTACTTC
*
8661280 TAGTAGTTAAAAGTATCTATCCATCATTTT
1 TAGTAGTTAAAAGTATCCAT-CATCATTTT
*
8661310 TAGTGGTTAAAAGTATCCATCA--ATTTT
1 TAGTAGTTAAAAGTATCCATCATCATTTT
* * * * *
8661337 TGGTGGTTAAAAGTGTCCATCTTCAACTTT
1 TAGTAGTTAAAAGTATCCATCATC-ATTTT
* *
8661367 TAGTAGTTAAAAGTATCCAT-AT-GTTTC
1 TAGTAGTTAAAAGTATCCATCATCATTTT
* *
8661394 TGGTGGTTAAAAGTATCCATGCATC-TTTT
1 TAGTAGTTAAAAGTATCCAT-CATCATTTT
8661423 CACTTCTGGT
Statistics
Matches: 91, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
27 44 0.48
29 8 0.09
30 39 0.43
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.41
Consensus pattern (29 bp):
TAGTAGTTAAAAGTATCCATCATCATTTT
Found at i:8661346 original size:57 final size:57
Alignment explanation
Indices: 8661285--8661418 Score: 166
Period size: 57 Copynumber: 2.3 Consensus size: 57
8661275 ACTTCTAGTA
* * *
8661285 GTTAAAAGTATCTATCCATC-ATTTTTAGTGGTTAAAAGTATCCATCAAT-TTT-TGGTG
1 GTTAAAAGTATCCAT-CATCAACTTTTAGTAGTTAAAAGTATCCAT--ATGTTTCTGGTG
* *
8661342 GTTAAAAGTGTCCATCTTCAACTTTTAGTAGTTAAAAGTATCCATATGTTTCTGGTG
1 GTTAAAAGTATCCATCATCAACTTTTAGTAGTTAAAAGTATCCATATGTTTCTGGTG
8661399 GTTAAAAGTATCCATGCATC
1 GTTAAAAGTATCCAT-CATC
8661419 TTTTCACTTC
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
55 2 0.03
56 6 0.09
57 55 0.83
58 3 0.05
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (57 bp):
GTTAAAAGTATCCATCATCAACTTTTAGTAGTTAAAAGTATCCATATGTTTCTGGTG
Found at i:8661469 original size:30 final size:30
Alignment explanation
Indices: 8661434--8661511 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
8661424 ACTTCTGGTG
* * *
8661434 GTTAAAAGTATTCATCCAACACTTTTGAT-
1 GTTAAAAGTATCCATCCAACACTTCTAATA
* * *
8661463 GATTAAAAATATCCATCCTATACTTCTAATA
1 G-TTAAAAGTATCCATCCAACACTTCTAATA
8661494 GTTAAAAGTATCCATCCA
1 GTTAAAAGTATCCATCCA
8661512 CTTTTGGTGG
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
29 1 0.03
30 37 0.95
31 1 0.03
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (30 bp):
GTTAAAAGTATCCATCCAACACTTCTAATA
Found at i:8662504 original size:17 final size:17
Alignment explanation
Indices: 8662460--8662507 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
8662450 TTGAAAAGCT
8662460 TTTTAAAAAAGAAGTAAA
1 TTTTAAAAAA-AAGTAAA
**
8662478 TTTTTTAAAAAA-TAAAA
1 TTTTAAAAAAAAGT-AAA
8662495 TTTTAAAAAAAAG
1 TTTTAAAAAAAAG
8662508 AGAGCTTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
16 1 0.04
17 15 0.62
18 8 0.33
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.33
Consensus pattern (17 bp):
TTTTAAAAAAAAGTAAA
Found at i:8663381 original size:4 final size:4
Alignment explanation
Indices: 8663367--8663398 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
8663357 TCTATCAGAG
8663367 TTTC TTTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC -TTTC TTTC TTTC TTTC TTTC TTTC TTT
8663399 TTCTATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:8666828 original size:2 final size:2
Alignment explanation
Indices: 8666823--8666854 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
8666813 TATATTTCAA
8666823 AT AT AT CAT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT A
8666855 ACCTAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:8686046 original size:107 final size:103
Alignment explanation
Indices: 8685846--8686052 Score: 274
Period size: 107 Copynumber: 2.0 Consensus size: 103
8685836 GCAAAGAAAG
*** *
8685846 CTCTGCTTCAAGCACAAAACAATAAATGTGAATTTTAACACTTAGCATATGATTATGTAGTTAAG
1 CTCTGCTTCAAGCACAAAACAATAAATACAAATTTTAACACTTAGCATATGATTAAGTAGTTAAG
8685911 ACCAAAACTTCATCTCTAAATCTGAAGAAATCAATTCT
66 ACCAAAACTTCATCTCTAAATCTGAAGAAATCAATTCT
8685949 CTCTGCTTCAAGCACAAAACAATAAACACATACAAATTTTAGA-ACTTAGCATATGATTAAGTAG
1 CTCTGCTTCAAGCACAAAACAAT--A-A-ATACAAATTTTA-ACACTTAGCATATGATTAAGTAG
* ** *
8686013 TTAAGGCTGAAA-TTCATCTCTATATCTGAAAGAAATCAAT
61 TTAAGACCAAAACTTCATCTCTAAATCTG-AAGAAATCAAT
8686053 AGACTGCATC
Statistics
Matches: 90, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
103 23 0.26
105 1 0.01
106 16 0.18
107 49 0.54
108 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (103 bp):
CTCTGCTTCAAGCACAAAACAATAAATACAAATTTTAACACTTAGCATATGATTAAGTAGTTAAG
ACCAAAACTTCATCTCTAAATCTGAAGAAATCAATTCT
Done.