Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167938.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_20, 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: 19866354
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 74000 characters in sequence are not A, C, G, or T
File 19 of 100
Found at i:5370937 original size:2 final size:2
Alignment explanation
Indices: 5370932--5370976 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
5370922 ATGTGTGTGC
5370932 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5370974 AT A
1 AT A
5370977 AACAGACTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5371136 original size:40 final size:40
Alignment explanation
Indices: 5371080--5371156 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
5371070 GGCTGAAATG
* *
5371080 AACAAAGATGCCCTTTAATAACACGTCTATTCGGCTAGTA
1 AACAAAGATGCCCTTTAATAACAAGTCTATTCAGCTAGTA
*
5371120 AACAAAGATGCGCTTTAATAACAAGTCTATTCAGCTA
1 AACAAAGATGCCCTTTAATAACAAGTCTATTCAGCTA
5371157 AATAGTGAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (40 bp):
AACAAAGATGCCCTTTAATAACAAGTCTATTCAGCTAGTA
Found at i:5377105 original size:16 final size:16
Alignment explanation
Indices: 5377045--5377107 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
5377035 CTCTATGATA
*
5377045 TATTTTTTT-ATTTTT
1 TATTTTTTTAAATTTT
**
5377060 TATTTTTTTTCATTTT
1 TATTTTTTTAAATTTT
* **
5377076 TCCTTTTTAAAAATTTT
1 T-ATTTTTTTAAATTTT
5377093 TATTTTTTTAAATTT
1 TATTTTTTTAAATTT
5377108 GTTTTAGGAA
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
15 9 0.25
16 16 0.44
17 11 0.31
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.75
Consensus pattern (16 bp):
TATTTTTTTAAATTTT
Found at i:5378165 original size:8 final size:8
Alignment explanation
Indices: 5378154--5378190 Score: 65
Period size: 8 Copynumber: 4.6 Consensus size: 8
5378144 GTTTTTTACT
5378154 TTTTTATA
1 TTTTTATA
5378162 TTTTTATA
1 TTTTTATA
5378170 TTTTTATA
1 TTTTTATA
*
5378178 TTTTTATG
1 TTTTTATA
5378186 TTTTT
1 TTTTT
5378191 TGGTTTTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (8 bp):
TTTTTATA
Found at i:5378220 original size:8 final size:8
Alignment explanation
Indices: 5378145--5378225 Score: 63
Period size: 8 Copynumber: 9.5 Consensus size: 8
5378135 ACTTGATTTG
*
5378145 TTTTTTAC
1 TTTTTTAT
5378153 TTTTTTAT
1 TTTTTTAT
*
5378161 ATTTTTAT
1 TTTTTTAT
*
5378169 ATTTTTAT
1 TTTTTTAT
*
5378177 ATTTTTAT
1 TTTTTTAT
*
5378185 GTTTTTTGGTT
1 -TTTTTT--AT
*
5378196 TTTTGTTTT
1 TTTT-TTAT
5378205 TTTCTTTAT
1 TTT-TTTAT
5378214 TTTTTTAT
1 TTTTTTAT
5378222 TTTT
1 TTTT
5378226 AATTATATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
8 39 0.62
9 16 0.25
10 5 0.08
11 3 0.05
ACGTcount: A:0.12, C:0.02, G:0.05, T:0.80
Consensus pattern (8 bp):
TTTTTTAT
Found at i:5378546 original size:14 final size:14
Alignment explanation
Indices: 5378514--5378555 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
5378504 TGTTACATAT
*
5378514 TTTATTGAA-TTTA
1 TTTATTAAATTTTA
*
5378527 TATATTAAATTTTA
1 TTTATTAAATTTTA
*
5378541 TTTATTTAATTTTA
1 TTTATTAAATTTTA
5378555 T
1 T
5378556 AAGTATATAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 7 0.29
14 17 0.71
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (14 bp):
TTTATTAAATTTTA
Found at i:5385126 original size:29 final size:29
Alignment explanation
Indices: 5385094--5385165 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
5385084 CCCGAATTTT
*
5385094 ATAAATTTTTATACTTTTA-TTATATTTAA
1 ATAAATTTTTA-ACTTTTACTTACATTTAA
* *
5385123 ATAAGTTTTTAATTTTTACTTTACATTTAA
1 ATAAATTTTTAACTTTTAC-TTACATTTAA
*
5385153 ATAAAATTTTAAC
1 ATAAATTTTTAAC
5385166 ATAGGTTAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
28 6 0.17
29 10 0.29
30 19 0.54
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (29 bp):
ATAAATTTTTAACTTTTACTTACATTTAA
Found at i:5385208 original size:20 final size:22
Alignment explanation
Indices: 5385180--5385219 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5385170 GTTAATCTTT
5385180 TATTC-AA-ATAAATAAAAACA
1 TATTCAAATATAAATAAAAACA
*
5385200 TATTTAAATATAAATAAAAA
1 TATTCAAATATAAATAAAAA
5385220 ACAAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 2 0.12
22 11 0.65
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (22 bp):
TATTCAAATATAAATAAAAACA
Found at i:5385255 original size:29 final size:29
Alignment explanation
Indices: 5385189--5385261 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
5385179 TTATTCAAAT
**
5385189 AAATAAAAACATATTTAAATATAAATAAA
1 AAATAAAAATTTATTTAAATATAAATAAA
*
5385218 AAACAAAAAATTTATTTAAATAT-AATAAA
1 AAA-TAAAAATTTATTTAAATATAAATAAA
*
5385247 ATTATAAAAATTTAT
1 A-AATAAAAATTTAT
5385262 CTATACGATA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 20 0.54
30 17 0.46
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (29 bp):
AAATAAAAATTTATTTAAATATAAATAAA
Found at i:5399598 original size:21 final size:21
Alignment explanation
Indices: 5399574--5399614 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5399564 ATTTTCCTCA
*
5399574 TCATCAGATTCACTCTCACTC
1 TCATCAGATTCACTATCACTC
*
5399595 TCATCAGATTCGCTATCACT
1 TCATCAGATTCACTATCACT
5399615 GTAAGATGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.34, G:0.07, T:0.34
Consensus pattern (21 bp):
TCATCAGATTCACTATCACTC
Found at i:5406950 original size:21 final size:21
Alignment explanation
Indices: 5406924--5406963 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5406914 AAAAATGGGA
5406924 GTGAGAACGGAGGTGATAAGG
1 GTGAGAACGGAGGTGATAAGG
**
5406945 GTGAGATTGGAGGTGATAA
1 GTGAGAACGGAGGTGATAA
5406964 AACCGGTGAT
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:0.33, C:0.03, G:0.45, T:0.20
Consensus pattern (21 bp):
GTGAGAACGGAGGTGATAAGG
Found at i:5409983 original size:2 final size:2
Alignment explanation
Indices: 5409976--5410003 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5409966 CTGTTTGTTT
5409976 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5410004 TGCGTACAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5412177 original size:20 final size:21
Alignment explanation
Indices: 5412143--5412181 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
5412133 TTTAATATTT
5412143 ATTAATTAAACAAAAAATACA
1 ATTAATTAAACAAAAAATACA
*
5412164 ATTAA-TAAATAAAAAATA
1 ATTAATTAAACAAAAAATA
5412182 AAGAAGACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (21 bp):
ATTAATTAAACAAAAAATACA
Found at i:5412390 original size:23 final size:21
Alignment explanation
Indices: 5412352--5412401 Score: 82
Period size: 23 Copynumber: 2.3 Consensus size: 21
5412342 ACTAGACCAA
5412352 CCACCCCTACGACACCTACAG
1 CCACCCCTACGACACCTACAG
5412373 CCACGCCCTACAGACACCTACAG
1 CCAC-CCCTAC-GACACCTACAG
5412396 CCACCC
1 CCACCC
5412402 TTACAACCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.15
22 8 0.30
23 15 0.56
ACGTcount: A:0.28, C:0.54, G:0.10, T:0.08
Consensus pattern (21 bp):
CCACCCCTACGACACCTACAG
Found at i:5413417 original size:20 final size:20
Alignment explanation
Indices: 5413392--5413430 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5413382 GTAATAATTA
* *
5413392 ACAATAATAATAATTAAATG
1 ACAATAACAATAATAAAATG
5413412 ACAATAACAATAATAAAAT
1 ACAATAACAATAATAAAAT
5413431 TTAAACGTTT
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:0.64, C:0.08, G:0.03, T:0.26
Consensus pattern (20 bp):
ACAATAACAATAATAAAATG
Found at i:5413498 original size:7 final size:8
Alignment explanation
Indices: 5413488--5413547 Score: 52
Period size: 9 Copynumber: 7.2 Consensus size: 8
5413478 TCCAAATATT
5413488 AAATAA-A
1 AAATAATA
5413495 AAATAATA
1 AAATAATA
*
5413503 AAAT-ATGC
1 AAATAAT-A
*
5413511 ATATAATA
1 AAATAATA
5413519 ATAATAATA
1 A-AATAATA
5413528 ATAATAATA
1 A-AATAATA
5413537 ATAATAATA
1 A-AATAATA
5413546 AA
1 AA
5413548 CTTTTCCCTA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
7 8 0.18
8 10 0.22
9 27 0.60
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (8 bp):
AAATAATA
Found at i:5413519 original size:3 final size:3
Alignment explanation
Indices: 5413513--5413546 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
5413503 AAATATGCAT
5413513 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5413547 ACTTTTCCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5413651 original size:19 final size:21
Alignment explanation
Indices: 5413621--5413672 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
5413611 AATGTTGGAG
*
5413621 AATTATTATTAAAAAT-AATA
1 AATTAATATTAAAAATAAATA
*
5413641 AA-TAATATTAAAACTAAATA
1 AATTAATATTAAAAATAAATA
5413661 AATTAATATTAA
1 AATTAATATTAA
5413673 CTATTCATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 11 0.39
20 8 0.29
21 9 0.32
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
AATTAATATTAAAAATAAATA
Found at i:5414625 original size:58 final size:57
Alignment explanation
Indices: 5414555--5415007 Score: 522
Period size: 58 Copynumber: 7.7 Consensus size: 57
5414545 TCTTATGTAG
*
5414555 GGAAAATTGATACTTTCAATTTTTCCCTAAAAATCATTTTTTTGAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAAT-ATTTTTTTGAAATTTATTTTTAA
* *
5414613 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTCAATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAATTT--ATTTTTAA
* * *
5414672 GAAAAATTGATACTTTCAACTTTT-TCTCAAAAATTCTTTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCT-AAAAA-T-ATTTTTTTG-AAATTTATTTTTAA
* * * * *
5414732 GAAAAATTGATACTTTCAATTTTTTCCTAAAAATATTTTTTGGAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAA-TTT-ATTTTTAA
* * *
5414791 GAAAAATTGATACTTTCAACTTTT-CCTCAAAAATCTTTTTTTTTTGAAAATTTACTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCT-AAAAA---TATTTTTTTG-AAATTTATTTTTAA
*
5414852 GGAAAATTGATACTTTCAACTTTTCCCT-AAAATA-TTTTTTGAAAATTTCTATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTG-AAA-TT-TATTTTTAA
* ***
5414910 GGAAAATTGATATTTTCAACTTTT-CCTCAAAAA-CCCTTTTTGAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCT-AAAAATATTTTTTTGAAATTTATTTTTAA
*
5414966 GGAAAATTGATACTTTCAACTTTTTCCTAAAAATATTTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTT
5415008 TTTGGAATTT
Statistics
Matches: 343, Mismatches: 30, Indels: 45
0.82 0.07 0.11
Matches are distributed among these distances:
56 47 0.14
57 33 0.10
58 81 0.24
59 81 0.24
60 40 0.12
61 38 0.11
62 20 0.06
63 3 0.01
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.47
Consensus pattern (57 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAATTTATTTTTAA
Found at i:5415011 original size:119 final size:118
Alignment explanation
Indices: 5414557--5415006 Score: 680
Period size: 119 Copynumber: 3.8 Consensus size: 118
5414547 TTATGTAGGG
* *
5414557 AAAATTGATACTTTCAATTTTTCC-CTAAAAATCATTTTTTTG-AAATTTATTTTTAAGGAAAAT
1 AAAATTGATACTTTCAACTTTTCCTC-AAAAATCTTTTTTTTGAAAATTTATTTTTAAGGAAAAT
*
5414620 TGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTCAATTTTCAAGA
65 TGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTCTATTTTCAAGA
* *
5414674 AAAATTGATACTTTCAACTTTTTCTCAAAAATTCTTTTTTTTGAAAATTTATTTTTAAGAAAAAT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA-TCTTTTTTTTGAAAATTTATTTTTAAGGAAAAT
* *
5414739 TGATACTTTCAATTTTTTCCTAAAAATATTTTTTGGAAATTT-TGATTTTCAAGA
65 TGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTCT-ATTTTCAAGA
*
5414793 AAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTTTGAAAATTTACTTTTAAGGAAAA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATC--TTTTTTTTGAAAATTTATTTTTAAGGAAAA
* *
5414858 TTGATACTTTCAACTTTTCCCT-AAAATATTTTTTGAAAATTTCTATTTTCAAGG
64 TTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTCTATTTTCAAGA
* **
5414912 AAAATTGATATTTTCAACTTTTCCTCAAAAA-C-CCTTTTTG-AAATTTATTTTTAAGGAAAATT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTTTAAGGAAAATT
*
5414974 GATACTTTCAACTTTTTCCTAAAAATATTTTTT
66 GATACTTTCAACTTTTCCCTAAAAATATTTTTT
5415007 TTTTGGAATT
Statistics
Matches: 306, Mismatches: 19, Indels: 18
0.89 0.06 0.05
Matches are distributed among these distances:
114 40 0.13
115 18 0.06
117 27 0.09
118 14 0.05
119 158 0.52
120 49 0.16
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (118 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTTTAAGGAAAATT
GATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTCTATTTTCAAGA
Found at i:5415045 original size:5 final size:5
Alignment explanation
Indices: 5415035--5415104 Score: 67
Period size: 5 Copynumber: 13.8 Consensus size: 5
5415025 TTATTTAAAG
5415035 AAAAT AAAAT AAAAAT AAAAT -AAA- AAAAT AAAA- AAAAGT AAAA- AAAAT
1 AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T AAAAT AAAAT
5415083 AAAAAAT AAAAT AAAGAT AAAA
1 --AAAAT AAAAT AAA-AT AAAA
5415105 AGAATATTAA
Statistics
Matches: 56, Mismatches: 0, Indels: 18
0.76 0.00 0.24
Matches are distributed among these distances:
4 14 0.25
5 23 0.41
6 14 0.25
7 5 0.09
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:5415051 original size:11 final size:11
Alignment explanation
Indices: 5415035--5415104 Score: 71
Period size: 11 Copynumber: 6.8 Consensus size: 11
5415025 TTATTTAAAG
5415035 AAAATAAAATA
1 AAAATAAAATA
5415046 AAAATAAAAT-
1 AAAATAAAATA
5415056 -AAA-AAAATA
1 AAAATAAAATA
*
5415065 AAAA-AAAGT-
1 AAAATAAAATA
5415074 AAAA-AAAATAA
1 AAAATAAAAT-A
5415085 AAAATAAAATA
1 AAAATAAAATA
*
5415096 AAGATAAAA
1 AAAATAAAA
5415105 AGAATATTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
8 5 0.10
9 11 0.22
10 7 0.14
11 23 0.45
12 5 0.10
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:5415064 original size:19 final size:19
Alignment explanation
Indices: 5415040--5415097 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 19
5415030 TAAAGAAAAT
5415040 AAAATAAAAATAAAATAAA
1 AAAATAAAAATAAAATAAA
*
5415059 AAAATAAAAA-AAAGTAAAA
1 AAAATAAAAATAAAAT-AAA
5415078 AAAATAAAAAATAAAATAAA
1 AAAAT-AAAAATAAAATAAA
5415098 GATAAAAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 4 0.12
19 18 0.53
20 8 0.24
21 4 0.12
ACGTcount: A:0.84, C:0.00, G:0.02, T:0.14
Consensus pattern (19 bp):
AAAATAAAAATAAAATAAA
Found at i:5415081 original size:27 final size:28
Alignment explanation
Indices: 5415046--5415110 Score: 89
Period size: 26 Copynumber: 2.4 Consensus size: 28
5415036 AAATAAAATA
5415046 AAAATAAAATAAAAAAATAAAAAAAAG-T
1 AAAA-AAAATAAAAAAATAAAAAAAAGAT
*
5415074 AAAAAAAAT-AAAAAATAAAATAAAGAT
1 AAAAAAAATAAAAAAATAAAAAAAAGAT
*
5415101 AAAAAGAATA
1 AAAAAAAATA
5415111 TTAAATAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 15 0.45
27 14 0.42
28 4 0.12
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.14
Consensus pattern (28 bp):
AAAAAAAATAAAAAAATAAAAAAAAGAT
Found at i:5415116 original size:27 final size:24
Alignment explanation
Indices: 5415030--5415119 Score: 82
Period size: 22 Copynumber: 3.7 Consensus size: 24
5415020 GATTTTTATT
5415030 TAAAGAAAATAAAATAAAAATAAA-A
1 TAAA-AAAATAAAAT-AAAATAAAGA
5415055 TAAAAAAATAAAA-AAAAGTAAA-A
1 TAAAAAAATAAAATAAAA-TAAAGA
*
5415078 -AAAATAA-AAAATAAAATAAAGA
1 TAAAAAAATAAAATAAAATAAAGA
5415100 TAAAAAGAATATTAAATAAA
1 TAAAAA-AATA--AAATAAA
5415120 CCTAATCTAA
Statistics
Matches: 55, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
21 8 0.15
22 15 0.27
23 9 0.16
24 11 0.20
25 5 0.09
27 7 0.13
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (24 bp):
TAAAAAAATAAAATAAAATAAAGA
Found at i:5416249 original size:16 final size:15
Alignment explanation
Indices: 5416230--5416268 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
5416220 ATACATATAT
*
5416230 TAATACATAATAATAA
1 TAATAAATAATAA-AA
5416246 TAATAAATAATAAAA
1 TAATAAATAATAAAA
5416261 TACATAAA
1 TA-ATAAA
5416269 ATACAAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (15 bp):
TAATAAATAATAAAA
Found at i:5416250 original size:9 final size:10
Alignment explanation
Indices: 5416215--5416273 Score: 54
Period size: 9 Copynumber: 5.9 Consensus size: 10
5416205 TAAATAAATA
5416215 AATATATACAT
1 AATA-ATACAT
5416226 ATATTAATACAT
1 A-A-TAATACAT
5416238 AATAATA-AT
1 AATAATACAT
5416247 AATAAATA-AT
1 AAT-AATACAT
5416257 AA-AATACAT
1 AATAATACAT
5416266 AA-AATACA
1 AATAATACA
5416274 AAAGAAAGAG
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
8 4 0.09
9 15 0.34
10 13 0.30
11 2 0.05
12 8 0.18
13 2 0.05
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.31
Consensus pattern (10 bp):
AATAATACAT
Found at i:5423662 original size:69 final size:68
Alignment explanation
Indices: 5423589--5423724 Score: 245
Period size: 68 Copynumber: 2.0 Consensus size: 68
5423579 TAAAGAAGAA
*
5423589 TGGCATGCCTTAAAGGGCAAGACTCGATTGATAAAAAAAATTATGTTCCTTTATTTGTATGAAAC
1 TGGCATGCCTCAAAGGGCAAGACTCGATTGAT-AAAAAAATTATGTTCCTTTATTTGTATGAAAC
5423654 ATTT
65 ATTT
*
5423658 TGGCATGCCTCAAAGGGCAAGCCTCGATTGATAAAAAAATTATGTTCCTTTATTTGTATGAAACA
1 TGGCATGCCTCAAAGGGCAAGACTCGATTGATAAAAAAATTATGTTCCTTTATTTGTATGAAACA
5423723 TT
66 TT
5423725 CTGTTCAGGC
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
68 35 0.54
69 30 0.46
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Consensus pattern (68 bp):
TGGCATGCCTCAAAGGGCAAGACTCGATTGATAAAAAAATTATGTTCCTTTATTTGTATGAAACA
TTT
Found at i:5428916 original size:36 final size:35
Alignment explanation
Indices: 5428754--5428970 Score: 157
Period size: 36 Copynumber: 6.1 Consensus size: 35
5428744 TTGACTTGTA
* * * * *
5428754 GTTTAATCTCGATTGTTATTATTTTTTTAACTCATG
1 GTTTAATCCCGATCGTCATTA-TTTCTTGACTCATG
* * * * * *
5428790 GTTTAGTCCCGATCGTCTTTATCCTCTTGATTTACG
1 GTTTAATCCCGATCGTCATTAT-TTCTTGACTCATG
* * * *
5428826 GTTTAATCTC-AGTCCTCATTATTTTTTGACTTATG
1 GTTTAATCCCGA-TCGTCATTATTTCTTGACTCATG
* * *
5428861 GTTTAATCTCGATCGTCATTATTTTTTTGACTCGTG
1 GTTTAATCCCGATCGTCATTA-TTTCTTGACTCATG
* * * * * *
5428897 ATTCAATCCCAATCTTCATTATTCCTTAACTCATG
1 GTTTAATCCCGATCGTCATTATTTCTTGACTCATG
*
5428932 GTTTAATCCCGATCGTCATTATTTTCTTGACTTATG
1 GTTTAATCCCGATCGTCATTA-TTTCTTGACTCATG
5428968 GTT
1 GTT
5428971 CAATTTCAAT
Statistics
Matches: 138, Mismatches: 38, Indels: 10
0.74 0.20 0.05
Matches are distributed among these distances:
35 56 0.41
36 82 0.59
ACGTcount: A:0.20, C:0.19, G:0.12, T:0.48
Consensus pattern (35 bp):
GTTTAATCCCGATCGTCATTATTTCTTGACTCATG
Found at i:5428962 original size:107 final size:108
Alignment explanation
Indices: 5428657--5429082 Score: 355
Period size: 107 Copynumber: 4.0 Consensus size: 108
5428647 TATAATCCTT
* * * * *
5428657 ATCGTCATTATTTTTTTGACTTGT-AGTTCAATCTCAGTCCTT-ATTATTCTTTTGGACTCGCGG
1 ATCGTCATTATTTTTTTGACTCGTGAGTTCAATCCCAAT-CTTCATTATTCTCTT-GACTCACGG
* * * * *
5428720 TTTAACCCCAATCCTTATTATTCTTTGACTTGTAGTTTAATCTCG
64 TTTAATCCCAATCCTCATTATTTTTTGACTTATGGTTTAATCTCG
* * * * * * * * * * * *
5428765 ATTGTTATTATTTTTTTAACTCATG-GTTTAGTCCCGATCGTCTTTATCCTCTTGATTTACGGTT
1 ATCGTCATTATTTTTTTGACTCGTGAGTTCAATCCCAATCTTCATTATTCTCTTGACTCACGGTT
* *
5428829 TAATCTCAGTCCTCATTATTTTTTGACTTATGGTTTAATCTCG
66 TAATCCCAATCCTCATTATTTTTTGACTTATGGTTTAATCTCG
* *
5428872 ATCGTCATTATTTTTTTGACTCGTGA-TTCAATCCCAATCTTCATTATTC-CTTAACTCATGGTT
1 ATCGTCATTATTTTTTTGACTCGTGAGTTCAATCCCAATCTTCATTATTCTCTTGACTCACGGTT
* * * * *
5428935 TAATCCCGATCGTCATTATTTTCTTGACTTATGGTTCAATTTCA
66 TAATCCCAATCCTCATTATTTT-TTGACTTATGGTTTAATCTCG
* ** * * * * * *
5428979 ATCCTCGGTATTCCTTTAGGCTCG-CAGTTCAA-CCCAATCCTCATTATTCT-TTGACTCATGGT
1 ATCGTCATTATT-TTTTTGACTCGTGAGTTCAATCCCAATCTTCATTATTCTCTTGACTCACGGT
** * *
5429041 TTAATCCCAATTGTCATTATTTTCTTAACTTGTGGTTTAATC
65 TTAATCCCAATCCTCATTATTTT-TTGACTTATGGTTTAATC
5429083 CCAGTCATTT
Statistics
Matches: 251, Mismatches: 60, Indels: 15
0.77 0.18 0.05
Matches are distributed among these distances:
106 28 0.11
107 175 0.70
108 48 0.19
ACGTcount: A:0.20, C:0.21, G:0.12, T:0.46
Consensus pattern (108 bp):
ATCGTCATTATTTTTTTGACTCGTGAGTTCAATCCCAATCTTCATTATTCTCTTGACTCACGGTT
TAATCCCAATCCTCATTATTTTTTGACTTATGGTTTAATCTCG
Found at i:5428973 original size:71 final size:71
Alignment explanation
Indices: 5428780--5429084 Score: 227
Period size: 71 Copynumber: 4.3 Consensus size: 71
5428770 TATTATTTTT
* * * * * * * * *
5428780 TTAACTCATGGTTTAGTCCCGATCGTCTTTATCCTCTTGATTTACGGTTTAATCTCAGTCCTCAT
1 TTAACTCATGGTTTAATCCCGATCGTCATTATTCTCTTGACTCATGGTTCAATCCCAATCCTCAT
**
5428845 TATTTT
66 TATTCC
* * * * * * * *
5428851 TTGACTTATGGTTTAATCTCGATCGTCATTATTTTTTTGACTCGTGATTCAATCCCAATCTTCAT
1 TTAACTCATGGTTTAATCCCGATCGTCATTATTCTCTTGACTCATGGTTCAATCCCAATCCTCAT
5428916 TATTCC
66 TATTCC
* * ** **
5428922 TTAACTCATGGTTTAATCCCGATCGTCATTATTTTCTTGACTTATGGTTCAATTTCAATCCTCGG
1 TTAACTCATGGTTTAATCCCGATCGTCATTATTCTCTTGACTCATGGTTCAATCCCAATCCTCAT
5428987 TATTCC
66 TATTCC
* *** * * * * **
5428993 TTTAGGCTCGCAGTTCAA-CCCAATCCTCATTATTCT-TTGACTCATGGTTTAATCCCAATTGTC
1 -TTA-ACTCATGGTTTAATCCCGATCGTCATTATTCTCTTGACTCATGGTTCAATCCCAATCCTC
*
5429056 ATTATTTTC
64 ATTA-TTCC
**
5429065 TTAACTTGTGGTTTAATCCC
1 TTAACTCATGGTTTAATCCC
5429085 AGTCATTTTT
Statistics
Matches: 177, Mismatches: 53, Indels: 8
0.74 0.22 0.03
Matches are distributed among these distances:
70 8 0.05
71 140 0.79
72 21 0.12
73 8 0.05
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.45
Consensus pattern (71 bp):
TTAACTCATGGTTTAATCCCGATCGTCATTATTCTCTTGACTCATGGTTCAATCCCAATCCTCAT
TATTCC
Found at i:5429175 original size:142 final size:143
Alignment explanation
Indices: 5429024--5429529 Score: 556
Period size: 142 Copynumber: 3.6 Consensus size: 143
5429014 AATCCTCATT
* * * * * * * *
5429024 ATTCTTTGACTCATGGTTTAATCCCAATTGTCATTATTTTCTTAACTTGTGGTTTAATCCCAGTC
1 ATTCCTTGACTCATGGTTTAATCTCGATTGTCATTATTTTCTTGACTCGTGATTCAGTCCCAGTC
* * ** * * *
5429089 ATTTTTATCCTCTTGACTCTTGATTTAGTCCCGGTTGTCTTTATCCTATTGACTTACGATTCAAT
66 ATCTTTATCCTCTTGACTCGTGATTTAGTCCCGGTCATCTTTATCCTCTTGACTTGCGGTTCAAT
* * *
5429154 CCCAGT-ATTGTG
131 CTCAGTCCTTATG
* * *
5429166 ATTCCTTGACTCATAGTTTAATCTCGATTATCATTATTTTCTTGACTCGTGATTCAGTCTCAGTC
1 ATTCCTTGACTCATGGTTTAATCTCGATTGTCATTATTTTCTTGACTCGTGATTCAGTCCCAGTC
* * * * * *
5429231 GTCTTCATCCTTTTGACTCGTGGTTTAGT-TCGATCATCTTTATCCTCTTGACTTGCGGTTCAAT
66 ATCTTTATCCTCTTGACTCGTGATTTAGTCCCGGTCATCTTTATCCTCTTGACTTGCGGTTCAAT
5429295 CTCAGTCCTTATG
131 CTCAGTCCTTATG
* * * * * * *
5429308 ATTTCTTGACTCGTGATTTAATCTCGATTGTTATTATTTTCTTGACTCGTGGTTTAGTCCAAGTC
1 ATTCCTTGACTCATGGTTTAATCTCGATTGTCATTATTTTCTTGACTCGTGATTCAGTCCCAGTC
* * * *
5429373 ATATTTATCCACTTGACTCGTGA-TT--TCCCGGTCATCTTTTTCCTCTTGACTTGCGGTTTAAT
66 ATCTTTATCCTCTTGACTCGTGATTTAGTCCCGGTCATCTTTATCCTCTTGACTTGCGGTTCAAT
*
5429435 CTTAGTCCTTATG
131 CTCAGTCCTTATG
* * * * **
5429448 ATTCATTGACTCGTGGTTTAATCTCGATCGTTATTATTTTCTTGACTTATGATTCAGTCCCAGTC
1 ATTCCTTGACTCATGGTTTAATCTCGATTGTCATTATTTTCTTGACTCGTGATTCAGTCCCAGTC
*
5429513 GTCTTTATCCT-TTGACT
66 ATCTTTATCCTCTTGACT
5429530 TGCGGTTCAA
Statistics
Matches: 302, Mismatches: 60, Indels: 7
0.82 0.16 0.02
Matches are distributed among these distances:
139 7 0.02
140 107 0.35
141 35 0.12
142 153 0.51
ACGTcount: A:0.18, C:0.22, G:0.15, T:0.46
Consensus pattern (143 bp):
ATTCCTTGACTCATGGTTTAATCTCGATTGTCATTATTTTCTTGACTCGTGATTCAGTCCCAGTC
ATCTTTATCCTCTTGACTCGTGATTTAGTCCCGGTCATCTTTATCCTCTTGACTTGCGGTTCAAT
CTCAGTCCTTATG
Found at i:5429282 original size:35 final size:36
Alignment explanation
Indices: 5429205--5429301 Score: 90
Period size: 35 Copynumber: 2.7 Consensus size: 36
5429195 ATCATTATTT
*
5429205 TCTTGACTCGTGATTCAGTCTCAGTCGTCTTCATCC
1 TCTTGACTCGTGATTCAGTCTCAGTCATCTTCATCC
* * * *
5429241 TTTTGACTCGTGGTTTAGT-TC-GATCATCTTTATCC
1 TCTTGACTCGTGATTCAGTCTCAG-TCATCTTCATCC
* * * *
5429276 TCTTGACTTGCGGTTCAATCTCAGTC
1 TCTTGACTCGTGATTCAGTCTCAGTC
5429302 CTTATGATTT
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
34 1 0.02
35 26 0.54
36 20 0.42
37 1 0.02
ACGTcount: A:0.14, C:0.26, G:0.18, T:0.42
Consensus pattern (36 bp):
TCTTGACTCGTGATTCAGTCTCAGTCATCTTCATCC
Found at i:5429331 original size:35 final size:36
Alignment explanation
Indices: 5429292--5429363 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 36
5429282 CTTGCGGTTC
5429292 AATCTC-AGTCCTTATGA-TTTCTTGACTCGTGATTT
1 AATCTCGA-TCCTTATGATTTTCTTGACTCGTGATTT
** * *
5429327 AATCTCGATTGTTATTATTTTCTTGACTCGTGGTTT
1 AATCTCGATCCTTATGATTTTCTTGACTCGTGATTT
5429363 A
1 A
5429364 GTCCAAGTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
35 12 0.39
36 19 0.61
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.49
Consensus pattern (36 bp):
AATCTCGATCCTTATGATTTTCTTGACTCGTGATTT
Found at i:5429573 original size:106 final size:107
Alignment explanation
Indices: 5429398--5429647 Score: 281
Period size: 106 Copynumber: 2.4 Consensus size: 107
5429388 ACTCGTGATT
* * * ** *
5429398 TCCCGGTCATCTTTTTCCTCTTGACTTGCGGTTTAATCTTAGTCCTTATGATTCATTGACTCGTG
1 TCCCAGTCATCTTTATCCTCTTGACTTGCGGTTCAATCCCAGTCCTTATGATTCATTGACTCGTA
** * * *
5429463 GTTTAATCTC-GATCGTTATTATTTTCTTGACTTATGATTCAG
66 GTTTAATAACAG-TCATTATTATTTTCTTGACTCATGATTCAA
* * * * *
5429505 TCCCAGTCGTCTTTATCCT-TTGACTTGCGGTTCAATCCCAGTCCTTGTGATTCCTTGGCTTGTA
1 TCCCAGTCATCTTTATCCTCTTGACTTGCGGTTCAATCCCAGTCCTTATGATTCATTGACTCGTA
*
5429569 GTTTAATAACAGTCATTATTATTTTCTTGACTCGTGATTCAA
66 GTTTAATAACAGTCATTATTATTTTCTTGACTCATGATTCAA
* * * *
5429611 TCCCAATCATCATTAT-TTCTTGACTCGCGGTTCAATC
1 TCCCAGTCATCTTTATCCTCTTGACTTGCGGTTCAATC
5429648 TTGATCTCTT
Statistics
Matches: 119, Mismatches: 22, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
105 1 0.01
106 101 0.85
107 17 0.14
ACGTcount: A:0.18, C:0.23, G:0.15, T:0.44
Consensus pattern (107 bp):
TCCCAGTCATCTTTATCCTCTTGACTTGCGGTTCAATCCCAGTCCTTATGATTCATTGACTCGTA
GTTTAATAACAGTCATTATTATTTTCTTGACTCATGATTCAA
Found at i:5429722 original size:104 final size:104
Alignment explanation
Indices: 5429609--5429800 Score: 246
Period size: 104 Copynumber: 1.8 Consensus size: 104
5429599 CTCGTGATTC
* * * *
5429609 AATCCCAATCATCATTA-TTTCTTGACTCGCGGTTCAATCTTGATCTCTTTACTTCTAAGTTACG
1 AATCCCAATC-TCATTATTTTCTTGACTCACAGTTCAATCCTGATCTCTTTACCTCTAAG-T-CG
*
5429673 -A-TTTAATCTCGATCCTCATTATTTTTCTGACATGTGGTTT
63 CAGTTTAATCTCAATCCTCATTATTTTTCTGACATGTGGTTT
* * * * *
5429713 AATCTCAATCTCTTTATTTTTTTGACTCATAGTTTAATCCTGATCTCTTTACCTCTAAGTCGCAG
1 AATCCCAATCTCATTATTTTCTTGACTCACAGTTCAATCCTGATCTCTTTACCTCTAAGTCGCAG
5429778 TTTAATCTCAATCCTCATTATTT
66 TTTAATCTCAATCCTCATTATTT
5429801 CTTTGAGTTA
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
102 2 0.03
103 7 0.09
104 66 0.88
ACGTcount: A:0.23, C:0.22, G:0.09, T:0.45
Consensus pattern (104 bp):
AATCCCAATCTCATTATTTTCTTGACTCACAGTTCAATCCTGATCTCTTTACCTCTAAGTCGCAG
TTTAATCTCAATCCTCATTATTTTTCTGACATGTGGTTT
Found at i:5429748 original size:35 final size:36
Alignment explanation
Indices: 5429674--5429751 Score: 88
Period size: 35 Copynumber: 2.2 Consensus size: 36
5429664 TAAGTTACGA
* * *
5429674 TTTAATCTCGATCCTCATTATTTTTCTGACATGTGG
1 TTTAATCTCAATCCTCATTATTTTTCTGACATATAG
* *
5429710 TTTAATCTCAAT-CTCTTTATTTTTTTGAC-TCATAG
1 TTTAATCTCAATCCTCATTATTTTTCTGACAT-ATAG
5429745 TTTAATC
1 TTTAATC
5429752 CTGATCTCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
34 1 0.03
35 24 0.67
36 11 0.31
ACGTcount: A:0.22, C:0.18, G:0.09, T:0.51
Consensus pattern (36 bp):
TTTAATCTCAATCCTCATTATTTTTCTGACATATAG
Found at i:5429818 original size:104 final size:104
Alignment explanation
Indices: 5429644--5429838 Score: 252
Period size: 104 Copynumber: 1.9 Consensus size: 104
5429634 CTCGCGGTTC
* * * **
5429644 AATCTTGATCTCTTTACTTCTAAGTTACGATTTAATCTCGATCCTCATTATTTTTCTGACATGTG
1 AATCCTGATCTCTTTACCTCTAAGTTACGATTTAATCTCAATCCTCATTATTTTTCTGACATACG
*
5429709 GTTTAATCTCAATCTCTTTATTTTTTTGACTCATAGTTT
66 ATTTAATCTCAATCTCTTTATTTTTTTGACTCATAGTTT
**
5429748 AATCCTGATCTCTTTACCTCTAAG-T-CGCAGTTTAATCTCAATCCTCATTATTTCTT-TGAGTT
1 AATCCTGATCTCTTTACCTCTAAGTTACG-A-TTTAATCTCAATCCTCATTATTT-TTCTGACAT
**
5429810 ACGATTTAATCTCGGTCTCTTTATTTTTT
63 ACGATTTAATCTCAATCTCTTTATTTTTT
5429839 AACTTGCAAT
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
102 2 0.03
103 2 0.03
104 72 0.92
105 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.49
Consensus pattern (104 bp):
AATCCTGATCTCTTTACCTCTAAGTTACGATTTAATCTCAATCCTCATTATTTTTCTGACATACG
ATTTAATCTCAATCTCTTTATTTTTTTGACTCATAGTTT
Found at i:5430327 original size:20 final size:18
Alignment explanation
Indices: 5430302--5430340 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
5430292 TTTAATATTT
5430302 ATTAATTAAACAAAAATATA
1 ATTAA-TAAACAAAAA-ATA
*
5430322 ATTAATAAATAAAAAATA
1 ATTAATAAACAAAAAATA
5430340 A
1 A
5430341 AAAGATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 9 0.50
20 5 0.28
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (18 bp):
ATTAATAAACAAAAAATA
Found at i:5431332 original size:28 final size:30
Alignment explanation
Indices: 5431287--5431351 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 30
5431277 TCAACCAACC
5431287 CTGAACCGGCTCAATCGAAC-CACCACTCAA
1 CTGAACCGGCTCAATCGAACTCA-CACTCAA
* *
5431317 CTGAACC-GCT-AGTCGAACTGACACTCAA
1 CTGAACCGGCTCAATCGAACTCACACTCAA
*
5431345 TTGAACC
1 CTGAACC
5431352 ACTTGTCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 20 0.65
29 4 0.13
30 7 0.23
ACGTcount: A:0.32, C:0.35, G:0.15, T:0.17
Consensus pattern (30 bp):
CTGAACCGGCTCAATCGAACTCACACTCAA
Found at i:5431692 original size:3 final size:3
Alignment explanation
Indices: 5431684--5431715 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5431674 AAATATGCAT
5431684 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
5431716 TTTTTCCTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:5433113 original size:13 final size:13
Alignment explanation
Indices: 5433095--5433119 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5433085 TTGACTACTG
5433095 AAATTGTTGCTTA
1 AAATTGTTGCTTA
5433108 AAATTGTTGCTT
1 AAATTGTTGCTT
5433120 CCAACTCTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (13 bp):
AAATTGTTGCTTA
Found at i:5434642 original size:75 final size:77
Alignment explanation
Indices: 5434546--5434686 Score: 223
Period size: 76 Copynumber: 1.9 Consensus size: 77
5434536 TTTCCTTTTT
* * * *
5434546 AAAATATATATATAACAGTTAATTTATCC-CTTTTAGCTTGACATTTTCAAAGTAGAGTATTTTT
1 AAAATATATATAAAACAGTTAATTTATCCTATTTTAGCTTGACATTTTCAAACTAAAGTATTTTT
5434610 TTTTTATGAAAA
66 TTTTTATGAAAA
*
5434622 AAAAT-TATATAAAACGGTTAATTTATCCTATTTTAGCTTGACATTTTCAAACTAAAGTATTTTT
1 AAAATATATATAAAACAGTTAATTTATCCTATTTTAGCTTGACATTTTCAAACTAAAGTATTTTT
5434686 T
66 T
5434687 AAAAAATTAT
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
75 21 0.36
76 38 0.64
ACGTcount: A:0.37, C:0.10, G:0.09, T:0.45
Consensus pattern (77 bp):
AAAATATATATAAAACAGTTAATTTATCCTATTTTAGCTTGACATTTTCAAACTAAAGTATTTTT
TTTTTATGAAAA
Found at i:5435411 original size:16 final size:16
Alignment explanation
Indices: 5435392--5435435 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
5435382 AAAACGTTTT
5435392 TATTAAAAAAAAATCA
1 TATTAAAAAAAAATCA
* * **
5435408 TATTAAAAACAATTTT
1 TATTAAAAAAAAATCA
5435424 TATTAAAAAAAA
1 TATTAAAAAAAA
5435436 TAAATCTTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (16 bp):
TATTAAAAAAAAATCA
Found at i:5443167 original size:77 final size:77
Alignment explanation
Indices: 5443073--5443221 Score: 246
Period size: 77 Copynumber: 1.9 Consensus size: 77
5443063 CAGATAGGTC
* *
5443073 TATATATAATTTAATGGTTTATCTCCCTTTGCACATGCAAATTATAAATGCACTGTTAAACTT-A
1 TATATACAATTTAATGGTTCATCTCCCTTTGCACATGCAAATTATAAATGCACTGTT-AACTTGA
5443137 TTTTCATTAATTT
65 TTTTCATTAATTT
* *
5443150 TATATACAATTTGATGGTTCATCTCCCTTTGCACATGCAAATTATAAATGTACTGTTAACTTGAT
1 TATATACAATTTAATGGTTCATCTCCCTTTGCACATGCAAATTATAAATGCACTGTTAACTTGAT
5443215 TTTCATT
66 TTTCATT
5443222 CTTCAAATTG
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
76 5 0.07
77 62 0.93
ACGTcount: A:0.31, C:0.15, G:0.09, T:0.44
Consensus pattern (77 bp):
TATATACAATTTAATGGTTCATCTCCCTTTGCACATGCAAATTATAAATGCACTGTTAACTTGAT
TTTCATTAATTT
Found at i:5444052 original size:18 final size:18
Alignment explanation
Indices: 5444029--5444076 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 18
5444019 AAAATAAAAA
5444029 ATAAAAATAAGTTTAAAT
1 ATAAAAATAAGTTTAAAT
** *
5444047 ATAAAAAAATATTTTTAATT
1 AT--AAAAATAAGTTTAAAT
5444067 ATAAAAATAA
1 ATAAAAATAA
5444077 AGAATGCTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
18 9 0.38
20 15 0.62
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
ATAAAAATAAGTTTAAAT
Found at i:5444056 original size:20 final size:20
Alignment explanation
Indices: 5444031--5444073 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5444021 AATAAAAAAT
5444031 AAAAATAAGTTTAAATATAA
1 AAAAATAAGTTTAAATATAA
** *
5444051 AAAAATATTTTTAATTATAA
1 AAAAATAAGTTTAAATATAA
5444071 AAA
1 AAA
5444074 TAAAGAATGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
AAAAATAAGTTTAAATATAA
Found at i:5444275 original size:27 final size:26
Alignment explanation
Indices: 5444215--5444276 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
5444205 ATTTTATAAT
5444215 TATTTTTTATTTTGTATTATTAAAAA
1 TATTTTTTATTTTGTATTATTAAAAA
* * *
5444241 TAATTTTTATTTT-TATTTTTCAAATA
1 TATTTTTTATTTTGTATTATT-AAAAA
5444267 TATTATTTTA
1 TATT-TTTTA
5444277 AATAAAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 6 0.20
26 19 0.63
27 5 0.17
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (26 bp):
TATTTTTTATTTTGTATTATTAAAAA
Found at i:5444971 original size:18 final size:18
Alignment explanation
Indices: 5444937--5444971 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5444927 TTAAATTAAA
* *
5444937 TTTATAATTAAATAATTT
1 TTTATAATAAAAAAATTT
5444955 TTTATAATAAAAAAATT
1 TTTATAATAAAAAAATT
5444972 AAAAATTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTATAATAAAAAAATTT
Found at i:5445074 original size:31 final size:32
Alignment explanation
Indices: 5445025--5445106 Score: 105
Period size: 31 Copynumber: 2.6 Consensus size: 32
5445015 TTTGATCAAT
* *
5445025 TTAATTATAATTAATTATTTAAA-AAATTTTAA
1 TTAATT-TAATTATTTATTTAAATAAATATTAA
5445057 TTAATTTAATTATTTA-TTAAATAAATATTAA
1 TTAATTTAATTATTTATTTAAATAAATATTAA
* *
5445088 TTAAATTAATTATTAATTT
1 TTAATTTAATTATTTATTT
5445107 TTTCAAATCG
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
30 5 0.11
31 31 0.70
32 8 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
TTAATTTAATTATTTATTTAAATAAATATTAA
Found at i:5445102 original size:27 final size:28
Alignment explanation
Indices: 5445025--5445103 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 28
5445015 TTTGATCAAT
5445025 TTAATTATAATTAATTATTTAAAAAATTTTAA
1 TTAATTA-AATTAATTA-TTAAAAAA--TTAA
* *
5445057 TTAATTTAATTATTTATTAAATAAA-T-A
1 TTAATTAAATTAATTATTAAA-AAATTAA
5445084 TTAATTAAATTAATTATTAA
1 TTAATTAAATTAATTATTAA
5445104 TTTTTTCAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
27 19 0.45
28 1 0.02
30 5 0.12
31 11 0.26
32 6 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TTAATTAAATTAATTATTAAAAAATTAA
Found at i:5446778 original size:3 final size:3
Alignment explanation
Indices: 5446764--5446804 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
5446754 ATCGTTCACC
5446764 AGA AGA AGGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
5446805 ACCCTCAGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:5449451 original size:55 final size:55
Alignment explanation
Indices: 5449367--5449474 Score: 180
Period size: 55 Copynumber: 2.0 Consensus size: 55
5449357 ATGTTTTTCT
* * *
5449367 TTAGTGCCATGTTAATGTTCAGAGTGCAATAGATATATGTTCTTTTGTACTGGCG
1 TTAGTGCAATGTGAATGTTCAGAGTGCAATAGATATATGTTCTTATGTACTGGCG
*
5449422 TTAGTGCAATGTGAATGTTCGGAGTGCAATAGATATATGTTCTTATGTACTGG
1 TTAGTGCAATGTGAATGTTCAGAGTGCAATAGATATATGTTCTTATGTACTGG
5449475 TTTTTACTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.39
Consensus pattern (55 bp):
TTAGTGCAATGTGAATGTTCAGAGTGCAATAGATATATGTTCTTATGTACTGGCG
Found at i:5465370 original size:2 final size:2
Alignment explanation
Indices: 5465363--5465392 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5465353 GCTATGATTA
5465363 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5465393 GAATACGAAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5476936 original size:21 final size:22
Alignment explanation
Indices: 5476895--5476939 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
5476885 ATTTAAACTA
*
5476895 ATCTTATTCATAATATTATCTT
1 ATCTTATTCATAATATAATCTT
5476917 ATCTTA-TCAT-ATCATAATCTT
1 ATCTTATTCATAAT-ATAATCTT
5476938 AT
1 AT
5476940 GCACTAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 13 0.62
22 6 0.29
ACGTcount: A:0.33, C:0.16, G:0.00, T:0.51
Consensus pattern (22 bp):
ATCTTATTCATAATATAATCTT
Found at i:5514469 original size:2 final size:2
Alignment explanation
Indices: 5514462--5514486 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5514452 AGTAACATCA
5514462 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
5514487 ATGGATCTTC
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:5519081 original size:2 final size:2
Alignment explanation
Indices: 5519076--5519104 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5519066 TGTGTGTGTG
5519076 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
5519105 GTGATACCTG
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:5520144 original size:3 final size:3
Alignment explanation
Indices: 5520136--5520160 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5520126 ATTTAAAAAG
5520136 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
5520161 TTTTATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:5524607 original size:16 final size:16
Alignment explanation
Indices: 5524583--5524613 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5524573 TCTAAATCCA
5524583 AATTAATTCAAACTCG
1 AATTAATTCAAACTCG
*
5524599 AATTGATTCAAACTC
1 AATTAATTCAAACTC
5524614 AAAATGAACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32
Consensus pattern (16 bp):
AATTAATTCAAACTCG
Found at i:5525976 original size:2 final size:2
Alignment explanation
Indices: 5525971--5526007 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5525961 ACGCACGTAC
*
5525971 AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5526008 CTTTTCATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:5526170 original size:17 final size:17
Alignment explanation
Indices: 5526134--5526189 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
5526124 AAAATATATA
*
5526134 TTTTTCATCTTTC-TATT
1 TTTTTCAT-TTTCTTAAT
5526151 TTTTTCATTTTCTTAAT
1 TTTTTCATTTTCTTAAT
*
5526168 TTTCTTAATTTT-TTAAT
1 TTT-TTCATTTTCTTAAT
5526185 TTTTT
1 TTTTT
5526190 ATTACCCTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
16 6 0.17
17 22 0.63
18 7 0.20
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTCATTTTCTTAAT
Found at i:5526185 original size:8 final size:8
Alignment explanation
Indices: 5526150--5526190 Score: 55
Period size: 9 Copynumber: 4.9 Consensus size: 8
5526140 ATCTTTCTAT
*
5526150 TTTTTTCA
1 TTTTTTAA
5526158 TTTTCTTAA
1 TTTT-TTAA
5526167 TTTTCTTAA
1 TTTT-TTAA
5526176 TTTTTTAA
1 TTTTTTAA
5526184 TTTTTTA
1 TTTTTTA
5526191 TTACCCTACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 15 0.48
9 16 0.52
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTTTTAA
Found at i:5526528 original size:11 final size:12
Alignment explanation
Indices: 5526490--5526530 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
5526480 ATATTATTTT
5526490 TAATATAAATATAA
1 TAAT-TAAATA-AA
5526504 -AATTAAATAAA
1 TAATTAAATAAA
5526515 TAATTAAA-AAA
1 TAATTAAATAAA
5526526 TAATT
1 TAATT
5526531 TTATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 10 0.38
12 13 0.50
13 3 0.12
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
TAATTAAATAAA
Found at i:5528618 original size:23 final size:24
Alignment explanation
Indices: 5528574--5528618 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
5528564 TGGACTTATT
*
5528574 TTTATTTTAAATAAAATTTAAAGA
1 TTTATTTTAAATAAAATATAAAGA
*
5528598 TTTATTTT-ACTAAAATATAAA
1 TTTATTTTAAATAAAATATAAA
5528619 ATAAAAGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (24 bp):
TTTATTTTAAATAAAATATAAAGA
Found at i:5530363 original size:22 final size:24
Alignment explanation
Indices: 5530336--5530382 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
5530326 ACACCTATTA
5530336 TTTA-TTTTAATCTCATT-TTTAT
1 TTTATTTTTAATCTCATTATTTAT
*
5530358 TTTATTTTTAATCTCTTTATTTAT
1 TTTATTTTTAATCTCATTATTTAT
5530382 T
1 T
5530383 CAAATGAACC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.18
23 12 0.55
24 6 0.27
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTATTTTTAATCTCATTATTTAT
Found at i:5549248 original size:21 final size:21
Alignment explanation
Indices: 5549206--5549249 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
5549196 AACTTTATCC
* *
5549206 AAGGTTTATTATTTAAGCTTG
1 AAGGCTTATTACTTAAGCTTG
* *
5549227 AAGGCTTATTACTTCAGTTTG
1 AAGGCTTATTACTTAAGCTTG
5549248 AA
1 AA
5549250 TAGGTTTGTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (21 bp):
AAGGCTTATTACTTAAGCTTG
Found at i:5551060 original size:52 final size:51
Alignment explanation
Indices: 5550972--5551117 Score: 150
Period size: 52 Copynumber: 2.8 Consensus size: 51
5550962 TGGACAAGAA
* *
5550972 GACTTGCAAAAAAAGAATTT-CAAGAGAAAGATGATTCTTAATAAGTAAATTT
1 GACTTGCAAAAGAAGAATTTAAAAG-GAAAGA-GATTCTTAATAAGTAAATTT
* * *
5551024 GACTTGCAATAGAAGAATTATAAAAGGAAAGAGATTCTTAATAGGTAAGTTT
1 GACTTGCAAAAGAAGAATT-TAAAAGGAAAGAGATTCTTAATAAGTAAATTT
* ** * * *
5551076 GACTTACAGGAGAAGAATTCTAAGAGGAGAGGGATTCTTAAT
1 GACTTGCAAAAGAAGAATT-TAAAAGGAAAGAGATTCTTAAT
5551118 GAGCAAGTCT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
52 70 0.88
53 7 0.09
54 3 0.04
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.27
Consensus pattern (51 bp):
GACTTGCAAAAGAAGAATTTAAAAGGAAAGAGATTCTTAATAAGTAAATTT
Found at i:5558904 original size:11 final size:11
Alignment explanation
Indices: 5558888--5558921 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
5558878 TATAAAAATT
5558888 TTTAATAT-TCA
1 TTTAATATAT-A
5558899 TTTAATATATA
1 TTTAATATATA
5558910 TTTAATATATA
1 TTTAATATATA
5558921 T
1 T
5558922 ATTTAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 21 0.95
12 1 0.05
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTAATATATA
Found at i:5558920 original size:13 final size:13
Alignment explanation
Indices: 5558903--5558927 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5558893 TATTCATTTA
5558903 ATATATATTTAAT
1 ATATATATTTAAT
5558916 ATATATATTTAA
1 ATATATATTTAA
5558928 ATTTGAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATATATTTAAT
Found at i:5559425 original size:13 final size:13
Alignment explanation
Indices: 5559394--5559419 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5559384 TTAAAACACA
5559394 TATATAATTTTTT
1 TATATAATTTTTT
5559407 TATATAATTTTTT
1 TATATAATTTTTT
5559420 ATTATATCAT
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:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TATATAATTTTTT
Found at i:5571137 original size:4 final size:4
Alignment explanation
Indices: 5571130--5571154 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5571120 ATTATTTATT
5571130 TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA T
5571155 TTTTAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:5583281 original size:12 final size:12
Alignment explanation
Indices: 5583245--5583284 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
5583235 ATTTAATTTT
5583245 ATTTAATT-TAA
1 ATTTAATTATAA
*
5583256 AATT-ATTA-AA
1 ATTTAATTATAA
5583266 ATTTAATTATAA
1 ATTTAATTATAA
5583278 ATTTAAT
1 ATTTAAT
5583285 CGAAAGTGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
10 8 0.33
11 7 0.29
12 9 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTTAATTATAA
Found at i:5590064 original size:41 final size:41
Alignment explanation
Indices: 5590007--5590089 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
5589997 GGCCTGTATG
*
5590007 ATTACTTCCTGTTTCTCATTTTCTTTGATATGAATTAGGAC
1 ATTACTTCCCGTTTCTCATTTTCTTTGATATGAATTAGGAC
5590048 ATTACTTCCCGTTTCTCATTTTCTTTGATATGAATTAGGAC
1 ATTACTTCCCGTTTCTCATTTTCTTTGATATGAATTAGGAC
5590089 A
1 A
5590090 CTGTTTCTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.23, C:0.18, G:0.12, T:0.47
Consensus pattern (41 bp):
ATTACTTCCCGTTTCTCATTTTCTTTGATATGAATTAGGAC
Found at i:5600109 original size:17 final size:18
Alignment explanation
Indices: 5600064--5600111 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
5600054 ATTTAATTTT
5600064 ATATTTATATTAAAAATA
1 ATATTTATATTAAAAATA
5600082 ATATTTATATTAAAAATA
1 ATATTTATATTAAAAATA
5600100 ATATTT-TATTAA
1 ATATTTATATTAA
5600112 TTTTTAATCG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 6 0.20
18 24 0.80
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
ATATTTATATTAAAAATA
Found at i:5623687 original size:2 final size:2
Alignment explanation
Indices: 5623680--5623708 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5623670 GTCGTCATGC
5623680 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
5623709 CCCTTTACAT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:5625190 original size:2 final size:2
Alignment explanation
Indices: 5625183--5625212 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5625173 CATGCAAATC
5625183 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5625213 GTAAGTACCT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5634788 original size:23 final size:24
Alignment explanation
Indices: 5634747--5634793 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
5634737 CTCTCCACCA
5634747 AAAATAAATAAATAAATC-TGCTT
1 AAAATAAATAAATAAATCTTGCTT
* **
5634770 AAAATCAATAAATTCATCTTGCTT
1 AAAATAAATAAATAAATCTTGCTT
5634794 CATGAAACAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.34
Consensus pattern (24 bp):
AAAATAAATAAATAAATCTTGCTT
Found at i:5641602 original size:71 final size:71
Alignment explanation
Indices: 5641462--5641594 Score: 212
Period size: 71 Copynumber: 1.9 Consensus size: 71
5641452 TCGAATACAT
* * * * *
5641462 GCAACTTCTTTTGAAATATTAGTATCGTTGAACATTTTCTTATGAAATTCTAGAATATTTAACAA
1 GCAACTTCTGTTGAAAGATGAGTATCGTTGAACATTTCCTCATGAAATTCTAGAATATTTAACAA
5641527 ATTTTA
66 ATTTTA
*
5641533 GCAACTTCTGTTGAAAGATGAGTATCGTTGAACCTTTCCTCATGAAATTCTAGAATATTTAA
1 GCAACTTCTGTTGAAAGATGAGTATCGTTGAACATTTCCTCATGAAATTCTAGAATATTTAA
5641595 TATATTTTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 56 1.00
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.40
Consensus pattern (71 bp):
GCAACTTCTGTTGAAAGATGAGTATCGTTGAACATTTCCTCATGAAATTCTAGAATATTTAACAA
ATTTTA
Found at i:5644005 original size:22 final size:25
Alignment explanation
Indices: 5643971--5644035 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 25
5643961 TAGTAAATAT
*
5643971 ATTTTTTTATTAAA-TAA-TATAAA
1 ATTTTATTATTAAATTAATTATAAA
5643994 ATTTTATT-TTAAATTAATTATAATTA
1 ATTTTATTATTAAATTAATTATAA--A
5644020 ATGTTTATCTATTAAA
1 AT-TTTAT-TATTAAA
5644036 AATATATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 5 0.15
23 10 0.29
24 5 0.15
26 3 0.09
27 5 0.15
28 1 0.03
29 5 0.15
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (25 bp):
ATTTTATTATTAAATTAATTATAAA
Found at i:5644011 original size:23 final size:24
Alignment explanation
Indices: 5643971--5644043 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 24
5643961 TAGTAAATAT
*
5643971 ATTTTTTTATTAAATAA-TATAAA
1 ATTTTATTATTAAATAATTATAAA
5643994 ATTTTATT-TTAAATTAATTATAATTA
1 ATTTTATTATTAAA-TAATTATAA--A
5644020 ATGTTTATCTATTAAA-AATATATA
1 AT-TTTAT-TATTAAATAAT-TATA
5644044 TATTTTGATG
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
22 5 0.12
23 10 0.24
24 5 0.12
26 3 0.07
27 8 0.20
28 5 0.12
29 5 0.12
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (24 bp):
ATTTTATTATTAAATAATTATAAA
Found at i:5644258 original size:22 final size:22
Alignment explanation
Indices: 5644233--5644286 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
5644223 TGATTCACTG
*
5644233 ATAATATATAAAATATATATTA
1 ATAATATATAAAATATAAATTA
* *
5644255 ATAATATATTAAATATAAATTT
1 ATAATATATAAAATATAAATTA
*
5644277 TTAATATATA
1 ATAATATATA
5644287 TTTATAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATAATATATAAAATATAAATTA
Found at i:5660108 original size:2 final size:2
Alignment explanation
Indices: 5660101--5660134 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5660091 AGTCATTTAT
5660101 TC TC 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 TC TC
5660135 ATTTCTTTTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:5668317 original size:6 final size:6
Alignment explanation
Indices: 5668306--5668372 Score: 61
Period size: 6 Copynumber: 11.3 Consensus size: 6
5668296 TAATATAATA
* *
5668306 TTAAAT TTAAAT TTTAAT TT-GAT TTAAAAT TTAAGAT TTAAAAT TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TT-AAAT TTAA-AT TT-AAAT TTAAAT
5668355 TTAAAT TT-AA- TTAAAT TT
1 TTAAAT TTAAAT TTAAAT TT
5668373 TATTTTTTTA
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
4 2 0.04
5 13 0.25
6 22 0.43
7 12 0.24
8 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (6 bp):
TTAAAT
Found at i:5668345 original size:14 final size:14
Alignment explanation
Indices: 5668326--5668364 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
5668316 ATTTTAATTT
5668326 GATTTAAAATTTAA
1 GATTTAAAATTTAA
5668340 GATTTAAAATTT-A
1 GATTTAAAATTTAA
5668353 -ATTT-AAATTTAA
1 GATTTAAAATTTAA
5668365 TTAAATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.25
12 5 0.21
13 1 0.04
14 12 0.50
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (14 bp):
GATTTAAAATTTAA
Found at i:5668370 original size:10 final size:11
Alignment explanation
Indices: 5668301--5668377 Score: 66
Period size: 12 Copynumber: 6.5 Consensus size: 11
5668291 TAAATTAATA
5668301 TAATATTAAATT
1 TAAT-TTAAATT
*
5668313 TAAATTTTAATT
1 T-AATTTAAATT
*
5668325 TGATTTAAAATT
1 TAATTT-AAATT
5668337 TAAGATTTAAAATT
1 T-A-ATTT-AAATT
5668351 TAATTTAAATT
1 TAATTTAAATT
5668362 TAA-TTAAATT
1 TAATTTAAATT
*
5668372 TTATTT
1 TAATTT
5668378 TTTTAACTCG
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
10 9 0.16
11 14 0.25
12 17 0.31
13 4 0.07
14 11 0.20
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (11 bp):
TAATTTAAATT
Found at i:5668500 original size:25 final size:23
Alignment explanation
Indices: 5668445--5668506 Score: 70
Period size: 25 Copynumber: 2.6 Consensus size: 23
5668435 TATATAAAAA
*
5668445 TAAATTTAAATTTTATATTCAAT
1 TAAATTTAAATTTTATACTCAAT
* *
5668468 AAATATTTAATTATTTATACTCAAAT
1 TAA-ATTTAAAT-TTTATACTC-AAT
5668494 TAAATTTAAATTT
1 TAAATTTAAATTT
5668507 AAGATATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
23 2 0.06
24 9 0.29
25 15 0.48
26 5 0.16
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (23 bp):
TAAATTTAAATTTTATACTCAAT
Found at i:5672229 original size:27 final size:26
Alignment explanation
Indices: 5672199--5672256 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
5672189 TAAACATAAG
5672199 ATAATATGATATTATTTAATTTAATTT
1 ATAATATGATATTATTTAATTTAA-TT
* * * *
5672226 ATAATATTATTTTATTTTATTTTATT
1 ATAATATGATATTATTTAATTTAATT
5672252 ATAAT
1 ATAAT
5672257 TTTGTACACT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 7 0.26
27 20 0.74
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (26 bp):
ATAATATGATATTATTTAATTTAATT
Found at i:5679644 original size:30 final size:28
Alignment explanation
Indices: 5679610--5679670 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 28
5679600 TTTCATTTTG
5679610 AAATTAAAATTATACATTA-TTTTATCATAA
1 AAATTAAAATTATA-A-TAGTTTTAT-ATAA
* *
5679640 AAATTAGAATTTTAATAGTTTTATATAA
1 AAATTAAAATTATAATAGTTTTATATAA
5679668 AAA
1 AAA
5679671 GAAAAAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 9 0.32
29 7 0.25
30 12 0.43
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (28 bp):
AAATTAAAATTATAATAGTTTTATATAA
Found at i:5680198 original size:3 final size:3
Alignment explanation
Indices: 5680190--5680220 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5680180 TTTTTAATTC
5680190 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5680221 TATTTTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5691750 original size:15 final size:16
Alignment explanation
Indices: 5691732--5691764 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5691722 TTTTCGTATA
5691732 TTTTATTT-ATATCAT
1 TTTTATTTCATATCAT
*
5691747 TTTTATTTCATGTCAT
1 TTTTATTTCATATCAT
5691763 TT
1 TT
5691765 ATTAAATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.21, C:0.09, G:0.03, T:0.67
Consensus pattern (16 bp):
TTTTATTTCATATCAT
Found at i:5692767 original size:27 final size:27
Alignment explanation
Indices: 5692731--5692787 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
5692721 TTTAATATAA
5692731 AAAACATTTTTCCAGTGAAAATGTAAT
1 AAAACATTTTTCCAGTGAAAATGTAAT
*
5692758 AAAACATTTTTCCAGTGAAAATGTTAT
1 AAAACATTTTTCCAGTGAAAATGTAAT
5692785 AAA
1 AAA
5692788 TGTAAACAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (27 bp):
AAAACATTTTTCCAGTGAAAATGTAAT
Found at i:5704763 original size:28 final size:30
Alignment explanation
Indices: 5704708--5704764 Score: 73
Period size: 28 Copynumber: 1.9 Consensus size: 30
5704698 ATAATTTACC
*
5704708 ATATAATAATAAAATTTATGTATTTATTATT
1 ATATAATAATAAAA-TTATGTATATATTATT
*
5704739 ATATAATAA-AAAA-TATTTATATATTA
1 ATATAATAATAAAATTATGTATATATTA
5704765 AATCACCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 11 0.46
30 4 0.17
31 9 0.38
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (30 bp):
ATATAATAATAAAATTATGTATATATTATT
Found at i:5707961 original size:31 final size:31
Alignment explanation
Indices: 5707923--5707992 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
5707913 TTATAATCAT
5707923 TAAATAATTAACTAATAAAATAAAATATAAA
1 TAAATAATTAACTAATAAAATAAAATATAAA
*
5707954 TAAATAATTAACTAATAAATTAAAATATAAA
1 TAAATAATTAACTAATAAAATAAAATATAAA
5707985 TAAATAAT
1 TAAATAAT
5707993 CAAATGAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (31 bp):
TAAATAATTAACTAATAAAATAAAATATAAA
Found at i:5711253 original size:21 final size:22
Alignment explanation
Indices: 5711229--5711271 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5711219 TAATTATGTG
*
5711229 TTGATTTTAT-TAAATTTTTAT
1 TTGATTTAATCTAAATTTTTAT
5711250 TTGATTTAATCTAAATTTTTAT
1 TTGATTTAATCTAAATTTTTAT
5711272 AGATATGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (22 bp):
TTGATTTAATCTAAATTTTTAT
Found at i:5717868 original size:26 final size:26
Alignment explanation
Indices: 5717828--5717886 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
5717818 AAATTATAAA
* ** *
5717828 AAATATTTAATATAATATTTAAATTTT
1 AAAT-TTTAAAATAATAAATAAATTAT
5717855 AAATTTTAAAATAATAAATAAATTAT
1 AAATTTTAAAATAATAAATAAATTAT
5717881 AAATTT
1 AAATTT
5717887 ATTAATTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 24 0.86
27 4 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
AAATTTTAAAATAATAAATAAATTAT
Found at i:5718000 original size:28 final size:28
Alignment explanation
Indices: 5717951--5718026 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 28
5717941 ATAATCAATA
* *
5717951 TTATAAATATT-ATATTA-ATTAATAAAT
1 TTATAAAT-TTAATATAATATTAAAAAAT
*
5717978 TTAT-AATTTAAATATCATATTAAAAAAT
1 TTATAAATTT-AATATAATATTAAAAAAT
*
5718006 TTTTAAATTTAATATAATATT
1 TTATAAATTTAATATAATATT
5718027 TAACAAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
25 2 0.05
26 3 0.07
27 9 0.22
28 22 0.54
29 5 0.12
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (28 bp):
TTATAAATTTAATATAATATTAAAAAAT
Found at i:5718504 original size:21 final size:22
Alignment explanation
Indices: 5718480--5718523 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
5718470 ATAATTTTTA
5718480 TTTATCAATT-TGT-AAATAAAT
1 TTTAT-AATTATGTAAAATAAAT
*
5718501 TTTATAATTATTTAAAATAAAT
1 TTTATAATTATGTAAAATAAAT
5718523 T
1 T
5718524 ATATTTTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 7 0.35
22 9 0.45
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTATAATTATGTAAAATAAAT
Found at i:5718730 original size:17 final size:17
Alignment explanation
Indices: 5718684--5718734 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 17
5718674 AAATTTATTG
5718684 AATTTATATATTTGATAAA
1 AATTT-TATATTT-ATAAA
**
5718703 TTTTTTA-ATTTATAAA
1 AATTTTATATTTATAAA
5718719 AATTTTATATTT-TAAA
1 AATTTTATATTTATAAA
5718735 CTTTTAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
16 14 0.52
17 8 0.30
18 2 0.07
19 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
AATTTTATATTTATAAA
Found at i:5735246 original size:14 final size:14
Alignment explanation
Indices: 5735237--5735268 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
5735227 AAAAAAAAAT
5735237 AAAACTAAAATAAA
1 AAAACTAAAATAAA
*
5735251 AATACTAAAATAAA
1 AAAACTAAAATAAA
5735265 AAAA
1 AAAA
5735269 GAAAATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.16
Consensus pattern (14 bp):
AAAACTAAAATAAA
Found at i:5736551 original size:23 final size:23
Alignment explanation
Indices: 5736525--5736584 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 23
5736515 TGAAATGTCC
5736525 TTAAATTATGTTTTTTTTTACA-T
1 TTAAATTAT-TTTTTTTTTACATT
* *
5736548 TTAAATT-TCTTATTTTTTATATT
1 TTAAATTAT-TTTTTTTTTACATT
5736571 TTAAAATTATTTTT
1 TT-AAATTATTTTT
5736585 AATAATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
22 11 0.37
23 10 0.33
24 8 0.27
25 1 0.03
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (23 bp):
TTAAATTATTTTTTTTTTACATT
Found at i:5737340 original size:28 final size:29
Alignment explanation
Indices: 5737307--5737369 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
5737297 ATGAAATTTT
* *
5737307 TAAAAAGTTAATTTTAATATA-TTTAATA
1 TAAAAAGTTAAATTTAATAAATTTTAATA
* * *
5737335 TTAAAATTTAAATTTCATAAATTTTAATA
1 TAAAAAGTTAAATTTAATAAATTTTAATA
5737364 TAAAAA
1 TAAAAA
5737370 TAATAAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
28 16 0.57
29 12 0.43
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (29 bp):
TAAAAAGTTAAATTTAATAAATTTTAATA
Found at i:5737417 original size:26 final size:27
Alignment explanation
Indices: 5737385--5737439 Score: 80
Period size: 24 Copynumber: 2.1 Consensus size: 27
5737375 AAAATAATTT
5737385 AAAATATA-AAAATTTT-AGATAT-TA
1 AAAATATATAAAATTTTGAGATATCTA
*
5737409 AAAATATATATAATTTTGAGATATCTA
1 AAAATATATAAAATTTTGAGATATCTA
5737436 AAAA
1 AAAA
5737440 AAAAGGCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 8 0.30
25 7 0.26
26 6 0.22
27 6 0.22
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.36
Consensus pattern (27 bp):
AAAATATATAAAATTTTGAGATATCTA
Found at i:5744596 original size:21 final size:22
Alignment explanation
Indices: 5744571--5744614 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
5744561 CTAAAGTATT
5744571 AAAATATATTTATA-TAGAATA
1 AAAATATATTTATACTAGAATA
* *
5744592 AAAATTTATTTATACTAGCATA
1 AAAATATATTTATACTAGAATA
5744614 A
1 A
5744615 TTTTTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.39
Consensus pattern (22 bp):
AAAATATATTTATACTAGAATA
Found at i:5752778 original size:22 final size:24
Alignment explanation
Indices: 5752754--5752796 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
5752744 TGTGTGTGCT
5752754 TTTTA-AAAT-TTTTTT-TAAAAA
1 TTTTACAAATATTTTTTGTAAAAA
5752775 TTTTACAAATATTTTTTGTAAA
1 TTTTACAAATATTTTTTGTAAA
5752797 TTTAAATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 4 0.21
23 6 0.32
24 4 0.21
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (24 bp):
TTTTACAAATATTTTTTGTAAAAA
Found at i:5758837 original size:23 final size:23
Alignment explanation
Indices: 5758807--5758860 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
5758797 GACGGTTAGT
5758807 TAGTTTTTTTCTATAACTTCTCC
1 TAGTTTTTTTCTATAACTTCTCC
*
5758830 TAGTTTTTTTCTATAACTTTTCC
1 TAGTTTTTTTCTATAACTTCTCC
*
5758853 TTGTTTTT
1 TAGTTTTT
5758861 AGATGCTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.15, C:0.17, G:0.06, T:0.63
Consensus pattern (23 bp):
TAGTTTTTTTCTATAACTTCTCC
Found at i:5774490 original size:31 final size:31
Alignment explanation
Indices: 5774455--5774519 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
5774445 CTCCTATTGC
5774455 AATGACACAAGCTTATAAACAAGACACTACT
1 AATGACACAAGCTTATAAACAAGACACTACT
5774486 AATGACACAAGCTTATAAACAAGACACTACT
1 AATGACACAAGCTTATAAACAAGACACTACT
5774517 AAT
1 AAT
5774520 CACCCAAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.49, C:0.22, G:0.09, T:0.20
Consensus pattern (31 bp):
AATGACACAAGCTTATAAACAAGACACTACT
Found at i:5783001 original size:28 final size:28
Alignment explanation
Indices: 5782946--5783001 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
5782936 TTTTGATTTG
*
5782946 AATTTAAATAATTATCTAAAAATCATTA
1 AATTTAAATAATTATCTAAAAATAATTA
*
5782974 AATTTAAATAATTTAT-TAAATATAATTA
1 AATTTAAATAA-TTATCTAAAAATAATTA
5783002 TTTGATAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (28 bp):
AATTTAAATAATTATCTAAAAATAATTA
Found at i:5783888 original size:23 final size:23
Alignment explanation
Indices: 5783861--5783914 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
5783851 TATATTTTTA
5783861 TTGTATTAAAATAAAATTTTGAT
1 TTGTATTAAAATAAAATTTTGAT
* * *
5783884 TTGTATTCAAATAAATTTTTTAT
1 TTGTATTAAAATAAAATTTTGAT
*
5783907 TTTTATTA
1 TTGTATTA
5783915 TAAACTTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (23 bp):
TTGTATTAAAATAAAATTTTGAT
Found at i:5789011 original size:2 final size:2
Alignment explanation
Indices: 5789004--5789050 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
5788994 ATCCAAAACA
*
5789004 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5789046 AT AT A
1 AT AT A
5789051 AATTGATGGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5791986 original size:17 final size:17
Alignment explanation
Indices: 5791964--5791999 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
5791954 AGTATTATGA
5791964 TGTGCTTAATAATGTGT
1 TGTGCTTAATAATGTGT
5791981 TGTGCTTAATAATGTGT
1 TGTGCTTAATAATGTGT
5791998 TG
1 TG
5792000 CTTCTGTGGG
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:0.22, C:0.06, G:0.25, T:0.47
Consensus pattern (17 bp):
TGTGCTTAATAATGTGT
Found at i:5799119 original size:8 final size:8
Alignment explanation
Indices: 5799106--5799137 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
5799096 ACCAAGCAAG
*
5799106 CTAAGCCA
1 CTAAGCTA
5799114 CTAAGCTA
1 CTAAGCTA
5799122 CTAAGCTA
1 CTAAGCTA
5799130 CTAAGCTA
1 CTAAGCTA
5799138 GTATGAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.38, C:0.28, G:0.12, T:0.22
Consensus pattern (8 bp):
CTAAGCTA
Found at i:5812876 original size:78 final size:76
Alignment explanation
Indices: 5812747--5812916 Score: 184
Period size: 78 Copynumber: 2.2 Consensus size: 76
5812737 ATTTAAGCAA
* * * **
5812747 AATCCAATTAAATTAAGAATTAAATTAATTAATAGAAATTTATTCTATTAAA-AGTAAA-ACTAA
1 AATCAAATCAAATTAAGAATTAAATTAATTAAGAGAAATTTAAACTATTAAATA-TAAATAC-AA
5812810 TTAATTTGGTCAG
64 TTAATTTGGTCAG
* *
5812823 AATCAAATC-AATTAAGAGTTAAAATTAATTGAAAGAGAAATTTAAACTATTAAATATAAATGCA
1 AATCAAATCAAATTAAGAATT-AAATTAATT--AAGAGAAATTTAAACTATTAAATATAAATACA
** *
5812887 ATTAATTTTTTTAG
63 ATTAATTTGGTCAG
5812901 AATCAAATCAAATTAA
1 AATCAAATCAAATTAA
5812917 TTAGAATTAA
Statistics
Matches: 78, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
75 10 0.13
76 16 0.21
78 44 0.56
79 8 0.10
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (76 bp):
AATCAAATCAAATTAAGAATTAAATTAATTAAGAGAAATTTAAACTATTAAATATAAATACAATT
AATTTGGTCAG
Found at i:5822219 original size:10 final size:10
Alignment explanation
Indices: 5822206--5822262 Score: 51
Period size: 10 Copynumber: 5.2 Consensus size: 10
5822196 AGAGTAATTT
5822206 AAAAATTATA
1 AAAAATTATA
*
5822216 AAAAATTTGTCTTA
1 AAAAA--T-TAT-A
5822230 AAAAATTATA
1 AAAAATTATA
*
5822240 AAAAATTTTA
1 AAAAATTATA
5822250 TAAAAATTATA
1 -AAAAATTATA
5822261 AA
1 AA
5822263 TTGAGAGTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
10 17 0.45
11 11 0.29
12 2 0.05
13 2 0.05
14 6 0.16
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (10 bp):
AAAAATTATA
Found at i:5822237 original size:24 final size:21
Alignment explanation
Indices: 5822205--5822262 Score: 80
Period size: 24 Copynumber: 2.6 Consensus size: 21
5822195 AAGAGTAATT
*
5822205 TAAAAATTATAAAAAATTTGTCT
1 TAAAAATTATAAAAAATTT-T-A
5822228 TAAAAAATTATAAAAAATTTTA
1 T-AAAAATTATAAAAAATTTTA
5822250 TAAAAATTATAAA
1 TAAAAATTATAAA
5822263 TTGAGAGTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
21 12 0.36
22 1 0.03
23 2 0.06
24 18 0.55
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
TAAAAATTATAAAAAATTTTA
Found at i:5822326 original size:17 final size:18
Alignment explanation
Indices: 5822292--5822327 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5822282 GATCTTACAT
*
5822292 TGATTTTTTTATTTTAAA
1 TGATTTTTTTATTATAAA
5822310 TGATTTTTTTA-TATAAA
1 TGATTTTTTTATTATAAA
5822327 T
1 T
5822328 ATATAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.64
Consensus pattern (18 bp):
TGATTTTTTTATTATAAA
Found at i:5822449 original size:7 final size:7
Alignment explanation
Indices: 5822437--5822470 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
5822427 TTAAGTATGC
5822437 ATTTAAA
1 ATTTAAA
5822444 ATTTAAA
1 ATTTAAA
5822451 ATTTAAA
1 ATTTAAA
*
5822458 ATTTAGA
1 ATTTAAA
5822465 ATTTAA
1 ATTTAA
5822471 TGGTAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (7 bp):
ATTTAAA
Found at i:5825091 original size:26 final size:25
Alignment explanation
Indices: 5825054--5825104 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
5825044 TTAAGTGAAT
*
5825054 ATTTTACTAAATTAATAAGTTGACAA
1 ATTTTACTAAA-TAATAACTTGACAA
5825080 ATTTTA-TGAAATAATAACTTGACAA
1 ATTTTACT-AAATAATAACTTGACAA
5825105 GGTTTGAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (25 bp):
ATTTTACTAAATAATAACTTGACAA
Found at i:5827498 original size:78 final size:77
Alignment explanation
Indices: 5827339--5827501 Score: 179
Period size: 78 Copynumber: 2.1 Consensus size: 77
5827329 ATTTAAGAAA
** * * *
5827339 AATCAAATTAAATTAAGGATTAAAATTAATAGAGAGAGATTTAATCTATTAAAAGTAAATATAAT
1 AATCAAATTAAATTAAAAATTAAAATTAATAGAGAGAAATTTAAGCTATTAAAAGTAAATACAAT
*
5827404 TAATTTAATTAT
66 TAATTTAATTAG
* * *
5827416 AATCAAATT-AATTAAAAATTAAAATTAATTGAGAGTGAAATTTAAGCTATTAAGTA-TAAATGC
1 AATCAAATTAAATTAAAAATTAAAATTAA-T-AGAGAGAAATTTAAGCTATTAA-AAGTAAATAC
*
5827479 AATTAATTTGA-TACG
63 AATTAATTTAATTA-G
5827494 AATCAAAT
1 AATCAAAT
5827502 GACATTAACT
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
76 17 0.24
77 12 0.17
78 42 0.58
79 1 0.01
ACGTcount: A:0.51, C:0.04, G:0.10, T:0.35
Consensus pattern (77 bp):
AATCAAATTAAATTAAAAATTAAAATTAATAGAGAGAAATTTAAGCTATTAAAAGTAAATACAAT
TAATTTAATTAG
Found at i:5828457 original size:39 final size:39
Alignment explanation
Indices: 5828403--5828477 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
5828393 TACTTGTTAC
5828403 TAATATTGATTAATTATCAAATTCAAAGCC-ATTTACCTT
1 TAATATTGATTAATTATCAAATTCAAA-CCTATTTACCTT
5828442 TAATATTGATTAATTATCAAATTCAAACCTATTTAC
1 TAATATTGATTAATTATCAAATTCAAACCTATTTAC
5828478 GTATAAAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
38 2 0.06
39 33 0.94
ACGTcount: A:0.40, C:0.15, G:0.04, T:0.41
Consensus pattern (39 bp):
TAATATTGATTAATTATCAAATTCAAACCTATTTACCTT
Found at i:5829729 original size:18 final size:17
Alignment explanation
Indices: 5829708--5829748 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
5829698 TATAAATGTT
5829708 AAAAAAAAG-TTAATAAA
1 AAAAAAAAGATTAA-AAA
*
5829725 AAAAATAAGATTAAAAA
1 AAAAAAAAGATTAAAAA
5829742 AAAAAAA
1 AAAAAAA
5829749 TAACTTTGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (17 bp):
AAAAAAAAGATTAAAAA
Done.