Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 102 of 136
Found at i:34387388 original size:24 final size:22
Alignment explanation
Indices: 34387340--34387397 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 22
34387330 GGCCCATATT
* *
34387340 AAATATATATTTAATATATATA
1 AAATATATATTTAATAAAAATA
*
34387362 AAATATATATTTGATTAAAAATAA
1 AAATATATATTT-AATAAAAAT-A
34387386 AAATATATATTT
1 AAATATATATTT
34387398 TTAATATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 12 0.39
23 6 0.19
24 13 0.42
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AAATATATATTTAATAAAAATA
Found at i:34388678 original size:27 final size:27
Alignment explanation
Indices: 34388604--34388678 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 27
34388594 TTAGCTGTGT
* * *
34388604 CGCCTATTAAATAGGCACCACCAGTGC
1 CGCCTATCAAATAGGCATCACCAGTAC
* * *
34388631 CGCCTATCAGATAAGG-GTCACTAGTAC
1 CGCCTATCAAAT-AGGCATCACCAGTAC
34388658 CGCCTATCAAATAGGCATCAC
1 CGCCTATCAAATAGGCATCAC
34388679 ACTCTTGTAT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
26 3 0.08
27 32 0.84
28 3 0.08
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.20
Consensus pattern (27 bp):
CGCCTATCAAATAGGCATCACCAGTAC
Found at i:34390058 original size:7 final size:7
Alignment explanation
Indices: 34390048--34390072 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
34390038 ATCCTGGATC
34390048 CTGAATG
1 CTGAATG
34390055 CTGAATG
1 CTGAATG
34390062 CTGAATG
1 CTGAATG
34390069 CTGA
1 CTGA
34390073 GCAATGTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (7 bp):
CTGAATG
Found at i:34405923 original size:20 final size:20
Alignment explanation
Indices: 34405898--34405937 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
34405888 AAAAATGAAT
*
34405898 AAAATTGTAAAAATTATTTA
1 AAAATTATAAAAATTATTTA
* *
34405918 AAAATTATAATAATTTTTTA
1 AAAATTATAAAAATTATTTA
34405938 CAATCTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
AAAATTATAAAAATTATTTA
Found at i:34406886 original size:13 final size:13
Alignment explanation
Indices: 34406868--34406892 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34406858 GAGAGAAACT
34406868 TTTTGTTGTTTGG
1 TTTTGTTGTTTGG
34406881 TTTTGTTGTTTG
1 TTTTGTTGTTTG
34406893 AGTTCTCAAG
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:0.00, C:0.00, G:0.28, T:0.72
Consensus pattern (13 bp):
TTTTGTTGTTTGG
Found at i:34417358 original size:17 final size:17
Alignment explanation
Indices: 34417328--34417361 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
34417318 CCACCAAAAT
*
34417328 ATAATATAATAATATTA
1 ATAATATAAAAATATTA
*
34417345 ATAATGTAAAAATATTA
1 ATAATATAAAAATATTA
34417362 TCTTAATTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
ATAATATAAAAATATTA
Found at i:34418461 original size:19 final size:18
Alignment explanation
Indices: 34418421--34418463 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
34418411 TCATAAAATG
* *
34418421 AAAATTCAGTGTAATCCT
1 AAAATTCAGAGTAATCCC
*
34418439 AAAATTCAAGAGTCATCCC
1 AAAATTC-AGAGTAATCCC
34418458 AAAATT
1 AAAATT
34418464 TTACATGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (18 bp):
AAAATTCAGAGTAATCCC
Found at i:34426546 original size:30 final size:29
Alignment explanation
Indices: 34426489--34426555 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 29
34426479 TCTAATTTTT
* * *
34426489 ATTAAAAATTATTAAATTTTTAGAAAATT
1 ATTAAAAATTATTAAATCTTCAGAAAATA
*
34426518 A-TAAAAATATATTTAAATCTTCATAAAATA
1 ATTAAAAAT-TA-TTAAATCTTCAGAAAATA
34426548 ATTAAAAA
1 ATTAAAAA
34426556 AACAATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 7 0.23
29 3 0.10
30 15 0.48
31 6 0.19
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (29 bp):
ATTAAAAATTATTAAATCTTCAGAAAATA
Found at i:34445225 original size:78 final size:77
Alignment explanation
Indices: 34445077--34445244 Score: 191
Period size: 78 Copynumber: 2.2 Consensus size: 77
34445067 CGAATATGTG
* * *
34445077 TATATATATAAGATCTTGAATTTAGTTAAAGGTAAGAATGTTATATATATATAAGGTTCGAATAT
1 TATATGTATAAGATCTTGAATTTAATTAAAGATAAGAATGTTATATATATATAAGGTTCGAATA-
34445142 GTATATATA-TATA
65 GTATATA-AGTATA
* * *
34445155 TATATGTATAAGATCTTGAATTTAATTAAAGATATGGATGTTATATTTATATATATAAGGTTTG-
1 TATATGTATAAGATCTTGAATTTAATTAAAGATAAGAATG-T-TA--TATATATATAAGGTTCGA
34445219 A-A-TATATAAGTATA
62 ATAGTATATAAGTATA
*
34445233 TACATGTATAAG
1 TATATGTATAAG
34445245 CTATATATAT
Statistics
Matches: 78, Mismatches: 7, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
77 1 0.01
78 56 0.72
79 1 0.01
80 3 0.04
81 1 0.01
82 16 0.21
ACGTcount: A:0.42, C:0.02, G:0.14, T:0.42
Consensus pattern (77 bp):
TATATGTATAAGATCTTGAATTTAATTAAAGATAAGAATGTTATATATATATAAGGTTCGAATAG
TATATAAGTATA
Found at i:34445881 original size:31 final size:31
Alignment explanation
Indices: 34445809--34445888 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 31
34445799 TGTGGAATAT
* * *
34445809 ATACATACATTTGGTTATATGCTCTTGATGA
1 ATACATATATTTGGTTATATGCTCTCGAAGA
* *
34445840 ATATAAATATTTGGTTATATGCAT-TCGAAGA
1 ATACATATATTTGGTTATATGC-TCTCGAAGA
* *
34445871 GTACATATATTTGATTAT
1 ATACATATATTTGGTTAT
34445889 CAATAAAATG
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
31 38 0.97
32 1 0.03
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (31 bp):
ATACATATATTTGGTTATATGCTCTCGAAGA
Found at i:34447919 original size:19 final size:19
Alignment explanation
Indices: 34447895--34447931 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
34447885 GAAAGAGGTA
34447895 TATTAATTAAATTAAAAAT
1 TATTAATTAAATTAAAAAT
*
34447914 TATTAATTAAGTTAAAAA
1 TATTAATTAAATTAAAAA
34447932 AAATAAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
TATTAATTAAATTAAAAAT
Found at i:34451195 original size:12 final size:11
Alignment explanation
Indices: 34451170--34451204 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
34451160 TCGATTGAAT
*
34451170 AAATTATTAAA
1 AAATTATAAAA
34451181 AAATTACTAAAA
1 AAATTA-TAAAA
34451193 AAATTATAAAA
1 AAATTATAAAA
34451204 A
1 A
34451205 TTTGGTTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (11 bp):
AAATTATAAAA
Found at i:34457996 original size:13 final size:13
Alignment explanation
Indices: 34457946--34457998 Score: 65
Period size: 13 Copynumber: 4.1 Consensus size: 13
34457936 AGTTCTTCAT
34457946 TGCTTTT-AGAAAG
1 TGCTTTTGA-AAAG
34457959 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
34457972 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
34457985 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
34457998 T
1 T
34457999 TTAGTTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
12 3 0.09
13 28 0.80
14 4 0.11
ACGTcount: A:0.32, C:0.08, G:0.25, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:34458009 original size:26 final size:26
Alignment explanation
Indices: 34457946--34457998 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
34457936 AGTTCTTCAT
34457946 TGCT-TTTAGAAAGTGCTTTTGAAAAG
1 TGCTGTTTA-AAAGTGCTTTTGAAAAG
**
34457972 TGCTGTGAAAAAGTGCTTTTGAAAAG
1 TGCTGTTTAAAAGTGCTTTTGAAAAG
34457998 T
1 T
34457999 TTAGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.32, C:0.08, G:0.25, T:0.36
Consensus pattern (26 bp):
TGCTGTTTAAAAGTGCTTTTGAAAAG
Found at i:34459123 original size:3 final size:3
Alignment explanation
Indices: 34459115--34459141 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
34459105 TGCCTACTTA
34459115 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
34459142 GAAATGTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:34460290 original size:13 final size:13
Alignment explanation
Indices: 34460272--34460310 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
34460262 TAAACAAAAG
*
34460272 TTTTCAGAAGCAT
1 TTTTCAGAAGCAA
*
34460285 TTTTCATAA-CAA
1 TTTTCAGAAGCAA
34460297 TTTTCAGAAGCAA
1 TTTTCAGAAGCAA
34460310 T
1 T
34460311 GAAAAACTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.38
Consensus pattern (13 bp):
TTTTCAGAAGCAA
Found at i:34478313 original size:228 final size:228
Alignment explanation
Indices: 34477901--34478542 Score: 752
Period size: 228 Copynumber: 2.8 Consensus size: 228
34477891 GGAGACGAAG
* * * *
34477901 AACAAGGTGAAGGGTAGACTCTTTCTGAATGTTATAATCAGCCAAAGTCCTCCCATCTTCCAATT
1 AACAAGGTGAAGGGTGGATTCTTTCTGGATGTTATAATCAGCCAAGGTCCTCCCATCTTCCAATT
* * * ** * * * * *
34477966 GTTTGCCGGCAAAGATGAGCCTTTGCTGATCAGGTGGGATTCCTTCCTTATCCTGAATCTTTGCC
66 GTTTGCCAGCGAAGATGAGACGCTGCTGGTCAGGTGGGATCCCTTCCTTGTCTTGAATCTTGGCC
* * * * * * * *
34478031 TTAACATTGTCAATGGTATCGGAGCTTTCAACCTCCAAGGTGATTGTTTTGCCGGTCAAAGTCTT
131 TTAACGTTGTCGATGGTGTCGGAGCTTTCGACCTCGAGGGTGATGGTCTTGCCGGTCAAAGTCTT
34478096 GACAAAAATCTGCAT-CCCTCCACGAA-GCCTCAA
196 GACAAAAATCTGCATGCCC-CCACGAAGGCCT-AA
*
34478129 AACAAGGTGAAGGGTGGATTCCTTT-TGGATATTATAATCAGCCAAGGTCCTCCCATCTTCCAAT
1 AACAAGGTGAAGGGTGGATT-CTTTCTGGATGTTATAATCAGCCAAGGTCCTCCCATCTTCCAAT
* * * *
34478193 TGTTTGCCAGCGAAGATCAAACGCTGTTGGTCAGGTGGGATGCCTTCCTTGTCTTGAATCTTGGC
65 TGTTTGCCAGCGAAGATGAGACGCTGCTGGTCAGGTGGGATCCCTTCCTTGTCTTGAATCTTGGC
* * * * * *
34478258 CTTAACGTTGTCGATGGTGTCGGAACTCTCGACTTCGAGGGTGATGGTCTTGCCGGTTAAGGTTT
130 CTTAACGTTGTCGATGGTGTCGGAGCTTTCGACCTCGAGGGTGATGGTCTTGCCGGTCAAAGTCT
* * *
34478323 TGACAAAGATTTGCATGCCCCCACGAAGGCGTAA
195 TGACAAAAATCTGCATGCCCCCACGAAGGCCTAA
* * * * ** * * **
34478357 GACGAGGTGGAGGGTGGATTCTTTCTGGATGTTATAATC-GGCAAGGGTCCGACCGTCTTCGAGC
1 AACAAGGTGAAGGGTGGATTCTTTCTGGATGTTATAATCAGCCAA-GGTCCTCCCATCTTCCAAT
* * *
34478421 TGTTTGCCAGCGAAAATGAGACGCTGCTGGTCGGGTGGGATCCCTTCCTTGTCTTGGATCTTGGC
65 TGTTTGCCAGCGAAGATGAGACGCTGCTGGTCAGGTGGGATCCCTTCCTTGTCTTGAATCTTGGC
* * *
34478486 CTTGACGTTGTCGATGGTGTCGGAGCTTTCGACCTCGAGTGTTATGGTCTTGCCGGT
130 CTTAACGTTGTCGATGGTGTCGGAGCTTTCGACCTCGAGGGTGATGGTCTTGCCGGT
34478543 AAGGGTTTTC
Statistics
Matches: 350, Mismatches: 59, Indels: 10
0.84 0.14 0.02
Matches are distributed among these distances:
227 8 0.02
228 332 0.95
229 10 0.03
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.30
Consensus pattern (228 bp):
AACAAGGTGAAGGGTGGATTCTTTCTGGATGTTATAATCAGCCAAGGTCCTCCCATCTTCCAATT
GTTTGCCAGCGAAGATGAGACGCTGCTGGTCAGGTGGGATCCCTTCCTTGTCTTGAATCTTGGCC
TTAACGTTGTCGATGGTGTCGGAGCTTTCGACCTCGAGGGTGATGGTCTTGCCGGTCAAAGTCTT
GACAAAAATCTGCATGCCCCCACGAAGGCCTAA
Found at i:34495188 original size:22 final size:21
Alignment explanation
Indices: 34495163--34495232 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 21
34495153 CAATAACAAC
34495163 AAAATAGTAGAAACATAATAGT
1 AAAATAGTAGAAA-ATAATAGT
* *
34495185 AAAATTGTAGCAAAATAGAGAG-
1 AAAATAGTAG-AAAATA-ATAGT
* *
34495207 AAAACAGTAAGAAAATAATATT
1 AAAATAGT-AGAAAATAATAGT
34495229 AAAA
1 AAAA
34495233 AAAGATTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
21 2 0.05
22 28 0.74
23 8 0.21
ACGTcount: A:0.61, C:0.04, G:0.14, T:0.20
Consensus pattern (21 bp):
AAAATAGTAGAAAATAATAGT
Found at i:34525385 original size:19 final size:17
Alignment explanation
Indices: 34525361--34525395 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
34525351 ATTGTTTGGA
34525361 TATTGTATAATTCTTGTTT
1 TATTGT-TAATT-TTGTTT
34525380 TATTGTTAATTTTGTT
1 TATTGTTAATTTTGTT
34525396 ACTATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.66
Consensus pattern (17 bp):
TATTGTTAATTTTGTTT
Found at i:34526832 original size:11 final size:11
Alignment explanation
Indices: 34526802--34526826 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
34526792 GAGAAATTTA
34526802 AGAGCAAATTG
1 AGAGCAAATTG
34526813 AGAGCAAATTG
1 AGAGCAAATTG
34526824 AGA
1 AGA
34526827 TTAAATATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.28, T:0.16
Consensus pattern (11 bp):
AGAGCAAATTG
Found at i:34526833 original size:51 final size:50
Alignment explanation
Indices: 34526778--34526877 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 50
34526768 AATTATTTAA
*
34526778 AAATAGGGGTTTAAGAGAAATTT-AAGAGCAAATTGAGAGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTGAAG-G-AAATTGAGAGCAAATTGAGATT
* * *
34526829 AAATATGGATTTGAGAGAAATTTGGAAGGAATTTGAGAGCAAATTGAGA
1 AAATAGGGATTTAAGAGAAATTT-GAAGGAAATTGAGAGCAAATTGAGA
34526878 GGAAATTGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
51 39 0.91
52 1 0.02
53 3 0.07
ACGTcount: A:0.44, C:0.03, G:0.27, T:0.26
Consensus pattern (50 bp):
AAATAGGGATTTAAGAGAAATTTGAAGGAAATTGAGAGCAAATTGAGATT
Found at i:34526851 original size:11 final size:11
Alignment explanation
Indices: 34526837--34526902 Score: 50
Period size: 11 Copynumber: 5.9 Consensus size: 11
34526827 TTAAATATGG
34526837 ATTTGAGAGAA
1 ATTTGAGAGAA
*
34526848 ATTTG-GAAGGA
1 ATTTGAG-AGAA
34526859 ATTTGAGAGCAA
1 ATTTGAGAG-AA
34526871 A-TTGAGAGGAA
1 ATTTGAGA-GAA
34526882 A-TTGAGA-AA
1 ATTTGAGAGAA
34526891 ATAATTGAGAGA
1 AT--TTGAGAGA
34526903 TGATTAGTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
9 3 0.07
10 1 0.02
11 30 0.67
12 10 0.22
13 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.29, T:0.24
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:34526880 original size:22 final size:22
Alignment explanation
Indices: 34526791--34526888 Score: 64
Period size: 22 Copynumber: 4.6 Consensus size: 22
34526781 TAGGGGTTTA
* *
34526791 AGAGAAATTTAAGAGCAAATTG
1 AGAGGAATTTGAGAGCAAATTG
* * **
34526813 AGAGCAAATTGAGATTAAA-T-
1 AGAGGAATTTGAGAGCAAATTG
*
34526833 A-TGG-ATTTGAGAG-AAATTTG
1 AGAGGAATTTGAGAGCAAA-TTG
34526853 -GAAGGAATTTGAGAGCAAATTG
1 AG-AGGAATTTGAGAGCAAATTG
*
34526875 AGAGGAAATTGAGA
1 AGAGGAATTTGAGA
34526889 AAATAATTGA
Statistics
Matches: 57, Mismatches: 11, Indels: 16
0.68 0.13 0.19
Matches are distributed among these distances:
17 3 0.05
18 7 0.12
19 2 0.04
20 1 0.02
21 3 0.05
22 37 0.65
23 4 0.07
ACGTcount: A:0.45, C:0.03, G:0.28, T:0.24
Consensus pattern (22 bp):
AGAGGAATTTGAGAGCAAATTG
Found at i:34527886 original size:38 final size:36
Alignment explanation
Indices: 34527844--34527922 Score: 97
Period size: 36 Copynumber: 2.1 Consensus size: 36
34527834 ATTAAAAATA
*
34527844 TTTATGATA-AAAAACACTACCATAAATATAATAAATGT
1 TTTATGATATAAAAA-AC-A-CATAAATATAACAAATGT
* *
34527882 TTTATTATATTAAAAACACATAAATATAACAAATGT
1 TTTATGATATAAAAAACACATAAATATAACAAATGT
34527918 TTTAT
1 TTTAT
34527923 TGTATTAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 22 0.59
37 1 0.03
38 10 0.27
39 4 0.11
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (36 bp):
TTTATGATATAAAAAACACATAAATATAACAAATGT
Found at i:34528800 original size:32 final size:32
Alignment explanation
Indices: 34528736--34528826 Score: 112
Period size: 32 Copynumber: 2.8 Consensus size: 32
34528726 TATTGTAATA
** *
34528736 TGTAAAATGATAATGAATAACAACTTTCATTT
1 TGTAAAATGATAACAAATTACAACTTTCATTT
* *
34528768 TGTGAAATGGTAACAAATTACAA-TTTCAATTT
1 TGTAAAATGATAACAAATTACAACTTTC-ATTT
*
34528800 TGTAAAATGATAACAAATTTCAACTTT
1 TGTAAAATGATAACAAATTACAACTTT
34528827 AGTTTTTTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
31 4 0.08
32 42 0.86
33 3 0.06
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (32 bp):
TGTAAAATGATAACAAATTACAACTTTCATTT
Found at i:34554326 original size:9 final size:9
Alignment explanation
Indices: 34554312--34554386 Score: 52
Period size: 9 Copynumber: 8.3 Consensus size: 9
34554302 ACCTTATAGA
34554312 AAAATTTAT
1 AAAATTTAT
34554321 AAAATTTAT
1 AAAATTTAT
34554330 AAAA---A-
1 AAAATTTAT
*
34554335 AATTATTTAT
1 AA-AATTTAT
34554345 AAAATTTAT
1 AAAATTTAT
*
34554354 AAAAACTTATT
1 -AAAATTTA-T
34554365 AAAAGTTT-T
1 AAAA-TTTAT
34554374 AAAAATTTAT
1 -AAAATTTAT
34554384 AAA
1 AAA
34554387 TATATATAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 20
0.68 0.05 0.26
Matches are distributed among these distances:
5 2 0.04
6 2 0.04
9 27 0.52
10 18 0.35
11 3 0.06
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (9 bp):
AAAATTTAT
Found at i:34554334 original size:10 final size:10
Alignment explanation
Indices: 34554311--34554410 Score: 69
Period size: 11 Copynumber: 9.5 Consensus size: 10
34554301 AACCTTATAG
34554311 AAAAATTTAT
1 AAAAATTTAT
34554321 -AAAATTTAT
1 AAAAATTTAT
*
34554330 AAAAAAATTATTT
1 --AAAAATT-TAT
34554343 ATAAAATTTAT
1 A-AAAATTTAT
*
34554354 AAAAACTTATT
1 AAAAATTTA-T
*
34554365 AAAAGTTT-T
1 AAAAATTTAT
34554374 AAAAATTTAT
1 AAAAATTTAT
* *
34554384 AAATATATAT
1 AAAAATTTAT
*
34554394 AAGAAAATTAT
1 AA-AAATTTAT
34554405 AGAAAA
1 A-AAAA
34554411 ATTTTGTTAT
Statistics
Matches: 70, Mismatches: 11, Indels: 17
0.71 0.11 0.17
Matches are distributed among these distances:
9 17 0.24
10 18 0.26
11 20 0.29
12 13 0.19
13 2 0.03
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (10 bp):
AAAAATTTAT
Found at i:34554340 original size:20 final size:20
Alignment explanation
Indices: 34554305--34554405 Score: 64
Period size: 21 Copynumber: 4.8 Consensus size: 20
34554295 AAACACAACC
*
34554305 TTATAGAAAAATTTATAAAAT
1 TTATA-AAAAAATTATAAAAT
34554326 TTATAAAAAAATTATTTATAAAAT
1 TTAT-AAAAAA--A-TTATAAAAT
*
34554350 TTAT-AAAAACTTATTAAAAGT
1 TTATAAAAAAATTA-TAAAA-T
*
34554371 TT-T-AAAAATTTATAAATAT
1 TTATAAAAAAATTATAAA-AT
* *
34554390 ATATAAGAAAATTATA
1 TTATAAAAAAATTATA
34554406 GAAAAATTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
19 9 0.14
20 16 0.25
21 21 0.32
22 6 0.09
24 13 0.20
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (20 bp):
TTATAAAAAAATTATAAAAT
Found at i:34554610 original size:96 final size:96
Alignment explanation
Indices: 34554446--34554638 Score: 341
Period size: 96 Copynumber: 2.0 Consensus size: 96
34554436 GTGATTAAAC
* * *
34554446 TTATAACGGGTTCTGAGTATGAGGTTTGAAAAATAATGAGTTTAGTGTTTGGTGGTTTAAGGTTA
1 TTATAACGGGTTCAGAGTATGAGGTTTGAAAAAGAATAAGTTTAGTGTTTGGTGGTTTAAGGTTA
34554511 ATAATAAATAATGGTTTTGATTAAAGAGTAA
66 ATAATAAATAATGGTTTTGATTAAAGAGTAA
34554542 TTATAACGGGTTCAGAGTATGAGGTTTGAAAAAGAATAAGTTTAGTGTTTGGTGGTTTAAGGTTA
1 TTATAACGGGTTCAGAGTATGAGGTTTGAAAAAGAATAAGTTTAGTGTTTGGTGGTTTAAGGTTA
* *
34554607 ATAATAAGTAATGGTTTTGATTAAGGAGTAA
66 ATAATAAATAATGGTTTTGATTAAAGAGTAA
34554638 T
1 T
34554639 GATACGAGAA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
96 92 1.00
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.38
Consensus pattern (96 bp):
TTATAACGGGTTCAGAGTATGAGGTTTGAAAAAGAATAAGTTTAGTGTTTGGTGGTTTAAGGTTA
ATAATAAATAATGGTTTTGATTAAAGAGTAA
Found at i:34555456 original size:9 final size:9
Alignment explanation
Indices: 34555442--34555516 Score: 52
Period size: 9 Copynumber: 8.3 Consensus size: 9
34555432 ACCTTATAGA
34555442 AAAATTTAT
1 AAAATTTAT
34555451 AAAATTTAT
1 AAAATTTAT
34555460 AAAA---A-
1 AAAATTTAT
*
34555465 AATTATTTAT
1 AA-AATTTAT
34555475 AAAATTTAT
1 AAAATTTAT
*
34555484 AAAAACTTATT
1 -AAAATTTA-T
34555495 AAAAGTTT-T
1 AAAA-TTTAT
34555504 AAAAATTTAT
1 -AAAATTTAT
34555514 AAA
1 AAA
34555517 TATATATAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 20
0.68 0.05 0.26
Matches are distributed among these distances:
5 2 0.04
6 2 0.04
9 27 0.52
10 18 0.35
11 3 0.06
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (9 bp):
AAAATTTAT
Found at i:34555464 original size:10 final size:10
Alignment explanation
Indices: 34555441--34555540 Score: 69
Period size: 11 Copynumber: 9.5 Consensus size: 10
34555431 AACCTTATAG
34555441 AAAAATTTAT
1 AAAAATTTAT
34555451 -AAAATTTAT
1 AAAAATTTAT
*
34555460 AAAAAAATTATTT
1 --AAAAATT-TAT
34555473 ATAAAATTTAT
1 A-AAAATTTAT
*
34555484 AAAAACTTATT
1 AAAAATTTA-T
*
34555495 AAAAGTTT-T
1 AAAAATTTAT
34555504 AAAAATTTAT
1 AAAAATTTAT
* *
34555514 AAATATATAT
1 AAAAATTTAT
*
34555524 AAGAAAATTAT
1 AA-AAATTTAT
34555535 AGAAAA
1 A-AAAA
34555541 ATTTTGTTAT
Statistics
Matches: 70, Mismatches: 11, Indels: 17
0.71 0.11 0.17
Matches are distributed among these distances:
9 17 0.24
10 18 0.26
11 20 0.29
12 13 0.19
13 2 0.03
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (10 bp):
AAAAATTTAT
Found at i:34555470 original size:20 final size:20
Alignment explanation
Indices: 34555435--34555535 Score: 64
Period size: 21 Copynumber: 4.8 Consensus size: 20
34555425 AAACACAACC
*
34555435 TTATAGAAAAATTTATAAAAT
1 TTATA-AAAAAATTATAAAAT
34555456 TTATAAAAAAATTATTTATAAAAT
1 TTAT-AAAAAA--A-TTATAAAAT
*
34555480 TTAT-AAAAACTTATTAAAAGT
1 TTATAAAAAAATTA-TAAAA-T
*
34555501 TT-T-AAAAATTTATAAATAT
1 TTATAAAAAAATTATAAA-AT
* *
34555520 ATATAAGAAAATTATA
1 TTATAAAAAAATTATA
34555536 GAAAAATTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
19 9 0.14
20 16 0.25
21 21 0.32
22 6 0.09
24 13 0.20
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (20 bp):
TTATAAAAAAATTATAAAAT
Found at i:34557572 original size:29 final size:30
Alignment explanation
Indices: 34557516--34557580 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
34557506 CTGGCCTGAA
*
34557516 TATATTATGTTATAAAAAGTAATTATATCAAT
1 TATA-TATGTTATAAAAAGTAAATATAT-AAT
* *
34557548 TATATATGTTA-AATAA-TAAATATATATT
1 TATATATGTTATAAAAAGTAAATATATAAT
34557576 TATAT
1 TATAT
34557581 TAAATTACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 7 0.23
29 8 0.27
30 4 0.13
31 7 0.23
32 4 0.13
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.46
Consensus pattern (30 bp):
TATATATGTTATAAAAAGTAAATATATAAT
Found at i:34560083 original size:12 final size:12
Alignment explanation
Indices: 34560066--34560090 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34560056 CTTGAAATGC
34560066 CTTCTCTTCACT
1 CTTCTCTTCACT
34560078 CTTCTCTTCACT
1 CTTCTCTTCACT
34560090 C
1 C
34560091 CTTTCTGCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.44, G:0.00, T:0.48
Consensus pattern (12 bp):
CTTCTCTTCACT
Found at i:34565753 original size:21 final size:20
Alignment explanation
Indices: 34565721--34565761 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
34565711 AAATCATGGA
*
34565721 TAATGTATTTAACTTCTCAG
1 TAATATATTTAACTTCTCAG
*
34565741 TAATATATATTAACTTTTCAG
1 TAATATAT-TTAACTTCTCAG
34565762 AGTGCCCTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.46
Consensus pattern (20 bp):
TAATATATTTAACTTCTCAG
Found at i:34568571 original size:5 final size:5
Alignment explanation
Indices: 34568561--34568587 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
34568551 AAAAATAGTG
34568561 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
34568588 GAAACAAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:34569768 original size:23 final size:23
Alignment explanation
Indices: 34569742--34569785 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
34569732 ATAATCGTGA
34569742 CATAA-AAGCAAACAAAACTGTGC
1 CATAAGAA-CAAACAAAACTGTGC
*
34569765 CATAAGAATAAACAAAACTGT
1 CATAAGAACAAACAAAACTGT
34569786 CGTGAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.55, C:0.18, G:0.11, T:0.16
Consensus pattern (23 bp):
CATAAGAACAAACAAAACTGTGC
Found at i:34572278 original size:21 final size:21
Alignment explanation
Indices: 34572252--34572297 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
34572242 TAAAATAGTC
34572252 ATAAATTTTGACATATTACTG
1 ATAAATTTTGACATATTACTG
34572273 ATAAATTTTGACATATTACTG
1 ATAAATTTTGACATATTACTG
34572294 ATAA
1 ATAA
34572298 TGAATTTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (21 bp):
ATAAATTTTGACATATTACTG
Found at i:34579031 original size:30 final size:25
Alignment explanation
Indices: 34578988--34579046 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 25
34578978 TTGGATGATT
34578988 ATTTTTTATAAAAAATTTAAGGTTTATTA
1 ATTTTTTATAAAAAA---AA-GTTTATTA
*
34579017 ATTTTTTTTCAAAAAAAAGTTTATTA
1 ATTTTTTAT-AAAAAAAAGTTTATTA
34579043 ATTT
1 ATTT
34579047 ATATTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 12 0.43
27 2 0.07
29 8 0.29
30 6 0.21
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (25 bp):
ATTTTTTATAAAAAAAAGTTTATTA
Found at i:34580779 original size:23 final size:22
Alignment explanation
Indices: 34580747--34580807 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 22
34580737 CCCGGCCCGT
*
34580747 TTTTTAATTAAAATTAAAATTATA
1 TTTTT-ATTAAAATTAAAACTA-A
34580771 TTTTTATTAAAATTAAAACTAA
1 TTTTTATTAAAATTAAAACTAA
*
34580793 TTGTTATTAAAATTA
1 TTTTTATTAAAATTA
34580808 TATCAAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.43
23 15 0.43
24 5 0.14
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTTTATTAAAATTAAAACTAA
Found at i:34580816 original size:22 final size:22
Alignment explanation
Indices: 34580753--34580816 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
34580743 CCGTTTTTTA
* * *
34580753 ATTAAAATTAAAATTATATTTTT
1 ATTAAAATTAAAA-CAAATTGTT
*
34580776 ATTAAAATTAAAACTAATTGTT
1 ATTAAAATTAAAACAAATTGTT
* *
34580798 ATTAAAATTATATCAAATT
1 ATTAAAATTAAAACAAATT
34580817 ATATTTTTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 21 0.62
23 13 0.38
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (22 bp):
ATTAAAATTAAAACAAATTGTT
Found at i:34580883 original size:19 final size:19
Alignment explanation
Indices: 34580859--34581015 Score: 66
Period size: 19 Copynumber: 8.4 Consensus size: 19
34580849 ATCTAACATT
34580859 TTGTTAATAAAATTATTAA
1 TTGTTAATAAAATTATTAA
* *
34580878 TTGTTACTAAAATTATCAAA
1 TTGTTAATAAAATTAT-TAA
* **
34580898 TTATATCAAATTATTCATTATTAA
1 TTGT-T--AA-TA-AAATTATTAA
*
34580922 TTGTTACT--AA-TATT--
1 TTGTTAATAAAATTATTAA
*
34580936 TTGTTAGTAAAATTATTAA
1 TTGTTAATAAAATTATTAA
34580955 TTGTTAAT----TGTATTAA
1 TTGTTAATAAAAT-TATTAA
* *
34580971 TTGTTAGTAAAATTATCAA
1 TTGTTAATAAAATTATTAA
* *
34580990 --ATTATATCAAATTATTAA
1 TTGTTA-ATAAAATTATTAA
34581008 TTGTTAAT
1 TTGTTAAT
34581016 TGTATTAATT
Statistics
Matches: 100, Mismatches: 19, Indels: 38
0.64 0.12 0.24
Matches are distributed among these distances:
14 7 0.07
15 1 0.01
16 19 0.19
17 8 0.08
18 10 0.10
19 29 0.29
20 10 0.10
21 2 0.02
23 2 0.02
24 7 0.07
25 5 0.05
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.48
Consensus pattern (19 bp):
TTGTTAATAAAATTATTAA
Found at i:34580919 original size:44 final size:44
Alignment explanation
Indices: 34580869--34581018 Score: 153
Period size: 44 Copynumber: 3.3 Consensus size: 44
34580859 TTGTTAATAA
34580869 AATTATTAATTGTTACTAAAATTATCAAATTATATCAAATTATT
1 AATTATTAATTGTTACTAAAATTATCAAATTATATCAAATTATT
* * * *
34580913 CATTATTAATTGTTACTAATATTTTGTTAGTAAAATTAT-T--AATTGTT
1 AATTATTAATTGTTACTAA-A----ATTA-TCAAATTATATCAAATTATT
*
34580960 AATTGTATTAATTGTTAGTAAAATTATCAAATTATATCAAATTATT
1 AA-T-TATTAATTGTTACTAAAATTATCAAATTATATCAAATTATT
*
34581006 AATTGTTAATTGT
1 AATTATTAATTGT
34581019 ATTAATTGTT
Statistics
Matches: 85, Mismatches: 10, Indels: 22
0.73 0.09 0.19
Matches are distributed among these distances:
43 8 0.09
44 31 0.36
45 2 0.02
46 8 0.09
47 7 0.08
48 2 0.02
49 19 0.22
50 8 0.09
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.49
Consensus pattern (44 bp):
AATTATTAATTGTTACTAAAATTATCAAATTATATCAAATTATT
Found at i:34580956 original size:33 final size:34
Alignment explanation
Indices: 34580914--34580986 Score: 103
Period size: 33 Copynumber: 2.1 Consensus size: 34
34580904 CAAATTATTC
*
34580914 ATTATTAATTGTTACTAATATT-TTGTTAGTAAA
1 ATTATTAATTGTTAATAATATTATTGTTAGTAAA
**
34580947 ATTATTAATTGTTAATTGTATTAATTGTTAGTAAA
1 ATTATTAATTGTTAATAATATT-ATTGTTAGTAAA
34580982 ATTAT
1 ATTAT
34580987 CAAATTATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
33 19 0.54
35 16 0.46
ACGTcount: A:0.37, C:0.01, G:0.10, T:0.52
Consensus pattern (34 bp):
ATTATTAATTGTTAATAATATTATTGTTAGTAAA
Found at i:34580975 original size:49 final size:51
Alignment explanation
Indices: 34580916--34581028 Score: 142
Period size: 53 Copynumber: 2.2 Consensus size: 51
34580906 AATTATTCAT
* **
34580916 TATTAATTGTTACTAATATT-T-TGTTAGTA-AAATTATTAATTGTTAATTG
1 TATTAATTGTTACTAAAATTATAAATTA-TACAAATTATTAATTGTTAATTG
*
34580965 TATTAATTGTTAGTAAAATTATCAAATTATATCAAATTATTAATTGTTAATTG
1 TATTAATTGTTACTAAAATTAT-AAATTATA-CAAATTATTAATTGTTAATTG
34581018 TATTAATTGTT
1 TATTAATTGTT
34581029 GTAACAAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
49 18 0.33
50 1 0.02
51 2 0.04
52 3 0.05
53 31 0.56
ACGTcount: A:0.37, C:0.03, G:0.09, T:0.51
Consensus pattern (51 bp):
TATTAATTGTTACTAAAATTATAAATTATACAAATTATTAATTGTTAATTG
Found at i:34583789 original size:7 final size:7
Alignment explanation
Indices: 34583777--34583806 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
34583767 CAAATAAGTT
34583777 GTTCATG
1 GTTCATG
34583784 GTTCATG
1 GTTCATG
34583791 GTTCATG
1 GTTCATG
*
34583798 GTCCATG
1 GTTCATG
34583805 GT
1 GT
34583807 CCATTTTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.13, C:0.17, G:0.30, T:0.40
Consensus pattern (7 bp):
GTTCATG
Found at i:34584177 original size:13 final size:13
Alignment explanation
Indices: 34584159--34584187 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
34584149 TCTTAAGCGA
34584159 TTTGCATAATTAG
1 TTTGCATAATTAG
34584172 TTTGCATAATTAG
1 TTTGCATAATTAG
34584185 TTT
1 TTT
34584188 TCTTTGGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.07, G:0.14, T:0.52
Consensus pattern (13 bp):
TTTGCATAATTAG
Found at i:34590208 original size:23 final size:23
Alignment explanation
Indices: 34590182--34590231 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
34590172 GGATTGCATG
* *
34590182 TAGAACCAATGAA-TGAAAATAAA
1 TAGAAACAATGAAGT-AAAAGAAA
*
34590205 TAGAAACGATGAAGTAAAAGAAA
1 TAGAAACAATGAAGTAAAAGAAA
34590228 TAGA
1 TAGA
34590232 TCGCATGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.60, C:0.06, G:0.18, T:0.16
Consensus pattern (23 bp):
TAGAAACAATGAAGTAAAAGAAA
Found at i:34617264 original size:19 final size:18
Alignment explanation
Indices: 34617242--34617289 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
34617232 TATTTTTAAG
34617242 ATTTTTATAAAAAATTCTA
1 ATTTTTA-AAAAAATTCTA
* * *
34617261 ATTTTTAATAAATTTTTA
1 ATTTTTAAAAAAATTCTA
34617279 ATTTTTAAAAA
1 ATTTTTAAAAA
34617290 TTTTATTAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTTTTAAAAAAATTCTA
Found at i:34617321 original size:19 final size:18
Alignment explanation
Indices: 34617264--34617323 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
34617254 AATTCTAATT
* **
34617264 TTTAATAAATTTTTAATT
1 TTTAATAATTTTTTAAAA
* *
34617282 TTTAAAAATTTTATTAGAA
1 TTTAATAATTTT-TTAAAA
34617301 TTTAATAATTTTTCTAAAA
1 TTTAATAATTTTT-TAAAA
34617320 TTTA
1 TTTA
34617324 TTATTTATTA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
18 11 0.33
19 22 0.67
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
TTTAATAATTTTTTAAAA
Found at i:34617479 original size:89 final size:88
Alignment explanation
Indices: 34617359--34617531 Score: 229
Period size: 89 Copynumber: 2.0 Consensus size: 88
34617349 ATAAGACCAT
* * *
34617359 GGGCTTAATTGCTTATTTGAAAAATTTTGAGGGTCTTTTTGAGGCATTTTGAAAGTTCAAGTACT
1 GGGCTTAATTGCTTATTTGAAAAAGTTTGAGGGCCTTTTTGAGGCATTTTAAAAGTTCAAGTACT
* * *
34617424 TAATTGAGTGGAAAAAAAAGTAG
66 CAATTGAATGCAAAAAAAAGTAG
* * * * * *
34617447 GGGCTTTATTGCTTCTTTTGAAGAAGTTTGAGGGCCTTTTTGATGTATTTTAAAAGTTCAAGTGC
1 GGGCTTAATTGCTT-ATTTGAAAAAGTTTGAGGGCCTTTTTGAGGCATTTTAAAAGTTCAAGTAC
34617512 TCAATTGAATGCAAAAAAAA
65 TCAATTGAATGCAAAAAAAA
34617532 AAAAAAGAGC
Statistics
Matches: 72, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
88 13 0.18
89 59 0.82
ACGTcount: A:0.32, C:0.09, G:0.23, T:0.37
Consensus pattern (88 bp):
GGGCTTAATTGCTTATTTGAAAAAGTTTGAGGGCCTTTTTGAGGCATTTTAAAAGTTCAAGTACT
CAATTGAATGCAAAAAAAAGTAG
Found at i:34619606 original size:24 final size:24
Alignment explanation
Indices: 34619578--34619655 Score: 129
Period size: 24 Copynumber: 3.2 Consensus size: 24
34619568 ACGATTTGAA
*
34619578 GCTCCCATAGGAGGACCACCTCTT
1 GCTCCCATAGAAGGACCACCTCTT
*
34619602 GCTCCCATAGAAGGACCACCCCTT
1 GCTCCCATAGAAGGACCACCTCTT
*
34619626 GCTCCCATCGAAGGACCACCTCTT
1 GCTCCCATAGAAGGACCACCTCTT
34619650 GCTCCC
1 GCTCCC
34619656 CTAGGAGAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.21, C:0.42, G:0.18, T:0.19
Consensus pattern (24 bp):
GCTCCCATAGAAGGACCACCTCTT
Found at i:34621437 original size:3 final size:3
Alignment explanation
Indices: 34621429--34621454 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
34621419 ATTAAAATTC
34621429 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
34621455 TATATAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:34626499 original size:29 final size:29
Alignment explanation
Indices: 34626469--34626567 Score: 159
Period size: 29 Copynumber: 3.5 Consensus size: 29
34626459 TTTTTTTGAT
34626469 ATATTTTGGTAAAT-AAAAAAAA-TT-TA
1 ATATTTTGGTAAATAAAAAAAAAGTTGTA
34626495 TATATTTTGGTAAATAAAAAAAAAGTTGTA
1 -ATATTTTGGTAAATAAAAAAAAAGTTGTA
*
34626525 ATATTTTCGTAAATAAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAAGTTGTA
34626554 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
34626568 TTTTATTTTT
Statistics
Matches: 67, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
27 14 0.21
28 8 0.12
29 43 0.64
30 2 0.03
ACGTcount: A:0.49, C:0.01, G:0.11, T:0.38
Consensus pattern (29 bp):
ATATTTTGGTAAATAAAAAAAAAGTTGTA
Found at i:34626829 original size:13 final size:13
Alignment explanation
Indices: 34626811--34626835 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34626801 CAATCAAATG
34626811 CACACAAAATAAA
1 CACACAAAATAAA
34626824 CACACAAAATAA
1 CACACAAAATAA
34626836 TATTAAAATA
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:34638602 original size:25 final size:25
Alignment explanation
Indices: 34638568--34638616 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
34638558 GAACTTAATA
* *
34638568 TTTTCTAATTTGGTACCTAAACTTT
1 TTTTCCAATTTGGTACCCAAACTTT
34638593 TTTTCCAATTTGGTACCCAAACTT
1 TTTTCCAATTTGGTACCCAAACTT
34638617 GTCACTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.08, T:0.47
Consensus pattern (25 bp):
TTTTCCAATTTGGTACCCAAACTTT
Found at i:34642627 original size:9 final size:9
Alignment explanation
Indices: 34642613--34642640 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
34642603 TGAGTTTTCA
34642613 AATTCGAAT
1 AATTCGAAT
34642622 AATTCGAAT
1 AATTCGAAT
34642631 AATTCGAAT
1 AATTCGAAT
34642640 A
1 A
34642641 TCAAACTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:34646727 original size:98 final size:99
Alignment explanation
Indices: 34646558--34646754 Score: 378
Period size: 98 Copynumber: 2.0 Consensus size: 99
34646548 GCACGTCTCG
34646558 GGGCCAACCCCGCTCCACGCGCGCCACTCCTCCGCGAGAGTTGCGCCTCCACGTCGCGCGTATTC
1 GGGCCAACCCCGCTCCACGCGCGCCACTCCTCCGCGAGAGTTGCGCCTCCACGTCGCGCGTATTC
34646623 TCCTCCAACAGTACCTGCATCAA-AAGATAGCAA
66 TCCTCCAACAGTACCTGCATCAACAAGATAGCAA
*
34646656 GGGCCGACCCCGCTCCACGCGCGCCACTCCTCCGCGAGAGTTGCGCCTCCACGTCGCGCGTATTC
1 GGGCCAACCCCGCTCCACGCGCGCCACTCCTCCGCGAGAGTTGCGCCTCCACGTCGCGCGTATTC
34646721 TCCTCCAACAGTACCTGCATCAACAAGATAGCAA
66 TCCTCCAACAGTACCTGCATCAACAAGATAGCAA
34646755 AAATCATGCC
Statistics
Matches: 97, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
98 87 0.90
99 10 0.10
ACGTcount: A:0.21, C:0.41, G:0.22, T:0.16
Consensus pattern (99 bp):
GGGCCAACCCCGCTCCACGCGCGCCACTCCTCCGCGAGAGTTGCGCCTCCACGTCGCGCGTATTC
TCCTCCAACAGTACCTGCATCAACAAGATAGCAA
Found at i:34646999 original size:34 final size:34
Alignment explanation
Indices: 34646956--34647022 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
34646946 TTCAAAGGTT
34646956 TTTTTTACTTTGTAGTATTTACTGTTCTTTTTGC
1 TTTTTTACTTTGTAGTATTTACTGTTCTTTTTGC
*
34646990 TTTTTTACTTTGTAGTATTTGCTGTTCTTTTTG
1 TTTTTTACTTTGTAGTATTTACTGTTCTTTTTG
34647023 TTTATATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.10, C:0.10, G:0.13, T:0.66
Consensus pattern (34 bp):
TTTTTTACTTTGTAGTATTTACTGTTCTTTTTGC
Found at i:34665576 original size:16 final size:17
Alignment explanation
Indices: 34665547--34665584 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
34665537 ATACGATATT
34665547 TAAT-TTTTAGATTT-A
1 TAATATTTTAGATTTAA
*
34665562 TAATATTTTATATTTAA
1 TAATATTTTAGATTTAA
34665579 TAATAT
1 TAATAT
34665585 AGTTAGTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 9 0.45
17 7 0.35
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TAATATTTTAGATTTAA
Found at i:34665920 original size:2 final size:2
Alignment explanation
Indices: 34665913--34665939 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
34665903 CACCACAGAA
34665913 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 A
34665940 ACCATAAATC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34676490 original size:11 final size:11
Alignment explanation
Indices: 34676477--34676538 Score: 65
Period size: 11 Copynumber: 5.6 Consensus size: 11
34676467 AATAAAAAAA
34676477 TTTAAAAAGTAT
1 TTTAAAAA-TAT
34676489 TTTAAAAATAT
1 TTTAAAAATAT
34676500 TTT-AAAAT-T
1 TTTAAAAATAT
***
34676509 AGAAAAAAGTAT
1 TTTAAAAA-TAT
34676521 TTTAAAAATAT
1 TTTAAAAATAT
34676532 TTTAAAA
1 TTTAAAA
34676539 TTAAAAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
9 1 0.02
10 9 0.22
11 17 0.41
12 14 0.34
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (11 bp):
TTTAAAAATAT
Found at i:34676521 original size:32 final size:31
Alignment explanation
Indices: 34676480--34676546 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 31
34676470 AAAAAAATTT
34676480 AAAAAGTATTTTAAAAATATTTTAAAATTAGA
1 AAAAAGTATTTTAAAAATATTTTAAAATTA-A
34676512 AAAAAGTATTTTAAAAATATTTTAAAATTAA
1 AAAAAGTATTTTAAAAATATTTTAAAATTAA
34676543 AAAA
1 AAAA
34676547 TTTAAAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 5 0.14
32 30 0.86
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (31 bp):
AAAAAGTATTTTAAAAATATTTTAAAATTAA
Found at i:34676552 original size:15 final size:18
Alignment explanation
Indices: 34676521--34676560 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 18
34676511 AAAAAAGTAT
34676521 TTTAAAAATATTTTAAAA
1 TTTAAAAATATTTTAAAA
34676539 -TTAAAAA-A-TTTAAAA
1 TTTAAAAATATTTTAAAA
34676554 TTTAAAA
1 TTTAAAA
34676561 TAAAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.33
16 7 0.33
17 7 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TTTAAAAATATTTTAAAA
Found at i:34676575 original size:22 final size:22
Alignment explanation
Indices: 34676532--34676575 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
34676522 TTAAAAATAT
* * *
34676532 TTTAAAATTAAAAAATTTAAAA
1 TTTAAAATAAAAAAAATAAAAA
34676554 TTTAAAATAAAAAAAATAAAAA
1 TTTAAAATAAAAAAAATAAAAA
34676576 AAATTTATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
TTTAAAATAAAAAAAATAAAAA
Found at i:34677070 original size:19 final size:20
Alignment explanation
Indices: 34677046--34677091 Score: 62
Period size: 17 Copynumber: 2.5 Consensus size: 20
34677036 ATTGTTTGGA
34677046 TATTGTATAAATTTTGTT-T
1 TATTGTATAAATTTTGTTAT
34677065 TATTGT-T-AATTTTGTTAT
1 TATTGTATAAATTTTGTTAT
*
34677083 TATTTTATA
1 TATTGTATA
34677092 GACATTTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 9 0.39
18 7 0.30
19 7 0.30
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (20 bp):
TATTGTATAAATTTTGTTAT
Found at i:34677269 original size:12 final size:12
Alignment explanation
Indices: 34677239--34677271 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
34677229 TATATATTTT
34677239 AAAATT-ATATA
1 AAAATTAATATA
34677250 AAAA-TAATATA
1 AAAATTAATATA
34677261 AAAATTAATAT
1 AAAATTAATAT
34677272 GGGCGGGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:34677731 original size:19 final size:20
Alignment explanation
Indices: 34677704--34677741 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
34677694 TTTGAAATAT
*
34677704 TATATTTTA-ATATTTAAAA
1 TATAGTTTACATATTTAAAA
*
34677723 TATAGTTTACATGTTTAAA
1 TATAGTTTACATATTTAAA
34677742 TTAAATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (20 bp):
TATAGTTTACATATTTAAAA
Found at i:34679562 original size:33 final size:32
Alignment explanation
Indices: 34679440--34679573 Score: 99
Period size: 33 Copynumber: 4.1 Consensus size: 32
34679430 AATTGACAGA
* *
34679440 TAAGACCATGGTTGGACCATGGCAATGTTTAAATG
1 TAAGACCATAGTTGGACTATGGC-A--TTTAAATG
* * *
34679475 TAAGACCATAGTTGGGCTATGACATTTTAATG
1 TAAGACCATAGTTGGACTATGGCATTTAAATG
* ** ** *
34679507 AAAAGACCATAACTGGGTTATGGCACTTTAAACG
1 -TAAGACCATAGTTGGACTATGGCA-TTTAAATG
* *
34679541 TAAGACCATGGTTGGACTATGGCA-ATAAATG
1 TAAGACCATAGTTGGACTATGGCATTTAAATG
34679572 TA
1 TA
34679574 TACGTGTAAG
Statistics
Matches: 77, Mismatches: 20, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
31 7 0.09
32 7 0.09
33 37 0.48
34 7 0.09
35 19 0.25
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.28
Consensus pattern (32 bp):
TAAGACCATAGTTGGACTATGGCATTTAAATG
Found at i:34679618 original size:105 final size:101
Alignment explanation
Indices: 34679440--34679636 Score: 286
Period size: 105 Copynumber: 1.9 Consensus size: 101
34679430 AATTGACAGA
* **
34679440 TAAGACCATGGTTGGACCATGGCAATGTTTAAATGTAAGACCATAGTTGGGCTATGACATTTTAA
1 TAAGACCATGGTTGGACCATGGCAATGTATAAATGTAAGACCATAGTTGGGCTATGACATCCTAA
34679505 TGAAAAGACCATAACTGGGTTATGGCACTTTAAACG
66 TGAAAAGACCATAACTGGGTTATGGCACTTTAAACG
* ** *
34679541 TAAGACCATGGTTGGACTATGGCAATAAATGTATACGTGTAAGACCATAGTTGGGCTATGGCATC
1 TAAGACCATGGTTGGACCATGGC----AATGTATAAATGTAAGACCATAGTTGGGCTATGACATC
*
34679606 CTAATGATAAGACCATAACTGGGTTATGGCA
62 CTAATGAAAAGACCATAACTGGGTTATGGCA
34679637 TTACGAGTGT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
101 22 0.26
105 62 0.74
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGGCAATGTATAAATGTAAGACCATAGTTGGGCTATGACATCCTAA
TGAAAAGACCATAACTGGGTTATGGCACTTTAAACG
Found at i:34679650 original size:33 final size:32
Alignment explanation
Indices: 34679577--34679654 Score: 84
Period size: 33 Copynumber: 2.4 Consensus size: 32
34679567 AAATGTATAC
** * *
34679577 GTGTAAGACCATAGTTGGGCTATGGCATCCTA
1 GTGTAAGACCATAACTGGGCTATGGCATACGA
* *
34679609 ATGATAAGACCATAACTGGGTTATGGCATTACGA
1 GTG-TAAGACCATAACTGGGCTATGGCA-TACGA
34679643 GTGTAAGACCAT
1 GTGTAAGACCAT
34679655 GGCAGGGCCA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
32 2 0.05
33 30 0.81
34 5 0.14
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.27
Consensus pattern (32 bp):
GTGTAAGACCATAACTGGGCTATGGCATACGA
Found at i:34689350 original size:15 final size:15
Alignment explanation
Indices: 34689330--34689363 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
34689320 CCCTTTCACA
* *
34689330 TTCCTCTTCCTTTCT
1 TTCCTCCTCCTCTCT
34689345 TTCCTCCTCCTCTCT
1 TTCCTCCTCCTCTCT
34689360 TTCC
1 TTCC
34689364 GTTCCTTGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (15 bp):
TTCCTCCTCCTCTCT
Found at i:34697082 original size:32 final size:33
Alignment explanation
Indices: 34697026--34697094 Score: 113
Period size: 32 Copynumber: 2.1 Consensus size: 33
34697016 CATGGTTAAT
34697026 ATTTTTAAAATTTTTTATGATTTTGTAAATAAA
1 ATTTTTAAAATTTTTTATGATTTTGTAAATAAA
* *
34697059 ATTTTTAAAA-TTTTTATGGTTTTGTAAATACA
1 ATTTTTAAAATTTTTTATGATTTTGTAAATAAA
34697091 ATTT
1 ATTT
34697095 ATTGTTTGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 24 0.71
33 10 0.29
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.55
Consensus pattern (33 bp):
ATTTTTAAAATTTTTTATGATTTTGTAAATAAA
Found at i:34698690 original size:593 final size:594
Alignment explanation
Indices: 34697553--34698740 Score: 2369
Period size: 593 Copynumber: 2.0 Consensus size: 594
34697543 TAAAATTTTA
34697553 CTTTTTTTACCATCATAAAAACATACAATTTAATTTCGTAAAAAAAAAATTCTAACTCCACCACT
1 CTTTTTTTACCATCATAAAAACATACAATTTAATTTCGTAAAAAAAAAATTCTAACTCCACCACT
34697618 AATCTCAACCCTTAAATAAGATAATCAAGACGTTGAAGCATGCTTGAACCCACTTAATCTTATAC
66 AATCTCAACCCTTAAATAAGATAATCAAGACGTTGAAGCATGCTTGAACCCACTTAATCTTATAC
34697683 TAATAATTTTTTTTACGTGAATATATTTTTTATATAAAAAATAAAATAATAAAAATACTCTCAAA
131 TAATAATTTTTTTTACGTGAATATATTTTTTATATAAAAAATAAAATAATAAAAATACTCTCAAA
34697748 ATAATATAAATTTTTTTTATTTCATTGGTATCCTATTAACGAAGTAAATTAACAACTTTTATCAA
196 ATAATATAAATTTTTTTTATTTCATTGGTATCCTATTAACGAAGTAAATTAACAACTTTTATCAA
34697813 GTATAGATATAGATGAGTTAAAAATCCCTGGGGAAAGGCGTGGGTGCACATGATGGTGGGGCCAC
261 GTATAGATATAGATGAGTTAAAAATCCCTGGGGAAAGGCGTGGGTGCACATGATGGTGGGGCCAC
34697878 TACCCACAAGTCAATAAAAAGGGGGCTCATTGGCACAGTGGCTCCGGTGAGCATAGTATTTGGAA
326 TACCCACAAGTCAATAAAAAGGGGGCTCATTGGCACAGTGGCTCCGGTGAGCATAGTATTTGGAA
34697943 GAGACACCCAAAAAGCAAAAACACAGGGTTGGGTTGGTGAATGGTGACACATGAAGCAACGCTTA
391 GAGACACCCAAAAAGCAAAAACACAGGGTTGGGTTGGTGAATGGTGACACATGAAGCAACGCTTA
34698008 TCTATGCCTCGAGCTGGCTAAGGAGAGACCATGTCTCCCCAATTATTTTGATTGGACTTTCCCTT
456 TCTATGCCTCGAGCTGGCTAAGGAGAGACCATGTCTCCCCAATTATTTTGATTGGACTTTCCCTT
34698073 CCCTCTCACTTCCATTTTACTTCCCCAGCACGTGTATTCTTCTGTTTCTCTTAGCTGTACTGTCT
521 CCCTCTCACTTCCATTTTACTTCCCCAGCACGTGTATTCTTCTGTTTCTCTTAGCTGTACTGTCT
34698138 CACGCCTTC
586 CACGCCTTC
34698147 CTTTTTTTA-CATCATAAAAACATACAATTTAATTTCGTAAAAAAAAAATTCTAACTCCACCACT
1 CTTTTTTTACCATCATAAAAACATACAATTTAATTTCGTAAAAAAAAAATTCTAACTCCACCACT
34698211 AATCTCAACCCTTAAATAAGATAATCAAGACGTTGAAGCATGCTTGAACCCACTTAATCTTATAC
66 AATCTCAACCCTTAAATAAGATAATCAAGACGTTGAAGCATGCTTGAACCCACTTAATCTTATAC
34698276 TAATAATTTTTTTTACGTGAATATATTTTTTATATAAAAAATAAAATAATAAAAATACTCTCAAA
131 TAATAATTTTTTTTACGTGAATATATTTTTTATATAAAAAATAAAATAATAAAAATACTCTCAAA
34698341 ATAATATAAATTTTTTTTATTTCATTGGTATCCTATTAACGAAGTAAATTAACAACTTTTATCAA
196 ATAATATAAATTTTTTTTATTTCATTGGTATCCTATTAACGAAGTAAATTAACAACTTTTATCAA
34698406 GTATAGATATAGATGAGTTAAAAATCCCTGGGGAAAGGCGTGGGTGCACATGATGGTGGGGCCAC
261 GTATAGATATAGATGAGTTAAAAATCCCTGGGGAAAGGCGTGGGTGCACATGATGGTGGGGCCAC
34698471 TACCCACAAGTCAATAAAAAGGGGGCTCATTGGCACAGTGGCTCCGGTGAGCATAGTATTTGGAA
326 TACCCACAAGTCAATAAAAAGGGGGCTCATTGGCACAGTGGCTCCGGTGAGCATAGTATTTGGAA
34698536 GAGACACCCAAAAAGCAAAAACACAGGGTTGGGTTGGTGAATGGTGACACATGAAGCAACGCTTA
391 GAGACACCCAAAAAGCAAAAACACAGGGTTGGGTTGGTGAATGGTGACACATGAAGCAACGCTTA
34698601 TCTATGCCTCGAGCTGGCTAAGGAGAGACCATGTCTCCCCAATTATTTTGATTGGACTTTCCCTT
456 TCTATGCCTCGAGCTGGCTAAGGAGAGACCATGTCTCCCCAATTATTTTGATTGGACTTTCCCTT
34698666 CCCTCTCACTTCCATTTTACTTCCCCAGCACGTGTATTCTTCTGTTTCTCTTAGCTGTACTGTCT
521 CCCTCTCACTTCCATTTTACTTCCCCAGCACGTGTATTCTTCTGTTTCTCTTAGCTGTACTGTCT
34698731 CACGCCTTC
586 CACGCCTTC
34698740 C
1 C
34698741 CCTTTTTCTT
Statistics
Matches: 594, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
593 585 0.98
594 9 0.02
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (594 bp):
CTTTTTTTACCATCATAAAAACATACAATTTAATTTCGTAAAAAAAAAATTCTAACTCCACCACT
AATCTCAACCCTTAAATAAGATAATCAAGACGTTGAAGCATGCTTGAACCCACTTAATCTTATAC
TAATAATTTTTTTTACGTGAATATATTTTTTATATAAAAAATAAAATAATAAAAATACTCTCAAA
ATAATATAAATTTTTTTTATTTCATTGGTATCCTATTAACGAAGTAAATTAACAACTTTTATCAA
GTATAGATATAGATGAGTTAAAAATCCCTGGGGAAAGGCGTGGGTGCACATGATGGTGGGGCCAC
TACCCACAAGTCAATAAAAAGGGGGCTCATTGGCACAGTGGCTCCGGTGAGCATAGTATTTGGAA
GAGACACCCAAAAAGCAAAAACACAGGGTTGGGTTGGTGAATGGTGACACATGAAGCAACGCTTA
TCTATGCCTCGAGCTGGCTAAGGAGAGACCATGTCTCCCCAATTATTTTGATTGGACTTTCCCTT
CCCTCTCACTTCCATTTTACTTCCCCAGCACGTGTATTCTTCTGTTTCTCTTAGCTGTACTGTCT
CACGCCTTC
Found at i:34700201 original size:15 final size:16
Alignment explanation
Indices: 34700181--34700213 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
34700171 ATATAATTTC
*
34700181 AATTTT-ATTTTTTAA
1 AATTTTGATTATTTAA
34700196 AATTTTGATTATTTAA
1 AATTTTGATTATTTAA
34700212 AA
1 AA
34700214 AAAATCATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
AATTTTGATTATTTAA
Found at i:34705102 original size:32 final size:32
Alignment explanation
Indices: 34705060--34705130 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
34705050 TTTGTTGGTT
*
34705060 TTGAAATTATTATGTCTTAAATTTGTTAGATA
1 TTGAAATTATTATGTCTTAAACTTGTTAGATA
* * * *
34705092 TTGAATTTATTATGTTTTAAGCTTGTTGGATA
1 TTGAAATTATTATGTCTTAAACTTGTTAGATA
34705124 TTGAAAT
1 TTGAAAT
34705131 GATTGACAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.03, G:0.15, T:0.51
Consensus pattern (32 bp):
TTGAAATTATTATGTCTTAAACTTGTTAGATA
Found at i:34706333 original size:21 final size:20
Alignment explanation
Indices: 34706308--34706347 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
34706298 TTATTCATAA
*
34706308 ATAAATTATTGTAATATATAT
1 ATAAATAATTGTAA-ATATAT
*
34706329 ATAAATAATTTTAAATATA
1 ATAAATAATTGTAAATATA
34706348 AATTTAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
ATAAATAATTGTAAATATAT
Found at i:34716318 original size:17 final size:17
Alignment explanation
Indices: 34716293--34716326 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
34716283 TTTGGAATAT
*
34716293 TTTATTTATAAAATTTA
1 TTTAATTATAAAATTTA
*
34716310 TTTAATTATAATATTTA
1 TTTAATTATAAAATTTA
34716327 AAATAATTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTAATTATAAAATTTA
Found at i:34717335 original size:17 final size:18
Alignment explanation
Indices: 34717315--34717348 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
34717305 CAATAAAAAA
34717315 TTTTAAAAA-ATAATTTC
1 TTTTAAAAATATAATTTC
34717332 TTTTAAAAATATAATTT
1 TTTTAAAAATATAATTT
34717349 TTTGATCGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTAAAAATATAATTTC
Found at i:34719952 original size:87 final size:86
Alignment explanation
Indices: 34719861--34720022 Score: 227
Period size: 87 Copynumber: 1.9 Consensus size: 86
34719851 TTCTTCACCC
** *
34719861 AATTGAGCACTTAAACTTTCAAAATGCATCAAAAAGGCCCTC-AAACTTCTTCAAAAAAAGTAAT
1 AATTGAGCACTTAAACTTTCAAAATGCATCAAAAACACCCTCAAAACTTCTTC-AAAAAAGCAAT
34719925 TAAGTCCCTGCTTTTTTTTACAA
65 TAAG-CCCTGCTTTTTTTTACAA
* * * * *
34719948 AATTGGGTACTTGAACTTTCAAAATGCATCAAAAACACCCTCAAAACTTTTTCATAAAAGCAATT
1 AATTGAGCACTTAAACTTTCAAAATGCATCAAAAACACCCTCAAAACTTCTTCAAAAAAGCAATT
34720013 AAGCCCTGCT
66 AAGCCCTGCT
34720023 ATTATTAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
86 7 0.11
87 50 0.76
88 9 0.14
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.30
Consensus pattern (86 bp):
AATTGAGCACTTAAACTTTCAAAATGCATCAAAAACACCCTCAAAACTTCTTCAAAAAAGCAATT
AAGCCCTGCTTTTTTTTACAA
Found at i:34720543 original size:88 final size:88
Alignment explanation
Indices: 34720358--34720543 Score: 225
Period size: 88 Copynumber: 2.1 Consensus size: 88
34720348 ATTTTATATT
* * * *
34720358 GGGGCTTAATTGCTTTTTCTGAAAAAGTTTGAGGGCCTTTTGATGCATTTTGAAAGTTTAAGTAC
1 GGGGCTTAATTGCTTTTTCTGAAAAAGTTTAAGAGCCTTTTGATACATTTTGAAAGTTCAAGTAC
* *
34720423 CCAATTGAGTGCAAAAAAAAGTA
66 CCAAATGAATGCAAAAAAAAGTA
* * *
34720446 GGAGCTTAATTGCTTTTT-TTAAAAGGTTTAAGAGCCTTTTTGATACATTTT-AAAGTTCAAGTA
1 GGGGCTTAATTGCTTTTTCTGAAAAAGTTTAAGAGCC-TTTTGATACATTTTGAAAGTTCAAGTA
*
34720509 CTCAAATGAATG-AAAAAATTAAGTA
65 CCCAAATGAATGCAAAAAA--AAGTA
*
34720534 GGGGTTTAAT
1 GGGGCTTAAT
34720544 CGCCTTTTAA
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
86 6 0.07
87 34 0.41
88 43 0.52
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36
Consensus pattern (88 bp):
GGGGCTTAATTGCTTTTTCTGAAAAAGTTTAAGAGCCTTTTGATACATTTTGAAAGTTCAAGTAC
CCAAATGAATGCAAAAAAAAGTA
Found at i:34721291 original size:126 final size:127
Alignment explanation
Indices: 34721135--34721387 Score: 499
Period size: 126 Copynumber: 2.0 Consensus size: 127
34721125 TTGAATATTT
34721135 TTTTTAATATATATATATATTTTTATATTTTTCTAATGTTATATGTTTTTAATATAGTAACATCT
1 TTTTTAATATATATATATATTTTTATATTTTTCTAATGTTATATGTTTTTAATATAGTAACATCT
34721200 TTTATGGTGTATTTTATTTAGTTGAAGATTATAAATTACTTTGGTTTTTTGGTTGGATCCAA
66 TTTATGGTGTATTTTATTTAGTTGAAGATTATAAATTACTTTGGTTTTTTGGTTGGATCCAA
34721262 TTTTTAATAT-TATATATATTTTTATATTTTTCTAATGTTATATGTTTTTAATATAGTAACATCT
1 TTTTTAATATATATATATATTTTTATATTTTTCTAATGTTATATGTTTTTAATATAGTAACATCT
34721326 TTTATGGTGTATTTTATTTAGTTGAAGATTATAAATTACTTTGGTTTTTTGGTTGGATCCAA
66 TTTATGGTGTATTTTATTTAGTTGAAGATTATAAATTACTTTGGTTTTTTGGTTGGATCCAA
34721388 AATCAATAGT
Statistics
Matches: 126, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
126 116 0.92
127 10 0.08
ACGTcount: A:0.28, C:0.05, G:0.12, T:0.55
Consensus pattern (127 bp):
TTTTTAATATATATATATATTTTTATATTTTTCTAATGTTATATGTTTTTAATATAGTAACATCT
TTTATGGTGTATTTTATTTAGTTGAAGATTATAAATTACTTTGGTTTTTTGGTTGGATCCAA
Found at i:34724097 original size:23 final size:23
Alignment explanation
Indices: 34724064--34724115 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
34724054 TTAGTTTGGA
* *
34724064 GTATAAAGTTTT-ATATTTTTATAT
1 GTAT-AAGTTTTGA-ATTTATACAT
34724088 GTATAAGTTTTGAATTTATACAT
1 GTATAAGTTTTGAATTTATACAT
34724111 GTATA
1 GTATA
34724116 TACAAGTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.52
Consensus pattern (23 bp):
GTATAAGTTTTGAATTTATACAT
Found at i:34726399 original size:19 final size:19
Alignment explanation
Indices: 34726367--34726405 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
34726357 GGTCTTTTAC
34726367 AAAAATAATACAAAAAAAT
1 AAAAATAATACAAAAAAAT
*
34726386 AAAAA-AATACCAAAATAAT
1 AAAAATAATA-CAAAAAAAT
34726405 A
1 A
34726406 TAATTTTTTT
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:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (19 bp):
AAAAATAATACAAAAAAAT
Found at i:34726898 original size:151 final size:149
Alignment explanation
Indices: 34726524--34727321 Score: 1187
Period size: 151 Copynumber: 5.3 Consensus size: 149
34726514 CAATTGTTCG
* * ** * *
34726524 TATTTTGGCCCTTTATTCGTATTTTTTTTCCAAATTTTATTACTTTAAAAAAAATACTATTTTCT
1 TATTTCGGCCCTTTGTTCGTATTTTTTCCCCAGATTTTATTACTTTAAAAAATATACTATTTTCT
* *
34726589 AATTTTTTTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTTTTTTTA
66 AATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTTTTTTTA
34726654 AATAAATT--AAAAAACCAT
131 AATAAATTAAAAAAAACC-T
* * * *
34726672 TATTTTGGCCCTTTGTTCGTATTTTTTCCCGA-ATTTTATTACTCTCAATAAAAATATATTATTT
1 TATTTCGGCCCTTTGTTCGTATTTTTTCCCCAGATTTTATTACT-T-TA-AAAAATATACTATTT
*
34726736 TCGT-ATTTTATTATTTTACATTATTTTAGTACATTATGTTCGAAATGTATTAATTTACTGTATT
63 TC-TAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGT-TT
34726800 TTTTAAATAAATT-AAAAAAACCT
126 TTTTAAATAAATTAAAAAAAACCT
*
34726823 TATTTCGGCCCTTTGTTCGTATTTTTTCCCCCAGAGTTTATTACTTTAAAAAACTATACTATTTT
1 TATTTCGGCCCTTTGTTCGTATTTTTT-CCCCAGATTTTATTACTTTAAAAAA-TATACTATTTT
* * *
34726888 CTAATTTTATTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTCATTTAGTGTGTTTT
64 CTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGT-TTTT
34726953 TTAAATAAATTTAAAAAAAACCAT
128 TTAAATAAA-TTAAAAAAAACC-T
**
34726977 TATTTCGGCCCTTTGTTCGTA-TTTTTCCCTGGATTTTATTACTTTTAAAAAATATACTATTTTC
1 TATTTCGGCCCTTTGTTCGTATTTTTTCCCCAGATTTTATTAC-TTTAAAAAATATACTATTTTC
*
34727041 TAATTTTTTTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTTTTTTT
65 TAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTTTTTTT
34727106 AAATAAATTAAAAAAAACCT
130 AAATAAATTAAAAAAAACCT
*
34727126 TATTTCGGCCCTTTGTTCGTATTTTTTCCCCCAGAGTTTATTACTTTAAAAAACTATACTATTTT
1 TATTTCGGCCCTTTGTTCGTATTTTTT-CCCCAGATTTTATTACTTTAAAAAA-TATACTATTTT
* *
34727191 CTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTG-TTTTT
64 CTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTTTTTT
*
34727255 TAAATAAATTAAAAAAAATCT
129 TAAATAAATTAAAAAAAACCT
* *
34727276 TATTTCGGCCCTTTGTTCGTATTTTTTTCCCGGATTTTATTACTTT
1 TATTTCGGCCCTTTGTTCGTATTTTTTCCCCAGATTTTATTACTTT
34727322 CAATAAAAAA
Statistics
Matches: 596, Mismatches: 37, Indels: 33
0.89 0.06 0.05
Matches are distributed among these distances:
147 11 0.02
148 29 0.05
149 39 0.07
150 153 0.26
151 214 0.36
152 95 0.16
153 33 0.06
154 22 0.04
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.51
Consensus pattern (149 bp):
TATTTCGGCCCTTTGTTCGTATTTTTTCCCCAGATTTTATTACTTTAAAAAATATACTATTTTCT
AATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTTTTTTTA
AATAAATTAAAAAAAACCT
Found at i:34727331 original size:303 final size:303
Alignment explanation
Indices: 34726524--34727331 Score: 1307
Period size: 303 Copynumber: 2.7 Consensus size: 303
34726514 CAATTGTTCG
* * ** * * *
34726524 TATTTTGGCCCTTTATTCGTATTTTTT-TTCCAAATTTTATTACTTTAAAAAA-AATACTATTTT
1 TATTTCGGCCCTTTGTTCGTATTTTTTCCCCCAGAGTTTATTACTTTAAAAAACTATACTATTTT
* *
34726587 CTAATTTTTTTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTTTTTT
66 CTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTG-TTTTT
* *
34726652 TAAATAAATT--AAAAAACCATTATTTTGGCCCTTTGTTCGTATTTTTTCCCGAATTTTATTACT
130 TAAATAAATTAAAAAAAACCATTATTTCGGCCCTTTGTTCGTATTTTTTCCCGGATTTTATTACT
* *
34726715 CTCAAT-AAAAATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTCGA
195 TTCAATAAAAAATATACTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTCGA
34726779 AATGTATTAATTTACTGTATTTTTTAAATAAATTAAAAAAACCT
260 AATGTATTAATTTACTGTATTTTTTAAATAAATTAAAAAAACCT
34726823 TATTTCGGCCCTTTGTTCGTATTTTTTCCCCCAGAGTTTATTACTTTAAAAAACTATACTATTTT
1 TATTTCGGCCCTTTGTTCGTATTTTTTCCCCCAGAGTTTATTACTTTAAAAAACTATACTATTTT
*
34726888 CTAATTTTATTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTCATTTAGTGTGTTTT
66 CTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTA--GTGTTTT
34726953 TTAAATAAATTTAAAAAAAACCATTATTTCGGCCCTTTGTTCGTA-TTTTTCCCTGGATTTTATT
129 TTAAATAAA-TTAAAAAAAACCATTATTTCGGCCCTTTGTTCGTATTTTTTCCC-GGATTTTATT
*
34727017 ACTTT---TAAAAAATATACTATTTTC-TAATTTTTTTATTTTACATTATTTTAGTACATTATGT
192 ACTTTCAATAAAAAATATACTATTTTCGT-ATTTTATTATTTTACATTATTTTAGTACATTATGT
*
34727078 TTGAAATGTATTAATTTACTGT-TTTTTTAAATAAATTAAAAAAAACCT
256 TCGAAATGTATTAATTTACTGTATTTTTTAAATAAATT-AAAAAAACCT
34727126 TATTTCGGCCCTTTGTTCGTATTTTTTCCCCCAGAGTTTATTACTTTAAAAAACTATACTATTTT
1 TATTTCGGCCCTTTGTTCGTATTTTTTCCCCCAGAGTTTATTACTTTAAAAAACTATACTATTTT
34727191 CTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTTTTTT
66 CTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTTTTTT
*
34727256 AAATAAATTAAAAAAAATC-TTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGGATTTTATTACT
131 AAATAAATTAAAAAAAACCATTATTTCGGCCCTTTGTTCGTA-TTTTTTCCCGGATTTTATTACT
34727320 TTCAATAAAAAA
195 TTCAATAAAAAA
34727332 CACATTAAAT
Statistics
Matches: 475, Mismatches: 18, Indels: 28
0.91 0.03 0.05
Matches are distributed among these distances:
299 47 0.10
300 47 0.10
301 87 0.18
302 30 0.06
303 213 0.45
304 8 0.02
305 43 0.09
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.50
Consensus pattern (303 bp):
TATTTCGGCCCTTTGTTCGTATTTTTTCCCCCAGAGTTTATTACTTTAAAAAACTATACTATTTT
CTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTTTTTT
AAATAAATTAAAAAAAACCATTATTTCGGCCCTTTGTTCGTATTTTTTCCCGGATTTTATTACTT
TCAATAAAAAATATACTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTCGAA
ATGTATTAATTTACTGTATTTTTTAAATAAATTAAAAAAACCT
Found at i:34728022 original size:26 final size:27
Alignment explanation
Indices: 34727967--34728023 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
34727957 TCATTATAAA
34727967 AAAAT-TATTTTTTTATAATAATTTAT
1 AAAATATATTTTTTTATAATAATTTAT
*
34727993 -AAATATATTTTTGTTAT-A-ACTTTAT
1 AAAATATATTTTT-TTATAATAATTTAT
34728018 AAAATA
1 AAAATA
34728024 CACAAATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
25 10 0.37
26 13 0.48
27 4 0.15
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (27 bp):
AAAATATATTTTTTTATAATAATTTAT
Found at i:34729304 original size:4 final size:4
Alignment explanation
Indices: 34729297--34729321 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
34729287 TTGATGGATG
34729297 GATA GATA GATA GATA GATA GATA G
1 GATA GATA GATA GATA GATA GATA G
34729322 GAGAAGTGCC
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:0.48, C:0.00, G:0.28, T:0.24
Consensus pattern (4 bp):
GATA
Found at i:34733839 original size:33 final size:32
Alignment explanation
Indices: 34733767--34733843 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 32
34733757 TAGATACATG
* * **
34733767 TGTAAGACCATAGCTGGGCTATGACATTCTGA
1 TGTAAGACCATAACTGGGCTATGACATACAAA
*
34733799 TGATAAGACCATAACTGGGTTATGACACTACAAA
1 TG-TAAGACCATAACTGGGCTATGACA-TACAAA
34733833 TGTAAGACCAT
1 TGTAAGACCAT
34733844 GGCAGGGCTA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
32 2 0.05
33 31 0.82
34 5 0.13
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (32 bp):
TGTAAGACCATAACTGGGCTATGACATACAAA
Found at i:34733855 original size:105 final size:98
Alignment explanation
Indices: 34733662--34733888 Score: 242
Period size: 105 Copynumber: 2.2 Consensus size: 98
34733652 AATGTTTAAA
* * * **
34733662 TGTAAGACCATAGTTTGGTTATGGAATTTTAATGAAAAGACCATAACTGGGTTATGACACCTTGA
1 TGTAAGACCATAGTTGGGCTAT-GAATTCTAATGAAAAGACCATAACTGGGTTATGACACCTCAA
* *
34733727 ATGTAAGACCGTGGTTAGACTATGGCAGTATAGATACATG
65 ATGTAAGACCATGGTCAGACTATGGCA--AT-G---CATG
* * *
34733767 TGTAAGACCATAGCTGGGCTATGACATTCTGATGATAAGACCATAACTGGGTTATGACA-CTACA
1 TGTAAGACCATAGTTGGGCTATGA-ATTCTAATGAAAAGACCATAACTGGGTTATGACACCT-CA
*
34733831 AATGTAAGACCATGG-CAGGGCTATGGCAATGCATG
64 AATGTAAGACCATGGTCA-GACTATGGCAATGCATG
*
34733866 TGTAAGACCATAGTTGGACTATG
1 TGTAAGACCATAGTTGGGCTATG
34733889 GCACAAAAAG
Statistics
Matches: 106, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
99 25 0.24
102 1 0.01
103 2 0.02
104 5 0.05
105 73 0.69
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.28
Consensus pattern (98 bp):
TGTAAGACCATAGTTGGGCTATGAATTCTAATGAAAAGACCATAACTGGGTTATGACACCTCAAA
TGTAAGACCATGGTCAGACTATGGCAATGCATG
Found at i:34735328 original size:20 final size:20
Alignment explanation
Indices: 34735305--34735342 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
34735295 AACCTTGTAT
34735305 GAAAAACTGAGAATCAAATC
1 GAAAAACTGAGAATCAAATC
*
34735325 GAAAAATTGAGAATCAAA
1 GAAAAACTGAGAATCAAA
34735343 CATGGGTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.11, G:0.16, T:0.16
Consensus pattern (20 bp):
GAAAAACTGAGAATCAAATC
Found at i:34735405 original size:14 final size:14
Alignment explanation
Indices: 34735386--34735413 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
34735376 GACAATGAGA
34735386 CCTATATTGAAAAT
1 CCTATATTGAAAAT
34735400 CCTATATTGAAAAT
1 CCTATATTGAAAAT
34735414 TATGCAATCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
CCTATATTGAAAAT
Found at i:34736050 original size:36 final size:36
Alignment explanation
Indices: 34736010--34736078 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
34736000 TCTCAGCTAT
* *
34736010 TTTTAATCTCAGTGATATAGCATTCAATCTCATTAC
1 TTTTAATCTCACTGATATAGCATCCAATCTCATTAC
*
34736046 TTTTAATCTCACTGCTATAGCATCCAATCTCAT
1 TTTTAATCTCACTGATATAGCATCCAATCTCAT
34736079 CACTACATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.29, C:0.23, G:0.07, T:0.41
Consensus pattern (36 bp):
TTTTAATCTCACTGATATAGCATCCAATCTCATTAC
Found at i:34736560 original size:14 final size:14
Alignment explanation
Indices: 34736541--34736572 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
34736531 TACAAGTTAC
34736541 AAAATAATAATAAT
1 AAAATAATAATAAT
34736555 AAAATAATAATAAT
1 AAAATAATAATAAT
34736569 AAAA
1 AAAA
34736573 CATCAAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (14 bp):
AAAATAATAATAAT
Found at i:34736640 original size:68 final size:69
Alignment explanation
Indices: 34736551--34736696 Score: 276
Period size: 68 Copynumber: 2.1 Consensus size: 69
34736541 AAAATAATAA
*
34736551 TAATAAAATAATAATAATAAAACATCAAGTTTATTTTACTAATCAAATGTTAGATTTTGTTACAA
1 TAATACAATAATAATAATAAAACATCAAGTTTATTTTACTAATCAAATGTTAGATTTTGTTACAA
34736616 CAAT
66 CAAT
34736620 TAATACAA-AATAATAATAAAACATCAAGTTTATTTTACTAATCAAATGTTAGATTTTGTTACAA
1 TAATACAATAATAATAATAAAACATCAAGTTTATTTTACTAATCAAATGTTAGATTTTGTTACAA
34736684 CAAT
66 CAAT
34736688 TAATACAAT
1 TAATACAAT
34736697 TAATTCAATT
Statistics
Matches: 75, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
68 68 0.91
69 7 0.09
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.37
Consensus pattern (69 bp):
TAATACAATAATAATAATAAAACATCAAGTTTATTTTACTAATCAAATGTTAGATTTTGTTACAA
CAAT
Found at i:34736697 original size:9 final size:9
Alignment explanation
Indices: 34736683--34736733 Score: 65
Period size: 9 Copynumber: 6.1 Consensus size: 9
34736673 TTTTGTTACA
34736683 ACAATTAAT
1 ACAATTAAT
34736692 ACAATTAAT
1 ACAATTAAT
*
34736701 TCAATT-A-
1 ACAATTAAT
34736708 ACAATTAAT
1 ACAATTAAT
34736717 ACAATT-A-
1 ACAATTAAT
34736724 ACAATTAAT
1 ACAATTAAT
34736733 A
1 A
34736734 ATTTGATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
7 11 0.31
8 4 0.11
9 21 0.58
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (9 bp):
ACAATTAAT
Found at i:34736713 original size:16 final size:16
Alignment explanation
Indices: 34736692--34736733 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
34736682 AACAATTAAT
*
34736692 ACAATTAATTCAATTA
1 ACAATTAATACAATTA
34736708 ACAATTAATACAATTA
1 ACAATTAATACAATTA
34736724 ACAATTAATA
1 ACAATTAATA
34736734 ATTTGATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (16 bp):
ACAATTAATACAATTA
Found at i:34736716 original size:25 final size:23
Alignment explanation
Indices: 34736682--34736736 Score: 83
Period size: 25 Copynumber: 2.3 Consensus size: 23
34736672 ATTTTGTTAC
34736682 AACAATTAATACAATTAATTCAATT
1 AACAATTAATACAATTAA--CAATT
34736707 AACAATTAATACAATTAACAATT
1 AACAATTAATACAATTAACAATT
*
34736730 AATAATT
1 AACAATT
34736737 TGATAATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 11 0.38
25 18 0.62
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.35
Consensus pattern (23 bp):
AACAATTAATACAATTAACAATT
Found at i:34736761 original size:16 final size:16
Alignment explanation
Indices: 34736740--34736781 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
34736730 AATAATTTGA
*
34736740 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
34736756 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
34736772 TAGTTTTAAT
1 TAATTTTAAT
34736782 TTGATTAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:34739155 original size:34 final size:34
Alignment explanation
Indices: 34739112--34739182 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
34739102 ATGCAAATAT
*
34739112 CATCACTTTATGCTATAGGACTTTAACCAAAGAA
1 CATCACTTTATGCTATAGAACTTTAACCAAAGAA
34739146 CATCACTTTATGCTATAGAACTTTAACCAAAGAA
1 CATCACTTTATGCTATAGAACTTTAACCAAAGAA
34739180 CAT
1 CAT
34739183 TCTTGTTGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (34 bp):
CATCACTTTATGCTATAGAACTTTAACCAAAGAA
Found at i:34745339 original size:21 final size:20
Alignment explanation
Indices: 34745306--34745345 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
34745296 GTTCTAATTC
* *
34745306 TAAAAATTCTAAAATATATT
1 TAAAAAATCTAAAAAATATT
34745326 TAAAAAATCTTAAAAAATAT
1 TAAAAAATC-TAAAAAATAT
34745346 ATTTTAGTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAAAAATCTAAAAAATATT
Found at i:34749033 original size:87 final size:87
Alignment explanation
Indices: 34748876--34749034 Score: 205
Period size: 87 Copynumber: 1.8 Consensus size: 87
34748866 TCAGGCCTTA
* * * * * *
34748876 ATATGGGAACAATTGTCAAGTTTAGGCACTAATTTGGACAAAAAAAAGTTTAGGCCCCGATGTGA
1 ATATGGGAACAATTGTCAAGTTTAGGCACTAACTTGGACAAAAAAAAGTTCAGACCCCAATATAA
*
34748941 GAAAGTTGTCAAGTTCAGGTTC
66 AAAAGTTGTCAAGTTCAGGTTC
**
34748963 ATATGGGAACAATTG-CTAAGTTTAGG-ACTTAACTTGGATTAAAAAAAGTTCAGACCCCAATAT
1 ATATGGGAACAATTGTC-AAGTTTAGGCAC-TAACTTGGACAAAAAAAAGTTCAGACCCCAATAT
34749026 AAAAAAGTT
64 AAAAAAGTT
34749035 ACTAAGTTTA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
86 3 0.05
87 58 0.95
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (87 bp):
ATATGGGAACAATTGTCAAGTTTAGGCACTAACTTGGACAAAAAAAAGTTCAGACCCCAATATAA
AAAAGTTGTCAAGTTCAGGTTC
Found at i:34751629 original size:6 final size:6
Alignment explanation
Indices: 34751618--34751644 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
34751608 AATATATCTC
34751618 TGGCAG TGGCAG TGGCAG TGGCAG TGG
1 TGGCAG TGGCAG TGGCAG TGGCAG TGG
34751645 TAAGAGGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.52, T:0.19
Consensus pattern (6 bp):
TGGCAG
Found at i:34752248 original size:116 final size:117
Alignment explanation
Indices: 34752109--34752341 Score: 459
Period size: 116 Copynumber: 2.0 Consensus size: 117
34752099 AAAATCTCAA
34752109 AATATCCAACTTCTCATTAGCCATAAATTTTAAAATTATACATGAATTTTGTTCTAATATATAAA
1 AATATCCAACTTCTCATTAGCCATAAATTTTAAAATTATACATGAATTTTGTTCTAATATATAAA
34752174 TTTATATATTAAAATTTGATTTGATTCAATTATCACAAATTATTAATAAAAC
66 TTTATATATTAAAATTTGATTTGATTCAATTATCACAAATTATTAATAAAAC
34752226 AATATCCAAC-TCTCATTAGCCATAAATTTTAAAATTATACATGAATTTTGTTCTAATATATAAA
1 AATATCCAACTTCTCATTAGCCATAAATTTTAAAATTATACATGAATTTTGTTCTAATATATAAA
34752290 TTTATATATTAAAATTTGATTTGATTCAATTATCACAAATTATTAATAAAAC
66 TTTATATATTAAAATTTGATTTGATTCAATTATCACAAATTATTAATAAAAC
34752342 TATTAATATA
Statistics
Matches: 116, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
116 106 0.91
117 10 0.09
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.42
Consensus pattern (117 bp):
AATATCCAACTTCTCATTAGCCATAAATTTTAAAATTATACATGAATTTTGTTCTAATATATAAA
TTTATATATTAAAATTTGATTTGATTCAATTATCACAAATTATTAATAAAAC
Found at i:34752367 original size:12 final size:13
Alignment explanation
Indices: 34752352--34752401 Score: 52
Period size: 14 Copynumber: 4.0 Consensus size: 13
34752342 TATTAATATA
34752352 ATATTAT-TTTAT
1 ATATTATATTTAT
* *
34752364 ATATTATATATAA
1 ATATTATATTTAT
34752377 ATAATTATATTTAT
1 AT-ATTATATTTAT
34752391 AT-TT-TATTTAT
1 ATATTATATTTAT
34752402 TTTTTAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
11 7 0.22
12 9 0.28
13 5 0.16
14 11 0.34
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATATTATATTTAT
Found at i:34754697 original size:176 final size:177
Alignment explanation
Indices: 34754402--34754759 Score: 709
Period size: 176 Copynumber: 2.0 Consensus size: 177
34754392 AAATTTAAAA
34754402 ATCTTGGTCTTGTCCTATTTCTCAATCCTAGGCATTTTAAATTGCACCATCTGTTTTTTCATAAG
1 ATCTTGGTCTTGTCCTATTTCTCAATCCTAGGCATTTTAAATTGCACCATCTGTTTTTTCATAAG
34754467 ATCGAACTCATCAATGATAGCATATGTTGAAAATTCTCAAGCTCTCTCTTTTTCGATGTATACCA
66 ATCGAACTCATCAATGATAGCATATGTTGAAAATTCTCAAGCTCTCTCTTTTTCGATGTATACCA
34754532 CTAAATAAGTTGAAAGAAAATCAACCTCCATTCTATTGCGAAGCCTT
131 CTAAATAAGTTGAAAGAAAATCAACCTCCATTCTATTGCGAAGCCTT
34754579 -TCTTGGTCTTGTCCTATTTCTCAATCCTAGGCATTTTAAATTGCACCATCTGTTTTTTCATAAG
1 ATCTTGGTCTTGTCCTATTTCTCAATCCTAGGCATTTTAAATTGCACCATCTGTTTTTTCATAAG
34754643 ATCGAACTCATCAATGATAGCATATGTTGAAAATTCTCAAGCTCTCTCTTTTTCGATGTATACCA
66 ATCGAACTCATCAATGATAGCATATGTTGAAAATTCTCAAGCTCTCTCTTTTTCGATGTATACCA
34754708 CTAAATAAGTTGAAAGAAAATCAACCTCCATTCTATTGCGAAGCCTT
131 CTAAATAAGTTGAAAGAAAATCAACCTCCATTCTATTGCGAAGCCTT
34754755 ATCTT
1 ATCTT
34754760 CACAAAATCA
Statistics
Matches: 180, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
176 176 0.98
177 4 0.02
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (177 bp):
ATCTTGGTCTTGTCCTATTTCTCAATCCTAGGCATTTTAAATTGCACCATCTGTTTTTTCATAAG
ATCGAACTCATCAATGATAGCATATGTTGAAAATTCTCAAGCTCTCTCTTTTTCGATGTATACCA
CTAAATAAGTTGAAAGAAAATCAACCTCCATTCTATTGCGAAGCCTT
Found at i:34757496 original size:51 final size:50
Alignment explanation
Indices: 34757396--34757505 Score: 193
Period size: 51 Copynumber: 2.2 Consensus size: 50
34757386 TGAGTACTTC
*
34757396 TGATCAGTGACAAGTGATAAGTGGTAGTTTAGCTACACTTATCTGATCAG
1 TGATAAGTGACAAGTGATAAGTGGTAGTTTAGCTACACTTATCTGATCAG
*
34757446 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATCAG
1 TGATAAGTGACAAGTGATAAGTGGTAG-TTTAGCTACACTTATCTGATCAG
34757497 TGATAAGTG
1 TGATAAGTG
34757506 GTAGCTTAGT
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
50 26 0.46
51 31 0.54
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (50 bp):
TGATAAGTGACAAGTGATAAGTGGTAGTTTAGCTACACTTATCTGATCAG
Found at i:34757529 original size:36 final size:37
Alignment explanation
Indices: 34757458--34757541 Score: 125
Period size: 36 Copynumber: 2.3 Consensus size: 37
34757448 ATAAGTGACA
*
34757458 AGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATC
1 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
*
34757495 AGTGATAAGTGGTAGC-TTAGTTACACTTATCTGATC
1 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
* *
34757531 GGTGACAAGTG
1 AGTGATAAGTG
34757542 ACAAGTGATA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 27 0.63
37 16 0.37
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.33
Consensus pattern (37 bp):
AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
Found at i:34757554 original size:87 final size:87
Alignment explanation
Indices: 34757408--34757592 Score: 307
Period size: 87 Copynumber: 2.1 Consensus size: 87
34757398 ATCAGTGACA
* *
34757408 AGTGATAAGTGGTAGTTTAGCTACACTTATCTGATCAGTGATAAGTGACAAGTGATAAGTGGTAG
1 AGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAG
* *
34757473 CTTTAGCTGCACTTATCTGATC
66 CTTTAGCTACACTTATCTAATC
* *
34757495 AGTGATAAGTGGTAGCTTAGTTACACTTATCTGATCGGTGACAAGTGACAAGTGATAAGTGGTAG
1 AGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAG
34757560 CTTTAGCTACACTTATCTAATC
66 CTTTAGCTACACTTATCTAATC
*
34757582 AGTGACAAGTG
1 AGTGATAAGTG
34757593 ACAAGTGATA
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 91 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (87 bp):
AGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAG
CTTTAGCTACACTTATCTAATC
Found at i:34757589 original size:51 final size:50
Alignment explanation
Indices: 34757495--34757603 Score: 182
Period size: 51 Copynumber: 2.2 Consensus size: 50
34757485 TTATCTGATC
* * *
34757495 AGTGATAAGTGGTAGCTTAGTTACACTTATCTGATCGGTGACAAGTGACA
1 AGTGATAAGTGGTAGCTTAGCTACACTTATCTAATCAGTGACAAGTGACA
34757545 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAGTGACAAGTGACA
1 AGTGATAAGTGGTAGC-TTAGCTACACTTATCTAATCAGTGACAAGTGACA
34757596 AGTGATAA
1 AGTGATAA
34757604 ATGTGATCCG
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
50 16 0.29
51 39 0.71
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (50 bp):
AGTGATAAGTGGTAGCTTAGCTACACTTATCTAATCAGTGACAAGTGACA
Found at i:34760234 original size:30 final size:30
Alignment explanation
Indices: 34760193--34760265 Score: 112
Period size: 30 Copynumber: 2.4 Consensus size: 30
34760183 AAGAACTTGA
*
34760193 GAAGACACGATATCTCGTTCAGGAGCTT-G
1 GAAGACTCGATATCTCGTTCAGGAGCTTAG
34760222 GAAAGACTCGATATCTCGTTCAGGAGCTTAG
1 G-AAGACTCGATATCTCGTTCAGGAGCTTAG
*
34760253 GAAGATTCGATAT
1 GAAGACTCGATAT
34760266 TTGATTTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
29 1 0.03
30 37 0.93
31 2 0.05
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (30 bp):
GAAGACTCGATATCTCGTTCAGGAGCTTAG
Found at i:34762602 original size:23 final size:26
Alignment explanation
Indices: 34762576--34762633 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
34762566 AGCCAGAATA
*
34762576 AGCTTCCTGA-T-A-GGCTCTTTGTT
1 AGCTTCCTGATTAATGGCTCTTTGTG
*
34762599 AGCTTCCCGATTAATGGCTCTTTGTG
1 AGCTTCCTGATTAATGGCTCTTTGTG
34762625 AGCTTCCTG
1 AGCTTCCTG
34762634 TTATATGACT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 9 0.31
24 1 0.03
25 1 0.03
26 18 0.62
ACGTcount: A:0.14, C:0.24, G:0.22, T:0.40
Consensus pattern (26 bp):
AGCTTCCTGATTAATGGCTCTTTGTG
Found at i:34764775 original size:19 final size:19
Alignment explanation
Indices: 34764735--34764785 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
34764725 ATATAAATCA
*
34764735 TTATTAAAAA-TATAAAAT
1 TTATAAAAAATTATAAAAT
*
34764753 TTATAAAAAAATTATGAAA-
1 TTAT-AAAAAATTATAAAAT
*
34764772 TTATTAAAAATTAT
1 TTATAAAAAATTAT
34764786 CTAAGTCCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 13 0.46
19 9 0.32
20 6 0.21
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
TTATAAAAAATTATAAAAT
Found at i:34764783 original size:18 final size:18
Alignment explanation
Indices: 34764718--34764785 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 18
34764708 TATTTTAAAA
34764718 ATTAAAAA-TATAAATCATT
1 ATTAAAAATTATAAA--ATT
34764737 ATTAAAAA-TATAAAATTT
1 ATTAAAAATTATAAAA-TT
* *
34764755 ATAAAAAAATTATGAAATT
1 AT-TAAAAATTATAAAATT
34764774 ATTAAAAATTAT
1 ATTAAAAATTAT
34764786 CTAAGTCCAT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
17 1 0.02
18 13 0.30
19 23 0.53
20 6 0.14
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (18 bp):
ATTAAAAATTATAAAATT
Found at i:34765305 original size:70 final size:70
Alignment explanation
Indices: 34765221--34765517 Score: 594
Period size: 70 Copynumber: 4.2 Consensus size: 70
34765211 TTTTAAAATT
34765221 ATTTTTTTTATAATTTTAATAATTACTAATGAATTTTTATATTTTGAAATATTTTTCTTATTATT
1 ATTTTTTTTATAATTTTAATAATTACTAATGAATTTTTATATTTTGAAATATTTTTCTTATTATT
34765286 TACAA
66 TACAA
34765291 ATTTTTTTTATAATTTTAATAATTACTAATGAATTTTTATATTTTGAAATATTTTTCTTATTATT
1 ATTTTTTTTATAATTTTAATAATTACTAATGAATTTTTATATTTTGAAATATTTTTCTTATTATT
34765356 TACAA
66 TACAA
34765361 ATTTTTTTTATAATTTTAATAATTACTAATGAATTTTTATATTTTGAAATATTTTTCTTATTATT
1 ATTTTTTTTATAATTTTAATAATTACTAATGAATTTTTATATTTTGAAATATTTTTCTTATTATT
34765426 TACAA
66 TACAA
34765431 ATTTTTTTTATAATTTTAATAATTACTAATGAATTTTTATATTTTGAAATATTTTTCTTATTATT
1 ATTTTTTTTATAATTTTAATAATTACTAATGAATTTTTATATTTTGAAATATTTTTCTTATTATT
34765496 TACAA
66 TACAA
34765501 ATTTTTTTTATAATTTT
1 ATTTTTTTTATAATTTT
34765518 TATAGTATTC
Statistics
Matches: 227, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 227 1.00
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.60
Consensus pattern (70 bp):
ATTTTTTTTATAATTTTAATAATTACTAATGAATTTTTATATTTTGAAATATTTTTCTTATTATT
TACAA
Found at i:34770991 original size:20 final size:20
Alignment explanation
Indices: 34770953--34770991 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
34770943 TCGTATAAAC
*
34770953 AAAAATATTATTTAAAAAAT
1 AAAAATATTATATAAAAAAT
34770973 AAAAATATT-TATAAGAAAA
1 AAAAATATTATATAA-AAAA
34770992 GAGTATATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (20 bp):
AAAAATATTATATAAAAAAT
Found at i:34780797 original size:29 final size:29
Alignment explanation
Indices: 34780746--34780805 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
34780736 AGTCTATATC
* **
34780746 TTTATAATTTTAAAATATTAAAT-CAAATT
1 TTTATAATTTTAAAAGACAAAATAC-AATT
*
34780775 TTTATAATTTTAGAAGACAAAATACAATT
1 TTTATAATTTTAAAAGACAAAATACAATT
34780804 TT
1 TT
34780806 ATCATTACTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 25 0.96
30 1 0.04
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (29 bp):
TTTATAATTTTAAAAGACAAAATACAATT
Found at i:34781156 original size:83 final size:82
Alignment explanation
Indices: 34780995--34781159 Score: 224
Period size: 83 Copynumber: 2.0 Consensus size: 82
34780985 TTACATTTTG
* ** * *
34780995 TAAAAGTGGTTAATTTTTAATTTTGGTCTTTTTAATATGTTTAAATTTGATATTTAATCCTTATA
1 TAAAAGTGGTTAATTTTCAATTTTGGTCTAATCAATATGCTTAAATTTGATATTTAATCCTTATA
* *
34781060 TTTTAATTTCTAACATA
66 ATTTAATCTCTAACATA
* *
34781077 TAAAAGTGGTTAATTTTCAGTTTTGGTC-AATCAATATGCTTAAATTTGAGATTTTTAATCCTTA
1 TAAAAGTGGTTAATTTTCAATTTTGGTCTAATCAATATGCTTAAATTT--GATATTTAATCCTTA
34781141 TAATTTAATCTCTAACATA
64 TAATTTAATCTCTAACATA
34781160 ATTTGGTCTC
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 15 0.21
82 26 0.36
83 31 0.43
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.49
Consensus pattern (82 bp):
TAAAAGTGGTTAATTTTCAATTTTGGTCTAATCAATATGCTTAAATTTGATATTTAATCCTTATA
ATTTAATCTCTAACATA
Found at i:34784164 original size:2 final size:2
Alignment explanation
Indices: 34784157--34784187 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
34784147 AACACATGTA
*
34784157 AT AT AT AT AT AT AT GT 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
34784188 GTAACCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34784637 original size:21 final size:21
Alignment explanation
Indices: 34784613--34784652 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
34784603 TTTATGCTAT
*
34784613 CAATCTTATAACTTATCAACA
1 CAATCTTATAACTCATCAACA
34784634 CAATCTTATAACTCATCAA
1 CAATCTTATAACTCATCAA
34784653 TTATACATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.25, G:0.00, T:0.33
Consensus pattern (21 bp):
CAATCTTATAACTCATCAACA
Done.