Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007889.1 Hibiscus syriacus cultivar Beakdansim tig00110271_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1663484
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 9
Found at i:600152 original size:6 final size:6
Alignment explanation
Indices: 600129--600163 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
600119 CTGGATCCAT
600129 ACCCTA A-CCTA A-CCTA ACCCTA ACCCTA ACCCTA A
1 ACCCTA ACCCTA ACCCTA ACCCTA ACCCTA ACCCTA A
600164 AGATATCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.36
6 18 0.64
ACGTcount: A:0.37, C:0.46, G:0.00, T:0.17
Consensus pattern (6 bp):
ACCCTA
Found at i:603035 original size:21 final size:21
Alignment explanation
Indices: 602996--603035 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
602986 TTCATTTTGA
* *
602996 TTTTGGGATTTAGGGTTTAAG
1 TTTTAGGATTTAGGATTTAAG
*
603017 TTTTAGGATTTATGATTTA
1 TTTTAGGATTTAGGATTTA
603036 GGGTATATGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.53
Consensus pattern (21 bp):
TTTTAGGATTTAGGATTTAAG
Found at i:603056 original size:28 final size:29
Alignment explanation
Indices: 603002--603078 Score: 81
Period size: 28 Copynumber: 2.8 Consensus size: 29
602992 TTGATTTTGG
*
603002 GATTTAGGGTTTAAGTTTTAGGATTT-AT
1 GATTTAGGGTTTAAGGTTTAGGATTTAAT
* *
603030 GATTTAGGGTATATGGTTTA-GAGTTTAAT
1 GATTTAGGGTTTAAGGTTTAGGA-TTTAAT
*
603059 G-TTT-GGGTTTAGGGTTTAGG
1 GATTTAGGGTTTAAGGTTTAGG
603079 TTAAATAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
27 14 0.34
28 24 0.59
29 3 0.07
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (29 bp):
GATTTAGGGTTTAAGGTTTAGGATTTAAT
Found at i:603073 original size:7 final size:7
Alignment explanation
Indices: 603004--603078 Score: 53
Period size: 7 Copynumber: 10.9 Consensus size: 7
602994 GATTTTGGGA
603004 TTTAGGG
1 TTTAGGG
* *
603011 TTTAAGT
1 TTTAGGG
*
603018 TTTAGGA
1 TTTAGGG
* *
603025 TTTATGA
1 TTTAGGG
603032 TTTAGGG
1 TTTAGGG
* *
603039 TATATGG
1 TTTAGGG
*
603046 TTTAGAG
1 TTTAGGG
**
603053 TTTAATG
1 TTTAGGG
603060 TTT-GGG
1 TTTAGGG
603066 TTTAGGG
1 TTTAGGG
603073 TTTAGG
1 TTTAGG
603079 TTAAATAAAT
Statistics
Matches: 51, Mismatches: 16, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
6 4 0.08
7 47 0.92
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (7 bp):
TTTAGGG
Found at i:610966 original size:30 final size:33
Alignment explanation
Indices: 610888--610953 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
610878 TTTTTACTTA
*
610888 CTATTACAATTATAATTTTATAAAAGCTTTTCT
1 CTATTACAATTATAAGTTTATAAAAGCTTTTCT
610921 CTATTACAATTATAAGTTTATAAAAGCTTTTCT
1 CTATTACAATTATAAGTTTATAAAAGCTTTTCT
610954 TTACAATGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.47
Consensus pattern (33 bp):
CTATTACAATTATAAGTTTATAAAAGCTTTTCT
Found at i:616270 original size:9 final size:9
Alignment explanation
Indices: 616256--616281 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
616246 CAAATTCTTA
616256 TATATTTTT
1 TATATTTTT
616265 TATATTTTT
1 TATATTTTT
616274 TATATTTT
1 TATATTTT
616282 CTATTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TATATTTTT
Found at i:616815 original size:24 final size:25
Alignment explanation
Indices: 616788--616846 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
616778 AATATCTAAA
616788 TTATATTTTTTC-TCATTTAAGTAT
1 TTATATTTTTTCTTCATTTAAGTAT
* * *
616812 TTATATTTTTTCTTTATTTATGTGT
1 TTATATTTTTTCTTCATTTAAGTAT
616837 TTA-ATTTTTT
1 TTATATTTTTT
616847 AAGTCAATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 19 0.61
25 12 0.39
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.69
Consensus pattern (25 bp):
TTATATTTTTTCTTCATTTAAGTAT
Found at i:623875 original size:21 final size:22
Alignment explanation
Indices: 623834--623881 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
623824 ATATATTTAT
623834 TAATATTTCTAATAATATAATA
1 TAATATTTCTAATAATATAATA
* *
623856 TAATATTT-TCATATTATAATA
1 TAATATTTCTAATAATATAATA
*
623877 AAATA
1 TAATA
623882 ATCAATTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (22 bp):
TAATATTTCTAATAATATAATA
Found at i:623896 original size:23 final size:23
Alignment explanation
Indices: 623845--623916 Score: 83
Period size: 23 Copynumber: 3.0 Consensus size: 23
623835 AATATTTCTA
*
623845 ATAATATAATATAATATTTTCATATT
1 ATAATA-AA-ATAATATATT-ATATT
623871 ATAATAAAATAATCA-ATTATATT
1 ATAATAAAATAAT-ATATTATATT
*
623894 ATAATAATATAATATATTATATT
1 ATAATAAAATAATATATTATATT
623917 TTTATTTTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
22 1 0.02
23 25 0.60
24 7 0.17
25 3 0.07
26 6 0.14
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (23 bp):
ATAATAAAATAATATATTATATT
Found at i:623906 original size:52 final size:53
Alignment explanation
Indices: 623843--623944 Score: 138
Period size: 52 Copynumber: 1.9 Consensus size: 53
623833 TTAATATTTC
*
623843 TAATAATATAATATA-ATATTTTCATATTATAATAA-A-ATAATCAATTATATTA
1 TAATAATATAATATATATATTTT--TATTATAATAATATATAATAAATTATATTA
*
623895 TAATAATATAATATATTATATTTTTATTTTAATAATATATAATAAATTAT
1 TAATAATATAATATA-TATATTTTTATTATAATAATATATAATAAATTAT
623945 TAATAAAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
52 25 0.57
53 1 0.02
54 18 0.41
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (53 bp):
TAATAATATAATATATATATTTTTATTATAATAATATATAATAAATTATATTA
Found at i:623949 original size:47 final size:51
Alignment explanation
Indices: 623845--623968 Score: 122
Period size: 52 Copynumber: 2.5 Consensus size: 51
623835 AATATTTCTA
*
623845 ATAATATAATATA--ATATTTTCATATTATAATAAAATAATCAATTATATTAT
1 ATAATATAATATATTATATTTT--TATTATAATAAAATAATCAATTAAATTAT
* *
623896 AATAATATAATATATTATATTTTTATTTTAATAATAT-AT-AA-TAAATTAT
1 -ATAATATAATATATTATATTTTTATTATAATAAAATAATCAATTAAATTAT
623945 -TAATA-AA-AT-TTATATTATTTATTA
1 ATAATATAATATATTATATT-TTTATTA
623969 ATTTCATAGA
Statistics
Matches: 65, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
44 7 0.11
45 8 0.12
46 2 0.03
47 5 0.08
49 7 0.11
50 2 0.03
51 2 0.03
52 25 0.38
54 7 0.11
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (51 bp):
ATAATATAATATATTATATTTTTATTATAATAAAATAATCAATTAAATTAT
Found at i:624017 original size:19 final size:18
Alignment explanation
Indices: 623993--624061 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
623983 ATATTATTAA
623993 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
624012 ATTATTTAT-ATATTTAAT
1 ATTATTAATAATA-ATAAT
624030 ATTAATATAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
624052 ATT-TTAATAA
1 ATTATTAATAA
624062 AGATATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
17 1 0.03
18 9 0.22
19 16 0.40
20 4 0.10
21 1 0.03
22 7 0.17
23 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:624036 original size:27 final size:27
Alignment explanation
Indices: 623956--624041 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 27
623946 AATAAAATTT
* *
623956 ATATTATTTAT-TAATTTCATAGAAATA
1 ATATTATTTATAT-ATTTAATATAAATA
* *
623983 ATATTA-TTAAAT-TATTAATAATGAATA
1 ATATTATTTATATAT-TTAAT-ATAAATA
624010 ATATTATTTATATATTTAATATTAATATA
1 ATATTATTTATATATTTAATA-TAA-ATA
624039 ATA
1 ATA
624042 ATCTAATAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
25 1 0.02
26 7 0.15
27 19 0.41
28 12 0.26
29 7 0.15
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (27 bp):
ATATTATTTATATATTTAATATAAATA
Found at i:624138 original size:16 final size:15
Alignment explanation
Indices: 624083--624160 Score: 50
Period size: 16 Copynumber: 4.7 Consensus size: 15
624073 TTAATTAGAT
624083 TATTAAAATATTATA
1 TATTAAAATATTATA
*
624098 TAATTTAAATATATAATACTT
1 T-A-TTAAA-ATAT--TA-TA
624119 TATTAAAATATTATTA
1 TATTAAAATATTA-TA
**
624135 TATTATTATATTA-A
1 TATTAAAATATTATA
624149 TATTAAATATAT
1 TATTAAA-ATAT
624161 AATACTTTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
14 6 0.12
15 5 0.10
16 15 0.31
17 5 0.10
18 8 0.16
19 5 0.10
20 3 0.06
21 2 0.04
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTAAAATATTATA
Found at i:624247 original size:14 final size:14
Alignment explanation
Indices: 624230--624270 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
624220 ATATTAATAT
*
624230 TTTTATTAATAAAA
1 TTTTAATAATAAAA
*
624244 TTTTAAAAATAAAA
1 TTTTAATAATAAAA
624258 TTTTAATAATAAA
1 TTTTAATAATAAA
624271 TAAATTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTTTAATAATAAAA
Found at i:624458 original size:14 final size:14
Alignment explanation
Indices: 624441--624474 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
624431 AAATGTAATT
624441 CATTTTACAGAAAA
1 CATTTTACAGAAAA
*
624455 CATTTTACGGAAAA
1 CATTTTACAGAAAA
*
624469 TATTTT
1 CATTTT
624475 CAATGAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (14 bp):
CATTTTACAGAAAA
Found at i:632224 original size:20 final size:20
Alignment explanation
Indices: 632173--632226 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
632163 TACGAACTCC
* *
632173 AATTTCGCAACACAGTTTTAA
1 AATTT-GCAACTCGGTTTTAA
*
632194 AATTCGCAACTCGGTTTTAA
1 AATTTGCAACTCGGTTTTAA
632214 AATTTGCAACTCG
1 AATTTGCAACTCG
632227 AATTTCTTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 25 0.86
21 4 0.14
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (20 bp):
AATTTGCAACTCGGTTTTAA
Found at i:632850 original size:20 final size:20
Alignment explanation
Indices: 632827--632864 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
632817 TTGAAACTTA
632827 AATTCGCAACACGAAAATGG
1 AATTCGCAACACGAAAATGG
632847 AATTCGCAACACGAAAAT
1 AATTCGCAACACGAAAAT
632865 CGCAACGCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.21, G:0.16, T:0.16
Consensus pattern (20 bp):
AATTCGCAACACGAAAATGG
Found at i:632919 original size:34 final size:34
Alignment explanation
Indices: 632881--632946 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
632871 GCGATTTTAG
* *
632881 TTTTCGCGTTGCGAATTTCGTGTTGCAAATTTCA
1 TTTTCGAGTTGCGAATTTCATGTTGCAAATTTCA
* *
632915 TTTTCGAGTTGCGATTTTCATGTTGCGAATTT
1 TTTTCGAGTTGCGAATTTCATGTTGCAAATTT
632947 AAGTTTCAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.17, C:0.15, G:0.21, T:0.47
Consensus pattern (34 bp):
TTTTCGAGTTGCGAATTTCATGTTGCAAATTTCA
Found at i:634497 original size:42 final size:42
Alignment explanation
Indices: 634438--634548 Score: 141
Period size: 42 Copynumber: 2.6 Consensus size: 42
634428 TGAGTACCCC
**
634438 CCACTTCGACACCGAGATCCATCACCTCATCGAGCCTCTTCT
1 CCACTTCGACACCGAGATCCATCACCTCATCGAGCCGATTCT
* * * *
634480 CCACTTCAACACCGAGATCCATCACCTGATTGAGTCGATTCT
1 CCACTTCGACACCGAGATCCATCACCTCATCGAGCCGATTCT
* * *
634522 ACACCTCGACACCGAGAGCCATCACCT
1 CCACTTCGACACCGAGATCCATCACCT
634549 ATTCCATCAC
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.25, C:0.40, G:0.14, T:0.22
Consensus pattern (42 bp):
CCACTTCGACACCGAGATCCATCACCTCATCGAGCCGATTCT
Found at i:634674 original size:21 final size:21
Alignment explanation
Indices: 634648--634859 Score: 137
Period size: 21 Copynumber: 10.1 Consensus size: 21
634638 ACCTCCACGG
*
634648 GATGAGTTAGGTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
** *
634669 GATGAGGCCGGTGCTTTATGT
1 GATGAGGTAGGTGCTTTACGT
*
634690 GATGAGGCCA-GTGCTTTACGT
1 GATGAGG-TAGGTGCTTTACGT
*
634711 GATGAGGTTGGTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
* * **
634732 GACGA--TAATGGTGCATGGCGT
1 GATGAGGT-A-GGTGCTTTACGT
634753 GATGAGGTAGG-GTCTTTACGT
1 GATGAGGTAGGTG-CTTTACGT
* * * *
634774 GGTGAGGTAGCTGTTTTACAT
1 GATGAGGTAGGTGCTTTACGT
**
634795 GATGA-CAATGGTGCTTTACGT
1 GATGAGGTA-GGTGCTTTACGT
* * ** *
634816 GGTGAGATATCTTCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
* *
634837 GATGAGGTAGTTGCTCTACGT
1 GATGAGGTAGGTGCTTTACGT
634858 GA
1 GA
634860 GATTGTTTCA
Statistics
Matches: 142, Mismatches: 39, Indels: 20
0.71 0.19 0.10
Matches are distributed among these distances:
19 1 0.01
20 2 0.01
21 134 0.94
22 4 0.03
23 1 0.01
ACGTcount: A:0.19, C:0.13, G:0.34, T:0.34
Consensus pattern (21 bp):
GATGAGGTAGGTGCTTTACGT
Found at i:634745 original size:63 final size:63
Alignment explanation
Indices: 634678--634851 Score: 152
Period size: 63 Copynumber: 2.8 Consensus size: 63
634668 TGATGAGGCC
* * * * * *
634678 GGTGCTTTATGTGATGAGGCCAGTG-CTTTACGTGATGAGGTTGGTGCTTTACGTGACGATAAT
1 GGTGCTTTACGTGATGAGG-CAGGGTCTTTACGTGATGAGGTAGCTGCTTTACATGACGACAAT
* ** * * * *
634741 GGTGCATGGCGTGATGAGGTAGGGTCTTTACGTGGTGAGGTAGCTGTTTTACATGATGACAAT
1 GGTGCTTTACGTGATGAGGCAGGGTCTTTACGTGATGAGGTAGCTGCTTTACATGACGACAAT
* ** *** *
634804 GGTGCTTTACGTGGTGAGATATCTTCTTTACGTGATGAGGTAGTTGCT
1 GGTGCTTTACGTGATGAGGCAGGGTCTTTACGTGATGAGGTAGCTGCT
634852 CTACGTGAGA
Statistics
Matches: 86, Mismatches: 24, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
62 3 0.03
63 83 0.97
ACGTcount: A:0.19, C:0.12, G:0.34, T:0.35
Consensus pattern (63 bp):
GGTGCTTTACGTGATGAGGCAGGGTCTTTACGTGATGAGGTAGCTGCTTTACATGACGACAAT
Found at i:634978 original size:4 final size:4
Alignment explanation
Indices: 634969--635030 Score: 88
Period size: 4 Copynumber: 15.5 Consensus size: 4
634959 TTTTTCAGCA
* *
634969 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAC TGAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* *
635017 GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TT
635031 TTAGCAGTCC
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:635203 original size:21 final size:21
Alignment explanation
Indices: 635179--635233 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
635169 ACCTCCTATT
* * *
635179 GTTCAGGATTCACCTATCATC
1 GTTCAGGATCCACCTACCACC
*
635200 GTTCAGGATCCACCTCCCACC
1 GTTCAGGATCCACCTACCACC
635221 GTTCAGGATCCAC
1 GTTCAGGATCCAC
635234 ATGGCATTCG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.22, C:0.36, G:0.16, T:0.25
Consensus pattern (21 bp):
GTTCAGGATCCACCTACCACC
Found at i:639367 original size:24 final size:23
Alignment explanation
Indices: 639336--639387 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
639326 AAACATCATC
*
639336 AAAATCCGAGTATTGATCAAGAT
1 AAAATCCGAGTATTGACCAAGAT
*
639359 AAAAGTCCGGGTATTGACCAAGAT
1 AAAA-TCCGAGTATTGACCAAGAT
*
639383 CAAAT
1 AAAAT
639388 TTCGAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.23
Consensus pattern (23 bp):
AAAATCCGAGTATTGACCAAGAT
Found at i:639533 original size:12 final size:12
Alignment explanation
Indices: 639512--639545 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
639502 GGTTGTGGGT
*
639512 TTTGAGATTGTG
1 TTTGATATTGTG
639524 TTTGATATTGTG
1 TTTGATATTGTG
*
639536 TTTGGTATTG
1 TTTGATATTG
639546 AAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:640492 original size:41 final size:40
Alignment explanation
Indices: 640447--640599 Score: 139
Period size: 41 Copynumber: 3.7 Consensus size: 40
640437 CAGAAATCGA
* *
640447 GTTGCGAATTTGAAATTCCGTGTTGCGAATACCAAATTCGC
1 GTTGCGAATTTGAAATT-CGCGTTGCGAATAACAAATTCGC
* *
640488 GTTGCGAATTTGAAAATCGCGTTGCGTAA-AAGAAATTCGC
1 GTTGCGAATTTGAAATTCGCGTTGCG-AATAACAAATTCGC
* * * * *
640528 ATTGCGAAATTGTCAAATTCGCGTTGCGAAT-TCAGAAATCGA
1 GTTGCG-AATT-TGAAATTCGCGTTGCGAATAACA-AATTCGC
* *
640570 GTTGCGAATTCGAAATTTCGTGTTGCGAAT
1 GTTGCGAATTTGAAA-TTCGCGTTGCGAAT
640600 TCGGAAACTG
Statistics
Matches: 91, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
40 25 0.27
41 42 0.46
42 24 0.26
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (40 bp):
GTTGCGAATTTGAAATTCGCGTTGCGAATAACAAATTCGC
Found at i:640580 original size:20 final size:20
Alignment explanation
Indices: 640387--640606 Score: 105
Period size: 20 Copynumber: 10.8 Consensus size: 20
640377 GGAAACTTGT
* *
640387 GTTGCGAATTTAAAAATCGC
1 GTTGCGAATTCAGAAATCGC
** *
640407 GTTGCGAA-AAAGAAATTCGT
1 GTTGCGAATTCAGAAA-TCGC
** *
640427 GTTGTAAATTCAGAAATCGA
1 GTTGCGAATTCAGAAATCGC
* *
640447 GTTGCGAATT-TGAAATTCCGT
1 GTTGCGAATTCAGAAA-T-CGC
* *
640468 GTTGCGAATACCA-AATTCGC
1 GTTGCGAAT-TCAGAAATCGC
*
640488 GTTGCGAATT-TGAAAATCGC
1 GTTGCGAATTCAG-AAATCGC
*
640508 GTTGCGTAA--AAGAAATTCGC
1 GTTGCG-AATTCAGAAA-TCGC
* *
640528 ATTGCGAAATTGTCA-AATTCGC
1 GTTGCG-AA-T-TCAGAAATCGC
*
640550 GTTGCGAATTCAGAAATCGA
1 GTTGCGAATTCAGAAATCGC
*
640570 GTTGCGAATTC-GAAATTTCGT
1 GTTGCGAATTCAGAAA--TCGC
*
640591 GTTGCGAATTCGGAAA
1 GTTGCGAATTCAGAAA
640607 CTGTGTTGCG
Statistics
Matches: 152, Mismatches: 29, Indels: 36
0.70 0.13 0.17
Matches are distributed among these distances:
19 18 0.12
20 81 0.53
21 35 0.23
22 15 0.10
23 2 0.01
24 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (20 bp):
GTTGCGAATTCAGAAATCGC
Found at i:640585 original size:62 final size:61
Alignment explanation
Indices: 640419--640586 Score: 171
Period size: 62 Copynumber: 2.7 Consensus size: 61
640409 TGCGAAAAAG
* ** * **
640419 AAATTCGTGTTGTAAATTCAGAAATCGAGTTGCGAATTTGAAATTCCGTGTTGCGAATACC
1 AAATTCGCGTTGCGAATTCAGAAATCGAGTTGCGAATTAGAAATTCCGCATTGCGAATACC
* * * **
640480 AAATTCGCGTTGCGAATT-TGAAAATCGCGTTGCGTAA-AAGAAATT-CGCATTGCGAAATTGTC
1 AAATTCGCGTTGCGAATTCAG-AAATCGAGTTGCG-AATTAGAAATTCCGCATTGCG-AA-TACC
*
640542 AAATTCGCGTTGCGAATTCAGAAATCGAGTTGCGAATTCGAAATT
1 AAATTCGCGTTGCGAATTCAGAAATCGAGTTGCGAATTAGAAATT
640587 TCGTGTTGCG
Statistics
Matches: 86, Mismatches: 15, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
60 8 0.09
61 37 0.43
62 40 0.47
63 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.30
Consensus pattern (61 bp):
AAATTCGCGTTGCGAATTCAGAAATCGAGTTGCGAATTAGAAATTCCGCATTGCGAATACC
Found at i:640600 original size:41 final size:39
Alignment explanation
Indices: 640306--640640 Score: 182
Period size: 40 Copynumber: 8.3 Consensus size: 39
640296 AAATAAAAGC
* * * ***
640306 TGTTGCAAATTCGGAAATCGAGTTGCAAAAACAAAATTCG
1 TGTTGCGAATTCAGAAATCGAGTTGC-GAATTGAAATTCG
* **
640346 TGTTGCGAATT-AGAAAATCTTA-TTGCGAAAAGGAAACTT-G
1 TGTTGCGAATTCAG-AAATC-GAGTTGCG-AATTGAAA-TTCG
* * * **
640386 TGTTGCGAATTTAAAAATCGCGTTGCGAAAAAGAAATTCG
1 TGTTGCGAATTCAGAAATCGAGTTGCG-AATTGAAATTCG
**
640426 TGTTGTAAATTCAGAAATCGAGTTGCGAATTTGAAATTCCG
1 TGTTGCGAATTCAGAAATCGAGTTGCGAA-TTGAAATT-CG
* * * *
640467 TGTTGCGAATACCA-AATTCGCGTTGCGAATTTGAAAATCG
1 TGTTGCGAAT-TCAGAAATCGAGTTGCGAA-TTGAAATTCG
* *
640507 CGTTGCGTAA--AAGAAATTCGCA-TTGCGAAATTGTCAAATTCG
1 TGTTGCG-AATTCAGAAA-TCG-AGTTGCG-AATTG--AAATTCG
*
640549 CGTTGCGAATTCAGAAATCGAGTTGCGAATTCGAAATTTCG
1 TGTTGCGAATTCAGAAATCGAGTTGCGAATT-GAAA-TTCG
* * * * *
640590 TGTTGCGAATTCGGAAA-CTGTGTTGCGAAATTGGAGTTTG
1 TGTTGCGAATTCAGAAATC-GAGTTGCG-AATTGAAATTCG
640630 TGTTGCGAATT
1 TGTTGCGAATT
640641 TGTTGGTTAT
Statistics
Matches: 236, Mismatches: 35, Indels: 48
0.74 0.11 0.15
Matches are distributed among these distances:
38 1 0.00
39 7 0.03
40 121 0.51
41 74 0.31
42 28 0.12
43 5 0.02
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (39 bp):
TGTTGCGAATTCAGAAATCGAGTTGCGAATTGAAATTCG
Found at i:640614 original size:20 final size:21
Alignment explanation
Indices: 640418--640640 Score: 110
Period size: 20 Copynumber: 10.9 Consensus size: 21
640408 TTGCGAAAAA
** *
640418 GAAATTCGTGTTGTAAATTCA
1 GAAATTCGTGTTGCGAATTCG
* *
640439 GAAA-TCGAGTTGCGAATT-T
1 GAAATTCGTGTTGCGAATTCG
*
640458 GAAATTCCGTGTTGCGAATAC-
1 GAAATT-CGTGTTGCGAATTCG
* * *
640479 CAAATTCGCGTTGCGAATT-T
1 GAAATTCGTGTTGCGAATTCG
* * **
640499 GAAAATCGCGTTGCGTAA--AA
1 GAAATTCGTGTTGCG-AATTCG
**
640519 GAAATTCGCATTGCGAAATT-G
1 GAAATTCGTGTTGCG-AATTCG
* * *
640540 TCAAATTCGCGTTGCGAATTCA
1 -GAAATTCGTGTTGCGAATTCG
*
640562 GAAA-TCGAGTTGCGAATTC-
1 GAAATTCGTGTTGCGAATTCG
640581 GAAATTTCGTGTTGCGAATTCG
1 GAAA-TTCGTGTTGCGAATTCG
*
640603 GAAACT-GTGTTGCGAAATT-G
1 GAAATTCGTGTTGCG-AATTCG
* *
640623 G-AGTTTGTGTTGCGAATT
1 GAAATTCGTGTTGCGAATT
640641 TGTTGGTTAT
Statistics
Matches: 162, Mismatches: 25, Indels: 32
0.74 0.11 0.15
Matches are distributed among these distances:
19 14 0.09
20 83 0.51
21 48 0.30
22 17 0.10
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (21 bp):
GAAATTCGTGTTGCGAATTCG
Found at i:641613 original size:21 final size:22
Alignment explanation
Indices: 641565--641618 Score: 85
Period size: 21 Copynumber: 2.5 Consensus size: 22
641555 TATTGCCTAA
641565 AAGTATCTATACCATAGGGTTG
1 AAGTATCTATACCATAGGGTTG
641587 AA-TATCTATACCATAGGGTT-
1 AAGTATCTATACCATAGGGTTG
*
641607 AAGTATCAATAC
1 AAGTATCTATAC
641619 TTGTAAGGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (22 bp):
AAGTATCTATACCATAGGGTTG
Found at i:644169 original size:3 final size:3
Alignment explanation
Indices: 644156--644750 Score: 782
Period size: 3 Copynumber: 198.7 Consensus size: 3
644146 ACTATTTTTT
* * * * * *
644156 AGA AAA AGA AGA AGA AGA AGA AGA AAA AAA AGA AGG AGG AGG AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* *
644204 AGA AGA AGA AGA AGA AGA AAA AGA AGA AGA AGGA AGA AGA GGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A-GA AGA AGA AGA AGA
*
644250 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA GGAA AGA A-A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA
* * * * *
644295 AGA AGA AGA AGA AGA GGA ATA AGA AGA TGA AGA AGA GGA AGA AGA GGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * *
644343 AGA AGA GAGA AGA AGA GGA GGA AGA AGGA AGA AGA GGA AGA AGA AG-
1 AGA AGA -AGA AGA AGA AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA
644389 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
644437 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A-A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
644484 AGA AGA AGA AGA AGAA AGA AGA AGA AGA AGA AGA AGGA AGA AGA AG-
1 AGA AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA A-GA AGA AGA AGA
* *
644530 AGA AGA AGA GAGA AGA AAA AGA A-A AGA AGA AGA AGA AGA GGA AGA
1 AGA AGA AGA -AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* *
644575 AGA AGA GAGA AGA GGA AGA AGA AAA AGA AGA GAGA AGA A-A GAGA AGA
1 AGA AGA -AGA AGA AGA AGA AGA AGA AGA AGA -AGA AGA AGA -AGA AGA
* *
644622 AGA GGA AGA AGA GGA AGA AG- AGA AGA AG- AGA AGA AGA GAGA AG-
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA -AGA AGA
* *
644665 AGA GGA AGA AGA GGA AGA AGA AGA AGA AG- AGA A-A AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
644711 AGA AGA AGA AGA AGA AGA AGA AGA AG- AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
644751 GGATAACAAA
Statistics
Matches: 527, Mismatches: 42, Indels: 46
0.86 0.07 0.07
Matches are distributed among these distances:
2 23 0.04
3 474 0.90
4 30 0.06
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:647481 original size:18 final size:16
Alignment explanation
Indices: 647433--647484 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 16
647423 ACTATAATTG
647433 ATAAGTAATAATACAAAA
1 ATAA-TAATAATA-AAAA
*
647451 ATAATGAAAAATAAAAA
1 ATAAT-AATAATAAAAA
647468 CATAGATAATAATAAAA
1 -ATA-ATAATAATAAAA
647485 TCGGATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 5 0.17
18 22 0.76
19 2 0.07
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.21
Consensus pattern (16 bp):
ATAATAATAATAAAAA
Found at i:650861 original size:17 final size:17
Alignment explanation
Indices: 650841--650907 Score: 50
Period size: 17 Copynumber: 3.9 Consensus size: 17
650831 TTTAATAAAA
650841 AATTATAATTTAAATAT
1 AATTATAATTTAAATAT
* *
650858 AATTCT-ATTAAAATTAT
1 AATTATAATTTAAA-TAT
*
650875 AATTA-AATTTTAATA-
1 AATTATAATTTAAATAT
*
650890 AATGATTAATTTTAAATA
1 AATTA-TAA-TTTAAATA
650908 AATATTTATA
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
15 4 0.11
16 8 0.21
17 19 0.50
18 7 0.18
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (17 bp):
AATTATAATTTAAATAT
Found at i:660821 original size:19 final size:19
Alignment explanation
Indices: 660797--660833 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
660787 AAATAAGAAT
660797 AATCCTTTGACCAGATATC
1 AATCCTTTGACCAGATATC
* *
660816 AATCCTTTTACCATATAT
1 AATCCTTTGACCAGATAT
660834 ATACACAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.38
Consensus pattern (19 bp):
AATCCTTTGACCAGATATC
Found at i:661514 original size:31 final size:31
Alignment explanation
Indices: 661476--661550 Score: 141
Period size: 31 Copynumber: 2.4 Consensus size: 31
661466 AAAATCAAAT
661476 TTGAATTTTTTTAGTGGTAGTAGATTTGAAC
1 TTGAATTTTTTTAGTGGTAGTAGATTTGAAC
*
661507 TTGAATTTTTTTAGTGGTAGTATATTTGAAC
1 TTGAATTTTTTTAGTGGTAGTAGATTTGAAC
661538 TTGAATTTTTTTA
1 TTGAATTTTTTTA
661551 TGGCTATCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.25, C:0.03, G:0.19, T:0.53
Consensus pattern (31 bp):
TTGAATTTTTTTAGTGGTAGTAGATTTGAAC
Found at i:667522 original size:54 final size:53
Alignment explanation
Indices: 667405--667524 Score: 159
Period size: 53 Copynumber: 2.2 Consensus size: 53
667395 CCCATAGAGT
* *
667405 GTACCGATACCCCTATGCCAATTTAGGCGCCGAAAAAACATAATTCCAAATGA
1 GTACCGATACCCCTATGCCAATTTAGGCGCCGAAAAAACAGAATGCCAAATGA
* * * * * *
667458 GTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAATAGAATGCCCAGTGG
1 GTACCGATACCCCTATGCCAATTTAGGCGCCGA-AAAAACAGAATGCCAAATGA
667512 GTACCGATACCCC
1 GTACCGATACCCC
667525 CTTAGAGGTA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
53 31 0.53
54 27 0.47
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (53 bp):
GTACCGATACCCCTATGCCAATTTAGGCGCCGAAAAAACAGAATGCCAAATGA
Found at i:667546 original size:18 final size:19
Alignment explanation
Indices: 667511--667547 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
667501 ATGCCCAGTG
667511 GGTACCGATACCCCCTTAGA
1 GGTACCGATA-CCCCTTAGA
667531 GGTACCGATA-CCCTTAG
1 GGTACCGATACCCCTTAG
667548 TCATTTAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.24, C:0.32, G:0.22, T:0.22
Consensus pattern (19 bp):
GGTACCGATACCCCTTAGA
Found at i:667749 original size:18 final size:19
Alignment explanation
Indices: 667715--667750 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
667705 TGCCCTAGTG
667715 GGTACCGATACCCCTTAGA
1 GGTACCGATACCCCTTAGA
667734 GGTACCGATA-CCCTTAG
1 GGTACCGATACCCCTTAG
667751 TCATTAACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.25, C:0.31, G:0.22, T:0.22
Consensus pattern (19 bp):
GGTACCGATACCCCTTAGA
Found at i:667772 original size:202 final size:202
Alignment explanation
Indices: 667383--667799 Score: 777
Period size: 203 Copynumber: 2.1 Consensus size: 202
667373 TTAAATAGGG
667383 AGGTACCGATA-CCCCATAGAGTGTACCGATACCCCTATGCCAATTTAGGCGCCGAAAAAACATA
1 AGGTACCGATACCCCCATAGAGTGTACCGATACCCCTATGCCAATTTAGGCGCCGAAAAAACATA
667447 ATTCCAAATGAGTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAATAGAATGCCCAGTGG
66 ATTCCAAATGAGTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAATAGAATGCCCAGTGG
667512 GTACCGATACCCCCTTAGAGGTACCGATACCCTTAGTCATTTAACGGTTGAAATATTTGAATTTT
131 GTACCGATACCCCCTTAGAGGTACCGATACCCTTAGTCATTTAACGGTTGAAATATTTGAATTTT
667577 ACACTGC
196 ACACTGC
*
667584 AGGTACCGATACCCCCATAGAGTGTACCGATACCCCTATGCCAATTTAGGCTCCGAGAAAAACAT
1 AGGTACCGATACCCCCATAGAGTGTACCGATACCCCTATGCCAATTTAGGCGCCGA-AAAAACAT
667649 AATTCCAAATGAGTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAATAGAATGCCCTAGT
65 AATTCCAAATGAGTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAATAGAATGCCC-AGT
667714 GGGTACCGATA-CCCCTTAGAGGTACCGATACCCTTAGTCA-TTAACGGTTGAAATATTTGAATT
129 GGGTACCGATACCCCCTTAGAGGTACCGATACCCTTAGTCATTTAACGGTTGAAATATTTGAATT
667777 TTACACTGC
194 TTACACTGC
*
667786 AGGTACTGATACCC
1 AGGTACCGATACCC
667800 ATTGAAGGTG
Statistics
Matches: 211, Mismatches: 2, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
201 11 0.05
202 88 0.42
203 98 0.46
204 14 0.07
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (202 bp):
AGGTACCGATACCCCCATAGAGTGTACCGATACCCCTATGCCAATTTAGGCGCCGAAAAAACATA
ATTCCAAATGAGTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAATAGAATGCCCAGTGG
GTACCGATACCCCCTTAGAGGTACCGATACCCTTAGTCATTTAACGGTTGAAATATTTGAATTTT
ACACTGC
Found at i:667813 original size:202 final size:201
Alignment explanation
Indices: 667383--667821 Score: 776
Period size: 202 Copynumber: 2.2 Consensus size: 201
667373 TTAAATAGGG
667383 AGGTACCGATACCCCATAGAGTGTACCGATACCCCTATGCCAATTTAGGCGCCGAAAAAACATAA
1 AGGTACCGATACCCCATAGAGTGTACCGATACCCCTATGCCAATTTAGGCGCCGAAAAAACATAA
667448 TTCCAAATGAGTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAATAGAATGCCCAGTGGG
66 TTCCAAATGAGTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAATAGAATGCCCAGTGGG
667513 TACCGATACCCCCTTAGAGGTACCGATACCCTTAGTCATTTAACGGTTGAAATATTTGAATTTTA
131 TACCGATACCCCCTTAGAGGTACCGATACCCTTAGTCATTTAACGGTTGAAATATTTGAATTTTA
667578 CACTGC
196 CACTGC
*
667584 AGGTACCGATACCCCCATAGAGTGTACCGATACCCCTATGCCAATTTAGGCTCCGAGAAAAACAT
1 AGGTACCGATA-CCCCATAGAGTGTACCGATACCCCTATGCCAATTTAGGCGCCGA-AAAAACAT
667649 AATTCCAAATGAGTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAATAGAATGCCCTAGT
64 AATTCCAAATGAGTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAATAGAATGCCC-AGT
667714 GGGTACCGATA-CCCCTTAGAGGTACCGATACCCTTAGTCA-TTAACGGTTGAAATATTTGAATT
128 GGGTACCGATACCCCCTTAGAGGTACCGATACCCTTAGTCATTTAACGGTTGAAATATTTGAATT
667777 TTACACTGC
193 TTACACTGC
* * *
667786 AGGTACTGATA-CCCATTGAAGGTGTACCAATACCCC
1 AGGTACCGATACCCCATAG-A-GTGTACCGATACCCC
667822 ACGCTCCCAG
Statistics
Matches: 229, Mismatches: 4, Indels: 9
0.95 0.02 0.04
Matches are distributed among these distances:
200 6 0.03
201 12 0.05
202 99 0.43
203 98 0.43
204 14 0.06
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (201 bp):
AGGTACCGATACCCCATAGAGTGTACCGATACCCCTATGCCAATTTAGGCGCCGAAAAAACATAA
TTCCAAATGAGTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAATAGAATGCCCAGTGGG
TACCGATACCCCCTTAGAGGTACCGATACCCTTAGTCATTTAACGGTTGAAATATTTGAATTTTA
CACTGC
Found at i:673464 original size:21 final size:21
Alignment explanation
Indices: 673440--673497 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 21
673430 TGTGCACTAG
673440 GTATCAATACCCCTTAAACGT
1 GTATCAATACCCCTTAAACGT
* * *
673461 GTATCGATACCCTCTTTGAATGT
1 GTATCAATACCC-C-TTAAACGT
673484 GTATCAATACCCCT
1 GTATCAATACCCCT
673498 ATAAGGGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 12 0.39
22 2 0.06
23 17 0.55
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.33
Consensus pattern (21 bp):
GTATCAATACCCCTTAAACGT
Found at i:673487 original size:23 final size:20
Alignment explanation
Indices: 673440--673516 Score: 66
Period size: 23 Copynumber: 3.6 Consensus size: 20
673430 TGTGCACTAG
*
673440 GTATCAATACCCCT-TAAACGT
1 GTATCGATACCCCTAT-AA-GT
*
673461 GTATCGATACCCTCTTTGAATGT
1 GTATCGATACCC-CTAT-AA-GT
* *
673484 GTATCAATACCCCTATAAGG
1 GTATCGATACCCCTATAAGT
673504 GTATCGATACCCC
1 GTATCGATACCCC
673517 CTATCGGGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
20 13 0.28
21 13 0.28
22 5 0.11
23 16 0.34
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (20 bp):
GTATCGATACCCCTATAAGT
Found at i:673519 original size:21 final size:22
Alignment explanation
Indices: 673439--673520 Score: 62
Period size: 21 Copynumber: 3.8 Consensus size: 22
673429 CTGTGCACTA
*
673439 GGTATCAATACCCCTTA-AACG
1 GGTATCAATACCCCCTATAACG
* * * * *
673460 TGTATCGATACCCTCTTTGAATG
1 GGTATCAATACCCCCTAT-AACG
*
673483 TGTATCAATA-CCCCTATAA-G
1 GGTATCAATACCCCCTATAACG
*
673503 GGTATCGATACCCCCTAT
1 GGTATCAATACCCCCTAT
673521 CGGGTTTAGG
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
20 9 0.19
21 21 0.45
22 5 0.11
23 12 0.26
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (22 bp):
GGTATCAATACCCCCTATAACG
Found at i:673930 original size:22 final size:24
Alignment explanation
Indices: 673884--673930 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
673874 AAGATTTTTC
*
673884 AATTTTTTTTTGAAATTTTCGAAAT
1 AATTTTTTTTTG-AATTTTCAAAAT
673909 AATTTTTTTTTG-ATTTT-AAAAT
1 AATTTTTTTTTGAATTTTCAAAAT
673931 TGTTTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 4 0.19
23 5 0.24
25 12 0.57
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (24 bp):
AATTTTTTTTTGAATTTTCAAAAT
Found at i:679595 original size:28 final size:28
Alignment explanation
Indices: 679555--679611 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
679545 CGTTACCGAA
679555 CCTAACTAAATCCAGTCTCAAGCAACAC
1 CCTAACTAAATCCAGTCTCAAGCAACAC
679583 CCTAACTAAATCCAGTCTCAAGCAACAC
1 CCTAACTAAATCCAGTCTCAAGCAACAC
679611 C
1 C
679612 TGCAAATCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.39, C:0.37, G:0.07, T:0.18
Consensus pattern (28 bp):
CCTAACTAAATCCAGTCTCAAGCAACAC
Found at i:691080 original size:18 final size:20
Alignment explanation
Indices: 691044--691081 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
691034 TCTCTTCTTC
691044 TACTTGGTGTTGTTACTGAT
1 TACTTGGTGTTGTTACTGAT
691064 TACTTGGT-TTG-TACTGAT
1 TACTTGGTGTTGTTACTGAT
691082 CTATCCCCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 3 0.17
20 8 0.44
ACGTcount: A:0.16, C:0.11, G:0.24, T:0.50
Consensus pattern (20 bp):
TACTTGGTGTTGTTACTGAT
Found at i:692622 original size:52 final size:54
Alignment explanation
Indices: 692566--692876 Score: 369
Period size: 52 Copynumber: 6.0 Consensus size: 54
692556 TTCGTGCTTC
* *
692566 GCACACCTAGTGCCG-AAC-GTTATTCATCCTCATAGGATGAATTCCGTGAAAT
1 GCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAAT
* ** * *
692618 GCACACTTA--GCCG-AATGG-TATTCATCCTTAAAGGATGAGTTCCGTGAAAT
1 GCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAAT
* * *
692668 ACACACTTAGTGTCGAAACGGTTA-TCCT-CACATAGGATGAATTCCGTGAAAT
1 GCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAAT
* *
692720 GCACACTTTGTACCGAAACGGTTATTC-TCCACATAGGATGAATTCCGTGAAAT
1 GCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAAT
*
692773 GC-CACTTAGTGCCGAAAC-GTTATTCATCCACATAGGATGAATTCCTTGAAAT
1 GCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAAT
** * * *
692825 ATACACTTAGTGTCAAAACGGTTATTCATCTACATAGGATG-A-TCCGTGAAAT
1 GCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAAT
692877 ACAGATTTAG
Statistics
Matches: 223, Mismatches: 26, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
50 43 0.19
51 8 0.04
52 100 0.45
53 50 0.22
54 22 0.10
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (54 bp):
GCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAAT
Found at i:692812 original size:105 final size:106
Alignment explanation
Indices: 692567--692879 Score: 376
Period size: 105 Copynumber: 3.0 Consensus size: 106
692557 TCGTGCTTCG
* *
692567 CACACCTAGTGCCG-AACGTTATTCATCCTCATAGGATGAATTCCGTGAAATGCACACTTAG-CC
1 CACACTTAGTGCCGAAACGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTCC
* ** * *
692630 G-AATGG-TATTCATCCTTAAAGGATGAGTTCCGTGAAATA
66 GAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATA
* * *
692669 CACACTTAGTGTCGAAACGGTTA-TCCT-CACATAGGATGAATTCCGTGAAATGCACACTTTGTA
1 CACACTTAGTGCCGAAAC-GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGT-
*
692732 CCGAAACGGTTATTC-TCCACATAGGATGAATTCCGTGAAATG
64 CCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATA
* ** *
692774 C-CACTTAGTGCCGAAACGTTATTCATCCACATAGGATGAATTCCTTGAAATATACACTTAGTGT
1 CACACTTAGTGCCGAAACGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGT-C
* *
692838 CAAAACGGTTATTCATCTACATAGGATG-A-TCCGTGAAATA
65 CGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATA
692878 CA
1 CA
692880 GATTTAGTTC
Statistics
Matches: 179, Mismatches: 22, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
102 44 0.25
103 10 0.06
104 36 0.20
105 72 0.40
106 17 0.09
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.28
Consensus pattern (106 bp):
CACACTTAGTGCCGAAACGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTCC
GAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATA
Found at i:692835 original size:157 final size:156
Alignment explanation
Indices: 692584--692876 Score: 414
Period size: 157 Copynumber: 1.9 Consensus size: 156
692574 AGTGCCGAAC
* * **
692584 GTTATTCATCCTCATAGGATGAATTCCGTGAAATGCACACTTAGCCGAATGGTATTCATCCTTAA
1 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGCCGAACGGTATTCATCCACAA
* * *
692649 AGGATGAGTTCCGTGAAATACACACTTAGTGTCGAAACGGTTA-TCCTC-ACATAGGATGAATTC
66 AGGATGAATTCCGTGAAATACACACTTAGTGTCAAAACGGTTATTCATCTACATAGGATG-A-TC
692712 CGTGAAATGCACACTTTGTACCGAAACG
129 CGTGAAATGCACACTTTGTACCGAAACG
*
692740 GTTATTC-TCCACATAGGATGAATTCCGTGAAATGC-CACTTAGTGCCGAAACGTTATTCATCCA
1 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTA--GCCG-AACGGTATTCATCCA
* * *
692803 CATAGGATGAATTCCTTGAAATATACACTTAGTGTCAAAACGGTTATTCATCTACATAGGATGAT
63 CAAAGGATGAATTCCGTGAAATACACACTTAGTGTCAAAACGGTTATTCATCTACATAGGATGAT
692868 CCGTGAAAT
128 CCGTGAAAT
692877 ACAGATTTAG
Statistics
Matches: 121, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
154 6 0.05
155 27 0.22
156 11 0.09
157 62 0.51
158 5 0.04
159 10 0.08
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.29
Consensus pattern (156 bp):
GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGCCGAACGGTATTCATCCACAA
AGGATGAATTCCGTGAAATACACACTTAGTGTCAAAACGGTTATTCATCTACATAGGATGATCCG
TGAAATGCACACTTTGTACCGAAACG
Found at i:699256 original size:54 final size:54
Alignment explanation
Indices: 699198--699550 Score: 456
Period size: 54 Copynumber: 6.6 Consensus size: 54
699188 TAAACAAATT
*** * * *
699198 ATGAATTCCGTGCTTTACACACCTAGTGCCAAAACGGTTATTCATCCTCATAGG
1 ATGAATTCCGTGAAATACACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
* ** **
699252 ATGAATTTCGTGAAATACACACTTAGTGCCGAAATAGTTATTCATCCTTATAGG
1 ATGAATTCCGTGAAATACACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
* * **
699306 ATGAATTCCGTGAAATGCACATTTAGTGCCGAAACGGTTATTCATCCTTATAGG
1 ATGAATTCCGTGAAATACACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
* * *
699360 ATGAATTCCGTGAAATGCACACTTAGTGTCGAAA-TGTTATTCATCCACATAGG
1 ATGAATTCCGTGAAATACACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
** * * *
699413 ATGAATTCAATGAAATACATACTTAGTGCTGAAACGGTTATTCACCCACATAGG
1 ATGAATTCCGTGAAATACACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
* * *
699467 ATGAATTCCGTGAAATACATACTTAGTGCCAAAATGGTTATTCATCCACATAGG
1 ATGAATTCCGTGAAATACACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
*
699521 ATGAATTCCGTGAAATACACATTTAGTGCC
1 ATGAATTCCGTGAAATACACACTTAGTGCC
699551 TATTAGGTAA
Statistics
Matches: 263, Mismatches: 35, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
53 44 0.17
54 219 0.83
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Consensus pattern (54 bp):
ATGAATTCCGTGAAATACACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
Found at i:699429 original size:161 final size:161
Alignment explanation
Indices: 699198--699548 Score: 452
Period size: 161 Copynumber: 2.2 Consensus size: 161
699188 TAAACAAATT
*** * * * * * *
699198 ATGAATTCCGTGCTTTACACACCTAGTGCCAAAACGGTTATTCATCCTCATAGGATGAATTTCGT
1 ATGAATTCCGTGAAATACACACTTAGTGTCGAAA-TGTTATTCATCCACATAGGATGAATTTCAT
* * ** * *
699263 GAAATACACACTTAGTGCCGAAATAGTTATTCATCCTTATAGGATGAATTCCGTGAAATGCACAT
65 GAAATACACACTTAGTGCCGAAACAGTTATTCACCCACATAGGATGAATTCCGTGAAATACACAC
* **
699328 TTAGTGCCGAAACGGTTATTCATCCTTATAGG
130 TTAGTGCCAAAACGGTTATTCATCCACATAGG
*
699360 ATGAATTCCGTGAAATGCACACTTAGTGTCGAAATGTTATTCATCCACATAGGATGAA-TTCAAT
1 ATGAATTCCGTGAAATACACACTTAGTGTCGAAATGTTATTCATCCACATAGGATGAATTTC-AT
* * * *
699424 GAAATACATACTTAGTGCTGAAACGGTTATTCACCCACATAGGATGAATTCCGTGAAATACATAC
65 GAAATACACACTTAGTGCCGAAACAGTTATTCACCCACATAGGATGAATTCCGTGAAATACACAC
*
699489 TTAGTGCCAAAATGGTTATTCATCCACATAGG
130 TTAGTGCCAAAACGGTTATTCATCCACATAGG
*
699521 ATGAATTCCGTGAAATACACATTTAGTG
1 ATGAATTCCGTGAAATACACACTTAGTG
699549 CCTATTAGGT
Statistics
Matches: 162, Mismatches: 26, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
160 3 0.02
161 132 0.81
162 27 0.17
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (161 bp):
ATGAATTCCGTGAAATACACACTTAGTGTCGAAATGTTATTCATCCACATAGGATGAATTTCATG
AAATACACACTTAGTGCCGAAACAGTTATTCACCCACATAGGATGAATTCCGTGAAATACACACT
TAGTGCCAAAACGGTTATTCATCCACATAGG
Found at i:699900 original size:20 final size:20
Alignment explanation
Indices: 699875--699926 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
699865 CCCTTCAGTG
*
699875 TCGATACCTCTACCATGGTA
1 TCGATACCCCTACCATGGTA
**
699895 TCGATACTACCCTATTATGGTA
1 TCGATAC--CCCTACCATGGTA
699917 TCGATACCCC
1 TCGATACCCC
699927 CTTCTGACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 10 0.37
22 17 0.63
ACGTcount: A:0.25, C:0.31, G:0.13, T:0.31
Consensus pattern (20 bp):
TCGATACCCCTACCATGGTA
Found at i:700124 original size:21 final size:21
Alignment explanation
Indices: 700082--700138 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
700072 CCTCACCATG
*
700082 GTATCGATAC-AATCT-CATCA
1 GTATCGATACTAAT-TGAATCA
* *
700102 GTATGGATACTGATTGAATCA
1 GTATCGATACTAATTGAATCA
700123 GTATCGATACTAATTG
1 GTATCGATACTAATTG
700139 TATAATTCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 10 0.33
21 20 0.67
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (21 bp):
GTATCGATACTAATTGAATCA
Found at i:701177 original size:64 final size:62
Alignment explanation
Indices: 701109--701287 Score: 188
Period size: 64 Copynumber: 2.8 Consensus size: 62
701099 TTGAACCCTT
*
701109 AGTGCATCGGTGCACTAAGAGTGCATCGATGCATGAAATGCATTCGATGTTTCA-AAATAGC-CA
1 AGTGCATCGATGCACT-AGAGTGCATCGATGCATGAAATGCATT-GATGTTTCATAAA-A-CTCA
701172 G
62 G
*
701173 AGTGCATCGATGCATGGCT-G-GTGCATCGATGCATCAAATGCATTTGATGTTTTCATAAAACTC
1 AGTGCATCGATGCA---CTAGAGTGCATCGATGCATGAAATGCA-TTGATG-TTTCATAAAACTC
*
701236 TG
61 AG
*
701238 AGTGTATCGATGCA-TAGTATGTGCATCGATGCATGAAATGCATTGATGTT
1 AGTGCATCGATGCACTAG-A-GTGCATCGATGCATGAAATGCATTGATGTT
701288 CAATTTATTC
Statistics
Matches: 99, Mismatches: 5, Indels: 23
0.78 0.04 0.18
Matches are distributed among these distances:
61 1 0.01
62 1 0.01
63 2 0.02
64 45 0.45
65 45 0.45
66 3 0.03
67 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (62 bp):
AGTGCATCGATGCACTAGAGTGCATCGATGCATGAAATGCATTGATGTTTCATAAAACTCAG
Found at i:701262 original size:65 final size:65
Alignment explanation
Indices: 701129--701287 Score: 202
Period size: 65 Copynumber: 2.5 Consensus size: 65
701119 TGCACTAAGA
* *
701129 GTGCATCGATGCATGAAATGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGAAATGCATTTGATGTTTTCAAAATAGCCAGAGTGCATCGATGCATAGCTG
* * *
701193 GTGCATCGATGCATCAAATGCATTTGATGTTTTCATAAA-A-CTCTGAGTGTATCGATGCATAG-
1 GTGCATCGATGCATGAAATGCATTTGATGTTTTCA-AAATAGC-CAGAGTGCATCGATGCATAGC
*
701255 TAT
64 T-G
701258 GTGCATCGATGCATGAAATGCA-TTGATGTT
1 GTGCATCGATGCATGAAATGCATTTGATGTT
701288 CAATTTATTC
Statistics
Matches: 84, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
64 37 0.44
65 44 0.52
66 3 0.04
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTTGATGTTTTCAAAATAGCCAGAGTGCATCGATGCATAGCTG
Found at i:701856 original size:13 final size:13
Alignment explanation
Indices: 701838--701862 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
701828 TGCCATTAGT
701838 TTCATAATCAATA
1 TTCATAATCAATA
701851 TTCATAATCAAT
1 TTCATAATCAAT
701863 TGTGAAATGG
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:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (13 bp):
TTCATAATCAATA
Found at i:702388 original size:21 final size:21
Alignment explanation
Indices: 702364--702407 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
702354 GTGCCGGAGG
* *
702364 AGGAGGAGCACGAGAAGAGCT
1 AGGAGCAGCACGAGAAGAACT
* *
702385 AGGAGCAGCTCGTGAAGAACT
1 AGGAGCAGCACGAGAAGAACT
702406 AG
1 AG
702408 CTCCTGGGGT
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:0.36, C:0.16, G:0.39, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAACT
Found at i:709315 original size:44 final size:44
Alignment explanation
Indices: 709248--709337 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
709238 GTCCGCTACC
709248 TTAGCTATCCACACTAAGAATTTTCCAACAAATTCACTAATTTG
1 TTAGCTATCCACACTAAGAATTTTCCAACAAATTCACTAATTTG
*
709292 TTAGCTATCCACACTAAGGATTTTCCAACAAATTCACTAATTTG
1 TTAGCTATCCACACTAAGAATTTTCCAACAAATTCACTAATTTG
709336 TT
1 TT
709338 CTTTCTTTTG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (44 bp):
TTAGCTATCCACACTAAGAATTTTCCAACAAATTCACTAATTTG
Found at i:709798 original size:21 final size:19
Alignment explanation
Indices: 709771--709825 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
709761 TTGGAGCATC
709771 AGTGCATCGATGCATACCCAAG
1 AGTGCATCGATGCAT---CAAG
*
709793 -GTGCATCGGTGCATCAAG
1 AGTGCATCGATGCATCAAG
709811 AGTGCATCGATGCAT
1 AGTGCATCGATGCAT
709826 GAAATGCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 4 0.13
19 13 0.43
21 13 0.43
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (19 bp):
AGTGCATCGATGCATCAAG
Found at i:709903 original size:64 final size:62
Alignment explanation
Indices: 709812--710015 Score: 216
Period size: 65 Copynumber: 3.2 Consensus size: 62
709802 TGCATCAAGA
*
709812 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATAGCCAGAGTGAATCGATGCATGGCTG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATA-CCAGAGTGCATCGATGCATGG-TG
* * *
709876 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ACTCTGAGTGCATCGATGCATAGTA
1 GTGCATCGATGCATGAAATGCATTCGATG-TTTCA-AAATAC-CAGAGTGCATCGATGCATGGT-
*
709940 T
62 G
* * *
709941 GTGCATCGATACATGAAATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAA--AATACCA-GAGTGCATCGATGCATGG--
710004 TG
61 TG
710006 GTGCATCGAT
1 GTGCATCGAT
710016 CCATTACATT
Statistics
Matches: 118, Mismatches: 12, Indels: 19
0.79 0.08 0.13
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 47 0.40
65 62 0.53
66 4 0.03
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.31
Consensus pattern (62 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATACCAGAGTGCATCGATGCATGGTG
Found at i:710830 original size:55 final size:53
Alignment explanation
Indices: 710741--710961 Score: 311
Period size: 53 Copynumber: 4.1 Consensus size: 53
710731 TCCTTATATT
*
710741 TGCACACAAAATGCTGTACGGTGATTCATCAACCCATGATGAATTATGTGAATA
1 TGCACACAAAGTGCTGTACGGTGATTCATCAACCCATGATGAATT-TGTGAATA
* *
710795 TGCACACAAAGTGCTTGTACGGTGATTGATTAACCCATGATGAATTTGTGAATA
1 TGCACACAAAGTGC-TGTACGGTGATTCATCAACCCATGATGAATTTGTGAATA
* * * **
710849 TGCACACGAA-TTCTTGTACAGTGATTCATCAACCCATGATGAATTCATGAATA
1 TGCACACAAAGTGC-TGTACGGTGATTCATCAACCCATGATGAATTTGTGAATA
*
710902 TGCACACAGAGTGCTGTACGGTGATTCATCAA-CCATGATGAATTTCGTGAATA
1 TGCACACAAAGTGCTGTACGGTGATTCATCAACCCATGATGAATTT-GTGAATA
710955 TGCACAC
1 TGCACAC
710962 TAAATGCCTG
Statistics
Matches: 148, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
52 12 0.08
53 75 0.51
54 32 0.22
55 29 0.20
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (53 bp):
TGCACACAAAGTGCTGTACGGTGATTCATCAACCCATGATGAATTTGTGAATA
Found at i:712041 original size:55 final size:55
Alignment explanation
Indices: 711753--712046 Score: 374
Period size: 55 Copynumber: 5.3 Consensus size: 55
711743 TTATGTGGGT
* * * * *
711753 TGCACACATAGTGTCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGGAT-
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACCCATGATGAATTCCGTGAATA
* * **
711807 TCGCACACAAAGTTCCTGTACGGTGATTCATTAACCCATGATGAATTATGTGAATA
1 T-GCACACAAAGTGCCTGTACGGTGATTCATCAACCCATGATGAATTCCGTGAATA
** *
711863 TGCACACAAAGTGTTTGTACGGTGATTCATCAACCCATGATGAATTTCGTGAATA
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACCCATGATGAATTCCGTGAATA
* *
711918 TGCACACGAAGTGCCTGTACGGTGATTCATCAACCCATGATGAATCCCGTGAATA
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACCCATGATGAATTCCGTGAATA
** ** *
711973 TAAACACGGAGTGCCTGTACGGTGATTCATTAACCCATGATGAATTCCGTGAATA
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACCCATGATGAATTCCGTGAATA
* * *
712028 TGTACACTAAGTGCATGTA
1 TGCACACAAAGTGCCTGTA
712047 GTACACATAG
Statistics
Matches: 209, Mismatches: 29, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
54 1 0.00
55 207 0.99
56 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (55 bp):
TGCACACAAAGTGCCTGTACGGTGATTCATCAACCCATGATGAATTCCGTGAATA
Found at i:712513 original size:18 final size:18
Alignment explanation
Indices: 712492--712527 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
712482 GTATCGATAC
712492 CAAAATTAGATTCGATGT
1 CAAAATTAGATTCGATGT
712510 CAAAATTAGATTCGATGT
1 CAAAATTAGATTCGATGT
712528 TGCTTGGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (18 bp):
CAAAATTAGATTCGATGT
Found at i:716649 original size:16 final size:16
Alignment explanation
Indices: 716611--716659 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
716601 TGTGAAATAA
716611 TATAT-AATAAATGTC
1 TATATGAATAAATGTC
*
716626 TATGTGAA-AAATGATC
1 TATATGAATAAATG-TC
716642 TATATGAATAAATGTC
1 TATATGAATAAATGTC
716658 TA
1 TA
716660 CGTGATATGC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 9 0.31
16 15 0.52
17 5 0.17
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37
Consensus pattern (16 bp):
TATATGAATAAATGTC
Found at i:716817 original size:23 final size:23
Alignment explanation
Indices: 716752--716817 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
716742 GAGTCGAGGG
* *
716752 TTCTACGCGGTCCTTTAGGACAA
1 TTCTACGCGGTCTTTTGGGACAA
* * *
716775 TTCTACGTGGT-TCTTCGGGACAT
1 TTCTACGCGGTCT-TTTGGGACAA
716798 TTCTACGCGGTCTTTTGGGA
1 TTCTACGCGGTCTTTTGGGA
716818 TATCTATATG
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
23 33 0.97
24 1 0.03
ACGTcount: A:0.15, C:0.23, G:0.26, T:0.36
Consensus pattern (23 bp):
TTCTACGCGGTCTTTTGGGACAA
Found at i:716858 original size:22 final size:21
Alignment explanation
Indices: 716806--716846 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
716796 ATTTCTACGC
*
716806 GGTCTTTTGGGATATCTATAT
1 GGTCATTTGGGATATCTATAT
*
716827 GGTTATTTGGGATATTCTAT
1 GGTCATTTGGGATA-TCTAT
716847 GTGGCACTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.20, C:0.07, G:0.24, T:0.49
Consensus pattern (21 bp):
GGTCATTTGGGATATCTATAT
Found at i:728840 original size:31 final size:31
Alignment explanation
Indices: 728797--728881 Score: 100
Period size: 31 Copynumber: 2.8 Consensus size: 31
728787 GGGCCTGAGA
* * **
728797 GCCTA-CCAAGAAAGTTCTCGGGGCCACGGG
1 GCCTACCCAAGAAAGATCTCAGGGCCACAAG
* * *
728827 GCCTACCCAAGAAAAATCTCAGTGCTACAAG
1 GCCTACCCAAGAAAGATCTCAGGGCCACAAG
728858 GCCTACCCAAGAAAGATCTCAGGG
1 GCCTACCCAAGAAAGATCTCAGGG
728882 TCGTATAGCC
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 5 0.11
31 40 0.89
ACGTcount: A:0.32, C:0.29, G:0.25, T:0.14
Consensus pattern (31 bp):
GCCTACCCAAGAAAGATCTCAGGGCCACAAG
Found at i:730425 original size:13 final size:13
Alignment explanation
Indices: 730407--730441 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
730397 CAGGTCGGGT
730407 CGGGTCGGGCAGG
1 CGGGTCGGGCAGG
730420 CGGGTCGGGCAGG
1 CGGGTCGGGCAGG
*
730433 CAGGTCGGG
1 CGGGTCGGG
730442 TCGACCCTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.09, C:0.23, G:0.60, T:0.09
Consensus pattern (13 bp):
CGGGTCGGGCAGG
Found at i:730425 original size:18 final size:18
Alignment explanation
Indices: 730397--730444 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
730387 TGGACTAGGT
*
730397 CAGGTCGGGTCGGGTCGGG
1 CAGGTCGGGTCGGG-CAGG
730416 CAGG-CGGGTCGGGCAGG
1 CAGGTCGGGTCGGGCAGG
730433 CAGGTCGGGTCG
1 CAGGTCGGGTCG
730445 ACCCTGTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 7 0.26
18 16 0.59
19 4 0.15
ACGTcount: A:0.08, C:0.23, G:0.56, T:0.12
Consensus pattern (18 bp):
CAGGTCGGGTCGGGCAGG
Found at i:733834 original size:250 final size:250
Alignment explanation
Indices: 733393--733893 Score: 984
Period size: 250 Copynumber: 2.0 Consensus size: 250
733383 AAACTCAGAC
733393 TCAGTCGTCGTTCGTTGGTTGATGTTGGCACTCTCTTGTTGGCTGTCGTCATTAGGCTGGGCTTG
1 TCAGTCGTCGTTCGTTGGTTGATGTTGGCACTCTCTTGTTGGCTGTCGTCATTAGGCTGGGCTTG
*
733458 TTTTGGCAAGGGAGAACCGATGGTCGTCGTGGTTGTTGTTGTCGAGATAGAGAACCAATGATGAT
66 TTTTGGCAAGGGAGAACCGATGGTCGTCGTGGTTGTTGTTGTCGAGAGAGAGAACCAATGATGAT
733523 CTGCATGCTGGTGAGCTTGCGTGGTTGGGCAGGGCTGAAATCGAGACTAGGATAGGTGCTTGATA
131 CTGCATGCTGGTGAGCTTGCGTGGTTGGGCAGGGCTGAAATCGAGACTAGGATAGGTGCTTGATA
733588 AATGTTGGACCAGTCGATTCATGGTTTTGAGGTCTTGAGATTTCTTAAGGATTAT
196 AATGTTGGACCAGTCGATTCATGGTTTTGAGGTCTTGAGATTTCTTAAGGATTAT
*
733643 TCAGTCGTCGTTCGTTGGTTGATGTTGGTACTCTCTTGTTGGCTGTCGTCATTAGGCTGGGCTTG
1 TCAGTCGTCGTTCGTTGGTTGATGTTGGCACTCTCTTGTTGGCTGTCGTCATTAGGCTGGGCTTG
733708 TTTTGGCAAGGGAGAACCGATGGTCGTCGTGGTTGTTGTTGTCGAGAGAGAGAACCAATGATGAT
66 TTTTGGCAAGGGAGAACCGATGGTCGTCGTGGTTGTTGTTGTCGAGAGAGAGAACCAATGATGAT
733773 CTGCATGCTGGTGAGCTTGCGTGGTTGGGCAGGGCTGAAATCGAGACTAGGATAGGTGCTTGATA
131 CTGCATGCTGGTGAGCTTGCGTGGTTGGGCAGGGCTGAAATCGAGACTAGGATAGGTGCTTGATA
733838 AATGTTGGACCAGTCGATTCATGGTTTTGAGGTCTTGAGATTTCTTAAGGATTAT
196 AATGTTGGACCAGTCGATTCATGGTTTTGAGGTCTTGAGATTTCTTAAGGATTAT
733893 T
1 T
733894 TACTGCATTC
Statistics
Matches: 249, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
250 249 1.00
ACGTcount: A:0.19, C:0.15, G:0.33, T:0.34
Consensus pattern (250 bp):
TCAGTCGTCGTTCGTTGGTTGATGTTGGCACTCTCTTGTTGGCTGTCGTCATTAGGCTGGGCTTG
TTTTGGCAAGGGAGAACCGATGGTCGTCGTGGTTGTTGTTGTCGAGAGAGAGAACCAATGATGAT
CTGCATGCTGGTGAGCTTGCGTGGTTGGGCAGGGCTGAAATCGAGACTAGGATAGGTGCTTGATA
AATGTTGGACCAGTCGATTCATGGTTTTGAGGTCTTGAGATTTCTTAAGGATTAT
Found at i:736080 original size:21 final size:21
Alignment explanation
Indices: 736046--736085 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
736036 GAACCGTCAC
* *
736046 ATTAACATTATTAATTATCAT
1 ATTAACATCATTAACTATCAT
*
736067 ATTAACATCGTTAACTATC
1 ATTAACATCATTAACTATC
736086 GTATCAATAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.42
Consensus pattern (21 bp):
ATTAACATCATTAACTATCAT
Found at i:739186 original size:73 final size:74
Alignment explanation
Indices: 739067--739213 Score: 287
Period size: 73 Copynumber: 2.0 Consensus size: 74
739057 TTTAATTTTG
739067 CAAAGAAAGCAAGTTAGTAAGTTATACATTTTTTGATCAGGTTACGAACTACTTCCTCGAACG-T
1 CAAAGAAAGCAAGTTAGTAAGTTATACATTTTTTGATCAGGTTACGAACTACTTCCTCGAACGTT
739131 TGAATCAAT
66 TGAATCAAT
739140 CAAAGAAAGCAAGTTAGTAAGTTATACATTTTTTGATCAGGTTACGAACTACTTCCTCGAACGTT
1 CAAAGAAAGCAAGTTAGTAAGTTATACATTTTTTGATCAGGTTACGAACTACTTCCTCGAACGTT
739205 TGAATCAAT
66 TGAATCAAT
739214 GCTTCAAGAT
Statistics
Matches: 73, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 63 0.86
74 10 0.14
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (74 bp):
CAAAGAAAGCAAGTTAGTAAGTTATACATTTTTTGATCAGGTTACGAACTACTTCCTCGAACGTT
TGAATCAAT
Found at i:740368 original size:20 final size:20
Alignment explanation
Indices: 740331--740369 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
740321 AATTACAATT
**
740331 AAATAAAATAAAGTAAATAC
1 AAATAAAATAAAAAAAATAC
*
740351 AAATATAATAAAAAAAATA
1 AAATAAAATAAAAAAAATA
740370 TATCGATGCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (20 bp):
AAATAAAATAAAAAAAATAC
Found at i:740889 original size:18 final size:18
Alignment explanation
Indices: 740863--740902 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
740853 AAAGGCGATG
740863 GCGGAATCAAATATGGCT
1 GCGGAATCAAATATGGCT
* *
740881 GCGGCATCATATATGGCT
1 GCGGAATCAAATATGGCT
740899 GCGG
1 GCGG
740903 TGGCTGCTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.25, C:0.20, G:0.33, T:0.23
Consensus pattern (18 bp):
GCGGAATCAAATATGGCT
Found at i:742841 original size:50 final size:49
Alignment explanation
Indices: 742787--742905 Score: 114
Period size: 50 Copynumber: 2.4 Consensus size: 49
742777 AAATACCCAG
* * * * *
742787 GTATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGGCGTCAGATCACC
1 GTATAGCGC-GATCAGGGGACGCGCTATACCCACGTGACGCCAAATCAAC
*** *
742837 GTATATTGAAAGA-CAGGGGACGCGTTATACCCACGTGACGCCAAATCAAC
1 GTATA--GCGCGATCAGGGGACGCGCTATACCCACGTGACGCCAAATCAAC
742887 GTATAGCGCGATTCAGGGG
1 GTATAGCGCGA-TCAGGGG
742906 TACACTTTAC
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
48 3 0.06
50 47 0.89
51 2 0.04
52 1 0.02
ACGTcount: A:0.26, C:0.25, G:0.31, T:0.18
Consensus pattern (49 bp):
GTATAGCGCGATCAGGGGACGCGCTATACCCACGTGACGCCAAATCAAC
Found at i:744895 original size:32 final size:32
Alignment explanation
Indices: 744842--744921 Score: 126
Period size: 32 Copynumber: 2.5 Consensus size: 32
744832 TTAATGGTGA
* *
744842 TGTTGATGTGACATT-TTTAATTATTTTTCAG
1 TGTTGATTTGATATTATTTAATTATTTTTCAG
744873 TGTTGATTTGATATTATTTAATTATTTTTCAG
1 TGTTGATTTGATATTATTTAATTATTTTTCAG
*
744905 TGTCGATTTGATATTAT
1 TGTTGATTTGATATTAT
744922 CTTATGAAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
31 13 0.29
32 32 0.71
ACGTcount: A:0.24, C:0.05, G:0.15, T:0.56
Consensus pattern (32 bp):
TGTTGATTTGATATTATTTAATTATTTTTCAG
Found at i:753042 original size:21 final size:21
Alignment explanation
Indices: 753016--753135 Score: 127
Period size: 21 Copynumber: 5.6 Consensus size: 21
753006 TCCTTAAGGA
*
753016 GTGGTCCTTCGGGACATATAT
1 GTGGTCCTTCAGGACATATAT
* *
753037 GTGGTCCTTCAGTACAAAATTCTAT
1 GTGGTCCTTCAGGAC---A-TATAT
* *
753062 GTTGTCCTTCAGGACATCTAT
1 GTGGTCCTTCAGGACATATAT
753083 GTGGTCCTTCAGGACAT-TAT
1 GTGGTCCTTCAGGACATATAT
*
753103 GTGGTCCTTC-GAGATATATAT
1 GTGGTCCTTCAG-GACATATAT
753124 GTGGTCCTTCAG
1 GTGGTCCTTCAG
753136 TACAAAATTC
Statistics
Matches: 85, Mismatches: 7, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
19 1 0.01
20 17 0.20
21 47 0.55
22 2 0.02
24 1 0.01
25 17 0.20
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (21 bp):
GTGGTCCTTCAGGACATATAT
Found at i:753086 original size:46 final size:45
Alignment explanation
Indices: 753016--753151 Score: 174
Period size: 46 Copynumber: 3.1 Consensus size: 45
753006 TCCTTAAGGA
753016 GTGGTCCTTCGGGACATATATGTGGTCCTTCAGTACAAAATTCTAT
1 GTGGTCCTTC-GGACATATATGTGGTCCTTCAGTACAAAATTCTAT
* * *
753062 GTTGTCCTTCAGGACATCTATGTGGTCCTTCAGGAC---A-T-TAT
1 GTGGTCCTTC-GGACATATATGTGGTCCTTCAGTACAAAATTCTAT
*
753103 GTGGTCCTTCGAGATATATATGTGGTCCTTCAGTACAAAATTCTAT
1 GTGGTCCTTCG-GACATATATGTGGTCCTTCAGTACAAAATTCTAT
753149 GTG
1 GTG
753152 CCCATAGTGG
Statistics
Matches: 76, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
40 1 0.01
41 33 0.43
42 1 0.01
43 1 0.01
44 1 0.01
45 1 0.01
46 38 0.50
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (45 bp):
GTGGTCCTTCGGACATATATGTGGTCCTTCAGTACAAAATTCTAT
Found at i:755662 original size:17 final size:16
Alignment explanation
Indices: 755631--755664 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
755621 CACGTGAGGA
755631 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
755647 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
755664 T
1 T
755665 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:758959 original size:21 final size:19
Alignment explanation
Indices: 758921--758966 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
758911 AATTAATCCT
758921 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
758941 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
758962 A-TAAT
1 ACTAAT
758967 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:768693 original size:21 final size:19
Alignment explanation
Indices: 768655--768700 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
768645 AATTAATCCT
768655 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
768675 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
768696 A-TAAT
1 ACTAAT
768701 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:781939 original size:36 final size:36
Alignment explanation
Indices: 781868--781939 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
781858 AATTGAAGAA
*
781868 AAGCAAATCATCTTAAGCCTTCACAAAAGAGTAGTG
1 AAGCAAATCATCTTAAGCCTTCACAAAAGAATAGTG
**
781904 AAGCAAATCATCTTAAGCCTTCACGGAAGAATAGTG
1 AAGCAAATCATCTTAAGCCTTCACAAAAGAATAGTG
781940 GAGCGAACCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.22
Consensus pattern (36 bp):
AAGCAAATCATCTTAAGCCTTCACAAAAGAATAGTG
Found at i:782031 original size:22 final size:22
Alignment explanation
Indices: 781989--782034 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
781979 TCCCTGAAGT
*
781989 AGGAGGGAGTGAACCTGTTGGC
1 AGGAGGGAGTGAACCTATTGGC
782011 AGGAGGGAGTGAACGC-ATTGGC
1 AGGAGGGAGTGAAC-CTATTGGC
782033 AG
1 AG
782035 AAGAATGTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.26, C:0.13, G:0.46, T:0.15
Consensus pattern (22 bp):
AGGAGGGAGTGAACCTATTGGC
Found at i:782099 original size:55 final size:55
Alignment explanation
Indices: 782013--782409 Score: 386
Period size: 55 Copynumber: 7.2 Consensus size: 55
782003 CTGTTGGCAG
* * * *
782013 GAGGGAGTGAACGCATTGGCAGAAGAATGTTCGAGTTCTATACTCCCTGAAACAA
1 GAGGGAGCGAACCCGTTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAACAA
* *
782068 GAGGGAGCGAACTCGTTGGCAGAAGATTGTTCGAGTTCTATACTCCCT-AAGGCAA
1 GAGGGAGCGAACCCGTTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAA-ACAA
* * ** * * ***
782123 GAGGGAACAAACCCGTTCACAGAAGATTGTTCGACTTCTATAATCCCTGACGTAA
1 GAGGGAGCGAACCCGTTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAACAA
** *** * *
782178 GAGGGAATGAACCCGTTTAAAGAAGATTGTTCGAGTTCAATACTCCCTGAAACAG
1 GAGGGAGCGAACCCGTTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAACAA
* * *
782233 GAAGGAGCGAACCCGTTGGTAGAAGATTGTTCGAGTTCTATACTCCCTGAAGATAA
1 GAGGGAGCGAACCCGTTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAA-ACAA
* * * * * * *
782289 -AGAGAGCAAACTCGTTGGCAGAAGAATGTTTGAGTTCCATACTCCCTAAAACAA
1 GAGGGAGCGAACCCGTTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAACAA
* * * * * *
782343 GAGGGAGAGAACCCGTTGGTAGCAGATTGTTCGA-TTCCAATAGTCCCTGAAGCAA
1 GAGGGAGCGAACCCGTTGGCAGAAGATTGTTCGAGTT-CTATACTCCCTGAAACAA
* *
782398 AAGGAAGCGAAC
1 GAGGGAGCGAAC
782410 TCGCTAGTCG
Statistics
Matches: 278, Mismatches: 59, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
54 7 0.03
55 268 0.96
56 3 0.01
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.22
Consensus pattern (55 bp):
GAGGGAGCGAACCCGTTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAACAA
Found at i:782313 original size:165 final size:164
Alignment explanation
Indices: 782033--782429 Score: 440
Period size: 165 Copynumber: 2.4 Consensus size: 164
782023 ACGCATTGGC
* * * *
782033 AGAAGAATGTTCGAGTTCTATACTCCCTGAAACAAGAGGGAGCGAACTCGTTGGCAGAAGATTGT
1 AGAAGATTGTTCGAGTTCAATACTCCCTGAAAC-AGAAGGAGCGAACTCGTTGGTAGAAGATTGT
* * * *
782098 TCGAGTTCTATACTCCCTAAGGCAAGAGGGAACAAACCCGTTCACAGAAGATTGTTCGACTTCTA
65 TCGAGTTCTATACTCCCTAAGACAAGAGAGAACAAACCCGTTCACAGAAGAATGTTCGACTTCCA
* *** *
782163 TAATCCCTGACGTAAGAGGGA-ATGAACCCGTTTAA
130 TAATCCCTAAAACAAGAGGGAGA-GAACCCGTTGAA
*
782198 AGAAGATTGTTCGAGTTCAATACTCCCTGAAACAGGAAGGAGCGAACCCGTTGGTAGAAGATTGT
1 AGAAGATTGTTCGAGTTCAATACTCCCTGAAACA-GAAGGAGCGAACTCGTTGGTAGAAGATTGT
* * * ** * *
782263 TCGAGTTCTATACTCCCTGAAGATAA-AGAGAGCAAACTCGTTGGCAGAAGAATGTTTGAGTTCC
65 TCGAGTTCTATACTCCCT-AAGACAAGAGAGAACAAACCCGTTCACAGAAGAATGTTCGACTTCC
* **
782327 ATACTCCCTAAAACAAGAGGGAGAGAACCCGTTGGT
129 ATAATCCCTAAAACAAGAGGGAGAGAACCCGTTGAA
* * * * * * *
782363 AGCAGATTGTTCGA-TTCCAATAGTCCCTGAAGCAAAAGGAAGCGAACTCGCTAGTCGAAGATTG
1 AGAAGATTGTTCGAGTT-CAATACTCCCTGAAACAGAAGG-AGCGAACTCGTTGGTAGAAGATTG
782427 TTC
64 TTC
782430 AAAGAAGAGA
Statistics
Matches: 195, Mismatches: 32, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
164 7 0.04
165 182 0.93
166 6 0.03
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.23
Consensus pattern (164 bp):
AGAAGATTGTTCGAGTTCAATACTCCCTGAAACAGAAGGAGCGAACTCGTTGGTAGAAGATTGTT
CGAGTTCTATACTCCCTAAGACAAGAGAGAACAAACCCGTTCACAGAAGAATGTTCGACTTCCAT
AATCCCTAAAACAAGAGGGAGAGAACCCGTTGAA
Found at i:796042 original size:3 final size:3
Alignment explanation
Indices: 796034--796065 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
796024 TCACTGCTTT
796034 GAA GAA GAA GAA GAA GAA GAA GAA G-A GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
796066 AATGTAGGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:800359 original size:22 final size:22
Alignment explanation
Indices: 800331--800410 Score: 110
Period size: 22 Copynumber: 3.7 Consensus size: 22
800321 GGTTACCTAT
800331 GTCCTTCGGGACATATGGATAG
1 GTCCTTCGGGACATATGGATAG
*
800353 GTCCTTCGGGATATATGGATAG
1 GTCCTTCGGGACATATGGATAG
* *
800375 GTCCTTCAGGACATA--GATGAC
1 GTCCTTCGGGACATATGGAT-AG
800396 GTCCTTCGGGACATA
1 GTCCTTCGGGACATA
800411 GATTTCACAT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 3 0.06
21 15 0.29
22 34 0.65
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.28
Consensus pattern (22 bp):
GTCCTTCGGGACATATGGATAG
Found at i:805838 original size:13 final size:13
Alignment explanation
Indices: 805820--805845 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
805810 GCTCAACCTA
805820 TATGTCTATAAAC
1 TATGTCTATAAAC
805833 TATGTCTATAAAC
1 TATGTCTATAAAC
805846 CCATATTTTA
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:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
TATGTCTATAAAC
Found at i:807279 original size:2 final size:2
Alignment explanation
Indices: 807272--807308 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
807262 TGCCTTTCAT
807272 TA TA TA TA 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 TA TA TA TA T
807309 TGTTTTTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:808784 original size:20 final size:20
Alignment explanation
Indices: 808759--808798 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
808749 CAACCACCCA
808759 GTATCACTCGAAATATTTGT
1 GTATCACTCGAAATATTTGT
808779 GTATCACTCGAAATATTTGT
1 GTATCACTCGAAATATTTGT
808799 ATAATATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
GTATCACTCGAAATATTTGT
Found at i:816488 original size:164 final size:159
Alignment explanation
Indices: 816178--816510 Score: 477
Period size: 164 Copynumber: 2.1 Consensus size: 159
816168 ATTCCTTAAT
* * * * * *
816178 AATATTATTTTATGTCTGCGAAGAACAAAAAAAATGGGTCCAGGAGCATAATTTGAGCACTTCCC
1 AATAGTATCTTATGTCTGAGAAGAACAAAAAAAATGGGTCCAGGAGCATAATTTAAGCACTACCA
* * *
816243 TAGAAGTGATACATTAATGACTCAGTAATAAGTACCCAAAAGTAAAAGCTTCACCAAATGTTAGA
66 TAGAAGTGATACATTAATGACTCAGCAATAAGTACCCAAAAATAAAAACTTCACCAAATGTTAGA
*
816308 CAACTTAATTTTGTAATGATACTAACTGA
131 CAACCTAATTTTGTAATGATACTAACTGA
* ** *
816337 AATTGTATCTTATGTCTGAGAAGAACATGAAAAATTGGTCCAGGAGCATAATTTAAGCACTACCA
1 AATAGTATCTTATGTCTGAGAAGAACAAAAAAAATGGGTCCAGGAGCATAATTTAAGCACTACCA
* *
816402 TAGAAGTGAAGTGATACATTAATGACTCAGCAGTAAGTATCCAAAAATAAAAACTTCACCAAATG
66 T---A--GAAGTGATACATTAATGACTCAGCAATAAGTACCCAAAAATAAAAACTTCACCAAATG
816467 TTAGACAACCTAATTTTGTAATGATACTAACTGA
126 TTAGACAACCTAATTTTGTAATGATACTAACTGA
816501 AATAGTATCT
1 AATAGTATCT
816511 AAGCAATTAG
Statistics
Matches: 152, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
159 56 0.37
162 1 0.01
164 95 0.62
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (159 bp):
AATAGTATCTTATGTCTGAGAAGAACAAAAAAAATGGGTCCAGGAGCATAATTTAAGCACTACCA
TAGAAGTGATACATTAATGACTCAGCAATAAGTACCCAAAAATAAAAACTTCACCAAATGTTAGA
CAACCTAATTTTGTAATGATACTAACTGA
Found at i:823472 original size:21 final size:21
Alignment explanation
Indices: 823448--823500 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
823438 GAATTTGTCG
*
823448 CGAAAGACCACATATATATCC
1 CGAAAGACCACATAGATATCC
*
823469 CG-AAGAACCACATAGATGTCC
1 CGAAAG-ACCACATAGATATCC
823490 C-AAATGACCAC
1 CGAAA-GACCAC
823501 TCCTTAAGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 3 0.11
21 23 0.85
22 1 0.04
ACGTcount: A:0.42, C:0.30, G:0.13, T:0.15
Consensus pattern (21 bp):
CGAAAGACCACATAGATATCC
Found at i:823787 original size:2 final size:2
Alignment explanation
Indices: 823780--823823 Score: 70
Period size: 2 Copynumber: 21.0 Consensus size: 2
823770 TGTCATTATC
823780 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT CAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT -AT AT AT
823824 TCTTGTATTC
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 36 0.90
3 4 0.10
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:828054 original size:26 final size:26
Alignment explanation
Indices: 828018--828101 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
828008 GCATGACACG
828018 GTCAGCGGAAGTTTCTAGAAGGTCCA
1 GTCAGCGGAAGTTTCTAGAAGGTCCA
828044 GTCAGCGGAAGTTTCTAGAAGGTCCA
1 GTCAGCGGAAGTTTCTAGAAGGTCCA
* *
828070 GTCAGCGGAAGTTTCTAGAAGATCTA
1 GTCAGCGGAAGTTTCTAGAAGGTCCA
828096 GTCAGC
1 GTCAGC
828102 ACACCTTCTG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (26 bp):
GTCAGCGGAAGTTTCTAGAAGGTCCA
Found at i:840415 original size:18 final size:17
Alignment explanation
Indices: 840394--840432 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
840384 ATCTCTCTAA
840394 CAAATGATATTGATTTTT
1 CAAATGAT-TTGATTTTT
*
840412 CAAATGCTTTGATTTTT
1 CAAATGATTTGATTTTT
840429 -AAAT
1 CAAAT
840433 TTTTTTTACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 9 0.45
18 7 0.35
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.49
Consensus pattern (17 bp):
CAAATGATTTGATTTTT
Found at i:842086 original size:22 final size:23
Alignment explanation
Indices: 842061--842103 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
842051 ATATAAAACT
842061 ATTATAAAATA-ATTAAATAATA
1 ATTATAAAATATATTAAATAATA
*
842083 ATTATAAGATATATTAAATAA
1 ATTATAAAATATATTAAATAA
842104 ATTTTCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
ATTATAAAATATATTAAATAATA
Found at i:843253 original size:2 final size:2
Alignment explanation
Indices: 843246--843274 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
843236 TTATTATAAC
843246 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
843275 CATTAAACAA
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:846183 original size:51 final size:51
Alignment explanation
Indices: 846128--846232 Score: 124
Period size: 51 Copynumber: 2.1 Consensus size: 51
846118 ACCTTTTGCA
* * * *
846128 GTAAGGCGCGCC-CCTTGCAGCGCGCTT-TACGCTGATCTAGCGCCACGTGGG
1 GTAAGGCGCACCTCC-TACAGCGCG-TTCTACGCTGATATAGCGCCACGTGAG
* *
846179 GTAAGGCGCACCTCCTACAGTGCGTTCTACGCTGATATGGCGCCACGTGAG
1 GTAAGGCGCACCTCCTACAGCGCGTTCTACGCTGATATAGCGCCACGTGAG
846230 GTA
1 GTA
846233 TAGCGCTGGG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
50 2 0.04
51 42 0.91
52 2 0.04
ACGTcount: A:0.17, C:0.30, G:0.31, T:0.21
Consensus pattern (51 bp):
GTAAGGCGCACCTCCTACAGCGCGTTCTACGCTGATATAGCGCCACGTGAG
Found at i:852928 original size:27 final size:27
Alignment explanation
Indices: 852873--852926 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
852863 AGGGGCGGAG
852873 TTAAAAAAATTATTTTAGGTGTCAAAA
1 TTAAAAAAATTATTTTAGGTGTCAAAA
852900 TTAAAAAAATATATTTTCA-GTGTCAAA
1 TTAAAAAAAT-TATTTT-AGGTGTCAAA
852927 TTTATAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 10 0.40
28 14 0.56
29 1 0.04
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.37
Consensus pattern (27 bp):
TTAAAAAAATTATTTTAGGTGTCAAAA
Found at i:854706 original size:22 final size:22
Alignment explanation
Indices: 854644--854686 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
854634 AACTTAAATT
**
854644 TAAAAAAATTAAA-AAAATAAA
1 TAAAAAAACAAAACAAAATAAA
854665 TAAAAAAACAAAACAAAATAAA
1 TAAAAAAACAAAACAAAATAAA
854687 AATAAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.14
Consensus pattern (22 bp):
TAAAAAAACAAAACAAAATAAA
Found at i:859610 original size:19 final size:19
Alignment explanation
Indices: 859586--859631 Score: 76
Period size: 18 Copynumber: 2.5 Consensus size: 19
859576 AAAATTGTTT
*
859586 TAAAATAAAAAGATGAGGA
1 TAAAATAAAAAGATAAGGA
859605 TAAAAT-AAAAGATAAGGA
1 TAAAATAAAAAGATAAGGA
859623 TAAAATAAA
1 TAAAATAAA
859632 TAAATAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.17
Consensus pattern (19 bp):
TAAAATAAAAAGATAAGGA
Found at i:861806 original size:12 final size:12
Alignment explanation
Indices: 861789--861816 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
861779 CTCACAGGCG
861789 CACACAGACACA
1 CACACAGACACA
861801 CACACAGACACA
1 CACACAGACACA
861813 CACA
1 CACA
861817 GCCACGCACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.43, G:0.07, T:0.00
Consensus pattern (12 bp):
CACACAGACACA
Found at i:862135 original size:18 final size:18
Alignment explanation
Indices: 862094--862135 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
862084 ACCGGGCCTC
*
862094 AAGCCC-AAATCAAACCA
1 AAGCCCAAAATAAAACCA
*
862111 AACCCCAAAATAAAACCA
1 AAGCCCAAAATAAAACCA
*
862129 AGGCCCA
1 AAGCCCA
862136 TTACATTATA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.52, C:0.36, G:0.07, T:0.05
Consensus pattern (18 bp):
AAGCCCAAAATAAAACCA
Found at i:866085 original size:20 final size:19
Alignment explanation
Indices: 866057--866112 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 19
866047 GATCAATTCC
* *
866057 TTTTACATTTACATGTTGTA
1 TTTTGCATTT-CATGTTGCA
866077 TTTTGCATTCTCAT-TTGCA
1 TTTTGCATT-TCATGTTGCA
866096 TATTTGCATTTTCATGT
1 T-TTTGCA-TTTCATGT
866113 ACATCTTTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
19 5 0.17
20 21 0.70
21 4 0.13
ACGTcount: A:0.20, C:0.14, G:0.11, T:0.55
Consensus pattern (19 bp):
TTTTGCATTTCATGTTGCA
Found at i:866121 original size:20 final size:20
Alignment explanation
Indices: 866078--866124 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
866068 CATGTTGTAT
* *
866078 TTTGCATTCTCATTTGCATA
1 TTTGCATTCTCATGTACATA
* *
866098 TTTGCATTTTCATGTACATC
1 TTTGCATTCTCATGTACATA
866118 TTTGCAT
1 TTTGCAT
866125 CTTAGCATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.19, C:0.19, G:0.11, T:0.51
Consensus pattern (20 bp):
TTTGCATTCTCATGTACATA
Found at i:868441 original size:54 final size:54
Alignment explanation
Indices: 868380--868500 Score: 154
Period size: 54 Copynumber: 2.2 Consensus size: 54
868370 TGGTTTTCAT
*
868380 GGGTTTCTTGATGTCTCCAAATGAATGTTT-AAGAAGCTAAGCCTATTTTTTTAG
1 GGGTTTCTTGATGTCTCCAAATGAATGTTTAAAGAAGCTAAGCCTA-ATTTTTAG
* * ** * *
868434 GGGTTTCTTAATGTTTTTAGATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAG
1 GGGTTTCTTGATGTCTCCAAATGAATGTTTAAAGAAGCTAAGCCTAATTTTTAG
*
868488 GGGTTTATTGATG
1 GGGTTTCTTGATG
868501 ATAACTATAA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
54 42 0.74
55 15 0.26
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.43
Consensus pattern (54 bp):
GGGTTTCTTGATGTCTCCAAATGAATGTTTAAAGAAGCTAAGCCTAATTTTTAG
Found at i:868871 original size:42 final size:42
Alignment explanation
Indices: 868800--868882 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
868790 TCTTACTTAG
* * * *
868800 TAAGTCCTTCGGGCCATCAGTATGGCTTTCGAGCATGATGCT
1 TAAGTCCTTCGGGCCATCAGCATGACTTTCAAGCAGGATGCT
868842 TAAGTCCTTCGGGCCATCCA-CATGACTTTCAAGCAGGATGC
1 TAAGTCCTTCGGGCCAT-CAGCATGACTTTCAAGCAGGATGC
868883 ATTTAAAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
42 34 0.94
43 2 0.06
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.28
Consensus pattern (42 bp):
TAAGTCCTTCGGGCCATCAGCATGACTTTCAAGCAGGATGCT
Found at i:869452 original size:136 final size:136
Alignment explanation
Indices: 869208--869912 Score: 833
Period size: 136 Copynumber: 5.2 Consensus size: 136
869198 CAATATTTTA
* * *
869208 AATGGAGAGTTCATAATGAGAAGAACTCATCCGATATAGGGAGAATAAGTTCATAATGAGAAGAA
1 AATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAA
* * * * ** * *
869273 CTTGTTTGACTTATTGCTCGGTTCACAACATTTCGAATCAGCAATGCGACGCTTGAAGGATTAAC
66 CTTGTTTGACCTATTGCTCGATTCACGACATTTTGAATCAGCAACACCACGCTTGAGGGATTAAC
869338 ATTTCC
131 ATTTCC
*
869344 AATGGAGAGTTCATAATGAGAATAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAA
1 AATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAA
* * ** * *
869409 CTTGTTTGACCTATTTCTCAATTCACGGTATTTTGAATCAGCAATACCTCGCTTGAGGGATTAAC
66 CTTGTTTGACCTATTGCTCGATTCACGACATTTTGAATCAGCAACACCACGCTTGAGGGATTAAC
*
869474 ATTTCT
131 ATTTCC
* * * *
869480 AATGGAGAGTTCATAATGAGAAAAACTCATCCGATAGAAGGAGAAAAAGTTCATAATGAGAA-AA
1 AATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAA
** ** * **
869544 CTTGTTCAACCTATTGCTCGGA-TCACGACATTTTGAATCATTAACACCTCTTTTGAGGGATTAA
66 CTTGTTTGACCTATTGCTC-GATTCACGACATTTTGAATCAGCAACACCACGCTTGAGGGATTAA
869608 CATTTCC
130 CATTTCC
* ** * * *
869615 AATGGATAGTTCATAATGAGAAGAACTCATTTGACAGAGGGAGAAGAAGCTCATAATAAGAAGAA
1 AATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAA
* * * *
869680 CTTGTTTGACCTATTGCTCGATTCACGACATTTCT-AATCTGTAAC-GCATCACTTGAGGGATTA
66 CTTGTTTGACCTATTGCTCGATTCACGACATTT-TGAATCAGCAACACCA-CGCTTGAGGGATTA
869743 ACATTTCC
129 ACATTTCC
* *
869751 AATGGAGAGTTCATAATGAGAAGAACTCATCTGAAAGAGGGAGAAGAAGTTCATAAAGAGAAGAA
1 AATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAA
** * * * * * * * *
869816 CTTGTTCAACCTATTGCTCGATTCATGTCATTTCGAATCAACAACGCCTCGCGTGAGGGATCAAC
66 CTTGTTTGACCTATTGCTCGATTCACGACATTTTGAATCAGCAACACCACGCTTGAGGGATTAAC
*
869881 ATTTCT
131 ATTTCC
* * * * *
869887 AGTAGAAAGATCATGATGAGAAGAAC
1 AATGGAGAGTTCATAATGAGAAGAAC
869913 CCGTAGCTTG
Statistics
Matches: 487, Mismatches: 75, Indels: 14
0.85 0.13 0.02
Matches are distributed among these distances:
135 115 0.24
136 370 0.76
137 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (136 bp):
AATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAA
CTTGTTTGACCTATTGCTCGATTCACGACATTTTGAATCAGCAACACCACGCTTGAGGGATTAAC
ATTTCC
Found at i:869692 original size:271 final size:272
Alignment explanation
Indices: 869208--869912 Score: 867
Period size: 271 Copynumber: 2.6 Consensus size: 272
869198 CAATATTTTA
* *
869208 AATGGAGAGTTCATAATGAGAAGAACTCATCCGATATAGGGAGAATAAGTTCATAATGAGAAGAA
1 AATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAAAAGTTCATAATGAGAAGAA
** * * ** *
869273 CTTGTTTGACTTATTGCTCGGTTCACAACATTTCGAATCAGCAATGCGACGCTTGAAGGATTAAC
66 CTTGTTCAACCTATTGCTCGGATCACAACATTTCGAATCAGCAACACCACGCTTGAAGGATTAAC
* * *
869338 ATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATGA
131 ATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGCTCATAATAA
* ** * * *
869403 GAAGAACTTGTTTGACCTATTTCTCAATTCACGGTATTT-TGAATCAGCAATACCTCGCTTGAGG
196 GAAGAACTTGTTTGACCTATTGCTCAATTCACGACATTTCT-AATCAGCAACACATCACTTGAGG
*
869467 GATTAACATTTCT
260 GATTAACATTTCC
* *
869480 AATGGAGAGTTCATAATGAGAAAAACTCATCCGATAGAAGGAGAAAAAGTTCATAATGAGAA-AA
1 AATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAAAAGTTCATAATGAGAAGAA
* * ** * ** *
869544 CTTGTTCAACCTATTGCTCGGATCACGACATTTTGAATCATTAACACCTCTTTTGAGGGATTAAC
66 CTTGTTCAACCTATTGCTCGGATCACAACATTTCGAATCAGCAACACCACGCTTGAAGGATTAAC
* ** *
869609 ATTTCCAATGGATAGTTCATAATGAGAAGAACTCATTTGACAGAGGGAGAAGAAGCTCATAATAA
131 ATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGCTCATAATAA
* * * *
869674 GAAGAACTTGTTTGACCTATTGCTCGATTCACGACATTTCTAATCTGTAACGCATCACTTGAGGG
196 GAAGAACTTGTTTGACCTATTGCTCAATTCACGACATTTCTAATCAGCAACACATCACTTGAGGG
869739 ATTAACATTTCC
261 ATTAACATTTCC
* * * *
869751 AATGGAGAGTTCATAATGAGAAGAACTCATCTGAAAGAGGGAGAAGAAGTTCATAAAGAGAAGAA
1 AATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAAAAGTTCATAATGAGAAGAA
*** * * * * * *
869816 CTTGTTCAACCTATTGCTC-GATTCATGTCATTTCGAATCAACAACGCCTCGCGTGAGGGATCAA
66 CTTGTTCAACCTATTGCTCGGA-TCACAACATTTCGAATCAGCAACACCACGCTTGAAGGATTAA
* * * * * *
869880 CATTTCTAGTAGAAAGATCATGATGAGAAGAAC
130 CATTTCCAATGGAGAGTTCATAATGAGAAGAAC
869913 CCGTAGCTTG
Statistics
Matches: 371, Mismatches: 59, Indels: 6
0.85 0.14 0.01
Matches are distributed among these distances:
271 232 0.63
272 139 0.37
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (272 bp):
AATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAAAAGTTCATAATGAGAAGAA
CTTGTTCAACCTATTGCTCGGATCACAACATTTCGAATCAGCAACACCACGCTTGAAGGATTAAC
ATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGCTCATAATAA
GAAGAACTTGTTTGACCTATTGCTCAATTCACGACATTTCTAATCAGCAACACATCACTTGAGGG
ATTAACATTTCC
Found at i:875166 original size:93 final size:96
Alignment explanation
Indices: 874997--875182 Score: 256
Period size: 93 Copynumber: 2.0 Consensus size: 96
874987 TCTCTGAACC
*
874997 TAAACTAAAATCAAAGAAAGATAGTAAGAATAATCGATAAAGACTTGAGTGATCCTTAAGTCTTT
1 TAAACTAAAATCAAAGAAAGA-AGTAAGAATAATCGATAAAGACTTGAGAGATCCTTAAGTCTTT
875062 CTTTCCTTATTTATA-CTTTCAATTTTTTTAT
65 CTTTCCTTATTTATATCTTTCAATTTTTTTAT
* * * *
875093 TAAACTAAAATCAAAGAAAG-A-TAATAATAATTGATTTAAGACTTGAGA-AGTCCTTGA-TCTT
1 TAAACTAAAATCAAAGAAAGAAGTAAGAATAATCGA-TAAAGACTTGAGAGA-TCCTTAAGTCTT
*
875154 TCTTTCCTTATTTATATTTTTCAATTTTT
64 TCTTTCCTTATTTATATCTTTCAATTTTT
875183 GATGATAACT
Statistics
Matches: 81, Mismatches: 6, Indels: 8
0.85 0.06 0.08
Matches are distributed among these distances:
93 32 0.40
94 29 0.36
96 20 0.25
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (96 bp):
TAAACTAAAATCAAAGAAAGAAGTAAGAATAATCGATAAAGACTTGAGAGATCCTTAAGTCTTTC
TTTCCTTATTTATATCTTTCAATTTTTTTAT
Found at i:876800 original size:32 final size:32
Alignment explanation
Indices: 876763--876827 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
876753 TACATATAAC
*
876763 AATATAATTACATTTATACATTTTTTTAATTT
1 AATATAATTACATTTATACATTTTGTTAATTT
876795 AATATAATTACATTTATACATTTTGTTAATTT
1 AATATAATTACATTTATACATTTTGTTAATTT
876827 A
1 A
876828 CTTGATATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (32 bp):
AATATAATTACATTTATACATTTTGTTAATTT
Found at i:876887 original size:14 final size:14
Alignment explanation
Indices: 876864--876894 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
876854 ACATATAATT
*
876864 TTTATTATTATATA
1 TTTATAATTATATA
876878 TTTATAATTATATA
1 TTTATAATTATATA
876892 TTT
1 TTT
876895 TTTAAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTATAATTATATA
Found at i:876898 original size:17 final size:16
Alignment explanation
Indices: 876856--876896 Score: 50
Period size: 14 Copynumber: 2.6 Consensus size: 16
876846 TTGATTAAAC
*
876856 ATATAATTTTTATTATT
1 ATAT-ATTTTTATAATT
876873 ATATA--TTTATAATT
1 ATATATTTTTATAATT
876887 ATATATTTTT
1 ATATATTTTT
876897 TAAAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
14 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
ATATATTTTTATAATT
Found at i:880930 original size:17 final size:18
Alignment explanation
Indices: 880897--880930 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
880887 TACATTATAT
*
880897 AAAATTTAAATTAAATAC
1 AAAATATAAATTAAATAC
880915 AAAATATAAA-TAAATA
1 AAAATATAAATTAAATA
880931 TAACATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAATATAAATTAAATAC
Found at i:880938 original size:17 final size:18
Alignment explanation
Indices: 880893--880938 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
880883 ATATTACATT
*
880893 ATATAAAATTTAAATTAA
1 ATATAAAATATAAATTAA
*
880911 ATACAAAATATAAA-TAA
1 ATATAAAATATAAATTAA
*
880928 ATATAACATAT
1 ATATAAAATAT
880939 TATTTAATAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (18 bp):
ATATAAAATATAAATTAA
Found at i:881010 original size:2 final size:2
Alignment explanation
Indices: 881003--881031 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
880993 TTGTATCATG
881003 TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
881032 CACAATTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:882488 original size:3 final size:3
Alignment explanation
Indices: 882480--882561 Score: 110
Period size: 3 Copynumber: 27.0 Consensus size: 3
882470 TTCATTTTAA
**
882480 ATT ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
882528 ATT ATT ATT ATT AAT AGT AAT ATT ATTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
882562 TAAATATTAC
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
3 67 0.96
4 3 0.04
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:884083 original size:54 final size:53
Alignment explanation
Indices: 883980--884084 Score: 124
Period size: 53 Copynumber: 2.0 Consensus size: 53
883970 ATAATTTTAC
* * * * *
883980 ATTTATTATTATTTTATTTATTTATAGTCATTGTTTAGTTATTTTTTTACTTA
1 ATTTATTATTATTTTATATATTTATAATCATTCTTTAATTATTGTTTTACTTA
884033 ATTT-TTATTATTTTAATATATTT-TAAATCATTACTTTAATTATTGTTTTACT
1 ATTTATTATTATTTT-ATATATTTAT-AATCATT-CTTTAATTATTGTTTTACT
884085 ATATTATAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
52 11 0.25
53 17 0.39
54 16 0.36
ACGTcount: A:0.28, C:0.05, G:0.04, T:0.64
Consensus pattern (53 bp):
ATTTATTATTATTTTATATATTTATAATCATTCTTTAATTATTGTTTTACTTA
Done.