Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, 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: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 98 of 109
Found at i:19625022 original size:21 final size:21
Alignment explanation
Indices: 19624984--19625023 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19624974 CAATTTCGCA
*
19624984 TTTTTTGGTCATTAGACAAAT
1 TTTTTTCGTCATTAGACAAAT
* *
19625005 TTTTTTCGTCTTTGGACAA
1 TTTTTTCGTCATTAGACAA
19625024 TATCTCATTT
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:0.12, G:0.15, T:0.50
Consensus pattern (21 bp):
TTTTTTCGTCATTAGACAAAT
Found at i:19627820 original size:3 final size:3
Alignment explanation
Indices: 19627812--19627855 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
19627802 TGTTCATAAA
19627812 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
19627856 CTTTGTACTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:19628132 original size:17 final size:16
Alignment explanation
Indices: 19628110--19628154 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
19628100 TCATATTAAA
19628110 TTTTATTAATTTAATTT
1 TTTTATTAATTT-ATTT
*
19628127 TTTTATTAAATTATTT
1 TTTTATTAATTTATTT
19628143 TATTT-TTAATTT
1 T-TTTATTAATTT
19628155 CATAAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 11 0.44
17 14 0.56
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTATTAATTTATTT
Found at i:19632495 original size:9 final size:9
Alignment explanation
Indices: 19632481--19632510 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
19632471 GATATTTTAT
19632481 TAATTAAAA
1 TAATTAAAA
19632490 TAATTAAAA
1 TAATTAAAA
19632499 TATATTAAAA
1 TA-ATTAAAA
19632509 TA
1 TA
19632511 TAAAAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TAATTAAAA
Found at i:19632507 original size:10 final size:10
Alignment explanation
Indices: 19632483--19632512 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
19632473 TATTTTATTA
19632483 ATTAAAATA-
1 ATTAAAATAT
19632492 ATTAAAATAT
1 ATTAAAATAT
19632502 ATTAAAATAT
1 ATTAAAATAT
19632512 A
1 A
19632513 AAAATTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:19633846 original size:23 final size:24
Alignment explanation
Indices: 19633819--19633868 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
19633809 TTTGAACGCA
19633819 AATTAATATATATTT-ATAAAAAT
1 AATTAATATATATTTAATAAAAAT
* * *
19633842 AATTAATATTTTTTTAATTAAAAT
1 AATTAATATATATTTAATAAAAAT
19633866 AAT
1 AAT
19633869 AAAATTATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AATTAATATATATTTAATAAAAAT
Found at i:19633898 original size:18 final size:19
Alignment explanation
Indices: 19633854--19633898 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
19633844 TTAATATTTT
19633854 TTTAATTAAAATAATAAAA
1 TTTAATTAAAATAATAAAA
*
19633873 -TTATATTAAAAT-TTAAAA
1 TTTA-ATTAAAATAATAAAA
19633891 TTTAATTA
1 TTTAATTA
19633899 GATTCGTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TTTAATTAAAATAATAAAA
Found at i:19635799 original size:1 final size:1
Alignment explanation
Indices: 19635793--19635818 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
19635783 TTTTATCTAT
19635793 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
19635819 CTGTTCTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:19641698 original size:15 final size:15
Alignment explanation
Indices: 19641665--19641697 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
19641655 AAAAAATATT
*
19641665 AAAATAAATAATTAA
1 AAAATAAATAATAAA
19641680 AAAATAAA-AATAAA
1 AAAATAAATAATAAA
19641694 AAAA
1 AAAA
19641698 AGTCAAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAATAAATAATAAA
Found at i:19641993 original size:31 final size:31
Alignment explanation
Indices: 19641939--19642013 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
19641929 TATCTTAATT
19641939 ATATATAAATATAATATTTTAATAAAATAAG
1 ATATATAAATATAATATTTTAATAAAATAAG
* *
19641970 ATAT-TAAATAATAAT-TTTATAATATAAT-AC
1 ATATATAAAT-ATAATATTT-TAATAAAATAAG
*
19642000 ATTTATAAATATAA
1 ATATATAAATATAA
19642014 AATTAATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
30 16 0.42
31 22 0.58
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (31 bp):
ATATATAAATATAATATTTTAATAAAATAAG
Found at i:19642010 original size:17 final size:16
Alignment explanation
Indices: 19641977--19642017 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
19641967 AAGATATTAA
19641977 ATAATAATTTTATAAT
1 ATAATAATTTTATAAT
19641993 ATAATACA-TTTATAAAT
1 ATAATA-ATTTTAT-AAT
19642010 ATAA-AATT
1 ATAATAATT
19642018 AATTAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.05
16 13 0.59
17 8 0.36
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAATAATTTTATAAT
Found at i:19646243 original size:21 final size:21
Alignment explanation
Indices: 19646219--19646269 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
19646209 AAGAAATGCT
19646219 ATGCTTTCTACCTATAAAATA
1 ATGCTTTCTACCTATAAAATA
19646240 ATGCTTTCTACCTATAAAATA
1 ATGCTTTCTACCTATAAAATA
*
19646261 ATACTTTCT
1 ATGCTTTCT
19646270 GTCCATAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.41
Consensus pattern (21 bp):
ATGCTTTCTACCTATAAAATA
Found at i:19651080 original size:12 final size:12
Alignment explanation
Indices: 19651049--19651082 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
19651039 TTTGATTTAC
*
19651049 AAAATTGAATAA
1 AAAAATGAATAA
19651061 AGAAAATGAATAA
1 A-AAAATGAATAA
19651074 AAAAATGAA
1 AAAAATGAA
19651083 AAGGTAGAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.18
Consensus pattern (12 bp):
AAAAATGAATAA
Found at i:19660068 original size:57 final size:57
Alignment explanation
Indices: 19659967--19660171 Score: 293
Period size: 57 Copynumber: 3.5 Consensus size: 57
19659957 GTAAAAAGTG
* * * *
19659967 GTGGCTGTGGTGGTTGTGGTGCAGGATGTGGGGGTGGTTGTGGAAGCATGGTGAATAGCA
1 GTGGTTGTGGTGGTTGTGGTGCTGGCTGT---GGTGGTTGTGGAAGCATGGTTAATAGCA
19660027 GTGGTTGTGGTGGTTGTGGTGCTGGCTGTGGTGGTTGTGGAAGCATGGTTAATAGCA
1 GTGGTTGTGGTGGTTGTGGTGCTGGCTGTGGTGGTTGTGGAAGCATGGTTAATAGCA
* *
19660084 GCGGTTGTGGTGGTTGTGGTGCTGGTTGTGGTGGTTGTGGAAGCATGGTTAATAGCA
1 GTGGTTGTGGTGGTTGTGGTGCTGGCTGTGGTGGTTGTGGAAGCATGGTTAATAGCA
* * * *
19660141 GTGGTTGTGGCGGCTGTGGCGGTGGCTGTGG
1 GTGGTTGTGGTGGTTGTGGTGCTGGCTGTGG
19660172 CAGTGGCTGT
Statistics
Matches: 133, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
57 107 0.80
60 26 0.20
ACGTcount: A:0.11, C:0.08, G:0.49, T:0.32
Consensus pattern (57 bp):
GTGGTTGTGGTGGTTGTGGTGCTGGCTGTGGTGGTTGTGGAAGCATGGTTAATAGCA
Found at i:19660165 original size:6 final size:6
Alignment explanation
Indices: 19660156--19660198 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
19660146 TGTGGCGGCT
* * * *
19660156 GTGGCG GTGGCT GTGGCA GTGGCT GTGGCG GTGGCT GTGGCG G
1 GTGGCG GTGGCG GTGGCG GTGGCG GTGGCG GTGGCG GTGGCG G
19660199 AGGTTGTGGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.02, C:0.16, G:0.58, T:0.23
Consensus pattern (6 bp):
GTGGCG
Found at i:19660206 original size:24 final size:24
Alignment explanation
Indices: 19660152--19660207 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
19660142 TGGTTGTGGC
*
19660152 GGCTGTGGCGGTGGCTGTGGCAGT
1 GGCTGTGGCGGTGGCTGTGGCAGA
*
19660176 GGCTGTGGCGGTGGCTGTGGCGGA
1 GGCTGTGGCGGTGGCTGTGGCAGA
*
19660200 GGTTGTGG
1 GGCTGTGG
19660208 AAGCAAGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.04, C:0.14, G:0.57, T:0.25
Consensus pattern (24 bp):
GGCTGTGGCGGTGGCTGTGGCAGA
Found at i:19660207 original size:12 final size:12
Alignment explanation
Indices: 19660152--19660198 Score: 85
Period size: 12 Copynumber: 3.9 Consensus size: 12
19660142 TGGTTGTGGC
19660152 GGCTGTGGCGGT
1 GGCTGTGGCGGT
*
19660164 GGCTGTGGCAGT
1 GGCTGTGGCGGT
19660176 GGCTGTGGCGGT
1 GGCTGTGGCGGT
19660188 GGCTGTGGCGG
1 GGCTGTGGCGG
19660199 AGGTTGTGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.02, C:0.17, G:0.57, T:0.23
Consensus pattern (12 bp):
GGCTGTGGCGGT
Found at i:19662830 original size:60 final size:58
Alignment explanation
Indices: 19662737--19662857 Score: 206
Period size: 60 Copynumber: 2.1 Consensus size: 58
19662727 CTCGTTTTGC
*
19662737 TTTGCAGGAAAGATGAAAAAGAGTGATAATGAAAAAAAAAATGATTAAAATTCATAATCA
1 TTTGCAGGAAAGATGAAAAAGAGTGATAATG--AAAAAAAATGATTAAAATTCACAATCA
*
19662797 TTTGCAGGAAAGATGAAAAAGAGTGATAATGAAAAACAATGATTAAAATTCACAATCA
1 TTTGCAGGAAAGATGAAAAAGAGTGATAATGAAAAAAAATGATTAAAATTCACAATCA
19662855 TTT
1 TTT
19662858 TTTTACCTTC
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
58 28 0.47
60 31 0.53
ACGTcount: A:0.52, C:0.07, G:0.17, T:0.25
Consensus pattern (58 bp):
TTTGCAGGAAAGATGAAAAAGAGTGATAATGAAAAAAAATGATTAAAATTCACAATCA
Found at i:19667516 original size:2 final size:2
Alignment explanation
Indices: 19667509--19667534 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19667499 AAAAGCAATC
19667509 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
19667535 TAGTTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19667670 original size:21 final size:22
Alignment explanation
Indices: 19667646--19667697 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
19667636 TTTAATTTTG
*
19667646 ATTTTGA-TAAATTTTTATAAA
1 ATTTTGAGTAAATTTTGATAAA
* *
19667667 ATTTT-AGTAACTTTTGATACA
1 ATTTTGAGTAAATTTTGATAAA
19667688 ATTTTG-GTAA
1 ATTTTGAGTAA
19667698 TCATTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (22 bp):
ATTTTGAGTAAATTTTGATAAA
Found at i:19668073 original size:22 final size:22
Alignment explanation
Indices: 19668048--19668227 Score: 135
Period size: 22 Copynumber: 8.2 Consensus size: 22
19668038 GACAATTAAG
* *
19668048 TTATCATTAATTTATTACTATA
1 TTATCAATAATTTATTACTAAA
** * *
19668070 TTATCAACGATTTACTACTAAG
1 TTATCAATAATTTATTACTAAA
* * *
19668092 TTATCAATGATATATTATTAAA
1 TTATCAATAATTTATTACTAAA
* *
19668114 TTATCAATAATTTACTACAAAA
1 TTATCAATAATTTATTACTAAA
* * * * *
19668136 TTAGCATTGATTTATTATTAAC
1 TTATCAATAATTTATTACTAAA
*
19668158 TTATGAATAATTTATTACTAAA
1 TTATCAATAATTTATTACTAAA
* * * *
19668180 TTATGAATGATTTACTATTAAA
1 TTATCAATAATTTATTACTAAA
* * * *
19668202 TTGTTAATGATTTACTACTAAA
1 TTATCAATAATTTATTACTAAA
19668224 TTAT
1 TTAT
19668228 TGATCATTTG
Statistics
Matches: 122, Mismatches: 36, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 122 1.00
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.46
Consensus pattern (22 bp):
TTATCAATAATTTATTACTAAA
Found at i:19668127 original size:44 final size:44
Alignment explanation
Indices: 19668026--19668383 Score: 209
Period size: 44 Copynumber: 8.0 Consensus size: 44
19668016 TCCAAAAAGT
* * * * * * * *
19668026 TTATCAATGATTGACAATTAAGTTATCATTAATTTATTACTATA
1 TTATCAATGATTTACTACTAAATTATCAATGATTTATTATTAAA
* * *
19668070 TTATCAACGATTTACTACTAAGTTATCAATGATATATTATTAAA
1 TTATCAATGATTTACTACTAAATTATCAATGATTTATTATTAAA
* * * * *
19668114 TTATCAATAATTTACTACAAAATTAGCATTGATTTATTATTAAC
1 TTATCAATGATTTACTACTAAATTATCAATGATTTATTATTAAA
* * * * *
19668158 TTATGAATAATTTATTACTAAATTATGAATGATTTACTATTAAA
1 TTATCAATGATTTACTACTAAATTATCAATGATTTATTATTAAA
* * ** * * *
19668202 TTGTTAATGATTTACTACTAAATTATTGATCATTT-GTAATAAA
1 TTATCAATGATTTACTACTAAATTATCAATGATTTATTATTAAA
* * ** *
19668245 GTTAT-AATTGATTTACTATTAATTTATTGATGATTTATTGCAAAGATATCAA
1 -TTATCAA-TGATTTACTACTAAATTATCAATGATTTATT------AT-TAAA
* * * * * * *
19668297 TAATTAACTAATTTACGACTAAATTATCACTAATTTATTACTAAA
1 TTATCAA-TGATTTACTACTAAATTATCAATGATTTATTATTAAA
* * *
19668342 TTATCAATAATTTA-TATATAAATTATCAATGATTTACTATTA
1 TTATCAATGATTTACTA-CTAAATTATCAATGATTTATTATTA
19668384 TGCTATTATG
Statistics
Matches: 241, Mismatches: 61, Indels: 24
0.74 0.19 0.07
Matches are distributed among these distances:
43 9 0.04
44 190 0.79
45 9 0.04
46 1 0.00
51 4 0.02
52 28 0.12
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (44 bp):
TTATCAATGATTTACTACTAAATTATCAATGATTTATTATTAAA
Found at i:19668148 original size:66 final size:66
Alignment explanation
Indices: 19668042--19668227 Score: 176
Period size: 66 Copynumber: 2.8 Consensus size: 66
19668032 ATGATTGACA
* * * * * * * *
19668042 ATTAAGTTATCATTAATTTATTACTATATTATCAACGATTTACTACTAAGTTATCAATGATATAT
1 ATTAAATTATCAATAATTTACTACTAAATTAGCAATGATTTACTACTAAATTATCAATAATATAT
19668107 T
66 T
* * * * * * *
19668108 ATTAAATTATCAATAATTTACTACAAAATTAGCATTGATTTATTATTAACTTATGAATAATTTAT
1 ATTAAATTATCAATAATTTACTACTAAATTAGCAATGATTTACTACTAAATTATCAATAATATAT
19668173 T
66 T
* * * * *
19668174 ACTAAATTATGAATGATTTACTATTAAATT-GTTAATGATTTACTACTAAATTAT
1 ATTAAATTATCAATAATTTACTACTAAATTAG-CAATGATTTACTACTAAATTAT
19668228 TGATCATTTG
Statistics
Matches: 95, Mismatches: 24, Indels: 2
0.79 0.20 0.02
Matches are distributed among these distances:
65 1 0.01
66 94 0.99
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (66 bp):
ATTAAATTATCAATAATTTACTACTAAATTAGCAATGATTTACTACTAAATTATCAATAATATAT
T
Found at i:19668229 original size:25 final size:23
Alignment explanation
Indices: 19668078--19668281 Score: 108
Period size: 22 Copynumber: 9.3 Consensus size: 23
19668068 TATTATCAAC
* *
19668078 GATTTACTACTAAGTTA-TCAAT
1 GATTTACTACTAAATTATTGAAT
* * * *
19668100 GATATATTATTAAATTA-TCAAT
1 GATTTACTACTAAATTATTGAAT
* * *
19668122 AATTTACTACAAAATTA--GCATT
1 GATTTACTACTAAATTATTG-AAT
* * *
19668144 GATTTATTATTAACTTA-TGAAT
1 GATTTACTACTAAATTATTGAAT
* *
19668166 AATTTATTACTAAATTA-TGAAT
1 GATTTACTACTAAATTATTGAAT
* *
19668188 GATTTACTATTAAATTGTT-AAT
1 GATTTACTACTAAATTATTGAAT
19668210 GATTTACTACTAAATTATTG-AT
1 GATTTACTACTAAATTATTGAAT
* * *
19668232 CATTT-GTAATAAAGTTA-T-AATT
1 GATTTACTACTAAA-TTATTGAA-T
* *
19668254 GATTTACTATTAATTTATTG-AT
1 GATTTACTACTAAATTATTGAAT
19668276 GATTTA
1 GATTTA
19668282 TTGCAAAGAT
Statistics
Matches: 139, Mismatches: 33, Indels: 20
0.72 0.17 0.10
Matches are distributed among these distances:
21 8 0.06
22 122 0.88
23 9 0.06
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (23 bp):
GATTTACTACTAAATTATTGAAT
Found at i:19668328 original size:11 final size:11
Alignment explanation
Indices: 19668314--19668369 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
19668304 CTAATTTACG
19668314 ACTAAATTATC
1 ACTAAATTATC
* *
19668325 ACTAATTTATT
1 ACTAAATTATC
19668336 ACTAAATTATC
1 ACTAAATTATC
* *
19668347 AATAATTTAT-
1 ACTAAATTATC
*
19668357 ATATAAATTATC
1 A-CTAAATTATC
19668369 A
1 A
19668370 ATGATTTACT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
10 1 0.03
11 34 0.94
12 1 0.03
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (11 bp):
ACTAAATTATC
Found at i:19668356 original size:22 final size:22
Alignment explanation
Indices: 19668305--19668377 Score: 94
Period size: 22 Copynumber: 3.3 Consensus size: 22
19668295 AATAATTAAC
** *
19668305 TAATTTACGACTAAATTATCAC
1 TAATTTATTACTAAATTATCAA
19668327 TAATTTATTACTAAATTATCAA
1 TAATTTATTACTAAATTATCAA
19668349 TAATTTATATA-TAAATTATCAA
1 TAATTTAT-TACTAAATTATCAA
*
19668371 TGATTTA
1 TAATTTA
19668378 CTATTATGCT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 44 0.96
23 2 0.04
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.44
Consensus pattern (22 bp):
TAATTTATTACTAAATTATCAA
Found at i:19668538 original size:22 final size:22
Alignment explanation
Indices: 19668305--19668667 Score: 87
Period size: 22 Copynumber: 16.8 Consensus size: 22
19668295 AATAATTAAC
* *
19668305 TAATTTACGACTAAATTATC-A
1 TAATTTACTATTAAATTATCTA
* * *
19668326 CTAATTTATTACTAAATTATCAA
1 -TAATTTACTATTAAATTATCTA
*
19668349 TAATTTA-TATATAAATTATCAA
1 TAATTTACTAT-TAAATTATCTA
* ***
19668371 TGATTTACTATTATGCTAT-TA
1 TAATTTACTATTAAATTATCTA
* * * ***
19668392 TGCATTTATTTTTTTGTTATC-A
1 T-AATTTACTATTAAATTATCTA
* * *
19668414 TTAATTTACTATTTAATTTTTTA
1 -TAATTTACTATTAAATTATCTA
* ** * *
19668437 TTATTTACTACAAAATAATCACA
1 TAATTTACTATTAAATTATC-TA
* * * *
19668460 TAA-TTATTATAAAATTAACCA
1 TAATTTACTATTAAATTATCTA
* * * *
19668481 TGATTTATTATCAAGTTATC-A
1 TAATTTACTATTAAATTATCTA
19668502 CTAATTTA-TATTAAATTATCTA
1 -TAATTTACTATTAAATTATCTA
19668524 TAATTTACTATTAAATTAT-T-
1 TAATTTACTATTAAATTATCTA
*
19668544 T-A---ACTATTAAGTTAT-TGA
1 TAATTTACTATTAAATTATCT-A
* * *
19668562 TAATTAACTACTACTAAGTTATAT-
1 TAATT---TACTATTAAATTATCTA
* *
19668586 TGATTTACTTTTAAATT-TC-A
1 TAATTTACTATTAAATTATCTA
** *
19668606 GTAATAAACTATTAAATTGTC-A
1 -TAATTTACTATTAAATTATCTA
* * *
19668628 TTGATTTATTATTAAATTATTTA
1 -TAATTTACTATTAAATTATCTA
*
19668651 TAATTTACTACTAAATT
1 TAATTTACTATTAAATT
19668668 TATCAATTAA
Statistics
Matches: 254, Mismatches: 61, Indels: 52
0.69 0.17 0.14
Matches are distributed among these distances:
16 13 0.05
18 1 0.00
19 2 0.01
20 2 0.01
21 49 0.19
22 160 0.63
23 10 0.04
24 4 0.02
25 12 0.05
26 1 0.00
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.48
Consensus pattern (22 bp):
TAATTTACTATTAAATTATCTA
Found at i:19668551 original size:16 final size:15
Alignment explanation
Indices: 19668526--19668559 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
19668516 ATTATCTATA
19668526 ATTTACTATTAAATT
1 ATTTACTATTAAATT
*
19668541 ATTTAACTATTAAGTT
1 ATTT-ACTATTAAATT
19668557 ATT
1 ATT
19668560 GATAATTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (15 bp):
ATTTACTATTAAATT
Found at i:19668670 original size:19 final size:19
Alignment explanation
Indices: 19668646--19668705 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 19
19668636 TTATTAAATT
19668646 ATTTATAATTTACTACTAA
1 ATTTATAATTTACTACTAA
19668665 ATTTATCAATTAACTACTACTAA
1 ATTTAT-AATT---TACTACTAA
*
19668688 ATTGA-AATTTACTTACTA
1 ATTTATAATTTAC-TACTA
19668706 TTAAATTATA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
18 3 0.09
19 11 0.31
20 4 0.11
21 4 0.11
23 13 0.37
ACGTcount: A:0.42, C:0.13, G:0.02, T:0.43
Consensus pattern (19 bp):
ATTTATAATTTACTACTAA
Found at i:19668680 original size:20 final size:19
Alignment explanation
Indices: 19668646--19668683 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
19668636 TTATTAAATT
*
19668646 ATTTATAATTTACTACTAA
1 ATTTATAATTAACTACTAA
19668665 ATTTATCAATTAACTACTA
1 ATTTAT-AATTAACTACTA
19668684 CTAAATTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTATAATTAACTACTAA
Found at i:19668718 original size:22 final size:20
Alignment explanation
Indices: 19668648--19668718 Score: 65
Period size: 22 Copynumber: 3.4 Consensus size: 20
19668638 ATTAAATTAT
*
19668648 TTATAATTTACTACTA-AAT
1 TTATAATTTACTACTATAAA
*
19668667 TTATCAATTAACTACTACTAAA
1 TTAT-AATTTACTACTA-TAAA
19668689 TTGA-AATTTACTTACTATTAAA
1 TT-ATAATTTAC-TACTA-TAAA
19668711 TTATAATT
1 TTATAATT
19668719 GATTTTTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
19 4 0.10
20 11 0.26
21 7 0.17
22 19 0.45
23 1 0.02
ACGTcount: A:0.42, C:0.11, G:0.01, T:0.45
Consensus pattern (20 bp):
TTATAATTTACTACTATAAA
Found at i:19669092 original size:24 final size:24
Alignment explanation
Indices: 19669056--19669132 Score: 65
Period size: 22 Copynumber: 3.4 Consensus size: 24
19669046 ATTTATCAGT
19669056 TATTTATTACTAAATTATCAATGA
1 TATTTATTACTAAATTATCAATGA
* *
19669080 TATTTACTT-CTAATTTATGAATG-
1 TATTTA-TTACTAAATTATCAATGA
* * *
19669103 -ATTTATCATTAAATTAT-AA-AA
1 TATTTATTACTAAATTATCAATGA
19669124 TATTTATTA
1 TATTTATTA
19669133 TTAAGCTGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
21 3 0.07
22 19 0.45
24 18 0.43
25 2 0.05
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.49
Consensus pattern (24 bp):
TATTTATTACTAAATTATCAATGA
Found at i:19669188 original size:22 final size:22
Alignment explanation
Indices: 19669145--19669206 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 22
19669135 AAGCTGTAAA
* **
19669145 TGATTT-CTATTAAATTGGTGG
1 TGATTTACTATTAAGTTATTGG
19669166 TGATTTACTATTAAGTTATTGG
1 TGATTTACTATTAAGTTATTGG
* * *
19669188 TAATTTATTATAAAGTTAT
1 TGATTTACTATTAAGTTAT
19669207 AATTAATTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 6 0.18
22 28 0.82
ACGTcount: A:0.31, C:0.03, G:0.16, T:0.50
Consensus pattern (22 bp):
TGATTTACTATTAAGTTATTGG
Found at i:19669217 original size:11 final size:11
Alignment explanation
Indices: 19669168--19669228 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
19669158 ATTGGTGGTG
*
19669168 ATTTACTATTA
1 ATTTATTATTA
* **
19669179 AGTTATTGGTA
1 ATTTATTATTA
*
19669190 ATTTATTATAA
1 ATTTATTATTA
* *
19669201 AGTTATAATTA
1 ATTTATTATTA
*
19669212 ATTTATTACTA
1 ATTTATTATTA
19669223 ATTTAT
1 ATTTAT
19669229 CGATAAATTA
Statistics
Matches: 36, Mismatches: 14, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
11 36 1.00
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.52
Consensus pattern (11 bp):
ATTTATTATTA
Found at i:19669535 original size:43 final size:44
Alignment explanation
Indices: 19669488--19669600 Score: 122
Period size: 43 Copynumber: 2.6 Consensus size: 44
19669478 ATGATTCACG
**
19669488 ATTAAGTTATTACTGATTTA-TATTAAATTATGCATAATTTATT
1 ATTAAGTTATTACTGATTTACTATTAAATTATAAATAATTTATT
* * ** *
19669531 ATTAAGTTGTTACTGATTAACTATTATGTTATAAATTATTTATT
1 ATTAAGTTATTACTGATTTACTATTAAATTATAAATAATTTATT
* * *
19669575 ACTAAGTTA-TATTGATTTACTTTTAA
1 ATTAAGTTATTACTGATTTACTATTAA
19669601 GTTTTCAATG
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
43 31 0.55
44 25 0.45
ACGTcount: A:0.35, C:0.05, G:0.08, T:0.51
Consensus pattern (44 bp):
ATTAAGTTATTACTGATTTACTATTAAATTATAAATAATTTATT
Found at i:19669663 original size:22 final size:22
Alignment explanation
Indices: 19669267--19669663 Score: 129
Period size: 22 Copynumber: 18.3 Consensus size: 22
19669257 TTAACTAATA
* * *
19669267 TACTACTAAATTATCACTAATT
1 TACTATTAAATTATCATTGATT
* * * *
19669289 TACAATTAAATTATTAGTAATT
1 TACTATTAAATTATCATTGATT
* * ***
19669311 TACTATTATATTATTAGCAATT
1 TACTATTAAATTATCATTGATT
* * *
19669333 TACTGTT-AAGT-T-ATTAATT
1 TACTATTAAATTATCATTGATT
*
19669352 TACTATTAAATTATCAATGATT
1 TACTATTAAATTATCATTGATT
* * * *
19669374 TATTATTACATTTTTATAT-ATT
1 TACTATTAAATTATCAT-TGATT
* *
19669396 TACTATTAGGA-TATCATTGACT
1 TACTATTA-AATTATCATTGATT
* *
19669418 TACTACTTAATTTATAATT-ATT
1 TACTA-TTAAATTATCATTGATT
** *
19669440 TA-TCACAAAATTAT-TTATGATT
1 TACT-ATTAAATTATCAT-TGATT
* *
19669462 TACCACTAAATTATC-TATGATT
1 TACTATTAAATTATCAT-TGATT
* * * * *
19669484 CACGATTAAGTTATTACTGATT
1 TACTATTAAATTATCATTGATT
*
19669506 TA-TATTAAATTATGCA-TAATT
1 TACTATTAAATTAT-CATTGATT
* * * * *
19669527 TATTATTAAGTTGTTACTGATT
1 TACTATTAAATTATCATTGATT
* ** *
19669549 AACTATTATGTTATAAATT-ATT
1 TACTATTAAATTAT-CATTGATT
* * *
19669571 TATTACTAAGTTAT-ATTGATT
1 TACTATTAAATTATCATTGATT
* * * *
19669592 TACTTTTAAGTTTTCAATGATT
1 TACTATTAAATTATCATTGATT
* *
19669614 AACTACTAAATTATCAATT-ATT
1 TACTATTAAATTATC-ATTGATT
*
19669636 TACTATTAATTTATCATTGATT
1 TACTATTAAATTATCATTGATT
19669658 TACTAT
1 TACTAT
19669664 CAATAAATTA
Statistics
Matches: 278, Mismatches: 75, Indels: 44
0.70 0.19 0.11
Matches are distributed among these distances:
19 11 0.04
20 8 0.03
21 44 0.16
22 200 0.72
23 15 0.05
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.49
Consensus pattern (22 bp):
TACTATTAAATTATCATTGATT
Found at i:19669737 original size:22 final size:22
Alignment explanation
Indices: 19669686--19669970 Score: 83
Period size: 22 Copynumber: 13.0 Consensus size: 22
19669676 TTAAATTGAA
* *
19669686 ATTGATTTATTGTTAAATTATT
1 ATTGATTTATTATTAAATTATC
* * *
19669708 ACTAATTTACTATTAAATTATC
1 ATTGATTTATTATTAAATTATC
**
19669730 ATTGATTTATTATTAAGCTATC
1 ATTGATTTATTATTAAATTATC
* * * * *
19669752 AATAATTAACTACTAAATTATC
1 ATTGATTTATTATTAAATTATC
* * *
19669774 ACTT-ATTTTTTGTTAAGTTATC
1 A-TTGATTTATTATTAAATTATC
* * ** *
19669796 CTTGATTTAGTATTATGTTATT
1 ATTGATTTATTATTAAATTATC
** * * ** *
19669818 ATACAATTA-CAACAATATTATA
1 ATTGATTTATTATTAA-ATTATC
* ** *
19669840 ATTGATTTATCATTAAGGTATT
1 ATTGATTTATTATTAAATTATC
* * * *
19669862 A-TCATATATTATTATATTATT
1 ATTGATTTATTATTAAATTATC
* **
19669883 ACTGATTTATTAAAAAAATTATC
1 ATTGATTTATT-ATTAAATTATC
* *
19669906 AATT-ATTTATCACTAAATTATC
1 -ATTGATTTATTATTAAATTATC
* * * *
19669928 GTTTATTTATTATTAAGTTATT
1 ATTGATTTATTATTAAATTATC
* * *
19669950 ATTAATTTACTACTAAATTAT
1 ATTGATTTATTATTAAATTAT
19669971 TGATGATTAT
Statistics
Matches: 181, Mismatches: 74, Indels: 16
0.67 0.27 0.06
Matches are distributed among these distances:
21 21 0.12
22 140 0.77
23 18 0.10
24 2 0.01
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.49
Consensus pattern (22 bp):
ATTGATTTATTATTAAATTATC
Found at i:19669758 original size:44 final size:44
Alignment explanation
Indices: 19669659--19669774 Score: 128
Period size: 44 Copynumber: 2.7 Consensus size: 44
19669649 TCATTGATTT
* * *
19669659 ACTATCAATAAATTA-TATTAAATTGA-AATTGATTTATTGTTAA
1 ACTATCAATAATTTACTATTAAATT-ATCATTGATTTATTATTAA
* * *
19669702 ATTATTACTAATTTACTATTAAATTATCATTGATTTATTATTAA
1 ACTATCAATAATTTACTATTAAATTATCATTGATTTATTATTAA
* * *
19669746 GCTATCAATAATTAACTACTAAATTATCA
1 ACTATCAATAATTTACTATTAAATTATCA
19669775 CTTATTTTTT
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
43 12 0.20
44 47 0.80
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (44 bp):
ACTATCAATAATTTACTATTAAATTATCATTGATTTATTATTAA
Found at i:19670972 original size:10 final size:9
Alignment explanation
Indices: 19670947--19670971 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
19670937 ATATAAAAAA
19670947 TAAAAAAGC
1 TAAAAAAGC
19670956 TAAAAAAGC
1 TAAAAAAGC
19670965 TAAAAAA
1 TAAAAAA
19670972 AATGAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.72, C:0.08, G:0.08, T:0.12
Consensus pattern (9 bp):
TAAAAAAGC
Found at i:19671883 original size:59 final size:59
Alignment explanation
Indices: 19671815--19672065 Score: 235
Period size: 58 Copynumber: 4.3 Consensus size: 59
19671805 AAATATTTCC
* *
19671815 AATTTTT-AAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAATAA
1 AATTTTTAAAAAAAATATTTTTAAGAAAAAGTTGAAAGTACCAATTTTCTTTGAAATAA
* ** * * * *
19671873 AATTTTTTAAAAAAGCATTTTT-GGCAAAAGTTGGAAGTACCAATTTTCTTTAAAAATAA
1 AATTTTTAAAAAAAATATTTTTAAGAAAAAGTTGAAAGTACCAATTTTCTTT-GAAATAA
* * *
19671932 AA-TTCTAAAAAAAATCATTTTTGAGAAAAAGTTGAAAGTATCAATTTT-TCTTGAAGATAA
1 AATTTTTAAAAAAAAT-ATTTTTAAGAAAAAGTTGAAAGTACCAATTTTCT-TTGAA-ATAA
* * * * * * *
19671992 AATTTTCAAAAAAAAAACATTTTAAAAAAAAGTTGGATGTACCAATTTTCCTT-AAA-AA
1 AATTTTTAAAAAAAATA-TTTTTAAGAAAAAGTTGAAAGTACCAATTTTCTTTGAAATAA
19672050 ATATTTTTAAAAAAAA
1 A-ATTTTTAAAAAAAA
19672066 GTTGAAAGTA
Statistics
Matches: 156, Mismatches: 27, Indels: 19
0.77 0.13 0.09
Matches are distributed among these distances:
58 44 0.28
59 43 0.28
60 32 0.21
61 37 0.24
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.36
Consensus pattern (59 bp):
AATTTTTAAAAAAAATATTTTTAAGAAAAAGTTGAAAGTACCAATTTTCTTTGAAATAA
Found at i:19671905 original size:58 final size:57
Alignment explanation
Indices: 19671817--19672006 Score: 204
Period size: 59 Copynumber: 3.2 Consensus size: 57
19671807 ATATTTCCAA
*
19671817 TTTTTAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAATAAAAT
1 TTTTTAAAAAAACATTTTT--GGAAAAGTTGAAAGTATCAATTTTCTTTGAAATAAAAT
* * * *
19671876 TTTTTAAAAAAGCATTTTTGGCAAAAGTTGGAAGTACCAATTTTCTTTAAAAATAAAA-
1 TTTTTAAAAAAACATTTTTGG-AAAAGTTGAAAGTATCAATTTTCTTT-GAAATAAAAT
* *
19671934 TTCTAAAAAAAATCATTTTTGAGAAAAAGTTGAAAGTATCAATTTT-TCTTGAAGATAAAAT
1 TTTTTAAAAAAA-CATTTTTG-G-AAAAGTTGAAAGTATCAATTTTCT-TTGAA-ATAAAAT
**
19671995 TTTCAAAAAAAA
1 TTTTTAAAAAAA
19672007 AACATTTTAA
Statistics
Matches: 110, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
57 2 0.02
58 33 0.30
59 36 0.33
60 29 0.26
61 10 0.09
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (57 bp):
TTTTTAAAAAAACATTTTTGGAAAAGTTGAAAGTATCAATTTTCTTTGAAATAAAAT
Found at i:19671964 original size:118 final size:119
Alignment explanation
Indices: 19671822--19672049 Score: 309
Period size: 121 Copynumber: 1.9 Consensus size: 119
19671812 TCCAATTTTT
* **
19671822 AAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAA-TTTTCTTTGAA-ATAAAATTTT-TTAAA
1 AAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTC-TTGAAGATAAAATTTTAAAAAA
* **** *
19671884 AAAGCATTTTTGGCAAAAGTTGGAAGTACCAATTTTCTTTAAAAATAAAATTCTA
65 AAAACATTTTAAAAAAAAGTTGGAAGTACCAATTTTCCTTAAAAATAAAATTCTA
*
19671939 AAAAAAATCATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAGATAAAATTTTCAAAAA
1 AAAAAAAT-ATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAGATAAAATTTT-AAAAA
*
19672004 AAAAACATTTTAAAAAAAAGTTGGATGTACCAATTTTCCTTAAAAA
64 AAAAACATTTTAAAAAAAAGTTGGAAGTACCAATTTTCCTTAAAAA
19672050 ATATTTTTAA
Statistics
Matches: 95, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
117 8 0.08
118 31 0.33
119 15 0.16
121 41 0.43
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.35
Consensus pattern (119 bp):
AAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAGATAAAATTTTAAAAAAA
AAACATTTTAAAAAAAAGTTGGAAGTACCAATTTTCCTTAAAAATAAAATTCTA
Found at i:19672039 original size:43 final size:43
Alignment explanation
Indices: 19671992--19672083 Score: 105
Period size: 43 Copynumber: 2.1 Consensus size: 43
19671982 TTGAAGATAA
* *
19671992 AATTTT-CAAAAAAAAAACATTTTAAAAAAAAGTTGGATGTACC
1 AATTTTCCAAAAAAAAAA-ATTTTAAAAAAAAGTTGAAAGTACC
** * * *
19672035 AATTTTCCTTAAAAAATATTTTTAAAAAAAAGTTGAAAGTATC
1 AATTTTCCAAAAAAAAAAATTTTAAAAAAAAGTTGAAAGTACC
19672078 AATTTT
1 AATTTT
19672084 TCTGAAAAAC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
43 33 0.80
44 8 0.20
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.35
Consensus pattern (43 bp):
AATTTTCCAAAAAAAAAAATTTTAAAAAAAAGTTGAAAGTACC
Found at i:19672063 original size:60 final size:58
Alignment explanation
Indices: 19671822--19672065 Score: 172
Period size: 59 Copynumber: 4.1 Consensus size: 58
19671812 TCCAATTTTT
* ** * * * **
19671822 AAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAATAAAATTTT-TT
1 AAAAAAACATTTTTAAAAAAAAGTTGGAAGTACCAATTTTCCTT-AAA-AAAATTTTAAA
* *** * *
19671881 AAAAAAGCATTTTT-GGCAAAAGTTGGAAGTACCAATTTTCTTTAAAAATAAAATTCT-AA
1 AAAAAAACATTTTTAAAAAAAAGTTGGAAGTACCAATTTTCCTT--AAA-AAAATTTTAAA
* * * * * *
19671940 AAAAAATCATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAGATAAAATTTTCAAA
1 AAAAAAACATTTTTAAAAAAAAGTTGGAAGTACCAATTTTCCTT-AA-A-AAAATTTT-AAA
* *
19672002 AAAAAAACA-TTTTAAAAAAAAGTTGGATGTACCAATTTTCCTTAAAAAATATTTTTAA
1 AAAAAAACATTTTTAAAAAAAAGTTGGAAGTACCAATTTTCCTTAAAAAA-ATTTTAAA
19672060 AAAAAA
1 AAAAAA
19672066 GTTGAAAGTA
Statistics
Matches: 152, Mismatches: 27, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
58 36 0.24
59 44 0.29
60 34 0.22
61 28 0.18
62 10 0.07
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.35
Consensus pattern (58 bp):
AAAAAAACATTTTTAAAAAAAAGTTGGAAGTACCAATTTTCCTTAAAAAAATTTTAAA
Found at i:19672092 original size:43 final size:42
Alignment explanation
Indices: 19672003--19672092 Score: 117
Period size: 43 Copynumber: 2.1 Consensus size: 42
19671993 ATTTTCAAAA
* * *
19672003 AAAAAACATTTTAAAAAAAAGTTGGATGTACCAATTTTCCTT
1 AAAAAACATTTTAAAAAAAAGTTGAAAGTACCAATTTTCCTG
* * *
19672045 AAAAAATATTTTTAAAAAAAAGTTGAAAGTATCAATTTTTCTG
1 AAAAAACA-TTTTAAAAAAAAGTTGAAAGTACCAATTTTCCTG
19672088 AAAAA
1 AAAAA
19672093 CAAAAAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
42 7 0.17
43 34 0.83
ACGTcount: A:0.50, C:0.08, G:0.09, T:0.33
Consensus pattern (42 bp):
AAAAAACATTTTAAAAAAAAGTTGAAAGTACCAATTTTCCTG
Found at i:19677379 original size:21 final size:22
Alignment explanation
Indices: 19677337--19677384 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
19677327 GATAAGAATT
*
19677337 TTTGAATTCTCAAATGCAAATC
1 TTTGAATTCTCAAATGAAAATC
19677359 TTTGAATT-TCAAA-GAACAATC
1 TTTGAATTCTCAAATGAA-AATC
19677380 TTTGA
1 TTTGA
19677385 GTTTTAAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 2 0.08
21 14 0.58
22 8 0.33
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (22 bp):
TTTGAATTCTCAAATGAAAATC
Found at i:19677865 original size:42 final size:42
Alignment explanation
Indices: 19677785--19677937 Score: 193
Period size: 42 Copynumber: 3.6 Consensus size: 42
19677775 ATGATTGTCA
* * * * *
19677785 ATGAGTAATTTATTTTTTCAAAAGTTTTGTTGCTTTTATTTAG
1 ATGAGCAATTTA-TTTTTCCAAAGTCTTATTGCCTTTATTTAG
*
19677828 ATGAGCCATTTATTTTTCCAAAGTCTTATTGCCTTTATTTAG
1 ATGAGCAATTTATTTTTCCAAAGTCTTATTGCCTTTATTTAG
*
19677870 ATGAGCTATTTATTTTTCCAAAGT-TCTATTGCCTTTATTTAG
1 ATGAGCAATTTATTTTTCCAAAGTCT-TATTGCCTTTATTTAG
19677912 A-GAAGCAATTTATTTTTCTCAAAGTC
1 ATG-AGCAATTTATTTTTC-CAAAGTC
19677938 GTTGAGCCTC
Statistics
Matches: 98, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
41 2 0.02
42 80 0.82
43 16 0.16
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.49
Consensus pattern (42 bp):
ATGAGCAATTTATTTTTCCAAAGTCTTATTGCCTTTATTTAG
Found at i:19678170 original size:17 final size:16
Alignment explanation
Indices: 19678126--19678171 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 16
19678116 GTTAATATAA
19678126 AAAAAATAAAAAAAATG
1 AAAAAAT-AAAAAAATG
*
19678143 AAAAAGCTAAAAAAATG
1 AAAAA-ATAAAAAAATG
19678160 AGAAAAATAAAA
1 A-AAAAATAAAA
19678172 GTTGAGGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 20 0.80
18 5 0.20
ACGTcount: A:0.78, C:0.02, G:0.09, T:0.11
Consensus pattern (16 bp):
AAAAAATAAAAAAATG
Found at i:19679112 original size:77 final size:76
Alignment explanation
Indices: 19678954--19679105 Score: 182
Period size: 77 Copynumber: 2.0 Consensus size: 76
19678944 AATTTTCAAA
* * * * *
19678954 AAAAAATATTTTTGAGGAAAATTGAAAATATCAATTTTCTTTGAAAATAAAATTTATAAAAATAT
1 AAAAAATATTTTTAAGGAAAATTGAAAATATCAATTTTCATTGAAAAAAAAATTTATAAAAAAAC
** *
19679019 TTCCAATTTTT
66 AACCAATTTTG
*
19679030 AAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCATTGAAAAAAAAATTT-TCAAAAAA
1 AAAAAATATTTTTAAGGAAAA-TTGAAAATATCAATTTTCATTGAAAAAAAAATTTAT-AAAAAA
*
19679094 ACAAGC-ATTTTG
64 ACAACCAATTTTG
19679106 GGAAAAAAAG
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
76 26 0.41
77 38 0.59
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (76 bp):
AAAAAATATTTTTAAGGAAAATTGAAAATATCAATTTTCATTGAAAAAAAAATTTATAAAAAAAC
AACCAATTTTG
Found at i:19684273 original size:30 final size:31
Alignment explanation
Indices: 19684223--19684302 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 31
19684213 ATTGATTTTT
19684223 TATTTAAATATTGATAAATTTTAGTCCATAAAT-A
1 TATTTAAATA--GAT-AATTTTA-TCCATAAATAA
* *
19684257 TATTTAAATA-ATAATTTTATCTATAGATAA
1 TATTTAAATAGATAATTTTATCCATAAATAA
*
19684287 TATTTAATTAGATAAT
1 TATTTAAATAGATAAT
19684303 AATATTTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 7 0.17
30 17 0.41
31 7 0.17
34 10 0.24
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (31 bp):
TATTTAAATAGATAATTTTATCCATAAATAA
Found at i:19685255 original size:19 final size:19
Alignment explanation
Indices: 19685214--19685258 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
19685204 TTTAAATTAG
*
19685214 TTTTTAATTAAATTTAAAA
1 TTTTTAAATAAATTTAAAA
19685233 -TTTTAAAT-AATTTAATAA
1 TTTTTAAATAAATTTAA-AA
19685251 TTTTTAAA
1 TTTTTAAA
19685259 ATATATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 7 0.30
18 9 0.39
19 7 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTTAAATAAATTTAAAA
Found at i:19688113 original size:14 final size:14
Alignment explanation
Indices: 19688094--19688136 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
19688084 TTCATTTTTT
*
19688094 AAATAAAAAAATCA
1 AAATAAAAAAATAA
19688108 AAAT-AAAAAATAA
1 AAATAAAAAAATAA
*
19688121 AAAGTAAAAAATTAA
1 AAA-TAAAAAAATAA
19688136 A
1 A
19688137 TTATTGGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 11 0.44
14 5 0.20
15 9 0.36
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.16
Consensus pattern (14 bp):
AAATAAAAAAATAA
Found at i:19689805 original size:63 final size:63
Alignment explanation
Indices: 19689732--19689852 Score: 215
Period size: 63 Copynumber: 1.9 Consensus size: 63
19689722 TTTCTGATAT
19689732 TCATTCTGAATTCAAATAACAAGAATCAATAAGTATATCAACAACTTAAATTGAACTTGACAA
1 TCATTCTGAATTCAAATAACAAGAATCAATAAGTATATCAACAACTTAAATTGAACTTGACAA
* * *
19689795 TCATTTTGAATTCAAATAACAAGAGTCGATAAGTATATCAACAACTTAAATTGAACTT
1 TCATTCTGAATTCAAATAACAAGAATCAATAAGTATATCAACAACTTAAATTGAACTT
19689853 TTGAGTGGGA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (63 bp):
TCATTCTGAATTCAAATAACAAGAATCAATAAGTATATCAACAACTTAAATTGAACTTGACAA
Found at i:19691331 original size:2 final size:2
Alignment explanation
Indices: 19691324--19691357 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
19691314 GGCTGTAAGG
19691324 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19691358 CCATGGTTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19695143 original size:14 final size:16
Alignment explanation
Indices: 19695126--19695164 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
19695116 TTTTTCTCAA
19695126 AAAATTTTA-CCT-TT
1 AAAATTTTATCCTATT
19695140 AAAATTTTATTCCTATT
1 AAAATTTTA-TCCTATT
19695157 AAAATTTT
1 AAAATTTT
19695165 TTAAATTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.41
16 3 0.14
17 10 0.45
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (16 bp):
AAAATTTTATCCTATT
Found at i:19697915 original size:27 final size:27
Alignment explanation
Indices: 19697885--19697941 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
19697875 TTTAAATTTG
**
19697885 GTTGTTG-TGTAAGTTTTTATTATTATT
1 GTTGTTGTTGT-AGTTGCTATTATTATT
*
19697912 GTTGTTGTTGTTGTTGCTATTATTATT
1 GTTGTTGTTGTAGTTGCTATTATTATT
19697939 GTT
1 GTT
19697942 ATTATCTTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.14, C:0.02, G:0.21, T:0.63
Consensus pattern (27 bp):
GTTGTTGTTGTAGTTGCTATTATTATT
Found at i:19698706 original size:20 final size:20
Alignment explanation
Indices: 19698683--19698721 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
19698673 ATTAATACCA
19698683 TAAAAATAT-ATTAAAATAAG
1 TAAAAAT-TCATTAAAATAAG
19698703 TAAAAATTCATTAAAATAA
1 TAAAAATTCATTAAAATAA
19698722 TATAACTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (20 bp):
TAAAAATTCATTAAAATAAG
Found at i:19698822 original size:16 final size:17
Alignment explanation
Indices: 19698801--19698833 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
19698791 TTAAAAAAAG
19698801 AATTTTTTTA-ATTCTA
1 AATTTTTTTACATTCTA
19698817 AATTTTTTTACATTCTA
1 AATTTTTTTACATTCTA
19698834 TGAGCATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (17 bp):
AATTTTTTTACATTCTA
Found at i:19700695 original size:18 final size:19
Alignment explanation
Indices: 19700672--19700707 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
19700662 TTTTCTCATT
*
19700672 TTTATTACTT-ATTTTTAA
1 TTTATTAATTAATTTTTAA
19700690 TTTATTAATTAATTTTTA
1 TTTATTAATTAATTTTTA
19700708 TTATTCTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTATTAATTAATTTTTAA
Found at i:19700889 original size:17 final size:15
Alignment explanation
Indices: 19700864--19700919 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 15
19700854 TAAAATTTTT
*
19700864 TTTTTATTAATTTTA
1 TTTTTATTAAGTTTA
19700879 TATTATTATTAAGTTTA
1 T-TT-TTATTAAGTTTA
**
19700896 TTTTTATTATTTATTA
1 TTTTTATTAAGT-TTA
19700912 TTTTTATT
1 TTTTTATT
19700920 TTAAAAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
15 8 0.23
16 15 0.43
17 12 0.34
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTTTATTAAGTTTA
Found at i:19700909 original size:22 final size:22
Alignment explanation
Indices: 19700873--19700922 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
19700863 TTTTTTATTA
19700873 ATTTTATATTATTATTAAGTTT
1 ATTTTATATTATTATTAAGTTT
**
19700895 ATTTT-TATTATTTATTATTTTT
1 ATTTTATATTA-TTATTAAGTTT
19700917 ATTTTA
1 ATTTTA
19700923 AAAATTAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (22 bp):
ATTTTATATTATTATTAAGTTT
Found at i:19701991 original size:22 final size:24
Alignment explanation
Indices: 19701947--19702035 Score: 69
Period size: 22 Copynumber: 3.7 Consensus size: 24
19701937 AAAAAAGAAA
* *
19701947 AAAAATAGAAATAGAAAATTAAAAGA-
1 AAAAATA-AAATA-ATAA-TAAAAAAT
*
19701973 AAAAATTAAA-AATAATAAAAAATT
1 AAAAATAAAATAATAATAAAAAA-T
*
19701997 AAAAATAAAATAATAAT-AATAAT
1 AAAAATAAAATAATAATAAAAAAT
*
19702020 -AAAATAAAATGATAAT
1 AAAAATAAAATAATAAT
19702036 TACAATTGCC
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
22 21 0.39
23 4 0.07
24 14 0.26
25 9 0.17
26 6 0.11
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (24 bp):
AAAAATAAAATAATAATAAAAAAT
Found at i:19701992 original size:17 final size:17
Alignment explanation
Indices: 19701972--19702004 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
19701962 AAATTAAAAG
19701972 AAAAAATTAAAAATAAT
1 AAAAAATTAAAAATAAT
19701989 AAAAAATTAAAAATAA
1 AAAAAATTAAAAATAA
19702005 AATAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAAAATTAAAAATAAT
Found at i:19702021 original size:31 final size:30
Alignment explanation
Indices: 19701939--19702023 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 30
19701929 GAAAAAGAAA
* * *
19701939 AAAAGAAAAAAA-ATAGA-AATAGAAAATT
1 AAAAGAAAAAAATAAAAATAATAAAAAATT
*
19701967 AAAAGAAAAAATTAAAAATAATAAAAAATT
1 AAAAGAAAAAAATAAAAATAATAAAAAATT
*
19701997 AAAA-ATAAAATAATAATAATAATAAAA
1 AAAAGA-AAAA-AATAAAAATAATAAAA
19702024 TAAAATGATA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
28 11 0.23
29 4 0.09
30 18 0.38
31 14 0.30
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (30 bp):
AAAAGAAAAAAATAAAAATAATAAAAAATT
Found at i:19702390 original size:48 final size:48
Alignment explanation
Indices: 19702233--19702733 Score: 370
Period size: 48 Copynumber: 10.5 Consensus size: 48
19702223 ATGGCTCACT
* * * * * ** *
19702233 TAAGTAGAGGTTCGACAATTTTAAAAATTTATCTTGAAAAAGCTCTTC
1 TAAGCAGAGGCTCAACAACTTTAAAAATTCATCTTGAAAAAATTCCTC
* * * *
19702281 TAAACAAAGGCT---TAACTTTAAAAA-TCATCTTGAAAAAGCTT-CTC
1 TAAGCAGAGGCTCAACAACTTTAAAAATTCATCTTGAAAAA-ATTCCTC
* * * * *
19702325 TCAGTAAAGGCTCAACAACTTTAAAACTTCACCTTGAAAAAATTCCTC
1 TAAGCAGAGGCTCAACAACTTTAAAAATTCATCTTGAAAAAATTCCTC
* * * * * *
19702373 TAAGCAGATGCTTAACAATTTTAAAAAATCATCCT-AAAAAAGCTCCTC
1 TAAGCAGAGGCTCAACAACTTTAAAAATTCATCTTGAAAAAA-TTCCTC
* * * * *
19702421 TAAACAGAGGCTCAATAATTTTAAAAAATCATCTTGAAAAAGCTT-CTC
1 TAAGCAGAGGCTCAACAACTTTAAAAATTCATCTTGAAAAA-ATTCCTC
* * * *
19702469 TTAA-TAGAGGCTTAACAACTTTAAAACTTCATCTTGAAAAAGTTCCTC
1 -TAAGCAGAGGCTCAACAACTTTAAAAATTCATCTTGAAAAAATTCCTC
19702517 TAAGCAGAGGCTCAACAACTTT-AAAATTCTTATCTTGAAAAAACTTCC-C
1 TAAGCAGAGGCTCAACAACTTTAAAAATTC--ATCTTGAAAAAA-TTCCTC
* * * * *
19702566 TCAGCAGAGACTCAATAACTTTAAAAA---ATCTTGAAAAAGTTTCTC
1 TAAGCAGAGGCTCAACAACTTTAAAAATTCATCTTGAAAAAATTCCTC
* * **
19702611 TCAA-CAGAGGCTCAACAACTTTAAAATTCTCATCTCGGAAAAGCTCTCCTC
1 T-AAGCAGAGGCTCAACAACTTTAAAAAT-TCATCT-TGAAAAAAT-TCCTC
* * *
19702662 --AGTAGAGGCTCAAAAACTTTAAAAATTCATCTT-AAAAAAGCTCCTC
1 TAAGCAGAGGCTCAACAACTTTAAAAATTCATCTTGAAAAAA-TTCCTC
*
19702708 TTAGCAGAGGCTCAACAACTTTAAAA
1 TAAGCAGAGGCTCAACAACTTTAAAA
19702734 TTCTTAACTT
Statistics
Matches: 357, Mismatches: 68, Indels: 56
0.74 0.14 0.12
Matches are distributed among these distances:
44 26 0.07
45 44 0.12
46 10 0.03
47 29 0.08
48 165 0.46
49 65 0.18
50 14 0.04
51 4 0.01
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (48 bp):
TAAGCAGAGGCTCAACAACTTTAAAAATTCATCTTGAAAAAATTCCTC
Found at i:19702444 original size:96 final size:95
Alignment explanation
Indices: 19702294--19702736 Score: 411
Period size: 96 Copynumber: 4.6 Consensus size: 95
19702284 ACAAAGGCTT
* * * * *
19702294 AACTTT-AAAAATCATCTTGAAAAAGCTTCTCTCAGTAAAGGCTCAACAACTTTAAAACTTCACC
1 AACTTTAAAAAATCATCTTGAAAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAA-TTCATC
* *
19702358 TTGAAAAAATTCCTCTAAGCAGATGCTTAAC
65 TTGAAAAAATTCCTCTAAGCAGAGGCTCAAC
* * * * * * *
19702389 AATTTTAAAAAATCATCCTAAAAAAGCTCCTCTAAACAGAGGCTCAATAATTTTAAAAAATCATC
1 AACTTTAAAAAATCATCTTGAAAAAGCTCCTCTAAGCAGAGGCTCAACAACTTT-AAAATTCATC
* * *
19702454 TTGAAAAAGCTT-CTCTTAA-TAGAGGCTTAAC
65 TTGAAAAA-ATTCCTC-TAAGCAGAGGCTCAAC
** *
19702485 AACTTTAAAACTTCATCTTGAAAAAGTTCCTCTAAGCAGAGGCTCAACAACTTTAAAATTCTTAT
1 AACTTTAAAAAATCATCTTGAAAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAATTC--AT
* * *
19702550 CTTGAAAAAACTTCC-CTCAGCAGAGACTCAAT
64 CTTGAAAAAA-TTCCTCTAAGCAGAGGCTCAAC
* *
19702582 AACTTT-AAAAA--ATCTTGAAAAAGTTTCTCTCAA-CAGAGGCTCAACAACTTTAAAATTCTCA
1 AACTTTAAAAAATCATCTTGAAAAAGCTCCTCT-AAGCAGAGGCTCAACAACTTTAAAA-T-TCA
* ** * *
19702643 TCTCGGAAAAGCTCTCCTC--AGTAGAGGCTCAAA
63 TCT-TGAAAAAAT-TCCTCTAAGCAGAGGCTCAAC
* * *
19702676 AACTTTAAAAATTCATCTTAAAAAAGCTCCTCTTAGCAGAGGCTCAACAACTTTAAAATTC
1 AACTTTAAAAAATCATCTTGAAAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAATTC
19702737 TTAACTTTTC
Statistics
Matches: 284, Mismatches: 45, Indels: 38
0.77 0.12 0.10
Matches are distributed among these distances:
94 62 0.22
95 28 0.10
96 118 0.42
97 75 0.26
98 1 0.00
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.28
Consensus pattern (95 bp):
AACTTTAAAAAATCATCTTGAAAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAATTCATCT
TGAAAAAATTCCTCTAAGCAGAGGCTCAAC
Found at i:19702683 original size:191 final size:191
Alignment explanation
Indices: 19702294--19702739 Score: 521
Period size: 191 Copynumber: 2.3 Consensus size: 191
19702284 ACAAAGGCTT
* * * *
19702294 AACTTTAAAAATCATCTTGAAAAAGCTT-CTCTCAGTAAAGGCTCAACAACTTTAAAA--CTTCA
1 AACTTTAAAATTCATCTTGAAAAAG-TTCCTCTAAGCAGAGGCTCAACAACTTTAAAATTCTT-A
* *
19702356 CCTTGAAAAAATTCCTCTAAGCAGATGCTTAACAATTTTAAAAAATCATCCTAAAAAAGCTCCTC
64 CCTTGAAAAAATTCCTCTAAGCAGATGCTCAACAACTTTAAAAAATCAT-CTAAAAAAGCTCCTC
* * * * * *
19702421 TAAACAGAGGCTCAATAATTTTAAAAAATCATCTTGAAAAAGCTTCTCTTAATAGAGGCTTAAC
128 TAAACAGAGGCTCAACAACTTTAAAAAATCATCTCGAAAAAGCTTCTCTCAATAGAGGCTCAAA
*
19702485 AACTTTAAAACTTCATCTTGAAAAAGTTCCTCTAAGCAGAGGCTCAACAACTTTAAAATTCTTAT
1 AACTTTAAAA-TTCATCTTGAAAAAGTTCCTCTAAGCAGAGGCTCAACAACTTTAAAATTCTTAC
* * * * *
19702550 CTTGAAAAAACTTCC-CTCAGCAGA-GACTCAATAACTTTAAAAAATC-T-TGAAAAAGTTTCTC
65 CTTGAAAAAA-TTCCTCTAAGCAGATG-CTCAACAACTTTAAAAAATCATCTAAAAAAGCTCCTC
* ** * *
19702611 TCAACAGAGGCTCAACAACTTTAAAATTCTCATCTCGGAAAAGC-TCTCCTCAGTAGAGGCTCAA
128 TAAACAGAGGCTCAACAACTTTAAAA-AATCATCTCGAAAAAGCTTCT-CTCAATAGAGGCTCAA
19702675 A
191 A
* * *
19702676 AACTTTAAAAATTCATCTTAAAAAAGCTCCTCTTAGCAGAGGCTCAACAACTTTAAAATTCTTA
1 AACTTT-AAAATTCATCTTGAAAAAGTTCCTCTAAGCAGAGGCTCAACAACTTTAAAATTCTTA
19702740 ACTTTTCTCG
Statistics
Matches: 220, Mismatches: 26, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
190 37 0.17
191 94 0.43
192 46 0.21
193 36 0.16
194 7 0.03
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (191 bp):
AACTTTAAAATTCATCTTGAAAAAGTTCCTCTAAGCAGAGGCTCAACAACTTTAAAATTCTTACC
TTGAAAAAATTCCTCTAAGCAGATGCTCAACAACTTTAAAAAATCATCTAAAAAAGCTCCTCTAA
ACAGAGGCTCAACAACTTTAAAAAATCATCTCGAAAAAGCTTCTCTCAATAGAGGCTCAAA
Found at i:19707374 original size:12 final size:12
Alignment explanation
Indices: 19707357--19707388 Score: 50
Period size: 10 Copynumber: 2.8 Consensus size: 12
19707347 CAAGCAAATG
19707357 TAGGTAAATATA
1 TAGGTAAATATA
19707369 TAGGT-AA-ATA
1 TAGGTAAATATA
19707379 TAGGTAAATA
1 TAGGTAAATA
19707389 ACTCTTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
10 8 0.44
11 4 0.22
12 6 0.33
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (12 bp):
TAGGTAAATATA
Found at i:19713342 original size:5 final size:5
Alignment explanation
Indices: 19713332--19713357 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
19713322 TTTGGGATTT
19713332 TTTTG TTTTG TTTTG TTTTG TTTTG T
1 TTTTG TTTTG TTTTG TTTTG TTTTG T
19713358 ATTAAACACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (5 bp):
TTTTG
Found at i:19714299 original size:22 final size:22
Alignment explanation
Indices: 19714272--19714313 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
19714262 TGAAAAAAAT
* *
19714272 AATTTTCTTGATTTTTTATTAA
1 AATTTTATTGATTTATTATTAA
*
19714294 AATTTTATTTATTTATTATT
1 AATTTTATTGATTTATTATT
19714314 TATTTTTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (22 bp):
AATTTTATTGATTTATTATTAA
Found at i:19714978 original size:17 final size:17
Alignment explanation
Indices: 19714956--19715000 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
19714946 AAAATTTTTC
19714956 TTTTATTTTTTTATTAA
1 TTTTATTTTTTTATTAA
* *
19714973 TTTTATATTATTATTAA
1 TTTTATTTTTTTATTAA
*
19714990 GTTTATTTTTT
1 TTTTATTTTTT
19715001 ATTTTAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (17 bp):
TTTTATTTTTTTATTAA
Found at i:19716037 original size:3 final size:3
Alignment explanation
Indices: 19716031--19716063 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
19716021 AAATAGAAAA
19716031 AAT AAT AAT AAT AAT -AT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
19716064 AATGGTGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:19716051 original size:14 final size:14
Alignment explanation
Indices: 19716029--19716063 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
19716019 AAAAATAGAA
19716029 AAAATAATAATAAT
1 AAAATAATAATAAT
*
19716043 AATATAATAATAAT
1 AAAATAATAATAAT
19716057 AAAATAA
1 AAAATAA
19716064 AATGGTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAATAATAATAAT
Found at i:19716609 original size:20 final size:20
Alignment explanation
Indices: 19716586--19716633 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
19716576 AAACTAAATG
19716586 GTGAAATCGAAAAAAGATAA
1 GTGAAATCGAAAAAAGATAA
* *
19716606 GTGAAATCGAAAAGAGGTAA
1 GTGAAATCGAAAAAAGATAA
*
19716626 GTAAAATC
1 GTGAAATC
19716634 TCACAGACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.54, C:0.06, G:0.23, T:0.17
Consensus pattern (20 bp):
GTGAAATCGAAAAAAGATAA
Found at i:19719546 original size:21 final size:20
Alignment explanation
Indices: 19719520--19719575 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 20
19719510 ACTATCAAAT
19719520 ATATAAATTACTTCAAAACAA
1 ATATAAATTACTTCAAAA-AA
* *
19719541 ATATAAA-T-CTT-AATAAT
1 ATATAAATTACTTCAAAAAA
19719558 ATATAAATTACTTCAAAA
1 ATATAAATTACTTCAAAA
19719576 TAAGATAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
17 8 0.28
18 4 0.14
19 6 0.21
20 4 0.14
21 7 0.24
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (20 bp):
ATATAAATTACTTCAAAAAA
Found at i:19719604 original size:37 final size:38
Alignment explanation
Indices: 19719517--19719604 Score: 124
Period size: 37 Copynumber: 2.3 Consensus size: 38
19719507 TAAACTATCA
* *
19719517 AATATATAAATTACTTCAAAACAAATATAAATCTTAAT
1 AATATATAAATTACTTCAAAACAAAGATAAATATTAAT
* * *
19719555 AATATATAAATTACTTCAAAA-TAAGATAACTATTAGT
1 AATATATAAATTACTTCAAAACAAAGATAAATATTAAT
19719592 AATATATAAATTA
1 AATATATAAATTA
19719605 TAACCTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
37 24 0.53
38 21 0.47
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (38 bp):
AATATATAAATTACTTCAAAACAAAGATAAATATTAAT
Found at i:19719836 original size:21 final size:22
Alignment explanation
Indices: 19719799--19719860 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 22
19719789 CAAAACTTTC
19719799 ACAAATAAAAAATAAATTACT-CA
1 ACAAAT-AAAAATAAATT-CTCCA
19719822 ACAAATAAAAA-AAATTCTCCA
1 ACAAATAAAAATAAATTCTCCA
19719843 ACAATACTAAAAATAAAT
1 ACAA-A-TAAAAATAAAT
19719861 CCAAAAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
20 2 0.06
21 11 0.31
22 6 0.17
23 12 0.34
24 4 0.11
ACGTcount: A:0.65, C:0.15, G:0.00, T:0.21
Consensus pattern (22 bp):
ACAAATAAAAATAAATTCTCCA
Found at i:19719855 original size:24 final size:22
Alignment explanation
Indices: 19719799--19719860 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 22
19719789 CAAAACTTTC
19719799 ACAAATAAAAAATAAATTACTCA
1 ACAAATAAAAAA-AAATTACTCA
19719822 ACAAAT-AAAAAAAATT-CTCCA
1 ACAAATAAAAAAAAATTACT-CA
*
19719843 ACAATACTAAAAATAAAT
1 ACAA-A-TAAAAAAAAAT
19719861 CCAAAAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
20 2 0.06
21 11 0.32
22 6 0.18
23 7 0.21
24 8 0.24
ACGTcount: A:0.65, C:0.15, G:0.00, T:0.21
Consensus pattern (22 bp):
ACAAATAAAAAAAAATTACTCA
Found at i:19720008 original size:59 final size:59
Alignment explanation
Indices: 19719934--19720092 Score: 214
Period size: 59 Copynumber: 2.7 Consensus size: 59
19719924 CAACAAATTC
* * *
19719934 CAACAAATTTATAACCAAAATCTAAACAAATTTCAACAAATATAA-AA-CTAACAAAAACT
1 CAACAAATTGATAACCAAAACCCAAACAAATTTCAACAAATA-AATAAGC-AACAAAAACT
* * *
19719993 TAACAAATTGGTAACCAAAACCCAAACAAATTTTAACAAATAAATAAGCAACAAAAACT
1 CAACAAATTGATAACCAAAACCCAAACAAATTTCAACAAATAAATAAGCAACAAAAACT
* *
19720052 CAACACATTGATAACCAAAACCCAAATAAATTTCAACAAAT
1 CAACAAATTGATAACCAAAACCCAAACAAATTTCAACAAAT
19720093 TTATAACAAA
Statistics
Matches: 87, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
58 2 0.02
59 84 0.97
60 1 0.01
ACGTcount: A:0.57, C:0.20, G:0.03, T:0.20
Consensus pattern (59 bp):
CAACAAATTGATAACCAAAACCCAAACAAATTTCAACAAATAAATAAGCAACAAAAACT
Found at i:19723669 original size:2 final size:2
Alignment explanation
Indices: 19723662--19723687 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19723652 TCTTTGGTAC
19723662 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
19723688 TGTTTTCCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19725562 original size:6 final size:6
Alignment explanation
Indices: 19725551--19725579 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
19725541 AAGAAAGGGA
19725551 GAGAGG GAGAGG GAGAGG GAGAGG GAGAG
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAG
19725580 AAATGGAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:19728668 original size:3 final size:3
Alignment explanation
Indices: 19728660--19728687 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
19728650 AACTTCACCT
19728660 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
19728688 AATCGTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:19731617 original size:24 final size:24
Alignment explanation
Indices: 19731590--19731645 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
19731580 ATGAATTCTT
19731590 AATAGGTAAAGTTGTATGCTTATA
1 AATAGGTAAAGTTGTATGCTTATA
19731614 AATAGGTAAAGTTGTATGCTTATA
1 AATAGGTAAAGTTGTATGCTTATA
19731638 AATAGGTA
1 AATAGGTA
19731646 TAAAAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.39, C:0.04, G:0.21, T:0.36
Consensus pattern (24 bp):
AATAGGTAAAGTTGTATGCTTATA
Found at i:19736017 original size:21 final size:21
Alignment explanation
Indices: 19735991--19736030 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
19735981 AATTTAAAAG
19735991 AAAATTTTT-TACTGAACACCC
1 AAAATTTTTATA-TGAACACCC
19736012 AAAATTTTTATATGAACAC
1 AAAATTTTTATATGAACAC
19736031 TCCCAAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAATTTTTATATGAACACCC
Found at i:19740406 original size:21 final size:21
Alignment explanation
Indices: 19740380--19740421 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
19740370 TACAAGACCT
*
19740380 CACAACAGCTTCCAGCTCAAA
1 CACAACAACTTCCAGCTCAAA
*
19740401 CACAACAACTTCCAGTTCAAA
1 CACAACAACTTCCAGCTCAAA
19740422 AAATGTTGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.36, G:0.07, T:0.17
Consensus pattern (21 bp):
CACAACAACTTCCAGCTCAAA
Found at i:19741092 original size:17 final size:15
Alignment explanation
Indices: 19741047--19741093 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 15
19741037 ATGAAATAAT
19741047 AAAATAT-TAACAA-
1 AAAATATATAACAAC
*
19741060 ATAATATATAACAAC
1 AAAATATATAACAAC
19741075 AAAATATAATAACTAAC
1 AAAATAT-ATAAC-AAC
19741092 AA
1 AA
19741094 TATGTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 6 0.21
14 6 0.21
15 6 0.21
16 5 0.18
17 5 0.18
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAATATATAACAAC
Found at i:19745108 original size:13 final size:13
Alignment explanation
Indices: 19745074--19745110 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
19745064 TTGAAATAGA
**
19745074 TTTAGGGTAAAAG
1 TTTAGGGTTTAAG
19745087 TTTAGGGTTTAAG
1 TTTAGGGTTTAAG
19745100 TTTAGGGTTTA
1 TTTAGGGTTTA
19745111 GGGTTTTGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.30, T:0.43
Consensus pattern (13 bp):
TTTAGGGTTTAAG
Found at i:19746564 original size:21 final size:21
Alignment explanation
Indices: 19746517--19746565 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
19746507 TTGTCTTCCT
* *
19746517 TTTTTTTATTTTTTGATTTAA
1 TTTTTTAATTTTTTGAATTAA
** *
19746538 AATTTTAATTTTTTTAATTAA
1 TTTTTTAATTTTTTGAATTAA
19746559 TTTTTTA
1 TTTTTTA
19746566 GATTATAAAA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTTTTAATTTTTTGAATTAA
Found at i:19748513 original size:2 final size:2
Alignment explanation
Indices: 19748506--19748544 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
19748496 ACAAGAAATG
19748506 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19748545 AACGCAGATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19756513 original size:6 final size:6
Alignment explanation
Indices: 19756481--19756505 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19756471 CCCACTCCTC
19756481 TCTCTT TCTCTT TCTCTT TCTCTT T
1 TCTCTT TCTCTT TCTCTT TCTCTT T
19756506 TTTCTTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TCTCTT
Found at i:19756516 original size:18 final size:20
Alignment explanation
Indices: 19756479--19756517 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
19756469 TCCCCACTCC
19756479 TCTCTCTTTCTCTTTCTCTT
1 TCTCTCTTTCTCTTTCTCTT
*
19756499 TCTCT-TTTTTCTTT-TCTT
1 TCTCTCTTTCTCTTTCTCTT
19756517 T
1 T
19756518 TCTAATTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 8 0.44
20 5 0.28
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (20 bp):
TCTCTCTTTCTCTTTCTCTT
Found at i:19757645 original size:15 final size:14
Alignment explanation
Indices: 19757602--19757645 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
19757592 GATTAAAATC
*
19757602 AAATTATAATTAGT
1 AAATTATAATTAAT
*
19757616 AAATAATTAATTAAT
1 AAATTA-TAATTAAT
19757631 AAATTATAATATAAT
1 AAATTATAAT-TAAT
19757646 TAAACAAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 9 0.36
15 16 0.64
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (14 bp):
AAATTATAATTAAT
Found at i:19768575 original size:2 final size:2
Alignment explanation
Indices: 19768568--19768592 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19768558 TTAAGATGTG
19768568 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 T
19768593 CATTCTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19770865 original size:182 final size:182
Alignment explanation
Indices: 19770558--19770923 Score: 723
Period size: 182 Copynumber: 2.0 Consensus size: 182
19770548 ATATATTATG
19770558 GAAACAACAAGAATGTTCTTACAAGTTGCAAAGGATGTACTAGGTTGCAGATTTGTATCAATAGC
1 GAAACAACAAGAATGTTCTTACAAGTTGCAAAGGATGTACTAGGTTGCAGATTTGTATCAATAGC
*
19770623 TTTCGTTTCATTGAAAGTGATAATGATCAATGTCGTTCTCTTAAATATATGTTCCTTACGCTTCC
66 TTTCGTTTCATTGAAAGTGATAATGATCAATGTCGTTCTCTTAAACATATGTTCCTTACGCTTCC
19770688 ACATCTCCTATCGTTTATGATTCAAGGACACAAAAAATATATGAGCTCCATC
131 ACATCTCCTATCGTTTATGATTCAAGGACACAAAAAATATATGAGCTCCATC
19770740 GAAACAACAAGAATGTTCTTACAAGTTGCAAAGGATGTACTAGGTTGCAGATTTGTATCAATAGC
1 GAAACAACAAGAATGTTCTTACAAGTTGCAAAGGATGTACTAGGTTGCAGATTTGTATCAATAGC
19770805 TTTCGTTTCATTGAAAGTGATAATGATCAATGTCGTTCTCTTAAACATATGTTCCTTACGCTTCC
66 TTTCGTTTCATTGAAAGTGATAATGATCAATGTCGTTCTCTTAAACATATGTTCCTTACGCTTCC
19770870 ACATCTCCTATCGTTTATGATTCAAGGACACAAAAAATATATGAGCTCCATC
131 ACATCTCCTATCGTTTATGATTCAAGGACACAAAAAATATATGAGCTCCATC
19770922 GA
1 GA
19770924 TCGAGCCTGT
Statistics
Matches: 183, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
182 183 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (182 bp):
GAAACAACAAGAATGTTCTTACAAGTTGCAAAGGATGTACTAGGTTGCAGATTTGTATCAATAGC
TTTCGTTTCATTGAAAGTGATAATGATCAATGTCGTTCTCTTAAACATATGTTCCTTACGCTTCC
ACATCTCCTATCGTTTATGATTCAAGGACACAAAAAATATATGAGCTCCATC
Found at i:19771511 original size:30 final size:30
Alignment explanation
Indices: 19771475--19771535 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
19771465 CGAAATCAAT
* * * *
19771475 AAAATATTATTTTTTAAATATAAATATTTA
1 AAAATATCATTATATAAATATAAATAATTA
*
19771505 AAAATATCATTATATAAATATATATAATTA
1 AAAATATCATTATATAAATATAAATAATTA
19771535 A
1 A
19771536 TTAATTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (30 bp):
AAAATATCATTATATAAATATAAATAATTA
Found at i:19772379 original size:21 final size:21
Alignment explanation
Indices: 19772352--19772403 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
19772342 AATAGAGAAC
19772352 AAAAAAAAAGAG-AACACACAA
1 AAAAAAAAAGAGTAA-ACACAA
* *
19772373 TAAAAAAAATAGTAAACACAA
1 AAAAAAAAAGAGTAAACACAA
19772394 AACAAAAAAA
1 AA-AAAAAAA
19772404 TTTTCGAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.77, C:0.12, G:0.06, T:0.06
Consensus pattern (21 bp):
AAAAAAAAAGAGTAAACACAA
Found at i:19772390 original size:23 final size:22
Alignment explanation
Indices: 19772349--19772403 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
19772339 GAGAATAGAG
*
19772349 AACAAAAAAAAAGAGAACACAC
1 AACAAAAAAAAAGAGAACACAA
*
19772371 AATAAAAAAAATAGTA-AACACAA
1 AACAAAAAAAA-AG-AGAACACAA
19772394 AACAAAAAAA
1 AACAAAAAAA
19772404 TTTTCGAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.36
23 17 0.61
24 1 0.04
ACGTcount: A:0.76, C:0.13, G:0.05, T:0.05
Consensus pattern (22 bp):
AACAAAAAAAAAGAGAACACAA
Found at i:19772604 original size:51 final size:51
Alignment explanation
Indices: 19772540--19772639 Score: 146
Period size: 51 Copynumber: 2.0 Consensus size: 51
19772530 TTTGGGTCGT
*
19772540 CGAAAACTAGAAAAGTTTGAATTTTTCAGCAACCATTGAATTTTTTGGCAC
1 CGAAAACTAGAAAAGTTTAAATTTTTCAGCAACCATTGAATTTTTTGGCAC
* * * **
19772591 CGAAATCTGGAAAAGTTTAAATTTTTCGGTGACCATTGAATTTTTTGGC
1 CGAAAACTAGAAAAGTTTAAATTTTTCAGCAACCATTGAATTTTTTGGC
19772640 CATTGAAATC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (51 bp):
CGAAAACTAGAAAAGTTTAAATTTTTCAGCAACCATTGAATTTTTTGGCAC
Found at i:19773404 original size:13 final size:12
Alignment explanation
Indices: 19773378--19773420 Score: 59
Period size: 13 Copynumber: 3.4 Consensus size: 12
19773368 TGATTTAAAC
*
19773378 AATATAAAACAAT
1 AATA-AAAATAAT
19773391 AATAAAAATTAAT
1 AATAAAAA-TAAT
19773404 AATAAAAATAAT
1 AATAAAAATAAT
19773416 AATAA
1 AATAA
19773421 TTGATATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 13 0.46
13 15 0.54
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (12 bp):
AATAAAAATAAT
Found at i:19785733 original size:34 final size:35
Alignment explanation
Indices: 19785685--19785750 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 35
19785675 GGTTTGGGTA
* *
19785685 ATTTTTTTTAATTTTTTA-ATTTTTTATATATTATT
1 ATTTTTGTTAA-TTTTGAGATTTTTTATATATTATT
*
19785720 ATTTTTGTT-ATTTTGAGTTTTTTTATATATT
1 ATTTTTGTTAATTTTGAGATTTTTTATATATT
19785751 TATGCATGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 5 0.19
34 14 0.52
35 8 0.30
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.73
Consensus pattern (35 bp):
ATTTTTGTTAATTTTGAGATTTTTTATATATTATT
Found at i:19785885 original size:21 final size:20
Alignment explanation
Indices: 19785800--19785904 Score: 70
Period size: 21 Copynumber: 5.0 Consensus size: 20
19785790 TAATTGTTTT
19785800 AATAATAATAAAAA-TAAAA
1 AATAATAATAAAAATTAAAA
* *
19785819 ATAAAATAAGATAATAATT-AAA
1 A-ATAAT-A-ATAAAAATTAAAA
* *
19785841 TATATATATTAAAAATGCTTAAAA
1 AATA-ATAATAAAAA---TTAAAA
*
19785865 AATAATAATAATAATCTAAAA
1 AATAATAATAAAAAT-TAAAA
*
19785886 AATAGTAATAAAAATTAAA
1 AATAATAATAAAAATTAAA
19785905 TCTTTTTTTA
Statistics
Matches: 65, Mismatches: 11, Indels: 19
0.68 0.12 0.20
Matches are distributed among these distances:
19 1 0.02
20 14 0.22
21 22 0.34
22 11 0.17
23 11 0.17
24 6 0.09
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.29
Consensus pattern (20 bp):
AATAATAATAAAAATTAAAA
Found at i:19786068 original size:12 final size:12
Alignment explanation
Indices: 19786004--19786068 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 12
19785994 TTATAAAAAG
*
19786004 AAAATTAATAAA
1 AAAATTAATAAT
19786016 AAAATGT-ATAA-
1 AAAAT-TAATAAT
19786027 AAAATTAA-AAT
1 AAAATTAATAAT
*
19786038 -TAA-TAATAAT
1 AAAATTAATAAT
* *
19786048 AATACTAATAAT
1 AAAATTAATAAT
19786060 AAAATTAAT
1 AAAATTAAT
19786069 GTTATTATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
9 3 0.07
10 8 0.19
11 7 0.17
12 23 0.55
13 1 0.02
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (12 bp):
AAAATTAATAAT
Found at i:19786303 original size:21 final size:21
Alignment explanation
Indices: 19786278--19786335 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
19786268 CCCTAAACTC
19786278 CAAACCTCTAAACCTTGAAAG
1 CAAACCTCTAAACCTTGAAAG
* *
19786299 CAAACCTC-AAACCATGAAAT
1 CAAACCTCTAAACCTTGAAAG
19786319 CAAAACC-CTAAATCCTT
1 C-AAACCTCTAAA-CCTT
19786336 TAAACCCTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 12 0.39
21 16 0.52
22 3 0.10
ACGTcount: A:0.45, C:0.31, G:0.05, T:0.19
Consensus pattern (21 bp):
CAAACCTCTAAACCTTGAAAG
Found at i:19786359 original size:21 final size:22
Alignment explanation
Indices: 19786333--19786418 Score: 72
Period size: 22 Copynumber: 4.0 Consensus size: 22
19786323 ACCCTAAATC
19786333 CTTTAAACCCTAAAACC-AAAA
1 CTTTAAACCCTAAAACCTAAAA
*
19786354 CTTTAAA-CCTCAAACCCTAAAA
1 CTTTAAACCCT-AAAACCTAAAA
* *
19786376 -TTGAAACCCTAAAATCCTAAAT
1 CTTTAAACCCTAAAA-CCTAAAA
* *
19786398 C-CTATACCCTAAAATCCTAAA
1 CTTTAAACCCTAAAA-CCTAAA
19786419 TTTTGAAAAC
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
20 3 0.06
21 20 0.38
22 30 0.57
ACGTcount: A:0.47, C:0.29, G:0.01, T:0.23
Consensus pattern (22 bp):
CTTTAAACCCTAAAACCTAAAA
Found at i:19787796 original size:40 final size:40
Alignment explanation
Indices: 19787707--19787796 Score: 119
Period size: 40 Copynumber: 2.2 Consensus size: 40
19787697 ACCTCTCAGA
*
19787707 TTTTAAATTTAAAGTTTGTTGCCTCTAGTGATAAAAGCTT
1 TTTTAAATTTAAAGTTTGTTGCCTCTAGTCATAAAAGCTT
* * *
19787747 TTTAAAATTTAAAGTTTGTTGCTTCTGGTCA-AAATAGCTT
1 TTTTAAATTTAAAGTTTGTTGCCTCTAGTCATAAA-AGCTT
*
19787787 TTTTTAATTT
1 TTTTAAATTT
19787797 CAAGAGCCTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 3 0.07
40 40 0.93
ACGTcount: A:0.29, C:0.09, G:0.13, T:0.49
Consensus pattern (40 bp):
TTTTAAATTTAAAGTTTGTTGCCTCTAGTCATAAAAGCTT
Found at i:19788046 original size:38 final size:38
Alignment explanation
Indices: 19787942--19788627 Score: 732
Period size: 38 Copynumber: 17.7 Consensus size: 38
19787932 GCATCTAGTC
* *
19787942 AAAGGAGCCTTTTAACATTTAAAGTTTGTTACCTTTGGTT
1 AAAGGAG-CTTTTGA-ATTTAAAGTTTGTTGCCTTTGGTT
*
19787982 AAAGGAGCTTTTGGAATTTAAAGTTTGTTGCCTTTCGTT
1 AAAGGAGCTTTT-GAATTTAAAGTTTGTTGCCTTTGGTT
* * * *
19788021 AAAGGAACTTTTGAATTTAAAGTTTGTTGCCTCTGATG
1 AAAGGAGCTTTTGAATTTAAAGTTTGTTGCCTTTGGTT
* * *
19788059 AAAGAAGCCTTTTAATATTTAAAGTTTGTTGCCATTGGTT
1 AAAGGAG-CTTTTGA-ATTTAAAGTTTGTTGCCTTTGGTT
* *
19788099 AAAGAAGGTTTTGAAATTTAAAGTTTGTTGCCTTTGGTT
1 AAAGGAGCTTTTG-AATTTAAAGTTTGTTGCCTTTGGTT
* * * *
19788138 AAAGGAGCTTTTGAATTTAAAGTTCGTTACCTCTT-ATC
1 AAAGGAGCTTTTGAATTTAAAGTTTGTTGCCT-TTGGTT
*
19788176 AAAGGAGTCTTTTAACATTTAAAGTTTGTTGCCTTTGGTT
1 AAAGGAG-CTTTTGA-ATTTAAAGTTTGTTGCCTTTGGTT
* * * *
19788216 AAAGGAGCTTTTAAATTTAAAGTTTGTT-ACTTCTGATG
1 AAAGGAGCTTTTGAATTTAAAGTTTGTTGCCTT-TGGTT
*
19788254 AAAGGAGCTTTTAACATTTAAAGTTTGTTGCCTTTGGTT
1 AAAGGAGCTTTTGA-ATTTAAAGTTTGTTGCCTTTGGTT
* *
19788293 AAAGGAG-TTTTGAAATTTAAAGTTTGTTACATTTGGTT
1 AAAGGAGCTTTTG-AATTTAAAGTTTGTTGCCTTTGGTT
*
19788331 AAAAGAGCTTTTGAATTTAAAGTTTGTTGCCTTTGGTT
1 AAAGGAGCTTTTGAATTTAAAGTTTGTTGCCTTTGGTT
* * * ** *
19788369 AAAAGAGCTTTAGAATTTAAAGTTTATTGCCCCTGGTC
1 AAAGGAGCTTTTGAATTTAAAGTTTGTTGCCTTTGGTT
* *
19788407 AGAGGAGCCTTTTAATATTTAAAGTTTGTTGCCTTTGGTT
1 AAAGGAG-CTTTTGA-ATTTAAAGTTTGTTGCCTTTGGTT
* *
19788447 AAAGGAGCTTTTGGAATTTAAAGTTTGTTGCC-TCGGATG
1 AAAGGAGCTTTT-GAATTTAAAGTTTGTTGCCTTTGG-TT
* * * *
19788486 AGATGAGTCTTTTAACATTTAAAGTTTGTTACCTTTGGTT
1 AAAGGAG-CTTTTGA-ATTTAAAGTTTGTTGCCTTTGGTT
* * * *
19788526 AAATGAGCTTTAGAATTTAAAATTTGTTGCCTTTGATT
1 AAAGGAGCTTTTGAATTTAAAGTTTGTTGCCTTTGGTT
* ** * *
19788564 AAAAGAGCTTTTGAATTTAAAGTTCATTGCCTATGGTG
1 AAAGGAGCTTTTGAATTTAAAGTTTGTTGCCTTTGGTT
*
19788602 AGAGGAGCTTTTTGAATTTAAAGTTT
1 AAAGGAGC-TTTTGAATTTAAAGTTT
19788628 TATAGTCTTT
Statistics
Matches: 544, Mismatches: 81, Indels: 43
0.81 0.12 0.06
Matches are distributed among these distances:
37 3 0.01
38 236 0.43
39 184 0.34
40 118 0.22
41 3 0.01
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (38 bp):
AAAGGAGCTTTTGAATTTAAAGTTTGTTGCCTTTGGTT
Found at i:19788085 original size:117 final size:115
Alignment explanation
Indices: 19787918--19788627 Score: 761
Period size: 117 Copynumber: 6.1 Consensus size: 115
19787908 TAAAGGAGAC
** * * *
19787918 ATTTAAAGTTCATTGCATCTAGTCAAAGGAGCCTTTTAACATTTAAAGTTTGTTACCTTTGGTTA
1 ATTTAAAGTTTGTTGCCTCTGGTCAAAGGAGCCTTTTAA-ATTTAAAGTTTGTTGCCTTTGGTTA
* *
19787983 AAGGAGCTTTTGGAATTTAAAGTTTGTTGCCTTTCGTTAAAGGAACTTTTGA
65 AAGGAGCTTTT-GAATTTAAAGTTTGTTGCCTTTCGTGAAAGGAGCTTTTGA
* * * *
19788035 ATTTAAAGTTTGTTGCCTCTGATGAAAGAAGCCTTTTAATATTTAAAGTTTGTTGCCATTGGTTA
1 ATTTAAAGTTTGTTGCCTCTGGTCAAAGGAGCCTTTTAA-ATTTAAAGTTTGTTGCCTTTGGTTA
* * * *
19788100 AAGAAGGTTTTGAAATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTGA
65 AAGGAGCTTTTG-AATTTAAAGTTTGTTGCCTTTCGTGAAAGGAGCTTTTGA
* * ** *
19788152 ATTTAAAGTTCGTTACCTCTTATCAAAGGAGTCTTTTAACATTTAAAGTTTGTTGCCTTTGGTTA
1 ATTTAAAGTTTGTTGCCTCTGGTCAAAGGAGCCTTTTAA-ATTTAAAGTTTGTTGCCTTTGGTTA
* * *
19788217 AAGGAGCTTTTAAATTTAAAGTTTGTT-AC-TTCTGATGAAAGGAGCTTTTAA
65 AAGGAGCTTTTGAATTTAAAGTTTGTTGCCTTTC-G-TGAAAGGAGCTTTTGA
* * * *
19788268 CATTTAAAGTTTGTTGCCTTTGGTTAAAGGAG--TTTTGAAATTTAAAGTTTGTTACATTTGGTT
1 -ATTTAAAGTTTGTTGCCTCTGGTCAAAGGAGCCTTTT-AAATTTAAAGTTTGTTGCCTTTGGTT
* * * * *
19788331 AAAAGAGCTTTTGAATTTAAAGTTTGTTGCCTTTGGTTAAAAGAGCTTTAGA
64 AAAGGAGCTTTTGAATTTAAAGTTTGTTGCCTTTCGTGAAAGGAGCTTTTGA
* * *
19788383 ATTTAAAGTTTATTGCCCCTGGTCAGAGGAGCCTTTTAATATTTAAAGTTTGTTGCCTTTGGTTA
1 ATTTAAAGTTTGTTGCCTCTGGTCAAAGGAGCCTTTTAA-ATTTAAAGTTTGTTGCCTTTGGTTA
* * *
19788448 AAGGAGCTTTTGGAATTTAAAGTTTGTTGCC--TCGGATGAGATGAGTCTTTTAA
65 AAGGAGCTTTT-GAATTTAAAGTTTGTTGCCTTTC-G-TGAAAGGAG-CTTTTGA
* * * * * *
19788501 CATTTAAAGTTTGTTACCTTTGGTTAAATGAG-C-TTTAGAATTTAAAATTTGTTGCCTTTGATT
1 -ATTTAAAGTTTGTTGCCTCTGGTCAAAGGAGCCTTTTA-AATTTAAAGTTTGTTGCCTTTGGTT
* ** * * *
19788564 AAAAGAGCTTTTGAATTTAAAGTTCATTGCCTATGGTGAGAGGAGCTTTTTGA
64 AAAGGAGCTTTTGAATTTAAAGTTTGTTGCCTTTCGTGAAAGGAGC-TTTTGA
19788617 ATTTAAAGTTT
1 ATTTAAAGTTT
19788628 TATAGTCTTT
Statistics
Matches: 500, Mismatches: 74, Indels: 40
0.81 0.12 0.07
Matches are distributed among these distances:
114 28 0.06
115 81 0.16
116 102 0.20
117 257 0.51
118 8 0.02
119 24 0.05
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (115 bp):
ATTTAAAGTTTGTTGCCTCTGGTCAAAGGAGCCTTTTAAATTTAAAGTTTGTTGCCTTTGGTTAA
AGGAGCTTTTGAATTTAAAGTTTGTTGCCTTTCGTGAAAGGAGCTTTTGA
Found at i:19788814 original size:3 final size:3
Alignment explanation
Indices: 19788808--19788852 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
19788798 TTGTTTTTTT
*
19788808 TTA TTA -TA TAA TT- TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19788853 ATCTTTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 6 0.16
3 31 0.84
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:19788827 original size:18 final size:17
Alignment explanation
Indices: 19788801--19788859 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 17
19788791 ACCAATTTTG
*
19788801 TTTTTTTTTATTATATAA
1 TTTTATTTTATTAT-TAA
19788819 TTTTATTTTATTATT-A
1 TTTTATTTTATTATTAA
19788835 TTATTATTATTATTATTAA
1 TT-TTATT-TTATTATTAA
19788854 TCTTTA
1 T-TTTA
19788860 AAACAAACGA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
16 3 0.08
17 6 0.17
18 21 0.58
19 5 0.14
20 1 0.03
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTATTTTATTATTAA
Found at i:19789154 original size:27 final size:25
Alignment explanation
Indices: 19789111--19789165 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
19789101 AACAGAGAAC
** *
19789111 AAAAAAAAAAAGGAACACACAATCAA
1 AAAAAAAAAAACAAACACA-AAACAA
19789137 AAAAAAAAACAACAAACACAAAACAA
1 AAAAAAAAA-AACAAACACAAAACAA
19789163 AAA
1 AAA
19789166 TTTTTTCCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.78, C:0.16, G:0.04, T:0.02
Consensus pattern (25 bp):
AAAAAAAAAAACAAACACAAAACAA
Found at i:19789365 original size:51 final size:50
Alignment explanation
Indices: 19789304--19789401 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 50
19789294 TTGGTCGTTG
*
19789304 GAAACTGAAAAAGTTTGAATTTTTCGACT-ACCATTGAATTTTTTGACATC
1 GAAACTGAAAAAATTTGAATTTTTCG-CTGACCATTGAATTTTTTGACATC
* * * *
19789354 GAAATCTGAAAAAATTTTAATTTTTTGGTGACCGTTGAATTTTTTGAC
1 GAAA-CTGAAAAAATTTGAATTTTTCGCTGACCATTGAATTTTTTGAC
19789402 CACCAAAATC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
50 5 0.12
51 36 0.88
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (50 bp):
GAAACTGAAAAAATTTGAATTTTTCGCTGACCATTGAATTTTTTGACATC
Found at i:19789704 original size:6 final size:6
Alignment explanation
Indices: 19789689--19789777 Score: 61
Period size: 6 Copynumber: 14.3 Consensus size: 6
19789679 TGCAGGGTTT
* * * * * *
19789689 TTTTTC TTTTTA TTTTTCA TTTTGA TTTTGA TTTTGA TTTTTTA TGTTAA
1 TTTTTA TTTTTA TTTTT-A TTTTTA TTTTTA TTTTTA -TTTTTA TTTTTA
* * * *
19789739 TTTTTA TGTTAA TTTTTA TTATTA TTATTA TTTTATA TT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT-TA TT
19789778 ATTGCTATTA
Statistics
Matches: 67, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
6 53 0.79
7 14 0.21
ACGTcount: A:0.20, C:0.02, G:0.06, T:0.72
Consensus pattern (6 bp):
TTTTTA
Found at i:19790199 original size:23 final size:23
Alignment explanation
Indices: 19790168--19790212 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
19790158 TGATTTAAAC
* *
19790168 AATATAAAACAATAATAAAAATT
1 AATAAAAAACAAAAATAAAAATT
*
19790191 AATAAAAAATAAAAATAAAAAT
1 AATAAAAAACAAAAATAAAAAT
19790213 AATTGATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (23 bp):
AATAAAAAACAAAAATAAAAATT
Found at i:19793927 original size:27 final size:29
Alignment explanation
Indices: 19793863--19793929 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
19793853 ATTTTTATCT
*
19793863 TATATATTTATATAAATTTTTTATAAATA
1 TATATATTAATATAAATTTTTTATAAATA
*
19793892 TATATATTAATAT-ATTTTTTTAATAAA-A
1 TATATATTAATATAAATTTTTT-ATAAATA
19793920 -ATATATTAAT
1 TATATATTAAT
19793930 TCTAATTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 10 0.29
28 8 0.23
29 17 0.49
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
TATATATTAATATAAATTTTTTATAAATA
Found at i:19795366 original size:18 final size:17
Alignment explanation
Indices: 19795343--19795376 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
19795333 TTTCTTTGTA
19795343 TTTTTTATTATTTTTTAC
1 TTTTTTATT-TTTTTTAC
19795361 TTTTTTATTTTTTTTA
1 TTTTTTATTTTTTTTA
19795377 AATTGACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTATTTTTTTTAC
Found at i:19795622 original size:21 final size:21
Alignment explanation
Indices: 19795599--19795639 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
19795589 AATCTGTTCA
19795599 TTTAAGATTTGTTTATATTTAT
1 TTTAAG-TTTGTTTATATTTAT
*
19795621 TTTAAGTTTGTTTGTATTT
1 TTTAAGTTTGTTTATATTT
19795640 GGTTATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.22, C:0.00, G:0.12, T:0.66
Consensus pattern (21 bp):
TTTAAGTTTGTTTATATTTAT
Found at i:19795694 original size:14 final size:15
Alignment explanation
Indices: 19795642--19795714 Score: 69
Period size: 15 Copynumber: 4.9 Consensus size: 15
19795632 TTGTATTTGG
* *
19795642 TTATTATTTATTTAT
1 TTATAATTTATTTAA
* *
19795657 TTTTAATTT-TATAA
1 TTATAATTTATTTAA
**
19795671 TTATATATTTATTTGT
1 TTATA-ATTTATTTAA
19795687 TTA-AATTTATTTAA
1 TTATAATTTATTTAA
19795701 TTATAATTTATTTA
1 TTATAATTTATTTA
19795715 TTACTCATAA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
14 18 0.40
15 22 0.49
16 5 0.11
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (15 bp):
TTATAATTTATTTAA
Found at i:19797420 original size:25 final size:23
Alignment explanation
Indices: 19797386--19797437 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 23
19797376 AAATGATATT
19797386 TAATAATTTTAAATTTTAATATTTA
1 TAATAATTTTAAATTTTAA-A-TTA
* * *
19797411 TAATATTTTTTATTTTTAAATTA
1 TAATAATTTTAAATTTTAAATTA
19797434 TAAT
1 TAAT
19797438 TTGTTTTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 7 0.29
24 1 0.04
25 16 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TAATAATTTTAAATTTTAAATTA
Found at i:19798143 original size:17 final size:17
Alignment explanation
Indices: 19798123--19798178 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
19798113 AAAAATTTAT
*
19798123 TTATTAATGAAATTATA
1 TTATTAATGAAATAATA
*
19798140 TTATT--TG-AATAATT
1 TTATTAATGAAATAATA
*
19798154 TTATTAATAAAATAATA
1 TTATTAATGAAATAATA
*
19798171 TTTTTAAT
1 TTATTAAT
19798179 TCATTAATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
14 10 0.32
15 2 0.06
16 1 0.03
17 18 0.58
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (17 bp):
TTATTAATGAAATAATA
Found at i:19801720 original size:10 final size:9
Alignment explanation
Indices: 19801705--19801730 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
19801695 CAAATCAGGA
19801705 TTTTTTTTC
1 TTTTTTTTC
19801714 TTTTTTTTC
1 TTTTTTTTC
19801723 TTTTTTTT
1 TTTTTTTT
19801731 GCCACTTAAT
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTC
Done.