Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008138.1 Hibiscus syriacus cultivar Beakdansim tig00110694_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: 3838456
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 18
Found at i:2650819 original size:20 final size:20
Alignment explanation
Indices: 2650774--2650820 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
2650764 TGACTTCTGT
2650774 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAGATTCGC
** * *
2650794 AATGCGATTTATATATTCGC
1 GTTGCGATTTACAGATTCGC
2650814 GTTGCGA
1 GTTGCGA
2650821 AATTGGAGTT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACAGATTCGC
Found at i:2651004 original size:26 final size:26
Alignment explanation
Indices: 2650961--2651053 Score: 91
Period size: 28 Copynumber: 3.6 Consensus size: 26
2650951 TTATATAATA
* * *
2650961 TACTATATAGTAT-A-ATAACATACG
1 TACTATATAATATAATATAATATATG
2650985 TACTATATAATATAATATAATATATG
1 TACTATATAATATAATATAATATATG
** *
2651011 TATGCTATACGATATAATATAATATATA
1 TA--CTATATAATATAATATAATATATG
*
2651039 TCCTATATAATATAA
1 TACTATATAATATAA
2651054 ACCATATAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
24 12 0.21
25 1 0.02
26 21 0.38
28 22 0.39
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.39
Consensus pattern (26 bp):
TACTATATAATATAATATAATATATG
Found at i:2651060 original size:14 final size:16
Alignment explanation
Indices: 2651027--2651064 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
2651017 ATACGATATA
*
2651027 ATATAATATATATCCT
1 ATATAATATATAACCT
2651043 ATATAATATA-AACC-
1 ATATAATATATAACCT
2651057 ATATAATA
1 ATATAATA
2651065 CATCTATACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 3 0.14
16 10 0.48
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (16 bp):
ATATAATATATAACCT
Found at i:2661999 original size:24 final size:24
Alignment explanation
Indices: 2661972--2662023 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
2661962 AACGGATATA
*
2661972 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
2661996 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
2662020 TCAA
1 TCAA
2662024 GTAACAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:2662110 original size:24 final size:24
Alignment explanation
Indices: 2661995--2662110 Score: 146
Period size: 24 Copynumber: 4.8 Consensus size: 24
2661985 CATAAATCAG
* *
2661995 GTCAAGTATCATATCAGAAAT-CAG
1 GTCAAGTATCAGATCAG-AATCCAT
* * *
2662019 GTCAAGTAACAGATCAAAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
2662043 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
*
2662067 ATC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
2662091 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
2662111 TCAAATCGAA
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
23 5 0.06
24 73 0.91
25 2 0.03
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:2662125 original size:24 final size:23
Alignment explanation
Indices: 2662028--2662128 Score: 105
Period size: 24 Copynumber: 4.2 Consensus size: 23
2662018 GGTCAAGTAA
*
2662028 CAGATCAAAATCCA-AGTCAAGTAT
1 CAGATCAGAATCCATA-TCAA-TAT
2662052 CAGATCAGAATCCATATCAGATAT
1 CAGATCAGAATCCATATCA-ATAT
*
2662076 CAGATCAGAATCCATGTCAAGTAT
1 CAGATCAGAATCCATATCAA-TAT
* * *
2662100 CAGATCAGAATTCAAATCGAAAAT
1 CAGATCAGAATCCATATC-AATAT
2662124 CAGAT
1 CAGAT
2662129 AAAATATTCA
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
23 1 0.01
24 62 0.93
25 4 0.06
ACGTcount: A:0.44, C:0.20, G:0.14, T:0.23
Consensus pattern (23 bp):
CAGATCAGAATCCATATCAATAT
Found at i:2662126 original size:48 final size:48
Alignment explanation
Indices: 2662028--2662133 Score: 144
Period size: 48 Copynumber: 2.2 Consensus size: 48
2662018 GGTCAAGTAA
* *
2662028 CAGATCAAAATCCAAGTCAAGTATCAGATCAGAATCCATATCAGATAT
1 CAGATCAAAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAAAT
* * *
2662076 CAGATCAGAATCCATGTCAAGTATCAGATCAGAATTCAAATC-GAAAAT
1 CAGATCAAAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAG-AAAT
2662124 CAGAT-AAAAT
1 CAGATCAAAAT
2662134 ATTCATGTGA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
47 5 0.10
48 46 0.90
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (48 bp):
CAGATCAAAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAAAT
Found at i:2675893 original size:26 final size:26
Alignment explanation
Indices: 2675863--2675913 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
2675853 GATATCATTG
*
2675863 AAATAATTAAATGATC-TAATTAAAAA
1 AAATAAATAAATGATCAT-ATTAAAAA
*
2675889 AAATAAATAAGTGATCATATTAAAA
1 AAATAAATAAATGATCATATTAAAA
2675914 TCTTTTATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.61, C:0.04, G:0.06, T:0.29
Consensus pattern (26 bp):
AAATAAATAAATGATCATATTAAAAA
Found at i:2676425 original size:4 final size:4
Alignment explanation
Indices: 2676416--2676442 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2676406 AAACATGAAC
2676416 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
2676443 GCAATGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:2676884 original size:17 final size:16
Alignment explanation
Indices: 2676853--2676887 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
2676843 TTATTTTTAT
2676853 ATTTTTTATAAATATA
1 ATTTTTTATAAATATA
*
2676869 ATTTTATTATATATATA
1 ATTTT-TTATAAATATA
2676886 AT
1 AT
2676888 ATGAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTTTTATAAATATA
Found at i:2677275 original size:21 final size:21
Alignment explanation
Indices: 2677249--2677293 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
2677239 ACATCTCATC
2677249 ATTTAACCAAAAAGTGGTATT
1 ATTTAACCAAAAAGTGGTATT
2677270 ATTTAACCAAAAAGTGGTATT
1 ATTTAACCAAAAAGTGGTATT
2677291 ATT
1 ATT
2677294 GTATAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (21 bp):
ATTTAACCAAAAAGTGGTATT
Found at i:2677421 original size:184 final size:186
Alignment explanation
Indices: 2677111--2677458 Score: 637
Period size: 184 Copynumber: 1.9 Consensus size: 186
2677101 TTATTAAGTT
2677111 TATAATTTTGAGTAAAGAACGAAGAATAAAATTTGAAAATGAACAATATGGATTGAATTCATTAT
1 TATAATTTTGAGTAAAGAACGAAGAATAAAATTTGAAAATGAACAATATGGATTGAATTCATTAT
* *
2677176 TTTAGGGGTTTTTATGTCCAAAGTGATTGGAATTGTTCATTACCTAAGAAATTGGATGTAATGAC
66 TTTAGGGGTTTTTATGTCCAAAGTGATGGGAATTGTTCATTACCTAAGAAATTGAATGTAATGAC
*
2677241 A-TCTCATCA-TTTAACCAAAAAGTGGTATTATTTAACCAAAAAGTGGTATTATTG
131 ATTCTCATCATTTTAACCAAAAAATGGTATTATTTAACCAAAAAGTGGTATTATTG
*
2677295 TATAATTTTGAGTAAAGAACGAAGAATAAAATTTGAAAATGATCAATATGGATTGAATTCATTAT
1 TATAATTTTGAGTAAAGAACGAAGAATAAAATTTGAAAATGAACAATATGGATTGAATTCATTAT
*
2677360 TTTAGGGGTTTTTATGTCCAAAGTGATGGGAATTGTTCATTACCTAAGAATTTGAATGTAATGAC
66 TTTAGGGGTTTTTATGTCCAAAGTGATGGGAATTGTTCATTACCTAAGAAATTGAATGTAATGAC
2677425 ATTCTCATCATTTTAACCAAAAAATGGTATTATT
131 ATTCTCATCATTTTAACCAAAAAATGGTATTATT
2677459 GGTAATAAGT
Statistics
Matches: 157, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
184 127 0.81
185 8 0.05
186 22 0.14
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (186 bp):
TATAATTTTGAGTAAAGAACGAAGAATAAAATTTGAAAATGAACAATATGGATTGAATTCATTAT
TTTAGGGGTTTTTATGTCCAAAGTGATGGGAATTGTTCATTACCTAAGAAATTGAATGTAATGAC
ATTCTCATCATTTTAACCAAAAAATGGTATTATTTAACCAAAAAGTGGTATTATTG
Found at i:2677879 original size:11 final size:11
Alignment explanation
Indices: 2677838--2677877 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
2677828 TTAATTATAT
2677838 AATAAATTTAA
1 AATAAATTTAA
*
2677849 ATTAAATTTTAA
1 AATAAA-TTTAA
2677861 AATAAATTTAA
1 AATAAATTTAA
2677872 TAATAA
1 -AATAA
2677878 TTATTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AATAAATTTAA
Found at i:2677879 original size:23 final size:22
Alignment explanation
Indices: 2677829--2677881 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
2677819 TTTAAATTTT
* *
2677829 TAATTATATAATAAATTTAAAT
1 TAATTATAAAATAAATTTAAAA
*
2677851 TAAATTTTAAAATAAATTTAATAA
1 T-AATTATAAAATAAATTTAA-AA
2677875 TAATTAT
1 TAATTAT
2677882 TTATTACTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 1 0.04
23 22 0.88
24 2 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAATTATAAAATAAATTTAAAA
Found at i:2678184 original size:15 final size:14
Alignment explanation
Indices: 2678138--2678200 Score: 65
Period size: 15 Copynumber: 4.4 Consensus size: 14
2678128 CATCAACAGA
*
2678138 ATAAACATT-TTAT
1 ATAAAAATTATTAT
*
2678151 ATAAAAATTATATTT
1 ATAAAAATTAT-TAT
2678166 ATAAAAATTATTAT
1 ATAAAAATTATTAT
*
2678180 AATAAATAATTTTTAT
1 -ATAAA-AATTATTAT
2678196 ATAAA
1 ATAAA
2678201 TTTTTCTTCT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
13 8 0.19
14 3 0.07
15 23 0.55
16 8 0.19
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (14 bp):
ATAAAAATTATTAT
Found at i:2678194 original size:28 final size:27
Alignment explanation
Indices: 2678150--2678202 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
2678140 AAACATTTTA
*
2678150 TATAAAAATTATATTTATAAAAATTAT
1 TATAAAAATAATATTTATAAAAATTAT
* *
2678177 TATAATAAATAATTTTTATATAAATT
1 TATAA-AAATAATATTTATAAAAATT
2678203 TTTCTTCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TATAAAAATAATATTTATAAAAATTAT
Found at i:2678654 original size:20 final size:20
Alignment explanation
Indices: 2678612--2678654 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
2678602 GGTAGGTATC
*
2678612 GATACATATATATAAGTATT
1 GATACATATATATAAGTACT
*
2678632 GATACATA-AGTATCAGTACT
1 GATACATATA-TATAAGTACT
2678652 GAT
1 GAT
2678655 GTACAACTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (20 bp):
GATACATATATATAAGTACT
Found at i:2684474 original size:17 final size:17
Alignment explanation
Indices: 2684452--2684484 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2684442 CGTAACAACT
2684452 TCAAAACAAATTTCAAA
1 TCAAAACAAATTTCAAA
2684469 TCAAAACAAATTTCAA
1 TCAAAACAAATTTCAA
2684485 TCTCTTGTTC
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:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (17 bp):
TCAAAACAAATTTCAAA
Found at i:2690664 original size:23 final size:24
Alignment explanation
Indices: 2690637--2690692 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 24
2690627 GCGAGCCACC
2690637 GAGCCGAGCC-A-CCAAGCCGAACT
1 GAGCCGAGCCAAGCCAAGCCG-ACT
2690660 GAGCCTTTGAGCCAAGCCAAGCCGACT
1 GAGCC---GAGCCAAGCCAAGCCGACT
2690687 GAGCCG
1 GAGCCG
2690693 TTGACGTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
23 5 0.18
24 1 0.04
26 5 0.18
27 9 0.32
28 8 0.29
ACGTcount: A:0.27, C:0.36, G:0.29, T:0.09
Consensus pattern (24 bp):
GAGCCGAGCCAAGCCAAGCCGACT
Found at i:2692366 original size:21 final size:22
Alignment explanation
Indices: 2692328--2692368 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2692318 TGAATACCCC
* *
2692328 ATTCAGTTCAATTGAATTTAAA
1 ATTCAGCTCAATTCAATTTAAA
2692350 ATTCAGCT-AATTCAATTTA
1 ATTCAGCTCAATTCAATTTA
2692369 TAATCCTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.41
Consensus pattern (22 bp):
ATTCAGCTCAATTCAATTTAAA
Found at i:2694005 original size:19 final size:19
Alignment explanation
Indices: 2693981--2694020 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
2693971 ACACTTCTCC
2693981 CATTTATCATTTTAAAACA
1 CATTTATCATTTTAAAACA
2694000 CATTTATCATTTTAAAACA
1 CATTTATCATTTTAAAACA
2694019 CA
1 CA
2694021 CTTAAAACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.40
Consensus pattern (19 bp):
CATTTATCATTTTAAAACA
Found at i:2696284 original size:20 final size:20
Alignment explanation
Indices: 2696255--2696292 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2696245 CCTATTCAAA
*
2696255 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
2696275 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
2696293 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:2704239 original size:59 final size:59
Alignment explanation
Indices: 2704141--2704261 Score: 149
Period size: 59 Copynumber: 2.1 Consensus size: 59
2704131 GGAGGGTTGG
* *
2704141 TTAGAGCCATATTATCGAGTTTTACTTTTTAACTTGACTAAGAGAG-TTCGATAGGACAC
1 TTAGAGCCATATTATCAAGTTTTACCTTTTAACTTGACTAAGA-AGCTTCGATAGGACAC
* * *
2704200 TTAGAGCCATATTATCAAG-TTTGCCTTTTCA-TTGCGACTAGGAAGCTTCGATAGGACAC
1 TTAGAGCCATATTATCAAGTTTTACCTTTTAACTT--GACTAAGAAGCTTCGATAGGACAC
2704259 TTA
1 TTA
2704262 TCCATCTATT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
57 2 0.04
58 11 0.20
59 41 0.76
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (59 bp):
TTAGAGCCATATTATCAAGTTTTACCTTTTAACTTGACTAAGAAGCTTCGATAGGACAC
Found at i:2710090 original size:19 final size:20
Alignment explanation
Indices: 2710061--2710099 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
2710051 AATTTGCATG
2710061 TAAATGTATCGATACATATA
1 TAAATGTATCGATACATATA
*
2710081 TAAA-GTATCGATATATATA
1 TAAATGTATCGATACATATA
2710100 ATTTCGAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (20 bp):
TAAATGTATCGATACATATA
Found at i:2710197 original size:142 final size:142
Alignment explanation
Indices: 2709923--2710224 Score: 394
Period size: 142 Copynumber: 2.1 Consensus size: 142
2709913 GTATGAACAA
* * * *
2709923 TATCGATACATATAGATCAAGTATCGATATTGCTTATTTCGAAACAACATTTGCAATATCTGAAA
1 TATCGATACATAT--ATAAAGTATCGATATTGATAATTTCGAAACAACATATGCAATATCTGAAA
* *
2709988 TGTCAATGTATCGTTACTAGTTATGATCGTATCGATACTTTTATTCCACTATGCTTCTCAAACAA
64 TGTCAAAGTATCGATACTAGTTATGATCGTATCGATACTTTTATTCCACTATGCTTCTCAAACAA
*
2710053 TTTGCATGTAAATG
129 TTTGCATGAAAATG
* * *
2710067 TATCGATACATATATAAAGTATCGATATAT-ATAATTTCGAAACAAGATATGGAATATCTTAAAT
1 TATCGATACATATATAAAGTATCGATAT-TGATAATTTCGAAACAACATATGCAATATCTGAAAT
* * * *
2710131 GTCAAAGTATTGATACTTGTTATG-CCTGTATCGATACTTTT-TTCCCAGTATGCTTCTCAAACA
65 GTCAAAGTATCGATACTAGTTATGATC-GTATCGATACTTTTATT-CCACTATGCTTCTCAAACA
2710194 ATTTGCATGAAAATG
128 ATTTGCATGAAAATG
* *
2710209 TATTGATATATATATA
1 TATCGATACATATATA
2710225 TATATATATA
Statistics
Matches: 139, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
141 3 0.02
142 122 0.88
143 1 0.01
144 13 0.09
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (142 bp):
TATCGATACATATATAAAGTATCGATATTGATAATTTCGAAACAACATATGCAATATCTGAAATG
TCAAAGTATCGATACTAGTTATGATCGTATCGATACTTTTATTCCACTATGCTTCTCAAACAATT
TGCATGAAAATG
Found at i:2710221 original size:2 final size:2
Alignment explanation
Indices: 2710214--2710294 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
2710204 AAATGTATTG
2710214 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2710256 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
2710295 GTATTGATGC
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2711246 original size:231 final size:232
Alignment explanation
Indices: 2710842--2711344 Score: 629
Period size: 231 Copynumber: 2.2 Consensus size: 232
2710832 TAATCATTGA
* *
2710842 TAATAATGTAAACGGTAAAATAAT-TACAACTTAACCGGTTAAAAATACAATAGGCGCAACCTGT
1 TAATAATGTACACAGTAAAAT-ATGTACAACTTAACCGGTTAAAAATACAATAGGCGCAACCTGT
* * * * **
2710906 TGCATTAAAGTTTCTACCGGTATAAGAATAATGTAAACGATAAAATATTTTCAGCCTAATTGGTA
65 TACATTAAAGTTTCTACCAGTATAAGAATAATATAAACGATAAAATATTTTCAACCTAACCGGTA
* ** * *
2710971 TAATCATAATGTAAACGGTATAATATTGACAACATAAACGGTTAAAACAATTTAGGCGCAACCTA
130 GAATCATAATGTAAACAATAAAATACTGACAACATAAACGGTTAAAACAATTTAGGCGCAACCTA
*
2711036 TTACTTTAAACTTCTTACCGTTTTGTTTATAGGTATAT
195 TTACTTTAAACTTCTTACCGATTTGTTTATAGGTATAT
* ***
2711074 TAATAATGTACACAGTAAAATATGTACACCTTAACCGGTTAAAAA-ACAATAGGTTTAACCTGTT
1 TAATAATGTACACAGTAAAATATGTACAACTTAACCGGTTAAAAATACAATAGGCGCAACCTGTT
* * * * *
2711138 ACATTAAAGTTTCTACCAGTATAATG-ATAATATAGATGGTAATAT-TGTTTGAACCTAACCGGT
66 ACATTAAAGTTTCTACCAGTATAA-GAATAATATAAACGATAAAATAT-TTTCAACCTAACCGGT
* * * ** * *
2711201 AGAATCATAATGTAAACAATAAAATGCTGGCGATTTAACCGGTTAAAGCAATTTAGGCGCAACCT
129 AGAATCATAATGTAAACAATAAAATACTGACAACATAAACGGTTAAAACAATTTAGGCGCAACCT
*
2711266 ATTACTTTAAACTTTTTACCGATTTGTTTATAGGTATAT
194 ATTACTTTAAACTTCTTACCGATTTGTTTATAGGTATAT
* * *
2711305 TAATAAGGT-CAATAATAAAATATGTACAACTTAACCGGTT
1 TAATAATGTAC-ACAGTAAAATATGTACAACTTAACCGGTT
2711345 GAAATATCAT
Statistics
Matches: 232, Mismatches: 35, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
230 2 0.01
231 190 0.82
232 40 0.17
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (232 bp):
TAATAATGTACACAGTAAAATATGTACAACTTAACCGGTTAAAAATACAATAGGCGCAACCTGTT
ACATTAAAGTTTCTACCAGTATAAGAATAATATAAACGATAAAATATTTTCAACCTAACCGGTAG
AATCATAATGTAAACAATAAAATACTGACAACATAAACGGTTAAAACAATTTAGGCGCAACCTAT
TACTTTAAACTTCTTACCGATTTGTTTATAGGTATAT
Found at i:2713161 original size:21 final size:21
Alignment explanation
Indices: 2713135--2713177 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2713125 ATTTAAAAAA
*
2713135 TATCGATCCTCATACAACTAG
1 TATCGATACTCATACAACTAG
* *
2713156 TATCGATACTTATTCAACTAG
1 TATCGATACTCATACAACTAG
2713177 T
1 T
2713178 TATAATTGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (21 bp):
TATCGATACTCATACAACTAG
Found at i:2716151 original size:23 final size:23
Alignment explanation
Indices: 2716100--2716155 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
2716090 ATAAATGCAT
2716100 CGAAGTGCCACGTAGAATTACAC
1 CGAAGTGCCACGTAGAATTACAC
* * **
2716123 CAAAGTGCCGCGTAGAATTGTAC
1 CGAAGTGCCACGTAGAATTACAC
*
2716146 TGAAGTGCCA
1 CGAAGTGCCA
2716156 TATATAATGT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (23 bp):
CGAAGTGCCACGTAGAATTACAC
Found at i:2721511 original size:29 final size:29
Alignment explanation
Indices: 2721457--2721512 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
2721447 GTAGCATCAT
** *
2721457 TTCACATATTTCATATCACTTTTATATAA
1 TTCACATATACCATATCACTTATATATAA
2721486 TTCACATATACCATAT-AGCTTATATAT
1 TTCACATATACCATATCA-CTTATATAT
2721513 TTTAATCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 1 0.04
29 22 0.96
ACGTcount: A:0.36, C:0.18, G:0.02, T:0.45
Consensus pattern (29 bp):
TTCACATATACCATATCACTTATATATAA
Found at i:2725917 original size:23 final size:23
Alignment explanation
Indices: 2725891--2725946 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
2725881 ATAAATGCAT
*
2725891 CGAAGTGCCACGTAGAATTGTAC
1 CGAAGTGCCACCTAGAATTGTAC
**
2725914 CGAAGTGCTGCCTAGAATTGTAC
1 CGAAGTGCCACCTAGAATTGTAC
*
2725937 TGAAGTGCCA
1 CGAAGTGCCA
2725947 TATATAATGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (23 bp):
CGAAGTGCCACCTAGAATTGTAC
Found at i:2729870 original size:110 final size:110
Alignment explanation
Indices: 2729654--2729978 Score: 377
Period size: 100 Copynumber: 3.0 Consensus size: 110
2729644 GTATGTATCG
* * * * *
2729654 ATACCTATATTTACAACTTAACAGGTTAAAATAAAATAGGTGTTACCTATTACGTTAAAATAACT
1 ATACATATATTTACAACTTAACCGGTTAAAATAAAATAGGTGCTACATATTACGTTAAACTAACT
**
2729719 ATC-AGTTTGTTTAAAGGTATAAATATTAATGT-AACATTAAAATAT
66 ATCGA-TTTGTTTAAAGGTAT-AATATTAATGTAAACGGTAAAATAT
* * ** * *
2729764 ATACATATATTTATAATTTAACCGGTTAAAATAAAATAGGCACTACTTATTACGTTAAACTAGCT
1 ATACATATATTTACAACTTAACCGGTTAAAATAAAATAGGTGCTACATATTACGTTAAACTAACT
* *
2729829 ATCGATTTCTTTAAAGGTATAATAATAATGTAAACGG-------T
66 ATCGATTTGTTTAAAGGTATAATATTAATGTAAACGGTAAAATAT
* * *
2729867 A-A-A-ATATTTACAACTTAACCGATTAAAATAAAATAGGTGCTACATATTTCGTTAAACTACCT
1 ATACATATATTTACAACTTAACCGGTTAAAATAAAATAGGTGCTACATATTACGTTAAACTAACT
2729929 ATCGATTTGTTTAAAGGTATAATATTAATGTAAACGGTAAAATAT
66 ATCGATTTGTTTAAAGGTATAATATTAATGTAAACGGTAAAATAT
*
2729974 TTACA
1 ATACA
2729979 ACATAATCGG
Statistics
Matches: 179, Mismatches: 25, Indels: 23
0.79 0.11 0.10
Matches are distributed among these distances:
100 86 0.48
101 1 0.01
102 1 0.01
103 2 0.01
107 1 0.01
108 1 0.01
109 11 0.06
110 75 0.42
111 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (110 bp):
ATACATATATTTACAACTTAACCGGTTAAAATAAAATAGGTGCTACATATTACGTTAAACTAACT
ATCGATTTGTTTAAAGGTATAATATTAATGTAAACGGTAAAATAT
Found at i:2729900 original size:100 final size:100
Alignment explanation
Indices: 2729770--2730141 Score: 478
Period size: 100 Copynumber: 3.7 Consensus size: 100
2729760 ATATATACAT
* * *
2729770 ATATTTATAATTTAACCGGTTAAAATAAAATAGGCACTACTTATTACGTTAAACTAGCTATCGAT
1 ATATTTACAACTTAACCGGTTAAAATAAAATAGGCACTACTTATTACGTTAAACTACCTATCGAT
* *
2729835 TTCTTTAAAGGTATAATAATAATGTAAACGGTAAA
66 TTGTTTAAAGGTATAATATTAATGTAAACGGTAAA
* ** * *
2729870 ATATTTACAACTTAACCGATTAAAATAAAATAGGTGCTACATATTTCGTTAAACTACCTATCGAT
1 ATATTTACAACTTAACCGGTTAAAATAAAATAGGCACTACTTATTACGTTAAACTACCTATCGAT
2729935 TTGTTTAAAGGTATAATATTAATGTAAACGGTAAA
66 TTGTTTAAAGGTATAATATTAATGTAAACGGTAAA
* * * ** * * * * *
2729970 ATATTTACAACATAATCGGTTACAATAAAATATACGCTACCTATTACGTTAAACTAACT-GCTGG
1 ATATTTACAACTTAACCGGTTAAAATAAAATAGGCACTACTTATTACGTTAAACTACCTATC-GA
* *
2730034 TTTGTCTAAAGGTATAATATTAATATAAACGGTAAA
65 TTTGTTTAAAGGTATAATATTAATGTAAACGGTAAA
* * *
2730070 CTATTTTCAACTTAACCGGTTAAAATAAAATAGG-AGCTACTTATTACGTTAAACTACCTACCGA
1 ATATTTACAACTTAACCGGTTAAAATAAAATAGGCA-CTACTTATTACGTTAAACTACCTATCGA
*
2730134 TTTATTTA
65 TTTGTTTA
2730142 GAGGCATATT
Statistics
Matches: 231, Mismatches: 38, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
99 1 0.00
100 229 0.99
101 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (100 bp):
ATATTTACAACTTAACCGGTTAAAATAAAATAGGCACTACTTATTACGTTAAACTACCTATCGAT
TTGTTTAAAGGTATAATATTAATGTAAACGGTAAA
Found at i:2730086 original size:200 final size:205
Alignment explanation
Indices: 2729660--2730141 Score: 575
Period size: 200 Copynumber: 2.4 Consensus size: 205
2729650 ATCGATACCT
* * * * *
2729660 ATATTTACAACTTAACAGGTTAAAATAAAATAGGTGTTACCTATTACGTTAAAATAACTATC-AG
1 ATATTTACAACTTAACCGGTTAAAATAAAATAGGTGCTACATATTACGTTAAACTACCTATCGA-
* *
2729724 TTTGTTTAAAGGTATAAATATTAATGTAACATTAAAATATATACATATATTTATAATTTAACCGG
65 TTTGTTTAAAGGTATAAATATTAATGTAACAGTAAAATATATACA-ATA-TCATAA-TT-A-CGG
* * * *
2729789 TTAAAATAAAATAGGCACTACTTATTACGTTAAACTAGCTATCGATTTCTTTAAAGGTATAATAA
125 TTAAAATAAAATAGACACTACCTATTACGTTAAACTAACTATCGATTTCTCTAAAGGTATAATAA
*
2729854 TAATGTAAACGGTAAA
190 TAATATAAACGGTAAA
* *
2729870 ATATTTACAACTTAACCGATTAAAATAAAATAGGTGCTACATATTTCGTTAAACTACCTATCGAT
1 ATATTTACAACTTAACCGGTTAAAATAAAATAGGTGCTACATATTACGTTAAACTACCTATCGAT
* * *
2729935 TTGTTTAAAGGTAT-AATATTAATGTAAACGGTAAAATATTTAC-A-A-CATAA-T-CGGTTACA
66 TTGTTTAAAGGTATAAATATTAATGT-AACAGTAAAATATATACAATATCATAATTACGGTTAAA
* * * * * *
2729994 ATAAAATATACGCTACCTATTACGTTAAACTAACT-GCTGGTTTGTCTAAAGGTATAATATTAAT
130 ATAAAATAGACACTACCTATTACGTTAAACTAACTATC-GATTTCTCTAAAGGTATAATAATAAT
2730058 ATAAACGGTAAA
194 ATAAACGGTAAA
* * * * *
2730070 CTATTTTCAACTTAACCGGTTAAAATAAAATAGGAGCTACTTATTACGTTAAACTACCTACCGAT
1 ATATTTACAACTTAACCGGTTAAAATAAAATAGGTGCTACATATTACGTTAAACTACCTATCGAT
*
2730135 TTATTTA
66 TTGTTTA
2730142 GAGGCATATT
Statistics
Matches: 238, Mismatches: 31, Indels: 16
0.84 0.11 0.06
Matches are distributed among these distances:
199 1 0.00
200 134 0.56
203 1 0.00
205 4 0.02
207 1 0.00
208 1 0.00
209 11 0.05
210 84 0.35
211 1 0.00
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.35
Consensus pattern (205 bp):
ATATTTACAACTTAACCGGTTAAAATAAAATAGGTGCTACATATTACGTTAAACTACCTATCGAT
TTGTTTAAAGGTATAAATATTAATGTAACAGTAAAATATATACAATATCATAATTACGGTTAAAA
TAAAATAGACACTACCTATTACGTTAAACTAACTATCGATTTCTCTAAAGGTATAATAATAATAT
AAACGGTAAA
Found at i:2730494 original size:37 final size:33
Alignment explanation
Indices: 2730422--2730495 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 33
2730412 TAATATGGAA
*
2730422 CAATCAACCAACAACTCAATAGAAAATCTCGAC
1 CAATCAACCAACAACTCAATAGAAAAACTCGAC
* *
2730455 CAATCAATCAACAACTC-ATCAGAAAAACTCGAG
1 CAATCAACCAACAACTCAAT-AGAAAAACTCGAC
*
2730488 CAACCAAC
1 CAATCAAC
2730496 TAACCAATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 2 0.06
33 33 0.94
ACGTcount: A:0.49, C:0.31, G:0.07, T:0.14
Consensus pattern (33 bp):
CAATCAACCAACAACTCAATAGAAAAACTCGAC
Found at i:2731560 original size:100 final size:100
Alignment explanation
Indices: 2731387--2731969 Score: 862
Period size: 100 Copynumber: 5.8 Consensus size: 100
2731377 TGAGTTAACA
* * * *
2731387 TTAAAATAAAATAGACACTAGCTATTACGTTAAACTAGCTACCGGTTTGTTTAAAGGTATAATAT
1 TTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTATAATAT
* *
2731452 TAAAGTAAACGGTAAAATATTTAAAACTTAACCGG
66 TAATGTAAACGGTAAAATATTTACAACTTAACCGG
* * *
2731487 TTAAAATAAAATAGGCGTTACTTATTACATTAAACTACCTACCGGTTTGTTTAAAGGTATAATAT
1 TTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTATAATAT
* *
2731552 TAATGTAAATGGTAAAATATTTAAAACTTAACCGG
66 TAATGTAAACGGTAAAATATTTACAACTTAACCGG
* * *
2731587 TTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTATCGATTTGTTTAAAGGTATACTAT
1 TTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTATAATAT
*
2731652 TAATGTAAACGGTAAACTATTTACAACTTAACCGG
66 TAATGTAAACGGTAAAATATTTACAACTTAACCGG
* * * * *
2731687 TTAAAACAAAATATGTGCTACCTATTACGTTAAACTACCTACCGATTTGTTTAAAGATATAATAT
1 TTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTATAATAT
* * *
2731752 TATTGTAAACGGTAAACTATTTACAACTTAACCTG
66 TAATGTAAACGGTAAAATATTTACAACTTAACCGG
* *
2731787 TTAAAATAAAATAGGCGCTACCTATTACGTTAATC-ACCTACCTGTTTGTTTAAAGGTATAATAT
1 TTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTATAATAT
*
2731851 TAATGTAAATGGTAAAATATTTACAACTTAACCGG
66 TAATGTAAACGGTAAAATATTTACAACTTAACCGG
* * * * * *
2731886 TTAAAATAAAATAGGCGTTATCTATTACGTTAAACTAGCTACCAGTTTGGTTAAAGGTATAATAA
1 TTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTATAATAT
*
2731951 TAATGTAAACAGTAAAATA
66 TAATGTAAACGGTAAAATA
2731970 AAATAGGCGT
Statistics
Matches: 436, Mismatches: 46, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
99 89 0.20
100 347 0.80
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (100 bp):
TTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTATAATAT
TAATGTAAACGGTAAAATATTTACAACTTAACCGG
Found at i:2731957 original size:299 final size:300
Alignment explanation
Indices: 2731408--2731966 Score: 897
Period size: 299 Copynumber: 1.9 Consensus size: 300
2731398 TAGACACTAG
* * *
2731408 CTATTACGTTAAACTAGCTACCGGTTTGTTTAAAGGTATAATATTAAAGTAAACGGTAAAATATT
1 CTATTACGTTAAACTACCTACCGATTTGTTTAAAGATATAATATTAAAGTAAACGGTAAAATATT
* *
2731473 TAAAACTTAACCGGTTAAAATAAAATAGGCGTTACTTATTACATTAAACTACCTACCGGTTTGTT
66 TAAAACTTAACCGGTTAAAATAAAATAGGCGCTACCTATTACATTAAACTACCTACCGGTTTGTT
2731538 TAAAGGTATAATATTAATGTAAATGGTAAAATATTTAAAACTTAACCGGTTAAAATAAAATAGGC
131 TAAAGGTATAATATTAATGTAAATGGTAAAATATTTAAAACTTAACCGGTTAAAATAAAATAGGC
* * * * *
2731603 GCTACCTATTACGTTAAACTACCTATCGATTTGTTTAAAGGTATACTATTAATGTAAACGGTAAA
196 GCTACCTATTACGTTAAACTACCTACCGATTTGGTTAAAGGTATAATAATAATGTAAACAGTAAA
2731668 CTATTTACAACTTAACCGGTTAAAACAAAATATGTGCTAC
261 CTATTTACAACTTAACCGGTTAAAACAAAATATGTGCTAC
** *
2731708 CTATTACGTTAAACTACCTACCGATTTGTTTAAAGATATAATATTATTGTAAACGGTAAACTATT
1 CTATTACGTTAAACTACCTACCGATTTGTTTAAAGATATAATATTAAAGTAAACGGTAAAATATT
* * * * *
2731773 TACAACTTAACCTGTTAAAATAAAATAGGCGCTACCTATTACGTTAATC-ACCTACCTGTTTGTT
66 TAAAACTTAACCGGTTAAAATAAAATAGGCGCTACCTATTACATTAAACTACCTACCGGTTTGTT
*
2731837 TAAAGGTATAATATTAATGTAAATGGTAAAATATTTACAACTTAACCGGTTAAAATAAAATAGGC
131 TAAAGGTATAATATTAATGTAAATGGTAAAATATTTAAAACTTAACCGGTTAAAATAAAATAGGC
* * *
2731902 GTTATCTATTACGTTAAACTAGCTACC-AGTTTGGTTAAAGGTATAATAATAATGTAAACAGTAA
196 GCTACCTATTACGTTAAACTACCTACCGA-TTTGGTTAAAGGTATAATAATAATGTAAACAGTAA
2731966 A
260 A
2731967 ATAAAATAGG
Statistics
Matches: 236, Mismatches: 22, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
298 1 0.00
299 133 0.56
300 102 0.43
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (300 bp):
CTATTACGTTAAACTACCTACCGATTTGTTTAAAGATATAATATTAAAGTAAACGGTAAAATATT
TAAAACTTAACCGGTTAAAATAAAATAGGCGCTACCTATTACATTAAACTACCTACCGGTTTGTT
TAAAGGTATAATATTAATGTAAATGGTAAAATATTTAAAACTTAACCGGTTAAAATAAAATAGGC
GCTACCTATTACGTTAAACTACCTACCGATTTGGTTAAAGGTATAATAATAATGTAAACAGTAAA
CTATTTACAACTTAACCGGTTAAAACAAAATATGTGCTAC
Found at i:2731977 original size:76 final size:76
Alignment explanation
Indices: 2731887--2732045 Score: 241
Period size: 76 Copynumber: 2.1 Consensus size: 76
2731877 CTTAACCGGT
2731887 TAAAATAAAATAGGCGTTATC-TATTACGTTAAACTAGCTACCAGTTTGGTT-AAAGGTATAATA
1 TAAAATAAAATAGGCGTTA-CATATTACGTTAAACTAGCTACCAGTTT-GTTAAAAGGTATAATA
2731950 ATAATGTAAACAG
64 ATAATGTAAACAG
* *** *
2731963 TAAAATAAAATAGGCGTTACATATTTCGTTAAACTAGCTATTGGTTTGTTAAAAGGTGTAATAAT
1 TAAAATAAAATAGGCGTTACATATTACGTTAAACTAGCTACCAGTTTGTTAAAAGGTATAATAAT
2732028 AATGTAAACAG
66 AATGTAAACAG
2732039 TAAAATA
1 TAAAATA
2732046 TTTACAACTT
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
75 4 0.05
76 72 0.95
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.33
Consensus pattern (76 bp):
TAAAATAAAATAGGCGTTACATATTACGTTAAACTAGCTACCAGTTTGTTAAAAGGTATAATAAT
AATGTAAACAG
Found at i:2733020 original size:22 final size:22
Alignment explanation
Indices: 2732978--2733020 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
2732968 TATTATTATT
*
2732978 ATAAACAAAACTAAAATTTTCA
1 ATAAACAAAAATAAAATTTTCA
*
2733000 ATAAA-AAAAATATAATATTTC
1 ATAAACAAAAATAAAAT-TTTC
2733021 CGGTAGTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
ATAAACAAAAATAAAATTTTCA
Found at i:2733262 original size:55 final size:54
Alignment explanation
Indices: 2733179--2733290 Score: 197
Period size: 55 Copynumber: 2.1 Consensus size: 54
2733169 AAAGCACATG
* *
2733179 TCACTTGAAGCCAAAACTTGTTTCCCTCATCACTTTCCAACTCAATCTAACAGT
1 TCACTTGAAGCCAAAACTTGATTCCCTCATCACTTTCCAACTCAATCCAACAGT
2733233 TCACTTGAAGCCAAAAACTTGATTCCCTCATCACTTTCCAACTCAATCCAACAGT
1 TCACTTGAAGCC-AAAACTTGATTCCCTCATCACTTTCCAACTCAATCCAACAGT
2733288 TCA
1 TCA
2733291 AAACTGCTAG
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
54 12 0.22
55 43 0.78
ACGTcount: A:0.31, C:0.32, G:0.07, T:0.29
Consensus pattern (54 bp):
TCACTTGAAGCCAAAACTTGATTCCCTCATCACTTTCCAACTCAATCCAACAGT
Found at i:2736207 original size:18 final size:18
Alignment explanation
Indices: 2736162--2736207 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
2736152 ACAGTAATAA
*
2736162 GTAAAGAAAGGATAAGCT
1 GTAAAGAAATGATAAGCT
* *
2736180 GTAAAGAAATGATAGGTT
1 GTAAAGAAATGATAAGCT
2736198 GTAAAGAAAT
1 GTAAAGAAAT
2736208 ATTGGTAGGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.50, C:0.02, G:0.26, T:0.22
Consensus pattern (18 bp):
GTAAAGAAATGATAAGCT
Found at i:2738037 original size:18 final size:19
Alignment explanation
Indices: 2738014--2738061 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
2738004 GATACCATGT
2738014 AGAAAACAGACTGTA-GAA
1 AGAAAACAGACTGTATGAA
* * *
2738032 AGAAAACATACTGTATTAC
1 AGAAAACAGACTGTATGAA
2738051 AGAAAACAGAC
1 AGAAAACAGAC
2738062 AAGTCTGTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.54, C:0.15, G:0.17, T:0.15
Consensus pattern (19 bp):
AGAAAACAGACTGTATGAA
Found at i:2741035 original size:52 final size:55
Alignment explanation
Indices: 2740968--2741075 Score: 168
Period size: 52 Copynumber: 2.0 Consensus size: 55
2740958 AAAGTGGTCG
* *
2740968 TGGTTGTGATGGTAAGGAAAAAACTTGC-AAAATT-GA-ATGTCCATGATGGACA
1 TGGTTATGAGGGTAAGGAAAAAACTTGCAAAAATTGGATATGTCCATGATGGACA
*
2741020 TGGTTATGAGGGTAAGGAAAAAACTTGCAAAAATTGGATATGTCCGTGATGGACA
1 TGGTTATGAGGGTAAGGAAAAAACTTGCAAAAATTGGATATGTCCATGATGGACA
2741075 T
1 T
2741076 TCATCCATAT
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
52 26 0.52
53 6 0.12
54 2 0.04
55 16 0.32
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.27
Consensus pattern (55 bp):
TGGTTATGAGGGTAAGGAAAAAACTTGCAAAAATTGGATATGTCCATGATGGACA
Found at i:2744463 original size:172 final size:172
Alignment explanation
Indices: 2744077--2744590 Score: 888
Period size: 172 Copynumber: 3.0 Consensus size: 172
2744067 ACAATGAAAA
* * *
2744077 TCCACTTGCATCCCACTATTTTCTTCCCTTGTGGTAGTTCTATTAGAGTCCAATTACCATTGCTT
1 TCCACTTGCATCCCACTATTTTCTTCCCTTGTGGTAGTTCTATTAGAATCCAAGTATCATTGCTT
* * * * * * * *
2744142 TCTAAGGCTTTAACTTCATCTTCAACTGTCTTTTTCCGCATTAGAATATTCAAGGCTTCTTGAAT
66 TCTAAGGGTTTAATTTCTTCTTCAAATGTCTTTTTCTGTATTAGAATCTTCAAGGCTTCCTGAAT
2744207 CG--TTTGGAATCTGTATACTATCAAGTGATGCAGTGAAAGC
131 CGATTTTGGAATCTGTATACTATCAAGTGATGCAGTGAAAGC
2744247 TCCACTTGCATCCCACTATTTTCTTCCCTTGTGGTAGTTCTATTAGAATCCAAGTATCATTGCTT
1 TCCACTTGCATCCCACTATTTTCTTCCCTTGTGGTAGTTCTATTAGAATCCAAGTATCATTGCTT
2744312 TCTAAGGGTTTAATTTCTTCTTCAAATGTCTTTTTCTGTATTAGAATCTTCAAGGCTTCCTGAAT
66 TCTAAGGGTTTAATTTCTTCTTCAAATGTCTTTTTCTGTATTAGAATCTTCAAGGCTTCCTGAAT
2744377 CGATTTTGGAATCTGTATACTATCAAGTGATGCAGTGAAAGC
131 CGATTTTGGAATCTGTATACTATCAAGTGATGCAGTGAAAGC
*
2744419 TCCACTTGCATCCCACTATTTTCTTCCCTTGTGGTAGTTCTATTAGAATTCAAGTATCATTGCTT
1 TCCACTTGCATCCCACTATTTTCTTCCCTTGTGGTAGTTCTATTAGAATCCAAGTATCATTGCTT
*
2744484 TCTAAGGGTTTAATTTCTTCTTCAAAAGTCTTTTTCTGTATTAGAATCTTCAAGGCTTCCTGAAT
66 TCTAAGGGTTTAATTTCTTCTTCAAATGTCTTTTTCTGTATTAGAATCTTCAAGGCTTCCTGAAT
*
2744549 CGATTTTGGAATCTGTATACTATCAAGTGATGTAGTGAAAGC
131 CGATTTTGGAATCTGTATACTATCAAGTGATGCAGTGAAAGC
2744591 ACTGTATGAC
Statistics
Matches: 328, Mismatches: 14, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
170 121 0.37
172 207 0.63
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (172 bp):
TCCACTTGCATCCCACTATTTTCTTCCCTTGTGGTAGTTCTATTAGAATCCAAGTATCATTGCTT
TCTAAGGGTTTAATTTCTTCTTCAAATGTCTTTTTCTGTATTAGAATCTTCAAGGCTTCCTGAAT
CGATTTTGGAATCTGTATACTATCAAGTGATGCAGTGAAAGC
Found at i:2757299 original size:3 final size:3
Alignment explanation
Indices: 2757293--2757388 Score: 133
Period size: 3 Copynumber: 32.7 Consensus size: 3
2757283 TTTTTATCCA
* ** *
2757293 TAT TAT TAT TAT TAA TAT TAT TAT TAT CCT TAT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
2757341 TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2757387 TA
1 TA
2757389 AATATATTAA
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
2 4 0.05
3 77 0.95
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2770205 original size:7 final size:7
Alignment explanation
Indices: 2770193--2770273 Score: 71
Period size: 7 Copynumber: 11.6 Consensus size: 7
2770183 ATTATGCTTG
2770193 AAGAAAA
1 AAGAAAA
2770200 AAGAAAA
1 AAGAAAA
*
2770207 GAAAAAGAA
1 -AAGAA-AA
2770216 AAGAAAGAA
1 AAG-AA-AA
2770225 AAGAAAA
1 AAGAAAA
2770232 AAG--AA
1 AAGAAAA
2770237 AAGAAAA
1 AAGAAAA
2770244 AA-AAAA
1 AAGAAAA
2770250 AA-AAAA
1 AAGAAAA
*
2770256 TAGAAAA
1 AAGAAAA
*
2770263 TAGAAAA
1 AAGAAAA
2770270 AAGA
1 AAGA
2770274 GAAGAAAAAG
Statistics
Matches: 64, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
5 5 0.08
6 11 0.17
7 30 0.47
8 8 0.12
9 10 0.16
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (7 bp):
AAGAAAA
Found at i:2770208 original size:5 final size:5
Alignment explanation
Indices: 2770198--2770286 Score: 69
Period size: 5 Copynumber: 17.6 Consensus size: 5
2770188 GCTTGAAGAA
2770198 AAAAG AAAAG AAAAAG AAAAG -AAAG AAAAG AAAAAAG AAAAG AAAA-
1 AAAAG AAAAG -AAAAG AAAAG AAAAG AAAAG --AAAAG AAAAG AAAAG
* * * *
2770244 AAAA- AAAAA AAATAG AAAAT AGAA- AAAAG AGAAG AAAAAG AAA
1 AAAAG AAAAG AAA-AG AAAAG AAAAG AAAAG AAAAG -AAAAG AAA
2770287 GGGGGTCAAG
Statistics
Matches: 70, Mismatches: 6, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
4 15 0.21
5 37 0.53
6 13 0.19
7 5 0.07
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:2770224 original size:20 final size:20
Alignment explanation
Indices: 2770199--2770261 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 20
2770189 CTTGAAGAAA
2770199 AAAGAAAAGAAAAAGAAAAG
1 AAAGAAAAGAAAAAGAAAAG
2770219 AAAGAAAAGAAAAAAGAAAAG
1 AAAGAAAAG-AAAAAGAAAAG
*
2770240 AAA-AAAA-AAAAAAAAATAG
1 AAAGAAAAGAAAAAGAAA-AG
2770259 AAA
1 AAA
2770262 ATAGAAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
18 8 0.20
19 5 0.12
20 13 0.32
21 14 0.35
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (20 bp):
AAAGAAAAGAAAAAGAAAAG
Found at i:2770230 original size:32 final size:32
Alignment explanation
Indices: 2770193--2770287 Score: 115
Period size: 32 Copynumber: 2.9 Consensus size: 32
2770183 ATTATGCTTG
2770193 AAGAAAAAAGAAAAGAAAAAGAAAAGAAAGAA
1 AAGAAAAAAGAAAAGAAAAAGAAAAGAAAGAA
*
2770225 AAGAAAAAAGAAAAGAAAAA-AAAA-AAAAAA
1 AAGAAAAAAGAAAAGAAAAAGAAAAGAAAGAA
*
2770255 ATAGAAAATAGAAAA-AAGAGAAGAAAAAGAAAG
1 A-AGAAAAAAGAAAAGAA-A-AAG-AAAAGAAAG
2770288 GGGGTCAAGG
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
30 8 0.15
31 17 0.31
32 22 0.41
34 4 0.07
35 3 0.06
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (32 bp):
AAGAAAAAAGAAAAGAAAAAGAAAAGAAAGAA
Found at i:2770268 original size:38 final size:36
Alignment explanation
Indices: 2770198--2770287 Score: 110
Period size: 38 Copynumber: 2.4 Consensus size: 36
2770188 GCTTGAAGAA
*
2770198 AAAAGAAAAGAAAAAGAAAAGAAAGAAAAGAAAAAAG
1 AAAAGAAAA-AAAAAGAAAAAAAAGAAAAGAAAAAAG
2770235 AAAAGAAAAAAAAA-AAAAAAATAGAAAATAGAAAAAAG
1 AAAAGAAAAAAAAAGAAAAAAA-AG-AAA-AGAAAAAAG
* *
2770273 AGAAGAAAAAGAAAG
1 AAAAGAAAAAAAAAG
2770288 GGGGTCAAGG
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
35 6 0.13
36 7 0.15
37 12 0.26
38 21 0.46
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (36 bp):
AAAAGAAAAAAAAAGAAAAAAAAGAAAAGAAAAAAG
Found at i:2771508 original size:82 final size:82
Alignment explanation
Indices: 2771409--2771835 Score: 687
Period size: 82 Copynumber: 5.2 Consensus size: 82
2771399 AAACATTAAA
*
2771409 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
1 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
*
2771474 AGAACATTCATTGAATT
66 AGAACAATCATTGAATT
* *
2771491 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAACCTGGTTTAGC
1 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
2771556 AGAACAATCATTGAATT
66 AGAACAATCATTGAATT
*
2771573 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
1 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
2771638 AGAACAATCATTGAATT
66 AGAACAATCATTGAATT
* * * *
2771655 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGATTATA-
1 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTT-TAG
* *
2771719 TAGAACCAAGCATTGAATT
65 CAGAA-CAATCATTGAATT
* *
2771738 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGA
1 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAG-
*
2771802 TAGAACAATCATTGAATT
65 CAGAACAATCATTGAATT
2771820 TGGAAGATGAATTTGC
1 TGGAAGATGAATTTGC
2771836 TCATAGTAAA
Statistics
Matches: 326, Mismatches: 15, Indels: 8
0.93 0.04 0.02
Matches are distributed among these distances:
81 1 0.00
82 250 0.77
83 75 0.23
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (82 bp):
TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
AGAACAATCATTGAATT
Found at i:2772647 original size:113 final size:113
Alignment explanation
Indices: 2772449--2773222 Score: 1167
Period size: 113 Copynumber: 6.8 Consensus size: 113
2772439 TAGCAAAGAT
* * *
2772449 TTGAATCCATCATTTGATGGAACAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATCCATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
2772514 AGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTAC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
* *
2772562 TTGAATCCGTCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATCCATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * * * **
2772627 AGAAAGAAGAAGAAGTTCATAATGAGAATAACTTGTTCAACTTTTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
* * * *
2772675 TTAAATTCATCATTTGATGGATCAACATTGT-CAGAGAAGGTTCATAATGAGAAGAACTCATCTG
1 TTGAATCCATCATTTGATGGATCAAC-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
2772739 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
* *
2772788 TTGAATCCGTCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATCCATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * * **
2772853 AGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
* * * * *
2772901 TTAAATTCATCATTTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATCCATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
2772966 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTAC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
* * * *
2773014 CTGAATCCATCATTTGGTGAATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATCCATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
2773079 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
* * *
2773127 TTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTG
1 TTGAATCCATCATTTGATGGATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTG
2773191 AAGAAGGAAG-AGAAAGTTCATAATGAGAAGAA
65 AAGAAGGAAGAAG-AAGTTCATAATGAGAAGAA
2773223 CTCATCAAGA
Statistics
Matches: 593, Mismatches: 64, Indels: 8
0.89 0.10 0.01
Matches are distributed among these distances:
112 6 0.01
113 584 0.98
114 3 0.01
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (113 bp):
TTGAATCCATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
Found at i:2772850 original size:226 final size:226
Alignment explanation
Indices: 2772456--2773222 Score: 1331
Period size: 226 Copynumber: 3.4 Consensus size: 226
2772446 GATTTGAATC
* * * *
2772456 CATCATTTGATGGAACAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
2772521 AGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTACTTGAATCCGTCATTTGATGGATCA
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCGTCATTTGATGGATCA
2772586 GCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATG
131 GCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATG
*
2772651 AGAATAACTTGTTCAACTTTTTGTTTAAATT
196 AGAAGAACTTGTTCAACTTTTTGTTTAAATT
*
2772682 CATCATTTGATGGATCAACATTGTCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
2772747 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCGTCATTTGATGGATCA
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCGTCATTTGATGGATCA
2772812 GCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATG
131 GCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATG
2772877 AGAAGAACTTGTTCAACTTTTTGTTTAAATT
196 AGAAGAACTTGTTCAACTTTTTGTTTAAATT
2772908 CATCATTTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * * *
2772973 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGAATCA
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCGTCATTTGATGGATCA
* *
2773038 TCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
131 GCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATG
* * * *
2773103 AGAAGAATTTGTTCAACCTTTTGCTTGAATT
196 AGAAGAACTTGTTCAACTTTTTGTTTAAATT
*
2773134 CATCATTTGATGGATCAACATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCATTTGATGGATCAACATTGCCAGAG-AAGGTTCATAATGAGAAGAACTCATCTGAAGAAGG
2773198 AAG-AGAAAGTTCATAATGAGAAGAA
65 AAGAAG-AAGTTCATAATGAGAAGAA
2773223 CTCATCAAGA
Statistics
Matches: 518, Mismatches: 21, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
225 3 0.01
226 515 0.99
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (226 bp):
CATCATTTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCGTCATTTGATGGATCA
GCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATG
AGAAGAACTTGTTCAACTTTTTGTTTAAATT
Found at i:2773479 original size:3 final size:3
Alignment explanation
Indices: 2773473--2773567 Score: 136
Period size: 3 Copynumber: 31.7 Consensus size: 3
2773463 TTTTTATCCA
* ** * *
2773473 TAT TAT TAT TAT TAA TAT TAT TAT TAT CCT TAT TAC TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
2773521 TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2773568 ATTTATATTA
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:2800259 original size:12 final size:13
Alignment explanation
Indices: 2800242--2800273 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
2800232 AACGCTTTTC
2800242 ATTATTATCT-TT
1 ATTATTATCTATT
2800254 ATTATTA-CTATT
1 ATTATTATCTATT
2800266 ATTATTAT
1 ATTATTAT
2800274 GATTATTGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 16 0.89
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTATTATCTATT
Found at i:2801409 original size:19 final size:19
Alignment explanation
Indices: 2801385--2801422 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2801375 TCCATGCGTG
2801385 GAATGGAAAAAAATAGCTC
1 GAATGGAAAAAAATAGCTC
2801404 GAATGGAAAAAAATAGCTC
1 GAATGGAAAAAAATAGCTC
2801423 AGATAGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.11, G:0.21, T:0.16
Consensus pattern (19 bp):
GAATGGAAAAAAATAGCTC
Found at i:2801432 original size:18 final size:19
Alignment explanation
Indices: 2801385--2801432 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
2801375 TCCATGCGTG
*
2801385 GAATGGAAAAAAATAGCTC
1 GAATAGAAAAAAATAGCTC
*
2801404 GAATGGAAAAAAATAGCTC
1 GAATAGAAAAAAATAGCTC
2801423 -AGATAGAAAA
1 GA-ATAGAAAA
2801433 CAAAAAAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 1 0.04
19 26 0.96
ACGTcount: A:0.56, C:0.08, G:0.21, T:0.15
Consensus pattern (19 bp):
GAATAGAAAAAAATAGCTC
Found at i:2803909 original size:54 final size:54
Alignment explanation
Indices: 2803808--2803910 Score: 152
Period size: 54 Copynumber: 1.9 Consensus size: 54
2803798 GAGTTCAGGG
* * * * *
2803808 TCGAAGGTCGCTCTTGTCGTGGCTACGGCAATAGGCAATGGTAAGGAAGACGGT
1 TCGAAGGTCGCTCTTATCGTGGCTACAGCAAGAGGCAACGATAAGGAAGACGGT
*
2803862 TCGAAGGTCGCTCTTATCGTGGCTACAGCAAGAGGCAACGATGAGGAAG
1 TCGAAGGTCGCTCTTATCGTGGCTACAGCAAGAGGCAACGATAAGGAAG
2803911 GATCATAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.20
Consensus pattern (54 bp):
TCGAAGGTCGCTCTTATCGTGGCTACAGCAAGAGGCAACGATAAGGAAGACGGT
Found at i:2805858 original size:6 final size:6
Alignment explanation
Indices: 2805847--2805875 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2805837 AAATGAAATG
2805847 GAGAAA GAGAAA GAGAAA GAGAAA GAGAA
1 GAGAAA GAGAAA GAGAAA GAGAAA GAGAA
2805876 TTTAAAAAAG
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:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (6 bp):
GAGAAA
Found at i:2807991 original size:21 final size:22
Alignment explanation
Indices: 2807965--2808018 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
2807955 GTAGGTTTGA
*
2807965 GATCGATCCATTT-AGACAAGG
1 GATCGATCCATTTCACACAAGG
*
2807986 GATCGATCC-TTTCACCCAAGG
1 GATCGATCCATTTCACACAAGG
2808007 GATCGAT-CATTT
1 GATCGATCCATTT
2808019 TTTTTAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (22 bp):
GATCGATCCATTTCACACAAGG
Found at i:2809442 original size:13 final size:13
Alignment explanation
Indices: 2809424--2809448 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2809414 CATAACCTTA
2809424 AGGATTAAGATTT
1 AGGATTAAGATTT
2809437 AGGATTAAGATT
1 AGGATTAAGATT
2809449 AATCATTTAT
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:0.40, C:0.00, G:0.24, T:0.36
Consensus pattern (13 bp):
AGGATTAAGATTT
Found at i:2810335 original size:21 final size:20
Alignment explanation
Indices: 2810292--2810339 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
2810282 CCTTACCCTC
2810292 ATCGATACTTTCACATCAAT
1 ATCGATACTTTCACATCAAT
*
2810312 ATCGATACTACTTCA-ATCAGT
1 ATCGATACT--TTCACATCAAT
2810333 ATCGATA
1 ATCGATA
2810340 TTGTTCACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 9 0.36
21 12 0.48
22 4 0.16
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.33
Consensus pattern (20 bp):
ATCGATACTTTCACATCAAT
Found at i:2832802 original size:20 final size:20
Alignment explanation
Indices: 2832773--2832813 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2832763 AAAGCTCTTA
*
2832773 TAGGATCATATAGATGCATG
1 TAGGAACATATAGATGCATG
*
2832793 TAGGAACATATAGTTGCATG
1 TAGGAACATATAGATGCATG
2832813 T
1 T
2832814 CGTGGAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (20 bp):
TAGGAACATATAGATGCATG
Found at i:2834751 original size:16 final size:16
Alignment explanation
Indices: 2834730--2834760 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2834720 AATTAAATAA
2834730 AAATAAAAACTAAAAT
1 AAATAAAAACTAAAAT
*
2834746 AAATAAAAATTAAAA
1 AAATAAAAACTAAAA
2834761 ACATTCCTCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (16 bp):
AAATAAAAACTAAAAT
Found at i:2836589 original size:9 final size:9
Alignment explanation
Indices: 2836575--2836609 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
2836565 TAGAGAGGGA
2836575 TGAAAAAAT
1 TGAAAAAAT
2836584 TGAAAAAAT
1 TGAAAAAAT
2836593 TG-AAAAAT
1 TGAAAAAAT
2836601 TGAAAAAAT
1 TGAAAAAAT
2836610 AAAATTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.23
Consensus pattern (9 bp):
TGAAAAAAT
Found at i:2836598 original size:8 final size:8
Alignment explanation
Indices: 2836578--2836624 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
2836568 AGAGGGATGA
2836578 AAAAATTG
1 AAAAATTG
2836586 AAAAAATTG
1 -AAAAATTG
2836595 AAAAATTG
1 AAAAATTG
*
2836603 AAAAAAT-
1 AAAAATTG
*
2836610 -AAAATTA
1 AAAAATTG
2836617 AAAAATTG
1 AAAAATTG
2836625 TCAAAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
6 5 0.15
8 20 0.61
9 8 0.24
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.23
Consensus pattern (8 bp):
AAAAATTG
Found at i:2836600 original size:17 final size:17
Alignment explanation
Indices: 2836578--2836624 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
2836568 AGAGGGATGA
2836578 AAAAATTGAAAAAATTG
1 AAAAATTGAAAAAATTG
2836595 AAAAATTGAAAAAA-T-
1 AAAAATTGAAAAAATTG
2836610 -AAAATT-AAAAAATTG
1 AAAAATTGAAAAAATTG
2836625 TCAAAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 6 0.21
14 7 0.25
16 1 0.04
17 14 0.50
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.23
Consensus pattern (17 bp):
AAAAATTGAAAAAATTG
Found at i:2836620 original size:22 final size:23
Alignment explanation
Indices: 2836588--2836635 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
2836578 AAAAATTGAA
*
2836588 AAAATTGAAAAATTG-AAAAAAT
1 AAAATTAAAAAATTGCAAAAAAT
2836610 AAAATTAAAAAATTGTCAAAAAAT
1 AAAATTAAAAAATTG-CAAAAAAT
2836634 AA
1 AA
2836636 TTGTAAGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.61
24 9 0.39
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.23
Consensus pattern (23 bp):
AAAATTAAAAAATTGCAAAAAAT
Found at i:2836637 original size:22 final size:20
Alignment explanation
Indices: 2836577--2836637 Score: 56
Period size: 22 Copynumber: 3.0 Consensus size: 20
2836567 GAGAGGGATG
2836577 AAAAAATTG--AAAA-AATT
1 AAAAAATTGAAAAAATAATT
*
2836594 GAAAAATTGAAAAAATAAAATT
1 AAAAAATTGAAAAAAT--AATT
2836616 AAAAAATTGTCAAAAAATAATT
1 AAAAAATTG--AAAAAATAATT
2836638 GTAAGTATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
17 8 0.23
19 4 0.11
22 16 0.46
24 7 0.20
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.25
Consensus pattern (20 bp):
AAAAAATTGAAAAAATAATT
Found at i:2837275 original size:45 final size:45
Alignment explanation
Indices: 2837226--2837399 Score: 244
Period size: 45 Copynumber: 3.9 Consensus size: 45
2837216 ATTCTAACAT
*
2837226 CTTTTCTGTTGATAATGAACCCATATCCATTTCAACTATAGTATA
1 CTTTTCTGTTGATAATGAACCCATATACATTTCAACTATAGTATA
* ** *
2837271 CTTTTAC-GATGATAATGTGCCCGTATACATTTCAACTATAGTATA
1 CTTTT-CTGTTGATAATGAACCCATATACATTTCAACTATAGTATA
*
2837316 CTTTTCTGTTGATAAT-ATACCCATATACATTTCAACTCTAGTATA
1 CTTTTCTGTTGATAATGA-ACCCATATACATTTCAACTATAGTATA
* *
2837361 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTAT
1 CTTTTCTGTTGATAATGAACCCATATACATTTCAACTAT
2837400 GGCATCTTTT
Statistics
Matches: 112, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
44 1 0.01
45 110 0.98
46 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (45 bp):
CTTTTCTGTTGATAATGAACCCATATACATTTCAACTATAGTATA
Found at i:2837421 original size:90 final size:90
Alignment explanation
Indices: 2837226--2837436 Score: 232
Period size: 90 Copynumber: 2.3 Consensus size: 90
2837216 ATTCTAACAT
* * **
2837226 CTTTTCTGTTGATAATGA-ACCCATATCCATTTCAACTATAGTATACTTTTACGATGATAATGTG
1 CTTTTCTGCTGATAAT-ACACCCATATACATTTCAACTATAGTATACTTTTACGATGATAATGCA
* *
2837290 CCCGTATACATTTCAACTATAGTATA
65 CCCATATACATTTCAACTATAGCATA
* * * *
2837316 CTTTTCTGTTGATAATATACCCATATACATTTCAACTCTAGTATACTTTT-CTGTTGATAATGCA
1 CTTTTCTGCTGATAATACACCCATATACATTTCAACTATAGTATACTTTTAC-GATGATAATGCA
* *
2837380 CCCATATGCATTTCAACTATGGCAT-
65 CCCATATACATTTCAACTATAGCATA
* *
2837405 CTTTTCATGCCT-ATAATGCACCCATATGCATT
1 CTTTTC-TG-CTGATAATACACCCATATACATT
2837437 ATTCTTTTAT
Statistics
Matches: 104, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
89 8 0.08
90 95 0.91
91 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.39
Consensus pattern (90 bp):
CTTTTCTGCTGATAATACACCCATATACATTTCAACTATAGTATACTTTTACGATGATAATGCAC
CCATATACATTTCAACTATAGCATA
Found at i:2837492 original size:79 final size:79
Alignment explanation
Indices: 2837361--2837522 Score: 254
Period size: 79 Copynumber: 2.1 Consensus size: 79
2837351 CTCTAGTATA
* * *
2837361 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATGGCATCTTTTCATGCCT-ATAATGCA
1 CTTTTATGTTGATAATGCACCCATATACATTTCAACTATGGCATCCTTTCATG-CTGATAATGCA
2837425 CCCATATGCATTATT
65 CCCATATGCATTATT
* * *
2837440 CTTTTATGTTGATAATGTACCCATATACATTTCAGCTATGGCATCCTTTCATGCTGATAATGCAT
1 CTTTTATGTTGATAATGCACCCATATACATTTCAACTATGGCATCCTTTCATGCTGATAATGCAC
2837505 CCATATGCATTATT
66 CCATATGCATTATT
2837519 CTTT
1 CTTT
2837523 ACATTTGTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
78 2 0.03
79 74 0.97
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (79 bp):
CTTTTATGTTGATAATGCACCCATATACATTTCAACTATGGCATCCTTTCATGCTGATAATGCAC
CCATATGCATTATT
Found at i:2838585 original size:112 final size:111
Alignment explanation
Indices: 2838388--2838616 Score: 334
Period size: 112 Copynumber: 2.1 Consensus size: 111
2838378 CTGAACTGTC
* * **
2838388 GAAATGGTAATTCACCTCATTATAAATACCATGGGTGGTACCCTTTATGCTGAAAATGCAACGTT
1 GAAATGGTAATTCACCTCATTATAAATACCATAGGTGGCACCCTTTATGCCAAAAATGCAACGTT
* * *
2838453 ATGCATTAAGCAAAATCGATCGATAACTTTCATACACGAAGTATGTA
66 ATGCATTAAACAAAATCGATCGAT-ACTATCATACACAAAGTATGTA
* * *
2838500 GAAATGGTAATTCACCTCATTATGAATACCATAGGTGGCA-CTTTTAATGCCAAAAATGCACCGT
1 GAAATGGTAATTCACCTCATTATAAATACCATAGGTGGCACCCTTT-ATGCCAAAAATGCAACGT
*
2838564 TATGCATTAAACAAAATCGATCGATACTATCATACACAAAGTATGTC
65 TATGCATTAAACAAAATCGATCGATACTATCATACACAAAGTATGTA
2838611 GAAATG
1 GAAATG
2838617 CACCTATAAC
Statistics
Matches: 105, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
111 29 0.28
112 76 0.72
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.28
Consensus pattern (111 bp):
GAAATGGTAATTCACCTCATTATAAATACCATAGGTGGCACCCTTTATGCCAAAAATGCAACGTT
ATGCATTAAACAAAATCGATCGATACTATCATACACAAAGTATGTA
Found at i:2843204 original size:22 final size:22
Alignment explanation
Indices: 2843138--2843204 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
2843128 GGTATGTGAA
*
2843138 ATATGTCCCGAAGGACCTATGC
1 ATATGTCCCGAAGGACCTATGT
*
2843160 ATATGTCCCGAAGGACCTGTGT
1 ATATGTCCCGAAGGACCTATGT
*
2843182 ATATGTCCCGAATGACCTATGT
1 ATATGTCCCGAAGGACCTATGT
2843204 A
1 A
2843205 ACCCTCGACT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (22 bp):
ATATGTCCCGAAGGACCTATGT
Found at i:2843467 original size:28 final size:28
Alignment explanation
Indices: 2843435--2843508 Score: 123
Period size: 28 Copynumber: 2.6 Consensus size: 28
2843425 TATAAACATA
*
2843435 TATAAC-TCATGCATGTTTTAATAATGAT
1 TATAACAT-ATGCATGTTCTAATAATGAT
2843463 TATAACATATGCATGTTCTAATAATGAT
1 TATAACATATGCATGTTCTAATAATGAT
2843491 TATAACATATGCATGTTC
1 TATAACATATGCATGTTC
2843509 ATAACTATTA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 43 0.98
29 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (28 bp):
TATAACATATGCATGTTCTAATAATGAT
Found at i:2848213 original size:13 final size:13
Alignment explanation
Indices: 2848195--2848221 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2848185 CATAGTTGAA
2848195 CAGTCTTCATATG
1 CAGTCTTCATATG
2848208 CAGTCTTCATATG
1 CAGTCTTCATATG
2848221 C
1 C
2848222 GTGTCTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:2855713 original size:35 final size:35
Alignment explanation
Indices: 2855639--2855706 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
2855629 TTCATGTTCA
2855639 AAATTCCAAAACACTTCAATTACATTCTAAACCTC
1 AAATTCCAAAACACTTCAATTACATTCTAAACCTC
* * * *
2855674 AAATTCCAAAATACTTTAATTATATTTTAAACC
1 AAATTCCAAAACACTTCAATTACATTCTAAACC
2855707 CTAAATTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.34
Consensus pattern (35 bp):
AAATTCCAAAACACTTCAATTACATTCTAAACCTC
Found at i:2856273 original size:31 final size:31
Alignment explanation
Indices: 2856234--2856305 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
2856224 TAAAAAGTAT
* *
2856234 CAAAATGGTTACTAATATTATCGATTTATAA
1 CAAAATGGTCACTAACATTATCGATTTATAA
* *
2856265 TAAAATGGTCACTAACGTTATCGATTTATAA
1 CAAAATGGTCACTAACATTATCGATTTATAA
2856296 CAAAATGGTC
1 CAAAATGGTC
2856306 TTCCACCATC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (31 bp):
CAAAATGGTCACTAACATTATCGATTTATAA
Found at i:2862429 original size:34 final size:34
Alignment explanation
Indices: 2862386--2862453 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
2862376 TCCAAATAAC
2862386 TATCTACTCCTTATTTATATATAGGAAAGATGTG
1 TATCTACTCCTTATTTATATATAGGAAAGATGTG
*
2862420 TATCTACTCCTTATTTATATGTAGGAAAGATGTG
1 TATCTACTCCTTATTTATATATAGGAAAGATGTG
2862454 AAGATACACA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (34 bp):
TATCTACTCCTTATTTATATATAGGAAAGATGTG
Found at i:2862629 original size:2 final size:2
Alignment explanation
Indices: 2862624--2862703 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
2862614 TATATGTGTG
2862624 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2862666 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2862704 GTTTTCTACT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2872395 original size:2 final size:2
Alignment explanation
Indices: 2872390--2872425 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2872380 CCCAAAAAAA
2872390 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2872426 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2872430 original size:2 final size:2
Alignment explanation
Indices: 2872425--2872449 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2872415 TATATATATA
2872425 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
2872450 ATGTATACAA
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2874216 original size:66 final size:63
Alignment explanation
Indices: 2873988--2874273 Score: 364
Period size: 63 Copynumber: 4.5 Consensus size: 63
2873978 AAACAAAATA
*
2873988 AAAAATCTTTGAGTCTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTCCTCTTG
1 AAAAATCTTTGAGTCTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
2874051 AAAAATCTTTGAGTCTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAAAATCTTTGAGTCTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * * * *
2874114 -AAAATCTTTGATTCTATTTCCCTTGAAAC-AAGTTTTGTCTCCCTTGAAATAGTTTCTCTTG
1 AAAAATCTTTGAGTCTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
* **
2874175 AAACACTCATCTTTGAGATC-GTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGATAACTTCTC
1 AAA-A---ATCTTTGAG-TCTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTC
2874238 TTG
61 TTG
* * *
2874241 AAGCATCATCTTTGAGTCAGTTTCTCTTGAAAC
1 AA--A-AATCTTTGAGTCTGTTTCCCTTGAAAC
2874274 CATTATCCCT
Statistics
Matches: 198, Mismatches: 15, Indels: 18
0.86 0.06 0.08
Matches are distributed among these distances:
61 29 0.15
62 29 0.15
63 63 0.32
64 2 0.01
65 22 0.11
66 48 0.24
67 4 0.02
68 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.41
Consensus pattern (63 bp):
AAAAATCTTTGAGTCTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:2874221 original size:125 final size:124
Alignment explanation
Indices: 2873989--2874273 Score: 344
Period size: 124 Copynumber: 2.2 Consensus size: 124
2873979 AACAAAATAA
* * *
2873989 AAAATCTTTGAGTCTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTCCTCTTGAAA
1 AAAATCTTTGAGTCTATTTCCCTTGAAACAAAGTTTTGTCTCCCTTGAAACAGTTCCTCTTGAAA
2874054 AATCTTTGAGTCTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
66 AATCTTTGAGTCTGTTTCCCTTGAAACAAAGTTTTG-CTCTCTTGAGACAGTTTCTCTTG
* * *
2874114 AAAATCTTTGATTCTATTTCCCTTGAAAC-AAGTTTTGTCTCCCTTGAAATAGTTTCTCTTGAAA
1 AAAATCTTTGAGTCTATTTCCCTTGAAACAAAGTTTTGTCTCCCTTGAAACAGTTCCTCTTGAAA
* **
2874178 CACTCATCTTTGAGATC-GTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGATAACTTCTCTTG
66 -A---ATCTTTGAG-TCTGTTTCCCTTGAAACAAAGTTTTG-CTCTCTTGAGACAGTTTCTCTTG
*
2874241 AAGCATCATCTTTGAGTC-AGTTTCTCTTGAAAC
1 AA--A--ATCTTTGAGTCTA-TTTCCCTTGAAAC
2874274 CATTATCCCT
Statistics
Matches: 139, Mismatches: 11, Indels: 14
0.85 0.07 0.09
Matches are distributed among these distances:
124 31 0.22
125 28 0.20
127 28 0.20
128 26 0.19
129 3 0.02
130 1 0.01
131 22 0.16
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.41
Consensus pattern (124 bp):
AAAATCTTTGAGTCTATTTCCCTTGAAACAAAGTTTTGTCTCCCTTGAAACAGTTCCTCTTGAAA
AATCTTTGAGTCTGTTTCCCTTGAAACAAAGTTTTGCTCTCTTGAGACAGTTTCTCTTG
Found at i:2874438 original size:83 final size:83
Alignment explanation
Indices: 2874315--2874487 Score: 224
Period size: 83 Copynumber: 2.1 Consensus size: 83
2874305 TCGCGTATGA
* * *
2874315 AACT-TGTCATCCCCCGACCAGACCTACTCATCAAGTAGGAGCCACATCAACCTTAGAAAATCTA
1 AACTGTGTCATCCACCGACCAGACCTACTCATCAAGTAGGAGCCACATCAACCCTAGAAAA-CCA
2874379 -CCGTCCTCATCATGTAGG
65 GCCGTCCTCATCATGTAGG
* * * *** * *
2874397 AACTGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGTCGTGTCACCCCTAGATAACCAG
1 AACTGTGTCATCCACCGACCAGACCTACTCATCAAGTAGGAGCCACATCAACCCTAGAAAACCAG
2874462 CCGTCCTCATCATGTAGG
66 CCGTCCTCATCATGTAGG
2874480 AACTGTGT
1 AACTGTGT
2874488 TATCACCCTC
Statistics
Matches: 78, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
82 6 0.08
83 72 0.92
ACGTcount: A:0.27, C:0.33, G:0.17, T:0.23
Consensus pattern (83 bp):
AACTGTGTCATCCACCGACCAGACCTACTCATCAAGTAGGAGCCACATCAACCCTAGAAAACCAG
CCGTCCTCATCATGTAGG
Found at i:2881147 original size:12 final size:11
Alignment explanation
Indices: 2881106--2881153 Score: 60
Period size: 12 Copynumber: 4.1 Consensus size: 11
2881096 GAAAAAAGGA
2881106 AAAATAATTAAT
1 AAAATAA-TAAT
*
2881118 AAAAAAATAAAT
1 AAAATAAT-AAT
2881130 AAAATAATAAT
1 AAAATAATAAT
2881141 AACAATAATAAT
1 AA-AATAATAAT
2881153 A
1 A
2881154 TACTAATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 6 0.19
12 26 0.81
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:2881160 original size:20 final size:21
Alignment explanation
Indices: 2881127--2881176 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
2881117 TAAAAAAATA
*
2881127 AATAAAATAATAA-TAACAAT
1 AATAATATAATAATTAACAAT
* *
2881147 AATAATATACTAATTAAGAAT
1 AATAATATAATAATTAACAAT
2881168 -ATAATATAA
1 AATAATATAA
2881177 ACCATATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (21 bp):
AATAATATAATAATTAACAAT
Found at i:2881392 original size:35 final size:36
Alignment explanation
Indices: 2881221--2881505 Score: 243
Period size: 35 Copynumber: 7.9 Consensus size: 36
2881211 TATATATTAT
* * * *
2881221 TTTTTAAAAAAGTTTTCAAAACTATATCTTATAT-AG
1 TTTTCAAAAATGTTTTTAAAAC-ATATATTATATAAG
* *
2881257 TTTTCAAAAATGATTTT--AA-A-ATATTATATATG
1 TTTTCAAAAATGTTTTTAAAACATATATTATATAAG
* *
2881289 TTTTCAAAAAATATTTTTAAAACTATATATTATATAAT
1 TTTTC-AAAAATGTTTTTAAAAC-ATATATTATATAAG
2881327 TTTTCAAGAAAATGTTTTTAAAACCATATATTATATAAG
1 TTTTC-A-AAAATGTTTTTAAAA-CATATATTATATAAG
* * **
2881366 TTTTC-AAAAT-TTTTTAAAACTTTATATAATATATT
1 TTTTCAAAAATGTTTTTAAAAC-ATATATTATATAAG
2881401 TTTTC-AAAATGTTTTTAAAA-ACTACTACTTATAT--G
1 TTTTCAAAAATGTTTTTAAAACA-TA-TA-TTATATAAG
* * *
2881436 TTTTCAAAAATGTTTTCAAAAC-TATATAATATACG
1 TTTTCAAAAATGTTTTTAAAACATATATTATATAAG
*
2881471 TTTTCAAAAATGTTTTCAAAACAATATATTATATA
1 TTTTCAAAAATGTTTTTAAAAC-ATATATTATATA
2881506 TTTCAAAATC
Statistics
Matches: 207, Mismatches: 22, Indels: 39
0.77 0.08 0.15
Matches are distributed among these distances:
31 8 0.04
32 7 0.03
33 15 0.07
34 5 0.02
35 63 0.30
36 43 0.21
37 16 0.08
38 17 0.08
39 32 0.15
40 1 0.00
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (36 bp):
TTTTCAAAAATGTTTTTAAAACATATATTATATAAG
Found at i:2881450 original size:12 final size:12
Alignment explanation
Indices: 2881433--2881491 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 12
2881423 TACTACTTAT
2881433 ATGTTTTCAAAA
1 ATGTTTTCAAAA
2881445 ATGTTTTCAAAA
1 ATGTTTTCAAAA
* * * *
2881457 CT-ATAT-AATAT
1 ATGTTTTCAA-AA
*
2881468 ACGTTTTCAAAA
1 ATGTTTTCAAAA
2881480 ATGTTTTCAAAA
1 ATGTTTTCAAAA
2881492 CAATATATTA
Statistics
Matches: 34, Mismatches: 10, Indels: 6
0.68 0.20 0.12
Matches are distributed among these distances:
10 2 0.06
11 3 0.09
12 27 0.79
13 2 0.06
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:2881467 original size:70 final size:69
Alignment explanation
Indices: 2881195--2881513 Score: 266
Period size: 71 Copynumber: 4.6 Consensus size: 69
2881185 ATATATACTT
* * * **
2881195 AAAAATATTTTTAAATTA-TATATTAT-T-TTTT-AAAAAAGTTTTCAAAACTATATCTTATATA
1 AAAAATGTTTTTAAA-AACTATATTATATGTTTTCAAAAATGTTTTCAAAACTATATAATATAT-
2881256 GTTTTC
64 GTTTTC
* * *
2881262 AAAAATGATTTT-AAAA-TAT-TATATATGTTTTCAAAAAATATTTTTAAAACTATATATTATAT
1 AAAAATGTTTTTAAAAACTATAT-TATATGTTTTC-AAAAATGTTTTCAAAACTATATA--ATAT
2881324 AAT-TTTTC
62 -ATGTTTTC
* *
2881332 AAGAAAATGTTTTTAAAACCATATATTATATAAGTTTTC-AAAAT-TTTTTAAAACTTTATATAA
1 -A-AAAATGTTTTTAAAAAC-TATATTATAT--GTTTTCAAAAATGTTTTCAAAAC--TATATAA
*
2881395 TATATTTTTTC
59 TATATGTTTTC
*
2881406 -AAAATGTTTTTAAAAACTACTACTTATATGTTTTCAAAAATGTTTTCAAAACTATATAATATAC
1 AAAAATGTTTTTAAAAACTA-TA-TTATATGTTTTCAAAAATGTTTTCAAAACTATATAATATAT
2881470 GTTTTC
64 GTTTTC
* * *
2881476 AAAAATGTTTTCAAAACAATATATTATAT-ATTTCAAAA
1 AAAAATGTTTTTAAAA-ACTATATTATATGTTTTCAAAA
2881514 TCATTTTACC
Statistics
Matches: 210, Mismatches: 17, Indels: 48
0.76 0.06 0.17
Matches are distributed among these distances:
64 1 0.00
65 7 0.03
66 3 0.01
67 14 0.07
69 27 0.13
70 35 0.17
71 43 0.20
72 30 0.14
73 5 0.02
74 19 0.09
75 13 0.06
76 7 0.03
77 6 0.03
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (69 bp):
AAAAATGTTTTTAAAAACTATATTATATGTTTTCAAAAATGTTTTCAAAACTATATAATATATGT
TTTC
Found at i:2882282 original size:23 final size:24
Alignment explanation
Indices: 2882256--2882305 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
2882246 TTCGAACTCG
2882256 AAGG-TCTTTTGTGTTTCAAGAGA
1 AAGGTTCTTTTGTGTTTCAAGAGA
*
2882279 AAGGTTTTTTTTGTGTTTCAAGAGA
1 AAGG-TTCTTTTGTGTTTCAAGAGA
2882304 AA
1 AA
2882306 CAATTTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 4 0.17
25 20 0.83
ACGTcount: A:0.28, C:0.06, G:0.24, T:0.42
Consensus pattern (24 bp):
AAGGTTCTTTTGTGTTTCAAGAGA
Found at i:2882438 original size:22 final size:22
Alignment explanation
Indices: 2882412--2882488 Score: 69
Period size: 22 Copynumber: 3.8 Consensus size: 22
2882402 AGAAACTGTC
*
2882412 TCAAGAGAGATAAAACTTTGTT
1 TCAAGAGAGACAAAACTTTGTT
*
2882434 TCAAG-G-G---AAA--TTGTC
1 TCAAGAGAGACAAAACTTTGTT
* *
2882449 TCAAGAGAAACAAAAATTTGTT
1 TCAAGAGAGACAAAACTTTGTT
2882471 TCAAGAGAGACAAAACTT
1 TCAAGAGAGACAAAACTT
2882489 AGTTCTAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
15 9 0.21
16 1 0.02
17 3 0.07
20 4 0.09
21 1 0.02
22 25 0.58
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.26
Consensus pattern (22 bp):
TCAAGAGAGACAAAACTTTGTT
Found at i:2882449 original size:37 final size:37
Alignment explanation
Indices: 2882393--2882478 Score: 127
Period size: 37 Copynumber: 2.3 Consensus size: 37
2882383 CAAAGATTGG
* * *
2882393 TGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAAACAAAAATT
* *
2882430 TGTTTCAAGGGAAATTGTCTCAAGAGAAACAAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAAACAAAAATT
2882467 TGTTTCAAGAGA
1 TGTTTCAAGAGA
2882479 GACAAAACTT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.28
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAAACAAAAATT
Found at i:2882508 original size:59 final size:58
Alignment explanation
Indices: 2882412--2882533 Score: 147
Period size: 59 Copynumber: 2.1 Consensus size: 58
2882402 AGAAACTGTC
* * ** *
2882412 TCAAGAGAGATAAAACTTTGTTTCAAGGGAAATTGTCTCAAGAGAAACAAAAATTTGTT
1 TCAAGAGAGACAAAACTTAGTTTCAAAAGAAACTGTCTCAAGAGAAAC-AAAATTTGTT
* * *
2882471 TCAAGAGAGACAAAACTTAG-TTCTAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTT
1 TCAAGAGAGACAAAACTTAGTTTC-AAAAGAAACTGTCTCAAGAGAAACAAAATTTGTT
2882529 TCAAG
1 TCAAG
2882534 GAAAACATAT
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
58 17 0.31
59 37 0.69
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (58 bp):
TCAAGAGAGACAAAACTTAGTTTCAAAAGAAACTGTCTCAAGAGAAACAAAATTTGTT
Found at i:2882590 original size:34 final size:34
Alignment explanation
Indices: 2882552--2882619 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
2882542 ATTCAATGAT
2882552 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
*
2882586 TTTGTTTCAAGGGAAACTGTCTCAATAGAGACAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
2882620 AGACAAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (34 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
Found at i:2882633 original size:163 final size:162
Alignment explanation
Indices: 2882335--2882641 Score: 444
Period size: 163 Copynumber: 1.9 Consensus size: 162
2882325 GTGTTTCAAG
2882335 AGAAACTGTCTCAAGGGAGGAAAAATTTTGTTTCAAGAAAAACATATTCAAAGATTGGTGTTTCA
1 AGAAACTGTCTCAAGGGAGGAAAAATTTTGTTTCAAGAAAAACATATTCAAAGATTGGTGTTTCA
*
2882400 AGAGAAACTGTCTCAAGAGAGATAAAACTTTGTTTCAAGGGAAATTGTCTCAAGAGAAACAAAAA
66 AGAGAAACTGTCTCAAGAGAGA-AAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAAACAAAAA
2882465 TTTGTTTCAAGAGAGACAAAACTTAGTTCTAAA
130 TTTGTTTCAAGAGAGACAAAACTTAGTTCTAAA
* * * *
2882498 AGAAACTGTCTCAAGGGA-GACGAAA-TTTGTTTCAAGGAAAACATATTCAATGATT-TTGTTTC
1 AGAAACTGTCTCAAGGGAGGA-AAAATTTTGTTTCAAGAAAAACATATTCAAAGATTGGTGTTTC
* * *
2882560 AAGGGAAACTGTCTCAAGAGAG-ACAA-TTTGTTTCAAGGGAAACTGTCTCAATAGAGACAAAGA
65 AAGAGAAACTGTCTCAAGAGAGAAAAACTTTGTTTCAAGGGAAACTGTCTC-A-AGAG--AAACA
2882623 CAAAATTTGTTTCAAGAGA
126 -AAAATTTGTTTCAAGAGA
2882642 AACTGTCTCA
Statistics
Matches: 130, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
158 22 0.17
159 4 0.03
160 4 0.03
161 27 0.21
162 34 0.26
163 39 0.30
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (162 bp):
AGAAACTGTCTCAAGGGAGGAAAAATTTTGTTTCAAGAAAAACATATTCAAAGATTGGTGTTTCA
AGAGAAACTGTCTCAAGAGAGAAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAAACAAAAAT
TTGTTTCAAGAGAGACAAAACTTAGTTCTAAA
Found at i:2882761 original size:36 final size:35
Alignment explanation
Indices: 2882711--2882815 Score: 151
Period size: 36 Copynumber: 3.0 Consensus size: 35
2882701 ATTCAAAGAT
*
2882711 TTTTTTCAAGGGAAACTGTCTTAAGAGAGACAAAA
1 TTTTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
2882746 TTTATTTCAAGGGAAACTGTCTCAAGAGAGA-AAAA
1 TTT-TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
2882781 TTGTTTT-AAGAGAAACTGTCTCAAGAGAGATAAAA
1 TT-TTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
2882816 CTTTGTTTTA
Statistics
Matches: 65, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
34 22 0.34
35 16 0.25
36 27 0.42
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (35 bp):
TTTTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:2882796 original size:34 final size:36
Alignment explanation
Indices: 2882704--2882824 Score: 149
Period size: 36 Copynumber: 3.3 Consensus size: 36
2882694 AAAACATATT
* *
2882704 CAAAGATTTTTTTCAAGGGAAACTGTCTTAAGAGAGA
1 CAAA-ATTGTTTTCAAGGGAAACTGTCTCAAGAGAGA
2882741 CAAAATT-TATTTCAAGGGAAACTGTCTCAAGAGAGA
1 CAAAATTGT-TTTCAAGGGAAACTGTCTCAAGAGAGA
*
2882777 -AAAATTGTTTT-AAGAGAAACTGTCTCAAGAGAGA
1 CAAAATTGTTTTCAAGGGAAACTGTCTCAAGAGAGA
*
2882811 TAAAACTTTGTTTT
1 CAAAA--TTGTTTT
2882825 AAGTAAATTA
Statistics
Matches: 77, Mismatches: 2, Indels: 10
0.87 0.02 0.11
Matches are distributed among these distances:
34 22 0.29
35 14 0.18
36 30 0.39
37 11 0.14
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.31
Consensus pattern (36 bp):
CAAAATTGTTTTCAAGGGAAACTGTCTCAAGAGAGA
Found at i:2883135 original size:40 final size:42
Alignment explanation
Indices: 2883080--2883178 Score: 114
Period size: 43 Copynumber: 2.4 Consensus size: 42
2883070 GGATTCTTCG
2883080 TTGT-GAAGTTGAAATCGT-GA-TGTGGGAACGATATCCTCCA
1 TTGTGGAA-TTGAAATCGTGGATTGTGGGAACGATATCCTCCA
* * *
2883120 TTGTGGAATTGAAATCGTGGATTTGTGGGTATGATATCCTCCG
1 TTGTGGAATTGAAATCGTGGA-TTGTGGGAACGATATCCTCCA
* *
2883163 TCGTGGAGTTGAAATC
1 TTGTGGAATTGAAATC
2883179 TGACTTGAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
40 14 0.28
41 5 0.10
43 31 0.62
ACGTcount: A:0.24, C:0.13, G:0.29, T:0.33
Consensus pattern (42 bp):
TTGTGGAATTGAAATCGTGGATTGTGGGAACGATATCCTCCA
Found at i:2884376 original size:95 final size:97
Alignment explanation
Indices: 2884177--2884376 Score: 298
Period size: 96 Copynumber: 2.1 Consensus size: 97
2884167 GGACAGCTCA
* * * * * *
2884177 ATATGTAAACACCTTTATCAGGTTAGCTGAATATTATCCATAAAGCTGGGGGCGTTTAACCAATT
1 ATATATAATCACCTTTATCAGGCTAGATGAATATTATCCATAAAGCTCGGGGCGCTTAACCAATT
2884242 GCTCTAGAGGGACAACTCAAGCTTTATTGTAT
66 GCTCTAGAGGGACAACTCAAGCTTTATTGTAT
*
2884274 AT-TATAATCACCTTTATCAGGCTAGATGAATCTTATCCATAAAG-TCGGGGCGCTTAACCAATT
1 ATATATAATCACCTTTATCAGGCTAGATGAATATTATCCATAAAGCTCGGGGCGCTTAACCAATT
* *
2884337 GCTTTAGAGGGAC-ACTCGAGCTTTATTGTAT
66 GCTCTAGAGGGACAACTCAAGCTTTATTGTAT
2884368 ATATATAAT
1 ATATATAAT
2884377 ATGGGTATAC
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
94 19 0.20
95 35 0.38
96 37 0.40
97 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (97 bp):
ATATATAATCACCTTTATCAGGCTAGATGAATATTATCCATAAAGCTCGGGGCGCTTAACCAATT
GCTCTAGAGGGACAACTCAAGCTTTATTGTAT
Found at i:2887170 original size:16 final size:16
Alignment explanation
Indices: 2887149--2887191 Score: 70
Period size: 15 Copynumber: 2.8 Consensus size: 16
2887139 AATAAAAGTC
2887149 CTACCCCACATGATAT
1 CTACCCCACATGATAT
*
2887165 CTA-CCCATATGATAT
1 CTACCCCACATGATAT
2887180 CTACCCCACATG
1 CTACCCCACATG
2887192 CTTATTATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.30, C:0.37, G:0.07, T:0.26
Consensus pattern (16 bp):
CTACCCCACATGATAT
Found at i:2888297 original size:6 final size:6
Alignment explanation
Indices: 2888286--2888329 Score: 61
Period size: 6 Copynumber: 7.0 Consensus size: 6
2888276 TTAGAAAGGA
*
2888286 AAAAAT AAAAAT AAAAAT AAAAAAA ATAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT -AAAAAT A-AAAAT AAAAAT AAAAAT
2888330 GAAATGAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 24 0.71
7 10 0.29
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:2888310 original size:20 final size:20
Alignment explanation
Indices: 2888285--2888328 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 20
2888275 TTTAGAAAGG
2888285 AAAAAATAAAAATAAAAATAA
1 AAAAAAT-AAAATAAAAATAA
2888306 AAAAAATAAAATAAAAATAA
1 AAAAAATAAAATAAAAATAA
2888326 AAA
1 AAA
2888329 TGAAATGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (20 bp):
AAAAAATAAAATAAAAATAA
Found at i:2889489 original size:20 final size:21
Alignment explanation
Indices: 2889456--2889505 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
2889446 AAAACAAACA
*
2889456 AATAAAATAATAA-TAACAAT
1 AATAATATAATAATTAACAAT
* *
2889476 AATAATATACTAATTAATAAT
1 AATAATATAATAATTAACAAT
2889497 -ATAATATAA
1 AATAATATAA
2889506 ACTATATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (21 bp):
AATAATATAATAATTAACAAT
Found at i:2889493 original size:15 final size:13
Alignment explanation
Indices: 2889461--2889499 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 13
2889451 AAACAAATAA
2889461 AATAATAATA-AC
1 AATAATAATATAC
2889473 AATAATAATATAC
1 AATAATAATATAC
2889486 TAATTAATAATATA
1 -AA-TAATAATATA
2889500 ATATAAACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 10 0.42
13 2 0.08
14 2 0.08
15 10 0.42
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (13 bp):
AATAATAATATAC
Found at i:2889501 original size:12 final size:11
Alignment explanation
Indices: 2889456--2889516 Score: 52
Period size: 12 Copynumber: 5.4 Consensus size: 11
2889446 AAAACAAACA
2889456 AATAAAATAAT
1 AATAAAATAAT
2889467 AATAACAATAAT
1 AATAA-AATAAT
* *
2889479 AATATACTAATT
1 AATAAAATAA-T
*
2889491 AATAATATAAT
1 AATAAAATAAT
*
2889502 -ATAAACTATAT
1 AATAAAATA-AT
2889513 AATA
1 AATA
2889517 TATACTTCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
10 6 0.15
11 12 0.31
12 21 0.54
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:2889614 original size:39 final size:35
Alignment explanation
Indices: 2889556--2889907 Score: 222
Period size: 35 Copynumber: 10.1 Consensus size: 35
2889546 ATTATTTTTT
* * *
2889556 AAAA-GTTTTCAAAACTATATCTCATATAGTTTTCA
1 AAAATGTTTT-AAAAATATATATTATATAGTTTTCA
*
2889591 AAAATGATTTTAAAAATAT-TA-TATA-AGCTTTCAA
1 AAAATG-TTTTAAAAATATATATTATATAGTTTTC-A
* * * *
2889625 AAAATATTTTTAAAACTATATTTTATATAATTTTTCAA
1 AAAAT-GTTTTAAAAATATATATTATAT-AGTTTTC-A
**
2889663 GAAAATGTTTTTAAAACCATATATTATATAAGTTTTC-
1 -AAAATG-TTTTAAAAATATATATTATAT-AGTTTTCA
*
2889700 AAAATGTTTTAAAAAGTTATATAATATATA-TTTTC-
1 AAAATGTTTTAAAAA--TATATATTATATAGTTTTCA
2889735 AAAATGTTTTAAAAAACTATATATTACATATATGTTTTCA
1 AAAATGTTTT-AAAAA-TATATATT--ATATA-GTTTTCA
* *
2889775 AAAATGTTTTCAAAACTATATAATATATATGTTTTCA
1 AAAATGTTTT-AAAAATATATATTATATA-GTTTTCA
* *
2889812 AAAA----CT--ATATAT-TA-TATATA-TTTT-A
1 AAAATGTTTTAAAAATATATATTATATAGTTTTCA
* *
2889837 AAAATGTTTTCAAAACTATATAATATAT-GTTTTCA
1 AAAATGTTTT-AAAAATATATATTATATAGTTTTCA
* *
2889872 AAAATGTTTCAAAACTATATATTATATA--TTTCA
1 AAAATGTTTTAAAAATATATATTATATAGTTTTCA
2889905 AAA
1 AAA
2889908 TCATTTTACC
Statistics
Matches: 258, Mismatches: 29, Indels: 62
0.74 0.08 0.18
Matches are distributed among these distances:
25 5 0.02
26 4 0.02
28 6 0.02
29 3 0.01
30 4 0.02
32 4 0.02
33 17 0.07
34 45 0.17
35 46 0.18
36 24 0.09
37 36 0.14
38 7 0.03
39 43 0.17
40 14 0.05
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (35 bp):
AAAATGTTTTAAAAATATATATTATATAGTTTTCA
Found at i:2889736 original size:74 final size:72
Alignment explanation
Indices: 2889606--2889899 Score: 240
Period size: 75 Copynumber: 4.1 Consensus size: 72
2889596 GATTTTAAAA
* * * **
2889606 ATATTATATAAGCTTTCAAAAAATATTTTTAAAACTATATTTTATATAATTTTTCAAGAAAATGT
1 ATATTATATAAGTTTTC-AAAAATGTTTTAAAAACTATATAATATAT-A-TTTTC---AAAATGT
*
2889671 TTT-TAAAACCAT
60 TTTAAAAAACCAT
*
2889683 ATATTATATAAGTTTTC-AAAATGTTTTAAAAAGTTATATAATATATATTTTCAAAATGTTTTAA
1 ATATTATATAAGTTTTCAAAAATGTTTTAAAAA-CTATATAATATATATTTTCAAAATGTTTTAA
*
2889747 AAAACTAT
65 AAAACCAT
* * *
2889755 ATATTACATATATGTTTTCAAAAATGTTTTCAAAACTATAT-A-ATATA---T----ATGTTTTC
1 ATATT--ATATAAGTTTTCAAAAATGTTTTAAAAACTATATAATATATATTTTCAAAATGTTTTA
*
2889811 AAAAACTAT
64 AAAAACCAT
* *
2889820 ATATTATATATA-TTTT-AAAAATGTTTTCAAAACTATATAATATATGTTTTCAAAAATG-TTT-
1 ATATTATATA-AGTTTTCAAAAATGTTTTAAAAACTATATAATATATATTTTC-AAAATGTTTTA
* *
2889881 CAAAACTAT
64 AAAAACCAT
2889890 ATATTATATA
1 ATATTATATA
2889900 TTTCAAAATC
Statistics
Matches: 186, Mismatches: 15, Indels: 39
0.77 0.06 0.16
Matches are distributed among these distances:
62 22 0.12
63 10 0.05
64 4 0.02
65 21 0.11
67 1 0.01
69 1 0.01
70 18 0.10
71 13 0.07
72 20 0.11
73 1 0.01
74 21 0.11
75 28 0.15
76 10 0.05
77 16 0.09
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (72 bp):
ATATTATATAAGTTTTCAAAAATGTTTTAAAAACTATATAATATATATTTTCAAAATGTTTTAAA
AAACCAT
Found at i:2889758 original size:37 final size:36
Alignment explanation
Indices: 2889508--2889908 Score: 204
Period size: 39 Copynumber: 11.6 Consensus size: 36
2889498 TAATATAAAC
* * *
2889508 TATATAATATATA-CTTCAAATATATTTT-TAAACTA
1 TATATAATATATATTTTCAAA-ATGTTTTAAAAACTA
*
2889543 TATAT--TAT-T-TTTT-AAAA-GTTTTCAAAACTA
1 TATATAATATATATTTTCAAAATGTTTTAAAAACTA
* * *
2889573 TATCTCATATA-GTTTTCAAAAATGATTTTAAAAA-TA
1 TATATAATATATATTTTC-AAAATG-TTTTAAAAACTA
** * *
2889609 T-TAT-ATA-A-GCTTTCAAAAAATATTTTTAAAACTA
1 TATATAATATATATTTTC--AAAATGTTTTAAAAACTA
* * * *
2889643 TATTTTATATA-ATTTTTCAAGAAAATGTTTTTAAAACCA
1 TATATAATATATA-TTTTC---AAAATGTTTTAAAAACTA
* *
2889682 TATATTATATA-AGTTTTCAAAATGTTTTAAAAAGT-
1 TATATAATATATA-TTTTCAAAATGTTTTAAAAACTA
2889717 TATATAATATATATTTTCAAAATGTTTTAAAAAACTA
1 TATATAATATATATTTTCAAAATGTTTT-AAAAACTA
* *
2889754 TATATTACATATATGTTTTCAAAAATGTTTTCAAAAC--
1 TATA-TA-ATATATATTTTC-AAAATGTTTTAAAAACTA
2889791 TATAT-A-ATATA---T----ATGTTTTCAAAAACTA
1 TATATAATATATATTTTCAAAATGTTTT-AAAAACTA
* * *
2889819 TATATTATATATATTTTAAAAATGTTTTCAAAAC--
1 TATATAATATATATTTTCAAAATGTTTTAAAAACTA
* *
2889853 TATATAATATATGTTTTCAAAAATG-TTTCAAAACTA
1 TATATAATATATATTTTC-AAAATGTTTTAAAAACTA
2889889 TATAT--TATATA-TTTCAAAAT
1 TATATAATATATATTTTCAAAAT
2889909 CATTTTACCT
Statistics
Matches: 297, Mismatches: 31, Indels: 79
0.73 0.08 0.19
Matches are distributed among these distances:
25 7 0.02
26 5 0.02
28 5 0.02
29 5 0.02
30 17 0.06
31 3 0.01
32 11 0.04
33 30 0.10
34 42 0.14
35 44 0.15
36 39 0.13
37 24 0.08
38 6 0.02
39 49 0.16
40 10 0.03
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (36 bp):
TATATAATATATATTTTCAAAATGTTTTAAAAACTA
Found at i:2889822 original size:26 final size:26
Alignment explanation
Indices: 2889778--2889840 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
2889768 GTTTTCAAAA
2889778 ATGTTTTC-AAAACTATATAATATAT
1 ATGTTTTCAAAAACTATATAATATAT
*
2889803 ATGTTTTCAAAAACTATATATTATAT
1 ATGTTTTCAAAAACTATATAATATAT
*
2889829 ATATTTT-AAAAA
1 ATGTTTTCAAAAA
2889841 TGTTTTCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 13 0.37
26 22 0.63
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.44
Consensus pattern (26 bp):
ATGTTTTCAAAAACTATATAATATAT
Found at i:2889863 original size:34 final size:34
Alignment explanation
Indices: 2889803--2889907 Score: 140
Period size: 34 Copynumber: 3.0 Consensus size: 34
2889793 TATAATATAT
2889803 ATGTTTTCAAAAACTATATATTATATATATTTTAAAA
1 ATGTTTTC-AAAACTATATA--ATATATATTTTAAAA
*
2889840 ATGTTTTCAAAACTATATAATATATGTTTTCAAAA
1 ATGTTTTCAAAACTATATAATATATATTTT-AAAA
* *
2889875 ATG-TTTCAAAACTATATATTATATATTTCAAAA
1 ATGTTTTCAAAACTATATAATATATATTTTAAAA
2889908 TCATTTTACC
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
33 4 0.06
34 33 0.52
35 7 0.11
36 11 0.17
37 8 0.13
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.44
Consensus pattern (34 bp):
ATGTTTTCAAAACTATATAATATATATTTTAAAA
Found at i:2889863 original size:62 final size:62
Alignment explanation
Indices: 2889738--2889875 Score: 217
Period size: 62 Copynumber: 2.2 Consensus size: 62
2889728 TATTTTCAAA
* *
2889738 ATGTTTTAAAAAACTATATATTACATATATGTTTTCAAAAATGTTTTCAAAACTATATAATATAT
1 ATGTTTTCAAAAACTATATATTA-ATATATATTTTCAAAAATGTTTTCAAAACTATAT-A-ATAT
2889803 ATGTTTTCAAAAACTATATATT-ATATATATTTT-AAAAATGTTTTCAAAACTATATAATAT
1 ATGTTTTCAAAAACTATATATTAATATATATTTTCAAAAATGTTTTCAAAACTATATAATAT
2889863 ATGTTTTCAAAAA
1 ATGTTTTCAAAAA
2889876 TGTTTCAAAA
Statistics
Matches: 71, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
60 17 0.24
61 1 0.01
62 22 0.31
63 10 0.14
65 21 0.30
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.43
Consensus pattern (62 bp):
ATGTTTTCAAAAACTATATATTAATATATATTTTCAAAAATGTTTTCAAAACTATATAATAT
Found at i:2889864 original size:36 final size:36
Alignment explanation
Indices: 2889803--2889907 Score: 146
Period size: 36 Copynumber: 3.0 Consensus size: 36
2889793 TATAATATAT
* *
2889803 ATGTTTTCAAAAACTATATATTATATATATTTTAAAA
1 ATGTTTTC-AAAACTATATAATATATATATTTCAAAA
*
2889840 ATGTTTTCAAAACTATATAATATATGT-TTTCAAAA
1 ATGTTTTCAAAACTATATAATATATATATTTCAAAA
2889875 ATG-TTTCAAAACTATAT-AT-TATATATTTCAAAA
1 ATGTTTTCAAAACTATATAATATATATATTTCAAAA
2889908 TCATTTTACC
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
32 4 0.06
33 10 0.16
34 14 0.22
35 10 0.16
36 17 0.27
37 8 0.13
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.44
Consensus pattern (36 bp):
ATGTTTTCAAAACTATATAATATATATATTTCAAAA
Found at i:2895205 original size:2 final size:2
Alignment explanation
Indices: 2895198--2895240 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2895188 AAAACTTCAA
2895198 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2895240 A
1 A
2895241 CTTCAACGAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2895478 original size:22 final size:21
Alignment explanation
Indices: 2895448--2895499 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
2895438 ATTTTAGAAT
*
2895448 TTATATTAA-ATTTAAGTTTAAA
1 TTATTTTAATATTTAA-TTT-AA
*
2895470 TTATTTTAATTTTTAATTTAA
1 TTATTTTAATATTTAATTTAA
2895491 TTATTTTAA
1 TTATTTTAA
2895500 GATAAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 11 0.41
22 11 0.41
23 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TTATTTTAATATTTAATTTAA
Found at i:2895492 original size:21 final size:23
Alignment explanation
Indices: 2895458--2895499 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
2895448 TTATATTAAA
2895458 TTTAAGTTTAAATTATTTTAATT
1 TTTAAGTTTAAATTATTTTAATT
2895481 TTTAA-TTT-AATTATTTTAA
1 TTTAAGTTTAAATTATTTTAA
2895500 GATAAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.58
22 3 0.16
23 5 0.26
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
TTTAAGTTTAAATTATTTTAATT
Found at i:2896587 original size:21 final size:22
Alignment explanation
Indices: 2896540--2896612 Score: 130
Period size: 22 Copynumber: 3.4 Consensus size: 22
2896530 AACTATGTCT
2896540 CGAAGGACCTATCCATAAGTCC
1 CGAAGGACCTATCCATAAGTCC
*
2896562 CGAAGGACCTATTCATAAGT-C
1 CGAAGGACCTATCCATAAGTCC
2896583 CGAAGGACCTATCCATAAGTCC
1 CGAAGGACCTATCCATAAGTCC
2896605 CGAAGGAC
1 CGAAGGAC
2896613 ATAGGTAACC
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.42
22 28 0.58
ACGTcount: A:0.33, C:0.29, G:0.21, T:0.18
Consensus pattern (22 bp):
CGAAGGACCTATCCATAAGTCC
Found at i:2898022 original size:20 final size:20
Alignment explanation
Indices: 2897997--2898048 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
2897987 CAACTTAAGT
*
2897997 AGTATCGGTACTACCCTCAC
1 AGTATCGATACTACCCTCAC
*
2898017 AGTATCGATACTACCCTCAT
1 AGTATCGATACTACCCTCAC
2898037 AGTATCGATACT
1 AGTATCGATACT
2898049 TCTATGCTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (20 bp):
AGTATCGATACTACCCTCAC
Found at i:2905554 original size:2 final size:2
Alignment explanation
Indices: 2905547--2905606 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
2905537 AATACACGCT
2905547 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2905589 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
2905607 ATGCTTGAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2908791 original size:60 final size:60
Alignment explanation
Indices: 2908698--2908864 Score: 214
Period size: 60 Copynumber: 2.8 Consensus size: 60
2908688 GATGAATTTG
* *
2908698 GGGATGAAATTAGAATGACCAAAAGTTTAAGGACCATTTTAGAAA-GACGA-TCATAGTCTA
1 GGGATAAAATTAGAATGACCAAAAGTTTAAGGACCAATTTA-AAATGA-GAGTCATAGTCTA
* * *
2908758 GGGATAAAATTAGAATGACCAAAAGTTTAAGGACTAATTTAAAATTAGAGTCATAGTTTA
1 GGGATAAAATTAGAATGACCAAAAGTTTAAGGACCAATTTAAAATGAGAGTCATAGTCTA
* * *
2908818 GGGATAAAATTAGAAT-ATTCAAAAGTTTAAAGACTAATTTAAAATGA
1 GGGATAAAATTAGAATGA-CCAAAAGTTTAAGGACCAATTTAAAATGA
2908865 AATTATAGTT
Statistics
Matches: 96, Mismatches: 8, Indels: 6
0.87 0.07 0.05
Matches are distributed among these distances:
59 6 0.06
60 90 0.94
ACGTcount: A:0.46, C:0.08, G:0.19, T:0.28
Consensus pattern (60 bp):
GGGATAAAATTAGAATGACCAAAAGTTTAAGGACCAATTTAAAATGAGAGTCATAGTCTA
Done.