Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008824.1 Hibiscus syriacus cultivar Beakdansim tig00111996_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: 4603428
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 19
Found at i:3076147 original size:28 final size:27
Alignment explanation
Indices: 3076046--3076147 Score: 106
Period size: 26 Copynumber: 3.9 Consensus size: 27
3076036 ATACTATATA
* *
3076046 ATATATAAATATATTAATTT-AAAAAC-
1 ATATATATATATA-TATTTTCAAAAACT
*
3076072 -TATATA-ATATATATTTTCAAAATCT
1 ATATATATATATATATTTTCAAAAACT
*
3076097 AAATAT-TATATATATTTTCAAAAACT
1 ATATATATATATATATTTTCAAAAACT
*
3076123 ATATATTATATATATATTTTTAAAA
1 ATATA-TATATATATATTTTCAAAA
3076148 TGTTTTCAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
23 5 0.08
24 10 0.16
25 6 0.09
26 26 0.41
27 1 0.02
28 16 0.25
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (27 bp):
ATATATATATATATATTTTCAAAAACT
Found at i:3076157 original size:39 final size:38
Alignment explanation
Indices: 3076111--3076256 Score: 188
Period size: 39 Copynumber: 3.8 Consensus size: 38
3076101 ATTATATATA
*
3076111 TTTTCAAAAACTATATATTATATATATATTTTTAAAAT
1 TTTTCAAAAACTATATATTATATATATATTTTCAAAAT
3076149 GTTTTCAAAAACTATATA-T-TATATATATTTTCAAAAT
1 -TTTTCAAAAACTATATATTATATATATATTTTCAAAAT
* **
3076186 ATTTTTAAAAACTATATATTATATATATGGTTTCAAAAT
1 -TTTTCAAAAACTATATATTATATATATATTTTCAAAAT
*
3076225 TTTATAAAAAAACTATATATTATATACTATAT
1 TTT-T-CAAAAACTATATATTATATA-TATAT
3076257 ATATATATAT
Statistics
Matches: 94, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
37 33 0.35
38 5 0.05
39 34 0.36
40 19 0.20
41 3 0.03
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (38 bp):
TTTTCAAAAACTATATATTATATATATATTTTCAAAAT
Found at i:3076165 original size:37 final size:37
Alignment explanation
Indices: 3076108--3076250 Score: 189
Period size: 37 Copynumber: 3.7 Consensus size: 37
3076098 AATATTATAT
*
3076108 ATATTTTCAAAAACTATATATTATATATATATTTTTAAA
1 ATATTTTCAAAAACTATATA-T-TATATATATTTTCAAA
*
3076147 ATGTTTTCAAAAACTATATATTATATATATTTTCAAA
1 ATATTTTCAAAAACTATATATTATATATATTTTCAAA
*
3076184 ATATTTTTAAAAACTATATATTATATATATGGTTTCAAA
1 ATATTTTCAAAAACTATATATTATATATAT--TTTCAAA
*
3076223 AT-TTTATAAAAAAACTATATATTATATA
1 ATATTT-T-CAAAAACTATATATTATATA
3076251 CTATATATAT
Statistics
Matches: 95, Mismatches: 5, Indels: 7
0.89 0.05 0.07
Matches are distributed among these distances:
37 43 0.45
38 4 0.04
39 29 0.31
40 19 0.20
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (37 bp):
ATATTTTCAAAAACTATATATTATATATATTTTCAAA
Found at i:3076255 original size:14 final size:13
Alignment explanation
Indices: 3076236--3076268 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
3076226 TTATAAAAAA
3076236 ACTATATATTATAT
1 ACTATATA-TATAT
3076250 ACTATATATATAT
1 ACTATATATATAT
3076263 A-TATAT
1 ACTATAT
3076269 TAAATAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.26
13 6 0.32
14 8 0.42
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (13 bp):
ACTATATATATAT
Found at i:3081000 original size:20 final size:20
Alignment explanation
Indices: 3080975--3081031 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
3080965 TAGTATGGTA
*
3080975 GTATCGATACCATGGTAAGT
1 GTATCGATACCATGGTAAGG
3080995 GTATCGATACCATGGTAAGG
1 GTATCGATACCATGGTAAGG
*
3081015 GTATCGATACCAGGGTA
1 GTATCGATACCATGGTA
3081032 TCGATACCAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (20 bp):
GTATCGATACCATGGTAAGG
Found at i:3081031 original size:14 final size:14
Alignment explanation
Indices: 3081012--3081042 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3081002 TACCATGGTA
3081012 AGGGTATCGATACC
1 AGGGTATCGATACC
3081026 AGGGTATCGATACC
1 AGGGTATCGATACC
3081040 AGG
1 AGG
3081043 AAACATCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.19, G:0.32, T:0.19
Consensus pattern (14 bp):
AGGGTATCGATACC
Found at i:3081128 original size:129 final size:129
Alignment explanation
Indices: 3080898--3081133 Score: 327
Period size: 129 Copynumber: 1.8 Consensus size: 129
3080888 CCATGATAAG
* *
3080898 GGGTATCGATACCAAGCAACATCGAATCTAATTTTGGTATCGATACAAGAAGGGGGTATCGGTAT
1 GGGTATCGATACCAAGAAACATCAAATCTAATTTTGGTATCGATACAAGAAGGGGGTATCGGTAT
* * * *
3080963 CATAGTATGGTAGTATCGATACCATGGTAAGTGTATCGATACCATGGTAAGGGTATCGATACCA
66 CATAGTATAGAAGTATCGATACCAGGGTAAGTGTATCAATACCATGGTAAGGGTATCGATACCA
* *
3081027 GGGTATCGATACCAGGAAACATCAAA-CTTAATTTTGGTATCGATATC-GGAAGGGGGTATCGGT
1 GGGTATCGATACCAAGAAACATCAAATC-TAATTTTGGTATCGATA-CAAGAAGGGGGTATCGGT
*
3081090 ATCATAGTATAGAAGTATATG-TACCAGGGT-AGTAGTATCAATAC
64 ATCATAGTATAGAAGTAT-CGATACCAGGGTAAGT-GTATCAATAC
3081134 TATGTAGATA
Statistics
Matches: 94, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
128 4 0.04
129 88 0.94
130 2 0.02
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (129 bp):
GGGTATCGATACCAAGAAACATCAAATCTAATTTTGGTATCGATACAAGAAGGGGGTATCGGTAT
CATAGTATAGAAGTATCGATACCAGGGTAAGTGTATCAATACCATGGTAAGGGTATCGATACCA
Found at i:3081546 original size:55 final size:54
Alignment explanation
Indices: 3081465--3081837 Score: 360
Period size: 55 Copynumber: 6.8 Consensus size: 54
3081455 GTACTACATG
* * * *
3081465 CACTTCGTGTGCATATTCACGGAATTCATCATGAGTTAATGAATCATCGTACATA
1 CACTT-GTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTACAGA
* * * **
3081520 CACCTTGTGTGCAAATCCACGAAATTCATCATAAGTTGATGAATCATTGTACAGGA
1 CA-CTTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTACA-GA
* * * *
3081576 -ACTTTGTGTACATATTCACGGAATTCATCACGAGTTGATGAATCACCATACAGA
1 CAC-TTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTACAGA
* ** *
3081630 CACTTCGTGTGTATATTCAC-AGAATTCATCACAAGTTGATGAATCACCGTACAGG
1 CACTT-GTGTGCATATTCACGA-AATTCATCATGAGTTGATGAATCACCGTACAGA
* * * *
3081685 CACTTCGTGTGCATATTCACGGAATTCATAATGAGTTGTTGAATCACCGTACTTG-
1 CACTT-GTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTAC-AGA
* * * * *
3081740 CACCTTGTGTGCAAATCCTCGAAATTCATCATGAGTTGATGAATTACCGTACAGG
1 CA-CTTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTACAGA
**
3081795 CACTATGTGTG--TAGCCCACGAAATTCATCATGAGTTGATGAAT
1 CACT-TGTGTGCATA-TTCACGAAATTCATCATGAGTTGATGAAT
3081838 TCCCGTATAA
Statistics
Matches: 266, Mismatches: 40, Indels: 25
0.80 0.12 0.08
Matches are distributed among these distances:
53 1 0.00
54 35 0.13
55 222 0.83
56 8 0.03
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (54 bp):
CACTTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTACAGA
Found at i:3081669 original size:110 final size:110
Alignment explanation
Indices: 3081466--3081837 Score: 423
Period size: 110 Copynumber: 3.4 Consensus size: 110
3081456 TACTACATGC
* * * *
3081466 ACTTCGTGTGCATATTCACGGAATTCATCATGAGTTAATGAATCATCGTACATACACCTTGTGTG
1 ACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCATACAGACACCTTGTGTG
* **
3081531 CAAATCCACGAAATTCATCATAAGTTGATGAATCATTGTACAGGA
66 CAAATCCACGAAATTCATCACAAGTTGATGAATCACCGTACAGGA
* * *
3081576 ACTTTGTGTACATATTCACGGAATTCATCACGAGTTGATGAATCACCATACAGACA-CTTCGTGT
1 ACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCATACAGACACCTT-GTGT
* * * *
3081640 GTATATTCAC-AGAATTCATCACAAGTTGATGAATCACCGTACAGGC
65 GCAAATCCACGA-AATTCATCACAAGTTGATGAATCACCGTACAGGA
* * * *
3081686 ACTTCGTGTGCATATTCACGGAATTCATAATGAGTTGTTGAATCACCGTACTTG-CACCTTGTGT
1 ACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCATAC-AGACACCTTGTGT
* ** * *
3081750 GCAAATCCTCGAAATTCATCATGAGTTGATGAATTACCGTACAGGC
65 GCAAATCCACGAAATTCATCACAAGTTGATGAATCACCGTACAGGA
** *
3081796 ACTAT-GTGTG--TAGCCCACGAAATTCATCATGAGTTGATGAAT
1 ACT-TCGTGTGCATA-TTCACGGAATTCATCATGAGTTGATGAAT
3081838 TCCCGTATAA
Statistics
Matches: 222, Mismatches: 33, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
108 2 0.01
109 28 0.13
110 186 0.84
111 6 0.03
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (110 bp):
ACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCATACAGACACCTTGTGTG
CAAATCCACGAAATTCATCACAAGTTGATGAATCACCGTACAGGA
Found at i:3088105 original size:22 final size:20
Alignment explanation
Indices: 3088080--3088124 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
3088070 GGCGTATTGG
*
3088080 TACCATAGTATGGTAGTATCGA
1 TACCATAGTAAGG--GTATCGA
*
3088102 TACCATGGTAAGGGTATCGA
1 TACCATAGTAAGGGTATCGA
3088122 TAC
1 TAC
3088125 TAGGCAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.48
22 11 0.52
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (20 bp):
TACCATAGTAAGGGTATCGA
Found at i:3088165 original size:95 final size:95
Alignment explanation
Indices: 3087995--3088221 Score: 285
Period size: 95 Copynumber: 2.4 Consensus size: 95
3087985 ATACCGATGA
* * * *
3087995 GGTAGTATCGATACCATGATAAGGGTTATCAATACCAAGCAACATCGAATTTAATTTTAGTATCG
1 GGTAGTATCGATACCATGGTAAGGG-TATCGATACTAAGCAACATCGAACTTAATTTTAGTATCG
** *
3088060 ATACTGGAAGGGCGTATTGGTACCATAGTAT
65 ATACCAGAAGGGCGTATCGGTACCATAGTAT
* *
3088091 GGTAGTATCGATACCATGGTAAGGGTATCGATACTAGGCAACATCGAACTTAATTTTGGTATCGA
1 GGTAGTATCGATACCATGGTAAGGGTATCGATACTAAGCAACATCGAACTTAATTTTAGTATCGA
* *
3088156 TACCAGAAGGGGGTATCGGTACCATTGTAT
66 TACCAGAAGGGCGTATCGGTACCATAGTAT
* * * * *
3088186 AGAAGTATCGGTACCAGGGT-AGTAGTATCGATACTA
1 GGTAGTATCGATACCATGGTAAG-GGTATCGATACTA
3088222 TGTAGACAAA
Statistics
Matches: 114, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
94 2 0.02
95 88 0.77
96 24 0.21
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.29
Consensus pattern (95 bp):
GGTAGTATCGATACCATGGTAAGGGTATCGATACTAAGCAACATCGAACTTAATTTTAGTATCGA
TACCAGAAGGGCGTATCGGTACCATAGTAT
Found at i:3088614 original size:55 final size:54
Alignment explanation
Indices: 3088545--3088922 Score: 427
Period size: 55 Copynumber: 6.9 Consensus size: 54
3088535 ATATGTGTAC
*
3088545 TACAGGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCA
1 TACAGGCAC-TTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
* * *
3088600 TACAGGCACCTTGTGTGTAAATCCACGGAATTCATCATGAGTTGATGAATCACCG
1 TACAGGCA-CTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
* ** *
3088655 TACAGGCACTTCGTGCGCATATTCATAGAATTCATCATGAGTTGATGAATCAACG
1 TACAGGCACTT-GTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
* *
3088710 TACAAGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATAAATCACCG
1 TACAGGCACTT-GTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
* * *
3088765 TATAGGCACTTCGTGTGCATATTCACGGAATTCATCAGGAGTTGATAAATCACCG
1 TACAGGCACTT-GTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
* * * * *** *
3088820 TATAGGCACCT-TGTGCGTAAATCTATATAATTCATCAAGAGTTGATGAATCACCG
1 TACAGGCACTTGTGTGCAT-ATTC-ACGGAATTCATCATGAGTTGATGAATCACCG
* * *** * *
3088875 TACATGCACATGTGTGCA-GCCCACGAAATTCATTATGAGTTGATGAAT
1 TACAGGCACTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAAT
3088923 TCCCGTATAT
Statistics
Matches: 278, Mismatches: 40, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
53 27 0.10
54 7 0.03
55 238 0.86
56 6 0.02
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.29
Consensus pattern (54 bp):
TACAGGCACTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
Found at i:3088854 original size:165 final size:163
Alignment explanation
Indices: 3088545--3088937 Score: 479
Period size: 165 Copynumber: 2.4 Consensus size: 163
3088535 ATATGTGTAC
* * * *
3088545 TACAGGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCATACAGGCACC
1 TACAAGCAC-TTGTGTGCATATTCACGGAATTCATCATGAGTTGATAAATCACCGTATAGGCA-C
* * * *
3088610 TTGTGTGTAAATCCACGGAATTCATCATGAGTTGATGAATCACCGTACAGGCACTTCGTGCGCAT
64 TTGTGTGCAAATCCACGGAATTCATCAGGAGTTGATAAATCACCGTACAGGCACTTCGTGCGCAA
*
3088675 ATTCATAGAATTCATCATGAGTTGATGAATCAACG
129 ATTCATAGAATTCATCAAGAGTTGATGAATCAACG
3088710 TACAAGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATAAATCACCGTATAGGCACT
1 TACAAGCACTT-GTGTGCATATTCACGGAATTCATCATGAGTTGATAAATCACCGTATAGGCACT
* * * *
3088775 TCGTGTGCATATTCACGGAATTCATCAGGAGTTGATAAATCACCGTATAGGCACCTT-GTGCGTA
65 T-GTGTGCAAATCCACGGAATTCATCAGGAGTTGATAAATCACCGTACAGGCA-CTTCGTGCGCA
* *
3088839 AA-TCTATATAATTCATCAAGAGTTGATGAATCACCG
128 AATTC-ATAGAATTCATCAAGAGTTGATGAATCAACG
* * *** * * * *
3088875 TACATGCACATGTGTGCA-GCCCACGAAATTCATTATGAGTTGATGAATTC-CCGTATATGCACT
1 TACAAGCACTTGTGTGCATATTCACGGAATTCATCATGAGTTGAT-AAATCACCGTATAGGCACT
3088938 AATTGTGCAT
Statistics
Matches: 199, Mismatches: 24, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
163 33 0.17
164 18 0.09
165 145 0.73
166 3 0.02
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.30
Consensus pattern (163 bp):
TACAAGCACTTGTGTGCATATTCACGGAATTCATCATGAGTTGATAAATCACCGTATAGGCACTT
GTGTGCAAATCCACGGAATTCATCAGGAGTTGATAAATCACCGTACAGGCACTTCGTGCGCAAAT
TCATAGAATTCATCAAGAGTTGATGAATCAACG
Found at i:3093707 original size:40 final size:40
Alignment explanation
Indices: 3093663--3093746 Score: 141
Period size: 40 Copynumber: 2.1 Consensus size: 40
3093653 AAATCTTAAA
* *
3093663 ACCAATCGATTCTTAATTATTTAACATGACAGACGTTGAT
1 ACCAATCGATTCTTAATAATTTAACATGACAGACGCTGAT
*
3093703 ACCAATCGATTCTTAATAATTTAACATGAGAGACGCTGAT
1 ACCAATCGATTCTTAATAATTTAACATGACAGACGCTGAT
3093743 ACCA
1 ACCA
3093747 CTTGTTAGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (40 bp):
ACCAATCGATTCTTAATAATTTAACATGACAGACGCTGAT
Found at i:3098705 original size:21 final size:21
Alignment explanation
Indices: 3098680--3098761 Score: 58
Period size: 22 Copynumber: 3.9 Consensus size: 21
3098670 ATTTATATAA
*
3098680 AAAAATTAAATATTTTATAATT
1 AAAAA-TAAATAATTTATAATT
* * *
3098702 AAAAAAAAACAGTTTATAATT
1 AAAAATAAATAATTTATAATT
** *
3098723 -AATTTAAATAATATATAATT
1 AAAAATAAATAATTTATAATT
* *
3098743 ATAAAATAAAAAAATTATA
1 A-AAAATAAATAATTTATA
3098762 TAAATTTTTA
Statistics
Matches: 44, Mismatches: 14, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
20 14 0.32
21 13 0.30
22 17 0.39
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (21 bp):
AAAAATAAATAATTTATAATT
Found at i:3099034 original size:184 final size:183
Alignment explanation
Indices: 3098713--3099057 Score: 618
Period size: 184 Copynumber: 1.9 Consensus size: 183
3098703 AAAAAAAACA
*
3098713 GTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAAAATTATATAAATTTTTAATTAAT
1 GTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAAATTATATAAATTTTTAATTAAT
*
3098778 TAATATTGATTTAGGTTTAAAAGTTATTGAATCTTAAATTATTAATTGAGTTTTAAATGGTTTGG
66 TAATATTGATTTAGATTTAAAAGTTATTGAATCTTAAATTATTAATTGAGTTTTAAATGGTTTGG
*
3098843 GCTGAGCCCAAATGTTATATATAATATATTTTAATTTTTTAATTCAGAAAATG
131 ACTGAGCCCAAATGTTATATATAATATATTTTAATTTTTTAATTCAGAAAATG
**
3098896 GTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTTATATAAATTTTTTAATTAA
1 GTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAAATTATATAAA-TTTTTAATTAA
*
3098961 TTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTG
65 TTAATATTGATTTAGATTTAAAAGTTATTGAATCTTAAATTATTAATTGAGTTTTAAATGGTTTG
*
3099026 GACTGAGCCCATATGTTATATATAATATATTT
130 GACTGAGCCCAAATGTTATATATAATATATTT
3099058 AATATTTAAA
Statistics
Matches: 154, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
183 50 0.32
184 104 0.68
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (183 bp):
GTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAAATTATATAAATTTTTAATTAAT
TAATATTGATTTAGATTTAAAAGTTATTGAATCTTAAATTATTAATTGAGTTTTAAATGGTTTGG
ACTGAGCCCAAATGTTATATATAATATATTTTAATTTTTTAATTCAGAAAATG
Found at i:3100165 original size:76 final size:75
Alignment explanation
Indices: 3099933--3100165 Score: 277
Period size: 77 Copynumber: 3.0 Consensus size: 75
3099923 TATATATAAG
* * * * * *
3099933 AAATAAGGTTGCGCTTAAAAATACCATGGTTCAGTAAGAAATAGGCTGCGATCTGGAATTATAAT
1 AAAT-AGGTTGCGCTCAAGAATATCATGGTTCACTAAG-AATAGGTTGTGATCTGGAATT-TAAT
3099998 ATTTTTATTAATA
63 ATTTTTATTAATA
* * * * * *
3100011 ACATAGGTTGAGCCCAAGAATATCATGGTTCACTCAAAAATTGGTTGTGATCTGGAATGTTAGTA
1 AAATAGGTTGCGCTCAAGAATATCATGGTTCACT-AAGAATAGGTTGTGATCTGGAAT-TTAATA
3100076 TTTTTATTAATA
64 TTTTTATTAATA
* * *
3100088 AAATGGGTTGCGCTCAAGAATGTCATGGTTCACTAAGAATAAGTTGTGATCTGGAATATTAATAT
1 AAATAGGTTGCGCTCAAGAATATCATGGTTCACTAAGAATAGGTTGTGATCTGGAAT-TTAATAT
3100153 TTTTATTAATA
65 TTTTATTAATA
3100164 AA
1 AA
3100166 TTTCGTTCCG
Statistics
Matches: 131, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
76 39 0.30
77 86 0.66
78 6 0.05
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (75 bp):
AAATAGGTTGCGCTCAAGAATATCATGGTTCACTAAGAATAGGTTGTGATCTGGAATTTAATATT
TTTATTAATA
Found at i:3100378 original size:77 final size:74
Alignment explanation
Indices: 3100281--3100507 Score: 224
Period size: 77 Copynumber: 3.0 Consensus size: 74
3100271 AAGAAATAAA
*
3100281 GTTGCACCCAAGAATGTCATGATTTACTAAGAAATATGTTACGATCTAGAGTGTTAAAATTTTTA
1 GTTGCACCCAAGAATGTCATG-TTTACTAAGAAATA-GTTACGATCT-GAATGTTAAAATTTTTA
*
3100346 TTAATAAAATGT
63 TTAATAAAATGG
* * * * * *
3100358 GTTTCACCCAAGAATATCATGGTTCACTAAGAAATAGATTGCGACCTGAAATGTTAATA-TTTTA
1 GTTGCACCCAAGAATGTCAT-GTTTACTAAGAAATAG-TTACGATCTG-AATGTTAAAATTTTTA
3100422 TTAATAAAATGG
63 TTAATAAAATGG
* * * * * *
3100434 GTTGCACTCAATAATGTTATGTTTACTAAGAAAGTAAATTACGATATGGAATGTTAATATTTTTT
1 GTTGCACCCAAGAATGTCATGTTTACTAAGAAA-T-AGTTACGATCT-GAATGTTAA-AATTTTT
3100499 ATT-ATAAAA
62 ATTAATAAAA
3100508 AATCCAAAGT
Statistics
Matches: 122, Mismatches: 20, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
75 12 0.10
76 48 0.39
77 54 0.44
78 8 0.07
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (74 bp):
GTTGCACCCAAGAATGTCATGTTTACTAAGAAATAGTTACGATCTGAATGTTAAAATTTTTATTA
ATAAAATGG
Found at i:3100487 original size:76 final size:75
Alignment explanation
Indices: 3100281--3100496 Score: 243
Period size: 76 Copynumber: 2.8 Consensus size: 75
3100271 AAGAAATAAA
** * * *
3100281 GTTGCACCCAAGAATGTCATGATTTACTAAGAAATATGTTACGATCTAGAGTGTTAAAATTTTTA
1 GTTGCACCCAAGAATGTCATG-TTTACTAAGAAATAAATTACGATCTGGAATGTTAATA-TTTTA
*
3100346 TTAATAAAATGT
64 TTAATAAAATGG
* * * * * * *
3100358 GTTTCACCCAAGAATATCATGGTTCACTAAGAAATAGATTGCGACCTGAAATGTTAATATTTTAT
1 GTTGCACCCAAGAATGTCAT-GTTTACTAAGAAATAAATTACGATCTGGAATGTTAATATTTTAT
3100423 TAATAAAATGG
65 TAATAAAATGG
* * * *
3100434 GTTGCACTCAATAATGTTATGTTTACTAAGAAAGTAAATTACGATATGGAATGTTAATATTTT
1 GTTGCACCCAAGAATGTCATGTTTACTAAGAAA-TAAATTACGATCTGGAATGTTAATATTTT
3100497 TTATTATAAA
Statistics
Matches: 114, Mismatches: 23, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
75 12 0.11
76 55 0.48
77 46 0.40
78 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (75 bp):
GTTGCACCCAAGAATGTCATGTTTACTAAGAAATAAATTACGATCTGGAATGTTAATATTTTATT
AATAAAATGG
Found at i:3100493 original size:341 final size:338
Alignment explanation
Indices: 3099840--3100506 Score: 772
Period size: 341 Copynumber: 2.0 Consensus size: 338
3099830 AGGTTGCGCT
3099840 TAAAATGTTACCAAAGTTTAAATTAATGGAGCATTGGATTTTCCCACAATAAGAAAATAAGTTAA
1 TAAAATGTTACCAAAGTTTAAATTAATGGAGCATTGGATTTTCCCACAATAAGAAAATAAGTTAA
* * * * * ** * *
3099905 AAATGAAAATGTTATGAATATATATAAGAAATAAGGTTGCGCTTAAAAATACCATGGTTCAGTAA
66 AAACGAAAATGTAATGAATATATAGAAGAAATAAAGTTGCACCCAAAAATACCATGATTCACTAA
* * * * *
3099970 GAAATAGGCTGCGATCTGGAATTATAATATTTTTATTAATAACATAGGTTGAGCCCAAGAATATC
131 GAAATAGGCTACGATCTAGAATTATAAAATTTTTATTAATAAAATAGGTTCAGCCCAAGAATATC
* * * * * * *
3100035 ATGGTTCACTCAAAAATTGGTTGTGATCTGGAATGTTAGTATTTTTATTAATAAAATGGGTTGCG
196 ATGGTTCACTCAAAAATAGATTGCGACCTGAAATGTTAATATTTTTATTAATAAAATGGGTTGCA
* ** *
3100100 CTCAAGAATGTCATGGTTCACTAAGAATAAGTTGTGATCTGGAATATTAATA-TTTTTATTAATA
261 CTCAAGAATGTCATGGTTCACTAAGAATAAATTACGATATGGAATATTAATATTTTTTATT-ATA
3100164 AATTTCGTTCCGGC
325 AATTTCGTTCCGGC
** * * * ** * * *
3100178 TAAAATGTTATTAGAGTTTAAGTTGATGGAGTTTTGTATTTTCTCACTATAAGAAAATAAGTTAA
1 TAAAATGTTACCAAAGTTTAAATTAATGGAGCATTGGATTTTCCCACAATAAGAAAATAAGTTAA
* * ** *
3100243 AGACGAAAATGTAATGATTATATATAAGAAGAAATAAAGTTGCACCCAAGAATGTCATGATTTAC
66 AAACGAAAATGTAATGA--ATATAT-AGAAGAAATAAAGTTGCACCCAAAAATACCATGATTCAC
* * *
3100308 TAAGAAATATGTTACGATCTAGAGTGT-TAAAATTTTTATTAATAAAAT-GTGTTTCA-CCCAAG
128 TAAGAAATAGGCTACGATCTAGAAT-TATAAAATTTTTATTAATAAAATAG-G-TTCAGCCCAAG
3100370 AATATCATGGTTCACT-AAGAAATAGATTGCGACCTGAAATGTTAATA-TTTTATTAATAAAATG
190 AATATCATGGTTCACTCAA-AAATAGATTGCGACCTGAAATGTTAATATTTTTATTAATAAAATG
* * * *
3100433 GGTTGCACTCAATAATGTTAT-GTTTACTAAGAAAGTAAATTACGATATGGAATGTTAATATTTT
254 GGTTGCACTCAAGAATGTCATGGTTCACTAAG-AA-TAAATTACGATATGGAATATTAATATTTT
3100497 TTATTATAAA
317 TTATTATAAA
3100507 AAATCCAAAG
Statistics
Matches: 272, Mismatches: 47, Indels: 17
0.81 0.14 0.05
Matches are distributed among these distances:
338 69 0.25
339 9 0.03
340 45 0.17
341 137 0.50
342 12 0.04
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (338 bp):
TAAAATGTTACCAAAGTTTAAATTAATGGAGCATTGGATTTTCCCACAATAAGAAAATAAGTTAA
AAACGAAAATGTAATGAATATATAGAAGAAATAAAGTTGCACCCAAAAATACCATGATTCACTAA
GAAATAGGCTACGATCTAGAATTATAAAATTTTTATTAATAAAATAGGTTCAGCCCAAGAATATC
ATGGTTCACTCAAAAATAGATTGCGACCTGAAATGTTAATATTTTTATTAATAAAATGGGTTGCA
CTCAAGAATGTCATGGTTCACTAAGAATAAATTACGATATGGAATATTAATATTTTTTATTATAA
ATTTCGTTCCGGC
Found at i:3100869 original size:27 final size:29
Alignment explanation
Indices: 3100823--3100879 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
3100813 GTATCGATAC
*
3100823 TTTTAAATTCGAAAGTTAT-AATATTTTT
1 TTTTAAATTCGAAAGTTATAAATAATTTT
*
3100851 TTTTAATTTCGAAAG-TATAAATAATTTT
1 TTTTAAATTCGAAAGTTATAAATAATTTT
3100879 T
1 T
3100880 CACAAATATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 3 0.12
28 23 0.88
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.53
Consensus pattern (29 bp):
TTTTAAATTCGAAAGTTATAAATAATTTT
Found at i:3101059 original size:99 final size:99
Alignment explanation
Indices: 3100951--3101281 Score: 377
Period size: 99 Copynumber: 3.3 Consensus size: 99
3100941 TTTGTTATGG
* * *
3100951 TCATGATAACGTAGTAGGTAGCGCATTTTTTTAATATAACTGTTAAAGTTACAAGTAT-AAATTG
1 TCATGATAACGTAGTAGGTAGCGC-CTTTTTTAATATAACTGTTTAAGTTATAAGTATGAAATTG
*
3101015 TTTATATGATGCAAAAGTAAGACAAAACATGTTTC
65 TTTATATTATGCAAAAGTAAGACAAAACATGTTTC
*
3101050 TCATGATAACGTAGTAGGTAGCGCCTTTTTT-ATGTTAA-TCGTTTAAGTTATAAGTATGAAATC
1 TCATGATAACGTAGTAGGTAGCGCCTTTTTTAAT-ATAACT-GTTTAAGTTATAAGTATGAAAT-
*
3101113 T-TTTATATTATGCAAAAGTAAGACAAAACATGTTAC
63 TGTTTATATTATGCAAAAGTAAGACAAAACATGTTTC
* * * * * **
3101149 TCATGATAACGTACTAAGTATCGCCTTTTTTAATGTCAACAT-TTTAAGTTATAAGCATGAAACC
1 TCATGATAACGTAGTAGGTAGCGCCTTTTTTAATAT-AAC-TGTTTAAGTTATAAGTATGAAATT
* * *
3101213 GTTTACATTATGCAAAAATAAGACAAAA-ATAGATTTA
64 GTTTATATTATGCAAAAGTAAGACAAAACAT-G-TTTC
* **
3101250 TCATGATAACATAGTAGGTAGCTTCTTTTTTA
1 TCATGATAACGTAGTAGGTAGCGCCTTTTTTA
3101282 TGCAAAAGTA
Statistics
Matches: 198, Mismatches: 23, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
97 3 0.02
98 24 0.12
99 92 0.46
100 50 0.25
101 28 0.14
102 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (99 bp):
TCATGATAACGTAGTAGGTAGCGCCTTTTTTAATATAACTGTTTAAGTTATAAGTATGAAATTGT
TTATATTATGCAAAAGTAAGACAAAACATGTTTC
Found at i:3101653 original size:73 final size:74
Alignment explanation
Indices: 3101517--3101753 Score: 218
Period size: 73 Copynumber: 3.3 Consensus size: 74
3101507 CATAACTTAT
* * * * * * * * * *
3101517 GTATCAATATTTTAACTATCGATCATATTCATCAACTTGTTCAATATCTAAAAATATCGATCATC
1 GTATCGATATTTTAAATTTAGATCTTATTTATCAACTTTTTCAATATTTAAAAGTATCGATCATA
3101582 ATCACATAA
66 ATCACATAA
* * *
3101591 GTATCGATATTTTAAATTTCA-ATCTT-TTTATCAGCTTTTTCAATTTTTAAAAGTATCAATCAT
1 GTATCGATATTTTAAATTT-AGATCTTATTTATCAACTTTTTCAATATTTAAAAGTATCGATCAT
* *
3101654 TA-CTGCATAA
65 AATC-ACATAA
* * *
3101664 GTATCTATTTTTTAAATTTAGATCTTATTT-T-AACTTTTTCAATATTTAAAAGTATCGATAATA
1 GTATCGATATTTTAAATTTAGATCTTATTTATCAACTTTTTCAATATTTAAAAGTATCGATCATA
*
3101727 AT-ATATTAA
66 ATCACA-TAA
*
3101736 GTATTGATA-TTTAAATTT
1 GTATCGATATTTTAAATTT
3101754 TTAAAATGTT
Statistics
Matches: 131, Mismatches: 26, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
71 10 0.08
72 39 0.30
73 59 0.45
74 23 0.18
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (74 bp):
GTATCGATATTTTAAATTTAGATCTTATTTATCAACTTTTTCAATATTTAAAAGTATCGATCATA
ATCACATAA
Found at i:3102258 original size:77 final size:76
Alignment explanation
Indices: 3102118--3102281 Score: 188
Period size: 77 Copynumber: 2.1 Consensus size: 76
3102108 ATCTTTGATA
* * * * * * ** *
3102118 ACATTTTAGGCGCAACCGATTTTATTATTAAAAATACTAAGATTCCATATTGCAACTTGTTTCTT
1 ACATTTTGGGCGCAACCAATTTTATTACTAAAAATACTAACATTACAAATCACAACTTATTTCTT
3102183 AGTTAAA-CATG
66 A-TTAAACCATG
*
3102194 ACATTCTTGGGCGCAACCAATTTTATTACTAAAAATATTAACATTACAAATCACAA-TCTATTTC
1 ACATT-TTGGGCGCAACCAATTTTATTACTAAAAATACTAACATTACAAATCACAACT-TATTTC
3102258 TTATTAAACCATG
64 TTATTAAACCATG
3102271 ACATTATTGGG
1 ACATT-TTGGG
3102282 TACAATCTAT
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
76 11 0.15
77 63 0.85
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (76 bp):
ACATTTTGGGCGCAACCAATTTTATTACTAAAAATACTAACATTACAAATCACAACTTATTTCTT
ATTAAACCATG
Found at i:3107761 original size:13 final size:13
Alignment explanation
Indices: 3107743--3107794 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
3107733 GTCATGAATC
3107743 TATGACGCACATT
1 TATGACGCACATT
* *
3107756 TATGACACATATT
1 TATGACGCACATT
* *
3107769 TATGATGCTCATT
1 TATGACGCACATT
*
3107782 TATGACGCGCATT
1 TATGACGCACATT
3107795 GAGCGTCATT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (13 bp):
TATGACGCACATT
Found at i:3110100 original size:36 final size:35
Alignment explanation
Indices: 3110016--3110117 Score: 127
Period size: 35 Copynumber: 2.9 Consensus size: 35
3110006 ATATAAGCGA
* *
3110016 GAAATGGTAATGGAAGATGGT-ACTGATATAGGCGT
1 GAAATGGTAATGGAAGATGGTGA-TGTTATAGGCAT
* *
3110051 GCAATGGTAATGGAAGATGATGATGTTATAGGCAT
1 GAAATGGTAATGGAAGATGGTGATGTTATAGGCAT
*
3110086 GAAAATGGTGATGGAAGATGGTGATGTT-TAGG
1 G-AAATGGTAATGGAAGATGGTGATGTTATAGG
3110118 TAGTATCTTA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
35 34 0.59
36 24 0.41
ACGTcount: A:0.33, C:0.04, G:0.35, T:0.27
Consensus pattern (35 bp):
GAAATGGTAATGGAAGATGGTGATGTTATAGGCAT
Found at i:3113679 original size:19 final size:17
Alignment explanation
Indices: 3113647--3113681 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
3113637 TGTAAGAGTC
3113647 TTTTTCTTTTCTTTTTG
1 TTTTTCTTTTCTTTTTG
3113664 TTTTTCTTCATTCTTTTT
1 TTTTTCTT--TTCTTTTT
3113682 CTCTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.80
Consensus pattern (17 bp):
TTTTTCTTTTCTTTTTG
Found at i:3114174 original size:36 final size:35
Alignment explanation
Indices: 3114081--3114191 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 35
3114071 TTGGTGGTTA
* * * *
3114081 TATAGGTATGAAATGGTAATGGAAGATGATAATGA
1 TATAGGCATGAAATGGTAATGGAAGATGGTGATGT
*
3114116 TATAGGCATGCAATGGTAATGGAAGATGGTGATGT
1 TATAGGCATGAAATGGTAATGGAAGATGGTGATGT
* *
3114151 TATAGGCGTGAAAATGGTGATGGAAGATGGTGATGT
1 TATAGGCATG-AAATGGTAATGGAAGATGGTGATGT
3114187 T-TAGG
1 TATAGG
3114192 TAGTATCTTA
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
35 43 0.64
36 24 0.36
ACGTcount: A:0.34, C:0.03, G:0.34, T:0.29
Consensus pattern (35 bp):
TATAGGCATGAAATGGTAATGGAAGATGGTGATGT
Found at i:3118200 original size:35 final size:35
Alignment explanation
Indices: 3118159--3118242 Score: 114
Period size: 35 Copynumber: 2.4 Consensus size: 35
3118149 ATTGGTGGTT
*
3118159 ATATAGGTATGAAATGGTAATAGAAGATGGTAATG
1 ATATAGGCATGAAATGGTAATAGAAGATGGTAATG
* * *
3118194 ATATAGGCATGCAATGGTAATGGAAGATGGTGATG
1 ATATAGGCATGAAATGGTAATAGAAGATGGTAATG
* *
3118229 TTATAGGCGTGAAA
1 ATATAGGCATGAAA
3118243 ATGGCGATGA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.38, C:0.04, G:0.31, T:0.27
Consensus pattern (35 bp):
ATATAGGCATGAAATGGTAATAGAAGATGGTAATG
Found at i:3118257 original size:36 final size:35
Alignment explanation
Indices: 3118159--3118263 Score: 104
Period size: 35 Copynumber: 3.0 Consensus size: 35
3118149 ATTGGTGGTT
* * *
3118159 ATATAGGTATGAAATGGTAAT-AGAAGATGGTAATG
1 ATATAGGCATGAAATGGCAATGA-AAGATGGTGATG
* * *
3118194 ATATAGGCATGCAATGGTAATGGAAGATGGTGATG
1 ATATAGGCATGAAATGGCAATGAAAGATGGTGATG
* * *
3118229 TTATAGGCGTGAAAATGGCGATGAAAGATGGTGAT
1 ATATAGGCATG-AAATGGCAATGAAAGATGGTGAT
3118264 ATTTAGGTAG
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
35 39 0.67
36 19 0.33
ACGTcount: A:0.37, C:0.04, G:0.32, T:0.27
Consensus pattern (35 bp):
ATATAGGCATGAAATGGCAATGAAAGATGGTGATG
Found at i:3122341 original size:8 final size:8
Alignment explanation
Indices: 3122325--3122370 Score: 74
Period size: 8 Copynumber: 5.8 Consensus size: 8
3122315 AACCAACTGC
3122325 AAAGAGAA
1 AAAGAGAA
*
3122333 AAAGGGAA
1 AAAGAGAA
3122341 AAAGAGAA
1 AAAGAGAA
*
3122349 AAAGGGAA
1 AAAGAGAA
3122357 AAAGAGAA
1 AAAGAGAA
3122365 AAAGAG
1 AAAGAG
3122371 GGAAGCTGCG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 34 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (8 bp):
AAAGAGAA
Found at i:3122346 original size:16 final size:16
Alignment explanation
Indices: 3122325--3122368 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
3122315 AACCAACTGC
3122325 AAAGAGAAAAAGGGAA
1 AAAGAGAAAAAGGGAA
3122341 AAAGAGAAAAAGGGAA
1 AAAGAGAAAAAGGGAA
3122357 AAAGAGAAAAAG
1 AAAGAGAAAAAG
3122369 AGGGAAGCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (16 bp):
AAAGAGAAAAAGGGAA
Found at i:3136903 original size:29 final size:29
Alignment explanation
Indices: 3136845--3137020 Score: 136
Period size: 29 Copynumber: 6.3 Consensus size: 29
3136835 TTTATACAAT
* *
3136845 TATCACCCTTTTAAAAAAGAATTACAAAAA
1 TATCACCCTTTT-CAAAATAATTACAAAAA
*
3136875 TATCACCCTTTTCAAAATAATTACTAAAA
1 TATCACCCTTTTCAAAATAATTACAAAAA
* * * *
3136904 TATCA--TTTCTTTAAAA-AA-TACGAAAT
1 TATCACCCTT-TTCAAAATAATTACAAAAA
**
3136930 TAT-A---TTTTTTAAA-AATTACGAAAAA
1 TATCACCCTTTTCAAAATAATTAC-AAAAA
* * *
3136955 TAGCACCATTTTCAAAATAATTACCAAAA
1 TATCACCCTTTTCAAAATAATTACAAAAA
* *
3136984 TATCACCATTTTCAAAATAATTACTAAAA
1 TATCACCCTTTTCAAAATAATTACAAAAA
3137013 TATCACCC
1 TATCACCC
3137021 GGTCAACGGT
Statistics
Matches: 121, Mismatches: 17, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
23 8 0.07
24 5 0.04
25 6 0.05
26 10 0.08
27 4 0.03
28 6 0.05
29 64 0.53
30 18 0.15
ACGTcount: A:0.48, C:0.17, G:0.02, T:0.33
Consensus pattern (29 bp):
TATCACCCTTTTCAAAATAATTACAAAAA
Found at i:3143356 original size:21 final size:21
Alignment explanation
Indices: 3143326--3143375 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
3143316 TTTCATACTT
*
3143326 GGAAACCATATGCAGAAATAC
1 GGAAATCATATGCAGAAATAC
*
3143347 TGAAATCATATGCAGAAATAC
1 GGAAATCATATGCAGAAATAC
3143368 GGAAATCA
1 GGAAATCA
3143376 GAATTCAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.48, C:0.16, G:0.18, T:0.18
Consensus pattern (21 bp):
GGAAATCATATGCAGAAATAC
Found at i:3144224 original size:29 final size:29
Alignment explanation
Indices: 3144182--3144364 Score: 114
Period size: 29 Copynumber: 6.6 Consensus size: 29
3144172 ATCAACCATT
* * *
3144182 TTACACAATTATCACCTTTTTAAAAAAAA
1 TTACAAAAATATCACCTTTTTCAAAAAAA
* *
3144211 TTACAAAAATATCACCCTTTTCAAAATAA
1 TTACAAAAATATCACCTTTTTCAAAAAAA
* ** **
3144240 TTACTAAAATAT-AATTTTTTTTAAAAAA
1 TTACAAAAATATCACCTTTTTCAAAAAAA
* * *
3144268 -TACGAAATTAT-A--TTTTT--TAAAAA
1 TTACAAAAATATCACCTTTTTCAAAAAAA
**
3144291 TTACAAAAATAGT-ACAATTTTCAAAAAAA
1 TTACAAAAATA-TCACCTTTTTCAAAAAAA
* * *
3144320 TTACCAAAATATC-CTCATTTTCAAAATAA
1 TTACAAAAATATCAC-CTTTTTCAAAAAAA
*
3144349 TTACTAAAATATCACC
1 TTACAAAAATATCACC
3144365 CGGTAAACGG
Statistics
Matches: 122, Mismatches: 23, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
23 5 0.04
24 8 0.07
25 7 0.06
27 14 0.11
28 12 0.10
29 75 0.61
30 1 0.01
ACGTcount: A:0.49, C:0.14, G:0.01, T:0.36
Consensus pattern (29 bp):
TTACAAAAATATCACCTTTTTCAAAAAAA
Found at i:3149081 original size:2 final size:2
Alignment explanation
Indices: 3149074--3149141 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
3149064 ACATGCATGC
3149074 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
3149116 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
3149142 CTCAATAGTA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3159646 original size:19 final size:18
Alignment explanation
Indices: 3159607--3159653 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 18
3159597 TGTTTGAAGC
*
3159607 AAGAAGAAGAAAAAATGAA
1 AAGAAAAAG-AAAAATGAA
3159626 AAGAAAAAGAAAAA-GAA
1 AAGAAAAAGAAAAATGAA
*
3159643 AA-AAAAGGAAA
1 AAGAAAAAGAAA
3159654 TGATTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 8 0.31
17 5 0.19
18 5 0.19
19 8 0.31
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (18 bp):
AAGAAAAAGAAAAATGAA
Found at i:3161164 original size:24 final size:24
Alignment explanation
Indices: 3161136--3161193 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
3161126 AAAGTTGTTA
3161136 GGGCCAAGAAGAAGAAATTATTGT
1 GGGCCAAGAAGAAGAAATTATTGT
3161160 GGGCCAAGAAGAAGAAATTATTGT
1 GGGCCAAGAAGAAGAAATTATTGT
*
3161184 GAGCCAAGAA
1 GGGCCAAGAA
3161194 TTGAGAGGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.43, C:0.10, G:0.29, T:0.17
Consensus pattern (24 bp):
GGGCCAAGAAGAAGAAATTATTGT
Found at i:3174586 original size:16 final size:17
Alignment explanation
Indices: 3174550--3174586 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
3174540 ATTGTAATAA
*
3174550 TTTTTCCTACAAAATGT
1 TTTTTACTACAAAATGT
3174567 TTTTTACTACAAAATGT
1 TTTTTACTACAAAATGT
3174584 TTT
1 TTT
3174587 GAAGAAACTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.30, C:0.14, G:0.05, T:0.51
Consensus pattern (17 bp):
TTTTTACTACAAAATGT
Found at i:3176293 original size:19 final size:19
Alignment explanation
Indices: 3176269--3176328 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
3176259 ATATTTTGTA
3176269 AAAATGTTGTTAACTGACG
1 AAAATGTTGTTAACTGACG
**
3176288 AAAATG-TGTTTTCT-A--
1 AAAATGTTGTTAACTGACG
3176303 AAAATGTTGTTAACTGACG
1 AAAATGTTGTTAACTGACG
3176322 AAAATGT
1 AAAATGT
3176329 GTTTTCGATG
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 6 0.18
16 6 0.18
17 2 0.06
18 6 0.18
19 13 0.39
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.35
Consensus pattern (19 bp):
AAAATGTTGTTAACTGACG
Found at i:3176310 original size:34 final size:34
Alignment explanation
Indices: 3176262--3176334 Score: 137
Period size: 34 Copynumber: 2.1 Consensus size: 34
3176252 AGCAATGATA
*
3176262 TTTTGTAAAAATGTTGTTAACTGACGAAAATGTG
1 TTTTCTAAAAATGTTGTTAACTGACGAAAATGTG
3176296 TTTTCTAAAAATGTTGTTAACTGACGAAAATGTG
1 TTTTCTAAAAATGTTGTTAACTGACGAAAATGTG
3176330 TTTTC
1 TTTTC
3176335 GATGATTACT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (34 bp):
TTTTCTAAAAATGTTGTTAACTGACGAAAATGTG
Found at i:3176879 original size:71 final size:71
Alignment explanation
Indices: 3176763--3176904 Score: 284
Period size: 71 Copynumber: 2.0 Consensus size: 71
3176753 AATCATCTAC
3176763 GGTAATATCAATAACCTCATTGTGAACTTTTTGGGGGTCCTTGCTATTCTGGGGCCATGTTCCAT
1 GGTAATATCAATAACCTCATTGTGAACTTTTTGGGGGTCCTTGCTATTCTGGGGCCATGTTCCAT
3176828 CGCGCA
66 CGCGCA
3176834 GGTAATATCAATAACCTCATTGTGAACTTTTTGGGGGTCCTTGCTATTCTGGGGCCATGTTCCAT
1 GGTAATATCAATAACCTCATTGTGAACTTTTTGGGGGTCCTTGCTATTCTGGGGCCATGTTCCAT
3176899 CGCGCA
66 CGCGCA
3176905 TATTGATCAT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.34
Consensus pattern (71 bp):
GGTAATATCAATAACCTCATTGTGAACTTTTTGGGGGTCCTTGCTATTCTGGGGCCATGTTCCAT
CGCGCA
Found at i:3177613 original size:2 final size:2
Alignment explanation
Indices: 3177606--3177638 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3177596 TATGTCAATT
3177606 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3177639 GCATCTACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3179159 original size:32 final size:32
Alignment explanation
Indices: 3179118--3179203 Score: 136
Period size: 32 Copynumber: 2.7 Consensus size: 32
3179108 TCACTAACAG
* **
3179118 ACTAACATTCTAACCTTTATTTTATTGTTCGA
1 ACTAACATTCTAACATTTATTTTATCATTCGA
3179150 ACTAACATTCTAACATTTATTTTATCATTCGA
1 ACTAACATTCTAACATTTATTTTATCATTCGA
*
3179182 ACTAACATTCTAACTTTTATTT
1 ACTAACATTCTAACATTTATTT
3179204 AATTTTTTCT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.31, C:0.19, G:0.03, T:0.47
Consensus pattern (32 bp):
ACTAACATTCTAACATTTATTTTATCATTCGA
Found at i:3179396 original size:16 final size:16
Alignment explanation
Indices: 3179377--3179408 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3179367 AAAATTTATA
*
3179377 TAATTTATTTCTTTTT
1 TAATTTATTTATTTTT
3179393 TAATTTATTTATTTTT
1 TAATTTATTTATTTTT
3179409 CCAACACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (16 bp):
TAATTTATTTATTTTT
Found at i:3191302 original size:15 final size:16
Alignment explanation
Indices: 3191284--3191367 Score: 57
Period size: 17 Copynumber: 5.1 Consensus size: 16
3191274 AAATGAAATG
3191284 AAAAAAAAGAAAAGAA
1 AAAAAAAAGAAAAGAA
3191300 AAATGAAAAAGAAAA-AA
1 AAA--AAAAAGAAAAGAA
**
3191317 GTAAAAAAATTAAAAGTAA
1 --AAAAAAAAGAAAAG-AA
* *
3191336 AAAAAAAAG-AAGGAC
1 AAAAAAAAGAAAAGAA
*
3191351 AAAAATAA-AAAAGAA
1 AAAAAAAAGAAAAGAA
3191366 AA
1 AA
3191368 GGGGGATCAA
Statistics
Matches: 52, Mismatches: 9, Indels: 15
0.68 0.12 0.20
Matches are distributed among these distances:
15 14 0.27
16 6 0.12
17 17 0.33
18 10 0.19
19 5 0.10
ACGTcount: A:0.80, C:0.01, G:0.12, T:0.07
Consensus pattern (16 bp):
AAAAAAAAGAAAAGAA
Found at i:3191303 original size:21 final size:21
Alignment explanation
Indices: 3191279--3191323 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
3191269 AGGGAAAATG
3191279 AAATGAAAAAAAAGAAAAG-AA
1 AAATGAAAAAAAA-AAAAGTAA
*
3191300 AAATGAAAAAGAAAAAAGTAA
1 AAATGAAAAAAAAAAAAGTAA
3191321 AAA
1 AAA
3191324 AATTAAAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (21 bp):
AAATGAAAAAAAAAAAAGTAA
Found at i:3191322 original size:26 final size:25
Alignment explanation
Indices: 3191273--3191341 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 25
3191263 ATAAAAAGGG
3191273 AAAATGAAATGAAAAAAAAGAAAAGA
1 AAAATGAAA-GAAAAAAAAGAAAAGA
*
3191299 AAAATGAAA-AAGAAAAAAGTAAA-A
1 AAAATGAAAGAA-AAAAAAGAAAAGA
* *
3191323 AAATTAAAAGTAAAAAAAA
1 AAAATGAAAG-AAAAAAAA
3191342 AAGAAGGACA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
24 10 0.27
25 16 0.43
26 11 0.30
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (25 bp):
AAAATGAAAGAAAAAAAAGAAAAGA
Found at i:3192152 original size:150 final size:150
Alignment explanation
Indices: 3191949--3192248 Score: 600
Period size: 150 Copynumber: 2.0 Consensus size: 150
3191939 CTTAATCAGG
3191949 CTCCACCCTCCCAAGAAAAATCAAAAGAGGTCCTAAATAAGAGGTTATACCATATACAATCTTAC
1 CTCCACCCTCCCAAGAAAAATCAAAAGAGGTCCTAAATAAGAGGTTATACCATATACAATCTTAC
3192014 GCAAACAATTTCAAGAGTAATCCAACCTTTCGTCAATTAAGGGGGTTAGAAAAGTAGTTATATCT
66 GCAAACAATTTCAAGAGTAATCCAACCTTTCGTCAATTAAGGGGGTTAGAAAAGTAGTTATATCT
3192079 GGAATCCTAGACAATGGCAA
131 GGAATCCTAGACAATGGCAA
3192099 CTCCACCCTCCCAAGAAAAATCAAAAGAGGTCCTAAATAAGAGGTTATACCATATACAATCTTAC
1 CTCCACCCTCCCAAGAAAAATCAAAAGAGGTCCTAAATAAGAGGTTATACCATATACAATCTTAC
3192164 GCAAACAATTTCAAGAGTAATCCAACCTTTCGTCAATTAAGGGGGTTAGAAAAGTAGTTATATCT
66 GCAAACAATTTCAAGAGTAATCCAACCTTTCGTCAATTAAGGGGGTTAGAAAAGTAGTTATATCT
3192229 GGAATCCTAGACAATGGCAA
131 GGAATCCTAGACAATGGCAA
3192249 TAGAAAACCA
Statistics
Matches: 150, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
150 150 1.00
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (150 bp):
CTCCACCCTCCCAAGAAAAATCAAAAGAGGTCCTAAATAAGAGGTTATACCATATACAATCTTAC
GCAAACAATTTCAAGAGTAATCCAACCTTTCGTCAATTAAGGGGGTTAGAAAAGTAGTTATATCT
GGAATCCTAGACAATGGCAA
Found at i:3193066 original size:13 final size:13
Alignment explanation
Indices: 3193048--3193072 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3193038 GTGTACACGT
3193048 CCATTACAAATAC
1 CCATTACAAATAC
3193061 CCATTACAAATA
1 CCATTACAAATA
3193073 TAATCAAACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (13 bp):
CCATTACAAATAC
Found at i:3194052 original size:111 final size:111
Alignment explanation
Indices: 3193914--3194136 Score: 446
Period size: 111 Copynumber: 2.0 Consensus size: 111
3193904 GGTAAAAGAT
3193914 AGACGATCTATGGTGGTGCTTGATGTGTTTGGGGTTTCGATCGAAATGTTTTGAGATGGCTTTTG
1 AGACGATCTATGGTGGTGCTTGATGTGTTTGGGGTTTCGATCGAAATGTTTTGAGATGGCTTTTG
3193979 CATTTTTTTGGTTTTCTTAGTTTTTGGTTTAGGGTCTAGAGAGAGG
66 CATTTTTTTGGTTTTCTTAGTTTTTGGTTTAGGGTCTAGAGAGAGG
3194025 AGACGATCTATGGTGGTGCTTGATGTGTTTGGGGTTTCGATCGAAATGTTTTGAGATGGCTTTTG
1 AGACGATCTATGGTGGTGCTTGATGTGTTTGGGGTTTCGATCGAAATGTTTTGAGATGGCTTTTG
3194090 CATTTTTTTGGTTTTCTTAGTTTTTGGTTTAGGGTCTAGAGAGAGG
66 CATTTTTTTGGTTTTCTTAGTTTTTGGTTTAGGGTCTAGAGAGAGG
3194136 A
1 A
3194137 ATAAGGATTT
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 112 1.00
ACGTcount: A:0.17, C:0.08, G:0.31, T:0.44
Consensus pattern (111 bp):
AGACGATCTATGGTGGTGCTTGATGTGTTTGGGGTTTCGATCGAAATGTTTTGAGATGGCTTTTG
CATTTTTTTGGTTTTCTTAGTTTTTGGTTTAGGGTCTAGAGAGAGG
Found at i:3194589 original size:32 final size:32
Alignment explanation
Indices: 3194540--3194659 Score: 136
Period size: 32 Copynumber: 3.7 Consensus size: 32
3194530 CTAACTTAAA
*
3194540 TAACATTCTAACCTTTATTTTATTGTTCGAAC
1 TAACATTCTAACATTTATTTTATTGTTCGAAC
* * *
3194572 TAACATTCCAACATTTATTTTATCGTTTGAAC
1 TAACATTCTAACATTTATTTTATTGTTCGAAC
* **
3194604 TAACATTCTAACTTTTA-TTTATTTGTTCTTAC
1 TAACATTCTAACATTTATTTTA-TTGTTCGAAC
3194636 TAAC-TTACTAACATTTTATTTTAT
1 TAACATT-CTAACA-TTTATTTTAT
3194660 CACACAAACT
Statistics
Matches: 73, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
31 6 0.08
32 58 0.79
33 5 0.07
34 4 0.05
ACGTcount: A:0.29, C:0.17, G:0.04, T:0.50
Consensus pattern (32 bp):
TAACATTCTAACATTTATTTTATTGTTCGAAC
Found at i:3194621 original size:64 final size:65
Alignment explanation
Indices: 3194540--3194660 Score: 167
Period size: 64 Copynumber: 1.9 Consensus size: 65
3194530 CTAACTTAAA
3194540 TAACATTCTAACCTTTATTT-TATTGTTCGAACTAACATT-CCAACA-TTTATTTTATCGTTTGA
1 TAACATTCTAACCTTTATTTAT-TTGTTCGAACTAAC-TTACCAACATTTTATTTTATCGTTTGA
3194602 AC
64 AC
* ** *
3194604 TAACATTCTAACTTTTATTTATTTGTTCTTACTAACTTACTAACATTTTATTTTATC
1 TAACATTCTAACCTTTATTTATTTGTTCGAACTAACTTACCAACATTTTATTTTATC
3194661 ACACAAACTA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
63 2 0.04
64 36 0.72
65 12 0.24
ACGTcount: A:0.29, C:0.17, G:0.04, T:0.50
Consensus pattern (65 bp):
TAACATTCTAACCTTTATTTATTTGTTCGAACTAACTTACCAACATTTTATTTTATCGTTTGAAC
Found at i:3199601 original size:16 final size:18
Alignment explanation
Indices: 3199566--3199601 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3199556 ATCAAGGTGG
3199566 GGGTTTTAGAGGAGTCTT
1 GGGTTTTAGAGGAGTCTT
3199584 GGGTTTTAG-GGA-TCTT
1 GGGTTTTAGAGGAGTCTT
3199600 GG
1 GG
3199602 ACGATTCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 3 0.17
18 9 0.50
ACGTcount: A:0.14, C:0.06, G:0.42, T:0.39
Consensus pattern (18 bp):
GGGTTTTAGAGGAGTCTT
Found at i:3210989 original size:69 final size:69
Alignment explanation
Indices: 3210878--3211017 Score: 262
Period size: 69 Copynumber: 2.0 Consensus size: 69
3210868 TAGTGTTCAT
* *
3210878 AATCAATATTCAAATCAAATGTTAAATGTTAAATTGGTCATAATGCAACTAAGATGTCAATAATG
1 AATCAATATTCAAATCAAATGTGAAATGGTAAATTGGTCATAATGCAACTAAGATGTCAATAATG
3210943 CAAA
66 CAAA
3210947 AATCAATATTCAAATCAAATGTGAAATGGTAAATTGGTCATAATGCAACTAAGATGTCAATAATG
1 AATCAATATTCAAATCAAATGTGAAATGGTAAATTGGTCATAATGCAACTAAGATGTCAATAATG
3211012 CAAA
66 CAAA
3211016 AA
1 AA
3211018 ATCATCCCAA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.29
Consensus pattern (69 bp):
AATCAATATTCAAATCAAATGTGAAATGGTAAATTGGTCATAATGCAACTAAGATGTCAATAATG
CAAA
Found at i:3217046 original size:15 final size:15
Alignment explanation
Indices: 3217026--3217062 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
3217016 ACTTCTTGTT
3217026 CCTCTTCATCGGAAC
1 CCTCTTCATCGGAAC
3217041 CCTCTTCATCGGAAC
1 CCTCTTCATCGGAAC
3217056 CCTCTTC
1 CCTCTTC
3217063 TTCGCTCCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.16, C:0.43, G:0.11, T:0.30
Consensus pattern (15 bp):
CCTCTTCATCGGAAC
Found at i:3222702 original size:22 final size:22
Alignment explanation
Indices: 3222674--3222760 Score: 86
Period size: 22 Copynumber: 4.0 Consensus size: 22
3222664 ATAACCTCAT
* *
3222674 CAGTGCTAAGGTA-TTTTAGTAG
1 CAGTGCTAACGTACTTCT-GTAG
*
3222696 CAGTGCTAACGTACTTCTGTAT
1 CAGTGCTAACGTACTTCTGTAG
* *
3222718 CAGTGCTAACGCACTTCTGTAT
1 CAGTGCTAACGTACTTCTGTAG
* **
3222740 CAGTACTAACACACTTCTGTA
1 CAGTGCTAACGTACTTCTGTA
3222761 CCAATGTAGA
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
22 55 0.95
23 3 0.05
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.33
Consensus pattern (22 bp):
CAGTGCTAACGTACTTCTGTAG
Found at i:3223979 original size:18 final size:19
Alignment explanation
Indices: 3223943--3223987 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
3223933 AAAATTAAAA
* *
3223943 ATCATATATATGTAGATAT
1 ATCATATATATATACATAT
3223962 ATCATA-ATATATACATAT
1 ATCATATATATATACATAT
*
3223980 AACATATA
1 ATCATATA
3223988 GGAATATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (19 bp):
ATCATATATATATACATAT
Found at i:3225006 original size:30 final size:30
Alignment explanation
Indices: 3224972--3225028 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
3224962 GGGCCATGAC
3224972 CTCTTAAAATTTTAAAAATTATAATTTAGA
1 CTCTTAAAATTTTAAAAATTATAATTTAGA
* * *
3225002 CTCTTAAGATTTTTAAAATTTTAATTT
1 CTCTTAAAATTTTAAAAATTATAATTT
3225029 TTCCCCCCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (30 bp):
CTCTTAAAATTTTAAAAATTATAATTTAGA
Found at i:3235989 original size:22 final size:24
Alignment explanation
Indices: 3235964--3236036 Score: 64
Period size: 25 Copynumber: 3.2 Consensus size: 24
3235954 AAAATATTGA
3235964 ATATACTTATAATA-TA-ATT-AT
1 ATATACTTATAATATTATATTAAT
* *
3235985 -TATATTTTTAATATTATATTAAT
1 ATATACTTATAATATTATATTAAT
* * *
3236008 ATATACTAAGATATATTATAATAAT
1 ATATACTTATA-ATATTATATTAAT
3236033 ATAT
1 ATAT
3236037 GATATTAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
20 11 0.28
21 2 0.05
22 3 0.08
23 2 0.05
24 6 0.15
25 16 0.40
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (24 bp):
ATATACTTATAATATTATATTAAT
Found at i:3239760 original size:12 final size:12
Alignment explanation
Indices: 3239723--3239762 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
3239713 TATTTTTTTT
*
3239723 ATAATAACAATA
1 ATAACAACAATA
*
3239735 ACAACAACAATA
1 ATAACAACAATA
*
3239747 ATAACAATAATA
1 ATAACAACAATA
3239759 ATAA
1 ATAA
3239763 ATTAACACTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.20
Consensus pattern (12 bp):
ATAACAACAATA
Found at i:3251557 original size:14 final size:15
Alignment explanation
Indices: 3251538--3251575 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
3251528 TCGTCACTTG
3251538 TCGTCACTAATAA-T
1 TCGTCACTAATAACT
3251552 TCGTCACTAATAACT
1 TCGTCACTAATAACT
*
3251567 TTGTCACTA
1 TCGTCACTA
3251576 TTATATCAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.37
Consensus pattern (15 bp):
TCGTCACTAATAACT
Found at i:3253037 original size:13 final size:13
Alignment explanation
Indices: 3252990--3253024 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
3252980 GTCATAACCC
*
3252990 GACCTGACCCGTT
1 GACCCGACCCGTT
*
3253003 CACCCGACCCGTT
1 GACCCGACCCGTT
3253016 GACCCGACC
1 GACCCGACC
3253025 TGACCCGTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.17, C:0.49, G:0.20, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:3256590 original size:2 final size:2
Alignment explanation
Indices: 3256583--3256623 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3256573 GAGTCATGCA
3256583 AT 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 AT A
3256624 GACTTCAGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3256958 original size:15 final size:15
Alignment explanation
Indices: 3256940--3256981 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
3256930 TCATTTATTT
3256940 ATATATTTGATTATA
1 ATATATTTGATTATA
* * *
3256955 ATATATTTAATTTTT
1 ATATATTTGATTATA
3256970 ATAT-TTTGATTA
1 ATATATTTGATTA
3256982 ATTAATAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (15 bp):
ATATATTTGATTATA
Found at i:3256962 original size:32 final size:29
Alignment explanation
Indices: 3256920--3256981 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 29
3256910 TTATTGTAAA
*
3256920 ATAAAATATTTCATTTATTTATATATTTGATT
1 ATAAAATATTT-AATT-TTTATAT-TTTGATT
*
3256952 ATAATATATTTAATTTTTATATTTTGATT
1 ATAAAATATTTAATTTTTATATTTTGATT
3256981 A
1 A
3256982 ATTAATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 8 0.29
30 7 0.25
31 3 0.11
32 10 0.36
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (29 bp):
ATAAAATATTTAATTTTTATATTTTGATT
Found at i:3257721 original size:37 final size:37
Alignment explanation
Indices: 3257665--3257735 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
3257655 TCCACGTGAG
*
3257665 TTATTTCTACTTAGAACATTTGCTTACTACTAATAAT
1 TTATTTCTACTAAGAACATTTGCTTACTACTAATAAT
3257702 TTATTTCTACCTAAG-ACATTTGCTTACTACTAAT
1 TTATTTCTA-CTAAGAACATTTGCTTACTACTAAT
3257736 CATTCAATCC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
37 28 0.88
38 4 0.12
ACGTcount: A:0.31, C:0.18, G:0.06, T:0.45
Consensus pattern (37 bp):
TTATTTCTACTAAGAACATTTGCTTACTACTAATAAT
Found at i:3257734 original size:19 final size:19
Alignment explanation
Indices: 3257680--3257734 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
3257670 TCTACTTAGA
*
3257680 ACATTTGCTTACTACTAAT
1 ACATTTGCTTACTACTAAG
* *
3257699 A-ATTT-ATTTCTACCTAAG
1 ACATTTGCTTACTA-CTAAG
3257717 ACATTTGCTTACTACTAA
1 ACATTTGCTTACTACTAA
3257735 TCATTCAATC
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
17 5 0.18
18 9 0.32
19 9 0.32
20 5 0.18
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.42
Consensus pattern (19 bp):
ACATTTGCTTACTACTAAG
Found at i:3258158 original size:62 final size:62
Alignment explanation
Indices: 3258061--3258238 Score: 271
Period size: 62 Copynumber: 3.0 Consensus size: 62
3258051 TTACTACTCA
*
3258061 TCAAATACTATAAACCTTGATTATCTAGATAGTTTAACCACGTACCATTTTTTCACAATGTG
1 TCAAATACTATAAACCTTGATTATCTAGATAGTTTAACCACGTACCATTTTTTCACAATGGG
3258123 TCAAATACTATAAACCTTGATTATCTAGATAGTTTAACCACGTACCATTTTTTCACAATATGGG
1 TCAAATACTATAAACCTTGATTATCTAGATAGTTTAACCACGTACCATTTTTTCAC-A-ATGGG
*
3258187 TCAAATACTATAAACCTTG---A--T--ATAGTTTAACCACATACCATTTTTTCACAAT
1 TCAAATACTATAAACCTTGATTATCTAGATAGTTTAACCACGTACCATTTTTTCACAAT
3258239 ATGGGTGCCC
Statistics
Matches: 112, Mismatches: 2, Indels: 11
0.90 0.02 0.09
Matches are distributed among these distances:
55 2 0.02
56 1 0.01
57 27 0.24
59 1 0.01
61 1 0.01
62 56 0.50
63 1 0.01
64 23 0.21
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (62 bp):
TCAAATACTATAAACCTTGATTATCTAGATAGTTTAACCACGTACCATTTTTTCACAATGGG
Found at i:3270217 original size:51 final size:52
Alignment explanation
Indices: 3269884--3270356 Score: 524
Period size: 55 Copynumber: 8.9 Consensus size: 52
3269874 TGACGAGTCT
* * * * *
3269884 GCTCCCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACATGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACT---ACAATCTTCAACAAACTTGTCC
** * * **
3269939 GCTCCCTATTAATTCAGGGAGTATAGAACTCGAACAATCTTCATA-AAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACT---ACAATCTTCA-ACAAACTTGTCC
* * *
3269994 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACT---ACAATCTTCAACAAACTTGTCC
* * ** **
3270049 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATGAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACT---ACAATCTTCAACAAACTTGTCC
* * *
3270104 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATTTTCAACAAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACT---ACAATCTTCAACAAACTTGTCC
*
3270159 GCTCCCTATTCCTTCAGAGAGTATAGGACT-CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTACAATCTTCAACAAACTTGTCC
*
3270210 GCTCCCTATTCCTTCAGAGAGTATAGGACT-CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTACAATCTTCAACAAACTTGTCC
* *
3270261 GCTCCCTATTCCTTCAAAGAGTATAGGACT-CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTACAATCTTCAACAAACTTGTCC
3270312 GCTCCCTATTCCTTCAGAGAGTATAGGACT-CAATCTTCAACAAAC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTACAATCTTCAACAAAC
3270357 GAATTTGCTT
Statistics
Matches: 389, Mismatches: 27, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
51 163 0.42
54 1 0.00
55 224 0.58
56 1 0.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.28
Consensus pattern (52 bp):
GCTCCCTATTCCTTCAGAGAGTATAGGACTACAATCTTCAACAAACTTGTCC
Found at i:3271664 original size:16 final size:17
Alignment explanation
Indices: 3271636--3271770 Score: 70
Period size: 16 Copynumber: 7.8 Consensus size: 17
3271626 CCTCCTTTTA
3271636 TTTCTCTTTTTTTCATT
1 TTTCTCTTTTTTTCATT
3271653 TTTCTC-TTTTTTCATT
1 TTTCTCTTTTTTTCATT
* *
3271669 TTTCATTTTTTCTTTC-CT
1 TTTC-TCTTTT-TTTCATT
*
3271687 TTTC-CATTTTTTC-TT
1 TTTCTCTTTTTTTCATT
*
3271702 CTTT-T-TTTCTTTTCGTT
1 -TTTCTCTTT-TTTTCATT
*
3271719 TTT-TCCATCATTTTT-ATTT
1 TTTCT-C-T-TTTTTTCA-TT
*
3271738 TTTCTCATTTTTTCATTT
1 TTTCTCTTTTTTTCA-TT
3271756 TTTCTCTTTTATTTC
1 TTTCTCTTTT-TTTC
3271771 TTCTTCAAGC
Statistics
Matches: 92, Mismatches: 11, Indels: 28
0.70 0.08 0.21
Matches are distributed among these distances:
15 7 0.08
16 29 0.32
17 14 0.15
18 21 0.23
19 19 0.21
20 2 0.02
ACGTcount: A:0.07, C:0.19, G:0.01, T:0.73
Consensus pattern (17 bp):
TTTCTCTTTTTTTCATT
Found at i:3271689 original size:19 final size:19
Alignment explanation
Indices: 3271662--3271701 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
3271652 TTTTCTCTTT
*
3271662 TTTCATTTTTCATTTTTTC
1 TTTCATTTTCCATTTTTTC
*
3271681 TTTCCTTTTCCATTTTTTC
1 TTTCATTTTCCATTTTTTC
3271700 TT
1 TT
3271702 CTTTTTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTCATTTTCCATTTTTTC
Found at i:3271708 original size:19 final size:18
Alignment explanation
Indices: 3271662--3271707 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
3271652 TTTTCTCTTT
3271662 TTTCATTTTTCATTTTTTC
1 TTTC-TTTTTCATTTTTTC
*
3271681 TTTCCTTTTCCATTTTTTC
1 TTT-CTTTTTCATTTTTTC
3271700 -TTCTTTTT
1 TTTCTTTTT
3271708 TTCTTTTCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 5 0.21
18 2 0.08
19 16 0.67
20 1 0.04
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTCTTTTTCATTTTTTC
Found at i:3271714 original size:18 final size:17
Alignment explanation
Indices: 3271636--3271772 Score: 79
Period size: 18 Copynumber: 7.9 Consensus size: 17
3271626 CCTCCTTTTA
*
3271636 TTTCTCTTTTTTTCATT
1 TTTCTCTTTTTTTCTTT
*
3271653 TTTCTC-TTTTTTCATT
1 TTTCTCTTTTTTTCTTT
* *
3271669 TTTCATTTTTTCTTTC-CT
1 TTTC-TCTTTT-TTTCTTT
*
3271687 TTTC-CATTTTTTCTTCT
1 TTTCTCTTTTTTTCTT-T
*
3271704 TTT-T-TTCTTTTCGTTT
1 TTTCTCTTTTTTTC-TTT
* *
3271720 TTTC-CATCATTTTTATTT
1 TTTCTC-T-TTTTTTCTTT
*
3271738 TTTCTCATTTTTTCATTT
1 TTTCTCTTTTTTTC-TTT
3271756 TTTCTCTTTTATTTCTT
1 TTTCTCTTTT-TTTCTT
3271773 CTTCAAGCAA
Statistics
Matches: 92, Mismatches: 14, Indels: 27
0.69 0.11 0.20
Matches are distributed among these distances:
15 4 0.04
16 27 0.29
17 18 0.20
18 30 0.33
19 13 0.14
ACGTcount: A:0.07, C:0.18, G:0.01, T:0.74
Consensus pattern (17 bp):
TTTCTCTTTTTTTCTTT
Found at i:3271759 original size:8 final size:8
Alignment explanation
Indices: 3271643--3271759 Score: 73
Period size: 8 Copynumber: 13.9 Consensus size: 8
3271633 TTATTTCTCT
3271643 TTTTTTCA
1 TTTTTTCA
3271651 TTTTTCTC-
1 TTTTT-TCA
3271659 TTTTTTCA
1 TTTTTTCA
3271667 -TTTTTCA
1 TTTTTTCA
*
3271674 TTTTTTCT
1 TTTTTTCA
3271682 TTCCTTTTCCA
1 TT--TTTT-CA
3271693 TTTTTTC-
1 TTTTTTCA
*
3271700 TTCTTTT-T
1 TT-TTTTCA
*
3271708 TTCTTTTCG
1 TT-TTTTCA
3271717 TTTTTTCCA
1 TTTTTT-CA
3271726 TCATTTTT-A
1 T--TTTTTCA
3271735 TTTTTTCTCA
1 -TTTTT-TCA
3271745 TTTTTTCA
1 TTTTTTCA
3271753 TTTTTTC
1 TTTTTTC
3271760 TCTTTTATTT
Statistics
Matches: 90, Mismatches: 4, Indels: 30
0.73 0.03 0.24
Matches are distributed among these distances:
7 11 0.12
8 48 0.53
9 17 0.19
10 6 0.07
11 8 0.09
ACGTcount: A:0.08, C:0.18, G:0.01, T:0.74
Consensus pattern (8 bp):
TTTTTTCA
Found at i:3281526 original size:47 final size:47
Alignment explanation
Indices: 3281427--3281532 Score: 133
Period size: 47 Copynumber: 2.2 Consensus size: 47
3281417 TGTTATCCAC
*
3281427 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCTTGTTCAA
1 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCTTATTCAA
* *
3281474 AAAAA-ATAAACCTAACCGCATGATATCTAGTTCGCATGCATTTATTCGAA
1 AAAAAGA-AATCCTAACCGCATGATATCTAATTCGCATGC--TTATTC-AA
*
3281524 AAAACGAAA
1 AAAAAGAAA
3281533 ATAAATGACT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
46 1 0.02
47 35 0.70
49 5 0.10
50 8 0.16
51 1 0.02
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.25
Consensus pattern (47 bp):
AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCTTATTCAA
Found at i:3285437 original size:16 final size:16
Alignment explanation
Indices: 3285416--3285476 Score: 77
Period size: 16 Copynumber: 3.8 Consensus size: 16
3285406 TAATAAATAA
* **
3285416 ACGAACATAAAGGCGC
1 ACGAACATAAACGAAC
*
3285432 ACGAACCTAAACGAAC
1 ACGAACATAAACGAAC
*
3285448 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
3285464 ACGAACATAAACG
1 ACGAACATAAACG
3285477 TTAGAGACCC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.51, C:0.25, G:0.16, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:3285457 original size:32 final size:32
Alignment explanation
Indices: 3285416--3285476 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
3285406 TAATAAATAA
** *
3285416 ACGAACATAAAGGCGCACGAACCTAAACGAAC
1 ACGAACATAAAGGAACACGAACATAAACGAAC
*
3285448 ACGAACATAAATGAACACGAACATAAACG
1 ACGAACATAAAGGAACACGAACATAAACG
3285477 TTAGAGACCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.51, C:0.25, G:0.16, T:0.08
Consensus pattern (32 bp):
ACGAACATAAAGGAACACGAACATAAACGAAC
Found at i:3285717 original size:12 final size:12
Alignment explanation
Indices: 3285700--3285750 Score: 77
Period size: 12 Copynumber: 4.3 Consensus size: 12
3285690 CTCGAGACTC
*
3285700 GAGCTCGATTCT
1 GAGCTCGATTCA
3285712 GAGCTCGATTCA
1 GAGCTCGATTCA
*
3285724 GAGCTTGATTCA
1 GAGCTCGATTCA
3285736 -AGCTCGATTCA
1 GAGCTCGATTCA
3285747 GAGC
1 GAGC
3285751 ACATTGCTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
11 10 0.29
12 25 0.71
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (12 bp):
GAGCTCGATTCA
Found at i:3286967 original size:38 final size:38
Alignment explanation
Indices: 3286892--3287020 Score: 137
Period size: 33 Copynumber: 3.5 Consensus size: 38
3286882 TCTAATTCAT
*
3286892 ATATTCAGGTCGGGTCGGGTCAGG--TTTTTTAAGTGTG
1 ATATTCGGGTCGGGTCGGGTC-GGATTTTTTTAAGTGTG
* *
3286929 ATATTCGGGTCGAGTCGGGTCGGATTTTTTTCAGTGTG
1 ATATTCGGGTCGGGTCGGGTCGGATTTTTTTAAGTGTG
* *
3286967 ATA-T----TCAGGTCGGGTCGAATTTTTTTAAGTGTG
1 ATATTCGGGTCGGGTCGGGTCGGATTTTTTTAAGTGTG
*
3287000 ATATTTGGGTCGGGTTCGGGT
1 ATATTCGGGTCGGG-TCGGGT
3287021 TTAAGGTGAA
Statistics
Matches: 76, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
33 28 0.37
34 1 0.01
36 2 0.03
37 20 0.26
38 19 0.25
39 6 0.08
ACGTcount: A:0.16, C:0.11, G:0.34, T:0.40
Consensus pattern (38 bp):
ATATTCGGGTCGGGTCGGGTCGGATTTTTTTAAGTGTG
Found at i:3287581 original size:17 final size:17
Alignment explanation
Indices: 3287559--3287622 Score: 92
Period size: 17 Copynumber: 3.7 Consensus size: 17
3287549 TATGGAATTG
*
3287559 GATTCCAATTCCTGATA
1 GATTCCAATTCCTGACA
3287576 GATTCCAATTCCTGACA
1 GATTCCAATTCCTGACA
*
3287593 GATTCCAATTCCTTCACA
1 GATTCCAATTCC-TGACA
*
3287611 GATTCCAGTTCC
1 GATTCCAATTCC
3287623 CTCATAAACA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
17 28 0.65
18 15 0.35
ACGTcount: A:0.27, C:0.30, G:0.11, T:0.33
Consensus pattern (17 bp):
GATTCCAATTCCTGACA
Found at i:3294168 original size:20 final size:21
Alignment explanation
Indices: 3294126--3294172 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
3294116 CAATTTAAAG
* *
3294126 TAAAGAATAAATAAATTATAT
1 TAAAGAATAAATAAATCAAAT
*
3294147 TAAA-AATAAATATATCAAAT
1 TAAAGAATAAATAAATCAAAT
3294167 TAAAGA
1 TAAAGA
3294173 GAAAATTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (21 bp):
TAAAGAATAAATAAATCAAAT
Found at i:3294644 original size:28 final size:28
Alignment explanation
Indices: 3294556--3294651 Score: 79
Period size: 28 Copynumber: 3.4 Consensus size: 28
3294546 ATTAGGAAAG
3294556 AAAGAAAAAAAAAATAACGATTAAAAAATG-
1 AAAG-AAAAAAAAATAAC-A-TAAAAAATGT
*** * * **
3294586 AAACTTAAAAAAAGAAAATGAGGAAAT-T
1 AAAGAAAAAAAAATAACAT-AAAAAATGT
3294614 AAAGAAAAAAAAATAACATAAAAAATGT
1 AAAGAAAAAAAAATAACATAAAAAATGT
3294642 AAAGAAAAAA
1 AAAGAAAAAA
3294652 TTTACAAATC
Statistics
Matches: 49, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
27 6 0.12
28 31 0.63
29 9 0.18
30 3 0.06
ACGTcount: A:0.73, C:0.03, G:0.10, T:0.14
Consensus pattern (28 bp):
AAAGAAAAAAAAATAACATAAAAAATGT
Found at i:3296466 original size:13 final size:13
Alignment explanation
Indices: 3296448--3296497 Score: 91
Period size: 13 Copynumber: 3.8 Consensus size: 13
3296438 GTAAATTTTC
*
3296448 TCTTTTATTCCTT
1 TCTTTTAATCCTT
3296461 TCTTTTAATCCTT
1 TCTTTTAATCCTT
3296474 TCTTTTAATCCTT
1 TCTTTTAATCCTT
3296487 TCTTTTAATCC
1 TCTTTTAATCC
3296498 CAAAATTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.14, C:0.24, G:0.00, T:0.62
Consensus pattern (13 bp):
TCTTTTAATCCTT
Found at i:3301484 original size:17 final size:17
Alignment explanation
Indices: 3301446--3301487 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3301436 AAGGGTTTTG
3301446 GTAAAAATGATTAAATA
1 GTAAAAATGATTAAATA
* *
3301463 ATAAAAAGTGATTTAA-A
1 GTAAAAA-TGATTAAATA
3301480 GTAAAAAT
1 GTAAAAAT
3301488 AAAGAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 1 0.05
17 13 0.62
18 7 0.33
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.29
Consensus pattern (17 bp):
GTAAAAATGATTAAATA
Found at i:3302054 original size:12 final size:12
Alignment explanation
Indices: 3302037--3302084 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
3302027 TTAGCATGTT
3302037 TTAAAATAAAAC
1 TTAAAATAAAAC
3302049 TTAAAATAAAA-
1 TTAAAATAAAAC
*
3302060 TAAAAATGAAAAC
1 TTAAAAT-AAAAC
*
3302073 TTGAAAAGAAAA
1 TT-AAAATAAAA
3302085 GAAAAGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
11 6 0.20
12 15 0.50
13 5 0.17
14 4 0.13
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.21
Consensus pattern (12 bp):
TTAAAATAAAAC
Found at i:3302071 original size:17 final size:17
Alignment explanation
Indices: 3302038--3302071 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3302028 TAGCATGTTT
* *
3302038 TAAAATAAAACTTAAAA
1 TAAAATAAAAATGAAAA
3302055 TAAAATAAAAATGAAAA
1 TAAAATAAAAATGAAAA
3302072 CTTGAAAAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (17 bp):
TAAAATAAAAATGAAAA
Found at i:3302073 original size:24 final size:24
Alignment explanation
Indices: 3302039--3302089 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
3302029 AGCATGTTTT
* *
3302039 AAAATAAAACTT-AAAATAAAATA
1 AAAATAAAACTTGAAAAGAAAAGA
3302062 AAAATGAAAACTTGAAAAGAAAAGA
1 AAAAT-AAAACTTGAAAAGAAAAGA
3302087 AAA
1 AAA
3302090 GAAAAGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 5 0.21
24 7 0.29
25 12 0.50
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.16
Consensus pattern (24 bp):
AAAATAAAACTTGAAAAGAAAAGA
Found at i:3302083 original size:5 final size:5
Alignment explanation
Indices: 3302075--3302099 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3302065 ATGAAAACTT
3302075 GAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA
3302100 AAACTTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:3302672 original size:15 final size:15
Alignment explanation
Indices: 3302652--3302680 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3302642 GAATTTAATA
3302652 TATGCAACAGTGATT
1 TATGCAACAGTGATT
3302667 TATGCAACAGTGAT
1 TATGCAACAGTGAT
3302681 ATATAAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (15 bp):
TATGCAACAGTGATT
Found at i:3306552 original size:26 final size:25
Alignment explanation
Indices: 3306521--3306572 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
3306511 CTTTCAGTGT
3306521 TTATTCTAAATTTATAGTG-TTTTTGA
1 TTATTCTAAATTTA-A-TGATTTTTGA
*
3306547 TTATTCTCAATTTAATGATTTTTGA
1 TTATTCTAAATTTAATGATTTTTGA
3306572 T
1 T
3306573 CTGATATGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 2 0.08
25 9 0.38
26 13 0.54
ACGTcount: A:0.27, C:0.06, G:0.10, T:0.58
Consensus pattern (25 bp):
TTATTCTAAATTTAATGATTTTTGA
Found at i:3311375 original size:22 final size:22
Alignment explanation
Indices: 3311347--3311404 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
3311337 TTGAAGGGAG
3311347 TATCGATACCATAGTATAAAAC
1 TATCGATACCATAGTATAAAAC
3311369 TATCGATACCATAGTATAAAAC
1 TATCGATACCATAGTATAAAAC
*
3311391 TATCTATACCATAG
1 TATCGATACCATAG
3311405 GAGGGGTGCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.29
Consensus pattern (22 bp):
TATCGATACCATAGTATAAAAC
Found at i:3312080 original size:138 final size:138
Alignment explanation
Indices: 3311920--3312173 Score: 352
Period size: 138 Copynumber: 1.8 Consensus size: 138
3311910 TATGTAATGA
* *
3311920 TTATCGATCGATTTTGTGTAATGCATAACGGTGCATTTTCATAACAGTA-TTGTGTCTACTTTTG
1 TTATCGATCGATTTTGTGTAATGCATAACGGTGCATTTTCATAACAATACTT-TGTCTACTTTCG
* * *
3311984 GCACTAGATGTGCAAT-CAT-GATATTCATAATGAGTTTGTGAATCACCATTTCGTTATACAATT
65 ACACTAGATGTGC-ATCCATGGA-ATTCATAATAACTTTGTGAATCACCATTTCGTTATACAATT
3312047 ATGTATAAAAG
128 ATGTATAAAAG
* * * *
3312058 TTATCGATCGATTTTGTTTAATGCATAACGGTGCATTTTCGTATCAATACTTTGTGTACTTTCGA
1 TTATCGATCGATTTTGTGTAATGCATAACGGTGCATTTTCATAACAATACTTTGTCTACTTTCGA
* **
3312123 CACTATATGTGCATCCATGGAATTCATAATAACTTTGTGAATTTCCATTTC
66 CACTAGATGTGCATCCATGGAATTCATAATAACTTTGTGAATCACCATTTC
3312174 AGCACTTCGG
Statistics
Matches: 101, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
137 2 0.02
138 95 0.94
139 4 0.04
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (138 bp):
TTATCGATCGATTTTGTGTAATGCATAACGGTGCATTTTCATAACAATACTTTGTCTACTTTCGA
CACTAGATGTGCATCCATGGAATTCATAATAACTTTGTGAATCACCATTTCGTTATACAATTATG
TATAAAAG
Found at i:3314432 original size:4 final size:4
Alignment explanation
Indices: 3314423--3314453 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
3314413 AAGTGTACAT
3314423 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
3314454 TGTTTTCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:3315104 original size:376 final size:378
Alignment explanation
Indices: 3314431--3315148 Score: 1176
Period size: 376 Copynumber: 1.9 Consensus size: 378
3314421 ATTTTATTTA
** *
3314431 TTTATTTATTTATTTATTTATTTTGTTTTCAATATTAACCCACCACGGCAAGTGGGTTACAAATG
1 TTTATTTATTTATTTATTTATTTTGTTTTCAATATTAACCCACCACAACAAGTGAGTTACAAATG
*
3314496 TAGCTCAATACGACAGTAAAATAAATATTTTGAAAAATACCATAAATGTTATAGTTATAGAGAAC
66 TAGCTCAATACGACAGTAAAATAAATATTTTGAAAAATACCATAAATGTTACAGTTATAGAGAAC
* * *
3314561 TTGTCAGGTTTTGATGATGATTTTTCTCAAGAAAAATATATTTTATTAGACTCATGTATCTAGGT
131 TTGCCAGGTTTAGATGATGATTTTTCTCAAGAAAAATATATTTTATTAGACTCATGTATCTACGT
* *
3314626 TTCGGGGGTTTAATAATTTAATATATTTATTGAAACTCGTCATGCACACGTAATGAATTTATTAT
196 TTCGGGGGTTTAATAATTTAATATATTTATTGAAACTCGTCATGCACACGTAACGAATTTATTAC
3314691 AATAATAATTTTTTAAATTTAAAAATTATTTTTATATATTA-TTATTATTTTGTAAAAACAATCG
261 AATAATAATTTTTTAAATTTAAAAATTATTTTTATATA-TACTTATTATTTTGTAAAAACAATCG
*
3314755 TGGAACT-GTCATGTGACAATTAGAAAAAGCTTAACAAGAAAATAAGTGTACAT
325 TGGAACTCGTCACGTGACAATTAGAAAAAGCTTAACAAGAAAATAAGTGTACAT
*
3314808 TTTATTTATTTATTTATTTATTTTGTTTTCAATATTAACCCACCACAACAAGTGAGTTACAAATT
1 TTTATTTATTTATTTATTTATTTTGTTTTCAATATTAACCCACCACAACAAGTGAGTTACAAATG
*
3314873 TAGCTCAATACGACAGTAAAA-AATTATTTTGAAAAATACCATAAATGTTACAGTTATAGAGAAC
66 TAGCTCAATACGACAGTAAAATAAATATTTTGAAAAATACCATAAATGTTACAGTTATAGAGAAC
* *
3314937 TTGCCAGGTTTAGATGATTATTTTTCTC-A-AAAAATATATTTTATTAGACTCATGTATGTACGT
131 TTGCCAGGTTTAGATGATGATTTTTCTCAAGAAAAATATATTTTATTAGACTCATGTATCTACGT
* * * * * *
3315000 TTCATGGGGTTTTATATTTTAATATATTTCTTGAAACTCGTCATGCTCACGTGACGAATTTATTA
196 TTC-GGGGGTTTAATAATTTAATATATTTATTGAAACTCGTCATGCACACGTAACGAATTTATTA
* *
3315065 CAATAATATTTTTTTTAATTTAAAAATTAATTTTTATATATACTTATTATTTTGTAAAAACAATC
260 CAATAATAATTTTTTAAATTTAAAAATT-ATTTTTATATATACTTATTATTTTGTAAAAACAATC
3315130 GTGGAACTCGTCACGTGAC
324 GTGGAACTCGTCACGTGAC
3315149 GAGTTCTTTT
Statistics
Matches: 315, Mismatches: 22, Indels: 8
0.91 0.06 0.02
Matches are distributed among these distances:
374 35 0.11
375 82 0.26
376 107 0.34
377 91 0.29
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (378 bp):
TTTATTTATTTATTTATTTATTTTGTTTTCAATATTAACCCACCACAACAAGTGAGTTACAAATG
TAGCTCAATACGACAGTAAAATAAATATTTTGAAAAATACCATAAATGTTACAGTTATAGAGAAC
TTGCCAGGTTTAGATGATGATTTTTCTCAAGAAAAATATATTTTATTAGACTCATGTATCTACGT
TTCGGGGGTTTAATAATTTAATATATTTATTGAAACTCGTCATGCACACGTAACGAATTTATTAC
AATAATAATTTTTTAAATTTAAAAATTATTTTTATATATACTTATTATTTTGTAAAAACAATCGT
GGAACTCGTCACGTGACAATTAGAAAAAGCTTAACAAGAAAATAAGTGTACAT
Found at i:3320142 original size:3 final size:3
Alignment explanation
Indices: 3320134--3320159 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3320124 TTTGAAATTG
3320134 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
3320160 GAAAGTTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3321208 original size:36 final size:36
Alignment explanation
Indices: 3321108--3321211 Score: 120
Period size: 36 Copynumber: 2.9 Consensus size: 36
3321098 TGTGGGGGCA
* * * *
3321108 ATGACTTAATGCTTCTAATGTAATGTAACATAATGT
1 ATGAGTTAATTCTTCTAATGTAATGTAATATAATGC
* * *
3321144 AGGAGTTAATGT-TTCTAATGTGATGTAATGTAATGC
1 ATGAGTTAAT-TCTTCTAATGTAATGTAATATAATGC
*
3321180 ATGAGTTAATTCTTTTAATGTAATGTAATATA
1 ATGAGTTAATTCTTCTAATGTAATGTAATATA
3321212 TCAGTTGCAA
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
35 1 0.02
36 54 0.98
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.41
Consensus pattern (36 bp):
ATGAGTTAATTCTTCTAATGTAATGTAATATAATGC
Found at i:3327736 original size:19 final size:19
Alignment explanation
Indices: 3327712--3327758 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
3327702 CAAAAATAAA
3327712 AAATAAAATTGAATTTTAT
1 AAATAAAATTGAATTTTAT
3327731 AAATAAAATTGAATTTTAT
1 AAATAAAATTGAATTTTAT
3327750 AAATAAAAT
1 AAATAAAAT
3327759 GAAAGATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (19 bp):
AAATAAAATTGAATTTTAT
Found at i:3330745 original size:22 final size:23
Alignment explanation
Indices: 3330720--3330763 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
3330710 ATGTTTTACC
3330720 ATTTTAAATAAAA-AAAAAATTA
1 ATTTTAAATAAAACAAAAAATTA
* *
3330742 ATTTTAATTAAAACAACAAATT
1 ATTTTAAATAAAACAAAAAATT
3330764 TAGGTCTGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (23 bp):
ATTTTAAATAAAACAAAAAATTA
Found at i:3333036 original size:18 final size:18
Alignment explanation
Indices: 3333013--3333048 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
3333003 ATTACCACCC
3333013 CCCTCTCTTTT-TTTCTTT
1 CCCTCT-TTTTATTTCTTT
3333031 CCCTCTTTTTATTTCTTT
1 CCCTCTTTTTATTTCTTT
3333049 TCTCTCCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.67
Consensus pattern (18 bp):
CCCTCTTTTTATTTCTTT
Found at i:3333344 original size:3 final size:3
Alignment explanation
Indices: 3333331--3333376 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
3333321 ATGTAAAATA
* *
3333331 AAT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT -AT AATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT
3333376 A
1 A
3333377 TTTATAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:3334011 original size:54 final size:54
Alignment explanation
Indices: 3333582--3334741 Score: 1504
Period size: 54 Copynumber: 21.5 Consensus size: 54
3333572 CTATTCTTTC
* * * * * * *
3333582 AGGGAGTATAGAACTCGAACAACCTTC-TGAAATCGGGTTCGCTCCCTATTGCTTT
1 AGGGAGTATGGAACTCGGAC-ATCTTCTTCAAA-CGGGTTCGCTCCCTCTTTCTCT
* * ** * *
3333637 AGGGAGTATAGAACTCGAACAATCTTCTGAAAACGGGTTCGCTCCATCTTTCTTT
1 AGGGAGTATGGAACTCGGAC-ATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
** * ** * * *
3333692 CAGGGAGTATAAAACTCGAACAATCTTC-AAAAATCGTG-TCTGCTCTCTATTTCT-T
1 -AGGGAGTATGGAACTCGGAC-ATCTTCTTCAAA-CGGGTTC-GCTCCCTCTTTCTCT
* * * ** * *
3333747 GCAGAGAGTAT-AAGACTCGAACCATCTTCAACAAACGGGTTCGCTTCCTCTTTCTTT
1 --AGGGAGTATGGA-ACTCGGA-CATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* ** *
3333804 CAGGGAGTATGGAACTCGAACATCTTCTTCTTACGGGGTTCACTCCCTCTTTCTCT
1 -AGGGAGTATGGAACTCGGACATCTTCTTCAAAC-GGGTTCGCTCCCTCTTTCTCT
* * * *
3333860 AGGGAGTATGGAACTCAGACATC-TCTTCAAACGGGTTCACTCCTTCTTTCTTT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* *
3333913 AAGGAGTATGGAACTCGGATATC-TCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* *
3333966 AGGAAGTATGGAACTCGGAAATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
*
3334020 AGGGAGTATGGAACTCTGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* *
3334074 AGGGAGTATGGAACTCGGATATATTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* *
3334128 AGGGAGTATGGAACTCAGACATCTTCTTCAAACGGGTTCGCTCCATCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* * * *
3334182 AGGGAGTATAGAACTCGGACATCTTCTTCAAATGGGTTCACT--C-CTTTCTTT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* *
3334233 AAGGAGTATGGAACTCGGATATC-TCTTCAAAC-GG-TCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* * * *
3334284 AGGAAGTATGGAACTCGAAAATCTTCTTCAAACGGGTTTGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
3334338 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* *
3334392 AGAGAGTATGAAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
3334446 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
3334500 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* *
3334554 AGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
*
3334608 AGGGAGTATGGAACTCGTACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* ** *
3334662 AGGGAGTATGGAATTCAAACA--ATCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* *
3334714 AGGGAGTATGGAACTCGAAAATCTTCTT
1 AGGGAGTATGGAACTCGGACATCTTCTT
3334742 TTGCTTCACT
Statistics
Matches: 995, Mismatches: 89, Indels: 43
0.88 0.08 0.04
Matches are distributed among these distances:
48 4 0.00
49 2 0.00
50 9 0.01
51 53 0.05
52 57 0.06
53 88 0.09
54 577 0.58
55 85 0.09
56 111 0.11
57 9 0.01
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.32
Consensus pattern (54 bp):
AGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
Found at i:3335201 original size:36 final size:36
Alignment explanation
Indices: 3335111--3335304 Score: 147
Period size: 36 Copynumber: 5.4 Consensus size: 36
3335101 ACTCTTATGA
* * * * *
3335111 GAAGGCTTAAAATGGATTTCCTTCACGACTCTTTGAT
1 GAAGGCTTAAGATGG-TTTGCTTCACTATTCTTTGGT
* ** *
3335148 GAAGACACAAGATGGTTTGCTTCATTATTCTTTGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTTTGGT
* * * * * *
3335184 GCATGCTTAAGACGGTTTGTTTCACTACTCTTTAGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTTTGGT
* *
3335220 AAAGGCTTAAGATGG-TTGCTTCACTATTATTTGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTTTGGT
* * * * ** *
3335255 GAAGACTTCAGATTGATCTGCTTCACTCCTCTTCGGT
1 GAAGGCTTAAGA-TGGTTTGCTTCACTATTCTTTGGT
3335292 GAAGGCTTAAGAT
1 GAAGGCTTAAGAT
3335305 TGACTTTGCT
Statistics
Matches: 117, Mismatches: 38, Indels: 5
0.73 0.24 0.03
Matches are distributed among these distances:
35 25 0.21
36 56 0.48
37 36 0.31
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (36 bp):
GAAGGCTTAAGATGGTTTGCTTCACTATTCTTTGGT
Found at i:3336643 original size:125 final size:122
Alignment explanation
Indices: 3336424--3336784 Score: 404
Period size: 125 Copynumber: 2.9 Consensus size: 122
3336414 ATCTTACATT
* * * * *
3336424 GGTACGGGCCTTCAAAATGCCCCAACATCTCAGATTGTAAGGCT-TGCTCTCAATGCCTTCTTGG
1 GGTACGGGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTCTTCT-TC-ATGCCTTATTGG
3336488 TCTGAATCTTGTCATCTTCACACAATGTGGGTGCAGTCATGCCCC-ATCAGTGTCTTATACC
64 TCTGAATCTTGTCATC-TCA-ACAATGTGGGTGCAGTCATGCCCCAAT-AGTGTCTTATACC
* ** *
3336549 GGTATGGGCCTTCAAAAAACCCCATCACCTCAAATTGTAAGGCTCCTTCTTCATGCCTTTTTGGT
1 GGTACGGGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCT-CTTCTTCATGCCTTATTGGT
* * * * * *
3336614 TTAAATCTTGTCATCTCAAC-ATGGCGTGGGTTCAGTCGTGCCCCAATATTGTCTTATACT
65 CTGAATCTTGTCATCTCAACAAT---GTGGGTGCAGTCATGCCCCAATAGTGTCTTATACC
* * * *
3336674 GGTACGGGCCTTTAAAATGCCTCATCACCTCAAATTCTAAGGCTCATTCTTCATGCCTCATTGGT
1 GGTACGGGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTC-TTCTTCATGCCTTATTGGT
* *
3336739 CTGAATCTTGTCATCTCAACCTAATGTGGGTTCAGTCGTGCCCCAA
65 CTGAATCTTGTCATCTCAA-C-AATGTGGGTGCAGTCATGCCCCAA
3336785 CATATCCTAA
Statistics
Matches: 202, Mismatches: 24, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
122 2 0.01
123 2 0.01
124 4 0.02
125 184 0.91
126 5 0.02
127 3 0.01
128 2 0.01
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.32
Consensus pattern (122 bp):
GGTACGGGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTCTTCTTCATGCCTTATTGGTC
TGAATCTTGTCATCTCAACAATGTGGGTGCAGTCATGCCCCAATAGTGTCTTATACC
Found at i:3338048 original size:14 final size:14
Alignment explanation
Indices: 3338031--3338082 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
3338021 TTTATTCTTT
3338031 TTTTTTTATTTTCA
1 TTTTTTTATTTTCA
* *
3338045 TTTTTTCATTTACAA
1 TTTTTTTATTTTC-A
*
3338060 TTTTTTCT-TTTTCT
1 TTTTTT-TATTTTCA
3338074 TTTTTTTAT
1 TTTTTTTAT
3338083 CTTTTCTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
13 1 0.03
14 18 0.60
15 11 0.37
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTTTATTTTCA
Found at i:3338118 original size:45 final size:45
Alignment explanation
Indices: 3338015--3338118 Score: 108
Period size: 45 Copynumber: 2.3 Consensus size: 45
3338005 TTTGGGTGAG
*
3338015 TTTTCT-TTTATTCTTTTTTTTTTATTTTCATTTTTTCATTTACAA
1 TTTTCTCTTT-TTCTTTTTTTTATATTTTCATTTTTTCATTTACAA
* * *
3338060 TTTTTTCTTTTTCTTTTTTTTATCTTTTC-TTTTTCTCTTTTA-ACA
1 TTTTCTCTTTTTCTTTTTTTTATATTTTCATTTTT-TCATTTACA-A
3338105 -TTTCTCTTCTTTCT
1 TTTTCTCTT-TTTCT
3338119 CTTCATGACG
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
44 13 0.26
45 34 0.68
46 3 0.06
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (45 bp):
TTTTCTCTTTTTCTTTTTTTTATATTTTCATTTTTTCATTTACAA
Found at i:3344387 original size:18 final size:18
Alignment explanation
Indices: 3344364--3344399 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
3344354 ATTACCACCC
3344364 CCCTCTCTTTT-TTTCTTT
1 CCCTCT-TTTTATTTCTTT
3344382 CCCTCTTTTTATTTCTTT
1 CCCTCTTTTTATTTCTTT
3344400 TCTCTCCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.67
Consensus pattern (18 bp):
CCCTCTTTTTATTTCTTT
Found at i:3344696 original size:3 final size:3
Alignment explanation
Indices: 3344678--3344730 Score: 63
Period size: 3 Copynumber: 17.3 Consensus size: 3
3344668 GCAAATGTAA
* *
3344678 AAT AAT AAAT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT -AT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3344723 AATT AAT A
1 AA-T AAT A
3344731 TTTATAATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:3357192 original size:5 final size:5
Alignment explanation
Indices: 3357182--3357227 Score: 56
Period size: 5 Copynumber: 8.8 Consensus size: 5
3357172 AACGGTCAAC
* *
3357182 GGTCG GGTCG GGTCG GGTCG GTTCG GGTCAAT GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC
3357228 AGACCGGTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
5 31 0.89
7 4 0.11
ACGTcount: A:0.04, C:0.20, G:0.52, T:0.24
Consensus pattern (5 bp):
GGTCG
Found at i:3364250 original size:7 final size:7
Alignment explanation
Indices: 3364238--3364274 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
3364228 GTCAAAGAAA
3364238 GTCAACG
1 GTCAACG
3364245 GTCAACG
1 GTCAACG
*
3364252 GTCACCG
1 GTCAACG
3364259 GTCAACG
1 GTCAACG
*
3364266 ATCAACG
1 GTCAACG
3364273 GT
1 GT
3364275 TGGGTCGGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:3364286 original size:5 final size:5
Alignment explanation
Indices: 3364276--3364334 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
3364266 ATCAACGGTT
* * *
3364276 GGGTC GGGTC GGGTC AACGATC GGGTC GGGTC GGGTC GGGTC AACGGTC
1 GGGTC GGGTC GGGTC --GGGTC GGGTC GGGTC GGGTC GGGTC --GGGTC
3364325 GGGTC GGGTC
1 GGGTC GGGTC
3364335 AGACCGGTCA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
5 37 0.84
7 7 0.16
ACGTcount: A:0.08, C:0.22, G:0.51, T:0.19
Consensus pattern (5 bp):
GGGTC
Found at i:3364301 original size:22 final size:22
Alignment explanation
Indices: 3364267--3364312 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
3364257 CGGTCAACGA
* *
3364267 TCAACGGTTGGGTCGGGTCGGG
1 TCAACGATCGGGTCGGGTCGGG
3364289 TCAACGATCGGGTCGGGTCGGG
1 TCAACGATCGGGTCGGGTCGGG
3364311 TC
1 TC
3364313 GGGTCAACGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.11, C:0.22, G:0.46, T:0.22
Consensus pattern (22 bp):
TCAACGATCGGGTCGGGTCGGG
Found at i:3364313 original size:27 final size:27
Alignment explanation
Indices: 3364258--3364334 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 27
3364248 AACGGTCACC
* *
3364258 GGTCAACGATCAACGGTTGGGTCGGGTCG
1 GGTCAACGATC--GGGTCGGGTCGGGTCG
3364287 GGTCAACGATCGGGTCGGGTCGGGTCG
1 GGTCAACGATCGGGTCGGGTCGGGTCG
*
3364314 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGATCGGGTCGGGTC
3364335 AGACCGGTCA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
27 34 0.76
29 11 0.24
ACGTcount: A:0.13, C:0.22, G:0.45, T:0.19
Consensus pattern (27 bp):
GGTCAACGATCGGGTCGGGTCGGGTCG
Found at i:3364355 original size:19 final size:19
Alignment explanation
Indices: 3364333--3364410 Score: 88
Period size: 19 Copynumber: 4.1 Consensus size: 19
3364323 TCGGGTCGGG
3364333 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
3364352 TCAGACAGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
3364371 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
3364390 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
3364410 T
1 T
3364411 GAAAACCGGT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
18 3 0.06
19 37 0.76
20 9 0.18
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:3364430 original size:9 final size:9
Alignment explanation
Indices: 3364337--3364430 Score: 62
Period size: 9 Copynumber: 9.8 Consensus size: 9
3364327 GTCGGGTCAG
*
3364337 ACCGGTCAA
1 ACCGGTTAA
*
3364346 ACCGGTTCAG
1 ACCGGTT-AA
* *
3364356 ACAGGTCAA
1 ACCGGTTAA
*
3364365 ACCGGTTCGA
1 ACCGGTT-AA
3364375 ACCGGTTGAA
1 ACCGGTT-AA
*
3364385 ACCGGTCAA
1 ACCGGTTAA
*
3364394 ACCGGTCAGA
1 ACCGGTTA-A
3364404 ACCGGTTGAAA
1 ACCGGTT--AA
3364415 ACCGGTTAA
1 ACCGGTTAA
*
3364424 ACTGGTT
1 ACCGGTT
3364431 TCCAGCAGCC
Statistics
Matches: 67, Mismatches: 13, Indels: 10
0.74 0.14 0.11
Matches are distributed among these distances:
9 30 0.45
10 28 0.42
11 8 0.12
12 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.27, T:0.18
Consensus pattern (9 bp):
ACCGGTTAA
Found at i:3367461 original size:21 final size:21
Alignment explanation
Indices: 3367392--3367453 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
3367382 ATTGATCCCG
** *
3367392 ATCTTAAGATTATCTTCAATA
1 ATCTTAACTTTATCTTCAACA
*
3367413 ATCTTAACTTTGTCTTCAACA
1 ATCTTAACTTTATCTTCAACA
3367434 ATCTTAACTTTATCTTCAAC
1 ATCTTAACTTTATCTTCAAC
3367454 TTCTTTAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.32, C:0.21, G:0.03, T:0.44
Consensus pattern (21 bp):
ATCTTAACTTTATCTTCAACA
Found at i:3375270 original size:205 final size:209
Alignment explanation
Indices: 3374929--3375343 Score: 802
Period size: 205 Copynumber: 2.0 Consensus size: 209
3374919 GGAAATATCA
3374929 ATTGAGTAAATTATTGTAATGTCGGAAATTTATTTAATAAGTTGATTTTTTTGGTTTAATTCTTA
1 ATTGAGTAAATTATTGTAATGTCGGAAATTTATTTAATAAGTTGATTTTTTTGGTTTAATTCTTA
3374994 AGTTGAGATTTAATTTCAAGTTTATCAAGTTGTGTGGTTGAATTTGGAAAGTCTAGAAAAAATTT
66 AGTTGAGATTTAATTTCAAGTTTATCAAGTTGTGTGGTTGAATTTGGAAAGTCTAGAAAAAATTT
3375059 AGGATTAAATTGCAAGCTTTTGAATGTTTAAGTCTTAATTTGAATATTTTTTTTGAGGTTTTGCA
131 AGGATTAAATTGCAAGCTTTTGAATGTTTAAGTCTTAATTTGAATATTTTTTTTGAGGTTTTGCA
3375124 AATTTCATGTAATT
196 AATTTCATGTAATT
3375138 ATTGAGTAAATTATTGTAATGTCGGAAATTTATTTAATAAG-TGA-TTTTTTGGTTTAATTCTTA
1 ATTGAGTAAATTATTGTAATGTCGGAAATTTATTTAATAAGTTGATTTTTTTGGTTTAATTCTTA
3375201 AGTTGAG-TTTAATTTCAAGTTTATCAAG-TGTGTGGTTGAATTTGGAAAGTCTAGAAAAAATTT
66 AGTTGAGATTTAATTTCAAGTTTATCAAGTTGTGTGGTTGAATTTGGAAAGTCTAGAAAAAATTT
3375264 AGGATTAAATTGCAAGCTTTTGAATGTTTAAGTCTTAATTTGAATATTTTTTTTGAGGTTTTGCA
131 AGGATTAAATTGCAAGCTTTTGAATGTTTAAGTCTTAATTTGAATATTTTTTTTGAGGTTTTGCA
3375329 AATTTCATGTAATT
196 AATTTCATGTAATT
3375343 A
1 A
3375344 ATGTGAAATG
Statistics
Matches: 206, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
205 115 0.56
206 21 0.10
207 26 0.13
208 3 0.01
209 41 0.20
ACGTcount: A:0.31, C:0.05, G:0.18, T:0.46
Consensus pattern (209 bp):
ATTGAGTAAATTATTGTAATGTCGGAAATTTATTTAATAAGTTGATTTTTTTGGTTTAATTCTTA
AGTTGAGATTTAATTTCAAGTTTATCAAGTTGTGTGGTTGAATTTGGAAAGTCTAGAAAAAATTT
AGGATTAAATTGCAAGCTTTTGAATGTTTAAGTCTTAATTTGAATATTTTTTTTGAGGTTTTGCA
AATTTCATGTAATT
Found at i:3376606 original size:18 final size:18
Alignment explanation
Indices: 3376554--3376704 Score: 125
Period size: 18 Copynumber: 8.7 Consensus size: 18
3376544 CTAAATGTTC
* *
3376554 ACAGTTATCAGA-CATTT
1 ACAGTTATTAGATGATTT
*
3376571 CACAGTTATCAGAT-ATTT
1 -ACAGTTATTAGATGATTT
3376589 ACAGTTATTAGATGATTT
1 ACAGTTATTAGATGATTT
*
3376607 TCAGTTATTAGATG-TTT
1 ACAGTTATTAGATGATTT
*
3376624 ATAGTTATTAGATGATTT
1 ACAGTTATTAGATGATTT
* * * *
3376642 TCAATTGTCAGAT-ATTT
1 ACAGTTATTAGATGATTT
*
3376659 ACAGTTA-CAGATG-TTT
1 ACAGTTATTAGATGATTT
* * *
3376675 ATAGATATTAGATGTTTT
1 ACAGTTATTAGATGATTT
*
3376693 ATAGTTATTAGA
1 ACAGTTATTAGA
3376705 CATATATTAA
Statistics
Matches: 111, Mismatches: 16, Indels: 12
0.80 0.12 0.09
Matches are distributed among these distances:
16 13 0.12
17 40 0.36
18 58 0.52
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.44
Consensus pattern (18 bp):
ACAGTTATTAGATGATTT
Found at i:3376612 original size:35 final size:35
Alignment explanation
Indices: 3376573--3376665 Score: 141
Period size: 35 Copynumber: 2.7 Consensus size: 35
3376563 AGACATTTCA
3376573 CAGTTATCAGATATTTACAGTTATTAGATGATTTT
1 CAGTTATCAGATATTTACAGTTATTAGATGATTTT
* * *
3376608 CAGTTATTAGATGTTTATAGTTATTAGATGATTTT
1 CAGTTATCAGATATTTACAGTTATTAGATGATTTT
* *
3376643 CAATTGTCAGATATTTACAGTTA
1 CAGTTATCAGATATTTACAGTTA
3376666 CAGATGTTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (35 bp):
CAGTTATCAGATATTTACAGTTATTAGATGATTTT
Found at i:3383340 original size:2 final size:2
Alignment explanation
Indices: 3383333--3383358 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3383323 TCATTTTTAA
3383333 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
3383359 TAATAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.