Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397265.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_146.0, 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: 8065533
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 116430 characters in sequence are not A, C, G, or T
File 8 of 18
Found at i:3292277 original size:45 final size:45
Alignment explanation
Indices: 3292208--3292305 Score: 110
Period size: 45 Copynumber: 2.2 Consensus size: 45
3292198 AAGTTTTAAC
* * *
3292208 AATATTTTCATCAAAGGATAAAAATATCC-TTTATTGCAAT-TAATT
1 AATATTTTCACCAAAAGATAAAAATA-CCTTTTATTACAATCTAA-T
* * *
3292253 AATATTTTCACCAAAATATGAAAATACCTTTTATTATAATCTAAT
1 AATATTTTCACCAAAAGATAAAAATACCTTTTATTACAATCTAAT
3292298 AATATTTT
1 AATATTTT
3292306 TGAGAAAAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
44 2 0.04
45 40 0.89
46 3 0.07
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.42
Consensus pattern (45 bp):
AATATTTTCACCAAAAGATAAAAATACCTTTTATTACAATCTAAT
Found at i:3292561 original size:42 final size:44
Alignment explanation
Indices: 3292467--3292567 Score: 143
Period size: 42 Copynumber: 2.3 Consensus size: 44
3292457 TTATTAAAGC
* *
3292467 TTTAATAATATTTTCATCAAAATATAAAATTAACCTTTATTTTAA
1 TTTAATAATATTTTCACCAAAATATAAAA-TAACCTTTATTATAA
* *
3292512 TTAAATAATATTTTCACCAAAATA-AAAA-ATCCTTTATTATAA
1 TTTAATAATATTTTCACCAAAATATAAAATAACCTTTATTATAA
3292554 TTTAATAATATTTT
1 TTTAATAATATTTT
3292568 TGGATTTAGA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
42 25 0.49
44 4 0.08
45 22 0.43
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (44 bp):
TTTAATAATATTTTCACCAAAATATAAAATAACCTTTATTATAA
Found at i:3292609 original size:130 final size:130
Alignment explanation
Indices: 3292456--3292699 Score: 320
Period size: 129 Copynumber: 1.9 Consensus size: 130
3292446 AAAAACACCT
* * *
3292456 TTTATTAAAGCTTTAATAATATTTTCATCAAAATATA-AAATTAACC-TTTATTTTAATTAAATA
1 TTTATTAAAGCTTTAATAATA-TTTCATCAAAAGATAGAAA--AACCTTTTATTGTAATCAAATA
*
3292519 ATATTTTCACCAAAATA-AAAAATCCT-TTATT-ATAATTTAATAATATTTTTGGATTTAGAAAA
63 ATATTTTCA-CAAAATACAAAAATACTGTT-TTCATAATTTAATAATATTTTTGGATTTAGAAAA
3292581 AAATA
126 AAATA
*
3292586 TTTATTTAAA-CTTTAATAATATTTCATCAAAAGATAGAAAATCCTTTTATTGTAATCAAATAAT
1 TTTA-TTAAAGCTTTAATAATATTTCATCAAAAGATAGAAAAACCTTTTATTGTAATCAAATAAT
* * *
3292650 ATTTTCACTAAGTACAAAAATACTGTTTTCATAATTTTATAATATTTTTG
65 ATTTTCACAAAATACAAAAATACTGTTTTCATAATTTAATAATATTTTTG
3292700 TATCAAAGCA
Statistics
Matches: 100, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
128 8 0.08
129 48 0.48
130 39 0.39
131 5 0.05
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (130 bp):
TTTATTAAAGCTTTAATAATATTTCATCAAAAGATAGAAAAACCTTTTATTGTAATCAAATAATA
TTTTCACAAAATACAAAAATACTGTTTTCATAATTTAATAATATTTTTGGATTTAGAAAAAAATA
Found at i:3292701 original size:265 final size:270
Alignment explanation
Indices: 3292149--3292706 Score: 592
Period size: 265 Copynumber: 2.1 Consensus size: 270
3292139 ATATTCTCTA
* * * * * *
3292149 TTATAATTTGATAATATTTTT-TGTCAAAAAACAAAAATATCTTTTATTTAAGTTTTAACAATAT
1 TTATAATTTCATAATATTTTTGTATCAAAAAACAAAAACACCTTTTATTAAAGCTTTAACAATAT
* * * *
3292213 TTTCATCAAAGGATAAAAATATCCTTTATTGCAATTAATTAATATTTTCACCAAAATATGAAAAT
66 TTTCATCAAAAGATAAAAATAACCTTTATTGCAATTAAATAATATTTTCACCAAAATATAAAAAT
** * *
3292278 ACCTTTTATTATAATCTAATAATATTTTTGAGAAAAGACAAATATTTCCTTTATTTAAGCTTAAA
131 ACCTTTTATTATAATCTAATAATATTTTTGAGAAAAGACAAATAAATCATTTATTTAAACTTAAA
** * * * *
3292343 TAATATGTTGGTCAAAAGAAAAAAAATATTGTTTATTGTAATTAAAAAACTTTTTACCAAAATAG
196 TAATATGTTCATCAAAAGAAAAAAAATACTGTTTATTGTAATCAAAAAACTTTTCACCAAAATAC
3292408 AAAAATACCC
261 AAAAATACCC
* * *
3292418 TT-T-A--TCACAATA-TTTTGTATCAAAAGACAAAAACACCTTTTATTAAAGCTTTAATAATAT
1 TTATAATTTCATAATATTTTTGTATCAAAAAACAAAAACACCTTTTATTAAAGCTTTAACAATAT
* * **
3292478 TTTCATCAAAATATAAAATTAACCTTTATTTTAATTAAATAATATTTTCACCAAAATA-AAAAAT
66 TTTCATCAAAAGATAAAAATAACCTTTATTGCAATTAAATAATATTTTCACCAAAATATAAAAAT
* ** *
3292542 -CC-TTTATTATAATTTAATAATATTTTTG-GATTTAGA-AAA-AAAT-ATTTATTTAAACTTTA
131 ACCTTTTATTATAATCTAATAATATTTTTGAGA-AAAGACAAATAAATCATTTATTTAAACTTAA
* * * * *
3292601 ATAATAT-TTCATCAAAAGATAGAAAATCCT-TTTATTGTAATCAAATAATA-TTTTCA-CTAAG
195 ATAATATGTTCATCAAAAGAAAAAAAATACTGTTTATTGTAATCAAA-AA-ACTTTTCACCAAAA
**
3292662 TACAAAAATACTGTT
258 TACAAAAATAC--CC
*
3292677 TTCATAATTTTATAATATTTTTGTATCAAA
1 TT-ATAATTTCATAATATTTTTGTATCAAA
3292707 GCAAGTTCAT
Statistics
Matches: 237, Mismatches: 40, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
257 27 0.11
258 24 0.10
259 23 0.10
260 2 0.01
261 6 0.03
262 29 0.12
263 2 0.01
264 15 0.06
265 105 0.44
267 1 0.00
268 1 0.00
269 2 0.01
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (270 bp):
TTATAATTTCATAATATTTTTGTATCAAAAAACAAAAACACCTTTTATTAAAGCTTTAACAATAT
TTTCATCAAAAGATAAAAATAACCTTTATTGCAATTAAATAATATTTTCACCAAAATATAAAAAT
ACCTTTTATTATAATCTAATAATATTTTTGAGAAAAGACAAATAAATCATTTATTTAAACTTAAA
TAATATGTTCATCAAAAGAAAAAAAATACTGTTTATTGTAATCAAAAAACTTTTCACCAAAATAC
AAAAATACCC
Found at i:3295520 original size:30 final size:30
Alignment explanation
Indices: 3295486--3295544 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
3295476 CTTCATCTTC
* *
3295486 ATCTTTATCTCCTTTCATGTCATCTTTTTT
1 ATCTTCATCTCCTTGCATGTCATCTTTTTT
3295516 ATCTTCATCTCCTTGCATGTCATCTTTTT
1 ATCTTCATCTCCTTGCATGTCATCTTTTT
3295545 CATCCCTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.14, C:0.25, G:0.05, T:0.56
Consensus pattern (30 bp):
ATCTTCATCTCCTTGCATGTCATCTTTTTT
Found at i:3297446 original size:21 final size:21
Alignment explanation
Indices: 3297420--3297464 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
3297410 TCCATCAACA
3297420 TTAGTTTTACTCTAAAATGGG
1 TTAGTTTTACTCTAAAATGGG
3297441 TTAGTTTTACTCTAAAATGGG
1 TTAGTTTTACTCTAAAATGGG
3297462 TTA
1 TTA
3297465 ACAATACCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (21 bp):
TTAGTTTTACTCTAAAATGGG
Found at i:3304916 original size:21 final size:20
Alignment explanation
Indices: 3304884--3304929 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
3304874 TGGTCTATGG
3304884 AATTAAATTAGTT-AGTTTAA
1 AATTAAATTAGTTCA-TTTAA
*
3304904 AATTGAATATAGTTCATTT-A
1 AATTAAAT-TAGTTCATTTAA
3304924 AATTAA
1 AATTAA
3304930 TTAATAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 13 0.59
21 8 0.36
22 1 0.05
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (20 bp):
AATTAAATTAGTTCATTTAA
Found at i:3307894 original size:171 final size:172
Alignment explanation
Indices: 3307650--3308552 Score: 1121
Period size: 171 Copynumber: 5.3 Consensus size: 172
3307640 ATCACAGTTG
* * *
3307650 TAATTTTACATTTATTAGTTTACAAGTTCAACAAATATAAAAAATTTT-TATACTTAAG-TGTAC
1 TAATTTTACATTTATTAGTTTACAAGTTCAACTAATAT-AAAAATTTTATATATTTAAGAT-TGC
** * *
3307713 ATTTTAGTTCAAATAATATAAATTTATTTTACATTTATTAGTTTACTAGTTCAACTAATATAAAA
64 ATCATAGTTCAAGTAATATAAATTTATTTTACATTTATTAGTTTACAAGTTCAACTAATATAAAA
* *
3307778 ATTTTATATA-TTAAGTTGGCATTATAGTTAAAGTAATATAAAT
129 ATTTTATATATTTAAGTTTGCATCATAGTTAAAGTAATATAAAT
* * * *
3307821 TAATTTTACATTTGTT-GATTTACAAGCTCAATTACTATAAAAATTTTATATATTTAAGATTGCA
1 TAATTTTACATTTATTAG-TTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGATTGCA
*
3307885 TCATAGTTCAAATAATATAAATTTATTTTACA--T-TT-G-TT---AGTT----TAATATAAAAA
65 TCATAGTTCAAGTAATATAAATTTATTTTACATTTATTAGTTTACAAGTTCAACTAATATAAAAA
* * * * *
3307938 TTTTATATATTTACGTTTGTATCATTGTTCAAGTAATATAAGT
130 TTTTATATATTTAAGTTTGCATCATAGTTAAAGTAATATAAAT
* *
3307981 TAATTTTACATTTATTAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGTAT
1 TAATTTTACATTTATTAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGATTGCAT
* * * * * *
3308046 TATTGTTCAAGTGATATAAATTAATTTTACATTCATTAGTTTACAAGTTCAACTAATATAAAAGT
66 CATAGTTCAAGTAATATAAATTTATTTTACATTTATTAGTTTACAAGTTCAACTAATATAAAAAT
* *
3308111 TTTATATATTTAA-TCTTGTATCATAGTTCATA-TAATATAAAT
131 TTTATATATTTAAGT-TTGCATCATAGTT-AAAGTAATATAAAT
* * * *
3308153 TTATTTTACATTTATTAGTTTACAAGTCCAACTAATATAAAAATATTATATA-TTAA-ATTTACA
1 TAATTTTACATTTATTAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGA-TTGCA
* * * * * *
3308216 TCATAGTTTAAGTAATATAAATTAATTTTATATTTTTTAGCTTACAAGTTCAACTATTATAAAAA
65 TCATAGTTCAAGTAATATAAATTTATTTTACATTTATTAGTTTACAAGTTCAACTAATATAAAAA
*
3308281 TTTTATATATTTAAGTTTGCATCATATTTCAAA-TAATATAAAT
130 TTTTATATATTTAAGTTTGCATCATAGTT-AAAGTAATATAAAT
* * *
3308324 TTATTTTACATTTATTAGTTTATAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCAT
1 TAATTTTACATTTATTAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGATTGCAT
* * * *
3308389 CATAGTTCAAGTAATATAAATTTATTTTAAATTTGTTAGTTTACAAGTTCAATTAATATAAAACT
66 CATAGTTCAAGTAATATAAATTTATTTTACATTTATTAGTTTACAAGTTCAACTAATATAAAAAT
* * * *
3308454 TTTATATATTTAAGTTTGCATCATAATTCATGTAGTATAAAT
131 TTTATATATTTAAGTTTGCATCATAGTTAAAGTAATATAAAT
*
3308496 T-ATTTTACATTTATCAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAG
1 TAATTTTACATTTATTAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAG
3308553 CTTTTGTTTA
Statistics
Matches: 636, Mismatches: 72, Indels: 48
0.84 0.10 0.06
Matches are distributed among these distances:
159 20 0.03
160 109 0.17
161 1 0.00
163 6 0.01
164 1 0.00
165 2 0.00
166 2 0.00
167 1 0.00
168 6 0.01
169 1 0.00
170 10 0.02
171 278 0.44
172 198 0.31
173 1 0.00
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.46
Consensus pattern (172 bp):
TAATTTTACATTTATTAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGATTGCAT
CATAGTTCAAGTAATATAAATTTATTTTACATTTATTAGTTTACAAGTTCAACTAATATAAAAAT
TTTATATATTTAAGTTTGCATCATAGTTAAAGTAATATAAAT
Found at i:3307918 original size:86 final size:86
Alignment explanation
Indices: 3307652--3308552 Score: 1147
Period size: 86 Copynumber: 10.7 Consensus size: 86
3307642 CACAGTTGTA
* * * * *
3307652 ATTTTACATTTATTAGTTTACAAGTTCAACAAATATAAAAAATTTT-TATACTTAAGTGTACATT
1 ATTTTACATTTATTAGTTTACAAGTTCAACTAATAT-AAAAATTTTATATATTTAAGTTTGCATC
*
3307716 TTAGTTCAAATAATATAAATTT
65 ATAGTTCAAATAATATAAATTT
* * *
3307738 ATTTTACATTTATTAGTTTACTAGTTCAACTAATATAAAAATTTTATATA-TTAAGTTGGCATTA
1 ATTTTACATTTATTAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCA
*
3307802 TAGTT-AAAGTAATATAAATTA
66 TAGTTCAAA-TAATATAAATTT
* * * * *
3307823 ATTTTACATTTGTT-GATTTACAAGCTCAATTACTATAAAAATTTTATATATTTAAGATTGCATC
1 ATTTTACATTTATTAG-TTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATC
3307887 ATAGTTCAAATAATATAAATTT
65 ATAGTTCAAATAATATAAATTT
* *
3307909 ATTTTACA--T-TT-G-TT---AGTT----TAATATAAAAATTTTATATATTTACGTTTGTATCA
1 ATTTTACATTTATTAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCA
* * * *
3307962 TTGTTCAAGTAATATAAGTTA
66 TAGTTCAAATAATATAAATTT
* *
3307983 ATTTTACATTTATTAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGTATTA
1 ATTTTACATTTATTAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCA
* * * *
3308048 TTGTTCAAGTGATATAAATTA
66 TAGTTCAAATAATATAAATTT
* * *
3308069 ATTTTACATTCATTAGTTTACAAGTTCAACTAATATAAAAGTTTTATATATTTAA-TCTTGTATC
1 ATTTTACATTTATTAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGT-TTGCATC
*
3308133 ATAGTTCATATAATATAAATTT
65 ATAGTTCAAATAATATAAATTT
* * * *
3308155 ATTTTACATTTATTAGTTTACAAGTCCAACTAATATAAAAATATTATATA-TTAAATTTACATCA
1 ATTTTACATTTATTAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCA
* * *
3308219 TAGTTTAAGTAATATAAATTA
66 TAGTTCAAATAATATAAATTT
* * * *
3308240 ATTTTATATTTTTTAGCTTACAAGTTCAACTATTATAAAAATTTTATATATTTAAGTTTGCATCA
1 ATTTTACATTTATTAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCA
*
3308305 TATTTCAAATAATATAAATTT
66 TAGTTCAAATAATATAAATTT
*
3308326 ATTTTACATTTATTAGTTTATAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCA
1 ATTTTACATTTATTAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCA
*
3308391 TAGTTCAAGTAATATAAATTT
66 TAGTTCAAATAATATAAATTT
* * * *
3308412 ATTTTAAATTTGTTAGTTTACAAGTTCAATTAATATAAAACTTTTATATATTTAAGTTTGCATCA
1 ATTTTACATTTATTAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCA
* ** *
3308477 TAATTCATGTAGTATAAA-TT
66 TAGTTCAAATAATATAAATTT
*
3308497 ATTTTACATTTATCAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAG
1 ATTTTACATTTATTAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAG
3308553 CTTTTGTTTA
Statistics
Matches: 716, Mismatches: 79, Indels: 41
0.86 0.09 0.05
Matches are distributed among these distances:
74 56 0.08
76 1 0.00
77 2 0.00
78 4 0.01
79 2 0.00
81 2 0.00
82 4 0.01
83 3 0.00
84 5 0.01
85 203 0.28
86 431 0.60
87 3 0.00
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.46
Consensus pattern (86 bp):
ATTTTACATTTATTAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCA
TAGTTCAAATAATATAAATTT
Found at i:3308324 original size:257 final size:258
Alignment explanation
Indices: 3307927--3308552 Score: 920
Period size: 257 Copynumber: 2.4 Consensus size: 258
3307917 TTTGTTAGTT
* * * *
3307927 TAATATAAAAATTTTATATATTTACGTTTGTATCATTGTTCAAGTAATATAAGTTAATTTTACAT
1 TAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACAT
* * *
3307992 TTATTAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGTATTATTGTTCAAG
66 TTATTAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCATTGTTCAAA
* *
3308057 TGATATAAATTAATTTTACATTCATTAGTTTACAAGTTCAACTAATATAAAAGTTTTATATATTT
131 TAATATAAATTAATTTTACATTCATTAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTT
* *
3308122 AA-TCTTGTATCATAGTTCATA-TAATATAAATTTATTTTACATTTATTAGTTTACAAGTCCAAC
196 AAGT-TTGCATCATAGTTCA-AGTAATATAAATTTATTTTAAATTTATTAGTTTACAAGTCCAAC
* * * * *
3308185 TAATATAAAAATATTATATA-TTAAATTTACATCATAGTTTAAGTAATATAAATTAATTTTATAT
1 TAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACAT
* * *
3308249 TTTTTAGCTTACAAGTTCAACTATTATAAAAATTTTATATATTTAAGTTTGCATCATAT-TTCAA
66 TTATTAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCAT-TGTTCAA
* * *
3308313 ATAATATAAATTTATTTTACATTTATTAGTTTATAAGTTCAACTAATATAAAAATTTTATATATT
130 ATAATATAAATTAATTTTACATTCATTAGTTTACAAGTTCAACTAATATAAAAATTTTATATATT
* * *
3308378 TAAGTTTGCATCATAGTTCAAGTAATATAAATTTATTTTAAATTTGTTAGTTTACAAGTTCAAT
195 TAAGTTTGCATCATAGTTCAAGTAATATAAATTTATTTTAAATTTATTAGTTTACAAGTCCAAC
* * * *
3308442 TAATATAAAACTTTTATATATTTAAGTTTGCATCATAATTCATGTAGTATAAATT-ATTTTACAT
1 TAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACAT
*
3308506 TTATCAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAG
66 TTATTAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAG
3308553 CTTTTGTTTA
Statistics
Matches: 326, Mismatches: 38, Indels: 9
0.87 0.10 0.02
Matches are distributed among these distances:
256 1 0.00
257 276 0.85
258 49 0.15
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.46
Consensus pattern (258 bp):
TAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACAT
TTATTAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAGTTTGCATCATTGTTCAAA
TAATATAAATTAATTTTACATTCATTAGTTTACAAGTTCAACTAATATAAAAATTTTATATATTT
AAGTTTGCATCATAGTTCAAGTAATATAAATTTATTTTAAATTTATTAGTTTACAAGTCCAAC
Found at i:3323490 original size:35 final size:35
Alignment explanation
Indices: 3323445--3323590 Score: 197
Period size: 35 Copynumber: 4.2 Consensus size: 35
3323435 CCAAGCTTTT
*
3323445 ACAATAGCTTTTCACAA-GCTCAACCACAACCTTCA
1 ACAATGGCTTTTCA-AAGGCTCAACCACAACCTTCA
*
3323480 ACAATGGCTTTTCAAAGGCTCAACCATAACCTTCA
1 ACAATGGCTTTTCAAAGGCTCAACCACAACCTTCA
* *
3323515 ACAATGGTTTTTCAAAGGCTCAACCACAACTTTCA
1 ACAATGGCTTTTCAAAGGCTCAACCACAACCTTCA
* * *
3323550 ATAATGGCTTTTCAAAGGCTCAGCCAC-ACCTTTTA
1 ACAATGGCTTTTCAAAGGCTCAACCACAACC-TTCA
3323585 ACAATG
1 ACAATG
3323591 ATTTTTTTCG
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
34 4 0.04
35 94 0.96
ACGTcount: A:0.34, C:0.28, G:0.11, T:0.27
Consensus pattern (35 bp):
ACAATGGCTTTTCAAAGGCTCAACCACAACCTTCA
Found at i:3331368 original size:177 final size:177
Alignment explanation
Indices: 3331061--3331419 Score: 619
Period size: 177 Copynumber: 2.0 Consensus size: 177
3331051 GAAGTAAACC
* *
3331061 TTTTCCATCTCATAATCCTACCCTTACATCTCAACATTTGTACTCAACGCCTTTCCAACCAATGA
1 TTTTCCATCTAATAATCCTACCCTTACATCTCAACATTTGTACTCAACACCTTTCCAACCAATGA
**
3331126 GGTTTCCATTCTAAATGAATTACGATATTACTTTTTACTTTTGGTTTTTGCTTTATAACAATTAG
66 GGTTTCCATTCTAAATGAATTACGATATTACTTTTTACTTTTGACTTTTGCTTTATAACAATTAG
* * *
3331191 ATGACTGTTAACAACATGAGAACTAATTTTCCTATTTATGTTTTACT
131 ATAACTGTTAACAACATGAAAACTAATTTTCCTATTTACGTTTTACT
* *
3331238 TTTTTCATCTAATAATCCTACCCTTCCATCTCAACATTTGTACTCAACACCTTTCCAACCAATGA
1 TTTTCCATCTAATAATCCTACCCTTACATCTCAACATTTGTACTCAACACCTTTCCAACCAATGA
* *
3331303 TGTTTCCATTCTAAATGAATTACGATATTACTTTTTACTTTTGACTTTTGTTTTATAACAATTAG
66 GGTTTCCATTCTAAATGAATTACGATATTACTTTTTACTTTTGACTTTTGCTTTATAACAATTAG
3331368 ATAACTGTTAACAACATGAAAACTAATTTTCCTATTTACGTTTTACT
131 ATAACTGTTAACAACATGAAAACTAATTTTCCTATTTACGTTTTACT
3331415 TTTTC
1 TTTTC
3331420 ATTTTATATG
Statistics
Matches: 170, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
177 170 1.00
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.43
Consensus pattern (177 bp):
TTTTCCATCTAATAATCCTACCCTTACATCTCAACATTTGTACTCAACACCTTTCCAACCAATGA
GGTTTCCATTCTAAATGAATTACGATATTACTTTTTACTTTTGACTTTTGCTTTATAACAATTAG
ATAACTGTTAACAACATGAAAACTAATTTTCCTATTTACGTTTTACT
Found at i:3341420 original size:15 final size:15
Alignment explanation
Indices: 3341400--3341429 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3341390 TATTTGGCTC
3341400 TTTCATTGTATTTAT
1 TTTCATTGTATTTAT
*
3341415 TTTCATTGTTTTTAT
1 TTTCATTGTATTTAT
3341430 GAATTTGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.07, G:0.07, T:0.70
Consensus pattern (15 bp):
TTTCATTGTATTTAT
Found at i:3342138 original size:30 final size:30
Alignment explanation
Indices: 3342103--3342185 Score: 103
Period size: 30 Copynumber: 2.8 Consensus size: 30
3342093 CTTTTGTATT
*
3342103 TTTTGAGTCAAATAAGCCCTTATACTTTTA
1 TTTTGAGTCAAATAAGTCCTTATACTTTTA
* ** **
3342133 TTTTGAATTGAATAAGTTATTATACTTTTA
1 TTTTGAGTCAAATAAGTCCTTATACTTTTA
*
3342163 TTTTGAGTCATATAAGTCCTTAT
1 TTTTGAGTCAAATAAGTCCTTAT
3342186 GATCAATAAT
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (30 bp):
TTTTGAGTCAAATAAGTCCTTATACTTTTA
Found at i:3344654 original size:19 final size:16
Alignment explanation
Indices: 3344615--3344657 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
3344605 ACGGGATTAA
3344615 TACCACCATCCCTGCT
1 TACCACCATCCCTGCT
3344631 TACCACCATCCCTGCT
1 TACCACCATCCCTGCT
3344647 TACCACCATCC
1 TACCACCATCC
3344658 TATAGGTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.21, C:0.51, G:0.05, T:0.23
Consensus pattern (16 bp):
TACCACCATCCCTGCT
Found at i:3353220 original size:17 final size:19
Alignment explanation
Indices: 3353190--3353225 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3353180 AATTTTGTCT
3353190 AATTTAATATTAGA-AAAA
1 AATTTAATATTAGACAAAA
3353208 AATTTAA-ATTAGACAAAA
1 AATTTAATATTAGACAAAA
3353226 TTTTGTCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.31
Consensus pattern (19 bp):
AATTTAATATTAGACAAAA
Found at i:3362058 original size:58 final size:58
Alignment explanation
Indices: 3361960--3362072 Score: 147
Period size: 58 Copynumber: 1.9 Consensus size: 58
3361950 CATAATTATC
* * ** * *
3361960 CAAAGTAGTTTGCATGTGACAATTTTACTTTGTGCAATTTAATACATGCTATGCAATG
1 CAAAGTAATATGCATGTGACAAAATTACTTTATGCAATTTAATAAATGCTATGCAATG
*
3362018 CAAAGTAATATGCATGTGACAAAATT-CTTTTATGCGATTTAATAAATGCTATGCA
1 CAAAGTAATATGCATGTGACAAAATTAC-TTTATGCAATTTAATAAATGCTATGCA
3362073 CGCTAAGATG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
57 1 0.02
58 46 0.98
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (58 bp):
CAAAGTAATATGCATGTGACAAAATTACTTTATGCAATTTAATAAATGCTATGCAATG
Found at i:3368568 original size:54 final size:52
Alignment explanation
Indices: 3368483--3368588 Score: 142
Period size: 54 Copynumber: 2.0 Consensus size: 52
3368473 CATCCTTTCC
*
3368483 CATCAACCCACTTAATAAACATATCTAGGGCATCCTCTTCCATCAGTCCACACA
1 CATCAACCCACTTAATAAACATATCTAGGGCATCCTCTCCCATCA-TCC-CACA
* * *
3368537 CATCAACCC-CTATAATAGACATATTTGGGGCATCCTCTCCCATCATCCCACA
1 CATCAACCCACT-TAATAAACATATCTAGGGCATCCTCTCCCATCATCCCACA
3368589 TAATAAGCAT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
52 4 0.09
53 5 0.11
54 38 0.81
ACGTcount: A:0.31, C:0.36, G:0.08, T:0.25
Consensus pattern (52 bp):
CATCAACCCACTTAATAAACATATCTAGGGCATCCTCTCCCATCATCCCACA
Found at i:3369188 original size:16 final size:16
Alignment explanation
Indices: 3369167--3369197 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3369157 CTTTTATATG
*
3369167 CATATATATTTGTATA
1 CATATATATATGTATA
3369183 CATATATATATGTAT
1 CATATATATATGTAT
3369198 GTATTTTTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (16 bp):
CATATATATATGTATA
Found at i:3369341 original size:19 final size:21
Alignment explanation
Indices: 3369304--3369351 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
3369294 CTACTCTGTG
*
3369304 AGCTTCAAATCATTTCC-TTA
1 AGCTTCAAATCACTTCCTTTA
*
3369324 AGCTTCAAAT-ACTTCCTTTG
1 AGCTTCAAATCACTTCCTTTA
3369344 AGCTTCAA
1 AGCTTCAA
3369352 CAAATTCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.38
Consensus pattern (21 bp):
AGCTTCAAATCACTTCCTTTA
Found at i:3372543 original size:30 final size:31
Alignment explanation
Indices: 3372516--3372589 Score: 130
Period size: 31 Copynumber: 2.4 Consensus size: 31
3372506 AAGTATGTAT
3372516 AAAATAATTTTAAATATTACAAATATGTAAA
1 AAAATAATTTTAAATATTACAAATATGTAAA
*
3372547 AAAAAAATTTTAAATATTACAAATATGTAAA
1 AAAATAATTTTAAATATTACAAATATGTAAA
3372578 AAAATAAGTTTT
1 AAAATAA-TTTT
3372590 TAATTAATGA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 36 0.90
32 4 0.10
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.35
Consensus pattern (31 bp):
AAAATAATTTTAAATATTACAAATATGTAAA
Found at i:3373296 original size:73 final size:73
Alignment explanation
Indices: 3373134--3373296 Score: 195
Period size: 73 Copynumber: 2.2 Consensus size: 73
3373124 CGAGGGACAT
* *
3373134 TGTTAGTAGACTAAGAACTTACTACCAAAAACTGAGTTCAGAGACAAAAACAACTTAATCGACTA
1 TGTTAGTAGACTAAGAGCCTACTACCAAAAACTGAGTTCAGAGACAAAAACAACTTAATCGACTA
* *
3373199 AGAAGTAT
66 AGAAGCAA
* * * * *
3373207 TGTTAGTCA-ACAAAGAGCCTACTGCCAGAAACT-AGGTTCAGAGATATAAACAACTTAATCGAC
1 TGTTAGT-AGACTAAGAGCCTACTACCAAAAACTGA-GTTCAGAGACAAAAACAACTTAATCGAC
*
3373270 TAAGTAGCAA
64 TAAGAAGCAA
*
3373280 TGTTAGTTGACTAAGAG
1 TGTTAGTAGACTAAGAG
3373297 TATTCTATTT
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
72 1 0.01
73 73 0.97
74 1 0.01
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.24
Consensus pattern (73 bp):
TGTTAGTAGACTAAGAGCCTACTACCAAAAACTGAGTTCAGAGACAAAAACAACTTAATCGACTA
AGAAGCAA
Found at i:3374819 original size:18 final size:19
Alignment explanation
Indices: 3374793--3374828 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3374783 GAGGAAGAAG
*
3374793 AAGACAAGAA-AAAAGCAA
1 AAGAAAAGAAGAAAAGCAA
3374811 AAGAAAAGAAGAAAAGCA
1 AAGAAAAGAAGAAAAGCA
3374829 TGGCCTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.72, C:0.08, G:0.19, T:0.00
Consensus pattern (19 bp):
AAGAAAAGAAGAAAAGCAA
Found at i:3388706 original size:36 final size:37
Alignment explanation
Indices: 3388646--3388715 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
3388636 AATGCATGCG
* * * *
3388646 ATAGATTTATTTTATGCCATTTAATGAATGCTATCGA
1 ATAGATTTATTTTATGACAATTAATAAATACTATCGA
3388683 ATAGATTTATTTTAT-ACAATTAATAAATACTAT
1 ATAGATTTATTTTATGACAATTAATAAATACTAT
3388716 GCATGAAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 14 0.48
37 15 0.52
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.44
Consensus pattern (37 bp):
ATAGATTTATTTTATGACAATTAATAAATACTATCGA
Found at i:3392969 original size:21 final size:21
Alignment explanation
Indices: 3392945--3392988 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3392935 TGCCTTAATT
* *
3392945 TTGAATAAATGTATCTATATA
1 TTGAAGAAATGTATCAATATA
* *
3392966 TTGAGGCAATGTATCAATATA
1 TTGAAGAAATGTATCAATATA
3392987 TT
1 TT
3392989 TTGGGCAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.41
Consensus pattern (21 bp):
TTGAAGAAATGTATCAATATA
Found at i:3396663 original size:21 final size:20
Alignment explanation
Indices: 3396622--3396677 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
3396612 TTGATTTATG
3396622 AAATTGAATTAATTAATTTA
1 AAATTGAATTAATTAATTTA
* *
3396642 AAATTGAATATGATTCATTT-
1 AAATTGAAT-TAATTAATTTA
*
3396662 AAATT-ATTTAATTAAT
1 AAATTGAATTAATTAAT
3396678 AAAATTATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 6 0.20
19 2 0.07
20 14 0.47
21 8 0.27
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (20 bp):
AAATTGAATTAATTAATTTA
Found at i:3397382 original size:14 final size:13
Alignment explanation
Indices: 3397363--3397392 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
3397353 ATTATTAAAT
3397363 AAAAAATTATTTTA
1 AAAAAATTA-TTTA
3397377 AAAAAATTATTTA
1 AAAAAATTATTTA
3397390 AAA
1 AAA
3397393 TATATATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AAAAAATTATTTA
Found at i:3397722 original size:21 final size:20
Alignment explanation
Indices: 3397690--3397729 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3397680 TGACTAATTA
*
3397690 TACTATTGATTAATAAAAGT
1 TACTATTAATTAATAAAAGT
*
3397710 TACTCATTAATTACTAAAAG
1 TACT-ATTAATTAATAAAAG
3397730 GTTATTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (20 bp):
TACTATTAATTAATAAAAGT
Found at i:3406493 original size:38 final size:38
Alignment explanation
Indices: 3406404--3406546 Score: 148
Period size: 38 Copynumber: 3.8 Consensus size: 38
3406394 ATACAAGGAC
* * ***
3406404 AATGGTATGATCCCCACTATTTA-GACAATTCACAAAT
1 AATGGTATGATCCCCACTATCTAGGACATTTCATGGAT
* *
3406441 AATGGTAAGGTCCCCACTATCTAGGACATTTCATGGAT
1 AATGGTATGATCCCCACTATCTAGGACATTTCATGGAT
* *
3406479 AATGGTATGATCCCCATTATCTAAGG-CATTTCTTGGAT
1 AATGGTATGATCCCCACTATCT-AGGACATTTCATGGAT
* *
3406517 AATGGTA-CATTCCCCGCTATCTAGGACATT
1 AATGGTATGA-TCCCCACTATCTAGGACATT
3406547 AAATAGAGTG
Statistics
Matches: 88, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
37 24 0.27
38 61 0.69
39 3 0.03
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (38 bp):
AATGGTATGATCCCCACTATCTAGGACATTTCATGGAT
Found at i:3410382 original size:19 final size:17
Alignment explanation
Indices: 3410370--3410408 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
3410360 TTTTTGTTGA
3410370 TTAATTTAGTTTTTATT
1 TTAATTTAGTTTTTATT
3410387 TTAA-TTAGTTTTT-TT
1 TTAATTTAGTTTTTATT
*
3410402 TCAATTT
1 TTAATTT
3410409 TTTGATTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 5 0.25
16 11 0.55
17 4 0.20
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (17 bp):
TTAATTTAGTTTTTATT
Found at i:3413780 original size:50 final size:50
Alignment explanation
Indices: 3413709--3413837 Score: 131
Period size: 50 Copynumber: 2.6 Consensus size: 50
3413699 GCTTCTTATC
* * *
3413709 AAAAAGGAA-AATCCTTGGTGGATTGTGTGGGTT-TTCGCTTGAT-CT-CG
1 AAAAAGCAAGAATCCTTTGTGGATTGTGTGGGTTATT-GCTTGATCCTATG
***
3413756 TAAAAAGCAAGAATTCCTTTGTGGATTGAAAGGGTTATTGCTTGATCCTATG
1 -AAAAAGCAAGAA-TCCTTTGTGGATTGTGTGGGTTATTGCTTGATCCTATG
*
3413808 AAAAAGCAAGAATCTCGTTGTGGATTGTGT
1 AAAAAGCAAGAATC-CTTTGTGGATTGTGT
3413838 AAGGTTTATC
Statistics
Matches: 65, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
48 8 0.12
49 2 0.03
50 27 0.42
51 27 0.42
52 1 0.02
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (50 bp):
AAAAAGCAAGAATCCTTTGTGGATTGTGTGGGTTATTGCTTGATCCTATG
Found at i:3414906 original size:11 final size:12
Alignment explanation
Indices: 3414890--3414933 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 12
3414880 TTTTATTCTA
3414890 TTTTCTTCAT-T
1 TTTTCTTCATCT
*
3414901 TTTTCTTCTTCT
1 TTTTCTTCATCT
3414913 TTTTCTT-ATCT
1 TTTTCTTCATCT
3414924 TTTTCATTCA
1 TTTTC-TTCA
3414934 CAATTTAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 17 0.61
12 10 0.36
13 1 0.04
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTCTTCATCT
Found at i:3418712 original size:21 final size:22
Alignment explanation
Indices: 3418687--3418730 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
3418677 AAGTGATTAA
3418687 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
*
3418708 TTTAAGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
3418730 T
1 T
3418731 ACTTTAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:3421494 original size:123 final size:123
Alignment explanation
Indices: 3421275--3421521 Score: 363
Period size: 123 Copynumber: 2.0 Consensus size: 123
3421265 ATTCTAGGTT
* * * * *
3421275 AGCTAAAAGACCTTGCATGGAAGATAAGATTCATTTTAATCAGTTACAAACTTTCCTTATCAATT
1 AGCTAAAAGACCTTACATGGAAGATAAGATTCATTCTAATCAGTTACAAACATCCCTAATCAATT
* *
3421340 AAATCAATTCTGTGATATTGGAGTTAACCTGAGTCAGTGAGGTAACAATCAGTTAGCA
66 AAATCAATTCTGTGATATAGGAGCTAACCTGAGTCAGTGAGGTAACAATCAGTTAGCA
*
3421398 AGCTAAAAGACCTTACATGGAAGAT-AGTATTCATTCTAATCAGTTA-AGAGCATCCCTAATCAA
1 AGCTAAAAGACCTTACATGGAAGATAAG-ATTCATTCTAATCAGTTACA-AACATCCCTAATCAA
* * *
3421461 TTAAATCAATTTTGTGTTATAGGAGCTAACCTGAGTTAGTGAGGTAACAATCAGTTAGCA
64 TTAAATCAATTCTGTGATATAGGAGCTAACCTGAGTCAGTGAGGTAACAATCAGTTAGCA
3421521 A
1 A
3421522 CTCCCTTAAT
Statistics
Matches: 111, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
122 3 0.03
123 108 0.97
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.31
Consensus pattern (123 bp):
AGCTAAAAGACCTTACATGGAAGATAAGATTCATTCTAATCAGTTACAAACATCCCTAATCAATT
AAATCAATTCTGTGATATAGGAGCTAACCTGAGTCAGTGAGGTAACAATCAGTTAGCA
Found at i:3425668 original size:15 final size:15
Alignment explanation
Indices: 3425648--3425733 Score: 52
Period size: 15 Copynumber: 5.5 Consensus size: 15
3425638 TTTTATTATT
3425648 TTTAGTTATTTTTTA
1 TTTAGTTATTTTTTA
3425663 TTTAGTT-TATTTTTA
1 TTTAGTTAT-TTTTTA
* * *
3425678 TTAAGTTA-ATTTAA
1 TTTAGTTATTTTTTA
3425692 TTTTATGTTTATTTATCTTAA
1 -TTTA-G-TTATTT-T-TT-A
*
3425713 TTTAGTTATTATTTA
1 TTTAGTTATTTTTTA
3425728 -TTAGTT
1 TTTAGTT
3425734 TTTATATTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 19
0.68 0.09 0.23
Matches are distributed among these distances:
14 11 0.20
15 23 0.42
16 3 0.05
17 4 0.07
18 6 0.11
19 2 0.04
20 5 0.09
21 1 0.02
ACGTcount: A:0.26, C:0.01, G:0.07, T:0.66
Consensus pattern (15 bp):
TTTAGTTATTTTTTA
Found at i:3453764 original size:16 final size:17
Alignment explanation
Indices: 3453727--3453764 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3453717 TCTAAAATCA
*
3453727 AAATTGAATAACTAATT
1 AAATTGAATAACTAACT
*
3453744 AAATTGAA-AATTAACT
1 AAATTGAATAACTAACT
3453760 AAATT
1 AAATT
3453765 TAATTTACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (17 bp):
AAATTGAATAACTAACT
Found at i:3457259 original size:30 final size:30
Alignment explanation
Indices: 3457223--3457288 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
3457213 CTAAACAAAC
3457223 TTTGGAAAGGGAGTTTAGTGTAGACTAAAA
1 TTTGGAAAGGGAGTTTAGTGTAGACTAAAA
3457253 TTTGGAAAGGGAGTTTAGTGTAGACTAAAA
1 TTTGGAAAGGGAGTTTAGTGTAGACTAAAA
3457283 TTTGGA
1 TTTGGA
3457289 TAGCATATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.32
Consensus pattern (30 bp):
TTTGGAAAGGGAGTTTAGTGTAGACTAAAA
Found at i:3474625 original size:33 final size:32
Alignment explanation
Indices: 3474520--3474630 Score: 132
Period size: 32 Copynumber: 3.4 Consensus size: 32
3474510 AACCACAATG
** *
3474520 ACTTGATCTTGAATTCACTTCAAGGGTCTACG
1 ACTTGATCTTGAATTTGCTTCAAGGGTCTACA
* * *
3474552 ACTTGATTTTGAAGTTGATTCAAGGGTCTACA
1 ACTTGATCTTGAATTTGCTTCAAGGGTCTACA
* *
3474584 ACTTGATCTTGAATTTGCTTCAAGGGTTTTGCA
1 ACTTGATCTTGAATTTGCTTCAAGGG-TCTACA
*
3474617 ACTCGATCTTGAAT
1 ACTTGATCTTGAAT
3474631 GAATATGTTT
Statistics
Matches: 66, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
32 49 0.74
33 17 0.26
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (32 bp):
ACTTGATCTTGAATTTGCTTCAAGGGTCTACA
Found at i:3474965 original size:48 final size:48
Alignment explanation
Indices: 3474877--3474981 Score: 140
Period size: 48 Copynumber: 2.2 Consensus size: 48
3474867 AATTGTAAAT
* * * *
3474877 TGGAAATCTAGAA-AGGCTTTGGTCTTAATATCTTCTTTCTTAGATATG
1 TGGAACTCTA-AAGAGGCTTTAGTCTTAAGATCTTCCTTCTTAGATATG
* *
3474925 TGTAACTCTAAAGAGGCTTTAGTCTTCAGATCTTCCTTCTTAGATATG
1 TGGAACTCTAAAGAGGCTTTAGTCTTAAGATCTTCCTTCTTAGATATG
3474973 TGGAACTCT
1 TGGAACTCT
3474982 TGAGGTTTTG
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
47 2 0.04
48 47 0.96
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (48 bp):
TGGAACTCTAAAGAGGCTTTAGTCTTAAGATCTTCCTTCTTAGATATG
Found at i:3475038 original size:46 final size:47
Alignment explanation
Indices: 3474890--3475044 Score: 154
Period size: 46 Copynumber: 3.3 Consensus size: 47
3474880 AAATCTAGAA
* * * * * *
3474890 AGGCTTTGGTCTTAATATCTTCTTTCTTAGATATGTGTAACTCTAAAG
1 AGGCTTTGATCTTCAGATCTTCCTTCTTAGATATGTGGAACTCT-TAG
3474938 AGGCTTT-AGTCTTCAGATCTTCCTTCTTAGATATGTGGAACTCTT-G
1 AGGCTTTGA-TCTTCAGATCTTCCTTCTTAGATATGTGGAACTCTTAG
* * * * * *
3474984 AGGTTTTGATCTTCAGATTTTCTTTCTTGGATTTGTGGAA-TTTTAG
1 AGGCTTTGATCTTCAGATCTTCCTTCTTAGATATGTGGAACTCTTAG
*
3475030 AGGCTTTGATGTTCA
1 AGGCTTTGATCTTCA
3475045 ACATCTTTTT
Statistics
Matches: 90, Mismatches: 14, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
45 3 0.03
46 48 0.53
47 1 0.01
48 38 0.42
ACGTcount: A:0.21, C:0.14, G:0.20, T:0.45
Consensus pattern (47 bp):
AGGCTTTGATCTTCAGATCTTCCTTCTTAGATATGTGGAACTCTTAG
Found at i:3493183 original size:21 final size:20
Alignment explanation
Indices: 3493159--3493198 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3493149 AAAAGTTTCA
*
3493159 AAATTACTTGGATGAGTTTTG
1 AAATTACTTGAATGA-TTTTG
*
3493180 AAATTGCTTGAATGATTTT
1 AAATTACTTGAATGATTTT
3493199 CAACTTGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (20 bp):
AAATTACTTGAATGATTTTG
Found at i:3493224 original size:21 final size:21
Alignment explanation
Indices: 3493173--3493226 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
3493163 TACTTGGATG
* *
3493173 AGTTTTGAAA-TTGCTTGAAT
1 AGTTTTTAAACTTGATTGAAT
* *
3493193 -GATTTTCAACTTGATTGAAT
1 AGTTTTTAAACTTGATTGAAT
3493213 AGTTTTTAAACTTG
1 AGTTTTTAAACTTG
3493227 TTTAAATAAG
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
19 6 0.23
20 9 0.35
21 11 0.42
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (21 bp):
AGTTTTTAAACTTGATTGAAT
Found at i:3493234 original size:21 final size:21
Alignment explanation
Indices: 3493195--3493234 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3493185 GCTTGAATGA
* *
3493195 TTTTCAACTTGATTGAATAGT
1 TTTTAAACTTGATTAAATAGT
*
3493216 TTTTAAACTTGTTTAAATA
1 TTTTAAACTTGATTAAATA
3493235 AGTTCTAGCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (21 bp):
TTTTAAACTTGATTAAATAGT
Found at i:3494683 original size:21 final size:22
Alignment explanation
Indices: 3494643--3494687 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
3494633 TCAGCCCATG
3494643 AAAGAAAACTAAAGAGAAAAGA
1 AAAGAAAACTAAAGAGAAAAGA
3494665 AAAGAAAA-TAATAGA-AAAAGA
1 AAAGAAAACTAA-AGAGAAAAGA
3494686 AA
1 AA
3494688 GTAACCTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.76, C:0.02, G:0.16, T:0.07
Consensus pattern (22 bp):
AAAGAAAACTAAAGAGAAAAGA
Found at i:3494800 original size:8 final size:8
Alignment explanation
Indices: 3494787--3494841 Score: 55
Period size: 8 Copynumber: 7.2 Consensus size: 8
3494777 AAGTGAGAAG
3494787 AGAAAGGA
1 AGAAAGGA
*
3494795 AGAAAGTA
1 AGAAAGGA
3494803 AGAAAGGA
1 AGAAAGGA
3494811 AGAAA-GA
1 AGAAAGGA
*
3494818 AGGAA-GA
1 AGAAAGGA
3494825 AGAGAA-G-
1 AGA-AAGGA
3494832 AGAAAGGA
1 AGAAAGGA
3494840 AG
1 AG
3494842 GTTTGGCCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
6 2 0.05
7 14 0.35
8 24 0.60
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02
Consensus pattern (8 bp):
AGAAAGGA
Found at i:3494808 original size:16 final size:15
Alignment explanation
Indices: 3494787--3494841 Score: 69
Period size: 16 Copynumber: 3.7 Consensus size: 15
3494777 AAGTGAGAAG
3494787 AGAAAGGAAGAAAGTA
1 AGAAAGGAAGAAAG-A
3494803 AGAAAGGAAGAAAGA
1 AGAAAGGAAGAAAGA
*
3494818 AGGAA-GAAGAGAAG-
1 AGAAAGGAAGA-AAGA
3494832 AGAAAGGAAG
1 AGAAAGGAAG
3494842 GTTTGGCCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
14 9 0.26
15 12 0.34
16 14 0.40
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02
Consensus pattern (15 bp):
AGAAAGGAAGAAAGA
Found at i:3497874 original size:12 final size:12
Alignment explanation
Indices: 3497853--3497887 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
3497843 TATTTTTCAT
3497853 ATTG-TTTATTC
1 ATTGATTTATTC
3497864 ATTGATTTATTC
1 ATTGATTTATTC
*
3497876 ATTAATTTATTC
1 ATTGATTTATTC
3497888 TTGGCCCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 4 0.18
12 18 0.82
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.60
Consensus pattern (12 bp):
ATTGATTTATTC
Found at i:3501916 original size:20 final size:20
Alignment explanation
Indices: 3501869--3501917 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
3501859 TACTCATAAT
*
3501869 TGTGAAGATATATAAAAATA
1 TGTGAAGTTATATAAAAATA
3501889 TGTGAAGTTATATAAAAATA
1 TGTGAAGTTATATAAAAATA
3501909 TGTGAAGTT
1 TGTGAAGTT
3501918 TAACTATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (20 bp):
TGTGAAGTTATATAAAAATA
Found at i:3507169 original size:96 final size:96
Alignment explanation
Indices: 3507005--3507197 Score: 377
Period size: 96 Copynumber: 2.0 Consensus size: 96
3506995 GAGATAATCG
3507005 TTTAAATCAAGTATCAAAACCAATACAAGTAAAGATTTTCACCGTCAAAATCATTTAATAACTTT
1 TTTAAATCAAGTATCAAAACCAATACAAGTAAAGATTTTCACCGTCAAAATCATTTAATAACTTT
3507070 TCTCAAATCAAATCAGTATAAACACGCATGC
66 TCTCAAATCAAATCAGTATAAACACGCATGC
3507101 TTTAAATCAAGTATCAAAACCAATACAAGTAAAGATTTTCACCGTCAAAATCATTTAATAACTTT
1 TTTAAATCAAGTATCAAAACCAATACAAGTAAAGATTTTCACCGTCAAAATCATTTAATAACTTT
*
3507166 TCTCAAATCAAATCAGTATAAACATGCATGC
66 TCTCAAATCAAATCAGTATAAACACGCATGC
3507197 T
1 T
3507198 CCCATAAAAT
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 96 1.00
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.30
Consensus pattern (96 bp):
TTTAAATCAAGTATCAAAACCAATACAAGTAAAGATTTTCACCGTCAAAATCATTTAATAACTTT
TCTCAAATCAAATCAGTATAAACACGCATGC
Found at i:3508873 original size:14 final size:14
Alignment explanation
Indices: 3508840--3508882 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
3508830 CCTCCAAGCC
*
3508840 TTTTTCTTCCTTCT
1 TTTTTCTTCTTTCT
*
3508854 TTTTTCTTTTTTCT
1 TTTTTCTTCTTTCT
* *
3508868 TCTTTCTCCTTTCT
1 TTTTTCTTCTTTCT
3508882 T
1 T
3508883 CCCTCTTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTCTTCTTTCT
Found at i:3508880 original size:21 final size:21
Alignment explanation
Indices: 3508840--3508882 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3508830 CCTCCAAGCC
**
3508840 TTTTTCTTCCTTCTTTTTTCT
1 TTTTTCTTCCTTCTCCTTTCT
*
3508861 TTTTTCTTCTTTCTCCTTTCT
1 TTTTTCTTCCTTCTCCTTTCT
3508882 T
1 T
3508883 CCCTCTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTTCTTCCTTCTCCTTTCT
Found at i:3509887 original size:17 final size:18
Alignment explanation
Indices: 3509865--3509905 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3509855 AAAATATTAA
3509865 TATTTTA-TTAAAAATAT
1 TATTTTACTTAAAAATAT
*
3509882 TATTTTACTTTAAAATAT
1 TATTTTACTTAAAAATAT
*
3509900 TCTTTT
1 TATTTT
3509906 CACCCATCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTTTACTTAAAAATAT
Found at i:3531786 original size:33 final size:33
Alignment explanation
Indices: 3531749--3531826 Score: 102
Period size: 33 Copynumber: 2.4 Consensus size: 33
3531739 TGTGTAATGC
3531749 TGATGTGATATGCTAACATATCATAATTGATAA
1 TGATGTGATATGCTAACATATCATAATTGATAA
** * * *
3531782 TGATGTGGCATACTAATATATCATAATTGATGA
1 TGATGTGATATGCTAACATATCATAATTGATAA
*
3531815 TAATGTGATATG
1 TGATGTGATATG
3531827 ATAATATGAC
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (33 bp):
TGATGTGATATGCTAACATATCATAATTGATAA
Found at i:3535211 original size:37 final size:38
Alignment explanation
Indices: 3535151--3535234 Score: 102
Period size: 37 Copynumber: 2.2 Consensus size: 38
3535141 TTTTAGGAAA
* * *
3535151 AAGCACAACCTTTACACCTAAATGCCTT-TCAAGGAT-C
1 AAGCACAACCTTTAAAACTAAATGCCTTCT-AAGAATCC
3535188 AAGCACAACCTTTATAAAC-AAATGCCTTCTAAGAATCC
1 AAGCACAACCTTTA-AAACTAAATGCCTTCTAAGAATCC
3535226 AAGCACAAC
1 AAGCACAAC
3535235 TTTTCTACCT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
37 28 0.68
38 13 0.32
ACGTcount: A:0.40, C:0.29, G:0.10, T:0.21
Consensus pattern (38 bp):
AAGCACAACCTTTAAAACTAAATGCCTTCTAAGAATCC
Found at i:3536482 original size:35 final size:34
Alignment explanation
Indices: 3536424--3536526 Score: 111
Period size: 35 Copynumber: 3.0 Consensus size: 34
3536414 AGATTCTTGC
* * *
3536424 TTTTTAACGGGATCAAACGATAA-CTTTACACTA
1 TTTTTAATGGGATCAAGCAATAACCTTTACACTA
* *
3536457 GTTTTTCCAA-GGGATCAAGCAATAACCCTTACATTTA
1 -TTTTT--AATGGGATCAAGCAATAACCTTTACA-CTA
3536494 TTTTTAATGGGATCAAGCAATAACCTTTACACT
1 TTTTTAATGGGATCAAGCAATAACCTTTACACT
3536527 TGCTATTTCA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
34 8 0.14
35 35 0.60
36 13 0.22
37 2 0.03
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (34 bp):
TTTTTAATGGGATCAAGCAATAACCTTTACACTA
Found at i:3536553 original size:71 final size:70
Alignment explanation
Indices: 3536424--3536556 Score: 169
Period size: 71 Copynumber: 1.9 Consensus size: 70
3536414 AGATTCTTGC
* *
3536424 TTTTTAACGGGATCAAACGATAACTTTACACTAGTTTTTCCAAGGGATCAAGCAATAACCCTTAC
1 TTTTTAACGGGATCAAACAATAACTTTACACTAGTATTTCCAAGGGATCAAGCAATAACCCTTAC
3536489 ATTTA
66 ATTTA
* * * * **
3536494 TTTTTAATGGGATCAAGCAATAACCTTTACACTTGCTATTT-CATGGGATCAAGTGATAACCCT
1 TTTTTAACGGGATCAAACAATAA-CTTTACACTAG-TATTTCCAAGGGATCAAGCAATAACCCT
3536557 AATATCGACT
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
70 20 0.38
71 29 0.55
72 4 0.08
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (70 bp):
TTTTTAACGGGATCAAACAATAACTTTACACTAGTATTTCCAAGGGATCAAGCAATAACCCTTAC
ATTTA
Found at i:3538129 original size:13 final size:13
Alignment explanation
Indices: 3538113--3538156 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
3538103 CAAATCGGGT
3538113 TTTCAAATGCTCA
1 TTTCAAATGCTCA
3538126 TTTCAAA--C-CA
1 TTTCAAATGCTCA
3538136 TTTTCAAATGCTCA
1 -TTTCAAATGCTCA
3538150 TTTCAAA
1 TTTCAAA
3538157 CCATTTTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
10 2 0.07
11 8 0.30
13 15 0.56
14 2 0.07
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.39
Consensus pattern (13 bp):
TTTCAAATGCTCA
Found at i:3538140 original size:24 final size:24
Alignment explanation
Indices: 3538112--3538167 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
3538102 TCAAATCGGG
3538112 TTTTCAAATGCTCATTTCAAACCA
1 TTTTCAAATGCTCATTTCAAACCA
3538136 TTTTCAAATGCTCATTTCAAACCA
1 TTTTCAAATGCTCATTTCAAACCA
3538160 TTTTCAAA
1 TTTTCAAA
3538168 ATACAGATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.39
Consensus pattern (24 bp):
TTTTCAAATGCTCATTTCAAACCA
Found at i:3538142 original size:11 final size:11
Alignment explanation
Indices: 3538126--3538167 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
3538116 CAAATGCTCA
3538126 TTTCAAACCAT
1 TTTCAAACCAT
3538137 TTTCAAATGCTCA-
1 TTTCAAA--C-CAT
3538150 TTTCAAACCAT
1 TTTCAAACCAT
3538161 TTTCAAA
1 TTTCAAA
3538168 ATACAGATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
10 2 0.07
11 15 0.56
13 8 0.30
14 2 0.07
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (11 bp):
TTTCAAACCAT
Found at i:3539268 original size:14 final size:15
Alignment explanation
Indices: 3539249--3539287 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
3539239 CTTTTCTTCA
3539249 TTTCTCTTCTTTCT-
1 TTTCTCTTCTTTCTC
*
3539263 TTTCTCTCCTTTCTC
1 TTTCTCTTCTTTCTC
3539278 TTT-TCTTCTT
1 TTTCTCTTCTT
3539288 GGTAGTGGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 19 0.86
15 3 0.14
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTCTCTTCTTTCTC
Found at i:3539284 original size:21 final size:22
Alignment explanation
Indices: 3539222--3539284 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 22
3539212 CTTCCTCCTG
*
3539222 TCTC-CCTTTCTCTCCTTCTTT
1 TCTCTCCTTTCTCTCTTTCTTT
*
3539243 TCT-TCATTTCTCTTCTTTCTTT
1 TCTCTCCTTTCTC-TCTTTCTTT
3539265 TCTCTCCTTTCTCT-TTTCTT
1 TCTCTCCTTTCTCTCTTTCTT
3539285 CTTGGTAGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
21 16 0.44
22 12 0.33
23 8 0.22
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (22 bp):
TCTCTCCTTTCTCTCTTTCTTT
Found at i:3553566 original size:21 final size:22
Alignment explanation
Indices: 3553528--3553574 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
3553518 TAACTACTCT
3553528 TAAAATTTAAAATAAAATAACC
1 TAAAATTTAAAATAAAATAACC
* *
3553550 TAAAATTT-AACTAAAATAACT
1 TAAAATTTAAAATAAAATAACC
3553571 TAAA
1 TAAA
3553575 TTAATCACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAATTTAAAATAAAATAACC
Found at i:3559841 original size:24 final size:25
Alignment explanation
Indices: 3559796--3559851 Score: 87
Period size: 24 Copynumber: 2.2 Consensus size: 25
3559786 CCTTAGTTGT
*
3559796 GGATTGTGCTCAGAGGATAAAGATGA
1 GGATTGTGCTCA-AGGATAAAGATAA
3559822 GGATTGTGCTC-AGGATAAAGATAA
1 GGATTGTGCTCAAGGATAAAGATAA
3559846 GGATTG
1 GGATTG
3559852 CTGAGACTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 18 0.62
26 11 0.38
ACGTcount: A:0.34, C:0.07, G:0.34, T:0.25
Consensus pattern (25 bp):
GGATTGTGCTCAAGGATAAAGATAA
Found at i:3583613 original size:22 final size:22
Alignment explanation
Indices: 3583571--3583613 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3583561 CGCTACAACA
* * *
3583571 TCAGACTCCTAATGCTGCAGCG
1 TCAGACTCCCAATCCTACAGCG
3583593 TCAGACTCCCAATCCTACAGC
1 TCAGACTCCCAATCCTACAGC
3583614 ACTATCCTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.37, G:0.16, T:0.21
Consensus pattern (22 bp):
TCAGACTCCCAATCCTACAGCG
Found at i:3588028 original size:24 final size:25
Alignment explanation
Indices: 3587964--3588029 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 25
3587954 TCTAAAATTT
* * * *
3587964 TGTTACACACCCTATTGAAAACAAG
1 TGTTACACACCATGTTCAAAACAAA
* *
3587989 TGGTTACACGCTATGTTCAAAA-AAA
1 T-GTTACACACCATGTTCAAAACAAA
3588014 TGTTACACACCATGTT
1 TGTTACACACCATGTT
3588030 GATAGATTAC
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
24 13 0.41
25 4 0.12
26 15 0.47
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (25 bp):
TGTTACACACCATGTTCAAAACAAA
Found at i:3589338 original size:28 final size:28
Alignment explanation
Indices: 3589306--3589365 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
3589296 TTATGTCAAC
3589306 AAAGAAATCACTTGACTTCAAAAAGAGA
1 AAAGAAATCACTTGACTTCAAAAAGAGA
* *
3589334 AAAGAAATCACTTGACTTTAAAAGGAGA
1 AAAGAAATCACTTGACTTCAAAAAGAGA
3589362 AAAG
1 AAAG
3589366 CAATTTCAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.53, C:0.12, G:0.17, T:0.18
Consensus pattern (28 bp):
AAAGAAATCACTTGACTTCAAAAAGAGA
Found at i:3603877 original size:12 final size:12
Alignment explanation
Indices: 3603860--3603888 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3603850 CTTAACAACT
3603860 CAAGTAGCTGCA
1 CAAGTAGCTGCA
3603872 CAAGTAGCTGCA
1 CAAGTAGCTGCA
3603884 CAAGT
1 CAAGT
3603889 GGCTACACTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.17
Consensus pattern (12 bp):
CAAGTAGCTGCA
Found at i:3604193 original size:21 final size:21
Alignment explanation
Indices: 3604169--3604213 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
3604159 AGTTTTATTG
*
3604169 ATATAGCAAGTGATATAGAGC
1 ATATACCAAGTGATATAGAGC
3604190 ATATACCAAGTGATATAGAGC
1 ATATACCAAGTGATATAGAGC
3604211 ATA
1 ATA
3604214 AATGAGAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.24
Consensus pattern (21 bp):
ATATACCAAGTGATATAGAGC
Found at i:3610629 original size:71 final size:70
Alignment explanation
Indices: 3610507--3610640 Score: 169
Period size: 71 Copynumber: 1.9 Consensus size: 70
3610497 AAACAAGGCA
* * *
3610507 TGTAACTTGATCTCTATTTTTTACTTCACTAAGACATAAACTTTTGGAGTTAAACAACTTAAACA
1 TGTAACTTGATCTCTATTTTATACTTCACTAAGACATAAACTCTTAGAGTTAAACAACTTAAACA
3610572 TAACG
66 TAACG
* * * * * * *
3610577 TGTAACTTGGTCTTTATCTTTATATTTCACTAAGACATTATCTCTTATAGTTAAACACCTTAAA
1 TGTAACTTGATCTCTAT-TTTATACTTCACTAAGACATAAACTCTTAGAGTTAAACAACTTAAA
3610641 TATGGCGTAT
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
70 15 0.28
71 38 0.72
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (70 bp):
TGTAACTTGATCTCTATTTTATACTTCACTAAGACATAAACTCTTAGAGTTAAACAACTTAAACA
TAACG
Found at i:3610799 original size:27 final size:27
Alignment explanation
Indices: 3610768--3610837 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 27
3610758 TAAACACCTT
3610768 AAACATGATGTGTAACAACTTTTTTTTC
1 AAACATGATGTGTAACAA-TTTTTTTTC
*
3610796 -AACAT-ATCATGTAACAATTTTTTTTC
1 AAACATGAT-GTGTAACAATTTTTTTTC
3610822 AAACATAGA-GTGTAAC
1 AAACAT-GATGTGTAAC
3610838 CTGGACTCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
26 11 0.31
27 24 0.67
29 1 0.03
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (27 bp):
AAACATGATGTGTAACAATTTTTTTTC
Found at i:3615508 original size:30 final size:29
Alignment explanation
Indices: 3615441--3615511 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 29
3615431 CCAGGGGACC
*
3615441 ATCGATGCTCCCCTCCCTTGGGAGCACCG
1 ATCGGTGCTCCCCTCCCTTGGGAGCACCG
* * *
3615470 ATCTGGTGCTGCCCTCCTTTGGTGAGCATCG
1 ATC-GGTGCTCCCCTCCCTTGG-GAGCACCG
3615501 ATCGGTGCTCC
1 ATCGGTGCTCC
3615512 TCCGATCAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 3 0.09
30 22 0.63
31 10 0.29
ACGTcount: A:0.11, C:0.35, G:0.27, T:0.27
Consensus pattern (29 bp):
ATCGGTGCTCCCCTCCCTTGGGAGCACCG
Found at i:3617953 original size:17 final size:17
Alignment explanation
Indices: 3617931--3617971 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3617921 TTGCCAAAGC
*
3617931 AATAAAGT-AAGACTGAG
1 AATAAAGTGAACACT-AG
3617948 AATAAA-TGAACACTAG
1 AATAAAGTGAACACTAG
3617964 AATAAAGT
1 AATAAAGT
3617972 TGAGAATAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.56, C:0.07, G:0.17, T:0.20
Consensus pattern (17 bp):
AATAAAGTGAACACTAG
Found at i:3619500 original size:62 final size:62
Alignment explanation
Indices: 3619424--3619556 Score: 221
Period size: 62 Copynumber: 2.1 Consensus size: 62
3619414 AAAATGTATT
* * *
3619424 AATACATGTTCATCATGTATCGATACATGAAACCCAGAAAAGGTTTTTTATGAGCATTTATC
1 AATACATGTTCATCATATATCGATACATGAAACCCAGAAAAGGATTTTTATGAGCATTGATC
* *
3619486 AATACATGTTCATCATATATCGATACGTGAAACCTAGAAAAGGATTTTTATGAGCATTGATC
1 AATACATGTTCATCATATATCGATACATGAAACCCAGAAAAGGATTTTTATGAGCATTGATC
3619548 AATACATGT
1 AATACATGT
3619557 CCCAAATGTA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 66 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (62 bp):
AATACATGTTCATCATATATCGATACATGAAACCCAGAAAAGGATTTTTATGAGCATTGATC
Found at i:3619870 original size:21 final size:21
Alignment explanation
Indices: 3619845--3619896 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 21
3619835 ATTTTCCAAA
3619845 AATTTTGATTTATTAAAAATTC
1 AATTTTGATTT-TTAAAAATTC
*
3619867 -ATTTT-ACTTTTAAAAATTC
1 AATTTTGATTTTTAAAAATTC
3619886 AAGTTTTGATT
1 AA-TTTTGATT
3619897 GATTTTGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 10 0.40
20 4 0.16
21 9 0.36
22 2 0.08
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.52
Consensus pattern (21 bp):
AATTTTGATTTTTAAAAATTC
Found at i:3621213 original size:42 final size:42
Alignment explanation
Indices: 3621142--3621228 Score: 111
Period size: 42 Copynumber: 2.1 Consensus size: 42
3621132 CTTTTAAATG
* * * *
3621142 ATTTGATTACGCTTGGGAAGCAAATTTTGAAAATCTTTGGAA
1 ATTTGATTACACTTGGGAAACAAACTTTGAAAATATTTGGAA
** *
3621184 ATTTGATTACACTTGGGAAATGAACTTTGAGAATATTTGGAA
1 ATTTGATTACACTTGGGAAACAAACTTTGAAAATATTTGGAA
3621226 ATT
1 ATT
3621229 GTTTATTTGC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (42 bp):
ATTTGATTACACTTGGGAAACAAACTTTGAAAATATTTGGAA
Found at i:3625500 original size:5 final size:5
Alignment explanation
Indices: 3625492--3625591 Score: 93
Period size: 5 Copynumber: 20.4 Consensus size: 5
3625482 TTATATTATA
* * *
3625492 TATTT TATTT TAATT TATTT TA-TT TCTTT TATTT TAATTT TAATTT T-TTA
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT T-ATTT T-ATTT TATTT
* *
3625542 TATTT TATTT TATTT TATTT T-TTAT T-TTT TATAT TA-TA TATTT TATTT
1 TATTT TATTT TATTT TATTT TATT-T TATTT TATTT TATTT TATTT TATTT
3625590 TA
1 TA
3625592 ATATTTTTAT
Statistics
Matches: 79, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
4 12 0.15
5 56 0.71
6 11 0.14
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.75
Consensus pattern (5 bp):
TATTT
Found at i:3625572 original size:50 final size:51
Alignment explanation
Indices: 3625480--3625603 Score: 139
Period size: 50 Copynumber: 2.4 Consensus size: 51
3625470 TAATATAGTT
*
3625480 TTTTATATTATATATTTTATTTTAATTTATTTTATTTCTTTTAT-TT-TA-A
1 TTTTAT-TTTTATATTTTATTTTAATTTATTTTATTTCTTTTATATTATATA
* *
3625529 TTTTAATTTTTTATATTTTATTTTATTTTATTTT-TTATTTTTTATATTATATA
1 TTTT-A-TTTTTATATTTTATTTTAATTTATTTTATT-TCTTTTATATTATATA
*
3625582 TTTTATTTTAATATTTTTATTT
1 TTTTATTTTTATA-TTTTATTT
3625604 NNNNNNNNNN
Statistics
Matches: 64, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
49 6 0.09
50 32 0.50
51 10 0.16
52 11 0.17
53 5 0.08
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.74
Consensus pattern (51 bp):
TTTTATTTTTATATTTTATTTTAATTTATTTTATTTCTTTTATATTATATA
Found at i:3625603 original size:14 final size:14
Alignment explanation
Indices: 3625479--3625603 Score: 76
Period size: 14 Copynumber: 8.6 Consensus size: 14
3625469 TTAATATAGT
*
3625479 TTTTTATATT-ATA
1 TTTTTATTTTAATA
*
3625492 TATTTTATTTTAATT
1 T-TTTTATTTTAATA
**
3625507 TATTTTATTTCTTTTA
1 T-TTTTATTT-TAATA
* *
3625523 TTTTAATTTTAATT
1 TTTTTATTTTAATA
* *
3625537 TTTTATATTTTATTT
1 TTTT-TATTTTAATA
*
3625552 TATTTTATTTT-TTA
1 T-TTTTATTTTAATA
*
3625566 TTTTTTATATT-ATA
1 -TTTTTATTTTAATA
3625580 TATTTTATTTTAATA
1 T-TTTTATTTTAATA
3625595 TTTTTATTT
1 TTTTTATTT
3625604 NNNNNNNNNN
Statistics
Matches: 89, Mismatches: 15, Indels: 15
0.75 0.13 0.13
Matches are distributed among these distances:
13 2 0.02
14 42 0.47
15 39 0.44
16 6 0.07
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTATTTTAATA
Found at i:3631334 original size:26 final size:26
Alignment explanation
Indices: 3631299--3631366 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
3631289 GTGTCCGTCA
* *
3631299 ACTTTTGGTGGTAAAATTATCCATCC
1 ACTTCTGGTGGCAAAATTATCCATCC
*
3631325 ACTTCTGGTGGCAAAATTATCTATCC
1 ACTTCTGGTGGCAAAATTATCCATCC
* *
3631351 CCTTCTGGTGACAAAA
1 ACTTCTGGTGGCAAAA
3631367 CTATTCTAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (26 bp):
ACTTCTGGTGGCAAAATTATCCATCC
Found at i:3636607 original size:25 final size:25
Alignment explanation
Indices: 3636579--3636630 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
3636569 GGGCACAAAC
*
3636579 AACTCAAGCAAAAATCAAATAAATA
1 AACTCAAGCAAAAACCAAATAAATA
* * *
3636604 AACTTAAGGAAAAGCCAAATAAATA
1 AACTCAAGCAAAAACCAAATAAATA
3636629 AA
1 AA
3636631 TAAAATTGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.63, C:0.13, G:0.08, T:0.15
Consensus pattern (25 bp):
AACTCAAGCAAAAACCAAATAAATA
Found at i:3639926 original size:21 final size:21
Alignment explanation
Indices: 3639902--3639942 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3639892 AAAGCTAAAT
3639902 AAATACTAACT-AAACTAAAAG
1 AAAT-CTAACTAAAACTAAAAG
*
3639923 AAATTTAACTAAAACTAAAA
1 AAATCTAACTAAAACTAAAA
3639943 TAAGATAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.63, C:0.12, G:0.02, T:0.22
Consensus pattern (21 bp):
AAATCTAACTAAAACTAAAAG
Found at i:3643891 original size:71 final size:70
Alignment explanation
Indices: 3643807--3643949 Score: 173
Period size: 71 Copynumber: 2.0 Consensus size: 70
3643797 TCTTGATAGT
*** * **
3643807 TTTCATTTTCTTTCTATCTAA-TGAGCTTTGCTTGATCAAGTC-TCAATACTCCAAAGGTGTGTC
1 TTTCATTTTCTTTCTAT-TAATTGAGCTTTGCCCAATCAAGTCTTC-ATACACCAAAGGCATGTC
3643870 TCGATAC
64 TCGATAC
* *
3643877 TTTCTATTTTCTTTCTGTTAATTGAGCTTTGCCCAATCAAGTCTTCATACACCAAGGGCATGTCT
1 TTTC-ATTTTCTTTCTATTAATTGAGCTTTGCCCAATCAAGTCTTCATACACCAAAGGCATGTCT
3643942 CGATAC
65 CGATAC
3643948 TT
1 TT
3643950 GACACTTGAG
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
70 7 0.11
71 53 0.85
72 2 0.03
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.41
Consensus pattern (70 bp):
TTTCATTTTCTTTCTATTAATTGAGCTTTGCCCAATCAAGTCTTCATACACCAAAGGCATGTCTC
GATAC
Found at i:3650963 original size:21 final size:22
Alignment explanation
Indices: 3650939--3650982 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
3650929 AAGTGATTAA
3650939 TTTAACTTATTTTA-GTTAAAT
1 TTTAACTTATTTTATGTTAAAT
** *
3650960 TTTAGGTTATTTTATTTTAAAT
1 TTTAACTTATTTTATGTTAAAT
3650982 T
1 T
3650983 ACTTTAAGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTAACTTATTTTATGTTAAAT
Found at i:3662695 original size:21 final size:21
Alignment explanation
Indices: 3662669--3662710 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3662659 AGCAAATTTA
3662669 ACACTCATACAATTAAGTCAT
1 ACACTCATACAATTAAGTCAT
3662690 ACACTCATACAATTAAGTCAT
1 ACACTCATACAATTAAGTCAT
3662711 TCGAGTTTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.24, G:0.05, T:0.29
Consensus pattern (21 bp):
ACACTCATACAATTAAGTCAT
Found at i:3667875 original size:34 final size:36
Alignment explanation
Indices: 3667810--3667876 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 36
3667800 CCCATAATTT
* *
3667810 TATAATAATTATAATATAATTAATTATATTAAAAAA
1 TATAATAATTATAATATAATTAATAAAATTAAAAAA
*
3667846 TATAATAATTA-AA-ATGATTAATAAAATTAAA
1 TATAATAATTATAATATAATTAATAAAATTAAA
3667877 TATTTACCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 15 0.54
35 2 0.07
36 11 0.39
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (36 bp):
TATAATAATTATAATATAATTAATAAAATTAAAAAA
Found at i:3671236 original size:13 final size:13
Alignment explanation
Indices: 3671218--3671242 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3671208 GAAATTGCGA
3671218 AATGTTGAGAAAG
1 AATGTTGAGAAAG
3671231 AATGTTGAGAAA
1 AATGTTGAGAAA
3671243 AAAGAAAGGT
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:0.00, G:0.28, T:0.24
Consensus pattern (13 bp):
AATGTTGAGAAAG
Found at i:3675134 original size:16 final size:16
Alignment explanation
Indices: 3675115--3675148 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3675105 CTTCTTCCTC
* *
3675115 CTTTCTTCCTTTCTTT
1 CTTTCTCCCATTCTTT
3675131 CTTTCTCCCATTCTTT
1 CTTTCTCCCATTCTTT
3675147 CT
1 CT
3675149 CACTTTGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.35, G:0.00, T:0.62
Consensus pattern (16 bp):
CTTTCTCCCATTCTTT
Found at i:3677115 original size:29 final size:29
Alignment explanation
Indices: 3677062--3677123 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
3677052 ATGAAGTGAT
* * * *
3677062 AACCCATGGTTTTAAATGGGTTCACTACA
1 AACCCATGGTTTTAAACGAGCTCACCACA
*
3677091 AACCCATGGTTTTTAACGAGCTCACCACA
1 AACCCATGGTTTTAAACGAGCTCACCACA
3677120 AACC
1 AACC
3677124 TATAGTAACT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.26
Consensus pattern (29 bp):
AACCCATGGTTTTAAACGAGCTCACCACA
Found at i:3677634 original size:72 final size:72
Alignment explanation
Indices: 3677509--3677663 Score: 211
Period size: 72 Copynumber: 2.2 Consensus size: 72
3677499 GAGAGTTTGT
* *
3677509 ATTTTTTATGTCTAGCTTGGTGTAGTCAACAATGCCTTCATCAAAGTCGACTATGGCTTCTTAAT
1 ATTTTTCAAGTCTAGCTTGGTGTAGTCAACAATGCCTTCATCAAAGTCGACTATGGCTTCTTAAT
3677574 TCTTTAA
66 TCTTTAA
* ** * * * * *
3677581 ATTTTTCAAGTCTGGCTTGGTGTAGTTGACTATGGCTTCATTAAGGTCTACTATGGCTTCTTAAT
1 ATTTTTCAAGTCTAGCTTGGTGTAGTCAACAATGCCTTCATCAAAGTCGACTATGGCTTCTTAAT
3677646 TCTTTAA
66 TCTTTAA
*
3677653 ATTTTGCAAGT
1 ATTTTTCAAGT
3677664 TTTCTACCTC
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.23, C:0.16, G:0.17, T:0.43
Consensus pattern (72 bp):
ATTTTTCAAGTCTAGCTTGGTGTAGTCAACAATGCCTTCATCAAAGTCGACTATGGCTTCTTAAT
TCTTTAA
Found at i:3678663 original size:15 final size:15
Alignment explanation
Indices: 3678643--3678671 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3678633 NNNNNNTATA
3678643 TTTAAATTTAATTTG
1 TTTAAATTTAATTTG
3678658 TTTAAATTTAATTT
1 TTTAAATTTAATTT
3678672 AAACATAATA
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:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
TTTAAATTTAATTTG
Found at i:3679750 original size:36 final size:37
Alignment explanation
Indices: 3679707--3679780 Score: 105
Period size: 36 Copynumber: 2.0 Consensus size: 37
3679697 TTGTATGATT
*
3679707 TTACTTATTTATTAGGCAAAA-TTATAAAAAGCATGA
1 TTACTTATTTATTAGGCAAAAGGTATAAAAAGCATGA
* * *
3679743 TTACTTATTTGTTAGGTAAAAGGTATAAAATGCATGA
1 TTACTTATTTATTAGGCAAAAGGTATAAAAAGCATGA
3679780 T
1 T
3679781 GTAATTGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
36 19 0.58
37 14 0.42
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.38
Consensus pattern (37 bp):
TTACTTATTTATTAGGCAAAAGGTATAAAAAGCATGA
Found at i:3682242 original size:29 final size:29
Alignment explanation
Indices: 3682200--3682258 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
3682190 TTTTAAATCC
3682200 TTTACGTATATAATTCGTATATACATATA
1 TTTACGTATATAATTCGTATATACATATA
* *
3682229 TTTATGTATATAATTCGTATATATATATA
1 TTTACGTATATAATTCGTATATACATATA
3682258 T
1 T
3682259 ATAGTCAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (29 bp):
TTTACGTATATAATTCGTATATACATATA
Found at i:3683871 original size:18 final size:19
Alignment explanation
Indices: 3683831--3683878 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
3683821 NNNNNNNTTT
3683831 AATATTATTTTATTCATAA
1 AATATTATTTTATTCATAA
*
3683850 AATATTATTTTATTTA-AA
1 AATATTATTTTATTCATAA
*
3683868 AATATTCTTTT
1 AATATTATTTT
3683879 CACTCATTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (19 bp):
AATATTATTTTATTCATAA
Found at i:3686054 original size:31 final size:31
Alignment explanation
Indices: 3686016--3686077 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
3686006 TCAGTCTTTC
3686016 TTAAGTATTCCTGTGGATGTTGATGAACCAT
1 TTAAGTATTCCTGTGGATGTTGATGAACCAT
*
3686047 TTAAGTATTCTTGTGGATGTTGATGAACCAT
1 TTAAGTATTCCTGTGGATGTTGATGAACCAT
3686078 CATCCTATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (31 bp):
TTAAGTATTCCTGTGGATGTTGATGAACCAT
Found at i:3698602 original size:27 final size:27
Alignment explanation
Indices: 3698572--3698631 Score: 120
Period size: 27 Copynumber: 2.2 Consensus size: 27
3698562 GAGAGTAAAA
3698572 GAGAATTTAAAGATAAAAGCTCTAGAG
1 GAGAATTTAAAGATAAAAGCTCTAGAG
3698599 GAGAATTTAAAGATAAAAGCTCTAGAG
1 GAGAATTTAAAGATAAAAGCTCTAGAG
3698626 GAGAAT
1 GAGAAT
3698632 GGGTTAGCCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.48, C:0.07, G:0.23, T:0.22
Consensus pattern (27 bp):
GAGAATTTAAAGATAAAAGCTCTAGAG
Found at i:3698899 original size:29 final size:29
Alignment explanation
Indices: 3698834--3698899 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
3698824 AGAAAAGGTA
3698834 TATGTGAAAAGGTACAAGAAAAAAAGCTG
1 TATGTGAAAAGGTACAAGAAAAAAAGCTG
** * *
3698863 TACATGAATAGGTACAAGAGAAGAAAG-TG
1 TATGTGAAAAGGTACAAGA-AAAAAAGCTG
3698892 TATGTGAA
1 TATGTGAA
3698900 CAAGTATATG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
29 24 0.80
30 6 0.20
ACGTcount: A:0.48, C:0.06, G:0.26, T:0.20
Consensus pattern (29 bp):
TATGTGAAAAGGTACAAGAAAAAAAGCTG
Found at i:3699172 original size:35 final size:35
Alignment explanation
Indices: 3699133--3699250 Score: 141
Period size: 35 Copynumber: 3.4 Consensus size: 35
3699123 TTGTTCCATA
* *
3699133 TGAAGTAGAGCTCCACTTATTTTAGTTGTTCTGCG
1 TGAAGTAGAGCTTCACTTGTTTTAGTTGTTCTGCG
* * *
3699168 TGAAGTA-ATGCTTTACTTGTTCTAGTTGTTCTGCA
1 TGAAGTAGA-GCTTCACTTGTTTTAGTTGTTCTGCG
*
3699203 TGAAGTAGCA-CTTCACTTGTTTTAGTTGTTTTGCG
1 TGAAGTAG-AGCTTCACTTGTTTTAGTTGTTCTGCG
*
3699238 TGAAGTAGTGCTT
1 TGAAGTAGAGCTT
3699251 TACTCATTTT
Statistics
Matches: 69, Mismatches: 10, Indels: 8
0.79 0.11 0.09
Matches are distributed among these distances:
34 1 0.01
35 67 0.97
37 1 0.01
ACGTcount: A:0.19, C:0.14, G:0.23, T:0.43
Consensus pattern (35 bp):
TGAAGTAGAGCTTCACTTGTTTTAGTTGTTCTGCG
Found at i:3699186 original size:70 final size:70
Alignment explanation
Indices: 3699111--3699254 Score: 193
Period size: 70 Copynumber: 2.1 Consensus size: 70
3699101 GTAGTTGTTC
*
3699111 TACTTGTAT-TAGTTGTTCCATATGAAGTAG-AGCTCCACTTATTTTAGTTGTTCTGCGTGAAGT
1 TACTTGT-TCTAGTTGTTCCACATGAAGTAGCA-CTCCACTTATTTTAGTTGTTCTGCGTGAAGT
3699174 AATGCTT
64 AATGCTT
** * * * *
3699181 TACTTGTTCTAGTTGTTCTGCATGAAGTAGCACTTCACTTGTTTTAGTTGTTTTGCGTGAAGTAG
1 TACTTGTTCTAGTTGTTCCACATGAAGTAGCACTCCACTTATTTTAGTTGTTCTGCGTGAAGTAA
3699246 TGCTT
66 TGCTT
3699251 TACT
1 TACT
3699255 CATTTTGCTT
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
69 1 0.02
70 63 0.97
71 1 0.02
ACGTcount: A:0.20, C:0.15, G:0.21, T:0.44
Consensus pattern (70 bp):
TACTTGTTCTAGTTGTTCCACATGAAGTAGCACTCCACTTATTTTAGTTGTTCTGCGTGAAGTAA
TGCTT
Found at i:3700415 original size:2 final size:2
Alignment explanation
Indices: 3700408--3700443 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3700398 CAAACTTGTG
3700408 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
3700444 TATTTAATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3702632 original size:16 final size:17
Alignment explanation
Indices: 3702604--3702636 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
3702594 TTTTATTATG
3702604 TTTTCTACATTTTTTTA
1 TTTTCTACATTTTTTTA
3702621 TTTTCT-CATTTTTTTA
1 TTTTCTACATTTTTTTA
3702637 AGGAGAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTCTACATTTTTTTA
Found at i:3703029 original size:18 final size:18
Alignment explanation
Indices: 3702957--3703029 Score: 67
Period size: 18 Copynumber: 4.1 Consensus size: 18
3702947 TTATTCGAGA
*
3702957 TGAGGTTGTTCTTGATAT
1 TGAGGTTATTCTTGATAT
* *
3702975 TGAGGTTATT-TCTAACAT
1 TGAGGTTATTCT-TGATAT
* * *
3702993 TAAGGTTATTCCTGCTAT
1 TGAGGTTATTCTTGATAT
*
3703011 TGAGGCTATTCTTGATAT
1 TGAGGTTATTCTTGATAT
3703029 T
1 T
3703030 AGAGTTGATG
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
17 1 0.02
18 40 0.98
ACGTcount: A:0.22, C:0.11, G:0.21, T:0.47
Consensus pattern (18 bp):
TGAGGTTATTCTTGATAT
Found at i:3703820 original size:25 final size:24
Alignment explanation
Indices: 3703773--3703821 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
3703763 TAAGTAAGCA
***
3703773 TAATAGCTATGGCCAATTTATGAG
1 TAATAGCTATGGCCAAGAAATGAG
3703797 TAATATGCTATGGCCAAGAAATGAG
1 TAATA-GCTATGGCCAAGAAATGAG
3703822 CGATAAAGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (24 bp):
TAATAGCTATGGCCAAGAAATGAG
Found at i:3705911 original size:35 final size:35
Alignment explanation
Indices: 3705872--3705994 Score: 131
Period size: 35 Copynumber: 3.5 Consensus size: 35
3705862 AGTGGTGCCC
* * *
3705872 TACTTATTTTAGTTGTTTTGTGTGAAGTAACGCTT
1 TACTTATTTTAGTTGTTCTGCGTGAAGTAGCGCTT
* * *
3705907 TACTTGTTTTAGTTGTTCTGCATGAAGTAGCACTT
1 TACTTATTTTAGTTGTTCTGCGTGAAGTAGCGCTT
* * * *
3705942 CACTT-GTTTAGGTGTTCTGCGTGAAGTAGTGCTT
1 TACTTATTTTAGTTGTTCTGCGTGAAGTAGCGCTT
* *
3705976 TACTCATTTTGGTTGTTCT
1 TACTTATTTTAGTTGTTCT
3705995 TTGTAGAATA
Statistics
Matches: 70, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
34 27 0.39
35 43 0.61
ACGTcount: A:0.17, C:0.13, G:0.22, T:0.48
Consensus pattern (35 bp):
TACTTATTTTAGTTGTTCTGCGTGAAGTAGCGCTT
Found at i:3705958 original size:34 final size:35
Alignment explanation
Indices: 3705894--3705970 Score: 102
Period size: 34 Copynumber: 2.2 Consensus size: 35
3705884 TTGTTTTGTG
* * * *
3705894 TGAAGTAACGCTTTACTTGTTTTAGTTGTTCTGCA
1 TGAAGTAGCACTTCACTTGTTTTAGGTGTTCTGCA
*
3705929 TGAAGTAGCACTTCACTTG-TTTAGGTGTTCTGCG
1 TGAAGTAGCACTTCACTTGTTTTAGGTGTTCTGCA
3705963 TGAAGTAG
1 TGAAGTAG
3705971 TGCTTTACTC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
34 21 0.57
35 16 0.43
ACGTcount: A:0.21, C:0.14, G:0.25, T:0.40
Consensus pattern (35 bp):
TGAAGTAGCACTTCACTTGTTTTAGGTGTTCTGCA
Found at i:3712197 original size:21 final size:21
Alignment explanation
Indices: 3712166--3712208 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 21
3712156 TGTCTTTTAA
3712166 ATACTTGAAATTT-A-GTTTT
1 ATACTTGAAATTTCATGTTTT
3712185 ATACTTAGAAAATTTCATGTTTT
1 ATACTT-G-AAATTTCATGTTTT
3712208 A
1 A
3712209 ATGTTTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 6 0.30
20 1 0.05
21 6 0.30
22 1 0.05
23 6 0.30
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.49
Consensus pattern (21 bp):
ATACTTGAAATTTCATGTTTT
Found at i:3714444 original size:32 final size:32
Alignment explanation
Indices: 3714408--3714471 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
3714398 ACATGTAGTT
3714408 GTTGATTTATTCATACTTTTGTAGGTGTTTAA
1 GTTGATTTATTCATACTTTTGTAGGTGTTTAA
*
3714440 GTTGATTTATTCGTACTTTTGTAGGTGTTTAA
1 GTTGATTTATTCATACTTTTGTAGGTGTTTAA
3714472 TGAAGGAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.20, C:0.06, G:0.20, T:0.53
Consensus pattern (32 bp):
GTTGATTTATTCATACTTTTGTAGGTGTTTAA
Found at i:3724637 original size:33 final size:33
Alignment explanation
Indices: 3724568--3724642 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
3724558 GAAGTGCTTC
* **
3724568 TTTATAGTTACTAGCTTGATAATAGCTCACTTT
1 TTTATAGTTACTAGCCTGATAATAGCTCACCCT
3724601 TTTATAGTTACTAGCCTGATAATAGCT-ATCCCT
1 TTTATAGTTACTAGCCTGATAATAGCTCA-CCCT
3724634 TTTATAGTT
1 TTTATAGTT
3724643 CTTCATCCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 1 0.03
33 37 0.97
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (33 bp):
TTTATAGTTACTAGCCTGATAATAGCTCACCCT
Found at i:3729664 original size:30 final size:30
Alignment explanation
Indices: 3729606--3729665 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
3729596 GAGGATCAAT
* **
3729606 CTTGTGAAGCAGAAATTTAAGGTTAAATAA
1 CTTGTAAAGCAGAAATTTAAGGGCAAATAA
* *
3729636 CTTGTAAAGTAGAAATTTAGGGGCAAATAA
1 CTTGTAAAGCAGAAATTTAAGGGCAAATAA
3729666 TAACGATGGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.43, C:0.07, G:0.22, T:0.28
Consensus pattern (30 bp):
CTTGTAAAGCAGAAATTTAAGGGCAAATAA
Found at i:3730950 original size:31 final size:31
Alignment explanation
Indices: 3730879--3730952 Score: 139
Period size: 31 Copynumber: 2.4 Consensus size: 31
3730869 GAATTGGGAC
*
3730879 TTGATATTGCTTTGAATTTTAGACTTTGGTA
1 TTGATATTGTTTTGAATTTTAGACTTTGGTA
3730910 TTGATATTGTTTTGAATTTTAGACTTTGGTA
1 TTGATATTGTTTTGAATTTTAGACTTTGGTA
3730941 TTGATATTGTTT
1 TTGATATTGTTT
3730953 CAACATTGGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.22, C:0.04, G:0.19, T:0.55
Consensus pattern (31 bp):
TTGATATTGTTTTGAATTTTAGACTTTGGTA
Found at i:3730967 original size:30 final size:31
Alignment explanation
Indices: 3730879--3730968 Score: 101
Period size: 31 Copynumber: 2.9 Consensus size: 31
3730869 GAATTGGGAC
* * **
3730879 TTGATATTGCTTTGAATTTTAGACTTTGGTA
1 TTGATATTGTTTTCAACATTAGACTTTGGTA
* **
3730910 TTGATATTGTTTTGAATTTTAGACTTTGGTA
1 TTGATATTGTTTTCAACATTAGACTTTGGTA
*
3730941 TTGATATTG-TTTCAACATTGGACTTTGG
1 TTGATATTGTTTTCAACATTAGACTTTGG
3730969 ATTTGGTATT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 15 0.28
31 39 0.72
ACGTcount: A:0.22, C:0.07, G:0.20, T:0.51
Consensus pattern (31 bp):
TTGATATTGTTTTCAACATTAGACTTTGGTA
Found at i:3734670 original size:21 final size:21
Alignment explanation
Indices: 3734599--3734672 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
3734589 TCTCAAAGAG
* * * *
3734599 AAGTATAGAGTCATTGCACTA
1 AAGTATAGAGACCTGGCACAA
*
3734620 AAGTATAAAGACCTGGCACAA
1 AAGTATAGAGACCTGGCACAA
*
3734641 AAGTATAGAGACCTTGCACAA
1 AAGTATAGAGACCTGGCACAA
* *
3734662 AGGTTTAGAGA
1 AAGTATAGAGA
3734673 TCTAGCTTCA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.22
Consensus pattern (21 bp):
AAGTATAGAGACCTGGCACAA
Found at i:3736514 original size:3 final size:3
Alignment explanation
Indices: 3736506--3736541 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
3736496 TATAGTATTG
*
3736506 CTA CTA CTA CTA CTA CTA CTA GTA CTA CTA CTA CTA
1 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA
3736542 GAGATAAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (3 bp):
CTA
Found at i:3739839 original size:21 final size:21
Alignment explanation
Indices: 3739808--3739873 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
3739798 ATCATAAATA
* *
3739808 ATCAGTCTTTGTTATGAATGC
1 ATCAGTATTTGTCATGAATGC
*
3739829 ATTAGTATTTGTCATGAATGC
1 ATCAGTATTTGTCATGAATGC
* *
3739850 ATCAGTCTTTGTCAAGAATTGC
1 ATCAGTATTTGTCATGAA-TGC
3739872 AT
1 AT
3739874 GATCATATCC
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
21 33 0.87
22 5 0.13
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (21 bp):
ATCAGTATTTGTCATGAATGC
Found at i:3741331 original size:17 final size:20
Alignment explanation
Indices: 3741306--3741358 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
3741296 ATTTTATCTA
3741306 AATAATTAAAATTAA-AAA-
1 AATAATTAAAATTAATAAAC
3741324 AA-AATT-AAATTAATAAAC
1 AATAATTAAAATTAATAAAC
3741342 TAATAATTAAAATTAAT
1 -AATAATTAAAATTAAT
3741359 TTAGTAGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 7 0.23
17 7 0.23
18 2 0.07
19 2 0.07
20 4 0.13
21 8 0.27
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (20 bp):
AATAATTAAAATTAATAAAC
Found at i:3742626 original size:109 final size:109
Alignment explanation
Indices: 3742457--3742783 Score: 591
Period size: 109 Copynumber: 3.0 Consensus size: 109
3742447 TCTTTTACTA
3742457 AAATTCTTCTTTCATCAAACACCTACAAAAGCACAAATAAATCAATAACAACCTATCTTAACCAC
1 AAATTCTTCTTTCATCAAACACCTACAAAAGCACAAATAAATCAATAACAACCTATCTTAACCAC
*
3742522 ATTAACACCAAATTAAGCATAAAATTAACTAAGCTTAGATTGAC
66 ATTAACACCAAATTAAGCATAAAATTAACTAAGATTAGATTGAC
* *
3742566 AAATTCTTCTTTCATCAAACACCTATAAAAGCACAAATAAATCAATAACAACCTAGCTTAACCAC
1 AAATTCTTCTTTCATCAAACACCTACAAAAGCACAAATAAATCAATAACAACCTATCTTAACCAC
*
3742631 ATTAACACCAAATTAAGCATAAAATTAACTAAGATTAGATTAAC
66 ATTAACACCAAATTAAGCATAAAATTAACTAAGATTAGATTGAC
*
3742675 AAATTCTTCTTTCATCAAACACCTACAAAAGCACAAATAAATCAATAACAATCTATCTTAACCAC
1 AAATTCTTCTTTCATCAAACACCTACAAAAGCACAAATAAATCAATAACAACCTATCTTAACCAC
* *
3742740 ATTAACACCAAATTAAGTATAAAATTAACTAAGATTATATTGAC
66 ATTAACACCAAATTAAGCATAAAATTAACTAAGATTAGATTGAC
3742784 TCACCTAGAA
Statistics
Matches: 208, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
109 208 1.00
ACGTcount: A:0.48, C:0.21, G:0.04, T:0.27
Consensus pattern (109 bp):
AAATTCTTCTTTCATCAAACACCTACAAAAGCACAAATAAATCAATAACAACCTATCTTAACCAC
ATTAACACCAAATTAAGCATAAAATTAACTAAGATTAGATTGAC
Found at i:3743249 original size:28 final size:28
Alignment explanation
Indices: 3743209--3743342 Score: 160
Period size: 28 Copynumber: 4.7 Consensus size: 28
3743199 GTAAAGGTTT
*
3743209 TGCCTAATCCTTGAAAATGCTGAGATTA
1 TGCCTAATCCTTGAAAAGGCTGAGATTA
*
3743237 TGCCTAATCCTTGAAAATGCTGAGATTA
1 TGCCTAATCCTTGAAAAGGCTGAGATTA
* * *
3743265 TGCCTAATCATTGAAAAGGCATATAGATTC
1 TGCCTAATCCTTGAAAAGGC-T-GAGATTA
** *
3743295 TGTTTAATCCTTGAAAAGGCTGAGGTTA
1 TGCCTAATCCTTGAAAAGGCTGAGATTA
* *
3743323 TGCTTGATCCTTGAAAAGGC
1 TGCCTAATCCTTGAAAAGGC
3743343 ATGGTTGTGC
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
28 68 0.74
29 2 0.02
30 22 0.24
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Consensus pattern (28 bp):
TGCCTAATCCTTGAAAAGGCTGAGATTA
Found at i:3744626 original size:12 final size:12
Alignment explanation
Indices: 3744609--3744634 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3744599 AGGGACAAAT
3744609 TTATTATAACAA
1 TTATTATAACAA
3744621 TTATTATAACAA
1 TTATTATAACAA
3744633 TT
1 TT
3744635 GTAAAGATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (12 bp):
TTATTATAACAA
Found at i:3752888 original size:20 final size:19
Alignment explanation
Indices: 3752852--3752890 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
3752842 ATTTTATAAA
*
3752852 ATTTTTAATTTTAAAATAT
1 ATTTTTAATATTAAAATAT
*
3752871 ATTTTTAAATATTGAAATAT
1 ATTTTT-AATATTAAAATAT
3752891 TAATATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
ATTTTTAATATTAAAATAT
Found at i:3753343 original size:2 final size:2
Alignment explanation
Indices: 3753336--3753364 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3753326 TTAAAATGAA
3753336 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 A
3753365 ACATTGTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3756409 original size:21 final size:21
Alignment explanation
Indices: 3756383--3756426 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3756373 CAACACATAT
*
3756383 ACTCTTACCTAAATTATGACA
1 ACTCTTACCTAAATTAAGACA
* *
3756404 ACTCTTATCTTAATTAAGACA
1 ACTCTTACCTAAATTAAGACA
3756425 AC
1 AC
3756427 AAATCTATCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.34
Consensus pattern (21 bp):
ACTCTTACCTAAATTAAGACA
Done.