Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 45 of 97
Found at i:18459153 original size:4 final size:4
Alignment explanation
Indices: 18459110--18459143 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
18459100 AAGTAAGGAG
*
18459110 AGAA AGGA AGAA AGAA AGAA AGAA AGAA AGAA AG
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AG
18459144 GCGAAAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:18461261 original size:24 final size:23
Alignment explanation
Indices: 18461233--18461285 Score: 97
Period size: 24 Copynumber: 2.3 Consensus size: 23
18461223 TTGTAAATAG
18461233 TATTAATGTAAATGTATGGTGGA
1 TATTAATGTAAATGTATGGTGGA
18461256 TAATTAATGTAAATGTATGGTGGA
1 T-ATTAATGTAAATGTATGGTGGA
18461280 TATTAA
1 TATTAA
18461286 AGACCTTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 6 0.21
24 23 0.79
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.40
Consensus pattern (23 bp):
TATTAATGTAAATGTATGGTGGA
Found at i:18461608 original size:23 final size:22
Alignment explanation
Indices: 18461582--18461660 Score: 68
Period size: 23 Copynumber: 3.5 Consensus size: 22
18461572 AATGCCTAAA
18461582 AACCAATCATGTAATACCCTATC
1 AACCAATCATGTAAT-CCCTATC
** * * *
18461605 AACCGGTCACGCAATGCCTATC
1 AACCAATCATGTAATCCCTATC
*
18461627 AACCAATCATGTAATGCCTTATC
1 AACCAATCATGTAAT-CCCTATC
* *
18461650 AATCAGTCATG
1 AACCAATCATG
18461661 CAGTGCTTAT
Statistics
Matches: 42, Mismatches: 13, Indels: 2
0.74 0.23 0.04
Matches are distributed among these distances:
22 17 0.40
23 25 0.60
ACGTcount: A:0.34, C:0.29, G:0.11, T:0.25
Consensus pattern (22 bp):
AACCAATCATGTAATCCCTATC
Found at i:18461672 original size:45 final size:45
Alignment explanation
Indices: 18461540--18461896 Score: 159
Period size: 45 Copynumber: 8.0 Consensus size: 45
18461530 GACTAGAGAG
* * * ** ** **
18461540 CAATCACGCAATGCCCTATCAAGTAGTCACTAAATGCCTAAAAAC
1 CAATCATGTAATGCCTTATCAACCAGTCACGCAATGCCTATCAAC
* * *
18461585 CAATCATGTAATACCCTATCAACCGGTCACGCAATGCCTATCAAC
1 CAATCATGTAATGCCTTATCAACCAGTCACGCAATGCCTATCAAC
* * * *
18461630 CAATCATGTAATGCCTTATCAATCAGTCATGCAGTGCTTATCAA-
1 CAATCATGTAATGCCTTATCAACCAGTCACGCAATGCCTATCAAC
* * * * * ** *
18461674 CAATCACGCAATGCCTTATCAACTAGTCACACAATGTCTAAAAAT
1 CAATCATGTAATGCCTTATCAACCAGTCACGCAATGCCTATCAAC
* *** * * ** **
18461719 CAGTCACACAATGCCTTA-CAAACCACTCATGCAATGATTAAAAAC
1 CAATCATGTAATGCCTTATC-AACCAGTCACGCAATGCCTATCAAC
* * * * *
18461764 TAGTCATGCAATGCC-TATCAACTAATCACGCAATGTCCTATCAAC
1 CAATCATGTAATGCCTTATCAACCAGTCACGCAATG-CCTATCAAC
* * * * * ** ** * *
18461809 TAGTCACGCAATGAC-TAAAAAGTAGTCACACAATGCTTTATCAAC
1 CAATCATGTAATGCCTTATCAACCAGTCACGCAATGC-CTATCAAC
* * *
18461854 CAGTCACGCAATGCC-TATCAA-CAGTCACGCAATGCCCTATCAA
1 CAATCATGTAATGCCTTATCAACCAGTCACGCAATG-CCTATCAA
18461897 TTAGTCACGC
Statistics
Matches: 244, Mismatches: 62, Indels: 13
0.76 0.19 0.04
Matches are distributed among these distances:
44 67 0.27
45 177 0.73
ACGTcount: A:0.37, C:0.28, G:0.11, T:0.24
Consensus pattern (45 bp):
CAATCATGTAATGCCTTATCAACCAGTCACGCAATGCCTATCAAC
Found at i:18461808 original size:112 final size:112
Alignment explanation
Indices: 18461653--18461912 Score: 314
Period size: 112 Copynumber: 2.3 Consensus size: 112
18461643 CCTTATCAAT
* * *
18461653 CAGTCATGCAGTGCTTATCAAC-AATCACGCAATG-CCTTATCAACTAGTCACACAATGTCTAAA
1 CAGTCATGCAATGCCTATCAACTAATCACGCAATGTCCTTATCAACTAGTCACACAATGACTAAA
* *
18461716 AA-TCAGTCACACAATGCCTTA-CAAACCACTCATGCAATGATTAAAAA
66 AAGT-AGTCACACAATGCCTTATC-AACCACTCACGCAATGACTAAAAA
*
18461763 CTAGTCATGCAATGCCTATCAACTAATCACGCAATGTCC-TATCAACTAGTCACGCAATGACTAA
1 C-AGTCATGCAATGCCTATCAACTAATCACGCAATGTCCTTATCAACTAGTCACACAATGACTAA
* * * **
18461827 AAAGTAGTCACACAATGCTTTATCAACCAGTCACGCAATGCCTATCAA
65 AAAGTAGTCACACAATGCCTTATCAACCACTCACGCAATGACTAAAAA
* * * *
18461875 CAGTCACGCAATGCCCTATCAATTAGTCACGCATTGTC
1 CAGTCATGCAATG-CCTATCAACTAATCACGCAATGTC
18461913 TAAAAATCAG
Statistics
Matches: 129, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
110 1 0.01
111 30 0.23
112 94 0.73
113 4 0.03
ACGTcount: A:0.36, C:0.28, G:0.12, T:0.24
Consensus pattern (112 bp):
CAGTCATGCAATGCCTATCAACTAATCACGCAATGTCCTTATCAACTAGTCACACAATGACTAAA
AAGTAGTCACACAATGCCTTATCAACCACTCACGCAATGACTAAAAA
Found at i:18461981 original size:22 final size:22
Alignment explanation
Indices: 18461543--18461980 Score: 225
Period size: 22 Copynumber: 19.6 Consensus size: 22
18461533 TAGAGAGCAA
**
18461543 TCACGCAATGCCCTATCAAGTAG
1 TCACGCAATG-CCTATCAACCAG
** ** *
18461566 TCACTAAATGCCTAAAAACCAA
1 TCACGCAATGCCTATCAACCAG
* * * *
18461588 TCATGTAATACCCTATCAACCGG
1 TCACGCAAT-GCCTATCAACCAG
*
18461611 TCACGCAATGCCTATCAACCAA
1 TCACGCAATGCCTATCAACCAG
* * *
18461633 TCATGTAATGCCTTATCAATCAG
1 TCACGCAATGCC-TATCAACCAG
* * * *
18461656 TCATGCAGTGCTTATCAA-CAA
1 TCACGCAATGCCTATCAACCAG
*
18461677 TCACGCAATGCCTTATCAACTAG
1 TCACGCAATGCC-TATCAACCAG
* * ** *
18461700 TCACACAATGTCTAAAAATCAG
1 TCACGCAATGCCTATCAACCAG
* *
18461722 TCACACAATGCCT-TACAAACCAC
1 TCACGCAATGCCTAT-C-AACCAG
* ** ** *
18461745 TCATGCAATGATTAAAAACTAG
1 TCACGCAATGCCTATCAACCAG
* * *
18461767 TCATGCAATGCCTATCAACTAA
1 TCACGCAATGCCTATCAACCAG
*
18461789 TCACGCAATGTCCTATCAACTAG
1 TCACGCAATG-CCTATCAACCAG
* ** **
18461812 TCACGCAATGACTAAAAAGTAG
1 TCACGCAATGCCTATCAACCAG
* *
18461834 TCACACAATGCTTTATCAACCAG
1 TCACGCAATGC-CTATCAACCAG
18461857 TCACGCAATGCCTATCAA-CAG
1 TCACGCAATGCCTATCAACCAG
**
18461878 TCACGCAATGCCCTATCAATTAG
1 TCACGCAATG-CCTATCAACCAG
* * ** *
18461901 TCACGCATTGTCTAAAAATCAG
1 TCACGCAATGCCTATCAACCAG
* * * ** *
18461923 TCACACAATACTTAAAAACCAA
1 TCACGCAATGCCTATCAACCAG
** * *
18461945 TCATACAATGACTAACAACCAG
1 TCACGCAATGCCTATCAACCAG
18461967 TCACGCAATGCCTA
1 TCACGCAATGCCTA
18461981 AGTCACACAA
Statistics
Matches: 310, Mismatches: 94, Indels: 23
0.73 0.22 0.05
Matches are distributed among these distances:
21 24 0.08
22 174 0.56
23 112 0.36
ACGTcount: A:0.37, C:0.28, G:0.11, T:0.24
Consensus pattern (22 bp):
TCACGCAATGCCTATCAACCAG
Found at i:18462017 original size:61 final size:60
Alignment explanation
Indices: 18461921--18462039 Score: 159
Period size: 61 Copynumber: 2.0 Consensus size: 60
18461911 TCTAAAAATC
*
18461921 AGTCACACAATACTTAAAAACCAATCATACAATGACTAACAACCAGTCACGCAATGCCTA
1 AGTCACACAATACTTAAAAACCAATCATACAATGACTAAAAACCAGTCACGCAATGCCTA
* * * * *
18461981 AGTCACACAATACCCTT-CAAACCACTCATGCAATGACTAAAAACTAGTCATGCAATGCC
1 AGTCACACAATA--CTTAAAAACCAATCATACAATGACTAAAAACCAGTCACGCAATGCC
18462040 AATCAACCAA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
60 12 0.24
61 36 0.71
62 3 0.06
ACGTcount: A:0.42, C:0.29, G:0.09, T:0.19
Consensus pattern (60 bp):
AGTCACACAATACTTAAAAACCAATCATACAATGACTAAAAACCAGTCACGCAATGCCTA
Found at i:18462253 original size:80 final size:80
Alignment explanation
Indices: 18462118--18462417 Score: 264
Period size: 80 Copynumber: 3.7 Consensus size: 80
18462108 TAAGTCATGT
* ** * * ** *
18462118 AATGCTTAAAACCCCTAAACCCAATGCCTAAAACCAGTCACATATGCCTTGTCAACCAAACACAC
1 AATGCCTAAAACCCCT-AACCCAACACATAAAACTAGTCACGCATGCCTTATCAACCAAACACAC
18462183 AAATCC-TAAGTCACAC
65 AAA-CCTTAAGTCACAC
* ** **
18462199 AATGCCTAAAACCCTTAACCCAACACATAAAACCT-GTCACGCATG-CTTCATCAACCAGTCATG
1 AATGCCTAAAACCCCTAACCCAACACATAAAA-CTAGTCACGCATGCCTT-ATCAACCAAACACA
**
18462262 CAAACCTTAAGTCATGC
64 CAAACCTTAAGTCACAC
* * * ** **
18462279 AATGCCTAAAACCCCTAACCCAACGCATAAAACTAGTCATGCATGCCTTATCAATCAGTCATGCA
1 AATGCCTAAAACCCCTAACCCAACACATAAAACTAGTCACGCATGCCTTATCAACCAAACACACA
* **
18462344 AACCTTAAGTTATGC
66 AACCTTAAGTCACAC
* ** * *
18462359 AATACCTAAAACCCCTAAACCCAACGTATAAAACTAGTCACACATGCCCTATCAACCAA
1 AATGCCTAAAACCCCT-AACCCAACACATAAAACTAGTCACGCATGCCTTATCAACCAA
18462418 TCATACATGC
Statistics
Matches: 186, Mismatches: 27, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
79 7 0.04
80 125 0.67
81 54 0.29
ACGTcount: A:0.39, C:0.32, G:0.09, T:0.20
Consensus pattern (80 bp):
AATGCCTAAAACCCCTAACCCAACACATAAAACTAGTCACGCATGCCTTATCAACCAAACACACA
AACCTTAAGTCACAC
Found at i:18462415 original size:161 final size:161
Alignment explanation
Indices: 18462067--18462421 Score: 367
Period size: 161 Copynumber: 2.2 Consensus size: 161
18462057 ATTTTCAATC
* * * * * *
18462067 AACTAGTCACGCAATCCCCCATCAATCAGTCACCCAAACCCTAAGTCATGTAATGCTTAAAACCC
1 AACTAGTCACGC-ATGCCCTATCAACCAGTCATCCAAACCCTAAGTCATGCAATGCCTAAAACCC
* * * *
18462132 CTAAACCCAATGCCTAAAACCAGTCACATATGCCTTGTCAACCAAACACACAAATCCTAAGTCAC
65 CTAAACCCAACGCATAAAACCAGTCACACATGCCTTATCAACCAAACACACAAATCCTAAGTCAC
* *
18462197 ACAATGCCTAAAACCCTTAACCCAACACATAA
130 ACAATACCTAAAACCCTAAACCCAACACATAA
* * *
18462229 AACCT-GTCACGCATG-CTTCATCAACCAGTCATGCAAACCTTAAGTCATGCAATGCCTAAAACC
1 AA-CTAGTCACGCATGCCCT-ATCAACCAGTCATCCAAACCCTAAGTCATGCAATGCCTAAAACC
* ** * ** ** *
18462292 CCT-AACCCAACGCATAAAACTAGTCATGCATGCCTTATCAATCAGTCATGCAAA-CCTTAAGTT
64 CCTAAACCCAACGCATAAAACCAGTCACACATGCCTTATCAACCAAACACACAAATCC-TAAGTC
** **
18462355 ATGCAATACCTAAAACCCCTAAACCCAACGTATAA
128 ACACAATACCTAAAA-CCCTAAACCCAACACATAA
* *
18462390 AACTAGTCACACATGCCCTATCAACCAATCAT
1 AACTAGTCACGCATGCCCTATCAACCAGTCAT
18462422 ACATGCCTTC
Statistics
Matches: 156, Mismatches: 31, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
159 2 0.01
160 59 0.38
161 82 0.53
162 11 0.07
163 2 0.01
ACGTcount: A:0.38, C:0.33, G:0.09, T:0.21
Consensus pattern (161 bp):
AACTAGTCACGCATGCCCTATCAACCAGTCATCCAAACCCTAAGTCATGCAATGCCTAAAACCCC
TAAACCCAACGCATAAAACCAGTCACACATGCCTTATCAACCAAACACACAAATCCTAAGTCACA
CAATACCTAAAACCCTAAACCCAACACATAA
Found at i:18463116 original size:17 final size:19
Alignment explanation
Indices: 18463094--18463132 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
18463084 TAGTAATGCT
18463094 TATGTATAAAT-TAA-ATA
1 TATGTATAAATATAATATA
*
18463111 TATGTATATATATAATATA
1 TATGTATAAATATAATATA
18463130 TAT
1 TAT
18463133 TACTTTCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 3 0.16
19 6 0.32
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (19 bp):
TATGTATAAATATAATATA
Found at i:18463181 original size:214 final size:216
Alignment explanation
Indices: 18462895--18463362 Score: 667
Period size: 221 Copynumber: 2.2 Consensus size: 216
18462885 ATGTTGATTT
* * * *
18462895 TATATAGTATATA-ATTATATGTATTATTTTATTACATATATAAAATTAATGACACAACTTATTT
1 TATAT-GTATATATATAATATATATTACTTTATTACATATATAAAATTAATGACACAACTTATAT
*
18462959 AATATAATG-TTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAACAATTTGTTATAAAA
65 AATATAATGTTTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAACAATATGTTATAAAA
*
18463023 ACTAAAGTAATAACTGATAAAGTTATTAAGTGTAATAATATAAATAAAG-TATTATAAGTTATAG
130 ACTAAAGTAATAACTAATAAAGTTATTAAGTGTAATAATATAAATAAAGCTATTATAAGTTATAG
*
18463087 TAATGCTTATGTATAAATTAAA
195 TAATACTTATGTATAAATTAAA
* * * * *
18463109 TATATGTATATATATAATATATATTACTTTCTTATATATATGAAATTAATGATACAACTTATATG
1 TATATGTATATATATAATATATATTACTTTATTACATATATAAAATTAATGACACAACTTATATA
* *
18463174 TTATAATGTTTTAATTTTTATATCAAAGTTTGTATAAATAATAATTAATTATAAACAATATGTTA
66 ATATAATG------TTTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAACAATATGTTA
* * * *
18463239 TAAAAATTAAGGTGATAACTAATAAAGTTATTAAGTGTAATCATATAAATAAAGTCTATTATAAG
125 TAAAAACTAAAGTAATAACTAATAAAGTTATTAAGTGTAATAATATAAATAAAG-CTATTATAAG
18463304 TTATAGTAATACTTATGTATAAATTAAA
189 TTATAGTAATACTTATGTATAAATTAAA
18463332 TATATGTATATATAT-A-ATATATTACTTTATT
1 TATATGTATATATATAATATATATTACTTTATT
18463363 TTATAGATAT
Statistics
Matches: 225, Mismatches: 19, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
213 7 0.03
214 55 0.24
221 111 0.49
222 1 0.00
223 51 0.23
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (216 bp):
TATATGTATATATATAATATATATTACTTTATTACATATATAAAATTAATGACACAACTTATATA
ATATAATGTTTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAACAATATGTTATAAAAA
CTAAAGTAATAACTAATAAAGTTATTAAGTGTAATAATATAAATAAAGCTATTATAAGTTATAGT
AATACTTATGTATAAATTAAA
Found at i:18463343 original size:2 final size:2
Alignment explanation
Indices: 18463331--18463404 Score: 82
Period size: 2 Copynumber: 38.0 Consensus size: 2
18463321 TATAAATTAA
* * * *
18463331 AT AT AT GT AT AT AT AT A- AT AT AT -T ACT TT AT -T TT AT AG AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
18463371 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
18463405 NNNNNNNNNN
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
1 3 0.05
2 57 0.93
3 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:18477444 original size:49 final size:49
Alignment explanation
Indices: 18477376--18477499 Score: 196
Period size: 49 Copynumber: 2.6 Consensus size: 49
18477366 TAATCTAGTG
*
18477376 TGATGATGATGACCCGGCTATGTGTGAGTAGGCAGTGCGCATAGGCCGA
1 TGATGATGATGACCCGGCTATGTATGAGTAGGCAGTGCGCATAGGCCGA
** *
18477425 TGATGATGATGACTTGGCTATGTATGAGTAGGGAGTGCGCATAGGCCGA
1 TGATGATGATGACCCGGCTATGTATGAGTAGGCAGTGCGCATAGGCCGA
*
18477474 TGATGATGATGATCCGGCTATG-ATGA
1 TGATGATGATGACCCGGCTATGTATGA
18477500 TGAATGAAGT
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
48 4 0.06
49 64 0.94
ACGTcount: A:0.24, C:0.15, G:0.35, T:0.26
Consensus pattern (49 bp):
TGATGATGATGACCCGGCTATGTATGAGTAGGCAGTGCGCATAGGCCGA
Found at i:18480064 original size:10 final size:10
Alignment explanation
Indices: 18480029--18480067 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
18480019 TTGTGGCTGA
18480029 ATTTGATGAT
1 ATTTGATGAT
*
18480039 ATTTCATGAT
1 ATTTGATGAT
*
18480049 ATTTTGGTGAT
1 A-TTTGATGAT
18480060 ATTTGATG
1 ATTTGATG
18480068 TTTGGTGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.26, C:0.03, G:0.21, T:0.51
Consensus pattern (10 bp):
ATTTGATGAT
Found at i:18491074 original size:3 final size:3
Alignment explanation
Indices: 18491039--18491087 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
18491029 AACAATGCTT
*
18491039 TTC TTC TT- TTC TT- TTGC TTC TATC TT- GTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TT-C TTC T-TC TTC TTC TTC TTC TTC TTC TTC
18491083 TTC TT
1 TTC TT
18491088 TCAGCTTCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 5 0.13
3 29 0.74
4 5 0.13
ACGTcount: A:0.02, C:0.27, G:0.04, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:18493892 original size:35 final size:33
Alignment explanation
Indices: 18493853--18494001 Score: 113
Period size: 35 Copynumber: 4.3 Consensus size: 33
18493843 TGAGCTTGTG
18493853 AAAAA-CCATTGTTGAATGGTTTTGCTTGATCTCGT
1 AAAAAGCCATTG-T-AA-GGTTTTGCTTGATCTCGT
* * *
18493888 AAAAAGCCATTGTAACGATTTTTCTTAATCTCGT
1 AAAAAGCCATTGTAA-GGTTTTGCTTGATCTCGT
* *
18493922 GAAAAAGCTATTGTAAGAGTTTTGTTTGATCTCGT
1 -AAAAAGCCATTGTAAG-GTTTTGCTTGATCTCGT
* * * * * *
18493957 -AAAGGCTATTGTGAGGGTTTCGTTTGATCTCAT
1 AAAAAGCCATTGT-AAGGTTTTGCTTGATCTCGT
18493990 AAAAAGCTCATT
1 AAAAAGC-CATT
18494002 TCCTTAAGTG
Statistics
Matches: 93, Mismatches: 15, Indels: 12
0.77 0.12 0.10
Matches are distributed among these distances:
33 26 0.28
34 25 0.27
35 36 0.39
36 6 0.06
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.38
Consensus pattern (33 bp):
AAAAAGCCATTGTAAGGTTTTGCTTGATCTCGT
Found at i:18493982 original size:33 final size:33
Alignment explanation
Indices: 18493928--18493992 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
18493918 TCGTGAAAAA
* *
18493928 GCTATTGTAAGAGTTTTGTTTGATCTCGTAAAG
1 GCTATTGTAAGAGTTTCGTTTGATCTCATAAAG
* *
18493961 GCTATTGTGAGGGTTTCGTTTGATCTCATAAA
1 GCTATTGTAAGAGTTTCGTTTGATCTCATAAA
18493993 AAGCTCATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.23, C:0.11, G:0.25, T:0.42
Consensus pattern (33 bp):
GCTATTGTAAGAGTTTCGTTTGATCTCATAAAG
Found at i:18496517 original size:342 final size:344
Alignment explanation
Indices: 18495893--18496892 Score: 1272
Period size: 342 Copynumber: 2.9 Consensus size: 344
18495883 TTACTATTAT
* * *
18495893 ATATATACTTTAATATAAATATATTTACTTTCTATTTTATGTTAAC-TTACAAAAATTATAACTT
1 ATATATACTTAAATATAAACATATTTACTTTCTATTTTGTGTTAACATTACAAAAATTATAACTT
* * * * *
18495957 ATAAAATTCTTAATTATAATATATATACCATTGTTTATATAAACTTATAATATATATACTTAAAG
66 ATAAAATTATTAATTATAATATATATACCTTTATTTATATAAACTTATAATATATAAACCTAAAG
* *
18496022 AG-AGCTTTTGAGATTAAAATAGTTTT-AGAACCTA-TCTATTTTTTTTAAATTTCATGAAATTA
131 AGAAG-TTGTGAGATTAAAATAGTTTTGA-AACCTAGT-TATTTTTTTTAAATTTCATGTAATTA
* * *
18496084 AGGACAAATCCATATAGTTAATTAAATTAATTCAAGAAACTATGATTATTAATTAACTTGTAATG
193 AGGACAAACCCATATATTTAATTAAATTAATTCATGAAACTATGATTATTAATTAACTTGTAATG
* *
18496149 TCTTTTAATATATA-TAGTT-TATATATTGTGTTAATTTATAAGAAATATATTTACTATTATATA
258 TCTTTTAATATATACT--TTATATATATTG-GTTCATTTATAAGAAATATAATTACTATTATATA
* *
18496212 TATACTAAAATA-TTT-T-TA-GTAC-
320 TAT--TAAAACACTTTATATATATACA
*
18496234 ATATATACTCTAAATATAAAGATATTTACTTTCTATTTTGTGTTAACATTACAAAAATTATAACT
1 ATATATACT-TAAATATAAACATATTTACTTTCTATTTTGTGTTAACATTACAAAAATTATAACT
* *
18496299 TATAAAATTATTAATTATAATATATATGCCTTTATTTATATAAACTTATAGTATATAAACCTAAA
65 TATAAAATTATTAATTATAATATATATACCTTTATTTATATAAACTTATAATATATAAACCTAAA
* * * *
18496364 GAGAAGTTGGGAGATTAAAATCGTTTTGAAACTTAGTT-TTTTTTTTAAATCTCATGTAATTAAG
130 GAGAAGTTGTGAGATTAAAATAGTTTTGAAACCTAGTTATTTTTTTTAAATTTCATGTAATTAAG
* * *
18496428 GACAAACCCATATATTTAATTAATTTAATTCATGAAACTATAATTATTAATTAACTTGTAATGCC
195 GACAAACCCATATATTTAATTAAATTAATTCATGAAACTATGATTATTAATTAACTTGTAATGTC
* *
18496493 TTTTAATATATACTTTATATATATTAGGTTCATTCATAAGGAATATAATTACTATTATATATATT
260 TTTTAATATATACTTTATATATATT-GGTTCATTTATAAGAAATATAATTACTATTATATATATT
18496558 AAAACACTTTTAGTATATATACA
324 AAAACAC-TTTA-TATATATACA
* * *
18496581 TATATATGTAGTTTAAAGATAAACATATTTACTTGT-TATTTTGTGTTAACACTACAAAAATTAT
1 -ATATA--TA-CTTAAATATAAACATATTTACTT-TCTATTTTGTGTTAACATTACAAAAATTAT
* *
18496645 AATTTATAAAATTATTAATTATAATATATATACCTTTATTTATATAAACTTATAATATATAAATC
61 AACTTATAAAATTATTAATTATAATATATATACCTTTATTTATATAAACTTATAATATATAAACC
* * * * * * *
18496710 TAAAGGGAAATTGTAATATTAGAATAGTTTTGAAACCTAGTTAATTTTTGT-AATTTCATGTAAT
126 TAAAGAGAAGTTGTGAGATTAAAATAGTTTTGAAACCTAGTTATTTTTTTTAAATTTCATGTAAT
* * * * * *
18496774 TAAGGACAAACTCATATAATTTTATTAAATTAATTAATGAAATTATGATTATTAATTGACTTGTG
191 TAAGGACAAACCCATAT-ATTTAATTAAATTAATTCATGAAACTATGATTATTAATTAACTTGTA
* * * *
18496839 ATGTCTTTTAATGTATACTTTATATACATTGAATTCATGTATAAGAAATATAAT
255 ATGTCTTTTAATATATACTTTATATATATTG-GTTCATTTATAAGAAATATAAT
18496893 CATACTAAAA
Statistics
Matches: 574, Mismatches: 62, Indels: 36
0.85 0.09 0.05
Matches are distributed among these distances:
340 6 0.01
341 11 0.02
342 173 0.30
343 104 0.18
344 5 0.01
345 2 0.00
346 3 0.01
348 5 0.01
350 172 0.30
351 93 0.16
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.44
Consensus pattern (344 bp):
ATATATACTTAAATATAAACATATTTACTTTCTATTTTGTGTTAACATTACAAAAATTATAACTT
ATAAAATTATTAATTATAATATATATACCTTTATTTATATAAACTTATAATATATAAACCTAAAG
AGAAGTTGTGAGATTAAAATAGTTTTGAAACCTAGTTATTTTTTTTAAATTTCATGTAATTAAGG
ACAAACCCATATATTTAATTAAATTAATTCATGAAACTATGATTATTAATTAACTTGTAATGTCT
TTTAATATATACTTTATATATATTGGTTCATTTATAAGAAATATAATTACTATTATATATATTAA
AACACTTTATATATATACA
Found at i:18496771 original size:350 final size:343
Alignment explanation
Indices: 18495890--18496892 Score: 1251
Period size: 350 Copynumber: 2.9 Consensus size: 343
18495880 TAATTACTAT
* *
18495890 TATATATATACTTT-AATATAAATATATTTACTTTCTATTTTATGTTAAC-TTACAAAAATTATA
1 TATATAT-TACTTTAAATATAAACATATTTACTTTCTATTTTGTGTTAACATTACAAAAATTATA
* * * *
18495953 ACTTATAAAATTCTTAATTATAATATATATACCATTGTTTATATAAACTTATAATATATATACTT
65 ACTTATAAAATTATTAATTATAATATATATACCTTTATTTATATAAACTTATAATATATAAAC-T
** * *
18496018 AAAGAGAGCTTTTGAGATTAAAATAGTTTT-AGAACCTA-TCTATTTTTTTTAAATTTCATGAAA
129 AAAGAGAAATTGTGAGATTAAAATAGTTTTGA-AACCTAGT-TATTTTTTTTAAATTTCATGTAA
* * *
18496081 TTAAGGACAAATCCATATAGTTAATTAAATTAATTCAAGAAACTATGATTATTAATTAACTTGTA
192 TTAAGGACAAACCCATATATTTAATTAAATTAATTCATGAAACTATGATTATTAATTAACTTGTA
* *
18496146 ATGTCTTTTAATATATA-TAGTT-TATATATTGTGTTAATTTATAAGAAATATATTTACTATTAT
257 ATGTCTTTTAATATATACT--TTATATATATTGTGTTAATTCATAAGAAATATAATTACTATTAT
* *
18496209 ATATATACTAAAATATTTTTAGTAC
320 ATATATA-TAAAACATTTTTAATAC
* *
18496234 -ATATA-TACTCTAAATATAAAGATATTTACTTTCTATTTTGTGTTAACATTACAAAAATTATAA
1 TATATATTACTTTAAATATAAACATATTTACTTTCTATTTTGTGTTAACATTACAAAAATTATAA
* *
18496297 CTTATAAAATTATTAATTATAATATATATGCCTTTATTTATATAAACTTATAGTATATAAACCTA
66 CTTATAAAATTATTAATTATAATATATATACCTTTATTTATATAAACTTATAATATATAAA-CTA
* * * * *
18496362 AAGAGAAGTTGGGAGATTAAAATCGTTTTGAAACTTAGTT-TTTTTTTTAAATCTCATGTAATTA
130 AAGAGAAATTGTGAGATTAAAATAGTTTTGAAACCTAGTTATTTTTTTTAAATTTCATGTAATTA
* *
18496426 AGGACAAACCCATATATTTAATTAATTTAATTCATGAAACTATAATTATTAATTAACTTGTAATG
195 AGGACAAACCCATATATTTAATTAAATTAATTCATGAAACTATGATTATTAATTAACTTGTAATG
* * *
18496491 CCTTTTAATATATACTTTATATATATTAG-GTTCATTCATAAGGAATATAATTACTATTATATAT
260 TCTTTTAATATATACTTTATATATATT-GTGTTAATTCATAAGAAATATAATTACTATTATATAT
18496555 AT-TAAAACACTTTTAGTATATATAC
324 ATATAAAACA--TTT--T-TA-ATAC
* * *
18496580 ATATATATGTAGTTTAAAGATAAACATATTTACTTGT-TATTTTGTGTTAACACTACAAAAATTA
1 -TATATAT-TACTTTAAATATAAACATATTTACTT-TCTATTTTGTGTTAACATTACAAAAATTA
*
18496644 TAATTTATAAAATTATTAATTATAATATATATACCTTTATTTATATAAACTTATAATATATAAAT
63 TAACTTATAAAATTATTAATTATAATATATATACCTTTATTTATATAAACTTATAATATATAAA-
* * * * * *
18496709 CTAAAGGGAAATTGTAATATTAGAATAGTTTTGAAACCTAGTTAATTTTTGT-AATTTCATGTAA
127 CTAAAGAGAAATTGTGAGATTAAAATAGTTTTGAAACCTAGTTATTTTTTTTAAATTTCATGTAA
* * * * *
18496773 TTAAGGACAAACTCATATAATTTTATTAAATTAATTAATGAAATTATGATTATTAATTGACTTGT
192 TTAAGGACAAACCCATAT-ATTTAATTAAATTAATTCATGAAACTATGATTATTAATTAACTTGT
* * * ** *
18496838 GATGTCTTTTAATGTATACTTTATATACATTGAATTCATGT-ATAAGAAATATAAT
256 AATGTCTTTTAATATATACTTTATATATATTGTGTTAAT-TCATAAGAAATATAAT
18496893 CATACTAAAA
Statistics
Matches: 574, Mismatches: 62, Indels: 39
0.85 0.09 0.06
Matches are distributed among these distances:
340 6 0.01
341 7 0.01
342 172 0.30
343 109 0.19
344 4 0.01
345 2 0.00
346 3 0.01
348 5 0.01
350 173 0.30
351 92 0.16
352 1 0.00
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.44
Consensus pattern (343 bp):
TATATATTACTTTAAATATAAACATATTTACTTTCTATTTTGTGTTAACATTACAAAAATTATAA
CTTATAAAATTATTAATTATAATATATATACCTTTATTTATATAAACTTATAATATATAAACTAA
AGAGAAATTGTGAGATTAAAATAGTTTTGAAACCTAGTTATTTTTTTTAAATTTCATGTAATTAA
GGACAAACCCATATATTTAATTAAATTAATTCATGAAACTATGATTATTAATTAACTTGTAATGT
CTTTTAATATATACTTTATATATATTGTGTTAATTCATAAGAAATATAATTACTATTATATATAT
ATAAAACATTTTTAATAC
Found at i:18520288 original size:53 final size:53
Alignment explanation
Indices: 18520230--18520335 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
18520220 TAAAAGGAAA
18520230 GCTATAACACACAAAGTAAAGAAGCAATTTATTTGAGTTTGAAAAATTGTTTT
1 GCTATAACACACAAAGTAAAGAAGCAATTTATTTGAGTTTGAAAAATTGTTTT
18520283 GCTATAACACACAAAGTAAAGAAGCAATTTATTTGAGTTTGAAAAATTGTTTT
1 GCTATAACACACAAAGTAAAGAAGCAATTTATTTGAGTTTGAAAAATTGTTTT
18520336 CTCTTCCATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (53 bp):
GCTATAACACACAAAGTAAAGAAGCAATTTATTTGAGTTTGAAAAATTGTTTT
Found at i:18524449 original size:11 final size:10
Alignment explanation
Indices: 18524428--18524458 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
18524418 AATTGTGAAT
18524428 AAAAGAAAAA
1 AAAAGAAAAA
18524438 AAAAGAAGAAA
1 AAAAGAA-AAA
18524449 AAAAGAAAAA
1 AAAAGAAAAA
18524459 GATAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:18524459 original size:17 final size:16
Alignment explanation
Indices: 18524426--18524469 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
18524416 TAAATTGTGA
18524426 ATAAAAGAAAAAAAAAG
1 ATAAAA-AAAAAAAAAG
18524443 A-AGAAAAAAAGAAAAAG
1 ATA-AAAAAAA-AAAAAG
18524460 ATAAAAAAAA
1 ATAAAAAAAA
18524470 TAGAATAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 5 0.21
17 18 0.75
18 1 0.04
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (16 bp):
ATAAAAAAAAAAAAAG
Found at i:18526755 original size:42 final size:41
Alignment explanation
Indices: 18526682--18526861 Score: 171
Period size: 42 Copynumber: 4.3 Consensus size: 41
18526672 CGGTTGTATA
* * * * *
18526682 AAATATCTCAAAATTTTCAAAGTTCGCTTTTGCAAGCGTATC
1 AAATATTTCAAAA-TCTCAAAGTCCACTTTTGCAAGCATATC
* * * *
18526724 AAGTATTTCAAAGATCTCTAAGTCCACTTTTGTAAGCATATA
1 AAATATTTCAAA-ATCTCAAAGTCCACTTTTGCAAGCATATC
* * ***
18526766 AAAAATCTCAAAATTCTCAAAGTTGGCTTTTGCAAGCATATC
1 AAATATTTCAAAA-TCTCAAAGTCCACTTTTGCAAGCATATC
* *
18526808 AAATATTTCAAAATGCTCAAAGTCCTCTTTTGCAAGCGTATC
1 AAATATTTCAAAAT-CTCAAAGTCCACTTTTGCAAGCATATC
*
18526850 AAGTATTTCAAA
1 AAATATTTCAAA
18526862 GATTTGCATG
Statistics
Matches: 110, Mismatches: 25, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
41 2 0.02
42 107 0.97
43 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (41 bp):
AAATATTTCAAAATCTCAAAGTCCACTTTTGCAAGCATATC
Found at i:18526861 original size:84 final size:84
Alignment explanation
Indices: 18526632--18526844 Score: 250
Period size: 84 Copynumber: 2.5 Consensus size: 84
18526622 TCTTTTTAAA
* ** * ** *
18526632 CATATCAAATATTTCAAAGATTTCCAAAGTCTGCTTGTTGC-GGTTGTATAAAATATCTCAAAAT
1 CATATCAAATATTTCAAAGATCT-CAAAGTCCACTT-TTGCAAG-CATATAAAAAATCTCAAAAT
*
18526696 TTTCAAAGTTCGCTTTTGCAAG
63 TCTCAAAGTTCGCTTTTGCAAG
* * * *
18526718 CGTATCAAGTATTTCAAAGATCTCTAAGTCCACTTTTGTAAGCATATAAAAAATCTCAAAATTCT
1 CATATCAAATATTTCAAAGATCTCAAAGTCCACTTTTGCAAGCATATAAAAAATCTCAAAATTCT
*
18526783 CAAAGTTGGCTTTTGCAAG
66 CAAAGTTCGCTTTTGCAAG
*
18526802 CATATCAAATATTTCAAA-ATGCTCAAAGTCCTCTTTTGCAAGC
1 CATATCAAATATTTCAAAGAT-CTCAAAGTCCACTTTTGCAAGC
18526845 GTATCAAGTA
Statistics
Matches: 107, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
83 2 0.02
84 75 0.70
85 10 0.09
86 20 0.19
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (84 bp):
CATATCAAATATTTCAAAGATCTCAAAGTCCACTTTTGCAAGCATATAAAAAATCTCAAAATTCT
CAAAGTTCGCTTTTGCAAG
Found at i:18527353 original size:51 final size:50
Alignment explanation
Indices: 18527193--18527385 Score: 291
Period size: 50 Copynumber: 3.8 Consensus size: 50
18527183 GAAATAATCA
*
18527193 AAGTCCAAACATCAACCAAACAAATATCCAAAGTCCAAATCTAATGTATC
1 AAGTCCAAACATCAACCAAACAAATATCCAAAGTCCAAATCAAATGTATC
18527243 AAGTCCAAACATCAACCAAACAAATATCCATAA-TCCAAATCAAATGTATC
1 AAGTCCAAACATCAACCAAACAAATATCCA-AAGTCCAAATCAAATGTATC
*
18527293 AAGTCCAAACATCGAAGCCAAACAAATATCCAAA-TCCAAATCAAATGTATT
1 AAGTCCAAACATC-AA-CCAAACAAATATCCAAAGTCCAAATCAAATGTATC
* *
18527344 AAGTTCAAACATCAAAGCCAAGCAAATATCCAAAGTCCAAAT
1 AAGTCCAAACATC-AA-CCAAACAAATATCCAAAGTCCAAAT
18527386 TGTTTATGTT
Statistics
Matches: 134, Mismatches: 5, Indels: 6
0.92 0.03 0.04
Matches are distributed among these distances:
50 59 0.44
51 53 0.40
52 22 0.16
ACGTcount: A:0.49, C:0.25, G:0.07, T:0.19
Consensus pattern (50 bp):
AAGTCCAAACATCAACCAAACAAATATCCAAAGTCCAAATCAAATGTATC
Found at i:18527353 original size:101 final size:102
Alignment explanation
Indices: 18527193--18527385 Score: 295
Period size: 101 Copynumber: 1.9 Consensus size: 102
18527183 GAAATAATCA
*
18527193 AAGTCCAAACATCAACCAAACAAATATCCAAAGTCCAAATCTAATGTATCAAGTCCAAACATC-A
1 AAGTCCAAACATCAACCAAACAAATATCCAAAGTCCAAATCAAATGTATCAAGTCCAAACATCAA
18527257 A-CCAAACAAATATCCATAA-TCCAAATCAAATGTATC
66 AGCCAAACAAATATCCA-AAGTCCAAATCAAATGTATC
* *
18527293 AAGTCCAAACATCGAAGCCAAACAAATATCCAAA-TCCAAATCAAATGTATTAAGTTCAAACATC
1 AAGTCCAAACATC-AA-CCAAACAAATATCCAAAGTCCAAATCAAATGTATCAAGTCCAAACATC
*
18527357 AAAGCCAAGCAAATATCCAAAGTCCAAAT
64 AAAGCCAAACAAATATCCAAAGTCCAAAT
18527386 TGTTTATGTT
Statistics
Matches: 84, Mismatches: 4, Indels: 7
0.88 0.04 0.07
Matches are distributed among these distances:
100 13 0.15
101 29 0.35
102 21 0.25
103 21 0.25
ACGTcount: A:0.49, C:0.25, G:0.07, T:0.19
Consensus pattern (102 bp):
AAGTCCAAACATCAACCAAACAAATATCCAAAGTCCAAATCAAATGTATCAAGTCCAAACATCAA
AGCCAAACAAATATCCAAAGTCCAAATCAAATGTATC
Found at i:18527454 original size:30 final size:30
Alignment explanation
Indices: 18527418--18527484 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
18527408 AAATAGACTG
18527418 CAAAGTGCTAGATAGCATGGACAATTAAAA
1 CAAAGTGCTAGATAGCATGGACAATTAAAA
18527448 CAAAGTGCTAGATAGCATGGACAATTAAAA
1 CAAAGTGCTAGATAGCATGGACAATTAAAA
18527478 CAAAGTG
1 CAAAGTG
18527485 TGCCGTAGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.46, C:0.13, G:0.21, T:0.19
Consensus pattern (30 bp):
CAAAGTGCTAGATAGCATGGACAATTAAAA
Found at i:18528390 original size:22 final size:22
Alignment explanation
Indices: 18528365--18528422 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
18528355 ATGAGTGACT
*
18528365 GGTTTTAGGCATTGGGTTTAAG
1 GGTTTTAGGCATTGGGTATAAG
* *
18528387 GGTTTTAAGCATTAGGTATAAG
1 GGTTTTAGGCATTGGGTATAAG
18528409 GGTTTTAGGCATTG
1 GGTTTTAGGCATTG
18528423 CGTGACTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.22, C:0.05, G:0.33, T:0.40
Consensus pattern (22 bp):
GGTTTTAGGCATTGGGTATAAG
Found at i:18528546 original size:22 final size:22
Alignment explanation
Indices: 18528521--18528597 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 22
18528511 TAGAGTTTGT
* *
18528521 GTGATTGATTAATAGGGCATTG
1 GTGATTGGTTGATAGGGCATTG
* *
18528543 GTGACTGGTTGATAGTGCATTG
1 GTGATTGGTTGATAGGGCATTG
*
18528565 CGTGATTGGTTGATAAGGCATTG
1 -GTGATTGGTTGATAGGGCATTG
*
18528588 GTGACTGGTT
1 GTGATTGGTT
18528598 TTTATTGATT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
22 27 0.59
23 19 0.41
ACGTcount: A:0.21, C:0.08, G:0.35, T:0.36
Consensus pattern (22 bp):
GTGATTGGTTGATAGGGCATTG
Found at i:18528638 original size:45 final size:45
Alignment explanation
Indices: 18528522--18528652 Score: 149
Period size: 45 Copynumber: 2.9 Consensus size: 45
18528512 AGAGTTTGTG
* ** *
18528522 TGATTGATTAATAGGGCATTGGTGACTGGTTGATAGTGCATTGCG
1 TGATTGGTTAATAGGGCATTGGTGACTGGTTTTTAGTGCATTGCA
* * *
18528567 TGATTGGTTGATAAGGCATTGGTGACTGGTTTTTATTG-ATTGCA
1 TGATTGGTTAATAGGGCATTGGTGACTGGTTTTTAGTGCATTGCA
** *
18528611 TGATTGGTTAATAGGGCATTACATGACTGATTTTTAG-GCATT
1 TGATTGGTTAATAGGGCATT-GGTGACTGGTTTTTAGTGCATT
18528653 TCATAACTAG
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
44 24 0.34
45 47 0.66
ACGTcount: A:0.23, C:0.08, G:0.29, T:0.40
Consensus pattern (45 bp):
TGATTGGTTAATAGGGCATTGGTGACTGGTTTTTAGTGCATTGCA
Found at i:18537015 original size:28 final size:28
Alignment explanation
Indices: 18536975--18537029 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
18536965 GAATATAATA
*
18536975 GGTGCAAGAACCAGGAACCAGAAGAATG
1 GGTGCAAGAACCAAGAACCAGAAGAATG
*
18537003 GGTGCAGGAACCAAGAACCAGAAGAAT
1 GGTGCAAGAACCAAGAACCAGAAGAAT
18537030 AAATTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.44, C:0.18, G:0.31, T:0.07
Consensus pattern (28 bp):
GGTGCAAGAACCAAGAACCAGAAGAATG
Found at i:18538017 original size:21 final size:23
Alignment explanation
Indices: 18537977--18538019 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
18537967 GTAACTAAAT
18537977 AACAAGGAAGAAGCTTATTGGTGA
1 AACAAGGAAGAAGC-TATTGGTGA
18538001 AACAAGGAAGAA-C-ATTGGT
1 AACAAGGAAGAAGCTATTGGT
18538020 TGACCAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
23 1 0.05
24 12 0.63
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (23 bp):
AACAAGGAAGAAGCTATTGGTGA
Found at i:18538177 original size:66 final size:67
Alignment explanation
Indices: 18538063--18538189 Score: 177
Period size: 66 Copynumber: 1.9 Consensus size: 67
18538053 AAAGAGTTTG
*
18538063 AGAAACAGAATCAATTTAGTCAACCAAGTCAGTCAACTAAGTACTCTCTGTCAG-AATTTGCAAA
1 AGAAACAGAATCAACTTAGTCAACCAAGTCAGTCAACTAAGTACTCTCTGTCAGCAATTTGCAAA
18538127 CC
66 CC
* * * * *
18538129 AGAAATAGAATCAACTTAGTCAATCAAGTCAGTCGACTAAG-AGTTCTCTGTCTGCAATTTG
1 AGAAACAGAATCAACTTAGTCAACCAAGTCAGTCAACTAAGTA-CTCTCTGTCAGCAATTTG
18538190 AACTAGAGCA
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
65 1 0.02
66 46 0.87
67 6 0.11
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (67 bp):
AGAAACAGAATCAACTTAGTCAACCAAGTCAGTCAACTAAGTACTCTCTGTCAGCAATTTGCAAA
CC
Found at i:18538963 original size:45 final size:44
Alignment explanation
Indices: 18538914--18539015 Score: 116
Period size: 45 Copynumber: 2.3 Consensus size: 44
18538904 AGGGCATTTC
* *
18538914 GTGACTGGTTTT-GTGTCATTACATGACTGGTTTGTAGGGAATTGT
1 GTGACTGGTTTTAG-G-CATTACATGACTGGTTTATAAGGAATTGT
* * *
18538959 GTGACTAGGTTTTAGGCATTGCATGATTGTTTTATAAGGAATTGT
1 GTGACT-GGTTTTAGGCATTACATGACTGGTTTATAAGGAATTGT
*
18539004 GTGACTGTTTTT
1 GTGACTGGTTTT
18539016 TGTAAGGCAT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
44 5 0.10
45 36 0.73
46 7 0.14
47 1 0.02
ACGTcount: A:0.20, C:0.08, G:0.28, T:0.44
Consensus pattern (44 bp):
GTGACTGGTTTTAGGCATTACATGACTGGTTTATAAGGAATTGT
Found at i:18539012 original size:23 final size:22
Alignment explanation
Indices: 18538937--18539015 Score: 61
Period size: 23 Copynumber: 3.5 Consensus size: 22
18538927 TGTCATTACA
*
18538937 TGACTGGTTTGTAGGGAATTGTG
1 TGACTGGTTT-TAAGGAATTGTG
* **
18538960 TGACTAGGTTTT-AGGCATTGCA
1 TGACT-GGTTTTAAGGAATTGTG
* *
18538982 TGATTGTTTTATAAGGAATTGTG
1 TGACTGGTTT-TAAGGAATTGTG
*
18539005 TGACTGTTTTT
1 TGACTGGTTTT
18539016 TGTAAGGCAT
Statistics
Matches: 43, Mismatches: 10, Indels: 7
0.72 0.17 0.12
Matches are distributed among these distances:
21 4 0.09
22 12 0.28
23 22 0.51
24 5 0.12
ACGTcount: A:0.20, C:0.06, G:0.29, T:0.44
Consensus pattern (22 bp):
TGACTGGTTTTAAGGAATTGTG
Found at i:18539022 original size:25 final size:25
Alignment explanation
Indices: 18538988--18539036 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
18538978 TGCATGATTG
*
18538988 TTTTATAAGGAATTGTGTGACTGTT
1 TTTTATAAGGAATTGCGTGACTGTT
* *
18539013 TTTTGTAAGGCATTGCGTGACTGT
1 TTTTATAAGGAATTGCGTGACTGT
18539037 CATTGCTTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.20, C:0.08, G:0.27, T:0.45
Consensus pattern (25 bp):
TTTTATAAGGAATTGCGTGACTGTT
Found at i:18540777 original size:16 final size:16
Alignment explanation
Indices: 18540756--18540787 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
18540746 GACTGATTGA
*
18540756 TAGGCATTGCGTGACT
1 TAGGCATTGCATGACT
18540772 TAGGCATTGCATGACT
1 TAGGCATTGCATGACT
18540788 AGTTTATAGA
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:0.19, G:0.28, T:0.31
Consensus pattern (16 bp):
TAGGCATTGCATGACT
Found at i:18546126 original size:14 final size:14
Alignment explanation
Indices: 18546107--18546152 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
18546097 AATAATTATA
* *
18546107 AAAACAATTATAAC
1 AAAACAAATATAAT
18546121 AAAACAAATATAAT
1 AAAACAAATATAAT
*
18546135 AAATCAAATATAAT
1 AAAACAAATATAAT
18546149 AAAA
1 AAAA
18546153 TTTAACATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAACAAATATAAT
Found at i:18546733 original size:80 final size:80
Alignment explanation
Indices: 18546600--18546759 Score: 302
Period size: 80 Copynumber: 2.0 Consensus size: 80
18546590 ATCGTCATCC
**
18546600 TCTACACAATCATCGTGCATCTAATCAGATGCATCGTCATTACTCATGAACGTCACAGCGTTGTT
1 TCTACACAATCATCGTGCATCTAATCAGATGCATCGTCATTACTCACAAACGTCACAGCGTTGTT
18546665 TGAGAATGGTAATGG
66 TGAGAATGGTAATGG
18546680 TCTACACAATCATCGTGCATCTAATCAGATGCATCGTCATTACTCACAAACGTCACAGCGTTGTT
1 TCTACACAATCATCGTGCATCTAATCAGATGCATCGTCATTACTCACAAACGTCACAGCGTTGTT
18546745 TGAGAATGGTAATGG
66 TGAGAATGGTAATGG
18546760 ACCCACTGCA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (80 bp):
TCTACACAATCATCGTGCATCTAATCAGATGCATCGTCATTACTCACAAACGTCACAGCGTTGTT
TGAGAATGGTAATGG
Found at i:18547395 original size:16 final size:16
Alignment explanation
Indices: 18547374--18547405 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
18547364 TGAAAAATGT
*
18547374 GTCACACAATGCCTAA
1 GTCACACAAGGCCTAA
18547390 GTCACACAAGGCCTAA
1 GTCACACAAGGCCTAA
18547406 AAACCAAACA
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:0.38, C:0.31, G:0.16, T:0.16
Consensus pattern (16 bp):
GTCACACAAGGCCTAA
Found at i:18547573 original size:22 final size:22
Alignment explanation
Indices: 18547547--18547687 Score: 86
Period size: 22 Copynumber: 6.8 Consensus size: 22
18547537 GCAACACCTA
*
18547547 AGTCATGCAATGCCTAAAAACT-
1 AGTCACGCAATGCCT-AAAACTC
*
18547569 AGTCACGCAATGCCTACAACTC
1 AGTCACGCAATGCCTAAAACTC
* *
18547591 AGTCACGCAATG-CT-TAAGTC
1 AGTCACGCAATGCCTAAAACTC
*
18547611 A-T-A--CAATACCTAAAAC-C
1 AGTCACGCAATGCCTAAAACTC
* *
18547628 AGTCACACAGTGCCTAAAAACT-
1 AGTCACGCAATGCCT-AAAACTC
* ** *
18547650 AGTCACGAAATATCTTAAAC-C
1 AGTCACGCAATGCCTAAAACTC
*
18547671 AGTCATGCAATGCCTAA
1 AGTCACGCAATGCCTAA
18547688 GTTATGAAGA
Statistics
Matches: 89, Mismatches: 20, Indels: 21
0.68 0.15 0.16
Matches are distributed among these distances:
16 4 0.04
17 4 0.04
18 4 0.04
19 2 0.02
20 5 0.06
21 29 0.33
22 41 0.46
ACGTcount: A:0.39, C:0.27, G:0.13, T:0.21
Consensus pattern (22 bp):
AGTCACGCAATGCCTAAAACTC
Found at i:18547578 original size:38 final size:39
Alignment explanation
Indices: 18547467--18547579 Score: 106
Period size: 38 Copynumber: 2.9 Consensus size: 39
18547457 TCATGTAATG
* * * *
18547467 CCTAAGTCACGCAATGTCTAAAAACTAGACACGCAATGA
1 CCTAAGTCATGCAATGCCTAAAAACTAGTCACGCAATCA
* * * * * *
18547506 -TTATGTCATGCAATGCTTAAAAGGC-AATCTCGCAA-CA
1 CCTAAGTCATGCAATGCCTAAAA-ACTAGTCACGCAATCA
18547543 CCTAAGTCATGCAATGCCTAAAAACTAGTCACGCAAT
1 CCTAAGTCATGCAATGCCTAAAAACTAGTCACGCAAT
18547580 GCCTACAACT
Statistics
Matches: 54, Mismatches: 16, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
37 2 0.04
38 51 0.94
39 1 0.02
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.22
Consensus pattern (39 bp):
CCTAAGTCATGCAATGCCTAAAAACTAGTCACGCAATCA
Found at i:18547685 original size:43 final size:42
Alignment explanation
Indices: 18547547--18547687 Score: 114
Period size: 43 Copynumber: 3.4 Consensus size: 42
18547537 GCAACACCTA
* *
18547547 AGTCATGCAATGCCTAAAAACTAGTCACGCAATGCC-TACAACTC
1 AGTCACGCAATGCCTAAAAACTAGTCACG-AATACCTTA-AAC-C
* ** *
18547591 AGTCACGCAATG-CTTAAGTC-A-T-AC-AATACCTAAAACC
1 AGTCACGCAATGCCTAAAAACTAGTCACGAATACCTTAAACC
* * *
18547628 AGTCACACAGTGCCTAAAAACTAGTCACGAAATATCTTAAACC
1 AGTCACGCAATGCCTAAAAACTAGTCACG-AATACCTTAAACC
*
18547671 AGTCATGCAATGCCTAA
1 AGTCACGCAATGCCTAA
18547688 GTTATGAAGA
Statistics
Matches: 74, Mismatches: 16, Indels: 15
0.70 0.15 0.14
Matches are distributed among these distances:
37 11 0.15
38 13 0.18
39 2 0.03
40 3 0.04
41 3 0.04
42 1 0.01
43 30 0.41
44 11 0.15
ACGTcount: A:0.39, C:0.27, G:0.13, T:0.21
Consensus pattern (42 bp):
AGTCACGCAATGCCTAAAAACTAGTCACGAATACCTTAAACC
Found at i:18547784 original size:38 final size:37
Alignment explanation
Indices: 18547737--18547845 Score: 112
Period size: 38 Copynumber: 2.9 Consensus size: 37
18547727 ATTAAGTCAT
* * *
18547737 ACAAAGCCTAAAAGCCAGTT-TCATATTGCCTAATTCAA
1 ACAATGCCTAAAAACCAGTTCGCA-A-TGCCTAATTCAA
*
18547775 ACAATGCCTAAAAACTAGTTCGCAATGCCTAATTCAA
1 ACAATGCCTAAAAACCAGTTCGCAATGCCTAATTCAA
* * * *
18547812 GCAATGTCTAAAAATCAGTCTCGTAATGCCTAAT
1 ACAATGCCTAAAAACCAGT-TCGCAATGCCTAAT
18547846 AACTAATTGA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
37 27 0.45
38 31 0.52
39 2 0.03
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.27
Consensus pattern (37 bp):
ACAATGCCTAAAAACCAGTTCGCAATGCCTAATTCAA
Found at i:18547807 original size:37 final size:38
Alignment explanation
Indices: 18547763--18547845 Score: 116
Period size: 37 Copynumber: 2.2 Consensus size: 38
18547753 AGTTTCATAT
18547763 TGCCTAATTCAAACAATGCCTAAAAA-CTAGT-TCGCAA
1 TGCCTAATTCAAACAATGCCTAAAAATC-AGTCTCGCAA
* * *
18547800 TGCCTAATTCAAGCAATGTCTAAAAATCAGTCTCGTAA
1 TGCCTAATTCAAACAATGCCTAAAAATCAGTCTCGCAA
18547838 TGCCTAAT
1 TGCCTAAT
18547846 AACTAATTGA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
37 27 0.66
38 14 0.34
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (38 bp):
TGCCTAATTCAAACAATGCCTAAAAATCAGTCTCGCAA
Found at i:18550503 original size:42 final size:42
Alignment explanation
Indices: 18550442--18550583 Score: 230
Period size: 42 Copynumber: 3.4 Consensus size: 42
18550432 ACGGCTTATG
* *
18550442 CGCATATAACCGGGTCAGCAACGGCTTATGTGCACTCCCACT
1 CGCATATAGCCGGGTCAGCAACGGCTTATGTGCACTCCTACT
**
18550484 TACATATAGCCGGGTCAGCAACGGCTTATGTGCACTCCTACT
1 CGCATATAGCCGGGTCAGCAACGGCTTATGTGCACTCCTACT
*
18550526 CGCATATAGCTGGGTCAGCAACGGCTTATGTGCACTCCTACT
1 CGCATATAGCCGGGTCAGCAACGGCTTATGTGCACTCCTACT
*
18550568 CGCACATAGCCGGGTC
1 CGCATATAGCCGGGTC
18550584 CAAATCAACA
Statistics
Matches: 91, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 91 1.00
ACGTcount: A:0.23, C:0.31, G:0.23, T:0.23
Consensus pattern (42 bp):
CGCATATAGCCGGGTCAGCAACGGCTTATGTGCACTCCTACT
Found at i:18551859 original size:26 final size:28
Alignment explanation
Indices: 18551813--18551865 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
18551803 GACAAGTGCT
*
18551813 GGGGAGAAAAATTTACTGA-TTTGCCCG
1 GGGGAGAAAAAATTACTGATTTTGCCCG
*
18551840 GGGGTGAAAAAATTAC-GATTTTGCCC
1 GGGGAGAAAAAATTACTGATTTTGCCC
18551866 CTATACTCCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.26
Consensus pattern (28 bp):
GGGGAGAAAAAATTACTGATTTTGCCCG
Found at i:18555496 original size:42 final size:42
Alignment explanation
Indices: 18555433--18555566 Score: 214
Period size: 42 Copynumber: 3.2 Consensus size: 42
18555423 ACGGCTTATG
* *
18555433 CGCATATAGCCGGGTCAGCAACGGCTTATGTGCACTCCCACT
1 CGCACATAGTCGGGTCAGCAACGGCTTATGTGCACTCCCACT
* *
18555475 CGCACATATTTGGGTCAGCAACGGCTTATGTGCACTCCCACT
1 CGCACATAGTCGGGTCAGCAACGGCTTATGTGCACTCCCACT
* *
18555517 CGCACATAGTCGGGTCAGCAATGGCTTATGTGCACTCCTACT
1 CGCACATAGTCGGGTCAGCAACGGCTTATGTGCACTCCCACT
18555559 CGCACATA
1 CGCACATA
18555567 ACCGGGTCCG
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 84 1.00
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.24
Consensus pattern (42 bp):
CGCACATAGTCGGGTCAGCAACGGCTTATGTGCACTCCCACT
Found at i:18564705 original size:255 final size:255
Alignment explanation
Indices: 18564254--18564762 Score: 883
Period size: 255 Copynumber: 2.0 Consensus size: 255
18564244 ACCAGCAACA
18564254 CATGACTAATTTGAGTTTGGGAATTCTTACCAACCGTACCTATACCATGAATTCTTCCTTTTGAA
1 CATGACTAATTTGAGTTTGGGAATTCTTACCAACCGTACCTATACCATGAATTCTTCCTTTTGAA
18564319 TCATCTCCAAAGGATACGGTTCCTCCCTTTCTCTTATCCAGCTGAGCAAACAACATTTCATGTCC
66 TCATCTCCAAAGGATACGGTTCCTCCCTTTCTCTTATCCAGCTGAGCAAACAACATTTCATGTCC
18564384 TATCATGTGCCGTGAACAACCACTGTCCAAGTACCAAAGCTATTTCTTCTTGAGTTGAGCTTTTG
131 TATCATGTGCCGTGAACAACCACTGTCCAAGTACCAAAGCTATTTCTTCTTGAGTTGAGCTTTTG
*
18564449 AACATGTCTCCTTTAAGTCCAACTCAACCTACAAAATAGAATTTCAGTTTTTCTTTATAC
196 AACATGTCTCCTTTAAGTCCAACTCAACCTACAAAACAGAATTTCAGTTTTTCTTTATAC
* * *
18564509 CATGACTAATTTGAGTTTGGGACTTCTTGCCAGCCGTACCTATACCATGAATTCTTCCTTTTGAA
1 CATGACTAATTTGAGTTTGGGAATTCTTACCAACCGTACCTATACCATGAATTCTTCCTTTTGAA
* * *
18564574 TCATCTCCAAAGGGTACGGTTCCTCCCTTTCTCTTATCCAGCTGAGCAAATAGCATTTCATGTCC
66 TCATCTCCAAAGGATACGGTTCCTCCCTTTCTCTTATCCAGCTGAGCAAACAACATTTCATGTCC
* * * * * *
18564639 TGTCATGTGCCGTGAATAGCCATTGTCCAAGTACCAAGGCTATTTTTTCTTGAGTTGAGCTTTTG
131 TATCATGTGCCGTGAACAACCACTGTCCAAGTACCAAAGCTATTTCTTCTTGAGTTGAGCTTTTG
* *
18564704 AACATGTCTCTTTTAAGTCCAACTCAACCTACAAAACATAATTTCAGTTTTTCTTTATA
196 AACATGTCTCCTTTAAGTCCAACTCAACCTACAAAACAGAATTTCAGTTTTTCTTTATA
18564763 GGTACCCATA
Statistics
Matches: 239, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
255 239 1.00
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (255 bp):
CATGACTAATTTGAGTTTGGGAATTCTTACCAACCGTACCTATACCATGAATTCTTCCTTTTGAA
TCATCTCCAAAGGATACGGTTCCTCCCTTTCTCTTATCCAGCTGAGCAAACAACATTTCATGTCC
TATCATGTGCCGTGAACAACCACTGTCCAAGTACCAAAGCTATTTCTTCTTGAGTTGAGCTTTTG
AACATGTCTCCTTTAAGTCCAACTCAACCTACAAAACAGAATTTCAGTTTTTCTTTATAC
Found at i:18568936 original size:14 final size:14
Alignment explanation
Indices: 18568904--18568948 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
18568894 GAAATTGAAA
* *
18568904 ATTACTTTCTTTTT
1 ATTAATTTCTATTT
*
18568918 GTTAATTTCTATTT
1 ATTAATTTCTATTT
18568932 ATTAATTTCTATTT
1 ATTAATTTCTATTT
18568946 ATT
1 ATT
18568949 TCTATATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.22, C:0.09, G:0.02, T:0.67
Consensus pattern (14 bp):
ATTAATTTCTATTT
Found at i:18574771 original size:18 final size:19
Alignment explanation
Indices: 18574738--18574774 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
18574728 TATTTGATTT
18574738 GGATATTTTTGAAAAGCTA
1 GGATATTTTTGAAAAGCTA
*
18574757 GGATA-TTTTGGAAAGCTA
1 GGATATTTTTGAAAAGCTA
18574775 TGAAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.35
Consensus pattern (19 bp):
GGATATTTTTGAAAAGCTA
Found at i:18579655 original size:24 final size:22
Alignment explanation
Indices: 18579627--18579675 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 22
18579617 AATCTTTTGA
18579627 ATATTTCTTTCATTAATTAATTAG
1 ATATTT-TTTC-TTAATTAATTAG
*
18579651 ATA--TTTTCTTAATTAATTGG
1 ATATTTTTTCTTAATTAATTAG
18579671 ATATT
1 ATATT
18579676 CAGCACGGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
20 14 0.64
21 4 0.18
22 1 0.05
24 3 0.14
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (22 bp):
ATATTTTTTCTTAATTAATTAG
Found at i:18579664 original size:20 final size:21
Alignment explanation
Indices: 18579634--18579675 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
18579624 TGAATATTTC
18579634 TTTCATTAATTAATTAGATAT
1 TTTCATTAATTAATTAGATAT
*
18579655 TTTC-TTAATTAATTGGATAT
1 TTTCATTAATTAATTAGATAT
18579675 T
1 T
18579676 CAGCACGGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (21 bp):
TTTCATTAATTAATTAGATAT
Found at i:18580166 original size:4 final size:4
Alignment explanation
Indices: 18580157--18580188 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
18580147 AGCTTGGTAA
*
18580157 CTTT CTTT CTTT CTTT CTTT CTTT CCTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
18580189 AATTCTCAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
CTTT
Found at i:18595460 original size:15 final size:15
Alignment explanation
Indices: 18595426--18595474 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
18595416 TTGCTTTTGG
18595426 TATG-TTGCTGAGAA
1 TATGATTGCTGAGAA
* * *
18595440 TGTGATTGTTGAGTA
1 TATGATTGCTGAGAA
18595455 TATGATTGCTGAGAA
1 TATGATTGCTGAGAA
18595470 TATGA
1 TATGA
18595475 CTTTATAGCG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 3 0.11
15 25 0.89
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.39
Consensus pattern (15 bp):
TATGATTGCTGAGAA
Found at i:18596014 original size:22 final size:21
Alignment explanation
Indices: 18595987--18596042 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 21
18595977 TAGATGCACC
* *
18595987 ATCTATCGATAGATGGTTCAAT
1 ATCTATTGATAGATGG-TAAAT
*
18596009 ATCTATTGATAAATGGTAAAT
1 ATCTATTGATAGATGGTAAAT
18596030 -TCTATTGATAGAT
1 ATCTATTGATAGAT
18596043 CAAACTATCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 12 0.40
21 4 0.13
22 14 0.47
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (21 bp):
ATCTATTGATAGATGGTAAAT
Found at i:18609469 original size:42 final size:42
Alignment explanation
Indices: 18609417--18609536 Score: 177
Period size: 42 Copynumber: 2.9 Consensus size: 42
18609407 CATCTCATAT
* *
18609417 GCAACGACTTATGTGCACTCCCACTCGCACATAGTCGGGTCA
1 GCAACGACTTATGTGCACTCCCACTCGCACATAGCCAGGTCA
* *
18609459 GCAATGACTTATGTGAACTCCCACTCGCACATAGCCAGGTCA
1 GCAACGACTTATGTGCACTCCCACTCGCACATAGCCAGGTCA
* * *
18609501 GCAACGGCTTATGTGCACTCCTACTAGCACATAGCC
1 GCAACGACTTATGTGCACTCCCACTCGCACATAGCC
18609537 GAGTCCACAT
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.26, C:0.33, G:0.20, T:0.22
Consensus pattern (42 bp):
GCAACGACTTATGTGCACTCCCACTCGCACATAGCCAGGTCA
Found at i:18612535 original size:36 final size:36
Alignment explanation
Indices: 18612488--18612560 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
18612478 AAGGAAGTAC
18612488 TTCAGTTCTCCCATCATGCTCATTTCAAATTCACCT
1 TTCAGTTCTCCCATCATGCTCATTTCAAATTCACCT
18612524 TTCAGTTCTCCCATCATGCTCATTTCAAATTCACCT
1 TTCAGTTCTCCCATCATGCTCATTTCAAATTCACCT
18612560 T
1 T
18612561 ACATTTCCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.22, C:0.33, G:0.05, T:0.40
Consensus pattern (36 bp):
TTCAGTTCTCCCATCATGCTCATTTCAAATTCACCT
Found at i:18625151 original size:26 final size:26
Alignment explanation
Indices: 18625113--18625164 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
18625103 TATAATATTT
* *
18625113 AATTTTTACTTTAAAATATTTATTATA
1 AATTGTTACTTTAAAAT-TTTAATATA
18625140 AATTGTTA-TTTAAAATTTTAATATA
1 AATTGTTACTTTAAAATTTTAATATA
18625165 GTTATTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 8 0.35
26 8 0.35
27 7 0.30
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (26 bp):
AATTGTTACTTTAAAATTTTAATATA
Found at i:18625359 original size:20 final size:21
Alignment explanation
Indices: 18625323--18625371 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
18625313 TTAATTTAAA
18625323 ATATT-AATTTCTCATAAATT
1 ATATTAAATTTCTCATAAATT
* *
18625343 ATATTAAATTT-TTATAATTT
1 ATATTAAATTTCTCATAAATT
18625363 ATAATTAAA
1 AT-ATTAAA
18625372 ACTTGAACCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (21 bp):
ATATTAAATTTCTCATAAATT
Found at i:18627190 original size:21 final size:21
Alignment explanation
Indices: 18627138--18627190 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
18627128 GCTTTTATTG
** * *
18627138 TTGGTGGATCTGTTTCAACTG
1 TTGGTGGATCTACTGCAACTA
* *
18627159 TTAGTGAATCTACTGCAACTA
1 TTGGTGGATCTACTGCAACTA
18627180 TTGGTGGATCT
1 TTGGTGGATCT
18627191 TTAAGAAGAC
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.15, G:0.25, T:0.40
Consensus pattern (21 bp):
TTGGTGGATCTACTGCAACTA
Found at i:18627214 original size:33 final size:33
Alignment explanation
Indices: 18627172--18627238 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
18627162 GTGAATCTAC
* *
18627172 TGCAACTATTGGTGGATCTTTAAGAAGACTTGT
1 TGCAACTATTAGTGGATCTTTAAGAAGACATGT
*
18627205 TGCAACTATTAGTGGATCTTTAAGAGGACATGT
1 TGCAACTATTAGTGGATCTTTAAGAAGACATGT
18627238 T
1 T
18627239 ATTGCTCTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (33 bp):
TGCAACTATTAGTGGATCTTTAAGAAGACATGT
Found at i:18629073 original size:43 final size:43
Alignment explanation
Indices: 18628998--18629107 Score: 141
Period size: 43 Copynumber: 2.6 Consensus size: 43
18628988 TCACCAGCTC
** ** *
18628998 ATGCGCACTCCCTACTCGCACATGGCTGGGTCATCAC-CGGGTT
1 ATGCGCACTCCCTACTCGCACATAACCAGGTCATC-CTCGGCTT
18629041 ATGCGCACTCCCTACTCGCACATAACCAGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACCAGGTCATCCTCGGCTT
* *
18629084 ATGTGCACTCCCTACTCGAACATA
1 ATGCGCACTCCCTACTCGCACATA
18629108 GCCGAGTCAA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
42 1 0.02
43 58 0.98
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCAGGTCATCCTCGGCTT
Found at i:18631496 original size:20 final size:20
Alignment explanation
Indices: 18631460--18631497 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
18631450 AAAAACACAC
**
18631460 AAATAATAAAATTTAAATTT
1 AAATAATAAAAAATAAATTT
18631480 AAATAATAAAAAATAAAT
1 AAATAATAAAAAATAAAT
18631498 ATCTCAAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATAATAAAAAATAAATTT
Found at i:18632043 original size:2 final size:2
Alignment explanation
Indices: 18632036--18632071 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
18632026 CCTTATTACA
18632036 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
18632072 NNNNNNNNNN
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:18632292 original size:2 final size:2
Alignment explanation
Indices: 18632285--18632321 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
18632275 NNTTAAAGTA
*
18632285 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18632322 ATAGTAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:18634589 original size:2 final size:2
Alignment explanation
Indices: 18634582--18634608 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18634572 GATGTTGGTT
18634582 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 T
18634609 GCCAAAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18645660 original size:51 final size:50
Alignment explanation
Indices: 18645586--18645712 Score: 200
Period size: 51 Copynumber: 2.5 Consensus size: 50
18645576 GTTACAGCAT
* *
18645586 TCATCCACTTCTGGTGGAAAAATTATCCTTAGATTCTAATGGTAAAATTA
1 TCATCCACTTCTGGTGGTAAAATTATCCTTAGATTCTAATAGTAAAATTA
* * *
18645636 TCCATCCACTTCTGATGGTAAAATTATTCTTAGATTCTGATAGTAAAATTA
1 T-CATCCACTTCTGGTGGTAAAATTATCCTTAGATTCTAATAGTAAAATTA
18645687 TCATCCACTTCTGGTGGTAAAATTAT
1 TCATCCACTTCTGGTGGTAAAATTAT
18645713 AATTAGAATT
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
50 25 0.36
51 45 0.64
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (50 bp):
TCATCCACTTCTGGTGGTAAAATTATCCTTAGATTCTAATAGTAAAATTA
Found at i:18645698 original size:25 final size:25
Alignment explanation
Indices: 18645586--18645712 Score: 114
Period size: 25 Copynumber: 5.0 Consensus size: 25
18645576 GTTACAGCAT
* *
18645586 TCATCCACTTCTGGTGGAAAAATTA
1 TCATCCACTTCTGATGGTAAAATTA
* * * *
18645611 TCCT-TAGATTCTAATGGTAAAATTA
1 TCATCCA-CTTCTGATGGTAAAATTA
18645636 TCCATCCACTTCTGATGGTAAAATTA
1 T-CATCCACTTCTGATGGTAAAATTA
* ** *
18645662 TTCTTAGA-TTCTGATAGTAAAATTA
1 -TCATCCACTTCTGATGGTAAAATTA
*
18645687 TCATCCACTTCTGGTGGTAAAATTA
1 TCATCCACTTCTGATGGTAAAATTA
18645712 T
1 T
18645713 AATTAGAATT
Statistics
Matches: 78, Mismatches: 19, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
24 5 0.06
25 50 0.64
26 21 0.27
27 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (25 bp):
TCATCCACTTCTGATGGTAAAATTA
Found at i:18647106 original size:20 final size:21
Alignment explanation
Indices: 18647071--18647109 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
18647061 AAAACTAATC
18647071 AATAATAAACAAATTAAAAGA
1 AATAATAAACAAATTAAAAGA
*
18647092 AATAATATA-AAATTAAAA
1 AATAATAAACAAATTAAAA
18647110 TAACTAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (21 bp):
AATAATAAACAAATTAAAAGA
Found at i:18649198 original size:22 final size:22
Alignment explanation
Indices: 18649164--18649235 Score: 126
Period size: 22 Copynumber: 3.3 Consensus size: 22
18649154 TGCTTCGAGT
* *
18649164 TTGAGCGCCGCGACTCTCAGTG
1 TTGAGCACTGCGACTCTCAGTG
18649186 TTGAGCACTGCGACTCTCAGTG
1 TTGAGCACTGCGACTCTCAGTG
18649208 TTGAGCACTGCGACTCTCAGTG
1 TTGAGCACTGCGACTCTCAGTG
18649230 TTGAGC
1 TTGAGC
18649236 GTCGCGGTGC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.26
Consensus pattern (22 bp):
TTGAGCACTGCGACTCTCAGTG
Found at i:18653380 original size:20 final size:21
Alignment explanation
Indices: 18653345--18653383 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
18653335 AAAACTAATC
18653345 AATAATAAACAAATTAAAAGA
1 AATAATAAACAAATTAAAAGA
*
18653366 AATAATATA-AAATTAAAA
1 AATAATAAACAAATTAAAA
18653384 TAACTAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (21 bp):
AATAATAAACAAATTAAAAGA
Found at i:18660823 original size:2 final size:2
Alignment explanation
Indices: 18660816--18660851 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
18660806 AAGCTGTCGA
*
18660816 AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18660852 TTGCAGAGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18663311 original size:28 final size:26
Alignment explanation
Indices: 18663278--18663329 Score: 77
Period size: 28 Copynumber: 1.9 Consensus size: 26
18663268 TGTTTATTTT
*
18663278 ATTTTATTTTATTTTCTAAATATTAATA
1 ATTTTAATTTATTTT-TAAAT-TTAATA
18663306 ATTTTAATTTATTTTTAAATTTAA
1 ATTTTAATTTATTTTTAAATTTAA
18663330 GATATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 4 0.17
27 5 0.22
28 14 0.61
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (26 bp):
ATTTTAATTTATTTTTAAATTTAATA
Found at i:18663627 original size:17 final size:17
Alignment explanation
Indices: 18663605--18663640 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
18663595 TGCTTAATAA
*
18663605 TTTAAAACATTGATATT
1 TTTAAAACATTCATATT
*
18663622 TTTAAAATATTCATATT
1 TTTAAAACATTCATATT
18663639 TT
1 TT
18663641 ATTTATGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAAACATTCATATT
Found at i:18663679 original size:23 final size:23
Alignment explanation
Indices: 18663653--18663706 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
18663643 TTATGATTTA
18663653 AATATTATTATAA-TTAAAATATT
1 AATATTATT-TAATTTAAAATATT
18663676 AATAATT-TTTAATTTAAAATATT
1 AAT-ATTATTTAATTTAAAATATT
*
18663699 AATTTTAT
1 AATATTAT
18663707 AAATCTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 5 0.19
23 19 0.70
24 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTATTTAATTTAAAATATT
Found at i:18667164 original size:21 final size:21
Alignment explanation
Indices: 18667140--18667194 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
18667130 TAGTTTTTAG
*
18667140 ACATTGCATGACTGATTTTGA
1 ACATTGCATGACTGACTTTGA
* *
18667161 ACATTGCATGATTGACTTTGG
1 ACATTGCATGACTGACTTTGA
*
18667182 ACATTGCGTGACT
1 ACATTGCATGACT
18667195 AGTTTTTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.36
Consensus pattern (21 bp):
ACATTGCATGACTGACTTTGA
Found at i:18667263 original size:23 final size:23
Alignment explanation
Indices: 18667232--18667289 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
18667222 GTTGATAGAT
18667232 ATTGTGTGACTTGTTAGTAAGGC
1 ATTGTGTGACTTGTTAGTAAGGC
* *
18667255 ATTGCGTGACTAGTTAGTAAGGC
1 ATTGTGTGACTTGTTAGTAAGGC
18667278 ATTGTGTGACTT
1 ATTGTGTGACTT
18667290 AAGCATTACT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.22, C:0.10, G:0.29, T:0.38
Consensus pattern (23 bp):
ATTGTGTGACTTGTTAGTAAGGC
Found at i:18667332 original size:22 final size:21
Alignment explanation
Indices: 18667301--18667381 Score: 99
Period size: 22 Copynumber: 3.8 Consensus size: 21
18667291 AGCATTACTT
*
18667301 AAAAATCAATCACGCAATGCC
1 AAAAACCAATCACGCAATGCC
18667322 AAAAAACCAATCACGCAATGCC
1 -AAAAACCAATCACGCAATGCC
* * * *
18667344 TAAAACCAATCATGTAATACC
1 AAAAACCAATCACGCAATGCC
18667365 TAAAAACCAATCACGCA
1 -AAAAACCAATCACGCA
18667382 GTGATTAAGT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
21 17 0.34
22 33 0.66
ACGTcount: A:0.49, C:0.28, G:0.07, T:0.15
Consensus pattern (21 bp):
AAAAACCAATCACGCAATGCC
Found at i:18670181 original size:21 final size:24
Alignment explanation
Indices: 18670151--18670232 Score: 128
Period size: 24 Copynumber: 3.4 Consensus size: 24
18670141 AAACAGAAAC
*
18670151 AGAATTATTAACAACAGGATCAGG
1 AGAATTATCAACAACAGGATCAGG
*
18670175 AGAATTATCAACAACAGAATCAGG
1 AGAATTATCAACAACAGGATCAGG
18670199 AGAATTATCAACAACAGGATCAGG
1 AGAATTATCAACAACAGGATCAGG
**
18670223 ATTATTATCA
1 AGAATTATCA
18670233 GAGACTTGTG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (24 bp):
AGAATTATCAACAACAGGATCAGG
Found at i:18675150 original size:19 final size:19
Alignment explanation
Indices: 18675126--18675162 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
18675116 CTTCTAAACT
18675126 TCAAATCATACTCCAATAC
1 TCAAATCATACTCCAATAC
18675145 TCAAATCATACTCCAATA
1 TCAAATCATACTCCAATA
18675163 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.27
Consensus pattern (19 bp):
TCAAATCATACTCCAATAC
Found at i:18682322 original size:13 final size:13
Alignment explanation
Indices: 18682304--18682340 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
18682294 ACGAGGTAAA
18682304 ACCAAAATTTATT
1 ACCAAAATTTATT
18682317 ACCAAAATTTATT
1 ACCAAAATTTATT
*
18682330 AACAAAATTTA
1 ACCAAAATTTA
18682341 AAGCTAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (13 bp):
ACCAAAATTTATT
Found at i:18684739 original size:39 final size:42
Alignment explanation
Indices: 18684661--18684740 Score: 112
Period size: 39 Copynumber: 2.0 Consensus size: 42
18684651 AAATGTGTTA
* *
18684661 TTAATCGTGTCGTGTCGTATATTGACATGTTTAATAAACGTG
1 TTAATCGTGTCATGTCGTATATTGACACGTTTAATAAACGTG
*
18684703 TTAATCGTGTCATGTC-T-TATT-ACACGTTTATTAAACGT
1 TTAATCGTGTCATGTCGTATATTGACACGTTTAATAAACGT
18684741 ATACGTGTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
39 15 0.43
40 4 0.11
41 1 0.03
42 15 0.43
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.42
Consensus pattern (42 bp):
TTAATCGTGTCATGTCGTATATTGACACGTTTAATAAACGTG
Found at i:18686207 original size:22 final size:23
Alignment explanation
Indices: 18686179--18686235 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
18686169 TTTATAAATC
*
18686179 ATTGCGTGATCTAA-TG-TTAGTA
1 ATTGCGTGA-CTAATTGATTAGGA
*
18686201 ATTGCGTGACTAATTGATTAGGC
1 ATTGCGTGACTAATTGATTAGGA
18686224 ATTGCGTGACTA
1 ATTGCGTGACTA
18686236 TTATTGTAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 4 0.13
22 11 0.35
23 16 0.52
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.37
Consensus pattern (23 bp):
ATTGCGTGACTAATTGATTAGGA
Found at i:18687580 original size:15 final size:16
Alignment explanation
Indices: 18687560--18687589 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
18687550 AAACCATATT
18687560 TTTTTATTTT-ATTAA
1 TTTTTATTTTGATTAA
18687575 TTTTTATTTTGATTA
1 TTTTTATTTTGATTA
18687590 TCATAGGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (16 bp):
TTTTTATTTTGATTAA
Found at i:18687966 original size:24 final size:24
Alignment explanation
Indices: 18687939--18687986 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
18687929 CTGCTGCTCC
* *
18687939 TCCTGCTTCTGCTGCTGCCCCTCA
1 TCCTACTTCGGCTGCTGCCCCTCA
*
18687963 TCCTACTTCGGGTGCTGCCCCTCA
1 TCCTACTTCGGCTGCTGCCCCTCA
18687987 AGTTGAGCGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.06, C:0.44, G:0.19, T:0.31
Consensus pattern (24 bp):
TCCTACTTCGGCTGCTGCCCCTCA
Found at i:18688215 original size:63 final size:63
Alignment explanation
Indices: 18688105--18688241 Score: 193
Period size: 63 Copynumber: 2.2 Consensus size: 63
18688095 GAATATGCAA
* * * *
18688105 ATGTAGATGCAGTCAATGCAGTTGGAGATCCAGTAGTTAATGCAGTTGGAGATCCAACGAGCG
1 ATGTAGATGCAATCAATGCAGCTGGAGATCCAGCAGTCAATGCAGTTGGAGATCCAACGAGCG
* * * *
18688168 ATGTAGATGCAATCAATGCAGCTGGAGATCTAGCAGTCAATGTAGTTGGAGATCCAGCGGGCG
1 ATGTAGATGCAATCAATGCAGCTGGAGATCCAGCAGTCAATGCAGTTGGAGATCCAACGAGCG
*
18688231 ATGCAGATGCA
1 ATGTAGATGCA
18688242 GACGCAATCA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.30, C:0.17, G:0.31, T:0.23
Consensus pattern (63 bp):
ATGTAGATGCAATCAATGCAGCTGGAGATCCAGCAGTCAATGCAGTTGGAGATCCAACGAGCG
Found at i:18689834 original size:26 final size:26
Alignment explanation
Indices: 18689805--18689856 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
18689795 AACACTATTC
*
18689805 TGTATCATTTCCATATTATTCTTTGT
1 TGTATCATTTACATATTATTCTTTGT
18689831 TGTATCATTTACATATTATTCTTTGT
1 TGTATCATTTACATATTATTCTTTGT
18689857 ATTCATTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.21, C:0.13, G:0.08, T:0.58
Consensus pattern (26 bp):
TGTATCATTTACATATTATTCTTTGT
Found at i:18692126 original size:70 final size:70
Alignment explanation
Indices: 18692052--18692204 Score: 272
Period size: 70 Copynumber: 2.2 Consensus size: 70
18692042 GAATCGTGTG
18692052 AGTAGTAAATATGGATCGCGTGAACCGTTAAGA-TTAGGAATCACGTGAGTATTAGATATTGACT
1 AGTAGTAAATATGGATCGCGTGAACCGTTAAGATTTA-GAATCACGTGAGTATTAGATATTGACT
18692116 CCCGTT
65 CCCGTT
* *
18692122 AGTAGTAAATATGGATCGCGTGAACCGTTAAGATTTAGAATCGCGTGAGTATTGGATATTGACTC
1 AGTAGTAAATATGGATCGCGTGAACCGTTAAGATTTAGAATCACGTGAGTATTAGATATTGACTC
18692187 CCGTT
66 CCGTT
18692192 AGTAGTAAATATG
1 AGTAGTAAATATG
18692205 AAGTGGTGTT
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
70 77 0.96
71 3 0.04
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (70 bp):
AGTAGTAAATATGGATCGCGTGAACCGTTAAGATTTAGAATCACGTGAGTATTAGATATTGACTC
CCGTT
Found at i:18694428 original size:14 final size:13
Alignment explanation
Indices: 18694397--18694431 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
18694387 AAATCTCCCA
*
18694397 TTCTTTTTTTTCT
1 TTCTTCTTTTTCT
18694410 TTCTTCTTTTTCT
1 TTCTTCTTTTTCT
18694423 TATCTTCTT
1 T-TCTTCTT
18694432 CTTGTATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (13 bp):
TTCTTCTTTTTCT
Found at i:18694430 original size:17 final size:16
Alignment explanation
Indices: 18694397--18694434 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
18694387 AAATCTCCCA
18694397 TTCTTTTTTTTCTTTC
1 TTCTTTTTTTTCTTTC
18694413 TTCTTTTTCTTATC-TTC
1 TTCTTTTT-TT-TCTTTC
18694430 TTCTT
1 TTCTT
18694435 GTATTCTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 8 0.40
17 10 0.50
18 2 0.10
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (16 bp):
TTCTTTTTTTTCTTTC
Found at i:18694644 original size:26 final size:26
Alignment explanation
Indices: 18694589--18694719 Score: 91
Period size: 26 Copynumber: 5.4 Consensus size: 26
18694579 TTACCTTAGA
* * ** *
18694589 CATTGCATGACTAGTTTTTGACAAGT
1 CATTGCGTGACTAGTTTCTGTTAAGG
18694615 CATTGCGTGACTAGTTTCTGTTAAGG
1 CATTGCGTGACTAGTTTCTGTTAAGG
* *
18694641 CATTGCGTGAGTAG--T-TGGT-AGG
1 CATTGCGTGACTAGTTTCTGTTAAGG
* *
18694663 CATTGCGTGAC---TTACT-TT-GGG
1 CATTGCGTGACTAGTTTCTGTTAAGG
* * *
18694684 CATTGCGTGCCTAGTTTTTGTTAATG
1 CATTGCGTGACTAGTTTCTGTTAAGG
18694710 CATTGCGTGA
1 CATTGCGTGA
18694720 TTTTTTTTTA
Statistics
Matches: 80, Mismatches: 17, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
21 13 0.16
22 14 0.17
23 3 0.04
24 4 0.05
25 2 0.03
26 44 0.55
ACGTcount: A:0.19, C:0.15, G:0.27, T:0.38
Consensus pattern (26 bp):
CATTGCGTGACTAGTTTCTGTTAAGG
Found at i:18699316 original size:118 final size:117
Alignment explanation
Indices: 18699114--18699413 Score: 370
Period size: 118 Copynumber: 2.6 Consensus size: 117
18699104 TAATGCAATG
* * * * * *** * * *
18699114 CCTAATAACTAGTGAACAAACGCCTCTAAACAAAAGGCGAATTGCACAAGTCACGCGCCACCGCT
1 CCTAAAAACTACTAAACAAAAGCCTCTAAACAACACATGAATTGCACAAGTCACACGCAACCACT
* ** *
18699179 CTCGCAATATATAACAACAGGTCACGTAATATATAAAAACC-AGTAACGCAAT
66 CTCGCAATACATAACAACAGGTCACACAATATATAAAAACCGA-TAACGCAAC
*
18699231 CCTAAAAAACTACTAAACAAAAGCCTCTAAACAACACATGAATTGCACAAGTCACATGCAACCAC
1 CCT-AAAAACTACTAAACAAAAGCCTCTAAACAACACATGAATTGCACAAGTCACACGCAACCAC
* *
18699296 TCTCGCAATACATAACAACAGGTCACACAATATATAAAAATCGATCACGCAAC
65 TCTCGCAATACATAACAACAGGTCACACAATATATAAAAACCGATAACGCAAC
* * * *
18699349 CCTAAAAACTCCTAAACAAAAGCC-CTAAACAACACATGGATTGCACAAGTCACGCGCCACCACT
1 CCTAAAAACTACTAAACAAAAGCCTCTAAACAACACATGAATTGCACAAGTCACACGCAACCACT
18699413 C
66 C
18699414 ACGCTACAAC
Statistics
Matches: 158, Mismatches: 23, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
116 37 0.23
117 23 0.15
118 97 0.61
119 1 0.01
ACGTcount: A:0.43, C:0.29, G:0.11, T:0.17
Consensus pattern (117 bp):
CCTAAAAACTACTAAACAAAAGCCTCTAAACAACACATGAATTGCACAAGTCACACGCAACCACT
CTCGCAATACATAACAACAGGTCACACAATATATAAAAACCGATAACGCAAC
Found at i:18699471 original size:54 final size:54
Alignment explanation
Indices: 18699407--18699515 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
18699397 GTCACGCGCC
18699407 ACCACTCACGCTACAACAAGTAATGCAATATATAAAAACCAGTCATGTAAGCCT
1 ACCACTCACGCTACAACAAGTAATGCAATATATAAAAACCAGTCATGTAAGCCT
18699461 ACCACTCACGCTACAACAAGTAATGCAATATATAAAAACCAGTCATGTAAGCCT
1 ACCACTCACGCTACAACAAGTAATGCAATATATAAAAACCAGTCATGTAAGCCT
18699515 A
1 A
18699516 AAAAACTACT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.43, C:0.26, G:0.11, T:0.20
Consensus pattern (54 bp):
ACCACTCACGCTACAACAAGTAATGCAATATATAAAAACCAGTCATGTAAGCCT
Found at i:18699632 original size:111 final size:111
Alignment explanation
Indices: 18699470--18699676 Score: 301
Period size: 111 Copynumber: 1.9 Consensus size: 111
18699460 TACCACTCAC
* * *
18699470 GCTACAACAAGTAATGCAATATATAAAAACCAGTCATGTAAGCCTAAAAAACTACTGAACAAAAG
1 GCTACAACAAGTAATGCAATATATAAAAACCAGTCACGCAAGCCTAAAAAACTACTAAACAAAAG
18699535 CCTCAAAACAACACATAAATTGCACAAGTCACGTGCCACCATTCTA
66 CCTCAAAACAACACATAAATTGCACAAGTCACGTGCCACCATTCTA
* * * *
18699581 GCTACAACAGGTAACT-CAATATAT-AAAACCAGTCACGCACTGCCTAAAAAACTACTAAATAAT
1 GCTACAACAAGTAA-TGCAATATATAAAAACCAGTCACGCA-AGCCTAAAAAACTACTAAACAAA
* *
18699644 AGCCTCAAAGCAACACATGAATTGCACAAGTCA
64 AGCCTCAAAACAACACATAAATTGCACAAGTCA
18699677 GTCACGCACC
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
110 13 0.15
111 71 0.84
112 1 0.01
ACGTcount: A:0.45, C:0.25, G:0.11, T:0.19
Consensus pattern (111 bp):
GCTACAACAAGTAATGCAATATATAAAAACCAGTCACGCAAGCCTAAAAAACTACTAAACAAAAG
CCTCAAAACAACACATAAATTGCACAAGTCACGTGCCACCATTCTA
Found at i:18700348 original size:30 final size:30
Alignment explanation
Indices: 18700312--18700371 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
18700302 TCTCCTGCTG
*
18700312 GAATATGTGTAACTGGTCCCTCACACTCAA
1 GAATATGTGCAACTGGTCCCTCACACTCAA
18700342 GAATATGTGCAACTGGTCCCTCACACTCAA
1 GAATATGTGCAACTGGTCCCTCACACTCAA
18700372 AGGCACCTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (30 bp):
GAATATGTGCAACTGGTCCCTCACACTCAA
Found at i:18701082 original size:102 final size:103
Alignment explanation
Indices: 18700924--18701164 Score: 331
Period size: 103 Copynumber: 2.3 Consensus size: 103
18700914 TACAAATAGG
* * * * **
18700924 TCACGTAATACTCAACAAATATTCAATCACATAATATTAATTCACGTAACGCCTGTCACACAACG
1 TCACGCAATGCTCAACAAATATTCAGTCACATAATATTAAGTCACGTAACAACTGTCACACAACG
*
18700989 CT-AACAAATATTCAGTCACGTAATGTCTATAAAGAAC
66 CTCAACAAATATTCAGTCACGTAATGCCTATAAAGAAC
** * ** *
18701026 TCACGCAATGCTCAACAAATATTCAGTCAGGTAATATTTAGTCACGTATTAACTGTCACGCAACG
1 TCACGCAATGCTCAACAAATATTCAGTCACATAATATTAAGTCACGTAACAACTGTCACACAACG
*
18701091 CTCAACATATATTCAGTCACGTAATGCCTATAAAGAAC
66 CTCAACAAATATTCAGTCACGTAATGCCTATAAAGAAC
* *
18701129 TCACGCAATGCTCAACAAATATTCAGGCACCTAATA
1 TCACGCAATGCTCAACAAATATTCAGTCACATAATA
18701165 CCAAATAAAT
Statistics
Matches: 121, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
102 55 0.45
103 66 0.55
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (103 bp):
TCACGCAATGCTCAACAAATATTCAGTCACATAATATTAAGTCACGTAACAACTGTCACACAACG
CTCAACAAATATTCAGTCACGTAATGCCTATAAAGAAC
Found at i:18701152 original size:48 final size:48
Alignment explanation
Indices: 18700991--18701163 Score: 193
Period size: 48 Copynumber: 3.5 Consensus size: 48
18700981 ACACAACGCT
18700991 AACAAATATTCAGTCACGTAATGTCTATAAAGAACTCACGCAATGCTC
1 AACAAATATTCAGTCACGTAATGTCTATAAAGAACTCACGCAATGCTC
* * * ** *
18701039 AACAAATATTCAGTCAGGTAATATTTAGTCACGTATTAACTGTCACGCAACGCTC
1 AACAAATATTCAGTCACGTAATGTCTA-T-A---AAGAAC--TCACGCAATGCTC
* *
18701094 AACATATATTCAGTCACGTAATGCCTATAAAGAACTCACGCAATGCTC
1 AACAAATATTCAGTCACGTAATGTCTATAAAGAACTCACGCAATGCTC
* *
18701142 AACAAATATTCAGGCACCTAAT
1 AACAAATATTCAGTCACGTAAT
18701164 ACCAAATAAA
Statistics
Matches: 101, Mismatches: 17, Indels: 14
0.77 0.13 0.11
Matches are distributed among these distances:
48 55 0.54
49 1 0.01
50 5 0.05
53 5 0.05
54 1 0.01
55 34 0.34
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (48 bp):
AACAAATATTCAGTCACGTAATGTCTATAAAGAACTCACGCAATGCTC
Found at i:18701993 original size:2 final size:2
Alignment explanation
Indices: 18701986--18702020 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
18701976 TAAATTAAGA
18701986 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18702021 TATGCCACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:18702304 original size:2 final size:2
Alignment explanation
Indices: 18702299--18702337 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
18702289 TATGTGTGTG
18702299 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18702338 GCCGATAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18710169 original size:21 final size:21
Alignment explanation
Indices: 18710147--18710187 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
18710137 AAGAATCGTA
*
18710147 TTAATATTTTAATAATAAATAT
1 TTAATA-TCTAATAATAAATAT
18710169 TTAATATCTAATAATAAAT
1 TTAATATCTAATAATAAAT
18710188 TATTCACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
TTAATATCTAATAATAAATAT
Found at i:18710664 original size:21 final size:22
Alignment explanation
Indices: 18710628--18710675 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
18710618 AAGATACAGA
*
18710628 ATTAATATTTTAATAATGAAATT
1 ATTAATATTCTAATAAT-AAATT
18710651 -TTAATA-TCTAATAATAAATT
1 ATTAATATTCTAATAATAAATT
18710671 ATTAA
1 ATTAA
18710676 ATTATTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 5 0.22
21 12 0.52
22 6 0.26
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (22 bp):
ATTAATATTCTAATAATAAATT
Found at i:18716930 original size:20 final size:21
Alignment explanation
Indices: 18716894--18716933 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
18716884 ATTCATTTCT
18716894 TTGATTAAAAAATTTAATTTG
1 TTGATTAAAAAATTTAATTTG
18716915 TTGATTAAAAAA-TTAATTT
1 TTGATTAAAAAATTTAATTT
18716934 AATTTTACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (21 bp):
TTGATTAAAAAATTTAATTTG
Found at i:18727083 original size:20 final size:20
Alignment explanation
Indices: 18727058--18727099 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
18727048 TATTTCCTGG
18727058 TTTCATTCAGTGCATATGCA
1 TTTCATTCAGTGCATATGCA
*
18727078 TTTCATTCAGTGCATGTGCA
1 TTTCATTCAGTGCATATGCA
18727098 TT
1 TT
18727100 CCTATCTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (20 bp):
TTTCATTCAGTGCATATGCA
Found at i:18727293 original size:24 final size:24
Alignment explanation
Indices: 18727262--18727325 Score: 101
Period size: 24 Copynumber: 2.7 Consensus size: 24
18727252 TAATATTCTT
*
18727262 TTTTAAAGTTATATTTCATAATAC
1 TTTTAAAGTTATATTTCAGAATAC
*
18727286 TTTTAAAGTTATATTTCAGACTAC
1 TTTTAAAGTTATATTTCAGAATAC
*
18727310 TGTTAAAGTTATATTT
1 TTTTAAAGTTATATTT
18727326 TACAACAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.50
Consensus pattern (24 bp):
TTTTAAAGTTATATTTCAGAATAC
Found at i:18732863 original size:11 final size:11
Alignment explanation
Indices: 18732838--18732873 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
18732828 TAGCATGTCT
18732838 TTGTTGTTTCC
1 TTGTTGTTTCC
18732849 ---TTGTTTCC
1 TTGTTGTTTCC
18732857 TTGTTGTTTCC
1 TTGTTGTTTCC
18732868 TTGTTG
1 TTGTTG
18732874 ACGATGGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 8 0.36
11 14 0.64
ACGTcount: A:0.00, C:0.17, G:0.19, T:0.64
Consensus pattern (11 bp):
TTGTTGTTTCC
Found at i:18743796 original size:5 final size:5
Alignment explanation
Indices: 18743784--18743813 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
18743774 TATTCTATCA
*
18743784 AACTT AACCT AACTT AACTT AACTT AACTT
1 AACTT AACTT AACTT AACTT AACTT AACTT
18743814 GGGCCACACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (5 bp):
AACTT
Found at i:18746161 original size:21 final size:20
Alignment explanation
Indices: 18746137--18746184 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
18746127 ATCTTACCTT
* *
18746137 TTTTTTACTTGTTTCCTTGAA
1 TTTTTCACTT-TTCCCTTGAA
*
18746158 TTTTCACACTTTTCCCTTGAA
1 TTTT-TCACTTTTCCCTTGAA
18746179 TTTTTC
1 TTTTTC
18746185 CACCTAGGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.05
21 17 0.77
22 4 0.18
ACGTcount: A:0.15, C:0.21, G:0.06, T:0.58
Consensus pattern (20 bp):
TTTTTCACTTTTCCCTTGAA
Found at i:18748329 original size:37 final size:37
Alignment explanation
Indices: 18748279--18748430 Score: 202
Period size: 37 Copynumber: 4.1 Consensus size: 37
18748269 GTTGTGTGAG
*
18748279 GATGTTGAAGTGTGTGAGTAAGGAGTGCACACATGAT
1 GATGTTGAAGTGTGCGAGTAAGGAGTGCACACATGAT
* *
18748316 GATGTT-AGAGTGTGCAAGTAGGGAGTGCACACATGAT
1 GATGTTGA-AGTGTGCGAGTAAGGAGTGCACACATGAT
* *
18748353 GATGTT-AGAGTGTGCGAGT-AGGAAATGCACAGATGAT
1 GATGTTGA-AGTGTGCGAGTAAGG-AGTGCACACATGAT
*
18748390 GATGTTGAAGTGTGTGAGTAAGGAGTGCACACATGAT
1 GATGTTGAAGTGTGCGAGTAAGGAGTGCACACATGAT
18748427 GATG
1 GATG
18748431 AATGCATATG
Statistics
Matches: 101, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
36 3 0.03
37 94 0.93
38 4 0.04
ACGTcount: A:0.30, C:0.09, G:0.36, T:0.26
Consensus pattern (37 bp):
GATGTTGAAGTGTGCGAGTAAGGAGTGCACACATGAT
Found at i:18763825 original size:2 final size:2
Alignment explanation
Indices: 18763820--18763880 Score: 59
Period size: 2 Copynumber: 30.5 Consensus size: 2
18763810 ACATGTTTAC
** ** * *
18763820 AT AT AT AT AT GC AT AT AT GC AT AT AT AT AC AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
18763862 AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT A
18763881 CCCATCATCA
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (2 bp):
AT
Found at i:18763845 original size:18 final size:18
Alignment explanation
Indices: 18763817--18763880 Score: 92
Period size: 18 Copynumber: 3.4 Consensus size: 18
18763807 CACACATGTT
18763817 TACATATATATATGCATATA
1 TACATATATATA--CATATA
*
18763837 TGCATATATATACATATA
1 TACATATATATACATATA
*
18763855 TACATATATATATATATA
1 TACATATATATACATATA
18763873 TACATATA
1 TACATATA
18763881 CCCATCATCA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
18 30 0.73
20 11 0.27
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (18 bp):
TACATATATATACATATA
Found at i:18763981 original size:43 final size:43
Alignment explanation
Indices: 18763916--18764025 Score: 141
Period size: 43 Copynumber: 2.6 Consensus size: 43
18763906 CGTCATCATC
* ** *
18763916 ATGCGCACTCCTTACTCGCACAT-GGCTAGGTCATCACCGGGTT
1 ATGCGCACTCCCTACTCGCACATAATC-AGGTCATCACCGGCTT
* * *
18763959 ATGCGCACTCCCTACTCACACATAATCGGGTCATCATCGGCTT
1 ATGCGCACTCCCTACTCGCACATAATCAGGTCATCACCGGCTT
18764002 ATGCGCACTCCCTACTCGCACATA
1 ATGCGCACTCCCTACTCGCACATA
18764026 GCTGAGTCAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
43 57 0.98
44 1 0.02
ACGTcount: A:0.22, C:0.35, G:0.18, T:0.25
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAATCAGGTCATCACCGGCTT
Found at i:18766377 original size:18 final size:18
Alignment explanation
Indices: 18766354--18766397 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
18766344 TAAGGGCCAT
*
18766354 GAATGAGCAAAATGCCTC
1 GAATGAGCAAAATGCCCC
18766372 GAATGAGCAAAATGCCCC
1 GAATGAGCAAAATGCCCC
18766390 GAATGAGC
1 GAATGAGC
18766398 CTATTGTGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.14
Consensus pattern (18 bp):
GAATGAGCAAAATGCCCC
Found at i:18769539 original size:20 final size:20
Alignment explanation
Indices: 18769514--18769551 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
18769504 GGAAGAAAAG
18769514 AGAAAAACCAAAGGAAAACT
1 AGAAAAACCAAAGGAAAACT
**
18769534 AGAAAATTCAAAGGAAAA
1 AGAAAAACCAAAGGAAAA
18769552 ATCGCGTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.66, C:0.11, G:0.16, T:0.08
Consensus pattern (20 bp):
AGAAAAACCAAAGGAAAACT
Found at i:18790152 original size:14 final size:14
Alignment explanation
Indices: 18790125--18790159 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
18790115 GACTTTGATG
18790125 ATATGATATATATAC
1 ATAT-ATATATATAC
*
18790140 ATATATATGTATAC
1 ATATATATATATAC
18790154 ATATAT
1 ATATAT
18790160 TTATCACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (14 bp):
ATATATATATATAC
Found at i:18790286 original size:2 final size:2
Alignment explanation
Indices: 18790279--18790308 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
18790269 TTAGGCAAAA
18790279 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
18790309 TTGCCTAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18791479 original size:4 final size:4
Alignment explanation
Indices: 18791472--18791508 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
18791462 AATATGTGTG
18791472 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
18791509 ATATATATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:18793356 original size:35 final size:34
Alignment explanation
Indices: 18793270--18793364 Score: 111
Period size: 34 Copynumber: 2.8 Consensus size: 34
18793260 GGAAAGGTAA
* *
18793270 AAAGGTTATGCTTGTTCTCGTGAAAAGGCATTGG
1 AAAGGTTGTGCTTGCTCTCGTGAAAAGGCATTGG
* **
18793304 AAAGGTTGTGCTAGCTCTCGTGAAAAGGC-TTTT
1 AAAGGTTGTGCTTGCTCTCGTGAAAAGGCATTGG
*
18793337 ATATGGTTTGTGCTTGCTCTCGTGAAAA
1 A-AAGG-TTGTGCTTGCTCTCGTGAAAA
18793365 AATAATGTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
33 3 0.06
34 29 0.56
35 20 0.38
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.35
Consensus pattern (34 bp):
AAAGGTTGTGCTTGCTCTCGTGAAAAGGCATTGG
Found at i:18793961 original size:24 final size:24
Alignment explanation
Indices: 18793931--18793986 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
18793921 TAAATCATTA
* *
18793931 AAAATTTTCAAATGTTTGAAAATT
1 AAAATTTCCAAATCTTTGAAAATT
18793955 AAAATTTCCAAATCTTTGAAAATT
1 AAAATTTCCAAATCTTTGAAAATT
18793979 AAAATTTC
1 AAAATTTC
18793987 AATAATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.39
Consensus pattern (24 bp):
AAAATTTCCAAATCTTTGAAAATT
Found at i:18797589 original size:46 final size:46
Alignment explanation
Indices: 18797522--18797609 Score: 149
Period size: 46 Copynumber: 1.9 Consensus size: 46
18797512 TTTTTATTTG
*
18797522 AAGCATCCTCATCTTAATTTATGATGATGGAATCAAATATGTCATT
1 AAGCATCCTCATCTCAATTTATGATGATGGAATCAAATATGTCATT
* *
18797568 AAGCATCCTCATCTCACTTTATGATGATGTAATCAAATATGT
1 AAGCATCCTCATCTCAATTTATGATGATGGAATCAAATATGT
18797610 TATCTTATCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.36
Consensus pattern (46 bp):
AAGCATCCTCATCTCAATTTATGATGATGGAATCAAATATGTCATT
Done.