Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167926.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_19, 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: 20060819
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 113000 characters in sequence are not A, C, G, or T
File 69 of 117
Found at i:12753873 original size:27 final size:27
Alignment explanation
Indices: 12753835--12753889 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
12753825 AAGTTCAATC
*
12753835 GTTGTTAATTTAGTGACGTTTGTATTA
1 GTTGCTAATTTAGTGACGTTTGTATTA
12753862 GTTGCTAATTTAGTGACGTTTGTATTA
1 GTTGCTAATTTAGTGACGTTTGTATTA
12753889 G
1 G
12753890 AAAAATGTCG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.05, G:0.24, T:0.49
Consensus pattern (27 bp):
GTTGCTAATTTAGTGACGTTTGTATTA
Found at i:12755913 original size:305 final size:314
Alignment explanation
Indices: 12755225--12756394 Score: 898
Period size: 321 Copynumber: 3.7 Consensus size: 314
12755215 AAATTTGAAT
* * * * * **
12755225 AAGTTTAATATCATGTATTTAATCTATCTAAATTGTTAAAATAGAA-ATATAACTATAAAAATAT
1 AAGTTTAATATCATGTATTGAAGCTATCCAAACTATTAAAATAGAATA-ATAA-TATAAATTTAT
* * *
12755289 ATTTTTGCCCTTTAATAGCA-CAAAAGTCTTAAACAAACAT-AAACAATAAAAGCATTTTGGCCT
64 ATTTTTGCCTTTTAATAGCATAAAAAGTCCTAAAC-AA-ATGAAAC-AT---A-C--TTT----T
* *
12755352 TTCACACATATCAA-T-CATGGAAACTAAATTCAATCATT-TGGACAAGTTTAATATCATGTATT
116 TTCACACATATCAACTGCA--GAAACCAAGTTCAATCATTCT--AC-A--TTAATATCATGTATT
* * * * * *
12755414 GAAGCTATCCAAATTGTTAAAACAGAAAAATAATAGCAACTTT-TCTTTTTACCTTTTAACAGCA
174 GAAGCTATCCAAACTGTTAAAATAGAATAATAATAGCAAATTTGTATTTTTGCCTTTTAACAGCA
* * * * *
12755478 AAAAAGGTTCTAAACAAAGGTAAACAACAACTTTTTCACATTTATCAACTATG-A-AAACCAAGT
239 AAAAA-GTCCTAAACAGACGTAAACGACAACTTTTTCACATATATCAA-T-TGTAGAAACCAAGT
* *
12755541 TCAATTATTCCAAA
301 TCAATCATTCCGAA
* * *
12755555 AAGTTTAATATCATGTATTGAAGCTATCCAAACTATTAAGATAAAACAATAATAGTAAATTTATA
1 AAGTTTAATATCATGTATTGAAGCTATCCAAACTATTAAAATAGAATAATAATA-TAAATTTATA
* *
12755620 TTTTTGCCTTTTAA-AGGCCTAAAAA-TCCTAAA-GAA-G-AACA-A-TTTTTTCACACATATCA
65 TTTTTGCCTTTTAATA-GCATAAAAAGTCCTAAACAAATGAAACATACTTTTTTCACACATATCA
* * * * * *
12755678 ACTGCGGAAACTAAGTTCAATCA-T-T-C-TTAAAATCGTGTATTGAAGCCACCCAAACTGTTAA
129 ACTGCAGAAACCAAGTTCAATCATTCTACATTAATATCATGTATTGAAGCTATCCAAACTGTTAA
* * * * *
12755739 AATATAATAATAATAGCAAATTTGTATTTTTGCCTTTTAACGGCAAAAACAATCCTAAATAGACA
194 AATAGAATAATAATAGCAAATTTGTATTTTTGCCTTTTAACAGCAAAAA-AGTCCTAAACAGACG
* * *
12755804 TAAACGACAACTTTTTCACATATATCAATTGTAGAAATCAAGTTCAATCATT-TGAC
258 TAAACGACAACTTTTTCACATATATCAATTGTAGAAACCAAGTTCAATCATTCCGAA
* * **
12755860 AAGTTTTATATCATGTATTGAAGCTATACAAACTATTAAAATAGAATAATAATATCAAATTTGCA
1 AAGTTTAATATCATGTATTGAAGCTATCCAAACTATTAAAATAGAATAATAATAT-AAATTTATA
*
12755925 -TTTTGCCTTTTAATAGCATAAAAAGTCCTAAACAAATGTAAATATTAGCTTTTTTTCACACATA
65 TTTTTGCCTTTTAATAGCATAAAAAGTCCTAAACAAATG-AAACA-TA-C-TTTTTTCACACATA
* * *
12755989 TCAACTGTAGAAACCAAGTTCAATTATTCTGACAAATTTAATATCATGTATTGAAGCTATGCAAA
126 TCAACTGCAGAAACCAAGTTCAATCATTCT-AC--A-TTAATATCATGTATTGAAGCTATCCAAA
* * * * * * * *
12756054 CTATTAAAATAGAATAATAACAACAAATTTGCATGTTTGCCTCTTAACAGCACAAAAGTCATAAA
187 CTGTTAAAATAGAATAATAATAGCAAATTTGTATTTTTGCCTTTTAACAGCAAAAAAGTCCTAAA
* * * * * * * *
12756119 CAGATGTAAATGATAACTTTTTCACACATATCAACTGTGGAAACCAAGTTCAATCATTCGGAT
252 CAGACGTAAACGACAACTTTTTCACATATATCAATTGTAGAAACCAAGTTCAATCATTCCGAA
* * * * *
12756182 AAGTTTAATATCATGTATT-AGAGCTATCCAAATTGTTAAAATAGAATAATAACAACAAATTTTT
1 AAGTTTAATATCATGTATTGA-AGCTATCCAAACTATTAAAATAGAATAATAA-TATAAATTTAT
* * ** * * * * * *
12756246 ATTTTTACCTATTAACGGCACAAAAAGTCTTAAATAAACGTAAAAAATA-TCTTTTTCATACATA
64 ATTTTTGCCTTTTAATAGCATAAAAAGTCCTAAACAAA--TGAAACATACT-TTTTTCACACATA
* * * * * * *
12756310 TCAACCGC-GAAAACAAAGTTTAATAATT-TGGATAAGTTTAATATCATGTATTGAAACTATCAA
126 TCAACTGCAG-AAACCAAGTTCAATCATTCT--A-CA--TTAATATCATGTATTGAAGCTATCCA
* *
12756373 AACTATTAAAATAGAACAATAA
185 AACTGTTAAAATAGAATAATAA
12756395 CTATAAATTT
Statistics
Matches: 688, Mismatches: 110, Indels: 93
0.77 0.12 0.10
Matches are distributed among these distances:
304 24 0.03
305 116 0.17
306 74 0.11
307 2 0.00
309 4 0.01
311 1 0.00
312 2 0.00
313 31 0.05
314 37 0.05
315 2 0.00
316 1 0.00
317 3 0.00
318 1 0.00
320 4 0.01
321 138 0.20
322 125 0.18
323 32 0.05
324 4 0.01
325 2 0.00
326 3 0.00
327 1 0.00
328 1 0.00
329 3 0.00
330 72 0.10
331 5 0.01
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.33
Consensus pattern (314 bp):
AAGTTTAATATCATGTATTGAAGCTATCCAAACTATTAAAATAGAATAATAATATAAATTTATAT
TTTTGCCTTTTAATAGCATAAAAAGTCCTAAACAAATGAAACATACTTTTTTCACACATATCAAC
TGCAGAAACCAAGTTCAATCATTCTACATTAATATCATGTATTGAAGCTATCCAAACTGTTAAAA
TAGAATAATAATAGCAAATTTGTATTTTTGCCTTTTAACAGCAAAAAAGTCCTAAACAGACGTAA
ACGACAACTTTTTCACATATATCAATTGTAGAAACCAAGTTCAATCATTCCGAA
Found at i:12756360 original size:161 final size:159
Alignment explanation
Indices: 12755351--12756434 Score: 882
Period size: 160 Copynumber: 6.8 Consensus size: 159
12755341 CATTTTGGCC
* *
12755351 TTTCACACATATCAATCATGG-AAACTAAATTCAATCATTTGGACAAGTTTAATATCATGTATTG
1 TTTCACACATATCAA-C-TGGAAAACCAAGTTCAATCATTT-GACAAGTTTAATATCATGTATTG
* * * * * * * * * *
12755415 AAGCTATCCAAATTGTTAAAACAGAAAAATAATAGCAACTTTTC-TTTTTACCTTTTAACAGCA-
63 AAGCTATCCAAACTATTAAAATAGAATAATAACAACAAATTTGCATTTTTGCCTTTTAACGGCAC
* * * *
12755478 AAAAAGGTTCTAAACAAAGGTAAACAACAACTT
128 AAAAA-GTCCTAAACAAACGTAAATAATAACTT
** * * ** *
12755511 TTTCACATTTATCAACTATGAAAACCAAGTTCAATTATTCCAAAAAGTTTAATATCATGTATTGA
1 TTTCACACATATCAACT-GGAAAACCAAGTTCAATCATT-TGACAAGTTTAATATCATGTATTGA
* * * * ** ** *
12755576 AGCTATCCAAACTATTAAGATAAAACAATAATAGTAAATTTATATTTTTGCCTTTTAAAGGC-CT
64 AGCTATCCAAACTATTAAAATAGAATAATAACAACAAATTTGCATTTTTGCCTTTTAACGGCAC-
* *
12755640 AAAAA-TCCTAAA-GAA-G--AACAAT---TT
128 AAAAAGTCCTAAACAAACGTAAATAATAACTT
* * * *
12755664 TTTCACACATATCAACTGCGGAAACTAAGTTCAATCA-TT--C----TTAAAATCGTGTATTGAA
1 TTTCACACATATCAACTG-GAAAACCAAGTTCAATCATTTGACAAGTTTAATATCATGTATTGAA
* * * * * * *
12755722 GCCACCCAAACTGTTAAAATATAATAATAATAGCAAATTTGTATTTTTGCCTTTTAACGGCA-AA
65 GCTATCCAAACTATTAAAATAGAATAATAACAACAAATTTGCATTTTTGCCTTTTAACGGCACAA
* * * * ** *
12755786 AACAATCCTAAATAGACATAAACGACAACTT
130 AA-AGTCCTAAACAAACGTAAATAATAACTT
* * * * *
12755817 TTTCACATATATCAATTGTAGAAATCAAGTTCAATCATTTGACAAGTTTTATATCATGTATTGAA
1 TTTCACACATATCAACTGGA-AAACCAAGTTCAATCATTTGACAAGTTTAATATCATGTATTGAA
* * * ** *
12755882 GCTATACAAACTATTAAAATAGAATAATAATATCAAATTTGCA-TTTTGCCTTTTAATAGCATAA
65 GCTATCCAAACTATTAAAATAGAATAATAACAACAAATTTGCATTTTTGCCTTTTAACGGCACAA
* * *
12755946 AAAGTCCTAAACAAATGTAAATATTAGCTTTT
130 AAAGTCCTAAACAAACGTAAATAATAAC--TT
* * *
12755978 TTTCACACATATCAACTGTAGAAACCAAGTTCAATTATTCTGACAAATTTAATATCATGTATTGA
1 TTTCACACATATCAACTGGA-AAACCAAGTTCAATCATT-TGACAAGTTTAATATCATGTATTGA
* * * *
12756043 AGCTATGCAAACTATTAAAATAGAATAATAACAACAAATTTGCATGTTTGCCTCTTAACAGCAC-
64 AGCTATCCAAACTATTAAAATAGAATAATAACAACAAATTTGCATTTTTGCCTTTTAACGGCACA
* * * *
12756107 AAAAGTCATAAACAGATGTAAATGATAACTT
129 AAAAGTCCTAAACAAACGTAAATAATAACTT
* * *
12756138 TTTCACACATATCAACTGTGGAAACCAAGTTCAATCATTCGGATAAGTTTAATATCATGTATT-A
1 TTTCACACATATCAACTG-GAAAACCAAGTTCAATCATT-TGACAAGTTTAATATCATGTATTGA
* * ** * *
12756202 GAGCTATCCAAATTGTTAAAATAGAATAATAACAACAAATTTTTATTTTTACCTATTAACGGCAC
64 -AGCTATCCAAACTATTAAAATAGAATAATAACAACAAATTTGCATTTTTGCCTTTTAACGGCAC
* * * *
12756267 AAAAAGTCTTAAATAAACGTAAAAAATATCTT
128 AAAAAGTCCTAAACAAACGTAAATAATAACTT
* * * * * *
12756299 TTTCATACATATCAACCGCGAAAACAAAGTTTAATAATTTGGATAAGTTTAATATCATGTATTGA
1 TTTCACACATATCAACTG-GAAAACCAAGTTCAATCATTT-GACAAGTTTAATATCATGTATTGA
* * * * * * * * * *
12756364 AACTATCAAAACTATTAAAATAGAACAATAACTATAAATTTACATTTTTACCTTGTAAAGGCATA
64 AGCTATCCAAACTATTAAAATAGAATAATAACAACAAATTTGCATTTTTGCCTTTTAACGGCACA
12756429 AAAAGT
129 AAAAGT
12756435 TGTAAACAGA
Statistics
Matches: 751, Mismatches: 138, Indels: 69
0.78 0.14 0.07
Matches are distributed among these distances:
144 4 0.01
145 69 0.09
146 7 0.01
147 1 0.00
150 4 0.01
152 1 0.00
153 64 0.09
154 2 0.00
156 6 0.01
158 2 0.00
159 37 0.05
160 257 0.34
161 188 0.25
162 94 0.13
163 15 0.02
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (159 bp):
TTTCACACATATCAACTGGAAAACCAAGTTCAATCATTTGACAAGTTTAATATCATGTATTGAAG
CTATCCAAACTATTAAAATAGAATAATAACAACAAATTTGCATTTTTGCCTTTTAACGGCACAAA
AAGTCCTAAACAAACGTAAATAATAACTT
Found at i:12756851 original size:19 final size:19
Alignment explanation
Indices: 12756823--12756859 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12756813 TGTTTATGCC
*
12756823 ACTATTATTACATTACTAT
1 ACTATAATTACATTACTAT
*
12756842 ACTATAATTATATTACTA
1 ACTATAATTACATTACTA
12756860 CTATACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.46
Consensus pattern (19 bp):
ACTATAATTACATTACTAT
Found at i:12756861 original size:22 final size:22
Alignment explanation
Indices: 12756836--12756878 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
12756826 ATTATTACAT
12756836 TACTATACTATAATTATATTAC
1 TACTATACTATAATTATATTAC
*
12756858 TACTATACTATTATTATATTA
1 TACTATACTATAATTATATTA
12756879 TTATAGTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.49
Consensus pattern (22 bp):
TACTATACTATAATTATATTAC
Found at i:12756868 original size:41 final size:38
Alignment explanation
Indices: 12756823--12756950 Score: 104
Period size: 41 Copynumber: 3.4 Consensus size: 38
12756813 TGTTTATGCC
12756823 ACTATTATTACATTACTATACTATAATT-ATATTACTACTAT
1 ACTATTATTACATTACTATACTAT-ATTGATATTA-TA-T-T
* * * *
12756864 ACTATTATTATATTATTATAGTATGTTGATATTATATT
1 ACTATTATTACATTACTATACTATATTGATATTATATT
* * * *
12756902 ACTATTATTATATT--TGTATTATATT-ATATTATAGT
1 ACTATTATTACATTACTATACTATATTGATATTATATT
*
12756937 A-TATTATTATATTA
1 ACTATTATTACATTA
12756951 TATTCGATTA
Statistics
Matches: 77, Mismatches: 8, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
34 12 0.16
35 10 0.13
36 8 0.10
38 15 0.19
39 1 0.01
40 4 0.05
41 27 0.35
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.53
Consensus pattern (38 bp):
ACTATTATTACATTACTATACTATATTGATATTATATT
Found at i:12756872 original size:3 final size:3
Alignment explanation
Indices: 12756866--12756999 Score: 71
Period size: 3 Copynumber: 48.0 Consensus size: 3
12756856 ACTACTATAC
* * *
12756866 TAT TAT TA- TAT TAT TA- TAG TAT GT-T GAT -AT TA- TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT
*
12756907 TAT TA- TAT T-T GTAT TA- TAT TA- TAT TA- TAG TA- TAT TAT TA-
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* **
12756946 TAT TA- TAT TCGAT TAT CA- TAT TAT GGT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT T--AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12756991 TAT TAT TAT
1 TAT TAT TAT
12757000 ATTTGATATT
Statistics
Matches: 103, Mismatches: 10, Indels: 36
0.69 0.07 0.24
Matches are distributed among these distances:
2 24 0.23
3 74 0.72
4 2 0.02
5 3 0.03
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:12756877 original size:5 final size:5
Alignment explanation
Indices: 12756848--12757002 Score: 79
Period size: 5 Copynumber: 29.6 Consensus size: 5
12756838 CTATACTATA
* * * *
12756848 ATTAT ATTACT ACTAT ACTATT ATTAT A-T-T ATTAT AGTAT GTTGAT
1 ATTAT ATTA-T ATTAT ATTA-T ATTAT ATTAT ATTAT ATTAT ATT-AT
* *
12756894 ATTAT ATTACT A-T-T ATTAT ATTTGT ATTAT ATTAT ATTAT AGTAT A-T-T
1 ATTAT ATTA-T ATTAT ATTAT A-TTAT ATTAT ATTAT ATTAT ATTAT ATTAT
* *
12756942 ATTAT ATTAT ATTCGATT ATCAT ATTAT GGTTATT ATTATT ATTATT ATTATT
1 ATTAT ATTAT ATT--A-T ATTAT ATTAT -ATTA-T ATTA-T ATTA-T ATTA-T
12756995 ATTAT ATT
1 ATTAT ATT
12757003 TGATATTATT
Statistics
Matches: 121, Mismatches: 13, Indels: 32
0.73 0.08 0.19
Matches are distributed among these distances:
3 6 0.05
4 5 0.04
5 62 0.51
6 43 0.36
7 2 0.02
8 3 0.02
ACGTcount: A:0.34, C:0.04, G:0.05, T:0.57
Consensus pattern (5 bp):
ATTAT
Found at i:12756944 original size:18 final size:18
Alignment explanation
Indices: 12756866--12757002 Score: 92
Period size: 18 Copynumber: 7.7 Consensus size: 18
12756856 ACTACTATAC
12756866 TATTATTATATTATTA-TA
1 TATTATTATATTA-TAGTA
* *
12756884 GTATGT-TGATATTATATTA
1 -TAT-TATTATATTATAGTA
12756903 CTATTATTATATT-T-GTA
1 -TATTATTATATTATAGTA
12756920 T-TATATTATATTATAGTA
1 TAT-TATTATATTATAGTA
* *
12756938 TATTATTATATTATATTC
1 TATTATTATATTATAGTA
* * *
12756956 GATTATCATATTATGGT-
1 TATTATTATATTATAGTA
12756973 TATTATTATTATTAT--TA
1 TATTATTA-TATTATAGTA
12756990 TTATTATTATATT
1 -TATTATTATATT
12757003 TGATATTATT
Statistics
Matches: 96, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
15 1 0.01
16 11 0.11
17 13 0.14
18 48 0.50
19 22 0.23
20 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (18 bp):
TATTATTATATTATAGTA
Found at i:12757009 original size:18 final size:17
Alignment explanation
Indices: 12756904--12757017 Score: 85
Period size: 18 Copynumber: 6.5 Consensus size: 17
12756894 ATTATATTAC
*
12756904 TATTATTATATTTGTAT
1 TATTATTATATTTATAT
12756921 TA-TATTATA-TTATAGT
1 TATTATTATATTTATA-T
12756937 ATATTATTATA-TTATAT
1 -TATTATTATATTTATAT
* *
12756954 TCGATTATCATA-TTATGGT
1 T--ATTATTATATTTAT-AT
12756973 TATTATTAT-TATTATTAT
1 TATTATTATAT-TTA-TAT
12756991 TATTATTATATTTGATAT
1 TATTATTATATTT-ATAT
*
12757009 TATTTTTAT
1 TATTATTAT
12757018 CATATTTTCT
Statistics
Matches: 80, Mismatches: 6, Indels: 21
0.75 0.06 0.20
Matches are distributed among these distances:
15 4 0.05
16 9 0.11
17 12 0.15
18 50 0.62
19 5 0.06
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (17 bp):
TATTATTATATTTATAT
Found at i:12757012 original size:3 final size:3
Alignment explanation
Indices: 12756893--12756999 Score: 72
Period size: 3 Copynumber: 38.0 Consensus size: 3
12756883 AGTATGTTGA
*
12756893 TAT TA- TAT TAC TAT TAT TA- TAT T-T GTAT TA- TAT TA- TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
* * **
12756933 TAG TA- TAT TAT TA- TAT TA- TAT TCGAT TAT CA- TAT TAT GGT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT T--AT TAT TAT TAT TAT TAT TAT
12756976 TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT
12757000 ATTTGATATT
Statistics
Matches: 83, Mismatches: 8, Indels: 26
0.71 0.07 0.22
Matches are distributed among these distances:
2 18 0.22
3 61 0.73
4 1 0.01
5 3 0.04
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:12760882 original size:11 final size:11
Alignment explanation
Indices: 12760862--12760890 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
12760852 AGGGCAAACA
12760862 TTTTTC-TTTT
1 TTTTTCATTTT
12760872 TTTTTCATTTT
1 TTTTTCATTTT
12760883 TTTTTCAT
1 TTTTTCAT
12760891 GCATTGCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTCATTTT
Found at i:12763331 original size:14 final size:14
Alignment explanation
Indices: 12763312--12763342 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
12763302 TTACTAAAAG
12763312 TATTGAATCAAGTT
1 TATTGAATCAAGTT
12763326 TATTGAATCAAGTT
1 TATTGAATCAAGTT
12763340 TAT
1 TAT
12763343 GTGACTCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.45
Consensus pattern (14 bp):
TATTGAATCAAGTT
Found at i:12768926 original size:60 final size:60
Alignment explanation
Indices: 12768810--12768946 Score: 168
Period size: 60 Copynumber: 2.3 Consensus size: 60
12768800 TAAGACTCGT
* * *
12768810 GGCATCATCCTAGTCATTAATCTACGACATTGACTCGATCTTGGTCGCTCTCAGACTCAC
1 GGCATCATCCCAGTCATTAATCTACGACATTGACTCGATCTTGATCACTCTCAGACTCAC
* * * **
12768870 GGCATCATCCCAGTCATTAATCTATGACCTTGATTCGATCTTGATCACT-TCTAGACTTGC
1 GGCATCATCCCAGTCATTAATCTACGACATTGACTCGATCTTGATCACTCTC-AGACTCAC
* *
12768930 GGCATCGTACCAGTCAT
1 GGCATCATCCCAGTCAT
12768947 CCAGCAAGAT
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
59 2 0.03
60 64 0.97
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.31
Consensus pattern (60 bp):
GGCATCATCCCAGTCATTAATCTACGACATTGACTCGATCTTGATCACTCTCAGACTCAC
Found at i:12769263 original size:19 final size:19
Alignment explanation
Indices: 12769236--12769279 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
12769226 TGTTTTTACC
*
12769236 ACTACTGTTACATTACTAT
1 ACTATTGTTACATTACTAT
* *
12769255 ACTATTGTTATATTATTAT
1 ACTATTGTTACATTACTAT
*
12769274 AGTATT
1 ACTATT
12769280 ATATTATATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.07, T:0.50
Consensus pattern (19 bp):
ACTATTGTTACATTACTAT
Found at i:12769270 original size:5 final size:5
Alignment explanation
Indices: 12769262--12769367 Score: 78
Period size: 5 Copynumber: 20.6 Consensus size: 5
12769252 TATACTATTG
12769262 TTATA TTAT- TATAGTA TTATA TTATA TTATTA TGGTATA TTGATA TTATA
1 TTATA TTATA T-TA-TA TTATA TTATA TTA-TA T--TATA TT-ATA TTATA
* * *
12769312 TTACCA -T-TA TTATA TTAGTA TTATA TTGTA TTATA GTATA -T-TA TTATA
1 TTA-TA TTATA TTATA TTA-TA TTATA TTATA TTATA TTATA TTATA TTATA
12769360 TTATA TTA
1 TTATA TTA
12769368 GGTTATCATA
Statistics
Matches: 83, Mismatches: 5, Indels: 26
0.73 0.04 0.23
Matches are distributed among these distances:
3 3 0.04
4 4 0.05
5 53 0.64
6 17 0.20
7 4 0.05
8 2 0.02
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.56
Consensus pattern (5 bp):
TTATA
Found at i:12769273 original size:3 final size:3
Alignment explanation
Indices: 12769265--12769431 Score: 53
Period size: 3 Copynumber: 59.7 Consensus size: 3
12769255 ACTATTGTTA
*
12769265 TAT TAT TA- TAG TAT TA- TAT TA- TAT TAT TAT GGTA- TAT TGA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT --TAT TAT T-AT TAT
* * * * *
12769308 TA- TAT TAC CAT TAT TA- TAT TAG TAT TA- TAT T-G TAT TA- TAG TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* ** *
12769350 TAT TAT TA- TAT TA- TAT TAGGT TAT CA- TAT TAT GGT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TA--T TAT TAT TAT TAT TAT TAT TAT TAT
* * *
12769394 TAT TAT TAA TAT TAT TA- TAT T-T GA- TAT TAT TTT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
12769432 GATTTTCTTT
Statistics
Matches: 120, Mismatches: 22, Indels: 44
0.65 0.12 0.24
Matches are distributed among these distances:
2 29 0.24
3 85 0.71
4 1 0.01
5 5 0.04
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:12769286 original size:13 final size:13
Alignment explanation
Indices: 12769268--12769364 Score: 60
Period size: 13 Copynumber: 7.5 Consensus size: 13
12769258 ATTGTTATAT
12769268 TATTATAGTATTA
1 TATTATAGTATTA
*
12769281 TATTATATTATTA
1 TATTATAGTATTA
* *
12769294 TGGTATATTGATATTA
1 T-AT-TATAG-TATTA
* *
12769310 TATTACCATTATTA
1 TATTA-TAGTATTA
12769324 TA-T-TAGTATTA
1 TATTATAGTATTA
12769335 TA-T-T-GTATTA
1 TATTATAGTATTA
* *
12769345 TAGTATATTATTA
1 TATTATAGTATTA
12769358 TATTATA
1 TATTATA
12769365 TTAGGTTATC
Statistics
Matches: 65, Mismatches: 12, Indels: 14
0.71 0.13 0.15
Matches are distributed among these distances:
10 8 0.12
11 11 0.17
12 1 0.02
13 25 0.38
14 10 0.15
15 4 0.06
16 6 0.09
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (13 bp):
TATTATAGTATTA
Found at i:12769291 original size:18 final size:18
Alignment explanation
Indices: 12769268--12769414 Score: 81
Period size: 18 Copynumber: 7.9 Consensus size: 18
12769258 ATTGTTATAT
12769268 TATTATAGTATTATATTA
1 TATTATAGTATTATATTA
12769286 TATTAT--TATGGTATATTGA
1 TATTATAGTAT--TATATT-A
* **
12769305 TATTATATTACCATTATTA
1 TATTATAGTATTA-TATTA
*
12769324 TA-T-TAGTATTATATTG
1 TATTATAGTATTATATTA
12769340 TATTATAGTA-TATTATTA
1 TATTATAGTATTA-TATTA
* * *
12769358 TATTATATTAGGT-TATCA
1 TATTATAGTA-TTATATTA
*
12769376 TATTATGGTCATTATTATTA
1 TATTATAGT-ATTA-TATTA
*
12769396 TTATTAATATTATTATATT
1 -TATT-ATAGTATTATATT
12769415 TGATATTATT
Statistics
Matches: 98, Mismatches: 15, Indels: 30
0.69 0.10 0.21
Matches are distributed among these distances:
16 9 0.09
17 8 0.08
18 43 0.44
19 12 0.12
20 13 0.13
21 10 0.10
22 3 0.03
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.55
Consensus pattern (18 bp):
TATTATAGTATTATATTA
Found at i:12769421 original size:21 final size:21
Alignment explanation
Indices: 12769397--12769436 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12769387 TTATTATTAT
*
12769397 TATTAATATTATTATATTTGA
1 TATTAATATTATTAGATTTGA
* *
12769418 TATTATTTTTATTAGATTT
1 TATTAATATTATTAGATTT
12769437 TCTTTCTTTT
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:0.00, G:0.05, T:0.62
Consensus pattern (21 bp):
TATTAATATTATTAGATTTGA
Found at i:12769884 original size:23 final size:21
Alignment explanation
Indices: 12769853--12769912 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 21
12769843 ACATATAAAT
12769853 TTTTCGATGAAGTTTCCAACGAGA
1 TTTT-GATGAAGTTTCCAA-GA-A
12769877 TTTTGATG-AGATTTCC-AGAA
1 TTTTGATGAAG-TTTCCAAGAA
*
12769897 -ATTGATGAAGTTTCCA
1 TTTTGATGAAGTTTCCA
12769913 GATTTGGTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
19 11 0.34
20 3 0.09
21 2 0.06
22 3 0.09
23 9 0.28
24 4 0.12
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (21 bp):
TTTTGATGAAGTTTCCAAGAA
Found at i:12777293 original size:62 final size:63
Alignment explanation
Indices: 12777213--12777330 Score: 152
Period size: 62 Copynumber: 1.9 Consensus size: 63
12777203 TTTTTTTTTA
*
12777213 AGATTATTGAAGACATTTTAGGC-AGAAAATGCCTTTAATAATCCCTTT-AAATTTTGACAAAG
1 AGATTATTGAAGACATTTTAGACTA-AAAATGCCTTTAATAATCCCTTTCAAATTTTGACAAAG
* * **
12777275 AGATTATTGAATG-TATTTTTGACTAAAAATGCCTTTGCTAATCCCTTTCAAATTTT
1 AGATTATTGAA-GACATTTTAGACTAAAAATGCCTTTAATAATCCCTTTCAAATTTT
12777331 TTAAGGAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
62 39 0.81
63 9 0.19
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.39
Consensus pattern (63 bp):
AGATTATTGAAGACATTTTAGACTAAAAATGCCTTTAATAATCCCTTTCAAATTTTGACAAAG
Found at i:12777356 original size:62 final size:62
Alignment explanation
Indices: 12777238--12777574 Score: 166
Period size: 63 Copynumber: 5.4 Consensus size: 62
12777228 TTTTAGGCAG
* *
12777238 AAAATGCCTTTAATAATCCCTTTAAATTTTGACAAAGAGATTATTGAATGTATTTTTGACTA
1 AAAATGCCTTTAATAATCCCTTTAAATTTTGACAAAGAAATTATTGAATGGATTTTTGACTA
** ** * *
12777300 AAAATGCCTTTGCTAATCCCTTTCAAATTTT-TTAAGGAAAATTATTGAA-GGCTTTTTTTTG-C
1 AAAATGCCTTTAATAATCCCTTT-AAATTTTGACAAAG-AAATTATTGAATGG---ATTTTTGAC
*
12777362 TG
61 TA
* * ** * *** * *
12777364 AAAATGCCTTCAATAATCCCCTCCATTTTTTTTAAAGAAAATTATTGAATGCGTTTTTTG-CTG
1 AAAATGCCTTTAATAATCCCTTTAAATTTTGACAAAG-AAATTATTGAATG-GATTTTTGACTA
* * * * * * * * * *
12777427 AAAATACCTTCAATAATCCCTTTTTATTTTTTATCAAAG-GATTATTCAAGGCGTTTTTTG-CCA
1 AAAATGCCTTTAATAATCCC-TTTAAATTTTGA-CAAAGAAATTATTGAATG-GATTTTTGACTA
** * * * * * *
12777490 AAAACACATTCAATAATCCCCTTAAATTTTGACAAGGAGATTATTGAA-GTCATTTTTGACTA
1 AAAATGCCTTTAATAATCCCTTTAAATTTTGACAAAGAAATTATTGAATG-GATTTTTGACTA
* *
12777552 AAAACGTCTTTAATAATTCCCTT
1 AAAATGCCTTTAATAA-TCCCTT
12777575 CAATTTTTTT
Statistics
Matches: 217, Mismatches: 45, Indels: 25
0.76 0.16 0.09
Matches are distributed among these distances:
61 11 0.05
62 56 0.26
63 93 0.43
64 45 0.21
65 11 0.05
66 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (62 bp):
AAAATGCCTTTAATAATCCCTTTAAATTTTGACAAAGAAATTATTGAATGGATTTTTGACTA
Found at i:12777379 original size:126 final size:125
Alignment explanation
Indices: 12777234--12777633 Score: 350
Period size: 126 Copynumber: 3.2 Consensus size: 125
12777224 GACATTTTAG
* *
12777234 GCAGAAAATGCCTTTAATAATCCCTTTAAATTTTGACAAAGAGATTATTGAATGTATTTTTGACT
1 GCAGAAAATGCCTTCAATAATCCCCTTAAATTTTGACAAAGAGATTATTGAATGTATTTTTGACT
** * *
12777299 AAAAATGCCTTTGCTAATCCCTTTCAAATTTTTTAAGGAAAATTATTGAAGGCTTTTTTTT
66 AAAAATGCCTTTAATAATCCCTTTCAAATTTTTTAA-AAAAATTATTAAAGGCTTTTTTTT
* ** * *** *
12777360 GCTGAAAATGCCTTCAATAATCCCCTCCATTTTTTTTAAAGAAAATTATTGAATGCGT-TTTTTG
1 GCAGAAAATGCCTTCAATAATCCCCTTAAATTTTGACAAAG-AGATTATTGAAT--GTATTTTTG
* * * ** ** * *
12777424 -CTGAAAATACCTTCAATAATCCCTTT-TTATTTTTTATCAAAGGATTATTCAAGGC-GTTTTTT
63 ACTAAAAATGCCTTTAATAATCCCTTTCAAATTTTTTA--AAAAAATTATTAAAGGCTTTTTTTT
** * *
12777486 GCCA-AAAACACATTCAATAATCCCCTTAAATTTTGACAAGGAGATTATTGAA-GTCATTTTTGA
1 G-CAGAAAATGCCTTCAATAATCCCCTTAAATTTTGACAAAGAGATTATTGAATGT-ATTTTTGA
* * *
12777549 CTAAAAACGTCTTTAATAATTCCC-TTCAATTTTTTTAAAAAAATTATTAAAGG-TATTTTTTT
64 CTAAAAATGCCTTTAATAA-TCCCTTTCAAATTTTTTAAAAAAATTATTAAAGGCT-TTTTTTT
** *
12777611 AAAGAAAATG-TTTCAATAATCCC
1 GCAGAAAATGCCTTCAATAATCCC
12777634 TTCCATTTTT
Statistics
Matches: 209, Mismatches: 51, Indels: 30
0.72 0.18 0.10
Matches are distributed among these distances:
122 2 0.01
124 32 0.15
125 36 0.17
126 85 0.41
127 45 0.22
128 7 0.03
129 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (125 bp):
GCAGAAAATGCCTTCAATAATCCCCTTAAATTTTGACAAAGAGATTATTGAATGTATTTTTGACT
AAAAATGCCTTTAATAATCCCTTTCAAATTTTTTAAAAAAATTATTAAAGGCTTTTTTTT
Found at i:12777382 original size:64 final size:63
Alignment explanation
Indices: 12777237--12777449 Score: 225
Period size: 63 Copynumber: 3.4 Consensus size: 63
12777227 ATTTTAGGCA
* ** * *
12777237 GAAAATGCCTTTAATAATCCCTTT-AAATTTTGACAAAG-AGATTATTGAATG-TATTTTTGACT
1 GAAAATGCCTTCAATAATCCCTTTCAAATTTT-TTAAAGAAAATTATTGAATGCTTTTTTTG-CT
* *** * *
12777299 AAAAATGCCTTTGCTAATCCCTTTCAAATTTTTTAAGGAAAATTATTGAAGGCTTTTTTTTGCT
1 GAAAATGCCTTCAATAATCCCTTTCAAATTTTTTAAAGAAAATTATTGAATGC-TTTTTTTGCT
* * ** *
12777363 GAAAATGCCTTCAATAATCCCCTCCATTTTTTTTAAAGAAAATTATTGAATGCGTTTTTTGCT
1 GAAAATGCCTTCAATAATCCCTTTCAAATTTTTTAAAGAAAATTATTGAATGCTTTTTTTGCT
*
12777426 GAAAATACCTTCAATAATCCCTTT
1 GAAAATGCCTTCAATAATCCCTTT
12777450 TTATTTTTTA
Statistics
Matches: 124, Mismatches: 23, Indels: 7
0.81 0.15 0.05
Matches are distributed among these distances:
62 24 0.19
63 48 0.39
64 45 0.36
65 7 0.06
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.41
Consensus pattern (63 bp):
GAAAATGCCTTCAATAATCCCTTTCAAATTTTTTAAAGAAAATTATTGAATGCTTTTTTTGCT
Found at i:12777456 original size:64 final size:63
Alignment explanation
Indices: 12777327--12777511 Score: 203
Period size: 63 Copynumber: 2.9 Consensus size: 63
12777317 CCCTTTCAAA
* * *
12777327 TTTTTTAAGGAAAATTATTGAAGGCTTTTTTTTGCTGAAAATGCCTTCAATAATCCCCTCCATT
1 TTTTTTAAAGAAAATTATTGAAGGC-GTTTTTTGCTGAAAATACCTTCAATAATCCCCTCCATT
* * **
12777391 TTTTTTAAAGAAAATTATTGAATGCGTTTTTTGCTGAAAATACCTTCAATAATCCCTTTTTATT
1 TTTTTTAAAGAAAATTATTGAAGGCGTTTTTTGCTGAAAATACCTTCAATAATCCC-CTCCATT
* * * ** * *
12777455 TTTTATCAAAG--GATTATTCAAGGCGTTTTTTGCCAAAAACACATTCAATAATCCCCT
1 TTTT-TTAAAGAAAATTATTGAAGGCGTTTTTTGCTGAAAATACCTTCAATAATCCCCT
12777512 TAAATTTTGA
Statistics
Matches: 103, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
62 1 0.01
63 66 0.64
64 31 0.30
65 5 0.05
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.42
Consensus pattern (63 bp):
TTTTTTAAAGAAAATTATTGAAGGCGTTTTTTGCTGAAAATACCTTCAATAATCCCCTCCATT
Found at i:12778082 original size:62 final size:59
Alignment explanation
Indices: 12777872--12778112 Score: 205
Period size: 61 Copynumber: 3.9 Consensus size: 59
12777862 ATCTTGTCTA
** *
12777872 AAAAATTGGAAGGGATTATTGAAGGCATTTTTTGCAAAAAAAATACCTTTAATAATTTCTTTT
1 AAAAATTTAAAGGGATTATTGAAGGCATTTTTTG-TAAAAAAA-ACCTTTAATAA-TTC-TTT
* * ** **
12777935 AAAAATTTAAAGGGAATTATTGAAGGCATTTTTAGTCAAAAATGCCTTTAATAATTCCCT
1 AAAAATTTAAAGGG-ATTATTGAAGGCATTTTTTGTAAAAAAAACCTTTAATAATTCTTT
* *** *
12777995 AAAATTTTTAAATAAAATTATTGAAGGTATTTTTTGTAAAAAAAACCTTTAATAATCTCATTT
1 AAAA-ATTTAAA-GGGATTATTGAAGGCATTTTTTGTAAAAAAAACCTTTAATAAT-TC-TTT
* * * * * *
12778058 AAAAATTTGAAGGAGATTATTGAAGGCGTTTTTAGT-GAAAACACCTTCAATAATT
1 AAAAATTTAAAGG-GATTATTGAAGGCATTTTTTGTAAAAAAAACCTTTAATAATT
12778113 TGTTCATCAA
Statistics
Matches: 141, Mismatches: 31, Indels: 15
0.75 0.17 0.08
Matches are distributed among these distances:
60 6 0.04
61 59 0.42
62 35 0.25
63 22 0.16
64 19 0.13
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (59 bp):
AAAAATTTAAAGGGATTATTGAAGGCATTTTTTGTAAAAAAAACCTTTAATAATTCTTT
Found at i:12778133 original size:96 final size:97
Alignment explanation
Indices: 12778032--12778222 Score: 260
Period size: 96 Copynumber: 2.0 Consensus size: 97
12778022 TATTTTTTGT
* *
12778032 AAAAAAAACCTTTAATAATCTCATTTAAAAATTTGAAGGAGATTATTGAAGGCGTTTTTAGTGAA
1 AAAAAAAACCTTTAATAATCTCATTTAAAAATTTGAAGGAGATTATTGAAGGCGTTTTCAGTCAA
*
12778097 AACAC-CT-TCAATAATTTGTTCATCAAAATGC
66 AA-ACGCTGTCAATAATTTGGTCATCAAAATGC
** * ** * * *
12778128 AAAAAATGCCTTTAATAATTTTGTTTAAAAATTTGGAGGAGATTATTGAATGTGTTTTCAGTCAA
1 AAAAAAAACCTTTAATAATCTCATTTAAAAATTTGAAGGAGATTATTGAAGGCGTTTTCAGTCAA
12778193 AAACGCTGTCAATAATTTGGTCATCAAAAT
66 AAACGCTGTCAATAATTTGGTCATCAAAAT
12778223 TTAAGGGGAT
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
95 2 0.02
96 59 0.72
97 21 0.26
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (97 bp):
AAAAAAAACCTTTAATAATCTCATTTAAAAATTTGAAGGAGATTATTGAAGGCGTTTTCAGTCAA
AAACGCTGTCAATAATTTGGTCATCAAAATGC
Found at i:12780227 original size:21 final size:21
Alignment explanation
Indices: 12780176--12780232 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
12780166 CATTGAGCAA
*
12780176 CAACAACAAAGACTTGATGAC
1 CAACAACAATGACTTGATGAC
*
12780197 CAA-AAGCAATG-CTTGAATGAG
1 CAACAA-CAATGACTTG-ATGAC
12780218 CAACAACAATGACTT
1 CAACAACAATGACTT
12780233 ATAGCTTTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
20 6 0.20
21 19 0.63
22 5 0.17
ACGTcount: A:0.46, C:0.21, G:0.16, T:0.18
Consensus pattern (21 bp):
CAACAACAATGACTTGATGAC
Found at i:12781289 original size:14 final size:14
Alignment explanation
Indices: 12781270--12781313 Score: 81
Period size: 14 Copynumber: 3.2 Consensus size: 14
12781260 AAACACCTTC
12781270 AATAATCCCTTACA
1 AATAATCCCTTACA
12781284 AATAATCCCTTACA
1 AATAATCCCTTACA
12781298 AATAATCCCTTA-A
1 AATAATCCCTTACA
12781311 AAT
1 AAT
12781314 CCCAATAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 4 0.13
14 26 0.87
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (14 bp):
AATAATCCCTTACA
Found at i:12781661 original size:20 final size:21
Alignment explanation
Indices: 12781631--12781673 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
12781621 ATCCCTCCCA
12781631 AAAATGGATAGGGGATTATTG
1 AAAATGGATAGGGGATTATTG
12781652 AAAA-GGATAGGGGATTATTG
1 AAAATGGATAGGGGATTATTG
12781672 AA
1 AA
12781674 GGTGTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.42, C:0.00, G:0.33, T:0.26
Consensus pattern (21 bp):
AAAATGGATAGGGGATTATTG
Found at i:12784680 original size:111 final size:111
Alignment explanation
Indices: 12784486--12784703 Score: 382
Period size: 111 Copynumber: 2.0 Consensus size: 111
12784476 AAACTTCTAC
* *
12784486 TACAAGAGAGGAAAATTAACCCTAAGAAAACAACAATGTTAGAGAAGAGCTACTTTACCCACCTA
1 TACAAGAGAGGAAAATTAACCCTAAGAAAACAACAATGTTAAAAAAGAGCTACTTTACCCACCTA
*
12784551 GCTATACACCACCCCATGCTCAAACTCCTCAAGTGATGTATCCATT
66 GCTATACACCACCCCATGCTCAAACTCCTCAAGTAATGTATCCATT
* * *
12784597 TACAAGAGAGGAAAATTAACCCTAAGAAAACAACAATTTTAAAAAAGAGCTACTTTATCCACCTG
1 TACAAGAGAGGAAAATTAACCCTAAGAAAACAACAATGTTAAAAAAGAGCTACTTTACCCACCTA
12784662 GCTATACACCACCCCATGCTCAAACTCCTCAAGTAATGTATC
66 GCTATACACCACCCCATGCTCAAACTCCTCAAGTAATGTATC
12784704 TATTGCCAAT
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
111 101 1.00
ACGTcount: A:0.40, C:0.26, G:0.12, T:0.22
Consensus pattern (111 bp):
TACAAGAGAGGAAAATTAACCCTAAGAAAACAACAATGTTAAAAAAGAGCTACTTTACCCACCTA
GCTATACACCACCCCATGCTCAAACTCCTCAAGTAATGTATCCATT
Found at i:12785386 original size:14 final size:14
Alignment explanation
Indices: 12785367--12785397 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12785357 TCACCTAGGG
12785367 TTTAGGATTTTATT
1 TTTAGGATTTTATT
*
12785381 TTTAGGGTTTTATT
1 TTTAGGATTTTATT
12785395 TTT
1 TTT
12785398 TGGGAAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (14 bp):
TTTAGGATTTTATT
Found at i:12787146 original size:3 final size:3
Alignment explanation
Indices: 12787138--12787185 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
12787128 CTTTCAAATC
12787138 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12787186 TTGTTTTGGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:12787277 original size:26 final size:25
Alignment explanation
Indices: 12787205--12787282 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 25
12787195 AACTAGCTTT
* *
12787205 TTATTATTATTTGTATTTTC-TTTTA
1 TTATT-TTATTAGTATATTCATTTTA
*
12787230 TTA-TTTATTA-TGTA-TCA-TTTA
1 TTATTTTATTAGTATATTCATTTTA
12787251 TTATTTTATTAGTATATTCATTATTA
1 TTATTTTATTAGTATATTCATT-TTA
12787277 -TATTTT
1 TTATTTT
12787283 TTTTATATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
21 9 0.21
22 9 0.21
23 8 0.19
24 4 0.09
25 10 0.23
26 3 0.07
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.67
Consensus pattern (25 bp):
TTATTTTATTAGTATATTCATTTTA
Found at i:12787298 original size:19 final size:18
Alignment explanation
Indices: 12787274--12787311 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
12787264 ATATTCATTA
*
12787274 TTATATTTTTTTTATATTT
1 TTATATATTTTTTAT-TTT
12787293 TTATATATTTTTTATTTT
1 TTATATATTTTTTATTTT
12787311 T
1 T
12787312 CGTTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (18 bp):
TTATATATTTTTTATTTT
Found at i:12787306 original size:11 final size:11
Alignment explanation
Indices: 12787202--12787307 Score: 58
Period size: 11 Copynumber: 9.6 Consensus size: 11
12787192 TGGAACTAGC
12787202 TTTTTAT-TAT
1 TTTTTATATAT
* * *
12787212 TATTTGTATTT
1 TTTTTATATAT
12787223 TCTTTTAT-TAT
1 T-TTTTATATAT
* *
12787234 TTATTATGTAT
1 TTTTTATATAT
**
12787245 CATTTAT-TAT
1 TTTTTATATAT
12787255 TTTATTAGTATAT
1 TTT-TTA-TATAT
**
12787268 TCATTATTATAT
1 TTTTTA-TATAT
*
12787280 TTTTTTTATA-
1 TTTTTATATAT
12787290 TTTTTATATAT
1 TTTTTATATAT
12787301 TTTTTAT
1 TTTTTAT
12787308 TTTTCGTTAA
Statistics
Matches: 70, Mismatches: 19, Indels: 13
0.69 0.19 0.13
Matches are distributed among these distances:
10 23 0.33
11 27 0.39
12 16 0.23
13 4 0.06
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (11 bp):
TTTTTATATAT
Found at i:12789969 original size:2 final size:2
Alignment explanation
Indices: 12789957--12789989 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
12789947 AAACAAAAAC
*
12789957 AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12789990 CAAAAGATGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:12791906 original size:3 final size:3
Alignment explanation
Indices: 12791898--12791946 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
12791888 AATGTATACT
12791898 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12791946 T
1 T
12791947 ATTTAACATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:12793346 original size:1 final size:1
Alignment explanation
Indices: 12793342--12793367 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
12793332 TGTAAATTCG
12793342 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
12793368 CCTTTTGCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:12794867 original size:65 final size:66
Alignment explanation
Indices: 12794774--12794909 Score: 220
Period size: 65 Copynumber: 2.1 Consensus size: 66
12794764 ATTTTGGCAG
* *
12794774 TATTGAAAAAGAGATTACTTAGTATTTTTGCAATATTGAG-AAAAAATTACTTGCTATTTTTGAA
1 TATTGAAAAAGAGATTACTTACTATTTTTGCAATATTGAGAAAAAAATTACTAGCTATTTTTGAA
12794838 A
66 A
* *
12794839 TATTGAGAAAGAGATTACTTACTATTTTTGCAATATTGAGAAAAAAAATTACTAGCTATTTTTGC
1 TATTGAAAAAGAGATTACTTACTATTTTTGCAATATTGAG-AAAAAAATTACTAGCTATTTTTGA
12794904 AA
65 AA
12794906 TATT
1 TATT
12794910 AAGACAAAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
65 38 0.58
67 27 0.42
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (66 bp):
TATTGAAAAAGAGATTACTTACTATTTTTGCAATATTGAGAAAAAAATTACTAGCTATTTTTGAA
A
Found at i:12794898 original size:34 final size:35
Alignment explanation
Indices: 12794763--12794924 Score: 187
Period size: 33 Copynumber: 4.8 Consensus size: 35
12794753 AAAGACAAAG
* * * *
12794763 TATTTTGGCAGTATTGA-AAAAGAGATTACTTAG-
1 TATTTTTGCAATATTGAGAAAAAAAATTACTTAGC
12794796 TATTTTTGCAATATTGAG--AAAAAATTACTT-GC
1 TATTTTTGCAATATTGAGAAAAAAAATTACTTAGC
* * *
12794828 TATTTTTGAAATATTGAG-AAAGAGATTACTTA-C
1 TATTTTTGCAATATTGAGAAAAAAAATTACTTAGC
12794861 TATTTTTGCAATATTGAGAAAAAAAATTAC-TAGC
1 TATTTTTGCAATATTGAGAAAAAAAATTACTTAGC
*
12794895 TATTTTTGCAATATTAAGACAAAAAAATTA
1 TATTTTTGCAATATTGAGA-AAAAAAATTA
12794925 ATTGGCATTA
Statistics
Matches: 111, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
31 1 0.01
32 27 0.24
33 45 0.41
34 28 0.25
35 10 0.09
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (35 bp):
TATTTTTGCAATATTGAGAAAAAAAATTACTTAGC
Found at i:12795079 original size:32 final size:32
Alignment explanation
Indices: 12795038--12795101 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
12795028 AAATATACCA
12795038 TACATTTACCAACACTTTATACAACCGTTAGT
1 TACATTTACCAACACTTTATACAACCGTTAGT
12795070 TACATTTACCAACACTTTATACAACCGTTAGT
1 TACATTTACCAACACTTTATACAACCGTTAGT
12795102 ATAGATAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.34
Consensus pattern (32 bp):
TACATTTACCAACACTTTATACAACCGTTAGT
Found at i:12795392 original size:25 final size:25
Alignment explanation
Indices: 12795364--12795413 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
12795354 ATATAAGCTA
* *
12795364 AAAAAATATTTATTCCTAATTTTTT
1 AAAAAATATTAATTCATAATTTTTT
12795389 AAAAAATATTAATTCATAATTTTTT
1 AAAAAATATTAATTCATAATTTTTT
12795414 CCTCTAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (25 bp):
AAAAAATATTAATTCATAATTTTTT
Found at i:12795564 original size:26 final size:30
Alignment explanation
Indices: 12795533--12795600 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
12795523 TGTAAGTATT
12795533 ATATTA-ATTAATAAA-TTTAT-AA-TTAA
1 ATATTAGATTAATAAATTTTATAAATTTAA
* *
12795559 ATATTAGACTAA-AAATTTTTTAAATTTAA
1 ATATTAGATTAATAAATTTTATAAATTTAA
*
12795588 ATATTATATTAAT
1 ATATTAGATTAAT
12795601 TTGGTTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
26 9 0.27
27 8 0.24
28 2 0.06
29 14 0.42
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (30 bp):
ATATTAGATTAATAAATTTTATAAATTTAA
Found at i:12799088 original size:21 final size:20
Alignment explanation
Indices: 12799063--12799105 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
12799053 TGAATTTTTA
12799063 GAAAAAGAAAATTT-TGATTT
1 GAAAAAG-AAATTTATGATTT
12799083 GAAAAAGAAATTTAATGATTT
1 GAAAAAGAAATTT-ATGATTT
12799104 GA
1 GA
12799106 TGAATGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.29
20 7 0.33
21 8 0.38
ACGTcount: A:0.51, C:0.00, G:0.16, T:0.33
Consensus pattern (20 bp):
GAAAAAGAAATTTATGATTT
Found at i:12801896 original size:16 final size:16
Alignment explanation
Indices: 12801872--12801906 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
12801862 CTTGATTACA
*
12801872 TATCTTTAACAATTGG
1 TATCCTTAACAATTGG
12801888 TATCCTTAACAATTGG
1 TATCCTTAACAATTGG
12801904 TAT
1 TAT
12801907 GAGCTTGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.43
Consensus pattern (16 bp):
TATCCTTAACAATTGG
Found at i:12802570 original size:38 final size:38
Alignment explanation
Indices: 12802519--12802595 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
12802509 TTAAGTTGTG
* *
12802519 TTGGATTAGGATGCATAAATTGAGAGGGAGTTTTGCCA
1 TTGGATTAGGATGCACAAATTAAGAGGGAGTTTTGCCA
*
12802557 TTGGATTAGGATGCACAAATTAAGGGGGAGTTTTGCCA
1 TTGGATTAGGATGCACAAATTAAGAGGGAGTTTTGCCA
12802595 T
1 T
12802596 GCATTACTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.29, C:0.09, G:0.31, T:0.31
Consensus pattern (38 bp):
TTGGATTAGGATGCACAAATTAAGAGGGAGTTTTGCCA
Found at i:12805267 original size:145 final size:146
Alignment explanation
Indices: 12805035--12805445 Score: 436
Period size: 145 Copynumber: 2.8 Consensus size: 146
12805025 GAGAAAGACC
** * * * *
12805035 AAATTACCAAAATACCCTTATAGGGG-ATTTTTGTAATTT-GACCTTCT-CGAACTCGGATTTTT
1 AAATTACCAAAATACCCTTATAGGGGTATTTTCATAATTTAG-CCTTTTCCGAACTCGAAATTTC
*** * * * * * *
12805097 GTGAAACCTTCCAGACCATCGTTTTATAATATTTCATGATTTTTGATGCATTTAAAATCACAGTG
65 ACAAAACTTTTCAGATCATAGTTTTATAATATTTCATGATTTTTAATGCATTTAAAATCACAGTA
*
12805162 GGGCCTCAAAAACTATG
130 GGACCTCAAAAACTATG
*
12805179 AAATTACCAAAATACCCTTATAGGGTTATTTTCATAATTTAGCC-TTTCCGAACTCGAAATTTCA
1 AAATTACCAAAATACCCTTATAGGGGTATTTTCATAATTTAGCCTTTTCCGAACTCGAAATTTCA
* * * * * *
12805243 CAAAACTTTTTAGATCCTAGTTTTATAATATTTCATGATTTTTTATCCATTTGAAATCATAGTAG
66 CAAAACTTTTCAGATCATAGTTTTATAATATTTCATGATTTTTAATGCATTTAAAATCACAGTAG
* * *
12805308 TACCTCAAAAAGTGTG
131 GACCTCAAAAACTATG
** * * *
12805324 AAATTACCAAAATACCCTTATAGGGGTATTTTTGTAATTTAGCCTTTTCTGAGCTCGGAATTTCA
1 AAATTACCAAAATACCCTTATAGGGGTATTTTCATAATTTAGCCTTTTCCGAACTCGAAATTTCA
** * * * * *
12805389 TGAAACTTTTCATATCATAATCTTATAATATTTCTTGATTTTTAATG-TTTTAAAATC
66 CAAAACTTTTCAGATCATAGTTTTATAATATTTCATGATTTTTAATGCATTTAAAATC
12805446 CCAAAAATGG
Statistics
Matches: 220, Mismatches: 43, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
144 27 0.12
145 138 0.63
146 55 0.25
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (146 bp):
AAATTACCAAAATACCCTTATAGGGGTATTTTCATAATTTAGCCTTTTCCGAACTCGAAATTTCA
CAAAACTTTTCAGATCATAGTTTTATAATATTTCATGATTTTTAATGCATTTAAAATCACAGTAG
GACCTCAAAAACTATG
Found at i:12805826 original size:1 final size:1
Alignment explanation
Indices: 12805774--12805807 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
12805764 GGAGGGCAGG
*
12805774 AAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
12805808 GGAAAACCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:12812005 original size:278 final size:280
Alignment explanation
Indices: 12811656--12812235 Score: 596
Period size: 278 Copynumber: 2.1 Consensus size: 280
12811646 GCATTTTAGG
* * * * * *
12811656 CCAAAAACG-CTTCAATAATCTAAGAATTATTCAAGGCATTTTCGGCCAGAAACACCTTTAGTAC
1 CCAAAAATGCCTTCAATAATCCAAGAATTATTCAAGGCATTTTCAGCCAGAAACACCTTCAATAA
* * * * ** *** * *
12811720 CCTCATTCAATATTTTGTTAAGGATTTTTCAAGGTGTTATCT-GGGTAAAATGCCTTTAATAATC
66 CCTCATTCAATATTGTGTAAAAGATTATTCAAGGCATTATCTAGACAAAAACGCCTTCAATAATC
* * * * * *
12811784 TCATCATAAATGCCTAAAGGGGATTATTCAAGGCGTTTTTAGCCAT-ATATGCCTTGACTAACTC
131 TCATCATAAACGCCTAAAAGGGATTATTCAAGGCATTTTTAGCCATAAAATGCCTTAACTAACCC
* ** * * * * *
12811848 TAAGCG-ATTATTCAAGGTGTTTTTTCACAAAAATGCCTTAAATGATCC-CAAAAAAATGGGA-A
196 CAAG-GAATTATTCAAGGCATTTTATCACAAAAATACCTTAAATAATCCAAAAAAAAATGAGAGA
*
12811910 GCGATTATTGAAAGCATTTTTCA
260 G-AATTATTGAAAGCATTTTT-A
* * * * *
12811933 CCAAAAATGCCTTTAATAATCCAGGAATTATTCAAGGCATTTTTAGCTAGAAACATCTTCAATAA
1 CCAAAAATGCCTTCAATAATCCAAGAATTATTCAAGGCATTTTCAGCCAGAAACACCTTCAATAA
* * * * *
12811998 TCTCATTCTATATTGTGTAAAAGATTATTGAATGCATTTTCTAGACAAAAACGCCTTCAATAATC
66 CCTCATTCAATATTGTGTAAAAGATTATTCAAGGCATTATCTAGACAAAAACGCCTTCAATAATC
** * * * *
12812063 TTTTCATAACCGCTTAAAAGGGATTATTCAAGGTATTTTTTGCCATAAAATGCCTTAACTAACCC
131 TCATCATAAACGCCTAAAAGGGATTATTCAAGGCATTTTTAGCCATAAAATGCCTTAACTAACCC
*
12812128 CAAGGAATTATTCAAGGCATTTTATCACAAAAATACCTTGAATAATCCAAAAAAAAATGAGAGAG
196 CAAGGAATTATTCAAGGCATTTTATCACAAAAATACCTTAAATAATCCAAAAAAAAATGAGAGAG
* * *
12812193 AATTATTGAAGGTATTTTTG
261 AATTATTGAAAGCATTTTTA
* *
12812213 GCAGAAAATGCCTTGAATAATCC
1 CCA-AAAATGCCTTCAATAATCC
12812236 CTTTTAAAAA
Statistics
Matches: 242, Mismatches: 54, Indels: 10
0.79 0.18 0.03
Matches are distributed among these distances:
277 8 0.03
278 76 0.31
279 55 0.23
280 56 0.23
281 45 0.19
282 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (280 bp):
CCAAAAATGCCTTCAATAATCCAAGAATTATTCAAGGCATTTTCAGCCAGAAACACCTTCAATAA
CCTCATTCAATATTGTGTAAAAGATTATTCAAGGCATTATCTAGACAAAAACGCCTTCAATAATC
TCATCATAAACGCCTAAAAGGGATTATTCAAGGCATTTTTAGCCATAAAATGCCTTAACTAACCC
CAAGGAATTATTCAAGGCATTTTATCACAAAAATACCTTAAATAATCCAAAAAAAAATGAGAGAG
AATTATTGAAAGCATTTTTA
Found at i:12812935 original size:294 final size:293
Alignment explanation
Indices: 12812399--12813183 Score: 873
Period size: 295 Copynumber: 2.7 Consensus size: 293
12812389 CACATACACT
* * * * *
12812399 TTCAATAACCCCACTAAATATTATGTTAGAGATTATTCAAGGCATTTTCTGGGTAAAAACACCTT
1 TTCAATAACCCCATTAAATATTTTGTTAGAGATTATTTAAGGTATTTTCTGGGTAAAAATACCTT
** * * * ** *
12812464 TAATAATCTCCTCATAAACACCTAAAGAGGATTATTCAAGTTGTTTTATCACAAAAATATCTTGA
66 TAATAATCTCCTCATAAATGCTTGAAGGGGATTATTCAAGGCGTTTTATCACAAAAATACCTTGA
** *
12812529 ATGATCTTAAAAAAATGAAAGAGAATTATTGAAGATGTTTTTGATAGAAAACACCTTGAATAATC
131 ATGATCCCAAAAAAATGAAAGAGAATTATTGAAGATGTTTTTGATAGAAAACACCTCGAATAATC
* * *
12812594 CCCTCTAAAAAATTAGAAAGGATTATTAAAGGCATTTTTAACCAAAAATACCTTCAATAATTAAG
196 CCCTCTAAAAAATTAGAAAGGATTATTAAAGGCACTTTTAACCAAAAACACCTTCAATAATCAAG
** * *
12812659 GATTTATCCAAGGTGTTTTTGG-CTAAAGTGCC
261 GATTTATCCAAGGCATTTTTGGCCAAAAATGCC
* * * *
12812691 TTCAATAACCCCATTTAATATTTTCTTA-AGGATTATTTAAGGTATTTTTTGGGCAAAAATACCT
1 TTCAATAACCCCATTAAATATTTTGTTAGA-GATTATTTAAGGTATTTTCTGGGTAAAAATACCT
* * *
12812755 TTAATAATCTCTTCATAAATGCTTGAAGGGGATTATTGAAGGCG-TTTATCACAAAAATGCCTTG
65 TTAATAATCTCCTCATAAATGCTTGAAGGGGATTATTCAAGGCGTTTTATCACAAAAATACCTTG
** * * *
12812819 AATGATCCCAAAAAAATGGGAG-GAGATTATTGAAGGTATTTTTTTTTATAGAAAACGCCTCGAA
130 AATGATCCCAAAAAAATGAAAGAGA-ATTATTGAA-G-A-TGTTTTTGATAGAAAACACCTCGAA
* * **
12812883 TAATCCCTTCTAAAAAATT-GAAAGGGATTATTAAAGGCGCTTTTGGCCAAAAACACCTTCAATA
191 TAATCCCCTCTAAAAAATTAGAAA-GGATTATTAAAGGCACTTTTAACCAAAAACACCTTCAATA
* * * *
12812947 ATCCATGATTTATTCAATGCATTTTTGGCCAAAAATGCC
255 ATCAAGGATTTATCCAAGGCATTTTTGGCCAAAAATGCC
* * *
12812986 TTCAATAACCCCATTCAATATTTTGTTAGAGATTATTTAAGGTATTTTCTGGATAAAAATGCCTT
1 TTCAATAACCCCATTAAATATTTTGTTAGAGATTATTTAAGGTATTTTCTGGGTAAAAATACCTT
* * * * * * *
12813051 CAATAATCTCCTCATAAATGCTTGAAGGGAATTTTTCAAGACATTTTATCATAAAAATACCTTCA
66 TAATAATCTCCTCATAAATGCTTGAAGGGGATTATTCAAGGCGTTTTATCACAAAAATACCTTGA
* * * * *** *
12813116 TTAATCCTTTCATAAAAAATAAAAGAG-ATTATTAAAGGCATTTTTGATAGAAAATACCTTC-AA
131 ATGATCC---CA-AAAAAATGAAAGAGAATTATTGAAGATGTTTTTGATAGAAAACACC-TCGAA
12813179 TAATC
191 TAATC
12813184 TCTTATAAAA
Statistics
Matches: 407, Mismatches: 71, Indels: 26
0.81 0.14 0.05
Matches are distributed among these distances:
290 2 0.00
291 46 0.11
292 89 0.22
293 5 0.01
294 95 0.23
295 101 0.25
296 46 0.11
297 2 0.00
298 1 0.00
299 10 0.02
300 9 0.02
301 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (293 bp):
TTCAATAACCCCATTAAATATTTTGTTAGAGATTATTTAAGGTATTTTCTGGGTAAAAATACCTT
TAATAATCTCCTCATAAATGCTTGAAGGGGATTATTCAAGGCGTTTTATCACAAAAATACCTTGA
ATGATCCCAAAAAAATGAAAGAGAATTATTGAAGATGTTTTTGATAGAAAACACCTCGAATAATC
CCCTCTAAAAAATTAGAAAGGATTATTAAAGGCACTTTTAACCAAAAACACCTTCAATAATCAAG
GATTTATCCAAGGCATTTTTGGCCAAAAATGCC
Found at i:12820665 original size:15 final size:15
Alignment explanation
Indices: 12820645--12820680 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
12820635 GGTGTAACTC
*
12820645 TTTATCTATGTTTGT
1 TTTATCAATGTTTGT
12820660 TTTATCAATGTTTGT
1 TTTATCAATGTTTGT
12820675 TTTATC
1 TTTATC
12820681 CAACTTGGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.17, C:0.08, G:0.11, T:0.64
Consensus pattern (15 bp):
TTTATCAATGTTTGT
Found at i:12821019 original size:55 final size:55
Alignment explanation
Indices: 12820952--12821094 Score: 171
Period size: 55 Copynumber: 2.6 Consensus size: 55
12820942 CAAAATATAA
* *
12820952 TAAAAAAATTAAAACATATAAGTCTATACTGACAATCTCTAACCA-TAGGTAAATG
1 TAAAAAAATTAAAACATAAAAGTCTATACTGACAATCTCTAACCATTA-GTAAAGG
* * * * * *
12821007 TAAAAAAATTAAAGCATAAAATTCTATATTGATAGTCTCTAACCATTAGTATAGG
1 TAAAAAAATTAAAACATAAAAGTCTATACTGACAATCTCTAACCATTAGTAAAGG
* * *
12821062 TAAGAAAATTAAAAAATACAAGTCTATACTGAC
1 TAAAAAAATTAAAACATAAAAGTCTATACTGAC
12821095 GGATGCTAAG
Statistics
Matches: 72, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
55 70 0.97
56 2 0.03
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.29
Consensus pattern (55 bp):
TAAAAAAATTAAAACATAAAAGTCTATACTGACAATCTCTAACCATTAGTAAAGG
Found at i:12821734 original size:18 final size:18
Alignment explanation
Indices: 12821711--12821767 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
12821701 TCAAAAGAAC
12821711 AAGAAAATGATGATGAGA
1 AAGAAAATGATGATGAGA
* *
12821729 AAGAAAAAGATGATGATA
1 AAGAAAATGATGATGAGA
* **
12821747 ATGATGATGATGATGATGA
1 AAGAAAATGATGATGA-GA
12821766 AA
1 AA
12821768 CATATGAGTT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
18 28 0.93
19 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.26, T:0.21
Consensus pattern (18 bp):
AAGAAAATGATGATGAGA
Found at i:12822217 original size:21 final size:20
Alignment explanation
Indices: 12822191--12822249 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 20
12822181 CCATACAGGT
12822191 CATTTTCACCATCGATATAG
1 CATTTTCACCATCGATATAG
*
12822211 CCATTTTCACCACCGATATAG
1 -CATTTTCACCATCGATATAG
*
12822232 CATGATTCACCATACGAT
1 CAT-TTTCACCAT-CGAT
12822250 CATCTTCTGC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.09
21 26 0.79
22 4 0.12
ACGTcount: A:0.31, C:0.29, G:0.10, T:0.31
Consensus pattern (20 bp):
CATTTTCACCATCGATATAG
Found at i:12823774 original size:157 final size:155
Alignment explanation
Indices: 12823416--12823976 Score: 495
Period size: 158 Copynumber: 3.6 Consensus size: 155
12823406 CGTAATTTAT
* * * *
12823416 TTTGTGATTCTGATTGTGTATTGTGATTATTGATGAAGC--AGATAG-GATAGTAATTAAAAGAT
1 TTTGTGATTCTGGTTGTGTATTATGATTATTGAT-AA-CATAGATAGTG-TAGTAATTGAAAGAC
* ** * *
12823478 TAAACATTACGGGACAAATGATATTGAACTATACAGTATTGTGTGCTTATTGAGATGAAATGACT
63 TAAACATTACAGGATGAATGATATTGAACTATATAGT-TT-T-TGATTATTGAGATGAAATGACT
* * *
12823543 TAGTGAATGTG--AACTATTGCATAACTTAC
125 TTGTGAAGGTGAAAACTATTGCATAACTTGC
* * * * ** * * *
12823572 TTTTTTATTCTGGCTGTATATTATGCGTGTTAATAA-ATTAAATAGTGTAGTAATTGAAAGACTA
1 TTTGTGATTCTGGTTGTGTATTATGATTATTGATAACA-TAGATAGTGTAGTAATTGAAAGACTA
* * * * *
12823636 AACATTACAGGATGGATGGTATTGAAATATATATGTTTTATGATTATTAAGATGCAATGACTTTG
65 AACATTACAGGATGAATGATATTGAACTATATA-GTTTT-TGATTATTGAGATGAAATGACTTTG
*
12823701 TGAAGGAGAAAACTATTGCATAACTTGC
128 TGAAGGTGAAAACTATTGCATAACTTGC
* *
12823729 TTTGTGATTCTTGTTGTGTATTATTATTATTGATAACATAGATAGTGTAGTAATTGAAAGACTAA
1 TTTGTGATTCTGGTTGTGTATTATGATTATTGATAACATAGATAGTGTAGTAATTGAAAGACTAA
* * * * * * *
12823794 ACCTTGCAAGACGATTGATATTGAACTATTTAGCATTTTGTACTTATTGAGATGAAATGACTTTG
66 ACATTACAGGATGAATGATATTGAACTATATAG-TTTTTG-A-TTATTGAGATGAAATGACTTTG
* * ** *
12823859 TAAAGGTGAAAACTATTGCGTATTTTGT
128 TGAAGGTGAAAACTATTGCATAACTTGC
* * * * * * * ***
12823887 TTTATGATTCTGGTTATGTATTGTGATTGTTGATAAAATAGATAATGTAATAATTGAACTCCTAA
1 TTTGTGATTCTGGTTGTGTATTATGATTATTGATAACATAGATAGTGTAGTAATTGAAAGACTAA
* *
12823952 ACATTATAGGATGAATGGTATTGAA
66 ACATTACAGGATGAATGATATTGAA
12823977 TTGTGTCATT
Statistics
Matches: 318, Mismatches: 76, Indels: 20
0.77 0.18 0.05
Matches are distributed among these distances:
155 30 0.09
156 75 0.24
157 99 0.31
158 114 0.36
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.39
Consensus pattern (155 bp):
TTTGTGATTCTGGTTGTGTATTATGATTATTGATAACATAGATAGTGTAGTAATTGAAAGACTAA
ACATTACAGGATGAATGATATTGAACTATATAGTTTTTGATTATTGAGATGAAATGACTTTGTGA
AGGTGAAAACTATTGCATAACTTGC
Found at i:12823896 original size:158 final size:157
Alignment explanation
Indices: 12823420--12823944 Score: 409
Period size: 157 Copynumber: 3.3 Consensus size: 157
12823410 ATTTATTTTG
* * * * ** * *
12823420 TGATTCTGATTGTGTATTGTGATTATTGATGAAGCAGATAG-GATAGTAATTAAAAGATTAAACA
1 TGATTCTGGTTATGTATTATGATTATTGATAAAATAGATAGTG-TAGTAATTGAAAGACTAAACA
** * * * * * * *
12823484 TTACGGGA-CAAATGATATTGAACTATACA-GTATTGTGTGCTTATTGAGATGAAATGACTTAGT
65 TTACAAGATC-GATGATATTGAAATATATATGT-TT-TATGATTATTAAGATGAAATGACTTTGT
* * * * *
12823547 GAATGTG--AACTATTGCATAACTTACTTTT
127 AAAGGAGAAAACTATTGCATAACTTGCTTTA
* * * * ** * * * *
12823576 TTATTCTGGCTGTATATTATGCGTGTTAATAAATTAAATAGTGTAGTAATTGAAAGACTAAACAT
1 TGATTCTGGTTATGTATTATGATTATTGATAAAATAGATAGTGTAGTAATTGAAAGACTAAACAT
* * * * *
12823641 TACAGGATGGATGGTATTGAAATATATATGTTTTATGATTATTAAGATGCAATGACTTTGTGAAG
66 TACAAGATCGATGATATTGAAATATATATGTTTTATGATTATTAAGATGAAATGACTTTGTAAAG
*
12823706 GAGAAAACTATTGCATAACTTGCTTTG
131 GAGAAAACTATTGCATAACTTGCTTTA
* * * * *
12823733 TGATTCTTGTTGTGTATTATTATTATTGATAACATAGATAGTGTAGTAATTGAAAGACTAAACCT
1 TGATTCTGGTTATGTATTATGATTATTGATAAAATAGATAGTGTAGTAATTGAAAGACTAAACAT
* * * * *
12823798 TGCAAGA-CGATTGATATTGAACTATTTA-GCATTT-TGTACTTATTGAGATGAAATGACTTTGT
66 TACAAGATCGA-TGATATTGAAATATATATG-TTTTATG-A-TTATTAAGATGAAATGACTTTGT
* * ** *
12823860 AAAGGTGAAAACTATTGCGTATTTTGTTTTA
127 AAAGGAGAAAACTATTGCATAACTTGCTTTA
* * * *
12823891 TGATTCTGGTTATGTATTGTGATTGTTGATAAAATAGATAATGTAATAATTGAA
1 TGATTCTGGTTATGTATTATGATTATTGATAAAATAGATAGTGTAGTAATTGAA
12823945 CTCCTAAACA
Statistics
Matches: 293, Mismatches: 67, Indels: 16
0.78 0.18 0.04
Matches are distributed among these distances:
155 28 0.10
156 76 0.26
157 98 0.33
158 91 0.31
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (157 bp):
TGATTCTGGTTATGTATTATGATTATTGATAAAATAGATAGTGTAGTAATTGAAAGACTAAACAT
TACAAGATCGATGATATTGAAATATATATGTTTTATGATTATTAAGATGAAATGACTTTGTAAAG
GAGAAAACTATTGCATAACTTGCTTTA
Found at i:12832872 original size:11 final size:11
Alignment explanation
Indices: 12832848--12832880 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
12832838 TTGGTTCCGC
12832848 TTTTCTTTTCTT
1 TTTTCTTTT-TT
12832860 TTTTCTTTTTT
1 TTTTCTTTTTT
12832871 TTTTCTTTTT
1 TTTTCTTTTT
12832881 CTCTTGGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:12832874 original size:18 final size:19
Alignment explanation
Indices: 12832848--12832885 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
12832838 TTGGTTCCGC
12832848 TTTTCTTTTCTTTTT-TCT
1 TTTTCTTTTCTTTTTCTCT
*
12832866 TTTTTTTTTCTTTTTCTCT
1 TTTTCTTTTCTTTTTCTCT
12832885 T
1 T
12832886 GGTTTGGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTCTTTTCTTTTTCTCT
Found at i:12833982 original size:16 final size:18
Alignment explanation
Indices: 12833951--12833988 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
12833941 TAAAATTTTA
12833951 AATTATATTATATTAAAT
1 AATTATATTATATTAAAT
*
12833969 AATTAT-TTAT-TTAACT
1 AATTATATTATATTAAAT
12833985 AATT
1 AATT
12833989 TTTTTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 4 0.21
18 6 0.32
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
AATTATATTATATTAAAT
Found at i:12835746 original size:1 final size:1
Alignment explanation
Indices: 12835703--12835728 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
12835693 AAAGACCATG
12835703 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
12835729 ATAAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:12836537 original size:16 final size:16
Alignment explanation
Indices: 12836507--12836550 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
12836497 AAAATTTCAA
*
12836507 ATTTCATTTTATATTTT
1 ATTTC-TTTTATATTGT
*
12836524 ATTTCTTTTTTATTGT
1 ATTTCTTTTATATTGT
12836540 ATTTTCTTTTA
1 A-TTTCTTTTA
12836551 AATATAATGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73
Consensus pattern (16 bp):
ATTTCTTTTATATTGT
Found at i:12840266 original size:2 final size:2
Alignment explanation
Indices: 12840254--12840307 Score: 72
Period size: 2 Copynumber: 27.0 Consensus size: 2
12840244 ACATACATGA
* * * *
12840254 AT AT AT GT AT AT AA AT AA AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12840296 AT AT AT AT AT AT
1 AT AT AT AT AT AT
12840308 GGAGACTCAC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:12844465 original size:12 final size:12
Alignment explanation
Indices: 12844445--12844502 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
12844435 GATTTTTAGA
*
12844445 TTATGTTTATTT
1 TTATATTTATTT
*
12844457 TTATATTTATAT
1 TTATATTTATTT
*
12844469 TTA-ATTGATATT
1 TTATATTTAT-TT
*
12844481 TTAAATTTATTT
1 TTATATTTATTT
*
12844493 TTATTTTTAT
1 TTATATTTAT
12844503 AAATATTTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
11 5 0.14
12 27 0.73
13 5 0.14
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (12 bp):
TTATATTTATTT
Found at i:12848132 original size:12 final size:12
Alignment explanation
Indices: 12848110--12848156 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
12848100 CTTTAACTTA
12848110 AACTAAATGAAG
1 AACTAAATGAAG
* *
12848122 ACCTAAGTGAAG
1 AACTAAATGAAG
*
12848134 AACTAATTGAAG
1 AACTAAATGAAG
12848146 AACTAAATGAA
1 AACTAAATGAA
12848157 AATGTAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (12 bp):
AACTAAATGAAG
Found at i:12855449 original size:12 final size:12
Alignment explanation
Indices: 12855432--12855474 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
12855422 CACTTAGACC
*
12855432 AAATGAAGACCT
1 AAATGAAGAACT
12855444 AAATGAAGAACT
1 AAATGAAGAACT
*
12855456 AATTGAAGAACT
1 AAATGAAGAACT
12855468 AAATGAA
1 AAATGAA
12855475 AATGTAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.56, C:0.09, G:0.16, T:0.19
Consensus pattern (12 bp):
AAATGAAGAACT
Found at i:12864828 original size:43 final size:43
Alignment explanation
Indices: 12864769--12864884 Score: 153
Period size: 43 Copynumber: 2.7 Consensus size: 43
12864759 CTCTCTTAGT
*
12864769 AGATGCTCAACAACTTTGAAAAATTTAAAAGGTTGCTCTAATT
1 AGATGCTCAACAACTTTGAAAAATTTAAAAGGTTGCTCTAATC
* * * * *
12864812 AGAGTG-TTAATAACTTTGAAAATTTTAAAAGGTTTCTCTCATC
1 AGA-TGCTCAACAACTTTGAAAAATTTAAAAGGTTGCTCTAATC
*
12864855 AGATGCTCAACAACTTTAAAAAATTTAAAA
1 AGATGCTCAACAACTTTGAAAAATTTAAAA
12864885 AGCTCATCTC
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
42 2 0.03
43 57 0.93
44 2 0.03
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (43 bp):
AGATGCTCAACAACTTTGAAAAATTTAAAAGGTTGCTCTAATC
Found at i:12864895 original size:43 final size:42
Alignment explanation
Indices: 12864769--12864972 Score: 142
Period size: 43 Copynumber: 4.8 Consensus size: 42
12864759 CTCTCTTAGT
* * * *
12864769 AGATGCTCAACAACTTTGAAAAATTTAAAAGGTTGCTCTAATT
1 AGATGCTCAACAACTTTAAAAAATTTAAAAAGTT-CTCTCATC
* * * * *
12864812 AGAGTG-TTAATAACTTTGAAAATTTTAAAAGGTTTCTCTCATC
1 AGA-TGCTCAACAACTTTAAAAAATTTAAAAAG-TTCTCTCATC
* *
12864855 AGATGCTCAACAACTTTAAAAAATTTAAAAAGCTCATCTCATT
1 AGATGCTCAACAACTTTAAAAAATTTAAAAAGTTC-TCTCATC
* * * * * * *
12864898 AGAGGTTCAACAAC-TTAGGAAATTTTAAGAATTTCCTTTCATC
1 AGATGCTCAACAACTTTA-AAAAATTTAAAAAGTT-CTCTCATC
* * * *
12864941 AAAGGCTTAATAACTTTAAAAAATTTAAAAAG
1 AGATGCTCAACAACTTTAAAAAATTTAAAAAG
12864973 CTTGGCTTAA
Statistics
Matches: 125, Mismatches: 29, Indels: 14
0.74 0.17 0.08
Matches are distributed among these distances:
42 7 0.06
43 110 0.88
44 8 0.06
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (42 bp):
AGATGCTCAACAACTTTAAAAAATTTAAAAAGTTCTCTCATC
Found at i:12864899 original size:86 final size:86
Alignment explanation
Indices: 12864769--12864974 Score: 240
Period size: 86 Copynumber: 2.4 Consensus size: 86
12864759 CTCTCTTAGT
* * * * *
12864769 AGATGCTCAACAACTTTGAAAAATTTAAAAGGTTGCTCTAATTAGAGTGTT-AATAACTTTGAAA
1 AGATGCTCAACAACTTTAAAAAATTTAAAAAGCTGCTCTAATTAGAG-GTTCAACAACTTAGAAA
12864833 ATTTTAA-AAGGTTT-CTCTCATC
65 ATTTTAAGAA--TTTCCTCTCATC
* *
12864855 AGATGCTCAACAACTTTAAAAAATTTAAAAAGCT-CATCTCATTAGAGGTTCAACAACTTAGGAA
1 AGATGCTCAACAACTTTAAAAAATTTAAAAAGCTGC-TCTAATTAGAGGTTCAACAACTTAGAAA
*
12864919 ATTTTAAGAATTTCCTTTCATC
65 ATTTTAAGAATTTCCTCTCATC
* * * *
12864941 AAAGGCTTAATAACTTTAAAAAATTTAAAAAGCT
1 AGATGCTCAACAACTTTAAAAAATTTAAAAAGCT
12864975 TGGCTTAACA
Statistics
Matches: 104, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
85 7 0.07
86 95 0.91
87 2 0.02
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (86 bp):
AGATGCTCAACAACTTTAAAAAATTTAAAAAGCTGCTCTAATTAGAGGTTCAACAACTTAGAAAA
TTTTAAGAATTTCCTCTCATC
Found at i:12864980 original size:32 final size:32
Alignment explanation
Indices: 12864944--12865006 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
12864934 TTTCATCAAA
*
12864944 GGCTTAATAACTTTAAAAAATTTAAAAAGCTT
1 GGCTTAACAACTTTAAAAAATTTAAAAAGCTT
* *
12864976 GGCTTAACAACTTTGAAAATTTTAAAAAGCT
1 GGCTTAACAACTTTAAAAAATTTAAAAAGCT
12865007 CATTTCATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (32 bp):
GGCTTAACAACTTTAAAAAATTTAAAAAGCTT
Found at i:12865013 original size:75 final size:76
Alignment explanation
Indices: 12864906--12865046 Score: 185
Period size: 75 Copynumber: 1.9 Consensus size: 76
12864896 TTAGAGGTTC
* * ** * * *
12864906 AACAACTTAGGAAATTTTAAGAATTTCCTTTCATCAAAGGCTTAATAAC-TTTAAAAAATTTAAA
1 AACAACTTAGAAAATTTTAAAAAGCTCATTTCATCAAAGGCTTAACAACTTTTAAAAAATGTAAA
12864970 AAGCTTGGCTT
66 AAGCTTGGCTT
* * *
12864981 AACAACTTTGAAAATTTTAAAAAGCTCATTTCATTAGAGGCTTAACAACTTTTAAAAAATGTAAA
1 AACAACTTAGAAAATTTTAAAAAGCTCATTTCATCAAAGGCTTAACAACTTTTAAAAAATGTAAA
12865046 A
66 A
12865047 GGCTCCTTAA
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
75 40 0.73
76 15 0.27
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (76 bp):
AACAACTTAGAAAATTTTAAAAAGCTCATTTCATCAAAGGCTTAACAACTTTTAAAAAATGTAAA
AAGCTTGGCTT
Found at i:12866458 original size:13 final size:12
Alignment explanation
Indices: 12866440--12866499 Score: 54
Period size: 13 Copynumber: 5.0 Consensus size: 12
12866430 GTAAGCCCAA
12866440 TTTTGTTTTATAT
1 TTTTG-TTTATAT
12866453 TTTTG-TTAT-T
1 TTTTGTTTATAT
12866463 TTTAT-TTTATAT
1 TTT-TGTTTATAT
*
12866475 TTTATGTATATAT
1 TTT-TGTTTATAT
*
12866488 TTTTCTTTATAT
1 TTTTGTTTATAT
12866500 CCTGTGTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
10 4 0.10
11 9 0.22
12 13 0.32
13 14 0.35
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (12 bp):
TTTTGTTTATAT
Found at i:12866592 original size:24 final size:24
Alignment explanation
Indices: 12866546--12866596 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
12866536 TTAATATATA
* * *
12866546 TATTTTATTTTATTTTTCCTTTTT
1 TATTTTATTTTATATGTACTTTTT
12866570 TATTTTATTTTATATGTA--TTTT
1 TATTTTATTTTATATGTACTTTTT
12866592 TATTT
1 TATTT
12866597 ATCTAATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 9 0.38
24 15 0.62
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (24 bp):
TATTTTATTTTATATGTACTTTTT
Found at i:12866606 original size:24 final size:22
Alignment explanation
Indices: 12866566--12866707 Score: 89
Period size: 24 Copynumber: 6.3 Consensus size: 22
12866556 TATTTTTCCT
12866566 TTTTTATTTTAT-T-TTATATGTA
1 TTTTTA-TTTATCTATTATAT-TA
12866588 TTTTTATTTATCTAATTATA-TA
1 TTTTTATTTATCT-ATTATATTA
*
12866610 --TTTATTTATCTGTTATTATTA
1 TTTTTATTTATCTATTA-TATTA
*
12866631 TTTTTTATTTATCTTATAATATTA
1 -TTTTTATTTATC-TATTATATTA
* *
12866655 TAATTAATTTATCTTATTATTATT-
1 T-TTTTATTTATC-TATTA-TATTA
* * * *
12866679 TTTCTAATTATCTATTAAATTT
1 TTTTTATTTATCTATTATATTA
12866701 TTTTTAT
1 TTTTTAT
12866708 CTGATTTTTG
Statistics
Matches: 95, Mismatches: 13, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
19 3 0.03
20 13 0.14
21 10 0.11
22 19 0.20
23 8 0.08
24 35 0.37
25 7 0.07
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.66
Consensus pattern (22 bp):
TTTTTATTTATCTATTATATTA
Found at i:12866618 original size:41 final size:41
Alignment explanation
Indices: 12866569--12866716 Score: 124
Period size: 41 Copynumber: 3.6 Consensus size: 41
12866559 TTTTCCTTTT
12866569 TTAT-TTTATTTTATATGTATTTTTATTTATCTAATTATATA
1 TTATATTTATTTTATAT-TATTTTTATTTATCTAATTATATA
*
12866610 TT-TATTTATCTGTTATTATTATTTTTTATTTATCTTA-TA-ATA
1 TTATATTTAT-T-TTA-TATTA-TTTTTATTTATCTAATTATATA
* * * * * *
12866652 TTATAATTAATTTATCTTATTATTATTTTTCTAATTATCTA
1 TTATATTTATTTTATATTATTTTTATTTATCTAATTATATA
* * * *
12866693 TTAAATTTTTTTTATCTGATTTTT
1 TTATATTTATTTTATATTATTTTT
12866717 GTTTTGAAAG
Statistics
Matches: 85, Mismatches: 14, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
39 12 0.14
40 7 0.08
41 30 0.35
42 7 0.08
43 12 0.14
44 17 0.20
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (41 bp):
TTATATTTATTTTATATTATTTTTATTTATCTAATTATATA
Found at i:12867549 original size:21 final size:21
Alignment explanation
Indices: 12867521--12867666 Score: 84
Period size: 21 Copynumber: 6.5 Consensus size: 21
12867511 TTTTTTTGAA
*
12867521 TTTATTTATTTATTTGTTTAT
1 TTTATTTATTTATTTATTTAT
12867542 TTGT-TTTATTTATTTATTTAT
1 TT-TATTTATTTATTTATTTAT
* *
12867563 TTTATTTATTAGATTAAGTTTAT
1 TTTATTTATT-TATTTA-TTTAT
* * *
12867586 TTAATATTCTTT-TTATCTTTAT
1 TTTAT-TTATTTATT-TATTTAT
12867608 TTTATTTTTATTT-TTGT-TTTACT
1 TTTA--TTTATTTATT-TATTTA-T
*
12867631 TTTTTTTATTTTATTTTATTTTATT
1 TTTATTTA-TTTA-TTTA-TTTA-T
12867656 TTTATTTATTT
1 TTTATTTATTT
12867667 TCACTTTTAT
Statistics
Matches: 97, Mismatches: 14, Indels: 25
0.71 0.10 0.18
Matches are distributed among these distances:
20 1 0.01
21 30 0.31
22 22 0.23
23 22 0.23
24 10 0.10
25 12 0.12
ACGTcount: A:0.20, C:0.02, G:0.03, T:0.75
Consensus pattern (21 bp):
TTTATTTATTTATTTATTTAT
Found at i:12867551 original size:17 final size:17
Alignment explanation
Indices: 12867520--12867667 Score: 89
Period size: 17 Copynumber: 8.8 Consensus size: 17
12867510 TTTTTTTTGA
12867520 ATTTATTTA-TTTATTT
1 ATTTATTTATTTTATTT
* *
12867536 GTTTATTTGTTTTATTT
1 ATTTATTTATTTTATTT
12867553 ATTTATTTATTTTATTT
1 ATTTATTTATTTTATTT
* * *
12867570 ATTAGATTAAGTTTATTT
1 ATT-TATTTATTTTATTT
*
12867588 A-ATATTCT-TTTTA--T
1 ATTTATT-TATTTTATTT
*
12867602 CTTTATTTTATTTTTATTT
1 ATTTA-TTTA-TTTTATTT
*
12867621 -TTGT-TTTACTTTTTTTT
1 ATT-TATTTA-TTTTATTT
12867638 ATTTTATTTTATTTTA-TT
1 A-TTTA-TTTATTTTATTT
12867656 -TTTATTTATTTT
1 ATTTATTTATTTT
12867668 CACTTTTATT
Statistics
Matches: 102, Mismatches: 16, Indels: 29
0.69 0.11 0.20
Matches are distributed among these distances:
14 1 0.01
15 11 0.11
16 20 0.20
17 41 0.40
18 17 0.17
19 8 0.08
20 4 0.04
ACGTcount: A:0.20, C:0.02, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTATTTATTTTATTT
Found at i:12867588 original size:4 final size:4
Alignment explanation
Indices: 12867520--12867572 Score: 70
Period size: 4 Copynumber: 12.8 Consensus size: 4
12867510 TTTTTTTTGA
* *
12867520 ATTT ATTT ATTT ATTT GTTT ATTT GTTTT ATTT ATTT ATTT ATTTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT -ATTT ATTT ATTT ATTT A-TTT ATTT
12867570 ATT
1 ATT
12867573 AGATTAAGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
4 36 0.84
5 7 0.16
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:12867613 original size:5 final size:5
Alignment explanation
Indices: 12867596--12867687 Score: 89
Period size: 5 Copynumber: 17.4 Consensus size: 5
12867586 TTAATATTCT
*
12867596 TTTTA TCTTTA TTTTA TTTTTA TTTTTG TTTTA CTTTT- TTTTA TTTTA
1 TTTTA T-TTTA TTTTA -TTTTA -TTTTA TTTTA -TTTTA TTTTA TTTTA
*
12867644 TTTTA TTTTA TTTT- TATTTA TTTTCA CTTTTA TTTTG TTTTA TT
1 TTTTA TTTTA TTTTA T-TTTA TTTT-A -TTTTA TTTTA TTTTA TT
12867688 ATTCTATTTT
Statistics
Matches: 75, Mismatches: 4, Indels: 16
0.79 0.04 0.17
Matches are distributed among these distances:
4 5 0.07
5 44 0.59
6 22 0.29
7 4 0.05
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:12867644 original size:37 final size:35
Alignment explanation
Indices: 12867545--12867697 Score: 114
Period size: 37 Copynumber: 4.1 Consensus size: 35
12867535 TGTTTATTTG
* * *
12867545 TTTTATTTA-TTTATTTATTTTA-TTTATTAGATTAA
1 TTTTATTTATTTTTTTTATTTTATTTTATT--TTTAT
*
12867580 GTTTATTTAATATTCTTTTTATCTTTATTTTATTTTTAT
1 TTTTATTT-AT-TT-TTTTTAT-TTTATTTTATTTTTAT
*
12867619 TTTTGTTTTACTTTTTTTTATTTTATTTTA-TTTTAT
1 TTTT-ATTTA-TTTTTTTTATTTTATTTTATTTTTAT
*
12867655 TTTTATTTATTTTCACTTTTATTTTGTTTTATTATTCTAT
1 TTTTATTTATTTT---TTTTATTTTATTTTATT-TT-TAT
12867695 TTT
1 TTT
12867698 CTTTAAATAA
Statistics
Matches: 96, Mismatches: 8, Indels: 23
0.76 0.06 0.18
Matches are distributed among these distances:
34 4 0.04
35 11 0.11
36 11 0.11
37 23 0.24
38 10 0.10
39 17 0.18
40 14 0.15
41 6 0.06
ACGTcount: A:0.20, C:0.04, G:0.03, T:0.74
Consensus pattern (35 bp):
TTTTATTTATTTTTTTTATTTTATTTTATTTTTAT
Found at i:12867872 original size:59 final size:59
Alignment explanation
Indices: 12867724--12867991 Score: 360
Period size: 59 Copynumber: 4.5 Consensus size: 59
12867714 AAAATATATA
* *
12867724 TTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAAAAAAG
1 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTC-AAAAAAATAG
* * * * * *
12867784 TTTTTGAGGAAAAGTTGAAAGTATTAATTTTTCTTGAAAATCAAAGTTTCCAAAGAATAT
1 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT-AAATTTTCAAAAAAATAG
* * **
12867844 TTTTTG-GTAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAAAGGG
1 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAAATAG
* *
12867902 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC-AAAAAATCAA
1 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAAAT-AG
*
12867961 CTTTTGAGGAAAAGTTGAAAGTATCAATTTT
1 TTTTTGAGGAAAAGTTGAAAGTATCAATTTT
12867992 CCCTGCACAA
Statistics
Matches: 180, Mismatches: 25, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
58 24 0.13
59 99 0.55
60 50 0.28
61 7 0.04
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.37
Consensus pattern (59 bp):
TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAAATAG
Found at i:12871021 original size:23 final size:22
Alignment explanation
Indices: 12870991--12871043 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
12870981 TGGTTGAAGG
* *
12870991 TTTTTTTTT-GTCATTTTAAGAT
1 TTTTTTTTTAGTAATGTT-AGAT
12871013 TTTTTTTTTAGTAATGTTAGAT
1 TTTTTTTTTAGTAATGTTAGAT
*
12871035 TTCTTTTTT
1 TTTTTTTTT
12871044 GCAATATGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 21 0.78
23 6 0.22
ACGTcount: A:0.17, C:0.04, G:0.09, T:0.70
Consensus pattern (22 bp):
TTTTTTTTTAGTAATGTTAGAT
Found at i:12871906 original size:19 final size:17
Alignment explanation
Indices: 12871882--12871952 Score: 70
Period size: 18 Copynumber: 3.9 Consensus size: 17
12871872 ACAATGGATG
*
12871882 AAAAATGAGAAAAAAGAA
1 AAAAAAGAGAAAAAA-AA
12871900 AAAAAATGATGAAAAAAAA
1 AAAAAA-GA-GAAAAAAAA
*
12871919 AGAAAAAAAGAAAAAAAA
1 A-AAAAAGAGAAAAAAAA
*
12871937 AAGAAAGAAGAAAAAA
1 AAAAAAG-AGAAAAAA
12871953 TGAGAAAATG
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
17 4 0.09
18 23 0.51
19 6 0.13
20 12 0.27
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (17 bp):
AAAAAAGAGAAAAAAAA
Found at i:12871914 original size:18 final size:15
Alignment explanation
Indices: 12871893--12871968 Score: 50
Period size: 18 Copynumber: 4.7 Consensus size: 15
12871883 AAAATGAGAA
12871893 AAAAGAAAAAAAATGATG
1 AAAAGAAAAAAAA--A-G
*
12871911 AAAA-AAAAAGAAA-
1 AAAAGAAAAAAAAAG
12871924 AAAAGAAAAAAAAA-
1 AAAAGAAAAAAAAAG
12871938 AGAAAGAAGAAAAAATGAG
1 A-AAAGAA-AAAAAA--AG
12871957 AAAATGAAAAAA
1 AAAA-GAAAAAA
12871969 GAGATTCAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
13 4 0.08
14 9 0.18
15 7 0.14
16 6 0.12
17 7 0.14
18 12 0.24
19 4 0.08
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.05
Consensus pattern (15 bp):
AAAAGAAAAAAAAAG
Found at i:12871916 original size:22 final size:21
Alignment explanation
Indices: 12871882--12871942 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 21
12871872 ACAATGGATG
*
12871882 AAAA-ATGAGAAAAAAGAAAA
1 AAAAGATGAAAAAAAAGAAAA
12871902 AAAATGATGAAAAAAAA-AGAAA
1 AAAA-GATGAAAAAAAAGA-AAA
*
12871924 AAAAGA-AAAAAAAAAGAAA
1 AAAAGATGAAAAAAAAGAAA
12871943 GAAGAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
20 14 0.40
21 4 0.11
22 17 0.49
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (21 bp):
AAAAGATGAAAAAAAAGAAAA
Found at i:12871921 original size:23 final size:20
Alignment explanation
Indices: 12871891--12871942 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 20
12871881 GAAAAATGAG
12871891 AAAAAAGAAAAAAAATGATGAAA
1 AAAAAAGAAAAAAAA-GA--AAA
12871914 AAAAAAG-AAAAAAAGAAAA
1 AAAAAAGAAAAAAAAGAAAA
12871933 AAAAAAGAAA
1 AAAAAAGAAA
12871943 GAAGAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.36
20 2 0.07
21 2 0.07
22 7 0.25
23 7 0.25
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.04
Consensus pattern (20 bp):
AAAAAAGAAAAAAAAGAAAA
Found at i:12871960 original size:10 final size:9
Alignment explanation
Indices: 12871881--12871960 Score: 58
Period size: 9 Copynumber: 8.6 Consensus size: 9
12871871 AACAATGGAT
*
12871881 GAAAAATGA
1 GAAAAAAGA
12871890 GAAAAAAGA
1 GAAAAAAGA
*
12871899 AAAAAAATGA
1 GAAAAAA-GA
*
12871909 TGAAAAAAAAA
1 -G-AAAAAAGA
12871920 GAAAAAA-A
1 GAAAAAAGA
12871928 GAAAAAA-A
1 GAAAAAAGA
12871936 -AAAGAAAGAA
1 GAAA-AAAG-A
12871946 GAAAAAATGA
1 GAAAAAA-GA
12871956 GAAAA
1 GAAAA
12871961 TGAAAAAAGA
Statistics
Matches: 59, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
7 3 0.05
8 12 0.20
9 20 0.34
10 13 0.22
11 5 0.08
12 6 0.10
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (9 bp):
GAAAAAAGA
Found at i:12871969 original size:26 final size:25
Alignment explanation
Indices: 12871881--12871970 Score: 78
Period size: 26 Copynumber: 3.6 Consensus size: 25
12871871 AACAATGGAT
*
12871881 GAAAAATGAGAAAA-AAG-AAAAAA
1 GAAAAATGAAAAAAGAAGAAAAAAA
** *
12871904 -AATGATGAAAAAAAAAGAAAAAAA
1 GAAAAATGAAAAAAGAAGAAAAAAA
** *
12871928 GAAAAAAAAAAGAAAGAAGAAAAAAT
1 GAAAAATGAAA-AAAGAAGAAAAAAA
12871954 GAGAAAATGAAAAAAGA
1 GA-AAAATGAAAAAAGA
12871971 GATTCAAATT
Statistics
Matches: 51, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
22 10 0.20
23 3 0.06
24 6 0.12
25 6 0.12
26 19 0.37
27 7 0.14
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.06
Consensus pattern (25 bp):
GAAAAATGAAAAAAGAAGAAAAAAA
Found at i:12871972 original size:15 final size:14
Alignment explanation
Indices: 12871916--12871972 Score: 66
Period size: 16 Copynumber: 4.1 Consensus size: 14
12871906 TGATGAAAAA
12871916 AAAAGAAAAAA-AG
1 AAAAGAAAAAAGAG
12871929 AAAA-AAAAAAGA-
1 AAAAGAAAAAAGAG
12871941 AAGAAGAAAAAATGAG
1 AA-AAGAAAAAA-GAG
12871957 AAAATGAAAAAAGAG
1 AAAA-GAAAAAAGAG
12871972 A
1 A
12871973 TTCAAATTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
12 8 0.21
13 7 0.18
14 6 0.16
15 8 0.21
16 9 0.24
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAAGAAAAAAGAG
Found at i:12873385 original size:41 final size:41
Alignment explanation
Indices: 12873322--12873617 Score: 364
Period size: 41 Copynumber: 7.1 Consensus size: 41
12873312 ATGATTGTCA
12873322 AGGAGCAATTTAC-TTTCAAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTC-AAAGTCGTGGTGCCTCTGTTTAG
* *
12873363 AGGAGTAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAA
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* * *
12873404 ATGAGTAATTTACTTTTCCAAAGTTGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAG
*
12873446 AGGAGCAATTTAC-TTTCTAAAGTCATGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTC-AAAGTCGTGGTGCCTCTGTTTAG
* *
12873487 AGGAGCAATTTACTTTTCAAAGTTGTGGTGCCTTTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* * * *
12873528 AGGAGCAATTTA-TTTTCCAAAGTCATTGAGCCTCTGATTAG
1 AGGAGCAATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAG
* * * * *
12873569 AGGAGCCATTTATGTTTCTCAAAGTCGTTGAGCCTCTGCTTAG
1 AGGAGCAATTTA-CTTT-TCAAAGTCGTGGTGCCTCTGTTTAG
12873612 AGGAGC
1 AGGAGC
12873618 TTTGGTAAAA
Statistics
Matches: 226, Mismatches: 21, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
40 5 0.02
41 148 0.65
42 41 0.18
43 31 0.14
44 1 0.00
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.37
Consensus pattern (41 bp):
AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
Found at i:12873587 original size:124 final size:124
Alignment explanation
Indices: 12873322--12873617 Score: 405
Period size: 124 Copynumber: 2.4 Consensus size: 124
12873312 ATGATTGTCA
* *
12873322 AGGAGCAATTTACTTTCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGTAATTTACTTTTCAAAGTC
1 AGGAGCAATTTACTTTCTAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTC
* * ** * *
12873387 GTGGTGCCTCTGTTTAAATGAGTAATTTACTTTTCCAAAGTTGTGGTGCCTCTGTTTAG
66 GTGGTGCCTCTGTTTAAAGGAGCAATTTACTTTTCCAAAGTCATGGAGCCTCTGATTAG
* *
12873446 AGGAGCAATTTACTTTCTAAAGTCATGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTT
1 AGGAGCAATTTACTTTCTAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTC
* * *
12873511 GTGGTGCCTTTGTTTAGAGGAGCAATTTA-TTTTCCAAAGTCATTGAGCCTCTGATTAG
66 GTGGTGCCTCTGTTTAAAGGAGCAATTTACTTTTCCAAAGTCATGGAGCCTCTGATTAG
* * * * *
12873569 AGGAGCCATTTATGTTTCTCAAAGTCGTTGAGCCTCTGCTTAGAGGAGC
1 AGGAGCAATTTA-CTTTCT-AAAGTCGTGGTGCCTCTGTTTAGAGGAGC
12873618 TTTGGTAAAA
Statistics
Matches: 151, Mismatches: 19, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
123 35 0.23
124 91 0.60
125 25 0.17
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.37
Consensus pattern (124 bp):
AGGAGCAATTTACTTTCTAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTC
GTGGTGCCTCTGTTTAAAGGAGCAATTTACTTTTCCAAAGTCATGGAGCCTCTGATTAG
Found at i:12873651 original size:13 final size:13
Alignment explanation
Indices: 12873635--12873664 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
12873625 AAAAAAAACC
12873635 AAAAAAACAAAAA
1 AAAAAAACAAAAA
12873648 AAAAAAACAAAAA
1 AAAAAAACAAAAA
12873661 AAAA
1 AAAA
12873665 TTAAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAA
Found at i:12873670 original size:22 final size:22
Alignment explanation
Indices: 12873623--12873673 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
12873613 GGAGCTTTGG
*
12873623 TAAAAAAAAACCAAAAAAACAA
1 TAAAAAAAAAACAAAAAAACAA
12873645 -AAAAAAAAAACAAAAAAA-AA
1 TAAAAAAAAAACAAAAAAACAA
*
12873665 TTAAAAAAA
1 TAAAAAAAA
12873674 TGAAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 2 0.08
21 24 0.92
ACGTcount: A:0.86, C:0.08, G:0.00, T:0.06
Consensus pattern (22 bp):
TAAAAAAAAAACAAAAAAACAA
Found at i:12873673 original size:10 final size:10
Alignment explanation
Indices: 12873624--12873664 Score: 55
Period size: 11 Copynumber: 3.9 Consensus size: 10
12873614 GAGCTTTGGT
12873624 AAAAAAAAACC
1 AAAAAAAAA-C
*
12873635 AAAAAAACAAA
1 AAAAAAA-AAC
12873646 AAAAAAAAAC
1 AAAAAAAAAC
12873656 AAAAAAAAA
1 AAAAAAAAA
12873665 TTAAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 11 0.41
11 14 0.52
12 2 0.07
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:12874000 original size:25 final size:24
Alignment explanation
Indices: 12873972--12874069 Score: 89
Period size: 25 Copynumber: 4.2 Consensus size: 24
12873962 TAATTATATA
12873972 TTTATTTATCTGTTATTATTATTTT
1 TTTATTTATCT-TTATTATTATTTT
* *
12873997 TTTATTTATCTTATAATATTA-TTG
1 TTTATTTATCTT-TATTATTATTTT
* *
12874021 TTGATTTATC-TTGTTATTATTTT
1 TTTATTTATCTTTATTATTATTTT
* *
12874044 TTTAATTATC--TATTA-AATTTT
1 TTTATTTATCTTTATTATTATTTT
12874065 TTTAT
1 TTTAT
12874070 CTGATTTTTA
Statistics
Matches: 60, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
21 9 0.15
22 10 0.17
23 11 0.18
24 12 0.20
25 18 0.30
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (24 bp):
TTTATTTATCTTTATTATTATTTT
Found at i:12874039 original size:50 final size:44
Alignment explanation
Indices: 12873950--12874083 Score: 125
Period size: 45 Copynumber: 3.0 Consensus size: 44
12873940 TTTATATGTA
*
12873950 TTTTTATTTATCTAATTATATATTTATTTATCTGTTATTATTATT
1 TTTTTATTTATCTAATAATATATTTATTTATCTGTTATTATT-TT
*
12873995 TTTTTATTTATCTTATAATATTATTGTTGATTTATCTTGTTATTA--TT
1 TTTTTATTTATCTAATAATA-TA-T-TT-ATTTATC-TGTTATTATTTT
* * *
12874042 TTTTTAATTATCTATTAA-AT-TTT-TTTATCTGATTTTTATTTT
1 TTTTTATTTATCTAATAATATATTTATTTATCTG-TTATTATTTT
12874084 GGAAGGCTGT
Statistics
Matches: 75, Mismatches: 6, Indels: 19
0.75 0.06 0.19
Matches are distributed among these distances:
39 2 0.03
40 11 0.15
42 4 0.05
43 1 0.01
45 19 0.25
46 3 0.04
47 18 0.24
48 2 0.03
49 7 0.09
50 8 0.11
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (44 bp):
TTTTTATTTATCTAATAATATATTTATTTATCTGTTATTATTTT
Found at i:12875018 original size:27 final size:26
Alignment explanation
Indices: 12874988--12875070 Score: 79
Period size: 27 Copynumber: 3.3 Consensus size: 26
12874978 TTAGATTAGG
12874988 TTTATTTAATATTCTTTTTATCTTTAT
1 TTTATTTAATATT-TTTTTATCTTTAT
12875015 TTTATTTTTAAT-TTTTTTTA-CTTTTAT
1 TTTA--TTTAATATTTTTTTATC-TTTAT
*
12875042 TTTATTT--TA-TTTTTTATTTTTA-
1 TTTATTTAATATTTTTTTATCTTTAT
12875064 TTTATTT
1 TTTATTT
12875071 TCACTTTTAT
Statistics
Matches: 50, Mismatches: 1, Indels: 15
0.76 0.02 0.23
Matches are distributed among these distances:
22 7 0.14
23 12 0.24
25 3 0.06
26 1 0.02
27 19 0.38
28 2 0.04
29 6 0.12
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (26 bp):
TTTATTTAATATTTTTTTATCTTTAT
Found at i:12875020 original size:5 final size:5
Alignment explanation
Indices: 12875003--12875101 Score: 80
Period size: 5 Copynumber: 18.8 Consensus size: 5
12874993 TTAATATTCT
12875003 TTTTA TCTTTA TTTTA TTTTTAA TTTT- TTTTA CTTTTA TTTTA TTTTA
1 TTTTA T-TTTA TTTTA -TTTT-A TTTTA TTTTA -TTTTA TTTTA TTTTA
*
12875051 TTTT- TTAT- TTTTA -TTTA TTTTCA CTTTTA TTTTGTA TTATTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTT-A -TTTTA -TTT-TA TT-TTA TTTTA
12875098 TTTT
1 TTTT
12875102 CTTTAAATAA
Statistics
Matches: 80, Mismatches: 3, Indels: 22
0.76 0.03 0.21
Matches are distributed among these distances:
4 14 0.17
5 29 0.36
6 29 0.36
7 8 0.10
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:12875024 original size:17 final size:16
Alignment explanation
Indices: 12874988--12875101 Score: 97
Period size: 17 Copynumber: 6.8 Consensus size: 16
12874978 TTAGATTAGG
* * *
12874988 TTTATTTAATATTCTT
1 TTTATTTTATTTTATT
12875004 TTTATCTTTATTTTATT
1 TTTAT-TTTATTTTATT
*
12875021 TTTAATTTT-TTTTACT
1 TTT-ATTTTATTTTATT
12875037 TTTATTTTATTTTATTT
1 TTTATTTTATTTTA-TT
12875054 TTTATTTT-TATTTATT
1 TTTATTTTAT-TTTATT
*
12875070 TTCACTTTTATTTTGTATT
1 TTTA-TTTTA-TTT-TATT
*
12875089 ATTATTTTATTTT
1 TTTATTTTATTTT
12875102 CTTTAAATAA
Statistics
Matches: 81, Mismatches: 8, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
15 5 0.06
16 26 0.32
17 34 0.42
18 9 0.11
19 7 0.09
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.75
Consensus pattern (16 bp):
TTTATTTTATTTTATT
Found at i:12875030 original size:7 final size:6
Alignment explanation
Indices: 12875002--12875101 Score: 72
Period size: 6 Copynumber: 17.7 Consensus size: 6
12874992 TTTAATATTC
* * *
12875002 TTTTTA TCTTTA -TTTTA TTTTTA -ATTT- TTTTTA CTTTTA -TTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
* * *
12875046 -TTTTA TTTTTTA TTTTTA --TTTA TTTTCA CTTTTA TTTTGTA TTATTA
1 TTTTTA -TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT-TA TTTTTA
12875093 -TTTTA TTTT
1 TTTTTA TTTT
12875102 CTTTAAATAA
Statistics
Matches: 74, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
4 4 0.05
5 24 0.32
6 36 0.49
7 10 0.14
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.77
Consensus pattern (6 bp):
TTTTTA
Found at i:12875041 original size:22 final size:20
Alignment explanation
Indices: 12875010--12875101 Score: 82
Period size: 22 Copynumber: 4.4 Consensus size: 20
12875000 TCTTTTTATC
12875010 TTTATTTTATTTTTAATTTTT
1 TTTATTTTATTTTT-ATTTTT
12875031 TTTACTTTTA-TTTTA-TTTT
1 TTTA-TTTTATTTTTATTTTT
*
12875050 ATT-TTTTATTTTTATTTATT
1 TTTATTTTATTTTTATTT-TT
*
12875070 TTCACTTTTATTTTGTATTATTAT
1 TTTA-TTTTATTTT-TATT-TT-T
12875094 TTTATTTT
1 TTTATTTT
12875102 CTTTAAATAA
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
17 5 0.09
18 5 0.09
19 8 0.14
20 4 0.07
21 8 0.14
22 14 0.24
23 9 0.16
24 5 0.09
ACGTcount: A:0.18, C:0.03, G:0.01, T:0.77
Consensus pattern (20 bp):
TTTATTTTATTTTTATTTTT
Found at i:12875060 original size:39 final size:40
Alignment explanation
Indices: 12875011--12875101 Score: 132
Period size: 39 Copynumber: 2.3 Consensus size: 40
12875001 CTTTTTATCT
* *
12875011 TTATTTTATTTTTAATTT-TTTTTACTTTTATTTTATTTTA
1 TTATTTTATTTTT-ATTTATTTTCACTTTTATTTTATATTA
*
12875051 TT-TTTTATTTTTATTTATTTTCACTTTTATTTTGTATTA
1 TTATTTTATTTTTATTTATTTTCACTTTTATTTTATATTA
12875090 TTATTTTATTTT
1 TTATTTTATTTT
12875102 CTTTAAATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
38 4 0.09
39 31 0.67
40 11 0.24
ACGTcount: A:0.19, C:0.03, G:0.01, T:0.77
Consensus pattern (40 bp):
TTATTTTATTTTTATTTATTTTCACTTTTATTTTATATTA
Found at i:12875275 original size:59 final size:57
Alignment explanation
Indices: 12875123--12875410 Score: 314
Period size: 59 Copynumber: 4.9 Consensus size: 57
12875113 AATAAAAAAA
*
12875123 AATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAGATAAA-TTTTCAAAAA
1 AATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAA-ATAAAGTTTTC-AAAG
* * *
12875181 AAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTGCTTGAAAATCAAAGTTTTCAAAG
1 AATA--TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAAT-AAAGTTTTCAAAG
* * *
12875242 AATATTTTTGGGGAAAAGTTGAAAGTATTAATTTTCCTTAAAAAAAAATTTTCAAA-
1 AATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAATAAAGTTTTCAAAG
* * * *
12875298 AAAAGGGTTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTCCAAAG
1 AATA---TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAAT-AAAGTTTTCAAAG
** *
12875360 AATATTTTT-GAAAAAAGTTGAAAGTATCAATTTT-CTTAAAAATAAATTTTT
1 AATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAATAAAGTTTT
12875411 GAGGAAAAGT
Statistics
Matches: 197, Mismatches: 22, Indels: 24
0.81 0.09 0.10
Matches are distributed among these distances:
56 9 0.05
57 20 0.10
58 30 0.15
59 69 0.35
60 39 0.20
61 22 0.11
62 8 0.04
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (57 bp):
AATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAATAAAGTTTTCAAAG
Found at i:12875359 original size:118 final size:119
Alignment explanation
Indices: 12875123--12875409 Score: 463
Period size: 118 Copynumber: 2.4 Consensus size: 119
12875113 AATAAAAAAA
*
12875123 AATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAGATAAATTTTCAAAAAAAAAGGT
1 AATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAAAGGT
* * * *
12875188 TTTTGAGGAAAAGTTGAAAGTATCAATTTTGCTTGAAAATCAAAGTTTTCAAAG
66 TTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTCCAAAG
* * *
12875242 AATATTTTTGGGGAAAAGTTGAAAGTATTAATTTTCCTTAAAAAAAAATTTTC-AAAAAAAGGGT
1 AATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAAAGGT
12875306 TTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTCCAAAG
66 TTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTCCAAAG
**
12875360 AATATTTTT-GAAAAAAGTTGAAAGTATCAATTTT-CTTAAAAATAAATTTT
1 AATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTT
12875410 TGAGGAAAAG
Statistics
Matches: 156, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
116 15 0.10
117 22 0.14
118 69 0.44
119 50 0.32
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.36
Consensus pattern (119 bp):
AATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAAAGGT
TTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTCCAAAG
Found at i:12883671 original size:117 final size:117
Alignment explanation
Indices: 12883405--12883794 Score: 576
Period size: 117 Copynumber: 3.4 Consensus size: 117
12883395 TTTTGTGCAG
* * * *
12883405 GGAAAATTGATACTTTCAACTTTT-CCCAAAAATATTCTTTT-GAAA-CTTTAATTTCGAGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATT-TTTTGGAAACCTTGATTTTCAAGGAAA
**
12883467 ATTGATACTTTCAACTTTTCCTCAAAAATTTATTTTTTTGAAAATTTA---TTAA
65 ATTGATACTTTCAACTTTTCCTCAAAAA--CCTTTTTTTGAAAATTTATTTTTAA
**
12883519 GGAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTGGAAACCTTGATTTTCAAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAACCTTGATTTTCAAGGAAAA
*
12883584 TTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTGAAAATTTATTTTTAA
66 TTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTTGAAAATTTATTTTTAA
* * * *
12883636 GAAAAATTGATACTTTTAACTTTTCCCCAAAAATATTCTTTGGAAACTTTGATTTTCAAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAACCTTGATTTTCAAGGAAAA
12883701 TTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTTTGAAAATTTATTTTTAA
66 TTGATACTTTCAACTTTTCCTCAAAAACC-TTTTTTTGAAAATTTATTTTTAA
*
12883754 GGAAAATTGATACTTTCAAGTTTTCCCCAAAAATATTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT
12883795 TATTTTTATT
Statistics
Matches: 249, Mismatches: 20, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
114 43 0.17
115 14 0.06
116 41 0.16
117 92 0.37
118 59 0.24
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (117 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAACCTTGATTTTCAAGGAAAA
TTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTTGAAAATTTATTTTTAA
Found at i:12883763 original size:176 final size:172
Alignment explanation
Indices: 12883405--12883795 Score: 493
Period size: 176 Copynumber: 2.2 Consensus size: 172
12883395 TTTTGTGCAG
* * *
12883405 GGAAAATTGATACTTTCAACTTTTCCCAAAAATATTCTTTTGAAACTTTAATTTCGAGAAAAATT
1 GGAAAATTGATACTTTCAACTTTTCCCAAAAACATTCTTTTGAAAATTTAATTTCAAGAAAAATT
* * *
12883470 GATACTTTCAACTTTTCCTCAAAAATTTATTTTTTTGAAAATTTATTAAGGAAAATTGATACTTT
66 GATACTTTCAACTTTTCCCCAAAAA-TTATTCTTTGGAAAATTTATTAAGGAAAATTGATACTTT
* *
12883535 CAACTTTTCCTTAAAAATATTTTTTGGAAACCTTGATTTTCAA
130 CAACTTTTCCTCAAAAATATTTTTTGGAAACATTGATTTTCAA
* * *
12883578 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCCTT-TTTTGAAAATTTATTTTTAAGAAAAA
1 GGAAAATTGATACTTTCAACTTTTCC-CAAAAA-CATTCTTTTGAAAATTTAATTTCAAGAAAAA
* *
12883642 TTGATACTTTTAACTTTTCCCCAAAAA-TATTCTTTGGAAACTTTGATTTTCAAGGAAAATTGAT
64 TTGATACTTTCAACTTTTCCCCAAAAATTATTCTTTGGAAAATTT-A--TT-AAGGAAAATTGAT
* * *
12883706 ACTTTCAACTTTTCCTCAAAAACCT-TTTTTTTGAAA-ATTTATTTTTAA
125 ACTTTCAACTTTTCCTCAAAAA--TATTTTTTGGAAACATTGATTTTCAA
* * *
12883754 GGAAAATTGATACTTTCAAGTTTTCCCCAAAAATATTTTTTT
1 GGAAAATTGATACTTTCAACTTTT-CCCAAAAACATTCTTTT
12883796 ATTTTTATTT
Statistics
Matches: 189, Mismatches: 19, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
172 14 0.07
173 27 0.14
174 53 0.28
175 6 0.03
176 76 0.40
177 12 0.06
178 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (172 bp):
GGAAAATTGATACTTTCAACTTTTCCCAAAAACATTCTTTTGAAAATTTAATTTCAAGAAAAATT
GATACTTTCAACTTTTCCCCAAAAATTATTCTTTGGAAAATTTATTAAGGAAAATTGATACTTTC
AACTTTTCCTCAAAAATATTTTTTGGAAACATTGATTTTCAA
Found at i:12883795 original size:59 final size:58
Alignment explanation
Indices: 12883405--12883795 Score: 495
Period size: 59 Copynumber: 6.7 Consensus size: 58
12883395 TTTTGTGCAG
* * * *
12883405 GGAAAATTGATACTTTCAACTTTTCC-CAAAAATATTCTTTTGAAACTTTAATTTCGA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTATTTTCAA
*
12883462 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATTTATTTTTTTGAAAATTTA--TT-AA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAA--TATTTTTTTGAAAATTTATTTTCAA
* * * *
12883519 GGAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTGGAAACCTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAA-ATTTATTTTCAA
*** *
12883578 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTATTTTCAA
* * * * * *
12883636 GAAAAATTGATACTTTTAACTTTTCCCCAAAAATATTCTTTGGAAACTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTT-ATTTTCAA
*
12883695 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCT-TTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAA--TATTTTTTTGAAAATTTATTTTCAA
* *
12883754 GGAAAATTGATACTTTCAAGTTTTCCCCAAAAATATTTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTT
12883796 ATTTTTATTT
Statistics
Matches: 287, Mismatches: 36, Indels: 21
0.83 0.10 0.06
Matches are distributed among these distances:
55 12 0.04
56 3 0.01
57 58 0.20
58 67 0.23
59 118 0.41
60 28 0.10
61 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (58 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTATTTTCAA
Found at i:12883852 original size:5 final size:5
Alignment explanation
Indices: 12883820--12883907 Score: 72
Period size: 5 Copynumber: 16.4 Consensus size: 5
12883810 AAAATAGAAT
*
12883820 AATAA AACAA AATAA AAGTGAA AA-AA AATAAAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AA-T-AA AATAA AAT--AA AATAA AATAA AATAA
*
12883868 AA-AA AAGTAA AACAGA AATAAA AATAA AATAA AGATAA AA
1 AATAA AA-TAA AATA-A AAT-AA AATAA AATAA A-ATAA AA
12883908 AGAATATTAA
Statistics
Matches: 69, Mismatches: 4, Indels: 20
0.74 0.04 0.22
Matches are distributed among these distances:
4 8 0.12
5 34 0.49
6 17 0.25
7 10 0.14
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (5 bp):
AATAA
Found at i:12883853 original size:17 final size:17
Alignment explanation
Indices: 12883810--12883908 Score: 78
Period size: 17 Copynumber: 5.6 Consensus size: 17
12883800 TTATTTAAAG
*
12883810 AAAATAGAATAATAAAAC
1 AAAATA-AAAAATAAAAC
*
12883828 AAAAT-AAAAGTGAAAA-
1 AAAATAAAAAAT-AAAAC
*
12883844 AAAATAAAAAATAAAAT
1 AAAATAAAAAATAAAAC
12883861 AAAATAAAAAAAAGTAAAAC
1 AAAAT--AAAAAA-TAAAAC
*
12883881 AGAAAT-AAAAATAAAAT
1 A-AAATAAAAAATAAAAC
12883898 AAAGATAAAAA
1 AAA-ATAAAAA
12883909 GAATATTAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
16 15 0.22
17 22 0.33
18 14 0.21
19 6 0.09
20 6 0.09
21 4 0.06
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (17 bp):
AAAATAAAAAATAAAAC
Found at i:12883853 original size:27 final size:25
Alignment explanation
Indices: 12883823--12883922 Score: 85
Period size: 28 Copynumber: 3.7 Consensus size: 25
12883813 ATAGAATAAT
12883823 AAAACAAAATAAAAGTGAAAAAAAATAA
1 AAAACAAAATAAAA-T-AAAAAAAAT-A
*
12883851 AAAATAAAATAAAATAAAAAAAAGT-
1 AAAACAAAATAAAATAAAAAAAA-TA
12883876 AAAACAGAAATAAAAATAAAATAAAGATA
1 AAAACA-AAAT-AAAATAAAA-AAA-ATA
* * *
12883905 AAAAGAATATTAAATAAA
1 AAAACAAAATAAAATAAA
12883923 CCTAATCTAA
Statistics
Matches: 61, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
25 5 0.08
26 12 0.20
27 18 0.30
28 20 0.33
29 6 0.10
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (25 bp):
AAAACAAAATAAAATAAAAAAAATA
Found at i:12883891 original size:37 final size:37
Alignment explanation
Indices: 12883820--12883908 Score: 119
Period size: 38 Copynumber: 2.4 Consensus size: 37
12883810 AAAATAGAAT
*
12883820 AATAAAACAAAATAAAAGTGAAAAAAAATAAAAAATAA
1 AATAAAATAAAA-AAAAGTGAAAAAAAATAAAAAATAA
12883858 AATAAAATAAAAAAAAGT-AAAACAGAAAT-AAAAATAA
1 AATAAAATAAAAAAAAGTGAAAA-A-AAATAAAAAATAA
12883895 AATAAAGATAAAAA
1 AATAAA-ATAAAAA
12883909 GAATATTAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
36 4 0.09
37 21 0.45
38 22 0.47
ACGTcount: A:0.79, C:0.02, G:0.06, T:0.13
Consensus pattern (37 bp):
AATAAAATAAAAAAAAGTGAAAAAAAATAAAAAATAA
Found at i:12883906 original size:43 final size:42
Alignment explanation
Indices: 12883820--12883907 Score: 108
Period size: 43 Copynumber: 2.0 Consensus size: 42
12883810 AAAATAGAAT
**
12883820 AATAAAACAAAATAAAAGTGAAAAAAAATAAAAAATAAAATAA
1 AATAAAACAAAATAAAACAGAAAAAAAAT-AAAAATAAAATAA
12883863 AATAAAA-AAAAGTAAAACAGAAATAAAAAT-AAAATAAAGATAA
1 AATAAAACAAAA-TAAAACAGAAA-AAAAATAAAAATAAA-ATAA
12883906 AA
1 AA
12883908 AGAATATTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
42 12 0.30
43 22 0.55
44 6 0.15
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (42 bp):
AATAAAACAAAATAAAACAGAAAAAAAATAAAAATAAAATAA
Found at i:12883938 original size:4 final size:4
Alignment explanation
Indices: 12883931--12883974 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
12883921 AACCTAATCT
* * *
12883931 AATA AATA AAAA AATA AATA AATA AACCA AATA AATA AAAA AAT
1 AATA AATA AATA AATA AATA AATA AA-TA AATA AATA AATA AAT
12883975 TAAAAAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
4 30 0.91
5 3 0.09
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (4 bp):
AATA
Found at i:12883986 original size:29 final size:29
Alignment explanation
Indices: 12883931--12883986 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
12883921 AACCTAATCT
*
12883931 AATAAATAAAAAAATAAATAAATAAACCA
1 AATAAATAAAAAAATAAATAAAAAAACCA
12883960 AATAAATAAAAAAATTAAA-AAAAAAAC
1 AATAAATAAAAAAA-TAAATAAAAAAAC
12883987 TTGGAGCGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.16
Consensus pattern (29 bp):
AATAAATAAAAAAATAAATAAAAAAACCA
Found at i:12884918 original size:25 final size:24
Alignment explanation
Indices: 12884855--12884937 Score: 82
Period size: 25 Copynumber: 3.5 Consensus size: 24
12884845 AAAATTTAAT
* *
12884855 AGATAATTAGAAAAATAATA-ATA
1 AGATAAATAAAAAAATAATATATA
* *
12884878 AGATAAAT-CAACAATAATATTATA
1 AGATAAATAAAAAAATAATA-TATA
12884902 AGATAAATAAAAAAATAATA-ATAA
1 AGATAAATAAAAAAATAATATAT-A
12884926 CAGATAAATAAA
1 -AGATAAATAAA
12884938 TATATAATTA
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
22 9 0.18
23 9 0.18
24 12 0.24
25 20 0.40
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.24
Consensus pattern (24 bp):
AGATAAATAAAAAAATAATATATA
Found at i:12884944 original size:25 final size:23
Alignment explanation
Indices: 12884839--12884974 Score: 92
Period size: 22 Copynumber: 6.0 Consensus size: 23
12884829 TAAAAATCAG
*
12884839 ATAAAAAA-AAT-TTAATAGATAA
1 ATAAAAAATAATAATAA-AGATAA
*
12884861 TTAGAAAAATAATAAT-AAGATAA
1 ATA-AAAAATAATAATAAAGATAA
* * *
12884884 ATCAACAATAATATTATAAGATAA
1 ATAAAAAATAATAATA-AAGATAA
12884908 ATAAAAAAATAATAATAACAGATAA
1 AT-AAAAAATAATAATAA-AGATAA
* *
12884933 AT-AAATAT-ATAAT-TAGATAA
1 ATAAAAAATAATAATAAAGATAA
12884953 AT-AAAAATACAT-ATAAA-ATAA
1 ATAAAAAATA-ATAATAAAGATAA
12884974 A
1 A
12884975 ATGAAAAAGA
Statistics
Matches: 91, Mismatches: 13, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
20 13 0.14
21 7 0.08
22 20 0.22
23 17 0.19
24 14 0.15
25 20 0.22
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.26
Consensus pattern (23 bp):
ATAAAAAATAATAATAAAGATAA
Found at i:12884966 original size:24 final size:23
Alignment explanation
Indices: 12884839--12884968 Score: 101
Period size: 24 Copynumber: 5.7 Consensus size: 23
12884829 TAAAAATCAG
* *
12884839 ATAAAAAAAATTTAAT-AGATAA
1 ATAAAAATAATATAATAAGATAA
* *
12884861 TTAGAAA-AATAATAATAAGATAA
1 ATAAAAATAAT-ATAATAAGATAA
* *
12884884 ATCAACAATAATATTATAAGATAA
1 AT-AAAAATAATATAATAAGATAA
12884908 ATAAAAA-AATAATAATAACAGATAA
1 ATAAAAATAAT-ATAAT-A-AGATAA
*
12884933 AT--AAAT-ATATAATTAGATAA
1 ATAAAAATAATATAATAAGATAA
12884953 ATAAAAATACATATAA
1 ATAAAAATA-ATATAA
12884969 AATAAAATGA
Statistics
Matches: 86, Mismatches: 10, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
20 8 0.09
21 3 0.03
22 21 0.24
23 20 0.23
24 23 0.27
25 11 0.13
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (23 bp):
ATAAAAATAATATAATAAGATAA
Found at i:12884974 original size:41 final size:40
Alignment explanation
Indices: 12884826--12884974 Score: 104
Period size: 41 Copynumber: 3.6 Consensus size: 40
12884816 CAGCCTTCCA
* * * * *
12884826 AAATAAAAATCAGATAAAAAAAATTTAATAGATAATTAGAA
1 AAATAAAAATAAGATAAAATAAA-TAAATATATAATTAGAT
* * * * *
12884867 AAATAATAATAAGAT-AAATCAA-CAATAATATTATAAGAT
1 AAATAAAAATAAGATAAAATAAATAAAT-ATATAATTAGAT
*
12884906 AAATAAAAAAATAATAATAACAGATAAATAAATATATAATTAGAT
1 AAAT--AAAAATAA-GATAA-A-ATAAATAAATATATAATTAGAT
*
12884951 AAATAAAAATACATATAAAATAAA
1 AAATAAAAATA-AGATAAAATAAA
12884975 ATGAAAAAGA
Statistics
Matches: 83, Mismatches: 16, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
38 3 0.04
39 12 0.14
40 5 0.06
41 25 0.30
42 3 0.04
43 12 0.14
44 2 0.02
45 18 0.22
46 3 0.04
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (40 bp):
AAATAAAAATAAGATAAAATAAATAAATATATAATTAGAT
Found at i:12885443 original size:42 final size:41
Alignment explanation
Indices: 12885274--12885536 Score: 339
Period size: 42 Copynumber: 6.3 Consensus size: 41
12885264 TTTAACCAAA
* * * *
12885274 GCTCCTCTAAGCAGAGGCTA-AACGACTTTGAGAAATATAAATG
1 GCTCCTCTAAACAGAGGC-ACCACGACTTTGA-AAA-GTAAATT
* * * * * * *
12885317 GCTTCTTTAATCAGAGGCTCAATGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
12885358 GCTCCTCTAAACAGAGGCACCAAGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
12885399 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATT
*
12885441 GCTCCTCTAAACAGAGGCACCACGACTTTGGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATT
*
12885483 TCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-AAAAGTAAATT
12885525 GCTCCTCTAAAC
1 GCTCCTCTAAAC
12885537 CACGACTTTG
Statistics
Matches: 198, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
41 69 0.35
42 104 0.53
43 25 0.13
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
Done.