Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008804.1 Hibiscus syriacus cultivar Beakdansim tig00111957_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 529415
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 2 of 3
Found at i:231575 original size:45 final size:45
Alignment explanation
Indices: 231502--231763 Score: 400
Period size: 45 Copynumber: 5.8 Consensus size: 45
231492 TGCATAACAT
**
231502 TGTATAAAAGGCATGAAATAATGCCATAAATGAAATGTATAATAG
1 TGTATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAG
* *
231547 TGTATATAAGGCATGAAAGGATGACATAAATGAAATGTATAATAG
1 TGTATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAG
*
231592 TGTATAAAAGGCATGAAATGATGCCATAAATGAAATGTATAATAG
1 TGTATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAG
231637 TGTATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAG
1 TGTATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAG
* *
231682 TGTATAAAAGGCATGAAAGGATGTCATAAATGAAATGCAT-ATGAG
1 TGTATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAAT-AG
* * ** *
231727 TGCATTATCGGCATGAAAGGATGCCATAATTGAAATG
1 TGTATAAAAGGCATGAAAGGATGCCATAAATGAAATG
231764 CATATGGGTG
Statistics
Matches: 200, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
44 2 0.01
45 198 0.99
ACGTcount: A:0.45, C:0.07, G:0.22, T:0.26
Consensus pattern (45 bp):
TGTATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAG
Found at i:231621 original size:22 final size:22
Alignment explanation
Indices: 231595--231666 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
231585 ATAATAGTGT
231595 ATAAAAGGCATGAAATGATGCC
1 ATAAAAGGCATGAAATGATGCC
* ** *
231617 ATAAATGAAATGTATAAT-AGTG-T
1 ATAAAAGGCATG-A-AATGA-TGCC
*
231640 ATAAAAGGCATGAAAGGATGCC
1 ATAAAAGGCATGAAATGATGCC
231662 ATAAA
1 ATAAA
231667 TGAAATGTAT
Statistics
Matches: 36, Mismatches: 9, Indels: 10
0.65 0.16 0.18
Matches are distributed among these distances:
21 4 0.11
22 16 0.44
23 11 0.31
24 5 0.14
ACGTcount: A:0.49, C:0.08, G:0.21, T:0.22
Consensus pattern (22 bp):
ATAAAAGGCATGAAATGATGCC
Found at i:231711 original size:22 final size:22
Alignment explanation
Indices: 231640--231711 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
231630 ATAATAGTGT
*
231640 ATAAAAGGCATGAAAGGATGCC
1 ATAAAAGGCATGAAAGGATGTC
* ** *
231662 ATAAATGAAATGTATAA-TAGTGT-
1 ATAAAAGGCATG-A-AAGGA-TGTC
231685 ATAAAAGGCATGAAAGGATGTC
1 ATAAAAGGCATGAAAGGATGTC
231707 ATAAA
1 ATAAA
231712 TGAAATGCAT
Statistics
Matches: 36, Mismatches: 9, Indels: 10
0.65 0.16 0.18
Matches are distributed among these distances:
21 5 0.14
22 16 0.44
23 11 0.31
24 4 0.11
ACGTcount: A:0.49, C:0.07, G:0.22, T:0.22
Consensus pattern (22 bp):
ATAAAAGGCATGAAAGGATGTC
Found at i:231744 original size:135 final size:135
Alignment explanation
Indices: 231502--231815 Score: 416
Period size: 135 Copynumber: 2.3 Consensus size: 135
231492 TGCATAACAT
* *
231502 TGTATAAAAGGCATGAAATAATGCCATAAATGAAATGTATAATAGTGTATATAAGGCATGAAAGG
1 TGTATAAAAGGCATGAAAGAATGCCATAAATGAAATGTATAATAGTGTATAAAAGGCATGAAAGG
* * *
231567 ATGACATAAATGAAATGTATAATAGTGTATAAAAGGCATGAAATGATGCCATAAATGAAATGTAT
66 ATGACATAAATGAAATGCATAATAGTGCATAAAAGGCATGAAAGGATGCCATAAATGAAATGTAT
231632 AATAG
131 AATAG
*
231637 TGTATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGTGTATAAAAGGCATGAAAGG
1 TGTATAAAAGGCATGAAAGAATGCCATAAATGAAATGTATAATAGTGTATAAAAGGCATGAAAGG
* * ** * *
231702 ATGTCATAAATGAAATGCAT-ATGAGTGCATTATCGGCATGAAAGGATGCCATAATTGAAATGCA
66 ATGACATAAATGAAATGCATAAT-AGTGCATAAAAGGCATGAAAGGATGCCATAAATGAAATGTA
*
231766 T-ATGGG
130 TAAT-AG
* * ** * *
231772 TGCATTATTGGCATGAAACAATGCCATAAATGAAAATGCATAAT
1 TGTATAAAAGGCATGAAAGAATGCCATAAATG-AAATGTATAAT
231816 GGTGCATTAT
Statistics
Matches: 156, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
134 4 0.03
135 142 0.91
136 10 0.06
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.26
Consensus pattern (135 bp):
TGTATAAAAGGCATGAAAGAATGCCATAAATGAAATGTATAATAGTGTATAAAAGGCATGAAAGG
ATGACATAAATGAAATGCATAATAGTGCATAAAAGGCATGAAAGGATGCCATAAATGAAATGTAT
AATAG
Found at i:231764 original size:45 final size:45
Alignment explanation
Indices: 231510--231841 Score: 364
Period size: 45 Copynumber: 7.4 Consensus size: 45
231500 ATTGTATAAA
**
231510 AGGCATGAAATAATGCCATAAATGAAATGTATAATAGTGTA-TAT
1 AGGCATGAAAGGATGCCATAAATGAAATGTATAATAGTGTATTAT
* * *
231554 AAGGCATGAAAGGATGACATAAATGAAATGTATAATAGTGTATAAA
1 -AGGCATGAAAGGATGCCATAAATGAAATGTATAATAGTGTATTAT
* * *
231600 AGGCATGAAATGATGCCATAAATGAAATGTATAATAGTGTATAAA
1 AGGCATGAAAGGATGCCATAAATGAAATGTATAATAGTGTATTAT
* *
231645 AGGCATGAAAGGATGCCATAAATGAAATGTATAATAGTGTATAAA
1 AGGCATGAAAGGATGCCATAAATGAAATGTATAATAGTGTATTAT
* * *
231690 AGGCATGAAAGGATGTCATAAATGAAATGCAT-ATGAGTGCATTAT
1 AGGCATGAAAGGATGCCATAAATGAAATGTATAAT-AGTGTATTAT
* * * * *
231735 CGGCATGAAAGGATGCCATAATTGAAATGCAT-ATGGGTGCATTAT
1 AGGCATGAAAGGATGCCATAAATGAAATGTATAAT-AGTGTATTAT
* ** * * *
231780 TGGCATGAAACAATGCCATAAATGAAAATGCATAATGGTGCATTAT
1 AGGCATGAAAGGATGCCATAAATG-AAATGTATAATAGTGTATTAT
* * *
231826 AAGTATGAAGGGATGC
1 AGGCATGAAAGGATGC
231842 TCTTAATGAA
Statistics
Matches: 256, Mismatches: 27, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
44 2 0.01
45 223 0.87
46 29 0.11
47 2 0.01
ACGTcount: A:0.43, C:0.08, G:0.23, T:0.26
Consensus pattern (45 bp):
AGGCATGAAAGGATGCCATAAATGAAATGTATAATAGTGTATTAT
Found at i:231785 original size:90 final size:90
Alignment explanation
Indices: 231502--231841 Score: 407
Period size: 90 Copynumber: 3.8 Consensus size: 90
231492 TGCATAACAT
* *
231502 TGTATAAAAGGCATGAAATAATGCCATAAATGAAATGTATAATAGTGTA-TATAAGGCATGAAAG
1 TGTATAAAAGGCATGAAATAATGCCATAAATGAAATGCATAATAGTGCATTAT-AGGCATGAAAG
*
231566 GATGACATAAATGAAATGTATAATAG
65 GATGCCATAAATGAAATGTATAATAG
* * * * *
231592 TGTATAAAAGGCATGAAATGATGCCATAAATGAAATGTATAATAGTGTATAAAAGGCATGAAAGG
1 TGTATAAAAGGCATGAAATAATGCCATAAATGAAATGCATAATAGTGCATTATAGGCATGAAAGG
231657 ATGCCATAAATGAAATGTATAATAG
66 ATGCCATAAATGAAATGTATAATAG
** * *
231682 TGTATAAAAGGCATGAAAGGATGTCATAAATGAAATGCAT-ATGAGTGCATTATCGGCATGAAAG
1 TGTATAAAAGGCATGAAATAATGCCATAAATGAAATGCATAAT-AGTGCATTATAGGCATGAAAG
* * *
231746 GATGCCATAATTGAAATGCAT-ATGGG
65 GATGCCATAAATGAAATGTATAAT-AG
* * ** * * * * *
231772 TGCATTATTGGCATGAAACAATGCCATAAATGAAAATGCATAATGGTGCATTATAAGTATGAAGG
1 TGTATAAAAGGCATGAAATAATGCCATAAATG-AAATGCATAATAGTGCATTATAGGCATGAAAG
231837 GATGC
65 GATGC
231842 TCTTAATGAA
Statistics
Matches: 219, Mismatches: 26, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
89 4 0.02
90 183 0.84
91 30 0.14
92 2 0.01
ACGTcount: A:0.43, C:0.08, G:0.22, T:0.26
Consensus pattern (90 bp):
TGTATAAAAGGCATGAAATAATGCCATAAATGAAATGCATAATAGTGCATTATAGGCATGAAAGG
ATGCCATAAATGAAATGTATAATAG
Found at i:238362 original size:16 final size:15
Alignment explanation
Indices: 238337--238370 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
238327 CTGCAATTTC
*
238337 TTAATATAATTAGTA
1 TTAATATAATTAATA
238352 TTAATTATAATTAATA
1 TTAA-TATAATTAATA
238368 TTA
1 TTA
238371 TGATATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TTAATATAATTAATA
Found at i:248432 original size:20 final size:20
Alignment explanation
Indices: 248407--248446 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
248397 TTTTCCCATG
248407 ATCCCTTGAATTCAATCACA
1 ATCCCTTGAATTCAATCACA
248427 ATCCCTTGAATTCAATCACA
1 ATCCCTTGAATTCAATCACA
248447 CAAGCCCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.30, G:0.05, T:0.30
Consensus pattern (20 bp):
ATCCCTTGAATTCAATCACA
Found at i:256129 original size:12 final size:13
Alignment explanation
Indices: 256101--256151 Score: 59
Period size: 12 Copynumber: 3.9 Consensus size: 13
256091 TATTGTGAAA
*
256101 AAAGAAATAAAAT
1 AAAGATATAAAAT
*
256114 ATAAAATATAAAAT
1 A-AAGATATAAAAT
*
256128 AAAGATAT-GAAT
1 AAAGATATAAAAT
256140 AAAGATATAAAA
1 AAAGATATAAAA
256152 GGATGAAGGG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 11 0.35
13 9 0.29
14 11 0.35
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.22
Consensus pattern (13 bp):
AAAGATATAAAAT
Found at i:262963 original size:22 final size:22
Alignment explanation
Indices: 262937--262978 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
262927 CCATTTCAAT
262937 ATCAACACCATCAACATCTTCC
1 ATCAACACCATCAACATCTTCC
** *
262959 ATCAAGGCCATCAATATCTT
1 ATCAACACCATCAACATCTT
262979 TATAATTCCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.33, G:0.05, T:0.26
Consensus pattern (22 bp):
ATCAACACCATCAACATCTTCC
Found at i:268453 original size:2 final size:2
Alignment explanation
Indices: 268446--268481 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
268436 AAATCCCATA
268446 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
268482 CATAAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:268868 original size:30 final size:30
Alignment explanation
Indices: 268775--268926 Score: 125
Period size: 30 Copynumber: 5.2 Consensus size: 30
268765 ATGTCTCATA
* *
268775 CAGAATCAGGAT-GCGGAACGAAGCCCCATA
1 CAGAATCAGGATAG-GGAACGAAGTCCCATG
* * *
268805 TAGAATC---AT-GGGAACGAAATCTCATG
1 CAGAATCAGGATAGGGAACGAAGTCCCATG
* * **
268831 GAGAATCAGGACAATGAACGAAGTCCCATG
1 CAGAATCAGGATAGGGAACGAAGTCCCATG
* * *
268861 CATAATCAAGATAGGGAATGAAGTCCCATG
1 CAGAATCAGGATAGGGAACGAAGTCCCATG
* * *
268891 CAGAATTAGGATAGGGAACGAAGTCCTATA
1 CAGAATCAGGATAGGGAACGAAGTCCCATG
268921 CAGAAT
1 CAGAAT
268927 AGAAATACAT
Statistics
Matches: 94, Mismatches: 24, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
26 18 0.19
27 3 0.03
29 1 0.01
30 72 0.77
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.17
Consensus pattern (30 bp):
CAGAATCAGGATAGGGAACGAAGTCCCATG
Found at i:275486 original size:30 final size:31
Alignment explanation
Indices: 275447--275595 Score: 148
Period size: 30 Copynumber: 5.0 Consensus size: 31
275437 CAAATAAAAA
*
275447 CAGGACGGGGAACGAAGTCCCATG-ATGAAT
1 CAGGGCGGGGAACGAAGTCCCATGCATGAAT
* * *
275477 AAGGGCGGGGAACAAAGTCCCATGCAT-AAG
1 CAGGGCGGGGAACGAAGTCCCATGCATGAAT
*
275507 CAGGGTGGGGAACGAAGTCCCATGCA-GAAT
1 CAGGGCGGGGAACGAAGTCCCATGCATGAAT
** * *
275537 CAGGATGGGGAACGAAGTCCCCTGCA-AAAT
1 CAGGGCGGGGAACGAAGTCCCATGCATGAAT
* * *
275567 CA-AGCGGGGAATGAAGTCTCATGCA-GAAT
1 CAGGGCGGGGAACGAAGTCCCATGCATGAAT
275596 AATTAATGCA
Statistics
Matches: 99, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
29 20 0.20
30 77 0.78
31 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.33, T:0.13
Consensus pattern (31 bp):
CAGGGCGGGGAACGAAGTCCCATGCATGAAT
Found at i:275547 original size:60 final size:59
Alignment explanation
Indices: 275452--275597 Score: 168
Period size: 60 Copynumber: 2.5 Consensus size: 59
275442 AAAAACAGGA
* * *
275452 CGGGGAACGAAGTCCCATG-ATGAATAAGGGCGGGGAACAAAGTCCCATGCATAAGCAGGG
1 CGGGGAACGAAGTCCCATGCA-GAATAAGGACGGGGAACAAAGTCCCATGCAAAAGCA-AG
* * * * * *
275512 TGGGGAACGAAGTCCCATGCAGAATCAGGATGGGGAACGAAGTCCCCTGCAAAATCAAG
1 CGGGGAACGAAGTCCCATGCAGAATAAGGACGGGGAACAAAGTCCCATGCAAAAGCAAG
* *
275571 CGGGGAATGAAGTCTCATGCAGAATAA
1 CGGGGAACGAAGTCCCATGCAGAATAA
275598 TTAATGCATC
Statistics
Matches: 72, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
59 24 0.33
60 47 0.65
61 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.32, T:0.14
Consensus pattern (59 bp):
CGGGGAACGAAGTCCCATGCAGAATAAGGACGGGGAACAAAGTCCCATGCAAAAGCAAG
Found at i:282550 original size:41 final size:41
Alignment explanation
Indices: 282493--282575 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
282483 GCGTAGTGTG
282493 TGGAAAGTAGGACGGGAGAGCTCTATCTCGATTTAGAATAA
1 TGGAAAGTAGGACGGGAGAGCTCTATCTCGATTTAGAATAA
282534 TGGAAAGTAGGACGGGAGAGCTCTATCTCGATTTAGAATAA
1 TGGAAAGTAGGACGGGAGAGCTCTATCTCGATTTAGAATAA
282575 T
1 T
282576 TTTTTGTTAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.25
Consensus pattern (41 bp):
TGGAAAGTAGGACGGGAGAGCTCTATCTCGATTTAGAATAA
Found at i:284784 original size:5 final size:5
Alignment explanation
Indices: 284766--284812 Score: 71
Period size: 5 Copynumber: 9.8 Consensus size: 5
284756 TCTACTTTTA
*
284766 TTTC- TTTC- TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCC TTTC
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTC
284813 AATTGTTGTG
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
4 8 0.20
5 33 0.80
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTCT
Found at i:285307 original size:249 final size:251
Alignment explanation
Indices: 284869--285368 Score: 959
Period size: 249 Copynumber: 2.0 Consensus size: 251
284859 TATTTTGTTA
*
284869 AATTGATATGAAACTAAAGGAATTATTTTTTTTCTGAAGAGAAGAATTAAATCTGTTAAATCATG
1 AATTGATATGAAACTAAAGGAATTAATTTTTTTCTGAAGAGAAGAATTAAATCTGTTAAATCATG
284934 AATTTGAGAAAAATATGAGAGTTGATCTGTATGAGAATATGGATGTAATTTTAATTATATTAACG
66 AATTTGAGAAAAATATGAGAGTTGATCTGTATGAGAATATGGATGTAATTTTAATTATATTAACG
284999 AAATATGGATGAATTTTTATTTGAAACAAGAGCTCGTTAATTTGAGAGTGTTTCTCTTTTA-T-T
131 AAATATGGATGAATTTTTATTTGAAACAAGAGCTCGTTAATTTGAGAGTGTTTCTCTTTTATTAT
285062 TATTTTTTTATGATAGTTTGATGTTGGCTTTTGAAAAAATGGATTGCAGTTTGATT
196 TATTTTTTTATGATAGTTTGATGTTGGCTTTTGAAAAAATGGATTGCAGTTTGATT
285118 AATTGATATGAAACTAAAGGAATTAATTTTTTTCTGAAGAGAAGAATTAAATCTGTTAAATCATG
1 AATTGATATGAAACTAAAGGAATTAATTTTTTTCTGAAGAGAAGAATTAAATCTGTTAAATCATG
285183 AATTTGAGAAAAATATGAGAGTTGATCTGTATGAGAATATGGATGTAATTTTAATTATATTAACG
66 AATTTGAGAAAAATATGAGAGTTGATCTGTATGAGAATATGGATGTAATTTTAATTATATTAACG
*
285248 AAATATGGATGAATTTTTATTTGAAACAAGAGCTCGTTAATTTGAGAGTTTTTCTCTTTTATTAT
131 AAATATGGATGAATTTTTATTTGAAACAAGAGCTCGTTAATTTGAGAGTGTTTCTCTTTTATTAT
*
285313 TTTTTTTTTATGATAGTTTGATGTTGGCTTTTGAAAAAATGGATTGCAGTTTGATT
196 TATTTTTTTATGATAGTTTGATGTTGGCTTTTGAAAAAATGGATTGCAGTTTGATT
285369 TACTGTTATA
Statistics
Matches: 246, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
249 189 0.77
250 1 0.00
251 56 0.23
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.42
Consensus pattern (251 bp):
AATTGATATGAAACTAAAGGAATTAATTTTTTTCTGAAGAGAAGAATTAAATCTGTTAAATCATG
AATTTGAGAAAAATATGAGAGTTGATCTGTATGAGAATATGGATGTAATTTTAATTATATTAACG
AAATATGGATGAATTTTTATTTGAAACAAGAGCTCGTTAATTTGAGAGTGTTTCTCTTTTATTAT
TATTTTTTTATGATAGTTTGATGTTGGCTTTTGAAAAAATGGATTGCAGTTTGATT
Found at i:291999 original size:34 final size:34
Alignment explanation
Indices: 291956--292024 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
291946 TCAAGTGGGA
* *
291956 GATTGTTGAAAATTCAACAAGGTAGGCACCGAAT
1 GATTGTTGAAAAATCAACAAGGTACGCACCGAAT
291990 GATTGTTGAAAAATCAACAAGGTACGCACCGAAT
1 GATTGTTGAAAAATCAACAAGGTACGCACCGAAT
292024 G
1 G
292025 TGCAAGTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.22
Consensus pattern (34 bp):
GATTGTTGAAAAATCAACAAGGTACGCACCGAAT
Found at i:292335 original size:29 final size:29
Alignment explanation
Indices: 292293--292351 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
292283 AGTTGTAATT
292293 CCTATTTTCTCATAGTGAAATTCTTCTAC
1 CCTATTTTCTCATAGTGAAATTCTTCTAC
292322 CCTATTTTCTCATAGTGAAATTCTTCTAC
1 CCTATTTTCTCATAGTGAAATTCTTCTAC
292351 C
1 C
292352 GTTTCCCATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.25, G:0.07, T:0.44
Consensus pattern (29 bp):
CCTATTTTCTCATAGTGAAATTCTTCTAC
Found at i:293782 original size:14 final size:13
Alignment explanation
Indices: 293763--293831 Score: 57
Period size: 14 Copynumber: 4.9 Consensus size: 13
293753 TAATTATATT
293763 ATTTAAGATTTAAA
1 ATTTAA-ATTTAAA
*
293777 ATTTAAAGTTTATA
1 ATTTAAA-TTTAAA
*
293791 ATTTAAATTTCAGA
1 ATTTAAATTT-AAA
* *
293805 GTTTAGAGTTTAAA
1 ATTTA-AATTTAAA
293819 ATTTAAAATTTAA
1 ATTT-AAATTTAA
293832 GATCATTTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
13 4 0.09
14 35 0.80
15 5 0.11
ACGTcount: A:0.45, C:0.01, G:0.09, T:0.45
Consensus pattern (13 bp):
ATTTAAATTTAAA
Found at i:293788 original size:21 final size:21
Alignment explanation
Indices: 293764--293834 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
293754 AATTATATTA
293764 TTTAAGATTTAAAATTTAAAG
1 TTTAAGATTTAAAATTTAAAG
*
293785 TTTATA-ATTT-AAATTTCAGAG
1 TTTA-AGATTTAAAATTT-AAAG
*
293806 TTT-AGAGTTTAAAATTTAAAA
1 TTTAAGA-TTTAAAATTTAAAG
293827 TTTAAGAT
1 TTTAAGAT
293835 CATTTAATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
19 1 0.02
20 7 0.17
21 23 0.56
22 10 0.24
ACGTcount: A:0.44, C:0.01, G:0.10, T:0.45
Consensus pattern (21 bp):
TTTAAGATTTAAAATTTAAAG
Found at i:294879 original size:20 final size:21
Alignment explanation
Indices: 294854--294905 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
294844 TTTTCCCAAT
*
294854 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
294874 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
294895 TCGCAATGCGA
1 TCGCAATGCGA
294906 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:294922 original size:20 final size:20
Alignment explanation
Indices: 294894--295028 Score: 103
Period size: 20 Copynumber: 6.7 Consensus size: 20
294884 AATTGGGAAA
294894 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
294914 ATTGCAATGAGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
294934 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
294955 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
294975 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
294995 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
295015 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
295029 TTTCAAAGCG
Statistics
Matches: 92, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.04
20 62 0.67
21 24 0.26
22 2 0.02
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:294956 original size:61 final size:61
Alignment explanation
Indices: 294891--295028 Score: 179
Period size: 61 Copynumber: 2.3 Consensus size: 61
294881 GCGAATTGGG
* * *
294891 AAAATCGCAATGCGATACTGACTATT-GCAATGAGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAATGCGATACTGACT-TTCGCAACGAGATACTGACTATCGCAACGCGATAATAC
* * * * *
294952 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTTTCGCAACGAGATACTGACTATCGCAACGCGATAATAC
*
295013 ATAATCGCAATGCGAT
1 AAAATCGCAATGCGAT
295029 TTTCAAAGCG
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 2 0.03
61 63 0.97
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (61 bp):
AAAATCGCAATGCGATACTGACTTTCGCAACGAGATACTGACTATCGCAACGCGATAATAC
Found at i:295725 original size:25 final size:24
Alignment explanation
Indices: 295671--295725 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
295661 TGTTTATTAT
* *
295671 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
295695 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
295721 TGTTT
1 TGTTT
295726 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:296883 original size:17 final size:18
Alignment explanation
Indices: 296848--296889 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
296838 TCCACTTCGG
*
296848 GCCATCACCTCGCCCAGA
1 GCCATCACCTCGACCAGA
*
296866 GCTATCACCTC-ACCAGA
1 GCCATCACCTCGACCAGA
296883 GCCATCA
1 GCCATCA
296890 TCTGATCGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.26, C:0.45, G:0.14, T:0.14
Consensus pattern (18 bp):
GCCATCACCTCGACCAGA
Found at i:297428 original size:19 final size:20
Alignment explanation
Indices: 297374--297440 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
297364 TAGTTTACTT
* *
297374 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
297394 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
297414 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
297433 TCGCAACG
1 TCGCAACG
297441 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:297448 original size:14 final size:14
Alignment explanation
Indices: 297429--297486 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
297419 ATGCGAAATG
297429 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
297443 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
297459 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
297475 AAAATTGCAACG
1 AAAATCGCAACG
297487 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:297471 original size:32 final size:33
Alignment explanation
Indices: 297413--297503 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
297403 GGAAATGGCT
297413 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
297446 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
297478 ATTGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
297504 TGCGATTTTC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:297547 original size:20 final size:19
Alignment explanation
Indices: 297513--297568 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
297503 ATGCGATTTT
*
297513 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
297532 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
297552 CATTTTCGTGTTGCGAT
1 CA-TTTCGCGTTGCGAT
297569 TTTAAGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 24 0.75
21 3 0.09
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:299441 original size:14 final size:14
Alignment explanation
Indices: 299422--299457 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
299412 ATTGTTTAAT
299422 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
299436 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
299450 TGATTTGT
1 TGATTTGT
299458 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:299565 original size:20 final size:20
Alignment explanation
Indices: 299540--299579 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
299530 ATGTTGAAGG
299540 CAAAACAGACTATCGCAACA
1 CAAAACAGACTATCGCAACA
*
299560 CAAAACTGACTATCGCAACA
1 CAAAACAGACTATCGCAACA
299580 AGAGAATCGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.30, G:0.10, T:0.12
Consensus pattern (20 bp):
CAAAACAGACTATCGCAACA
Found at i:299608 original size:19 final size:19
Alignment explanation
Indices: 299584--299648 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
299574 GCAACAAGAG
299584 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
299603 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
299622 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
299636 AATCGCAATGCGA
1 AATCGCAATGCGA
299649 TTTTCATTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
14 11 0.26
15 1 0.02
16 2 0.05
17 2 0.05
19 27 0.63
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:299713 original size:20 final size:20
Alignment explanation
Indices: 299674--299763 Score: 146
Period size: 20 Copynumber: 4.5 Consensus size: 20
299664 GCGATTTTGT
299674 CGTTGCGATAGCCA-TTTCG
1 CGTTGCGATAGCCATTTTCG
299693 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
* *
299713 CGTTGCGATCGCTATTTTCG
1 CGTTGCGATAGCCATTTTCG
*
299733 CGTTGCGATAGCCATTGTCG
1 CGTTGCGATAGCCATTTTCG
299753 CGTTGCGATAG
1 CGTTGCGATAG
299764 TCAAATGAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
19 14 0.22
20 51 0.78
ACGTcount: A:0.14, C:0.24, G:0.28, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:303267 original size:19 final size:19
Alignment explanation
Indices: 303242--303372 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
303232 GGAAATTACT
303242 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
303261 ATTGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
303275 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
303294 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
303308 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
303327 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
303341 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
303360 ATCGCAACGCGAA
1 ATCGCAATGCGAA
303373 TTTAATTTCG
Statistics
Matches: 82, Mismatches: 15, Indels: 30
0.65 0.12 0.24
Matches are distributed among these distances:
14 26 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 38 0.46
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:303284 original size:33 final size:33
Alignment explanation
Indices: 303242--303368 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
303232 GGAAATTACT
*
303242 ATCGCAATGCGAAATGAAAATTGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
303275 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
303307 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
303341 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
303369 CGAATTTAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.01
33 82 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:303349 original size:66 final size:66
Alignment explanation
Indices: 303243--303375 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
303233 GAAATTACTA
* *
303243 TCGCAATGCGAAATGAAAATTGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
303308 T
66 T
*
303309 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
303374 T
66 T
303375 T
1 T
303376 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:303390 original size:19 final size:19
Alignment explanation
Indices: 303368--303409 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
303358 AAATCGCAAC
303368 GCGAATTTAATTTCGCGTT
1 GCGAATTTAATTTCGCGTT
* *
303387 GCGATTTTCATTTCGCGTT
1 GCGAATTTAATTTCGCGTT
303406 GCGA
1 GCGA
303410 TTCTCATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (19 bp):
GCGAATTTAATTTCGCGTT
Found at i:303429 original size:19 final size:19
Alignment explanation
Indices: 303377--303421 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
303367 CGCGAATTTA
*
303377 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTCTC
303396 ATTTCGCGTTGCGATTCTC
1 ATTTCGCGTTGCGATTCTC
303415 ATTTCGC
1 ATTTCGC
303422 ATTACGATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTCTC
Found at i:303555 original size:14 final size:14
Alignment explanation
Indices: 303536--303572 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
303526 CATCAATTAA
303536 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
303550 ACAAATCACCTTTT
1 ACAAATCAACTTTT
303564 ACAAATCAA
1 ACAAATCAA
303573 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:304972 original size:42 final size:41
Alignment explanation
Indices: 304913--305118 Score: 164
Period size: 42 Copynumber: 4.9 Consensus size: 41
304903 GTGAATCGGG
*
304913 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAATGGTGGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * * *
304955 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAATGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * *
304997 CTCTTCAATGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAATGGTGGGAG-GGACTCTTCAAGGATGACAGTGGC
* * *
305039 CTCTTGAATGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAATGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * * *
305081 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAG
1 CTCTTGAATGGTGGGAG-GGACTCTTCAAGGATGACAG
305119 GCGAGTCGGG
Statistics
Matches: 126, Mismatches: 30, Indels: 16
0.73 0.17 0.09
Matches are distributed among these distances:
41 9 0.07
42 106 0.84
43 11 0.09
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAATGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:304979 original size:21 final size:21
Alignment explanation
Indices: 304913--304979 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
304903 GTGAATCGGG
*
304913 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
304933 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
304955 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
304976 CTCT
1 CTCT
304980 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:305054 original size:84 final size:84
Alignment explanation
Indices: 304943--305118 Score: 334
Period size: 84 Copynumber: 2.1 Consensus size: 84
304933 CCTCTTCAAC
*
304943 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAATGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
305008 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
*
305027 GATGACAGTGGCCTCTTGAATGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
305092 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
305111 GATGACAG
1 GATGACAG
305119 GCGAGTCGGG
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 90 1.00
ACGTcount: A:0.23, C:0.16, G:0.38, T:0.22
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:305499 original size:89 final size:90
Alignment explanation
Indices: 305329--305513 Score: 277
Period size: 89 Copynumber: 2.0 Consensus size: 90
305319 ATATTTTAAA
* *
305329 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTA
305394 GCAGAATTGGCAGCAACCGAAT-AATTT
63 GCAGAATTGGCAGCAACCGAATAAATTT
305421 ACTTCAACCAAAAGACAAAACAAAAAGAC-AATACTAACTTCACAGTGTT-AATAAACAGTTTAG
1 ACTTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAG
*
305484 CAGTATTGGCAGCAACCGAATAAATTT
64 CAGAATTGGCAGCAACCGAATAAATTT
305511 ACT
1 ACT
305514 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
89 33 0.38
90 8 0.09
92 21 0.24
93 19 0.22
94 6 0.07
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
GAATTGGCAGCAACCGAATAAATTT
Found at i:305748 original size:62 final size:63
Alignment explanation
Indices: 305679--305804 Score: 236
Period size: 62 Copynumber: 2.0 Consensus size: 63
305669 AAGTAGACAC
305679 CCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTA-CGATCTCCTCACACAAGGCATTGA
1 CCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACACAAGGCATTGA
*
305741 CCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTGA
1 CCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACACAAGGCATTGA
305804 C
1 C
305805 TCTCACTTAA
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
62 38 0.61
63 24 0.39
ACGTcount: A:0.25, C:0.37, G:0.18, T:0.21
Consensus pattern (63 bp):
CCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACACAAGGCATTGA
Found at i:307258 original size:20 final size:20
Alignment explanation
Indices: 307229--307267 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
307219 TTTTGGTTGA
307229 AATGAAAATCGCAACGAGAT
1 AATGAAAATCGCAACGAGAT
*
307249 AATGAGAATCGCAACGAGA
1 AATGAAAATCGCAACGAGA
307268 GAATCGCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.15, G:0.23, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAT
Found at i:307271 original size:14 final size:14
Alignment explanation
Indices: 307252--307278 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
307242 ACGAGATAAT
307252 GAGAATCGCAACGA
1 GAGAATCGCAACGA
307266 GAGAATCGCAACG
1 GAGAATCGCAACG
307279 CGAAATGAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.22, G:0.30, T:0.07
Consensus pattern (14 bp):
GAGAATCGCAACGA
Found at i:307332 original size:20 final size:20
Alignment explanation
Indices: 307309--307354 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
307299 GCAATCGCAA
*
307309 TGCGATTTTTGGTTTCGCGT
1 TGCGATTTTTGATTTCGCGT
*
307329 TGCG-TTTTTTATTTCGCGT
1 TGCGATTTTTGATTTCGCGT
307348 TGCGATT
1 TGCGATT
307355 CGTTGCGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.07, C:0.15, G:0.26, T:0.52
Consensus pattern (20 bp):
TGCGATTTTTGATTTCGCGT
Found at i:307902 original size:20 final size:20
Alignment explanation
Indices: 307877--307927 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
307867 GCGCTATGTA
307877 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
307897 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
307917 TATCTCGTTGC
1 AATCGCGTTGC
307928 AATTTTGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:307963 original size:20 final size:20
Alignment explanation
Indices: 307938--307991 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
307928 AATTTTGTAT
307938 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
307958 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
307978 TATCGCATTGCGAT
1 TATCGCATTGCGAT
307992 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:307994 original size:61 final size:61
Alignment explanation
Indices: 307878--307994 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
307868 CGCTATGTAA
* * * * *
307878 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCAATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCAATTTTGTATT
* * * *
307939 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCAATTTT
307995 CCCAATTCGC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCAATTTTGTATT
Found at i:308010 original size:61 final size:61
Alignment explanation
Indices: 307878--308012 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
307868 CGCTATGTAA
* * * * * ** *
307878 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCAATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCAATTTTCCAAT
* * * *
307939 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCAATTTT-CCAAT
308001 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
308013 TTACTTATTC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 58 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCAATTTTCCAAT
Found at i:314160 original size:63 final size:63
Alignment explanation
Indices: 314072--314213 Score: 164
Period size: 64 Copynumber: 2.2 Consensus size: 63
314062 TTAAATTTTT
* *** *
314072 AAAAAAT-AAATCAAATAAGGAAATATTAAA-TTTAAAAAAT-GTTATATAAAAAATGTTAAAAG
1 AAAAAATAAAAT-AAATAAGAAAATATTAAATTTTAAAAAATAAAAATAT-AAAAATATTAAAAG
*
314134 AAAAAATAAAATAAATGAAGAAAATATTAAATTTTAGAAAATAAAAATATAAAAATATTAAAAG
1 AAAAAATAAAATAAAT-AAGAAAATATTAAATTTTAAAAAATAAAAATATAAAAATATTAAAAG
*
314198 AGAAAATAAAAATAAA
1 AAAAAAT-AAAATAAA
314214 ACAAAATAGA
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
62 11 0.16
63 17 0.25
64 28 0.41
65 12 0.18
ACGTcount: A:0.68, C:0.01, G:0.07, T:0.25
Consensus pattern (63 bp):
AAAAAATAAAATAAATAAGAAAATATTAAATTTTAAAAAATAAAAATATAAAAATATTAAAAG
Found at i:314214 original size:5 final size:5
Alignment explanation
Indices: 314200--314263 Score: 58
Period size: 5 Copynumber: 12.4 Consensus size: 5
314190 ATTAAAAGAG
* * *
314200 AAAAT AAAAAT AAAAC AAAAT AGAAT AAAAT AATAAT -AAAT AAAAG AGAAAT
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT A-AAAT
*
314252 ATAAT AAAAT AA
1 AAAAT AAAAT AA
314264 TAAATAATAA
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
4 3 0.06
5 32 0.68
6 12 0.26
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:314219 original size:23 final size:25
Alignment explanation
Indices: 314193--314267 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 25
314183 TAAAAATATT
314193 AAAAGAGAAAATAAAAAT-A-AAAC
1 AAAAGAGAAAATAAAAATAATAAAC
* * *
314216 AAAATAGAATAA-AATAATAATAAAT
1 AAAAGAGAA-AATAAAAATAATAAAC
314241 AAAAGAGAAATATAATAAAATAATAAA
1 AAAAGAGAAA-AT-A-AAAATAATAAA
314268 TAATAATAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
23 13 0.32
24 4 0.10
25 12 0.30
27 1 0.03
28 10 0.25
ACGTcount: A:0.75, C:0.01, G:0.07, T:0.17
Consensus pattern (25 bp):
AAAAGAGAAAATAAAAATAATAAAC
Found at i:314252 original size:26 final size:25
Alignment explanation
Indices: 314200--314270 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 25
314190 ATTAAAAGAG
* * *
314200 AAAATAAAAATAAAACAAAATAGAAT
1 AAAATAATAAT-AAATAAAAGAGAAT
314226 AAAATAATAATAAATAAAAGAGAAAT
1 AAAATAATAATAAATAAAAGAG-AAT
*
314252 ATAATAAAATAATAAATAA
1 A-AA-ATAATAATAAATAA
314271 TAATAGTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
25 9 0.24
26 14 0.37
27 2 0.05
28 13 0.34
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (25 bp):
AAAATAATAATAAATAAAAGAGAAT
Found at i:314258 original size:31 final size:29
Alignment explanation
Indices: 314202--314273 Score: 99
Period size: 31 Copynumber: 2.4 Consensus size: 29
314192 TAAAAGAGAA
314202 AATAAAAATAAAACAAAATAGAATAAAAT
1 AATAAAAATAAAACAAAATAGAATAAAAT
* *
314231 AATAATAAATAAAAGAGAAATATAATAAAAT
1 AATAA-AAATAAAACA-AAATAGAATAAAAT
314262 AATAAATAATAA
1 AATAAA-AATAA
314274 TAGTAAAGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 5 0.13
30 10 0.26
31 23 0.61
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.21
Consensus pattern (29 bp):
AATAAAAATAAAACAAAATAGAATAAAAT
Found at i:314273 original size:15 final size:14
Alignment explanation
Indices: 314171--314270 Score: 66
Period size: 15 Copynumber: 7.0 Consensus size: 14
314161 TAAATTTTAG
314171 AAAATAA-AAATATA
1 AAAATAATAAATA-A
*
314185 AAAATATTAAA-AGA
1 AAAATAATAAATA-A
314199 GAAAATAA-AAATAA
1 -AAAATAATAAATAA
314213 AACAA-AATAGAATAA
1 AA-AATAATA-AATAA
314228 AATAATAATAAATAA
1 AA-AATAATAAATAA
* * *
314243 AAGAGAA-ATATAA
1 AAAATAATAAATAA
314256 TAAAATAATAAATAA
1 -AAAATAATAAATAA
314271 TAATAGTAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
13 9 0.13
14 23 0.34
15 31 0.46
16 4 0.06
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.20
Consensus pattern (14 bp):
AAAATAATAAATAA
Found at i:314352 original size:18 final size:18
Alignment explanation
Indices: 314314--314352 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
314304 GTTATTTTTA
* *
314314 AAATAAAAGATAATTAGT
1 AAATAAAAGAAAATAAGT
*
314332 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAATAAGT
314350 AAA
1 AAA
314353 CAAATAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAATAAGT
Found at i:318184 original size:31 final size:31
Alignment explanation
Indices: 318138--318216 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
318128 AATAGATACA
* * *
318138 AATTTTATAAATTTAATGATTAGTTTATAGT
1 AATTTGATAAATTTAATGATTAATTTATAAT
*
318169 AATTTGATAATTTTAATGATTAATTTATAAT
1 AATTTGATAAATTTAATGATTAATTTATAAT
*
318200 AGTTTGATAAATTTAAT
1 AATTTGATAAATTTAAT
318217 AATGATGTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.51
Consensus pattern (31 bp):
AATTTGATAAATTTAATGATTAATTTATAAT
Found at i:324408 original size:44 final size:44
Alignment explanation
Indices: 324345--324438 Score: 145
Period size: 44 Copynumber: 2.1 Consensus size: 44
324335 TACACCAATA
* * *
324345 ACAGTACATAAAACTTAAAAACATCCCCTAG-CATAAAAGCCTTT
1 ACAGTACATAAAACTTAAAAACACCCCCT-GCCATAAAAACCTTC
324389 ACAGTACATAAAACTTAAAAACACCCCCTGCCATAAAAACCTTC
1 ACAGTACATAAAACTTAAAAACACCCCCTGCCATAAAAACCTTC
324433 ACAGTA
1 ACAGTA
324439 GAATAGAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
43 1 0.02
44 45 0.98
ACGTcount: A:0.46, C:0.28, G:0.06, T:0.20
Consensus pattern (44 bp):
ACAGTACATAAAACTTAAAAACACCCCCTGCCATAAAAACCTTC
Found at i:325619 original size:20 final size:20
Alignment explanation
Indices: 325594--325637 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
325584 AAAGAACATA
325594 AAAAGAGAGCTAGGTTTAGC
1 AAAAGAGAGCTAGGTTTAGC
*
325614 AAAAGAGAGCTGGGTTTAGC
1 AAAAGAGAGCTAGGTTTAGC
325634 AAAA
1 AAAA
325638 TAGTCACTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.30, T:0.18
Consensus pattern (20 bp):
AAAAGAGAGCTAGGTTTAGC
Found at i:331837 original size:18 final size:18
Alignment explanation
Indices: 331814--331853 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
331804 CTCAGGGATG
331814 CAGCTGACCTCCAGTCTA
1 CAGCTGACCTCCAGTCTA
331832 CAGCTGACCTCCAGTCTA
1 CAGCTGACCTCCAGTCTA
331850 CAGC
1 CAGC
331854 AGGGGAAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.40, G:0.17, T:0.20
Consensus pattern (18 bp):
CAGCTGACCTCCAGTCTA
Found at i:332985 original size:32 final size:32
Alignment explanation
Indices: 332948--333031 Score: 100
Period size: 32 Copynumber: 2.7 Consensus size: 32
332938 TAAAAGTTTG
332948 ATAAAATTTAATGATCATTTTATAAC-ATATAA
1 ATAAAATTTAATGATCATTTTATAACAAT-TAA
* * **
332980 ATAAAATTTAATGACCATTTTGTAACAATTCG
1 ATAAAATTTAATGATCATTTTATAACAATTAA
*
333012 A-CAAATTTAATGATCATTTT
1 ATAAAATTTAATGATCATTTT
333032 GTTCAGTTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
31 17 0.38
32 26 0.58
33 2 0.04
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (32 bp):
ATAAAATTTAATGATCATTTTATAACAATTAA
Found at i:334563 original size:43 final size:43
Alignment explanation
Indices: 334502--334586 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
334492 GGAGCTTAAC
*
334502 CGTTTTTTTCTGAACTTTCTGATCGTGGGTGAAAAATGCCCAA
1 CGTTTTTTTCTGAACTTTCAGATCGTGGGTGAAAAATGCCCAA
* *
334545 CGTTTTTTTCTTAACTTTCAGATCGTGGGTGGAAAATGCCCA
1 CGTTTTTTTCTGAACTTTCAGATCGTGGGTGAAAAATGCCCA
334587 TTAAATTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (43 bp):
CGTTTTTTTCTGAACTTTCAGATCGTGGGTGAAAAATGCCCAA
Found at i:340923 original size:20 final size:20
Alignment explanation
Indices: 340877--340942 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
340867 ATAATATATA
*
340877 AAAACAATTAAAAAACTTAAAT
1 AAAATAATTAAAAAAC--AAAT
340899 AAAATAATTAAAACAACAAAT
1 AAAATAATTAAAA-AACAAAT
* *
340920 -AAATAATAAAAAAACAAAC
1 AAAATAATTAAAAAACAAAT
340939 AAAA
1 AAAA
340943 ACAACATAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
19 6 0.15
20 14 0.36
21 4 0.10
22 12 0.31
23 3 0.08
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (20 bp):
AAAATAATTAAAAAACAAAT
Found at i:342742 original size:39 final size:39
Alignment explanation
Indices: 342671--343546 Score: 1116
Period size: 39 Copynumber: 22.6 Consensus size: 39
342661 AAGAAAAATA
* * *
342671 ATCTCAAGTGAGAT-AAATCTTCTGTTTTGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACT
*
342709 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACT
* * *
342748 ATCTCAAGCGAGATAAAATCTTCTATTTCGAGCGAAACA
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACT
* * * *
342787 ATCTCAAGTGAGATAAAATCTTCTGTTTCAAGCGAAACA
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACT
** * **
342826 ATCTCAAGCGAGATAAAAAATTTTGTTTCGATTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACT
* * **
342865 ATCTCAAGCGAGATAAAAATATTATGTTTCGAATGAAACT
1 ATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGGGAAACT
342905 ATCTCAAGCGAGATAAAATCTTCTGTTTCG-GGGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACT
* *
342943 ATCTCAATCGAGATAAAATCTTTTGTTTCGAGGGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACT
* * *
342982 ATCTCAAGCGAGACAAAATTTTTTGTTTCGAGGGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACT
* * * *
343021 AT-TCAAGCGAGACAAAATCTTCTGTTTTGAGTGACACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACT
* * * * * *
343059 ATCTCAAGTGAGACAAAATCTTTTGTTTTGAAGAAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACT
* *
343098 ATCTCAAGCGAGACAAAATCTTCTGTTTCGAGAGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACT
* * * *
343137 ATGTCAACCAAGATAAAATCTTCTGTTTTGAGGGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACT
** *
343176 ATCTCAAGCGAGATAAAAAAATTTTGTTTCGAGGGAAACT
1 ATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGGGAAACT
* *
343216 ATCTCAAGCGAGATAAAATCTT-TATTT-TAGGGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACT
* *
343253 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGAG-ACCT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACT
* * ***
343291 ATCTCAAGCGAGACAAAATCCTCTGTTTCGAATAAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACT
* **
343330 ATCTCAAGCGAGATAAAATCTTCTGTTTCAAAAGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACT
*
343369 ATCTCAAACGAGATAAAATCTTCTGTTTCGAGGGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACT
* * *
343408 ATTTCAAACGAGACAAAATCTTCTGTTTCGAGGGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACT
*
343447 ATCTCAAACGAGATAAAATCTTCTGTTTCGAGGGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACT
* *
343486 ATCTCAAGAGAGATAAAATCTTCTATTTCGAGGGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACT
*
343525 ATCTCAAGAGAGATAAAATCTT
1 ATCTCAAGCGAGATAAAATCTT
343547 ATTTAAAACA
Statistics
Matches: 742, Mismatches: 88, Indels: 15
0.88 0.10 0.02
Matches are distributed among these distances:
37 31 0.04
38 120 0.16
39 520 0.70
40 71 0.10
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (39 bp):
ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACT
Found at i:343714 original size:37 final size:37
Alignment explanation
Indices: 343672--343758 Score: 113
Period size: 37 Copynumber: 2.4 Consensus size: 37
343662 AATAAGAATG
* *
343672 TCTCAAGCGAGACAAAATTTATTTTTAGCGAAAACT-A
1 TCTCAAGAGAGACAAAATTTATTTTTA-AGAAAACTAA
* * *
343709 TCTCAAGTGAGATAAAATTTGTTTTTAAGAAAACTAA
1 TCTCAAGAGAGACAAAATTTATTTTTAAGAAAACTAA
343746 TCTCAAGAGAGAC
1 TCTCAAGAGAGAC
343759 GACCCTTTGT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
36 7 0.16
37 36 0.84
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (37 bp):
TCTCAAGAGAGACAAAATTTATTTTTAAGAAAACTAA
Found at i:344908 original size:12 final size:12
Alignment explanation
Indices: 344888--344981 Score: 75
Period size: 13 Copynumber: 7.7 Consensus size: 12
344878 CATGTGCTTC
*
344888 TTGCCTTTTTCT
1 TTGCTTTTTTCT
344900 TTGCTTTTTT-T
1 TTGCTTTTTTCT
**
344911 TTATTTTTTCTCT
1 TTGCTTTTT-TCT
344924 TTG-TTTTTTCT
1 TTGCTTTTTTCT
* *
344935 ATGTTTTTTTCTCT
1 TTG-CTTTTT-TCT
*
344949 TTTCTTTTTCTCT
1 TTGCTTTTT-TCT
*
344962 TTTCTTTTTTCT
1 TTGCTTTTTTCT
344974 TTGCTTTT
1 TTGCTTTT
344982 CTGTTTTTTT
Statistics
Matches: 68, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
11 13 0.19
12 25 0.37
13 26 0.38
14 4 0.06
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.77
Consensus pattern (12 bp):
TTGCTTTTTTCT
Found at i:344942 original size:25 final size:24
Alignment explanation
Indices: 344893--344997 Score: 82
Period size: 25 Copynumber: 4.5 Consensus size: 24
344883 GCTTCTTGCC
344893 TTTT-TCTTTGCTTTTTT-TT-TATT
1 TTTTCTCTTTG-TTTTTTCTTGT-TT
344916 TTTTCTCTTTGTTTTTTCTATGTTT
1 TTTTCTCTTTGTTTTTTCT-TGTTT
344941 TTTTCTCTTT-TCTTTTTCTCT-TTT
1 TTTTCTCTTTGT-TTTTTCT-TGTTT
* *
344965 CTTTTTTCTTTG-CTTTTC-TGTTT
1 -TTTTCTCTTTGTTTTTTCTTGTTT
344988 TTTT-TCTTTG
1 TTTTCTCTTTG
344998 ATTTGATCTT
Statistics
Matches: 71, Mismatches: 3, Indels: 18
0.77 0.03 0.20
Matches are distributed among these distances:
21 6 0.08
22 5 0.07
23 13 0.18
24 16 0.23
25 30 0.42
26 1 0.01
ACGTcount: A:0.02, C:0.14, G:0.06, T:0.78
Consensus pattern (24 bp):
TTTTCTCTTTGTTTTTTCTTGTTT
Found at i:344965 original size:32 final size:32
Alignment explanation
Indices: 344906--344966 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
344896 TTCTTTGCTT
* * *
344906 TTTTTTTATTTTTTCTCTTTGTTTTTTCTATG
1 TTTTTTTATCTTTTCTCTTTCTCTTTTCTATG
* *
344938 TTTTTTTCTCTTTTCTTTTTCTCTTTTCT
1 TTTTTTTATCTTTTCTCTTTCTCTTTTCT
344967 TTTTTCTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (32 bp):
TTTTTTTATCTTTTCTCTTTCTCTTTTCTATG
Found at i:344988 original size:7 final size:7
Alignment explanation
Indices: 344941--344973 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
344931 TTCTATGTTT
344941 TTTTCTC
1 TTTTCTC
344948 TTTTCT-
1 TTTTCTC
344954 TTTTCTC
1 TTTTCTC
*
344961 TTTTCTT
1 TTTTCTC
344968 TTTTCT
1 TTTTCT
344974 TTGCTTTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTCTC
Found at i:348660 original size:28 final size:28
Alignment explanation
Indices: 348628--348685 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
348618 AATAAACTTA
* *
348628 AATAAAATAATTAAAACA-ACAAATAAAT
1 AATAAAAAAAATAAAACATA-AAATAAAT
*
348656 AATAAAAAAAATACAACATAAAATAAAT
1 AATAAAAAAAATAAAACATAAAATAAAT
348684 AA
1 AA
348686 AATAAACCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 25 0.96
29 1 0.04
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (28 bp):
AATAAAAAAAATAAAACATAAAATAAAT
Found at i:348699 original size:20 final size:21
Alignment explanation
Indices: 348656--348700 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
348646 ACAAATAAAT
348656 AATAAAAAAAATACAACATAA
1 AATAAAAAAAATACAACATAA
* *
348677 AATAAATAAAATA-AACCTAA
1 AATAAAAAAAATACAACATAA
348697 AATA
1 AATA
348701 TGAGGACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (21 bp):
AATAAAAAAAATACAACATAA
Found at i:348888 original size:50 final size:51
Alignment explanation
Indices: 348832--348928 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
348822 AACGACTAAC
**
348832 ATGCAAAAAATAAAA-ATTAGTAACTAAATCAGAAA-TAAACAGTGACCAAA
1 ATGCAAAAAATAAAATAACAGTAACTAAATCAGAAACT-AACAGTGACCAAA
* *
348882 ATGCAAAAAATAAAATAACAGTAGCTAAATTAGAAACTAACAGTGAC
1 ATGCAAAAAATAAAATAACAGTAACTAAATCAGAAACTAACAGTGAC
348929 TAAATTAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
50 15 0.37
51 25 0.61
52 1 0.02
ACGTcount: A:0.58, C:0.12, G:0.11, T:0.19
Consensus pattern (51 bp):
ATGCAAAAAATAAAATAACAGTAACTAAATCAGAAACTAACAGTGACCAAA
Found at i:351751 original size:22 final size:22
Alignment explanation
Indices: 351721--351769 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
351711 TAAAGGAAGT
351721 AAAA-ACGAAAAA-AATAATGAA
1 AAAATACGAAAAACAAT-ATGAA
*
351742 AAAATACGAAAAACAATATTAA
1 AAAATACGAAAAACAATATGAA
351764 AAAATA
1 AAAATA
351770 ATAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 4 0.16
22 18 0.72
23 3 0.12
ACGTcount: A:0.73, C:0.06, G:0.06, T:0.14
Consensus pattern (22 bp):
AAAATACGAAAAACAATATGAA
Found at i:351769 original size:10 final size:10
Alignment explanation
Indices: 351729--351800 Score: 58
Period size: 11 Copynumber: 6.8 Consensus size: 10
351719 GTAAAAACGA
351729 AAAAAATAAT
1 AAAAAATAAT
351739 GAAAAAATACGA-
1 -AAAAAATA--AT
*
351751 AAAACAATATT
1 AAAA-AATAAT
351762 AAAAAATAAT
1 AAAAAATAAT
*
351772 -AAAAATAAA
1 AAAAAATAAT
351781 AATAACAATAAT
1 AA-AA-AATAAT
351793 AAAAAATA
1 AAAAAATA
351801 GTAATATAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
9 8 0.16
10 10 0.20
11 20 0.40
12 11 0.22
13 1 0.02
ACGTcount: A:0.75, C:0.04, G:0.03, T:0.18
Consensus pattern (10 bp):
AAAAAATAAT
Found at i:351783 original size:15 final size:15
Alignment explanation
Indices: 351763--351797 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
351753 AACAATATTA
*
351763 AAAAATAATAAAAAT
1 AAAAATAACAAAAAT
*
351778 AAAAATAACAATAAT
1 AAAAATAACAAAAAT
351793 AAAAA
1 AAAAA
351798 ATAGTAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAATAACAAAAAT
Found at i:351788 original size:31 final size:31
Alignment explanation
Indices: 351729--351818 Score: 92
Period size: 31 Copynumber: 2.8 Consensus size: 31
351719 GTAAAAACGA
* *
351729 AAAAAATAATGAAAAAATACGAAA-AACAATATT
1 AAAAAATAAT--AAAAATA-AAAATAACAATAAT
351762 AAAAAATAATAAAAATAAAAATAACAATAAT
1 AAAAAATAATAAAAATAAAAATAACAATAAT
* *
351793 AAAAAATAGTAATATAATATAAATAA
1 AAAAAATAATAA-A-AATAAAAATAA
351819 ATAGAAAACT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
30 3 0.06
31 26 0.52
32 1 0.02
33 20 0.40
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.21
Consensus pattern (31 bp):
AAAAAATAATAAAAATAAAAATAACAATAAT
Found at i:353119 original size:2 final size:2
Alignment explanation
Indices: 353112--353193 Score: 150
Period size: 2 Copynumber: 42.0 Consensus size: 2
353102 AAATAAACAC
353112 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
353153 -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
353194 GTTATAATTT
Statistics
Matches: 78, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 76 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:353846 original size:65 final size:65
Alignment explanation
Indices: 353627--353911 Score: 227
Period size: 65 Copynumber: 4.3 Consensus size: 65
353617 AGAGAAGTTA
* * * * * * *
353627 TCTCAAAAGAGACAAAATTCGTTTCAAGGGAAAC-GATCTCAAAGATTTTGTTGTTTCATGAGAA
1 TCTCAAGAGAGACAAAATTTGTTTAAAGGAAAACAGAT-TAAAAGA--TT-TTGTTTCAAGGGAA
*
353691 ACGG
62 ACTG
* * * * * * *
353695 TCTCAAG-GTTA-ACAAAATTTTATTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGA
1 TCTCAAGAG--AGACAAAA-TTTGTTTAAAGGAAAACAGATTAAAAGA-TTT-TGTTTCAAGGGA
353758 AACTG
61 AACTG
* * *
353763 TCTCGAGAGAGACGAAATTTGTTTAAAGGAAAACAGATTAAAAGATTTTGTTTCAAGGGAAACTT
1 TCTCAAGAGAGACAAAATTTGTTTAAAGGAAAACAGATTAAAAGATTTTGTTTCAAGGGAAACTG
* * * * * * * *
353828 TCTTAATAGAGGCAAAATTTGTTTCAAGGGAAATAGATTCAAAGATTTTGTTTCATGGGAAACTG
1 TCTCAAGAGAGACAAAATTTGTTTAAAGGAAAACAGATTAAAAGATTTTGTTTCAAGGGAAACTG
353893 TCTCAAGAGAGA-AAAATTT
1 TCTCAAGAGAGACAAAATTT
353912 TAAGAGAAAA
Statistics
Matches: 178, Mismatches: 32, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
64 7 0.04
65 78 0.44
66 3 0.02
67 25 0.14
68 41 0.23
69 22 0.12
70 2 0.01
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.31
Consensus pattern (65 bp):
TCTCAAGAGAGACAAAATTTGTTTAAAGGAAAACAGATTAAAAGATTTTGTTTCAAGGGAAACTG
Found at i:353956 original size:36 final size:36
Alignment explanation
Indices: 353886--354002 Score: 145
Period size: 36 Copynumber: 3.4 Consensus size: 36
353876 TGTTTCATGG
* *
353886 GAAACTGTCTCAAGAGAGA-AAAA----TTTTAAGA
1 GAAACTGTCTCAAGAGAAACAAAATTTGTTTTAAAA
* *
353917 GAAAATGTCTCAAGAGATACAAAATTTGTTTTAAAA
1 GAAACTGTCTCAAGAGAAACAAAATTTGTTTTAAAA
* *
353953 GAAACTGTCTCAAGGGAAACGAAATTTGTTTTAAAA
1 GAAACTGTCTCAAGAGAAACAAAATTTGTTTTAAAA
353989 GAAACTGTCTCAAG
1 GAAACTGTCTCAAG
354003 GGAGATGAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
31 17 0.23
32 4 0.05
36 53 0.72
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.26
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAAACAAAATTTGTTTTAAAA
Found at i:354003 original size:36 final size:36
Alignment explanation
Indices: 353909--354019 Score: 159
Period size: 36 Copynumber: 3.1 Consensus size: 36
353899 GAGAGAAAAA
* * * * *
353909 TTTTAAGAGAAAATGTCTCAAGAGATACAAAATTTG
1 TTTTAAAAGAAACTGTCTCAAGGGAAACGAAATTTG
353945 TTTTAAAAGAAACTGTCTCAAGGGAAACGAAATTTG
1 TTTTAAAAGAAACTGTCTCAAGGGAAACGAAATTTG
* *
353981 TTTTAAAAGAAACTGTCTCAAGGGAGATGAAATTTG
1 TTTTAAAAGAAACTGTCTCAAGGGAAACGAAATTTG
354017 TTT
1 TTT
354020 CAAGGAAAAC
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 68 1.00
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.32
Consensus pattern (36 bp):
TTTTAAAAGAAACTGTCTCAAGGGAAACGAAATTTG
Found at i:357888 original size:21 final size:23
Alignment explanation
Indices: 357836--357888 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 23
357826 GGCCTTATGC
*
357836 ATCGATGCACATTCAAGGCGTGC
1 ATCGATGCACATTCAAGGCGTGA
* * *
357859 ATCGGTGCACCTTC-ATG-GTGA
1 ATCGATGCACATTCAAGGCGTGA
357880 ATCGATGCA
1 ATCGATGCA
357889 TGTTAAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 11 0.44
22 2 0.08
23 12 0.48
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.25
Consensus pattern (23 bp):
ATCGATGCACATTCAAGGCGTGA
Found at i:363840 original size:65 final size:64
Alignment explanation
Indices: 363642--363849 Score: 221
Period size: 65 Copynumber: 3.2 Consensus size: 64
363632 TGCACTAAGA
* * * *
363642 GTGCACCGATGCATGAAATGCATTCGATGTTTCAAAATAGCCA-GAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTC-AATTAACCATGAGTGCATCGATGCATGGTTG
* * *
363706 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAACTC-TGAGTGCATCGATGCATAGT
1 GTGCATCGATGCATGAAATGCATTCGATG-TTTCAAT-TAAC-CATGAGTGCATCGATGCATGGT
363769 AT-
63 -TG
*
363771 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAA-TTA-ACCATGAGTGCATCGATGCATGG-T
363834 TG
63 TG
*
363836 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
363850 CACTTTGAAA
Statistics
Matches: 121, Mismatches: 12, Indels: 21
0.79 0.08 0.14
Matches are distributed among these distances:
63 4 0.03
64 48 0.40
65 68 0.56
66 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAACCATGAGTGCATCGATGCATGGTTG
Found at i:371237 original size:2 final size:2
Alignment explanation
Indices: 371230--371303 Score: 95
Period size: 2 Copynumber: 39.0 Consensus size: 2
371220 AAATTATAAC
371230 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
371270 -T AT AT GAT AT AA AT -T AT A- 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
371304 GTGTTTATTT
Statistics
Matches: 64, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
1 5 0.08
2 57 0.89
3 2 0.03
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:372606 original size:25 final size:23
Alignment explanation
Indices: 372552--372606 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
372542 TATTTTCTAT
*
372552 TTTTA-TTTTTATTTTCTATATC
1 TTTTATTTTTTATTTTCTATATA
*
372574 TCTTTATTTTTTAGTTTTCTATTTA
1 T-TTTATTTTTTA-TTTTCTATATA
372599 TTTATATT
1 TTT-TATT
372607 ATATTACTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 1 0.04
23 4 0.15
24 8 0.30
25 14 0.52
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73
Consensus pattern (23 bp):
TTTTATTTTTTATTTTCTATATA
Found at i:372624 original size:25 final size:24
Alignment explanation
Indices: 372596--372652 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
372586 AGTTTTCTAT
372596 TTATTTATATTATATTACTATT-TTA
1 TTATTT-TATTAT-TTACTATTATTA
**
372621 TTATTGTTATTATTTGTTATTATTA
1 TTATT-TTATTATTTACTATTATTA
372646 TTATTTT
1 TTATTTT
372653 TTCGTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 8 0.29
25 19 0.68
26 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (24 bp):
TTATTTTATTATTTACTATTATTA
Found at i:372640 original size:16 final size:16
Alignment explanation
Indices: 372621--372651 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
372611 TACTATTTTA
*
372621 TTATTGTTATTATTTG
1 TTATTATTATTATTTG
372637 TTATTATTATTATTT
1 TTATTATTATTATTT
372652 TTTCGTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (16 bp):
TTATTATTATTATTTG
Found at i:376685 original size:95 final size:94
Alignment explanation
Indices: 376505--376685 Score: 283
Period size: 94 Copynumber: 1.9 Consensus size: 94
376495 ATATTATTTA
* * *
376505 TATACAATACAGCTTGAGTTGTCCCTCTAGAGCAATTGATTAAACGCCCGGCTTTATGGATAATA
1 TATACAATAAAGCCTGAGTTGTCCCTCTAGAGCAATTGATTAAACGCCCGGCTTTATGGATAAGA
*
376570 TTCAGCTAGCCTGATAAAGGTGATTATAC
66 TTCAGCTAACCTGATAAAGGTGATTATAC
*
376599 TATACAATAAAGCCTGAGTTGTCCCTCTA-AGGCAATTGGTTAAACGCCCTGGCTTTATGGATAA
1 TATACAATAAAGCCTGAGTTGTCCCTCTAGA-GCAATTGATTAAACGCCC-GGCTTTATGGATAA
*
376663 GATTTAGCTAACCTGATAAAGGT
64 GATTCAGCTAACCTGATAAAGGT
376686 ATTTAAATTG
Statistics
Matches: 79, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
93 1 0.01
94 44 0.56
95 34 0.43
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (94 bp):
TATACAATAAAGCCTGAGTTGTCCCTCTAGAGCAATTGATTAAACGCCCGGCTTTATGGATAAGA
TTCAGCTAACCTGATAAAGGTGATTATAC
Found at i:377989 original size:19 final size:19
Alignment explanation
Indices: 377967--378025 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
377957 AAAAATGACT
377967 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
377986 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
378000 ATCGCAATGCGAAATTAAA
1 ATCGCAATGCGAAATGAAA
*
378019 ATTGCAA
1 ATCGCAA
378026 CGACAAAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 10 0.32
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 15 0.48
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:378009 original size:33 final size:33
Alignment explanation
Indices: 377967--378046 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 33
377957 AAAAATGACT
* *
377967 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
378000 ATCGCAATGCGAAATTAAAATTGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
378033 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
378047 CTAAATTCGC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:378098 original size:33 final size:33
Alignment explanation
Indices: 378056--378202 Score: 161
Period size: 33 Copynumber: 4.3 Consensus size: 33
378046 ACTAAATTCG
*
378056 CGTTGCGATTTTCATTTCGCATTACGATTC-CGT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTC-T
**
378089 CGTTGCGATTTTCATTTTACATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* * * *
378122 CATTGCGATTCTAATTTCGCATTGCGATAATCATTTCCG
1 CGTTGCGATTTTCATTTCGCATTGCGAT--TC---T-CT
378161 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
378194 CGTTGCGAT
1 CGTTGCGAT
378203 AGTAATTTCC
Statistics
Matches: 94, Mismatches: 13, Indels: 14
0.78 0.11 0.12
Matches are distributed among these distances:
33 61 0.65
34 2 0.02
35 2 0.02
37 2 0.02
38 1 0.01
39 26 0.28
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:378146 original size:19 final size:19
Alignment explanation
Indices: 378052--378192 Score: 95
Period size: 19 Copynumber: 7.9 Consensus size: 19
378042 CGAAACTAAA
* *
378052 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTCTCAT
*
378071 TTCGCATTACGATTC-C--
1 TTCGCATTGCGATTCTCAT
* *
378087 GTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTCTCAT
**
378104 TTTACATTGCGATTCTC--
1 TTCGCATTGCGATTCTCAT
*
378121 -T--CATTGCGATTCTAAT
1 TTCGCATTGCGATTCTCAT
**
378137 TTCGCATTGCGATAATCAT
1 TTCGCATTGCGATTCTCAT
* *
378156 TTCCGCGTTGCGATTTTCAT
1 TT-CGCATTGCGATTCTCAT
378176 TTCGCATTGCGATTCTC
1 TTCGCATTGCGATTCTC
378193 TCGTTGCGAT
Statistics
Matches: 92, Mismatches: 19, Indels: 22
0.69 0.14 0.17
Matches are distributed among these distances:
14 19 0.21
15 1 0.01
16 4 0.04
17 2 0.02
18 1 0.01
19 49 0.53
20 16 0.17
ACGTcount: A:0.16, C:0.23, G:0.17, T:0.43
Consensus pattern (19 bp):
TTCGCATTGCGATTCTCAT
Found at i:378168 original size:20 final size:18
Alignment explanation
Indices: 378135--378223 Score: 60
Period size: 20 Copynumber: 4.9 Consensus size: 18
378125 TGCGATTCTA
*
378135 ATTTCGCATTGCGATAATC
1 ATTTCGCGTTGCGAT-ATC
*
378154 ATTTCCGCGTTGCGATTTTC
1 ATTT-CGCGTTGCGA-TATC
*
378174 ATTTCGCATTGCGAT-TC
1 ATTTCGCGTTGCGATATC
* *
378191 ---TCTCGTTGCGATAGTA
1 ATTTCGCGTTGCGATA-TC
378207 ATTTCCGCGTTGCGATA
1 ATTT-CGCGTTGCGATA
378224 GACATTAAGA
Statistics
Matches: 55, Mismatches: 7, Indels: 15
0.71 0.09 0.19
Matches are distributed among these distances:
14 10 0.18
16 1 0.02
17 2 0.04
18 1 0.02
19 14 0.25
20 26 0.47
21 1 0.02
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.39
Consensus pattern (18 bp):
ATTTCGCGTTGCGATATC
Found at i:378185 original size:72 final size:74
Alignment explanation
Indices: 378083--378223 Score: 214
Period size: 72 Copynumber: 1.9 Consensus size: 74
378073 CGCATTACGA
* *
378083 TTCCGTCGTTGCGATTTTCATTTTACATTGCGATTCTCTCATTGCGATTCTAATTT-CGCATTGC
1 TTCCGTCGTTGCGATTTTCATTTCACATTGCGATTCTCTCATTGCGATACTAATTTCCGCATTGC
378147 GATAATCAT
66 GATAATCAT
* * * *
378156 TTCCG-CGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTAATTTCCGCGTTGC
1 TTCCGTCGTTGCGATTTTCATTTCACATTGCGATTCTCTCATTGCGATACTAATTTCCGCATTGC
378220 GATA
66 GATA
378224 GACATTAAGA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
72 45 0.74
73 16 0.26
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (74 bp):
TTCCGTCGTTGCGATTTTCATTTCACATTGCGATTCTCTCATTGCGATACTAATTTCCGCATTGC
GATAATCAT
Found at i:378211 original size:33 final size:33
Alignment explanation
Indices: 378056--378222 Score: 147
Period size: 33 Copynumber: 4.8 Consensus size: 33
378046 ACTAAATTCG
* *
378056 CGTTGCGATTTTCATTTCGCATTACGATTC-CGT
1 CGTTGCGATTTTAATTTCGCATTGCGATTCTC-T
* **
378089 CGTTGCGATTTTCATTTTACATTGCGATTCTCT
1 CGTTGCGATTTTAATTTCGCATTGCGATTCTCT
* * *
378122 CATTGCGATTCTAATTTCGCATTGCGATAATCATTTCCG
1 CGTTGCGATTTTAATTTCGCATTGCGAT--TC---T-CT
*
378161 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTAATTTCGCATTGCGATTCTCT
** *
378194 CGTTGCGATAGTAATTTCCGCGTTGCGAT
1 CGTTGCGATTTTAATTT-CGCATTGCGAT
378223 AGACATTAAG
Statistics
Matches: 109, Mismatches: 17, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
33 66 0.61
34 12 0.11
35 2 0.02
37 2 0.02
38 1 0.01
39 26 0.24
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.42
Consensus pattern (33 bp):
CGTTGCGATTTTAATTTCGCATTGCGATTCTCT
Found at i:378268 original size:20 final size:20
Alignment explanation
Indices: 378195--378268 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
378185 CGATTCTCTC
* *
378195 GTTGCGATAGTAATTTCCGC
1 GTTGCGATAGTCATTTCCGT
* **
378215 GTTGCGATAGACA-TTAAGAT
1 GTTGCGATAGTCATTTCCG-T
378235 GATTGCGA-ACGTCATTTCCGT
1 G-TTGCGATA-GTCATTTCCGT
378256 GTTGCGATAGTCA
1 GTTGCGATAGTCA
378269 AATGAATGCC
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.07
20 23 0.56
21 12 0.29
22 3 0.07
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCGT
Found at i:380530 original size:12 final size:13
Alignment explanation
Indices: 380500--380530 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
380490 TACCGTGGTT
380500 TTTCTTTGGGGAC
1 TTTCTTTGGGGAC
380513 TTTCTTTGGGGA-
1 TTTCTTTGGGGAC
380525 TTTCTT
1 TTTCTT
380531 CTTCTTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.06, C:0.13, G:0.26, T:0.55
Consensus pattern (13 bp):
TTTCTTTGGGGAC
Found at i:380756 original size:24 final size:24
Alignment explanation
Indices: 380729--380775 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
380719 ATCATCACAA
380729 TCCGAGTATTGACCAAGATCAAAG
1 TCCGAGTATTGACCAAGATCAAAG
*
380753 TCCGGGTATTGACCAAGATCAAA
1 TCCGAGTATTGACCAAGATCAAA
380776 TTTCGAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (24 bp):
TCCGAGTATTGACCAAGATCAAAG
Found at i:380789 original size:24 final size:24
Alignment explanation
Indices: 380729--380789 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
380719 ATCATCACAA
* *
380729 TCCGAGTATTGACCAAGATCAAAG
1 TCCGAATACTGACCAAGATCAAAG
** * *
380753 TCCGGGTATTGACCAAGATCAAAT
1 TCCGAATACTGACCAAGATCAAAG
*
380777 TTCGAATACTGAC
1 TCCGAATACTGAC
380790 TAGTACTCAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (24 bp):
TCCGAATACTGACCAAGATCAAAG
Found at i:381063 original size:167 final size:165
Alignment explanation
Indices: 380750--381081 Score: 646
Period size: 167 Copynumber: 2.0 Consensus size: 165
380740 ACCAAGATCA
380750 AAGTCCGGGTATTGACCAAGATCAAATTTCGAATACTGACTAGTACTCACAATTTTTTCTGTGGC
1 AAGTCCGGGTATTGACCAAGATCAAATTTCGAATACTGACTAGTACTCACAATTTTTTCTGTGGC
380815 TCATCATCGTCTAACTGGTCATACGAAAACCGGAATTTGGTGCTGAAAGTTGATTGGGATTTGGA
66 TCATCATCGTCTAACTGGTCATACGAAAACCGGAATTTGGTGCTGAAAGTTGATTGGGATTTGGA
380880 TTAGGGAAAGGTTGTGGGTTTTGAGATTGTGTTTG
131 TTAGGGAAAGGTTGTGGGTTTTGAGATTGTGTTTG
380915 AAGTCCGGGTATTGACCAAGATCAAATTTCGAATACTGACTAGTACTCACAATTTTTTCTGTTGG
1 AAGTCCGGGTATTGACCAAGATCAAATTTCGAATACTGACTAGTACTCACAATTTTTTCTG-TGG
380980 CTCATCATCGTCTAACTGGTCAATACGAAAACCGGAATTTGGTGCTGAAAGTTGATTGGGATTTG
65 CTCATCATCGTCTAACTGGTC-ATACGAAAACCGGAATTTGGTGCTGAAAGTTGATTGGGATTTG
381045 GATTAGGGAAAGGTTGTGGGTTTTGAGATTGTGTTTG
129 GATTAGGGAAAGGTTGTGGGTTTTGAGATTGTGTTTG
381082 GTATTGGAAA
Statistics
Matches: 165, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
165 61 0.37
166 24 0.15
167 80 0.48
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (165 bp):
AAGTCCGGGTATTGACCAAGATCAAATTTCGAATACTGACTAGTACTCACAATTTTTTCTGTGGC
TCATCATCGTCTAACTGGTCATACGAAAACCGGAATTTGGTGCTGAAAGTTGATTGGGATTTGGA
TTAGGGAAAGGTTGTGGGTTTTGAGATTGTGTTTG
Found at i:381811 original size:20 final size:19
Alignment explanation
Indices: 381796--381908 Score: 136
Period size: 20 Copynumber: 5.7 Consensus size: 19
381786 GTCAGAATCT
*
381796 CATTGCGATTTACAGATTCG
1 CATTGCGATTTAC-GATTCA
*
381816 CATTGCGATTTACGTATTCG
1 CATTGCGATTTACG-ATTCA
381836 CATTGCGATTTACGTATTCA
1 CATTGCGATTTACG-ATTCA
*
381856 CATTGCGATTTACGGATACA
1 CATTGCGATTTAC-GATTCA
*
381876 CATTGCGATTTACGTATTCT
1 CATTGCGATTTACG-ATTCA
*
381896 CGTTGCGATTTAC
1 CATTGCGATTTAC
381909 AGATACGTGT
Statistics
Matches: 85, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
19 2 0.02
20 82 0.96
21 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (19 bp):
CATTGCGATTTACGATTCA
Found at i:381840 original size:40 final size:39
Alignment explanation
Indices: 381798--382067 Score: 181
Period size: 40 Copynumber: 6.7 Consensus size: 39
381788 CAGAATCTCA
* * *
381798 TTGCGATTTACAGATTCGCATTGCGATTTACGTATTCGCA
1 TTGCGATTTAC-GATTCGCGTTGCGATTTACGTATACGCG
* * * * *
381838 TTGCGATTTACGTATTCACATTGCGATTTACGGATACACA
1 TTGCGATTTACG-ATTCGCGTTGCGATTTACGTATACGCG
* *
381878 TTGCGATTTACGTATTCTCGTTGCGATTTACAG-ATACGTG
1 TTGCGATTTACG-ATTCGCGTTGCGATTTAC-GTATACGCG
*
381918 TTGCGATTTACGTATT-GTCGTTGCGATTTTACGTAT-TGTCG
1 TTGCGATTTACG-ATTCG-CGTTGCGA-TTTACGTATACG-CG
* *
381959 TTGCGATTTACGGATAT-GCGTTGCGATTTTACGGATACTCG
1 TTGCGATTTAC-GAT-TCGCGTTGCGA-TTTACGTATACGCG
* * ** * *
382000 TTGCGATAGT-CAGAATCGCGTTGCGATTTATATGTTCGCG
1 TTGCGAT-TTAC-GATTCGCGTTGCGATTTACGTATACGCG
* * *
382040 TTGCGATTTTCATATTCACGTTGCGATT
1 TTGCGATTTAC-GATTCGCGTTGCGATT
382068 CTGGAAAATC
Statistics
Matches: 190, Mismatches: 28, Indels: 24
0.79 0.12 0.10
Matches are distributed among these distances:
39 2 0.01
40 124 0.65
41 60 0.32
42 4 0.02
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (39 bp):
TTGCGATTTACGATTCGCGTTGCGATTTACGTATACGCG
Found at i:381920 original size:20 final size:20
Alignment explanation
Indices: 381798--382006 Score: 123
Period size: 20 Copynumber: 10.3 Consensus size: 20
381788 CAGAATCTCA
* *
381798 TTGCGATTTACAGATTCG-CA
1 TTGCGATTTAC-GATACGTCG
* *
381818 TTGCGATTTACGTATTCG-CA
1 TTGCGATTTACG-ATACGTCG
* * *
381838 TTGCGATTTACGTATTC-ACA
1 TTGCGATTTACG-ATACGTCG
* *
381858 TTGCGATTTACGGATAC-ACA
1 TTGCGATTTAC-GATACGTCG
*
381878 TTGCGATTTACGTATTC-TCG
1 TTGCGATTTACG-ATACGTCG
381898 TTGCGATTTACAGATACGT-G
1 TTGCGATTTAC-GATACGTCG
*
381918 TTGCGATTTACG-TATTGTCG
1 TTGCGATTTACGATA-CGTCG
*
381938 TTGCGATTTTACG-TATTGTCG
1 TTGCGA-TTTACGATA-CGTCG
*
381959 TTGCGATTTACGGATATG-CG
1 TTGCGATTTAC-GATACGTCG
381979 TTGCGATTTTACGGATAC-TCG
1 TTGCGA-TTTAC-GATACGTCG
382000 TTGCGAT
1 TTGCGAT
382007 AGTCAGAATC
Statistics
Matches: 169, Mismatches: 7, Indels: 26
0.84 0.03 0.13
Matches are distributed among these distances:
18 2 0.01
19 5 0.03
20 116 0.69
21 44 0.26
22 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACGATACGTCG
Found at i:381922 original size:60 final size:59
Alignment explanation
Indices: 381798--382006 Score: 220
Period size: 60 Copynumber: 3.5 Consensus size: 59
381788 CAGAATCTCA
* * * * * * * *
381798 TTGCGATTTACAGATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCACA
1 TTGCGATTTACGGATACTCATTGCGATTTACGTATTCTCGTTGCGATTTACG-ATACGCG
* *
381858 TTGCGATTTACGGATACACATTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGTG
1 TTGCGATTTACGGATACTCATTGCGATTTACGTATTCTCGTTGCGATTTAC-GATACGCG
* ** * * *
381918 TTGCGATTTACGTATTGTCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATATGCG
1 TTGCGATTTACGGATACTCATTGCGA-TTTACGTATTCTCGTTGCGATTTAC-GATACGCG
*
381979 TTGCGATTTTACGGATACTCGTTGCGAT
1 TTGCGA-TTTACGGATACTCATTGCGAT
382007 AGTCAGAATC
Statistics
Matches: 125, Mismatches: 21, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
60 70 0.56
61 38 0.30
62 17 0.14
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (59 bp):
TTGCGATTTACGGATACTCATTGCGATTTACGTATTCTCGTTGCGATTTACGATACGCG
Found at i:382021 original size:41 final size:41
Alignment explanation
Indices: 381858--382028 Score: 117
Period size: 41 Copynumber: 4.2 Consensus size: 41
381848 CGTATTCACA
* * * *
381858 TTGCGA-TTTACGGATACACATTGCGATTTAC-G-TATTCTCG
1 TTGCGATTTTACGGATACTCGTTGCGATGTACAGATA-T-GCG
* *
381898 TTGCGA-TTTACAGATACGT-GTTGCGATTTAC-G-TATTGTCG
1 TTGCGATTTTACGGATAC-TCGTTGCGATGTACAGATA-TG-CG
* ** * *
381938 TTGCGATTTTACGTATTGTCGTTGCGATTTACGGATATGCG
1 TTGCGATTTTACGGATACTCGTTGCGATGTACAGATATGCG
381979 TTGCGATTTTACGGATACTCGTTGCGATAGT-CAGA-ATCGCG
1 TTGCGATTTTACGGATACTCGTTGCGAT-GTACAGATAT-GCG
382020 TTGCGATTT
1 TTGCGATTT
382029 ATATGTTCGC
Statistics
Matches: 110, Mismatches: 13, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
40 43 0.39
41 61 0.55
42 4 0.04
43 2 0.02
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.39
Consensus pattern (41 bp):
TTGCGATTTTACGGATACTCGTTGCGATGTACAGATATGCG
Found at i:382038 original size:20 final size:20
Alignment explanation
Indices: 382015--382067 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
382005 ATAGTCAGAA
*
382015 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
382035 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
*
382055 TCACGTTGCGATT
1 TCGCGTTGCGATT
382068 CTGGAAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:382182 original size:19 final size:19
Alignment explanation
Indices: 382158--382210 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
382148 ATTCTGGAGA
382158 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTTATT
382177 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTTATT
*
382196 TCGCATTGCGATTTT
1 TCGCGTTGCGATTTT
382211 GTTGGTCATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.11, C:0.17, G:0.21, T:0.51
Consensus pattern (19 bp):
TCGCGTTGCGATTTTTATT
Found at i:384940 original size:20 final size:20
Alignment explanation
Indices: 384896--384940 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
384886 AATAAATTAA
384896 AAAATTTATAAAATGGTCAT
1 AAAATTTATAAAATGGTCAT
* * * *
384916 TAAATTTATCAAATTGTTAT
1 AAAATTTATAAAATGGTCAT
384936 AAAAT
1 AAAAT
384941 AATCATTAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (20 bp):
AAAATTTATAAAATGGTCAT
Found at i:389160 original size:20 final size:19
Alignment explanation
Indices: 389121--389170 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 19
389111 TGATGCAATT
389121 GGTATCGATACTGAGAGAA
1 GGTATCGATACTGAGAGAA
389140 GGTATCGATACT-ATGGAGAA
1 GGTATCGATACTGA--GAGAA
389160 GGTATCGATAC
1 GGTATCGATAC
389171 CATTAATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 1 0.03
19 12 0.41
20 16 0.55
ACGTcount: A:0.34, C:0.12, G:0.30, T:0.24
Consensus pattern (19 bp):
GGTATCGATACTGAGAGAA
Found at i:389844 original size:55 final size:56
Alignment explanation
Indices: 389594--390352 Score: 1025
Period size: 56 Copynumber: 13.7 Consensus size: 56
389584 GACACTATGA
* * *
389594 GTGCAAAA-TTAAGAAATTCATAATGAGTTTATGAATTTCCTTATGGGAACTTTGT
1 GTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGT
* * * *
389649 GGGCAAAAGCTAAGAAATTTATAATGAGTTTATGAATTTTCGTATGGACACTTTGT
1 GTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGT
*
389705 GTGAAAAAGCTAAGAAATTCATAATGAGTTTATGAATTT-CGTA-GGGCACTTTGT
1 GTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGT
* * * * *
389759 GTGTAAAA-CTAAGAAATTCGTAATAAGTTTATGAATTT-TGTATGGGCAATTTGT
1 GTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGT
* * ** * *
389813 GTGAAAAAGCTAATAAATTCATAACAAGTTTATGAATTTCCGTATGAGAACTTTGT
1 GTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGT
** * * *
389869 GTGCAAAA-CTAAGAAATTCATAACAAGTTTATGAATTTTCGTATAGACACTTTGT
1 GTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGT
* * * *
389924 GTGCAAAAGCTAAAAAATTTATAATGAGTTTATGAATTTCCGTATGGGAACTTTAT
1 GTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGT
*
389980 GTGCAAAAGCTAAG-AATTCATAATGAGTTTATGAATTTCCGTATAGGCACTTTGT
1 GTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGT
*
390035 GTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGAGCACTTTGT
1 GTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGT
* * *
390091 GTGCAAATGATAAGAAATTCATAATGAGTTTATGAATTTCCATATGGGCACTTTGT
1 GTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGT
* *
390147 GTGCAAATGCTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTTTGT
1 GTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGT
* * *
390203 ATGCAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTTT
1 GTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGT
* * * *
390258 GGTGCAAAAGCTAAGAAATTTATAATAAGTCTATGAATTTCCATAT-GGCACTTTGT
1 -GTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGT
* * * *
390314 GTGCAAAA-CTAATAAATTCATTATTAGCTTATGAATTTC
1 GTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTC
390353 TATAATGGTA
Statistics
Matches: 626, Mismatches: 70, Indels: 17
0.88 0.10 0.02
Matches are distributed among these distances:
53 31 0.05
54 59 0.09
55 190 0.30
56 313 0.50
57 33 0.05
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (56 bp):
GTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGT
Found at i:389967 original size:111 final size:111
Alignment explanation
Indices: 389594--390352 Score: 1028
Period size: 111 Copynumber: 6.9 Consensus size: 111
389584 GACACTATGA
* * * *
389594 GTGCAAAA-TTAAGAAATTCATAATGAGTTTATGAATTTCCTTATGGGAACTTTGTGGGCAAAAG
1 GTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAA-
* * * *
389658 CTAAGAAATTTATAATGAGTTTATGAATTTTCGTATGGACACTTTGT
65 CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGT
* *
389705 GTGAAAAAGCTAAGAAATTCATAATGAGTTTATGAATTT-CGTA-GGGCACTTTGTGTGTAAAAC
1 GTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAC
* * *
389768 TAAGAAATTCGTAATAAGTTTATGAATTT-TGTATGGGCAATTTGT
66 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGT
* * ** * *
389813 GTGAAAAAGCTAATAAATTCATAACAAGTTTATGAATTTCCGTATGAGAACTTTGTGTGCAAAAC
1 GTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAC
* * * *
389878 TAAGAAATTCATAACAAGTTTATGAATTTTCGTATAGACACTTTGT
66 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGT
* * * *
389924 GTGCAAAAGCTAAAAAATTTATAATGAGTTTATGAATTTCCGTATGGGAACTTTATGTGCAAAAG
1 GTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAA-
* *
389989 CTAAG-AATTCATAATGAGTTTATGAATTTCCGTATAGGCACTTTGT
65 CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGT
*
390035 GTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGAGCACTTTGTGTGCAAATG
1 GTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAA--
* *
390100 A-TAAGAAATTCATAATGAGTTTATGAATTTCCATATGGGCACTTTGT
64 ACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGT
* * *
390147 GTGCAAATGCTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTTTGTATGCAAAAC
1 GTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAC
*
390212 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTTT
66 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGT
* * * *
390258 GGTGCAAAAGCTAAGAAATTTATAATAAGTCTATGAATTTCCATAT-GGCACTTTGTGTGCAAAA
1 -GTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAA
* * * *
390322 CTAATAAATTCATTATTAGCTTATGAATTTC
65 CTAAGAAATTCATAATAAGTTTATGAATTTC
390353 TATAATGGTA
Statistics
Matches: 578, Mismatches: 60, Indels: 20
0.88 0.09 0.03
Matches are distributed among these distances:
108 49 0.08
109 31 0.05
110 61 0.11
111 265 0.46
112 171 0.30
113 1 0.00
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (111 bp):
GTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAC
TAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGT
Found at i:395944 original size:111 final size:111
Alignment explanation
Indices: 395734--396262 Score: 805
Period size: 111 Copynumber: 4.8 Consensus size: 111
395724 AGTAAAAAAT
* * * *
395734 TAAGAAATTCATAATGAGTTTATGAATTTTCGTATAGACACTTTGTGGGCAAAAGCTAAGAAATT
1 TAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAA-CTAAGAAATT
* * *
395799 CATAATGAGTTTATGAATTTCCGTATGGGAACTTTGTGTGCAAAAGA
65 CATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGC
* * * *
395846 AAAGAAATTCATAATGAGTTAATGAATTTCCTTATGGGCACTTTGTGTGCAAAATTAAGAAATTC
1 TAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTC
*
395911 ATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTACAAAAGC
66 ATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGC
*
395957 TAAGAAATTCAAAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTC
1 TAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTC
* * *
396022 ATAATAAGTTTATGAATTTCCGTATGGTCACTTTGTGTGTAAAAGG
66 ATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGC
* * *
396068 TAA-AAATTCATAACGAGTTTATGAATTTTCGTATGGGCATTTTGTGTGCAAAACTAAGAAATTC
1 TAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTC
396132 ATAATAAGTTTATGAATTTCCGTAT-GGCACTTTGTGTGCAAAAGC
66 ATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGC
* * *
396177 TAAGAAATTCATAATAAGTCTT-TGAATTTCCTTAT-GGCAATTTGTGTGCAAAAGCTAAGAAAT
1 TAAGAAATTCATAATGAGT-TTATGAATTTCCGTATGGGCACTTTGTGTGCAAAA-CTAAGAAAT
396240 TCATAATAAGTTTATGAATTTCC
64 TCATAATAAGTTTATGAATTTCC
396263 TTATTGGTAG
Statistics
Matches: 381, Mismatches: 33, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
109 37 0.10
110 138 0.36
111 159 0.42
112 47 0.12
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.35
Consensus pattern (111 bp):
TAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAAATTC
ATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGC
Found at i:396266 original size:55 final size:56
Alignment explanation
Indices: 395734--396262 Score: 775
Period size: 55 Copynumber: 9.6 Consensus size: 56
395724 AGTAAAAAAT
* * * * *
395734 TAAGAAATTCATAATGAGTTTATGAATTTTCGTATAGACACTTTGTGGGCAAAAGC
1 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGC
* * *
395790 TAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGAACTTTGTGTGCAAAAGA
1 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGC
* * * * *
395846 AAAGAAATTCATAATGAGTTAATGAATTTCCTTATGGGCACTTTGTGTGCAAAA-T
1 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGC
*
395901 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTACAAAAGC
1 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGC
* *
395957 TAAGAAATTCAAAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAA-C
1 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGC
* * *
396012 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGTCACTTTGTGTGTAAAAGG
1 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGC
** * *
396068 TAA-AAATTCATAACGAGTTTATGAATTTTCGTATGGGCATTTTGTGTGCAAAA-C
1 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGC
396122 TAAGAAATTCATAATAAGTTTATGAATTTCCGTAT-GGCACTTTGTGTGCAAAAGC
1 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGC
* *
396177 TAAGAAATTCATAATAAGTCTT-TGAATTTCCTTAT-GGCAATTTGTGTGCAAAAGC
1 TAAGAAATTCATAATAAGT-TTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGC
396232 TAAGAAATTCATAATAAGTTTATGAATTTCC
1 TAAGAAATTCATAATAAGTTTATGAATTTCC
396263 TTATTGGTAG
Statistics
Matches: 429, Mismatches: 38, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
54 22 0.05
55 251 0.59
56 156 0.36
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.35
Consensus pattern (56 bp):
TAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGC
Found at i:396334 original size:110 final size:108
Alignment explanation
Indices: 395782--396338 Score: 464
Period size: 111 Copynumber: 5.0 Consensus size: 108
395772 CACTTTGTGG
* * ** *
395782 GCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGAACTTTGTGTGCAAAAGAA
1 GCAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT-GGCACTGGGTGTGCAAAAG-C
* * * * * * **
395847 AAGAAATTCATAATGAGT-TAATGAATTTCCTTATGGGCACTTTGTGT
63 TAGAAATTCATAATAAGTCT-TTGAATTACCGTAT-GGCAATACGTGT
* ** *
395894 GCAAAATTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTACAAAAGCTA
1 GCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT-GGCACTGGGTGTGCAAAAGCT-
* * * * **
395959 AGAAATTCAAAATGAGT-TTATGAATTTCCGTATGGGCACTTTGTGT
64 AGAAATTCATAATAAGTCTT-TGAATTACCGTAT-GGCAATACGTGT
** * *
396005 GCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGTCACTTTGTGTGTAAAAGGTA
1 GCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGG-CACTGGGTGTGCAAAAGCTA
* ** ** * **
396070 AAAATTCATAACGAGT-TTATGAATTTTCGTATGGGCATTTTGTGT
65 GAAATTCATAATAAGTCTT-TGAATTACCGTAT-GGCAATACGTGT
**
396115 GCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGCACTTTGTGTGCAAAAGCTAA
1 GCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGCACTGGGTGTGCAAAAGCT-A
* * **
396180 GAAATTCATAATAAGTCTTTGAATTTCCTTATGGCAATTTGTGT
65 GAAATTCATAATAAGTCTTTGAATTACCGTATGGCAATACGTGT
* * * *
396224 GCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCCTTATTGGTAGTGGGTGTGCAACCCA-
1 GCAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTCCGTA-TGGCACTGGGTGTGCAA--AAG
*
396288 CT-TAAATT-ATAATAAGT-TTGTGAATTACCGTATTGG-AACTACGTGT
62 CTAGAAATTCATAATAAGTCTT-TGAATTACCGTA-TGGCAA-TACGTGT
396334 GCAAA
1 GCAAA
396339 CTATAAAGTT
Statistics
Matches: 396, Mismatches: 37, Indels: 26
0.86 0.08 0.06
Matches are distributed among these distances:
108 2 0.01
109 55 0.14
110 164 0.41
111 166 0.42
112 8 0.02
113 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (108 bp):
GCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGCACTGGGTGTGCAAAAGCTAG
AAATTCATAATAAGTCTTTGAATTACCGTATGGCAATACGTGT
Found at i:399192 original size:12 final size:12
Alignment explanation
Indices: 399175--399213 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
399165 TGTGTTGTTT
399175 TTATTTTATTTA
1 TTATTTTATTTA
399187 TTATTTTATTT-
1 TTATTTTATTTA
*
399198 TTATTTAAGTTTA
1 TTATTTTA-TTTA
399211 TTA
1 TTA
399214 AATGTTTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 7 0.29
12 14 0.58
13 3 0.12
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (12 bp):
TTATTTTATTTA
Found at i:409153 original size:14 final size:14
Alignment explanation
Indices: 409134--409194 Score: 67
Period size: 14 Copynumber: 4.5 Consensus size: 14
409124 TACACCTAAG
*
409134 AAGAAAAATAA-ATA
1 AAGAAAAA-AAGAAA
409148 AAGAAAAACAAGAAA
1 AAGAAAAA-AAGAAA
409163 AAG--AAAAA-AAA
1 AAGAAAAAAAGAAA
409174 AAGAAAAAAAGAAA
1 AAGAAAAAAAGAAA
409188 AAGAAAA
1 AAGAAAA
409195 TGAGAGGTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
11 6 0.15
12 2 0.05
13 8 0.20
14 20 0.49
15 5 0.12
ACGTcount: A:0.84, C:0.02, G:0.11, T:0.03
Consensus pattern (14 bp):
AAGAAAAAAAGAAA
Found at i:409162 original size:9 final size:8
Alignment explanation
Indices: 409131--409189 Score: 64
Period size: 8 Copynumber: 7.0 Consensus size: 8
409121 TATTACACCT
409131 AAGAAGAAA
1 AAGAA-AAA
* *
409140 AATAAATA
1 AAGAAAAA
409148 AAGAAAAA
1 AAGAAAAA
409156 CAAGAAAAA
1 -AAGAAAAA
*
409165 GAAAAAAAA
1 -AAGAAAAA
409174 AAGAAAAA
1 AAGAAAAA
409182 AAGAAAAA
1 AAGAAAAA
409190 GAAAATGAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
8 23 0.55
9 19 0.45
ACGTcount: A:0.83, C:0.02, G:0.12, T:0.03
Consensus pattern (8 bp):
AAGAAAAA
Found at i:409168 original size:6 final size:6
Alignment explanation
Indices: 409157--409194 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
409147 AAAGAAAAAC
409157 AAGAAA AAGAAA AA-AAA AAGAAAAA AAGAAA AAGAAA A
1 AAGAAA AAGAAA AAGAAA AAG--AAA AAGAAA AAGAAA A
409195 TGAGAGGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.17
6 18 0.62
8 6 0.21
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (6 bp):
AAGAAA
Done.