Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008142.1 Hibiscus syriacus cultivar Beakdansim tig00110704_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: 459836
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
File 1 of 2
Found at i:8809 original size:38 final size:38
Alignment explanation
Indices: 8758--8834 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
8748 CCATCTCCCC
8758 CTAATCCACTAGTTATGAACTCTCTATTACGGTCACCA
1 CTAATCCACTAGTTATGAACTCTCTATTACGGTCACCA
* * * * *
8796 CTAATCCGCTAGTTATTAACTCTTTGTTCCGGTCACCA
1 CTAATCCACTAGTTATGAACTCTCTATTACGGTCACCA
8834 C
1 C
8835 CAACACCTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.25, C:0.30, G:0.12, T:0.34
Consensus pattern (38 bp):
CTAATCCACTAGTTATGAACTCTCTATTACGGTCACCA
Found at i:12636 original size:22 final size:24
Alignment explanation
Indices: 12611--12660 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
12601 CCCCAATATA
* * *
12611 TTTTATT-GTTTATATTTAGAGTT
1 TTTTATTCATTTATAGTCAGAGTT
12634 TTTTATTCATTTATAGTCAGAGTT
1 TTTTATTCATTTATAGTCAGAGTT
12658 TTT
1 TTT
12661 AATCATTCTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.22, C:0.04, G:0.12, T:0.62
Consensus pattern (24 bp):
TTTTATTCATTTATAGTCAGAGTT
Found at i:12770 original size:64 final size:66
Alignment explanation
Indices: 12687--12815 Score: 219
Period size: 64 Copynumber: 2.0 Consensus size: 66
12677 ATTTAAATTG
*
12687 TTTTAAGGAAAATATAATAT-ACTTTATCATTTTAATTTTAAAATAT-TTTTTTAAAGTAATGTT
1 TTTTAAGGAAAATATAATATAAC-TTATCATTTTAATTTTAAAATATCTTTTTAAAAGTAATGTT
12750 AA
65 AA
12752 TTTTAA-GAAAATATAATATAACTTATCATTTTAATTTTAAAATATCTTTTTAAAAGTAATGTTA
1 TTTTAAGGAAAATATAATATAACTTATCATTTTAATTTTAAAATATCTTTTTAAAAGTAATGTTA
12816 CACACGCCTT
Statistics
Matches: 61, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
64 36 0.59
65 25 0.41
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (66 bp):
TTTTAAGGAAAATATAATATAACTTATCATTTTAATTTTAAAATATCTTTTTAAAAGTAATGTTA
A
Found at i:13079 original size:32 final size:31
Alignment explanation
Indices: 13043--13130 Score: 90
Period size: 30 Copynumber: 2.8 Consensus size: 31
13033 TGAGATGATT
* * *
13043 ATTAAGTTTTATTGAATCGTTAAAAAGTGGTC
1 ATTAAATTTTATCGAATCGTTAAAAA-TGCTC
* *
13075 ATTAAACTTTATCGAA-C-TATTAAAATGCTC
1 ATTAAATTTTATCGAATCGT-TAAAAATGCTC
*
13105 ATTAAATTTTATCGAATTGTTAAAAA
1 ATTAAATTTTATCGAATCGTTAAAAA
13131 ATGATTAATA
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
30 20 0.44
31 11 0.24
32 14 0.31
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (31 bp):
ATTAAATTTTATCGAATCGTTAAAAATGCTC
Found at i:13143 original size:32 final size:32
Alignment explanation
Indices: 13037--13145 Score: 96
Period size: 32 Copynumber: 3.5 Consensus size: 32
13027 ATATTATGAG
* * * *
13037 ATGATTATTAAGTTTTATTGAATCGTTAAAAA
1 ATGATCATTAAATTTTATCGAATTGTTAAAAA
* * * * *
13069 GTGGTCATTAAACTTTATCGAACTATT--AAA
1 ATGATCATTAAATTTTATCGAATTGTTAAAAA
*
13099 ATGCTCATTAAATTTTATCGAATTGTTAAAAA
1 ATGATCATTAAATTTTATCGAATTGTTAAAAA
* *
13131 ATGATTAATAAATTT
1 ATGATCATTAAATTT
13146 ATTGAAAATT
Statistics
Matches: 58, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
30 25 0.43
32 33 0.57
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.41
Consensus pattern (32 bp):
ATGATCATTAAATTTTATCGAATTGTTAAAAA
Found at i:13321 original size:24 final size:25
Alignment explanation
Indices: 13289--13339 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
13279 TATTTTTATT
*
13289 CCTCCTAAAAAATTT-AAGTTCATC
1 CCTCCTAAAAAATTTAAAATTCATC
*
13313 CCTCCTAAAAAGTTTAAAATTCATC
1 CCTCCTAAAAAATTTAAAATTCATC
13338 CC
1 CC
13340 CTAACATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.31
Consensus pattern (25 bp):
CCTCCTAAAAAATTTAAAATTCATC
Found at i:13937 original size:2 final size:2
Alignment explanation
Indices: 13932--13958 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13922 TTTGTGTGTG
13932 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
13959 TTGTGGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14938 original size:55 final size:55
Alignment explanation
Indices: 14850--14960 Score: 177
Period size: 55 Copynumber: 2.0 Consensus size: 55
14840 GTGCTCCACT
* * * *
14850 GTTATTGGTGTGAATCCACTTTACACTGCAACTTTCGATAATAGTGGTTTCAGCC
1 GTTATTGGTGTAAATCCACTTTACAATGCAACTTTCGATAACAGTAGTTTCAGCC
*
14905 GTTATTGGTGTAAATCCACTTTACAATGTAACTTTCGATAACAGTAGTTTCAGCC
1 GTTATTGGTGTAAATCCACTTTACAATGCAACTTTCGATAACAGTAGTTTCAGCC
14960 G
1 G
14961 CCACCGCTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (55 bp):
GTTATTGGTGTAAATCCACTTTACAATGCAACTTTCGATAACAGTAGTTTCAGCC
Found at i:17379 original size:84 final size:84
Alignment explanation
Indices: 17238--17406 Score: 284
Period size: 84 Copynumber: 2.0 Consensus size: 84
17228 CTGTTAAGAA
* * *
17238 TAGATGAAGATGATGGGGTTGCAGATGTTGGAATTCGAACTCTGCGAGACTTCGAGTTTTCTTCT
1 TAGATGAAGAGGATGGGGTTGCAGATATTGGAATTCGAACTCTGCGAGACTTCGAGTTTTCGTCT
17303 CGAGTGATTATTTTCATTT
66 CGAGTGATTATTTTCATTT
* *
17322 TAGATGAAGAGGATGGGGTTGTAGATATTTGAATTCGAACTCTGCGAGACTTCGAGTTTTCGTCT
1 TAGATGAAGAGGATGGGGTTGCAGATATTGGAATTCGAACTCTGCGAGACTTCGAGTTTTCGTCT
*
17387 CTAGTGATTATTTTCATTT
66 CGAGTGATTATTTTCATTT
17406 T
1 T
17407 GAAGAATTGT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 79 1.00
ACGTcount: A:0.23, C:0.12, G:0.25, T:0.39
Consensus pattern (84 bp):
TAGATGAAGAGGATGGGGTTGCAGATATTGGAATTCGAACTCTGCGAGACTTCGAGTTTTCGTCT
CGAGTGATTATTTTCATTT
Found at i:41671 original size:29 final size:30
Alignment explanation
Indices: 41608--41671 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
41598 AGAATAAAAA
*
41608 CTAAAAATATAAAAATTATTAAAAATTCTT
1 CTAAAAATATAAAAATTATTAAAAATACTT
* *
41638 TTAAAAATA-AAAAA-TATTCAAAATAACTT
1 CTAAAAATATAAAAATTATTAAAAAT-ACTT
41667 CTAAA
1 CTAAA
41672 TCTTCATACA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 9 0.31
29 12 0.41
30 8 0.28
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (30 bp):
CTAAAAATATAAAAATTATTAAAAATACTT
Found at i:42551 original size:110 final size:109
Alignment explanation
Indices: 42349--42551 Score: 244
Period size: 110 Copynumber: 1.9 Consensus size: 109
42339 CTAACTACCT
* * * * * ** *
42349 GTTAGTGTAATAAGATAAGATTTAAGTCTTTTAAACCATGTCTAGAGTTCATGTTCCAATGTTGT
1 GTTAGTGTAACAAGATAAGAATTAAGTCTTTTAAACAATATCTAGAGTTCATATTCCAACATCGT
* * * *
42414 GAATAGGGATGATAACATGTCAAATTTTTAACCAATCACATTCA
66 AAATAAGAATGATAACACGTCAAATTTTTAACCAATCACATTCA
* * **
42458 GTTAGTGTAACGAGATAAGACATTAAGTCTTTTAAACAATATCTAGGGTTCATATTCTGACATCG
1 GTTAGTGTAACAAGATAAGA-ATTAAGTCTTTTAAACAATATCTAGAGTTCATATTCCAACATCG
*
42523 TAAATAAGAATGATAACACGTCAGATTTT
65 TAAATAAGAATGATAACACGTCAAATTTT
42552 CGATCAATCC
Statistics
Matches: 76, Mismatches: 17, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
109 18 0.24
110 58 0.76
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (109 bp):
GTTAGTGTAACAAGATAAGAATTAAGTCTTTTAAACAATATCTAGAGTTCATATTCCAACATCGT
AAATAAGAATGATAACACGTCAAATTTTTAACCAATCACATTCA
Found at i:50008 original size:61 final size:61
Alignment explanation
Indices: 49912--50037 Score: 236
Period size: 60 Copynumber: 2.1 Consensus size: 61
49902 GTGGAACAAA
49912 GAATGTGCAAATAAAATAATATTAATTAAATATTCTAATAAAAATAAACCAAATTTCAAGAG
1 GAATGTGCAAATAAAATAATATTAATTAAATATTCTAAT-AAAATAAACCAAATTTCAAGAG
49974 GAATGTGCAAAT-AAATAATATTAATTAAATATTCTAATAAAATAAACCAAATTTCAAGAG
1 GAATGTGCAAATAAAATAATATTAATTAAATATTCTAATAAAATAAACCAAATTTCAAGAG
50034 GAAT
1 GAAT
50038 AAGAACAAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
60 26 0.41
61 26 0.41
62 12 0.19
ACGTcount: A:0.54, C:0.08, G:0.09, T:0.29
Consensus pattern (61 bp):
GAATGTGCAAATAAAATAATATTAATTAAATATTCTAATAAAATAAACCAAATTTCAAGAG
Found at i:50138 original size:22 final size:23
Alignment explanation
Indices: 50093--50138 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
50083 AGAGAGAAAA
* *
50093 TAACTTTATAGAAAGTACTTAAT
1 TAACTTTATAAAAAGTACTCAAT
*
50116 TAACTTT-TAAAAAGTTCTCAAT
1 TAACTTTATAAAAAGTACTCAAT
50138 T
1 T
50139 TAGTATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (23 bp):
TAACTTTATAAAAAGTACTCAAT
Found at i:52749 original size:31 final size:31
Alignment explanation
Indices: 52664--52749 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 31
52654 ATTTTCTAAA
**
52664 ATTATAAAATAATTATTAAA-TTATTGAGTT
1 ATTATAAAATAATTATTAAATTTATAAAGTT
* * * *
52694 ATTATCAAATAATAATTTATTTTATCAAAG-T
1 ATTATAAAATAATTATTAAATTTAT-AAAGTT
52725 ATTATAAAATAATTATTAAATTTAT
1 ATTATAAAATAATTATTAAATTTAT
52750 TAGAATTTAT
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
30 16 0.36
31 26 0.59
32 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (31 bp):
ATTATAAAATAATTATTAAATTTATAAAGTT
Found at i:53214 original size:29 final size:29
Alignment explanation
Indices: 53175--53234 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
53165 GTCGAGGCTT
53175 GGTCGCCGGGAGTACATGGCGACCTTGTA
1 GGTCGCCGGGAGTACATGGCGACCTTGTA
* *
53204 GGTCGCTGGGAGTGCATGGCGACCTTGTA
1 GGTCGCCGGGAGTACATGGCGACCTTGTA
53233 GG
1 GG
53235 GGAGTGCATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.15, C:0.22, G:0.42, T:0.22
Consensus pattern (29 bp):
GGTCGCCGGGAGTACATGGCGACCTTGTA
Found at i:53241 original size:23 final size:23
Alignment explanation
Indices: 53211--53256 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
53201 GTAGGTCGCT
53211 GGGAGTGCATGGCGACCTTGTAG
1 GGGAGTGCATGGCGACCTTGTAG
53234 GGGAGTGCATGGCGACCTTGTAG
1 GGGAGTGCATGGCGACCTTGTAG
53257 CTGTGTTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.43, T:0.22
Consensus pattern (23 bp):
GGGAGTGCATGGCGACCTTGTAG
Found at i:53289 original size:16 final size:16
Alignment explanation
Indices: 53268--53301 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
53258 TGTGTTGGGT
53268 GTTGGGTGCTAGGGAC
1 GTTGGGTGCTAGGGAC
*
53284 GTTGGGTGCTGGGGAC
1 GTTGGGTGCTAGGGAC
53300 GT
1 GT
53302 GCATGGCGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.09, C:0.12, G:0.53, T:0.26
Consensus pattern (16 bp):
GTTGGGTGCTAGGGAC
Found at i:53339 original size:40 final size:40
Alignment explanation
Indices: 53284--53369 Score: 163
Period size: 40 Copynumber: 2.1 Consensus size: 40
53274 TGCTAGGGAC
53284 GTTGGGTGCTGGGGACGTGCATGGCGACCTGTGTTGGGGT
1 GTTGGGTGCTGGGGACGTGCATGGCGACCTGTGTTGGGGT
*
53324 GTTGGGTGCTGGGGACGTGCATGGCGACCTGTGTTGTGGT
1 GTTGGGTGCTGGGGACGTGCATGGCGACCTGTGTTGGGGT
53364 GTTGGG
1 GTTGGG
53370 GACGTGCATG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.07, C:0.14, G:0.50, T:0.29
Consensus pattern (40 bp):
GTTGGGTGCTGGGGACGTGCATGGCGACCTGTGTTGGGGT
Found at i:53739 original size:23 final size:21
Alignment explanation
Indices: 53705--53753 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
53695 TTAAGATGAT
* *
53705 TTTAATTTAAAATGTTATTATA
1 TTTAATTAAAAATGTTA-TAAA
*
53727 TTTAACTTAAAAATTTTATAAA
1 TTTAA-TTAAAAATGTTATAAA
53749 TTTAA
1 TTTAA
53754 AATACTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
TTTAATTAAAAATGTTATAAA
Found at i:54346 original size:3 final size:3
Alignment explanation
Indices: 54338--54371 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
54328 GAATTAACAT
54338 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
54372 TAAAAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:55503 original size:38 final size:37
Alignment explanation
Indices: 55434--55530 Score: 97
Period size: 38 Copynumber: 2.6 Consensus size: 37
55424 GGTGTATTCA
* * *
55434 GTTCATTTATGTTCACTAATAAACTCTTTTAT-AGACTC
1 GTTCATTTATGTTCA-TAACAAACACGTTTATCA-ACTC
* *
55472 GTTCATTTATGTTCATGAACAATCACGTTTATCAACTT
1 GTTCATTTATGTTCAT-AACAAACACGTTTATCAACTC
**
55510 GTTCATTTCGGTTCATAACAA
1 GTTCATTTATGTTCATAACAA
55531 GTTGATTTAC
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
37 6 0.12
38 43 0.86
39 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (37 bp):
GTTCATTTATGTTCATAACAAACACGTTTATCAACTC
Found at i:56934 original size:28 final size:28
Alignment explanation
Indices: 56858--56944 Score: 70
Period size: 31 Copynumber: 2.9 Consensus size: 28
56848 ATTATACAAG
*
56858 TTTGATAAATTTAATGATCATTTTGTAATAA
1 TTTGATAAATTTAAT--T-ATTTTATAATAA
*
56889 TTT-ATAGAATCCAATAATTATTTTATAATAA
1 TTTGATA-AAT---TTAATTATTTTATAATAA
56920 TTTGATAAATTTAA-TACTTTTATAA
1 TTTGATAAATTTAATTA-TTTTATAA
56945 GTTTAAAAGT
Statistics
Matches: 47, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
27 2 0.04
28 11 0.23
30 3 0.06
31 23 0.49
32 4 0.09
34 4 0.09
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.48
Consensus pattern (28 bp):
TTTGATAAATTTAATTATTTTATAATAA
Found at i:64703 original size:2 final size:2
Alignment explanation
Indices: 64696--64751 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
64686 TTTAAAGAAC
64696 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
64738 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
64752 TTGCTTAAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72005 original size:41 final size:41
Alignment explanation
Indices: 71960--72119 Score: 286
Period size: 41 Copynumber: 3.9 Consensus size: 41
71950 TAATATTTTG
*
71960 AACTAAGCATTAGCTCACTAATTTGATAATTCCAAATTTCA
1 AACTAAGCATTAGCTCACTAATATGATAATTCCAAATTTCA
*
72001 AACTAAGCATTAGCTCACTAATATGATCATTCCAAATTTCA
1 AACTAAGCATTAGCTCACTAATATGATAATTCCAAATTTCA
72042 AAC-AATGCATTAGCTCACTAATATGATAATTCCAAATTTCA
1 AACTAA-GCATTAGCTCACTAATATGATAATTCCAAATTTCA
72083 AACTAAGCATTAGCTCACTAATATGATAATTCCAAAT
1 AACTAAGCATTAGCTCACTAATATGATAATTCCAAAT
72120 CTAAACCTTA
Statistics
Matches: 114, Mismatches: 3, Indels: 4
0.94 0.02 0.03
Matches are distributed among these distances:
40 2 0.02
41 110 0.96
42 2 0.02
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.32
Consensus pattern (41 bp):
AACTAAGCATTAGCTCACTAATATGATAATTCCAAATTTCA
Found at i:73683 original size:20 final size:20
Alignment explanation
Indices: 73660--73714 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
73650 AAAATTATAT
*
73660 AATAATCACTACATTTATTA
1 AATAATCACTAAATTTATTA
73680 AATAATCACTAAATTTATTA
1 AATAATCACTAAATTTATTA
*
73700 AATAACCACTAAATT
1 AATAATCACTAAATT
73715 ATATCAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (20 bp):
AATAATCACTAAATTTATTA
Found at i:73684 original size:23 final size:22
Alignment explanation
Indices: 73653--73714 Score: 69
Period size: 20 Copynumber: 3.0 Consensus size: 22
73643 AAAGTTTAAA
*
73653 ATTATATAATAATCACTACATTT
1 ATTA-ATAATAATCACTAAATTT
73676 ATT-A-AATAATCACTAAATTT
1 ATTAATAATAATCACTAAATTT
*
73696 ATT-A-AATAACCACTAAATT
1 ATTAATAATAATCACTAAATT
73715 ATATCAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 33 0.89
21 1 0.03
23 3 0.08
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (22 bp):
ATTAATAATAATCACTAAATTT
Found at i:73823 original size:20 final size:20
Alignment explanation
Indices: 73795--73840 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
73785 ATCACTGATT
*
73795 ATTTTATAAT-AATTTAATAA
1 ATTTAATAATAAATTT-ATAA
73815 ATTTAATAATAAATTTATAA
1 ATTTAATAATAAATTTATAA
*
73835 TTTTAA
1 ATTTAA
73841 AAATTTGATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTAATAATAAATTTATAA
Found at i:74461 original size:15 final size:15
Alignment explanation
Indices: 74423--74461 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
74413 CATCTTTGAT
74423 TATATTTTAATTTTA
1 TATATTTTAATTTTA
*
74438 TATAATTTAATTTT-
1 TATATTTTAATTTTA
74452 TATTATTTTA
1 TA-TATTTTA
74462 TTAGTGAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 2 0.10
15 19 0.90
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATATTTTAATTTTA
Found at i:82674 original size:36 final size:36
Alignment explanation
Indices: 82624--82699 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
82614 GTTATAGCAA
*
82624 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
82660 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
82696 AAAA
1 AAAA
82700 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:83434 original size:27 final size:29
Alignment explanation
Indices: 83404--83475 Score: 94
Period size: 31 Copynumber: 2.5 Consensus size: 29
83394 TTGTATATAT
83404 GTACCCAGGGTTTCA-TT-TAAAAAAAAC
1 GTACCCAGGGTTTCATTTCTAAAAAAAAC
* *
83431 GTACCCAGGGTTTCACTTTTCTGAAAAAAAT
1 GTACCCAGGGTTTCA--TTTCTAAAAAAAAC
83462 GTACCCAGGGTTTC
1 GTACCCAGGGTTTC
83476 CTAGGGTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 15 0.38
30 2 0.05
31 22 0.56
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (29 bp):
GTACCCAGGGTTTCATTTCTAAAAAAAAC
Found at i:90592 original size:16 final size:16
Alignment explanation
Indices: 90571--90606 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
90561 AAACTTTAAA
90571 ACTTTTTAATTTAATC
1 ACTTTTTAATTTAATC
90587 ACTTTTTAATTTAATC
1 ACTTTTTAATTTAATC
90603 ACTT
1 ACTT
90607 AATTTTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.56
Consensus pattern (16 bp):
ACTTTTTAATTTAATC
Found at i:90610 original size:13 final size:14
Alignment explanation
Indices: 90575--90616 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 14
90565 TTTAAAACTT
90575 TTTAATTTAATCAC
1 TTTAATTTAATCAC
90589 TTTTTAATTTAATCAC
1 --TTTAATTTAATCAC
*
90605 -TTAATTTTATCA
1 TTTAATTTAATCA
90617 AAATAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 11 0.44
16 14 0.56
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTAATTTAATCAC
Found at i:96164 original size:21 final size:21
Alignment explanation
Indices: 96138--96182 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
96128 GATTTCTGGG
* *
96138 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
96159 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
96180 CAA
1 CAA
96183 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:96995 original size:31 final size:31
Alignment explanation
Indices: 96957--97112 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
96947 AGGGTCGAGG
*
96957 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
96988 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
97019 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
97050 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
97081 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
97112 G
1 G
97113 GTCCTTCGGG
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
31 116 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:98698 original size:2 final size:2
Alignment explanation
Indices: 98691--98736 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
98681 AAAAATCAAG
98691 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
98733 TA TA
1 TA TA
98737 ACTGAAATTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:105768 original size:2 final size:2
Alignment explanation
Indices: 105761--105787 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
105751 AATAAAAATG
105761 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
105788 ATTATGTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:109344 original size:2 final size:2
Alignment explanation
Indices: 109337--109368 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
109327 CATCCCTTTA
109337 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
109369 GAGATTGGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:118195 original size:41 final size:41
Alignment explanation
Indices: 118121--118403 Score: 165
Period size: 41 Copynumber: 6.9 Consensus size: 41
118111 CGTTTGTTAA
* *
118121 AAAACGCCGCAATAGAGTGGTAA-AT-TAGCGGCGTTTATACC
1 AAAACGCCGCAAT--AGTGTTAACATATAGTGGCGTTTATACC
*
118162 ACAAACGCCGCAATAGT-TTAACATATAGTGGCGTTT-TAGCT
1 A-AAACGCCGCAATAGTGTTAACATATAGTGGCGTTTATA-CC
* * *
118203 AAAACGCAGTAATAGATCG-TAA-AT-TAGCGGCGTTTATACC
1 AAAACGCCGCAATAG-T-GTTAACATATAGTGGCGTTTATACC
* * * * *
118243 ACAAACGCCGTAATAG-ATTACACATATAGTGGCATTTATTCTT
1 A-AAACGCCGCAATAGTGTTA-ACATATAGTGGCGTTTATAC-C
* * * * * * * *
118286 AAAACACCGTAATAGTGATAATAAATAGTGGTGTTTTTA-A
1 AAAACGCCGCAATAGTGTTAACATATAGTGGCGTTTATACC
* * **
118326 ATAAATGCCGCAATAGTGTTAATCA-ATAGTGGCGTTTTTAGA
1 A-AAACGCCGCAATAGTGTTAA-CATATAGTGGCGTTTATACC
*
118368 AAAACGCCGCAATAGTTTTAATCA-ATAGTGGCGTTT
1 AAAACGCCGCAATAGTGTTAA-CATATAGTGGCGTTT
118404 TTTAACAAAC
Statistics
Matches: 193, Mismatches: 31, Indels: 36
0.74 0.12 0.14
Matches are distributed among these distances:
39 5 0.03
40 33 0.17
41 96 0.50
42 56 0.29
43 3 0.02
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (41 bp):
AAAACGCCGCAATAGTGTTAACATATAGTGGCGTTTATACC
Found at i:118195 original size:82 final size:82
Alignment explanation
Indices: 118109--118382 Score: 254
Period size: 82 Copynumber: 3.3 Consensus size: 82
118099 GGTTTAATGC
*
118109 GGCGTTTGTTA-AAAAACGCCGCAATAGAGTGGTAAATTAGCGGCGTTTATACCACAAACGCCGC
1 GGCGTTT-TTAGAAAAACGCCGCAATAGAGTAGTAAATTAGCGGCGTTTATACCACAAACGCCGC
118173 AATAGTTTAACATATAGT
65 AATAGTTTAACATATAGT
* * * * *
118191 GGCG-TTTTAGCTAAAACGCAGTAATAGA-TCGTAAATTAGCGGCGTTTATACCACAAACGCCGT
1 GGCGTTTTTAG-AAAAACGCCGCAATAGAGTAGTAAATTAGCGGCGTTTATACCACAAACGCCGC
*
118254 AATAGATTACACATATAGT
65 AATAGTTTA-ACATATAGT
* *** * * * * * * * * * *
118273 GGCATTTATTCTTAAAACACCGTAATAGTGATAATAAA-TAGTGGTGTTTTTA-AATAAATGCCG
1 GGCGTTT-TTAGAAAAACGCCGCAATAGAG-TAGTAAATTAGCGGCGTTTATACCACAAACGCCG
118336 CAATAGTGTTAATCA-ATAGT
64 CAATAGT-TTAA-CATATAGT
118356 GGCGTTTTTAGAAAAACGCCGCAATAG
1 GGCGTTTTTAGAAAAACGCCGCAATAG
118383 TTTTAATCAA
Statistics
Matches: 155, Mismatches: 28, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
80 3 0.02
81 43 0.28
82 45 0.29
83 41 0.26
84 18 0.12
85 5 0.03
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.28
Consensus pattern (82 bp):
GGCGTTTTTAGAAAAACGCCGCAATAGAGTAGTAAATTAGCGGCGTTTATACCACAAACGCCGCA
ATAGTTTAACATATAGT
Found at i:118245 original size:81 final size:83
Alignment explanation
Indices: 118121--118275 Score: 251
Period size: 81 Copynumber: 1.9 Consensus size: 83
118111 CGTTTGTTAA
* * *
118121 AAAACGCCGCAATAGAGTGGTAAATTAGCGGCGTTTATACCACAAACGCCGCAATAGTTTA-ACA
1 AAAACGCAGCAATAGAGTCGTAAATTAGCGGCGTTTATACCACAAACGCCGCAATAGATTACACA
118185 TATAGTGGCGTTTTAGCT
66 TATAGTGGCGTTTTAGCT
* *
118203 AAAACGCAGTAATAGA-TCGTAAATTAGCGGCGTTTATACCACAAACGCCGTAATAGATTACACA
1 AAAACGCAGCAATAGAGTCGTAAATTAGCGGCGTTTATACCACAAACGCCGCAATAGATTACACA
118267 TATAGTGGC
66 TATAGTGGC
118276 ATTTATTCTT
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
81 41 0.61
82 26 0.39
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (83 bp):
AAAACGCAGCAATAGAGTCGTAAATTAGCGGCGTTTATACCACAAACGCCGCAATAGATTACACA
TATAGTGGCGTTTTAGCT
Found at i:118404 original size:41 final size:40
Alignment explanation
Indices: 118286--118445 Score: 187
Period size: 41 Copynumber: 4.0 Consensus size: 40
118276 ATTTATTCTT
* * * *
118286 AAAACACCGTAATAGTGATAATAAATAGTGGTGTTTTTAA
1 AAAACACCGCAATAGTGTTAATCAATAGTGGCGTTTTTAA
**
118326 ATAAATGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGA
1 A-AAACACCGCAATAGTGTTAATCAATAGTGGCGTTTTTA-A
* *
118368 AAAACGCCGCAATAGTTTTAATCAATAGTGGCGTTTTTTAA
1 AAAACACCGCAATAGTGTTAATCAATAGTGGCG-TTTTTAA
* * *
118409 CAAACACCACAATAGTG-TAATCAATAGTGGCCTTTTT
1 AAAACACCGCAATAGTGTTAATCAATAGTGGCGTTTTT
118446 TTTGTATAAA
Statistics
Matches: 104, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
39 5 0.05
40 15 0.14
41 76 0.73
42 8 0.08
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (40 bp):
AAAACACCGCAATAGTGTTAATCAATAGTGGCGTTTTTAA
Found at i:118446 original size:41 final size:40
Alignment explanation
Indices: 118268--118447 Score: 127
Period size: 41 Copynumber: 4.4 Consensus size: 40
118258 GATTACACAT
* ** *
118268 ATAGTGGCATTTATTCTT-AAAACACCGTAATAGTGATAATAA
1 ATAGTGGCCTTT-TT-TTAAAAACACCACAATAGTG-TAATCA
* *
118310 ATAGTGG--TGTTTTTAAATAA-ATGCCGCAATAGTGTTAATCA
1 ATAGTGGCCTTTTTTTAAA-AACA--CCACAATAGTG-TAATCA
* ** * * *
118351 ATAGTGGCGTTTTTAGAAAAACGCCGCAATAGTTTTAATCA
1 ATAGTGGCCTTTTTTTAAAAACACCACAATAG-TGTAATCA
*
118392 ATAGTGG-CGTTTTTTAACAAACACCACAATAGTGTAATCA
1 ATAGTGGCCTTTTTTTAA-AAACACCACAATAGTGTAATCA
118432 ATAGTGGCCTTTTTTT
1 ATAGTGGCCTTTTTTT
118448 TGTATAAACG
Statistics
Matches: 111, Mismatches: 17, Indels: 21
0.74 0.11 0.14
Matches are distributed among these distances:
38 2 0.02
39 5 0.05
40 24 0.22
41 63 0.57
42 10 0.09
43 7 0.06
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.35
Consensus pattern (40 bp):
ATAGTGGCCTTTTTTTAAAAACACCACAATAGTGTAATCA
Found at i:119939 original size:125 final size:124
Alignment explanation
Indices: 119705--120029 Score: 333
Period size: 125 Copynumber: 2.6 Consensus size: 124
119695 TTGTATCCAG
* ** * ** *
119705 AAACGCCGCTATAG-GTACGTACTTTAGTGGTATTTTTATACAAACGCCACTATAGAA-TCATA-
1 AAACGCCGCTATAGACTA-GTACTTTAGTGGCGTTTTAATAC-AACGCTGCTATA-AACTCGTAC
* * * * * * *
119767 CGTTAGTGGCATTTT-TAT-ACAAACGCCGCTATATACTAGTATTTTAGTGGCATTTTTATAC
63 CCTTAGTGGCGTTTTGAATGA-AAACGCCGCTAAAGACTAGTAATTTAGTAGCATTTTTATAC
*
119828 AAACGCCGCTATATACTCA-TACTTTAGTGGCGTTTTAA-ATCTAAGCGCTGCTATAAACTCGTA
1 AAACGCCGCTATAGACT-AGTACTTTAGTGGCGTTTTAATA-C-AA-CGCTGCTATAAACTCGTA
* * * *
119891 -CTTTAGTGGCGTTTTGAATGAAAACGCCGCTAAAGACTCGTAATTTAGTAGCGTTTTTATAT
62 CCCTTAGTGGCGTTTTGAATGAAAACGCCGCTAAAGACTAGTAATTTAGTAGCATTTTTATAC
*
119953 AAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATACAACGCTGCTATAAACTCGTACCCT
1 AAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTAATACAACGCTGCTATAAACTCGTACCCT
*
120018 TAGTGGCTTTTT
66 TAGTGGCGTTTT
120030 TAGATAAACG
Statistics
Matches: 169, Mismatches: 23, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
122 1 0.01
123 52 0.31
124 42 0.25
125 72 0.43
126 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (124 bp):
AAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTAATACAACGCTGCTATAAACTCGTACCCT
TAGTGGCGTTTTGAATGAAAACGCCGCTAAAGACTAGTAATTTAGTAGCATTTTTATAC
Found at i:120021 original size:41 final size:41
Alignment explanation
Indices: 119705--120031 Score: 306
Period size: 41 Copynumber: 7.9 Consensus size: 41
119695 TTGTATCCAG
** **
119705 AAACGCCGCTAT-AGGTACGTACTTTAGTGGTATTTTTATAC
1 AAACGCCGCTATAAACT-CGTACTTTAGTGGCGTTTTTATAC
* * * *
119746 AAACGCCACTATAGAA-TCATACGTTAGTGGCATTTTTATAC
1 AAACGCCGCTATA-AACTCGTACTTTAGTGGCGTTTTTATAC
* * * *
119787 AAACGCCGCTATATACTAGTATTTTAGTGGCATTTTTATAC
1 AAACGCCGCTATAAACTCGTACTTTAGTGGCGTTTTTATAC
* * *
119828 AAACGCCGCTATATACTCATACTTTAGTGGCG-TTTTAAATC
1 AAACGCCGCTATAAACTCGTACTTTAGTGGCGTTTTTATA-C
* * *
119869 TAAGCGCTGCTATAAACTCGTACTTTAGTGGCGTTTTGAATGA-
1 -AAACGCCGCTATAAACTCGTACTTTAGTGGCGTTTT-TAT-AC
* * *
119912 AAACGCCGCTA-AAGACTCGTAATTTAGTAGCGTTTTTATAT
1 AAACGCCGCTATAA-ACTCGTACTTTAGTGGCGTTTTTATAC
* *
119953 AAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATAC
1 AAACGCCGCTATAAACTCGTACTTTAGTGGCGTTTTTATAC
* * *
119994 -AACGCTGCTATAAACTCGTACCCTTAGTGGCTTTTTTA
1 AAACGCCGCTATAAACTCGTA-CTTTAGTGGCGTTTTTA
120032 GATAAACGTC
Statistics
Matches: 237, Mismatches: 37, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
40 25 0.11
41 147 0.62
42 59 0.25
43 4 0.02
44 1 0.00
45 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.35
Consensus pattern (41 bp):
AAACGCCGCTATAAACTCGTACTTTAGTGGCGTTTTTATAC
Found at i:120049 original size:82 final size:81
Alignment explanation
Indices: 119705--120071 Score: 323
Period size: 82 Copynumber: 4.5 Consensus size: 81
119695 TTGTATCCAG
* ** *
119705 AAACGCCGCTATAG-GTACGTACTTTAGTGGTATTTTTATACAAACGCCACTATAGAA-TCATAC
1 AAACGCCGCTATAGACTA-GTACTTTAGTGGCGTTTTTATACAAACGCCGCTATA-AACTCATAC
* *
119768 GTTAGTGGCATTTTTATAC
64 TTTAGTGGC-TTTTTATAT
* * * *
119787 AAACGCCGCTATATACTAGTATTTTAGTGGCATTTTTATACAAACGCCGCTATATACTCATACTT
1 AAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCTATAAACTCATACTT
* *
119852 TAGTGGCGTTTTAAATCT
66 TAGTGGC-TTTT-TATAT
* * * * * *
119870 AAGCGCTGCTATAAACTCGTACTTTAGTGGCGTTTTGAATGA-AAACGCCGCTA-AAGACTCGTA
1 AAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTT-TAT-ACAAACGCCGCTATAA-ACTCATA
* *
119933 ATTTAGTAGCGTTTTTATAT
63 CTTTAGTGGC-TTTTTATAT
* * *
119953 AAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATAC-AACGCTGCTATAAACTCGTACCC
1 AAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCTATAAACTCATA-CT
*
120017 TTAGTGGCTTTTTTAGAT
65 TTAGTGGC-TTTTTATAT
* * * * *
120035 AAACGTCGCAATAGATATAATA-TTTTGTGGCGTTTTT
1 AAACGCCGCTATAGA-CTAGTACTTTAGTGGCGTTTTT
120072 TAAGATAAAC
Statistics
Matches: 235, Mismatches: 40, Indels: 20
0.80 0.14 0.07
Matches are distributed among these distances:
81 18 0.08
82 110 0.47
83 74 0.31
84 32 0.14
85 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (81 bp):
AAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCTATAAACTCATACTT
TAGTGGCTTTTTATAT
Found at i:120079 original size:43 final size:42
Alignment explanation
Indices: 120020--120114 Score: 147
Period size: 43 Copynumber: 2.3 Consensus size: 42
120010 CGTACCCTTA
**
120020 GTGGC-TTTTTTAGATAAACGTCGCAATAGATATAATATTTT
1 GTGGCGTTTTTTAGATAAACACCGCAATAGATATAATATTTT
120061 GTGGCGTTTTTTAAGATAAACACCGCAATAGATATAATATTTT
1 GTGGCGTTTTTT-AGATAAACACCGCAATAGATATAATATTTT
*
120104 GCGGCGTTTTT
1 GTGGCGTTTTT
120115 ACTATAGGCT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
41 5 0.10
42 6 0.12
43 38 0.78
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (42 bp):
GTGGCGTTTTTTAGATAAACACCGCAATAGATATAATATTTT
Found at i:128177 original size:21 final size:21
Alignment explanation
Indices: 128107--128201 Score: 77
Period size: 21 Copynumber: 4.5 Consensus size: 21
128097 AGGGAAGTAG
* *
128107 AGAGAGCAGCAGCAGAAGCA-
1 AGAGAGAAGCAGCAGCAGCAC
* * * * *
128127 ACCAGAGCAGCAGCGGAAGCAG
1 A-GAGAGAAGCAGCAGCAGCAC
* *
128149 AGAAAGAAGCTGC-GACAGCAC
1 AGAGAGAAGCAGCAG-CAGCAC
128170 AGAGAGAAGCAGCAGCAGCAC
1 AGAGAGAAGCAGCAGCAGCAC
128191 AGAGAGAAGCA
1 AGAGAGAAGCA
128202 TCATATCAGT
Statistics
Matches: 61, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
20 2 0.03
21 57 0.93
22 2 0.03
ACGTcount: A:0.43, C:0.22, G:0.34, T:0.01
Consensus pattern (21 bp):
AGAGAGAAGCAGCAGCAGCAC
Found at i:128880 original size:43 final size:43
Alignment explanation
Indices: 128822--129202 Score: 421
Period size: 43 Copynumber: 8.9 Consensus size: 43
128812 TTTTTAGCAG
* * * * *
128822 AAACGCCG-TAAAACATCAACACCTACTGCGGCGTTTTAACAAA
1 AAACGCCGCT-AAATATCAACACCTATTGCGGCGTTTTTATAAC
* * * * * * *
128865 AAACACCGCTAAACATCATA-ACATATTGCGGCGTTTGTCTGAG
1 AAACGCCGCTAAATATCA-ACACCTATTGCGGCGTTTTTATAAC
* * * *
128908 AAACGCTGCTAAATATTAACACCTATTACGGCGTTTTTATGAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATAAC
* *
128951 AAACGCCGCTAAATATCAACACCTTTTGCGGCGTTTTTATAAA
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATAAC
** * * *
128994 AAAAACCACTAAATATCAACACCTATAGCGGCGTTTGTT-GAA-
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTT-TTATAAC
* *
129036 AAACGCTGCTAAATATCAACACCTATTGCGGCGTTTTTATGAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATAAC
*
129079 AAACGCCGCTAAATATCAACACCTATTGCAGCGTTTTTATAAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATAAC
* * *
129122 AAACGCCACTAAATATCAACACCTATTGCGACGTTTTTCA-CAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTT-ATAAC
*
129165 AAACGCCGCTAAATATCAATACCTATTGCGGCGTTTTT
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTT
129203 TTTGTGAAAA
Statistics
Matches: 284, Mismatches: 47, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
41 2 0.01
42 33 0.12
43 244 0.86
44 5 0.02
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATAAC
Found at i:129070 original size:171 final size:171
Alignment explanation
Indices: 128888--129200 Score: 448
Period size: 171 Copynumber: 1.8 Consensus size: 171
128878 CATCATAACA
* * * * * *
128888 TATTGCGGCGTTTGTCTGAGAAACGCTGCTAAATATTAACACCTATTACGGCGTTTTTATGACAA
1 TATTGCGGCGTTTGTATGACAAACGCCGCTAAATATCAACACCTATTACAGCGTTTTTATAACAA
* * *
128953 ACGCCGCTAAATATCAACACCTTTTGCGGCGTTTTT-ATAAAAAAAACCACTAAATATCAACACC
66 ACGCCACTAAATATCAACACCTATTGCGACGTTTTTCA-AAAAAAAACCACTAAATATCAACACC
129017 TATAGCGGCGTTTGTTGAAAAACGCTGCTAAATATCAACACC
130 TATAGCGGCGTTTGTTGAAAAACGCTGCTAAATATCAACACC
* *
129059 TATTGCGGCGTTTTTATGACAAACGCCGCTAAATATCAACACCTATTGCAGCGTTTTTATAACAA
1 TATTGCGGCGTTTGTATGACAAACGCCGCTAAATATCAACACCTATTACAGCGTTTTTATAACAA
* * ** * *
129124 ACGCCACTAAATATCAACACCTATTGCGACGTTTTTCACACAAACGCCGCTAAATATCAATACCT
66 ACGCCACTAAATATCAACACCTATTGCGACGTTTTTCAAAAAAAAACCACTAAATATCAACACCT
*
129189 ATTGCGGCGTTT
131 ATAGCGGCGTTT
129201 TTTTTGTGAA
Statistics
Matches: 123, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
171 122 0.99
172 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (171 bp):
TATTGCGGCGTTTGTATGACAAACGCCGCTAAATATCAACACCTATTACAGCGTTTTTATAACAA
ACGCCACTAAATATCAACACCTATTGCGACGTTTTTCAAAAAAAAACCACTAAATATCAACACCT
ATAGCGGCGTTTGTTGAAAAACGCTGCTAAATATCAACACC
Found at i:130914 original size:2 final size:2
Alignment explanation
Indices: 130907--130964 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
130897 CGCTTTCCGC
130907 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
130949 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
130965 ATTTGTTGTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:139237 original size:18 final size:18
Alignment explanation
Indices: 139210--139245 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
139200 GGTCATAACT
139210 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
*
139228 CGACCTGACCCGTTGACC
1 CGACCCGACCCGTTGACC
139246 GTTGACCGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.47, G:0.22, T:0.14
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:141795 original size:24 final size:24
Alignment explanation
Indices: 141685--141778 Score: 136
Period size: 24 Copynumber: 3.9 Consensus size: 24
141675 TTTTCGATTT
141685 GATTTCTGATCTGATACTTGACATG
1 GATTT-TGATCTGATACTTGACATG
141710 GATTTTGATCTGATA-TCTGACATG
1 GATTTTGATCTGATACT-TGACATG
* *
141734 GATTCTGATCTGATACTTGACCTG
1 GATTTTGATCTGATACTTGACATG
*
141758 GATTTTGATATGATACTTGAC
1 GATTTTGATCTGATACTTGAC
141779 GTGAATTATG
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
23 1 0.02
24 56 0.89
25 6 0.10
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.40
Consensus pattern (24 bp):
GATTTTGATCTGATACTTGACATG
Found at i:155588 original size:34 final size:34
Alignment explanation
Indices: 155550--155617 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
155540 TCATGGTCGT
*
155550 AATCATTCTAAATTAATATTTATATAACTTACAA
1 AATCATTCTAAATTAATATTTACATAACTTACAA
*
155584 AATCATTCTAAATTAGTATTTACATAACTTACAA
1 AATCATTCTAAATTAATATTTACATAACTTACAA
155618 CATTCATCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.40
Consensus pattern (34 bp):
AATCATTCTAAATTAATATTTACATAACTTACAA
Found at i:157855 original size:64 final size:64
Alignment explanation
Indices: 157783--157911 Score: 249
Period size: 64 Copynumber: 2.0 Consensus size: 64
157773 AGGGTATCCT
*
157783 ATTGAAGGGGTGTCTACACGAATTTTTCTTTCGTTTAATGATTTGGAAATAAGTTCATCTCGTA
1 ATTGAAGGGGTGTCTACACGAATTTTTCTTTCGTTTAATGATTTAGAAATAAGTTCATCTCGTA
157847 ATTGAAGGGGTGTCTACACGAATTTTTCTTTCGTTTAATGATTTAGAAATAAGTTCATCTCGTA
1 ATTGAAGGGGTGTCTACACGAATTTTTCTTTCGTTTAATGATTTAGAAATAAGTTCATCTCGTA
157911 A
1 A
157912 AGATTCACTC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.40
Consensus pattern (64 bp):
ATTGAAGGGGTGTCTACACGAATTTTTCTTTCGTTTAATGATTTAGAAATAAGTTCATCTCGTA
Found at i:158815 original size:24 final size:24
Alignment explanation
Indices: 158783--158841 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
158773 CTTCATGGAA
158783 GAAGACTTTGATAACGGTGTCTAT
1 GAAGACTTTGATAACGGTGTCTAT
158807 GAAGACTTTGATAACGGTGTCTAT
1 GAAGACTTTGATAACGGTGTCTAT
*
158831 GAAAACTTTGA
1 GAAGACTTTGA
158842 GTAGACGAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (24 bp):
GAAGACTTTGATAACGGTGTCTAT
Found at i:164250 original size:2 final size:2
Alignment explanation
Indices: 164188--164241 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
164178 ATATAAAGAA
164188 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
164230 AT AT AT AT AT AT
1 AT AT AT AT AT AT
164242 CTCATATATG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:172244 original size:2 final size:2
Alignment explanation
Indices: 172237--172263 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
172227 CAGACCTGAT
172237 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
172264 GAGATTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:175076 original size:17 final size:17
Alignment explanation
Indices: 175051--175086 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
175041 AAAACTATTA
175051 TAAAATTTGGTAACCGG
1 TAAAATTTGGTAACCGG
* *
175068 TAAACTTTGGTCACCGG
1 TAAAATTTGGTAACCGG
175085 TA
1 TA
175087 GGTATCGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (17 bp):
TAAAATTTGGTAACCGG
Found at i:176113 original size:72 final size:73
Alignment explanation
Indices: 175903--176391 Score: 547
Period size: 72 Copynumber: 6.6 Consensus size: 73
175893 TGTTATAATG
* ** *
175903 AAACCGGTATGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTAATGTTTATATTATTAATTA
1 AAACCGGTAGGTATTTTAATGTAATAGGTAGCGCCTA-TTTTTTTACCGTTTACATTATT-A--A
175968 GCAACCTT-AAAA
62 -CAACCTTCAAAA
* * * * *
175980 AAATCGGTAGATAATTTAATGTAATAGGTAGTGCCTATTTTTTTACCGTTTACATTATTAACATC
1 AAACCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTACCGTTTACATTATTAACAAC
176045 CTTCAAAA
66 CTTCAAAA
* * *
176053 AAACCGATAGGTATTTTAATATAATAGGTAGCGCCTATTTTTTTACCG-TTACATTATTAACAAT
1 AAACCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTACCGTTTACATTATTAACAAC
176117 CTTCAAAA
66 CTTCAAAA
* * * * *
176125 AAACCGGTAGGCAGTTTAATATAATAGGTTGCGCCTATTTTTTTTTACCGTTTACATTATTAGCA
1 AAACCGGTAGGTATTTTAATGTAATAGGTAGCGCCTA--TTTTTTTACCGTTTACATTATTAACA
*
176190 ACCTTCAAAT
64 ACCTTCAAAA
* * * *
176200 AAA-CGGTAGGTAGTTTAATGTAATAGGT-GACACATATTGTTTTACCGTTTACATTATTAACAA
1 AAACCGGTAGGTATTTTAATGTAATAGGTAG-CGCCTATTTTTTTACCGTTTACATTATTAACAA
* *
176263 CTTTAAAAA
65 CCTTCAAAA
* * * * * *
176272 AAACCGGTAGATATTTTAATGTAATAGATAACACTTATTTTTTATACCGTTTACATTATTAGCAA
1 AAACCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTT-TACCGTTTACATTATTAACAA
*
176337 CCTTAAAAAA
65 CCTT-CAAAA
* *
176347 AAATCGGTAGGTATTTTAATGTAATAGGT-GACACCTATTTTTTTA
1 AAACCGGTAGGTATTTTAATGTAATAGGTAG-CGCCTATTTTTTTA
176392 AAAAAGAAAA
Statistics
Matches: 356, Mismatches: 46, Indels: 23
0.84 0.11 0.05
Matches are distributed among these distances:
72 95 0.27
73 80 0.22
74 63 0.18
75 67 0.19
76 19 0.05
77 32 0.09
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (73 bp):
AAACCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTACCGTTTACATTATTAACAAC
CTTCAAAA
Found at i:176289 original size:219 final size:226
Alignment explanation
Indices: 175903--176390 Score: 604
Period size: 219 Copynumber: 2.2 Consensus size: 226
175893 TGTTATAATG
* * * *
175903 AAACCGGTATGTATTTTAATGTAATAGGTAGCGCCTA-TTTTTTTTAATGTTTATATTATTAATT
1 AAACCGGTAGGTATTTTAATGTAATAGGTTGCGCCTATTTTTTTTTAACGTTTATATCATTAATT
* *
175967 AGCAACCTTAAAAAAATCGGTAGATAATTTAATGTAATAGGTAGTGCCTATTTTTTTACCGTTTA
66 AGCAACCTTAAAAAAATCGGTAGATAATTTAATGTAATAGGTAGTACCTATTGTTTTACCGTTTA
* * * * * *
176032 CATTATTAACATCCTTCAAAAAAACCGATAGGTATTTTAATATAATAGGTAGCGCCTATTTTTT-
131 CATTATTAACAACCTTAAAAAAAACCGATAGATATTTTAATATAATAGATAACACCTATTTTTTA
* *
176096 TACCG-TTACATTATTAACAATCTT-CAAAA
196 TACCGTTTACATTATTAACAACCTTAAAAAA
* * * *
176125 AAACCGGTAGGCAGTTTAATATAATAGGTTGCGCCTATTTTTTTTTACCG-TT-TA-CATT-ATT
1 AAACCGGTAGGTATTTTAATGTAATAGGTTGCGCCTATTTTTTTTTAACGTTTATATCATTAATT
* * *
176186 AGCAACCTTCAAATAAA-CGGTAGGTAGTTTAATGTAATAGGT-G-ACACATATTGTTTTACCGT
66 AGCAACCTT-AAAAAAATCGGTAGATAATTTAATGTAATAGGTAGTAC-C-TATTGTTTTACCGT
* * * *
176248 TTACATTATTAACAACTTTAAAAAAAACCGGTAGATATTTTAATGTAATAGATAACACTTATTTT
128 TTACATTATTAACAACCTTAAAAAAAACCGATAGATATTTTAATATAATAGATAACACCTATTTT
*
176313 TTATACCGTTTACATTATTAGCAACCTTAAAAAA
193 TTATACCGTTTACATTATTAACAACCTTAAAAAA
* *
176347 AAATCGGTAGGTATTTTAATGTAATAGG-TGACACCTATTTTTTT
1 AAACCGGTAGGTATTTTAATGTAATAGGTTG-CGCCTATTTTTTT
176391 AAAAAAGAAA
Statistics
Matches: 227, Mismatches: 31, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
217 1 0.00
218 2 0.01
219 105 0.46
220 14 0.06
221 21 0.09
222 74 0.33
223 10 0.04
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (226 bp):
AAACCGGTAGGTATTTTAATGTAATAGGTTGCGCCTATTTTTTTTTAACGTTTATATCATTAATT
AGCAACCTTAAAAAAATCGGTAGATAATTTAATGTAATAGGTAGTACCTATTGTTTTACCGTTTA
CATTATTAACAACCTTAAAAAAAACCGATAGATATTTTAATATAATAGATAACACCTATTTTTTA
TACCGTTTACATTATTAACAACCTTAAAAAA
Found at i:177296 original size:20 final size:20
Alignment explanation
Indices: 177260--177297 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
177250 ATCCTATTCC
**
177260 CTGATAATCTTTTATTCCCA
1 CTGATAATCTTACATTCCCA
177280 CTGATAATCTTACATTCC
1 CTGATAATCTTACATTCC
177298 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.42
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCA
Found at i:177701 original size:15 final size:15
Alignment explanation
Indices: 177683--177716 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
177673 AAAGAAAATA
177683 TGACCAAACATAATT
1 TGACCAAACATAATT
**
177698 TGACTTAACATAATT
1 TGACCAAACATAATT
177713 TGAC
1 TGAC
177717 TTTTTATGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (15 bp):
TGACCAAACATAATT
Found at i:177717 original size:15 final size:15
Alignment explanation
Indices: 177689--177718 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
177679 AATATGACCA
177689 AACATAATTTGACTT
1 AACATAATTTGACTT
177704 AACATAATTTGACTT
1 AACATAATTTGACTT
177719 TTTATGTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (15 bp):
AACATAATTTGACTT
Found at i:178428 original size:23 final size:27
Alignment explanation
Indices: 178380--178466 Score: 112
Period size: 23 Copynumber: 3.4 Consensus size: 27
178370 AGGTTTTATA
* *
178380 TTTAATTTTATATTATAGATATTAATT
1 TTTAATATTAAATTATAGATATTAATT
178407 TTTAA-A-TAAATTA-A-ATATTAATT
1 TTTAATATTAAATTATAGATATTAATT
*
178430 TTTAATATTATATTATAGATATTAA-T
1 TTTAATATTAAATTATAGATATTAATT
178456 TTTAATATTAA
1 TTTAATATTAA
178467 TTTTTAAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
23 14 0.27
24 2 0.04
25 12 0.23
26 12 0.23
27 12 0.23
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (27 bp):
TTTAATATTAAATTATAGATATTAATT
Found at i:178451 original size:14 final size:12
Alignment explanation
Indices: 178391--178530 Score: 81
Period size: 13 Copynumber: 11.2 Consensus size: 12
178381 TTAATTTTAT
178391 ATTATAGATATTA
1 ATTATA-ATATTA
* *
178404 ATTTTTAA-ATAA
1 A-TTATAATATTA
178416 ATTA-AATATTA
1 ATTATAATATTA
*
178427 ATTTTTAATATTA
1 A-TTATAATATTA
178440 TATTATAGATATTA
1 -ATTATA-ATATTA
*
178454 ATTTTAATATTA
1 ATTATAATATTA
* *
178466 ATTTTTAA-ATAA
1 A-TTATAATATTA
178478 ATTA-AATATTA
1 ATTATAATATTA
* *
178489 TTTTTTAATATTA
1 -ATTATAATATTA
*
178502 TATTAAAGATATTA
1 -ATTATA-ATATTA
*
178516 ATTTTAATATTA
1 ATTATAATATTA
178528 ATT
1 ATT
178531 TTTTAAATAA
Statistics
Matches: 99, Mismatches: 17, Indels: 23
0.71 0.12 0.17
Matches are distributed among these distances:
10 4 0.04
11 11 0.11
12 28 0.28
13 39 0.39
14 17 0.17
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (12 bp):
ATTATAATATTA
Found at i:178466 original size:39 final size:36
Alignment explanation
Indices: 178420--178565 Score: 100
Period size: 36 Copynumber: 4.2 Consensus size: 36
178410 AAATAAATTA
*
178420 AATATTAATTTTTAATATTATATTATAGATA-T-TAATTTT
1 AATATTAATTTTTAA-A-TAAATTA-A-ATATTAT-ATTTT
*
178459 AATATTAATTTTTAAATAAATTAAATATTATTTTTT
1 AATATTAATTTTTAAATAAATTAAATATTATATTTT
* *
178495 AATATT-A----T--ATTAA--AGATATTA-ATTTT
1 AATATTAATTTTTAAATAAATTAAATATTATATTTT
*
178521 AATATTAATTTTTTAAATAAATTAAATATTGATTTTTT
1 AATATTAA-TTTTTAAATAAATTAAATATT-ATATTTT
178559 AATATTA
1 AATATTA
178566 TATTATAGAT
Statistics
Matches: 85, Mismatches: 8, Indels: 29
0.70 0.07 0.24
Matches are distributed among these distances:
26 10 0.12
27 8 0.09
29 4 0.05
31 1 0.01
32 1 0.01
34 4 0.05
35 4 0.05
36 18 0.21
37 8 0.09
38 12 0.14
39 15 0.18
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (36 bp):
AATATTAATTTTTAAATAAATTAAATATTATATTTT
Found at i:178469 original size:62 final size:62
Alignment explanation
Indices: 178398--178586 Score: 333
Period size: 62 Copynumber: 3.0 Consensus size: 62
178388 TATATTATAG
*
178398 ATATTAATTTTTAAATAAATTAAATATTAATTTTTAATATTATATTATAGATATTAATTTTA
1 ATATTAATTTTTAAATAAATTAAATATTATTTTTTAATATTATATTATAGATATTAATTTTA
*
178460 ATATTAATTTTTAAATAAATTAAATATTATTTTTTAATATTATATTAAAGATATTAATTTTA
1 ATATTAATTTTTAAATAAATTAAATATTATTTTTTAATATTATATTATAGATATTAATTTTA
178522 ATATTAATTTTTTAAATAAATTAAATATTGATTTTTTAATATTATATTATAGATATTTAATTTTA
1 ATATTAA-TTTTTAAATAAATTAAATATT-ATTTTTTAATATTATATTATAGATA-TTAATTTTA
178587 TATCATATAA
Statistics
Matches: 121, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
62 67 0.55
63 21 0.17
64 24 0.20
65 9 0.07
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (62 bp):
ATATTAATTTTTAAATAAATTAAATATTATTTTTTAATATTATATTATAGATATTAATTTTA
Found at i:178641 original size:20 final size:19
Alignment explanation
Indices: 178581--178642 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
178571 TAGATATTTA
*
178581 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
178600 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
178618 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
178638 ATTTT
1 ATTTT
178643 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:182210 original size:12 final size:12
Alignment explanation
Indices: 182195--182249 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
182185 GTTATTTAAA
182195 CGGGTATTGGGC
1 CGGGTATTGGGC
*
182207 CGGGTATTGGGT
1 CGGGTATTGGGC
182219 CGGGTATTGGGC
1 CGGGTATTGGGC
* * *
182231 CGAGAATCGGGC
1 CGGGTATTGGGC
182243 CGGGTAT
1 CGGGTAT
182250 ATATATATAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.13, C:0.16, G:0.47, T:0.24
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:182311 original size:13 final size:13
Alignment explanation
Indices: 182281--182324 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
182271 ATATATAAAT
*
182281 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
182293 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
182306 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
182319 ATCGGG
1 ATCGGG
182325 TAATCGGGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.14, C:0.16, G:0.52, T:0.18
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:195228 original size:27 final size:27
Alignment explanation
Indices: 195198--195250 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
195188 ATTCCCCAAC
*
195198 TTCTTTTTCTTCACTTTTCTTCTTTTT
1 TTCTTTCTCTTCACTTTTCTTCTTTTT
195225 TTCTTTCTCTTCACTTTTCTTCTTTT
1 TTCTTTCTCTTCACTTTTCTTCTTTT
195251 CCTCTTCTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.04, C:0.25, G:0.00, T:0.72
Consensus pattern (27 bp):
TTCTTTCTCTTCACTTTTCTTCTTTTT
Found at i:195256 original size:27 final size:27
Alignment explanation
Indices: 195199--195256 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
195189 TTCCCCAACT
* **
195199 TCTTTTTCTTCACTTTTCTTCTTTTTT
1 TCTTTCTCTTCACTTTTCTTCTTTTCC
195226 TCTTTCTCTTCACTTTTCTTCTTTTCC
1 TCTTTCTCTTCACTTTTCTTCTTTTCC
195253 TCTT
1 TCTT
195257 CTCACACACG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (27 bp):
TCTTTCTCTTCACTTTTCTTCTTTTCC
Found at i:197399 original size:28 final size:28
Alignment explanation
Indices: 197365--197423 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
197355 TAACTGTTTA
197365 ACTATATTTTTCGTCACGCCTCTTAACG
1 ACTATATTTTTCGTCACGCCTCTTAACG
197393 ACTATATTTTTCGTCACGCCTCTTAACG
1 ACTATATTTTTCGTCACGCCTCTTAACG
197421 ACT
1 ACT
197424 GTTAACGGCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.22, C:0.29, G:0.10, T:0.39
Consensus pattern (28 bp):
ACTATATTTTTCGTCACGCCTCTTAACG
Found at i:202193 original size:20 final size:20
Alignment explanation
Indices: 202168--202205 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
202158 TTTGGTTCAC
*
202168 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAGTG
202188 GGAATAAAAGATTACCAG
1 GGAATAAAAGATTACCAG
202206 GGAATATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.21
Consensus pattern (20 bp):
GGAATAAAAGATTACCAGTG
Found at i:202208 original size:18 final size:19
Alignment explanation
Indices: 202168--202211 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
202158 TTTGGTTCAC
*
202168 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAG-G
202188 GGAATAAAAGATTACCA-G
1 GGAATAAAAGATTACCAGG
202206 GGAATA
1 GGAATA
202212 TGATTACTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
20 16 0.70
ACGTcount: A:0.45, C:0.09, G:0.25, T:0.20
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGG
Found at i:208885 original size:57 final size:57
Alignment explanation
Indices: 208794--208910 Score: 164
Period size: 57 Copynumber: 2.1 Consensus size: 57
208784 TTATTTACAA
* * * * *
208794 AATTAAGTGATCAATATTTAAAATAAAATCTGTCTATAGTTAAATGATCATAAGTGT
1 AATTAAGAGATCAATATTCAAAATAAAATATGTCTATAGTCAAATAATCATAAGTGT
*
208851 AATTAAGAGATCAATCA-TCAAAATAAAATATGTCTATAGTCAAATAATCATACGTGT
1 AATTAAGAGATCAAT-ATTCAAAATAAAATATGTCTATAGTCAAATAATCATAAGTGT
208908 AAT
1 AAT
208911 GTAGAACTCC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 52 0.98
58 1 0.02
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.33
Consensus pattern (57 bp):
AATTAAGAGATCAATATTCAAAATAAAATATGTCTATAGTCAAATAATCATAAGTGT
Found at i:211592 original size:18 final size:19
Alignment explanation
Indices: 211571--211611 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
211561 TTTTTAATAA
211571 AAATACATGA-AATAATT-T
1 AAATACAT-ATAATAATTCT
*
211589 AAATATATATAATAATTCT
1 AAATACATATAATAATTCT
211608 AAAT
1 AAAT
211612 TTTCAAGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 14 0.70
19 5 0.25
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (19 bp):
AAATACATATAATAATTCT
Found at i:212328 original size:25 final size:25
Alignment explanation
Indices: 212280--212330 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
212270 CAATTAACAA
*
212280 ATCTCATCCAACTAGAGACTATTTT
1 ATCTCATCCAACTAGAAACTATTTT
*
212305 ATCTCATCTAACTAGAAA-TCATTTT
1 ATCTCATCCAACTAGAAACT-ATTTT
212330 A
1 A
212331 CTCCGAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.37
Consensus pattern (25 bp):
ATCTCATCCAACTAGAAACTATTTT
Found at i:220115 original size:27 final size:27
Alignment explanation
Indices: 220077--220129 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
220067 CTGCAACCAT
220077 GCAAAGTTTAAACGTCATGGTGGTCTC
1 GCAAAGTTTAAACGTCATGGTGGTCTC
* *
220104 GCAAAGTTTAAATGTCATGTTGGTCT
1 GCAAAGTTTAAACGTCATGGTGGTCT
220130 GGAACGTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (27 bp):
GCAAAGTTTAAACGTCATGGTGGTCTC
Found at i:223938 original size:20 final size:20
Alignment explanation
Indices: 223915--223979 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
223905 TCATAAACAC
223915 AATATTCATAAAATAAATTA
1 AATATTCATAAAATAAATTA
* * *
223935 AATATT-A-AATGATTATTTA
1 AATATTCATAA-AATAAATTA
* * *
223954 AATATGCATAACATCAATTA
1 AATATTCATAAAATAAATTA
223974 AATATT
1 AATATT
223980 AAACTAATAA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
18 2 0.06
19 12 0.35
20 18 0.53
21 2 0.06
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.38
Consensus pattern (20 bp):
AATATTCATAAAATAAATTA
Found at i:224518 original size:30 final size:32
Alignment explanation
Indices: 224482--224541 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
224472 GCTCGTGAAC
224482 TTTCGAGTT-GACTCGAACTT-CAATTTTTTA
1 TTTCGAGTTCGACTCGAACTTACAATTTTTTA
*
224512 TTTCGAGTTCGAGTCGAACTTGACAATTTT
1 TTTCGAGTTCGACTCGAACTT-ACAATTTT
224542 AAGTTCTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 9 0.35
31 10 0.38
33 7 0.27
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (32 bp):
TTTCGAGTTCGACTCGAACTTACAATTTTTTA
Found at i:228286 original size:16 final size:16
Alignment explanation
Indices: 228265--228310 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
228255 ATTGGATTAA
228265 GGGTTT-AGGATTTAGG
1 GGGTTTAAGG-TTTAGG
228281 GGGTTTAAGGTTTAGG
1 GGGTTTAAGGTTTAGG
* *
228297 TGTTTTAAGGTTTA
1 GGGTTTAAGGTTTA
228311 TGGTTTATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 24 0.89
17 3 0.11
ACGTcount: A:0.20, C:0.00, G:0.37, T:0.43
Consensus pattern (16 bp):
GGGTTTAAGGTTTAGG
Found at i:228292 original size:7 final size:7
Alignment explanation
Indices: 228264--228366 Score: 89
Period size: 7 Copynumber: 14.1 Consensus size: 7
228254 AATTGGATTA
228264 AGGGTTT
1 AGGGTTT
*
228271 AGGATTT
1 AGGGTTT
228278 AGGGGGTTT
1 A--GGGTTT
*
228287 AAGGTTT
1 AGGGTTT
228294 AGGTGTTTT
1 AGG-G-TTT
*
228303 AAGGTTT
1 AGGGTTT
*
228310 ATGGTTT
1 AGGGTTT
*
228317 ATGGTTT
1 AGGGTTT
**
228324 ATAGTTT
1 AGGGTTT
**
228331 ATAGTTT
1 AGGGTTT
228338 AGGGTTT
1 AGGGTTT
228345 AGGGTTT
1 AGGGTTT
228352 AGGGTTT
1 AGGGTTT
228359 AGGGTTT
1 AGGGTTT
228366 A
1 A
228367 TGACTCATTG
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
7 70 0.84
8 2 0.02
9 11 0.13
ACGTcount: A:0.19, C:0.00, G:0.34, T:0.47
Consensus pattern (7 bp):
AGGGTTT
Found at i:228849 original size:16 final size:16
Alignment explanation
Indices: 228790--228841 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
228780 TATTTTTTAA
*
228790 AAATTATTA-ATATTT
1 AAATTATTATATTTTT
*
228805 AAATTGAATCATATTTTT
1 AAATT--ATTATATTTTT
*
228823 AATTTATTATATTTTT
1 AAATTATTATATTTTT
228839 AAA
1 AAA
228842 ATTTTATAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
15 5 0.17
16 12 0.41
17 3 0.10
18 9 0.31
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (16 bp):
AAATTATTATATTTTT
Found at i:228889 original size:28 final size:29
Alignment explanation
Indices: 228830--228890 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
228820 TTTAATTTAT
* * *
228830 TATATTTTTAAAATTTTATAGAATTTTTAA
1 TATATTTTTAAAATTCTATA-AATTATCAA
228860 TATATTTTTAAAATTCTAT-AATTATCAA
1 TATATTTTTAAAATTCTATAAATTATCAA
228888 TAT
1 TAT
228891 TGTATTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 10 0.36
30 18 0.64
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (29 bp):
TATATTTTTAAAATTCTATAAATTATCAA
Found at i:231909 original size:22 final size:22
Alignment explanation
Indices: 231877--231926 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
231867 TAGTTTTGTT
* *
231877 TTTAAAATTTTAAAAGTTCATTC
1 TTTAAATTTTTAAAAGTTC-GTC
*
231900 TTTAAATTTTTATAAGTTCGTC
1 TTTAAATTTTTAAAAGTTCGTC
231922 TTTAA
1 TTTAA
231927 CATAAAGTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.34, C:0.08, G:0.06, T:0.52
Consensus pattern (22 bp):
TTTAAATTTTTAAAAGTTCGTC
Found at i:241213 original size:51 final size:50
Alignment explanation
Indices: 241137--241263 Score: 173
Period size: 51 Copynumber: 2.5 Consensus size: 50
241127 TTAGCAGTAA
**
241137 AGCGCGCCCCCTGCACCGCGCTATACGATGATTTGGCGCCACGTGGGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGT-GGGTAT
*
241188 AGCGCGCCCCCTGCACCGCGCTATACGGTGAGCTGGCGCCACGTGGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGTAT
* * * * *
241238 AGTGCGGCCCCTACAACGCACTATAC
1 AGCGCGCCCCCTGCACCGCGCTATAC
241264 TTGTATATCT
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
50 27 0.40
51 41 0.60
ACGTcount: A:0.17, C:0.35, G:0.30, T:0.17
Consensus pattern (50 bp):
AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGTAT
Found at i:241415 original size:12 final size:10
Alignment explanation
Indices: 241374--241414 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
241364 TTTATCACAC
241374 CAAATTCTCT
1 CAAATTCTCT
241384 CAAATTCTCT
1 CAAATTCTCT
241394 -AAATTTCTCT
1 CAAA-TTCTCT
*
241404 CAAATACTCT
1 CAAATTCTCT
241414 C
1 C
241415 TTTTTAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:241463 original size:13 final size:14
Alignment explanation
Indices: 241435--241463 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
241425 ATATTTTATA
241435 ATATTTTTACTATT
1 ATATTTTTACTATT
241449 ATATTTTTACT-TT
1 ATATTTTTACTATT
241462 AT
1 AT
241464 TTAATATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATTTTTACTATT
Found at i:243182 original size:18 final size:18
Alignment explanation
Indices: 243159--243193 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
243149 GCAGCCACCG
243159 CAACCATATATGATGCCA
1 CAACCATATATGATGCCA
243177 CAACCATATATGATGCC
1 CAACCATATATGATGCC
243194 GTCATCGCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.29, G:0.11, T:0.23
Consensus pattern (18 bp):
CAACCATATATGATGCCA
Found at i:243692 original size:41 final size:42
Alignment explanation
Indices: 243647--243730 Score: 125
Period size: 41 Copynumber: 2.0 Consensus size: 42
243637 GCCTGGCCTG
* *
243647 TTTAACTAAACAGGCCAGGCCCAGGCCTTTTTAAAAG-CTTA
1 TTTAACTAAACAGGCCAGGCCCAGGCCTATTAAAAAGCCTTA
**
243688 TTTAACTAAACAGGCCAGGCTTAGGCCTATTAAAAAGCCTTA
1 TTTAACTAAACAGGCCAGGCCCAGGCCTATTAAAAAGCCTTA
243730 T
1 T
243731 AAGCCTGATA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
41 33 0.87
42 5 0.13
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (42 bp):
TTTAACTAAACAGGCCAGGCCCAGGCCTATTAAAAAGCCTTA
Found at i:243877 original size:17 final size:18
Alignment explanation
Indices: 243855--243894 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
243845 TATTGTTAAA
243855 CAGGCTTTTAAACAGG-C
1 CAGGCTTTTAAACAGGCC
*
243872 CAGGCTTTTAAATAGGCC
1 CAGGCTTTTAAACAGGCC
243890 CAGGC
1 CAGGC
243895 CAGGCCTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.23
Consensus pattern (18 bp):
CAGGCTTTTAAACAGGCC
Found at i:247960 original size:50 final size:50
Alignment explanation
Indices: 247888--247995 Score: 146
Period size: 50 Copynumber: 2.2 Consensus size: 50
247878 TATAGCGCAC
**
247888 TGCAGGGGCTACGCTATACCCACGTGGCGCCAGCTCACCGTATAACGCGG
1 TGCAGGGGCTACGCTATACCCACGTGGCGCCAAATCACCGTATAACGCGG
* * *
247938 TGCAGGGG-TACTCTATACCCCACGTGGCGCCAAATCATCGTATAGCGCGG
1 TGCAGGGGCTACGCTATA-CCCACGTGGCGCCAAATCACCGTATAACGCGG
*
247988 TACAGGGG
1 TGCAGGGG
247996 GCACGCTTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
49 8 0.16
50 43 0.84
ACGTcount: A:0.21, C:0.31, G:0.31, T:0.18
Consensus pattern (50 bp):
TGCAGGGGCTACGCTATACCCACGTGGCGCCAAATCACCGTATAACGCGG
Found at i:248711 original size:2 final size:2
Alignment explanation
Indices: 248704--248729 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
248694 AACTGAATGC
248704 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
248730 TATTGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:249570 original size:2 final size:2
Alignment explanation
Indices: 249563--249590 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
249553 AAATACACAA
249563 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
249591 TATGGGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:250140 original size:2 final size:2
Alignment explanation
Indices: 250133--250196 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
250123 TGAATAAATC
250133 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
250175 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
250197 GAACTTTAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:252584 original size:33 final size:33
Alignment explanation
Indices: 252547--252613 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
252537 TCGAGATCAA
252547 ACTTCTCAAGCCATCTGAATCAAGATAAATTAT
1 ACTTCTCAAGCCATCTGAATCAAGATAAATTAT
* *
252580 ACTTCTTAATCCATCTGAATCAAGATAAATTAT
1 ACTTCTCAAGCCATCTGAATCAAGATAAATTAT
252613 A
1 A
252614 GCCAAGTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.33
Consensus pattern (33 bp):
ACTTCTCAAGCCATCTGAATCAAGATAAATTAT
Found at i:253004 original size:48 final size:48
Alignment explanation
Indices: 252933--253030 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
252923 TTTTCTTAAC
*
252933 AATATATCATGGAGCAACTTGCAAACTGGAGAAGGAAATTATGACATA
1 AATATATCATGGAGCAACTTGCAAACTAGAGAAGGAAATTATGACATA
* *
252981 AATATATCGTGGAGCAACTTGCAAACTAGAGAATGAAATTATGACATA
1 AATATATCATGGAGCAACTTGCAAACTAGAGAAGGAAATTATGACATA
253029 AA
1 AA
253031 AGCTCGGTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.23
Consensus pattern (48 bp):
AATATATCATGGAGCAACTTGCAAACTAGAGAAGGAAATTATGACATA
Found at i:257075 original size:24 final size:27
Alignment explanation
Indices: 257048--257103 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 27
257038 TGGTAGTTAC
257048 AATTTGGGG-TTTA-AGGTTGA-GTAT
1 AATTTGGGGATTTAGAGGTTGAGGTAT
*
257072 AA-TTGGGGATTTAGAGTTTGAGTGTAT
1 AATTTGGGGATTTAGAGGTTGAG-GTAT
257099 AATTT
1 AATTT
257104 AGAATTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 6 0.23
24 6 0.23
25 6 0.23
27 6 0.23
28 2 0.08
ACGTcount: A:0.27, C:0.00, G:0.30, T:0.43
Consensus pattern (27 bp):
AATTTGGGGATTTAGAGGTTGAGGTAT
Found at i:260860 original size:21 final size:21
Alignment explanation
Indices: 260836--260894 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
260826 TCAAATCCCT
260836 CAACTAAGCCTGTAACATCTG
1 CAACTAAGCCTGTAACATCTG
**
260857 CAAC-AATGCCTGTAATGTCTG
1 CAACTAA-GCCTGTAACATCTG
* * *
260878 CTACTAAGTCTGCAACA
1 CAACTAAGCCTGTAACA
260895 AAACCAGTAT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
20 2 0.07
21 25 0.86
22 2 0.07
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.25
Consensus pattern (21 bp):
CAACTAAGCCTGTAACATCTG
Found at i:261815 original size:26 final size:27
Alignment explanation
Indices: 261766--261816 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
261756 AATGTGTTTG
*
261766 AAGGTATCACGGTATCATTTAGTTATC
1 AAGGTATCACGGAATCATTTAGTTATC
261793 AAGGTATCAC-GAATCATTTAGTTA
1 AAGGTATCACGGAATCATTTAGTTA
261817 ATAGTTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (27 bp):
AAGGTATCACGGAATCATTTAGTTATC
Found at i:263750 original size:57 final size:58
Alignment explanation
Indices: 263686--263796 Score: 170
Period size: 58 Copynumber: 1.9 Consensus size: 58
263676 CTTAGCATGT
* * *
263686 CAAACTTATCATGTGATAAAAG-AAAATATTATTTTCTGTTAAGGTTTTGAGTTTGAG
1 CAAACTTATCATATGATAAAAGAAAAATATTATTTTCCGTCAAGGTTTTGAGTTTGAG
* *
263743 CAAACTTATCATATGATAAAAGAAAAATATTGTTTTCCGTCGAGGTTTTGAGTT
1 CAAACTTATCATATGATAAAAGAAAAATATTATTTTCCGTCAAGGTTTTGAGTT
263797 CGAGAGGGTT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
57 21 0.44
58 27 0.56
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (58 bp):
CAAACTTATCATATGATAAAAGAAAAATATTATTTTCCGTCAAGGTTTTGAGTTTGAG
Found at i:272557 original size:3 final size:3
Alignment explanation
Indices: 272549--272586 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
272539 AACTATGTAT
272549 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
272587 TTAATACATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:272897 original size:37 final size:37
Alignment explanation
Indices: 272748--273023 Score: 315
Period size: 37 Copynumber: 7.4 Consensus size: 37
272738 TGTATACAAT
* * * *
272748 ATATATAGTTTTGAAAAATATTTTTCTATAACATATATA
1 ATATATAGTTTTTAAAAATA-TTTT-AAAAATATATATA
272787 ATATATAG-TTTTAAAAATATTTTGAAAACATATATATA
1 ATATATAGTTTTTAAAAATATTTT-AAAA-ATATATATA
*
272825 ATATATAGTTTTTAAAAATTATTTTGAAAATATATATA
1 ATATATAGTTTTTAAAAA-TATTTTAAAAATATATATA
* * *
272863 ATATATAGTTTTTGAAAACATTTTAAAAACATATATA
1 ATATATAGTTTTTAAAAATATTTTAAAAATATATATA
* *
272900 ATATATAGTTTTAAAAAATATTTTGAAAATATATATA
1 ATATATAGTTTTTAAAAATATTTTAAAAATATATATA
* * *
272937 ATATATAATTTTTGAAAACATTTTGAAAAAATATATATA
1 ATATATAGTTTTTAAAAATATTTT--AAAAATATATATA
** *
272976 ATATATA-TTTTTTGAAGT-TTTTAAAAATATATATA
1 ATATATAGTTTTTAAAAATATTTTAAAAATATATATA
*
273011 CTATATAGTTTTT
1 ATATATAGTTTTT
273024 TTAAATATAT
Statistics
Matches: 206, Mismatches: 25, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
35 19 0.09
36 5 0.02
37 78 0.38
38 59 0.29
39 39 0.19
40 6 0.03
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (37 bp):
ATATATAGTTTTTAAAAATATTTTAAAAATATATATA
Found at i:273020 original size:26 final size:26
Alignment explanation
Indices: 272991--273043 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
272981 TATTTTTTGA
272991 AGTTTTTAAAAATATATATACTATAT
1 AGTTTTTAAAAATATATATACTATAT
** * *
273017 AGTTTTTTTAAATATATTTATTATAT
1 AGTTTTTAAAAATATATATACTATAT
273043 A
1 A
273044 TAGTATAGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (26 bp):
AGTTTTTAAAAATATATATACTATAT
Found at i:273024 original size:28 final size:28
Alignment explanation
Indices: 272993--273047 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
272983 TTTTTTGAAG
272993 TTTTTAAAAATATATA-TACTATATAGTT
1 TTTTTAAAAATATATATTA-TATATAGTT
* *
273021 TTTTTAAATATATTTATTATATATAGT
1 TTTTTAAAAATATATATTATATATAGT
273048 ATAGTCATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (28 bp):
TTTTTAAAAATATATATTATATATAGTT
Found at i:273025 original size:37 final size:37
Alignment explanation
Indices: 272748--273023 Score: 283
Period size: 38 Copynumber: 7.4 Consensus size: 37
272738 TGTATACAAT
* * * *
272748 ATATATAGTTTTGAAAAATATTTTTCTATAACATATATA
1 ATATATAGTTTTTAAAAA-ATTTTT-AAAAATATATATA
*
272787 ATATATAG-TTTTAAAAATATTTTGAAAACATATATATA
1 ATATATAGTTTTTAAAAA-ATTTTTAAAA-ATATATATA
* *
272825 ATATATAGTTTTTAAAAATTATTTTGAAAATATATATA
1 ATATATAGTTTTTAAAAAAT-TTTTAAAAATATATATA
* *
272863 ATATATAGTTTTTGAAAACA-TTTTAAAAACATATATA
1 ATATATAGTTTTT-AAAAAATTTTTAAAAATATATATA
*
272900 ATATATAG-TTTTAAAAAATATTTTGAAAATATATATA
1 ATATATAGTTTTTAAAAAAT-TTTTAAAAATATATATA
* * *
272937 ATATATAATTTTTGAAAACATTTTGAAAAAATATATATA
1 ATATATAGTTTTT-AAAAAATTTT-TAAAAATATATATA
** *
272976 ATATATA-TTTTT-TGAAGTTTTTAAAAATATATATA
1 ATATATAGTTTTTAAAAAATTTTTAAAAATATATATA
*
273011 CTATATAGTTTTT
1 ATATATAGTTTTT
273024 TTAAATATAT
Statistics
Matches: 202, Mismatches: 25, Indels: 23
0.81 0.10 0.09
Matches are distributed among these distances:
35 24 0.12
36 14 0.07
37 47 0.23
38 65 0.32
39 52 0.26
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (37 bp):
ATATATAGTTTTTAAAAAATTTTTAAAAATATATATA
Found at i:279312 original size:23 final size:23
Alignment explanation
Indices: 279286--279329 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
279276 TAACACTGAT
* *
279286 TTTCTAAAATAAGATTAATATAA
1 TTTCAAAAAAAAGATTAATATAA
*
279309 TTTCAAAAAAAATATTAATAT
1 TTTCAAAAAAAAGATTAATAT
279330 GTGAATCATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (23 bp):
TTTCAAAAAAAAGATTAATATAA
Found at i:283364 original size:18 final size:18
Alignment explanation
Indices: 283322--283372 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
283312 ATTATAAAAA
*
283322 ATATTATTATTTTTATCG
1 ATATTATTATTTTAATCG
283340 ATATTATTATTATTAATCG
1 ATATTATTATT-TTAATCG
*
283359 -TTTTATCTATTTTA
1 ATATTAT-TATTTTA
283373 TTAACATATC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 19 0.66
19 10 0.34
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.61
Consensus pattern (18 bp):
ATATTATTATTTTAATCG
Found at i:287606 original size:1 final size:1
Alignment explanation
Indices: 287595--287625 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
287585 AAGTGCTTGC
*
287595 TTTTGTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
287626 GTATTCTCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:302606 original size:35 final size:35
Alignment explanation
Indices: 302492--302606 Score: 94
Period size: 35 Copynumber: 3.4 Consensus size: 35
302482 TGAGAAGACT
* *
302492 AAAGAAAGGGATAGTAACGATGATGAAAAAGCTAA
1 AAAGAAAAGGAAAGTAACGATGATGAAAAAGCTAA
* * * * * *
302527 AAAGAAAAAGAGAGTCA-G-TCATGAAAAGGGT--
1 AAAGAAAAGGAAAGTAACGATGATGAAAAAGCTAA
* * *
302558 AAAGAAAACGAAAGTGACGATGATGAAAAAACTAA
1 AAAGAAAAGGAAAGTAACGATGATGAAAAAGCTAA
*
302593 AAAGAAAGGGAAAG
1 AAAGAAAAGGAAAG
302607 CCGATCATGG
Statistics
Matches: 60, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
31 14 0.23
32 1 0.02
33 19 0.32
34 1 0.02
35 25 0.42
ACGTcount: A:0.57, C:0.06, G:0.26, T:0.11
Consensus pattern (35 bp):
AAAGAAAAGGAAAGTAACGATGATGAAAAAGCTAA
Found at i:302615 original size:66 final size:66
Alignment explanation
Indices: 302508--302698 Score: 204
Period size: 66 Copynumber: 2.9 Consensus size: 66
302498 AGGGATAGTA
* * * * * *
302508 ACGATGATGAAAAAGCTAAAAAGAAAAAGAGAGTC-AGTCATGAAAAGGGTAAAGAAAACGAAAG
1 ACGATGATGAAAAAACTAAAAAGAAAGAGAAAGCCGA-TCATGAAAAGGCTAAAGAAAAAGAAAG
*
302572 TG
65 CG
* * ** *
302574 ACGATGATGAAAAAACTAAAAAGAAAGGGAAAGCCGATCATGGAAAGATTAAAGAAAAAGAGAGC
1 ACGATGATGAAAAAACTAAAAAGAAAGAGAAAGCCGATCATGAAAAGGCTAAAGAAAAAGAAAGC
302639 G
66 G
* ** ** *
302640 ACGAAGATGAAAAGTCTAAAAAGGGAGAGAAAGCCGATCATGTAAAGGCTAAAGAAAAA
1 ACGATGATGAAAAAACTAAAAAGAAAGAGAAAGCCGATCATGAAAAGGCTAAAGAAAAA
302699 AAGAGTGGCG
Statistics
Matches: 104, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
66 103 0.99
67 1 0.01
ACGTcount: A:0.54, C:0.09, G:0.26, T:0.12
Consensus pattern (66 bp):
ACGATGATGAAAAAACTAAAAAGAAAGAGAAAGCCGATCATGAAAAGGCTAAAGAAAAAGAAAGC
G
Found at i:302717 original size:21 final size:21
Alignment explanation
Indices: 302691--302740 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
302681 GTAAAGGCTA
* *
302691 AAGAAAAAAAGAGTGGCGATG
1 AAGAAAAAAAGAGCGACGATG
**
302712 AAGAAAGTAAGAGCGACGATG
1 AAGAAAAAAAGAGCGACGATG
*
302733 ATGAAAAA
1 AAGAAAAA
302741 GCTAAAAAGA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.54, C:0.06, G:0.30, T:0.10
Consensus pattern (21 bp):
AAGAAAAAAAGAGCGACGATG
Found at i:302746 original size:153 final size:153
Alignment explanation
Indices: 302573--302862 Score: 377
Period size: 153 Copynumber: 1.9 Consensus size: 153
302563 AAACGAAAGT
** * *
302573 GACGATGATGAAAAAACTAAAAAGAAAGGGAAAGCCGA-TCATGGAAAGATTAAAGAAAAAGAGA
1 GACGATGATGAAAAAACTAAAAAGAAAAAGAAAG-AGAGTCATGGAAAGAGTAAAGAAAAAGAGA
* ** *
302637 GCGACGAAGATG-AAAAGTCTAAAAAGGGAGAGAAAGCCGATCATGTAAAGGCTAAAGAAAAAAA
65 GCGACGAAGATGAAAAAAT-TAAAAAGAAAGAGAAAGCCGATCATGGAAAGGCTAAAGAAAAAAA
*
302701 GAGTGGCGATGAAGAAAGTAAGAGC
129 GAGCGGCGATGAAGAAAGTAAGAGC
* * * *
302726 GACGATGATGAAAAAGCTAAAAAGAAAAAGAGAGAGAGTCATGGAAAGGGTAAAGAAAACGAGAG
1 GACGATGATGAAAAAACTAAAAAGAAAAAGAAAGAGAGTCATGGAAAGAGTAAAGAAAAAGAGAG
* * * * * *
302791 TGACGATGATGAAAAAATTAAAAAGAAAGGGAAAGCCGGTTATGGAAAGGCTAAAGAAAAAGAGA
66 CGACGAAGATGAAAAAATTAAAAAGAAAGAGAAAGCCGATCATGGAAAGGCTAAAGAAAAAAAGA
302856 GCGGCGA
131 GCGGCGA
302863 AGATGAAAAG
Statistics
Matches: 116, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
152 2 0.02
153 109 0.94
154 5 0.04
ACGTcount: A:0.51, C:0.08, G:0.29, T:0.11
Consensus pattern (153 bp):
GACGATGATGAAAAAACTAAAAAGAAAAAGAAAGAGAGTCATGGAAAGAGTAAAGAAAAAGAGAG
CGACGAAGATGAAAAAATTAAAAAGAAAGAGAAAGCCGATCATGGAAAGGCTAAAGAAAAAAAGA
GCGGCGATGAAGAAAGTAAGAGC
Found at i:302774 original size:87 final size:87
Alignment explanation
Indices: 302634--302804 Score: 202
Period size: 87 Copynumber: 2.0 Consensus size: 87
302624 AAAGAAAAAG
** * * *
302634 AGAGCGACGAAGATGAAAAGTCTAAAAAGGGAGAGAAAGCCGATCATGTAAAGGCTAAAGAAAAA
1 AGAGCGACGAAGATGAAAAGTCTAAAAAGAAAAAGAAAGCAGATCATGGAAAGGCTAAAGAAAAA
*
302699 AAGAGTGGCGATGAAGAAAGTA
66 AAGAGTGACGATGAAGAAAGTA
* * *
302721 AGAGCGACGATGATGAAAAAG-CTAAAAAGAAAAAGAGAG-AGAGTCATGGAAAGGGTAAAGAAA
1 AGAGCGACGAAGATG-AAAAGTCTAAAAAGAAAAAGAAAGCAGA-TCATGGAAAGGCTAAAGAAA
** *
302784 ACGAGAGTGACGATGATGAAA
64 AAAAGAGTGACGATGAAGAAA
302805 AAATTAAAAA
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
86 2 0.03
87 63 0.90
88 5 0.07
ACGTcount: A:0.50, C:0.08, G:0.30, T:0.11
Consensus pattern (87 bp):
AGAGCGACGAAGATGAAAAGTCTAAAAAGAAAAAGAAAGCAGATCATGGAAAGGCTAAAGAAAAA
AAGAGTGACGATGAAGAAAGTA
Found at i:302799 original size:66 final size:66
Alignment explanation
Indices: 302721--303150 Score: 200
Period size: 66 Copynumber: 6.2 Consensus size: 66
302711 GAAGAAAGTA
* * *
302721 AGAGCGACGATGATGAAAAAGCTAAAAAGAAAAAGAGAG-AGAGTCATGGAAAGGGTAAAGAAAA
1 AGAGCGACGATGATGAAAAAACTAAAAAGAAAAAGAAAGCAG-GTCATGGAAAGGCTAAAGAAAA
*
302785 CG
65 AG
* * ** * *
302787 AGAGTGACGATGATGAAAAAATTAAAAAGAAAGGGAAAGCCGGTTATGGAAAGGCTAAAGAAAAA
1 AGAGCGACGATGATGAAAAAACTAAAAAGAAAAAGAAAGCAGGTCATGGAAAGGCTAAAGAAAAA
302852 G
66 G
* * ** * ** * * * ** *
302853 AGAGCGGCGAAGATGAAAAGTCTGAAAAGGGAGAGAAAGCCGATCATTTAAAGGCTAAAAAAAAA
1 AGAGCGACGATGATGAAAAAACTAAAAAGAAAAAGAAAGCAGGTCATGGAAAGGCTAAAGAAAAA
302918 G
66 G
* * *
302919 AGAGTGACAATGAAGAAAGTGAGAACGACGATGATGAAAAAGCTAAAAAGAAAAAG-AGAGTCAG
1 AGAGCGACGATGATG-AA---A-AA--AC--T-A--AAA-AG--AAAAAG--AAAGCAG-GTCA-
* *
302983 TCGTGAAAAGGGTAAA-AGAAACG
47 T-G-G-AAAGGCTAAAGA-AAAAG
* * ** *** *
303006 AGAGTGACGAGGATGAAAAAACTAAAAAGAAAGGGAAAGCCTATCATGGAAATGCTAAAGAAAAA
1 AGAGCGACGATGATGAAAAAACTAAAAAGAAAAAGAAAGCAGGTCATGGAAAGGCTAAAGAAAAA
303071 G
66 G
* * * ** * * * *
303072 AGACCGACGAAGATGAAAAATCTAAAAAGGGAGAGAAAGCCGATCATGTAAAGGCTAAAGAAAAA
1 AGAGCGACGATGATGAAAAAACTAAAAAGAAAAAGAAAGCAGGTCATGGAAAGGCTAAAGAAAAA
303137 G
66 G
* *
303138 AGAGTGATGATGA
1 AGAGCGACGATGA
303151 AGAGAGTGAG
Statistics
Matches: 271, Mismatches: 67, Indels: 52
0.69 0.17 0.13
Matches are distributed among these distances:
66 192 0.71
67 5 0.02
68 1 0.00
69 1 0.00
70 8 0.03
71 1 0.00
72 4 0.01
73 1 0.00
74 2 0.01
75 4 0.01
77 1 0.00
78 4 0.01
79 2 0.01
80 2 0.01
81 3 0.01
82 3 0.01
83 8 0.03
84 1 0.00
86 3 0.01
87 25 0.09
ACGTcount: A:0.51, C:0.09, G:0.28, T:0.12
Consensus pattern (66 bp):
AGAGCGACGATGATGAAAAAACTAAAAAGAAAAAGAAAGCAGGTCATGGAAAGGCTAAAGAAAAA
G
Found at i:302872 original size:219 final size:219
Alignment explanation
Indices: 302508--303194 Score: 1085
Period size: 219 Copynumber: 3.1 Consensus size: 219
302498 AGGGATAGTA
*
302508 ACGATGATGAAAAAGCTAAAAAGAAAAAGAGAGTCAGTCATGAAAAGGGTAAAGAAAACGAAAGT
1 ACGATGATGAAAAAGCTAAAAAGAAAAAGAGAGTCAGTCATGAAAAGGGTAAAGAAAACGAGAGT
**
302573 GACGATGATGAAAAAACTAAAAAGAAAGGGAAAGCCGATCATGGAAAGATTAAAGAAAAAGAGAG
66 GACGATGATGAAAAAACTAAAAAGAAAGGGAAAGCCGATCATGGAAAGGCTAAAGAAAAAGAGAG
302638 CGACGAAGATGAAAAGTCTAAAAAGGGAGAGAAAGCCGATCATGTAAAGGCTAAAGAAAAAAAGA
131 CGACGAAGATGAAAAGTCTAAAAAGGGAGAGAAAGCCGATCATGTAAAGGCTAAAGAAAAAAAGA
* *
302703 GTGGCGATGAAGAAAGTAAGAGCG
196 GTGACGATGAAGAAAGTGAGAGCG
** *
302727 ACGATGATGAAAAAGCTAAAAAGAAAAAGAGAGAGAGTCATGGAAAGGGTAAAGAAAACGAGAGT
1 ACGATGATGAAAAAGCTAAAAAGAAAAAGAGAGTCAGTCATGAAAAGGGTAAAGAAAACGAGAGT
* * *
302792 GACGATGATGAAAAAATTAAAAAGAAAGGGAAAGCCGGTTATGGAAAGGCTAAAGAAAAAGAGAG
66 GACGATGATGAAAAAACTAAAAAGAAAGGGAAAGCCGATCATGGAAAGGCTAAAGAAAAAGAGAG
* * *
302857 CGGCGAAGATGAAAAGTCTGAAAAGGGAGAGAAAGCCGATCATTTAAAGGCTAAA-AAAAAAGAG
131 CGACGAAGATGAAAAGTCTAAAAAGGGAGAGAAAGCCGATCATGTAAAGGCTAAAGAAAAAA-AG
* *
302921 AGTGACAATGAAGAAAGTGAGAACG
195 AGTGACGATGAAGAAAGTGAGAGCG
*
302946 ACGATGATGAAAAAGCTAAAAAGAAAAAGAGAGTCAGTCGTGAAAAGGGTAAA-AGAAACGAGAG
1 ACGATGATGAAAAAGCTAAAAAGAAAAAGAGAGTCAGTCATGAAAAGGGTAAAGA-AAACGAGAG
* * *
303010 TGACGAGGATGAAAAAACTAAAAAGAAAGGGAAAGCCTATCATGGAAATGCTAAAGAAAAAGAGA
65 TGACGATGATGAAAAAACTAAAAAGAAAGGGAAAGCCGATCATGGAAAGGCTAAAGAAAAAGAGA
* * *
303075 CCGACGAAGATGAAAAATCTAAAAAGGGAGAGAAAGCCGATCATGTAAAGGCTAAAGAAAAAGAG
130 GCGACGAAGATGAAAAGTCTAAAAAGGGAGAGAAAGCCGATCATGTAAAGGCTAAAGAAAAAAAG
* *
303140 AGTGATGATGAAGAGAGTGAGAGCG
195 AGTGACGATGAAGAAAGTGAGAGCG
* *
303165 ACGATGATGAAAATG--ATAAAGAAAAAGAGA
1 ACGATGATGAAAAAGCTAAAAAGAAAAAGAGA
303195 ACGACCACGA
Statistics
Matches: 427, Mismatches: 38, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
217 14 0.03
218 7 0.02
219 401 0.94
220 5 0.01
ACGTcount: A:0.52, C:0.08, G:0.28, T:0.12
Consensus pattern (219 bp):
ACGATGATGAAAAAGCTAAAAAGAAAAAGAGAGTCAGTCATGAAAAGGGTAAAGAAAACGAGAGT
GACGATGATGAAAAAACTAAAAAGAAAGGGAAAGCCGATCATGGAAAGGCTAAAGAAAAAGAGAG
CGACGAAGATGAAAAGTCTAAAAAGGGAGAGAAAGCCGATCATGTAAAGGCTAAAGAAAAAAAGA
GTGACGATGAAGAAAGTGAGAGCG
Found at i:303261 original size:33 final size:33
Alignment explanation
Indices: 303224--303318 Score: 111
Period size: 33 Copynumber: 2.9 Consensus size: 33
303214 AAAGAAAACG
* *
303224 GGTCATGCAAAGGATAAGGAAGAAGTGGGA-GCC
1 GGTCATGCAAAGGATAAGGAAGAAG-AGAACGCC
* * *
303257 GGTCATGTAAAGGACAAGGAAGAAGAGAACGGC
1 GGTCATGCAAAGGATAAGGAAGAAGAGAACGCC
**
303290 GGTCATGCAAAGGATAAAAAAGAAGAGAA
1 GGTCATGCAAAGGATAAGGAAGAAGAGAA
303319 TGCCAATCAT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
32 2 0.04
33 50 0.96
ACGTcount: A:0.44, C:0.11, G:0.35, T:0.11
Consensus pattern (33 bp):
GGTCATGCAAAGGATAAGGAAGAAGAGAACGCC
Found at i:305973 original size:33 final size:33
Alignment explanation
Indices: 305928--305992 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
305918 GAAAAAGGAA
305928 GTGCGGATGATGAAAAGCA-TAAAGAAAAAGAGG
1 GTGCGGATGATGAAAAG-ATTAAAGAAAAAGAGG
*
305961 GTGCTGGA-GATGAGAAGATTAAAGAAAAAGAG
1 GTGC-GGATGATGAAAAGATTAAAGAAAAAGAG
305993 AGCGACGAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 1 0.03
33 25 0.86
34 3 0.10
ACGTcount: A:0.48, C:0.05, G:0.34, T:0.14
Consensus pattern (33 bp):
GTGCGGATGATGAAAAGATTAAAGAAAAAGAGG
Found at i:306045 original size:66 final size:67
Alignment explanation
Indices: 305975--306553 Score: 565
Period size: 66 Copynumber: 8.8 Consensus size: 67
305965 TGGAGATGAG
* *
305975 AAGATTAAAGAAAAAGAGAGCGACGAGGATGAAAAAG-CTAAGAAGAAAGGGAGAGCCGATCATG
1 AAGATTAAAGAAAAAGAGAGCGACGAGGATGAAAAAGTCTAAGAAGAAAGAGAAAGCCGATCATG
306039 GA
66 GA
* * * * * * * *
306041 AAGATTAAAGAAAAAGAGAGTGAAGATGACG-AAAAGTTTAAAAAGAGAGAGAAAGCCGATCATA
1 AAGATTAAAGAAAAAGAGAGCGACGAGGATGAAAAAGTCTAAGAAGAAAGAGAAAGCCGATCATG
306105 GA
66 GA
* * * * * *
306107 AAGGA-TAAAGAAAAAGAGAGCGACGAGGATGAAAAA-ACTAAGAAGAATGGGAGAGCCGGTCAC
1 AA-GATTAAAGAAAAAGAGAGCGACGAGGATGAAAAAGTCTAAGAAGAAAGAGAAAGCCGATCAT
*
306170 GGT
65 GGA
* * * *
306173 AAGATTAAAGAAAAAAATAGCGAAGATGATG-AAAAGTCTAA-AACGAAAGAGAAAGCCGATCAT
1 AAGATTAAAGAAAAAGAGAGCGACGAGGATGAAAAAGTCTAAGAA-GAAAGAGAAAGCCGATCAT
**
306236 ATAA
65 -GGA
* * * * * *
306240 AAGA-TAAAGAAAAAGAGATCGACGAGGATGAAAAA-ACTAAGAAAAAAGGGAGAGCCGGTCATG
1 AAGATTAAAGAAAAAGAGAGCGACGAGGATGAAAAAGTCTAAGAAGAAAGAGAAAGCCGATCATG
306303 GA
66 GA
* * * * *
306305 AAGATTAAAGAAAAAGAGAGCGAAGATGACG-AAAAGTCTAAAAAGAAAGAGAAAGCCGATCATA
1 AAGATTAAAGAAAAAGAGAGCGACGAGGATGAAAAAGTCTAAGAAGAAAGAGAAAGCCGATCATG
*
306369 AA
66 GA
* * * * *
306371 AAGAATAAAGAAATAGAGAGCGACGAGGATGAAAAAG-CTAAGAAGAAATG-GACAGTCGGTCAT
1 AAGATTAAAGAAAAAGAGAGCGACGAGGATGAAAAAGTCTAAGAAGAAA-GAGAAAGCCGATCAT
306434 GGA
65 GGA
* * * * *
306437 AAGATTAAAGAAAAAGAGAGCGAAGATGACG-AAAAGTCTAAAAAGAAAGAGAAAGCCGATCATA
1 AAGATTAAAGAAAAAGAGAGCGACGAGGATGAAAAAGTCTAAGAAGAAAGAGAAAGCCGATCATG
306501 GA
66 GA
* * * * *
306503 AAGAATAAAGAAAAAGAGAACGACAAAGATGAAAAGAGT-AAAGAA-AAAGAG
1 AAGATTAAAGAAAAAGAGAGCGACGAGGATGAAAA-AGTCTAAGAAGAAAGAG
306554 GACGACCATG
Statistics
Matches: 405, Mismatches: 91, Indels: 34
0.76 0.17 0.06
Matches are distributed among these distances:
65 28 0.07
66 345 0.85
67 29 0.07
68 3 0.01
ACGTcount: A:0.54, C:0.08, G:0.27, T:0.11
Consensus pattern (67 bp):
AAGATTAAAGAAAAAGAGAGCGACGAGGATGAAAAAGTCTAAGAAGAAAGAGAAAGCCGATCATG
GA
Done.