Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008373.1 Hibiscus syriacus cultivar Beakdansim tig00111129_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: 1027749
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:731 original size:36 final size:36
Alignment explanation
Indices: 684--755 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
674 CCTAGCATTC
*
684 GCCAAGAACCAGATTCGGATCCTGTTGCCTCTGAAA
1 GCCAAGAACCAGATTCGGATCCTGTTGCATCTGAAA
*
720 GCCAAGAACCAGATTCGGATCTTGTTGCATCTGAAA
1 GCCAAGAACCAGATTCGGATCCTGTTGCATCTGAAA
756 TAGAAGGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (36 bp):
GCCAAGAACCAGATTCGGATCCTGTTGCATCTGAAA
Found at i:5402 original size:14 final size:14
Alignment explanation
Indices: 5383--5409 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5373 GGTACCGTAC
5383 ATGTGCTATTTATA
1 ATGTGCTATTTATA
5397 ATGTGCTATTTAT
1 ATGTGCTATTTAT
5410 CTTGGGTCGA
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:0.26, C:0.07, G:0.15, T:0.52
Consensus pattern (14 bp):
ATGTGCTATTTATA
Found at i:13990 original size:6 final size:6
Alignment explanation
Indices: 13979--14015 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
13969 AGTTAATTAA
13979 AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG A
1 AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG A
14016 GTGGTAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
AAGGGG
Found at i:16559 original size:20 final size:20
Alignment explanation
Indices: 16521--16561 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
16511 AAAATTTATG
*
16521 AAATTTAATTTGAATTATTT
1 AAATTTAATTTGAAATATTT
16541 AAATTTAATTAT-AAATATTT
1 AAATTTAATT-TGAAATATTT
16561 A
1 A
16562 TAATGTTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
AAATTTAATTTGAAATATTT
Found at i:18261 original size:2 final size:2
Alignment explanation
Indices: 18244--18282 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
18234 TTTACTCGTC
*
18244 TA TA TT TA TA -A 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
18283 AATCATTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20548 original size:16 final size:16
Alignment explanation
Indices: 20518--20560 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
20508 ATCATGAATT
20518 TTTAAATACATATTTAA
1 TTTAAATA-ATATTTAA
*
20535 TTTAAATAATATTTCA
1 TTTAAATAATATTTAA
*
20551 TTAAAATAAT
1 TTTAAATAAT
20561 TACTTGATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTAAATAATATTTAA
Found at i:21176 original size:21 final size:20
Alignment explanation
Indices: 21152--21191 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
21142 TATCATTTTG
*
21152 TAAAAAAATAATATTTAAAAA
1 TAAAAAAATAA-ATGTAAAAA
*
21173 TAAAAATATAAATGTAAAA
1 TAAAAAAATAAATGTAAAA
21192 TATATTTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (20 bp):
TAAAAAAATAAATGTAAAAA
Found at i:24833 original size:16 final size:16
Alignment explanation
Indices: 24812--24843 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
24802 AATAAATAAG
24812 CGAACATAAACGAACA
1 CGAACATAAACGAACA
24828 CGAACATAAACGAACA
1 CGAACATAAACGAACA
24844 AATTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.25, G:0.12, T:0.06
Consensus pattern (16 bp):
CGAACATAAACGAACA
Found at i:24937 original size:16 final size:16
Alignment explanation
Indices: 24913--24973 Score: 104
Period size: 16 Copynumber: 3.8 Consensus size: 16
24903 TAATAAATAA
24913 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
24929 ACAAACATAAACGAAC
1 ACGAACATAAACGAAC
*
24945 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
24961 ACGAACATAAACG
1 ACGAACATAAACG
24974 TTGGAGACCC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.57, C:0.23, G:0.11, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:26522 original size:24 final size:24
Alignment explanation
Indices: 26485--26540 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
26475 TATTAGGTTA
* * *
26485 AACATAAATGAACGCACATAAACG
1 AACATAACTAAACGAACATAAACG
*
26509 AACATAACTAAACGAATATAAACG
1 AACATAACTAAACGAACATAAACG
26533 AACATAAC
1 AACATAAC
26541 CGAACGTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.57, C:0.20, G:0.09, T:0.14
Consensus pattern (24 bp):
AACATAACTAAACGAACATAAACG
Found at i:28351 original size:29 final size:31
Alignment explanation
Indices: 28283--28348 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 31
28273 TGTTCAAAGT
* *
28283 TTGGCCACCAACCAAGATGAAATTTCTAATAAG
1 TTGGCCACCAACCAAGATGAAATTTC--ACAAC
28316 TTGGCCACCAACCAAGATGAAATTTC-CAAC
1 TTGGCCACCAACCAAGATGAAATTTCACAAC
28346 TTG
1 TTG
28349 CCAACTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 5 0.16
33 26 0.84
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.24
Consensus pattern (31 bp):
TTGGCCACCAACCAAGATGAAATTTCACAAC
Found at i:39599 original size:30 final size:30
Alignment explanation
Indices: 39565--39668 Score: 73
Period size: 30 Copynumber: 3.2 Consensus size: 30
39555 AGAAGTTAAT
39565 TGGGATGCTCTTCTATGTTTCTTAGCCATG
1 TGGGATGCTCTTCTATGTTTCTTAGCCATG
* * * * * *
39595 TGGGATTGTTTTATTCTCATATTTTCTCTTTAGACTTT
1 TGGGA-TG--CT-CT-TC-TATGTT-TC-TTAGCCATG
*
39633 TGGGATGCTCTTCTATGTTTTTTAGCCATG
1 TGGGATGCTCTTCTATGTTTCTTAGCCATG
39663 TGGGAT
1 TGGGAT
39669 TGTTTTTAAA
Statistics
Matches: 53, Mismatches: 13, Indels: 16
0.65 0.16 0.20
Matches are distributed among these distances:
30 17 0.32
31 3 0.06
32 5 0.09
33 3 0.06
34 2 0.04
35 3 0.06
36 5 0.09
37 4 0.08
38 11 0.21
ACGTcount: A:0.14, C:0.15, G:0.21, T:0.49
Consensus pattern (30 bp):
TGGGATGCTCTTCTATGTTTCTTAGCCATG
Found at i:40695 original size:25 final size:25
Alignment explanation
Indices: 40632--40698 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
40622 GCAACTTTTG
*
40632 AAAAGTGACTTTTAAAAGTGTTGTA
1 AAAAGTGTCTTTTAAAAGTGTTGTA
**
40657 AAAACGAAT-TTTTAAAAGTGTTGTA
1 AAAA-GTGTCTTTTAAAAGTGTTGTA
*
40682 AAAAGTGTCGTTTAAAA
1 AAAAGTGTCTTTTAAAA
40699 TTTAACTATT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
24 2 0.06
25 31 0.91
26 1 0.03
ACGTcount: A:0.43, C:0.04, G:0.18, T:0.34
Consensus pattern (25 bp):
AAAAGTGTCTTTTAAAAGTGTTGTA
Found at i:51897 original size:21 final size:20
Alignment explanation
Indices: 51859--51938 Score: 106
Period size: 20 Copynumber: 4.0 Consensus size: 20
51849 CAGATTGCCT
51859 AGGGGGTACAGATTCCCCCC
1 AGGGGGTACAGATTCCCCCC
* *
51879 AAGGGGTACAGATTCCCCCT
1 AGGGGGTACAGATTCCCCCC
*
51899 AGGGGGAACAGATTCCCCCCC
1 AGGGGGTACAGATT-CCCCCC
**
51920 AGGGGGTATTGATTCCCCC
1 AGGGGGTACAGATTCCCCC
51939 ATGTCTAACG
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 35 0.69
21 16 0.31
ACGTcount: A:0.21, C:0.33, G:0.29, T:0.17
Consensus pattern (20 bp):
AGGGGGTACAGATTCCCCCC
Found at i:51902 original size:40 final size:41
Alignment explanation
Indices: 51856--51938 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
51846 AATCAGATTG
*
51856 CCTAGGGGGTACAGATT-CCCCCCAAGGGGTACAGATTCCC
1 CCTAGGGGGAACAGATTCCCCCCCAAGGGGTACAGATTCCC
* **
51896 CCTAGGGGGAACAGATTCCCCCCCAGGGGGTATTGATTCCC
1 CCTAGGGGGAACAGATTCCCCCCCAAGGGGTACAGATTCCC
51937 CC
1 CC
51939 ATGTCTAACG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
40 16 0.42
41 22 0.58
ACGTcount: A:0.20, C:0.34, G:0.28, T:0.18
Consensus pattern (41 bp):
CCTAGGGGGAACAGATTCCCCCCCAAGGGGTACAGATTCCC
Found at i:52334 original size:35 final size:33
Alignment explanation
Indices: 52285--52357 Score: 83
Period size: 35 Copynumber: 2.2 Consensus size: 33
52275 CCTTTTGTAA
* * * *
52285 AGGGGAAATGTTCTAGCTTATCCCGTGTAAAATCT
1 AGGGAAAAAGTTCTAGCTTAGCCCG-G-AAAAACT
*
52320 AGGGAAAAAGTTCTAGTTTAGCCCGGAAAAACT
1 AGGGAAAAAGTTCTAGCTTAGCCCGGAAAAACT
52353 AGGGA
1 AGGGA
52358 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
33 11 0.33
34 1 0.03
35 21 0.64
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (33 bp):
AGGGAAAAAGTTCTAGCTTAGCCCGGAAAAACT
Found at i:53240 original size:19 final size:20
Alignment explanation
Indices: 53216--53263 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
53206 AATGATTTTC
*
53216 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
53235 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
53255 TTTTGAAAA
1 TTTTGAAAA
53264 ATGATTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:55183 original size:2 final size:2
Alignment explanation
Indices: 55176--55205 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
55166 ATTTGTTTCA
*
55176 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55206 GTAACCCACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:55973 original size:12 final size:12
Alignment explanation
Indices: 55948--56017 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
55938 ACGGAGATAT
* *
55948 CAGAAATCAAAA
1 CAGAATTCAGAA
55960 CAGAATTCAGAA
1 CAGAATTCAGAA
55972 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
55984 CAAAATCCA-AA
1 CAGAATTCAGAA
*
55995 TCAGAAATCAGAA
1 -CAGAATTCAGAA
*
56008 TAGAATTCAG
1 CAGAATTCAG
56018 GTCATGTATC
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
11 4 0.09
12 37 0.82
13 4 0.09
ACGTcount: A:0.54, C:0.17, G:0.13, T:0.16
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:55975 original size:24 final size:25
Alignment explanation
Indices: 55946--56017 Score: 85
Period size: 24 Copynumber: 3.0 Consensus size: 25
55936 AAACGGAGAT
*
55946 ATCAGAAATCAAAACAGAATTCAGA
1 ATCAGAAATCAGAACAGAATTCAGA
* * *
55971 A-CAGATATCAGAACAAAATCCA-A
1 ATCAGAAATCAGAACAGAATTCAGA
*
55994 ATCAGAAATCAGAATAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
56018 GTCATGTATC
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
23 2 0.05
24 34 0.92
25 1 0.03
ACGTcount: A:0.54, C:0.17, G:0.12, T:0.17
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAGA
Found at i:56054 original size:48 final size:48
Alignment explanation
Indices: 55946--56037 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
55936 AAACGGAGAT
*
55946 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAAAATCCAA
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAAAATCCAA
* **
55994 ATCAGAAATCAGAATAGAATTCAGGTCATG-TATCAGAACAAAAT
1 ATCAGAAATCAGAACAGAATTCAGAACA-GATATCAGAACAAAAT
56038 TCAAGTTGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 38 0.97
49 1 0.03
ACGTcount: A:0.52, C:0.16, G:0.13, T:0.18
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAAAATCCAA
Found at i:68892 original size:22 final size:22
Alignment explanation
Indices: 68866--68909 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
68856 CTCTATTTCA
*
68866 ACATGACGACCTTCAAGCATAG
1 ACATGACGACCTTCAAACATAG
68888 ACATGACGACCTTCAAACATAG
1 ACATGACGACCTTCAAACATAG
68910 CAATTACCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.27, G:0.16, T:0.18
Consensus pattern (22 bp):
ACATGACGACCTTCAAACATAG
Found at i:71543 original size:30 final size:30
Alignment explanation
Indices: 71498--71599 Score: 127
Period size: 30 Copynumber: 3.5 Consensus size: 30
71488 ACCCAAAAAT
*
71498 AAAAGTTGGGTACCTATTTGCACCATTAAA
1 AAAAGTTAGGTACCTATTTGCACCATTAAA
* *
71528 AAAGGTTATGTACCTATTTGCACCATTAAA
1 AAAAGTTAGGTACCTATTTGCACCATTAAA
* * *
71558 AAAAGTTAGGTGCCTAATTGCA-CA-CAAA
1 AAAAGTTAGGTACCTATTTGCACCATTAAA
*
71586 AAAAGTTGGGTACC
1 AAAAGTTAGGTACC
71600 ACATTACACA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
28 15 0.24
29 2 0.03
30 45 0.73
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (30 bp):
AAAAGTTAGGTACCTATTTGCACCATTAAA
Found at i:71609 original size:28 final size:28
Alignment explanation
Indices: 71555--71609 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
71545 TTGCACCATT
* *
71555 AAAAAAAGTTAGGTGCCTAATTGCACAC
1 AAAAAAAGTTAGGTACCTAATTACACAC
*
71583 AAAAAAAGTTGGGTACC-ACATTACACA
1 AAAAAAAGTTAGGTACCTA-ATTACACA
71610 TAAATGCCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 1 0.04
28 22 0.96
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.20
Consensus pattern (28 bp):
AAAAAAAGTTAGGTACCTAATTACACAC
Found at i:78788 original size:85 final size:84
Alignment explanation
Indices: 78624--78788 Score: 183
Period size: 85 Copynumber: 2.0 Consensus size: 84
78614 GAGATTTATA
* * * * *
78624 ATTTATAAAATAATAGATTCATATAAATGACTAATAATACCCACCAGAAAGCAAAACTCGAGGCT
1 ATTTATAAAATAATAAATTCATATAAATGACTAATAATACCAACAAAAAACCAAAACTCGAGGCT
* *
78689 CTTACTTATTTGTCCCCCC
66 CTTAATTATATGTCCCCCC
* * *
78708 ATTTTTAAAAGTAATAAATTCATATAAATGACTAATCATACCTAACAAAAAAACCAATA-TC-AG
1 ATTTATAAAA-TAATAAATTCATATAAATGACTAATAATACC-AAC-AAAAAACCAAAACTCGAG
78771 GCTC-TAATTCATATGTCC
63 GCTCTTAATT-ATATGTCC
78789 TAAAGGGTGA
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
84 13 0.19
85 42 0.63
86 4 0.06
87 8 0.12
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (84 bp):
ATTTATAAAATAATAAATTCATATAAATGACTAATAATACCAACAAAAAACCAAAACTCGAGGCT
CTTAATTATATGTCCCCCC
Found at i:80715 original size:20 final size:20
Alignment explanation
Indices: 80677--80715 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
80667 TCTCGTATTA
* *
80677 TTCACATCAATTAAGATAAT
1 TTCAAATCAAGTAAGATAAT
*
80697 TTCAAATCAAGTAATATAA
1 TTCAAATCAAGTAAGATAA
80716 AGATATCTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.33
Consensus pattern (20 bp):
TTCAAATCAAGTAAGATAAT
Found at i:83915 original size:71 final size:71
Alignment explanation
Indices: 83835--83967 Score: 198
Period size: 71 Copynumber: 1.9 Consensus size: 71
83825 CGGCCACAAT
83835 TAAAGGATTTAA-AACTATAAAGGGGCTTTGGTTTTTGCGCCCCAGACATT-GAGTTATGGTGGG
1 TAAAGGATTTAACAA-TATAAAGGGGCTTTGGTTTTTGCGCCCCAGAC-TTAGAGTTATGGTGGG
83898 CGTTTAAA
64 CGTTTAAA
* * * *
83906 TAAAGGATTTAACAATATAATGGGGCTTTGGTTTTTGCTCTCCAGACTTAGAGTTTTGGTGG
1 TAAAGGATTTAACAATATAAAGGGGCTTTGGTTTTTGCGCCCCAGACTTAGAGTTATGGTGG
83968 TTCTGCGCAT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
70 2 0.04
71 52 0.93
72 2 0.04
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.35
Consensus pattern (71 bp):
TAAAGGATTTAACAATATAAAGGGGCTTTGGTTTTTGCGCCCCAGACTTAGAGTTATGGTGGGCG
TTTAAA
Found at i:85364 original size:12 final size:12
Alignment explanation
Indices: 85347--85413 Score: 81
Period size: 12 Copynumber: 5.9 Consensus size: 12
85337 GAGTTAAAAT
85347 AAATTATTAATA
1 AAATTATTAATA
85359 AAATTATTAATA
1 AAATTATTAATA
*
85371 AAATTATAAATA
1 AAATTATTAATA
85383 AAA-TATT--T-
1 AAATTATTAATA
85391 AAATTATATAA-A
1 AAATTAT-TAATA
85403 AAATTATTAAT
1 AAATTATTAAT
85414 TTTTTAAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
8 3 0.06
9 4 0.09
10 1 0.02
11 6 0.13
12 33 0.70
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATTATTAATA
Found at i:85412 original size:20 final size:20
Alignment explanation
Indices: 85346--85412 Score: 55
Period size: 23 Copynumber: 3.1 Consensus size: 20
85336 AGAGTTAAAA
85346 TAAATTAT-TAATAAAATTAT
1 TAAATTATATAA-AAAATTAT
** *
85366 TAATAAAATTATAAATAAAATATT
1 TAA-ATTA-TATAAA-AAATTA-T
85390 TAAATTATATAAAAAATTAT
1 TAAATTATATAAAAAATTAT
85410 TAA
1 TAA
85413 TTTTTTAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
20 7 0.19
21 7 0.19
22 8 0.22
23 10 0.28
24 4 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAATTATATAAAAAATTAT
Found at i:93298 original size:15 final size:15
Alignment explanation
Indices: 93278--93342 Score: 89
Period size: 15 Copynumber: 4.5 Consensus size: 15
93268 CAACTCGTTT
93278 AGTCAACTCAGACAG
1 AGTCAACTCAGACAG
93293 AGTCAACTCAGACAG
1 AGTCAACTCAGACAG
**
93308 AGTCAACTC-G-TTG
1 AGTCAACTCAGACAG
*
93321 AGTCAACTTAGACAG
1 AGTCAACTCAGACAG
93336 AGTCAAC
1 AGTCAAC
93343 CCGTTGACTT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
13 9 0.21
14 2 0.05
15 32 0.74
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (15 bp):
AGTCAACTCAGACAG
Found at i:93323 original size:28 final size:28
Alignment explanation
Indices: 93292--93349 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
93282 AACTCAGACA
*
93292 GAGTCAACTCAGACAGAGTCAACTCGTT
1 GAGTCAACTCAGACAGAGTCAACCCGTT
*
93320 GAGTCAACTTAGACAGAGTCAACCCGTT
1 GAGTCAACTCAGACAGAGTCAACCCGTT
93348 GA
1 GA
93350 CTTTGACTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.21
Consensus pattern (28 bp):
GAGTCAACTCAGACAGAGTCAACCCGTT
Found at i:94291 original size:18 final size:17
Alignment explanation
Indices: 94268--94301 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
94258 AAAAAATGAC
*
94268 TAAAATATCCCTAAAGTG
1 TAAAATAACCC-AAAGTG
94286 TAAAATAACCCAAAGT
1 TAAAATAACCCAAAGT
94302 ACTTCCAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.18, G:0.09, T:0.24
Consensus pattern (17 bp):
TAAAATAACCCAAAGTG
Found at i:96566 original size:23 final size:23
Alignment explanation
Indices: 96513--96568 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
96503 ATTAATGTAC
* * * *
96513 TTCGGGACAATTCTATGTGGTCC
1 TTCGAGACAATTATACGTGGTCA
* *
96536 TTCAAGACAATTATACGTTGTCA
1 TTCGAGACAATTATACGTGGTCA
96559 TTCGAGACAA
1 TTCGAGACAA
96569 ATTTTACGCG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (23 bp):
TTCGAGACAATTATACGTGGTCA
Found at i:97921 original size:43 final size:43
Alignment explanation
Indices: 97873--98100 Score: 230
Period size: 43 Copynumber: 5.3 Consensus size: 43
97863 AGGTAACGAT
* * *
97873 ATTTAGCGGCGTTTGTCTTACAAATTCCGTAATAGGTGTTGAG
1 ATTTAGCGGCGTTTTTCTTACAAACTCCGCAATAGGTGTTGAG
* * * *
97916 GTTTAGCGGC-TTTTTCCTACAAACGCTGCAATAGGTGTTGAG
1 ATTTAGCGGCGTTTTTCTTACAAACTCCGCAATAGGTGTTGAG
* * * *
97958 ATTTAGCGGCATTTTT-TCACAAACTACGCAATAGGTTTTGAG
1 ATTTAGCGGCGTTTTTCTTACAAACTCCGCAATAGGTGTTGAG
* * * *
98000 ATTTAGGGGCGTTTTTCTCACAAACGT-CACAATAGGTATTGAG
1 ATTTAGCGGCGTTTTTCTTACAAAC-TCCGCAATAGGTGTTGAG
* ** *
98043 ATTTAGCGACGTTTTTCAAATAAA-TGCCGCAATAGGTGTTGAG
1 ATTTAGCGGCGTTTTTCTTACAAACT-CCGCAATAGGTGTTGAG
*
98086 ATTTAGTGGCGTTTT
1 ATTTAGCGGCGTTTT
98101 CCCCACAAAC
Statistics
Matches: 153, Mismatches: 27, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
41 1 0.01
42 69 0.45
43 82 0.54
44 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (43 bp):
ATTTAGCGGCGTTTTTCTTACAAACTCCGCAATAGGTGTTGAG
Found at i:97951 original size:85 final size:85
Alignment explanation
Indices: 97851--98110 Score: 258
Period size: 85 Copynumber: 3.0 Consensus size: 85
97841 TGGTAACAAA
* ** * *
97851 AAACGCCGCAATAGGTAACGATATTTAGCGGCGTTTGTCTTACAAATTCCGTAATAGGTGTTGAG
1 AAACGCTGCAATAGGTATTGAGATTTAGCGGCGTTT-TCTTACAAATTCCGCAATAGGTGTTGAG
*
97916 GTTTAGCGGCTTTTTCCT-AC
65 ATTTAGCGGCTTTTTCCTCAC
* * * * *
97936 AAACGCTGCAATAGGTGTTGAGATTTAGCGGCATTTT-TTCACAAACTACGCAATAGGTTTTGAG
1 AAACGCTGCAATAGGTATTGAGATTTAGCGGCGTTTTCTT-ACAAATTCCGCAATAGGTGTTGAG
*
98000 ATTTAGGGGCGTTTTT-CTCAC
65 ATTTAGCGGC-TTTTTCCTCAC
* * ** * *
98021 AAACG-TCACAATAGGTATTGAGATTTAGCGACGTTTTTCAAATAAATGCCGCAATAGGTGTTGA
1 AAACGCT-GCAATAGGTATTGAGATTTAGCGGCG-TTTTCTTACAAATTCCGCAATAGGTGTTGA
* * *
98085 GATTTAGTGGCGTTTTCCCCAC
64 GATTTAGCGGCTTTTTCCTCAC
98107 AAAC
1 AAAC
98111 ATCATAAAAT
Statistics
Matches: 142, Mismatches: 26, Indels: 13
0.78 0.14 0.07
Matches are distributed among these distances:
83 2 0.01
84 32 0.23
85 68 0.48
86 40 0.28
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (85 bp):
AAACGCTGCAATAGGTATTGAGATTTAGCGGCGTTTTCTTACAAATTCCGCAATAGGTGTTGAGA
TTTAGCGGCTTTTTCCTCAC
Found at i:98639 original size:23 final size:21
Alignment explanation
Indices: 98609--98666 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
98599 GCTGATATGT
* *
98609 TGCTTCTCTCTGTGCTGTCGC
1 TGCTTCTCTCTGTACTGCCGC
98630 TGCTTCTCTCTGTACTGCCGC
1 TGCTTCTCTCTGTACTGCCGC
* *
98651 TGTTTCTCTCTCTACT
1 TGCTTCTCTCTGTACT
98667 TCTGTTGCTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.03, C:0.34, G:0.17, T:0.45
Consensus pattern (21 bp):
TGCTTCTCTCTGTACTGCCGC
Found at i:104366 original size:18 final size:17
Alignment explanation
Indices: 104343--104379 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
104333 TATCAAAATG
104343 AAATAAGACAACAATACA
1 AAATAAGACAACAA-ACA
104361 AAATAAGACAACAAACA
1 AAATAAGACAACAAACA
104378 AA
1 AA
104380 CTAAACCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.70, C:0.16, G:0.05, T:0.08
Consensus pattern (17 bp):
AAATAAGACAACAAACA
Found at i:114808 original size:22 final size:22
Alignment explanation
Indices: 114734--114800 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
114724 TATAAATCTT
114734 TGATGTAATATATATTACACAG
1 TGATGTAATATATATTACACAG
114756 TGATGTAATATATATTACACAG
1 TGATGTAATATATATTACACAG
114778 TGATGTAATATATATTACACAG
1 TGATGTAATATATATTACACAG
114800 T
1 T
114801 AATATAATGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.37
Consensus pattern (22 bp):
TGATGTAATATATATTACACAG
Found at i:116937 original size:17 final size:17
Alignment explanation
Indices: 116917--116992 Score: 75
Period size: 17 Copynumber: 4.4 Consensus size: 17
116907 TGCAAGCTTA
*
116917 AATGAGCTAGTTTAATT
1 AATGAACTAGTTTAATT
*
116934 AATGAA-TCAGTTTAAATG
1 AATGAACT-AGTTT-AATT
116952 AATGAACTAGTTTAATT
1 AATGAACTAGTTTAATT
*
116969 ACTGAACTAGCTTT-ATT
1 AATGAACTAG-TTTAATT
116986 GAATGAA
1 -AATGAA
116993 AAATCATACT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
16 1 0.02
17 25 0.51
18 22 0.45
19 1 0.02
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (17 bp):
AATGAACTAGTTTAATT
Found at i:116957 original size:18 final size:18
Alignment explanation
Indices: 116917--116992 Score: 61
Period size: 18 Copynumber: 4.3 Consensus size: 18
116907 TGCAAGCTTA
* *
116917 AATGAGCTAGTTT-AATT
1 AATGAACTAGTTTAAATG
116934 AATGAA-TCAGTTTAAATG
1 AATGAACT-AGTTTAAATG
*
116952 AATGAACTAGTTT-AATT
1 AATGAACTAGTTTAAATG
* *
116969 ACTGAACTAGCTTT-ATTG
1 AATGAACTAG-TTTAAATG
116987 AATGAA
1 AATGAA
116993 AAATCATACT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
16 1 0.02
17 22 0.46
18 24 0.50
19 1 0.02
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (18 bp):
AATGAACTAGTTTAAATG
Found at i:119253 original size:25 final size:26
Alignment explanation
Indices: 119185--119254 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 26
119175 TTATTTTGGG
*
119185 TTTAAAGTTTAAGGTTTAAATGTATGA
1 TTTAAAGATTAAGGTTT-AATGTATGA
* *
119212 TAT-AAGATTTAGGGTTTAA-GTATGA
1 TTTAAAGA-TTAAGGTTTAATGTATGA
*
119237 TTTAAAGATTAAAGTTTA
1 TTTAAAGATTAAGGTTTA
119255 GGATTTAGGA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
25 16 0.46
26 9 0.26
27 10 0.29
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.43
Consensus pattern (26 bp):
TTTAAAGATTAAGGTTTAATGTATGA
Found at i:138542 original size:20 final size:20
Alignment explanation
Indices: 138517--138741 Score: 140
Period size: 20 Copynumber: 11.3 Consensus size: 20
138507 CCCATGCTCT
* * *
138517 AAAATCTAGCTTCAAACCTA
1 AAAATCAAGTTTCCAACCTA
138537 AAAATCCAA--TTCTCAACCTA
1 AAAAT-CAAGTTTC-CAACCTA
* **
138557 ATAATC-AGTTTTTAACCTA
1 AAAATCAAGTTTCCAACCTA
*
138576 AAAATCAAGTTTCCAACTTA
1 AAAATCAAGTTTCCAACCTA
**
138596 AAAATCAAGTTTTTAACCTA
1 AAAATCAAGTTTCCAACCTA
** *
138616 AAAATTGAGGTTCCAACCTA
1 AAAATCAAGTTTCCAACCTA
* * *
138636 AAAATCAGGTATCCAA-CTC
1 AAAATCAAGTTTCCAACCTA
* *
138655 AAAATC-AGCTTT-TAACATA
1 AAAATCAAG-TTTCCAACCTA
* * *
138674 AAAATTCATGTTTTCAACTTA
1 AAAA-TCAAGTTTCCAACCTA
* *
138695 AAAATC-AGGTTCCAACCCA
1 AAAATCAAGTTTCCAACCTA
* *
138714 AAAATTCAGGTTTCCAACTTA
1 AAAA-TCAAGTTTCCAACCTA
138735 AAAATCA
1 AAAATCA
138742 GATTCAAATC
Statistics
Matches: 153, Mismatches: 40, Indels: 24
0.71 0.18 0.11
Matches are distributed among these distances:
18 4 0.03
19 42 0.27
20 82 0.54
21 25 0.16
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (20 bp):
AAAATCAAGTTTCCAACCTA
Found at i:138651 original size:60 final size:58
Alignment explanation
Indices: 138570--138710 Score: 167
Period size: 59 Copynumber: 2.4 Consensus size: 58
138560 ATCAGTTTTT
* * * *
138570 AACCTAAAAATCAAGTTTCCAACTTAAAAATCAAGTTTTTAACCTAAAAATTGA-GGTTCC
1 AACCTAAAAATC-AGGTTCCAAC-TAAAAATC-AGCTTTTAACATAAAAATTCATGGTTCC
* * *
138630 AACCTAAAAATCAGGTATCCAACTCAAAATCAGCTTTTAACATAAAAATTCATGTTTTC
1 AACCTAAAAATCAGGT-TCCAACTAAAAATCAGCTTTTAACATAAAAATTCATGGTTCC
*
138689 AACTTAAAAATCAGGTTCCAAC
1 AACCTAAAAATCAGGTTCCAAC
138711 CCAAAAATTC
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
58 24 0.34
59 29 0.41
60 18 0.25
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (58 bp):
AACCTAAAAATCAGGTTCCAACTAAAAATCAGCTTTTAACATAAAAATTCATGGTTCC
Found at i:138659 original size:79 final size:79
Alignment explanation
Indices: 138576--138742 Score: 196
Period size: 79 Copynumber: 2.1 Consensus size: 79
138566 TTTTAACCTA
* * * *
138576 AAAATCAAG-TTTCCAACTTAAAAA-TCAAGTTTTTAACCTAAAAATTGAGGTTCCAACCTAAAA
1 AAAATC-AGCTTT-CAACATAAAAATTCAAGTTTTCAACCTAAAAA-TCAGGTTCCAACCCAAAA
138639 A-TCAGGTATCCAACTC
63 ATTCAGGTATCCAACTC
* * *
138655 AAAATCAGCTTTTAACATAAAAATTCATGTTTTCAACTTAAAAATCAGGTTCCAACCCAAAAATT
1 AAAATCAGCTTTCAACATAAAAATTCAAGTTTTCAACCTAAAAATCAGGTTCCAACCCAAAAATT
* *
138720 CAGGTTTCCAACTTA
66 CAGGTATCCAAC-TC
138735 AAAATCAG
1 AAAATCAG
138743 ATTCAAATCT
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
78 28 0.37
79 38 0.51
80 9 0.12
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (79 bp):
AAAATCAGCTTTCAACATAAAAATTCAAGTTTTCAACCTAAAAATCAGGTTCCAACCCAAAAATT
CAGGTATCCAACTC
Found at i:138742 original size:20 final size:20
Alignment explanation
Indices: 138550--138742 Score: 153
Period size: 20 Copynumber: 9.8 Consensus size: 20
138540 ATCCAATTCT
* *
138550 CAACCTAATAATCA-GTTTT
1 CAACCTAAAAATCAGGTTTC
* *
138569 TAACCTAAAAATCAAGTTTC
1 CAACCTAAAAATCAGGTTTC
* * *
138589 CAACTTAAAAATCAAGTTTT
1 CAACCTAAAAATCAGGTTTC
* *
138609 TAACCTAAAAATTGAGG-TTC
1 CAACCTAAAAA-TCAGGTTTC
*
138629 CAACCTAAAAATCAGGTATC
1 CAACCTAAAAATCAGGTTTC
* *
138649 CAA-CTCAAAATCAGCTTT-
1 CAACCTAAAAATCAGGTTTC
* * * *
138667 TAACATAAAAATTCATGTTTT
1 CAACCTAAAAA-TCAGGTTTC
*
138688 CAACTTAAAAATCAGG-TTC
1 CAACCTAAAAATCAGGTTTC
*
138707 CAACCCAAAAATTCAGGTTTC
1 CAACCTAAAAA-TCAGGTTTC
*
138728 CAACTTAAAAATCAG
1 CAACCTAAAAATCAG
138743 ATTCAAATCT
Statistics
Matches: 136, Mismatches: 30, Indels: 15
0.75 0.17 0.08
Matches are distributed among these distances:
18 2 0.01
19 44 0.32
20 66 0.49
21 24 0.18
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (20 bp):
CAACCTAAAAATCAGGTTTC
Found at i:139588 original size:120 final size:120
Alignment explanation
Indices: 139455--139681 Score: 418
Period size: 120 Copynumber: 1.9 Consensus size: 120
139445 TTTGTTCTAC
**
139455 TTCACTTTCATCATTCAGGCATATCATTTAGGCATTGGATTCATTTATATTATACCCAATATCAC
1 TTCACTTTCATCATTCAGGCATATCATTTAGGCATTAAATTCATTTATATTATACCCAATATCAC
139520 TTAACACTTCACCTTTTAATTTAATCAATTTACACATTGGTTCGGGTTCTTTACT
66 TTAACACTTCACCTTTTAATTTAATCAATTTACACATTGGTTCGGGTTCTTTACT
*
139575 TTCACTTTCATCATTCAGGCCTATCATTTAGGCATTAAATTCATTTATATTATACCCAATATCAC
1 TTCACTTTCATCATTCAGGCATATCATTTAGGCATTAAATTCATTTATATTATACCCAATATCAC
*
139640 TTAACATTTCACCTTTTAATTTAATCAATTTACACATTGGTT
66 TTAACACTTCACCTTTTAATTTAATCAATTTACACATTGGTT
139682 TGGATCCACC
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 103 1.00
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (120 bp):
TTCACTTTCATCATTCAGGCATATCATTTAGGCATTAAATTCATTTATATTATACCCAATATCAC
TTAACACTTCACCTTTTAATTTAATCAATTTACACATTGGTTCGGGTTCTTTACT
Found at i:140981 original size:5 final size:6
Alignment explanation
Indices: 140966--140990 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
140956 TTATTTATAT
140966 TTTTTC TTTTTC TTTTTC TTTTTC T
1 TTTTTC TTTTTC TTTTTC TTTTTC T
140991 CTATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:143296 original size:15 final size:15
Alignment explanation
Indices: 143276--143306 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
143266 CAACAAATAA
143276 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
143291 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
143306 A
1 A
143307 TTTAAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:151146 original size:39 final size:39
Alignment explanation
Indices: 151086--151193 Score: 137
Period size: 39 Copynumber: 2.8 Consensus size: 39
151076 AATAAAAAGA
* * **
151086 TATAGTT-ATCTAGACTTCTAAATCAAATAAAATAGTGT
1 TATAGTTAATCTAAACTACTAAATCAAATAAAATACAGT
*
151124 TATAGTTAATCTAAACTACTAAATCAAATAAGATACAGT
1 TATAGTTAATCTAAACTACTAAATCAAATAAAATACAGT
* * *
151163 TATAGTTAATTTAAATTACTAATTCAAATAA
1 TATAGTTAATCTAAACTACTAAATCAAATAA
151194 TTTACTACTT
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
38 7 0.11
39 54 0.89
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.36
Consensus pattern (39 bp):
TATAGTTAATCTAAACTACTAAATCAAATAAAATACAGT
Found at i:155244 original size:114 final size:114
Alignment explanation
Indices: 155044--155258 Score: 430
Period size: 114 Copynumber: 1.9 Consensus size: 114
155034 ATTCCCGGGG
155044 ATCATATGTAAACAGTATAAGATTACTTGTTTCTAAAGAAATAACGCTAAAATTTTATTTGCATA
1 ATCATATGTAAACAGTATAAGATTACTTGTTTCTAAAGAAATAACGCTAAAATTTTATTTGCATA
155109 ACCTTTTGCAACTTGACTTTGAATATGGGTAGGTGACGCATGACAGAAT
66 ACCTTTTGCAACTTGACTTTGAATATGGGTAGGTGACGCATGACAGAAT
155158 ATCATATGTAAACAGTATAAGATTACTTGTTTCTAAAGAAATAACGCTAAAATTTTATTTGCATA
1 ATCATATGTAAACAGTATAAGATTACTTGTTTCTAAAGAAATAACGCTAAAATTTTATTTGCATA
155223 ACCTTTTGCAACTTGACTTTGAATATGGGTAGGTGA
66 ACCTTTTGCAACTTGACTTTGAATATGGGTAGGTGA
155259 TGCCTGATAA
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 101 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (114 bp):
ATCATATGTAAACAGTATAAGATTACTTGTTTCTAAAGAAATAACGCTAAAATTTTATTTGCATA
ACCTTTTGCAACTTGACTTTGAATATGGGTAGGTGACGCATGACAGAAT
Found at i:167794 original size:2 final size:2
Alignment explanation
Indices: 167787--167814 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
167777 GAACTGTAAG
167787 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
167815 CATTTTTATA
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:167842 original size:21 final size:22
Alignment explanation
Indices: 167818--167860 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
167808 TATATATCAT
*
167818 TTTTATATTTGTAATT-ATGTA
1 TTTTATATTTCTAATTGATGTA
* *
167839 TTTTTTCTTTCTAATTGATGTA
1 TTTTATATTTCTAATTGATGTA
167861 AAATGAACAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.23, C:0.05, G:0.09, T:0.63
Consensus pattern (22 bp):
TTTTATATTTCTAATTGATGTA
Found at i:168907 original size:35 final size:35
Alignment explanation
Indices: 168841--168955 Score: 221
Period size: 35 Copynumber: 3.3 Consensus size: 35
168831 CATACGGGAA
168841 CATACGAGCCAATGGTTCTCCCCCATGCATACGAGC
1 CATACGAGCCAATGGTTCT-CCCCATGCATACGAGC
168877 CATACGAGCCAATGGTTCTCCCCATGCATACGAGC
1 CATACGAGCCAATGGTTCTCCCCATGCATACGAGC
168912 CATACGAGCCAATGGTTCTCCCCATGCATACGAGC
1 CATACGAGCCAATGGTTCTCCCCATGCATACGAGC
168947 CATACGAGC
1 CATACGAGC
168956 GTTCTCCCCA
Statistics
Matches: 79, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
35 60 0.76
36 19 0.24
ACGTcount: A:0.26, C:0.35, G:0.20, T:0.19
Consensus pattern (35 bp):
CATACGAGCCAATGGTTCTCCCCATGCATACGAGC
Found at i:168962 original size:30 final size:27
Alignment explanation
Indices: 168926--168993 Score: 95
Period size: 26 Copynumber: 2.5 Consensus size: 27
168916 CGAGCCAATG
168926 GTTCTCCCCATGCATACGAGCCATACGAGC
1 GTTCTCCCCATGC---CGAGCCATACGAGC
168956 GTTCTCCCCATG-CGAGCCATACGAGC
1 GTTCTCCCCATGCCGAGCCATACGAGC
168982 GTTCT-CCCATGC
1 GTTCTCCCCATGC
168994 GAGGTGGCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
25 6 0.16
26 19 0.51
30 12 0.32
ACGTcount: A:0.19, C:0.38, G:0.21, T:0.22
Consensus pattern (27 bp):
GTTCTCCCCATGCCGAGCCATACGAGC
Found at i:168996 original size:25 final size:26
Alignment explanation
Indices: 168942--168996 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
168932 CCCATGCATA
168942 CGAGCCATACGAGCGTTCTCCCCATG
1 CGAGCCATACGAGCGTTCTCCCCATG
168968 CGAGCCATACGAGCGTTCT-CCCATG
1 CGAGCCATACGAGCGTTCTCCCCATG
168993 CGAG
1 CGAG
168997 GTGGCCATGC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 10 0.34
26 19 0.66
ACGTcount: A:0.20, C:0.36, G:0.25, T:0.18
Consensus pattern (26 bp):
CGAGCCATACGAGCGTTCTCCCCATG
Found at i:169027 original size:41 final size:42
Alignment explanation
Indices: 168981--169065 Score: 163
Period size: 41 Copynumber: 2.0 Consensus size: 42
168971 GCCATACGAG
168981 CGTTCTCCCATGCGAGGTGGCCATGCAGTGG-ATAGAGAGGT
1 CGTTCTCCCATGCGAGGTGGCCATGCAGTGGAATAGAGAGGT
169022 CGTTCTCCCATGCGAGGTGGCCATGCAGTGGAATAGAGAGGT
1 CGTTCTCCCATGCGAGGTGGCCATGCAGTGGAATAGAGAGGT
169064 CG
1 CG
169066 CCATGCACCT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 31 0.72
42 12 0.28
ACGTcount: A:0.20, C:0.22, G:0.36, T:0.21
Consensus pattern (42 bp):
CGTTCTCCCATGCGAGGTGGCCATGCAGTGGAATAGAGAGGT
Found at i:169162 original size:28 final size:29
Alignment explanation
Indices: 169077--169166 Score: 155
Period size: 29 Copynumber: 3.1 Consensus size: 29
169067 CATGCACCTA
*
169077 GGCGACCTTTTAGGTCGCCATGTAGTCCC
1 GGCGACCTTGTAGGTCGCCATGTAGTCCC
*
169106 GGCGACCTTGTAGGTCGCCATGTACTCCC
1 GGCGACCTTGTAGGTCGCCATGTAGTCCC
169135 GGCGACCTTGTA-GTCGCCATGTAGTCCC
1 GGCGACCTTGTAGGTCGCCATGTAGTCCC
169163 GGCG
1 GGCG
169167 CCATTCCCGT
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
28 19 0.33
29 39 0.67
ACGTcount: A:0.13, C:0.32, G:0.30, T:0.24
Consensus pattern (29 bp):
GGCGACCTTGTAGGTCGCCATGTAGTCCC
Found at i:169228 original size:23 final size:24
Alignment explanation
Indices: 169182--169228 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
169172 CCCGTCCATT
169182 CCCATCATCCATTCACCATGCAGC
1 CCCATCATCCATTCACCATGCAGC
169206 CCCATCATCCATTCA-CATGCAGC
1 CCCATCATCCATTCACCATGCAGC
169229 ATATAGATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.26, C:0.45, G:0.09, T:0.21
Consensus pattern (24 bp):
CCCATCATCCATTCACCATGCAGC
Found at i:169440 original size:23 final size:23
Alignment explanation
Indices: 169413--169458 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
169403 GAATCTATAT
169413 GGCTGCATGTGAATGGATGATGG
1 GGCTGCATGTGAATGGATGATGG
169436 GGCTGCATGTGAATGGATGATGG
1 GGCTGCATGTGAATGGATGATGG
169459 AATGGACGAT
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:0.22, C:0.09, G:0.43, T:0.26
Consensus pattern (23 bp):
GGCTGCATGTGAATGGATGATGG
Found at i:169583 original size:43 final size:43
Alignment explanation
Indices: 169522--169608 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
169512 GCTGCATGGT
*
169522 GACCTTTCTATTCCACTGCATGGCCACCTCGCATGGGGAGAAC
1 GACCTCTCTATTCCACTGCATGGCCACCTCGCATGGGGAGAAC
169565 GACCTCTCTATTCCACTGCATGGCCACCTCGCATGGGGAGAAC
1 GACCTCTCTATTCCACTGCATGGCCACCTCGCATGGGGAGAAC
169608 G
1 G
169609 CTCGTATGGC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.21, C:0.33, G:0.24, T:0.22
Consensus pattern (43 bp):
GACCTCTCTATTCCACTGCATGGCCACCTCGCATGGGGAGAAC
Found at i:169634 original size:25 final size:26
Alignment explanation
Indices: 169592--169646 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 26
169582 GCATGGCCAC
169592 CTCGCATGGGGAGAACGCTCGTATGG
1 CTCGCATGGGGAGAACGCTCGTATGG
169618 CTCGCAT-GGGAGAACGCTCGTATGG
1 CTCGCATGGGGAGAACGCTCGTATGG
169643 CTCG
1 CTCG
169647 TATGCATGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 22 0.76
26 7 0.24
ACGTcount: A:0.18, C:0.25, G:0.36, T:0.20
Consensus pattern (26 bp):
CTCGCATGGGGAGAACGCTCGTATGG
Found at i:169705 original size:35 final size:35
Alignment explanation
Indices: 169633--169741 Score: 197
Period size: 34 Copynumber: 3.2 Consensus size: 35
169623 ATGGGAGAAC
169633 GCTCGTATGGCTCGTATGCATGGGGA-AACCATTG
1 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
169667 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
1 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
169702 GCTCGTATGGCTCGTA-GCAT-GGGAGAACCATTG
1 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
169735 GCTCGTA
1 GCTCGTA
169742 GTTCCCGTAT
Statistics
Matches: 74, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
33 20 0.27
34 30 0.41
35 24 0.32
ACGTcount: A:0.20, C:0.21, G:0.33, T:0.26
Consensus pattern (35 bp):
GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
Found at i:169870 original size:3 final size:3
Alignment explanation
Indices: 169845--170057 Score: 238
Period size: 3 Copynumber: 71.0 Consensus size: 3
169835 CAAAAAAGGG
* * * * *
169845 AGA AGA AAA AAA AG- AGA AGGA AGA AGA AGG TGA A-A GGA AGGA AGA
1 AGA AGA AGA AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA A-GA AGA
* * * *
169890 AGA AGA AGGA GGA GGA AGA AGG AGA AGA AGA AGG AGA AG- AGA AGA
1 AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
169935 AGA AGA AGA AG- AGA AGA AGA AGA AG- AGA AGAA AGA AGA GAGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA -AGA AGA
* *
169980 AGG AGA AGA AGG AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
170028 AGA AGA AAA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
170058 CATATAAGTT
Statistics
Matches: 180, Mismatches: 20, Indels: 20
0.82 0.09 0.09
Matches are distributed among these distances:
2 9 0.05
3 157 0.87
4 14 0.08
ACGTcount: A:0.62, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:171851 original size:21 final size:21
Alignment explanation
Indices: 171822--171874 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
171812 ATTCTGACTA
171822 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
171843 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
171864 TCGCAATGCGA
1 TCGCATTGCGA
171875 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:172102 original size:22 final size:22
Alignment explanation
Indices: 172077--172146 Score: 113
Period size: 22 Copynumber: 3.2 Consensus size: 22
172067 CTAAGGCGAC
172077 ATCAGTCCCCATCTCCGACGAA
1 ATCAGTCCCCATCTCCGACGAA
*
172099 ATCAGTCCCCATCTCCGACGAT
1 ATCAGTCCCCATCTCCGACGAA
* *
172121 ATCAGTCTCCATCTCCGGCGAA
1 ATCAGTCCCCATCTCCGACGAA
172143 ATCA
1 ATCA
172147 TTCACGGTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.26, C:0.39, G:0.14, T:0.21
Consensus pattern (22 bp):
ATCAGTCCCCATCTCCGACGAA
Found at i:172538 original size:20 final size:20
Alignment explanation
Indices: 172513--172559 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
172503 GATTCTTGCA
172513 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
** *
172533 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCAAATTCGCG
172553 TTGCGAT
1 TTGCGAT
172560 TTTCATTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCG
Found at i:172557 original size:40 final size:40
Alignment explanation
Indices: 172513--172599 Score: 102
Period size: 40 Copynumber: 2.2 Consensus size: 40
172503 GATTCTTGCA
*
172513 TTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCAAATTCACGTTGCGATAGTCATTTTCGTG
** ** * **
172553 TTGCGATTTTCATTTTCATGTTGCGATTTTCATTTTCGTG
1 TTGCGATAGTCAAATTCACGTTGCGATAGTCATTTTCGTG
172593 TTGCGAT
1 TTGCGAT
172600 TTAAAGTTTC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.16, C:0.16, G:0.22, T:0.46
Consensus pattern (40 bp):
TTGCGATAGTCAAATTCACGTTGCGATAGTCATTTTCGTG
Found at i:172609 original size:20 final size:20
Alignment explanation
Indices: 172527--172601 Score: 114
Period size: 20 Copynumber: 3.8 Consensus size: 20
172517 GATAGTCAAA
* **
172527 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
172547 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
*
172567 TTCATGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
172587 TTCGTGTTGCGATTT
1 TTCGTGTTGCGATTT
172602 AAAGTTTCAG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.12, C:0.16, G:0.21, T:0.51
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:172610 original size:40 final size:40
Alignment explanation
Indices: 172532--172610 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
172522 TCAAATTCGC
** *
172532 GTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTTCAT
1 GTTGCGATAGTCATTTTCGTGTTGCGATTTAAAGTTTCAT
**
172572 GTTGCGATTTTCATTTTCGTGTTGCGATTTAAAGTTTCA
1 GTTGCGATAGTCATTTTCGTGTTGCGATTTAAAGTTTCA
172611 GAAACTATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.49
Consensus pattern (40 bp):
GTTGCGATAGTCATTTTCGTGTTGCGATTTAAAGTTTCAT
Found at i:174511 original size:20 final size:20
Alignment explanation
Indices: 174486--174642 Score: 135
Period size: 20 Copynumber: 8.5 Consensus size: 20
174476 AGAATAGTTT
174486 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
174506 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
174526 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
174546 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
174562 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
174579 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
* *
174595 A--ATCGCAACGCAAAAATG
1 ACTATCGCAATGCGAAAATG
**
174613 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
174633 ACTATCGCAA
1 ACTATCGCAA
174643 CGAAAGAATC
Statistics
Matches: 116, Mismatches: 7, Indels: 28
0.77 0.05 0.19
Matches are distributed among these distances:
14 14 0.12
16 10 0.09
17 8 0.07
18 5 0.04
19 7 0.06
20 72 0.62
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.17
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:174599 original size:33 final size:34
Alignment explanation
Indices: 174529--174622 Score: 100
Period size: 33 Copynumber: 2.8 Consensus size: 34
174519 GAAAATGACT
** * * *
174529 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAACGCGAAAATGAAAATCGCAACAACAAA
*
174563 ATCGCAATGCG-AAATGAAAATCGCAACAACAAA
1 ATCGCAACGCGAAAATGAAAATCGCAACAACAAA
* **
174596 ATCGCAACGCAAAAATGACTATCGCAA
1 ATCGCAACGCGAAAATGAAAATCGCAA
174623 TGCGAATTTG
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
33 26 0.53
34 23 0.47
ACGTcount: A:0.46, C:0.23, G:0.18, T:0.13
Consensus pattern (34 bp):
ATCGCAACGCGAAAATGAAAATCGCAACAACAAA
Found at i:174641 original size:87 final size:87
Alignment explanation
Indices: 174509--174674 Score: 278
Period size: 87 Copynumber: 1.9 Consensus size: 87
174499 GAAAATGACT
* * *
174509 ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAGAGAATCGCAATGCG
1 ATCGCAACGCAAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAATGCG
174574 AAATGAAAATCGCAACAACAAA
66 AAATGAAAATCGCAACAACAAA
* **
174596 ATCGCAACGCAAAAATGACTATCGCAATGCGAATTTGACTATCGCAACGAAAGAATCGCAATGCG
1 ATCGCAACGCAAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAATGCG
174661 AAATGAAAATCGCA
66 AAATGAAAATCGCA
174675 TTGCGATTCT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.43, C:0.22, G:0.19, T:0.16
Consensus pattern (87 bp):
ATCGCAACGCAAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAATGCG
AAATGAAAATCGCAACAACAAA
Found at i:174781 original size:20 final size:20
Alignment explanation
Indices: 174689--174812 Score: 155
Period size: 20 Copynumber: 6.3 Consensus size: 20
174679 GATTCTCTCG
**
174689 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
* **
174709 TTACGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
174729 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
174749 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
174769 TTGCGATAGTCATTTT--CA
1 TTGCGATAGTCATTTTCGCA
* *
174787 -CGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
174806 TTGCGAT
1 TTGCGAT
174813 TTTAAGTTTC
Statistics
Matches: 92, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
17 14 0.15
18 1 0.01
19 1 0.01
20 76 0.83
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:174823 original size:37 final size:37
Alignment explanation
Indices: 174751--174823 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
174741 TTTTCGCATT
* *
174751 GCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCAC
1 GCGATAGTCATTTTCGCGTTGCGATAGTAAGTTTCAC
**
174788 GCGATAGTCATTTTCGCGTTGCGATTTTAAGTTTCA
1 GCGATAGTCATTTTCGCGTTGCGATAGTAAGTTTCA
174824 GATTCTATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (37 bp):
GCGATAGTCATTTTCGCGTTGCGATAGTAAGTTTCAC
Found at i:176790 original size:14 final size:14
Alignment explanation
Indices: 176771--176806 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
176761 ATTGTTTAAT
176771 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
176785 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
176799 TGATTTGT
1 TGATTTGT
176807 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:176951 original size:14 final size:14
Alignment explanation
Indices: 176932--176985 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
176922 GGAAATGACT
176932 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
176946 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
176965 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
176979 ATCGCAA
1 ATCGCAA
176986 TGCGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:177000 original size:34 final size:33
Alignment explanation
Indices: 176912--177007 Score: 147
Period size: 33 Copynumber: 2.8 Consensus size: 33
176902 AAAACAGACT
* **
176912 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
176946 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
176979 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
177008 CGAAACTAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 32 0.55
34 26 0.45
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:177003 original size:20 final size:19
Alignment explanation
Indices: 176945--177012 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 19
176935 GCAACGAGAG
176945 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
176964 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
176978 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
176998 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
177013 CTAAATTGGC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
19 12 0.30
20 13 0.32
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:177079 original size:33 final size:33
Alignment explanation
Indices: 177028--177106 Score: 122
Period size: 33 Copynumber: 2.4 Consensus size: 33
177018 TTGGCGTTGT
177028 GATTTTCATTTTCGCATTGCGATTCTCTCATTGC
1 GATTTTCA-TTTCGCATTGCGATTCTCTCATTGC
*
177062 GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
1 GATTTTCATTTCGCATTGCGATTCTCTCATTGC
**
177095 GATAGTCATTTC
1 GATTTTCATTTC
177107 CGTGTTGCGA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 34 0.81
34 8 0.19
ACGTcount: A:0.15, C:0.23, G:0.16, T:0.46
Consensus pattern (33 bp):
GATTTTCATTTCGCATTGCGATTCTCTCATTGC
Found at i:177115 original size:20 final size:19
Alignment explanation
Indices: 177090--177177 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 19
177080 CGATTCTCTC
177090 GTTGCGATAGTCATTTCCGT
1 GTTGCGATAGTCATTT-CGT
177110 GTTGCGATAGTCAATTTCGT
1 GTTGCGATAGTC-ATTTCGT
*
177130 GTTGCTATAGTCATTTTCGT
1 GTTGCGATAGTCA-TTTCGT
*
177150 GTTGCGATAGTCATATTCGC
1 GTTGCGATAGTCAT-TTCGT
177170 GTTGCGAT
1 GTTGCGAT
177178 TTTCGCGTTG
Statistics
Matches: 62, Mismatches: 3, Indels: 6
0.87 0.04 0.08
Matches are distributed among these distances:
19 2 0.03
20 56 0.90
21 4 0.06
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.41
Consensus pattern (19 bp):
GTTGCGATAGTCATTTCGT
Found at i:177174 original size:40 final size:40
Alignment explanation
Indices: 177089--177177 Score: 135
Period size: 40 Copynumber: 2.2 Consensus size: 40
177079 GCGATTCTCT
177089 CGTTGCGATAGTCATTTCCGTGTTGCGATAGTCAATTTCG
1 CGTTGCGATAGTCATTTCCGTGTTGCGATAGTCAATTTCG
* * *
177129 TGTTGCTATAGTCATTTTCGTGTTGCGATAGTC-ATATTCG
1 CGTTGCGATAGTCATTTCCGTGTTGCGATAGTCAAT-TTCG
177169 CGTTGCGAT
1 CGTTGCGAT
177178 TTTCGCGTTG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
39 2 0.05
40 41 0.95
ACGTcount: A:0.17, C:0.18, G:0.25, T:0.40
Consensus pattern (40 bp):
CGTTGCGATAGTCATTTCCGTGTTGCGATAGTCAATTTCG
Found at i:177184 original size:14 final size:14
Alignment explanation
Indices: 177165--177191 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
177155 GATAGTCATA
177165 TTCGCGTTGCGATT
1 TTCGCGTTGCGATT
177179 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
177192 AGTCAAATGA
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:0.07, C:0.22, G:0.30, T:0.41
Consensus pattern (14 bp):
TTCGCGTTGCGATT
Found at i:179598 original size:24 final size:24
Alignment explanation
Indices: 179564--179617 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
179554 CTGAAAAATC
179564 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
179588 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
179612 ATCAAA
1 ATCAAA
179618 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:180484 original size:20 final size:20
Alignment explanation
Indices: 180459--180525 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
180449 AAATTCAGTA
180459 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
*
180479 TTGCGATAGTCAGAATCTCA
1 TTGCGATAGTCAGAATCTCG
* * *
180499 TTGCGATAGTTAGATTCGCG
1 TTGCGATAGTCAGAATCTCG
180519 TTGCGAT
1 TTGCGAT
180526 TTACGTATTC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:180535 original size:20 final size:20
Alignment explanation
Indices: 180512--180584 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
180502 CGATAGTTAG
*
180512 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
180532 ATTCGCATTGCGTTTTACGT
1 ATTCGCATTGCGATTTACGT
180552 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
180572 ATTCGCATTGCGA
1 ATTCGCATTGCGA
180585 GTTAGGAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.18, C:0.21, G:0.22, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:180541 original size:40 final size:41
Alignment explanation
Indices: 180497--180588 Score: 129
Period size: 40 Copynumber: 2.3 Consensus size: 41
180487 GTCAGAATCT
*
180497 CATTGCGATAGTTA-G-ATTCGCGTTGCGATTTACGTATTCG
1 CATTGCGAT-GTTACGTATTCGCATTGCGATTTACGTATTCG
*
180537 CATTGCG-TTTTACGTATTCGCATTGCGATTTACGTATTCG
1 CATTGCGATGTTACGTATTCGCATTGCGATTTACGTATTCG
180577 CATTGCGA-GTTA
1 CATTGCGATGTTA
180589 GGAAAATCGC
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
38 3 0.07
39 2 0.04
40 41 0.89
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (41 bp):
CATTGCGATGTTACGTATTCGCATTGCGATTTACGTATTCG
Found at i:180605 original size:21 final size:21
Alignment explanation
Indices: 180581--180626 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
180571 TATTCGCATT
*
180581 GCGAGTTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
180602 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
180623 GCGA
1 GCGA
180627 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:181002 original size:29 final size:29
Alignment explanation
Indices: 180960--181028 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 29
180950 ACTAAATTGG
*
180960 AATTTTATCATTCTAAAATATCAAAATAA
1 AATTTTATCATTCTAAAAGATCAAAATAA
* * * *
180989 AATTTTATCATTCTAAAGGGTTAAAATAC
1 AATTTTATCATTCTAAAAGATCAAAATAA
181018 AATTTTATCAT
1 AATTTTATCAT
181029 GTCCTAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.41
Consensus pattern (29 bp):
AATTTTATCATTCTAAAAGATCAAAATAA
Found at i:190963 original size:19 final size:21
Alignment explanation
Indices: 190939--190977 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
190929 CTTTGCTACA
190939 TTTATG-TTATTTGG-ATTTT
1 TTTATGTTTATTTGGTATTTT
190958 TTTATGTTTATTTGGTATTT
1 TTTATGTTTATTTGGTATTT
190978 GGTACTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 8 0.44
21 4 0.22
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (21 bp):
TTTATGTTTATTTGGTATTTT
Found at i:192328 original size:16 final size:17
Alignment explanation
Indices: 192297--192329 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
192287 TATTTTCATT
192297 TTTTAATAATAAAATTA
1 TTTTAATAATAAAATTA
*
192314 TTTTCATAA-AAAATTA
1 TTTTAATAATAAAATTA
192330 AGTTATAGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTTAATAATAAAATTA
Found at i:200860 original size:18 final size:18
Alignment explanation
Indices: 200834--200868 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
200824 TCGAAATGAC
*
200834 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
200852 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
200869 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:202366 original size:216 final size:216
Alignment explanation
Indices: 201983--202392 Score: 784
Period size: 216 Copynumber: 1.9 Consensus size: 216
201973 ATAAAGGTTC
201983 CTGAACATTTTCCTAATACACACGAAAATATAGTGGGATTCTAATGTATCAACCTTAAATGTCTG
1 CTGAACATTTTCCTAATACACACGAAAATATAGTGGGATTCTAATGTATCAACCTTAAATGTCTG
202048 GCTAGATCGGTTAGTAATCGATTCTCCTCAATAGGACCTTGTTCCTGGAATTCGATCAAATTTCA
66 GCTAGATCGGTTAGTAATCGATTCTCCTCAATAGGACCTTGTTCCTGGAATTCGATCAAATTTCA
*
202113 TAAGTTTCATGTTATCCAAAATGATAACTACAATGGCCTCTGAAAATACTTGGATTCTTTAGTGG
131 TAAGTTTCATGTTATCCAAAATGATAACTACAATGGCCTCTGAAAATACTTGGATTCTCTAGTGG
202178 GATTCTAATGTACAATGGCCT
196 GATTCTAATGTACAATGGCCT
* *
202199 CTGAACGTTTTCCTAATGCACACGAAAATATAGTGGGATTCTAATGTATCAACCTTAAATGTCTG
1 CTGAACATTTTCCTAATACACACGAAAATATAGTGGGATTCTAATGTATCAACCTTAAATGTCTG
202264 GCTAGATCGGTTAGTAATCGATTCTCCTCAATAGGACCTTGTTCCTGGAATTCGATCAAATTTCA
66 GCTAGATCGGTTAGTAATCGATTCTCCTCAATAGGACCTTGTTCCTGGAATTCGATCAAATTTCA
*
202329 TAAGTTTCATGTTATCCAAAATGATAACTATAATGGCCTCTGAAAATACTTGGATTCTCTAGTG
131 TAAGTTTCATGTTATCCAAAATGATAACTACAATGGCCTCTGAAAATACTTGGATTCTCTAGTG
202393 TGTTCCCTAA
Statistics
Matches: 190, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
216 190 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34
Consensus pattern (216 bp):
CTGAACATTTTCCTAATACACACGAAAATATAGTGGGATTCTAATGTATCAACCTTAAATGTCTG
GCTAGATCGGTTAGTAATCGATTCTCCTCAATAGGACCTTGTTCCTGGAATTCGATCAAATTTCA
TAAGTTTCATGTTATCCAAAATGATAACTACAATGGCCTCTGAAAATACTTGGATTCTCTAGTGG
GATTCTAATGTACAATGGCCT
Found at i:204334 original size:20 final size:20
Alignment explanation
Indices: 204309--204381 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
204299 TTTTTGGCTC
*
204309 AAAGGATCGATCCCCTAGAA
1 AAAGGATCGATCCCCTTGAA
*
204329 AAAGGATCGATCCCTTTGACA
1 AAAGGATCGATCCCCTTGA-A
* * *
204350 AAAGAATCAATCCCCTTTAA
1 AAAGGATCGATCCCCTTGAA
204370 AAAGGATCGATC
1 AAAGGATCGATC
204382 TCGGACAACA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (20 bp):
AAAGGATCGATCCCCTTGAA
Found at i:206733 original size:18 final size:20
Alignment explanation
Indices: 206694--206730 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
206684 TGATATGTGT
*
206694 TATATGTGGTCCTTCGGGGA
1 TATATGTGGTCATTCGGGGA
206714 TATA-GTGGTCATTCGGG
1 TATATGTGGTCATTCGGG
206731 ATAAATTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.16, C:0.14, G:0.35, T:0.35
Consensus pattern (20 bp):
TATATGTGGTCATTCGGGGA
Found at i:211280 original size:17 final size:17
Alignment explanation
Indices: 211226--211290 Score: 57
Period size: 17 Copynumber: 4.1 Consensus size: 17
211216 GAAATATAAG
*
211226 TTCAAAC-ATCCATAAA
1 TTCAAACAATCCACAAA
* *
211242 TTCAAAAAATTCAC--A
1 TTCAAACAATCCACAAA
*
211257 GTCAAACAATCCACAAA
1 TTCAAACAATCCACAAA
*
211274 TTCAAACATTCCA-AAA
1 TTCAAACAATCCACAAA
211290 T
1 T
211291 ATCCAAAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
15 12 0.32
16 10 0.26
17 16 0.42
ACGTcount: A:0.51, C:0.25, G:0.02, T:0.23
Consensus pattern (17 bp):
TTCAAACAATCCACAAA
Found at i:213187 original size:21 final size:21
Alignment explanation
Indices: 213163--213221 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
213153 AACAGAACCC
213163 CAGGGGGTATCGATTCCCCTA
1 CAGGGGGTATCGATTCCCCTA
* * *
213184 CAGGGGGAATCGGTTCCCCTT
1 CAGGGGGTATCGATTCCCCTA
*
213205 CAAGGGGTATCGATTCC
1 CAGGGGGTATCGATTCC
213222 TCTGCACCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.27, G:0.31, T:0.24
Consensus pattern (21 bp):
CAGGGGGTATCGATTCCCCTA
Found at i:217068 original size:22 final size:21
Alignment explanation
Indices: 217026--217065 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
217016 GAGTTTATTT
*
217026 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
217047 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
217066 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:222602 original size:15 final size:13
Alignment explanation
Indices: 222582--222615 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 13
222572 TTTTTTAAAA
222582 AAATATAATTATATT
1 AAATATAA-TATA-T
222597 AAATATAATATAT
1 AAATATAATATAT
222610 AAATAT
1 AAATAT
222616 TTAAAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 4 0.21
15 8 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAATATAATATAT
Found at i:222622 original size:22 final size:21
Alignment explanation
Indices: 222584--222626 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
222574 TTTTAAAAAA
*
222584 ATATAATTATATTAAATATAAT
1 ATATAAATATATTAAAT-TAAT
222606 ATATAAATAT-TTAAAATTAAT
1 ATATAAATATATT-AAATTAAT
222627 TTATCATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATATAAATATATTAAATTAAT
Found at i:227557 original size:19 final size:19
Alignment explanation
Indices: 227512--227562 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
227502 GAAACACTTA
*
227512 GTGCATCAGTGCACTAAGG
1 GTGCATCGGTGCACTAAGG
227531 GTGCATCGGTGCACTAAGG
1 GTGCATCGGTGCACTAAGG
*
227550 GTGCATCGATGCA
1 GTGCATCGGTGCA
227563 TAAAATGCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.24, C:0.22, G:0.33, T:0.22
Consensus pattern (19 bp):
GTGCATCGGTGCACTAAGG
Found at i:227635 original size:65 final size:63
Alignment explanation
Indices: 227550--227704 Score: 215
Period size: 65 Copynumber: 2.4 Consensus size: 63
227540 TGCACTAAGG
227550 GTGCATCGATGCATAAAATGCATTCGATG-TTCCA-AACAAGCCTGGAGTGCATCGATGCATGGT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCCATAA-AAGCCT-GAGTGCAT-GATGCATGG-
*
227613 CT
62 CA
* * * *
227615 GTGCATTGATGCATAAAATGCATTTGATGTTTCTATAAAATCCTGAGTGCATGATGCATGGCA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCCATAAAAGCCTGAGTGCATGATGCATGGCA
227678 GTGCATCGATGCATAAAATGCATTCGA
1 GTGCATCGATGCATAAAATGCATTCGA
227705 AATGGGGTGG
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
63 26 0.32
64 9 0.11
65 35 0.43
66 9 0.11
67 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (63 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCCATAAAAGCCTGAGTGCATGATGCATGGCA
Found at i:228333 original size:27 final size:27
Alignment explanation
Indices: 228303--228359 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
228293 CTAAATGATG
* * *
228303 CAAAAATCTAATAAACCAATATAAGTT
1 CAAAAACCAAATAAACAAATATAAGTT
* *
228330 CAAAAACCAAATATATAAATATAAGTT
1 CAAAAACCAAATAAACAAATATAAGTT
228357 CAA
1 CAA
228360 GCATTCAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.58, C:0.14, G:0.04, T:0.25
Consensus pattern (27 bp):
CAAAAACCAAATAAACAAATATAAGTT
Found at i:230400 original size:24 final size:24
Alignment explanation
Indices: 230371--230423 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
230361 TTCATGGTGT
230371 ATCGATGCACATTCATAGGGATGC
1 ATCGATGCACATTCATAGGGATGC
230395 ATCGATGCACATTCATAGGGATGC
1 ATCGATGCACATTCATAGGGATGC
230419 ATCGA
1 ATCGA
230424 GGCATTATGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.25
Consensus pattern (24 bp):
ATCGATGCACATTCATAGGGATGC
Found at i:233979 original size:18 final size:18
Alignment explanation
Indices: 233956--233993 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
233946 TGATTTTTCC
233956 ATTTAAGGTTCGTTAAGG
1 ATTTAAGGTTCGTTAAGG
233974 ATTTAAGGTTCGTTAAGG
1 ATTTAAGGTTCGTTAAGG
233992 AT
1 AT
233994 CTCTATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.05, G:0.26, T:0.39
Consensus pattern (18 bp):
ATTTAAGGTTCGTTAAGG
Found at i:234286 original size:22 final size:21
Alignment explanation
Indices: 234244--234283 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
234234 GAGATTATTT
*
234244 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
234265 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
234284 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:235780 original size:19 final size:19
Alignment explanation
Indices: 235756--235800 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
235746 CCGAATTCTT
235756 GAGAACACTCTCTCCCAAA
1 GAGAACACTCTCTCCCAAA
235775 GAGAACACTCTCTCCCAAA
1 GAGAACACTCTCTCCCAAA
235794 GAGAACA
1 GAGAACA
235801 ATACAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.40, C:0.33, G:0.13, T:0.13
Consensus pattern (19 bp):
GAGAACACTCTCTCCCAAA
Found at i:236292 original size:65 final size:63
Alignment explanation
Indices: 236243--236395 Score: 220
Period size: 65 Copynumber: 2.4 Consensus size: 63
236233 TGCACTAAGG
236243 GTGCATCGATGCATAAAATGCATTCGATG-TTCCA-AACAAGCCTGGAGTGCATCGATGCATGGT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCCATAA-AAGCCT-GAGTGCATCGATGCATGG-
236306 C
63 C
* * *
236307 TGTGCATTGATGCATAAAATACATTCGATGTTTCCATAAAATCCTGAGTGCATCGATGCATGGC
1 -GTGCATCGATGCATAAAATGCATTCGATGTTTCCATAAAAGCCTGAGTGCATCGATGCATGGC
236371 AGTGCATCGATGCATAAAATGCATT
1 -GTGCATCGATGCATAAAATGCATT
236396 TGAAATGGGG
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
64 23 0.29
65 45 0.56
66 10 0.12
67 2 0.03
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (63 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCCATAAAAGCCTGAGTGCATCGATGCATGGC
Found at i:242863 original size:21 final size:22
Alignment explanation
Indices: 242829--242872 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
242819 AGACCTATAC
* *
242829 AAATATTTATAAAT-TGTTGCA
1 AAATATTGAAAAATATGTTGCA
242850 AAATATTGAAAAATAGTGTTGCA
1 AAATATTGAAAAATA-TGTTGCA
242873 GTATTATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.63
23 7 0.37
ACGTcount: A:0.45, C:0.05, G:0.14, T:0.36
Consensus pattern (22 bp):
AAATATTGAAAAATATGTTGCA
Found at i:243164 original size:20 final size:20
Alignment explanation
Indices: 243141--243184 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
243131 GAGAAGAATT
243141 TTTATTGAAAGGTTAAGACC
1 TTTATTGAAAGGTTAAGACC
*
243161 TTTATTGAAAGGTTAAGTCC
1 TTTATTGAAAGGTTAAGACC
243181 TTTA
1 TTTA
243185 AATGAAATGA
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:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (20 bp):
TTTATTGAAAGGTTAAGACC
Found at i:243291 original size:23 final size:22
Alignment explanation
Indices: 243265--243314 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
243255 ACTTTTGGGG
243265 TGAAATGAAATAATTATTTTTCA
1 TGAAAT-AAATAATTATTTTTCA
**
243288 TGAAAATACTTAATTATTTTTCA
1 TG-AAATAAATAATTATTTTTCA
243311 TGAA
1 TGAA
243315 TAGTCATGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 2 0.08
23 18 0.75
24 4 0.17
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (22 bp):
TGAAATAAATAATTATTTTTCA
Found at i:254147 original size:210 final size:211
Alignment explanation
Indices: 253783--254202 Score: 788
Period size: 210 Copynumber: 2.0 Consensus size: 211
253773 AACAACAAAC
253783 GTTCACAACAGTAAGCACAACCGTAGTGAGAAATCGAACACAATCTTTGTCTTTATCTATCACCG
1 GTTCACAACAGTAAGCACAACCGTAGTGAGAAATCGAACACAATC-TTGTCTTTATCTATCACCG
*
253848 GAAAATGACTTTGGAAGAATCGGAGAATTGAAATGAAAGTACTTGAAAGAAATTAGTAAAAAGTT
65 GAAAATGACTTTGGAAGAATCGGAGAATTGAAATGAAAGTACTTGAAAGAAATTAATAAAAAGTT
253913 GTGTGTTGAGATGTGTCACAACTTAGCCTTCATATAGGGAGAGGAATTTGTATTGAAAGGTTAAG
130 GTGTGTTGAGATGTGTCACAACTTAGCCTTCATATAGGGAGAGGAATTTGTATTGAAAGGTTAAG
253978 GCCTTTAAATGAAATAT
195 GCCTTTAAATGAAATAT
* * *
253995 GTTCACAACAGTAAGCACAACTGTAGTGAGCAATCGAACACAATC-TGTCTTTATCTATCACTGG
1 GTTCACAACAGTAAGCACAACCGTAGTGAGAAATCGAACACAATCTTGTCTTTATCTATCACCGG
254059 AAAATGACTTTGGAAGAATCGGAGAATTGAAATGAAAGTACTTGAAAGAAATTAATAAAAAGTTG
66 AAAATGACTTTGGAAGAATCGGAGAATTGAAATGAAAGTACTTGAAAGAAATTAATAAAAAGTTG
254124 TGTGTTGAGATGTGTCACAACTTAGCCTTCATATAGGGAGAGGAATTTGTATTGAAAGGTTAAGG
131 TGTGTTGAGATGTGTCACAACTTAGCCTTCATATAGGGAGAGGAATTTGTATTGAAAGGTTAAGG
254189 CCTTTAAATGAAAT
196 CCTTTAAATGAAAT
254203 GACTTAACCA
Statistics
Matches: 204, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
210 161 0.79
212 43 0.21
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (211 bp):
GTTCACAACAGTAAGCACAACCGTAGTGAGAAATCGAACACAATCTTGTCTTTATCTATCACCGG
AAAATGACTTTGGAAGAATCGGAGAATTGAAATGAAAGTACTTGAAAGAAATTAATAAAAAGTTG
TGTGTTGAGATGTGTCACAACTTAGCCTTCATATAGGGAGAGGAATTTGTATTGAAAGGTTAAGG
CCTTTAAATGAAATAT
Found at i:256241 original size:22 final size:22
Alignment explanation
Indices: 256211--256256 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
256201 AATCAACTAG
256211 AACCAAAATTAACCCAAACCAA
1 AACCAAAATTAACCCAAACCAA
* ** *
256233 AACCGAAATTTGCCCAAATCAA
1 AACCAAAATTAACCCAAACCAA
256255 AA
1 AA
256257 ACAACCCGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.54, C:0.28, G:0.04, T:0.13
Consensus pattern (22 bp):
AACCAAAATTAACCCAAACCAA
Found at i:257508 original size:29 final size:30
Alignment explanation
Indices: 257475--257548 Score: 114
Period size: 29 Copynumber: 2.5 Consensus size: 30
257465 TAAACCCGTC
257475 CCCGTCCCCGTTTAACATAAACAG-TTTTT
1 CCCGTCCCCGTTTAACATAAACAGTTTTTT
* * *
257504 CCCGTCCCCATTTAGCATAAACGGTTTTTT
1 CCCGTCCCCGTTTAACATAAACAGTTTTTT
257534 CCCGTCCCCGTTTAA
1 CCCGTCCCCGTTTAA
257549 TTCGATTTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 21 0.54
30 18 0.46
ACGTcount: A:0.20, C:0.34, G:0.12, T:0.34
Consensus pattern (30 bp):
CCCGTCCCCGTTTAACATAAACAGTTTTTT
Found at i:264740 original size:21 final size:21
Alignment explanation
Indices: 264716--264755 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
264706 CATTATCTAT
264716 ATCATCATCACTACCACCACC
1 ATCATCATCACTACCACCACC
264737 ATCATCATCACTACCACCA
1 ATCATCATCACTACCACCA
264756 TCATGAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.45, G:0.00, T:0.20
Consensus pattern (21 bp):
ATCATCATCACTACCACCACC
Found at i:264741 original size:18 final size:18
Alignment explanation
Indices: 264718--264759 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
264708 TTATCTATAT
264718 CATCATCA-CTACCACCAC
1 CATCATCATC-ACCACCAC
*
264736 CATCATCATCACTACCAC
1 CATCATCATCACCACCAC
264754 CATCAT
1 CATCAT
264760 GAATAGTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.33, C:0.45, G:0.00, T:0.21
Consensus pattern (18 bp):
CATCATCATCACCACCAC
Found at i:279702 original size:65 final size:64
Alignment explanation
Indices: 279576--279722 Score: 190
Period size: 65 Copynumber: 2.3 Consensus size: 64
279566 AGAGTGCAAA
* *
279576 GATGCATAAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGGTGCATC
1 GATGCATAAAATGCATTCGATGTTTCAAAATACCCACAGTGCATCGATGCATGGCTGGTGCATC
* * *
279640 GATGCATCAAATGCATTCGATGTTTTCATAAA-ACCCTCAGTGCATCGATGCATGG-TATGTGCA
1 GATGCATAAAATGCATTCGATG-TTTCA-AAATACCCACAGTGCATCGATGCATGGCT-GGTGCA
279703 TC
63 TC
* *
279705 AATGCATGAAATGCATTC
1 GATGCATAAAATGCATTC
279723 TGTTGGGATT
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
64 22 0.30
65 48 0.66
66 3 0.04
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.29
Consensus pattern (64 bp):
GATGCATAAAATGCATTCGATGTTTCAAAATACCCACAGTGCATCGATGCATGGCTGGTGCATC
Found at i:280269 original size:20 final size:22
Alignment explanation
Indices: 280244--280283 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
280234 AGTCGTATAT
280244 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
280264 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
280284 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:280336 original size:20 final size:21
Alignment explanation
Indices: 280311--280352 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
280301 CCCAGAATAG
*
280311 AGGGAATCGGTA-CCCTTCAT
1 AGGGAATCGATACCCCTTCAT
280331 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
280352 A
1 A
280353 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:280414 original size:21 final size:21
Alignment explanation
Indices: 280388--280428 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
280378 CTGTTGAACA
280388 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
280409 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
280429 AGACATTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.15, C:0.29, G:0.41, T:0.15
Consensus pattern (21 bp):
GGGGGGAATCGGTACCCCCTG
Found at i:280489 original size:20 final size:19
Alignment explanation
Indices: 280464--280537 Score: 70
Period size: 20 Copynumber: 4.1 Consensus size: 19
280454 AAAACCTGCA
280464 GGGGGTATCTGTACCCCCTG
1 GGGGGTATCTGTA-CCCCTG
280484 GGGGGTATCTGTA-CCC--
1 GGGGGTATCTGTACCCCTG
280500 ---GGTATCTGTACCCCTG
1 GGGGGTATCTGTACCCCTG
* *
280516 GGGGGAATCTATACCCCCTG
1 GGGGGTATCTGTA-CCCCTG
280536 GG
1 GG
280538 CAATCTTGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
13 10 0.22
14 3 0.07
18 3 0.07
19 8 0.18
20 21 0.47
ACGTcount: A:0.14, C:0.28, G:0.34, T:0.24
Consensus pattern (19 bp):
GGGGGTATCTGTACCCCTG
Done.