Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, 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: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 15 of 133
Found at i:3826450 original size:23 final size:22
Alignment explanation
Indices: 3826407--3826450 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
3826397 ATAATTAGAT
*
3826407 ATTTATCATAATAAATTTAAAC
1 ATTTATCATAATAAATATAAAC
*
3826429 ATTTATCATGCATAAATATAAA
1 ATTTATCAT-AATAAATATAAA
3826451 AACTTAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (22 bp):
ATTTATCATAATAAATATAAAC
Found at i:3827577 original size:3 final size:3
Alignment explanation
Indices: 3827562--3827591 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3827552 AAATATATAT
*
3827562 TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3827592 GTAGACTCGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3828047 original size:102 final size:103
Alignment explanation
Indices: 3827936--3828541 Score: 751
Period size: 105 Copynumber: 5.9 Consensus size: 103
3827926 TTAAATCATA
* * *
3827936 AATCAAAGAATAAAGAGATCGAGATTAAATCACGAGTCAAA-A-AATAACAACAATCGAGATTAA
1 AATCGAAGAATAAAAAGATCGAGATTAAATCACGAGTCAAAGATAACAACAACAATCGAGATTAA
* * *
3827999 ACTACAATTTTAAATTAAAGAGGTCAGGATTGAGTCGCG
66 ACTACGATTTTAAATTAAAGAGATCAGGATTGA-ACGCG
* * *
3828038 ATTCGAAGAATAAAACGATCGAGATTAAATCACGAGTTAAAAGATAACAACAACAATCGAGATTA
1 AATCGAAGAATAAAAAGATCGAGATTAAATCACGAG-TCAAAGATAACAACAACAATCGAGATTA
3828103 AACTACGATTTTAAATTAAAGAGATC-GAGATTGAACTGCG
65 AACTACGATTTTAAATTAAAGAGATCAG-GATTGAAC-GCG
3828143 AATCGAAGAATAAAAAGATCGAGATTAAATCACGAGTCAGAAGATAACAACAACAATCGAGATTA
1 AATCGAAGAATAAAAAGATCGAGATTAAATCACGAGTCA-AAGATAACAACAACAATCGAGATTA
* *
3828208 AACTACGATTTTAAATTAAAGAGATCGGGATTGAACCGTG
65 AACTACGATTTTAAATTAAAGAGATCAGGATTGAA-CGCG
* * * * *
3828248 AATTGAAGAGTAAAAAGATCGAGATTAAACCACAAGTCAGAAGATAACAACAACAATTGAGATTA
1 AATCGAAGAATAAAAAGATCGAGATTAAATCACGAGTCA-AAGATAACAACAACAATCGAGATTA
* *
3828313 AATTACGATTTTAAATTAAAGAGATCAAGATTGAACTGCG
65 AACTACGATTTTAAATTAAAGAGATCAGGATTGAAC-GCG
* * * *
3828353 AATCGAAGAATAAAAAGATCGAGATTAAACCACGAGTCAAA-A-AATAACAACAGTCAAGATTAA
1 AATCGAAGAATAAAAAGATCGAGATTAAATCACGAGTCAAAGATAACAACAACAATCGAGATTAA
** *
3828416 ACTGTGATTTTAAATTAAAGAGATCAGGATTGAATCGTG
66 ACTACGATTTTAAATTAAAGAGATCAGGATTGAA-CGCG
* * * ** * * *
3828455 AATC-AGAGAATAAAGAGACCGAAATTAAATCGTGAGT-AAA-AAAATAACAACAATTGAGATTA
1 AATCGA-AGAATAAAAAGATCGAGATTAAATCACGAGTCAAAGATAACAACAACAATCGAGATTA
**
3828517 AACTGTGATTTTAAATTAAAGAGAT
65 AACTACGATTTTAAATTAAAGAGAT
3828542 TGAGAGAATA
Statistics
Matches: 449, Mismatches: 43, Indels: 24
0.87 0.08 0.05
Matches are distributed among these distances:
101 5 0.01
102 152 0.34
103 6 0.01
104 8 0.02
105 276 0.61
106 2 0.00
ACGTcount: A:0.48, C:0.12, G:0.17, T:0.22
Consensus pattern (103 bp):
AATCGAAGAATAAAAAGATCGAGATTAAATCACGAGTCAAAGATAACAACAACAATCGAGATTAA
ACTACGATTTTAAATTAAAGAGATCAGGATTGAACGCG
Found at i:3828118 original size:51 final size:51
Alignment explanation
Indices: 3828062--3828223 Score: 121
Period size: 51 Copynumber: 3.1 Consensus size: 51
3828052 ACGATCGAGA
3828062 TTAAATCACGAGTTAAAAGATAACAACAACAATCGAGATTAAACTACGATT
1 TTAAATCACGAGTTAAAAGATAACAACAACAATCGAGATTAAACTACGATT
* * * ** ** ** * ** **
3828113 TTAAATTAAAGAGAT-CGAGAT-TGAACTGCGAATCGAAGAATAAAAAGATCGAGA
1 TTAAA-TCACGAGTTAAAAGATAACAACAAC-AATCG-AG-ATTAAACTA-CGATT
* *
3828167 TTAAATCACGAGTCAGAAGATAACAACAACAATCGAGATTAAACTACGATT
1 TTAAATCACGAGTTAAAAGATAACAACAACAATCGAGATTAAACTACGATT
3828218 TTAAAT
1 TTAAAT
3828224 TAAAGAGATC
Statistics
Matches: 75, Mismatches: 29, Indels: 14
0.64 0.25 0.12
Matches are distributed among these distances:
50 4 0.05
51 23 0.31
52 14 0.19
53 13 0.17
54 17 0.23
55 4 0.05
ACGTcount: A:0.48, C:0.14, G:0.15, T:0.23
Consensus pattern (51 bp):
TTAAATCACGAGTTAAAAGATAACAACAACAATCGAGATTAAACTACGATT
Found at i:3828270 original size:210 final size:207
Alignment explanation
Indices: 3827936--3828546 Score: 845
Period size: 210 Copynumber: 3.0 Consensus size: 207
3827926 TTAAATCATA
* *
3827936 AATCAAAGAATAAAGAGATCGAGATTAAATCACGAGTCAAAAAATAACAACAATCGAGATTAAAC
1 AATCGAAGAATAAAAAGATCGAGATTAAATCACGAGTCAAAAAATAACAACAATCGAGATTAAAC
* * * * *
3828001 TACAATTTTAAATTAAAGAGGTCAGGATTGAGTCGCG-ATTCGAAGAATAAAACGATCGAGATTA
66 TACGATTTTAAATTAAAGAGATCAGGATTGAATCGTGAATT-GAAGAATAAAAAGATCGAGATTA
*
3828065 AATCACGAGTTAAAAGATAACAACAACAATCGAGATTAAACTACGATTTTAAATTAAAGAGATCG
130 AATCACGAGTTAAAAGATAACAACAACAATTGAGATTAAACTACGATTTTAAATTAAAGAGATCG
3828130 AGATTGAACTGCG
195 AGATTGAACTGCG
*
3828143 AATCGAAGAATAAAAAGATCGAGATTAAATCACGAGTCAGAAGATAACAACAACAATCGAGATTA
1 AATCGAAGAATAAAAAGATCGAGATTAAATCACGAGTCA-AA-A-AATAACAACAATCGAGATTA
* * *
3828208 AACTACGATTTTAAATTAAAGAGATCGGGATTGAACCGTGAATTGAAGAGTAAAAAGATCGAGAT
63 AACTACGATTTTAAATTAAAGAGATCAGGATTGAATCGTGAATTGAAGAATAAAAAGATCGAGAT
* * * * *
3828273 TAAACCACAAGTCAGAAGATAACAACAACAATTGAGATTAAATTACGATTTTAAATTAAAGAGAT
128 TAAATCACGAGTTAAAAGATAACAACAACAATTGAGATTAAACTACGATTTTAAATTAAAGAGAT
*
3828338 CAAGATTGAACTGCG
193 CGAGATTGAACTGCG
* * *
3828353 AATCGAAGAATAAAAAGATCGAGATTAAACCACGAGTCAAAAAATAACAACAGTCAAGATTAAAC
1 AATCGAAGAATAAAAAGATCGAGATTAAATCACGAGTCAAAAAATAACAACAATCGAGATTAAAC
** * * * *
3828418 TGTGATTTTAAATTAAAGAGATCAGGATTGAATCGTGAA-TCAGAGAATAAAGAGACCGAAATTA
66 TACGATTTTAAATTAAAGAGATCAGGATTGAATCGTGAATTGA-AGAATAAAAAGATCGAGATTA
** * ** *
3828482 AATCGTGAG-TAAAA-A-AATAACAACAATTGAGATTAAACTGTGATTTTAAATTAAAGAGATTG
130 AATCACGAGTTAAAAGATAACAACAACAATTGAGATTAAACTACGATTTTAAATTAAAGAGATCG
3828544 AGA
195 AGA
3828547 GAATAAAGAG
Statistics
Matches: 356, Mismatches: 43, Indels: 13
0.86 0.10 0.03
Matches are distributed among these distances:
204 44 0.12
205 1 0.00
206 5 0.01
207 114 0.32
208 3 0.01
209 3 0.01
210 183 0.51
211 3 0.01
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.22
Consensus pattern (207 bp):
AATCGAAGAATAAAAAGATCGAGATTAAATCACGAGTCAAAAAATAACAACAATCGAGATTAAAC
TACGATTTTAAATTAAAGAGATCAGGATTGAATCGTGAATTGAAGAATAAAAAGATCGAGATTAA
ATCACGAGTTAAAAGATAACAACAACAATTGAGATTAAACTACGATTTTAAATTAAAGAGATCGA
GATTGAACTGCG
Found at i:3829131 original size:69 final size:71
Alignment explanation
Indices: 3829046--3829186 Score: 207
Period size: 70 Copynumber: 2.0 Consensus size: 71
3829036 GCTTTTGTAC
* * *
3829046 AGAAAAATTTGATACTTCCAACTTCTTC-CCAAAATATTTTTT-AGAAACTTTAATTTCGGGTAA
1 AGAAAAATTTGATACTTCCAACTTCTTCTCAAAAATATTTTTTGA-AAACTTTAATTTCGAGAAA
3829109 AATTGAA
65 AATTGAA
* *
3829116 AGAAAAA-TTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAAACTTTAATTTCGAGAAAA
1 AGAAAAATTTGATACTTCCAACTTCTTCTCAAAAATATTTTTTGAAAACTTTAATTTCGAGAAAA
3829180 ATTGAA
66 ATTGAA
3829186 A
1 A
3829187 CTTTCAACTT
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
69 18 0.28
70 45 0.70
71 1 0.02
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (71 bp):
AGAAAAATTTGATACTTCCAACTTCTTCTCAAAAATATTTTTTGAAAACTTTAATTTCGAGAAAA
ATTGAA
Found at i:3829241 original size:59 final size:59
Alignment explanation
Indices: 3829115--3829860 Score: 607
Period size: 58 Copynumber: 12.8 Consensus size: 59
3829105 GTAAAATTGA
* * *
3829115 AAGAAAAATTGATACTTTCAACTTTTTCTC--AAAAATATTTTTTGAAAACTTTAATTTC
1 AAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTTTGAAAA-TTTAATTTT
* * * ** *
3829173 GAGAAAAATTGAAACTTTCAACTTTTTCTCAAAAAAACCTTTTTTGAAAATTTATTTTT
1 AAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTTTGAAAATTTAATTTT
* * * *
3829232 AAGAAAAATTGATGCTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAACTTTAATTTC
1 AAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTTTGAAAA-TTTAATTTT
* ** *
3829292 GAGAAAAATTGATACTTTCAACTTTTTTTC-AAAAAATTTTTTTTGAAAATTTATTTTT
1 AAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTTTGAAAATTTAATTTT
* *
3829350 AAGAAAAATTGATACTTTCAACTTTTTCC-C--AAAAATATTTTTTGAAAATTTTAATTTC
1 AAGAAAAATTGATACTTTCAAC-TTTTCCTCAAAAAAATTTTTTTTGAAAA-TTTAATTTT
* * ** *
3829408 GAGAAAAATTGATACTTTCAACTTTTCCTTAAAAAAACCTTTTTTGAAAATTTATTTTT
1 AAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTTTGAAAATTTAATTTT
* * ** * * *
3829467 AAGGAAAATTGATACTTTCAATTTTTCC-C-CCAAATTTTTTTTTGGAAACTTTAATTTC
1 AAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTTT-GAAAATTTAATTTT
* * * * * *
3829525 GAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTG--AATTTTATTTA
1 AAGAAAAATTGATACTTTCAACTTTTCCTCAAAAA-AATTTTTTTTGAAAATTTAATTTT
* * *** ** **** * **** * *
3829583 AAGAAAGTAAAATAATAAAAT-AAAATAAAATAAAAATAAAAGAATATT-AAACA-ATAA----
1 AAG-AA--AAATTGATACTTTCAACTTTTCCTCAAAA-AAATTTTTTTTGAAA-ATTTAATTTT
* *
3829640 AATAAAAATTGATACATTT-AACTTTTCCTCAAAAAAATATTTTTTGAAAATTT-ATGTTT
1 AAGAAAAATTGATAC-TTTCAACTTTTCCTCAAAAAAATTTTTTTTGAAAATTTAAT-TTT
* * *
3829699 AAAAAAAATTGATACTTTCAAATTTT-CTCAAAAAATTTTTTTTTGAAAACTTTAATTTT
1 AAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTTTGAAAA-TTTAATTTT
* * ** *
3829758 GAGAAAAATTGATACTTTTAACTTTTCCTCAAAAAAA-CCTTTTTGAAAATTTATTTTT
1 AAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTTTGAAAATTTAATTTT
* * *
3829816 GAGAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTT
1 AAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTTT
3829861 TGAATTTTAT
Statistics
Matches: 542, Mismatches: 114, Indels: 63
0.75 0.16 0.09
Matches are distributed among these distances:
54 15 0.03
55 13 0.02
56 2 0.00
57 34 0.06
58 198 0.37
59 168 0.31
60 89 0.16
61 22 0.04
62 1 0.00
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.42
Consensus pattern (59 bp):
AAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTTTGAAAATTTAATTTT
Found at i:3829250 original size:117 final size:117
Alignment explanation
Indices: 3829115--3829858 Score: 787
Period size: 117 Copynumber: 6.4 Consensus size: 117
3829105 GTAAAATTGA
*
3829115 AAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAAACTTTAATTTCGAGAAAA
1 AAGAAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGAAAACTTTAATTTCGAGAAAA
* *
3829180 ATTGAAACTTTCAACTTTTTCTCAAAAAAACCTTTTTTGAAAATTTATTTTT
66 ATTGATACTTTCAACTTTTCCTCAAAAAAACCTTTTTTGAAAATTTATTTTT
* *
3829232 AAGAAAAATTGATGCTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAACTTTAATTTCGAGAA
1 AAGAAAAATTGATACTTTCAACTTTTTCCCAAAAATA--TTTTTTGAAAACTTTAATTTCGAGAA
** **
3829297 AAATTGATACTTTCAACTTTTTTTC-AAAAAATTTTTTTTGAAAATTTATTTTT
64 AAATTGATACTTTCAACTTTTCCTCAAAAAAACCTTTTTTGAAAATTTATTTTT
*
3829350 AAGAAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGAAAATTTTAATTTCGAGAAAA
1 AAGAAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGAAAACTTTAATTTCGAGAAAA
*
3829415 ATTGATACTTTCAACTTTTCCTTAAAAAAACCTTTTTTGAAAATTTATTTTT
66 ATTGATACTTTCAACTTTTCCTCAAAAAAACCTTTTTTGAAAATTTATTTTT
* * * * * *
3829467 AAGGAAAATTGATACTTTCAA-TTTTTCCCCCAAATTTTTTTTTGGAAACTTTAATTTCGAGGAA
1 AAGAAAAATTGATACTTTCAACTTTTT-CCCAAAAATATTTTTTGAAAACTTTAATTTCGAGAAA
* *** * *
3829531 AATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTG-AATTTTA-TTTA
65 AATTGATACTTTCAACTTTTCCTCAAAAA-AACCTTTTTTGAAAATTTATTTTT
* * *** * * *** *** * * * ***
3829583 AAGAAAGTAAAATAATAAAATAAAATAAAAT---AAAAATA---AAAGAATA-TTAAACAATAAA
1 AAG-AA--AAATTGATACTTTCAACT-TTTTCCCAAAAATATTTTTTGAAAACTT-TA-ATTTCG
* ** *
3829641 ATAAAAATTGATACATTT-AACTTTTCCTCAAAAAAATATTTTTTGAAAATTTATGTTT
60 AGAAAAATTGATAC-TTTCAACTTTTCCTCAAAAAAACCTTTTTTGAAAATTTATTTTT
* * * * *
3829699 AAAAAAAATTGATACTTTCAA-ATTTTCTCAAAAAATTTTTTTTTGAAAACTTTAATTTTGAGAA
1 AAGAAAAATTGATACTTTCAACTTTTTC-CCAAAAA-TATTTTTTGAAAACTTTAATTTCGAGAA
*
3829763 AAATTGATACTTTTAACTTTTCCTCAAAAAAACC-TTTTTGAAAATTTATTTTT
64 AAATTGATACTTTCAACTTTTCCTCAAAAAAACCTTTTTTGAAAATTTATTTTT
* *
3829816 GAGAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT
1 AAGAAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTT
3829859 TTTGAATTTT
Statistics
Matches: 510, Mismatches: 91, Indels: 53
0.78 0.14 0.08
Matches are distributed among these distances:
111 1 0.00
113 12 0.02
114 13 0.03
115 42 0.08
116 73 0.14
117 195 0.38
118 106 0.21
119 64 0.13
120 3 0.01
121 1 0.00
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.42
Consensus pattern (117 bp):
AAGAAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGAAAACTTTAATTTCGAGAAAA
ATTGATACTTTCAACTTTTCCTCAAAAAAACCTTTTTTGAAAATTTATTTTT
Found at i:3829623 original size:29 final size:29
Alignment explanation
Indices: 3829590--3829648 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
3829580 TTAAAGAAAG
*
3829590 TAAAATAATA-AAATAAAATAAAATAAAAA
1 TAAAAGAATATAAA-AAAATAAAATAAAAA
* *
3829619 TAAAAGAATATTAAACAATAAAATAAAAA
1 TAAAAGAATATAAAAAAATAAAATAAAAA
3829648 T
1 T
3829649 TGATACATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (29 bp):
TAAAAGAATATAAAAAAATAAAATAAAAA
Found at i:3829897 original size:5 final size:5
Alignment explanation
Indices: 3829887--3829952 Score: 62
Period size: 5 Copynumber: 12.4 Consensus size: 5
3829877 AAAGTAAAAT
* *
3829887 AATAA AATAA AATAA AATAA AATAAA AATAA GGA-AA AGTAA AATAAA
1 AATAA AATAA AATAA AATAA AAT-AA AATAA -AATAA AATAA AAT-AA
3829934 AATAAA AATAAA AATAA AA
1 AAT-AA AAT-AA AATAA AA
3829953 GACTATTAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
5 30 0.57
6 23 0.43
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17
Consensus pattern (5 bp):
AATAA
Found at i:3829902 original size:10 final size:11
Alignment explanation
Indices: 3829875--3829952 Score: 79
Period size: 10 Copynumber: 6.9 Consensus size: 11
3829865 TTTTATTTAA
3829875 AAAAAGTAAAAT
1 AAAAA-TAAAAT
3829887 AATAAAATAAAAT
1 -A-AAAATAAAAT
3829900 -AAAATAAAAT
1 AAAAATAAAAT
**
3829910 AAAAAT-AAGG
1 AAAAATAAAAT
*
3829920 AAAAGTAAAAT
1 AAAAATAAAAT
3829931 AAAAATAAAAAT
1 AAAAAT-AAAAT
3829943 AAAAATAAAA
1 AAAAATAAAA
3829953 GACTATTAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
10 17 0.31
11 16 0.29
12 11 0.20
13 7 0.13
14 4 0.07
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:3829916 original size:6 final size:6
Alignment explanation
Indices: 3829890--3829952 Score: 62
Period size: 6 Copynumber: 10.5 Consensus size: 6
3829880 GTAAAATAAT
3829890 AAAAT- AAAAT- AAAAT- AAAATA AAAATA AGGAAA-A GTAAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA A--AAATA --AAAATA AAAATA
3829938 AAAATA AAAATA AAA
1 AAAATA AAAATA AAA
3829953 GACTATTAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
5 15 0.29
6 28 0.54
7 4 0.08
8 4 0.08
9 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:3830530 original size:5 final size:6
Alignment explanation
Indices: 3830506--3830571 Score: 51
Period size: 6 Copynumber: 10.2 Consensus size: 6
3830496 AAATAAGCAG
* * * *
3830506 ATAAATA ATAAAA ATAAAA ATAAAA ATATATAT ATATATA TTAAATA ATGAAA
1 ATAAA-A ATAAAA ATAAAA ATAAAA ATA-A-AA ATA-AAA ATAAA-A ATAAAA
3830559 ATAAAA ATAAAA A
1 ATAAAA ATAAAA A
3830572 GTCCATTGGG
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
6 30 0.62
7 12 0.25
8 6 0.12
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (6 bp):
ATAAAA
Found at i:3830875 original size:102 final size:102
Alignment explanation
Indices: 3830689--3830903 Score: 304
Period size: 102 Copynumber: 2.1 Consensus size: 102
3830679 TATAATCGCA
* * *
3830689 AGTCAAAAAATAACAACAATCGAGATTAAACTACGATTTTAAATTAAAGAGATCGAGATTGAATC
1 AGTCAGAAAATAACAACAATCAAGATTAAACTACGATTTTAAATTAAAGAGATCGAGATTGAACC
* *
3830754 ATAAATCAAAGAATGAAGAGATCGAGATTAAACTGCG
66 ATAAATCAAAGAATAAAGAGACCGAGATTAAACTGCG
* * * * *
3830791 AGTTAGAAAATAATAACAATCAAGATTGAACTACGATTTTAAATTAAAGAGATTGGGATTGAACC
1 AGTCAGAAAATAACAACAATCAAGATTAAACTACGATTTTAAATTAAAGAGATCGAGATTGAACC
*** *
3830856 ATAAATTGGAGAATAAAGAGACCGGGATTAAACTGCG
66 ATAAATCAAAGAATAAAGAGACCGAGATTAAACTGCG
3830893 AGTCAGAAAAT
1 AGTCAGAAAAT
3830904 GACGTTAACT
Statistics
Matches: 98, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
102 98 1.00
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.23
Consensus pattern (102 bp):
AGTCAGAAAATAACAACAATCAAGATTAAACTACGATTTTAAATTAAAGAGATCGAGATTGAACC
ATAAATCAAAGAATAAAGAGACCGAGATTAAACTGCG
Found at i:3831388 original size:110 final size:108
Alignment explanation
Indices: 3831266--3831982 Score: 646
Period size: 110 Copynumber: 6.5 Consensus size: 108
3831256 CGATTAGGAG
* * * * * *
3831266 AACACCGTGAATCAAAATTATATCTGGAGATCTTACAAATCATGCTCGGAGGTCTTACAAAATCG
1 AACACCGCGAATCAAAATTATACCTGAAGGTCTTAGAAATCATGCTCGGAGGTCTTACAGAATCG
* * * * * * *
3831331 ACTGAGACAATACCATAAGTCAACAAATAAGAAATCAATTGGGAT
66 ACTGGGATAACATCATAAGTCAA-AGATAA-AAATCGATCGGGAT
* * * * * * * * *
3831376 AAAATCGCGAATCAAATTTATGCCTGGAGGTTTTAGAAATCATGCCCAGAGGTCTTACAGAATTG
1 AACACCGCGAATCAAAATTATACCTGAAGGTCTTAGAAATCATGCTCGGAGGTCTTACAGAATCG
* * * *
3831441 ATTGAGATAACACCATAAGTTGAAAGATAAATAATCGATCGGGAT
66 ACTGGGATAACATCATAAG-TCAAAGATAAA-AATCGATCGGGAT
* ** * * *
3831486 AACATCGTAAATCAAAATTATGTCC-GGAGGTCTTAGAAATCATGCTCGAAGGTCTTACAGAATC
1 AACACCGCGAATCAAAATTAT-ACCTGAAGGTCTTAGAAATCATGCTCGGAGGTCTTACAGAATC
* *
3831550 GACTGGGATAACATCACAAGTCAAAAGATAAAGAATCGATCGAGAT
65 GACTGGGATAACATCATAAGTC-AAAGATAAA-AATCGATCGGGAT
* * * * *
3831596 AACACCACGAATCGAAATTATACCTGAAGGTCTTAGAAATCATGCCCGAAGATCTTACAGAATCG
1 AACACCGCGAATCAAAATTATACCTGAAGGTCTTAGAAATCATGCTCGGAGGTCTTACAGAATCG
* ** *
3831661 ATTGGGATAACATCGCAAGTCGAAAGATAAGAAATCGATTGGGAT
66 ACTGGGATAACATCATAAGTC-AAAGATAA-AAATCGATCGGGAT
** * * ** *
3831706 AACACTACGAATCGAAATTATGCCTGAAAATCTTAGAAATAATGC-CTGGAGGTCTTACAGAATC
1 AACACCGCGAATCAAAATTATACCTGAAGGTCTTAGAAATCATGCTC-GGAGGTCTTACAGAATC
* *
3831770 GATTGGGATAACATCGTAAGTCGAAAGATAAAAAATCGATCGGGAT
65 GACTGGGATAACATCATAAGTC-AAAGAT-AAAAATCGATCGGGAT
* * * * *
3831816 AACACCGCGAATCAAAATTATACCCGAAGGTCTTAAAAATCATACTCGGAGATCTTATAGAATCG
1 AACACCGCGAATCAAAATTATACCTGAAGGTCTTAGAAATCATGCTCGGAGGTCTTACAGAATCG
* ** * * *
3831881 ACTAGGATAACATCACGAGTTGAAAGATAAGAAATTGATCGAGAT
66 ACTGGGATAACATCATAAG-TCAAAGATAA-AAATCGATCGGGAT
* * * * * * * * *
3831926 AACATCACGAATCGAAATAATGCCTGGAGGTTTTAAAAATCATGCCCGGAGGTCTTA
1 AACACCGCGAATCAAAATTATACCTGAAGGTCTTAGAAATCATGCTCGGAGGTCTTA
3831983 GAAATCATGT
Statistics
Matches: 505, Mismatches: 91, Indels: 22
0.82 0.15 0.04
Matches are distributed among these distances:
109 7 0.01
110 488 0.97
111 10 0.02
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.24
Consensus pattern (108 bp):
AACACCGCGAATCAAAATTATACCTGAAGGTCTTAGAAATCATGCTCGGAGGTCTTACAGAATCG
ACTGGGATAACATCATAAGTCAAAGATAAAAATCGATCGGGAT
Found at i:3831544 original size:220 final size:216
Alignment explanation
Indices: 3831249--3831982 Score: 735
Period size: 220 Copynumber: 3.3 Consensus size: 216
3831239 GTCAAAAAAT
** * * * ** *
3831249 TAAG-AATCGATTAGGAGAACACCGTGAATCAAAATTATATCTGGAGATCTTACAAATCATGCTC
1 TAAGAAATCGATCGGGATAACATCGTAAATCAAAATTATGCCTGGAGATCTTAGAAATCATGCTC
* * * * * * *
3831313 GGAGGTCTTACAAAATCGACTGAGACAATACCATAAGTCAACAAATAAGAAATCAATTGGGATAA
66 GGAGGTCTTACAGAATCGACTGGGATAACATCATAAGTCAA-AAATAA-AAATCGATCGGGATAA
* * * * * * *
3831378 AATCGCGAATCAAATTTATGCCTGGAGGTTTTAGAAATCATGCCCAGAGGTCTTACAGAATTGAT
129 CACCGCGAATCAAA-TTATACCTGAAGGTCTTAGAAATCATGCCC-GAGATCTTACAGAATCGAT
* *
3831443 TGAGATAACACCATAAGTTGAAAGA
192 TGAGATAACATCACAAGTTGAAAGA
*
3831468 TAA-ATAATCGATCGGGATAACATCGTAAATCAAAATTATGTCC-GGAGGTCTTAGAAATCATGC
1 TAAGA-AATCGATCGGGATAACATCGTAAATCAAAATTATG-CCTGGAGATCTTAGAAATCATGC
* * *
3831531 TCGAAGGTCTTACAGAATCGACTGGGATAACATCACAAGTCAAAAGATAAAGAATCGATCGAGAT
64 TCGGAGGTCTTACAGAATCGACTGGGATAACATCATAAGTCAAAA-ATAAA-AATCGATCGGGAT
*
3831596 AACACCACGAATCGAAATTATACCTGAAGGTCTTAGAAATCATGCCCGAAGATCTTACAGAATCG
127 AACACCGCGAATC-AAATTATACCTGAAGGTCTTAGAAATCATGCCCG-AGATCTTACAGAATCG
* * *
3831661 ATTGGGATAACATCGCAAGTCGAAAGA
190 ATTGAGATAACATCACAAGTTGAAAGA
* * * * *
3831688 TAAGAAATCGATTGGGATAACA-C-TACGAATCGAAATTATGCCTGAAAATCTTAGAAATAATGC
1 TAAGAAATCGATCGGGATAACATCGTA--AATCAAAATTATGCCTGGAGATCTTAGAAATCATGC
* * *
3831751 -CTGGAGGTCTTACAGAATCGATTGGGATAACATCGTAAGTCGAAAGATAAAAAATCGATCGGGA
64 TC-GGAGGTCTTACAGAATCGACTGGGATAACATCATAAGTC-AAAAAT-AAAAATCGATCGGGA
* * * * *
3831815 TAACACCGCGAATCAAAATTATACCCGAAGGTCTTAAAAATCATACTCGGAGATCTTATAGAATC
126 TAACACCGCGAATC-AAATTATACCTGAAGGTCTTAGAAATCATGC-CCGAGATCTTACAGAATC
* *
3831880 GACT-AGGATAACATCACGAGTTGAAAGA
189 GATTGA-GATAACATCACAAGTTGAAAGA
* * *** * * * * * *
3831908 TAAGAAATTGATCGAGATAACATCACGAATCGAAATAATGCCTGGAGGTTTTAAAAATCATGCCC
1 TAAGAAATCGATCGGGATAACATCGTAAATCAAAATTATGCCTGGAGATCTTAGAAATCATGCTC
3831973 GGAGGTCTTA
66 GGAGGTCTTA
3831983 GAAATCATGT
Statistics
Matches: 428, Mismatches: 68, Indels: 37
0.80 0.13 0.07
Matches are distributed among these distances:
218 2 0.00
219 11 0.03
220 400 0.93
221 15 0.04
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.24
Consensus pattern (216 bp):
TAAGAAATCGATCGGGATAACATCGTAAATCAAAATTATGCCTGGAGATCTTAGAAATCATGCTC
GGAGGTCTTACAGAATCGACTGGGATAACATCATAAGTCAAAAATAAAAATCGATCGGGATAACA
CCGCGAATCAAATTATACCTGAAGGTCTTAGAAATCATGCCCGAGATCTTACAGAATCGATTGAG
ATAACATCACAAGTTGAAAGA
Found at i:3831849 original size:330 final size:329
Alignment explanation
Indices: 3831237--3831982 Score: 870
Period size: 330 Copynumber: 2.3 Consensus size: 329
3831227 ACTAAACCGT
* * * ** * * *
3831237 AAGTCAAAAAATTAAGAATCGAT-TAGGAGAACACCGTGAATCAAAATTATATCTGGAGATCTTA
1 AAGTCAAAAGA-TAAGAATCGATCGA-GATAACACCACGAATCGAAATTATACCTGGAGGTCTTA
* * * *
3831301 CAAATCATGCTCGGAGGTCTTACAAAATCGACTGAGACAATACCATAAGTCAACAAATAAGAAAT
64 AAAATCATGCCCGGAGGTCTTACAAAATCGACTGAGACAACACCACAAGTCAACAAATAAGAAAT
* * ** * *
3831366 CAATTGGGATAAAATCGCGAATCAAATTTATGCCTGGAGGTTTTAGAAATCATGCCCAGAGGTCT
129 CAATTGGGATAAAATCACGAATCAAATTTATGCCTGAAAATCTTAGAAATAATGCCCAGAGGTCT
* * * * *
3831431 TACAGAATTGATTGAGATAACACCATAAGTTGAAAGATAAATAATCGATCGGGATAACATCGTAA
194 TACAGAATCGATTGAGATAACACCATAAGTCGAAAGATAAAAAATCGATCGGGATAACACCGCAA
** * * * * *
3831496 ATCAAAATTATGTCCGGAGGTCTTAGAAATCATGCTCGAAGGTCTTACAGAATCGACTGGGATAA
259 ATCAAAATTATACCCGAAGGTCTTAAAAATCATACTCGAAGATCTTACAGAATCGACTAGGATAA
3831561 CATCAC
324 CATCAC
* *
3831567 AAGTCAAAAGATAAAGAATCGATCGAGATAACACCACGAATCGAAATTATACCTGAAGGTCTTAG
1 AAGTCAAAAGAT-AAGAATCGATCGAGATAACACCACGAATCGAAATTATACCTGGAGGTCTTAA
* * * * * * * * *
3831632 AAATCATGCCCGAAGATCTTACAGAATCGATTGGGATAACATCGCAAGTCGAA-AGATAAGAAAT
65 AAATCATGCCCGGAGGTCTTACAAAATCGACTGAGACAACACCACAAGTC-AACAAATAAGAAAT
* * **
3831696 CGATTGGGATAACA-CTACGAATCGAAA-TTATGCCTGAAAATCTTAGAAATAATGCCTGGAGGT
129 CAATTGGGATAAAATC-ACGAATC-AAATTTATGCCTGAAAATCTTAGAAATAATGCCCAGAGGT
* * *
3831759 CTTACAGAATCGATTGGGATAACATCGTAAGTCGAAAGATAAAAAATCGATCGGGATAACACCGC
192 CTTACAGAATCGATTGAGATAACACCATAAGTCGAAAGATAAAAAATCGATCGGGATAACACCGC
* * *
3831824 GAATCAAAATTATACCCGAAGGTCTTAAAAATCATACTCGGAGATCTTATAGAATCGACTAGGAT
257 AAATCAAAATTATACCCGAAGGTCTTAAAAATCATACTCGAAGATCTTACAGAATCGACTAGGAT
3831889 AACATCAC
322 AACATCAC
* ** * * * * *
3831897 GAGTTGAAAGATAAGAAATTGATCGAGATAACATCACGAATCGAAATAATGCCTGGAGGTTTTAA
1 AAGTCAAAAGATAAG-AATCGATCGAGATAACACCACGAATCGAAATTATACCTGGAGGTCTTAA
3831962 AAATCATGCCCGGAGGTCTTA
65 AAATCATGCCCGGAGGTCTTA
3831983 GAAATCATGT
Statistics
Matches: 348, Mismatches: 62, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
329 5 0.01
330 337 0.97
331 6 0.02
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (329 bp):
AAGTCAAAAGATAAGAATCGATCGAGATAACACCACGAATCGAAATTATACCTGGAGGTCTTAAA
AATCATGCCCGGAGGTCTTACAAAATCGACTGAGACAACACCACAAGTCAACAAATAAGAAATCA
ATTGGGATAAAATCACGAATCAAATTTATGCCTGAAAATCTTAGAAATAATGCCCAGAGGTCTTA
CAGAATCGATTGAGATAACACCATAAGTCGAAAGATAAAAAATCGATCGGGATAACACCGCAAAT
CAAAATTATACCCGAAGGTCTTAAAAATCATACTCGAAGATCTTACAGAATCGACTAGGATAACA
TCAC
Found at i:3831970 original size:22 final size:21
Alignment explanation
Indices: 3831940--3832004 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
3831930 TCACGAATCG
*
3831940 AAATAATGCCTGGAGGTTTTAA
1 AAATCATGCC-GGAGGTTTTAA
* *
3831962 AAATCATGCCCGGAGGTCTTAG
1 AAATCATG-CCGGAGGTTTTAA
*
3831984 AAATCATGTCCGAAGGTTTTA
1 AAATCATG-CCGGAGGTTTTA
3832005 CAGAATCAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
22 34 0.94
23 2 0.06
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.29
Consensus pattern (21 bp):
AAATCATGCCGGAGGTTTTAA
Found at i:3832042 original size:132 final size:133
Alignment explanation
Indices: 3831829--3832133 Score: 312
Period size: 132 Copynumber: 2.3 Consensus size: 133
3831819 ACCGCGAATC
* * * * * * * *
3831829 AAAATTATACCC-GAAGGTCTTA-AAAATCATACTCGGAGATCTTATAGAATCGACTAGGATAAC
1 AAAATCATACCCAG-AGGTCTTACAAAATCATGCCCGAAGGTTTTACAGAATCAACTAGGATAAC
* * * * * * *
3831892 ATCACGAGTTGAAAGATAAGAAATTGATC-GAGATAACATCACGAATCGAAATAATGCCTGGAGG
65 ACCACAAGTCGAAAGATAAAAAATCGATCGGA-ATAACATCACAAATCGAAATAATGCCTGAAGG
*
3831956 TTTTA
129 TCTTA
* * * * *
3831961 AAAATCATGCCCGGAGGTCTTA-GAAATCATGTCCGAAGGTTTTACAGAATCAACTGGGATAACA
1 AAAATCATACCCAGAGGTCTTACAAAATCATGCCCGAAGGTTTTACAGAATCAACTAGGATAACA
** * *
3832025 CCACAAGTCGAAAGATAAAAAATCGATCGGAATAACATCGTAAATCGAATTTATGCCTGAAGGTC
66 CCACAAGTCGAAAGATAAAAAATCGATCGGAATAACATCACAAATCGAAATAATGCCTGAAGGTC
3832090 TTA
131 TTA
* * *
3832093 GAAATCATACTCAGAGGTCTTACAAAATCATGCCCGGAGGT
1 AAAATCATACCCAGAGGTCTTACAAAATCATGCCCGAAGGT
3832134 CTTGAAAGTT
Statistics
Matches: 139, Mismatches: 31, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
132 121 0.87
133 18 0.13
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (133 bp):
AAAATCATACCCAGAGGTCTTACAAAATCATGCCCGAAGGTTTTACAGAATCAACTAGGATAACA
CCACAAGTCGAAAGATAAAAAATCGATCGGAATAACATCACAAATCGAAATAATGCCTGAAGGTC
TTA
Found at i:3832113 original size:22 final size:22
Alignment explanation
Indices: 3832085--3832140 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
3832075 TTATGCCTGA
*
3832085 AGGTCTTAGAAATCATACTCAG
1 AGGTCTTAGAAATCATACCCAG
* * *
3832107 AGGTCTTACAAAATCATGCCCGG
1 AGGTCTTA-GAAATCATACCCAG
3832130 AGGTCTT-GAAA
1 AGGTCTTAGAAA
3832141 GTTGTGCCTA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 3 0.11
22 8 0.29
23 17 0.61
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (22 bp):
AGGTCTTAGAAATCATACCCAG
Found at i:3834107 original size:9 final size:9
Alignment explanation
Indices: 3834070--3834108 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
3834060 CTTTTGTTTG
*
3834070 TTTTTTTCTT
1 TTTTTTT-TA
3834080 TTTTTTTTA
1 TTTTTTTTA
3834089 CTTTTTTTTA
1 -TTTTTTTTA
3834099 TTTTTTTTA
1 TTTTTTTTA
3834108 T
1 T
3834109 GTCCCATCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 11 0.41
10 16 0.59
ACGTcount: A:0.08, C:0.05, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:3834691 original size:15 final size:13
Alignment explanation
Indices: 3834673--3834718 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 13
3834663 CTTTTTCTCT
3834673 TTTTTCTTTTTTTG
1 TTTTT-TTTTTTTG
3834687 ATTTTTTTTGTTTTG
1 -TTTTTTTT-TTTTG
3834702 TTTTTTTTTTTT-
1 TTTTTTTTTTTTG
3834714 TTTTT
1 TTTTT
3834719 AAATCTTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.17
13 4 0.13
14 11 0.37
15 10 0.33
ACGTcount: A:0.02, C:0.02, G:0.07, T:0.89
Consensus pattern (13 bp):
TTTTTTTTTTTTG
Found at i:3834700 original size:23 final size:23
Alignment explanation
Indices: 3834674--3834718 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3834664 TTTTTCTCTT
3834674 TTTTCTTTTTTTGATTTTTTTTG
1 TTTTCTTTTTTTGATTTTTTTTG
* **
3834697 TTTTGTTTTTTTTTTTTTTTTT
1 TTTTCTTTTTTTGATTTTTTTT
3834719 AAATCTTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.02, C:0.02, G:0.07, T:0.89
Consensus pattern (23 bp):
TTTTCTTTTTTTGATTTTTTTTG
Found at i:3837661 original size:31 final size:31
Alignment explanation
Indices: 3837623--3837685 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
3837613 AAGCAAAGAA
3837623 TTTAAGAAAAATCTTTAATCTTTGGAAATGT
1 TTTAAGAAAAATCTTTAATCTTTGGAAATGT
3837654 TTTAAGAAAAATCTTTAATCTTTGGAAATGT
1 TTTAAGAAAAATCTTTAATCTTTGGAAATGT
3837685 T
1 T
3837686 CTTTTGCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43
Consensus pattern (31 bp):
TTTAAGAAAAATCTTTAATCTTTGGAAATGT
Found at i:3840955 original size:21 final size:22
Alignment explanation
Indices: 3840908--3840956 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
3840898 TTTATTTTTT
*
3840908 TTTATTTTTTATATAATTAATA
1 TTTATTTTTTATAAAATTAATA
*
3840930 ATTATTTTTTA-AAAA-TATATA
1 TTTATTTTTTATAAAATTA-ATA
3840951 TTTATT
1 TTTATT
3840957 ATTGTTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.09
21 11 0.48
22 10 0.43
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTATTTTTTATAAAATTAATA
Found at i:3846719 original size:15 final size:15
Alignment explanation
Indices: 3846699--3846740 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
3846689 TTGAATATAG
*
3846699 ATAAATGATTGTTAT
1 ATAAATGATTATTAT
* *
3846714 ATAAATCATAATTAT
1 ATAAATGATTATTAT
3846729 ATAAATGATTAT
1 ATAAATGATTAT
3846741 AATCATTTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (15 bp):
ATAAATGATTATTAT
Found at i:3847551 original size:24 final size:22
Alignment explanation
Indices: 3847524--3847587 Score: 58
Period size: 24 Copynumber: 2.8 Consensus size: 22
3847514 TATTTATGTT
*
3847524 TAAATAAAAATAATTATTGTATGA
1 TAAAT-AAAATAATTATTGAAT-A
**
3847548 TAAATGATCATAATTATTTGAATA
1 TAAAT-AAAATAATTA-TTGAATA
3847572 TAAATAAAAT-ATTATT
1 TAAATAAAATAATTATT
3847588 CATAAAAGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
21 2 0.06
22 4 0.12
23 3 0.09
24 19 0.58
25 5 0.15
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.41
Consensus pattern (22 bp):
TAAATAAAATAATTATTGAATA
Found at i:3847677 original size:18 final size:18
Alignment explanation
Indices: 3847651--3847686 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3847641 TTTTTATTCA
*
3847651 TTTATTATAAATATTTTT
1 TTTAATATAAATATTTTT
*
3847669 TTTAATATAATTATTTTT
1 TTTAATATAAATATTTTT
3847687 ACTATTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTAATATAAATATTTTT
Found at i:3851725 original size:21 final size:21
Alignment explanation
Indices: 3851682--3851725 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3851672 AAAGGAATAA
**
3851682 TTACTTTTAAAAAAGTATTTT
1 TTACTTTTAAAAAAGTAAATT
3851703 TTACTCTTTAAAAAA-TAAATT
1 TTACT-TTTAAAAAAGTAAATT
3851724 TT
1 TT
3851726 TTAATTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (21 bp):
TTACTTTTAAAAAAGTAAATT
Found at i:3861909 original size:11 final size:11
Alignment explanation
Indices: 3861895--3861932 Score: 53
Period size: 10 Copynumber: 3.6 Consensus size: 11
3861885 TCTCATTCCC
3861895 TCTCTCTCTTT
1 TCTCTCTCTTT
3861906 TCTCTC-CTTT
1 TCTCTCTCTTT
*
3861916 TC-CTCTCTCT
1 TCTCTCTCTTT
3861926 TCTCTCT
1 TCTCTCT
3861933 TTGTTTCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
9 3 0.12
10 11 0.46
11 10 0.42
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (11 bp):
TCTCTCTCTTT
Found at i:3866843 original size:14 final size:13
Alignment explanation
Indices: 3866821--3866864 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
3866811 ATTTTCTCTC
*
3866821 TTTTATCATCTTTT
1 TTTTTTCAT-TTTT
3866835 TTTTTTCATTTTTT
1 TTTTTTCA-TTTTT
3866849 CTTTTTTCATTTTT
1 -TTTTTTCATTTTT
3866863 TT
1 TT
3866865 CCATCCATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 2 0.07
14 16 0.59
15 9 0.33
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTTCATTTTT
Found at i:3866843 original size:31 final size:28
Alignment explanation
Indices: 3866808--3866864 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 28
3866798 AATTTGACTA
3866808 TTCATTTTCTCTCTTTTATCATCTTTTTTTT
1 TTCATTTT-T-TCTTTTATCAT-TTTTTTTT
*
3866839 TTCATTTTTTCTTTTTTCATTTTTTT
1 TTCATTTTTTCTTTTATCATTTTTTT
3866865 CCATCCATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 6 0.24
29 10 0.40
30 1 0.04
31 8 0.32
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (28 bp):
TTCATTTTTTCTTTTATCATTTTTTTTT
Found at i:3866848 original size:8 final size:8
Alignment explanation
Indices: 3866835--3866863 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
3866825 ATCATCTTTT
3866835 TTTTTTCA
1 TTTTTTCA
3866843 TTTTTTC-
1 TTTTTTCA
3866850 TTTTTTCA
1 TTTTTTCA
3866858 TTTTTT
1 TTTTTT
3866864 TCCATCCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTTCA
Found at i:3866853 original size:15 final size:15
Alignment explanation
Indices: 3866808--3866863 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
3866798 AATTTGACTA
3866808 TTCATTTTCTCTCTTTT
1 TTCATTTT-T-TCTTTT
* *
3866825 ATCATCTTTT-TTTT
1 TTCATTTTTTCTTTT
3866839 TTCATTTTTTCTTTT
1 TTCATTTTTTCTTTT
3866854 TTCATTTTTT
1 TTCATTTTTT
3866864 TCCATCCATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
14 12 0.35
15 15 0.44
16 1 0.03
17 6 0.18
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (15 bp):
TTCATTTTTTCTTTT
Found at i:3871436 original size:26 final size:24
Alignment explanation
Indices: 3871407--3871477 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 24
3871397 AATTTAGAAA
*
3871407 AAATTTCTCACTTAGGAATTTTATAG
1 AAATTTCTCA-TTAGAAATTTT-TAG
* * *
3871433 AAATTTATCATTTGAAATTTTTAT
1 AAATTTCTCATTAGAAATTTTTAG
3871457 AAATTTCATCATTAGATAATT
1 AAATTTC-TCATTAGA-AATT
3871478 ATTATTTATT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
24 8 0.22
25 16 0.43
26 13 0.35
ACGTcount: A:0.38, C:0.08, G:0.07, T:0.46
Consensus pattern (24 bp):
AAATTTCTCATTAGAAATTTTTAG
Found at i:3871577 original size:16 final size:16
Alignment explanation
Indices: 3871535--3871581 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
3871525 TAATTATGCA
3871535 AAAATACTAAAAAAAT
1 AAAATACTAAAAAAAT
* *
3871551 -AAACACATAAATAAAT
1 AAAATAC-TAAAAAAAT
3871567 AAAATACTAAAAAAA
1 AAAATACTAAAAAAA
3871582 CCTTAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 5 0.20
16 15 0.60
17 5 0.20
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAATACTAAAAAAAT
Found at i:3883581 original size:15 final size:15
Alignment explanation
Indices: 3883561--3883591 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3883551 AAGAAAAAAG
3883561 ATGGTTATGGACTTA
1 ATGGTTATGGACTTA
3883576 ATGGTTATGGACTTA
1 ATGGTTATGGACTTA
3883591 A
1 A
3883592 AAGGTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.06, G:0.26, T:0.39
Consensus pattern (15 bp):
ATGGTTATGGACTTA
Found at i:3886284 original size:24 final size:23
Alignment explanation
Indices: 3886257--3886314 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 23
3886247 TTTTACCCTC
3886257 TTCCATTTTTTTCCTTTTCTTTAT
1 TTCC-TTTTTTTCCTTTTCTTTAT
* *
3886281 TTCCTTTTCTTTTCTTTTCTTTTT
1 TTCCTTTT-TTTCCTTTTCTTTAT
3886305 TTCCTTTTTT
1 TTCCTTTTTT
3886315 AATATTATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 6 0.19
24 25 0.81
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (23 bp):
TTCCTTTTTTTCCTTTTCTTTAT
Found at i:3886285 original size:14 final size:13
Alignment explanation
Indices: 3886263--3886312 Score: 61
Period size: 14 Copynumber: 3.9 Consensus size: 13
3886253 CCTCTTCCAT
3886263 TTTTTTCCTTTTC
1 TTTTTTCCTTTTC
3886276 TTTATTTCCTTTTC
1 TTT-TTTCCTTTTC
3886290 --TTTT-CTTTTC
1 TTTTTTCCTTTTC
3886300 TTTTTTTCCTTTT
1 -TTTTTTCCTTTT
3886313 TTAATATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
10 6 0.19
11 3 0.09
12 1 0.03
13 7 0.22
14 15 0.47
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTTTCCTTTTC
Found at i:3887645 original size:20 final size:20
Alignment explanation
Indices: 3887607--3887658 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
3887597 ATAATTATTT
3887607 TATATATAAATTTATTTAAA
1 TATATATAAATTTATTTAAA
*
3887627 TATAT-TAATTTTATATTAAAA
1 TATATATAAATTTAT-TT-AAA
3887648 TAATATATAAA
1 T-ATATATAAA
3887659 ATACAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 8 0.31
20 7 0.27
21 4 0.15
22 4 0.15
23 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TATATATAAATTTATTTAAA
Found at i:3887916 original size:29 final size:29
Alignment explanation
Indices: 3887867--3887934 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
3887857 TATTATATTA
* *
3887867 ATTAACATA-TTTATAATTTAAATATCAT
1 ATTAAAATATTTTAAAATTTAAATATCAT
* *
3887895 ATTAAAATATTTTAAAATTTAATTATTAT
1 ATTAAAATATTTTAAAATTTAAATATCAT
*
3887924 AAT-AAATATTT
1 ATTAAAATATTT
3887935 AACTATAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 16 0.47
29 18 0.53
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (29 bp):
ATTAAAATATTTTAAAATTTAAATATCAT
Found at i:3888238 original size:2 final size:2
Alignment explanation
Indices: 3888231--3888259 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3888221 TATGATGGTT
3888231 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3888260 GCATAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3889197 original size:36 final size:35
Alignment explanation
Indices: 3889151--3889224 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 35
3889141 AATCAATCTC
*
3889151 TTAATATAATTACGAAAATAC-TCTTCTTATCATAA
1 TTAATATAATTACGAAAATACAT-TTCTCATCATAA
**
3889186 TTAATCATAATTATTAAAATACATTTCTCATCATAA
1 TTAAT-ATAATTACGAAAATACATTTCTCATCATAA
3889222 TTA
1 TTA
3889225 TAAAATTGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
35 5 0.15
36 28 0.82
37 1 0.03
ACGTcount: A:0.43, C:0.14, G:0.01, T:0.42
Consensus pattern (35 bp):
TTAATATAATTACGAAAATACATTTCTCATCATAA
Found at i:3895541 original size:62 final size:63
Alignment explanation
Indices: 3895472--3895637 Score: 205
Period size: 62 Copynumber: 2.7 Consensus size: 63
3895462 AATATAAGAG
*
3895472 GATTATTTAAGGTATTTTGATCCAAAAATACCTTAAATAATC-CTCAGTAATTTTTT-AAAGGA
1 GATTATTTAAGGTATTTTGATCCAAAAATACCTTAAATAATCTC-CAATAATTTTTTAAAAGGA
* ** * *
3895534 GATTATTTAAGGTATTTTTATCCAAAAATTTCTTAAATAATCTCCAATATTTTTTTAAAATGA
1 GATTATTTAAGGTATTTTGATCCAAAAATACCTTAAATAATCTCCAATAATTTTTTAAAAGGA
* *
3895597 -ATTATTTAAGGTATTTTTGGTTC-AAAATCACCTTAAATAAT
1 GATTATTTAAGGTA-TTTTGATCCAAAAAT-ACCTTAAATAAT
3895638 TCTCTTTAAA
Statistics
Matches: 89, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
62 67 0.75
63 22 0.25
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (63 bp):
GATTATTTAAGGTATTTTGATCCAAAAATACCTTAAATAATCTCCAATAATTTTTTAAAAGGA
Found at i:3897160 original size:26 final size:25
Alignment explanation
Indices: 3897112--3897160 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
3897102 CTCTTTGGGT
* *
3897112 TTTTAATTTTAATTTTATTTTATGA
1 TTTTAATTTTAATTATATCTTATGA
*
3897137 TTTTAATTTTCCATTATATCTTAT
1 TTTTAATTTT-AATTATATCTTAT
3897161 CCTATATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 10 0.50
26 10 0.50
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (25 bp):
TTTTAATTTTAATTATATCTTATGA
Found at i:3903414 original size:129 final size:130
Alignment explanation
Indices: 3903182--3903441 Score: 432
Period size: 129 Copynumber: 2.0 Consensus size: 130
3903172 CTGACTCCAT
*
3903182 TGAACCCCAGACCTCTCCCTGTGCATTCGGAACATCAATCAGTTGATGTCTCAAATCCTGGAAAC
1 TGAACCCCAGACCTCTCCCGGTGCATTCGGAACATCAATCAGTTGATGTCTCAAATCCTGGAAAC
* *
3903247 TGTAAAGCGTCTAGAAAAAGGCAAACACATTAGGCCATATATAAGTCATTACGTG-AAGAAAACA
66 TGTAAAGCGTCTAGAAAAAGGCAAACACATTAGCCCATATAGAAGTCATTACGTGAAAGAAAACA
* * * *
3903311 TGAACCCCAGGCCTCTCCCGGTGCATTCGGGACATCAATCAGTTGATGTGTCAAATCCTGGAAAG
1 TGAACCCCAGACCTCTCCCGGTGCATTCGGAACATCAATCAGTTGATGTCTCAAATCCTGGAAAC
* *
3903376 TGTAAAGCGTCTAGGAAAAGGCAAACACATTAGCCCATATAGATGTCATTACGTGAAAGAAAACA
66 TGTAAAGCGTCTAGAAAAAGGCAAACACATTAGCCCATATAGAAGTCATTACGTGAAAGAAAACA
3903441 T
1 T
3903442 TTAGCCCATA
Statistics
Matches: 121, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
129 111 0.92
130 10 0.08
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (130 bp):
TGAACCCCAGACCTCTCCCGGTGCATTCGGAACATCAATCAGTTGATGTCTCAAATCCTGGAAAC
TGTAAAGCGTCTAGAAAAAGGCAAACACATTAGCCCATATAGAAGTCATTACGTGAAAGAAAACA
Found at i:3903458 original size:36 final size:37
Alignment explanation
Indices: 3903405--3903477 Score: 130
Period size: 36 Copynumber: 2.0 Consensus size: 37
3903395 GGCAAACACA
*
3903405 TTAGCCCATATAGATGTCATTACGTGAAAGAAAACAT
1 TTAGCCCATATAGATGTCATAACGTGAAAGAAAACAT
3903442 TTAGCCCATATA-ATGTCATAACGTGAAAGAAAACAT
1 TTAGCCCATATAGATGTCATAACGTGAAAGAAAACAT
3903478 GAACCCCAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 23 0.66
37 12 0.34
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.26
Consensus pattern (37 bp):
TTAGCCCATATAGATGTCATAACGTGAAAGAAAACAT
Found at i:3904026 original size:27 final size:27
Alignment explanation
Indices: 3903995--3904053 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
3903985 CGCTCCACAT
3903995 CAATACCCTTGAAATCTAATCCACCGC
1 CAATACCCTTGAAATCTAATCCACCGC
***
3904022 CAATATGGTTGAAATCTAATCCACCGC
1 CAATACCCTTGAAATCTAATCCACCGC
3904049 CAATA
1 CAATA
3904054 TGGTATGCCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.36, C:0.31, G:0.10, T:0.24
Consensus pattern (27 bp):
CAATACCCTTGAAATCTAATCCACCGC
Found at i:3904054 original size:27 final size:27
Alignment explanation
Indices: 3904003--3904057 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
3903993 ATCAATACCC
3904003 TTGAAATCTAATCCACCGCCAATATGG
1 TTGAAATCTAATCCACCGCCAATATGG
3904030 TTGAAATCTAATCCACCGCCAATATGG
1 TTGAAATCTAATCCACCGCCAATATGG
3904057 T
1 T
3904058 ATGCCCAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (27 bp):
TTGAAATCTAATCCACCGCCAATATGG
Found at i:3905820 original size:15 final size:16
Alignment explanation
Indices: 3905780--3905823 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
3905770 ATTGTGGGAT
*
3905780 TTTTTTTATATATATA
1 TTTTTTAATATATATA
* *
3905796 TTTATAAATAT-TATA
1 TTTTTTAATATATATA
3905811 TTTTTTAATATAT
1 TTTTTTAATATAT
3905824 GTATATTAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTTTAATATATATA
Found at i:3905904 original size:23 final size:22
Alignment explanation
Indices: 3905862--3905905 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3905852 AAAAATATAG
*
3905862 TTTTTATTTTTTGATGATTATT
1 TTTTTATTTTTTGATAATTATT
3905884 TTTTTATTCATTTT-ATAATTAT
1 TTTTTATT--TTTTGATAATTAT
3905906 AACTAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 8 0.42
23 7 0.37
24 4 0.21
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (22 bp):
TTTTTATTTTTTGATAATTATT
Found at i:3910768 original size:4 final size:4
Alignment explanation
Indices: 3910759--3910792 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
3910749 ATGAAAATAC
*
3910759 AAAG AAAG AAAG AAGAG AAAG AAAG AAGG AAAG A
1 AAAG AAAG AAAG AA-AG AAAG AAAG AAAG AAAG A
3910793 GAATGGGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:3910779 original size:13 final size:13
Alignment explanation
Indices: 3910761--3910792 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
3910751 GAAAATACAA
3910761 AGAAAGAAAGAAG
1 AGAAAGAAAGAAG
3910774 AGAAAGAAAGAAG
1 AGAAAGAAAGAAG
3910787 -GAAAGA
1 AGAAAGA
3910793 GAATGGGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
AGAAAGAAAGAAG
Found at i:3910781 original size:17 final size:18
Alignment explanation
Indices: 3910759--3910795 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
3910749 ATGAAAATAC
3910759 AAAGAAAGAAAG-AAGAG
1 AAAGAAAGAAAGAAAGAG
*
3910776 AAAGAAAGAAGGAAAGAG
1 AAAGAAAGAAAGAAAGAG
3910794 AA
1 AA
3910796 TGGGAGAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (18 bp):
AAAGAAAGAAAGAAAGAG
Found at i:3911627 original size:20 final size:22
Alignment explanation
Indices: 3911589--3911629 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
3911579 GAAGTTAGTT
3911589 CAAAAGAGAGGACTGGAAGGAA
1 CAAAAGAGAGGACTGGAAGGAA
3911611 CAAAAG-GAGGA-TGGAAGGA
1 CAAAAGAGAGGACTGGAAGGA
3911630 TTTTTTGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
21 5 0.26
22 6 0.32
ACGTcount: A:0.49, C:0.07, G:0.39, T:0.05
Consensus pattern (22 bp):
CAAAAGAGAGGACTGGAAGGAA
Found at i:3913303 original size:2 final size:2
Alignment explanation
Indices: 3913298--3913329 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3913288 TGTGTGTGTG
*
3913298 TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3913330 GCTCTTTGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3928516 original size:20 final size:19
Alignment explanation
Indices: 3928491--3928535 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
3928481 ATTTGGTGTT
3928491 TTCTTCTCCATTTC-TTTTTA
1 TTCTTCT-C-TTTCGTTTTTA
3928511 TTCTTCTCTTTCGTTTTTA
1 TTCTTCTCTTTCGTTTTTA
3928530 TT-TTCT
1 TTCTTCT
3928536 ATATAGTGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.33
19 9 0.38
20 7 0.29
ACGTcount: A:0.07, C:0.22, G:0.02, T:0.69
Consensus pattern (19 bp):
TTCTTCTCTTTCGTTTTTA
Found at i:3928527 original size:18 final size:20
Alignment explanation
Indices: 3928491--3928527 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
3928481 ATTTGGTGTT
*
3928491 TTCTTCTCCATTTCTTTTTA
1 TTCTTCTCCATTTCGTTTTA
3928511 TTCTTCT-C-TTTCGTTTT
1 TTCTTCTCCATTTCGTTTT
3928528 TATTTTCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 1 0.06
20 7 0.44
ACGTcount: A:0.05, C:0.24, G:0.03, T:0.68
Consensus pattern (20 bp):
TTCTTCTCCATTTCGTTTTA
Found at i:3935316 original size:22 final size:22
Alignment explanation
Indices: 3935291--3935353 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 22
3935281 CTTTGTCCAT
* * *
3935291 AATTTTTTTTTTTGATGTTCAA
1 AATTTTATTTTTTCATATTCAA
* * *
3935313 AATTATGTTTTTTCATATTTAA
1 AATTTTATTTTTTCATATTCAA
3935335 AATATTTATTTTTT-ATATT
1 AAT-TTTATTTTTTCATATT
3935354 TTTAAATTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
22 25 0.76
23 8 0.24
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (22 bp):
AATTTTATTTTTTCATATTCAA
Found at i:3935366 original size:22 final size:22
Alignment explanation
Indices: 3935311--3935368 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
3935301 TTTGATGTTC
*
3935311 AAAATTATGTTTTTTCATATTT
1 AAAATTATATTTTTTCATATTT
*
3935333 AAAATATTTATTTTTT-ATATTTT
1 AAAAT-TATATTTTTTCATA-TTT
*
3935356 TAAATTATATTTT
1 AAAATTATATTTT
3935369 AATTTTGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 15 0.50
23 15 0.50
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (22 bp):
AAAATTATATTTTTTCATATTT
Found at i:3940886 original size:6 final size:6
Alignment explanation
Indices: 3940875--3940905 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
3940865 TGGCCCTGAA
*
3940875 CCAAAC CCAAAC CCAAAC CCAAAC CCGAAC C
1 CCAAAC CCAAAC CCAAAC CCAAAC CCAAAC C
3940906 ACCCACCCGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.45, C:0.52, G:0.03, T:0.00
Consensus pattern (6 bp):
CCAAAC
Found at i:3952361 original size:23 final size:25
Alignment explanation
Indices: 3952325--3952370 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
3952315 ATTTTTTGGC
* *
3952325 TGATTTGTCTGTTA-TTTTTTTATT
1 TGATTTATCTGTTAGCTTTTTTATT
3952349 TGATTTATC-GTTAGCTTTTTTA
1 TGATTTATCTGTTAGCTTTTTTA
3952371 GGTAATAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.15, C:0.07, G:0.13, T:0.65
Consensus pattern (25 bp):
TGATTTATCTGTTAGCTTTTTTATT
Found at i:3952692 original size:14 final size:14
Alignment explanation
Indices: 3952673--3952703 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
3952663 AAAAAGAAGA
3952673 TTTTTTTGG-AAAT
1 TTTTTTTGGAAAAT
3952686 TTTTTTTGGAAAAT
1 TTTTTTTGGAAAAT
3952700 TTTT
1 TTTT
3952704 ATTTTTTCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.65
Consensus pattern (14 bp):
TTTTTTTGGAAAAT
Found at i:3953547 original size:21 final size:21
Alignment explanation
Indices: 3953523--3953562 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3953513 AAAAAGATAA
3953523 AAAAAATAAAA-ACTAAAAACT
1 AAAAAATAAAAGA-TAAAAACT
*
3953544 AAAAGATAAAAGATAAAAA
1 AAAAAATAAAAGATAAAAA
3953563 TATTAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.78, C:0.05, G:0.05, T:0.12
Consensus pattern (21 bp):
AAAAAATAAAAGATAAAAACT
Found at i:3955153 original size:16 final size:16
Alignment explanation
Indices: 3955129--3955202 Score: 57
Period size: 16 Copynumber: 4.8 Consensus size: 16
3955119 TTAGGGTCTC
*
3955129 ATTTTAGGGTTTTAGG
1 ATTTCAGGGTTTTAGG
*
3955145 ATTTCAGGGTTTTTGG
1 ATTTCAGGGTTTTAGG
3955161 ATTT-ATGGG-TTTATGG
1 ATTTCA-GGGTTTTA-GG
* * *
3955177 -TTTAAAGGTTTAAGG
1 ATTTCAGGGTTTTAGG
3955192 -TTTCAGGGTTT
1 ATTTCAGGGTTT
3955203 CGAGGTTTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
15 20 0.43
16 27 0.57
ACGTcount: A:0.19, C:0.03, G:0.30, T:0.49
Consensus pattern (16 bp):
ATTTCAGGGTTTTAGG
Found at i:3955201 original size:15 final size:14
Alignment explanation
Indices: 3955131--3955268 Score: 78
Period size: 15 Copynumber: 9.2 Consensus size: 14
3955121 AGGGTCTCAT
*
3955131 TTTAGGGTTTTAGGA
1 TTTAGGG-TTTAGGG
* *
3955146 TTTCAGGGTTTTTGGA
1 TTT-AGGG-TTTAGGG
*
3955162 TTTATGGGTTTATGG
1 TTTA-GGGTTTAGGG
* *
3955177 TTTAAAGGTTTAAGG
1 TTT-AGGGTTTAGGG
*
3955192 TTTCAGGGTTTCGAGG
1 TTT-AGGGTTTAG-GG
* * * *
3955208 TTTATGATTTCAAGA
1 TTTAGGGTTT-AGGG
*
3955223 TTTAAGGTTTCAGGG
1 TTTAGGGTTT-AGGG
*
3955238 TTTAGGGTTTAGGA
1 TTTAGGGTTTAGGG
3955252 TTTAGGGTTTAGGG
1 TTTAGGGTTTAGGG
3955266 TTT
1 TTT
3955269 TAGTTTTTTT
Statistics
Matches: 96, Mismatches: 22, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
14 19 0.20
15 54 0.56
16 23 0.24
ACGTcount: A:0.20, C:0.04, G:0.31, T:0.46
Consensus pattern (14 bp):
TTTAGGGTTTAGGG
Found at i:3955210 original size:38 final size:37
Alignment explanation
Indices: 3955162--3955255 Score: 125
Period size: 38 Copynumber: 2.5 Consensus size: 37
3955152 GGTTTTTGGA
* *
3955162 TTTATGGGTTTATGGTTTAAAGGTTTAAGGTTTCAGGG
1 TTTA-GGGTTTATGATTTAAAGATTTAAGGTTTCAGGG
* *
3955200 TTTCGAGGTTTATGATTTCAAGATTTAAGGTTTCAGGG
1 TTTAG-GGTTTATGATTTAAAGATTTAAGGTTTCAGGG
*
3955238 TTTAGGGTTTAGGATTTA
1 TTTAGGGTTTATGATTTA
3955256 GGGTTTAGGG
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
37 12 0.25
38 36 0.75
ACGTcount: A:0.22, C:0.04, G:0.29, T:0.45
Consensus pattern (37 bp):
TTTAGGGTTTATGATTTAAAGATTTAAGGTTTCAGGG
Found at i:3955246 original size:7 final size:7
Alignment explanation
Indices: 3955131--3955268 Score: 78
Period size: 7 Copynumber: 18.4 Consensus size: 7
3955121 AGGGTCTCAT
3955131 TTTAGGG
1 TTTAGGG
*
3955138 TTTTAGGA
1 -TTTAGGG
3955146 TTTCAGGG
1 TTT-AGGG
* *
3955154 TTTTTGGA
1 -TTTAGGG
3955162 TTTATGGG
1 TTTA-GGG
*
3955170 TTTATGG
1 TTTAGGG
*
3955177 TTTAAAGG
1 TTT-AGGG
*
3955185 TTTAAGG
1 TTTAGGG
3955192 TTTCAGGG
1 TTT-AGGG
*
3955200 TTTCGAGG
1 TTTAG-GG
* *
3955208 TTTATGA
1 TTTAGGG
* *
3955215 TTTCAAGA
1 TTT-AGGG
*
3955223 TTTAAGG
1 TTTAGGG
3955230 TTTCAGGG
1 TTT-AGGG
3955238 TTTAGGG
1 TTTAGGG
*
3955245 TTTAGGA
1 TTTAGGG
3955252 TTTAGGG
1 TTTAGGG
3955259 TTTAGGG
1 TTTAGGG
3955266 TTT
1 TTT
3955269 TAGTTTTTTT
Statistics
Matches: 104, Mismatches: 18, Indels: 17
0.75 0.13 0.12
Matches are distributed among these distances:
7 55 0.53
8 46 0.44
9 3 0.03
ACGTcount: A:0.20, C:0.04, G:0.31, T:0.46
Consensus pattern (7 bp):
TTTAGGG
Found at i:3955885 original size:12 final size:12
Alignment explanation
Indices: 3955868--3955894 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3955858 TATATGTATG
3955868 TATACATATATA
1 TATACATATATA
3955880 TATACATATATA
1 TATACATATATA
3955892 TAT
1 TAT
3955895 GAGAGAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (12 bp):
TATACATATATA
Found at i:3958715 original size:96 final size:96
Alignment explanation
Indices: 3958530--3958770 Score: 263
Period size: 96 Copynumber: 2.5 Consensus size: 96
3958520 CCAGTGTTAA
* * * *
3958530 CTAATTTGGGCTTAAAGTGCCAGCTAAATTGGGT-TTAAAGTTTGGGTGCCAACTAATTTGAACT
1 CTAATTTGGGTTTAAAGTGTCAGCTAAATT-GGTCTTAAAGTTTAGGTGCCAACTAATCTGAACT
* *
3958594 TAAGTGCCATCTACTCTGTGCTTGAGTGCTAG
65 TAAGTGCCAACTACTCTGTGCTTGAGTGCCAG
* * * * *
3958626 CTAATTTGGGTTTAATGTATCAACTAAATTGGTCTTAAAGTTTAGGTGCCAGCTAATCTGAGCTT
1 CTAATTTGGGTTTAAAGTGTCAGCTAAATTGGTCTTAAAGTTTAGGTGCCAACTAATCTGAACTT
* * *
3958691 AGGT-CTCAACTAGTCTAG-GTTTGAGTGCCAG
66 AAGTGC-CAACTACTCT-GTGCTTGAGTGCCAG
* * * * *
3958722 CTAGTTTGGGTTTAAAGTGTCAGCTAAACTAGACTTAAAATTTAGGTGC
1 CTAATTTGGGTTTAAAGTGTCAGCTAAATTGGTCTTAAAGTTTAGGTGC
3958771 TGGTTAATAT
Statistics
Matches: 120, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
95 4 0.03
96 115 0.96
97 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (96 bp):
CTAATTTGGGTTTAAAGTGTCAGCTAAATTGGTCTTAAAGTTTAGGTGCCAACTAATCTGAACTT
AAGTGCCAACTACTCTGTGCTTGAGTGCCAG
Found at i:3959141 original size:27 final size:29
Alignment explanation
Indices: 3959098--3959151 Score: 69
Period size: 27 Copynumber: 1.9 Consensus size: 29
3959088 TAGACCTCCT
*
3959098 TATTTCTTTATTGTTTTT-TT-TTTTTAC
1 TATTTCTTTATTCTTTTTCTTCTTTTTAC
3959125 TATTTCTCTT-TTCTTTTTCTTCTTTTT
1 TATTTCT-TTATTCTTTTTCTTCTTTTT
3959152 TTAGGCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 14 0.61
28 4 0.17
29 5 0.22
ACGTcount: A:0.07, C:0.13, G:0.02, T:0.78
Consensus pattern (29 bp):
TATTTCTTTATTCTTTTTCTTCTTTTTAC
Found at i:3960558 original size:16 final size:18
Alignment explanation
Indices: 3960527--3960565 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
3960517 GCTCACAAAT
*
3960527 AAAACATAGCTTTTTTTA
1 AAAACATAGCTTTTTTGA
3960545 AAAACAT-G-TTTTTTGA
1 AAAACATAGCTTTTTTGA
3960561 AAAAC
1 AAAAC
3960566 CAAACATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 1 0.05
18 7 0.35
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (18 bp):
AAAACATAGCTTTTTTGA
Found at i:3964322 original size:4 final size:4
Alignment explanation
Indices: 3964307--3964360 Score: 63
Period size: 4 Copynumber: 13.5 Consensus size: 4
3964297 ACAAATATAG
* * * * *
3964307 GAAT GTAT GAAT GAAT GAAT GAAT GATT GAAT GAAT AAAC AAAT GAAT
1 GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT
3964355 GAAT GA
1 GAAT GA
3964361 TAAAGCTTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.22, T:0.26
Consensus pattern (4 bp):
GAAT
Found at i:3973700 original size:22 final size:21
Alignment explanation
Indices: 3973674--3973717 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
3973664 TTAAAGTTTG
3973674 GATTTTAGGGTTTAAGATTTTA
1 GATTTTAGGGTTT-AGATTTTA
*
3973696 GATTTTAGGGTTTTGATTTTA
1 GATTTTAGGGTTTAGATTTTA
3973717 G
1 G
3973718 GGTTTAAGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.52
Consensus pattern (21 bp):
GATTTTAGGGTTTAGATTTTA
Found at i:3973700 original size:36 final size:36
Alignment explanation
Indices: 3973654--3973725 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
3973644 GGTTTTTAGA
*
3973654 ATTTTGGATTTTAAAGTTTGGATTTTAGGGTTTAAG
1 ATTTTAGATTTTAAAGTTTGGATTTTAGGGTTTAAG
** *
3973690 ATTTTAGATTTTAGGGTTTTGATTTTAGGGTTTAAG
1 ATTTTAGATTTTAAAGTTTGGATTTTAGGGTTTAAG
3973726 GTCTGGGGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.24, C:0.00, G:0.25, T:0.51
Consensus pattern (36 bp):
ATTTTAGATTTTAAAGTTTGGATTTTAGGGTTTAAG
Found at i:3973715 original size:14 final size:15
Alignment explanation
Indices: 3973691--3973722 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
3973681 GGGTTTAAGA
3973691 TTTTAGATTTTAGGG
1 TTTTAGATTTTAGGG
3973706 TTTT-GATTTTAGGG
1 TTTTAGATTTTAGGG
3973720 TTT
1 TTT
3973723 AAGGTCTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.16, C:0.00, G:0.25, T:0.59
Consensus pattern (15 bp):
TTTTAGATTTTAGGG
Found at i:3973723 original size:21 final size:22
Alignment explanation
Indices: 3973677--3973723 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
3973667 AAGTTTGGAT
*
3973677 TTTAGGGTTTAAGATTTTAGAT
1 TTTAGGGTTTAAGATTTTAGAG
* *
3973699 TTTAGGGTTT-TGATTTTAGGG
1 TTTAGGGTTTAAGATTTTAGAG
3973720 TTTA
1 TTTA
3973724 AGGTCTGGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53
Consensus pattern (22 bp):
TTTAGGGTTTAAGATTTTAGAG
Found at i:3973738 original size:36 final size:36
Alignment explanation
Indices: 3973660--3973740 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
3973650 TAGAATTTTG
** * *
3973660 GATTTTAAAGTTTGGATTTTAGGGTTTAAGATTTTA
1 GATTTTAGGGTTTGGATTTTAGGGTTTAAGATCTGA
* * *
3973696 GATTTTAGGGTTTTGATTTTAGGGTTTAAGGTCTGG
1 GATTTTAGGGTTTGGATTTTAGGGTTTAAGATCTGA
*
3973732 GGTTTTAGG
1 GATTTTAGG
3973741 TTTACGATTT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.21, C:0.01, G:0.30, T:0.48
Consensus pattern (36 bp):
GATTTTAGGGTTTGGATTTTAGGGTTTAAGATCTGA
Found at i:3973750 original size:36 final size:36
Alignment explanation
Indices: 3973660--3973760 Score: 87
Period size: 36 Copynumber: 2.8 Consensus size: 36
3973650 TAGAATTTTG
** * * *
3973660 GATTTTAAAGTTTGGATTTTAGGGTTTAAGATTTTA
1 GATTTTAGGGTTTCGATTTTAGGGTTTAAGATCTGA
* * *
3973696 GATTTTAGGGTTTTGATTTTAGGGTTTAAGGTCTGG
1 GATTTTAGGGTTTCGATTTTAGGGTTTAAGATCTGA
* *
3973732 GGTTTTA-GGTTTACGATTTAAAGGGTTTA
1 GATTTTAGGGTTT-CGATTT-TAGGGTTTA
3973761 GGGTTTCAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
35 5 0.09
36 40 0.75
37 8 0.15
ACGTcount: A:0.23, C:0.02, G:0.28, T:0.48
Consensus pattern (36 bp):
GATTTTAGGGTTTCGATTTTAGGGTTTAAGATCTGA
Found at i:3973797 original size:24 final size:24
Alignment explanation
Indices: 3973731--3973843 Score: 78
Period size: 22 Copynumber: 4.9 Consensus size: 24
3973721 TTAAGGTCTG
* * **
3973731 GGGTTTTAGG-TTTACGATTTAAA
1 GGGTTTAAGGTTTTAGGATTTTGA
* *
3973754 GGGTTTAGGGTTTCA--ATTTTGA
1 GGGTTTAAGGTTTTAGGATTTTGA
*
3973776 -TGTTTAAAGGTTTTAGGATTTTGA
1 GGGTTT-AAGGTTTTAGGATTTTGA
3973800 GGGTTTAAGGTTTTA--ATTTT-A
1 GGGTTTAAGGTTTTAGGATTTTGA
* *
3973821 GGGTTTGAAGGGTTTAGGGTTTT
1 GGGTTT-AAGGTTTTAGGATTTT
3973844 AATTACGAGG
Statistics
Matches: 71, Mismatches: 11, Indels: 15
0.73 0.11 0.15
Matches are distributed among these distances:
21 11 0.15
22 25 0.35
23 8 0.11
24 23 0.32
25 4 0.06
ACGTcount: A:0.21, C:0.02, G:0.30, T:0.47
Consensus pattern (24 bp):
GGGTTTAAGGTTTTAGGATTTTGA
Found at i:3973820 original size:30 final size:30
Alignment explanation
Indices: 3973786--3973847 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
3973776 TGTTTAAAGG
*
3973786 TTTTAGGATTTTG-AGGGTTTAAGGTTTTAA
1 TTTTAGG-GTTTGAAGGGTTTAAGGTTTTAA
*
3973816 TTTTAGGGTTTGAAGGGTTTAGGGTTTTAA
1 TTTTAGGGTTTGAAGGGTTTAAGGTTTTAA
3973846 TT
1 TT
3973848 ACGAGGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (30 bp):
TTTTAGGGTTTGAAGGGTTTAAGGTTTTAA
Found at i:3973837 original size:46 final size:46
Alignment explanation
Indices: 3973739--3973845 Score: 117
Period size: 46 Copynumber: 2.3 Consensus size: 46
3973729 TGGGGTTTTA
* * * *
3973739 GGTTTACGATTTAAAGGGTTTAGGGTTTCAATTTTGATGTTTAAAG
1 GGTTTAGGATTTTAAGGGTTTAAGGTTTCAATTTTGAGGTTTAAAG
* * * *
3973785 GTTTTAGGATTTTGAGGGTTTAAGGTTTTAATTTT-AGGGTTTGAAG
1 GGTTTAGGATTTTAAGGGTTTAAGGTTTCAATTTTGA-GGTTTAAAG
*
3973831 GGTTTAGGGTTTTAA
1 GGTTTAGGATTTTAA
3973846 TTACGAGGTT
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
45 1 0.02
46 48 0.98
ACGTcount: A:0.23, C:0.02, G:0.29, T:0.46
Consensus pattern (46 bp):
GGTTTAGGATTTTAAGGGTTTAAGGTTTCAATTTTGAGGTTTAAAG
Found at i:3974204 original size:3 final size:3
Alignment explanation
Indices: 3974196--3974238 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
3974186 ATTCATTTGA
* *
3974196 ATT ATT ATT ATT ATT ACT ATT ATT GTT ATT ATT ATT GATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT
3974239 GTAAAACAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:3976228 original size:15 final size:15
Alignment explanation
Indices: 3976208--3976237 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3976198 ATTAATCATT
*
3976208 AAATTTTAAATTTTA
1 AAATTTAAAATTTTA
3976223 AAATTTAAAATTTTA
1 AAATTTAAAATTTTA
3976238 TCATGTAAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AAATTTAAAATTTTA
Found at i:3976319 original size:24 final size:24
Alignment explanation
Indices: 3976292--3976340 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
3976282 CCAACTTCCT
*
3976292 TGTTTCCTTATCATTATCTACATA
1 TGTTTCCCTATCATTATCTACATA
3976316 TGTTTCCCTATCATTATCTACATA
1 TGTTTCCCTATCATTATCTACATA
3976340 T
1 T
3976341 CAATGTCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.22, G:0.04, T:0.49
Consensus pattern (24 bp):
TGTTTCCCTATCATTATCTACATA
Found at i:3981156 original size:6 final size:6
Alignment explanation
Indices: 3981140--3981169 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
3981130 CCATCTCAAC
*
3981140 CAAAAA TAAAAA CAAAAA CAAAAA CAAAAA
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA
3981170 ATTTCAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.83, C:0.13, G:0.00, T:0.03
Consensus pattern (6 bp):
CAAAAA
Found at i:3984998 original size:16 final size:17
Alignment explanation
Indices: 3984968--3985001 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3984958 AATAGGAGAG
*
3984968 AAAAAAGAGAGAAAAGA
1 AAAAAAAAGAGAAAAGA
3984985 AAAAAAAAGA-AAAAGA
1 AAAAAAAAGAGAAAAGA
3985001 A
1 A
3985002 GGGAGGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGAGAAAAGA
Found at i:3985460 original size:6 final size:6
Alignment explanation
Indices: 3985447--3985482 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
3985437 CTTTAAATTA
* *
3985447 TGATAT TAATAT TAATAT TGATAT TGATAT TGATAT
1 TGATAT TGATAT TGATAT TGATAT TGATAT TGATAT
3985483 AATTTTCACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (6 bp):
TGATAT
Found at i:3985808 original size:19 final size:18
Alignment explanation
Indices: 3985784--3985847 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 18
3985774 CTCGAAATTA
*
3985784 ATAAAATATTTTTTAAAAT
1 ATAAAATATTTTTT-TAAT
3985803 ATAAAAGATTATTTTTTTAAT
1 AT-AAA-A-TATTTTTTTAAT
3985824 ATAAAATATTATTTTTAAT
1 ATAAAATATT-TTTTTAAT
3985843 ATAAA
1 ATAAA
3985848 TATAAAATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
18 4 0.10
19 16 0.40
20 6 0.15
21 6 0.15
22 8 0.20
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
ATAAAATATTTTTTTAAT
Found at i:3985817 original size:21 final size:21
Alignment explanation
Indices: 3985793--3985841 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
3985783 AATAAAATAT
3985793 TTTTTAAAATATAAAAGATTA
1 TTTTTAAAATATAAAAGATTA
** *
3985814 TTTTTTTAATATAAAATATTA
1 TTTTTAAAATATAAAAGATTA
3985835 TTTTTAA
1 TTTTTAA
3985842 TATAAATATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TTTTTAAAATATAAAAGATTA
Found at i:3991978 original size:18 final size:19
Alignment explanation
Indices: 3991945--3991981 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3991935 ATCCTCAAAA
3991945 CTTGAACTCGAACTCTTCT
1 CTTGAACTCGAACTCTTCT
*
3991964 CTTGAA-TCGAGCTCTTCT
1 CTTGAACTCGAACTCTTCT
3991982 AAGCTTGCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.19, C:0.30, G:0.14, T:0.38
Consensus pattern (19 bp):
CTTGAACTCGAACTCTTCT
Found at i:3992605 original size:64 final size:65
Alignment explanation
Indices: 3992476--3992605 Score: 226
Period size: 64 Copynumber: 2.0 Consensus size: 65
3992466 CTTTCTTAAG
* * *
3992476 TTAATTTATTTCTCAAAATCAATATTATCAAAATTGTATTGAGTCCAAAATGAATAAGTTTACTT
1 TTAATCTATTTCTCAAAATCAATATTATCAAAATTGTATTGAGTCCAAAATAAATAAGTTCACTT
3992541 TTAATCTATTTCTCAAAATCAATATTATC-AAATTGTATTGAGTCCAAAATAAATAAGTTCACTT
1 TTAATCTATTTCTCAAAATCAATATTATCAAAATTGTATTGAGTCCAAAATAAATAAGTTCACTT
3992605 T
1 T
3992606 AAAAATAATA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
64 34 0.55
65 28 0.45
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.41
Consensus pattern (65 bp):
TTAATCTATTTCTCAAAATCAATATTATCAAAATTGTATTGAGTCCAAAATAAATAAGTTCACTT
Found at i:4000901 original size:18 final size:19
Alignment explanation
Indices: 4000874--4000913 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
4000864 CATGGTATGA
4000874 TTTTTGTTTTGTTTTG-GT
1 TTTTTGTTTTGTTTTGAGT
* *
4000892 TTTTTTTTTTTTTTTGAGT
1 TTTTTGTTTTGTTTTGAGT
4000911 TTT
1 TTT
4000914 GGGACTGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.03, C:0.00, G:0.15, T:0.82
Consensus pattern (19 bp):
TTTTTGTTTTGTTTTGAGT
Found at i:4007503 original size:12 final size:11
Alignment explanation
Indices: 4007486--4007519 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
4007476 TTGGAAACAG
4007486 AAAAAGATAAA
1 AAAAAGATAAA
4007497 CAAAAAGATAAA
1 -AAAAAGATAAA
4007509 AAAAA-ATAAA
1 AAAAAGATAAA
4007519 A
1 A
4007520 GATGAAGGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 6 0.27
11 5 0.23
12 11 0.50
ACGTcount: A:0.82, C:0.03, G:0.06, T:0.09
Consensus pattern (11 bp):
AAAAAGATAAA
Found at i:4020079 original size:1 final size:1
Alignment explanation
Indices: 4020073--4020098 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
4020063 TCTTCTTCTC
4020073 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
4020099 CCAGGCTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4026116 original size:26 final size:26
Alignment explanation
Indices: 4026086--4026169 Score: 77
Period size: 26 Copynumber: 3.4 Consensus size: 26
4026076 GAAATTTGTT
4026086 TATAATTATTTTAGTCTTTTTGTAAA
1 TATAATTATTTTAGTCTTTTTGTAAA
* *** *
4026112 TATAATTATTCT-G-AAATTTGT--T
1 TATAATTATTTTAGTCTTTTTGTAAA
* *
4026134 TATAATTATTTAAGTCTTTTTATAAA
1 TATAATTATTTTAGTCTTTTTGTAAA
4026160 TATAATTATT
1 TATAATTATT
4026170 CTAAAGTATT
Statistics
Matches: 42, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
22 10 0.24
23 1 0.02
24 9 0.21
25 1 0.02
26 21 0.50
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.56
Consensus pattern (26 bp):
TATAATTATTTTAGTCTTTTTGTAAA
Found at i:4026132 original size:48 final size:48
Alignment explanation
Indices: 4026071--4026171 Score: 175
Period size: 48 Copynumber: 2.1 Consensus size: 48
4026061 GAGCAGTTTA
* * *
4026071 ATTCCGAAATTTGTTTATAATTATTTTAGTCTTTTTGTAAATATAATT
1 ATTCTGAAATTTGTTTATAATTATTTAAGTCTTTTTATAAATATAATT
4026119 ATTCTGAAATTTGTTTATAATTATTTAAGTCTTTTTATAAATATAATT
1 ATTCTGAAATTTGTTTATAATTATTTAAGTCTTTTTATAAATATAATT
4026167 ATTCT
1 ATTCT
4026172 AAAGTATTGA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.33, C:0.06, G:0.07, T:0.54
Consensus pattern (48 bp):
ATTCTGAAATTTGTTTATAATTATTTAAGTCTTTTTATAAATATAATT
Found at i:4026494 original size:19 final size:19
Alignment explanation
Indices: 4026470--4026510 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
4026460 AATTATTATT
4026470 TAAAATATAATT-TTAAAAA
1 TAAAATA-AATTATTAAAAA
*
4026489 TAAAATAATTTATTAAAAA
1 TAAAATAAATTATTAAAAA
4026508 TAA
1 TAA
4026511 TAAAATATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAAATAAATTATTAAAAA
Found at i:4026512 original size:17 final size:16
Alignment explanation
Indices: 4026464--4026513 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
4026454 AAATACAATT
*
4026464 ATTATTTAAAAT-ATA
1 ATTATTAAAAATAATA
4026479 ATT-TTAAAAATAAAATA
1 ATTATTAAAAAT--AATA
4026496 ATTTATTAAAAATAATA
1 A-TTATTAAAAATAATA
4026513 A
1 A
4026514 AATATGAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
14 7 0.24
15 3 0.10
17 9 0.31
18 2 0.07
19 8 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTATTAAAAATAATA
Found at i:4026993 original size:22 final size:22
Alignment explanation
Indices: 4026946--4026999 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 22
4026936 ATTATATAGG
* * *
4026946 TAAAATACATAAAATTTTTTAT
1 TAAAATAAATAAAAATTTTGAT
4026968 TAAAAGTAAATAAAAATTTTGA-
1 TAAAA-TAAATAAAAATTTTGAT
*
4026990 TAAAAAAAAT
1 TAAAATAAAT
4027000 TGAATCAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 4 0.15
22 10 0.37
23 13 0.48
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (22 bp):
TAAAATAAATAAAAATTTTGAT
Found at i:4027195 original size:47 final size:47
Alignment explanation
Indices: 4027144--4027290 Score: 140
Period size: 47 Copynumber: 3.1 Consensus size: 47
4027134 TATTTATTTA
4027144 ATAAATATATCAAAATTTATTAAAATTTTATATGTTTAATTTCTATG
1 ATAAATATATCAAAATTTATTAAAATTTTATATGTTTAATTTCTATG
* *** * * ** *
4027191 ATAAA-ATTTTTTAATTTATGTTAATATTTT-TA-CTAAAATATT-TATTTA
1 ATAAATATATCAAAATTTA--TTAAAATTTTATATGTTTAAT-TTCTA--TG
4027239 ATAAATATATCAAAATTTATTAAAATTTTATATGTTTAATTTCTATG
1 ATAAATATATCAAAATTTATTAAAATTTTATATGTTTAATTTCTATG
4027286 ATAAA
1 ATAAA
4027291 ATTTTTTTAA
Statistics
Matches: 73, Mismatches: 18, Indels: 18
0.67 0.17 0.17
Matches are distributed among these distances:
46 15 0.21
47 24 0.33
48 19 0.26
49 15 0.21
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (47 bp):
ATAAATATATCAAAATTTATTAAAATTTTATATGTTTAATTTCTATG
Found at i:4027252 original size:95 final size:97
Alignment explanation
Indices: 4027110--4027305 Score: 378
Period size: 95 Copynumber: 2.0 Consensus size: 97
4027100 ACGATAAAAA
4027110 TTATGTTAATATTTTTACTAAAAATATTTATTTAATAAATATATCAAAATTTATTAAAATTTTAT
1 TTATGTTAATATTTTTACTAAAAATATTTATTTAATAAATATATCAAAATTTATTAAAATTTTAT
4027175 ATGTTTAATTTCTATGATAAAA-TTTTTTAAT
66 ATGTTTAATTTCTATGATAAAATTTTTTTAAT
4027206 TTATGTTAATATTTTTACT-AAAATATTTATTTAATAAATATATCAAAATTTATTAAAATTTTAT
1 TTATGTTAATATTTTTACTAAAAATATTTATTTAATAAATATATCAAAATTTATTAAAATTTTAT
4027270 ATGTTTAATTTCTATGATAAAATTTTTTTAAT
66 ATGTTTAATTTCTATGATAAAATTTTTTTAAT
4027302 TTAT
1 TTAT
4027306 CAATTTTAAT
Statistics
Matches: 99, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
95 67 0.68
96 32 0.32
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (97 bp):
TTATGTTAATATTTTTACTAAAAATATTTATTTAATAAATATATCAAAATTTATTAAAATTTTAT
ATGTTTAATTTCTATGATAAAATTTTTTTAAT
Found at i:4031845 original size:10 final size:10
Alignment explanation
Indices: 4031826--4031856 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
4031816 TATAAGGGAA
4031826 TTTAAGAATTT
1 TTTAA-AATTT
4031837 TTTAAAATTT
1 TTTAAAATTT
4031847 TTTAAAATTT
1 TTTAAAATTT
4031857 ATATATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.75
11 5 0.25
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (10 bp):
TTTAAAATTT
Found at i:4037331 original size:14 final size:14
Alignment explanation
Indices: 4037312--4037340 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4037302 TTTGGCGGCT
4037312 ATGCAGAGAAAGAG
1 ATGCAGAGAAAGAG
4037326 ATGCAGAGAAAGAG
1 ATGCAGAGAAAGAG
4037340 A
1 A
4037341 GGGGAAGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.34, T:0.07
Consensus pattern (14 bp):
ATGCAGAGAAAGAG
Found at i:4043253 original size:11 final size:11
Alignment explanation
Indices: 4043239--4043293 Score: 51
Period size: 12 Copynumber: 5.0 Consensus size: 11
4043229 TATATTAAAT
*
4043239 AAATTTTATTA
1 AAATTTAATTA
*
4043250 AAATTAAAATTA
1 AAATT-TAATTA
4043262 AAATTTAATTA
1 AAATTTAATTA
*
4043273 ATAATATAA-T-
1 A-AATTTAATTA
4043283 AAATTTAATTA
1 AAATTTAATTA
4043294 TATCACATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
9 6 0.17
10 2 0.06
11 12 0.34
12 15 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AAATTTAATTA
Found at i:4043288 original size:21 final size:21
Alignment explanation
Indices: 4043235--4043293 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 21
4043225 AATTTATATT
*
4043235 AAATAAATTTTATTAAAATTA
1 AAATAAATTTAATTAAAATTA
4043256 AAATTAAAATTTAATTAATAA-TA
1 AAA-T-AAATTTAATTAA-AATTA
*
4043279 TAATAAATTTAATTA
1 AAATAAATTTAATTA
4043294 TATCACATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 14 0.42
22 2 0.06
23 15 0.45
24 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATAAATTTAATTAAAATTA
Found at i:4049348 original size:78 final size:78
Alignment explanation
Indices: 4049266--4049415 Score: 174
Period size: 78 Copynumber: 1.9 Consensus size: 78
4049256 TTAGGTTATG
* * * * *
4049266 TTGGGTCAAGGTCATTTTGAGTTTTGAGTTTTTCGGATTCGGTTATTTTTGGATTTGGACCGAGT
1 TTGGGTCAAGGTCATTTTAAGTGTGGAATTTTTCGGATTCAGTTATTTTTGGATTTGGACCGAGT
4049331 TCAAGATAGTCTA
66 TCAAGATAGTCTA
** * * * * * *
4049344 TTGGGTTTAGGTCTTTTTAAGTGTGGAATTTTTTGGGTTTAGTTATTTTTGGATTTGGGCTGAGT
1 TTGGGTCAAGGTCATTTTAAGTGTGGAATTTTTCGGATTCAGTTATTTTTGGATTTGGACCGAGT
*
4049409 TTAAGAT
66 TCAAGAT
4049416 CGTTTTGTTT
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
78 58 1.00
ACGTcount: A:0.18, C:0.07, G:0.28, T:0.47
Consensus pattern (78 bp):
TTGGGTCAAGGTCATTTTAAGTGTGGAATTTTTCGGATTCAGTTATTTTTGGATTTGGACCGAGT
TCAAGATAGTCTA
Found at i:4052308 original size:24 final size:24
Alignment explanation
Indices: 4052262--4052306 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
4052252 ATGTTTATAT
4052262 ATAAAATATTAATTTTATCTTTTA
1 ATAAAATATTAATTTTATCTTTTA
*
4052286 ATAAATTA-TAATTTTA-CTTTT
1 ATAAAATATTAATTTTATCTTTT
4052307 TTTACACTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 8 0.40
24 7 0.35
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (24 bp):
ATAAAATATTAATTTTATCTTTTA
Found at i:4056453 original size:41 final size:41
Alignment explanation
Indices: 4056386--4056464 Score: 99
Period size: 41 Copynumber: 1.9 Consensus size: 41
4056376 TTGTATAATC
*
4056386 ATAACATTTATGAATAATAATCTATTTATATT-AAATAGTT
1 ATAACATTTATCAATAATAATCTATTTATATTCAAATAGTT
* *
4056426 ATAACAATTTATCATATGATAAT-TATTTGTATTCAAATA
1 ATAAC-ATTTATCA-ATAATAATCTATTTATATTCAAATA
4056465 TAATTATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 5 0.15
41 16 0.48
42 12 0.36
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.44
Consensus pattern (41 bp):
ATAACATTTATCAATAATAATCTATTTATATTCAAATAGTT
Found at i:4064107 original size:16 final size:17
Alignment explanation
Indices: 4064088--4064131 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 17
4064078 AATTTTGAAA
4064088 ATTTTTTATTTTAT-TT
1 ATTTTTTATTTTATATT
*
4064104 ATTTTTTCTTTTATCATT
1 ATTTTTTATTTTAT-ATT
4064122 ATATTTTTAT
1 AT-TTTTTAT
4064132 ATTAAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 13 0.57
18 4 0.17
19 6 0.26
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (17 bp):
ATTTTTTATTTTATATT
Found at i:4065000 original size:20 final size:18
Alignment explanation
Indices: 4064967--4065015 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 18
4064957 CATATTTTTT
4064967 AATATAAAAAAATTTAAA
1 AATATAAAAAAATTTAAA
*
4064985 AATCATAAAAATAATTTTAA
1 AAT-ATAAAAA-AATTTAAA
4065005 AATATAAAAAA
1 AATATAAAAAA
4065016 GTAAGAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 4 0.14
19 14 0.50
20 10 0.36
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (18 bp):
AATATAAAAAAATTTAAA
Found at i:4065386 original size:30 final size:30
Alignment explanation
Indices: 4065346--4065426 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 30
4065336 TAGTTTAATG
4065346 TTATAA-ATGATTTTAAATTATAGTAAAATA
1 TTATAATATGATTTTAAATTATA-TAAAATA
* *
4065376 TT-TAATATGATATTAAATT-T-TAAAATT
1 TTATAATATGATTTTAAATTATATAAAATA
*
4065403 TTATAATATAATATTTAAATTATA
1 TTATAATATGAT-TTTAAATTATA
4065427 AATTTATTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
27 8 0.19
28 8 0.19
29 11 0.26
30 15 0.36
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (30 bp):
TTATAATATGATTTTAAATTATATAAAATA
Found at i:4065431 original size:28 final size:28
Alignment explanation
Indices: 4065369--4065428 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
4065359 TAAATTATAG
* * *
4065369 TAAAATATT-TAATATGATATTAAATTT
1 TAAAATTTTATAATATAATATTAAATTA
4065396 TAAAATTTTATAATATAATATTTAAATTA
1 TAAAATTTTATAATATAATA-TTAAATTA
4065425 TAAA
1 TAAA
4065429 TTTATTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 8 0.29
28 9 0.32
29 11 0.39
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (28 bp):
TAAAATTTTATAATATAATATTAAATTA
Found at i:4065437 original size:28 final size:27
Alignment explanation
Indices: 4065369--4065437 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 27
4065359 TAAATTATAG
* * *
4065369 TAAAATATTTAATATGATATTAAATTT
1 TAAAATTTTTAATATAATATTAAATTA
4065396 TAAAATTTTATAATATAATATTTAAATTA
1 TAAAATTTT-TAATATAATA-TTAAATTA
4065425 T-AAATTTATTAAT
1 TAAAATTT-TTAAT
4065438 TATTATGATA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 8 0.22
28 19 0.53
29 9 0.25
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (27 bp):
TAAAATTTTTAATATAATATTAAATTA
Found at i:4071728 original size:27 final size:29
Alignment explanation
Indices: 4071684--4071738 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
4071674 AAAAACTTTT
*
4071684 ATCTGTGATAATTGAAAT-TTTTGTAAGC
1 ATCTGTGATAATTGAAATCTTTTCTAAGC
4071712 ATCT-TGAT-ATTGAAAATCTTTTCTAAG
1 ATCTGTGATAATTG-AAATCTTTTCTAAG
4071739 TTTTCCAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 4 0.17
27 8 0.33
28 12 0.50
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.44
Consensus pattern (29 bp):
ATCTGTGATAATTGAAATCTTTTCTAAGC
Found at i:4072351 original size:20 final size:20
Alignment explanation
Indices: 4072314--4072351 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4072304 ATTTACAAAT
*
4072314 AAATAAATACATAAATAGTC
1 AAATAAATAAATAAATAGTC
*
4072334 AAATAAATAAATATATAG
1 AAATAAATAAATAAATAG
4072352 ACAGACAATT
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:0.63, C:0.05, G:0.05, T:0.26
Consensus pattern (20 bp):
AAATAAATAAATAAATAGTC
Found at i:4073415 original size:22 final size:22
Alignment explanation
Indices: 4073389--4073494 Score: 78
Period size: 22 Copynumber: 4.9 Consensus size: 22
4073379 TTCACAATTG
*
4073389 AAATTCAAAAGTT-TGCAATTAA
1 AAATTCAAAAATTCT-CAATTAA
* *
4073411 AAATTTAAAAATTCTCAATTTA
1 AAATTCAAAAATTCTCAATTAA
* *
4073433 AAATTCAAGAATTCTCAACTT-G
1 AAATTCAAAAATTCTCAA-TTAA
* *
4073455 AAGTTTAAAAATTCGT-AATT--
1 AAATTCAAAAATTC-TCAATTAA
*
4073475 AAATTCAAATATTCTCAATT
1 AAATTCAAAAATTCTCAATT
4073495 TGAATTTAAA
Statistics
Matches: 68, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.01
20 15 0.22
21 2 0.03
22 46 0.68
23 4 0.06
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (22 bp):
AAATTCAAAAATTCTCAATTAA
Found at i:4073489 original size:42 final size:43
Alignment explanation
Indices: 4073412--4073504 Score: 122
Period size: 42 Copynumber: 2.2 Consensus size: 43
4073402 TGCAATTAAA
4073412 AATTTAAAAATTCTCAATTTAAAATTCAAGAATTCTCAACTTG
1 AATTTAAAAATTCTCAATTTAAAATTCAAGAATTCTCAACTTG
*
4073455 AAGTTTAAAAATTCGT-AA-TT-AAATTCAA-ATATTCTCAATTTG
1 AA-TTTAAAAATTC-TCAATTTAAAATTCAAGA-ATTCTCAACTTG
4073497 AATTTAAA
1 AATTTAAA
4073505 GGCTTGCAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
41 7 0.15
42 21 0.46
43 4 0.09
44 13 0.28
45 1 0.02
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (43 bp):
AATTTAAAAATTCTCAATTTAAAATTCAAGAATTCTCAACTTG
Found at i:4073716 original size:18 final size:18
Alignment explanation
Indices: 4073568--4073764 Score: 93
Period size: 18 Copynumber: 10.9 Consensus size: 18
4073558 GAATTCAAAT
*
4073568 ATTCATAAAAG-TTCAAG
1 ATTCACAAAAGATTCAAG
* * *
4073585 GTTCGCAAAAGATTCAAT
1 ATTCACAAAAGATTCAAG
*
4073603 ATTTTA-AAAA-ATTCAAG
1 A-TTCACAAAAGATTCAAG
** *
4073620 ATTCGTACAAG-TTCAAAG
1 ATTCACAAAAGATTC-AAG
4073638 ATTCACAAAAGATTTTCAA-
1 ATTCACAAAAGA--TTCAAG
** * **
4073657 ATTTGCTAGTGATTCAAG
1 ATTCACAAAAGATTCAAG
* * *
4073675 ACTCACAAAAAATTTCAAAA
1 ATTCACAAAAGA-TTC-AAG
4073695 ATTCACAAAAGATTCAAG
1 ATTCACAAAAGATTCAAG
** *
4073713 ATTCGTAAAA-AGTCAAAG
1 ATTCACAAAAGATTC-AAG
**
4073731 ATTTGCAAAAGATTCAAG
1 ATTCACAAAAGATTCAAG
4073749 ATTCACAAAA-ATTCAA
1 ATTCACAAAAGATTCAA
4073765 AAATTCGTAA
Statistics
Matches: 129, Mismatches: 38, Indels: 26
0.67 0.20 0.13
Matches are distributed among these distances:
16 2 0.02
17 35 0.27
18 57 0.44
19 18 0.14
20 14 0.11
21 3 0.02
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.28
Consensus pattern (18 bp):
ATTCACAAAAGATTCAAG
Found at i:4073759 original size:36 final size:36
Alignment explanation
Indices: 4073586--4073782 Score: 141
Period size: 36 Copynumber: 5.4 Consensus size: 36
4073576 AAGTTCAAGG
* * *
4073586 TTCGCAAAAGATTCAATATTTTA-AAAAATTC-AAGA
1 TTCGCAAAAGATTCAAGA-TTCACAAAAATTCAAAAA
* * ***
4073621 TTCGTACAAG-TTCAAAGATTCACAAAAGATTTTCAAA
1 TTCGCAAAAGATTC-AAGATTCACAAAA-ATTCAAAAA
* * ** *
4073658 TTTGCTAGTGATTCAAGACTCACAAAAAATTTCAAAAA
1 TTCGCAAAAGATTCAAGATTCAC-AAAAA-TTCAAAAA
* ** * *
4073696 TTCACAAAAGATTCAAGATTCGTAAAAAGTCAAAGA
1 TTCGCAAAAGATTCAAGATTCACAAAAATTCAAAAA
*
4073732 TTTGCAAAAGATTCAAGATTCACAAAAATTCAAAAA
1 TTCGCAAAAGATTCAAGATTCACAAAAATTCAAAAA
*
4073768 TTCGTAAAAG-TTCAA
1 TTCGCAAAAGATTCAA
4073783 ATATTTGAAA
Statistics
Matches: 120, Mismatches: 35, Indels: 14
0.71 0.21 0.08
Matches are distributed among these distances:
34 6 0.05
35 20 0.17
36 47 0.39
37 20 0.17
38 27 0.22
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.28
Consensus pattern (36 bp):
TTCGCAAAAGATTCAAGATTCACAAAAATTCAAAAA
Done.