Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168481.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_8, 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: 25818110
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 67000 characters in sequence are not A, C, G, or T
File 27 of 127
Found at i:5806352 original size:17 final size:16
Alignment explanation
Indices: 5806302--5806352 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 16
5806292 TTAGTACTCC
*
5806302 TTATTTTTT-TTATCT
1 TTATTTTTTATTTTCT
*
5806317 TTA-TTTTTATTTTATT
1 TTATTTTTTATTTT-CT
5806333 TTATTTTTTGATTTTCT
1 TTATTTTTT-ATTTTCT
5806350 TTA
1 TTA
5806353 AATAAAATTC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 5 0.17
15 6 0.21
16 4 0.14
17 9 0.31
18 5 0.17
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (16 bp):
TTATTTTTTATTTTCT
Found at i:5806432 original size:58 final size:57
Alignment explanation
Indices: 5806365--5806502 Score: 231
Period size: 58 Copynumber: 2.4 Consensus size: 57
5806355 TAAAATTCCA
*
5806365 AAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTCTAAAAAATATTTTTGAGG
1 AAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTCTAAAAAACA-TTTTGAGG
* * *
5806423 AAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTTTTCTGAAAAACATTTTGGGG
1 AAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTCTAAAAAACATTTTGAGG
5806480 AAAAGTTGAAAGTATCAATTTTC
1 AAAAGTTGAAAGTATCAATTTTC
5806503 TTTGTACAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
57 29 0.39
58 46 0.61
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (57 bp):
AAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTCTAAAAAACATTTTGAGG
Found at i:5815272 original size:16 final size:16
Alignment explanation
Indices: 5815251--5815287 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
5815241 ATGACATGAT
*
5815251 GCATAAAAAGATATAA
1 GCATAAAAAGATAGAA
*
5815267 GCATAAAGAGATAGAA
1 GCATAAAAAGATAGAA
5815283 GCATA
1 GCATA
5815288 TATGAATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.08, G:0.19, T:0.16
Consensus pattern (16 bp):
GCATAAAAAGATAGAA
Found at i:5818841 original size:48 final size:49
Alignment explanation
Indices: 5818757--5818897 Score: 185
Period size: 48 Copynumber: 2.9 Consensus size: 49
5818747 GTCGAGCTTT
* *
5818757 TGCTTAAATGAGCTTTTTTCAAGATGAATTTTTAAAGTTGTTGAACCTC
1 TGCTTAAAAGAGCTTTTTCCAAGATGAATTTTTAAAGTTGTTGAACCTC
* * *
5818806 TGCTTAAAAGATC-TTTTCCAAGATGAATTTTTAAAGTTATTAAACCTC
1 TGCTTAAAAGAGCTTTTTCCAAGATGAATTTTTAAAGTTGTTGAACCTC
* * * * *
5818854 TGCTTATAAGAGCTTTTTCTAAGATAAATCTTTAAACTTGTTGA
1 TGCTTAAAAGAGCTTTTTCCAAGATGAATTTTTAAAGTTGTTGA
5818898 GCATTTGCTT
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
48 43 0.55
49 35 0.45
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (49 bp):
TGCTTAAAAGAGCTTTTTCCAAGATGAATTTTTAAAGTTGTTGAACCTC
Found at i:5818907 original size:49 final size:49
Alignment explanation
Indices: 5818757--5818915 Score: 171
Period size: 49 Copynumber: 3.3 Consensus size: 49
5818747 GTCGAGCTTT
5818757 TGCTTA-AATGAGCTTTTT-TCAAGATGAATTTTTAAAGTTGTTGAACCTC
1 TGCTTATAA-GAGCTTTTTCT-AAGATGAATTTTTAAAGTTGTTGAACCTC
* * * * *
5818806 TGCTTAAAAGATC-TTTTCCAAGATGAATTTTTAAAGTTATTAAACCTC
1 TGCTTATAAGAGCTTTTTCTAAGATGAATTTTTAAAGTTGTTGAACCTC
* * * * * *
5818854 TGCTTATAAGAGCTTTTTCTAAGATAAATCTTTAAACTTGTTGAGCATT
1 TGCTTATAAGAGCTTTTTCTAAGATGAATTTTTAAAGTTGTTGAACCTC
*
5818903 TGCTTATAGGAGC
1 TGCTTATAAGAGC
5818916 ATTCATTATC
Statistics
Matches: 91, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
48 42 0.46
49 47 0.52
50 2 0.02
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (49 bp):
TGCTTATAAGAGCTTTTTCTAAGATGAATTTTTAAAGTTGTTGAACCTC
Found at i:5823025 original size:11 final size:11
Alignment explanation
Indices: 5823011--5823042 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
5823001 AAAAAATAAG
5823011 AAAAAATTTTT
1 AAAAAATTTTT
5823022 -AAAAATTTTT
1 AAAAAATTTTT
5823032 AAAAAATTTTT
1 AAAAAATTTTT
5823043 TTTACCTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
AAAAAATTTTT
Found at i:5823903 original size:18 final size:17
Alignment explanation
Indices: 5823893--5823946 Score: 74
Period size: 17 Copynumber: 3.1 Consensus size: 17
5823883 TTTTTTGGTA
5823893 TTTTGTATTTTGGT-TTT
1 TTTTGTATTTT-GTATTT
*
5823910 TTTTATATTTTGTATTT
1 TTTTGTATTTTGTATTT
5823927 TTTTGGTATTTTGTATTT
1 TTTT-GTATTTTGTATTT
5823945 TT
1 TT
5823947 GTTTAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
16 2 0.06
17 17 0.52
18 14 0.42
ACGTcount: A:0.11, C:0.00, G:0.13, T:0.76
Consensus pattern (17 bp):
TTTTGTATTTTGTATTT
Found at i:5823918 original size:24 final size:25
Alignment explanation
Indices: 5823881--5823927 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
5823871 TCTGTTTTAT
*
5823881 TTTTTTTTGGTATTTTGTATTTTGG
1 TTTTTTTTGATATTTTGTATTTTGG
5823906 TTTTTTTT-ATATTTTGTATTTT
1 TTTTTTTTGATATTTTGTATTTT
5823928 TTTGGTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.11, C:0.00, G:0.13, T:0.77
Consensus pattern (25 bp):
TTTTTTTTGATATTTTGTATTTTGG
Found at i:5823955 original size:18 final size:17
Alignment explanation
Indices: 5823906--5823960 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 17
5823896 TGTATTTTGG
5823906 TTTTTTTTATATTTTGTA
1 TTTTTTTTA-ATTTTGTA
5823924 TTTTTTTGGT-ATTTTGTA
1 TTTTTTT--TAATTTTGTA
5823942 TTTTTGTTTAATTTT-TA
1 TTTTT-TTTAATTTTGTA
5823959 TT
1 TT
5823961 ATTATATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
17 5 0.15
18 25 0.76
19 2 0.06
20 1 0.03
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76
Consensus pattern (17 bp):
TTTTTTTTAATTTTGTA
Found at i:5823996 original size:18 final size:17
Alignment explanation
Indices: 5823955--5823999 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
5823945 TTGTTTAATT
5823955 TTTATTATTATATTTAA
1 TTTATTATTATATTTAA
* *
5823972 TAATATTATTATTATTTTA
1 T-TTATTATTA-TATTTAA
5823991 TTTATTATT
1 TTTATTATT
5824000 TTTTCTGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 1 0.04
18 15 0.65
19 7 0.30
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTATTATTATATTTAA
Found at i:5824000 original size:12 final size:12
Alignment explanation
Indices: 5823955--5824001 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
5823945 TTGTTTAATT
*
5823955 TTTATTATTATA
1 TTTATTATTTTA
* *
5823967 TTTAATAATATTA
1 TTT-ATTATTTTA
5823980 -TTATTATTTTA
1 TTTATTATTTTA
5823991 TTTATTATTTT
1 TTTATTATTTT
5824002 TTCTGTGACC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
11 7 0.25
12 15 0.54
13 6 0.21
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:5824357 original size:49 final size:48
Alignment explanation
Indices: 5824292--5824945 Score: 715
Period size: 47 Copynumber: 13.7 Consensus size: 48
5824282 GTTAAAAAGG
* * *
5824292 GCTCATCTCAGCAGAGGCTCAACAATTTTAAAAATTTCATC-TAAAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATTTCATCTTGAAAAA
* * * * *
5824340 GGCTCATCTTAGTAGAGGCTCAACAATTTTAAAATTTCAT-TTGGAAAA
1 -GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCATCTTGAAAAA
* * * *
5824388 GCTCATCTCAGCAGAGGCTTAACAACTTTAAAATCTCATC-TAAAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCATCTTGAAAAA
* *
5824435 ACTCCTCTCAACAGAGGCTCAACAACTTTAAAA-TTCATCTTGAAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCATCTTGAAAAA
* *
5824482 GCTCCTCTTAGCAGAGGCTCAACAACTTTAAAAAATTC-TCTTGAAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATTTCATCTTGAAAAA
* *
5824530 GCTCCTCTCAACAGAGGCTCAACAACTTTAAAAATCTT-ATCTTGAAAAGG
1 GCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAAT-TTCATCTTGAAAA-A
* * *
5824580 GCTCCTCTCAGCAAAGGCTCAACAACTTTAAAATCTCAT-TTGGAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCATCTTGAAAAA
* * * *
5824627 GCTCCTCTCATCAGAGGCGT-AATAACTTTAAAATCTCATC-TGGAAAA
1 GCTCCTCTCAGCAGAGGC-TCAACAACTTTAAAATTTCATCTTGAAAAA
* * * *
5824674 GCTTCTTTCAGCAGAGGCTCAACAATTTTTGAAATCTT-ATCTTGAAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAA-CTTTAAAAT-TTCATCTTGAAAAA
* * * *
5824723 GCTCCTCTCAGTAGAGGCTCAATAACTTTAAAAATATCATCTTGAAAAGG
1 GCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATTTCATCTTGAAAA-A
* *
5824773 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATTC-TCGTGAAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCATCTTGAAAAA
* * * * *
5824820 -CTCCTCTCAACAAAAGCTCAACAACTTTAAAA-TCCATCTTGAAAGA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCATCTTGAAAAA
* *
5824866 GCTACTCTCAGCAGAGGCTCAACAACTTTAAAAATT-ATCTTGAAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCATCTTGAAAAA
* *
5824913 GCTCCTCTTAGCTGAGGCTCAACAACTTTAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA
5824946 ATCTCATATG
Statistics
Matches: 515, Mismatches: 69, Indels: 44
0.82 0.11 0.07
Matches are distributed among these distances:
45 2 0.00
46 43 0.08
47 228 0.44
48 92 0.18
49 96 0.19
50 54 0.10
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (48 bp):
GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCATCTTGAAAAA
Found at i:5824634 original size:192 final size:192
Alignment explanation
Indices: 5824292--5824949 Score: 800
Period size: 192 Copynumber: 3.4 Consensus size: 192
5824282 GTTAAAAAGG
* * * * * * *
5824292 GCTCATCTCAGCAGAGGCTCAACAATTTTAAAAATTTCATC-TAAAAAAGGCTCATCTTAGTAGA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAAATT-ATCTTGAAAAA-GCTCCTCTCAGCAGA
* * *
5824356 GGCTCAACAA-TTTTAAAAT-TTCAT-TTGGAAAA--GCTCATCTCAGCAGAGGCTTAACAACTT
64 GGCTCAACAACTTTAAAAATCTT-ATCTT-GAAAAGGGCTCCTCTCAGCAGAGGCTCAACAACTT
* **
5824416 TAAAATCTCATCTAAAAAAACTCCTCTCAACAGAGGCTCAACAACTTTAAAATTCATCTTGAAAA
127 TAAAATCTCATTTGGAAAAACTCCTCTCAACAGAGGCTCAACAACTTTAAAATTCATCTTGAAAA
5824481 A
192 A
* * *
5824482 GCTCCTCTTAGCAGAGGCTCAACAACTTTAAAAAATTCTCTTGAAAAAGCTCCTCTCAACAGAGG
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAAATTATCTTGAAAAAGCTCCTCTCAGCAGAGG
*
5824547 CTCAACAACTTTAAAAATCTTATCTTGAAAAGGGCTCCTCTCAGCAAAGGCTCAACAACTTTAAA
66 CTCAACAACTTTAAAAATCTTATCTTGAAAAGGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAA
* * * *
5824612 ATCTCATTTGGAAAAGCTCCTCTCATCAGAGGCGT-AATAACTTTAAAATCTCATC-TGGAAAA
131 ATCTCATTTGGAAAAACTCCTCTCAACAGAGGC-TCAACAACTTTAAAAT-TCATCTTGAAAAA
* * * * ** *
5824674 GCTTCTTTCAGCAGAGGCTCAACAATTTTTGAAATCTTATCTTGAAAAAGCTCCTCTCAGTAGAG
1 GCTCCTCTCAGCAGAGGCTCAACAA-CTTTAAAAAATTATCTTGAAAAAGCTCCTCTCAGCAGAG
* * *
5824739 GCTCAATAACTTTAAAAATATCATCTTGAAAAGGGCTCCTCTCAGCAGAGGCTCAACAACTTTAA
65 GCTCAACAACTTTAAAAATCTTATCTTGAAAAGGGCTCCTCTCAGCAGAGGCTCAACAACTTT-A
* * * * *
5824804 AAAT-TC--TCGTGAAAAACTCCTCTCAACAAAAGCTCAACAACTTTAAAATCCATCTTGAAAGA
129 AAATCTCATTTG-GAAAAACTCCTCTCAACAGAGGCTCAACAACTTTAAAATTCATCTTGAAAAA
* * *
5824866 GCTACTCTCAGCAGAGGCTCAACAACTTT-AAAAATTATCTTGAAAAAGCTCCTCTTAGCTGAGG
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAAATTATCTTGAAAAAGCTCCTCTCAGCAGAGG
5824930 CTCAACAACTTTAAAAATCT
66 CTCAACAACTTTAAAAATCT
5824950 CATATGTTCT
Statistics
Matches: 401, Mismatches: 54, Indels: 26
0.83 0.11 0.05
Matches are distributed among these distances:
189 23 0.06
190 102 0.25
191 14 0.03
192 158 0.39
193 99 0.25
194 5 0.01
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (192 bp):
GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAAATTATCTTGAAAAAGCTCCTCTCAGCAGAGG
CTCAACAACTTTAAAAATCTTATCTTGAAAAGGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAA
ATCTCATTTGGAAAAACTCCTCTCAACAGAGGCTCAACAACTTTAAAATTCATCTTGAAAAA
Found at i:5824826 original size:239 final size:235
Alignment explanation
Indices: 5824286--5824945 Score: 796
Period size: 239 Copynumber: 2.8 Consensus size: 235
5824276 CTCTCAGTTA
* * * * *
5824286 AAAAGGGCTCATCTCAGCAGAGGCTCAACAATTTTAAAAATTTCATCTAAAAAAGGCTCATCTTA
1 AAAAGGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATTTC-TCTGAAAAA--CTCCTCTCA
* * * * *
5824351 GTAGAGGCTCAACAATTTTAAAATTTCATTTGGAAAAGCTCATCTCAGCAGAGGCTTAACAACTT
63 GCAAAGGCTCAACAACTTTAAAATCTCATTTGGAAAAGCTCCTCTCAGCAGAGGC-TAACAACTT
* * * *
5824416 TAAAATCTCATCTAAAAAAACTCCTCTCAACAGAGGCTCAACAACTTTAAAATTCATCTTGAAAA
127 TAAAATCTCATCTGAAAAAGCTCCTTTCAGCAGAGGCTCAACAACTTTAAAATTCATCTTGAAAA
*
5824481 AGCTCCTCTTAGCAGAGGCTCAACAACTTTAAAAAATTCTCTTG
192 AGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAAATTCTCTTG
* * * *
5824525 AAAA-AGCTCCTCTCAACAGAGGCTCAACAACTTTAAAAATCTTATCTTGAAAAGGGCTCCTCTC
1 AAAAGGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAAT-TTCTC-TGAAAA--ACTCCTCTC
* *
5824589 AGCAAAGGCTCAACAACTTTAAAATCTCATTTGGAAAAGCTCCTCTCATCAGAGGCGTAATAACT
62 AGCAAAGGCTCAACAACTTTAAAATCTCATTTGGAAAAGCTCCTCTCAGCAGAGGC-TAACAACT
* * * * *
5824654 TTAAAATCTCATCTGGAAAAGCTTCTTTCAGCAGAGGCTCAACAATTTTTGAAATCTTATCTTGA
126 TTAAAATCTCATCTGAAAAAGCTCCTTTCAGCAGAGGCTCAACAA-CTTTAAAAT-TCATCTTGA
* *
5824719 AAAAGCTCCTCTCAGTAGAGGCTCAATAACTTT-AAAAATATCATCTTG
189 AAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAAAT-TC-TCTTG
*
5824767 AAAAGGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAA-TTCTCGTGAAAAACTCCTCTCAAC
1 AAAAGGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATTTCTC-TGAAAAACTCCTCTCAGC
* *
5824831 AAAAGCTCAACAACTTTAAAATC-CATCTT-GAAAGAGCTACTCTCAGCAGAGGCTCAACAACTT
65 AAAGGCTCAACAACTTTAAAATCTCAT-TTGGAAA-AGCTCCTCTCAGCAGAGGCT-AACAACTT
*
5824894 TAAAAAT-T-ATCTTGAAAAAGCTCCTCTT-AGCTGAGGCTCAACAACTTTAAAA
127 T-AAAATCTCATC-TGAAAAAGCTCCT-TTCAGCAGAGGCTCAACAACTTTAAAA
5824946 ATCTCATATG
Statistics
Matches: 362, Mismatches: 44, Indels: 31
0.83 0.10 0.07
Matches are distributed among these distances:
238 51 0.14
239 199 0.55
240 20 0.06
241 50 0.14
242 9 0.02
243 33 0.09
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (235 bp):
AAAAGGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATTTCTCTGAAAAACTCCTCTCAGCA
AAGGCTCAACAACTTTAAAATCTCATTTGGAAAAGCTCCTCTCAGCAGAGGCTAACAACTTTAAA
ATCTCATCTGAAAAAGCTCCTTTCAGCAGAGGCTCAACAACTTTAAAATTCATCTTGAAAAAGCT
CCTCTCAGCAGAGGCTCAACAACTTTAAAAAATTCTCTTG
Found at i:5831561 original size:168 final size:168
Alignment explanation
Indices: 5831273--5831610 Score: 543
Period size: 168 Copynumber: 2.0 Consensus size: 168
5831263 TTTTTATGGT
* * *
5831273 ATTTTCAATGATCTCACCTAATATCATCATATTTGTAAAGTTTTTGATTGCATTGCCTATCAATC
1 ATTTTCAATGATCTCACCTAATATCATCATATCTGTAAAGTTTTTGATTACATTACCTATCAATC
* * * *
5831338 TCTCATAGTATGGTACTTTCAGGGTGTTCACAAATAAAACAGTTATTTTTTTCTCAGTGAGAGGA
66 TCTCATAGTACGGTACTTTCAAGGTGTTCACAAATAAAACAGTTATTTCTTTCTCAGTAAGAGGA
5831403 GGTTGAACTTGTGCAGCCATGTCTCTCCATCTTTATGC
131 GGTTGAACTTGTGCAGCCATGTCTCTCCATCTTTATGC
* * *
5831441 ATTTTTAATGATCTCACCTGATATCA-CTATATCTGTAAAGTTTTTGGTTACATTACCTATCAAT
1 ATTTTCAATGATCTCACCTAATATCATC-ATATCTGTAAAGTTTTTGATTACATTACCTATCAAT
* * *
5831505 CTTTCATAGTACGGTACTTTCAAGGTGTTCATAAATAAAACAGTTGTTTCTTTCTCAGTAAGAGG
65 CTCTCATAGTACGGTACTTTCAAGGTGTTCACAAATAAAACAGTTATTTCTTTCTCAGTAAGAGG
5831570 AGGTTGAACTTGTGCAGCCATGTCTCTCCATCTTTATGC
130 AGGTTGAACTTGTGCAGCCATGTCTCTCCATCTTTATGC
5831609 AT
1 AT
5831611 ATTCTTTGAA
Statistics
Matches: 156, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
167 1 0.01
168 155 0.99
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (168 bp):
ATTTTCAATGATCTCACCTAATATCATCATATCTGTAAAGTTTTTGATTACATTACCTATCAATC
TCTCATAGTACGGTACTTTCAAGGTGTTCACAAATAAAACAGTTATTTCTTTCTCAGTAAGAGGA
GGTTGAACTTGTGCAGCCATGTCTCTCCATCTTTATGC
Found at i:5836710 original size:24 final size:25
Alignment explanation
Indices: 5836678--5836734 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
5836668 TTTCTTTTTT
5836678 TTTATTTTTT-TTATTATTATTAAA-
1 TTTATTTTTTATT-TTATTATTAAAG
* *
5836702 TTTATTTTTTATTTTGTTTTTAAAG
1 TTTATTTTTTATTTTATTATTAAAG
5836727 TTTATTTT
1 TTTATTTT
5836735 GAAAAATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 19 0.66
25 10 0.34
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.74
Consensus pattern (25 bp):
TTTATTTTTTATTTTATTATTAAAG
Found at i:5837864 original size:23 final size:22
Alignment explanation
Indices: 5837824--5837913 Score: 72
Period size: 23 Copynumber: 3.9 Consensus size: 22
5837814 CCATCCCCCA
* * *
5837824 TTTTTTTTCTGTTCTATTTTTT
1 TTTTTTTTATTTTGTATTTTTT
*
5837846 TTTTTTTGTATTTTGTATTTTGAT
1 TTTTTTT-TATTTTGTATTTT-TT
* *
5837870 TTTTTTATATTTTATATTTTTAT
1 TTTTTTTTATTTTGTATTTTT-T
*
5837893 TTAATTTTTATTATTGTATTT
1 TT-TTTTTTATT-TTGTATTT
5837914 AATAATAATT
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
22 7 0.13
23 25 0.47
24 14 0.26
25 7 0.13
ACGTcount: A:0.16, C:0.02, G:0.06, T:0.77
Consensus pattern (22 bp):
TTTTTTTTATTTTGTATTTTTT
Found at i:5837901 original size:19 final size:19
Alignment explanation
Indices: 5837873--5837916 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
5837863 TTTTGATTTT
5837873 TTTATATTTTATATT-TT-TA
1 TTTA-ATTTT-TATTATTGTA
5837892 TTTAATTTTTATTATTGTA
1 TTTAATTTTTATTATTGTA
5837911 TTTAAT
1 TTTAAT
5837917 AATAATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.17
18 7 0.30
19 12 0.52
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTAATTTTTATTATTGTA
Found at i:5837901 original size:29 final size:30
Alignment explanation
Indices: 5837839--5837907 Score: 74
Period size: 28 Copynumber: 2.4 Consensus size: 30
5837829 TTTCTGTTCT
* *
5837839 ATTTTTTTT-TTTTTGTATTTTGTATTTTG
1 ATTTTTTTTATTTTTATATTTTGTATTTTA
5837868 A-TTTTTTTATATTTTATATTTT-TA-TTTA
1 ATTTTTTTTAT-TTTTATATTTTGTATTTTA
*
5837896 ATTTTTATTATT
1 ATTTTTTTTATT
5837908 GTATTTAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
28 12 0.35
29 12 0.35
30 10 0.29
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.77
Consensus pattern (30 bp):
ATTTTTTTTATTTTTATATTTTGTATTTTA
Found at i:5840325 original size:29 final size:29
Alignment explanation
Indices: 5840293--5840357 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
5840283 GTCCTAAAAT
5840293 ATTATTTCTA-TTAATA-TAATAATATTAAA
1 ATTATTT-TACTTAATATTAA-AATATTAAA
*
5840322 ATTATATTACTTAATATTAAAATATTAAA
1 ATTATTTTACTTAATATTAAAATATTAAA
*
5840351 AATATTT
1 ATTATTT
5840358 AAACTATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 2 0.06
29 26 0.84
30 3 0.10
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (29 bp):
ATTATTTTACTTAATATTAAAATATTAAA
Found at i:5840359 original size:18 final size:17
Alignment explanation
Indices: 5840334--5840369 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
5840324 TATATTACTT
5840334 AATATTAAAATATTAAA
1 AATATTAAAATATTAAA
*
5840351 AATATTTAAACTATTAAA
1 AATA-TTAAAATATTAAA
5840369 A
1 A
5840370 GAGTTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
AATATTAAAATATTAAA
Found at i:5840501 original size:22 final size:25
Alignment explanation
Indices: 5840455--5840500 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
5840445 TAGTAATATA
5840455 AATACATTTGTCAAATTATAAAAAT
1 AATACATTTGTCAAATTATAAAAAT
*
5840480 AATACATTT-T-AAATTAGAAAA
1 AATACATTTGTCAAATTATAAAA
5840501 TATTAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 1 0.05
25 9 0.45
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (25 bp):
AATACATTTGTCAAATTATAAAAAT
Found at i:5845525 original size:59 final size:59
Alignment explanation
Indices: 5845462--5845590 Score: 161
Period size: 59 Copynumber: 2.2 Consensus size: 59
5845452 TACATGAAAC
* *
5845462 TTTTAAATATCA-TGAATAAAAATGAAATATTAATAAAAGTAGTGGATGACAAATGCAAT
1 TTTTAAAGATCATTG-ATAAAAATGAAATATTAATAAAAGTAGTAGATGACAAATGCAAT
* * * * **
5845521 TTTTAAAGATCATTGATGAAAATGAGATATTAATAAAAGTCGTAGATGATAAATATAACT
1 TTTTAAAGATCATTGATAAAAATGAAATATTAATAAAAGTAGTAGATGACAAATGCAA-T
5845581 TTTTAAAGAT
1 TTTTAAAGAT
5845591 TTTAAATAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
59 47 0.78
60 13 0.22
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.33
Consensus pattern (59 bp):
TTTTAAAGATCATTGATAAAAATGAAATATTAATAAAAGTAGTAGATGACAAATGCAAT
Found at i:5845569 original size:30 final size:30
Alignment explanation
Indices: 5845481--5845574 Score: 70
Period size: 31 Copynumber: 3.1 Consensus size: 30
5845471 TCATGAATAA
* *
5845481 AAATGAAATATTAATAAAAGTAGTGGATGAC
1 AAATG-AATATTAATAAAAGTCGTAGATGAC
* * *
5845512 AAATGCAAT-TT--TTAAAGATCATTGATGA-
1 AAATG-AATATTAATAAAAG-TCGTAGATGAC
*
5845540 AAATGAGATATTAATAAAAGTCGTAGATGAT
1 AAATGA-ATATTAATAAAAGTCGTAGATGAC
5845571 AAAT
1 AAAT
5845575 ATAACTTTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
27 1 0.02
28 12 0.24
29 9 0.18
30 10 0.20
31 17 0.35
ACGTcount: A:0.49, C:0.04, G:0.17, T:0.30
Consensus pattern (30 bp):
AAATGAATATTAATAAAAGTCGTAGATGAC
Found at i:5846801 original size:17 final size:17
Alignment explanation
Indices: 5846779--5846811 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5846769 AAAAAAGAAA
*
5846779 ATTTATTTCTTTTCATC
1 ATTTATTTCGTTTCATC
5846796 ATTTATTTCGTTTCAT
1 ATTTATTTCGTTTCAT
5846812 ATGAAAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.15, G:0.03, T:0.64
Consensus pattern (17 bp):
ATTTATTTCGTTTCATC
Found at i:5848756 original size:5 final size:5
Alignment explanation
Indices: 5848746--5848772 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
5848736 TAAATAAAGA
5848746 AATTT AATTT AATTT AATTT AATTT AA
1 AATTT AATTT AATTT AATTT AATTT AA
5848773 ACTCTATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
AATTT
Found at i:5849887 original size:3 final size:3
Alignment explanation
Indices: 5849879--5849915 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5849869 ACCAGTGTTC
5849879 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5849916 CTGTGAACGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5855092 original size:22 final size:23
Alignment explanation
Indices: 5855067--5855119 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
5855057 ATTTTTGTAG
*
5855067 TTTAATTT-TTTAA-ATTAAATAA
1 TTTAATTTATTTAATA-AAAATAA
5855089 TTT-ATTTATTTAATAAAAATAA
1 TTTAATTTATTTAATAAAAATAA
5855111 TTTAATTTA
1 TTTAATTTA
5855120 ATTTTAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 4 0.15
22 17 0.63
23 6 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTAATTTATTTAATAAAAATAA
Found at i:5855127 original size:22 final size:20
Alignment explanation
Indices: 5855082--5855134 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 20
5855072 TTTTTTAAAT
5855082 TAAATAATTT-ATTTATTTAA
1 TAAATAATTTAATTTATTT-A
5855102 TAAAAATAATTTAATTTAATTT-
1 T--AAATAATTTAATTT-ATTTA
5855124 TAAATAATTTA
1 TAAATAATTTA
5855135 TTCAAAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
20 11 0.38
22 10 0.34
23 4 0.14
24 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAAATAATTTAATTTATTTA
Found at i:5855736 original size:24 final size:23
Alignment explanation
Indices: 5855683--5855737 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
5855673 TCTTTCTCTT
*
5855683 TTTTTTTATTTTTTTTAATTATA
1 TTTTTTTATTTTTTATAATTATA
*
5855706 TTCTTTTTATTTTTCTAT-ATTTTAA
1 TT-TTTTTATTTTT-TATAATTAT-A
5855731 TTTTTTT
1 TTTTTTT
5855738 TTTAAGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 2 0.07
24 20 0.74
25 5 0.19
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTTTTTATTTTTTATAATTATA
Found at i:5855883 original size:17 final size:17
Alignment explanation
Indices: 5855842--5855883 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
5855832 TTAAAGAGAA
*
5855842 TCATA-TTTTTAATTTT
1 TCATATTTTTTAAATTT
* *
5855858 TGATTTTTTTTAAATTT
1 TCATATTTTTTAAATTT
5855875 TCATATTTT
1 TCATATTTT
5855884 CTTTGATCTT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (17 bp):
TCATATTTTTTAAATTT
Found at i:5856661 original size:29 final size:28
Alignment explanation
Indices: 5856605--5856661 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
5856595 ATTGTATCTT
5856605 ATATAAAAATTAAATATTAATTTATGTTG
1 ATATAAAAATTAAATATT-ATTTATGTTG
*
5856634 ATATAAAAATATAAAATATT-TTTTTGTT
1 ATATAAAAAT-T-AAATATTATTTATGTT
5856662 AAATATATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 17 0.68
30 1 0.04
31 7 0.28
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (28 bp):
ATATAAAAATTAAATATTATTTATGTTG
Found at i:5856736 original size:16 final size:17
Alignment explanation
Indices: 5856717--5856750 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5856707 TTTTATTTTC
5856717 ATATCAT-TTTCGTATT
1 ATATCATATTTCGTATT
5856733 ATATCATCATTTCGTATT
1 ATATCAT-ATTTCGTATT
5856751 TTGGATTGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.26, C:0.15, G:0.06, T:0.53
Consensus pattern (17 bp):
ATATCATATTTCGTATT
Found at i:5859886 original size:33 final size:33
Alignment explanation
Indices: 5859844--5859926 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 33
5859834 AAACCCATGT
5859844 ATCTTTTGCATCATCCACATTTCCACTACTTTC
1 ATCTTTTGCATCATCCACATTTCCACTACTTTC
* * * *
5859877 ATCTTTTGCATCATCCTCGTTTTCGCTACTTTC
1 ATCTTTTGCATCATCCACATTTCCACTACTTTC
*
5859910 ATCTTTTGC-TCAACCAC
1 ATCTTTTGCATCATCCAC
5859927 CCAAAATTCA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 6 0.14
33 38 0.86
ACGTcount: A:0.18, C:0.33, G:0.06, T:0.43
Consensus pattern (33 bp):
ATCTTTTGCATCATCCACATTTCCACTACTTTC
Found at i:5869128 original size:15 final size:15
Alignment explanation
Indices: 5869108--5869202 Score: 58
Period size: 14 Copynumber: 6.4 Consensus size: 15
5869098 CTTATAAATT
5869108 TATTAATTAATATAA
1 TATTAATTAATATAA
5869123 TATTAA-TAAT-TATA
1 TATTAATTAATATA-A
* *
5869137 TATGAA-AAATA-AA
1 TATTAATTAATATAA
** *
5869150 TATTTTTTAAATATTA
1 TATTAATT-AATATAA
5869166 TATTAATTAATA-AA
1 TATTAATTAATATAA
5869180 T-TATAATTTAAATATAA
1 TAT-TAA-TT-AATATAA
5869197 TATTAA
1 TATTAA
5869203 ACATTAAACA
Statistics
Matches: 60, Mismatches: 10, Indels: 18
0.68 0.11 0.20
Matches are distributed among these distances:
13 7 0.12
14 19 0.32
15 16 0.27
16 11 0.18
17 6 0.10
18 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (15 bp):
TATTAATTAATATAA
Found at i:5871266 original size:9 final size:8
Alignment explanation
Indices: 5871241--5871269 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
5871231 CATATGTTTA
5871241 TTTTTA-T
1 TTTTTATT
5871248 TTTTTATT
1 TTTTTATT
5871256 TTTTTATT
1 TTTTTATT
5871264 TTTTTA
1 TTTTTA
5871270 GATGTACCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 6 0.29
8 15 0.71
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTTATT
Found at i:5872297 original size:24 final size:24
Alignment explanation
Indices: 5872242--5872299 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
5872232 TAAAAATATA
* *
5872242 AAAAAAAAATTATTTTTTAAAATT
1 AAAAAAAAATGACTTTTTAAAATT
* *
5872266 TAATAAAAATGACCTTTTTAAAA-T
1 AAAAAAAAATGA-CTTTTTAAAATT
5872290 AAAAAAAAAT
1 AAAAAAAAAT
5872300 AAATTTTGTT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
24 18 0.67
25 9 0.33
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.34
Consensus pattern (24 bp):
AAAAAAAAATGACTTTTTAAAATT
Found at i:5872298 original size:25 final size:24
Alignment explanation
Indices: 5872239--5872298 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 24
5872229 TGTTAAAAAT
* *
5872239 ATAAAAAAAAAATTATTTTTTAAA
1 ATAAAAAAAAAATGACTTTTTAAA
** *
5872263 ATTTAATAAAAATGACCTTTTTAAA
1 ATAAAAAAAAAATGA-CTTTTTAAA
5872288 ATAAAAAAAAA
1 ATAAAAAAAAA
5872299 TAAATTTTGT
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
24 11 0.41
25 16 0.59
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (24 bp):
ATAAAAAAAAAATGACTTTTTAAA
Found at i:5872321 original size:25 final size:24
Alignment explanation
Indices: 5872225--5872323 Score: 65
Period size: 25 Copynumber: 3.9 Consensus size: 24
5872215 AAAAGCATGG
*
5872225 ATTTTGTTAAAAATATAAAAAAAAA
1 ATTTTGTT-AAAATATAAAAAATAA
* * *
5872250 ATTATTTTTTAAAATTTAATAAAAATGA
1 A-T-TTTGTTAAAATAT-A-AAAAATAA
** *
5872278 CCTTT-TTAAAATAAAAAAAAATAA
1 ATTTTGTTAAAAT-ATAAAAAATAA
5872302 ATTTTGTTGAAAATATAAAAAA
1 ATTTTGTT-AAAATATAAAAAA
5872324 ATATTTTTCA
Statistics
Matches: 55, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
24 10 0.18
25 18 0.33
26 15 0.27
27 6 0.11
28 6 0.11
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (24 bp):
ATTTTGTTAAAATATAAAAAATAA
Found at i:5872325 original size:26 final size:25
Alignment explanation
Indices: 5872225--5872326 Score: 91
Period size: 26 Copynumber: 4.0 Consensus size: 25
5872215 AAAAGCATGG
5872225 ATTTTGTTAAAAATATAAAAAAA-AA
1 ATTTTGTT-AAAATATAAAAAAATAA
* * *
5872250 ATTATTTTTTAAAATTTAATAAAAATGA
1 A-T-TTTGTTAAAATATAA-AAAAATAA
** *
5872278 CCTTT-TTAAAATAAAAAAAAATAA
1 ATTTTGTTAAAATATAAAAAAATAA
5872302 ATTTTGTTGAAAATATAAAAAAATA
1 ATTTTGTT-AAAATATAAAAAAATA
5872327 TTTTTCAAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
24 10 0.17
25 12 0.20
26 27 0.45
27 10 0.17
28 1 0.02
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (25 bp):
ATTTTGTTAAAATATAAAAAAATAA
Found at i:5872366 original size:21 final size:20
Alignment explanation
Indices: 5872323--5872367 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
5872313 AATATAAAAA
* *
5872323 AATATTTTTCAAAAATTTTT
1 AATATTTTTCAAAAATATGT
*
5872343 AATATATTTTGAAAAATATGT
1 AATAT-TTTTCAAAAATATGT
5872364 AATA
1 AATA
5872368 AAAAATAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (20 bp):
AATATTTTTCAAAAATATGT
Found at i:5873864 original size:21 final size:23
Alignment explanation
Indices: 5873840--5873893 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
5873830 TTGGACATTC
5873840 TTGGCA-AAAAG-AGACAAGCAA
1 TTGGCATAAAAGAAGACAAGCAA
*
5873861 TTGGACATAACAGAAGACAAGCAA
1 TTGG-CATAAAAGAAGACAAGCAA
5873885 TTCGGCATA
1 TT-GGCATA
5873894 CATAATTGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 4 0.14
22 2 0.07
23 4 0.14
24 16 0.57
25 2 0.07
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (23 bp):
TTGGCATAAAAGAAGACAAGCAA
Found at i:5874087 original size:34 final size:34
Alignment explanation
Indices: 5874041--5874108 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
5874031 ATAGTGCATC
* *
5874041 TGAAAATGTATATCCAAAATGTTTAAAAAATTTT
1 TGAAAATATATATCCAAAAGGTTTAAAAAATTTT
*
5874075 TGAAAATATATATCCGAAAGGTTTAAAAAATTTT
1 TGAAAATATATATCCAAAAGGTTTAAAAAATTTT
5874109 CGGATATGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (34 bp):
TGAAAATATATATCCAAAAGGTTTAAAAAATTTT
Found at i:5874659 original size:17 final size:17
Alignment explanation
Indices: 5874637--5874677 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
5874627 CTTTATATAT
5874637 ATATATATATTTAGTAA
1 ATATATATATTTAGTAA
* *
5874654 ATATAT-TTTTTATTAA
1 ATATATATATTTAGTAA
5874670 ATA-ATATA
1 ATATATATA
5874678 AATTATTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 2 0.10
16 12 0.60
17 6 0.30
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
ATATATATATTTAGTAA
Found at i:5874715 original size:26 final size:26
Alignment explanation
Indices: 5874651--5874715 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
5874641 ATATATTTAG
* *
5874651 TAAATATATTTTT-TATTAAATAATA
1 TAAATATATTTTTAGATTAAATAAAA
*
5874676 TAAAT-TATTATTTAGATTAATTAAAA
1 TAAATATATT-TTTAGATTAAATAAAA
*
5874702 TTAATATATTTTTA
1 TAAATATATTTTTA
5874716 TTAAAAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
24 4 0.12
25 8 0.24
26 17 0.52
27 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (26 bp):
TAAATATATTTTTAGATTAAATAAAA
Found at i:5885165 original size:63 final size:63
Alignment explanation
Indices: 5885091--5885219 Score: 249
Period size: 63 Copynumber: 2.0 Consensus size: 63
5885081 TCAAACACTA
*
5885091 AAACTGAAGAAATATTTGTTCCTCTAATTATATAATTAAATACAAGTAACAATACAGATACTC
1 AAACTAAAGAAATATTTGTTCCTCTAATTATATAATTAAATACAAGTAACAATACAGATACTC
5885154 AAACTAAAGAAATATTTGTTCCTCTAATTATATAATTAAATACAAGTAACAATACAGATACTC
1 AAACTAAAGAAATATTTGTTCCTCTAATTATATAATTAAATACAAGTAACAATACAGATACTC
5885217 AAA
1 AAA
5885220 TGAATTCCTA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.31
Consensus pattern (63 bp):
AAACTAAAGAAATATTTGTTCCTCTAATTATATAATTAAATACAAGTAACAATACAGATACTC
Found at i:5887851 original size:3 final size:3
Alignment explanation
Indices: 5887843--5887875 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5887833 AAATAAAATT
5887843 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5887876 GACATATGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5888024 original size:21 final size:21
Alignment explanation
Indices: 5887974--5888025 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
5887964 AATAATAGTG
5887974 TATTAAATAAAATAAATGAAAA
1 TATTAAATAAAATAAA-GAAAA
*
5887996 T-TTTAATAAAATAAA-AAAA
1 TATTAAATAAAATAAAGAAAA
5888015 TAATTAAATAA
1 T-ATTAAATAA
5888026 TTACTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 5 0.19
21 20 0.77
22 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (21 bp):
TATTAAATAAAATAAAGAAAA
Found at i:5888103 original size:2 final size:2
Alignment explanation
Indices: 5888096--5888127 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5888086 ATACTTTGTA
5888096 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5888128 CAATCAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5890222 original size:2 final size:2
Alignment explanation
Indices: 5890217--5890258 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
5890207 TTTTTTCTTT
* *
5890217 TA TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5890259 AACCCTAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:5892924 original size:30 final size:31
Alignment explanation
Indices: 5892874--5892943 Score: 106
Period size: 30 Copynumber: 2.3 Consensus size: 31
5892864 ATCGGGTCAT
5892874 TTATATATTCATATAATATTTTATACAAAAA
1 TTATATATTCATATAATATTTTATACAAAAA
* * *
5892905 TTATAT-TTTATATGATATTTTATATAAAAA
1 TTATATATTCATATAATATTTTATACAAAAA
5892935 TTATATATT
1 TTATATATT
5892944 ACAATTTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
30 27 0.77
31 8 0.23
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (31 bp):
TTATATATTCATATAATATTTTATACAAAAA
Found at i:5897030 original size:13 final size:14
Alignment explanation
Indices: 5897012--5897047 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
5897002 AGTTAAATAA
5897012 AAATTAAAA-TTAT
1 AAATTAAAATTTAT
5897025 AAATTAAAATTTAT
1 AAATTAAAATTTAT
5897039 AAATTAAAA
1 AAATTAAAA
5897048 AGTTTTAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATTAAAATTTAT
Found at i:5897114 original size:13 final size:13
Alignment explanation
Indices: 5897096--5897147 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
5897086 AAAAATTAAT
5897096 TAATTTTAATATA
1 TAATTTTAATATA
*
5897109 TAATTTTAGATAAA
1 TAATTTTA-ATATA
*
5897123 TATTTTTAATA-A
1 TAATTTTAATATA
* *
5897135 AAATATTAATATA
1 TAATTTTAATATA
5897148 ATTTTTATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
12 9 0.28
13 12 0.38
14 11 0.34
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (13 bp):
TAATTTTAATATA
Found at i:5897252 original size:37 final size:36
Alignment explanation
Indices: 5897222--5897290 Score: 104
Period size: 37 Copynumber: 1.9 Consensus size: 36
5897212 TTATATATTA
5897222 TTAATTTTTATATT-AAATTTTATTAATTTATTGAT
1 TTAATTTTTATATTAAAATTTTATTAATTTATTGAT
* *
5897257 TTAATTTTTTTATTAAAAATTTTATTAAATTATT
1 TTAATTTTTATATT-AAAATTTTATTAATTTATT
5897291 TTTAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 13 0.43
37 17 0.57
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (36 bp):
TTAATTTTTATATTAAAATTTTATTAATTTATTGAT
Found at i:5897291 original size:13 final size:13
Alignment explanation
Indices: 5897238--5897292 Score: 51
Period size: 12 Copynumber: 4.4 Consensus size: 13
5897228 TTTATATTAA
*
5897238 ATTTTATTAATTT
1 ATTTTATTAAATT
* *
5897251 A-TTGATTTAATT
1 ATTTTATTAAATT
* *
5897263 TTTTTATTAAA-A
1 ATTTTATTAAATT
5897275 ATTTTATTAAATT
1 ATTTTATTAAATT
5897288 ATTTT
1 ATTTT
5897293 TAAAAAAATT
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
12 18 0.58
13 13 0.42
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (13 bp):
ATTTTATTAAATT
Found at i:5900213 original size:2 final size:2
Alignment explanation
Indices: 5900206--5900238 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5900196 CAGAAGGAAA
*
5900206 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5900239 GTGCAAGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5908155 original size:2 final size:2
Alignment explanation
Indices: 5908148--5908179 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5908138 ATGGACATAC
*
5908148 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5908180 GCAAGTTTCT
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5915939 original size:47 final size:47
Alignment explanation
Indices: 5915885--5915984 Score: 182
Period size: 47 Copynumber: 2.1 Consensus size: 47
5915875 TTAATCAGTA
5915885 TTACTGTTGTTAATAGAGCTGTTTGATTATCTGCACTCTGCAGGCAG
1 TTACTGTTGTTAATAGAGCTGTTTGATTATCTGCACTCTGCAGGCAG
*
5915932 TTACTGTTGTTAATAGAGCTGTTTGTTTATCTGCACTCTGCAGGCAG
1 TTACTGTTGTTAATAGAGCTGTTTGATTATCTGCACTCTGCAGGCAG
*
5915979 TGACTG
1 TTACTG
5915985 CGATGGTTCA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (47 bp):
TTACTGTTGTTAATAGAGCTGTTTGATTATCTGCACTCTGCAGGCAG
Found at i:5917694 original size:202 final size:202
Alignment explanation
Indices: 5917332--5917736 Score: 702
Period size: 202 Copynumber: 2.0 Consensus size: 202
5917322 GCTCATAGAA
* *
5917332 AGGACCTCAAATTAGATTGCTTAATGTGGCATTTCTTTCAATGATGACATCTGCAAAAAGATTAC
1 AGGACCTCAAATTAGATTGCTTAATGTGGCATTTCTTTCAAGGATGACATCTGCAAAAAGAGTAC
5917397 ACTGAATGTTTTCTTTCTGTTGATTGTTATTTCATATATATTGTATGGTGTAAGGTTTGATCCTA
66 ACTGAATGTTTTCTTTCTGTTGATTGTTATTTCATATATATTGTATGGTGTAAGGTTTGATCCTA
*
5917462 GTTTTACAAGATGAGGAAAAAAATTTCTTCTATTGATTTTGGGCTAGAAATCTATATCTTTTGTG
131 GTTTTACAAGATGAGGAAAAAAACTTCTTCTATTGATTTTGGGCTAGAAATCTATATCTTTTGTG
5917527 GAAACTT
196 GAAACTT
* * * *
5917534 AGGACTTCAAGTTAGATTGCTTAATGTGGCATTTCTTTCGAGGATGAGATCTGCAAAAAGAGTAC
1 AGGACCTCAAATTAGATTGCTTAATGTGGCATTTCTTTCAAGGATGACATCTGCAAAAAGAGTAC
* * *
5917599 ACTGAATGTTTTTTTTCTGTTGGTTGTTATTTCATATATATTGTATGGTGTAAGGTTTGATCCTT
66 ACTGAATGTTTTCTTTCTGTTGATTGTTATTTCATATATATTGTATGGTGTAAGGTTTGATCCTA
* *
5917664 GTTTTACAAGATGAGGGAAAAAACTTCTTCTATTGTTTTTGGGCTAGAAATCTATATCTTTTGTG
131 GTTTTACAAGATGAGGAAAAAAACTTCTTCTATTGATTTTGGGCTAGAAATCTATATCTTTTGTG
5917729 GAAACTT
196 GAAACTT
5917736 A
1 A
5917737 ACCCTGGATA
Statistics
Matches: 191, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
202 191 1.00
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (202 bp):
AGGACCTCAAATTAGATTGCTTAATGTGGCATTTCTTTCAAGGATGACATCTGCAAAAAGAGTAC
ACTGAATGTTTTCTTTCTGTTGATTGTTATTTCATATATATTGTATGGTGTAAGGTTTGATCCTA
GTTTTACAAGATGAGGAAAAAAACTTCTTCTATTGATTTTGGGCTAGAAATCTATATCTTTTGTG
GAAACTT
Found at i:5917847 original size:29 final size:29
Alignment explanation
Indices: 5917805--5917880 Score: 152
Period size: 29 Copynumber: 2.6 Consensus size: 29
5917795 AATTCTCAAA
5917805 CTGTTGTTGGATGTAAGACAGTTATTTGT
1 CTGTTGTTGGATGTAAGACAGTTATTTGT
5917834 CTGTTGTTGGATGTAAGACAGTTATTTGT
1 CTGTTGTTGGATGTAAGACAGTTATTTGT
5917863 CTGTTGTTGGATGTAAGA
1 CTGTTGTTGGATGTAAGA
5917881 ACGAGAATCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.21, C:0.07, G:0.29, T:0.43
Consensus pattern (29 bp):
CTGTTGTTGGATGTAAGACAGTTATTTGT
Found at i:5924774 original size:11 final size:11
Alignment explanation
Indices: 5924758--5924782 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5924748 TCTTAGTTTA
5924758 TTTTTTTTATT
1 TTTTTTTTATT
5924769 TTTTTTTTATT
1 TTTTTTTTATT
5924780 TTT
1 TTT
5924783 GTGGTGCTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTATT
Found at i:5925047 original size:5 final size:5
Alignment explanation
Indices: 5925037--5925062 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5925027 AATATATGTA
5925037 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
5925063 TTTTTCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:5925235 original size:29 final size:29
Alignment explanation
Indices: 5925170--5925241 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
5925160 AATTTCATTT
*
5925170 AATTAAAAGTTTAATTGAATTAAAATAAA
1 AATTAAAAATTTAATTGAATTAAAATAAA
* *
5925199 AATAAAAAATTTAATT-AATTATAATAAA
1 AATTAAAAATTTAATTGAATTAAAATAAA
* *
5925227 GTATTAAAAAATTAA
1 -AATTAAAAATTTAA
5925242 ATAACAATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
28 11 0.31
29 25 0.69
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (29 bp):
AATTAAAAATTTAATTGAATTAAAATAAA
Found at i:5925838 original size:16 final size:17
Alignment explanation
Indices: 5925806--5925838 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5925796 TTTATATATA
*
5925806 AAAATAACAATAATGAT
1 AAAATAACAAAAATGAT
5925823 AAAATAA-AAAAATGAT
1 AAAATAACAAAAATGAT
5925839 TATTAGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.70, C:0.03, G:0.06, T:0.21
Consensus pattern (17 bp):
AAAATAACAAAAATGAT
Found at i:5926222 original size:6 final size:6
Alignment explanation
Indices: 5926207--5926250 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
5926197 TATTTAGATG
* *
5926207 TAAAAA TAATAA TAATAA T-AAAA TAAAAA TAAAAA TAAAAA TAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAA
5926251 TTATTAGAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
5 4 0.11
6 31 0.89
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (6 bp):
TAAAAA
Found at i:5926231 original size:17 final size:18
Alignment explanation
Indices: 5926207--5926251 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
5926197 TATTTAGATG
*
5926207 TAAAAATAATAATAATAA
1 TAAAAATAATAATAAAAA
*
5926225 T-AAAATAAAAATAAAAA
1 TAAAAATAATAATAAAAA
5926242 TAAAAATAAT
1 TAAAAATAAT
5926252 TATTAGAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (18 bp):
TAAAAATAATAATAAAAA
Found at i:5926233 original size:23 final size:23
Alignment explanation
Indices: 5926207--5926250 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
5926197 TATTTAGATG
* *
5926207 TAAAAATAATAATAATAATAAAA
1 TAAAAATAAAAATAAAAATAAAA
5926230 TAAAAATAAAAATAAAAATAA
1 TAAAAATAAAAATAAAAATAA
5926251 TTATTAGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (23 bp):
TAAAAATAAAAATAAAAATAAAA
Found at i:5927408 original size:22 final size:23
Alignment explanation
Indices: 5927358--5927408 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
5927348 ATTAAAAGTC
* *
5927358 TTAATTGCCTTCATACATTTTTG
1 TTAATTGCCCTCATACATTTTCG
*
5927381 TTAATTGCCCTCGTACA-TTTCG
1 TTAATTGCCCTCATACATTTTCG
5927403 TTAATT
1 TTAATT
5927409 ACAAAAATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.49
Consensus pattern (23 bp):
TTAATTGCCCTCATACATTTTCG
Found at i:5927451 original size:24 final size:25
Alignment explanation
Indices: 5927422--5927471 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
5927412 AAAATACTTC
*
5927422 AAGTGAATACTAAAAA-TTTATAAT
1 AAGTGAATACTAAAAAGTATATAAT
5927446 AAGTGAATACTAAAAAGTATATAAT
1 AAGTGAATACTAAAAAGTATATAAT
5927471 A
1 A
5927472 TGTATTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.56, C:0.04, G:0.10, T:0.30
Consensus pattern (25 bp):
AAGTGAATACTAAAAAGTATATAAT
Found at i:5927624 original size:6 final size:6
Alignment explanation
Indices: 5927613--5927656 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
5927603 ACAAGAATTT
*
5927613 TTTTAA TTTTAA TTTTAA -TTTAA -TTTGA -TTTAA TTTTAA TTTTA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTA
5927657 TTGTTTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
5 13 0.37
6 22 0.63
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (6 bp):
TTTTAA
Found at i:5928098 original size:4 final size:4
Alignment explanation
Indices: 5928091--5928126 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
5928081 TAATTTTAAT
*
5928091 TTTA TTTA TTTA TTTA TTTAA TTTA ATTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTT-A TTTA TTTA TTTA TTT
5928127 GATTATCTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:5928114 original size:17 final size:17
Alignment explanation
Indices: 5928079--5928126 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
5928069 TTCAATTTTT
* *
5928079 TTTAATT-TTAATTTTA
1 TTTAATTATTTATTTAA
*
5928095 TTTATTTATTTATTTAA
1 TTTAATTATTTATTTAA
5928112 TTTAATTATTTATTT
1 TTTAATTATTTATTT
5928127 GATTATCTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 6 0.22
17 21 0.78
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTAATTATTTATTTAA
Found at i:5928175 original size:16 final size:16
Alignment explanation
Indices: 5928144--5928178 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5928134 TATTATTTTT
**
5928144 AAATATATTTTTATAA
1 AAATATATTTAAATAA
5928160 AAATATATTTAAATAA
1 AAATATATTTAAATAA
5928176 AAA
1 AAA
5928179 CCTTACCAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATATATTTAAATAA
Found at i:5928383 original size:15 final size:16
Alignment explanation
Indices: 5928362--5928392 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5928352 CTTTATAATT
*
5928362 TTTTTAAAAAATAAAG
1 TTTTAAAAAAATAAAG
5928378 TTTTAAAAAAATAAA
1 TTTTAAAAAAATAAA
5928393 ATACTATTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
TTTTAAAAAAATAAAG
Found at i:5932885 original size:23 final size:23
Alignment explanation
Indices: 5932857--5932912 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
5932847 ATATTTGAAA
**
5932857 TTTGAATGTGAATCTTTAAATTT
1 TTTGAATGAAAATCTTTAAATTT
*
5932880 TTTGAATGAAAATCTTTAACTTT
1 TTTGAATGAAAATCTTTAAATTT
* *
5932903 TATGTATGAA
1 TTTGAATGAA
5932913 TCTCTAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.48
Consensus pattern (23 bp):
TTTGAATGAAAATCTTTAAATTT
Found at i:5932889 original size:21 final size:21
Alignment explanation
Indices: 5932865--5932925 Score: 59
Period size: 23 Copynumber: 2.8 Consensus size: 21
5932855 AATTTGAATG
5932865 TGAATCTTTAAATTTTTTGAA
1 TGAATCTTTAAATTTTTTGAA
* * *
5932886 TGAAAATCTTTAACTTTTATGTA
1 TG--AATCTTTAAATTTTTTGAA
* *
5932909 TGAATCTCTAAAATTTT
1 TGAATCTTTAAATTTTT
5932926 CAAATGAGAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
21 13 0.42
23 18 0.58
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.49
Consensus pattern (21 bp):
TGAATCTTTAAATTTTTTGAA
Found at i:5933205 original size:17 final size:17
Alignment explanation
Indices: 5933161--5933205 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
5933151 TAACTTGAAA
* * *
5933161 TTCTGGTGAAACTAAAT
1 TTCTTGTGAATCTAAAG
5933178 TTCTTGTGAATCTAAAG
1 TTCTTGTGAATCTAAAG
5933195 TTCTTGTGAAT
1 TTCTTGTGAAT
5933206 ATGAAGTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (17 bp):
TTCTTGTGAATCTAAAG
Found at i:5933212 original size:17 final size:17
Alignment explanation
Indices: 5933173--5933213 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
5933163 CTGGTGAAAC
* *
5933173 TAAATTTCTTGTGAATC
1 TAAAGTTCTTGTGAATA
5933190 TAAAGTTCTTGTGAATA
1 TAAAGTTCTTGTGAATA
*
5933207 TGAAGTT
1 TAAAGTT
5933214 TTTATGAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.32, C:0.07, G:0.17, T:0.44
Consensus pattern (17 bp):
TAAAGTTCTTGTGAATA
Found at i:5933998 original size:43 final size:43
Alignment explanation
Indices: 5933841--5934073 Score: 156
Period size: 43 Copynumber: 5.5 Consensus size: 43
5933831 ATAAAAGAGT
* * * * * * * *
5933841 CCATATCTTATTTTAAAGTTGTTCTGCCTCTCTGTAGAGAAGC
1 CCATTTCTTATTTTAAAGTTATTTTACCTTTGTATAGAGAAAC
* * * ** *
5933884 CTATTTCTTATTTTAAAGTCATTTT-GCTTCATTTAGA-AGAAC
1 CCATTTCTTATTTTAAAGTTATTTTACCTTTGTATAGAGA-AAC
* * *
5933926 ACA-TTCCTATTTTACA-TT-TGTTTACCCTTTGTATAGAGAAAC
1 CCATTTCTTATTTTAAAGTTAT-TTTA-CCTTTGTATAGAGAAAC
* *
5933968 CCATTTCTTATTTTAAAGTTATTTTACCTTTGGT-TAGAGGAAT
1 CCATTTCTTATTTTAAAGTTATTTTACCTTT-GTATAGAGAAAC
* * * *
5934011 CCATTTCTTATTTTAAAGTCA-TTTAGCCTTTGAATAGAGGAGC
1 CCATTTCTTATTTTAAAGTTATTTTA-CCTTTGTATAGAGAAAC
*
5934054 CCATTTTTTATTTTAAAGTT
1 CCATTTCTTATTTTAAAGTT
5934074 GTTTATCCTC
Statistics
Matches: 148, Mismatches: 31, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
39 1 0.01
40 4 0.03
41 12 0.08
42 28 0.19
43 94 0.64
44 8 0.05
45 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (43 bp):
CCATTTCTTATTTTAAAGTTATTTTACCTTTGTATAGAGAAAC
Found at i:5934092 original size:43 final size:43
Alignment explanation
Indices: 5933886--5934097 Score: 180
Period size: 43 Copynumber: 5.0 Consensus size: 43
5933876 AGAGAAGCCT
* * ** * * *
5933886 ATTTCTTATTTTAAAGTCATTT-TGCTTCATTTAGAAGAACAC
1 ATTTCTTATTTTAAAGTTATTTATCCTTTGTATAGAGGAACCC
* * * * * *
5933928 A-TTCCTATTTTACATTTGTTTACCCTTTGTATAGAGAAACCC
1 ATTTCTTATTTTAAAGTTATTTATCCTTTGTATAGAGGAACCC
*
5933970 ATTTCTTATTTTAAAGTTATTT-TACCTTTGGT-TAGAGGAATCC
1 ATTTCTTATTTTAAAGTTATTTAT-CCTTT-GTATAGAGGAACCC
* * * *
5934013 ATTTCTTATTTTAAAGTCATTTAGCCTTTGAATAGAGGAGCCC
1 ATTTCTTATTTTAAAGTTATTTATCCTTTGTATAGAGGAACCC
* * * *
5934056 ATTTTTTATTTTAAAGTTGTTTATCCTCTGTTTAGAGGAACC
1 ATTTCTTATTTTAAAGTTATTTATCCTTTGTATAGAGGAACC
5934098 TATTACTTGA
Statistics
Matches: 131, Mismatches: 33, Indels: 11
0.75 0.19 0.06
Matches are distributed among these distances:
41 15 0.11
42 15 0.11
43 99 0.76
44 2 0.02
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (43 bp):
ATTTCTTATTTTAAAGTTATTTATCCTTTGTATAGAGGAACCC
Found at i:5934339 original size:6 final size:6
Alignment explanation
Indices: 5934328--5934365 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
5934318 AACAGGAATT
*
5934328 TTTTAA TTTTAA -TTTGA -TTTAA TTTTAA TTTTAA TTTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTT
5934366 TTTTAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 8 0.28
6 21 0.72
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (6 bp):
TTTTAA
Found at i:5934371 original size:16 final size:16
Alignment explanation
Indices: 5934329--5934360 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5934319 ACAGGAATTT
*
5934329 TTTAATTTTAATTTGA
1 TTTAATTTTAATTTTA
5934345 TTTAATTTTAATTTTA
1 TTTAATTTTAATTTTA
5934361 ATTTTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (16 bp):
TTTAATTTTAATTTTA
Found at i:5935921 original size:26 final size:26
Alignment explanation
Indices: 5935870--5935927 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
5935860 TTTGTGTTTG
* **
5935870 GGCCCATTGAGGTTCGAGCCTGATTA
1 GGCCCATTGAGGTTAGAGCCCAATTA
5935896 GGCCCATTGAGGTCTAG-GCCCAATTA
1 GGCCCATTGAGGT-TAGAGCCCAATTA
5935922 GGCCCA
1 GGCCCA
5935928 CCAATTATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 26 0.93
27 2 0.07
ACGTcount: A:0.21, C:0.28, G:0.29, T:0.22
Consensus pattern (26 bp):
GGCCCATTGAGGTTAGAGCCCAATTA
Found at i:5936066 original size:3 final size:3
Alignment explanation
Indices: 5936058--5936089 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5936048 GTTAACTTGT
5936058 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5936090 TATTCTCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5936596 original size:19 final size:19
Alignment explanation
Indices: 5936574--5936610 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5936564 TAGGTTTGAT
*
5936574 TGAATTTTTCGATGAAGTA
1 TGAATTTTTAGATGAAGTA
5936593 TGAATTTTTAGATGAAGT
1 TGAATTTTTAGATGAAGT
5936611 TTCCAGTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.03, G:0.22, T:0.43
Consensus pattern (19 bp):
TGAATTTTTAGATGAAGTA
Found at i:5938602 original size:12 final size:12
Alignment explanation
Indices: 5938587--5938616 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5938577 TTTGTTTTTA
5938587 TTTTTTAAATTT
1 TTTTTTAAATTT
*
5938599 TTTTTTAGATTT
1 TTTTTTAAATTT
5938611 TTTTTT
1 TTTTTT
5938617 GGAAAAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (12 bp):
TTTTTTAAATTT
Found at i:5938733 original size:14 final size:13
Alignment explanation
Indices: 5938709--5938770 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 13
5938699 AAAATATGGG
5938709 TAAAAATAAATAAA
1 TAAAAATAAA-AAA
5938723 T--AAAT-AAAAA
1 TAAAAATAAAAAA
5938733 TAAAAATAAGAAAA
1 TAAAAATAA-AAAA
* *
5938747 TAAAAAGAAAATA
1 TAAAAATAAAAAA
5938760 -AAAAATGAAAA
1 TAAAAAT-AAAA
5938771 CCTATGGTCG
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
10 4 0.10
11 2 0.05
12 13 0.32
13 8 0.20
14 13 0.32
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:5938739 original size:20 final size:18
Alignment explanation
Indices: 5938710--5938770 Score: 68
Period size: 20 Copynumber: 3.2 Consensus size: 18
5938700 AAATATGGGT
*
5938710 AAAAATAAATAAATAAATA
1 AAAAAAAAATAAA-AAATA
5938729 AAAATAAAAATAAGAAAATA
1 AAAA-AAAAATAA-AAAATA
*
5938749 AAAAGAAAATAAAAAATGA
1 AAAAAAAAATAAAAAAT-A
5938768 AAA
1 AAA
5938771 CCTATGGTCG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
18 5 0.14
19 15 0.41
20 16 0.43
21 1 0.03
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (18 bp):
AAAAAAAAATAAAAAATA
Found at i:5938770 original size:24 final size:24
Alignment explanation
Indices: 5938709--5938763 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 24
5938699 AAAATATGGG
*
5938709 TAAAAATAA-ATAAATAAATAAAAA
1 TAAAAATAAGA-AAATAAAAAAAAA
5938733 TAAAAATAAGAAAATAAAAAGAAAA
1 TAAAAATAAGAAAATAAAAA-AAAA
5938758 TAAAAA
1 TAAAAA
5938764 ATGAAAACCT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 17 0.61
25 11 0.39
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (24 bp):
TAAAAATAAGAAAATAAAAAAAAA
Found at i:5939629 original size:11 final size:11
Alignment explanation
Indices: 5939605--5939638 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
5939595 AAAAGAAAAG
5939605 AAAGAAAC-AA
1 AAAGAAACGAA
*
5939615 AAAGAAAGGAA
1 AAAGAAACGAA
5939626 AAAGAAACGAA
1 AAAGAAACGAA
5939637 AA
1 AA
5939639 TAATATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 7 0.33
11 14 0.67
ACGTcount: A:0.76, C:0.06, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAGAAACGAA
Found at i:5939646 original size:5 final size:5
Alignment explanation
Indices: 5939638--5939685 Score: 60
Period size: 5 Copynumber: 9.2 Consensus size: 5
5939628 AGAAACGAAA
* *
5939638 ATAAT ATAAT AATAAT ATAAAT ATAAT ATGAT ATAGT ATAAT ATAAT A
1 ATAAT ATAAT -ATAAT AT-AAT ATAAT ATAAT ATAAT ATAAT ATAAT A
5939686 GAACAGAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
5 27 0.73
6 10 0.27
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:5939827 original size:16 final size:16
Alignment explanation
Indices: 5939808--5939847 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
5939798 TAGGCTTAGG
5939808 CCAAAATGGGCCCAGA
1 CCAAAATGGGCCCAGA
*
5939824 CCAAAATGGGCCTAGA
1 CCAAAATGGGCCCAGA
*
5939840 CAAAAATG
1 CCAAAATG
5939848 AGTGTCTACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.42, C:0.25, G:0.23, T:0.10
Consensus pattern (16 bp):
CCAAAATGGGCCCAGA
Found at i:5940622 original size:238 final size:237
Alignment explanation
Indices: 5940036--5940627 Score: 642
Period size: 238 Copynumber: 2.5 Consensus size: 237
5940026 TGATCGGGAT
* * * *
5940036 AGAATCACAAATCATAAGGAATGATCTGGATTGAGCCT-AGATCGAGTAACCGGGACAAAATCAC
1 AGAACCACGAATCATAAGGAATGATCTGGATTGAG-CTAAGATCGAGTGACTGGGACAAAATCAC
* * * * * **
5940100 AAGTC-AAATAAAATGACCAAGACTGAGTCAAGGTCAAGAACAGATGATCGGGATGAAACCACGC
65 AAGTCAAAATAAAATGACCAAGATTGAGTCAAGATCGA-AATAGATGATCGAGATGAAACCACAA
*
5940164 ATCATAAGAAATGATCTAGACTAAGCCAAGATGGAACAACTGGGACAAAACCACAAGTTAAAATA
129 ATCATAAGAAATGATCTAGACTAAGCCAAGATCGAACAACTGGGACAAAACCACAAGTTAAAATA
* *
5940229 AAGTGACCAAGATCGAGTTCAGGTCAAGAATAGATGATCAATAC
194 AAGTGACCAAGACCGAGTTCAGGTCAAGAATAAATGATCAATAC
* * * *
5940273 AGAACCACGAATCATAAGGAATGATCTGGATTGAGCTAAGATCGAGTGA-TCGAGACGAAACCAT
1 AGAACCACGAATCATAAGGAATGATCTGGATTGAGCTAAGATCGAGTGACT-GGGACAAAATCAC
* * * * * * * **
5940337 AAGTTAAAATAAAATAACCAGGATCGAGTCAA-AGTTGAGAATAGATGATTGAGATGGAATTACA
65 AAGTCAAAATAAAATGACCAAGATTGAGTCAAGA-TCGA-AATAGATGATCGAGATGAAACCACA
* * * * **
5940401 AATCATAAGGAATGATCTGGACTAAGCCAAGATCGAGCAACTGGGATAAAATTACAAGTTAAAAT
128 AATCATAAGAAATGATCTAGACTAAGCCAAGATCGAACAACTGGGACAAAACCACAAGTTAAAAT
* ** *
5940466 AAAGTGACTAAGACCGAG-TCAAGGTTGAGAATAAATGATCGAGAT-G
193 AAAGTGACCAAGACCGAGTTC-AGGTCAAGAATAAATGATC-A-ATAC
* * * * *
5940512 A-AAGCATGAATCATTA-GAGATGATCTGGATTGAGCTAAGATCAAGGGACTGGGACAAAATCAC
1 AGAACCACGAATCATAAGGA-ATGATCTGGATTGAGCTAAGATCGAGTGACTGGGACAAAATCAC
* *
5940575 AAGTCAAAATAAAGTGACTAAGATTGAGTCAAGATCGAAAGTAGATGATCGAG
65 AAGTCAAAATAAAATGACCAAGATTGAGTCAAGATCGAAA-TAGATGATCGAG
5940628 GTAATGCAAA
Statistics
Matches: 290, Mismatches: 54, Indels: 21
0.79 0.15 0.06
Matches are distributed among these distances:
236 2 0.01
237 62 0.21
238 220 0.76
239 4 0.01
240 2 0.01
ACGTcount: A:0.43, C:0.15, G:0.23, T:0.19
Consensus pattern (237 bp):
AGAACCACGAATCATAAGGAATGATCTGGATTGAGCTAAGATCGAGTGACTGGGACAAAATCACA
AGTCAAAATAAAATGACCAAGATTGAGTCAAGATCGAAATAGATGATCGAGATGAAACCACAAAT
CATAAGAAATGATCTAGACTAAGCCAAGATCGAACAACTGGGACAAAACCACAAGTTAAAATAAA
GTGACCAAGACCGAGTTCAGGTCAAGAATAAATGATCAATAC
Found at i:5940627 original size:119 final size:118
Alignment explanation
Indices: 5940012--5940627 Score: 530
Period size: 119 Copynumber: 5.2 Consensus size: 118
5940002 GATCATGTTG
* * * *
5940012 AGGTCGAAAGCAGATGATCGGGAT-AGAATCACAAATCATAAGGAATGATCTGGATTGAGCCT-A
1 AGGTCGAAA-TAGATGATCGAGATGA-AACCACGAATCATAAGGAATGATCTGGATTGAG-CTAA
* * * *
5940075 GATCGAGTAACCGGGACAAAATCACAAG-TCAAATAAAATGACCAAGA-CTGAGTCA
63 GATCGAGCAACTGGGACAAAATCACAAGTTAAAATAAAGTGACCAAGATC-GAGTCA
* * * * * * * * *
5940130 AGGTCAAGAACAGATGATCGGGATGAAACCACGCATCATAAGAAATGATCTAGACTAAGCCAAGA
1 AGGTCGA-AATAGATGATCGAGATGAAACCACGAATCATAAGGAATGATCTGGATTGAGCTAAGA
* * *
5940195 TGGAACAACTGGGACAAAACCACAAGTTAAAATAAAGTGACCAAGATCGAGTTC-
65 TCGAGCAACTGGGACAAAATCACAAGTTAAAATAAAGTGACCAAGATCGAG-TCA
* *
5940249 AGGTCAAGAATAGATGATC-A-ATACAGAACCACGAATCATAAGGAATGATCTGGATTGAGCTAA
1 AGGTCGA-AATAGATGATCGAGAT-GA-AACCACGAATCATAAGGAATGATCTGGATTGAGCTAA
** * * * * * * *
5940312 GATCGAGTGA-TCGAGACGAAACCATAAGTTAAAATAAAATAACCAGGATCGAGTCA
63 GATCGAGCAACT-GGGACAAAATCACAAGTTAAAATAAAGTGACCAAGATCGAGTCA
* * * * ** * * * *
5940368 AAGTTGAGAATAGATGATTGAGATGGAATTACAAATCATAAGGAATGATCTGGACTAAGCCAAGA
1 AGGTCGA-AATAGATGATCGAGATGAAACCACGAATCATAAGGAATGATCTGGATTGAGCTAAGA
* * * *
5940433 TCGAGCAACTGGGATAAAATTACAAGTTAAAATAAAGTGACTAAGACCGAGTCA
65 TCGAGCAACTGGGACAAAATCACAAGTTAAAATAAAGTGACCAAGATCGAGTCA
* * * * *
5940487 AGGTTGAGAATAAATGATCGAGATGAAAGCATGAATCATTA-GAGATGATCTGGATTGAGCTAAG
1 AGGTCGA-AATAGATGATCGAGATGAAACCACGAATCATAAGGA-ATGATCTGGATTGAGCTAAG
* ** * * *
5940551 ATCAAGGGACTGGGACAAAATCACAAGTCAAAATAAAGTGACTAAGATTGAGTCA
64 ATCGAGCAACTGGGACAAAATCACAAGTTAAAATAAAGTGACCAAGATCGAGTCA
*
5940606 AGATCGAAAGTAGATGATCGAG
1 AGGTCGAAA-TAGATGATCGAG
5940628 GTAATGCAAA
Statistics
Matches: 400, Mismatches: 83, Indels: 29
0.78 0.16 0.06
Matches are distributed among these distances:
117 3 0.01
118 78 0.19
119 312 0.78
120 5 0.01
121 2 0.00
ACGTcount: A:0.43, C:0.14, G:0.23, T:0.19
Consensus pattern (118 bp):
AGGTCGAAATAGATGATCGAGATGAAACCACGAATCATAAGGAATGATCTGGATTGAGCTAAGAT
CGAGCAACTGGGACAAAATCACAAGTTAAAATAAAGTGACCAAGATCGAGTCA
Found at i:5941446 original size:12 final size:11
Alignment explanation
Indices: 5941425--5941451 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5941415 CAATTTAACC
5941425 TTTTTCTTTTT
1 TTTTTCTTTTT
5941436 TTTTTCTTTTT
1 TTTTTCTTTTT
5941447 TTTTT
1 TTTTT
5941452 GGATCAAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:5951575 original size:10 final size:10
Alignment explanation
Indices: 5951560--5951595 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
5951550 ATTTCTTTTG
5951560 TTTTTTTAAT
1 TTTTTTTAAT
5951570 TTTTTTTAAT
1 TTTTTTTAAT
**
5951580 TTTTTAGAAT
1 TTTTTTTAAT
5951590 TTTTTT
1 TTTTTT
5951596 CTTTTTTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (10 bp):
TTTTTTTAAT
Found at i:5952612 original size:14 final size:15
Alignment explanation
Indices: 5952587--5952625 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
5952577 AATTAGAACA
5952587 AAAAAGGAAAGAAA-G
1 AAAAA-GAAAGAAAGG
*
5952602 AAATAGAAAGAAAGG
1 AAAAAGAAAGAAAGG
5952617 AAAAAGAAA
1 AAAAAGAAA
5952626 CTAAAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (15 bp):
AAAAAGAAAGAAAGG
Found at i:5952641 original size:5 final size:5
Alignment explanation
Indices: 5952631--5952679 Score: 66
Period size: 5 Copynumber: 10.2 Consensus size: 5
5952621 AGAAACTAAA
* *
5952631 ATAAT ATAAT A-AAT ATAAT A-AAT ATAAT ATGAT ATAGT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
5952679 A
1 A
5952680 GAACAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
4 8 0.21
5 30 0.79
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (5 bp):
ATAAT
Found at i:5952647 original size:9 final size:10
Alignment explanation
Indices: 5952631--5952679 Score: 66
Period size: 9 Copynumber: 5.1 Consensus size: 10
5952621 AGAAACTAAA
5952631 ATAATATAAT
1 ATAATATAAT
5952641 A-AATATAAT
1 ATAATATAAT
5952650 A-AATATAAT
1 ATAATATAAT
* *
5952659 ATGATATAGT
1 ATAATATAAT
5952669 ATAATATAAT
1 ATAATATAAT
5952679 A
1 A
5952680 GAACAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
9 18 0.53
10 16 0.47
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (10 bp):
ATAATATAAT
Found at i:5952713 original size:3 final size:3
Alignment explanation
Indices: 5952705--5952757 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
5952695 ATAAAAAAGA
*
5952705 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5952753 AAT AA
1 AAT AA
5952758 AAATCTAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:5955396 original size:4 final size:4
Alignment explanation
Indices: 5955382--5955418 Score: 56
Period size: 4 Copynumber: 9.0 Consensus size: 4
5955372 CATGCATTTG
*
5955382 CATT ACATT CATT CATT CATT CATT CATC CATT CATT
1 CATT -CATT CATT CATT CATT CATT CATT CATT CATT
5955419 ATCATAACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.46
Consensus pattern (4 bp):
CATT
Found at i:5969795 original size:110 final size:110
Alignment explanation
Indices: 5969590--5969948 Score: 326
Period size: 110 Copynumber: 3.3 Consensus size: 110
5969580 CACTATCCAC
* * *
5969590 TCATTTGATCTCAACTCATGTCAGATCATCTTTT-GACTCGCGATATCCATCT-GATTATTTTTA
1 TCATTTGATCTCAACTCATGTCAGATCAT-TTTTAGACTCGCGACATCAATCTAG-TAATTTTTA
* * * ***
5969653 ACCTTGACTCAATCTTGGTCATTTTTTGACTTGTGGCATTGTCCCAA
64 ACCTCGACTTAGTCTTGGTCGCCTTTTGACTTGTGGCATTGTCCCAA
* * * * *
5969700 TCATTTGATCTCTACTCATGTCAGATTATTTTTAGACTCGCAACATCAATCTAGTCATTTTTGAC
1 TCATTTGATCTCAACTCATGTCAGATCATTTTTAGACTCGCGACATCAATCTAGTAATTTTTAAC
* * ** ** *
5969765 CTCGACTTAGTTTTGGTCGCCTTTTAACTTGCAGCATCATCCCAC
66 CTCGACTTAGTCTTGGTCGCCTTTTGACTTGTGGCATTGTCCCAA
* * * * * * * *
5969810 TTATTTGATCTCAACTCATGTCAAATCATCTTTAGACTCGCGACATTAGTCCAATAATTTTTTAC
1 TCATTTGATCTCAACTCATGTCAGATCATTTTTAGACTCGCGACATCAATCTAGTAATTTTTAAC
* * * * * ** *
5969875 ATCGACTTGGTCTTGGTAGCCTTCTGACTTATGGCATTGTCTGAG
66 CTCGACTTAGTCTTGGTCGCCTTTTGACTTGTGGCATTGTCCCAA
* * *
5969920 TCATTTGATCTCGACTCGTGTTAGATCAT
1 TCATTTGATCTCAACTCATGTCAGATCAT
5969949 CTTCAGACCT
Statistics
Matches: 196, Mismatches: 51, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
109 4 0.02
110 191 0.97
111 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (110 bp):
TCATTTGATCTCAACTCATGTCAGATCATTTTTAGACTCGCGACATCAATCTAGTAATTTTTAAC
CTCGACTTAGTCTTGGTCGCCTTTTGACTTGTGGCATTGTCCCAA
Found at i:5970660 original size:3 final size:3
Alignment explanation
Indices: 5970652--5970719 Score: 75
Period size: 3 Copynumber: 22.7 Consensus size: 3
5970642 GTTAACTTGT
* * * *
5970652 TTA TTA TTA TCA TTA TTA TTT TTA TTA TTA TTA CTA TTA TTA GTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
5970699 TCCA TTA TTA TTA TTA TTA TT
1 T-TA TTA TTA TTA TTA TTA TT
5970720 TTTTTATTTT
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
2 1 0.02
3 51 0.96
4 1 0.02
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:5971547 original size:18 final size:17
Alignment explanation
Indices: 5971521--5971567 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
5971511 GATTGCAGGT
*
5971521 TTTTCCTTTTTCATTTTA
1 TTTTACTTTTT-ATTTTA
5971539 TTTTACTTTTATATTTTA
1 TTTTACTTTT-TATTTTA
5971557 TTTTA-TTTTTA
1 TTTTACTTTTTA
5971568 ACCCATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 2 0.07
17 4 0.15
18 20 0.74
19 1 0.04
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTACTTTTTATTTTA
Found at i:5972163 original size:22 final size:22
Alignment explanation
Indices: 5972138--5972185 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
5972128 GTCAATTTTC
5972138 ATTTTCACCTAACATTTATAAT
1 ATTTTCACCTAACATTTATAAT
* *
5972160 ATTTTCGCCTAACTTTTATAAT
1 ATTTTCACCTAACATTTATAAT
5972182 ATTT
1 ATTT
5972186 AATTGCTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.31, C:0.17, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTTTCACCTAACATTTATAAT
Found at i:5972235 original size:17 final size:17
Alignment explanation
Indices: 5972207--5972241 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5972197 CTTATTTTTA
5972207 TATTTATTGCATGGTATT
1 TATTTATTGCATGG-ATT
5972225 TATTT-TTGCATGGATT
1 TATTTATTGCATGGATT
5972241 T
1 T
5972242 GCATGATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 8 0.47
18 5 0.29
ACGTcount: A:0.20, C:0.06, G:0.17, T:0.57
Consensus pattern (17 bp):
TATTTATTGCATGGATT
Found at i:5972329 original size:16 final size:16
Alignment explanation
Indices: 5972308--5972363 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
5972298 TGATTTATTA
*
5972308 ATATATTTGGATGATT
1 ATATATTTGAATGATT
*
5972324 ATATATTT-AATTGAAT
1 ATATATTTGAA-TGATT
* * *
5972340 GTTTATTTGCATGATT
1 ATATATTTGAATGATT
5972356 ATATATTT
1 ATATATTT
5972364 AATTGCATAT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
15 1 0.03
16 28 0.93
17 1 0.03
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.54
Consensus pattern (16 bp):
ATATATTTGAATGATT
Found at i:5972418 original size:31 final size:30
Alignment explanation
Indices: 5972346--5972438 Score: 102
Period size: 31 Copynumber: 3.1 Consensus size: 30
5972336 GAATGTTTAT
*
5972346 TTGCATGA-TTATATATT-TAATTGCAT-A
1 TTGCATGATTTATATATTATTATTGCATGA
*
5972373 TTTTGCATGGTTTATATATTATTATTGACATGA
1 --TTGCATGATTTATATATTATTATTG-CATGA
*
5972406 TTGCATGATTTATATGTTATTATTTGCATGA
1 TTGCATGATTTATATATTATTA-TTGCATGA
5972437 TT
1 TT
5972439 ATATATTTAA
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
29 7 0.13
30 9 0.16
31 32 0.58
32 6 0.11
33 1 0.02
ACGTcount: A:0.28, C:0.06, G:0.14, T:0.52
Consensus pattern (30 bp):
TTGCATGATTTATATATTATTATTGCATGA
Found at i:5972472 original size:12 final size:12
Alignment explanation
Indices: 5972424--5972496 Score: 55
Period size: 12 Copynumber: 6.4 Consensus size: 12
5972414 TTTATATGTT
5972424 ATTATTTGCATG
1 ATTATTTGCATG
*
5972436 ATTATAT--AT-
1 ATTATTTGCATG
*
5972445 -TTAATTGCATG
1 ATTATTTGCATG
*
5972456 TTTATTTGCATG
1 ATTATTTGCATG
*** *
5972468 ATTATTAATATT
1 ATTATTTGCATG
5972480 ATTATTTGCATG
1 ATTATTTGCATG
5972492 ATTAT
1 ATTAT
5972497 ATATTTAATT
Statistics
Matches: 44, Mismatches: 13, Indels: 8
0.68 0.20 0.12
Matches are distributed among these distances:
8 4 0.09
10 4 0.09
12 36 0.82
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.53
Consensus pattern (12 bp):
ATTATTTGCATG
Found at i:5972493 original size:56 final size:57
Alignment explanation
Indices: 5972311--5972550 Score: 230
Period size: 56 Copynumber: 4.2 Consensus size: 57
5972301 TTTATTAATA
* * *
5972311 TATTTGGATGATTATATATTTAATTGAATGTTTATTTGCATGATTATATATTTAATTGCA-
1 TATTTGCATGATTATATATTTAATTGCATGTTTATTTGCATGATTAT-TATAT-ATT--AT
* * *
5972371 TATTTTGCATGGTTTATATATTATTATTGACATG---A-TTGCATGA-T-TTATATGTTAT
1 TA-TTTGCAT-GATTATATATT-TAATTG-CATGTTTATTTGCATGATTATTATATATTAT
5972426 TATTTGCATGATTATATATTTAATTGCATGTTTATTTGCATGATTATTA-ATATTAT
1 TATTTGCATGATTATATATTTAATTGCATGTTTATTTGCATGATTATTATATATTAT
* * * *
5972482 TATTTGCATGATTATATATTTAATTGCATGTCTAATTACATGATGATTA-AT-TTATT
1 TATTTGCATGATTATATATTTAATTGCATGTTTATTTGCATGATTATTATATATTA-T
*
5972538 TATTTGTATGATT
1 TATTTGCATGATT
5972551 GCCTAATTAT
Statistics
Matches: 154, Mismatches: 14, Indels: 28
0.79 0.07 0.14
Matches are distributed among these distances:
51 4 0.03
52 5 0.03
53 10 0.06
54 9 0.06
55 13 0.08
56 69 0.45
57 7 0.05
58 1 0.01
59 1 0.01
60 10 0.06
61 7 0.05
62 10 0.06
63 5 0.03
64 3 0.02
ACGTcount: A:0.30, C:0.05, G:0.12, T:0.53
Consensus pattern (57 bp):
TATTTGCATGATTATATATTTAATTGCATGTTTATTTGCATGATTATTATATATTAT
Found at i:5972595 original size:33 final size:33
Alignment explanation
Indices: 5972557--5972640 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 33
5972547 GATTGCCTAA
* * *
5972557 TTATATATTTAATTGTATATTTATTTGCATGGT
1 TTATATATTTAATTGCATATTTATTTACATGAT
*
5972590 TTATATATTTAATTGCATGTTTATTTACATGAT
1 TTATATATTTAATTGCATATTTATTTACATGAT
*
5972623 TTACAT-TGTTAATTGCAT
1 TTATATAT-TTAATTGCAT
5972641 GATTATTATA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
32 1 0.02
33 44 0.98
ACGTcount: A:0.29, C:0.06, G:0.11, T:0.55
Consensus pattern (33 bp):
TTATATATTTAATTGCATATTTATTTACATGAT
Found at i:5972597 original size:21 final size:20
Alignment explanation
Indices: 5972572--5972613 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
5972562 TATTTAATTG
*
5972572 TATATTTATTTGCATGGTTTA
1 TATATTTAATTGCAT-GTTTA
5972593 TATATTTAATTGCATGTTTA
1 TATATTTAATTGCATGTTTA
5972613 T
1 T
5972614 TTACATGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.26, C:0.05, G:0.12, T:0.57
Consensus pattern (20 bp):
TATATTTAATTGCATGTTTA
Found at i:5972971 original size:18 final size:18
Alignment explanation
Indices: 5972901--5972971 Score: 58
Period size: 18 Copynumber: 4.1 Consensus size: 18
5972891 CATGAATGGT
* *
5972901 TATTAATATATTT-TATGG
1 TATT-ATATATTTGCATGA
* *
5972919 TATTTTATATTTGCATAA
1 TATTATATATTTGCATGA
*
5972937 TAATA-AT-TTTGCATGA
1 TATTATATATTTGCATGA
*
5972953 TATTATATATTTACATGA
1 TATTATATATTTGCATGA
5972971 T
1 T
5972972 TGTTATCATT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
16 12 0.29
17 11 0.27
18 18 0.44
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.52
Consensus pattern (18 bp):
TATTATATATTTGCATGA
Found at i:5973442 original size:10 final size:10
Alignment explanation
Indices: 5973424--5973470 Score: 60
Period size: 10 Copynumber: 4.8 Consensus size: 10
5973414 GAGGGGAGAC
*
5973424 AAAGGAAAGG
1 AAAGTAAAGG
*
5973434 AAAGTAAAGT
1 AAAGTAAAGG
5973444 AAAGTAAAGG
1 AAAGTAAAGG
*
5973454 AATGTAAAGG
1 AAAGTAAAGG
5973464 AAA-TAAA
1 AAAGTAAA
5973471 ATCCCCATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
9 4 0.12
10 28 0.88
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.13
Consensus pattern (10 bp):
AAAGTAAAGG
Found at i:5973447 original size:15 final size:15
Alignment explanation
Indices: 5973424--5973470 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
5973414 GAGGGGAGAC
*
5973424 AAAGGAAAGGAAAGT
1 AAAGTAAAGGAAAGT
* *
5973439 AAAGTAAAGTAAAGG
1 AAAGTAAAGGAAAGT
*
5973454 AATGTAAAGGAAA-T
1 AAAGTAAAGGAAAGT
5973468 AAA
1 AAA
5973471 ATCCCCATTT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.13
Consensus pattern (15 bp):
AAAGTAAAGGAAAGT
Found at i:5974613 original size:28 final size:28
Alignment explanation
Indices: 5974564--5974620 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
5974554 GAAATATAAG
* * *
5974564 AAAAAAGATGAAAAAATGAAAAATGAAA
1 AAAAAAGATAAAAAAAGGAAAAAGGAAA
5974592 AAAAAAG-TAAAAAAAGGAAAAAAGGAAA
1 AAAAAAGATAAAAAAAGG-AAAAAGGAAA
5974620 A
1 A
5974621 CTTAAACTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 8 0.32
28 17 0.68
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (28 bp):
AAAAAAGATAAAAAAAGGAAAAAGGAAA
Found at i:5975348 original size:20 final size:24
Alignment explanation
Indices: 5975297--5975354 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
5975287 CCTTGATAAC
5975297 TACATTTGCATCATGGTTAGAGCA
1 TACATTTGCATCATGGTTAGAGCA
*
5975321 TGCATTTGCATCAT-G-TAGAG-A
1 TACATTTGCATCATGGTTAGAGCA
*
5975342 -ACATTTGAATCAT
1 TACATTTGCATCAT
5975355 AGTATGACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 11 0.35
21 1 0.03
22 5 0.16
23 1 0.03
24 13 0.42
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (24 bp):
TACATTTGCATCATGGTTAGAGCA
Found at i:5975654 original size:23 final size:23
Alignment explanation
Indices: 5975583--5975657 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
5975573 TTTAAAGGAA
* *
5975583 AATTTTTTTAATGTGAATCTTTG
1 AATTTTTTGAATGTAAATCTTTG
* * * **
5975606 AA-ATTTTGGATGTAAATCCTAA
1 AATTTTTTGAATGTAAATCTTTG
*
5975628 AATTTTTTGAATGAAAATCTTTG
1 AATTTTTTGAATGTAAATCTTTG
5975651 AATTTTT
1 AATTTTT
5975658 GCTGTGAACC
Statistics
Matches: 38, Mismatches: 13, Indels: 2
0.72 0.25 0.04
Matches are distributed among these distances:
22 15 0.39
23 23 0.61
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.49
Consensus pattern (23 bp):
AATTTTTTGAATGTAAATCTTTG
Found at i:5975820 original size:17 final size:17
Alignment explanation
Indices: 5975798--5975841 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
5975788 TGTGAAACTC
5975798 TTGTGAATCTAAAATTT
1 TTGTGAATCTAAAATTT
*
5975815 TTGTGAATCTAAAGTTT
1 TTGTGAATCTAAAATTT
*
5975832 TTGCGAATCT
1 TTGTGAATCT
5975842 TTCTTTCTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.45
Consensus pattern (17 bp):
TTGTGAATCTAAAATTT
Found at i:5975897 original size:17 final size:16
Alignment explanation
Indices: 5975846--5975900 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
5975836 GAATCTTTCT
5975846 TTCTTGCGAAATCGAAA
1 TTCTTGCGAAAT-GAAA
* *
5975863 TTCTTGCGAACCTAAAA
1 TTCTTGCGAA-ATGAAA
*
5975880 TTCTTGAGAATATGAAA
1 TTCTTGCGAA-ATGAAA
5975897 TTCT
1 TTCT
5975901 GGCAAATCTG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
17 30 0.97
18 1 0.03
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Consensus pattern (16 bp):
TTCTTGCGAAATGAAA
Done.