Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167982.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_24, 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: 18142777
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 63000 characters in sequence are not A, C, G, or T
File 76 of 84
Found at i:16462183 original size:20 final size:21
Alignment explanation
Indices: 16462150--16462191 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
16462140 ACTAAAAGGA
16462150 TTTAAGCCTCTGGTGAA-TTC
1 TTTAAGCCTCTGGTGAAGTTC
16462170 TTTAA-CCTCTTGGTGAAGTTC
1 TTTAAGCCTC-TGGTGAAGTTC
16462191 T
1 T
16462192 CCAAAAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 12 0.60
21 4 0.20
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (21 bp):
TTTAAGCCTCTGGTGAAGTTC
Found at i:16465676 original size:55 final size:55
Alignment explanation
Indices: 16465541--16465730 Score: 224
Period size: 55 Copynumber: 3.4 Consensus size: 55
16465531 TTTTTTAGGT
* *
16465541 AAAAATAATTTCAAAACATTTTTGAGAAAAAGTTGAAGTATTAAGTATTTTTAAAC
1 AAAAA-AATTTCAAAAAATTTTTGAGAAAAAGTTGAAGTATCAAGTATTTTTAAAC
* *
16465597 AAATAATATTTCAAAAAATATTTTGAGAAAAAGTTGAAGTATCAA-TTTTTTTAAAC
1 AAA-AAAATTTCAAAAAAT-TTTTGAGAAAAAGTTGAAGTATCAAGTATTTTTAAAC
* * *
16465653 AAAAAAAATTCAAAAAATGTTTTGAGAAAAAGTTGAAGTATC-AGT-TCTCCTTAAAT
1 AAAAAAATTTCAAAAAAT-TTTTGAGAAAAAGTTGAAGTATCAAGTAT-T-TTTAAAC
16465709 AAAAAATATTTCAAAAATATTT
1 AAAAAA-ATTTCAAAAA-ATTT
16465731 AAGGAAAATT
Statistics
Matches: 117, Mismatches: 10, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
54 2 0.02
55 38 0.32
56 38 0.32
57 37 0.32
58 2 0.02
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.35
Consensus pattern (55 bp):
AAAAAAATTTCAAAAAATTTTTGAGAAAAAGTTGAAGTATCAAGTATTTTTAAAC
Found at i:16465738 original size:56 final size:54
Alignment explanation
Indices: 16465541--16465731 Score: 197
Period size: 56 Copynumber: 3.4 Consensus size: 54
16465531 TTTTTTAGGT
* *
16465541 AAAAATAATTTCAAAACAT-TTTTGAGAAAAAGTTGAAGTATTAAGTATTTTTAAACA
1 AAAAAT-ATTTCAAAA-ATATTTAGAGAAAAAGTTGAAGTA-TCAGT-TTTTTAAACA
* * *
16465598 AATAATATTTCAAAAAATATTTTGAGAAAAAGTTGAAGTATCAATTTTTTTAAACA
1 AAAAATATTTC-AAAAATATTTAGAGAAAAAGTTGAAGTATC-AGTTTTTTAAACA
* * * * *
16465654 AAAAA-AATTCAAAAAATGTTTTGAGAAAAAGTTGAAGTATCAGTTCTCCTTAAATA
1 AAAAATATTTC-AAAAATATTTAGAGAAAAAGTTGAAGTATCAGTT-T-TTTAAACA
16465710 AAAAATATTTCAAAAATATTTA
1 AAAAATATTTCAAAAATATTTA
16465732 AGGAAAATTT
Statistics
Matches: 116, Mismatches: 12, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
54 3 0.03
55 35 0.30
56 42 0.36
57 36 0.31
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (54 bp):
AAAAATATTTCAAAAATATTTAGAGAAAAAGTTGAAGTATCAGTTTTTTAAACA
Found at i:16465753 original size:112 final size:112
Alignment explanation
Indices: 16465541--16465758 Score: 266
Period size: 112 Copynumber: 1.9 Consensus size: 112
16465531 TTTTTTAGGT
* * * *
16465541 AAAAATAATTTCAAAACATTTTTGAGAAAAAGTTGAAGTATTAAGTATTTTTAAACAAATAATAT
1 AAAAATAAATTCAAAAAATTTTTGAGAAAAAGTTGAAGTATTAAGTATTCTTAAACAAAAAATAT
* *
16465606 TTCAAAAAATATTTTGAGAAAAAGTTGAAGTATCAATTTTTTTAAAC
66 TTCAAAAAATATTTAGAGAAAAAGTTGAAATATCAATTTTTTTAAAC
* *
16465653 AAAAA-AAATTCAAAAAATGTTTTGAGAAAAAGTTGAAGTA-TCAGT-TCTCCTTAAATAAAAAA
1 AAAAATAAATTCAAAAAAT-TTTTGAGAAAAAGTTGAAGTATTAAGTAT-T-CTTAAACAAAAAA
**
16465715 TATTTC-AAAAATATTTA-AGGAAAATTTTGAAATAATCAATTTTT
63 TATTTCAAAAAATATTTAGA-GAAAAAGTTGAAAT-ATCAATTTTT
16465759 GCTTAAATAA
Statistics
Matches: 91, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
110 2 0.02
111 37 0.41
112 52 0.57
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.35
Consensus pattern (112 bp):
AAAAATAAATTCAAAAAATTTTTGAGAAAAAGTTGAAGTATTAAGTATTCTTAAACAAAAAATAT
TTCAAAAAATATTTAGAGAAAAAGTTGAAATATCAATTTTTTTAAAC
Found at i:16466703 original size:17 final size:17
Alignment explanation
Indices: 16466681--16466721 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
16466671 ATAATTTTAA
* *
16466681 ATAAAACAAATAATATG
1 ATAAAAAAAACAATATG
16466698 ATAAAAAAAACAATATG
1 ATAAAAAAAACAATATG
16466715 A-AAAAAA
1 ATAAAAAA
16466722 TATGAAGTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.17
Consensus pattern (17 bp):
ATAAAAAAAACAATATG
Found at i:16469367 original size:18 final size:18
Alignment explanation
Indices: 16469297--16469367 Score: 70
Period size: 18 Copynumber: 3.9 Consensus size: 18
16469287 ATTTGAGAAT
*
16469297 GATACATTTGTGGTGGGG
1 GATACATTTGTGGTGGAG
*
16469315 GATACATTTGTGGTAGAG
1 GATACATTTGTGGTGGAG
* * * * *
16469333 GATAAATTAGAGATGGAA
1 GATACATTTGTGGTGGAG
*
16469351 GATACATTTGTGTTGGA
1 GATACATTTGTGGTGGA
16469368 TAATAACCAT
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.30, C:0.04, G:0.34, T:0.32
Consensus pattern (18 bp):
GATACATTTGTGGTGGAG
Found at i:16469872 original size:16 final size:17
Alignment explanation
Indices: 16469842--16469873 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16469832 CATCATTATA
16469842 ATTCTTTTCTTCTATTC
1 ATTCTTTTCTTCTATTC
16469859 ATTCTTTT-TTCTATT
1 ATTCTTTTCTTCTATT
16469874 TGTTTGTGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTCTTTTCTTCTATTC
Found at i:16472089 original size:19 final size:18
Alignment explanation
Indices: 16472067--16472106 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
16472057 TTCCACTCCA
16472067 TTTTC-TATTTTGATTTTAT
1 TTTTCTTATTTT-A-TTTAT
16472086 TTTTCTTATTTTATTTAT
1 TTTTCTTATTTTATTTAT
16472104 TTT
1 TTT
16472107 ATTTTGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
19 6 0.30
20 6 0.30
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.78
Consensus pattern (18 bp):
TTTTCTTATTTTATTTAT
Found at i:16472098 original size:14 final size:14
Alignment explanation
Indices: 16472072--16472116 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
16472062 CTCCATTTTC
16472072 TATTTTGATTTTATT
1 TATTTT-ATTTTATT
16472087 T-TTCTTATTTTATT
1 TATT-TTATTTTATT
*
16472101 TATTTTATTTTGTT
1 TATTTTATTTTATT
16472115 TA
1 TA
16472117 CATTTATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 22 0.81
15 5 0.19
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (14 bp):
TATTTTATTTTATT
Found at i:16479004 original size:56 final size:55
Alignment explanation
Indices: 16478933--16479236 Score: 290
Period size: 56 Copynumber: 5.4 Consensus size: 55
16478923 TTTTTTAGGT
*
16478933 AAAAATAATTTCAAAAAATTTTTGAGAAAAAGTTGAAGTATTAAGTTTTTTTAAATA
1 AAAAAT-ATTTCAAAAAATTTTTGAGAAAAAGTTGAAGTATCAA-TTTTTTTAAATA
* *
16478990 AATAATATTTCAAAAAATATTTTGAGGAAAAGTTGAAGTATCAA-TTTTTTAAATA
1 AAAAATATTTCAAAAAAT-TTTTGAGAAAAAGTTGAAGTATCAATTTTTTTAAATA
* * * * * *
16479045 AAAAAAATTT-TAAAAATGTTTTGAGAGAAAGTTAAAATATCAATTTTCCTTAAATA
1 AAAAATATTTCAAAAAAT-TTTTGAGAAAAAGTTGAAGTATCAATTTT-TTTAAATA
* * * ** *
16479101 AAAAATATTTCAAAAAATGTATAAGAAAAAGTAAAAGTATAAATTTTCTTTAAATAA
1 AAAAATATTTCAAAAAATTTTTGAGAAAAAGTTGAAGTATCAATTTT-TTTAAAT-A
* * * ***
16479158 AAAAATGTTTCAAAAAAAATATTTGA-AGAAAAGTTGAATTATCAATTTTCCCAATATA
1 AAAAATATTTC--AAAAAATTTTTGAGA-AAAAGTTGAAGTATCAATTTTTTTAA-ATA
16479216 AAAAATATTTCAAAAATATTT
1 AAAAATATTTCAAAAA-ATTT
16479237 AAGGAAAAAG
Statistics
Matches: 202, Mismatches: 35, Indels: 20
0.79 0.14 0.08
Matches are distributed among these distances:
54 27 0.13
55 22 0.11
56 62 0.31
57 48 0.24
58 14 0.07
59 29 0.14
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.36
Consensus pattern (55 bp):
AAAAATATTTCAAAAAATTTTTGAGAAAAAGTTGAAGTATCAATTTTTTTAAATA
Found at i:16479021 original size:57 final size:56
Alignment explanation
Indices: 16478933--16479244 Score: 287
Period size: 57 Copynumber: 5.6 Consensus size: 56
16478923 TTTTTTAGGT
* *
16478933 AAAAATAATTTCAAAAAAT-TTTTGAGAAAAAGTTGAAGTATTAAGTTTTTTTAAATA
1 AAAAAT-ATTTCAAAAAATATTTTGAGGAAAAGTTGAAGTATCAA-TTTTTTTAAATA
*
16478990 AATAATATTTCAAAAAATATTTTGAGGAAAAGTTGAAGTATCAA-TTTTTTAAATA
1 AAAAATATTTCAAAAAATATTTTGAGGAAAAGTTGAAGTATCAATTTTTTTAAATA
* * * * * *
16479045 AAAAAAATTT-TAAAAATGTTTTGA-GAGAAAGTTAAAATATCAATTTTCCTTAAATA
1 AAAAATATTTCAAAAAATATTTTGAGGA-AAAGTTGAAGTATCAATTTT-TTTAAATA
* * * * ** *
16479101 AAAAATATTTCAAAAAAT-GTATAAGAAAAAGTAAAAGTATAAATTTTCTTTAAATAA
1 AAAAATATTTCAAAAAATATTTTGAGGAAAAGTTGAAGTATCAATTTT-TTTAAAT-A
* * * * ***
16479158 AAAAATGTTTCAAAAAAAATATTTGAAGAAAAGTTGAATTATCAATTTTCCCAATATA
1 AAAAATATTTCAAAAAATAT-TTTGAGGAAAAGTTGAAGTATCAATTTTTTTAA-ATA
*
16479216 AAAAATATTTC-AAAAATA-TTTAAGGAAAA
1 AAAAATATTTCAAAAAATATTTTGAGGAAAA
16479245 AGTCGAAATA
Statistics
Matches: 207, Mismatches: 38, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
53 2 0.01
54 26 0.13
55 31 0.15
56 55 0.27
57 58 0.28
58 13 0.06
59 22 0.11
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.35
Consensus pattern (56 bp):
AAAAATATTTCAAAAAATATTTTGAGGAAAAGTTGAAGTATCAATTTTTTTAAATA
Found at i:16479217 original size:115 final size:109
Alignment explanation
Indices: 16478932--16479274 Score: 293
Period size: 111 Copynumber: 3.0 Consensus size: 109
16478922 ATTTTTTAGG
* * * * * * * * *
16478932 TAAAAATAATTTCAAAAAATTTTTGAGAAAAAGTTGAAGTATTAAGTTTT-TTTAAATAAATAAT
1 TAAAAA-AATTTTAAAAAAATTTTGAGAGAAAGTTAAAATATCAA-TTTTCCTCAAATAAAAAAT
* * ** *
16478996 ATTTCAAAAAATATTTTGAGGAAAAGTTGAAGTATCAA-TTT-TTTAAA
64 ATTTC-AAAAA-A-TTTAAGAAAAAGTAAAAGTATAAATTTTCTTTAAA
** *
16479043 TAAAAAAAATTTTAAAAATGTTTTGAGAGAAAGTTAAAATATCAATTTTCCTTAAATAAAAAATA
1 T-AAAAAAATTTTAAAAAAATTTTGAGAGAAAGTTAAAATATCAATTTTCCTCAAATAAAAAATA
16479108 TTTCAAAAAATGTATAAGAAAAAGTAAAAGTATAAATTTTCTTTAAA
65 TTTCAAAAAAT-T-TAAGAAAAAGTAAAAGTATAAATTTTCTTTAAA
* *
16479155 TAAAAAAATGTTTCAAAAAAAATATTTGA-AGAAAAGTTGAATTATCAATTTTCC-CAATATAAA
1 TAAAAAAAT-TTT--AAAAAAAT-TTTGAGAG-AAAGTTAAAATATCAATTTTCCTCAA-ATAAA
* *
16479218 AAATATTTCAAAAATATTTAAGGAAAAAGTCGAAA-TAATAAATTTTCCTTAAA
60 AAATATTTCAAAAA-ATTTAA-GAAAAAGT-AAAAGT-ATAAATTTTCTTTAAA
16479271 TAAA
1 TAAA
16479275 GCATTATTTT
Statistics
Matches: 195, Mismatches: 21, Indels: 27
0.80 0.09 0.11
Matches are distributed among these distances:
108 1 0.01
109 2 0.01
110 26 0.13
111 60 0.31
112 15 0.08
114 13 0.07
115 54 0.28
116 24 0.12
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.35
Consensus pattern (109 bp):
TAAAAAAATTTTAAAAAAATTTTGAGAGAAAGTTAAAATATCAATTTTCCTCAAATAAAAAATAT
TTCAAAAAATTTAAGAAAAAGTAAAAGTATAAATTTTCTTTAAA
Found at i:16479263 original size:57 final size:53
Alignment explanation
Indices: 16478933--16479274 Score: 177
Period size: 56 Copynumber: 6.0 Consensus size: 53
16478923 TTTTTTAGGT
* * * * ***
16478933 AAAAATAATTTCAAAAAATTTTTGAGAAAAAGTTGAAGTATTAAGTTTTTTTAAATA
1 AAAAAT-ATTTC-AAAAATATTTAAGAAAAAG-TGAAATA-TAAATTTTCCCAAATA
* * * * * **
16478990 AATAATATTTCAAAAAATATTTTGAGGAAAAGTTGAAGTATCAATTTT-TTAAATA
1 AAAAATATTTC-AAAAATA-TTTAAGAAAAAG-TGAAATATAAATTTTCCCAAATA
* * * * * * * *
16479045 AAAAAAATTTTAAAAATGTTTTGAGAGAAAGTTAAAATATCAATTTTCCTTAAATA
1 AAAAATATTTCAAAAAT-ATTTAAGAAAAAG-TGAAATATAAATTTTCC-CAAATA
* **
16479101 AAAAATATTTCAAAAA-ATGTATAAGAAAAAGTAAAAGTATAAATTTTCTTTAAATAA
1 AAAAATATTTCAAAAATAT-T-TAAGAAAAAGTGAAA-TATAAATTTTC-CCAAAT-A
* * *
16479158 AAAAATGTTTCAAAAAAAATATTTGAAG-AAAAGTTGAATTATCAATTTTCCCAATATA
1 AAAAATATTTC---AAAAATATTT-AAGAAAAAG-TGAAATATAAATTTTCCCAA-ATA
*
16479216 AAAAATATTTCAAAAATATTTAAGGAAAAAGTCGAAATAATAAATTTTCCTTAAATA
1 AAAAATATTTCAAAAATATTTAA-GAAAAAGT-GAAAT-ATAAATTTTCC-CAAATA
16479273 AA
1 AA
16479275 GCATTATTTT
Statistics
Matches: 233, Mismatches: 31, Indels: 42
0.76 0.10 0.14
Matches are distributed among these distances:
54 33 0.14
55 33 0.14
56 70 0.30
57 50 0.21
58 15 0.06
59 18 0.08
60 12 0.05
61 2 0.01
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.35
Consensus pattern (53 bp):
AAAAATATTTCAAAAATATTTAAGAAAAAGTGAAATATAAATTTTCCCAAATA
Found at i:16479355 original size:17 final size:18
Alignment explanation
Indices: 16479323--16479356 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
16479313 TAAGAAAATT
16479323 TTGAAATATCAATTTTTC
1 TTGAAATATCAATTTTTC
*
16479341 TTGAAAT-TTAATTTTT
1 TTGAAATATCAATTTTT
16479357 TTAAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (18 bp):
TTGAAATATCAATTTTTC
Found at i:16480239 original size:22 final size:22
Alignment explanation
Indices: 16480214--16480259 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
16480204 AAAAATATGA
*
16480214 AATAGAAATAATTTAAAAATTT
1 AATAGAAATAATATAAAAATTT
* * *
16480236 AATATAAATTATATATAAATTT
1 AATAGAAATAATATAAAAATTT
16480258 AA
1 AA
16480260 CAAAAACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
AATAGAAATAATATAAAAATTT
Found at i:16482824 original size:18 final size:18
Alignment explanation
Indices: 16482786--16482825 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
16482776 ATTTGAGAAT
* *
16482786 GATACATTTGTGGTGGGG
1 GATACATTTGTGGTAGAG
16482804 GATACATTTGTGGTAGAG
1 GATACATTTGTGGTAGAG
16482822 GATA
1 GATA
16482826 AATTAGAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.25, C:0.05, G:0.38, T:0.33
Consensus pattern (18 bp):
GATACATTTGTGGTAGAG
Found at i:16485035 original size:51 final size:51
Alignment explanation
Indices: 16484915--16485061 Score: 134
Period size: 51 Copynumber: 2.9 Consensus size: 51
16484905 AACTGTAATT
** **
16484915 GAGAGATTTTTTTGATTTAATTCCAAAATCAATTGGCATTAATAATGATGTA
1 GAGAGATTTTTGAGATTTAATTCCAAAATCAATTCACATTAA-AATGATGTA
* * * * *
16484967 GAGAGGTTATCGAGATTTAATTCCATAATCAATTCACATTAAAATGATAG-G
1 GAGAGATTTTTGAGATTTAATTCCAAAATCAATTCACATTAAAATGAT-GTA
* * ** * *
16485018 GAGAGATTTTTGGGATTTGATTTTAGAATCAATTCTCATTAAAA
1 GAGAGATTTTTGAGATTTAATTCCAAAATCAATTCACATTAAAA
16485062 CTGAAACCAA
Statistics
Matches: 76, Mismatches: 18, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
51 41 0.54
52 35 0.46
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (51 bp):
GAGAGATTTTTGAGATTTAATTCCAAAATCAATTCACATTAAAATGATGTA
Found at i:16485580 original size:14 final size:14
Alignment explanation
Indices: 16485556--16485607 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
16485546 CCATTTTCTG
*
16485556 TTTTGATTTTATTT
1 TTTTTATTTTATTT
*
16485570 TTCTTATTTTATTT
1 TTTTTATTTTATTT
*
16485584 TTTTTATTTTGTTT
1 TTTTTATTTTATTT
16485598 ATTTTTATTT
1 -TTTTTATTT
16485608 ACTCTTGCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
14 24 0.73
15 9 0.27
ACGTcount: A:0.13, C:0.02, G:0.04, T:0.81
Consensus pattern (14 bp):
TTTTTATTTTATTT
Found at i:16485592 original size:23 final size:24
Alignment explanation
Indices: 16485562--16485607 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
16485552 TCTGTTTTGA
16485562 TTTTATTTT-TCTTA-TTTTATTTT
1 TTTTATTTTGT-TTATTTTTATTTT
16485585 TTTTATTTTGTTTATTTTTATTT
1 TTTTATTTTGTTTATTTTTATTT
16485608 ACTCTTGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.13, C:0.02, G:0.02, T:0.83
Consensus pattern (24 bp):
TTTTATTTTGTTTATTTTTATTTT
Found at i:16489733 original size:12 final size:12
Alignment explanation
Indices: 16489711--16489758 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
16489701 AAAAGGTGTG
16489711 CAAACAAAAAAAA
1 CAAA-AAAAAAAA
*
16489724 TAAAAAAAAAAA
1 CAAAAAAAAAAA
**
16489736 CAAAAAAAATTA
1 CAAAAAAAAAAA
16489748 CAAAAAAAAAA
1 CAAAAAAAAAA
16489759 GAGAGCAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
12 26 0.90
13 3 0.10
ACGTcount: A:0.85, C:0.08, G:0.00, T:0.06
Consensus pattern (12 bp):
CAAAAAAAAAAA
Found at i:16489738 original size:21 final size:23
Alignment explanation
Indices: 16489712--16489758 Score: 80
Period size: 21 Copynumber: 2.1 Consensus size: 23
16489702 AAAGGTGTGC
16489712 AAACAAAAAAAA-TA-AAAAAAA
1 AAACAAAAAAAATTACAAAAAAA
16489733 AAACAAAAAAAATTACAAAAAAA
1 AAACAAAAAAAATTACAAAAAAA
16489756 AAA
1 AAA
16489759 GAGAGCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 12 0.50
22 2 0.08
23 10 0.42
ACGTcount: A:0.87, C:0.06, G:0.00, T:0.06
Consensus pattern (23 bp):
AAACAAAAAAAATTACAAAAAAA
Found at i:16489793 original size:25 final size:25
Alignment explanation
Indices: 16489749--16489798 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
16489739 AAAAAATTAC
16489749 AAAAAAAAAAGAGAGCAAAAAAGAA
1 AAAAAAAAAAGAGAGCAAAAAAGAA
*
16489774 AAAATAAAAAAGA-AGGAAAAAAGAA
1 AAAA-AAAAAAGAGAGCAAAAAAGAA
16489799 GGCTTAGATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (25 bp):
AAAAAAAAAAGAGAGCAAAAAAGAA
Found at i:16491345 original size:17 final size:18
Alignment explanation
Indices: 16491304--16491347 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
16491294 GAATATTCTT
16491304 TTTGCAAATATGAAAGTC
1 TTTGCAAATATGAAAGTC
*
16491322 CTTGCAAACT-TGAAA-TC
1 TTTGCAAA-TATGAAAGTC
16491339 TTTGCAAAT
1 TTTGCAAAT
16491348 CTAGAACCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 1 0.04
17 9 0.39
18 12 0.52
19 1 0.04
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (18 bp):
TTTGCAAATATGAAAGTC
Found at i:16492413 original size:14 final size:14
Alignment explanation
Indices: 16492394--16492431 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
16492384 TTCTGTTTTG
16492394 ATTTTATTTT-TCTT
1 ATTTTATTTTGT-TT
16492408 ATTTTATTTTGTTT
1 ATTTTATTTTGTTT
16492422 ATTTTTATTT
1 A-TTTTATTT
16492432 ACTCTTGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.79
Consensus pattern (14 bp):
ATTTTATTTTGTTT
Found at i:16502646 original size:27 final size:27
Alignment explanation
Indices: 16502608--16502689 Score: 164
Period size: 27 Copynumber: 3.0 Consensus size: 27
16502598 CCCCTAACAT
16502608 TCTTATCACATAATACATATTACATTC
1 TCTTATCACATAATACATATTACATTC
16502635 TCTTATCACATAATACATATTACATTC
1 TCTTATCACATAATACATATTACATTC
16502662 TCTTATCACATAATACATATTACATTC
1 TCTTATCACATAATACATATTACATTC
16502689 T
1 T
16502690 GTGAACTAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (27 bp):
TCTTATCACATAATACATATTACATTC
Found at i:16505161 original size:2 final size:2
Alignment explanation
Indices: 16505154--16505181 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16505144 CTCATTGTGC
16505154 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
16505182 TGTAAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16505736 original size:12 final size:12
Alignment explanation
Indices: 16505715--16505752 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
16505705 AAATCTATTT
16505715 AAAT-ATATTAA
1 AAATAATATTAA
16505726 AAATAATATT-A
1 AAATAATATTAA
16505737 AAATAATATATAA
1 AAATAATAT-TAA
16505750 AAA
1 AAA
16505753 ATAAAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 14 0.58
12 6 0.25
13 4 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATAATATTAA
Found at i:16505739 original size:11 final size:11
Alignment explanation
Indices: 16505710--16505755 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
16505700 TACCTAAATC
*
16505710 TATTTAAAT-A
1 TATTAAAATAA
16505720 TATTAAAAATAA
1 TATT-AAAATAA
16505732 TATTAAAATAA
1 TATTAAAATAA
16505743 TATATAAAA-AA
1 TAT-TAAAATAA
16505754 TA
1 TA
16505756 AAATTTATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
10 4 0.12
11 18 0.56
12 10 0.31
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
TATTAAAATAA
Found at i:16507672 original size:57 final size:57
Alignment explanation
Indices: 16507552--16507712 Score: 209
Period size: 58 Copynumber: 2.8 Consensus size: 57
16507542 ACATGAGTTG
* * * *
16507552 AAATATTTCAAAAAATGTTCGAGAAAAAGTTGAAATATCAATTTTTCTTAAATAAAA
1 AAATATTTTAAAAAATGTTTGAGAAAAAGTTGAAGTATCAATTTTTCTAAAATAAAA
*
16507609 AAATATTTTAAGAAAATGTTTGAGAAAAAGTTGAAGTATTAATTTTTCTAAAAT-AAA
1 AAATATTTTAA-AAAATGTTTGAGAAAAAGTTGAAGTATCAATTTTTCTAAAATAAAA
** *
16507666 AAATA-TTTCCAAAATATTTGAGAAAAAAGTTGAGAGTATCAATTTTT
1 AAATATTTTAAAAAATGTTTGAG-AAAAAGTTGA-AGTATCAATTTTT
16507713 TCTTAGAATT
Statistics
Matches: 92, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
55 11 0.12
56 13 0.14
57 30 0.33
58 38 0.41
ACGTcount: A:0.48, C:0.05, G:0.11, T:0.35
Consensus pattern (57 bp):
AAATATTTTAAAAAATGTTTGAGAAAAAGTTGAAGTATCAATTTTTCTAAAATAAAA
Found at i:16510440 original size:112 final size:110
Alignment explanation
Indices: 16510272--16510590 Score: 308
Period size: 112 Copynumber: 2.9 Consensus size: 110
16510262 TGAAAAAGCA
** * * * *
16510272 TTTTTTAGGTAAAAATAATTTC-AAAAATTTTTTTAGAAAACGTTGAAGTATTAATTTTTTTTAA
1 TTTTTTAAATAAAAA-AA-TTCAAAAAATATTTTGAGAAAAAGTTGAAGTATTAATTTTTCTTAA
*** * *
16510336 AACAAATAATATTTCAAAAAATATTTTAAGGAAAAGTTGATGTATTAAT
64 AA-AAATAATATTTCAAAAAATA-TTTAAGGAAAAGAAAAAGTATAAAT
* *
16510385 TTTTTTAAATAAAAAAATTCAAAAAATATTTTGAGAAAAAGTTGAAGTATAAATTTTCCTTAAAT
1 TTTTTTAAATAAAAAAATTCAAAAAATATTTTGAGAAAAAGTTGAAGTATTAATTTTTCTTAAA-
* * *
16510450 AAAAT--TATTTCAAAAAATGTATAAGAAAAAGAAAAAGTATAAAT
65 AAAATAATATTTCAAAAAATATTTAAGGAAAAGAAAAAGTATAAAT
* * * * **
16510494 TTTCTTTAAAAAAAAAAATTCAAAAAAAATATTTGA-AGAAAAGTTGAATTATTAA-GTTTCCCA
1 TTT-TTTAAATAAAAAAATTCAAAAAATAT-TTTGAGA-AAAAGTTGAAGTATTAATTTTTCTTA
*
16510557 AAATAAAGAATATTTC-AAAAATATTTAAGGAAAA
63 AAA-AAATAATATTTCAAAAAATATTTAAGGAAAA
16510591 AGTCGAAAAA
Statistics
Matches: 170, Mismatches: 28, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
109 22 0.13
110 47 0.28
111 38 0.22
112 49 0.29
113 14 0.08
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (110 bp):
TTTTTTAAATAAAAAAATTCAAAAAATATTTTGAGAAAAAGTTGAAGTATTAATTTTTCTTAAAA
AAATAATATTTCAAAAAATATTTAAGGAAAAGAAAAAGTATAAAT
Found at i:16510448 original size:55 final size:55
Alignment explanation
Indices: 16510281--16510620 Score: 244
Period size: 55 Copynumber: 6.1 Consensus size: 55
16510271 ATTTTTTAGG
* * * **
16510281 TAAAAATAATTTC-AAAAATTTTTTTAGAAAACGTTGAAGTATTAATTTTTTTTAAA
1 TAAAAA-AA-TTCAAAAAATATTTTAAGAAAAAGTTGAAGTATTAATTTTCCTTAAA
* * *
16510337 -ACAAATAATATTTCAAAAAATATTTTAAGGAAAAGTTGATGTATTAATTTT-TTTAAA
1 TA-AAA-AA-A-TTCAAAAAATATTTTAAGAAAAAGTTGAAGTATTAATTTTCCTTAAA
* *
16510394 TAAAAAAATTCAAAAAATATTTTGAGAAAAAGTTGAAGTATAAATTTTCCTTAAA
1 TAAAAAAATTCAAAAAATATTTTAAGAAAAAGTTGAAGTATTAATTTTCCTTAAA
* * * * *** * *
16510449 TAAAATTATTTCAAAAAAT-GTATAAGAAAAAGAAAAAGTATAAATTTTCTTTAAA
1 TAAAA-AAATTCAAAAAATATTTTAAGAAAAAGTTGAAGTATTAATTTTCCTTAAA
* * * * **
16510504 AAAAAAAATTCAAAAAAAATATTTGAAG-AAAAGTTGAATTATTAAGTTTCCCAAAA
1 TAAAAAAATTC--AAAAAATATTTTAAGAAAAAGTTGAAGTATTAATTTTCCTTAAA
* * ** *
16510560 TAAAGAATATTTC-AAAAATA-TTTAAGGAAAAAGTCGAAAAAATCAATTTTCCTTAAA
1 TAAA-AA-AATTCAAAAAATATTTTAA-GAAAAAGTTG-AAGTATTAATTTTCCTTAAA
16510617 TAAA
1 TAAA
16510621 GCATTATTTT
Statistics
Matches: 225, Mismatches: 44, Indels: 29
0.76 0.15 0.10
Matches are distributed among these distances:
54 44 0.20
55 53 0.24
56 53 0.24
57 39 0.17
58 36 0.16
ACGTcount: A:0.52, C:0.05, G:0.08, T:0.34
Consensus pattern (55 bp):
TAAAAAAATTCAAAAAATATTTTAAGAAAAAGTTGAAGTATTAATTTTCCTTAAA
Found at i:16510578 original size:111 final size:110
Alignment explanation
Indices: 16510334--16510592 Score: 283
Period size: 111 Copynumber: 2.3 Consensus size: 110
16510324 AATTTTTTTT
* * *** * * *
16510334 AAAACAAATAATATTTCAAAAAATATTTTAAGG-AAAAGTTGATGTATTAATTTTTTTAAATAAA
1 AAAATAAA-AATATTTCAAAAAATA-TATAAGGAAAAAGAAAAAGTATAAATTTTTTTAAAAAAA
* * *
16510398 AAAATTCAAAAAATATTTTGAGAAAAAGTTGAAGTATAAATTTTCCT
64 AAAATTCAAAAAAAATTTTGAGAAAAAGTTGAAGTATAAAGTTTCCC
* * *
16510445 TAAATAAAATTATTTCAAAAAATGTATAA-GAAAAAGAAAAAGTATAAATTTTCTTTAAAAAAAA
1 AAAATAAAAATATTTCAAAAAATATATAAGGAAAAAGAAAAAGTATAAATTTT-TTTAAAAAAAA
* *
16510509 AAATTCAAAAAAAATATTTGA-AGAAAAGTTGAATTATTAAGTTTCCC
65 AAATTCAAAAAAAAT-TTTGAGA-AAAAGTTGAAGTATAAAGTTTCCC
*
16510556 AAAATAAAGAATATTTC-AAAAATATTTAAGGAAAAAG
1 AAAATAAA-AATATTTCAAAAAATATATAAGGAAAAAG
16510593 TCGAAAAAAT
Statistics
Matches: 122, Mismatches: 20, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
108 1 0.01
109 20 0.16
110 39 0.32
111 48 0.39
112 14 0.11
ACGTcount: A:0.54, C:0.05, G:0.09, T:0.32
Consensus pattern (110 bp):
AAAATAAAAATATTTCAAAAAATATATAAGGAAAAAGAAAAAGTATAAATTTTTTTAAAAAAAAA
AATTCAAAAAAAATTTTGAGAAAAAGTTGAAGTATAAAGTTTCCC
Found at i:16514201 original size:18 final size:18
Alignment explanation
Indices: 16514131--16514201 Score: 74
Period size: 18 Copynumber: 3.9 Consensus size: 18
16514121 ATTTGAGAAT
**
16514131 GATACATTTATGGTGGGG
1 GATACATTTATGGTGGAA
* *
16514149 GATACATTTGTGGTAGAA
1 GATACATTTATGGTGGAA
16514167 GATACA-TTA-GAGATGGAA
1 GATACATTTATG-G-TGGAA
16514185 GATACATTTATGGTGGA
1 GATACATTTATGGTGGA
16514202 TAATAACCAT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
16 1 0.02
17 3 0.07
18 34 0.79
19 4 0.09
20 1 0.02
ACGTcount: A:0.32, C:0.06, G:0.31, T:0.31
Consensus pattern (18 bp):
GATACATTTATGGTGGAA
Found at i:16516924 original size:19 final size:18
Alignment explanation
Indices: 16516902--16516941 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
16516892 TTCCACTCCA
16516902 TTTTC-TATTTTGATTTTAT
1 TTTTCTTATTTT-A-TTTAT
16516921 TTTTCTTATTTTATTTAT
1 TTTTCTTATTTTATTTAT
16516939 TTT
1 TTT
16516942 ATTTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
19 6 0.30
20 6 0.30
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.78
Consensus pattern (18 bp):
TTTTCTTATTTTATTTAT
Found at i:16516933 original size:14 final size:13
Alignment explanation
Indices: 16516909--16516957 Score: 55
Period size: 14 Copynumber: 3.7 Consensus size: 13
16516899 CCATTTTCTA
*
16516909 TTTTGATTTTATT
1 TTTTTATTTTATT
16516922 TTTCTTATTTTATT
1 TTT-TTATTTTATT
*
16516936 TATTTTATTTT-TA
1 T-TTTTATTTTATT
16516949 TTTTTATTT
1 TTTTTATTT
16516958 ACTCTTGCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 8 0.25
13 5 0.16
14 17 0.53
15 2 0.06
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (13 bp):
TTTTTATTTTATT
Found at i:16516934 original size:5 final size:5
Alignment explanation
Indices: 16516907--16516957 Score: 52
Period size: 5 Copynumber: 10.0 Consensus size: 5
16516897 CTCCATTTTC
*
16516907 TATTT TGATTT TATTT T-TCT TATTT TA-TT TATTT TATTTT TATTTT
1 TATTT T-ATTT TATTT TATTT TATTT TATTT TATTT TA-TTT TA-TTT
16516953 TATTT
1 TATTT
16516958 ACTCTTGCTA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
4 7 0.17
5 17 0.43
6 16 0.40
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (5 bp):
TATTT
Found at i:16517107 original size:46 final size:45
Alignment explanation
Indices: 16517057--16517144 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 45
16517047 CTTTTCAAAT
* *
16517057 AAATTCAT-GAATCTCACCAAACTATTGAAAAATTTTCATAAATTTA
1 AAATTCATGGAATC-CACCAAACCATTGAAAAA-TTCCATAAATTTA
*
16517103 AAATTTATGGAATCCACCAAACCATTGAAAAATTCCATAAAT
1 AAATTCATGGAATCCACCAAACCATTGAAAAATTCCATAAAT
16517145 AAATTTCAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
45 9 0.24
46 24 0.63
47 5 0.13
ACGTcount: A:0.47, C:0.17, G:0.06, T:0.31
Consensus pattern (45 bp):
AAATTCATGGAATCCACCAAACCATTGAAAAATTCCATAAATTTA
Found at i:16517907 original size:16 final size:15
Alignment explanation
Indices: 16517878--16517919 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
16517868 AATTTAAGAT
* *
16517878 TATTTTTTTCTTTCC
1 TATTTTTTTATTTTC
16517893 TATTTTTTTATTTTC
1 TATTTTTTTATTTTC
16517908 -ATTGTTTTTATT
1 TATT-TTTTTATT
16517920 CTATTTAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 3 0.12
15 21 0.88
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.76
Consensus pattern (15 bp):
TATTTTTTTATTTTC
Found at i:16520729 original size:20 final size:20
Alignment explanation
Indices: 16520706--16520744 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
16520696 AAAAAAAAAG
16520706 AAAAAGAA-AAGAAAATTGAA
1 AAAAAGAATAAG-AAATTGAA
*
16520726 AAAATGAATAAGAAATTGA
1 AAAAAGAATAAGAAATTGA
16520745 TGGGGTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (20 bp):
AAAAAGAATAAGAAATTGAA
Found at i:16523484 original size:56 final size:56
Alignment explanation
Indices: 16523336--16523593 Score: 228
Period size: 56 Copynumber: 4.6 Consensus size: 56
16523326 GATTATTTCG
* ** *
16523336 ACTTTTTCCTTAAATA-TTTTTGAAATATTCTTTATATTTGGA-AAAATTGATA-TTTCA
1 ACTTTTT-CTTAAACATTTTTTGAAATATT-TTT-TATTTAAAGAAAATTAATACTTT-A
* * *
16523393 AC-TTTTCTTCAAATATCTTTTTTGAAA-ATTTTTTTATTTAAAGAAAATTTATACTTTT
1 ACTTTTTCTT-AAACA--TTTTTTGAAATA-TTTTTTATTTAAAGAAAATTAATACTTTA
* * * *
16523451 ACTTTTTCTTATACATTTTTTGAAATATTTTTTATTTAAGGAAAATTGATACTTCA
1 ACTTTTTCTTAAACATTTTTTGAAATATTTTTTATTTAAAGAAAATTAATACTTTA
16523507 ACTTTTT-TTCAAAACATTTTTTG-AATA-TTTTTATTTAAA-AAAATTAATACTTTA
1 ACTTTTTCTT--AAACATTTTTTGAAATATTTTTTATTTAAAGAAAATTAATACTTTA
* * *
16523561 ACTTTTTCTCAAAAAATTTTTGAAATTATTTTT
1 ACTTTTTCTTAAACATTTTTTGAAA-TATTTTT
16523594 ACCTAAAAAA
Statistics
Matches: 169, Mismatches: 17, Indels: 31
0.78 0.08 0.14
Matches are distributed among these distances:
53 10 0.06
54 22 0.13
55 19 0.11
56 59 0.35
57 20 0.12
58 18 0.11
59 21 0.12
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.53
Consensus pattern (56 bp):
ACTTTTTCTTAAACATTTTTTGAAATATTTTTTATTTAAAGAAAATTAATACTTTA
Found at i:16524538 original size:56 final size:56
Alignment explanation
Indices: 16524441--16525120 Score: 545
Period size: 56 Copynumber: 11.7 Consensus size: 56
16524431 AATTAAATTC
* *
16524441 TAAGTAAAAATTGATACTCTTAACTTTTTTCTC-AAATATTTTGGAAATATTTTTTATT
1 TAAG-AAAAATTGATACT-TCAAC-TTTTTCTCAAAATATTTTTGAAATATTTTTTATT
** * * * *
16524499 TTGGGAAAATTAATACTTCAACTTTTTCTCAAACA-ATTTTTTAAAATGTTTTTTTATTT
1 TAAGAAAAATTGATACTTCAACTTTTTCTCAAA-ATA-TTTTTGAAAT-ATTTTTTA-TT
* **
16524558 TAA-AAAAATTGATATTTCAACTTTTTCTCTAGCAT-TTTTTGAAATATTTTTTAATT
1 TAAGAAAAATTGATACTTCAACTTTTTCTC-AAAATATTTTTGAAATATTTTTT-ATT
* * * * *
16524614 TAAGGAAAATTAATACTTCAACTTCTCCTCAAAACATTTTTTTG-AA-ATTTTTTATT
1 TAAGAAAAATTGATACTTCAACTTTTTCTC-AAA-ATATTTTTGAAATATTTTTTATT
** * * * * *
16524670 TAAGAAAAATTGATTTTTTAACTTTTCCTTAAAACATTTTTTTTGAAAT-TTTTTTGTT
1 TAAGAAAAATTGATACTTCAACTTTTTC-TCAAA-A-TATTTTTGAAATATTTTTTATT
* *
16524728 TAAAAAAAATTGATACTTCAACTTTTCCTCAAAATATTTTTTTGAAATATTTTTTTTATT
1 TAAGAAAAATTGATACTTCAACTTTTTCTCAAAATA--TTTTTGAAATA--TTTTTTATT
* * *
16524788 TAAGAAAAATTGATACTTCAACTTTTCCTCAAAATATTTTTTG-AATTTTTTTTGTT
1 TAAGAAAAATTGATACTTCAACTTTTTCTCAAAATA-TTTTTGAAATATTTTTTATT
* *
16524844 TAATAAAAATTGATACTTCAA-TTTCTCCTCAAAATATTTTTTTGAAATATTATTTTTTTATT
1 TAAGAAAAATTGATACTTCAACTTT-TTCTCAAAATA--TTTTTG-AA-A-TA-TTTTTTATT
* * * * *
16524906 TTAGGAAAATTGATATTTCAATTTTTTCTCAAAATAGATTTTGAAAT-TTTTTTATT
1 TAAGAAAAATTGATACTTCAACTTTTTCTCAAAATA-TTTTTGAAATATTTTTTATT
* * * *
16524962 TAAGAAAATTTGATATTTCATCTTTTTCTCAAAACATTTTTTTGAAATATTATTTGTTTATT
1 TAAGAAAAATTGATACTTCAACTTTTTCTC-AAA-ATATTTTTG-AA-A-TATTT-TTTATT
** * * * *
16525024 TAAGAAATTTTGATATTTCAAC-TTTTCTTCAAAACATTTTTAAAAAATTTTTTATT
1 TAAGAAAAATTGATACTTCAACTTTTTC-TCAAAATATTTTTGAAATATTTTTTATT
* * *
16525080 TAAGAAAAATTAATATTTCAACTTTTTCTCAAAATGTTTTT
1 TAAGAAAAATTGATACTTCAACTTTTTCTCAAAATATTTTT
16525121 TTAAATTATT
Statistics
Matches: 514, Mismatches: 71, Indels: 76
0.78 0.11 0.11
Matches are distributed among these distances:
55 12 0.02
56 158 0.31
57 106 0.21
58 80 0.16
59 22 0.04
60 53 0.10
61 17 0.03
62 63 0.12
63 3 0.01
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (56 bp):
TAAGAAAAATTGATACTTCAACTTTTTCTCAAAATATTTTTGAAATATTTTTTATT
Found at i:16524540 original size:115 final size:115
Alignment explanation
Indices: 16524421--16524656 Score: 250
Period size: 115 Copynumber: 2.0 Consensus size: 115
16524411 TTAACATTTA
16524421 TTTTTAAAA-AAATTAAATTCTAAGTAAAAATTGATACTCTT-AACTTTTT-TCTCA-AATATTT
1 TTTTTAAAAGAAATTAAATTCTAA--AAAAATTGATA-T-TTCAACTTTTTCTCT-AGAAT-TTT
** * *
16524482 TGGAAATATTTTTT-ATTTTGGGAAAATTAATACTTCAACTTTTTCTC-AAACAAT
60 TGGAAATATTTTTTAATTTAAGGAAAATTAATACTTCAACTTCTCCTCAAAACAAT
*** ** * * *
16524536 TTTTTAAAATGTTTTTTTATTTTAAAAAAATTGATATTTCAACTTTTTCTCTAGCATTTTTTGAA
1 TTTTTAAAA-GAAATTAAATTCTAAAAAAATTGATATTTCAACTTTTTCTCTAGAATTTTTGGAA
*
16524601 ATATTTTTTAATTTAAGGAAAATTAATACTTCAACTTCTCCTCAAAACATT
65 ATATTTTTTAATTTAAGGAAAATTAATACTTCAACTTCTCCTCAAAACAAT
16524652 TTTTT
1 TTTTT
16524657 GAAATTTTTT
Statistics
Matches: 101, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
113 2 0.02
114 26 0.26
115 54 0.53
116 11 0.11
117 8 0.08
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.48
Consensus pattern (115 bp):
TTTTTAAAAGAAATTAAATTCTAAAAAAATTGATATTTCAACTTTTTCTCTAGAATTTTTGGAAA
TATTTTTTAATTTAAGGAAAATTAATACTTCAACTTCTCCTCAAAACAAT
Found at i:16524777 original size:13 final size:13
Alignment explanation
Indices: 16524759--16524783 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16524749 CTTTTCCTCA
16524759 AAATATTTTTTTG
1 AAATATTTTTTTG
16524772 AAATATTTTTTT
1 AAATATTTTTTT
16524784 TATTTAAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
AAATATTTTTTTG
Found at i:16524852 original size:118 final size:116
Alignment explanation
Indices: 16524441--16525133 Score: 696
Period size: 118 Copynumber: 5.9 Consensus size: 116
16524431 AATTAAATTC
* * **
16524441 TAAGTAAAAATTGATACTCTT-AACTTTTTTCTC-AAATA-TTTTGGAAATATTTTTTATTTTGG
1 TAAG-AAAAATTGATA-T-TTCAAC-TTTTCCTCAAAATATTTTTTGAAAT-TTTTTTATTTAAG
* *
16524503 GAAAATTAATACTTCAACTTTTTCTCAAACA-A-TTTTTT-AAA-ATGTTTTTTTATTT
61 AAAAATTAATACTTCAACTTTTCCTCAAA-ATATTTTTTTGAAATAT-TTTTTTTA-TT
* * ** *
16524558 TAA-AAAAATTGATATTTCAACTTTTTCTC-TAGCATTTTTTGAAATATTTTTTAATTTAAGGAA
1 TAAGAAAAATTGATATTTCAACTTTTCCTCAAAATATTTTTTGAAAT-TTTTTT-ATTTAAGAAA
* *
16524621 AATTAATACTTCAACTTCTCCTCAAAACATTTTTTTG-AA-A--TTTTTTATT
64 AATTAATACTTCAACTTTTCCTCAAAATATTTTTTTGAAATATTTTTTTTATT
* * * * * *
16524670 TAAGAAAAATTGATTTTTTAACTTTTCCTTAAAACATTTTTTTTGAAATTTTTTTGTTTAAAAAA
1 TAAGAAAAATTGATATTTCAACTTTTCC-TCAAA-ATATTTTTTGAAATTTTTTTATTTAAGAAA
*
16524735 AATTGATACTTCAACTTTTCCTCAAAATATTTTTTTGAAATATTTTTTTTATT
64 AATTAATACTTCAACTTTTCCTCAAAATATTTTTTTGAAATATTTTTTTTATT
* * * *
16524788 TAAGAAAAATTGATACTTCAACTTTTCCTCAAAATATTTTTTGAATTTTTTTTGTTTAATAAAAA
1 TAAGAAAAATTGATATTTCAACTTTTCCTCAAAATATTTTTTGAAATTTTTTTATTTAAGAAAAA
*
16524853 TTGATACTTCAA-TTTCTCCTCAAAATATTTTTTTGAAATATTATTTTTTTATT
66 TTAATACTTCAACTTT-TCCTCAAAATATTTTTTTGAAATA-T-TTTTTTTATT
* * * * ** *
16524906 TTAGGAAAATTGATATTTCAATTTTTTCTCAAAATAGATTTTGAAATTTTTTTATTTAAGAAAAT
1 TAAGAAAAATTGATATTTCAACTTTTCCTCAAAATATTTTTTGAAATTTTTTTATTTAAGAAAAA
* * * * *
16524971 TTGATATTTCATCTTTTTCTCAAAACATTTTTTTGAAATATTATTTGTTTATT
66 TTAATACTTCAACTTTTCCTCAAAATATTTTTTTGAAATATT-TTT-TTTATT
** * * ** *
16525024 TAAGAAATTTTGATATTTCAACTTTTCTTCAAAACATTTTTAAAAAATTTTTTATTTAAGAAAAA
1 TAAGAAAAATTGATATTTCAACTTTTCCTCAAAATATTTTTTGAAATTTTTTTATTTAAGAAAAA
* * *
16525089 TTAATATTTCAACTTTTTCTCAAAATGTTTTTTT-AAATTATTTTT
66 TTAATACTTCAACTTTTCCTCAAAATATTTTTTTGAAA-TATTTTT
16525134 AGCTAAAAAG
Statistics
Matches: 493, Mismatches: 62, Indels: 42
0.83 0.10 0.07
Matches are distributed among these distances:
112 5 0.01
113 40 0.08
114 63 0.13
115 56 0.11
116 87 0.18
117 18 0.04
118 221 0.45
119 3 0.01
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (116 bp):
TAAGAAAAATTGATATTTCAACTTTTCCTCAAAATATTTTTTGAAATTTTTTTATTTAAGAAAAA
TTAATACTTCAACTTTTCCTCAAAATATTTTTTTGAAATATTTTTTTTATT
Found at i:16524856 original size:174 final size:172
Alignment explanation
Indices: 16524504--16525133 Score: 630
Period size: 174 Copynumber: 3.6 Consensus size: 172
16524494 TTATTTTGGG
* * * * * * *
16524504 AAAATTAATACTTCAACTTTTTC-TCAAACAATTTTTTAAAATGTTTTTTTATTTTAAAAAAATT
1 AAAATTGATATTTCAACTTTTCCTTAAAACATTTTTTTGAAA--TTTTTTTATTTAAAAAAAATT
* ** * * *
16524568 GATATTTCAACTTTTTCTC-TAGCATTTTTTGAAATATTTTTTAATTTAAGGAAAATTAATACTT
64 GATATTTCAACTTTTTCTCAAAATATTTTTTGAAATATTTTTTTATTTAAGAAAAATTGATACTT
* * *
16524632 CAACTTCTCCTCAAAACATTTTTTTGAA-ATTTTTTATTTAAGA
129 CAACTTTTCCTCAAAACATTTTTTTGAATATTTTTTGTTTAATA
* * *
16524675 AAAATTGATTTTTTAACTTTTCCTTAAAACATTTTTTTTGAAATTTTTTTGTTTAAAAAAAATTG
1 AAAATTGATATTTCAACTTTTCCTTAAAACA-TTTTTTTGAAATTTTTTTATTTAAAAAAAATTG
* *
16524740 ATACTTCAACTTTTCCTCAAAATATTTTTTTGAAATATTTTTTTTATTTAAGAAAAATTGATACT
65 ATATTTCAACTTTTTCTCAAAATA-TTTTTTGAAATA-TTTTTTTATTTAAGAAAAATTGATACT
* *
16524805 TCAACTTTTCCTCAAAATA-TTTTTTGAATTTTTTTTGTTTAATA
128 TCAACTTTTCCTCAAAACATTTTTTTGAATATTTTTTGTTTAATA
* * * * **
16524849 AAAATTGATACTTCAA-TTTCTCCTCAAAATATTTTTTTGAAATATTATTTTTTTATTTTAGGAA
1 AAAATTGATATTTCAACTTT-TCCTTAAAACATTTTTTTG--A-A--ATTTTTTTATTTAAAAAA
* ** *
16524913 AATTGATATTTCAATTTTTTCTCAAAATAGATTTTG-AA-ATTTTTTTATTTAAGAAAATTTGAT
60 AATTGATATTTCAACTTTTTCTCAAAATATTTTTTGAAATATTTTTTTATTTAAGAAAAATTGAT
* * * * *
16524976 ATTTCATCTTTTTCTCAAAACATTTTTTTGAAATATTATTTGTTTATTTA
125 ACTTCAACTTTTCCTCAAAACATTTTTTTG-AATATTTTTTGTTTA-ATA
** * *
16525026 AGAAATTTTGATATTTCAACTTTT-CTTCAAAACA-TTTTTAAAAAATTTTTTATTTAAGAAAAA
1 A-AAA--TTGATATTTCAACTTTTCCTT-AAAACATTTTTTTGAAATTTTTTTATTTAAAAAAAA
* * *
16525089 TTAATATTTCAACTTTTTCTCAAAATGTTTTTTTAAATTATTTTT
62 TTGATATTTCAACTTTTTCTCAAAATATTTTTTGAAA-TATTTTT
16525134 AGCTAAAAAG
Statistics
Matches: 377, Mismatches: 59, Indels: 40
0.79 0.12 0.08
Matches are distributed among these distances:
171 54 0.14
172 8 0.02
173 41 0.11
174 161 0.43
175 11 0.03
176 17 0.05
177 15 0.04
178 43 0.11
179 7 0.02
180 17 0.05
181 3 0.01
ACGTcount: A:0.35, C:0.09, G:0.05, T:0.51
Consensus pattern (172 bp):
AAAATTGATATTTCAACTTTTCCTTAAAACATTTTTTTGAAATTTTTTTATTTAAAAAAAATTGA
TATTTCAACTTTTTCTCAAAATATTTTTTGAAATATTTTTTTATTTAAGAAAAATTGATACTTCA
ACTTTTCCTCAAAACATTTTTTTGAATATTTTTTGTTTAATA
Found at i:16527866 original size:23 final size:23
Alignment explanation
Indices: 16527840--16527896 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
16527830 AACAAAATAT
*
16527840 ATTTAAATTAAATTATATTTTAA
1 ATTTAAATTAAATTATATTTGAA
**
16527863 ATTTATAATT-TTTTATATTTGAA
1 ATTTA-AATTAAATTATATTTGAA
16527886 A--TAAATTAAAT
1 ATTTAAATTAAAT
16527897 AAAGTAATCT
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
20 4 0.15
21 3 0.11
23 16 0.59
24 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
ATTTAAATTAAATTATATTTGAA
Found at i:16528377 original size:25 final size:26
Alignment explanation
Indices: 16528328--16528377 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
16528318 GTTCATTGAT
* *
16528328 TTTTAAATTTTATTTTTTATATATTA
1 TTTTAAATATTATTTTTAATATATTA
*
16528354 TTTT-AATATTATTTTTAATGTATT
1 TTTTAAATATTATTTTTAATATATT
16528378 TAAATAGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (26 bp):
TTTTAAATATTATTTTTAATATATTA
Found at i:16531426 original size:27 final size:27
Alignment explanation
Indices: 16531394--16531475 Score: 164
Period size: 27 Copynumber: 3.0 Consensus size: 27
16531384 TTTAGTTCAC
16531394 AGAATGTAATATGTATTATGTGATAAG
1 AGAATGTAATATGTATTATGTGATAAG
16531421 AGAATGTAATATGTATTATGTGATAAG
1 AGAATGTAATATGTATTATGTGATAAG
16531448 AGAATGTAATATGTATTATGTGATAAG
1 AGAATGTAATATGTATTATGTGATAAG
16531475 A
1 A
16531476 ATGTTAGGGG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (27 bp):
AGAATGTAATATGTATTATGTGATAAG
Found at i:16541632 original size:20 final size:21
Alignment explanation
Indices: 16541607--16541658 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
16541597 TTTTTCAATT
*
16541607 TAAAATAAGAAATAG-CAAGAG
1 TAAAATAAGAAATAGACAA-AA
16541628 T-AAATAA-AAATAGACAAAA
1 TAAAATAAGAAATAGACAAAA
16541647 TAAAATAAGAAA
1 TAAAATAAGAAA
16541659 AATAAAATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 8 0.30
20 15 0.56
21 4 0.15
ACGTcount: A:0.69, C:0.04, G:0.12, T:0.15
Consensus pattern (21 bp):
TAAAATAAGAAATAGACAAAA
Found at i:16541649 original size:15 final size:15
Alignment explanation
Indices: 16541629--16541665 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
16541619 TAGCAAGAGT
16541629 AAATAAAAAT-AGACA
1 AAATAAAAATAAGA-A
16541644 AAAT-AAAATAAGAA
1 AAATAAAAATAAGAA
16541658 AAATAAAA
1 AAATAAAA
16541666 TCAAAACAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.14
Consensus pattern (15 bp):
AAATAAAAATAAGAA
Found at i:16541653 original size:14 final size:14
Alignment explanation
Indices: 16541629--16541666 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
16541619 TAGCAAGAGT
16541629 AAATAAAA-ATAGACA
1 AAATAAAATA-AGA-A
16541644 AAATAAAATAAGAA
1 AAATAAAATAAGAA
16541658 AAATAAAAT
1 AAATAAAAT
16541667 CAAAACAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 10 0.45
15 11 0.50
16 1 0.05
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (14 bp):
AAATAAAATAAGAA
Found at i:16542250 original size:51 final size:50
Alignment explanation
Indices: 16542169--16542316 Score: 138
Period size: 51 Copynumber: 2.9 Consensus size: 50
16542159 TGATTGTATG
** * *
16542169 TTTTAATGAGAATTGATTCCGAAATCAAATCTCAAAAATCTCTC-C-TTAT
1 TTTTAATGAGAATTGATTATGGAATTAAATC-CAAAAATCTCTCACATTAT
* * *
16542218 CATTTTAATGTGAATTGATTATGGAATTAAATCCCGACAATCTCTGCACATTAT
1 --TTTTAATGAGAATTGATTATGGAATTAAAT-CCAAAAATCTCT-CACATTAT
* **
16542272 TTTTAGTGCCAATTGATTATGGAATTAAATCCTAAAAATCTCTCA
1 TTTTAATGAGAATTGATTATGGAATTAAATCC-AAAAATCTCTCA
16542317 ATTGCAATTG
Statistics
Matches: 80, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
51 38 0.47
52 37 0.46
53 1 0.01
54 4 0.05
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (50 bp):
TTTTAATGAGAATTGATTATGGAATTAAATCCAAAAATCTCTCACATTAT
Found at i:16543410 original size:115 final size:115
Alignment explanation
Indices: 16543200--16543432 Score: 252
Period size: 115 Copynumber: 2.0 Consensus size: 115
16543190 TTATACAACG
* **
16543200 AGTCAAAAAAATAATCTAGACTAAGCTAAGATCGAATGATCGGGATGATACCACGAGTCTAAAAA
1 AGTCAAAAAAATAATCTAGACTAAGCTAAGATCGAATGATCGAGACAATACCACGAGTCTAAAAA
* * * * * *
16543265 CAACCAAGATCGAGTTGAGGTTAAAGATGAATAACCGAGACGATGTCGCA
66 CAACCAAGATCGAATTAAGGTAAAAAATGAATAACCAAGACGATATCGCA
* * * * * *
16543315 AGTCAAAAAAATGATCTGGACTAAG-TCGAGATCGAATGATCGAGACAATGCCATGAGTCTGAAA
1 AGTCAAAAAAATAATCTAGACTAAGCT-AAGATCGAATGATCGAGACAATACCACGAGTCTAAAA
** * * * * *
16543379 ATGACTAGGATTGAATTAAGGTAAAAAATGAATGACCAAGATGATATCGCA
65 ACAACCAAGATCGAATTAAGGTAAAAAATGAATAACCAAGACGATATCGCA
16543430 AGT
1 AGT
16543433 TAGGAAAATA
Statistics
Matches: 95, Mismatches: 22, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
114 1 0.01
115 94 0.99
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.21
Consensus pattern (115 bp):
AGTCAAAAAAATAATCTAGACTAAGCTAAGATCGAATGATCGAGACAATACCACGAGTCTAAAAA
CAACCAAGATCGAATTAAGGTAAAAAATGAATAACCAAGACGATATCGCA
Found at i:16544338 original size:25 final size:27
Alignment explanation
Indices: 16544310--16544370 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 27
16544300 CGATCTAAGC
16544310 TTTCTTTTTTTC-CT-TTTTTTTATTT
1 TTTCTTTTTTTCTCTCTTTTTTTATTT
* *
16544335 TTTC-TTTTTGCTCTCTTTTTTTGTTT
1 TTTCTTTTTTTCTCTCTTTTTTTATTT
16544361 TTT-TTTTTTT
1 TTTCTTTTTTT
16544371 GACTTTTTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 6 0.20
25 6 0.20
26 18 0.60
ACGTcount: A:0.02, C:0.11, G:0.03, T:0.84
Consensus pattern (27 bp):
TTTCTTTTTTTCTCTCTTTTTTTATTT
Found at i:16552437 original size:27 final size:27
Alignment explanation
Indices: 16552406--16552461 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
16552396 ACCTCCAACA
16552406 CTCTTATCACATAATACATATTACATT
1 CTCTTATCACATAATACATATTACATT
16552433 CTCTTATCACATAATACATATTACATT
1 CTCTTATCACATAATACATATTACATT
16552460 CT
1 CT
16552462 GTGAACCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.36, C:0.23, G:0.00, T:0.41
Consensus pattern (27 bp):
CTCTTATCACATAATACATATTACATT
Found at i:16555355 original size:11 final size:12
Alignment explanation
Indices: 16555339--16555391 Score: 56
Period size: 11 Copynumber: 4.3 Consensus size: 12
16555329 AAATTTATTT
16555339 AAATAA-ATTAA
1 AAATAATATTAA
16555350 AAATAATATT-A
1 AAATAATATTAA
16555361 AAATAATATATAAA
1 AAATAATAT-T-AA
*
16555375 AAATAAAATTTAA
1 AAATAATA-TTAA
16555388 AAAT
1 AAAT
16555392 CAATGAACAG
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
11 16 0.44
12 4 0.11
13 6 0.17
14 9 0.25
15 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATAATATTAA
Found at i:16558672 original size:15 final size:15
Alignment explanation
Indices: 16558652--16558683 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
16558642 ACAAAATCTT
16558652 TAAGTTTTCGAAGAA
1 TAAGTTTTCGAAGAA
*
16558667 TAAGTTTTTGAAGAA
1 TAAGTTTTCGAAGAA
16558682 TA
1 TA
16558684 TTTGCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.19, T:0.38
Consensus pattern (15 bp):
TAAGTTTTCGAAGAA
Found at i:16560285 original size:55 final size:55
Alignment explanation
Indices: 16560051--16560616 Score: 460
Period size: 56 Copynumber: 9.9 Consensus size: 55
16560041 TTTTTTAGCT
* * * * *
16560051 AAAAATAATTTCAAAAACA-AATTTGAGAAAAACTTGAAATATCAATTTTTCTTAAACA
1 AAAAAAAATTTCAAAAA-ATATTTTGAGGAAAAGTTGAAGTATCAATTTTT-TT-AA-A
* * * * * *
16560109 AACAAATAATATTTTGAAAAAATGTTTTGAGAAAAAGATGAAATATCAAATTTTCTTAAA
1 AA-AAA-AA-A-TTTCAAAAAATATTTTGAGGAAAAGTTGAAGTATC-AATTTTTTTAAA
* ** *
16560169 TAAAAAAATTTCAAAATTTATTTTGAGGAAAAATTGAAGTATCAATTTTTATTAAA
1 AAAAAAAATTTCAAAAAATATTTTGAGGAAAAGTTGAAGTATCAATTTTT-TTAAA
* *
16560225 CAAAAAAACTTCAAAAAATATTTTGAGGAAAAGTTGAAGTATCAATTTTTTTAAA
1 AAAAAAAATTTCAAAAAATATTTTGAGGAAAAGTTGAAGTATCAATTTTTTTAAA
* * * *
16560280 CAAAAAAATTTCAAAAAATGTTTTAAGGAAAAGTTGAAATATCAATTTTTCTT-AA
1 AAAAAAAATTTCAAAAAATATTTTGAGGAAAAGTTGAAGTATCAATTTTT-TTAAA
* * * * * * *
16560335 ATAAAAATTTTCAAAAAAAACATGTTTTCAGGAGAAGTTGAAGTATTAATTTTCCTTAAA
1 AAAAAAAATTTC---AAAAA-ATATTTTGAGGAAAAGTTGAAGTATCAATTTT-TTTAAA
* *
16560395 TAAAAAAATATTTCAAAAAATATTTTAAGAAAAAGTTGAAGTATCAATTTTTCTTAAA
1 -AAAAAAA-ATTTCAAAAAATATTTTGAGGAAAAGTTGAAGTATCAATTTTT-TTAAA
** * * *
16560453 AAAAAAAATTTCAAAAAAT-GCTTGAGAAAAAGTTGAAATATCAATTTTCTTAAA
1 AAAAAAAATTTCAAAAAATATTTTGAGGAAAAGTTGAAGTATCAATTTTTTTAAA
* * * * * **
16560507 TAAAAAAATATTTTAAAAAAAATGTTTGA-GAAAAGTTGAAGTGTTAAGTTTCCTAAA
1 -AAAAAAA-ATTTCAAAAAATAT-TTTGAGGAAAAGTTGAAGTATCAATTTTTTTAAA
* *
16560564 ATAAAAAATATTTC-CAAAATA-TTTGAGAAAAAAGTTGAGAGTATCAATTTTTT
1 A-AAAAAA-ATTTCAAAAAATATTTTGAG-GAAAAGTTGA-AGTATCAATTTTTT
16560617 CTTAAATAAA
Statistics
Matches: 417, Mismatches: 66, Indels: 51
0.78 0.12 0.10
Matches are distributed among these distances:
54 10 0.02
55 100 0.24
56 116 0.28
57 50 0.12
58 45 0.11
59 41 0.10
60 5 0.01
61 10 0.02
62 34 0.08
63 6 0.01
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.34
Consensus pattern (55 bp):
AAAAAAAATTTCAAAAAATATTTTGAGGAAAAGTTGAAGTATCAATTTTTTTAAA
Found at i:16563329 original size:54 final size:56
Alignment explanation
Indices: 16563275--16563528 Score: 290
Period size: 55 Copynumber: 4.6 Consensus size: 56
16563265 AGGTAAAAAT
16563275 AATTTCAAAAAAT-TTTTGAGAAAAAGTTGAAGTATTAATTTT-TTTAAA-ACAAATA
1 AATTTCAAAAAATATTTTGAGAAAAAGTTGAAGTATTAATTTTCTTTAAATAC-AA-A
*
16563330 ATATTTCAAAAAATATTTTGAGGAAAAGTTGAAGTATTAATTTT-TTTAAATA-AAA
1 A-ATTTCAAAAAATATTTTGAGAAAAAGTTGAAGTATTAATTTTCTTTAAATACAAA
* * *
16563385 AAATTCAAAAAATGTTTTGAGAAAAAGTTGAAGTATCAATTTTCTTTAAATACAAA
1 AATTTCAAAAAATATTTTGAGAAAAAGTTGAAGTATTAATTTTCTTTAAATACAAA
* * ** * *
16563441 ATATTTC-AAAAA-ATTATAAGAAAAAGTAAAAGTATAAATTTTCTTTAAATAAAAAA
1 A-ATTTCAAAAAATATTTTGAGAAAAAGTTGAAGTATTAATTTTCTTTAAAT-ACAAA
*
16563497 AATTTCAAAAAAAATATTTGA-AGAAAAGTTGA
1 AATTTCAAAAAATAT-TTTGAGA-AAAAGTTGA
16563529 CTTATCAATT
Statistics
Matches: 171, Mismatches: 17, Indels: 19
0.83 0.08 0.09
Matches are distributed among these distances:
54 38 0.22
55 48 0.28
56 33 0.19
57 41 0.24
58 11 0.06
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.35
Consensus pattern (56 bp):
AATTTCAAAAAATATTTTGAGAAAAAGTTGAAGTATTAATTTTCTTTAAATACAAA
Found at i:16563351 original size:57 final size:56
Alignment explanation
Indices: 16563269--16563608 Score: 320
Period size: 57 Copynumber: 6.0 Consensus size: 56
16563259 TTTTTTAGGT
*
16563269 AAAAATAATTTCAAAAAAT-TTTTGAGAAAAAGTTGAAGTATTAATTTTTTTAAA-A
1 AAAAAT-ATTTCAAAAAATATTTTGAGAAAAAGTTGAAGTATCAATTTTTTTAAATA
* *
16563324 CAAATAATATTTCAAAAAATATTTTGAGGAAAAGTTGAAGTATTAATTTTTTTAAATA
1 -AAA-AATATTTCAAAAAATATTTTGAGAAAAAGTTGAAGTATCAATTTTTTTAAATA
*
16563382 AAAAA-A-TTCAAAAAATGTTTTGAGAAAAAGTTGAAGTATCAATTTTCTTTAAATA
1 AAAAATATTTCAAAAAATATTTTGAGAAAAAGTTGAAGTATCAATTTT-TTTAAATA
* * * ** *
16563437 CAAAATATTTC-AAAAA-ATTATAAGAAAAAGTAAAAGTATAAATTTTCTTTAAATA
1 AAAAATATTTCAAAAAATATTTTGAGAAAAAGTTGAAGTATCAATTTT-TTTAAATA
* * ** ***
16563492 AAAAAAATTTCAAAAAAAATATTTGA-AGAAAAGTTGACTTATCAATTTTCCCAAAATA
1 AAAAATATTTCAAAAAATAT-TTTGAGA-AAAAGTTGAAGTATCAATTTT-TTTAAATA
* * ** *
16563550 AAGAATATTTC-AAAAATA-TTTAAGGAAAAAGTCAAAATAATCAATTTTTCTTAAATA
1 AAAAATATTTCAAAAAATATTTTGA-GAAAAAGTTGAAGT-ATCAATTTTT-TTAAATA
16563607 AA
1 AA
16563609 GCATTATTTT
Statistics
Matches: 236, Mismatches: 34, Indels: 27
0.79 0.11 0.09
Matches are distributed among these distances:
54 37 0.16
55 59 0.25
56 36 0.15
57 69 0.29
58 35 0.15
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (56 bp):
AAAAATATTTCAAAAAATATTTTGAGAAAAAGTTGAAGTATCAATTTTTTTAAATA
Found at i:16563374 original size:55 final size:55
Alignment explanation
Indices: 16563268--16563570 Score: 285
Period size: 55 Copynumber: 5.4 Consensus size: 55
16563258 TTTTTTTAGG
*
16563268 TAAAAATAATTTCAAAAAAT-TTTTGAGAAAAAGTTGAAGTATTAATTTTTTTAAAA
1 TAAAAAT-ATTTCAAAAAATATTTTGAGAAAAAGTTGAAGTATCAA-TTTTTTAAAA
* * * *
16563324 CAAATAATATTTCAAAAAATATTTTGAGGAAAAGTTGAAGTATTAATTTTTTTAAA
1 TAAA-AATATTTCAAAAAATATTTTGAGAAAAAGTTGAAGTATCAATTTTTTAAAA
* * *
16563380 TAAAAA-AATTCAAAAAATGTTTTGAGAAAAAGTTGAAGTATCAATTTTCTTTAAA
1 TAAAAATATTTCAAAAAATATTTTGAGAAAAAGTTGAAGTATCAATTTT-TTAAAA
* * ** * *
16563435 TACAAAATATTTC-AAAAA-ATTATAAGAAAAAGTAAAAGTATAAATTTTCTTTAAA
1 TA-AAAATATTTCAAAAAATATTTTGAGAAAAAGTTGAAGTATCAATTTT-TTAAAA
* * ** **
16563490 TAAAAAAAATTTCAAAAAAAATATTTGA-AGAAAAGTTGACTTATCAATTTTCCCAAAA
1 T-AAAAATATTTCAAAAAATAT-TTTGAGA-AAAAGTTGAAGTATCAATTTT-TTAAAA
16563548 TAAAGAATATTTC-AAAAATATTT
1 TAAA-AATATTTCAAAAAATATTT
16563571 AAGGAAAAAG
Statistics
Matches: 208, Mismatches: 28, Indels: 22
0.81 0.11 0.09
Matches are distributed among these distances:
54 38 0.18
55 51 0.25
56 44 0.21
57 44 0.21
58 31 0.15
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.35
Consensus pattern (55 bp):
TAAAAATATTTCAAAAAATATTTTGAGAAAAAGTTGAAGTATCAATTTTTTAAAA
Found at i:16563419 original size:111 final size:109
Alignment explanation
Indices: 16563258--16563608 Score: 363
Period size: 111 Copynumber: 3.1 Consensus size: 109
16563248 TTGAAAAAGT
** *
16563258 TTTTTTTAGGTAAAAATAATTTCAAAAAATTTTTGAGAAAAAGTTGAAGTATTAATTTTTTTAAA
1 TTTTTTTAAATAAAAA-AATTTCAAAAAATTTTTGAGAAAAAGTTGAAGTATCAATTTTTTTAAA
* ** *
16563323 ACAAATAATATTTCAAAAAATATTTTGAGGAAAAGTTGAAGTATTAA
65 ACAAA-AATATTTC-AAAAATATTTTAAGGAAAAGTAAAAGTATAAA
16563370 TTTTTTTAAATAAAAAAA-TTCAAAAAATGTTTTGAGAAAAAGTTGAAGTATCAATTTTCTTTAA
1 TTTTTTTAAATAAAAAAATTTCAAAAAAT-TTTTGAGAAAAAGTTGAAGTATCAATTTT-TTTAA
* *
16563434 ATAC-AAAATATTTCAAAAA-ATTATAAGAAAAAGTAAAAGTATAAA
64 A-ACAAAAATATTTCAAAAATATTTTAAGGAAAAGTAAAAGTATAAA
* ** **
16563479 TTTTCTTTAAATAAAAAAAATTTCAAAAAAAATATTTGA-AGAAAAGTTGACTTATCAATTTTCC
1 TTTT-TTTAAAT-AAAAAAATTTC--AAAAAATTTTTGAGA-AAAAGTTGAAGTATCAATTTTTT
* * *
16563543 CAAAATAAAGAATATTTCAAAAATA-TTTAAGGAAAAAGTCAAAA-TAATCAA
61 TAAAACAAA-AATATTTCAAAAATATTTTAAGG-AAAAGT-AAAAGT-ATAAA
16563594 TTTTTCTTAAATAAA
1 TTTTT-TTAAATAAA
16563609 GCATTATTTT
Statistics
Matches: 204, Mismatches: 19, Indels: 30
0.81 0.08 0.12
Matches are distributed among these distances:
109 24 0.12
110 22 0.11
111 46 0.23
112 31 0.15
113 44 0.22
114 19 0.09
115 18 0.09
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (109 bp):
TTTTTTTAAATAAAAAAATTTCAAAAAATTTTTGAGAAAAAGTTGAAGTATCAATTTTTTTAAAA
CAAAAATATTTCAAAAATATTTTAAGGAAAAGTAAAAGTATAAA
Found at i:16564542 original size:17 final size:17
Alignment explanation
Indices: 16564520--16564560 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
16564510 CTAATTTTAA
* *
16564520 ATAAAACAAATAATATG
1 ATAAAAAAAACAATATG
16564537 ATAAAAAAAACAATATG
1 ATAAAAAAAACAATATG
16564554 A-AAAAAA
1 ATAAAAAA
16564561 TATGAAATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.17
Consensus pattern (17 bp):
ATAAAAAAAACAATATG
Found at i:16565722 original size:2 final size:2
Alignment explanation
Indices: 16565715--16565741 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16565705 CTTAATTTAT
16565715 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
16565742 TTGTTGGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16567211 original size:18 final size:18
Alignment explanation
Indices: 16567141--16567211 Score: 70
Period size: 18 Copynumber: 3.9 Consensus size: 18
16567131 ATTAGAGAAT
**
16567141 GATACATTTGTGGTGGGG
1 GATACATTTGTGGTGGAA
* *
16567159 GATACATTTGTGGTAGAT
1 GATACATTTGTGGTGGAA
* * *
16567177 GATACATTAGAGATGGAA
1 GATACATTTGTGGTGGAA
*
16567195 GATATATTTGTGGTGGA
1 GATACATTTGTGGTGGA
16567212 TAATAACCAT
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.28, C:0.04, G:0.34, T:0.34
Consensus pattern (18 bp):
GATACATTTGTGGTGGAA
Found at i:16567732 original size:16 final size:17
Alignment explanation
Indices: 16567702--16567733 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16567692 CATCATTATA
16567702 ATTCTTTTGTTCTATTC
1 ATTCTTTTGTTCTATTC
16567719 ATTCTTTT-TTCTATT
1 ATTCTTTTGTTCTATT
16567734 TGTTTGTACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.12, C:0.16, G:0.03, T:0.69
Consensus pattern (17 bp):
ATTCTTTTGTTCTATTC
Found at i:16569404 original size:52 final size:52
Alignment explanation
Indices: 16569347--16569495 Score: 176
Period size: 51 Copynumber: 2.9 Consensus size: 52
16569337 AACTGTAATT
** *
16569347 GAGAGATTTTTGGGATTTAATTCCAGAATCAATTGGCATTAAAAATTAT-GTG
1 GAGAGATTTTTGGGATTTAATTCCAGAATCAATTCACATTAAAAATGATAG-G
* *** *
16569399 GAGAGATTATCAAGATTTAATTCCATAATCAATTCACATT-AAAATGATAGG
1 GAGAGATTTTTGGGATTTAATTCCAGAATCAATTCACATTAAAAATGATAGG
* * *
16569450 GAGAGATTTTTGGGATTTGATTTCAGAATCAATTCTCATTAAAAAT
1 GAGAGATTTTTGGGATTTAATTCCAGAATCAATTCACATTAAAAAT
16569496 AAAATCAAAT
Statistics
Matches: 79, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
51 40 0.51
52 39 0.49
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (52 bp):
GAGAGATTTTTGGGATTTAATTCCAGAATCAATTCACATTAAAAATGATAGG
Found at i:16573702 original size:20 final size:20
Alignment explanation
Indices: 16573673--16573713 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
16573663 AAGCCTATTG
*
16573673 AAAATTTGAAAAAAAAATTA
1 AAAATATGAAAAAAAAATTA
* *
16573693 AAAATATGAAGAAGAAATTA
1 AAAATATGAAAAAAAAATTA
16573713 A
1 A
16573714 TGGGTCAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.22
Consensus pattern (20 bp):
AAAATATGAAAAAAAAATTA
Found at i:16574018 original size:14 final size:14
Alignment explanation
Indices: 16573993--16574030 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
16573983 AAAAAGGTGT
16573993 GCAAAC-AAAAAAA
1 GCAAACAAAAAAAA
16574006 GCAAACAAAAAAAA
1 GCAAACAAAAAAAA
16574020 GCAAA-AAAAAA
1 GCAAACAAAAAA
16574031 CCAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.79, C:0.13, G:0.08, T:0.00
Consensus pattern (14 bp):
GCAAACAAAAAAAA
Found at i:16574038 original size:13 final size:13
Alignment explanation
Indices: 16573993--16574072 Score: 60
Period size: 14 Copynumber: 6.0 Consensus size: 13
16573983 AAAAAGGTGT
*
16573993 GCAAACAAAAAAA
1 GCAAAAAAAAAAA
16574006 GCAAACAAAAAAAA
1 GCAAA-AAAAAAAA
16574020 GC--AAAAAAAAA
1 GCAAAAAAAAAAA
*
16574031 CCAAAAAAAATTACAA
1 GCAAAAAAAA--A-AA
16574047 --AAAAAAGAAAAA
1 GCAAAAAA-AAAAA
16574059 GCAAAAAATAAAAA
1 GCAAAAAA-AAAAA
16574073 ATAAAAAGAG
Statistics
Matches: 55, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
11 9 0.16
12 3 0.05
13 12 0.22
14 26 0.47
15 3 0.05
16 2 0.04
ACGTcount: A:0.79, C:0.11, G:0.06, T:0.04
Consensus pattern (13 bp):
GCAAAAAAAAAAA
Found at i:16574092 original size:26 final size:26
Alignment explanation
Indices: 16574001--16574081 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 26
16573991 GTGCAAACAA
**
16574001 AAAAAGCAAACAAA-AAAAAGCAAAA-
1 AAAAAGCAAA-AAATAAAAAAAAAAAG
*
16574026 AAAAACCAAAAAA-AATTACAAAAAAAAG
1 AAAAAGCAAAAAATAA--A-AAAAAAAAG
16574054 AAAAAGCAAAAAATAAAAAATAAAAAG
1 AAAAAGCAAAAAATAAAAAA-AAAAAG
16574081 A
1 A
16574082 GAAGGAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
24 5 0.11
25 9 0.20
26 4 0.09
27 14 0.30
28 12 0.26
29 2 0.04
ACGTcount: A:0.80, C:0.09, G:0.06, T:0.05
Consensus pattern (26 bp):
AAAAAGCAAAAAATAAAAAAAAAAAG
Found at i:16575636 original size:17 final size:18
Alignment explanation
Indices: 16575595--16575637 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
16575585 AATCCTTTTT
* *
16575595 TTTGCAAATCTGAAAGTC
1 TTTGCAAACCTGAAAATC
*
16575613 CTTGCAAACCT-AAAATC
1 TTTGCAAACCTGAAAATC
16575630 TTTGCAAA
1 TTTGCAAA
16575638 TATAGAACAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (18 bp):
TTTGCAAACCTGAAAATC
Found at i:16575715 original size:86 final size:85
Alignment explanation
Indices: 16575568--16575724 Score: 210
Period size: 86 Copynumber: 1.8 Consensus size: 85
16575558 AACCTTTAAA
* * *
16575568 AAACTTGAAATCTTGTGAATCCTTTTTTTTGCAAATCTGAAAGTCCTTGCAAACCTAAAATCTTT
1 AAACTTGAAATCTTGCGAATCCTTTTTCTTGCAAATCTGAAAGACCTTGCAAACCTAAAATCTTT
16575633 GCAAATATAGAACATTTTTG
66 GCAAATATAGAACATTTTTG
* ** *
16575653 AAACTTGAAATCTTGCGAAT-CTTTCATTCTTGCGAATCTGAAA-ACCTTTGCAAATTTTAAATC
1 AAACTTGAAATCTTGCGAATCCTTT--TTCTTGCAAATCTGAAAGACC-TTGCAAACCTAAAATC
16575716 TTTGCAAAT
63 TTTGCAAAT
16575725 TTATTAAACT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
84 4 0.06
85 21 0.34
86 37 0.60
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (85 bp):
AAACTTGAAATCTTGCGAATCCTTTTTCTTGCAAATCTGAAAGACCTTGCAAACCTAAAATCTTT
GCAAATATAGAACATTTTTG
Found at i:16576745 original size:14 final size:14
Alignment explanation
Indices: 16576726--16576763 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
16576716 TTCTGTTTTC
16576726 ATTTTATTTT-TCTT
1 ATTTTATTTTGT-TT
16576740 ATTTTATTTTGTTT
1 ATTTTATTTTGTTT
16576754 ATTTTTATTT
1 A-TTTTATTT
16576764 ACTCTTGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.79
Consensus pattern (14 bp):
ATTTTATTTTGTTT
Found at i:16586788 original size:27 final size:27
Alignment explanation
Indices: 16586757--16586812 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
16586747 ACCCCTAACG
16586757 CTCTTATCACATAATACATATTACATT
1 CTCTTATCACATAATACATATTACATT
*
16586784 CTCTTATCACATAATGCATATTACATT
1 CTCTTATCACATAATACATATTACATT
16586811 CT
1 CT
16586813 GTGAACCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (27 bp):
CTCTTATCACATAATACATATTACATT
Found at i:16587355 original size:47 final size:49
Alignment explanation
Indices: 16587277--16587369 Score: 154
Period size: 48 Copynumber: 1.9 Consensus size: 49
16587267 TGTTATATAG
16587277 ATCAAGTGTACAAATTTTGAAAACAAATATTAATAAA-ATTGATATATT
1 ATCAAGTGTACAAATTTTGAAAACAAATATTAATAAATATTGATATATT
* *
16587325 ATCAAGTGTGCAAATTTTGAAAA-AAATATTAATAAATATTTATAT
1 ATCAAGTGTACAAATTTTGAAAACAAATATTAATAAATATTGATAT
16587370 TTTTTTATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
47 13 0.31
48 29 0.69
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (49 bp):
ATCAAGTGTACAAATTTTGAAAACAAATATTAATAAATATTGATATATT
Found at i:16591838 original size:58 final size:56
Alignment explanation
Indices: 16591720--16591846 Score: 148
Period size: 61 Copynumber: 2.2 Consensus size: 56
16591710 ACATGAGTTG
*
16591720 AAAT-ATTTCAAAAAATGCATGAGAAAAAGTTGAAATATCAATTTTTCTTAAATAAAA
1 AAATAATTTAAAAAAATGCATGAGAAAAAGTTGAAATATCAATTTTTCTTAAAT--AA
** *
16591777 AAATAATTTAAAAAAATGTTTGAGAAAAAAGTTGAGAGTATCAATTTTTTCTTAAATAA
1 AAATAATTTAAAAAAATGCATGAG-AAAAAGTTGA-AATATCAA-TTTTTCTTAAATAA
16591836 AATATTAATTT
1 AA-A-TAATTT
16591847 TTTTCTAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
57 4 0.07
58 16 0.27
59 14 0.23
60 8 0.13
61 18 0.30
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.35
Consensus pattern (56 bp):
AAATAATTTAAAAAAATGCATGAGAAAAAGTTGAAATATCAATTTTTCTTAAATAA
Found at i:16594671 original size:56 final size:56
Alignment explanation
Indices: 16594476--16594812 Score: 244
Period size: 54 Copynumber: 6.0 Consensus size: 56
16594466 TTTTTTAGCT
* * * * *
16594476 AAAAATAATTTCAAAAACTTTTTTAGAAAAAGTTGAAGTATTAA--TTT-TAAAACA
1 AAAAAT-ATTTCAAAAAATGTTTAAGAAAAAGTTGAAGTATTAATTTTTCTTAAATA
* * * *
16594530 AATAATATTTCAAAAAATATTTTGAGGAAAAGTTGAAGTATTAATTTTT-TTAAAT-
1 AAAAATATTTCAAAAAAT-GTTTAAGAAAAAGTTGAAGTATTAATTTTTCTTAAATA
* * * *
16594585 AAAAA-ACTTCCAAAAATGTTTTGAGAAAAAGTTGAAGTATCAATTTTTCTTAAATA
1 AAAAATATTTCAAAAAATG-TTTAAGAAAAAGTTGAAGTATTAATTTTTCTTAAATA
* *** * *
16594641 AAAAATATTTCAAAAAATGTATAAGAAAAAGAAAAAGTA-TAAATTTTCTTTAAACA
1 AAAAATATTTCAAAAAATGTTTAAGAAAAAGTTGAAGTATTAATTTTTC-TTAAATA
* ** * *
16594697 AAAAAAATTTCAAAAAAAAATTTGAAG-AAAAGTTGAATTATTAA-TTTTCTCAAAATA
1 AAAAATATTTC-AAAAAATGTTT-AAGAAAAAGTTGAAGTATTAATTTTTCT-TAAATA
* * * ** * *
16594754 AAGAATATTTC-AAAAATATTTAAGGAAAAAGTGGAAAAAATCAATTTTCCTTAAATA
1 AAAAATATTTCAAAAAATGTTTAA-GAAAAAGTTG-AAGTATTAATTTTTCTTAAATA
16594811 AA
1 AA
16594813 GCATTATTTT
Statistics
Matches: 226, Mismatches: 41, Indels: 29
0.76 0.14 0.10
Matches are distributed among these distances:
53 11 0.05
54 67 0.30
55 27 0.12
56 51 0.23
57 59 0.26
58 11 0.05
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (56 bp):
AAAAATATTTCAAAAAATGTTTAAGAAAAAGTTGAAGTATTAATTTTTCTTAAATA
Found at i:16594688 original size:55 final size:55
Alignment explanation
Indices: 16594565--16594713 Score: 149
Period size: 56 Copynumber: 2.7 Consensus size: 55
16594555 GGAAAAGTTG
* * * * * * ***
16594565 AAGTATTAATTTTTTTAAAT-AAAAAACTTCCAAAAATGTTTTGAGAAAAAGTTG
1 AAGTATAAATTTTCTTAAATAAAAAAATTTCAAAAAATGTTATAAGAAAAAGAAA
*
16594619 AAGTATCAATTTTTCTTAAATAAAAAATATTTCAAAAAATG-TATAAGAAAAAGAAA
1 AAGTAT-AAATTTTCTTAAATAAAAAA-ATTTCAAAAAATGTTATAAGAAAAAGAAA
*
16594675 AAGTATAAATTTTCTTTAAACAAAAAAAATTTCAAAAAA
1 AAGTATAAATTTTC-TTAAA-TAAAAAAATTTCAAAAAA
16594714 AAATTTGAAG
Statistics
Matches: 78, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
54 6 0.08
55 18 0.23
56 37 0.47
57 17 0.22
ACGTcount: A:0.54, C:0.06, G:0.07, T:0.33
Consensus pattern (55 bp):
AAGTATAAATTTTCTTAAATAAAAAAATTTCAAAAAATGTTATAAGAAAAAGAAA
Found at i:16594782 original size:113 final size:109
Alignment explanation
Indices: 16594500--16594784 Score: 285
Period size: 113 Copynumber: 2.6 Consensus size: 109
16594490 AAACTTTTTT
* * *
16594500 AGAAAAAGTTGAAGTATTAA-TTTT-AAAACAAATAATATTTCAAAAAATATTTTGAGG-AAAAG
1 AGAAAAAGTTGAAGTATTAATTTTTCAAAATAAAAAATATTTC-AAAAATA-TTTAAGGAAAAAG
*** * * * ***
16594562 TTGAAGTATTAATTTTTTTAAATAAAAAACTTCCAAAAATGTTTTG
64 AAAAAGTATAAATTTTTTTAAAAAAAAAACTTCAAAAAAAAATTTG
* *
16594608 AGAAAAAGTTGAAGTATCAATTTTTCTTAAATAAAAAATATTTCAAAAA-ATGTATAA-GAAAAA
1 AGAAAAAGTTGAAGTATTAATTTTTC-AAAATAAAAAATATTTCAAAAATAT-T-TAAGGAAAAA
*
16594671 GAAAAAGTATAAATTTTCTTTAAACAAAAAAAATTTCAAAAAAAAATTTG
63 GAAAAAGTATAAATTTT-TTT-AA-AAAAAAAACTTCAAAAAAAAATTTG
* *
16594721 A-AGAAAAGTTGAATTATTAATTTTCTCAAAATAAAGAATATTTCAAAAATATTTAAGGAAAAAG
1 AGA-AAAAGTTGAAGTATTAATTTT-TCAAAATAAAAAATATTTCAAAAATATTTAAGGAAAAAG
16594785 TGGAAAAAAT
Statistics
Matches: 145, Mismatches: 19, Indels: 21
0.78 0.10 0.11
Matches are distributed among these distances:
108 20 0.14
109 7 0.05
110 24 0.17
111 17 0.12
112 6 0.04
113 67 0.46
114 4 0.03
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.33
Consensus pattern (109 bp):
AGAAAAAGTTGAAGTATTAATTTTTCAAAATAAAAAATATTTCAAAAATATTTAAGGAAAAAGAA
AAAGTATAAATTTTTTTAAAAAAAAAACTTCAAAAAAAAATTTG
Found at i:16594813 original size:57 final size:54
Alignment explanation
Indices: 16594623--16594812 Score: 138
Period size: 57 Copynumber: 3.4 Consensus size: 54
16594613 AAGTTGAAGT
*
16594623 ATCAATTTTTCTTAAATAAAAAATATTTCAAAAAATGTATAAGAAAAA--GAAAAA
1 ATCAATTTTCCTTAAATAAAAAATATTTCAAAAAAT-T-TAAGAAAAAGTGAAAAA
* * * * **
16594677 GTATAAATTTTCTTTAAACAAAAAAAATTTCAAAAAAAAATTTGAAG-AAAAGTTG-AATT
1 --ATCAATTTTCCTTAAATAAAAAATATTTC---AAAAAATTT-AAGAAAAAG-TGAAAAA
* * *
16594736 ATTAATTTT-CTCAAAATAAAGAATATTTCAAAAATATTTAAGGAAAAAGTGGAAAAA
1 ATCAATTTTCCT-TAAATAAAAAATATTTCAAAAA-ATTTAA-GAAAAAGT-GAAAAA
16594793 ATCAATTTTCCTTAAATAAA
1 ATCAATTTTCCTTAAATAAA
16594813 GCATTATTTT
Statistics
Matches: 103, Mismatches: 17, Indels: 27
0.70 0.12 0.18
Matches are distributed among these distances:
54 7 0.07
55 6 0.06
56 31 0.30
57 43 0.42
58 6 0.06
59 9 0.09
60 1 0.01
ACGTcount: A:0.55, C:0.06, G:0.07, T:0.32
Consensus pattern (54 bp):
ATCAATTTTCCTTAAATAAAAAATATTTCAAAAAATTTAAGAAAAAGTGAAAAA
Found at i:16595724 original size:17 final size:17
Alignment explanation
Indices: 16595702--16595742 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
16595692 ATAATTTTAA
* *
16595702 ATAAAACAAATAATATG
1 ATAAAAAAAACAATATG
16595719 ATAAAAAAAACAATATG
1 ATAAAAAAAACAATATG
16595736 A-AAAAAA
1 ATAAAAAA
16595743 TATGAAATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.17
Consensus pattern (17 bp):
ATAAAAAAAACAATATG
Found at i:16596905 original size:2 final size:2
Alignment explanation
Indices: 16596898--16596930 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
16596888 CTTAATTTAT
16596898 TA TA 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 TA TA T
16596931 TTCTTGGCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16598354 original size:18 final size:18
Alignment explanation
Indices: 16598331--16598401 Score: 79
Period size: 18 Copynumber: 3.9 Consensus size: 18
16598321 ATTAGAGAAT
**
16598331 GATACATTTGTGGTGGGG
1 GATACATTTGTGGTGGAA
* *
16598349 GATACATTTGTGGTAGAT
1 GATACATTTGTGGTGGAA
* * *
16598367 GATACATTAGAGATGGAA
1 GATACATTTGTGGTGGAA
16598385 GATACATTTGTGGTGGA
1 GATACATTTGTGGTGGA
16598402 TAATAACCAT
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.28, C:0.06, G:0.34, T:0.32
Consensus pattern (18 bp):
GATACATTTGTGGTGGAA
Found at i:16598920 original size:16 final size:17
Alignment explanation
Indices: 16598890--16598921 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16598880 CATAATTATA
16598890 ATTCTTTTGTTCTATTC
1 ATTCTTTTGTTCTATTC
16598907 ATTCTTTT-TTCTATT
1 ATTCTTTTGTTCTATT
16598922 TCTTTGTGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.12, C:0.16, G:0.03, T:0.69
Consensus pattern (17 bp):
ATTCTTTTGTTCTATTC
Found at i:16600655 original size:52 final size:52
Alignment explanation
Indices: 16600548--16600658 Score: 127
Period size: 52 Copynumber: 2.1 Consensus size: 52
16600538 AGATTTTTGT
* * ** * *
16600548 GATTAAATTCCATAATCAATTGGCATTAAAAATGATGTGGAAAAATTATCAA
1 GATTTAATTCCATAATCAATTCGCATTAAAAATGAAATGCAAAAATAATCAA
*
16600600 GATTTAATTCCATAATCAATTCTCATTAAAAATGAAAT-CAAATAA-AATCATA
1 GATTTAATTCCATAATCAATTCGCATTAAAAATGAAATGCAAA-AATAATCA-A
16600652 GATTTAA
1 GATTTAA
16600659 GGGGAATTGA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
51 7 0.14
52 43 0.86
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.32
Consensus pattern (52 bp):
GATTTAATTCCATAATCAATTCGCATTAAAAATGAAATGCAAAAATAATCAA
Found at i:16601146 original size:9 final size:9
Alignment explanation
Indices: 16601131--16601174 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
16601121 CTGTTTTGAT
16601131 TTTATTTT-
1 TTTATTTTA
16601139 TCTTATTTTA
1 T-TTATTTTA
16601149 TTTATTTTA
1 TTTATTTTA
*
16601158 TTTATTTATT
1 TTTATTT-TA
16601168 TTTATTT
1 TTTATTT
16601175 ACTCTTGCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
8 1 0.03
9 22 0.69
10 9 0.28
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTATTTTA
Found at i:16601148 original size:14 final size:14
Alignment explanation
Indices: 16601124--16601174 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
16601114 CCATTTTCTG
16601124 TTTTGATTTTATTT-
1 TTTT-ATTTTATTTA
16601138 TTCTTATTTTATTTA
1 TT-TTATTTTATTTA
16601153 TTTTA-TTTATTTA
1 TTTTATTTTATTTA
16601166 TTTTTATTT
1 -TTTTATTT
16601175 ACTCTTGCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
13 8 0.24
14 19 0.58
15 6 0.18
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (14 bp):
TTTTATTTTATTTA
Found at i:16602135 original size:15 final size:14
Alignment explanation
Indices: 16602115--16602154 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
16602105 TTGAGATTAT
*
16602115 TTTTTTTCTTTTCGA
1 TTTTTTTATTTTC-A
16602130 TTTTTTTATTTTCA
1 TTTTTTTATTTTCA
16602144 TTGTTTTTATT
1 TT-TTTTTATT
16602155 ATGTTTAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 3 0.13
15 20 0.87
ACGTcount: A:0.10, C:0.07, G:0.05, T:0.78
Consensus pattern (14 bp):
TTTTTTTATTTTCA
Found at i:16605332 original size:22 final size:23
Alignment explanation
Indices: 16605285--16605335 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
16605275 GGTGTGCAAA
*
16605285 AAAAAAGCAAACAAAAAAAGGCC
1 AAAAAAGCAAACAAAAAAAGGAC
**
16605308 AAAAAAG-AAACAAAAAAATTAC
1 AAAAAAGCAAACAAAAAAAGGAC
16605330 AAAAAA
1 AAAAAA
16605336 AAAGAGAGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.76, C:0.12, G:0.08, T:0.04
Consensus pattern (23 bp):
AAAAAAGCAAACAAAAAAAGGAC
Found at i:16607441 original size:52 final size:51
Alignment explanation
Indices: 16607382--16607528 Score: 154
Period size: 51 Copynumber: 2.9 Consensus size: 51
16607372 AATCGTAATT
**
16607382 GAGAGATTTTTAGGATTTAATTCCATAATCAATTGGCATTAAAAATAAT-GTG
1 GAGAGATTTTTAGGATTTAATTCCATAATCAATTCACATT-AAAATAATAG-G
* * ** *
16607434 GATAGATTGTCGGGATTTAATTCCATAATCAATTCACATTAAAATGATAGG
1 GAGAGATTTTTAGGATTTAATTCCATAATCAATTCACATTAAAATAATAGG
* ** *
16607485 GAGAGATTTTTTA-GATTTAATTTCGGAATCAATTCTCATTAAAA
1 GAGAGA-TTTTTAGGATTTAATTCCATAATCAATTCACATTAAAA
16607529 CAGAAATCAA
Statistics
Matches: 78, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
51 40 0.51
52 38 0.49
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (51 bp):
GAGAGATTTTTAGGATTTAATTCCATAATCAATTCACATTAAAATAATAGG
Found at i:16608047 original size:20 final size:19
Alignment explanation
Indices: 16608019--16608068 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
16608009 TTCCATTCCA
16608019 TTTTC-TATTTTGATTTTAT
1 TTTTCTTATTTT-ATTTTAT
*
16608038 TTTTCTTATTTTATTTTGT
1 TTTTCTTATTTTATTTTAT
*
16608057 TTATTTTTATTT
1 TT-TTCTTATTT
16608069 ACTCTTGCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.14, C:0.04, G:0.04, T:0.78
Consensus pattern (19 bp):
TTTTCTTATTTTATTTTAT
Found at i:16608050 original size:14 final size:14
Alignment explanation
Indices: 16608031--16608068 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
16608021 TTCTATTTTG
16608031 ATTTTATTTT-TCTT
1 ATTTTATTTTGT-TT
16608045 ATTTTATTTTGTTT
1 ATTTTATTTTGTTT
16608059 ATTTTTATTT
1 A-TTTTATTT
16608069 ACTCTTGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.79
Consensus pattern (14 bp):
ATTTTATTTTGTTT
Found at i:16621710 original size:23 final size:23
Alignment explanation
Indices: 16621655--16621711 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
16621645 AGATTACTTT
*
16621655 ATTTAATTT--ATTTCAAATATA
1 ATTTAATTTAAATTTAAAATATA
* *
16621676 AA-AAATTATAAATTTAAAATATA
1 ATTTAATT-TAAATTTAAAATATA
16621699 ATTTAATTTAAAT
1 ATTTAATTTAAAT
16621712 ATATTTGTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
20 4 0.15
21 2 0.07
23 17 0.63
24 4 0.15
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAATTTAAATTTAAAATATA
Found at i:16625635 original size:15 final size:15
Alignment explanation
Indices: 16625615--16625646 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
16625605 ACAAAATCTT
16625615 TAAGTTTTCGAAGAA
1 TAAGTTTTCGAAGAA
*
16625630 TAAGTTTTTGAAGAA
1 TAAGTTTTCGAAGAA
16625645 TA
1 TA
16625647 TTTGCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.19, T:0.38
Consensus pattern (15 bp):
TAAGTTTTCGAAGAA
Found at i:16627173 original size:56 final size:56
Alignment explanation
Indices: 16627033--16627650 Score: 506
Period size: 56 Copynumber: 10.7 Consensus size: 56
16627023 TTTTAAAAAA
* *
16627033 TTTGA-GAAAAAGTAGAAATATCAATTTTTCTTAAATAAACAAATAATATTTCGAAAAAATGT
1 TTTGAGGAAAAA-TTGAAATATCAATTTTTCTTAAAT--A-AAA-AA-ATTTC-AAAAAATAT
* * * **
16627095 TTTGA-GAAAAAGATGAAATATCAAATTTTCTTAAATAAAAAAGTTTCAAAATTTAT
1 TTTGAGGAAAAA-TTGAAATATCAATTTTTCTTAAATAAAAAAATTTCAAAAAATAT
* * *
16627151 TTTGAGGAAAAATTGAAGTATCAATTTTCCTAAAATAAAAAAATAATATTTCAAAAAAATAT
1 TTTGAGGAAAAATTGAAATATCAATTTTTCTTAAAT---AAAA-AA-ATTTC-AAAAAATAT
* * * * **
16627213 TTTGAGGAAAAATTGAAGTGTCAATTTTTATTAAACAAAAAAAAATCAAAAAATAT
1 TTTGAGGAAAAATTGAAATATCAATTTTTCTTAAATAAAAAAATTTCAAAAAATAT
* * * *
16627269 TTTGAGGAAAAGTT-AAAGTATCAATTTTTTTTAAACAAAAAAATTTCAAAAAATGT
1 TTTGAGGAAAAATTGAAA-TATCAATTTTTCTTAAATAAAAAAATTTCAAAAAATAT
* * *
16627325 TTTAAGGAAAAGTTGAAATATCAATTTTTCTTAAAT-AAAAAATTTCAAAAAAATGT
1 TTTGAGGAAAAATTGAAATATCAATTTTTCTTAAATAAAAAAATTTC-AAAAAATAT
* * * *
16627381 TTTGAGGAGAAATTGAAGTATTAATATTTCTTAAATAAAAAAATATTTCAAAAAATAT
1 TTTGAGGAAAAATTGAAATATCAATTTTTCTTAAAT-AAAAAA-ATTTCAAAAAATAT
* * * *
16627439 TTTTA-AAAAAAGTTAAAATATCAATTTTTCTTAAATAAAAAATATTTCAAAAAAT-G
1 TTTGAGGAAAAA-TTGAAATATCAATTTTTCTTAAATAAAAAA-ATTTCAAAAAATAT
* *
16627495 CTTGA-GAAAAAGTTGAAATATCAATTTTTCTTAAATAAAAAAATATTTTAAAAAA-AT
1 TTTGAGGAAAAA-TTGAAATATCAATTTTTCTTAAAT-AAAAAA-ATTTCAAAAAATAT
* * * *
16627552 GTTTGA-GAAAAAGTT-AAAGTAT-TATTTTTCCTAAAATAAAAAATATTTC-CAAAACA-
1 -TTTGAGGAAAAA-TTGAAA-TATCAATTTTT-CTTAAATAAAAAA-ATTTCAAAAAATAT
* * *
16627608 TTTGAGAAAAAAGTTGAGAGTATTAATTTTTTCTTAAATAAAA
1 TTTGAGGAAAAA-TTGA-AATATCAA-TTTTTCTTAAATAAAA
16627651 TATTAATTTT
Statistics
Matches: 469, Mismatches: 62, Indels: 54
0.80 0.11 0.09
Matches are distributed among these distances:
55 17 0.04
56 197 0.42
57 81 0.17
58 75 0.16
59 21 0.04
60 3 0.01
61 4 0.01
62 71 0.15
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (56 bp):
TTTGAGGAAAAATTGAAATATCAATTTTTCTTAAATAAAAAAATTTCAAAAAATAT
Found at i:16627471 original size:114 final size:114
Alignment explanation
Indices: 16627033--16627650 Score: 607
Period size: 114 Copynumber: 5.4 Consensus size: 114
16627023 TTTTAAAAAA
* * *
16627033 TTTGA-GAAAAAGTAGAAATATCAATTTTTCTTAAATAAACAAATAATATTTCGAAAAAATGTTT
1 TTTGAGGAAAAAGTTGAAGTATCAATTTTTCTTAAAT-AA-AAA-AATATTTC-AAAAAATATTT
* * **
16627097 TGAGAAAAAGATGAAATATCAAATTTTCTTAAATAAAAAAGTTTCAAAATTTAT
62 TGAGAAAAAGTTGAAATATCAATTTTTCTTAAATAAAAAA-TTTCAAAAAATAT
* *
16627151 TTTGAGGAAAAA-TTGAAGTATCAATTTTCCTAAAATAAAAAAATAATATTTCAAAAAAATATTT
1 TTTGAGGAAAAAGTTGAAGTATCAATTTTTCTTAAAT--AAAAA-AATATTTC-AAAAAATATTT
* * * * **
16627215 TGAGGAAAAA-TTGAAGTGTCAATTTTTATTAAACAAAAAAAAATCAAAAAATAT
62 TGA-GAAAAAGTTGAAATATCAATTTTTCTTAAA-TAAAAAATTTCAAAAAATAT
* * * * *
16627269 TTTGAGG-AAAAGTTAAAGTATCAATTTTTTTTAAA-CAAAAAA-ATTTCAAAAAATGTTTTAAG
1 TTTGAGGAAAAAGTTGAAGTATCAATTTTTCTTAAATAAAAAAATATTTCAAAAAATATTTTGAG
* *
16627331 GAAAAGTTGAAATATCAATTTTTCTTAAATAAAAAATTTCAAAAAAATGT
66 AAAAAGTTGAAATATCAATTTTTCTTAAATAAAAAATTTC-AAAAAATAT
* * * * *
16627381 TTTGAGGAGAAA-TTGAAGTATTAATATTTCTTAAATAAAAAAATATTTCAAAAAATATTTTTAA
1 TTTGAGGAAAAAGTTGAAGTATCAATTTTTCTTAAATAAAAAAATATTTCAAAAAATATTTTGAG
* *
16627445 AAAAAGTTAAAATATCAATTTTTCTTAAATAAAAAATATTTCAAAAAAT-G
66 AAAAAGTTGAAATATCAATTTTTCTTAAAT-AAAAA-ATTTCAAAAAATAT
* * *
16627495 CTTGA-GAAAAAGTTGAAATATCAATTTTTCTTAAATAAAAAAATATTTTAAAAAA-ATGTTTGA
1 TTTGAGGAAAAAGTTGAAGTATCAATTTTTCTTAAATAAAAAAATATTTCAAAAAATAT-TTTGA
* * * *
16627558 GAAAAAGTT-AAAGTAT-TATTTTTCCTAAAATAAAAAATATTTC-CAAAACA-
65 GAAAAAGTTGAAA-TATCAATTTTT-CTTAAAT-AAAAA-ATTTCAAAAAATAT
* *
16627608 TTTGAGAAAAAAGTTGAGAGTATTAATTTTTTCTTAAATAAAA
1 TTTGAGGAAAAAGTTGA-AGTATCAA-TTTTTCTTAAATAAAA
16627651 TATTAATTTT
Statistics
Matches: 421, Mismatches: 59, Indels: 42
0.81 0.11 0.08
Matches are distributed among these distances:
111 13 0.03
112 66 0.16
113 38 0.09
114 133 0.32
115 22 0.05
116 21 0.05
117 4 0.01
118 103 0.24
119 21 0.05
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (114 bp):
TTTGAGGAAAAAGTTGAAGTATCAATTTTTCTTAAATAAAAAAATATTTCAAAAAATATTTTGAG
AAAAAGTTGAAATATCAATTTTTCTTAAATAAAAAATTTCAAAAAATAT
Found at i:16627654 original size:23 final size:24
Alignment explanation
Indices: 16627628--16627676 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
16627618 AAGTTGAGAG
*
16627628 TATTAA-TTTTTTCTTAAATAAAA
1 TATTAATTTTTTTCTAAAATAAAA
16627651 TATTAATTTTTTTCTAAAATAAAA
1 TATTAATTTTTTTCTAAAATAAAA
16627675 TA
1 TA
16627677 AAAAAGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (24 bp):
TATTAATTTTTTTCTAAAATAAAA
Found at i:16630321 original size:53 final size:53
Alignment explanation
Indices: 16630262--16630401 Score: 174
Period size: 54 Copynumber: 2.5 Consensus size: 53
16630252 TTGAAAAAGC
** *
16630262 ATTTTTTAGGTAAAAATAATTTCAAAAAAT-TTTTGAGAAAAAGTTGAAGTATTA
1 ATTTTTTAAATAAAAA-AA-TTCAAAAAATATTTTGAGAAAAAGTTGAAGTATCA
16630316 ATTTTTTTAAATAAAAAAATTCAAAAAATATTTTGAGAAAAAGTTGAAGTATCA
1 A-TTTTTTAAATAAAAAAATTCAAAAAATATTTTGAGAAAAAGTTGAAGTATCA
*
16630370 ATTTTCCTTAAATAAAGAATATTTCAAAAAAT
1 ATTTT--TTAAATAAA-AA-AATTCAAAAAAT
16630402 GTATAAGAAA
Statistics
Matches: 76, Mismatches: 4, Indels: 9
0.85 0.04 0.10
Matches are distributed among these distances:
53 14 0.18
54 27 0.36
55 22 0.29
56 2 0.03
57 11 0.14
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.37
Consensus pattern (53 bp):
ATTTTTTAAATAAAAAAATTCAAAAAATATTTTGAGAAAAAGTTGAAGTATCA
Found at i:16630422 original size:56 final size:55
Alignment explanation
Indices: 16630272--16630554 Score: 247
Period size: 56 Copynumber: 5.1 Consensus size: 55
16630262 ATTTTTTAGG
* * * *
16630272 TAAAAATAATTTCAAAAAATTTTTGAGAAAAAGTTGAAGTATTAATTTT-TTTAAA
1 TAAAAAT-ATTTCAAAAAATTTATAAGAAAAAGTTGAAGTATCAATTTTCCTTAAA
* * *
16630327 TAAAAA-AATTCAAAAAATATTTTGAGAAAAAGTTGAAGTATCAATTTTCCTTAAA
1 TAAAAATATTTCAAAAAAT-TTATAAGAAAAAGTTGAAGTATCAATTTTCCTTAAA
* * * *
16630382 TAAAGAATATTTCAAAAAATGTATAAGAAAAA-TTAAAAGTATAAATTTTCTTTAAA
1 TAAA-AATATTTCAAAAAATTTATAAGAAAAAGTT-GAAGTATCAATTTTCCTTAAA
* * * **
16630438 TCGAAAAAT-TTTCAAAAAAAAATT-GAAG-AAAAGTTGAATTATCAATTTTCCCAAAA
1 T--AAAAATATTTC--AAAAAATTTATAAGAAAAAGTTGAAGTATCAATTTTCCTTAAA
** *
16630494 TAAAGAATATTTCAAAAATATTTA-AAGAAAAAGTCAAAATAATCAATTTTCCTTAAA
1 TAAA-AATATTTCAAAAA-ATTTATAAGAAAAAGTTGAAGT-ATCAATTTTCCTTAAA
16630551 TAAA
1 TAAA
16630555 GCATTATTTT
Statistics
Matches: 187, Mismatches: 25, Indels: 30
0.77 0.10 0.12
Matches are distributed among these distances:
53 11 0.06
54 36 0.19
55 26 0.14
56 67 0.36
57 37 0.20
58 10 0.05
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.33
Consensus pattern (55 bp):
TAAAAATATTTCAAAAAATTTATAAGAAAAAGTTGAAGTATCAATTTTCCTTAAA
Found at i:16630487 original size:112 final size:112
Alignment explanation
Indices: 16630272--16630554 Score: 321
Period size: 112 Copynumber: 2.5 Consensus size: 112
16630262 ATTTTTTAGG
* * * *
16630272 TAAA-AATAATTTCAAAAAATTTTTGAGAAAAAGTT-GAAGTATTAATTTT-TTTAAATAAAAAA
1 TAAAGAAT-ATTTCAAAAAATTTATAAGAAAAAGTTAAAAGTATAAATTTTCTTTAAATAAAAAA
** **
16630334 ATTCAAAAAATATTTTGAGAAAAAGTTGAAGTATCAATTTTCCTTAAA
65 ATTCAAAAAATAAATTGAGAAAAAGTTGAAGTATCAATTTTCCCAAAA
*
16630382 TAAAGAATATTTCAAAAAATGTATAAGAAAAA-TTAAAAGTATAAATTTTCTTTAAATCGAAAAA
1 TAAAGAATATTTCAAAAAATTTATAAGAAAAAGTTAAAAGTATAAATTTTCTTTAAAT--AAAAA
** *
16630446 TTTTCAAAAAA-AAATTGA-AGAAAAGTTGAATTATCAATTTTCCCAAAA
64 AATTCAAAAAATAAATTGAGA-AAAAGTTGAAGTATCAATTTTCCCAAAA
* * *
16630494 TAAAGAATATTTCAAAAATATTTA-AAGAAAAAGTCAAAA-TAATCAATTTTCCTTAAATAAA
1 TAAAGAATATTTCAAAAA-ATTTATAAGAAAAAGTTAAAAGT-ATAAATTTTCTTTAAATAAA
16630555 GCATTATTTT
Statistics
Matches: 148, Mismatches: 16, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
109 2 0.01
110 37 0.25
111 14 0.09
112 57 0.39
113 38 0.26
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.33
Consensus pattern (112 bp):
TAAAGAATATTTCAAAAAATTTATAAGAAAAAGTTAAAAGTATAAATTTTCTTTAAATAAAAAAA
TTCAAAAAATAAATTGAGAAAAAGTTGAAGTATCAATTTTCCCAAAA
Found at i:16632236 original size:2 final size:2
Alignment explanation
Indices: 16632229--16632253 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16632219 TAATTTATTT
16632229 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 T
16632254 TTCTTGGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16633680 original size:18 final size:18
Alignment explanation
Indices: 16633636--16633680 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
16633626 GATATATTAG
16633636 AGAATGATACATTTGTGGT
1 AGAA-GATACATTTGTGGT
* **
16633655 GGGGGATACATTTGTGGT
1 AGAAGATACATTTGTGGT
16633673 AGAAGATA
1 AGAAGATA
16633681 TTTAGAGATG
Statistics
Matches: 20, Mismatches: 6, Indels: 1
0.74 0.22 0.04
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.31, C:0.04, G:0.33, T:0.31
Consensus pattern (18 bp):
AGAAGATACATTTGTGGT
Found at i:16634230 original size:16 final size:17
Alignment explanation
Indices: 16634200--16634231 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16634190 CATCATTATA
16634200 ATTCTTTTCTTCTATTC
1 ATTCTTTTCTTCTATTC
16634217 ATTCTTTT-TTCTATT
1 ATTCTTTTCTTCTATT
16634232 TGTTTGTGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTCTTTTCTTCTATTC
Found at i:16635898 original size:52 final size:52
Alignment explanation
Indices: 16635841--16635991 Score: 180
Period size: 51 Copynumber: 2.9 Consensus size: 52
16635831 AACTGTAATT
* * *
16635841 GAGAGATTTTTTAGATTAAATTCCAGAATCAATTGACATTAAAAATGAT-GTG
1 GAGAGATTTTTGAGATTTAATTCCAGAATCAATTCACATTAAAAATGATAG-G
* * * *
16635893 GAGAGATTATCGAGATTTAATTCCATAATCGATTCACATT-AAAATGATAGG
1 GAGAGATTTTTGAGATTTAATTCCAGAATCAATTCACATTAAAAATGATAGG
* * * *
16635944 GAGAGATTTTTGGGATTTGATTTCAGAATCAATTCTCATTAAAAATGA
1 GAGAGATTTTTGAGATTTAATTCCAGAATCAATTCACATTAAAAATGA
16635992 AATCAAATAA
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
51 41 0.50
52 41 0.50
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.34
Consensus pattern (52 bp):
GAGAGATTTTTGAGATTTAATTCCAGAATCAATTCACATTAAAAATGATAGG
Found at i:16636494 original size:19 final size:18
Alignment explanation
Indices: 16636472--16636528 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
16636462 TTCTACTTCA
16636472 TTTTC-TATTTTGATTTTAT
1 TTTTCTTATTTT-A-TTTAT
16636491 TTTTCTTATTTTATTTAT
1 TTTTCTTATTTTATTTAT
* *
16636509 TTAT-TTATTTATTTTTAT
1 TTTTCTTATTT-TATTTAT
16636527 TT
1 TT
16636529 ACTCTTGCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
17 6 0.18
18 16 0.47
19 6 0.18
20 6 0.18
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.77
Consensus pattern (18 bp):
TTTTCTTATTTTATTTAT
Found at i:16636514 original size:22 final size:22
Alignment explanation
Indices: 16636486--16636529 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
16636476 CTATTTTGAT
*
16636486 TTTATTTTTCTTA-TTTTATTTA
1 TTTATTTAT-TTATTTTTATTTA
16636508 TTTATTTATTTATTTTTATTTA
1 TTTATTTATTTATTTTTATTTA
16636530 CTCTTGCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTATTTATTTATTTTTATTTA
Found at i:16636517 original size:12 final size:13
Alignment explanation
Indices: 16636484--16636522 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
16636474 TTCTATTTTG
*
16636484 ATTTTATTTTTCTT
1 ATTTTATTTAT-TT
16636498 ATTTTATTTATTT
1 ATTTTATTTATTT
16636511 A-TTTATTTATTT
1 ATTTTATTTATTT
16636523 TTATTTACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 11 0.46
13 3 0.12
14 10 0.42
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (13 bp):
ATTTTATTTATTT
Found at i:16640335 original size:20 final size:20
Alignment explanation
Indices: 16640312--16640350 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
16640302 AAAAAAAAAG
16640312 AAAAAGAA-AAGAAAATTGAA
1 AAAAAGAAGAAG-AAATTGAA
*
16640332 AAAATGAAGAAGAAATTGA
1 AAAAAGAAGAAGAAATTGA
16640351 TAGGCAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.69, C:0.00, G:0.18, T:0.13
Consensus pattern (20 bp):
AAAAAGAAGAAGAAATTGAA
Found at i:16640652 original size:14 final size:14
Alignment explanation
Indices: 16640635--16640673 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
16640625 AAAGGTGTGT
*
16640635 AAAAAAAATTACAA
1 AAAAAAAATAACAA
* *
16640649 AAAAAAGAGAACAA
1 AAAAAAAATAACAA
16640663 AAAAAAAATAA
1 AAAAAAAATAA
16640674 AAAGAAAAGG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.82, C:0.05, G:0.05, T:0.08
Consensus pattern (14 bp):
AAAAAAAATAACAA
Found at i:16640665 original size:27 final size:25
Alignment explanation
Indices: 16640635--16640689 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 25
16640625 AAAGGTGTGT
*
16640635 AAAAAAAATTACAAAA-AAAAGAGAACA
1 AAAAAAAAATA-AAAAGAAAAG-GAA-A
16640662 AAAAAAAAATAAAAAGAAAAGGAAA
1 AAAAAAAAATAAAAAGAAAAGGAAA
16640687 AAA
1 AAA
16640690 GAAGGCTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 4 0.15
26 7 0.27
27 15 0.58
ACGTcount: A:0.82, C:0.04, G:0.09, T:0.05
Consensus pattern (25 bp):
AAAAAAAAATAAAAAGAAAAGGAAA
Found at i:16641789 original size:114 final size:114
Alignment explanation
Indices: 16641555--16641795 Score: 268
Period size: 115 Copynumber: 2.1 Consensus size: 114
16641545 TGATAGCTTT
* * ** * * * *
16641555 ATTTTCTTAACTTGCGACATCATCTTGGTCATTCATCTTTGATCTCAATTCTATCTGGTCTTTTT
1 ATTTTTTTGACTTGCGACATCATCTTGGTCATTCATCTTCAACCTCAACTCGATCTGGTCTCTTT
** ** * *
16641620 TAAACTTGTGGCATTGTCTCGATCATTCGATCTCAACTTAGTCCAGATC
66 TAAACTTACGGCATCATCCCGATCATTCGATCTCAACTCAGTCCAGATC
*
16641669 ATTTTTTTGACTTGCGACATCATCTTGGTCATTCATCTTCAACCTCAACTCGGTCTTGGT-TACT
1 ATTTTTTTGACTTGCGACATCATCTTGGTCATTCATCTTCAACCTCAACTCGATC-TGGTCT-CT
* * * * * *
16641733 TTTAGACTTACGGTATCATCCCGATCATTCGATCTTAGCTCAGTCTAGTTC
64 TTTAAACTTACGGCATCATCCCGATCATTCGATCTCAACTCAGTCCAGATC
16641784 ATTTTTTTGACT
1 ATTTTTTTGACT
16641796 CACTGCATAA
Statistics
Matches: 104, Mismatches: 21, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
114 48 0.46
115 56 0.54
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (114 bp):
ATTTTTTTGACTTGCGACATCATCTTGGTCATTCATCTTCAACCTCAACTCGATCTGGTCTCTTT
TAAACTTACGGCATCATCCCGATCATTCGATCTCAACTCAGTCCAGATC
Found at i:16642213 original size:18 final size:17
Alignment explanation
Indices: 16642190--16642233 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
16642180 TCCTTTTTCC
16642190 TGCAAATCTGAAAGTCCT
1 TGCAAATCTGAAA-TCCT
*
16642208 TGCAAA-CTTGAAATCTT
1 TGCAAATC-TGAAATCCT
16642225 TGCAAATCT
1 TGCAAATCT
16642234 ACAACATCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (17 bp):
TGCAAATCTGAAATCCT
Found at i:16642229 original size:17 final size:17
Alignment explanation
Indices: 16642207--16642258 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
16642197 CTGAAAGTCC
16642207 TTGCAAACTTGAAATCT
1 TTGCAAACTTGAAATCT
**
16642224 TTGCAAATCTACAACATCT
1 TTGCAAA-CTTGAA-ATCT
*
16642243 TCG-AAACTTGAAATCT
1 TTGCAAACTTGAAATCT
16642259 CGCGAATCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
16 4 0.14
17 11 0.39
18 7 0.25
19 6 0.21
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.33
Consensus pattern (17 bp):
TTGCAAACTTGAAATCT
Found at i:16643355 original size:24 final size:24
Alignment explanation
Indices: 16643323--16643369 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
16643313 TTCCATTCCA
16643323 TTTTCTATTTTGATTTTATTTTTC
1 TTTTCTATTTTGATTTTATTTTTC
* *
16643347 TTTTTTATTTTGTTTTTATTTTT
1 TTTTCTATTTTGATTTTATTTTT
16643370 ATTTACTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.11, C:0.04, G:0.04, T:0.81
Consensus pattern (24 bp):
TTTTCTATTTTGATTTTATTTTTC
Found at i:16645423 original size:5 final size:6
Alignment explanation
Indices: 16645407--16645431 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
16645397 CCTTTATCTT
16645407 TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA T
16645432 GATAAGATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:16653570 original size:27 final size:27
Alignment explanation
Indices: 16653539--16653592 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
16653529 ACCCCCAACA
16653539 CTCTTATCACATAATACATATTACATT
1 CTCTTATCACATAATACATATTACATT
16653566 CTCTTATCACATAATACATATTACATT
1 CTCTTATCACATAATACATATTACATT
16653593 TTGTGAACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (27 bp):
CTCTTATCACATAATACATATTACATT
Found at i:16654812 original size:14 final size:15
Alignment explanation
Indices: 16654793--16654823 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
16654783 TTTATATTGC
16654793 ATAATATTTAAA-AA
1 ATAATATTTAAATAA
16654807 ATAATATTTAAATAA
1 ATAATATTTAAATAA
16654822 AT
1 AT
16654824 TTTTAAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
ATAATATTTAAATAA
Found at i:16655953 original size:9 final size:9
Alignment explanation
Indices: 16655939--16655963 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
16655929 AATTAAATGT
16655939 ATTTATTTA
1 ATTTATTTA
16655948 ATTTATTTA
1 ATTTATTTA
16655957 ATTTATT
1 ATTTATT
16655964 ATCTCCAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
ATTTATTTA
Found at i:16656018 original size:24 final size:24
Alignment explanation
Indices: 16656003--16656073 Score: 133
Period size: 24 Copynumber: 3.0 Consensus size: 24
16655993 ATTTAAATTT
16656003 AAATTAAATGTATTATTTATTTTA
1 AAATTAAATGTATTATTTATTTTA
16656027 AAATTAAATGTATTATTTATTTTA
1 AAATTAAATGTATTATTTATTTTA
*
16656051 AAATTAAATGTATTATGTATTTT
1 AAATTAAATGTATTATTTATTTT
16656074 CGAAAATAGA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.54
Consensus pattern (24 bp):
AAATTAAATGTATTATTTATTTTA
Done.