Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397266.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_20.0, 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: 7441454
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 92215 characters in sequence are not A, C, G, or T
File 5 of 18
Found at i:1900005 original size:27 final size:27
Alignment explanation
Indices: 1899973--1900030 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
1899963 GAGGCCCAAG
*
1899973 AGGGTGCCAGCCCTCCAAGACCCATGT
1 AGGGTGCCAGCCCACCAAGACCCATGT
*
1900000 AGGGTGTCAGCCCACCAAGACCCATGT
1 AGGGTGCCAGCCCACCAAGACCCATGT
1900027 AGGG
1 AGGG
1900031 ATTTCCCTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.24, C:0.33, G:0.29, T:0.14
Consensus pattern (27 bp):
AGGGTGCCAGCCCACCAAGACCCATGT
Found at i:1900101 original size:15 final size:15
Alignment explanation
Indices: 1900081--1900138 Score: 91
Period size: 15 Copynumber: 3.9 Consensus size: 15
1900071 TCCCAAATGG
1900081 TTTTGGAGGGAAATC
1 TTTTGGAGGGAAATC
1900096 TTTTGGAGGGAAATC
1 TTTTGGAGGGAAATC
* *
1900111 CTTTGGAGGGAAA-A
1 TTTTGGAGGGAAATC
1900125 TTTTGGAGGGAAAT
1 TTTTGGAGGGAAAT
1900139 GGATGGGGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
14 12 0.31
15 27 0.69
ACGTcount: A:0.29, C:0.05, G:0.34, T:0.31
Consensus pattern (15 bp):
TTTTGGAGGGAAATC
Found at i:1900136 original size:29 final size:30
Alignment explanation
Indices: 1900082--1900138 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
1900072 CCCAAATGGT
*
1900082 TTTGGAGGGAAATCTTTTGGAGGGAAATCC
1 TTTGGAGGGAAATATTTTGGAGGGAAATCC
1900112 TTTGGAGGGAAA-ATTTTGGAGGGAAAT
1 TTTGGAGGGAAATATTTTGGAGGGAAAT
1900139 GGATGGGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (30 bp):
TTTGGAGGGAAATATTTTGGAGGGAAATCC
Found at i:1903864 original size:32 final size:34
Alignment explanation
Indices: 1903810--1903873 Score: 89
Period size: 32 Copynumber: 1.9 Consensus size: 34
1903800 ATAAATTTTG
*
1903810 AAATGAAACAAAAATCTATGTTTTGTTAATATTT
1 AAATGAAACAAAAATCTATGTTTTATTAATATTT
1903844 AAAT-AAA-AAAAAT-TAGTGTTTTATTAATAT
1 AAATGAAACAAAAATCTA-TGTTTTATTAATAT
1903874 CTCAGAATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 2 0.07
32 19 0.68
33 3 0.11
34 4 0.14
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.41
Consensus pattern (34 bp):
AAATGAAACAAAAATCTATGTTTTATTAATATTT
Found at i:1910358 original size:211 final size:212
Alignment explanation
Indices: 1909981--1910373 Score: 499
Period size: 211 Copynumber: 1.9 Consensus size: 212
1909971 AGGTGAATTT
* *
1909981 TTGTTCTAGTTGTAATATTGAATTTGTATTGTTCACTGTTGAAGTGAACAGTTTATTATGTATAT
1 TTGTTCTAGTTGTAATATTGAATTTGTATTGTCCACTATTGAAGTGAACAGTTTATTATGTATAT
* * * * *
1910046 TTCTTCCAATAGACATTTTTAGTCAATATTTTTATACCAATACACACCTAGCTCTACAAAAAAAA
66 ATCTTCCAATAAAAATTTTTAGTCAAAATTTTTATACCAATACACACCCAGCTCTACAAAAAAAA
* * ** *
1910111 AAAGAAAGAAAGTCGTTGTTGTGTTGATGTAAAGTTTTAACCATGGGAAAATAAAAGCTTTGAAA
131 AAAGAAAGAAAGTCATTGTTGGGTTGATACAAAGTTTTAACCATGGAAAAATAAAAGCTTTGAAA
1910176 ATCTTGGTTTTAAAATG
196 ATCTTGGTTTTAAAATG
* * * *
1910193 TTGTTCTAGTTGTAAT-TCTGAATTTGTATTGTCCACTATTGAGGTGAAGAG-TTGTTATGTATC
1 TTGTTCTAGTTGTAATAT-TGAATTTGTATTGTCCACTATTGAAGTGAACAGTTTATTATGTATA
*** * * *
1910256 TATCTTCTGGTAAAAATTTTTTGTCAAAATTTTTATAGCAATACACACCCAGCTTTA-AAAAAAA
65 TATCTTCCAATAAAAATTTTTAGTCAAAATTTTTATACCAATACACACCCAGCTCTACAAAAAAA
**
1910320 GGAA-AAA-AAAGTCATTATTGTTGGGTTGATACAAAGTTTTAACCATGGAAAAAT
130 AAAAGAAAGAAAGTC---ATTGTTGGGTTGATACAAAGTTTTAACCATGGAAAAAT
1910374 GAAGACTCCG
Statistics
Matches: 153, Mismatches: 24, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
208 6 0.04
209 3 0.02
210 9 0.06
211 90 0.59
212 45 0.29
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (212 bp):
TTGTTCTAGTTGTAATATTGAATTTGTATTGTCCACTATTGAAGTGAACAGTTTATTATGTATAT
ATCTTCCAATAAAAATTTTTAGTCAAAATTTTTATACCAATACACACCCAGCTCTACAAAAAAAA
AAAGAAAGAAAGTCATTGTTGGGTTGATACAAAGTTTTAACCATGGAAAAATAAAAGCTTTGAAA
ATCTTGGTTTTAAAATG
Found at i:1920722 original size:22 final size:23
Alignment explanation
Indices: 1920688--1920731 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
1920678 ACCCTTCAAC
* *
1920688 TTTATTATCTTAT-TAAAAATAT
1 TTTATAATATTATATAAAAATAT
*
1920710 TTTATAATATTATATTAAAATA
1 TTTATAATATTATATAAAAATA
1920732 AATATATAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTATAATATTATATAAAAATAT
Found at i:1920738 original size:19 final size:17
Alignment explanation
Indices: 1920715--1920773 Score: 57
Period size: 19 Copynumber: 3.3 Consensus size: 17
1920705 AATATTTTAT
1920715 AATATTATATTAAAATAA
1 AATATTATA-TAAAATAA
*
1920733 ATATATAATATAAGAATAA
1 A-ATATTATATAA-AATAA
*
1920752 AA-ATTAAAATAAAATAA
1 AATATT-ATATAAAATAA
1920769 AATAT
1 AATAT
1920774 AAAATTAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
17 9 0.26
18 12 0.35
19 13 0.38
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (17 bp):
AATATTATATAAAATAA
Found at i:1920768 original size:23 final size:23
Alignment explanation
Indices: 1920737--1920781 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1920727 AAATAAATAT
*
1920737 ATAATATAAGAATA-AAAATTAAA
1 ATAAAATAA-AATATAAAATTAAA
1920760 ATAAAATAAAATATAAAATTAA
1 ATAAAATAAAATATAAAATTAA
1920782 TATTTATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (23 bp):
ATAAAATAAAATATAAAATTAAA
Found at i:1920777 original size:48 final size:51
Alignment explanation
Indices: 1920716--1920839 Score: 134
Period size: 53 Copynumber: 2.4 Consensus size: 51
1920706 ATATTTTATA
* *
1920716 ATATTATATTAAAATAAATATATAATATAAGA-ATAA-AAATTAAAATAAAAT
1 ATATAATA-TAAAATAAATATATAATAT-AGATAAAACAAATTAAAATAAAAT
1920767 A-A-AATATAAAATTAATATTTATATAATATAGATAAAACAAATTAAAATAAAAT
1 ATATAATATAAAA-TAA-A--TATATAATATAGATAAAACAAATTAAAATAAAAT
1920820 ATATAATAT-AAA-AAATATAT
1 ATATAATATAAAATAAATATAT
1920840 TAAAGAAATG
Statistics
Matches: 63, Mismatches: 2, Indels: 18
0.76 0.02 0.22
Matches are distributed among these distances:
48 5 0.08
49 11 0.17
50 2 0.03
51 5 0.08
52 15 0.24
53 16 0.25
54 4 0.06
55 5 0.08
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.33
Consensus pattern (51 bp):
ATATAATATAAAATAAATATATAATATAGATAAAACAAATTAAAATAAAAT
Found at i:1920834 original size:21 final size:21
Alignment explanation
Indices: 1920810--1921132 Score: 58
Period size: 23 Copynumber: 14.3 Consensus size: 21
1920800 AAAACAAATT
1920810 AAAATAAAATATATAATATAA
1 AAAATAAAATATATAATATAA
* * * * *
1920831 AAAATATATTAAAGAAATGAAAAA
1 AAAATAAAATATA-TAAT--ATAA
*
1920855 AAATATAAAAATATAATAATAAATA
1 AAA-AT-AAAATAT-ATAATATA-A
1920880 AAAATAAAATATATGACAT-TAA
1 AAAATAAAATATAT-A-ATATAA
* *
1920902 AAATATATTTAAA-ATATGATATTA
1 AAA-ATA---AAATATATAATATAA
* *
1920926 TATA-AAAAT-TAATAATAT-A
1 AAAATAAAATAT-ATAATATAA
* *
1920945 AATAT-AAATATATTAAAAATAA
1 AAAATAAAATATA-T-AATATAA
*
1920967 AATATAAAATATTATAATAATAAATA
1 AAAATAAAATA-TATAAT-AT--A-A
1920993 AAAATAAAATATATGACAT-TAA
1 AAAATAAAATATAT-A-ATATAA
* *
1921015 AAATATATTTAAGAAATGATATTATATA
1 AAA-ATA---AA-ATAT-ATAATATA-A
1921043 AAAATTAATAATATA-AATATAA
1 AAAA-TAA-AATATATAATATAA
* *
1921065 ATATATTAAAA-ATAAAATATAA
1 A-A-AATAAAATATATAATATAA
* *
1921087 AATATTATAATA-ATAA-AT-A
1 AA-AATAAAATATATAATATAA
* *
1921106 AAAATAAAATATATGATATTA
1 AAAATAAAATATATAATATAA
1921127 AAAATA
1 AAAATA
1921133 TATTTAAGAA
Statistics
Matches: 227, Mismatches: 29, Indels: 92
0.65 0.08 0.26
Matches are distributed among these distances:
18 7 0.03
19 19 0.08
20 12 0.05
21 35 0.15
22 35 0.15
23 36 0.16
24 20 0.09
25 19 0.08
26 26 0.11
27 10 0.04
28 8 0.04
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (21 bp):
AAAATAAAATATATAATATAA
Found at i:1920837 original size:53 final size:51
Alignment explanation
Indices: 1920734--1920837 Score: 140
Period size: 53 Copynumber: 2.0 Consensus size: 51
1920724 TTAAAATAAA
*
1920734 TATATAATATAAGAATAAAAATTAAAATAAAATAAAATATAAAATTAATATT
1 TATATAATATAAGAAAAAAAATTAAAATAAAATAAAATATAAAA-TAATATT
1920786 TATATAATAT-AGATAAAACAAATTAAAATAAAATATATAATATAAAA-AATAT
1 TATATAATATAAGA-AAAA-AAATTAAAATAAAATA-A-AATATAAAATAATAT
1920838 ATTAAAGAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
51 3 0.06
52 13 0.28
53 21 0.45
54 1 0.02
55 9 0.19
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (51 bp):
TATATAATATAAGAAAAAAAATTAAAATAAAATAAAATATAAAATAATATT
Found at i:1920950 original size:6 final size:6
Alignment explanation
Indices: 1920939--1921005 Score: 50
Period size: 6 Copynumber: 11.0 Consensus size: 6
1920929 AAAAATTAAT
* *
1920939 AATATA AATATA AATAT- ATTAAA AATA-A AATATAA AATATTA TAATAATA
1 AATATA AATATA AATATA AATATA AATATA AATAT-A AATA-TA -AAT-ATA
*
1920989 AATAAA AATA-A AATATA
1 AATATA AATATA AATATA
1921006 TGACATTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
5 13 0.26
6 21 0.42
7 9 0.18
8 6 0.12
9 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AATATA
Found at i:1921010 original size:113 final size:113
Alignment explanation
Indices: 1920850--1921295 Score: 793
Period size: 113 Copynumber: 4.0 Consensus size: 113
1920840 TAAAGAAATG
1920850 AAAA-AAAATATAAAA-A-TATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
1 AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
1920912 AA-AATATGATATTATATAAAAATTAATAATATAAATATAAATATATTA
66 AAGAA-ATGATATTATATAAAAATTAATAATATAAATATAAATATATTA
1920960 AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
1 AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
1921025 AAGAAATGATATTATATAAAAATTAATAATATAAATATAAATATATTA
66 AAGAAATGATATTATATAAAAATTAATAATATAAATATAAATATATTA
*
1921073 AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTT
1 AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
1921138 AAGAAATGATATTATATAAAAATTAATAA-A-AAATATAAATATATTA
66 AAGAAATGATATTATATAAAAATTAATAATATAAATATAAATATATTA
*
1921184 AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTT
1 AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
*
1921249 -A-AAATGATATTATAT-AAAATTAATAATAAAAATATAAATATATTA
66 AAGAAATGATATTATATAAAAATTAATAATATAAATATAAATATATTA
1921294 AA
1 AA
1921296 CTATATTTTT
Statistics
Matches: 329, Mismatches: 1, Indels: 12
0.96 0.00 0.04
Matches are distributed among these distances:
108 11 0.03
109 15 0.05
110 23 0.07
111 92 0.28
112 2 0.01
113 184 0.56
114 2 0.01
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (113 bp):
AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
AAGAAATGATATTATATAAAAATTAATAATATAAATATAAATATATTA
Found at i:1921063 original size:6 final size:6
Alignment explanation
Indices: 1921052--1921118 Score: 50
Period size: 6 Copynumber: 11.0 Consensus size: 6
1921042 AAAAATTAAT
* *
1921052 AATATA AATATA AATAT- ATTAAA AATA-A AATATAA AATATTA TAATAATA
1 AATATA AATATA AATATA AATATA AATATA AATAT-A AATA-TA -AAT-ATA
*
1921102 AATAAA AATA-A AATATA
1 AATATA AATATA AATATA
1921119 TGATATTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
5 13 0.26
6 21 0.42
7 9 0.18
8 6 0.12
9 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AATATA
Found at i:1921063 original size:23 final size:23
Alignment explanation
Indices: 1920924--1920992 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
1920914 AATATGATAT
1920924 TATATAAAAATTAATAATATAAA
1 TATATAAAAATTAATAATATAAA
*
1920947 TATA-AATATATTAA-AA-ATAAA
1 TATATAA-AAATTAATAATATAAA
1920968 -ATATAAAATATT-ATAATAATAAA
1 TATATAAAA-ATTAATAAT-ATAAA
1920991 TA
1 TA
1920993 AAAATAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
20 5 0.14
21 12 0.32
22 4 0.11
23 15 0.41
24 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
TATATAAAAATTAATAATATAAA
Found at i:1921216 original size:224 final size:220
Alignment explanation
Indices: 1920850--1921295 Score: 781
Period size: 224 Copynumber: 2.0 Consensus size: 220
1920840 TAAAGAAATG
1920850 AAAAAAAATATAAAAATATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTTAAA
1 AAAAAAAATATAAAAATATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTTAAA
1920915 ATATGATATTATATAAAAATTAATAATATAAATATAAATATATTAAAAATAAAATATAAAATATT
66 ATATGATATTATATAAAAATTAATAATATAAATATAAATATATTAAAAATAAAATATAAAATATT
1920980 ATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTTAAGAAATGATATTATATAAA
131 ATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT-A-AAATGATATTATAT-AA
*
1921045 AATTAATAATATAAATATAAATATATTA
193 AATTAATAATAAAAATATAAATATATTA
*
1921073 AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTT
1 AAAA-AAAATATAAAA-A-TATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
1921138 AAGAA-ATGATATTATATAAAAATTAATAA-A-AAATATAAATATATTAAAAATAAAATATAAAA
63 AA-AATATGATATTATATAAAAATTAATAATATAAATATAAATATATTAAAAATAAAATATAAAA
*
1921200 TATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAAATGATATTATATA
127 TATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTTAAAATGATATTATATA
1921265 AAATTAATAATAAAAATATAAATATATTA
192 AAATTAATAATAAAAATATAAATATATTA
1921294 AA
1 AA
1921296 CTATATTTTT
Statistics
Matches: 216, Mismatches: 3, Indels: 10
0.94 0.01 0.04
Matches are distributed among these distances:
221 31 0.14
222 14 0.06
223 5 0.02
224 91 0.42
225 2 0.01
226 71 0.33
227 2 0.01
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (220 bp):
AAAAAAAATATAAAAATATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTTAAA
ATATGATATTATATAAAAATTAATAATATAAATATAAATATATTAAAAATAAAATATAAAATATT
ATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTTAAAATGATATTATATAAAAT
TAATAATAAAAATATAAATATATTA
Found at i:1921252 original size:12 final size:15
Alignment explanation
Indices: 1921221--1921268 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
1921211 TAAATAAAAA
1921221 TAAAATATATGATAT
1 TAAAATATATGATAT
1921236 TAAAA-ATAT-AT-T
1 TAAAATATATGATAT
*
1921248 TAAAATGATATTATA-
1 TAAAAT-ATATGATAT
1921263 TAAAAT
1 TAAAAT
1921269 TAATAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 6 0.21
13 2 0.07
14 8 0.28
15 13 0.45
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (15 bp):
TAAAATATATGATAT
Found at i:1921252 original size:33 final size:33
Alignment explanation
Indices: 1920950--1921253 Score: 127
Period size: 33 Copynumber: 8.5 Consensus size: 33
1920940 ATATAAATAT
1920950 AAATATATTAAAAATAAAATATAAAATATTATA
1 AAATATATTAAAAATAAAATATAAAATATTATA
* ** *
1920983 ATAATA-AATAAAAATAAAATATATGACATTA-A
1 A-AATATATTAAAAATAAAATATAAAATATTATA
*
1921015 AAATATATTTAAGAAATGATATTATATAAAA-ATTAATA
1 AAATATA-TTAA-AAAT-A-A-AATATAAAATATT-ATA
* *
1921053 ATATAAATATAAATATATTAAAAATAAAATATAAAATATTATA
1 AAATATAT-TAAA-A-A-T-AAAAT---A--TAAAATATTATA
* **
1921096 ATAATA-AATAAAAATAAAATATATGATATTA-A
1 A-AATATATTAAAAATAAAATATAAAATATTATA
* *
1921128 AAATATATTTAAGAAATGATATTATATAAAAATTAATAAAAAATA
1 AAATATA-TTAA-AAAT-A-A-AATAT-AAAA-T-AT----TATA
1921173 TAAATATATTAAAAATAAAATATAAAATATTATA
1 -AAATATATTAAAAATAAAATATAAAATATTATA
* **
1921207 ATAATA-AATAAAAATAAAATATATGATATTA-A
1 A-AATATATTAAAAATAAAATATAAAATATTATA
*
1921239 AAATATATTTAAAAT
1 AAATATATTAAAAAT
1921254 GATATTATAT
Statistics
Matches: 206, Mismatches: 28, Indels: 75
0.67 0.09 0.24
Matches are distributed among these distances:
31 12 0.06
32 15 0.07
33 59 0.29
34 19 0.09
35 3 0.01
36 5 0.02
37 13 0.06
38 21 0.10
39 5 0.02
40 9 0.04
41 6 0.03
42 5 0.02
43 11 0.05
44 11 0.05
45 5 0.02
46 7 0.03
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (33 bp):
AAATATATTAAAAATAAAATATAAAATATTATA
Found at i:1921465 original size:15 final size:15
Alignment explanation
Indices: 1921445--1921498 Score: 81
Period size: 15 Copynumber: 3.6 Consensus size: 15
1921435 TTTTCCCTGT
*
1921445 AATCACATTGCTTGC
1 AATCACATTACTTGC
1921460 AATCACATTACTTGC
1 AATCACATTACTTGC
* *
1921475 AATCACATTACCTGT
1 AATCACATTACTTGC
1921490 AATCACATT
1 AATCACATT
1921499 GCATTGTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.33
Consensus pattern (15 bp):
AATCACATTACTTGC
Found at i:1934064 original size:2 final size:2
Alignment explanation
Indices: 1934057--1934094 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1934047 GCTTTGTTAC
1934057 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1934095 GAAAAAACTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1940378 original size:30 final size:30
Alignment explanation
Indices: 1940342--1940402 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
1940332 TACTATGATC
1940342 TGTAGCTTTTCCTCAAAATGGTTTCTCTGT
1 TGTAGCTTTTCCTCAAAATGGTTTCTCTGT
1940372 TGTAGCTTTTCCTCAAAATGGTTTCTCTGT
1 TGTAGCTTTTCCTCAAAATGGTTTCTCTGT
1940402 T
1 T
1940403 TTTTTCTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.48
Consensus pattern (30 bp):
TGTAGCTTTTCCTCAAAATGGTTTCTCTGT
Found at i:1948522 original size:20 final size:21
Alignment explanation
Indices: 1948479--1948522 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1948469 GAAAAACAAC
* *
1948479 AAAGTTTAAGAACAAAATACA
1 AAAGTTCAAGAACAAAATAAA
*
1948500 AAAGTTCAAGAA-ATAATAAA
1 AAAGTTCAAGAACAAAATAAA
1948520 AAA
1 AAA
1948523 AGTAATAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.66, C:0.07, G:0.09, T:0.18
Consensus pattern (21 bp):
AAAGTTCAAGAACAAAATAAA
Found at i:1964063 original size:16 final size:16
Alignment explanation
Indices: 1964044--1964084 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1964034 TTTAAACTCT
**
1964044 TTTTTTTAAAATTTTA
1 TTTTTTTAAAAAATTA
*
1964060 TTTTTTAAAAAAATTA
1 TTTTTTTAAAAAATTA
1964076 TTTTTTTAA
1 TTTTTTTAA
1964085 GAGTTTTTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTTTTTAAAAAATTA
Found at i:1975248 original size:71 final size:70
Alignment explanation
Indices: 1975173--1975412 Score: 259
Period size: 71 Copynumber: 3.4 Consensus size: 70
1975163 CATGTCGTTA
* * *
1975173 CAGTATTATGGGGTGACACACCACGTTGGTTAGATATCATTGACATCTTGTGGTGGCATGTTGAG
1 CAGTATTATAGGGTGACACACCACGTT-GTTAGATATCATTGACATCTTGTGGTGACATGTTGAA
*
1975238 TTATTG
65 TCATTG
* *** ** * * *
1975244 CAGTATTATAGGGTAACATGTCATTTTTGTTAGATGA-CTTTGACGTCTTGTGGTGACATGTTAA
1 CAGTATTATAGGGTGACACACCA-CGTTGTTAGAT-ATCATTGACATCTTGTGGTGACATGTTGA
1975308 ATCATTG
64 ATCATTG
* * * *
1975315 CAATATTATAGGGTGACACACCACGCTTCTTAGATGTCATTGACATCTTGTGGTGACATGTTGAC
1 CAGTATTATAGGGTGACACACCACG-TTGTTAGATATCATTGACATCTTGTGGTGACATGTTGAA
1975380 TCATTG
65 TCATTG
*
1975386 TAGTATTAT-GAGGTGACACACCACGTT
1 CAGTATTATAG-GGTGACACACCACGTT
1975413 TTAATTATTA
Statistics
Matches: 136, Mismatches: 28, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
70 3 0.02
71 130 0.96
72 3 0.02
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (70 bp):
CAGTATTATAGGGTGACACACCACGTTGTTAGATATCATTGACATCTTGTGGTGACATGTTGAAT
CATTG
Found at i:1975765 original size:13 final size:13
Alignment explanation
Indices: 1975744--1975776 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1975734 TTCTAAAGCG
*
1975744 TATTGGCGACGCA
1 TATTAGCGACGCA
1975757 TATTAGCGACGCA
1 TATTAGCGACGCA
1975770 TATTAGC
1 TATTAGC
1975777 AATCATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (13 bp):
TATTAGCGACGCA
Found at i:1979437 original size:30 final size:30
Alignment explanation
Indices: 1979367--1979502 Score: 123
Period size: 31 Copynumber: 4.4 Consensus size: 30
1979357 AAAAAGAAAT
* * *
1979367 AAATATTGTTACACGCTATGCATACTAAGTA
1 AAATGTTGTTACATGCTATGCATAC-AAGTC
*
1979398 AAATGTTGTTAAATGCTATGCATACAAGTC
1 AAATGTTGTTACATGCTATGCATACAAGTC
* *
1979428 AAGTGTTGTTACATAG-TAAGCATAACAAGTC
1 AAATGTTGTTACAT-GCTATGCAT-ACAAGTC
* * * *
1979459 AAATATTGTTACATACTGA-GCACACCAAATC
1 AAATGTTGTTACATGCT-ATGCATA-CAAGTC
1979490 AAATGTTGTTACA
1 AAATGTTGTTACA
1979503 CGCCAATGCG
Statistics
Matches: 87, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
30 23 0.26
31 63 0.72
32 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (30 bp):
AAATGTTGTTACATGCTATGCATACAAGTC
Found at i:1980691 original size:35 final size:35
Alignment explanation
Indices: 1980652--1980772 Score: 120
Period size: 35 Copynumber: 3.5 Consensus size: 35
1980642 AGCAGTGCTC
*
1980652 CATTTATTCTAATTGTTTTGTGTGAAGTAGTGTTT
1 CATTTGTTCTAATTGTTTTGTGTGAAGTAGTGTTT
* ** * *
1980687 CATTTGTTTTAATTGTTTTGCATTAAGTAGCG-TT
1 CATTTGTTCTAATTGTTTTGTGTGAAGTAGTGTTT
* * *
1980721 CACTTGTTCTAGTTGTTTTATGTGAAGTAGTGCTTT
1 CATTTGTTCTAATTGTTTTGTGTGAAGTAGTG-TTT
* *
1980757 -ATTTTTTCCAATTGTT
1 CATTTGTTCTAATTGTT
1980773 CTCATTATTC
Statistics
Matches: 66, Mismatches: 18, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
34 26 0.39
35 38 0.58
36 2 0.03
ACGTcount: A:0.19, C:0.09, G:0.18, T:0.54
Consensus pattern (35 bp):
CATTTGTTCTAATTGTTTTGTGTGAAGTAGTGTTT
Found at i:1980749 original size:34 final size:35
Alignment explanation
Indices: 1980658--1980750 Score: 102
Period size: 34 Copynumber: 2.7 Consensus size: 35
1980648 GCTCCATTTA
* * *
1980658 TTCTAATTGTTTTGTGTGAAGTAGTGTTTCATTTG
1 TTCTAATTGTTTTATGTGAAGTAGCGTTTCACTTG
*
1980693 TTTTAATTGTTTTGCAT-T-AAGTAGCG-TTCACTTG
1 TTCTAATTGTTTT--ATGTGAAGTAGCGTTTCACTTG
*
1980727 TTCTAGTTGTTTTATGTGAAGTAG
1 TTCTAATTGTTTTATGTGAAGTAG
1980751 TGCTTTATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
32 2 0.04
33 1 0.02
34 24 0.50
35 19 0.40
36 1 0.02
37 1 0.02
ACGTcount: A:0.19, C:0.08, G:0.22, T:0.52
Consensus pattern (35 bp):
TTCTAATTGTTTTATGTGAAGTAGCGTTTCACTTG
Found at i:1981033 original size:15 final size:15
Alignment explanation
Indices: 1980989--1981036 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
1980979 TCTTAAGTTG
* *
1980989 TAATGCCTTAGGTAG
1 TAATGCCTTAGGCAA
*
1981004 TAATACCTTAGGCAA
1 TAATGCCTTAGGCAA
*
1981019 TAATGCCATAGGCAA
1 TAATGCCTTAGGCAA
1981034 TAA
1 TAA
1981037 GGTGTTATTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.27
Consensus pattern (15 bp):
TAATGCCTTAGGCAA
Found at i:1982393 original size:102 final size:102
Alignment explanation
Indices: 1982129--1982424 Score: 285
Period size: 102 Copynumber: 2.9 Consensus size: 102
1982119 AGTTAATGGC
* * * * *
1982129 ATAACATCATTATAGCCAAATAATGAGCGATAAAG-TTAGTGGCTAAAATATGAATGATGAATTA
1 ATAATATCATTATAGCCAAAAAATAAGCGATAAAGCTT-GTGGCTAAAATAAGAATGATGAACTA
* *
1982193 TGGTAAAAAAAATGAGCAATAAAGCTTACAAGCAATAGAA
65 TGGT-CAAAAAATGAGTAATAAAGCTTAC-AGCAATAGAA
* * * * ** *
1982233 AAAATATCATTAAAGCCAAAATATAAGCGATAAAGCTTGTGGTTGAAGTTAA-AGTGATGAACTA
1 ATAATATCATTATAGCCAAAAAATAAGCGATAAAGCTTGTGGCT-AAAATAAGAATGATGAACTA
* * * *
1982297 TGGTCAAAAAATGAGTGATGAAGCTTAC-G-ACTAGTATT
65 TGGTCAAAAAATGAGTAATAAAGCTTACAGCAATAG-A-A
** * *
1982335 ATAATATCATTATAGAAAAAAAATAAGCGATAAAGCATGCGGCTAAAATAAGAATGATGAACTAT
1 ATAATATCATTATAGCCAAAAAATAAGCGATAAAGCTTGTGGCTAAAATAAGAATGATGAACTAT
* * *
1982400 AGTCAAAGAATGAGTAACAAAGCTT
66 GGTCAAAAAATGAGTAATAAAGCTT
1982425 GTGACTAATA
Statistics
Matches: 153, Mismatches: 34, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
100 4 0.03
101 7 0.05
102 68 0.44
103 20 0.13
104 48 0.31
105 6 0.04
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.25
Consensus pattern (102 bp):
ATAATATCATTATAGCCAAAAAATAAGCGATAAAGCTTGTGGCTAAAATAAGAATGATGAACTAT
GGTCAAAAAATGAGTAATAAAGCTTACAGCAATAGAA
Found at i:1983640 original size:2 final size:2
Alignment explanation
Indices: 1983633--1983661 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1983623 TAAGAGAAAC
1983633 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1983662 AATGTAGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2002566 original size:11 final size:12
Alignment explanation
Indices: 2002546--2002578 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
2002536 CTGATACCCA
2002546 TTTATATAATAT
1 TTTATATAATAT
2002558 TTTAT-TAATA-
1 TTTATATAATAT
2002568 TTTATATAATA
1 TTTATATAATA
2002579 GATAATAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 5 0.25
11 10 0.50
12 5 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TTTATATAATAT
Found at i:2002865 original size:20 final size:21
Alignment explanation
Indices: 2002842--2002890 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
2002832 TATAATTATT
2002842 TATATATATATATACTTT-TA
1 TATATATATATATACTTTCTA
* * *
2002862 TATAAACATATTTACTTTCTA
1 TATATATATATATACTTTCTA
2002883 T-TATATAT
1 TATATATAT
2002891 TTTGTAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (21 bp):
TATATATATATATACTTTCTA
Found at i:2010166 original size:22 final size:22
Alignment explanation
Indices: 2010141--2010183 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2010131 GAAATTGATT
*
2010141 AGACTGGATTTTAAGTATTGCG
1 AGACTAGATTTTAAGTATTGCG
*
2010163 AGACTAGTTTTTAAGTATTGC
1 AGACTAGATTTTAAGTATTGC
2010184 ATGACTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.40
Consensus pattern (22 bp):
AGACTAGATTTTAAGTATTGCG
Found at i:2010267 original size:22 final size:22
Alignment explanation
Indices: 2010208--2010278 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 22
2010198 GCGTAACTAG
* *
2010208 TTTTTAGGCATTACATGA-TTA
1 TTTTTAGGCATTACGTGACTGA
* * *
2010229 GTTATAGGCATTGCGTGACTGA
1 TTTTTAGGCATTACGTGACTGA
* *
2010251 TTTTTAGGTATTACGTGATTGA
1 TTTTTAGGCATTACGTGACTGA
2010273 TTTTTA
1 TTTTTA
2010279 AGCAATGCCT
Statistics
Matches: 39, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
21 14 0.36
22 25 0.64
ACGTcount: A:0.24, C:0.08, G:0.21, T:0.46
Consensus pattern (22 bp):
TTTTTAGGCATTACGTGACTGA
Found at i:2010316 original size:23 final size:23
Alignment explanation
Indices: 2010290--2010394 Score: 115
Period size: 23 Copynumber: 4.6 Consensus size: 23
2010280 GCAATGCCTA
*
2010290 AGTCACATAATGCCTTACTAACT
1 AGTCACACAATGCCTTACTAACT
**
2010313 AGTCATGCAATGCCTTACTAACT
1 AGTCACACAATGCCTTACTAACT
* * *
2010336 AGTCACCCAATGACTTACTAACA
1 AGTCACACAATGCCTTACTAACT
*
2010359 AGTCA-AGCAATGCC-TACCAACT
1 AGTCACA-CAATGCCTTACTAACT
*
2010381 AGTCACGCAATGCC
1 AGTCACACAATGCC
2010395 CAAAGTCAGT
Statistics
Matches: 68, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
22 18 0.26
23 50 0.74
ACGTcount: A:0.34, C:0.30, G:0.12, T:0.24
Consensus pattern (23 bp):
AGTCACACAATGCCTTACTAACT
Found at i:2010357 original size:46 final size:45
Alignment explanation
Indices: 2010298--2010392 Score: 136
Period size: 46 Copynumber: 2.1 Consensus size: 45
2010288 TAAGTCACAT
* * * *
2010298 AATGCCTTACTAACTAGTCATGCAATGCCTTACTAACTAGTCACCC
1 AATGACTTACTAACAAGTCAAGCAATGCC-TACCAACTAGTCACCC
*
2010344 AATGACTTACTAACAAGTCAAGCAATGCCTACCAACTAGTCACGC
1 AATGACTTACTAACAAGTCAAGCAATGCCTACCAACTAGTCACCC
2010389 AATG
1 AATG
2010393 CCCAAAGTCA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 18 0.41
46 26 0.59
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.24
Consensus pattern (45 bp):
AATGACTTACTAACAAGTCAAGCAATGCCTACCAACTAGTCACCC
Found at i:2010440 original size:21 final size:21
Alignment explanation
Indices: 2010387--2010440 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
2010377 AACTAGTCAC
* *
2010387 GCAATGCCCAAAGTCAGTTAT
1 GCAATGCCTAAAGTAAGTTAT
**
2010408 GCAATGTATAAAGTAAGTTAT
1 GCAATGCCTAAAGTAAGTTAT
2010429 GCAATGCCTAAA
1 GCAATGCCTAAA
2010441 AACTAGTCAC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.26
Consensus pattern (21 bp):
GCAATGCCTAAAGTAAGTTAT
Found at i:2013667 original size:29 final size:29
Alignment explanation
Indices: 2013633--2013688 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
2013623 ATTTTAAACA
*
2013633 ATTTAAATAAGTTT-TTTATTTTCTATTAT
1 ATTTAAATAAGTTTATATATTTT-TATTAT
*
2013662 ATTTAATTAAGTTTATATATTTTTATT
1 ATTTAAATAAGTTTATATATTTTTATT
2013689 TTGGGTGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (29 bp):
ATTTAAATAAGTTTATATATTTTTATTAT
Found at i:2015249 original size:15 final size:16
Alignment explanation
Indices: 2015229--2015258 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2015219 CTGTTATGTA
2015229 GATTTT-ATTTTTAAT
1 GATTTTAATTTTTAAT
2015244 GATTTTAATTTTTAA
1 GATTTTAATTTTTAA
2015259 AAATTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (16 bp):
GATTTTAATTTTTAAT
Found at i:2016547 original size:32 final size:33
Alignment explanation
Indices: 2016482--2016547 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
2016472 AAACTAATGG
* *
2016482 ATAAAGTAAATATAAAGTAATGATGCCATGCAT
1 ATAAAGTAAATATAAACTAATGAAGCCATGCAT
* *
2016515 ATAAAGTAAATATATACTTAT-AAGCCATGCAT
1 ATAAAGTAAATATAAACTAATGAAGCCATGCAT
2016547 A
1 A
2016548 GTCAAGATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 11 0.38
33 18 0.62
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.29
Consensus pattern (33 bp):
ATAAAGTAAATATAAACTAATGAAGCCATGCAT
Found at i:2025687 original size:2 final size:2
Alignment explanation
Indices: 2025676--2025714 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
2025666 CTTTAGAGTT
*
2025676 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2025715 AATGAGTCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2027033 original size:18 final size:18
Alignment explanation
Indices: 2027012--2027046 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2027002 AAAAAAGAAA
*
2027012 AAGAAAAAAAGAAAGGGT
1 AAGAAAAAAACAAAGGGT
*
2027030 AAGAGAAAAACAAAGGG
1 AAGAAAAAAACAAAGGG
2027047 CGATAGTGGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.03, G:0.29, T:0.03
Consensus pattern (18 bp):
AAGAAAAAAACAAAGGGT
Found at i:2030145 original size:5 final size:5
Alignment explanation
Indices: 2030135--2030174 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
2030125 AAGAGAATAC
* *
2030135 TATAA TATAA TATAA TATAA TCTAA TCTAA TATATA TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATA-A TATA
2030175 TATTGATACA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 27 0.84
6 5 0.16
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:2031081 original size:4 final size:4
Alignment explanation
Indices: 2031074--2031098 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2031064 TATATAGCAT
2031074 TCCA TCCA TCCA TCCA TCCA TCCA T
1 TCCA TCCA TCCA TCCA TCCA TCCA T
2031099 ATAGACATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.48, G:0.00, T:0.28
Consensus pattern (4 bp):
TCCA
Found at i:2039799 original size:14 final size:15
Alignment explanation
Indices: 2039768--2039806 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
2039758 TCATAAGTAT
*
2039768 ATATAAATAGTTTTA
1 ATATAAATAGTTTGA
2039783 ATATAAA-AGTTTGA
1 ATATAAATAGTTTGA
2039797 ATAATAAATA
1 AT-ATAAATA
2039807 ATTAAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 8 0.38
15 12 0.57
16 1 0.05
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (15 bp):
ATATAAATAGTTTGA
Found at i:2045905 original size:9 final size:9
Alignment explanation
Indices: 2045893--2045920 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
2045883 ATTTTTTTAA
2045893 AAAAAAAAT
1 AAAAAAAAT
2045902 AAAAAAAAT
1 AAAAAAAAT
2045911 AAAAAAAAT
1 AAAAAAAAT
2045920 A
1 A
2045921 TAATTGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:2049852 original size:7 final size:7
Alignment explanation
Indices: 2049842--2049866 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2049832 ACTCTCAACC
2049842 CTCCTAT
1 CTCCTAT
2049849 CTCCTAT
1 CTCCTAT
2049856 CTCCTAT
1 CTCCTAT
2049863 CTCC
1 CTCC
2049867 GTCTACCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.48, G:0.00, T:0.40
Consensus pattern (7 bp):
CTCCTAT
Found at i:2052531 original size:27 final size:26
Alignment explanation
Indices: 2052501--2052583 Score: 78
Period size: 27 Copynumber: 3.1 Consensus size: 26
2052491 CAAAAGTATC
2052501 TGGATATCTTTATTCATCA-AAGGTGGA
1 TGGATA-CTTTATTCATCAGAA-GTGGA
* *
2052528 TGGATACTTTTACTCGTCAGAAGTGGA
1 TGGATAC-TTTATTCATCAGAAGTGGA
* * *
2052555 TAGATACCTTTATTCATTAGAAGTAGA
1 TGGATA-CTTTATTCATCAGAAGTGGA
2052582 TG
1 TG
2052584 AACAACTTTA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.02
27 41 0.91
28 3 0.07
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.36
Consensus pattern (26 bp):
TGGATACTTTATTCATCAGAAGTGGA
Found at i:2052619 original size:27 final size:27
Alignment explanation
Indices: 2052546--2052624 Score: 76
Period size: 27 Copynumber: 2.9 Consensus size: 27
2052536 TTTACTCGTC
* *
2052546 AGAAGTGGATAGATACCTTTA-TTCATT
1 AGAAGTGAATAGATACCTTTACTT-ACT
2052573 AGAAGT-AGAT-GA-ACAACTTTACTTACT
1 AGAAGTGA-ATAGATAC--CTTTACTTACT
2052600 AGAAGTGAATAGATACCTTTACTTA
1 AGAAGTGAATAGATACCTTTACTTA
2052625 TAAGAACTAG
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
25 2 0.05
26 2 0.05
27 32 0.74
28 5 0.12
29 2 0.05
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (27 bp):
AGAAGTGAATAGATACCTTTACTTACT
Found at i:2052648 original size:54 final size:54
Alignment explanation
Indices: 2052545--2052663 Score: 136
Period size: 54 Copynumber: 2.2 Consensus size: 54
2052535 TTTTACTCGT
* * * *
2052545 CAGAAGTGGATAGATACCTTTATTCATTAGAAGTAGATGAACAACTTTACTTAC
1 CAGAAGTGAATAGATACCTTTATTCATAAGAACTAGATGAACAACTTTACCTAC
*
2052599 TAGAAGTGAATAGATACCTTTACTT-ATAAGAACTAGATGGATAC-A-TTTACCTAC
1 CAGAAGTGAATAGATACCTTTA-TTCATAAGAACTAGAT-GA-ACAACTTTACCTAC
*
2052653 CAAAAGTGAAT
1 CAGAAGTGAAT
2052664 GAATACATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
54 48 0.87
55 5 0.09
56 2 0.04
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (54 bp):
CAGAAGTGAATAGATACCTTTATTCATAAGAACTAGATGAACAACTTTACCTAC
Found at i:2052669 original size:27 final size:27
Alignment explanation
Indices: 2052639--2052711 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
2052629 AACTAGATGG
2052639 ATACATTTACCTACCAAAAGTGAATGA
1 ATACATTTACCTACCAAAAGTGAATGA
* *
2052666 ATACATTTACCCACCAAAAGTGAATGG
1 ATACATTTACCTACCAAAAGTGAATGA
** *
2052693 ATATTTTTACCTATCAAAA
1 ATACATTTACCTACCAAAA
2052712 TTTGATAAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (27 bp):
ATACATTTACCTACCAAAAGTGAATGA
Found at i:2055202 original size:19 final size:19
Alignment explanation
Indices: 2055153--2055202 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
2055143 AAATGATTAG
* *
2055153 TCAATGTGGAAGATAAAAA
1 TCAAGGTGGAATATAAAAA
2055172 TCAAGGTGGAATATAAAAA
1 TCAAGGTGGAATATAAAAA
2055191 TCAAGGTGGAAT
1 TCAAGGTGGAAT
2055203 TTACTTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.48, C:0.06, G:0.24, T:0.22
Consensus pattern (19 bp):
TCAAGGTGGAATATAAAAA
Found at i:2061662 original size:29 final size:29
Alignment explanation
Indices: 2061600--2061727 Score: 87
Period size: 29 Copynumber: 4.7 Consensus size: 29
2061590 ATGTTATATG
* *
2061600 GTAAAAAAAAAGTTATTA-TA-A-GGTAT
1 GTAAAAAAAAAATTATTATTACATGCTAT
2061626 GTTGAAAAAAAAAATTATTATTACATGCTAT
1 G-T-AAAAAAAAAATTATTATTACATGCTAT
*
2061657 GT--AAAAAAAA-TGTTA-TAC-T-C-AT
1 GTAAAAAAAAAATTATTATTACATGCTAT
* * * *
2061679 GTTAAAAAAATATTATTGTTACATGCCAT
1 GTAAAAAAAAAATTATTATTACATGCTAT
* *
2061708 GTTAAAAAAAAATTACTATT
1 GTAAAAAAAAAATTATTATT
2061728 GCACATCATG
Statistics
Matches: 81, Mismatches: 9, Indels: 21
0.73 0.08 0.19
Matches are distributed among these distances:
22 4 0.05
23 1 0.01
24 8 0.10
25 6 0.07
26 8 0.10
27 10 0.12
28 16 0.20
29 21 0.26
30 2 0.02
31 5 0.06
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.34
Consensus pattern (29 bp):
GTAAAAAAAAAATTATTATTACATGCTAT
Found at i:2061737 original size:29 final size:27
Alignment explanation
Indices: 2061631--2061738 Score: 75
Period size: 29 Copynumber: 4.0 Consensus size: 27
2061621 GGTATGTTGA
*
2061631 AAAAAAAAATTATTATTACATGCTATG-T
1 AAAAAAAAATTACTATTACAT-C-ATGTT
2061659 -AAAAAAAATGT--TA-TAC-TCATGTT
1 AAAAAAAAAT-TACTATTACATCATGTT
* * *
2061682 AAAAAAATATTATTGTTACATGCCATGTT
1 AAAAAAAAATTACTATTACAT--CATGTT
2061711 AAAAAAAAATTACTATTGCACATCATGT
1 AAAAAAAAATTACTATT--ACATCATGT
2061739 ACAAAAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 21
0.71 0.06 0.23
Matches are distributed among these distances:
22 3 0.05
23 3 0.05
24 9 0.14
25 4 0.06
26 5 0.08
27 10 0.16
28 1 0.02
29 25 0.39
31 4 0.06
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.34
Consensus pattern (27 bp):
AAAAAAAAATTACTATTACATCATGTT
Found at i:2061826 original size:30 final size:30
Alignment explanation
Indices: 2061667--2061838 Score: 85
Period size: 29 Copynumber: 6.1 Consensus size: 30
2061657 GTAAAAAAAA
*
2061667 TGTTATAC-TCATG-TTAAAAAAATATTAT
1 TGTTACACATCATGTTTAAAAAAATATTAT
*** * *
2061695 TGTTACATGCCATG-TTAAAAAAAAATTAC
1 TGTTACACATCATGTTTAAAAAAATATTAT
* * *
2061724 TATTGCACATCATG--TACAAAAATA-TA-
1 TGTTACACATCATGTTTAAAAAAATATTAT
* *** * *
2061750 --TTAGACGGGATGTTAAAAAAAATAATAT
1 TGTTACACATCATGTTTAAAAAAATATTAT
* *
2061778 TGTTACATATCAT-ATTAAAAAAATATTAT
1 TGTTACACATCATGTTTAAAAAAATATTAT
* * * *
2061807 TGTTACACGTTATGTTTAAAAAATTTTTAT
1 TGTTACACATCATGTTTAAAAAAATATTAT
2061837 TG
1 TG
2061839 CGTTTAAAAT
Statistics
Matches: 103, Mismatches: 33, Indels: 14
0.69 0.22 0.09
Matches are distributed among these distances:
24 7 0.07
26 8 0.08
27 4 0.04
28 14 0.14
29 49 0.48
30 21 0.20
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.38
Consensus pattern (30 bp):
TGTTACACATCATGTTTAAAAAAATATTAT
Found at i:2062397 original size:10 final size:10
Alignment explanation
Indices: 2062382--2062412 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2062372 TTTATCAAAT
2062382 TATAATTAAA
1 TATAATTAAA
2062392 TATAATTAAA
1 TATAATTAAA
*
2062402 AATAATTAAA
1 TATAATTAAA
2062412 T
1 T
2062413 TTATTTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
TATAATTAAA
Found at i:2062438 original size:15 final size:16
Alignment explanation
Indices: 2062400--2062458 Score: 52
Period size: 15 Copynumber: 3.8 Consensus size: 16
2062390 AATATAATTA
2062400 AAAATAATTAAATTTATT
1 AAAATAATT--ATTTATT
**
2062418 TTAATAATTATTT-TT
1 AAAATAATTATTTATT
*
2062433 AAAATACTT-TTTATT
1 AAAATAATTATTTATT
2062448 AAAA-AATTATT
1 AAAATAATTATT
2062459 CATCACAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
14 6 0.18
15 16 0.48
16 4 0.12
18 7 0.21
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
AAAATAATTATTTATT
Found at i:2063257 original size:35 final size:35
Alignment explanation
Indices: 2063211--2063284 Score: 148
Period size: 35 Copynumber: 2.1 Consensus size: 35
2063201 TATTCGCACG
2063211 GCCATCAGAACCGCCATTGCAAGAGAGCGTAGAAT
1 GCCATCAGAACCGCCATTGCAAGAGAGCGTAGAAT
2063246 GCCATCAGAACCGCCATTGCAAGAGAGCGTAGAAT
1 GCCATCAGAACCGCCATTGCAAGAGAGCGTAGAAT
2063281 GCCA
1 GCCA
2063285 GCATCCCTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.34, C:0.27, G:0.26, T:0.14
Consensus pattern (35 bp):
GCCATCAGAACCGCCATTGCAAGAGAGCGTAGAAT
Found at i:2070302 original size:30 final size:29
Alignment explanation
Indices: 2070256--2070414 Score: 155
Period size: 30 Copynumber: 5.4 Consensus size: 29
2070246 TTATATTAAT
*
2070256 TTAAGAC-AACTTATTTTATCTTGTCTAAA
1 TTAAGACAAACATATTTT-TCTTGTCTAAA
* * * *
2070285 TTGAGACAAATATA-TTTTCTTATCTACA
1 TTAAGACAAACATATTTTTCTTGTCTAAA
* * *
2070313 TTAAGACCAAAAATATTTTTCTTATATTAAA
1 TTAAGA-CAAACATATTTTTCTTGT-CTAAA
2070344 TTAAGACAAACATATTTTCTCTTGTCTAAA
1 TTAAGACAAACATATTTT-TCTTGTCTAAA
* *
2070374 TTAAGACCAAACAT-GTTTTATTGTCTAAA
1 TTAAGA-CAAACATATTTTTCTTGTCTAAA
2070403 -TAAGACAAACAT
1 TTAAGACAAACAT
2070415 GTTAAAGCTG
Statistics
Matches: 110, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
27 7 0.06
28 19 0.17
29 26 0.24
30 37 0.34
31 21 0.19
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.40
Consensus pattern (29 bp):
TTAAGACAAACATATTTTTCTTGTCTAAA
Found at i:2070403 original size:59 final size:58
Alignment explanation
Indices: 2070276--2070414 Score: 156
Period size: 61 Copynumber: 2.4 Consensus size: 58
2070266 TTATTTTATC
* * * * *
2070276 TTGTCTAAATTGAGACAAATATATTTTCTTATCTACATTAAGACCAAAAATATTTTTC
1 TTGTCTAAATTAAGACAAACATATTTTCTTATCTAAATTAAGACCAAAAATAGTTTTA
* * * *
2070334 TTATATTAAATTAAGACAAACATATTTTCTCTTGTCTAAATTAAGACCAAACAT-GTTTTA
1 TTGT-CTAAATTAAGACAAACATA-TTT-TCTTATCTAAATTAAGACCAAAAATAGTTTTA
2070394 TTGTCTAAA-TAAGACAAACAT
1 TTGTCTAAATTAAGACAAACAT
2070415 GTTAAAGCTG
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
58 15 0.22
59 20 0.30
60 10 0.15
61 22 0.33
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (58 bp):
TTGTCTAAATTAAGACAAACATATTTTCTTATCTAAATTAAGACCAAAAATAGTTTTA
Found at i:2070407 original size:89 final size:88
Alignment explanation
Indices: 2070246--2070408 Score: 220
Period size: 89 Copynumber: 1.8 Consensus size: 88
2070236 CCTCTGAACA
* * * * *
2070246 TTATATTAATTTAAGACAACTTATTTTATCTTGTCTAAATTGAGACAAATATATTTTCTTATCTA
1 TTATATTAAATTAAGACAACATATTTTATCTTGTCTAAATTAAGACAAACATATTTTATTATCTA
*
2070311 CATTAAGACCAAAAATATTTTTC
66 CAATAAGACCAAAAATATTTTTC
* * *
2070334 TTATATTAAATTAAGACAAACATATTTTCTCTTGTCTAAATTAAGACCAAACATGTTTTATTGTC
1 TTATATTAAATTAAGAC-AACATATTTTATCTTGTCTAAATTAAGA-CAAACATATTTTATTATC
2070399 TA-AATAAGAC
64 TACAATAAGAC
2070409 AAACATGTTA
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
88 16 0.25
89 32 0.50
90 16 0.25
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.42
Consensus pattern (88 bp):
TTATATTAAATTAAGACAACATATTTTATCTTGTCTAAATTAAGACAAACATATTTTATTATCTA
CAATAAGACCAAAAATATTTTTC
Found at i:2079272 original size:23 final size:23
Alignment explanation
Indices: 2079222--2079272 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
2079212 GATTAATTCA
2079222 CAATGACCTACCAACCAATAATG
1 CAATGACCTACCAACCAATAATG
* * * *
2079245 TAATGACCTATCAACCAGTCATG
1 CAATGACCTACCAACCAATAATG
2079268 CAATG
1 CAATG
2079273 CTTAACCCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.27, G:0.12, T:0.22
Consensus pattern (23 bp):
CAATGACCTACCAACCAATAATG
Found at i:2085018 original size:23 final size:23
Alignment explanation
Indices: 2084992--2085036 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2084982 TCAGCCTTCG
*
2084992 TTAAGTTTT-TTTTTTTTGAATTT
1 TTAAGTTTTAATTTTTTT-AATTT
2085015 TTAAGTTTTAATTTTTTTAATT
1 TTAAGTTTTAATTTTTTTAATT
2085037 GAATGGGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71
Consensus pattern (23 bp):
TTAAGTTTTAATTTTTTTAATTT
Found at i:2085829 original size:33 final size:36
Alignment explanation
Indices: 2085792--2085859 Score: 97
Period size: 33 Copynumber: 2.0 Consensus size: 36
2085782 CACACCTATA
2085792 AAAATTTTA-AAATTT-TTCTAACAA-AATTTTTTT
1 AAAATTTTATAAATTTGTTCTAACAATAATTTTTTT
* *
2085825 AAAATTTTATAATTTTGTTCTTACAATAATTTTTT
1 AAAATTTTATAAATTTGTTCTAACAATAATTTTTT
2085860 ATTAAGTGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 9 0.30
34 5 0.17
35 8 0.27
36 8 0.27
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.54
Consensus pattern (36 bp):
AAAATTTTATAAATTTGTTCTAACAATAATTTTTTT
Found at i:2086128 original size:49 final size:49
Alignment explanation
Indices: 2086056--2086153 Score: 151
Period size: 49 Copynumber: 2.0 Consensus size: 49
2086046 TTTTTACTTG
*
2086056 CTAGCATTCTTTGTACAATAAACCTCTAGTCAGAAACTCAATTTTCATA
1 CTAGCATTCTTTGTACAATAAACCTCTACTCAGAAACTCAATTTTCATA
* * * *
2086105 CTAGCATTTTTTGTGCAATAAACCTCTACTCAGTAACTTAATTTTCATA
1 CTAGCATTCTTTGTACAATAAACCTCTACTCAGAAACTCAATTTTCATA
2086154 TCATGATAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (49 bp):
CTAGCATTCTTTGTACAATAAACCTCTACTCAGAAACTCAATTTTCATA
Found at i:2092370 original size:19 final size:21
Alignment explanation
Indices: 2092345--2092394 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 21
2092335 AGGGACAAGA
*
2092345 ATAAATATTTATGA-ATTTTT
1 ATAAATATTTATAAGATTTTT
2092365 -TAAATATTT-TAAGATTTTT
1 ATAAATATTTATAAGATTTTT
2092384 ATAAATATTTA
1 ATAAATATTTA
2092395 AAAAGTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.08
19 15 0.58
20 9 0.35
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (21 bp):
ATAAATATTTATAAGATTTTT
Found at i:2092376 original size:9 final size:10
Alignment explanation
Indices: 2092345--2092394 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
2092335 AGGGACAAGA
2092345 ATAAATATTT
1 ATAAATATTT
*
2092355 ATGAAT-TTT
1 ATAAATATTT
*
2092364 TTAAATATTT
1 ATAAATATTT
*
2092374 -TAAGATTTTT
1 ATAA-ATATTT
2092384 ATAAATATTT
1 ATAAATATTT
2092394 A
1 A
2092395 AAAAGTTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
9 10 0.31
10 19 0.59
11 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (10 bp):
ATAAATATTT
Found at i:2092395 original size:19 final size:20
Alignment explanation
Indices: 2092345--2092405 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
2092335 AGGGACAAGA
*
2092345 ATAAATATTTATGAATTTTT
1 ATAAATATTTAAGAATTTTT
2092365 -TAAATATTTTAAG-ATTTTT
1 ATAAATA-TTTAAGAATTTTT
* *
2092384 ATAAATATTTAAAAAGTTTT
1 ATAAATATTTAAGAATTTTT
2092404 AT
1 AT
2092406 GTTTTTCTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
19 17 0.49
20 18 0.51
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (20 bp):
ATAAATATTTAAGAATTTTT
Found at i:2094471 original size:23 final size:23
Alignment explanation
Indices: 2094445--2094488 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2094435 ACAGTAAGTG
*
2094445 AGTCATGTAATCCCATATCAAAA
1 AGTCATGCAATCCCATATCAAAA
**
2094468 AGTCATGCAATTTCATATCAA
1 AGTCATGCAATCCCATATCAA
2094489 CTAGTCACAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (23 bp):
AGTCATGCAATCCCATATCAAAA
Found at i:2094577 original size:69 final size:67
Alignment explanation
Indices: 2094482--2094850 Score: 296
Period size: 69 Copynumber: 5.4 Consensus size: 67
2094472 ATGCAATTTC
* * * * * *
2094482 ATATCAACTAGTCACACGACTATATAATAACTAGTAACGTCACTTCATATTTACTACTAACCTGA
1 ATATCAACTAGTCACGCGATTCTATAATAACTAGTAACG-CACTCCATATTTACTACTCACCTAA
2094547 TTGA
65 TT-A
* * * *
2094551 ATATCAACTAGTCACGTGCTTCTATAATAACTAGTCACACG-ACTCTATATGTACTACTCACAC-
1 ATATCAACTAGTCACGCGATTCTATAATAACTAGT-A-ACGCACTCCATATTTACTACTCAC-CT
*
2094614 AATTTT
63 AA-TTA
* * * * * *
2094620 ATAAT-AACTAGTAACACGATTCCATAATAACTAGTAACACCAGTCCATATTTACTACTTACGCT
1 AT-ATCAACTAGTCACGCGATTCTATAATAACTAGTAAC-GCACTCCATATTTACTACTCAC-CT
*
2094684 ACTTA
63 AATTA
* * ** * * *
2094689 ATATCAACTAGTCATGCGATTCCATAATAGTTAGTCATGCGACTCCATATTTACTACTCACGTAA
1 ATATCAACTAGTCACGCGATTCTATAATAACTAGTAACGC-ACTCCATATTTACTACTCACCTAA
*
2094754 TTTT
65 -TTA
* * * *
2094758 ATAAT-AACTAGTTATGAGATTCTATAATAACTAGTAACGCCACTCCATATTTACTACTCACGTG
1 AT-ATCAACTAGTCACGCGATTCTATAATAACTAGTAACG-CACTCCATATTTACTACTCACCT-
*
2094822 ACTTA
63 AATTA
*
2094827 ATATTAACTAGTCACGCGATTCTA
1 ATATCAACTAGTCACGCGATTCTA
2094851 ATCTTAACAG
Statistics
Matches: 236, Mismatches: 49, Indels: 30
0.75 0.16 0.10
Matches are distributed among these distances:
67 2 0.01
68 8 0.03
69 212 0.90
70 11 0.05
71 3 0.01
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.33
Consensus pattern (67 bp):
ATATCAACTAGTCACGCGATTCTATAATAACTAGTAACGCACTCCATATTTACTACTCACCTAAT
TA
Found at i:2094597 original size:23 final size:23
Alignment explanation
Indices: 2094570--2094659 Score: 92
Period size: 23 Copynumber: 3.9 Consensus size: 23
2094560 AGTCACGTGC
*
2094570 TTCTATAATAACTAGTCACACGA
1 TTCTATAATAACTAGTAACACGA
* * * * *
2094593 CTCTAT-ATGTACTACTCACACAA
1 TTCTATAAT-AACTAGTAACACGA
*
2094616 TTTTATAATAACTAGTAACACGA
1 TTCTATAATAACTAGTAACACGA
*
2094639 TTCCATAATAACTAGTAACAC
1 TTCTATAATAACTAGTAACAC
2094660 CAGTCCATAT
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
22 2 0.04
23 49 0.92
24 2 0.04
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.31
Consensus pattern (23 bp):
TTCTATAATAACTAGTAACACGA
Found at i:2094675 original size:23 final size:23
Alignment explanation
Indices: 2094620--2094668 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
2094610 ACACAATTTT
* *
2094620 ATAATAACTAGTAACACGATTCC
1 ATAATAACTAGTAACACCAGTCC
2094643 ATAATAACTAGTAACACCAGTCC
1 ATAATAACTAGTAACACCAGTCC
2094666 ATA
1 ATA
2094669 TTTACTACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.45, C:0.22, G:0.08, T:0.24
Consensus pattern (23 bp):
ATAATAACTAGTAACACCAGTCC
Found at i:2094693 original size:138 final size:139
Alignment explanation
Indices: 2094487--2094848 Score: 446
Period size: 138 Copynumber: 2.6 Consensus size: 139
2094477 ATTTCATATC
* * * * *
2094487 AACTAGTCACACGACTATATAATAACTAGTAACGTCACTTCATATTTACTACTAAC-CTGA-TTG
1 AACTAGTAACACGATTCTATAATAACTAGTAACGCCACTCCATATTTACTACTAACGCTGACTT-
* * * *
2094550 AATATCAACTAGTCACGTGCTTCTATAATAACTAGTCACACGACTCTATATGTACTACTCACACA
65 AATATCAACTAGTCACGCGATTCCATAATAACTAGTCACACGACTCCATATGTACTACTCACACA
2094615 ATTTTATAAT
130 ATTTTATAAT
* * * *
2094625 AACTAGTAACACGATTCCATAATAACTAGTAACACCAGTCCATATTTACTACTTACGCT-ACTTA
1 AACTAGTAACACGATTCTATAATAACTAGTAACGCCACTCCATATTTACTACTAACGCTGACTTA
* ** ** * **
2094689 ATATCAACTAGTCATGCGATTCCATAATAGTTAGTCATGCGACTCCATATTTACTACTCACGTAA
66 ATATCAACTAGTCACGCGATTCCATAATAACTAGTCACACGACTCCATATGTACTACTCACACAA
2094754 TTTTATAAT
131 TTTTATAAT
** *
2094763 AACTAGTTATGA-GATTCTATAATAACTAGTAACGCCACTCCATATTTACTACTCACG-TGACTT
1 AACTAG-TAACACGATTCTATAATAACTAGTAACGCCACTCCATATTTACTACTAACGCTGACTT
*
2094826 AATATTAACTAGTCACGCGATTC
65 AATATCAACTAGTCACGCGATTC
2094849 TAATCTTAAC
Statistics
Matches: 191, Mismatches: 29, Indels: 8
0.84 0.13 0.04
Matches are distributed among these distances:
137 1 0.01
138 183 0.96
139 7 0.04
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.33
Consensus pattern (139 bp):
AACTAGTAACACGATTCTATAATAACTAGTAACGCCACTCCATATTTACTACTAACGCTGACTTA
ATATCAACTAGTCACGCGATTCCATAATAACTAGTCACACGACTCCATATGTACTACTCACACAA
TTTTATAAT
Found at i:2094894 original size:23 final size:23
Alignment explanation
Indices: 2094868--2094921 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
2094858 CAGCTCAAGT
*
2094868 GATTTCAAATTTATTAGTCACAC
1 GATTTCAAATCTATTAGTCACAC
* *
2094891 GATTCCAAATCTATTAGTCACGC
1 GATTTCAAATCTATTAGTCACAC
*
2094914 GGTTTCAA
1 GATTTCAA
2094922 CTAGGCACCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.35
Consensus pattern (23 bp):
GATTTCAAATCTATTAGTCACAC
Found at i:2095298 original size:26 final size:26
Alignment explanation
Indices: 2095251--2095318 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
2095241 TGCCTTTCTC
*
2095251 TTTGTTAAATGATGCAAAAAAGAAAAA
1 TTTG-TAAATGATACAAAAAAGAAAAA
** *
2095278 TTTGTAAATGATACACCAAAGAATAA
1 TTTGTAAATGATACAAAAAAGAAAAA
*
2095304 TTAG-AAGATGATACA
1 TTTGTAA-ATGATACA
2095319 GAACAATGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
25 2 0.06
26 29 0.83
27 4 0.11
ACGTcount: A:0.51, C:0.07, G:0.15, T:0.26
Consensus pattern (26 bp):
TTTGTAAATGATACAAAAAAGAAAAA
Found at i:2099413 original size:94 final size:94
Alignment explanation
Indices: 2099193--2099385 Score: 266
Period size: 94 Copynumber: 2.1 Consensus size: 94
2099183 CATCAATCAC
* * * * * *
2099193 TCATGCAA-AGACCTATCAACCAATCACGTAATATTAAACCCTAATGCAAGCACGCAGAGCCTAA
1 TCATGCAATAG-CCTATCAACTAGTCACGCAATGTTAAACCCTAATGCAAGCACACACAGCCTAA
*
2099257 GTGACGGCATGCCTAAATCCAGTTATCTTG
65 GTGACGCCATGCCTAAATCCAGTTATCTTG
*
2099287 TCATGCAATAGCCTATCAACTAGTCACGCAATGTTAAACCCTAATGCAATCACACACA-CCTTAA
1 TCATGCAATAGCCTATCAACTAGTCACGCAATGTTAAACCCTAATGCAAGCACACACAGCC-TAA
2099351 GTGACGCCATGCCTAAATCCAGTTAT-TCTG
65 GTGACGCCATGCCTAAATCCAGTTATCT-TG
2099381 TCATG
1 TCATG
2099386 TAATGATTTA
Statistics
Matches: 88, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
93 3 0.03
94 83 0.94
95 2 0.02
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (94 bp):
TCATGCAATAGCCTATCAACTAGTCACGCAATGTTAAACCCTAATGCAAGCACACACAGCCTAAG
TGACGCCATGCCTAAATCCAGTTATCTTG
Found at i:2115350 original size:87 final size:87
Alignment explanation
Indices: 2115204--2115379 Score: 316
Period size: 87 Copynumber: 2.0 Consensus size: 87
2115194 ATGATGGGAA
* *
2115204 GAGCTCAAAGGTTGTTCTAACTTTAAGCTCTGGTTGTCTGCTAGATCAAGACATGAATGCACAGA
1 GAGCTCAAAGGTTGTTCCAACTTTAAGCTCTGGTTGTCTGCCAGATCAAGACATGAATGCACAGA
2115269 ATCAAAATAACAGTGACATGCT
66 ATCAAAATAACAGTGACATGCT
*
2115291 GAGCTCAAAGGTTGTTCCAACTTTAAGCTCTGGTTGTCTGCCAGATCAAGACTTGAATGCACAGA
1 GAGCTCAAAGGTTGTTCCAACTTTAAGCTCTGGTTGTCTGCCAGATCAAGACATGAATGCACAGA
*
2115356 ATCAAAATAATAGTGACATGCT
66 ATCAAAATAACAGTGACATGCT
2115378 GA
1 GA
2115380 TTAACCATGT
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 85 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (87 bp):
GAGCTCAAAGGTTGTTCCAACTTTAAGCTCTGGTTGTCTGCCAGATCAAGACATGAATGCACAGA
ATCAAAATAACAGTGACATGCT
Found at i:2117383 original size:15 final size:14
Alignment explanation
Indices: 2117346--2117383 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
2117336 TTTATGATAA
2117346 TTTTTTAAATATAT
1 TTTTTTAAATATAT
*
2117360 TTTTATAAATTATAT
1 TTTTTTAAA-TATAT
2117375 TTTTTTAAA
1 TTTTTTAAA
2117384 AATAATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTTTAAATATAT
Found at i:2117392 original size:14 final size:14
Alignment explanation
Indices: 2117342--2117392 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
2117332 ACTTTTTATG
2117342 ATAATTTTTTAAAT
1 ATAATTTTTTAAAT
2117356 AT-ATTTTTATAAATT
1 ATAATTTTT-TAAA-T
* *
2117371 ATATTTTTTTAAAA
1 ATAATTTTTTAAAT
2117385 ATAATTTT
1 ATAATTTT
2117393 ATTGACACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 6 0.19
14 13 0.42
15 7 0.23
16 5 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATAATTTTTTAAAT
Found at i:2117501 original size:25 final size:25
Alignment explanation
Indices: 2117473--2117523 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
2117463 GCTTATGCCA
* * *
2117473 AAAGGAGAATATATACAATTACGTG
1 AAAGGAGAACATACACAATCACGTG
2117498 AAAGGAGAACATACACAATCACGTG
1 AAAGGAGAACATACACAATCACGTG
2117523 A
1 A
2117524 GGAGACTGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.49, C:0.14, G:0.20, T:0.18
Consensus pattern (25 bp):
AAAGGAGAACATACACAATCACGTG
Found at i:2125628 original size:59 final size:59
Alignment explanation
Indices: 2125564--2125686 Score: 167
Period size: 59 Copynumber: 2.1 Consensus size: 59
2125554 AGCGACCTCT
* * * *
2125564 TTCATATCCATGATCATAATTATTAAATGATGTTGTATTCACTATAGAGAAT-GAATGGA
1 TTCATAACCATGACCATAATTATTAAATGATGTCGCATTCACTATAGAGAATAGAAT-GA
* * *
2125623 TTCATAACCATGACCATAATTATTAAATGATGTCGCATTCATTTTAGGGAATAGAATGA
1 TTCATAACCATGACCATAATTATTAAATGATGTCGCATTCACTATAGAGAATAGAATGA
2125682 TTCAT
1 TTCAT
2125687 GATTTTTGTT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 52 0.93
60 4 0.07
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (59 bp):
TTCATAACCATGACCATAATTATTAAATGATGTCGCATTCACTATAGAGAATAGAATGA
Found at i:2126864 original size:2 final size:2
Alignment explanation
Indices: 2126822--2126848 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2126812 TTTCGCTATC
2126822 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2126849 AGTATAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2127169 original size:706 final size:699
Alignment explanation
Indices: 2125764--2127169 Score: 2282
Period size: 699 Copynumber: 2.0 Consensus size: 699
2125754 AGTAAATTTA
2125764 CTTTCAATCAAGAGACAAAATATAATATATACTACATGATAGCAAAATTCATATTAAAGTTAATT
1 CTTTCAATCAAGAGACAAAATATAATATATACTACATGATAGCAAAATTCATATTAAAGTTAATT
* *
2125829 TTTATGAAATAAAATATTAAAGAGATATCAAGTTACTTACCTAATTTGCTATAACAAAAAATTAA
66 TTTATGAAATAAAATATTAAAGAGATATCAAATTACTTACCTAATTTGCTACAACAAAAAATTAA
*
2125894 AGACCAACCATCGAAATTTTTTTAAAACTTGAGGATGATGAAAACAAAATAATAATAACACTTAC
131 AGACCAACCATCGAAATCTTTTTAAAACTTGAGGATGATGAAAACAAAATAATAATAACACTTAC
** * * * * * *
2125959 TTAATTTGCTAAAATCAGAAATTAAAACCCAATTATTGAAATTCTTATGAAGCTTGAACGGTGAT
196 TTAAAATGCAAAAATCAAAAATCAAAACCCAATTATTGAAATCCTTATGAAACTTGAAAGGTGAT
* *
2126024 AAAAACAAAATAATACTTGATTCTGCTTCATTTAATATATATCCATTCACCAATGTTTCCATGTA
261 AAAAACAAAATAATACTTGATTATGCTTCATTTAATATATATCCATTCACCAATATTTCCATGTA
* * * **
2126089 ATAATGCTCGAAATAAAGATTTTGCTATCATATATATATATGTATATAAGTATAACAAATATATG
326 ATAATGCTCAAAATAAAGATTTCGCTATCATATATATATATATATATAAGTATAACAAATATACA
** *
2126154 GTTAAATTTGGAATTTGGAATTTGCAATGGTGTTAATTAACTAGTTTAAATAATAATATTTTATT
391 AATAAATTTGGAATTTGAAATTTGCAATGGTGTTAATTAACTAGTTTAAATAATAATATTTTATT
* *
2126219 TTACCATTATATATATGAAGCACAATTTAGCAAGATCGAATTTTGTCGAATCTGCAAGAGGCAAA
456 TTACCATTATATATATGAAGCACAATTTAGCAAGATCGAATTTCGTCGAATCCGCAAGAGGCAAA
* *
2126284 AATAGACAAAAGAATGAGGAAATTCTGGTTTTTTATTCTTCAGGGAAAAGAAAGAGATGTTGTTA
521 AATAGACAAAAGAATGAGGAAATTCTGGTTTTTTATTCTTCAGGGAAAAGAAAGAGATGCTGTCA
*
2126349 CGTTTTAAAAGTGACCAAAGGAAGTGACAAGCTATTTTCAACAAGACGAGAACTAGATGCTATAA
586 CCTTTTAAAAGTGACCAAAGGAAGTGACAAGCTATTTTCAACAAGACGAGAACTAGATGCTATAA
2126414 ATTTATACCACTGTATAAAGTTGTGATTCCTTTGTGATTAAGGATTTTC
651 ATTTATACCACTGTATAAAGTTGTGATTCCTTTGTGATTAAGGATTTTC
*
2126463 CTTTCAATCAAG-GAACAAAATATAATATATACTACATGATAGCAAAATTCATATTAAAGTTGAT
1 CTTTCAATCAAGAG-ACAAAATATAATATATACTACATGATAGCAAAATTCATATTAAAGTTAAT
* * *
2126527 TTTTATTAAATAAAATATTAAAGAGATATCAAATTACTTACCTAATTTGTTACAATAAAAAATTA
65 TTTTATGAAATAAAATATTAAAGAGATATCAAATTACTTACCTAATTTGCTACAACAAAAAATTA
* * *
2126592 AAGACCAACCATTGAAATCTTTTTAAAACTTGAGGATGATGAAAATAAAATAATAATAATACTTA
130 AAGACCAACCATCGAAATCTTTTTAAAACTTGAGGATGATGAAAACAAAATAATAATAACACTT-
* * *
2126657 ATTTGTTAAAAT-CAAAAATCAAAAATCAAAACCCAATTATTGCAATCCTTTTGAAACTTGAAAG
194 A---CTTAAAATGCAAAAATCAAAAATCAAAACCCAATTATTGAAATCCTTATGAAACTTGAAAG
2126721 GTGATAAAAACAAAATAATACTTGATTATGCTTCATTTAATATATATATCCATTCACCAATATTT
256 GTGATAAAAACAAAATAATACTTGATTATGCTTCATTT-A-ATATATATCCATTCACCAATATTT
* *
2126786 TCATGTAATAATGCTCAAAATAAAGATTTCGCTATCATATATATATATATATAT-A-TATATATA
319 CCATGTAATAATGCTCAAAATAAAGATTTCGCTATCATATATATATATATATATAAGTATA-ACA
* * *
2126849 AGTATAACAAATATATGGTT-GAATTTGAAATTTGCAATGGTGTTAATTAACTGGTTTAAATAAT
383 AATAT-ACAAATAAAT--TTGGAATTTGAAATTTGCAATGGTGTTAATTAACTAGTTTAAATAAT
2126913 AATATTTTATTTTACCATTATATATATGAAGCACAATTTAGCAAGATCGAATTTCGTCGAATCCG
445 AATATTTTATTTTACCATTATATATATGAAGCACAATTTAGCAAGATCGAATTTCGTCGAATCCG
*
2126978 CAAGAGGCAAAAATAGACAAAAGAATTGAGGAAATTCTGGTTTTTTATTCTTCAGGGGAAAGAAA
510 CAAGAGGCAAAAATAGACAAAAGAA-TGAGGAAATTCTGGTTTTTTATTCTTCAGGGAAAAGAAA
2127043 GAGATGCTGTCACCTTTTAAAAGTGACCAAAGGAAGTGACAAGCTATTTTCAACAAGACGAGAAC
574 GAGATGCTGTCACCTTTTAAAAGTGACCAAAGGAAGTGACAAGCTATTTTCAACAAGACGAGAAC
*
2127108 TGGATGCTATAAATTTATACCACTGTATAAAGTTGTGATTCCTTTGTGATTAAGGATTTTC
639 TAGATGCTATAAATTTATACCACTGTATAAAGTTGTGATTCCTTTGTGATTAAGGATTTTC
2127169 C
1 C
2127170 AAGTCCAAGA
Statistics
Matches: 652, Mismatches: 43, Indels: 17
0.92 0.06 0.02
Matches are distributed among these distances:
698 1 0.00
699 181 0.28
700 1 0.00
702 85 0.13
703 13 0.02
704 78 0.12
705 130 0.20
706 163 0.25
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.34
Consensus pattern (699 bp):
CTTTCAATCAAGAGACAAAATATAATATATACTACATGATAGCAAAATTCATATTAAAGTTAATT
TTTATGAAATAAAATATTAAAGAGATATCAAATTACTTACCTAATTTGCTACAACAAAAAATTAA
AGACCAACCATCGAAATCTTTTTAAAACTTGAGGATGATGAAAACAAAATAATAATAACACTTAC
TTAAAATGCAAAAATCAAAAATCAAAACCCAATTATTGAAATCCTTATGAAACTTGAAAGGTGAT
AAAAACAAAATAATACTTGATTATGCTTCATTTAATATATATCCATTCACCAATATTTCCATGTA
ATAATGCTCAAAATAAAGATTTCGCTATCATATATATATATATATATAAGTATAACAAATATACA
AATAAATTTGGAATTTGAAATTTGCAATGGTGTTAATTAACTAGTTTAAATAATAATATTTTATT
TTACCATTATATATATGAAGCACAATTTAGCAAGATCGAATTTCGTCGAATCCGCAAGAGGCAAA
AATAGACAAAAGAATGAGGAAATTCTGGTTTTTTATTCTTCAGGGAAAAGAAAGAGATGCTGTCA
CCTTTTAAAAGTGACCAAAGGAAGTGACAAGCTATTTTCAACAAGACGAGAACTAGATGCTATAA
ATTTATACCACTGTATAAAGTTGTGATTCCTTTGTGATTAAGGATTTTC
Found at i:2138237 original size:7 final size:7
Alignment explanation
Indices: 2138225--2138254 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
2138215 ACGTACGCCC
2138225 GCAGCCT
1 GCAGCCT
2138232 GCAGCCT
1 GCAGCCT
2138239 GCAGCCT
1 GCAGCCT
2138246 GCAG-CT
1 GCAGCCT
2138252 GCA
1 GCA
2138255 AGTCAAACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.17, C:0.40, G:0.30, T:0.13
Consensus pattern (7 bp):
GCAGCCT
Found at i:2142643 original size:138 final size:138
Alignment explanation
Indices: 2142390--2142644 Score: 325
Period size: 138 Copynumber: 1.8 Consensus size: 138
2142380 ATAGCCAGGT
* * *
2142390 GCCAACAGAACAAGAAAACAACATGATTACTTTCCTCATGCAATGAAGAATATAACAACAACAAA
1 GCCAACAGAACAAGAAAACAACATGATTACATCCCTCATGCAATGAAGAAAATAACAACAACAAA
* * * **
2142455 GCAGAACTGCAGCAAAGCTAAGATAAAAAGCCTATGATAGGAAAGGAAGGGGAAATTTTGGTGCA
66 GCAGAACTGCAGCAAAGCCAAAATAAAAAGCCTATCATAGGAAACAAAGGGGAAATTTTGGTGCA
2142520 ATAAAAGA
131 ATAAAAGA
* * * * * *
2142528 GCCAACAGTACAGGCAAACAACATGGTTACATCCCTCATGCAATTG-AGAAAATAACAATAACAT
1 GCCAACAGAACAAGAAAACAACATGATTACATCCCTCATGCAA-TGAAGAAAATAACAACAACAA
* * *
2142592 AGCAGAACTTCAGCAAAGCACAAAAT-AAAGGCCTATCATGGGAAACAAAGGGG
65 AGCAGAACTGCAGCAAAGC-CAAAATAAAAAGCCTATCATAGGAAACAAAGGGG
2142645 GAAAAAATGG
Statistics
Matches: 98, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
138 92 0.94
139 6 0.06
ACGTcount: A:0.46, C:0.18, G:0.19, T:0.16
Consensus pattern (138 bp):
GCCAACAGAACAAGAAAACAACATGATTACATCCCTCATGCAATGAAGAAAATAACAACAACAAA
GCAGAACTGCAGCAAAGCCAAAATAAAAAGCCTATCATAGGAAACAAAGGGGAAATTTTGGTGCA
ATAAAAGA
Found at i:2146632 original size:30 final size:30
Alignment explanation
Indices: 2146596--2146666 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 30
2146586 CTGTTTGGGT
* *
2146596 GCTGTGCGGGCCTGCATACCGCGCGCCCCA
1 GCTGTGCGGGCCTGCATACCACGCACCCCA
* * *
2146626 GCTGTGCAGGCTTGCATACCACGCACCCCT
1 GCTGTGCGGGCCTGCATACCACGCACCCCA
*
2146656 GCTATGCGGGC
1 GCTGTGCGGGC
2146667 TAGCTAGCCC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.13, C:0.39, G:0.31, T:0.17
Consensus pattern (30 bp):
GCTGTGCGGGCCTGCATACCACGCACCCCA
Found at i:2146715 original size:30 final size:29
Alignment explanation
Indices: 2146679--2146736 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
2146669 GCTAGCCCCG
*
2146679 GGCCTGCGTACCACGCGCCCATGCTGTGCT
1 GGCCTGCGTACCACGCACCC-TGCTGTGCT
* *
2146709 GGCCTGCGTGCCGCGCACCCTGCTGTGC
1 GGCCTGCGTACCACGCACCCTGCTGTGC
2146737 GAGCTGGCAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.07, C:0.41, G:0.33, T:0.19
Consensus pattern (29 bp):
GGCCTGCGTACCACGCACCCTGCTGTGCT
Found at i:2156507 original size:9 final size:9
Alignment explanation
Indices: 2156495--2156545 Score: 57
Period size: 9 Copynumber: 5.7 Consensus size: 9
2156485 CGCCGCCGCC
2156495 TGTTGCTGT
1 TGTTGCTGT
2156504 TGTTGCTGT
1 TGTTGCTGT
* *
2156513 TGCTGCTGC
1 TGTTGCTGT
* *
2156522 AGTTGTTGT
1 TGTTGCTGT
*
2156531 TGTTGTTGT
1 TGTTGCTGT
2156540 TGTTGC
1 TGTTGC
2156546 GTAGCCGCTA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.02, C:0.12, G:0.33, T:0.53
Consensus pattern (9 bp):
TGTTGCTGT
Found at i:2159269 original size:22 final size:22
Alignment explanation
Indices: 2159229--2159270 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2159219 TCTCAAAATA
*
2159229 TAATATTTAAATTATTAATTTT
1 TAATATTTAAAATATTAATTTT
2159251 TAATATTTAAAA-ATATAATT
1 TAATATTTAAAATAT-TAATT
2159271 AAAAATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TAATATTTAAAATATTAATTTT
Found at i:2171145 original size:19 final size:19
Alignment explanation
Indices: 2171094--2171147 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
2171084 TTCAATCATT
* *
2171094 AATATTTTTATTATTTTAAT
1 AATATTTTTA-TATTTAAAA
** *
2171114 AATATAATAATATTTAAAA
1 AATATTTTTATATTTAAAA
2171133 AATATTTTTATATTT
1 AATATTTTTATATTT
2171148 TATTAATTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AATATTTTTATATTTAAAA
Found at i:2175193 original size:25 final size:23
Alignment explanation
Indices: 2175158--2175207 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 23
2175148 ACATTCAAAT
*
2175158 ATTAAATAACTTTAG-AAGCACAA
1 ATTAAATAACTTGAGAAAG-ACAA
2175181 ATTAAATAGAACTTGAGAAAGACAA
1 ATTAAAT--AACTTGAGAAAGACAA
2175206 AT
1 AT
2175208 CAATTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 7 0.30
25 13 0.57
26 3 0.13
ACGTcount: A:0.54, C:0.10, G:0.12, T:0.24
Consensus pattern (23 bp):
ATTAAATAACTTGAGAAAGACAA
Found at i:2175485 original size:109 final size:110
Alignment explanation
Indices: 2175302--2175518 Score: 319
Period size: 109 Copynumber: 2.0 Consensus size: 110
2175292 AGCAAGTCCT
* *
2175302 CCAAACAAAAACAATGCAAAGCATACCTTAAAAACCCATGTACACTAATGCCAATGCCGAGAGAT
1 CCAAACAAAAACAATGCAAAGCACACCTTAAAAACCCATGCACACTAATGCCAATGCCGAGAGAT
*
2175367 AAGAAAGAAAAAACAAAATAACAGAATAAATACAAAAAATTAACC
66 AAGAAAGAAAAAACAAAATAACAAAATAAATACAAAAAATTAACC
** * * * * *
2175412 CCAAACATGAACAATGCAAA-CACCCCTTAAAAACCCATGCATAGTGATGCCAATGCCGAGAGCT
1 CCAAACAAAAACAATGCAAAGCACACCTTAAAAACCCATGCACACTAATGCCAATGCCGAGAGAT
* *
2175476 AAGATAGAAAAAACAAACTAACAAAATAAATACAAAAAATTAA
66 AAGAAAGAAAAAACAAAATAACAAAATAAATACAAAAAATTAA
2175519 ACAAACTCCA
Statistics
Matches: 95, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
109 77 0.81
110 18 0.19
ACGTcount: A:0.54, C:0.21, G:0.11, T:0.14
Consensus pattern (110 bp):
CCAAACAAAAACAATGCAAAGCACACCTTAAAAACCCATGCACACTAATGCCAATGCCGAGAGAT
AAGAAAGAAAAAACAAAATAACAAAATAAATACAAAAAATTAACC
Found at i:2179040 original size:21 final size:20
Alignment explanation
Indices: 2179008--2179046 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2178998 TGTATTTAAA
2179008 ATTTAAGTAACTTGTATGTAT
1 ATTTAAGTAACTT-TATGTAT
2179029 ATTTCAAG-AACTTTATGT
1 ATTT-AAGTAACTTTATGT
2179047 TACTCAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 9 0.53
22 3 0.18
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (20 bp):
ATTTAAGTAACTTTATGTAT
Found at i:2179735 original size:19 final size:19
Alignment explanation
Indices: 2179703--2179741 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
2179693 TCATAAATTC
*
2179703 TTTTAATGTTAAAACAAATA
1 TTTTAATG-TAAAAAAAATA
2179723 TTTT-ATGTAAAAAAAATA
1 TTTTAATGTAAAAAAAATA
2179741 T
1 T
2179742 GATTCATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 3 0.17
20 4 0.22
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (19 bp):
TTTTAATGTAAAAAAAATA
Found at i:2212795 original size:22 final size:22
Alignment explanation
Indices: 2212770--2212812 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2212760 ACCAAACAAA
2212770 AAAATTTATTATAAAAAAAATT
1 AAAATTTATTATAAAAAAAATT
* * *
2212792 AAAATTTTTTTTTAAAAAAAT
1 AAAATTTATTATAAAAAAAAT
2212813 ATTATGAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AAAATTTATTATAAAAAAAATT
Found at i:2213185 original size:17 final size:17
Alignment explanation
Indices: 2213163--2213218 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
2213153 TAAAAATAAT
2213163 AAATAATAATTTAATTA
1 AAATAATAATTTAATTA
2213180 AAATAATTAA-TTAATTA
1 AAATAA-TAATTTAATTA
* * *
2213197 TAAATATTTATTTAATTT
1 -AAATAATAATTTAATTA
2213215 AAAT
1 AAAT
2213219 TTAAAATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 19 0.58
18 14 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AAATAATAATTTAATTA
Found at i:2236957 original size:16 final size:17
Alignment explanation
Indices: 2236905--2236957 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 17
2236895 AGAAATGGAA
2236905 ATAAATATTTTAATAAT
1 ATAAATATTTTAATAAT
2236922 -T-AATATTTATATATTAAT
1 ATAAATATTT-TA-A-TAAT
2236940 ATAAATA-TTTAATAAT
1 ATAAATATTTTAATAAT
2236956 AT
1 AT
2236958 TTATTTTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
15 7 0.23
16 9 0.29
17 2 0.06
18 6 0.19
19 3 0.10
20 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATAAATATTTTAATAAT
Found at i:2237004 original size:41 final size:38
Alignment explanation
Indices: 2236903--2237004 Score: 106
Period size: 41 Copynumber: 2.7 Consensus size: 38
2236893 TAAGAAATGG
2236903 AAATAAATATTTTAATAATTAATA---TTTATATATTA
1 AAATAAATATTTTAATAATTAATATTTTTTATATATTA
* * *
2236938 ATATAAATA-TTTAATAA-TATTTATTTTTTCATTTTATTCA
1 AAATAAATATTTTAATAATTA-ATATTTTTT-A-TATATT-A
2236978 AAATAAATATTTTAATAATTAATATTT
1 AAATAAATATTTTAATAATTAATATTT
2237005 ATATATTATA
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
33 2 0.04
34 10 0.19
35 8 0.15
37 3 0.06
38 1 0.02
39 5 0.09
40 9 0.17
41 13 0.25
42 2 0.04
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (38 bp):
AAATAAATATTTTAATAATTAATATTTTTTATATATTA
Found at i:2237434 original size:20 final size:20
Alignment explanation
Indices: 2237394--2237430 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2237384 CCTATTTTTT
2237394 ATTTTTTAAATATAATAATA
1 ATTTTTTAAATATAATAATA
2237414 ATTTTTTAAAT-TAATAA
1 ATTTTTTAAATATAATAA
2237431 ATAAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTTTTAAATATAATAATA
Found at i:2249347 original size:27 final size:27
Alignment explanation
Indices: 2249281--2249353 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
2249271 AAAGAAGTTT
* *
2249281 AAAACACAAAAATAACAATACATTATAC
1 AAAAC-CAAAAAAAAAAATACATTATAC
** *
2249309 AACCCCACAAAAAAAAATACATTATAC
1 AAAACCAAAAAAAAAAATACATTATAC
*
2249336 AAAACTAAAAAATAAAAA
1 AAAACCAAAAAA-AAAAA
2249354 ATATATATTT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
27 27 0.77
28 8 0.23
ACGTcount: A:0.67, C:0.18, G:0.00, T:0.15
Consensus pattern (27 bp):
AAAACCAAAAAAAAAAATACATTATAC
Found at i:2250635 original size:16 final size:16
Alignment explanation
Indices: 2250616--2250666 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 16
2250606 ATTTTATCTT
2250616 TTATTAATTTTAAAAA
1 TTATTAATTTTAAAAA
* *
2250632 TTATT-ATTATATAAA
1 TTATTAATTTTAAAAA
*
2250647 TTATATATTTTTTAAAAA
1 TTAT-TA-ATTTTAAAAA
2250665 TT
1 TT
2250667 TTCTCTCTGT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
15 12 0.44
16 6 0.22
18 9 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATTAATTTTAAAAA
Found at i:2251705 original size:2 final size:2
Alignment explanation
Indices: 2251698--2251723 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2251688 CATCCAATCA
2251698 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
2251724 GAACCATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2253865 original size:6 final size:6
Alignment explanation
Indices: 2253854--2253881 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2253844 CAGAGACCTC
2253854 TTTTGT TTTTGT TTTTGT TTTTGT TTTT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTT
2253882 AGGCTCGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (6 bp):
TTTTGT
Found at i:2254239 original size:2 final size:2
Alignment explanation
Indices: 2254232--2254264 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2254222 NNNNNNNNNN
2254232 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2254265 CCTGATTCCC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2257393 original size:12 final size:12
Alignment explanation
Indices: 2257376--2257402 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2257366 ACACAAGTTG
2257376 AATAGTCAAGGT
1 AATAGTCAAGGT
2257388 AATAGTCAAGGT
1 AATAGTCAAGGT
2257400 AAT
1 AAT
2257403 GGAACCAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.26
Consensus pattern (12 bp):
AATAGTCAAGGT
Found at i:2258923 original size:3 final size:3
Alignment explanation
Indices: 2258915--2258951 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
2258905 CATTAACAGA
*
2258915 AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2258952 TCACAACTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:2259596 original size:10 final size:10
Alignment explanation
Indices: 2259581--2259614 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
2259571 TGTATAATCC
2259581 TTTTAAAAAA
1 TTTTAAAAAA
**
2259591 TTTTAAATTA
1 TTTTAAAAAA
2259601 TTTTAAAAAA
1 TTTTAAAAAA
2259611 TTTT
1 TTTT
2259615 TATTTTTATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TTTTAAAAAA
Found at i:2260612 original size:2 final size:2
Alignment explanation
Indices: 2260605--2260640 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2260595 GTATAATAAG
2260605 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2260641 GAGGCACGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2265303 original size:14 final size:14
Alignment explanation
Indices: 2265274--2265312 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
2265264 ATTTACAATC
2265274 AATAATTAT-A-AA
1 AATAATTATAACAA
2265286 AATAATTATAACAA
1 AATAATTATAACAA
*
2265300 AATAATAATAACA
1 AATAATTATAACA
2265313 TCTAATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 9 0.38
13 1 0.04
14 14 0.58
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (14 bp):
AATAATTATAACAA
Found at i:2276989 original size:29 final size:30
Alignment explanation
Indices: 2276957--2277014 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
2276947 AATAAATAAT
*
2276957 TTTTTATTATAT-TTAATTAAATTTTTATA
1 TTTTTATTATATATTAAATAAATTTTTATA
* *
2276986 TTTTTATTTTATATTAAATAAGTTTTTAT
1 TTTTTATTATATATTAAATAAATTTTTAT
2277015 TATTAACATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (30 bp):
TTTTTATTATATATTAAATAAATTTTTATA
Found at i:2277151 original size:19 final size:18
Alignment explanation
Indices: 2277123--2277158 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2277113 TATTAATGAT
2277123 ATTTAATTAATTATAAAAA
1 ATTTAATTAATT-TAAAAA
*
2277142 ATTTATTTAATTTAAAA
1 ATTTAATTAATTTAAAA
2277159 TAAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTTAATTAATTTAAAAA
Found at i:2278810 original size:17 final size:17
Alignment explanation
Indices: 2278778--2278816 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2278768 CAAAGTTAAA
*
2278778 ATAATTATATTAATTAT
1 ATAATTATAGTAATTAT
* *
2278795 TTAATTATAGTCATTAT
1 ATAATTATAGTAATTAT
2278812 ATAAT
1 ATAAT
2278817 ATTATTATAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (17 bp):
ATAATTATAGTAATTAT
Found at i:2294667 original size:128 final size:128
Alignment explanation
Indices: 2294465--2294735 Score: 398
Period size: 128 Copynumber: 2.1 Consensus size: 128
2294455 CCTAAACTAG
* * * * * *
2294465 TATAAGAGCCCCTCTCTTCTATGATAAAGAGATGTCTCATGATAAGTCAAGTGGTATCAAAACAT
1 TATAAGAGTCCATCTCTTCTATGATAAAAAGACGTCCCATGATAAGTCAAGTGGTATCAAAACAA
* *
2294530 ATTCGAATCTTTATTGATGTGGGCCCCATGAGAAATATAAGGTTTGAAGTAGACTTAAATTAA
66 ATTCGAATCTTTATTGATGTGGGCCCCATGAGAAATATAAGGTTTGAAATAGACATAAATTAA
* *
2294593 TATAAGAGTCCATCTCTTCTATGATAAAAAGACGTCCCATGCTAAGTCAAGTGGTATCAAAGCAA
1 TATAAGAGTCCATCTCTTCTATGATAAAAAGACGTCCCATGATAAGTCAAGTGGTATCAAAACAA
* ** * *
2294658 ATTTGAATCTTTATTGATGTGGGTTCCATGAGAGATATAAGGTTTGAAATATACATAAATTAA
66 ATTCGAATCTTTATTGATGTGGGCCCCATGAGAAATATAAGGTTTGAAATAGACATAAATTAA
*
2294721 TATAAGAGTCTATCT
1 TATAAGAGTCCATCT
2294736 TGCACAAAGA
Statistics
Matches: 127, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
128 127 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (128 bp):
TATAAGAGTCCATCTCTTCTATGATAAAAAGACGTCCCATGATAAGTCAAGTGGTATCAAAACAA
ATTCGAATCTTTATTGATGTGGGCCCCATGAGAAATATAAGGTTTGAAATAGACATAAATTAA
Found at i:2294780 original size:24 final size:23
Alignment explanation
Indices: 2294745--2294789 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
2294735 TTGCACAAAG
2294745 AAAAAAAAAGAAAAGAAATAACA
1 AAAAAAAAAGAAAAGAAATAACA
*
2294768 AAAAAAAAGAGAAAAGAGATAA
1 AAAAAAAA-AGAAAAGAAATAA
2294790 GTTATGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.80, C:0.02, G:0.13, T:0.04
Consensus pattern (23 bp):
AAAAAAAAAGAAAAGAAATAACA
Found at i:2295676 original size:2 final size:2
Alignment explanation
Indices: 2295669--2295704 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2295659 NNNNNNNNNN
*
2295669 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2295705 AAGAACATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2295749 original size:21 final size:21
Alignment explanation
Indices: 2295725--2295764 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2295715 TCCTTTCAAA
*
2295725 TTCTAGTTTTGTTTTTCTTCG
1 TTCTAGTTATGTTTTTCTTCG
*
2295746 TTCTTGTTATGTTTTTCTT
1 TTCTAGTTATGTTTTTCTT
2295765 GCACTATAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.05, C:0.12, G:0.12, T:0.70
Consensus pattern (21 bp):
TTCTAGTTATGTTTTTCTTCG
Found at i:2296955 original size:7 final size:7
Alignment explanation
Indices: 2296943--2296973 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
2296933 TATTTTCTTT
2296943 TCACTAA
1 TCACTAA
2296950 TCACTAA
1 TCACTAA
2296957 TCACTAA
1 TCACTAA
2296964 TCACTAA
1 TCACTAA
2296971 TCA
1 TCA
2296974 TTTACATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (7 bp):
TCACTAA
Found at i:2305046 original size:4 final size:4
Alignment explanation
Indices: 2305030--2305064 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
2305020 TTTACTTGCT
* *
2305030 ATAC ATAC GTAC ATAC ATAC ATAC ATTC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
2305065 TATATATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.46, C:0.23, G:0.03, T:0.29
Consensus pattern (4 bp):
ATAC
Found at i:2305079 original size:16 final size:16
Alignment explanation
Indices: 2305060--2305090 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2305050 ATACATTCAT
2305060 ACATATATATATATAC
1 ACATATATATATATAC
*
2305076 ACATATATGTATATA
1 ACATATATATATATA
2305091 TAAATCATGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.39
Consensus pattern (16 bp):
ACATATATATATATAC
Done.