Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007925.1 Hibiscus syriacus cultivar Beakdansim tig00110331_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1316088
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:1036472 original size:3 final size:3
Alignment explanation
Indices: 1036464--1036535 Score: 117
Period size: 3 Copynumber: 23.3 Consensus size: 3
1036454 AGTGGTTGGG
1036464 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1036512 TAA TAA TAAA TATT TAA TAA TAA T
1 TAA TAA T-AA TA-A TAA TAA TAA T
1036536 TTTTTGACCC
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
3 60 0.92
4 5 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1037140 original size:44 final size:44
Alignment explanation
Indices: 1037091--1037732 Score: 138
Period size: 44 Copynumber: 14.6 Consensus size: 44
1037081 TGAAAACATC
* *
1037091 GATCCACCTCCTTCTGTGATGGAATCGAACGAGATATCGATGAT
1 GATCCACCTCCTTCTGTGATGGAATCGAACGAAATATCGATGCT
* * * * *
1037135 GATCCATCTCCTTCTCTTTTTGATGATAGAATCGAGC-AAAAAGTTGATGCT
1 GATCCA---CC-TC-C-TTCTG-TGATGGAATCGAACGAAATA-TCGATGCT
* * * * * *** *
1037186 GATCCAACTCCTTCTGCGATGGATTTGAGCGAAATAAAAATGTT
1 GATCCACCTCCTTCTGTGATGGAATCGAACGAAATATCGATGCT
* * * * * *
1037230 GATCCATCTCCTTATGTGACGGAATCGAACGAGATGTCGGTGCT
1 GATCCACCTCCTTCTGTGATGGAATCGAACGAAATATCGATGCT
* * * * * * *
1037274 GATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAATTGACGCT
1 GATCCACCTCCTTCTGTGATGGAATCGAACGAAATATCGATGCT
* ** * * * *
1037318 GATCCAACTCCCTCTCATTCTGTGTTATAATCGAGCTAAA-AGTTGACGCT
1 GATCC-A---CCTC-C-TTCTGTGATGGAATCGAACGAAATA-TCGATGCT
* * * * * * *
1037368 GATCCAACTCCTTCTGTGATTGATTTGAGCGAAA-A---ATACC
1 GATCCACCTCCTTCTGTGATGGAATCGAACGAAATATCGATGCT
* * * * * *
1037408 GATCCACCTCCTTCTGTGATGGATTTGAATGAGATGTCGGTGCT
1 GATCCACCTCCTTCTGTGATGGAATCGAACGAAATATCGATGCT
* * * * * * * *
1037452 GATCTACCTCATTTTGTGATAGAATCGAGCTAAA-AGTTGACGCT
1 GATCCACCTCCTTCTGTGATGGAATCGAACGAAATA-TCGATGCT
* * * * *
1037496 GGTCCAACTCCTTCTGCGATGGATTTGAA--AAA-AT-G-T--T
1 GATCCACCTCCTTCTGTGATGGAATCGAACGAAATATCGATGCT
** * * * * * * * *
1037533 GATCCATATCTTTCTGTGATAGATTTGAACGAGATGTCGGTGTT
1 GATCCACCTCCTTCTGTGATGGAATCGAACGAAATATCGATGCT
* * * * * *
1037577 GATCTACCTCATTCTGTGATAGAATC-AAGCTAAA-AGTTGACGCT
1 GATCCACCTCCTTCTGTGATGGAATCGAA-CGAAATA-TCGATGCT
* * * * * *
1037621 GATCCAACTCCTTCTATGATGGATTTGAGCGAAAAAT--AT-C-
1 GATCCACCTCCTTCTGTGATGGAATCGAACGAAATATCGATGCT
* * * *
1037661 GATCCATCTCATTCTGTGATGGATTCGAACGAGATATCCG-TGCT
1 GATCCACCTCCTTCTGTGATGGAATCGAACGAAATAT-CGATGCT
* * * *
1037705 GATCTACCTCCTTTTATGATAGAATCGA
1 GATCCACCTCCTTCTGTGATGGAATCGA
1037733 GCAAAAAGTT
Statistics
Matches: 423, Mismatches: 138, Indels: 74
0.67 0.22 0.12
Matches are distributed among these distances:
37 24 0.06
39 2 0.00
40 63 0.15
41 3 0.01
42 7 0.02
43 3 0.01
44 226 0.53
45 12 0.03
46 4 0.01
47 4 0.01
48 7 0.02
49 4 0.01
50 40 0.09
51 24 0.06
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (44 bp):
GATCCACCTCCTTCTGTGATGGAATCGAACGAAATATCGATGCT
Found at i:1037496 original size:178 final size:179
Alignment explanation
Indices: 1037164--1037506 Score: 490
Period size: 178 Copynumber: 1.9 Consensus size: 179
1037154 TTGATGATAG
* **
1037164 AATCGAGCAAAAAGTTGATGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAATAAAAATGT
1 AATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGAGCG--A-AAAAATAC
* * *
1037229 TGATCCATCTCCTTATGTGACGGAATCGAACGAGATGTCGGTGCTGATCTACCTCCTTCTGTGAT
63 CGATCCACCTCCTTATGTGACGGAATCGAACGAGATGTCGGTGCTGATCTACCTCATTCTGTGAT
1037294 AGAATCGAGCAAAAAATTGACGCTGATCCAACTCCCTCTCATTCTGTGTTAT
128 AGAATCGAGCAAAAAATTGACGCTGATCCAACTCCCTCTCATTCTGTGTTAT
* * *
1037346 AATCGAGCTAAAAGTTGACGCTGATCCAACTCCTTCTGTGATTGATTTGAGCG-AAAAATACCGA
1 AATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAAAATACCGA
* * * * * *
1037410 TCCACCTCCTTCTGTGATGGATTTGAATGAGATGTCGGTGCTGATCTACCTCATTTTGTGATAGA
66 TCCACCTCCTTATGTGACGGAATCGAACGAGATGTCGGTGCTGATCTACCTCATTCTGTGATAGA
* * *
1037475 ATCGAGCTAAAAGTTGACGCTGGTCCAACTCC
131 ATCGAGCAAAAAATTGACGCTGATCCAACTCC
1037507 TTCTGCGATG
Statistics
Matches: 143, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
178 94 0.66
182 49 0.34
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (179 bp):
AATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAAAATACCGA
TCCACCTCCTTATGTGACGGAATCGAACGAGATGTCGGTGCTGATCTACCTCATTCTGTGATAGA
ATCGAGCAAAAAATTGACGCTGATCCAACTCCCTCTCATTCTGTGTTAT
Found at i:1037521 original size:128 final size:128
Alignment explanation
Indices: 1037331--1037783 Score: 633
Period size: 128 Copynumber: 3.6 Consensus size: 128
1037321 CCAACTCCCT
* * * *
1037331 CTCATTCTGTGTTATAATCGAGCTAAAAGTTGACGCTGATCCAACTCCTTCTGTGATTGATTTGA
1 CTCATTCTGTGATAGAATCGAGCTAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
* * * *
1037396 GCGAAAAATACCGATCCACCTCCTTCTGTGATGGATTTGAATGAGATGTCGGTGCTGATCTAC
66 GCGAAAAATATCGATCCATCTCATTCTGTGATGGATTTGAACGAGATGTCGGTGCTGATCTAC
* *
1037459 CTCATTTTGTGATAGAATCGAGCTAAAAGTTGACGCTGGTCCAACTCCTTCTGCGATGGATTTGA
1 CTCATTCTGTGATAGAATCGAGCTAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
* * * * * *
1037524 ---AAAAATGTTGATCCATATCTTTCTGTGATAGATTTGAACGAGATGTCGGTGTTGATCTAC
66 GCGAAAAATATCGATCCATCTCATTCTGTGATGGATTTGAACGAGATGTCGGTGCTGATCTAC
* **
1037584 CTCATTCTGTGATAGAATCAAGCTAAAAGTTGACGCTGATCCAACTCCTTCTATGATGGATTTGA
1 CTCATTCTGTGATAGAATCGAGCTAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
* * *
1037649 GCGAAAAATATCGATCCATCTCATTCTGTGATGGATTCGAACGAGATATCCGTGCTGATCTAC
66 GCGAAAAATATCGATCCATCTCATTCTGTGATGGATTTGAACGAGATGTCGGTGCTGATCTAC
* * * * * *
1037712 CTCCTTTTATGATAGAATCGAGCAAAAAGTTAACGCTGATCCAACTTCTTCTGCGATGGATTTGA
1 CTCATTCTGTGATAGAATCGAGCTAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
1037777 GCGAAAA
66 GCGAAAA
1037784 TTTGAACAAA
Statistics
Matches: 284, Mismatches: 38, Indels: 6
0.87 0.12 0.02
Matches are distributed among these distances:
125 111 0.39
128 173 0.61
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.32
Consensus pattern (128 bp):
CTCATTCTGTGATAGAATCGAGCTAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
GCGAAAAATATCGATCCATCTCATTCTGTGATGGATTTGAACGAGATGTCGGTGCTGATCTAC
Found at i:1046672 original size:64 final size:64
Alignment explanation
Indices: 1046592--1046744 Score: 166
Period size: 64 Copynumber: 2.4 Consensus size: 64
1046582 GGGTGTATCG
* * * * *
1046592 ATGCACAGGAAGTGCATCGATGCA-TCCATTAAAAATGGAAACATCGAATGCAATTAGTGCATCA
1 ATGCATAGGTAGTGCATCGATGCACCCCATT-AAAATGAAAACATCGAAGGCAATTAGTGCATCA
* ** * *
1046656 ATGCATAAGG-AGTGCATCGATGCACCCCCTTAAAATGAAAACATCGAAGGTGATTAGTGTATCG
1 ATGCAT-AGGTAGTGCATCGATGCACCCCATTAAAATGAAAACATCGAAGGCAATTAGTGCATCA
* *
1046720 ATGCATGGGTAGTGCATCAATGCAC
1 ATGCATAGGTAGTGCATCGATGCAC
1046745 ATGTTAAAGA
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
63 2 0.03
64 66 0.88
65 7 0.09
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (64 bp):
ATGCATAGGTAGTGCATCGATGCACCCCATTAAAATGAAAACATCGAAGGCAATTAGTGCATCA
Found at i:1046777 original size:20 final size:20
Alignment explanation
Indices: 1046752--1046789 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1046742 CACATGTTAA
*
1046752 AGAATGCATTGATGCACTGT
1 AGAATGCATCGATGCACTGT
1046772 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
1046790 TCAAGGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:1047580 original size:18 final size:18
Alignment explanation
Indices: 1047557--1047608 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
1047547 GGGTCTACGC
*
1047557 GGTCCTTTGGGACATAGT
1 GGTCCTTCGGGACATAGT
*
1047575 GGTCCTTCGGGATATAGT
1 GGTCCTTCGGGACATAGT
1047593 GGTCCTTCGGGACATA
1 GGTCCTTCGGGACATA
1047609 TGTGTTATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.17, C:0.19, G:0.33, T:0.31
Consensus pattern (18 bp):
GGTCCTTCGGGACATAGT
Found at i:1050895 original size:19 final size:19
Alignment explanation
Indices: 1050871--1050922 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
1050861 GAATGCAATT
*
1050871 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGA
1050890 AGTGCATCGATGCATAAGA
1 AGTGCATCGATGCATAAGA
1050909 AGTGCATCGATGCA
1 AGTGCATCGATGCA
1050923 CCCCCTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGA
Found at i:1050915 original size:83 final size:83
Alignment explanation
Indices: 1050812--1050986 Score: 228
Period size: 83 Copynumber: 2.1 Consensus size: 83
1050802 TTCAGTGTGT
* * *
1050812 ATCGATGCATAGGAAGTGCATCGATACA-CCCATTAAAAATGGAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAAGAAGTGCATCGATACACCCCATT-AAAATGAAAACATCGAAGGCAATTAGTGC
1050876 ATCGATGCATAAGG-AGTGC
65 ATCGATGCAT-AGGTAGTGC
* * ** *
1050895 ATCGATGCATAAGAAGTGCATCGATGCACCCCCTTAAAATGAAAACATCGAAGGTGATTAGTGTA
1 ATCGATGCATAAGAAGTGCATCGATACACCCCATTAAAATGAAAACATCGAAGGCAATTAGTGCA
* *
1050960 TCGATGCATGGGTAGTGT
66 TCGATGCATAGGTAGTGC
1050978 ATCGATGCA
1 ATCGATGCA
1050987 CATGTTAAAG
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
82 2 0.03
83 73 0.91
84 5 0.06
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (83 bp):
ATCGATGCATAAGAAGTGCATCGATACACCCCATTAAAATGAAAACATCGAAGGCAATTAGTGCA
TCGATGCATAGGTAGTGC
Found at i:1052429 original size:24 final size:24
Alignment explanation
Indices: 1052402--1052451 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
1052392 GACATATATG
*
1052402 TATGAAATGA-TAATAGTAATTGTT
1 TATG-AATGATTAATAGTAAATGTT
* *
1052426 TATGCATGATTACTAGTAAATGTT
1 TATGAATGATTAATAGTAAATGTT
1052450 TA
1 TA
1052452 CATTATATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (24 bp):
TATGAATGATTAATAGTAAATGTT
Found at i:1054952 original size:20 final size:21
Alignment explanation
Indices: 1054912--1054952 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1054902 AACTTAAAGG
1054912 ATTAAAATGGTAAAAACAAAA
1 ATTAAAATGGTAAAAACAAAA
* *
1054933 ATTAAAA-GGTTAAAATAAAA
1 ATTAAAATGGTAAAAACAAAA
1054953 TAACAGAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.66, C:0.02, G:0.10, T:0.22
Consensus pattern (21 bp):
ATTAAAATGGTAAAAACAAAA
Found at i:1055470 original size:12 final size:12
Alignment explanation
Indices: 1055455--1055479 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1055445 ATAAGTGGAA
1055455 GAATAAAACATG
1 GAATAAAACATG
1055467 GAATAAAACATG
1 GAATAAAACATG
1055479 G
1 G
1055480 GGTGGTGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.08, G:0.20, T:0.16
Consensus pattern (12 bp):
GAATAAAACATG
Found at i:1055563 original size:3 final size:3
Alignment explanation
Indices: 1055555--1055582 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1055545 AGTGCTTGGG
1055555 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1055583 TTTTTGATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1056000 original size:23 final size:23
Alignment explanation
Indices: 1055974--1056023 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
1055964 AACAAAATAT
1055974 ATTCCAAATTTCAAAAGAAAAAG
1 ATTCCAAATTTCAAAAGAAAAAG
1055997 ATTCCAAATTTCAAAAGAAAAAG
1 ATTCCAAATTTCAAAAGAAAAAG
1056020 ATTC
1 ATTC
1056024 AGTGAATGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.54, C:0.14, G:0.08, T:0.24
Consensus pattern (23 bp):
ATTCCAAATTTCAAAAGAAAAAG
Found at i:1057869 original size:69 final size:69
Alignment explanation
Indices: 1057787--1057924 Score: 231
Period size: 69 Copynumber: 2.0 Consensus size: 69
1057777 TTTACCTCAC
* * *
1057787 GGTTGGCGTAAAACACTTCAAGTTCTCGATTTCTAGCCAGAATATCGTGTGTTTCGTTGAGTAAC
1 GGTTGACGTAAAACACTTCAAGTTCTCGATTTCTAACCAGAATATCATGTGTTTCGTTGAGTAAC
1057852 AATA
66 AATA
* *
1057856 GGTTGACGTAAAACACTTTAAGTTCTCGATTTCTAACTAGAATATCATGTGTTTCGTTGAGTAAC
1 GGTTGACGTAAAACACTTCAAGTTCTCGATTTCTAACCAGAATATCATGTGTTTCGTTGAGTAAC
1057921 AATA
66 AATA
1057925 TAATGGTTGA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.35
Consensus pattern (69 bp):
GGTTGACGTAAAACACTTCAAGTTCTCGATTTCTAACCAGAATATCATGTGTTTCGTTGAGTAAC
AATA
Found at i:1073743 original size:17 final size:18
Alignment explanation
Indices: 1073711--1073746 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1073701 ATTACTCATA
*
1073711 TTTGTTTTTTTCATTTTT
1 TTTGTTTTTATCATTTTT
1073729 TTTGTTTTTAT-ATTTTT
1 TTTGTTTTTATCATTTTT
1073746 T
1 T
1073747 ATTCATGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.08, C:0.03, G:0.06, T:0.83
Consensus pattern (18 bp):
TTTGTTTTTATCATTTTT
Found at i:1083990 original size:17 final size:17
Alignment explanation
Indices: 1083962--1084002 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1083952 GTCCTAAGTT
*
1083962 GAAAAA-AAAAGAAGAA
1 GAAAAAGAAAAGAAAAA
*
1083978 GAAGAAGAAAAGAAAAA
1 GAAAAAGAAAAGAAAAA
1083995 GAAAAAGA
1 GAAAAAGA
1084003 GGAAAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (17 bp):
GAAAAAGAAAAGAAAAA
Found at i:1083997 original size:23 final size:22
Alignment explanation
Indices: 1083962--1084023 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 22
1083952 GTCCTAAGTT
1083962 GAAAAAAAAAGAAGAAGAAGAA
1 GAAAAAAAAAGAAGAAGAAGAA
* *
1083984 GAAAAGAAAAAGAAAAAGAGGAA
1 GAAAA-AAAAAGAAGAAGAAGAA
*
1084007 AAAATAACAAAAGAAGA
1 GAAA-AA-AAAAGAAGA
1084024 GAAAATAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 5 0.15
23 19 0.58
24 9 0.27
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.02
Consensus pattern (22 bp):
GAAAAAAAAAGAAGAAGAAGAA
Found at i:1084020 original size:18 final size:18
Alignment explanation
Indices: 1083997--1084031 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1083987 AAGAAAAAGA
*
1083997 AAAAGAGGAAAAAATAAC
1 AAAAGAAGAAAAAATAAC
*
1084015 AAAAGAAGAGAAAATAA
1 AAAAGAAGAAAAAATAA
1084032 GGTGGGTTCA
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:0.74, C:0.03, G:0.17, T:0.06
Consensus pattern (18 bp):
AAAAGAAGAAAAAATAAC
Found at i:1084943 original size:105 final size:106
Alignment explanation
Indices: 1084756--1085312 Score: 895
Period size: 105 Copynumber: 5.4 Consensus size: 106
1084746 GGTTTTACCC
* * *
1084756 AGAGTCAATTTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACGG
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
1084821 CGAAGGGACCGCTGGTTGTCAATAGACATTTCTC-AATTCT
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCT
*
1084861 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGTCAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
1084926 CGAAGGGACCGCTGGTTGCCAA-TAA-A----T-AATTTC-
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCT
* * *
1084959 AGGGCCAATTTTAACTTCACAACAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1085024 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTC-
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCT
1085064 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
1085129 TGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTC-
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCT
1085169 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
1085234 CGAAGGGACCACTGGTTGTCAACAAACATTTCTCAAATT-T
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCT
*
1085274 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1085313 GGAACAATAC
Statistics
Matches: 421, Mismatches: 22, Indels: 18
0.91 0.05 0.04
Matches are distributed among these distances:
98 82 0.19
99 7 0.02
100 1 0.00
103 1 0.00
104 2 0.00
105 328 0.78
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (106 bp):
AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCT
Found at i:1085117 original size:203 final size:207
Alignment explanation
Indices: 1084755--1085312 Score: 901
Period size: 203 Copynumber: 2.7 Consensus size: 207
1084745 AGGTTTTACC
* *
1084755 CAGAGTCAATTTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
1084820 GCGAAGGGACCGCTGGTTGTCAATAGACATTTCTC-AATTCTAGAGCCAATTTCAACTTCACAAC
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTC-AGAGCCAATTTCAACTTCACAAC
*
1084884 GAAGGATATTGGACTCCAGTCAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGCCAA-
130 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGCCAAC
* *
1084948 TAA-A-T-AATTT
195 AAACATTCAAATT
* * *
1084958 CAGGGCCAATTTTAACTTCACAACAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1085023 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACG
* *
1085088 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACA
131 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGCCAACA
1085153 AACATTTCTCAAATT
196 AACA--T-TCAAATT
1085168 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
1085233 ACGAAGGGACCACTGGTTGTCAACAAACATTTCTCAAATTTAGAGTCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACG
1085298 AAGGATATTGGACTC
131 AAGGATATTGGACTC
1085313 GGAACAATAC
Statistics
Matches: 328, Mismatches: 19, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
203 176 0.54
204 7 0.02
205 1 0.00
209 1 0.00
210 143 0.44
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (207 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACG
AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGCCAACA
AACATTCAAATT
Found at i:1087141 original size:16 final size:17
Alignment explanation
Indices: 1087110--1087144 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1087100 ATTACTCATA
*
1087110 TTTGTTTTTTTCATTTT
1 TTTGTTTTTATCATTTT
1087127 TTTGTTTTTAT-ATTTT
1 TTTGTTTTTATCATTTT
1087143 TT
1 TT
1087145 ATTCATGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.09, C:0.03, G:0.06, T:0.83
Consensus pattern (17 bp):
TTTGTTTTTATCATTTT
Found at i:1088487 original size:26 final size:27
Alignment explanation
Indices: 1088449--1088510 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
1088439 GATCTTGCCC
*
1088449 CATCCCAATAAATTCT-ATTTTTCTCT
1 CATCCCAATAAATTCTAATTTTTCCCT
* *
1088475 CGTCCCAATAAATTTTAATTTTTCCCT
1 CATCCCAATAAATTCTAATTTTTCCCT
1088502 CATCCCAAT
1 CATCCCAAT
1088511 TTTATCATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 14 0.45
27 17 0.55
ACGTcount: A:0.27, C:0.29, G:0.02, T:0.42
Consensus pattern (27 bp):
CATCCCAATAAATTCTAATTTTTCCCT
Found at i:1089146 original size:2 final size:2
Alignment explanation
Indices: 1089141--1089168 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1089131 AAATAAGCAA
1089141 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
1089169 TATCAACTGC
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:1092694 original size:19 final size:19
Alignment explanation
Indices: 1092649--1092698 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 19
1092639 TTTATCTTCA
*
1092649 TTATCTTAATTTTGATTGTT
1 TTATCTTAATCTTGA-TGTT
1092669 TTAATCTTAATCTTG-TGTT
1 TT-ATCTTAATCTTGATGTT
1092688 CTTATCTTAAT
1 -TTATCTTAAT
1092699 TTTTAAGTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 12 0.44
20 4 0.15
21 11 0.41
ACGTcount: A:0.22, C:0.10, G:0.08, T:0.60
Consensus pattern (19 bp):
TTATCTTAATCTTGATGTT
Found at i:1093001 original size:10 final size:10
Alignment explanation
Indices: 1092988--1093014 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1092978 AAAAAAAATG
1092988 AATTTAGATA
1 AATTTAGATA
1092998 AATTTAGATA
1 AATTTAGATA
1093008 AATTTAG
1 AATTTAG
1093015 GCAAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (10 bp):
AATTTAGATA
Found at i:1095606 original size:23 final size:20
Alignment explanation
Indices: 1095567--1095619 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
1095557 CATAATTATT
*
1095567 TAAAAAATTAAATAAAAATAC
1 TAAAAAATTTAATAAAAAT-C
1095588 TAAAAACATTTAATAAAAAATC
1 TAAAAA-ATTTAAT-AAAAATC
1095610 -AAAAAATTTA
1 TAAAAAATTTA
1095620 GGTTGAACCG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 5 0.17
21 11 0.38
22 7 0.24
23 6 0.21
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAAAAATTTAATAAAAATC
Found at i:1095614 original size:22 final size:21
Alignment explanation
Indices: 1095568--1095615 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
1095558 ATAATTATTT
1095568 AAAAAATTAAATAAAAATACTA
1 AAAAAATTAAATAAAAATAC-A
* *
1095590 AAAACATTTAATAAAAA-ATCA
1 AAAAAATTAAATAAAAATA-CA
1095611 AAAAA
1 AAAAA
1095616 TTTAGGTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACA
Found at i:1096119 original size:31 final size:32
Alignment explanation
Indices: 1096081--1096150 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
1096071 TCAAGTCGAT
1096081 TTTTTTTTAAAAAAA-TCGAGATCGGGTT-GG
1 TTTTTTTTAAAAAAATTCGAGATCGGGTTAGG
* *
1096111 ATTTTTTTTAAAAAAATTCGGGTTCGGGTTAGG
1 -TTTTTTTTAAAAAAATTCGAGATCGGGTTAGG
1096144 TTTTTTT
1 TTTTTTT
1096151 AAGTTTGATA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
31 15 0.43
32 18 0.51
33 2 0.06
ACGTcount: A:0.26, C:0.06, G:0.21, T:0.47
Consensus pattern (32 bp):
TTTTTTTTAAAAAAATTCGAGATCGGGTTAGG
Found at i:1096119 original size:32 final size:34
Alignment explanation
Indices: 1096078--1096150 Score: 100
Period size: 31 Copynumber: 2.3 Consensus size: 34
1096068 TATTCAAGTC
1096078 GATTTTTTTTTAAAAAAA-TCGAGATCGGGTT-G
1 GATTTTTTTTTAAAAAAATTCGAGATCGGGTTAG
* *
1096110 GA-TTTTTTTTAAAAAAATTCGGGTTCGGGTTAG
1 GATTTTTTTTTAAAAAAATTCGAGATCGGGTTAG
1096143 G-TTTTTTT
1 GATTTTTTT
1096151 AAGTTTGATA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
31 15 0.42
32 13 0.36
33 8 0.22
ACGTcount: A:0.26, C:0.05, G:0.22, T:0.47
Consensus pattern (34 bp):
GATTTTTTTTTAAAAAAATTCGAGATCGGGTTAG
Found at i:1100469 original size:35 final size:35
Alignment explanation
Indices: 1100423--1100492 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
1100413 TCAATTCTCA
*
1100423 AATTTATAATTTACGCAAAATTCATTTAGGATGTG
1 AATTTATAATTTACCCAAAATTCATTTAGGATGTG
*
1100458 AATTTATAATTTACCCAAAATTCATTTAGGGTGTG
1 AATTTATAATTTACCCAAAATTCATTTAGGATGTG
1100493 TTTGATAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (35 bp):
AATTTATAATTTACCCAAAATTCATTTAGGATGTG
Found at i:1100785 original size:16 final size:15
Alignment explanation
Indices: 1100764--1100795 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
1100754 CATTTTAATA
1100764 AAAATATTTAAGTATT
1 AAAATATTTAA-TATT
1100780 AAAATATTTAATATT
1 AAAATATTTAATATT
1100795 A
1 A
1100796 TTATAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (15 bp):
AAAATATTTAATATT
Found at i:1100837 original size:19 final size:19
Alignment explanation
Indices: 1100794--1100839 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
1100784 TATTTAATAT
*
1100794 TATTATAATATAATTTTAA
1 TATTATATTATAATTTTAA
*
1100813 TA--ATATTATATTTTTAA
1 TATTATATTATAATTTTAA
1100830 TATTATATTA
1 TATTATATTA
1100840 ATATATACTC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 15 0.65
19 8 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTATATTATAATTTTAA
Found at i:1100842 original size:11 final size:10
Alignment explanation
Indices: 1100784--1100843 Score: 54
Period size: 11 Copynumber: 6.0 Consensus size: 10
1100774 AGTATTAAAA
1100784 TATTTAATAT
1 TATTTAATAT
1100794 TATTATAATAT
1 TATT-TAATAT
* *
1100805 AATTTTAATAA
1 TA-TTTAATAT
1100816 TA-TT-ATAT
1 TATTTAATAT
1100824 T-TTTAATAT
1 TATTTAATAT
1100833 TATATTAATAT
1 TAT-TTAATAT
1100844 ATACTCAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
8 6 0.15
9 7 0.17
10 5 0.12
11 20 0.50
12 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TATTTAATAT
Found at i:1101308 original size:30 final size:30
Alignment explanation
Indices: 1101274--1101334 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
1101264 TTTCTAGAAA
* *
1101274 ATGTATTTCATTGTACATAAAACAGTTTTC
1 ATGTAATTCATTGTACATAAAACAATTTTC
* *
1101304 ATGTAATTCATTTTACGTAAAACAATTTTC
1 ATGTAATTCATTGTACATAAAACAATTTTC
1101334 A
1 A
1101335 AATAATCCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (30 bp):
ATGTAATTCATTGTACATAAAACAATTTTC
Found at i:1101346 original size:30 final size:30
Alignment explanation
Indices: 1101282--1101354 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
1101272 AAATGTATTT
* * * ** *
1101282 CATTGTACATAAAACAGTTTTCATGTAATT
1 CATTTTACGTAAAACAATTTTCAAATAATC
1101312 CATTTTACGTAAAACAATTTTCAAATAATC
1 CATTTTACGTAAAACAATTTTCAAATAATC
1101342 CATTTTACGTAAA
1 CATTTTACGTAAA
1101355 TTATTTTCCA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (30 bp):
CATTTTACGTAAAACAATTTTCAAATAATC
Found at i:1104055 original size:18 final size:18
Alignment explanation
Indices: 1104010--1104060 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
1104000 ATCGTTGATC
*
1104010 ATTGACCGTTGACCGTTG
1 ATTGACCGTTGACCGCTG
* *
1104028 ATCGATCGTTGACCGACT-
1 ATTGACCGTTGACCG-CTG
1104046 ATTGACCGTTGACCG
1 ATTGACCGTTGACCG
1104061 TCATTGACTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 26 0.96
19 1 0.04
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.29
Consensus pattern (18 bp):
ATTGACCGTTGACCGCTG
Found at i:1104527 original size:34 final size:28
Alignment explanation
Indices: 1104455--1104513 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
1104445 GCTGATCGTG
1104455 ATCGGCAGACTCAGTAGTAGGCTTCCTT
1 ATCGGCAGACTCAGTAGTAGGCTTCCTT
1104483 ATCGGCAGACTCAGTAGTAGGCTTCCTT
1 ATCGGCAGACTCAGTAGTAGGCTTCCTT
1104511 ATC
1 ATC
1104514 AGACTACTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.29
Consensus pattern (28 bp):
ATCGGCAGACTCAGTAGTAGGCTTCCTT
Found at i:1105400 original size:23 final size:23
Alignment explanation
Indices: 1105374--1105436 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
1105364 AACTCGTATA
*
1105374 AAATGTCCCGAAAGACCGCGTAG
1 AAATGTCCCGAAAGACAGCGTAG
* *
1105397 AAATGTCCCGAATGACATCGTAG
1 AAATGTCCCGAAAGACAGCGTAG
* * *
1105420 AATTGTCCTGAAGGACA
1 AAATGTCCCGAAAGACA
1105437 ACATATAAGT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (23 bp):
AAATGTCCCGAAAGACAGCGTAG
Found at i:1105769 original size:19 final size:19
Alignment explanation
Indices: 1105754--1105791 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1105744 CACACATAGT
*
1105754 ATAACATGTAACACATACA
1 ATAACATATAACACATACA
1105773 ATAACATATAACACATACA
1 ATAACATATAACACATACA
1105792 CTCATATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.21, G:0.03, T:0.21
Consensus pattern (19 bp):
ATAACATATAACACATACA
Found at i:1107049 original size:21 final size:21
Alignment explanation
Indices: 1107016--1107093 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
1107006 ACGACTCCTT
* *
1107016 AAGGATCACATATATATTCCA
1 AAGGACCACATATATGTTCCA
* *
1107037 AAGGACCAAATATATGTACCA
1 AAGGACCACATATATGTTCCA
*
1107058 AAGAACCACATATATGTTCCA
1 AAGGACCACATATATGTTCCA
**
1107079 AAGGATTACATATAT
1 AAGGACCACATATAT
1107094 ATCCTGAAGA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.26
Consensus pattern (21 bp):
AAGGACCACATATATGTTCCA
Found at i:1107110 original size:42 final size:42
Alignment explanation
Indices: 1107011--1107111 Score: 105
Period size: 42 Copynumber: 2.4 Consensus size: 42
1107001 GAAGGACGAC
* * *
1107011 TCCTTAAGGATCACATATATATTCCAAAGGACCAAATATATG
1 TCCTAAAGAATCACATATATATTCCAAAGGACCAAATATATA
* * ** *
1107053 TACC-AAAGAACCACATATATGTTCCAAAGGATTACATATATA
1 T-CCTAAAGAATCACATATATATTCCAAAGGACCAAATATATA
*
1107095 TCCTGAAGAATCACATA
1 TCCTAAAGAATCACATA
1107112 GAACCCTCAA
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
41 2 0.04
42 43 0.91
43 2 0.04
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.27
Consensus pattern (42 bp):
TCCTAAAGAATCACATATATATTCCAAAGGACCAAATATATA
Found at i:1110603 original size:21 final size:21
Alignment explanation
Indices: 1110577--1110616 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1110567 CAGAACCCCA
*
1110577 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
1110598 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
1110617 TCAAAGGGGG
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:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:1110646 original size:21 final size:21
Alignment explanation
Indices: 1110598--1110660 Score: 90
Period size: 21 Copynumber: 2.9 Consensus size: 21
1110588 ATTCCCCTGT
1110598 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTT-CCC-TCAA
*
1110621 AGGGGGAATCGGTTCCCTCAA
1 GGGGGGAATCGGTTCCCTCAA
*
1110642 GGGGGGAATCGATTCCCTC
1 GGGGGGAATCGGTTCCCTC
1110661 TGCACCAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 21 0.57
22 3 0.08
23 13 0.35
ACGTcount: A:0.19, C:0.25, G:0.35, T:0.21
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCTCAA
Found at i:1118203 original size:11 final size:11
Alignment explanation
Indices: 1118168--1118195 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1118158 AACTCATACA
1118168 CATTTTAAATT
1 CATTTTAAATT
1118179 CATTTTAAATT
1 CATTTTAAATT
1118190 CATTTT
1 CATTTT
1118196 TAACTCATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (11 bp):
CATTTTAAATT
Found at i:1119388 original size:34 final size:33
Alignment explanation
Indices: 1119331--1119398 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
1119321 TTTTGTAAAG
* *
1119331 GGGAAAGGTTCTAGCTAAGCCCGTGTAAAATCTA
1 GGGAAAGGTTATAGCTAAGCCCGTG-AAAAACTA
* * *
1119365 GGGAAAGGTTATAGTTTATCCCGTGAAAAACTA
1 GGGAAAGGTTATAGCTAAGCCCGTGAAAAACTA
1119398 G
1 G
1119399 TGAATTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
33 8 0.28
34 21 0.72
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (33 bp):
GGGAAAGGTTATAGCTAAGCCCGTGAAAAACTA
Found at i:1121932 original size:21 final size:21
Alignment explanation
Indices: 1121903--1122008 Score: 108
Period size: 21 Copynumber: 5.0 Consensus size: 21
1121893 ATCAGATTGT
1121903 CCAAGGGGTACATATTCCCCC
1 CCAAGGGGTACATATTCCCCC
*
1121924 CCAGGGGGTACATATTCCTCCC
1 CCAAGGGGTACATATTCC-CCC
* **
1121946 TGCAAGGGGTACCGATT-CCCC
1 -CCAAGGGGTACATATTCCCCC
* * *
1121967 CCAGGGGGAACAGATTCCCCC
1 CCAAGGGGTACATATTCCCCC
1121988 CCAAGGGGTAC-TGATTCCCCC
1 CCAAGGGGTACAT-ATTCCCCC
1122009 TGTCTAACGA
Statistics
Matches: 69, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
20 12 0.17
21 41 0.59
22 4 0.06
23 12 0.17
ACGTcount: A:0.21, C:0.37, G:0.25, T:0.18
Consensus pattern (21 bp):
CCAAGGGGTACATATTCCCCC
Found at i:1124767 original size:21 final size:23
Alignment explanation
Indices: 1124742--1124904 Score: 85
Period size: 20 Copynumber: 7.9 Consensus size: 23
1124732 CATATTTTCC
*
1124742 AGGGGTTACATA-T-CCCCTGCA
1 AGGGGTTACAGATTCCCCCTGCA
1124763 AGGGG-TACAGATTCCCCCTGC-
1 AGGGGTTACAGATTCCCCCTGCA
* *
1124784 AGGGGGTACCGATTCCCCC--CA
1 AGGGGTTACAGATTCCCCCTGCA
*
1124805 AGGGG-TACCGATTCCCCC--C-
1 AGGGGTTACAGATTCCCCCTGCA
* *
1124824 AGGGG-AACAGATTCCCCC--CC
1 AGGGGTTACAGATTCCCCCTGCA
* *
1124844 AGGGGGTACCGATT-CCCC--CA
1 AGGGGTTACAGATTCCCCCTGCA
**
1124864 AGGGGGAACAGATTCCCCC--CA
1 AGGGGTTACAGATTCCCCCTGCA
* *
1124885 TGGGG-TACTGATTCCCCCTG
1 AGGGGTTACAGATTCCCCCTG
1124905 TCTAACGGTC
Statistics
Matches: 121, Mismatches: 12, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
19 17 0.14
20 53 0.44
21 32 0.26
22 19 0.16
ACGTcount: A:0.20, C:0.35, G:0.28, T:0.17
Consensus pattern (23 bp):
AGGGGTTACAGATTCCCCCTGCA
Found at i:1124811 original size:20 final size:20
Alignment explanation
Indices: 1124761--1124902 Score: 153
Period size: 20 Copynumber: 7.0 Consensus size: 20
1124751 ATATCCCCTG
1124761 CAAGGGGTACAGATTCCCCC
1 CAAGGGGTACAGATTCCCCC
* *
1124781 TGCAGGGGGTACCGATTCCCCC
1 --CAAGGGGTACAGATTCCCCC
*
1124803 CAAGGGGTACCGATTCCCCC
1 CAAGGGGTACAGATTCCCCC
*
1124823 C-AGGGGAACAGATTCCCCCC
1 CAAGGGGTACAGATT-CCCCC
* *
1124843 CAGGGGGTACCGATT-CCCC
1 CAAGGGGTACAGATTCCCCC
*
1124862 CAAGGGGGAACAGATTCCCCC
1 CAA-GGGGTACAGATTCCCCC
* *
1124883 CATGGGGTACTGATTCCCCC
1 CAAGGGGTACAGATTCCCCC
1124903 TGTCTAACGG
Statistics
Matches: 102, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
19 17 0.17
20 51 0.50
21 16 0.16
22 18 0.18
ACGTcount: A:0.20, C:0.37, G:0.27, T:0.15
Consensus pattern (20 bp):
CAAGGGGTACAGATTCCCCC
Found at i:1124842 original size:40 final size:40
Alignment explanation
Indices: 1124761--1124902 Score: 187
Period size: 40 Copynumber: 3.5 Consensus size: 40
1124751 ATATCCCCTG
* * *
1124761 CAAGGGGTACAGATTCCCCCTGCAGGGGGTACCGATTCCCCC
1 CAAGGGGTACCGATTCCCCC--CAGGGGGAACAGATTCCCCC
1124803 CAAGGGGTACCGATTCCCCCCA-GGGGAACAGATTCCCCCC
1 CAAGGGGTACCGATTCCCCCCAGGGGGAACAGATT-CCCCC
* *
1124843 CAGGGGGTACCGATTCCCCCAAGGGGGAACAGATTCCCCC
1 CAAGGGGTACCGATTCCCCCCAGGGGGAACAGATTCCCCC
* *
1124883 CATGGGGTACTGATTCCCCC
1 CAAGGGGTACCGATTCCCCC
1124903 TGTCTAACGG
Statistics
Matches: 91, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
39 10 0.11
40 50 0.55
41 12 0.13
42 19 0.21
ACGTcount: A:0.20, C:0.37, G:0.27, T:0.15
Consensus pattern (40 bp):
CAAGGGGTACCGATTCCCCCCAGGGGGAACAGATTCCCCC
Found at i:1124859 original size:60 final size:61
Alignment explanation
Indices: 1124763--1124903 Score: 205
Period size: 60 Copynumber: 2.3 Consensus size: 61
1124753 ATCCCCTGCA
* * *
1124763 AGGGGTACAGATTCCCCCTGCAGGGGGTACCGATTCCCCCCAA-GGGGTACCGATTCCCCCC
1 AGGGGTACAGATTCCCCCTCCAGGGGGTACCGATT-CCCCCAAGGGGGAACAGATTCCCCCC
*
1124824 AGGGGAACAGATTCCCCC-CCAGGGGGTACCGATTCCCCCAAGGGGGAACAGATTCCCCCC
1 AGGGGTACAGATTCCCCCTCCAGGGGGTACCGATTCCCCCAAGGGGGAACAGATTCCCCCC
*
1124884 ATGGGGTACTGATTCCCCCT
1 A-GGGGTACAGATTCCCCCT
1124904 GTCTAACGGT
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
59 7 0.10
60 32 0.45
61 32 0.45
ACGTcount: A:0.20, C:0.36, G:0.28, T:0.16
Consensus pattern (61 bp):
AGGGGTACAGATTCCCCCTCCAGGGGGTACCGATTCCCCCAAGGGGGAACAGATTCCCCCC
Found at i:1125275 original size:34 final size:32
Alignment explanation
Indices: 1125236--1125305 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1125226 TTTTGTAAAG
* *
1125236 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAACTTAGCCCG-G-AAAAACTA
*
1125270 GGGAAAGGTTCTAATTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAACTTAGCCCGGAAAAACTA
1125302 GGGA
1 GGGA
1125306 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAACTTAGCCCGGAAAAACTA
Found at i:1125631 original size:21 final size:20
Alignment explanation
Indices: 1125606--1125644 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1125596 TTGATGTTTT
1125606 GATATAACAAATGAGTTTTAA
1 GATATAACAAATGA-TTTTAA
**
1125627 GATATTGCAAATGATTTT
1 GATATAACAAATGATTTT
1125645 CTTAGTTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.38
Consensus pattern (20 bp):
GATATAACAAATGATTTTAA
Found at i:1125880 original size:20 final size:21
Alignment explanation
Indices: 1125840--1125963 Score: 135
Period size: 21 Copynumber: 6.0 Consensus size: 21
1125830 ATCAGATTGT
*
1125840 CCAGGGGGTACATATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
*
1125861 TCAGGGGGTACAGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
* **
1125882 TGCAGGGGGTATTGATTCCCCC
1 -CCAGGGGGTACAGATTCCCCC
*
1125904 CCAGGGGGTACCGATT-CCCC
1 CCAGGGGGTACAGATTCCCCC
* * *
1125924 CCAAGGGGAACAGATTCCACC
1 CCAGGGGGTACAGATTCCCCC
*
1125945 CCA-GGGGTACTGATTCCCC
1 CCAGGGGGTACAGATTCCCC
1125964 TGTCTAACGG
Statistics
Matches: 86, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
20 30 0.35
21 38 0.44
22 18 0.21
ACGTcount: A:0.19, C:0.35, G:0.27, T:0.19
Consensus pattern (21 bp):
CCAGGGGGTACAGATTCCCCC
Found at i:1125889 original size:43 final size:40
Alignment explanation
Indices: 1125840--1125963 Score: 126
Period size: 43 Copynumber: 3.0 Consensus size: 40
1125830 ATCAGATTGT
1125840 CCAGGGGGTACATATTCCCCCTCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACATATTCCCCC-CAGGGGGTACAGATTCCCC
* *
1125881 CTGCAGGGGGTA-TTGATTCCCCCCCAGGGGGTACCGATTCCCC
1 C--CAGGGGGTACAT-ATT-CCCCCCAGGGGGTACAGATTCCCC
* * * *
1125924 CCAAGGGGAACAGATTCCACCCCA-GGGGTACTGATTCCCC
1 CCAGGGGGTACATATTCC-CCCCAGGGGGTACAGATTCCCC
1125964 TGTCTAACGG
Statistics
Matches: 70, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
40 17 0.24
41 16 0.23
42 1 0.01
43 31 0.44
44 5 0.07
ACGTcount: A:0.19, C:0.35, G:0.27, T:0.19
Consensus pattern (40 bp):
CCAGGGGGTACATATTCCCCCCAGGGGGTACAGATTCCCC
Found at i:1127141 original size:22 final size:22
Alignment explanation
Indices: 1127116--1127163 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
1127106 GTTATATATT
1127116 CCCCTGCAGGGGGTACAGATTC
1 CCCCTGCAGGGGGTACAGATTC
*
1127138 CCCCTGCAGGGGGTACCGATTC
1 CCCCTGCAGGGGGTACAGATTC
1127160 CCCC
1 CCCC
1127164 CCCCCATGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.15, C:0.40, G:0.29, T:0.17
Consensus pattern (22 bp):
CCCCTGCAGGGGGTACAGATTC
Found at i:1128176 original size:20 final size:20
Alignment explanation
Indices: 1128139--1128301 Score: 150
Period size: 20 Copynumber: 8.1 Consensus size: 20
1128129 ATCATATTTT
* *
1128139 CCAGGGGTTACATA-TCCCC
1 CCAGGGGGTACAGATTCCCC
1128158 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
** *
1128178 CTGCAAAGGGTACCGATTCCCCC
1 C--CAGGGGGTACAGATT-CCCC
*
1128201 CCAGGGGGTACCGATTCCCC
1 CCAGGGGGTACAGATTCCCC
* * *
1128221 CTAGGGGGAATAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
* *
1128241 GCCAAGGGGTACCGATTCCCC
1 -CCAGGGGGTACAGATTCCCC
*
1128262 CCAGGGGGGACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
* *
1128282 CCAGGGGATACTG-TTCCCC
1 CCAGGGGGTACAGATTCCCC
1128301 C
1 C
1128302 TGACTAACGG
Statistics
Matches: 117, Mismatches: 22, Indels: 10
0.79 0.15 0.07
Matches are distributed among these distances:
19 19 0.16
20 53 0.45
21 28 0.24
22 12 0.10
23 5 0.04
ACGTcount: A:0.20, C:0.36, G:0.28, T:0.17
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:1128190 original size:22 final size:22
Alignment explanation
Indices: 1128163--1128222 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 22
1128153 TCCCCCCAGG
* *
1128163 GGGTACAGATTCCCCCTGCAAA
1 GGGTACCGATTCCCCCTCCAAA
**
1128185 GGGTACCGATTCCCCC-CCAGG
1 GGGTACCGATTCCCCCTCCAAA
1128206 GGGTACCGATTCCCCCT
1 GGGTACCGATTCCCCCT
1128223 AGGGGGAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 18 0.55
22 15 0.45
ACGTcount: A:0.18, C:0.38, G:0.25, T:0.18
Consensus pattern (22 bp):
GGGTACCGATTCCCCCTCCAAA
Found at i:1128237 original size:41 final size:41
Alignment explanation
Indices: 1128154--1128302 Score: 158
Period size: 41 Copynumber: 3.6 Consensus size: 41
1128144 GGTTACATAT
* ** * *
1128154 CCCCCCAGGGGGTACAGATTCCCCCTGCAAAGGGTACCGATTC
1 CCCCCCAGGGGGTACCGATTCCCCCT--AGGGGGAACAGATTC
*
1128197 CCCCCCAGGGGGTACCGATTCCCCCTAGGGGGAATAGATTC
1 CCCCCCAGGGGGTACCGATTCCCCCTAGGGGGAACAGATTC
* * * *
1128238 CCCGCCAAGGGGTACCGATTCCCCCCAGGGGGGACAGATT-
1 CCCCCCAGGGGGTACCGATTCCCCCTAGGGGGAACAGATTC
* *
1128278 CCCCCCAGGGGATACTG-TTCCCCCT
1 CCCCCCAGGGGGTACCGATTCCCCCT
1128303 GACTAACGGT
Statistics
Matches: 90, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
39 7 0.08
40 13 0.14
41 45 0.50
43 25 0.28
ACGTcount: A:0.19, C:0.38, G:0.28, T:0.16
Consensus pattern (41 bp):
CCCCCCAGGGGGTACCGATTCCCCCTAGGGGGAACAGATTC
Found at i:1128621 original size:34 final size:32
Alignment explanation
Indices: 1128582--1128651 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1128572 TTTTGTAAAG
* *
1128582 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAACTTAGCCCG-G-AAAAACTA
*
1128616 GGGAAAGGTTCTAATTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAACTTAGCCCGGAAAAACTA
1128648 GGGA
1 GGGA
1128652 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAACTTAGCCCGGAAAAACTA
Found at i:1129212 original size:21 final size:21
Alignment explanation
Indices: 1129186--1129249 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 21
1129176 ATCAGATTGT
1129186 CCAGGGGGTACATATTCCCCC
1 CCAGGGGGTACATATTCCCCC
*
1129207 CCAGGGGGTACAGA-TCCCCC
1 CCAGGGGGTACATATTCCCCC
1129227 CTGCAGGGGGTAC-TGATTCCCCC
1 C--CAGGGGGTACAT-ATTCCCCC
1129250 TGTCTAACGG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
20 7 0.19
21 13 0.35
22 11 0.30
23 6 0.16
ACGTcount: A:0.17, C:0.38, G:0.28, T:0.17
Consensus pattern (21 bp):
CCAGGGGGTACATATTCCCCC
Found at i:1129250 original size:22 final size:22
Alignment explanation
Indices: 1129187--1129251 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
1129177 TCAGATTGTC
*
1129187 CAGGGGGTACAT-ATTCCCCC-C
1 CAGGGGGTAC-TGATTCCCCCTG
* *
1129208 CAGGGGGTACAGATCCCCCCTG
1 CAGGGGGTACTGATTCCCCCTG
1129230 CAGGGGGTACTGATTCCCCCTG
1 CAGGGGGTACTGATTCCCCCTG
1129252 TCTAACGGTC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 17 0.46
22 20 0.54
ACGTcount: A:0.17, C:0.35, G:0.29, T:0.18
Consensus pattern (22 bp):
CAGGGGGTACTGATTCCCCCTG
Found at i:1130431 original size:22 final size:22
Alignment explanation
Indices: 1130406--1130495 Score: 121
Period size: 22 Copynumber: 4.2 Consensus size: 22
1130396 TATATATTCT
*
1130406 CCTGCAGGGGGTACAGATTCCC
1 CCTGCAGGGGGTACCGATTCCC
1130428 CCTGCAGGGGGTACCGATTCCC
1 CCTGCAGGGGGTACCGATTCCC
1130450 CCT--AGGGGGTACCGATTCCC
1 CCTGCAGGGGGTACCGATTCCC
** * *
1130470 CCCCCATGGGGTACTGATTCCC
1 CCTGCAGGGGGTACCGATTCCC
1130492 CCTG
1 CCTG
1130496 TCTAACGGTC
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
20 19 0.32
22 41 0.68
ACGTcount: A:0.14, C:0.37, G:0.29, T:0.20
Consensus pattern (22 bp):
CCTGCAGGGGGTACCGATTCCC
Found at i:1130458 original size:42 final size:42
Alignment explanation
Indices: 1130411--1130494 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
1130401 ATTCTCCTGC
**
1130411 AGGGGGTACAGATTCCCCCTGCAGGGGGTACCGATTCCCCCT
1 AGGGGGTACAGATTCCCCCCCCAGGGGGTACCGATTCCCCCT
* * *
1130453 AGGGGGTACCGATTCCCCCCCCATGGGGTACTGATTCCCCCT
1 AGGGGGTACAGATTCCCCCCCCAGGGGGTACCGATTCCCCCT
1130495 GTCTAACGGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.15, C:0.36, G:0.29, T:0.20
Consensus pattern (42 bp):
AGGGGGTACAGATTCCCCCCCCAGGGGGTACCGATTCCCCCT
Found at i:1131493 original size:42 final size:40
Alignment explanation
Indices: 1131445--1131543 Score: 126
Period size: 42 Copynumber: 2.4 Consensus size: 40
1131435 ATCAGATTGT
* * *
1131445 CCAGGGGGTATATATTCCCCCTAGGGGGTACAGATTCCCC
1 CCAGGGGGTATAGATTCCCCCCAGGGGGAACAGATTCCCC
**
1131485 CTGCAGGGGGTACCGATTCCCCCCAGGGGGAACAGATTCCCC
1 C--CAGGGGGTATAGATTCCCCCCAGGGGGAACAGATTCCCC
*
1131527 CCAGGGGGTATTGATTC
1 CCAGGGGGTATAGATTC
1131544 ACCCTGTCTA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
40 15 0.30
42 35 0.70
ACGTcount: A:0.19, C:0.30, G:0.30, T:0.20
Consensus pattern (40 bp):
CCAGGGGGTATAGATTCCCCCCAGGGGGAACAGATTCCCC
Found at i:1131543 original size:20 final size:20
Alignment explanation
Indices: 1131445--1131536 Score: 121
Period size: 20 Copynumber: 4.5 Consensus size: 20
1131435 ATCAGATTGT
* *
1131445 CCAGGGGGTATATATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
1131465 CTAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
1131485 CTGCAGGGGGTACCGATTCCCC
1 C--CAGGGGGTACAGATTCCCC
*
1131507 CCAGGGGGAACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
1131527 CCAGGGGGTA
1 CCAGGGGGTA
1131537 TTGATTCACC
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
20 44 0.71
22 18 0.29
ACGTcount: A:0.20, C:0.32, G:0.32, T:0.17
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:1135642 original size:22 final size:21
Alignment explanation
Indices: 1135601--1135685 Score: 82
Period size: 21 Copynumber: 4.0 Consensus size: 21
1135591 ATCAGATTGT
* *
1135601 CCAAGGGTTACATATTCCCCC
1 CCAAGGGGTACAGATTCCCCC
1135622 CCAAGGGGTACAGATTCCCCC
1 CCAAGGGGTACAGATTCCCCC
* * *
1135643 TGCAGGGGGCATC-GATTCCCCC
1 -CCAAGGGGTA-CAGATTCCCCC
* *
1135665 CCAGGGGGTACCGATTCCCCC
1 CCAAGGGGTACAGATTCCCCC
1135686 AATGGGGAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
20 1 0.02
21 36 0.67
22 16 0.30
23 1 0.02
ACGTcount: A:0.19, C:0.39, G:0.25, T:0.18
Consensus pattern (21 bp):
CCAAGGGGTACAGATTCCCCC
Found at i:1135692 original size:20 final size:20
Alignment explanation
Indices: 1135619--1135725 Score: 58
Period size: 20 Copynumber: 5.2 Consensus size: 20
1135609 TACATATTCC
*
1135619 CCCCCAA-GGGGTACAGATT
1 CCCCCAAGGGGGCACAGATT
*
1135638 CCCCCTGCAGGGGGCATC-GATT
1 CCCCC--AAGGGGGCA-CAGATT
* * *
1135660 CCCCCCCAGGGGGTACCGATT
1 -CCCCCAAGGGGGCACAGATT
* * *
1135681 CCCCCAATGGGGAATAGATT
1 CCCCCAAGGGGGCACAGATT
* *
1135701 CCCCTC-ATGGGGCACTGATT
1 CCCC-CAAGGGGGCACAGATT
1135721 CCCCC
1 CCCCC
1135726 TGTCTAACGG
Statistics
Matches: 70, Mismatches: 11, Indels: 14
0.74 0.12 0.15
Matches are distributed among these distances:
19 6 0.09
20 35 0.50
21 14 0.20
22 9 0.13
23 6 0.09
ACGTcount: A:0.19, C:0.37, G:0.26, T:0.18
Consensus pattern (20 bp):
CCCCCAAGGGGGCACAGATT
Found at i:1136695 original size:42 final size:40
Alignment explanation
Indices: 1136647--1136751 Score: 129
Period size: 43 Copynumber: 2.5 Consensus size: 40
1136637 ATCAGATTAT
1136647 CCAGGGGGTACATATTCCCCCCAGGGGGTACAGATTCCCCC
1 CCAGGGGGTAC-TATTCCCCCCAGGGGGTACAGATTCCCCC
* * *
1136688 TGCAGGGGGTACCGATTCCCCCCCAGGGGGTACTGATTCCCCC
1 -CCAGGGGGTA-CTATT-CCCCCCAGGGGGTACAGATTCCCCC
*
1136731 CCAAGGGGTACTGATTCCCCC
1 CCAGGGGGTACT-ATTCCCCC
1136752 TGTCTAACGG
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
41 6 0.11
42 23 0.43
43 25 0.46
ACGTcount: A:0.17, C:0.37, G:0.28, T:0.18
Consensus pattern (40 bp):
CCAGGGGGTACTATTCCCCCCAGGGGGTACAGATTCCCCC
Found at i:1136696 original size:22 final size:21
Alignment explanation
Indices: 1136647--1136751 Score: 140
Period size: 21 Copynumber: 5.0 Consensus size: 21
1136637 ATCAGATTAT
*
1136647 CCAGGGGGTACATATT-CCCC
1 CCAGGGGGTACAGATTCCCCC
1136667 CCAGGGGGTACAGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
* *
1136688 TGCAGGGGGTACCGATTCCCCC
1 -CCAGGGGGTACAGATTCCCCC
*
1136710 CCAGGGGGTACTGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
* *
1136731 CCAAGGGGTACTGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
1136752 TGTCTAACGG
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
20 15 0.19
21 43 0.56
22 19 0.25
ACGTcount: A:0.17, C:0.37, G:0.28, T:0.18
Consensus pattern (21 bp):
CCAGGGGGTACAGATTCCCCC
Found at i:1140542 original size:38 final size:38
Alignment explanation
Indices: 1140491--1140583 Score: 143
Period size: 38 Copynumber: 2.4 Consensus size: 38
1140481 CTCGTATAAA
* *
1140491 TGTCCCGAAGGACCTATCAT-CTCGAAGGATGTCATCTG
1 TGTCCCGAAGGACCTATCATCCT-GAAGGATGTAATCCG
*
1140529 TGTCCCGAAGGACCTGTCATCCTGAAGGATGTAATCCG
1 TGTCCCGAAGGACCTATCATCCTGAAGGATGTAATCCG
1140567 TGTCCCGAAGGACCTAT
1 TGTCCCGAAGGACCTAT
1140584 TATATGTCTT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
38 48 0.96
39 2 0.04
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.25
Consensus pattern (38 bp):
TGTCCCGAAGGACCTATCATCCTGAAGGATGTAATCCG
Found at i:1140792 original size:46 final size:46
Alignment explanation
Indices: 1140735--1140839 Score: 167
Period size: 46 Copynumber: 2.3 Consensus size: 46
1140725 ATGTGTAGCC
* *
1140735 ATGT-ATTTCATATCATATCACATGTATCACGTATTATATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACATATTACATATTCAT
*
1140780 ATGTCATTTCATATCATATCACATGTATCACATATTGCATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACATATTACATATTCAT
*
1140826 ATATCATTTCATAT
1 ATGTCATTTCATAT
1140840 AGTCACATAG
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
45 4 0.07
46 51 0.93
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (46 bp):
ATGTCATTTCATATCATATCACATGTATCACATATTACATATTCAT
Found at i:1141305 original size:34 final size:35
Alignment explanation
Indices: 1141246--1141315 Score: 115
Period size: 34 Copynumber: 2.0 Consensus size: 35
1141236 TTTCGTTTAG
*
1141246 GGGGAATCGATACCCCCCCAGGGGGAATCTGTTCCC
1 GGGGAATCGATA-CCCCCCAAGGGGAATCTGTTCCC
1141282 GGGGAATCGATA-CCCCCAAGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCAAGGGGAATCTGTTCCC
1141316 CCTGCACATA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
34 21 0.64
36 12 0.36
ACGTcount: A:0.21, C:0.31, G:0.30, T:0.17
Consensus pattern (35 bp):
GGGGAATCGATACCCCCCAAGGGGAATCTGTTCCC
Found at i:1141316 original size:19 final size:18
Alignment explanation
Indices: 1141260--1141317 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 18
1141250 AATCGATACC
1141260 CCCCCAGGGGGAATCTGTT
1 CCCCCA-GGGGAATCTGTT
*
1141279 --CCC-GGGGAATC-GATA
1 CCCCCAGGGGAATCTG-TT
1141294 CCCCCAAGGGGAATCTGTT
1 CCCCC-AGGGGAATCTGTT
1141313 CCCCC
1 CCCCC
1141318 TGCACATACT
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
14 1 0.03
15 9 0.29
17 6 0.19
19 14 0.45
20 1 0.03
ACGTcount: A:0.19, C:0.36, G:0.28, T:0.17
Consensus pattern (18 bp):
CCCCCAGGGGAATCTGTT
Found at i:1144263 original size:96 final size:95
Alignment explanation
Indices: 1144108--1144339 Score: 326
Period size: 96 Copynumber: 2.4 Consensus size: 95
1144098 ATTGCATTCT
* *
1144108 AGTTTCAGGTTGTATTGAGTTGAATGGAATCATTGAAGGCATAAGAGTTATATGTGAAAAAGATC
1 AGTTTCAGGTTGTATTGAGTTGAATGGAGTCATTGAAGGCACAAGAGTTATATGTGAAAAAGATC
1144173 TCACTATATTTACAGTATTTGTTACATTTTG
66 TCACTATATTTACAGTATTTGTTACA-TTTG
* *
1144204 -GTTTCAGATTGTATTCAGTTGAAGTGGAGTCATTGAAGGCACAAGAGTT-TACCTG-GAAAAAG
1 AGTTTCAGGTTGTATTGAGTTGAA-TGGAGTCATTGAAGGCACAAGAGTTATA--TGTGAAAAAG
* * *
1144266 ATTTCAGTATATTTACAGTATTTGTTGCATTTG
63 ATCTCACTATATTTACAGTATTTGTTACATTTG
*
1144299 AGTTTCAGGTTGTATTGAGCTGAATGGGAGTCATTGAAGGC
1 AGTTTCAGGTTGTATTGAGTTGAAT-GGAGTCATTGAAGGC
1144340 GTATGAGTTA
Statistics
Matches: 121, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
95 28 0.23
96 91 0.75
97 2 0.02
ACGTcount: A:0.30, C:0.09, G:0.24, T:0.37
Consensus pattern (95 bp):
AGTTTCAGGTTGTATTGAGTTGAATGGAGTCATTGAAGGCACAAGAGTTATATGTGAAAAAGATC
TCACTATATTTACAGTATTTGTTACATTTG
Found at i:1150616 original size:174 final size:173
Alignment explanation
Indices: 1150297--1150646 Score: 610
Period size: 174 Copynumber: 2.0 Consensus size: 173
1150287 AATAATATTA
* *
1150297 TTTTTATGAAATTAATAAATATAATTAATTTTATTAATAATTGATTATATATTATTAAAATAAAA
1 TTTTTATGAAATTAATAAATATAATTAATTTTATTAATAATTAATTATATACTATTAAAATAAAA
*
1150362 TATTATATTATATTATAAAAATTACCAAAAAATATAATTTAATAATTAATATTTTATAAAAATGA
66 TATAATATTATATTATAAAAATTACCAAAAAATATAATTTAATAATTAATATTTTATAAAAATGA
*
1150427 TACTAAAATAATAATATTTTGAGTGTTTATGTTTTGAAGTGAAT
131 TACT-AAATAATAATATTTTGAGTGTTTATGCTTTGAAGTGAAT
1150471 TTTTTATGAAATTAATAAATATAATTAATTTTATTAATAATTAATTATATACTATTAAAATATAA
1 TTTTTATGAAATTAATAAATATAATTAATTTTATTAATAATTAATTATATACTATTAAAATA-AA
*
1150536 ATATAATATTATATTATAAAAATTACCAATAAATATAATTTAATAATTAATATTTTATAAAAAAA
65 ATATAATATTATATTATAAAAATTACCAAAAAATATAATTTAATAATTAATATTTTAT--AAAAA
1150601 TGATACTAAAATAATAATATTTTGAGTGTTTATGCTTTGAAGTGAA
128 TGATACT-AAATAATAATATTTTGAGTGTTTATGCTTTGAAGTGAA
1150647 AAGTTTGTAA
Statistics
Matches: 168, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
174 60 0.36
175 58 0.35
177 50 0.30
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.44
Consensus pattern (173 bp):
TTTTTATGAAATTAATAAATATAATTAATTTTATTAATAATTAATTATATACTATTAAAATAAAA
TATAATATTATATTATAAAAATTACCAAAAAATATAATTTAATAATTAATATTTTATAAAAATGA
TACTAAATAATAATATTTTGAGTGTTTATGCTTTGAAGTGAAT
Found at i:1150758 original size:12 final size:12
Alignment explanation
Indices: 1150746--1150804 Score: 68
Period size: 12 Copynumber: 5.1 Consensus size: 12
1150736 CCGAGTTTTA
1150746 AATATTA-TATT
1 AATATTATTATT
*
1150757 AAAATTA-TATT
1 AATATTATTATT
*
1150768 ATTATTATTATT
1 AATATTATTATT
*
1150780 ATTATTATTATT
1 AATATTATTATT
*
1150792 AATATTACTATT
1 AATATTATTATT
1150804 A
1 A
1150805 TTAATGTTAC
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
11 15 0.36
12 27 0.64
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (12 bp):
AATATTATTATT
Found at i:1150772 original size:3 final size:3
Alignment explanation
Indices: 1150760--1150807 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
1150750 TTATATTAAA
* *
1150760 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT AAT ATT ACT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1150807 A
1 A
1150808 ATGTTACATA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:1152049 original size:2 final size:2
Alignment explanation
Indices: 1152038--1152070 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1152028 GTTTTATCCA
1152038 AT AT -T 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
1152071 TAATGCATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1153432 original size:39 final size:38
Alignment explanation
Indices: 1153378--1153458 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 38
1153368 CACCCTAATC
1153378 AAATATTGGTGGCGACTCCTCGAATCGTATTTTTATCGT
1 AAATATTGGTGGCGACTCCTCGAATCGTA-TTTTATCGT
1153417 AAATATTGGTGGCGACTCCTCGAATCGTATTTTATCGT
1 AAATATTGGTGGCGACTCCTCGAATCGTATTTTATCGT
1153455 AAAT
1 AAAT
1153459 GAATTTCTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 13 0.31
39 29 0.69
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (38 bp):
AAATATTGGTGGCGACTCCTCGAATCGTATTTTATCGT
Found at i:1160335 original size:125 final size:125
Alignment explanation
Indices: 1160110--1160365 Score: 395
Period size: 125 Copynumber: 2.0 Consensus size: 125
1160100 AAGTTAGGAT
* * * *
1160110 ATGTTGGGGCATGACTGAAACCACATCATGTTGAGATGACAAGATTCAGACCAATGAGGCATGAA
1 ATGTTGGGCCACGACTGAAACCACATCATGTTGAGATGACAAGATTCAGACCAAGGAGGCATAAA
* * *
1160175 GAATGAGCCTTACAATTTGAGGTGATGAGGCATTTTGAGGGTCCGTACCGGTATAAGATA
66 GAACGAGCCTTACAATTTGAGGTGATGAGGCATTTTGAAGGTCCGTACCAGTATAAGATA
* *
1160235 ATGTTGGGCCACGACTGAACCCACATCATGTTGAGATGATAAGATTCAGACCAAGGAGGCATAAA
1 ATGTTGGGCCACGACTGAAACCACATCATGTTGAGATGACAAGATTCAGACCAAGGAGGCATAAA
* * **
1160300 GAACGAGCCTTACAATTTGAGGTGATGGGGTATTTTGAAGGTGTGTACCAGTATAAGATA
66 GAACGAGCCTTACAATTTGAGGTGATGAGGCATTTTGAAGGTCCGTACCAGTATAAGATA
1160360 ATGTTG
1 ATGTTG
1160366 TGGCACTAGT
Statistics
Matches: 118, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
125 118 1.00
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.25
Consensus pattern (125 bp):
ATGTTGGGCCACGACTGAAACCACATCATGTTGAGATGACAAGATTCAGACCAAGGAGGCATAAA
GAACGAGCCTTACAATTTGAGGTGATGAGGCATTTTGAAGGTCCGTACCAGTATAAGATA
Found at i:1161682 original size:37 final size:37
Alignment explanation
Indices: 1161630--1161788 Score: 137
Period size: 37 Copynumber: 4.3 Consensus size: 37
1161620 ATGAGATTGG
* *
1161630 AGCAAAGTCAATCTTAAGCCTTCACTGAAGAGTAGTAA
1 AGCAAA-TCCATCTTAAGCCTTCACTGAAGAGTAGTGA
* * ** *
1161668 AGCAAATCCATCTTAATCTTTCACCAAAGATTAGTGA
1 AGCAAATCCATCTTAAGCCTTCACTGAAGAGTAGTGA
**
1161705 AGCAAA-CCATCTTAATTCTTCA-TCGAAGAGTAGTGA
1 AGCAAATCCATCTTAAGCCTTCACT-GAAGAGTAGTGA
* * * * *
1161741 AGCAAATCCATTTTAAGCATTCTCAGAAGAGT-GTTGG
1 AGCAAATCCATCTTAAGCCTTCACTGAAGAGTAG-TGA
1161778 AGCAAA-CCATC
1 AGCAAATCCATC
1161789 AGATTATTAG
Statistics
Matches: 97, Mismatches: 20, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
36 35 0.36
37 56 0.58
38 6 0.06
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.26
Consensus pattern (37 bp):
AGCAAATCCATCTTAAGCCTTCACTGAAGAGTAGTGA
Found at i:1161739 original size:36 final size:37
Alignment explanation
Indices: 1161630--1161756 Score: 141
Period size: 37 Copynumber: 3.4 Consensus size: 37
1161620 ATGAGATTGG
* * * * *
1161630 AGCAAAGTCAATCTTAAGCCTTCACTGAAGAGTAGTAA
1 AGCAAA-TCCATCTTAATCTTTCACCGAAGAGTAGTGA
* *
1161668 AGCAAATCCATCTTAATCTTTCACCAAAGATTAGTGA
1 AGCAAATCCATCTTAATCTTTCACCGAAGAGTAGTGA
*
1161705 AGCAAA-CCATCTTAAT-TCTTCATCGAAGAGTAGTGA
1 AGCAAATCCATCTTAATCT-TTCACCGAAGAGTAGTGA
*
1161741 AGCAAATCCATTTTAA
1 AGCAAATCCATCTTAA
1161757 GCATTCTCAG
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
35 1 0.01
36 31 0.41
37 38 0.50
38 6 0.08
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.28
Consensus pattern (37 bp):
AGCAAATCCATCTTAATCTTTCACCGAAGAGTAGTGA
Found at i:1162382 original size:56 final size:56
Alignment explanation
Indices: 1162166--1162539 Score: 320
Period size: 56 Copynumber: 6.8 Consensus size: 56
1162156 GTGAAGCAAG
* * * * * * *
1162166 AGAAGA-TGTTCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCAGTCTT-C
1 AGAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCAAACCCGT-TTGT
* * * * * ****
1162220 AGAAGA-TGTTCTAGTTGC-ATACTCCCT-AAAGAAAGAGTGAGCAAACCCATAAAA
1 AGAAGATTATTCGAGTT-CTATACTTCCTGAAAGAAAGAGGGAGCAAACCCGTTTGT
* * * *
1162274 AGAAGA-TGTTCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCAAACCCGTTTGT
1 AGAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCAAACCCGTTTGT
* * * *
1162328 AGAAGATTATTCGAGCTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCTGTTTGC
1 AGAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCAAACCCGTTTGT
* *
1162384 AGAAGATTATTCGAGTTATATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGT
1 AGAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCAAACCCGTTTGT
* * * * **
1162440 AGAACATTATTCGAGTTTTATACTTCCTGAAAGAAAGATGGAGAAAACTTGTTTGT
1 AGAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCAAACCCGTTTGT
* * *
1162496 GGAAGATTGTTCGAG-TCTTATAC-TCTCTG-AAGAAATAGGGAGCA
1 AGAAGATTATTCGAGTTC-TATACTTC-CTGAAAGAAAGAGGGAGCA
1162540 GACACGATTG
Statistics
Matches: 270, Mismatches: 43, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
53 1 0.00
54 92 0.34
55 33 0.12
56 144 0.53
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (56 bp):
AGAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCAAACCCGTTTGT
Found at i:1162551 original size:45 final size:45
Alignment explanation
Indices: 1162500--1162806 Score: 254
Period size: 55 Copynumber: 6.2 Consensus size: 45
1162490 GTTTGTGGAA
1162500 GATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACAC
1 GATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACAC
1162545 GATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACAC
1 GATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACAC
* * * *
1162590 GATTGTTCGAGTCTTATACTCTCTAAAGGAATAGGGAGCATACATGATTGTTGAA
1 GATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAG----CA-GA-----CAC
* *
1162645 GATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGTAGACAC
1 GATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACAC
* *
1162690 GATTGTTGAAAATTGTTCGAGTCATATACTCTCTGAAGGAATAGGGAGCAGACAC
1 -------G---ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACAC
* *
1162745 GATTGTTGAAGATTGTTCGAGTCTTATATTTTCTGAAGAAATAGGGAGCAGACAC
1 ----------GATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACAC
1162800 GATTGTT
1 GATTGTT
1162807 GAAGATTGTT
Statistics
Matches: 221, Mismatches: 18, Indels: 46
0.78 0.06 0.16
Matches are distributed among these distances:
45 89 0.40
49 2 0.01
50 4 0.02
51 1 0.00
52 1 0.00
55 120 0.54
58 4 0.02
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (45 bp):
GATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACAC
Found at i:1162674 original size:55 final size:55
Alignment explanation
Indices: 1162590--1163115 Score: 658
Period size: 55 Copynumber: 9.7 Consensus size: 55
1162580 GAGCAGACAC
* * *
1162590 GATTGTTCGAGTCTTATACTCTCTAAAGGAATAGGGAGCATACATGATTGTTGAA
1 GATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAA
*
1162645 GATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGTAGACACGATTGTTGAA
1 GATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAA
* *
1162700 AATTGTTCGAGTCATATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAA
1 GATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAA
* * *
1162755 GATTGTTCGAGTCTTATATTTTCTGAAGAAATAGGGAGCAGACACGATTGTTGAA
1 GATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAA
* *
1162810 GATTGTTCGAGTCTTATACTCTCTAAAGGAATAGGGAGCGGACACGATTGTTGAA
1 GATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAA
* *
1162865 GATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACATGTTTGTTGAA
1 GATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAA
* * * * * * *
1162920 GGTTGTTCAATTCCTATACTCTCTGAAGAAATAAGGAGC-GAACACGTTTGTTGAA
1 GATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAG-ACACGATTGTTGAA
* * *
1162975 GA----TCGAGTCCTATACTCTCTGAATGAATAGGGAGCAGACACGTTTGTTGAA
1 GATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAA
* * * * *
1163026 GA----TCGAGTCCTATACTGTCTGAAGGAATAGGGAACAGACCCG-TTTTATGAA
1 GATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT-TGAA
* * * * * *
1163077 GATTGTTTGAGTTTTACACTCCCTGAAGCAAGAGGGAGC
1 GATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGC
1163116 GAACCTGCTG
Statistics
Matches: 416, Mismatches: 48, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
50 3 0.01
51 86 0.21
52 1 0.00
54 1 0.00
55 325 0.78
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (55 bp):
GATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAA
Found at i:1163310 original size:11 final size:12
Alignment explanation
Indices: 1163290--1163360 Score: 56
Period size: 14 Copynumber: 5.6 Consensus size: 12
1163280 TGTCCGAGTT
1163290 TTAAATATTATA
1 TTAAATATTATA
1163302 TTAAA-ATTATA
1 TTAAATATTATA
*
1163313 TT-ATTATTATTA
1 TTAAATATTA-TA
*
1163325 TTATATTATTATTA
1 TTA-AATATTA-TA
1163339 TTATAACTATTATA
1 TTA-AA-TATTATA
1163353 TTATAATA
1 TTA-AATA
1163361 CATTATTATT
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
10 1 0.02
11 12 0.23
12 9 0.17
13 2 0.04
14 23 0.44
15 5 0.10
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (12 bp):
TTAAATATTATA
Found at i:1163319 original size:3 final size:3
Alignment explanation
Indices: 1163307--1163403 Score: 92
Period size: 3 Copynumber: 32.7 Consensus size: 3
1163297 TTATATTAAA
* *
1163307 ATT A-T ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATA ACT ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
1163352 ATT ATA ATAC ATT ATT ATT ATT ATT ATT ACT ATT ATT AAT GTT ATAT
1 ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
1163399 ATT AT
1 ATT AT
1163404 ATTTTACAGG
Statistics
Matches: 76, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
2 6 0.08
3 65 0.86
4 5 0.07
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:1169989 original size:16 final size:16
Alignment explanation
Indices: 1169968--1170004 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
1169958 TCCCCTTCTA
1169968 GATTTCGATCTGCCAT
1 GATTTCGATCTGCCAT
1169984 GATTTCGATCTGCCAT
1 GATTTCGATCTGCCAT
1170000 GATTT
1 GATTT
1170005 GAATTTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.41
Consensus pattern (16 bp):
GATTTCGATCTGCCAT
Found at i:1172196 original size:37 final size:37
Alignment explanation
Indices: 1172103--1172196 Score: 84
Period size: 37 Copynumber: 2.5 Consensus size: 37
1172093 AATTTCTTTG
* *
1172103 TTAATCAAAATGTTGATATGAATTTATGATTCTCCAA
1 TTAATCAAAATATTGAGATGAATTTATGATTCTCCAA
* * * * *
1172140 CTAATTATAATAATT-AGATGACTTTATGATTCAT-CTA
1 TTAATCAAAAT-ATTGAGATGAATTTATGATTC-TCCAA
*
1172177 TTAATCACAATATTGAGATG
1 TTAATCAAAATATTGAGATG
1172197 TTGTAAGTTG
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
36 3 0.07
37 38 0.86
38 3 0.07
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (37 bp):
TTAATCAAAATATTGAGATGAATTTATGATTCTCCAA
Found at i:1176707 original size:17 final size:17
Alignment explanation
Indices: 1176682--1176721 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1176672 ACAATTTTGC
*
1176682 TTCTCTTTTTTTCCTTT
1 TTCTTTTTTTTTCCTTT
*
1176699 TTCTTTTTTTTTTCTTT
1 TTCTTTTTTTTTCCTTT
1176716 TT-TTTT
1 TTCTTTT
1176722 CTTCGATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
TTCTTTTTTTTTCCTTT
Found at i:1176712 original size:11 final size:11
Alignment explanation
Indices: 1176696--1176721 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1176686 CTTTTTTTCC
1176696 TTTTTCTTTTT
1 TTTTTCTTTTT
1176707 TTTTTCTTTTT
1 TTTTTCTTTTT
1176718 TTTT
1 TTTT
1176722 CTTCGATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:1187353 original size:168 final size:168
Alignment explanation
Indices: 1187074--1187409 Score: 656
Period size: 168 Copynumber: 2.0 Consensus size: 168
1187064 AAGCTCCGTT
1187074 TTTTATATAATTTATGTTGATATGTATCTGAGAAATTATTGGAAGTTGAATTAAATATCAAAGGC
1 TTTTATATAATTTATGTTGATATGTATCTGAGAAATTATTGGAAGTTGAATTAAATATCAAAGGC
1187139 GTTCGAATGGAATTTTTATGGTCGATCAGTATGGCACGAAAAATCGAGGTAATACTTTACTACCT
66 GTTCGAATGGAATTTTTATGGTCGATCAGTATGGCACGAAAAATCGAGGTAATACTTTACTACCT
1187204 CTTTAAGCTTTATGGAACATGTTTAATATTGGTAAATGC
131 CTTTAAGCTTTATGGAACATG-TTAATATTGGTAAATGC
1187243 TTTTATATAATTTATGTTGATATGTATCTGAG-AATTATTGGAAGTTGAATTAAATATCAAAGGC
1 TTTTATATAATTTATGTTGATATGTATCTGAGAAATTATTGGAAGTTGAATTAAATATCAAAGGC
1187307 GTTCGAATGGAATTTTTATGGTCGATCAGTATGGCACGAAAAATCGAGGTAATACTTTACTACCT
66 GTTCGAATGGAATTTTTATGGTCGATCAGTATGGCACGAAAAATCGAGGTAATACTTTACTACCT
1187372 CTTTAAGCTTTATGGAACATGTTAATATTGGTAAATGC
131 CTTTAAGCTTTATGGAACATGTTAATATTGGTAAATGC
1187410 ATGAATAAGA
Statistics
Matches: 167, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
167 17 0.10
168 118 0.71
169 32 0.19
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (168 bp):
TTTTATATAATTTATGTTGATATGTATCTGAGAAATTATTGGAAGTTGAATTAAATATCAAAGGC
GTTCGAATGGAATTTTTATGGTCGATCAGTATGGCACGAAAAATCGAGGTAATACTTTACTACCT
CTTTAAGCTTTATGGAACATGTTAATATTGGTAAATGC
Found at i:1187761 original size:17 final size:18
Alignment explanation
Indices: 1187729--1187765 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1187719 GGATTAATAA
1187729 ATCTGAAAAGATATATTG
1 ATCTGAAAAGATATATTG
*
1187747 ATCTGATAA-ATATATTG
1 ATCTGAAAAGATATATTG
1187764 AT
1 AT
1187766 GTGCATAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (18 bp):
ATCTGAAAAGATATATTG
Found at i:1188350 original size:13 final size:13
Alignment explanation
Indices: 1188332--1188359 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1188322 AAATTACCAA
1188332 AATGGCCTATACT
1 AATGGCCTATACT
1188345 AATGGCCTATACT
1 AATGGCCTATACT
1188358 AA
1 AA
1188360 GTAAATATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (13 bp):
AATGGCCTATACT
Found at i:1189984 original size:43 final size:43
Alignment explanation
Indices: 1189640--1189972 Score: 537
Period size: 43 Copynumber: 7.8 Consensus size: 43
1189630 TTAATTACCG
* *
1189640 TTACAGTTCCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1189683 TTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1189726 TTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* *
1189769 TTACAGTTCCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
*
1189812 TTACAG-TTCCCCAGGTCTCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* * *
1189854 TTACAGTTCCCCCAGGTTCATTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* *
1189897 TTACAGTTT-CCCAGGTTCTTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* *
1189939 TTACAGTTTCCCCAGG-CTCTTTGCTATGTGCAAG
1 TTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAG
1189973 TATAAGACCT
Statistics
Matches: 271, Mismatches: 17, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
42 94 0.35
43 177 0.65
ACGTcount: A:0.17, C:0.26, G:0.25, T:0.32
Consensus pattern (43 bp):
TTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
Found at i:1189984 original size:85 final size:85
Alignment explanation
Indices: 1189640--1189972 Score: 533
Period size: 85 Copynumber: 3.9 Consensus size: 85
1189630 TTAATTACCG
* *
1189640 TTACAGTTCCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCTT
1 TTACAGTT-CCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTCCCTT
1189705 TGCTGTGTGCAAGGGTAAGCC
65 TGCTGTGTGCAAGGGTAAGCC
1189726 TTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTCCCTT
1 TTACAG-TTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTCCCTT
*
1189791 TGTTGTGTGCAAGGGTAAGCC
65 TGCTGTGTGCAAGGGTAAGCC
* * *
1189812 TTACAGTTCCCCAGGTCTCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTTCATTT
1 TTACAGTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTCCCTTT
1189877 GCTGTGTGCAAGGGTAAGCC
66 GCTGTGTGCAAGGGTAAGCC
* * * * *
1189897 TTACAGTTTCCCAGGTTCTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGG-CTCTTT
1 TTACAGTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTCCCTTT
*
1189961 GCTATGTGCAAG
66 GCTGTGTGCAAG
1189973 TATAAGACCT
Statistics
Matches: 230, Mismatches: 16, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
84 14 0.06
85 128 0.56
86 86 0.37
87 2 0.01
ACGTcount: A:0.17, C:0.26, G:0.25, T:0.32
Consensus pattern (85 bp):
TTACAGTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTCCCTTT
GCTGTGTGCAAGGGTAAGCC
Found at i:1191004 original size:28 final size:25
Alignment explanation
Indices: 1190947--1191020 Score: 73
Period size: 28 Copynumber: 2.8 Consensus size: 25
1190937 AAATAAGTAT
1190947 ATAAATAAGATACAATAATATATATCTA
1 ATAAATAAGAT--AATAATAT-TATCTA
1190975 ATAAATAAGATATATAATATTACTCTTA
1 ATAAATAAGATA-ATAATATTA-TC-TA
1191003 AT-AAT-A-ATAATAATATTA
1 ATAAATAAGATAATAATATTA
1191021 ATTAATTAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
24 9 0.21
25 3 0.07
26 4 0.09
27 12 0.28
28 15 0.35
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.36
Consensus pattern (25 bp):
ATAAATAAGATAATAATATTATCTA
Found at i:1191069 original size:26 final size:25
Alignment explanation
Indices: 1191000--1191061 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 25
1190990 AATATTACTC
*
1191000 TTAATAATAATAATAATATTAATTAA
1 TTAATAATAATAA-AATATTAATAAA
*
1191026 TTAATACTAATACAAATATT-ATAAA
1 TTAATAATAATA-AAATATTAATAAA
1191051 TTAATAATAAT
1 TTAATAATAAT
1191062 TAAGAATAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 14 0.44
26 17 0.53
27 1 0.03
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.40
Consensus pattern (25 bp):
TTAATAATAATAAAATATTAATAAA
Found at i:1201033 original size:2 final size:2
Alignment explanation
Indices: 1201026--1201058 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1201016 TCCCAACTCA
1201026 AT AT 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 AT AT A
1201059 AATTCTTCAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1201231 original size:2 final size:2
Alignment explanation
Indices: 1201224--1201252 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1201214 GTCATTTAAT
1201224 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1201253 TATTAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1201641 original size:22 final size:23
Alignment explanation
Indices: 1201598--1201646 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
1201588 AGAAAATGTC
*
1201598 TTTTAACATATATTAAATAATT-
1 TTTTAACATATATTAAAGAATTG
*
1201620 TTTTAATATAT-TTAAAAGAATTG
1 TTTTAACATATATT-AAAGAATTG
1201643 TTTT
1 TTTT
1201647 GGATTGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 2 0.09
22 17 0.74
23 4 0.17
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (23 bp):
TTTTAACATATATTAAAGAATTG
Found at i:1201821 original size:25 final size:26
Alignment explanation
Indices: 1201777--1201826 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
1201767 ACTTCAAATA
*
1201777 TGACAATAATTAAATTGTCACTTTTG
1 TGACAATAATTAAAATGTCACTTTTG
*
1201803 TGACAATAA-TAAAATGTCATTTTT
1 TGACAATAATTAAAATGTCACTTTT
1201827 AGCGTCTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (26 bp):
TGACAATAATTAAAATGTCACTTTTG
Found at i:1209046 original size:15 final size:15
Alignment explanation
Indices: 1209026--1209082 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
1209016 CCGGATGTTA
*
1209026 CGGGTACCCAGTAAT
1 CGGGTACCCGGTAAT
**
1209041 CGGGTACCCGGATTTT
1 CGGGTACCCGG-TAAT
1209057 ACGGGTACCCGGTAAT
1 -CGGGTACCCGGTAAT
1209073 CGGGTACCCG
1 CGGGTACCCG
1209083 ATACCCGGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 20 0.57
16 4 0.11
17 11 0.31
ACGTcount: A:0.19, C:0.28, G:0.32, T:0.21
Consensus pattern (15 bp):
CGGGTACCCGGTAAT
Found at i:1209059 original size:32 final size:32
Alignment explanation
Indices: 1209014--1209082 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
1209004 CCGTGTCCCG
1209014 ACCCGGATGTTACGGGTACCCAGTAATCGGGT
1 ACCCGGATGTTACGGGTACCCAGTAATCGGGT
* *
1209046 ACCCGGATTTTACGGGTACCCGGTAATCGGGT
1 ACCCGGATGTTACGGGTACCCAGTAATCGGGT
1209078 ACCCG
1 ACCCG
1209083 ATACCCGGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.20, C:0.28, G:0.30, T:0.22
Consensus pattern (32 bp):
ACCCGGATGTTACGGGTACCCAGTAATCGGGT
Found at i:1209063 original size:17 final size:17
Alignment explanation
Indices: 1209014--1209082 Score: 65
Period size: 15 Copynumber: 4.3 Consensus size: 17
1209004 CCGTGTCCCG
*
1209014 ACCCGGATGTTACGGGT
1 ACCCGGATATTACGGGT
* *
1209031 ACCCAG-TAAT-CGGGT
1 ACCCGGATATTACGGGT
*
1209046 ACCCGGATTTTACGGGT
1 ACCCGGATATTACGGGT
*
1209063 ACCCGG-TAAT-CGGGT
1 ACCCGGATATTACGGGT
1209078 ACCCG
1 ACCCG
1209083 ATACCCGGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
15 20 0.48
16 6 0.14
17 16 0.38
ACGTcount: A:0.20, C:0.28, G:0.30, T:0.22
Consensus pattern (17 bp):
ACCCGGATATTACGGGT
Found at i:1209278 original size:10 final size:9
Alignment explanation
Indices: 1209263--1209287 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1209253 ATAATTATAT
1209263 ATAAAAAAA
1 ATAAAAAAA
1209272 ATAAAAAAA
1 ATAAAAAAA
1209281 ATAAAAA
1 ATAAAAA
1209288 CTAACCGGGT
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:1211460 original size:21 final size:21
Alignment explanation
Indices: 1211436--1211485 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1211426 GCTTTGGAAT
* *
1211436 TTTTCCTGGGATGCAACTAGC
1 TTTTCATGGGATGCAACCAGC
* *
1211457 TTTTTATGGGATGTAACCAGC
1 TTTTCATGGGATGCAACCAGC
1211478 TTTTCATG
1 TTTTCATG
1211486 TAAAATTGCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (21 bp):
TTTTCATGGGATGCAACCAGC
Found at i:1217485 original size:41 final size:41
Alignment explanation
Indices: 1217439--1217516 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
1217429 ATTGTATCAC
*
1217439 TAGTCTTAGTTGGTGATTTGTGACTACAA-TTATTTTTTCAA
1 TAGTCTTAGTTGGTGATTTATGACTA-AACTTATTTTTTCAA
*
1217480 TAGTCTTAGTTGGTGATTTATGATTAAACTTATTTTT
1 TAGTCTTAGTTGGTGATTTATGACTAAACTTATTTTT
1217517 GTCACTATTG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 2 0.06
41 32 0.94
ACGTcount: A:0.24, C:0.08, G:0.17, T:0.51
Consensus pattern (41 bp):
TAGTCTTAGTTGGTGATTTATGACTAAACTTATTTTTTCAA
Found at i:1218289 original size:35 final size:35
Alignment explanation
Indices: 1218212--1218290 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 35
1218202 GTATTTAAAT
*
1218212 ACAAACTTACAATAAGAATTAAATGGTAAATGATA
1 ACAAAATTACAATAAGAATTAAATGGTAAATGATA
*
1218247 ACCAAATTACAATAACTGATATTAAATGGT-AAT-A-A
1 ACAAAATTACAATAA--GA-ATTAAATGGTAAATGATA
1218282 ACAAAATTA
1 ACAAAATTA
1218291 ATTGAAATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
35 22 0.58
36 1 0.03
37 5 0.13
38 10 0.26
ACGTcount: A:0.54, C:0.10, G:0.09, T:0.27
Consensus pattern (35 bp):
ACAAAATTACAATAAGAATTAAATGGTAAATGATA
Found at i:1218518 original size:12 final size:12
Alignment explanation
Indices: 1218501--1218527 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1218491 ACTCCTCGCT
1218501 GTCATCGTCGTC
1 GTCATCGTCGTC
1218513 GTCATCGTCGTC
1 GTCATCGTCGTC
1218525 GTC
1 GTC
1218528 CTGAGCAGGT
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:0.07, C:0.33, G:0.26, T:0.33
Consensus pattern (12 bp):
GTCATCGTCGTC
Found at i:1220617 original size:18 final size:17
Alignment explanation
Indices: 1220585--1220630 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
1220575 GAATTATATT
1220585 AGTAAAATATTAAATAA
1 AGTAAAATATTAAATAA
1220602 AGTAAAATACTTAAATAA
1 AGTAAAATA-TTAAATAA
*
1220620 ATTAAATATAT
1 AGTAAA-ATAT
1220631 AATATTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 9 0.35
18 14 0.54
19 3 0.12
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (17 bp):
AGTAAAATATTAAATAA
Found at i:1221581 original size:112 final size:112
Alignment explanation
Indices: 1221384--1221956 Score: 934
Period size: 112 Copynumber: 5.1 Consensus size: 112
1221374 TTGTCGGTTT
* **
1221384 GTGTCGATACTTTATAAAAATATATTAATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
*
1221449 GGTCTATAAATGACAAAACAGGTAAAGAGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
1221496 GTGTCGATACTTTATAAAAATGTATCTATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
* **
1221561 AGTCTATAAATGACAAAACAGGTAAAGCGCTACTAGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
1221608 GTGACGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
* *
1221673 GGTCTATAAATGAAAAAACAGGTAAAACGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
1221720 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
* *
1221785 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * * *
1221832 GTATCGATACTTTATAAAAATGTATCGATCCATAACAATAAAACACGT--AAAAATGACAAAATC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
* *
1221895 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
1221942 GTGTCGACACTTTAT
1 GTGTCGATACTTTAT
1221957 TATAAGTATC
Statistics
Matches: 435, Mismatches: 26, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
110 74 0.17
112 361 0.83
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:1222181 original size:162 final size:162
Alignment explanation
Indices: 1221904--1222236 Score: 585
Period size: 162 Copynumber: 2.1 Consensus size: 162
1221894 CGGTCTATAA
* *
1221904 ATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGACACTTTATTATAAGTATCGA
1 ATGACAAAACAGGTAAAGAGCTACCAGATATGTTGATAGTGTCGACACTTTATTATAAGTATCGA
* *
1221969 CACTTTTGAAATTTAAAAGAGAAGAAGTTATAGCACTAATAAAATGTCGATACTTTATAAAAATG
66 CACTTTTGAAATTTAAAAGAAAAGAAGTTATAGCACCAATAAAATGTCGATACTTTATAAAAATG
1222034 TATCGATCCATAACAATATAACAGGTAAAAAT
131 TATCGATCCATAACAATATAACAGGTAAAAAT
* *
1222066 ATGACAAAACTGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTATTATAAGTATCGA
1 ATGACAAAACAGGTAAAGAGCTACCAGATATGTTGATAGTGTCGACACTTTATTATAAGTATCGA
* * *
1222131 CACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATG
66 CACTTTTGAAATTTAAAAGAAAAGAAGTTATAGCACCAATAAAATGTCGATACTTTATAAAAATG
1222196 TATCGATCCATAACAATATAACAGGTAAAAAT
131 TATCGATCCATAACAATATAACAGGTAAAAAT
1222228 ATGACAAAA
1 ATGACAAAA
1222237 TTGATCTCGA
Statistics
Matches: 162, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
162 162 1.00
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (162 bp):
ATGACAAAACAGGTAAAGAGCTACCAGATATGTTGATAGTGTCGACACTTTATTATAAGTATCGA
CACTTTTGAAATTTAAAAGAAAAGAAGTTATAGCACCAATAAAATGTCGATACTTTATAAAAATG
TATCGATCCATAACAATATAACAGGTAAAAAT
Found at i:1222911 original size:23 final size:23
Alignment explanation
Indices: 1222882--1222929 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
1222872 AAATAGCTCA
*
1222882 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTAATACATT
*
1222905 ATATAAGCGCTACCTAATATATT
1 ATATAAGCGCTACCTAATACATT
1222928 AT
1 AT
1222930 TGTACTTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATACATT
Found at i:1223390 original size:21 final size:21
Alignment explanation
Indices: 1223364--1223408 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
1223354 TTGCATTGTA
1223364 ATTTTCCAAATTCGCGTTGCG
1 ATTTTCCAAATTCGCGTTGCG
*
1223385 ATTTTCCTAATTCGCGTTGCG
1 ATTTTCCAAATTCGCGTTGCG
1223406 ATT
1 ATT
1223409 ACGTAAATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (21 bp):
ATTTTCCAAATTCGCGTTGCG
Found at i:1223425 original size:20 final size:20
Alignment explanation
Indices: 1223402--1223528 Score: 218
Period size: 20 Copynumber: 6.3 Consensus size: 20
1223392 TAATTCGCGT
*
1223402 TGCGATTACGTAAATCGCAA
1 TGCGAATACGTAAATCGCAA
1223422 TGCGAATACGTAAATCGCAA
1 TGCGAATACGTAAATCGCAA
1223442 TGCGAATACGTAAATCGCAA
1 TGCGAATACGTAAATCGCAA
1223462 TGCGAATACGTAAATCGCAA
1 TGCGAATACGTAAATCGCAA
*
1223482 TGCGAATACATAAATCGCAA
1 TGCGAATACGTAAATCGCAA
*
1223502 CGCGAATACGTAAATCGCAA
1 TGCGAATACGTAAATCGCAA
*
1223522 CGCGAAT
1 TGCGAAT
1223529 TTGACTATCA
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 103 1.00
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (20 bp):
TGCGAATACGTAAATCGCAA
Found at i:1223752 original size:22 final size:22
Alignment explanation
Indices: 1223727--1223788 Score: 106
Period size: 22 Copynumber: 2.8 Consensus size: 22
1223717 ACATCCGTCC
1223727 CCATCTCCGACGAAATCAGTCT
1 CCATCTCCGACGAAATCAGTCT
*
1223749 CCATCTCCGACGATATCAGTCT
1 CCATCTCCGACGAAATCAGTCT
*
1223771 CCATCTCCGGCGAAATCA
1 CCATCTCCGACGAAATCA
1223789 TTCACGGTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.26, C:0.37, G:0.15, T:0.23
Consensus pattern (22 bp):
CCATCTCCGACGAAATCAGTCT
Found at i:1224182 original size:20 final size:20
Alignment explanation
Indices: 1224124--1224208 Score: 82
Period size: 20 Copynumber: 4.3 Consensus size: 20
1224114 GCGATTCTGT
**
1224124 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATAGTCATTTTCG
**
1224143 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
1224163 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* * **
1224183 TGTTGTGATTTTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
1224203 TGTTGC
1 CGTTGC
1224209 AATTTTAAGT
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 12 0.22
20 43 0.78
ACGTcount: A:0.14, C:0.18, G:0.24, T:0.45
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1224213 original size:20 final size:20
Alignment explanation
Indices: 1224174--1224214 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1224164 GTTGCGATAG
**
1224174 TCATTTTCGTGTTGTGATTT
1 TCATTTTCGTGTTGCAATTT
1224194 TCATTTTCGTGTTGCAATTT
1 TCATTTTCGTGTTGCAATTT
1224214 T
1 T
1224215 AAGTTTCAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.12, G:0.17, T:0.59
Consensus pattern (20 bp):
TCATTTTCGTGTTGCAATTT
Done.