Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009592.1 Hibiscus syriacus cultivar Beakdansim tig00116971_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: 7920512
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 39
Found at i:2752694 original size:30 final size:30
Alignment explanation
Indices: 2752660--2752740 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
2752650 TAATTCACTT
**
2752660 ATCACATTTCTCATGTCATATTCTCATATG
1 ATCACATAACTCATGTCATATTCTCATATG
*
2752690 ATCACATAACTCATGTCACT-TTCTCATGTG
1 ATCACATAACTCATGTCA-TATTCTCATATG
* *
2752720 GTCACATAGCTCATGTCATAT
1 ATCACATAACTCATGTCATAT
2752741 AATCTCTTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
29 1 0.02
30 42 0.95
31 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.38
Consensus pattern (30 bp):
ATCACATAACTCATGTCATATTCTCATATG
Found at i:2757262 original size:21 final size:21
Alignment explanation
Indices: 2757189--2757255 Score: 116
Period size: 21 Copynumber: 3.2 Consensus size: 21
2757179 TTGGGCAAGG
*
2757189 GGTACCGATACCCCATGAATA
1 GGTACCAATACCCCATGAATA
2757210 GGTACCAATACCCCATGAATA
1 GGTACCAATACCCCATGAATA
*
2757231 GGTACCAATACCCTATGAATA
1 GGTACCAATACCCCATGAATA
2757252 GGTA
1 GGTA
2757256 TTGATACATA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (21 bp):
GGTACCAATACCCCATGAATA
Found at i:2771581 original size:26 final size:26
Alignment explanation
Indices: 2771519--2771570 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
2771509 ATAGGTGTCG
*
2771519 CCACTAAAATAATTGTTAATAAATTA
1 CCACTAAAATAATTGTTAATAAAATA
2771545 CCACTAAAATAATTGTTAATAAAATA
1 CCACTAAAATAATTGTTAATAAAATA
2771571 TCATTATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.33
Consensus pattern (26 bp):
CCACTAAAATAATTGTTAATAAAATA
Found at i:2772304 original size:60 final size:59
Alignment explanation
Indices: 2772158--2772304 Score: 156
Period size: 60 Copynumber: 2.4 Consensus size: 59
2772148 AACATAATGA
* * * * *
2772158 ATAGTCGATTGACATTTTTGTAACTTTTAATAGTCAGGGGACTCAATAAAGCAACTCCCT
1 ATAGTCAATGGACA-TTTTGTAACTTTTAATAGTCAAGAGACTCAACAAAGCAACTCCCT
* *
2772218 ATAGTCGGAA-GAACATTTTGTAACTTTTAATAGTCAAGAGACTCAACAAAGCAA-TATCCT
1 ATAGTC--AATGGACATTTTGTAACTTTTAATAGTCAAGAGACTCAACAAAGCAACT-CCCT
2772278 ATAGTCAATGGACTATTTGTGT-ACTTT
1 ATAGTCAATGGAC-ATTT-TGTAACTTT
2772305 ACCCTTAATA
Statistics
Matches: 73, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
58 2 0.03
59 4 0.05
60 60 0.82
61 6 0.08
62 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Consensus pattern (59 bp):
ATAGTCAATGGACATTTTGTAACTTTTAATAGTCAAGAGACTCAACAAAGCAACTCCCT
Found at i:2778639 original size:59 final size:61
Alignment explanation
Indices: 2778531--2778659 Score: 142
Period size: 59 Copynumber: 2.1 Consensus size: 61
2778521 TCGAGTGAAA
* * *
2778531 ATTTTGTA-ACTTTTAATAGTCAGAGGATTCAACAAAGCAATTCCCTATAGTCGA-AGATC
1 ATTTTGTACACTTTTAATAGTCAGAGGACTCAACAAAGCAATTCCCTATAGTCAATAGACC
* * *
2778590 ATTTTGTACA-TTTTAATAGT-TGAGGGACTCAACAAAGTAATAT-CTTATAGTCAATAGACC
1 ATTTTGTACACTTTTAATAGTCAGA-GGACTCAACAAAGCAAT-TCCCTATAGTCAATAGACC
2778650 ATTTGTGTAC
1 ATTT-TGTAC
2778660 TTTACCCTTA
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
58 2 0.03
59 42 0.71
60 10 0.17
61 5 0.08
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (61 bp):
ATTTTGTACACTTTTAATAGTCAGAGGACTCAACAAAGCAATTCCCTATAGTCAATAGACC
Found at i:2780490 original size:2 final size:2
Alignment explanation
Indices: 2780483--2780519 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2780473 TTTTTAAAAC
2780483 AT AT 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 AT AT A
2780520 CCCCCATCCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2780705 original size:12 final size:12
Alignment explanation
Indices: 2780680--2780749 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
2780670 ACGAAGATAT
* *
2780680 CAGAAATCAAAA
1 CAGAATTCAGAA
2780692 CAGAATTCAGAA
1 CAGAATTCAGAA
2780704 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
2780716 CAGAATCCAGAT
1 CAGAATTCAGAA
*
2780728 CAGAAATCAGAA
1 CAGAATTCAGAA
2780740 CAGAATTCAG
1 CAGAATTCAG
2780750 GTCATTTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 2 0.04
12 44 0.92
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:2780712 original size:24 final size:24
Alignment explanation
Indices: 2780680--2780749 Score: 104
Period size: 24 Copynumber: 2.9 Consensus size: 24
2780670 ACGAAGATAT
*
2780680 CAGAAATCAAAACAGAATTCAGAA
1 CAGAAATCAGAACAGAATTCAGAA
* * *
2780704 CAGATATCAGAACAGAATCCAGAT
1 CAGAAATCAGAACAGAATTCAGAA
2780728 CAGAAATCAGAACAGAATTCAG
1 CAGAAATCAGAACAGAATTCAG
2780750 GTCATTTATC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAGAA
Found at i:2780760 original size:24 final size:24
Alignment explanation
Indices: 2780678--2780770 Score: 100
Period size: 24 Copynumber: 4.0 Consensus size: 24
2780668 TAACGAAGAT
* *
2780678 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGATATCAGAACAGAATTCAG
* *
2780702 AACAGATATCAGAACAGAATCCAG
1 ATCAGATATCAGAACAGAATTCAG
*
2780726 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGATATCAGAACAGAATTCAG
* **
2780750 GTCATTTATC--AACAGAATTCA
1 ATCAGATATCAGAACAGAATTCA
2780771 AGTCGAAATC
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
22 11 0.19
24 47 0.81
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.19
Consensus pattern (24 bp):
ATCAGATATCAGAACAGAATTCAG
Found at i:2780760 original size:48 final size:45
Alignment explanation
Indices: 2780678--2780783 Score: 115
Period size: 48 Copynumber: 2.3 Consensus size: 45
2780668 TAACGAAGAT
*
2780678 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATC--AACAGAATCCA
** ** *
2780725 GATCAGAAATCAGAACAGAATTCAGGTCATTTATCAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGAACAGATATCAACAGAATCCA
2780771 AGTC-GAAATCAGA
1 A-TCAGAAATCAGA
2780784 TAAAATATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
45 10 0.20
46 12 0.24
48 29 0.57
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.19
Consensus pattern (45 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAACAGAATCCA
Found at i:2781932 original size:18 final size:18
Alignment explanation
Indices: 2781911--2781946 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2781901 CTTCCATCCG
*
2781911 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
2781929 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
2781947 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:2783265 original size:15 final size:15
Alignment explanation
Indices: 2783245--2783278 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
2783235 GGTCAACTCC
2783245 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
2783260 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
2783275 GGTC
1 GGTC
2783279 GGGTCGGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.24, C:0.26, G:0.35, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:2783278 original size:8 final size:7
Alignment explanation
Indices: 2783244--2783275 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
2783234 TGGTCAACTC
2783244 CGGTCAA
1 CGGTCAA
2783251 CGGTCAA
1 CGGTCAA
2783258 CGGGTCAA
1 C-GGTCAA
2783266 CGGTCAA
1 CGGTCAA
2783273 CGG
1 CGG
2783276 GTCGGGTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:2783292 original size:18 final size:17
Alignment explanation
Indices: 2783266--2783334 Score: 74
Period size: 18 Copynumber: 4.2 Consensus size: 17
2783256 AACGGGTCAA
2783266 CGGTCAACGGGTCGGGT
1 CGGTCAACGGGTCGGGT
2783283 CGGTTCAACGGGTC--G-
1 CGG-TCAACGGGTCGGGT
*
2783298 -GGTAAACGGGTCGGGT
1 CGGTCAACGGGTCGGGT
*
2783314 CGGGTCAACGGATCGGGT
1 C-GGTCAACGGGTCGGGT
2783332 CGG
1 CGG
2783335 GTTGTGACCG
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
13 9 0.21
14 2 0.05
15 1 0.02
16 1 0.02
17 5 0.12
18 25 0.58
ACGTcount: A:0.14, C:0.22, G:0.46, T:0.17
Consensus pattern (17 bp):
CGGTCAACGGGTCGGGT
Found at i:2783294 original size:13 final size:13
Alignment explanation
Indices: 2783278--2783313 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
2783268 GTCAACGGGT
* *
2783278 CGGGTCGGTTCAA
1 CGGGTCGGGTAAA
2783291 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
2783304 CGGGTCGGGT
1 CGGGTCGGGT
2783314 CGGGTCAACG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.14, C:0.19, G:0.47, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:2783309 original size:31 final size:31
Alignment explanation
Indices: 2783271--2783331 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
2783261 GTCAACGGTC
* *
2783271 AACGGGTCGGGTCGGTTCAACGGGTCGGGTA
1 AACGGGTCGGGTCGGGTCAACGGATCGGGTA
2783302 AACGGGTCGGGTCGGGTCAACGGATCGGGT
1 AACGGGTCGGGTCGGGTCAACGGATCGGGT
2783332 CGGGTTGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.16, C:0.20, G:0.46, T:0.18
Consensus pattern (31 bp):
AACGGGTCGGGTCGGGTCAACGGATCGGGTA
Found at i:2786654 original size:3 final size:3
Alignment explanation
Indices: 2786648--2786728 Score: 134
Period size: 3 Copynumber: 28.3 Consensus size: 3
2786638 CAAAAAAATG
2786648 TAA TAA TAA T-A TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2786693 TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2786729 TAAACTTTGG
Statistics
Matches: 74, Mismatches: 0, Indels: 8
0.90 0.00 0.10
Matches are distributed among these distances:
2 8 0.11
3 66 0.89
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2786680 original size:17 final size:17
Alignment explanation
Indices: 2786648--2786726 Score: 142
Period size: 17 Copynumber: 4.6 Consensus size: 17
2786638 CAAAAAAATG
2786648 TAATAATAATATAATAA
1 TAATAATAATATAATAA
2786665 T-ATAATAATAATAATAA
1 TAATAATAAT-ATAATAA
2786682 TAATAATAATATAATAA
1 TAATAATAATATAATAA
2786699 TAATAATAATATAATAA
1 TAATAATAATATAATAA
2786716 TAATAATAATA
1 TAATAATAATA
2786727 ATTAAACTTT
Statistics
Matches: 60, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.13
17 44 0.73
18 8 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TAATAATAATATAATAA
Found at i:2787123 original size:134 final size:134
Alignment explanation
Indices: 2786883--2787651 Score: 980
Period size: 134 Copynumber: 5.7 Consensus size: 134
2786873 ACTGTCACTT
* * * *
2786883 AGGGAATATCAGATCT-GGGGATGTTGATCCATTCCGCTGACATTGAGGGAAGATTGAATCGGGG
1 AGGGAATATCATATCTGGGGGA-GTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGG
2786947 CAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAAAGATATATGTTCCTCTTCT
65 CAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAAAGATATATGTTCCTCTTCT
2787012 TCTGA
130 TCTGA
* * *
2787017 AGGGAATATCATAT-TGAGGGGAGTTGATCAATTCCGTTGTCACTCAAGGAAGATTGAATCGGGG
1 AGGGAATATCATATCTG-GGGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGG
* * * *
2787081 TAGACTTGTTCCGCTGTCAATCAGGGAGTATCAAATCTTGAAAG--AGATGGATTTGTTCCTCTT
65 CAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAAAGAT--ATATGTTCCTCTT
2787144 CTTCTGA
128 CTTCTGA
* * *
2787151 AGGGAATATCATATCTGAGGGAGTTGATCCATTCCACTGTCACTCAGGGAAGATTGAATAGGGGC
1 AGGGAATATCATATCTGGGGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGC
* * *
2787216 AGACTTGTTCCGTTGTCACTCAGGGAATATCAAATCTAGAAA-AAGAGAGATATGTT-CTACTTC
66 AGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAA-AGATATATGTTCCT-CTTC
2787279 TTCTGA
129 TTCTGA
* ** * *
2787285 AGGGAATATCATATCTGGAGGAGTTGATCCATTTTGTTGTCACTCAGGGAAGATTGAATCGGGAC
1 AGGGAATATCATATCTGGGGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGC
* * * * ** * * *
2787350 ATACTTGTTCCGCTGTCACTCAAGGAATATCAAATCTAGAAAGAGAGGGAT-TTTTTCTGTTTCT
66 AGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAAAGATATATGTTCCT-CTTCT
2787414 TCTGA
130 TCTGA
* * *
2787419 AGGGAATATCAGAGCTGGGGG-GTTTATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGC
1 AGGGAATATCATATCTGGGGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGC
* * * * *
2787483 ATACTTGTTCCACTGTCACTCAGGGAATATTAAATCTTGAAAGAGA-ATGATATGTTCCGCTTCT
66 AGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAAAGAT-ATATGTTCCTCTTCT
2787547 TCTGA
130 TCTGA
** * *
2787552 AGGGAATATCATATCTGGGGGAGTTGATCCATTTTGCTGTCACTCAGGGAAGATTAAATCGGGGT
1 AGGGAATATCATATCTGGGGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGC
* * * *
2787617 AGACTTGTTTCACTATTACTCAGGGAATATCAAAT
66 AGACTTGTTCCGCTGTCACTCAGGGAATATCAAAT
2787652 TCGCAAATTA
Statistics
Matches: 551, Mismatches: 70, Indels: 28
0.85 0.11 0.04
Matches are distributed among these distances:
132 4 0.01
133 116 0.21
134 420 0.76
135 8 0.01
136 3 0.01
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (134 bp):
AGGGAATATCATATCTGGGGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGC
AGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAAAGATATATGTTCCTCTTCTT
CTGA
Found at i:2787566 original size:267 final size:268
Alignment explanation
Indices: 2786883--2787651 Score: 1107
Period size: 268 Copynumber: 2.9 Consensus size: 268
2786873 ACTGTCACTT
* * *
2786883 AGGGAATATCAGATCTGGGGATGTTGATCCATTCCGCTGACATTGAGGGAAGATTGAATCGGGGC
1 AGGGAATATCAGATCTGGGGA-GTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGC
* *
2786948 AGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAAAGAT-ATATGTTCCTCTTCT
65 AGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGATGATATGTTCCACTTCT
* ** *
2787012 TCTGAAGGGAATATCATAT-TGAGGGGAGTTGATCAATTCCGTTGTCACTCAAGGAAGATTGAAT
130 TCTGAAGGGAATATCATATCTG-GGGGAGTTGATCCATTTTGTTGTCACTCAGGGAAGATTGAAT
* * * *
2787076 CGGGGTAGACTTGTTCCGCTGTCAATCAGGGAGTATCAAATCTTGAAAGAGATGGATTTGTTCCT
194 CGGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTAGAAAGAGAGGGATTTGTTCCT
2787141 CTTCTTCTGA
259 CTTCTTCTGA
* * *
2787151 AGGGAATATCATATCTGAGGGAGTTGATCCATTCCACTGTCACTCAGGGAAGATTGAATAGGGGC
1 AGGGAATATCAGATCTG-GGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGC
* * * *
2787216 AGACTTGTTCCGTTGTCACTCAGGGAATATCAAATCTAGAAAAAGAGA-GATATGTTCTACTTCT
65 AGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGATGATATGTTCCACTTCT
*
2787280 TCTGAAGGGAATATCATATCTGGAGGAGTTGATCCATTTTGTTGTCACTCAGGGAAGATTGAATC
130 TCTGAAGGGAATATCATATCTGGGGGAGTTGATCCATTTTGTTGTCACTCAGGGAAGATTGAATC
** * * *
2787345 GGGACATACTTGTTCCGCTGTCACTCAAGGAATATCAAATCTAGAAAGAGAGGGATTT-TTTCTG
195 GGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTAGAAAGAGAGGGATTTGTTCCT-
*
2787409 TTTCTTCTGA
259 CTTCTTCTGA
* * *
2787419 AGGGAATATCAGAGCTGGGGGGTTTATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGCA
1 AGGGAATATCAGATCTGGGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGCA
* * * *
2787484 TACTTGTTCCACTGTCACTCAGGGAATATTAAATCTTGAAAGAGA-ATGATATGTTCCGCTTCTT
66 GACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGATGATATGTTCCACTTCTT
* *
2787548 CTGAAGGGAATATCATATCTGGGGGAGTTGATCCATTTTGCTGTCACTCAGGGAAGATTAAATCG
131 CTGAAGGGAATATCATATCTGGGGGAGTTGATCCATTTTGTTGTCACTCAGGGAAGATTGAATCG
* * * *
2787613 GGGTAGACTTGTTTCACTATTACTCAGGGAATATCAAAT
196 GGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAAT
2787652 TCGCAAATTA
Statistics
Matches: 444, Mismatches: 52, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
266 1 0.00
267 195 0.44
268 242 0.55
269 6 0.01
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (268 bp):
AGGGAATATCAGATCTGGGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGCA
GACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGATGATATGTTCCACTTCTT
CTGAAGGGAATATCATATCTGGGGGAGTTGATCCATTTTGTTGTCACTCAGGGAAGATTGAATCG
GGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTAGAAAGAGAGGGATTTGTTCCTCT
TCTTCTGA
Found at i:2796061 original size:12 final size:12
Alignment explanation
Indices: 2796044--2796085 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
2796034 GTAGGATATC
2796044 AAACTAAAACTT
1 AAACTAAAACTT
2796056 AAACT-AAACGTT
1 AAACTAAAAC-TT
2796068 --ACTAAAACTT
1 AAACTAAAACTT
2796078 AAACTAAA
1 AAACTAAA
2796086 CGTTAGATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
10 5 0.19
11 8 0.31
12 13 0.50
ACGTcount: A:0.57, C:0.17, G:0.02, T:0.24
Consensus pattern (12 bp):
AAACTAAAACTT
Found at i:2796071 original size:22 final size:22
Alignment explanation
Indices: 2796046--2796090 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2796036 AGGATATCAA
2796046 ACTAAAACTTAAACTAAACGTT
1 ACTAAAACTTAAACTAAACGTT
2796068 ACTAAAACTTAAACTAAACGTT
1 ACTAAAACTTAAACTAAACGTT
2796090 A
1 A
2796091 GATATGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.51, C:0.18, G:0.04, T:0.27
Consensus pattern (22 bp):
ACTAAAACTTAAACTAAACGTT
Found at i:2799055 original size:36 final size:36
Alignment explanation
Indices: 2798979--2799201 Score: 292
Period size: 36 Copynumber: 6.2 Consensus size: 36
2798969 AAAGATGAAC
* *
2798979 ACTTGAATCGAAAGTG-CGACGCCTTC-TTCCATTCG
1 ACTTGAATCGAAAGTGTCGATG-CTTCTTTCCGTTCG
*
2799014 TCTTGAATCGAAAGTGTCGATGCTT-TCTTCCGTTCG
1 ACTTGAATCGAAAGTGTCGATGCTTCT-TTCCGTTCG
* * *
2799050 ACTTGAATCGGAAGTGCCGATGCTTCATTCCGTTCG
1 ACTTGAATCGAAAGTGTCGATGCTTCTTTCCGTTCG
* *
2799086 ACTTGAATCGAAAGTGACGTTGCTTCTTTCCGTTCG
1 ACTTGAATCGAAAGTGTCGATGCTTCTTTCCGTTCG
*
2799122 ACTTGAATCGGAAGTGTC-ATTGCTTCTTTCCGTTCG
1 ACTTGAATCGAAAGTGTCGA-TGCTTCTTTCCGTTCG
* *
2799158 ACTTGAATCGAAAGTGTCGTTGCTTCCTTCCGTTCG
1 ACTTGAATCGAAAGTGTCGATGCTTCTTTCCGTTCG
2799194 ACTTGAAT
1 ACTTGAAT
2799202 TAGAAGTGCC
Statistics
Matches: 165, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
35 18 0.11
36 147 0.89
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (36 bp):
ACTTGAATCGAAAGTGTCGATGCTTCTTTCCGTTCG
Found at i:2802211 original size:29 final size:26
Alignment explanation
Indices: 2802179--2802235 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
2802169 TGAAAATAAC
*
2802179 ATTATAGATAATATTTATAAAATAATATG
1 ATTATAGA-AAT-TATATAAAATAAT-TG
*
2802208 ATTATAGAAATTATATTAAATAATTG
1 ATTATAGAAATTATATAAAATAATTG
2802234 AT
1 AT
2802236 ACCATTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 4 0.15
27 11 0.42
28 3 0.12
29 8 0.31
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (26 bp):
ATTATAGAAATTATATAAAATAATTG
Found at i:2804349 original size:30 final size:31
Alignment explanation
Indices: 2804313--2804372 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
2804303 ATTTATTTGA
2804313 TATTTTATCTAAACTTAAG-GGTCAAATTAG
1 TATTTTATCTAAACTTAAGAGGTCAAATTAG
* *
2804343 TATTTTATCTAAACTTCAGAGGTTAAATTA
1 TATTTTATCTAAACTTAAGAGGTCAAATTA
2804373 AAACCAGTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 18 0.67
31 9 0.33
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.42
Consensus pattern (31 bp):
TATTTTATCTAAACTTAAGAGGTCAAATTAG
Found at i:2806679 original size:17 final size:18
Alignment explanation
Indices: 2806651--2806685 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
2806641 TAAAAATAAA
2806651 TTAACGCGATTATTTATT
1 TTAACGCGATTATTTATT
2806669 TTAAC-CGATTATTTATT
1 TTAACGCGATTATTTATT
2806686 GAGATGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (18 bp):
TTAACGCGATTATTTATT
Found at i:2807983 original size:18 final size:18
Alignment explanation
Indices: 2807936--2808020 Score: 93
Period size: 18 Copynumber: 4.7 Consensus size: 18
2807926 TATTCTTTTG
*
2807936 TTCTAATCC--AAAGAAT
1 TTCTAATCCAAAAAGTAT
*
2807952 TTCTAATTATCAAAAAGTAT
1 TTCTAA-T-CCAAAAAGTAT
*
2807972 TTCTACTCCAAAAAGTAT
1 TTCTAATCCAAAAAGTAT
**
2807990 TTCTAATCCAATGAGTAT
1 TTCTAATCCAAAAAGTAT
2808008 TTCTAATCCAAAA
1 TTCTAATCCAAAA
2808021 TACACATTAT
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
16 6 0.11
17 1 0.02
18 37 0.66
19 1 0.02
20 11 0.20
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (18 bp):
TTCTAATCCAAAAAGTAT
Found at i:2808107 original size:14 final size:14
Alignment explanation
Indices: 2808090--2808118 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2808080 TTTTTAATCC
2808090 AAAATACACATTAT
1 AAAATACACATTAT
2808104 AAAATACACATTAT
1 AAAATACACATTAT
2808118 A
1 A
2808119 TTTAGAGGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAATACACATTAT
Found at i:2808170 original size:17 final size:17
Alignment explanation
Indices: 2808148--2808198 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
2808138 ATATATCCAT
2808148 TGGTCTATTAATTTCTA
1 TGGTCTATTAATTTCTA
* *
2808165 TGGTCTAATAACATATCTA
1 TGGTCT-ATTA-ATTTCTA
2808184 -GG-CTATTAATTTCTA
1 TGGTCTATTAATTTCTA
2808199 GTCTAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 6 0.21
16 3 0.11
17 8 0.29
18 5 0.18
19 6 0.21
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (17 bp):
TGGTCTATTAATTTCTA
Found at i:2810726 original size:7 final size:7
Alignment explanation
Indices: 2810714--2810743 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
2810704 TAAGTTTTTG
2810714 AGGGTTT
1 AGGGTTT
2810721 AGGGTTT
1 AGGGTTT
*
2810728 AAGGTTT
1 AGGGTTT
2810735 AGGGTTT
1 AGGGTTT
2810742 AG
1 AG
2810744 AATAATCCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (7 bp):
AGGGTTT
Found at i:2811260 original size:18 final size:19
Alignment explanation
Indices: 2811239--2811300 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
2811229 TGTTAAATTT
*
2811239 TTATTAAAT-TTTTTAAAA
1 TTATTAAATATTATTAAAA
*
2811257 TTA-TAAATATTATTAAAT
1 TTATTAAATATTATTAAAA
*
2811275 TTATCAAAATATTA-TACAAA
1 TTAT-TAAATATTATTA-AAA
2811295 TTATTA
1 TTATTA
2811301 CAACATTATC
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
17 5 0.14
18 13 0.37
19 3 0.09
20 14 0.40
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (19 bp):
TTATTAAATATTATTAAAA
Found at i:2811274 original size:17 final size:19
Alignment explanation
Indices: 2811238--2811289 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
2811228 ATGTTAAATT
* *
2811238 TTTATTAAAT-TTTTTAAA
1 TTTATAAAATATTATTAAA
*
2811256 ATTAT-AAATATTATTAAA
1 TTTATAAAATATTATTAAA
2811274 TTTATCAAAATATTAT
1 TTTAT-AAAATATTAT
2811290 ACAAATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 4 0.14
18 15 0.54
20 9 0.32
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTATAAAATATTATTAAA
Found at i:2811391 original size:11 final size:11
Alignment explanation
Indices: 2811372--2811425 Score: 74
Period size: 11 Copynumber: 4.9 Consensus size: 11
2811362 AATTTTTTTT
*
2811372 ATTTTATAATA
1 ATTTAATAATA
2811383 ATTTAATAA-A
1 ATTTAATAATA
*
2811393 ATTTAATAATT
1 ATTTAATAATA
2811404 ATTTAATAATA
1 ATTTAATAATA
2811415 ATTTTAATAAT
1 A-TTTAATAAT
2811426 TTTAATGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
10 10 0.26
11 19 0.50
12 9 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
ATTTAATAATA
Found at i:2811401 original size:21 final size:22
Alignment explanation
Indices: 2811372--2811425 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
2811362 AATTTTTTTT
*
2811372 ATTTTATAATAATTTAATAA-A
1 ATTTAATAATAATTTAATAATA
*
2811393 ATTTAATAATTATTTAATAATA
1 ATTTAATAATAATTTAATAATA
2811415 ATTTTAATAAT
1 A-TTTAATAAT
2811426 TTTAATGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 18 0.62
22 2 0.07
23 9 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTTAATAATAATTTAATAATA
Found at i:2811429 original size:21 final size:19
Alignment explanation
Indices: 2811378--2811431 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 19
2811368 TTTTATTTTA
2811378 TAATAA-TTTAATAAAATT
1 TAATAATTTTAATAAAATT
2811396 TAATAATTATTTAATAATAATTT
1 TAATAA-T-TTTAATAA-AA-TT
2811419 TAATAATTTTAAT
1 TAATAATTTTAAT
2811432 GTTTTAGCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
18 6 0.19
21 14 0.45
22 3 0.10
23 8 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TAATAATTTTAATAAAATT
Found at i:2819104 original size:81 final size:81
Alignment explanation
Indices: 2818969--2819127 Score: 219
Period size: 81 Copynumber: 2.0 Consensus size: 81
2818959 GAACATACTC
* * * * *
2818969 GTCAGACACCTACCGATTTCTGATACTCACACCAGAGGTCAAGTAACATTGGTTGTTTCTATCTT
1 GTCAGACACATACCGATATCTCACACTCACACCAGAAGTCAAGTAACATTGGTTGTTTCTATCTT
2819034 TCTAACTAAATTGCTT
66 TCTAACTAAATTGCTT
* * * *
2819050 GTCAGACACATACTGATATCTCACACTCACACCCGAATTCAAGTAACATTGGTTGTTTCTTTCTT
1 GTCAGACACATACCGATATCTCACACTCACACCAGAAGTCAAGTAACATTGGTTGTTTCTATCTT
* *
2819115 TCTGACTGAATTG
66 TCTAACTAAATTG
2819128 TTCAATGTAG
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 67 1.00
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (81 bp):
GTCAGACACATACCGATATCTCACACTCACACCAGAAGTCAAGTAACATTGGTTGTTTCTATCTT
TCTAACTAAATTGCTT
Found at i:2820499 original size:3 final size:3
Alignment explanation
Indices: 2820491--2820519 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2820481 CTAAACTTGA
2820491 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
2820520 ATGGTTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2820643 original size:18 final size:19
Alignment explanation
Indices: 2820607--2820643 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2820597 TTGAGTCATT
*
2820607 ATATTGTTTTTTATTTTAA
1 ATATTGTTTTTTATGTTAA
2820626 ATATTGTTTTTT-TGTTAA
1 ATATTGTTTTTTATGTTAA
2820644 TTTTATTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (19 bp):
ATATTGTTTTTTATGTTAA
Found at i:2821374 original size:28 final size:28
Alignment explanation
Indices: 2821321--2821374 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
2821311 AGAATTTAAT
* *
2821321 TTATTTTTAATTAGATAATTAAAAATAA
1 TTATTTTTAATTAAATAAATAAAAATAA
*
2821349 TTATTTTT-ATTAAATTAAATATAAAT
1 TTATTTTTAATTAAA-TAAATAAAAAT
2821375 TATAAAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (28 bp):
TTATTTTTAATTAAATAAATAAAAATAA
Found at i:2826740 original size:2 final size:2
Alignment explanation
Indices: 2826733--2826787 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
2826723 TAAATAACAC
2826733 AT AT 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 AT AT
2826775 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
2826788 AAGGGAATGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2836389 original size:20 final size:20
Alignment explanation
Indices: 2836364--2836496 Score: 117
Period size: 20 Copynumber: 6.5 Consensus size: 20
2836354 TTATCCTAAT
2836364 TCGCAATGCGAATTTGTAAA
1 TCGCAATGCGAATTTGTAAA
* **
2836384 TCGCAATACGAATACGT-AA
1 TCGCAATGCGAATTTGTAAA
*
2836403 TCGCAATTGCGAATTATGAAAA
1 TCGCAA-TGCGAATT-TGTAAA
* **
2836425 TCGCAACGCGAATACGTAAA
1 TCGCAATGCGAATTTGTAAA
* *
2836445 TCGCAATGCGAATTAAGAAAA
1 TCGCAATGCGAATT-TGTAAA
* *
2836466 TCGCAATGCGAATCTG-ACTA
1 TCGCAATGCGAATTTGTA-AA
2836486 TCGCAATGCGA
1 TCGCAATGCGA
2836497 TTTACATAGC
Statistics
Matches: 90, Mismatches: 18, Indels: 10
0.76 0.15 0.08
Matches are distributed among these distances:
19 9 0.10
20 49 0.54
21 24 0.27
22 8 0.09
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATTTGTAAA
Found at i:2836429 original size:41 final size:41
Alignment explanation
Indices: 2836364--2836478 Score: 171
Period size: 41 Copynumber: 2.8 Consensus size: 41
2836354 TTATCCTAAT
* *
2836364 TCGCAATGCGAATT-TGTAAATCGCAATACGAATACGT-AA
1 TCGCAATGCGAATTATGAAAATCGCAATGCGAATACGTAAA
*
2836403 TCGCAATTGCGAATTATGAAAATCGCAACGCGAATACGTAAA
1 TCGCAA-TGCGAATTATGAAAATCGCAATGCGAATACGTAAA
*
2836445 TCGCAATGCGAATTAAGAAAATCGCAATGCGAAT
1 TCGCAATGCGAATTATGAAAATCGCAATGCGAAT
2836479 CTGACTATCG
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
39 6 0.09
40 8 0.12
41 46 0.68
42 8 0.12
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (41 bp):
TCGCAATGCGAATTATGAAAATCGCAATGCGAATACGTAAA
Found at i:2836489 original size:41 final size:41
Alignment explanation
Indices: 2836364--2836496 Score: 134
Period size: 41 Copynumber: 3.3 Consensus size: 41
2836354 TTATCCTAAT
* *
2836364 TCGCAATGCGAATT-TGTAAATCGCAATACGAA--T-ACGTAA
1 TCGCAATGCGAATTATGAAAATCGCAATGCGAATCTGAC-T-A
* *
2836403 TCGCAATTGCGAATTATGAAAATCGCAACGCGAATAC-GTA-AA
1 TCGCAA-TGCGAATTATGAAAATCGCAATGCGAAT-CTG-ACTA
*
2836445 TCGCAATGCGAATTAAGAAAATCGCAATGCGAATCTGACTA
1 TCGCAATGCGAATTATGAAAATCGCAATGCGAATCTGACTA
2836486 TCGCAATGCGA
1 TCGCAATGCGA
2836497 TTTACATAGC
Statistics
Matches: 78, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
39 6 0.08
40 10 0.13
41 54 0.69
42 7 0.09
45 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (41 bp):
TCGCAATGCGAATTATGAAAATCGCAATGCGAATCTGACTA
Found at i:2836489 original size:61 final size:61
Alignment explanation
Indices: 2836364--2836496 Score: 153
Period size: 61 Copynumber: 2.2 Consensus size: 61
2836354 TTATCCTAAT
** * *
2836364 TCGCAATGCGAATTTGTAAATCGCAATACGAATACGTAATCGCAATTGCGAATTATGAAAA
1 TCGCAATGCGAATACGTAAATCGCAATACGAATAAGAAATCGCAATTGCGAATTATGAAAA
* * * **
2836425 TCGCAACGCGAATACGTAAATCGCAATGCGAATTAAGAAAATCGCAA-TGCGAA-TCTGACTA
1 TCGCAATGCGAATACGTAAATCGCAATACGAA-TAAG-AAATCGCAATTGCGAATTATGAAAA
2836486 TCGCAATGCGA
1 TCGCAATGCGA
2836497 TTTACATAGC
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
61 43 0.72
62 9 0.15
63 8 0.13
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (61 bp):
TCGCAATGCGAATACGTAAATCGCAATACGAATAAGAAATCGCAATTGCGAATTATGAAAA
Found at i:2837083 original size:19 final size:19
Alignment explanation
Indices: 2837019--2837103 Score: 72
Period size: 19 Copynumber: 4.7 Consensus size: 19
2837009 TAGTTTCGAG
2837019 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGC-GA
**
2837039 AATGACTATCGCAA--CG-
1 AATGAAAATCGCAACGCGA
*
2837055 -A-GAGAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
*
2837072 AATGAAAATCGCAACGCAA
1 AATGAAAATCGCAACGCGA
**
2837091 AACCAAAATCGCA
1 AATGAAAATCGCA
2837104 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
14 9 0.17
15 1 0.02
16 2 0.04
17 1 0.02
18 2 0.04
19 25 0.48
20 12 0.23
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.11
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGA
Found at i:2837140 original size:14 final size:14
Alignment explanation
Indices: 2837121--2837176 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
2837111 TTTCATTTCG
2837121 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2837135 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
2837154 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2837168 CGTTGCGAT
1 CGTTGCGAT
2837177 AGTCATTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.25, T:0.41
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2837150 original size:33 final size:33
Alignment explanation
Indices: 2837104--2837197 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
2837094 CAAAATCGCA
*
2837104 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
2837137 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
*
2837170 TTGCGATAGTCATTTCCGCGTTGCGATT
1 TTGCGATTGTCATTT-CGCGTTGCGATT
2837198 TTCATTCTCT
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 46 0.79
34 12 0.21
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (33 bp):
TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
Found at i:2837202 original size:20 final size:19
Alignment explanation
Indices: 2837099--2837225 Score: 103
Period size: 20 Copynumber: 7.1 Consensus size: 19
2837089 AAAACCAAAA
*
2837099 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2837118 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
2837132 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
2837151 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
2837165 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
2837184 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
2837204 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
2837224 TC
1 TC
2837226 AACCAAAAGA
Statistics
Matches: 85, Mismatches: 11, Indels: 24
0.71 0.09 0.20
Matches are distributed among these distances:
14 20 0.24
16 4 0.05
17 5 0.06
19 23 0.27
20 32 0.38
21 1 0.01
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2839103 original size:94 final size:93
Alignment explanation
Indices: 2838912--2839287 Score: 625
Period size: 94 Copynumber: 4.1 Consensus size: 93
2838902 TAAATTGCTT
* *
2838912 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
2838973 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
2839002 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
2839067 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
*
2839096 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
2839161 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * *
2839190 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
2839255 ATTTGTCTTTGTTTTGTCTTTTAGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
2839283 AGTAA
1 AGTAA
2839288 TGCAATCCAT
Statistics
Matches: 274, Mismatches: 7, Indels: 7
0.95 0.02 0.02
Matches are distributed among these distances:
90 35 0.13
92 3 0.01
93 28 0.10
94 208 0.76
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:2839405 original size:19 final size:19
Alignment explanation
Indices: 2839378--2839487 Score: 87
Period size: 19 Copynumber: 6.3 Consensus size: 19
2839368 TCTTTTGGTT
*
2839378 GAAATGAAAATCGCAACGC
1 GAAACGAAAATCGCAACGC
2839397 GAAACGAAAATCGCAA--C
1 GAAACGAAAATCGCAACGC
* * *
2839414 G--A-GAGAATCGTAACAC
1 GAAACGAAAATCGCAACGC
*
2839430 GAAATGAAAATCGCAA--C
1 GAAACGAAAATCGCAACGC
2839447 G--AC-AAAATCGCAACGC
1 GAAACGAAAATCGCAACGC
*
2839463 GAAACCAAAAATCGCAACGC
1 GAAA-CGAAAATCGCAACGC
2839483 GAAAC
1 GAAAC
2839488 TATAATCTCG
Statistics
Matches: 74, Mismatches: 6, Indels: 22
0.73 0.06 0.22
Matches are distributed among these distances:
14 19 0.26
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 26 0.35
20 17 0.23
ACGTcount: A:0.49, C:0.24, G:0.19, T:0.08
Consensus pattern (19 bp):
GAAACGAAAATCGCAACGC
Found at i:2839433 original size:33 final size:33
Alignment explanation
Indices: 2839384--2839481 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 33
2839374 GGTTGAAATG
*
2839384 AAAATCGCAACGCGAAACGAAAATCGCAACGAG
1 AAAATCGCAACGCGAAACGAAAATCGCAACGAC
* * * *
2839417 AGAATCGTAACACGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACGAAAATCGCAACGAC
*
2839450 AAAATCGCAACGCGAAACCAAAAATCGCAACG
1 AAAATCGCAACGCGAAA-CGAAAATCGCAACG
2839482 CGAAACTATA
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 42 0.78
34 12 0.22
ACGTcount: A:0.49, C:0.24, G:0.18, T:0.08
Consensus pattern (33 bp):
AAAATCGCAACGCGAAACGAAAATCGCAACGAC
Found at i:2839473 original size:20 final size:20
Alignment explanation
Indices: 2839450--2839487 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2839440 TCGCAACGAC
2839450 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAACCA
2839470 AAAATCGCAACGCGAAAC
1 AAAATCGCAACGCGAAAC
2839488 TATAATCTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.29, G:0.16, T:0.05
Consensus pattern (20 bp):
AAAATCGCAACGCGAAACCA
Found at i:2839538 original size:33 final size:33
Alignment explanation
Indices: 2839493--2839556 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
2839483 GAAACTATAA
2839493 TCTCGTTGCGATTTTAATTTCGCATTGCGATTC
1 TCTCGTTGCGATTTTAATTTCGCATTGCGATTC
* ** *
2839526 TCTCGTTTCGATTTTCGTTTCGCGTTGCGAT
1 TCTCGTTGCGATTTTAATTTCGCATTGCGAT
2839557 AGTCATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.47
Consensus pattern (33 bp):
TCTCGTTGCGATTTTAATTTCGCATTGCGATTC
Found at i:2841493 original size:13 final size:13
Alignment explanation
Indices: 2841447--2841484 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
2841437 TTGATTGTTT
2841447 AATTGATTTGTAA
1 AATTGATTTGTAA
*
2841460 AAGATGATTTGTAA
1 AA-TTGATTTGTAA
2841474 AATTGATTTGT
1 AATTGATTTGT
2841485 TTAATTGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (13 bp):
AATTGATTTGTAA
Found at i:2841702 original size:14 final size:14
Alignment explanation
Indices: 2841683--2841737 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
2841673 TCATTTCGCA
2841683 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
2841697 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
2841714 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
2841730 TTGCGATT
1 TTGCGATT
2841738 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:2841708 original size:33 final size:33
Alignment explanation
Indices: 2841671--2841755 Score: 170
Period size: 33 Copynumber: 2.6 Consensus size: 33
2841661 ATTATGTTGA
2841671 TTTCATTTCGCATTGCGATTCTCTCGTTGCGAT
1 TTTCATTTCGCATTGCGATTCTCTCGTTGCGAT
2841704 TTTCATTTCGCATTGCGATTCTCTCGTTGCGAT
1 TTTCATTTCGCATTGCGATTCTCTCGTTGCGAT
2841737 TTTCATTTCGCATTGCGAT
1 TTTCATTTCGCATTGCGAT
2841756 AGTCATTTTC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.46
Consensus pattern (33 bp):
TTTCATTTCGCATTGCGATTCTCTCGTTGCGAT
Found at i:2841721 original size:19 final size:19
Alignment explanation
Indices: 2841671--2841775 Score: 86
Period size: 19 Copynumber: 6.0 Consensus size: 19
2841661 ATTATGTTGA
2841671 TTTCATTTCGCATTGCGA-
1 TTTCATTTCGCATTGCGAT
*
2841689 -TTC-TCTCG--TTGCGAT
1 TTTCATTTCGCATTGCGAT
2841704 TTTCATTTCGCATTGCGA-
1 TTTCATTTCGCATTGCGAT
*
2841722 -TTC-TCTCG--TTGCGAT
1 TTTCATTTCGCATTGCGAT
2841737 TTTCATTTCGCATTGCGAT
1 TTTCATTTCGCATTGCGAT
** *
2841756 AGTCATTTTCGCGTTGCGAT
1 TTTCA-TTTCGCATTGCGAT
2841776 AGACATTAAG
Statistics
Matches: 69, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
14 12 0.17
16 14 0.20
17 14 0.20
19 16 0.23
20 13 0.19
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (19 bp):
TTTCATTTCGCATTGCGAT
Found at i:2841767 original size:20 final size:20
Alignment explanation
Indices: 2841742--2841782 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2841732 GCGATTTTCA
*
2841742 TTTCGCATTGCGATAGTCAT
1 TTTCGCATTGCGATAGACAT
*
2841762 TTTCGCGTTGCGATAGACAT
1 TTTCGCATTGCGATAGACAT
2841782 T
1 T
2841783 AAGATGATTG
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:0.20, C:0.20, G:0.22, T:0.39
Consensus pattern (20 bp):
TTTCGCATTGCGATAGACAT
Found at i:2844240 original size:24 final size:24
Alignment explanation
Indices: 2844213--2844266 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2844203 TTGAAAAATC
*
2844213 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
* *
2844237 ATCAAAGTCCGGGTATTAACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
2844261 ATCAAA
1 ATCAAA
2844267 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:2845155 original size:20 final size:20
Alignment explanation
Indices: 2845132--2845291 Score: 157
Period size: 20 Copynumber: 8.0 Consensus size: 20
2845122 AGAATCTCGT
* *
2845132 TGCGATTAGGAAAATCGCAA
1 TGCGATTACGTAAATCGCAA
**
2845152 TGCGAACACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
2845172 TGCGATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
*
2845192 TGCGAATTA-GAAAAATCGCAA
1 TGCG-ATTACG-TAAATCGCAA
* *
2845213 TGCGATTTCGTAAATCGCAT
1 TGCGATTACGTAAATCGCAA
* *
2845233 TGCGATTTACGT-ATTCGCAT
1 TGCGA-TTACGTAAATCGCAA
*
2845253 TGCGATTTACGT-AATCGCAT
1 TGCGA-TTACGTAAATCGCAA
2845273 TGCGATTTACGT-AATCGCA
1 TGCGA-TTACGTAAATCGCA
2845292 TTGTGATTTT
Statistics
Matches: 123, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
20 100 0.81
21 23 0.19
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (20 bp):
TGCGATTACGTAAATCGCAA
Found at i:2845219 original size:41 final size:40
Alignment explanation
Indices: 2845132--2845237 Score: 133
Period size: 41 Copynumber: 2.6 Consensus size: 40
2845122 AGAATCTCGT
* * *
2845132 TGCGATTAGGAAAATCGCAATGCGAACACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAATGCGAACACGAAAATCGCAA
*
2845172 TGCGATTACGTAAATCGCAATGCGAATTA-GAAAAATCGCAA
1 TGCGATTACGTAAATCGCAATGCGAA-CACG-AAAATCGCAA
* *
2845213 TGCGATTTCGTAAATCGCATTGCGA
1 TGCGATTACGTAAATCGCAATGCGA
2845238 TTTACGTATT
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
40 25 0.43
41 33 0.57
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.23
Consensus pattern (40 bp):
TGCGATTACGTAAATCGCAATGCGAACACGAAAATCGCAA
Found at i:2845251 original size:61 final size:61
Alignment explanation
Indices: 2845131--2845318 Score: 197
Period size: 61 Copynumber: 3.1 Consensus size: 61
2845121 GAGAATCTCG
*** * *
2845131 TTGCG-ATTAGGAAAATCGCAATGCGAACACGTAAATCGCAATGCGA-TTACGTAAATCGCA
1 TTGCGAATTA-GAAAATCGCAATGCGATTTCGTAAATCGCATTGCGATTTACGTAATTCGCA
*
2845191 ATGCGAATTAGAAAAATCGCAATGCGATTTCGTAAATCGCATTGCGATTTACGT-ATTCGCA
1 TTGCGAATTAG-AAAATCGCAATGCGATTTCGTAAATCGCATTGCGATTTACGTAATTCGCA
* * * * * *
2845252 TTGCGATTTACG-TAATCGCATTGCGATTTACGT-AATCGCATTGTGATTTTCCTAATTCGCA
1 TTGCGAATTA-GAAAATCGCAATGCGATTT-CGTAAATCGCATTGCGATTTACGTAATTCGCA
2845313 TTGCGA
1 TTGCGA
2845319 TTTACGTATT
Statistics
Matches: 109, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
60 37 0.34
61 65 0.60
62 7 0.06
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (61 bp):
TTGCGAATTAGAAAATCGCAATGCGATTTCGTAAATCGCATTGCGATTTACGTAATTCGCA
Found at i:2845266 original size:41 final size:41
Alignment explanation
Indices: 2845159--2845338 Score: 206
Period size: 41 Copynumber: 4.4 Consensus size: 41
2845149 CAATGCGAAC
* * *
2845159 ACGTAAATCGCAATGCGA-TTACGTAAATCGCAATGCGAATT
1 ACGT-AATCGCATTGCGATTTACGTAAATCGCATTGCGATTT
* *
2845200 A-GAAAAATCGCAATGCGATTT-CGTAAATCGCATTGCGATTT
1 ACG--TAATCGCATTGCGATTTACGTAAATCGCATTGCGATTT
*
2845241 ACGTATTCGCATTGCGATTTACGT-AATCGCATTGCGATTT
1 ACGTAATCGCATTGCGATTTACGTAAATCGCATTGCGATTT
* * * *
2845281 ACGTAATCGCATTGTGATTTTCCTAATTCGCATTGCGATTT
1 ACGTAATCGCATTGCGATTTACGTAAATCGCATTGCGATTT
*
2845322 ACGTATTCGCATTGCGA
1 ACGTAATCGCATTGCGA
2845339 ATTAGGAAAA
Statistics
Matches: 120, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
40 51 0.43
41 66 0.55
42 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (41 bp):
ACGTAATCGCATTGCGATTTACGTAAATCGCATTGCGATTT
Found at i:2845292 original size:20 final size:20
Alignment explanation
Indices: 2845159--2845338 Score: 195
Period size: 20 Copynumber: 8.8 Consensus size: 20
2845149 CAATGCGAAC
*
2845159 ACGTAAATCGCAATGCGA-TT
1 ACGT-AATCGCATTGCGATTT
* *
2845179 ACGTAAATCGCAATGCGAATT
1 ACGT-AATCGCATTGCGATTT
* *
2845200 A-GAAAAATCGCAATGCGATTT
1 ACG--TAATCGCATTGCGATTT
2845221 -CGTAAATCGCATTGCGATTT
1 ACGT-AATCGCATTGCGATTT
*
2845241 ACGTATTCGCATTGCGATTT
1 ACGTAATCGCATTGCGATTT
2845261 ACGTAATCGCATTGCGATTT
1 ACGTAATCGCATTGCGATTT
*
2845281 ACGTAATCGCATTGTGATTT
1 ACGTAATCGCATTGCGATTT
* *
2845301 TCCTAATTCGCATTGCGATTT
1 ACGTAA-TCGCATTGCGATTT
*
2845322 ACGTATTCGCATTGCGA
1 ACGTAATCGCATTGCGA
2845339 ATTAGGAAAA
Statistics
Matches: 140, Mismatches: 13, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
20 102 0.73
21 38 0.27
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (20 bp):
ACGTAATCGCATTGCGATTT
Found at i:2845312 original size:81 final size:80
Alignment explanation
Indices: 2845166--2845381 Score: 238
Period size: 81 Copynumber: 2.6 Consensus size: 80
2845156 AACACGTAAA
* *
2845166 TCGCAATGCGATTACGTAAATCGCAATGCGAATTAGAAAAATCGCAATGCGATTTCGTAAATCGC
1 TCGCATTGCGATTACGTAAATCGCAATGCGAATTAG-AAAATCGCAATGCGATTTCCTAAATCGC
2845231 ATTGCGATTTACGTAT
65 ATTGCGATTTACGTAT
* * * * * *
2845247 TCGCATTGCGATTTACGT-AATCGCATTGCGATTTACG-TAATCGCATTGTGATTTTCCTAATTC
1 TCGCATTGCGA-TTACGTAAATCGCAATGCGAATTA-GAAAATCGCAATGCGA-TTTCCTAAATC
2845310 GCATTGCGATTTACGTAT
63 GCATTGCGATTTACGTAT
* * * ** *
2845328 TCGCATTGCGAATTAGGAAAATTGCAACACGAATTTGAGAAATCGCAATGCGAT
1 TCGCATTGCG-ATTACGTAAATCGCAATGCGAATTAGA-AAATCGCAATGCGAT
2845382 AGTTAGAATC
Statistics
Matches: 109, Mismatches: 19, Indels: 13
0.77 0.13 0.09
Matches are distributed among these distances:
80 11 0.10
81 67 0.61
82 20 0.18
83 11 0.10
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (80 bp):
TCGCATTGCGATTACGTAAATCGCAATGCGAATTAGAAAATCGCAATGCGATTTCCTAAATCGCA
TTGCGATTTACGTAT
Found at i:2845320 original size:61 final size:60
Alignment explanation
Indices: 2845205--2845338 Score: 198
Period size: 61 Copynumber: 2.2 Consensus size: 60
2845195 GAATTAGAAA
* *
2845205 AATCGCAATGCGATTTCGTAAATCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTCGTAAATCGCATTGCGATTTACCTATTCGCATTGCGATTTACGT
* *
2845265 AATCGCATTGCGATTTACGT-AATCGCATTGTGATTTTCCTAATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTT-CGTAAATCGCATTGCGATTTACCT-ATTCGCATTGCGATTTACGT
*
2845326 ATTCGCATTGCGA
1 AATCGCATTGCGA
2845339 ATTAGGAAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
60 32 0.48
61 35 0.52
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (60 bp):
AATCGCATTGCGATTTCGTAAATCGCATTGCGATTTACCTATTCGCATTGCGATTTACGT
Found at i:2847563 original size:353 final size:353
Alignment explanation
Indices: 2846752--2848805 Score: 3856
Period size: 353 Copynumber: 5.8 Consensus size: 353
2846742 CATGTGTTTG
2846752 GATATGATACTTTTAGAAAACAAAGGGTCGGTCTAATGTAGGTGTCACCCGTCTGCGTTTATGGT
1 GATATGATACTTTTAGAAAACAAAGGGTCGGTCTAATGTAGGTGTCACCCGTCTGCGTTTATGGT
2846817 TATGATCTCTGATTTACATGTTATGATGCACAGCCTAAGCAAATTCATGAGATCAAAGACTTCCT
66 TATGATCTCTGATTTACATGTTATGATGCACAGCCTAAGCAAATTCATGAGATCAAAGACTTCCT
*
2846882 TCTCAATGCCAGAAGGAAAGATGCACGTTC-GTGAAGATCAAGAAGAGCAGAGATGTAGTTAAGT
131 TCTCACTGCCAGAAGGAAAGATGCACGTTCGGTGAAGATCAAGAAGAGCAGAGATGTAGTTAAGT
2846946 TCAAGGTCCGTTGCTCCAAGTACTTGTACACAC-TT-TGTGTCCGATGCCGAGAAGGCTGACAAG
196 TCAAGGTCCGTTGCTCCAAGTACTTGTACACACTTTGTGTGTCCGATGCCGAGAAGGCTGACAAG
2847009 TTGAAGCAGTCCCTTCCTCCAGGTAAATTGTTATGCATTAATAGAGTAGCCTC-TTCTCTT-TTT
261 TTGAAGCAGTCCCTTCCTCCAGGTAAATTGTTATGCATTAATAGAGTAGCCTCTTTCT-TTGTTT
2847072 TGAATGAACCAGCGTGTTATAGAATTGTA
325 TGAATGAACCAGCGTGTTATAGAATTGTA
*
2847101 GATATGATACTTTTAGAAACCAAAGGGTCGGTCTAATGTAGGTGTCACCCGTCTGCGTTTATGGT
1 GATATGATACTTTTAGAAAACAAAGGGTCGGTCTAATGTAGGTGTCACCCGTCTGCGTTTATGGT
2847166 TATGATCTCTGATTTACATGTTATGATGCACAGCCTAAGCAAATTCATGAGATCAAAGACTTCCT
66 TATGATCTCTGATTTACATGTTATGATGCACAGCCTAAGCAAATTCATGAGATCAAAGACTTCCT
2847231 TCTCACTGCCAGAAGGAAAGATGCACGTTCGGTGAAGATCAAGAAGAGCAGAGATGTAGTTAAGT
131 TCTCACTGCCAGAAGGAAAGATGCACGTTCGGTGAAGATCAAGAAGAGCAGAGATGTAGTTAAGT
*
2847296 TCAAGGTCCGTTGCTCCAAGTACTTGTACACAGTTTGTGTGTCCGATGCCGAGAAGGCTGACAAG
196 TCAAGGTCCGTTGCTCCAAGTACTTGTACACACTTTGTGTGTCCGATGCCGAGAAGGCTGACAAG
2847361 TTGAAGCAGTCCCTTCCTCCAGGTAAATTGTTATGCATTAATAGAGTAGCCTCTTTCTTTGTTTT
261 TTGAAGCAGTCCCTTCCTCCAGGTAAATTGTTATGCATTAATAGAGTAGCCTCTTTCTTTGTTTT
2847426 GAATGAACCAGCGTGTTATAGAATTGTA
326 GAATGAACCAGCGTGTTATAGAATTGTA
*
2847454 GATATGATACTTTTAGAAAACAAAGGGTCAGTCTAATGTAGGTGTCACCCGTCTGCGTTTATGGT
1 GATATGATACTTTTAGAAAACAAAGGGTCGGTCTAATGTAGGTGTCACCCGTCTGCGTTTATGGT
2847519 TATGATCTCTGATTTACATGTTATGATGCACAGCCTAAGCAAATTCATGAGATCAAAGACTTCCT
66 TATGATCTCTGATTTACATGTTATGATGCACAGCCTAAGCAAATTCATGAGATCAAAGACTTCCT
2847584 TCTCACTGCCAGAAGGAAAGATGCACGTTCGGTGAAGATCAAGAAGAGCAGAGATGTAGTTAAGT
131 TCTCACTGCCAGAAGGAAAGATGCACGTTCGGTGAAGATCAAGAAGAGCAGAGATGTAGTTAAGT
* *
2847649 TCAAGGTCCGTTGCTCCAAGTACTTGTACACACTTTGTGTGTCCGATGCCTAGATGGCTGACAAG
196 TCAAGGTCCGTTGCTCCAAGTACTTGTACACACTTTGTGTGTCCGATGCCGAGAAGGCTGACAAG
2847714 TTGAAGCAGTCCCTTCCTCCAGGTAAATTGTTATGCATTAATAGAGTAGCCTCTTTCTTTGTTTT
261 TTGAAGCAGTCCCTTCCTCCAGGTAAATTGTTATGCATTAATAGAGTAGCCTCTTTCTTTGTTTT
2847779 GAATGAACCAGCGTGTTATAGAATTGTA
326 GAATGAACCAGCGTGTTATAGAATTGTA
2847807 GATATGATACTTTTAGAAAACAAA--GTCGGTCTAATGTAGGTGTCACCCGTCTGCGTTTATGGT
1 GATATGATACTTTTAGAAAACAAAGGGTCGGTCTAATGTAGGTGTCACCCGTCTGCGTTTATGGT
*
2847870 TATGATCTCTGATTTACATGTTATGATGCACAGCCTAAGCATATTCATGAGATCAAAGACTTCCT
66 TATGATCTCTGATTTACATGTTATGATGCACAGCCTAAGCAAATTCATGAGATCAAAGACTTCCT
*
2847935 TCTCACTGCCAGAAGGAAAGATGCACGTTTGGTGAAGATCAAGAAGAGCAGAGATGTAGTTAAGT
131 TCTCACTGCCAGAAGGAAAGATGCACGTTCGGTGAAGATCAAGAAGAGCAGAGATGTAGTTAAGT
2848000 TCAAGGTCCGTTGCTCCAAGTACTTGTACACACTTTGTGTGTCCGATGCCGAGAAGGCTGACAAG
196 TCAAGGTCCGTTGCTCCAAGTACTTGTACACACTTTGTGTGTCCGATGCCGAGAAGGCTGACAAG
*
2848065 TTGAAGCAGTCCCTTCCTCTAGGTAAATTGTTATGCATTAATAGAGTAGCCTCTTTCTTTGTTTT
261 TTGAAGCAGTCCCTTCCTCCAGGTAAATTGTTATGCATTAATAGAGTAGCCTCTTTCTTTGTTTT
2848130 GAATGAACCAGCGTGTTATAGAATTGTA
326 GAATGAACCAGCGTGTTATAGAATTGTA
2848158 GATATGATACTTTTAGAAAACAAAGGGTCGGTCTAATGTAGGTGTCACCCGTCTG-GATTTATGG
1 GATATGATACTTTTAGAAAACAAAGGGTCGGTCTAATGTAGGTGTCACCCGTCTGCG-TTTATGG
2848222 TTATGATCTCTGATTTACATGTTATGATGCACAGCCTAAGCAAATTCATGAGATCAAAGACTTCC
65 TTATGATCTCTGATTTACATGTTATGATGCACAGCCTAAGCAAATTCATGAGATCAAAGACTTCC
*
2848287 TTCTCACTGCCAGAAGAAAAGATGCACGTTCGGTGAAGATCAAGAAGAGCAGAGATGTAGTTAAG
130 TTCTCACTGCCAGAAGGAAAGATGCACGTTCGGTGAAGATCAAGAAGAGCAGAGATGTAGTTAAG
* *
2848352 TTCAAGGTCCGTTTCTCCAAGTACTTGTACACACTTTGTGTGTCCGATGCAGAGAAGGCTGACAA
195 TTCAAGGTCCGTTGCTCCAAGTACTTGTACACACTTTGTGTGTCCGATGCCGAGAAGGCTGACAA
*
2848417 GTTGAAGCAGTCCCTTTCTCCAGGTAAATTGTTATGCATTAATAGAGTAGCCTCTTCTCTTTGTT
260 GTTGAAGCAGTCCCTTCCTCCAGGTAAATTGTTATGCATTAATAGAGTAGCCTCTT-TCTTTGTT
2848482 TTGAATGAACCAGCGTGTTATAGAATTGTA
324 TTGAATGAACCAGCGTGTTATAGAATTGTA
*
2848512 GATATGATACTTTTAGAAAACAAAGGGTCGGTCTAATGTAGGAGTCACCC-TCTGCGTTTATGGT
1 GATATGATACTTTTAGAAAACAAAGGGTCGGTCTAATGTAGGTGTCACCCGTCTGCGTTTATGGT
*
2848576 TATGATCTCTGATTTACATGCTATGATGCACAGCCTAAGCAAATTCATGAGATCAAAGACTTCCT
66 TATGATCTCTGATTTACATGTTATGATGCACAGCCTAAGCAAATTCATGAGATCAAAGACTTCCT
2848641 TCTCACTGCCAGAAGGAAAGATGCACGTTCGGTGAAGATCAAGAAGAGCAGAGATGTAGTTAAGT
131 TCTCACTGCCAGAAGGAAAGATGCACGTTCGGTGAAGATCAAGAAGAGCAGAGATGTAGTTAAGT
* * *
2848706 TCAAGGTCCGTTGCTCCATGTAATTGTACACAGTTTGTGTGTCCGATGCCGAGAAGGCTGACAAG
196 TCAAGGTCCGTTGCTCCAAGTACTTGTACACACTTTGTGTGTCCGATGCCGAGAAGGCTGACAAG
2848771 TTGAAGCAGTCCCTTCCTCCAGGTAAATTGTTATG
261 TTGAAGCAGTCCCTTCCTCCAGGTAAATTGTTATG
2848806 TGTCGAGAAT
Statistics
Matches: 1665, Mismatches: 30, Indels: 16
0.97 0.02 0.01
Matches are distributed among these distances:
349 158 0.09
350 66 0.04
351 347 0.21
352 84 0.05
353 922 0.55
354 88 0.05
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (353 bp):
GATATGATACTTTTAGAAAACAAAGGGTCGGTCTAATGTAGGTGTCACCCGTCTGCGTTTATGGT
TATGATCTCTGATTTACATGTTATGATGCACAGCCTAAGCAAATTCATGAGATCAAAGACTTCCT
TCTCACTGCCAGAAGGAAAGATGCACGTTCGGTGAAGATCAAGAAGAGCAGAGATGTAGTTAAGT
TCAAGGTCCGTTGCTCCAAGTACTTGTACACACTTTGTGTGTCCGATGCCGAGAAGGCTGACAAG
TTGAAGCAGTCCCTTCCTCCAGGTAAATTGTTATGCATTAATAGAGTAGCCTCTTTCTTTGTTTT
GAATGAACCAGCGTGTTATAGAATTGTA
Found at i:2848097 original size:704 final size:705
Alignment explanation
Indices: 2846752--2848805 Score: 3854
Period size: 704 Copynumber: 2.9 Consensus size: 705
2846742 CATGTGTTTG
2846752 GATATGATACTTTTAGAAAACAAAGGGTCGGTCTAATGTAGGTGTCACCCGTCTGCGTTTATGGT
1 GATATGATACTTTTAGAAAACAAAGGGTCGGTCTAATGTAGGTGTCACCCGTCTGCGTTTATGGT
2846817 TATGATCTCTGATTTACATGTTATGATGCACAGCCTAAGCAAATTCATGAGATCAAAGACTTCCT
66 TATGATCTCTGATTTACATGTTATGATGCACAGCCTAAGCAAATTCATGAGATCAAAGACTTCCT
*
2846882 TCTCAATGCCAGAAGGAAAGATGCACGTTC-GTGAAGATCAAGAAGAGCAGAGATGTAGTTAAGT
131 TCTCACTGCCAGAAGGAAAGATGCACGTTCGGTGAAGATCAAGAAGAGCAGAGATGTAGTTAAGT
2846946 TCAAGGTCCGTTGCTCCAAGTACTTGTACACAC-TT-TGTGTCCGATGCCGAGAAGGCTGACAAG
196 TCAAGGTCCGTTGCTCCAAGTACTTGTACACACTTTGTGTGTCCGATGCCGAGAAGGCTGACAAG
2847009 TTGAAGCAGTCCCTTCCTCCAGGTAAATTGTTATGCATTAATAGAGTAGCCTC-TTCTCTT-TTT
261 TTGAAGCAGTCCCTTCCTCCAGGTAAATTGTTATGCATTAATAGAGTAGCCTCTTTCT-TTGTTT
*
2847072 TGAATGAACCAGCGTGTTATAGAATTGTAGATATGATACTTTTAGAAACCAAAGGGTCGGTCTAA
325 TGAATGAACCAGCGTGTTATAGAATTGTAGATATGATACTTTTAGAAAACAAA-GGTCGGTCTAA
2847137 TGTAGGTGTCACCCGTCTGCGTTTATGGTTATGATCTCTGATTTACATGTTATGATGCACAGCCT
389 TGTAGGTGTCACCCGTCTGCGTTTATGGTTATGATCTCTGATTTACATGTTATGATGCACAGCCT
2847202 AAGCAAATTCATGAGATCAAAGACTTCCTTCTCACTGCCAGAAGGAAAGATGCACGTTCGGTGAA
454 AAGCAAATTCATGAGATCAAAGACTTCCTTCTCACTGCCAGAAGGAAAGATGCACGTTCGGTGAA
2847267 GATCAAGAAGAGCAGAGATGTAGTTAAGTTCAAGGTCCGTTGCTCCAAGTACTTGTACACAGTTT
519 GATCAAGAAGAGCAGAGATGTAGTTAAGTTCAAGGTCCGTTGCTCCAAGTACTTGTACACAGTTT
2847332 GTGTGTCCGATGCCGAGAAGGCTGACAAGTTGAAGCAGTCCCTTCCTCCAGGTAAATTGTTATGC
584 GTGTGTCCGATGCCGAGAAGGCTGACAAGTTGAAGCAGTCCCTTCCTCCAGGTAAATTGTTATGC
2847397 ATTAATAGAGTAGCCTCTTTCTTTGTTTTGAATGAACCAGCGTGTTATAGAATTGTA
649 ATTAATAGAGTAGCCTCTTTCTTTGTTTTGAATGAACCAGCGTGTTATAGAATTGTA
*
2847454 GATATGATACTTTTAGAAAACAAAGGGTCAGTCTAATGTAGGTGTCACCCGTCTGCGTTTATGGT
1 GATATGATACTTTTAGAAAACAAAGGGTCGGTCTAATGTAGGTGTCACCCGTCTGCGTTTATGGT
2847519 TATGATCTCTGATTTACATGTTATGATGCACAGCCTAAGCAAATTCATGAGATCAAAGACTTCCT
66 TATGATCTCTGATTTACATGTTATGATGCACAGCCTAAGCAAATTCATGAGATCAAAGACTTCCT
2847584 TCTCACTGCCAGAAGGAAAGATGCACGTTCGGTGAAGATCAAGAAGAGCAGAGATGTAGTTAAGT
131 TCTCACTGCCAGAAGGAAAGATGCACGTTCGGTGAAGATCAAGAAGAGCAGAGATGTAGTTAAGT
* *
2847649 TCAAGGTCCGTTGCTCCAAGTACTTGTACACACTTTGTGTGTCCGATGCCTAGATGGCTGACAAG
196 TCAAGGTCCGTTGCTCCAAGTACTTGTACACACTTTGTGTGTCCGATGCCGAGAAGGCTGACAAG
2847714 TTGAAGCAGTCCCTTCCTCCAGGTAAATTGTTATGCATTAATAGAGTAGCCTCTTTCTTTGTTTT
261 TTGAAGCAGTCCCTTCCTCCAGGTAAATTGTTATGCATTAATAGAGTAGCCTCTTTCTTTGTTTT
2847779 GAATGAACCAGCGTGTTATAGAATTGTAGATATGATACTTTTAGAAAACAAA-GTCGGTCTAATG
326 GAATGAACCAGCGTGTTATAGAATTGTAGATATGATACTTTTAGAAAACAAAGGTCGGTCTAATG
2847843 TAGGTGTCACCCGTCTGCGTTTATGGTTATGATCTCTGATTTACATGTTATGATGCACAGCCTAA
391 TAGGTGTCACCCGTCTGCGTTTATGGTTATGATCTCTGATTTACATGTTATGATGCACAGCCTAA
* *
2847908 GCATATTCATGAGATCAAAGACTTCCTTCTCACTGCCAGAAGGAAAGATGCACGTTTGGTGAAGA
456 GCAAATTCATGAGATCAAAGACTTCCTTCTCACTGCCAGAAGGAAAGATGCACGTTCGGTGAAGA
*
2847973 TCAAGAAGAGCAGAGATGTAGTTAAGTTCAAGGTCCGTTGCTCCAAGTACTTGTACACACTTTGT
521 TCAAGAAGAGCAGAGATGTAGTTAAGTTCAAGGTCCGTTGCTCCAAGTACTTGTACACAGTTTGT
*
2848038 GTGTCCGATGCCGAGAAGGCTGACAAGTTGAAGCAGTCCCTTCCTCTAGGTAAATTGTTATGCAT
586 GTGTCCGATGCCGAGAAGGCTGACAAGTTGAAGCAGTCCCTTCCTCCAGGTAAATTGTTATGCAT
2848103 TAATAGAGTAGCCTCTTTCTTTGTTTTGAATGAACCAGCGTGTTATAGAATTGTA
651 TAATAGAGTAGCCTCTTTCTTTGTTTTGAATGAACCAGCGTGTTATAGAATTGTA
2848158 GATATGATACTTTTAGAAAACAAAGGGTCGGTCTAATGTAGGTGTCACCCGTCTG-GATTTATGG
1 GATATGATACTTTTAGAAAACAAAGGGTCGGTCTAATGTAGGTGTCACCCGTCTGCG-TTTATGG
2848222 TTATGATCTCTGATTTACATGTTATGATGCACAGCCTAAGCAAATTCATGAGATCAAAGACTTCC
65 TTATGATCTCTGATTTACATGTTATGATGCACAGCCTAAGCAAATTCATGAGATCAAAGACTTCC
*
2848287 TTCTCACTGCCAGAAGAAAAGATGCACGTTCGGTGAAGATCAAGAAGAGCAGAGATGTAGTTAAG
130 TTCTCACTGCCAGAAGGAAAGATGCACGTTCGGTGAAGATCAAGAAGAGCAGAGATGTAGTTAAG
* *
2848352 TTCAAGGTCCGTTTCTCCAAGTACTTGTACACACTTTGTGTGTCCGATGCAGAGAAGGCTGACAA
195 TTCAAGGTCCGTTGCTCCAAGTACTTGTACACACTTTGTGTGTCCGATGCCGAGAAGGCTGACAA
*
2848417 GTTGAAGCAGTCCCTTTCTCCAGGTAAATTGTTATGCATTAATAGAGTAGCCTCTTCTCTTTGTT
260 GTTGAAGCAGTCCCTTCCTCCAGGTAAATTGTTATGCATTAATAGAGTAGCCTCTT-TCTTTGTT
2848482 TTGAATGAACCAGCGTGTTATAGAATTGTAGATATGATACTTTTAGAAAACAAAGGGTCGGTCTA
324 TTGAATGAACCAGCGTGTTATAGAATTGTAGATATGATACTTTTAGAAAACAAA-GGTCGGTCTA
* *
2848547 ATGTAGGAGTCACCC-TCTGCGTTTATGGTTATGATCTCTGATTTACATGCTATGATGCACAGCC
388 ATGTAGGTGTCACCCGTCTGCGTTTATGGTTATGATCTCTGATTTACATGTTATGATGCACAGCC
2848611 TAAGCAAATTCATGAGATCAAAGACTTCCTTCTCACTGCCAGAAGGAAAGATGCACGTTCGGTGA
453 TAAGCAAATTCATGAGATCAAAGACTTCCTTCTCACTGCCAGAAGGAAAGATGCACGTTCGGTGA
* *
2848676 AGATCAAGAAGAGCAGAGATGTAGTTAAGTTCAAGGTCCGTTGCTCCATGTAATTGTACACAGTT
518 AGATCAAGAAGAGCAGAGATGTAGTTAAGTTCAAGGTCCGTTGCTCCAAGTACTTGTACACAGTT
2848741 TGTGTGTCCGATGCCGAGAAGGCTGACAAGTTGAAGCAGTCCCTTCCTCCAGGTAAATTGTTATG
583 TGTGTGTCCGATGCCGAGAAGGCTGACAAGTTGAAGCAGTCCCTTCCTCCAGGTAAATTGTTATG
2848806 TGTCGAGAAT
Statistics
Matches: 1319, Mismatches: 24, Indels: 14
0.97 0.02 0.01
Matches are distributed among these distances:
702 158 0.12
703 68 0.05
704 631 0.48
705 143 0.11
706 296 0.22
707 23 0.02
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (705 bp):
GATATGATACTTTTAGAAAACAAAGGGTCGGTCTAATGTAGGTGTCACCCGTCTGCGTTTATGGT
TATGATCTCTGATTTACATGTTATGATGCACAGCCTAAGCAAATTCATGAGATCAAAGACTTCCT
TCTCACTGCCAGAAGGAAAGATGCACGTTCGGTGAAGATCAAGAAGAGCAGAGATGTAGTTAAGT
TCAAGGTCCGTTGCTCCAAGTACTTGTACACACTTTGTGTGTCCGATGCCGAGAAGGCTGACAAG
TTGAAGCAGTCCCTTCCTCCAGGTAAATTGTTATGCATTAATAGAGTAGCCTCTTTCTTTGTTTT
GAATGAACCAGCGTGTTATAGAATTGTAGATATGATACTTTTAGAAAACAAAGGTCGGTCTAATG
TAGGTGTCACCCGTCTGCGTTTATGGTTATGATCTCTGATTTACATGTTATGATGCACAGCCTAA
GCAAATTCATGAGATCAAAGACTTCCTTCTCACTGCCAGAAGGAAAGATGCACGTTCGGTGAAGA
TCAAGAAGAGCAGAGATGTAGTTAAGTTCAAGGTCCGTTGCTCCAAGTACTTGTACACAGTTTGT
GTGTCCGATGCCGAGAAGGCTGACAAGTTGAAGCAGTCCCTTCCTCCAGGTAAATTGTTATGCAT
TAATAGAGTAGCCTCTTTCTTTGTTTTGAATGAACCAGCGTGTTATAGAATTGTA
Found at i:2848854 original size:20 final size:20
Alignment explanation
Indices: 2848829--2848919 Score: 72
Period size: 20 Copynumber: 5.0 Consensus size: 20
2848819 TAAATTAAAT
*
2848829 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
*
2848849 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
* *
2848869 ATT--CT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
* *
2848881 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
2848901 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
2848920 TTATTCTATT
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
12 3 0.06
13 2 0.04
14 1 0.02
15 4 0.07
17 3 0.06
18 1 0.02
19 2 0.04
20 38 0.70
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:2848906 original size:52 final size:52
Alignment explanation
Indices: 2848828--2848975 Score: 271
Period size: 53 Copynumber: 2.8 Consensus size: 52
2848818 CTAAATTAAA
*
2848828 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
2848880 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
2848933 TATTAGATAGGATCATTTTTAATTAGATAGAATCA-TTTTTATT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATT
2848976 ATGTTGCTAA
Statistics
Matches: 94, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
51 8 0.09
52 35 0.37
53 51 0.54
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:2848959 original size:20 final size:20
Alignment explanation
Indices: 2848934--2848973 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2848924 TCTATTAGTT
*
2848934 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
2848954 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
2848974 TTATGTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:2853558 original size:20 final size:20
Alignment explanation
Indices: 2853533--2853623 Score: 63
Period size: 20 Copynumber: 5.0 Consensus size: 20
2853523 TAAATTAAAT
*
2853533 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
* *
2853553 ATTAGATAGAATCAATTTTT
1 ATTAGATAGAATCAGTTTTA
* *
2853573 ATT--CT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
* *
2853585 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
2853605 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
2853624 TTATTCTATT
Statistics
Matches: 52, Mismatches: 11, Indels: 16
0.66 0.14 0.20
Matches are distributed among these distances:
12 3 0.06
13 2 0.04
14 1 0.02
15 3 0.06
17 3 0.06
18 1 0.02
19 2 0.04
20 37 0.71
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:2853648 original size:53 final size:52
Alignment explanation
Indices: 2853532--2853681 Score: 264
Period size: 53 Copynumber: 2.8 Consensus size: 52
2853522 CTAAATTAAA
* *
2853532 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAATTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCATTTTTTATTCTATTAGT
2853584 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCA-TTTTTTATTCTATTAGT
2853637 TATTAGATAGGATCATTTTTAATTAGATAGAATCATTTTATTATT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCATTTT-TTATT
2853682 TGCTAATTTT
Statistics
Matches: 94, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
52 38 0.40
53 56 0.60
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.48
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCATTTTTTATTCTATTAGT
Found at i:2853663 original size:20 final size:20
Alignment explanation
Indices: 2853638--2853675 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2853628 TCTATTAGTT
*
2853638 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
2853658 ATTAGATAGAATCATTTT
1 ATTAGATAGAATCATTTT
2853676 ATTATTTGCT
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:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:2854871 original size:349 final size:353
Alignment explanation
Indices: 2853798--2854988 Score: 2229
Period size: 353 Copynumber: 3.4 Consensus size: 353
2853788 TTCTTCTTTA
2853798 TTATGCATTAATAGAGTAGCCTCTTTCTTTGTTTTGAATGAACCAGCGTGTTATAGAATTGTAGA
1 TTATGCATTAATAGAGTAGCCTCTTTCTTTGTTTTGAATGAACCAGCGTGTTATAGAATTGTAGA
2853863 TATGATACTTTTAGAAAACAAAGGGTCGGTCTAATGTAGGTGTCACCCGTCTGCGTTTATGGTTA
66 TATGATACTTTTAGAAAACAAAGGGTCGGTCTAATGTAGGTGTCACCCGTCTGCGTTTATGGTTA
2853928 TGATCTCTGATTTACATGTTATGATGCACAGCCTAAGCAAATTCATGAGATCAAAGACTTCCTTC
131 TGATCTCTGATTTACATGTTATGATGCACAGCCTAAGCAAATTCATGAGATCAAAGACTTCCTTC
*
2853993 TCACTGCCAGAAGGAAAGATGCACGTTTGGTGAAGATCAAGAAGAGCAGAGATGTAGTTAAGTTC
196 TCACTGCCAGAAGGAAAGATGCACGTTCGGTGAAGATCAAGAAGAGCAGAGATGTAGTTAAGTTC
* *
2854058 AAGGTCCGTTGCTCCAAGTACTTGTACACACTTTGTATGTCCGATGCCAAGAAGGCTGACAAGTT
261 AAGGTCCGTTGCTCCAAGTACTTGTACACACTTTGTGTGTCCGATGCCGAGAAGGCTGACAAGTT
2854123 GAAGCAGTCCCTTCCTCCAGGTAAATTG
326 GAAGCAGTCCCTTCCTCCAGGTAAATTG
2854151 TTATGCATTAATAGAGTAGCCTCTTTCTTTGTTTTGAATGAACCAGCGTGTTATAGAATTGTAGA
1 TTATGCATTAATAGAGTAGCCTCTTTCTTTGTTTTGAATGAACCAGCGTGTTATAGAATTGTAGA
* *
2854216 TATGATACTTTTAGAAAACAAAGGGTCGGTCTAATGTAGGTGTCACTCGTCTGCATTTATGGTTA
66 TATGATACTTTTAGAAAACAAAGGGTCGGTCTAATGTAGGTGTCACCCGTCTGCGTTTATGGTTA
2854281 TGATCTCTGATTTACATGTTATGATGCACAGCCTAAGCAAATTCATGAGATCAAAGACTTCCTTC
131 TGATCTCTGATTTACATGTTATGATGCACAGCCTAAGCAAATTCATGAGATCAAAGACTTCCTTC
2854346 TCACTGCCAGAAGGAAAGATGCACGTTCGGTGAAGATCAAGAAGAGCAGAGATGTAGTTAAGTTC
196 TCACTGCCAGAAGGAAAGATGCACGTTCGGTGAAGATCAAGAAGAGCAGAGATGTAGTTAAGTTC
*
2854411 AAGGTCCGTTGCTCCAAGTACTTGTACACACTTTGTGTGTCCGATGCAGAGAAGGCTGACAAGTT
261 AAGGTCCGTTGCTCCAAGTACTTGTACACACTTTGTGTGTCCGATGCCGAGAAGGCTGACAAGTT
*
2854476 GAAGCAGTCCCTCCCTCCAGGT-AATTG
326 GAAGCAGTCCCTTCCTCCAGGTAAATTG
2854503 TTAT---TTAATAGAGTAGCCTC-TTCTCTTGTTTTGAATGAACCAGCGTGTTATAGAATTGTAG
1 TTATGCATTAATAGAGTAGCCTCTTTCT-TTGTTTTGAATGAACCAGCGTGTTATAGAATTGTAG
*
2854564 ATATGATACTATTAGAAAACAAAGGGTCGGTCTAATGTAGGTGTCACCC-TCTGCGTTTATGGTT
65 ATATGATACTTTTAGAAAACAAAGGGTCGGTCTAATGTAGGTGTCACCCGTCTGCGTTTATGGTT
2854628 ATGATCTCTGATTTACATGTTATGATGCACAGCCTAAGCAAATTCATGAGATCAAAGACTTCCTT
130 ATGATCTCTGATTTACATGTTATGATGCACAGCCTAAGCAAATTCATGAGATCAAAGACTTCCTT
*
2854693 CTCACTGCCAGAAGGAAAGATGCACGTTCGGTGAAGATCAAGAAGAGCA-TG-TGTAGTT-AGTT
195 CTCACTGCCAGAAGGAAAGATGCACGTTCGGTGAAGATCAAGAAGAGCAGAGATGTAGTTAAGTT
2854755 CAAGGTCCGTTGCTCCAAGTACTTGTACACACTTTGTGTGTCCGATGCCGAGAAGGCTGACAAGT
260 CAAGGTCCGTTGCTCCAAGTACTTGTACACACTTTGTGTGTCCGATGCCGAGAAGGCTGACAAGT
2854820 TGAAGCAGTCCCTTCCTCCAGGTAAATTG
325 TGAAGCAGTCCCTTCCTCCAGGTAAATTG
2854849 TTATGCATTAATAGAGTAGCCTCTTTCTTTGTTTTGAATGAACCAGCGTGTTATAGAATTGTAGA
1 TTATGCATTAATAGAGTAGCCTCTTTCTTTGTTTTGAATGAACCAGCGTGTTATAGAATTGTAGA
2854914 TATGATACTTTTAGAAAACAAAGGGTCGGTCTAATGTAGGTGTCACCCGTCTGCGTTTATGGTTA
66 TATGATACTTTTAGAAAACAAAGGGTCGGTCTAATGTAGGTGTCACCCGTCTGCGTTTATGGTTA
2854979 TGATCTCTGA
131 TGATCTCTGA
2854989 ACTTCCTTCT
Statistics
Matches: 817, Mismatches: 14, Indels: 17
0.96 0.02 0.02
Matches are distributed among these distances:
345 90 0.11
346 16 0.02
347 1 0.00
348 132 0.16
349 199 0.24
350 30 0.04
352 9 0.01
353 340 0.42
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (353 bp):
TTATGCATTAATAGAGTAGCCTCTTTCTTTGTTTTGAATGAACCAGCGTGTTATAGAATTGTAGA
TATGATACTTTTAGAAAACAAAGGGTCGGTCTAATGTAGGTGTCACCCGTCTGCGTTTATGGTTA
TGATCTCTGATTTACATGTTATGATGCACAGCCTAAGCAAATTCATGAGATCAAAGACTTCCTTC
TCACTGCCAGAAGGAAAGATGCACGTTCGGTGAAGATCAAGAAGAGCAGAGATGTAGTTAAGTTC
AAGGTCCGTTGCTCCAAGTACTTGTACACACTTTGTGTGTCCGATGCCGAGAAGGCTGACAAGTT
GAAGCAGTCCCTTCCTCCAGGTAAATTG
Found at i:2864435 original size:16 final size:16
Alignment explanation
Indices: 2864414--2864455 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
2864404 ATAAGAGAAT
2864414 GAATTAAAATATAATC
1 GAATTAAAATATAATC
2864430 GAATTAAAATATAATC
1 GAATTAAAATATAATC
2864446 GAATTAAAAT
1 GAATTAAAAT
2864456 TAGATTCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.31
Consensus pattern (16 bp):
GAATTAAAATATAATC
Found at i:2864930 original size:2 final size:2
Alignment explanation
Indices: 2864925--2864969 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2864915 ATATATTGTG
2864925 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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 TA TA TA
2864967 TA T
1 TA T
2864970 TCATATGCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2865860 original size:26 final size:26
Alignment explanation
Indices: 2865830--2865974 Score: 179
Period size: 26 Copynumber: 6.0 Consensus size: 26
2865820 TAAAACGAAT
2865830 CCATAAATGAAATGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATG
2865856 CCATAAATGAAATGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATG
*
2865882 -CAT---T--AAGGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATG
*
2865902 CTATAAATGAAATGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATG
*
2865928 -CAT---T--AAGGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATG
2865948 CCATAAATGAAATGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATG
2865974 C
1 C
2865975 ATTAGGGCAT
Statistics
Matches: 101, Mismatches: 6, Indels: 24
0.77 0.05 0.18
Matches are distributed among these distances:
20 30 0.30
21 5 0.05
22 2 0.02
24 2 0.02
25 5 0.05
26 57 0.56
ACGTcount: A:0.44, C:0.11, G:0.25, T:0.20
Consensus pattern (26 bp):
CCATAAATGAAATGCATGAAAGGATG
Found at i:2865894 original size:20 final size:20
Alignment explanation
Indices: 2865869--2865993 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
2865859 TAAATGAAAT
2865869 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
2865889 GCATGAAAGGATGCTATAAATGAAAT
1 GCATGAAAGGATGC-AT---T--AAG
2865915 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
2865935 GCATGAAAGGATGCCATAAATGAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
2865961 GCATGAAAGGATGCATTAGG
1 GCATGAAAGGATGCATTAAG
2865981 GCATGAAAGGATG
1 GCATGAAAGGATG
2865994 TCATAAATGA
Statistics
Matches: 88, Mismatches: 5, Indels: 24
0.75 0.04 0.21
Matches are distributed among these distances:
20 43 0.49
21 5 0.06
22 2 0.02
24 2 0.02
25 5 0.06
26 31 0.35
ACGTcount: A:0.42, C:0.10, G:0.29, T:0.20
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:2865910 original size:46 final size:46
Alignment explanation
Indices: 2865843--2866006 Score: 301
Period size: 46 Copynumber: 3.6 Consensus size: 46
2865833 TAAATGAAAT
2865843 GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAG
*
2865889 GCATGAAAGGATGCTATAAATGAAATGCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAG
*
2865935 GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAGG
1 GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAG
*
2865981 GCATGAAAGGATGTCATAAATGAAAT
1 GCATGAAAGGATGCCATAAATGAAAT
2866007 TAACGAATAA
Statistics
Matches: 114, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 114 1.00
ACGTcount: A:0.43, C:0.10, G:0.26, T:0.21
Consensus pattern (46 bp):
GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAG
Found at i:2866487 original size:81 final size:81
Alignment explanation
Indices: 2866370--2866567 Score: 292
Period size: 81 Copynumber: 2.4 Consensus size: 81
2866360 ATGGTCTAGT
2866370 TGTGTATTTGACAGAAATGTGTCAATCATGTC-AGTTAGATGAAAGGTTAAATACCTTTGAGTAA
1 TGTGTATTTGACAGAAATGTGTCAATCATG-CAAGTTAGATGAAAGGTTAAATACCTTTGAGTAA
2866434 AAGACTAAAAGCCTAAC
65 AAGACTAAAAGCCTAAC
* * * *
2866451 TGTGTCTTTGGCAGAAATGTGTCAATCATGCAAGTTAGATGAAAGGTTAAATACTTTTGGGTAAA
1 TGTGTATTTGACAGAAATGTGTCAATCATGCAAGTTAGATGAAAGGTTAAATACCTTTGAGTAAA
* *
2866516 AGACTAAATGTCTAAC
66 AGACTAAAAGCCTAAC
* *
2866532 GGTGTATTTGACAGAAA-GATGTCAATAATGCAAGTT
1 TGTGTATTTGACAGAAATG-TGTCAATCATGCAAGTT
2866568 GGATAAATGA
Statistics
Matches: 105, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
80 2 0.02
81 103 0.98
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (81 bp):
TGTGTATTTGACAGAAATGTGTCAATCATGCAAGTTAGATGAAAGGTTAAATACCTTTGAGTAAA
AGACTAAAAGCCTAAC
Found at i:2870117 original size:4 final size:4
Alignment explanation
Indices: 2870110--2870135 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2870100 TTCTCTATAT
2870110 ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC AT
2870136 GGACGGAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:2870249 original size:17 final size:17
Alignment explanation
Indices: 2870227--2870260 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2870217 ATAGATGCCA
2870227 ATATTT-TTTAAAGATAT
1 ATATTTCTTTAAA-ATAT
2870244 ATATTTCTTTAAAATAT
1 ATATTTCTTTAAAATAT
2870261 GTTAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (17 bp):
ATATTTCTTTAAAATAT
Found at i:2872517 original size:30 final size:30
Alignment explanation
Indices: 2872461--2872559 Score: 155
Period size: 30 Copynumber: 3.3 Consensus size: 30
2872451 GAAGGACCTA
* *
2872461 TCCAGAGGTCACAAAGA-CCCCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
2872490 TCCAGAGGTCATAAAGATCCTCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
2872520 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
2872550 TCCATAGGTC
1 TCCAGAGGTC
2872560 CCGAAGAACC
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
29 16 0.25
30 48 0.75
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.21
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:2872576 original size:60 final size:59
Alignment explanation
Indices: 2872458--2872576 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 59
2872448 CCCGAAGGAC
* * *
2872458 CTATCCAGAGGTCACAAAGACCCCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGACCCCGGTAACTGTCCAGAGGTCACAAAGAACCTAGGTAA
* * * * *
2872517 CTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCATAGGTCCCGAAGAACCTAGGTAA
1 CTATCCAGAGGTCACAAAGA-CCCCGGTAACTGTCCAGAGGTCACAAAGAACCTAGGTAA
2872577 ACTTTCCATA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
59 19 0.37
60 32 0.63
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.20
Consensus pattern (59 bp):
CTATCCAGAGGTCACAAAGACCCCGGTAACTGTCCAGAGGTCACAAAGAACCTAGGTAA
Found at i:2873921 original size:21 final size:21
Alignment explanation
Indices: 2873891--2873935 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2873881 ATTCTGTCGT
* *
2873891 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2873912 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2873933 TTG
1 TTG
2873936 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2877103 original size:20 final size:20
Alignment explanation
Indices: 2877078--2877121 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
2877068 TTTGGATTGA
2877078 CAAATGCTACAGTTACCTTT
1 CAAATGCTACAGTTACCTTT
2877098 CAAATGCTACAGTTACCTTT
1 CAAATGCTACAGTTACCTTT
2877118 CAAA
1 CAAA
2877122 CACTTATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.25, G:0.09, T:0.32
Consensus pattern (20 bp):
CAAATGCTACAGTTACCTTT
Found at i:2880948 original size:13 final size:13
Alignment explanation
Indices: 2880930--2880963 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
2880920 TAAGATTTTC
*
2880930 TTTGAAAATCATT
1 TTTGAAAATCAAT
2880943 TTTG-AAATCAAT
1 TTTGAAAATCAAT
2880955 TTTGAAAAT
1 TTTGAAAAT
2880964 TACTCCCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:2883228 original size:23 final size:23
Alignment explanation
Indices: 2883201--2883278 Score: 76
Period size: 21 Copynumber: 3.6 Consensus size: 23
2883191 CACTCCTGAG
2883201 TGTATCGATACACATTCAAGGAA
1 TGTATCGATACACATTCAAGGAA
*
2883224 TGTATCGGTACACATTCATA-G--
1 TGTATCGATACACATTCA-AGGAA
* * *
2883245 TGTATCGATACATA-GCGAGGAA
1 TGTATCGATACACATTCAAGGAA
2883267 -GTATCGATACAC
1 TGTATCGATACAC
2883279 TTTGCACAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
19 1 0.02
20 2 0.04
21 23 0.51
23 18 0.40
24 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.27
Consensus pattern (23 bp):
TGTATCGATACACATTCAAGGAA
Found at i:2883250 original size:21 final size:20
Alignment explanation
Indices: 2883199--2883256 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 20
2883189 TACACTCCTG
2883199 AGTGTATCGATACACATTCA
1 AGTGTATCGATACACATTCA
*
2883219 AGGAATGTATCGGTACACATTCA
1 A-G--TGTATCGATACACATTCA
2883242 TAGTGTATCGATACA
1 -AGTGTATCGATACA
2883257 TAGCGAGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 1 0.03
21 12 0.38
23 18 0.56
24 1 0.03
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (20 bp):
AGTGTATCGATACACATTCA
Found at i:2906998 original size:63 final size:62
Alignment explanation
Indices: 2906868--2907009 Score: 146
Period size: 63 Copynumber: 2.3 Consensus size: 62
2906858 CGATGCATTC
* *
2906868 TTTAAA-ATGTGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTCGATGTTTTCAT
1 TTTAAAGA-GTGCATCGATGCACTAACCATGCATCGATACACAAAGCA-CTTCGATGTTTTCAT
* * ** * *
2906931 TTTAAGGGGTGCATCGATGCACTAACTGTGCATCGGTACACTCAAAGCA-TTCGATG-TTTCTT
1 TTTAAAGAGTGCATCGATGCACTAACCATGCATCGATACA--CAAAGCACTTCGATGTTTTCAT
2906993 CTTTAAAGAGTGCATCG
1 -TTTAAAGAGTGCATCG
2907010 GTACACATTG
Statistics
Matches: 65, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
62 5 0.08
63 54 0.83
65 6 0.09
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (62 bp):
TTTAAAGAGTGCATCGATGCACTAACCATGCATCGATACACAAAGCACTTCGATGTTTTCAT
Found at i:2910011 original size:16 final size:16
Alignment explanation
Indices: 2909978--2910011 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2909968 ATTGAAACTC
* *
2909978 AACTCGAACTCGAAAA
1 AACTCAAACTCAAAAA
2909994 AACTCAAACTCAAAAA
1 AACTCAAACTCAAAAA
2910010 AA
1 AA
2910012 TTTAAAAGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.24, G:0.06, T:0.12
Consensus pattern (16 bp):
AACTCAAACTCAAAAA
Found at i:2910072 original size:12 final size:12
Alignment explanation
Indices: 2910055--2910094 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
2910045 TCGATTGGAA
2910055 CTCAATTTTAAG
1 CTCAATTTTAAG
*
2910067 CTCAA-TTCAAG
1 CTCAATTTTAAG
*
2910078 CTCAATTTTGAG
1 CTCAATTTTAAG
2910090 CTCAA
1 CTCAA
2910095 GTCAAGCTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.35
Consensus pattern (12 bp):
CTCAATTTTAAG
Found at i:2910081 original size:23 final size:23
Alignment explanation
Indices: 2910055--2910105 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
2910045 TCGATTGGAA
*
2910055 CTCAATTTTAAGCTCAATTCAAG
1 CTCAATTTTAAGCTCAAGTCAAG
*
2910078 CTCAATTTTGAGCTCAAGTCAAG
1 CTCAATTTTAAGCTCAAGTCAAG
2910101 CTCAA
1 CTCAA
2910106 GACTGCTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (23 bp):
CTCAATTTTAAGCTCAAGTCAAG
Found at i:2912085 original size:14 final size:14
Alignment explanation
Indices: 2912066--2912095 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2912056 TATAATTATC
*
2912066 AATAATGTATTTTT
1 AATAATGTAATTTT
2912080 AATAATGTAATTTT
1 AATAATGTAATTTT
2912094 AA
1 AA
2912096 AAAATCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTAATTTT
Found at i:2914123 original size:20 final size:22
Alignment explanation
Indices: 2914086--2914136 Score: 79
Period size: 20 Copynumber: 2.4 Consensus size: 22
2914076 TGGTGAGGTA
2914086 GTATCGATATTCTGTTCATAGG
1 GTATCGATATTCTGTTCATAGG
2914108 GTATCGATA-T-TGTTCATAGG
1 GTATCGATATTCTGTTCATAGG
*
2914128 GTATTGATA
1 GTATCGATA
2914137 CCTAAGTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 18 0.64
21 1 0.04
22 9 0.32
ACGTcount: A:0.25, C:0.10, G:0.24, T:0.41
Consensus pattern (22 bp):
GTATCGATATTCTGTTCATAGG
Found at i:2914455 original size:27 final size:27
Alignment explanation
Indices: 2914423--2914476 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
2914413 ATATTGAAAG
*
2914423 GTCGATATCGATACTAAAGGGCTTAGT
1 GTCGATATCAATACTAAAGGGCTTAGT
2914450 GTCGATATCAATACTAAAGGGCTTAGT
1 GTCGATATCAATACTAAAGGGCTTAGT
2914477 ATAGATACCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (27 bp):
GTCGATATCAATACTAAAGGGCTTAGT
Found at i:2914483 original size:27 final size:27
Alignment explanation
Indices: 2914426--2914483 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
2914416 TTGAAAGGTC
* * *
2914426 GATATCGATACTAAAGGGCTTAGTGTC
1 GATATCAATACTAAAGGGCTTAGTATA
2914453 GATATCAATACTAAAGGGCTTAGTATA
1 GATATCAATACTAAAGGGCTTAGTATA
2914480 GATA
1 GATA
2914484 CCATCATGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (27 bp):
GATATCAATACTAAAGGGCTTAGTATA
Found at i:2916597 original size:15 final size:16
Alignment explanation
Indices: 2916563--2916599 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2916553 CATAGCTAAT
*
2916563 TCATTCAGCATTTAAA
1 TCATTCAGCACTTAAA
2916579 TCATTCAGCACTT-AA
1 TCATTCAGCACTTAAA
2916594 TCATTC
1 TCATTC
2916600 TGAAGTAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.38
Consensus pattern (16 bp):
TCATTCAGCACTTAAA
Found at i:2917408 original size:3 final size:3
Alignment explanation
Indices: 2917396--2917449 Score: 92
Period size: 3 Copynumber: 18.0 Consensus size: 3
2917386 TTTGTATTGT
2917396 ATA ATAA ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2917441 ATA ATA ATA
1 ATA ATA ATA
2917450 GTTTCTAATT
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 44 0.90
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2923685 original size:10 final size:10
Alignment explanation
Indices: 2923670--2923705 Score: 54
Period size: 10 Copynumber: 3.4 Consensus size: 10
2923660 AAAAAAATTC
2923670 TATTATTATA
1 TATTATTATA
2923680 TATTATTATA
1 TATTATTATA
2923690 TATATATATATA
1 TAT-TAT-TATA
2923702 TATT
1 TATT
2923706 TGTCTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 13 0.54
11 4 0.17
12 7 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TATTATTATA
Found at i:2924277 original size:15 final size:15
Alignment explanation
Indices: 2924257--2924286 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2924247 TATCTCAACT
2924257 TGTTATTTAAAAATA
1 TGTTATTTAAAAATA
*
2924272 TGTTATTTATAAATA
1 TGTTATTTAAAAATA
2924287 AATATATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (15 bp):
TGTTATTTAAAAATA
Found at i:2925650 original size:14 final size:14
Alignment explanation
Indices: 2925633--2925670 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
2925623 TCTGGATCGG
2925633 CCCGAACCGATCAA
1 CCCGAACCGATCAA
2925647 CCCGAACCGATCAA
1 CCCGAACCGATCAA
*
2925661 CCCGACCCGA
1 CCCGAACCGA
2925671 CTCGATTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.32, C:0.47, G:0.16, T:0.05
Consensus pattern (14 bp):
CCCGAACCGATCAA
Found at i:2927939 original size:155 final size:156
Alignment explanation
Indices: 2927657--2927967 Score: 615
Period size: 155 Copynumber: 2.0 Consensus size: 156
2927647 TAAAATCTTA
2927657 AAATTCATTTATACTTAGTTTGTTATATCGAAACATCAAAATGTTTTCAACAATCTCCCCCTTTT
1 AAATTCATTTATACTTAGTTTGTTATATCGAAACATCAAAATGTTTTCAACAATCTCCCCCTTTT
2927722 TGATATAACAAAACATTTAGTAATTTTAAGATTTTCAATTTGAAAAAAAATATATCAAGTTTTGA
66 TGATATAACAAAACATTTAGTAATTTTAAGATTTTCAATTTGAAAAAAAATATATCAAGTTTTGA
2927787 AATTACTCCCCC-TACTATAACACAC
131 AATTACTCCCCCTTACTATAACACAC
2927812 AAATTCATTTATACTTAGTTTGTTATATCGAAACATCAAAATGTTTTCAACAATCTCCCCCTTTT
1 AAATTCATTTATACTTAGTTTGTTATATCGAAACATCAAAATGTTTTCAACAATCTCCCCCTTTT
2927877 TGATATAACAAAACATTTAGTAATTTTAAGATTTTCAATTTGAAAAAAAATATATCAAGTTTTGA
66 TGATATAACAAAACATTTAGTAATTTTAAGATTTTCAATTTGAAAAAAAATATATCAAGTTTTGA
2927942 AATTACTCCCCCTTACTATAACACAC
131 AATTACTCCCCCTTACTATAACACAC
2927968 TTCTCCCTCT
Statistics
Matches: 155, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
155 142 0.92
156 13 0.08
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (156 bp):
AAATTCATTTATACTTAGTTTGTTATATCGAAACATCAAAATGTTTTCAACAATCTCCCCCTTTT
TGATATAACAAAACATTTAGTAATTTTAAGATTTTCAATTTGAAAAAAAATATATCAAGTTTTGA
AATTACTCCCCCTTACTATAACACAC
Found at i:2936556 original size:123 final size:123
Alignment explanation
Indices: 2936337--2936586 Score: 491
Period size: 123 Copynumber: 2.0 Consensus size: 123
2936327 GACATTTCCT
2936337 AATAGCATTGAAATGTCGAATTGGAATAAAGACCATTGGAATACCTGTTAATCTCCCTAAGATCC
1 AATAGCATTGAAATGTCGAATTGGAATAAAGACCATTGGAATACCTGTTAATCTCCCTAAGATCC
2936402 ATTCAACGATGATTCTGAAGATGATCAATTCGACAAGAATTGTCTGTATTGAAAAGTG
66 ATTCAACGATGATTCTGAAGATGATCAATTCGACAAGAATTGTCTGTATTGAAAAGTG
2936460 AATAGCATTGAAATGTCGAATTGGAATAAAGACCATTGGAATACCTGTTAATCTCCCTAAGATCC
1 AATAGCATTGAAATGTCGAATTGGAATAAAGACCATTGGAATACCTGTTAATCTCCCTAAGATCC
*
2936525 ATTCAACGATGATTCTGAAGATGATCAATTCGATAAGAATTGTCTGTATTGAAAAGTG
66 ATTCAACGATGATTCTGAAGATGATCAATTCGACAAGAATTGTCTGTATTGAAAAGTG
2936583 AATA
1 AATA
2936587 CTCTGGAAGT
Statistics
Matches: 126, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
123 126 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (123 bp):
AATAGCATTGAAATGTCGAATTGGAATAAAGACCATTGGAATACCTGTTAATCTCCCTAAGATCC
ATTCAACGATGATTCTGAAGATGATCAATTCGACAAGAATTGTCTGTATTGAAAAGTG
Found at i:2938401 original size:15 final size:15
Alignment explanation
Indices: 2938368--2938402 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2938358 GAGAAATGAG
**
2938368 ATAAGCTATGTGACT
1 ATAAGCTATGTGAAA
2938383 ATAAGCTATGTGAAA
1 ATAAGCTATGTGAAA
2938398 ATAAG
1 ATAAG
2938403 TTATATGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.29
Consensus pattern (15 bp):
ATAAGCTATGTGAAA
Found at i:2938660 original size:21 final size:22
Alignment explanation
Indices: 2938636--2938691 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 22
2938626 AATCCTATGG
2938636 AACATATATGTGGTTC-TTCGA
1 AACATATATGTGGTTCATTCGA
* * * *
2938657 AACACATAT-TGGGTCATTTGG
1 AACATATATGTGGTTCATTCGA
*
2938678 AATATATATGTGGT
1 AACATATATGTGGT
2938692 ACTTAAGGAG
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
20 5 0.19
21 18 0.69
22 3 0.12
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (22 bp):
AACATATATGTGGTTCATTCGA
Found at i:2938733 original size:21 final size:21
Alignment explanation
Indices: 2938707--2938746 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2938697 AGGAGAATTC
2938707 TATGTGGTCATTCGGGACATA
1 TATGTGGTCATTCGGGACATA
*
2938728 TATGTGGTCCTTCGGGACA
1 TATGTGGTCATTCGGGACA
2938747 AATTTTATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.33
Consensus pattern (21 bp):
TATGTGGTCATTCGGGACATA
Found at i:2939716 original size:67 final size:67
Alignment explanation
Indices: 2939638--2939771 Score: 205
Period size: 67 Copynumber: 2.0 Consensus size: 67
2939628 GGTATGAAGA
* * * * * *
2939638 CTCTGGCAGGTTCAGTTGTTGCTGGTAATTACTTGTATAGGTTCAACATCGACTGGTAATTCCTT
1 CTCTGGCAGGTTCAGTCGCTGCTAGTAATTACTCGTATAGGTTCAACACCGACTAGTAATTCCTT
2939703 AT
66 AT
*
2939705 CTCTGGCAGGTTCAGTCGCTGCTAGTAATTCCTCGTATAGGTTCAACACCGACTAGTAATTCCTT
1 CTCTGGCAGGTTCAGTCGCTGCTAGTAATTACTCGTATAGGTTCAACACCGACTAGTAATTCCTT
2939770 AT
66 AT
2939772 GGACCTAAGG
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.36
Consensus pattern (67 bp):
CTCTGGCAGGTTCAGTCGCTGCTAGTAATTACTCGTATAGGTTCAACACCGACTAGTAATTCCTT
AT
Found at i:2967513 original size:2 final size:2
Alignment explanation
Indices: 2967506--2967578 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
2967496 CGTATACCCA
2967506 AT AT 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 AT AT
2967548 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 A
2967579 CAATAAAGCT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2970029 original size:27 final size:27
Alignment explanation
Indices: 2969999--2970059 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
2969989 AATGGACTCT
*
2969999 AGTCGAGAAGATCAATTTTTCGAGTCG
1 AGTCGAGAAAATCAATTTTTCGAGTCG
* ** *
2970026 AGTCGAAAAAATTGATTTTTTGAGTCG
1 AGTCGAGAAAATCAATTTTTCGAGTCG
*
2970053 AATCGAG
1 AGTCGAG
2970060 TTTTACTCAC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (27 bp):
AGTCGAGAAAATCAATTTTTCGAGTCG
Found at i:2972433 original size:21 final size:21
Alignment explanation
Indices: 2972393--2972433 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2972383 ATTGAAGTTC
*
2972393 TACTTTTCTTTCGTATTTTTT
1 TACTTTTCTTTCCTATTTTTT
2972414 TACTTTTCTTTCACTATTTT
1 TACTTTTCTTTC-CTATTTT
2972434 CTTTTCACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.12, C:0.17, G:0.02, T:0.68
Consensus pattern (21 bp):
TACTTTTCTTTCCTATTTTTT
Found at i:2981625 original size:41 final size:40
Alignment explanation
Indices: 2981531--2981698 Score: 160
Period size: 41 Copynumber: 4.2 Consensus size: 40
2981521 TAACGTCTAT
* * * * *
2981531 TTTAGTGGTGTTTTTATATACACGCCGCTAAAGAC-CGTAA
1 TTTAGT-GAGTTTTTATACAAACGCCGCTAAAGACTCATAC
* * *
2981571 TTTAGTGACTTTTTTTACAAACGCCGTTAAAGACTCATAC
1 TTTAGTGAGTTTTTATACAAACGCCGCTAAAGACTCATAC
* *
2981611 TTTAGTGATGTTTTTATACAAACACCGCTAAAAACTCATAC
1 TTTAGTGA-GTTTTTATACAAACGCCGCTAAAGACTCATAC
* * * *
2981652 TTTAGT-AGCATTTTTGTACAAATGCCGCTAAAGACTCTTAT
1 TTTAGTGAG--TTTTTATACAAACGCCGCTAAAGACTCATAC
2981693 TTTAGT
1 TTTAGT
2981699 ACACAACAAG
Statistics
Matches: 105, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
39 23 0.22
40 18 0.17
41 64 0.61
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (40 bp):
TTTAGTGAGTTTTTATACAAACGCCGCTAAAGACTCATAC
Found at i:2981697 original size:82 final size:80
Alignment explanation
Indices: 2981528--2981698 Score: 200
Period size: 80 Copynumber: 2.1 Consensus size: 80
2981518 TCATAACGTC
* * * * * * *
2981528 TATTTTAGTGGTGTTTTTATATACACGCCGCTAAAGACCGTAATTTAGTGACTTTTTTTACAAAC
1 TATTTTAGTGATGTTTTTATACAAACACCGCTAAAAACCATAATTTAGTGACTTTTTGTACAAAC
*
2981593 GCCGTTAAAGACTCA
66 GCCGCTAAAGACTCA
* *
2981608 TACTTTAGTGATGTTTTTATACAAACACCGCTAAAAACTCATACTTTAGT-AGCATTTTTGTACA
1 TATTTTAGTGATGTTTTTATACAAACACCGCTAAAAAC-CATAATTTAGTGA-C-TTTTTGTACA
* *
2981672 AATGCCGCTAAAGACTCT
63 AACGCCGCTAAAGACTCA
2981690 TATTTTAGT
1 TATTTTAGT
2981699 ACACAACAAG
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
80 33 0.44
81 10 0.13
82 32 0.43
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (80 bp):
TATTTTAGTGATGTTTTTATACAAACACCGCTAAAAACCATAATTTAGTGACTTTTTGTACAAAC
GCCGCTAAAGACTCA
Found at i:2988485 original size:40 final size:40
Alignment explanation
Indices: 2988430--2988552 Score: 246
Period size: 40 Copynumber: 3.1 Consensus size: 40
2988420 TGCAGGTTTA
2988430 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
2988470 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
2988510 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
2988550 TAA
1 TAA
2988553 CACTACGGTG
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 83 1.00
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:2990968 original size:24 final size:24
Alignment explanation
Indices: 2990941--2990986 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2990931 TTTTAAATCT
2990941 TTTTATTTAT-TTATTTTCTTTTCC
1 TTTT-TTTATCTTATTTTCTTTTCC
* *
2990965 TTTTTTTCTCTTTTTTTCTTTT
1 TTTTTTTATCTTATTTTCTTTT
2990987 TTCTTGCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (24 bp):
TTTTTTTATCTTATTTTCTTTTCC
Found at i:2991159 original size:18 final size:21
Alignment explanation
Indices: 2991132--2991173 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 21
2991122 GTTATAACCA
2991132 ATTTAAGAAA-AC-ATAC-GT
1 ATTTAAGAAATACTATACGGT
*
2991150 ATTTATGAAATACTATACGGT
1 ATTTAAGAAATACTATACGGT
2991171 ATT
1 ATT
2991174 AACATTAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 9 0.45
19 2 0.10
20 4 0.20
21 5 0.25
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.36
Consensus pattern (21 bp):
ATTTAAGAAATACTATACGGT
Found at i:2991637 original size:18 final size:18
Alignment explanation
Indices: 2991614--2991649 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2991604 CCGCGTAGAA
*
2991614 ATGTCCCGAATGACCACT
1 ATGTCCCGAAGGACCACT
2991632 ATGTCCCGAAGGACCACT
1 ATGTCCCGAAGGACCACT
2991650 CCTTAAGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.19
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACT
Found at i:2992051 original size:17 final size:17
Alignment explanation
Indices: 2992029--2992061 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2992019 ATATCACAAG
2992029 TACATGTAATAACATAT
1 TACATGTAATAACATAT
*
2992046 TACATGTAATCACATA
1 TACATGTAATAACATA
2992062 GATCGTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.33
Consensus pattern (17 bp):
TACATGTAATAACATAT
Found at i:2993627 original size:2 final size:2
Alignment explanation
Indices: 2993620--2993664 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
2993610 ACATAAACGC
* *
2993620 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2993662 AT A
1 AT A
2993665 CATACCATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Done.