Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008747.1 Hibiscus syriacus cultivar Beakdansim tig00111837_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: 12616935
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 51
Found at i:2164981 original size:26 final size:26
Alignment explanation
Indices: 2164948--2165109 Score: 177
Period size: 26 Copynumber: 6.7 Consensus size: 26
2164938 ATGCCTTAGC
2164948 GCATCCTTTCATGCATTTCATTTATG
1 GCATCCTTTCATGCATTTCATTTATG
* *
2164974 GTATCCTTTCATGC----C-TTAAT-
1 GCATCCTTTCATGCATTTCATTTATG
*
2164994 GCATCCTTTCATGTATTTCATTTATG
1 GCATCCTTTCATGCATTTCATTTATG
*
2165020 GCATCCTTTCATGTATTTCATTTATG
1 GCATCCTTTCATGCATTTCATTTATG
* *
2165046 GCATCC-TT--T-CA-TTCCTTAAT-
1 GCATCCTTTCATGCATTTCATTTATG
2165066 GCATCCTTTCATGCATTTCATTTATG
1 GCATCCTTTCATGCATTTCATTTATG
*
2165092 GCATCCTTTCATGAATTT
1 GCATCCTTTCATGCATTT
2165110 TAAGTTATGA
Statistics
Matches: 113, Mismatches: 11, Indels: 24
0.76 0.07 0.16
Matches are distributed among these distances:
20 18 0.16
21 13 0.12
22 2 0.02
23 2 0.02
24 3 0.03
25 13 0.12
26 62 0.55
ACGTcount: A:0.20, C:0.23, G:0.10, T:0.47
Consensus pattern (26 bp):
GCATCCTTTCATGCATTTCATTTATG
Found at i:2165032 original size:72 final size:72
Alignment explanation
Indices: 2164948--2165109 Score: 279
Period size: 72 Copynumber: 2.2 Consensus size: 72
2164938 ATGCCTTAGC
* * *
2164948 GCATCCTTTCATGCATTTCATTTATGGTATCCTTTCATGCCTTAATGCATCCTTTCATGTATTTC
1 GCATCCTTTCATGAATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTC
2165013 ATTTATG
66 ATTTATG
* *
2165020 GCATCCTTTCATGTATTTCATTTATGGCATCCTTTCATTCCTTAATGCATCCTTTCATGCATTTC
1 GCATCCTTTCATGAATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTC
2165085 ATTTATG
66 ATTTATG
2165092 GCATCCTTTCATGAATTT
1 GCATCCTTTCATGAATTT
2165110 TAAGTTATGA
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 85 1.00
ACGTcount: A:0.20, C:0.23, G:0.10, T:0.47
Consensus pattern (72 bp):
GCATCCTTTCATGAATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTC
ATTTATG
Found at i:2169492 original size:82 final size:82
Alignment explanation
Indices: 2169359--2169603 Score: 311
Period size: 81 Copynumber: 3.0 Consensus size: 82
2169349 CTTTTAGCAT
* * * * *
2169359 TTAATCTTTTAGTCGAAGGTGTTTAA-CATTCATATAACTGGCATAATTGACACATTTTTTGCCA
1 TTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTTTTGCCA
2169423 AATGCACAGCTAGGCCA
66 AATGCACAGCTAGGCCA
* *
2169440 TTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGTCATAATTGACACATTTCTT-CCA
1 TTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTTTTGCCA
2169504 AATGCACAGCTAGGCTC-
66 AATGCACAGCTAGGC-CA
* * * * *
2169521 TTAATATTTTACTCAAAGATATTTAACATTTCATCTAAAC-GGCATAGTTGACA-ATTTTCTGCC
1 TTAATCTTTTACTCAAAGGTATTTAACCTTTCATCT-AACTGGCATAATTGACACATTTTTTGCC
* *
2169584 AAATGCACATCTAGGTCA
65 AAATGCACAGCTAGGCCA
2169602 TT
1 TT
2169604 GATCGCTTGT
Statistics
Matches: 143, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
80 6 0.04
81 103 0.72
82 34 0.24
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.36
Consensus pattern (82 bp):
TTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTTTTGCCA
AATGCACAGCTAGGCCA
Found at i:2174218 original size:269 final size:267
Alignment explanation
Indices: 2173732--2174270 Score: 961
Period size: 269 Copynumber: 2.0 Consensus size: 267
2173722 TGTTCACATC
2173732 ATGTTTGGAACGTGATGAAGAAGGAATAATAAGGGAGGAACACTTTACATTGCTTATGCATGAAT
1 ATGTTTGGAACGTGATGAAGAAGGAATAATAAGGGAGGAACACTTTACATTGCTTATGCATGAAT
*
2173797 TTGCATGAGAATTTAAAGTTTGCATAACATTCATTGCATTAATAAGTGTGTTGTTCATTCAAGCA
66 TTGCATGAGAATTTAAAGTTTGCATAACATTCATTGCATTAATAAGTGTGCTGTTCATTCAAGCA
* *
2173862 TGCATTGCATTTAAATCATCTAGTTCATTCATCAAATTAGTTCTTTTATTAGACTAAATCTTAAT
131 TGCATTGCATTTAAATCATCTACTTCATTCATCAAATTAGTTCATTTATTAGACTAAATCTTAAT
*
2173927 TGTTTCATGCATATTTTCAATTAAATATTGAATAAAGTTCACCTTTGTGTCTAGGTGCATGAGAG
196 TGTTTCATGCATATTTTCAATTAAATATTGAATAAAGTTCACCTTTGTGTCTAGGTGCATGAGAA
*
2173992 AATTTGA
261 AAGTTGA
*
2173999 ATGTTTGATGAACGTGATGAAGAAGGAATAATAAGGGAGGAACACTTTACTTTGCTTATGCATGA
1 ATGTTTG--GAACGTGATGAAGAAGGAATAATAAGGGAGGAACACTTTACATTGCTTATGCATGA
2174064 ATTTGCATGAGAATTTAAAGTTTGCATAACATTCATTGCATTAATAAGTGTGCTGTTCATTCAAG
64 ATTTGCATGAGAATTTAAAGTTTGCATAACATTCATTGCATTAATAAGTGTGCTGTTCATTCAAG
* * *
2174129 CATGCATTGCATTTAAATCATCTACTTCATTCATCAAATTAGTTCATTTATTATATTAATTCTTA
129 CATGCATTGCATTTAAATCATCTACTTCATTCATCAAATTAGTTCATTTATTAGACTAAATCTTA
* *
2174194 ATTGTTTCATGCATGTTTTCAATTAAATATTGAATGAAGTTCACCTTTGTGTCTAGGTGCATGAG
194 ATTGTTTCATGCATATTTTCAATTAAATATTGAATAAAGTTCACCTTTGTGTCTAGGTGCATGAG
2174259 AAAAGTTGA
259 AAAAGTTGA
2174268 ATG
1 ATG
2174271 GTTTCATCAT
Statistics
Matches: 259, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
267 7 0.03
269 252 0.97
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (267 bp):
ATGTTTGGAACGTGATGAAGAAGGAATAATAAGGGAGGAACACTTTACATTGCTTATGCATGAAT
TTGCATGAGAATTTAAAGTTTGCATAACATTCATTGCATTAATAAGTGTGCTGTTCATTCAAGCA
TGCATTGCATTTAAATCATCTACTTCATTCATCAAATTAGTTCATTTATTAGACTAAATCTTAAT
TGTTTCATGCATATTTTCAATTAAATATTGAATAAAGTTCACCTTTGTGTCTAGGTGCATGAGAA
AAGTTGA
Found at i:2175500 original size:12 final size:12
Alignment explanation
Indices: 2175483--2175516 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
2175473 GTGTTAGTAA
2175483 AAAAATAAAAAC
1 AAAAATAAAAAC
2175495 AAAAATAAAAAC
1 AAAAATAAAAAC
*
2175507 AAAAACAAAA
1 AAAAATAAAA
2175517 GAAAGAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.85, C:0.09, G:0.00, T:0.06
Consensus pattern (12 bp):
AAAAATAAAAAC
Found at i:2175510 original size:5 final size:6
Alignment explanation
Indices: 2175483--2175516 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
2175473 GTGTTAGTAA
* *
2175483 AAAAAT AAAAAC AAAAAT AAAAAC AAAAAC AAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAA
2175517 GAAAGAAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.85, C:0.09, G:0.00, T:0.06
Consensus pattern (6 bp):
AAAAAC
Found at i:2185644 original size:23 final size:20
Alignment explanation
Indices: 2185614--2185671 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 20
2185604 GCACCCCTGC
2185614 AGTGCATCCATGCACC-TGCCACT
1 AGTGCATCCATGCACCATG----T
*
2185637 AGTGCATCGATGCACCATGT
1 AGTGCATCCATGCACCATGT
2185657 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
2185672 TCCATTTCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 15 0.47
23 15 0.47
24 2 0.06
ACGTcount: A:0.24, C:0.33, G:0.21, T:0.22
Consensus pattern (20 bp):
AGTGCATCCATGCACCATGT
Found at i:2185717 original size:20 final size:20
Alignment explanation
Indices: 2185692--2185743 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
2185682 ATGCAATTAG
*
2185692 TGCATCCATGTATCATT-CTA
1 TGCATCCATGCATC-TTACTA
* *
2185712 TGCATCGATGCATCTTACTG
1 TGCATCCATGCATCTTACTA
2185732 TGCATCCATGCA
1 TGCATCCATGCA
2185744 CCAAGGCTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (20 bp):
TGCATCCATGCATCTTACTA
Found at i:2186166 original size:34 final size:33
Alignment explanation
Indices: 2186109--2186179 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 33
2186099 CTTAGTAAAG
*
2186109 GGGAAAGGTTCTAGCTAAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTAAGCCCGTG-AAAAACTA
**
2186143 GGGAAAGGTTCTAATTTAA-CCCGTGAAAAACTA
1 GGGAAAGGTTCT-AGCTAAGCCCGTGAAAAACTA
2186176 GGGA
1 GGGA
2186180 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 11 0.33
34 18 0.55
35 4 0.12
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.21
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTAAGCCCGTGAAAAACTA
Found at i:2186995 original size:23 final size:22
Alignment explanation
Indices: 2186924--2187005 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 22
2186914 ACACTTAACA
2186924 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCA-CCC-TTGAAT
* * *
2186948 GTGCATCGATACA-CCATGAAG
1 GTGCATCGATGCACCCTTGAAT
*
2186969 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCAC-CCTTGAAT
2186992 GTGCATCGATGCAC
1 GTGCATCGATGCAC
2187006 AAGGCCATGA
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
21 15 0.31
22 2 0.04
23 19 0.40
24 12 0.25
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (22 bp):
GTGCATCGATGCACCCTTGAAT
Found at i:2188698 original size:19 final size:19
Alignment explanation
Indices: 2188676--2188724 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
2188666 ACATTTCATT
2188676 CATCGATGCACATACCATG
1 CATCGATGCACATACCATG
2188695 CATCGATGCACATACCATG
1 CATCGATGCACATACCATG
2188714 CATCGATGCAC
1 CATCGATGCAC
2188725 TCAGAGTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.31, C:0.33, G:0.16, T:0.20
Consensus pattern (19 bp):
CATCGATGCACATACCATG
Found at i:2188806 original size:45 final size:46
Alignment explanation
Indices: 2188711--2188817 Score: 139
Period size: 45 Copynumber: 2.3 Consensus size: 46
2188701 TGCACATACC
*
2188711 ATGCATCGATGCACTCAGAGTTTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACTCAGAGTTTTATGAAAACATCGAATACATTTG
*
2188757 ATGCATCGATGCACTCAG-GCTATTT-TG-AAACATCGAATACATTTT
1 ATGCATCGATGCACTCAGAG-T-TTTATGAAAACATCGAATACATTTG
* *
2188802 ATGCAGCGTTGCACTC
1 ATGCATCGATGCACTC
2188818 TTAGTGCACC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
45 31 0.56
46 21 0.38
47 3 0.05
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (46 bp):
ATGCATCGATGCACTCAGAGTTTTATGAAAACATCGAATACATTTG
Found at i:2190308 original size:44 final size:42
Alignment explanation
Indices: 2190152--2190414 Score: 260
Period size: 43 Copynumber: 6.1 Consensus size: 42
2190142 AAGGTAATTA
* ** * *
2190152 GCGGCGTTTGTATCCAAAACCGTCGCTATAGATTTGACCTTTT
1 GCGGCATTTGT-TCCAAAAATGCCGCTATAGATCTGACCTTTT
* * *
2190195 GCGGTATTTGTTCCAAAAATGTCACTATAGATCTAGACCTTTT
1 GCGGCATTTGTTCCAAAAATGCCGCTATAGATCT-GACCTTTT
*
2190238 GCGGCATTTGTTCCAAAAATGCCGCTATAGATCTGACCTTCT
1 GCGGCATTTGTTCCAAAAATGCCGCTATAGATCTGACCTTTT
* * *
2190280 GTGGCGTTTGTATCAAATAAATGCCGCTATAGATCTGACCTTTT
1 GCGGCATTTGT-TCCAA-AAATGCCGCTATAGATCTGACCTTTT
* * *
2190324 ACGGCATTTGTTCCAAAAACGCCGCTATATATCTCGACCTTTT
1 GCGGCATTTGTTCCAAAAATGCCGCTATAGATCT-GACCTTTT
* * * * *
2190367 GC-G-ATGTTAGTTCTAAAAACGCCACTATAGATCTTAACCTATT
1 GCGGCAT-TT-GTTCCAAAAATGCCGCTATAGATC-TGACCTTTT
2190410 GCGGC
1 GCGGC
2190415 CGTTTTTGTT
Statistics
Matches: 185, Mismatches: 26, Indels: 16
0.81 0.11 0.07
Matches are distributed among these distances:
41 2 0.01
42 54 0.29
43 94 0.51
44 35 0.19
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.33
Consensus pattern (42 bp):
GCGGCATTTGTTCCAAAAATGCCGCTATAGATCTGACCTTTT
Found at i:2199994 original size:21 final size:21
Alignment explanation
Indices: 2199968--2200007 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2199958 AACTGCCCAG
*
2199968 TATAGAGTGTATCGGTACTTC
1 TATAGAGAGTATCGGTACTTC
*
2199989 TATAGAGAGTATTGGTACT
1 TATAGAGAGTATCGGTACT
2200008 ACCTTTGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.38
Consensus pattern (21 bp):
TATAGAGAGTATCGGTACTTC
Found at i:2200101 original size:32 final size:32
Alignment explanation
Indices: 2200065--2200128 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
2200055 TGACGGTATC
* *
2200065 GATACTAAGCATGTGGTACTGATACTACTATT
1 GATACTAAGCATATGGTACCGATACTACTATT
*
2200097 GATACTAAGCCTATGGTACCGATACTACTATT
1 GATACTAAGCATATGGTACCGATACTACTATT
2200129 TAAGTAGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (32 bp):
GATACTAAGCATATGGTACCGATACTACTATT
Found at i:2203949 original size:13 final size:13
Alignment explanation
Indices: 2203946--2203987 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
2203936 CGTTGACCCA
*
2203946 ACCCGACCTGTTG
1 ACCCGACCCGTTG
2203959 ACCCGACCCGTTG
1 ACCCGACCCGTTG
*
2203972 ACCCGACCCATTG
1 ACCCGACCCGTTG
2203985 ACC
1 ACC
2203988 GTTGACCGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.19, C:0.45, G:0.19, T:0.17
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:2203980 original size:18 final size:18
Alignment explanation
Indices: 2203926--2203968 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
2203916 TGACCGGTCA
2203926 CAACCCGACCCGTTGACC
1 CAACCCGACCCGTTGACC
*
2203944 CAACCCGACCTGTTGACC
1 CAACCCGACCCGTTGACC
*
2203962 CGACCCG
1 CAACCCG
2203969 TTGACCCGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.49, G:0.19, T:0.12
Consensus pattern (18 bp):
CAACCCGACCCGTTGACC
Found at i:2206393 original size:47 final size:48
Alignment explanation
Indices: 2206304--2206413 Score: 118
Period size: 47 Copynumber: 2.3 Consensus size: 48
2206294 AAATATTTTA
* * * *
2206304 TCTGATTTCCGA-ATTGAATTCTGTTCTGATACGTTACCTGAATTATGT
1 TCTGATTTCTGATA-TGGATTCTGTTCTGATACGTTACATGAATTATAT
* *
2206352 TCTGA-TTCTGATATGGATTCTGTTCTGATATC-TTATATGAATTCTAT
1 TCTGATTTCTGATATGGATTCTGTTCTGATA-CGTTACATGAATTATAT
*
2206399 TTTGATTTCTGATAT
1 TCTGATTTCTGATAT
2206414 CTCCGTTTAC
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
47 36 0.69
48 16 0.31
ACGTcount: A:0.23, C:0.14, G:0.15, T:0.48
Consensus pattern (48 bp):
TCTGATTTCTGATATGGATTCTGTTCTGATACGTTACATGAATTATAT
Found at i:2206395 original size:24 final size:24
Alignment explanation
Indices: 2206318--2206396 Score: 90
Period size: 24 Copynumber: 3.3 Consensus size: 24
2206308 ATTTCCGAAT
**
2206318 TGAATTCTGTTCTGATA-CGTTACC
1 TGAATTCTGTTCTGATATC-TTATA
* *
2206342 TGAATTATGTTCTGAT-TCTGATA
1 TGAATTCTGTTCTGATATCTTATA
*
2206365 TGGATTCTGTTCTGATATCTTATA
1 TGAATTCTGTTCTGATATCTTATA
2206389 TGAATTCT
1 TGAATTCT
2206397 ATTTTGATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
23 16 0.36
24 29 0.64
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.47
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTTATA
Found at i:2206404 original size:24 final size:23
Alignment explanation
Indices: 2206342--2206413 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 23
2206332 ATACGTTACC
* *
2206342 TGAATTATGTTCTGATTCTGATA
1 TGAATTCTATTCTGATTCTGATA
* * *
2206365 TGGATTCTGTTCTGATATCTTATA
1 TGAATTCTATTCTGAT-TCTGATA
*
2206389 TGAATTCTATTTTGATTTCTGATA
1 TGAATTCTATTCTGA-TTCTGATA
2206413 T
1 T
2206414 CTCCGTTTAC
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
23 14 0.35
24 25 0.62
25 1 0.03
ACGTcount: A:0.24, C:0.10, G:0.15, T:0.51
Consensus pattern (23 bp):
TGAATTCTATTCTGATTCTGATA
Found at i:2208570 original size:18 final size:18
Alignment explanation
Indices: 2208547--2208606 Score: 75
Period size: 18 Copynumber: 3.2 Consensus size: 18
2208537 ACTGGTCACA
*
2208547 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
*
2208565 ACCCGACCCGACCTGTTG
1 ACCCGACCCGACCCGTTG
2208583 ACCCGACCCGTTGACCCGTTG
1 ACCCGACCC---GACCCGTTG
2208604 ACC
1 ACC
2208607 GTTGACCCGT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
18 25 0.69
21 11 0.31
ACGTcount: A:0.17, C:0.47, G:0.20, T:0.17
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:2208585 original size:13 final size:13
Alignment explanation
Indices: 2208569--2208600 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2208559 CCGTTTACCC
*
2208569 GACCCGACCTGTT
1 GACCCGACCCGTT
2208582 GACCCGACCCGTT
1 GACCCGACCCGTT
2208595 GACCCG
1 GACCCG
2208601 TTGACCGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.44, G:0.25, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:2208610 original size:7 final size:8
Alignment explanation
Indices: 2208587--2208626 Score: 66
Period size: 8 Copynumber: 5.2 Consensus size: 8
2208577 CTGTTGACCC
2208587 GACCCGTT
1 GACCCGTT
2208595 GACCCGTT
1 GACCCGTT
2208603 GA-CCGTT
1 GACCCGTT
2208610 GACCCGTT
1 GACCCGTT
2208618 GA-CCGTT
1 GACCCGTT
2208625 GA
1 GA
2208627 TCGGCGTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 14 0.45
8 17 0.55
ACGTcount: A:0.15, C:0.33, G:0.28, T:0.25
Consensus pattern (8 bp):
GACCCGTT
Found at i:2208610 original size:15 final size:15
Alignment explanation
Indices: 2208590--2208626 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
2208580 TTGACCCGAC
2208590 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
2208605 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
2208620 CCGTTGA
1 CCGTTGA
2208627 TCGGCGTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.14, C:0.32, G:0.27, T:0.27
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:2211022 original size:47 final size:48
Alignment explanation
Indices: 2210933--2211042 Score: 118
Period size: 47 Copynumber: 2.3 Consensus size: 48
2210923 AAATATTTTA
* * * *
2210933 TCTGATTTCCGA-ATTGAATTCTGTTCTGATACGTTACCTGAATTATGT
1 TCTGATTTCTGATA-TGGATTCTGTTCTGATACGTTACATGAATTATAT
* *
2210981 TCTGA-TTCTGATATGGATTCTGTTCTGATATC-TTATATGAATTCTAT
1 TCTGATTTCTGATATGGATTCTGTTCTGATA-CGTTACATGAATTATAT
*
2211028 TTTGATTTCTGATAT
1 TCTGATTTCTGATAT
2211043 CTTCGTTTAC
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
47 36 0.69
48 16 0.31
ACGTcount: A:0.23, C:0.14, G:0.15, T:0.48
Consensus pattern (48 bp):
TCTGATTTCTGATATGGATTCTGTTCTGATACGTTACATGAATTATAT
Found at i:2211024 original size:24 final size:24
Alignment explanation
Indices: 2210947--2211025 Score: 90
Period size: 24 Copynumber: 3.3 Consensus size: 24
2210937 ATTTCCGAAT
**
2210947 TGAATTCTGTTCTGATA-CGTTACC
1 TGAATTCTGTTCTGATATC-TTATA
* *
2210971 TGAATTATGTTCTGAT-TCTGATA
1 TGAATTCTGTTCTGATATCTTATA
*
2210994 TGGATTCTGTTCTGATATCTTATA
1 TGAATTCTGTTCTGATATCTTATA
2211018 TGAATTCT
1 TGAATTCT
2211026 ATTTTGATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
23 16 0.36
24 29 0.64
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.47
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTTATA
Found at i:2211033 original size:24 final size:23
Alignment explanation
Indices: 2210971--2211042 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 23
2210961 ATACGTTACC
* *
2210971 TGAATTATGTTCTGATTCTGATA
1 TGAATTCTATTCTGATTCTGATA
* * *
2210994 TGGATTCTGTTCTGATATCTTATA
1 TGAATTCTATTCTGAT-TCTGATA
*
2211018 TGAATTCTATTTTGATTTCTGATA
1 TGAATTCTATTCTGA-TTCTGATA
2211042 T
1 T
2211043 CTTCGTTTAC
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
23 14 0.35
24 25 0.62
25 1 0.03
ACGTcount: A:0.24, C:0.10, G:0.15, T:0.51
Consensus pattern (23 bp):
TGAATTCTATTCTGATTCTGATA
Found at i:2213787 original size:73 final size:73
Alignment explanation
Indices: 2213702--2213848 Score: 240
Period size: 73 Copynumber: 2.0 Consensus size: 73
2213692 ATCTCATTTT
* * *
2213702 AAAATATAACACAAGGTATACACATATTTTGAGATGAAATTATCCATGCTTATTACTTATCTAAT
1 AAAATATAACACAAGATATACACATATTTTGAGATGAAAATATCCATGCTTATTACTTAGCTAAT
2213767 ATTTATTA
66 ATTTATTA
* * *
2213775 AAAATATAACACAAGATATACACATCTTTTGAGATGAAAATGTCCATGCTTATTACTTAGCTGAT
1 AAAATATAACACAAGATATACACATATTTTGAGATGAAAATATCCATGCTTATTACTTAGCTAAT
2213840 ATTTATTA
66 ATTTATTA
2213848 A
1 A
2213849 TAAAATTATG
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.37
Consensus pattern (73 bp):
AAAATATAACACAAGATATACACATATTTTGAGATGAAAATATCCATGCTTATTACTTAGCTAAT
ATTTATTA
Found at i:2214625 original size:242 final size:242
Alignment explanation
Indices: 2214200--2214683 Score: 968
Period size: 242 Copynumber: 2.0 Consensus size: 242
2214190 TTATTAATTG
2214200 GTCTAAAGATGAGTTAATATTTGATAGACTTTCAAACCACAATTGTTGTAATAAATGTTTGAAAA
1 GTCTAAAGATGAGTTAATATTTGATAGACTTTCAAACCACAATTGTTGTAATAAATGTTTGAAAA
2214265 CTATAAGGTATTTTATGTGAGCATTACATTAGTCTAAAGGATAATCTATTGTTCAATATGCATGA
66 CTATAAGGTATTTTATGTGAGCATTACATTAGTCTAAAGGATAATCTATTGTTCAATATGCATGA
2214330 ACCAAATTACCTCACTAGTTAAAGGAGTTGTTTTTGTTCCTAGAGGTTACAGGTTCGAGCACAAG
131 ACCAAATTACCTCACTAGTTAAAGGAGTTGTTTTTGTTCCTAGAGGTTACAGGTTCGAGCACAAG
2214395 CAACTGTAGGGTGATTTCACATTCATTGTCAAATGGTTAAGTGTAGT
196 CAACTGTAGGGTGATTTCACATTCATTGTCAAATGGTTAAGTGTAGT
2214442 GTCTAAAGATGAGTTAATATTTGATAGACTTTCAAACCACAATTGTTGTAATAAATGTTTGAAAA
1 GTCTAAAGATGAGTTAATATTTGATAGACTTTCAAACCACAATTGTTGTAATAAATGTTTGAAAA
2214507 CTATAAGGTATTTTATGTGAGCATTACATTAGTCTAAAGGATAATCTATTGTTCAATATGCATGA
66 CTATAAGGTATTTTATGTGAGCATTACATTAGTCTAAAGGATAATCTATTGTTCAATATGCATGA
2214572 ACCAAATTACCTCACTAGTTAAAGGAGTTGTTTTTGTTCCTAGAGGTTACAGGTTCGAGCACAAG
131 ACCAAATTACCTCACTAGTTAAAGGAGTTGTTTTTGTTCCTAGAGGTTACAGGTTCGAGCACAAG
2214637 CAACTGTAGGGTGATTTCACATTCATTGTCAAATGGTTAAGTGTAGT
196 CAACTGTAGGGTGATTTCACATTCATTGTCAAATGGTTAAGTGTAGT
2214684 TAAAATAGAT
Statistics
Matches: 242, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
242 242 1.00
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (242 bp):
GTCTAAAGATGAGTTAATATTTGATAGACTTTCAAACCACAATTGTTGTAATAAATGTTTGAAAA
CTATAAGGTATTTTATGTGAGCATTACATTAGTCTAAAGGATAATCTATTGTTCAATATGCATGA
ACCAAATTACCTCACTAGTTAAAGGAGTTGTTTTTGTTCCTAGAGGTTACAGGTTCGAGCACAAG
CAACTGTAGGGTGATTTCACATTCATTGTCAAATGGTTAAGTGTAGT
Found at i:2218387 original size:2 final size:2
Alignment explanation
Indices: 2218380--2218448 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
2218370 TGTTCTACAT
2218380 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
2218422 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2218449 CATCCCTTCA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2219168 original size:79 final size:78
Alignment explanation
Indices: 2219067--2219342 Score: 361
Period size: 79 Copynumber: 3.6 Consensus size: 78
2219057 TTTCAACTTT
* * * *
2219067 GGCATCATTTCATGCTAATAATGCACCCATATGCATTATTCTGTTATGCCGATAATGAACCCGTA
1 GGCATCCTTTCATGCCATTAATGCACCCATATGCATTATTCTTTTATGCCGATAATG-ACCCGTA
2219132 TACATATAAGCTAA
65 TACATATAAGCTAA
2219146 GGCATCCTTTCATGCCATTAATGCACCCATATGCATTATTCTTTTATGCCGATAAT-----G--T
1 GGCATCCTTTCATGCCATTAATGCACCCATATGCATTATTCTTTTATGCCGATAATGACCCGTAT
2219204 ACATATCAA-CTAA
66 ACATAT-AAGCTAA
* * * *
2219217 GGCATCCTTTCATACCGTTAATGCACCCATATGCATTATTCTCTTATGCCGATAATGTACCCATA
1 GGCATCCTTTCATGCCATTAATGCACCCATATGCATTATTCTTTTATGCCGATAATG-ACCCGTA
*
2219282 TACATATCAGCTAA
65 TACATATAAGCTAA
* * *
2219296 GGTATCCTTTCATGCAATTAATGCACCCATATGAATTATTCTTTTAT
1 GGCATCCTTTCATGCCATTAATGCACCCATATGCATTATTCTTTTAT
2219343 TCATTCGTTT
Statistics
Matches: 172, Mismatches: 15, Indels: 20
0.83 0.07 0.10
Matches are distributed among these distances:
71 64 0.37
72 2 0.01
73 1 0.01
78 1 0.01
79 104 0.60
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (78 bp):
GGCATCCTTTCATGCCATTAATGCACCCATATGCATTATTCTTTTATGCCGATAATGACCCGTAT
ACATATAAGCTAA
Found at i:2219202 original size:34 final size:34
Alignment explanation
Indices: 2219164--2219282 Score: 91
Period size: 34 Copynumber: 3.4 Consensus size: 34
2219154 TTCATGCCAT
2219164 TAATGCACCCATATGCATTATTCTTTTATGCCGA
1 TAATGCACCCATATGCATTATTCTTTTATGCCGA
* * * * * *
2219198 TAATGTA--CATAT-CAACTAAGGCATCCTTTCATACCGT
1 TAATGCACCCATATGC-A-T----TATTCTTTTATGCCGA
*
2219235 TAATGCACCCATATGCATTATTCTCTTATGCCGA
1 TAATGCACCCATATGCATTATTCTTTTATGCCGA
*
2219269 TAATGTACCCATAT
1 TAATGCACCCATAT
2219283 ACATATCAGC
Statistics
Matches: 62, Mismatches: 14, Indels: 18
0.66 0.15 0.19
Matches are distributed among these distances:
31 1 0.02
32 6 0.10
33 1 0.02
34 29 0.47
37 17 0.27
38 1 0.02
39 6 0.10
40 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.35
Consensus pattern (34 bp):
TAATGCACCCATATGCATTATTCTTTTATGCCGA
Found at i:2219248 original size:71 final size:72
Alignment explanation
Indices: 2219132--2219342 Score: 291
Period size: 71 Copynumber: 2.9 Consensus size: 72
2219122 TGAACCCGTA
2219132 TACATAT-AAGCTAAGGCATCCTTTCATGCCATTAATGCACCCATATGCATTATTCTTTTATGCC
1 TACATATCAAGCTAAGGCATCCTTTCATGCCATTAATGCACCCATATGCATTATTCTTTTATGCC
2219196 GATAATG
66 GATAATG
* * *
2219203 TACATATCAA-CTAAGGCATCCTTTCATACCGTTAATGCACCCATATGCATTATTCTCTTATGCC
1 TACATATCAAGCTAAGGCATCCTTTCATGCCATTAATGCACCCATATGCATTATTCTTTTATGCC
2219267 GATAATG
66 GATAATG
* * *
2219274 TACCCATATACATATCAGCTAAGGTATCCTTTCATGCAATTAATGCACCCATATGAATTATTCTT
1 TA--CATAT-C--A--AGCTAAGGCATCCTTTCATGCCATTAATGCACCCATATGCATTATTCTT
2219339 TTAT
59 TTAT
2219343 TCATTCGTTT
Statistics
Matches: 122, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
71 67 0.55
72 2 0.02
73 5 0.04
74 1 0.01
76 1 0.01
78 1 0.01
79 45 0.37
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (72 bp):
TACATATCAAGCTAAGGCATCCTTTCATGCCATTAATGCACCCATATGCATTATTCTTTTATGCC
GATAATG
Found at i:2219773 original size:22 final size:21
Alignment explanation
Indices: 2219724--2219778 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
2219714 CTGGCCCTTT
* *
2219724 GGTATCGATACCCCTGCTTAT
1 GGTATCGATACCCCTGATTAG
2219745 GGTATCGATACTACCCT-ATTAG
1 GGTATCGATAC--CCCTGATTAG
2219767 GGTATCGATACC
1 GGTATCGATACC
2219779 TTCTTCATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 1 0.03
21 11 0.37
22 14 0.47
23 4 0.13
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (21 bp):
GGTATCGATACCCCTGATTAG
Found at i:2219886 original size:95 final size:95
Alignment explanation
Indices: 2219787--2219967 Score: 226
Period size: 95 Copynumber: 1.9 Consensus size: 95
2219777 CCTTCTTCAT
*
2219787 GTATCGATACCAAAATTA-ATTTTGATGTAGCCCGGTATCGATACCACCT-CCATGGAATCGATA
1 GTATCGATACCAAAATTAGA-TTTGATGTAGACCGGTATCGATACC-CCTACCATGGAATCGATA
*
2219850 CC-CCTATGCTAT-GGTACCGATACCCTATCTAG
64 CCACAT-TGCT-TGGGTACCGATACCCTATCTAG
* ** * * *
2219882 GTATCGATACCTAAATTAGATTTGATGTTTACTGGTATCGATACCCTTACCATGGTATCGATACC
1 GTATCGATACCAAAATTAGATTTGATGTAGACCGGTATCGATACCCCTACCATGGAATCGATACC
2219947 ACATTGCTTGGGTACCGATAC
66 ACATTGCTTGGGTACCGATAC
2219968 TGGTTGAATC
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
94 3 0.04
95 68 0.92
96 3 0.04
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.31
Consensus pattern (95 bp):
GTATCGATACCAAAATTAGATTTGATGTAGACCGGTATCGATACCCCTACCATGGAATCGATACC
ACATTGCTTGGGTACCGATACCCTATCTAG
Found at i:2219889 original size:19 final size:21
Alignment explanation
Indices: 2219838--2219892 Score: 69
Period size: 19 Copynumber: 2.7 Consensus size: 21
2219828 TACCACCTCC
*
2219838 ATGGAATCGATACCCCTATGCT
1 ATGGTATCGATA-CCCTATGCT
*
2219860 ATGGTACCGATACCCTAT-CT
1 ATGGTATCGATACCCTATGCT
2219880 A-GGTATCGATACC
1 ATGGTATCGATACC
2219893 TAAATTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 11 0.37
20 3 0.10
21 6 0.20
22 10 0.33
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27
Consensus pattern (21 bp):
ATGGTATCGATACCCTATGCT
Found at i:2223897 original size:46 final size:46
Alignment explanation
Indices: 2223837--2223940 Score: 120
Period size: 46 Copynumber: 2.3 Consensus size: 46
2223827 AGCATCCCAA
* * *
2223837 CATGCTTATAATACACCATTATACCATTTCCATTT-TGGCATCCTTT
1 CATGCTTTTTATACACCATTATA-CATTTCCATTTATGGCATCCTTG
* * * *
2223883 CATGCTTTTTATACACTATTATACATTTTCTTTTATGGCATTCTTG
1 CATGCTTTTTATACACCATTATACATTTCCATTTATGGCATCCTTG
*
2223929 CATGCATTTTAT
1 CATGCTTTTTAT
2223941 GTTATGTTTC
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
45 9 0.18
46 40 0.82
ACGTcount: A:0.24, C:0.21, G:0.08, T:0.47
Consensus pattern (46 bp):
CATGCTTTTTATACACCATTATACATTTCCATTTATGGCATCCTTG
Found at i:2224007 original size:2 final size:2
Alignment explanation
Indices: 2224000--2224026 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2223990 TGTTGTACAT
2224000 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2224027 CATCATCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2224595 original size:60 final size:60
Alignment explanation
Indices: 2224523--2224671 Score: 244
Period size: 60 Copynumber: 2.5 Consensus size: 60
2224513 TTTCCTATAC
*
2224523 GAAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACATAAAGTGACCTTATCT
1 GAAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACAAAGTGACCTTATCT
* * * *
2224583 GAAAATTAATACACTTAGTATAATTTCTTTATCATTTTAGCACACAAAGTGCCCTTATCT
1 GAAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACAAAGTGACCTTATCT
*
2224643 GGAAATTCATACACTTAGTATGATTTCCT
1 GAAAATTCATACACTTAGTATGATTTCCT
2224672 CTTTTATATC
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 80 1.00
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (60 bp):
GAAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACAAAGTGACCTTATCT
Found at i:2224812 original size:79 final size:78
Alignment explanation
Indices: 2224681--2224992 Score: 335
Period size: 79 Copynumber: 3.9 Consensus size: 78
2224671 TCTTTTATAT
* * * * ** *
2224681 CGATAATGCACCCATATGCATTTCAACTTTGGCAT-CTTTTCATGCCAATAATGCACCTATATGC
1 CGATAATGTACCCATATACATATCAGCTAAGGCATCCTTTT-ATGCCATTAATGCACCTATATGC
2224745 ATTATTCTGTTACT-C
65 ATTATTCT-TTA-TGC
* * * * * *
2224760 CGATAATGTACCTATCTACATATTAGCTAAGTCATCCTTTTATGCCATTAATGCACCCATATACA
1 CGATAATGTACCCATATACATATCAGCTAAGGCATCCTTTTATGCCATTAATGCACCTATATGCA
2224825 TTATTCCTTTATGC
66 TTATT-CTTTATGC
* * * * *
2224839 CGATAATATACCCATATACATATCATCTAAGGCATCATTTCATACCATTAATGCA-CTCATATGC
1 CGATAATGTACCCATATACATATCAGCTAAGGCATCCTTTTATGCCATTAATGCACCT-ATATGC
2224903 ATTATTCTTTTATGC
65 ATTATTC-TTTATGC
* * *
2224918 CGATAATGTACCCATATACATATCAGCTATGGCATGCCATTAATGCCATTAATGCACCCT-TATG
1 CGATAATGTACCCATATACATATCAGCTAAGGCAT-CCTTTTATGCCATTAATGCA-CCTATATG
2224982 CATTATTCTTT
64 CATTATTCTTT
2224993 TATTCATTAG
Statistics
Matches: 194, Mismatches: 31, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
78 3 0.02
79 154 0.79
80 35 0.18
82 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (78 bp):
CGATAATGTACCCATATACATATCAGCTAAGGCATCCTTTTATGCCATTAATGCACCTATATGCA
TTATTCTTTATGC
Found at i:2225429 original size:22 final size:21
Alignment explanation
Indices: 2225377--2225430 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
2225367 CTGGCCCTTT
* *
2225377 GGTATCGATACTCCTGCTTAT
1 GGTATCGATACTCCTGATTAG
*
2225398 GGTATTGATACTACCCT-ATTAG
1 GGTATCGATACT--CCTGATTAG
2225420 GGTATCGATAC
1 GGTATCGATAC
2225431 CCCCTTCATG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 11 0.41
22 13 0.48
23 3 0.11
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.35
Consensus pattern (21 bp):
GGTATCGATACTCCTGATTAG
Found at i:2225523 original size:95 final size:95
Alignment explanation
Indices: 2225420--2225595 Score: 219
Period size: 95 Copynumber: 1.9 Consensus size: 95
2225410 ACCCTATTAG
* * * * * *
2225420 GGTATCGATACCCCCT-TCATGTATCGATACCAAAATTAGTTTCAATGTAGCCCGGTATCGATAC
1 GGTATCGATACCCCATCT-AGGCATCGATACCAAAATTAGATTCAATGTAGACCAGTATCGATAC
2225484 CCTCACCATGGTATCGATAACCCTATGATAT
65 CCTCACCATGGTATCGATAACCCTATGATAT
* * ** *
2225515 GGTATCGATACCCCATCTAGGCATCGATACCCAAATTAGATTCGATGTTTACTAGTATCGATACC
1 GGTATCGATACCCCATCTAGGCATCGATACCAAAATTAGATTCAATGTAGACCAGTATCGATACC
* *
2225580 TTTACCATGGTATCGA
66 CTCACCATGGTATCGA
2225596 CGCCACATTG
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
95 66 0.99
96 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.30
Consensus pattern (95 bp):
GGTATCGATACCCCATCTAGGCATCGATACCAAAATTAGATTCAATGTAGACCAGTATCGATACC
CTCACCATGGTATCGATAACCCTATGATAT
Found at i:2225779 original size:206 final size:208
Alignment explanation
Indices: 2225546--2225956 Score: 808
Period size: 206 Copynumber: 2.0 Consensus size: 208
2225536 CATCGATACC
2225546 CAAATTAGATTCGATGTTTACTAGTATCGATACCTTTACCATGGTATCGACGCCACATTGCTTGG
1 CAAATTAGATTCGATGTTTACTAGTATCGATACCTTTACCATGGTATCGACGCCACATTGCTTGG
2225611 GGTGTCGATATTGGTTGAATTAGTATCGATACCTCTCAGATGATTTAGCCTAATTTTTGCTTATG
66 GGTGTCGATATTGGTTGAATTAGTATCGATACCTCTCAGATGATTTAGCCTAATTTTTGCTTATG
2225676 GTATCGATACCACTTCATTAAGTACTGATACCCCTGCCTAGA-TTTTCAGTTTTCAACCCGAAA-
131 GTATCGATACCACTTCATTAAGTACTGATACCCCTGCCTAGATTTTTCAGTTTTCAACCCGAAAT
2225739 TTACCCAACTATA
196 TTACCCAACTATA
2225752 CAAATTAGATTCGATGTTTACTAGTATCGATACCTTTACCATGGTATCGACGCCACATTGCTTGG
1 CAAATTAGATTCGATGTTTACTAGTATCGATACCTTTACCATGGTATCGACGCCACATTGCTTGG
2225817 GGTGTCGATATTGGTTGAATTAGTATCGATACCTCTCAGATGATTTAGCCTAATTTTTGCTTATG
66 GGTGTCGATATTGGTTGAATTAGTATCGATACCTCTCAGATGATTTAGCCTAATTTTTGCTTATG
2225882 GTATCGATACCACTTCATTAAGTACTGATACCCCTGCCTAGATTTTTCAGTTTTCAACCCGAAAT
131 GTATCGATACCACTTCATTAAGTACTGATACCCCTGCCTAGATTTTTCAGTTTTCAACCCGAAAT
2225947 TTACCCAACT
196 TTACCCAACT
2225957 TTGGCTAATT
Statistics
Matches: 203, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
206 172 0.85
207 21 0.10
208 10 0.05
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (208 bp):
CAAATTAGATTCGATGTTTACTAGTATCGATACCTTTACCATGGTATCGACGCCACATTGCTTGG
GGTGTCGATATTGGTTGAATTAGTATCGATACCTCTCAGATGATTTAGCCTAATTTTTGCTTATG
GTATCGATACCACTTCATTAAGTACTGATACCCCTGCCTAGATTTTTCAGTTTTCAACCCGAAAT
TTACCCAACTATA
Found at i:2230127 original size:29 final size:29
Alignment explanation
Indices: 2230085--2230160 Score: 127
Period size: 29 Copynumber: 2.6 Consensus size: 29
2230075 GGAGCAGGAG
2230085 GGAGTGCATGGCGACCTACAAGGTCGCCA
1 GGAGTGCATGGCGACCTACAAGGTCGCCA
*
2230114 GGAGTGCATGGCGACCTACAAGGTCGCCC
1 GGAGTGCATGGCGACCTACAAGGTCGCCA
2230143 GGAG-GTCATGGCGACCTA
1 GGAGTG-CATGGCGACCTA
2230161 TGCTTGTGGA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 1 0.02
29 44 0.98
ACGTcount: A:0.22, C:0.28, G:0.36, T:0.14
Consensus pattern (29 bp):
GGAGTGCATGGCGACCTACAAGGTCGCCA
Found at i:2231161 original size:3 final size:3
Alignment explanation
Indices: 2231155--2231204 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
2231145 AAATATAATA
* *
2231155 ATT ATT ATT ATT AAT A-T AAT ATAT ATT ATT ATT ATT ATT ATTT ATT
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT A-TT ATT
2231201 ATT A
1 ATT A
2231205 AATAAATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 34 0.81
4 6 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:2231171 original size:21 final size:21
Alignment explanation
Indices: 2231146--2231204 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
2231136 TTTTTTCATA
2231146 AATATAATAATTATTATTATT
1 AATATAATAATTATTATTATT
2231167 AATATAAT-ATATATTATTATT
1 AATATAATAAT-TATTATTATT
* *
2231188 -AT-TATTATTTATTATTA
1 AATATAATAATTATTATTA
2231205 AATAAATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 11 0.32
20 5 0.15
21 18 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AATATAATAATTATTATTATT
Found at i:2232724 original size:3 final size:3
Alignment explanation
Indices: 2232711--2232775 Score: 82
Period size: 3 Copynumber: 22.3 Consensus size: 3
2232701 TTATTTGTAA
*
2232711 TAT TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGCT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT
*
2232755 AAT TAT TAT TA- TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
2232776 TATTTATATA
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
2 5 0.09
3 48 0.87
4 2 0.04
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2232778 original size:12 final size:12
Alignment explanation
Indices: 2232690--2232782 Score: 74
Period size: 12 Copynumber: 8.1 Consensus size: 12
2232680 TTAATTCCTT
*
2232690 TTATTTA-ATCA
1 TTATTTATATTA
* *
2232701 TTATTTGTAATA
1 TTATTTATATTA
2232713 TTATTT-TATTA
1 TTATTTATATTA
2232724 TTA-TTATTATTA
1 TTATTTA-TATTA
2232736 TTA-TTATTATTA
1 TTATTTA-TATTA
*
2232748 TTGCTTTA-ATTA
1 TT-ATTTATATTA
2232760 TTA-TTATATTA
1 TTATTTATATTA
2232771 TTATTTAT-TTA
1 TTATTTATATTA
2232782 T
1 T
2232783 ATAAATATAT
Statistics
Matches: 69, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
10 5 0.07
11 24 0.35
12 37 0.54
14 3 0.04
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (12 bp):
TTATTTATATTA
Found at i:2232785 original size:18 final size:17
Alignment explanation
Indices: 2232718--2232784 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 17
2232708 TAATATTATT
2232718 TTATTA-TTATTAT-TA
1 TTATTATTTATTATATA
2232733 TTATTA-TTATTAT-TA
1 TTATTATTTATTATATA
* *
2232748 TTGCTTTAATTATTATTATA
1 TT--ATTATTTATTA-TATA
2232768 TTATTATTTATT-TATA
1 TTATTATTTATTATATA
2232784 T
1 T
2232785 AAATATATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
15 17 0.39
16 5 0.11
17 3 0.07
18 14 0.32
19 1 0.02
20 4 0.09
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (17 bp):
TTATTATTTATTATATA
Found at i:2233101 original size:21 final size:20
Alignment explanation
Indices: 2233077--2233124 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
2233067 TTCTAAACAA
2233077 ATAAATATCTTAT-TTAAAAAT
1 ATAAATAT-TT-TCTTAAAAAT
*
2233098 ATAATATATTTTCTTAAAATT
1 ATAA-ATATTTTCTTAAAAAT
2233119 ATAAAT
1 ATAAAT
2233125 TTGAAATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 3 0.12
21 17 0.71
22 4 0.17
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAAATATTTTCTTAAAAAT
Found at i:2234926 original size:30 final size:30
Alignment explanation
Indices: 2234891--2234949 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
2234881 GAATGTCATG
* *
2234891 GAAGAAGTTGCAGTCCAGATAAGCAATATA
1 GAAGAAGTTGCAGTACAGACAAGCAATATA
* *
2234921 GAAGAAGTTGTAGTATAGACAAGCAATAT
1 GAAGAAGTTGCAGTACAGACAAGCAATAT
2234950 GGCCCATAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.22
Consensus pattern (30 bp):
GAAGAAGTTGCAGTACAGACAAGCAATATA
Found at i:2235267 original size:12 final size:13
Alignment explanation
Indices: 2235250--2235278 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2235240 ACATTCACAT
2235250 ATTTACA-TTTGC
1 ATTTACATTTTGC
2235262 ATTTACATTTTGC
1 ATTTACATTTTGC
2235275 ATTT
1 ATTT
2235279 TTTTCTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.24, C:0.14, G:0.07, T:0.55
Consensus pattern (13 bp):
ATTTACATTTTGC
Found at i:2250220 original size:5 final size:5
Alignment explanation
Indices: 2250205--2250269 Score: 59
Period size: 5 Copynumber: 13.6 Consensus size: 5
2250195 AAACGAAGCC
* *
2250205 AAATGA AAATA AAAT- -AATA AAATA AAAT- AAATA AAAGA ATATTA AAA-A
1 AAAT-A AAATA AAATA AAATA AAATA AAATA AAATA AAATA A-AATA AAATA
2250253 AAATA AAA-A AAATA AAA
1 AAATA AAATA AAATA AAA
2250270 AAATAAGTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
3 3 0.06
4 12 0.24
5 27 0.55
6 7 0.14
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:2250238 original size:9 final size:9
Alignment explanation
Indices: 2250205--2250275 Score: 56
Period size: 9 Copynumber: 7.7 Consensus size: 9
2250195 AAACGAAGCC
2250205 AAATGAAAAT
1 AAAT-AAAAT
*
2250215 AAA-ATAAT
1 AAATAAAAT
2250223 AAAATAAAAT
1 -AAATAAAAT
*
2250233 AAATAAAAG
1 AAATAAAAT
*
2250242 AATATTAAAAA
1 AA-A-TAAAAT
*
2250253 AAATAAAAA
1 AAATAAAAT
2250262 AAATAAAA-
1 AAATAAAAT
2250270 AAATAA
1 AAATAA
2250276 GTTTAGGGAT
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
8 10 0.19
9 27 0.51
10 9 0.17
11 7 0.13
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (9 bp):
AAATAAAAT
Found at i:2250251 original size:25 final size:24
Alignment explanation
Indices: 2250217--2250264 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2250207 ATGAAAATAA
*
2250217 AATAATAAAATAAAATAAATAAAAG
1 AATAATAAAA-AAAATAAAAAAAAG
*
2250242 AATATTAAAAAAAATAAAAAAAA
1 AATAATAAAAAAAATAAAAAAAA
2250265 TAAAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (24 bp):
AATAATAAAAAAAATAAAAAAAAG
Found at i:2250256 original size:20 final size:18
Alignment explanation
Indices: 2250205--2250272 Score: 66
Period size: 18 Copynumber: 3.6 Consensus size: 18
2250195 AAACGAAGCC
*
2250205 AAATGAAAATAAAAT-AATA
1 AAAT-AAAA-AAAATAAAAA
*
2250224 AAATAAAATAAATAAAAGA
1 AAATAAAAAAAATAAAA-A
*
2250243 ATATTAAAAAAAATAAAAA
1 A-AATAAAAAAAATAAAAA
2250262 AAATAAAAAAA
1 AAATAAAAAAA
2250273 TAAGTTTAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
17 4 0.10
18 15 0.37
19 8 0.20
20 14 0.34
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (18 bp):
AAATAAAAAAAATAAAAA
Found at i:2250272 original size:8 final size:8
Alignment explanation
Indices: 2250215--2250275 Score: 59
Period size: 9 Copynumber: 6.9 Consensus size: 8
2250205 AAATGAAAAT
*
2250215 AAAATAAT
1 AAAATAAA
2250223 AAAATAAA
1 AAAATAAA
2250231 ATAAATAAA
1 A-AAATAAA
2250240 AGAATATTAAAA
1 A-AA-A-T-AAA
2250252 AAAATAAAA
1 AAAAT-AAA
2250261 AAAATAAA
1 AAAATAAA
2250269 AAAATAA
1 AAAATAA
2250276 GTTTAGGGAT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
8 18 0.38
9 20 0.43
10 2 0.04
11 3 0.06
12 4 0.09
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (8 bp):
AAAATAAA
Found at i:2251472 original size:7 final size:7
Alignment explanation
Indices: 2251460--2251486 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2251450 ATAAAAGAAA
2251460 AATAAAG
1 AATAAAG
2251467 AATAAAG
1 AATAAAG
2251474 AATAAAG
1 AATAAAG
2251481 AATAAA
1 AATAAA
2251487 ATAGAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (7 bp):
AATAAAG
Found at i:2251716 original size:38 final size:37
Alignment explanation
Indices: 2251546--2251772 Score: 168
Period size: 35 Copynumber: 6.1 Consensus size: 37
2251536 TATAAAATAT
*
2251546 GTTTTCAAAAATCGTTTTTAAAAAAATTATATATTATAT--
1 GTTTTCAAAAAT-G-TTTT--AAAAACTATATATTATATAC
* *
2251585 GTTTTCAAAAGTAT-TTTTGAAAGC--TATATTATATAC
1 GTTTTCAAAA--ATGTTTTAAAAACTATATATTATATAC
* *
2251621 GTTTTCAAAAATGCTTTCAAAACTATATATTATAT--
1 GTTTTCAAAAATGTTTTAAAAACTATATATTATATAC
2251656 GTTTAT-AAAAATGTTTTAAAAACTATATATTATATAC
1 GTTT-TCAAAAATGTTTTAAAAACTATATATTATATAC
* * *
2251693 GTTTTCGAGAAATGTTTTTAAAACTATATTATATATATAT
1 GTTTTC-AAAAATGTTTTAAAAACTATA-TAT-TATATAC
* * * *
2251733 ATATATTCAAAAA--TATTCAAAACTATATATTATATTC
1 GT-T-TTCAAAAATGTTTTAAAAACTATATATTATATAC
2251770 GTT
1 GTT
2251773 ATATATATAC
Statistics
Matches: 154, Mismatches: 18, Indels: 35
0.74 0.09 0.17
Matches are distributed among these distances:
34 12 0.08
35 38 0.25
36 16 0.10
37 20 0.13
38 26 0.17
39 25 0.16
40 7 0.05
41 7 0.05
42 3 0.02
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (37 bp):
GTTTTCAAAAATGTTTTAAAAACTATATATTATATAC
Found at i:2252408 original size:5 final size:5
Alignment explanation
Indices: 2252398--2252460 Score: 63
Period size: 5 Copynumber: 12.0 Consensus size: 5
2252388 ATGTTAGATT
* * * *
2252398 ATAAA ATAAA AGAAA TATCAA ATAAAA ATTAAA TTAAA TTAAA ATAAA
1 ATAAA ATAAA ATAAA -ATAAA AT-AAA A-TAAA ATAAA ATAAA ATAAA
2252446 ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA
2252461 TCAAAGAAGG
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
5 39 0.80
6 9 0.18
7 1 0.02
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (5 bp):
ATAAA
Found at i:2252436 original size:16 final size:16
Alignment explanation
Indices: 2252398--2252460 Score: 58
Period size: 16 Copynumber: 4.0 Consensus size: 16
2252388 ATGTTAGATT
*
2252398 ATAAAATAAAAGA-AAT
1 ATAAAATAAAA-ATAAA
* *
2252414 ATCAAATAAAAATTAA
1 ATAAAATAAAAATAAA
* *
2252430 ATTAAATTAAAATAAA
1 ATAAAATAAAAATAAA
2252446 ATAAAAT-AAAATAAA
1 ATAAAATAAAAATAAA
2252461 TCAAAGAAGG
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
15 9 0.23
16 30 0.77
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (16 bp):
ATAAAATAAAAATAAA
Found at i:2252622 original size:35 final size:37
Alignment explanation
Indices: 2252583--2252653 Score: 103
Period size: 35 Copynumber: 2.0 Consensus size: 37
2252573 TGTTAAAAGA
*
2252583 GAAAATAAAAATAA-A-AAAATAAAA-AAAAGAAGTGG
1 GAAAATAAAAATAATACAAAACAAAATAAAA-AAGTGG
2252618 GAAAATAAAAATAATACAAAACAAAATAAAAAAGTG
1 GAAAATAAAAATAATACAAAACAAAATAAAAAAGTG
2252654 TTAAATAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 14 0.44
36 1 0.03
37 13 0.41
38 4 0.12
ACGTcount: A:0.73, C:0.03, G:0.11, T:0.13
Consensus pattern (37 bp):
GAAAATAAAAATAATACAAAACAAAATAAAAAAGTGG
Found at i:2253349 original size:12 final size:12
Alignment explanation
Indices: 2253332--2253378 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
2253322 AAAGATAAAA
2253332 TAAAATAATATT
1 TAAAATAATATT
*
2253344 TAAAATAATATCC
1 TAAAATAATAT-T
**
2253357 T-AAATCCTATT
1 TAAAATAATATT
2253368 TAAAATAATAT
1 TAAAATAATAT
2253379 CCTAAATCAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
11 1 0.04
12 25 0.93
13 1 0.04
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (12 bp):
TAAAATAATATT
Found at i:2253367 original size:24 final size:24
Alignment explanation
Indices: 2253340--2253386 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
2253330 AATAAAATAA
2253340 TATTTAAAATAATATCCTAAATCC
1 TATTTAAAATAATATCCTAAATCC
2253364 TATTTAAAATAATATCCTAAATC
1 TATTTAAAATAATATCCTAAATC
2253387 ATAATTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (24 bp):
TATTTAAAATAATATCCTAAATCC
Found at i:2253397 original size:24 final size:24
Alignment explanation
Indices: 2253334--2253398 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
2253324 AGATAAAATA
* *
2253334 AAATAATATTTAAAATAATATCCT
1 AAATCATAATTAAAATAATATCCT
* *
2253358 AAATCCTATTTAAAATAATATCCT
1 AAATCATAATTAAAATAATATCCT
*
2253382 AAATCATAATTGAAATA
1 AAATCATAATTAAAATA
2253399 CAAACATCTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.35
Consensus pattern (24 bp):
AAATCATAATTAAAATAATATCCT
Found at i:2254127 original size:123 final size:123
Alignment explanation
Indices: 2253925--2254152 Score: 334
Period size: 123 Copynumber: 1.9 Consensus size: 123
2253915 TTATTCATTA
*
2253925 TGAAGTTGAGCTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGTAAATTGAAT
1 TGAAGTTGAGCTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAAAATTGAAT
* * *
2253990 CGCTTTGTGATTAATAT-ATTTCGTTGTGAAGTTGAAATTGTGGAAGGATAATTCGCTG
66 CGCTTCGAGATTAATATCA-TTCGCTGTGAAGTTGAAATTGTGGAAGGATAATTCGCTG
* * *
2254048 TGAAGTTGAGCTTTGAATTGGATGTCCTTCGTTGTGAAGTTGAAATCCATTCTTGAAAATTGCAT
1 TGAAGTTGAGCTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAAAATTG-AA
* * *
2254113 TGGC-TCGAGTTTAATATCATTCGCTGTGAAGTTGACATTG
65 TCGCTTCGAGATTAATATCATTCGCTGTGAAGTTGAAATTG
2254153 ACTTTTACAA
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
123 88 0.95
124 5 0.05
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (123 bp):
TGAAGTTGAGCTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAAAATTGAAT
CGCTTCGAGATTAATATCATTCGCTGTGAAGTTGAAATTGTGGAAGGATAATTCGCTG
Found at i:2260410 original size:40 final size:41
Alignment explanation
Indices: 2260366--2260479 Score: 108
Period size: 40 Copynumber: 2.7 Consensus size: 41
2260356 AATAAACTAT
2260366 AAAAAATGTTAAAAGAAAAAATAAAAATAAAACAAAATAAA
1 AAAAAATGTTAAAAGAAAAAATAAAAATAAAACAAAATAAA
* ** **
2260407 AAAAAGAAG--AAGTGGGAAAATAAAAATAAAACAAAATAAA
1 AAAAA-ATGTTAAAAGAAAAAATAAAAATAAAACAAAATAAA
*
2260447 ATAAAAAGTGTTAAATA-AAATAATAAATAATAA
1 A-AAAAA-TGTTAAA-AGAAAAAATAAA-AATAA
2260480 TAGTAAAGAT
Statistics
Matches: 55, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
40 29 0.53
41 10 0.18
42 2 0.04
43 9 0.16
44 5 0.09
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.17
Consensus pattern (41 bp):
AAAAAATGTTAAAAGAAAAAATAAAAATAAAACAAAATAAA
Found at i:2260453 original size:16 final size:16
Alignment explanation
Indices: 2260423--2260452 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2260413 AAGAAGTGGG
2260423 AAAATAAAAATAAAAC
1 AAAATAAAAATAAAAC
2260439 AAAAT-AAAATAAAA
1 AAAATAAAAATAAAA
2260453 AGTGTTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAATAAAAATAAAAC
Found at i:2260540 original size:18 final size:18
Alignment explanation
Indices: 2260517--2260559 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
2260507 ATTGTTTTTA
* *
2260517 AAATAAGAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
2260535 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
2260553 AAATAAA
1 AAATAAA
2260560 TAATCTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:2265734 original size:8 final size:8
Alignment explanation
Indices: 2265721--2265761 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
2265711 CTCATTTTCA
2265721 GAGAATTT
1 GAGAATTT
2265729 GAGAATTT
1 GAGAATTT
*
2265737 -AGAGTTT
1 GAGAATTT
*
2265744 GGGAATTT
1 GAGAATTT
2265752 GAGAATTT
1 GAGAATTT
2265760 GA
1 GA
2265762 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:2266060 original size:128 final size:128
Alignment explanation
Indices: 2265832--2266588 Score: 1327
Period size: 128 Copynumber: 5.9 Consensus size: 128
2265822 TAATCGGAGT
* *
2265832 ACTATTCACATGAAGGCACGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCATAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
2265897 CATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
2265960 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
2266025 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
2266088 ACTATTCACATGAAGGCGTGTTCCCGGGGGCGCGACTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
2266153 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACAATAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* * *
2266216 ACTATTCACATTAAGGCGCGTTCCCGGGGGCTCTCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
2266281 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
2266344 ACTATTCACATGAAGGCGCGTTCCCGGGGGAGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
2266409 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *** * * * *
2266472 TC-AGGGGACATGAAGGCGCGTTCCTGGGGGCTCGCCTTCCATTATTTTGTCATAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
*
2266536 TCATTGCCCCATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
2266589 AATCAGGTAA
Statistics
Matches: 602, Mismatches: 26, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
127 1 0.00
128 601 1.00
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:2267059 original size:33 final size:34
Alignment explanation
Indices: 2266989--2267088 Score: 130
Period size: 34 Copynumber: 3.0 Consensus size: 34
2266979 AAATTTAATG
* *
2266989 TTAAATTTCGAGTACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
2267023 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
2267056 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
2267089 AACATTTATC
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 27 0.49
34 28 0.51
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:2267638 original size:21 final size:21
Alignment explanation
Indices: 2267608--2267701 Score: 145
Period size: 21 Copynumber: 4.5 Consensus size: 21
2267598 TATGGTATAA
*
2267608 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
2267629 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
2267650 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
*
2267671 AACCCTGCGGGCTTGGAATGT
1 AACCCTGCGGGCTAGGAATGT
2267692 AACCCTGCGG
1 AACCCTGCGG
2267702 AGATGGCATA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
20 3 0.04
21 62 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.34, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:2267725 original size:42 final size:42
Alignment explanation
Indices: 2267608--2267728 Score: 147
Period size: 42 Copynumber: 2.9 Consensus size: 42
2267598 TATGGTATAA
*
2267608 AACCCTGCGGGCTAGGCATGTAACCTGGCGGGCTAGGAATGT
1 AACCCTGCGGGCTAGGCATGTAACCTGGCGGGCTTGGAATGT
* *
2267650 AACCCTGCGGGCTCGGAATGTAACCCT-GCGGGCTTGGAATGT
1 AACCCTGCGGGCTAGGCATGTAA-CCTGGCGGGCTTGGAATGT
* * * *
2267692 AACCCTGCGGAGAT-GGCATATAAACTGGTGGGCTTGG
1 AACCCTGCGG-GCTAGGCATGTAACCTGGCGGGCTTGG
2267729 CATATGAAGT
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
41 2 0.03
42 61 0.90
43 5 0.07
ACGTcount: A:0.21, C:0.23, G:0.35, T:0.21
Consensus pattern (42 bp):
AACCCTGCGGGCTAGGCATGTAACCTGGCGGGCTTGGAATGT
Found at i:2267731 original size:21 final size:21
Alignment explanation
Indices: 2267705--2267752 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2267695 CCTGCGGAGA
*
2267705 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
2267726 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
2267747 GGGCAT
1 TGGCAT
2267753 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:2269519 original size:17 final size:19
Alignment explanation
Indices: 2269497--2269540 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2269487 ATAATTATAT
2269497 AAATATTAT-TTTA-ATAA
1 AAATATTATATTTACATAA
*
2269514 AAATATAATATTTACATAA
1 AAATATTATATTTACATAA
*
2269533 ATATATTA
1 AAATATTA
2269541 ATATAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 4 0.18
19 10 0.45
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATATTATATTTACATAA
Found at i:2269532 original size:19 final size:18
Alignment explanation
Indices: 2269484--2269571 Score: 55
Period size: 17 Copynumber: 5.1 Consensus size: 18
2269474 TTCTAAATAA
* *
2269484 ATAATAATT-ATATAAAT
1 ATAATATTTAATAAAAAT
*
2269501 ATTAT-TTTAATAAAAAT
1 ATAATATTTAATAAAAAT
*
2269518 ATAATATTTACATAAATAT
1 ATAATATTTA-ATAAAAAT
2269537 ATTAATA--T-A-AAAAAT
1 A-TAATATTTAATAAAAAT
2269552 AATAACTATTTAA-AAAAAT
1 -ATAA-TATTTAATAAAAAT
2269571 A
1 A
2269572 CTAACATAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 17
0.71 0.08 0.22
Matches are distributed among these distances:
15 8 0.14
16 6 0.11
17 15 0.27
18 7 0.12
19 15 0.27
20 5 0.09
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAATATTTAATAAAAAT
Found at i:2269581 original size:34 final size:34
Alignment explanation
Indices: 2269512--2269583 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
2269502 TTATTTTAAT
* * *
2269512 AAAAATATAATATTTACATAAATATATTAATATA
1 AAAAATATAATATTTACATAAAAATACTAACATA
2269546 AAAAATAATAACTATTTA-A-AAAAATACTAACATA
1 AAAAAT-ATAA-TATTTACATAAAAATACTAACATA
2269580 AAAA
1 AAAA
2269584 TAAATTTCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 22 0.67
35 5 0.15
36 6 0.18
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (34 bp):
AAAAATATAATATTTACATAAAAATACTAACATA
Found at i:2271004 original size:15 final size:15
Alignment explanation
Indices: 2270984--2271021 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
2270974 AAATTATTAA
2270984 ACATATATTAAAAAT
1 ACATATATTAAAAAT
2270999 ACATATATTAAAAAT
1 ACATATATTAAAAAT
2271014 ACAT-TATT
1 ACATATATT
2271022 GATAATTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (15 bp):
ACATATATTAAAAAT
Found at i:2271148 original size:40 final size:40
Alignment explanation
Indices: 2271093--2271175 Score: 148
Period size: 40 Copynumber: 2.1 Consensus size: 40
2271083 ATTCGAATTT
*
2271093 GAGTTCGAGGTTGAATCGAGCCCAAAATCGAGCTTCAATC
1 GAGTTCGAGGTTGAATCGAGCCCAAAATCAAGCTTCAATC
*
2271133 GAGTTCGAGGTTGAATCGAGCTCAAAATCAAGCTTCAATC
1 GAGTTCGAGGTTGAATCGAGCCCAAAATCAAGCTTCAATC
2271173 GAG
1 GAG
2271176 CTCCTGAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.23
Consensus pattern (40 bp):
GAGTTCGAGGTTGAATCGAGCCCAAAATCAAGCTTCAATC
Found at i:2272876 original size:17 final size:17
Alignment explanation
Indices: 2272819--2272868 Score: 100
Period size: 17 Copynumber: 2.9 Consensus size: 17
2272809 AACGACGGTG
2272819 GGGGCCACTGGTGAGTA
1 GGGGCCACTGGTGAGTA
2272836 GGGGCCACTGGTGAGTA
1 GGGGCCACTGGTGAGTA
2272853 GGGGCCACTGGTGAGT
1 GGGGCCACTGGTGAGT
2272869 GGTGGCCATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.16, C:0.18, G:0.48, T:0.18
Consensus pattern (17 bp):
GGGGCCACTGGTGAGTA
Found at i:2273790 original size:2 final size:2
Alignment explanation
Indices: 2273783--2273809 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2273773 AAAGATACCT
2273783 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2273810 TAATTATAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2275299 original size:16 final size:17
Alignment explanation
Indices: 2275278--2275313 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2275268 ATTTTCTAAA
*
2275278 AGAAATTATATTT-GGT
1 AGAAATCATATTTGGGT
2275294 AGAAATCATATTTGGGT
1 AGAAATCATATTTGGGT
2275311 AGA
1 AGA
2275314 TATATTGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (17 bp):
AGAAATCATATTTGGGT
Found at i:2278116 original size:2 final size:2
Alignment explanation
Indices: 2278109--2278187 Score: 149
Period size: 2 Copynumber: 39.5 Consensus size: 2
2278099 TAATGTAATC
2278109 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
*
2278151 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2278188 ATAAAGTTGA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2278813 original size:25 final size:25
Alignment explanation
Indices: 2278765--2278813 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
2278755 CAAACGTTCT
* *
2278765 TCAAAATTCTTTCTTCAAACATTTC
1 TCAAAATTCTTTCATAAAACATTTC
*
2278790 TCAAAATTCTTTCATAAAAGATTT
1 TCAAAATTCTTTCATAAAACATTT
2278814 TCGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.37, C:0.18, G:0.02, T:0.43
Consensus pattern (25 bp):
TCAAAATTCTTTCATAAAACATTTC
Found at i:2279193 original size:29 final size:30
Alignment explanation
Indices: 2279113--2279196 Score: 98
Period size: 29 Copynumber: 2.8 Consensus size: 30
2279103 TACTACACAT
** **
2279113 ACTTGGCCACCAATGCCAAATAGTACTTGG
1 ACTTGGCCACCAATGTTAAATAGTACGAGG
* *
2279143 ACTTGGCCACCAAGGTTGAATAGTA-GAGG
1 ACTTGGCCACCAATGTTAAATAGTACGAGG
*
2279172 ACTTGGCCAACAATGTTAAATAGTA
1 ACTTGGCCACCAATGTTAAATAGTA
2279197 TAGGGACCAA
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 24 0.53
30 21 0.47
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (30 bp):
ACTTGGCCACCAATGTTAAATAGTACGAGG
Found at i:2281566 original size:23 final size:23
Alignment explanation
Indices: 2281535--2281590 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
2281525 TAGTTACCAT
*
2281535 ATTTTTTATTGCTTATTTGAATCC
1 ATTTTTTATTGCATATTT-AATCC
2281559 -TTTTTTA-TGCATATTTAATCC
1 ATTTTTTATTGCATATTTAATCC
2281580 ATGTTTTTATT
1 AT-TTTTTATT
2281591 TGTCTATGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 5 0.18
22 9 0.32
23 13 0.46
24 1 0.04
ACGTcount: A:0.21, C:0.11, G:0.07, T:0.61
Consensus pattern (23 bp):
ATTTTTTATTGCATATTTAATCC
Found at i:2282457 original size:17 final size:16
Alignment explanation
Indices: 2282424--2282464 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
2282414 AACATCCTAA
2282424 ATTTTAATTTACATTT
1 ATTTTAATTTACATTT
2282440 ATTTTGAATTT-CATTT
1 ATTTT-AATTTACATTT
*
2282456 -TATTAATTT
1 ATTTTAATTT
2282465 TGGGGACTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 5 0.22
15 3 0.13
16 10 0.43
17 5 0.22
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (16 bp):
ATTTTAATTTACATTT
Found at i:2284297 original size:18 final size:18
Alignment explanation
Indices: 2284252--2284310 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
2284242 TTGAATTGTT
* *
2284252 TGAAATGATCGAAATAAA
1 TGAAATGATTGAATTAAA
*
2284270 TGAATTGATTGAATTAAA
1 TGAAATGATTGAATTAAA
* *
2284288 TGAAAAGATTGGATTAAA
1 TGAAATGATTGAATTAAA
2284306 TGAAA
1 TGAAA
2284311 CGACCATAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.51, C:0.02, G:0.19, T:0.29
Consensus pattern (18 bp):
TGAAATGATTGAATTAAA
Found at i:2288513 original size:32 final size:32
Alignment explanation
Indices: 2288445--2288554 Score: 114
Period size: 32 Copynumber: 3.4 Consensus size: 32
2288435 CTAAGTTGAC
* * * *
2288445 CTTGGGTGGGCTCTGAGGCCCCAATGCA-TTT
1 CTTGGGTAGGCTCTAAGGCCCCAAGGTACTTT
*
2288476 CCTTGGGTAGGATCTAAGGCCCCAAGGTACTTT
1 -CTTGGGTAGGCTCTAAGGCCCCAAGGTACTTT
* * * **
2288509 CTTGGTTAGGCTCTTAGGCCCTAAGGTACTCC
1 CTTGGGTAGGCTCTAAGGCCCCAAGGTACTTT
2288541 CTTGGGTAGGCTCT
1 CTTGGGTAGGCTCT
2288555 CAAGACCCAA
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
32 62 0.95
33 3 0.05
ACGTcount: A:0.15, C:0.25, G:0.29, T:0.30
Consensus pattern (32 bp):
CTTGGGTAGGCTCTAAGGCCCCAAGGTACTTT
Found at i:2289665 original size:2 final size:2
Alignment explanation
Indices: 2289660--2289693 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2289650 TGTTTCTCTC
2289660 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
2289694 TTCATGATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2290310 original size:71 final size:71
Alignment explanation
Indices: 2290233--2290376 Score: 288
Period size: 71 Copynumber: 2.0 Consensus size: 71
2290223 TACGAATTTT
2290233 TAGTAATATATAAACCAATTTTCTTCATTTAAAAGTCACTTCTGAAATTTGTTAAAAATAAATTT
1 TAGTAATATATAAACCAATTTTCTTCATTTAAAAGTCACTTCTGAAATTTGTTAAAAATAAATTT
2290298 TTTAGG
66 TTTAGG
2290304 TAGTAATATATAAACCAATTTTCTTCATTTAAAAGTCACTTCTGAAATTTGTTAAAAATAAATTT
1 TAGTAATATATAAACCAATTTTCTTCATTTAAAAGTCACTTCTGAAATTTGTTAAAAATAAATTT
2290369 TTTAGG
66 TTTAGG
2290375 TA
1 TA
2290377 TTCGACCTAC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (71 bp):
TAGTAATATATAAACCAATTTTCTTCATTTAAAAGTCACTTCTGAAATTTGTTAAAAATAAATTT
TTTAGG
Found at i:2294131 original size:157 final size:157
Alignment explanation
Indices: 2293845--2294159 Score: 630
Period size: 157 Copynumber: 2.0 Consensus size: 157
2293835 CTATTCTTAA
2293845 TCGTTAACTTTTACAATTATCGATAGTCGATACACAAGCTCACTAACCTATTTTTCTTCTTAAAA
1 TCGTTAACTTTTACAATTATCGATAGTCGATACACAAGCTCACTAACCTATTTTTCTTCTTAAAA
2293910 AGCACTGGTGCTCCCCATGGCGATATACTCGATCAAATTAAACCCCTCTCTTATAAATCTTGAAT
66 AGCACTGGTGCTCCCCATGGCGATATACTCGATCAAATTAAACCCCTCTCTTATAAATCTTGAAT
2293975 CTAAGCCTCTAACTCCTTTAACTCAAT
131 CTAAGCCTCTAACTCCTTTAACTCAAT
2294002 TCGTTAACTTTTACAATTATCGATAGTCGATACACAAGCTCACTAACCTATTTTTCTTCTTAAAA
1 TCGTTAACTTTTACAATTATCGATAGTCGATACACAAGCTCACTAACCTATTTTTCTTCTTAAAA
2294067 AGCACTGGTGCTCCCCATGGCGATATACTCGATCAAATTAAACCCCTCTCTTATAAATCTTGAAT
66 AGCACTGGTGCTCCCCATGGCGATATACTCGATCAAATTAAACCCCTCTCTTATAAATCTTGAAT
2294132 CTAAGCCTCTAACTCCTTTAACTCAAT
131 CTAAGCCTCTAACTCCTTTAACTCAAT
2294159 T
1 T
2294160 AGTTCCATGC
Statistics
Matches: 158, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
157 158 1.00
ACGTcount: A:0.30, C:0.26, G:0.10, T:0.34
Consensus pattern (157 bp):
TCGTTAACTTTTACAATTATCGATAGTCGATACACAAGCTCACTAACCTATTTTTCTTCTTAAAA
AGCACTGGTGCTCCCCATGGCGATATACTCGATCAAATTAAACCCCTCTCTTATAAATCTTGAAT
CTAAGCCTCTAACTCCTTTAACTCAAT
Found at i:2325591 original size:18 final size:18
Alignment explanation
Indices: 2325561--2325596 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2325551 ACAAAGTGCC
2325561 GAAAGTACACAAGGTACT
1 GAAAGTACACAAGGTACT
*
2325579 GAAAGTACGCAAGGTACT
1 GAAAGTACACAAGGTACT
2325597 AACATGATTA
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:0.42, C:0.17, G:0.25, T:0.17
Consensus pattern (18 bp):
GAAAGTACACAAGGTACT
Found at i:2332241 original size:32 final size:32
Alignment explanation
Indices: 2332158--2332233 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
2332148 TTGTCACATC
* *
2332158 CAGATAATGCACCGTAGTGTCAGCTTTGCATT
1 CAGATAATGCACCGTAGTGTCAACTTTCCATT
2332190 CAGATAATGCACCGTAGTGTCAACTTTCCATT
1 CAGATAATGCACCGTAGTGTCAACTTTCCATT
2332222 CAGATAATGCAC
1 CAGATAATGCAC
2332234 ATCAGTGTGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (32 bp):
CAGATAATGCACCGTAGTGTCAACTTTCCATT
Found at i:2339745 original size:16 final size:16
Alignment explanation
Indices: 2339724--2339754 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2339714 GTCTTCTAAA
2339724 CAATTTTAAGAAAAAT
1 CAATTTTAAGAAAAAT
2339740 CAATTTTAAGAAAAA
1 CAATTTTAAGAAAAA
2339755 AAATTTGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (16 bp):
CAATTTTAAGAAAAAT
Found at i:2339759 original size:15 final size:16
Alignment explanation
Indices: 2339725--2339760 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2339715 TCTTCTAAAC
*
2339725 AATTTTAAGAAAAATC
1 AATTTTAAGAAAAATA
2339741 AATTTTAAGAAAAA-A
1 AATTTTAAGAAAAATA
2339756 AATTT
1 AATTT
2339761 GGTATACGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (16 bp):
AATTTTAAGAAAAATA
Found at i:2341065 original size:102 final size:102
Alignment explanation
Indices: 2340924--2341178 Score: 312
Period size: 102 Copynumber: 2.5 Consensus size: 102
2340914 GTTATCTCAG
* * * * * *
2340924 GTGAGATAAAATTTTATTTCGAGTGAAACAATTTTAAAATTTGTGTTTCAAGGGAAAACTACCTT
1 GTGAGAT-CAATTTTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAACCACCTC
* *
2340989 GAGCGAGACAAAATATGTTTTTAGAAAAACAATCGCAA
65 AAGCAAGACAAAATATGTTTTTAGAAAAACAATCGCAA
**
2341027 GTGAGATCAATTTTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAACCGTCTCA
1 GTGAGATCAATTTTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAACCACCTCA
** * * * *
2341092 AGCAAGATGAAATTTGTTTTTAGGAAAATAATCTCAA
66 AGCAAGACAAAATATGTTTTTAGAAAAACAATCGCAA
* * * * *
2341129 GAGAGATCAATTTTGTTTCAAGTGAAACAACTGCGAAATTTGGGTTTCAA
1 GTGAGATCAATTTTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTCAA
2341179 TGGAGACTAC
Statistics
Matches: 131, Mismatches: 21, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
102 124 0.95
103 7 0.05
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.32
Consensus pattern (102 bp):
GTGAGATCAATTTTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAACCACCTCA
AGCAAGACAAAATATGTTTTTAGAAAAACAATCGCAA
Found at i:2341210 original size:102 final size:102
Alignment explanation
Indices: 2340933--2341224 Score: 289
Period size: 102 Copynumber: 2.9 Consensus size: 102
2340923 GGTGAGATAA
* * * ** * * ** * * *
2340933 AATTTTATTTCGAGTGAAACAATTTTAAAATTTGTGTTTCAAGGGAAAACTACCTTGAGCGAGAC
1 AATTTTGTTTCAAGTGAAACAACTGCAAAATTTGGGTTTCAAGGGAAAACCACCTCAACCAAGAT
* * *
2340998 AAAATATGTTTTTAGAAAAACAATCGCAAGTGAGATC
66 GAAATTTGTTTTTAGAAAAACAATCGCAAGAGAGATC
* * * ** *
2341035 AATTTTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAACCGTCTCAAGCAAGAT
1 AATTTTGTTTCAAGTGAAACAACTGCAAAATTTGGGTTTCAAGGGAAAACCACCTCAACCAAGAT
* * *
2341100 GAAATTTGTTTTTAGGAAAATAATCTCAAGAGAGATC
66 GAAATTTGTTTTTAGAAAAACAATCGCAAGAGAGATC
* * * * *
2341137 AATTTTGTTTCAAGTGAAACAACTGCGAAATTTGGGTTTCAATGG-AGACTACCTCAACCGAGAT
1 AATTTTGTTTCAAGTGAAACAACTGCAAAATTTGGGTTTCAAGGGAAAACCACCTCAACCAAGAT
* *
2341201 GAAACTTTGTTTTGAGAGAAACAA
66 GAAA-TTTGTTTTTAGAAAAACAA
2341225 CCTCAAAGGT
Statistics
Matches: 158, Mismatches: 31, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
101 17 0.11
102 141 0.89
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (102 bp):
AATTTTGTTTCAAGTGAAACAACTGCAAAATTTGGGTTTCAAGGGAAAACCACCTCAACCAAGAT
GAAATTTGTTTTTAGAAAAACAATCGCAAGAGAGATC
Found at i:2341315 original size:36 final size:35
Alignment explanation
Indices: 2341268--2341393 Score: 120
Period size: 36 Copynumber: 3.7 Consensus size: 35
2341258 CAAAGGTTTA
*
2341268 TGTTTCAAGAGAAACTTTCTCAAGCAAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGCAAGA-AAAATT
* **
2341304 TGTTTCAAGAGAAACAATCTC-A--AAG---GTTT
1 TGTTTCAAGAGAAACTATCTCAAGCAAGAAAAATT
*
2341333 ATGTTTCAAGAGAAACTATCTCAAGCGAGAAAAAATT
1 -TGTTTCAAGAGAAACTATCTCAAGCAAG-AAAAATT
* *
2341370 TGTTTCAAGAGAAAATGTCTCAAG
1 TGTTTCAAGAGAAACTATCTCAAG
2341394 GGAGACAGGC
Statistics
Matches: 72, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
29 2 0.03
30 20 0.28
31 1 0.01
33 5 0.07
35 1 0.01
36 41 0.57
37 2 0.03
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (35 bp):
TGTTTCAAGAGAAACTATCTCAAGCAAGAAAAATT
Found at i:2341354 original size:30 final size:30
Alignment explanation
Indices: 2341215--2341356 Score: 151
Period size: 30 Copynumber: 4.5 Consensus size: 30
2341205 CTTTGTTTTG
*
2341215 AGAGAAACAACCTCAAAGGTTTATGTTTCA
1 AGAGAAACAATCTCAAAGGTTTATGTTTCA
*
2341245 AGAGAAACAACCTCAAAGGTTTATGTTTCA
1 AGAGAAACAATCTCAAAGGTTTATGTTTCA
** **
2341275 AGAGAAACTTTCTCAAGCAAGACAAAATT-TGTTTCA
1 AGAGAAACAATCTC-A--AAG----GTTTATGTTTCA
2341311 AGAGAAACAATCTCAAAGGTTTATGTTTCA
1 AGAGAAACAATCTCAAAGGTTTATGTTTCA
*
2341341 AGAGAAACTATCTCAA
1 AGAGAAACAATCTCAA
2341357 GCGAGAAAAA
Statistics
Matches: 94, Mismatches: 10, Indels: 16
0.78 0.08 0.13
Matches are distributed among these distances:
29 2 0.02
30 63 0.67
31 1 0.01
33 6 0.06
35 1 0.01
36 19 0.20
37 2 0.02
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (30 bp):
AGAGAAACAATCTCAAAGGTTTATGTTTCA
Found at i:2341392 original size:66 final size:66
Alignment explanation
Indices: 2341238--2341383 Score: 256
Period size: 66 Copynumber: 2.2 Consensus size: 66
2341228 CAAAGGTTTA
* * *
2341238 TGTTTCAAGAGAAACAACCTCAAAGGTTTATGTTTCAAGAGAAACTTTCTCAAGCAAGACAAAAT
1 TGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTATCTCAAGCAAGAAAAAAT
2341303 T
66 T
*
2341304 TGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTATCTCAAGCGAGAAAAAAT
1 TGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTATCTCAAGCAAGAAAAAAT
2341369 T
66 T
2341370 TGTTTCAAGAGAAA
1 TGTTTCAAGAGAAA
2341384 ATGTCTCAAG
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 76 1.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.27
Consensus pattern (66 bp):
TGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTATCTCAAGCAAGAAAAAAT
T
Found at i:2354646 original size:16 final size:17
Alignment explanation
Indices: 2354625--2354656 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2354615 ATCTTTTAAA
2354625 CAATTTTAAGA-AAAAT
1 CAATTTTAAGACAAAAT
2354641 CAATTTTAAGACAAAA
1 CAATTTTAAGACAAAA
2354657 AACTGGTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.56, C:0.09, G:0.06, T:0.28
Consensus pattern (17 bp):
CAATTTTAAGACAAAAT
Found at i:2355140 original size:25 final size:27
Alignment explanation
Indices: 2355110--2355165 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
2355100 CAACTACACA
*
2355110 TATGAAAC-AAATATATAATATATA-G
1 TATGAAACGAAATAAATAATATATATG
*
2355135 TATGAAACTGTAATAAATAATATATATG
1 TATGAAAC-GAAATAAATAATATATATG
2355163 TAT
1 TAT
2355166 ATATATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 8 0.31
27 14 0.54
28 4 0.15
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.36
Consensus pattern (27 bp):
TATGAAACGAAATAAATAATATATATG
Found at i:2356017 original size:12 final size:13
Alignment explanation
Indices: 2355992--2356017 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2355982 GATTGTAAGC
2355992 TCTTCCCTTTTTT
1 TCTTCCCTTTTTT
2356005 TCTTCCCTTTTTT
1 TCTTCCCTTTTTT
2356018 GTAGTTTTGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (13 bp):
TCTTCCCTTTTTT
Found at i:2356797 original size:104 final size:102
Alignment explanation
Indices: 2356653--2356901 Score: 293
Period size: 104 Copynumber: 2.4 Consensus size: 102
2356643 AGATAAAAAA
* * * * * *
2356653 TATTTCGAGTGAAACAATTTTAAAATTTGCTCTTCAAGGGAAAACTATCGT-AAGAGAGACGAAA
1 TATTTCAAGTGAAAAAAATTCAAAATTTGCTTTTCAAGGGAAAACTATC-TCAAGAGAAACGAAA
2356717 TTTGGTTTTAGGAAAACAATCTCAAGTGAGATCAATTTT
65 TTTGGTTTTAGGAAAACAATCTCAAGTGAGATCAA-TTT
* * * * * * *
2356756 TGTTTCAAGTGAAAAAAAATTCAAAATTTGTTTTTCGAGGGAAAACTGTCTCAAGCGAAATGGAA
1 TATTTCAAGTG-AAAAAAATTCAAAATTTGCTTTTCAAGGGAAAACTATCTCAAGAGAAACGAAA
* *
2356821 TTTGTTTTTAGGAAAACAATCTCAAGTGATATCAATTT
65 TTTGGTTTTAGGAAAACAATCTCAAGTGAGATCAATTT
* * **
2356859 TATTTCAAGTGAAACAACTTCAAAATTTGGGTTTCAAGGGAAA
1 TATTTCAAGTGAAAAAAATTCAAAATTTGCTTTTCAAGGGAAA
2356902 TTGTCTCAAG
Statistics
Matches: 123, Mismatches: 21, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
102 27 0.22
103 23 0.19
104 73 0.59
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (102 bp):
TATTTCAAGTGAAAAAAATTCAAAATTTGCTTTTCAAGGGAAAACTATCTCAAGAGAAACGAAAT
TTGGTTTTAGGAAAACAATCTCAAGTGAGATCAATTT
Found at i:2356948 original size:66 final size:66
Alignment explanation
Indices: 2356889--2357071 Score: 235
Period size: 66 Copynumber: 2.8 Consensus size: 66
2356879 CAAAATTTGG
*
2356889 GTTTCAAGGGAAATTGTCTCAAGTGAGA-AGAAACTTTGTTTCGAA-AGAAACAATCTCAAAGGT
1 GTTTCAAGAGAAATTGTCTCAAGTGAGACA-AAA-TTTGTTTC-AAGAGAAACAATCTCAAAGGT
2356952 TTAT
63 TTAT
* * ** * * *
2356956 GTTTCAAGAGAAACTATCTTTAGCGAGATAAAATTTGTTTCAAGAGAAACGATCTCAAAGGTTTA
1 GTTTCAAGAGAAATTGTCTCAAGTGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTA
2357021 T
66 T
* *
2357022 GTTTCAAGAAAAATTGTCTCAAGTAAGACAAAATTTGTTTCAAGAGAAAC
1 GTTTCAAGAGAAATTGTCTCAAGTGAGACAAAATTTGTTTCAAGAGAAAC
2357072 TGTCTCGGGG
Statistics
Matches: 99, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
65 2 0.02
66 71 0.72
67 25 0.25
68 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (66 bp):
GTTTCAAGAGAAATTGTCTCAAGTGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTA
T
Found at i:2356968 original size:30 final size:30
Alignment explanation
Indices: 2356925--2357030 Score: 81
Period size: 30 Copynumber: 3.3 Consensus size: 30
2356915 GAAGAAACTT
2356925 TGTTTCGAA-AGAAACAATCTCAAAGGTTTA
1 TGTTTC-AAGAGAAACAATCTCAAAGGTTTA
* ***
2356955 TGTTTCAAGAGAAACTATCTTTAGCGAGATAAAATT-
1 TGTTTCAAGAGAAACAATC--T--C-A-A-AGGTTTA
*
2356991 TGTTTCAAGAGAAACGATCTCAAAGGTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
2357021 TGTTTCAAGA
1 TGTTTCAAGA
2357031 AAAATTGTCT
Statistics
Matches: 59, Mismatches: 8, Indels: 18
0.69 0.09 0.21
Matches are distributed among these distances:
29 5 0.08
30 26 0.44
31 1 0.02
32 2 0.03
34 2 0.03
35 1 0.02
36 19 0.32
37 3 0.05
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (30 bp):
TGTTTCAAGAGAAACAATCTCAAAGGTTTA
Found at i:2361853 original size:21 final size:20
Alignment explanation
Indices: 2361815--2361853 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2361805 TTCTTTTGGC
*
2361815 TTTCTTCTTTTTGTACTCTT
1 TTTCTTCTTTTTGAACTCTT
*
2361835 TTTCTTTTGTTTTGAACTC
1 TTTCTTCT-TTTTGAACTC
2361854 CATGATTGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.08, C:0.18, G:0.08, T:0.67
Consensus pattern (20 bp):
TTTCTTCTTTTTGAACTCTT
Found at i:2362464 original size:86 final size:87
Alignment explanation
Indices: 2362300--2362475 Score: 246
Period size: 86 Copynumber: 2.0 Consensus size: 87
2362290 GTAGATGGAA
* * * *
2362300 ATGGAAATAGTATCTTAAACAAGTTAAACAAGAAACTATACTATAGAGAGTATAACCCTGGACTT
1 ATGGAAATAATATCTTAAACAAGTTAAACAAGAAACTATAATATAGAGAGTATAACCCCGGAATT
2362365 TACAAACTCGAATAAGGGAT-G
66 TACAAACTCGAATAAGGGATAG
* * *
2362386 ATGGAAATAATATCTTAGACAAGTTAAATAAGAAACTATAATATAGAGAGTATAGCCCCGGAATT
1 ATGGAAATAATATCTTAAACAAGTTAAACAAGAAACTATAATATAGAGAGTATAACCCCGGAATT
* * * *
2362451 TATAAATTTGAATAATGGATAG
66 TACAAACTCGAATAAGGGATAG
2362473 ATG
1 ATG
2362476 TTTAGGACTT
Statistics
Matches: 78, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
86 74 0.95
87 4 0.05
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.27
Consensus pattern (87 bp):
ATGGAAATAATATCTTAAACAAGTTAAACAAGAAACTATAATATAGAGAGTATAACCCCGGAATT
TACAAACTCGAATAAGGGATAG
Found at i:2365761 original size:24 final size:24
Alignment explanation
Indices: 2365693--2365772 Score: 88
Period size: 24 Copynumber: 3.3 Consensus size: 24
2365683 TTCAATTTGA
*
2365693 ATTCTGTTATGATACCTGACATGG
1 ATTCTGTTATGATACCTGACCTGG
* * *
2365717 ATTTTGTTCTAATACCTGACCTGG
1 ATTCTGTTATGATACCTGACCTGG
* * *
2365741 ATTCTATTATGATATCTGACCTGA
1 ATTCTGTTATGATACCTGACCTGG
*
2365765 ATTATGTT
1 ATTCTGTT
2365773 TTAATTTTTG
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.42
Consensus pattern (24 bp):
ATTCTGTTATGATACCTGACCTGG
Found at i:2372516 original size:16 final size:16
Alignment explanation
Indices: 2372495--2372537 Score: 77
Period size: 16 Copynumber: 2.6 Consensus size: 16
2372485 TTAAACAATT
2372495 TTAAGAAAAATCATTC
1 TTAAGAAAAATCATTC
2372511 TTAAGAAAAATCATTC
1 TTAAGAAAAATCATTC
2372527 TTAAGACAAAA
1 TTAAGA-AAAA
2372538 AACTAGTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 22 0.85
17 4 0.15
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.28
Consensus pattern (16 bp):
TTAAGAAAAATCATTC
Found at i:2375570 original size:16 final size:16
Alignment explanation
Indices: 2375546--2375576 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2375536 CCTACCGTGT
2375546 ATATATATGATATGTG
1 ATATATATGATATGTG
*
2375562 ATATTTATGATATGT
1 ATATATATGATATGT
2375577 TTGTTTTGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.48
Consensus pattern (16 bp):
ATATATATGATATGTG
Found at i:2384614 original size:17 final size:17
Alignment explanation
Indices: 2384592--2384631 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
2384582 CGATGCAAGT
*
2384592 GGTATCGATATTGATGG
1 GGTATCGATACTGATGG
2384609 GGTATCGATACTGATGG
1 GGTATCGATACTGATGG
2384626 GGTATC
1 GGTATC
2384632 AACACTAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.23, C:0.10, G:0.35, T:0.33
Consensus pattern (17 bp):
GGTATCGATACTGATGG
Found at i:2385468 original size:81 final size:81
Alignment explanation
Indices: 2385380--2386014 Score: 920
Period size: 81 Copynumber: 7.9 Consensus size: 81
2385370 TTAATGGTGA
* *
2385380 AGCTGTGCATTTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGGTTAAATACCTTTGAGT
1 AGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGT
2385445 AAAAGATTAATGGCCT
66 AAAAGATTAATGGCCT
* *
2385461 AGTTGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATA-CTTATGAG
1 AGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTT-TGAG
2385525 TAAAAGATTAATGGCCT
65 TAAAAGATTAATGGCCT
* * * * *
2385542 ATCTGTGCATTTGGCAGAAAGATGTTAATTATGCCAGTTAGATGAAAGGTTGAATATCTTTGAGT
1 AGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGT
2385607 AAAAGATTAATGGCCT
66 AAAAGATTAATGGCCT
2385623 AGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGT
1 AGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGT
2385688 AAAAGATTAATGGCCT
66 AAAAGATTAATGGCCT
* * * * *
2385704 AGTTGTACATTTGGCAGAAAGGTGTCAATTATGGCAGTAAGGTGAAAGGTTAAATACCTTTGAGT
1 AGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGT
2385769 AAAAGATTAATGGCCT
66 AAAAGATTAATGGCCT
* * * *
2385785 AGATGTGCATTTGGAAGAAATGTGTCAATTATAG-CAGTAAGATGAAAGGTTAAATACCTTTGAG
1 AGCTGTGCATTTGGCAGAAAGGTGTCAATTAT-GCCAGTTAGATGAAAGGTTAAATACCTTTGAG
2385849 TAAAAGATTAATGGCCT
65 TAAAAGATTAATGGCCT
* * * * *
2385866 AGCTAT---TTTGGCAGAAATGTATCAATTATGCCATTTAGATGAAAGGTTAAATATCTTTGAGT
1 AGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGT
*
2385928 AAAAGATTAATGACCT
66 AAAAGATTAATGGCCT
* * * * * * * * *
2385944 AGCTGTGTATTTGGCACAAAAGTGTTAATCATGCAAGTTAGATGAAAGGCTAAATGCCTTTGGGT
1 AGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGT
2386009 AAAAGA
66 AAAAGA
2386015 CTAAAAGATT
Statistics
Matches: 502, Mismatches: 45, Indels: 14
0.89 0.08 0.02
Matches are distributed among these distances:
77 1 0.00
78 69 0.14
80 3 0.01
81 425 0.85
82 4 0.01
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (81 bp):
AGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGT
AAAAGATTAATGGCCT
Found at i:2389290 original size:67 final size:67
Alignment explanation
Indices: 2389182--2389311 Score: 251
Period size: 67 Copynumber: 1.9 Consensus size: 67
2389172 AAGAATTTTA
2389182 TGTAAAATTATAGCCTAGTAGAGTAGTTATACAAGAGAGATAATGACATAAGTAATTGTTAAATT
1 TGTAAAATTATAGCCTAGTAGAGTAGTTATACAAGAGAGATAATGACATAAGTAATTGTTAAATT
2389247 TG
66 TG
*
2389249 TGTAAAATTATAGCCTAGTAGAGTAGTTATACAAGAGAGATAATGACCTAAGTAATTGTTAAA
1 TGTAAAATTATAGCCTAGTAGAGTAGTTATACAAGAGAGATAATGACATAAGTAATTGTTAAA
2389312 AGTTATCGTC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (67 bp):
TGTAAAATTATAGCCTAGTAGAGTAGTTATACAAGAGAGATAATGACATAAGTAATTGTTAAATT
TG
Found at i:2391650 original size:16 final size:16
Alignment explanation
Indices: 2391596--2391656 Score: 79
Period size: 16 Copynumber: 3.9 Consensus size: 16
2391586 ATAATTGGTA
2391596 TTAACC-GACCTGTTT
1 TTAACCTGACCTGTTT
* *
2391611 TTAACCTAACATGTTT
1 TTAACCTGACCTGTTT
* *
2391627 TCAACCTGGCCTGTTT
1 TTAACCTGACCTGTTT
2391643 TTAACCTGACCTGT
1 TTAACCTGACCTGT
2391657 AAATGATCCG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
15 6 0.16
16 31 0.84
ACGTcount: A:0.21, C:0.26, G:0.13, T:0.39
Consensus pattern (16 bp):
TTAACCTGACCTGTTT
Found at i:2391867 original size:13 final size:13
Alignment explanation
Indices: 2391851--2391877 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2391841 GACCTATTAT
2391851 ATAAAATTATTTA
1 ATAAAATTATTTA
2391864 ATAAAATTATTTA
1 ATAAAATTATTTA
2391877 A
1 A
2391878 ATGTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:2391954 original size:23 final size:24
Alignment explanation
Indices: 2391916--2391965 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
2391906 ATACAAAGAA
*
2391916 AAATTAATATATTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
2391940 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
2391963 AAA
1 AAA
2391966 AAATAATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:2395829 original size:60 final size:61
Alignment explanation
Indices: 2395748--2395888 Score: 196
Period size: 60 Copynumber: 2.3 Consensus size: 61
2395738 TCTTAGTTTT
* * * *
2395748 AAATTTATTTAATTTAGTCCAAATTTAATGATT-TAATATATTAATTTAAGCTTCATATTTC
1 AAATTTGTTCAATTTAATCCAAATTTAATG-TTATAATATATTAATTTAAGCTTCATATTTA
* *
2395809 AACTTT-TTCAATTTAATCCAAATTTAATGTTATAATTTATTAATTTAAGCTTCATATTTA
1 AAATTTGTTCAATTTAATCCAAATTTAATGTTATAATATATTAATTTAAGCTTCATATTTA
*
2395869 AAATTTGTTCAATTTGATCC
1 AAATTTGTTCAATTTAATCC
2395889 TTATATATTT
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
59 2 0.03
60 52 0.73
61 17 0.24
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (61 bp):
AAATTTGTTCAATTTAATCCAAATTTAATGTTATAATATATTAATTTAAGCTTCATATTTA
Done.