Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008243.1 Hibiscus syriacus cultivar Beakdansim tig00110893_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: 10265705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 25 of 49
Found at i:5323336 original size:20 final size:20
Alignment explanation
Indices: 5323313--5323362 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
5323303 GGAATTTGAA
5323313 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
5323333 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
5323353 TTCTAGAAAA
1 TTCTGGAAAA
5323363 CATCTGGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:5323495 original size:26 final size:28
Alignment explanation
Indices: 5323445--5323509 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 28
5323435 AATTTTATAA
*
5323445 ATATATTTAATTATATTAAAGTAA-TAGT
1 ATATA-TTAATTATATTAAAATAATTAGT
5323473 ACTATATTAATT-T-TTAAAATAATTAGT
1 A-TATATTAATTATATTAAAATAATTAGT
*
5323500 ATATTTTAAT
1 ATATATTAAT
5323510 ATCTTTACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 16 0.48
27 6 0.18
28 7 0.21
29 4 0.12
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.49
Consensus pattern (28 bp):
ATATATTAATTATATTAAAATAATTAGT
Found at i:5323914 original size:42 final size:42
Alignment explanation
Indices: 5323855--5323974 Score: 213
Period size: 42 Copynumber: 2.9 Consensus size: 42
5323845 ATGAATTACA
*
5323855 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
5323897 TTCCGGAAAATGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
5323939 TTCCGGAAAACGAATTACGTGAAACAAACACTGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
5323975 TTCGGGGAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:5324129 original size:26 final size:26
Alignment explanation
Indices: 5324100--5324179 Score: 84
Period size: 26 Copynumber: 3.3 Consensus size: 26
5324090 CTTGTTTATT
5324100 TTTTAATGTGTTTAGGTTCGTTTAAA
1 TTTTAATGTGTTTAGGTTCGTTTAAA
*
5324126 TTTTAATTTGTGTTTA--TT--ATT---
1 TTTTAA--TGTGTTTAGGTTCGTTTAAA
5324147 TTTTAATGTGTTTAGGTTCGTTTAAA
1 TTTTAATGTGTTTAGGTTCGTTTAAA
5324173 TTTTAAT
1 TTTTAAT
5324180 ATTGTGTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 18
0.68 0.03 0.29
Matches are distributed among these distances:
19 8 0.19
21 8 0.19
23 2 0.05
24 2 0.05
26 15 0.35
28 8 0.19
ACGTcount: A:0.23, C:0.03, G:0.15, T:0.60
Consensus pattern (26 bp):
TTTTAATGTGTTTAGGTTCGTTTAAA
Found at i:5324158 original size:47 final size:48
Alignment explanation
Indices: 5324095--5324200 Score: 205
Period size: 47 Copynumber: 2.2 Consensus size: 48
5324085 GTTCGCTTGT
5324095 TTATTTTTTAATGTGTTTAGGTTCGTTTAAATTTTAAT-TTGTGTTTA
1 TTATTTTTTAATGTGTTTAGGTTCGTTTAAATTTTAATATTGTGTTTA
5324142 TTATTTTTTAATGTGTTTAGGTTCGTTTAAATTTTAATATTGTGTTTA
1 TTATTTTTTAATGTGTTTAGGTTCGTTTAAATTTTAATATTGTGTTTA
5324190 TTATTTTTTAA
1 TTATTTTTTAA
5324201 GGCGTTCGTG
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 38 0.66
48 20 0.34
ACGTcount: A:0.23, C:0.02, G:0.13, T:0.62
Consensus pattern (48 bp):
TTATTTTTTAATGTGTTTAGGTTCGTTTAAATTTTAATATTGTGTTTA
Found at i:5324973 original size:2 final size:2
Alignment explanation
Indices: 5324956--5325002 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
5324946 ATTATTTGAC
*
5324956 TA TA CA TA TA -A 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
5324997 -A TA TA T
1 TA TA TA T
5325003 TCGAATTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5326921 original size:14 final size:15
Alignment explanation
Indices: 5326892--5326923 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5326882 AAATAATTAA
5326892 AATAATATATTTTAT
1 AATAATATATTTTAT
5326907 AATAATATA-TTTAT
1 AATAATATATTTTAT
5326921 AAT
1 AAT
5326924 TATTTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATAATATATTTTAT
Found at i:5326976 original size:42 final size:41
Alignment explanation
Indices: 5326907--5327010 Score: 129
Period size: 42 Copynumber: 2.5 Consensus size: 41
5326897 TATATTTTAT
*
5326907 AATAATATA-TTTATAATTATTTATTATATTTTAAACAGTTA
1 AATAATATATTTTATAA-TATTTATTATATTTTAAACAATTA
* * * *
5326948 AATTAGTATATTTTATAATATTTTTTATATTTTTAATAATTA
1 AA-TAATATATTTTATAATATTTATTATATTTTAAACAATTA
5326990 AATAATATATTTTAATAATAT
1 AATAATATATTTT-ATAATAT
5327011 AAAAACAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
41 12 0.22
42 35 0.65
43 7 0.13
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (41 bp):
AATAATATATTTTATAATATTTATTATATTTTAAACAATTA
Found at i:5327893 original size:46 final size:46
Alignment explanation
Indices: 5327841--5327971 Score: 210
Period size: 47 Copynumber: 2.8 Consensus size: 46
5327831 GGTAGAGCGC
5327841 TACCTAAAATATTATTTTTTCTATCGGAAATATTAATATCAACCGT
1 TACCTAAAATATTATTTTTTCTATCGGAAATATTAATATCAACCGT
*
5327887 TACCTAAAATATTATTTTTTTCTATCGGAAATATTAATATCAGCCGT
1 TACCTAAAATATTA-TTTTTTCTATCGGAAATATTAATATCAACCGT
* * *
5327934 TACCTAAAATATTATTTTTT-TACCGAAAATGTTAATAT
1 TACCTAAAATATTATTTTTTCTATCGGAAATATTAATAT
5327972 AAAAAATATT
Statistics
Matches: 80, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
45 15 0.19
46 20 0.25
47 45 0.56
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.43
Consensus pattern (46 bp):
TACCTAAAATATTATTTTTTCTATCGGAAATATTAATATCAACCGT
Found at i:5327921 original size:47 final size:47
Alignment explanation
Indices: 5327841--5327954 Score: 212
Period size: 47 Copynumber: 2.4 Consensus size: 47
5327831 GGTAGAGCGC
5327841 TACCTAAAATATTA-TTTTTTCTATCGGAAATATTAATATCAACCGT
1 TACCTAAAATATTATTTTTTTCTATCGGAAATATTAATATCAACCGT
*
5327887 TACCTAAAATATTATTTTTTTCTATCGGAAATATTAATATCAGCCGT
1 TACCTAAAATATTATTTTTTTCTATCGGAAATATTAATATCAACCGT
5327934 TACCTAAAATATTATTTTTTT
1 TACCTAAAATATTATTTTTTT
5327955 ACCGAAAATG
Statistics
Matches: 66, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
46 14 0.21
47 52 0.79
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.45
Consensus pattern (47 bp):
TACCTAAAATATTATTTTTTTCTATCGGAAATATTAATATCAACCGT
Found at i:5328552 original size:4 final size:4
Alignment explanation
Indices: 5328545--5328590 Score: 56
Period size: 4 Copynumber: 10.8 Consensus size: 4
5328535 CATACATGTA
*
5328545 TATG TATG TATG TATG CATG TATG TATG TATTG TATTG TACTG TAT
1 TATG TATG TATG TATG TATG TATG TATG TA-TG TA-TG TA-TG TAT
5328591 ATGATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
4 25 0.66
5 13 0.34
ACGTcount: A:0.24, C:0.04, G:0.22, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:5329679 original size:5 final size:5
Alignment explanation
Indices: 5329669--5329710 Score: 57
Period size: 5 Copynumber: 8.4 Consensus size: 5
5329659 ATCTTACCAG
* **
5329669 ATCAA ATCAA ATCAA ATCAA ATCAA AACCC ATCAA ATCAA AT
1 ATCAA ATCAA ATCAA ATCAA ATCAA ATCAA ATCAA ATCAA AT
5329711 AAAAACCCGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.57, C:0.24, G:0.00, T:0.19
Consensus pattern (5 bp):
ATCAA
Found at i:5329715 original size:20 final size:20
Alignment explanation
Indices: 5329679--5329718 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5329669 ATCAAATCAA
*
5329679 ATCAAATCAAATCAAAACCC
1 ATCAAATCAAATAAAAACCC
5329699 ATCAAATCAAATAAAAACCC
1 ATCAAATCAAATAAAAACCC
5329719 GTCGAATTCG
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:0.57, C:0.28, G:0.00, T:0.15
Consensus pattern (20 bp):
ATCAAATCAAATAAAAACCC
Found at i:5330125 original size:23 final size:24
Alignment explanation
Indices: 5330093--5330139 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
5330083 TAAAACAATT
5330093 AAATCATAATTCA-ATATAAATATA
1 AAATCATAATT-ATATATAAATATA
*
5330117 AAATC-TAATTATATATATATATA
1 AAATCATAATTATATATAAATATA
5330140 CGATAAGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 15 0.71
24 5 0.24
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.38
Consensus pattern (24 bp):
AAATCATAATTATATATAAATATA
Found at i:5332089 original size:80 final size:79
Alignment explanation
Indices: 5331939--5332099 Score: 207
Period size: 80 Copynumber: 2.0 Consensus size: 79
5331929 ATTAATATTT
* * * * * *
5331939 TTTAACATTTTCGGTAAAGCGTTACTTAAAACATTATTTTTTCTACTGAAAATGTTAATATTTGG
1 TTTAACATTTCCGGTAAAACGCTACCTAAAACATTATTTTTTCTACTGAAAATGTTAATATTAGA
* *
5332004 TGCTACTTAAAATG
66 CGCTACCTAAAATG
* *
5332018 TTTAACATTTCCGTTAAAACGCTACCTAAAATATTATTTTTTTCTA-TCGAAAATGTTAATATTA
1 TTTAACATTTCCGGTAAAACGCTACCTAAAACATTA-TTTTTTCTACT-GAAAATGTTAATATTA
5332082 GACGCTACCTAAAATG
64 GACGCTACCTAAAATG
5332098 TT
1 TT
5332100 ATTTTTCTAC
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
79 31 0.44
80 39 0.56
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.42
Consensus pattern (79 bp):
TTTAACATTTCCGGTAAAACGCTACCTAAAACATTATTTTTTCTACTGAAAATGTTAATATTAGA
CGCTACCTAAAATG
Found at i:5335082 original size:271 final size:272
Alignment explanation
Indices: 5334570--5335113 Score: 1065
Period size: 272 Copynumber: 2.0 Consensus size: 272
5334560 TAAAAAGTTC
5334570 GATGGTGCAGACTTTGGCTTTTGGAAGATGCAGATTGAAGATTTTCTGTATCAGAAAAATCTATA
1 GATGGTGCAGACTTTGGCTTTTGGAAGATGCAGATTGAAGATTTTCTGTATCAGAAAAATCTATA
5334635 TCAACTCTTTCAGGAAAGCAACCAGAGGGCATGAAGAATGAAGACTGAGTTCTTCTCGACAGACA
66 TCAACTCTTTCAGGAAAGCAACCAGAGGGCATGAAGAATGAAGACTGAGTTCTTCTCGACAGACA
5334700 AGCCCTCGGAGTTATCCGACTGACGTTATCCCGCAATGTTGCTTTCAACATATCAAAGGAAAAGA
131 AGCCCTCGGAGTTATCCGACTGACGTTATCCCGCAATGTTGCTTTCAACATATCAAAGGAAAAGA
5334765 CCACGGCGGGTCTTATGACGGCTCTCTCCAGTTATGTATGAGAAGCCATCGGCCTC-AACAAAGT
196 CCACGGCGGGTCTTATGACGGCTCTCTCCAGTTATGTATGAGAAGCCATCGGCCTCAAACAAAGT
5334829 TCATTTGATGAG
261 TCATTTGATGAG
5334841 GATGGTGCAGACTTTGGCTTTTGGAAGATGCAGATTGAAGATTTTCTGTATCAGAAAAATCTATA
1 GATGGTGCAGACTTTGGCTTTTGGAAGATGCAGATTGAAGATTTTCTGTATCAGAAAAATCTATA
5334906 TCAACCTCTTTCAGGAAAGCAACCAGAGGGCATGAAGAATGAAGACTGAGTTCTTCTCGACAGAC
66 TCAA-CTCTTTCAGGAAAGCAACCAGAGGGCATGAAGAATGAAGACTGAGTTCTTCTCGACAGAC
5334971 AAGCCCTCGGAGTTATCCGACTGACGTTATCCCGCAATGTTGCTTTCAACATATCAAAGGAAAAG
130 AAGCCCTCGGAGTTATCCGACTGACGTTATCCCGCAATGTTGCTTTCAACATATCAAAGGAAAAG
5335036 ACCACGGCGGGTCTTATGACGGCTCTCTCCAG-TATGTATGAGAAGCCATCGGCCTCAAACAAAG
195 ACCACGGCGGGTCTTATGACGGCTCTCTCCAGTTATGTATGAGAAGCCATCGGCCTCAAACAAAG
5335100 TTCATTTGATGAG
260 TTCATTTGATGAG
5335113 G
1 G
5335114 CGATTATTCA
Statistics
Matches: 271, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
271 93 0.34
272 178 0.66
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (272 bp):
GATGGTGCAGACTTTGGCTTTTGGAAGATGCAGATTGAAGATTTTCTGTATCAGAAAAATCTATA
TCAACTCTTTCAGGAAAGCAACCAGAGGGCATGAAGAATGAAGACTGAGTTCTTCTCGACAGACA
AGCCCTCGGAGTTATCCGACTGACGTTATCCCGCAATGTTGCTTTCAACATATCAAAGGAAAAGA
CCACGGCGGGTCTTATGACGGCTCTCTCCAGTTATGTATGAGAAGCCATCGGCCTCAAACAAAGT
TCATTTGATGAG
Found at i:5346936 original size:5 final size:5
Alignment explanation
Indices: 5346926--5346962 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
5346916 AACGGTCAAC
*
5346926 GGTCG GGTCG GGTC- AGTCG GGTC- GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
5346963 AGACCGGTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
4 7 0.25
5 21 0.75
ACGTcount: A:0.03, C:0.22, G:0.54, T:0.22
Consensus pattern (5 bp):
GGTCG
Found at i:5346958 original size:9 final size:9
Alignment explanation
Indices: 5346926--5346959 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
5346916 AACGGTCAAC
5346926 GGTCGGGTCG
1 GGTC-GGTCG
*
5346936 GGTCAGTCG
1 GGTCGGTCG
5346945 GGTCGGTCG
1 GGTCGGTCG
5346954 GGTCGG
1 GGTCGG
5346960 GTCAGACCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 18 0.82
10 4 0.18
ACGTcount: A:0.03, C:0.21, G:0.56, T:0.21
Consensus pattern (9 bp):
GGTCGGTCG
Found at i:5346971 original size:23 final size:23
Alignment explanation
Indices: 5346925--5346971 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
5346915 CAACGGTCAA
* *
5346925 CGGTCGGGTCGGGTCAGTCGGGT
1 CGGTCGGGTCGGGTCAGACCGGT
5346948 CGGTCGGGTCGGGTCAGACCGGT
1 CGGTCGGGTCGGGTCAGACCGGT
5346971 C
1 C
5346972 ATACCGGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.06, C:0.26, G:0.49, T:0.19
Consensus pattern (23 bp):
CGGTCGGGTCGGGTCAGACCGGT
Found at i:5346983 original size:19 final size:18
Alignment explanation
Indices: 5346959--5347018 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 18
5346949 GGTCGGGTCG
*
5346959 GGTCAGACCGGTCATACC
1 GGTCAGACCGGTCAAACC
5346977 GGTTCAGACCGGTCGAAACC
1 GG-TCAGACCGGTC-AAACC
*
5346997 GGTCAAACCGGTCAGAACC
1 GGTCAGACCGGTCA-AACC
5347016 GGT
1 GGT
5347019 TTCCAGCAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
18 3 0.08
19 28 0.76
20 6 0.16
ACGTcount: A:0.25, C:0.30, G:0.30, T:0.15
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:5346989 original size:10 final size:9
Alignment explanation
Indices: 5346959--5347018 Score: 66
Period size: 9 Copynumber: 6.3 Consensus size: 9
5346949 GGTCGGGTCG
5346959 GGTCAGACC
1 GGTCAGACC
*
5346968 GGTCATACC
1 GGTCAGACC
5346977 GGTTCAGACC
1 GG-TCAGACC
*
5346987 GGTCGAAACC
1 GGTC-AGACC
*
5346997 GGTCAAACC
1 GGTCAGACC
5347006 GGTCAGAACC
1 GGTCAG-ACC
5347016 GGT
1 GGT
5347019 TTCCAGCAGC
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
9 22 0.50
10 22 0.50
ACGTcount: A:0.25, C:0.30, G:0.30, T:0.15
Consensus pattern (9 bp):
GGTCAGACC
Found at i:5350589 original size:42 final size:42
Alignment explanation
Indices: 5350524--5350651 Score: 150
Period size: 42 Copynumber: 3.0 Consensus size: 42
5350514 ATCATCATAT
* * *
5350524 TTGAACGAGAGTAAGTCGGTCGAAAGCTCGA-TCCGACAATTA
1 TTGAACGAGAGTAGGTCGTTCGAAAGCTCGAGT-CGACAATGA
* *
5350566 TTGAGCGAGAGTAGGTCGTTCGAAGGCTCGAGTCGACAATGA
1 TTGAACGAGAGTAGGTCGTTCGAAAGCTCGAGTCGACAATGA
* * * * *
5350608 TTGAAAGAGAGTAGGTCGTTCGAGAGATCAACTCGACAATGA
1 TTGAACGAGAGTAGGTCGTTCGAAAGCTCGAGTCGACAATGA
5350650 TT
1 TT
5350652 AGTCACATTG
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
42 72 0.99
43 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (42 bp):
TTGAACGAGAGTAGGTCGTTCGAAAGCTCGAGTCGACAATGA
Found at i:5360238 original size:2 final size:2
Alignment explanation
Indices: 5360231--5360259 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5360221 TTTTTAAAAC
5360231 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5360260 CCCCCATCCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5360455 original size:24 final size:24
Alignment explanation
Indices: 5360428--5360527 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
5360418 GATATCAAAA
*
5360428 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
5360452 ATCATAACAGAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
5360476 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
5360500 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
5360524 ATCA
1 ATCA
5360528 GATAAAATAT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:5360527 original size:48 final size:48
Alignment explanation
Indices: 5360421--5360529 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
5360411 AAACGGAGAT
* * * * *
5360421 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
5360469 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
5360517 ATCAGAAATCAGA
1 ATCAGAAATCAGA
5360530 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:5363009 original size:10 final size:9
Alignment explanation
Indices: 5362996--5363045 Score: 54
Period size: 10 Copynumber: 5.8 Consensus size: 9
5362986 GACAAAGTTT
5362996 TGGTCAACAG
1 TGGTCAAC-G
5363006 TGGTCAACG
1 TGGTCAACG
5363015 TCGGTCAACG
1 T-GGTCAACG
5363025 -GGTCAAC-
1 TGGTCAACG
5363032 -GGTCAACG
1 TGGTCAACG
5363040 -GGTCAA
1 TGGTCAA
5363046 TGGGTCGGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
7 7 0.18
8 13 0.34
9 2 0.05
10 16 0.42
ACGTcount: A:0.26, C:0.24, G:0.32, T:0.18
Consensus pattern (9 bp):
TGGTCAACG
Found at i:5363036 original size:15 final size:15
Alignment explanation
Indices: 5363016--5363045 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5363006 TGGTCAACGT
5363016 CGGTCAACGGGTCAA
1 CGGTCAACGGGTCAA
5363031 CGGTCAACGGGTCAA
1 CGGTCAACGGGTCAA
5363046 TGGGTCGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.33, T:0.13
Consensus pattern (15 bp):
CGGTCAACGGGTCAA
Found at i:5363037 original size:7 final size:8
Alignment explanation
Indices: 5362997--5363051 Score: 58
Period size: 8 Copynumber: 6.5 Consensus size: 8
5362987 ACAAAGTTTT
5362997 GGTCAACAG
1 GGTCAAC-G
5363006 TGGTCAACG
1 -GGTCAACG
5363015 TCGGTCAACG
1 --GGTCAACG
5363025 GGTCAAC-
1 GGTCAACG
5363032 GGTCAACG
1 GGTCAACG
*
5363040 GGTCAATG
1 GGTCAACG
5363048 GGTC
1 GGTC
5363052 GGGTCGGGTC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
7 7 0.17
8 18 0.44
9 1 0.02
10 15 0.37
ACGTcount: A:0.24, C:0.24, G:0.35, T:0.18
Consensus pattern (8 bp):
GGTCAACG
Found at i:5363064 original size:23 final size:23
Alignment explanation
Indices: 5363038--5363083 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
5363028 CAACGGTCAA
*
5363038 CGGGTCAATGGGTCGGGTCGGGT
1 CGGGTCAACGGGTCGGGTCGGGT
5363061 CGGGTCAACGGGTCGGGTCGGGT
1 CGGGTCAACGGGTCGGGTCGGGT
5363084 TATGACCGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.09, C:0.20, G:0.52, T:0.20
Consensus pattern (23 bp):
CGGGTCAACGGGTCGGGTCGGGT
Found at i:5365844 original size:2 final size:2
Alignment explanation
Indices: 5365837--5365875 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5365827 TCTAATCAAG
5365837 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5365876 TTAAAAACGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5366408 original size:106 final size:105
Alignment explanation
Indices: 5366224--5366433 Score: 339
Period size: 106 Copynumber: 2.0 Consensus size: 105
5366214 AGACAACATA
* * *
5366224 TTAACATCTAGCTCAAATTGTCGTTAATTTTTTATCGAAAAAGATGAATTTAGAACATGATGAAT
1 TTAACATCTAGCTCAAATTGCCGTTAATTTTTTATCAAAAAAGATGAATTTAGAACATAATGAAT
* *
5366289 AGTTGGGTGACCATTTTTTAACTTTTAGTAGTTGAAGGAT
66 AGTTGGGTGACCATTTTGTAACTTTTAATAGTTGAAGGAT
* * *
5366329 TTAACATCTAGTTCAAATTGCCGTTATTTTTTTTATCAAAAAAGATGAATTTGGAACATAATGAA
1 TTAACATCTAGCTCAAATTGCCGTTA-ATTTTTTATCAAAAAAGATGAATTTAGAACATAATGAA
5366394 TAGTTGGGTGACCATTTTGTAACTTTTAATAGTTGAAGGA
65 TAGTTGGGTGACCATTTTGTAACTTTTAATAGTTGAAGGA
5366434 CTCAGCAAAG
Statistics
Matches: 96, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
105 24 0.25
106 72 0.75
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.39
Consensus pattern (105 bp):
TTAACATCTAGCTCAAATTGCCGTTAATTTTTTATCAAAAAAGATGAATTTAGAACATAATGAAT
AGTTGGGTGACCATTTTGTAACTTTTAATAGTTGAAGGAT
Found at i:5367847 original size:13 final size:13
Alignment explanation
Indices: 5367829--5367860 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
5367819 TTGTATTTTA
*
5367829 TTCAATTTCGGTG
1 TTCAATTACGGTG
5367842 TTCAATTACGGTG
1 TTCAATTACGGTG
5367855 TTCAAT
1 TTCAAT
5367861 CCTCCTGAAT
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:0.22, C:0.16, G:0.19, T:0.44
Consensus pattern (13 bp):
TTCAATTACGGTG
Found at i:5371552 original size:2 final size:2
Alignment explanation
Indices: 5371547--5371589 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5371537 AAAACACATA
5371547 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
5371589 A
1 A
5371590 AAGTTTATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5379199 original size:60 final size:60
Alignment explanation
Indices: 5379030--5379214 Score: 194
Period size: 60 Copynumber: 3.1 Consensus size: 60
5379020 TAGTTACTTG
* * *
5379030 TTTTGACCAAAAATATAGTTTAGCGACTTAAAGCAAA-AAAGGGGCATAGTTTAGGGGCTTA
1 TTTTGACCAAAAA-ATAGTTTAGGGACTTAAAGCAAATAAA-GGGTATAGTTTAGGGGTTTA
* * * ** * ** * * *
5379091 CTTTGACCAAAAAATAGTTTAGGTACTTAAAGTAGTTACA-TATAATAGTTCAAGGATTTA
1 TTTTGACCAAAAAATAGTTTAGGGACTTAAAGCAAATAAAGGGT-ATAGTTTAGGGGTTTA
*
5379151 TTTTAACCAAAAAATAGTTTAGGGACTTAAAGCAAATAAAGGGTATAGTTTAGGGGTTTA
1 TTTTGACCAAAAAATAGTTTAGGGACTTAAAGCAAATAAAGGGTATAGTTTAGGGGTTTA
5379211 TTTT
1 TTTT
5379215 TAGTTTAAGC
Statistics
Matches: 95, Mismatches: 26, Indels: 7
0.74 0.20 0.05
Matches are distributed among these distances:
60 80 0.84
61 15 0.16
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.33
Consensus pattern (60 bp):
TTTTGACCAAAAAATAGTTTAGGGACTTAAAGCAAATAAAGGGTATAGTTTAGGGGTTTA
Found at i:5380159 original size:15 final size:15
Alignment explanation
Indices: 5380139--5380169 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5380129 CTTCTTGCTT
5380139 TTGTGTGCATGGAAA
1 TTGTGTGCATGGAAA
5380154 TTGTGTGCATGGAAA
1 TTGTGTGCATGGAAA
5380169 T
1 T
5380170 CAGAAGCAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.32, T:0.35
Consensus pattern (15 bp):
TTGTGTGCATGGAAA
Found at i:5397049 original size:324 final size:324
Alignment explanation
Indices: 5396454--5397052 Score: 947
Period size: 324 Copynumber: 1.8 Consensus size: 324
5396444 ATGTTCCTTA
*
5396454 ATAATTAATTCAAAACAAATTATTAAACGTTCAATAAAAGAATCATACTTTAAATATTGTTTCAA
1 ATAATTAATTCAAAACAAATTATTAAACGTTCAATAAAAGAATCATACTTTAAATATTGTTCCAA
* * *
5396519 TTTTACAATTTCCACCATCTACGATAATATATAAGTGACTAAGTATCAATTTTGGGCGATGTGTG
66 TTTTACAATGTCCACCATCTACAATAATATATAAGTGACTAAATATCAATTTTGGGCGATGTGTG
** * *
5396584 GGTGTTTATCCTTCCTCGCGTGTAATCGACTTCCGGATTCTTAAAAAATGAATTTTTGGTAAATG
131 GGTGTTTATCCTTCCTAACGTGTAATCGACTTCCGAATTCTTAAAAAATGAATTTTTGGTAAACG
*
5396649 CACACCAACTTTTATCTTTAAATGATTTTTTCCGAATTGATTAAAAGATATTTTTAGGTATTCGA
196 CACACCAACTTTTATCTTTAAATGATTTTTTCCAAATTGATTAAAAGATATTTTTAGGTATTCGA
5396714 TCTACCTAACCAAAAGGTCGATACTTTAAATATTGATTCAAATTTACAATTTCCACCAGTTATG
261 TCTACCTAACCAAAAGGTCGATACTTTAAATATTGATTCAAATTTACAATTTCCACCAGTTATG
5396778 ATAATTAATTCAAAACAAATTATTAAACGTTCAATAAAATG-ATCATACTTTAAATATTGATTCC
1 ATAATTAATTCAAAACAAATTATTAAACGTTCAATAAAA-GAATCATACTTTAAATATTG-TTCC
* * *
5396842 CA-TTTACAATGTCCACCAAT-TACAATAATATATAAGTGACTAAATATTAATTTTGGGCGTTGT
64 AATTTTACAATGTCCACC-ATCTACAATAATATATAAGTGACTAAATATCAATTTTGGGCGATGT
* ** *
5396905 G-GGGTGTTTATCCTTTCC-AACGTGTAATCGTCTTTTGAATTCTTAAAAAATGATTTTTTGGTA
128 GTGGGTGTTTATCC-TTCCTAACGTGTAATCGACTTCCGAATTCTTAAAAAATGAATTTTTGGTA
* *
5396968 AACGCATATCAACTTTTATCTTTTAAATGATTTTTTCCAAATTGATTAAAAGATATTTTTAGGTA
192 AACGCACACCAACTTTTATC-TTTAAATGATTTTTTCCAAATTGATTAAAAGATATTTTTAGGTA
*
5397033 TTCGATCTAGCTAACCAAAA
256 TTCGATCTACCTAACCAAAA
5397053 TGTTGATGAA
Statistics
Matches: 251, Mismatches: 19, Indels: 10
0.90 0.07 0.04
Matches are distributed among these distances:
323 67 0.27
324 177 0.71
325 7 0.03
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (324 bp):
ATAATTAATTCAAAACAAATTATTAAACGTTCAATAAAAGAATCATACTTTAAATATTGTTCCAA
TTTTACAATGTCCACCATCTACAATAATATATAAGTGACTAAATATCAATTTTGGGCGATGTGTG
GGTGTTTATCCTTCCTAACGTGTAATCGACTTCCGAATTCTTAAAAAATGAATTTTTGGTAAACG
CACACCAACTTTTATCTTTAAATGATTTTTTCCAAATTGATTAAAAGATATTTTTAGGTATTCGA
TCTACCTAACCAAAAGGTCGATACTTTAAATATTGATTCAAATTTACAATTTCCACCAGTTATG
Found at i:5406406 original size:18 final size:18
Alignment explanation
Indices: 5406383--5406589 Score: 136
Period size: 18 Copynumber: 11.2 Consensus size: 18
5406373 TTAAGAATTG
*
5406383 GATTTTAGGTTGTAATCA
1 GATTTTAGGTTGTAACCA
**
5406401 GATTTTAGGTTGTAAACTT
1 GATTTTAGGTTGT-AACCA
5406420 G-TTCTTAGGTTGTAACCA
1 GATT-TTAGGTTGTAACCA
5406438 GATTTTAGGTTGTAA-CA
1 GATTTTAGGTTGTAACCA
*
5406455 TGTTTTTAGGTTGTAACCA
1 -GATTTTAGGTTGTAACCA
* *
5406474 GATTTTAAGTTGTAA-TA
1 GATTTTAGGTTGTAACCA
*
5406491 TGTTTTTAGGTTGTAACC-
1 -GATTTTAGGTTGTAACCA
* * *
5406509 GAATGTTAGGTTGCAAACA
1 G-ATTTTAGGTTGTAACCA
* ** **
5406528 TGTTTTTATATTGTAAATA
1 -GATTTTAGGTTGTAACCA
**
5406547 GGATTTTAGCCTGTAAACCTA
1 -GATTTTAGGTTGT-AACC-A
5406568 -ATTTTAGGTTGTCAACCA
1 GATTTTAGGTTGT-AACCA
5406586 GATT
1 GATT
5406590 GTAGATTGAA
Statistics
Matches: 144, Mismatches: 32, Indels: 25
0.72 0.16 0.12
Matches are distributed among these distances:
17 4 0.03
18 83 0.58
19 53 0.37
20 3 0.02
21 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.43
Consensus pattern (18 bp):
GATTTTAGGTTGTAACCA
Found at i:5406471 original size:36 final size:36
Alignment explanation
Indices: 5406385--5406589 Score: 205
Period size: 36 Copynumber: 5.6 Consensus size: 36
5406375 AAGAATTGGA
* *
5406385 TTTTAGGTTGTAATCAGATTTTAGGTTGTAAACTTGT
1 TTTTAGGTTGTAACCAGATTTTAGGTTGT-AACATGT
*
5406422 TCTTAGGTTGTAACCAGATTTTAGGTTGTAACATGT
1 TTTTAGGTTGTAACCAGATTTTAGGTTGTAACATGT
* *
5406458 TTTTAGGTTGTAACCAGATTTTAAGTTGTAATATGT
1 TTTTAGGTTGTAACCAGATTTTAGGTTGTAACATGT
* *
5406494 TTTTAGGTTGTAACC-GAATGTTAGGTTGCAAACATGT
1 TTTTAGGTTGTAACCAG-ATTTTAGGTTG-TAACATGT
** ** ** * **
5406531 TTTTATATTGTAAATAGGATTTTAGCCTGTAAACCTAA
1 TTTTAGGTTGTAACCA-GATTTTAGGTTGT-AACATGT
5406569 TTTTAGGTTGTCAACCAGATT
1 TTTTAGGTTGT-AACCAGATT
5406590 GTAGATTGAA
Statistics
Matches: 137, Mismatches: 25, Indels: 11
0.79 0.14 0.06
Matches are distributed among these distances:
35 1 0.01
36 63 0.46
37 44 0.32
38 25 0.18
39 4 0.03
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.43
Consensus pattern (36 bp):
TTTTAGGTTGTAACCAGATTTTAGGTTGTAACATGT
Found at i:5415107 original size:20 final size:21
Alignment explanation
Indices: 5415068--5415128 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 21
5415058 TTTTGGTGCA
* *
5415068 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCTTT
*
5415088 GAGGGAACCGATTCCTCCTTT
1 GAGGGAACCGATTCCCCCTTT
5415109 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
5415129 CACAGGGGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 10 0.29
21 8 0.24
22 1 0.03
23 15 0.44
ACGTcount: A:0.21, C:0.33, G:0.26, T:0.20
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCTTT
Found at i:5420879 original size:20 final size:23
Alignment explanation
Indices: 5420838--5420885 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
5420828 TCTCTCTTAA
5420838 GATACACATTATTAAGGAGTACT
1 GATACACATTATTAAGGAGTACT
5420861 -ATACACATTATT-A-GAGTACT
1 GATACACATTATTAAGGAGTACT
5420881 GATAC
1 GATAC
5420886 TTTTGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.29
21 5 0.21
22 12 0.50
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (23 bp):
GATACACATTATTAAGGAGTACT
Found at i:5421549 original size:39 final size:40
Alignment explanation
Indices: 5421494--5421576 Score: 107
Period size: 39 Copynumber: 2.1 Consensus size: 40
5421484 GAACTGAATT
* * *
5421494 TTTTTCTTCTCGAATTTGTTATACCCACAGAATCA-AACTC
1 TTTTTCTTCTCAAATTTGTTATACCCAAAAAAT-AGAACTC
*
5421534 TTTTT-TTCTCAAATTTGTTATGCCCAAAAAATAGAACTC
1 TTTTTCTTCTCAAATTTGTTATACCCAAAAAATAGAACTC
5421573 TTTT
1 TTTT
5421577 ATGCTTTCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 1 0.03
39 32 0.84
40 5 0.13
ACGTcount: A:0.29, C:0.20, G:0.07, T:0.43
Consensus pattern (40 bp):
TTTTTCTTCTCAAATTTGTTATACCCAAAAAATAGAACTC
Found at i:5422407 original size:8 final size:8
Alignment explanation
Indices: 5422384--5422465 Score: 65
Period size: 8 Copynumber: 10.2 Consensus size: 8
5422374 TAGGAGCCAT
*
5422384 TTTGAGAA
1 TTTGAGAG
5422392 TTTGAGAG
1 TTTGAGAG
5422400 TTTGAGAG
1 TTTGAGAG
** *
5422408 AGTGATAG
1 TTTGAGAG
* *
5422416 TTTCAAAG
1 TTTGAGAG
*
5422424 TTAGAGAG
1 TTTGAGAG
*
5422432 TTTGAGAA
1 TTTGAGAG
*
5422440 TTTAAGAG
1 TTTGAGAG
*
5422448 TTTAAGAG
1 TTTGAGAG
*
5422456 ATTGAGAG
1 TTTGAGAG
5422464 TT
1 TT
5422466 AGGGAACTAT
Statistics
Matches: 56, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
8 56 1.00
ACGTcount: A:0.34, C:0.01, G:0.29, T:0.35
Consensus pattern (8 bp):
TTTGAGAG
Found at i:5429969 original size:17 final size:17
Alignment explanation
Indices: 5429947--5429984 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
5429937 TCTCTGTGCT
5429947 TATTTT-CAAAATCAAAA
1 TATTTTCCAAAATC-AAA
5429964 TATTTTCCAAAATCAAA
1 TATTTTCCAAAATCAAA
5429981 TATT
1 TATT
5429985 GACTTTGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.39
Consensus pattern (17 bp):
TATTTTCCAAAATCAAA
Found at i:5430864 original size:9 final size:9
Alignment explanation
Indices: 5430850--5430891 Score: 57
Period size: 9 Copynumber: 4.4 Consensus size: 9
5430840 CAGGAGTGAG
5430850 AGAAAAAGA
1 AGAAAAAGA
5430859 AGAAAAAGA
1 AGAAAAAGA
5430868 AGAAGAAAGGA
1 AGAA-AAA-GA
*
5430879 AGAAGAAGA
1 AGAAAAAGA
5430888 AGAA
1 AGAA
5430892 CGAGGGTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 19 0.63
10 5 0.17
11 6 0.20
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (9 bp):
AGAAAAAGA
Found at i:5430870 original size:3 final size:3
Alignment explanation
Indices: 5430850--5430891 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
5430840 CAGGAGTGAG
* * *
5430850 AGA AAA AGA AGA AAA AGA AGA AGA A-A GGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
5430892 CGAGGGTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 1 0.03
3 31 0.97
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:5432730 original size:14 final size:15
Alignment explanation
Indices: 5432711--5432739 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5432701 TTGCAGCAAC
5432711 AACAAAA-AGTTACA
1 AACAAAATAGTTACA
5432725 AACAAAATAGTTACA
1 AACAAAATAGTTACA
5432740 GTAGTTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.62, C:0.14, G:0.07, T:0.17
Consensus pattern (15 bp):
AACAAAATAGTTACA
Found at i:5435013 original size:22 final size:23
Alignment explanation
Indices: 5434988--5435034 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
5434978 ATAAAGTACA
*
5434988 ATAACATACTA-GTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
5435010 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
5435033 AT
1 AT
5435035 TTACCTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:5436107 original size:20 final size:19
Alignment explanation
Indices: 5436082--5436150 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 19
5436072 GATAGACACT
*
5436082 TTACATATAACCACTACCTA
1 TTACATATAA-AACTACCTA
5436102 TTACATTATATAAACGATACCTA
1 TTACA-TATA-AAAC--TACCTA
**
5436125 TTACATATAAGTGCTACCTA
1 TTACATATAA-AACTACCTA
5436145 TTACAT
1 TTACAT
5436151 CATATGTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
20 17 0.41
21 7 0.17
22 6 0.15
23 11 0.27
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (19 bp):
TTACATATAAAACTACCTA
Found at i:5436114 original size:23 final size:23
Alignment explanation
Indices: 5436086--5436130 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5436076 GACACTTTAC
5436086 ATAT-AACCACTACCTATTACATT
1 ATATAAACCA-TACCTATTACATT
*
5436109 ATATAAACGATACCTATTACAT
1 ATATAAACCATACCTATTACAT
5436131 ATAAGTGCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.42, C:0.22, G:0.02, T:0.33
Consensus pattern (23 bp):
ATATAAACCATACCTATTACATT
Found at i:5436593 original size:37 final size:38
Alignment explanation
Indices: 5436543--5436627 Score: 136
Period size: 37 Copynumber: 2.2 Consensus size: 38
5436533 TCAAGTTGTA
*
5436543 GATTTTGATTTCCTTTTGCTTGGCATC-ATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCAATGAGATTTG
*
5436580 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCA-ATGAGATTTG
5436619 GATTTTGAT
1 GATTTTGAT
5436628 GAGCATCGGA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
37 26 0.59
39 18 0.41
ACGTcount: A:0.16, C:0.14, G:0.21, T:0.48
Consensus pattern (38 bp):
GATTTTGATTTCCTTTTGCTTGGCACCAATGAGATTTG
Found at i:5436909 original size:18 final size:18
Alignment explanation
Indices: 5436886--5436922 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5436876 CGAAATATAT
5436886 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
5436904 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
5436922 A
1 A
5436923 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:5437586 original size:23 final size:23
Alignment explanation
Indices: 5437560--5437622 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
5437550 ATATAACCAC
5437560 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* **
5437583 TACCTATTACATTACATAAGGGA
1 TACCTATTACATTATATAAACGA
*
5437606 TACCTATTACATCATAT
1 TACCTATTACATTATAT
5437623 GTTTACCTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:5439834 original size:183 final size:183
Alignment explanation
Indices: 5439493--5439835 Score: 589
Period size: 183 Copynumber: 1.9 Consensus size: 183
5439483 TTAAAATTAC
* *
5439493 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
* *
5439558 ATTATAAAGTGTCGATATAGGTTGTAGACATATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACATATTCGCGCATAAAACCGGTATATTTATACCAGTT
*
5439623 ATATTACCAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACCAAATTACCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
5439676 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
*
5439741 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCAGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACATATTCGCGCATAAAACCGGTATATTTATACCAGTT
* **
5439806 ATATT-GCAAATTTACCTATTTTATTATAAT
131 ATATTACCAAA-TTACCTATTACATTATAAT
5439836 ATGTTGAAAG
Statistics
Matches: 150, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
182 4 0.03
183 146 0.97
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.36
Consensus pattern (183 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACATATTCGCGCATAAAACCGGTATATTTATACCAGTT
ATATTACCAAATTACCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
Found at i:5441261 original size:3 final size:3
Alignment explanation
Indices: 5441253--5441306 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
5441243 ACTTGTTTGG
* * *
5441253 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC ATC GTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
*
5441301 TTC ATC
1 ATC ATC
5441307 GTCAGCTTCA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.26, C:0.33, G:0.04, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:5441270 original size:12 final size:12
Alignment explanation
Indices: 5441253--5441310 Score: 80
Period size: 12 Copynumber: 4.8 Consensus size: 12
5441243 ACTTGTTTGG
* *
5441253 ATCATCATCTTC
1 ATCATCGTCATC
*
5441265 ATCATCATCATC
1 ATCATCGTCATC
5441277 ATCATCGTCATC
1 ATCATCGTCATC
5441289 ATCATCGTCATC
1 ATCATCGTCATC
*
5441301 TTCATCGTCA
1 ATCATCGTCA
5441311 GCTTCATCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.26, C:0.33, G:0.05, T:0.36
Consensus pattern (12 bp):
ATCATCGTCATC
Found at i:5441276 original size:18 final size:18
Alignment explanation
Indices: 5441253--5441321 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
5441243 ACTTGTTTGG
* *
5441253 ATCATCATCTTCATCATC
1 ATCATCATCATCTTCATC
*
5441271 ATCATCATCATCGTCATC
1 ATCATCATCATCTTCATC
*
5441289 ATCATCGTCATCTTCATC
1 ATCATCATCATCTTCATC
* * *
5441307 GTCAGCTTCATCTTC
1 ATCATCATCATCTTC
5441322 TGCGACCGCT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.23, C:0.33, G:0.06, T:0.38
Consensus pattern (18 bp):
ATCATCATCATCTTCATC
Found at i:5441315 original size:12 final size:12
Alignment explanation
Indices: 5441266--5441318 Score: 70
Period size: 12 Copynumber: 4.4 Consensus size: 12
5441256 ATCATCTTCA
* *
5441266 TCATCATCATCA
1 TCATCGTCATCT
*
5441278 TCATCGTCATCA
1 TCATCGTCATCT
5441290 TCATCGTCATCT
1 TCATCGTCATCT
*
5441302 TCATCGTCAGCT
1 TCATCGTCATCT
5441314 TCATC
1 TCATC
5441319 TTCTGCGACC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.23, C:0.34, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:5443705 original size:199 final size:198
Alignment explanation
Indices: 5442778--5443897 Score: 2150
Period size: 198 Copynumber: 5.6 Consensus size: 198
5442768 TTTAAATTAG
*
5442778 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACTGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
**
5442843 ATTGTACCGGAAAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
5442908 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTATGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
5442973 AAA
196 AAA
* *
5442976 TATCGACACAAACTATATTAGTGTAGACACGTTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
5443041 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
5443106 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
5443171 AAA
196 AAA
5443174 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
5443239 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
5443304 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
5443369 AAA
196 AAA
*
5443372 TATCGAAACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
5443437 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
5443502 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
5443567 AAAA
195 AAAA
5443571 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
5443636 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
5443701 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
5443766 AAAA
195 AAAA
5443770 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
5443835 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTAAACTTTTGGGTTCGATGATTTTGGG
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
5443898 TACCTAAAAT
Statistics
Matches: 910, Mismatches: 11, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
198 578 0.64
199 332 0.36
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (198 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAA
Found at i:5444708 original size:3 final size:3
Alignment explanation
Indices: 5444700--5444753 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
5444690 ACTTGTTTGG
* * *
5444700 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC ATC GTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
*
5444748 TTC ATC
1 ATC ATC
5444754 GTCAGCTTCA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.26, C:0.33, G:0.04, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:5444717 original size:12 final size:12
Alignment explanation
Indices: 5444700--5444757 Score: 80
Period size: 12 Copynumber: 4.8 Consensus size: 12
5444690 ACTTGTTTGG
* *
5444700 ATCATCATCTTC
1 ATCATCGTCATC
*
5444712 ATCATCATCATC
1 ATCATCGTCATC
5444724 ATCATCGTCATC
1 ATCATCGTCATC
5444736 ATCATCGTCATC
1 ATCATCGTCATC
*
5444748 TTCATCGTCA
1 ATCATCGTCA
5444758 GCTTCATCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.26, C:0.33, G:0.05, T:0.36
Consensus pattern (12 bp):
ATCATCGTCATC
Found at i:5444723 original size:18 final size:18
Alignment explanation
Indices: 5444700--5444768 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
5444690 ACTTGTTTGG
* *
5444700 ATCATCATCTTCATCATC
1 ATCATCATCATCTTCATC
*
5444718 ATCATCATCATCGTCATC
1 ATCATCATCATCTTCATC
*
5444736 ATCATCGTCATCTTCATC
1 ATCATCATCATCTTCATC
* * *
5444754 GTCAGCTTCATCTTC
1 ATCATCATCATCTTC
5444769 TGCGACCGCT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.23, C:0.33, G:0.06, T:0.38
Consensus pattern (18 bp):
ATCATCATCATCTTCATC
Found at i:5444762 original size:12 final size:12
Alignment explanation
Indices: 5444713--5444765 Score: 70
Period size: 12 Copynumber: 4.4 Consensus size: 12
5444703 ATCATCTTCA
* *
5444713 TCATCATCATCA
1 TCATCGTCATCT
*
5444725 TCATCGTCATCA
1 TCATCGTCATCT
5444737 TCATCGTCATCT
1 TCATCGTCATCT
*
5444749 TCATCGTCAGCT
1 TCATCGTCATCT
5444761 TCATC
1 TCATC
5444766 TTCTGCGACC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.23, C:0.34, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:5446953 original size:198 final size:199
Alignment explanation
Indices: 5446226--5447346 Score: 2176
Period size: 199 Copynumber: 5.6 Consensus size: 199
5446216 TTTAAATTAG
*
5446226 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACTGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
**
5446291 ATTGTACCGGAAAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
5446356 CGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
5446419 AAAA
196 AAAA
5446423 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
5446488 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
5446553 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
5446618 AAAA
196 AAAA
5446622 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
5446687 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
5446752 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
5446816 AAAA
196 AAAA
5446820 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
5446885 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
5446950 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
5447015 AAAAA
195 AAAAA
5447020 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
5447085 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
5447150 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
5447215 AAAA
196 AAAA
5447219 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
5447284 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTAAACTTTTGGGTTCGATGATTTTGGG
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
5447347 GACCTAAAAT
Statistics
Matches: 916, Mismatches: 4, Indels: 6
0.99 0.00 0.01
Matches are distributed among these distances:
197 133 0.15
198 252 0.28
199 333 0.36
200 198 0.22
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAAA
Found at i:5448121 original size:3 final size:3
Alignment explanation
Indices: 5448113--5448181 Score: 66
Period size: 3 Copynumber: 23.0 Consensus size: 3
5448103 ACTTGTTTGG
* * * *
5448113 ATC ATC ATC TTC ATC ATC ATC ATC ATC GTC GTC ATC ATC ATC GTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * *
5448161 TTC ATC GTC AGC TTC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC
5448182 TGCGACCGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.23, C:0.33, G:0.07, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:5449979 original size:198 final size:198
Alignment explanation
Indices: 5449641--5451004 Score: 2617
Period size: 198 Copynumber: 6.9 Consensus size: 198
5449631 TTTAAATTAG
*
5449641 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACTGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
**
5449706 ATTGTACCGGAAAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
5449771 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
5449836 AAA
196 AAA
5449839 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
5449904 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
5449969 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
5450034 AAAA
195 AAAA
5450038 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
5450103 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
5450168 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTT-CATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
5450232 AAA
196 AAA
*
5450235 TATCGACACAAACTATATTAGTGTCGATACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
5450300 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
5450365 CGACAC-TTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
5450428 AAAA
195 AAAA
5450432 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
5450497 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
5450562 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACTCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
5450627 AAA
196 AAA
5450630 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
5450695 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTAAACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
5450760 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
5450825 AAA
196 AAA
5450828 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
5450893 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTAAACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
5450958 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
5451005 GGCCATATTG
Statistics
Matches: 1152, Mismatches: 8, Indels: 11
0.98 0.01 0.01
Matches are distributed among these distances:
195 36 0.03
196 16 0.01
197 284 0.25
198 543 0.47
199 273 0.24
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (198 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAA
Found at i:5450845 original size:593 final size:594
Alignment explanation
Indices: 5449641--5451004 Score: 2617
Period size: 593 Copynumber: 2.3 Consensus size: 594
5449631 TTTAAATTAG
*
5449641 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACTGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
**
5449706 ATTGTACCGGAAAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
5449771 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
5449836 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGT
196 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGT
5449901 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
261 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
5449966 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGA
326 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGA
5450031 AAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAAC
391 AAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAAC
*
5450096 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
456 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTAAACTTTTGGGTTCGATGATT
5450161 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCATTCATTCT
521 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCATTCATTCT
5450226 GGAAAAAAA
586 GGAAAAAAA
*
5450235 TATCGACACAAACTATATTAGTGTCGATACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
5450300 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
5450365 CGACAC-TTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
5450428 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
195 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
5450493 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
260 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
*
5450558 GGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACTCTGTTTTCCATTCATTCTGG
325 GGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG
5450623 -AAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAA
390 AAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAA
5450687 CCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTAAACTTTTGGGTTCGATGAT
455 CCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTAAACTTTTGGGTTCGATGAT
5450752 TTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATT
520 TTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTT-CATTCATT
5450817 CTGGAAAAAAA
584 CTGGAAAAAAA
5450828 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
5450893 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTAAACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
5450958 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
5451005 GGCCATATTG
Statistics
Matches: 757, Mismatches: 8, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
592 233 0.31
593 354 0.47
594 132 0.17
595 4 0.01
596 34 0.04
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (594 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGT
ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGA
AAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAAC
CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTAAACTTTTGGGTTCGATGATT
TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCATTCATTCT
GGAAAAAAA
Found at i:5451155 original size:19 final size:19
Alignment explanation
Indices: 5451123--5451170 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
5451113 TTATATTCAC
5451123 ATACAAAA-TATAAATCGT
1 ATACAAAATTATAAATCGT
*
5451141 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
5451160 ATACAAAATTA
1 ATACAAAATTA
5451171 ACCCTACATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:5453003 original size:33 final size:33
Alignment explanation
Indices: 5452966--5453031 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
5452956 CATCTTAATA
*
5452966 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
5452999 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
5453032 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:5455370 original size:17 final size:18
Alignment explanation
Indices: 5455348--5455390 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
5455338 ATATATCCGG
5455348 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
5455365 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
5455385 TATCAT
1 TATCAT
5455391 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:5455408 original size:20 final size:19
Alignment explanation
Indices: 5455353--5455399 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
5455343 TCCGGTATCA
5455353 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
5455372 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
5455393 TTTTACC
1 TTTTACC
5455400 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:5455545 original size:19 final size:19
Alignment explanation
Indices: 5455521--5455578 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
5455511 ACTTTTAAAT
5455521 TTACCGGTTTATCATTTTG
1 TTACCGGTTTATCATTTTG
*
5455540 TTACCGGTTTTATCATATT-
1 TTACCGG-TTTATCATTTTG
* *
5455559 TTACCTGGTATATCGTTTTG
1 TTACC-GGTTTATCATTTTG
5455579 GATCGATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
19 20 0.62
20 12 0.38
ACGTcount: A:0.17, C:0.16, G:0.16, T:0.52
Consensus pattern (19 bp):
TTACCGGTTTATCATTTTG
Found at i:5462195 original size:38 final size:39
Alignment explanation
Indices: 5462153--5462226 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
5462143 AAAATACATG
*
5462153 CATATTTGATTTGTAAC-ATAATTTAGAGTTAATTATAT
1 CATATTTGATTCGTAACAATAATTTAGAGTTAATTATAT
5462191 CATATTTGATTCGTAACAATAATTTAGAGTTAATTA
1 CATATTTGATTCGTAACAATAATTTAGAGTTAATTA
5462227 ATTCTTAAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
38 16 0.47
39 18 0.53
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.45
Consensus pattern (39 bp):
CATATTTGATTCGTAACAATAATTTAGAGTTAATTATAT
Found at i:5464524 original size:23 final size:23
Alignment explanation
Indices: 5464498--5464545 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
5464488 ATAAAGTACA
*
5464498 ATAACATACTAGGTAGAGCTTAT
1 ATAACATAATAGGTAGAGCTTAT
** *
5464521 ATAATGTAATAGGTAGTGCTTAT
1 ATAACATAATAGGTAGAGCTTAT
5464544 AT
1 AT
5464546 TTACCTAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGAGCTTAT
Found at i:5464996 original size:23 final size:23
Alignment explanation
Indices: 5464970--5465032 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
5464960 ATATAACCAC
5464970 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
5464993 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
5465016 TACCTATTACATCATAT
1 TACCTATTACATTATAT
5465033 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:5465208 original size:22 final size:22
Alignment explanation
Indices: 5465178--5465219 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5465168 TCATTTGCAC
5465178 AAAAAATTATTT-GATATTTTAT
1 AAAAAATTATTTAGA-ATTTTAT
*
5465200 AAAATATTATTTAGAATTTT
1 AAAAAATTATTTAGAATTTT
5465220 TAATTTAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (22 bp):
AAAAAATTATTTAGAATTTTAT
Found at i:5465422 original size:23 final size:23
Alignment explanation
Indices: 5465396--5465458 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
5465386 ATATAACCAC
5465396 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
5465419 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
5465442 TACCTATTACATCATAT
1 TACCTATTACATTATAT
5465459 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:5465601 original size:425 final size:426
Alignment explanation
Indices: 5464619--5465668 Score: 1887
Period size: 426 Copynumber: 2.4 Consensus size: 426
5464609 TTATAATATG
5464619 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
*
5464684 TCAATTTTTTGAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
66 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
*
5464749 AAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA-TA-A-T
131 -AAAAA--A--T-ATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAACAACATT
*
5464811 -AATATATATCGTAATGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATCTTAA
190 AAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATCTTAA
5464875 AACTCACTCAAAAGATAACCTTAAATTAATGTTTTCAACAGTGAAAAAGTATGGACACTTTTATA
255 AACTCACTCAAAAGATAACCTTAAATTAATGTTTTCAACAGTGAAAAAGTATGGACACTTTTATA
*
5464940 AAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACAT
320 AAAAAGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACAT
5465005 TATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
385 TATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
5465047 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
5465112 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
5465177 C-AAAAA-ATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAACAACATTAAATA
130 CAAAAAATATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAACAACATTAAATA
5465240 TATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATCTTAAAACTC
195 TATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATCTTAAAACTC
*
5465305 ACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAA
260 ACTCAAAAGATAACCTTAAATTAATGTTTTCAACAGTG-AAAAAGTATGGACACTTTTATAAAAA
5465370 AGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTATA
324 AGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTATA
5465435 TAAGCGCTACCTATTACATCATATTTTTACCTATTATA
389 TAAGCGCTACCTATTACATCATATTTTTACCTATTATA
*
5465473 TTGAAAGTGTCCATACCTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
5465538 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
66 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
5465603 AAAAAATTATTTGATTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAACAACATTA
131 AAAAAA-TA-TT-A--TTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAACAACATTA
5465668 A
191 A
5465669 CCAAAGATAA
Statistics
Matches: 603, Mismatches: 6, Indels: 22
0.96 0.01 0.03
Matches are distributed among these distances:
421 45 0.07
422 1 0.00
423 1 0.00
424 1 0.00
425 167 0.28
426 201 0.33
427 4 0.01
428 70 0.12
429 62 0.10
430 1 0.00
432 50 0.08
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (426 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
AAAAAATATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAACAACATTAAATAT
ATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATCTTAAAACTCA
CTCAAAAGATAACCTTAAATTAATGTTTTCAACAGTGAAAAAGTATGGACACTTTTATAAAAAAG
ATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTATATA
AGCGCTACCTATTACATCATATTTTTACCTATTATA
Found at i:5465933 original size:39 final size:39
Alignment explanation
Indices: 5465879--5465964 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
5465869 CAAGTTGTAG
*
5465879 ATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGA
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
* *
5465918 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGG
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
5465957 ATTTTGAT
1 ATTTTGAT
5465965 GAGCATCGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.49
Consensus pattern (39 bp):
ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
Found at i:5466244 original size:18 final size:18
Alignment explanation
Indices: 5466221--5466257 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5466211 CGAAATATAT
5466221 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
5466239 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
5466257 A
1 A
5466258 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:5466719 original size:23 final size:23
Alignment explanation
Indices: 5466689--5466742 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
5466679 TTTACAATAT
* * *
5466689 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAACGATACATATTAC
5466712 ATTATATAAACGATACATATTAC
1 ATTATATAAACGATACATATTAC
5466735 ATTATATA
1 ATTATATA
5466743 CTTGTAGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.37
Consensus pattern (23 bp):
ATTATATAAACGATACATATTAC
Found at i:5469060 original size:198 final size:198
Alignment explanation
Indices: 5468723--5470250 Score: 2936
Period size: 198 Copynumber: 7.7 Consensus size: 198
5468713 GATTATGTTG
*
5468723 GGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGG-AAATAAATATCGACACAAACT
1 GGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACT
*
5468787 ATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACTGGTTAG
66 ATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTTAG
5468852 ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATA
131 ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATA
5468917 TAT
196 TAT
5468920 GGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACT
1 GGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACT
*
5468985 ATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCAGTATAATTGTACCGGTTAG
66 ATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTTAG
5469050 ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATA
131 ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATA
5469115 TAT
196 TAT
*
5469118 GGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGG-AAATAAATATCGACACAAACT
1 GGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACT
*
5469182 ATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTTAT
66 ATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTTAG
* *
5469247 ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATTATGTTGGGATCGACACTTTTTATA
131 ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATA
5469312 TAT
196 TAT
*
5469315 GGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGG-AAATAAATATCGACACAAACT
1 GGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACT
5469379 ATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTTAG
66 ATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTTAG
5469444 ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATA
131 ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATA
5469509 TAT
196 TAT
*
5469512 GGATCAACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACT
1 GGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACT
5469577 ATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTTAG
66 ATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTTAG
*
5469642 ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGATACTTTTTATA
131 ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATA
5469707 TAT
196 TAT
*
5469710 AGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACT
1 GGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACT
5469775 ATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTTAG
66 ATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTTAG
5469840 ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATA
131 ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATA
5469905 TAT
196 TAT
5469908 GGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACT
1 GGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACT
5469973 ATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTTAG
66 ATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTTAG
5470038 ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATA
131 ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATA
5470103 TAT
196 TAT
5470106 GGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACT
1 GGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACT
5470171 ATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTTAG
66 ATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTTAG
5470236 ATTGAAAAATTACAT
131 ATTGAAAAATTACAT
5470251 CCTTTTGGCC
Statistics
Matches: 1311, Mismatches: 18, Indels: 3
0.98 0.01 0.00
Matches are distributed among these distances:
197 428 0.33
198 883 0.67
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (198 bp):
GGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACT
ATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTTAG
ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATA
TAT
Found at i:5469702 original size:15 final size:15
Alignment explanation
Indices: 5469665--5469702 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
5469655 ATATTACATT
*
5469665 ATACTTTTGGGTTCG
1 ATACTTTTGGGATCG
5469680 ATGA-TTTTGGGATCG
1 AT-ACTTTTGGGATCG
5469695 ATACTTTT
1 ATACTTTT
5469703 TATATATAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
14 1 0.05
15 18 0.90
16 1 0.05
ACGTcount: A:0.18, C:0.11, G:0.24, T:0.47
Consensus pattern (15 bp):
ATACTTTTGGGATCG
Found at i:5469723 original size:592 final size:593
Alignment explanation
Indices: 5468723--5470250 Score: 2950
Period size: 592 Copynumber: 2.6 Consensus size: 593
5468713 GATTATGTTG
5468723 GGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATAAATATCGACACAAACTA
1 GGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATAAATATCGACACAAACTA
*
5468788 TATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACTGGTTAGA
66 TATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTTAGA
5468853 TTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATAT
131 TTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATAT
5468918 ATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAA
196 ATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAA
*
5468983 CTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCAGTATAATTGTACCGGTT
261 CTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTT
5469048 AGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTA
326 AGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTA
* *
5469113 TATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGG-AAATAAATATCGACAC
391 TATATAGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACAC
5469177 AAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCG
456 AAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCG
* *
5469242 GTTATATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATTATGTTGGGATCGACACTTT
521 GTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATGTTGGGATCGACACTTT
5469307 TTATATAT
586 TTATATAT
5469315 GGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATAAATATCGACACAAACTA
1 GGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATAAATATCGACACAAACTA
5469380 TATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTTAGA
66 TATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTTAGA
5469445 TTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATAT
131 TTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATAT
*
5469510 ATGGATCAACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAA
196 ATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAA
5469575 CTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTT
261 CTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTT
*
5469640 AGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGATACTTTTTA
326 AGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTA
5469705 TATATAGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACAC
391 TATATAGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACAC
5469770 AAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCG
456 AAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCG
*
5469835 GTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTT
521 GTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATGTTGGGATCGACACTTT
5469900 TTATATAT
586 TTATATAT
*
5469908 GGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACT
1 GGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGG-AAATAAATATCGACACAAACT
5469973 ATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTTAG
65 ATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTTAG
5470038 ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATA
130 ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATA
5470103 TATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAA
195 TATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAA
5470168 ACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGT
260 ACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGT
5470233 TAGATTGAAAAATTACAT
325 TAGATTGAAAAATTACAT
5470251 CCTTTTGGCC
Statistics
Matches: 923, Mismatches: 11, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
592 433 0.47
593 193 0.21
594 297 0.32
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (593 bp):
GGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATAAATATCGACACAAACTA
TATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTTAGA
TTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATAT
ATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAA
CTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCGGTT
AGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTA
TATATAGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACAC
AAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATAATTGTACCG
GTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATGTTGGGATCGACACTTT
TTATATAT
Found at i:5470406 original size:19 final size:19
Alignment explanation
Indices: 5470375--5470423 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
5470365 TTATATTCAC
5470375 ATACGAAAA-TATAAATCGT
1 ATAC-AAAATTATAAATCGT
*
5470394 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
5470413 ATACAAAATTA
1 ATACAAAATTA
5470424 ACCCTACATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.55, C:0.10, G:0.04, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:5472252 original size:33 final size:33
Alignment explanation
Indices: 5472215--5472280 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
5472205 CATCTTAATA
*
5472215 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
5472248 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
5472281 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:5472354 original size:21 final size:21
Alignment explanation
Indices: 5472314--5472378 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
5472304 CACCTTATGC
* *
5472314 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
5472335 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
5472356 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
5472377 CT
1 CT
5472379 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:5474631 original size:17 final size:18
Alignment explanation
Indices: 5474609--5474651 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
5474599 ATATATCCGG
5474609 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
5474626 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
5474646 TATCAT
1 TATCAT
5474652 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:5474669 original size:20 final size:19
Alignment explanation
Indices: 5474614--5474660 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
5474604 TCCGGTATCA
5474614 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
5474633 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
5474654 TTTTACC
1 TTTTACC
5474661 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:5474808 original size:20 final size:20
Alignment explanation
Indices: 5474782--5474827 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
5474772 CACTTTTAAA
5474782 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
5474801 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
5474822 TTTACC
1 TTTACC
5474828 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:5478383 original size:2 final size:2
Alignment explanation
Indices: 5478376--5478401 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5478366 TGAAAAGGAC
5478376 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
5478402 AAGAAAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5480546 original size:16 final size:17
Alignment explanation
Indices: 5480519--5480552 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5480509 GTTTATCATA
*
5480519 ATTAATTAAGAATAGAG
1 ATTAATTAAGAAAAGAG
5480536 ATTAA-TAAGAAAAGAG
1 ATTAATTAAGAAAAGAG
5480552 A
1 A
5480553 AAAGACATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.59, C:0.00, G:0.18, T:0.24
Consensus pattern (17 bp):
ATTAATTAAGAAAAGAG
Found at i:5484977 original size:374 final size:377
Alignment explanation
Indices: 5483958--5485825 Score: 2926
Period size: 376 Copynumber: 5.0 Consensus size: 377
5483948 AAACATAAGA
* * *
5483958 GTAAATTACATATTCAATCACTCAATTATTTATATAGTTTTGTTTTCATCACTCAACTATTTTTT
1 GTAAATTACATATTTAGTCACTCAATTATTTATATAGTTTTGTTTTGATCACTCAACTATTTTTT
5484023 TCAAAATCATCACTAAACTTAAGTTTTTATTCTATTTTGGTCACCTAATTCGATTCTA-TTTTTT
66 TCAAAATCATCACTAAACTTAAGTTTTTATTCTATTTTGGTCACCTAATTCGATTCTATTTTTTT
* *
5484087 TCTAAATTTATAATATATAAGAATATTTGTCAATTTTTTACTTATGCCTTTAATTTTTTTATT-A
131 TGTAAATTTACAATATATAAGAATATTTGTCAATTTTTTACTTATGCCTTTAATTTTTTTATTAA
* *
5484151 -TTATTTTTTTAAATTTATAATGCTATCTACCAATTTTTTACTTAACTTTACAAGAAGGGTAAAG
196 TTTATTTTTTAAAATTTATAATGCTATCTACCAA-TTTTTA-TTAACTTTACAACAAGGGTAAAG
5484215 TACTTGTTTCACATTGCTATGGGTGTAATTTGCCCTTTAAAAAATGTTTGGTACGATTAATCTAA
259 TACTTGTTTCACATTGCTATGGGTGTAATTTGCCCTTTAAAAAATGTTTGGTACGATTAATCTAA
5484280 TTTTTAAAACATTTTCAAATTGCTTTGGCATGGACCTAAAAGAAATATTTTTAG
324 TTTTTAAAACATTTTCAAATTGCTTTGGCATGGACCTAAAAGAAATATTTTTAG
* *
5484334 GTAAATTCCATATTTATTCACTCAATTATTTATATAGTTTTGTTTTGATCACTCAACTATTTTTT
1 GTAAATTACATATTTAGTCACTCAATTATTTATATAGTTTTGTTTTGATCACTCAACTATTTTTT
* * *
5484399 TCAAAATCATCACTAAACTTAAGCTTTTATTCTATTTTAGTCATCTAATTCGATTCTATTTTTTT
66 TCAAAATCATCACTAAACTTAAGTTTTTATTCTATTTTGGTCACCTAATTCGATTCTA--TTTTT
* *
5484464 TTTGTAAATTTACAATATATAAGAATATTTGTCAAATTTTTACTTATGCCTTTAGTTTTTTTATT
129 TTTGTAAATTTACAATATATAAGAATATTTGTCAATTTTTTACTTATGCCTTTAATTTTTTTATT
* *
5484529 AATTTATATTTTAAAATTTATAATGCTATCTACCAA-ATTT-TT-ACTTTACAACAAGGGTAAAG
194 AATTTATTTTTTAAAATTTATAATGCTATCTACCAATTTTTATTAACTTTACAACAAGGGTAAAG
* * * *
5484591 TACTTGTTTCACATCGCTATGGGTGTAATTTACCCTTTAAAAAATGCTCGGTACGATTAATCTAA
259 TACTTGTTTCACATTGCTATGGGTGTAATTTGCCCTTTAAAAAATGTTTGGTACGATTAATCTAA
* * * * * *
5484656 TTTTTAGAACATTTTCATATTTCTTTGGAATGGAACTTAAA-AAATATTTTTAG
324 TTTTTAAAACATTTTCAAATTGCTTTGGCATGGACCTAAAAGAAATATTTTTAG
** *
5484709 GTAAATTACATATTTAGTCACTCAATTATTTATATAGTTTCATTTTGATCATTCAACTATTTTTT
1 GTAAATTACATATTTAGTCACTCAATTATTTATATAGTTTTGTTTTGATCACTCAACTATTTTTT
* *
5484774 TCAAAATCATCACTAAACTTAAGTTTTTATTCTATTTTAGTCATCTAATTCGATTCTATTTTTTT
66 TCAAAATCATCACTAAACTTAAGTTTTTATTCTATTTTGGTCACCTAATTCGATTCTA-TTTTTT
*
5484839 TTGTAAATTTACAATATATAAGAATATTTGTCAATTTTTTACTTATGCCTTTAATTTTTCTATTA
130 TTGTAAATTTACAATATATAAGAATATTTGTCAATTTTTTACTTATGCCTTTAATTTTTTTATTA
* *
5484904 ATTTATATTTTAAAATTTATAATGCTATCTACCAA-ATTT-TT-ACTTTACAACAAGGGTAAAGT
195 ATTTATTTTTTAAAATTTATAATGCTATCTACCAATTTTTATTAACTTTACAACAAGGGTAAAGT
* * * *
5484966 ACTTGTTTCACATCGCTATGGGTGTAATTTACCCTTTAAAAAATGCTCGGTACGATTAATCTAAT
260 ACTTGTTTCACATTGCTATGGGTGTAATTTGCCCTTTAAAAAATGTTTGGTACGATTAATCTAAT
* *
5485031 TTTTAGAACATTTTCACATTGCTTTGGCATGGACCTAAAAGAAATATTTTTAG
325 TTTTAAAACATTTTCAAATTGCTTTGGCATGGACCTAAAAGAAATATTTTTAG
* *
5485084 GTAAATTACATATTTATTCACTCAATTATTTATGTAGTTTTGTTTTGATCACTCAACTA-TTTTT
1 GTAAATTACATATTTAGTCACTCAATTATTTATATAGTTTTGTTTTGATCACTCAACTATTTTTT
*
5485148 TCAAAATCATCACTAAAATTAAGTTTTTATTCTATTTTGGTCACCTAATTCGATTCTATTTTTTT
66 TCAAAATCATCACTAAACTTAAGTTTTTATTCTATTTTGGTCACCTAATTCGATTCTATTTTTTT
* *
5485213 TCTAAATTTATAATATATAAGAATATTTGTCAATTTTTTACTTATGCCTTTAA-TTTTTTATTAA
131 TGTAAATTTACAATATATAAGAATATTTGTCAATTTTTTACTTATGCCTTTAATTTTTTTATTAA
* *
5485277 TTTATTTTTTTAAATTTATAATGCTATCTACCAATTTTTTACTTAACTTTACAAGAAGGGTAAAG
196 TTTATTTTTTAAAATTTATAATGCTATCTACCAA-TTTTTA-TTAACTTTACAACAAGGGTAAAG
5485342 TACTTGTTTCACATTGCTATGGGTGTAATTTGCCCTTTAAAAAATGTTTGGTACGATTAATCTAA
259 TACTTGTTTCACATTGCTATGGGTGTAATTTGCCCTTTAAAAAATGTTTGGTACGATTAATCTAA
5485407 TTTTTAAAACATTTTCAAATTGCTTTGGCATGGACCTAAAAGAAATATTTTTAG
324 TTTTTAAAACATTTTCAAATTGCTTTGGCATGGACCTAAAAGAAATATTTTTAG
* * *
5485461 GTAAATTTCA-ATTTAGTCACTCAATTATTTATAGAGTTTTGTTTTGACCACTCAACTA-TTTTT
1 GTAAATTACATATTTAGTCACTCAATTATTTATATAGTTTTGTTTTGATCACTCAACTATTTTTT
5485524 TCAAAATCATCACTAAACTTAAGTTTTTATTCTATTTTGGTCACCTAATTCGATTCTA-----TT
66 TCAAAATCATCACTAAACTTAAGTTTTTATTCTATTTTGGTCACCTAATTCGATTCTATTTTTTT
* *
5485584 TG------T-CAATTTATAAGAATATTTGTCAATTTTTTTTACTTACGCCTTTAATTTTTTTATT
131 TGTAAATTTACAATATATAAGAATATTTGTCAA--TTTTTTACTTATGCCTTTAATTTTTTTATT
* *
5485642 AATTT-TTTTTTAAAATTTATAATGCGATCTACCAATTTTTTACTTGACTTTACAACAAGGGTAA
194 AATTTATTTTTTAAAATTTATAATGCTATCTACCAA-TTTTTA-TTAACTTTACAACAAGGGTAA
5485706 AGTACTTGTTTCACATTGCTATGGGTGTAATTTGCCCTTTAAAAAATGTTTGGTACGATTAATCT
257 AGTACTTGTTTCACATTGCTATGGGTGTAATTTGCCCTTTAAAAAATGTTTGGTACGATTAATCT
* * * *
5485771 AATTTTTAAAACATTTTCACATTGCTTTGGCATGGGCCTAAAATAAATAATTTTA
322 AATTTTTAAAACATTTTCAAATTGCTTTGGCATGGACCTAAAAGAAATATTTTTA
5485826 ATGGGATTTT
Statistics
Matches: 1400, Mismatches: 78, Indels: 38
0.92 0.05 0.03
Matches are distributed among these distances:
364 21 0.01
365 1 0.00
366 190 0.14
367 14 0.01
371 3 0.00
372 42 0.03
373 58 0.04
374 294 0.21
375 195 0.14
376 339 0.24
377 143 0.10
379 68 0.05
380 1 0.00
381 31 0.02
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.46
Consensus pattern (377 bp):
GTAAATTACATATTTAGTCACTCAATTATTTATATAGTTTTGTTTTGATCACTCAACTATTTTTT
TCAAAATCATCACTAAACTTAAGTTTTTATTCTATTTTGGTCACCTAATTCGATTCTATTTTTTT
TGTAAATTTACAATATATAAGAATATTTGTCAATTTTTTACTTATGCCTTTAATTTTTTTATTAA
TTTATTTTTTAAAATTTATAATGCTATCTACCAATTTTTATTAACTTTACAACAAGGGTAAAGTA
CTTGTTTCACATTGCTATGGGTGTAATTTGCCCTTTAAAAAATGTTTGGTACGATTAATCTAATT
TTTAAAACATTTTCAAATTGCTTTGGCATGGACCTAAAAGAAATATTTTTAG
Found at i:5485420 original size:751 final size:751
Alignment explanation
Indices: 5483958--5485825 Score: 2954
Period size: 751 Copynumber: 2.5 Consensus size: 751
5483948 AAACATAAGA
* * *
5483958 GTAAATTACATATTCAATCACTCAATTATTTATATAGTTTTGTTTTCATCACTCAACTATTTTTT
1 GTAAATTACATATTTAGTCACTCAATTATTTATATAGTTTTGTTTTGATCACTCAACTATTTTTT
5484023 TCAAAATCATCACTAAACTTAAGTTTTTATTCTATTTTGGTCACCTAATTCGATTCTATTTTTTT
66 TCAAAATCATCACTAAACTTAAGTTTTTATTCTATTTTGGTCACCTAATTCGATTCTATTTTTTT
* *
5484088 CTAAATTTATAATATATAAGAATATTTGTCAATTTTTTACTTATGCCTTTAATTTTTTTATT-A-
131 GTAAATTTACAATATATAAGAATATTTGTCAATTTTTTACTTATGCCTTTAATTTTTTTATTAAT
* *
5484151 TTATTTTTTTAAATTTATAATGCTATCTACCAATTTTTTACTTAACTTTACAAGAAGGGTAAAGT
196 TTATTTTTTAAAATTTATAATGCTATCTACCAA-TTTTTA-TTAACTTTACAACAAGGGTAAAGT
5484216 ACTTGTTTCACATTGCTATGGGTGTAATTTGCCCTTTAAAAAATGTTTGGTACGATTAATCTAAT
259 ACTTGTTTCACATTGCTATGGGTGTAATTTGCCCTTTAAAAAATGTTTGGTACGATTAATCTAAT
* *
5484281 TTTTAAAACATTTTCAAATTGCTTTGGCATGGACCTAAAAGAAATATTTTTAGGTAAATTCCATA
324 TTTTAAAACATTTTCACATTGCTTTGGCATGGACCTAAAAGAAATATTTTTAGGTAAATTACATA
5484346 TTTATTCACTCAATTATTTATATAGTTTTGTTTTGATCACTCAACTATTTTTTTCAAAATCATCA
389 TTTATTCACTCAATTATTTATATAGTTTTGTTTTGATCACTCAACTATTTTTTTCAAAATCATCA
* * *
5484411 CTAAACTTAAGCTTTTATTCTATTTTAGTCATCTAATTCGATTCTATTTTTTTTTTGTAAATTTA
454 CTAAAATTAAGCTTTTATTCTATTTTAGTCACCTAATTCGATTCTA-TTTTTTTTTCTAAATTTA
*
5484476 CAATATATAAGAATATTTGTCAAATTTTTACTTATGCCTTTAGTTTTTTTATTAATTTATATTTT
518 CAATATATAAGAATATTTGTCAAATTTTTACTTATGCCTTTAGATTTTTTATTAATTTATATTTT
5484541 AAAATTTATAATGCTATCTACCAAATTTTTACTTTACAACAAGGGTAAAGTACTTGTTTCACATC
583 AAAATTTATAATGCTATCTACCAAATTTTTACTTTACAACAAGGGTAAAGTACTTGTTTCACATC
*
5484606 GCTATGGGTGTAATTTACCCTTTAAAAAATGCTCGGTACGATTAATCTAATTTTTAGAACATTTT
648 GCTATGGGTGTAATTTACCCTTTAAAAAATGCTCGGTACGATTAATCTAATTTTTAAAACATTTT
* * *
5484671 CATATTTCTTTGGAATGGAACTTAAA-AAATATTTTTAG
713 CAAATTGCTTTGGAATGGAACTAAAAGAAATATTTTTAG
** *
5484709 GTAAATTACATATTTAGTCACTCAATTATTTATATAGTTTCATTTTGATCATTCAACTATTTTTT
1 GTAAATTACATATTTAGTCACTCAATTATTTATATAGTTTTGTTTTGATCACTCAACTATTTTTT
* *
5484774 TCAAAATCATCACTAAACTTAAGTTTTTATTCTATTTTAGTCATCTAATTCGATTCTATTTTTTT
66 TCAAAATCATCACTAAACTTAAGTTTTTATTCTATTTTGGTCACCTAATTCGATTCTA--TTTTT
*
5484839 TTGTAAATTTACAATATATAAGAATATTTGTCAATTTTTTACTTATGCCTTTAATTTTTCTATTA
129 TTGTAAATTTACAATATATAAGAATATTTGTCAATTTTTTACTTATGCCTTTAATTTTTTTATTA
* *
5484904 ATTTATATTTTAAAATTTATAATGCTATCTACCAA-ATTT-TT-ACTTTACAACAAGGGTAAAGT
194 ATTTATTTTTTAAAATTTATAATGCTATCTACCAATTTTTATTAACTTTACAACAAGGGTAAAGT
* * * *
5484966 ACTTGTTTCACATCGCTATGGGTGTAATTTACCCTTTAAAAAATGCTCGGTACGATTAATCTAAT
259 ACTTGTTTCACATTGCTATGGGTGTAATTTGCCCTTTAAAAAATGTTTGGTACGATTAATCTAAT
*
5485031 TTTTAGAACATTTTCACATTGCTTTGGCATGGACCTAAAAGAAATATTTTTAGGTAAATTACATA
324 TTTTAAAACATTTTCACATTGCTTTGGCATGGACCTAAAAGAAATATTTTTAGGTAAATTACATA
*
5485096 TTTATTCACTCAATTATTTATGTAGTTTTGTTTTGATCACTCAACTA-TTTTTTCAAAATCATCA
389 TTTATTCACTCAATTATTTATATAGTTTTGTTTTGATCACTCAACTATTTTTTTCAAAATCATCA
* * *
5485160 CTAAAATTAAGTTTTTATTCTATTTTGGTCACCTAATTCGATTCTA-TTTTTTTTCTAAATTTAT
454 CTAAAATTAAGCTTTTATTCTATTTTAGTCACCTAATTCGATTCTATTTTTTTTTCTAAATTTAC
* * *
5485224 AATATATAAGAATATTTGTCAATTTTTTACTTATGCCTTTA-ATTTTTTATTAATTTATTTTTTT
519 AATATATAAGAATATTTGTCAAATTTTTACTTATGCCTTTAGATTTTTTATTAATTTATATTTTA
* *
5485288 AAATTTATAATGCTATCTACCAATTTTTTACTTAACTTTACAAGAAGGGTAAAGTACTTGTTTCA
584 AAATTTATAATGCTATCTACCAA--ATTT--TT-ACTTTACAACAAGGGTAAAGTACTTGTTTCA
* * * *
5485353 CATTGCTATGGGTGTAATTTGCCCTTTAAAAAATGTTTGGTACGATTAATCTAATTTTTAAAACA
644 CATCGCTATGGGTGTAATTTACCCTTTAAAAAATGCTCGGTACGATTAATCTAATTTTTAAAACA
* *
5485418 TTTTCAAATTGCTTTGGCATGGACCTAAAAGAAATATTTTTAG
709 TTTTCAAATTGCTTTGGAATGGAACTAAAAGAAATATTTTTAG
* * *
5485461 GTAAATTTCA-ATTTAGTCACTCAATTATTTATAGAGTTTTGTTTTGACCACTCAACTA-TTTTT
1 GTAAATTACATATTTAGTCACTCAATTATTTATATAGTTTTGTTTTGATCACTCAACTATTTTTT
5485524 TCAAAATCATCACTAAACTTAAGTTTTTATTCTATTTTGGTCACCTAATTCGATTCTA----TTT
66 TCAAAATCATCACTAAACTTAAGTTTTTATTCTATTTTGGTCACCTAATTCGATTCTATTTTTTT
* *
5485585 G------T-CAATTTATAAGAATATTTGTCAATTTTTTTTACTTACGCCTTTAATTTTTTTATTA
131 GTAAATTTACAATATATAAGAATATTTGTCAA--TTTTTTACTTATGCCTTTAATTTTTTTATTA
* *
5485643 ATTT-TTTTTTAAAATTTATAATGCGATCTACCAATTTTTTACTTGACTTTACAACAAGGGTAAA
194 ATTTATTTTTTAAAATTTATAATGCTATCTACCAA-TTTTTA-TTAACTTTACAACAAGGGTAAA
5485707 GTACTTGTTTCACATTGCTATGGGTGTAATTTGCCCTTTAAAAAATGTTTGGTACGATTAATCTA
257 GTACTTGTTTCACATTGCTATGGGTGTAATTTGCCCTTTAAAAAATGTTTGGTACGATTAATCTA
* * *
5485772 ATTTTTAAAACATTTTCACATTGCTTTGGCATGGGCCTAAAATAAATAATTTTA
322 ATTTTTAAAACATTTTCACATTGCTTTGGCATGGACCTAAAAGAAATATTTTTA
5485826 ATGGGATTTT
Statistics
Matches: 1033, Mismatches: 67, Indels: 42
0.90 0.06 0.04
Matches are distributed among these distances:
737 22 0.02
738 29 0.03
739 33 0.03
740 3 0.00
742 2 0.00
743 130 0.13
744 4 0.00
746 43 0.04
747 56 0.05
748 3 0.00
749 59 0.06
750 252 0.24
751 275 0.27
752 21 0.02
753 69 0.07
754 1 0.00
755 31 0.03
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.46
Consensus pattern (751 bp):
GTAAATTACATATTTAGTCACTCAATTATTTATATAGTTTTGTTTTGATCACTCAACTATTTTTT
TCAAAATCATCACTAAACTTAAGTTTTTATTCTATTTTGGTCACCTAATTCGATTCTATTTTTTT
GTAAATTTACAATATATAAGAATATTTGTCAATTTTTTACTTATGCCTTTAATTTTTTTATTAAT
TTATTTTTTAAAATTTATAATGCTATCTACCAATTTTTATTAACTTTACAACAAGGGTAAAGTAC
TTGTTTCACATTGCTATGGGTGTAATTTGCCCTTTAAAAAATGTTTGGTACGATTAATCTAATTT
TTAAAACATTTTCACATTGCTTTGGCATGGACCTAAAAGAAATATTTTTAGGTAAATTACATATT
TATTCACTCAATTATTTATATAGTTTTGTTTTGATCACTCAACTATTTTTTTCAAAATCATCACT
AAAATTAAGCTTTTATTCTATTTTAGTCACCTAATTCGATTCTATTTTTTTTTCTAAATTTACAA
TATATAAGAATATTTGTCAAATTTTTACTTATGCCTTTAGATTTTTTATTAATTTATATTTTAAA
ATTTATAATGCTATCTACCAAATTTTTACTTTACAACAAGGGTAAAGTACTTGTTTCACATCGCT
ATGGGTGTAATTTACCCTTTAAAAAATGCTCGGTACGATTAATCTAATTTTTAAAACATTTTCAA
ATTGCTTTGGAATGGAACTAAAAGAAATATTTTTAG
Found at i:5495326 original size:29 final size:29
Alignment explanation
Indices: 5495272--5495327 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
5495262 AAACTATGCA
* *
5495272 TTTAGTACATAAACTATCAGTGTTTTCGT
1 TTTAGTACATAAACTATCAATATTTTCGT
*
5495301 TTTAGTATC-TAAACTTTCAATATTTTC
1 TTTAGTA-CATAAACTATCAATATTTTC
5495328 AAAATCATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 22 0.96
30 1 0.04
ACGTcount: A:0.29, C:0.14, G:0.09, T:0.48
Consensus pattern (29 bp):
TTTAGTACATAAACTATCAATATTTTCGT
Found at i:5499001 original size:14 final size:14
Alignment explanation
Indices: 5498982--5499011 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5498972 TGCTGCTTAC
*
5498982 CACTAGAACCAACT
1 CACTAGAACAAACT
5498996 CACTAGAACAAACT
1 CACTAGAACAAACT
5499010 CA
1 CA
5499012 TTGATAACAA
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:0.47, C:0.33, G:0.07, T:0.13
Consensus pattern (14 bp):
CACTAGAACAAACT
Found at i:5499378 original size:21 final size:21
Alignment explanation
Indices: 5499334--5499384 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
5499324 ATGGACTATA
* * *
5499334 ACGTCAGCATCGTGGATAGTC
1 ACGTCAGTATCGTGAATAGGC
*
5499355 ACGTCAGTATCGTGAATTGGC
1 ACGTCAGTATCGTGAATAGGC
*
5499376 ACGTTAGTA
1 ACGTCAGTA
5499385 CTGTAATGGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (21 bp):
ACGTCAGTATCGTGAATAGGC
Found at i:5516827 original size:87 final size:87
Alignment explanation
Indices: 5516675--5516835 Score: 241
Period size: 87 Copynumber: 1.9 Consensus size: 87
5516665 TATCCCCCGC
* *
5516675 TGGTGGCACTGCAAATTCTTCTCCTTCATGGTAGTACCCAGGGACTAAGTCGTAATCAGAGTCCG
1 TGGTGGCACTGCAAATTCATCCCCTTCATGGTAGTACCCAGGGACTAAGTCGTAATCAGAGTCCG
5516740 GTGGAAGTGTGAAATCCACCAT
66 GTGGAAGTGTGAAATCCACCAT
* * ** * * *
5516762 TGGTGGCATTGCGAATTCATCCCCTTCATGGTAGTAGTCAGGGCCTAAGTCGTAATCGGATTCCG
1 TGGTGGCACTGCAAATTCATCCCCTTCATGGTAGTACCCAGGGACTAAGTCGTAATCAGAGTCCG
5516827 GTGGAAGTG
66 GTGGAAGTG
5516836 CAAACTCATC
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 65 1.00
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (87 bp):
TGGTGGCACTGCAAATTCATCCCCTTCATGGTAGTACCCAGGGACTAAGTCGTAATCAGAGTCCG
GTGGAAGTGTGAAATCCACCAT
Found at i:5517114 original size:165 final size:165
Alignment explanation
Indices: 5516823--5517164 Score: 490
Period size: 165 Copynumber: 2.1 Consensus size: 165
5516813 GTAATCGGAT
* *
5516823 TCCGGTGGAAGTGCAAACTCATCTCCTTCACCATCGTAGTCAGGGCCCAAGTCGAAATCGAATTC
1 TCCGGTGGCACTGCAAACTCATCTCCTTCACCATCGTAGTCAGGGCCCAAGTCGAAATCGAATTC
* * * * *
5516888 AGGTGGAAGTGCAAAATCCGCCCTTAGTGGCACTGTAATTTTATCTCCCTGAGGGTTGTAGTCGG
66 AGGTGGAAGTGCAAAATCCGCCATCAGTGGCACTGTAATTTTATCTCCCTGACGCTTGTAGTCGA
*
5516953 AGCCTATGTCGTGGTCAGGCACACCTAAATCCGCC
131 AGCCTAAGTCGTGGTCAGGCACACCTAAATCCGCC
* *
5516988 TCCGGTGGCACTGCAAA-TACATCTCCTTCACCATCGTAGTCGGGGCCTAAGTCGAAATCGAATT
1 TCCGGTGGCACTGCAAACT-CATCTCCTTCACCATCGTAGTCAGGGCCCAAGTCGAAATCGAATT
* *
5517052 CAGGTGGAAGTGCAAAATCCG-CATGCAGTGGCACTGTAATTTTTTCTCCGTGACGCTTGTAGTC
65 CAGGTGGAAGTGCAAAATCCGCCAT-CAGTGGCACTGTAATTTTATCTCCCTGACGCTTGTAGTC
* * **
5517116 GAAGTCTAAGTCGTGGTTAGGTGCACCTAAATCCGCC
129 GAAGCCTAAGTCGTGGTCAGGCACACCTAAATCCGCC
* *
5517153 ACCGGTGTCACT
1 TCCGGTGGCACT
5517165 ATGAATCCGT
Statistics
Matches: 157, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
164 3 0.02
165 154 0.98
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (165 bp):
TCCGGTGGCACTGCAAACTCATCTCCTTCACCATCGTAGTCAGGGCCCAAGTCGAAATCGAATTC
AGGTGGAAGTGCAAAATCCGCCATCAGTGGCACTGTAATTTTATCTCCCTGACGCTTGTAGTCGA
AGCCTAAGTCGTGGTCAGGCACACCTAAATCCGCC
Found at i:5518280 original size:19 final size:19
Alignment explanation
Indices: 5518256--5518293 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5518246 TAGTCACATT
5518256 TAGTTAGCATTTAAAGGAA
1 TAGTTAGCATTTAAAGGAA
5518275 TAGTTAGCATTTAAAGGAA
1 TAGTTAGCATTTAAAGGAA
5518294 GTGTTTACGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (19 bp):
TAGTTAGCATTTAAAGGAA
Found at i:5522189 original size:2 final size:2
Alignment explanation
Indices: 5522182--5522269 Score: 167
Period size: 2 Copynumber: 44.0 Consensus size: 2
5522172 GTAGAAGAAG
5522182 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
*
5522224 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5522266 AT AT
1 AT AT
5522270 GTAAGAGCAT
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5527173 original size:2 final size:2
Alignment explanation
Indices: 5527166--5527190 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5527156 GTTTAGATTC
5527166 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 A
5527191 ATGATGCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5536073 original size:20 final size:20
Alignment explanation
Indices: 5536048--5536107 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
5536038 CATTGATGAT
5536048 TCACTGACGTTATAAATCGG
1 TCACTGACGTTATAAATCGG
5536068 TCACTGACGTTATAAATCGG
1 TCACTGACGTTATAAATCGG
*
5536088 TCATTGACGTTATAAATCGG
1 TCACTGACGTTATAAATCGG
5536108 AAAACATCGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (20 bp):
TCACTGACGTTATAAATCGG
Found at i:5540339 original size:10 final size:10
Alignment explanation
Indices: 5540324--5540348 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5540314 TGCTTTGTAC
5540324 GAGTGAAAGA
1 GAGTGAAAGA
5540334 GAGTGAAAGA
1 GAGTGAAAGA
5540344 GAGTG
1 GAGTG
5540349 TTACCAGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.12
Consensus pattern (10 bp):
GAGTGAAAGA
Found at i:5546157 original size:13 final size:13
Alignment explanation
Indices: 5546139--5546163 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5546129 ATTTTAATGT
5546139 TGAAAGTTAGAGG
1 TGAAAGTTAGAGG
5546152 TGAAAGTTAGAG
1 TGAAAGTTAGAG
5546164 ATGGAAGAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.36, T:0.24
Consensus pattern (13 bp):
TGAAAGTTAGAGG
Found at i:5554458 original size:24 final size:24
Alignment explanation
Indices: 5554431--5554514 Score: 98
Period size: 24 Copynumber: 3.5 Consensus size: 24
5554421 AATTATGTTG
* * * *
5554431 TGATACCTAACCTGAATTCTGATA
1 TGATACATGACCTGGATTCTGATC
* *
5554455 TGATA-TTGACATGGATTCTGATC
1 TGATACATGACCTGGATTCTGATC
5554478 TGATACATGACCTGGATTCTGATC
1 TGATACATGACCTGGATTCTGATC
*
5554502 TGATACTTGACCT
1 TGATACATGACCT
5554515 AATTTATGTT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
23 18 0.35
24 33 0.65
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (24 bp):
TGATACATGACCTGGATTCTGATC
Found at i:5554740 original size:18 final size:18
Alignment explanation
Indices: 5554713--5554760 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 18
5554703 TGTGTGTGTG
*
5554713 TGTATGTTTTAAAAGATC
1 TGTATCTTTTAAAAGATC
5554731 TGTATCTTTTTTAAAAGATC
1 TGTATC--TTTTAAAAGATC
5554751 TGTATCTTTT
1 TGTATCTTTT
5554761 TACTGGTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 9 0.33
20 18 0.67
ACGTcount: A:0.27, C:0.08, G:0.12, T:0.52
Consensus pattern (18 bp):
TGTATCTTTTAAAAGATC
Found at i:5554762 original size:19 final size:20
Alignment explanation
Indices: 5554719--5554761 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
5554709 TGTGTGTATG
5554719 TTTTAAAAGATCTGTATCTT
1 TTTTAAAAGATCTGTATCTT
5554739 TTTTAAAAGATCTGTATCTT
1 TTTTAAAAGATCTGTATCTT
5554759 TTT
1 TTT
5554762 ACTGGTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.53
Consensus pattern (20 bp):
TTTTAAAAGATCTGTATCTT
Found at i:5569509 original size:1 final size:1
Alignment explanation
Indices: 5569503--5569531 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
5569493 TAGGGATTGG
5569503 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5569532 GCAGAAGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5570562 original size:2 final size:2
Alignment explanation
Indices: 5570555--5570583 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5570545 AAGAAATTTG
5570555 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5570584 TTAATGAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5571229 original size:60 final size:58
Alignment explanation
Indices: 5571165--5571294 Score: 127
Period size: 59 Copynumber: 2.2 Consensus size: 58
5571155 CATAAATGAC
** * * *
5571165 TCTCCGACTATAAGATATTGTTTTGTTGAGTCATC-CGACTATCAAAAGTTATAAAATAGT
1 TCTCCGACTATAAGATATTACTTT-ATGAGTC-TCTCAACTATCAAAAGTTATAAAAT-GG
* * * * *
5571225 TCTCCAATTATATGATGTTACTTTATGAGTCTCTCAACTATTAAAAGTTATAAAATGG
1 TCTCCGACTATAAGATATTACTTTATGAGTCTCTCAACTATCAAAAGTTATAAAATGG
5571283 TCATCCGACTAT
1 TC-TCCGACTAT
5571295 TCATTATGTT
Statistics
Matches: 56, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
58 5 0.09
59 33 0.59
60 18 0.32
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (58 bp):
TCTCCGACTATAAGATATTACTTTATGAGTCTCTCAACTATCAAAAGTTATAAAATGG
Found at i:5572805 original size:23 final size:23
Alignment explanation
Indices: 5572779--5572844 Score: 123
Period size: 23 Copynumber: 2.9 Consensus size: 23
5572769 TGTACTTCTG
5572779 TGCTGAATCAGTCAACACTGTTT
1 TGCTGAATCAGTCAACACTGTTT
5572802 TGCTGAATCAGTCAACACTGTTT
1 TGCTGAATCAGTCAACACTGTTT
*
5572825 TGCTGAATTAGTCAACACTG
1 TGCTGAATCAGTCAACACTG
5572845 AATCATTCAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.33
Consensus pattern (23 bp):
TGCTGAATCAGTCAACACTGTTT
Found at i:5573093 original size:3 final size:3
Alignment explanation
Indices: 5573085--5573121 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5573075 ACACCTATAA
5573085 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5573122 TCTCTTTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5581160 original size:21 final size:20
Alignment explanation
Indices: 5581134--5581209 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 20
5581124 CAACAGTAGA
5581134 TTCAGATGCCACCGCAGACAT
1 TTCAGATGCCACCGCA-ACAT
* *
5581155 TTCAGATGGCACCACAACCATT
1 TTCAGATGCCACCGCAA-CA-T
*
5581177 TTC-GATGCCACCGCATCCAT
1 TTCAGATGCCACCGCA-ACAT
*
5581197 TTCAGCTGCCACC
1 TTCAGATGCCACC
5581210 ATCACAGGGT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
20 5 0.11
21 36 0.80
22 4 0.09
ACGTcount: A:0.25, C:0.37, G:0.16, T:0.22
Consensus pattern (20 bp):
TTCAGATGCCACCGCAACAT
Found at i:5583194 original size:102 final size:101
Alignment explanation
Indices: 5582987--5583204 Score: 224
Period size: 102 Copynumber: 2.1 Consensus size: 101
5582977 AGCTTGTAGT
* * * * * *
5582987 TGAATGCCTTCCCCTTGAACTTGAAGCATCATTTCATATGGGTTTTAAACTGAGTGTTGTGTTGC
1 TGAATGCCTTCCCCTGGAACTTGAAGCATCATGTCAAATGGGTATTAAACAGAGTGTTGTGTCGC
* * **
5583052 AAACATCTCCATATTGAGGTCAAAAAAACTTACAGT
66 AAACATCTCCATATTCAAGTCAAAAAAACTTACAAA
* * *
5583088 TGAATGCCTCCCCCTGGAACTTGAAGGCATCATGTCAAATTGGTATTAAACAGATTGTTGTGTCG
1 TGAATGCCTTCCCCTGGAACTTGAA-GCATCATGTCAAATGGGTATTAAACAGAGTGTTGTGTCG
** * * *
5583153 -AGGGCATCTCCATATTCAAGTTAAAGAAA-TTGGCAAA
65 CA-AACATCTCCATATTCAAGTCAAAAAAACTT-ACAAA
*
5583190 TGAATACCTTCCCCT
1 TGAATGCCTTCCCCT
5583205 TGAATTGGAA
Statistics
Matches: 94, Mismatches: 20, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
101 26 0.28
102 68 0.72
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (101 bp):
TGAATGCCTTCCCCTGGAACTTGAAGCATCATGTCAAATGGGTATTAAACAGAGTGTTGTGTCGC
AAACATCTCCATATTCAAGTCAAAAAAACTTACAAA
Found at i:5585463 original size:19 final size:19
Alignment explanation
Indices: 5585441--5585487 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
5585431 AAATGTTGGG
*
5585441 TTTTTTTAA-TATAAATTTA
1 TTTTTTTAATTATAAA-TAA
*
5585460 TTTTTTTAATTTTAAATAA
1 TTTTTTTAATTATAAATAA
5585479 TTTTTTTAA
1 TTTTTTTAA
5585488 AATTACCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTTTTAATTATAAATAA
Found at i:5586712 original size:30 final size:30
Alignment explanation
Indices: 5586678--5586738 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
5586668 GGGAGGAGTT
*
5586678 AGAAAATTTATTTTT-GAGTGTCAAATTTAG
1 AGAAAATTTATTTTTAG-GTGTCAAAATTAG
5586708 AGAAAATTTATTTTTAGGTGTCAAAATTAG
1 AGAAAATTTATTTTTAGGTGTCAAAATTAG
5586738 A
1 A
5586739 AATTGTATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.39, C:0.03, G:0.16, T:0.41
Consensus pattern (30 bp):
AGAAAATTTATTTTTAGGTGTCAAAATTAG
Found at i:5587592 original size:12 final size:12
Alignment explanation
Indices: 5587575--5587604 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
5587565 TAGTTTATCT
5587575 GAGATAGAACGA
1 GAGATAGAACGA
5587587 GAGATAGAACGA
1 GAGATAGAACGA
5587599 GAGATA
1 GAGATA
5587605 TCTCTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (12 bp):
GAGATAGAACGA
Found at i:5598924 original size:24 final size:24
Alignment explanation
Indices: 5598870--5598918 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
5598860 GCCCAAAGAA
5598870 TACTTTTATTAGATAAACAATCAT
1 TACTTTTATTAGATAAACAATCAT
5598894 TACTTTTATTAGATAAACAATCAT
1 TACTTTTATTAGATAAACAATCAT
5598918 T
1 T
5598919 GGTTTTTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.12, G:0.04, T:0.43
Consensus pattern (24 bp):
TACTTTTATTAGATAAACAATCAT
Found at i:5600490 original size:21 final size:25
Alignment explanation
Indices: 5600440--5600490 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 25
5600430 ATTGAAAACA
*
5600440 ATTAAATAGTTAAGAGATCTGATTG
1 ATTAAATAGTTAAAAGATCTGATTG
5600465 A-TAAA-A-TTAAAAGAT-TGA-TG
1 ATTAAATAGTTAAAAGATCTGATTG
5600485 ATTAAA
1 ATTAAA
5600491 GTAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
20 3 0.12
21 7 0.29
22 8 0.33
23 1 0.04
24 4 0.17
25 1 0.04
ACGTcount: A:0.49, C:0.02, G:0.16, T:0.33
Consensus pattern (25 bp):
ATTAAATAGTTAAAAGATCTGATTG
Found at i:5600874 original size:18 final size:18
Alignment explanation
Indices: 5600851--5600893 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
5600841 CATTATTCAA
5600851 ATAATTAA-ATAATTATTC
1 ATAATTAAGATAA-TATTC
5600869 ATAATTAAGATAATATTC
1 ATAATTAAGATAATATTC
5600887 ATAATTA
1 ATAATTA
5600894 TTTTTTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (18 bp):
ATAATTAAGATAATATTC
Done.