Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008272.1 Hibiscus syriacus cultivar Beakdansim tig00110929_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: 465257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:287721 original size:3 final size:3
Alignment explanation
Indices: 287713--287739 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
287703 CTTCACGCAA
287713 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
287740 CTTTGACATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:293828 original size:41 final size:41
Alignment explanation
Indices: 293762--293842 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
293752 AATTTATAAT
*
293762 TAAACTATAATAATAAATATGTCATTAATATTCTTTTAAAAA
1 TAAACTATAATAATAAATATATCATTAATATT-TTTTAAAAA
* * *
293804 TAAACTAT-ATATTAAATTTATCATTGATATTTTTTAAAA
1 TAAACTATAATAATAAATATATCATTAATATTTTTTAAAA
293843 TAAGGACACC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 8 0.23
41 19 0.54
42 8 0.23
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.44
Consensus pattern (41 bp):
TAAACTATAATAATAAATATATCATTAATATTTTTTAAAAA
Found at i:304926 original size:22 final size:21
Alignment explanation
Indices: 304874--304934 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
304864 GATTTCTGGG
*
304874 CAAGGGGAATTGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
304895 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
*
304916 CAATGGGGAATCGATACCC
1 CAA-GGGGAATCGGTACCC
304935 CTCAAGCGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
21 23 0.62
22 14 0.38
ACGTcount: A:0.30, C:0.23, G:0.28, T:0.20
Consensus pattern (21 bp):
CAAGGGGAATCGGTACCCATT
Found at i:306111 original size:16 final size:16
Alignment explanation
Indices: 306092--306122 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
306082 TATATGAAAT
*
306092 ATTATATGACTATGTG
1 ATTATATGAATATGTG
306108 ATTATATGAATATGT
1 ATTATATGAATATGT
306123 TCTACGCGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.03, G:0.16, T:0.45
Consensus pattern (16 bp):
ATTATATGAATATGTG
Found at i:306476 original size:23 final size:23
Alignment explanation
Indices: 306444--306504 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
306434 TATAGTATTA
306444 CGGTGCAATTCTACGCGGCACTC
1 CGGTGCAATTCTACGCGGCACTC
* * *
306467 CGGTGTAATTCTACGTGGCACTT
1 CGGTGCAATTCTACGCGGCACTC
* *
306490 TGGTGCAATTATACG
1 CGGTGCAATTCTACG
306505 AGCTGTGGTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.20, C:0.25, G:0.26, T:0.30
Consensus pattern (23 bp):
CGGTGCAATTCTACGCGGCACTC
Found at i:312764 original size:33 final size:33
Alignment explanation
Indices: 312722--312784 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
312712 ACAAAATATG
*
312722 CGTATCATTTACAACTAAGTTCTTTAATCGGGT
1 CGTATCATTTACAACTAAGTTATTTAATCGGGT
312755 CGTATCATTTACAACTAAGTTATTTAATCG
1 CGTATCATTTACAACTAAGTTATTTAATCG
312785 AGTAACATGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (33 bp):
CGTATCATTTACAACTAAGTTATTTAATCGGGT
Found at i:318045 original size:2 final size:2
Alignment explanation
Indices: 318038--318067 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
318028 TGAAATTCAC
318038 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
318068 GTGTGTATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:323666 original size:178 final size:185
Alignment explanation
Indices: 323286--323801 Score: 611
Period size: 193 Copynumber: 2.8 Consensus size: 185
323276 TTGAAGTCAT
* * * * * *** *
323286 CAGTAACACCATAAGATTTGTCACCATCACTCTAAATTTTATATACATGAC-GAAATAACAAGTC
1 CAGTAACACCATACGATTTGTCACTATCGCTCT--A-CTTATATATATGACAGAAATGGTAAGCC
*
323350 TCTAACGATGAAAACAAATTGTTAAATCTCAGATTAAGTAACTTAATAATATTCTATTAA-TAAG
63 TCTAACGATGAAAACAAATTGTTAGATCTCAGATTAAGTAACTTAATAATATTCTATTAATTAAG
* * *
323414 AAGAACAATGTGATACTTCGTTAAAGCTTAAATCCCAGACGATGTTATAAAGAAAAAA
128 AGGAACAATGTGATACTTCATTAAAGCTTAAATCCCAGACGACGTTATAAAGAAAAAA
* *
323472 CAGTAACACTATACGATTTGTTACTATC-C-CT-C-TA-A-ATATGAC-GAAATGGTAAGCCTCT
1 CAGTAACACCATACGATTTGTCACTATCGCTCTACTTATATATATGACAGAAATGGTAAGCCTCT
* * * *
323530 AACGGTGAAAACAAATTGTTAGATTTCAGCTTAAGTAACTTAATAATATTCTGTTAATTAAGAGG
66 AACGATGAAAACAAATTGTTAGATCTCAGATTAAGTAACTTAATAATATTCTATTAATTAAGAGG
* * *
323595 AACAATGCGATACTTCATTAGAGTTTAAATCCCAGACGACGTTATAAA-AGAAAAA
131 AACAATGTGATACTTCATTAAAGCTTAAATCCCAGACGACGTTATAAAGA-AAAAA
323650 CAGTAACACCATACGATTTGTCACTATCGCTCTAAAGCCTTATATATATGACATGATGAAATGGT
1 CAGTAACACCATACGATTTGTCACTATCGCTCT--A--CTTATATATATGAC---A-GAAATGGT
* * * *
323715 AAGTCTCTAACGCTGAAAACAAATTGTTAGATCTCAGATTAAGTAACTTTATAATATTCTATCAA
58 AAGCCTCTAACGATGAAAACAAATTGTTAGATCTCAGATTAAGTAACTTAATAATATTCTATTAA
*
323780 TTAAGAGGAATAATGTGATACT
123 TTAAGAGGAACAATGTGATACT
323802 CCGTGAAGAT
Statistics
Matches: 281, Mismatches: 32, Indels: 27
0.83 0.09 0.08
Matches are distributed among these distances:
177 71 0.25
178 81 0.29
179 3 0.01
180 2 0.01
184 2 0.01
185 2 0.01
186 26 0.09
187 1 0.00
188 7 0.02
193 86 0.31
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (185 bp):
CAGTAACACCATACGATTTGTCACTATCGCTCTACTTATATATATGACAGAAATGGTAAGCCTCT
AACGATGAAAACAAATTGTTAGATCTCAGATTAAGTAACTTAATAATATTCTATTAATTAAGAGG
AACAATGTGATACTTCATTAAAGCTTAAATCCCAGACGACGTTATAAAGAAAAAA
Found at i:323836 original size:3 final size:3
Alignment explanation
Indices: 323828--323860 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
323818 TTTTTATCCA
323828 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
323861 AAATAATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:325663 original size:2 final size:2
Alignment explanation
Indices: 325656--325706 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
325646 AGTCATGTAA
325656 AT AT AT AT AT AT AT AT AT AT AT A- 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
325697 AT AT AT AT AT
1 AT AT AT AT AT
325707 TTGCTTAAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:326359 original size:18 final size:16
Alignment explanation
Indices: 326333--326392 Score: 68
Period size: 18 Copynumber: 3.6 Consensus size: 16
326323 TTTCTTTCAA
326333 ATTTTTTATTACTTATT
1 ATTTTTTATTA-TTATT
326350 ATTATTTTATATATTATT
1 ATT-TTTTAT-TATTATT
326368 ATTTTTTATT-TTATTT
1 ATTTTTTATTATTA-TT
*
326384 ATTTATTAT
1 ATTTTTTAT
326393 ATTCAAGAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
15 3 0.08
16 11 0.28
17 9 0.23
18 14 0.36
19 2 0.05
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.72
Consensus pattern (16 bp):
ATTTTTTATTATTATT
Found at i:326365 original size:22 final size:22
Alignment explanation
Indices: 326339--326392 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
326329 TCAAATTTTT
326339 TATTACTTA-TTATTATTTTATA
1 TATTA-TTATTTATTATTTTATA
* *
326361 TATTATTATTTTTTATTTTATT
1 TATTATTATTTATTATTTTATA
326383 TATTTATTAT
1 TA-TTATTAT
326393 ATTCAAGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 3 0.11
22 18 0.64
23 7 0.25
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (22 bp):
TATTATTATTTATTATTTTATA
Found at i:326366 original size:15 final size:15
Alignment explanation
Indices: 326346--326387 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
326336 TTTTATTACT
326346 TATTATTATTTTATA
1 TATTATTATTTTATA
*
326361 TATTATTATTTTTTA
1 TATTATTATTTTATA
*
326376 TTTTATTTATTT
1 TATTA-TTATTT
326388 ATTATATTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 18 0.75
16 6 0.25
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TATTATTATTTTATA
Found at i:327899 original size:26 final size:27
Alignment explanation
Indices: 327851--327912 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
327841 CATACATGCA
* *
327851 TTGTATTTTGCATTGTACATTTTTACGT
1 TTGTA-TTTACATTGTACATTTTTACAT
327879 TTGTATTTACATT-TACATTTTTACAT
1 TTGTATTTACATTGTACATTTTTACAT
*
327905 TTGCATTT
1 TTGTATTT
327913 GGCATCTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 19 0.61
27 7 0.23
28 5 0.16
ACGTcount: A:0.21, C:0.11, G:0.10, T:0.58
Consensus pattern (27 bp):
TTGTATTTACATTGTACATTTTTACAT
Found at i:329964 original size:89 final size:90
Alignment explanation
Indices: 329813--329993 Score: 355
Period size: 89 Copynumber: 2.0 Consensus size: 90
329803 GTACCCTCAT
329813 TTGGTTAAAGGTCAATACATTACACCAAGATTGGTGAAGGTGTCACCAAAGCCTTATGCTCA-TG
1 TTGGTTAAAGGTCAATACATTACACCAAGATTGGTGAAGGTGTCACCAAAGCCTTATGCTCATTG
329877 CTATGATCAAAAATAGCTTCTGTAA
66 CTATGATCAAAAATAGCTTCTGTAA
329902 TTGGTTAAAGGTCAATACATTACACCAAGATTGGTGAAGGTGTCACCAAAGCCTTATGCTCATTG
1 TTGGTTAAAGGTCAATACATTACACCAAGATTGGTGAAGGTGTCACCAAAGCCTTATGCTCATTG
329967 CTATGATCAAAAATAGCTTCTGTAA
66 CTATGATCAAAAATAGCTTCTGTAA
329992 TT
1 TT
329994 TTCACTTGGG
Statistics
Matches: 91, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
89 62 0.68
90 29 0.32
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (90 bp):
TTGGTTAAAGGTCAATACATTACACCAAGATTGGTGAAGGTGTCACCAAAGCCTTATGCTCATTG
CTATGATCAAAAATAGCTTCTGTAA
Found at i:333600 original size:110 final size:111
Alignment explanation
Indices: 333405--333617 Score: 340
Period size: 110 Copynumber: 1.9 Consensus size: 111
333395 GTGCTCATAG
* * *
333405 TAGAAATAAGATGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGT
1 TAGAAATAAGATGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTCGGT
* *
333470 ATGAACCCCAAAACCAATCATTGG-ATTTAAAGATGAATTTGCTCA
66 AGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTGCTCA
333515 TAGAAATAAGGA-GACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTCGG
1 TAGAAATAA-GATGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTCGG
* *
333579 TAGGAACCCCATAACCGATCATTGGAATTGAAAGATGAA
65 TAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAA
333618 CTGCATGATC
Statistics
Matches: 94, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
110 80 0.85
111 14 0.15
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (111 bp):
TAGAAATAAGATGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTCGGT
AGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTGCTCA
Found at i:335713 original size:48 final size:47
Alignment explanation
Indices: 335623--335748 Score: 155
Period size: 48 Copynumber: 2.6 Consensus size: 47
335613 AATCCAAGAA
* *
335623 AAATGATGAATATGTTGTCAACTGTTTTACATCCAAGCAGAAGCCACAGG
1 AAATGATG-ATATGTTGTCAAATGTTTTACATCCAAACAGAAG-C-CAGG
*
335673 GAATGATGATATGTTGTCAAATG-TTTACATCCAAACAGAAGCCAGG
1 AAATGATGATATGTTGTCAAATGTTTTACATCCAAACAGAAGCCAGG
* * *
335719 AAATGATGAATGTGTTATCAAACGTTTTAC
1 AAATGATG-ATATGTTGTCAAATGTTTTAC
335749 GAACCAGTGA
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
46 11 0.16
47 13 0.19
48 22 0.33
49 14 0.21
50 7 0.10
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (47 bp):
AAATGATGATATGTTGTCAAATGTTTTACATCCAAACAGAAGCCAGG
Found at i:336143 original size:22 final size:22
Alignment explanation
Indices: 336112--336164 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
336102 ATCTATACTC
*
336112 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
336134 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
336156 TTCAAAGAT
1 TTCAAAGAT
336165 AAAAGCTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:336769 original size:113 final size:113
Alignment explanation
Indices: 336572--337447 Score: 1251
Period size: 113 Copynumber: 7.9 Consensus size: 113
336562 GATTCAAATC
* * * *
336572 CATCATTCAATAGATCAACATTTCC-G-GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAATG
1 CATCATTCGATGGATCAACTTTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* *
336635 AAGAAGAAGTTCATAATGAGAATAACTTGTTCAACTTTTTGCTCGAATT
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATT
336684 CATCATTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
336749 AGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCTCGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATT
336797 CATCATTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
336862 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT-GCTCGAATT
* * *
336910 CATTATTCGATGGATCAACATTACCAG-GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAA-G
1 CATCATTCGATGGATCAACTTTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGG
*
336973 --GAAGAAG-TCATAATGAGAAGAACTTGTTCAA-CTTTTCGCTTGAATT
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT-GCTCGAATT
* * * *
337019 CATTATTCGATGGATCAACATTACCAG-GAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
337083 AGAAGAAGTTCATAATAAGAAGAA-TTGTTCAACCTTTTAC-CTG-A-T
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC-GAATT
* * *
337128 CATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAA-AAGGA
1 CATCATTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
** *
337192 AGAAGAAGTTCATAAT--GAAG-A-TTG-TCAACCTTTACCT-GAATC
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATT
* *
337234 CATCATTTGATGGATCAGC-TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
337298 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC-CTGAATC
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC-GAATT
* *
337346 CATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
337411 AGAAGAAGTTCATAATGAGAAGAA-TTGTTCAACCTTT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
337448 GCTTGATTCC
Statistics
Matches: 712, Mismatches: 29, Indels: 46
0.90 0.04 0.06
Matches are distributed among these distances:
104 1 0.00
105 49 0.07
106 44 0.06
107 4 0.01
108 35 0.05
109 114 0.16
110 40 0.06
111 27 0.04
112 87 0.12
113 308 0.43
114 3 0.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (113 bp):
CATCATTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATT
Found at i:337738 original size:3 final size:3
Alignment explanation
Indices: 337730--337773 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
337720 TTTTTATCCA
*
337730 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
337774 AAATATAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:338648 original size:41 final size:39
Alignment explanation
Indices: 338583--338660 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
338573 CCCTCTCTGT
338583 TTTAGAGAGAAGGCAGAGCTTCTCTCTCCTAGAGAGAGA
1 TTTAGAGAGAAGGCAGAGCTTCTCTCTCCTAGAGAGAGA
338622 TTTAGAGAGAAGGCAGAGCTTCTCTCTCCTAGAGAGAGA
1 TTTAGAGAGAAGGCAGAGCTTCTCTCTCCTAGAGAGAGA
338661 AGCTGAAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.31, C:0.18, G:0.28, T:0.23
Consensus pattern (39 bp):
TTTAGAGAGAAGGCAGAGCTTCTCTCTCCTAGAGAGAGA
Found at i:339587 original size:2 final size:2
Alignment explanation
Indices: 339580--339622 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
339570 TAGTCATGTA
*
339580 AT AT AT AT AT AT AT AT CT AT AT AT A- 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
339621 AT
1 AT
339623 TGCTTAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:343242 original size:19 final size:18
Alignment explanation
Indices: 343220--343266 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
343210 AGGTTTAGGG
343220 TTTAATAATGATTCAATAA
1 TTTAATAATGATTCAA-AA
*
343239 TTTAATAATTATTCAAAA
1 TTTAATAATGATTCAAAA
343257 -TTAA-AATGAT
1 TTTAATAATGAT
343267 GAACAAACTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 5 0.19
17 4 0.15
18 2 0.08
19 15 0.58
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (18 bp):
TTTAATAATGATTCAAAA
Found at i:356164 original size:16 final size:16
Alignment explanation
Indices: 356143--356199 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
356133 TTAATTGATT
356143 ATTTTTATATCA-TTTA
1 ATTTTTAT-TCATTTTA
*
356159 ATTTTTATTTATTTTA
1 ATTTTTATTCATTTTA
*
356175 ATTTTATTATTAAATTTTA
1 A-TTT-TTATT-CATTTTA
356194 ATTTTT
1 ATTTTT
356200 GTTTCTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
15 2 0.06
16 13 0.37
17 5 0.14
18 8 0.23
19 7 0.20
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTTTATTCATTTTA
Found at i:356190 original size:29 final size:29
Alignment explanation
Indices: 356123--356197 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
356113 AATTATAAAC
*
356123 TTATTAAATTTTAATTGATTATTTTTATA
1 TTATTAAATTTTAATTTATTATTTTTATA
* * *
356152 TCATTTAATTTTTATTTATT-TTAATTT-TA
1 TTATTAAATTTTAATTTATTATT--TTTATA
356181 TTATTAAATTTTAATTT
1 TTATTAAATTTTAATTT
356198 TTGTTTCTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
28 2 0.05
29 32 0.86
30 3 0.08
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (29 bp):
TTATTAAATTTTAATTTATTATTTTTATA
Found at i:356397 original size:2 final size:2
Alignment explanation
Indices: 356390--356415 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
356380 AATAAAATTA
356390 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
356416 CTTAAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:356499 original size:15 final size:14
Alignment explanation
Indices: 356475--356512 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
356465 AAATATAATA
356475 ATTT-TATAAATATT
1 ATTTATATAAA-ATT
356489 ATTTATATAAAATT
1 ATTTATATAAAATT
356503 ATATTATATA
1 AT-TTATATA
356513 TTTATAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTTATATAAAATT
Found at i:356508 original size:19 final size:21
Alignment explanation
Indices: 356484--356531 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 21
356474 AATTTTATAA
356484 ATATTAT-T-TATATAAAATT
1 ATATTATATATATATAAAATT
*
356503 ATATTATATATTTATAAAATT
1 ATATTATATATATATAAAATT
356524 A-A-TATATA
1 ATATTATATA
356532 AAATATTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 13 0.50
20 2 0.08
21 11 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATTATATATATATAAAATT
Found at i:356793 original size:16 final size:16
Alignment explanation
Indices: 356772--356821 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
356762 TTATTTTTAT
356772 TTGAGTTTAAAATTAA
1 TTGAGTTTAAAATTAA
356788 TTGAGTTTTAAAATATCAA
1 TTGAG-TTTAAAAT-T-AA
*
356807 TAG-GTTTAAAATTAA
1 TTGAGTTTAAAATTAA
356822 CATTTAGTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 2 0.07
16 6 0.20
17 16 0.53
18 2 0.07
19 4 0.13
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (16 bp):
TTGAGTTTAAAATTAA
Found at i:367138 original size:16 final size:17
Alignment explanation
Indices: 367101--367138 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
367091 CACCATAAAA
367101 ATTTAAAATTATTATAT
1 ATTTAAAATTATTATAT
367118 ATTTAAAATTA-TATAT
1 ATTTAAAATTATTATAT
*
367134 TTTTA
1 ATTTA
367139 TTGAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTAAAATTATTATAT
Found at i:377634 original size:34 final size:34
Alignment explanation
Indices: 377591--377668 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 34
377581 TCGAGCCGAG
377591 TATATATATTTAAATTAAATATATAAA-TATTATA-
1 TATATATATTTAAATTAAAT-T-TAAATTATTATAT
* *
377625 TATATATATTTTAATTTAATTTAAATTTATTATAT
1 TATATATATTTAAATTAAATTTAAA-TTATTATAT
377660 TATATATAT
1 TATATATAT
377669 ATAATAATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
32 4 0.10
33 1 0.03
34 25 0.64
35 9 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (34 bp):
TATATATATTTAAATTAAATTTAAATTATTATAT
Found at i:377685 original size:37 final size:39
Alignment explanation
Indices: 377591--377692 Score: 97
Period size: 39 Copynumber: 2.7 Consensus size: 39
377581 TCGAGCCGAG
* * *
377591 TATATAT-ATTTAAATTAA-ATATATAAATATTATATATA
1 TATATATAATTTAATTTAATATTTAT-TATATTATATATA
*
377629 TATATTTTAATTTAATTTAA-ATTTATTATATTATATATA
1 TATA-TATAATTTAATTTAATATTTATTATATTATATATA
*
377668 TATA-ATAA-TTATTTTTAATATTTAT
1 TATATATAATTTA-ATTTAATATTTAT
377693 CGGGCCGAGT
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
36 3 0.06
37 8 0.15
38 10 0.19
39 18 0.33
40 15 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (39 bp):
TATATATAATTTAATTTAATATTTATTATATTATATATA
Found at i:386125 original size:31 final size:30
Alignment explanation
Indices: 386090--386147 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
386080 AAATTATGTA
386090 TTTAGTA-CTTAAACTATCAGTTTTTTTATAT
1 TTTAGTATC-TAAACTATCA-TTTTTTTATAT
*
386121 TTTAGTATCTAAACTTTCATTTTTTTA
1 TTTAGTATCTAAACTATCATTTTTTTA
386148 ATCATACCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 8 0.32
31 16 0.64
32 1 0.04
ACGTcount: A:0.28, C:0.10, G:0.05, T:0.57
Consensus pattern (30 bp):
TTTAGTATCTAAACTATCATTTTTTTATAT
Found at i:387408 original size:18 final size:18
Alignment explanation
Indices: 387382--387417 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
387372 CAAAATTTTA
387382 TTAAGAGTTTTGAAACTT
1 TTAAGAGTTTTGAAACTT
*
387400 TTAATAGTTTTGAAACTT
1 TTAAGAGTTTTGAAACTT
387418 CATACTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.47
Consensus pattern (18 bp):
TTAAGAGTTTTGAAACTT
Found at i:389104 original size:31 final size:31
Alignment explanation
Indices: 389068--389126 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
389058 AACTTAAAGG
* *
389068 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
389099 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
389127 CTATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:389162 original size:21 final size:22
Alignment explanation
Indices: 389138--389188 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
389128 TATACAACTA
389138 AAAT-AATAAAT-TATTTAAAAT
1 AAATCAATAAATAT-TTTAAAAT
**
389159 AAATCAATCCATATTTTAAAAT
1 AAATCAATAAATATTTTAAAAT
389181 AAATCAAT
1 AAATCAAT
389189 CCTTACTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 4 0.15
22 21 0.81
23 1 0.04
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (22 bp):
AAATCAATAAATATTTTAAAAT
Found at i:389202 original size:22 final size:22
Alignment explanation
Indices: 389153--389201 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
389143 ATAAATTATT
**
389153 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
389175 TAAAATAAATCAATCCTTACTAA
1 TAAAATAAATCAATCCATA-TAA
389198 TAAA
1 TAAA
389202 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:389205 original size:54 final size:53
Alignment explanation
Indices: 389141--389386 Score: 245
Period size: 54 Copynumber: 4.5 Consensus size: 53
389131 ACAACTAAAA
*
389141 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCTTAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT-CATAC
* *** *
389195 TAATAAATTATTTAAAATAAATCAATCTATACAACTACAAT-AAT-AA--AT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCATAC
*
389244 -AATCAA-TATTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATCAATC-ATAC
389306 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT-CATAC
*
389360 AAATAAATTATTTAAAATAAATCAATC
1 TAATAAATTATTTAAAATAAATCAATC
389387 TATACTAATA
Statistics
Matches: 158, Mismatches: 15, Indels: 38
0.75 0.07 0.18
Matches are distributed among these distances:
47 18 0.11
48 6 0.04
49 1 0.01
50 1 0.01
53 4 0.03
54 79 0.50
55 8 0.05
56 6 0.04
57 3 0.02
58 4 0.03
60 1 0.01
61 2 0.01
62 1 0.01
63 6 0.04
64 18 0.11
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (53 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCATAC
Found at i:389291 original size:14 final size:14
Alignment explanation
Indices: 389274--389327 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
389264 CAATCCATAC
389274 AAATAAATTATTTA
1 AAATAAATTATTTA
*
389288 AAATAAATCAATCTATA
1 AAATAAAT-TAT-T-TA
*
389305 CTAATAAATTATTTA
1 -AAATAAATTATTTA
389320 AAATAAAT
1 AAATAAAT
389328 CAATCCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.47
15 4 0.12
16 2 0.06
17 4 0.12
18 7 0.22
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:389291 original size:32 final size:32
Alignment explanation
Indices: 389250--389531 Score: 282
Period size: 32 Copynumber: 9.8 Consensus size: 32
389240 AATCAATCAA
*
389250 TATTTAAAATAAATCAATCCATACAAATAAAT
1 TATTTAAAATAAATCAATCCATACTAATAAAT
*
389282 TATTTAAAATAAATCAATCTATACTAATAAAT
1 TATTTAAAATAAATCAATCCATACTAATAAAT
389314 TATTTAAAATAAATCAAT-C---C--AT--A-
1 TATTTAAAATAAATCAATCCATACTAATAAAT
*
389337 T-TTTAAAATAAATCAATCCATACAAATAAAT
1 TATTTAAAATAAATCAATCCATACTAATAAAT
*
389368 TATTTAAAATAAATCAATCTATACTAATAAAT
1 TATTTAAAATAAATCAATCCATACTAATAAAT
389400 TATTTAAAATAAATCAAT-C---C--AT--A-
1 TATTTAAAATAAATCAATCCATACTAATAAAT
*
389423 T-TTTAAAATAAATCAATGCATACTAATAAAT
1 TATTTAAAATAAATCAATCCATACTAATAAAT
389454 TATTTAAAATAAATCAAT-C---C--AT--A-
1 TATTTAAAATAAATCAATCCATACTAATAAAT
*
389477 T-TTTAAAATAAATCAATTCATACTAATAAAT
1 TATTTAAAATAAATCAATCCATACTAATAAAT
* *
389508 TATTTAAAATAAATAAATCTATAC
1 TATTTAAAATAAATCAATCCATAC
389532 AACTACAATA
Statistics
Matches: 211, Mismatches: 9, Indels: 60
0.75 0.03 0.21
Matches are distributed among these distances:
22 48 0.23
23 6 0.03
24 3 0.01
26 9 0.04
28 9 0.04
30 3 0.01
31 4 0.02
32 129 0.61
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.35
Consensus pattern (32 bp):
TATTTAAAATAAATCAATCCATACTAATAAAT
Found at i:389342 original size:22 final size:22
Alignment explanation
Indices: 389316--389358 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
389306 TAATAAATTA
389316 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
389338 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
389359 CAAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:389367 original size:22 final size:22
Alignment explanation
Indices: 389318--389366 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
389308 ATAAATTATT
***
389318 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATAAAA
389340 TAAAATAAATCAATCCATACAAA
1 TAAAATAAATCAATCCATA-AAA
389363 TAAA
1 TAAA
389367 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAATAAATCAATCCATAAAA
Found at i:389377 original size:14 final size:14
Alignment explanation
Indices: 389360--389413 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
389350 CAATCCATAC
389360 AAATAAATTATTTA
1 AAATAAATTATTTA
*
389374 AAATAAATCAATCTATA
1 AAATAAAT-TAT-T-TA
*
389391 CTAATAAATTATTTA
1 -AAATAAATTATTTA
389406 AAATAAAT
1 AAATAAAT
389414 CAATCCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.47
15 4 0.12
16 2 0.06
17 4 0.12
18 7 0.22
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:389428 original size:22 final size:22
Alignment explanation
Indices: 389402--389444 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
389392 TAATAAATTA
389402 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
389424 TTTAAAATAAATCAATGCATA
1 TTTAAAATAAATCAATCCATA
389445 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:389428 original size:54 final size:53
Alignment explanation
Indices: 389370--389750 Score: 470
Period size: 54 Copynumber: 7.0 Consensus size: 53
389360 AAATAAATTA
389370 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATC-ATACTAATAAATTATTTAAAATAAATCAATCCATAT
389424 TTTAAAATAAATCAATGCATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAAT-CATACTAATAAATTATTTAAAATAAATCAATCCATAT
* * *
389478 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATAAATCTATACA
1 TTTAAAATAAATCAA-TCATACTAATAAATTATTTAAAATAAATCAATCCATA-T
** * *
389533 ACTACAAT-AAT-AA--AT-C-AATCAA-TATTTTAAAATAAATCAATCCATACAAATAAATT
1 TTTAAAATAAATCAATCATACTAATAAATTA-TTTAAAATAAATCAAT-C---C--AT--A-T
*
389589 ATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCAATAT
1 -TTTAAAATAAATCAAT-CATACTAATAAATTATTTAAAATAAATCAATCCATAT
389644 TTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAAT-CATACTAATAAATTATTTAAAATAAATCAATCCATAT
*
389698 TTTAAAGTAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAAT-CATACTAATAAATTATTTAAAATAAATCAATCCATA
389751 CAACTACAAT
Statistics
Matches: 286, Mismatches: 20, Indels: 42
0.82 0.06 0.12
Matches are distributed among these distances:
47 2 0.01
48 20 0.07
49 2 0.01
50 2 0.01
53 2 0.01
54 209 0.73
55 8 0.03
56 2 0.01
57 5 0.02
58 5 0.02
59 2 0.01
62 2 0.01
63 2 0.01
64 21 0.07
65 2 0.01
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.35
Consensus pattern (53 bp):
TTTAAAATAAATCAATCATACTAATAAATTATTTAAAATAAATCAATCCATAT
Found at i:389453 original size:22 final size:22
Alignment explanation
Indices: 389404--389452 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
389394 ATAAATTATT
**
389404 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
389426 TAAAATAAATCAATGCATACTAA
1 TAAAATAAATCAATCCATA-TAA
389449 TAAA
1 TAAA
389453 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:389482 original size:22 final size:22
Alignment explanation
Indices: 389456--389498 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
389446 TAATAAATTA
389456 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
389478 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
389499 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:389507 original size:22 final size:22
Alignment explanation
Indices: 389458--389506 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
389448 ATAAATTATT
**
389458 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
389480 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
389503 TAAA
1 TAAA
389507 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:389587 original size:220 final size:220
Alignment explanation
Indices: 389236--389821 Score: 987
Period size: 220 Copynumber: 2.6 Consensus size: 220
389226 CAACTACAAT
* *
389236 AATAAATCAATCAATA-TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
*
389300 CTATACTAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAAT
66 CTATAC-AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAAT
* *
389364 AAATTATTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAA
124 AAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCAATATTTTAA
*
389429 AATAAATCAATGCATACTAATAAATTATTTAA
189 AATAAATCAATACATACTAATAAATTATTTAA
* *
389461 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATAAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
*
389526 CTATACAACTACAATAATAAATCAATCAATATTTTAAAATAAATCAATCCATACAAATAAATTAT
66 CTATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTAT
389591 TTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCAATATTTTAAAATAAAT
131 TTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCAATATTTTAAAATAAAT
389656 CAATACATACTAATAAATTATTTAA
196 CAATACATACTAATAAATTATTTAA
*
389681 AATAAATCAATCCATATTTTAAAGTAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* *
389746 CCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
66 CTATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTAT
389811 TTAAAATAAAT
131 TTAAAATAAAT
389822 TATTTTAAAA
Statistics
Matches: 344, Mismatches: 15, Indels: 9
0.93 0.04 0.02
Matches are distributed among these distances:
220 271 0.79
222 1 0.00
224 1 0.00
225 17 0.05
226 54 0.16
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (220 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CTATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTAT
TTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCAATATTTTAAAATAAAT
CAATACATACTAATAAATTATTTAA
Found at i:389597 original size:32 final size:32
Alignment explanation
Indices: 389558--389821 Score: 224
Period size: 32 Copynumber: 9.4 Consensus size: 32
389548 CAATCAATAT
*
389558 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
389590 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
389622 TTTAAAATAAATC-A---AT-C-AAT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
389644 TTTAAAATAAATCAATACATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
389676 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
389698 TTTAAAGTAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
389730 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
389760 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
389778 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
389810 TTTAAAATAAAT
1 TTTAAAATAAAT
389822 TATTTTAAAA
Statistics
Matches: 192, Mismatches: 4, Indels: 72
0.72 0.01 0.27
Matches are distributed among these distances:
20 1 0.01
22 42 0.22
23 5 0.03
24 4 0.02
25 1 0.01
26 23 0.12
27 2 0.01
28 9 0.05
30 3 0.02
31 6 0.03
32 96 0.50
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:389702 original size:22 final size:22
Alignment explanation
Indices: 389676--389718 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
389666 TAATAAATTA
389676 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
389698 TTTAAAGTAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
389719 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.14, G:0.02, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:389804 original size:18 final size:19
Alignment explanation
Indices: 389760--389807 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 19
389750 ACAACTACAA
*
389760 TAATAAATCAATCCATATTT
1 TAATAAATCAATCCATA-TC
389780 TAAAATAAATCAATCCATA-C
1 T--AATAAATCAATCCATATC
389800 TAATAAAT
1 TAATAAAT
389808 TATTTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 7 0.28
20 2 0.08
22 16 0.64
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (19 bp):
TAATAAATCAATCCATATC
Found at i:389820 original size:94 final size:96
Alignment explanation
Indices: 389667--389935 Score: 266
Period size: 94 Copynumber: 2.7 Consensus size: 96
389657 AATACATACT
* * ** *
389667 AATAAATTA-TTTAAAATAAATCAATCCATATTTTAAAGTAAATCAATCCATACTAATAAATTA-
1 AATAAATTATTTTAAAATAAATCAATCCATA-TAT-AA-TAAAT-TAT-TTTA-AAATAAATTAT
389730 TTTAAAATAAATCAATCCATAC-AACTACAA-TA-AT-A
60 TTTAAAATAAATCAATCCATACTAA-TA-AATTATATAA
* *
389765 AATCAATCCATATTTTAAAATAAATCAATCCATA-CTAATAAATTA-TTTAAAATAAATTATTTT
1 AATAAAT---TATTTTAAAATAAATCAATCCATATATAATAAATTATTTTAAAATAAATTATTTT
*
389828 AAAATAAATCAATCCATACTAATAAATTATTTAA
63 AAAATAAATCAATCCATACTAATAAATTATATAA
*
389862 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTAAAATAAATTATTTT
1 AATAAATTATTTTAAAATAAATCAATCCATA---TATAATAAATTATTTTAAAATAAATTATTTT
*
389927 ATAATAAAT
63 AAAATAAAT
389936 TATGTTAAAA
Statistics
Matches: 146, Mismatches: 11, Indels: 27
0.79 0.06 0.15
Matches are distributed among these distances:
94 35 0.24
95 28 0.19
96 3 0.02
97 8 0.05
98 20 0.14
99 28 0.19
100 1 0.01
101 2 0.01
102 21 0.14
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (96 bp):
AATAAATTATTTTAAAATAAATCAATCCATATATAATAAATTATTTTAAAATAAATTATTTTAAA
ATAAATCAATCCATACTAATAAATTATATAA
Found at i:389830 original size:15 final size:15
Alignment explanation
Indices: 389801--389965 Score: 154
Period size: 15 Copynumber: 10.5 Consensus size: 15
389791 AATCCATACT
389801 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
389815 AATAAATTATTTTAA
1 AATAAATTATTTTAA
* ** *
389830 AATAAATCAATCCATACT
1 AATAAAT-TAT-TTTA-A
389848 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
389862 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
389877 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
389899 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
389914 AATAAATTATTTTAT
1 AATAAATTATTTTAA
*
389929 AATAAATTATGTTAA
1 AATAAATTATTTTAA
389944 AATAAATTATTTTAA
1 AATAAATTATTTTAA
389959 AATAAAT
1 AATAAAT
389966 AACCTTATTA
Statistics
Matches: 123, Mismatches: 16, Indels: 23
0.76 0.10 0.14
Matches are distributed among these distances:
14 18 0.15
15 76 0.62
16 2 0.02
17 4 0.03
18 9 0.07
19 3 0.02
20 1 0.01
22 10 0.08
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:389843 original size:47 final size:47
Alignment explanation
Indices: 389721--389935 Score: 260
Period size: 47 Copynumber: 4.5 Consensus size: 47
389711 AATCCATACT
*
389721 AATAAATTA-TTTAAAATAAATCAATCCATAC-AACTACAA-TA-AT-A
1 AATAAATTATTTTAAAATAAATCAATCCATACTAA-TA-AATTATTTAA
*
389765 AATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAAT---TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
389815 AATAAATTATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATTATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
389862 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTAA
1 AATAAATTATTTTAAAATAAATCAATCCATA----CTAATAAATTA-TTTAA
*
389914 AATAAATTATTTTATAATAAAT
1 AATAAATTATTTTAAAATAAAT
389936 TATGTTAAAA
Statistics
Matches: 152, Mismatches: 6, Indels: 18
0.86 0.03 0.10
Matches are distributed among these distances:
44 6 0.04
47 75 0.49
48 26 0.17
49 3 0.02
50 7 0.05
51 9 0.06
52 26 0.17
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (47 bp):
AATAAATTATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:396422 original size:15 final size:15
Alignment explanation
Indices: 396402--396438 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
396392 GATATTAGCT
*
396402 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
396417 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
396432 GGGCGGG
1 GGGCGGG
396439 TAATGTCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.70, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:401936 original size:21 final size:21
Alignment explanation
Indices: 401912--401951 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
401902 ATTCGGAACA
401912 CGAATTTCAACTATCGCAATG
1 CGAATTTCAACTATCGCAATG
*
401933 CGAATTTGAACTATCGCAA
1 CGAATTTCAACTATCGCAA
401952 ATTATTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.28
Consensus pattern (21 bp):
CGAATTTCAACTATCGCAATG
Found at i:402574 original size:3 final size:3
Alignment explanation
Indices: 402562--402622 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
402552 CATCTCAGTC
402562 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
402609 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
402623 GAATTGTAGA
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.04
3 55 0.96
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:406713 original size:32 final size:32
Alignment explanation
Indices: 406658--406773 Score: 117
Period size: 32 Copynumber: 3.7 Consensus size: 32
406648 AGAGGACGAG
*
406658 GATTCCAACATCAA-GGAGTGAGGAGGAGAAC
1 GATTGCAACATCAATGGAGTGAGGAGGAGAAC
* ** *
406689 GATTACAACATCAATGGAGTGAGGACAACAAC
1 GATTGCAACATCAATGGAGTGAGGAGGAGAAC
* * * * *
406721 AATTGCAGCATCAATGGAATGAAGAGGAGGAC
1 GATTGCAACATCAATGGAGTGAGGAGGAGAAC
* *
406753 GACTGCAACATTAATGGAGTG
1 GATTGCAACATCAATGGAGTG
406774 TGGACGACGA
Statistics
Matches: 66, Mismatches: 18, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
31 13 0.20
32 53 0.80
ACGTcount: A:0.40, C:0.16, G:0.28, T:0.16
Consensus pattern (32 bp):
GATTGCAACATCAATGGAGTGAGGAGGAGAAC
Found at i:415118 original size:19 final size:20
Alignment explanation
Indices: 415080--415118 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
415070 ATTAAAGTAC
*
415080 TATTTAAATATGTGTAACAT
1 TATTTAAATATGTCTAACAT
*
415100 TATTTAACTAT-TCTAACAT
1 TATTTAAATATGTCTAACAT
415119 GAACTAGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.46
Consensus pattern (20 bp):
TATTTAAATATGTCTAACAT
Found at i:415345 original size:21 final size:21
Alignment explanation
Indices: 415321--415361 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
415311 GGTAAAAAGT
* *
415321 TACCTTAAACATTATTATTTA
1 TACCTAAAACATTAATATTTA
415342 TACCTAAAACATTAATATTT
1 TACCTAAAACATTAATATTT
415362 TTTAACATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (21 bp):
TACCTAAAACATTAATATTTA
Found at i:425240 original size:31 final size:31
Alignment explanation
Indices: 425199--425258 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
425189 TCACCAAAAA
* * *
425199 AAAATAATGATGTGTCATGTAGCACATCACT
1 AAAATAATGATATGACATATAGCACATCACT
* *
425230 AAAATTATGATATGACATATATCACATCA
1 AAAATAATGATATGACATATAGCACATCA
425259 TCAACAACGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.30
Consensus pattern (31 bp):
AAAATAATGATATGACATATAGCACATCACT
Found at i:425458 original size:19 final size:20
Alignment explanation
Indices: 425434--425472 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
425424 ATTTTATTAA
425434 TAAACTACAT-AAACATATT
1 TAAACTACATCAAACATATT
**
425453 TAAACTTTATCAAACATATT
1 TAAACTACATCAAACATATT
425473 ATTTTCATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAACTACATCAAACATATT
Found at i:426115 original size:28 final size:28
Alignment explanation
Indices: 426079--426135 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
426069 GTCTTCGTTT
*
426079 ACATTATGTCGTCGAG-TCAGTGTTTGAA
1 ACATTATGTCGTCGAGCT-AGTGCTTGAA
*
426107 ACATTATGTTGTCGAGCTAGTGCTTGAA
1 ACATTATGTCGTCGAGCTAGTGCTTGAA
426135 A
1 A
426136 TCAACGACGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 25 0.96
29 1 0.04
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (28 bp):
ACATTATGTCGTCGAGCTAGTGCTTGAA
Found at i:430256 original size:18 final size:18
Alignment explanation
Indices: 430229--430299 Score: 74
Period size: 18 Copynumber: 3.9 Consensus size: 18
430219 AAAAACCTCA
*
430229 TCAGACTCATCTTCATCC
1 TCAGAATCATCTTCATCC
* *
430247 TCAGAATCATCTTCTTCA
1 TCAGAATCATCTTCATCC
430265 TCAGAA-C-TACTTTCATCC
1 TCAGAATCAT-C-TTCATCC
*
430283 TAAGAATCATCTTCATC
1 TCAGAATCATCTTCATC
430300 GGAACTACTT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
16 1 0.02
17 2 0.05
18 37 0.86
19 2 0.05
20 1 0.02
ACGTcount: A:0.28, C:0.31, G:0.06, T:0.35
Consensus pattern (18 bp):
TCAGAATCATCTTCATCC
Found at i:430334 original size:20 final size:20
Alignment explanation
Indices: 430309--430369 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
430299 CGGAACTACT
430309 TTCATCCTAGAATCATCTTC
1 TTCATCCTAGAATCATCTTC
* *
430329 TTCATCATA-ACT-A-C-T-
1 TTCATCCTAGAATCATCTTC
430344 TTCATCCTAGAATCATCTTC
1 TTCATCCTAGAATCATCTTC
430364 TTCATC
1 TTCATC
430370 ATAACTACTT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 8 0.25
16 3 0.09
17 2 0.06
18 2 0.06
19 3 0.09
20 14 0.44
ACGTcount: A:0.26, C:0.30, G:0.03, T:0.41
Consensus pattern (20 bp):
TTCATCCTAGAATCATCTTC
Found at i:430341 original size:35 final size:36
Alignment explanation
Indices: 430240--430395 Score: 241
Period size: 35 Copynumber: 4.5 Consensus size: 36
430230 CAGACTCATC
430240 TTCATCCTCAGAATCATCTTCTTCATCAGAACTACT
1 TTCATCCTCAGAATCATCTTCTTCATCAGAACTACT
* *
430276 TTCATCCTAAGAATCA---TCTTCATCGGAACTACT
1 TTCATCCTCAGAATCATCTTCTTCATCAGAACTACT
*
430309 TTCATCCT-AGAATCATCTTCTTCATCATAACTACT
1 TTCATCCTCAGAATCATCTTCTTCATCAGAACTACT
*
430344 TTCATCCT-AGAATCATCTTCTTCATCATAACTACT
1 TTCATCCTCAGAATCATCTTCTTCATCAGAACTACT
430379 TTCATCCTCAGAATCAT
1 TTCATCCTCAGAATCAT
430396 AGTCATCGTC
Statistics
Matches: 112, Mismatches: 4, Indels: 8
0.90 0.03 0.06
Matches are distributed among these distances:
32 7 0.06
33 24 0.21
35 58 0.52
36 23 0.21
ACGTcount: A:0.29, C:0.29, G:0.05, T:0.37
Consensus pattern (36 bp):
TTCATCCTCAGAATCATCTTCTTCATCAGAACTACT
Found at i:432268 original size:28 final size:28
Alignment explanation
Indices: 432237--432304 Score: 127
Period size: 28 Copynumber: 2.4 Consensus size: 28
432227 GATTATTGAC
*
432237 CAAATTAATACCTTTTAAATTTCGATCA
1 CAAATTATTACCTTTTAAATTTCGATCA
432265 CAAATTATTACCTTTTAAATTTCGATCA
1 CAAATTATTACCTTTTAAATTTCGATCA
432293 CAAATTATTACC
1 CAAATTATTACC
432305 AACTAATCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.38, C:0.19, G:0.03, T:0.40
Consensus pattern (28 bp):
CAAATTATTACCTTTTAAATTTCGATCA
Found at i:432558 original size:21 final size:20
Alignment explanation
Indices: 432521--432567 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
432511 TTTAAATTTG
432521 ATTTGATTAAATATGATTAA
1 ATTTGATTAAATATGATTAA
* *
432541 TATTTGATTTAGAT-TGATTCA
1 -ATTTGA-TTAAATATGATTAA
432562 ATTTGA
1 ATTTGA
432568 ATTCAAGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 6 0.26
21 12 0.52
22 5 0.22
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (20 bp):
ATTTGATTAAATATGATTAA
Found at i:432899 original size:34 final size:34
Alignment explanation
Indices: 432828--432926 Score: 96
Period size: 34 Copynumber: 2.9 Consensus size: 34
432818 ATTAAAATAA
* * * * *
432828 TATCTATTTAAGTTTGAATAGTAAAAGATAACT-T
1 TATCTGTTTAAATTTGAATATTAAAATAT-ATTAT
*
432862 TATCT-TTTGAATATTTTAA-ATTAAAATATATTAT
1 TATCTGTTT-AA-ATTTGAATATTAAAATATATTAT
432896 TATCTGTTTAAATTTGAATATTAAAATATAT
1 TATCTGTTTAAATTTGAATATTAAAATATAT
432927 GTAGATAGAG
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
33 11 0.20
34 35 0.65
35 8 0.15
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.47
Consensus pattern (34 bp):
TATCTGTTTAAATTTGAATATTAAAATATATTAT
Found at i:432921 original size:68 final size:64
Alignment explanation
Indices: 432776--432921 Score: 163
Period size: 68 Copynumber: 2.2 Consensus size: 64
432766 CCTACATAAC
* *
432776 TTTGAATATT-AAAGATAATTATATTTTTTTTGAATATTTCAAATTAAAATAATATCTATTTAAG
1 TTTGAATATTAAAAGATAATTATA-TTCTTTTGAATATTTCAAATTAAAATAATATCTATTTAAA
* * *
432840 TTTGAATAGTAAAAGATAACTT-TA-TCTTTTGAATATTTTAAATTAAAATATATTATTATCTGT
1 TTTGAATATTAAAAGATAA-TTATATTCTTTTGAATATTTCAAATT-AAA-ATA--A-TATCTAT
432903 TTAAA
60 TTAAA
432908 TTTGAATATTAAAA
1 TTTGAATATTAAAA
432922 TATATGTAGA
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
63 18 0.26
64 12 0.17
65 13 0.19
66 2 0.03
67 1 0.01
68 23 0.33
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (64 bp):
TTTGAATATTAAAAGATAATTATATTCTTTTGAATATTTCAAATTAAAATAATATCTATTTAAA
Found at i:433099 original size:13 final size:13
Alignment explanation
Indices: 433080--433143 Score: 119
Period size: 13 Copynumber: 4.9 Consensus size: 13
433070 AGACTTTGTT
433080 TGAGTTGACTCAA
1 TGAGTTGACTCAA
*
433093 CGAGTTGACTCAA
1 TGAGTTGACTCAA
433106 TGAGTTGACTCAA
1 TGAGTTGACTCAA
433119 TGAGTTGACTCAA
1 TGAGTTGACTCAA
433132 TGAGTTGACTCA
1 TGAGTTGACTCA
433144 GTTGGACCGG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 49 1.00
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (13 bp):
TGAGTTGACTCAA
Found at i:436262 original size:21 final size:20
Alignment explanation
Indices: 436233--436275 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
436223 TTTGTTTTTT
436233 GCTTTAAAAACAGAGTTTCA
1 GCTTTAAAAACAGAGTTTCA
436253 GCTTTAAAAACAGAGTTTCA
1 GCTTTAAAAACAGAGTTTCA
436273 GCT
1 GCT
436276 GATTCGAGGG
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:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (20 bp):
GCTTTAAAAACAGAGTTTCA
Found at i:451286 original size:228 final size:224
Alignment explanation
Indices: 450880--451324 Score: 766
Period size: 228 Copynumber: 2.0 Consensus size: 224
450870 GTAAATTATC
* *
450880 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATTTATTATTATCTTTAGTTA
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATTTATTATTATATTTAGTTA
**
450945 ATATTGTTAAATTTAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGT
66 ATATTGTTAAATTTAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTTTGT
*
451010 GTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAA
131 GTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTGAAA
451075 CATAAATTACATAACTTTCAAAAAAGTATA
196 CATAAATTACATAACTTT-AAAAAAGTATA
*
451105 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TG-AAA-ATATTTATTATTATATTTAG
451170 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
63 TTAATATTGTTAAATTTAAA-TCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
451235 TTGTGT-AATTAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAAATT
127 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATT
451299 GAAACATAAATTACATAACTTTAAAA
192 GAAACATAAATTACATAACTTTAAAA
451325 GCAGTTTAAA
Statistics
Matches: 208, Mismatches: 8, Indels: 6
0.94 0.04 0.03
Matches are distributed among these distances:
225 36 0.17
226 2 0.01
227 7 0.03
228 115 0.55
229 48 0.23
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (224 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATTTATTATTATATTTAGTTA
ATATTGTTAAATTTAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTTTGT
GTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTGAAA
CATAAATTACATAACTTTAAAAAAGTATA
Found at i:451413 original size:20 final size:19
Alignment explanation
Indices: 451390--451436 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
451380 CGATATACCA
451390 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
451410 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
451430 GGTAAAA
1 GGTAAAA
451437 TTAAAAGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:453957 original size:33 final size:32
Alignment explanation
Indices: 453896--453960 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
453886 AAATAGAAGG
*
453896 AGTGGTGAAAGAAGTAGAGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGTGTTAAGGGGTGA
*
453928 AGTGGTGAAAGAAGTTTCG-GTGTTAAGGGGTGA
1 AGTGGTGAAAGAAG--TAGAGTGTTAAGGGGTGA
453961 TATTAAGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 14 0.48
33 13 0.45
34 2 0.07
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.25
Consensus pattern (32 bp):
AGTGGTGAAAGAAGTAGAGTGTTAAGGGGTGA
Found at i:456732 original size:395 final size:397
Alignment explanation
Indices: 455865--457277 Score: 2626
Period size: 395 Copynumber: 3.6 Consensus size: 397
455855 TTAAGGGTCA
* *
455865 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCA
455930 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
455995 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
456060 ATGTGTCGACACTAATATAGTTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTG
196 ATGTGTCGACACTAATATAG-TTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTG
*
456125 CATCAATAAAGTGTCGATCTATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC-AAAGTAT
260 CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
*
456189 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
325 AATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
*
456254 AAATAATA
390 AAATAATG
*
456262 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCA
456327 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
456392 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
130 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
456457 AATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTAAAAACAAGGTG
195 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTG
456521 CATCAATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
260 CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
456585 AATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGG-TTTATGAGAGAATAAGTCT
325 AATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
456649 AAATAATG
390 AAATAATG
*
456657 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCA
456722 ATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
456786 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
456851 ATGTGTCGACACTAATATAG-TTGTGTCGATATTTTTTTTCCAGAATGAA-TAAAAACAAGGTGC
196 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGC
456914 ATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
261 ATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
456979 ATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
326 ATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
457044 AATAATG
391 AATAATG
457051 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATTAAAAACAAGGTGCACC
* *
457116 CATAAAGTGTCGATCCATATATAAAACGTGTCGATCCC-AAATCATCGAACCCAAAAGTATAATG
65 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* * *
457180 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
130 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
*
457245 AATGTGTCGACACTAATATATTTTGTGTCGATA
195 AATGTGTCGACACTAATATAGTTTGTGTCGATA
457278 CTAATTTAAA
Statistics
Matches: 993, Mismatches: 15, Indels: 17
0.97 0.01 0.02
Matches are distributed among these distances:
392 50 0.05
393 228 0.23
394 63 0.06
395 296 0.30
396 132 0.13
397 95 0.10
398 129 0.13
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (397 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCA
ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGC
ATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
ATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
AATAATG
Found at i:456965 original size:197 final size:198
Alignment explanation
Indices: 455865--457277 Score: 2615
Period size: 197 Copynumber: 7.1 Consensus size: 198
455855 TTAAGGGTCA
*
455865 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
455930 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
455995 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
456060 ATG
196 ATG
456063 TGTCGACACTAATATAGTTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCAT
1 TGTCGACACTAATATAG-TTTGTGTCGATA-TTTTTTTCCAGAATGAATTAAAAACAAGGTGCAT
*
456128 CAATAAAGTGTCGATCTATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC-AAAGTATAAT
64 CAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
456192 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
129 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
*
456257 TAATA
194 TAATG
* *
456262 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
456327 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
456392 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
130 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
456457 AATG
195 AATG
456461 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
456526 ATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
456590 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGG-TTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
456654 ATG
196 ATG
456657 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
456722 ATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
456786 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
456851 ATG
196 ATG
456854 TGTCGACACTAATATAG-TTGTGTCGATATTTTTTTTCCAGAATGAA-TAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
456917 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
65 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
456982 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
130 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
457047 AATG
195 AATG
*
457051 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATTAAAAACAAGGTGCATC
* *
457116 CATAAAGTGTCGATCCATATATAAAACGTGTCGATCCC-AAATCATCGAACCCAAAAGTATAATG
65 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* * *
457180 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
130 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
457245 AATG
195 AATG
*
457249 TGTCGACACTAATATATTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
457278 CTAATTTAAA
Statistics
Matches: 1187, Mismatches: 18, Indels: 20
0.97 0.01 0.02
Matches are distributed among these distances:
196 246 0.21
197 333 0.28
198 200 0.17
199 321 0.27
200 87 0.07
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (198 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
ATG
Found at i:458763 original size:3 final size:3
Alignment explanation
Indices: 458743--458835 Score: 96
Period size: 3 Copynumber: 31.0 Consensus size: 3
458733 TGAAGCTGAC
* * * * * ** *
458743 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
458791 GAT GAT GAC GAT GAT GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
458836 CCAAACAAGT
Statistics
Matches: 71, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.35, C:0.05, G:0.34, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:458778 original size:42 final size:42
Alignment explanation
Indices: 458731--458819 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
458721 GGTCGCAGAA
*
458731 GATGAAGCTGACGATGAAGATGACGATGATGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
* * *
458773 GATGAAGCTGGCGATGAAGATGATGACGATGATGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
458815 GATGA
1 GATGA
458820 TGATGAAGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.22
Consensus pattern (42 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
Found at i:458806 original size:12 final size:12
Alignment explanation
Indices: 458728--458835 Score: 99
Period size: 12 Copynumber: 9.0 Consensus size: 12
458718 ATCGGTCGCA
* *
458728 GAAGATGAAGCT
1 GAAGATGATGAT
* *
458740 GACGATGAAGAT
1 GAAGATGATGAT
*
458752 GACGATGATGAT
1 GAAGATGATGAT
* *
458764 GATGATGACGAT
1 GAAGATGATGAT
* **
458776 GAAGCTGGCGAT
1 GAAGATGATGAT
*
458788 GAAGATGATGAC
1 GAAGATGATGAT
*
458800 GATGATGATGAT
1 GAAGATGATGAT
*
458812 GATGATGATGAT
1 GAAGATGATGAT
458824 GAAGATGATGAT
1 GAAGATGATGAT
458836 CCAAACAAGT
Statistics
Matches: 81, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 81 1.00
ACGTcount: A:0.36, C:0.06, G:0.34, T:0.23
Consensus pattern (12 bp):
GAAGATGATGAT
Found at i:458832 original size:18 final size:18
Alignment explanation
Indices: 458731--458835 Score: 111
Period size: 18 Copynumber: 5.8 Consensus size: 18
458721 GGTCGCAGAA
* * *
458731 GATGAAGCTGACGATGAA
1 GATGAAGATGATGATGAT
*
458749 GATGACGATGATGATGAT
1 GATGAAGATGATGATGAT
* * * **
458767 GATGACGATGAAGCTGGC
1 GATGAAGATGATGATGAT
*
458785 GATGAAGATGATGACGAT
1 GATGAAGATGATGATGAT
*
458803 GATGATGATGATGATGAT
1 GATGAAGATGATGATGAT
458821 GATGAAGATGATGAT
1 GATGAAGATGATGAT
458836 CCAAACAAGT
Statistics
Matches: 70, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 70 1.00
ACGTcount: A:0.35, C:0.07, G:0.34, T:0.24
Consensus pattern (18 bp):
GATGAAGATGATGATGAT
Found at i:460628 original size:183 final size:184
Alignment explanation
Indices: 460286--460945 Score: 1173
Period size: 184 Copynumber: 3.7 Consensus size: 184
460276 CTTTCAACAT
**
460286 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTAT-AATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
*
460350 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAAAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
460415 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
460469 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
460534 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
460599 AATGTGTCGATACGATTT-AAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
460652 ATT-TAATGT-A-AGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
460714 GGTCTACAACC--TATCG--ACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
460775 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* *
460829 ATTATAATGTAATAGATAA-TTTGTAATATAACCGGTATAAATATA-C-GTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
*
460891 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
460946 CCATTTAAAA
Statistics
Matches: 461, Mismatches: 7, Indels: 20
0.94 0.01 0.04
Matches are distributed among these distances:
176 63 0.14
177 63 0.14
178 12 0.03
179 32 0.07
180 69 0.15
181 35 0.08
182 6 0.01
183 75 0.16
184 106 0.23
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (184 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:463510 original size:22 final size:21
Alignment explanation
Indices: 463485--463537 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 21
463475 AGGTAAACAT
463485 ATGTAATAGTAGCCCTTATATA
1 ATGTAATAGTA-CCCTTATATA
* *
463507 ATGTAATAGGTATCGTTATATA
1 ATGTAATA-GTACCCTTATATA
463529 ATGTAATAG
1 ATGTAATAG
463538 GTAATGGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 1 0.04
22 24 0.86
23 3 0.11
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (21 bp):
ATGTAATAGTACCCTTATATA
Found at i:463538 original size:22 final size:23
Alignment explanation
Indices: 463500--463550 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 23
463490 ATAGTAGCCC
463500 TTATATAATGTAATAGGT-ATCG
1 TTATATAATGTAATAGGTAATCG
*
463522 TTATATAATGTAATAGGTAATGG
1 TTATATAATGTAATAGGTAATCG
463545 TTATAT
1 TTATAT
463551 TGTAAAGTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.37, C:0.02, G:0.18, T:0.43
Consensus pattern (23 bp):
TTATATAATGTAATAGGTAATCG
Found at i:464187 original size:412 final size:414
Alignment explanation
Indices: 463386--464362 Score: 1703
Period size: 412 Copynumber: 2.4 Consensus size: 414
463376 AATTCGCAGT
463386 ACACTGTTAAAAAAATTGAAACAT-AATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTT-AAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTA-A
463450 AAAGTATGGACACTTTCAATATAATAGGTAAAC--AT-ATGTAATA-GTAGCCCTTATATAATGT
64 AAAG-ATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGT
463511 AATAGGTATCGTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTATAAA
128 AATAGGTATCGTT-TAT-A--TAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTATAAA
463576 AGTGTCCATACTTTTTTCACTGTGGAAAACATTATTTAAGGTTATCTTTTGAGTGAGTTTTAAGA
189 AGTGTCCATACTTTTTTCACTGTGGAAAACATTATTTAAGGTTATCTTTTGAGTGAGTTTTAAGA
463641 TATTAATTTAGTAATTAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTAAATTT
254 TATTAATTTAGTAATTAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTAAATTT
463706 AAAATTCTAAATATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATGAAATTA
319 AAAATTCTAAATATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATGAAATTA
463771 TTAAATCAATATTGTAGGTGGAAAACATGAA
384 TTAAATCAATATTGTAGGTGGAAAACATGAA
463802 ACACTGTTAAAAAATTGAAACATAAATTACATAAG-TTTAAAAAAAGTATCGATCCTTTTTAAAA
1 ACACTGTTAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTAAAA
463866 A-ATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAAT
66 AGATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAAT
463930 AGGTATCGTTTATATAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTT-TAAAAGTGTCC
131 AGGTATCGTTTATATAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTATAAAAGTGTCC
*
463994 CTACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATA-TAA
196 ATACTTTTTTCACTGTGGAAAACATT-ATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAA
464058 TTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTATAAATTTAA
260 TTTAGTAA-T-TAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTA-T-TAAATTTAA
464123 AATTCTAAATAATATTTTATAAAATAT-AAAACAATCAAATAA-TTTTT-TGCAAATGAAA-TAT
321 AATTCTAAAT-ATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATGAAATTAT
464184 TAAATCAATATTGTAGGTGGAAAACATGAA
385 TAAATCAATATTGTAGGTGGAAAACATGAA
464214 ACACTGTTAAAAAATTGAAACATAAATTACAT-AGTTTTAAAAAAAGTATCGATCCTTTTTATAA
1 ACACTGTTAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCC-TTTT-TAA
464278 AAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGT
64 AAAG-ATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGT
464343 AATAGGTATCGTTTATATAA
128 AATAGGTATCGTTTATATAA
464363 GTAATATGTA
Statistics
Matches: 544, Mismatches: 1, Indels: 32
0.94 0.00 0.06
Matches are distributed among these distances:
411 49 0.09
412 187 0.34
413 57 0.10
414 19 0.03
415 86 0.16
416 146 0.27
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (414 bp):
ACACTGTTAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTAAAA
AGATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAAT
AGGTATCGTTTATATAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTATAAAAGTGTCC
ATACTTTTTTCACTGTGGAAAACATTATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAAT
TTAGTAATTAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTAAATTTAAAATTC
TAAATATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATC
AATATTGTAGGTGGAAAACATGAA
Found at i:464373 original size:22 final size:23
Alignment explanation
Indices: 464311--464374 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
464301 ATAGGTAAAC
* * **
464311 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGTTT
464334 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGTTT
*
464357 ATATAA-GTAATATGTATC
1 ATATAATGTAATAGGTATC
464375 TATCTCGCAT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 11 0.31
23 25 0.69
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGTTT
Found at i:464981 original size:18 final size:19
Alignment explanation
Indices: 464946--464982 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
464936 TGGTTATTGT
* *
464946 AAAGTGTCTATCCTTTTTA
1 AAAGTGTCCATACTTTTTA
464965 AAAGTGTCCATACTTTTT
1 AAAGTGTCCATACTTTTT
464983 TCACTGTGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.46
Consensus pattern (19 bp):
AAAGTGTCCATACTTTTTA
Done.