Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008569.1 Hibiscus syriacus cultivar Beakdansim tig00111493_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: 1513883
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 8
Found at i:465956 original size:19 final size:19
Alignment explanation
Indices: 465932--465969 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
465922 CTTGAATCGC
465932 ACTGGGAAGCATCTTGTTT
1 ACTGGGAAGCATCTTGTTT
465951 ACTGGGAAGCATCTTGTTT
1 ACTGGGAAGCATCTTGTTT
465970 TTTGTCGTAC
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:0.21, C:0.16, G:0.26, T:0.37
Consensus pattern (19 bp):
ACTGGGAAGCATCTTGTTT
Found at i:468551 original size:47 final size:47
Alignment explanation
Indices: 468482--468577 Score: 183
Period size: 47 Copynumber: 2.0 Consensus size: 47
468472 ACCAGTGTTA
*
468482 TTTATTTCTTTTTAGTTTGTTTGCTGGTTCGTGCTGGAATTTTGGTT
1 TTTATTTCTTTTTAGTTTGTTTGCTAGTTCGTGCTGGAATTTTGGTT
468529 TTTATTTCTTTTTAGTTTGTTTGCTAGTTCGTGCTGGAATTTTGGTT
1 TTTATTTCTTTTTAGTTTGTTTGCTAGTTCGTGCTGGAATTTTGGTT
468576 TT
1 TT
468578 CTTAAGTATT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.09, C:0.08, G:0.22, T:0.60
Consensus pattern (47 bp):
TTTATTTCTTTTTAGTTTGTTTGCTAGTTCGTGCTGGAATTTTGGTT
Found at i:470969 original size:19 final size:19
Alignment explanation
Indices: 470945--470987 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
470935 CCAGTTTCAT
470945 CAACCCGACCCGATTGCAC
1 CAACCCGACCCGATTGCAC
* *
470964 CAACCCGACCCGGTTGCAG
1 CAACCCGACCCGATTGCAC
470983 CAACC
1 CAACC
470988 GAGTTGCCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.26, C:0.47, G:0.19, T:0.09
Consensus pattern (19 bp):
CAACCCGACCCGATTGCAC
Found at i:474095 original size:46 final size:47
Alignment explanation
Indices: 473982--474101 Score: 188
Period size: 47 Copynumber: 2.6 Consensus size: 47
473972 GAATAAATGT
473982 ATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTCTCGAACAAAAC
1 ATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTCTCGAACAAAAC
* *
474029 ATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTCTCGTAC-AAGC
1 ATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTCTCGAACAAAAC
* **
474075 ATGCGAATTAGTTATCATGCGGTTAGG
1 ATGCGAACTAGAAATCATGCGGTTAGG
474102 ACTTTTTGTG
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
46 27 0.40
47 41 0.60
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Consensus pattern (47 bp):
ATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTCTCGAACAAAAC
Found at i:480951 original size:36 final size:36
Alignment explanation
Indices: 480866--481080 Score: 146
Period size: 36 Copynumber: 6.0 Consensus size: 36
480856 TGGAGAAAAG
480866 TCAATCTTAAGCCTTCACCGAAGAGG--AGTGAAGCAGA
1 TCAATCTTAAGCCTTCACC--AGAGGATAGTGAAGCA-A
*
480903 TCAATCTAAAGCCTTCA-CAGGAGGATAGTGAAGCAA
1 TCAATCTTAAGCCTTCACCA-GAGGATAGTGAAGCAA
*
480939 ACAATCTTAAGCCTTCACCAGA-GATTAGTGAAGCAA
1 TCAATCTTAAGCCTTCACCAGAGGA-TAGTGAAGCAA
* * *
480975 TCCA-CTTTAAGCCTTCACTGAAGAGG--AGTGAAACAA
1 TCAATC-TTAAGCCTTCAC--CAGAGGATAGTGAAGCAA
* * * * * *
481011 TCCATTTTAAGTCTTCACTA-AAGAGTAGTGGAGC-A
1 TCAATCTTAAGCCTTCACCAGAGGA-TAGTGAAGCAA
* *
481046 TC-ATATTAAGCCTTCACC-GAAGGGTAGTGAAGCAA
1 TCAATCTTAAGCCTTCACCAG-AGGATAGTGAAGCAA
481081 ATCCATCCAT
Statistics
Matches: 143, Mismatches: 19, Indels: 34
0.73 0.10 0.17
Matches are distributed among these distances:
33 2 0.01
34 23 0.16
35 13 0.09
36 74 0.52
37 27 0.19
38 3 0.02
39 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (36 bp):
TCAATCTTAAGCCTTCACCAGAGGATAGTGAAGCAA
Found at i:481388 original size:42 final size:41
Alignment explanation
Indices: 481322--481423 Score: 123
Period size: 42 Copynumber: 2.5 Consensus size: 41
481312 TTCACAATGT
* * * *
481322 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
1 ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
* * *
481363 CTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
1 -ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
*
481405 ATAAGTCCTTCGGGCCATC
1 ATAAATCCTTCGGGCCATC
481424 CATAAAATCT
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 16 0.32
42 34 0.68
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.29
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
Found at i:481563 original size:215 final size:205
Alignment explanation
Indices: 481198--481844 Score: 999
Period size: 215 Copynumber: 3.1 Consensus size: 205
481188 ATTTCACAAT
* * *
481198 TGATAAGTTCTTCGGGCCATCCATAAGACCTCCGGGTAGGATGTTTTCACATGAATTTGAGAATG
1 TGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATG
* *
481263 AAAAAATGATGTTGGAAATTTTGAAAACGAAGAATGTGAGTTTCAAAATTTCACAATGTATAAGT
66 AAAAAATGATGTTGGAAATTTTGAAAACAAAGAATGCGAGTTTCAAAATTTCACAATGTATAAGT
481328 CCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTT
131 CCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTT
481393 TAGAGCAAGA
196 TAGAGCAAGA
* * *
481403 TGATAAGTCCTTCGGGCCATCCATAAAATCTTCGGGTAGGATGTTTTCACATTAATTTGAAAATG
1 TGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATG
481468 AAAAAATGATGTTTTAAGATGATGAAAATTTTGAAAACAAAGAATGCGAGTTTCAAAATTTCACA
66 AAAAAATGATG---T----TG--G-AAATTTTGAAAACAAAGAATGCGAGTTTCAAAATTTCACA
481533 ATGTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATC
121 ATGTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATC
481598 TGTAAGCCTTTAGAGCAAGA
186 TGTAAGCCTTTAGAGCAAGA
481618 TGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATG
1 TGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATG
* * *
481683 AAAAAATGATGTTGGAATTTTTTAAAACAAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGT
66 AAAAAATGATGTTGGAAATTTTGAAAACAAAGAATGCGAGTTTCAAAATTTCACAATGTATAAGT
* * * * *
481748 CCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGTTTAAATCCTTTGGGTCAT-TAATAAGTCT
131 CCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCT-GTAAGCCT
* *
481812 TTCGAGCATGA
195 TTAGAGCAAGA
* *
481823 TGTTTAAATCCTTCGGGCCATC
1 TG-ATAAGTCCTTCGGGCCATC
481845 AGTAAGTCTT
Statistics
Matches: 407, Mismatches: 23, Indels: 23
0.90 0.05 0.05
Matches are distributed among these distances:
204 1 0.00
205 185 0.45
206 18 0.04
208 3 0.01
212 3 0.01
214 1 0.00
215 196 0.48
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (205 bp):
TGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATG
AAAAAATGATGTTGGAAATTTTGAAAACAAAGAATGCGAGTTTCAAAATTTCACAATGTATAAGT
CCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTT
TAGAGCAAGA
Found at i:481603 original size:42 final size:41
Alignment explanation
Indices: 481537--481638 Score: 123
Period size: 42 Copynumber: 2.5 Consensus size: 41
481527 TTCACAATGT
* * * *
481537 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
1 ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
* * *
481578 CTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
1 -ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
*
481620 ATAAGTCCTTCGGGCCATC
1 ATAAATCCTTCGGGCCATC
481639 CATAAAACCT
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 16 0.32
42 34 0.68
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.29
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
Found at i:481891 original size:41 final size:42
Alignment explanation
Indices: 481747--481926 Score: 220
Period size: 42 Copynumber: 4.3 Consensus size: 42
481737 AATTTATAAG
*
481747 TCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGTTTAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTAGAGCATGATGTTTAAA
* * * * *
481789 TCCTTTGGGTCATTAATAAGTCTTTCGAGCATGATGTTTAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTAGAGCATGATGTTTAAA
*
481831 TCCTTCGGGCCATCAGTAAGTCTTTAGAGCATGATGCTT-AA
1 TCCTTCGGGCCATCAGTAAGTCTTTAGAGCATGATGTTTAAA
* * * * * *
481872 TCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG-ATAAG
1 TCCTTCGGGCCATCAGTAAGTCTTTAGAGCATGATGTTTAAA
*
481913 TCCTTCCGGCCATC
1 TCCTTCGGGCCATC
481927 CATAAAACCT
Statistics
Matches: 118, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
40 1 0.01
41 47 0.40
42 70 0.59
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (42 bp):
TCCTTCGGGCCATCAGTAAGTCTTTAGAGCATGATGTTTAAA
Found at i:482119 original size:42 final size:40
Alignment explanation
Indices: 482040--482148 Score: 119
Period size: 42 Copynumber: 2.6 Consensus size: 40
482030 ATTTCACAAT
* * * *
482040 TGATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGA
1 TGATAAATCCTTCGGGCCATCA-TAAGCCTTTAGAGCAAGA
* *
482081 TGTTTAAATCCTTCGGGTCATCTATAAGCCTTTAGAGCAAGA
1 TG-ATAAATCCTTCGGGCCATC-ATAAGCCTTTAGAGCAAGA
*
482123 TGATAAGTCCTTCGGGCCATCCATAA
1 TGATAAATCCTTCGGGCCAT-CATAA
482149 AACCTTCGGG
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
41 21 0.38
42 34 0.61
43 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (40 bp):
TGATAAATCCTTCGGGCCATCATAAGCCTTTAGAGCAAGA
Found at i:482305 original size:215 final size:216
Alignment explanation
Indices: 481831--482364 Score: 840
Period size: 215 Copynumber: 2.5 Consensus size: 216
481821 GATGTTTAAA
*
481831 TCCTTCGGGCCATCAGTAAGTCTTTAGAGCATGATGCTT-AATCCTTCGGGTCATCTGTAAGCCT
1 TCCTTCGGGCCATCAGTAAGTCTTTAGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGCCT
* *
481895 TTAGAGCAAGATGATAAGTCCTTCCGGCCATCCATAAAACCTTCAGGTAGGATGTTTTCACATGA
66 TTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCAGGTAGGATGTTTTCAAATGA
*
481960 ATTTGAAAATGAAAAAAAATGATGATTTGAGAAGATGAAATTTTTGAAAACGAAGAATGCGATTT
131 ATTTGAAAATG-AAAAAAACGATGATTTGAGAAGATGAAATTTTTGAAAACGAAGAATGCGATTT
482025 TCAAAATTTCACAATTGATAAG
195 TCAAAATTTCACAATTGATAAG
* *
482047 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTATAAGCCT
1 TCCTTCGGGCCATCAGTAAGTCTTTAGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGCCT
* *
482112 TTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTATGATGTTTTCAAATGA
66 TTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCAGGTAGGATGTTTTCAAATGA
*
482177 ATTTGAAAATG-AAAAAACGATGTTTTGAGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTT
131 ATTTGAAAATGAAAAAAACGATGATTTGAGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTT
*
482241 CAAAATTTCACAATTTATAAG
196 CAAAATTTCACAATTGATAAG
* * * *
482262 TCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGCTTAAATCCTTTGGGCCATC-AGTAAGTC
1 TCCTTCGGGCCATCAGTAAGTCTTTAGAGCATGATGCTTAAATCCTTCGGGTCATCTA-TAAGCC
* * * * * *
482326 TTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTATAA
65 TTTAGAGCAAGATG-ATAAGTCCTTCGGGCCATCCATAA
482365 GCCTTTAGAG
Statistics
Matches: 294, Mismatches: 21, Indels: 6
0.92 0.07 0.02
Matches are distributed among these distances:
214 1 0.00
215 140 0.48
216 57 0.19
217 96 0.33
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (216 bp):
TCCTTCGGGCCATCAGTAAGTCTTTAGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGCCT
TTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCAGGTAGGATGTTTTCAAATGA
ATTTGAAAATGAAAAAAACGATGATTTGAGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTT
CAAAATTTCACAATTGATAAG
Found at i:482321 original size:42 final size:42
Alignment explanation
Indices: 482262--482400 Score: 165
Period size: 42 Copynumber: 3.3 Consensus size: 42
482252 AATTTATAAG
*
482262 TCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGCTTAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTAGAGCATGATGCTTAAA
* * *
482304 TCCTTTGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTAGAGCATGATGCTTAAA
* * * * *
482346 TCCTTCGGGTCATCTA-TAAGCCTTTAGAGCAGGATG-ATAAG
1 TCCTTCGGGCCATC-AGTAAGTCTTTAGAGCATGATGCTTAAA
*
482387 TCCTTCGGGTCATC
1 TCCTTCGGGCCATC
482401 CATAAGATCT
Statistics
Matches: 86, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
41 17 0.20
42 68 0.79
43 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (42 bp):
TCCTTCGGGCCATCAGTAAGTCTTTAGAGCATGATGCTTAAA
Found at i:483072 original size:19 final size:19
Alignment explanation
Indices: 483044--483086 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
483034 CCAGTTTCAT
*
483044 CAACCTGACCCGGTTGCAC
1 CAACCCGACCCGGTTGCAC
*
483063 CAACCCGACCCGGTTGCAG
1 CAACCCGACCCGGTTGCAC
483082 CAACC
1 CAACC
483087 GAGTTGCCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.23, C:0.44, G:0.21, T:0.12
Consensus pattern (19 bp):
CAACCCGACCCGGTTGCAC
Found at i:490784 original size:11 final size:12
Alignment explanation
Indices: 490758--490786 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
490748 TAACTCTATA
490758 ATAATAAAATTC
1 ATAATAAAATTC
490770 ATAATAAAA-TC
1 ATAATAAAATTC
490781 ATAATA
1 ATAATA
490787 TTAAAGTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (12 bp):
ATAATAAAATTC
Found at i:490813 original size:75 final size:75
Alignment explanation
Indices: 490647--490838 Score: 190
Period size: 75 Copynumber: 2.6 Consensus size: 75
490637 AAATAAATTT
* * *
490647 AAATATCAATACTCAAACCACAATATTAAATTTAAAACAGTAAAATCCATAAACAAACCACAATA
1 AAATTTCAATACTCAAACCACAATATTAAATCTAAAACAATAAAATCCATAAACAAACCACAATA
490712 TTAAAATATC
66 TTAAAATATC
* * * * * * * * *
490722 AAATTTCAAGATTCAAACTACAATATTAACTCTATAATAATAAAATTCATAATA-AAATCATAAT
1 AAATTTCAATACTCAAACCACAATATTAAATCTAAAACAATAAAATCCATAA-ACAAACCACAAT
* *
490786 ATTAAAGTGTC
65 ATTAAAATATC
* * * *
490797 AGATCTT-AATACTCAAACCATAATATTAAGTCTAAAAAAATA
1 AAAT-TTCAATACTCAAACCACAATATTAAATCTAAAACAATA
490839 TTAACTCTAA
Statistics
Matches: 93, Mismatches: 22, Indels: 4
0.78 0.18 0.03
Matches are distributed among these distances:
75 90 0.97
76 3 0.03
ACGTcount: A:0.53, C:0.15, G:0.03, T:0.29
Consensus pattern (75 bp):
AAATTTCAATACTCAAACCACAATATTAAATCTAAAACAATAAAATCCATAAACAAACCACAATA
TTAAAATATC
Found at i:490840 original size:17 final size:17
Alignment explanation
Indices: 490818--490850 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
490808 CTCAAACCAT
*
490818 AATATTAAGTCTAAAAA
1 AATATTAACTCTAAAAA
490835 AATATTAACTCTAAAA
1 AATATTAACTCTAAAA
490851 TTTCATTAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.09, G:0.03, T:0.30
Consensus pattern (17 bp):
AATATTAACTCTAAAAA
Found at i:493101 original size:18 final size:18
Alignment explanation
Indices: 493074--493109 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
493064 TAAAGTGATG
*
493074 AGTGAGATCATCTCCACA
1 AGTGAAATCATCTCCACA
493092 AGTGAAATCATCTCCACA
1 AGTGAAATCATCTCCACA
493110 GTACATCAAT
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:0.36, C:0.28, G:0.14, T:0.22
Consensus pattern (18 bp):
AGTGAAATCATCTCCACA
Found at i:497847 original size:32 final size:31
Alignment explanation
Indices: 497765--497847 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 31
497755 TAGCAAACCC
* * * *
497765 GAAATTAACCAGATCCTAAAGCAACCCGAACT
1 GAAATTAACC-GAACCGAAAGCAACCCAAACA
* *
497797 GAATTTAACCAAACCCGAAAGCAACCCAAACA
1 GAAATTAACCGAA-CCGAAAGCAACCCAAACA
497829 GAAATTAATCCGAACCGAA
1 GAAATTAA-CCGAACCGAA
497848 TAATAAATTA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
31 1 0.02
32 36 0.88
33 4 0.10
ACGTcount: A:0.47, C:0.28, G:0.12, T:0.13
Consensus pattern (31 bp):
GAAATTAACCGAACCGAAAGCAACCCAAACA
Found at i:500721 original size:23 final size:23
Alignment explanation
Indices: 500678--500732 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
500668 GGTTCCCTTT
* * *
500678 AAAAATAA-AAATAATATAAAAT
1 AAAAAAAATAAATAATACAAAAC
* *
500700 AAAAGAAATAAATAATGCAAAAC
1 AAAAAAAATAAATAATACAAAAC
500723 AAAAAAAATA
1 AAAAAAAATA
500733 TCAATGTACC
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 6 0.23
23 20 0.77
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (23 bp):
AAAAAAAATAAATAATACAAAAC
Found at i:501637 original size:6 final size:6
Alignment explanation
Indices: 501626--501663 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
501616 GAAAAACAAG
* *
501626 ATGATA ATGATA ATGATA ATGATA ATAATA ATAATA AT
1 ATGATA ATGATA ATGATA ATGATA ATGATA ATGATA AT
501664 AACAAGAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (6 bp):
ATGATA
Found at i:502437 original size:18 final size:18
Alignment explanation
Indices: 502414--502448 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
502404 ACTGAATATT
502414 TGTCCCGAAGAACCACTA
1 TGTCCCGAAGAACCACTA
*
502432 TGTCCCGAAGCACCACT
1 TGTCCCGAAGAACCACT
502449 GATAATCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.37, G:0.17, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGAACCACTA
Found at i:504861 original size:19 final size:20
Alignment explanation
Indices: 504822--504864 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
504812 ATCAGATTGT
504822 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
504842 CCAGGGGGTATC-GATTCCCC
1 CCAGGGGGTA-CAGATTCCCC
504862 CCA
1 CCA
504865 TTCTGGGCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.19, C:0.37, G:0.28, T:0.16
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:508250 original size:34 final size:35
Alignment explanation
Indices: 508192--508273 Score: 114
Period size: 34 Copynumber: 2.4 Consensus size: 35
508182 TCCAGGGGGT
508192 ACAGATTCTCCCC-AGGGGGTATCGATTCCCCAAGA
1 ACAGATTC-CCCCTAGGGGGTATCGATTCCCCAAGA
** *
508227 ACAGATTCCCCCTA-GGGGTATCGATTCCCCGGGT
1 ACAGATTCCCCCTAGGGGGTATCGATTCCCCAAGA
508261 ACAGATTCCCCCT
1 ACAGATTCCCCCT
508274 GCATGGTTTG
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
34 34 0.79
35 9 0.21
ACGTcount: A:0.22, C:0.34, G:0.22, T:0.22
Consensus pattern (35 bp):
ACAGATTCCCCCTAGGGGGTATCGATTCCCCAAGA
Found at i:511727 original size:20 final size:20
Alignment explanation
Indices: 511702--511761 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
511692 ATCAGATTGT
511702 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
511722 CCAGGGGGAACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
511742 CTAGGGGGTATC-GATTCCCC
1 CCAGGGGGTA-CAGATTCCCC
511762 GGGAACAGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 35 0.97
21 1 0.03
ACGTcount: A:0.20, C:0.33, G:0.30, T:0.17
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:511774 original size:15 final size:15
Alignment explanation
Indices: 511754--511809 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
511744 AGGGGGTATC
511754 GATTCCCCGGGAACA
1 GATTCCCCGGGAACA
*
511769 GATTCCCCCAGGGGTATC-
1 GATT-CCCC--GGG-AACA
*
511787 GATTCCCCGGGTACA
1 GATTCCCCGGGAACA
511802 GATTCCCC
1 GATTCCCC
511810 CCTGCATGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
14 1 0.03
15 15 0.45
16 4 0.12
17 4 0.12
18 7 0.21
19 2 0.06
ACGTcount: A:0.20, C:0.36, G:0.25, T:0.20
Consensus pattern (15 bp):
GATTCCCCGGGAACA
Found at i:511788 original size:33 final size:35
Alignment explanation
Indices: 511727--511810 Score: 145
Period size: 33 Copynumber: 2.5 Consensus size: 35
511717 TCCCCCCAGG
511727 GGGAACAGATTCCCCCTAGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTAGGGGGTATCGATTCCCC
511762 GGGAACAGATTCCCCC-A-GGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTAGGGGGTATCGATTCCCC
*
511795 GGGTACAGATTCCCCC
1 GGGAACAGATTCCCCC
511811 CTGCATGGTT
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
33 31 0.65
34 1 0.02
35 16 0.33
ACGTcount: A:0.20, C:0.33, G:0.27, T:0.19
Consensus pattern (35 bp):
GGGAACAGATTCCCCCTAGGGGGTATCGATTCCCC
Found at i:511950 original size:21 final size:21
Alignment explanation
Indices: 511924--511965 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
511914 ATTTGAATAT
*
511924 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
511945 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
511966 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:513216 original size:17 final size:19
Alignment explanation
Indices: 513190--513224 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
513180 TCAACACTTC
513190 TTGTACAAAT-CTTATTCT
1 TTGTACAAATCCTTATTCT
513208 TTGTA-AAATCCTTATTC
1 TTGTACAAATCCTTATTC
513225 AAATCACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.49
Consensus pattern (19 bp):
TTGTACAAATCCTTATTCT
Found at i:513922 original size:18 final size:18
Alignment explanation
Indices: 513899--513951 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
513889 ACTGAATATT
*
513899 TGTCCCAAAGGATCACTA
1 TGTCCCAAAGGACCACTA
*
513917 TGTCCCAAAGGACCATTA
1 TGTCCCAAAGGACCACTA
*
513935 TGTCCCGAAGGACCACT
1 TGTCCCAAAGGACCACT
513952 GATAATCCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (18 bp):
TGTCCCAAAGGACCACTA
Found at i:515601 original size:152 final size:151
Alignment explanation
Indices: 515231--515568 Score: 364
Period size: 152 Copynumber: 2.2 Consensus size: 151
515221 CCTTGAAATT
* * * *** *
515231 TGATATATCACTG-GAA-AAAAATGATGTTTTGAATTTAGACATCACTGAAAAT-TCATTTTGAG
1 TGATATATCAATGAAAAGAAAAATGACGTTTTGAATTTAGATGGCACT--AAATGTAATTTTGAG
* * * * *
515293 GTGATATATCACTGAAAAGTCATGGTGAAATTATTATGATAGGGTCTGATCAATTATTAAATAAG
64 GTTATTTATCACTGAAAAGTCATGGTGAAATTATTATGATAGGGTATGATCAATGAGTAAATAAG
* * *
515358 CACTGAAAAGTTCATAAATTAGA
129 CACTCAAAAGTTCAGAAATGAGA
* ** ** *
515381 TGATATATCAATGAAAGGAAAAATGACGTTTTTCATTTAGATTTCACTAAAATGTCATTTTGAGG
1 TGATATATCAATGAAAAGAAAAATGACGTTTTGAATTTAGATGGCACT-AAATGTAATTTTGAGG
* *
515446 TTATTTATCACTGAAAAGTCATGGTGGAATTATTATGATAGGGTATGATCAATGAGTAAATATG-
65 TTATTTATCACTGAAAAGTCATGGTGAAATTATTATGATAGGGTATGATCAATGAGTAAATAAGC
*
515510 A-TCAACAAGTTCAGAAATGAGG
130 ACTCAA-AAGTTCAGAAATGAGA
*
515532 TGATATATCACTGAAAAGAAAAA-GAACGTTTTGAATT
1 TGATATATCAATGAAAAGAAAAATG-ACGTTTTGAATT
515569 ATTATGATAG
Statistics
Matches: 160, Mismatches: 23, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
150 16 0.10
151 51 0.32
152 93 0.58
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.33
Consensus pattern (151 bp):
TGATATATCAATGAAAAGAAAAATGACGTTTTGAATTTAGATGGCACTAAATGTAATTTTGAGGT
TATTTATCACTGAAAAGTCATGGTGAAATTATTATGATAGGGTATGATCAATGAGTAAATAAGCA
CTCAAAAGTTCAGAAATGAGA
Found at i:515917 original size:36 final size:35
Alignment explanation
Indices: 515857--515935 Score: 113
Period size: 36 Copynumber: 2.2 Consensus size: 35
515847 TTGAATCTTT
* * *
515857 AAAAAAATATTTTTTCACAGCTTCCTTAAATCTAC
1 AAAAAAATATCTTTTAACAACTTCCTTAAATCTAC
*
515892 AAAAAAATATACTTTTAACAACTTCCTTGAATCTAC
1 AAAAAAATAT-CTTTTAACAACTTCCTTAAATCTAC
515928 AAAAAAAT
1 AAAAAAAT
515936 TCAAACAATG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 10 0.26
36 29 0.74
ACGTcount: A:0.47, C:0.18, G:0.03, T:0.33
Consensus pattern (35 bp):
AAAAAAATATCTTTTAACAACTTCCTTAAATCTAC
Found at i:521855 original size:21 final size:21
Alignment explanation
Indices: 521831--521896 Score: 105
Period size: 21 Copynumber: 3.1 Consensus size: 21
521821 ATGATTTTAA
* *
521831 AAAATTGAAAGTTTAAGTACT
1 AAAACTGATAGTTTAAGTACT
521852 AAAACTGATAGTTTAAGTACT
1 AAAACTGATAGTTTAAGTACT
*
521873 AAAACTGATAGTTTAATTACT
1 AAAACTGATAGTTTAAGTACT
521894 AAA
1 AAA
521897 GGCGTAATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (21 bp):
AAAACTGATAGTTTAAGTACT
Found at i:522463 original size:29 final size:29
Alignment explanation
Indices: 522430--522584 Score: 310
Period size: 29 Copynumber: 5.3 Consensus size: 29
522420 TCCCCAAGCA
522430 TAGGTCGCCAAGCACTCCGGGCGACCTTG
1 TAGGTCGCCAAGCACTCCGGGCGACCTTG
522459 TAGGTCGCCAAGCACTCCGGGCGACCTTG
1 TAGGTCGCCAAGCACTCCGGGCGACCTTG
522488 TAGGTCGCCAAGCACTCCGGGCGACCTTG
1 TAGGTCGCCAAGCACTCCGGGCGACCTTG
522517 TAGGTCGCCAAGCACTCCGGGCGACCTTG
1 TAGGTCGCCAAGCACTCCGGGCGACCTTG
522546 TAGGTCGCCAAGCACTCCGGGCGACCTTG
1 TAGGTCGCCAAGCACTCCGGGCGACCTTG
522575 TAGGTCGCCA
1 TAGGTCGCCA
522585 TACAATCCTC
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 126 1.00
ACGTcount: A:0.17, C:0.34, G:0.31, T:0.17
Consensus pattern (29 bp):
TAGGTCGCCAAGCACTCCGGGCGACCTTG
Found at i:523217 original size:21 final size:21
Alignment explanation
Indices: 523192--523235 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
523182 AATTTAGTTA
523192 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
523213 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
523234 AT
1 AT
523236 ATTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:523249 original size:28 final size:28
Alignment explanation
Indices: 523212--523265 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
523202 TAGTATAAAT
*
523212 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAATTTGTTAGTTTAAGTTATATTA
523240 TATTAATTTGTTAGTTTAAGTTATAT
1 TATTAATTTGTTAGTTTAAGTTATAT
523266 ATTAGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (28 bp):
TATTAATTTGTTAGTTTAAGTTATATTA
Found at i:526128 original size:21 final size:20
Alignment explanation
Indices: 526104--526143 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
526094 TAGTGGTGGT
526104 TCATAATTTTGATCGAGTTGG
1 TCATAATTTTG-TCGAGTTGG
* *
526125 TCATACTTTTGTCGTGTTG
1 TCATAATTTTGTCGAGTTG
526144 TGCATACGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.17, C:0.12, G:0.23, T:0.47
Consensus pattern (20 bp):
TCATAATTTTGTCGAGTTGG
Found at i:526804 original size:21 final size:21
Alignment explanation
Indices: 526780--526882 Score: 66
Period size: 21 Copynumber: 4.6 Consensus size: 21
526770 AATAATGAAA
*
526780 TTATTATTAATATTTAATGAT
1 TTATTAGTAATATTTAATGAT
526801 TTATTAGTAATGATTAGTAATAATGAT
1 TTATTAGTAAT-A-T--T--TAATGAT
* *
526828 ATTATTATTAATTTTTAATGAT
1 -TTATTAGTAATATTTAATGAT
*
526850 TTGA-TAGTAATGATTTAAT-AA
1 TT-ATTAGTAAT-ATTTAATGAT
*
526871 TTATTACTAATA
1 TTATTAGTAATA
526883 ATTATGGAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 21
0.70 0.08 0.23
Matches are distributed among these distances:
20 2 0.03
21 27 0.42
22 15 0.23
23 1 0.02
24 1 0.02
25 1 0.02
26 1 0.02
27 7 0.11
28 10 0.15
ACGTcount: A:0.40, C:0.01, G:0.09, T:0.50
Consensus pattern (21 bp):
TTATTAGTAATATTTAATGAT
Found at i:526810 original size:49 final size:50
Alignment explanation
Indices: 526755--526871 Score: 188
Period size: 49 Copynumber: 2.4 Consensus size: 50
526745 CTTGTCTAAT
526755 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTT-A
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
* *
526804 TTAGTAATGATTAGTAATAATGATATTATTATTAATTTTTAATGATTTGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
526854 -TAGTAATGATT--TAATAAT
1 TTAGTAATGATTAGTAATAAT
526872 TATTACTAAT
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
47 7 0.11
49 57 0.88
50 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (50 bp):
TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
Found at i:527024 original size:17 final size:17
Alignment explanation
Indices: 526999--527040 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
526989 AATGATTTAG
526999 TAATTATTATTAATAAT
1 TAATTATTATTAATAAT
* *
527016 TATTTATTATTAATATT
1 TAATTATTATTAATAAT
527033 TAATTATT
1 TAATTATT
527041 TGATACTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TAATTATTATTAATAAT
Found at i:527050 original size:21 final size:22
Alignment explanation
Indices: 527012--527069 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
527002 TTATTATTAA
*
527012 TAATTATTTATTATTAAT-ATT
1 TAATTATTTATTACTAATGATT
527033 TAATTATTTGA-TACTAATGATT
1 TAATTATTT-ATTACTAATGATT
* *
527055 T-ATTAATGATTACTA
1 TAATTATTTATTACTA
527070 GTAATGAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 1 0.03
21 25 0.81
22 5 0.16
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.53
Consensus pattern (22 bp):
TAATTATTTATTACTAATGATT
Found at i:527090 original size:14 final size:13
Alignment explanation
Indices: 527058--527284 Score: 103
Period size: 12 Copynumber: 18.3 Consensus size: 13
527048 AATGATTTAT
*
527058 TAATG-ATTACTAG
1 TAATGAATTA-TAA
527071 TAATGAAATTATAA
1 TAATG-AATTATAA
*
527085 TAATGATTTAGTAA
1 TAATGAATTA-TAA
*
527099 TAAT-CATTATAA
1 TAATGAATTATAA
527111 TAATG-ATT-TAA
1 TAATGAATTATAA
*
527122 TAATG-ATTTTAA
1 TAATGAATTATAA
* * * *
527134 TATTTAATGAT-T
1 TAATGAATTATAA
* *
527146 TGATG-ATT-TAG
1 TAATGAATTATAA
*
527157 TAATGATTTGATAA
1 TAATGAATT-ATAA
*
527171 TAAT-CATTATAA
1 TAATGAATTATAA
*
527183 T-ATGATTTAGTAA
1 TAATGAATTA-TAA
*
527196 TAAT-CATTATAA
1 TAATGAATTATAA
527208 TAAT-AATT-TAA
1 TAATGAATTATAA
*
527219 TAAT-AATGATAA
1 TAATGAATTATAA
527231 TAATG-ATT-TAA
1 TAATGAATTATAA
*
527242 TAATGATTTTATAA
1 TAATGA-ATTATAA
* *
527256 TAATGATTTAATAC
1 TAATGAATT-ATAA
527270 TAAT-AATT-TAA
1 TAATGAATTATAA
527281 TAAT
1 TAAT
527285 TATTACTAAT
Statistics
Matches: 165, Mismatches: 30, Indels: 40
0.70 0.13 0.17
Matches are distributed among these distances:
10 1 0.01
11 43 0.26
12 47 0.28
13 32 0.19
14 38 0.23
15 4 0.02
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.44
Consensus pattern (13 bp):
TAATGAATTATAA
Found at i:527138 original size:97 final size:99
Alignment explanation
Indices: 526988--527225 Score: 271
Period size: 97 Copynumber: 2.4 Consensus size: 99
526978 GATTTAATAC
* * * *
526988 TAATGATTTAGTAAT--T-ATTATTAATAATTATTTATTATTAATATTTAATTATTTGAT-A-CT
1 TAATGATTTAGTAATAATCATTA-TAATAATAATTTAATAATAATATTTAATTATTTAATGATCT
*
527048 AATGATTTATTAATGATTACT-AGTAATGAA-ATTATAA
65 AATGATTTAGTAATGATT--TGA-TAAT-AACATTATAA
* * * *
527085 TAATGATTTAGTAATAATCATTATAATAATGATTTAATAATGAT-TTTAA-TATTTAATGATTTG
1 TAATGATTTAGTAATAATCATTATAATAATAATTTAATAATAATATTTAATTATTTAATGATCTA
527148 ATGATTTAGTAATGATTTGATAATAATCATTATAA
66 ATGATTTAGTAATGATTTGATAATAA-CATTATAA
527183 T-ATGATTTAGTAATAATCATTATAATAATAATTTAATAATAAT
1 TAATGATTTAGTAATAATCATTATAATAATAATTTAATAATAAT
527226 GATAATAATG
Statistics
Matches: 123, Mismatches: 10, Indels: 16
0.83 0.07 0.11
Matches are distributed among these distances:
96 2 0.02
97 67 0.54
98 15 0.12
99 35 0.28
100 4 0.03
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (99 bp):
TAATGATTTAGTAATAATCATTATAATAATAATTTAATAATAATATTTAATTATTTAATGATCTA
ATGATTTAGTAATGATTTGATAATAACATTATAA
Found at i:527187 original size:25 final size:25
Alignment explanation
Indices: 527078--527282 Score: 135
Period size: 26 Copynumber: 8.4 Consensus size: 25
527068 TAGTAATGAA
*
527078 ATTATAATAATGATTTAGTAATAATC
1 ATTATAAT-ATGATTTAATAATAATC
*
527104 ATTATAATAATGATTTAATAATGAT-
1 ATTATAAT-ATGATTTAATAATAATC
* * *
527129 -TT-T-A-AT-ATTTAATGATTTGATG
1 ATTATAATATGATTTAAT-A-ATAATC
* *
527151 ATT-TAGTAATGATTTGATAATAATC
1 ATTATAAT-ATGATTTAATAATAATC
*
527176 ATTATAATATGATTTAGTAATAATC
1 ATTATAATATGATTTAATAATAATC
* *
527201 ATTATAATAATAATTTAATAATAATG
1 ATTATAAT-ATGATTTAATAATAATC
* *
527227 ATAAT-A-ATGATTTAATAATGAT-
1 ATTATAATATGATTTAATAATAATC
* * *
527249 TTTATAATAATGATTTAATACTAATA
1 ATTATAAT-ATGATTTAATAATAATC
527275 ATT-TAATA
1 ATTATAATA
527283 ATTATTACTA
Statistics
Matches: 143, Mismatches: 22, Indels: 30
0.73 0.11 0.15
Matches are distributed among these distances:
19 7 0.05
20 3 0.02
21 4 0.03
22 4 0.03
23 19 0.13
24 3 0.02
25 48 0.34
26 49 0.34
27 6 0.04
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (25 bp):
ATTATAATATGATTTAATAATAATC
Found at i:527221 original size:11 final size:11
Alignment explanation
Indices: 527193--527319 Score: 78
Period size: 11 Copynumber: 11.0 Consensus size: 11
527183 TATGATTTAG
*
527193 TAATAATCATT
1 TAATAATAATT
527204 ATAATAATAATT
1 -TAATAATAATT
*
527216 TAATAATAATGA
1 TAATAATAAT-T
*
527228 TAATAATGATT
1 TAATAATAATT
*
527239 TAATAATGATTTT
1 TAATAAT-A-ATT
*
527252 ATAATAATGATT
1 -TAATAATAATT
527264 TAATACTAATAATT
1 T-A-A-TAATAATT
*
527278 TAATAATTA-T
1 TAATAATAATT
* *
527288 TACTAATGATT
1 TAATAATAATT
*
527299 TAATAATTA-T
1 TAATAATAATT
*
527309 TACTAATAATT
1 TAATAATAATT
527320 ATGGAATAAT
Statistics
Matches: 90, Mismatches: 16, Indels: 19
0.72 0.13 0.15
Matches are distributed among these distances:
10 16 0.18
11 32 0.36
12 23 0.26
13 4 0.04
14 15 0.17
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (11 bp):
TAATAATAATT
Found at i:527246 original size:85 final size:84
Alignment explanation
Indices: 527108--527268 Score: 209
Period size: 85 Copynumber: 1.9 Consensus size: 84
527098 ATAATCATTA
* * * * * *
527108 TAATAATGATTTAATAATGATTTTAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATA
1 TAATAATCATTTAATAATGAATTTAATATATAATGATATAATGATTTAATAATGATTTGATAATA
527173 ATCATTATAATATGATTTAG
66 ATCATT-TAATATGATTTAG
*
527193 TAATAATCATTATAATAAT-AATTTAATA-ATAATGATAATAATGATTTAATAATGATTTTATAA
1 TAATAATCATT-TAATAATGAATTTAATATATAATGAT-ATAATGATTTAATAATGATTTGATAA
*
527256 TAATGATTTAATA
64 TAATCATTTAATA
527269 CTAATAATTT
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
84 12 0.18
85 47 0.71
86 7 0.11
ACGTcount: A:0.45, C:0.01, G:0.09, T:0.45
Consensus pattern (84 bp):
TAATAATCATTTAATAATGAATTTAATATATAATGATATAATGATTTAATAATGATTTGATAATA
ATCATTTAATATGATTTAG
Found at i:527329 original size:24 final size:21
Alignment explanation
Indices: 527208--527319 Score: 97
Period size: 21 Copynumber: 5.4 Consensus size: 21
527198 ATCATTATAA
* *
527208 TAATAATTTAATAATAATGATAA
1 TAATAATTTAATAATTAT--TAC
* *
527231 TAATGATTTAATAATGATT--
1 TAATAATTTAATAATTATTAC
* * *
527250 TTATAA--TAATGATTTAATAC
1 TAATAATTTAAT-AATTATTAC
527270 TAATAATTTAATAATTATTAC
1 TAATAATTTAATAATTATTAC
*
527291 TAATGATTTAATAATTATTAC
1 TAATAATTTAATAATTATTAC
527312 TAATAATT
1 TAATAATT
527320 ATGGAATAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
17 4 0.06
18 4 0.06
19 4 0.06
20 5 0.07
21 35 0.49
22 4 0.06
23 16 0.22
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (21 bp):
TAATAATTTAATAATTATTAC
Found at i:527451 original size:21 final size:21
Alignment explanation
Indices: 527422--527489 Score: 92
Period size: 21 Copynumber: 3.5 Consensus size: 21
527412 GATTTAATAC
*
527422 TAATGATTTAGTAATTATTAT
1 TAATAATTTAGTAATTATTAT
527443 TAATAATTTAGTAATTATTAT
1 TAATAATTTAGTAATTATTAT
527464 TAATAA-TTA-T--TTATTAT
1 TAATAATTTAGTAATTATTAT
527481 TAAT-ATTTA
1 TAATAATTTA
527490 ATTATTTGAT
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
16 1 0.02
17 14 0.31
19 1 0.02
20 3 0.07
21 26 0.58
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (21 bp):
TAATAATTTAGTAATTATTAT
Found at i:527545 original size:14 final size:13
Alignment explanation
Indices: 527508--527798 Score: 83
Period size: 12 Copynumber: 23.7 Consensus size: 13
527498 ATACTAATGA
*
527508 TATATTAATG-AT
1 TATAATAATGAAT
*
527520 TACTAGTAATGAAAT
1 TA-TAATAATG-AAT
*
527535 TATAATAATGATT
1 TATAATAATGAAT
*
527548 TAGTAATAAT-CAT
1 TA-TAATAATGAAT
527561 TATAATAAT-AAT
1 TATAATAATGAAT
527573 T-TAATAATG-AT
1 TATAATAATGAAT
* * *
527584 TTTAATATTTAAT
1 TATAATAATGAAT
* * *
527597 GAT-TTGATG-AT
1 TATAATAATGAAT
* *
527608 T-TAGTAATGATT
1 TATAATAATGAAT
*
527620 TGATAATAAT-CAT
1 T-ATAATAATGAAT
*
527633 TATAAT-ATGATT
1 TATAATAATGAAT
*
527645 TAGTAATAAT--TT
1 TA-TAATAATGAAT
527657 TATAATAATG-AT
1 TATAATAATGAAT
* *
527669 T-TAATATTTAAT
1 TATAATAATGAAT
* * *
527681 GAT-TTGATG-AT
1 TATAATAATGAAT
* *
527692 T-TAGTAATGATT
1 TATAATAATGAAT
*
527704 TAGTAATAAT-CAT
1 TA-TAATAATGAAT
527717 TATAATAAT-AAT
1 TATAATAATGAAT
527729 T-TAATAAT-AAT
1 TATAATAATGAAT
* *
527740 GATAATAATGATT
1 TATAATAATGAAT
*
527753 TAGTAATAAT--TT
1 TA-TAATAATGAAT
*
527765 TATAATAATGATT
1 TATAATAATGAAT
*
527778 TAATACTAAT-AAT
1 T-ATAATAATGAAT
527791 T-TAATAAT
1 TATAATAAT
527799 TATTACTAAT
Statistics
Matches: 207, Mismatches: 45, Indels: 55
0.67 0.15 0.18
Matches are distributed among these distances:
10 2 0.01
11 60 0.29
12 63 0.30
13 36 0.17
14 42 0.20
15 4 0.02
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (13 bp):
TATAATAATGAAT
Found at i:527545 original size:27 final size:25
Alignment explanation
Indices: 527508--527671 Score: 94
Period size: 25 Copynumber: 6.6 Consensus size: 25
527498 ATACTAATGA
*
527508 TATATTAATGATTACTAGTAATGAA-AT
1 TATAATAATGATT--TAGTAAT-AACAT
527535 TATAATAATGATTTAGTAATAATCAT
1 TATAATAATGATTTAGTAATAA-CAT
* * * **
527561 TATAATAATAATTTAATAATGATTT
1 TATAATAATGATTTAGTAATAACAT
* *
527586 TAATATTTAATGATTT-G--AT--GAT
1 T-ATA-ATAATGATTTAGTAATAACAT
*
527608 T-TAGTAATGATTT-GATAATAATCAT
1 TATAATAATGATTTAG-TAATAA-CAT
**
527633 TATAAT-ATGATTTAGTAATAATTT
1 TATAATAATGATTTAGTAATAACAT
527657 TATAATAATGATTTA
1 TATAATAATGATTTA
527672 ATATTTAATG
Statistics
Matches: 108, Mismatches: 16, Indels: 28
0.71 0.11 0.18
Matches are distributed among these distances:
19 10 0.09
20 2 0.02
22 4 0.04
24 11 0.10
25 33 0.31
26 28 0.26
27 20 0.19
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (25 bp):
TATAATAATGATTTAGTAATAACAT
Found at i:527642 original size:25 final size:25
Alignment explanation
Indices: 527612--527742 Score: 85
Period size: 25 Copynumber: 5.3 Consensus size: 25
527602 GATGATTTAG
527612 TAATGATTT-GATAATAATCATTATAA
1 TAATGATTTAG-TAATAAT-ATTATAA
*
527638 T-ATGATTTAGTAATAATTTTATAA
1 TAATGATTTAGTAATAATATTATAA
* * * * *
527662 TAATGATTTAATATTTA-ATGAT-T
1 TAATGATTTAGTAATAATATTATAA
* *
527685 TGATGATTTAGTAATGAT-TTAGTAA
1 TAATGATTTAGTAATAATATTA-TAA
* *
527710 TAATCATTATAATAATAAT-TTAATAA
1 TAATGATT-TAGTAATAATATT-ATAA
527736 TAATGAT
1 TAATGAT
527743 AATAATGATT
Statistics
Matches: 80, Mismatches: 18, Indels: 14
0.71 0.16 0.12
Matches are distributed among these distances:
23 15 0.19
24 11 0.14
25 32 0.40
26 21 0.26
27 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.46
Consensus pattern (25 bp):
TAATGATTTAGTAATAATATTATAA
Found at i:527662 original size:11 final size:12
Alignment explanation
Indices: 527612--527798 Score: 73
Period size: 11 Copynumber: 14.3 Consensus size: 12
527602 GATGATTTAG
527612 TAATGATTTGATAA
1 TAAT-ATTT-ATAA
527626 TAATCA-TTATAA
1 TAAT-ATTTATAA
527638 T-ATGATTTAGTAA
1 TAAT-ATTTA-TAA
527651 TAAT-TTTATAA
1 TAATATTTATAA
*
527662 TAATGATTTAATATT
1 TAAT-ATTT-ATA-A
527677 TAATGATTTGATGATTTA
1 TAAT-ATTT-AT-A---A
527695 GTAATGATTTAGTAA
1 -TAAT-ATTTA-TAA
527710 TAATCA-TTATAA
1 TAAT-ATTTATAA
*
527722 TAATAATT-TAA
1 TAATATTTATAA
* *
527733 TAATAATGATAA
1 TAATATTTATAA
527745 TAATGATTTAGTAA
1 TAAT-ATTTA-TAA
527759 TAAT-TTTATAA
1 TAATATTTATAA
*
527770 TAATGATTTAATAC
1 TAAT-ATTT-ATAA
*
527784 TAATAATT-TAA
1 TAATATTTATAA
527795 TAAT
1 TAAT
527799 TATTACTAAT
Statistics
Matches: 142, Mismatches: 12, Indels: 41
0.73 0.06 0.21
Matches are distributed among these distances:
11 34 0.24
12 32 0.23
13 21 0.15
14 29 0.20
15 12 0.08
16 1 0.01
18 3 0.02
19 10 0.07
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (12 bp):
TAATATTTATAA
Found at i:527679 original size:7 final size:8
Alignment explanation
Indices: 527662--527694 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
527652 AATTTTATAA
527662 TAATGATT
1 TAATGATT
527670 TAAT-ATT
1 TAATGATT
527677 TAATGATT
1 TAATGATT
*
527685 TGATGATT
1 TAATGATT
527693 TA
1 TA
527695 GTAATGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (8 bp):
TAATGATT
Found at i:527681 original size:84 final size:83
Alignment explanation
Indices: 527578--527754 Score: 277
Period size: 84 Copynumber: 2.1 Consensus size: 83
527568 ATAATTTAAT
527578 AATGATTTTAATATTTAATGATTTGATGATTTAGTAATGATTT-GATAATAATCATTATAAT-AT
1 AATGA-TTTAATATTTAATGATTTGATGATTTAGTAATGATTTAG-TAATAATCATTATAATAAT
* * *
527641 GATTTAGTAATAATTTTATAAT
64 AATTTAATAATAA--TGATAAT
527663 AATGATTTAATATTTAATGATTTGATGATTTAGTAATGATTTAGTAATAATCATTATAATAATAA
1 AATGATTTAATATTTAATGATTTGATGATTTAGTAATGATTTAGTAATAATCATTATAATAATAA
527728 TTTAATAATAATGATAAT
66 TTTAATAATAATGATAAT
527746 AATGATTTA
1 AATGATTTA
527755 GTAATAATTT
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
83 15 0.17
84 53 0.61
85 19 0.22
ACGTcount: A:0.42, C:0.01, G:0.10, T:0.46
Consensus pattern (83 bp):
AATGATTTAATATTTAATGATTTGATGATTTAGTAATGATTTAGTAATAATCATTATAATAATAA
TTTAATAATAATGATAAT
Found at i:527733 original size:23 final size:23
Alignment explanation
Indices: 527707--527835 Score: 104
Period size: 23 Copynumber: 5.6 Consensus size: 23
527697 AATGATTTAG
* *
527707 TAATAATCATTATAATAATAATT
1 TAATAATAATTATAATAATGATT
*
527730 TAATAATAATGATAATAATGATT
1 TAATAATAATTATAATAATGATT
*
527753 TAGTAATAATTTTATAATAATGATT
1 TAATAATAA--TTATAATAATGATT
*
527778 TAATACTAATAATT-TAATAATTA-T
1 T-A-A-TAATAATTATAATAATGATT
* * *
527802 TACTAATGATT-TAATAATTA-T
1 TAATAATAATTATAATAATGATT
*
527823 TACTAATAATTAT
1 TAATAATAATTAT
527836 GGAATAATAA
Statistics
Matches: 90, Mismatches: 10, Indels: 13
0.80 0.09 0.12
Matches are distributed among these distances:
21 27 0.30
22 1 0.01
23 29 0.32
24 2 0.02
25 22 0.24
26 3 0.03
28 6 0.07
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (23 bp):
TAATAATAATTATAATAATGATT
Found at i:527809 original size:60 final size:59
Alignment explanation
Indices: 527620--527832 Score: 163
Period size: 60 Copynumber: 3.6 Consensus size: 59
527610 AGTAATGATT
* * * *
527620 TGATAATAATCA-TTA-TAATATGATTTAGTAATAAT-TTTATAATAATGATTTAATATTTAA
1 TGATAATAATGATTTAGTAATA--ATTTAGTAATAATCATTATAATAAT-AATTAATA-ATAA
* * *
527680 TGAT-TTGATGATTTAGTAATGATTTAGTAATAATCATTATAATAATAATTTAATAATAA
1 TGATAATAATGATTTAGTAATAATTTAGTAATAATCATTATAATAATAA-TTAATAATAA
* *
527739 TGATAATAATGATTTAGTAATAATTTTA-TAATAATGATT-TAATACTAA-TAATTTAATAA
1 TGATAATAATGATTTAGTAATAA-TTTAGTAATAATCATTATAATAATAATTAA--TAATAA
* * * * *
527798 TTATTACTAATGATTTAATAATTA-TTACTAATAAT
1 TGA-TAATAATGATTTAGTAATAATTTAGTAATAAT
527833 TATGGAATAA
Statistics
Matches: 127, Mismatches: 16, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
57 3 0.02
58 3 0.02
59 48 0.38
60 65 0.51
61 8 0.06
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.46
Consensus pattern (59 bp):
TGATAATAATGATTTAGTAATAATTTAGTAATAATCATTATAATAATAATTAATAATAA
Found at i:527843 original size:24 final size:21
Alignment explanation
Indices: 527781--527833 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
527771 AATGATTTAA
527781 TACTAATAATTTAATAATTAT
1 TACTAATAATTTAATAATTAT
*
527802 TACTAATGATTTAATAATTAT
1 TACTAATAATTTAATAATTAT
527823 TACTAATAATT
1 TACTAATAATT
527834 ATGGAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (21 bp):
TACTAATAATTTAATAATTAT
Found at i:527970 original size:24 final size:24
Alignment explanation
Indices: 527922--527966 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
527912 TTTAAATATT
*
527922 TAATGATTTAGTAATTATTATTAA
1 TAATGATTTAGTAATTAATATTAA
*
527946 TAATGATTTA-TTATTAATATT
1 TAATGATTTAGTAATTAATATT
527967 TAATTATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (24 bp):
TAATGATTTAGTAATTAATATTAA
Found at i:527973 original size:17 final size:17
Alignment explanation
Indices: 527933--527974 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
527923 AATGATTTAG
527933 TAATTATTATTAATAAT
1 TAATTATTATTAATAAT
* * *
527950 GATTTATTATTAATATT
1 TAATTATTATTAATAAT
527967 TAATTATT
1 TAATTATT
527975 TGATACTAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TAATTATTATTAATAAT
Found at i:528035 original size:14 final size:12
Alignment explanation
Indices: 527977--528026 Score: 57
Period size: 11 Copynumber: 4.0 Consensus size: 12
527967 TAATTATTTG
527977 ATACTAATGATT
1 ATACTAATGATT
527989 -TACTAATGATT
1 ATACTAATGATT
*
528000 ACTAGTAATGAAATT
1 A-TACTAATG--ATT
528015 ATACTAATGATT
1 ATACTAATGATT
528027 TGATACTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
11 11 0.34
12 3 0.09
13 7 0.22
14 7 0.22
15 4 0.12
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (12 bp):
ATACTAATGATT
Found at i:530264 original size:11 final size:11
Alignment explanation
Indices: 530250--530288 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
530240 TTAAACTATT
530250 CTTTAATATAA
1 CTTTAATATAA
*
530261 CTTTAACTAT-T
1 CTTTAA-TATAA
530272 CTTTAATATAA
1 CTTTAATATAA
530283 CTTTAA
1 CTTTAA
530289 CTAATAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (11 bp):
CTTTAATATAA
Found at i:530269 original size:30 final size:30
Alignment explanation
Indices: 530235--530321 Score: 91
Period size: 30 Copynumber: 3.2 Consensus size: 30
530225 TTCCTTAAAC
530235 AACTATTAAACTATTCTTT-A-AT-A---T
1 AACTATTAAACTATTCTTTAATATAACTTT
530259 AACT-TT-AACTATTCTTTAATATAACTTT
1 AACTATTAAACTATTCTTTAATATAACTTT
* * *
530287 AACTAATAAACTATTATTTAATATAACTTA
1 AACTATTAAACTATTCTTTAATATAACTTT
530317 AACTA
1 AACTA
530322 AAAAATTAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
22 11 0.21
23 3 0.06
24 6 0.12
25 1 0.02
28 5 0.10
29 1 0.02
30 25 0.48
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.44
Consensus pattern (30 bp):
AACTATTAAACTATTCTTTAATATAACTTT
Found at i:530271 original size:22 final size:22
Alignment explanation
Indices: 530243--530291 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
530233 ACAACTATTA
530243 AACTATTCTTTAATATAACTTT
1 AACTATTCTTTAATATAACTTT
530265 AACTATTCTTTAATATAACTTT
1 AACTATTCTTTAATATAACTTT
530287 AACTA
1 AACTA
530292 ATAAACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (22 bp):
AACTATTCTTTAATATAACTTT
Found at i:530308 original size:15 final size:16
Alignment explanation
Indices: 530264--530314 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 16
530254 AATATAACTT
*
530264 TAACTATTCTTTAATA
1 TAACTATTATTTAATA
**
530280 TAACT-TTAACTAATA
1 TAACTATTATTTAATA
530295 -AACTATTATTTAATA
1 TAACTATTATTTAATA
530310 TAACT
1 TAACT
530315 TAAACTAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 4 0.14
15 15 0.54
16 9 0.32
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (16 bp):
TAACTATTATTTAATA
Found at i:530322 original size:30 final size:30
Alignment explanation
Indices: 530265--530322 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
530255 ATATAACTTT
* *
530265 AACTATTCTTTAATATAACTTTAACTAATA
1 AACTATTATTTAATATAACTTAAACTAATA
530295 AACTATTATTTAATATAACTTAAACTAA
1 AACTATTATTTAATATAACTTAAACTAA
530323 AAAATTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (30 bp):
AACTATTATTTAATATAACTTAAACTAATA
Found at i:530334 original size:27 final size:29
Alignment explanation
Indices: 530274--530335 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 29
530264 TAACTATTCT
* *
530274 TTAATATAACTTTAACTAATAAACTATTAT
1 TTAATATAACTTAAACTAATAAAC-ATTAA
530304 TTAATATAACTTAAACTAA-AAA-ATTAA
1 TTAATATAACTTAAACTAATAAACATTAA
530331 TTAAT
1 TTAAT
530336 TAATTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 9 0.30
29 3 0.10
30 18 0.60
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (29 bp):
TTAATATAACTTAAACTAATAAACATTAA
Found at i:530533 original size:21 final size:21
Alignment explanation
Indices: 530507--530546 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
530497 TTTCTATATG
530507 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
530528 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
530547 ACTAATTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:530787 original size:27 final size:29
Alignment explanation
Indices: 530752--530816 Score: 91
Period size: 28 Copynumber: 2.3 Consensus size: 29
530742 AAAATGTAAC
530752 TTAATTATTTA-ACTAACT-ACAAACTAA
1 TTAATTATTTAGACTAACTAACAAACTAA
* *
530779 TTAAATA-TTAGACTAACTAACACACTAA
1 TTAATTATTTAGACTAACTAACAAACTAA
530807 TTAATTATTT
1 TTAATTATTT
530817 TTTTAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 3 0.09
27 13 0.41
28 14 0.44
29 2 0.06
ACGTcount: A:0.46, C:0.14, G:0.02, T:0.38
Consensus pattern (29 bp):
TTAATTATTTAGACTAACTAACAAACTAA
Found at i:530929 original size:21 final size:20
Alignment explanation
Indices: 530881--530929 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
530871 ATATAACTTA
*
530881 AACTAAACTAATAATAATAT
1 AACTAAACTAACAATAATAT
530901 AACTTAAACTAACACACTAAT-T
1 AAC-TAAACTAACA-A-TAATAT
530923 AACTAAA
1 AACTAAA
530930 ATTTTGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 3 0.12
21 13 0.52
22 5 0.20
23 4 0.16
ACGTcount: A:0.57, C:0.16, G:0.00, T:0.27
Consensus pattern (20 bp):
AACTAAACTAACAATAATAT
Found at i:530948 original size:39 final size:39
Alignment explanation
Indices: 530903--530987 Score: 154
Period size: 39 Copynumber: 2.2 Consensus size: 39
530893 AATAATATAA
530903 CTTAAACTAAC-ACACTAATTAACTAAAATTTTGTTTTAC
1 CTTAAACTAACTA-ACTAATTAACTAAAATTTTGTTTTAC
530942 CTTAAACTAACTAACTAATTAACTAAAATTTTGTTTTAC
1 CTTAAACTAACTAACTAATTAACTAAAATTTTGTTTTAC
530981 CTTAAAC
1 CTTAAAC
530988 CATAAACTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
39 44 0.98
40 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.02, T:0.39
Consensus pattern (39 bp):
CTTAAACTAACTAACTAATTAACTAAAATTTTGTTTTAC
Found at i:531011 original size:39 final size:38
Alignment explanation
Indices: 530903--531011 Score: 121
Period size: 39 Copynumber: 2.8 Consensus size: 38
530893 AATAATATAA
* **
530903 CTTAAACTAACACACTAATTAACTAAAATTTTGTTTTAC
1 CTTAAACCAACA-ACTAACAAACTAAAATTTTGTTTTAC
* **
530942 CTTAAACTAACTAACTAATTAACTAAAATTTTGTTTTAC
1 CTTAAACCAAC-AACTAACAAACTAAAATTTTGTTTTAC
530981 CTTAAACCATA-AACTAACAAACTAATAATTT
1 CTTAAACCA-ACAACTAACAAACTAA-AATTT
531012 AAAATAATAA
Statistics
Matches: 64, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
38 12 0.19
39 50 0.78
40 2 0.03
ACGTcount: A:0.44, C:0.17, G:0.02, T:0.37
Consensus pattern (38 bp):
CTTAAACCAACAACTAACAAACTAAAATTTTGTTTTAC
Found at i:531036 original size:9 final size:9
Alignment explanation
Indices: 531004--531041 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
530994 CTAACAAACT
531004 AATAATTTAA
1 AATAA-TTAA
531014 AATAA-TAA
1 AATAATTAA
*
531022 ACTAATTAA
1 AATAATTAA
531031 AATAATTAA
1 AATAATTAA
531040 AA
1 AA
531042 AACTTACCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 13 0.52
10 5 0.20
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (9 bp):
AATAATTAA
Found at i:531247 original size:12 final size:11
Alignment explanation
Indices: 531216--531251 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
531206 ACGTGAGCGG
531216 GCTGCAATAAT
1 GCTGCAATAAT
*
531227 GCAGCAATAAGT
1 GCTGCAATAA-T
531239 GCTGCAATAAT
1 GCTGCAATAAT
531250 GC
1 GC
531252 AGTTGAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (11 bp):
GCTGCAATAAT
Found at i:544227 original size:33 final size:32
Alignment explanation
Indices: 544162--544241 Score: 108
Period size: 32 Copynumber: 2.5 Consensus size: 32
544152 GACCTAAACA
* * *
544162 AAAAATCAACCAATTCAATATTGACCATACCC
1 AAAAATCAACCGATCCAATATTGACCAAACCC
*
544194 AAAAATCAACTGATCCAATATTGATCCAAACCC
1 AAAAATCAACCGATCCAATATTGA-CCAAACCC
544227 AAAAA-CAACCGATCC
1 AAAAATCAACCGATCC
544242 GATAATCACT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
32 30 0.71
33 12 0.29
ACGTcount: A:0.47, C:0.29, G:0.05, T:0.19
Consensus pattern (32 bp):
AAAAATCAACCGATCCAATATTGACCAAACCC
Found at i:544390 original size:15 final size:15
Alignment explanation
Indices: 544370--544401 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
544360 TAATCTAGAG
544370 CCGAAATGACCCAAC
1 CCGAAATGACCCAAC
544385 CCGAAATGACCCAAC
1 CCGAAATGACCCAAC
544400 CC
1 CC
544402 AAACCCGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.44, G:0.12, T:0.06
Consensus pattern (15 bp):
CCGAAATGACCCAAC
Found at i:548403 original size:14 final size:14
Alignment explanation
Indices: 548386--548421 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
548376 AAAAAATAAA
*
548386 AAATTAAAGTAATG
1 AAATTAAAGGAATG
*
548400 AAATTAAAGGACTG
1 AAATTAAAGGAATG
548414 AAATTAAA
1 AAATTAAA
548422 TAAATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.58, C:0.03, G:0.14, T:0.25
Consensus pattern (14 bp):
AAATTAAAGGAATG
Found at i:553583 original size:21 final size:21
Alignment explanation
Indices: 553541--553583 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
553531 TTTCTGGGTT
* * *
553541 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
553562 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
553583 A
1 A
553584 CGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:553649 original size:67 final size:68
Alignment explanation
Indices: 553565--553714 Score: 205
Period size: 68 Copynumber: 2.2 Consensus size: 68
553555 CCATTCAAGG
* *
553565 GGAACCGATACCCCCTCAACG-AAATGAATTTCCAGAATGCTAGAGGGGAATCGGTACCCCCA-G
1 GGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATA-CCCCAGG
553628 GGGA
65 GGGA
* * * *
553632 GGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCAGGG
1 GGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCAGGG
*
553697 GGG
66 GGA
*
553700 GGAACCGATTCCCCC
1 GGAACCGATACCCCC
553715 ATGAGAAAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
67 25 0.34
68 48 0.66
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.17
Consensus pattern (68 bp):
GGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCAGGG
GGA
Found at i:554051 original size:29 final size:29
Alignment explanation
Indices: 554017--554088 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
554007 CATATTATGA
**
554017 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
554046 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
554075 TACATGACTTGAAT
1 TACATGACATGAAT
554089 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:554144 original size:30 final size:30
Alignment explanation
Indices: 554110--554172 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
554100 GTTATATGAA
*
554110 CTATGTGATAAAGGTATGTAAATGA-TATGT
1 CTATGTGATAAAGGTATGGAAAT-ACTATGT
*
554140 CTATGTGTTAAAGGTATGGAAATACTATGT
1 CTATGTGATAAAGGTATGGAAATACTATGT
554170 CTA
1 CTA
554173 CGCGATATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.35, C:0.06, G:0.22, T:0.37
Consensus pattern (30 bp):
CTATGTGATAAAGGTATGGAAATACTATGT
Found at i:554442 original size:23 final size:22
Alignment explanation
Indices: 554382--554449 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
554372 TTATGGACAT
554382 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
554404 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
554426 AATTCTACGGGGCACTTCGGTGC
1 AATTCTAC-GGGCACTTCGGTGC
554449 A
1 A
554450 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 30 0.67
23 15 0.33
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.26
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:560642 original size:67 final size:68
Alignment explanation
Indices: 560512--560662 Score: 198
Period size: 68 Copynumber: 2.2 Consensus size: 68
560502 CCATTCAAGG
* *
560512 GGAACCGATACCCCCTTAACGAAATGAATTTCCAGAATGCTAGAGGGGAATCGATACCCCCA-GG
1 GGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCAGGG
560576 GGA
66 GGA
* * * *
560579 GGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATA-CCCCAGG
1 GGAACCGATACCCCCTCAACG-AAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA-G
*
560643 GGGGG
64 GGGGA
*
560648 GGAACCGATTCCCCC
1 GGAACCGATACCCCC
560663 ATGAGAAAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
67 24 0.33
68 31 0.42
69 18 0.25
ACGTcount: A:0.28, C:0.27, G:0.26, T:0.18
Consensus pattern (68 bp):
GGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCAGGG
GGA
Found at i:560999 original size:29 final size:29
Alignment explanation
Indices: 560965--561036 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
560955 CATATTATGA
**
560965 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
560994 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
561023 TACATGACTTGAAT
1 TACATGACATGAAT
561037 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:561092 original size:30 final size:30
Alignment explanation
Indices: 561058--561120 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
561048 GTTATATGAA
561058 CTATGTGATAAAGGTATGTAAATGA-TATGT
1 CTATGTGATAAAGGTATGTAAAT-ACTATGT
*
561088 CTATGTGTTAAAGGTATGTAAATACTATGT
1 CTATGTGATAAAGGTATGTAAATACTATGT
561118 CTA
1 CTA
561121 CGCGATATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 1 0.03
30 30 0.97
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (30 bp):
CTATGTGATAAAGGTATGTAAATACTATGT
Found at i:561390 original size:23 final size:22
Alignment explanation
Indices: 561330--561397 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
561320 TTATGGACAT
561330 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
561352 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
561374 AATTCTACGGGGCACTTCGGTGC
1 AATTCTAC-GGGCACTTCGGTGC
561397 A
1 A
561398 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 30 0.67
23 15 0.33
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.26
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:563051 original size:20 final size:20
Alignment explanation
Indices: 563000--563051 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
562990 ATAGTTTCTA
*
563000 ATTTAATCTT-TTTAATTTTC
1 ATTT-ATCTTATTTAATATTC
*
563020 TTTTAT-TTATTTAATATTC
1 ATTTATCTTATTTAATATTC
563039 ATTTATCTTATTT
1 ATTTATCTTATTT
563052 TACAATCTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 2 0.07
19 16 0.59
20 9 0.33
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTTATCTTATTTAATATTC
Found at i:565481 original size:25 final size:27
Alignment explanation
Indices: 565448--565500 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
565438 ATTTCAAAAT
565448 TATAATTAT-AA-AAAATATTAATTTA
1 TATAATTATAAATAAAATATTAATTTA
* *
565473 TATATTTATAAATAAAATATTTATTTA
1 TATAATTATAAATAAAATATTAATTTA
565500 T
1 T
565501 TTAGAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.33
26 2 0.08
27 14 0.58
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
TATAATTATAAATAAAATATTAATTTA
Found at i:565667 original size:104 final size:104
Alignment explanation
Indices: 565467--565675 Score: 226
Period size: 104 Copynumber: 2.0 Consensus size: 104
565457 AAAAAATATT
* * * *
565467 AATTTATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAATGACTTCTAGGTGC
1 AATTTATATATTTATAAATAAAATACTTATTTATTTAAAAATATCAGAAAATGACATCCAGGTGC
* *
565532 CTTAAGACAGCTCTTTTCTTCGATATAAAAAAAATAAAA
66 CTTAAGACAGCTCCTTTCTTCAATATAAAAAAAATAAAA
** * *
565571 AATTTATA-ATTTATAAAATAGGATACTTATTTATTTAAAAATATTAGAAAATAGACATCCAGTT
1 AATTTATATATTTAT-AAATAAAATACTTATTTATTTAAAAATATCAGAAAAT-GACATCCAGGT
*** *
565635 TTTTTAAGACTGC-CCTTTCTT-AATATTGAAAAATAAATAAA
64 GCCTTAAGACAGCTCCTTTCTTCAATA-T-AAAAA-AAATAAA
565676 TATTAAAACA
Statistics
Matches: 86, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
103 9 0.10
104 48 0.56
105 22 0.26
106 7 0.08
ACGTcount: A:0.44, C:0.09, G:0.08, T:0.38
Consensus pattern (104 bp):
AATTTATATATTTATAAATAAAATACTTATTTATTTAAAAATATCAGAAAATGACATCCAGGTGC
CTTAAGACAGCTCCTTTCTTCAATATAAAAAAAATAAAA
Found at i:565713 original size:20 final size:20
Alignment explanation
Indices: 565678--565717 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
565668 TAAATAAATA
*
565678 TTAAAACATGATTAAAATAAG
1 TTAAAACATAATT-AAATAAG
565699 TTAAAA-ATAATTAAATAAG
1 TTAAAACATAATTAAATAAG
565718 ATTTTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 5 0.28
21 6 0.33
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (20 bp):
TTAAAACATAATTAAATAAG
Found at i:565760 original size:2 final size:2
Alignment explanation
Indices: 565748--565782 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
565738 TATTATTTAT
*
565748 TA TA TA AA 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 T
565783 TTATGGATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:565809 original size:12 final size:13
Alignment explanation
Indices: 565792--565826 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
565782 TTTATGGATA
565792 AATAATAATTA-T
1 AATAATAATTAGT
565804 AATAATAA-TAGT
1 AATAATAATTAGT
565816 AATAATAATTA
1 AATAATAATTA
565827 AAAGTAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.10
12 17 0.81
13 2 0.10
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (13 bp):
AATAATAATTAGT
Found at i:567178 original size:3 final size:3
Alignment explanation
Indices: 567170--567225 Score: 66
Period size: 3 Copynumber: 20.0 Consensus size: 3
567160 ATTATTTATT
* *
567170 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA TAA TAT TAA -AA CAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
567214 TAA TAA TAA TAA
1 TAA TAA TAA TAA
567226 ATAAAACAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
2 8 0.17
3 39 0.83
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:567194 original size:19 final size:20
Alignment explanation
Indices: 567170--567226 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 20
567160 ATTATTTATT
*
567170 TAATAATAATAATA-TAATA
1 TAATAATAATAATATTAAAA
567189 TAATAATAATAATATTAAAA
1 TAATAATAATAATATTAAAA
* *
567209 CAA-AATAATAATAATAAA
1 TAATAATAATAATATTAAA
567227 TAAAACAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 28 0.82
20 6 0.18
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (20 bp):
TAATAATAATAATATTAAAA
Found at i:567198 original size:22 final size:22
Alignment explanation
Indices: 567170--567235 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
567160 ATTATTTATT
* *
567170 TAATAATAATAATATAATATAA
1 TAATAATAATAATATAACAAAA
* *
567192 TAATAATAATATTAAAACAAAA
1 TAATAATAATAATATAACAAAA
*
567214 TAATAATAATAAATAAAACAAA
1 TAATAATAAT-AATATAACAAA
567236 TGAAATAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
22 28 0.74
23 10 0.26
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (22 bp):
TAATAATAATAATATAACAAAA
Found at i:567781 original size:113 final size:113
Alignment explanation
Indices: 567577--567937 Score: 641
Period size: 113 Copynumber: 3.2 Consensus size: 113
567567 AGAATCATGC
*
567577 AAAAGATTGAATAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCAT
1 AAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCAT
*
567642 TATGAACTCGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCG
65 TATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
* *
567691 AAAAGTTGAACAAGTTGTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATT
*
567756 ATGAACTCGACCTGGTAATGCTGATCTATCGAATGATGAATTCAAGCG
66 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
567804 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATT
* *
567869 ACGAACCCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
66 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
*
567917 AAAAGTTGAACAAATTCTTCT
1 AAAAGTTGAACAAGTTCTTCT
567938 TCCTTCTTCA
Statistics
Matches: 236, Mismatches: 11, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
113 231 0.98
114 5 0.02
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (113 bp):
AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATT
ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
Found at i:567859 original size:226 final size:216
Alignment explanation
Indices: 567577--568202 Score: 802
Period size: 226 Copynumber: 2.9 Consensus size: 216
567567 AGAATCATGC
*
567577 AAAAGATTGAATAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCAT
1 AAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCAT
*
567642 TATGAACTCGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTT
65 TATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTT
*
567707 GTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGT
130 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCG--CT-G-
567772 AATGCTGATCTATCGAATGATGAATTCAAGCG-
191 -AT-C--A---ATCGAATGATGAATTCAAGCGA
567804 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATT
* * *
567869 ACGAACCCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAATTC
66 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTC
* * ** ** *** * ** * * *
567934 TTCTTCCTTCTTCAGAT-GAGTT-CTTC-TCATTATGAACTCGT-TCACT-GGTAA-T-GCTGAT
131 TTC-TCATTATGAACTTCTTCTTCCTTCTTCA-GATGAGTTCTTCTCATTATG-AACTCGCTGAT
*
567992 CCATCGAATGATGAATTCAAGCG-
193 CAATCGAATGATGAATTCAAGCGA
**
568015 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCCTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATT
**
568080 ATGAACTCTTCCACTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGT
66 ATGAACTC-GAC-CTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGT
568145 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
129 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
568203 TTTCAGAAAT
Statistics
Matches: 343, Mismatches: 44, Indels: 34
0.81 0.10 0.08
Matches are distributed among these distances:
211 90 0.26
212 8 0.02
213 58 0.17
214 11 0.03
215 9 0.03
216 3 0.01
217 2 0.01
219 1 0.00
220 2 0.01
222 1 0.00
223 2 0.01
224 9 0.03
225 11 0.03
226 124 0.36
227 12 0.03
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (216 bp):
AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATT
ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTC
TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGCTGATCAA
TCGAATGATGAATTCAAGCGA
Found at i:567945 original size:96 final size:98
Alignment explanation
Indices: 567835--568039 Score: 344
Period size: 98 Copynumber: 2.1 Consensus size: 98
567825 CATTATGAAC
567835 TTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTACGAACCCG-AC-CTGGTAATGCTGATCCAT
1 TTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTACGAACCCGTACACTGGTAATGCTGATCCAT
567898 CGAATGATGAATTCAAGCGAAAAGTTGAACAAA
66 CGAATGATGAATTCAAGCGAAAAGTTGAACAAA
* * * *
567931 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGTTCACTGGTAATGCTGATCCAT
1 TTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTACGAACCCGTACACTGGTAATGCTGATCCAT
*
567996 CGAATGATGAATTCAAGCGAAAAGTTGAACAAG
66 CGAATGATGAATTCAAGCGAAAAGTTGAACAAA
568029 TTCTTC-TCATT
1 TTCTTCTTCATT
568040 ATGAACTTCT
Statistics
Matches: 101, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
96 40 0.40
97 5 0.05
98 56 0.55
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (98 bp):
TTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTACGAACCCGTACACTGGTAATGCTGATCCAT
CGAATGATGAATTCAAGCGAAAAGTTGAACAAA
Found at i:568062 original size:115 final size:114
Alignment explanation
Indices: 567931--568204 Score: 521
Period size: 115 Copynumber: 2.4 Consensus size: 114
567921 GTTGAACAAA
567931 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGTTCACTGGTAATGCTGATCCAT
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC-TTCACTGGTAATGCTGATCCAT
567996 CGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAAC
65 CGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAAC
*
568046 TTCTTCTTCCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCCACTGGTAATGCTGATCCAT
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTT-CACTGGTAATGCTGATCCAT
568111 CGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAAC
65 CGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAAC
568161 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTT
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTT
568205 TCAGAAATGT
Statistics
Matches: 156, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
114 2 0.01
115 154 0.99
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.38
Consensus pattern (114 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCACTGGTAATGCTGATCCATC
GAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAAC
Found at i:568687 original size:22 final size:22
Alignment explanation
Indices: 568638--568689 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
568628 GATAAAGCTT
* * *
568638 TCATATTTGAAAAGAGAATCTG
1 TCATCTTTAAAAAGAGAATCTA
*
568660 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
*
568682 TTATCTTT
1 TCATCTTT
568690 GAAGAGTGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAATCTA
Found at i:569134 original size:50 final size:48
Alignment explanation
Indices: 569047--569238 Score: 134
Period size: 54 Copynumber: 4.0 Consensus size: 48
569037 ATAACTGGTT
* * * * *
569047 TGTAAAACATTTGACAACATATTC-TTCATCTCATGTGGTTTTAGCTCAGA
1 TGTAAAACACTTGACAACACATTCATCCTTTTC-TGTGG-TTT-GCTCAGA
569097 TGTAAAACACTTGACAACACATTCATCCTTTTCTGT-G---G----GA
1 TGTAAAACACTTGACAACACATTCATCCTTTTCTGTGGTTTGCTCAGA
569137 TGTAAAACACTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGA
1 TGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG-TT-TGCTCAGA
* * *
569187 TGTTCGTAAAGA-ATTTGACAATACATTTATCCTTTTCTGTGGCTTCTGCTCA
1 ---T-GTAAA-ACACTTGACAACACATTCATCCTTTTCTGTGG-TT-TGCTCA
569239 AATTTCTCAA
Statistics
Matches: 118, Mismatches: 8, Indels: 28
0.77 0.05 0.18
Matches are distributed among these distances:
40 38 0.32
41 1 0.01
44 1 0.01
46 1 0.01
49 1 0.01
50 27 0.23
51 5 0.04
53 1 0.01
54 42 0.36
55 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (48 bp):
TGTAAAACACTTGACAACACATTCATCCTTTTCTGTGGTTTGCTCAGA
Found at i:569150 original size:40 final size:40
Alignment explanation
Indices: 569095--569174 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
569085 TTTTAGCTCA
569095 GATGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG
1 GATGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG
569135 GATGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG
1 GATGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG
569175 CTTCTGCTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.33
Consensus pattern (40 bp):
GATGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG
Found at i:571508 original size:114 final size:114
Alignment explanation
Indices: 571308--571525 Score: 373
Period size: 114 Copynumber: 1.9 Consensus size: 114
571298 GATCATGCAG
* * * *
571308 TTCATCTTTCAATTCCAATGATTGGTTCTGGGATTCCTACCGAACCAGATTAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGATTCATACCAAACCAGATCAGATAACTCAAAGA
571373 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACAATAAACAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACAATAAACAAA
* * *
571422 TTCATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGATTCATACCAAACCAGATCAGATAACTCAAAGA
571487 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTAC
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTAC
571526 TATGAGAACG
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 97 1.00
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGGGATTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACAATAAACAAA
Found at i:575841 original size:47 final size:46
Alignment explanation
Indices: 575788--575886 Score: 110
Period size: 48 Copynumber: 2.1 Consensus size: 46
575778 AAATAGTTTG
* ** *
575788 AAATAAAATGTAATTATGCAAAGATGC-AAATGCAAACATGAAAATGT
1 AAATAAAACGTAAAAATGAAAAGATGCAAAATGC-AA-ATGAAAATGT
* *
575835 AAATAAAAACGTAAAAATGAAAATATGCAAAATGCAAATGCAAATGT
1 AAAT-AAAACGTAAAAATGAAAAGATGCAAAATGCAAATGAAAATGT
575882 AAATA
1 AAATA
575887 TGTGAATGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
46 1 0.02
47 17 0.39
48 20 0.45
49 6 0.14
ACGTcount: A:0.58, C:0.08, G:0.13, T:0.21
Consensus pattern (46 bp):
AAATAAAACGTAAAAATGAAAAGATGCAAAATGCAAATGAAAATGT
Found at i:575844 original size:20 final size:20
Alignment explanation
Indices: 575821--575859 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
575811 ATGCAAATGC
* *
575821 AAACATGAAAATGTAAATAA
1 AAACATAAAAATGAAAATAA
*
575841 AAACGTAAAAATGAAAATA
1 AAACATAAAAATGAAAATA
575860 TGCAAAATGC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.67, C:0.05, G:0.10, T:0.18
Consensus pattern (20 bp):
AAACATAAAAATGAAAATAA
Found at i:575978 original size:7 final size:7
Alignment explanation
Indices: 575944--575985 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
575934 ATAAAAGTAT
575944 AAATGCA
1 AAATGCA
* *
575951 CAATGAA
1 AAATGCA
575958 AAATGCA
1 AAATGCA
575965 AAGATGCA
1 AA-ATGCA
575973 AAATGC-
1 AAATGCA
575979 AAATGCA
1 AAATGCA
575986 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:578258 original size:19 final size:19
Alignment explanation
Indices: 578207--578261 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
578197 CTTAATATTG
*
578207 AAAAATAAATAAAT-A-TT
1 AAAAATAATTAAATAAGTT
578224 AAAACA-AGATTAAAATAAGTT
1 AAAA-ATA-ATT-AAATAAGTT
578245 AAAAATAATTAAATAAG
1 AAAAATAATTAAATAAG
578262 ATTTTAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
17 5 0.16
18 3 0.10
19 11 0.35
20 5 0.16
21 7 0.23
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.25
Consensus pattern (19 bp):
AAAAATAATTAAATAAGTT
Found at i:578289 original size:24 final size:24
Alignment explanation
Indices: 578243--578314 Score: 62
Period size: 23 Copynumber: 3.1 Consensus size: 24
578233 TTAAAATAAG
* *
578243 TTAA-AAATAATTAAATA-AGATT
1 TTAATAAATAAATAAATATATATT
578265 TTAATAAATAAAATAAATAT-TA-T
1 TTAATAAAT-AAATAAATATATATT
* * *
578288 TTATTATATAAATATATATATATT
1 TTAATAAATAAATAAATATATATT
578312 TTA
1 TTA
578315 TGGCTAAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
22 13 0.32
23 14 0.35
24 13 0.32
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (24 bp):
TTAATAAATAAATAAATATATATT
Found at i:578338 original size:12 final size:12
Alignment explanation
Indices: 578321--578353 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
578311 TTTATGGCTA
578321 AATAATAAT-GAT
1 AATAATAATAG-T
578333 AATAATAATAGT
1 AATAATAATAGT
578345 AATAATAAT
1 AATAATAAT
578354 TAAAAGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 19 0.95
13 1 0.05
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (12 bp):
AATAATAATAGT
Found at i:579624 original size:3 final size:3
Alignment explanation
Indices: 579616--579677 Score: 69
Period size: 3 Copynumber: 22.0 Consensus size: 3
579606 ATTATTTATT
* * *
579616 TAA TAA TAA TAA T-A TAA T-A TAA TAG TAA TAA TAA TAT TAA -AA CAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
579661 -AA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
579678 ATAAAACAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
2 8 0.16
3 43 0.84
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:579649 original size:25 final size:25
Alignment explanation
Indices: 579616--579687 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
579606 ATTATTTATT
* * *
579616 TAATAATAATAATATAATATAATAG
1 TAATAATAATAATATAACAAAATAA
* *
579641 TAATAATAATATTAAAACAAAATAA
1 TAATAATAATAATATAACAAAATAA
*
579666 TAATAATAATAAATAAAACAAA
1 TAATAATAAT-AATATAACAAA
579688 TGAAATAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
25 30 0.75
26 10 0.25
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (25 bp):
TAATAATAATAATATAACAAAATAA
Found at i:584218 original size:21 final size:22
Alignment explanation
Indices: 584194--584234 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
584184 ACTTGAAATC
584194 ATAAAATAAAAAAA-TTAAAAA
1 ATAAAATAAAAAAACTTAAAAA
*
584215 ATAATATAAAAAAACTTAAA
1 ATAAAATAAAAAAACTTAAA
584235 CAAAAGATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (22 bp):
ATAAAATAAAAAAACTTAAAAA
Found at i:588464 original size:7 final size:7
Alignment explanation
Indices: 588452--588501 Score: 93
Period size: 7 Copynumber: 7.3 Consensus size: 7
588442 ATAAATAGAT
588452 GATGGAA
1 GATGGAA
588459 GATGGAA
1 GATGGAA
588466 GATGGAA
1 GATGGAA
588473 GATGGAA
1 GATGGAA
588480 GATGGAA
1 GATGGAA
588487 GATGGAA
1 GATGGAA
588494 GAT-GAA
1 GATGGAA
588500 GA
1 GA
588502 ATGAAGAAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
6 5 0.12
7 38 0.88
ACGTcount: A:0.44, C:0.00, G:0.42, T:0.14
Consensus pattern (7 bp):
GATGGAA
Found at i:589145 original size:23 final size:24
Alignment explanation
Indices: 589101--589147 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
589091 ATATAAAATA
*
589101 TATTTTTATTATAATTATATTTTT
1 TATTTATATTATAATTATATTTTT
*
589125 TATTTATATT-TATTTATATTTTT
1 TATTTATATTATAATTATATTTTT
589148 ATTATAGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (24 bp):
TATTTATATTATAATTATATTTTT
Found at i:593139 original size:2 final size:2
Alignment explanation
Indices: 593132--593237 Score: 109
Period size: 2 Copynumber: 56.0 Consensus size: 2
593122 TTTCGTCTCC
* * *
593132 TA TA TA TA TA TA TA TA TT TA -A T- TA TA TA TA TT TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
593172 TA T- TA TA T- TA TA T- TT TT TA T- TA TA TA TA TA TCA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
593210 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
593238 GATGTATTAA
Statistics
Matches: 89, Mismatches: 7, Indels: 16
0.79 0.06 0.14
Matches are distributed among these distances:
1 7 0.08
2 80 0.90
3 2 0.02
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:595169 original size:4 final size:4
Alignment explanation
Indices: 595151--595217 Score: 55
Period size: 4 Copynumber: 16.2 Consensus size: 4
595141 CCCCTATATA
* * * **
595151 TATT TTTT TAAT TATT TATT TATT TATT TATT TACTA TATT CCTT T-TT
1 TATT TATT TATT TATT TATT TATT TATT TATT TA-TT TATT TATT TATT
595199 TATT TATAT TATAT TATT T
1 TATT TAT-T TAT-T TATT T
595218 TTATTATATA
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
3 3 0.06
4 36 0.71
5 12 0.24
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.70
Consensus pattern (4 bp):
TATT
Found at i:595217 original size:14 final size:14
Alignment explanation
Indices: 595198--595237 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
595188 TATTCCTTTT
595198 TTATTTATATTATA
1 TTATTTATATTATA
*
595212 TTATTTTTATTATA
1 TTATTTATATTATA
595226 TATATCTTATAT
1 T-TAT-TTATAT
595238 CATTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:595221 original size:40 final size:40
Alignment explanation
Indices: 595154--595230 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 40
595144 CTATATATAT
595154 TTTTTTAATTATTTATTTATTTATTTATT-TACTATATTCC
1 TTTTTTAATTATTTATTTATTTATTTATTATA-TATATTCC
*
595194 TTTTTTATTTATATTATATTA-TT-TTTATTATATATAT
1 TTTTTTAATTAT-TTAT-TTATTTATTTATTATATATAT
595231 CTTATATCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
40 22 0.67
41 8 0.24
42 3 0.09
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (40 bp):
TTTTTTAATTATTTATTTATTTATTTATTATATATATTCC
Found at i:595327 original size:39 final size:37
Alignment explanation
Indices: 595286--595414 Score: 135
Period size: 39 Copynumber: 3.5 Consensus size: 37
595276 TTACTATGTA
595286 TATATATTTTTTCTTAATATTATATTTTATACGTTATT
1 TATATATTTTTTCTTAATATTATATTTT-TACGTTATT
*
595324 ATATATATTTTTTCTTAATATTCTATTTTT--GTT-TT
1 -TATATATTTTTTCTTAATATTATATTTTTACGTTATT
* * * *
595359 TATTTATTTATAT-ATATATATTATATTTTTACTTTATT
1 TATATATTT-TTTCTTA-ATATTATATTTTTACGTTATT
595397 T-TAT-TTTTTTCTTAATAT
1 TATATATTTTTTCTTAATAT
595415 CTTGTATATC
Statistics
Matches: 75, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
34 10 0.13
35 22 0.29
36 8 0.11
37 4 0.05
38 4 0.05
39 27 0.36
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.67
Consensus pattern (37 bp):
TATATATTTTTTCTTAATATTATATTTTTACGTTATT
Found at i:595352 original size:17 final size:17
Alignment explanation
Indices: 595288--595414 Score: 76
Period size: 18 Copynumber: 7.0 Consensus size: 17
595278 ACTATGTATA
595288 TATATTTTTTCTTAATAT
1 TATA-TTTTTCTTAATAT
*
595306 TATATTTTATACGTTATTAT
1 TATATTTT-T-C-TTAATAT
595326 ATATATTTTTTCTTAATAT
1 -TATA-TTTTTCTTAATAT
* * **
595345 TCTATTTTTGTTTTTAT
1 TATATTTTTCTTAATAT
* *
595362 T-TATTTATATATATATAT
1 TATATTTTTCT-TA-ATAT
* *
595380 TATATTTTTACTTTATTT
1 TATATTTTT-CTTAATAT
*
595398 TATTTTTTTCTTAATAT
1 TATATTTTTCTTAATAT
595415 CTTGTATATC
Statistics
Matches: 83, Mismatches: 17, Indels: 19
0.70 0.14 0.16
Matches are distributed among these distances:
16 7 0.08
17 22 0.27
18 23 0.28
19 14 0.17
20 8 0.10
21 5 0.06
22 4 0.05
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATATTTTTCTTAATAT
Found at i:598304 original size:17 final size:18
Alignment explanation
Indices: 598282--598318 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
598272 TCTTATGCAC
598282 ATCAATA-GT-TTTATCAG
1 ATCAATATGTCTTT-TCAG
598299 ATCAATATGTCTTTTCAG
1 ATCAATATGTCTTTTCAG
598317 AT
1 AT
598319 TTATTAATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 8 0.44
19 3 0.17
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (18 bp):
ATCAATATGTCTTTTCAG
Found at i:601719 original size:17 final size:18
Alignment explanation
Indices: 601697--601733 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
601687 TCTTATGCAC
601697 ATCAATA-GT-TTTATCAG
1 ATCAATATGTCTTT-TCAG
601714 ATCAATATGTCTTTTCAG
1 ATCAATATGTCTTTTCAG
601732 AT
1 AT
601734 TTATTAATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 8 0.44
19 3 0.17
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (18 bp):
ATCAATATGTCTTTTCAG
Done.