Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001701.1 Hibiscus syriacus cultivar Beakdansim tig00003403_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: 790467
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:507578 original size:251 final size:249
Alignment explanation
Indices: 506977--507720 Score: 1152
Period size: 251 Copynumber: 3.0 Consensus size: 249
506967 CAACAAGTTG
* * *
506977 TTTTGTATAATAATGAGAAAGCGATTTTCAACGTTTCTTATTCAATCTTTTCCAAAAATGAAATT
1 TTTTGTATAAGAATGAGAAAGAGATTTTCAACGTTTCTCATTCAATCTTTTCCAAAAATGAAATT
*
507042 TTTGAAAAGTAAGAAGTTTTCTTACCCAGTAAATTATTTCCCACAAATTTGTAAATCCTTGGGTT
66 TTTGAAAAGTAAGAAGTTTTCTTA-CCAGTAAATTATTTCCCACAAATTTGTAAATCCTTGGGTC
* * *
507107 ATCTGTCAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATTTGTTGGTCTTTCGAGCAAGA
130 ATCTGTCAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCATCTGTTAGTCTTTCGAGCAAGA
* * *
507172 TGATAAGTCCTT-CGGCCATCCGTCAAACCTTTGGGGAGGATGTTTACATATGAT
195 TGATAAGTCCTTAGGGCCATCCGTCAAACCTTTGGGAAAGATGTTTACATATGAT
* *
507226 TTTTGTATAAGAATGAAAAAGTGA-TTTCAACGTTTCTCATTCAATCTTTTCCAAAAATGAAATT
1 TTTTGTATAAGAATGAGAAAGAGATTTTCAACGTTTCTCATTCAATCTTTTCCAAAAATGAAATT
*
507290 TTTGAAAAATAAGAAGTTTTCTTACCTAGTAAATTATTTCCCACAAATTTGTAAATCCTTCGGGT
66 TTTGAAAAGTAAGAAGTTTTCTTACC-AGTAAATTATTTCCCACAAATTTGTAAATCCTT-GGGT
* *
507355 CATATGTCAGTCTTTCGAGCATGATGCTTAAATCCTTTGGGGTCATCTGTTAGTCTTTCGAGCAA
129 CATCTGTCAGTCTTTCGAGCATGATGCTTAAATCC-TTAGGGTCATCTGTTAGTCTTTCGAGCAA
** * *
507420 GATGATAAGTAATTAGGGCCATCCCTCAAACCTTTGGGTAAGATGTTTACATATGAT
193 GATGATAAGTCCTTAGGGCCATCCGTCAAACCTTTGGGAAAGATGTTTACATATGAT
*
507477 TTTTGTATAAGAATGAGAAAGAGATTTTCAACGTTTCTCATTCAATCTTTTCCAAAGATGAAATT
1 TTTTGTATAAGAATGAGAAAGAGATTTTCAACGTTTCTCATTCAATCTTTTCCAAAAATGAAATT
* *
507542 TTTGAAAAGTAAGAAGTTTTCTTACCAGTAAATTATTTCCCACAAAATTGTAAATTCTTTGGGTC
66 TTTGAAAAGTAAGAAGTTTTCTTACCAGTAAATTATTTCCCACAAATTTGTAAA-TCCTTGGGTC
* * * *
507607 ATCTGTTAGTCTTTCGAGCATGATGTTTAAATCCTTAGGGTCATCTGTCAGTCTTTCGAGCAACA
130 ATCTGTCAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCATCTGTTAGTCTTTCGAGCAAGA
* **
507672 TGATAAGTCCTTAGGGCAATCCGTCAGGCCTTT-GGAAAGGATGTTTACA
195 TGATAAGTCCTTAGGGCCATCCGTCAAACCTTTGGGAAA-GATGTTTACA
507721 CTCTTTATTG
Statistics
Matches: 453, Mismatches: 35, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
247 2 0.00
248 95 0.21
249 62 0.14
250 103 0.23
251 123 0.27
252 68 0.15
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (249 bp):
TTTTGTATAAGAATGAGAAAGAGATTTTCAACGTTTCTCATTCAATCTTTTCCAAAAATGAAATT
TTTGAAAAGTAAGAAGTTTTCTTACCAGTAAATTATTTCCCACAAATTTGTAAATCCTTGGGTCA
TCTGTCAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCATCTGTTAGTCTTTCGAGCAAGAT
GATAAGTCCTTAGGGCCATCCGTCAAACCTTTGGGAAAGATGTTTACATATGAT
Found at i:507698 original size:41 final size:42
Alignment explanation
Indices: 507592--507698 Score: 110
Period size: 42 Copynumber: 2.6 Consensus size: 42
507582 CACAAAATTG
* * * * ** *
507592 TAAATTCTTTGGGTCATCTGTTAGTCTTTCGAGCATGATGTT
1 TAAATCCTTAGGGTCATCCGTCAGTCTTTCGAGCAACATGTA
*
507634 TAAATCCTTAGGGTCATCTGTCAGTCTTTCGAGCAACATG-A
1 TAAATCCTTAGGGTCATCCGTCAGTCTTTCGAGCAACATGTA
*
507675 TAAGTCCTTAGGG-CAATCCGTCAG
1 TAAATCCTTAGGGTC-ATCCGTCAG
507699 GCCTTTGGAA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
40 1 0.02
41 20 0.36
42 35 0.62
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (42 bp):
TAAATCCTTAGGGTCATCCGTCAGTCTTTCGAGCAACATGTA
Found at i:507983 original size:19 final size:19
Alignment explanation
Indices: 507959--508016 Score: 70
Period size: 17 Copynumber: 3.3 Consensus size: 19
507949 TGTCTGTTTC
*
507959 TATTATTAATTATATATGT
1 TATTATTAATTATATATAT
507978 TATTATT-A-TATATATA-
1 TATTATTAATTATATATAT
*
507994 TATTATTAATAATA-ATAT
1 TATTATTAATTATATATAT
508012 TATTA
1 TATTA
508017 AATAATATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
16 7 0.21
17 11 0.32
18 9 0.26
19 7 0.21
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
TATTATTAATTATATATAT
Found at i:508020 original size:16 final size:17
Alignment explanation
Indices: 507959--508024 Score: 66
Period size: 16 Copynumber: 3.9 Consensus size: 17
507949 TGTCTGTTTC
*
507959 TATTATT-AATTATATA
1 TATTATTAAATAATATA
* *
507975 TGTTATTATTATATATATA
1 TATTATTA-AATA-ATATA
507994 TATTATT-AATAATA-A
1 TATTATTAAATAATATA
508009 TATTATTAAATAATAT
1 TATTATTAAATAATAT
508025 TACAAAAGAC
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
15 8 0.20
16 16 0.40
17 3 0.08
18 2 0.05
19 11 0.28
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
TATTATTAAATAATATA
Found at i:508022 original size:13 final size:14
Alignment explanation
Indices: 507978--508026 Score: 64
Period size: 13 Copynumber: 3.4 Consensus size: 14
507968 TTATATATGT
507978 TATTATTATATATATA
1 TATTATTATA-ATA-A
507994 TATTATTAATAATAA
1 TATTATT-ATAATAA
508009 TATTATTA-AATAA
1 TATTATTATAATAA
508022 TATTA
1 TATTA
508027 CAAAAGACCA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
13 10 0.31
14 1 0.03
15 8 0.25
16 10 0.31
17 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TATTATTATAATAA
Found at i:512299 original size:21 final size:21
Alignment explanation
Indices: 512270--512344 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
512260 GTATGTTTAG
512270 GATCGATCCCTTCACCAAAAT
1 GATCGATCCCTTCACCAAAAT
* **
512291 GATCAATCCC-TCGAGGAAAAT
1 GATCGATCCCTTC-ACCAAAAT
512312 GATCGATCCCTTTCACC-AAAT
1 GATCGATCCC-TTCACCAAAAT
*
512333 GATTGATCCCTT
1 GATCGATCCCTT
512345 GTACATAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
20 4 0.09
21 37 0.84
22 1 0.02
23 2 0.05
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (21 bp):
GATCGATCCCTTCACCAAAAT
Found at i:516936 original size:44 final size:43
Alignment explanation
Indices: 516780--517086 Score: 200
Period size: 43 Copynumber: 7.1 Consensus size: 43
516770 TGTGTACAAA
* ** * * *
516780 AAACGCCGCAATAGGTGACGATATATAG-TGCGTTTGTTCATA-
1 AAACGCCGCAATAGATGTTGATATTTAGCGGCGTTT-TTCTTAC
* * * * * *
516822 AAATGCCGCAATAGGTGTTGTTATGTAGCGGCATTTTTATTAC
1 AAACGCCGCAATAGATGTTGATATTTAGCGGCGTTTTTCTTAC
* *
516865 AAACG-CGCAATAGGTGTTGATTTTTAGCGGCGTTTTTCTTAC
1 AAACGCCGCAATAGATGTTGATATTTAGCGGCGTTTTTCTTAC
* **
516907 AAACGCCGCAAATAGATGTTGATCTTTAGCGGCGTTTTTCCCAC
1 AAACGCCGC-AATAGATGTTGATATTTAGCGGCGTTTTTCTTAC
** * * * *
516951 AAACGTTGCAGTAGTTGTTTATATTTAGCGACGTTTTTATCTT--
1 AAACGCCGCAATAGATGTTGATATTTAGCGGCG-TTTT-TCTTAC
* * *
516994 AAACGCCGCAATA-ATTATTGAGATTTAGCGGCGTTTTT-TCCAC
1 AAACGCCGCAATAGA-TGTTGATATTTAGCGGCGTTTTTCT-TAC
** * *
517037 ACAA-GCCGCAATATG-TGTTGATATTTCCCGACGTTTTTTCATAC
1 A-AACGCCGCAATA-GATGTTGATATTTAGCGGCG-TTTTTCTTAC
517081 AAACGC
1 AAACGC
517087 AGCTAAAGGA
Statistics
Matches: 205, Mismatches: 44, Indels: 30
0.73 0.16 0.11
Matches are distributed among these distances:
40 1 0.00
41 1 0.00
42 68 0.33
43 80 0.39
44 53 0.26
45 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (43 bp):
AAACGCCGCAATAGATGTTGATATTTAGCGGCGTTTTTCTTAC
Found at i:517115 original size:43 final size:44
Alignment explanation
Indices: 517068--517159 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 44
517058 TATTTCCCGA
* *
517068 CGTTTTT-TCATACAAACGCAGCTAAAGGACCGATACATAGCGG
1 CGTTTTTAGCATACAAACGCAGCTAAAAGACCGATACATAGCGG
* * * * *
517111 CGTTTTTAGGATACAAACGCCGCTAAAAGATCGGTATATAGCGG
1 CGTTTTTAGCATACAAACGCAGCTAAAAGACCGATACATAGCGG
517155 CGTTT
1 CGTTT
517160 CTATCAACGC
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 7 0.17
44 34 0.83
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (44 bp):
CGTTTTTAGCATACAAACGCAGCTAAAAGACCGATACATAGCGG
Found at i:517450 original size:23 final size:23
Alignment explanation
Indices: 517424--517474 Score: 81
Period size: 21 Copynumber: 2.3 Consensus size: 23
517414 ATATGATGCT
517424 TCTCTCTGTGC-T-GCTGCTGCC
1 TCTCTCTGTGCTTCGCTGCTGCC
517445 TCTCTCTGTGCTTCGCTGCTG-C
1 TCTCTCTGTGCTTCGCTGCTGCC
517467 TCTCTCTG
1 TCTCTCTG
517475 CTTCCCTTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.39
22 10 0.36
23 7 0.25
ACGTcount: A:0.00, C:0.37, G:0.22, T:0.41
Consensus pattern (23 bp):
TCTCTCTGTGCTTCGCTGCTGCC
Found at i:517469 original size:20 final size:20
Alignment explanation
Indices: 517424--517478 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
517414 ATATGATGCT
*
517424 TCTCTCTGTGCTGCTGCTGCC
1 TCTCTCTGTGCTTCTGCTG-C
517445 TCTCTCTGTGCTTC-GCTGC
1 TCTCTCTGTGCTTCTGCTGC
*
517464 TGCTCTCTCTGCTTC
1 T-CTCTCTGTGCTTC
517479 CCTTGCTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 2 0.06
20 16 0.52
21 13 0.42
ACGTcount: A:0.00, C:0.38, G:0.20, T:0.42
Consensus pattern (20 bp):
TCTCTCTGTGCTTCTGCTGC
Found at i:524834 original size:42 final size:40
Alignment explanation
Indices: 524713--524834 Score: 106
Period size: 42 Copynumber: 3.0 Consensus size: 40
524703 ATTTGTATCC
*
524713 AAAAACGCCACTAAAGTATAACTTTTTAGCGGCATTTTTTA
1 AAAAACGCCACTAAAATATAACTTTTTA-CGGCATTTTTTA
** * *
524754 CCAAACGCCAC-AAAAT-TAAGAGTATTTTACGGCGTTTTTCTA
1 AAAAACGCCACTAAAATAT-A-ACT-TTTTACGGCATTTTT-TA
*
524796 AAAAACGCCACTAAAATATTA-TTCTTTACCGGCATTTTT
1 AAAAACGCCACTAAAATATAACTT-TTTA-CGGCATTTTT
524835 GGATACAAAC
Statistics
Matches: 64, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
39 1 0.02
40 6 0.09
41 25 0.39
42 26 0.41
43 5 0.08
44 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.34
Consensus pattern (40 bp):
AAAAACGCCACTAAAATATAACTTTTTACGGCATTTTTTA
Found at i:526166 original size:40 final size:42
Alignment explanation
Indices: 526114--526211 Score: 148
Period size: 41 Copynumber: 2.4 Consensus size: 42
526104 TTTATACAAA
* *
526114 AAAAAATGCCACTATTGATT-ACACTATTGTGGCGTTTGT-T
1 AAAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTCT
526154 AAAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTCT
1 AAAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTCT
*
526196 -AAGAACGCCACTATTG
1 AAAAAACGCCACTATTG
526212 CGGCGTTTGA
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
40 19 0.36
41 33 0.62
42 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (42 bp):
AAAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTCT
Found at i:526360 original size:42 final size:41
Alignment explanation
Indices: 526313--526443 Score: 124
Period size: 42 Copynumber: 3.1 Consensus size: 41
526303 AAACGTTGCT
*
526313 AATTTACCACTCTATTCTGGCATTTTGGCTAAATCACCGCAA
1 AATTTACCACTCTATTCTAGC-TTTTGGCTAAATCACCGCAA
* * * * * *
526355 AATTTA-TACTCTATTGTAGCTTTTGTGGTATAAACGCCGC-T
1 AATTTACCACTCTATTCTAGCTTTTG-GCTA-AATCACCGCAA
*
526396 AATTTACCACTCTATTAC-AGCGTTTTGGCTAAATCACCGTAA
1 AATTTACCACTCTATT-CTAGC-TTTTGGCTAAATCACCGCAA
526438 AATTTA
1 AATTTA
526444 TACGACGGCG
Statistics
Matches: 69, Mismatches: 14, Indels: 12
0.73 0.15 0.13
Matches are distributed among these distances:
40 5 0.07
41 26 0.38
42 33 0.48
43 5 0.07
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (41 bp):
AATTTACCACTCTATTCTAGCTTTTGGCTAAATCACCGCAA
Found at i:526366 original size:41 final size:40
Alignment explanation
Indices: 526321--526446 Score: 112
Period size: 41 Copynumber: 3.0 Consensus size: 40
526311 CTAATTTACC
*
526321 ACTCTATTCTGGCATTTTGGCTAAATCACCGCAAAATTTAT
1 ACTCTATTCTAGC-TTTTGGCTAAATCACCGCAAAATTTAT
* * * * * *
526362 ACTCTATTGTAGCTTTTGTGGTATAAACGCCGC-TAATTTACC
1 ACTCTATTCTAGCTTTTG-GCTA-AATCACCGCAAAATTTA-T
*
526404 ACTCTATTAC-AGCGTTTTGGCTAAATCACCGTAAAATTTAT
1 ACTCTATT-CTAGC-TTTTGGCTAAATCACCGCAAAATTTAT
526445 AC
1 AC
526447 GACGGCGTAT
Statistics
Matches: 65, Mismatches: 14, Indels: 12
0.71 0.15 0.13
Matches are distributed among these distances:
40 5 0.08
41 28 0.43
42 27 0.42
43 5 0.08
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (40 bp):
ACTCTATTCTAGCTTTTGGCTAAATCACCGCAAAATTTAT
Found at i:526422 original size:83 final size:82
Alignment explanation
Indices: 526293--526446 Score: 238
Period size: 83 Copynumber: 1.9 Consensus size: 82
526283 TATTGCGGCG
** *
526293 TTTTTGGTATAAACGTTGCTAATTTACCACTCTATTCTGGCATTTTGGCTAAATCACCGCAAAAT
1 TTTTTGGTATAAACGCCGCTAATTTACCACTCTATTCTAGCATTTTGGCTAAATCACCGCAAAAT
526358 TTATACTCTATTGTAGC
66 TTATACTCTATTGTAGC
* *
526375 TTTTGTGGTATAAACGCCGCTAATTTACCACTCTATTAC-AGCGTTTTGGCTAAATCACCGTAAA
1 TTTT-TGGTATAAACGCCGCTAATTTACCACTCTATT-CTAGCATTTTGGCTAAATCACCGCAAA
526439 ATTTATAC
64 ATTTATAC
526447 GACGGCGTAT
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
82 4 0.06
83 60 0.92
84 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (82 bp):
TTTTTGGTATAAACGCCGCTAATTTACCACTCTATTCTAGCATTTTGGCTAAATCACCGCAAAAT
TTATACTCTATTGTAGC
Found at i:528028 original size:20 final size:21
Alignment explanation
Indices: 527990--528031 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
527980 CCTTTGCAAA
527990 AAAAAATCGATCCCTTTTAGG
1 AAAAAATCGATCCCTTTTAGG
*
528011 AAAAGATCGATCCC-TTTAGG
1 AAAAAATCGATCCCTTTTAGG
528031 A
1 A
528032 CAAATTTGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (21 bp):
AAAAAATCGATCCCTTTTAGG
Found at i:531356 original size:22 final size:23
Alignment explanation
Indices: 531310--531355 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
531300 CAATGACCAT
* *
531310 ATCTTAATTTAATAAAAACAAAA
1 ATCTTAACTAAATAAAAACAAAA
531333 ATCTTAACTAAATAAAAACAAAA
1 ATCTTAACTAAATAAAAACAAAA
531356 TTGACCAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (23 bp):
ATCTTAACTAAATAAAAACAAAA
Found at i:536626 original size:15 final size:15
Alignment explanation
Indices: 536601--536661 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 15
536591 TTAAAAGAGA
536601 AAATAAAAATAA-AACT
1 AAAT-AAAATAATAA-T
536617 AAATAAAATAATAAT
1 AAATAAAATAATAAT
536632 AAATAAAAGGT-A-AAT
1 AAATAAAA--TAATAAT
536647 ATAATAAAATAATAA
1 A-AATAAAATAATAA
536662 ATAATAGTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
14 1 0.03
15 21 0.54
16 16 0.41
17 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.23
Consensus pattern (15 bp):
AAATAAAATAATAAT
Found at i:536639 original size:31 final size:31
Alignment explanation
Indices: 536601--536661 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
536591 TTAAAAGAGA
536601 AAATAAAA-ATAAA-ACTAAATAAAATAATAAT
1 AAATAAAAGATAAATA-T-AATAAAATAATAAT
*
536632 AAATAAAAGGTAAATATAATAAAATAATAA
1 AAATAAAAGATAAATATAATAAAATAATAA
536662 ATAATAGTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 21 0.78
32 5 0.19
33 1 0.04
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.23
Consensus pattern (31 bp):
AAATAAAAGATAAATATAATAAAATAATAAT
Found at i:536665 original size:15 final size:15
Alignment explanation
Indices: 536618--536667 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
536608 AATAAAACTA
536618 AATAAAATAAT-AAT
1 AATAAAATAATAAAT
*
536632 AAATAAAAGGTAA-ATAT
1 -AATAAAA--TAATAAAT
536649 AATAAAATAATAAAT
1 AATAAAATAATAAAT
536664 AATA
1 AATA
536668 GTAGTAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 3 0.10
15 14 0.48
16 7 0.24
17 5 0.17
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (15 bp):
AATAAAATAATAAAT
Found at i:536728 original size:18 final size:18
Alignment explanation
Indices: 536707--536749 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
536697 GTTGTTTTTA
*
536707 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
536725 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
536743 AAATAAA
1 AAATAAA
536750 TAATCTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:537404 original size:200 final size:200
Alignment explanation
Indices: 536924--537392 Score: 654
Period size: 200 Copynumber: 2.3 Consensus size: 200
536914 CATATGGTTT
* *
536924 ATATGCCCTCGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATTGCCCTTCTCGT-C
1 ATATGCCTTCGAGCTGAATGGAATCGAACTCGAAAG-TTTTGTTGACAGATTGCCCTTCTC-TCC
* *
536988 TTGAGCTATGCTGTAAATTCGACTGGGAGATAGTTCTTTGTTGCTAAATCGCAGCCAACCTAGGT
64 TTGAGCTATGCTGTAAATTCGACTGGGAGATAGTTCATTGTAGCTAAATCGCAGCCAACCTAGGT
* ** *
537053 CTTCTTCTTAACTTAAAGACCTCATTTTAAACTTTAACTAGAAAGTAGTTCCTCGTTGCTACCAT
129 CTTCTTCTTAACTTAAAGACCTCAGTTTAAACTCGAACGAGAAAGTAGTTCCTCGTTGCTACCAT
537118 ACGATTA
194 ACGATTA
* * * * *
537125 ATATGCCTTCGAGTTGAATGGAATCAAACTCGCAAGTTTTGTTGACAGATAGCCCTTCTCGCCTT
1 ATATGCCTTCGAGCTGAATGGAATCGAACTCGAAAGTTTTGTTGACAGATTGCCCTTCTCTCCTT
* * *
537190 GAGCTATGCTGTAAATTCGGCTGGGAGATAGTTCATTGTAGCTAAATTGCAGCCAACTTAGGTCT
66 GAGCTATGCTGTAAATTCGACTGGGAGATAGTTCATTGTAGCTAAATCGCAGCCAACCTAGGTCT
* ** *
537255 TCTTCTTGACTTAAAGACCTTGGTTTAAACATCGAACGA-AAAGTAGTTCCTCGTTGCTACCATG
131 TCTTCTTAACTTAAAGACCTCAGTTTAAAC-TCGAACGAGAAAGTAGTTCCTCGTTGCTACCATA
* *
537319 CGGTTG
195 CGATTA
* * * * *
537325 ATATGTCTTCGAGCTAAATGGAATTGAACTTGAAAGTTTTATTGACAGATTGCCCTTCTCTCCTT
1 ATATGCCTTCGAGCTGAATGGAATCGAACTCGAAAGTTTTGTTGACAGATTGCCCTTCTCTCCTT
537390 GAG
66 GAG
537393 TTTTACTGTA
Statistics
Matches: 234, Mismatches: 32, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
200 198 0.85
201 36 0.15
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.33
Consensus pattern (200 bp):
ATATGCCTTCGAGCTGAATGGAATCGAACTCGAAAGTTTTGTTGACAGATTGCCCTTCTCTCCTT
GAGCTATGCTGTAAATTCGACTGGGAGATAGTTCATTGTAGCTAAATCGCAGCCAACCTAGGTCT
TCTTCTTAACTTAAAGACCTCAGTTTAAACTCGAACGAGAAAGTAGTTCCTCGTTGCTACCATAC
GATTA
Found at i:537950 original size:42 final size:41
Alignment explanation
Indices: 537729--538213 Score: 170
Period size: 42 Copynumber: 11.3 Consensus size: 41
537719 TTTGGATGAC
* * * * *
537729 TCCCCTTCACGGGAAAGTCAAGTGGTATATTCTTCAGGTGGT
1 TCCCCTTCACGGGAAAGCCATGTGATATATCCTT-AGATGGT
* * * * * * **
537771 TCCCCTTCGCGGGTCTGAA-CCAAGTGAGATGATCTTTGGATGAC
1 TCCCCTTCACGGG---AAAGCCATGTGATAT-ATCCTTAGATGGT
* * * *
537815 TCCCCTTCACGGGAAAGTCATGTGGTATATTCCTCAGGTGGT
1 TCCCCTTCACGGGAAAGCCATGTGATATA-TCCTTAGATGGT
* * * * * **
537857 TCCCCTTCGCGGGTCTAAA-CCAAGTGAGATGATCTTTGGATGAC
1 TCCCCTTCACGGG---AAAGCCATGTGATAT-ATCCTTAGATGGT
*
537901 TCCCCTTCATGGGAAAGCCATGTGATATATTCCTTAGATGGT
1 TCCCCTTCACGGGAAAGCCATGTGATATA-TCCTTAGATGGT
** * * * * **
537943 TCCCCTTCGTGGGTCTGAA-CCAAGTGATATGATCTTTGGATGAC
1 TCCCCTTCACGGG---AAAGCCATGTGATAT-ATCCTTAGATGGT
* * * *
537987 TCCCCTTCACGGGAAAGTCATGTGGTATATTCCTCAGGTGGT
1 TCCCCTTCACGGGAAAGCCATGTGATATA-TCCTTAGATGGT
* * * * * **
538029 TCCCCTTCGCGGGTCTAAA-CCAAGTGAGATGATCTTTGGATGAC
1 TCCCCTTCACGGG---AAAGCCATGTGATAT-ATCCTTAGATGGT
* * *
538073 TCTCTTTCATGGGAAAGCCATGTGATATACTCCTTAGATGGT
1 TCCCCTTCACGGGAAAGCCATGTGATATA-TCCTTAGATGGT
* * * * * * **
538115 TCCCCTTCGCGGGTCTGAA-CCAAGTGAGATGATCTTTGGATGAC
1 TCCCCTTCACGGG---AAAGCCATGTGATAT-ATCCTTAGATGGT
* * *
538159 TCCCCTTCACGGGAAAGCCATGTGGTATATTCTTCAGGTGGT
1 TCCCCTTCACGGGAAAGCCATGTGATATATCCTT-AGATGGT
*
538201 TCCCCTTCGCGGG
1 TCCCCTTCACGGG
538214 TCTGAACCAG
Statistics
Matches: 308, Mismatches: 105, Indels: 60
0.65 0.22 0.13
Matches are distributed among these distances:
41 20 0.06
42 141 0.46
44 127 0.41
45 20 0.06
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.30
Consensus pattern (41 bp):
TCCCCTTCACGGGAAAGCCATGTGATATATCCTTAGATGGT
Found at i:538279 original size:86 final size:86
Alignment explanation
Indices: 537467--538268 Score: 1214
Period size: 86 Copynumber: 9.3 Consensus size: 86
537457 ATTCTTTAGT
** ** * * *
537467 TGACTCCTTTTCACGGGAAAACCAAGTGGTATATTCTTCAGGTGGTTCCCCTTTGCAGGTCTGAA
1 TGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCGGGTCTGAA
*
537532 CCAGGTGAGATGATCTTTGGA
66 CCAAGTGAGATGATCTTTGGA
*
537553 TGACTCCCCTTCACGGGAAAGTCATGTAGTATATTCTTCAGGTGGTTCCCCTTCGCGGGTCTGAA
1 TGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCGGGTCTGAA
* *
537618 CCAGGTGAGATGATTTTTGGA
66 CCAAGTGAGATGATCTTTGGA
* *
537639 TTACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCTCTTCGCGGGTCTGAA
1 TGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCGGGTCTGAA
* * * *
537704 CTAGGTGATATGATATTTGGA
66 CCAAGTGAGATGATCTTTGGA
*
537725 TGACTCCCCTTCACGGGAAAGTCAAGTGGTATATTCTTCAGGTGGTTCCCCTTCGCGGGTCTGAA
1 TGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCGGGTCTGAA
537790 CCAAGTGAGATGATCTTTGGA
66 CCAAGTGAGATGATCTTTGGA
* *
537811 TGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCCTCAGGTGGTTCCCCTTCGCGGGTCTAAA
1 TGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCGGGTCTGAA
537876 CCAAGTGAGATGATCTTTGGA
66 CCAAGTGAGATGATCTTTGGA
* * * * *
537897 TGACTCCCCTTCATGGGAAAGCCATGTGATATATTCCTT-AGATGGTTCCCCTTCGTGGGTCTGA
1 TGACTCCCCTTCACGGGAAAGTCATGTGGTATATT-CTTCAGGTGGTTCCCCTTCGCGGGTCTGA
*
537961 ACCAAGTGATATGATCTTTGGA
65 ACCAAGTGAGATGATCTTTGGA
* *
537983 TGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCCTCAGGTGGTTCCCCTTCGCGGGTCTAAA
1 TGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCGGGTCTGAA
538048 CCAAGTGAGATGATCTTTGGA
66 CCAAGTGAGATGATCTTTGGA
* * * * * * *
538069 TGACTCTCTTTCATGGGAAAGCCATGTGATATACTCCTT-AGATGGTTCCCCTTCGCGGGTCTGA
1 TGACTCCCCTTCACGGGAAAGTCATGTGGTATA-TTCTTCAGGTGGTTCCCCTTCGCGGGTCTGA
538133 ACCAAGTGAGATGATCTTTGGA
65 ACCAAGTGAGATGATCTTTGGA
*
538155 TGACTCCCCTTCACGGGAAAGCCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCGGGTCTGAA
1 TGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCGGGTCTGAA
*
538220 CC-AGTTGAGATTATCTTTGGA
66 CCAAG-TGAGATGATCTTTGGA
*
538241 TGACTCCCCTTTACGGGAAAGTCATGTG
1 TGACTCCCCTTCACGGGAAAGTCATGTG
538269 AGATGTTCTT
Statistics
Matches: 652, Mismatches: 59, Indels: 10
0.90 0.08 0.01
Matches are distributed among these distances:
85 8 0.01
86 639 0.98
87 5 0.01
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (86 bp):
TGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCGGGTCTGAA
CCAAGTGAGATGATCTTTGGA
Found at i:541495 original size:16 final size:16
Alignment explanation
Indices: 541474--541519 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
541464 GAAAAAGGTC
*
541474 CTACCCCATATGCTAT
1 CTACCCCACATGCTAT
*
541490 CTACCCCACATGTTAT
1 CTACCCCACATGCTAT
*
541506 CTATCCCACATGCT
1 CTACCCCACATGCT
541520 TGTTATTCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.24, C:0.39, G:0.07, T:0.30
Consensus pattern (16 bp):
CTACCCCACATGCTAT
Found at i:542463 original size:20 final size:20
Alignment explanation
Indices: 542397--542463 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 20
542387 CAAAAAATGT
542397 TAAAAGAAAA-AATAAAATA
1 TAAAAGAAAATAATAAAATA
* *
542416 -AATGAAGAAAATATTAAATTTCA
1 TAA--AAGAAAATAATAAA-AT-A
542439 TAAAAGAAAATAATAAAATA
1 TAAAAGAAAATAATAAAATA
542459 TAAAA
1 TAAAA
542464 AAATGTTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
18 2 0.05
20 13 0.34
21 6 0.16
22 14 0.37
23 1 0.03
24 2 0.05
ACGTcount: A:0.70, C:0.01, G:0.06, T:0.22
Consensus pattern (20 bp):
TAAAAGAAAATAATAAAATA
Found at i:542510 original size:20 final size:20
Alignment explanation
Indices: 542478--542530 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
542468 GTTAAAAGAG
542478 AAAATAA-AAATAAAACA-A
1 AAAATAATAAATAAAACAGA
*
542496 AATAATAATAAATAAAAGAGA
1 AA-AATAATAAATAAAACAGA
542517 AAAATAATAAATAA
1 AAAATAATAAATAA
542531 TAGTAGTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 2 0.06
19 5 0.16
20 21 0.68
21 3 0.10
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.17
Consensus pattern (20 bp):
AAAATAATAAATAAAACAGA
Found at i:542597 original size:18 final size:18
Alignment explanation
Indices: 542574--542616 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
542564 TGTTTTTTTA
* *
542574 AAATAAAAGATAAGACTT
1 AAATAAAAGAAAAGAATT
*
542592 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
542610 AAATAAA
1 AAATAAA
542617 TAATCTAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:545964 original size:30 final size:30
Alignment explanation
Indices: 545930--546057 Score: 121
Period size: 30 Copynumber: 4.3 Consensus size: 30
545920 TACTAGTGCC
*
545930 AAATAGTACAGGGACTTGGCCATCAATGTT
1 AAATAGTACAGGGACTTGGCCACCAATGTT
* * * * *
545960 AAATAGTAAAAGGACTCGGCCATCAAGGTT
1 AAATAGTACAGGGACTTGGCCACCAATGTT
* * * * * *
545990 AATTATTACCGGGGCTTGGTCACCAATTTT
1 AAATAGTACAGGGACTTGGCCACCAATGTT
* * *
546020 AAATAGTATAGAGACTTTGCCACCAATGTT
1 AAATAGTACAGGGACTTGGCCACCAATGTT
546050 AAATAGTA
1 AAATAGTA
546058 TAAGAACCAA
Statistics
Matches: 74, Mismatches: 24, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 74 1.00
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.28
Consensus pattern (30 bp):
AAATAGTACAGGGACTTGGCCACCAATGTT
Found at i:548201 original size:23 final size:23
Alignment explanation
Indices: 548148--548204 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
548138 GCACTGATGT
* * *
548148 ACCACGTAGAAATGTCCTGAAGG
1 ACCATGTAGAAATGACCCGAAGG
548171 ACCATGTAGAAATGACCCGAAGG
1 ACCATGTAGAAATGACCCGAAGG
**
548194 ACTGTGTAGAA
1 ACCATGTAGAA
548205 TTTGTCCCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.37, C:0.19, G:0.26, T:0.18
Consensus pattern (23 bp):
ACCATGTAGAAATGACCCGAAGG
Found at i:554676 original size:28 final size:28
Alignment explanation
Indices: 554636--554721 Score: 154
Period size: 28 Copynumber: 3.1 Consensus size: 28
554626 AAGAGAAGAA
554636 CCCGATCATTTGCTATGAATGCAAAAAG
1 CCCGATCATTTGCTATGAATGCAAAAAG
*
554664 CCCGATCATTTGCTATGAATGCAAAAAA
1 CCCGATCATTTGCTATGAATGCAAAAAG
*
554692 CCCGATCATTTTCTATGAATGCAAAAAG
1 CCCGATCATTTGCTATGAATGCAAAAAG
554720 CC
1 CC
554722 GGGGCATGTC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 55 1.00
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (28 bp):
CCCGATCATTTGCTATGAATGCAAAAAG
Found at i:561444 original size:20 final size:20
Alignment explanation
Indices: 561419--561470 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
561409 CACTTAGGGA
*
561419 ACCGATTCCCCTTAAGGGGT
1 ACCGATTCCCCCTAAGGGGT
561439 ACCGATTCCCCCTAAGGGGT
1 ACCGATTCCCCCTAAGGGGT
*
561459 ACCGACTCCCCC
1 ACCGATTCCCCC
561471 CACGCTCCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.19, C:0.40, G:0.21, T:0.19
Consensus pattern (20 bp):
ACCGATTCCCCCTAAGGGGT
Found at i:564829 original size:24 final size:23
Alignment explanation
Indices: 564772--564830 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 23
564762 CAGCCAAAAC
*
564772 TGCCACATAGAATTGCACCGAAG
1 TGCCACATAGAATTGCAACGAAG
564795 TG-CAGCATAGAATATGCAACGAAG
1 TGCCA-CATAGAAT-TGCAACGAAG
*
564819 TGCCACGTAGAA
1 TGCCACATAGAA
564831 ATGTCCTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 2 0.06
23 10 0.32
24 17 0.55
25 2 0.06
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (23 bp):
TGCCACATAGAATTGCAACGAAG
Found at i:564875 original size:23 final size:23
Alignment explanation
Indices: 564821--564876 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
564811 CAACGAAGTG
564821 CCACGTAGAAATGTCCTAAAGGA
1 CCACGTAGAAATGTCCTAAAGGA
* * * *
564844 CCACATAGACATGTCTTGAAGGA
1 CCACGTAGAAATGTCCTAAAGGA
*
564867 CCATGTAGAA
1 CCACGTAGAA
564877 TTTGTCTCGA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (23 bp):
CCACGTAGAAATGTCCTAAAGGA
Found at i:564892 original size:24 final size:24
Alignment explanation
Indices: 564839--564916 Score: 72
Period size: 23 Copynumber: 3.3 Consensus size: 24
564829 AAATGTCCTA
* *
564839 AAGGACCACATAGACA--TGTCTTG
1 AAGGACCATATAGA-ATTTGTCTCG
*
564862 AAGGACCATGTAGAATTTGTCTCG
1 AAGGACCATATAGAATTTGTCTCG
* * *
564886 AATGACCATATAGAA-TTATCCCG
1 AAGGACCATATAGAATTTGTCTCG
564909 AAGGACCA
1 AAGGACCA
564917 CGTAGAACCC
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
22 1 0.02
23 25 0.56
24 19 0.42
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (24 bp):
AAGGACCATATAGAATTTGTCTCG
Found at i:564915 original size:23 final size:24
Alignment explanation
Indices: 564861--564916 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
564851 GACATGTCTT
* * *
564861 GAAGGACCATGTAGAATTTGTCTC
1 GAAGGACCATATAGAATTTATCCC
*
564885 GAATGACCATATAGAA-TTATCCC
1 GAAGGACCATATAGAATTTATCCC
564908 GAAGGACCA
1 GAAGGACCA
564917 CGTAGAACCC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 13 0.48
24 14 0.52
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (24 bp):
GAAGGACCATATAGAATTTATCCC
Found at i:564922 original size:23 final size:24
Alignment explanation
Indices: 564861--564923 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 24
564851 GACATGTCTT
* *
564861 GAAGGACCATGTAGAATTTGTCTC
1 GAAGGACCATGTAGAATTTATCCC
* *
564885 GAATGACCATATAGAA-TTATCCC
1 GAAGGACCATGTAGAATTTATCCC
*
564908 GAAGGACCACGTAGAA
1 GAAGGACCATGTAGAA
564924 CCCTCGACTA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 18 0.56
24 14 0.44
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (24 bp):
GAAGGACCATGTAGAATTTATCCC
Found at i:594351 original size:179 final size:177
Alignment explanation
Indices: 594032--594381 Score: 666
Period size: 179 Copynumber: 2.0 Consensus size: 177
594022 TCTTGAGGGT
594032 AAGTCGATTGGTTGCAAATGGGTGTATAAGAAGAAACCAACAGTAACAGAAAAAAGGGGAGAAGT
1 AAGTCGATTGGTTGCAAATGGGTGTATAAGAAGAAACCAACAGTAACAGAAAAAAGGGGAGAAGT
594097 TCAAGGCTCGCTTGGTAGCAAAGGTTTTTCACAGAAGAAAGGAGTTGATTATGATGAAATCTTTT
66 TCAAGGCTCGCTTGGTAGCAAAGGTTTTTCACAGAAGAAAGGAGTTGATTATGATGAAATCTTTT
594162 CTCCTGTGGTCAGTCACACTTCAATCCGAGCA-TACTTACAGGTAAG
131 CTCCTGTGGTCAGTCACACTTCAATCCGAGCAGTACTTACAGGTAAG
594208 AAGTCGATTGGTTGCAAATGGGTGTATAAGAAGAAACCAACAGTAACAGAAAAAGAGGGGGAGAA
1 AAGTCGATTGGTTGCAAATGGGTGTATAAGAAGAAACCAACAGTAACAGAAAAA-A-GGGGAGAA
594273 GTTCAAGGCTCGCTTGGTAGCAAAGGGTTTTTCACAGAAGAAAGGAGTTGATTATGATGAAATCT
64 GTTCAAGGCTCGCTTGGTAGCAAA-GGTTTTTCACAGAAGAAAGGAGTTGATTATGATGAAATCT
594338 TTTCTCCTGTGGTCAGTCACACTTCAATCCGAGCAGTACTTACA
128 TTTCTCCTGTGGTCAGTCACACTTCAATCCGAGCAGTACTTACA
594382 TTGGTGGCTA
Statistics
Matches: 170, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
176 54 0.32
177 1 0.01
178 32 0.19
179 75 0.44
180 8 0.05
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.25
Consensus pattern (177 bp):
AAGTCGATTGGTTGCAAATGGGTGTATAAGAAGAAACCAACAGTAACAGAAAAAAGGGGAGAAGT
TCAAGGCTCGCTTGGTAGCAAAGGTTTTTCACAGAAGAAAGGAGTTGATTATGATGAAATCTTTT
CTCCTGTGGTCAGTCACACTTCAATCCGAGCAGTACTTACAGGTAAG
Found at i:599646 original size:14 final size:14
Alignment explanation
Indices: 599627--599664 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
599617 TTAGGCAGCT
*
599627 GAGATAGAAGGACC
1 GAGATAGAAGGAAC
*
599641 GAGATAGAAGGAAT
1 GAGATAGAAGGAAC
599655 GAGATAGAAG
1 GAGATAGAAG
599665 TGAAAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.47, C:0.05, G:0.37, T:0.11
Consensus pattern (14 bp):
GAGATAGAAGGAAC
Found at i:601106 original size:30 final size:30
Alignment explanation
Indices: 601064--601122 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
601054 TGTAAAATTT
**
601064 GATTTTGCACTTAATTGAATTTATCAAAAA
1 GATTTTGCACTTAATCAAATTTATCAAAAA
601094 GATTTTAG-ACTTAATCAAATTTATCAAAA
1 GATTTT-GCACTTAATCAAATTTATCAAAA
601123 TTTATCAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.39
Consensus pattern (30 bp):
GATTTTGCACTTAATCAAATTTATCAAAAA
Found at i:607740 original size:43 final size:43
Alignment explanation
Indices: 607674--607757 Score: 132
Period size: 43 Copynumber: 2.0 Consensus size: 43
607664 ATAAATTGCA
** *
607674 GAAACATTTCAATATATTGGGAACCCAGTGTTACGTAGAACGC
1 GAAACATTTCAATATATCAGGAACCCAATGTTACGTAGAACGC
*
607717 GAAACGTTTCAATATATCAGGAACCCAATGTTACGTAGAAC
1 GAAACATTTCAATATATCAGGAACCCAATGTTACGTAGAAC
607758 ATGAAGTCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (43 bp):
GAAACATTTCAATATATCAGGAACCCAATGTTACGTAGAACGC
Found at i:615927 original size:21 final size:21
Alignment explanation
Indices: 615903--615968 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
615893 TCTCACGATT
615903 ATATCAAAGCCATGATAAACA
1 ATATCAAAGCCATGATAAACA
* * **
615924 ATATCATA--CATAATAGTC-
1 ATATCAAAGCCATGATAAACA
615942 ATATCAAAGCCATGATAAACA
1 ATATCAAAGCCATGATAAACA
615963 ATATCA
1 ATATCA
615969 TACATATTAG
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
18 7 0.21
19 7 0.21
20 7 0.21
21 13 0.38
ACGTcount: A:0.50, C:0.18, G:0.08, T:0.24
Consensus pattern (21 bp):
ATATCAAAGCCATGATAAACA
Found at i:616046 original size:13 final size:12
Alignment explanation
Indices: 616015--616059 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
616005 ACAATACAAA
616015 ACTTTCATATCTC
1 ACTTTCATAT-TC
* *
616028 ATTTTCATCTTAC
1 ACTTTCATATT-C
616041 ACTTTCATATTC
1 ACTTTCATATTC
616053 ACTTTCA
1 ACTTTCA
616060 CATTTAGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 9 0.33
13 18 0.67
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (12 bp):
ACTTTCATATTC
Found at i:616147 original size:37 final size:38
Alignment explanation
Indices: 616092--616164 Score: 105
Period size: 37 Copynumber: 1.9 Consensus size: 38
616082 CTTTCACATT
*
616092 TCAAAATTCATTCTCAGATTCAGAACTTGTTTTCAAAC
1 TCAAAATTCATTCTCAGATTCAGAACTTATTTTCAAAC
*
616130 TCAAAACTT-ATT-TCAGATTCATAACTTATTTTCAA
1 TCAAAA-TTCATTCTCAGATTCAGAACTTATTTTCAA
616165 GTTCATAGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
37 21 0.66
38 9 0.28
39 2 0.06
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.40
Consensus pattern (38 bp):
TCAAAATTCATTCTCAGATTCAGAACTTATTTTCAAAC
Found at i:616155 original size:18 final size:18
Alignment explanation
Indices: 616091--616160 Score: 61
Period size: 18 Copynumber: 3.8 Consensus size: 18
616081 ACTTTCACAT
616091 TTCAAAA-TTCATTCTCAGA
1 TTCAAAACTT-ATT-TCAGA
* * *
616110 TTCAGAACTTGTTTTCAAA
1 TTCAAAACTT-ATTTCAGA
*
616129 CTCAAAACTTATTTCAGA
1 TTCAAAACTTATTTCAGA
*
616147 TTCATAACTTATTT
1 TTCAAAACTTATTT
616161 TCAAGTTCAT
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
18 18 0.45
19 18 0.45
20 4 0.10
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.41
Consensus pattern (18 bp):
TTCAAAACTTATTTCAGA
Found at i:616169 original size:19 final size:19
Alignment explanation
Indices: 616110--616171 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
616100 CATTCTCAGA
* * *
616110 TTCAGAACTTGTTTTCAAA
1 TTCATAACTTATTTTCAAG
* *
616129 CTCAAAACTTA-TTTC-AG
1 TTCATAACTTATTTTCAAG
616146 ATTCATAACTTATTTTCAAG
1 -TTCATAACTTATTTTCAAG
616166 TTCATA
1 TTCATA
616172 GCCCAATGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 1 0.03
18 13 0.38
19 18 0.53
20 2 0.06
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.42
Consensus pattern (19 bp):
TTCATAACTTATTTTCAAG
Found at i:619581 original size:23 final size:23
Alignment explanation
Indices: 619528--619583 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
619518 TTACATTTTG
**
619528 GTTACAAACCAAAATTTTGGGGT
1 GTTACAATTCAAAATTTTGGGGT
619551 GTTACAATTCAAAATTTTGGGGT
1 GTTACAATTCAAAATTTTGGGGT
619574 GTTACAATTC
1 GTTACAATTC
619584 TTTCCCCTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (23 bp):
GTTACAATTCAAAATTTTGGGGT
Found at i:623064 original size:16 final size:13
Alignment explanation
Indices: 623032--623071 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 13
623022 TTCTATCAAA
623032 GTCAAAGTCAATG
1 GTCAAAGTCAATG
623045 GTCAACAGTCATACTG
1 GTCAA-AGTCA-A-TG
623061 GTCAAAGTCAA
1 GTCAAAGTCAA
623072 CAGTCAACAG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 5 0.21
14 6 0.25
15 6 0.25
16 7 0.29
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (13 bp):
GTCAAAGTCAATG
Found at i:631624 original size:39 final size:37
Alignment explanation
Indices: 631547--631627 Score: 126
Period size: 37 Copynumber: 2.1 Consensus size: 37
631537 ATCATCATTT
631547 TATCAAAACCATAATAAAAATATCATAATAATAGTCA
1 TATCAAAACCATAATAAAAATATCATAATAATAGTCA
* *
631584 TATCAAAGCCATGATAAACAATATCATACATAATAGTCA
1 TATCAAAACCATAATAAA-AATATCATA-ATAATAGTCA
631623 TATCA
1 TATCA
631628 TATTCTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
37 16 0.40
38 9 0.22
39 15 0.38
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (37 bp):
TATCAAAACCATAATAAAAATATCATAATAATAGTCA
Found at i:631805 original size:19 final size:19
Alignment explanation
Indices: 631747--631824 Score: 59
Period size: 19 Copynumber: 4.2 Consensus size: 19
631737 GGACTCATTC
* **
631747 TCAGATTCAGAACTTGTTT
1 TCAGATTCATAACTTAATT
* * *
631766 TCAGACTCAAAACGT-ATT
1 TCAGATTCATAACTTAATT
631784 TCAGATTCATAACTTAATT
1 TCAGATTCATAACTTAATT
* * * *
631803 TCATATTCGTATCTTATTT
1 TCAGATTCATAACTTAATT
631822 TCA
1 TCA
631825 AGTTCATAGC
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
18 14 0.30
19 33 0.70
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42
Consensus pattern (19 bp):
TCAGATTCATAACTTAATT
Found at i:634620 original size:14 final size:15
Alignment explanation
Indices: 634601--634629 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
634591 TTTGGGGTCA
634601 AAAAATT-AACTTTT
1 AAAAATTAAACTTTT
634615 AAAAATTAAACTTTT
1 AAAAATTAAACTTTT
634630 GTTCCATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAAATTAAACTTTT
Found at i:634993 original size:12 final size:12
Alignment explanation
Indices: 634956--634998 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
634946 TTCGTCTGAT
*
634956 TTTATCTATTTA
1 TTTATATATTTA
*
634968 TTTATTTATTTA
1 TTTATATATTTA
*
634980 TTTATATATATA
1 TTTATATATTTA
634992 -TTATATA
1 TTTATATA
634999 ATCTGCAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 7 0.25
12 21 0.75
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTATATATTTA
Found at i:635063 original size:37 final size:35
Alignment explanation
Indices: 635022--635328 Score: 179
Period size: 36 Copynumber: 8.5 Consensus size: 35
635012 TTTGAAATAT
635022 ATATAAT-ATATATAGTTTTTAGAAAAACATTTTGAAA
1 ATATAATAATATATAGTTTTT---AAAACATTTTGAAA
* **
635059 ATAT-ATAAAATAGGGTTTTTAAAACATTTTGAAA
1 ATATAATAATATATAGTTTTTAAAACATTTTGAAA
* * *
635093 ACCTAT-ATAATATATAGTTTTGAAATCATTTTAAAA
1 A--TATAATAATATATAGTTTTTAAAACATTTTGAAA
635129 ATATATATAATATATAGTTTTTAAAACATTTTTGAAA
1 ATATA-ATAATATATAGTTTTTAAAACA-TTTTGAAA
* * *
635166 A-ATTATATAATATATAATTTTAAAAAACATTTTTTTAAA
1 ATA-TA-ATAATATATAGTTTT-TAAAACA--TTTTGAAA
* *
635205 ACT-T-AT-ATA-ATATTTTTTAAATCATTTTTGAAA
1 A-TATAATAATATATAGTTTTTAAAACA-TTTTGAAA
* * * *
635238 GCTAT-ATAATATATAGTTTTGAAAACTTTTTTTTAAA
1 -ATATAATAATATATAGTTTTTAAAAC--ATTTTGAAA
* ** *
635275 AAAT-ATAATATATAG--TTTAAAGATGTTTTTAGAA
1 ATATAATAATATATAGTTTTTAAA-ACATTTTGA-AA
635309 ATATATATAATATATAGTTT
1 ATATA-ATAATATATAGTTT
635329 ATATTATATT
Statistics
Matches: 216, Mismatches: 31, Indels: 45
0.74 0.11 0.15
Matches are distributed among these distances:
33 15 0.07
34 36 0.17
35 11 0.05
36 89 0.41
37 48 0.22
38 7 0.03
39 10 0.05
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.45
Consensus pattern (35 bp):
ATATAATAATATATAGTTTTTAAAACATTTTGAAA
Found at i:635113 original size:36 final size:35
Alignment explanation
Indices: 635011--635292 Score: 216
Period size: 36 Copynumber: 7.8 Consensus size: 35
635001 CTGCAAATGT
635011 TTTTGAAATA-TATATAATATATATAGTTTTTAGAAAAACA
1 TTTTGAAA-ACTATAT-A-ATATATAGTTTTT---AAAACA
* **
635051 TTTTGAAAA-TATATAAAATAGGGTTTTTAAAACA
1 TTTTGAAAACTATATAATATATAGTTTTTAAAACA
* *
635085 TTTTGAAAACCTATATAATATATAGTTTTGAAATCA
1 TTTTGAAAA-CTATATAATATATAGTTTTTAAAACA
* *
635121 TTTTAAAAATATATATAATATATAGTTTTTAAAACA
1 TTTTGAAAA-CTATATAATATATAGTTTTTAAAACA
* * *
635157 TTTTTGAAAAATTATATAATATATAATTTTAAAAAACA
1 -TTTTG-AAAACTATATAATATATAGTTTT-TAAAACA
* * *
635195 TTTTTTTAAAACT-TAT-ATA-ATATTTTTTAAATCA
1 --TTTTGAAAACTATATAATATATAGTTTTTAAAACA
* * *
635229 TTTTTGAAAGCTATATAATATATAGTTTTGAAAACTTT
1 -TTTTGAAAACTATATAATATATAGTTTTTAAAAC--A
* *
635267 TTTTTAAAA-AATATAATATATAGTTT
1 TTTTGAAAACTATATAATATATAGTTT
635293 AAAGATGTTT
Statistics
Matches: 200, Mismatches: 31, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
33 10 0.05
34 23 0.12
35 10 0.05
36 81 0.41
37 41 0.20
38 16 0.08
39 11 0.05
40 8 0.04
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (35 bp):
TTTTGAAAACTATATAATATATAGTTTTTAAAACA
Found at i:635179 original size:144 final size:145
Alignment explanation
Indices: 635010--635324 Score: 337
Period size: 144 Copynumber: 2.2 Consensus size: 145
635000 TCTGCAAATG
*
635010 TTTTTGAAATATATATAATATATATAGT-TTTTAGAAAAACA-TTTTGAAAA-TATATAAAATAG
1 TTTTTGAAAAATATATAATATATATA-TATTTTA-AAAAACATTTTTGAAAACT-TATAAAATA-
635072 GGTTTTTAAAACA-TTTTGAAAACCTATATAATATATAGTTTTG-AAA-TCATTTTAAAAATATA
62 -GTTTTTAAAACATTTTTG-AAACCTATATAATATATAGTTTTGAAAACTCATTTTAAAAA-A-A
635134 TATAATATATAGTTTTTAAAACA
123 TATAATATATAGTTTTTAAAACA
* * *
635157 TTTTTGAAAAAT-TAT-ATA-ATATATAATTTTAAAAAACATTTTTTTAAAACTTATATAATATT
1 TTTTTGAAAAATATATAATATATATAT-ATTTTAAAAAACA-TTTTTGAAAACTTATAAAATAGT
* * ** *
635219 TTTTAAATCATTTTTGAAAGCTATATAATATATAGTTTTGAAAACTTTTTTTTAAAAAATATAAT
64 TTTTAAAACATTTTTGAAACCTATATAATATATAGTTTTGAAAACTCATTTTAAAAAAATATAAT
**
635284 ATATAG--TTTAAAGATG
129 ATATAGTTTTTAAA-ACA
*
635300 TTTTTAGAAATATATATAATATATA
1 TTTTT-GAAAAATATATAATATATA
635325 GTTTATATTA
Statistics
Matches: 143, Mismatches: 12, Indels: 26
0.79 0.07 0.14
Matches are distributed among these distances:
142 6 0.04
143 7 0.05
144 64 0.45
145 20 0.14
146 31 0.22
147 15 0.10
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (145 bp):
TTTTTGAAAAATATATAATATATATATATTTTAAAAAACATTTTTGAAAACTTATAAAATAGTTT
TTAAAACATTTTTGAAACCTATATAATATATAGTTTTGAAAACTCATTTTAAAAAAATATAATAT
ATAGTTTTTAAAACA
Found at i:635350 original size:14 final size:14
Alignment explanation
Indices: 635333--635373 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
635323 TAGTTTATAT
635333 TATATTATTATTAG
1 TATATTATTATTAG
*
635347 TATATTATTATTAT
1 TATATTATTATTAG
*
635361 TATTTTAGTTATT
1 TATATTA-TTATT
635374 TGTTTTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (14 bp):
TATATTATTATTAG
Found at i:636549 original size:23 final size:21
Alignment explanation
Indices: 636519--636605 Score: 70
Period size: 22 Copynumber: 4.0 Consensus size: 21
636509 TTTAACATAT
636519 TTTA-TATTTTTTTGTTTTTTA
1 TTTATTATTTTTTT-TTTTTTA
* *
636540 CTTTATTATTATTTATTATTTTA
1 -TTTATTATT-TTTTTTTTTTTA
636563 TTTATTATTTATTTTCCTTTTTTA
1 TTTATTATTT-TTTT--TTTTTTA
* *
636587 -TTCTTATTTTTTATTTTTT
1 TTTATTATTTTTTTTTTTTT
636606 CATTCTCTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
20 6 0.11
21 1 0.02
22 19 0.35
23 18 0.33
24 10 0.19
ACGTcount: A:0.17, C:0.05, G:0.01, T:0.77
Consensus pattern (21 bp):
TTTATTATTTTTTTTTTTTTA
Found at i:636588 original size:13 final size:12
Alignment explanation
Indices: 636533--636603 Score: 58
Period size: 13 Copynumber: 5.9 Consensus size: 12
636523 TATTTTTTTG
*
636533 TTTTTTACTTTA
1 TTTTTTATTTTA
*
636545 -TTATTA-TTTA
1 TTTTTTATTTTA
636555 TTATTTTA-TTTA
1 TT-TTTTATTTTA
* *
636567 TTATTTATTTTCC
1 TTTTTTATTTT-A
636580 TTTTTTATTCTTA
1 TTTTTTATT-TTA
636593 TTTTTTATTTT
1 TTTTTTATTTT
636604 TTCATTCTCT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
10 4 0.08
11 10 0.21
12 15 0.31
13 17 0.35
14 2 0.04
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTTATTTTA
Found at i:636594 original size:45 final size:48
Alignment explanation
Indices: 636545--636652 Score: 113
Period size: 45 Copynumber: 2.3 Consensus size: 48
636535 TTTTACTTTA
636545 TTATTATTTATTATTTT-ATT-TATTATTT-ATTT-TCCTTTT-TTATTC
1 TTATTATTTATT-TTTTCATTCTATT-TTTGATTTATCCTTTTATTATTC
* *
636590 TTATTTTTTATTTTTTCATTCTCTTTTTGATTTATCCTTTTATTATT-
1 TTATTATTTATTTTTTCATTCTATTTTTGATTTATCCTTTTATTATTC
*
636637 TTCTTTATTT-TTTTTT
1 TT-ATTATTTATTTTTT
636653 ACAGTTTCCC
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
44 4 0.08
45 17 0.32
46 7 0.13
47 15 0.28
48 10 0.19
ACGTcount: A:0.16, C:0.08, G:0.01, T:0.75
Consensus pattern (48 bp):
TTATTATTTATTTTTTCATTCTATTTTTGATTTATCCTTTTATTATTC
Found at i:636600 original size:7 final size:7
Alignment explanation
Indices: 636516--636605 Score: 56
Period size: 7 Copynumber: 12.1 Consensus size: 7
636506 ATTTTTAACA
*
636516 TATTTTA
1 TATTTTT
636523 TATTTTTT
1 TA-TTTTT
*
636531 TGTTTTT
1 TATTTTT
*
636538 TACTTTAT
1 TA-TTTTT
*
636546 TATTATT
1 TATTTTT
636553 TATTATTT
1 TATT-TTT
*
636561 TATTTAT
1 TATTTTT
636568 TATTTATTT
1 TA-TT-TTT
*
636577 TCCTTTTT
1 T-ATTTTT
*
636585 TA-TTCT
1 TATTTTT
636591 TATTTTT
1 TATTTTT
636598 TATTTTT
1 TATTTTT
636605 T
1 T
636606 CATTCTCTTT
Statistics
Matches: 63, Mismatches: 13, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
6 5 0.08
7 30 0.48
8 23 0.37
9 5 0.08
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.77
Consensus pattern (7 bp):
TATTTTT
Found at i:636616 original size:20 final size:20
Alignment explanation
Indices: 636580--636622 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
636570 TTTATTTTCC
*
636580 TTTTTTATTCTTATTTTTTA
1 TTTTTTATTCTTATTTTTGA
*
636600 TTTTTTCATTC-TCTTTTTGA
1 TTTTTT-ATTCTTATTTTTGA
636620 TTT
1 TTT
636623 ATCCTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.12, C:0.09, G:0.02, T:0.77
Consensus pattern (20 bp):
TTTTTTATTCTTATTTTTGA
Found at i:636696 original size:26 final size:25
Alignment explanation
Indices: 636665--636739 Score: 82
Period size: 26 Copynumber: 3.0 Consensus size: 25
636655 AGTTTCCCTA
636665 TCTTTTGATTTATTTAATATATTTT
1 TCTTTTGATTTATTTAATATATTTT
* * *
636690 TCCTTTTGATTTTTTTATTGTTTATTTT
1 T-CTTTTGATTTATTTA--ATATATTTT
636718 TC-TTTGATTTATTTAA-ATATTT
1 TCTTTTGATTTATTTAATATATTT
636740 ATTTATTCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
23 5 0.12
25 1 0.02
26 26 0.63
27 1 0.02
28 8 0.20
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.69
Consensus pattern (25 bp):
TCTTTTGATTTATTTAATATATTTT
Found at i:639454 original size:95 final size:94
Alignment explanation
Indices: 639339--639592 Score: 350
Period size: 95 Copynumber: 2.7 Consensus size: 94
639329 AATATTATAT
*
639339 ATATACAATGAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGATAA
1 ATATAAAAT-AAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGATAA
*
639404 GATTCAACTAGCCTGATAAAGGTGTTTACA
65 GATTCAACTAGCCTGATAAAGGTGATTACA
** *
639434 ATATAAAATAAAGCTTGAGTTGTTGCTCTAGAGCAATTGGTTAAATGCCCCG-CTTTATGGATAA
1 ATATAAAAT-AAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGATAA
* * * *
639498 TATTCAGCTAGCCTGGTAAAGGTGATTATA
65 GATTCAACTAGCCTGATAAAGGTGATTACA
*
639528 ATATTATACAATAA-CATTGAGTTGTCCCTCTAGAGTAATTGGTTAAACGCCCCGACTTTATGGA
1 ATA-TA-A-AATAAGC-TTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGA
639592 T
62 T
639593 TCAGCTAGCC
Statistics
Matches: 140, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
94 40 0.29
95 50 0.36
96 37 0.26
97 13 0.09
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (94 bp):
ATATAAAATAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGATAAG
ATTCAACTAGCCTGATAAAGGTGATTACA
Found at i:640668 original size:80 final size:80
Alignment explanation
Indices: 640382--641070 Score: 914
Period size: 80 Copynumber: 8.5 Consensus size: 80
640372 CACTTTAACA
* *
640382 AAAGACCTTCGAGTT-GATTACACTCAGCTCAAAGGCATATCATTTGCAGCATAGCTAAAGGCAA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
* *
640446 GAAGGGTTATCTGCC
66 GAAGGGCTACCTGCC
* * * **
640461 AATAAAAGATCTTCGAGTTCGATTAGACTCGGCTCAAAGGTGCATCATTTGCAGCATAGCTCAAG
1 ----AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAG
* *
640526 GCGAA-AAGGGTTATCTGCC
62 GC-AAGAAGGGCTACCTGCC
* **
640545 AAAAAAAGACCTTTGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTTTAGCATAGCTCAAG
1 ----AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAG
* * *
640610 GTAAGAAGGGCTTCCTTCC
62 GCAAGAAGGGCTACCTGCC
** * *
640629 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAAAATAGCTCTAGGAAA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
640694 GAAGGGCTACCTGCC
66 GAAGGGCTACCTGCC
* * *
640709 AAAGACCTTCGAGTTAGATTACAGTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGAAA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
640774 GAAGGGCTACCTGCC
66 GAAGGGCTACCTGCC
* * **
640789 AAAGACCTTCGAGTTCGATTACAATCAGCTTAAAGGCACATCATTTGCAATATAGCTCAAGGCAA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
640854 GAAGGGCTACCTGCC
66 GAAGGGCTACCTGCC
*
640869 AAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
* *
640934 GAAGTGCTACATGCC
66 GAAGGGCTACCTGCC
* *
640949 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGTATAGCTCAAGGCGA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
* *
641014 GAAGGGCTATCAGCCAAC
66 GAAGGGCTACCTG-C--C
* *
641032 AAAAGACCTTTGAGTTCGATTACATTCAGCTCAAAGGCA
1 -AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCA
641071 TATCTAGTAC
Statistics
Matches: 542, Mismatches: 57, Indels: 13
0.89 0.09 0.02
Matches are distributed among these distances:
80 364 0.67
81 1 0.00
83 17 0.03
84 158 0.29
85 2 0.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (80 bp):
AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
GAAGGGCTACCTGCC
Found at i:641142 original size:84 final size:84
Alignment explanation
Indices: 640378--641146 Score: 435
Period size: 80 Copynumber: 9.4 Consensus size: 84
640368 AAAGCACTTT
* * * * * * * *
640378 AACAAAAGACCTTCGAGTT-GATTACACTCAGCTCAAAGGCATATCATTTGCAGCATAGCTAAAG
1 AACAAAAGACCGTCGAGTTCGATTACATTCAGCTCAAAGGCACATCATGTACAGTATAACTCAAG
* *
640442 GC-AAGAAGGGTTATCTGCC
66 GCGAA-AAGGGCTATCAGCC
* * * * * * ** * * * *
640461 AATAAAAGATCTTCGAGTTCGATTAGACTCGGCTCAAAGGTGCATCATTTGCAGCATAGCTCAAG
1 AACAAAAGACCGTCGAGTTCGATTACATTCAGCTCAAAGGCACATCATGTACAGTATAACTCAAG
* *
640526 GCGAAAAGGGTTATCTGCC
66 GCGAAAAGGGCTATCAGCC
* * * * * ** * *
640545 AAAAAAAGACCTTTGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTTTAGCATAGCTCAAG
1 AACAAAAGACCGTCGAGTTCGATTACATTCAGCTCAAAGGCACATCATGTACAGTATAACTCAAG
*
640610 G-TAAGAAGGGCT-T---CC
66 GCGAA-AAGGGCTATCAGCC
** * * * * * ** * *
640625 TTCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAAAATAGCTCTAG
1 AACAAAAGACCGTCGAGTTCGATTACATTCAGCTCAAAGGCACATCATGTACAGTATAACTCAAG
* * *
640690 G-AAAGAAGGGCTACCTG-C
66 GCGAA-AAGGGCTATCAGCC
* * * * * * *
640708 --C-AAAGACCTTCGAGTTAGATTACAGTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAG
1 AACAAAAGACCGTCGAGTTCGATTACATTCAGCTCAAAGGCACATCATGTACAGTATAACTCAAG
* * *
640770 G-AAAGAAGGGCTACCTG-C
66 GCGAA-AAGGGCTATCAGCC
* * * * * * *
640788 --C-AAAGACCTTCGAGTTCGATTACAATCAGCTTAAAGGCACATCATTTGCAATATAGCTCAAG
1 AACAAAAGACCGTCGAGTTCGATTACATTCAGCTCAAAGGCACATCATGTACAGTATAACTCAAG
* *
640850 GC-AAGAAGGGCTACCTG-C
66 GCGAA-AAGGGCTATCAGCC
* * * * * * *
640868 --C-AAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAG
1 AACAAAAGACCGTCGAGTTCGATTACATTCAGCTCAAAGGCACATCATGTACAGTATAACTCAAG
*
640930 GC-AAGAAGTGCTA-CATG-C
66 GCGAA-AAGGGCTATCA-GCC
* * * * *
640948 --C-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGTATAGCTCAAG
1 AACAAAAGACCGTCGAGTTCGATTACATTCAGCTCAAAGGCACATCATGTACAGTATAACTCAAG
*
641010 GCGAGAAGGGCTATCAGCC
66 GCGAAAAGGGCTATCAGCC
* * *
641029 AACAAAAGACCTTTGAGTTCGATTACATTCAGCTCAAAGGCATATC-TAGTACAGTATAACTCAA
1 AACAAAAGACCGTCGAGTTCGATTACATTCAGCTCAAAGGCACATCAT-GTACAGTATAACTCAA
* * *
641093 GGCGAAAAGGGTTATCTGTC
65 GGCGAAAAGGGCTATCAGCC
* *** *
641113 AATAAAATTTCGTCGAGTTCGATTCCATTCAGCT
1 AACAAAAGACCGTCGAGTTCGATTACATTCAGCT
641147 TGATGACACA
Statistics
Matches: 601, Mismatches: 69, Indels: 31
0.86 0.10 0.04
Matches are distributed among these distances:
79 1 0.00
80 357 0.59
81 5 0.01
83 23 0.04
84 213 0.35
85 2 0.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (84 bp):
AACAAAAGACCGTCGAGTTCGATTACATTCAGCTCAAAGGCACATCATGTACAGTATAACTCAAG
GCGAAAAGGGCTATCAGCC
Found at i:641848 original size:2 final size:2
Alignment explanation
Indices: 641841--641876 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
641831 TTCATCTAAT
641841 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
641877 ATCTCCAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:641947 original size:36 final size:36
Alignment explanation
Indices: 641883--642084 Score: 151
Period size: 36 Copynumber: 5.6 Consensus size: 36
641873 TATAATCTCC
* * *
641883 AAATGTTTTTGAAATACATATAATATATATAGTTTTGA
1 AAATATTTTTAAAATATATAT-A-ATATATAGTTTTGA
* * *
641921 AAATGTTTTTTAAATATATATAATATATAGTTTTAA
1 AAATATTTTTAAAATATATATAATATATAGTTTTGA
* * * ** *
641957 AAAAACATTTTGAAA-ATATATAATATAGGGTTTTTA
1 AAATA-TTTTTAAAATATATATAATATATAGTTTTGA
* * **
641993 AAACATTTTGAAAACCTATATAATATATA-TTTTG-
1 AAATATTTTTAAAATATATATAATATATAGTTTTGA
* **
642027 AAATCATTTTAAAAATATATATAATATATAGTTTTTT
1 AAAT-ATTTTTAAAATATATATAATATATAGTTTTGA
* *
642064 AAA-ATTTTGAAAATTTATATA
1 AAATATTTTTAAAATATATATA
642085 TTTTTAAAAA
Statistics
Matches: 134, Mismatches: 25, Indels: 13
0.78 0.15 0.08
Matches are distributed among these distances:
34 3 0.02
35 48 0.36
36 53 0.40
37 11 0.08
38 19 0.14
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.45
Consensus pattern (36 bp):
AAATATTTTTAAAATATATATAATATATAGTTTTGA
Found at i:642071 original size:35 final size:36
Alignment explanation
Indices: 641889--642084 Score: 177
Period size: 35 Copynumber: 5.5 Consensus size: 36
641879 CTCCAAATGT
* * **
641889 TTTTG-AAATACATATAATATATATAGTTTTGAAAATG
1 TTTTGAAAATATATAT-A-ATATATAGTTTTTAAAACA
** *
641926 TTTTTTAAATATATATAATATATAGTTTTAAAAAAACA
1 TTTTGAAAATATATATAATATATAGTTTT--TAAAACA
**
641964 TTTTG-AAA-ATATATAATATAGGGTTTTTAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTAAAACA
** * *
641998 TTTTGAAAACCTATATAATATATA-TTTTGAAATCA
1 TTTTGAAAATATATATAATATATAGTTTTTAAAACA
* *
642033 TTTTAAAAATATATATAATATATAGTTTTTTAAA-A
1 TTTTGAAAATATATATAATATATAGTTTTTAAAACA
*
642068 TTTTGAAAATTTATATA
1 TTTTGAAAATATATATA
642085 TTTTTAAAAA
Statistics
Matches: 131, Mismatches: 22, Indels: 14
0.78 0.13 0.08
Matches are distributed among these distances:
34 11 0.08
35 49 0.37
36 46 0.35
37 8 0.06
38 17 0.13
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (36 bp):
TTTTGAAAATATATATAATATATAGTTTTTAAAACA
Found at i:642170 original size:25 final size:24
Alignment explanation
Indices: 642111--642197 Score: 67
Period size: 24 Copynumber: 3.6 Consensus size: 24
642101 CATATATATA
642111 TTTTTT-AAATCAT-TTTTGAAAAC
1 TTTTTTAAAAT-ATATTTTGAAAAC
* * *
642134 -TATATAATATATAGTTTTGAAAAC
1 TTTTTTAAAATATA-TTTTGAAAAC
642158 TTTTTTAAAATATATATTT-AAAA-
1 TTTTTTAAAATATAT-TTTGAAAAC
642181 TGTTTTTAGAAATATAT
1 T-TTTTTA-AAATATAT
642198 ATATTAGTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
22 5 0.10
23 4 0.08
24 21 0.41
25 21 0.41
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.49
Consensus pattern (24 bp):
TTTTTTAAAATATATTTTGAAAAC
Found at i:642172 original size:34 final size:36
Alignment explanation
Indices: 642104--642173 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
642094 AAAAATTCAT
* * *
642104 ATATATATTTTTTAAATCATTTTTGAAAACTATATA
1 ATATATAGTTTTGAAAACATTTTTGAAAACTATATA
*
642140 ATATATAGTTTTGAAAAC-TTTTTTAAAA-TATATA
1 ATATATAGTTTTGAAAACATTTTTGAAAACTATATA
642174 TTTAAAATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 6 0.20
35 9 0.30
36 15 0.50
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (36 bp):
ATATATAGTTTTGAAAACATTTTTGAAAACTATATA
Found at i:642214 original size:17 final size:17
Alignment explanation
Indices: 642192--642239 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
642182 GTTTTTAGAA
642192 ATATATATATTAGTTAT
1 ATATATATATTAGTTAT
642209 ATATATATTATTAG-TAT
1 ATATATA-TATTAGTTAT
642226 AT-TAT-TATTA-TTAT
1 ATATATATATTAGTTAT
642240 TTTAGTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 8 0.28
16 3 0.10
17 12 0.41
18 6 0.21
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (17 bp):
ATATATATATTAGTTAT
Found at i:643401 original size:10 final size:10
Alignment explanation
Indices: 643388--643459 Score: 56
Period size: 10 Copynumber: 6.9 Consensus size: 10
643378 TTTTAACATC
643388 TTTTATATTT
1 TTTTATATTT
* *
643398 TTTTGTTTTT
1 TTTTATATTT
643408 TACTTTATTATTAT
1 T--TTTA-TATT-T
*
643422 TTTTTTATTT
1 TTTTATATTT
643432 TTTT-TATTT
1 TTTTATATTT
*
643441 TTTTTTATTT
1 TTTTATATTT
*
643451 TTTTCTATT
1 TTTTATATT
643460 CATTCTTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
9 9 0.18
10 27 0.53
11 4 0.08
12 6 0.12
13 3 0.06
14 2 0.04
ACGTcount: A:0.14, C:0.03, G:0.01, T:0.82
Consensus pattern (10 bp):
TTTTATATTT
Found at i:643407 original size:27 final size:25
Alignment explanation
Indices: 643368--643454 Score: 69
Period size: 27 Copynumber: 3.5 Consensus size: 25
643358 TCTTTGTTCC
643368 TTTTTTTTATTTTTAACATCTT-TTA-TA
1 TTTTTTTT-TTTTT-AC-T-TTATTATTA
643395 TTTTTTTGTTTTTTACTTTATTATTA
1 TTTTTTT-TTTTTTACTTTATTATTA
*
643421 TTTTTTTATTTTT--TTTATT-TT-
1 TTTTTTTTTTTTTACTTTATTATTA
*
643442 TTTTTATTTTTTT
1 TTTTTTTTTTTTT
643455 CTATTCATTC
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
21 11 0.20
22 2 0.04
23 6 0.11
24 2 0.04
25 9 0.17
26 11 0.20
27 12 0.22
28 1 0.02
ACGTcount: A:0.15, C:0.03, G:0.01, T:0.80
Consensus pattern (25 bp):
TTTTTTTTTTTTTACTTTATTATTA
Found at i:643434 original size:26 final size:26
Alignment explanation
Indices: 643369--643434 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 26
643359 CTTTGTTCCT
*
643369 TTTTTTTATTTTTAACATCTTTTATA
1 TTTTTTTATTTTTTACATCTTTTATA
*
643395 TTTTTTTGTTTTTTAC-T-TTATTATTA
1 TTTTTTTATTTTTTACATCTT-TTA-TA
643421 TTTTTTTATTTTTT
1 TTTTTTTATTTTTT
643435 TTATTTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 2 0.06
25 4 0.11
26 29 0.83
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.77
Consensus pattern (26 bp):
TTTTTTTATTTTTTACATCTTTTATA
Found at i:643595 original size:3 final size:3
Alignment explanation
Indices: 643589--643619 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
643579 TATTGTTTAT
*
643589 TTA TTA TTA TTA TTA TTA TTA TTA TTC TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
643620 GTTTTTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:647812 original size:16 final size:17
Alignment explanation
Indices: 647787--647818 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
647777 GTATTCAGGA
647787 TTTTTATTTCTTTTTTC
1 TTTTTATTTCTTTTTTC
647804 TTTTT-TTTCTTTTTT
1 TTTTTATTTCTTTTTT
647819 GAAAAGTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTTATTTCTTTTTTC
Found at i:650567 original size:20 final size:20
Alignment explanation
Indices: 650529--650568 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
650519 TTTTTTTAAT
*
650529 AAAAAACAAAAAAGGCAAAA
1 AAAAAACAAAAAAGCCAAAA
*
650549 AAAAAACAAAAAATCCAAAA
1 AAAAAACAAAAAAGCCAAAA
650569 TTTCAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.80, C:0.12, G:0.05, T:0.03
Consensus pattern (20 bp):
AAAAAACAAAAAAGCCAAAA
Found at i:662898 original size:18 final size:18
Alignment explanation
Indices: 662871--662909 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
662861 ATTACTATAG
662871 TTTTATTTTT-TAATTTT
1 TTTTATTTTTGTAATTTT
*
662888 TTTTAATTTTTGTCATTTT
1 TTTT-ATTTTTGTAATTTT
662907 TTT
1 TTT
662910 GTACAGACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 6 0.32
19 9 0.47
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTTATTTTTGTAATTTT
Found at i:666022 original size:17 final size:17
Alignment explanation
Indices: 666000--666042 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
665990 TAATTTGATT
*
666000 AATGAACTAGTTTAATG
1 AATGAACTAGTTTAATC
666017 AATGAACTAGTTTAATC
1 AATGAACTAGTTTAATC
666034 AATGAACTA
1 AATGAACTA
666043 ACATTTATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (17 bp):
AATGAACTAGTTTAATC
Found at i:676744 original size:6 final size:6
Alignment explanation
Indices: 676695--676743 Score: 80
Period size: 6 Copynumber: 8.2 Consensus size: 6
676685 TCTGGCTCTT
* *
676695 CGTCTC CGTCTC CGTCTC CGTCTC CGTCTC CGTCTC CATCTC CATCTC
1 CGTCTC CGTCTC CGTCTC CGTCTC CGTCTC CGTCTC CGTCTC CGTCTC
676743 C
1 C
676744 ACTTTATTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.04, C:0.51, G:0.12, T:0.33
Consensus pattern (6 bp):
CGTCTC
Found at i:677097 original size:73 final size:73
Alignment explanation
Indices: 677014--677151 Score: 233
Period size: 73 Copynumber: 1.9 Consensus size: 73
677004 GGATGAAAAT
*
677014 TTTATTTAAAAGGAATTATTAGAA-AATTTTATTAGTAAAAGGAAATTTCTTTTGAGTATTGAAT
1 TTTATTTAAAAGGAATTATTA-AAGAATTTTATTAGTAAAAGGAAATTTCTTTTGAGTATAGAAT
677078 TGTTTTTTA
65 TGTTTTTTA
* *
677087 TTTATTTAAAATGAATTATTAAAGAATTTTCTTAGTAAAAGGAAATTTCTTTTGAGTATAGAATT
1 TTTATTTAAAAGGAATTATTAAAGAATTTTATTAGTAAAAGGAAATTTCTTTTGAGTATAGAATT
677152 AAATTTCATT
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
72 2 0.03
73 59 0.97
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.46
Consensus pattern (73 bp):
TTTATTTAAAAGGAATTATTAAAGAATTTTATTAGTAAAAGGAAATTTCTTTTGAGTATAGAATT
GTTTTTTA
Found at i:679826 original size:43 final size:43
Alignment explanation
Indices: 679779--679882 Score: 136
Period size: 43 Copynumber: 2.4 Consensus size: 43
679769 CAAAATCCGT
* * * * * *
679779 TAAAGGTTATGTTTTTTAGTGACTTTTTTTTTACAAACGCCGC
1 TAAAGGTTATGATATTTAGCGACATTTGTTTTACAAACGCCAC
* *
679822 TAAAGGTAATGATATTTAGCGGCATTTGTTTTACAAACGCCAC
1 TAAAGGTTATGATATTTAGCGACATTTGTTTTACAAACGCCAC
679865 TAAAGGTTATGATATTTA
1 TAAAGGTTATGATATTTA
679883 TCAGCATTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.40
Consensus pattern (43 bp):
TAAAGGTTATGATATTTAGCGACATTTGTTTTACAAACGCCAC
Found at i:679890 original size:43 final size:43
Alignment explanation
Indices: 679807--679891 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
679797 GTGACTTTTT
* *
679807 TTTTACAAACGCCGCTAAAGGTAATGATATTTAGCGGCATTTG
1 TTTTACAAACGCCACTAAAGGTAATGATATTTAGCAGCATTTG
* *
679850 TTTTACAAACGCCACTAAAGGTTATGATATTTATCAGCATTT
1 TTTTACAAACGCCACTAAAGGTAATGATATTTAGCAGCATTT
679892 TCTCAAATGC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (43 bp):
TTTTACAAACGCCACTAAAGGTAATGATATTTAGCAGCATTTG
Found at i:680178 original size:21 final size:21
Alignment explanation
Indices: 680152--680207 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
680142 ATTATCCAAT
* *
680152 AAACTTGACATCTATAACAAC-
1 AAACTTGAAATCCATAAC-ACG
680173 AAACTTGAAATCCATAACACG
1 AAACTTGAAATCCATAACACG
680194 AAACTTGAAATCCA
1 AAACTTGAAATCCA
680208 CAATAATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 2 0.06
21 30 0.94
ACGTcount: A:0.48, C:0.23, G:0.07, T:0.21
Consensus pattern (21 bp):
AAACTTGAAATCCATAACACG
Found at i:681430 original size:14 final size:14
Alignment explanation
Indices: 681393--681440 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
681383 CGAGCCAAGC
*
681393 CGACTGAGTCAACAT
1 CGACTGAGTTAAC-T
681408 GCG-CTGAGTTAACT
1 -CGACTGAGTTAACT
681422 CGACTGAGTTAACT
1 CGACTGAGTTAACT
681436 C-ACTG
1 CGACTG
681441 GGTCAACTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 6 0.20
14 13 0.43
15 9 0.30
16 2 0.07
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (14 bp):
CGACTGAGTTAACT
Found at i:686862 original size:24 final size:24
Alignment explanation
Indices: 686799--686900 Score: 73
Period size: 24 Copynumber: 4.2 Consensus size: 24
686789 ATTTGATTTT
* * * *
686799 TGATTTGAATTTTATTCTGACATA
1 TGATATGAATTATGTTCTGATATA
* * *
686823 TGATTTGTAA-TCTGTTCTGAT-TCG
1 TGATATG-AATTATGTTCTGATAT-A
*
686847 TGATATGGATTATGTTCTGATATA
1 TGATATGAATTATGTTCTGATATA
* * *
686871 TGATATGAATTATGTTTTGTTTTA
1 TGATATGAATTATGTTCTGATATA
686895 TGATAT
1 TGATAT
686901 CTCCGTTTAT
Statistics
Matches: 62, Mismatches: 12, Indels: 8
0.76 0.15 0.10
Matches are distributed among these distances:
23 2 0.03
24 57 0.92
25 3 0.05
ACGTcount: A:0.25, C:0.06, G:0.18, T:0.51
Consensus pattern (24 bp):
TGATATGAATTATGTTCTGATATA
Found at i:695737 original size:22 final size:22
Alignment explanation
Indices: 695698--695777 Score: 99
Period size: 22 Copynumber: 3.7 Consensus size: 22
695688 GATTACCTAT
695698 GTCCTTC-GGACATATGGACAG
1 GTCCTTCGGGACATATGGACAG
*
695719 GTCCTTCGGGATATATGGACAG
1 GTCCTTCGGGACATATGGACAG
* * *
695741 GTCTTTCGAGACATATGGACAT
1 GTCCTTCGGGACATATGGACAG
* *
695763 GTTCTTTGGGACATA
1 GTCCTTCGGGACATA
695778 GACTTCGTAT
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 7 0.14
22 42 0.86
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.30
Consensus pattern (22 bp):
GTCCTTCGGGACATATGGACAG
Found at i:697286 original size:32 final size:32
Alignment explanation
Indices: 697197--697273 Score: 127
Period size: 32 Copynumber: 2.4 Consensus size: 32
697187 AAGAGTCGAG
*
697197 GATTACCTATGTCCTTCGGGACATATGAATAA
1 GATTACCTATGTCCTTCGGGACATATGAACAA
* *
697229 GATTACCTATGTCCTTCGGGACATATGGACAT
1 GATTACCTATGTCCTTCGGGACATATGAACAA
697261 GATTACCTATGTC
1 GATTACCTATGTC
697274 ATTTAGGACA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32
Consensus pattern (32 bp):
GATTACCTATGTCCTTCGGGACATATGAACAA
Found at i:698104 original size:16 final size:16
Alignment explanation
Indices: 698083--698117 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
698073 ATCAGAGCTA
* *
698083 AGGTTTAGTCGGTTCT
1 AGGTTTAGCCAGTTCT
698099 AGGTTTAGCCAGTTCT
1 AGGTTTAGCCAGTTCT
698115 AGG
1 AGG
698118 CTTAAACCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.14, G:0.31, T:0.37
Consensus pattern (16 bp):
AGGTTTAGCCAGTTCT
Found at i:705554 original size:12 final size:12
Alignment explanation
Indices: 705537--705561 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
705527 GTTGACTCAA
705537 CTCTCAGGTATG
1 CTCTCAGGTATG
705549 CTCTCAGGTATG
1 CTCTCAGGTATG
705561 C
1 C
705562 CATATGTGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.28, G:0.24, T:0.32
Consensus pattern (12 bp):
CTCTCAGGTATG
Found at i:707577 original size:2 final size:2
Alignment explanation
Indices: 707570--707596 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
707560 ATGGATTGCT
707570 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
707597 TTAGTATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:707657 original size:2 final size:2
Alignment explanation
Indices: 707650--707687 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
707640 TCAATCTACA
707650 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
707688 TACGACATAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:707777 original size:13 final size:13
Alignment explanation
Indices: 707756--707797 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
707746 AATGACATGC
*
707756 AATGTAAGTCATA
1 AATGCAAGTCATA
707769 AATGCAAGTCATA
1 AATGCAAGTCATA
**
707782 AATGCGTGTCATA
1 AATGCAAGTCATA
707795 AAT
1 AAT
707798 TTATGACACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.29
Consensus pattern (13 bp):
AATGCAAGTCATA
Found at i:707870 original size:13 final size:13
Alignment explanation
Indices: 707852--707903 Score: 77
Period size: 13 Copynumber: 4.0 Consensus size: 13
707842 AATGACGTAC
*
707852 AATGCGTGTCATA
1 AATGCGCGTCATA
707865 AATGCGCGTCATA
1 AATGCGCGTCATA
* *
707878 AATACGTGTCATA
1 AATGCGCGTCATA
707891 AATGCGCGTCATA
1 AATGCGCGTCATA
707904 GATTTATGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:707876 original size:96 final size:96
Alignment explanation
Indices: 707707--707893 Score: 241
Period size: 96 Copynumber: 1.9 Consensus size: 96
707697 CAATCACGCC
* * * * * * *
707707 ACACAAATGTGTGTTATCTTTTTTAATGATGTGTGCTTCAATGACATGCAATGTAAGTCATAAAT
1 ACACAAATGTGTGTCATCTTATTTAATGACGGGGGCTTCAATGACATACAATGCAAGTCATAAAT
*
707772 GCAAGTCATAAATGCGTGTCATAAATTTATG
66 GCAAGTCATAAATACGTGTCATAAATTTATG
* **
707803 ACACAAATGTGTGTCATCTTCATTT-ATGACGGGGGCTTCAATGACGTACAATGCGTGTCATAAA
1 ACACAAATGTGTGTCATCTT-ATTTAATGACGGGGGCTTCAATGACATACAATGCAAGTCATAAA
**
707867 TGCGCGTCATAAATACGTGTCATAAAT
65 TGCAAGTCATAAATACGTGTCATAAAT
707894 GCGCGTCATA
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
96 74 0.96
97 3 0.04
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (96 bp):
ACACAAATGTGTGTCATCTTATTTAATGACGGGGGCTTCAATGACATACAATGCAAGTCATAAAT
GCAAGTCATAAATACGTGTCATAAATTTATG
Found at i:713007 original size:30 final size:32
Alignment explanation
Indices: 712968--713032 Score: 80
Period size: 35 Copynumber: 2.0 Consensus size: 32
712958 CAATCTAAAC
712968 ATGTCTTAACT-C-TAATTCCTAATAAAATAA
1 ATGTCTTAACTACTTAATTCCTAATAAAATAA
*
712998 ATGTTTTAACTCAACCTTAATTCCTAATAAAATAA
1 ATGTCTTAACT--A-CTTAATTCCTAATAAAATAA
713033 TAAATCTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 10 0.34
34 1 0.03
35 18 0.62
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.37
Consensus pattern (32 bp):
ATGTCTTAACTACTTAATTCCTAATAAAATAA
Found at i:713696 original size:41 final size:41
Alignment explanation
Indices: 713574--713862 Score: 260
Period size: 41 Copynumber: 7.1 Consensus size: 41
713564 TTCTAAACAT
* * * * * *
713574 AAACGCCACTAAAGTACGAGTATTTAGCGGTGTTTCTACAA
1 AAACACCACTAAAGTACGAGTATATAGCAGCGTTTGTATAA
* * * * * *
713615 AAACACCATTAATGCACAAGTATTTAGCAGTGTTTGTATAA
1 AAACACCACTAAAGTACGAGTATATAGCAGCGTTTGTATAA
* * *
713656 AAACACCACTAAAGTACGAGTCTATAGTAGCGTTTTTATAA
1 AAACACCACTAAAGTACGAGTATATAGCAGCGTTTGTATAA
* * * * *
713697 AAAC-GCACTAAAGTACGAGTTTATAGCGGCGTTTATACAA
1 AAACACCACTAAAGTACGAGTATATAGCAGCGTTTGTATAA
* * * *
713737 AAACCCCACTAAAGTATGAGTCTTTAGC-GACGTTTGTATAA
1 AAACACCACTAAAGTACGAGTATATAGCAG-CGTTTGTATAA
* * * *
713778 AAACACCACGAAAATATGAGTTTATAGCAGCGTTTGTATAA
1 AAACACCACTAAAGTACGAGTATATAGCAGCGTTTGTATAA
* * * *
713819 AAAC-CCACTACAGTACGAGTATTTAGCGGCGTTTGTATAC
1 AAACACCACTAAAGTACGAGTATATAGCAGCGTTTGTATAA
713859 AAAC
1 AAAC
713863 GCTTTTTGGT
Statistics
Matches: 203, Mismatches: 42, Indels: 7
0.81 0.17 0.03
Matches are distributed among these distances:
40 67 0.33
41 135 0.67
42 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (41 bp):
AAACACCACTAAAGTACGAGTATATAGCAGCGTTTGTATAA
Found at i:713804 original size:122 final size:122
Alignment explanation
Indices: 713574--713861 Score: 355
Period size: 122 Copynumber: 2.3 Consensus size: 122
713564 TTCTAAACAT
* * * *
713574 AAACGCCACTAAAGTACGAGTATTTAGCGGTGTTTCTACAAAAACACCATTAATGCACAAGTATT
1 AAACG-CACTAAAGTACGAGTATTTAGCGGCGTTTATACAAAAACACCACTAAAGCACAAGTATT
* * * * *
713639 TAGCAGTGTTTGTATAAAAACACCACTAAAGTACGAGTCTATAGTAGCGTTTTTATAA
65 TAGCAGCGTTTGTATAAAAACACCACGAAAATACGAGTCTATAGCAGCGTTTGTATAA
* * ** *
713697 AAACGCACTAAAGTACGAGT-TTATAGCGGCGTTTATACAAAAACCCCACTAAAGTATGAGTCTT
1 AAACGCACTAAAGTACGAGTATT-TAGCGGCGTTTATACAAAAACACCACTAAAGCACAAGTATT
* *
713761 TAGC-GACGTTTGTATAAAAACACCACGAAAATATGAGTTTATAGCAGCGTTTGTATAA
65 TAGCAG-CGTTTGTATAAAAACACCACGAAAATACGAGTCTATAGCAGCGTTTGTATAA
* *
713819 AAACCCACTACAGTACGAGTATTTAGCGGCGTTTGTATACAAA
1 AAACGCACTAAAGTACGAGTATTTAGCGGCG-TT-TATACAAA
713862 CGCTTTTTGG
Statistics
Matches: 142, Mismatches: 18, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
121 3 0.02
122 122 0.86
123 9 0.06
124 8 0.06
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (122 bp):
AAACGCACTAAAGTACGAGTATTTAGCGGCGTTTATACAAAAACACCACTAAAGCACAAGTATTT
AGCAGCGTTTGTATAAAAACACCACGAAAATACGAGTCTATAGCAGCGTTTGTATAA
Found at i:713826 original size:81 final size:80
Alignment explanation
Indices: 713639--713862 Score: 261
Period size: 81 Copynumber: 2.8 Consensus size: 80
713629 CACAAGTATT
* * * * *
713639 TAGCAGTGTTTGTATAAAAACACCACTAAAGTACGAGTCTATAG-TAGCGTTTTTATAAAAACGC
1 TAGCAGCGTTTGTATAAAAAC-CCACTAAAGTACGAGTCTTTAGCGA-CGTTTGTATAAAAACCC
* *
713703 ACTAAAGTACGAGTTTA
64 ACGAAAATACGAGTTTA
* * * *
713720 TAGCGGCGTTTATACAAAAACCCCACTAAAGTATGAGTCTTTAGCGACGTTTGTATAAAAACACC
1 TAGCAGCGTTTGTATAAAAA-CCCACTAAAGTACGAGTCTTTAGCGACGTTTGTATAAAAAC-CC
*
713785 ACGAAAATATGAGTTTA
64 ACGAAAATACGAGTTTA
* * * *
713802 TAGCAGCGTTTGTATAAAAACCCACTACAGTACGAGTATTTAGCGGCGTTTGTATACAAAC
1 TAGCAGCGTTTGTATAAAAACCCACTAAAGTACGAGTCTTTAGCGACGTTTGTATAAAAAC
713863 GCTTTTTGGT
Statistics
Matches: 120, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
81 86 0.72
82 34 0.28
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (80 bp):
TAGCAGCGTTTGTATAAAAACCCACTAAAGTACGAGTCTTTAGCGACGTTTGTATAAAAACCCAC
GAAAATACGAGTTTA
Found at i:759550 original size:13 final size:13
Alignment explanation
Indices: 759516--759558 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
759506 AAAACAAAGA
759516 AAAGATAATTCCT
1 AAAGATAATTCCT
*
759529 AAGAGATAATTTCT
1 AA-AGATAATTCCT
*
759543 AAAGATAATTCTT
1 AAAGATAATTCCT
759556 AAA
1 AAA
759559 ATATTTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (13 bp):
AAAGATAATTCCT
Found at i:763309 original size:5 final size:5
Alignment explanation
Indices: 763300--763357 Score: 55
Period size: 5 Copynumber: 11.4 Consensus size: 5
763290 AATAAAATAA
* * * *
763300 AAATG GAATG GAATG GAATG AAATG AAATG AAATG AAAT- AAATTTA AAATG
1 AAATG AAATG AAATG AAATG AAATG AAATG AAATG AAATG AAA--TG AAATG
763351 AAATG AA
1 AAATG AA
763358 GCATGCTAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
4 3 0.06
5 40 0.85
6 1 0.02
7 3 0.06
ACGTcount: A:0.57, C:0.00, G:0.21, T:0.22
Consensus pattern (5 bp):
AAATG
Found at i:769028 original size:16 final size:17
Alignment explanation
Indices: 769003--769035 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
768993 TTGTTATAGC
769003 ATTATCTTATT-TTTTT
1 ATTATCTTATTATTTTT
*
769019 ATTATTTTATTATTTTT
1 ATTATCTTATTATTTTT
769036 CTTTTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTATCTTATTATTTTT
Found at i:769033 original size:19 final size:19
Alignment explanation
Indices: 769009--769047 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
768999 TAGCATTATC
769009 TTATTTTT-TTATTATTTTA
1 TTATTTTTCTT-TTATTTTA
769028 TTATTTTTCTTTTATTTTA
1 TTATTTTTCTTTTATTTTA
769047 T
1 T
769048 GGATTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (19 bp):
TTATTTTTCTTTTATTTTA
Found at i:772192 original size:102 final size:102
Alignment explanation
Indices: 772012--772203 Score: 321
Period size: 102 Copynumber: 1.9 Consensus size: 102
772002 TCACGGGATG
* * * *
772012 ACTCTACTTGACTAGCTTGGGGGTAGAAGGTATGTTCCCTTTCACTTAGAGTGTGGAATGGTAGT
1 ACTCTACCTGACTAGCTCGGGGGTAGAAGGTATGCTCCCTTTCACTTAGAGTGTGGAATGATAGT
*
772077 GTGATGAGCTGACTCCCCTTAAAGTATGCTAAAAAAA
66 GTGATGAGATGACTCCCCTTAAAGTATGCTAAAAAAA
*
772114 ACTCTACCTGACTAGCTCGGGGGTAGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGATAGT
1 ACTCTACCTGACTAGCTCGGGGGTAGAAGGTATGCTCCCTTTCACTTAGAGTGTGGAATGATAGT
*
772179 GTGATGAGATGACTCCCCTTGAAGT
66 GTGATGAGATGACTCCCCTTAAAGT
772204 GTTAAAAAAA
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 83 1.00
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (102 bp):
ACTCTACCTGACTAGCTCGGGGGTAGAAGGTATGCTCCCTTTCACTTAGAGTGTGGAATGATAGT
GTGATGAGATGACTCCCCTTAAAGTATGCTAAAAAAA
Found at i:778824 original size:51 final size:51
Alignment explanation
Indices: 778765--778866 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
778755 TGCAAGTATT
778765 GTGTTCTTGGTAAATAGACTAAAGTTCGTTTCAAGACTGGGAAGCACACAA
1 GTGTTCTTGGTAAATAGACTAAAGTTCGTTTCAAGACTGGGAAGCACACAA
778816 GTGTTCTTGGTAAATAGACTAAAGTTCGTTTCAAGACTGGGAAGCACACAA
1 GTGTTCTTGGTAAATAGACTAAAGTTCGTTTCAAGACTGGGAAGCACACAA
778867 CTAAAGAGAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (51 bp):
GTGTTCTTGGTAAATAGACTAAAGTTCGTTTCAAGACTGGGAAGCACACAA
Found at i:784115 original size:17 final size:17
Alignment explanation
Indices: 784093--784127 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
784083 AACATTTTCT
784093 TCGCACTAAACAAACAC
1 TCGCACTAAACAAACAC
784110 TCGCACTAAACAAACAC
1 TCGCACTAAACAAACAC
784127 T
1 T
784128 TTTGTGCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.34, G:0.06, T:0.14
Consensus pattern (17 bp):
TCGCACTAAACAAACAC
Found at i:786877 original size:37 final size:36
Alignment explanation
Indices: 786805--786878 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 36
786795 GTTGGAAAAT
*
786805 ATTTATATATTTTCTTTAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAATCATAAA
*
786841 ATTTATATAATTGTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATT-TTCTTTAAAAAATT-AAAATCATAAA
786878 A
1 A
786879 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
36 8 0.24
37 19 0.58
38 6 0.18
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.45
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAAATTAAAATCATAAA
Found at i:788616 original size:54 final size:54
Alignment explanation
Indices: 788486--788720 Score: 314
Period size: 54 Copynumber: 4.4 Consensus size: 54
788476 TTATATGTAT
* *
788486 TATAGGCACTAAGTGTGCAACCCACATAATTCATCA-ATATTGATGAACAACCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCG
788539 TATAGGCACTAAGTGTGCAAACCCAC-GAAATTCATCATATGTTGATGAACAACCG
1 TATAGGCACTAAGTGTGC-AACCCACAG-AATTCATCATATGTTGATGAACAACCG
*
788594 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCA
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCG
** * * * ** *
788648 TATAGGCACTATTTGTGCAAACCAC-GAAATTCATAATATGTTTATGAATGATCG
1 TATAGGCACTAAGTGTGCAACCCACAG-AATTCATCATATGTTGATGAACAACCG
*
788702 TATAGGCACTATGTGTGCA
1 TATAGGCACTAAGTGTGCA
788721 TCTTAATGAA
Statistics
Matches: 164, Mismatches: 13, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
53 19 0.12
54 110 0.67
55 35 0.21
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (54 bp):
TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCG
Found at i:788675 original size:108 final size:108
Alignment explanation
Indices: 788486--788720 Score: 355
Period size: 108 Copynumber: 2.2 Consensus size: 108
788476 TTATATGTAT
* *
788486 TATAGGCACTAAGTGTGCAACCCACATAATTCATCAATATTGATGAACAACCGTATAGGCACTAA
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCAATATTGATGAACAACCATATAGGCACTAA
*
788551 GTGTGCAAACCCACGAAATTCATCATATGTTGATGAACAACCG
66 GTGTGCAAACCCACGAAATTCATAATATGTTGATGAACAACCG
*
788594 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCATATAGGCACTA
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCA-ATATTGATGAACAACCATATAGGCACTA
** * ** *
788659 TTTGTGCAAA-CCACGAAATTCATAATATGTTTATGAATGATCG
65 AGTGTGCAAACCCACGAAATTCATAATATGTTGATGAACAACCG
*
788702 TATAGGCACTATGTGTGCA
1 TATAGGCACTAAGTGTGCA
788721 TCTTAATGAA
Statistics
Matches: 115, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
108 81 0.70
109 34 0.30
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (108 bp):
TATAGGCACTAAGTGTGCAACCCACAGAATTCATCAATATTGATGAACAACCATATAGGCACTAA
GTGTGCAAACCCACGAAATTCATAATATGTTGATGAACAACCG
Found at i:789440 original size:11 final size:11
Alignment explanation
Indices: 789426--789457 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
789416 AAATTAATAA
789426 AATAAATAAAT
1 AATAAATAAAT
789437 AATAAATAAAT
1 AATAAATAAAT
*
789448 ATTAAATAAA
1 AATAAATAAA
789458 AAAAATATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AATAAATAAAT
Done.