Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_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: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 89
Found at i:650085 original size:23 final size:23
Alignment explanation
Indices: 650055--650102 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
650045 TCTCCAACTA
650055 AATCTCTTTTAATATCTAAATTT
1 AATCTCTTTTAATATCTAAATTT
650078 AATCTCTTTTAATATCTAAATTT
1 AATCTCTTTTAATATCTAAATTT
650101 AA
1 AA
650103 ATAGATAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (23 bp):
AATCTCTTTTAATATCTAAATTT
Found at i:652035 original size:6 final size:6
Alignment explanation
Indices: 652024--652078 Score: 92
Period size: 6 Copynumber: 8.8 Consensus size: 6
652014 CCGAGGAGAA
652024 GAAAAC GAAAAC GAAAAAC GAAAAC GAAAAC GAAAAC GAAAAAC GAAAAC
1 GAAAAC GAAAAC G-AAAAC GAAAAC GAAAAC GAAAAC G-AAAAC GAAAAC
652074 GAAAA
1 GAAAA
652079 ACGAGGGAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
6 35 0.74
7 12 0.26
ACGTcount: A:0.69, C:0.15, G:0.16, T:0.00
Consensus pattern (6 bp):
GAAAAC
Found at i:652043 original size:13 final size:13
Alignment explanation
Indices: 652025--652082 Score: 109
Period size: 13 Copynumber: 4.5 Consensus size: 13
652015 CGAGGAGAAG
652025 AAAACGAAAACGA
1 AAAACGAAAACGA
652038 AAAACGAAAACG-
1 AAAACGAAAACGA
652050 AAAACGAAAACGA
1 AAAACGAAAACGA
652063 AAAACGAAAACGA
1 AAAACGAAAACGA
652076 AAAACGA
1 AAAACGA
652083 GGGAGAAGTG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
12 12 0.27
13 32 0.73
ACGTcount: A:0.69, C:0.16, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAACGAAAACGA
Found at i:652048 original size:19 final size:19
Alignment explanation
Indices: 652024--652082 Score: 102
Period size: 19 Copynumber: 3.1 Consensus size: 19
652014 CCGAGGAGAA
652024 GAAAACGAAAACGAAAAAC
1 GAAAACGAAAACGAAAAAC
652043 GAAAACGAAAACG-AAAAC
1 GAAAACGAAAACGAAAAAC
652061 GAAAAACGAAAACGAAAAAC
1 G-AAAACGAAAACGAAAAAC
652081 GA
1 GA
652083 GGGAGAAGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.16
19 26 0.68
20 6 0.16
ACGTcount: A:0.68, C:0.15, G:0.17, T:0.00
Consensus pattern (19 bp):
GAAAACGAAAACGAAAAAC
Found at i:652052 original size:25 final size:25
Alignment explanation
Indices: 652024--652078 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
652014 CCGAGGAGAA
652024 GAAAACGAAAACGAAAAACGAAAAC
1 GAAAACGAAAACGAAAAACGAAAAC
652049 GAAAACGAAAACGAAAAACGAAAAC
1 GAAAACGAAAACGAAAAACGAAAAC
652074 GAAAA
1 GAAAA
652079 ACGAGGGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.69, C:0.15, G:0.16, T:0.00
Consensus pattern (25 bp):
GAAAACGAAAACGAAAAACGAAAAC
Found at i:657455 original size:3 final size:3
Alignment explanation
Indices: 657449--657560 Score: 167
Period size: 3 Copynumber: 38.0 Consensus size: 3
657439 GCATTTTTTT
**
657449 TTA TTA TTA TTA TT- TTA TTA -TA TTA TTA TTA TTA AGA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
657495 TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
657542 TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA
657561 AATAAATATA
Statistics
Matches: 99, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
2 6 0.06
3 90 0.91
4 3 0.03
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:657574 original size:25 final size:24
Alignment explanation
Indices: 657485--657575 Score: 73
Period size: 24 Copynumber: 3.8 Consensus size: 24
657475 TATTATTAAG
* *
657485 ATTATTATTATTAT-TATTATTATT
1 ATTATTATAAATATATATTA-TATT
* *
657509 ATTATTATTATTA-ATATTATATT
1 ATTATTATAAATATATATTATATT
* *
657532 ATTATTATTATTAT-TATTAT-TT
1 ATTATTATAAATATATATTATATT
657554 ATTATTAAATAAATATATATTA
1 ATTATT--ATAAATATATATTA
657576 CAAATTACAA
Statistics
Matches: 60, Mismatches: 2, Indels: 9
0.85 0.03 0.13
Matches are distributed among these distances:
22 8 0.13
23 23 0.38
24 24 0.40
25 5 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
ATTATTATAAATATATATTATATT
Found at i:657615 original size:22 final size:23
Alignment explanation
Indices: 657585--657627 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
657575 ACAAATTACA
*
657585 ATCAGACCCAGA-AGGCCCAAAT
1 ATCAAACCCAGACAGGCCCAAAT
*
657607 ATCAAACCCAGACTGGCCCAA
1 ATCAAACCCAGACAGGCCCAA
657628 CAACAAACCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.40, C:0.35, G:0.16, T:0.09
Consensus pattern (23 bp):
ATCAAACCCAGACAGGCCCAAAT
Found at i:658901 original size:39 final size:39
Alignment explanation
Indices: 658858--658934 Score: 95
Period size: 38 Copynumber: 2.0 Consensus size: 39
658848 TGGTCACTAT
*
658858 TTTATT-TTATTATTGCCCCTTTAATTTCAAT-ATTTTTAA
1 TTTATTATTATTA-T-CCCCTATAATTTCAATAATTTTTAA
* *
658897 TTTATTATTTTTATCCCCTATAATTTTAATAATTTTTA
1 TTTATTATTATTATCCCCTATAATTTCAATAATTTTTA
658935 TTTTTGTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 14 0.42
39 14 0.42
40 5 0.15
ACGTcount: A:0.27, C:0.12, G:0.01, T:0.60
Consensus pattern (39 bp):
TTTATTATTATTATCCCCTATAATTTCAATAATTTTTAA
Found at i:658907 original size:14 final size:15
Alignment explanation
Indices: 658877--658909 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
658867 TTATTGCCCC
658877 TTTAATTTCAATATT
1 TTTAATTTCAATATT
*
658892 TTTAATTT-ATTATT
1 TTTAATTTCAATATT
658906 TTTA
1 TTTA
658910 TCCCCTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTAATTTCAATATT
Found at i:668890 original size:20 final size:22
Alignment explanation
Indices: 668844--668901 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
668834 TACATCTACA
668844 CTCTTCAAAGATGATAAATTCT
1 CTCTTCAAAGATGATAAATTCT
*
668866 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAAATTCT
* *
668888 CTTTTCGAAGATGA
1 CTCTTCAAAGATGA
668902 AAGCTTTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (22 bp):
CTCTTCAAAGATGATAAATTCT
Found at i:669685 original size:164 final size:165
Alignment explanation
Indices: 669414--669743 Score: 583
Period size: 164 Copynumber: 2.0 Consensus size: 165
669404 TAAAAATGAG
* *
669414 CATTATCTTGAGATTGGGGTATGTTACCCAATCAACATGTTATTTTAAAAAATAGTGAGAAAACG
1 CATTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTTAAAAAATAATGAGAAAACG
*
669479 ATTTCCATAGTTTCTTATTGTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTC
66 ATTTCCATAGTTTCTCATTGTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTC
669544 CTT-AGTTTTTTACTTAGTAAACTATTTCCAACAT
131 CTTAAGTTTTTTACTTAGTAAACTATTTCCAACAT
*
669578 CATTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTTGAAAAATAATGAGAAAACG
1 CATTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTTAAAAAATAATGAGAAAACG
*
669643 ATTTCCATAGTTTCTCATT-TAATCTTTTTTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTT
66 ATTTCCATAGTTTCTCATTGT-ATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTT
*
669707 CCTTAATTTTTTTACTTAGTAAACTATTTCCAACAT
130 CCTTAAGTTTTTTACTTAGTAAACTATTTCCAACAT
669743 C
1 C
669744 CGTAAGCCCT
Statistics
Matches: 158, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
163 1 0.01
164 126 0.80
165 31 0.20
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (165 bp):
CATTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTTAAAAAATAATGAGAAAACG
ATTTCCATAGTTTCTCATTGTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTC
CTTAAGTTTTTTACTTAGTAAACTATTTCCAACAT
Found at i:670360 original size:73 final size:73
Alignment explanation
Indices: 669740--670333 Score: 927
Period size: 73 Copynumber: 8.0 Consensus size: 73
669730 CTATTTCCAA
* * * * *
669740 CATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCATTTTGATCTTAAACC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
669805 CTCAGGGT
66 CTCAGGGT
* *
669813 AATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAATC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
669878 CTCAGGGT
66 CTCAGGGT
* * *
669886 TATCTATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGTTTTTTGATCTTAAACC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
669951 CTCAGGGT
66 CTCAGGGT
*
669959 CGTCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
670024 CTCAGGGT
66 CTCAGGGT
* * *
670032 CATCTGTAAGACCTACAGTGCATGATGTTTCCAAAAAGCATTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGA---TCTTAA
670097 ACCCTCAGGGT
63 ACCCTCAGGGT
*
670108 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTACAA
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAT-CTT--AA
* *
670173 AGCCTTAGGGT
63 ACCCTCAGGGT
* *
670184 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGAGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
670249 CTCAGGGT
66 CTCAGGGT
* * *
670257 CATCTGTAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAAG
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTT-AAAC
670322 CCTCAGGGT
65 CCTCAGGGT
670331 CAT
1 CAT
670334 TCATAAGACC
Statistics
Matches: 485, Mismatches: 29, Indels: 13
0.92 0.06 0.02
Matches are distributed among these distances:
73 327 0.67
74 19 0.04
75 2 0.00
76 137 0.28
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (73 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
CTCAGGGT
Found at i:670497 original size:3 final size:3
Alignment explanation
Indices: 670491--670549 Score: 77
Period size: 3 Copynumber: 20.0 Consensus size: 3
670481 TCGCATTTTT
**
670491 TTA TTA TTA TT- TTA TTA -TA TTA TTA TTA TTA AGA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
670537 TTA TTTA TTA TTA
1 TTA -TTA TTA TTA
670550 AATAAATATA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 4 0.08
3 42 0.86
4 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:670604 original size:22 final size:21
Alignment explanation
Indices: 670574--670631 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 21
670564 ACAAATTATA
*
670574 ATCAGACCCAGAA-GGCCCAAAT
1 ATCAAACCCA-AACGGCCC-AAT
670596 ATCAAACCCAAACTGGCCCAAT
1 ATCAAACCCAAAC-GGCCCAAT
*
670618 AACAAACCCTAAAC
1 ATCAAACCC-AAAC
670632 CCATCTAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 2 0.06
22 20 0.65
23 9 0.29
ACGTcount: A:0.45, C:0.34, G:0.10, T:0.10
Consensus pattern (21 bp):
ATCAAACCCAAACGGCCCAAT
Found at i:670631 original size:23 final size:23
Alignment explanation
Indices: 670587--670631 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
670577 AGACCCAGAA
*
670587 GGCCCAAATATCAAACCCAAACT
1 GGCCCAAATAACAAACCCAAACT
670610 GGCCC-AATAACAAACCCTAAAC
1 GGCCCAAATAACAAACCC-AAAC
670632 CCATCTAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.44, C:0.36, G:0.09, T:0.11
Consensus pattern (23 bp):
GGCCCAAATAACAAACCCAAACT
Found at i:672637 original size:11 final size:13
Alignment explanation
Indices: 672600--672639 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 13
672590 TGTTTAATAA
672600 AATATA-TATATT
1 AATATATTATATT
*
672612 AATATATTATCTT
1 AATATATTATATT
672625 AA-A-ATTATATT
1 AATATATTATATT
672636 AATA
1 AATA
672640 AACTTAACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 8 0.33
13 7 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
AATATATTATATT
Found at i:672708 original size:17 final size:18
Alignment explanation
Indices: 672682--672716 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
672672 TGAATTTTTA
*
672682 AATTTCTAA-TAATAAAG
1 AATTTATAATTAATAAAG
672699 AATTTATAATTAATAAAG
1 AATTTATAATTAATAAAG
672717 TGCCAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (18 bp):
AATTTATAATTAATAAAG
Found at i:676156 original size:33 final size:33
Alignment explanation
Indices: 676114--676195 Score: 146
Period size: 33 Copynumber: 2.5 Consensus size: 33
676104 ACCTCACCAT
*
676114 AGATGATCATGATACACGGTCAATGTTAAACAA
1 AGATGATCATGATACACGGTCAAAGTTAAACAA
*
676147 AGATGATCATGATACACGGTCAAAGTTATACAA
1 AGATGATCATGATACACGGTCAAAGTTAAACAA
676180 AGATGATCATGATACA
1 AGATGATCATGATACA
676196 TGAACCGTCC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.24
Consensus pattern (33 bp):
AGATGATCATGATACACGGTCAAAGTTAAACAA
Found at i:676944 original size:19 final size:19
Alignment explanation
Indices: 676920--676956 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
676910 ATGACCAACA
*
676920 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
676939 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
676957 CAGTATCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:677007 original size:20 final size:20
Alignment explanation
Indices: 676982--677053 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
676972 GTTTCCAGAT
*
676982 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTATGACTA
* * *
677002 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTATG-ACTA
* *
677022 TCGCAATGCGATTCTGACTA
1 TCGCAACGCGATTATGACTA
677042 TCGCAACGCGAT
1 TCGCAACGCGAT
677054 AATACAAAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 1 0.02
20 40 0.95
21 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTATGACTA
Found at i:677074 original size:41 final size:40
Alignment explanation
Indices: 676982--677075 Score: 118
Period size: 40 Copynumber: 2.3 Consensus size: 40
676972 GTTTCCAGAT
* * * **
676982 TCGCAACGCGATTTTGACTATCGCAATGCGAATATGTAAA
1 TCGCAATGCGATTCTGACTATCGCAACGCGAATATCAAAA
677022 TCGCAATGCGATTCTGACTATCGCAACGCG-ATAATACAAAA
1 TCGCAATGCGATTCTGACTATCGCAACGCGAAT-AT-CAAAA
677063 TCGCAATGCGATT
1 TCGCAATGCGATT
677076 TTCAAAGCGC
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
39 2 0.04
40 29 0.62
41 16 0.34
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (40 bp):
TCGCAATGCGATTCTGACTATCGCAACGCGAATATCAAAA
Found at i:677720 original size:20 final size:19
Alignment explanation
Indices: 677623--677722 Score: 86
Period size: 20 Copynumber: 5.4 Consensus size: 19
677613 AAATCGCAAC
677623 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCA-TTTCGCGTT
677642 GCGATTTTCATTTCGCGTT
1 GCGATTTTCATTTCGCGTT
*
677661 GCGA--TT-A--TCTCGTT
1 GCGATTTTCATTTCGCGTT
** *
677675 GCGATAGTCATTTTCGTGTT
1 GCGATTTTCA-TTTCGCGTT
*
677695 GCGATTTTCATTTTCGTGTT
1 GCGATTTTCA-TTTCGCGTT
677715 GCGATTTT
1 GCGATTTT
677723 AAGTTTCAGA
Statistics
Matches: 68, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 3 0.04
19 21 0.31
20 32 0.47
ACGTcount: A:0.12, C:0.17, G:0.23, T:0.48
Consensus pattern (19 bp):
GCGATTTTCATTTCGCGTT
Found at i:677729 original size:20 final size:20
Alignment explanation
Indices: 677686--677729 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
677676 CGATAGTCAT
* *
677686 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
677706 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
677726 TTTC
1 TTTC
677730 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:679691 original size:33 final size:33
Alignment explanation
Indices: 679631--679729 Score: 126
Period size: 33 Copynumber: 2.9 Consensus size: 33
679621 CACGAAACTT
** *
679631 AAAATCGCAATGCGGAAATGACTATCGCAATGGG
1 AAAATCGCAATGC-GAAATGAAAATCGCAACGGG
* * *
679665 ATAATCGCAATGCGAAATAAAAATCGCAACGTG
1 AAAATCGCAATGCGAAATGAAAATCGCAACGGG
679698 AAAATCGCAATGCGAAAATGAAAATCGCAACG
1 AAAATCGCAATGCG-AAATGAAAATCGCAACG
679730 CGAATTTAGT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.16
Consensus pattern (33 bp):
AAAATCGCAATGCGAAATGAAAATCGCAACGGG
Found at i:679719 original size:20 final size:20
Alignment explanation
Indices: 679696--679733 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
679686 AATCGCAACG
*
679696 TGAAAATCGCAATGCGAAAA
1 TGAAAATCGCAACGCGAAAA
679716 TGAAAATCGCAACGCGAA
1 TGAAAATCGCAACGCGAA
679734 TTTAGTTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.13
Consensus pattern (20 bp):
TGAAAATCGCAACGCGAAAA
Found at i:679761 original size:19 final size:20
Alignment explanation
Indices: 679734--679772 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
679724 GCAACGCGAA
*
679734 TTTAGTTTCGCGTTGCGATT
1 TTTAGTTTCGCATTGCGATT
*
679754 TTTA-TTTCGTATTGCGATT
1 TTTAGTTTCGCATTGCGATT
679773 ATCCCGTTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.13, C:0.13, G:0.21, T:0.54
Consensus pattern (20 bp):
TTTAGTTTCGCATTGCGATT
Found at i:679803 original size:20 final size:20
Alignment explanation
Indices: 679777--679825 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
679767 GCGATTATCC
*
679777 CGTTGCGATAGTTATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
679797 TGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
679817 CGTTGCGAT
1 CGTTGCGAT
679826 TTTAAGTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.14, C:0.16, G:0.27, T:0.43
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:679835 original size:20 final size:20
Alignment explanation
Indices: 679812--679855 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
679802 CGATAGTCAT
679812 TTTCGCGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
* *
679832 TTTCGTGTTGTGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
679852 TTTC
1 TTTC
679856 AGAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.11, G:0.23, T:0.52
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTAAG
Found at i:679848 original size:34 final size:32
Alignment explanation
Indices: 679739--679848 Score: 76
Period size: 40 Copynumber: 3.1 Consensus size: 32
679729 GCGAATTTAG
* *
679739 TTTCGCGTTGCGATTTTTATTTCGTATTGCGAT
1 TTTCGCGTTGCGA-TTTTATTTCGTGTTGTGAT
* * *
679772 TATCCCGTTGCGATAGTTATTTTCGTGTTGCGATAGTCAT
1 TTTCGCGTTGCGAT-TTTA-TTTCGTGTT--G-T-G--AT
679812 TTTCGCGTTGCGATTTTAAGTTTCGTGTTGTGAT
1 TTTCGCGTTGCGATTTT-A-TTTCGTGTTGTGAT
679846 TTT
1 TTT
679849 AAGTTTCAGA
Statistics
Matches: 59, Mismatches: 9, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
32 1 0.02
33 14 0.24
34 13 0.22
36 2 0.03
37 1 0.02
38 2 0.03
39 2 0.03
40 24 0.41
ACGTcount: A:0.14, C:0.15, G:0.23, T:0.49
Consensus pattern (32 bp):
TTTCGCGTTGCGATTTTATTTCGTGTTGTGAT
Found at i:680416 original size:21 final size:21
Alignment explanation
Indices: 680339--680453 Score: 79
Period size: 21 Copynumber: 5.5 Consensus size: 21
680329 CACTTGTCAT
** * *
680339 CGTTCAAGAGGCTTCTCCTAT
1 CGTTCAAGAGGCCCCTCCCAC
**
680360 CGTTCAAGAGGCCCCTATCATC
1 CGTTCAAGAGGCCCCTCCCA-C
* **
680382 C-CTCAAGAATCCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCCAC
** *
680402 CGTTCAAGAGGCCCCTGTCAT
1 CGTTCAAGAGGCCCCTCCCAC
* *
680423 CGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCCAC
*
680444 CATTCAAGAG
1 CGTTCAAGAG
680454 CCCGATTCAC
Statistics
Matches: 68, Mismatches: 24, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
20 2 0.03
21 65 0.96
22 1 0.01
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (21 bp):
CGTTCAAGAGGCCCCTCCCAC
Found at i:680439 original size:42 final size:42
Alignment explanation
Indices: 680333--680453 Score: 129
Period size: 42 Copynumber: 2.9 Consensus size: 42
680323 TCGACTCACT
* * *
680333 TGTCATCGTTCAAGAGG-CTTCTCCTATCGTTCAAGAGGCCCC
1 TGTCATCGTTCAAGAGGTC-CCTCCCACCGTTCAAGAGGCCCC
* ** *
680375 TATCATCCCTCAAGA-ATCCCCTCCCACCGTTCAAGAGGCCCC
1 TGTCATCGTTCAAGAGGT-CCCTCCCACCGTTCAAGAGGCCCC
* *
680417 TGTCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 TGTCATCGTTCAAGAGGTCCCTCCCACCGTTCAAGAG
680454 CCCGATTCAC
Statistics
Matches: 63, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
42 61 0.97
43 2 0.03
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (42 bp):
TGTCATCGTTCAAGAGGTCCCTCCCACCGTTCAAGAGGCCCC
Found at i:682013 original size:19 final size:19
Alignment explanation
Indices: 681989--682070 Score: 67
Period size: 20 Copynumber: 4.2 Consensus size: 19
681979 AACGCTAAAC
*
681989 TCAAAATCGCATGTGAAAG
1 TCAAAATCGCATGCGAAAG
*
682008 TCAAAATCGTAATGCGAAAG
1 TCAAAATCG-CATGCGAAAG
* **
682028 CCAAAATCGCAACACGAAAG
1 TCAAAATCGC-ATGCGAAAG
* *
682048 TC-AATTCGCATTGTGAAAG
1 TCAAAATCGCA-TGCGAAAG
682067 TCAA
1 TCAA
682071 TTCGCATTGC
Statistics
Matches: 48, Mismatches: 11, Indels: 7
0.73 0.17 0.11
Matches are distributed among these distances:
18 1 0.02
19 22 0.46
20 25 0.52
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.20
Consensus pattern (19 bp):
TCAAAATCGCATGCGAAAG
Found at i:682071 original size:19 final size:19
Alignment explanation
Indices: 682043--682079 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
682033 ATCGCAACAC
682043 GAAAGTCAATTCGCATTGT
1 GAAAGTCAATTCGCATTGT
682062 GAAAGTCAATTCGCATTG
1 GAAAGTCAATTCGCATTG
682080 CGATAGTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (19 bp):
GAAAGTCAATTCGCATTGT
Found at i:682143 original size:20 final size:20
Alignment explanation
Indices: 682120--682185 Score: 105
Period size: 20 Copynumber: 3.3 Consensus size: 20
682110 GTTGAAATAG
*
682120 TCAAATTCCCGTTGCGATAA
1 TCAAATTCGCGTTGCGATAA
*
682140 TCAAATTCGCGTTGCGATAG
1 TCAAATTCGCGTTGCGATAA
*
682160 TCAAATTCGCGTTGCGATAT
1 TCAAATTCGCGTTGCGATAA
682180 TCAAAT
1 TCAAAT
682186 GAATGTGTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (20 bp):
TCAAATTCGCGTTGCGATAA
Found at i:682379 original size:18 final size:18
Alignment explanation
Indices: 682356--682390 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
682346 AAGCCGGTTG
*
682356 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
682374 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
682391 GCCCTTTGCT
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:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:684672 original size:24 final size:24
Alignment explanation
Indices: 684638--684691 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
684628 CTGAAACATC
684638 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
684662 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
684686 ATCAAA
1 ATCAAA
684692 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:685367 original size:17 final size:17
Alignment explanation
Indices: 685345--685379 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
685335 CGGATGGGGA
685345 AGGATGTCGTTGGATAT
1 AGGATGTCGTTGGATAT
685362 AGGATGTCGTTGGATAT
1 AGGATGTCGTTGGATAT
685379 A
1 A
685380 AGAACGGATG
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:0.26, C:0.06, G:0.34, T:0.34
Consensus pattern (17 bp):
AGGATGTCGTTGGATAT
Found at i:685554 original size:20 final size:20
Alignment explanation
Indices: 685529--685597 Score: 86
Period size: 20 Copynumber: 3.4 Consensus size: 20
685519 GAAATTCAGT
685529 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* **
685549 GTTGCGATTTTGT-ATTATCGC
1 GTTGCGA--TAGTCAGAATCGC
685570 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
685590 GTTGCGAT
1 GTTGCGAT
685598 TTACATATTC
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
19 3 0.08
20 21 0.52
21 13 0.32
22 3 0.08
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.33
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:685555 original size:41 final size:41
Alignment explanation
Indices: 685509--685677 Score: 136
Period size: 41 Copynumber: 4.2 Consensus size: 41
685499 CTAAAACCTA
*
685509 TTGCGAATTTGAAAT-TCAGTGTTGCGATAGTCAGAATCGCG
1 TTGCGAATTTGAAATATC-GCGTTGCGATAGTCAGAATCGCG
* * *
685550 TTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCGCG
1 TTGCGAATTTGAAATATCGCGTTGCGATAGTCAGAATCGCG
* * ** * *
685591 TTGCG-ATTT-ACATATTCGCATTGCGATTTTCTAAAATAGCG
1 TTGCGAATTTGAAATA-TCGCGTTGCGATAGTC-AGAATCGCG
** *
685632 -T--GAATTTGGAAA-ATCGCAATGCGATAGTCAAAATCGCG
1 TTGCGAATTT-GAAATATCGCGTTGCGATAGTCAGAATCGCG
685670 TTGCGAAT
1 TTGCGAAT
685678 CTGGAAACTG
Statistics
Matches: 101, Mismatches: 18, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
38 9 0.09
39 20 0.20
40 18 0.18
41 52 0.51
42 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (41 bp):
TTGCGAATTTGAAATATCGCGTTGCGATAGTCAGAATCGCG
Found at i:686353 original size:3 final size:3
Alignment explanation
Indices: 686345--686396 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
686335 TATTAAATAT
* * *
686345 TTA TTA TTA ATA TTA TTA CTA TTA TTA TTA TTA ATA TTAA TTA GTT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA -TTA
686391 TTA TTA
1 TTA TTA
686397 CATATTTTGC
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
2 2 0.05
3 33 0.82
4 5 0.12
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:688149 original size:2 final size:2
Alignment explanation
Indices: 688142--688177 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
688132 TTCTTTATGC
688142 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
688178 CGTGCATGTA
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):
AT
Found at i:694640 original size:6 final size:6
Alignment explanation
Indices: 694629--694657 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
694619 ACGTGATAAT
694629 AAATTA AAATTA AAATTA AAATTA AAATT
1 AAATTA AAATTA AAATTA AAATTA AAATT
694658 TATTTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
AAATTA
Found at i:709215 original size:7 final size:7
Alignment explanation
Indices: 709205--709229 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
709195 TTGTCCCTTA
709205 AGCATGC
1 AGCATGC
709212 AGCATGC
1 AGCATGC
709219 AGCATGC
1 AGCATGC
709226 AGCA
1 AGCA
709230 CCTAAGCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.28, G:0.28, T:0.12
Consensus pattern (7 bp):
AGCATGC
Found at i:712924 original size:32 final size:32
Alignment explanation
Indices: 712880--712944 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 32
712870 AACATTCTCA
712880 AATCTATCACCATAAACATCAATGAAAACAAC
1 AATCTATCACCATAAACATCAATGAAAACAAC
712912 AATCTAAT-ACCATAAACATCAATGAAAACAAC
1 AATCT-ATCACCATAAACATCAATGAAAACAAC
712944 A
1 A
712945 TTCTCAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 30 0.94
33 2 0.06
ACGTcount: A:0.55, C:0.23, G:0.03, T:0.18
Consensus pattern (32 bp):
AATCTATCACCATAAACATCAATGAAAACAAC
Found at i:716409 original size:19 final size:19
Alignment explanation
Indices: 716385--716433 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
716375 AAATAGAGTT
716385 CATCGATGCATGGCTAGTG
1 CATCGATGCATGGCTAGTG
*
716404 CATCGATGCATGGCTGGTG
1 CATCGATGCATGGCTAGTG
716423 CATCGATGCAT
1 CATCGATGCAT
716434 CAAATGCATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.20, C:0.22, G:0.31, T:0.27
Consensus pattern (19 bp):
CATCGATGCATGGCTAGTG
Found at i:716554 original size:65 final size:64
Alignment explanation
Indices: 716400--716565 Score: 178
Period size: 65 Copynumber: 2.6 Consensus size: 64
716390 ATGCATGGCT
* * *
716400 AGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTTGATGTTTTCATAAAACTCTG
1 AGTGCATCGATGCATGGTTGGTGCATCAATGCATCAAATGCATTCGATG-TTTCATAAAACTCTG
* * * *
716465 AGTGCATCGTTGCATAGTAT-GTGCATCAATGCATGAAATGCATTCGATG-TTCA-AAATATTCC
1 AGTGCATCGATGCATGGT-TGGTGCATCAATGCATCAAATGCATTCGATGTTTCATAAA-ACT-C
716527 ATG
63 -TG
*
716530 -GTGCATCGATGCATGGATTGGTGCATCAGTGCATCA
1 AGTGCATCGATGCATGG-TTGGTGCATCAATGCATCA
716566 CTTTAAAAAT
Statistics
Matches: 84, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
62 3 0.04
63 6 0.07
64 16 0.19
65 58 0.69
66 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.31
Consensus pattern (64 bp):
AGTGCATCGATGCATGGTTGGTGCATCAATGCATCAAATGCATTCGATGTTTCATAAAACTCTG
Found at i:717031 original size:2 final size:2
Alignment explanation
Indices: 717024--717050 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
717014 TAGCCAATTG
717024 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
717051 GCTTAAGCTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:719237 original size:23 final size:22
Alignment explanation
Indices: 719207--719287 Score: 83
Period size: 23 Copynumber: 3.6 Consensus size: 22
719197 GTATGGCCTT
719207 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
719229 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
719251 GTGTATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
*
719274 GATGCATCAATGCA
1 G-TGCATCGATGCA
719288 TTGTTAAGTG
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
21 15 0.33
22 2 0.04
23 19 0.41
24 10 0.22
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:719263 original size:21 final size:22
Alignment explanation
Indices: 719207--719269 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
719197 GTATGGCCTT
719207 GTGCATCGATGCACATTCAAGGC
1 GTGCATCGATGCACATTC-AGGC
* * *
719230 GTGCATCGGTGCACCTTCATG-
1 GTGCATCGATGCACATTCAGGC
*
719251 GTGTATCGATGCACATTCA
1 GTGCATCGATGCACATTCA
719270 AAGGGATGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 16 0.47
22 2 0.06
23 16 0.47
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAGGC
Found at i:719954 original size:25 final size:25
Alignment explanation
Indices: 719926--719992 Score: 125
Period size: 25 Copynumber: 2.7 Consensus size: 25
719916 CCCGTCCCTA
*
719926 TCCCCGTTTAAAAAACCCGTACCCG
1 TCCCCGCTTAAAAAACCCGTACCCG
719951 TCCCCGCTTAAAAAACCCGTACCCG
1 TCCCCGCTTAAAAAACCCGTACCCG
719976 TCCCCGCTTAAAAAACC
1 TCCCCGCTTAAAAAACC
719993 ACGGGGATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.30, C:0.42, G:0.10, T:0.18
Consensus pattern (25 bp):
TCCCCGCTTAAAAAACCCGTACCCG
Found at i:720159 original size:30 final size:30
Alignment explanation
Indices: 720098--720164 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 30
720088 TCGGGCCGGG
* *
720098 TATATATATTTAAATTAAATATATATATAT
1 TATATATTTTTAAATTAAATATAAATATAT
* * * *
720128 TATATATTTTTTAATTTAATTTAAATTTAT
1 TATATATTTTTAAATTAAATATAAATATAT
720158 TA-ATATT
1 TATATATT
720165 ATATATATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
29 5 0.16
30 26 0.84
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
TATATATTTTTAAATTAAATATAAATATAT
Found at i:720282 original size:36 final size:36
Alignment explanation
Indices: 720235--720315 Score: 117
Period size: 36 Copynumber: 2.2 Consensus size: 36
720225 TTACTAAACT
** *
720235 CGTCCCCGTCCCCGTTTAACATAAACGGTTTTTTCC
1 CGTCCCCGTCCCCGTTTAACATAAACAATTTTTCCC
* *
720271 CGTCCTCGTCCCCGTTTAGCATAAACAATTTTTCCC
1 CGTCCCCGTCCCCGTTTAACATAAACAATTTTTCCC
720307 CGTCCCCGT
1 CGTCCCCGT
720316 TTAATTCGGT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.16, C:0.38, G:0.14, T:0.32
Consensus pattern (36 bp):
CGTCCCCGTCCCCGTTTAACATAAACAATTTTTCCC
Found at i:724859 original size:2 final size:2
Alignment explanation
Indices: 724852--724877 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
724842 TGAATAAATA
724852 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
724878 GATTAAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:726267 original size:3 final size:3
Alignment explanation
Indices: 726261--726321 Score: 72
Period size: 3 Copynumber: 20.7 Consensus size: 3
726251 TAATATTTAT
* * *
726261 TAA TAA TAA -AA TAA TAA TAA TAA TTA TTA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
726308 TAA T-A TAAA TAA TA
1 TAA TAA T-AA TAA TA
726322 TTCAAATGAA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
2 4 0.08
3 45 0.88
4 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:726287 original size:27 final size:27
Alignment explanation
Indices: 726248--726321 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
726238 ATTAGGCTTG
*
726248 TAATAATATTTATTAATAATAAAATAA
1 TAATAATAATTATTAATAATAAAATAA
*
726275 TAATAATAATTATT-ATAATTATAATAA
1 TAATAATAATTATTAATAA-TAAAATAA
*
726302 TAATAATAA-TATAAATAATA
1 TAATAATAATTATTAATAATA
726322 TTCAAATGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 9 0.21
27 33 0.79
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
TAATAATAATTATTAATAATAAAATAA
Found at i:726322 original size:9 final size:10
Alignment explanation
Indices: 726248--726322 Score: 70
Period size: 9 Copynumber: 7.9 Consensus size: 10
726238 ATTAGGCTTG
*
726248 TAATAATATT
1 TAATAATATA
*
726258 TATTAATAATA
1 TAATAAT-ATA
*
726269 AAATAATA-A
1 TAATAATATA
726278 TAATAAT-TA
1 TAATAATATA
*
726287 TTATAAT-TA
1 TAATAATATA
726296 TAATAATA-A
1 TAATAATATA
726305 TAATAATATA
1 TAATAATATA
726315 -AATAATAT
1 TAATAATAT
726323 TCAAATGAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
9 39 0.72
10 8 0.15
11 7 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
TAATAATATA
Found at i:726792 original size:113 final size:113
Alignment explanation
Indices: 726658--727207 Score: 753
Period size: 113 Copynumber: 4.9 Consensus size: 113
726648 TAGAGTCATG
* * * * *
726658 CAAAAGGTCGAACAAGCTCTTCTTATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
726723 TTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAA
66 TTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAA
* * * * **
726771 CAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTTTTTCTTCTTCAGAAAAGTTCTTCTCA
1 CAAAAAGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * *
726836 TTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAA
66 TTATGAACT-TTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAA
* * *
726884 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* **
726949 TTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGGATT-TGA
66 TTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAA
**
726996 GTAAAAGATTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 CAAAAAG-TTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * ** *
727061 ATTATGAACTTTCTCTGGAAAAGATGATCCATCGAGTGATGGATTTGAG
65 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAA
* * * * *
727110 TAGAAGGTTGAACAAGCTCTTCTCATTATGAAATTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
727175 TTATGAACTTTCTCTGGAAAAGCTGATCCATCG
66 TTATGAACTTTCTCTGGAAAAGTTGATCCATCG
727208 TGATGGATTT
Statistics
Matches: 387, Mismatches: 46, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
112 7 0.02
113 375 0.97
114 5 0.01
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (113 bp):
CAAAAAGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAA
Found at i:728380 original size:19 final size:17
Alignment explanation
Indices: 728356--728404 Score: 64
Period size: 16 Copynumber: 2.8 Consensus size: 17
728346 AAAATAAAAG
728356 AATAAATTGAATTTTCGAA
1 AATAAATTGAATTTTC--A
*
728375 AATAAATTGAA-TCTCA
1 AATAAATTGAATTTTCA
728391 AATAAATTGAATTT
1 AATAAATTGAATTT
728405 AGAGGAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 12 0.44
17 1 0.04
18 3 0.11
19 11 0.41
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (17 bp):
AATAAATTGAATTTTCA
Found at i:732308 original size:9 final size:9
Alignment explanation
Indices: 732285--732315 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
732275 GAAAAATAAT
732285 GAATGTAAA
1 GAATGTAAA
732294 -AATGTAAA
1 GAATGTAAA
732302 GAATGTAAA
1 GAATGTAAA
732311 GAATG
1 GAATG
732316 ATTGCCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.55, C:0.00, G:0.23, T:0.23
Consensus pattern (9 bp):
GAATGTAAA
Found at i:736109 original size:15 final size:15
Alignment explanation
Indices: 736086--736117 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
736076 AAAATAATGC
736086 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
736101 AATGCATGTATGCAA
1 AATGAATGTATGCAA
736116 AA
1 AA
736118 GATATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:741616 original size:3 final size:3
Alignment explanation
Indices: 741610--741664 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
741600 TAATATTTAT
* *
741610 TAA TAA TAA -AA TAA TAA TAA TTA TAA TTA TAA TAA TAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
741656 TAAA TAA TA
1 T-AA TAA TA
741665 TTCAAATGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 4 0.09
3 39 0.87
4 2 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:741622 original size:21 final size:20
Alignment explanation
Indices: 741598--741666 Score: 56
Period size: 21 Copynumber: 3.5 Consensus size: 20
741588 TTAGGCTTGT
741598 AATAATATTTATTAATAATAA
1 AATAATA-TTATTAATAATAA
* *
741619 AATAATAATAATT-ATAATTAT
1 AATAAT-ATTATTAATAA-TAA
741640 AATAATA--A-TAATAATATA
1 AATAATATTATTAATAATA-A
741658 AATAATATT
1 AATAATATT
741667 CAAATGAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
17 3 0.08
18 12 0.31
20 5 0.13
21 18 0.46
22 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AATAATATTATTAATAATAA
Found at i:743141 original size:45 final size:44
Alignment explanation
Indices: 743074--743227 Score: 188
Period size: 45 Copynumber: 3.4 Consensus size: 44
743064 CGGTGCACTA
743074 AGAGTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATAGCC
1 AGAGTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATA-CC
*
743119 AGAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ACTC
1 AGAGTGCATCGATGCATGAAATGCATTCGATG-TTTCA-AAATAC-C
* * *
743165 TGAGTGTATCGATGCATGAAATGCATTCGGTG-TTCAAAATATTCC
1 AGAGTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATA--CC
743210 ATG-GTGCATCGATGCATG
1 A-GAGTGCATCGATGCATG
743228 GATTGGTGCA
Statistics
Matches: 95, Mismatches: 7, Indels: 14
0.82 0.06 0.12
Matches are distributed among these distances:
43 3 0.03
44 5 0.05
45 47 0.49
46 37 0.39
47 3 0.03
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.30
Consensus pattern (44 bp):
AGAGTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATACC
Found at i:748085 original size:18 final size:18
Alignment explanation
Indices: 748049--748094 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
748039 TCTTTTAGTA
*
748049 TTTAATTTT-TTTTTAATT
1 TTTAATTTTAGTTTTAA-T
748067 TTTAATTTTAGTTTT-AT
1 TTTAATTTTAGTTTTAAT
748084 TTT-ATTTTAGT
1 TTTAATTTTAGT
748095 GCTCTCACAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 8 0.31
17 4 0.15
18 10 0.38
19 4 0.15
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (18 bp):
TTTAATTTTAGTTTTAAT
Found at i:749043 original size:5 final size:5
Alignment explanation
Indices: 749006--749044 Score: 60
Period size: 5 Copynumber: 7.6 Consensus size: 5
748996 AAAAAAATAA
*
749006 AAATT AAATT AAATT AAATT AAATA AAAGTT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAA-TT AAATT AAA
749045 AGAAATAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 27 0.87
6 4 0.13
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (5 bp):
AAATT
Found at i:749050 original size:21 final size:20
Alignment explanation
Indices: 749006--749052 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
748996 AAAAAAATAA
* **
749006 AAATTAAATTAAATTAAATT
1 AAATAAAATTAAATTAAAAG
749026 AAATAAAAGTTAAATTAAAAG
1 AAATAAAA-TTAAATTAAAAG
749047 AAATAA
1 AAATAA
749053 GATAACATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (20 bp):
AAATAAAATTAAATTAAAAG
Found at i:749050 original size:26 final size:24
Alignment explanation
Indices: 748992--749072 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 24
748982 AGGGTTAGAA
748992 TAAAA-AAA-AAATAAAAATTAAAT
1 TAAAAGAAATAAAT-AAAATTAAAT
**
749015 TAAATTAAATTAAATAAAAGTTAAAT
1 TAAAAGAAA-TAAATAAAA-TTAAAT
*
749041 TAAAAGAAATAAGATAACATTCAAAT
1 TAAAAGAAATAA-ATAAAATT-AAAT
749067 TAAAAG
1 TAAAAG
749073 GATTTTACTG
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
23 4 0.08
24 3 0.06
25 9 0.19
26 32 0.67
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (24 bp):
TAAAAGAAATAAATAAAATTAAAT
Found at i:751511 original size:3 final size:3
Alignment explanation
Indices: 751503--751562 Score: 77
Period size: 3 Copynumber: 19.7 Consensus size: 3
751493 TTTGGGCTTG
* *
751503 TAA TAA TAA TAA TAT TAA TAA TAAA TAA TAA TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
751549 TAA T-A TAAA TAA TA
1 TAA TAA T-AA TAA TA
751563 TTTAAATGAA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 2 0.04
3 43 0.86
4 5 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:751995 original size:22 final size:23
Alignment explanation
Indices: 751964--752011 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
751954 GACTTGGACC
*
751964 TAAACCAACATAA-AAATAAA-AA
1 TAAACAAACA-AATAAATAAATAA
751986 TAAACAAACAAATAAATAAATAA
1 TAAACAAACAAATAAATAAATAA
752009 TAA
1 TAA
752012 GTATATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 2 0.09
22 16 0.70
23 5 0.22
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.17
Consensus pattern (23 bp):
TAAACAAACAAATAAATAAATAA
Found at i:752142 original size:37 final size:37
Alignment explanation
Indices: 752024--752410 Score: 487
Period size: 37 Copynumber: 10.4 Consensus size: 37
752014 ATATTATAAA
*
752024 ATATATTATATATA-TTTCGAAAAACGTTTTCAAAATCT
1 ATATATTATATATATTTTC-AAAAATGTTTTCAAAA-CT
** *
752062 ATATATTATATATATTTT-AATTATTTTTTCAAAACT
1 ATATATTATATATATTTTCAAAAATGTTTTCAAAACT
*
752098 ATATATTATATATATTTTTCAAAAACGTTTT-AAAACT
1 ATATATTATATATA-TTTTCAAAAATGTTTTCAAAACT
*
752135 ATATA-T-TATATATTTTCGAAAAATATTTTCAAAACT
1 ATATATTATATATATTTTC-AAAAATGTTTTCAAAACT
752171 ATATTATATATATATATATATTCAAAAATGTTTTCAAAACT
1 ATA-TAT-TATATATAT-T-TTCAAAAATGTTTTCAAAACT
* * * *
752212 ATATATTATATAAAATTTCAAACATGTTTTCCAAACT
1 ATATATTATATATATTTTCAAAAATGTTTTCAAAACT
* * * *
752249 ATATATTATATATGTTTTCAAATATGTTTTTAAAATT
1 ATATATTATATATATTTTCAAAAATGTTTTCAAAACT
* *
752286 ATATATTATATATATTTTCAAACATGTTTTCCAAACT
1 ATATATTATATATATTTTCAAAAATGTTTTCAAAACT
*
752323 ATATATTATATATATTTTCAAAAATGTTTTTAAAACT
1 ATATATTATATATATTTTCAAAAATGTTTTCAAAACT
* *
752360 ATATATTATATATATTTTCAAACATGTTTTTCCAAACT
1 ATATATTATATATATTTTCAAAAATG-TTTTCAAAACT
752398 ATATATTATATAT
1 ATATATTATATAT
752411 GCTATGTATA
Statistics
Matches: 304, Mismatches: 33, Indels: 24
0.84 0.09 0.07
Matches are distributed among these distances:
34 5 0.02
35 15 0.05
36 26 0.09
37 169 0.56
38 44 0.14
39 11 0.04
40 10 0.03
41 21 0.07
42 3 0.01
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.47
Consensus pattern (37 bp):
ATATATTATATATATTTTCAAAAATGTTTTCAAAACT
Found at i:759620 original size:15 final size:15
Alignment explanation
Indices: 759600--759631 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
759590 ACTTGGTTTC
759600 TTGTAATTGCCTTTA
1 TTGTAATTGCCTTTA
759615 TTGTAATTGCCTTTA
1 TTGTAATTGCCTTTA
759630 TT
1 TT
759632 TCCAAATAAA
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:0.19, C:0.12, G:0.12, T:0.56
Consensus pattern (15 bp):
TTGTAATTGCCTTTA
Found at i:760075 original size:25 final size:26
Alignment explanation
Indices: 760039--760100 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 26
760029 TCTGATTGGA
*
760039 TGAAA-TCAATTGAAATTTGGGGAAT
1 TGAAATTCAATTGAAATTGGGGGAAT
*
760064 TGAAATTC-ATTGGAATTGGGGGAAT
1 TGAAATTCAATTGAAATTGGGGGAAT
*
760089 TGAAATCCAATT
1 TGAAATTCAATT
760101 CCACCACTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 27 0.84
26 5 0.16
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.32
Consensus pattern (26 bp):
TGAAATTCAATTGAAATTGGGGGAAT
Found at i:763755 original size:15 final size:15
Alignment explanation
Indices: 763735--763768 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
763725 ATTATCGATG
763735 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
763750 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
763765 AATT
1 AATT
763769 AAAATTTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:763936 original size:12 final size:11
Alignment explanation
Indices: 763907--763937 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
763897 TAATATTCCC
763907 AGTAATATGTT
1 AGTAATATGTT
763918 AGTAATATGTT
1 AGTAATATGTT
763929 AGGTAATAT
1 A-GTAATAT
763938 TACATTCCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.63
12 7 0.37
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.42
Consensus pattern (11 bp):
AGTAATATGTT
Found at i:766485 original size:2 final size:2
Alignment explanation
Indices: 766478--766502 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
766468 TCGTTTCCAT
766478 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 T
766503 TAAAGTTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:767004 original size:42 final size:41
Alignment explanation
Indices: 766916--767036 Score: 106
Period size: 40 Copynumber: 2.9 Consensus size: 41
766906 TTGTGATTTA
* * *
766916 TAGTGGCATTTTTGTTCACAAAC-GCTGCTAATT-TCA-TATATT
1 TAGT-GCATTTTTG-CCACAAACGGC-GCTAATTCT-ATTGTATG
766958 TAGTGACATTTTTGCCACAAACGGCGCTAATTCTATTGTATG
1 TAGTG-CATTTTTGCCACAAACGGCGCTAATTCTATTGTATG
* * * *
767000 TAGTG-GTTTTTTCCACAAACGCCGCTAATGCTATTGT
1 TAGTGCATTTTTGCCACAAACGGCGCTAATTCTATTGT
767037 TTTTAGTGGC
Statistics
Matches: 68, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
40 28 0.41
41 16 0.24
42 24 0.35
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (41 bp):
TAGTGCATTTTTGCCACAAACGGCGCTAATTCTATTGTATG
Found at i:767026 original size:40 final size:42
Alignment explanation
Indices: 766966--767068 Score: 120
Period size: 40 Copynumber: 2.5 Consensus size: 42
766956 TTTAGTGACA
* * *
766966 TTTTTGCCACAAACGGCGCTAATTCTATTGTATGTAGT-G-G
1 TTTTTTCCACAAACGCCGCTAATGCTATTGTATGTAGTGGCG
* *
767006 TTTTTTCCACAAACGCCGCTAATGCTATTGTTTTTAGTGGCG
1 TTTTTTCCACAAACGCCGCTAATGCTATTGTATGTAGTGGCG
* **
767048 TTATTTATACAAACGCCGCTA
1 TTTTTTCCACAAACGCCGCTA
767069 TATATTATGA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
40 33 0.62
41 1 0.02
42 19 0.36
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.38
Consensus pattern (42 bp):
TTTTTTCCACAAACGCCGCTAATGCTATTGTATGTAGTGGCG
Found at i:768699 original size:14 final size:14
Alignment explanation
Indices: 768676--768711 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
768666 AAATTGTTAG
*
768676 AAAATAAATATATT
1 AAAATAAATAAATT
*
768690 AAATTAAATAAATT
1 AAAATAAATAAATT
768704 AAAATAAA
1 AAAATAAA
768712 GTTAGTCCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAATAAATAAATT
Found at i:773171 original size:18 final size:18
Alignment explanation
Indices: 773121--773174 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
773111 TATGTGATAT
* * *
773121 GTGGTCCTTCGGGATATA
1 GTGGTCATTCGGGACAAA
*
773139 GTGGTCATTTGGGACAAA
1 GTGGTCATTCGGGACAAA
773157 GTGGTCATTCGGGACAAA
1 GTGGTCATTCGGGACAAA
773175 TTCTATGCGC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.28
Consensus pattern (18 bp):
GTGGTCATTCGGGACAAA
Found at i:775029 original size:18 final size:18
Alignment explanation
Indices: 775006--775049 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
774996 AGTTAGCACC
775006 TGTTATTATTGAAAGGGG
1 TGTTATTATTGAAAGGGG
775024 TGTTATTATTGAAAGGGG
1 TGTTATTATTGAAAGGGG
775042 TGCTTATT
1 TG-TTATT
775050 CTTTGGACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.25, C:0.02, G:0.30, T:0.43
Consensus pattern (18 bp):
TGTTATTATTGAAAGGGG
Found at i:777170 original size:21 final size:21
Alignment explanation
Indices: 777129--777172 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
777119 GTGGTCCTTC
* *
777129 GGAACATATATGTAATCCTTT
1 GGAACATATATGCAATACTTT
*
777150 GGAACATATATGCAGTACTTT
1 GGAACATATATGCAATACTTT
777171 GG
1 GG
777173 TATACTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (21 bp):
GGAACATATATGCAATACTTT
Found at i:777266 original size:18 final size:17
Alignment explanation
Indices: 777238--777274 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
777228 GGATATATGT
777238 GATATGTGGTCCTTCGG
1 GATATGTGGTCCTTCGG
777255 GATATAGTGGTCCTTCGG
1 GATAT-GTGGTCCTTCGG
777273 GA
1 GA
777275 CAAATTCTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.16, C:0.16, G:0.35, T:0.32
Consensus pattern (17 bp):
GATATGTGGTCCTTCGG
Found at i:778817 original size:22 final size:22
Alignment explanation
Indices: 778789--778844 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
778779 ATGATAAAAA
778789 ATGGTGGTCGGCGCCATCGCCT
1 ATGGTGGTCGGCGCCATCGCCT
* *
778811 ATGGTGGTCGGCGTCGTCGCCT
1 ATGGTGGTCGGCGCCATCGCCT
*
778833 ATGGTGGCCGGC
1 ATGGTGGTCGGC
778845 CAGGAAAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.07, C:0.29, G:0.41, T:0.23
Consensus pattern (22 bp):
ATGGTGGTCGGCGCCATCGCCT
Found at i:779387 original size:26 final size:27
Alignment explanation
Indices: 779358--779423 Score: 125
Period size: 26 Copynumber: 2.5 Consensus size: 27
779348 GTTACTGTTC
779358 ATTGGTTTTGATCTTTTTTT-GTTACA
1 ATTGGTTTTGATCTTTTTTTGGTTACA
779384 ATTGGTTTTGATCTTTTTTTGGTTACA
1 ATTGGTTTTGATCTTTTTTTGGTTACA
779411 ATTGGTTTTGATC
1 ATTGGTTTTGATC
779424 ATTTCGGTGC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
26 20 0.51
27 19 0.49
ACGTcount: A:0.15, C:0.08, G:0.18, T:0.59
Consensus pattern (27 bp):
ATTGGTTTTGATCTTTTTTTGGTTACA
Found at i:784268 original size:117 final size:117
Alignment explanation
Indices: 784062--784520 Score: 530
Period size: 117 Copynumber: 3.9 Consensus size: 117
784052 TAATCAAGAA
* *
784062 TGGATTTCAACTTCACGACGAAGGATATCCAATTCAATGCTCAACTTCACAACGAAGGGGTCATC
1 TGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATC
* *
784127 TACGATTTCAACTTCACGACGAAGGATATCGTGCCCACATTCATCTTTATAT
66 CACGATTTCAACTTCACGACGAAGGATATCGTGCCCACATTAATCTTTATAT
** * *
784179 TGGATTTCAACTTCACGAAAAAGGATATCAAATTCAAGGCTCAACTTCACAACGAAGGGGTCATC
1 TGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATC
* * * *
784244 CACGATTTCAACTTCGCGACGAAGGATATCGTTCTCACCAGCAACATTTATCTTTAGAT
66 CACGATTTCAACTTCACGACGAAGGATATCG---T-GCC--C-ACATTAATCTTTATAT
* * * * *
784303 TGGATTTCAACTTCACGACGAAGAATATCCAATTCATA-ACTCAAATTCATAATGAAGGGGCCAT
1 TGGATTTCAACTTCACGACGAAGGATATCCAATTCA-AGGCTCAACTTCACAACGAAGGGGCCAT
* * * * ** * **
784367 CCACGATTTTAACTTCACGACGAATGATACCGTGCCTACAAGAAACATACAATACT
65 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACATTAATC-T-TTATA-T
*
784423 TGGATTTCAACTTCACGACGAAGGATTTCCAATTCAAGGCTCAACTTCACAACGAA-GGGCCAT-
1 TGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATC
*
784486 CACGATTTCAACTTCAC-AGTGAAGGATATCGTGCC
66 CACGATTTCAACTTCACGA-CGAAGGATATCGTGCC
784521 ATAAGAAGCA
Statistics
Matches: 288, Mismatches: 41, Indels: 25
0.81 0.12 0.07
Matches are distributed among these distances:
117 96 0.33
118 30 0.10
119 10 0.03
120 52 0.18
121 3 0.01
123 1 0.00
124 95 0.33
125 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (117 bp):
TGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATC
CACGATTTCAACTTCACGACGAAGGATATCGTGCCCACATTAATCTTTATAT
Found at i:784360 original size:124 final size:122
Alignment explanation
Indices: 784062--784577 Score: 526
Period size: 124 Copynumber: 4.3 Consensus size: 122
784052 TAATCAAGAA
* *
784062 TGGATTTCAACTTCACGACGAAGGATATCCAATTCAATGCTCAACTTCACAACGAAGGGGTCATC
1 TGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATC
* * *
784127 TACGATTTCAACTTCACGACGAAGGATATCG--T-GCC--C-ACATTCATCTTTATAT
66 CACGATTTCAACTTCACGACGAAGGATATCGTCTCACCAGCAACATTTATCTTTA-AT
** * *
784179 TGGATTTCAACTTCACGAAAAAGGATATCAAATTCAAGGCTCAACTTCACAACGAAGGGGTCATC
1 TGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATC
*
784244 CACGATTTCAACTTCGCGACGAAGGATATCGTTCTCACCAGCAACATTTATCTTTAGAT
66 CACGATTTCAACTTCACGACGAAGGATATCG-TCTCACCAGCAACATTTATCTTTA-AT
* * * * *
784303 TGGATTTCAACTTCACGACGAAGAATATCCAATTCATA-ACTCAAATTCATAATGAAGGGGCCAT
1 TGGATTTCAACTTCACGACGAAGGATATCCAATTCA-AGGCTCAACTTCACAACGAAGGGGCCAT
* * * * * ** *
784367 CCACGATTTTAACTTCACGACGAATGATACCGTGC-CTACAAGAAACA--TA-CAATACT
65 CCACGATTTCAACTTCACGACGAAGGATATCGT-CTC-ACCAGCAACATTTATCTTTAAT
*
784423 TGGATTTCAACTTCACGACGAAGGATTTCCAATTCAAGGCTCAACTTCACAACGAA-GGGCCAT-
1 TGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATC
* ** *** *
784486 CACGATTTCAACTTCAC-AGTGAAGGATATCGTGC-CATAAG-AAGCATCCCTCTCTATAT
66 CACGATTTCAACTTCACGA-CGAAGGATATCGT-CTCACCAGCAA-CATTTATCTTTA-AT
*
784544 TGGATTTCAACTTCAC-AGTGAAGGATATCCAATT
1 TGGATTTCAACTTCACGA-CGAAGGATATCCAATT
784578 TAAAGAAGGA
Statistics
Matches: 336, Mismatches: 45, Indels: 32
0.81 0.11 0.08
Matches are distributed among these distances:
116 2 0.01
117 97 0.29
118 29 0.09
119 8 0.02
120 54 0.16
121 36 0.11
122 2 0.01
123 3 0.01
124 104 0.31
125 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (122 bp):
TGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATC
CACGATTTCAACTTCACGACGAAGGATATCGTCTCACCAGCAACATTTATCTTTAAT
Found at i:784548 original size:241 final size:241
Alignment explanation
Indices: 784062--784577 Score: 623
Period size: 241 Copynumber: 2.1 Consensus size: 241
784052 TAATCAAGAA
* * *
784062 TGGATTTCAACTTCACGACGAAGGATATCCAATTCAATGCTCAACTTCACAACGAAGGGGTCATC
1 TGGATTTCAACTTCACGACGAAGGATATCCAATTCAATACTCAAATTCACAACGAAGGGGCCATC
* * *** * **
784127 TACGATTTCAACTTCACGACGAAGGATATCGTGCCCACATTCATCTTTATATTGGATTTCAACTT
66 CACGATTTCAACTTCACGACGAAGGATACCGTGCCCACAAGAAACTCAATATTGGATTTCAACTT
*
784192 CACGAAAAAGGATATCAAATTCAAGGCTCAACTTCACAACGAAGGGGTCATCCACGATTTCAACT
131 CACGAAAAAGGATATCAAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGATTTCAACT
* * * ** *
784257 TCGCGACGAAGGATATCGTTCTCACCAGCAACATTTATCTTTAGAT
196 TCACGACGAAGGATATCGTGCTCACAAGCAACATCCATCTCTAGAT
* * *
784303 TGGATTTCAACTTCACGACGAAGAATATCCAATTC-ATAACTCAAATTCATAATGAAGGGGCCAT
1 TGGATTTCAACTTCACGACGAAGGATATCCAATTCAAT-ACTCAAATTCACAACGAAGGGGCCAT
* * *
784367 CCACGATTTTAACTTCACGACGAATGATACCGTGCCTACAAGAAACATACAATACTTGGATTTCA
65 CCACGATTTCAACTTCACGACGAAGGATACCGTGCCCACAAGAAAC-T-CAATA-TTGGATTTCA
** * *
784432 ACTTCACGACGAAGGATTTCCAATTCAAGGCTCAACTTCACAACGAA-GGGCCAT-CACGATTTC
127 ACTTCACGAAAAAGGATATCAAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGATTTC
* * * *
784495 AACTTCAC-AGTGAAGGATATCGTGC-CATAAG-AAGCATCCCTCTCTATAT
192 AACTTCACGA-CGAAGGATATCGTGCTCACAAGCAA-CATCCATCTCTAGAT
*
784544 TGGATTTCAACTTCAC-AGTGAAGGATATCCAATT
1 TGGATTTCAACTTCACGA-CGAAGGATATCCAATT
784578 TAAAGAAGGA
Statistics
Matches: 234, Mismatches: 34, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
240 5 0.02
241 137 0.59
242 30 0.13
243 9 0.04
244 53 0.23
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (241 bp):
TGGATTTCAACTTCACGACGAAGGATATCCAATTCAATACTCAAATTCACAACGAAGGGGCCATC
CACGATTTCAACTTCACGACGAAGGATACCGTGCCCACAAGAAACTCAATATTGGATTTCAACTT
CACGAAAAAGGATATCAAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGATTTCAACT
TCACGACGAAGGATATCGTGCTCACAAGCAACATCCATCTCTAGAT
Found at i:785340 original size:3 final size:3
Alignment explanation
Indices: 785332--785365 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
785322 GGATAAAAAT
785332 ATA ATA ATA ATA ATA ATA ATA ATA ATA TATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
785366 TATTATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:793599 original size:20 final size:20
Alignment explanation
Indices: 793563--793602 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
793553 ATCAAATATA
*
793563 ATAAAAATATTATTTATTAT
1 ATAAAAATAATATTTATTAT
793583 ATAAAAATTAATA-TTATTAT
1 ATAAAAA-TAATATTTATTAT
793603 TTTTAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATAAAAATAATATTTATTAT
Found at i:793723 original size:19 final size:19
Alignment explanation
Indices: 793687--793767 Score: 67
Period size: 19 Copynumber: 4.3 Consensus size: 19
793677 ATAAATCAAA
* **
793687 ATATTAAAATTAGTATATT
1 ATATTAAAATAAAAATATT
*
793706 CTATTAAAATAAAAATATT
1 ATATTAAAATAAAAATATT
** * *
793725 ATA-TATTATATTAATTATT
1 ATATTAAAATA-AAAATATT
793744 -TATTAAAATAAAAATATT
1 ATATTAAAATAAAAATATT
793762 ATATTA
1 ATATTA
793768 CTTTTTAAAA
Statistics
Matches: 46, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
18 13 0.28
19 33 0.72
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (19 bp):
ATATTAAAATAAAAATATT
Found at i:794016 original size:22 final size:22
Alignment explanation
Indices: 793933--794006 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 22
793923 ATTATTAAAA
*
793933 TAAAAATAAAATATCATATATTAT
1 TAAAAATATAATAT-A-ATATTAT
* * *
793957 T-ATAATATAGT-T-ATAATAT
1 TAAAAATATAATATAATATTAT
*
793976 TAAAAATATAATATTATATTAT
1 TAAAAATATAATATAATATTAT
793998 TAAAAATAT
1 TAAAAATAT
794007 TAGTAAATAT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
19 7 0.17
20 8 0.20
21 1 0.03
22 16 0.40
23 7 0.17
24 1 0.03
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (22 bp):
TAAAAATATAATATAATATTAT
Found at i:794604 original size:15 final size:15
Alignment explanation
Indices: 794584--794615 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
794574 ATGTCATCGT
794584 TTAAAAAATTATTAG
1 TTAAAAAATTATTAG
794599 TTAAAAAATTATTAG
1 TTAAAAAATTATTAG
794614 TT
1 TT
794616 TTCATTGTTG
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:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (15 bp):
TTAAAAAATTATTAG
Found at i:797701 original size:62 final size:63
Alignment explanation
Indices: 797620--797741 Score: 228
Period size: 62 Copynumber: 2.0 Consensus size: 63
797610 TTGAAGTCTG
*
797620 TTTGGGTTTTTTTTCCCTTATCTTTTCATCGAATCCTCTCAACAATTTTTGCTGATAGATTGC
1 TTTGGGTTTTTTTCCCCTTATCTTTTCATCGAATCCTCTCAACAATTTTTGCTGATAGATTGC
797683 TTTGGG-TTTTTTCCCCTTATCTTTTCATCGAATCCTCTCAACAATTTTTGCTGATAGAT
1 TTTGGGTTTTTTTCCCCTTATCTTTTCATCGAATCCTCTCAACAATTTTTGCTGATAGAT
797742 CACTTTCCTA
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
62 52 0.90
63 6 0.10
ACGTcount: A:0.18, C:0.21, G:0.12, T:0.48
Consensus pattern (63 bp):
TTTGGGTTTTTTTCCCCTTATCTTTTCATCGAATCCTCTCAACAATTTTTGCTGATAGATTGC
Found at i:798142 original size:13 final size:13
Alignment explanation
Indices: 798126--798153 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
798116 TGTATGAGAA
798126 AGAGAAGAAGAGG
1 AGAGAAGAAGAGG
798139 AGAGAAGAAGAGG
1 AGAGAAGAAGAGG
798152 AG
1 AG
798154 GCACTCTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (13 bp):
AGAGAAGAAGAGG
Found at i:800626 original size:25 final size:25
Alignment explanation
Indices: 800597--800644 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
800587 CTAGGAGAAA
800597 TTTTAAAGGGTTAAATTATATTTAT
1 TTTTAAAGGGTTAAATTATATTTAT
*
800622 TTTTAAATGGTTAAATTATATTT
1 TTTTAAAGGGTTAAATTATATTT
800645 TAGACTCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.54
Consensus pattern (25 bp):
TTTTAAAGGGTTAAATTATATTTAT
Found at i:802265 original size:23 final size:23
Alignment explanation
Indices: 802246--802329 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
802236 TCATTCAGGG
802246 CAATTTTATGTGGTCCTTCAAGA
1 CAATTTTATGTGGTCCTTCAAGA
802269 CAATTTTATGTGGTCCTTCGGAA-A
1 CAATTTTATGTGGTCCTTC--AAGA
*
802293 -AATTATATGTGGTCCTTCAAGA
1 CAATTTTATGTGGTCCTTCAAGA
* *
802315 TAATTCTATGTGGTC
1 CAATTTTATGTGGTC
802330 ATTTGGGACA
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
21 2 0.04
22 1 0.02
23 49 0.89
24 1 0.02
25 2 0.04
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.39
Consensus pattern (23 bp):
CAATTTTATGTGGTCCTTCAAGA
Found at i:802348 original size:46 final size:46
Alignment explanation
Indices: 802225--802350 Score: 130
Period size: 46 Copynumber: 2.7 Consensus size: 46
802215 GAGTTGAGAG
* * * *
802225 ATTCTATGTAGTCATTCAGGG-CAATTTTATGTGGTCCTTCAAGACA
1 ATTCTATGTGGTCATT-TGGGACAAATATATGTGGTCCTTCAAGACA
* * * * *
802271 ATTTTATGTGGTC-CTTCGGAAAAATTATATGTGGTCCTTCAAGATA
1 ATTCTATGTGGTCATTTGGGACAAA-TATATGTGGTCCTTCAAGACA
*
802317 ATTCTATGTGGTCATTTGGGACAAATCTATGTGG
1 ATTCTATGTGGTCATTTGGGACAAATATATGTGG
802351 CACTTCGGTG
Statistics
Matches: 63, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
44 2 0.03
45 3 0.05
46 50 0.79
47 8 0.13
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.38
Consensus pattern (46 bp):
ATTCTATGTGGTCATTTGGGACAAATATATGTGGTCCTTCAAGACA
Found at i:803735 original size:6 final size:6
Alignment explanation
Indices: 803724--803753 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
803714 CACACTTTGA
*
803724 ATGAGT ATGAGT ATGAGT ATGAGT GTGAGT
1 ATGAGT ATGAGT ATGAGT ATGAGT ATGAGT
803754 TTAATAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (6 bp):
ATGAGT
Found at i:809864 original size:21 final size:21
Alignment explanation
Indices: 809838--809882 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 21
809828 CCGAAAATAT
809838 TAAAAA-AATTAATATTTTAAG
1 TAAAAATAA-TAATATTTTAAG
809859 TAAAAATAATAATATTTTAAG
1 TAAAAATAATAATATTTTAAG
809880 TAA
1 TAA
809883 TTTTTTTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAAG
Found at i:812474 original size:251 final size:250
Alignment explanation
Indices: 812031--812499 Score: 640
Period size: 251 Copynumber: 1.9 Consensus size: 250
812021 TGTATGTATC
* * * * * *
812031 TGAATGCCTGACTCTCCTTTCATCTGAAGTTTTGCGGTCATGAAGTCAGCTAATAAGGGCCCCTA
1 TGAATGCCGGACTCTCCCTTCATCCGAAGTTTTGCAGCCATGAAGTCAGCTAATAAGCGCCCCTA
* * * * * *
812096 TAAACCATATTGATAGTCTAATGGCTCACAGAAATGCTTTCTTCTTTTTTGTAATTATTGTCTAA
66 AAAACCATATGGATAGTCTAATGGCTCACAAAAATGCTTTCCTCTCTTTTGGAATTATTGTCTAA
* * *
812161 TGTAATTTTATAACTAAATTTTGGTTTTTATACTCTCGACTTTTTTTGACACATTAAAGATAATG
131 TGTAATTTTATAACTAAATTTTGGTTTTTACAATCTC-ACTTTTTTTGACACATTAAAGATAACG
*
812226 AGGCTTATGTCTTAGTTTCGTTTACAATTATCTATTAGGATTTAGGGGCATTTATT
195 AGGCTTATGTATTAGTTTCGTTTACAATTATCTATTAGGATTTAGGGGCATTTATT
* * *
812282 TGAATGCCGGACTCTCCCTTCATCCGTAA-TTTTGCAGCCATGAATTCGGCTAATAAGCGTCCCT
1 TGAATGCCGGACTCTCCCTTCATCCG-AAGTTTTGCAGCCATGAAGTCAGCTAATAAGCGCCCCT
* *
812346 AAAAACCTTATGGATAGTCTAATGGCTCACAAAAATGCTTTCCTC-CTTTTGGAATTATTTTCTA
65 AAAAACCATATGGATAGTCTAATGGCTCACAAAAATGCTTTCCTCTCTTTTGGAATTATTGTCTA
* *
812410 ATGTAATTTTATAATTAAATTTTGG-TTTTACAATCT-AGTTGAGTTTTTGGACACATTAAAGAT
130 ATGTAATTTTATAACTAAATTTTGGTTTTTACAATCTCACTT---TTTTT-GACACATTAAAGAT
*
812473 AACGAGGCTTATGTATTAGTTTTGTTT
191 AACGAGGCTTATGTATTAGTTTCGTTT
812500 TATAATTGAA
Statistics
Matches: 189, Mismatches: 24, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
247 3 0.02
249 9 0.05
250 45 0.24
251 130 0.69
252 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (250 bp):
TGAATGCCGGACTCTCCCTTCATCCGAAGTTTTGCAGCCATGAAGTCAGCTAATAAGCGCCCCTA
AAAACCATATGGATAGTCTAATGGCTCACAAAAATGCTTTCCTCTCTTTTGGAATTATTGTCTAA
TGTAATTTTATAACTAAATTTTGGTTTTTACAATCTCACTTTTTTTGACACATTAAAGATAACGA
GGCTTATGTATTAGTTTCGTTTACAATTATCTATTAGGATTTAGGGGCATTTATT
Found at i:816481 original size:30 final size:30
Alignment explanation
Indices: 816437--816493 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
816427 TACACTTAAA
816437 TTTTTAATACTAAACTTTTAAACAATTCAT
1 TTTTTAATACTAAACTTTTAAACAATTCAT
* *
816467 TTTTTGATATTAAACTTTTAAACAATT
1 TTTTTAATACTAAACTTTTAAACAATT
816494 TACTCTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.49
Consensus pattern (30 bp):
TTTTTAATACTAAACTTTTAAACAATTCAT
Found at i:817740 original size:22 final size:21
Alignment explanation
Indices: 817674--817741 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 21
817664 CTTCCGATAA
* *
817674 AATTAATATTAAATTTAAAATT
1 AATTAAAATTAAA-TTAATATT
* *
817696 CATCATAAAATTAAATTATTATT
1 AAT--TAAAATTAAATTAATATT
*
817719 AATTAAATATTTAATTAATATT
1 AATTAAA-ATTAAATTAATATT
817741 A
1 A
817742 TATTCTTTTA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
21 4 0.11
22 15 0.42
23 8 0.22
24 9 0.25
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (21 bp):
AATTAAAATTAAATTAATATT
Found at i:817796 original size:35 final size:35
Alignment explanation
Indices: 817726--817797 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 35
817716 ATTAATTAAA
* *
817726 TATTTAATTAATATTATATTCTTTTAATTATTTTT
1 TATTTAATTAATATTATATTCTTTAAATTAATTTT
*
817761 TATTTAATTTATATT-TATT-TTTAAATTTAAATTTT
1 TATTTAATTAATATTATATTCTTTAAA-TT-AATTTT
817796 TA
1 TA
817798 AAGTAAGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 5 0.16
34 6 0.19
35 21 0.66
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (35 bp):
TATTTAATTAATATTATATTCTTTAAATTAATTTT
Found at i:819465 original size:17 final size:17
Alignment explanation
Indices: 819443--819476 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
819433 TAAGAATGTG
819443 TTGAGAGCCTTAAATAA
1 TTGAGAGCCTTAAATAA
819460 TTGAGAGCCTTAAATAA
1 TTGAGAGCCTTAAATAA
819477 AGAGTATTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (17 bp):
TTGAGAGCCTTAAATAA
Found at i:839157 original size:40 final size:41
Alignment explanation
Indices: 839100--839301 Score: 146
Period size: 40 Copynumber: 4.8 Consensus size: 41
839090 GATGGTTTGT
839100 CATCCTCATCACGTAGGAACCGTGTCATCCCCCGACCAAAC
1 CATCCTCATCACGTAGGAACCGTGTCATCCCCCGACCAAAC
* * * *
839141 C-TCCTCATCACGTAGGATCCGTATCA-CCCCTAGATAACC-AGC
1 CATCCTCATCACGTAGGAACCGTGTCATCCCC-CG---ACCAAAC
* * * *
839183 CATCCTCATCACGTAGGAACCGTGTTATCGTCCCTA-AAGATGAC
1 CATCCTCATCACGTAGGAACCGTGTCATC-CCCCGACCA-A--AC
*
839227 ATGTCATCCTCATCACGTAGGAACTGTGTCATCCCCCGACCAAAC
1 ----CATCCTCATCACGTAGGAACCGTGTCATCCCCCGACCAAAC
* * *
839272 C-TCCTTATCAAGTAGGATCCGTGTCA-CCCC
1 CATCCTCATCACGTAGGAACCGTGTCATCCCC
839302 TAGATAACCA
Statistics
Matches: 124, Mismatches: 21, Indels: 34
0.69 0.12 0.19
Matches are distributed among these distances:
39 8 0.06
40 45 0.36
41 3 0.02
42 4 0.03
43 25 0.20
44 2 0.02
45 4 0.03
47 5 0.04
48 28 0.23
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.22
Consensus pattern (41 bp):
CATCCTCATCACGTAGGAACCGTGTCATCCCCCGACCAAAC
Found at i:839320 original size:131 final size:131
Alignment explanation
Indices: 839097--839478 Score: 507
Period size: 131 Copynumber: 2.9 Consensus size: 131
839087 AAAGATGGTT
* *
839097 TGTCATCCTCATCACGTAGGAACCGTGTCATCCCCCGACCAAACCTCCTCATCACGTAGGATCCG
1 TGTCATCCTCATCACGTAGGAACTGTGTCATCCCCCGACCAAACCTCCTTATCACGTAGGATCCG
* * *
839162 TATCACCCCTAGATAACCAGCCATCCTCATCACGTAGGAACCGTGTTATCGTCCCTAAAGATGAC
66 TGTCACCCCTAGATAACCAGTCATCCTCATCACGTAGGAACCGTGTTATCATCCCTAAAGATGAC
839227 A
131 A
*
839228 TGTCATCCTCATCACGTAGGAACTGTGTCATCCCCCGACCAAACCTCCTTATCAAGTAGGATCCG
1 TGTCATCCTCATCACGTAGGAACTGTGTCATCCCCCGACCAAACCTCCTTATCACGTAGGATCCG
** * * ** * **
839293 TGTCACCCCTAGATAACCAGTTGTCCTCATCACGAAGAAACAATGTTATTATCCCTAAAGATGGT
66 TGTCACCCCTAGATAACCAGTCATCCTCATCACGTAGGAACCGTGTTATCATCCCTAAAGATGAC
839358 A
131 A
* * * * * ** *
839359 TGTCATCCTCATCACATAGGAATTGTGTCATCTCCCGACCATACAT-CTTCATCACGTTTGAACC
1 TGTCATCCTCATCACGTAGGAACTGTGTCATCCCCCGACCAAACCTCCTT-ATCACGTAGGATCC
* **
839423 GTGTCACCCCTAGATAAACAGTCATCCTCATCGTGTAGGAACCGTGTTATCA-CCCT
65 GTGTCACCCCTAGATAACCAGTCATCCTCATCACGTAGGAACCGTGTTATCATCCCT
839479 TCCTAAAGAT
Statistics
Matches: 216, Mismatches: 34, Indels: 3
0.85 0.13 0.01
Matches are distributed among these distances:
130 7 0.03
131 209 0.97
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.26
Consensus pattern (131 bp):
TGTCATCCTCATCACGTAGGAACTGTGTCATCCCCCGACCAAACCTCCTTATCACGTAGGATCCG
TGTCACCCCTAGATAACCAGTCATCCTCATCACGTAGGAACCGTGTTATCATCCCTAAAGATGAC
A
Found at i:840007 original size:220 final size:220
Alignment explanation
Indices: 839619--840380 Score: 1025
Period size: 220 Copynumber: 3.5 Consensus size: 220
839609 TCATCCCCAA
* * * * *
839619 CAACAAATAATTTACCTGAAAACGACCATATCTCTTCAACACGGATGAGCAGCGTCATCTTCAAC
1 CAACAAATAATTTACCTAAAAATGAACAGATCTCTTCAACACGGATGAGCAACGTCATCTTCAAC
* * *
839684 ATCAAATTATCTTCAGGTTGACCCGATCTCCTCAA-AGCGAATGAGAAGTGTCATCCTCAGACAA
66 ATCAAATTATCTCCAGATTGACCCGATCTCCTCAACA-CGAATGAGAAGTGTCATCCTAAGACAA
* *
839748 TCAGA-TCTCCTCAACGCGAAGGAACCGTGTTGTCTCCAAATTATATCCTGATTGACCTGATTTC
130 TCAGACT-TCCTCAACGCGAAGGAACCGTGTTGTCTCCAAATTATCTCCAGATTGACCTGATTTC
*
839812 CTCAACGCGAAGGAACAACGTCATCTT
194 CTTAACGCGAAGGAACAACGTCATCTT
** *
839839 CAACAAATAATTTACCTAAAAATGAACAGATCTCTTCAACACGGATGAATAACGTCGTCTTCAAC
1 CAACAAATAATTTACCTAAAAATGAACAGATCTCTTCAACACGGATGAGCAACGTCATCTTCAAC
* *
839904 ATCAAATTATCTCCAGATTGACCCGATCTCCTCAACACGAATGAGCA-TCATCATCCTAAGACAA
66 ATCAAATTATCTCCAGATTGACCCGATCTCCTCAACACGAATGAGAAGT-GTCATCCTAAGACAA
* * * * * *
839968 TAAGACTTCCTCAACACGAAGGAACCGTATTGCCTCCAAATTTTCTCCAGATTGACCTTATTTCC
130 TCAGACTTCCTCAACGCGAAGGAACCGTGTTGTCTCCAAATTATCTCCAGATTGACCTGATTTCC
840033 TTAACGCGAAGGAACAACGTCATCTT
195 TTAACGCGAAGGAACAACGTCATCTT
* * ** *
840059 CAATAAATAATTTACCTAAAAATGACCAGATCTCTTCAACACGGATGAGCAGTGTCGTCTTCAAC
1 CAACAAATAATTTACCTAAAAATGAACAGATCTCTTCAACACGGATGAGCAACGTCATCTTCAAC
* ** * *
840124 ATCAAATTATCTCTAGATTGACCCGATCTCCTCAACGTGAATGAGTAGTGTCATTCTCAA-ACAA
66 ATCAAATTATCTCCAGATTGACCCGATCTCCTCAACACGAATGAGAAGTGTCATCCT-AAGACAA
* *
840188 TCAGACTTCCGCAACGCGAAGGAACCGTGTTGTCTCCAAATTATCTCCAGATTGACCTGACTTCC
130 TCAGACTTCCTCAACGCGAAGGAACCGTGTTGTCTCCAAATTATCTCCAGATTGACCTGATTTCC
* *
840253 TTAACGAGAAGGAACAACATCATCTT
195 TTAACGCGAAGGAACAACGTCATCTT
** * * *
840279 CAACAAATAATTTATTTGAAAGTG-ACTAGATCTCTTCAACACGGATGAGCAGA-GTCATCTTTA
1 CAACAAATAATTTACCTAAAAATGAAC-AGATCTCTTCAACACGGATGAGCA-ACGTCATCTTCA
* *
840342 ACACCAAATTATCTCCAGATTGACTCGAT-TCCCTCAACA
64 ACATCAAATTATCTCCAGATTGACCCGATCT-CCTCAACA
840381 AGAAGGAACA
Statistics
Matches: 477, Mismatches: 57, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
219 3 0.01
220 469 0.98
221 5 0.01
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.26
Consensus pattern (220 bp):
CAACAAATAATTTACCTAAAAATGAACAGATCTCTTCAACACGGATGAGCAACGTCATCTTCAAC
ATCAAATTATCTCCAGATTGACCCGATCTCCTCAACACGAATGAGAAGTGTCATCCTAAGACAAT
CAGACTTCCTCAACGCGAAGGAACCGTGTTGTCTCCAAATTATCTCCAGATTGACCTGATTTCCT
TAACGCGAAGGAACAACGTCATCTT
Found at i:842032 original size:5 final size:5
Alignment explanation
Indices: 842022--842070 Score: 71
Period size: 5 Copynumber: 9.8 Consensus size: 5
842012 CTCTTTTCAC
* * *
842022 TTTTA TTTTA TTTTA TTTCA TTTTA TTTTG TTTTA TTTTA TTTTC TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
842071 GTAAAAATTG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.14, C:0.04, G:0.02, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:842071 original size:20 final size:20
Alignment explanation
Indices: 842016--842072 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
842006 TTTCAACTCT
*
842016 TTTCACTTTTATTTTATTTTA
1 TTTCA-TTTTATTTTGTTTTA
842037 TTTCATTTTATTTTGTTTTA
1 TTTCATTTTATTTTGTTTTA
* *
842057 TTTTATTTTCTTTTGT
1 TTTCATTTTATTTTGT
842073 AAAAATTGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 28 0.85
21 5 0.15
ACGTcount: A:0.14, C:0.07, G:0.04, T:0.75
Consensus pattern (20 bp):
TTTCATTTTATTTTGTTTTA
Found at i:842630 original size:54 final size:54
Alignment explanation
Indices: 842555--842709 Score: 247
Period size: 54 Copynumber: 2.9 Consensus size: 54
842545 GAATTCCGTA
** *
842555 GGTTGCACACATAGTGCCGATACGGTAATTCATAAACTCATTATGAATTATGTG
1 GGTTGCACACATAGTAACGATACGGTAATTCACAAACTCATTATGAATTATGTG
* * *
842609 GGTTGTACACATAGTATCGATACGGTAATTCACAAACTCATTATGAATTCTGTG
1 GGTTGCACACATAGTAACGATACGGTAATTCACAAACTCATTATGAATTATGTG
*
842663 GGTTACACACATAGTAACGATACGGTAATTCACAAACTCATTATGAA
1 GGTTGCACACATAGTAACGATACGGTAATTCACAAACTCATTATGAA
842710 AATATGTCAA
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 93 1.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Consensus pattern (54 bp):
GGTTGCACACATAGTAACGATACGGTAATTCACAAACTCATTATGAATTATGTG
Found at i:843427 original size:20 final size:21
Alignment explanation
Indices: 843384--843427 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
843374 AAACTAACTT
** *
843384 ACATCCATAAATCTCCTTATA
1 ACATCCATAAATCTCCAAAGA
843405 ACATCCA-AAATCTCCAAAGA
1 ACATCCATAAATCTCCAAAGA
843425 ACA
1 ACA
843428 CTCAAAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.45, C:0.30, G:0.02, T:0.23
Consensus pattern (21 bp):
ACATCCATAAATCTCCAAAGA
Found at i:850018 original size:21 final size:21
Alignment explanation
Indices: 849994--850039 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
849984 TATCAAGTAG
849994 CTCGTTTCGATTCATTAAGAA
1 CTCGTTTCGATTCATTAAGAA
850015 CTCGTTTCGATTCATTAAGAA
1 CTCGTTTCGATTCATTAAGAA
850036 CTCG
1 CTCG
850040 AACTCGAGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (21 bp):
CTCGTTTCGATTCATTAAGAA
Found at i:851380 original size:31 final size:31
Alignment explanation
Indices: 851341--851408 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
851331 ATAGGCTAAA
851341 TAGT-GAGGGAAAAATGGTCATTTCCAATAC
1 TAGTGGAGGGAAAAATGGTCATTTCCAATAC
* *
851371 TAGTGGAGGGCAAAATGGTTATTTCCAATAC
1 TAGTGGAGGGAAAAATGGTCATTTCCAATAC
851402 TAGTGGA
1 TAGTGGA
851409 AATACCTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 4 0.11
31 31 0.89
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (31 bp):
TAGTGGAGGGAAAAATGGTCATTTCCAATAC
Found at i:852066 original size:31 final size:31
Alignment explanation
Indices: 852031--852091 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
852021 AATTCGGTGA
*
852031 ATTCAATATGTCCTTCTCACTAGGAACTCCC
1 ATTCAATATGTCATTCTCACTAGGAACTCCC
852062 ATTCAATATGTCATTCTCACTAGGAACTCC
1 ATTCAATATGTCATTCTCACTAGGAACTCC
852092 AAAACTCTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.33
Consensus pattern (31 bp):
ATTCAATATGTCATTCTCACTAGGAACTCCC
Found at i:855423 original size:22 final size:21
Alignment explanation
Indices: 855371--855430 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
855361 GATTTCTGGG
855371 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
855392 CAA-GGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
*
855412 CAATGGGGAATCGATACCC
1 CAA-GGGGAATCGGTACCC
855431 CCCTCAAACG
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 20 0.56
21 3 0.08
22 13 0.36
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGGTACCCATT
Found at i:855510 original size:23 final size:22
Alignment explanation
Indices: 855466--855510 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
855456 AATCTCATAG
*
855466 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
855488 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
855511 AAATTGTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.29, C:0.33, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:855963 original size:20 final size:20
Alignment explanation
Indices: 855938--855983 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
855928 ATAAGTCGAG
855938 AGATGTAGGGAAATAGAAAT
1 AGATGTAGGGAAATAGAAAT
855958 AGATGTAGGGAAATAGAAAT
1 AGATGTAGGGAAATAGAAAT
855978 AGATGT
1 AGATGT
855984 TTATAAAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.48, C:0.00, G:0.30, T:0.22
Consensus pattern (20 bp):
AGATGTAGGGAAATAGAAAT
Found at i:857110 original size:103 final size:103
Alignment explanation
Indices: 856787--857102 Score: 553
Period size: 103 Copynumber: 3.1 Consensus size: 103
856777 GGGTCTACGC
856787 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
*
856852 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGC
66 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
* * *
856890 AGTCCTTCGGAACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGTGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
856955 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
856993 GGTCCTTCGGGACATATATGTATTCTTTGGAAC-TGTGTGAAGTCTGGTGAGGACACATACTTGA
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGA-GACACATACTTGA
* * *
857057 TCCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
65 TCCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
857096 GGTCCTT
1 GGTCCTT
857103 ATGGACATTA
Statistics
Matches: 202, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
102 16 0.08
103 186 0.92
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:857146 original size:23 final size:23
Alignment explanation
Indices: 857120--857164 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
857110 TTATTATATA
*
857120 GCACGATGGTGCAATTCTACGTG
1 GCACGACGGTGCAATTCTACGTG
**
857143 GCACTCCGGTGCAATTCTACGT
1 GCACGACGGTGCAATTCTACGT
857165 AGCGGTGCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GCACGACGGTGCAATTCTACGTG
Done.