Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008463.1 Hibiscus syriacus cultivar Beakdansim tig00111276_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: 1833679
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 11
Found at i:670404 original size:20 final size:20
Alignment explanation
Indices: 670368--670405 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
670358 CAACCCAGGC
*
670368 ACATGTCTATTGTTTGATAA
1 ACATGTCTATGGTTTGATAA
670388 ACATGT-TATGGTATTGAT
1 ACATGTCTATGGT-TTGAT
670406 TGATCCAGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (20 bp):
ACATGTCTATGGTTTGATAA
Found at i:674701 original size:24 final size:24
Alignment explanation
Indices: 674672--674725 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
674662 CAGGTAGTGT
*
674672 ATCGATGCACACGTTATGGAATGC
1 ATCGATGCACACGTTATGGAATAC
674696 ATCGATGCACACGTTATGGAATAC
1 ATCGATGCACACGTTATGGAATAC
674720 ATCGAT
1 ATCGAT
674726 ACACTGTAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.26
Consensus pattern (24 bp):
ATCGATGCACACGTTATGGAATAC
Found at i:675297 original size:18 final size:18
Alignment explanation
Indices: 675276--675319 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
675266 CCAGTGGTTC
*
675276 TTCGGGACGTAATGGTCT
1 TTCGGGACGTAATGGTCA
*
675294 TTCGGGACGTAGTGGTCA
1 TTCGGGACGTAATGGTCA
675312 TTCGGGAC
1 TTCGGGAC
675320 AAATATTCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.18, G:0.36, T:0.30
Consensus pattern (18 bp):
TTCGGGACGTAATGGTCA
Found at i:682598 original size:22 final size:22
Alignment explanation
Indices: 682570--682611 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
682560 GATAATTTTT
682570 AGCTCAGCAGTACTCGAGTTTG
1 AGCTCAGCAGTACTCGAGTTTG
682592 AGCTCAGCAGTACTCGAGTT
1 AGCTCAGCAGTACTCGAGTT
682612 CGACTCGGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (22 bp):
AGCTCAGCAGTACTCGAGTTTG
Found at i:683003 original size:31 final size:30
Alignment explanation
Indices: 682946--683034 Score: 81
Period size: 31 Copynumber: 3.0 Consensus size: 30
682936 TTTTTCATTT
* * **
682946 AAGTACTTAAAGTGT-TTTTTTATCAAAAC
1 AAGTACCTAAAGTATCTTTTTGGTCAAAAC
** *
682975 AAGTATTTAAAGTTATCTTTTTGGTCAAAAT
1 AAGTACCTAAAG-TATCTTTTTGGTCAAAAC
* *
683006 AGGTACCTAAAGTATTTTTTTGGTCAAAA
1 AAGTACCTAAAGTATCTTTTTGGTCAAAA
683035 TAGGTACTTA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
29 11 0.22
30 18 0.37
31 20 0.41
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (30 bp):
AAGTACCTAAAGTATCTTTTTGGTCAAAAC
Found at i:683028 original size:30 final size:31
Alignment explanation
Indices: 682982--683047 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 31
682972 AACAAGTATT
682982 TAAAGTTATCTTTTTGGTCAAAATAGGTACC
1 TAAAGTTATCTTTTTGGTCAAAATAGGTACC
* *
683013 TAAAG-TATTTTTTTGGTCAAAATAGGTACT
1 TAAAGTTATCTTTTTGGTCAAAATAGGTACC
683043 TAAAG
1 TAAAG
683048 AATCCAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 28 0.85
31 5 0.15
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (31 bp):
TAAAGTTATCTTTTTGGTCAAAATAGGTACC
Found at i:684055 original size:40 final size:40
Alignment explanation
Indices: 684000--684079 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
683990 TAGGTTAGTT
*
684000 TTTTTAGGAGAATTTCATAAACGATTTTACCATTTTAGGA
1 TTTTTAAGAGAATTTCATAAACGATTTTACCATTTTAGGA
* *
684040 TTTTTAAGATAATTTCATAAATGATTTTACCATTTTAGGA
1 TTTTTAAGAGAATTTCATAAACGATTTTACCATTTTAGGA
684080 GTCCAAAACC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (40 bp):
TTTTTAAGAGAATTTCATAAACGATTTTACCATTTTAGGA
Found at i:691817 original size:40 final size:39
Alignment explanation
Indices: 691755--691867 Score: 104
Period size: 42 Copynumber: 2.8 Consensus size: 39
691745 GAGTAGTACA
*
691755 ATAGCGGCGGTTTTT-TACAAACGCCGCAATAGGTGTATT
1 ATAGTGGC-GTTTTTATACAAACGCCGCAATAGGTGTATT
* **
691794 ATAGTGGCGTTTTTATAACAAACGTCGCAAAATATTTGTATT
1 ATAGTGGCGTTTTTAT-ACAAACGCCGC--AATAGGTGTATT
* * *
691836 TTAGTGGCGTTTGTATGA-AAACGCCGCTATAG
1 ATAGTGGCGTTTTTAT-ACAAACGCCGCAATAG
691868 ACTTCTACTT
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
38 6 0.10
39 11 0.18
40 10 0.17
41 8 0.13
42 25 0.42
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (39 bp):
ATAGTGGCGTTTTTATACAAACGCCGCAATAGGTGTATT
Found at i:691939 original size:41 final size:41
Alignment explanation
Indices: 691835--691929 Score: 156
Period size: 41 Copynumber: 2.3 Consensus size: 41
691825 ATATTTGTAT
691835 TTTAGTGGCGTTTGTATGAAAACGCCGCTATAGACTTC-TAC
1 TTTAGTGGCGTTTGTATGAAAACGCCGCTATAGAC-TCGTAC
*
691876 TTTAGTGGCGTTCGTATGAAAACGCCGCTATAGACTCGTAC
1 TTTAGTGGCGTTTGTATGAAAACGCCGCTATAGACTCGTAC
*
691917 TTTAGTAGCGTTT
1 TTTAGTGGCGTTT
691930 TTGTTAAAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
40 2 0.04
41 48 0.96
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (41 bp):
TTTAGTGGCGTTTGTATGAAAACGCCGCTATAGACTCGTAC
Found at i:699812 original size:21 final size:21
Alignment explanation
Indices: 699790--699865 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
699780 AGGGAAGTAG
* *
699790 AGAGAGCAGCAACGGAAGCAG
1 AGAGAGAAGCAACGGAAGCAC
* * *
699811 AGAAAGAAGCAGCGGCAGCAC
1 AGAGAGAAGCAACGGAAGCAC
* * *
699832 AGAGAGAAGTAGCGGCAGCAC
1 AGAGAGAAGCAACGGAAGCAC
699853 AGAGAGAAGCAAC
1 AGAGAGAAGCAAC
699866 ATATCAGAAG
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.43, C:0.20, G:0.36, T:0.01
Consensus pattern (21 bp):
AGAGAGAAGCAACGGAAGCAC
Found at i:700318 original size:43 final size:43
Alignment explanation
Indices: 700269--700377 Score: 114
Period size: 43 Copynumber: 2.5 Consensus size: 43
700259 CCAAACTTTA
700269 GCGGCGTTTT-AATAAAAAACGCCCCTAAAGCTCAACACC-TATT
1 GCGGCGTTTTCAAT-AAAAACGCCCCTAAAGCTCAAC-CCTTATT
* * **
700312 GCGGCGTTTTCAATAGAAACGCCGCTAATTCTCAACCCTTATT
1 GCGGCGTTTTCAATAAAAACGCCCCTAAAGCTCAACCCTTATT
* * * *
700355 GCGTCATTTTCGATACAAACGCC
1 GCGGCGTTTTCAATAAAAACGCC
700378 GCTTAATCTG
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
42 2 0.04
43 51 0.91
44 3 0.05
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (43 bp):
GCGGCGTTTTCAATAAAAACGCCCCTAAAGCTCAACCCTTATT
Found at i:700417 original size:86 final size:87
Alignment explanation
Indices: 700326--700529 Score: 229
Period size: 86 Copynumber: 2.4 Consensus size: 87
700316 CGTTTTCAAT
* * * ** * *
700326 AGAAACGCCGCTAATTC-TCAAC-CCTTATTGCGTC-ATTTTCGATACAAACGCCGCTTAATCTG
1 AGAAACGCCGCTAA-ACATCAACACC-TATTGCGGCGATTTTCGA-AAAAACGCCGCAAAATATC
700388 AAAACCTACTGCGACGTTTGT-GGG
63 AAAACCTACTGCGACGTTTGTAGGG
* * * *
700412 AGAAACGCCGCTAAACATCATCACCTATTGCGGCGTTTTTTGAAAAAACGCCGCAAAATATCAAC
1 AGAAACGCCGCTAAACATCAACACCTATTGCGGCGATTTTCGAAAAAACGCCGCAAAATATCAAA
*
700477 ACCTACTGCGGCGTTTGTAGGG
66 ACCTACTGCGACGTTTGTAGGG
*
700499 A-AAACGCCGCTAAACATCAAAACCTATTGCG
1 AGAAACGCCGCTAAACATCAACACCTATTGCG
700530 ACATTTTTGT
Statistics
Matches: 100, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
85 1 0.01
86 87 0.87
87 12 0.12
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (87 bp):
AGAAACGCCGCTAAACATCAACACCTATTGCGGCGATTTTCGAAAAAACGCCGCAAAATATCAAA
ACCTACTGCGACGTTTGTAGGG
Found at i:700418 original size:43 final size:42
Alignment explanation
Indices: 700371--700555 Score: 165
Period size: 43 Copynumber: 4.3 Consensus size: 42
700361 TTTTCGATAC
* *
700371 AAACGCCGCTTAATC-TGAAAACCTACTGCGACGTTTGTGGGA
1 AAACGCCGC-TAAACATCAAAACCTACTGCGACGTTTGTGGGA
** * * * **
700413 GAAACGCCGCTAAACATCATCACCTATTGCGGCGTTTTTTGAAA
1 -AAACGCCGCTAAACATCAAAACCTACTGCGACG-TTTGTGGGA
* * * *
700457 AAACGCCGCAAAATATCAACACCTACTGCGGCGTTTGTAGGGA
1 AAACGCCGCTAAACATCAAAACCTACTGCGACGTTTGT-GGGA
* * * *
700500 AAACGCCGCTAAACATCAAAACCTATTGCGACATTTTTGTGA
1 AAACGCCGCTAAACATCAAAACCTACTGCGACGTTTGTGGGA
700542 CAAACGCCGCTAAA
1 -AAACGCCGCTAAA
700556 TAACAAAGCT
Statistics
Matches: 114, Mismatches: 24, Indels: 8
0.78 0.16 0.05
Matches are distributed among these distances:
42 11 0.10
43 97 0.85
44 6 0.05
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.23
Consensus pattern (42 bp):
AAACGCCGCTAAACATCAAAACCTACTGCGACGTTTGTGGGA
Found at i:700537 original size:86 final size:85
Alignment explanation
Indices: 700389--700577 Score: 247
Period size: 86 Copynumber: 2.2 Consensus size: 85
700379 CTTAATCTGA
* ** * *
700389 AAACCTACTGCGACGTTTGTGGGAGAAACGCCGCTAAACATCATCACCTATTGCGGCGTTTTT-T
1 AAACCTACTGCGGCGTTTGTGGGAGAAACGCCGCTAAACATCAAAACCTATTGCGACATTTTTGT
*
700453 GAAAAAACGCCGCAAAATATC
66 G-AAAAACGCCGCAAAATAAC
700474 AACACCTACTGCGGCGTTTGTAGGGA-AAACGCCGCTAAACATCAAAACCTATTGCGACATTTTT
1 AA-ACCTACTGCGGCGTTTGT-GGGAGAAACGCCGCTAAACATCAAAACCTATTGCGACATTTTT
* *
700538 GTGACAAACGCCGCTAAATAAC
64 GTGAAAAACGCCGCAAAATAAC
* *
700560 AAAGCTATTGCGGCGTTT
1 AAACCTACTGCGGCGTTT
700578 TTTGTTAAAA
Statistics
Matches: 91, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
85 16 0.18
86 69 0.76
87 6 0.07
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (85 bp):
AAACCTACTGCGGCGTTTGTGGGAGAAACGCCGCTAAACATCAAAACCTATTGCGACATTTTTGT
GAAAAACGCCGCAAAATAAC
Found at i:700580 original size:43 final size:42
Alignment explanation
Indices: 700414--700587 Score: 170
Period size: 43 Copynumber: 4.1 Consensus size: 42
700404 TTTGTGGGAG
* * **
700414 AAACGCCGCTAAACATCATCACCTATTGCGGCGTTTTTTGAAA
1 AAACGCCGCTAAATATCA-AACCTATTGCGGCGTTTTTTGTGA
* * * * *
700457 AAACGCCGCAAAATATCAACACCTACTGCGGCGTTTGTAGGGA
1 AAACGCCGCTAAATATCAA-ACCTATTGCGGCGTTTTTTGTGA
* * *
700500 AAACGCCGCTAAACATCAAAACCTATTGCGAC-ATTTTTGTGA
1 AAACGCCGCTAAATATC-AAACCTATTGCGGCGTTTTTTGTGA
* * *
700542 CAAACGCCGCTAAATAACAAAGCTATTGCGGCGTTTTTTGTTA
1 -AAACGCCGCTAAATATCAAACCTATTGCGGCGTTTTTTGTGA
700585 AAA
1 AAA
700588 AATGCCGCTA
Statistics
Matches: 105, Mismatches: 22, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
42 21 0.20
43 82 0.78
44 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (42 bp):
AAACGCCGCTAAATATCAAACCTATTGCGGCGTTTTTTGTGA
Found at i:705475 original size:3 final size:3
Alignment explanation
Indices: 705463--705552 Score: 173
Period size: 3 Copynumber: 30.3 Consensus size: 3
705453 CTTACCTTAC
705463 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
705510 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
705553 CAAGGCCCGA
Statistics
Matches: 86, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 84 0.98
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:709888 original size:157 final size:158
Alignment explanation
Indices: 709602--709916 Score: 623
Period size: 157 Copynumber: 2.0 Consensus size: 158
709592 CCCAAATTAA
709602 GGGTTAGTGACTAAATTTTAAAATTTCAAAATTTGGGGATAAAATTATAATAGTTGAATAGTTTA
1 GGGTTAGTGACTAAATTTTAAAATTTCAAAATTTGGGGATAAAATTATAATAGTTGAATAGTTTA
709667 ATGATTTATGTGGAGATATTTCCTGAAAGTTGTTAGTAAATATTAAAGGAGTCAAAGGGCAAATG
66 ATGATTTATGTGGAGATATTTCCTGAAAGTTGTTAGTAAATATTAAAGGAGTCAAAGGGCAAATG
709732 AGTAATTAAACAATG-AAATAATTAAAT
131 AGTAATTAAACAATGAAAATAATTAAAT
709759 GGGTTAGTGACTAAATTTTAAAATTTCAAAATTTGGGGATAAAATTATAATAGTTGAATAGTTTA
1 GGGTTAGTGACTAAATTTTAAAATTTCAAAATTTGGGGATAAAATTATAATAGTTGAATAGTTTA
709824 ATGATTTATGTGGAGATATTTCCTGAAAGTTGTTAGTAAATATTAAAGGAGTCAAAGGGCAAATG
66 ATGATTTATGTGGAGATATTTCCTGAAAGTTGTTAGTAAATATTAAAGGAGTCAAAGGGCAAATG
709889 AGTAATTAAACAATGAAAATAATTAAAT
131 AGTAATTAAACAATGAAAATAATTAAAT
709917 AATAATTAAT
Statistics
Matches: 157, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
157 145 0.92
158 12 0.08
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.34
Consensus pattern (158 bp):
GGGTTAGTGACTAAATTTTAAAATTTCAAAATTTGGGGATAAAATTATAATAGTTGAATAGTTTA
ATGATTTATGTGGAGATATTTCCTGAAAGTTGTTAGTAAATATTAAAGGAGTCAAAGGGCAAATG
AGTAATTAAACAATGAAAATAATTAAAT
Found at i:711765 original size:31 final size:31
Alignment explanation
Indices: 711695--712007 Score: 280
Period size: 31 Copynumber: 10.0 Consensus size: 31
711685 GTCGAGGGTT
* * *
711695 TACCTATGTTCTACGGAACATATTGACAGAA
1 TACCTATGTTCTTCGGAACATATGGACAGTA
*
711726 TTACCTATG-TCTTTCGGGACATATGGACAGTA
1 -TACCTATGTTC-TTCGGAACATATGGACAGTA
* * *
711758 TACCTATGTTCTACAGAACATATGGACAGAA
1 TACCTATGTTCTTCGGAACATATGGACAGTA
* *
711789 TTACCTATG-TCTTTCGGGACATATGAACAGTA
1 -TACCTATGTTC-TTCGGAACATATGGACAGTA
* *
711821 TACCTATGTTCTACGGAACATATGGACAGAA
1 TACCTATGTTCTTCGGAACATATGGACAGTA
711852 TTACCTATG-TCTTTCAGG-ACATATGGACAGTA
1 -TACCTATGTTC-TTC-GGAACATATGGACAGTA
* *
711884 TACCTATGTTCTAT-AGAACATATGGATA-TAA
1 TACCTATGTTCT-TCGGAACATATGGACAGT-A
* *
711915 TTACCTATG-TCTTTCGGGACATATGGATAGTA
1 -TACCTATGTTC-TTCGGAACATATGGACAGTA
** * *
711947 TACCTATGTTCTAAGGAACATATGGACATTT
1 TACCTATGTTCTTCGGAACATATGGACAGTA
* * *
711978 TACCTAGGTTCTTCGGGACCTATGGACAGT
1 TACCTATGTTCTTCGGAACATATGGACAGT
712008 TGCCGAGGTT
Statistics
Matches: 229, Mismatches: 35, Indels: 35
0.77 0.12 0.12
Matches are distributed among these distances:
30 2 0.01
31 123 0.54
32 101 0.44
33 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (31 bp):
TACCTATGTTCTTCGGAACATATGGACAGTA
Found at i:711794 original size:63 final size:63
Alignment explanation
Indices: 711695--712007 Score: 470
Period size: 63 Copynumber: 5.0 Consensus size: 63
711685 GTCGAGGGTT
* *
711695 TACCTATGTTCTACGGAACATATTGACAGAATTACCTATGTCTTTCGGGACATATGGACAGTA
1 TACCTATGTTCTACAGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGACAGTA
*
711758 TACCTATGTTCTACAGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGAACAGTA
1 TACCTATGTTCTACAGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGACAGTA
* *
711821 TACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCAGGACATATGGACAGTA
1 TACCTATGTTCTACAGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGACAGTA
* * * *
711884 TACCTATGTTCTATAGAACATATGGATATAATTACCTATGTCTTTCGGGACATATGGATAGTA
1 TACCTATGTTCTACAGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGACAGTA
** * *
711947 TACCTATGTTCTA-AGGAACATATGGACA-TTTTACCTAGGT-TCTTCGGGACCTATGGACAGT
1 TACCTATGTTCTACA-GAACATATGGACAGAATTACCTATGTCT-TTCGGGACATATGGACAGT
712008 TGCCGAGGTT
Statistics
Matches: 230, Mismatches: 18, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
61 1 0.00
62 27 0.12
63 202 0.88
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (63 bp):
TACCTATGTTCTACAGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGACAGTA
Found at i:722552 original size:34 final size:33
Alignment explanation
Indices: 722510--722580 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 33
722500 AATAGTAATA
*
722510 AACAAAATTAAGCAAAATAAATTAACAA-AAAGTCC
1 AACAAATTTAA-CAAAATAAATTAA-AATAAA-TCC
722545 AACAAATTTAACAAAATAAATTAAAATAAATCC
1 AACAAATTTAACAAAATAAATTAAAATAAATCC
722578 AAC
1 AAC
722581 CATATTAACG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
33 8 0.24
34 16 0.47
35 10 0.29
ACGTcount: A:0.63, C:0.14, G:0.03, T:0.20
Consensus pattern (33 bp):
AACAAATTTAACAAAATAAATTAAAATAAATCC
Found at i:722676 original size:14 final size:13
Alignment explanation
Indices: 722630--722666 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
722620 TAAAATAAAT
*
722630 TACAATAAAAAAG
1 TACAATAAAAAAC
*
722643 TCCAATAAAAAAC
1 TACAATAAAAAAC
722656 TACAATAAAAA
1 TACAATAAAAA
722667 GTACTAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.68, C:0.14, G:0.03, T:0.16
Consensus pattern (13 bp):
TACAATAAAAAAC
Found at i:722952 original size:9 final size:9
Alignment explanation
Indices: 722938--722962 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
722928 ACCGGCCTGT
722938 GAAAACTGG
1 GAAAACTGG
722947 GAAAACTGG
1 GAAAACTGG
722956 GAAAACT
1 GAAAACT
722963 AATAAAACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.12, G:0.28, T:0.12
Consensus pattern (9 bp):
GAAAACTGG
Found at i:724855 original size:21 final size:20
Alignment explanation
Indices: 724825--724885 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
724815 TCTGCAAAAA
724825 AAAT-AATTAAGTAAAATATT
1 AAATAAATTAA-TAAAATATT
724845 AAATAAATTAAATACAAAATATT
1 AAATAAATT-AAT--AAAATATT
724868 -AA-AAATATAATAAAATAT
1 AAATAAAT-TAATAAAATAT
724886 ACCTTAGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
19 7 0.19
20 4 0.11
21 12 0.33
22 5 0.14
23 8 0.22
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (20 bp):
AAATAAATTAATAAAATATT
Found at i:724918 original size:10 final size:10
Alignment explanation
Indices: 724905--724934 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
724895 AGAGATTATA
*
724905 AGAGTATTTG
1 AGAGAATTTG
724915 AGAGAATTTG
1 AGAGAATTTG
724925 AGAGAATTTG
1 AGAGAATTTG
724935 GTGTGATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.30, T:0.33
Consensus pattern (10 bp):
AGAGAATTTG
Found at i:725873 original size:19 final size:19
Alignment explanation
Indices: 725845--725885 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
725835 TTAATTATTT
*
725845 TTACAATATATTTAAATAA
1 TTACAATATATTAAAATAA
* *
725864 TTACAGTATATTAAAATTA
1 TTACAATATATTAAAATAA
725883 TTA
1 TTA
725886 TATCTAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (19 bp):
TTACAATATATTAAAATAA
Found at i:734210 original size:20 final size:20
Alignment explanation
Indices: 734185--734225 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
734175 GTATCGTGTT
* *
734185 ACAAATTGATGATGTTAGTG
1 ACAAATCGATAATGTTAGTG
734205 ACAAATCGATAATGTTAGTG
1 ACAAATCGATAATGTTAGTG
734225 A
1 A
734226 GTAATTTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (20 bp):
ACAAATCGATAATGTTAGTG
Found at i:735253 original size:18 final size:18
Alignment explanation
Indices: 735230--735271 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
735220 TAAAAGTTAA
735230 AATAATCTAATAAAATAG
1 AATAATCTAATAAAATAG
735248 AATAATCTAATAAAATAG
1 AATAATCTAATAAAATAG
735266 AATAAT
1 AATAAT
735272 AATCAAAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (18 bp):
AATAATCTAATAAAATAG
Found at i:735523 original size:6 final size:6
Alignment explanation
Indices: 735512--735573 Score: 124
Period size: 6 Copynumber: 10.3 Consensus size: 6
735502 GACACGTATT
735512 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
735560 ACCACG ACCACG AC
1 ACCACG ACCACG AC
735574 GGCGGCGGCG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.34, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:740039 original size:21 final size:21
Alignment explanation
Indices: 740015--740054 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
740005 ACCAAAATCT
**
740015 TTATTTAAGTACAAAGCAACC
1 TTATTTAAACACAAAGCAACC
740036 TTATTTAAACACAAAGCAA
1 TTATTTAAACACAAAGCAA
740055 ATTTTTTGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.28
Consensus pattern (21 bp):
TTATTTAAACACAAAGCAACC
Found at i:757700 original size:24 final size:24
Alignment explanation
Indices: 757599--757707 Score: 94
Period size: 24 Copynumber: 4.5 Consensus size: 24
757589 GAATATTTTA
* *
757599 TCTGATTTCTGATTTGAATTCTGT
1 TCTGATATCTGATCTGAATTCTGT
* * *
757623 TTTGACATCTGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTCTGT
* * *
757647 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTCTGT
* *
757671 TCTGATATCTGATTTGAATTATGT
1 TCTGATATCTGATCTGAATTCTGT
* *
757695 TTTGATTTCTGAT
1 TCTGATATCTGAT
757708 ATCTCCGTTT
Statistics
Matches: 65, Mismatches: 18, Indels: 4
0.75 0.21 0.05
Matches are distributed among these distances:
23 1 0.02
24 63 0.97
25 1 0.02
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.49
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTCTGT
Found at i:760769 original size:17 final size:17
Alignment explanation
Indices: 760727--760761 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
760717 CCAGTAGCAT
760727 GGTCGGTTCGCTAACCG
1 GGTCGGTTCGCTAACCG
760744 GGTCGGTTCGCTAACCG
1 GGTCGGTTCGCTAACCG
760761 G
1 G
760762 TCCGGTTCTT
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:0.11, C:0.29, G:0.37, T:0.23
Consensus pattern (17 bp):
GGTCGGTTCGCTAACCG
Found at i:768512 original size:24 final size:24
Alignment explanation
Indices: 768416--768524 Score: 85
Period size: 24 Copynumber: 4.5 Consensus size: 24
768406 GAATATTTTA
* * *
768416 TCTGATTTCTGATTTGAATTCTGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
768440 TTTGACATATGATCTGAAATATGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
768464 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTATGT
768488 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* *
768512 TTTGATTTCTGAT
1 TCTGATATCTGAT
768525 ATCTCCGTTT
Statistics
Matches: 62, Mismatches: 21, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
23 1 0.02
24 60 0.97
25 1 0.02
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTATGT
Found at i:772615 original size:3 final size:3
Alignment explanation
Indices: 772607--772639 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
772597 TAAATGACAT
*
772607 TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
772640 ATTCCTAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:773268 original size:20 final size:20
Alignment explanation
Indices: 773243--773289 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
773233 ATTGTCACGT
773243 TAGCACCATAAACTGTCACA
1 TAGCACCATAAACTGTCACA
773263 TAGCACCATAAACTGTCACA
1 TAGCACCATAAACTGTCACA
773283 TAGCACC
1 TAGCACC
773290 CTAACGGTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.32, G:0.11, T:0.19
Consensus pattern (20 bp):
TAGCACCATAAACTGTCACA
Found at i:777529 original size:10 final size:10
Alignment explanation
Indices: 777514--777604 Score: 65
Period size: 10 Copynumber: 8.1 Consensus size: 10
777504 CATTTAAATG
777514 ATAAACGAAC
1 ATAAACGAAC
777524 ATAAACGAAC
1 ATAAACGAAC
*
777534 GTAAACGAACGAAC
1 --ATA--AACGAAC
777548 ATAAACGAAC
1 ATAAACGAAC
*
777558 ATAATAAATGAAC
1 ---ATAAACGAAC
777571 ATAAACGAACAC
1 ATAAACG-A-AC
*
777583 AATAAATGAAC
1 -ATAAACGAAC
777594 ATAAACGAAC
1 ATAAACGAAC
777604 A
1 A
777605 ACACAAACAC
Statistics
Matches: 65, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
10 33 0.51
11 3 0.05
12 7 0.11
13 15 0.23
14 7 0.11
ACGTcount: A:0.59, C:0.18, G:0.11, T:0.12
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:777544 original size:14 final size:14
Alignment explanation
Indices: 777517--777557 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
777507 TTAAATGATA
777517 AACGAACATAAACG
1 AACGAACATAAACG
777531 AACG----TAAACG
1 AACGAACATAAACG
777541 AACGAACATAAACG
1 AACGAACATAAACG
777555 AAC
1 AAC
777558 ATAATAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
10 10 0.43
14 13 0.57
ACGTcount: A:0.56, C:0.22, G:0.15, T:0.07
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:777570 original size:13 final size:13
Alignment explanation
Indices: 777535--777597 Score: 53
Period size: 13 Copynumber: 5.0 Consensus size: 13
777525 TAAACGAACG
777535 TAAACGAACGA-ACA
1 TAAACGAAC-ATA-A
777549 TAAACGAACATAA
1 TAAACGAACATAA
*
777562 TAAATGAAC---A
1 TAAACGAACATAA
*
777572 TAAACGAACACAA
1 TAAACGAACATAA
*
777585 TAAATGAACATAA
1 TAAACGAACATAA
777598 ACGAACAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
10 9 0.22
13 22 0.54
14 10 0.24
ACGTcount: A:0.60, C:0.16, G:0.10, T:0.14
Consensus pattern (13 bp):
TAAACGAACATAA
Found at i:777574 original size:23 final size:23
Alignment explanation
Indices: 777514--777604 Score: 121
Period size: 23 Copynumber: 3.9 Consensus size: 23
777504 CATTTAAATG
*
777514 ATAAACGAACATAAACGAACGTA
1 ATAAACGAACATAAACGAACATA
777537 A-ACGAACGAACATAAACGAACATA
1 ATA--AACGAACATAAACGAACATA
* *
777561 ATAAATGAACATAAACGAACACA
1 ATAAACGAACATAAACGAACATA
*
777584 ATAAATGAACATAAACGAACA
1 ATAAACGAACATAAACGAACA
777605 ACACAAACAC
Statistics
Matches: 62, Mismatches: 3, Indels: 6
0.87 0.04 0.08
Matches are distributed among these distances:
22 1 0.02
23 40 0.65
24 20 0.32
25 1 0.02
ACGTcount: A:0.59, C:0.18, G:0.11, T:0.12
Consensus pattern (23 bp):
ATAAACGAACATAAACGAACATA
Found at i:777936 original size:43 final size:39
Alignment explanation
Indices: 777884--777979 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 39
777874 TTCATGAACG
777884 TAAATGAACGAACAAGCCCTTTGTTCATGTTCGTTCATTTAA
1 TAAATGAACGAACAA--CC-TTGTTCATGTTCGTTCATTTAA
* *
777926 TTAAACGAACGCAA-AATCTTGTTCATGTTCGTTCATTTAA
1 -TAAATGAACG-AACAACCTTGTTCATGTTCGTTCATTTAA
*
777966 TAAATAAACGAACA
1 TAAATGAACGAACA
777980 TAAACAAACT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
38 2 0.04
39 9 0.19
40 22 0.47
41 1 0.02
43 11 0.23
44 2 0.04
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33
Consensus pattern (39 bp):
TAAATGAACGAACAACCTTGTTCATGTTCGTTCATTTAA
Found at i:779121 original size:18 final size:19
Alignment explanation
Indices: 779086--779122 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
779076 CACGGAATGT
779086 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
779106 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
779123 TGATTATTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:780920 original size:2 final size:2
Alignment explanation
Indices: 780913--781051 Score: 190
Period size: 2 Copynumber: 70.0 Consensus size: 2
780903 TTTTCGTGAG
*
780913 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G- GG GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * *
780954 GA GA GA GA GA GA GA GA GG GA GA GA GA GA GG GA GA GA GA GC GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * *
780996 GA GA GA GA GA GA GG GA GA GA GA GA GA GA GA GA GG GA GG GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* *
781038 GG GA GG GA GA GA GA
1 GA GA GA GA GA GA GA
781052 AGTTGCGACT
Statistics
Matches: 119, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
1 1 0.01
2 118 0.99
ACGTcount: A:0.43, C:0.01, G:0.56, T:0.00
Consensus pattern (2 bp):
GA
Found at i:786012 original size:24 final size:24
Alignment explanation
Indices: 785985--786036 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
785975 AACGGATAAA
*
785985 TCAAAAATCAAAACATAATCCAGG
1 TCAAAAATCAAAACAAAATCCAGG
* * * *
786009 TCAAATATGAGATCAAAATCCAGG
1 TCAAAAATCAAAACAAAATCCAGG
786033 TCAA
1 TCAA
786037 GTATTAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.19, G:0.12, T:0.19
Consensus pattern (24 bp):
TCAAAAATCAAAACAAAATCCAGG
Found at i:786045 original size:24 final size:24
Alignment explanation
Indices: 786001--786118 Score: 114
Period size: 24 Copynumber: 5.0 Consensus size: 24
785991 ATCAAAACAT
* *
786001 AATCCAGGTCAAATATGAGATCAA
1 AATCCAGGTCAAGTATCAGATCAA
* *
786025 AATCCAGGTCAAGTATTAGATCAG
1 AATCCAGGTCAAGTATCAGATCAA
* * * *
786049 AATCCAAGTCAAATATCATATCAG
1 AATCCAGGTCAAGTATCAGATCAA
*
786073 AATCCATGTC-AGATATCAGATC-A
1 AATCCAGGTCAAG-TATCAGATCAA
* *
786096 AATCCATGTCAAGTATCATATCA
1 AATCCAGGTCAAGTATCAGATCA
786119 GAATTCAAAT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
23 19 0.24
24 60 0.76
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCAGATCAA
Found at i:786077 original size:48 final size:47
Alignment explanation
Indices: 786001--786122 Score: 147
Period size: 48 Copynumber: 2.6 Consensus size: 47
785991 ATCAAAACAT
* * * * *
786001 AATCCAGGTCAAATATGAGATCAAAATCCAGGTCA-AGTATTAGATCA
1 AATCCAAGTCAAATATCATATCAGAATCCAGGTCAGA-TATCAGATCA
*
786048 GAATCCAAGTCAAATATCATATCAGAATCCATGTCAGATATCAGATCA
1 -AATCCAAGTCAAATATCATATCAGAATCCAGGTCAGATATCAGATCA
* *
786096 AATCCATGTCAAGTATCATATCAGAAT
1 AATCCAAGTCAAATATCATATCAGAAT
786123 TCAAATTGAA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
47 25 0.38
48 39 0.60
49 1 0.02
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (47 bp):
AATCCAAGTCAAATATCATATCAGAATCCAGGTCAGATATCAGATCA
Found at i:791781 original size:4 final size:4
Alignment explanation
Indices: 791772--791796 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
791762 CGTACGATAG
791772 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
791797 TGTGACTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:794404 original size:2 final size:2
Alignment explanation
Indices: 794397--794421 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
794387 TGTATGTATG
794397 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
794422 GATGAATGAT
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:798470 original size:16 final size:16
Alignment explanation
Indices: 798449--798483 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
798439 AGGAGTCTTA
*
798449 GATTATTCTTTGGTTT
1 GATTATTCTTTGATTT
798465 GATTATTCTTTGATTT
1 GATTATTCTTTGATTT
798481 GAT
1 GAT
798484 ATGAATTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.06, G:0.17, T:0.60
Consensus pattern (16 bp):
GATTATTCTTTGATTT
Found at i:802889 original size:4 final size:4
Alignment explanation
Indices: 802880--802906 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
802870 GTAATTGCAA
802880 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
802907 GTCCAATACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:803238 original size:108 final size:105
Alignment explanation
Indices: 803034--803239 Score: 243
Period size: 108 Copynumber: 1.9 Consensus size: 105
803024 AATAAATTAC
* *
803034 TTGGATTCAGGTGTGTCTAACATGGGTATGCGTCCAACACAAGCATATACAATTTTTTCGAAGAT
1 TTGGACTCAGGTGTGTCTAACATGGGTATGCGTCCAACACAAG-ATATACAATTTTTTCCAAGAT
* * * * * * *
803099 TTCCATGTATTCGGATAGTCCTTGGAGGTTGGATACGGATG
65 TCCCATATACTCGAAGAGACCTTGGAAGTTGGATACGGATG
* * *
803140 TTGGACTCAGGTGTATGTCTAACATGGGTATGTGTCCAACAC-AGATGTGTTCAATTTTTTCCAA
1 TTGGACTCAGGTG--TGTCTAACATGGGTATGCGTCCAACACAAGA--TATACAATTTTTTCCAA
*
803204 GATTCCCATATACTCTAAGAGACCTTGGAAGTTGGA
62 GATTCCCATATACTCGAAGAGACCTTGGAAGTTGGA
803240 CACAGGTGTC
Statistics
Matches: 83, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
106 13 0.16
107 2 0.02
108 68 0.82
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (105 bp):
TTGGACTCAGGTGTGTCTAACATGGGTATGCGTCCAACACAAGATATACAATTTTTTCCAAGATT
CCCATATACTCGAAGAGACCTTGGAAGTTGGATACGGATG
Found at i:812975 original size:7 final size:7
Alignment explanation
Indices: 812963--812989 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
812953 TTCTGTCAAA
812963 AAAAAAT
1 AAAAAAT
812970 AAAAAAT
1 AAAAAAT
812977 AAAAAAT
1 AAAAAAT
812984 AAAAAA
1 AAAAAA
812990 GAAGAAGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:815708 original size:2 final size:2
Alignment explanation
Indices: 815701--815750 Score: 91
Period size: 2 Copynumber: 24.5 Consensus size: 2
815691 GCATATTCGA
815701 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
815743 AT AGT AT A
1 AT A-T AT A
815751 ATTCTTTGAA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 45 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:816615 original size:29 final size:28
Alignment explanation
Indices: 816562--816622 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 28
816552 TATTGATGGG
*
816562 TTTAATATTTAAATTAAACTCATATTCCT
1 TTTAATATTCAAATTAAACTCATATT-CT
816591 TTTAATATTGCAAATTAAGA-T-ATATTCT
1 TTTAATATT-CAAATTAA-ACTCATATTCT
816619 TTTA
1 TTTA
816623 TTTGAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 6 0.21
29 14 0.48
30 8 0.28
31 1 0.03
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (28 bp):
TTTAATATTCAAATTAAACTCATATTCT
Found at i:820086 original size:63 final size:67
Alignment explanation
Indices: 820005--820161 Score: 168
Period size: 63 Copynumber: 2.4 Consensus size: 67
819995 AGGTATTTAT
* *
820005 TATCTATTTAACA-TTGAATATTAAAAGAT-AA-TTATATAC-TTTGAATATTTCAAATT-AAA-
1 TATCTATTTAA-ATTTGAATATTAAAAAATGAATTTAAAT-CTTTTGAATATTTCAAATTAAAAG
820064 ATAA
64 ATAA
* *
820068 TATCTATTTAAATTTGAATA--AAAAAATGAGTTTAAATCTTTTGGATATTTCAAATTAAAAGAT
1 TATCTATTTAAATTTGAATATTAAAAAATGAATTTAAATCTTTTGAATATTTCAAATTAAAAGAT
820131 AA
66 AA
*
820133 TATTATATGTTTAAATTTGAATATTAAAA
1 TA-TCTA--TTTAAATTTGAATATTAAAA
820162 CATATTTAGT
Statistics
Matches: 78, Mismatches: 5, Indels: 15
0.80 0.05 0.15
Matches are distributed among these distances:
61 6 0.08
62 3 0.04
63 39 0.50
64 3 0.04
65 6 0.08
66 3 0.04
68 14 0.18
70 4 0.05
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.42
Consensus pattern (67 bp):
TATCTATTTAAATTTGAATATTAAAAAATGAATTTAAATCTTTTGAATATTTCAAATTAAAAGAT
AA
Found at i:825745 original size:14 final size:14
Alignment explanation
Indices: 825726--825756 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
825716 TATTTGAAAG
825726 ATAATTTATCGAAT
1 ATAATTTATCGAAT
825740 ATAATTTATCGAAT
1 ATAATTTATCGAAT
825754 ATA
1 ATA
825757 TCAATGTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (14 bp):
ATAATTTATCGAAT
Found at i:829860 original size:18 final size:18
Alignment explanation
Indices: 829834--829884 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
829824 GGATTATCAA
*
829834 TGGTCCTTCGGGACATAG
1 TGGTCCTTCAGGACATAG
*
829852 TGGTTCTTCAGGACATAG
1 TGGTCCTTCAGGACATAG
829870 TGGTCCTTCAGGACA
1 TGGTCCTTCAGGACA
829885 AATATTCAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (18 bp):
TGGTCCTTCAGGACATAG
Found at i:833766 original size:88 final size:81
Alignment explanation
Indices: 833612--833784 Score: 267
Period size: 80 Copynumber: 2.0 Consensus size: 81
833602 GCAATAGATA
833612 TTTTGTATTACTGTGAATATTACAAGGCTTAAATAAAAGTACCTAAATTTATGCTTTCACGAATA
1 TTTTGTATTACTGTGAATATTACAAGGCTTAAATAAAAGTACCTAAATTTATGCTTTCACGAATA
833677 GGTTTCTAAAGT-TTT
66 GGTTTCTAAAGTATTT
833692 TTTTGTATTACTGTGAATATTACAAGGCTTAAATATAAAATAAGTACCTAAATTGTATTGCTTTT
1 TTTTGTATTACTGTGAATATTACAAGGCTT-AA-AT--AA-AAGTACCTAAATT-TA-TGC-TTT
833757 CACGAATAGGTTTCTAAAGTATTT
58 CACGAATAGGTTTCTAAAGTATTT
833781 TTTT
1 TTTT
833785 AATTTATCCT
Statistics
Matches: 84, Mismatches: 0, Indels: 9
0.90 0.00 0.10
Matches are distributed among these distances:
80 30 0.36
81 2 0.02
82 2 0.02
84 2 0.02
85 13 0.15
86 2 0.02
87 3 0.04
88 23 0.27
89 7 0.08
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (81 bp):
TTTTGTATTACTGTGAATATTACAAGGCTTAAATAAAAGTACCTAAATTTATGCTTTCACGAATA
GGTTTCTAAAGTATTT
Found at i:835828 original size:14 final size:14
Alignment explanation
Indices: 835809--835839 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
835799 GATATAATTA
835809 AAGTTGGCTAAAAT
1 AAGTTGGCTAAAAT
835823 AAGTTGGCTAAAAT
1 AAGTTGGCTAAAAT
835837 AAG
1 AAG
835840 ATAGTCCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.06, G:0.23, T:0.26
Consensus pattern (14 bp):
AAGTTGGCTAAAAT
Found at i:839418 original size:16 final size:16
Alignment explanation
Indices: 839397--839427 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
839387 ATACCCGACT
*
839397 CATACCCGATCCAAAC
1 CATACCCGACCCAAAC
839413 CATACCCGACCCAAA
1 CATACCCGACCCAAA
839428 ATTTAGCGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.45, G:0.06, T:0.10
Consensus pattern (16 bp):
CATACCCGACCCAAAC
Found at i:839588 original size:18 final size:18
Alignment explanation
Indices: 839565--839617 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
839555 AATAATAAAT
839565 TAATTTAAATAAAAATGA
1 TAATTTAAATAAAAATGA
* *
839583 TAATTT-ATTAAAAATGT
1 TAATTTAAATAAAAATGA
839600 TAGATTTATAATAAAAAT
1 TA-ATTTA-AATAAAAAT
839618 AATAGGAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 11 0.38
18 10 0.34
20 8 0.28
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.40
Consensus pattern (18 bp):
TAATTTAAATAAAAATGA
Found at i:839594 original size:17 final size:18
Alignment explanation
Indices: 839574--839622 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
839564 TTAATTTAAA
839574 TAAAAATGATA-ATTTAT
1 TAAAAATGATAGATTTAT
*
839591 TAAAAATGTTAGATTTAT
1 TAAAAATGATAGATTTAT
*
839609 AATAAAAATAATAG
1 --TAAAAATGATAG
839623 GAAGTTTACT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 10 0.38
18 6 0.23
20 10 0.38
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (18 bp):
TAAAAATGATAGATTTAT
Found at i:845214 original size:146 final size:146
Alignment explanation
Indices: 844969--845487 Score: 792
Period size: 146 Copynumber: 3.6 Consensus size: 146
844959 CAGGATCTCC
*
844969 GATCAATATTCTGAACAGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGG
1 GATCAATATTCCGAACAGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGG
845034 ACGATCAGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGCGGTTTTTAGCCTCTTGCC
66 ACGATCAGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGCGGTTTTTAGCCTCTTGCC
*
845099 GGTGATCGGAATATTT
131 GGTGATCGGAATCTTT
845115 GATCAATATTCCGAAC-GATCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAG
1 GATCAATATTCCGAACAG-TCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAG
* *
845179 GACGATCAGACGGTGGAAGGTGACGGATCGGAGAAAACAAATCCGGGCAGTTTTTAGCCTCTTGC
65 GACGATCAGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGCGGTTTTTAGCCTCTTGC
* *
845244 CGGTTATCAGAATCTTT
130 CGGTGATCGGAATCTTT
* *
845261 GATCAATATTTCAAACAGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGG
1 GATCAATATTCCGAACAGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGG
* * * *
845326 ACGATCGGACGGTGGACGGTGATGGATCGGAGAAAATAAATCCGGACGGTTTTTAGCCTCTTGCC
66 ACGATCAGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGCGGTTTTTAGCCTCTTGCC
**
845391 GGTGATCGGAATCTGC
131 GGTGATCGGAATCTTT
* * * * *
845407 GATCAATATTCCGAACGGTGAAAAGTTGCGCGATA--CCAACACAAACAACCTATTGAAAAATCA
1 GATCAATATTCCGAACAGTCAAAAGTTGCG-GA-AGGCCATCACGAACAACATATTGAAAAATCA
* * *
845470 GGTCAATCGGACGGTGGA
64 GGACGATCAGACGGTGGA
845488 TGACGGCAGA
Statistics
Matches: 342, Mismatches: 27, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
145 1 0.00
146 337 0.99
147 3 0.01
148 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (146 bp):
GATCAATATTCCGAACAGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGG
ACGATCAGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGCGGTTTTTAGCCTCTTGCC
GGTGATCGGAATCTTT
Found at i:847905 original size:46 final size:47
Alignment explanation
Indices: 847799--847917 Score: 186
Period size: 47 Copynumber: 2.6 Consensus size: 47
847789 AAATGTATGT
*
847799 GAACTAGAAATCATGCGGTTAGGTATATTTTCTCGAACAAAGCATGC
1 GAACTAGAAATCATGCGGTTAGGTTTATTTTCTCGAACAAAGCATGC
*
847846 GAACTAGAAATCATGCGGTTATGTTTATTTTCTCGAAC-AAGCATGC
1 GAACTAGAAATCATGCGGTTAGGTTTATTTTCTCGAACAAAGCATGC
* * *
847892 GAATTAGATATCATGCGATTAGGTTT
1 GAACTAGAAATCATGCGGTTAGGTTT
847918 TCTTTTTGTG
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
46 30 0.45
47 36 0.55
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (47 bp):
GAACTAGAAATCATGCGGTTAGGTTTATTTTCTCGAACAAAGCATGC
Found at i:848678 original size:6 final size:6
Alignment explanation
Indices: 848667--848709 Score: 70
Period size: 6 Copynumber: 7.2 Consensus size: 6
848657 ATTAACACCT
848667 TTTGCA TTTGCA TTTGGCA TTTGCA TTTGCA TTTGCA -TTGCA T
1 TTTGCA TTTGCA TTT-GCA TTTGCA TTTGCA TTTGCA TTTGCA T
848710 GTATTTGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.14
6 24 0.69
7 6 0.17
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.49
Consensus pattern (6 bp):
TTTGCA
Found at i:848691 original size:19 final size:18
Alignment explanation
Indices: 848667--848709 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 18
848657 ATTAACACCT
848667 TTTGCATTTGCATTTGGCA
1 TTTGCATTTGCATTT-GCA
848686 TTTGCATTTGCATTTGCA
1 TTTGCATTTGCATTTGCA
848704 -TTGCAT
1 TTTGCAT
848710 GTATTTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 6 0.25
18 3 0.12
19 15 0.62
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.49
Consensus pattern (18 bp):
TTTGCATTTGCATTTGCA
Found at i:852556 original size:125 final size:125
Alignment explanation
Indices: 852330--852558 Score: 293
Period size: 125 Copynumber: 1.8 Consensus size: 125
852320 TAGGATATGT
*
852330 TGGGGCACGACTGAACCCCTATCATGTTGAGATGACAAAACCCAGACCAAAGAGGCATGAAGAAC
1 TGGGGCACGACTGAACCCCTATCATGTTGAGATGACAAAACCAAGACCAAAGAGGCATGAAGAAC
852395 GAGCCTTACAAATAGAGGTGATGGGGCATTTCGAAGGCCTGCACCAGTATGAGATGATGA
66 GAGCCTTACAAATAGAGGTGATGGGGCATTTCGAAGGCCTGCACCAGTATGAGATGATGA
* ** * **
852455 TGGGGTACGACTGAACCCAC-ATCATGTTGAGATGATGAGATTAAGACC-AAGAAGGCATTG-AG
1 TGGGGCACGACTGAACCC-CTATCATGTTGAGATGACAAAACCAAGACCAAAG-AGGCA-TGAAG
* * * * * *
852517 AATGAGCCTTACAATTTGAGGTGTTGGGGCGTTTTGAAGGCC
63 AACGAGCCTTACAAATAGAGGTGATGGGGCATTTCGAAGGCC
852559 CATATCAGTA
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
124 3 0.03
125 82 0.93
126 3 0.03
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.21
Consensus pattern (125 bp):
TGGGGCACGACTGAACCCCTATCATGTTGAGATGACAAAACCAAGACCAAAGAGGCATGAAGAAC
GAGCCTTACAAATAGAGGTGATGGGGCATTTCGAAGGCCTGCACCAGTATGAGATGATGA
Found at i:853799 original size:36 final size:36
Alignment explanation
Indices: 853757--853878 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 36
853747 AGCAAAGTCA
853757 ATCTTAAGCCTTCACTAAAGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACTAAAGAGTAGTGAAGCAAACC
* * * * * *
853793 GTCTTAAGCATGCACCAAAGAATAATGAAGCAAACC
1 ATCTTAAGCCTTCACTAAAGAGTAGTGAAGCAAACC
** * * *
853829 ATCTTGTGTCTTCA-TCAAAGAGTCGTGAAGGAAATCC
1 ATCTTAAGCCTTCACT-AAAGAGTAGTGAAGCAAA-CC
*
853866 ATTTTAAGCCTTC
1 ATCTTAAGCCTTC
853879 TCATAAGAGT
Statistics
Matches: 63, Mismatches: 21, Indels: 3
0.72 0.24 0.03
Matches are distributed among these distances:
36 52 0.83
37 11 0.17
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (36 bp):
ATCTTAAGCCTTCACTAAAGAGTAGTGAAGCAAACC
Found at i:854386 original size:54 final size:54
Alignment explanation
Indices: 854248--854885 Score: 853
Period size: 54 Copynumber: 11.9 Consensus size: 54
854238 AGTGAAGCAA
* * * *
854248 AAGAAGATTTTCGAGTTCCATACTCCCTAGAGAAAAAGAGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* * *
854302 AAG-A-TTGTTCGAGTTTCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
*
854354 AAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
*
854408 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAATCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
854462 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* * * *
854516 AAGAAGATTTTCGAGTTCCATACTTCCTAGAGAAAGAGGGAGCGAACCCATTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
*
854570 AAGAAGATATCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* * * *
854624 AAGAAGATTTCTGAGTTCCATACTTCCTAGAGAAAGAGGGAGTGAACCCG--TG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* * * * * * *
854676 -TGAAGATATCAGAGTTCCATACTCCTTAAAGAAAGAAGGATCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
**
854729 AAG-AGATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* * * *
854782 AAGAAGATTTTCGAGTTCCATACTTCCTAGAGAAAGAGGGAGTGAACCCCG--T-
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAA-CCCGTTTG
* * * * * *
854834 AAGAAGATTATTCGAGTTCTATACTGCCTGAAAGAAAGAGGGAGCGGACCCG
1 AAGAAGA-TGTCCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCG
854886 ATTGTTGAAG
Statistics
Matches: 524, Mismatches: 51, Indels: 19
0.88 0.09 0.03
Matches are distributed among these distances:
51 40 0.08
52 55 0.10
53 73 0.14
54 352 0.67
55 4 0.01
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.22
Consensus pattern (54 bp):
AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
Found at i:855005 original size:55 final size:55
Alignment explanation
Indices: 854836--855300 Score: 659
Period size: 55 Copynumber: 8.4 Consensus size: 55
854826 AACCCCGTAA
* * * * *
854836 GAAGATTATTCGAGT-TCTATACTGC-CTGAAAGAAAGAGGGAGCGGACCCGATTGTT
1 GAAGATTGTTCGAGTCT-TATACT-CTCTG-AAGGAATAGGGAGCAGACACGATTGTT
* * *
854892 GAAGATTGTTCGAGTCTTATACTCTCTCTGAAGAAATAGGGAGTAGACACGACTGTT
1 GAAGATTGTTCGAGTCTTATA--CTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
* *
854949 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
* *
855004 GAAGATTGTTCGAGTCTTATACTCTTTGAAGGAATAGGGAGCGGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
* *
855059 GAAGATTGTTCGAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
* * * * * *
855114 GAAGAATGTTTGAGTATTATACTCTCTGAAGGAATAGGGAGAAAACACGGTTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
*
855169 GAAGGTTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
855224 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
855279 GAAGA-TGTTCGAGT-TCTATACT
1 GAAGATTGTTCGAGTCT-TATACT
855301 TCCTAAAAAA
Statistics
Matches: 371, Mismatches: 33, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
53 1 0.00
54 15 0.04
55 287 0.77
56 18 0.05
57 45 0.12
58 5 0.01
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
Found at i:855379 original size:54 final size:53
Alignment explanation
Indices: 854249--855464 Score: 683
Period size: 54 Copynumber: 22.5 Consensus size: 53
854239 GTGAAGCAAA
* * * *
854249 AGAAGATTTTCGAGTTCCATACTCCCTAGAGAAAAAGAGAGCGAACCCG-TTT
1 AGAAGATTTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGATTT
*
854301 -GAAGATTGTTCGAGTT-TCATACTCCCTAGAGAAAGAGGGAGCGAACCCG-TTT
1 AGAAGATT-TTCGAGTTCT-ATACTCCCTAAAGAAAGAGGGAGCGAACCCGATTT
* * *
854353 GAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCG-TTT
1 --AGAAGATTTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGATTT
* * * * *
854407 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAATCCG-TTT
1 --AGAAGATTTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGATTT
* * * *
854461 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG-TTT
1 --AGAAGATTTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGATTT
* * *
854515 GAAGAAGATTTTCGAGTTCCATACTTCCTAGAGAAAGAGGGAGCGAACCC-ATTT
1 --AGAAGATTTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGATTT
* * * *
854569 GAAGAAGATATCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG-TTT
1 --AGAAGATTTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGATTT
* * * * *
854623 GAAGAAGA-TTTCTGAGTTCCATACTTCCTAGAGAAAGAGGGAGTGAACCCG-TGT
1 --AGAAGATTTTC-GAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGATTT
* * * * *
854677 -GAAGA-TATCAGAGTTCCATACTCCTTAAAGAAAGAAGGATCGAACCCG-TTT
1 AGAAGATTTTC-GAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGATTT
* *
854728 -GAAGAGATGTTT-GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG-TTT
1 AG-A-AGAT-TTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGATTT
* * * * *
854781 GAAGAAGATTTTCGAGTTCCATACTTCCTAGAGAAAGAGGGAGTGAACCCCG--TA
1 --AGAAGATTTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAA-CCCGATTT
* *
854835 AGAAGATTATTCGAGTTCTATACTGCCTGAAAGAAAGAGGGAGCGGACCCGATTGT
1 AGAAGATT-TTCGAGTTCTATACTCCCT-AAAGAAAGAGGGAGCGAACCCGATT-T
* * * * *
854891 TGAAGATTGTTCGAG-TCTTATACTCTCTCTGAAGAAATAGGGAG-TAGACACGACTGTT
1 AGAAGATT-TTCGAGTTC-TATACTC-C-CTAAAGAAAGAGGGAGCGA-ACCCGA-T-TT
* * * *
854949 -GAAGATTGTTCGAG-TCTTATACTCTCTGAAGAAATAGGGAGC-AGACACGATCGTT
1 AGAAGATT-TTCGAGTTC-TATACTCCCTAAAGAAAGAGGGAGCGA-ACCCGAT--TT
** * * * * *
855004 -GAAGATTGTTCGAG-TCTTATACTCTTTGAAGGAATAGGGAGCGGACACGATTGT
1 AGAAGATT-TTCGAGTTC-TATACTCCCTAAAGAAAGAGGGAGCGAACCCGATT-T
* * * *
855058 TGAAGATTGTTCGAG-TCTTATACTCTCTGAATGAATAGA--GAGC-AGACACGATTGT
1 AGAAGATT-TTCGAGTTC-TATACTCCCT-AAAGAA-AGAGGGAGCGA-ACCCGATT-T
* * * * * ** * *
855113 TGAAGAATGTTT-GAGTAT-TATACTCTCTGAAGGAATAGGGAGAAAACACGGTTGT
1 AGAAG-AT-TTTCGAGT-TCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGATT-T
* * * * * * *
855168 TGAAGGTTGTTCGAG-TCTTATACTCTCTGAAGGAATAGGGAGC-AGACACGATTGT
1 AGAAGATT-TTCGAGTTC-TATACTCCCTAAAGAAAGAGGGAGCGA-ACCCGATT-T
* * * * * *
855223 TGAAGATTGTTCGAG-TCTTATACTCTCTGAAGGAATAGGGAGC-AGACACGATTGT
1 AGAAGATT-TTCGAGTTC-TATACTCCCTAAAGAAAGAGGGAGCGA-ACCCGATT-T
* * * * *
855278 TGAAGATGTTCGAGTTCTATACTTCCTAAAAAAAGAAGGAGCGAACCCGATTT
1 AGAAGATTTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGATTT
* * ***
855331 CAGAAGATTTGCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCAAACCCGAAGGC
1 -AGAAGATTTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCG-ATTT
* * * *
855386 ATAAGATTGTTCGAGTTC-CTACTCCCTAAAGAAATAGGGAGCGAACCC-ATTGGC
1 AGAAGATT-TTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGATT--T
855440 AGAAGATTATTCGAGTT-TCATACTC
1 AGAAGATT-TTCGAGTTCT-ATACTC
855465 TCTGAAGCAA
Statistics
Matches: 1007, Mismatches: 99, Indels: 113
0.83 0.08 0.09
Matches are distributed among these distances:
51 50 0.05
52 50 0.05
53 72 0.07
54 476 0.47
55 280 0.28
56 28 0.03
57 46 0.05
58 4 0.00
59 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (53 bp):
AGAAGATTTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGATTT
Found at i:856257 original size:146 final size:146
Alignment explanation
Indices: 855993--856511 Score: 781
Period size: 146 Copynumber: 3.6 Consensus size: 146
855983 CAGGATCTCC
*
855993 GATCAATATTCTGAACAGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGG
1 GATCAATATTCCGAACAGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGG
*
856058 ACGATCAGACGGTGGACGGTGACGGATCGAAGAAAACAAATCCGGGCGGTTTTTAGCCTCTTGCC
66 ACGATCAGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGCGGTTTTTAGCCTCTTGCC
* *
856123 GGTGATCGGAATATTT
131 GGTGATCGGAATCTGT
*
856139 GATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGG
1 GATCAATATTCCGAACAGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGG
* *
856204 ACGATCAGACGGTGGAAGGTGACGGATCGGAGAAAACAAATCCGGGCAGTTTTTAGCCTCTTGCC
66 ACGATCAGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGCGGTTTTTAGCCTCTTGCC
* *
856269 GGTTATCAGAATCTGT
131 GGTGATCGGAATCTGT
* *
856285 GATCAATATTTCGAACAGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATTAGG
1 GATCAATATTCCGAACAGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGG
* * * * *
856350 ACGATCGGACGGTGGACGGTGATGGATCGGAGAAAATAAATCCGGACGGTTTTTAACCTCTTGCC
66 ACGATCAGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGCGGTTTTTAGCCTCTTGCC
*
856415 GGTGATCGGAATCTGC
131 GGTGATCGGAATCTGT
* * * * *
856431 GATCAATATTCCGAACGGTGAAAAGTTGCGCGATA--CCAACACAAACAACCTATTGAAAAATCA
1 GATCAATATTCCGAACAGTCAAAAGTTGCG-GA-AGGCCATCACGAACAACATATTGAAAAATCA
* * *
856494 GGTCAATCGGACGGTGGA
64 GGACGATCAGACGGTGGA
856512 TGACGGCAGA
Statistics
Matches: 340, Mismatches: 31, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
146 337 0.99
147 2 0.01
148 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (146 bp):
GATCAATATTCCGAACAGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGG
ACGATCAGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGCGGTTTTTAGCCTCTTGCC
GGTGATCGGAATCTGT
Found at i:859259 original size:16 final size:16
Alignment explanation
Indices: 859234--859266 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
859224 GCCATCCATT
*
859234 TATACTCATCCAATGA
1 TATACGCATCCAATGA
859250 TATACGCATCCAATGA
1 TATACGCATCCAATGA
859266 T
1 T
859267 CCTAAATCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.24, G:0.09, T:0.30
Consensus pattern (16 bp):
TATACGCATCCAATGA
Found at i:861825 original size:72 final size:73
Alignment explanation
Indices: 861686--861826 Score: 184
Period size: 72 Copynumber: 1.9 Consensus size: 73
861676 GAATATATAC
* *
861686 AATTGAAAATATTTAAAAATAATATTTTTAGTTAAGCACAATCTAAAATATTTATTTTTAATATT
1 AATTAAAAATATTTAAAAATAATATTTTTAGTTAAGCACAATCTAAAATATTAATTTTTAATATT
861751 TTTAGTTG
66 TTTAGTTG
*
861759 AATTAAAAATATTATAAAGAATAATATTTTTA-TT-A-TA-AA-CTAAAAATATTAATTTTTTAA
1 AATTAAAAATATT-TAAA-AATAATATTTTTAGTTAAGCACAATCT-AAAATATTAA-TTTTTAA
861819 TATTTTTA
62 TATTTTTA
861827 ATTACGTATT
Statistics
Matches: 61, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
70 2 0.03
71 11 0.18
72 16 0.26
73 13 0.21
74 6 0.10
75 13 0.21
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (73 bp):
AATTAAAAATATTTAAAAATAATATTTTTAGTTAAGCACAATCTAAAATATTAATTTTTAATATT
TTTAGTTG
Found at i:866194 original size:84 final size:84
Alignment explanation
Indices: 866047--866217 Score: 315
Period size: 84 Copynumber: 2.0 Consensus size: 84
866037 AACAGCATGC
* *
866047 TCCAGGCAGAAAATCCGAGGTCTCAGATATTTGTTACAGGTGTTCCATCCTTCGTAAATCTTAGT
1 TCCAGGCAGAAAATCCGAGGTCTCAGATATTTGTTACAGGTGTTCCATCCTTCGGAAACCTTAGT
866112 TATTGATGGAAATGGTGAA
66 TATTGATGGAAATGGTGAA
*
866131 TCCAGGCAGAAAATCCGAGGTCTCAGATATTTGTTACAGGTGTTCTATCCTTCGGAAACCTTAGT
1 TCCAGGCAGAAAATCCGAGGTCTCAGATATTTGTTACAGGTGTTCCATCCTTCGGAAACCTTAGT
866196 TATTGATGGAAATGGTGAA
66 TATTGATGGAAATGGTGAA
866215 TCC
1 TCC
866218 TTGGAAGGAA
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.32
Consensus pattern (84 bp):
TCCAGGCAGAAAATCCGAGGTCTCAGATATTTGTTACAGGTGTTCCATCCTTCGGAAACCTTAGT
TATTGATGGAAATGGTGAA
Found at i:870195 original size:15 final size:16
Alignment explanation
Indices: 870177--870208 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
870167 AATACTTAGA
870177 ATAAATAT-TGATAAT
1 ATAAATATATGATAAT
870192 ATAAATATATGATAAT
1 ATAAATATATGATAAT
870208 A
1 A
870209 AAAACATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (16 bp):
ATAAATATATGATAAT
Found at i:873689 original size:36 final size:36
Alignment explanation
Indices: 873642--873917 Score: 439
Period size: 36 Copynumber: 7.7 Consensus size: 36
873632 TGGATGATTT
*
873642 ACTTCACTACTCTTCCGTGAAGGTTAAAAATAACTA
1 ACTTCACTACTCTTCCGTGAAGGTTGAAAATAACTA
*
873678 ACTTCACTACTCTTCCGTGAATGTTGAAAATAACTA
1 ACTTCACTACTCTTCCGTGAAGGTTGAAAATAACTA
*
873714 ACTTCACTACTCTTCCGTGAAGGTTGAAAATGA-TGA
1 ACTTCACTACTCTTCCGTGAAGGTTGAAAATAACT-A
**
873750 ACTTCACTACTCTTCCGTGAAGGTTGAAAAGGA-TGA
1 ACTTCACTACTCTTCCGTGAAGGTTGAAAATAACT-A
873786 ACTTCACTACTCTTCCGTGAAGGTTGAAAATAACTA
1 ACTTCACTACTCTTCCGTGAAGGTTGAAAATAACTA
**
873822 ACTTCACTACTCTTTTGTGAAGGTTGAAAATAACTA
1 ACTTCACTACTCTTCCGTGAAGGTTGAAAATAACTA
873858 ACTTCACTACTCTTCCGTGAAGGTTGAAAATAACTA
1 ACTTCACTACTCTTCCGTGAAGGTTGAAAATAACTA
* *
873894 ACTTCACTACTATTTCGTGAAGGT
1 ACTTCACTACTCTTCCGTGAAGGT
873918 CTTATGAATA
Statistics
Matches: 225, Mismatches: 13, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
35 1 0.00
36 223 0.99
37 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (36 bp):
ACTTCACTACTCTTCCGTGAAGGTTGAAAATAACTA
Found at i:873769 original size:108 final size:107
Alignment explanation
Indices: 873610--873917 Score: 451
Period size: 108 Copynumber: 2.9 Consensus size: 107
873600 CTGATCTTGA
* * * *
873610 TTCACTACTCTTCTGTGAAGGCTG--GATGATTTACTTCACTACTCTTCCGTGAAGGTTAAAAAT
1 TTCACTACTCTTCTGTGAAGGTTGAAAATGA-TAACTTCACTACTCTTCCGTGAAGGTTGAAAAT
*
873673 AACTAACTTCACTACTCTTCCGTGAATGTTGAAAATAACTAAC
65 AACTAACTTCACTACTCTTCCGTGAAGGTTGAAAATAACTAAC
* *
873716 TTCACTACTCTTCCGTGAAGGTTGAAAATGATGAACTTCACTACTCTTCCGTGAAGGTTGAAAAG
1 TTCACTACTCTTCTGTGAAGGTTGAAAATGAT-AACTTCACTACTCTTCCGTGAAGGTTGAAAAT
*
873781 GA-TGAACTTCACTACTCTTCCGTGAAGGTTGAAAATAACTAAC
65 AACT-AACTTCACTACTCTTCCGTGAAGGTTGAAAATAACTAAC
* *
873824 TTCACTACTCTTTTGTGAAGGTTGAAAATAACTAACTTCACTACTCTTCCGTGAAGGTTGAAAAT
1 TTCACTACTCTTCTGTGAAGGTTGAAAATGA-TAACTTCACTACTCTTCCGTGAAGGTTGAAAAT
* *
873889 AACTAACTTCACTACTATTTCGTGAAGGT
65 AACTAACTTCACTACTCTTCCGTGAAGGT
873918 CTTATGAATA
Statistics
Matches: 181, Mismatches: 15, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
106 22 0.12
107 2 0.01
108 155 0.86
109 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (107 bp):
TTCACTACTCTTCTGTGAAGGTTGAAAATGATAACTTCACTACTCTTCCGTGAAGGTTGAAAATA
ACTAACTTCACTACTCTTCCGTGAAGGTTGAAAATAACTAAC
Found at i:873998 original size:21 final size:20
Alignment explanation
Indices: 873969--874048 Score: 97
Period size: 20 Copynumber: 4.0 Consensus size: 20
873959 CTGACAGATA
*
873969 ACCCTAAGGTTTTACAAATTT
1 ACCCGAAGGTTTTACAAA-TT
873990 ACCCGAAGGTTTTACAAATT
1 ACCCGAAGGTTTTACAAATT
** * * *
874010 ACTTGGAGGATTTACAAATG
1 ACCCGAAGGTTTTACAAATT
874030 ACCCGAAGGTTTTACAAAT
1 ACCCGAAGGTTTTACAAAT
874049 GAATGAGAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
20 32 0.65
21 17 0.35
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Consensus pattern (20 bp):
ACCCGAAGGTTTTACAAATT
Found at i:879251 original size:2 final size:2
Alignment explanation
Indices: 879244--879303 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
879234 ACCATATAAC
879244 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
879286 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
879304 CATGTCATGT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:879667 original size:30 final size:30
Alignment explanation
Indices: 879604--879692 Score: 108
Period size: 30 Copynumber: 3.0 Consensus size: 30
879594 CCCGAATGGC
* **
879604 CTATCCAGAGGTCACAAAG-ACCCCGACAA
1 CTATCCAGAGGTCACAAAGAACCTCGGTAA
*
879633 CTATCCAGAGGTCATAAAGAACCTCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTCGGTAA
* * *
879663 CTATCCATAGGTCCCAAAGAACCTAGGTAA
1 CTATCCAGAGGTCACAAAGAACCTCGGTAA
879693 ATTATCCATA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 18 0.35
30 33 0.65
ACGTcount: A:0.37, C:0.28, G:0.18, T:0.17
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCTCGGTAA
Found at i:879702 original size:31 final size:31
Alignment explanation
Indices: 879631--879725 Score: 95
Period size: 30 Copynumber: 3.1 Consensus size: 31
879621 AGACCCCGAC
* ** *
879631 AACTATCCAGAGGTCATAAAGAACCTCGGT-
1 AACTATCCATAGGTCCCAAAGAACCTAGGTA
879661 AACTATCCATAGGTCCCAAAGAACCTAGGTA
1 AACTATCCATAGGTCCCAAAGAACCTAGGTA
* * * *
879692 AATTATCCATATGTCTCGAAAG-ACGTAGGTA
1 AACTATCCATAGGTC-CCAAAGAACCTAGGTA
879723 AAC
1 AAC
879726 CCTCGACTCT
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
30 26 0.48
31 23 0.43
32 5 0.09
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (31 bp):
AACTATCCATAGGTCCCAAAGAACCTAGGTA
Found at i:880980 original size:20 final size:23
Alignment explanation
Indices: 880955--881011 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 23
880945 TCCCCTTGAA
880955 GTGCATCGATGCATGC-T-AC-T
1 GTGCATCGATGCATGCTTAACAT
*
880975 GTGCATCGATGCATTCTTTAACAT
1 GTGCATCGATGCATGC-TTAACAT
880999 GTGCATCGATGCA
1 GTGCATCGATGCA
881012 CTACCCATGC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 15 0.47
22 1 0.03
23 2 0.06
24 14 0.44
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (23 bp):
GTGCATCGATGCATGCTTAACAT
Found at i:882348 original size:171 final size:171
Alignment explanation
Indices: 882063--882412 Score: 619
Period size: 171 Copynumber: 2.0 Consensus size: 171
882053 ACCACATAAG
* *
882063 TCTACCAGCTTGTGGGCTACATTGATTTCTTGGATAGAGACTGTCTTCATGTCATTGTCTTTTTC
1 TCTACCATCTTGTGGGCTACATTGATTGCTTGGATAGAGACTGTCTTCATGTCATTGTCTTTTTC
* *
882128 CTGAATCTTACCTGCTTTCTCCTGAAGTTGTAGATAATATTGCTCATTTTCTTTAATAAGAGAGC
66 CTGAATCTTACCTGCTATCTCCTGAAGTTGTAGACAATATTGCTCATTTTCTTTAATAAGAGAGC
*
882193 CTTTGTGTTCAATAAGTTCTTGTACAAGATCTCCATAGTCT
131 CTTTGTGTTCAAGAAGTTCTTGTACAAGATCTCCATAGTCT
*
882234 TCTACCATCTTGTGGGCTACATTGATTGCTTGGATAGAGATTGTCTTCATGTCATTGTCTTTTTC
1 TCTACCATCTTGTGGGCTACATTGATTGCTTGGATAGAGACTGTCTTCATGTCATTGTCTTTTTC
* *
882299 CTGAATCTTATCTGCTATCTCCTGAAGTTGTAGACAATATTTCTCATTTTCTTTAATAAGAGAGC
66 CTGAATCTTACCTGCTATCTCCTGAAGTTGTAGACAATATTGCTCATTTTCTTTAATAAGAGAGC
*
882364 CTTTGTGTTCAAGAAGTTCTTGTACAAGATCTTCATAGTCT
131 CTTTGTGTTCAAGAAGTTCTTGTACAAGATCTCCATAGTCT
882405 TCTACCAT
1 TCTACCAT
882413 ATTTGTTAAT
Statistics
Matches: 170, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
171 170 1.00
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.42
Consensus pattern (171 bp):
TCTACCATCTTGTGGGCTACATTGATTGCTTGGATAGAGACTGTCTTCATGTCATTGTCTTTTTC
CTGAATCTTACCTGCTATCTCCTGAAGTTGTAGACAATATTGCTCATTTTCTTTAATAAGAGAGC
CTTTGTGTTCAAGAAGTTCTTGTACAAGATCTCCATAGTCT
Found at i:887949 original size:31 final size:31
Alignment explanation
Indices: 887929--888068 Score: 235
Period size: 31 Copynumber: 4.5 Consensus size: 31
887919 ATAGATTCCA
* *
887929 AAGAACCTAGGTAATCAGTCCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
*
887960 AAGAACATAGGTAAACAGTCAATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
887991 AAGAACATAGGTAAACAGTCCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
* *
888022 AAGAACATAGGTAAACAATCCATATGTCCCA
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
888053 AAGAACATAGGTAAAC
1 AAGAACATAGGTAAAC
888069 CCTCGACCCT
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 103 1.00
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.19
Consensus pattern (31 bp):
AAGAACATAGGTAAACAGTCCATATGTCCCG
Found at i:889068 original size:21 final size:21
Alignment explanation
Indices: 889044--889088 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
889034 TTTTGTTCGT
* *
889044 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
889065 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
889086 TTG
1 TTG
889089 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:889968 original size:2 final size:2
Alignment explanation
Indices: 889961--889993 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
889951 TATTTTCCTT
889961 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
889994 TCATATCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:891097 original size:2 final size:2
Alignment explanation
Indices: 891090--891118 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
891080 TATTTTCCTT
891090 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
891119 TCATATCATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:893497 original size:31 final size:31
Alignment explanation
Indices: 893475--893645 Score: 288
Period size: 31 Copynumber: 5.5 Consensus size: 31
893465 ATAGATTCCA
* *
893475 AAGAACCTAGGTAATCAGTCCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
*
893506 AAGAACATAGGTAAACAGTCAATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
893537 AAGAACATAGGTAAACAGTCCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
* *
893568 AAGAACATAGGTAAACAATCCATATGTCCCA
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
*
893599 AAGAACATAGGTAAACAGTTCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
893630 AAGAACATAGGTAAAC
1 AAGAACATAGGTAAAC
893646 CCTCGACCCT
Statistics
Matches: 131, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 131 1.00
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.20
Consensus pattern (31 bp):
AAGAACATAGGTAAACAGTCCATATGTCCCG
Found at i:894650 original size:21 final size:21
Alignment explanation
Indices: 894626--894670 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
894616 TTTTGTTCGT
* *
894626 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
894647 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
894668 TTG
1 TTG
894671 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:899053 original size:20 final size:20
Alignment explanation
Indices: 899005--899058 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
898995 CAGCGAAGGA
* * *
899005 AATTGGGGATTCAGAAAATG
1 AATTAGGGATTAAGAAAACG
899025 AATTAGGGATTAAGAAATACG
1 AATTAGGGATTAAGAAA-ACG
899046 AATT-GGGAATTAA
1 AATTAGGG-ATTAA
899059 AACATATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.44, C:0.04, G:0.26, T:0.26
Consensus pattern (20 bp):
AATTAGGGATTAAGAAAACG
Found at i:901530 original size:18 final size:18
Alignment explanation
Indices: 901507--901551 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
901497 CAACATTCCA
901507 GTAATCTTATTCCCACCG
1 GTAATCTTATTCCCACCG
*
901525 GTAATCTTATTCCCACTG
1 GTAATCTTATTCCCACCG
901543 GTAATCTTA
1 GTAATCTTA
901552 CTTCTGTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.24, C:0.27, G:0.11, T:0.38
Consensus pattern (18 bp):
GTAATCTTATTCCCACCG
Found at i:904259 original size:20 final size:19
Alignment explanation
Indices: 904234--904272 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
904224 GTTCCATCGA
*
904234 ATATTTTTTTATTTGATTTT
1 ATATTTTTTT-TTTAATTTT
904254 ATATTTTTTTTTTAATTTT
1 ATATTTTTTTTTTAATTTT
904273 GAAAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (19 bp):
ATATTTTTTTTTTAATTTT
Found at i:905410 original size:21 final size:21
Alignment explanation
Indices: 905359--905411 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
905349 ATTATGACTA
905359 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
905380 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
905401 TCGCAATGCGA
1 TCGCAATGCGA
905412 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:905444 original size:21 final size:21
Alignment explanation
Indices: 905401--905473 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
905391 TTTTCCCAAT
** *
905401 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGAAAA
905421 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
* *
905442 TCGCATTGCGAATTTGAAAAA
1 TCGCAATGCGAATTTGGAAAA
*
905463 TCGCAACGCGA
1 TCGCAATGCGA
905474 TACTGACTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 12 0.27
21 33 0.73
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:905486 original size:41 final size:41
Alignment explanation
Indices: 905459--905596 Score: 161
Period size: 41 Copynumber: 3.4 Consensus size: 41
905449 GCGAATTTGA
905459 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * * *
905500 AAAATCGTAACGCGATACTGACTTTCGCAACTCGATACT-T
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
** * * *
905540 AATTTCGCAACGCAATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
905581 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
905597 TTTCAAAGCG
Statistics
Matches: 78, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
40 32 0.41
41 46 0.59
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:905487 original size:20 final size:20
Alignment explanation
Indices: 905462--905576 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
905452 AATTTGAAAA
905462 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
905482 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
905503 ATCGTAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * *
905523 TTCGCAACTCGATACTTAAT
1 ATCGCAACGCGATACTGACT
* *
905543 TTCGCAACGCAATACTGACT
1 ATCGCAACGCGATACTGACT
* *
905563 TTCGCAACGAGATA
1 ATCGCAACGCGATA
905577 ATACATAATC
Statistics
Matches: 76, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
19 2 0.03
20 58 0.76
21 14 0.18
22 2 0.03
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:907469 original size:18 final size:18
Alignment explanation
Indices: 907448--907495 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
907438 TCCACTTCGG
907448 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
907466 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
907484 GAGCCATCACCT
1 GAGCCATCACCT
907496 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:908055 original size:20 final size:20
Alignment explanation
Indices: 908030--908075 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
908020 TAGTTTACTT
908030 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
908050 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
908070 TCGCAA
1 TCGCAA
908076 TGCGAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:908084 original size:19 final size:19
Alignment explanation
Indices: 908041--908099 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
908031 CGCAACACGA
*
908041 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAATGC-G
*
908061 AAATGGCTATCGCAATGCG
1 AAATGACTATCGCAATGCG
**
908080 AAATGAAAATCGCAATGCG
1 AAATGACTATCGCAATGCG
908099 A
1 A
908100 TTTGTGTTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (19 bp):
AAATGACTATCGCAATGCG
Found at i:908130 original size:14 final size:14
Alignment explanation
Indices: 908111--908169 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
908101 TTGTGTTTCG
908111 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
908125 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
908142 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
908158 CGTTGCGATTTT
1 CGTTGCGATTTT
908170 CATTTTGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 20 0.53
15 3 0.08
16 2 0.05
17 2 0.05
18 3 0.08
19 8 0.21
ACGTcount: A:0.08, C:0.17, G:0.25, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:908143 original size:33 final size:33
Alignment explanation
Indices: 908106--908185 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
908096 GCGATTTGTG
908106 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
908139 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
* *
908172 TTTTGCATTGCGAT
1 TTTCGCGTTGCGAT
908186 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:908204 original size:20 final size:20
Alignment explanation
Indices: 908179--908244 Score: 114
Period size: 20 Copynumber: 3.3 Consensus size: 20
908169 TCATTTTGCA
*
908179 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGTCATTTCCGCG
908199 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTCCGCG
*
908219 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTCCGCG
908239 TTGCGA
1 TTGCGA
908245 AAGTAAGTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.15, C:0.24, G:0.26, T:0.35
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGCG
Found at i:908255 original size:20 final size:19
Alignment explanation
Indices: 908190--908270 Score: 81
Period size: 20 Copynumber: 4.1 Consensus size: 19
908180 TGCGATAGCC
* *
908190 ATTTCCGCGTTGCGATAGTC
1 ATTT-CGCGTTGCGAAAGTA
*
908210 ATTTCCGCGTTGCGATAGTCA
1 ATTT-CGCGTTGCGAAAGT-A
*
908231 TTTTCGCGTTGCGAAAGTA
1 ATTTCGCGTTGCGAAAGTA
*
908250 AGTTTCGTGTTGCGAAAGTA
1 A-TTTCGCGTTGCGAAAGTA
908270 A
1 A
908271 ACTATTCTTC
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
19 1 0.02
20 50 0.93
21 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.35
Consensus pattern (19 bp):
ATTTCGCGTTGCGAAAGTA
Found at i:908262 original size:40 final size:40
Alignment explanation
Indices: 908179--908264 Score: 111
Period size: 40 Copynumber: 2.1 Consensus size: 40
908169 TCATTTTGCA
* *
908179 TTGCGATAGCCATTTCCGCGTTGCGATAGTCATTTCCGCG
1 TTGCGATAGCCATTTCCGCGTTGCGAAAGTAATTTCCGCG
* * *
908219 TTGCGATAGTCATTTTCGCGTTGCGAAAGTAAGTTT-CGTG
1 TTGCGATAGCCATTTCCGCGTTGCGAAAGTAA-TTTCCGCG
908259 TTGCGA
1 TTGCGA
908265 AAGTAAACTA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 37 0.93
41 3 0.08
ACGTcount: A:0.17, C:0.21, G:0.27, T:0.35
Consensus pattern (40 bp):
TTGCGATAGCCATTTCCGCGTTGCGAAAGTAATTTCCGCG
Found at i:908645 original size:21 final size:21
Alignment explanation
Indices: 908614--908672 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
908604 CTCACCTGTC
*
908614 ATCCCTCAAGAGTCCCCTCTA
1 ATCCCTCAAGAGTCCCCTATA
** * *
908635 ATCGTTCAAGAGGCCCCTATC
1 ATCCCTCAAGAGTCCCCTATA
908656 ATCCCTCAAGAGTCCCC
1 ATCCCTCAAGAGTCCCC
908673 CCCACCGTTC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.24, C:0.41, G:0.14, T:0.22
Consensus pattern (21 bp):
ATCCCTCAAGAGTCCCCTATA
Found at i:908699 original size:41 final size:42
Alignment explanation
Indices: 908609--908699 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 42
908599 CCCGACTCAC
* * *
908609 CTGTCATCCCTCAAGAGTCCCCTCTAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
* *
908651 CTATCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
908692 CTGTCATC
1 CTGTCATC
908700 TTTGAAGAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 22 0.51
42 21 0.49
ACGTcount: A:0.22, C:0.41, G:0.15, T:0.22
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:908708 original size:41 final size:42
Alignment explanation
Indices: 908612--908729 Score: 114
Period size: 42 Copynumber: 2.8 Consensus size: 42
908602 GACTCACCTG
** * *
908612 TCATCCCTCAAGA-GTCCCCTCTAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGGTCCCC-CCCACCGTTCAAGAGGCCACTA
*
908654 TCATCCCTCAAGA-GTCCCCCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGGTCCCCCCCACCGTTCAAGAGGCCACTA
** * * * *
908695 TCATCTTTGAAGAGGTCCCTCCCACCATTCCAGAG
1 TCATCCCTCAAGAGGTCCCCCCCACCGTTCAAGAG
908730 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 27 0.42
42 37 0.58
ACGTcount: A:0.23, C:0.39, G:0.16, T:0.22
Consensus pattern (42 bp):
TCATCCCTCAAGAGGTCCCCCCCACCGTTCAAGAGGCCACTA
Found at i:910241 original size:19 final size:19
Alignment explanation
Indices: 910196--910244 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
910186 ATCGCAACGA
*
910196 GAAAATCACAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
910215 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
910234 GAAAATCGCAA
1 GAAAATCGCAA
910245 CAAGTAAATT
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:0.51, C:0.16, G:0.18, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:910294 original size:18 final size:18
Alignment explanation
Indices: 910271--910308 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
910261 CAAGTTAAAT
910271 ATGGTTAATTTAAGTGAA
1 ATGGTTAATTTAAGTGAA
910289 ATGGTTAATTTAAGTGAA
1 ATGGTTAATTTAAGTGAA
910307 AT
1 AT
910309 TACGAGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (18 bp):
ATGGTTAATTTAAGTGAA
Found at i:911718 original size:26 final size:26
Alignment explanation
Indices: 911680--911735 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
911670 AGCATCTCCA
*
911680 CCCGGATGTTGTACTCTCAGCCATGG
1 CCCGGATGCTGTACTCTCAGCCATGG
911706 CCCGGATGCTGTACTCTCAGCCATGG
1 CCCGGATGCTGTACTCTCAGCCATGG
911732 CCCG
1 CCCG
911736 AAGCAGGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.14, C:0.36, G:0.27, T:0.23
Consensus pattern (26 bp):
CCCGGATGCTGTACTCTCAGCCATGG
Found at i:912057 original size:33 final size:33
Alignment explanation
Indices: 912002--912133 Score: 165
Period size: 33 Copynumber: 3.8 Consensus size: 33
911992 AGATAATGAA
912002 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGACTATCGCAACGAGAG
* *
912036 AATCGCAACGCAAAATGACTATCGCAATGAGAG
1 AATCGCAACGCGAAATGACTATCGCAACGAGAG
*
912069 AATCGCAACGCGAAATGACTATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGACTATCGCAA--CG--A-GAG
**
912107 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGACTATCGCAA
912134 TGCGATTTTG
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
33 46 0.53
34 11 0.13
35 1 0.01
37 1 0.01
38 27 0.31
ACGTcount: A:0.42, C:0.23, G:0.22, T:0.13
Consensus pattern (33 bp):
AATCGCAACGCGAAATGACTATCGCAACGAGAG
Found at i:912059 original size:19 final size:19
Alignment explanation
Indices: 911983--912138 Score: 116
Period size: 19 Copynumber: 8.6 Consensus size: 19
911973 TGAAATGAAA
* **
911983 ATCGCAACGAGATAATGAAA
1 ATCGCAACGCGA-AATGACT
912003 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
*
912023 ATCGCAA--CGAGA-GA--
1 ATCGCAACGCGAAATGACT
*
912037 ATCGCAACGCAAAATGACT
1 ATCGCAACGCGAAATGACT
* *
912056 ATCGCAA--TGAGA-GA--
1 ATCGCAACGCGAAATGACT
912070 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
**
912089 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
**
912108 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
*
912127 ATCGCAATGCGA
1 ATCGCAACGCGA
912139 TTTTGGTTTC
Statistics
Matches: 111, Mismatches: 14, Indels: 23
0.75 0.09 0.16
Matches are distributed among these distances:
14 14 0.13
16 10 0.09
17 9 0.08
18 1 0.01
19 54 0.49
20 21 0.19
21 2 0.02
ACGTcount: A:0.42, C:0.22, G:0.22, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:912182 original size:33 final size:33
Alignment explanation
Indices: 912134--912205 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
912124 AAAATCGCAA
**
912134 TGCGATTTTGGTTTCGCGTTACGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTACGATTATCTCGT
* *
912167 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTACGATTATCTCGT
912200 TGCGAT
1 TGCGAT
912206 AGTTATTTCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.21, G:0.24, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTACGATTATCTCGT
Found at i:912214 original size:33 final size:33
Alignment explanation
Indices: 912145--912226 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 33
912135 GCGATTTTGG
* *
912145 TTTCGCGTTACGATTATCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTATCTCGTTGCGATGTTCA
*
912178 TTTCGCGTTGCGATTCTCTCGTTGCGATAGTT-A
1 TTTCGCGTTGCGATTATCTCGTTGCGAT-GTTCA
*
912211 TTTCCGCGTTGTGATT
1 TTT-CGCGTTGCGATT
912227 TTCATTCTCG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
33 30 0.70
34 13 0.30
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (33 bp):
TTTCGCGTTGCGATTATCTCGTTGCGATGTTCA
Found at i:912792 original size:20 final size:20
Alignment explanation
Indices: 912769--912841 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
912759 TGATAGTAAG
*
912769 ATTCGCATTACGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
912789 ATTCGCATTGCGATTTACTT
1 ATTCGCATTGCGATTTACGT
* *
912809 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
912829 ATTCGCATTGCGA
1 ATTCGCATTGCGA
912842 ATTATGAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:912862 original size:21 final size:21
Alignment explanation
Indices: 912838--912893 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
912828 TATTCGCATT
*
912838 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
* *
912859 GCGAA-TACGTAAATCGCAAT
1 GCGAATTACGAAAATCGCAAC
* *
912879 ACGAATTAGGAAAAT
1 GCGAATTACGAAAAT
912894 TGCATTGCGA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.45, C:0.16, G:0.20, T:0.20
Consensus pattern (21 bp):
GCGAATTACGAAAATCGCAAC
Found at i:912957 original size:20 final size:21
Alignment explanation
Indices: 912913--912964 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
912903 ATAGTCAGTA
*
912913 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
912934 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
912954 TCGCATTGCGA
1 TCGCATTGCGA
912965 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:912979 original size:41 final size:41
Alignment explanation
Indices: 912771--912979 Score: 138
Period size: 41 Copynumber: 5.1 Consensus size: 41
912761 ATAGTAAGAT
* * * ***
912771 TCGCATTACGATTTACGTATTCGCATTGCGATTTA-CTTAA
1 TCGCATTGCGATTTACTTATTCGCATTGCGAATTAGGAAAA
* * *
912811 TCGCGTTGCGATTTACGTATTCGCATTGCGAATTATGAAAA
1 TCGCATTGCGATTTACTTATTCGCATTGCGAATTAGGAAAA
** * * * * *
912852 TCGCAACGCGA-ATACGTAAATCGCAATACGAATTAGGAAAA
1 TCGCATTGCGATTTAC-TTATTCGCATTGCGAATTAGGAAAA
* * * * *** *
912893 TTGCATTGCGA--TAGTCAGTATCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTACTTA-T-TCGCATTGCGAATTAGGAAAA
*
912934 TCGCATTGCGATTTACTTATTCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGATTTACTTATTCGCATTGCGAATTAGGAAAA
912975 TCGCA
1 TCGCA
912980 ACGCGAAATT
Statistics
Matches: 126, Mismatches: 37, Indels: 11
0.72 0.21 0.06
Matches are distributed among these distances:
39 2 0.02
40 37 0.29
41 82 0.65
42 1 0.01
43 4 0.03
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (41 bp):
TCGCATTGCGATTTACTTATTCGCATTGCGAATTAGGAAAA
Found at i:913006 original size:21 final size:22
Alignment explanation
Indices: 912954--913006 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
912944 ATTTACTTAT
912954 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
** *
912975 TCGCAACGCGAAATT-GGAAAT
1 TCGCATTGCGAAATTGGGAAAA
*
912996 TTGCATTGCGA
1 TCGCATTGCGA
913007 TAGTCATAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:931054 original size:103 final size:102
Alignment explanation
Indices: 930935--931134 Score: 364
Period size: 103 Copynumber: 2.0 Consensus size: 102
930925 CACGGTAATG
930935 AAAAAAAACCTGATGTACTATTTCTAAAAGGTAGTTTTAAAAAATCAATATGAAAATATACAAAT
1 AAAAAAAACCTGATGTACTATTTCTAAAAGGTAGTTTTAAAAAATCAATATGAAAATATACAAAT
931000 ATTAAATAAAAGTTTTTTTTTATTATTTAATGAATGAA
66 ATTAAATAAAAG-TTTTTTTTATTATTTAATGAATGAA
* * *
931038 AAAAAAAACCTTATGTACTATTTCTAAAAGGTTGTTTTAAAAAATCAATATGAAAATATATAAAT
1 AAAAAAAACCTGATGTACTATTTCTAAAAGGTAGTTTTAAAAAATCAATATGAAAATATACAAAT
931103 ATTAAATAAAAGTTTTTTTTATTATTTAATGA
66 ATTAAATAAAAGTTTTTTTTATTATTTAATGA
931135 TATTAGTTTT
Statistics
Matches: 94, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
102 20 0.21
103 74 0.79
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.39
Consensus pattern (102 bp):
AAAAAAAACCTGATGTACTATTTCTAAAAGGTAGTTTTAAAAAATCAATATGAAAATATACAAAT
ATTAAATAAAAGTTTTTTTTATTATTTAATGAATGAA
Found at i:931729 original size:16 final size:17
Alignment explanation
Indices: 931708--931740 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
931698 ACAAGTACCT
931708 ACAAAAG-AAAATAAAA
1 ACAAAAGCAAAATAAAA
931724 ACAAAAGCAAAATAAAA
1 ACAAAAGCAAAATAAAA
931741 TAAAAACTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.79, C:0.09, G:0.06, T:0.06
Consensus pattern (17 bp):
ACAAAAGCAAAATAAAA
Done.