Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008428.1 Hibiscus syriacus cultivar Beakdansim tig00111213_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: 6915314
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 30
Found at i:421562 original size:5 final size:5
Alignment explanation
Indices: 421548--421577 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
421538 GTGCTTCAAC
421548 TTTC- TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
421578 CTTTTTGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:425208 original size:16 final size:17
Alignment explanation
Indices: 425164--425205 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
425154 AATTGGAGTG
425164 CAAAAAGAAAGAAAAGA
1 CAAAAAGAAAGAAAAGA
*
425181 C-AAAAGAAAGAAAATA
1 CAAAAAGAAAGAAAAGA
425197 CAAAAAGAA
1 CAAAAAGAA
425206 GAAGAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.76, C:0.07, G:0.14, T:0.02
Consensus pattern (17 bp):
CAAAAAGAAAGAAAAGA
Found at i:428170 original size:23 final size:23
Alignment explanation
Indices: 428125--428170 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
428115 TTATACCTAT
*
428125 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
428148 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
428171 TATATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:429790 original size:24 final size:25
Alignment explanation
Indices: 429744--429798 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
429734 ACAGTTATGC
*
429744 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
429768 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
429793 CA-TTGA
1 CACTTGA
429799 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:434955 original size:11 final size:11
Alignment explanation
Indices: 434939--434968 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
434929 ATGGTTTGAA
434939 TGAGCTGGTGG
1 TGAGCTGGTGG
434950 TGAGCTGGTGG
1 TGAGCTGGTGG
434961 TGAGCTGG
1 TGAGCTGG
434969 CCTTAGATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.10, C:0.10, G:0.53, T:0.27
Consensus pattern (11 bp):
TGAGCTGGTGG
Found at i:437434 original size:21 final size:22
Alignment explanation
Indices: 437408--437453 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
437398 TATTTTTTTC
437408 AAAAAAAC-AAAAAAAGGCAAA
1 AAAAAAACAAAAAAAAGGCAAA
437429 AAAAAAACAAAAAAAAGGCAAA
1 AAAAAAACAAAAAAAAGGCAAA
437451 AAA
1 AAA
437454 GCCAAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.83, C:0.09, G:0.09, T:0.00
Consensus pattern (22 bp):
AAAAAAACAAAAAAAAGGCAAA
Found at i:437450 original size:11 final size:11
Alignment explanation
Indices: 437416--437453 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
437406 TCAAAAAAAC
437416 AAAAAAAGGCA
1 AAAAAAAGGCA
**
437427 AAAAAAAAACA
1 AAAAAAAGGCA
437438 AAAAAAAGGCA
1 AAAAAAAGGCA
437449 AAAAA
1 AAAAA
437454 GCCAAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.82, C:0.08, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAAAGGCA
Found at i:445950 original size:9 final size:9
Alignment explanation
Indices: 445936--445962 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
445926 TAATAACTCG
445936 GATATTTCT
1 GATATTTCT
445945 GATATTTCT
1 GATATTTCT
445954 GATATTTCT
1 GATATTTCT
445963 ACCCATACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (9 bp):
GATATTTCT
Found at i:449534 original size:9 final size:9
Alignment explanation
Indices: 449520--449546 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
449510 TAATAACTCG
449520 GATATTTCT
1 GATATTTCT
449529 GATATTTCT
1 GATATTTCT
449538 GATATTTCT
1 GATATTTCT
449547 ACCCATACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (9 bp):
GATATTTCT
Found at i:453117 original size:9 final size:9
Alignment explanation
Indices: 453103--453129 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
453093 TAATAACTCG
453103 GATATTTCT
1 GATATTTCT
453112 GATATTTCT
1 GATATTTCT
453121 GATATTTCT
1 GATATTTCT
453130 ACCCATACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (9 bp):
GATATTTCT
Found at i:457122 original size:9 final size:9
Alignment explanation
Indices: 457108--457134 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
457098 TAATAACTCG
457108 GATATTTCT
1 GATATTTCT
457117 GATATTTCT
1 GATATTTCT
457126 GATATTTCT
1 GATATTTCT
457135 ACCCATACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (9 bp):
GATATTTCT
Found at i:474439 original size:24 final size:21
Alignment explanation
Indices: 474404--474446 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
474394 GGCACATTGT
*
474404 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
474427 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
474447 GTCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:476892 original size:19 final size:22
Alignment explanation
Indices: 476848--476890 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
476838 TTTCTTCCTT
476848 TTTGAGTGCTTTCAATTTCTTC
1 TTTGAGTGCTTTCAATTTCTTC
* *
476870 TTTGAGTGCTTTGATTTTCTT
1 TTTGAGTGCTTTCAATTTCTT
476891 TGCTGGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.14, G:0.16, T:0.58
Consensus pattern (22 bp):
TTTGAGTGCTTTCAATTTCTTC
Found at i:477904 original size:19 final size:20
Alignment explanation
Indices: 477861--477914 Score: 83
Period size: 19 Copynumber: 2.7 Consensus size: 20
477851 GAAACCCCTT
477861 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGA-TTTTAAA
477882 TGAAAATACATGATTTT-AA
1 TGAAAATACATGATTTTAAA
*
477901 TGAAGATACATGAT
1 TGAAAATACATGAT
477915 CTTGGCCGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 15 0.47
20 4 0.12
21 13 0.41
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:479780 original size:24 final size:24
Alignment explanation
Indices: 479730--479779 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
479720 AACACAGCCC
* *
479730 TTGGCACTTCAAATGACGTTTCTT
1 TTGGAACTTCAAATGACATTTCTT
*
479754 TTGGAACTTCAAATGGCATATTCTT
1 TTGGAACTTCAAATGACAT-TTCTT
479779 T
1 T
479780 GAAACATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (24 bp):
TTGGAACTTCAAATGACATTTCTT
Found at i:481637 original size:15 final size:17
Alignment explanation
Indices: 481612--481645 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
481602 TAAAGGTCTT
481612 AAATAACTAATAAA-TA
1 AAATAACTAATAAACTA
481628 AAATAA-TAATAAACTA
1 AAATAACTAATAAACTA
481644 AA
1 AA
481646 CATATATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAACTAATAAACTA
Found at i:486315 original size:25 final size:22
Alignment explanation
Indices: 486286--486331 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
486276 TTTTTAACCC
486286 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
486311 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
486332 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:490705 original size:19 final size:19
Alignment explanation
Indices: 490674--490715 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
490664 AGGGGATAAT
490674 AATATAAGTAATGAAATGA
1 AATATAAGTAATGAAATGA
* *
490693 AATATTAAG-AATGGAGTGA
1 AATA-TAAGTAATGAAATGA
490712 AATA
1 AATA
490716 AAGAAAGGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.55, C:0.00, G:0.19, T:0.26
Consensus pattern (19 bp):
AATATAAGTAATGAAATGA
Found at i:497127 original size:19 final size:21
Alignment explanation
Indices: 497084--497135 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
497074 GAAACCTATT
*
497084 TGAAAATACATGATTTTTAAA
1 TGAAGATACATGATTTTTAAA
497105 TGAAGATACATGA-TTTT-AA
1 TGAAGATACATGATTTTTAAA
497124 TGAAGATACATG
1 TGAAGATACATG
497136 CTCTTGGCAG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 14 0.47
20 4 0.13
21 12 0.40
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (21 bp):
TGAAGATACATGATTTTTAAA
Found at i:503316 original size:19 final size:18
Alignment explanation
Indices: 503292--503347 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 18
503282 TCTTTTTGAA
503292 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
* *
503310 CTTCTTTTCCTCTTCTTTT
1 -TTCTTTTTCTTTTCTTTT
503329 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
503347 T
1 T
503348 GCACACCAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 9 0.28
19 23 0.72
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:505379 original size:20 final size:19
Alignment explanation
Indices: 505342--505380 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
505332 AAATAAAGAT
**
505342 GTGAAAACATATGTTATGC
1 GTGAAAACATATAATATGC
505361 GTGAAAATCATATAATATGC
1 GTGAAAA-CATATAATATGC
505381 AAGTGAATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (19 bp):
GTGAAAACATATAATATGC
Found at i:507620 original size:10 final size:9
Alignment explanation
Indices: 507573--507627 Score: 53
Period size: 8 Copynumber: 6.3 Consensus size: 9
507563 TCTTTTTGAA
507573 TTTCTTCTT
1 TTTCTTCTT
507582 TTTCTT-TT
1 TTTCTTCTT
507590 TTTCTT-TT
1 TTTCTTCTT
* **
507598 CTGATTC-T
1 TTTCTTCTT
507606 TTTCTTCATT
1 TTTCTTC-TT
507616 TTTCTTCTT
1 TTTCTTCTT
507625 TTT
1 TTT
507628 GTACTCCAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
8 18 0.49
9 11 0.30
10 8 0.22
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (9 bp):
TTTCTTCTT
Found at i:508389 original size:19 final size:21
Alignment explanation
Indices: 508346--508397 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
508336 GAAACCCCTT
508346 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
508367 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
508386 TGAAGATACATG
1 TGAAAATACATG
508398 CTCTTGGCAG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:509409 original size:20 final size:19
Alignment explanation
Indices: 509372--509410 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
509362 AAGTAAATAT
**
509372 GTGAAAACATATGTTATGC
1 GTGAAAACATATAATATGC
509391 GTGAAAATCATATAATATGC
1 GTGAAAA-CATATAATATGC
509411 AAGTGAATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (19 bp):
GTGAAAACATATAATATGC
Found at i:509866 original size:15 final size:16
Alignment explanation
Indices: 509838--509868 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
509828 CATTTCTATC
509838 CATTTCCTTTTCTTAT
1 CATTTCCTTTTCTTAT
509854 CATTTCC-TTTCTTAT
1 CATTTCCTTTTCTTAT
509869 TTCATATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTCCTTTTCTTAT
Found at i:514832 original size:13 final size:13
Alignment explanation
Indices: 514810--514839 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
514800 ACTAAACACC
514810 TTTC-ACATACCT
1 TTTCAACATACCT
514822 TTTCAACATACCT
1 TTTCAACATACCT
514835 TTTCA
1 TTTCA
514840 TATTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:517596 original size:23 final size:24
Alignment explanation
Indices: 517567--517622 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 24
517557 GAATTGTTGA
517567 TGAGTGCTTCCAACTTT-TT-TTTT
1 TGAGTGCTTCCAA-TTTCTTCTTTT
*
517590 TGAGTGCTTTCAATTTCTTCTTTT
1 TGAGTGCTTCCAATTTCTTCTTTT
517614 TGAGTGCTT
1 TGAGTGCTT
517623 ATTTTCTGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 3 0.10
23 14 0.47
24 13 0.43
ACGTcount: A:0.12, C:0.16, G:0.16, T:0.55
Consensus pattern (24 bp):
TGAGTGCTTCCAATTTCTTCTTTT
Found at i:517635 original size:22 final size:24
Alignment explanation
Indices: 517586--517636 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
517576 CCAACTTTTT
**
517586 TTTTTGAGTGCTTTCAATTTCTTC
1 TTTTTGAGTGCTTTCAATTTCTGA
*
517610 TTTTTGAGTGC-TT-ATTTTCTGA
1 TTTTTGAGTGCTTTCAATTTCTGA
517632 TTTTT
1 TTTTT
517637 TTTCTTGCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 11 0.46
23 2 0.08
24 11 0.46
ACGTcount: A:0.12, C:0.12, G:0.14, T:0.63
Consensus pattern (24 bp):
TTTTTGAGTGCTTTCAATTTCTGA
Found at i:517638 original size:24 final size:24
Alignment explanation
Indices: 517567--517622 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
517557 GAATTGTTGA
* *
517567 TGAGTGCTTCCAACTT-TTTTTTT
1 TGAGTGCTTTCAATTTCTTTTTTT
*
517590 TGAGTGCTTTCAATTTCTTCTTTT
1 TGAGTGCTTTCAATTTCTTTTTTT
517614 TGAGTGCTT
1 TGAGTGCTT
517623 ATTTTCTGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 14 0.48
24 15 0.52
ACGTcount: A:0.12, C:0.16, G:0.16, T:0.55
Consensus pattern (24 bp):
TGAGTGCTTTCAATTTCTTTTTTT
Found at i:525202 original size:24 final size:23
Alignment explanation
Indices: 525153--525203 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
525143 AATGAAAATC
**
525153 AAAGCACTCAAAAGAAGAAATTG
1 AAAGCACTCAAAAGAAGAAAAAG
525176 AAAGCACTCGAAAAGAAGAAAAAG
1 AAAGCACTC-AAAAGAAGAAAAAG
525200 AAAG
1 AAAG
525204 AAAGAAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.61, C:0.12, G:0.20, T:0.08
Consensus pattern (23 bp):
AAAGCACTCAAAAGAAGAAAAAG
Found at i:526350 original size:24 final size:24
Alignment explanation
Indices: 526315--526365 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
526305 TCACTTCAAG
* *
526315 TTGAAGATTCAAGAAACATGTCTT
1 TTGAAGAATCAAGAAACATGACTT
* *
526339 TTGAAGAATCAATAAACGTGACTT
1 TTGAAGAATCAAGAAACATGACTT
526363 TTG
1 TTG
526366 GTGATCCACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (24 bp):
TTGAAGAATCAAGAAACATGACTT
Found at i:536272 original size:22 final size:21
Alignment explanation
Indices: 536243--536326 Score: 78
Period size: 23 Copynumber: 3.9 Consensus size: 21
536233 TTTAGTGCAG
536243 AGGGAACCGATACCCCCTTGA
1 AGGGAACCGATACCCCCTTGA
*
536264 ATGGGAACCGATTCCCCCTTTGA
1 A-GGGAACCGATACCCCC-TTGA
* * ***
536287 AGGGGAACTGATTCCCCCCACA
1 A-GGGAACCGATACCCCCTTGA
*
536309 AGGGAATCGATACCCCCT
1 AGGGAACCGATACCCCCT
536327 GAGGGTTCTG
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
21 14 0.27
22 17 0.33
23 20 0.39
ACGTcount: A:0.26, C:0.33, G:0.23, T:0.18
Consensus pattern (21 bp):
AGGGAACCGATACCCCCTTGA
Found at i:536286 original size:23 final size:22
Alignment explanation
Indices: 536244--536304 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 22
536234 TTAGTGCAGA
* *
536244 GGGAACCGATACCCCCTTGAAT
1 GGGAACCGATTCCCCCTTGAAG
536266 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-TTGAAG
*
536289 GGGAACTGATTCCCCC
1 GGGAACCGATTCCCCC
536305 CACAAGGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 15 0.43
23 20 0.57
ACGTcount: A:0.23, C:0.33, G:0.25, T:0.20
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTGAAG
Found at i:537929 original size:18 final size:18
Alignment explanation
Indices: 537908--537948 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
537898 AAAACAACAC
537908 GAGGAACAAGCACGAG-CA
1 GAGGAACAAGCAC-AGCCA
537926 GAGGAACAAGCACAGCCA
1 GAGGAACAAGCACAGCCA
537944 GAGGA
1 GAGGA
537949 TCAAATGCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.44, C:0.22, G:0.34, T:0.00
Consensus pattern (18 bp):
GAGGAACAAGCACAGCCA
Found at i:543965 original size:20 final size:21
Alignment explanation
Indices: 543923--543966 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
543913 AATTTAAACT
543923 ATAATAAAAGTTATAAATAAA
1 ATAATAAAAGTTATAAATAAA
*
543944 ATAATATAA-TTAT-AATACAA
1 ATAATAAAAGTTATAAATA-AA
543964 ATA
1 ATA
543967 TATTTTACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 9 0.43
21 8 0.38
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (21 bp):
ATAATAAAAGTTATAAATAAA
Found at i:545518 original size:35 final size:34
Alignment explanation
Indices: 545472--545538 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 34
545462 GGGTGCCCCT
545472 TCAAAAGGTGCTTTTATGAGGTATGCTTTGACATA
1 TCAAAAGGTGCTTTTATGAGGTATGC-TTGACATA
545507 TCAAAAGGTGCTTTTATGAGGTATGCTTGACA
1 TCAAAAGGTGCTTTTATGAGGTATGCTTGACA
545539 CATTAATAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 6 0.19
35 26 0.81
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (34 bp):
TCAAAAGGTGCTTTTATGAGGTATGCTTGACATA
Found at i:545550 original size:34 final size:35
Alignment explanation
Indices: 545472--545550 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
545462 GGGTGCCCCT
*
545472 TCAAAAGGTGCTTTTATGAGGTATGCTTTGACATA
1 TCAAAAGGTGCTTTTATGAGGTATGCTTTGACACA
545507 TCAAAAGGTGCTTTTATGAGGTATGC-TTGACACA
1 TCAAAAGGTGCTTTTATGAGGTATGCTTTGACACA
* *
545541 TTAATAGGTG
1 TCAAAAGGTG
545551 TGGGAATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
34 15 0.37
35 26 0.63
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.35
Consensus pattern (35 bp):
TCAAAAGGTGCTTTTATGAGGTATGCTTTGACACA
Found at i:551430 original size:20 final size:21
Alignment explanation
Indices: 551407--551448 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
551397 ATTTTGCGGA
551407 TATGGTAA-TAATTTGAATGT
1 TATGGTAATTAATTTGAATGT
* *
551427 TATGTTAATTATTTTGAATGT
1 TATGGTAATTAATTTGAATGT
551448 T
1 T
551449 TTATTTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (21 bp):
TATGGTAATTAATTTGAATGT
Found at i:556841 original size:22 final size:22
Alignment explanation
Indices: 556813--556858 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
556803 TTTGGGCTGT
556813 CAACTTGATCAGCTTGTTGAGC
1 CAACTTGATCAGCTTGTTGAGC
*
556835 CAACTTGATCAGCTTGTTGGGC
1 CAACTTGATCAGCTTGTTGAGC
556857 CA
1 CA
556859 GCCCATAGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (22 bp):
CAACTTGATCAGCTTGTTGAGC
Found at i:558554 original size:38 final size:38
Alignment explanation
Indices: 558476--558555 Score: 94
Period size: 38 Copynumber: 2.1 Consensus size: 38
558466 AACAAGTTGG
* *
558476 AAAATATTTATATATTTTCTTTAAAAATTTAAATTCAT
1 AAAATATTTATATATTTTCTTTAAAAATTGAAAATCAT
558514 AAAAT-TTATATATATATTT-TTTACAAAATTGAAAAT-AT
1 AAAATATT-TATATAT-TTTCTTTA-AAAATTGAAAATCAT
558552 AAAA
1 AAAA
558556 AGTTTTAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
37 2 0.05
38 22 0.59
39 13 0.35
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (38 bp):
AAAATATTTATATATTTTCTTTAAAAATTGAAAATCAT
Found at i:564858 original size:77 final size:79
Alignment explanation
Indices: 564759--564907 Score: 189
Period size: 77 Copynumber: 1.9 Consensus size: 79
564749 TTAATTAATT
* **
564759 TCTTATTTAATTAATTCAAATTAAATATTC-ATT-GAAGACTTATAATCTGAATTACAATC-TTT
1 TCTTATTTAATTAATTCAAATTAAATA-TCAATTAAAAGACTTATAATCAAAATTACAATCTTTT
564821 AATGTTTATTTAAAA
65 AATGTTTATTTAAAA
* * * *
564836 TCTTATTTAATT-ATTCCGAATTAAATATCAATTAAAAGAGTTGTAATCAAAATTACACTCTTTT
1 TCTTATTTAATTAATT-CAAATTAAATATCAATTAAAAGACTTATAATCAAAATTACAATCTTTT
564900 AATGTTTA
65 AATGTTTA
564908 CTTACTATAT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
76 5 0.08
77 25 0.41
78 20 0.33
79 11 0.18
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (79 bp):
TCTTATTTAATTAATTCAAATTAAATATCAATTAAAAGACTTATAATCAAAATTACAATCTTTTA
ATGTTTATTTAAAA
Found at i:581551 original size:25 final size:25
Alignment explanation
Indices: 581522--581573 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
581512 AACAACAAAG
* *
581522 AATTGCAAGTACTCAAAAAGAAGAA
1 AATTGAAAGCACTCAAAAAGAAGAA
*
581547 AATTGAAAGCACTCAAAAATAAGAA
1 AATTGAAAGCACTCAAAAAGAAGAA
581572 AA
1 AA
581574 AGAAAAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.60, C:0.12, G:0.13, T:0.15
Consensus pattern (25 bp):
AATTGAAAGCACTCAAAAAGAAGAA
Found at i:581580 original size:25 final size:25
Alignment explanation
Indices: 581532--581578 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
581522 AATTGCAAGT
*
581532 ACTCAAAAAGAAGAAAATTGAAAGC
1 ACTCAAAAAGAAGAAAATAGAAAGC
*
581557 ACTCAAAAATAAGAAAA-AGAAA
1 ACTCAAAAAGAAGAAAATAGAAA
581579 AGAAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.66, C:0.11, G:0.13, T:0.11
Consensus pattern (25 bp):
ACTCAAAAAGAAGAAAATAGAAAGC
Found at i:584093 original size:21 final size:20
Alignment explanation
Indices: 584069--584107 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
584059 TATGTTATAT
*
584069 CATGAATTACTTAGCTCATGA
1 CATGAATT-CGTAGCTCATGA
*
584090 CATGCATTCGTAGCTCAT
1 CATGAATTCGTAGCTCAT
584108 ATCACTCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.33
Consensus pattern (20 bp):
CATGAATTCGTAGCTCATGA
Found at i:585440 original size:10 final size:10
Alignment explanation
Indices: 585416--585453 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
585406 AATAAGAATG
585416 AATTGAAACTA
1 AATTGAAA-TA
585427 AATTGAAATA
1 AATTGAAATA
585437 AATTGAAA-A
1 AATTGAAATA
585446 AATTGAAA
1 AATTGAAA
585454 ATGATGAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 9 0.33
10 10 0.37
11 8 0.30
ACGTcount: A:0.61, C:0.03, G:0.11, T:0.26
Consensus pattern (10 bp):
AATTGAAATA
Found at i:588778 original size:72 final size:72
Alignment explanation
Indices: 588661--588805 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
588651 TGAGCGATAA
588661 CTTAAAAGGAAGATCTTCAAGAGGAGTAGCAAACATTCGGCCACCAAATGGAAACAAGAGCCCAA
1 CTTAAAAGGAAGATCTTCAAGAGGAGTAGCAAACATTCGGCCACCAAATGGAAACAAGAGCCCAA
588726 TACTTTC
66 TACTTTC
588733 CTTAAAAGGAAGATCTTCAAGAGGAGTAGCAAACATTCGGCCACCAAATGGAAACAAGAGCCCAA
1 CTTAAAAGGAAGATCTTCAAGAGGAGTAGCAAACATTCGGCCACCAAATGGAAACAAGAGCCCAA
588798 TACTTTC
66 TACTTTC
588805 C
1 C
588806 GAAAGCTCAC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.18
Consensus pattern (72 bp):
CTTAAAAGGAAGATCTTCAAGAGGAGTAGCAAACATTCGGCCACCAAATGGAAACAAGAGCCCAA
TACTTTC
Found at i:594557 original size:24 final size:21
Alignment explanation
Indices: 594523--594565 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
594513 TGCACAAGAT
*
594523 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
594545 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
594566 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:601100 original size:59 final size:59
Alignment explanation
Indices: 601002--601122 Score: 161
Period size: 59 Copynumber: 2.1 Consensus size: 59
600992 AGCAGGCTGT
** * *
601002 ATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGTC
1 ATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGTC
* ** * *
601061 ATATTCGGGACTGTACTTAAGGATACCTAGTACAGATGGTGGACATGACCTTATGTGTC
1 ATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGTC
601120 ATA
1 ATA
601123 CTCAGGATTG
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (59 bp):
ATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGTC
Found at i:613943 original size:13 final size:13
Alignment explanation
Indices: 613925--613958 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
613915 TGATATGGTC
613925 TTGATGAAGGATG
1 TTGATGAAGGATG
*
613938 TTGATGAAGGTTG
1 TTGATGAAGGATG
*
613951 ATGATGAA
1 TTGATGAA
613959 ATGACAATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (13 bp):
TTGATGAAGGATG
Found at i:615647 original size:39 final size:36
Alignment explanation
Indices: 615612--615681 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
615602 AATTCAAAAG
*
615612 GCTCTTCTTTATTTGAATTTTCCTCCAAACGTTCAA
1 GCTCTTCTTCATTTGAATTTTCCTCCAAACGTTCAA
* *
615648 GCTTTTCTTCATTTGAATTTTCCTCCAAATGTTC
1 GCTCTTCTTCATTTGAATTTTCCTCCAAACGTTC
615682 TCCTTCAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.20, C:0.24, G:0.09, T:0.47
Consensus pattern (36 bp):
GCTCTTCTTCATTTGAATTTTCCTCCAAACGTTCAA
Found at i:616734 original size:7 final size:6
Alignment explanation
Indices: 616716--616758 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
616706 GATGTAGGGG
*
616716 TCTTTT TCTTTT ATC-TTT TGTTTT TCTTCTT TCTTTT TCTTTT
1 TCTTTT TCTTTT -TCTTTT TCTTTT TCTT-TT TCTTTT TCTTTT
616759 GTTGCAGTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 1 0.03
6 23 0.72
7 8 0.25
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.79
Consensus pattern (6 bp):
TCTTTT
Found at i:616734 original size:13 final size:12
Alignment explanation
Indices: 616716--616758 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
616706 GATGTAGGGG
616716 TCTTTTTCTTTT
1 TCTTTTTCTTTT
*
616728 ATC-TTTTGTTTT
1 -TCTTTTTCTTTT
616740 TCTTCTTTCTTTT
1 TCTT-TTTCTTTT
616753 TCTTTT
1 TCTTTT
616759 GTTGCAGTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 2 0.08
12 11 0.42
13 13 0.50
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.79
Consensus pattern (12 bp):
TCTTTTTCTTTT
Found at i:616756 original size:24 final size:24
Alignment explanation
Indices: 616716--616761 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
616706 GATGTAGGGG
616716 TCTTTTTCTTTTATCTTTTGTTTT
1 TCTTTTTCTTTTATCTTTTGTTTT
616740 TCTTCTTTCTTTT-TCTTTTGTT
1 TCTT-TTTCTTTTATCTTTTGTT
616762 GCAGTACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.78
Consensus pattern (24 bp):
TCTTTTTCTTTTATCTTTTGTTTT
Found at i:617365 original size:22 final size:21
Alignment explanation
Indices: 617340--617380 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
617330 GGTTGCGGAA
617340 TTGATGGTCTTTATGGATGATG
1 TTGATGGTCTTTAT-GATGATG
*
617362 TTGATGGTGTTTATGATGA
1 TTGATGGTCTTTATGATGA
617381 AATAGAGACG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.20, C:0.02, G:0.32, T:0.46
Consensus pattern (21 bp):
TTGATGGTCTTTATGATGATG
Found at i:630555 original size:13 final size:12
Alignment explanation
Indices: 630531--630571 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
630521 GTACTGCAAC
630531 AAAAGCAAAAACA
1 AAAAG-AAAAACA
630544 AAGAAGAAAAACA
1 AA-AAGAAAAACA
*
630557 AAAAGAAAAAGA
1 AAAAGAAAAACA
630569 AAA
1 AAA
630572 GACTCTTACA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 12 0.46
13 11 0.42
14 3 0.12
ACGTcount: A:0.80, C:0.07, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAACA
Found at i:652766 original size:6 final size:6
Alignment explanation
Indices: 652710--652763 Score: 63
Period size: 6 Copynumber: 8.8 Consensus size: 6
652700 GTCTTTTCTT
* * * *
652710 TTTTTA TTTTTA TTTTTA TTTTTA TATTTA TTTTTC TTCTTTG TTTTTG
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT-TTTA TTTTTA
652759 TTTTT
1 TTTTT
652764 GTTGCAGCAC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
6 38 0.88
7 5 0.12
ACGTcount: A:0.11, C:0.04, G:0.04, T:0.81
Consensus pattern (6 bp):
TTTTTA
Found at i:652975 original size:17 final size:17
Alignment explanation
Indices: 652953--652998 Score: 76
Period size: 17 Copynumber: 2.7 Consensus size: 17
652943 ATAAAATAAG
652953 AAATGAATGAAAGAATA
1 AAATGAATGAAAGAATA
652970 AAATGAATG-AAGAATA
1 AAATGAATGAAAGAATA
652986 AAATGAAATGAAA
1 AAATG-AATGAAA
652999 ATGAAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 12 0.44
17 13 0.48
18 2 0.07
ACGTcount: A:0.65, C:0.00, G:0.17, T:0.17
Consensus pattern (17 bp):
AAATGAATGAAAGAATA
Found at i:652980 original size:21 final size:21
Alignment explanation
Indices: 652954--653009 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
652944 TAAAATAAGA
*
652954 AATGAATGAAAGAATAAAATG
1 AATGAATGAAAAAATAAAATG
*
652975 AATGAA-GAATAAAATGAAATG
1 AATGAATGAA-AAAATAAAATG
652996 AA--AATGAAATAAAT
1 AATGAATGAAA-AAAT
653010 GAATAGAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
19 3 0.10
20 10 0.33
21 17 0.57
ACGTcount: A:0.64, C:0.00, G:0.16, T:0.20
Consensus pattern (21 bp):
AATGAATGAAAAAATAAAATG
Found at i:652984 original size:16 final size:16
Alignment explanation
Indices: 652953--653012 Score: 77
Period size: 16 Copynumber: 3.7 Consensus size: 16
652943 ATAAAATAAG
652953 AAATGAATGAAAGAATA
1 AAATGAATG-AAGAATA
652970 AAATGAATGAAGAATA
1 AAATGAATGAAGAATA
*
652986 AAATGAAATGAA-AATG
1 AAATG-AATGAAGAATA
*
653002 AAATAAATGAA
1 AAATGAATGAA
653013 TAGAGATGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.15
16 19 0.47
17 15 0.38
ACGTcount: A:0.65, C:0.00, G:0.17, T:0.18
Consensus pattern (16 bp):
AAATGAATGAAGAATA
Found at i:663697 original size:15 final size:15
Alignment explanation
Indices: 663656--663689 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 15
663646 TGATAATTAA
663656 GAAAGGAAATGGAAATG
1 GAAA-GAAAT-GAAATG
663673 GAAAGAAATGAAATG
1 GAAAGAAATGAAATG
663688 GA
1 GA
663690 TATAAATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 5 0.29
17 4 0.24
ACGTcount: A:0.56, C:0.00, G:0.32, T:0.12
Consensus pattern (15 bp):
GAAAGAAATGAAATG
Found at i:670176 original size:59 final size:58
Alignment explanation
Indices: 670110--670329 Score: 323
Period size: 59 Copynumber: 3.7 Consensus size: 58
670100 CTTCAATAGA
* * * *
670110 AAATTCATACAATTAATATGATTTCCTTATCATTTTAGCACACGATGTACCCTATCTG
1 AAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCTG
* * *
670168 TAAATTCATACACTTAGCATGATTTCCTTATCATTTTAGCACATGAAGTGCCATATCTAG
1 -AAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT-G
* * *
670228 AAATTGATACACTTAGTATGATTTTCTTATCGTTTTAGCACACGAAGTGCCCTATCTGG
1 AAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT-G
670287 AAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACAC
1 AAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACAC
670330 TTGGTGCCAT
Statistics
Matches: 143, Mismatches: 17, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
59 142 0.99
60 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (58 bp):
AAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCTG
Found at i:670318 original size:118 final size:118
Alignment explanation
Indices: 670110--670328 Score: 357
Period size: 118 Copynumber: 1.9 Consensus size: 118
670100 CTTCAATAGA
* *
670110 AAATTCATACAATTAATATGATTTCCTTATCATTTTAGCACACGATGTACCCTATCTGTAAATTC
1 AAATTCATACAATTAATATGATTTCCTTATCATTTTAGCACACGAAGTACCCTATCTGGAAATTC
670175 ATACACTTAGCATGATTTCCTTATCATTTTAGCACATGAAGTGCCATATCTAG
66 ATACACTTAGCATGATTTCCTTATCATTTTAGCACATGAAGTGCCATATCTAG
* * * * * *
670228 AAATTGATACACTTAGTATGATTTTCTTATCGTTTTAGCACACGAAGTGCCCTATCTGGAAATTC
1 AAATTCATACAATTAATATGATTTCCTTATCATTTTAGCACACGAAGTACCCTATCTGGAAATTC
*
670293 ATACACTTAGTATGATTTCCTTATCATTTTAGCACA
66 ATACACTTAGCATGATTTCCTTATCATTTTAGCACA
670329 CTTGGTGCCA
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
118 92 1.00
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (118 bp):
AAATTCATACAATTAATATGATTTCCTTATCATTTTAGCACACGAAGTACCCTATCTGGAAATTC
ATACACTTAGCATGATTTCCTTATCATTTTAGCACATGAAGTGCCATATCTAG
Found at i:670767 original size:19 final size:20
Alignment explanation
Indices: 670699--670768 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 20
670689 GTGGCCCAGT
*
670699 ATCGATACCCTTACCATGGC
1 ATCGATACCCTTACTATGGC
* *
670719 ATCGATACTACTATACTATGGT
1 ATCGATAC-CCT-TACTATGGC
670741 ATCGATACCCTTA-TATGGC
1 ATCGATACCCTTACTATGGC
*
670760 ATCAATACC
1 ATCGATACC
670769 AAAATTAGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
19 13 0.31
20 10 0.24
21 4 0.10
22 15 0.36
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (20 bp):
ATCGATACCCTTACTATGGC
Found at i:670782 original size:95 final size:94
Alignment explanation
Indices: 670615--670825 Score: 271
Period size: 95 Copynumber: 2.2 Consensus size: 94
670605 ATTTCTGGCC
** * * * *
670615 TACCATGGTATCGATACTACCCTACTTTGGTATTGATACCCCCTTCTAGTATCAATACCAAAATT
1 TACCATGGTATCGATACTACTATACTATGGTATCGATA-CCCCTTATAGCATCAATACCAAAATT
*
670680 AGATTCGATGTGGCCCAGTATCGATACCCT
65 AGATTCGATGTGACCCAGTATCGATACCCT
*
670710 TACCATGGCATCGATACTACTATACTATGGTATCGATA-CCCTTATATGGCATCAATACCAAAAT
1 TACCATGGTATCGATACTACTATACTATGGTATCGATACCCCTTATA--GCATCAATACCAAAAT
* * * *
670774 TAGGTTCGATGTTACCCGGTTTCGATACCCT
64 TAGATTCGATGTGACCCAGTATCGATACCCT
*
670805 AACCATGGTATCGATACTACT
1 TACCATGGTATCGATACTACT
670826 TCGTTAGGTA
Statistics
Matches: 100, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
93 7 0.07
95 93 0.93
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.31
Consensus pattern (94 bp):
TACCATGGTATCGATACTACTATACTATGGTATCGATACCCCTTATAGCATCAATACCAAAATTA
GATTCGATGTGACCCAGTATCGATACCCT
Found at i:678091 original size:19 final size:20
Alignment explanation
Indices: 678048--678098 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
678038 GAAACCCCTT
* **
678048 TGAAAATACATAATTTTTTA
1 TGAAAATACATGATTTTCAA
678068 TGAAAATACATGA-TTTCAA
1 TGAAAATACATGATTTTCAA
678087 TGAAAATACATG
1 TGAAAATACATG
678099 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTCAA
Found at i:691147 original size:20 final size:21
Alignment explanation
Indices: 691118--691163 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
691108 AGTAAATAAG
*
691118 AATG-AATGAAAGAAA-AGGA
1 AATGAAATGAAAGAAAGAGAA
*
691137 AATGAAATGAAATAAAGAGAA
1 AATGAAATGAAAGAAAGAGAA
691158 AATGAA
1 AATGAA
691164 GATACTTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 4 0.17
20 10 0.43
21 9 0.39
ACGTcount: A:0.65, C:0.00, G:0.22, T:0.13
Consensus pattern (21 bp):
AATGAAATGAAAGAAAGAGAA
Found at i:691308 original size:26 final size:28
Alignment explanation
Indices: 691279--691336 Score: 66
Period size: 31 Copynumber: 2.0 Consensus size: 28
691269 TTGAGTGTAC
691279 TTTGC-AACTTT-TTCTTCTCTTTTCTT
1 TTTGCTAACTTTCTTCTTCTCTTTTCTT
*
691305 TTTGCTTTGAATTTTCTTCTTCTCTTTTCTT
1 TTTGC--T-AACTTTCTTCTTCTCTTTTCTT
691336 T
1 T
691337 CTTTTGCACT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 5 0.19
30 5 0.19
31 16 0.62
ACGTcount: A:0.07, C:0.21, G:0.05, T:0.67
Consensus pattern (28 bp):
TTTGCTAACTTTCTTCTTCTCTTTTCTT
Found at i:706052 original size:24 final size:24
Alignment explanation
Indices: 706020--706081 Score: 106
Period size: 24 Copynumber: 2.5 Consensus size: 24
706010 CCTAAATGAG
706020 ACTAGGTGACTATCTTGGTAGCTA
1 ACTAGGTGACTATCTTGGTAGCTA
*
706044 ACTAGGTGACTCTCTTGGTAGCTA
1 ACTAGGTGACTATCTTGGTAGCTA
706068 ACTAGGTGAACTAT
1 ACTAGGTG-ACTAT
706082 AGCATAATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
24 31 0.89
25 4 0.11
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (24 bp):
ACTAGGTGACTATCTTGGTAGCTA
Found at i:709523 original size:24 final size:24
Alignment explanation
Indices: 709496--709548 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
709486 ATCAGTAAAT
*
709496 AAAAGTCAAGCACTCCAAAAGAAG
1 AAAAGTCAAGCACTCAAAAAGAAG
* *
709520 AAAAATCCAGCACTCAAAAAGAAG
1 AAAAGTCAAGCACTCAAAAAGAAG
709544 AAAAG
1 AAAAG
709549 AAAAGAAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.58, C:0.19, G:0.15, T:0.08
Consensus pattern (24 bp):
AAAAGTCAAGCACTCAAAAAGAAG
Found at i:715763 original size:20 final size:20
Alignment explanation
Indices: 715719--715775 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
715709 CCATTTGGCC
* * *
715719 AAAAGCATGTAATTTC-ATT
1 AAAATCATGTATTTTCAATA
715738 AAAATCATGTATTTTCAATA
1 AAAATCATGTATTTTCAATA
715758 AAAATCATGTATTTTCAA
1 AAAATCATGTATTTTCAA
715776 AGGGGTTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 14 0.41
20 20 0.59
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.39
Consensus pattern (20 bp):
AAAATCATGTATTTTCAATA
Found at i:723807 original size:19 final size:19
Alignment explanation
Indices: 723783--723819 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
723773 TACACGATTT
723783 TTTTAATGAAAATACATGA
1 TTTTAATGAAAATACATGA
*
723802 TTTTAATGAAGATACATG
1 TTTTAATGAAAATACATG
723820 CTCTTGGACG
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:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (19 bp):
TTTTAATGAAAATACATGA
Found at i:728928 original size:8 final size:8
Alignment explanation
Indices: 728917--728944 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
728907 CAAAAAATAG
728917 AAAATAAT
1 AAAATAAT
728925 AAAATAAT
1 AAAATAAT
728933 AAAATAAT
1 AAAATAAT
728941 AAAA
1 AAAA
728945 ATCCAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAATAAT
Found at i:732532 original size:2 final size:2
Alignment explanation
Indices: 732525--732553 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
732515 CTTTTAATTG
732525 AT 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 AT A
732554 ATTCGGAATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:742686 original size:163 final size:163
Alignment explanation
Indices: 742416--742742 Score: 654
Period size: 163 Copynumber: 2.0 Consensus size: 163
742406 AGGTGCACGG
742416 CATTGTCTTGTGGATCTATGCAGTGTTTGTGTTTCTAAATCTATTGAATGCTCCTCAACAACTTG
1 CATTGTCTTGTGGATCTATGCAGTGTTTGTGTTTCTAAATCTATTGAATGCTCCTCAACAACTTG
742481 TGAAACATGCTCAACTTCAGGTTCATTTATTTGTTGTTCTTGAAATTCTCCAAGTTTAGTATGTC
66 TGAAACATGCTCAACTTCAGGTTCATTTATTTGTTGTTCTTGAAATTCTCCAAGTTTAGTATGTC
742546 TACCCTTTCATTTCTTTAAGAGAAATTCTCTTT
131 TACCCTTTCATTTCTTTAAGAGAAATTCTCTTT
742579 CATTGTCTTGTGGATCTATGCAGTGTTTGTGTTTCTAAATCTATTGAATGCTCCTCAACAACTTG
1 CATTGTCTTGTGGATCTATGCAGTGTTTGTGTTTCTAAATCTATTGAATGCTCCTCAACAACTTG
742644 TGAAACATGCTCAACTTCAGGTTCATTTATTTGTTGTTCTTGAAATTCTCCAAGTTTAGTATGTC
66 TGAAACATGCTCAACTTCAGGTTCATTTATTTGTTGTTCTTGAAATTCTCCAAGTTTAGTATGTC
742709 TACCCTTTCATTTCTTTAAGAGAAATTCTCTTT
131 TACCCTTTCATTTCTTTAAGAGAAATTCTCTTT
742742 C
1 C
742743 GAGAAAAACT
Statistics
Matches: 164, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
163 164 1.00
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (163 bp):
CATTGTCTTGTGGATCTATGCAGTGTTTGTGTTTCTAAATCTATTGAATGCTCCTCAACAACTTG
TGAAACATGCTCAACTTCAGGTTCATTTATTTGTTGTTCTTGAAATTCTCCAAGTTTAGTATGTC
TACCCTTTCATTTCTTTAAGAGAAATTCTCTTT
Found at i:745700 original size:2 final size:2
Alignment explanation
Indices: 745693--745719 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
745683 CACCTTGCAA
745693 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
745720 CACGTTCTTA
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:746233 original size:128 final size:128
Alignment explanation
Indices: 746005--746260 Score: 512
Period size: 128 Copynumber: 2.0 Consensus size: 128
745995 TCGATTCGAA
746005 CAATGATATCAGCATATTTACCGAAATCGATAAAACTAGAACATGCATCTCATACATATCGCATC
1 CAATGATATCAGCATATTTACCGAAATCGATAAAACTAGAACATGCATCTCATACATATCGCATC
746070 ATCCAAGAATTTAACCAGAATTTAGATGTACAAGTGGCTCTAACAACACTGTTGGGACCGTTT
66 ATCCAAGAATTTAACCAGAATTTAGATGTACAAGTGGCTCTAACAACACTGTTGGGACCGTTT
746133 CAATGATATCAGCATATTTACCGAAATCGATAAAACTAGAACATGCATCTCATACATATCGCATC
1 CAATGATATCAGCATATTTACCGAAATCGATAAAACTAGAACATGCATCTCATACATATCGCATC
746198 ATCCAAGAATTTAACCAGAATTTAGATGTACAAGTGGCTCTAACAACACTGTTGGGACCGTTT
66 ATCCAAGAATTTAACCAGAATTTAGATGTACAAGTGGCTCTAACAACACTGTTGGGACCGTTT
746261 GCACACCCCA
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
128 128 1.00
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (128 bp):
CAATGATATCAGCATATTTACCGAAATCGATAAAACTAGAACATGCATCTCATACATATCGCATC
ATCCAAGAATTTAACCAGAATTTAGATGTACAAGTGGCTCTAACAACACTGTTGGGACCGTTT
Found at i:760221 original size:15 final size:15
Alignment explanation
Indices: 760203--760242 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
760193 TTCATCAGGA
*
760203 ACATGTTCCTCAATG
1 ACATATTCCTCAATG
*
760218 ACATATTCCTGAATG
1 ACATATTCCTCAATG
760233 ACATATTCCT
1 ACATATTCCT
760243 TCCTTTCCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (15 bp):
ACATATTCCTCAATG
Found at i:762213 original size:77 final size:77
Alignment explanation
Indices: 762086--762240 Score: 310
Period size: 77 Copynumber: 2.0 Consensus size: 77
762076 CCTAAGTTAC
762086 AAGAAAATACGATTCGACATATCATCTTGGTGGTTAACTCTTTTATGTATTACATCCTTATGCCC
1 AAGAAAATACGATTCGACATATCATCTTGGTGGTTAACTCTTTTATGTATTACATCCTTATGCCC
762151 TTTATATCTAGA
66 TTTATATCTAGA
762163 AAGAAAATACGATTCGACATATCATCTTGGTGGTTAACTCTTTTATGTATTACATCCTTATGCCC
1 AAGAAAATACGATTCGACATATCATCTTGGTGGTTAACTCTTTTATGTATTACATCCTTATGCCC
762228 TTTATATCTAGA
66 TTTATATCTAGA
762240 A
1 A
762241 TAGACACAAG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (77 bp):
AAGAAAATACGATTCGACATATCATCTTGGTGGTTAACTCTTTTATGTATTACATCCTTATGCCC
TTTATATCTAGA
Found at i:763416 original size:174 final size:175
Alignment explanation
Indices: 763126--763476 Score: 695
Period size: 174 Copynumber: 2.0 Consensus size: 175
763116 TTTAGGAATA
763126 CTCCCTTAAAGGCAAAGCAAACATTGGTTGCATATGGTAAGAACGTGCTTGCATCACCTAATTTA
1 CTCCCTTAAAGGCAAAGCAAACATTGGTTGCATATGGTAAGAACGTGCTTGCATCACCTAATTTA
763191 ATAAATAGTGGGTTTGAGTCCTTAACACCACCCCTTAGTTAAGTTTGCAAAGATCGGAGCTACAC
66 ATAAATAGTGGGTTTGAGTCCTTAACACCACCCCTTAGTTAAGTTTGCAAAGATCGGAGCTACAC
763256 TCTTCATATTATAGTTTCTTCTTTAATTTATAT-AGATACTATTT
131 TCTTCATATTATAGTTTCTTCTTTAATTTATATAAGATACTATTT
763300 CTCCCTTAAAGGCAAAGCAAACATTGGTTGCATATGGTAAGAACGTGCTTGCATCACCTAATTTA
1 CTCCCTTAAAGGCAAAGCAAACATTGGTTGCATATGGTAAGAACGTGCTTGCATCACCTAATTTA
763365 ATAAATAGTGGGTTTGAGTCCTTAACACCACCCCTTAGTTAAGTTTGCAAAGATCGGAGCTACAC
66 ATAAATAGTGGGTTTGAGTCCTTAACACCACCCCTTAGTTAAGTTTGCAAAGATCGGAGCTACAC
763430 TCTTCATATTATAGTTTCTTCTTTAATTTATATAAGATACTATTT
131 TCTTCATATTATAGTTTCTTCTTTAATTTATATAAGATACTATTT
763475 CT
1 CT
763477 TTTCATTTCC
Statistics
Matches: 176, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
174 163 0.93
175 13 0.07
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.35
Consensus pattern (175 bp):
CTCCCTTAAAGGCAAAGCAAACATTGGTTGCATATGGTAAGAACGTGCTTGCATCACCTAATTTA
ATAAATAGTGGGTTTGAGTCCTTAACACCACCCCTTAGTTAAGTTTGCAAAGATCGGAGCTACAC
TCTTCATATTATAGTTTCTTCTTTAATTTATATAAGATACTATTT
Found at i:770644 original size:18 final size:18
Alignment explanation
Indices: 770607--770640 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
770597 TTTTAAGATT
770607 TTATATTCGATTTAAATA
1 TTATATTCGATTTAAATA
770625 TTATATTCGA-TTAAAT
1 TTATATTCGATTTAAAT
770641 TATTCGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (18 bp):
TTATATTCGATTTAAATA
Found at i:771020 original size:24 final size:23
Alignment explanation
Indices: 770988--771066 Score: 76
Period size: 24 Copynumber: 3.5 Consensus size: 23
770978 ACCATGTTCG
*
770988 GTATCGATACTACTTTACATAGTA
1 GTATCGATACTACTTCA-ATAGTA
* *
771012 GTATCGATACTCAC-TGAA-CG--
1 GTATCGATACT-ACTTCAATAGTA
771032 GTATCGATACTACTTCATATAGTA
1 GTATCGATACTACTTCA-ATAGTA
771056 GTATCGATACT
1 GTATCGATACT
771067 CCTTGAACAG
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
19 2 0.04
20 13 0.29
21 1 0.02
22 2 0.04
23 1 0.02
24 24 0.53
25 2 0.04
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (23 bp):
GTATCGATACTACTTCAATAGTA
Found at i:771035 original size:44 final size:44
Alignment explanation
Indices: 770986--771085 Score: 157
Period size: 44 Copynumber: 2.3 Consensus size: 44
770976 ATACCATGTT
*
770986 CGGTATCGATACTACTTTACATAGTAGTATCGATACTCAC-TGAA
1 CGGTATCGATACTACTTCACATAGTAGTATCGATACTC-CTTGAA
*
771030 CGGTATCGATACTACTTCATATAGTAGTATCGATACTCCTTGAA
1 CGGTATCGATACTACTTCACATAGTAGTATCGATACTCCTTGAA
*
771074 CAGTATCGATAC
1 CGGTATCGATAC
771086 CATTGAGTTG
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
43 1 0.02
44 51 0.98
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (44 bp):
CGGTATCGATACTACTTCACATAGTAGTATCGATACTCCTTGAA
Found at i:771990 original size:23 final size:23
Alignment explanation
Indices: 771946--771990 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
771936 CGCCAACTAC
**
771946 GCCTATTGGAAGAATACGATGAT
1 GCCTATTGGAAGAATAAAATGAT
771969 GCCTATTGGAAGAATAAAATGA
1 GCCTATTGGAAGAATAAAATGA
771991 AGTTATGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.24
Consensus pattern (23 bp):
GCCTATTGGAAGAATAAAATGAT
Found at i:780585 original size:97 final size:97
Alignment explanation
Indices: 780414--780601 Score: 349
Period size: 97 Copynumber: 1.9 Consensus size: 97
780404 CAAATATTTT
*
780414 TATTTTTTGTCAAGCTTCCACCAAAATTTTAATTGCCAATTCACCCCCTCTTGGCTATTTCATCT
1 TATTTTTTGTCAAGCTTCCACCAAAATTTTAATTGCCAATTCACCCCCTCTTGGCTATTTCATCC
*
780479 GATCAATTGACTCAACAGAACGTTTGGAGGAA
66 AATCAATTGACTCAACAGAACGTTTGGAGGAA
780511 TATTTTTTGTCAAGCTTCCACCAAAATTTTAATTGCCAATTCACCCCCTCTTGGCTATTTCATCC
1 TATTTTTTGTCAAGCTTCCACCAAAATTTTAATTGCCAATTCACCCCCTCTTGGCTATTTCATCC
*
780576 AATCGATTGACTCAACAGAACGTTTG
66 AATCAATTGACTCAACAGAACGTTTG
780602 AAGATGAATA
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
97 88 1.00
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.36
Consensus pattern (97 bp):
TATTTTTTGTCAAGCTTCCACCAAAATTTTAATTGCCAATTCACCCCCTCTTGGCTATTTCATCC
AATCAATTGACTCAACAGAACGTTTGGAGGAA
Found at i:782629 original size:44 final size:44
Alignment explanation
Indices: 782566--782654 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
782556 GGGCTGTTAG
782566 ATCTCGGAGCTAGACCCAACGGTTGAAACATGGTTGCATTTAAA
1 ATCTCGGAGCTAGACCCAACGGTTGAAACATGGTTGCATTTAAA
782610 ATCTCGGAGCTAGACCCAACGGTTGAAACATGGTTGCATTTAAA
1 ATCTCGGAGCTAGACCCAACGGTTGAAACATGGTTGCATTTAAA
782654 A
1 A
782655 CTTTTAGGGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (44 bp):
ATCTCGGAGCTAGACCCAACGGTTGAAACATGGTTGCATTTAAA
Found at i:783642 original size:25 final size:26
Alignment explanation
Indices: 783609--783662 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 26
783599 GGTAATTTAT
*
783609 TTTATTTTTCTTTAAAATTCTT-TAAA
1 TTTATTTTTCTCTAAAATT-TTATAAA
783635 TTTA-TTTTCTCTAAAATTTTATAAA
1 TTTATTTTTCTCTAAAATTTTATAAA
783660 TTT
1 TTT
783663 TAAATTAAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 2 0.08
25 20 0.77
26 4 0.15
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTATTTTTCTCTAAAATTTTATAAA
Found at i:785981 original size:18 final size:18
Alignment explanation
Indices: 785957--786003 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
785947 AAGACAAAAG
*
785957 CAAAAAGAAAAATAAGTT
1 CAAAAAGAAAAAGAAGTT
*
785975 TAAAAAGAAAAAGAAGTT
1 CAAAAAGAAAAAGAAGTT
785993 CAAAAAGAAAA
1 CAAAAAGAAAA
786004 TCAAACTCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.70, C:0.04, G:0.13, T:0.13
Consensus pattern (18 bp):
CAAAAAGAAAAAGAAGTT
Found at i:787175 original size:36 final size:36
Alignment explanation
Indices: 787123--787194 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
787113 AATTGAAGGA
*
787123 GAACGTTTGGAGAAAAATTCAAATGAAGAAAAGCTT
1 GAACGTTTGAAGAAAAATTCAAATGAAGAAAAGCTT
*
787159 GAACGTTTGAATAAAAATTCAAATGAAGAAAAGCTT
1 GAACGTTTGAAGAAAAATTCAAATGAAGAAAAGCTT
787195 TTTGAAGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.49, C:0.08, G:0.19, T:0.24
Consensus pattern (36 bp):
GAACGTTTGAAGAAAAATTCAAATGAAGAAAAGCTT
Found at i:787799 original size:23 final size:23
Alignment explanation
Indices: 787765--787820 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
787755 GAGACTCAAA
* *
787765 CTCGATTGAAGCTCGATT-TGGAG
1 CTCGATTCAAGCTCAATTGT-GAG
787788 CTCGATTCAAGCTCAATTGTGAG
1 CTCGATTCAAGCTCAATTGTGAG
*
787811 CTCAATTCAA
1 CTCGATTCAA
787821 AATCGACTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 28 0.97
24 1 0.03
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (23 bp):
CTCGATTCAAGCTCAATTGTGAG
Found at i:789872 original size:7 final size:7
Alignment explanation
Indices: 789860--789940 Score: 81
Period size: 7 Copynumber: 11.6 Consensus size: 7
789850 AATCGAATTA
789860 AGGGTTT
1 AGGGTTT
789867 AGGGTTT
1 AGGGTTT
**
789874 ATAGTTT
1 AGGGTTT
*
789881 AGGGTAT
1 AGGGTTT
*
789888 AGGGCTT
1 AGGGTTT
*
789895 AGGGCTT
1 AGGGTTT
789902 AGGGTTT
1 AGGGTTT
*
789909 AAGGTTT
1 AGGGTTT
*
789916 AAGGTTT
1 AGGGTTT
*
789923 AAGGTTT
1 AGGGTTT
*
789930 ATGGTTT
1 AGGGTTT
789937 AGGG
1 AGGG
789941 ATCATTGCAA
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 63 1.00
ACGTcount: A:0.21, C:0.02, G:0.37, T:0.40
Consensus pattern (7 bp):
AGGGTTT
Found at i:792742 original size:12 final size:12
Alignment explanation
Indices: 792727--792751 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
792717 CATTACTTAT
792727 TTTATTATTCCA
1 TTTATTATTCCA
792739 TTTATTATTCCA
1 TTTATTATTCCA
792751 T
1 T
792752 CATTAATCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTATTATTCCA
Found at i:801351 original size:65 final size:64
Alignment explanation
Indices: 801281--801441 Score: 191
Period size: 65 Copynumber: 2.5 Consensus size: 64
801271 AATTAAATTG
* * * * *
801281 AACATCAAATGCATTTCATGCATCGATGCACATA-CCATGCATCGATGCACTGGGGAT-TTTATG
1 AACATCGAATGCATTTAATGCATCGATGCAC-TAGACATACATCGATGCACTCGGGATATTT-TG
801344 AA
64 -A
* *
801346 AACATCGAATGCATTTAATGCATCGATGCACTAGACATACATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTAATGCATCGATGCACTAGACATACATCGATGCACTCGGGATATTTTGA
* * *
801410 AACATCGAATACACTTGATGCATCGATGCACT
1 AACATCGAATGCATTTAATGCATCGATGCACT
801442 CTTAGTGCAC
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 32 0.38
65 49 0.58
66 3 0.04
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTAATGCATCGATGCACTAGACATACATCGATGCACTCGGGATATTTTGA
Found at i:803404 original size:21 final size:20
Alignment explanation
Indices: 803369--803413 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
803359 GAATTATGAG
*
803369 AAATTGTTTTTAAAATAT-AA
1 AAATTATTTTTAAAAT-TGAA
803389 AAATTATTTTTCAAAATTGAA
1 AAATTATTTTT-AAAATTGAA
803410 AAAT
1 AAAT
803414 GAAAATAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.42
Consensus pattern (20 bp):
AAATTATTTTTAAAATTGAA
Found at i:807294 original size:21 final size:21
Alignment explanation
Indices: 807229--807323 Score: 86
Period size: 23 Copynumber: 4.4 Consensus size: 21
807219 TTGTGCTTCA
*
807229 TGCATCGATACACC-T-AACAG
1 TGCATCGATACACCTTGAA-TG
*
807249 TGCATCGATGCATCCTTGAATG
1 TGCATCGATACA-CCTTGAATG
* *
807271 TGCATCGATACACCATGAAGG
1 TGCATCGATACACCTTGAATG
* *
807292 TGCACCGATGCACGCCTTGAATG
1 TGCATCGAT--ACACCTTGAATG
807315 TGCATCGAT
1 TGCATCGAT
807324 GCACAGGGTC
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
20 11 0.18
21 17 0.28
22 13 0.22
23 19 0.32
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.24
Consensus pattern (21 bp):
TGCATCGATACACCTTGAATG
Found at i:807317 original size:23 final size:23
Alignment explanation
Indices: 807248--807328 Score: 96
Period size: 23 Copynumber: 3.7 Consensus size: 23
807238 ACACCTAACA
*
807248 GTGCATCGATGCA-TCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
* *
807270 GTGCATCGAT--ACACCATGAAG
1 GTGCATCGATGCACACCTTGAAT
* *
807291 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
807314 GTGCATCGATGCACA
1 GTGCATCGATGCACA
807329 GGGTCATGCA
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
20 1 0.02
21 15 0.32
22 10 0.21
23 21 0.45
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.23
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Found at i:807319 original size:44 final size:42
Alignment explanation
Indices: 807229--807323 Score: 129
Period size: 44 Copynumber: 2.2 Consensus size: 42
807219 TTGTGCTTCA
* *
807229 TGCATCGATACACCTAACAGTGCATCGATGCATCCTTGAATG
1 TGCATCGATACACCTAACAGTGCACCGATGCAGCCTTGAATG
*
807271 TGCATCGATACACCATGAA-GGTGCACCGATGCACGCCTTGAATG
1 TGCATCGATACACC-T-AACAGTGCACCGATGCA-GCCTTGAATG
807315 TGCATCGAT
1 TGCATCGAT
807324 GCACAGGGTC
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
42 14 0.30
43 13 0.28
44 20 0.43
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.24
Consensus pattern (42 bp):
TGCATCGATACACCTAACAGTGCACCGATGCAGCCTTGAATG
Found at i:807344 original size:43 final size:43
Alignment explanation
Indices: 807229--807344 Score: 112
Period size: 43 Copynumber: 2.7 Consensus size: 43
807219 TTGTGCTTCA
* *
807229 TGCATCGATACACC--TAACAGTGCATCGATGCATCCTTGAATG
1 TGCATCGATACACCAGGAACA-TGCATCGATGCAGCCTTGAATG
* ** *
807271 TGCATCGATACACCATGAAGGTGCACCGATGCACGCCTTGAATG
1 TGCATCGATACACCAGGAACATGCATCGATGCA-GCCTTGAATG
* **
807315 TGCATCGATGCA-CAGGGTCATGCATCGATG
1 TGCATCGATACACCAGGAACATGCATCGATG
807345 TATCTGTCGG
Statistics
Matches: 59, Mismatches: 12, Indels: 5
0.78 0.16 0.07
Matches are distributed among these distances:
42 14 0.24
43 23 0.39
44 22 0.37
ACGTcount: A:0.27, C:0.26, G:0.24, T:0.23
Consensus pattern (43 bp):
TGCATCGATACACCAGGAACATGCATCGATGCAGCCTTGAATG
Found at i:810026 original size:65 final size:64
Alignment explanation
Indices: 809949--810071 Score: 167
Period size: 64 Copynumber: 1.9 Consensus size: 64
809939 GAACGCATTT
* * *
809949 CATGTATCGATGCACTGAGGAT-TTTATGAAAAAATCGAATGCATTTGATGCATCGATGCACCAG
1 CATGCATCGATGCACTCAGGATATTT-TG-AAAAATCGAATGCACTTGATGCATCGATGCACCAG
810013 A
64 A
* * *
810014 CATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGATGCATCGATGC
1 CATGCATCGATGCACTCAGGATATTTTGAAAAATCGAATGCACTTGATGCATCGATGC
810072 TCTCTTAGTG
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
64 28 0.55
65 20 0.39
66 3 0.06
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (64 bp):
CATGCATCGATGCACTCAGGATATTTTGAAAAATCGAATGCACTTGATGCATCGATGCACCAGA
Found at i:811217 original size:2 final size:2
Alignment explanation
Indices: 811210--811235 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
811200 TATAACATAA
811210 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
811236 TAAATCTATT
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:817336 original size:95 final size:95
Alignment explanation
Indices: 817237--817441 Score: 243
Period size: 95 Copynumber: 2.2 Consensus size: 95
817227 AGAAGGGGAC
* * **
817237 ATCGATGCCATAGT-GTAGTAGTATCGATACCATGGAAAAGGCATCGATACCAGGCCACATCGAA
1 ATCGATACCATAGTAG-AGTAGTATCGATACCATGGAAAAGGCATCGATACCAAGAAACATCGAA
**
817301 -TCTAATTTTGGTATCGATATTATATGGGGGT
65 GT-TAAAATTGGTATCGATATTATATGGGGGT
** *
817332 ATCGATACCATAGTAGAGTAGTATCGATACCATGTTAAAGGTATCGATACCAAGAAACATCGAAG
1 ATCGATACCATAGTAGAGTAGTATCGATACCATGGAAAAGGCATCGATACCAAGAAACATCGAAG
**** *
817397 TTAAAATTGGTATCGATACCGGAAGGGGGT
66 TTAAAATTGGTATCGATATTATATGGGGGT
*
817427 AACGATACCATAGTA
1 ATCGATACCATAGTA
817442 TAGAAGTGCC
Statistics
Matches: 93, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
95 91 0.98
96 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (95 bp):
ATCGATACCATAGTAGAGTAGTATCGATACCATGGAAAAGGCATCGATACCAAGAAACATCGAAG
TTAAAATTGGTATCGATATTATATGGGGGT
Found at i:817377 original size:20 final size:20
Alignment explanation
Indices: 817329--817383 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 20
817319 ATTATATGGG
*
817329 GGTATCGATACCATAGTAGA
1 GGTATCGATACCATAGTAAA
817349 GTAGTATCGATACCAT-GTTAAA
1 G--GTATCGATACCATAG-TAAA
817371 GGTATCGATACCA
1 GGTATCGATACCA
817384 AGAAACATCG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 13 0.42
21 1 0.03
22 17 0.55
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (20 bp):
GGTATCGATACCATAGTAAA
Found at i:817918 original size:46 final size:46
Alignment explanation
Indices: 817865--818186 Score: 446
Period size: 46 Copynumber: 7.0 Consensus size: 46
817855 AAATCGAAAA
*
817865 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAACGGGTGC
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGC
* *
817911 CATAATTAAAATGCATGAAAGTATGCATTAAGGCATGAACGGATAC
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGC
* *
817957 CATAATTAAAATGCATGAAAGGATGCATGAAGGCATGGACGGATGC
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGC
* * * *
818003 CATAACTAAAATGCATGAAATGATGCATGAAGGCATGAACGAATGC
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGC
* * * * *
818049 CATAACTAAAATGCATGAAATGATGCATGATGGCATGAACGTATGC
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGC
* * *
818095 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATTC
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGC
* * * *
818141 CATAAATTATAATGCATGAAAAGATGCATTAAAGCATGAATGGATG
1 CAT-AATTAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATG
818187 TATTAATACT
Statistics
Matches: 250, Mismatches: 25, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
46 214 0.86
47 36 0.14
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.22
Consensus pattern (46 bp):
CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGC
Found at i:818120 original size:26 final size:25
Alignment explanation
Indices: 817865--818167 Score: 99
Period size: 20 Copynumber: 13.0 Consensus size: 25
817855 AAATCGAAAA
817865 CATAATTAAAATGCATGAAAGGATG-
1 CATAA-TAAAATGCATGAAAGGATGC
* * *
817890 CAT--T--AAGGCATGAACGGGTGC
1 CATAATAAAATGCATGAAAGGATGC
*
817911 CATAATTAAAATGCATGAAAGTATG-
1 CATAA-TAAAATGCATGAAAGGATGC
* * *
817936 CAT--T--AAGGCATGAACGGATAC
1 CATAATAAAATGCATGAAAGGATGC
817957 CATAATTAAAATGCATGAAAGGATG-
1 CATAA-TAAAATGCATGAAAGGATGC
* * * *
817982 C---AT-GAAGGCATGGACGGATGC
1 CATAATAAAATGCATGAAAGGATGC
*
818003 CATAACTAAAATGCATGAAATGATG-
1 CATAA-TAAAATGCATGAAAGGATGC
* * * *
818028 C---AT-GAAGGCATGAACGAATGC
1 CATAATAAAATGCATGAAAGGATGC
*
818049 CATAACTAAAATGCATGAAATGATG-
1 CATAA-TAAAATGCATGAAAGGATGC
* * * *
818074 CATGAT----GGCATGAACGTATGC
1 CATAATAAAATGCATGAAAGGATGC
818095 CATAACTAAAATGCATGAAAGGATG-
1 CATAA-TAAAATGCATGAAAGGATGC
* *
818120 CAT--T--AAGGCATGAAAGGATTC
1 CATAATAAAATGCATGAAAGGATGC
* *
818141 CATAAATTATAATGCATGAAAAGATGC
1 CAT-AA-TAAAATGCATGAAAGGATGC
818168 ATTAAAGCAT
Statistics
Matches: 194, Mismatches: 47, Indels: 72
0.62 0.15 0.23
Matches are distributed among these distances:
20 74 0.38
21 17 0.09
22 6 0.03
24 5 0.03
25 18 0.09
26 60 0.31
27 14 0.07
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.22
Consensus pattern (25 bp):
CATAATAAAATGCATGAAAGGATGC
Found at i:821039 original size:14 final size:14
Alignment explanation
Indices: 821020--821047 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
821010 AAAGATTAAA
821020 GAAGATAATATCTC
1 GAAGATAATATCTC
821034 GAAGATAATATCTC
1 GAAGATAATATCTC
821048 AAAGTTATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
GAAGATAATATCTC
Found at i:822489 original size:24 final size:25
Alignment explanation
Indices: 822448--822495 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
822438 AAAGTTTTAT
*
822448 TTTTCTTCTTTTTGAGTGCTTCAAA
1 TTTTCTACTTTTTGAGTGCTTCAAA
822473 TTTTCTAC-TTTTGAGTGCTTCAA
1 TTTTCTACTTTTTGAGTGCTTCAA
822496 TTTATTTGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.17, C:0.17, G:0.12, T:0.54
Consensus pattern (25 bp):
TTTTCTACTTTTTGAGTGCTTCAAA
Found at i:825703 original size:25 final size:22
Alignment explanation
Indices: 825658--825704 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
825648 TAGGATGATG
825658 TATTATCTTTTAGGATTAGATT
1 TATTATCTTTTAGGATTAGATT
*
825680 TATTATTTTATTAGGAATTAAGATT
1 TATTATCTT-TTAGG-ATT-AGATT
825705 GGGTTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.38
23 5 0.24
24 3 0.14
25 5 0.24
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (22 bp):
TATTATCTTTTAGGATTAGATT
Found at i:825787 original size:15 final size:17
Alignment explanation
Indices: 825764--825797 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
825754 TTAATATATG
825764 TTTAGTTTATTA-TTAT
1 TTTAGTTTATTAGTTAT
825780 TTTA-TTTATTAGTTAT
1 TTTAGTTTATTAGTTAT
825796 TT
1 TT
825798 AGGACCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTAGTTTATTAGTTAT
Found at i:826612 original size:14 final size:14
Alignment explanation
Indices: 826560--826596 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
826550 TCAAAAAAAC
826560 AAAAAAAAGGCAAA
1 AAAAAAAAGGCAAA
*
826574 AAAAAAAGGGCAAA
1 AAAAAAAAGGCAAA
826588 AAAACAAAA
1 AAAA-AAAA
826597 AAAAAAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 17 0.85
15 3 0.15
ACGTcount: A:0.78, C:0.08, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGGCAAA
Found at i:830509 original size:15 final size:17
Alignment explanation
Indices: 830486--830519 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
830476 TTAATATATG
830486 TTTAGTTTATTA-TTAT
1 TTTAGTTTATTAGTTAT
830502 TTTA-TTTATTAGTTAT
1 TTTAGTTTATTAGTTAT
830518 TT
1 TT
830520 AGGACCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTAGTTTATTAGTTAT
Found at i:837742 original size:95 final size:94
Alignment explanation
Indices: 837623--837901 Score: 330
Period size: 95 Copynumber: 2.9 Consensus size: 94
837613 TAATGTAGTC
* * *
837623 TCGATACCATGGTAAGGGTATCGATACCAGGTAACATCGAACCTAATTTTGGTATCAATACCAGA
1 TCGATACCATGGTTAGGGTATCGATACCAGGAAACATCGAACCTAATTTTGGTATCAATACCGGA
*
837688 AGGGGGCATCAGTACCATAGTATAG-CGATA
66 AGGGGGTATC-GTACCATAGTATAGTCG-TA
** * * *
837718 TCGATACCATGGTTAGGGTATCGATACCAGGCCACATCGAATCTAATTTTGGTATCGATACTGGA
1 TCGATACCATGGTTAGGGTATCGATACCAGGAAACATCGAACCTAATTTTGGTATCAATACCGGA
* * *
837783 TGGGGGTATCGATACCATAGTAAAGTTGTA
66 AGGGGGTATCG-TACCATAGTATAGTCGTA
* ** **
837813 TCGATACCAT-GTTAAGGGTATCGATACCAAGAAACATCGAAGTTAAAGTTGGTATCAATACCGG
1 TCGATACCATGGTT-AGGGTATCGATACCAGGAAACATCGAACCTAATTTTGGTATCAATACCGG
*
837877 AA-AGGGTATCGGTACCATAGTATAG
65 AAGGGGGTATC-GTACCATAGTATAG
837902 AAATATTGAT
Statistics
Matches: 157, Mismatches: 23, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
94 23 0.15
95 133 0.85
96 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (94 bp):
TCGATACCATGGTTAGGGTATCGATACCAGGAAACATCGAACCTAATTTTGGTATCAATACCGGA
AGGGGGTATCGTACCATAGTATAGTCGTA
Found at i:837835 original size:20 final size:21
Alignment explanation
Indices: 837786--837841 Score: 78
Period size: 22 Copynumber: 2.7 Consensus size: 21
837776 TACTGGATGG
837786 GGGTATCGATACCATAGTAAA
1 GGGTATCGATACCATAGTAAA
* *
837807 GTTGTATCGATACCAT-GTTAA
1 G-GGTATCGATACCATAGTAAA
837828 GGGTATCGATACCA
1 GGGTATCGATACCA
837842 AGAAACATCG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.39
21 6 0.19
22 13 0.42
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (21 bp):
GGGTATCGATACCATAGTAAA
Found at i:838454 original size:46 final size:46
Alignment explanation
Indices: 838288--838608 Score: 322
Period size: 46 Copynumber: 7.0 Consensus size: 46
838278 AAATCGAAAA
* * * * *
838288 CATAATTAAAATGCATGAAATGATGCATTAAGGCATGAACAGATAC
1 CATAACTAAAATGCATGAAAGGATGCATGAAGGCATGAACGGATGC
* * * * * * *
838334 CATAA-TATACTGTATAAAAGGATGCATTAAGGCATGAATGGATGA
1 CATAACTAAAATGCATGAAAGGATGCATGAAGGCATGAACGGATGC
* * * * *
838379 CATAATTAAAATGCATGAAATGATACATGAAAGCATAAACGGATGC
1 CATAACTAAAATGCATGAAAGGATGCATGAAGGCATGAACGGATGC
* * * *
838425 CATAAGTAAAATGTAGGAAAGGATTCATGAAGGCATGAACGGATGC
1 CATAACTAAAATGCATGAAAGGATGCATGAAGGCATGAACGGATGC
* * *
838471 CATAACTAAAATGCATGAAAGGATGCATGAAGGCATGAATGAATGT
1 CATAACTAAAATGCATGAAAGGATGCATGAAGGCATGAACGGATGC
* * *
838517 CATAACTAAAATACATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAACTAAAATGCATGAAAGGATGCATGAAGGCATGAACGGATGC
* * * * *
838563 CATAAGCTGTAAA-GCATGAAAAGATGCATTAAAGCATGAATGGATG
1 CATAA-CT-AAAATGCATGAAAGGATGCATGAAGGCATGAACGGATG
838609 AATTAATACT
Statistics
Matches: 228, Mismatches: 44, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
45 36 0.16
46 158 0.69
47 31 0.14
48 3 0.01
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (46 bp):
CATAACTAAAATGCATGAAAGGATGCATGAAGGCATGAACGGATGC
Found at i:838608 original size:20 final size:20
Alignment explanation
Indices: 838572--838614 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
838562 CCATAAGCTG
*
838572 TAAAGCATGAAAAGATGCAT
1 TAAAGCATGAAAAGATGAAT
**
838592 TAAAGCATGAATGGATGAAT
1 TAAAGCATGAAAAGATGAAT
838612 TAA
1 TAA
838615 TACTTGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.07, G:0.21, T:0.23
Consensus pattern (20 bp):
TAAAGCATGAAAAGATGAAT
Found at i:848776 original size:18 final size:19
Alignment explanation
Indices: 848737--848776 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
848727 TAATTCCTAA
848737 TAAAATAATAAATCTGATCC
1 TAAAATAATAAATC-GATCC
*
848757 TAAAATAATTAATC-ATCC
1 TAAAATAATAAATCGATCC
848775 TA
1 TA
848777 TATTAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
20 13 0.68
ACGTcount: A:0.50, C:0.15, G:0.03, T:0.33
Consensus pattern (19 bp):
TAAAATAATAAATCGATCC
Found at i:854397 original size:13 final size:13
Alignment explanation
Indices: 854379--854405 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
854369 AAATTTTGGC
854379 TTTTTTGTTTTTT
1 TTTTTTGTTTTTT
854392 TTTTTTGTTTTTT
1 TTTTTTGTTTTTT
854405 T
1 T
854406 GAAAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (13 bp):
TTTTTTGTTTTTT
Found at i:870199 original size:25 final size:24
Alignment explanation
Indices: 870166--870212 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
870156 AAAAGAAAAG
870166 AAAGAAAGAAAGAAAAGACAAAATC
1 AAAGAAAGAAAGAAAAGA-AAAATC
*
870191 AAAGCAAGAAAGAAAAGAAAAA
1 AAAGAAAGAAAGAAAAGAAAAA
870213 GTGAAATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.74, C:0.06, G:0.17, T:0.02
Consensus pattern (24 bp):
AAAGAAAGAAAGAAAAGAAAAATC
Found at i:873077 original size:16 final size:16
Alignment explanation
Indices: 873051--873087 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
873041 CATTTATATC
873051 CCTTT-CATTT-CTTT
1 CCTTTCCATTTCCTTT
873065 CCATTTCCATTTCCTTT
1 CC-TTTCCATTTCCTTT
873082 CCTTTC
1 CCTTTC
873088 TTATTTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.10
15 3 0.15
16 9 0.45
17 6 0.30
ACGTcount: A:0.08, C:0.35, G:0.00, T:0.57
Consensus pattern (16 bp):
CCTTTCCATTTCCTTT
Found at i:875642 original size:16 final size:16
Alignment explanation
Indices: 875618--875649 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
875608 TCATTATGTC
*
875618 CTATGGTTATAATAAT
1 CTATAGTTATAATAAT
875634 CTATAGTTATAATAAT
1 CTATAGTTATAATAAT
875650 AATATTCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (16 bp):
CTATAGTTATAATAAT
Found at i:876538 original size:19 final size:20
Alignment explanation
Indices: 876514--876556 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
876504 AGCATGTATC
876514 TTCATT-AAAATCATCTATT
1 TTCATTAAAAATCATCTATT
*
876533 TTCATTAAAAATCATGTATT
1 TTCATTAAAAATCATCTATT
876553 TTCA
1 TTCA
876557 AAGGGGTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.37, C:0.14, G:0.02, T:0.47
Consensus pattern (20 bp):
TTCATTAAAAATCATCTATT
Found at i:884314 original size:12 final size:13
Alignment explanation
Indices: 884285--884327 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
884275 ATAACAAAAG
884285 AAAAGAAAGAAAT
1 AAAAGAAAGAAAT
884298 AAAAGAAA-AAAT
1 AAAAGAAAGAAAT
* * *
884310 CAAAGCAAGAAAA
1 AAAAGAAAGAAAT
884323 AAAAG
1 AAAAG
884328 TGAAATCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.77, C:0.05, G:0.14, T:0.05
Consensus pattern (13 bp):
AAAAGAAAGAAAT
Done.