Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007928.1 Hibiscus syriacus cultivar Beakdansim tig00110334_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: 336612
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
File 2 of 2
Found at i:263007 original size:19 final size:21
Alignment explanation
Indices: 262970--263012 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
262960 TAACTTTTTC
262970 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
262990 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
263010 TTT
1 TTT
263013 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:263018 original size:19 final size:20
Alignment explanation
Indices: 262969--263018 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
262959 TTAACTTTTT
*
262969 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
262989 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
263008 CTTTTACCTTT
1 CTTTTACCTTT
263019 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:270198 original size:21 final size:22
Alignment explanation
Indices: 270173--270213 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
270163 TGATTTTTGC
270173 ATATGA-TGTTATCATGAACAT
1 ATATGATTGTTATCATGAACAT
*
270194 ATATGATTTTTATCATGAAC
1 ATATGATTGTTATCATGAAC
270214 GTTATTTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (22 bp):
ATATGATTGTTATCATGAACAT
Found at i:270459 original size:60 final size:59
Alignment explanation
Indices: 270359--270488 Score: 172
Period size: 60 Copynumber: 2.2 Consensus size: 59
270349 CAGCAGGTTG
** * *
270359 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGA-AGGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGT-GGACACGACCTTATGTGT
** *
270418 CATATTCGGGAACTGTACTTAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
1 CATATTCGGGAA-TACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
270478 CATATTCGGGA
1 CATATTCGGGA
270489 TTGCACTACG
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
59 15 0.24
60 47 0.76
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.28
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
Found at i:270575 original size:20 final size:20
Alignment explanation
Indices: 270550--270592 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
270540 TATATTGGGC
* * *
270550 TATTGTTTATTGTTTATGGT
1 TATTGTCTATGGTATATGGT
270570 TATTGTCTATGGTATATGGT
1 TATTGTCTATGGTATATGGT
270590 TAT
1 TAT
270593 GGAATAATGG
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:0.19, C:0.02, G:0.21, T:0.58
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGT
Found at i:270724 original size:45 final size:44
Alignment explanation
Indices: 270589--270783 Score: 295
Period size: 44 Copynumber: 4.4 Consensus size: 44
270579 TGGTATATGG
* *
270589 TTATGGA-ATAATGGTAAGTGTATTGGTAAAATAAGCTTGCGAGC
1 TTATGGATA-AATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
* *
270633 TTATGGATAAATGGCAAGTGTATTGGTAAAATAAGCTTACGAGC
1 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
270677 TTATGGATAAATGGTAAGTATATTGGTAAAAATAAGCTTACGAGC
1 TTATGGATAAATGGTAAGTATATTGGT-AAAATAAGCTTACGAGC
*
270722 TTAAGGATAAATGGTAAG-ATATTGGTAAAATAAGCTTACGAGC
1 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
270765 TTATGGTATTAAATGGTAA
1 TTATGG-A-TAAATGGTAA
270784 AATATTGCAC
Statistics
Matches: 141, Mismatches: 6, Indels: 7
0.92 0.04 0.05
Matches are distributed among these distances:
43 22 0.16
44 74 0.52
45 45 0.32
ACGTcount: A:0.38, C:0.07, G:0.24, T:0.31
Consensus pattern (44 bp):
TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
Found at i:274304 original size:17 final size:17
Alignment explanation
Indices: 274282--274317 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
274272 TTTAAGTAAG
274282 GATTAAAATTGGCATTT
1 GATTAAAATTGGCATTT
274299 GATTAAAATTGGCATTT
1 GATTAAAATTGGCATTT
274316 GA
1 GA
274318 AAACTTGGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.39
Consensus pattern (17 bp):
GATTAAAATTGGCATTT
Found at i:274789 original size:17 final size:18
Alignment explanation
Indices: 274767--274803 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
274757 GCAAAAATTA
274767 ATGAAA-TC-AATATAAAC
1 ATGAAATTCAAAT-TAAAC
274784 ATGAAATTCAAATTAAAC
1 ATGAAATTCAAATTAAAC
274802 AT
1 AT
274804 TCAAACCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 9 0.50
19 3 0.17
ACGTcount: A:0.57, C:0.11, G:0.05, T:0.27
Consensus pattern (18 bp):
ATGAAATTCAAATTAAAC
Found at i:274841 original size:23 final size:24
Alignment explanation
Indices: 274815--274864 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
274805 CAAACCATTC
*
274815 AAACAAACATATCCAAAA-ATCCA
1 AAACAAACAAATCCAAAACATCCA
* *
274838 AAACATACAAATCCAAAACATTCA
1 AAACAAACAAATCCAAAACATCCA
274862 AAA
1 AAA
274865 TGTTTTAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.62, C:0.24, G:0.00, T:0.14
Consensus pattern (24 bp):
AAACAAACAAATCCAAAACATCCA
Found at i:274851 original size:15 final size:15
Alignment explanation
Indices: 274831--274863 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
274821 ACATATCCAA
274831 AAATCCAAAACATAC
1 AAATCCAAAACATAC
*
274846 AAATCCAAAACATTC
1 AAATCCAAAACATAC
274861 AAA
1 AAA
274864 ATGTTTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.61, C:0.24, G:0.00, T:0.15
Consensus pattern (15 bp):
AAATCCAAAACATAC
Found at i:283493 original size:10 final size:10
Alignment explanation
Indices: 283478--283516 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
283468 ACAAATAAAG
283478 TTTGTTAATA
1 TTTGTTAATA
283488 TTTGTT-ATAA
1 TTTGTTAAT-A
*
283498 ATTGTTAATA
1 TTTGTTAATA
283508 TTTGTTAAT
1 TTTGTTAAT
283517 TTTATAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (10 bp):
TTTGTTAATA
Found at i:283791 original size:197 final size:194
Alignment explanation
Indices: 283569--283978 Score: 592
Period size: 197 Copynumber: 2.1 Consensus size: 194
283559 CCAATAATTT
**
283569 TTTTATATTGAGAAATTAATATTTATTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAGT
1 TTTTATATTGAGAAATTAATATTTATTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAAA
* *
283634 TTTTATTTTGAGAAAATATTGTGACAAAAT-AATTGTAACATAATTTTTTATTTTGACT-AATGT
66 ATTTATTTTGAGAAAATATTGTGACAAAATAAATT-TAACATAATTTTTTATTTTCACTAAAT-T
* * * * *
283697 TAATATGTTAGTGTGGCTAAATAAATTTGTTACAATTTGTTAATGTGAAAGAATATATTTGTCCT
129 TAATATGGTAGTGTGACTAAATAAATTTGGTACAATTTATTAATGTGAAA-AATAT-TTT-TCAT
283762 GATA-
191 GA-AC
*
283766 TTTTATATTGAGAAATTATTATTTATTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAAA
1 TTTTATATTGAGAAATTAATATTTATTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAAA
* *
283831 ATTTATTTTGAGAAAATATTGTGACAAAATAAATTTGATATAATTTTTTATTTTCACTAAATTTA
66 ATTTATTTTGAGAAAATATTGTGACAAAATAAATTTAACATAATTTTTTATTTTCACTAAATTTA
* * *
283896 CTATGGTATTGTGACTAAATAAATTTGGTACAATTTATTATTGTGAAAAATATTTTTCATGAAC
131 ATATGGTAGTGTGACTAAATAAATTTGGTACAATTTATTAATGTGAAAAATATTTTTCATGAAC
* *
283960 TTTCATATTGAAAAATTAA
1 TTTTATATTGAGAAATTAA
283979 CAATTGTTAT
Statistics
Matches: 192, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
193 1 0.01
194 21 0.11
195 3 0.02
196 5 0.03
197 155 0.81
198 7 0.04
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (194 bp):
TTTTATATTGAGAAATTAATATTTATTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAAA
ATTTATTTTGAGAAAATATTGTGACAAAATAAATTTAACATAATTTTTTATTTTCACTAAATTTA
ATATGGTAGTGTGACTAAATAAATTTGGTACAATTTATTAATGTGAAAAATATTTTTCATGAAC
Found at i:284285 original size:145 final size:144
Alignment explanation
Indices: 284003--284285 Score: 298
Period size: 145 Copynumber: 2.0 Consensus size: 144
283993 ATTTTGAGAT
* *
284003 AATATTGTGAATAAATAAATTTGACACAATTTTTTATTTTAATTAAATTTAACATAATAGTATTA
1 AATATTGTGAATAAATAAATTTGACACAATTTCTTATTTTAATTAAATTTAACATAATAGTATGA
* **** * * *
284068 TTAAATAAATTTGTTACAATTAGTTATAAATAATTGTTATTATAATTATATAAATTTGTCATAAT
66 CTAAATAAATTTGTTACAATTAGTTATAAATAAAAAATATTAT-ATTATATAAATTTATAATAAC
* *
284133 TAGTTATTTAAAGAA
130 AAATTATTTAAAGAA
* * * * * ** **
284148 AATATTGTGACTAAATAAATTTGACATAATTTCTTATTTTGATTAAATTTCATATGTTTTTATGA
1 AATATTGTGAATAAATAAATTTGACACAATTTCTTATTTTAATTAAATTTAACATAATAGTATGA
* * * * *
284213 CTAAATAAATTTGTTACAATTTGTTATTATTAAAAAAATATTAT-TTTTATAATTTTTATAATAA
66 CTAAATAAATTTGTTACAATTAGTTATAAAT-AAAAAATATTATATTATATAA-ATTTATAATAA
284277 CAAATTATT
129 CAAATTATT
284286 ATTTTCTATA
Statistics
Matches: 110, Mismatches: 26, Indels: 4
0.79 0.19 0.03
Matches are distributed among these distances:
144 7 0.06
145 95 0.86
146 8 0.07
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.47
Consensus pattern (144 bp):
AATATTGTGAATAAATAAATTTGACACAATTTCTTATTTTAATTAAATTTAACATAATAGTATGA
CTAAATAAATTTGTTACAATTAGTTATAAATAAAAAATATTATATTATATAAATTTATAATAACA
AATTATTTAAAGAA
Found at i:289574 original size:3 final size:3
Alignment explanation
Indices: 289568--289618 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
289558 AAATTATTAG
289568 TAA TAA TAA TAA TAA T-A TAA TAA T-A TAA TAA TAA TAA TAA TCAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
289612 T-A TAA TA
1 TAA TAA TA
289619 TATATTTTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 6 0.14
3 35 0.80
4 3 0.07
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:289586 original size:28 final size:30
Alignment explanation
Indices: 289555--289616 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 30
289545 AATATGTAAT
* *
289555 TATAAATTAT-TAGTAATAATAATAAT-AA
1 TATAAATAATATAATAATAATAATAATCAA
289583 TAT-AATAATATAATAATAATAATAATCAA
1 TATAAATAATATAATAATAATAATAATCAA
289612 TATAA
1 TATAA
289617 TATATATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 5 0.17
28 18 0.62
29 5 0.17
30 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (30 bp):
TATAAATAATATAATAATAATAATAATCAA
Found at i:289598 original size:22 final size:21
Alignment explanation
Indices: 289573--289618 Score: 78
Period size: 19 Copynumber: 2.3 Consensus size: 21
289563 ATTAGTAATA
289573 ATAATAATAAT-ATAAT-AAT
1 ATAATAATAATAATAATCAAT
289592 ATAATAATAATAATAATCAAT
1 ATAATAATAATAATAATCAAT
289613 ATAATA
1 ATAATA
289619 TATATTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 11 0.44
20 5 0.20
21 9 0.36
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAATAATAATAATAATCAAT
Found at i:289915 original size:51 final size:51
Alignment explanation
Indices: 289799--290699 Score: 317
Period size: 55 Copynumber: 16.6 Consensus size: 51
289789 TAACCAGCGG
* * ** *
289799 GTTCGCTCCCTATTGCTTCAGGGAGTATAGAACTCGAGAAATCTTTTGA-AAACGG
1 GTTCGCTCCCTATTCCTTCAGAGAGTATAGAACT--AG--ATC-TTCAACAAACGT
* * * *
289854 GTTCGTTCCCTCTTTCTTCAGGGAGTATAGAACTAGATCTTCAACAAACGT
1 GTTCGCTCCCTATTCCTTCAGAGAGTATAGAACTAGATCTTCAACAAACGT
* *
289905 GTACGCTCCCTATTCCTTCAGAGAGTATTGGACTTGAAC-AAATCTTCAACAAACGT
1 GTTCGCTCCCTATTCCTTCAGAGAGTA-T--A---GAACTAGATCTTCAACAAACGT
* * * *
289961 GTCCCCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAACAAACGT
1 GTTCGCTCCCTATTCCTTCAGAGAGTATAGAACTAGATCTTCAACAAACGT
*
290012 GTTCGCTCCCTATTCCTTCAGAGAGTATA-AGACTCGAACAATCTTCAACAAATCGT
1 GTTCGCTCCCTATTCCTTCAGAGAGTATAGA-ACT---A-GATCTTCAACAAA-CGT
*
290068 G-TCTGCTCCCTATT-CTTCCAGAGAGTATA-AGACTCGAATAATCTTCAACAAACGT
1 GTTC-GCTCCCTATTCCTT-CAGAGAGTATAGA-ACT---A-GATCTTCAACAAACGT
* * * * *
290123 G-TCTACTCCATATTTCTTCAGAGAGTATA-AGACTTGAACAATCTTCAACAATCGT
1 GTTC-GCTCCCTATTCCTTCAGAGAGTATAGA-AC-T--A-GATCTTCAACAAACGT
* * ** *
290178 G-TCTGCTCTCTATTCCTTCAGAGAGTATA-AGACTCAAACATCTTCTTCAATCGT
1 GTTC-GCTCCCTATTCCTTCAGAGAGTATAGA-ACT---AGATCTTCAACAAACGT
* *
290232 G-TCTGCTCCCTATTCCTTCAGAGAGTATA-AGACTCGAATAATCTTCAACAATCGT
1 GTTC-GCTCCCTATTCCTTCAGAGAGTATAGA-ACT---A-GATCTTCAACAAACGT
* * *
290287 G-TCTGCTCCCCATTCCTTCAGATAGTATA-AGACTCGAATAATCTTCAACAAACGT
1 GTTC-GCTCCCTATTCCTTCAGAGAGTATAGA-ACT---A-GATCTTCAACAAACGT
* * * *
290342 G-TCTACTCCCTATTTCTTCAGAGAGTATA-AGACTCGAACAATCTTCAACAATCGT
1 GTTC-GCTCCCTATTCCTTCAGAGAGTATAGA-ACT---A-GATCTTCAACAAACGT
* * * * * *
290397 GTAT-GCTCCATATTCCTTCAAAGAGTATA-AGACTCGAACAATATTCAACAATCAT
1 GT-TCGCTCCCTATTCCTTCAGAGAGTATAGA-ACT---A-GATCTTCAACAAACGT
* * *
290452 G-TCTGCTCTCTATTCCTTCAGAGAGTATA-AGACTCGAACAATCTTCAACAATCGT
1 GTTC-GCTCCCTATTCCTTCAGAGAGTATAGA-ACT---A-GATCTTCAACAAACGT
* * * * *
290507 G-TCTGCTCTCTAGTCCTTCAGAGAGTATA-AGACTCGAACAATTTTCAACAATCGT
1 GTTC-GCTCCCTATTCCTTCAGAGAGTATAGA-ACT---A-GATCTTCAACAAACGT
* * * ** *
290562 G-TCTGTTCTCTATTCCTTCAGAGAGTATA-ACACTCGAACATCTTCTTCAATCGT
1 GTTC-GCTCCCTATTCCTTCAGAGAGTATAGA-ACT---AGATCTTCAACAAACGT
* * * *
290616 -TTCTGCTCCATATTCCTTCAGAGAGTATA-AGACTCGAACAATCTTCAACAATCAT
1 GTTC-GCTCCCTATTCCTTCAGAGAGTATAGA-ACT---A-GATCTTCAACAAACGT
*
290671 G-TCTGCTCTCTATTCCTTCAGAGAGTATA
1 GTTC-GCTCCCTATTCCTTCAGAGAGTATA
290700 AGACTCGAAT
Statistics
Matches: 740, Mismatches: 79, Indels: 54
0.85 0.09 0.06
Matches are distributed among these distances:
50 6 0.01
51 75 0.10
52 1 0.00
53 4 0.01
54 96 0.13
55 461 0.62
56 92 0.12
57 5 0.01
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (51 bp):
GTTCGCTCCCTATTCCTTCAGAGAGTATAGAACTAGATCTTCAACAAACGT
Found at i:290150 original size:55 final size:55
Alignment explanation
Indices: 289890--290708 Score: 1134
Period size: 55 Copynumber: 15.0 Consensus size: 55
289880 ATAGAACTAG
* ** *
289890 ATCTTCAACAAACGTGTAC-GCTCCCTATTCCTTCAGAGAGTATTGGACTTGAACAA
1 ATCTTCAACAATCGTGT-CTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAAC-A
* ** *
289946 ATCTTCAACAAACGTGTCCCCTCCCTATTCCTTCAGAGAGTATAGGACTCG----
1 ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
*
289997 ATCTTCAACAAACGTGT-TCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
1 ATCTTCAACAATCGTGTCT-GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
*
290052 ATCTTCAACAAATCGTGTCTGCTCCCTATT-CTTCCAGAGAGTATAAGACTCGAATA
1 ATCTTCAAC-AATCGTGTCTGCTCCCTATTCCTT-CAGAGAGTATAAGACTCGAACA
* * * * *
290108 ATCTTCAACAAACGTGTCTACTCCATATTTCTTCAGAGAGTATAAGACTTGAACA
1 ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
* *
290163 ATCTTCAACAATCGTGTCTGCTCTCTATTCCTTCAGAGAGTATAAGACTCAAAC-
1 ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
** *
290217 ATCTTCTTCAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAATA
1 ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
* * *
290272 ATCTTCAACAATCGTGTCTGCTCCCCATTCCTTCAGATAGTATAAGACTCGAATA
1 ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
* * *
290327 ATCTTCAACAAACGTGTCTACTCCCTATTTCTTCAGAGAGTATAAGACTCGAACA
1 ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
* * *
290382 ATCTTCAACAATCGTGTATGCTCCATATTCCTTCAAAGAGTATAAGACTCGAACA
1 ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
* * *
290437 ATATTCAACAATCATGTCTGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACA
1 ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
* *
290492 ATCTTCAACAATCGTGTCTGCTCTCTAGTCCTTCAGAGAGTATAAGACTCGAACA
1 ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
* * * *
290547 ATTTTCAACAATCGTGTCTGTTCTCTATTCCTTCAGAGAGTATAACACTCGAAC-
1 ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
** * *
290601 ATCTTCTTCAATCGTTTCTGCTCCATATTCCTTCAGAGAGTATAAGACTCGAACA
1 ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
* *
290656 ATCTTCAACAATCATGTCTGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAA
1 ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAA
290709 TATCTTCTTC
Statistics
Matches: 683, Mismatches: 68, Indels: 25
0.88 0.09 0.03
Matches are distributed among these distances:
51 47 0.07
54 95 0.14
55 444 0.65
56 96 0.14
57 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (55 bp):
ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
Found at i:290339 original size:219 final size:220
Alignment explanation
Indices: 289890--290708 Score: 1163
Period size: 219 Copynumber: 3.7 Consensus size: 220
289880 ATAGAACTAG
* ** *
289890 ATCTTCAACAAACGTGTAC-GCTCCCTATTCCTTCAGAGAGTATTGGACTTGAACAAATCTTCAA
1 ATCTTCAACAAACGTGT-CTACTCCCTATTCCTTCAGAGAGTATAAGACTCGAAC-AATCTTCAA
* ** * * * *
289954 CAAACGTGTCCCCTCCCTATTCCTTCAGAGAGTATAGGACTCG----ATCTTCAACAAACGTGT-
64 CAATCGTGTCTGCTCCATATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCATGTC
290014 TCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAATCGTGTCTGCTCCCT
129 T-GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC-AATCGTGTCTGCTCCCT
290079 ATT-CTTCCAGAGAGTATAAGACTCGAATA
192 ATTCCTT-CAGAGAGTATAAGACTCGAATA
* * *
290108 ATCTTCAACAAACGTGTCTACTCCATATTTCTTCAGAGAGTATAAGACTTGAACAATCTTCAACA
1 ATCTTCAACAAACGTGTCTACTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACA
* ** *
290173 ATCGTGTCTGCTCTC-TATTCCTTCAGAGAGTATAAGACTCAAAC-ATCTTCTTCAATCGTGTCT
66 ATCGTGTCTGCTC-CATATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCATGTCT
* *
290236 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAATAATCTTCAACAATCGTGTCTGCTCCCCATT
130 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATT
*
290301 CCTTCAGATAGTATAAGACTCGAATA
195 CCTTCAGAGAGTATAAGACTCGAATA
*
290327 ATCTTCAACAAACGTGTCTACTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACA
1 ATCTTCAACAAACGTGTCTACTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACA
* * *
290392 ATCGTGTATGCTCCATATTCCTTCAAAGAGTATAAGACTCGAACAATATTCAACAATCATGTCTG
66 ATCGTGTCTGCTCCATATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCATGTCTG
* * *
290457 CTCTCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCTCTAGTC
131 CTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
*
290522 CTTCAGAGAGTATAAGACTCGAACA
196 CTTCAGAGAGTATAAGACTCGAATA
* * ** * * **
290547 ATTTTCAACAATCGTGTCTGTTCTCTATTCCTTCAGAGAGTATAACACTCGAAC-ATCTTCTTCA
1 ATCTTCAACAAACGTGTCTACTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACA
*
290611 ATCGTTTCTGCTCCATATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCATGTCTG
66 ATCGTGTCTGCTCCATATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCATGTCTG
*
290676 CTCTCTATTCCTTCAGAGAGTATAAGACTCGAA
131 CTCCCTATTCCTTCAGAGAGTATAAGACTCGAA
290709 TATCTTCTTC
Statistics
Matches: 547, Mismatches: 45, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
217 46 0.08
218 49 0.09
219 244 0.45
220 207 0.38
221 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (220 bp):
ATCTTCAACAAACGTGTCTACTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACA
ATCGTGTCTGCTCCATATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCATGTCTG
CTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
CTTCAGAGAGTATAAGACTCGAATA
Found at i:290751 original size:54 final size:53
Alignment explanation
Indices: 290693--290825 Score: 142
Period size: 54 Copynumber: 2.5 Consensus size: 53
290683 TTCCTTCAGA
* *
290693 GAGTATAAGACTCGAATATCTTCTTCATACGGGTTTGCTCCCTCTTTCTTTAGG
1 GAGTATAAGACTCGAATATCTTCTTCAAACGGGTTCGCTCCCTCTTT-TTTAGG
* * ** *
290747 GAGTAT-AGAATTTGAATAATCTTCCGCAAATGGGTTCGCTCCCTCTTTTTTAGG
1 GAGTATAAG-ACTCGAAT-ATCTTCTTCAAACGGGTTCGCTCCCTCTTTTTTAGG
* * *
290801 GAGTATAAAACCCGAACATCTTCTT
1 GAGTATAAGACTCGAATATCTTCTT
290826 TTTCTTCACT
Statistics
Matches: 62, Mismatches: 14, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
53 8 0.13
54 28 0.45
55 26 0.42
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (53 bp):
GAGTATAAGACTCGAATATCTTCTTCAAACGGGTTCGCTCCCTCTTTTTTAGG
Found at i:290975 original size:37 final size:38
Alignment explanation
Indices: 290914--290992 Score: 108
Period size: 37 Copynumber: 2.1 Consensus size: 38
290904 CTCAAGGTAA
290914 TGCTTCACTACTCTTCGGTGAAGGCTTACAAATTGA-TT
1 TGCTTCACTACTCTTCGGTGAAGGCTTA-AAATTGACTT
* * *
290952 TGCTTCACTCCT-TTTGGTGAAGGCTTAAGATTGACTT
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAAATTGACTT
290989 TGCT
1 TGCT
290993 CCAATCTCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 6 0.16
37 20 0.54
38 11 0.30
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (38 bp):
TGCTTCACTACTCTTCGGTGAAGGCTTAAAATTGACTT
Found at i:297855 original size:6 final size:6
Alignment explanation
Indices: 297836--297865 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
297826 AAAAAATAAG
*
297836 AATGCA AATACA AATGCA AATGCA AATGCA
1 AATGCA AATGCA AATGCA AATGCA AATGCA
297866 CGAGGTGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.53, C:0.17, G:0.13, T:0.17
Consensus pattern (6 bp):
AATGCA
Found at i:298400 original size:9 final size:9
Alignment explanation
Indices: 298381--298412 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
298371 ATGAGGATGC
298381 AAATGCAATA
1 AAAT-CAATA
298391 AAATCAATA
1 AAATCAATA
298400 AAATCAATA
1 AAATCAATA
298409 AAAT
1 AAAT
298413 AGACATAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.82
10 4 0.18
ACGTcount: A:0.66, C:0.09, G:0.03, T:0.22
Consensus pattern (9 bp):
AAATCAATA
Found at i:299553 original size:17 final size:17
Alignment explanation
Indices: 299531--299563 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
299521 CAAAATCGTT
299531 TTCATTTTAAATAAAAA
1 TTCATTTTAAATAAAAA
*
299548 TTCATTTTAATTAAAA
1 TTCATTTTAAATAAAA
299564 GAACAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (17 bp):
TTCATTTTAAATAAAAA
Found at i:303608 original size:10 final size:10
Alignment explanation
Indices: 303593--303631 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
303583 ACAAATAAAG
303593 TTTGTTAATA
1 TTTGTTAATA
303603 TTTGTT-ATAA
1 TTTGTTAAT-A
*
303613 ATTGTTAATA
1 TTTGTTAATA
303623 TTTGTTAAT
1 TTTGTTAAT
303632 TTTATAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (10 bp):
TTTGTTAATA
Found at i:303766 original size:32 final size:33
Alignment explanation
Indices: 303677--303766 Score: 85
Period size: 32 Copynumber: 2.7 Consensus size: 33
303667 TTGTCCTCCA
* * *
303677 ATAAATTTTTTATATTGAGAAATTAATATTTGTT
1 ATAAA-TTTTTATTTTGAGAAAATAATATTTGTC
* * **
303711 ATAAATTGTTATTATGACTAAATAA-ATTTGTC
1 ATAAATTTTTATTTTGAGAAAATAATATTTGTC
303743 A-AAAGTTTTTATTTTGAGAAAATA
1 ATAAA-TTTTTATTTTGAGAAAATA
303767 TTGTGACAAA
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
31 3 0.07
32 22 0.50
33 14 0.32
34 5 0.11
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.47
Consensus pattern (33 bp):
ATAAATTTTTATTTTGAGAAAATAATATTTGTC
Found at i:304031 original size:197 final size:196
Alignment explanation
Indices: 303684--304063 Score: 584
Period size: 197 Copynumber: 1.9 Consensus size: 196
303674 CCAATAAATT
* * **
303684 TTTTATATTGAGAAATTAATATTTGTTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAGT
1 TTTTATAATGAGAAATTAATATTTATTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAAA
* *
303749 TTTTATTTTGAGAAAATATTGTGACAAAATAATTGTAACATAATTTTTTATTTTGACTAATGTTA
66 ATTTATTTTGAGAAAATATTGTGACAAAATAATTGTAACATAATTTTTTATTTTCACTAATGTTA
* * *
303814 ATATGTTAGTGTGGCTAAATAAATTTGTTACAATTTGTTAATGTGAAAGAATATATTTGTCCTGA
131 ATATGGTAGTGTGACTAAATAAATTTGTTACAATTTATTAATGTGAAA-AATATATTTGTCCTGA
303879 TA
195 TA
*
303881 TTTTATAATGAGAAATTATTATTTATTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAAA
1 TTTTATAATGAGAAATTAATATTTATTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAAA
* *
303946 ATTTATTTTGAGAAAATATTGTGACAAAATAAATT-TGATATAATTTTTTATTTTCACTAAAT-T
66 ATTTATTTTGAGAAAATATTGTGACAAAAT-AATTGTAACATAATTTTTTATTTTCACT-AATGT
* * *
304009 TACTATGGTATTGTGACTAAATAAATTTGTTACAATTTATTATTGTGAAAAATAT
129 TAATATGGTAGTGTGACTAAATAAATTTGTTACAATTTATTAATGTGAAAAATAT
304064 TTTTCATGAA
Statistics
Matches: 166, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
196 5 0.03
197 154 0.93
198 7 0.04
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.45
Consensus pattern (196 bp):
TTTTATAATGAGAAATTAATATTTATTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAAA
ATTTATTTTGAGAAAATATTGTGACAAAATAATTGTAACATAATTTTTTATTTTCACTAATGTTA
ATATGGTAGTGTGACTAAATAAATTTGTTACAATTTATTAATGTGAAAAATATATTTGTCCTGAT
A
Found at i:304052 original size:100 final size:98
Alignment explanation
Indices: 303720--304064 Score: 237
Period size: 100 Copynumber: 3.5 Consensus size: 98
303710 TATAAATTGT
* * *
303720 TATTATGACTAAATAAATTTGTCAAAAGTTT-TTATTTTGAGAAAATATTGTGACAAAAT-AATT
1 TATTGTGACTAAATAAATTTGTCACAA-TTTATTATTGTGA-AAAATATTGTGACAAAATAAATT
* * *
303783 GTAACATAATTTTTTATTTTGACT-AATGTTAATATG
64 ATAATATAATTTTTTATTTTCACTAAAT-TT-ATATG
* * * * * * * *** **
303819 TTAGTGTGGCTAAATAAATTTGTTACAATTTGTTAATGTGAAAGAATATATTTGTCCTGATATTT
1 -TATTGTGACTAAATAAATTTGTCACAATTTATTATTGTGAAA-AATAT-TGTGACAAAATAAAT
* * * *
303884 TATAATGAGAAATTATTATTTATTA-TAAATTGT-TAT-
63 TATAAT-ATAATTTTTTATTT-TCACTAAATT-TATATG
* *
303920 TA---TGACTAAATAAATTTGTCAAAAAAATTTATT-TTGAG-AAAATATTGTGACAAAATAAAT
1 TATTGTGACTAAATAAATTTGTC---ACAATTTATTATTGTGAAAAATATTGTGACAAAATAAAT
*
303980 T-TGATATAATTTTTTATTTTCACTAAATTTACTATGG
63 TATAATATAATTTTTTATTTTCACTAAATTTA-TAT-G
*
304017 TATTGTGACTAAATAAATTTGTTACAATTTATTATTGTGAAAAATATT
1 TATTGTGACTAAATAAATTTGTCACAATTTATTATTGTGAAAAATATT
304065 TTTCATGAAC
Statistics
Matches: 183, Mismatches: 41, Indels: 43
0.69 0.15 0.16
Matches are distributed among these distances:
93 3 0.02
94 17 0.09
95 6 0.03
96 9 0.05
97 32 0.17
98 6 0.03
99 16 0.09
100 61 0.33
101 6 0.03
102 8 0.04
103 13 0.07
104 6 0.03
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (98 bp):
TATTGTGACTAAATAAATTTGTCACAATTTATTATTGTGAAAAATATTGTGACAAAATAAATTAT
AATATAATTTTTTATTTTCACTAAATTTATATG
Found at i:304400 original size:145 final size:144
Alignment explanation
Indices: 304118--304400 Score: 307
Period size: 145 Copynumber: 2.0 Consensus size: 144
304108 ATTTTGAGAT
* *
304118 AATATTGTGAATAAATAAATTTGACACAATTTTTTATTTTAATTAAATTTAACATAATAGTATTA
1 AATATTGTGAATAAATAAATTTGACACAATTTCTTATTTTAATTAAATTTAACATAATAGTATGA
* **** * * *
304183 TTAAATAAATTTGTTACAATTAGTTATAAATAATTTTTATTATAATTATATAAATTTGTCATAAT
66 CTAAATAAATTTGTTACAATTAGTTATAAATAAAAAATATTAT-ATTATATAAATTTATAATAAC
* *
304248 TAGTTATTTAAAGAA
130 AAATTATTTAAAGAA
* * * * ** **
304263 AATATTGTGACTAAATAAATTTGACATAATTTCTTATTTTGATTAAATTTAATATGTTTTTATGA
1 AATATTGTGAATAAATAAATTTGACACAATTTCTTATTTTAATTAAATTTAACATAATAGTATGA
* * * * *
304328 CTAAATAAATTTGTTACAATTTGTTATTATTAAAAAAATATTAT-TTTTATAATTTTTATAATAA
66 CTAAATAAATTTGTTACAATTAGTTATAAAT-AAAAAATATTATATTATATAA-ATTTATAATAA
304392 CAAATTATT
129 CAAATTATT
304401 ATTTTCTATA
Statistics
Matches: 111, Mismatches: 25, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
144 7 0.06
145 96 0.86
146 8 0.07
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (144 bp):
AATATTGTGAATAAATAAATTTGACACAATTTCTTATTTTAATTAAATTTAACATAATAGTATGA
CTAAATAAATTTGTTACAATTAGTTATAAATAAAAAATATTATATTATATAAATTTATAATAACA
AATTATTTAAAGAA
Found at i:309259 original size:92 final size:92
Alignment explanation
Indices: 309102--309285 Score: 341
Period size: 92 Copynumber: 2.0 Consensus size: 92
309092 AGTAAGAAAA
309102 AAAATCTGAAATGTTTACTTTGCTTGTATTTCTTTCAACTAGTAGGAAAACGATTACAATGGTTC
1 AAAATCTGAAATGTTTACTTTGCTTGTATTTCTTTCAACTAGTAGGAAAACGATTACAATGGTTC
* *
309167 TTCTTTTTTTCCTTGTTTTTCGAATGG
66 TTCTTCTTTTCCTGGTTTTTCGAATGG
309194 AAAATCTGAAATGTTTACTTTGCTTGTATTTCTTTCAACTAGTAGGAAAACGATTACAATGGTTC
1 AAAATCTGAAATGTTTACTTTGCTTGTATTTCTTTCAACTAGTAGGAAAACGATTACAATGGTTC
*
309259 TTCTTCTTTTCCTGGTTTTTTGAATGG
66 TTCTTCTTTTCCTGGTTTTTCGAATGG
309286 TGGGGATATA
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 89 1.00
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.45
Consensus pattern (92 bp):
AAAATCTGAAATGTTTACTTTGCTTGTATTTCTTTCAACTAGTAGGAAAACGATTACAATGGTTC
TTCTTCTTTTCCTGGTTTTTCGAATGG
Found at i:309769 original size:3 final size:3
Alignment explanation
Indices: 309763--309809 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
309753 TAGTATTAAA
*
309763 AAT AAT AAT -AT ATT AAT -AT AAT AAT AAT AAT AAT AAT CAAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
309806 AAT A
1 AAT A
309810 TATATTTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 6 0.16
3 29 0.76
4 3 0.08
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:310106 original size:51 final size:51
Alignment explanation
Indices: 310049--310215 Score: 208
Period size: 51 Copynumber: 3.2 Consensus size: 51
310039 AAACGGGTTT
* * * *
310049 GCTCCCTCTTTCTTCAGGGAGTATAGAACTAGATCTTCAACAAACGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTAGATCTTCAACAAACGTGTCC
* *
310100 GCTCCCTATTCCTTCAGAGAGTATAGGACTTGAACAAATCTTCAATAAACGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGAC-T----AGATCTTCAACAAACGTGTCC
* * *
310156 ACTCCCTATTCCTTCAGAGAGTATAGGACTTGATCTTCAACAAACGTGTTC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTAGATCTTCAACAAACGTGTCC
310207 GCTCCCTAT
1 GCTCCCTAT
310216 GGTTACAGAT
Statistics
Matches: 99, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
51 50 0.51
52 1 0.01
55 1 0.01
56 47 0.47
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (51 bp):
GCTCCCTATTCCTTCAGAGAGTATAGGACTAGATCTTCAACAAACGTGTCC
Found at i:310161 original size:56 final size:56
Alignment explanation
Indices: 310081--310215 Score: 199
Period size: 56 Copynumber: 2.5 Consensus size: 56
310071 ATAGAACTAG
*
310081 ATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTTGAACAA
1 ATCTTCAACAAACGTGTCCACTCCCTATTCCTTCAGAGAGTATAGGACTTGAACAA
*
310137 ATCTTCAATAAACGTGTCCACTCCCTATTCCTTCAGAGAGTATAGGACTTG-----
1 ATCTTCAACAAACGTGTCCACTCCCTATTCCTTCAGAGAGTATAGGACTTGAACAA
* *
310188 ATCTTCAACAAACGTGTTCGCTCCCTAT
1 ATCTTCAACAAACGTGTCCACTCCCTAT
310216 GGTTACAGAT
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
51 25 0.34
56 49 0.66
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (56 bp):
ATCTTCAACAAACGTGTCCACTCCCTATTCCTTCAGAGAGTATAGGACTTGAACAA
Found at i:310632 original size:296 final size:296
Alignment explanation
Indices: 310098--310688 Score: 1038
Period size: 296 Copynumber: 2.0 Consensus size: 296
310088 ACAAACGTGT
*
310098 CCGCTCCCTATTCCTTCAGAGAGTATAGGACTTGAACAAATCTTCAATAAACGTGTCCACTCCCT
1 CCGCTCCCTATTCCTTCAGAGAGTATAGGACTTGAACAAATCTTCAACAAACGTGTCCACTCCCT
* *
310163 ATTCCTTCAGAGAGTATAGGACTTGATCTTCAACAAACGTGTTCGCTCCCTATGGTTACAGATTG
66 ATTCCTTCAGAGAGTATAGGACTCGATCTTCAACAAACGTGTCCGCTCCCTATGGTTACAGATTG
310228 ACTCCAACAATGGTGATAGCTTGAGATGTTGGCGTGATTGGCTGCCGCTCATGCACATGGATGGG
131 ACTCCAACAATGGTGATAGCTTGAGATGTTGGCGTGATTGGCTGCCGCTCATGCACATGGATGGG
*
310293 AACAGCTCCTGTGCTTAAATTGATTTACTTGTAATTATTTTGGGGCTGTTGGATTTTTATTGGGC
196 AACAGCTCCTGTGCTTAAACTGATTTACTTGTAATTATTTTGGGGCTGTTGGATTTTTATTGGGC
*
310358 TTGTATTGGGCTCCGAGATTGCTTTTGTTGTAGTGA
261 TTGCATTGGGCTCCGAGATTGCTTTTGTTGTAGTGA
**
310394 CCGCTCCCTATTCCTTCAGAGAGTATAGGACTTGAACAAATCTTCAACAAACGTGTCTGCTCCCT
1 CCGCTCCCTATTCCTTCAGAGAGTATAGGACTTGAACAAATCTTCAACAAACGTGTCCACTCCCT
* ** * *
310459 ATTCCTTCAGAGAGTATATGACTCGATCTTCAACAAACGTGTCCGCTCTTTATTGTTGCAGATTG
66 ATTCCTTCAGAGAGTATAGGACTCGATCTTCAACAAACGTGTCCGCTCCCTATGGTTACAGATTG
* *
310524 GCTCCAACAATGGTGATAGCTTGAGATGTTGTCGTGATTGGCTGCCGCTCATGCACATGGATGGG
131 ACTCCAACAATGGTGATAGCTTGAGATGTTGGCGTGATTGGCTGCCGCTCATGCACATGGATGGG
310589 AACAGCTCCTGTGCTTAAACTGATTTACTTGTAATTATTTTGGGGCTGTTGGATTTTTATTGGGC
196 AACAGCTCCTGTGCTTAAACTGATTTACTTGTAATTATTTTGGGGCTGTTGGATTTTTATTGGGC
* *
310654 TTGCATTGGGCTCCGGGATTGCTTTTTTTGTAGTG
261 TTGCATTGGGCTCCGAGATTGCTTTTGTTGTAGTG
310689 GCCTTGAGCT
Statistics
Matches: 279, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
296 279 1.00
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (296 bp):
CCGCTCCCTATTCCTTCAGAGAGTATAGGACTTGAACAAATCTTCAACAAACGTGTCCACTCCCT
ATTCCTTCAGAGAGTATAGGACTCGATCTTCAACAAACGTGTCCGCTCCCTATGGTTACAGATTG
ACTCCAACAATGGTGATAGCTTGAGATGTTGGCGTGATTGGCTGCCGCTCATGCACATGGATGGG
AACAGCTCCTGTGCTTAAACTGATTTACTTGTAATTATTTTGGGGCTGTTGGATTTTTATTGGGC
TTGCATTGGGCTCCGAGATTGCTTTTGTTGTAGTGA
Found at i:310738 original size:3 final size:3
Alignment explanation
Indices: 310732--310776 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
310722 TTAGTATTAT
*
310732 TAA TAA TAA T-A TAT TAA T-A TAA TAA TAA TAA TAA TCAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
310775 TA
1 TA
310777 TATATTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
2 6 0.17
3 27 0.75
4 3 0.08
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:310756 original size:19 final size:21
Alignment explanation
Indices: 310732--310776 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
310722 TTAGTATTAT
*
310732 TAATAATAATATATTAATATAA
1 TAATAATAATA-ATCAATATAA
310754 TAATAATAATAATCAATATAA
1 TAATAATAATAATCAATATAA
310775 TA
1 TA
310777 TATATTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
TAATAATAATAATCAATATAA
Found at i:311073 original size:51 final size:52
Alignment explanation
Indices: 310960--311139 Score: 166
Period size: 51 Copynumber: 3.3 Consensus size: 52
310950 CCAGCGGGTT
* * ** * *
310960 CGCTCCCTATTGCTTCAGGGAGTATAGAACTCGAGAAATCTTTTGA-AAACGGGTT
1 CGCTCCCTATTCCTTCAGGGAGTATAGAACT--A-AGATC-TTCAACAAACGTGTC
* *
311015 CGCTCCCTCTTTCTTCAGGGAGTATAGAACT-AGATCTTCAACAAACGTGTC
1 CGCTCCCTATTCCTTCAGGGAGTATAGAACTAAGATCTTCAACAAACGTGTC
* * *
311066 CGCTCCCTATTCCTTCAGAGAGTATAGGACTTGAACAAATCTTCAACAAACGTGTC
1 CGCTCCCTATTCCTTCAGGGAGTATAGAAC-T--A-AGATCTTCAACAAACGTGTC
*
311122 CGCTCCTTATTCCTTCAG
1 CGCTCCCTATTCCTTCAG
311140 AAGGTAGGTA
Statistics
Matches: 106, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
50 3 0.03
51 37 0.35
52 1 0.01
55 29 0.27
56 36 0.34
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (52 bp):
CGCTCCCTATTCCTTCAGGGAGTATAGAACTAAGATCTTCAACAAACGTGTC
Found at i:311436 original size:3 final size:3
Alignment explanation
Indices: 311430--311480 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
311420 TTATTAGTAT
* *
311430 TAA TAA TAA TAA -CA TAT TAA T-A TAA TAA TAA TAA TAA TAA TCAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
311474 T-A TAA TA
1 TAA TAA TA
311481 TATATTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
2 5 0.12
3 32 0.80
4 3 0.08
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:311458 original size:22 final size:23
Alignment explanation
Indices: 311421--311463 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
311411 AATTATAAAT
*
311421 TATTAGTATTAATAATAATAACA
1 TATTAATATTAATAATAATAACA
311444 TATTAATA-TAATAATAATAA
1 TATTAATATTAATAATAATAA
311464 TAATAATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
TATTAATATTAATAATAATAACA
Found at i:312061 original size:27 final size:27
Alignment explanation
Indices: 312009--312061 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
311999 CTTTTTATAA
* * *
312009 TAATAATAATAATAGTAGTAGTAATAT
1 TAATAATAATAAAAGCAGTAGCAATAT
312036 TAATAATAATAAAAGCA-TAGACAATA
1 TAATAATAATAAAAGCAGTAG-CAATA
312062 ATATTAATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 3 0.14
27 19 0.86
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (27 bp):
TAATAATAATAAAAGCAGTAGCAATAT
Found at i:312064 original size:3 final size:3
Alignment explanation
Indices: 312005--312047 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
311995 ATATCTTTTT
* * * *
312005 ATA ATA ATA ATA ATA ATA GTA GTA GTA ATA TTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
312048 AAGCATAGAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:312867 original size:14 final size:15
Alignment explanation
Indices: 312838--312938 Score: 77
Period size: 16 Copynumber: 6.8 Consensus size: 15
312828 AATGAATAAA
312838 TATATTTAATATACTT
1 TATATTT-ATATACTT
312854 TATATTTA-ATAC-T
1 TATATTTATATACTT
312867 TATATTTATATACTT
1 TATATTTATATACTT
* * *
312882 TAATACTTATATTC-A
1 T-ATATTTATATACTT
* *
312897 AACACTTTAT-TACTT
1 TATA-TTTATATACTT
*
312912 TATA-TTATATATTT
1 TATATTTATATACTT
312926 TATACTTTATATA
1 TATA-TTTATATA
312939 TAAAGTACCA
Statistics
Matches: 66, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
13 13 0.20
14 20 0.30
15 9 0.14
16 24 0.36
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (15 bp):
TATATTTATATACTT
Found at i:312871 original size:22 final size:22
Alignment explanation
Indices: 312854--312937 Score: 84
Period size: 22 Copynumber: 3.9 Consensus size: 22
312844 TAATATACTT
312854 TATA-TTTAATACTTATATTTA
1 TATACTTTAATACTTATATTTA
*
312875 TATACTTTAATACTTATATTCA
1 TATACTTTAATACTTATATTTA
* * *
312897 AACACTTTATTACTT-TATATTA
1 TATACTTTAATACTTATAT-TTA
*
312919 TATA-TTTTATACTTTATAT
1 TATACTTTAATAC-TTATAT
312938 ATAAAGTACC
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
21 13 0.26
22 34 0.68
23 3 0.06
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.55
Consensus pattern (22 bp):
TATACTTTAATACTTATATTTA
Found at i:313061 original size:7 final size:7
Alignment explanation
Indices: 313032--313070 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
313022 ATTAAACAAC
313032 ACTTTATT
1 ACTTTA-T
313040 ACTTTAT
1 ACTTTAT
313047 A-TTATAT
1 ACTT-TAT
313054 ACTTTAT
1 ACTTTAT
313061 ACTTTAT
1 ACTTTAT
313068 ACT
1 ACT
313071 AAGATGACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
6 2 0.07
7 19 0.66
8 8 0.28
ACGTcount: A:0.31, C:0.13, G:0.00, T:0.56
Consensus pattern (7 bp):
ACTTTAT
Found at i:313301 original size:2 final size:2
Alignment explanation
Indices: 313296--313333 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
313286 TTATATAGTT
*
313296 TA TA TA TA TA TA TA TA TA TA T- TA TA TA GTT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
313334 CTATGCATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.94
3 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:313978 original size:7 final size:7
Alignment explanation
Indices: 313949--313987 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
313939 ATTAAACAAC
313949 ACTTTATT
1 ACTTTA-T
313957 ACTTTAT
1 ACTTTAT
313964 A-TTATAT
1 ACTT-TAT
313971 ACTTTAT
1 ACTTTAT
313978 ACTTTAT
1 ACTTTAT
313985 ACT
1 ACT
313988 AAGATGACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
6 2 0.07
7 19 0.66
8 8 0.28
ACGTcount: A:0.31, C:0.13, G:0.00, T:0.56
Consensus pattern (7 bp):
ACTTTAT
Found at i:314088 original size:7 final size:7
Alignment explanation
Indices: 314076--314120 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
314066 AATACATATA
314076 TTAGGGT
1 TTAGGGT
314083 TTAGGGT
1 TTAGGGT
314090 TTAGGGT
1 TTAGGGT
***
314097 TTAAAAT
1 TTAGGGT
314104 TTAGGGT
1 TTAGGGT
314111 TTAGGGT
1 TTAGGGT
314118 TTA
1 TTA
314121 TATAAACTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.44
Consensus pattern (7 bp):
TTAGGGT
Found at i:314203 original size:2 final size:2
Alignment explanation
Indices: 314198--314246 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
314188 TTATATAGTT
**
314198 TA TA TA TA TA GG T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
314239 TA TA TA TA
1 TA TA TA TA
314247 CATGGTTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:314646 original size:21 final size:21
Alignment explanation
Indices: 314617--314668 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
314607 TCCATTTATA
* *
314617 TTAGGGTTTGTAGTTTAAGGT
1 TTAGGGTTTATAGTTTAAAGT
* *
314638 TTAGTGTTTATGGTTTAAAGT
1 TTAGGGTTTATAGTTTAAAGT
*
314659 TTAGGATTTA
1 TTAGGGTTTA
314669 GGAGTTATGA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (21 bp):
TTAGGGTTTATAGTTTAAAGT
Found at i:314905 original size:22 final size:21
Alignment explanation
Indices: 314862--314923 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 21
314852 GTTCAGGGGA
** *
314862 TTAAGGTTTAGGGTCAAGGAT
1 TTAAGGTTTAGGGTTTATGAT
314883 TTAAAGGTTTAGGGTTTATGAT
1 TT-AAGGTTTAGGGTTTATGAT
* *
314905 TTAGGGTTTAGAGTTTATG
1 TTAAGGTTTAGGGTTTATG
314924 GTTTTTATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 17 0.49
22 18 0.51
ACGTcount: A:0.26, C:0.02, G:0.31, T:0.42
Consensus pattern (21 bp):
TTAAGGTTTAGGGTTTATGAT
Found at i:314909 original size:14 final size:14
Alignment explanation
Indices: 314889--314927 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
314879 GGATTTAAAG
314889 GTTTAGGGTTTATGA
1 GTTTAGGGTTTA-GA
314904 -TTTAGGGTTTAGA
1 GTTTAGGGTTTAGA
*
314917 GTTTATGGTTT
1 GTTTAGGGTTT
314928 TTATAAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 2 0.09
14 20 0.91
ACGTcount: A:0.18, C:0.00, G:0.31, T:0.51
Consensus pattern (14 bp):
GTTTAGGGTTTAGA
Found at i:315245 original size:17 final size:18
Alignment explanation
Indices: 315205--315249 Score: 65
Period size: 17 Copynumber: 2.5 Consensus size: 18
315195 ATAAAATCTC
315205 AATTCTCAATTTCCCTCTA
1 AATTCTCAATTT-CCTCTA
315224 AATTCTCAATTT-CTCTA
1 AATTCTCAATTTCCTCTA
*
315241 TATTCTCAA
1 AATTCTCAA
315250 ATTTTCCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 13 0.52
19 12 0.48
ACGTcount: A:0.29, C:0.27, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTCTCAATTTCCTCTA
Found at i:315255 original size:19 final size:18
Alignment explanation
Indices: 315205--315255 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
315195 ATAAAATCTC
*
315205 AATTCTCAATTTCCCTCTA
1 AATTCTCAATTT-TCTCTA
315224 AATTCTCAA-TTTCTCTA
1 AATTCTCAATTTTCTCTA
*
315241 TATTCTCAAATTTTC
1 AATTCTC-AATTTTC
315256 CCAATTTCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 11 0.39
18 4 0.14
19 13 0.46
ACGTcount: A:0.27, C:0.25, G:0.00, T:0.47
Consensus pattern (18 bp):
AATTCTCAATTTTCTCTA
Found at i:315432 original size:13 final size:13
Alignment explanation
Indices: 315406--315468 Score: 63
Period size: 13 Copynumber: 4.5 Consensus size: 13
315396 ATATACTTTT
315406 TATAGTTTACACATA
1 TATAGTTT--ACATA
315421 TATAGTTTACATATA
1 TATAGTTTAC--ATA
315436 TATAGTTTACATA
1 TATAGTTTACATA
* **
315449 TAAAGTTTTTATA
1 TATAGTTTACATA
315462 TATAGTT
1 TATAGTT
315469 CATATAAACA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
13 21 0.50
15 21 0.50
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (13 bp):
TATAGTTTACATA
Found at i:315447 original size:15 final size:14
Alignment explanation
Indices: 315406--315553 Score: 83
Period size: 15 Copynumber: 10.1 Consensus size: 14
315396 ATATACTTTT
*
315406 TATAGTTTACACATA
1 TATAGTTTA-ATATA
315421 TATAGTTTACATATA
1 TATAGTTTA-ATATA
315436 TATAGTTTACATATA
1 TATAGTTTA-ATATA
*
315451 -A-AGTTT-TTATA
1 TATAGTTTAATATA
* *
315462 TATAGTTCATATAAA
1 TATAGTTTA-ATATA
* *
315477 CATAATTT-ATATA
1 TATAGTTTAATATA
*
315490 TATAACTTATAATAATTA
1 TAT-AGTT-TAAT-A-TA
315508 TATAGTTTATAATATAAA
1 TATAG-TT-TAATAT--A
315526 TATAGTTT-ATATA
1 TATAGTTTAATATA
315539 TATAGTTT-ATATA
1 TATAGTTTAATATA
315552 TA
1 TA
315554 AACTTATATT
Statistics
Matches: 109, Mismatches: 12, Indels: 26
0.74 0.08 0.18
Matches are distributed among these distances:
11 4 0.04
12 1 0.01
13 31 0.28
14 4 0.04
15 42 0.39
16 4 0.04
17 5 0.05
18 18 0.17
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (14 bp):
TATAGTTTAATATA
Found at i:315528 original size:18 final size:19
Alignment explanation
Indices: 315507--315542 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
315497 TATAATAATT
315507 ATATAGTTTATA-ATATAA
1 ATATAGTTTATATATATAA
315525 ATATAGTTTATATATATA
1 ATATAGTTTATATATATA
315543 GTTTATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (19 bp):
ATATAGTTTATATATATAA
Found at i:315541 original size:13 final size:13
Alignment explanation
Indices: 315418--315553 Score: 84
Period size: 13 Copynumber: 10.4 Consensus size: 13
315408 TAGTTTACAC
315418 ATATATAGTTTACAT
1 ATATATAGTTT--AT
*
315433 ATATATAGTTTAC
1 ATATATAGTTTAT
* *
315446 ATATAAAGTTTTT
1 ATATATAGTTTAT
315459 ATATATAGTTCATAT
1 ATATATAGTT--TAT
* * *
315474 AAACATAATTTAT
1 ATATATAGTTTAT
**
315487 ATATATAACTTAT
1 ATATATAGTTTAT
315500 A-ATA-A--TTAT
1 ATATATAGTTTAT
* *
315509 ATAGTTTA-TAATAT
1 ATA-TATAGT-TTAT
*
315523 AAATATAGTTTAT
1 ATATATAGTTTAT
315536 ATATATAGTTTAT
1 ATATATAGTTTAT
315549 ATATA
1 ATATA
315554 AACTTATATT
Statistics
Matches: 95, Mismatches: 18, Indels: 18
0.73 0.14 0.14
Matches are distributed among these distances:
9 5 0.05
10 1 0.01
11 2 0.02
12 4 0.04
13 57 0.60
14 6 0.06
15 20 0.21
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (13 bp):
ATATATAGTTTAT
Found at i:315579 original size:30 final size:31
Alignment explanation
Indices: 315483--315580 Score: 100
Period size: 31 Copynumber: 3.2 Consensus size: 31
315473 TAAACATAAT
*
315483 TTATATATATAACTTATAATA-AT-TATATAG
1 TTATATATA-AACTTATATTATATATATATAG
315513 TTTATAATATAAA--TATAGTT-TATATATATAG
1 -TTAT-ATATAAACTTATA-TTATATATATATAG
315544 TTTATATATAAACTTATATTATATATATATA-
1 -TTATATATAAACTTATATTATATATATATAG
315575 TTATAT
1 TTATAT
315581 TTTTTTCAAT
Statistics
Matches: 59, Mismatches: 1, Indels: 15
0.79 0.01 0.20
Matches are distributed among these distances:
29 4 0.07
30 16 0.27
31 20 0.34
32 19 0.32
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (31 bp):
TTATATATAAACTTATATTATATATATATAG
Found at i:315580 original size:13 final size:13
Alignment explanation
Indices: 315483--315580 Score: 55
Period size: 13 Copynumber: 7.5 Consensus size: 13
315473 TAAACATAAT
315483 TTATATATATA-A
1 TTATATATATATA
*
315495 CT-TATA-ATA-A
1 TTATATATATATA
*
315505 TTATATAGTTTATA
1 TTATATA-TATATA
* *
315519 ATATAAATATAGT-
1 TTATATATATA-TA
315532 TTATATATATAGT-
1 TTATATATATA-TA
315545 TTATATATAAACTTATA
1 TTATATAT--A--TATA
315562 TTATATATATATA
1 TTATATATATATA
315575 TTATAT
1 TTATAT
315581 TTTTTTCAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
10 5 0.07
11 8 0.12
12 1 0.01
13 34 0.50
14 7 0.10
15 2 0.03
16 1 0.01
17 10 0.15
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (13 bp):
TTATATATATATA
Found at i:316864 original size:21 final size:20
Alignment explanation
Indices: 316835--316875 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
316825 AAAATATAAA
*
316835 AAATATAAATTAAATTATTAT
1 AAATATAAAATAAA-TATTAT
*
316856 AAATTTAAAATAAATATTAT
1 AAATATAAAATAAATATTAT
316876 TTTTATCTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATATAAAATAAATATTAT
Found at i:319197 original size:101 final size:101
Alignment explanation
Indices: 319022--319224 Score: 406
Period size: 101 Copynumber: 2.0 Consensus size: 101
319012 CGCATACAAA
319022 CAAATTTATCAACTAAATACCAAGAAGATGTTTGTGATTTCTTAAAGCTTGCTAAACAAAATACA
1 CAAATTTATCAACTAAATACCAAGAAGATGTTTGTGATTTCTTAAAGCTTGCTAAACAAAATACA
319087 AACTCCAGTGGTAGGATTCATTGCCCATTAAAAGAT
66 AACTCCAGTGGTAGGATTCATTGCCCATTAAAAGAT
319123 CAAATTTATCAACTAAATACCAAGAAGATGTTTGTGATTTCTTAAAGCTTGCTAAACAAAATACA
1 CAAATTTATCAACTAAATACCAAGAAGATGTTTGTGATTTCTTAAAGCTTGCTAAACAAAATACA
319188 AACTCCAGTGGTAGGATTCATTGCCCATTAAAAGAT
66 AACTCCAGTGGTAGGATTCATTGCCCATTAAAAGAT
319224 C
1 C
319225 GTAACAACTG
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 102 1.00
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (101 bp):
CAAATTTATCAACTAAATACCAAGAAGATGTTTGTGATTTCTTAAAGCTTGCTAAACAAAATACA
AACTCCAGTGGTAGGATTCATTGCCCATTAAAAGAT
Found at i:331151 original size:10 final size:10
Alignment explanation
Indices: 331136--331169 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
331126 ATTTTACCAC
331136 ACAAAAAAAA
1 ACAAAAAAAA
331146 ACAAAAAAAA
1 ACAAAAAAAA
*
331156 A-ACAAAAAA
1 ACAAAAAAAA
331165 ACAAA
1 ACAAA
331170 TAATATGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (10 bp):
ACAAAAAAAA
Found at i:331154 original size:11 final size:11
Alignment explanation
Indices: 331138--331165 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
331128 TTTACCACAC
331138 AAAAAAAAACA
1 AAAAAAAAACA
331149 AAAAAAAAACA
1 AAAAAAAAACA
331160 AAAAAA
1 AAAAAA
331166 CAAATAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:333713 original size:22 final size:23
Alignment explanation
Indices: 333667--333735 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 23
333657 ATACAATAAA
**
333667 TAATATTATTTATCATAAAAT-T
1 TAATATTATTTATTTTAAAATAT
333689 TAATATTA-TTATTTTAAAATAT
1 TAATATTATTTATTTTAAAATAT
* *
333711 TAAAATAATTTATTATT-AAATAT
1 TAATATTATTTATT-TTAAAATAT
333734 TA
1 TA
333736 TTTGTATAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
21 10 0.25
22 15 0.38
23 13 0.32
24 2 0.05
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (23 bp):
TAATATTATTTATTTTAAAATAT
Found at i:333792 original size:33 final size:32
Alignment explanation
Indices: 333734--333797 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
333724 TATTAAATAT
*
333734 TATTTGTATAATTTTATTAATAAAAATATTAA
1 TATTGGTATAATTTTATTAATAAAAATATTAA
333766 TATTGGTAT-ATTTTATTGAAATAAAAATATTA
1 TATTGGTATAATTTTATT--AATAAAAATATTA
333798 TAATTATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 8 0.28
32 8 0.28
33 13 0.45
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (32 bp):
TATTGGTATAATTTTATTAATAAAAATATTAA
Found at i:333902 original size:27 final size:28
Alignment explanation
Indices: 333872--333932 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
333862 TTAATATCTT
* *
333872 TATTAAA-ATATTATTAGATATTATT-AA
1 TATTAAATATATAAATA-ATATTATTCAA
*
333899 TATTAAATATATAAATAATATTATTCAT
1 TATTAAATATATAAATAATATTATTCAA
333927 TATTAA
1 TATTAA
333933 TAATTTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 15 0.52
28 14 0.48
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (28 bp):
TATTAAATATATAAATAATATTATTCAA
Found at i:333903 original size:9 final size:9
Alignment explanation
Indices: 333878--334003 Score: 50
Period size: 9 Copynumber: 14.2 Consensus size: 9
333868 TCTTTATTAA
333878 AATATTATT
1 AATATTATT
333887 AGATATTATT
1 A-ATATTATT
333897 AATATTA--
1 AATATTATT
*
333904 AATA-TATA
1 AATATTATT
*
333912 AATAATATT
1 AATATTATT
*
333921 ATTCATTATT
1 AAT-ATTATT
*
333931 AATAAT-TT
1 AATATTATT
*
333939 AA-AATATT
1 AATATTATT
* *
333947 -ATTTCTATG
1 AATAT-TATT
**
333956 AA-ATTAAA
1 AATATTATT
* *
333964 AATAATATA
1 AATATTATT
*
333973 AATTTTATT
1 AATATTATT
333982 AATAATTTATT
1 AAT-A-TTATT
333993 AATATTATT
1 AATATTATT
334002 AA
1 AA
334004 AATAAAATAT
Statistics
Matches: 88, Mismatches: 17, Indels: 24
0.68 0.13 0.19
Matches are distributed among these distances:
6 2 0.02
7 8 0.09
8 14 0.16
9 38 0.43
10 18 0.20
11 8 0.09
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (9 bp):
AATATTATT
Found at i:334106 original size:9 final size:10
Alignment explanation
Indices: 334048--334106 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
334038 TGATTATATT
334048 TATTATTAAA
1 TATTATTAAA
* **
334058 AATATATTTTA
1 TAT-TATTAAA
334069 TATTATTAAA
1 TATTATTAAA
*
334079 TATTAATAATA
1 TATTATTAA-A
334090 TATT-TTAAA
1 TATTATTAAA
334099 TATT-TTAA
1 TATTATTAA
334107 TAATTAATAT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
9 9 0.23
10 18 0.46
11 12 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TATTATTAAA
Found at i:334108 original size:28 final size:26
Alignment explanation
Indices: 334022--334115 Score: 82
Period size: 28 Copynumber: 3.3 Consensus size: 26
334012 ATAATATCTT
*
334022 ATATTTATAATATAATTGATTATA-TTTA
1 ATATTAATAATAT-ATT--TTATATTTTA
* *
334050 TTATTAAAAATATATTTTATATTATTAA
1 ATATTAATAATATATTTTATATT-TT-A
334078 ATATTAATAATATATTTTAAATATTTTA
1 ATATTAATAATATATTTT--ATATTTTA
334106 ATAATTAATA
1 AT-ATTAATA
334116 TTTTGATTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
25 5 0.09
26 1 0.02
27 5 0.09
28 30 0.55
29 9 0.16
30 5 0.09
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (26 bp):
ATATTAATAATATATTTTATATTTTA
Found at i:334109 original size:22 final size:21
Alignment explanation
Indices: 334066--334119 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 21
334056 AAAATATATT
334066 TTATATTATTAAATATTAATAA
1 TTATATT-TTAAATATTAATAA
334088 -TATATTTTAAATATTTTAATAA
1 TTATATTTTAAATA--TTAATAA
334110 TTAATATTTT
1 TT-ATATTTT
334120 GATTAAATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 7 0.25
21 6 0.21
22 7 0.25
23 1 0.04
24 7 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTATATTTTAAATATTAATAA
Found at i:335540 original size:79 final size:78
Alignment explanation
Indices: 335435--335583 Score: 201
Period size: 79 Copynumber: 1.9 Consensus size: 78
335425 AGTGTTCAAT
* * * * *
335435 AATAACAAAATCGGTAGAAAAATAATGTTTTAGGTAACGTTTTACTGGATATATTAACAAAACCA
1 AATAACAAAACCGATAGAAAAATAATGTTTTAGGTAACGTTTTACCGGAAATATTAA-AAAAACA
335500 ATAAAACGCCCAAA
65 ATAAAACGCCCAAA
** *
335514 AATAA-AAAACCGATAGAAATAATAATGTTTTAGGTAATTTTTTACCGGAAATATTAAAAAAATA
1 AATAACAAAACCGATAGAAA-AATAATGTTTTAGGTAACGTTTTACCGGAAATATTAAAAAAACA
335578 ATAAAA
65 ATAAAA
335584 AAACCTATAA
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
78 23 0.38
79 38 0.62
ACGTcount: A:0.51, C:0.10, G:0.11, T:0.28
Consensus pattern (78 bp):
AATAACAAAACCGATAGAAAAATAATGTTTTAGGTAACGTTTTACCGGAAATATTAAAAAAACAA
TAAAACGCCCAAA
Found at i:335723 original size:3 final size:3
Alignment explanation
Indices: 335717--335749 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
335707 AATTTAAAAA
335717 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
335750 GACGAAGGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Done.