Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 60 of 226
Found at i:23703642 original size:34 final size:34
Alignment explanation
Indices: 23703599--23703668 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
23703589 GAATATCGGG
23703599 TTTGTTTGTTGACATCTTTATTGTGATTAATGGA
1 TTTGTTTGTTGACATCTTTATTGTGATTAATGGA
23703633 TTTGTTTGTTGACATCTTTATTGTGATTAATGGA
1 TTTGTTTGTTGACATCTTTATTGTGATTAATGGA
23703667 TT
1 TT
23703669 AAATAACTGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.20, C:0.06, G:0.20, T:0.54
Consensus pattern (34 bp):
TTTGTTTGTTGACATCTTTATTGTGATTAATGGA
Found at i:23706754 original size:29 final size:30
Alignment explanation
Indices: 23706709--23706766 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
23706699 GGTTGAATCA
* *
23706709 AAATTAAAGTTTCATGTATATAATTGCACC
1 AAATCAAAGTTTCATGTATAGAATTGCACC
*
23706739 AAATCAAAGTTT-ATGTATCGAATTGCAC
1 AAATCAAAGTTTCATGTATAGAATTGCAC
23706767 AATGACTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (30 bp):
AAATCAAAGTTTCATGTATAGAATTGCACC
Found at i:23713525 original size:30 final size:29
Alignment explanation
Indices: 23713474--23713564 Score: 103
Period size: 30 Copynumber: 3.0 Consensus size: 29
23713464 GATTCCATAG
*
23713474 GTCCCTGTATGTTTCATAAATTTAATATTTA
1 GTCCCTGTAT-TTTTATAAATTTAA-ATTTA
23713505 GTCCCTGTATTTTTATAAATTTGAAATTTA
1 GTCCCTGTATTTTTATAAATTT-AAATTTA
* *
23713535 GTCTCTTTATTTTT-TAAATTTTAAAATTTA
1 GTCCCTGTATTTTTATAAA-TTT-AAATTTA
23713565 AGTTCAATAG
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
29 4 0.07
30 38 0.70
31 12 0.22
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.53
Consensus pattern (29 bp):
GTCCCTGTATTTTTATAAATTTAAATTTA
Found at i:23716719 original size:17 final size:18
Alignment explanation
Indices: 23716676--23716720 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
23716666 TTAAATCATA
23716676 TACATATTTTTTTATTAT
1 TACATATTTTTTTATTAT
23716694 TACAT-TTTTTTTATT-T
1 TACATATTTTTTTATTAT
23716710 T-CATAGTTTTT
1 TACATA-TTTTT
23716721 ATATATACGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 3 0.12
16 2 0.08
17 15 0.60
18 5 0.20
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.69
Consensus pattern (18 bp):
TACATATTTTTTTATTAT
Found at i:23719559 original size:21 final size:19
Alignment explanation
Indices: 23719535--23719587 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 19
23719525 ATTGGAATAT
23719535 AATATTTAATTATTATATTTA
1 AATATTTAATTA-T-TATTTA
*
23719556 AATATTTAAATATTATTTA
1 AATATTTAATTATTATTTA
*
23719575 TATATTCTAATTA
1 AATATT-TAATTA
23719588 AATTTAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 11 0.39
20 6 0.21
21 11 0.39
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
AATATTTAATTATTATTTA
Found at i:23723505 original size:2 final size:2
Alignment explanation
Indices: 23723498--23723534 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
23723488 NNNNNNNNNC
23723498 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23723535 TGAAGTGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:23725731 original size:91 final size:92
Alignment explanation
Indices: 23725606--23725798 Score: 291
Period size: 91 Copynumber: 2.1 Consensus size: 92
23725596 TTGATTTTAG
* *
23725606 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAACAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
* *
23725671 ATTTAAT-ATTAATTATTTTAAATTGTA
66 ATGTAATAATT-ATTATTTTAAATTATA
* * *
23725698 TAAATTCATGTAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTAT
1 TAAATTCATATAAGAACAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
23725762 ATGTAATAATTATTATTTTAAATTATA
66 ATGTAATAATTATTATTTTAAATTATA
*
23725789 CAAATTCATA
1 TAAATTCATA
23725799 AAATATAATT
Statistics
Matches: 91, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
91 73 0.80
92 18 0.20
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.47
Consensus pattern (92 bp):
TAAATTCATATAAGAACAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
ATGTAATAATTATTATTTTAAATTATA
Found at i:23725961 original size:120 final size:120
Alignment explanation
Indices: 23725829--23726121 Score: 500
Period size: 120 Copynumber: 2.4 Consensus size: 120
23725819 AATTATTTTA
* * * *
23725829 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TCTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT--AATTTATATT
*
23725892 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATCATTAAG
64 TTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATCATTAAG
*
23725949 AATTTTATTAAATTATATATTTTAATTATACTATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
23726014 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATCATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATCATTAAG
23726069 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
23726122 TAAATATGAT
Statistics
Matches: 164, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
119 5 0.03
120 157 0.96
121 2 0.01
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATCATTAAG
Found at i:23726104 original size:16 final size:16
Alignment explanation
Indices: 23726083--23726124 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
23726073 TTATTAAATT
*
23726083 ATATATTTTAATTATA
1 ATATATTTTAATAATA
23726099 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
23726114 AT-TATGTTTAA
1 ATATAT-TTTAA
23726125 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:23726109 original size:15 final size:15
Alignment explanation
Indices: 23726074--23726115 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
23726064 TTAAGAATTT
*
23726074 TATTAAATTAT-ATA
1 TATTTAATTATAATA
23726088 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
23726102 TATTTAATAATAAT
1 TATTTAATTATAAT
23726116 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:23726255 original size:18 final size:17
Alignment explanation
Indices: 23726227--23726261 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
23726217 ATTATTAAGA
*
23726227 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
23726244 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
23726262 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:23726354 original size:157 final size:157
Alignment explanation
Indices: 23726058--23726374 Score: 589
Period size: 157 Copynumber: 2.0 Consensus size: 157
23726048 ATAAGAATAT
*
23726058 TAATCATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATCATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
*
23726123 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
23726188 TAATAATTTACCAAAACAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
*
23726215 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATCATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
23726280 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
23726345 TAATCATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
23726372 TAA
1 TAA
23726375 GGGTATTCTA
Statistics
Matches: 155, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 155 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATCATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:23726516 original size:16 final size:16
Alignment explanation
Indices: 23726497--23726548 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
23726487 GATTTGCTAT
* * *
23726497 TACACATCTATTCCAT
1 TACACCTCTAATCCAA
23726513 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
23726529 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
23726545 TACA
1 TACA
23726549 GCGAACCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.37, C:0.35, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:23732224 original size:20 final size:20
Alignment explanation
Indices: 23732186--23732225 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
23732176 CGTAAAATAA
**
23732186 TTTCTGAAAAATGTTTTACT
1 TTTCTGAAAAATGACTTACT
*
23732206 TTTCTGTAAAATGACTTACT
1 TTTCTGAAAAATGACTTACT
23732226 GGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.47
Consensus pattern (20 bp):
TTTCTGAAAAATGACTTACT
Found at i:23733613 original size:27 final size:27
Alignment explanation
Indices: 23733583--23733652 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
23733573 AATAATCAAT
*
23733583 TCAATATCCAACAATGTTAAAACATA-A
1 TCAATATCCAACAAT-TCAAAACATATA
* *
23733610 TCAATATCTAACCAATTCAAGACATATA
1 TCAATATCCAA-CAATTCAAAACATATA
*
23733638 TCAAAATCCAACAAT
1 TCAATATCCAACAAT
23733653 CTAAAATCTG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 22 0.61
28 14 0.39
ACGTcount: A:0.50, C:0.21, G:0.03, T:0.26
Consensus pattern (27 bp):
TCAATATCCAACAATTCAAAACATATA
Found at i:23735353 original size:21 final size:21
Alignment explanation
Indices: 23735329--23735389 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
23735319 TTATAAAGTT
23735329 ATCATGACTTAAAATATATTG
1 ATCATGACTTAAAATATATTG
* * *
23735350 ATCATGATTTTATAA-A-GTT-
1 ATCATGA-CTTAAAATATATTG
*
23735369 ACCATGACTTAAAATATATTG
1 ATCATGACTTAAAATATATTG
23735390 CCCAAAAGCT
Statistics
Matches: 29, Mismatches: 7, Indels: 8
0.66 0.16 0.18
Matches are distributed among these distances:
18 5 0.17
19 7 0.24
20 4 0.14
21 8 0.28
22 5 0.17
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (21 bp):
ATCATGACTTAAAATATATTG
Found at i:23737655 original size:6 final size:6
Alignment explanation
Indices: 23737644--23737674 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
23737634 AATATTTCCC
*
23737644 ACAGAA ACAGAA ACAGAA ACAAAA ACAGAA A
1 ACAGAA ACAGAA ACAGAA ACAGAA ACAGAA A
23737675 ATACAAACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.71, C:0.16, G:0.13, T:0.00
Consensus pattern (6 bp):
ACAGAA
Found at i:23741142 original size:11 final size:11
Alignment explanation
Indices: 23741126--23741190 Score: 64
Period size: 11 Copynumber: 6.0 Consensus size: 11
23741116 AATTAATCAC
23741126 ATTAATATTAA
1 ATTAATATTAA
23741137 ATTAATA--AA
1 ATTAATATTAA
* *
23741146 A-TATTATCAA
1 ATTAATATTAA
*
23741156 GATAAATATTAA
1 -ATTAATATTAA
23741168 ATTAATATTAA
1 ATTAATATTAA
23741179 TATTAATATTAA
1 -ATTAATATTAA
23741191 TTGTTTCTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
8 4 0.09
9 3 0.07
10 2 0.05
11 18 0.41
12 17 0.39
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (11 bp):
ATTAATATTAA
Found at i:23741179 original size:6 final size:6
Alignment explanation
Indices: 23741160--23741191 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
23741150 TATCAAGATA
23741160 AATATT AA-ATT AATATT AATATT AATATT AAT
1 AATATT AATATT AATATT AATATT AATATT AAT
23741192 TGTTTCTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
AATATT
Found at i:23741186 original size:23 final size:22
Alignment explanation
Indices: 23741126--23741190 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
23741116 AATTAATCAC
23741126 ATTAATATTAAATTAATA--AA
1 ATTAATATTAAATTAATATTAA
* * *
23741146 A-TATTATCAAGATAAATATTAA
1 ATTAATATTAA-ATTAATATTAA
23741168 ATTAATATTAATATTAATATTAA
1 ATTAATATTAA-ATTAATATTAA
23741191 TTGTTTCTTG
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
19 7 0.21
20 7 0.21
22 3 0.09
23 17 0.50
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
ATTAATATTAAATTAATATTAA
Found at i:23741679 original size:52 final size:50
Alignment explanation
Indices: 23741604--23741710 Score: 151
Period size: 52 Copynumber: 2.1 Consensus size: 50
23741594 AAAAGCTAAA
* * * *
23741604 TAAATAAAAATGAGATTCTATTAGATTAATTATCTTTTTTAACTTAAAAATC
1 TAAATAAAAATAAAATTCAATTAGATTAATTA--TTTTTGAACTTAAAAATC
*
23741656 TAAATAAAAATAAAATTCAATTAGATTAATTATTTTTGAACTTATAAATC
1 TAAATAAAAATAAAATTCAATTAGATTAATTATTTTTGAACTTAAAAATC
23741706 TAAAT
1 TAAAT
23741711 TTGACTCAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
50 21 0.42
52 29 0.58
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (50 bp):
TAAATAAAAATAAAATTCAATTAGATTAATTATTTTTGAACTTAAAAATC
Found at i:23742626 original size:12 final size:12
Alignment explanation
Indices: 23742609--23742633 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23742599 GTAAAACACT
23742609 TAAATAATATTA
1 TAAATAATATTA
23742621 TAAATAATATTA
1 TAAATAATATTA
23742633 T
1 T
23742634 GTTGTAGAAT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAATAATATTA
Found at i:23744760 original size:27 final size:27
Alignment explanation
Indices: 23744719--23744770 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
23744709 TAGTATTGGC
23744719 GCCTATCTGGAAGGCGCCAATGGTGGT
1 GCCTATCTGGAAGGCGCCAATGGTGGT
* *
23744746 GCCTATTTGGGAGGCGCCAATGGTG
1 GCCTATCTGGAAGGCGCCAATGGTG
23744771 AACAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.17, C:0.21, G:0.38, T:0.23
Consensus pattern (27 bp):
GCCTATCTGGAAGGCGCCAATGGTGGT
Found at i:23744894 original size:19 final size:19
Alignment explanation
Indices: 23744870--23745341 Score: 167
Period size: 19 Copynumber: 25.4 Consensus size: 19
23744860 ATATCCCCAC
23744870 ATTATAATATTCATACAAA
1 ATTATAATATTCATACAAA
*
23744889 ATTATAATA-T--TACAAT
1 ATTATAATATTCATACAAA
* *
23744905 A-T-TCATA--CA-AAAAA
1 ATTATAATATTCATACAAA
**
23744919 ATTGCAATATTCATACAAA
1 ATTATAATATTCATACAAA
23744938 ATTATAATATTACAATATTCATACAA
1 ATTATAATATT-C-ATA--C--A-AA
* *
23744964 CATTACAATATTCATAAAAA
1 -ATTATAATATTCATACAAA
23744984 ATTATAATATTCATACAAA
1 ATTATAATATTCATACAAA
* *
23745003 ATTACAATA-T--TACAAT
1 ATTATAATATTCATACAAA
* *
23745019 A-T-TCATA--CA-AAAAA
1 ATTATAATATTCATACAAA
*
23745033 ATTACAATATTCATACAAA
1 ATTATAATATTCATACAAA
23745052 ATTATAATA-T--TAC--A
1 ATTATAATATTCATACAAA
23745066 A-TAT--TCATTCA-A-AAA
1 ATTATAAT-ATTCATACAAA
*
23745081 AATATAATATTCATACAAA
1 ATTATAATATTCATACAAA
*
23745100 ATTACAATATTCATACAAAAAA
1 ATTATAATATTCATAC---AAA
**
23745122 ATTGCAATATTCATACAAAA
1 ATTATAATATTCATAC-AAA
23745142 CTATAATATTACAATATTCATACAAAAA
1 --AT--TA-T--AATATTCATAC--AAA
23745170 ATTTATAATATTCATACAAA
1 A-TTATAATATTCATACAAA
*
23745190 ATTACAATATTCATACAAA
1 ATTATAATATTCATACAAA
* * *
23745209 A--A-ATTATTAATCCAAA
1 ATTATAATATTCATACAAA
*
23745225 ACTAT-A-A---ATAC-AA
1 ATTATAATATTCATACAAA
*
23745238 ATT-T-A-ATT-ATAAAATA
1 ATTATAATATTCATACAA-A
* *
23745254 ATTACAATATTCATACAAC
1 ATTATAATATTCATACAAA
* *
23745273 ATTACAATATTCATAAAAAA
1 ATTATAATATTCAT-ACAAA
23745293 ATTATAATATTCATACAAAAA
1 ATTATAATATTCATAC--AAA
*
23745314 ATTTAAAATATTCATACAAA
1 A-TTATAATATTCATACAAA
*
23745334 ATTCTAAT
1 ATTATAAT
23745342 CTAAACTATA
Statistics
Matches: 347, Mismatches: 46, Indels: 120
0.68 0.09 0.23
Matches are distributed among these distances:
11 1 0.00
12 4 0.01
13 8 0.02
14 24 0.07
15 7 0.02
16 40 0.12
17 7 0.02
18 11 0.03
19 117 0.34
20 36 0.10
21 8 0.02
22 45 0.13
23 1 0.00
24 2 0.01
25 6 0.02
26 4 0.01
27 22 0.06
28 4 0.01
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTATAATATTCATACAAA
Found at i:23744928 original size:30 final size:27
Alignment explanation
Indices: 23744870--23745200 Score: 195
Period size: 27 Copynumber: 14.1 Consensus size: 27
23744860 ATATCCCCAC
* *
23744870 ATTATAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTACAAT
23744897 ATTACAATATTCATAC-AAA--A-AA-
1 ATTACAATATTCATACAAAATTACAAT
* *
23744919 ATTGCAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTACAAT
23744946 ATTACAATATTCATAC---A--AC---
1 ATTACAATATTCATACAAAATTACAAT
* *
23744965 ATTACAATATTCATAAAAAATTATAAT
1 ATTACAATATTCATACAAAATTACAAT
23744992 ATT-C-------ATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
23745011 ATTACAATATTCATAC-AAA--A-AA-
1 ATTACAATATTCATACAAAATTACAAT
*
23745033 ATTACAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTACAAT
*
23745060 ATTACAATATTCATTCAAAA--A-AAT
1 ATTACAATATTCATACAAAATTACAAT
23745084 A-T--AATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
* *
23745108 ATT-C-ATA--CA-AAAAAATTGC-A-
1 ATTACAATATTCATACAAAATTACAAT
* *
23745128 A-TA-----TTCATACAAAACTATAAT
1 ATTACAATATTCATACAAAATTACAAT
23745149 ATTACAATATTCATAC-AAA--A-AAT
1 ATTACAATATTCATACAAAATTACAAT
*
23745172 -TTATAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
23745198 ATT
1 ATT
23745201 CATACAAAAA
Statistics
Matches: 239, Mismatches: 17, Indels: 96
0.68 0.05 0.27
Matches are distributed among these distances:
18 2 0.01
19 38 0.16
20 3 0.01
21 16 0.07
22 57 0.24
23 20 0.08
24 13 0.05
25 8 0.03
26 17 0.07
27 65 0.27
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (27 bp):
ATTACAATATTCATACAAAATTACAAT
Found at i:23744937 original size:49 final size:46
Alignment explanation
Indices: 23744870--23745217 Score: 274
Period size: 49 Copynumber: 7.6 Consensus size: 46
23744860 ATATCCCCAC
*
23744870 ATTATAATATTCATACAAAATTATAATATTACAATATTCATACAAAAAA
1 ATTACAATATTCATACAAAA--A-AATATTACAATATTCATACAAAAAA
* *
23744919 ATTGCAATATTCATACAAAATTATAATATTACAATATTCATAC---AAC
1 ATTACAATATTCATACAAAA--A-AATATTACAATATTCATACAAAAAA
*
23744965 ATTACAATATTCAT----AAAAA-ATTATAATATTCATACAAAATTACAA
1 ATTACAATATTCATACAAAAAAATATTACAATATTCATAC-AAA--A-AA
23745010 TATTACAATATTCATAC-AAAAAA-ATTACAATATTCATACAAAATTATAA
1 -ATTACAATATTCATACAAAAAAATATTACAATATTCATAC-AAA--A-AA
*
23745059 TATTACAATATTCATTCAAAAAAATA-T--AATATTCATAC---AAA
1 -ATTACAATATTCATACAAAAAAATATTACAATATTCATACAAAAAA
*
23745100 ATTACAATATTCATAC-AAAAAA-ATTGCAATATTCATACAAAACTATAA
1 ATTACAATATTCATACAAAAAAATATTACAATATTCATAC-AAA--A-AA
*
23745148 TATTACAATATTCATAC-AAAAAAT-TTATAATATTCATAC---AAA
1 -ATTACAATATTCATACAAAAAAATATTACAATATTCATACAAAAAA
*
23745190 ATTACAATATTCATACAAAAAATTATTA
1 ATTACAATATTCATACAAAAAAATATTA
23745218 ATCCAAAACT
Statistics
Matches: 259, Mismatches: 13, Indels: 60
0.78 0.04 0.18
Matches are distributed among these distances:
38 16 0.06
39 9 0.03
40 16 0.06
41 29 0.11
42 11 0.04
43 4 0.02
44 1 0.00
45 1 0.00
46 29 0.11
47 1 0.00
48 13 0.05
49 121 0.47
50 7 0.03
51 1 0.00
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (46 bp):
ATTACAATATTCATACAAAAAAATATTACAATATTCATACAAAAAA
Found at i:23744948 original size:68 final size:64
Alignment explanation
Indices: 23744870--23745341 Score: 305
Period size: 68 Copynumber: 7.1 Consensus size: 64
23744860 ATATCCCCAC
*
23744870 ATTATAATATTCATACAAAATTATAATATTACAATATTCATACAAAAAAATTGCAATATTCATAC
1 ATTATAATATTCATACAAAA--A-AA-ATTACAATATTCATACAAAAAAATTACAATATTCATAC
23744935 AAA
62 AAA
* * * *
23744938 ATTATAATATTACAATATTCATACAACATTACAATATTCAT---AAAAAATTATAATATTCATAC
1 ATTATAATATT-C-ATA--CAAAAAAAATTACAATATTCATACAAAAAAATTACAATATTCATAC
23745000 AAA
62 AAA
*
23745003 ATTACAATATTACAATATTCATACAAAAAAATTACAATATTCATACAAAATTATAATATTACAAT
1 ATTATAATATT-C-ATA--C--A-AAAAAAATTACAATATTCATAC-AAA--A-AA-ATTACAAT
*
23745068 ATTCATTCAAAAA
54 ATTCA-T-ACAAA
* *
23745081 AATATAATATTCATAC----AAAATTACAATATTCATACAAAAAAATTGCAATATTCATACAAA
1 ATTATAATATTCATACAAAAAAAATTACAATATTCATACAAAAAAATTACAATATTCATACAAA
* *
23745141 ACTATAATATTACAATATTCATACAAAAAATTTATAATATTCATAC---AAAATTACAATATTCA
1 ATTATAATATT-C-ATA--CA-A-AAAAAA-TTACAATATTCATACAAAAAAATTACAATATTCA
23745203 TACAAA
59 TACAAA
* * * * * *
23745209 A--A-ATTATTAATCCAAAACTATAAA-TACAA-ATTTAATTATAAAATAATTACAATATTCATA
1 ATTATAATATTCATACAAAA--A-AAATTACAATA-TTCA-TACAAAAAAATTACAATATTCATA
*
23745269 CAAC
61 CAAA
* * * *
23745273 ATTACAATATTCAT---AAAAAAATTATAATATTCATACAAAAAATTTAAAATATTCATACAAA
1 ATTATAATATTCATACAAAAAAAATTACAATATTCATACAAAAAAATTACAATATTCATACAAA
*
23745334 ATTCTAAT
1 ATTATAAT
23745342 CTAAACTATA
Statistics
Matches: 326, Mismatches: 37, Indels: 89
0.72 0.08 0.20
Matches are distributed among these distances:
59 3 0.01
60 22 0.07
61 39 0.12
62 26 0.08
63 5 0.02
64 26 0.08
65 46 0.14
66 5 0.02
67 27 0.08
68 64 0.20
69 2 0.01
70 8 0.02
71 14 0.04
72 5 0.02
74 2 0.01
75 2 0.01
76 15 0.05
77 2 0.01
78 13 0.04
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.33
Consensus pattern (64 bp):
ATTATAATATTCATACAAAAAAAATTACAATATTCATACAAAAAAATTACAATATTCATACAAA
Found at i:23745061 original size:41 final size:41
Alignment explanation
Indices: 23744899--23745336 Score: 155
Period size: 49 Copynumber: 10.0 Consensus size: 41
23744889 ATTATAATAT
**
23744899 TACAATATTCATACAAAAAAATTGCAATATTCATACAAAAT
1 TACAATATTCATACAAAAAAATTATAATATTCATACAAAAT
* * * * *
23744940 TATAATATTACAATATTCATACAACATTACAATATTCATAAAAAAT
1 TACAATATT-C-ATA--CA-AAAAAATTATAATATTCATACAAAAT
* *
23744986 TATAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAAT
1 TACAATATTCATAC-AAA--A-AA-ATTATAATATTCATAC---AAAAT
* * *
23745035 TACAATATTCATACAAAATTATAATATTACAATATTCATTCAAAAAAA
1 TACAATATTCATAC-AAA--A-AA-ATTATAATATTCA-T-ACAAAAT
* *
23745083 TATAATATTCATAC---AAAATTACAATATTCATACAAAAAAAT
1 TACAATATTCATACAAAAAAATTATAATATTCATAC---AAAAT
* *
23745124 TGCAATATTCATACAAAACTATAATATTACAATATTCATACAAAAAATT
1 TACAATATTCATAC-AAA--A-AA-ATTATAATATTCATAC--AAAA-T
* *
23745173 TATAATATTCATAC---AAAATTACAATATTCATACAAAA-
1 TACAATATTCATACAAAAAAATTATAATATTCATACAAAAT
* * * * * *
23745210 -A-ATTATTAATCCAAAACTATAAATACAAATTTAATT-ATAAAATAAT
1 TACAATATTCATACAAAA--A-AATTA-TAA--T-ATTCATACAA-AAT
* * *
23745256 TACAATATTCATAC---AACATTACAATATTCATAAAAAAAT
1 TACAATATTCATACAAAAAAATTATAATATTCAT-ACAAAAT
* * *
23745295 TATAATATTCATACAAAAAATTTAAAATATTCATACAAAAT
1 TACAATATTCATACAAAAAAATTATAATATTCATACAAAAT
23745336 T
1 T
23745337 CTAATCTAAA
Statistics
Matches: 315, Mismatches: 36, Indels: 92
0.71 0.08 0.21
Matches are distributed among these distances:
35 8 0.03
36 1 0.00
38 5 0.02
39 24 0.08
40 18 0.06
41 55 0.17
42 25 0.08
43 6 0.02
44 10 0.03
45 10 0.03
46 46 0.15
47 2 0.01
48 33 0.10
49 70 0.22
50 1 0.00
51 1 0.00
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (41 bp):
TACAATATTCATACAAAAAAATTATAATATTCATACAAAAT
Found at i:23745123 original size:89 final size:89
Alignment explanation
Indices: 23745005--23745312 Score: 388
Period size: 89 Copynumber: 3.5 Consensus size: 89
23744995 CATACAAAAT
* *
23745005 TACAATATTACAATATTCATACAAAAAAATTACAATATTCATACAAAATTATAATATTACAATAT
1 TACAAAATTACAATATTCATACAAAAAAATTACAATATTCATACAAAACTATAATATTACAATAT
23745070 TCATTCAAAAAAATATAATATTCA
66 TCATTCAAAAAAATATAATATTCA
*
23745094 TACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAACTATAATATTACAATAT
1 TACAAAATTACAATATTCATACAAAAAAATTACAATATTCATACAAAACTATAATATTACAATAT
* *
23745159 TCATACAAAAAATTTATAATATTCA
66 TCATTCAAAAAA-ATATAATATTCA
* *
23745184 TACAAAATTACAATATTCATAC-AAAAAA-T----TATTAATCCAAAACTATAA-A-TACAA-AT
1 TACAAAATTACAATATTCATACAAAAAAATTACAATATTCATACAAAACTATAATATTACAATA-
* *
23745240 TTAATT-ATAAAATAATTACAATATTCA
65 TTCATTCA-AAAA-AA-TATAATATTCA
* *
23745267 TACAACATTACAATATTCAT--AAAAAAATTATAATATTCATACAAAA
1 TACAAAATTACAATATTCATACAAAAAAATTACAATATTCATACAAAA
23745313 AATTTAAAAT
Statistics
Matches: 194, Mismatches: 14, Indels: 24
0.84 0.06 0.10
Matches are distributed among these distances:
81 2 0.01
82 19 0.10
83 32 0.16
84 17 0.09
87 11 0.06
88 1 0.01
89 79 0.41
90 33 0.17
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (89 bp):
TACAAAATTACAATATTCATACAAAAAAATTACAATATTCATACAAAACTATAATATTACAATAT
TCATTCAAAAAAATATAATATTCA
Found at i:23750916 original size:44 final size:43
Alignment explanation
Indices: 23750806--23751033 Score: 212
Period size: 43 Copynumber: 5.3 Consensus size: 43
23750796 TAAAAATGCT
* *
23750806 TTTAGTGGCGTTTTCT-ATAAAAGCGTCGCTAAAGGTCATGCTT-
1 TTTAGCGGCGTTTT-TGATAAAAGCGCCGCTAAAGGTCATG-TTC
* * *
23750849 TTTAGCTGCGTTTGTGATAAAAGCGCCGCTAAAGATCATGTTTC
1 TTTAGCGGCGTTTTTGATAAAAGCGCCGCTAAAGGTCATG-TTC
* * *
23750893 TTTAGCGGCGTTTTTGGGT-AAAGCGTCGCTAAAGGTCCTGTTC
1 TTTAGCGGCGTTTTT-GATAAAAGCGCCGCTAAAGGTCATGTTC
* * * *
23750936 TTTAGTGGCATTTTTAATAAAAGCGCTGCTAAAGGTC-TCGTTC
1 TTTAGCGGCGTTTTTGATAAAAGCGCCGCTAAAGGTCAT-GTTC
** * * * **
23750979 TTTAGCGGCGTTTTTTTTCAAAGCACCACTAAAGGTCATGACC
1 TTTAGCGGCGTTTTTGATAAAAGCGCCGCTAAAGGTCATGTTC
23751022 TTTAGCGGCGTT
1 TTTAGCGGCGTT
23751034 GTCAATAGCG
Statistics
Matches: 151, Mismatches: 28, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
42 3 0.02
43 114 0.75
44 32 0.21
45 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (43 bp):
TTTAGCGGCGTTTTTGATAAAAGCGCCGCTAAAGGTCATGTTC
Found at i:23750994 original size:87 final size:87
Alignment explanation
Indices: 23750825--23750993 Score: 229
Period size: 87 Copynumber: 2.0 Consensus size: 87
23750815 GTTTTCTATA
* *
23750825 AAAGCGTCGCTAAAGGTCATGCTTTTTAGCTGCGTTTGTGATAAAAGCGCCGCTAAAGATCATGT
1 AAAGCGTCGCTAAAGGTCATGCTTTTTAGCTGCATTTGTAATAAAAGCGCCGCTAAAGATCATGT
23750890 TTCTTTAGCGGCGTTTTTGGGT
66 TTCTTTAGCGGCGTTTTTGGGT
* * * *
23750912 AAAGCGTCGCTAAAGGTCCTG-TTCTTTAG-TGGCATTTTTAATAAAAGCGCTGCTAAAGGTC-T
1 AAAGCGTCGCTAAAGGTCATGCTT-TTTAGCT-GCATTTGTAATAAAAGCGCCGCTAAAGATCAT
23750974 CG-TTCTTTAGCGGCGTTTTT
64 -GTTTCTTTAGCGGCGTTTTT
23750994 TTTCAAAGCA
Statistics
Matches: 73, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
86 22 0.30
87 51 0.70
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.36
Consensus pattern (87 bp):
AAAGCGTCGCTAAAGGTCATGCTTTTTAGCTGCATTTGTAATAAAAGCGCCGCTAAAGATCATGT
TTCTTTAGCGGCGTTTTTGGGT
Found at i:23753741 original size:19 final size:19
Alignment explanation
Indices: 23753717--23753760 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
23753707 TTATTAAAAT
23753717 ATTATAACAAATT-TAGAAA
1 ATTATAA-AAATTATAGAAA
23753736 ATTATAAAAATTATAGAAA
1 ATTATAAAAATTATAGAAA
*
23753755 AATATA
1 ATTATA
23753761 TTTTATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (19 bp):
ATTATAAAAATTATAGAAA
Found at i:23763293 original size:18 final size:18
Alignment explanation
Indices: 23763257--23763295 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
23763247 TTATTATTGT
**
23763257 TAAAATTTTCTATTAAAA
1 TAAAATTTTAAATTAAAA
*
23763275 TAAAATTTTAAATTTAAA
1 TAAAATTTTAAATTAAAA
23763293 TAA
1 TAA
23763296 TTTATTATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAATTTTAAATTAAAA
Found at i:23764634 original size:23 final size:25
Alignment explanation
Indices: 23764604--23764657 Score: 85
Period size: 23 Copynumber: 2.2 Consensus size: 25
23764594 TTATACAGTT
*
23764604 AAAAATACTAGAT-ATATC-TATAA
1 AAAAATACTAGATAAAATCATATAA
23764627 AAAAATACTAGATAAAATCATATAA
1 AAAAATACTAGATAAAATCATATAA
23764652 AAAAAT
1 AAAAAT
23764658 TTGAGCTACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 13 0.46
24 4 0.14
25 11 0.39
ACGTcount: A:0.63, C:0.07, G:0.04, T:0.26
Consensus pattern (25 bp):
AAAAATACTAGATAAAATCATATAA
Found at i:23777415 original size:5 final size:5
Alignment explanation
Indices: 23777407--23777438 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
23777397 TGTAGTCTAC
23777407 TTTTA TTTTA TTTTA -TTTA -TTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
23777439 TTACATACGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 8 0.31
5 18 0.69
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:23778787 original size:4 final size:4
Alignment explanation
Indices: 23778778--23778802 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
23778768 TCACTTGGTG
23778778 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
23778803 ATGTCCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:23780210 original size:46 final size:47
Alignment explanation
Indices: 23780139--23780228 Score: 112
Period size: 46 Copynumber: 1.9 Consensus size: 47
23780129 GTCGAAATTA
* * *
23780139 AATTATATATTTTTATAATAGTAAAA-ATATAAATTTATTATTTTAAT
1 AATTATATATCTTTATAATAGTAAAAGAT-TAAATTAAATATTTTAAT
**
23780186 AATT-TATATCTTTATAATTTTAAAAGATTAAATTAAATATTTT
1 AATTATATATCTTTATAATAGTAAAAGATTAAATTAAATATTTT
23780229 GGTTTGAGTC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
46 31 0.84
47 6 0.16
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (47 bp):
AATTATATATCTTTATAATAGTAAAAGATTAAATTAAATATTTTAAT
Found at i:23789707 original size:50 final size:50
Alignment explanation
Indices: 23789651--23789751 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
23789641 TTTAATGAAC
23789651 TCAAAAAATATTTATTTATTTTATATTTTCGTACATGTCCAACATATCCT
1 TCAAAAAATATTTATTTATTTTATATTTTCGTACATGTCCAACATATCCT
23789701 TCAAAAAATATTTATTTATTTTATATTTTCGTACATGTCCAACATATCCT
1 TCAAAAAATATTTATTTATTTTATATTTTCGTACATGTCCAACATATCCT
23789751 T
1 T
23789752 ACTTTGATAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.34, C:0.16, G:0.04, T:0.47
Consensus pattern (50 bp):
TCAAAAAATATTTATTTATTTTATATTTTCGTACATGTCCAACATATCCT
Found at i:23789984 original size:21 final size:21
Alignment explanation
Indices: 23789951--23789992 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
23789941 AGCTATATAT
*
23789951 ATTAAATGAT-AAAAATTAAA
1 ATTAAATCATAAAAAATTAAA
23789971 ATTAATATCATAAAAAATTAAA
1 ATTAA-ATCATAAAAAATTAAA
23789993 TTATTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 4 0.21
22 10 0.53
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (21 bp):
ATTAAATCATAAAAAATTAAA
Found at i:23805942 original size:21 final size:21
Alignment explanation
Indices: 23805918--23805970 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
23805908 CATTGTTTCT
*
23805918 AATCTCACCGCTACAGTACCC
1 AATCTCACCGCTACAGTAACC
* *
23805939 AATCTCACTGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
23805960 AATCTCACCGC
1 AATCTCACCGC
23805971 CACCGCTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:23809302 original size:14 final size:14
Alignment explanation
Indices: 23809283--23809312 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
23809273 ATAAAGAAAT
23809283 TTGTAATTTAAGCA
1 TTGTAATTTAAGCA
23809297 TTGTAATTTAAGCA
1 TTGTAATTTAAGCA
23809311 TT
1 TT
23809313 CACATTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (14 bp):
TTGTAATTTAAGCA
Found at i:23809510 original size:21 final size:21
Alignment explanation
Indices: 23809442--23809512 Score: 60
Period size: 21 Copynumber: 3.5 Consensus size: 21
23809432 CAATTTAATC
* *
23809442 ATAATTTTAAAAAATTCAA-A
1 ATAAATTTAAAAAATACAATA
*
23809462 A-AAATAT-AAAAATAC-ATGA
1 ATAAATTTAAAAAATACAAT-A
**
23809481 ATATTTTTAAAAAATACAATA
1 ATAAATTTAAAAAATACAATA
23809502 ATAAATTTAAA
1 ATAAATTTAAA
23809513 TTTATATTAA
Statistics
Matches: 38, Mismatches: 8, Indels: 9
0.69 0.15 0.16
Matches are distributed among these distances:
17 1 0.03
18 7 0.18
19 6 0.16
20 4 0.11
21 18 0.47
22 2 0.05
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.32
Consensus pattern (21 bp):
ATAAATTTAAAAAATACAATA
Found at i:23810197 original size:3 final size:3
Alignment explanation
Indices: 23810184--23810214 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
23810174 TCAAATATAA
*
23810184 ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
23810215 CTCAAAACTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:23817301 original size:21 final size:20
Alignment explanation
Indices: 23817267--23817316 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
23817257 TAAAATAAGC
*
23817267 ATAAATTATTAAAATTATATT
1 ATAAA-TATTAAAACTATATT
*
23817288 ATAAATATTAAAAACTATGTT
1 ATAAATATT-AAAACTATATT
23817309 A-AAATATT
1 ATAAATATT
23817317 TTTAAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (20 bp):
ATAAATATTAAAACTATATT
Found at i:23817313 original size:20 final size:19
Alignment explanation
Indices: 23817268--23817316 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
23817258 AAAATAAGCA
* *
23817268 TAAATTATTAAAATTATAT
1 TAAAATATTAAAACTATAT
*
23817287 TATAAATATTAAAAACTATGT
1 TA-AAATATT-AAAACTATAT
23817308 TAAAATATT
1 TAAAATATT
23817317 TTTAAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 2 0.08
20 13 0.52
21 10 0.40
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
TAAAATATTAAAACTATAT
Found at i:23819043 original size:20 final size:20
Alignment explanation
Indices: 23819014--23819052 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
23819004 TTTTAAAATA
23819014 TTTTTAAAAT-ACTTTTTTAT
1 TTTTTAAAATGA-TTTTTTAT
*
23819034 TTTTTTAAATGATTTTTTA
1 TTTTTAAAATGATTTTTTA
23819053 GTGTTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (20 bp):
TTTTTAAAATGATTTTTTAT
Found at i:23822350 original size:17 final size:18
Alignment explanation
Indices: 23822319--23822363 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
23822309 GAAAATACTA
*
23822319 ATAAAAAGTATAATTTA-G
1 ATAAAAA-TAGAATTTAGG
23822337 ATAAAAATAGAATTTAGG
1 ATAAAAATAGAATTTAGG
*
23822355 AAAAAAATA
1 ATAAAAATA
23822364 AGAGACTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.27
Consensus pattern (18 bp):
ATAAAAATAGAATTTAGG
Found at i:23823508 original size:18 final size:17
Alignment explanation
Indices: 23823466--23823508 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
23823456 TTTTTAAGTT
*
23823466 TATAATATTTTATATTA
1 TATAATTTTTTATATTA
* *
23823483 TGTTATTTTTATATATTA
1 TATAATTTTT-TATATTA
23823501 TATAATTT
1 TATAATTT
23823509 AGAACACACT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATAATTTTTTATATTA
Found at i:23823608 original size:25 final size:24
Alignment explanation
Indices: 23823580--23823642 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 24
23823570 AATAATGTTA
*
23823580 AAATAACAATATAAAAAATTTCAAT
1 AAATAAAAATATAAAAAATTT-AAT
* *
23823605 AAATAAAAAAATAAAAAATTTATT
1 AAATAAAAATATAAAAAATTTAAT
**
23823629 AAATATTAATATAA
1 AAATAAAAATATAA
23823643 TATAATATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 13 0.41
25 19 0.59
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (24 bp):
AAATAAAAATATAAAAAATTTAAT
Found at i:23823631 original size:24 final size:25
Alignment explanation
Indices: 23823580--23823633 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
23823570 AATAATGTTA
* *
23823580 AAATAACAATATAAAAAATTTCAAT
1 AAATAAAAAAATAAAAAATTTCAAT
*
23823605 AAATAAAAAAATAAAAAATTT-ATT
1 AAATAAAAAAATAAAAAATTTCAAT
23823629 AAATA
1 AAATA
23823634 TTAATATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.28
Consensus pattern (25 bp):
AAATAAAAAAATAAAAAATTTCAAT
Found at i:23824604 original size:24 final size:24
Alignment explanation
Indices: 23824577--23824624 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
23824567 AAAGACAAGG
23824577 TAAAACATTAAAATAGTCATTTTT
1 TAAAACATTAAAATAGTCATTTTT
23824601 TAAAACATTAAAATAGTCATTTTT
1 TAAAACATTAAAATAGTCATTTTT
23824625 GTTTGTCTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (24 bp):
TAAAACATTAAAATAGTCATTTTT
Found at i:23827550 original size:35 final size:35
Alignment explanation
Indices: 23827506--23827593 Score: 95
Period size: 35 Copynumber: 2.5 Consensus size: 35
23827496 TTGAAAATAT
**
23827506 AGAAGTTTTTAAAACATGGGAATTTCTGAAAACACG
1 AGAA-TTTTTAAAACACCGGAATTTCTGAAAACACG
* * * *
23827542 AGAATTTTTTAAATACCGGAATTTTTGAAAACATG
1 AGAATTTTTAAAACACCGGAATTTCTGAAAACACG
*
23827577 AGGATTTTTGAAAACAC
1 AGAATTTTT-AAAACAC
23827594 GAAGATTTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
35 33 0.79
36 9 0.21
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.32
Consensus pattern (35 bp):
AGAATTTTTAAAACACCGGAATTTCTGAAAACACG
Found at i:23827584 original size:17 final size:18
Alignment explanation
Indices: 23827426--23827677 Score: 145
Period size: 18 Copynumber: 14.2 Consensus size: 18
23827416 TTTTTAAAAA
*
23827426 AAAACACGAAAAATTTTT-
1 AAAACACG-AGAATTTTTG
*
23827444 AAGAACACGAGAATTTTAG
1 AA-AACACGAGAATTTTTG
* * **
23827463 -AGACACGAAAATTCTTAAA
1 AAAACACGAGAATT-TT-TG
*
23827482 AAAACACGA-AAATTTTG
1 AAAACACGAGAATTTTTG
* *
23827499 AAAATA-TAGAAGTTTTT-
1 AAAACACGAGAA-TTTTTG
* * *
23827516 AAAACATGGGAATTTCTG
1 AAAACACGAGAATTTTTG
*
23827534 AAAACACGAGAATTTTTT
1 AAAACACGAGAATTTTTG
23827552 AAATAC-CG-GAATTTTTG
1 AAA-ACACGAGAATTTTTG
* *
23827569 AAAACATGAGGATTTTTG
1 AAAACACGAGAATTTTTG
23827587 AAAACACGA-AGATTTTTG
1 AAAACACGAGA-ATTTTTG
*
23827605 AAAGCACG-GAAATTTTTG
1 AAAACACGAG-AATTTTTG
*
23827623 AAAATACGA-AAGTTTTT-
1 AAAACACGAGAA-TTTTTG
*
23827640 AAAACATTG-GAA-TTTTG
1 AAAACA-CGAGAATTTTTG
*
23827657 AAAACACGAGGA-TTTTG
1 AAAACACGAGAATTTTTG
23827674 AAAA
1 AAAA
23827678 ATGGATTTTT
Statistics
Matches: 181, Mismatches: 32, Indels: 43
0.71 0.12 0.17
Matches are distributed among these distances:
16 8 0.04
17 62 0.34
18 91 0.50
19 13 0.07
20 7 0.04
ACGTcount: A:0.46, C:0.10, G:0.16, T:0.29
Consensus pattern (18 bp):
AAAACACGAGAATTTTTG
Found at i:23827594 original size:53 final size:54
Alignment explanation
Indices: 23827482--23827626 Score: 149
Period size: 53 Copynumber: 2.7 Consensus size: 54
23827472 AATTCTTAAA
* * ** *
23827482 AAAACACGAA-AATTTTGAAAATATAGAAGTTTTT-AAAACATGGGAATTTCTG
1 AAAACACGAAGATTTTTGAAAACACGGAAATTTTTGAAAACATGGGAATTTCTG
* *
23827534 AAAACACG-AGAATTTTTTAAATAC-CGG-AATTTTTGAAAACATGAGG-ATTTTTG
1 AAAACACGAAG-ATTTTTGAAA-ACACGGAAATTTTTGAAAACATG-GGAATTTCTG
*
23827587 AAAACACGAAGATTTTTGAAAGCACGGAAATTTTTGAAAA
1 AAAACACGAAGATTTTTGAAAACACGGAAATTTTTGAAAA
23827627 TACGAAAGTT
Statistics
Matches: 76, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
51 1 0.01
52 15 0.20
53 43 0.57
54 17 0.22
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.30
Consensus pattern (54 bp):
AAAACACGAAGATTTTTGAAAACACGGAAATTTTTGAAAACATGGGAATTTCTG
Found at i:23827620 original size:36 final size:36
Alignment explanation
Indices: 23827527--23827677 Score: 122
Period size: 35 Copynumber: 4.3 Consensus size: 36
23827517 AAACATGGGA
* * *
23827527 ATTTCTGAAAACA-CGAGAATTTTTTAAATAC-CGGA-
1 ATTTTTGAAAACATCG-GAATTTTTGAAA-ACACGAAG
*
23827562 ATTTTTGAAAACAT-GAGGATTTTTGAAAACACGAAG
1 ATTTTTGAAAACATCG-GAATTTTTGAAAACACGAAG
* *
23827598 ATTTTTGAAAGCA-CGGAAATTTTTGAAAATACGAA-
1 ATTTTTGAAAACATCGG-AATTTTTGAAAACACGAAG
* *
23827633 AGTTTTT-AAAACATTGGAA-TTTTGAAAACACGAGG
1 A-TTTTTGAAAACATCGGAATTTTTGAAAACACGAAG
23827668 A-TTTTGAAAA
1 ATTTTTGAAAA
23827678 ATGGATTTTT
Statistics
Matches: 96, Mismatches: 11, Indels: 19
0.76 0.09 0.15
Matches are distributed among these distances:
33 4 0.04
34 19 0.20
35 37 0.39
36 36 0.38
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.32
Consensus pattern (36 bp):
ATTTTTGAAAACATCGGAATTTTTGAAAACACGAAG
Found at i:23827777 original size:36 final size:35
Alignment explanation
Indices: 23827695--23827815 Score: 129
Period size: 36 Copynumber: 3.4 Consensus size: 35
23827685 TTTATTTTTT
* * *
23827695 ATTTTTT-AAAACACGAATATTTTTGAAATA-TGA
1 ATTTTTTGAAAACACGAAAATTTTTGAAACAGAGA
* * *
23827728 TTTTTTTAAAAAACAAGAAAATTTTTGAAACACGAGA
1 ATTTTTT-GAAAACACGAAAATTTTTGAAACA-GAGA
23827765 ATTTTTTGAAAACACGAAAATTTTTGAAACATGAGAA
1 ATTTTTTGAAAACACGAAAATTTTTGAAACA-GAG-A
23827802 ATTTTTTTGAAAAC
1 A-TTTTTTGAAAAC
23827816 TCGCTTTTTT
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
33 6 0.08
35 20 0.27
36 25 0.34
37 10 0.14
38 12 0.16
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (35 bp):
ATTTTTTGAAAACACGAAAATTTTTGAAACAGAGA
Found at i:23827790 original size:18 final size:18
Alignment explanation
Indices: 23827746--23827807 Score: 90
Period size: 18 Copynumber: 3.4 Consensus size: 18
23827736 AAAAACAAGA
23827746 AAATTTTTGAAACACGAG
1 AAATTTTTGAAACACGAG
*
23827764 AATTTTTTGAAAACACGA-
1 AAATTTTTG-AAACACGAG
*
23827782 AAATTTTTGAAACATGAG
1 AAATTTTTGAAACACGAG
23827800 AAATTTTT
1 AAATTTTT
23827808 TTGAAAACTC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
17 7 0.18
18 24 0.62
19 8 0.21
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (18 bp):
AAATTTTTGAAACACGAG
Found at i:23827842 original size:16 final size:17
Alignment explanation
Indices: 23827823--23827861 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
23827813 AACTCGCTTT
*
23827823 TTTTTTAAACTCGA-AA
1 TTTTTTAAACACGACAA
*
23827839 TTTTTGAAACACGACAA
1 TTTTTTAAACACGACAA
23827856 TTTTTT
1 TTTTTT
23827862 TAAAATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (17 bp):
TTTTTTAAACACGACAA
Found at i:23827842 original size:18 final size:19
Alignment explanation
Indices: 23827749--23827843 Score: 58
Period size: 17 Copynumber: 5.2 Consensus size: 19
23827739 AACAAGAAAA
*
23827749 TTTTTG-AAACACGAGAA-T
1 TTTTTGAAAACTCGA-AATT
* *
23827767 TTTTTGAAAACACGAAA-A
1 TTTTTGAAAACTCGAAATT
*
23827785 TTTTTG-AAACATGAGAAATT
1 TTTTTGAAAAC-T-CGAAATT
*
23827805 TTTTTGAAAACTCG--CTT
1 TTTTTGAAAACTCGAAATT
**
23827822 TTTTTTTAAACTCGAAATT
1 TTTTTGAAAACTCGAAATT
23827841 TTT
1 TTT
23827844 GAAACACGAC
Statistics
Matches: 61, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
17 18 0.30
18 14 0.23
19 18 0.30
20 7 0.11
21 4 0.07
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.42
Consensus pattern (19 bp):
TTTTTGAAAACTCGAAATT
Found at i:23827860 original size:18 final size:17
Alignment explanation
Indices: 23827738--23827861 Score: 88
Period size: 18 Copynumber: 6.9 Consensus size: 17
23827728 TTTTTTTAAA
* *
23827738 AAACAAGAAAATTTTTG
1 AAACACGAAATTTTTTG
23827755 AAACACGAGAATTTTTTG
1 AAACACGA-AATTTTTTG
*
23827773 AAAACACGAAAATTTTTG
1 -AAACACGAAATTTTTTG
*
23827791 AAACATGAGAAATTTTTTTG
1 AAACA--CGAAA-TTTTTTG
* *** *
23827811 AAAACTCGCTTTTTTTTT
1 -AAACACGAAATTTTTTG
*
23827829 AAACTCGAAA-TTTTTG
1 AAACACGAAATTTTTTG
23827845 AAACACGACAATTTTTT
1 AAACACGA-AATTTTTT
23827862 TAAAATTGTA
Statistics
Matches: 83, Mismatches: 16, Indels: 15
0.73 0.14 0.13
Matches are distributed among these distances:
16 12 0.14
17 21 0.25
18 27 0.33
19 13 0.16
20 6 0.07
21 4 0.05
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.37
Consensus pattern (17 bp):
AAACACGAAATTTTTTG
Found at i:23828337 original size:18 final size:17
Alignment explanation
Indices: 23828304--23828336 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
23828294 GCCTTTCCCT
23828304 TTTTTTCCTTCTTTTTC
1 TTTTTTCCTTCTTTTTC
23828321 TTTTTTCTCTT-TTTTT
1 TTTTTTC-CTTCTTTTT
23828337 TTGTTGGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTCCTTCTTTTTC
Found at i:23828525 original size:17 final size:18
Alignment explanation
Indices: 23828503--23828557 Score: 69
Period size: 17 Copynumber: 3.1 Consensus size: 18
23828493 TGGGCTTTGG
23828503 GCTGC-TTCTTTTTTTTT
1 GCTGCTTTCTTTTTTTTT
23828520 GCTGCTTTTCCTTTTTTTTT
1 GCTGC-TTT-CTTTTTTTTT
*
23828540 -CTGCTTTGTTTTTTTTT
1 GCTGCTTTCTTTTTTTTT
23828557 G
1 G
23828558 GGCTGCTTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
17 14 0.42
18 3 0.09
19 6 0.18
20 10 0.30
ACGTcount: A:0.00, C:0.16, G:0.13, T:0.71
Consensus pattern (18 bp):
GCTGCTTTCTTTTTTTTT
Found at i:23828553 original size:19 final size:19
Alignment explanation
Indices: 23828508--23828557 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
23828498 TTTGGGCTGC
23828508 TTCTTTTTTTTTGCTGCTT
1 TTCTTTTTTTTTGCTGCTT
23828527 TTCCTTTTTTTTT-CTGC-T
1 TT-CTTTTTTTTTGCTGCTT
*
23828545 TTGTTTTTTTTTG
1 TTCTTTTTTTTTG
23828558 GGCTGCTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 9 0.32
18 3 0.11
19 6 0.21
20 10 0.36
ACGTcount: A:0.00, C:0.14, G:0.10, T:0.76
Consensus pattern (19 bp):
TTCTTTTTTTTTGCTGCTT
Found at i:23828563 original size:20 final size:18
Alignment explanation
Indices: 23828511--23828567 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 18
23828501 GGGCTGCTTC
23828511 TTTTTTTTTGCTGCTTT-
1 TTTTTTTTTGCTGCTTTG
*
23828528 TCCTTTTTTTTTCTGCTTTG
1 T--TTTTTTTTGCTGCTTTG
23828548 TTTTTTTTTGGGCTGCTTTG
1 TTTTTTTTT--GCTGCTTTG
23828568 GGCTTGACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
17 1 0.03
18 8 0.24
19 15 0.45
20 9 0.27
ACGTcount: A:0.00, C:0.14, G:0.16, T:0.70
Consensus pattern (18 bp):
TTTTTTTTTGCTGCTTTG
Found at i:23828675 original size:4 final size:4
Alignment explanation
Indices: 23828668--23828708 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
23828658 TGTTTCCCTC
*
23828668 TTCT TTCT TTGT TTC- TTCT CTT-T TTCT TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTCT TT
23828709 TCCGATCAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
3 5 0.16
4 25 0.78
5 2 0.06
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:23828680 original size:19 final size:19
Alignment explanation
Indices: 23828650--23828702 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
23828640 CCGACTGTTA
*
23828650 TTTTTTTTTGTTTC-CCTC
1 TTTTTCTTTGTTTCTCCTC
*
23828668 TTCTTTCTTTGTTTCTTCTC
1 TT-TTTCTTTGTTTCTCCTC
*
23828688 TTTTTCTTTCTTTCT
1 TTTTTCTTTGTTTCT
23828703 TTCTTTTCCG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 2 0.07
19 23 0.77
20 5 0.17
ACGTcount: A:0.00, C:0.23, G:0.04, T:0.74
Consensus pattern (19 bp):
TTTTTCTTTGTTTCTCCTC
Found at i:23829222 original size:30 final size:30
Alignment explanation
Indices: 23829187--23829295 Score: 98
Period size: 30 Copynumber: 3.6 Consensus size: 30
23829177 TAAATGTAGC
*
23829187 AAAAGTTTTGGGGCAAAAGTGTAATTTTGA
1 AAAAGTTTAGGGGCAAAAGTGTAATTTTGA
****
23829217 AAAAGTTTAGAGATTGAAA-TGTAATTTTGA
1 AAAAGTTTAG-GGGCAAAAGTGTAATTTTGA
*
23829247 GAAAGTTTAGGGGTCAAAAG-GTAATTTT-A
1 AAAAGTTTAGGGG-CAAAAGTGTAATTTTGA
*
23829276 GAAAAGATTAGGGGTCAAAA
1 -AAAAGTTTAGGGG-CAAAA
23829296 AAATTAAAAA
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
29 2 0.03
30 57 0.90
31 4 0.06
ACGTcount: A:0.41, C:0.03, G:0.26, T:0.30
Consensus pattern (30 bp):
AAAAGTTTAGGGGCAAAAGTGTAATTTTGA
Found at i:23833942 original size:17 final size:19
Alignment explanation
Indices: 23833922--23833966 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
23833912 TTTGTTAACA
23833922 ATATTTTT-ATT-TTTATT
1 ATATTTTTAATTATTTATT
23833939 ATATTTTTAAATTATTTATT
1 ATATTTTT-AATTATTTATT
23833959 ATATTTTT
1 ATATTTTT
23833967 TAAAAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.32
19 3 0.12
20 14 0.56
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
ATATTTTTAATTATTTATT
Found at i:23833977 original size:23 final size:21
Alignment explanation
Indices: 23833933--23833988 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
23833923 TATTTTTATT
*
23833933 TTTATTATA-TTTTTAAATTA
1 TTTATTATATTTTTTAAAATA
23833953 TTTATTATATTTTTTAAAAAATA
1 TTTATTATATTTTTT--AAAATA
*
23833976 TTTA-TGTATTTTT
1 TTTATTATATTTTT
23833989 ATATGTTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.29
21 5 0.16
22 8 0.26
23 9 0.29
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTATTATATTTTTTAAAATA
Found at i:23835164 original size:14 final size:12
Alignment explanation
Indices: 23835133--23835157 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23835123 ATTACAATTA
23835133 AAAATATTTTTT
1 AAAATATTTTTT
23835145 AAAATATTTTTT
1 AAAATATTTTTT
23835157 A
1 A
23835158 TACAATAAAT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AAAATATTTTTT
Found at i:23837095 original size:29 final size:28
Alignment explanation
Indices: 23837036--23837097 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
23837026 CGATTTCACG
*
23837036 AAAAATGACCCATTCCGGTAAATAATCA
1 AAAAATGACCCATTCCGGTAAATAATAA
* * **
23837064 AAAAATCGGCCCATTTCGGTAAATTTTAA
1 AAAAAT-GACCCATTCCGGTAAATAATAA
23837093 AAAAA
1 AAAAA
23837098 AACGGCTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.24
Consensus pattern (28 bp):
AAAAATGACCCATTCCGGTAAATAATAA
Found at i:23840078 original size:253 final size:253
Alignment explanation
Indices: 23839630--23840133 Score: 981
Period size: 253 Copynumber: 2.0 Consensus size: 253
23839620 CTTTCGAACC
23839630 TGAAAATGGTGAGAGAGACATAAAAGGAGGGGTCTCTCCCTATCTCACAAGTGGGGAGAACAATG
1 TGAAAATGGTGAGAGAGACATAAAAGGAGGGGTCTCTCCCTATCTCACAAGTGGGGAGAACAATG
*
23839695 AAGTTAAAAGCATTTGGGAAGATATTATTATTAAATGAATTCATTCAGTTTATTAAAAATGTAAT
66 AAGTTAAAAGCATTTGGGAAGATATTATTATTAAATGAATTCATTCAGTTTATTAAAAACGTAAT
*
23839760 GACCCAAAATTCACGGGTATCGAAAAAGTGTAATATCGGGCCTCCGTCTTAATAAACCAAGTTTG
131 GACCCAAAATTCACGGGCATCGAAAAAGTGTAATATCGGGCCTCCGTCTTAATAAACCAAGTTTG
23839825 TAAATAATTATTAAAAATATTTATGAGTCTAGTAGTGTGTTTAATTAGATTTTAATCT
196 TAAATAATTATTAAAAATATTTATGAGTCTAGTAGTGTGTTTAATTAGATTTTAATCT
*
23839883 TGAAAATGGTGAGAGAGACATAAAAGGTGGGGTCTCTCCCTATCTCACAAGTGGGGAGAACAATG
1 TGAAAATGGTGAGAGAGACATAAAAGGAGGGGTCTCTCCCTATCTCACAAGTGGGGAGAACAATG
23839948 AAGTTAAAAGCATTTGGGAAGATATTATTATTAAATGAATTCATTCAGTTTATTAAAAACGTAAT
66 AAGTTAAAAGCATTTGGGAAGATATTATTATTAAATGAATTCATTCAGTTTATTAAAAACGTAAT
23840013 GACCCAAAATTCACGGGCATCGAAAAAGTGTAATATCGGGCCTCCGTCTTAATAAACCAAGTTTG
131 GACCCAAAATTCACGGGCATCGAAAAAGTGTAATATCGGGCCTCCGTCTTAATAAACCAAGTTTG
23840078 TAAATAATTATTAAAAATATTTATGAGTCTAGTAGTGTGTTTAATTAGATTTTAAT
196 TAAATAATTATTAAAAATATTTATGAGTCTAGTAGTGTGTTTAATTAGATTTTAAT
23840134 TAAGTGAATT
Statistics
Matches: 248, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
253 248 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (253 bp):
TGAAAATGGTGAGAGAGACATAAAAGGAGGGGTCTCTCCCTATCTCACAAGTGGGGAGAACAATG
AAGTTAAAAGCATTTGGGAAGATATTATTATTAAATGAATTCATTCAGTTTATTAAAAACGTAAT
GACCCAAAATTCACGGGCATCGAAAAAGTGTAATATCGGGCCTCCGTCTTAATAAACCAAGTTTG
TAAATAATTATTAAAAATATTTATGAGTCTAGTAGTGTGTTTAATTAGATTTTAATCT
Found at i:23840344 original size:2 final size:2
Alignment explanation
Indices: 23840337--23840364 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
23840327 AATTAATGAA
23840337 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23840365 TAAAGCCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23840478 original size:30 final size:28
Alignment explanation
Indices: 23840439--23840500 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
23840429 ATGGATTTAA
* *
23840439 ATTACTTATTATTTAAGTACATATATATTT
1 ATTACTTATTA-TTAAGTA-AAAGATATTT
*
23840469 ATTATTTATTATTAAGTAAAAGATATTT
1 ATTACTTATTATTAAGTAAAAGATATTT
23840497 ATTA
1 ATTA
23840501 ATTAAATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 12 0.41
29 7 0.24
30 10 0.34
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (28 bp):
ATTACTTATTATTAAGTAAAAGATATTT
Found at i:23842989 original size:18 final size:17
Alignment explanation
Indices: 23842940--23842989 Score: 59
Period size: 16 Copynumber: 3.0 Consensus size: 17
23842930 AAATATTGAA
*
23842940 AAATATTTAT-TTTTAT
1 AAATATTTATATTTTTT
*
23842956 AAAT-TTTATACTTTTT
1 AAATATTTATATTTTTT
23842972 AAATAATTTATATTTTTT
1 AAAT-ATTTATATTTTTT
23842990 TTGAATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 5 0.18
16 12 0.43
18 11 0.39
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
AAATATTTATATTTTTT
Found at i:23847975 original size:13 final size:13
Alignment explanation
Indices: 23847954--23848005 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
23847944 GCTAAAACTC
*
23847954 TTTTAATAATGTT
1 TTTTAATAATATT
*
23847967 TTTTTATAATA-T
1 TTTTAATAATATT
23847979 TTTTAAT-ATATTT
1 TTTTAATAATA-TT
23847992 TTTTATATAATATT
1 TTTTA-ATAATATT
23848006 AGAGGCAAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 3 0.09
12 7 0.22
13 15 0.47
14 4 0.12
15 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (13 bp):
TTTTAATAATATT
Found at i:23848001 original size:26 final size:25
Alignment explanation
Indices: 23847954--23848005 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 25
23847944 GCTAAAACTC
23847954 TTTTAATAATGTTTTTTTATAATAT
1 TTTTAATAATGTTTTTTTATAATAT
23847979 TTTTAATATAT-TTTTTTATATAATAT
1 TTTTAATA-ATGTTTTTT-TATAATAT
23848005 T
1 T
23848006 AGAGGCAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (25 bp):
TTTTAATAATGTTTTTTTATAATAT
Found at i:23849570 original size:18 final size:18
Alignment explanation
Indices: 23849549--23849583 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
23849539 ACCCAAGTAT
23849549 CCAACCCAACCTAATTAC
1 CCAACCCAACCTAATTAC
*
23849567 CCAACTCAACCTAATTA
1 CCAACCCAACCTAATTA
23849584 AAAAAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (18 bp):
CCAACCCAACCTAATTAC
Found at i:23850111 original size:17 final size:18
Alignment explanation
Indices: 23850079--23850112 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23850069 AGGTGTCAAC
*
23850079 TATTTTTTAATTTTTATG
1 TATTTTTTAATATTTATG
23850097 TATTTTTT-ATATTTAT
1 TATTTTTTAATATTTAT
23850113 ATTTAATGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (18 bp):
TATTTTTTAATATTTATG
Found at i:23850522 original size:33 final size:31
Alignment explanation
Indices: 23850485--23850555 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 31
23850475 AAAATACTTT
* * *
23850485 ATTTTATTTGTATTATTTTTATACTTTTAAATA
1 ATTTTAATGGTATTAATTTTAT-CTTTTAAA-A
* *
23850518 ATTTTAATGGTTTTAATTTTATTTTTTAAAA
1 ATTTTAATGGTATTAATTTTATCTTTTAAAA
23850549 ATTTTAA
1 ATTTTAA
23850556 AAAAATTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
31 8 0.24
32 7 0.21
33 18 0.55
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.62
Consensus pattern (31 bp):
ATTTTAATGGTATTAATTTTATCTTTTAAAA
Found at i:23852206 original size:21 final size:22
Alignment explanation
Indices: 23852166--23852208 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
23852156 AATTTACTAT
* *
23852166 AATTTTTAAAAAATATTATTAA
1 AATTTTCAAAAAATAGTATTAA
23852188 AATTTTCAAAAAA-AGTATTAA
1 AATTTTCAAAAAATAGTATTAA
23852209 TTGTCGATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
AATTTTCAAAAAATAGTATTAA
Found at i:23852451 original size:19 final size:21
Alignment explanation
Indices: 23852415--23852467 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
23852405 TTTTCTTTTT
*
23852415 TCTTTTTATTGTTAAAATATTA-
1 TCTTTTT-TT-TTGAAATATTAG
*
23852437 T-TTTTTTTTTGAAATTTTAG
1 TCTTTTTTTTTGAAATATTAG
23852457 TCTTTTTTTTT
1 TCTTTTTTTTT
23852468 ATTTTTGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 9 0.33
20 3 0.11
21 14 0.52
22 1 0.04
ACGTcount: A:0.21, C:0.04, G:0.06, T:0.70
Consensus pattern (21 bp):
TCTTTTTTTTTGAAATATTAG
Found at i:23854324 original size:25 final size:24
Alignment explanation
Indices: 23854287--23854343 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 24
23854277 TTTAAAAAAA
* *
23854287 TTAAAAATCTATATTTTTATACTTTTT
1 TTAAAAA-CTATA-CTTTATA-TATTT
23854314 TTAAAAA-TATACTTTATATATTT
1 TTAAAAACTATACTTTATATATTT
23854337 TTAAAAA
1 TTAAAAA
23854344 ATAATTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 11 0.39
24 6 0.21
25 4 0.14
27 7 0.25
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (24 bp):
TTAAAAACTATACTTTATATATTT
Found at i:23854865 original size:22 final size:22
Alignment explanation
Indices: 23854840--23854921 Score: 62
Period size: 22 Copynumber: 3.8 Consensus size: 22
23854830 GGGTCGAAAT
23854840 TAAATTATAATTTTTATAATAA
1 TAAATTATAATTTTTATAATAA
* *
23854862 TAAAATATAATTTCATTATTAT-A
1 TAAATTATAATTT--TTATAATAA
** * *
23854885 T-TTTTATAATTTTTAAAATAT
1 TAAATTATAATTTTTATAATAA
*
23854906 TAAATCA-AATTTTTAT
1 TAAATTATAATTTTTAT
23854922 GCTTTTAGTC
Statistics
Matches: 44, Mismatches: 12, Indels: 9
0.68 0.18 0.14
Matches are distributed among these distances:
20 5 0.11
21 9 0.20
22 22 0.50
23 2 0.05
24 6 0.14
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TAAATTATAATTTTTATAATAA
Found at i:23869446 original size:21 final size:20
Alignment explanation
Indices: 23869406--23869446 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
23869396 GGTATGAAAA
* *
23869406 TTTGTGAGAATTTGGGTTTT
1 TTTGTGAGAATTTAGATTTT
23869426 TTTGTGGAGAATTTAGATTTT
1 TTTGT-GAGAATTTAGATTTT
23869447 ACAAGGGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.54
Consensus pattern (20 bp):
TTTGTGAGAATTTAGATTTT
Found at i:23882968 original size:15 final size:14
Alignment explanation
Indices: 23882930--23882979 Score: 57
Period size: 15 Copynumber: 3.5 Consensus size: 14
23882920 TTAAAGTCAA
*
23882930 GATA-AAAGAGGGG
1 GATATAAAGAGGGT
*
23882943 GATAAAAAGAGGGT
1 GATATAAAGAGGGT
23882957 GATGATAAAGAGGAGT
1 GAT-ATAAAGAGG-GT
23882973 GATATAA
1 GATATAA
23882980 GGAAATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 4 0.12
14 11 0.34
15 12 0.38
16 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.36, T:0.16
Consensus pattern (14 bp):
GATATAAAGAGGGT
Found at i:23884306 original size:59 final size:59
Alignment explanation
Indices: 23884243--23884393 Score: 212
Period size: 59 Copynumber: 2.6 Consensus size: 59
23884233 GAACCAAAAA
*
23884243 GCTAAGTTTAGATACTTAATTGGACAAAAAAAAGTTCAAGGATCAAATTGAACCTTGAC
1 GCTAAGTTTAGATACCTAATTGGACAAAAAAAAGTTCAAGGATCAAATTGAACCTTGAC
* * * * * *
23884302 GCTAAGTTTAGATACCCAATCGGATAAAAAAAAGTTTAAGTATCAAATTGAACCTTGAG
1 GCTAAGTTTAGATACCTAATTGGACAAAAAAAAGTTCAAGGATCAAATTGAACCTTGAC
* **
23884361 GCCAAGTTTAGGCACCTAATTGGACAAAAAAAA
1 GCTAAGTTTAGATACCTAATTGGACAAAAAAAA
23884394 AACACATTAG
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 79 1.00
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (59 bp):
GCTAAGTTTAGATACCTAATTGGACAAAAAAAAGTTCAAGGATCAAATTGAACCTTGAC
Found at i:23884845 original size:20 final size:20
Alignment explanation
Indices: 23884798--23884846 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
23884788 TAAACTAATT
*
23884798 TTTAATTAATACTTATATAA
1 TTTAATAAATACTTATATAA
*
23884818 TTAAAATAAATA-TTATATAAA
1 TT-TAATAAATACTTATAT-AA
23884839 TTTAATAA
1 TTTAATAA
23884847 TCGGACATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTAATAAATACTTATATAA
Found at i:23885350 original size:23 final size:26
Alignment explanation
Indices: 23885323--23885386 Score: 89
Period size: 24 Copynumber: 2.5 Consensus size: 26
23885313 TTTATAAATA
23885323 AATTTATTTAAAATTAATG-TTT-TT
1 AATTTATTTAAAATTAATGTTTTGTT
*
23885347 ATTTTATTT-AAATTAATGTTTTGTT
1 AATTTATTTAAAATTAATGTTTTGTT
23885372 AATTTATTTATAAAT
1 AATTTATTTA-AAAT
23885387 AATAAATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 9 0.26
24 11 0.32
25 10 0.29
27 4 0.12
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (26 bp):
AATTTATTTAAAATTAATGTTTTGTT
Found at i:23886616 original size:12 final size:12
Alignment explanation
Indices: 23886601--23886697 Score: 57
Period size: 12 Copynumber: 8.2 Consensus size: 12
23886591 TAACCTATAA
23886601 ATATAGAAAATT
1 ATATAGAAAATT
23886613 ATAT-G-AAA--
1 ATATAGAAAATT
*
23886621 GTATA-AAAATT
1 ATATAGAAAATT
*
23886632 ATATAAAATAATT
1 ATATAGAA-AATT
*
23886645 AAAATGATGAAAATT
1 -ATAT-A-GAAAATT
23886660 ATAATA-AAAATT
1 AT-ATAGAAAATT
23886672 ATA-AGAAAA-T
1 ATATAGAAAATT
23886682 ATATAAGAAAATT
1 ATAT-AGAAAATT
23886695 ATA
1 ATA
23886698 GAAAAGTTTG
Statistics
Matches: 66, Mismatches: 5, Indels: 27
0.67 0.05 0.28
Matches are distributed among these distances:
8 3 0.05
9 3 0.05
10 8 0.12
11 10 0.15
12 20 0.30
13 8 0.12
14 5 0.08
15 7 0.11
16 2 0.03
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (12 bp):
ATATAGAAAATT
Found at i:23886639 original size:10 final size:10
Alignment explanation
Indices: 23886602--23886702 Score: 66
Period size: 10 Copynumber: 9.9 Consensus size: 10
23886592 AACCTATAAA
23886602 TATAGAAAAT
1 TATAGAAAAT
*
23886612 TATATG-AAAG
1 TATA-GAAAAT
23886622 TATA-AAAAT
1 TATAGAAAAT
*
23886631 TATATAAAAT
1 TATAGAAAAT
* *
23886641 AAT-TAAAAT
1 TATAGAAAAT
*
23886650 GAT-GAAAAT
1 TATAGAAAAT
*
23886659 TATAATAAAAAT
1 TAT-A-GAAAAT
23886671 TATAAGAAAAT
1 TAT-AGAAAAT
23886682 ATATAAGAAAAT
1 -TAT-AGAAAAT
23886694 TATAGAAAA
1 TATAGAAAA
23886703 GTTTGTTATT
Statistics
Matches: 76, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
9 22 0.29
10 24 0.32
11 9 0.12
12 21 0.28
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.30
Consensus pattern (10 bp):
TATAGAAAAT
Found at i:23886649 original size:19 final size:19
Alignment explanation
Indices: 23886599--23886641 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
23886589 ATTAACCTAT
23886599 AAATATAGAAAATTATATGA
1 AAATATA-AAAATTATATGA
*
23886619 AAGTATAAAAATTATAT-A
1 AAATATAAAAATTATATGA
23886637 AAATA
1 AAATA
23886642 ATTAAAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 10 0.48
20 6 0.29
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (19 bp):
AAATATAAAAATTATATGA
Found at i:23886692 original size:23 final size:22
Alignment explanation
Indices: 23886623--23886702 Score: 71
Period size: 23 Copynumber: 3.8 Consensus size: 22
23886613 ATATGAAAGT
*
23886623 ATAAAAATTATA-TAAA--ATA
1 ATAAAAATTATAGAAAATTATA
* *
23886642 ATTAAAATGAT-GAAAATTATA
1 ATAAAAATTATAGAAAATTATA
23886663 ATAAAAATTATAAGAAAATATATA
1 ATAAAAATTAT-AGAAAAT-TATA
*
23886687 A-GAAAATTATAGAAAA
1 ATAAAAATTATAGAAAA
23886703 GTTTGTTATT
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
19 12 0.24
21 12 0.24
22 6 0.12
23 14 0.29
24 5 0.10
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (22 bp):
ATAAAAATTATAGAAAATTATA
Found at i:23887001 original size:17 final size:17
Alignment explanation
Indices: 23886979--23887013 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
23886969 ATTAGAAATT
*
23886979 ATTAAAATATTACAAAA
1 ATTAAAAAATTACAAAA
*
23886996 ATTAAAAAATTATAAAA
1 ATTAAAAAATTACAAAA
23887013 A
1 A
23887014 ACTTATATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
ATTAAAAAATTACAAAA
Found at i:23887293 original size:28 final size:28
Alignment explanation
Indices: 23887261--23887314 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
23887251 CTAATTGCTA
*
23887261 ACTTTT-GATTAAGAGTTCAATTGATTGT
1 ACTTTTCGATTAAGA-CTCAATTGATTGT
*
23887289 ACTTTTCGATTAGGACTCAATTGATT
1 ACTTTTCGATTAAGACTCAATTGATT
23887315 TTTTTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.44
Consensus pattern (28 bp):
ACTTTTCGATTAAGACTCAATTGATTGT
Found at i:23887673 original size:14 final size:14
Alignment explanation
Indices: 23887650--23887683 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
23887640 TTTTTAGTGT
23887650 TAAA-ATAAATAAA
1 TAAATATAAATAAA
23887663 TAAATATAAATAAA
1 TAAATATAAATAAA
23887677 TATAATA
1 TA-AATA
23887684 ATTTTACTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.21
14 11 0.58
15 4 0.21
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
TAAATATAAATAAA
Found at i:23887817 original size:25 final size:23
Alignment explanation
Indices: 23887787--23887833 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
23887777 CCACGTTAAC
23887787 ATATATGAAATAATCATATATATAT
1 ATATATG-AATAATCATAT-TATAT
*
23887812 ATATATGAATAATCTTATTATA
1 ATATATGAATAATCATATTATA
23887834 AAATTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.19
24 10 0.48
25 7 0.33
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (23 bp):
ATATATGAATAATCATATTATAT
Found at i:23891931 original size:6 final size:6
Alignment explanation
Indices: 23891920--23891948 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
23891910 CTTTGGTTAC
23891920 TGGAAG TGGAAG TGGAAG TGGAAG TGGAA
1 TGGAAG TGGAAG TGGAAG TGGAAG TGGAA
23891949 TCAACCATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.48, T:0.17
Consensus pattern (6 bp):
TGGAAG
Found at i:23899939 original size:21 final size:21
Alignment explanation
Indices: 23899913--23899954 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
23899903 GGAGTGGTTG
23899913 ATTTTCTATTTTTAAAAGTAA
1 ATTTTCTATTTTTAAAAGTAA
23899934 ATTTTCTATTTTTAAAAGTAA
1 ATTTTCTATTTTTAAAAGTAA
23899955 CTTCTTGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (21 bp):
ATTTTCTATTTTTAAAAGTAA
Found at i:23905560 original size:126 final size:126
Alignment explanation
Indices: 23905326--23905704 Score: 670
Period size: 126 Copynumber: 3.0 Consensus size: 126
23905316 GATAAAATCA
* *
23905326 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACATGGATGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
*
23905391 AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGAAAATAGTATAAAAAAACGCTTC
66 AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAAAAACGCTTC
* * *
23905452 AGGTAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACACGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
*
23905517 AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAAAAATGCTTC
66 AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAAAAACGCTTC
23905578 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* *
23905643 TGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTAT-AAAAAACGCTTC
66 AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAAAAACGCTTC
23905703 AA
1 AA
23905705 TCGACTAGCT
Statistics
Matches: 240, Mismatches: 13, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
125 13 0.05
126 227 0.95
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28
Consensus pattern (126 bp):
AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAAAAACGCTTC
Found at i:23907770 original size:24 final size:23
Alignment explanation
Indices: 23907743--23907788 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
23907733 TATGTTTTTT
* *
23907743 TTTTTATTACTTTGTTCACGTTTA
1 TTTTGATTA-TTTATTCACGTTTA
23907767 TTTTGATTATTTATTCACGTTT
1 TTTTGATTATTTATTCACGTTT
23907789 TCATTATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.17, C:0.11, G:0.09, T:0.63
Consensus pattern (23 bp):
TTTTGATTATTTATTCACGTTTA
Found at i:23913335 original size:40 final size:38
Alignment explanation
Indices: 23913280--23913416 Score: 114
Period size: 40 Copynumber: 3.5 Consensus size: 38
23913270 GCGTTTAGAT
* *
23913280 AAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTCTG
1 AAAAAACGCCACTAAAAAT-GAGCATTAGCGGCGCTT-TG
* *
23913320 AAAAAACGCCACTAAAGATTGAGCATTAGTGGCGTACTTTG
1 AAAAAACGCCACTAAA-AATGAGCATTAGCGGCG--CTTTG
* ** * *
23913361 -GAAAACGCTGCTAAAAATGAGCATTAGCGGCGTTTTTC
1 AAAAAACGCCACTAAAAATGAGCATTAGCGGCG-CTTTG
* *
23913399 AAAAAGCGCCACAAAAAA
1 AAAAAACGCCACTAAAAA
23913417 CCTAAGCACA
Statistics
Matches: 76, Mismatches: 17, Indels: 9
0.75 0.17 0.09
Matches are distributed among these distances:
38 3 0.04
39 27 0.36
40 39 0.51
41 4 0.05
42 3 0.04
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (38 bp):
AAAAAACGCCACTAAAAATGAGCATTAGCGGCGCTTTG
Found at i:23913393 original size:39 final size:40
Alignment explanation
Indices: 23913280--23913393 Score: 126
Period size: 40 Copynumber: 2.9 Consensus size: 40
23913270 GCGTTTAGAT
*
23913280 AAAAAACGCCGCTAAAAATCAAGCATTAGCGGCG-CTTCTG
1 AAAAAACGCCGCTAAAAAT-GAGCATTAGCGGCGTCTTCTG
* * *
23913320 AAAAAACGCCACTAAAGATTGAGCATTAGTGGCGTACTT-TG
1 AAAAAACGCCGCTAAA-AATGAGCATTAGCGGCGT-CTTCTG
* *
23913361 -GAAAACGCTGCTAAAAATGAGCATTAGCGGCGT
1 AAAAAACGCCGCTAAAAATGAGCATTAGCGGCGT
23913394 TTTTCAAAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
39 16 0.26
40 39 0.63
41 4 0.06
42 3 0.05
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.20
Consensus pattern (40 bp):
AAAAAACGCCGCTAAAAATGAGCATTAGCGGCGTCTTCTG
Found at i:23913506 original size:41 final size:41
Alignment explanation
Indices: 23913449--23913563 Score: 142
Period size: 40 Copynumber: 2.8 Consensus size: 41
23913439 TCTGAGTTTT
* **
23913449 TGGGGCTTTAGTGGCGTTTTTTAAAAAGCGTTGCTAATGCA
1 TGGGGCTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCA
* *
23913490 TGGGGCTTTAGCGGCG-TTTTTGAAAAGCGCCGCTAATGCT
1 TGGGGCTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCA
* * **
23913530 TAGGGTTTTAGCGGCGTTTTCCAAAAAGCGCCGC
1 TGGGGCTTTAGCGGCGTTTTTTAAAAAGCGCCGC
23913564 AAAAAACCTA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
40 34 0.54
41 29 0.46
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.31
Consensus pattern (41 bp):
TGGGGCTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCA
Found at i:23913668 original size:153 final size:153
Alignment explanation
Indices: 23913384--23913675 Score: 469
Period size: 153 Copynumber: 1.9 Consensus size: 153
23913374 AAAATGAGCA
* * *
23913384 TTAGCGGCGTTTTTCAAAAAGCGCCACAAAAAACCTAAGCACAACGACGTCGTTTTCTGAGTTTT
1 TTAGCGGCGTTTTCCAAAAAGCGCCACAAAAAACCTAAGCACAACGACGCCATTTTCTGAGTTTT
* * *
23913449 TGGGGCTTTAGTGGCGTTTTTTAAAAAGCGTTGCTAATGCATGGGGCTTTAGCGGCGTTTTTGAA
66 AGGGGCTTTAGTGGCGTTTTTTAAAAAGCGTCGCTAAAGCATGGGGCTTTAGCGGCGTTTTTGAA
23913514 AAGCGCCGCTAATGCTTAGGGTT
131 AAGCGCCGCTAATGCTTAGGGTT
* * * *
23913537 TTAGCGGCGTTTTCCAAAAAGCGCCGCAAAAAACCTAAGCCCAACTACGCCATTTTTTGAGTTTT
1 TTAGCGGCGTTTTCCAAAAAGCGCCACAAAAAACCTAAGCACAACGACGCCATTTTCTGAGTTTT
*
23913602 AGGGGCTTTAGTGGCGTTTTTTAAAAAGCGTCGCTAAAGCAT-GGGCTTTTGCGGCGTTTTTGGA
66 AGGGGCTTTAGTGGCGTTTTTTAAAAAGCGTCGCTAAAGCATGGGGCTTTAGCGGCGTTTTT-GA
23913666 AAAGCGCCGC
130 AAAGCGCCGC
23913676 AAAAAATATT
Statistics
Matches: 127, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
152 18 0.14
153 109 0.86
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (153 bp):
TTAGCGGCGTTTTCCAAAAAGCGCCACAAAAAACCTAAGCACAACGACGCCATTTTCTGAGTTTT
AGGGGCTTTAGTGGCGTTTTTTAAAAAGCGTCGCTAAAGCATGGGGCTTTAGCGGCGTTTTTGAA
AAGCGCCGCTAATGCTTAGGGTT
Found at i:23913716 original size:16 final size:16
Alignment explanation
Indices: 23913697--23913743 Score: 76
Period size: 16 Copynumber: 2.8 Consensus size: 16
23913687 TATCTATTTA
23913697 TTATTATTTAATTGGT
1 TTATTATTTAATTGGT
23913713 TTATTATTTAATTGGT
1 TTATTATTTAATTGGT
23913729 TTATTTATATTAATT
1 TTA-TTAT-TTAATT
23913744 AAAATTCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
16 19 0.66
17 4 0.14
18 6 0.21
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.64
Consensus pattern (16 bp):
TTATTATTTAATTGGT
Found at i:23914001 original size:14 final size:14
Alignment explanation
Indices: 23913982--23914016 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
23913972 ACTATTTTAA
23913982 GGTTTATAGATTAT
1 GGTTTATAGATTAT
*
23913996 GGTTTATAGTTTAT
1 GGTTTATAGATTAT
23914010 GCGTTTA
1 G-GTTTA
23914017 AGGCTTAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.23, C:0.03, G:0.23, T:0.51
Consensus pattern (14 bp):
GGTTTATAGATTAT
Found at i:23914063 original size:21 final size:21
Alignment explanation
Indices: 23913977--23914065 Score: 63
Period size: 21 Copynumber: 4.2 Consensus size: 21
23913967 GAGTTACTAT
*
23913977 TTTAAGGTTTATAGATTATGG
1 TTTAAGGTTTATAGATTAAGG
* *
23913998 TTTATA-GTTTATGCGTTTAAGG
1 TTTA-AGGTTTAT-AGATTAAGG
* * ** * *
23914020 CTTAAGGGTTACGGTTTATGG
1 TTTAAGGTTTATAGATTAAGG
*
23914041 TTTAAGATTTATAGATTAAGG
1 TTTAAGGTTTATAGATTAAGG
23914062 TTTA
1 TTTA
23914066 GGGGTTAAGG
Statistics
Matches: 50, Mismatches: 15, Indels: 6
0.70 0.21 0.08
Matches are distributed among these distances:
21 36 0.72
22 14 0.28
ACGTcount: A:0.27, C:0.03, G:0.24, T:0.46
Consensus pattern (21 bp):
TTTAAGGTTTATAGATTAAGG
Found at i:23914073 original size:14 final size:14
Alignment explanation
Indices: 23914014--23914127 Score: 61
Period size: 14 Copynumber: 8.1 Consensus size: 14
23914004 GTTTATGCGT
*
23914014 TTAAGGCTTAAGGG
1 TTAAGGTTTAAGGG
* * *
23914028 TTACGGTTTATGGT
1 TTAAGGTTTAAGGG
* *
23914042 TTAAGATTTATA-GA
1 TTAAGGTTTA-AGGG
*
23914056 TTAAGGTTTAGGGG
1 TTAAGGTTTAAGGG
*
23914070 TTAAGGGTT-AGGAG
1 TTAAGGTTTAAGG-G
* * *
23914084 TTGAGGGTTAAGAG
1 TTAAGGTTTAAGGG
* * *
23914098 TTAAGGGTTATGGT
1 TTAAGGTTTAAGGG
*
23914112 TTATGGTTTAAGGG
1 TTAAGGTTTAAGGG
23914126 TT
1 TT
23914128 GGGTGATACG
Statistics
Matches: 73, Mismatches: 23, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
13 2 0.03
14 69 0.95
15 2 0.03
ACGTcount: A:0.25, C:0.02, G:0.34, T:0.39
Consensus pattern (14 bp):
TTAAGGTTTAAGGG
Found at i:23914079 original size:7 final size:7
Alignment explanation
Indices: 23914056--23914127 Score: 56
Period size: 7 Copynumber: 10.3 Consensus size: 7
23914046 GATTTATAGA
*
23914056 TTAAGGT
1 TTAAGGG
*
23914063 TTAGGGG
1 TTAAGGG
23914070 TTAAGGG
1 TTAAGGG
23914077 TT-AGGAG
1 TTAAGG-G
*
23914084 TTGAGGG
1 TTAAGGG
*
23914091 TTAAGAG
1 TTAAGGG
23914098 TTAAGGG
1 TTAAGGG
* *
23914105 TTATGGT
1 TTAAGGG
* *
23914112 TTATGGT
1 TTAAGGG
23914119 TTAAGGG
1 TTAAGGG
23914126 TT
1 TT
23914128 GGGTGATACG
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
6 3 0.06
7 47 0.89
8 3 0.06
ACGTcount: A:0.24, C:0.00, G:0.39, T:0.38
Consensus pattern (7 bp):
TTAAGGG
Found at i:23919312 original size:73 final size:75
Alignment explanation
Indices: 23919230--23919373 Score: 256
Period size: 74 Copynumber: 1.9 Consensus size: 75
23919220 TATAATATAA
* *
23919230 TATTTGATTAAAAT-ATTTTTTTTAAAGGTTATGTTTTTAGTGGCG-TTTTTGTGAGAAGCGCCG
1 TATTTGATTAAAATAATTTTTTTTAAAGGTTATGTTTTTAGCGGCGTTTTTTGCGAGAAGCGCCG
23919293 CTAAAGATAT
66 CTAAAGATAT
23919303 TATTTGATTAAAATAATTTTTTTTAAAGGTTATGTTTTTAGCGGCGTTTTTTGCGAGAAGCGCCG
1 TATTTGATTAAAATAATTTTTTTTAAAGGTTATGTTTTTAGCGGCGTTTTTTGCGAGAAGCGCCG
23919368 CTAAAG
66 CTAAAG
23919374 GTTTGTTCTT
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
73 14 0.21
74 30 0.45
75 23 0.34
ACGTcount: A:0.27, C:0.08, G:0.21, T:0.44
Consensus pattern (75 bp):
TATTTGATTAAAATAATTTTTTTTAAAGGTTATGTTTTTAGCGGCGTTTTTTGCGAGAAGCGCCG
CTAAAGATAT
Found at i:23919387 original size:43 final size:44
Alignment explanation
Indices: 23919339--23919587 Score: 253
Period size: 43 Copynumber: 5.8 Consensus size: 44
23919329 AGGTTATGTT
* *
23919339 TTTAGCGGCGTTTTTTGCGAGAAGCGCCGCTAAAGGT-TTGTTC
1 TTTAGCGGCGTTTTTTGCGAAAAGCGCCGCTAAAGGTCTTGATC
* * *
23919382 TTTAGCGGCGTTTTTTGCGAGAAGCGCCGCTAAAGATCATGATC
1 TTTAGCGGCGTTTTTTGCGAAAAGCGCCGCTAAAGGTCTTGATC
* * * * *
23919426 TTTAGCGGCGTTTGTGGC-AAAAGCGCCGTTAAAGGTCGTGGTC
1 TTTAGCGGCGTTTTTTGCGAAAAGCGCCGCTAAAGGTCTTGATC
* * * *
23919469 TATAGCGGCG-TTTGT-CGAAAAGCGCCGCTAAAGGTCGTGGTC
1 TTTAGCGGCGTTTTTTGCGAAAAGCGCCGCTAAAGGTCTTGATC
* * *
23919511 TTTAGCGGCGTTTGTCG-GAAAAGCACCGCTAAAGGT-TGTGATC
1 TTTAGCGGCGTTTTTTGCGAAAAGCGCCGCTAAAGGTCT-TGATC
* *
23919554 TTTAGCGGCATTTTTT-CTAGAAA-CGCCGCTAAAG
1 TTTAGCGGCGTTTTTTGCGA-AAAGCGCCGCTAAAG
23919588 TTAGCGATGC
Statistics
Matches: 172, Mismatches: 27, Indels: 14
0.81 0.13 0.07
Matches are distributed among these distances:
41 1 0.01
42 35 0.20
43 113 0.66
44 23 0.13
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (44 bp):
TTTAGCGGCGTTTTTTGCGAAAAGCGCCGCTAAAGGTCTTGATC
Found at i:23919518 original size:85 final size:86
Alignment explanation
Indices: 23919339--23919567 Score: 266
Period size: 85 Copynumber: 2.7 Consensus size: 86
23919329 AGGTTATGTT
* * * * * * *
23919339 TTTAGCGGCGTTTTTTGCGAGAAGCGCCGCTAAAGGTTTGTTCTTTAGCGGCGTTTTTTGCGAGA
1 TTTAGCGGCGTTTGTGGC-AAAAGCGCCGCTAAAGGTGTGATCTTTAGCGGCGTTTTGTGCGAAA
23919404 AGCGCCGCTAAAGATCATGATC
65 AGCGCCGCTAAAGATCATGATC
* * *
23919426 TTTAGCGGCGTTTGTGGCAAAAGCGCCGTTAAAGGTCGTGGTCTATAGCGGCG-TTTGT-CGAAA
1 TTTAGCGGCGTTTGTGGCAAAAGCGCCGCTAAAGGT-GTGATCTTTAGCGGCGTTTTGTGCGAAA
* * *
23919489 AGCGCCGCTAAAGGTCGTGGTC
65 AGCGCCGCTAAAGATCATGATC
* *
23919511 TTTAGCGGCGTTTGTCGG-AAAAGCACCGCTAAAGGTTGTGATCTTTAGCGGCATTTT
1 TTTAGCGGCGTTTGT-GGCAAAAGCGCCGCTAAAGG-TGTGATCTTTAGCGGCGTTTT
23919568 TTCTAGAAAC
Statistics
Matches: 121, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
85 66 0.55
86 26 0.21
87 29 0.24
ACGTcount: A:0.20, C:0.19, G:0.31, T:0.30
Consensus pattern (86 bp):
TTTAGCGGCGTTTGTGGCAAAAGCGCCGCTAAAGGTGTGATCTTTAGCGGCGTTTTGTGCGAAAA
GCGCCGCTAAAGATCATGATC
Found at i:23921927 original size:24 final size:25
Alignment explanation
Indices: 23921874--23921929 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
23921864 TTTCAACTCT
* *
23921874 TATGAGCTTCCTGTTATTCAGCTCA
1 TATGAGCTTACTGTTATACAGCTCA
*
23921899 CATGAGCTTACTGTT-TACAGCTCA
1 TATGAGCTTACTGTTATACAGCTCA
23921923 TATGAGC
1 TATGAGC
23921930 ATACATGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 14 0.52
25 13 0.48
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (25 bp):
TATGAGCTTACTGTTATACAGCTCA
Found at i:23923876 original size:23 final size:23
Alignment explanation
Indices: 23923850--23923900 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
23923840 GAAAGGTATG
23923850 TGTAATATCCC-GAAAATTACTAC
1 TGTAATA-CCCTGAAAATTACTAC
23923873 TGTAATACCCTGAAAATTACTAC
1 TGTAATACCCTGAAAATTACTAC
*
23923896 AGTAA
1 TGTAA
23923901 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 3 0.12
23 23 0.88
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (23 bp):
TGTAATACCCTGAAAATTACTAC
Found at i:23930059 original size:17 final size:14
Alignment explanation
Indices: 23930022--23930080 Score: 55
Period size: 17 Copynumber: 3.7 Consensus size: 14
23930012 TGTGATGAAT
23930022 TTATTGAATTTATA
1 TTATTGAATTTATA
23930036 TTGATTGAATTGGTATA
1 TT-ATTGAATT--TATA
23930053 TATATTGAATTTATTGA
1 T-TATTGAATTTA-T-A
23930070 TTATTTGAATT
1 TTA-TTGAATT
23930081 GAAATGAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
14 2 0.05
15 10 0.26
16 3 0.08
17 22 0.58
18 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (14 bp):
TTATTGAATTTATA
Found at i:23934658 original size:18 final size:18
Alignment explanation
Indices: 23934625--23934659 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23934615 TTTATTTTTG
* *
23934625 CGAAAGCTACGTCTATTA
1 CGAAAGCTAAGACTATTA
23934643 CGAAAGCTAAGACTATT
1 CGAAAGCTAAGACTATT
23934660 CAATCTGGCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (18 bp):
CGAAAGCTAAGACTATTA
Found at i:23935852 original size:18 final size:18
Alignment explanation
Indices: 23935811--23935850 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
23935801 TTTTCTGTCC
* *
23935811 AAAATTAATCTATTTTCT
1 AAAATTAACCTATTTCCT
23935829 AAAATTAACCTATTTCCCT
1 AAAATTAACCTATTT-CCT
23935848 AAA
1 AAA
23935851 TTTAGAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATTAACCTATTTCCT
Found at i:23938633 original size:6 final size:7
Alignment explanation
Indices: 23938621--23938647 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
23938611 GAAAAAAAAA
23938621 TATTTTT
1 TATTTTT
23938628 TATTTTT
1 TATTTTT
23938635 TATTTTT
1 TATTTTT
23938642 TATTTT
1 TATTTT
23938648 AGGGTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TATTTTT
Found at i:23948077 original size:15 final size:16
Alignment explanation
Indices: 23948052--23948081 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
23948042 TAGTTTGAGA
23948052 AAAATTAATAAAAACT
1 AAAATTAATAAAAACT
23948068 AAAA-TAATAAAAAC
1 AAAATTAATAAAAAC
23948082 CGAGACATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (16 bp):
AAAATTAATAAAAACT
Done.