Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 89
Found at i:4420934 original size:41 final size:41
Alignment explanation
Indices: 4420876--4420953 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
4420866 TTGCAGAAGA
*
4420876 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
*
4420917 GTCGCAACGAGAGAAATGACAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
4420954 CGCAACGCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.44, C:0.18, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:4420950 original size:21 final size:21
Alignment explanation
Indices: 4420877--4420952 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
4420867 TGCAGAAGAG
* *
4420877 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGACAA
**
4420898 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGACAA
4420918 TCGCAACGAGAGAAATGACAA
1 TCGCAACGAGAGAAATGACAA
4420939 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
4420953 TCGCAACGCG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.35
21 31 0.65
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGACAA
Found at i:4420956 original size:14 final size:14
Alignment explanation
Indices: 4420937--4420992 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
4420927 GAGAAATGAC
4420937 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
4420951 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
4420970 AATCGC-ACGAGAG
1 AATCGCAACGAGAG
4420983 AATCGCAACG
1 AATCGCAACG
4420993 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
13 8 0.24
14 12 0.35
16 4 0.12
18 2 0.06
19 8 0.24
ACGTcount: A:0.43, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:4420985 original size:32 final size:32
Alignment explanation
Indices: 4420929--4421008 Score: 124
Period size: 32 Copynumber: 2.5 Consensus size: 32
4420919 CGCAACGAGA
*
4420929 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGC-ACGAGAGAATCGCAACGC
4420962 GAAATGAAAATCGCACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCACGAGAGAATCGCAACGC
**
4420994 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
4421009 TTGCGATTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
32 31 0.70
33 13 0.30
ACGTcount: A:0.45, C:0.24, G:0.23, T:0.09
Consensus pattern (32 bp):
GAAATGAAAATCGCACGAGAGAATCGCAACGC
Found at i:4421043 original size:14 final size:14
Alignment explanation
Indices: 4421024--4421113 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
4421014 ATTCATTTCG
4421024 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
4421038 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
4421057 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
4421071 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
4421090 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
4421104 CGTTGCGATT
1 CGTTGCGATT
4421114 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
16 6 0.10
17 6 0.10
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:4421055 original size:33 final size:33
Alignment explanation
Indices: 4421015--4421121 Score: 214
Period size: 33 Copynumber: 3.2 Consensus size: 33
4421005 CGCATTGCGA
4421015 TTCATTTCGCGTTGCGATTCTCTCGTTGCGATT
1 TTCATTTCGCGTTGCGATTCTCTCGTTGCGATT
4421048 TTCATTTCGCGTTGCGATTCTCTCGTTGCGATT
1 TTCATTTCGCGTTGCGATTCTCTCGTTGCGATT
4421081 TTCATTTCGCGTTGCGATTCTCTCGTTGCGATT
1 TTCATTTCGCGTTGCGATTCTCTCGTTGCGATT
4421114 TTCATTTC
1 TTCATTTC
4421122 AACCAAAAGA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 74 1.00
ACGTcount: A:0.09, C:0.24, G:0.20, T:0.47
Consensus pattern (33 bp):
TTCATTTCGCGTTGCGATTCTCTCGTTGCGATT
Found at i:4421062 original size:19 final size:19
Alignment explanation
Indices: 4421015--4421099 Score: 82
Period size: 19 Copynumber: 5.0 Consensus size: 19
4421005 CGCATTGCGA
4421015 TTCATTTCGCGTTGCGA--
1 TTCATTTCGCGTTGCGATT
*
4421032 TTC---TCTCGTTGCGATT
1 TTCATTTCGCGTTGCGATT
4421048 TTCATTTCGCGTTGCGA--
1 TTCATTTCGCGTTGCGATT
*
4421065 TTC---TCTCGTTGCGATT
1 TTCATTTCGCGTTGCGATT
4421081 TTCATTTCGCGTTGCGATT
1 TTCATTTCGCGTTGCGATT
4421100 CTCTCGTTGC
Statistics
Matches: 54, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
14 20 0.37
16 6 0.11
17 6 0.11
19 22 0.41
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.46
Consensus pattern (19 bp):
TTCATTTCGCGTTGCGATT
Found at i:4423036 original size:93 final size:93
Alignment explanation
Indices: 4422807--4423365 Score: 1063
Period size: 93 Copynumber: 6.1 Consensus size: 93
4422797 TAGATTGCTT
* *
4422807 AGTAAATTTATTCGGTTGCTGCCAATTCTACTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4422872 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
4422899 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4422964 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
4422992 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4423057 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
4423085 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGAA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4423150 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
4423178 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4423243 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
4423270 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4423335 -TTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
4423361 AGTAA
1 AGTAA
4423366 TGCAATCCAT
Statistics
Matches: 462, Mismatches: 4, Indels: 3
0.99 0.01 0.01
Matches are distributed among these distances:
91 6 0.01
92 197 0.43
93 259 0.56
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:4423038 original size:185 final size:186
Alignment explanation
Indices: 4422807--4423365 Score: 1063
Period size: 185 Copynumber: 3.0 Consensus size: 186
4422797 TAGATTGCTT
* *
4422807 AGTAAATTTATTCGGTTGCTGCCAATTCTACTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4422872 TTTGTCTTTGTTTTGTC-TTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
4422936 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
4422992 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4423057 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
*
4423122 GTGTATTCTTTAACACTGTGAAATAGAATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
4423178 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4423243 -TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
4423307 GTGTATTCTTTAACACTGTGAAATAGTA-TTGTCTTTGTTTTGTCTTTTGGTTG-A
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
4423361 AGTAA
1 AGTAA
4423366 TGCAATCCAT
Statistics
Matches: 369, Mismatches: 4, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
183 6 0.02
184 25 0.07
185 171 0.46
186 167 0.45
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:4423452 original size:19 final size:19
Alignment explanation
Indices: 4423412--4423540 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
4423402 TAGTTTACTT
* *
4423412 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
*
4423432 TCGCAACGTGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
4423451 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
4423470 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
4423484 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
4423503 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
4423517 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
4423536 TCGCA
1 TCGCA
4423541 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 19 0.22
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 45 0.51
20 12 0.14
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:4423491 original size:33 final size:32
Alignment explanation
Indices: 4423448--4423540 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
4423438 CGTGAAACCA
**
4423448 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
4423480 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
4423513 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
4423541 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:4423538 original size:52 final size:52
Alignment explanation
Indices: 4423412--4423540 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 52
4423402 TAGTTTACTT
** *
4423412 TCGCAACACGAAACTTAAAATCGCAACGTGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
4423464 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
4423517 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
4423541 TTGCGATTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 41 0.67
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:4423558 original size:19 final size:19
Alignment explanation
Indices: 4423536--4423653 Score: 121
Period size: 19 Copynumber: 6.7 Consensus size: 19
4423526 GAAACCAAAA
*
4423536 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
4423555 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
4423571 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
4423588 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
4423604 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
4423621 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
4423640 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
4423654 AAGTTTCGTG
Statistics
Matches: 82, Mismatches: 7, Indels: 20
0.75 0.06 0.18
Matches are distributed among these distances:
14 15 0.18
16 11 0.13
17 11 0.13
19 45 0.55
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:4423577 original size:14 final size:14
Alignment explanation
Indices: 4423558--4423614 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
4423548 TTTCATTTCG
4423558 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
4423572 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
4423589 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
4423605 CGTTGCGATT
1 CGTTGCGATT
4423615 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:4423583 original size:33 final size:33
Alignment explanation
Indices: 4423541--4423633 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
4423531 CAAAATCGCA
*
4423541 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
4423574 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
4423607 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
4423634 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:4423659 original size:19 final size:19
Alignment explanation
Indices: 4423605--4423669 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
4423595 GCGATTCTGT
*
4423605 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGA-TTTAAGTTTCG
**
4423624 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTAAGTTTCG
4423643 CGTTGCGATTTAAGTTTCG
1 CGTTGCGATTTAAGTTTCG
*
4423662 TGTTGCGA
1 CGTTGCGA
4423670 AAGTAAACTA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
18 3 0.08
19 37 0.93
ACGTcount: A:0.11, C:0.17, G:0.28, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTAAGTTTCG
Found at i:4425488 original size:12 final size:12
Alignment explanation
Indices: 4425473--4425508 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
4425463 TGATTCAATA
4425473 GTTTAATTGATT
1 GTTTAATTGATT
**
4425485 GTTTTTTTGATT
1 GTTTAATTGATT
4425497 GTTTAATTGATT
1 GTTTAATTGATT
4425509 TGTAAAAGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.17, T:0.64
Consensus pattern (12 bp):
GTTTAATTGATT
Found at i:4425594 original size:14 final size:14
Alignment explanation
Indices: 4425575--4425613 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
4425565 ATTGTTTAAT
4425575 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
4425589 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
4425603 TGATTGTGTAA
1 TGATT-TGTAA
4425614 TTGATGCGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.36, C:0.00, G:0.23, T:0.41
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:4425729 original size:19 final size:19
Alignment explanation
Indices: 4425713--4425819 Score: 152
Period size: 19 Copynumber: 5.8 Consensus size: 19
4425703 AAAAATGACT
4425713 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
4425732 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4425751 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
4425765 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
4425784 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
4425804 ATCGCAATGCGGAAAT
1 ATCGCAATGC-GAAAT
4425820 CGCAATGCGT
Statistics
Matches: 80, Mismatches: 2, Indels: 11
0.86 0.02 0.12
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.49
20 25 0.31
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:4425791 original size:52 final size:52
Alignment explanation
Indices: 4425713--4425828 Score: 191
Period size: 52 Copynumber: 2.2 Consensus size: 52
4425703 AAAAATGACT
4425713 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAA-CGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAAGCG-GA-A
4425765 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCGGAA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAA-GCGGAA
4425818 ATCGCAATGCG
1 ATCGCAATGCG
4425829 TTTATATTTC
Statistics
Matches: 61, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
52 29 0.48
53 28 0.46
54 2 0.03
55 2 0.03
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.15
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAAGCGGAA
Found at i:4425821 original size:14 final size:14
Alignment explanation
Indices: 4425802--4425828 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4425792 GCGGAAATGA
4425802 AAATCGCAATGCGG
1 AAATCGCAATGCGG
4425816 AAATCGCAATGCG
1 AAATCGCAATGCG
4425829 TTTATATTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (14 bp):
AAATCGCAATGCGG
Found at i:4425879 original size:19 final size:19
Alignment explanation
Indices: 4425855--4426067 Score: 238
Period size: 19 Copynumber: 12.4 Consensus size: 19
4425845 CGATTCTCTC
4425855 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4425874 TTGCGA-TTTCA-TTCGCA
1 TTGCGATTTTCATTTCGCA
*
4425891 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
4425905 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4425924 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
4425943 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
4425957 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4425976 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
4425995 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
4426009 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4426028 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
4426042 TTG-GATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4426060 TTGCGATT
1 TTGCGATT
4426068 CTCTCGTTGC
Statistics
Matches: 166, Mismatches: 6, Indels: 44
0.77 0.03 0.20
Matches are distributed among these distances:
13 8 0.05
14 21 0.13
15 1 0.01
16 25 0.15
17 31 0.19
18 8 0.05
19 72 0.43
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:4425926 original size:33 final size:33
Alignment explanation
Indices: 4425874--4426081 Score: 223
Period size: 33 Copynumber: 6.2 Consensus size: 33
4425864 TCATTTCGCA
4425874 TTGCGA-TTTCA-TTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
4425905 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
4425941 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
4425976 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
4426009 TTGCGATTTTCATTTCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTTCGCATTGCGATTCTC-TCG
4426042 TTG-GATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
4426074 TTGCGATT
1 TTGCGATT
4426082 GTAATTTCCG
Statistics
Matches: 147, Mismatches: 14, Indels: 30
0.77 0.07 0.16
Matches are distributed among these distances:
31 16 0.11
32 39 0.27
33 60 0.41
34 1 0.01
35 5 0.03
36 4 0.03
37 2 0.01
38 8 0.05
39 3 0.02
40 9 0.06
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:4425963 original size:52 final size:52
Alignment explanation
Indices: 4425834--4426040 Score: 393
Period size: 52 Copynumber: 4.0 Consensus size: 52
4425824 ATGCGTTTAT
4425834 ATTTCGCATTGCGATTCTCTC-TTGCGATTTTCATTTCGCATTGCGA-TTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
4425884 A-TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
4425935 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
4425987 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
4426039 AT
1 AT
4426041 GTTGGATTTT
Statistics
Matches: 154, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
49 19 0.12
50 26 0.17
51 5 0.03
52 104 0.68
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:4428272 original size:12 final size:12
Alignment explanation
Indices: 4428257--4428281 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4428247 TTCTTCGGGA
4428257 CTTTTTCTTCTT
1 CTTTTTCTTCTT
4428269 CTTTTTCTTCTT
1 CTTTTTCTTCTT
4428281 C
1 C
4428282 AGGATTATGA
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:4429185 original size:20 final size:20
Alignment explanation
Indices: 4429157--4429246 Score: 121
Period size: 20 Copynumber: 4.6 Consensus size: 20
4429147 AAATTTCAGT
* * *
4429157 GTTGTGATTTACATATTCTC
1 GTTGCGATTTACAGATTATC
*
4429177 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTATC
4429197 GTTGCGATTTACAGA-T-TC
1 GTTGCGATTTACAGATTATC
*
4429215 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTATC
4429235 GTTGCGATTTAC
1 GTTGCGATTTAC
4429247 GGATACGCGT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
18 16 0.26
19 2 0.03
20 44 0.71
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.42
Consensus pattern (20 bp):
GTTGCGATTTACAGATTATC
Found at i:4429220 original size:38 final size:39
Alignment explanation
Indices: 4429157--4429341 Score: 168
Period size: 40 Copynumber: 4.8 Consensus size: 39
4429147 AAATTTCAGT
* *
4429157 GTTGTGATTTACATATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGA-TCTCGTTGCGATTTACGGATTATC
4429197 GTTGCGATTTACAGAT-TCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATCTCGTTGCGATTTACGGATTATC
* * *
4429235 GTTGCGATTTACGGATACGCGTTGCGATATACGGA-TA-C
1 GTTGCGATTTACAGAT-CTCGTTGCGATTTACGGATTATC
** * *
4429273 GCATTGCGATTTACCCATACGCGTTGCGA-TTACGGA-TACAC
1 G--TTGCGATTTACAGAT-CTCGTTGCGATTTACGGATTA-TC
* *
4429314 G-TGCGATTTACGGA-CGCGTTGCGATTTA
1 GTTGCGATTTACAGATCTCGTTGCGATTTA
4429342 TGTGTTCGCG
Statistics
Matches: 128, Mismatches: 10, Indels: 17
0.83 0.06 0.11
Matches are distributed among these distances:
36 10 0.08
37 3 0.02
38 50 0.39
39 11 0.09
40 52 0.41
41 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.35
Consensus pattern (39 bp):
GTTGCGATTTACAGATCTCGTTGCGATTTACGGATTATC
Found at i:4429238 original size:58 final size:58
Alignment explanation
Indices: 4429157--4429341 Score: 180
Period size: 58 Copynumber: 3.2 Consensus size: 58
4429147 AAATTTCAGT
* * * * * *
4429157 GTTGTGATTTACATATTCTCGTTGCGATTTACGGATTA-TCGTTGCGATTTACAGATTC
1 GTTGCGATTTACACATTATCGTTGCGATTTACGGA-TACACGTTGCGATTTACGGATAC
** * *
4429215 GTTGCGATTTACGGATTATCGTTGCGATTTACGGATACGCGTTGCGATATACGGATAC
1 GTTGCGATTTACACATTATCGTTGCGATTTACGGATACACGTTGCGATTTACGGATAC
* * **
4429273 GCATTGCGATTTACCCA-TACGCGTTGCGA-TTACGGATACACG-TGCGATTTACGGACGC
1 G--TTGCGATTTACACATTA-TCGTTGCGATTTACGGATACACGTTGCGATTTACGGATAC
4429331 GTTGCGATTTA
1 GTTGCGATTTA
4429342 TGTGTTCGCG
Statistics
Matches: 108, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
56 10 0.09
57 2 0.02
58 62 0.57
59 14 0.13
60 20 0.19
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.35
Consensus pattern (58 bp):
GTTGCGATTTACACATTATCGTTGCGATTTACGGATACACGTTGCGATTTACGGATAC
Found at i:4429271 original size:20 final size:20
Alignment explanation
Indices: 4429176--4429341 Score: 177
Period size: 20 Copynumber: 8.6 Consensus size: 20
4429166 TACATATTCT
*
4429176 CGTTGCGATTTACGGATTA-T
1 CGTTGCGATTTACGGA-TACG
* *
4429196 CGTTGCGATTTACAGAT--T
1 CGTTGCGATTTACGGATACG
*
4429214 CGTTGCGATTTACGGATTA-T
1 CGTTGCGATTTACGGA-TACG
4429234 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
*
4429254 CGTTGCGATATACGGATACG
1 CGTTGCGATTTACGGATACG
* **
4429274 CATTGCGATTTACCCATACG
1 CGTTGCGATTTACGGATACG
*
4429294 CGTTGCGA-TTACGGATACA
1 CGTTGCGATTTACGGATACG
4429313 CG-TGCGATTTACGG--ACG
1 CGTTGCGATTTACGGATACG
4429330 CGTTGCGATTTA
1 CGTTGCGATTTA
4429342 TGTGTTCGCG
Statistics
Matches: 128, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.03
18 30 0.23
19 20 0.16
20 74 0.58
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.33
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACG
Found at i:4429353 original size:20 final size:20
Alignment explanation
Indices: 4429328--4429380 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
4429318 GATTTACGGA
* *
4429328 CGCGTTGCGATTTAT-GTGTT
1 CGCGTTGCGATTT-TCATATT
4429348 CGCGTTGC-ATTTTCATATT
1 CGCGTTGCGATTTTCATATT
4429367 CGCGTTGCGATTTT
1 CGCGTTGCGATTTT
4429381 GGAAAATCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 1 0.03
19 15 0.52
20 13 0.45
ACGTcount: A:0.11, C:0.19, G:0.25, T:0.45
Consensus pattern (20 bp):
CGCGTTGCGATTTTCATATT
Found at i:4429396 original size:21 final size:21
Alignment explanation
Indices: 4429366--4429448 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
4429356 ATTTTCATAT
*
4429366 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
4429387 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
4429408 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
4429429 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
4429449 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:4432068 original size:17 final size:17
Alignment explanation
Indices: 4432028--4432068 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
4432018 TAGGCGGAGC
*
4432028 ATTATCAGATATTAGAT
1 ATTATCGGATATTAGAT
4432045 ATTATCGGATATTAGAT
1 ATTATCGGATATTAGAT
4432062 ATTATCG
1 ATTATCG
4432069 AATCTGAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (17 bp):
ATTATCGGATATTAGAT
Found at i:4432097 original size:17 final size:17
Alignment explanation
Indices: 4432075--4432109 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
4432065 ATCGAATCTG
*
4432075 AATTTTTAGATATTTAA
1 AATTTTTAGATATCTAA
4432092 AATTTTTAGATATCTAA
1 AATTTTTAGATATCTAA
4432109 A
1 A
4432110 GTAATGGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (17 bp):
AATTTTTAGATATCTAA
Found at i:4433860 original size:14 final size:14
Alignment explanation
Indices: 4433841--4433868 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4433831 AAGCAACTCT
4433841 CCTTTTTCTAAGAC
1 CCTTTTTCTAAGAC
4433855 CCTTTTTCTAAGAC
1 CCTTTTTCTAAGAC
4433869 AAAGATCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.29, G:0.07, T:0.43
Consensus pattern (14 bp):
CCTTTTTCTAAGAC
Found at i:4434316 original size:9 final size:8
Alignment explanation
Indices: 4434298--4434329 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
4434288 AGAGAAAGAG
4434298 AAAGAAAA
1 AAAGAAAA
4434306 AAAGAAAA
1 AAAGAAAA
4434314 AAAGAAAAA
1 AAAG-AAAA
4434323 AAAGAAA
1 AAAGAAA
4434330 GAAACTTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAGAAAA
Found at i:4434319 original size:16 final size:17
Alignment explanation
Indices: 4434298--4434329 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4434288 AGAGAAAGAG
4434298 AAAG-AAAAAAAGAAAA
1 AAAGAAAAAAAAGAAAA
4434314 AAAGAAAAAAAAGAAA
1 AAAGAAAAAAAAGAAA
4434330 GAAACTTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAAAAGAAAA
Found at i:4434594 original size:35 final size:35
Alignment explanation
Indices: 4434548--4434622 Score: 116
Period size: 35 Copynumber: 2.1 Consensus size: 35
4434538 AATTGAAAAA
4434548 CGGATTGGATATCCGAATTTTCAGATCGG-ATCAGT
1 CGGATTGGATATCCGAATTTTCAGATCGGAAT-AGT
* *
4434583 CGGATTGGATATCTGAATTTTCGGATCGGAATAGT
1 CGGATTGGATATCCGAATTTTCAGATCGGAATAGT
4434618 CGGAT
1 CGGAT
4434623 CAGATTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 35 0.95
36 2 0.05
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (35 bp):
CGGATTGGATATCCGAATTTTCAGATCGGAATAGT
Found at i:4435755 original size:5 final size:5
Alignment explanation
Indices: 4435735--4435886 Score: 60
Period size: 5 Copynumber: 29.2 Consensus size: 5
4435725 TAAAGTAGCT
*
4435735 AAATA ATAAT- AAATA AAATA AAATAAA AAATA AAAGTAA AAATA AATTAA
1 AAATA A-AATA AAATA AAATA AAAT--A AAATA AAA-T-A AAATA AAAT-A
* * * * * *
4435785 AAAGA AAAGTA ATAAAA GAAATA AAGTA AAATA GAATG AGATGA AAATA
1 AAATA AAA-TA A-AATA -AAATA AAATA AAATA AAATA AAAT-A AAATA
* * * * * * *
4435834 AAA-A TAA-A AAATG AAATC AAAGA AAACA AAAGA AAATA AAATT AAA-A
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA
4435881 AAATA A
1 AAATA A
4435887 TATATATATA
Statistics
Matches: 109, Mismatches: 25, Indels: 26
0.68 0.16 0.16
Matches are distributed among these distances:
4 12 0.11
5 68 0.62
6 17 0.16
7 12 0.11
ACGTcount: A:0.74, C:0.01, G:0.08, T:0.17
Consensus pattern (5 bp):
AAATA
Found at i:4435764 original size:12 final size:12
Alignment explanation
Indices: 4435735--4435787 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 12
4435725 TAAAGTAGCT
4435735 AAATAATAATAAATA
1 AAATAA-AAT-AA-A
4435750 AAATAAAATAAA
1 AAATAAAATAAA
4435762 AAATAAAAGT-AA
1 AAATAAAA-TAAA
*
4435774 AAATAAATTAAA
1 AAATAAAATAAA
4435786 AA
1 AA
4435788 GAAAAGTAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
11 1 0.03
12 22 0.63
13 3 0.09
14 3 0.09
15 6 0.17
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (12 bp):
AAATAAAATAAA
Found at i:4435766 original size:24 final size:24
Alignment explanation
Indices: 4435734--4435787 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
4435724 ATAAAGTAGC
*
4435734 TAAATAATAATAAAT-AAAATAAAA
1 TAAAAAATAA-AAATAAAAATAAAA
* *
4435758 TAAAAAATAAAAGTAAAAATAAAT
1 TAAAAAATAAAAATAAAAATAAAA
4435782 TAAAAA
1 TAAAAA
4435788 GAAAAGTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 3 0.12
24 23 0.88
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (24 bp):
TAAAAAATAAAAATAAAAATAAAA
Found at i:4435781 original size:23 final size:24
Alignment explanation
Indices: 4435749--4435809 Score: 72
Period size: 23 Copynumber: 2.5 Consensus size: 24
4435739 AATAATAAAT
*
4435749 AAAATAAAATAAAAAATAAAAGTA
1 AAAATAAAATAAAAAAGAAAAGTA
*
4435773 AAAAT-AAATTAAAAAGAAAAGTA
1 AAAATAAAATAAAAAAGAAAAGTA
4435796 ATAAA-AGAAATAAA
1 A-AAATA-AAATAAA
4435810 GTAAAATAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 17 0.55
24 8 0.26
25 6 0.19
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (24 bp):
AAAATAAAATAAAAAAGAAAAGTA
Found at i:4435956 original size:3 final size:3
Alignment explanation
Indices: 4435948--4435973 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4435938 ACAAAAAAGA
4435948 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
4435974 ACCTAATACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4436093 original size:2 final size:2
Alignment explanation
Indices: 4436086--4436133 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
4436076 AAATAAAATA
4436086 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4436127 AT AT AT A
1 AT AT AT A
4436134 CATAAAACAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4438132 original size:167 final size:167
Alignment explanation
Indices: 4437925--4439140 Score: 1647
Period size: 167 Copynumber: 7.3 Consensus size: 167
4437915 GAATGTAATT
*
4437925 GAACTCGAAGGTC-T--TTGGCAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTGCC
1 GAACTCGAAGGTCTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCC
* * * *
4437987 TTGGAGCTGAGCGTAGTCGAACTTGAAGGTCTTT-GTTGACAGATAAACCTTTTAGCCTTGAGTT
66 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTT
* * * *
4438051 ATGATATAAATGATATGCCTTTGAGCTGAGCGTAGTC
131 ATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTC
*
4438088 GAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
1 GAACTCGAAGGTC-TTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
* * * * *
4438153 CTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGGTGGCAGATATCACTTCTAGCCTTGAGC
65 CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGT
* * * *
4438218 TATGCTGCAAATAATGTACCTTGGAGCCGAGCGTAGTC
130 TATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTC
* *
4438256 GAACTCGAAGGTCTTTGATTGGCAGATAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATGTGC
1 GAACTCGAAGGTC-TTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
* ** *
4438321 CTTGGAGATGAGCGTAGTTTAACTCGAAGGTATTTGGTTGGCAGATAACCCTTCTAGCCTTGAGT
65 CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGT
* ** *
4438386 TATACTACAAATGATGTGCCTTGCAGCTGAGCGTAGTC
130 TATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTC
* * * * *
4438424 GAACTCGAAGGTCTTTGTTGACAGCTAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCC
1 GAACTCGAAGGTCTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCC
* * ** *
4438489 TTTGAGCTGAGCGTAGTTGAACTCGAAGGTCTTTTATTGGCAGACAACCCTTCTAGCCTTGAGTT
66 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTT
4438554 A-GCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTC
131 ATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTC
* *** * * *
4438590 GAACTCGAAGGTCTTTGGGTGGCAGATAGTACTTATAGCCTTGAGCTATACTGCAAATGATGTGC
1 GAACTCGAAGGTC-TTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
*
4438655 CTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGT
65 CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGT
4438720 TA-GCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTC
130 TATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTC
* *** * * *
4438757 GAACTCGAAGGTCTTTGGGTGGCAGATAGTACTTATAGCCTTGAGCTATACTGCAAATGATGTGC
1 GAACTCGAAGGTC-TTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
* *
4438822 CTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGAAGATAACCCTTCTAGCCTTGAGT
65 CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGT
* *
4438887 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATC
130 TATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTC
*
4438925 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATAATGTGC
1 GAACTCGAAGGTC-TTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
* * * * * *
4438990 ATTGGAGTTGAGCGTAGTCAAACTCGAATGTCTTTTGG-TGGAAGATATCCCTTCTAGCCTTGAG
65 CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTAGCCTTGAG
* * *
4439054 CTATGCT-TCAAATCATGTGCCTTGGAGCTGAGCATAGTC
129 TTATGCTGT-AAATGATGTGCCTTGGAGCTGAGCGTAGTC
* * ** * *
4439093 GTACTCGAAGGTCTTGGCTGAAAGATAACACTTCTCGCCTTGAGTTAT
1 GAACTCGAAGGTCTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
4439141 ACTACCGATA
Statistics
Matches: 946, Mismatches: 98, Indels: 14
0.89 0.09 0.01
Matches are distributed among these distances:
163 13 0.01
165 1 0.00
166 44 0.05
167 480 0.51
168 403 0.43
169 5 0.01
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (167 bp):
GAACTCGAAGGTCTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCC
TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTT
ATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTC
Found at i:4438148 original size:84 final size:84
Alignment explanation
Indices: 4437925--4439140 Score: 1687
Period size: 84 Copynumber: 14.6 Consensus size: 84
4437915 GAATGTAATT
*
4437925 GAACTCGAAGGTC--T--TTGGCAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTGC
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
4437986 CTTGGAGCTGAGCGTAGTC
66 CTTGGAGCTGAGCGTAGTC
* * * * * ** *
4438005 GAACTTGAAGGTCTTT-GTTGACAGATAAACCTTTTAGCCTTGAGTTATGATATAAATGATATGC
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
*
4438069 CTTTGAGCTGAGCGTAGTC
66 CTTGGAGCTGAGCGTAGTC
*
4438088 GAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
4438153 CTTGGAGCTGAGCGTAGTC
66 CTTGGAGCTGAGCGTAGTC
* * * * * * *
4438172 AAACTCGAAGGTCTTTGGGTGGCAGATATCACTTCTAGCCTTGAGCTATGCTGCAAATAATGTAC
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
*
4438237 CTTGGAGCCGAGCGTAGTC
66 CTTGGAGCTGAGCGTAGTC
* *
4438256 GAACTCGAAGGTCTTTGATTGGCAGATAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATGTGC
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
* *
4438321 CTTGGAGATGAGCGTAGTT
66 CTTGGAGCTGAGCGTAGTC
* * * *
4438340 TAACTCGAAGGTATTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATACTACAAATGATGTGC
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
*
4438405 CTTGCAGCTGAGCGTAGTC
66 CTTGGAGCTGAGCGTAGTC
* * * *
4438424 GAACTCGAAGGTCTTT-GTTGACAGCTAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGC
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
* *
4438488 CTTTGAGCTGAGCGTAGTT
66 CTTGGAGCTGAGCGTAGTC
** * *
4438507 GAACTCGAAGGTCTTTTATTGGCAGACAACCCTTCTAGCCTTGAGTTA-GCTGTAAATGATGTGC
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
4438571 CTTGGAGCTGAGCGTAGTC
66 CTTGGAGCTGAGCGTAGTC
* *** * * *
4438590 GAACTCGAAGGTCTTTGGGTGGCAGATAGTACTTATAGCCTTGAGCTATACTGCAAATGATGTGC
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
*
4438655 CTTAGAGCTGAGCGTAGTC
66 CTTGGAGCTGAGCGTAGTC
*
4438674 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTA-GCTGTAAATGATGTGC
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
4438738 CTTGGAGCTGAGCGTAGTC
66 CTTGGAGCTGAGCGTAGTC
* *** * * *
4438757 GAACTCGAAGGTCTTTGGGTGGCAGATAGTACTTATAGCCTTGAGCTATACTGCAAATGATGTGC
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
*
4438822 CTTAGAGCTGAGCGTAGTC
66 CTTGGAGCTGAGCGTAGTC
*
4438841 GAACTCGAAGGTCTTTGGTTGGAAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
*
4438906 CTTGGAGCTGAGCGTAATC
66 CTTGGAGCTGAGCGTAGTC
*
4438925 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATAATGTGC
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
* *
4438990 ATTGGAGTTGAGCGTAGTC
66 CTTGGAGCTGAGCGTAGTC
* * * * * * *
4439009 AAACTCGAATGTCTTTTGG-TGGAAGATATCCCTTCTAGCCTTGAGCTATGCTTCAAATCATGTG
1 GAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTG
*
4439073 CCTTGGAGCTGAGCATAGTC
65 CCTTGGAGCTGAGCGTAGTC
* * ** * *
4439093 GTACTCGAAGGTC-TTGGCTGAAAGATAACACTTCTCGCCTTGAGTTAT
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
4439141 ACTACCGATA
Statistics
Matches: 997, Mismatches: 130, Indels: 15
0.87 0.11 0.01
Matches are distributed among these distances:
80 12 0.01
82 5 0.01
83 316 0.32
84 659 0.66
85 5 0.01
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (84 bp):
GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
CTTGGAGCTGAGCGTAGTC
Found at i:4441466 original size:95 final size:95
Alignment explanation
Indices: 4441288--4441532 Score: 296
Period size: 95 Copynumber: 2.5 Consensus size: 95
4441278 AGCCGGGAAA
* * *
4441288 TTTAACCAATTGCTCTAGAGGGACAACTTAATACCATTGTATAG-ATATTATAATCACCTTTATC
1 TTTAACCAATTGCTCTAGAGGGACAAC-TCA-AGC-TT-TATTGTATATTATAATCACCTTTATC
*
4441352 AGACTAGCTAAATATTATCCATAAAGAT-GGGGAG
62 AGACTAGCTAAATATTATCCATAAAG-TCAGGGAG
* *
4441386 TTTAACCAATTTCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAATCACCTTTATCAGGC
1 TTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAATCACCTTTATCAGAC
* * *
4441451 TAGTTAAATCTTATCCATAAAGTCAGGGCG
66 TAGCTAAATATTATCCATAAAGTCAGGGAG
** * * *
4441481 TCGAACCAATTGCTTTAGAGGGACAGCTCAAGCTTTATTATATATATATAAT
1 TTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAT-TATAAT
4441533 ATTATAATCT
Statistics
Matches: 129, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
94 5 0.04
95 88 0.68
96 8 0.06
97 2 0.02
98 26 0.20
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (95 bp):
TTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAATCACCTTTATCAGAC
TAGCTAAATATTATCCATAAAGTCAGGGAG
Found at i:4444273 original size:12 final size:12
Alignment explanation
Indices: 4444252--4444434 Score: 75
Period size: 12 Copynumber: 14.0 Consensus size: 12
4444242 GTAGCTAAAT
* *
4444252 AATAATAAATTA
1 AATAAAAAATAA
*
4444264 AATATAAAATAA
1 AATAAAAAATAA
4444276 AATAAAAAATAA
1 AATAAAAAATAA
4444288 AAGTGAAAATAAATTAA
1 AA-T--AAA-AAA-TAA
*
4444305 AATGAAAAATAA
1 AATAAAAAATAA
*
4444317 TAA-AAGAAATAA
1 -AATAAAAAATAA
*
4444329 AAGAAATAAAGTAA
1 AATAAA-AAA-TAA
*
4444343 AATAGAATGATATGAA
1 AATA-AA--AAAT-AA
*
4444359 AATAAAAATAAAA
1 AATAAAAA-ATAA
4444372 AATGAAATCAAATAA
1 AAT-AAA--AAATAA
4444387 AATAAAATAA-AA
1 AATAAAA-AATAA
* *
4444399 CAAAAAAAAATTA
1 -AATAAAAAATAA
*
4444412 AATAAAAAA-AT
1 AATAAAAAATAA
*
4444423 TATAAAAAATAA
1 AATAAAAAATAA
4444435 TATATATATA
Statistics
Matches: 130, Mismatches: 21, Indels: 40
0.68 0.11 0.21
Matches are distributed among these distances:
11 10 0.08
12 48 0.37
13 24 0.18
14 15 0.12
15 14 0.11
16 14 0.11
17 5 0.04
ACGTcount: A:0.73, C:0.01, G:0.05, T:0.20
Consensus pattern (12 bp):
AATAAAAAATAA
Found at i:4444275 original size:5 final size:5
Alignment explanation
Indices: 4444248--4444418 Score: 100
Period size: 5 Copynumber: 33.6 Consensus size: 5
4444238 AAAAGTAGCT
*
4444248 AAATA ATAATA AATTA AATATA AAATA AAATAAA AAATA AAAGTGA AAATA
1 AAATA A-AATA AAATA AA-ATA AAATA AAAT--A AAATA AAA-T-A AAATA
* * * * *
4444299 AATTA AAATGA AAA-A TAATA AAA-G AAATA AAA-G AAATA AAGTA AAATA
1 AAATA AAAT-A AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA
* * * * * *
4444347 GAATG ATATGA AAATA AAA-A TAA-A AAATG AAATC AAATA AAATA AAATA
1 AAATA AAAT-A AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA
* * *
4444396 AAACA AAAAA AAATT AAATA AAA
1 AAATA AAATA AAATA AAATA AAA
4444419 AAATTATAAA
Statistics
Matches: 126, Mismatches: 28, Indels: 24
0.71 0.16 0.13
Matches are distributed among these distances:
4 15 0.12
5 84 0.67
6 18 0.14
7 9 0.07
ACGTcount: A:0.73, C:0.01, G:0.06, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:4444326 original size:29 final size:29
Alignment explanation
Indices: 4444267--4444434 Score: 89
Period size: 29 Copynumber: 5.7 Consensus size: 29
4444257 TAAATTAAAT
**
4444267 ATAAAATAAAATAAAAAATAAAAGTGAAA
1 ATAAAATAAAATAAAAAATAAAAAAGAAA
* *
4444296 ATAAATTAAAATGAAAAATAATAAAAG-AA
1 ATAAAATAAAATAAAAAATAA-AAAAGAAA
* * *
4444325 ATAAAA-GAAAT--AAAGTAAAATAGAATGA
1 ATAAAATAAAATAAAAAATAAAAAAGAA--A
* **
4444353 TATGAAAATAAAAATAAAAAAT--GAAATCAA
1 -AT-AAAAT-AAAATAAAAAATAAAAAAGAAA
* **
4444383 ATAAAATAAAATAAAACAAAAAAAAATTAA
1 ATAAAATAAAATAAAA-AATAAAAAAGAAA
4444413 ATAAAA-AAATTATAAAAAATAA
1 ATAAAATAAA--ATAAAAAATAA
4444435 TATATATATA
Statistics
Matches: 106, Mismatches: 18, Indels: 29
0.69 0.12 0.19
Matches are distributed among these distances:
25 4 0.04
26 7 0.07
27 9 0.08
28 12 0.11
29 33 0.31
30 24 0.23
31 6 0.06
32 7 0.07
34 4 0.04
ACGTcount: A:0.74, C:0.01, G:0.06, T:0.19
Consensus pattern (29 bp):
ATAAAATAAAATAAAAAATAAAAAAGAAA
Found at i:4444405 original size:39 final size:37
Alignment explanation
Indices: 4444255--4444405 Score: 103
Period size: 41 Copynumber: 3.7 Consensus size: 37
4444245 GCTAAATAAT
*
4444255 AATAAATTAAATATAAAATAAAATAAAAAAT-AAAAGTGAA
1 AATAAA-TAAA-ATAAAATAAAA-AAAAAATAAAAAATG-A
*
4444295 AATAAATTAAAATGAAAAATAATAAAAGAAAT--AAAA-GA
1 AATAAA-TAAAAT--AAAATAA-AAAAAAAATAAAAAATGA
4444333 AATAAAGTAAAATAGAATGATATGAAAATAAAAATAAAAAATGA
1 AATAAA-TAAAATA-AA--ATA--AAAA-AAAAATAAAAAATGA
4444377 AATCAAATAAAATAAAATAAAACAAAAAA
1 AAT-AAATAAAATAAAATAAAA-AAAAAA
4444406 AAATTAAATA
Statistics
Matches: 93, Mismatches: 4, Indels: 29
0.74 0.03 0.23
Matches are distributed among these distances:
36 1 0.01
37 2 0.02
38 13 0.14
39 14 0.15
40 18 0.19
41 22 0.24
42 2 0.02
43 6 0.06
44 12 0.13
45 3 0.03
ACGTcount: A:0.73, C:0.01, G:0.07, T:0.19
Consensus pattern (37 bp):
AATAAATAAAATAAAATAAAAAAAAAATAAAAAATGA
Found at i:4444419 original size:15 final size:15
Alignment explanation
Indices: 4444248--4444421 Score: 73
Period size: 17 Copynumber: 11.1 Consensus size: 15
4444238 AAAAGTAGCT
*
4444248 AAATAATAATAAATTAA
1 AAATAA-AATAAA-AAA
*
4444265 ATATAAAATAAAATAAA
1 AAATAAAAT-AAA-AAA
*
4444282 AAATAAAAGTGAAAATA
1 AAATAAAA-T-AAAAAA
* *
4444299 AATTAAAATGAAAAA
1 AAATAAAATAAAAAA
* * *
4444314 TAATAAAA-GAAATA
1 AAATAAAATAAAAAA
* **
4444328 AAA-GAAATAAAGTA
1 AAATAAAATAAAAAA
* * **
4444342 AAATAGAATGATATGA
1 AAATAAAAT-AAAAAA
4444358 AAATAAAAATAAAAAA
1 AAAT-AAAATAAAAAA
* *
4444374 TGAAATCAAATAAAATA
1 --AAATAAAATAAAAAA
*
4444391 AAATAAAACAAAAAA
1 AAATAAAATAAAAAA
*
4444406 AAATTAAATAAAAAA
1 AAATAAAATAAAAAA
4444421 A
1 A
4444422 TTATAAAAAA
Statistics
Matches: 118, Mismatches: 31, Indels: 18
0.71 0.19 0.11
Matches are distributed among these distances:
13 3 0.03
14 14 0.12
15 39 0.33
16 14 0.12
17 40 0.34
18 8 0.07
ACGTcount: A:0.74, C:0.01, G:0.06, T:0.20
Consensus pattern (15 bp):
AAATAAAATAAAAAA
Found at i:4444695 original size:19 final size:20
Alignment explanation
Indices: 4444668--4444707 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
4444658 AAATGTTAGG
4444668 AAAAGAAATAAT-AATAATA
1 AAAAGAAATAATAAATAATA
*
4444687 AAAATAAATAATAAATAATA
1 AAAAGAAATAATAAATAATA
4444707 A
1 A
4444708 TATATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (20 bp):
AAAAGAAATAATAAATAATA
Found at i:4444701 original size:7 final size:7
Alignment explanation
Indices: 4444673--4444707 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
4444663 TTAGGAAAAG
4444673 AAATAAT
1 AAATAAT
4444680 -AATAAT
1 AAATAAT
4444686 AAA-AAT
1 AAATAAT
4444692 AAATAAT
1 AAATAAT
4444699 AAATAAT
1 AAATAAT
4444706 AA
1 AA
4444708 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 12 0.46
7 14 0.54
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAATAAT
Found at i:4444714 original size:2 final size:2
Alignment explanation
Indices: 4444707--4444749 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
4444697 ATAAATAATA
4444707 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4444749 A
1 A
4444750 AAAGAAATGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4446191 original size:2 final size:2
Alignment explanation
Indices: 4446184--4446220 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4446174 TACTATAAAC
4446184 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4446221 GAAAATTTAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4452750 original size:20 final size:21
Alignment explanation
Indices: 4452727--4452774 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
4452717 AAAGTTTGAT
*
4452727 TCCTTC-ACTAAAAGGATCAA
1 TCCTTCAACAAAAAGGATCAA
4452747 TCCTTCAACAAAAAGGATCAA
1 TCCTTCAACAAAAAGGATCAA
4452768 TCACTTC
1 TC-CTTC
4452775 CCCTAAAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 6 0.24
21 15 0.60
22 4 0.16
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (21 bp):
TCCTTCAACAAAAAGGATCAA
Found at i:4455829 original size:23 final size:22
Alignment explanation
Indices: 4455781--4455829 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
4455771 ATAGAATGTC
4455781 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
4455802 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
4455825 AAGGA
1 AAGGA
4455830 AAAATGTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:4456778 original size:31 final size:31
Alignment explanation
Indices: 4456740--4456880 Score: 237
Period size: 31 Copynumber: 4.5 Consensus size: 31
4456730 AGGGTCGAGG
4456740 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4456771 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* **
4456802 GTTTACCTATGTTATTTAGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4456833 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
4456864 GATTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
4456881 AGAATCTATG
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 102 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:4457382 original size:21 final size:21
Alignment explanation
Indices: 4457358--4457400 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
4457348 AAAGAATATA
4457358 TTGTATAA-GCTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
4457379 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
4457400 T
1 T
4457401 AAATGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:4463436 original size:12 final size:12
Alignment explanation
Indices: 4463421--4463450 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
4463411 GGTAGATTTA
4463421 AATTTATCTTTC
1 AATTTATCTTTC
4463433 AATTTATCTTTC
1 AATTTATCTTTC
4463445 AATTTA
1 AATTTA
4463451 CTTGTTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (12 bp):
AATTTATCTTTC
Found at i:4465126 original size:29 final size:29
Alignment explanation
Indices: 4465076--4465142 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
4465066 TTAGGAACCG
* * *
4465076 AACTGGAAAGAAATAAATGTTAGGCAGTA
1 AACTGGAAAGAAATAAACGTTACGCACTA
*
4465105 AACTGGAACGAAA-AGAACGTTACGCACTA
1 AACTGGAAAGAAATA-AACGTTACGCACTA
*
4465134 AACTAGAAA
1 AACTGGAAA
4465143 AATGCTTACG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
28 1 0.03
29 30 0.97
ACGTcount: A:0.49, C:0.13, G:0.21, T:0.16
Consensus pattern (29 bp):
AACTGGAAAGAAATAAACGTTACGCACTA
Found at i:4467771 original size:46 final size:46
Alignment explanation
Indices: 4467719--4467855 Score: 170
Period size: 46 Copynumber: 3.0 Consensus size: 46
4467709 ATAAAATTTC
* * * *
4467719 TTATCAATATATTTACCATTTAATCCCATGAGCTCGTAAGCTTATT
1 TTATCAATATACTTACCATATAATCACATAAGCTCGTAAGCTTATT
4467765 TTATCAATATACTTACCATATAATCACATAAGCTCGTAAGCTTATT
1 TTATCAATATACTTACCATATAATCACATAAGCTCGTAAGCTTATT
* * * * * *
4467811 TTACCCATATACCTGCCAT-TATTC-CATAAGCTCGTAAGATTATT
1 TTATCAATATACTTACCATATAATCACATAAGCTCGTAAGCTTATT
4467855 T
1 T
4467856 GCATGGTTAC
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
44 20 0.25
45 4 0.05
46 57 0.70
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (46 bp):
TTATCAATATACTTACCATATAATCACATAAGCTCGTAAGCTTATT
Found at i:4468089 original size:58 final size:58
Alignment explanation
Indices: 4467956--4468089 Score: 162
Period size: 58 Copynumber: 2.3 Consensus size: 58
4467946 ATAAGCACTG
* * * **
4467956 TAGTGTTATCCCGAGTATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTT
1 TAGTG-TATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
* ** *
4468015 AAGTACAGTCCC-AATATGACACATAAGGTCGTGCCCACCATATACACTGGGTATCCTT
1 TAGTGTA-TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
4468073 TAGTGTATCCCGAATAT
1 TAGTGTATCCCGAATAT
4468090 ACAGCCTGTT
Statistics
Matches: 61, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
57 4 0.07
58 50 0.82
59 7 0.11
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.29
Consensus pattern (58 bp):
TAGTGTATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
Found at i:4468420 original size:24 final size:24
Alignment explanation
Indices: 4468378--4468426 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
4468368 AATCTTCCTG
**
4468378 ATGATGTATAAAATGTCTAAGTAC
1 ATGATGTATAAAACATCTAAGTAC
*
4468402 ATGATGTATAAAACATCTACGTAC
1 ATGATGTATAAAACATCTAAGTAC
4468426 A
1 A
4468427 ATGTCATGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (24 bp):
ATGATGTATAAAACATCTAAGTAC
Found at i:4469974 original size:30 final size:30
Alignment explanation
Indices: 4469940--4469998 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
4469930 TTTGGTCCCT
* *
4469940 AAACTTT-TCAAAGTTTATACTTTAGTCACC
1 AAACTTTACCAAA-TTTATAATTTAGTCACC
*
4469970 AAACTTTACCAAATTTATAATTTGGTCAC
1 AAACTTTACCAAATTTATAATTTAGTCAC
4469999 TAATTGAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.39
Consensus pattern (30 bp):
AAACTTTACCAAATTTATAATTTAGTCACC
Found at i:4471893 original size:6 final size:6
Alignment explanation
Indices: 4471882--4471929 Score: 60
Period size: 6 Copynumber: 7.7 Consensus size: 6
4471872 ATCTCTCATT
* *
4471882 TTTTTC TTTTTC TTCTTTC TTTTTG TTTTCTT TTTTTC TTTTTC TTTT
1 TTTTTC TTTTTC TT-TTTC TTTTTC TTTT-TC TTTTTC TTTTTC TTTT
4471930 AATATATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
6 26 0.70
7 11 0.30
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:4471902 original size:13 final size:12
Alignment explanation
Indices: 4471882--4471929 Score: 60
Period size: 13 Copynumber: 3.8 Consensus size: 12
4471872 ATCTCTCATT
4471882 TTTTTCTTTTTC
1 TTTTTCTTTTTC
*
4471894 TTCTTTCTTTTTG
1 TT-TTTCTTTTTC
*
4471907 TTTTCTTTTTTTC
1 TTTT-TCTTTTTC
4471920 TTTTTCTTTT
1 TTTTTCTTTT
4471930 AATATATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
12 9 0.30
13 21 0.70
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (12 bp):
TTTTTCTTTTTC
Found at i:4471904 original size:19 final size:20
Alignment explanation
Indices: 4471882--4471929 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
4471872 ATCTCTCATT
4471882 TTTTTCTTTTTC-TTCTTTC
1 TTTTTCTTTTTCTTTCTTTC
* *
4471901 TTTTT-GTTTTCTTTTTTTC
1 TTTTTCTTTTTCTTTCTTTC
4471920 TTTTTCTTTT
1 TTTTTCTTTT
4471930 AATATATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 5 0.21
19 16 0.67
20 3 0.12
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (20 bp):
TTTTTCTTTTTCTTTCTTTC
Found at i:4471918 original size:14 final size:14
Alignment explanation
Indices: 4471880--4471929 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 14
4471870 GCATCTCTCA
4471880 TTTTTTTCTTTTTC
1 TTTTTTTCTTTTTC
*
4471894 TTCTTTCTTTTTGTTTTC
1 -T-TTT-TTTCT-TTTTC
4471912 TTTTTTTCTTTTTC
1 TTTTTTTCTTTTTC
4471926 TTTT
1 TTTT
4471930 AATATATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
14 9 0.30
15 5 0.17
16 6 0.20
17 5 0.17
18 5 0.17
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (14 bp):
TTTTTTTCTTTTTC
Found at i:4475382 original size:3 final size:3
Alignment explanation
Indices: 4475374--4475399 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4475364 GAATAGGGTT
4475374 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
4475400 ATCAATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:4475465 original size:46 final size:46
Alignment explanation
Indices: 4475398--4475534 Score: 165
Period size: 46 Copynumber: 3.0 Consensus size: 46
4475388 GTTGTTGTTG
* *
4475398 TTATCAATATATTTACCATTTAATCCAATAAGCTTGTAAGCTTATT
1 TTATCAATATACTTACCATTTAATCCAATAAGCTCGTAAGCTTATT
*
4475444 TTATCAATATACTTACCATTTAAT-CACATAAGATCGTAAGCTTATT
1 TTATCAATATACTTACCATTTAATCCA-ATAAGCTCGTAAGCTTATT
* * * *
4475490 TTA-CACATATACCTGCCA-TTATTCC-ATAATCTCGTAAGCTTATT
1 TTATCA-ATATACTTACCATTTAATCCAATAAGCTCGTAAGCTTATT
4475534 T
1 T
4475535 GCATGGTTAC
Statistics
Matches: 80, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
44 18 0.22
45 8 0.10
46 54 0.68
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.41
Consensus pattern (46 bp):
TTATCAATATACTTACCATTTAATCCAATAAGCTCGTAAGCTTATT
Found at i:4475759 original size:58 final size:58
Alignment explanation
Indices: 4475634--4475763 Score: 172
Period size: 58 Copynumber: 2.2 Consensus size: 58
4475624 TAAAAGCACC
* * * **
4475634 GTATCCCGAGTATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGT
1 GTATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGT
** *
4475692 ACAGT-CCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGT
1 GTA-TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGT
4475750 GTATCCCGAATATG
1 GTATCCCGAATATG
4475764 CAGCCTGCTA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
57 1 0.02
58 58 0.97
59 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (58 bp):
GTATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGT
Found at i:4476079 original size:24 final size:24
Alignment explanation
Indices: 4476048--4476096 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
4476038 AGTCTTCATG
4476048 ATGATGTATAAAACATCTAAGTAC
1 ATGATGTATAAAACATCTAAGTAC
*
4476072 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTAAGTAC
4476096 A
1 A
4476097 ATGTCATGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (24 bp):
ATGATGTATAAAACATCTAAGTAC
Found at i:4481008 original size:21 final size:21
Alignment explanation
Indices: 4480984--4481029 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
4480974 ATCGAAACCT
* *
4480984 GTTGTGGTGGCATATGAAATA
1 GTTGTGGAGCCATATGAAATA
* *
4481005 GTTGTGGAGCCATCTGAAATG
1 GTTGTGGAGCCATATGAAATA
4481026 GTTG
1 GTTG
4481030 CATCCCCATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.09, G:0.35, T:0.33
Consensus pattern (21 bp):
GTTGTGGAGCCATATGAAATA
Found at i:4482986 original size:2 final size:2
Alignment explanation
Indices: 4482979--4483034 Score: 84
Period size: 2 Copynumber: 30.0 Consensus size: 2
4482969 TAAAAATAAT
4482979 TA TA TA TA TA T- TA TA TA TA TA TA TA TA T- 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
4483019 TA T- TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
4483035 ATTAATAAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
1 4 0.08
2 46 0.92
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4483038 original size:15 final size:16
Alignment explanation
Indices: 4482974--4483038 Score: 98
Period size: 15 Copynumber: 4.1 Consensus size: 16
4482964 AATATTAAAA
4482974 ATAATTATATATATATT
1 ATAA-TATATATATATT
4482991 ATATATATATATATATT
1 ATA-ATATATATATATT
4483008 AT-ATATATATATATT
1 ATAATATATATATATT
4483023 ATAATATATATA-ATT
1 ATAATATATATATATT
4483038 A
1 A
4483039 ATAAATTTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
15 19 0.41
16 9 0.20
17 17 0.37
18 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATAATATATATATATT
Found at i:4483072 original size:19 final size:19
Alignment explanation
Indices: 4483026--4483087 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
4483016 ATATATTATA
* *
4483026 ATATATATAATTAATAAAT
1 ATATATTTAATTAAAAAAT
* *
4483045 TTA-ATTTAAATAAAAAAT
1 ATATATTTAATTAAAAAAT
* *
4483063 ATATATTTAATTTAAATAT
1 ATATATTTAATTAAAAAAT
4483082 ATATAT
1 ATATAT
4483088 ATACCCGGCC
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
18 14 0.41
19 20 0.59
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATATATTTAATTAAAAAAT
Found at i:4483136 original size:12 final size:12
Alignment explanation
Indices: 4483088--4483141 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
4483078 ATATATATAT
*
4483088 ATACCCGGCCCG
1 ATACCCGGCCCA
*
4483100 ATTCCCGGCCCA
1 ATACCCGGCCCA
*
4483112 ATA-CCGACCCA
1 ATACCCGGCCCA
4483123 ATACCCGGCCCA
1 ATACCCGGCCCA
4483135 ATACCCG
1 ATACCCG
4483142 TTTAAATAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
11 10 0.28
12 26 0.72
ACGTcount: A:0.24, C:0.48, G:0.17, T:0.11
Consensus pattern (12 bp):
ATACCCGGCCCA
Found at i:4483246 original size:25 final size:25
Alignment explanation
Indices: 4483212--4483264 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
4483202 TAAATCCCTG
4483212 CGGTATTTTAAACGGGGAC-GGGTAC
1 CGGTATTTTAAACGGGGACAGGG-AC
*
4483237 CGGTTTTTTAAACGGGGACAGGGAC
1 CGGTATTTTAAACGGGGACAGGGAC
4483262 CGG
1 CGG
4483265 GGGACCAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 23 0.88
26 3 0.12
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.23
Consensus pattern (25 bp):
CGGTATTTTAAACGGGGACAGGGAC
Found at i:4489461 original size:30 final size:31
Alignment explanation
Indices: 4489395--4489467 Score: 121
Period size: 32 Copynumber: 2.4 Consensus size: 31
4489385 GATATGCTTT
*
4489395 AACAAGTTTCTATTGCTACAGAGATGGTCTTC
1 AACAAGTTTCTATTGCTACAGAGA-GGTCCTC
4489427 AACAAGTTTCTATTGCTACAGAGA-GTCCTC
1 AACAAGTTTCTATTGCTACAGAGAGGTCCTC
4489457 AACAAGTTTCT
1 AACAAGTTTCT
4489468 GGGAAAAGTA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
30 16 0.40
32 24 0.60
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (31 bp):
AACAAGTTTCTATTGCTACAGAGAGGTCCTC
Found at i:4495055 original size:1 final size:1
Alignment explanation
Indices: 4495049--4495076 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
4495039 TCATATGCTG
4495049 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
4495077 GTATCTTCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:4496686 original size:19 final size:20
Alignment explanation
Indices: 4496658--4496696 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4496648 TTTGGGAAAA
*
4496658 ATCGG-TTTTTTTTAACCGG
1 ATCGGATTTTTTTAAACCGG
4496677 ATCGGATTTTTTTAAACCGG
1 ATCGGATTTTTTTAAACCGG
4496697 TTATTTTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.44
Consensus pattern (20 bp):
ATCGGATTTTTTTAAACCGG
Found at i:4496773 original size:22 final size:24
Alignment explanation
Indices: 4496729--4496780 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
4496719 AAAAACCTAG
* *
4496729 ACCGGTTTTTTTACACGATAAAAA
1 ACCGGTTTTTATACACGAAAAAAA
4496753 ACCGGTTTTTAT-C-CGAAAAAAA
1 ACCGGTTTTTATACACGAAAAAAA
4496775 ACCGGT
1 ACCGGT
4496781 CTGGGTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 14 0.54
23 1 0.04
24 11 0.42
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (24 bp):
ACCGGTTTTTATACACGAAAAAAA
Found at i:4499060 original size:21 final size:21
Alignment explanation
Indices: 4499036--4499075 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4499026 AGTTTATTTT
4499036 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
4499057 TAAACTTTGTTTCAATTAT
1 TAAACTTTATTTCAATTAT
4499076 TGAACTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:4499122 original size:33 final size:33
Alignment explanation
Indices: 4499072--4499170 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
4499062 TTTGTTTCAA
*
4499072 TTATTGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
4499104 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
4499137 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
4499170 T
1 T
4499171 ATGTTGAGTT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 10 0.16
33 52 0.84
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.46
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:4502325 original size:43 final size:43
Alignment explanation
Indices: 4502264--4502361 Score: 187
Period size: 43 Copynumber: 2.3 Consensus size: 43
4502254 ACACGAGCAT
*
4502264 CAAACCTAGAAAACATTAGTTGGTTACGGGAGTAATATTTCAA
1 CAAACCTAGAAAACATTAGATGGTTACGGGAGTAATATTTCAA
4502307 CAAACCTAGAAAACATTAGATGGTTACGGGAGTAATATTTCAA
1 CAAACCTAGAAAACATTAGATGGTTACGGGAGTAATATTTCAA
4502350 CAAACCTAGAAA
1 CAAACCTAGAAA
4502362 GTATAAATCT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.24
Consensus pattern (43 bp):
CAAACCTAGAAAACATTAGATGGTTACGGGAGTAATATTTCAA
Found at i:4514137 original size:21 final size:21
Alignment explanation
Indices: 4514113--4514158 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
4514103 TGGAGATCGT
4514113 CGCCACTACCATCATGACCGC
1 CGCCACTACCATCATGACCGC
* *
4514134 CGCCACTCCCATCATGACTGC
1 CGCCACTACCATCATGACCGC
4514155 CGCC
1 CGCC
4514159 TTGCACCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.50, G:0.15, T:0.15
Consensus pattern (21 bp):
CGCCACTACCATCATGACCGC
Found at i:4514667 original size:14 final size:13
Alignment explanation
Indices: 4514632--4514671 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
4514622 ACTGGTCGAG
4514632 CTGAGTCAACTCA
1 CTGAGTCAACTCA
*
4514645 CTAAGTCAACTCGA
1 CTGAGTCAACTC-A
*
4514659 TTGAGTCAACTCA
1 CTGAGTCAACTCA
4514672 AATAGAGTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.25
Consensus pattern (13 bp):
CTGAGTCAACTCA
Found at i:4515976 original size:27 final size:27
Alignment explanation
Indices: 4515946--4516005 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
4515936 TTCGATATTC
4515946 AAATGACTGA-AATATCCTTAAACCCTA
1 AAATGACTGATAATA-CCTTAAACCCTA
* * *
4515973 AAATGA-TTATAATACCTTGAACTCTA
1 AAATGACTGATAATACCTTAAACCCTA
4515999 AAATGAC
1 AAATGAC
4516006 CGAATTAACC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 18 0.64
27 10 0.36
ACGTcount: A:0.45, C:0.18, G:0.08, T:0.28
Consensus pattern (27 bp):
AAATGACTGATAATACCTTAAACCCTA
Found at i:4519274 original size:23 final size:24
Alignment explanation
Indices: 4519224--4519274 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
4519214 ACTACACTCA
* * * *
4519224 ATTTACTTTTTCCAATACATTTCT
1 ATTTACTTTTGCCAAAACATCTCG
4519248 ATTTA-TTTTGCCAAAACATCTCG
1 ATTTACTTTTGCCAAAACATCTCG
4519271 ATTT
1 ATTT
4519275 GCTGCCACAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.27, C:0.20, G:0.04, T:0.49
Consensus pattern (24 bp):
ATTTACTTTTGCCAAAACATCTCG
Found at i:4521747 original size:20 final size:20
Alignment explanation
Indices: 4521718--4521756 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4521708 AGGGCTCATA
*
4521718 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
4521738 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
4521757 GTTGTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:4525263 original size:20 final size:20
Alignment explanation
Indices: 4525234--4525272 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4525224 AGGGCTCATA
*
4525234 TAGGATCATATAGATGTATT
1 TAGGAGCATATAGATGTATT
*
4525254 TAGGAGCATATAGTTGTAT
1 TAGGAGCATATAGATGTAT
4525273 AAGGTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.38
Consensus pattern (20 bp):
TAGGAGCATATAGATGTATT
Found at i:4534564 original size:2 final size:2
Alignment explanation
Indices: 4534557--4534588 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4534547 AAAAGAGTAA
4534557 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4534589 TTATTCGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4537388 original size:24 final size:24
Alignment explanation
Indices: 4537327--4537378 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
4537317 CAGCTCCTAT
* * *
4537327 AAATTGTACCGAAGTGCCACGTAG
1 AAATTGCACCAAAGTGCCACATAG
4537351 AAATTGCACCAAAGTGCCACATAG
1 AAATTGCACCAAAGTGCCACATAG
4537375 AAAT
1 AAAT
4537379 GTCTCGAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (24 bp):
AAATTGCACCAAAGTGCCACATAG
Found at i:4537397 original size:23 final size:22
Alignment explanation
Indices: 4537367--4537445 Score: 68
Period size: 23 Copynumber: 3.5 Consensus size: 22
4537357 CACCAAAGTG
4537367 CCACATAGAAATGTCTCGAAAGA
1 CCACATAGAAATGTC-CGAAAGA
* * *
4537390 CCACATAGTATTGTCCAAAAGGA
1 CCACATAGAAATGTCCGAAA-GA
* * *
4537413 CCACGTAGAACTGTCCCGAAGGA
1 CCACATAGAAATGT-CCGAAAGA
*
4537436 CCACGTAGAA
1 CCACATAGAA
4537446 TTATCCCGAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
22 4 0.09
23 38 0.83
24 4 0.09
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.16
Consensus pattern (22 bp):
CCACATAGAAATGTCCGAAAGA
Found at i:4537452 original size:23 final size:23
Alignment explanation
Indices: 4537408--4537460 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
4537398 TATTGTCCAA
*
4537408 AAGGACCACGTAGAACTGTCCCG
1 AAGGACCACGTAGAACTATCCCG
*
4537431 AAGGACCACGTAGAATTATCCCG
1 AAGGACCACGTAGAACTATCCCG
*
4537454 AATGACC
1 AAGGACC
4537461 GTGTAAAACC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.34, C:0.28, G:0.23, T:0.15
Consensus pattern (23 bp):
AAGGACCACGTAGAACTATCCCG
Found at i:4538573 original size:11 final size:11
Alignment explanation
Indices: 4538557--4538582 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4538547 TTCATTTTAC
4538557 CCAAAAATTTT
1 CCAAAAATTTT
4538568 CCAAAAATTTT
1 CCAAAAATTTT
4538579 CCAA
1 CCAA
4538583 CTTCCTCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (11 bp):
CCAAAAATTTT
Found at i:4541450 original size:14 final size:14
Alignment explanation
Indices: 4541418--4541459 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
4541408 TCAATTCATC
4541418 CATAACATCCAAAA
1 CATAACATCCAAAA
4541432 CATAA-ATCCAAACA
1 CATAACATCCAAA-A
*
4541446 TATAAGCATCCAAA
1 CATAA-CATCCAAA
4541460 TTCAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 7 0.29
14 10 0.42
16 7 0.29
ACGTcount: A:0.55, C:0.26, G:0.02, T:0.17
Consensus pattern (14 bp):
CATAACATCCAAAA
Found at i:4543423 original size:19 final size:19
Alignment explanation
Indices: 4543399--4543437 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
4543389 CCAGAACCCG
*
4543399 TGGGGGGTATCGATTCCCC
1 TGGGGGGAATCGATTCCCC
*
4543418 TGGGGGGAATCGGTTCCCC
1 TGGGGGGAATCGATTCCCC
4543437 T
1 T
4543438 TCAACGGGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.10, C:0.26, G:0.38, T:0.26
Consensus pattern (19 bp):
TGGGGGGAATCGATTCCCC
Found at i:4547312 original size:22 final size:21
Alignment explanation
Indices: 4547270--4547309 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4547260 AAGACTATTT
*
4547270 TCATTTTTTAATTTTGAAATA
1 TCATTTTTTAATTTTAAAATA
4547291 TCATTTTTGT-ATTTTAAAA
1 TCATTTTT-TAATTTTAAAA
4547310 ATAAAGTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (21 bp):
TCATTTTTTAATTTTAAAATA
Found at i:4551536 original size:2 final size:2
Alignment explanation
Indices: 4551523--4551574 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
4551513 TATAACAAAA
*
4551523 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4551565 AT AT AT AT AT
1 AT AT AT AT AT
4551575 CATCATCAAC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4558504 original size:34 final size:34
Alignment explanation
Indices: 4558465--4558532 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
4558455 TTAACATAAT
4558465 TTCATCATCATTAATTATTTGGGTAAAGTACATA
1 TTCATCATCATTAATTATTTGGGTAAAGTACATA
4558499 TTCATCATCATTAATTATTTGGGTAAAGTACATA
1 TTCATCATCATTAATTATTTGGGTAAAGTACATA
4558533 AATGATTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (34 bp):
TTCATCATCATTAATTATTTGGGTAAAGTACATA
Found at i:4559130 original size:21 final size:21
Alignment explanation
Indices: 4559101--4559153 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
4559091 ATTCTGACTA
4559101 TCGCATTGCGA-TTTCCTAAAT
1 TCGCATTGCGATTTTCCT-AAT
*
4559122 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
*
4559143 TCGCAATGCGA
1 TCGCATTGCGA
4559154 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 22 0.79
22 6 0.21
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCTAAT
Found at i:4559168 original size:20 final size:20
Alignment explanation
Indices: 4559143--4559188 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
4559133 TTTTCCTAAT
*
4559143 TCGCAATGCGAATAC-GTAAA
1 TCGCAATGCAAAT-CTGTAAA
4559163 TCGCAATGCAAATCTGTAAA
1 TCGCAATGCAAATCTGTAAA
4559183 TCGCAA
1 TCGCAA
4559189 CGAGATTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (20 bp):
TCGCAATGCAAATCTGTAAA
Found at i:4559942 original size:60 final size:60
Alignment explanation
Indices: 4559843--4559994 Score: 223
Period size: 60 Copynumber: 2.5 Consensus size: 60
4559833 ATAAAATACG
* *
4559843 CGTTGCGATTTTACATATTGTCGTTGCGATTTACGGATACGCATTGCGATTTACATATTCT
1 CGTTGCGA-TTTACATATTCTCGTTGCGATTTACAGATACGCATTGCGATTTACATATTCT
* *
4559904 CGTTGCGATTTACATATTCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACATATTCTCGTTGCGATTTACAGATACGCATTGCGATTTACATATTCT
** * *
4559964 CGTTGCGATTTACGGATACGCGTTGCGATTT
1 CGTTGCGATTTACATATTCTCGTTGCGATTT
4559995 TACGTATTGT
Statistics
Matches: 83, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
60 75 0.90
61 8 0.10
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (60 bp):
CGTTGCGATTTACATATTCTCGTTGCGATTTACAGATACGCATTGCGATTTACATATTCT
Found at i:4560009 original size:41 final size:40
Alignment explanation
Indices: 4559864--4560111 Score: 248
Period size: 40 Copynumber: 6.2 Consensus size: 40
4559854 TACATATTGT
* * * * * * *
4559864 CGTTGCGATTTACGGATACGCATTGCGATTTACATATTCT
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACAGATACG
*
4559904 CGTTGCGATTTACATATTCTCGTTGCGATTTACAGATACG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACAGATACG
*
4559944 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACAGATACG
* *
4559984 CGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACG
1 CGTTGCGA-TTTACGTATTCTCGTTGCGATTTACAGATACG
* * * *
4560025 CGTTACGATTTTACGGATACTCGTTGCGATAGT-CAGA-ATCG
1 CGTTGCGA-TTTACGTATTCTCGTTGCGAT-TTACAGATA-CG
** * * * * *
4560066 CGTTGCGATTTATATGTTCGCGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACAGATACG
4560106 CGTTGC
1 CGTTGC
4560112 AATTCTGGAA
Statistics
Matches: 176, Mismatches: 27, Indels: 10
0.83 0.13 0.05
Matches are distributed among these distances:
39 1 0.01
40 105 0.60
41 69 0.39
42 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (40 bp):
CGTTGCGATTTACGTATTCTCGTTGCGATTTACAGATACG
Found at i:4560039 original size:21 final size:20
Alignment explanation
Indices: 4559838--4560054 Score: 197
Period size: 20 Copynumber: 10.7 Consensus size: 20
4559828 TGAAAATAAA
4559838 ATACGCGTTGCGATTTTAC--
1 ATACGCGTTGCGA-TTTACGG
*
4559857 ATATTGTCGTTGCGATTTACGG
1 ATA-CG-CGTTGCGATTTACGG
* **
4559879 ATACGCATTGCGATTTACAT
1 ATACGCGTTGCGATTTACGG
* * **
4559899 ATTCTCGTTGCGATTTACAT
1 ATACGCGTTGCGATTTACGG
* * *
4559919 ATTCTCGTTGCGATTTACAG
1 ATACGCGTTGCGATTTACGG
*
4559939 ATACGCGTTGCGATTTACGT
1 ATACGCGTTGCGATTTACGG
* *
4559959 ATTCTCGTTGCGATTTACGG
1 ATACGCGTTGCGATTTACGG
*
4559979 ATACGCGTTGCGATTTTACGT
1 ATACGCGTTGCGA-TTTACGG
*
4560000 AT-TGTCGTTGCGATTTACGG
1 ATACG-CGTTGCGATTTACGG
*
4560020 ATACGCGTTACGATTTTACGG
1 ATACGCGTTGCGA-TTTACGG
*
4560041 ATACTCGTTGCGAT
1 ATACGCGTTGCGAT
4560055 AGTCAGAATC
Statistics
Matches: 165, Mismatches: 25, Indels: 15
0.80 0.12 0.07
Matches are distributed among these distances:
19 3 0.02
20 115 0.70
21 44 0.27
22 3 0.02
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (20 bp):
ATACGCGTTGCGATTTACGG
Found at i:4560070 original size:61 final size:60
Alignment explanation
Indices: 4559942--4560077 Score: 157
Period size: 61 Copynumber: 2.2 Consensus size: 60
4559932 TTTACAGATA
* * * * * * *
4559942 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTAT
1 CGCGTTGCGATTTACGGATACGCGTTACGATTTACGGATACGCGTTGCGATGTCACGAAT
* *
4560002 TGTCGTTGCGATTTACGGATACGCGTTACGATTTTACGGATACTCGTTGCGATAGTCA-GAAT
1 CG-CGTTGCGATTTACGGATACGCGTTACGA-TTTACGGATACGCGTTGCGAT-GTCACGAAT
4560064 CGCGTTGCGATTTA
1 CGCGTTGCGATTTA
4560078 TATGTTCGCG
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
60 1 0.02
61 36 0.57
62 24 0.38
63 2 0.03
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTACGATTTACGGATACGCGTTGCGATGTCACGAAT
Found at i:4560086 original size:20 final size:20
Alignment explanation
Indices: 4560063--4560111 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
4560053 ATAGTCAGAA
*
4560063 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
4560083 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
4560103 TCGCGTTGC
1 TCGCGTTGC
4560112 AATTCTGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.12, C:0.20, G:0.24, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:4562452 original size:29 final size:29
Alignment explanation
Indices: 4562407--4562465 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
4562397 CACTAAACTG
*
4562407 TAATGAAGTTGTATAAGAA-TCAATGAAAC
1 TAATGAAGCTGTATAAGAAGT-AATGAAAC
*
4562436 TAATGAAGCTGTCTAAGAAGTAATGAAAC
1 TAATGAAGCTGTATAAGAAGTAATGAAAC
4562465 T
1 T
4562466 GAAGTTGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 26 0.96
30 1 0.04
ACGTcount: A:0.46, C:0.08, G:0.19, T:0.27
Consensus pattern (29 bp):
TAATGAAGCTGTATAAGAAGTAATGAAAC
Found at i:4564484 original size:18 final size:18
Alignment explanation
Indices: 4564461--4564496 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
4564451 CTTAAAAAAC
4564461 CCCTAAACCCGACCCGAA
1 CCCTAAACCCGACCCGAA
4564479 CCCTAAACCCGACCCGAA
1 CCCTAAACCCGACCCGAA
4564497 TATCAAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.50, G:0.11, T:0.06
Consensus pattern (18 bp):
CCCTAAACCCGACCCGAA
Found at i:4564860 original size:24 final size:25
Alignment explanation
Indices: 4564831--4564879 Score: 91
Period size: 24 Copynumber: 2.0 Consensus size: 25
4564821 AGGTTAATAT
4564831 ATTATTTAAAATTTT-AAAATAAAA
1 ATTATTTAAAATTTTAAAAATAAAA
4564855 ATTATTTAAAATTTTAAAAATAAAA
1 ATTATTTAAAATTTTAAAAATAAAA
4564880 GTATTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
ATTATTTAAAATTTTAAAAATAAAA
Found at i:4564884 original size:24 final size:24
Alignment explanation
Indices: 4564833--4564889 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
4564823 GTTAATATAT
*
4564833 TATTTAAAATTTTAAAATAAAAAT
1 TATTTAAAATTTTAAAATAAAAAG
4564857 TATTTAAAATTTTAAAA-ATAAAAG
1 TATTTAAAATTTTAAAATA-AAAAG
*
4564881 TATTAAAAA
1 TATTTAAAA
4564890 GAAGTAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 1 0.03
24 29 0.97
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (24 bp):
TATTTAAAATTTTAAAATAAAAAG
Found at i:4565673 original size:47 final size:48
Alignment explanation
Indices: 4565621--4565711 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 48
4565611 CTGCTTAGAC
* * *
4565621 TCTAATTAAGTTATCTCGTTAATATCTTGAATCG-AGTTAAATTGAAA
1 TCTAATTAAGTTACCTCGTTAAGATCTTGAATCGAAATTAAATTGAAA
*
4565668 TCTAATTAAGTTACCTCGTTAAGATCTTGAGTCGAAATTAAATT
1 TCTAATTAAGTTACCTCGTTAAGATCTTGAATCGAAATTAAATT
4565712 CGAGTTGAGC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 31 0.79
48 8 0.21
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (48 bp):
TCTAATTAAGTTACCTCGTTAAGATCTTGAATCGAAATTAAATTGAAA
Found at i:4572507 original size:34 final size:34
Alignment explanation
Indices: 4572424--4572508 Score: 86
Period size: 34 Copynumber: 2.5 Consensus size: 34
4572414 AGATTTAACC
* *
4572424 AATATATATATATATATATTAATATTCAAATTTA
1 AATAGATATATATATATATTAATATTAAAATTTA
*
4572458 AATAGATA-ATGATATATTTTAAT-TTAAAATATTCA
1 AATAGATATAT-ATATATATTAATATTAAAAT-TT-A
*
4572493 AA-AGGTATATATATAT
1 AATAGATATATATATAT
4572509 CTTTTAATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 8 0.19
34 30 0.70
35 5 0.12
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (34 bp):
AATAGATATATATATATATTAATATTAAAATTTA
Found at i:4572516 original size:70 final size:68
Alignment explanation
Indices: 4572428--4572631 Score: 208
Period size: 64 Copynumber: 3.1 Consensus size: 68
4572418 TTAACCAATA
* *
4572428 TATATATATATATATTAATATTCAAATTTAAATAGATAATGATATATTTTAATTTAAAATATTCA
1 TATATATATATCTATTAATATTCAAA-TTAAATAGATAAT-ATATATTTTAATTTGAAATATTCA
4572493 AAAGG
64 AAAGG
* * *
4572498 TATATATATATCTTTTAATATGCAACTTAAATAG---ATAT-TATTTTAATTTGAAATATTCAAA
1 TATATATATATCTATTAATATTCAAATTAAATAGATAATATATATTTTAATTTGAAATATTCAAA
4572559 A-G
66 AGG
* * * * * * *
4572561 AACA-AT-TATCCTACTGATATTCAAATTAAAGAGATAA-ATATCTTTTAATTTGGAATATTCAA
1 TATATATATAT-CTATTAATATTCAAATTAAATAGATAATATATATTTTAATTTGAAATATTCAA
4572623 AAGG
65 AAGG
*
4572627 GATAT
1 TATAT
4572632 GAATTTAATT
Statistics
Matches: 110, Mismatches: 17, Indels: 17
0.76 0.12 0.12
Matches are distributed among these distances:
61 3 0.03
62 19 0.17
63 3 0.03
64 25 0.23
65 25 0.23
66 5 0.05
69 8 0.07
70 22 0.20
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (68 bp):
TATATATATATCTATTAATATTCAAATTAAATAGATAATATATATTTTAATTTGAAATATTCAAA
AGG
Found at i:4576297 original size:34 final size:34
Alignment explanation
Indices: 4576249--4576350 Score: 111
Period size: 34 Copynumber: 3.0 Consensus size: 34
4576239 ATTTACTCAA
*
4576249 AATATATATCTTTTAATATTTAAATTTAAATAGAT
1 AATA-ATATTTTTTAATATTTAAATTTAAATAGAT
*
4576284 AATAATATTTTTTAAT-TTAAAATATTCAAA-AGAT
1 AATAATATTTTTTAATATTTAAAT-TT-AAATAGAT
* *
4576318 -ATAAATACTTTTTAATATTTAAACTTAAATAGA
1 AAT-AATATTTTTTAATATTTAAATTTAAATAGA
4576351 GTTGTTTTAA
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
33 11 0.19
34 34 0.60
35 12 0.21
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (34 bp):
AATAATATTTTTTAATATTTAAATTTAAATAGAT
Found at i:4576359 original size:62 final size:63
Alignment explanation
Indices: 4576293--4576413 Score: 183
Period size: 63 Copynumber: 1.9 Consensus size: 63
4576283 TAATAATATT
*
4576293 TTTTAATTTAAAATATTCAAAA-GATATAAATACT-TTTTAATATTTAAACTTAAATAGAGTTG
1 TTTTAATTTAAAATATTCAAAAGGATATAAATA-TATTTTAATATTCAAACTTAAATAGAGTTG
* * *
4576355 TTTTAATTTGAAATATTCAAAAGGATATAATTATATTTTAATATTCAAAGTTAAATAGA
1 TTTTAATTTAAAATATTCAAAAGGATATAAATATATTTTAATATTCAAACTTAAATAGA
4576414 TAATAAATGT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
62 22 0.42
63 31 0.58
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.43
Consensus pattern (63 bp):
TTTTAATTTAAAATATTCAAAAGGATATAAATATATTTTAATATTCAAACTTAAATAGAGTTG
Found at i:4577879 original size:20 final size:19
Alignment explanation
Indices: 4577856--4577922 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 19
4577846 CTTTCGATAC
*
4577856 GAATACCAAGTCTTCGGTAT
1 GAATACCAAG-CTTCAGTAT
* *
4577876 GAATACCTAACCTTTAGTAT
1 GAATACC-AAGCTTCAGTAT
*
4577896 GGATACCAAGCTTTCAGTAT
1 GAATACCAAGC-TTCAGTAT
4577916 GAATACC
1 GAATACC
4577923 TAATCTTTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 3 0.08
20 33 0.87
21 2 0.05
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (19 bp):
GAATACCAAGCTTCAGTAT
Found at i:4577902 original size:40 final size:40
Alignment explanation
Indices: 4577858--4577935 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 40
4577848 TTCGATACGA
*
4577858 ATACCAAG-TCTTCGGTATGAATACCTAACCTTTAGTATGG
1 ATACCAAGCT-TTCAGTATGAATACCTAACCTTTAGTATGG
*
4577898 ATACCAAGCTTTCAGTATGAATACCTAATCTTTAGTAT
1 ATACCAAGCTTTCAGTATGAATACCTAACCTTTAGTAT
4577936 ACATACTAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 34 0.97
41 1 0.03
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (40 bp):
ATACCAAGCTTTCAGTATGAATACCTAACCTTTAGTATGG
Done.