Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008094.1 Hibiscus syriacus cultivar Beakdansim tig00110610_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: 9952466
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 27 of 43
Found at i:5582703 original size:23 final size:23
Alignment explanation
Indices: 5582673--5582722 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
5582663 TCAAAGGGAA
*
5582673 AAAATAAAATAACA-TAAAAAAAT
1 AAAAT-AAATAAAAGTAAAAAAAT
*
5582696 AAAATAAATAAAAGTAATAAAAT
1 AAAATAAATAAAAGTAAAAAAAT
5582719 AAAA
1 AAAA
5582723 ACATAATGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (23 bp):
AAAATAAATAAAAGTAAAAAAAT
Found at i:5584975 original size:106 final size:106
Alignment explanation
Indices: 5584790--5585240 Score: 789
Period size: 106 Copynumber: 4.3 Consensus size: 106
5584780 TTGAAATTGG
* *
5584790 ATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGG
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGG
5584855 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
** *
5584896 ATATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGGTTATTGACAACCAGCGG
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGG
5584961 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* *
5585002 ATATCCTTCGTTGTGAAGTCGAAATTGGCTCTGAAATTGGGAAA-TGTTTATTGACAACCAGCGG
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGG
5585066 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* *
5585107 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-AGGAAATTATTTGTTGACAACCAGCG
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA-GAAATTGTTTATTGACAACCAGCG
5585171 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
65 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
5585213 ATATCCTTCGTTGCGAAGTTGAAATTGG
1 ATATCCTTCGTTGTGAAGTTGAAATTGG
5585241 GAAGTTGTTT
Statistics
Matches: 328, Mismatches: 15, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
105 101 0.31
106 227 0.69
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (106 bp):
ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGG
TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
Found at i:5585117 original size:105 final size:105
Alignment explanation
Indices: 5584790--5586068 Score: 1960
Period size: 105 Copynumber: 12.2 Consensus size: 105
5584780 TTGAAATTGG
* * * *
5584790 ATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGG
1 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATGTTTATTGACAACCAGCGG
5584855 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
65 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* * *
5584896 ATATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGGTTATTGACAACCAGCGG
1 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TGTTTATTGACAACCAGCGG
5584961 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
65 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* *
5585002 ATATCCTTCGTTGTGAAGTCGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGT
1 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGT
5585067 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
66 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* * * *
5585107 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTATTTGTTGACAACCAGCGG
1 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TGTTTATTGACAACCAGCGG
5585172 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
65 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* * *
5585213 ATATCCTTCGTTGCGAAGTTGAAATTGG----G-AA----G--TTGTTTATTGACAACCAGCGGT
1 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGT
5585267 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
66 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* *
5585307 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAATTTTTTTATTGACAACCAGCGG
1 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATGTTTATTGACAACCAGCGG
* *
5585372 TCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTTGAGTCCA
65 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* * *
5585413 ATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAGT-TGTTGTTGACAACCAGCGG
1 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGT-TTATTGACAACCAGCGG
*
5585477 TCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
65 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
5585518 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGT-TGTTATTGACAACCAGCGG
1 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGT-TTATTGACAACCAGCGG
*
5585582 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCA
65 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* *
5585623 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGT-TGTTGTTGACAACCAGCGG
1 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGT-TTATTGACAACCAGCGG
*
5585687 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCA
65 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* * *
5585728 ATATCTTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGT-TGTTGTTGACAACCAGCGG
1 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGT-TTATTGACAACCAGCGG
*
5585792 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCA
65 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* * *
5585833 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGT
1 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGT
5585898 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
66 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* * * *
5585938 ATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGT
1 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGT
* *
5586003 CCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTTGGA-TTCA
66 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TGGAGTCCA
* * *
5586043 AGATCCTTCGTTGAGAAGTTGAAATT
1 ATATCCTTCGCTGTGAAGTTGAAATT
5586069 TACTCTCGAG
Statistics
Matches: 1108, Mismatches: 48, Indels: 35
0.93 0.04 0.03
Matches are distributed among these distances:
94 85 0.08
97 1 0.00
98 1 0.00
99 2 0.00
101 2 0.00
102 1 0.00
103 1 0.00
104 1 0.00
105 682 0.62
106 332 0.30
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGT
CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
Found at i:5589755 original size:18 final size:17
Alignment explanation
Indices: 5589734--5589784 Score: 75
Period size: 18 Copynumber: 2.9 Consensus size: 17
5589724 AATCAAAGGG
5589734 AAAAAATAAAATAACATA
1 AAAAAATAAAATAA-ATA
5589752 AAAAAATAAAATAAATA
1 AAAAAATAAAATAAATA
*
5589769 AAAGTAATAAAATAAA
1 AAA-AAATAAAATAAA
5589785 AACATAATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 6 0.19
18 25 0.81
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (17 bp):
AAAAAATAAAATAAATA
Found at i:5589762 original size:23 final size:23
Alignment explanation
Indices: 5589736--5589785 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
5589726 TCAAAGGGAA
*
5589736 AAAATAAAATAACA-TAAAAAAAT
1 AAAAT-AAATAAAAGTAAAAAAAT
*
5589759 AAAATAAATAAAAGTAATAAAAT
1 AAAATAAATAAAAGTAAAAAAAT
5589782 AAAA
1 AAAA
5589786 ACATAATGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (23 bp):
AAAATAAATAAAAGTAAAAAAAT
Found at i:5600763 original size:31 final size:31
Alignment explanation
Indices: 5600728--5600789 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
5600718 CGTTGGAGAC
* *
5600728 CATATTGCAAATGGACTAAATGTTGGGGGAT
1 CATATTGCAAACGAACTAAATGTTGGGGGAT
*
5600759 CATATTGTAAACGAACTAAATGTTGGGGGAT
1 CATATTGCAAACGAACTAAATGTTGGGGGAT
5600790 TGTATTACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (31 bp):
CATATTGCAAACGAACTAAATGTTGGGGGAT
Found at i:5603989 original size:21 final size:21
Alignment explanation
Indices: 5603926--5604039 Score: 92
Period size: 21 Copynumber: 5.6 Consensus size: 21
5603916 TTATTTTTAT
*
5603926 TTTAAGGTTTAGGATTTAAGG-
1 TTTAGGGTTTAGGATTT-AGGA
* ** *
5603947 TTT-GGGGTT-GGGGTTATGA
1 TTTAGGGTTTAGGATTTAGGA
*
5603966 TTTAGGGTTTAGGACTTAGGA
1 TTTAGGGTTTAGGATTTAGGA
** *
5603987 TTTAATGTTTAGGATTTATGA
1 TTTAGGGTTTAGGATTTAGGA
*
5604008 TTTAGGGTTTA-GATTTAGAA
1 TTTAGGGTTTAGGATTTAGGA
*
5604028 TTTAGGATTTAG
1 TTTAGGGTTTAG
5604040 AGTTTAAATT
Statistics
Matches: 71, Mismatches: 18, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
18 2 0.03
19 7 0.10
20 26 0.37
21 36 0.51
ACGTcount: A:0.25, C:0.01, G:0.30, T:0.45
Consensus pattern (21 bp):
TTTAGGGTTTAGGATTTAGGA
Found at i:5603990 original size:14 final size:14
Alignment explanation
Indices: 5603964--5604039 Score: 75
Period size: 14 Copynumber: 5.5 Consensus size: 14
5603954 TTGGGGTTAT
*
5603964 GATTTAGGGTTTAG
1 GATTTAGGATTTAG
* *
5603978 GACTTAGGATTTAAT
1 GATTTAGGATTT-AG
*
5603993 G-TTTAGGATTTAT
1 GATTTAGGATTTAG
*
5604006 GATTTAGGGTTTA-
1 GATTTAGGATTTAG
*
5604019 GATTTAGAATTTAG
1 GATTTAGGATTTAG
5604033 GATTTAG
1 GATTTAG
5604040 AGTTTAAATT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
13 14 0.27
14 36 0.69
15 2 0.04
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.45
Consensus pattern (14 bp):
GATTTAGGATTTAG
Found at i:5604036 original size:27 final size:27
Alignment explanation
Indices: 5603994--5604045 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
5603984 GGATTTAATG
* * *
5603994 TTTAGGATTTATGATTTAGGGTTTAGA
1 TTTAGAATTTAGGATTTAGAGTTTAGA
5604021 TTTAGAATTTAGGATTTAGAGTTTA
1 TTTAGAATTTAGGATTTAGAGTTTA
5604046 AATTAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (27 bp):
TTTAGAATTTAGGATTTAGAGTTTAGA
Found at i:5604040 original size:14 final size:13
Alignment explanation
Indices: 5603994--5604045 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
5603984 GGATTTAATG
*
5603994 TTTAGGATTTATGA
1 TTTAGAATTTA-GA
**
5604008 TTTAGGGTTTAGA
1 TTTAGAATTTAGA
5604021 TTTAGAATTTAGGA
1 TTTAGAATTTA-GA
*
5604035 TTTAGAGTTTA
1 TTTAGAATTTA
5604046 AATTAAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
13 11 0.33
14 22 0.67
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (13 bp):
TTTAGAATTTAGA
Found at i:5604049 original size:20 final size:20
Alignment explanation
Indices: 5603994--5604049 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
5603984 GGATTTAATG
*
5603994 TTTAGGATTTATG-ATTTAGGG
1 TTTA-GATTTA-GAATTTAGGA
5604015 TTTAGATTTAGAATTTAGGA
1 TTTAGATTTAGAATTTAGGA
5604035 TTTAGAGTTTA-AATT
1 TTTAGA-TTTAGAATT
5604050 AAATAAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 1 0.03
20 23 0.72
21 8 0.25
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.48
Consensus pattern (20 bp):
TTTAGATTTAGAATTTAGGA
Found at i:5604172 original size:18 final size:17
Alignment explanation
Indices: 5604136--5604177 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
5604126 TTATCTTAAT
*
5604136 AAGAAAATAAAAAATTA
1 AAGAAAAGAAAAAATTA
5604153 AATGAAAAGAAAGAAA-TA
1 AA-GAAAAGAAA-AAATTA
5604171 AAGAAAA
1 AAGAAAA
5604178 TGATAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 12 0.55
19 3 0.14
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (17 bp):
AAGAAAAGAAAAAATTA
Found at i:5604741 original size:19 final size:19
Alignment explanation
Indices: 5604693--5604743 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
5604683 GTATATTGTT
*
5604693 ATTTCTTTTA-TTTAATAA
1 ATTTATTTTATTTTAATAA
*
5604711 ATTTATTATTATTTTACTAA
1 ATTTATT-TTATTTTAATAA
5604731 ATATT-TTTTATTT
1 AT-TTATTTTATTT
5604744 GATTGTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 6 0.21
19 9 0.32
20 11 0.39
21 2 0.07
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTTATTTTATTTTAATAA
Found at i:5604949 original size:14 final size:14
Alignment explanation
Indices: 5604930--5604956 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5604920 ATTTAAATTG
5604930 TTAGAATTTATTTT
1 TTAGAATTTATTTT
5604944 TTAGAATTTATTT
1 TTAGAATTTATTT
5604957 AAATGGGTTT
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:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (14 bp):
TTAGAATTTATTTT
Found at i:5605958 original size:2 final size:2
Alignment explanation
Indices: 5605951--5606008 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
5605941 TTGGTAAGAA
5605951 AT AT AT AT AT AT AT AT AT A- 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
5605992 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
5606009 GTTCAAATGG
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5606657 original size:21 final size:21
Alignment explanation
Indices: 5606605--5606658 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
5606595 CATCTTAGCT
* *
5606605 GGTTTAGATGCCATATTCGCC
1 GGTTTAGATGCCATACTCACC
* * *
5606626 AGTTCAAATGCCATACTCACC
1 GGTTTAGATGCCATACTCACC
5606647 GGTTTAGATGCC
1 GGTTTAGATGCC
5606659 TCCACCGCAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (21 bp):
GGTTTAGATGCCATACTCACC
Found at i:5607040 original size:15 final size:14
Alignment explanation
Indices: 5606991--5607046 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 14
5606981 ATGACATGAA
5606991 TTATGTTTTTACTTT
1 TTATGTTTTTA-TTT
5607006 TTAT-TTGGTTTATTT
1 TTATGTT--TTTATTT
5607021 ATTATGTTTTTATATT
1 -TTATGTTTTTAT-TT
*
5607037 TTATATTTTT
1 TTATGTTTTT
5607047 TGTCTTTATA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 2 0.06
15 21 0.60
16 10 0.29
17 2 0.06
ACGTcount: A:0.18, C:0.02, G:0.07, T:0.73
Consensus pattern (14 bp):
TTATGTTTTTATTT
Found at i:5616389 original size:20 final size:20
Alignment explanation
Indices: 5616352--5616390 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5616342 AGATTGAGTG
* * *
5616352 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
5616372 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
5616391 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:5616576 original size:21 final size:21
Alignment explanation
Indices: 5616550--5616589 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5616540 CAGAACCCCA
*
5616550 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
5616571 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
5616590 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:5616618 original size:20 final size:21
Alignment explanation
Indices: 5616572--5616632 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
5616562 TTCCCCTGTG
5616572 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
5616595 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
5616615 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
5616633 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:5654983 original size:26 final size:26
Alignment explanation
Indices: 5654954--5655014 Score: 99
Period size: 25 Copynumber: 2.4 Consensus size: 26
5654944 TTTATAGCCT
*
5654954 TTGTTTTGCTTATAGAGAAATTCACA
1 TTGTTTTACTTATAGAGAAATTCACA
5654980 TTG-TTTACTTATAGAGAAATTCACA
1 TTGTTTTACTTATAGAGAAATTCACA
5655005 TTG-TTTACTT
1 TTGTTTTACTT
5655015 CTCCCTCTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 31 0.91
26 3 0.09
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (26 bp):
TTGTTTTACTTATAGAGAAATTCACA
Found at i:5654992 original size:25 final size:25
Alignment explanation
Indices: 5654962--5655014 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
5654952 CTTTGTTTTG
5654962 CTTATAGAGAAATTCACATTGTTTA
1 CTTATAGAGAAATTCACATTGTTTA
5654987 CTTATAGAGAAATTCACATTGTTTA
1 CTTATAGAGAAATTCACATTGTTTA
5655012 CTT
1 CTT
5655015 CTCCCTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (25 bp):
CTTATAGAGAAATTCACATTGTTTA
Found at i:5659703 original size:90 final size:89
Alignment explanation
Indices: 5659593--5659759 Score: 316
Period size: 90 Copynumber: 1.9 Consensus size: 89
5659583 TAATCCCGGA
*
5659593 TATTTAATTTTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTTTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGAT
5659658 TATGGTAACTTGGATATAATTGGAT
65 TATGGTAACTTGGATATAATTGGAT
5659683 TATTAAATTTTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
1 TATTAAATTTTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
5659748 ATGGTAACTTGG
66 ATGGTAACTTGG
5659760 CTTTAAAAGG
Statistics
Matches: 76, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
89 25 0.33
90 51 0.67
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.43
Consensus pattern (89 bp):
TATTAAATTTTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
ATGGTAACTTGGATATAATTGGAT
Found at i:5669435 original size:49 final size:50
Alignment explanation
Indices: 5669352--5669462 Score: 161
Period size: 49 Copynumber: 2.2 Consensus size: 50
5669342 TACTATGCCT
* * *
5669352 CCTTAGTGGTGCGAGTTTACTAATCGGAGGACTTGATATTATAT-ATTAG
1 CCTTAGTGGCGCGAGTGTACTAATCGGAGCACTTGATATTATATGATTAG
* * *
5669401 CCTTAGTGGCGCGAGTGTACTGATTGGAGCACTTGATATTATATGTTTAG
1 CCTTAGTGGCGCGAGTGTACTAATCGGAGCACTTGATATTATATGATTAG
5669451 CCTTAGTGGCGC
1 CCTTAGTGGCGC
5669463 CGGACTACAT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
49 39 0.71
50 16 0.29
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.35
Consensus pattern (50 bp):
CCTTAGTGGCGCGAGTGTACTAATCGGAGCACTTGATATTATATGATTAG
Found at i:5672442 original size:17 final size:17
Alignment explanation
Indices: 5672399--5672442 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
5672389 AAAAAATAAC
* *
5672399 ATATATATATGTATTTA
1 ATATATATATATATCTA
*
5672416 ATATAAATATATATCTA
1 ATATATATATATATCTA
*
5672433 ATATTTATAT
1 ATATATATAT
5672443 GATTAATGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (17 bp):
ATATATATATATATCTA
Found at i:5680231 original size:12 final size:11
Alignment explanation
Indices: 5680214--5680247 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
5680204 ACATTTAATA
5680214 TATTTTATATTT
1 TATTTTAT-TTT
5680226 TATTTTATTTT
1 TATTTTATTTT
*
5680237 CATTTTATTTT
1 TATTTTATTTT
5680248 AATATAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (11 bp):
TATTTTATTTT
Found at i:5681588 original size:72 final size:77
Alignment explanation
Indices: 5681510--5681650 Score: 202
Period size: 79 Copynumber: 1.9 Consensus size: 77
5681500 CTTTATAATT
*
5681510 TAGGATTTTTAATTTGATTA-TTTTA-TTA-T-T-ATATTTTATTTAGGAATTAGTTATTTTATT
1 TAGGATTTTTAATTTGATTATTTTTATTTATTATAATATTTTATATAGGAATTAGTTATTTTATT
5681570 TAATAGTCTCGA
66 TAATAGTCTCGA
* *
5681582 TAGGATTTTTAATTTGATTATTTTTATCTTTATTATAATATTTTATATAGGAATTATTTATTTTG
1 TAGGATTTTTAATTTGATTATTTTTA--TTTATTATAATATTTTATATAGGAATTAGTTATTTTA
5681647 TTTA
64 TTTA
5681651 CTTAGAAAAC
Statistics
Matches: 59, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
72 20 0.34
73 5 0.08
76 3 0.05
77 1 0.02
78 1 0.02
79 29 0.49
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.59
Consensus pattern (77 bp):
TAGGATTTTTAATTTGATTATTTTTATTTATTATAATATTTTATATAGGAATTAGTTATTTTATT
TAATAGTCTCGA
Found at i:5683954 original size:71 final size:74
Alignment explanation
Indices: 5683870--5684006 Score: 199
Period size: 71 Copynumber: 1.9 Consensus size: 74
5683860 CAAATTTTAA
* * *
5683870 TTTCACTTGAAAAAAAAATTCATCTAACTCGAGATAGTTTT-CTC-AAACAACATTTTATCTCAC
1 TTTCACTTGAAAAAAAAATTCATCTAACTCGAGAAAGTTTTCCTCAAAACAAAATTTAATCTCAC
5683933 TTAAGATAG
66 TTAAGATAG
* * *
5683942 TTTCTCTT-AAAAAAAAATTCATGTCACTCGAGAAAGTTTTCCTCAAAACAAAATTTAATCTCAC
1 TTTCACTTGAAAAAAAAATTCATCTAACTCGAGAAAGTTTTCCTCAAAACAAAATTTAATCTCAC
5684006 T
66 T
5684007 ACAAATAGTT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
71 29 0.51
72 10 0.18
73 18 0.32
ACGTcount: A:0.39, C:0.19, G:0.07, T:0.34
Consensus pattern (74 bp):
TTTCACTTGAAAAAAAAATTCATCTAACTCGAGAAAGTTTTCCTCAAAACAAAATTTAATCTCAC
TTAAGATAG
Found at i:5683980 original size:36 final size:36
Alignment explanation
Indices: 5683870--5684006 Score: 107
Period size: 36 Copynumber: 3.8 Consensus size: 36
5683860 CAAATTTTAA
* *
5683870 TTTCACTTGAAAAAAAAATTCATCTAACTCGAGATAG
1 TTTCTCTT-AAAAAAAAATTCATCTCACTCGAGATAG
* * * * * **
5683907 TTT-TCTCAAACAACATTTTATCTCACTTAAGATAG
1 TTTCTCTTAAAAAAAAATTCATCTCACTCGAGATAG
* *
5683942 TTTCTCTTAAAAAAAAATTCATGTCACTCGAGAAAG
1 TTTCTCTTAAAAAAAAATTCATCTCACTCGAGATAG
* * *
5683978 TTT-TCCTCAAAACAAAATTTAATCTCACT
1 TTTCT-CTTAAAA-AAAAATTCATCTCACT
5684007 ACAAATAGTT
Statistics
Matches: 75, Mismatches: 22, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
35 25 0.33
36 34 0.45
37 16 0.21
ACGTcount: A:0.39, C:0.19, G:0.07, T:0.34
Consensus pattern (36 bp):
TTTCTCTTAAAAAAAAATTCATCTCACTCGAGATAG
Found at i:5686854 original size:17 final size:17
Alignment explanation
Indices: 5686808--5686871 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
5686798 AGTAGATATT
* **
5686808 TTAATTAATGAACCAAT
1 TTAATTAATGAACTAGC
*
5686825 TTAAATGAATGAACTAGC
1 TT-AATTAATGAACTAGC
5686843 TTAATTAATGAACTAGC
1 TTAATTAATGAACTAGC
*
5686860 TTTATTGAATGA
1 TTAATT-AATGA
5686872 TACAACATAC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
17 21 0.54
18 18 0.46
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (17 bp):
TTAATTAATGAACTAGC
Found at i:5691553 original size:18 final size:19
Alignment explanation
Indices: 5691521--5691563 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
5691511 TTTAAGTAGT
5691521 AATAAAAACGATTAAA-TA
1 AATAAAAACGATTAAAGTA
* *
5691539 AATAAAAATGGTTAAAGTA
1 AATAAAAACGATTAAAGTA
5691558 AA-AAAA
1 AATAAAA
5691564 TAAGAGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.21
Consensus pattern (19 bp):
AATAAAAACGATTAAAGTA
Found at i:5704176 original size:28 final size:27
Alignment explanation
Indices: 5704145--5704203 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
5704135 TATTCCAGGG
* *
5704145 TTTAGAGGTACTTTAGGTTATTTTACAC
1 TTTAGAGGCA-TTTAGGTCATTTTACAC
* *
5704173 TTTAGTGGCATTTTGGTCATTTTACAC
1 TTTAGAGGCATTTAGGTCATTTTACAC
5704200 TTTA
1 TTTA
5704204 TGGGTAATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.22, C:0.12, G:0.17, T:0.49
Consensus pattern (27 bp):
TTTAGAGGCATTTAGGTCATTTTACAC
Found at i:5718156 original size:19 final size:19
Alignment explanation
Indices: 5718129--5718170 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5718119 TCATTCGGCC
5718129 AAAAGCATGTACTTTAATT
1 AAAAGCATGTACTTTAATT
* * *
5718148 AAAATCATGTATTTTCATT
1 AAAAGCATGTACTTTAATT
5718167 AAAA
1 AAAA
5718171 AATCATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (19 bp):
AAAAGCATGTACTTTAATT
Found at i:5719652 original size:30 final size:30
Alignment explanation
Indices: 5719583--5719640 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
5719573 ATTTAAGGCA
5719583 AAAATGTTTTTGGACTTGAATTGAATTTGC
1 AAAATGTTTTTGGACTTGAATTGAATTTGC
*
5719613 AAAATGTTTTTGGATTTGAATTGAATTT
1 AAAATGTTTTTGGACTTGAATTGAATTT
5719641 ATTCAAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTGC
Found at i:5719748 original size:21 final size:21
Alignment explanation
Indices: 5719722--5719779 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
5719712 AGGGTGTCAA
*
5719722 AGTGCATCCATGCATCCTTGC
1 AGTGCATCCATGCATCCCTGC
5719743 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
*
5719764 AGTGCATCGATGCATC
1 AGTGCATCCATGCATC
5719780 TGCACTAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.21, C:0.33, G:0.21, T:0.26
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:5719811 original size:20 final size:22
Alignment explanation
Indices: 5719766--5719821 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 22
5719756 ATCCCTGCAG
*
5719766 TGCATCGATGCATCTGCACTAA
1 TGCATCGATGCATCAGCACTAA
*
5719788 TGCATCGATGCATCAG-GC-AA
1 TGCATCGATGCATCAGCACTAA
*
5719808 TGCATCCATGCATC
1 TGCATCGATGCATC
5719822 CAAACATCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 15 0.48
21 1 0.03
22 15 0.48
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.25
Consensus pattern (22 bp):
TGCATCGATGCATCAGCACTAA
Found at i:5719870 original size:8 final size:8
Alignment explanation
Indices: 5719859--5719904 Score: 55
Period size: 8 Copynumber: 6.2 Consensus size: 8
5719849 ATGCATCCTT
5719859 TCCATGCA
1 TCCATGCA
5719867 TCCATGCA
1 TCCATGCA
*
5719875 TCGATGCA
1 TCCATGCA
5719883 T-CATG--
1 TCCATGCA
5719888 -CCATGCA
1 TCCATGCA
5719895 TCCATGCA
1 TCCATGCA
5719903 TC
1 TC
5719905 AAGGCTGCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
5 4 0.12
7 3 0.09
8 25 0.78
ACGTcount: A:0.24, C:0.35, G:0.15, T:0.26
Consensus pattern (8 bp):
TCCATGCA
Found at i:5719893 original size:20 final size:20
Alignment explanation
Indices: 5719868--5719905 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5719858 TTCCATGCAT
*
5719868 CCATGCATCGATGCATCATG
1 CCATGCATCCATGCATCATG
5719888 CCATGCATCCATGCATCA
1 CCATGCATCCATGCATCA
5719906 AGGCTGCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.16, T:0.24
Consensus pattern (20 bp):
CCATGCATCCATGCATCATG
Found at i:5719895 original size:12 final size:13
Alignment explanation
Indices: 5719849--5719901 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
5719839 TAGTGCATCG
* *
5719849 ATGCATCCTTTCC
1 ATGCATCCATGCC
5719862 ATGCATCCATGCATC
1 ATGCATCCATGC--C
5719877 GATGCAT-CATGCC
1 -ATGCATCCATGCC
5719890 ATGCATCCATGC
1 ATGCATCCATGC
5719902 ATCAAGGCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
12 6 0.18
13 16 0.47
15 6 0.18
16 6 0.18
ACGTcount: A:0.23, C:0.34, G:0.15, T:0.28
Consensus pattern (13 bp):
ATGCATCCATGCC
Found at i:5720302 original size:34 final size:32
Alignment explanation
Indices: 5720259--5720327 Score: 102
Period size: 34 Copynumber: 2.1 Consensus size: 32
5720249 TTTTGTAAAT
*
5720259 GGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTAG
1 GGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTAG
*
5720293 GGAAAGGTTCTAGTTTAGCCCGGAAAAACTAG
1 GGAAAGGTTCTAGCTTAGCCCGGAAAAACTAG
5720325 GGA
1 GGA
5720328 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.32, C:0.16, G:0.30, T:0.22
Consensus pattern (32 bp):
GGAAAGGTTCTAGCTTAGCCCGGAAAAACTAG
Found at i:5721879 original size:19 final size:20
Alignment explanation
Indices: 5721836--5721881 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
5721826 TCTAAATCCT
*
5721836 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
5721856 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
5721875 TTTTCAA
1 TTTTCAA
5721882 GAGAAAATCG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.26, C:0.13, G:0.07, T:0.54
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:5722571 original size:23 final size:23
Alignment explanation
Indices: 5722541--5722594 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
5722531 TGACAATCGG
*
5722541 AACGGTTTGCAAAGGGGGGTCGA
1 AACGGTTTGCAAAGAGGGGTCGA
*
5722564 AACGGTTTGCAAAGAGGGGTCGG
1 AACGGTTTGCAAAGAGGGGTCGA
*
5722587 AATGGTTT
1 AACGGTTT
5722595 TTGTGTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.26, C:0.11, G:0.41, T:0.22
Consensus pattern (23 bp):
AACGGTTTGCAAAGAGGGGTCGA
Found at i:5723443 original size:30 final size:30
Alignment explanation
Indices: 5723396--5723455 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
5723386 AAACTTTGAA
*
5723396 TAAATTTAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
5723425 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
5723456 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 11 0.39
31 7 0.25
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:5725775 original size:12 final size:12
Alignment explanation
Indices: 5725758--5725797 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
5725748 AATGGGCAAT
5725758 TGATATGGAATG
1 TGATATGGAATG
*
5725770 TGATATGAAATG
1 TGATATGGAATG
5725782 TGATTATTGGAATG
1 TGA-TA-TGGAATG
5725796 TG
1 TG
5725798 TATTGAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 14 0.58
13 2 0.08
14 8 0.33
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.38
Consensus pattern (12 bp):
TGATATGGAATG
Found at i:5727304 original size:20 final size:20
Alignment explanation
Indices: 5727281--5727344 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 20
5727271 TAGTATTTAG
5727281 ATAAAT-TTATTAATAATTTT
1 ATAAATATT-TTAATAATTTT
* *
5727301 AT-AATCTTTTAATAAATTTA
1 ATAAATATTTTAAT-AATTTT
*
5727321 ATAAGTATTTT-ATAATTTT
1 ATAAATATTTTAATAATTTT
*
5727340 TTAAA
1 ATAAA
5727345 CTTTATTGAC
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
19 16 0.46
20 13 0.37
21 6 0.17
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
ATAAATATTTTAATAATTTT
Found at i:5727314 original size:19 final size:20
Alignment explanation
Indices: 5727290--5727339 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
5727280 GATAAATTTA
*
5727290 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
5727309 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
5727330 TT-ATAATTTT
1 TTAATAATTTT
5727340 TTAAACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:5727342 original size:31 final size:30
Alignment explanation
Indices: 5727258--5727343 Score: 93
Period size: 31 Copynumber: 2.8 Consensus size: 30
5727248 TTGATAATAA
* *
5727258 AATAATTATTTTAT-AGTATTTAGATAAATTT
1 AATAA-TATTTTATAATTTTTTA-ATAAATTT
* *
5727289 ATTAATAATTTTATAATCTTTTAATAAATTT
1 AATAAT-ATTTTATAATTTTTTAATAAATTT
5727320 AATAAGTATTTTATAATTTTTTAA
1 AATAA-TATTTTATAATTTTTTAA
5727344 ACTTTATTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 39 0.85
32 6 0.13
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (30 bp):
AATAATATTTTATAATTTTTTAATAAATTT
Found at i:5728099 original size:31 final size:31
Alignment explanation
Indices: 5728064--5728150 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
5728054 TTAATAAAGT
5728064 TTAAAAAATTATAAAATATTTATTAAATTTA
1 TTAAAAAATTATAAAATATTTATTAAATTTA
* * *
5728095 TTAAAAGATTATAAAAT-TATTAATCAATTTA
1 TTAAAAAATTATAAAATAT-TTATTAAATTTA
* * *
5728126 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAATATTTATTA
5728151 TATTATCGAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
30 1 0.02
31 43 0.96
32 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (31 bp):
TTAAAAAATTATAAAATATTTATTAAATTTA
Found at i:5736242 original size:35 final size:35
Alignment explanation
Indices: 5736200--5736279 Score: 133
Period size: 35 Copynumber: 2.3 Consensus size: 35
5736190 GGGGTTGGGC
5736200 ATGTAATTGAAGTATTTTAGAATTTGAGGTTTAGA
1 ATGTAATTGAAGTATTTTAGAATTTGAGGTTTAGA
* * *
5736235 ATTTAATTGAAGTATTTTGGAATTTGGGGTTTAGA
1 ATGTAATTGAAGTATTTTAGAATTTGAGGTTTAGA
5736270 ATGTAATTGA
1 ATGTAATTGA
5736280 TGATTGTGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.44
Consensus pattern (35 bp):
ATGTAATTGAAGTATTTTAGAATTTGAGGTTTAGA
Found at i:5746707 original size:17 final size:17
Alignment explanation
Indices: 5746685--5746741 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 17
5746675 GAATCGAGAC
5746685 TTATTGCAAAAAGACAT
1 TTATTGCAAAAAGACAT
* *
5746702 TTATTGTATTAGAAGATTCAT
1 TTATTGCA--AAAAGA--CAT
5746723 TTATTGCAAAAAGACAT
1 TTATTGCAAAAAGACAT
5746740 TT
1 TT
5746742 GTTATATTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 12 0.38
19 10 0.31
21 10 0.31
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (17 bp):
TTATTGCAAAAAGACAT
Found at i:5746723 original size:21 final size:21
Alignment explanation
Indices: 5746699--5746761 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
5746689 TGCAAAAAGA
5746699 CATTTATTGTATTAGAAGATT
1 CATTTATTGTATTAGAAGATT
* *
5746720 CATTTATTGCA--AAAAGA--
1 CATTTATTGTATTAGAAGATT
* *
5746737 CATTTGTTATATTAGAAGATT
1 CATTTATTGTATTAGAAGATT
5746758 CATT
1 CATT
5746762 CTTTAAGAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
17 8 0.25
19 10 0.31
21 14 0.44
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.43
Consensus pattern (21 bp):
CATTTATTGTATTAGAAGATT
Found at i:5746736 original size:38 final size:38
Alignment explanation
Indices: 5746685--5746761 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
5746675 GAATCGAGAC
*
5746685 TTATTGCAAAAAGACATTTATTGTATTAGAAGATTCAT
1 TTATTGCAAAAAGACATTTATTATATTAGAAGATTCAT
*
5746723 TTATTGCAAAAAGACATTTGTTATATTAGAAGATTCAT
1 TTATTGCAAAAAGACATTTATTATATTAGAAGATTCAT
5746761 T
1 T
5746762 CTTTAAGAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.40
Consensus pattern (38 bp):
TTATTGCAAAAAGACATTTATTATATTAGAAGATTCAT
Found at i:5764579 original size:23 final size:23
Alignment explanation
Indices: 5764547--5764590 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
5764537 TAATATATAT
5764547 ATATGAAAATAACTATCCTATAAC
1 ATATGAAAATAACTAT-CTATAAC
*
5764571 ATATG-AAATAAGTATCTATA
1 ATATGAAAATAACTATCTATA
5764591 GGTATAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 9 0.47
24 5 0.26
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.32
Consensus pattern (23 bp):
ATATGAAAATAACTATCTATAAC
Found at i:5769371 original size:44 final size:43
Alignment explanation
Indices: 5769321--5769417 Score: 115
Period size: 44 Copynumber: 2.2 Consensus size: 43
5769311 ACCACTTGAG
*** * * *
5769321 ATATCGATACTACTTTACATAGTAGTATCGATACCCCCTGGA-CA
1 ATATCGATACTAAACTACAAAGTAGTACCGATA-CCCAT-GACCA
5769365 ATATCGATACTAAACTACAAAGTAGTACCGATACCCATGACCA
1 ATATCGATACTAAACTACAAAGTAGTACCGATACCCATGACCA
5769408 ATATCGATAC
1 ATATCGATAC
5769418 CATTGGGATG
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 2 0.04
43 16 0.35
44 28 0.61
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (43 bp):
ATATCGATACTAAACTACAAAGTAGTACCGATACCCATGACCA
Found at i:5773104 original size:19 final size:20
Alignment explanation
Indices: 5773080--5773130 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
5773070 CGGCCAAGAG
* *
5773080 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
5773099 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
5773119 CATGTATTTTCA
1 CATGTATTTTCA
5773131 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:5777464 original size:6 final size:6
Alignment explanation
Indices: 5777455--5777488 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
5777445 ATTTTCGTTC
5777455 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA -TTTTTA TTT
5777489 GATTTATTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:5777493 original size:18 final size:18
Alignment explanation
Indices: 5777455--5777493 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5777445 ATTTTCGTTC
*
5777455 TTTTTATTTTTATTTTTA
1 TTTTTATTTTTATTTTGA
5777473 TTTTTATTTTT-TATTTGA
1 TTTTTATTTTTAT-TTTGA
5777491 TTT
1 TTT
5777494 ATTAGAGTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 1 0.05
18 18 0.95
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (18 bp):
TTTTTATTTTTATTTTGA
Found at i:5780901 original size:927 final size:925
Alignment explanation
Indices: 5779155--5781795 Score: 4262
Period size: 927 Copynumber: 2.9 Consensus size: 925
5779145 AAGGAAGAAT
* *
5779155 TTCAAAATCTAATGATTACCATGATCTTCACAAAATCCACAAATTAAGGAGGAAAAATCGGAATT
1 TTCAAAATCTAATGATTA-TATGATCTTCACAAAATCCACAAATTAAGGAGGAAAAATTGGAATT
* *
5779220 CAAGAAGTTGGCAAGACCAGAAGAGGTTTTCGCATAAGGCGTGGACACGTCTTATTCATCCCGAG
65 CAAGAAGTTGGCAAGACCAGAAGAGGTTTTCGCATAAGGCGTGGACAAG-CTTATTCATCCTGAG
*
5779285 CTATCGTAGAAGAAGTCTTCAGTTAAGGCGTGGGCGCGCCTTACCAGTCCGTACAACCCTAAATT
129 CTATCGTAGAAGAAGTCTTCAGTTAAGGCGTGGGTGCGCCTTACCAGTCCGTACAACCCTAAATT
* *
5779350 AGTGTTACGAATTTACAAAGGAAAAAGAGTTTAATGACGGTTAGAAGA--CTTTTGAATTATTCT
194 AGTGTTACAAATTTACAAAGGAAAAAGAGTTTAATAACGGTTAGAAGACTCTTTTGAATTATTCT
5779413 TATCTTTAGAAAAAGATGAGGGTATTTAAAACCCTATTTTTATGGGATTTACTTTTAATAAACTT
259 TATCTTTAGAAAAAGATGAGGGTATTTAAAACCCTATTTTTAT-GGATTTACTTTTAATAAACTT
5779478 CCTTATCTAGAATAGGGAAGTTCTTATAAAAGGTGAGGTTGGGATTTCATAGGAGGCATGAAGTT
323 CCTTATCTAGAATAGGGAAGTTCTTATAAAAGGTGAGGTTGGGATTTCATAGGAGGCATGAAGTT
* *
5779543 TTTCATCAAG---------TG--TTCTTTATGTTTTTCTTTTGGTGTTTTTTCAATTATGAGTAG
388 TTTCATCAAGTTTTCATTATGTTTTCTTTAAGTTTTTCTTTTGGTGTTCTTTCAATTATGAGTAG
* * *
5779597 CTAAATACTTTTGTTCAAACTGGAGGATAATTGAAGTTTTGGTTCTTCAAGGATTGTGAGATATA
453 CTAAATACTTTTGTTCCAACTGGAGGATAATTGAAGTTTTGGTTATTCAAGGATTGTGAGATCTA
* *
5779662 AATAATTTTCATTGTTCTTTTACTTCTTTGCTATTTATATATCTTCTATTTTTATTAAGAATTAT
518 AATAATTTTCATTGTTCTTTTACTTCTTTGCTATTTATATATCTTATGTTTTTATTAAGAATTAT
*
5779727 TATCTTGATTGATTGTGCAAAGGGCCCGTTTTTCAATTATCAGGTTGATAAATCGCTATTTAGAA
583 TATCTTGATTGATTGTGCAAAGGGCCCGTTTTTCAATTATCAGGTTGATAAATCGATATTTAGAA
* *
5779792 CTTGAAATTCGTAATTGTTTAAACGTTCTAATATTAGTGGTAAAGTAACATAGTTGATTTTGATT
648 CTTTAAATACGTAATTGTTTAAACGTTCTAATATTAGTGGTAAAGTAACATAGTTGATTTTGATT
5779857 ATGTTATAAAGGTATATAACCTAGTCTAAATGAATCGAGCTTGTGTATTCGTTGGCTAGAATTGG
713 ATGTTATAAAGGTATATAACCTAGTCTAAATGAATCGAGCTTGTGTATTCGTTGGCTAGAATTGG
5779922 TGGTCCCTCTAGTGGTTTGATAAGATGCATATTAGACATATATTCTATGATATTTTCCTCATATT
778 TGGTCCCTCTAGTGGTTTGATAAGATGCATATTAGACATATATTCTATGATATTTTCCTCATATT
*
5779987 TGAATAACTAAAATTGATTAAATCATGGATTTTGATTATATTTCGTATTTTGTGGATTAGGTTGA
843 TGAATAACTAAAATTGATTAAATCATGGATTTTGATTATATTTCATATTTTGTGGATTAGGTTGA
5780052 AGATTTGGATTAAACAAG
908 AGATTTGGATTAAACAAG
5780070 TTCAAAATCTAATGATTAGTATGATCTTCACAAAATCCACAAATTAAGGAGGAAAAATTGGAATT
1 TTCAAAATCTAATGATTA-TATGATCTTCACAAAATCCACAAATTAAGGAGGAAAAATTGGAATT
*
5780135 CAAGAAGTTGGCAAGACCAGAAGAGGTTTTTGCATAAGGCGTGGACATAGCTTATTCATCCTGAG
65 CAAGAAGTTGGCAAGACCAGAAGAGGTTTTCGCATAAGGCGTGGACA-AGCTTATTCATCCTGAG
* *
5780200 CTATCGCAGAAGAAGTCTTCAGTTAAGGCGTGGGTGTGCCTTACCAGTCCGTACAACCCTAAATT
129 CTATCGTAGAAGAAGTCTTCAGTTAAGGCGTGGGTGCGCCTTACCAGTCCGTACAACCCTAAATT
* *
5780265 AGTGTTATAAATTTACAAAGGAAAAATAGTTTAATAACGGTTAGAAGACTCTTTTGAATTATTCT
194 AGTGTTACAAATTTACAAAGGAAAAAGAGTTTAATAACGGTTAGAAGACTCTTTTGAATTATTCT
5780330 TATCTTTAGAAAAAGATGAGGGTATTTAAAACCCTATTTTTATGAGATTTACTTTTAATAAACTT
259 TATCTTTAGAAAAAGATGAGGGTATTTAAAACCCTATTTTTATG-GATTTACTTTTAATAAACTT
5780395 CCTTATCTAGAATAGGGAAGTTCTTATAAAAGGTGAGGTTGGGATTTCATAGGAGGCATGAAGTT
323 CCTTATCTAGAATAGGGAAGTTCTTATAAAAGGTGAGGTTGGGATTTCATAGGAGGCATGAAGTT
5780460 TTTCATCAAGTTTTCATTATGTTTTCTTTAAGTTTTT-TATTTGGTGTTCTTTCAATTATGAGTA
388 TTTCATCAAGTTTTCATTATGTTTTCTTTAAGTTTTTCT-TTTGGTGTTCTTTCAATTATGAGTA
*
5780524 GCTAAATACTTTTGTTCCAA-TGGAGGATAATTGAAGTTTTGGTTATTTAAGGATTGTGAGATCT
452 GCTAAATACTTTTGTTCCAACTGGAGGATAATTGAAGTTTTGGTTATTCAAGGATTGTGAGATCT
*
5780588 AAATAATTTTCATTGTTCTTTTACTTCTTTGCTATTTATATATCTTTTGTTTTTATTAAGAATTA
517 AAATAATTTTCATTGTTCTTTTACTTCTTTGCTATTTATATATCTTATGTTTTTATTAAGAATTA
* *
5780653 TTCTCTTGCTTGATTGTGCAAAGGGCCCGTTTTTCAATTATCAGGTTGATAAATCGATATTTAGA
582 TTATCTTGATTGATTGTGCAAAGGGCCCGTTTTTCAATTATCAGGTTGATAAATCGATATTTAGA
*
5780718 ACTTTAAATCCGTAATTGTTTAAACGTTCTAATATTAGTGGTAAAGTAACATAGTTGATTTTGAT
647 ACTTTAAATACGTAATTGTTTAAACGTTCTAATATTAGTGGTAAAGTAACATAGTTGATTTTGAT
* * *
5780783 TATGTTATAAAGGTATATAAACTAGTCTAAATGAATCGAGATTGTGTATTC-TATAGCTAGAATT
712 TATGTTATAAAGGTATATAACCTAGTCTAAATGAATCGAGCTTGTGTATTCGT-TGGCTAGAATT
5780847 GGTGGTCCCTCTAGTGGTTTGATAAGATGCATATTAGACATATATTCTATGATATTTTCCTCATA
776 GGTGGTCCCTCTAGTGGTTTGATAAGATGCATATTAGACATATATTCTATGATATTTTCCTCATA
5780912 TTTGAATAACTAAAATTGATTAAATCATGGATTTTGATTATATTTCATATTTTGTGGATTAGGTT
841 TTTGAATAACTAAAATTGATTAAATCATGGATTTTGATTATATTTCATATTTTGTGGATTAGGTT
5780977 GAAGATTTGGATTAAACAAG
906 GAAGATTTGGATTAAACAAG
*
5780997 TTCAAAATCTAATGATTATCATGATCTTCACAAAATCC-CAAAATTAAGGTGGAAAAATTGGAAT
1 TTCAAAATCTAATGATTAT-ATGATCTTCACAAAATCCAC-AAATTAAGGAGGAAAAATTGGAAT
* *
5781061 TCAAGAAGTTGGCAAGACCAGAAGAGGTTTTCGCATAAGGTGTGGACACGGCTTATTCATCCTGA
64 TCAAGAAGTTGGCAAGACCAGAAGAGGTTTTCGCATAAGGCGTGGACA-AGCTTATTCATCCTGA
* * *
5781126 GCTATCGTAGAAGAAGTCTTTAGGTAAGGCATGGGTGCGCCTTACCAGTCCGTACAACCCTAAAT
128 GCTATCGTAGAAGAAGTCTTCAGTTAAGGCGTGGGTGCGCCTTACCAGTCCGTACAACCCTAAAT
* * * * *
5781191 TAGGGTTACAAATTTACAAAGGAAAAAGAGTTTAATTATGGCTGGAAGACTCTTTTGAATTATTC
193 TAGTGTTACAAATTTACAAAGGAAAAAGAGTTTAATAACGGTTAGAAGACTCTTTTGAATTATTC
* * * * * * *
5781256 TCATCTCTAGAAAAGGATGAGGGCATTTAAAACCCCTATTTTTGTTGGATTTTC-TTTAAGGGAA
258 TTATCTTTAGAAAAAGATGAGGGTATTTAAAA-CCCTATTTTT-ATGGATTTACTTTTAA--TAA
* * * * * * * * * * *
5781320 TCTTCCTTATCTACAATAAGAAAATCCTTATAAAAGGGGAGATAGGGATTTCATAAGG-GACATC
319 ACTTCCTTATCTAGAATAGGGAAGTTCTTATAAAAGGTGAGGTTGGGATTTCAT-AGGAGGCATG
* *
5781384 AAG-TTTTCATTAAGTTTTTCATTAAGTTTTCTTTAAGTTTTTCTTTTGGTGTTCTTTCAATTAT
383 AAGTTTTTCATCAAG-TTTTCATTATGTTTTCTTTAAGTTTTTCTTTTGGTGTTCTTTCAATTAT
*
5781448 GAGTAGCTAAATACTTTTGTTCCAACAGGAGGATAATTGAAGTTTTGGTTATTCAAGGATTGTGA
447 GAGTAGCTAAATACTTTTGTTCCAACTGGAGGATAATTGAAGTTTTGGTTATTCAAGGATTGTGA
* *
5781513 GATCTAAATAATTTTCATTGTTCTTTTACTTCTTTACTATTTATATATATTATGTTTTTATTAAG
512 GATCTAAATAATTTTCATTGTTCTTTTACTTCTTTGCTATTTATATATCTTATGTTTTTATTAAG
* * * ** * * *
5781578 AATTATTGTCATGATTGATTGTACAAAGTTCCCGTTGTTCAATTATCAAGTTGATAAAT-TACTA
577 AATTATTATCTTGATTGATTGTGCAAAGGGCCCGTTTTTCAATTATCAGGTTGATAAATCGA-TA
* * * *
5781642 TTTAGAATTTTAAATATGTAATTGTTTAAATGTTCTAATATTAGTGGTAAAGTAACATAGTTGAA
641 TTTAGAACTTTAAATACGTAATTGTTTAAACGTTCTAATATTAGTGGTAAAGTAACATAGTTGAT
*
5781707 TTTGATTATGTTATGAAGGTATATAACCTAGTCTAAATGAATCGAGCTTGTGTATTCGTTGGCTA
706 TTTGATTATGTTATAAAGGTATATAACCTAGTCTAAATGAATCGAGCTTGTGTATTCGTTGGCTA
*
5781772 GACTTGGTGGTCCCTCTAGTGGTT
771 GAATTGGTGGTCCCTCTAGTGGTT
5781796 AATGTTATTG
Statistics
Matches: 1606, Mismatches: 91, Indels: 43
0.92 0.05 0.02
Matches are distributed among these distances:
915 228 0.14
916 2 0.00
917 153 0.10
926 5 0.00
927 709 0.44
928 82 0.05
929 128 0.08
930 298 0.19
931 1 0.00
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.38
Consensus pattern (925 bp):
TTCAAAATCTAATGATTATATGATCTTCACAAAATCCACAAATTAAGGAGGAAAAATTGGAATTC
AAGAAGTTGGCAAGACCAGAAGAGGTTTTCGCATAAGGCGTGGACAAGCTTATTCATCCTGAGCT
ATCGTAGAAGAAGTCTTCAGTTAAGGCGTGGGTGCGCCTTACCAGTCCGTACAACCCTAAATTAG
TGTTACAAATTTACAAAGGAAAAAGAGTTTAATAACGGTTAGAAGACTCTTTTGAATTATTCTTA
TCTTTAGAAAAAGATGAGGGTATTTAAAACCCTATTTTTATGGATTTACTTTTAATAAACTTCCT
TATCTAGAATAGGGAAGTTCTTATAAAAGGTGAGGTTGGGATTTCATAGGAGGCATGAAGTTTTT
CATCAAGTTTTCATTATGTTTTCTTTAAGTTTTTCTTTTGGTGTTCTTTCAATTATGAGTAGCTA
AATACTTTTGTTCCAACTGGAGGATAATTGAAGTTTTGGTTATTCAAGGATTGTGAGATCTAAAT
AATTTTCATTGTTCTTTTACTTCTTTGCTATTTATATATCTTATGTTTTTATTAAGAATTATTAT
CTTGATTGATTGTGCAAAGGGCCCGTTTTTCAATTATCAGGTTGATAAATCGATATTTAGAACTT
TAAATACGTAATTGTTTAAACGTTCTAATATTAGTGGTAAAGTAACATAGTTGATTTTGATTATG
TTATAAAGGTATATAACCTAGTCTAAATGAATCGAGCTTGTGTATTCGTTGGCTAGAATTGGTGG
TCCCTCTAGTGGTTTGATAAGATGCATATTAGACATATATTCTATGATATTTTCCTCATATTTGA
ATAACTAAAATTGATTAAATCATGGATTTTGATTATATTTCATATTTTGTGGATTAGGTTGAAGA
TTTGGATTAAACAAG
Found at i:5781400 original size:11 final size:11
Alignment explanation
Indices: 5781384--5781424 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
5781374 AAGGGACATC
5781384 AAGTTTTCATT
1 AAGTTTTCATT
5781395 AAGTTTTTCATT
1 AAG-TTTTCATT
*
5781407 AAGTTTTCTTT
1 AAGTTTTCATT
5781418 AAGTTTT
1 AAGTTTT
5781425 TCTTTTGGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.24, C:0.07, G:0.10, T:0.59
Consensus pattern (11 bp):
AAGTTTTCATT
Found at i:5781429 original size:12 final size:12
Alignment explanation
Indices: 5781387--5781426 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
5781377 GGACATCAAG
5781387 TTTTCATTAAGT
1 TTTTCATTAAGT
5781399 TTTTCATTAAG-
1 TTTTCATTAAGT
*
5781410 TTTTCTTTAAGT
1 TTTTCATTAAGT
5781422 TTTTC
1 TTTTC
5781427 TTTTGGTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.20, C:0.10, G:0.07, T:0.62
Consensus pattern (12 bp):
TTTTCATTAAGT
Found at i:5781438 original size:23 final size:23
Alignment explanation
Indices: 5781384--5781440 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
5781374 AAGGGACATC
* *
5781384 AAGTTTTCATTAAGTTTTTCATT
1 AAGTGTTCTTTAAGTTTTTCATT
* *
5781407 AAGTTTTCTTTAAGTTTTTCTTT
1 AAGTGTTCTTTAAGTTTTTCATT
**
5781430 TGGTGTTCTTT
1 AAGTGTTCTTT
5781441 CAATTATGAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.18, C:0.09, G:0.12, T:0.61
Consensus pattern (23 bp):
AAGTGTTCTTTAAGTTTTTCATT
Found at i:5783903 original size:102 final size:102
Alignment explanation
Indices: 5783727--5783921 Score: 318
Period size: 102 Copynumber: 1.9 Consensus size: 102
5783717 TCAACCTCAG
* *
5783727 AAAGACCAACATAAAGGACTCAAAAGCGAAAAACCGAAGGATTTTGTCATAAATCCTCATTTTCC
1 AAAGACCAACATAAAGGACTCAAAAGCGAAAAACCGAAGGAATTTATCATAAATCCTCATTTTCC
*
5783792 CGCTAGATTCGCTAATTCCAAGAAAGAAACAGAAGAT
66 CGCTAGATTCGCTAAGTCCAAGAAAGAAACAGAAGAT
* * * *
5783829 AAAGACCAACCTAAAGGACTCAAAAGCGAAAAACTGAAGGAATTTATCATAGATCCTCCTTTTCC
1 AAAGACCAACATAAAGGACTCAAAAGCGAAAAACCGAAGGAATTTATCATAAATCCTCATTTTCC
*
5783894 CTCTAGATTCGCTAAGTCCAAGAAAGAA
66 CGCTAGATTCGCTAAGTCCAAGAAAGAA
5783922 GCCAAAGAAA
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
102 85 1.00
ACGTcount: A:0.42, C:0.22, G:0.15, T:0.21
Consensus pattern (102 bp):
AAAGACCAACATAAAGGACTCAAAAGCGAAAAACCGAAGGAATTTATCATAAATCCTCATTTTCC
CGCTAGATTCGCTAAGTCCAAGAAAGAAACAGAAGAT
Found at i:5786409 original size:11 final size:11
Alignment explanation
Indices: 5786390--5786435 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
5786380 TCTTTTATTG
5786390 AAAAA-AAAAA
1 AAAAACAAAAA
*
5786400 CAAAACAAAAA
1 AAAAACAAAAA
5786411 AAAAACAAAAA
1 AAAAACAAAAA
*
5786422 AAGAAAGAAAAA
1 AA-AAACAAAAA
5786434 AA
1 AA
5786436 GAAGCAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
10 4 0.13
11 17 0.55
12 10 0.32
ACGTcount: A:0.89, C:0.07, G:0.04, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAA
Found at i:5786411 original size:16 final size:16
Alignment explanation
Indices: 5786390--5786420 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5786380 TCTTTTATTG
5786390 AAAAAAAAAACAAAAC
1 AAAAAAAAAACAAAAC
5786406 AAAAAAAAAACAAAA
1 AAAAAAAAAACAAAA
5786421 AAAGAAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAACAAAAC
Found at i:5786436 original size:12 final size:11
Alignment explanation
Indices: 5786389--5786438 Score: 55
Period size: 12 Copynumber: 4.3 Consensus size: 11
5786379 CTCTTTTATT
5786389 GAAAAAAAAAA
1 GAAAAAAAAAA
*
5786400 CAAAACAAAAAA
1 GAAAA-AAAAAA
*
5786412 AAAACAAAAAAA
1 GAAA-AAAAAAA
5786424 GAAAGAAAAAAA
1 GAAA-AAAAAAA
5786436 GAA
1 GAA
5786439 GCAAAATTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
11 4 0.12
12 28 0.85
13 1 0.03
ACGTcount: A:0.86, C:0.06, G:0.08, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:5788746 original size:433 final size:435
Alignment explanation
Indices: 5787923--5788785 Score: 1399
Period size: 433 Copynumber: 2.0 Consensus size: 435
5787913 GTCCCTCTAG
5787923 TGGTTAATGTTGTTGGTGGATTAAATCTTAAGCGCTTGTCTAGGGTTGTTCATTAACAAGGGAAA
1 TGGTTAATGTTGTTGGTGGATTAAATCTTAAGCGCTTGTCTAGGGTTGTTCATTAACAAGGGAAA
* * *
5787988 TAATCAAAGAGCTTCTCTTGATTATCAAGAAACTAAGGATAGACAGGTTGTTAGAGCTTCTTAAT
66 TAATCAAAGAGCTTCTCTTGATTATCAAAAAACTAAGGAGAGACAGGTTGTTAGAGCTTCTCAAT
* * *
5788053 AACCATAACCAATTTAGTGAAAAGTAAAAAATTTTATCATTGCATCTATGATCAATTTTTTGAAC
131 AACCATAACCAATTTAGTGAAAAGTAAAAAATTTTATCATTGAATCTATGATCAATTCTCTGAAC
* * *
5788118 CAATCCTGAAATTATACCTTTAGTTGGATATTTCCTTAATATTAATCTCTCTAAATTCATGGTGG
196 CAATCATGAAATTATACCTCTAGTTAGATATTTCCTTAATATTAATCTCTCTAAATTCATGGTGG
*
5788183 ATTTTAAATGCTTTTTATTTTTGATTTATTCTCAATTTTAAAACCCCTTTTATTTTCTTTAATTT
261 ATTTTAAATGCTTTTTATTTTTGATTTATTCTCAATTTTAAAACCCCTTTTATTTACTTTAATTT
* * * *
5788248 TCATTAAAATAGGTCTATCCAATCCCTGTGGATTCGACCTTGCTTATCGCTACTACAAATTTATA
326 TCATTAAAATAAGTCTACCCAATCCCTGTGGATTCGACCTTACTTATCACTACTACAAATTTATA
* * *
5788313 TTTCTTAGAGCAAGTATTATTATTTGTTGGATTCGACACCAATCA
391 TTTCTAAAAGCAAGTATTATTATTTGTTAGATTCGACACCAATCA
5788358 TGGTTAATGTTGTTGGTGGATTAAATCTTAAGCGCTTGTCTAGGGTTGTTCATTAAC-AGGGAAA
1 TGGTTAATGTTGTTGGTGGATTAAATCTTAAGCGCTTGTCTAGGGTTGTTCATTAACAAGGGAAA
*
5788422 TAATCAAAGAGCTTCTCTTGATTATCAAAAAACTAAGGAGAGACATGTTGTTAGAGCTTCTCAAT
66 TAATCAAAGAGCTTCTCTTGATTATCAAAAAACTAAGGAGAGACAGGTTGTTAGAGCTTCTCAAT
* * *
5788487 AACCATAACCAATTTAGTTAAAAGTAGAAGATTTTATCATTGAAT-TATGATCAATTCTCTGAAC
131 AACCATAACCAATTTAGTGAAAAGTAAAAAATTTTATCATTGAATCTATGATCAATTCTCTGAAC
* * * ** *
5788551 CAATTATGAAATTATACCTCTAGTTAGATATTTTCTTAATATTAATTTCTCTAAATTTTTGGTTG
196 CAATCATGAAATTATACCTCTAGTTAGATATTTCCTTAATATTAATCTCTCTAAATTCATGGTGG
* * * *
5788616 ATTTTAAATGTTTTTTCTTTTTGATTCT-TTCTCGATTTTAAAACCTCTTTTATTTACTTTAATT
261 ATTTTAAATGCTTTTTATTTTTGATT-TATTCTCAATTTTAAAACCCCTTTTATTTACTTTAATT
* *
5788680 TTCATTAAAATAAGTCTACCCAATCCCTGTGGATTCGACCTTACTTATCACTACTATAATTTTAT
325 TTCATTAAAATAAGTCTACCCAATCCCTGTGGATTCGACCTTACTTATCACTACTACAAATTTAT
5788745 ATTTCTAAAAGCAAGTATTATTATTTGTTAGATTCGACACC
390 ATTTCTAAAAGCAAGTATTATTATTTGTTAGATTCGACACC
5788786 CACCACTCCA
Statistics
Matches: 394, Mismatches: 33, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
433 227 0.58
434 110 0.28
435 57 0.14
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (435 bp):
TGGTTAATGTTGTTGGTGGATTAAATCTTAAGCGCTTGTCTAGGGTTGTTCATTAACAAGGGAAA
TAATCAAAGAGCTTCTCTTGATTATCAAAAAACTAAGGAGAGACAGGTTGTTAGAGCTTCTCAAT
AACCATAACCAATTTAGTGAAAAGTAAAAAATTTTATCATTGAATCTATGATCAATTCTCTGAAC
CAATCATGAAATTATACCTCTAGTTAGATATTTCCTTAATATTAATCTCTCTAAATTCATGGTGG
ATTTTAAATGCTTTTTATTTTTGATTTATTCTCAATTTTAAAACCCCTTTTATTTACTTTAATTT
TCATTAAAATAAGTCTACCCAATCCCTGTGGATTCGACCTTACTTATCACTACTACAAATTTATA
TTTCTAAAAGCAAGTATTATTATTTGTTAGATTCGACACCAATCA
Found at i:5794427 original size:14 final size:11
Alignment explanation
Indices: 5794393--5794418 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5794383 ACGATAAGGG
5794393 TTTTGAAATGA
1 TTTTGAAATGA
5794404 TTTTGAAATGA
1 TTTTGAAATGA
5794415 TTTT
1 TTTT
5794419 AATGAAATGT
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:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (11 bp):
TTTTGAAATGA
Found at i:5800311 original size:21 final size:21
Alignment explanation
Indices: 5800263--5800313 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
5800253 AATAAAAATT
* *
5800263 CTTTGCAAAGTGTATCTATGGA
1 CTTT-CAAAGTGTATCGATGCA
* *
5800285 CATTCAATGTGTATCGATGCA
1 CTTTCAAAGTGTATCGATGCA
5800306 CTTTCAAA
1 CTTTCAAA
5800314 TAAATGAACA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (21 bp):
CTTTCAAAGTGTATCGATGCA
Found at i:5801963 original size:23 final size:23
Alignment explanation
Indices: 5801866--5801953 Score: 149
Period size: 23 Copynumber: 3.8 Consensus size: 23
5801856 TTCTTAAGAA
5801866 GGTACAATTCTACGCGGCACTTC
1 GGTACAATTCTACGCGGCACTTC
*
5801889 GGTACAATTCTACGCGGCACTTT
1 GGTACAATTCTACGCGGCACTTC
5801912 GGTACAATTCTACGCGGCACTTC
1 GGTACAATTCTACGCGGCACTTC
* *
5801935 GGTGCAATTCTACGTGGCA
1 GGTACAATTCTACGCGGCA
5801954 TTTTGGTGCA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (23 bp):
GGTACAATTCTACGCGGCACTTC
Found at i:5804505 original size:19 final size:19
Alignment explanation
Indices: 5804481--5804527 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
5804471 ACATTAAGAA
5804481 ATGAGCAAAAGTTTGATTT
1 ATGAGCAAAAGTTTGATTT
5804500 ATGAGCAAAAGTTTGATTT
1 ATGAGCAAAAGTTTGATTT
*
5804519 ATGTGCAAA
1 ATGAGCAAA
5804528 GCACATAGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.34
Consensus pattern (19 bp):
ATGAGCAAAAGTTTGATTT
Found at i:5805525 original size:21 final size:21
Alignment explanation
Indices: 5805499--5805539 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5805489 TCTGGGCAAA
5805499 GTGTATCGATGCACATTCAAT
1 GTGTATCGATGCACATTCAAT
*
5805520 GTGTATCGATGCACTTTCAA
1 GTGTATCGATGCACATTCAA
5805540 ATAAATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (21 bp):
GTGTATCGATGCACATTCAAT
Found at i:5807175 original size:23 final size:23
Alignment explanation
Indices: 5807107--5807167 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
5807097 ACATTTTATA
5807107 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
5807130 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
5807153 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
5807168 TTTATACGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:5809438 original size:13 final size:13
Alignment explanation
Indices: 5809413--5809451 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
5809403 AAACGAAAAT
*
5809413 AACTCAAAAATAA
1 AACTGAAAAATAA
*
5809426 AACTGAAACATAA
1 AACTGAAAAATAA
5809439 AACTGAAAAATAA
1 AACTGAAAAATAA
5809452 CACTATTTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.67, C:0.13, G:0.05, T:0.15
Consensus pattern (13 bp):
AACTGAAAAATAA
Found at i:5814859 original size:10 final size:10
Alignment explanation
Indices: 5814844--5814870 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
5814834 AGTGACTAAT
5814844 TTAAAATAAA
1 TTAAAATAAA
5814854 TTAAAATAAA
1 TTAAAATAAA
5814864 TTAAAAT
1 TTAAAAT
5814871 TAAGAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
TTAAAATAAA
Found at i:5822311 original size:21 final size:21
Alignment explanation
Indices: 5822285--5822335 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
5822275 AAAGGAGTAC
5822285 TGATACCCCTTGAAGAGGTAT
1 TGATACCCCTTGAAGAGGTAT
5822306 TGATACCCCTTGAAGAGGTAT
1 TGATACCCCTTGAAGAGGTAT
*
5822327 CGATACCCC
1 TGATACCCC
5822336 ATATTATGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.25
Consensus pattern (21 bp):
TGATACCCCTTGAAGAGGTAT
Found at i:5824204 original size:19 final size:19
Alignment explanation
Indices: 5824180--5824216 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5824170 TCAAGATGAA
*
5824180 TTGATTTTGAAAGTAAAAG
1 TTGATTTTGAAAATAAAAG
5824199 TTGATTTTGAAAATAAAA
1 TTGATTTTGAAAATAAAA
5824217 ATGAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.16, T:0.38
Consensus pattern (19 bp):
TTGATTTTGAAAATAAAAG
Found at i:5825034 original size:20 final size:20
Alignment explanation
Indices: 5825011--5825048 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5825001 ATATGAACTT
*
5825011 AATTTTAACAATCGGTATCA
1 AATTTCAACAATCGGTATCA
*
5825031 AATTTCAACAATTGGTAT
1 AATTTCAACAATCGGTAT
5825049 TGCATAAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (20 bp):
AATTTCAACAATCGGTATCA
Found at i:5825406 original size:21 final size:20
Alignment explanation
Indices: 5825364--5825420 Score: 82
Period size: 21 Copynumber: 2.9 Consensus size: 20
5825354 TATATTTTCC
5825364 AACAATTGGTAT-C-TTTTT
1 AACAATTGGTATCCTTTTTT
*
5825382 AACAATTGATATCCTTTTGTT
1 AACAATTGGTATCCTTTT-TT
5825403 AACAATTGGTATCCTTTT
1 AACAATTGGTATCCTTTT
5825421 CATTAAACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 11 0.32
19 1 0.03
20 3 0.09
21 19 0.56
ACGTcount: A:0.28, C:0.14, G:0.11, T:0.47
Consensus pattern (20 bp):
AACAATTGGTATCCTTTTTT
Found at i:5825739 original size:16 final size:16
Alignment explanation
Indices: 5825718--5825748 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5825708 TATATCTATG
*
5825718 AGTGTATCGATACACT
1 AGTGTACCGATACACT
5825734 AGTGTACCGATACAC
1 AGTGTACCGATACAC
5825749 CCTATAGTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (16 bp):
AGTGTACCGATACACT
Found at i:5825758 original size:20 final size:20
Alignment explanation
Indices: 5825733--5825772 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5825723 ATCGATACAC
5825733 TAGTGTA-CCGATACACCCTA
1 TAGTGTATCC-ATACACCCTA
*
5825753 TAGTGTATCCATATACCCTA
1 TAGTGTATCCATACACCCTA
5825773 GCTACAACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (20 bp):
TAGTGTATCCATACACCCTA
Found at i:5827325 original size:65 final size:64
Alignment explanation
Indices: 5827256--5827399 Score: 184
Period size: 65 Copynumber: 2.2 Consensus size: 64
5827246 GCATCAATGC
* **
5827256 ATAAAATGCATTCGATGTTT-CA-AACAAGCCTGGAGTGCATCGATGCATGGTCTGTGAATCGAT
1 ATAAAATGCATTCGATGTTTCCATAA-AAGCCT-AAGTGCATCGATGCATGG-AAGTGAATCGAT
5827319 GA
63 GA
* * * *
5827321 ATAAAATGCATTCAATGTTTCCATAAAATCCTAAGTGCATCGATGCATGGAAGTGCATCGATGC
1 ATAAAATGCATTCGATGTTTCCATAAAAGCCTAAGTGCATCGATGCATGGAAGTGAATCGATGA
5827385 ATAAAATGCATTCGA
1 ATAAAATGCATTCGA
5827400 AATGGAGTGT
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
64 24 0.35
65 36 0.52
66 7 0.10
67 2 0.03
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (64 bp):
ATAAAATGCATTCGATGTTTCCATAAAAGCCTAAGTGCATCGATGCATGGAAGTGAATCGATGA
Found at i:5827399 original size:18 final size:18
Alignment explanation
Indices: 5827356--5827395 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
5827346 AAATCCTAAG
* *
5827356 TGCATCGATGCATGGAAG
1 TGCATCGATGCATGAAAA
5827374 TGCATCGATGCAT-AAAA
1 TGCATCGATGCATGAAAA
5827391 TGCAT
1 TGCAT
5827396 TCGAAATGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (18 bp):
TGCATCGATGCATGAAAA
Found at i:5827733 original size:21 final size:21
Alignment explanation
Indices: 5827709--5827749 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5827699 AAAATTACTG
*
5827709 CCCTTACTATAATTCATCTTC
1 CCCTTACTATAATACATCTTC
5827730 CCCTTACTATAATACATCTT
1 CCCTTACTATAATACATCTT
5827750 AATCTTCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.32, G:0.00, T:0.41
Consensus pattern (21 bp):
CCCTTACTATAATACATCTTC
Found at i:5827991 original size:27 final size:27
Alignment explanation
Indices: 5827952--5828005 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
5827942 CTAAATGATG
* * *
5827952 CAAAAATCTAATAAACCAATATAAGTT
1 CAAAAACCAAATAAACAAATATAAGTT
* *
5827979 CAAAAACCAAATATATAAATATAAGTT
1 CAAAAACCAAATAAACAAATATAAGTT
5828006 TAAACATTCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.57, C:0.13, G:0.04, T:0.26
Consensus pattern (27 bp):
CAAAAACCAAATAAACAAATATAAGTT
Found at i:5829982 original size:21 final size:22
Alignment explanation
Indices: 5829926--5830024 Score: 94
Period size: 21 Copynumber: 4.5 Consensus size: 22
5829916 ATCCCGACGG
*
5829926 GTGTATCGATGCACATTCAAGGA
1 GTGTATCGATGCACATTC-ATGA
* * *
5829949 GTGCATCGGTGCACCTTCATGA
1 GTGTATCGATGCACATTCATGA
*
5829971 -TGTATCGATGCACATTCATAGG
1 GTGTATCGATGCACATTCAT-GA
* *
5829993 GATGCATCGATGCACCTTCAT-A
1 G-TGTATCGATGCACATTCATGA
5830015 GTGTATCGAT
1 GTGTATCGAT
5830025 TCATTATGCA
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
21 24 0.39
22 5 0.08
23 15 0.25
24 17 0.28
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.29
Consensus pattern (22 bp):
GTGTATCGATGCACATTCATGA
Found at i:5830001 original size:24 final size:23
Alignment explanation
Indices: 5829930--5830015 Score: 97
Period size: 24 Copynumber: 3.8 Consensus size: 23
5829920 CGACGGGTGT
5829930 ATCGATGCACATTCA-AGGAGTGC
1 ATCGATGCACATTCATAGGA-TGC
* * *
5829953 ATCGGTGCACCTTCAT--GATGT
1 ATCGATGCACATTCATAGGATGC
5829974 ATCGATGCACATTCATAGGGATGC
1 ATCGATGCACATTCATA-GGATGC
*
5829998 ATCGATGCACCTTCATAG
1 ATCGATGCACATTCATAG
5830016 TGTATCGATT
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
21 16 0.31
22 2 0.04
23 14 0.27
24 20 0.38
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (23 bp):
ATCGATGCACATTCATAGGATGC
Found at i:5830013 original size:45 final size:44
Alignment explanation
Indices: 5829926--5830024 Score: 148
Period size: 45 Copynumber: 2.2 Consensus size: 44
5829916 ATCCCGACGG
*
5829926 GTGTATCGATGCACATTCAAGGAGTGCATCGGTGCACCTTCAT-
1 GTGTATCGATGCACATTCAAGGAGTGCATCGATGCACCTTCATA
5829969 GATGTATCGATGCACATTCATAGG-GATGCATCGATGCACCTTCATA
1 G-TGTATCGATGCACATTCA-AGGAG-TGCATCGATGCACCTTCATA
5830015 GTGTATCGAT
1 GTGTATCGAT
5830025 TCATTATGCA
Statistics
Matches: 51, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
43 1 0.02
44 19 0.37
45 30 0.59
46 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.29
Consensus pattern (44 bp):
GTGTATCGATGCACATTCAAGGAGTGCATCGATGCACCTTCATA
Found at i:5841476 original size:6 final size:6
Alignment explanation
Indices: 5841469--5841502 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
5841459 GCCGTCCGGC
*
5841469 TCGTGC TCGTGG TCGTGG TCGTGG TCGTGG TCGT
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGT
5841503 CGACACTTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.21, G:0.44, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:5847177 original size:29 final size:29
Alignment explanation
Indices: 5847135--5847193 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
5847125 ATTTTCACCT
5847135 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
*
5847164 AACTAAATTGATGTAAGCAATGGCATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
5847193 A
1 A
5847194 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:5854163 original size:130 final size:130
Alignment explanation
Indices: 5854022--5854269 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
5854012 TATTTATATA
*
5854022 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * *
5854087 TTAGCACATGATCATGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
5854152 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * *
5854217 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
5854270 GAAGAAAATT
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:5854300 original size:130 final size:129
Alignment explanation
Indices: 5854036--5854300 Score: 309
Period size: 130 Copynumber: 2.0 Consensus size: 129
5854026 ATTTGGTCCT
* *
5854036 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * *** * * **** *
5854101 TGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
5854166 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
5854231 TGATATGTGTTATTGGTGACACATGTCACCTCCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
5854295 -A
128 CA
5854296 AAATT
1 AAATT
5854301 TGGGTCTTGG
Statistics
Matches: 113, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
130 100 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.35
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:5854628 original size:27 final size:26
Alignment explanation
Indices: 5854595--5854654 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
5854585 AGTTGATACA
*
5854595 ATATTTTAAAAGAATAAA-TTAATATTT
1 ATATTTT-AAA-AATAAATTTAATAATT
* *
5854622 ATATTTTTAAACTAAATTTAATAATT
1 ATATTTTAAAAATAAATTTAATAATT
5854648 ATATTTT
1 ATATTTT
5854655 TCATATTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 5 0.17
26 17 0.59
27 7 0.24
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (26 bp):
ATATTTTAAAAATAAATTTAATAATT
Found at i:5854753 original size:16 final size:18
Alignment explanation
Indices: 5854732--5854765 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
5854722 ATTTCTTATT
5854732 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
5854748 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
5854766 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:5854912 original size:21 final size:21
Alignment explanation
Indices: 5854888--5854930 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5854878 TATTACCTTA
5854888 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
5854909 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
5854930 A
1 A
5854931 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:5854948 original size:35 final size:35
Alignment explanation
Indices: 5854899--5854984 Score: 93
Period size: 35 Copynumber: 2.5 Consensus size: 35
5854889 ATTGAAGTAT
** * *
5854899 TTTAGAATTTAATTGAAGTATTTTAG-AATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTGA-GG
* *
5854934 TTTAGAATAAAATTGAATTACTTTGGAAATTGAGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTGAGG
*
5854969 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
5854985 TGACTGTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
35 38 0.88
36 5 0.12
ACGTcount: A:0.38, C:0.01, G:0.20, T:0.41
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTGAGG
Found at i:5855167 original size:29 final size:29
Alignment explanation
Indices: 5855115--5855172 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
5855105 GTAAATGGAA
* *
5855115 TAAATGTTGGGGGACTGTATTGCAAGTTT
1 TAAATGTTGGGGGACTGAAATGCAAGTTT
5855144 TAAATGTTGGGGGACCT-AAATGCAAGTTT
1 TAAATGTTGGGGGA-CTGAAATGCAAGTTT
5855173 CAGAAATGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.28, C:0.09, G:0.29, T:0.34
Consensus pattern (29 bp):
TAAATGTTGGGGGACTGAAATGCAAGTTT
Found at i:5855841 original size:83 final size:86
Alignment explanation
Indices: 5855663--5855830 Score: 272
Period size: 83 Copynumber: 2.0 Consensus size: 86
5855653 CATTTAACCG
* *
5855663 GAAATATTATCAAGTACAATAACATATTAGATACCGCTTATATAATGTAATAGGTAGCGCTTATA
1 GAAATATTATCAAGCACAATAACATATTAGATACCGCTTATATAATGTAATAGGTAACGCTTATA
5855728 TAATAAAATAAGTTAATTACT
66 TAATAAAATAAGTTAATTACT
* *
5855749 GAAACATTATCAAGCACAATAACATATTAG-TAGCGC-T-TATAATGTAATAGGTAACGCTTATA
1 GAAATATTATCAAGCACAATAACATATTAGATACCGCTTATATAATGTAATAGGTAACGCTTATA
5855811 TAATAAAATAA-TTAATTACT
66 TAATAAAATAAGTTAATTACT
5855831 TAATTTATTA
Statistics
Matches: 78, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
82 9 0.12
83 35 0.45
84 1 0.01
85 5 0.06
86 28 0.36
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (86 bp):
GAAATATTATCAAGCACAATAACATATTAGATACCGCTTATATAATGTAATAGGTAACGCTTATA
TAATAAAATAAGTTAATTACT
Found at i:5856333 original size:199 final size:199
Alignment explanation
Indices: 5855951--5856341 Score: 633
Period size: 199 Copynumber: 2.0 Consensus size: 199
5855941 TTTGGGATGT
* *
5855951 GTGCACCTCGTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAATTTAAAAAGTGTCGATAC
1 GTGCACCTAGTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAATTTAAAAAATGTCGATAC
*
5856016 ATTATGCAGACATATTTTCTCATAAAACCGATATATTTATACCTGTTACATTGTAAATTTACCTA
66 ATTATGCAGACATATTTTCTCATAAAACCGATATATTTATACCAGTTACATTGTAAATTTACCTA
* *
5856081 TTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATATAATTTTAAATGTATCGACACTTT
131 TTACACTATAATTATCGATTTCGATGTTTTTGGGATCGATATAATTTTAAATGTATCGACACTTT
5856146 ATGC
196 ATGC
* *
5856150 GTGCACCTAGTTTGTCATTCATTCTGGACAAAAAGTATCGACACAAATTTAAAAAATGTCGATAC
1 GTGCACCTAGTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAATTTAAAAAATGTCGATAC
* * * *
5856215 ATTATGTAGACCTATTTTCTCATAAAACCGGTAT-TTTCTACCAGTTACATTGTAAATTTACCTA
66 ATTATGCAGACATATTTTCTCATAAAACCGATATATTTATACCAGTTACATTGTAAATTTACCTA
**
5856279 TTACACTATAATTATCGATTTCGATGTTTTTGGGATCGATA-CGTTTAATAAATGTATCGACAC
131 TTACACTATAATTATCGATTTCGATGTTTTTGGGATCGATATAATTT--TAAATGTATCGACAC
5856342 ATTTGTTTAC
Statistics
Matches: 177, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
197 3 0.02
198 67 0.38
199 107 0.60
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (199 bp):
GTGCACCTAGTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAATTTAAAAAATGTCGATAC
ATTATGCAGACATATTTTCTCATAAAACCGATATATTTATACCAGTTACATTGTAAATTTACCTA
TTACACTATAATTATCGATTTCGATGTTTTTGGGATCGATATAATTTTAAATGTATCGACACTTT
ATGC
Found at i:5857871 original size:18 final size:18
Alignment explanation
Indices: 5857848--5857882 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5857838 AAATTTATAC
5857848 TGAAATTCAAACTCAAAT
1 TGAAATTCAAACTCAAAT
* *
5857866 TGAAATTTAAATTCAAA
1 TGAAATTCAAACTCAAA
5857883 CTCCAATTAA
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:0.51, C:0.11, G:0.06, T:0.31
Consensus pattern (18 bp):
TGAAATTCAAACTCAAAT
Found at i:5857901 original size:24 final size:24
Alignment explanation
Indices: 5857848--5857901 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
5857838 AAATTTATAC
5857848 TGAAATTCAAACTCAAATTGAAAT
1 TGAAATTCAAACTCAAATTGAAAT
* *
5857872 TTAAATTCAAACTCCAATT-AAAT
1 TGAAATTCAAACTCAAATTGAAAT
5857895 ATGAAAT
1 -TGAAAT
5857902 GAACATGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.50, C:0.13, G:0.06, T:0.31
Consensus pattern (24 bp):
TGAAATTCAAACTCAAATTGAAAT
Found at i:5861102 original size:199 final size:198
Alignment explanation
Indices: 5860751--5861796 Score: 1333
Period size: 200 Copynumber: 5.2 Consensus size: 198
5860741 GTAATTTTAA
* ** * *
5860751 AAAAAGTATTGACACAAATTTTTAAAGTGTCGATACATTATGTAGAGCTATTCTCTCATAAAACC
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACC
* * * * * *
5860816 AGTATATTTATACCGATTACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCAATTTTT
66 AGTAT-TTTCTACCGGTTACATTGTAAAATTACCTATTACATTATAATTATCGGTTTCGATATTT
* * * **
5860881 TTGGGATCGATACAATTTTAAATTTATCGACACTTTATGCGTGCCCCTAGTTTATCATTCATTTC
130 TTGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGCATTCA-TTC
*
5860946 TGCAC
194 TGGAC
* * * *
5860951 AAAATGTATCGACACAAATTTAAAAAGTATCGATACATAATGTAGACCTATTTTCTCATAAAATC
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACC
* * * * * ** *
5861016 AGTATTTTCTACCTGTTACATTGTAAAGTTACATATTACAATGTAATTATTAGTTTCGATGTTTT
66 AGTATTTTCTACCGGTTACATTGTAAAATTACCTATTACATTATAATTATCGGTTTCGATATTTT
* * * *
5861081 TGGGATCGATACAATTTTAAATGTATCGAAACTTTATGTGTGCACCTCGTTGGGCATTCATTTTG
131 TGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGCATTCATTCTG
5861146 GAC
196 GAC
* * * * *
5861149 AAAACGTATTGAAACAATTTTAAAAAGTGTTGATACATTATGTAGACCTATTTTCTCATAAAACC
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACC
* ** * * * *
5861214 GGTATTTTCTATTGGTTACATTGTGAATTTACCTATTACATTGTAATTATCGGTTTTGATATTTT
66 AGTATTTTCTACCGGTTACATTGTAAAATTACCTATTACATTATAATTATCGGTTTCGATATTTT
* *
5861279 TGGGATCGATACAATTTTAAATGTATCGACATTTTATGCGTGCAACTCGTTTGGCCATTCATTCT
131 TGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTTGG-CATTCATTCT
5861344 GGAC
195 GGAC
* * *
5861348 AAAAAATATTGACACAAATTTTAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACC
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACC
** * *
5861413 -GATATTTTCTACCGGTTACATTACAAAATTACCTATTACATTCTAATTAGCGGTTTCGATATTT
66 AG-TATTTTCTACCGGTTACATTGTAAAATTACCTATTACATTATAATTATCGGTTTCGATATTT
* **
5861477 TTGGGATCAATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTCGTTTTGGCATTCATT
130 TTGGGATCGATACAATTT-TAAATGTATCGACACTTTATGCGTGCACCTCG-TTTGGCATTCATT
*
5861542 ATGGAC
193 CTGGAC
*
5861548 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTA-ACCTATTTTCTTATAAAAC
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATG-TAGACCTATTTTCTCATAAAAC
* ** *
5861612 CGGTATTTTCTATAGGTTACATTGTAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTT
65 CAGTATTTTCTACCGGTTACATTGTAAAATTACCTATTACATTATAATTATCGGTTTCGATATTT
** * * *
5861677 TTGGGATCGATACTTTTTATAAATGTATTGACACTTTATACGTGCACCTTGTTTGGGCATTCATT
130 TTGGGATCGATACAATTT-TAAATGTATCGACACTTTATGCGTGCACCTCGTTT-GGCATTCATT
5861742 CTGGGA-
193 CT-GGAC
* * * *
5861748 AAAAAGTATCGACACAAGTTTGAAAAGTGTCGATACGTTATGTTGACCT
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCT
5861797 GTTACTTTAA
Statistics
Matches: 741, Mismatches: 96, Indels: 18
0.87 0.11 0.02
Matches are distributed among these distances:
198 166 0.22
199 246 0.33
200 318 0.43
201 11 0.01
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (198 bp):
AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACC
AGTATTTTCTACCGGTTACATTGTAAAATTACCTATTACATTATAATTATCGGTTTCGATATTTT
TGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGCATTCATTCTG
GAC
Found at i:5868474 original size:86 final size:85
Alignment explanation
Indices: 5868327--5868624 Score: 395
Period size: 86 Copynumber: 3.5 Consensus size: 85
5868317 CGTTTTTTCA
* * *
5868327 CAAAAAACGCCGCAATAGATATTGATATTTAGCGGCGTTTGT-ATGATAAACGCAGCAATAGGTG
1 CAAAAAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTGTCAT-AAAAACGCTGCAATAGGTG
* *
5868391 TTGATGTTTAGCAGCGTTTGT
65 TTGATATTTAGCAGCGTTTTT
*
5868412 CATAAAAACGCCGCAATAGGTATTGATATTTAGCGACGTTTGTCATAAAAACGCTGCAATAGGTG
1 CA-AAAAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTGTCATAAAAACGCTGCAATAGGTG
5868477 TTGATATTTAGCAGCGTTTTT
65 TTGATATTTAGCAGCGTTTTT
* * * *
5868498 CAGACAAACGCTGCAATAGGTGTTGATATTTAGCGGCGTTTGTCATAAAAGCG-TCGCAATAGGT
1 CA-AAAAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTGTCATAAAAACGCT-GCAATAGGT
* *
5868562 GTTAATATTTAGCAGCATTTTT
64 GTTGATATTTAGCAGCGTTTTT
* *
5868584 CAAACAAATGCCGCAATAGGT-TATGATGTTTAGCGGCGTTT
1 CAAA-AAACGCCGCAATAGGTAT-TGATATTTAGCGGCGTTT
5868625 TTCGCTAAAC
Statistics
Matches: 190, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
85 5 0.03
86 183 0.96
87 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (85 bp):
CAAAAAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTGTCATAAAAACGCTGCAATAGGTGT
TGATATTTAGCAGCGTTTTT
Found at i:5868627 original size:43 final size:43
Alignment explanation
Indices: 5868329--5868624 Score: 346
Period size: 43 Copynumber: 6.9 Consensus size: 43
5868319 TTTTTTCACA
* *
5868329 AAAAACGCCGCAATAGATATTGATATTTAGCGGCGTTTGT-AT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAT
* * * *
5868371 GATAAACGCAGCAATAGGTGTTGATGTTTAGCAGCGTTTGTCAT
1 -AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAT
* *
5868415 AAAAACGCCGCAATAGGTATTGATATTTAGCGACGTTTGTCAT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAT
* * * *
5868458 AAAAACGCTGCAATAGGTGTTGATATTTAGCAGCGTTTTTCAG
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAT
* *
5868501 ACAAACGCTGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAT
* * * * * *
5868544 AAAAGCGTCGCAATAGGTGTTAATATTTAGCAGCATTTTTCA-
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAT
* *
5868586 AACAAATGCCGCAATAGGT-TATGATGTTTAGCGGCGTTT
1 AA-AAACGCCGCAATAGGTGT-TGATATTTAGCGGCGTTT
5868625 TTCGCTAAAC
Statistics
Matches: 213, Mismatches: 37, Indels: 6
0.83 0.14 0.02
Matches are distributed among these distances:
42 3 0.01
43 208 0.98
44 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (43 bp):
AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAT
Found at i:5868647 original size:86 final size:87
Alignment explanation
Indices: 5868320--5868710 Score: 365
Period size: 86 Copynumber: 4.6 Consensus size: 87
5868310 TTTGCGGCGT
* *
5868320 TTTTTCACAAAAAACGCCGCAATA-GATATTGATATTTAGCGGCGTTTGT-ATGATAAACG-CAG
1 TTTTTCACAACAAACGCCGCAATAGGTTATTGATATTTAGCGGCGTTTGTCAT-A-AAACGCCA-
*
5868382 CAATAGGTGTTGATGTTTAGCAGCG
63 CAATAGGTGTTGATATTTAGCAGCG
* * * **
5868407 TTTGTCATAA-AAACGCCGCAATAGG-TATTGATATTTAGCGACGTTTGTCATAAAAACGCTGCA
1 TTTTTCACAACAAACGCCGCAATAGGTTATTGATATTTAGCGGCGTTTGTCAT-AAAACGCCACA
5868470 ATAGGTGTTGATATTTAGCAGCG
65 ATAGGTGTTGATATTTAGCAGCG
* * * * *
5868493 TTTTTCA-GACAAACGCTGCAATAGG-TGTTGATATTTAGCGGCGTTTGTCATAAAAGCGTCGCA
1 TTTTTCACAACAAACGCCGCAATAGGTTATTGATATTTAGCGGCGTTTGTCATAAAA-CGCCACA
* *
5868556 ATAGGTGTTAATATTTAGCAGCA
65 ATAGGTGTTGATATTTAGCAGCG
* * * * *
5868579 TTTTTCA-AACAAATGCCGCAATAGGTTA-TGATGTTTAGCGGCGTTTTTCGCTAAACCGCCACA
1 TTTTTCACAACAAACGCCGCAATAGGTTATTGATATTTAGCGGCGTTTGTC-ATAAAACGCCACA
* * * *
5868642 GTAGGTGTTGATGTCTT-GCAACA
65 ATAGGTGTTGATAT-TTAGCAGCG
** * * * *
5868665 TTTTTTTC-ACAAACGCCGCAGTAGG-TATTGATGTTTTGCGGTGTTT
1 TTTTTCACAACAAACGCCGCAATAGGTTATTGATATTTAGCGGCGTTT
5868711 CTGCTAAAAA
Statistics
Matches: 258, Mismatches: 36, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
85 7 0.03
86 232 0.90
87 19 0.07
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (87 bp):
TTTTTCACAACAAACGCCGCAATAGGTTATTGATATTTAGCGGCGTTTGTCATAAAACGCCACAA
TAGGTGTTGATATTTAGCAGCG
Found at i:5869149 original size:24 final size:21
Alignment explanation
Indices: 5869122--5869173 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 21
5869112 TCTTCTGATA
*
5869122 TGCTGCTTCTCTCTGTGTTGCCGC
1 TGCTGCTT-TCTCT-TCTT-CCGC
*
5869146 TGCTTCTTTCTCTTCTTCCGC
1 TGCTGCTTTCTCTTCTTCCGC
5869167 TGCTGCT
1 TGCTGCT
5869174 CTGGCTGCTG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 10 0.40
22 3 0.12
23 5 0.20
24 7 0.28
ACGTcount: A:0.00, C:0.35, G:0.19, T:0.46
Consensus pattern (21 bp):
TGCTGCTTTCTCTTCTTCCGC
Found at i:5871753 original size:42 final size:42
Alignment explanation
Indices: 5871705--5872071 Score: 383
Period size: 42 Copynumber: 8.8 Consensus size: 42
5871695 TTGTAAATAC
*
5871705 AAACGCCACTAAAGTACGAGTC-ATTAGCAGTGTTTGTATTCA
1 AAACGCCACTAAAGTACGAGTCTA-TAGCAGCGTTTGTATTCA
* * *
5871747 AAACGCCACTACAGTACGAGTCTATAGC-GACTTTTGCATTCA
1 AAACGCCACTAAAGTACGAGTCTATAGCAG-CGTTTGTATTCA
*
5871789 AAACGCCACTAAAGTACGAGTCTATAGC-GACGTTTGTA-TAA
1 AAACGCCACTAAAGTACGAGTCTATAGCAG-CGTTTGTATTCA
*
5871830 AAACGCCACTAAAGTACGAGTC-ATTAGCAGTGTTTGTATTCA
1 AAACGCCACTAAAGTACGAGTCTA-TAGCAGCGTTTGTATTCA
* *
5871872 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATTGA
1 AAACGCCACTAAAGTACGAGTCTATAGCAGCGTTTGTATTCA
* * * * *
5871914 AAACGCCACTAAAGTAAGAGTCTATAGCGGCATTTATA-TAA
1 AAACGCCACTAAAGTACGAGTCTATAGCAGCGTTTGTATTCA
* * ** * *
5871955 AAATGCCACTAAAGTACTAGTCTATAGTGGCGTTTATA-TAA
1 AAACGCCACTAAAGTACGAGTCTATAGCAGCGTTTGTATTCA
* * * * * *
5871996 AAATGCTACTAAAGTACGTGTCTTTAG-AGGCATTTGCATTCA
1 AAACGCCACTAAAGTACGAGTCTATAGCA-GCGTTTGTATTCA
* *
5872038 AAACGCCACTAAAGTA-GAGTTTATAGCGGCGTTT
1 AAACGCCACTAAAGTACGAGTCTATAGCAGCGTTT
5872072 TTGGATACAA
Statistics
Matches: 278, Mismatches: 38, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
40 1 0.00
41 115 0.41
42 160 0.58
43 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (42 bp):
AAACGCCACTAAAGTACGAGTCTATAGCAGCGTTTGTATTCA
Found at i:5871874 original size:83 final size:84
Alignment explanation
Indices: 5871705--5872071 Score: 412
Period size: 83 Copynumber: 4.4 Consensus size: 84
5871695 TTGTAAATAC
* * * *
5871705 AAACGCCACTAAAGTACGAGTC-ATTAGCAGTGTTTGTATTCAAAACGCCACTACAGTACGAGTC
1 AAACGCCACTAAAGTACGAGTCTA-TAGCGGCGTTTGTATTAAAAACGCCACTAAAGTACGAGTC
*
5871769 TATAGCGACT-TTTGCATTCA
65 TATAGC-AGTGTTTGCATTCA
*
5871789 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTA-TAAAAACGCCACTAAAGTACGAGTC-
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATTAAAAACGCCACTAAAGTACGAGTCT
*
5871852 ATTAGCAGTGTTTGTATTCA
66 A-TAGCAGTGTTTGCATTCA
* *
5871872 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATTGAAAACGCCACTAAAGTAAGAGTCT
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATTAAAAACGCCACTAAAGTACGAGTCT
* ** *
5871937 ATAGCGGCATTT--ATATAA
66 ATAGCAGTGTTTGCAT-TCA
* * * * * * *
5871955 AAATGCCACTAAAGTACTAGTCTATAGTGGCGTTTATA-TAAAAATGCTACTAAAGTACGTGTCT
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATTAAAAACGCCACTAAAGTACGAGTCT
*
5872019 TTAG-AG-GCATTTGCATTCA
66 ATAGCAGTG--TTTGCATTCA
*
5872038 AAACGCCACTAAAGTA-GAGTTTATAGCGGCGTTT
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTT
5872072 TTGGATACAA
Statistics
Matches: 242, Mismatches: 31, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
81 1 0.00
82 47 0.19
83 126 0.52
84 66 0.27
85 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (84 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATTAAAAACGCCACTAAAGTACGAGTCT
ATAGCAGTGTTTGCATTCA
Found at i:5871927 original size:125 final size:124
Alignment explanation
Indices: 5871705--5872071 Score: 495
Period size: 125 Copynumber: 3.0 Consensus size: 124
5871695 TTGTAAATAC
*
5871705 AAACGCCACTAAAGTACGAGTCATTAGCAGTGTTTGTATTCAAAACGCCACTACAGTACGAGTCT
1 AAACGCCACTAAAGTACGAGTCATTAGCAGTGTTTGTATTCAAAACGCCACTAAAGTACGAGTCT
* * * *
5871770 ATAGCGACTTTTGCATTCAAAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
66 ATAGCGGCATTTGCATTCAAAACGCCACTAAAGTA-GAGTCTATAGCGGCGTTTATATAA
5871830 AAACGCCACTAAAGTACGAGTCATTAGCAGTGTTTGTATTCAAAACGCCACTAAAGTACGAGTCT
1 AAACGCCACTAAAGTACGAGTCATTAGCAGTGTTTGTATTCAAAACGCCACTAAAGTACGAGTCT
* * * *
5871895 ATAGCGGCGTTTGTATTGAAAACGCCACTAAAGTAAGAGTCTATAGCGGCATTTATATAA
66 ATAGCGGCATTTGCATTCAAAACGCCACTAAAGT-AGAGTCTATAGCGGCGTTTATATAA
* * ** * * * * * *
5871955 AAATGCCACTAAAGTACTAGTC-TATAGTGGCGTTTATA-TAAAAATGCTACTAAAGTACGTGTC
1 AAACGCCACTAAAGTACGAGTCAT-TAGCAGTGTTTGTATTCAAAACGCCACTAAAGTACGAGTC
* * *
5872018 TTTAGAGGCATTTGCATTCAAAACGCCACTAAAGTAGAGTTTATAGCGGCGTTT
65 TATAGCGGCATTTGCATTCAAAACGCCACTAAAGTAGAGTCTATAGCGGCGTTT
5872072 TTGGATACAA
Statistics
Matches: 215, Mismatches: 25, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
123 17 0.08
124 52 0.24
125 145 0.67
126 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (124 bp):
AAACGCCACTAAAGTACGAGTCATTAGCAGTGTTTGTATTCAAAACGCCACTAAAGTACGAGTCT
ATAGCGGCATTTGCATTCAAAACGCCACTAAAGTAGAGTCTATAGCGGCGTTTATATAA
Found at i:5872084 original size:42 final size:43
Alignment explanation
Indices: 5871701--5872134 Score: 311
Period size: 42 Copynumber: 10.4 Consensus size: 43
5871691 GCGTTTGTAA
* *
5871701 ATACAAACGCCACTAAAGTACGAGTC-ATTAGC--AGTGTTTGT
1 ATACAAACGCCACTAAAGTACGAGTCTA-TAGCGGCGTTTTTGT
* * * *
5871742 ATTCAAAACGCCACTACAGTACGAGTCTATAGCGAC--TTTTGC
1 ATAC-AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTTTGT
* *
5871784 ATTCAAAACGCCACTAAAGTACGAGTCTATAGCGACG--TTTGT
1 ATAC-AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTTTGT
* * *
5871826 ATAAAAACGCCACTAAAGTACGAGTC-ATTAGC--AGTGTTTGT
1 ATACAAACGCCACTAAAGTACGAGTCTA-TAGCGGCGTTTTTGT
*
5871867 ATTCAAAACGCCACTAAAGTACGAGTCTATAGCGGCG--TTTGT
1 ATAC-AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTTTGT
* * *
5871909 ATTGA-AAACGCCACTAAAGTAAGAGTCTATAGCGGC--ATTTAT
1 A-T-ACAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTTTGT
* * * * *
5871951 ATAAAAATGCCACTAAAGTACTAGTCTATAGTGGCG--TTTAT
1 ATACAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTTTGT
* * * * * * * *
5871992 ATAAAAATGCTACTAAAGTACGTGTCTTTAGAGGC--ATTTGC
1 ATACAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTTTGT
* * *
5872033 ATTCAAAACGCCACTAAAGTA-GAGTTTATAGCGGCGTTTTTGG
1 ATAC-AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTTTGT
* *
5872076 ATACAAACGCCACAAAATGT-C-AGATCTATAGCGGCGTTTCTAG-
1 ATACAAACGCCACTAAA-GTACGAG-TCTATAGCGGCGTTT-TTGT
5872119 ATACAAACGCCACTAA
1 ATACAAACGCCACTAA
5872135 TTACCTTTTA
Statistics
Matches: 326, Mismatches: 42, Indels: 48
0.78 0.10 0.12
Matches are distributed among these distances:
39 1 0.00
40 2 0.01
41 114 0.35
42 165 0.51
43 41 0.13
44 3 0.01
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.27
Consensus pattern (43 bp):
ATACAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTTTGT
Found at i:5872652 original size:43 final size:41
Alignment explanation
Indices: 5872617--5872781 Score: 131
Period size: 41 Copynumber: 4.0 Consensus size: 41
5872607 TATATATTTA
*
5872617 ACATT-TTGCGGCGTTTATACAAAAAAACGCCACTATTGATT
1 ACATTATTGCGGAGTTTAT-CAAAAAAACGCCACTATTGATT
* * *
5872658 ACATTATTGTGGAGTTTGTTAAAAAAACGCCACTATTGATT
1 ACATTATTGCGGAGTTTATCAAAAAAACGCCACTATTGATT
* * ***
5872699 AAAACTATTGCGGCA-TTT-TTGTAAAAACGCCACTATTGATT
1 -ACATTATTGCGG-AGTTTATCAAAAAAACGCCACTATTGATT
* * * * * *
5872740 AACACTATTACGGCGTTTGTC-TAAAAACGCCACTATTTATT
1 -ACATTATTGCGGAGTTTATCAAAAAAACGCCACTATTGATT
5872781 A
1 A
5872782 TAAATATTGC
Statistics
Matches: 105, Mismatches: 14, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
40 1 0.01
41 80 0.76
42 23 0.22
43 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34
Consensus pattern (41 bp):
ACATTATTGCGGAGTTTATCAAAAAAACGCCACTATTGATT
Found at i:5872682 original size:41 final size:42
Alignment explanation
Indices: 5872637--5872798 Score: 165
Period size: 41 Copynumber: 3.9 Consensus size: 42
5872627 GCGTTTATAC
* *
5872637 AAAAAAACGCCACTATTGATT-ACATTATTGTGGAGTTTGTT
1 AAAAAAACGCCACTATTGATTAACACTATTGCGGAGTTTGTT
*
5872678 AAAAAAACGCCACTATTGATTAAAACTATTGCGGCA-TTT-TT
1 AAAAAAACGCCACTATTGATTAACACTATTGCGG-AGTTTGTT
** * *
5872719 GTAAAAACGCCACTATTGATTAACACTATTACGGCGTTTGTCT
1 AAAAAAACGCCACTATTGATTAACACTATTGCGGAGTTTGT-T
* * *
5872762 --AAAAACGCCACTATTTATTATA-AATATTGCGGCGTTT
1 AAAAAAACGCCACTATTGATTA-ACACTATTGCGGAGTTT
5872799 TAAGAATAAA
Statistics
Matches: 104, Mismatches: 11, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
41 88 0.85
42 14 0.13
43 2 0.02
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Consensus pattern (42 bp):
AAAAAAACGCCACTATTGATTAACACTATTGCGGAGTTTGTT
Found at i:5872838 original size:83 final size:82
Alignment explanation
Indices: 5872639--5872842 Score: 222
Period size: 82 Copynumber: 2.5 Consensus size: 82
5872629 GTTTATACAA
* *
5872639 AAAAACGCCACTATTGATT-ACATTATTGTGGAGTTTGTTAAAAAAACGCCACTATTGATTAAAA
1 AAAAACGCCACTATTGATTAACACTATTGTGGCGTTTGTT-AAAAAACGCCACTATTGATTAAAA
*
5872703 CTATTGCGGCATTTTTGT
65 CTATTGCGGCATTTTAGT
** *
5872721 AAAAACGCCACTATTGATTAACACTATTACGGCGTTTGTCT-AAAAACGCCACTATTTATTATAA
1 AAAAACGCCACTATTGATTAACACTATTGTGGCGTTTGT-TAAAAAACGCCACTATTGATTA-AA
*
5872785 A-TATTGCGGCGTTTTAAG-
64 ACTATTGCGGCATTTT-AGT
* *
5872803 AATAAATGCCACTATATG-TGTAA-TCTATTGTGGCGTTTGT
1 AA-AAACGCCACTAT-TGAT-TAACACTATTGTGGCGTTTGT
5872843 GGTATAAATG
Statistics
Matches: 104, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
82 53 0.51
83 45 0.43
84 6 0.06
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (82 bp):
AAAAACGCCACTATTGATTAACACTATTGTGGCGTTTGTTAAAAAACGCCACTATTGATTAAAAC
TATTGCGGCATTTTAGT
Found at i:5872850 original size:42 final size:41
Alignment explanation
Indices: 5872686--5872998 Score: 144
Period size: 42 Copynumber: 7.5 Consensus size: 41
5872676 TTAAAAAAAC
* * * * *
5872686 GCCACTAT-TGATTAAAACTATTGCGGCATTT-TTGTAAAAAC
1 GCCACTATATG-TT-AATCTATTGCGGCGTTTGTGGTATAAAT
* * * * *
5872727 GCCACTAT-TGATTAACACTATTACGGCGTTTGT-CTAAAAAC
1 GCCACTATATG-TTAA-TCTATTGCGGCGTTTGTGGTATAAAT
* * ** * *
5872768 GCCACTATTTATTATAAATATTGCGGCGTTT-TAAGAATAAAT
1 GCCACTATATGTTA-ATCTATTGCGGCGTTTGT-GGTATAAAT
*
5872810 GCCACTATATGTGTAATCTATTGTGGCGTTTGTGGTATAAAT
1 GCCACTATATGT-TAATCTATTGCGGCGTTTGTGGTATAAAT
* * *
5872852 GCCGCTA-AT-TTACCGATCTATTACGGCGTTT-TGGCTA-AAAC
1 GCCACTATATGTTA---ATCTATTGCGGCGTTTGTGG-TATAAAT
* * *
5872893 ACCACTATATGTTAATCTATTGCGGCATTTGTGGTATAAAC
1 GCCACTATATGTTAATCTATTGCGGCGTTTGTGGTATAAAT
* * * * *
5872934 GCCGCTA-AT-TTACCACTCTATTACGGCGTTTGTTGTAAAAAC
1 GCCACTATATGTTA--A-TCTATTGCGGCGTTTGTGGTATAAAT
* *
5872976 GCCGCTATATGTCAACTCTATTG
1 GCCACTATATGTTAA-TCTATTG
5872999 AAGCGTTTTT
Statistics
Matches: 218, Mismatches: 33, Indels: 41
0.75 0.11 0.14
Matches are distributed among these distances:
39 5 0.02
40 22 0.10
41 83 0.38
42 98 0.45
43 8 0.04
44 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (41 bp):
GCCACTATATGTTAATCTATTGCGGCGTTTGTGGTATAAAT
Found at i:5872925 original size:82 final size:83
Alignment explanation
Indices: 5872811--5872964 Score: 258
Period size: 82 Copynumber: 1.9 Consensus size: 83
5872801 AGAATAAATG
* * *
5872811 CCACTATATGTGTAATCTATTGTGGCGTTTGTGGTATAAATGCCGCTAATTTACCGA-TCTATTA
1 CCACTATATGTGTAATCTATTGCGGCATTTGTGGTATAAACGCCGCTAATTTACC-ACTCTATTA
5872875 CGGCGTTTTGGCTAAAACA
65 CGGCGTTTTGGCTAAAACA
5872894 CCACTATATGT-TAATCTATTGCGGCATTTGTGGTATAAACGCCGCTAATTTACCACTCTATTAC
1 CCACTATATGTGTAATCTATTGCGGCATTTGTGGTATAAACGCCGCTAATTTACCACTCTATTAC
5872958 GGCGTTT
66 GGCGTTT
5872965 GTTGTAAAAA
Statistics
Matches: 67, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
81 1 0.01
82 55 0.82
83 11 0.16
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (83 bp):
CCACTATATGTGTAATCTATTGCGGCATTTGTGGTATAAACGCCGCTAATTTACCACTCTATTAC
GGCGTTTTGGCTAAAACA
Found at i:5872973 original size:82 final size:83
Alignment explanation
Indices: 5872811--5872998 Score: 256
Period size: 82 Copynumber: 2.3 Consensus size: 83
5872801 AGAATAAATG
* * *
5872811 CCACTATATGTGTAATCTATTGTGGCGTTTGTGGTATAAATGCCGCTAATTTACCGATCTATTAC
1 CCACTATATGT-TAATCTATTGCGGCATTTGTGGTATAAACGCCGCTAATTTACCGATCTATTAC
5872876 GGCGTTTTGGCT-AAAACA
65 GGCGTTTTGGCTAAAAACA
5872894 CCACTATATGTTAATCTATTGCGGCATTTGTGGTATAAACGCCGCTAATTTACC-ACTCTATTAC
1 CCACTATATGTTAATCTATTGCGGCATTTGTGGTATAAACGCCGCTAATTTACCGA-TCTATTAC
* *
5872958 GGCGTTTGTTG-TAAAAACG
65 GGCGTTT-TGGCTAAAAACA
* *
5872977 CCGCTATATGTCAACTCTATTG
1 CCACTATATGTTAA-TCTATTG
5872999 AAGCGTTTTT
Statistics
Matches: 94, Mismatches: 7, Indels: 7
0.87 0.06 0.06
Matches are distributed among these distances:
81 1 0.01
82 56 0.60
83 30 0.32
84 7 0.07
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.36
Consensus pattern (83 bp):
CCACTATATGTTAATCTATTGCGGCATTTGTGGTATAAACGCCGCTAATTTACCGATCTATTACG
GCGTTTTGGCTAAAAACA
Found at i:5873005 original size:42 final size:42
Alignment explanation
Indices: 5872888--5873024 Score: 111
Period size: 42 Copynumber: 3.3 Consensus size: 42
5872878 CGTTTTGGCT
* * * * * *
5872888 AAAACACCACTATATGTTAA-TCTATTGCGGCATTTGTGGTA
1 AAAACGCCGCTATATGTCAACTCTATTGAGGCGTTTGTTGTA
* * *
5872929 TAAACGCCGCTA-ATTTACCACTCTATT-ACGGCGTTTGTTGTA
1 AAAACGCCGCTATATGT-CAACTCTATTGA-GGCGTTTGTTGTA
* **
5872971 AAAACGCCGCTATATGTCAACTCTATTGAAGCGTTT-TTACA
1 AAAACGCCGCTATATGTCAACTCTATTGAGGCGTTTGTTGTA
5873012 ACAAACGCCGCTA
1 A-AAACGCCGCTA
5873025 AAGTATCAAT
Statistics
Matches: 75, Mismatches: 15, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
40 3 0.04
41 14 0.19
42 54 0.72
43 4 0.05
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (42 bp):
AAAACGCCGCTATATGTCAACTCTATTGAGGCGTTTGTTGTA
Found at i:5873375 original size:42 final size:42
Alignment explanation
Indices: 5873284--5873393 Score: 123
Period size: 42 Copynumber: 2.6 Consensus size: 42
5873274 ATTATAGATT
* * * ** *
5873284 AACCCTATTATGGCATTTATAT-AAAAATGCCGCTATTGATG
1 AACCCTATTATGGCGTTTGTATAAAAAATGCCACTATAAACG
* *
5873325 AACTCTATTACGGCGTTTGTATAAAAAATGCCACTATAAACG
1 AACCCTATTATGGCGTTTGTATAAAAAATGCCACTATAAACG
**
5873367 AACCCTATTATGATGTTTGTATAAAAA
1 AACCCTATTATGGCGTTTGTATAAAAA
5873394 CCCCGCTAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
41 18 0.32
42 38 0.68
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (42 bp):
AACCCTATTATGGCGTTTGTATAAAAAATGCCACTATAAACG
Found at i:5876856 original size:23 final size:23
Alignment explanation
Indices: 5876843--5876914 Score: 90
Period size: 23 Copynumber: 3.1 Consensus size: 23
5876833 ATAATTCTAC
5876843 GTGGTCATTCGGGACAATACTAT
1 GTGGTCATTCGGGACAATACTAT
* *
5876866 GTGGTCCTTCAGGACAATACTAT
1 GTGGTCATTCGGGACAATACTAT
* * * *
5876889 GTGGTCCTTCAGGACATTTCTAT
1 GTGGTCATTCGGGACAATACTAT
5876912 GTG
1 GTG
5876915 CCACTTCGGT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.33
Consensus pattern (23 bp):
GTGGTCATTCGGGACAATACTAT
Found at i:5881522 original size:23 final size:23
Alignment explanation
Indices: 5881461--5881558 Score: 74
Period size: 23 Copynumber: 4.2 Consensus size: 23
5881451 CCTGTGGTTT
* *
5881461 TTCGGGACATTTCTATATAGTCC
1 TTCGGGACATTTCTATGTGGTCC
* * * * *
5881484 TTTGGGGCAATACTATGGGGTCC
1 TTCGGGACATTTCTATGTGGTCC
5881507 TTCGGGACATTTCTATGTGG-CAC
1 TTCGGGACATTTCTATGTGGTC-C
* *
5881530 TTCGGTACAATTTCTACGTGG-CAC
1 TTCGGGAC-ATTTCTATGTGGTC-C
5881554 TTCGG
1 TTCGG
5881559 TGCAATTTAT
Statistics
Matches: 59, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
22 1 0.02
23 39 0.66
24 19 0.32
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (23 bp):
TTCGGGACATTTCTATGTGGTCC
Found at i:5881550 original size:24 final size:24
Alignment explanation
Indices: 5881506--5881571 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
5881496 CTATGGGGTC
* *
5881506 CTTCGGGAC-ATTTCTATGTGGCA
1 CTTCGGTACAATTTCTACGTGGCA
5881529 CTTCGGTACAATTTCTACGTGGCA
1 CTTCGGTACAATTTCTACGTGGCA
* *
5881553 CTTCGGTGCAATTTATACG
1 CTTCGGTACAATTTCTACG
5881572 AGTTGTGGTG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
23 8 0.21
24 30 0.79
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.35
Consensus pattern (24 bp):
CTTCGGTACAATTTCTACGTGGCA
Done.