Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007926.1 Hibiscus syriacus cultivar Beakdansim tig00110332_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: 10075380
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 29 of 42
Found at i:6128012 original size:20 final size:19
Alignment explanation
Indices: 6127966--6128036 Score: 115
Period size: 19 Copynumber: 3.7 Consensus size: 19
6127956 GAAACAAAAA
*
6127966 TCGCATTGCGATTTTTATT
1 TCGCGTTGCGATTTTTATT
6127985 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTTATT
*
6128004 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTTATT
6128024 TCGCGTTGCGATT
1 TCGCGTTGCGATT
6128037 GTCTGGTCGC
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 31 0.63
20 18 0.37
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (19 bp):
TCGCGTTGCGATTTTTATT
Found at i:6128061 original size:33 final size:33
Alignment explanation
Indices: 6128019--6128106 Score: 124
Period size: 33 Copynumber: 2.6 Consensus size: 33
6128009 GTTGCGATTT
* *
6128019 TCATTTCGCGTTGCGATTGTCTGGTCGCTG-TAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGC-GATAG
*
6128052 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
6128085 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
6128107 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
32 1 0.02
33 34 0.68
34 15 0.30
ACGTcount: A:0.10, C:0.25, G:0.25, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:6128108 original size:20 final size:20
Alignment explanation
Indices: 6128074--6128131 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
6128064 GCGATTCTCT
**
6128074 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
6128094 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
6128114 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
6128132 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:6130213 original size:21 final size:21
Alignment explanation
Indices: 6130189--6130255 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
6130179 TCATTCCTCG
6130189 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
6130210 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
6130231 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
6130252 AGAG
1 AGAG
6130256 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:6130213 original size:42 final size:42
Alignment explanation
Indices: 6130133--6130255 Score: 115
Period size: 42 Copynumber: 2.9 Consensus size: 42
6130123 GCCCGACTCA
* * * * * *
6130133 CCTATCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
*
6130175 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
* * * *
6130217 ACTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCCTCCCACCATTCAAGAG
6130256 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 61 0.91
43 2 0.03
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.23
Consensus pattern (42 bp):
CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
Found at i:6131633 original size:14 final size:14
Alignment explanation
Indices: 6131614--6131649 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
6131604 ATTGTTTAAT
6131614 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
6131628 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
6131642 TGATTTGT
1 TGATTTGT
6131650 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:6131859 original size:19 final size:19
Alignment explanation
Indices: 6131828--6131958 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
6131818 CGAAATTAAA
6131828 TTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
6131847 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
6131863 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
6131880 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
6131894 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
6131913 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
* *
6131929 CTCG--TTGCGATTTTTAT
1 TTCGCATTGCGATTTTCAT
6131946 TTCGCATTGCGAT
1 TTCGCATTGCGAT
6131959 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 23 0.27
16 12 0.14
17 13 0.15
19 36 0.43
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:6131876 original size:33 final size:32
Alignment explanation
Indices: 6131834--6131958 Score: 180
Period size: 33 Copynumber: 3.8 Consensus size: 32
6131824 TAAATTCGCA
6131834 TTGCGATTTTCATTTCGCATTGCGATTCCCTCG
1 TTGCGATTTTCATTTCGCATTGCGATT-CCTCG
**
6131867 TTGCGATTTTCATTTCGCATTGCGAAATT-AGCG
1 TTGCGATTTTCATTTCGCATTGCG--ATTCCTCG
6131900 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTC-CTCG
*
6131933 TTGCGATTTTTATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
6131959 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 5, Indels: 8
0.86 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 77 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (32 bp):
TTGCGATTTTCATTTCGCATTGCGATTCCTCG
Found at i:6131921 original size:66 final size:66
Alignment explanation
Indices: 6131825--6131957 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
6131815 ACGCGAAATT
*
6131825 AAATTCGCATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
6131890 G
66 G
* * *
6131891 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTTATTTCGCATTGC
1 AAATTAGCATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
6131956 G
66 G
6131957 A
1 A
6131958 TAGTAATTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (66 bp):
AAATTAGCATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:6134262 original size:12 final size:12
Alignment explanation
Indices: 6134245--6134269 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6134235 TCTTCGGGGA
6134245 CTTTTTCTTCTT
1 CTTTTTCTTCTT
6134257 CTTTTTCTTCTT
1 CTTTTTCTTCTT
6134269 C
1 C
6134270 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:6134478 original size:24 final size:24
Alignment explanation
Indices: 6134444--6134497 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
6134434 CTTAAACATC
* *
6134444 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
6134468 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
6134492 ATCAAA
1 ATCAAA
6134498 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:6135568 original size:20 final size:20
Alignment explanation
Indices: 6135543--6135580 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6135533 ATTCATTTGA
*
6135543 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
6135563 CTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
6135581 CGCAATGCGA
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:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:6135636 original size:33 final size:33
Alignment explanation
Indices: 6135599--6135676 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
6135589 GAAATGAAAA
***
6135599 TCGCATTGCGATTTTCTCGA-TGCGATTTTCATT
1 TCGCATTGCGATTTTCTC-ATTGCGATAGCCATT
6135632 TCGCATTGCGATTTTCTCATTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCATTGCGATAGCCATT
*
6135665 TCGCGTTGCGAT
1 TCGCATTGCGAT
6135677 AGTCTGTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 1 0.03
33 39 0.98
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.41
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCATTGCGATAGCCATT
Found at i:6135641 original size:19 final size:16
Alignment explanation
Indices: 6135599--6135657 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 16
6135589 GAAATGAAAA
6135599 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
6135615 TCG-A-TGCGATTTTC
1 TCGCATTGCGATTTTC
6135629 ATTTCGCATTGCGATTTTC
1 ---TCGCATTGCGATTTTC
6135648 T--CATTGCGAT
1 TCGCATTGCGAT
6135658 AGCCATTTCG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
14 19 0.50
15 1 0.03
16 4 0.11
17 3 0.08
18 1 0.03
19 10 0.26
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (16 bp):
TCGCATTGCGATTTTC
Found at i:6135783 original size:14 final size:14
Alignment explanation
Indices: 6135764--6135800 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
6135754 CATCAATTAA
6135764 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
6135778 ACAAATCATCTTTT
1 ACAAATCAACATTT
6135792 ACAAATCAA
1 ACAAATCAA
6135801 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:6137704 original size:20 final size:19
Alignment explanation
Indices: 6137669--6137735 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
6137659 GAAACTTAAA
6137669 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
6137688 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
6137708 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
6137727 ATCGCAACG
1 ATCGCAACG
6137736 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:6137743 original size:14 final size:14
Alignment explanation
Indices: 6137724--6137781 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
6137714 ATGCGAAATG
6137724 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
6137738 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
6137754 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
6137770 AAAATCGCAACG
1 AAAATCGCAACG
6137782 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:6137766 original size:32 final size:33
Alignment explanation
Indices: 6137708--6137786 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
6137698 GGAAATGGCT
*
6137708 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
6137741 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
6137773 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
6137787 CACAAATCGT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:6137838 original size:14 final size:14
Alignment explanation
Indices: 6137815--6137872 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
6137805 TTTCATTTCA
6137815 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
* *
6137829 CGTTGTGATTTCATTT
1 CGTTGCGATTT--TGT
*
6137845 CGCATTGTGATTTTGT
1 CG--TTGCGATTTTGT
6137861 CGTTGCGATTTT
1 CGTTGCGATTTT
6137873 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.53
16 8 0.22
18 9 0.25
ACGTcount: A:0.10, C:0.14, G:0.24, T:0.52
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:6137879 original size:33 final size:33
Alignment explanation
Indices: 6137798--6137888 Score: 139
Period size: 32 Copynumber: 2.8 Consensus size: 33
6137788 ACAAATCGTA
* *
6137798 TTGCGATTTTCATTTCACGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
* *
6137831 TTGTGA-TTTCATTTCGCATTGTGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
6137863 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
6137889 AGCCATTTCC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
32 28 0.55
33 23 0.45
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:6137907 original size:20 final size:19
Alignment explanation
Indices: 6137873--6137927 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
6137863 TTGCGATTTT
*
6137873 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
6137892 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
6137912 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
6137928 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:6138435 original size:18 final size:18
Alignment explanation
Indices: 6138409--6138453 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
6138399 GTCGATCAGA
*
6138409 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
6138427 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
6138445 TGATGGCTC
1 TGATGGCTC
6138454 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:6139798 original size:20 final size:20
Alignment explanation
Indices: 6139773--6139815 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
6139763 AATAGTTTCT
6139773 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
6139793 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
6139813 GAA
1 GAA
6139816 TTCGACTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.19, G:0.19, T:0.09
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:6140121 original size:22 final size:22
Alignment explanation
Indices: 6140094--6140137 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
6140084 GATGGAGATA
6140094 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
6140116 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
6140138 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:6140350 original size:20 final size:20
Alignment explanation
Indices: 6140325--6140417 Score: 159
Period size: 20 Copynumber: 4.7 Consensus size: 20
6140315 GATTATGTAT
6140325 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
6140345 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
**
6140365 TATATCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
6140385 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
6140405 TATCTCGTTGCGA
1 TATCGCGTTGCGA
6140418 TTTTTTATTA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:6140436 original size:21 final size:21
Alignment explanation
Indices: 6140403--6140503 Score: 59
Period size: 20 Copynumber: 4.9 Consensus size: 21
6140393 TGCGAAAGTA
* * *
6140403 AGTATCTCGTTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
6140424 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
*
6140444 AGTATCGCATTGCGATTTTCCC
1 AGTATCGCATTGCGATTTT-TC
* *
6140466 AAT-TCGCGTTGCGATTTACTT-
1 AGTATCGCATTGCGATTT--TTC
6140487 A-T-TCGCATTGCGATTTT
1 AGTATCGCATTGCGATTTT
6140504 CCCAATTCGC
Statistics
Matches: 62, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
18 1 0.02
20 30 0.48
21 27 0.44
22 3 0.05
23 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.43
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:6140478 original size:41 final size:41
Alignment explanation
Indices: 6140387--6140521 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
6140377 AAAGTAAGTA
* * * ** *
6140387 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
6140427 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
6140469 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
6140510 TCGCGTTGCGAT
1 TCGCGTTGCGAT
6140522 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:6140513 original size:21 final size:20
Alignment explanation
Indices: 6140448--6140540 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
6140438 ATAGTCAGTA
*
6140448 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* **
6140469 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
*
6140489 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* **
6140510 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
6140530 TCGCATTGCGA
1 TCGCATTGCGA
6140541 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACCAAT
Found at i:6140522 original size:41 final size:41
Alignment explanation
Indices: 6140448--6140540 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
6140438 ATAGTCAGTA
6140448 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
6140489 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
6140530 TCGCATTGCGA
1 TCGCATTGCGA
6140541 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:6141223 original size:23 final size:25
Alignment explanation
Indices: 6141178--6141224 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
6141168 AAATTCATAA
*
6141178 AATTTTAGATAAAATAAACTTAAAG
1 AATTTTAGAGAAAATAAACTTAAAG
*
6141203 AATTTTATAGAAAA-AAA-TTAAA
1 AATTTTAGAGAAAATAAACTTAAA
6141225 TTACCTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 3 0.15
25 12 0.60
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (25 bp):
AATTTTAGAGAAAATAAACTTAAAG
Found at i:6144083 original size:25 final size:25
Alignment explanation
Indices: 6144051--6144105 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
6144041 TTGGGTATAG
*
6144051 AAATAAATATAAAAAAGTTAAATAT
1 AAATAAATATAAAAAAGTTAAATAA
* *
6144076 AAATAAATATAAATAAGTTAAGTAA
1 AAATAAATATAAAAAAGTTAAATAA
6144101 AAATA
1 AAATA
6144106 TCATGAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.27
Consensus pattern (25 bp):
AAATAAATATAAAAAAGTTAAATAA
Found at i:6153841 original size:26 final size:26
Alignment explanation
Indices: 6153805--6153882 Score: 129
Period size: 26 Copynumber: 3.0 Consensus size: 26
6153795 GTTCTGTTCG
6153805 TTTATGTTCACGAAGAAGCTCGTTTA
1 TTTATGTTCACGAAGAAGCTCGTTTA
6153831 TTTATGTTCACGAAGAAGCTCGTTTA
1 TTTATGTTCACGAAGAAGCTCGTTTA
* * *
6153857 TTTATGTTCATGAACAAACTCGTTTA
1 TTTATGTTCACGAAGAAGCTCGTTTA
6153883 CCCGATTCTC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (26 bp):
TTTATGTTCACGAAGAAGCTCGTTTA
Found at i:6154091 original size:22 final size:22
Alignment explanation
Indices: 6154066--6154118 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
6154056 AAATGAATGA
6154066 TAAACAAA-TACTAAAACAACAC
1 TAAACAAACT-CTAAAACAACAC
** *
6154088 TAAACAAACTCTAAATGAACAT
1 TAAACAAACTCTAAAACAACAC
6154110 TAAACAAAC
1 TAAACAAAC
6154119 ATGTTCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 26 0.96
23 1 0.04
ACGTcount: A:0.60, C:0.21, G:0.02, T:0.17
Consensus pattern (22 bp):
TAAACAAACTCTAAAACAACAC
Found at i:6154239 original size:23 final size:23
Alignment explanation
Indices: 6154202--6154245 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
6154192 ATGTTCATGA
*
6154202 ACATGTTCGCAAACATTAAATGC
1 ACATGTTCGCAAACAATAAATGC
**
6154225 ACATGTTCGTGAACAATAAAT
1 ACATGTTCGCAAACAATAAAT
6154246 AAACGAACAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (23 bp):
ACATGTTCGCAAACAATAAATGC
Found at i:6156045 original size:158 final size:159
Alignment explanation
Indices: 6155878--6156309 Score: 473
Period size: 158 Copynumber: 2.7 Consensus size: 159
6155868 TTATCTATTT
*
6155878 AATTTAGATATTAAAAGAGTTTTGATTGGAGTAAAACTCTCAGGTTTAATATTATAAATTTAAAA
1 AATTTAGATATTAAAAGAGTTTTGATTAGAGTAAAACTCTCAGGTTTAATATTATAAATTTAAAA
* *
6155943 TATATTATTTGTTTAAATTTAAATATTAAAAGAGTTTTGGTTTGGAGTAAAACTT-TCA-AGTT-
66 -ATATTA-TTATTT-AATTTAAATATTAAAAGAGTTTT-G-TTAGAGTAAAACTTCTCATAGTTA
6156005 ATAT-TATAAATTTAAAAGATATTAT-T-TG-TTA
126 ATATGT-TAAATTTAAAAGATATTATATATGTTTA
* * * *
6156036 AATTTAGATATTAAAAGAG-TTGGTTTTGAGTAAAAACTCTCAGGTTGAATA-TATAAA--TAAA
1 AATTTAGATATTAAAAGAGTTTTGATTAGAGT-AAAACTCTCAGGTTTAATATTATAAATTTAAA
* * *
6156097 GATATTA--ATTTAATTTAGATATTAAAAGAGTTTTGATTAGAGTAAAA-TTCTCATATTTAATA
65 AATATTATTATTTAATTTAAATATTAAAAGAGTTTTG-TTAGAGTAAAACTTCTCATAGTTAATA
6156159 TGTTAAATTTAAAAGATATTATAATATGTTTA
129 TGTTAAATTTAAAAGATATTAT-ATATGTTTA
* * * * * *
6156191 AATTTATATATTAAAAGAGTTTTGGTTAGAGTAAAATTCTTA-GATTAATATTTTAAATGTTAAA
1 AATTTAGATATTAAAAGAGTTTTGATTAGAGTAAAACTCTCAGGTTTAATATTATAAAT-TTAAA
* * *
6156255 AA-ATTATTATCTATTTTATATATTAAAAGAGTTTTAGTTAGAGTAAAACTCTCTC
65 AATATTATTATTTAATTTAAATATTAAAAGAGTTTT-GTTAGAGTAAAACT-TCTC
6156310 GAAATTCCCT
Statistics
Matches: 232, Mismatches: 23, Indels: 35
0.80 0.08 0.12
Matches are distributed among these distances:
148 2 0.01
149 14 0.06
150 25 0.11
151 26 0.11
152 1 0.00
153 1 0.00
154 14 0.06
155 38 0.16
156 9 0.04
157 19 0.08
158 42 0.18
159 35 0.15
160 2 0.01
161 4 0.02
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.43
Consensus pattern (159 bp):
AATTTAGATATTAAAAGAGTTTTGATTAGAGTAAAACTCTCAGGTTTAATATTATAAATTTAAAA
ATATTATTATTTAATTTAAATATTAAAAGAGTTTTGTTAGAGTAAAACTTCTCATAGTTAATATG
TTAAATTTAAAAGATATTATATATGTTTA
Found at i:6156128 original size:72 final size:75
Alignment explanation
Indices: 6155878--6156211 Score: 295
Period size: 78 Copynumber: 4.3 Consensus size: 75
6155868 TTATCTATTT
* * *
6155878 AATTTAGATATTAAAAGAGTTTTGATTGGAGTAAAACTCTCAGGTTTAATATTATAAATTTAAAA
1 AATTTAGATATTAAAAGAG-TTGGTTTGGAGTAAAACTCTCAAG-TT-ATATTATAAA-TTAAAA
* *
6155943 TATATTATTTGTTTA
62 GATATTATATG-TTA
* *
6155958 AATTTAAATATTAAAAGAGTTTTGGTTTGGAGTAAAACTTTCAAGTTATATTATAAATTTAAAAG
1 AATTTAGATATTAAAAGAG--TTGGTTTGGAGTAAAACTCTCAAGTTATATTATAAA-TTAAAAG
*
6156023 ATATTATTTGTTA
63 ATATTATATGTTA
* *
6156036 AATTTAGATATTAAAAGAGTTGGTTTTGAGTAAAAACTCTCAGGTTGA-ATATATAAA-T-AAAG
1 AATTTAGATATTAAAAGAGTTGGTTTGGAGT-AAAACTCTCAAGTT-ATAT-TATAAATTAAAAG
6156098 ATATTA-AT-TT-
63 ATATTATATGTTA
* * * * *
6156108 AATTTAGATATTAAAAGAGTTTTGATTAGAGTAAAATTCTCATATTTAATATGT-TAAATTTAAA
1 AATTTAGATATTAAAAGAG-TTGGTTTGGAGTAAAACTCTCA-AGTT-ATAT-TATAAA-TTAAA
6156172 AGATATTATAATATGTTTA
61 AGATA-T-T-ATATG-TTA
*
6156191 AATTTATATATTAAAAGAGTT
1 AATTTAGATATTAAAAGAGTT
6156212 TTGGTTAGAG
Statistics
Matches: 217, Mismatches: 20, Indels: 32
0.81 0.07 0.12
Matches are distributed among these distances:
72 28 0.13
73 18 0.08
74 4 0.02
75 11 0.05
76 19 0.09
77 15 0.07
78 29 0.13
79 28 0.13
80 22 0.10
81 21 0.10
82 4 0.02
83 18 0.08
ACGTcount: A:0.42, C:0.03, G:0.13, T:0.42
Consensus pattern (75 bp):
AATTTAGATATTAAAAGAGTTGGTTTGGAGTAAAACTCTCAAGTTATATTATAAATTAAAAGATA
TTATATGTTA
Found at i:6156202 original size:83 final size:76
Alignment explanation
Indices: 6155867--6156307 Score: 268
Period size: 76 Copynumber: 5.7 Consensus size: 76
6155857 AAACAATACT
* * * * *
6155867 ATTATCTATTTAATTTAGATATTAAAAGAGTTTTGATTGGAGTAAAACTCTCAGGTTTAATAT-T
1 ATTAT-TATCTAATTTATATATTAAAAGAGTTTTGATTAGAGTAAAATTCTCA-GATTAATATGT
6155931 ATAAAT-TTAAAATA
64 -TAAATGTTAAAA-A
* * * * *
6155945 TATTATTTGTTTAAATTTAAATATTAAAAGAGTTTTGGTTTGGAGTAAAACTT-TCA-AGTT-AT
1 -ATTA-TTATCT-AATTTATATATTAAAAGAGTTTT-GATTAGAGTAAAA-TTCTCAGA-TTAAT
6156007 AT-TATAAAT-TTAAAAGA
60 ATGT-TAAATGTTAAAA-A
* * * * * * *
6156024 TATTATT-TGTTAAATTTAGATATTAAAAGAG-TTGGTTTTGAGTAAAAACTCTCAGGTTGAATA
1 -ATTATTAT-CT-AATTTATATATTAAAAGAGTTTTGATTAGAGT-AAAATTCTCAGATT-AATA
* *
6156087 T-ATAAA---T-AAAG
61 TGTTAAATGTTAAAAA
* * *
6156098 A-TATTAATTTAATTTAGATATTAAAAGAGTTTTGATTAGAGTAAAATTCTCATATTTAATATGT
1 ATTATT-ATCTAATTTATATATTAAAAGAGTTTTGATTAGAGTAAAATTCTCAGA-TTAATATGT
6156162 TAAAT-TTAAAAGA
64 TAAATGTTAAAA-A
* * *
6156175 TATTATAATATGTTTAAATTTATATATTAAAAGAGTTTTGGTTAGAGTAAAATTCTTAGATTAAT
1 -ATTAT--TA--TCT-AATTTATATATTAAAAGAGTTTTGATTAGAGTAAAATTCTCAGATTAAT
*
6156240 ATTTTAAATGTTAAAAA
60 ATGTTAAATGTTAAAAA
* *
6156257 ATTATTATCTATTTTATATATTAAAAGAGTTTT-AGTTAGAGTAAAACTCTC
1 ATTATTATCTAATTTATATATTAAAAGAGTTTTGA-TTAGAGTAAAATTCTC
6156308 TCGAAATTCC
Statistics
Matches: 302, Mismatches: 31, Indels: 61
0.77 0.08 0.15
Matches are distributed among these distances:
72 37 0.12
73 18 0.06
74 1 0.00
75 4 0.01
76 49 0.16
77 14 0.05
78 28 0.09
79 40 0.13
80 26 0.09
81 21 0.07
82 18 0.06
83 46 0.15
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.43
Consensus pattern (76 bp):
ATTATTATCTAATTTATATATTAAAAGAGTTTTGATTAGAGTAAAATTCTCAGATTAATATGTTA
AATGTTAAAAA
Found at i:6176978 original size:31 final size:31
Alignment explanation
Indices: 6176940--6177004 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
6176930 AGAGTCGAGG
*
6176940 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTAGGTTCTACGGAACATATGGACA
** * *
6176971 GTTTACCTAGGTTCTTTGGGACCTATGGACA
1 GTTTACCTAGGTTCTACGGAACATATGGACA
6177002 GTT
1 GTT
6177005 GCTGAGGTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTTCTACGGAACATATGGACA
Found at i:6177015 original size:30 final size:30
Alignment explanation
Indices: 6176963--6177058 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
6176953 CTACGGAACA
* *
6176963 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAG-TTACCGAGGTTCTTTGTGACC
* * *
6176994 TATGGACAGTTGCTGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTGTGACC
* * *
6177024 TCTGGATAGTTACCG-GGGTCTTTGTGACC
1 TATGGACAGTTACCGAGGTTCTTTGTGACC
6177053 TATGGA
1 TATGGA
6177059 TAGGTCCTTC
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
29 17 0.32
30 27 0.51
31 9 0.17
ACGTcount: A:0.19, C:0.18, G:0.28, T:0.35
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTGTGACC
Found at i:6181862 original size:23 final size:23
Alignment explanation
Indices: 6181836--6181913 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
6181826 CACCACAGCT
6181836 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
6181859 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * *
6181882 CGTAAAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
6181905 TATAATAAT
1 CAT-ATAAT
6181914 GTCCATAAGG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 41 0.91
24 4 0.09
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:6183294 original size:21 final size:21
Alignment explanation
Indices: 6183268--6183322 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
6183258 TCTGGGCTAT
6183268 GTGCACCGATGCACATTCAAG
1 GTGCACCGATGCACATTCAAG
6183289 GTGCACCGATGCACATTCAAG
1 GTGCACCGATGCACATTCAAG
6183310 GTGCACCGATGCA
1 GTGCACCGATGCA
6183323 TCAAGGGTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.27, C:0.29, G:0.25, T:0.18
Consensus pattern (21 bp):
GTGCACCGATGCACATTCAAG
Found at i:6185041 original size:23 final size:23
Alignment explanation
Indices: 6185015--6185082 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
6185005 CCTTATATGG
*
6185015 CACTTCGGTGCATTTCTATGAGA
1 CACTTCGGTGCATTTCTACGAGA
* * * *
6185038 CACTACGGTGCAATTCTACGTGG
1 CACTTCGGTGCATTTCTACGAGA
*
6185061 CACTTCGGTGCATTTATACGAG
1 CACTTCGGTGCATTTCTACGAG
6185083 CTGTGGTGAC
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.31
Consensus pattern (23 bp):
CACTTCGGTGCATTTCTACGAGA
Found at i:6189515 original size:19 final size:20
Alignment explanation
Indices: 6189491--6189533 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
6189481 TGAATACAAG
6189491 TATAGGAAAATGA-TATATA
1 TATAGGAAAATGACTATATA
* *
6189510 TATAGGAAGATGACTATCTA
1 TATAGGAAAATGACTATATA
6189530 TATA
1 TATA
6189534 TATAGGATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.47, C:0.05, G:0.16, T:0.33
Consensus pattern (20 bp):
TATAGGAAAATGACTATATA
Found at i:6189995 original size:23 final size:23
Alignment explanation
Indices: 6189927--6189995 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
6189917 CAACCTTATA
*
6189927 TGGCACTTCGGTGTATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* *
6189950 CGGCACTAT-GGTGCAATTCTACG
1 TGGCACT-TCGGTGCATTTCTACG
*
6189973 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
6189996 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
22 1 0.03
23 36 0.95
24 1 0.03
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.33
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:6197009 original size:8 final size:7
Alignment explanation
Indices: 6196977--6197006 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
6196967 TCTAAAGCCT
6196977 CGAAACC
1 CGAAACC
6196984 CGAAACC
1 CGAAACC
6196991 CGAAACC
1 CGAAACC
6196998 CAGAAACC
1 C-GAAACC
6197006 C
1 C
6197007 AGAGGCGGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.43, C:0.43, G:0.13, T:0.00
Consensus pattern (7 bp):
CGAAACC
Found at i:6201731 original size:26 final size:26
Alignment explanation
Indices: 6201668--6201752 Score: 81
Period size: 26 Copynumber: 3.4 Consensus size: 26
6201658 AGGTTTTATA
* * *
6201668 TTTAATTTTATATTATAT-TTGATTT
1 TTTAATATTATATTAAATATTAATTT
*
6201693 TTTAA-A-TAAATTAAATATTAATTT
1 TTTAATATTATATTAAATATTAATTT
6201717 TTTAATATTATATTATAGATATTAA--T
1 TTTAATATTATATTA-A-ATATTAATTT
6201743 TTTAATATTA
1 TTTAATATTA
6201753 ATTTTTTTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
23 8 0.16
24 11 0.22
25 6 0.12
26 17 0.34
27 1 0.02
28 7 0.14
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (26 bp):
TTTAATATTATATTAAATATTAATTT
Found at i:6201797 original size:26 final size:25
Alignment explanation
Indices: 6201740--6201812 Score: 67
Period size: 26 Copynumber: 2.7 Consensus size: 25
6201730 TATAGATATT
*
6201740 AATTTTAATATTAATTTTTTTTAAATA
1 AATTATAATATTAA--TTTTTTAAATA
6201767 AATTA-AATATTAATTTTTTAATATTA
1 AATTATAATATTAATTTTTTAA-A-TA
*
6201793 TATTATAGATATTTAATTTT
1 AATTATA-ATA-TTAATTTT
6201813 ATATCATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
24 8 0.21
25 1 0.03
26 14 0.36
27 5 0.13
28 3 0.08
29 8 0.21
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (25 bp):
AATTATAATATTAATTTTTTAAATA
Found at i:6201849 original size:66 final size:65
Alignment explanation
Indices: 6201692--6201832 Score: 192
Period size: 66 Copynumber: 2.1 Consensus size: 65
6201682 ATATTTGATT
* *
6201692 TTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATATTAATTTTAATATTAATTT
1 TTTT-AATAAATTAAATATAAATTTTTTAATATTATATTATAGATATTAATTTTAATATTAAATT
*
6201757 T
65 A
*
6201758 TTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATATTTAATTTTATATCATATA
1 TTTT-AATAAATTAAATATAAATTTTTTAATATTATATTATAGATA-TTAATTTTA-AT-AT-TA
6201823 AATTA
61 AATTA
6201828 TTTTA
1 TTTTA
6201833 TATATTATTA
Statistics
Matches: 69, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
66 46 0.67
67 9 0.13
68 2 0.03
69 3 0.04
70 9 0.13
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (65 bp):
TTTTAATAAATTAAATATAAATTTTTTAATATTATATTATAGATATTAATTTTAATATTAAATTA
Found at i:6201868 original size:20 final size:19
Alignment explanation
Indices: 6201808--6201869 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
6201798 TAGATATTTA
*
6201808 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
6201827 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
6201845 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
6201865 ATTTT
1 ATTTT
6201870 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:6202393 original size:31 final size:31
Alignment explanation
Indices: 6202342--6202401 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
6202332 TAGTTGTATG
* ** *
6202342 AATTATTTAAATTTTTGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
6202373 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
6202402 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.43
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:6218121 original size:64 final size:64
Alignment explanation
Indices: 6218040--6218199 Score: 198
Period size: 64 Copynumber: 2.5 Consensus size: 64
6218030 GAAGGTGTAT
** *
6218040 TGATGCATTGGTAGTGCATCGATGCACACTTTTAA-AATAAAAACATCGAATGCAATTCATGCA-
1 TGATGCATAAGTAGTGCATCGATGCATACTTTTAATAAT-AAAACATCGAATGCAATTCATGCAC
*** * * *
6218103 TCGATGCATAAGTAGTGCATCGATGCATACCAGTAATAATACAACATCGAATGCATTTTATGCAC
1 T-GATGCATAAGTAGTGCATCGATGCATACTTTTAATAATAAAACATCGAATGCAATTCATGCAC
*
6218168 TGATGCATCAGTAGTGCATCGATGCATACTTT
1 TGATGCATAAGTAGTGCATCGATGCATACTTT
6218200 CATTGAAAGA
Statistics
Matches: 81, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
63 1 0.01
64 76 0.94
65 4 0.05
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (64 bp):
TGATGCATAAGTAGTGCATCGATGCATACTTTTAATAATAAAACATCGAATGCAATTCATGCAC
Found at i:6218721 original size:31 final size:31
Alignment explanation
Indices: 6218683--6218807 Score: 225
Period size: 31 Copynumber: 4.0 Consensus size: 31
6218673 AGGGTCGAGG
6218683 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
6218714 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
6218745 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
6218776 GTTTACCTAGGTTCTTCGGGATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
6218807 G
1 G
6218808 GTCCTTCGGG
Statistics
Matches: 92, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
31 91 0.99
32 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:6222003 original size:30 final size:30
Alignment explanation
Indices: 6221944--6222032 Score: 135
Period size: 30 Copynumber: 3.0 Consensus size: 30
6221934 CCCGAAGGAC
* * *
6221944 CTATCCAGAGGTCACACAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
6221973 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
6222003 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
6222033 ACTGTCCATA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
29 18 0.33
30 37 0.67
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:6222068 original size:31 final size:31
Alignment explanation
Indices: 6222028--6222127 Score: 123
Period size: 31 Copynumber: 3.2 Consensus size: 31
6222018 AAAGATCCTC
*
6222028 GGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAAACTGTCCATATGTTCCATAGAACATA
* * *
6222059 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTAAACTGTCCATATGT-TCCATAGAACATA
*
6222090 -GTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT-AAACTGTCCATATGTTCCATAGAACATA
6222121 GGTAAAC
1 GGTAAAC
6222128 CCTCGACTCT
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
30 6 0.11
31 45 0.79
32 6 0.11
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (31 bp):
GGTAAACTGTCCATATGTTCCATAGAACATA
Found at i:6223342 original size:21 final size:21
Alignment explanation
Indices: 6223318--6223362 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
6223308 TGTTGTTCGT
* *
6223318 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
6223339 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
6223360 TTG
1 TTG
6223363 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:6226562 original size:30 final size:30
Alignment explanation
Indices: 6226503--6226591 Score: 135
Period size: 30 Copynumber: 3.0 Consensus size: 30
6226493 CCCGAAGGAC
* * *
6226503 CTATCCAGAGGTCACACAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
6226532 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
6226562 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
6226592 ACTGTCTATA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
29 18 0.33
30 37 0.67
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:6226627 original size:31 final size:31
Alignment explanation
Indices: 6226587--6226687 Score: 123
Period size: 31 Copynumber: 3.2 Consensus size: 31
6226577 AAAGATCCTC
* *
6226587 GGTAAACTGTCTATATGTTCCTTAGAACATA
1 GGTAAACTGTCCATATGTTCCATAGAACATA
* * *
6226618 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTAAACTGTCCATATGT-TCCATAGAACATA
*
6226649 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT-AAACTGTCCATATGTTCCATAGAACATA
6226681 GGTAAAC
1 GGTAAAC
6226688 CCTCGACTCT
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
31 32 0.55
32 26 0.45
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (31 bp):
GGTAAACTGTCCATATGTTCCATAGAACATA
Found at i:6226680 original size:32 final size:32
Alignment explanation
Indices: 6226590--6226686 Score: 119
Period size: 32 Copynumber: 3.1 Consensus size: 32
6226580 GATCCTCGGT
* *
6226590 AAACTGTCTATATGTTCCTTAGAACATAGGT-
1 AAACTGTCCATATGTTCCGTAGAACATAGGTA
* *
6226621 ATACTGTCCATATG-TCTCG-AAAGACATAGGTA
1 AAACTGTCCATATGTTC-CGTAGA-ACATAGGTA
6226653 AAACTGTCCATATGTTCCGTAGAACATAGGTA
1 AAACTGTCCATATGTTCCGTAGAACATAGGTA
6226685 AA
1 AA
6226687 CCCTCGACTC
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
30 4 0.07
31 21 0.38
32 26 0.47
33 4 0.07
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (32 bp):
AAACTGTCCATATGTTCCGTAGAACATAGGTA
Found at i:6227906 original size:21 final size:21
Alignment explanation
Indices: 6227882--6227926 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
6227872 TGTTGTTCGT
* *
6227882 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
6227903 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
6227924 TTG
1 TTG
6227927 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:6231125 original size:30 final size:30
Alignment explanation
Indices: 6231066--6231154 Score: 135
Period size: 30 Copynumber: 3.0 Consensus size: 30
6231056 CCCGAAGGAC
* * *
6231066 CTATCCAGAGGTCACACAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
6231095 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
6231125 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
6231155 ACTGTCCATA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
29 18 0.33
30 37 0.67
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:6231190 original size:31 final size:31
Alignment explanation
Indices: 6231150--6231250 Score: 132
Period size: 31 Copynumber: 3.2 Consensus size: 31
6231140 AAAGATCCTC
*
6231150 GGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAAACTGTCCATATGTTCCATAGAACATA
* * *
6231181 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTAAACTGTCCATATGT-TCCATAGAACATA
*
6231212 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT-AAACTGTCCATATGTTCCATAGAACATA
6231244 GGTAAAC
1 GGTAAAC
6231251 CCTCGACTCT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
31 33 0.56
32 26 0.44
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (31 bp):
GGTAAACTGTCCATATGTTCCATAGAACATA
Found at i:6231959 original size:2 final size:2
Alignment explanation
Indices: 6231952--6231999 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
6231942 ATACAATTCC
6231952 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6231994 TA TA TA
1 TA TA TA
6232000 ACTCATGTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6232083 original size:29 final size:29
Alignment explanation
Indices: 6232029--6232084 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
6232019 TTTCTCTTGT
* *
6232029 TATCATATAAATCATTGCCATATAACACA
1 TATCATATAAATCATTACCACATAACACA
*
6232058 TATCATATAAATTCA-TACCACCTAACA
1 TATCATATAAA-TCATTACCACATAACA
6232085 TGTAATACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 20 0.87
30 3 0.13
ACGTcount: A:0.45, C:0.23, G:0.02, T:0.30
Consensus pattern (29 bp):
TATCATATAAATCATTACCACATAACACA
Found at i:6232497 original size:21 final size:21
Alignment explanation
Indices: 6232473--6232517 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
6232463 TGTTGTTCGT
* *
6232473 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
6232494 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
6232515 TTG
1 TTG
6232518 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:6235165 original size:31 final size:31
Alignment explanation
Indices: 6235127--6235249 Score: 212
Period size: 31 Copynumber: 4.0 Consensus size: 31
6235117 GGGTCGAGGG
6235127 TTTACCTATGTTCTTCGGGACATATGGACTA
1 TTTACCTATGTTCTTCGGGACATATGGACTA
*
6235158 TTTACCTATGTTCTTCGGGACATATGGACTG
1 TTTACCTATGTTCTTCGGGACATATGGACTA
6235189 TTTACCTATGTTCTTCGGGACATATGGACTA
1 TTTACCTATGTTCTTCGGGACATATGGACTA
*
6235220 TTTACCTAGGTTCTTCGGGATC-TATGGACT
1 TTTACCTATGTTCTTCGGGA-CATATGGACT
6235250 GGTCCTTCGG
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (31 bp):
TTTACCTATGTTCTTCGGGACATATGGACTA
Found at i:6237561 original size:23 final size:23
Alignment explanation
Indices: 6237530--6237589 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
6237520 CACCATAGCT
*
6237530 CGTATAATTGCACCAAAGTGCCA
1 CGTAGAATTGCACCAAAGTGCCA
* * *
6237553 CGTAGAATTACACCAGAGTGCCG
1 CGTAGAATTGCACCAAAGTGCCA
6237576 CGTAGAATTGCACC
1 CGTAGAATTGCACC
6237590 GTAGTACTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.32, C:0.27, G:0.22, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCAAAGTGCCA
Found at i:6239142 original size:21 final size:21
Alignment explanation
Indices: 6239100--6239160 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
6239090 TTCGCTTGAG
*
6239100 GGGTATCGATTCCCTATTGAAT
1 GGGTATCGATTCCC-CTTGAAT
6239122 GGGTATCGATTCCCCTTGAAT
1 GGGTATCGATTCCCCTTGAAT
*
6239143 GGGTACCGATTCCCCTTG
1 GGGTATCGATTCCCCTTG
6239161 CCCAGAAATC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
21 23 0.62
22 14 0.38
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.33
Consensus pattern (21 bp):
GGGTATCGATTCCCCTTGAAT
Found at i:6242863 original size:23 final size:23
Alignment explanation
Indices: 6242803--6242863 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
6242793 CACCACAGCC
* *
6242803 CGTATAATTGCACCAAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
6242826 CGTAGAATTGCACCGGAGTGTCG
1 CGTAGAATTGCACCGAAGTGCCA
6242849 CGTAGAATTGCACCG
1 CGTAGAATTGCACCG
6242864 TAGTTCCATA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.21
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:6244418 original size:21 final size:21
Alignment explanation
Indices: 6244376--6244436 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
6244366 TTCGCTTGAG
*
6244376 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
6244398 GGGTACCGATTCCCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
6244419 GGGTACCGATTCCCCTTG
1 GGGTACCGATTCCCCTTG
6244437 CCCAGAAATC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 24 0.63
22 14 0.37
ACGTcount: A:0.18, C:0.28, G:0.25, T:0.30
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:6254653 original size:26 final size:26
Alignment explanation
Indices: 6254624--6254689 Score: 123
Period size: 26 Copynumber: 2.5 Consensus size: 26
6254614 CGTTATATGA
*
6254624 TATTTTAATTATTTAATTTTTGTTTG
1 TATTTTAATTATTTAATTTGTGTTTG
6254650 TATTTTAATTATTTAATTTGTGTTTG
1 TATTTTAATTATTTAATTTGTGTTTG
6254676 TATTTTAATTATTT
1 TATTTTAATTATTT
6254690 GAGTTTGACA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (26 bp):
TATTTTAATTATTTAATTTGTGTTTG
Found at i:6257247 original size:17 final size:19
Alignment explanation
Indices: 6257219--6257267 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
6257209 TATTTTGAAA
6257219 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
6257237 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
6257256 CACCGATGCACT
1 CATCGATGCACT
6257268 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:6257263 original size:64 final size:64
Alignment explanation
Indices: 6257088--6257267 Score: 213
Period size: 65 Copynumber: 2.8 Consensus size: 64
6257078 AATTAAATTG
* * * *
6257088 AACATCGAATGCATTTCATGCATCGATGCACACACCATGCACCGATGTACTGAGGATTTTATGAA
1 AACATCGAATGCATTTGATGCATCGATGCAC-CATCATGCACCGATGCACTCAGGATTTTATGAA
* * *
6257153 AACATCGAATGCATTTGATGCATCGATGCACCAGTCATGCATCGATGCACTCTGGCTATTT-TG-
1 AACATCGAATGCATTTGATGCATCGATGCACCA-TCATGCACCGATGCACTCAGGAT-TTTATGA
6257216 A
64 A
* *
6257217 AACATCGAATGCACTTGATGCATCGATGCACTC-TTAGTGCACCGATGCACT
1 AACATCGAATGCATTTGATGCATCGATGCAC-CATCA-TGCACCGATGCACT
6257268 AAGGGTCCAA
Statistics
Matches: 101, Mismatches: 10, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
63 2 0.02
64 46 0.46
65 50 0.50
66 3 0.03
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACCATCATGCACCGATGCACTCAGGATTTTATGAA
Found at i:6265236 original size:2 final size:2
Alignment explanation
Indices: 6265229--6265297 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
6265219 AATCTTAAGC
6265229 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6265271 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
6265298 CAATTGGCTA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6265414 original size:27 final size:27
Alignment explanation
Indices: 6265376--6265435 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
6265366 GAGAAATGTT
6265376 AAGTG-TTAAAATTTTTAAAAAGGGAG
1 AAGTGTTTAAAATTTTTAAAAAGGGAG
6265402 AAGTGTTTAAAATTTTTAAAAAGGGAG
1 AAGTGTTTAAAATTTTTAAAAAGGGAG
6265429 AAGTGTT
1 AAGTGTT
6265436 ATAGTAAGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 5 0.15
27 28 0.85
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (27 bp):
AAGTGTTTAAAATTTTTAAAAAGGGAG
Found at i:6265880 original size:65 final size:64
Alignment explanation
Indices: 6265761--6265970 Score: 214
Period size: 65 Copynumber: 3.2 Consensus size: 64
6265751 ATTTTTAGAG
* * * *
6265761 TGATGCACCGATGCATCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGC
1 TGATGCATCGATGCA-CCATCCATGCACCGATGCACTCAGGATATT---TTGAAACATCGAATGC
6265823 ATT
62 ATT
* * *
6265826 TCATGCATCGATGCACACA-CCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCAAATGCA
1 TGATGCATCGATGCAC-CATCCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCA
6265889 TT
63 TT
* * * * *
6265891 TGATGCATCGATGCACCATTCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACCATCCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
6265955 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
6265971 TCTTAGTGCA
Statistics
Matches: 122, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 48 0.39
65 68 0.56
66 3 0.02
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (64 bp):
TGATGCATCGATGCACCATCCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:6265970 original size:17 final size:19
Alignment explanation
Indices: 6265942--6265990 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
6265932 TATTTTGAAA
6265942 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
6265960 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
6265979 CACCGATGCACT
1 CATCGATGCACT
6265991 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:6267109 original size:65 final size:63
Alignment explanation
Indices: 6266998--6267140 Score: 164
Period size: 65 Copynumber: 2.2 Consensus size: 63
6266988 TGCATTCTAC
* *
6266998 AGTGCATCGATGCATTACCCATGCATCGATACACAAATTACCTTCGATGTTTTCATT-TTTAAAG
1 AGTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATG-TTTC-TTCTTTAAAG
* * * * * *
6267062 GGATGCATCGATGCACT-CCTTATGCATTGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAG
1 AG-TGCATCGATGCACTACC-CATGCATCGATACACAAATTACATTCGATGTTTCTTCTTTAAAG
6267126 AGTGCATCGATGCAC
1 AGTGCATCGATGCAC
6267141 ATTCAATGTG
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
63 15 0.22
64 15 0.22
65 37 0.55
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (63 bp):
AGTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATGTTTCTTCTTTAAAG
Found at i:6267153 original size:65 final size:65
Alignment explanation
Indices: 6267018--6267162 Score: 152
Period size: 65 Copynumber: 2.2 Consensus size: 65
6267008 TGCATTACCC
* * * * * **
6267018 ATGCATCGATACACAAATTACCTTCGATGTTTTCATTTTTAAAGGGATGCATCGATGCACTCCTT
1 ATGCATAGATACACCAATTGCATTCGATGTTTTCATTTTTAAAGAGATGCATCGATGCACTCAAT
* *
6267083 ATGCATTGATGCACCAATTGCATTCGATG-TTTC-TTCTTTAAAGAG-TGCATCGATGCACATTC
1 ATGCATAGATACACCAATTGCATTCGATGTTTTCATT-TTTAAAGAGATGCATCGATGCAC--TC
6267145 AAT
63 AAT
*
6267148 GTGCATAGATACACC
1 ATGCATAGATACACC
6267163 TTACCCAGAA
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
63 15 0.23
64 12 0.18
65 39 0.59
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (65 bp):
ATGCATAGATACACCAATTGCATTCGATGTTTTCATTTTTAAAGAGATGCATCGATGCACTCAAT
Found at i:6278169 original size:3 final size:3
Alignment explanation
Indices: 6278163--6278243 Score: 103
Period size: 3 Copynumber: 26.7 Consensus size: 3
6278153 CTCCATTTTC
6278163 TAT TAT TAT TATT TAT TAT TAT TAT TAT T-T TAT ATAT TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
* *
6278209 TAT TAT TA- TATT TAT TAT TAT TAA AAT TAT TAT TA
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TA
6278244 CAAACAGGCC
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
2 4 0.06
3 57 0.83
4 8 0.12
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:6279805 original size:121 final size:118
Alignment explanation
Indices: 6279666--6279903 Score: 266
Period size: 122 Copynumber: 2.0 Consensus size: 118
6279656 TTTAATCCTA
* * * * * *
6279666 TTTTAATATTTATTTA-TTTTCCAATAT-TAAG-AAAGGGCAGTCTTAAAATAACTGGATGTCCA
1 TTTTAATAATTATTTATTTTTCCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCC-
*
6279728 TTTTTCTGATATTTTTAAATAAATAAAATATCTTATTTTATAAATTATATATTAATTG
65 -TTTTCTGATATTTCTAAATAAAT-AAATATCTTA-TTTATAAA-TATATATTAATTG
** * ** * *
6279786 TTTTAATTAATTATTTATTTTTTTAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTATAAGTCC
1 TTTTAA-TAATTATTTATTTTTCCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCC
*
6279851 TTTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATATTAATT
65 TTTTCTGATATTTCTAAATAAATAAATATCTTATTTATAAATATATATTAATT
6279904 AATATATATT
Statistics
Matches: 99, Mismatches: 15, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
119 12 0.12
120 14 0.14
121 18 0.18
122 31 0.31
123 3 0.03
124 21 0.21
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.47
Consensus pattern (118 bp):
TTTTAATAATTATTTATTTTTCCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCCT
TTTCTGATATTTCTAAATAAATAAATATCTTATTTATAAATATATATTAATTG
Found at i:6291515 original size:20 final size:22
Alignment explanation
Indices: 6291479--6291518 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
6291469 TATTTATTAA
6291479 TAAATTCTAAGTTTATTTTCTC
1 TAAATTCTAAGTTTATTTTCTC
6291501 TAAATTC-AA-TTTATTTTC
1 TAAATTCTAAGTTTATTTTC
6291519 GAAAATTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 2 0.11
22 7 0.39
ACGTcount: A:0.30, C:0.12, G:0.03, T:0.55
Consensus pattern (22 bp):
TAAATTCTAAGTTTATTTTCTC
Found at i:6292031 original size:114 final size:114
Alignment explanation
Indices: 6291831--6292050 Score: 332
Period size: 114 Copynumber: 1.9 Consensus size: 114
6291821 CACGTTCTCG
* * *
6291831 TAGTAGAAATAAGTAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
1 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGATTC
* * * * * *
6291896 GGTATGATCCCCAAAATCAATCATTAGATTTGAAAGATGAATTTGCTCA
66 GGTAGGAACCACAAAACCAATCATTAGAATTAAAAGATGAATTTGCTCA
*
6291945 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTC
1 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGATTC
* *
6292010 GGTAGGAACCACAGAACCAATCATTGGAATTAAAAGATGAA
66 GGTAGGAACCACAAAACCAATCATTAGAATTAAAAGATGAA
6292051 CTGCATGATC
Statistics
Matches: 94, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
114 94 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.30
Consensus pattern (114 bp):
TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGATTC
GGTAGGAACCACAAAACCAATCATTAGAATTAAAAGATGAATTTGCTCA
Found at i:6293135 original size:225 final size:224
Alignment explanation
Indices: 6292778--6293782 Score: 959
Period size: 225 Copynumber: 4.3 Consensus size: 224
6292768 AGTACCAGTT
*
6292778 AAAGTTCATAATGATAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
*
6292843 TCAACCTTTTGTTTGAATTCATCATTTGATGGATCAATATTGCCAGGTAGAGTTCATAATGAGAA
66 TCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAA
* **
6292908 GAACTCGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCTCAAAT
131 GAACTCGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAAT
*
6292973 CCATCACTTGATGGATCAACTTTTCCAGAG
196 TCATCA-TTGATGGATCAACTTTTCCAGAG
*
6293003 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTAATAATGAGAAGAATTTGT
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
*
6293068 TCGACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAA
66 TCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAA
* * * * * *
6293133 GAACTCGTCGTCAAGAAGGAAGAATAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGA
131 GAACTCGTCATC-TGAA-GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGA
*
6293198 ATTCATCATTCTATGGATCAACTTTTCC--AG
194 ATTCATCATT-GATGGATCAACTTTTCCAGAG
* *
6293228 AAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAATTCATAATGAGAAGAATTTGT
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
** ** * * *
6293292 TCAACCTTTTGCAT-AATTCTATCACAGAATGAGATAGATCAGCATCAGCTTTTCCAGAG-AAAG
66 TCAACCTTTTGTTTGAATTC-AT--C---ATTTGATGGATCA--A-CA---TTGCCAG-GTAGAG
6293355 TTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
118 TTCATAATGAGAAGAACTCGTCATCTGAAGAA-GAAG-A-AA-TTCATAATGAGAAGAATTTGTT
* * *
6293417 CAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAG-G
179 CAACCTTTTGCTTGAATTCATCA-TTGATGGATCAACTTTTCCAGAG
*
6293463 TAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA-GAAG-A-AA-TTCATAATGAGAAGAAT
1 -AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
** *** * *
6293524 TTGTTCAACCTTTTGCAT-AATTCTATCACAGAAGGAGATAGATCAGCATTAGCTTTTCCAGAG-
62 TTGTTCAACCTTTTGTTTGAATTC-AT--C---ATTTGATGGATCAACATT-G-----CCAG-GT
* * * * **
6293587 AAAGTTCATAATGAGAAGAA--C-TCATCTGAAAAAGAAGAAGTTCACAATGAGAAGAGCTTGTT
114 AGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTT
* * *
6293649 CAACCTTTTGCAT-AATTCTATCACAGAAGGAGATAGATCAGCATCAACTTTTCCAGAG
179 CAACCTTTTGCTTGAATTC-AT--C--------ATTGAT--GGATCAACTTTTCCAGAG
* * * * * *
6293707 AAAGTTCATAATAAGAAGAACTCATTTGAAGAAGAAATAAGAAGTTCATAATGAGAAGAACTTAT
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
6293772 TCAACCTTTTG
66 TCAACCTTTTG
6293783 AATGACTCTA
Statistics
Matches: 669, Mismatches: 59, Indels: 85
0.82 0.07 0.10
Matches are distributed among these distances:
223 5 0.01
224 44 0.07
225 169 0.25
226 6 0.01
227 63 0.09
229 10 0.01
230 5 0.01
231 12 0.02
232 39 0.06
233 5 0.01
234 58 0.09
235 32 0.05
236 119 0.18
237 2 0.00
238 2 0.00
239 13 0.02
240 12 0.02
241 7 0.01
242 2 0.00
243 33 0.05
244 31 0.05
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (224 bp):
AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
TCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAA
GAACTCGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAAT
TCATCATTGATGGATCAACTTTTCCAGAG
Found at i:6293416 original size:124 final size:124
Alignment explanation
Indices: 6293214--6293931 Score: 858
Period size: 124 Copynumber: 5.9 Consensus size: 124
6293204 CATTCTATGG
* *
6293214 ATCAACTTTTCC--AGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAATTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* *
6293276 AATGAGAAGAATTTGTTCAACCTTTTGCATAATTCTATCACAGAATGAGATAGATCAGC
66 AATGAGAAGAACTTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATCAGC
*
6293335 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* ** * * *
6293400 AATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTC-AT--C------A-TTTGAT--GG
66 AATGAGAAGAACTTGTTCAACCTTTTGCAT-AATTCTATCACAGAAGGAGATAGATCAGC
* * *
6293448 ATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA-GAAG-A-AA-T
1 ATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGT
*
6293508 TCATAATGAGAAGAATTTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATCAGC
62 TCATAATGAGAAGAACTTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATCAGC
* * *
6293571 ATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG-A-AA--AAGAAGAAGTTCAC
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
6293632 AATGAGAAGAGCTTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATCAGC
66 AATGAGAAGAACTTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATCAGC
* * * *
6293691 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATTTGAAGAAGAAATAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * * * * * *
6293756 AATGAGAAGAACTTATTCAACCTTTTGAATGACTCTATCACAGAAGGAAATAGGTCAAC
66 AATGAGAAGAACTTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATCAGC
* * * *
6293815 ATCAACTTTTCCAGGGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAATTTTAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * *
6293880 AATAAGAAGAACTTGTTCAACCCTTTTCCA-AATTAC-ATCATAGAAGGAGATA
66 AATGAGAAGAACTTGTTCAA-CCTTTTGCATAATT-CTATCACAGAAGGAGATA
6293932 TTATCATCCC
Statistics
Matches: 514, Mismatches: 53, Indels: 57
0.82 0.08 0.09
Matches are distributed among these distances:
111 5 0.01
112 36 0.07
113 33 0.06
114 2 0.00
115 9 0.02
116 13 0.03
117 3 0.01
118 3 0.01
119 3 0.01
120 109 0.21
121 17 0.03
122 3 0.01
123 62 0.12
124 203 0.39
125 13 0.03
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.27
Consensus pattern (124 bp):
ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATCAGC
Found at i:6293556 original size:236 final size:234
Alignment explanation
Indices: 6292893--6293906 Score: 1053
Period size: 236 Copynumber: 4.3 Consensus size: 234
6292883 TGCCAGGTAG
*
6292893 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAA-GAAG-A-AA-TTCATAATGAGAAGAATTTG
1 AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* ** * *
6292954 TTTAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGA
63 TTCAACCTTTTGCTTGAATTCATCATTTGATGGATCAACTTTTCCAG-GAAAGTTCATAATGAGA
* * **
6293019 AGAA--CTCATCTGAAGAAGGAAGAAGAAGTTAATAATGAGAAGAATTTGTTCGACCTTTTGTTT
127 AGAACTCTCATCTGAAGAA-GAAG-A-AA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCAT
*** * * *
6293082 GAATTC-AT--C---ATTTGATGGATCA--A-CA---TTGCCAG-GTAG
188 -AATTCTATCACAGAAGGAGATAGATCAGCATCAGCTTTTCCAGAG-AA
* * *
6293118 AGTTCATAATGAGAAGAACTCGTCGTCAAGAAGGAAGAATAAGTTCATAATGAGAAGAACTTGTT
1 AGTTCATAATGAGAAGAACTCATC-TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
6293183 CAACTTTTTGCTTGAATTCATCATTCT-ATGGATCAACTTTTCCA-GAAAGTTCATAATGAGAAG
65 CAACCTTTTGCTTGAATTCATCATT-TGATGGATCAACTTTTCCAGGAAAGTTCATAATGAGAAG
6293246 AACT-T-ATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCATAAT
129 AACTCTCATCTG-A-A-GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCATAAT
*
6293309 TCTATCACAGAATGAGATAGATCAGCATCAGCTTTTCCAGAGAA
191 TCTATCACAGAAGGAGATAGATCAGCATCAGCTTTTCCAGAGAA
*
6293353 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * *
6293418 AACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGA
66 AACCTTTTGCTTGAATTCATCATTTGATGGATCAACTTTTCCAGG-AAAGTTCATAATGAGAAGA
6293483 ACTCGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCATAATTCT
130 ACTC-TCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCATAATTCT
*
6293548 ATCACAGAAGGAGATAGATCAGCATTAGCTTTTCCAGAGAA
194 ATCACAGAAGGAGATAGATCAGCATCAGCTTTTCCAGAGAA
* *
6293589 AGTTCATAATGAGAAGAACTCATCTG-A-AA--AAGAAGAAGTTCACAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * *
6293650 AACCTTTTGCAT-AATTCTATCACAGAAGGAGATAGATCAGCATCAACTTTTCCAGAGAAAGTTC
66 AACCTTTTGCTTGAATTC-AT--C------A-TTTGAT--GGATCAACTTTTCCAG-GAAAGTTC
* * * * *
6293714 ATAATAAGAAGAA--CTCATTTGAAGAAGAAATAAGAAGTTCATAATGAGAAGAACTTATTCAAC
118 ATAATGAGAAGAACTCTCATCTGAAGAAG----AAGAAATTCATAATGAGAAGAATTTGTTCAAC
* * * * * * * *
6293777 CTTTTGAATGACTCTATCACAGAAGGAAATAGGTCAACATCAACTTTTCCAGGGAA
179 CTTTTGCATAATTCTATCACAGAAGGAGATAGATCAGCATCAGCTTTTCCAGAGAA
* * * *
6293833 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAATTTTATAATAAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
6293898 AACCCTTTT
66 AA-CCTTTT
6293907 CCAAATTACA
Statistics
Matches: 677, Mismatches: 60, Indels: 80
0.83 0.07 0.10
Matches are distributed among these distances:
222 4 0.01
223 12 0.02
224 37 0.05
225 47 0.07
226 6 0.01
227 62 0.09
228 4 0.01
229 10 0.01
231 6 0.01
232 43 0.06
233 1 0.00
234 78 0.12
235 32 0.05
236 138 0.20
237 1 0.00
238 2 0.00
239 5 0.01
240 13 0.02
241 5 0.01
243 31 0.05
244 102 0.15
245 1 0.00
246 2 0.00
248 29 0.04
249 6 0.01
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (234 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACCTTTTGCTTGAATTCATCATTTGATGGATCAACTTTTCCAGGAAAGTTCATAATGAGAAGAA
CTCTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCATAATTCTAT
CACAGAAGGAGATAGATCAGCATCAGCTTTTCCAGAGAA
Found at i:6293751 original size:356 final size:347
Alignment explanation
Indices: 6292749--6293782 Score: 1246
Period size: 348 Copynumber: 3.0 Consensus size: 347
6292739 GATTTAAATC
** * * * * * * *
6292749 CATCATTCAATGGATCAACAGTACCAGTTAAAGTTCATAATGATAAGAACTCATC-TGAAGAAGG
1 CATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCAAGAAGG
* * ** *** *
6292813 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATC
66 AAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCATGAATTCATCAGGAGATAGATC
* * *
6292878 AA-TATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTG-A-AGAAGAAGAAATTCATA
131 AACT-TTTCCA-G-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAGAAGAAGAAATTCACA
* * * * * *
6292940 ATGAGAAGAATTTGTTTAACCTTTTGC-TCAAATCCATCAC---------TTGAT--GGATCAAC
190 ATGAGAAGAACTTGTTCAACCTTTTGCAT-AATTCTATCACAGAAGGAGATAGATCAGCATCAAC
*
6292993 TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTAATAATGAG
254 TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
*
6293058 AAGAATTTGTTCGACCTTTTGTTTGAATT
319 AAGAATTTGTTCAACCTTTTGTTTGAATT
*
6293087 CATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCGTCAAGAAGG
1 CATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCAAGAAGG
* * * * **** *
6293152 AAGAATAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCTATGGATC
66 AAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCATGAATTCATCAGGAGATAGATC
* *
6293217 AACTTTTCCAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCATAATGAG
131 AACTTTTCCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA-GAAGAAGAAATTCACAATGAG
* * *
6293282 AAGAATTTGTTCAACCTTTTGCATAATTCTATCACAGAATGAGATAGATCAGCATCAGCTTTTCC
195 AAGAACTTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATCAGCATCAACTTTTCC
6293347 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
260 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
6293412 TTGTTCAACCTTTTGTTTGAATT
325 TTGTTCAACCTTTTGTTTGAATT
*
6293435 CATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATC-TGAA-G
1 CATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCAAGAAGG
*
6293498 AAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCAT-AATTCTATCACAGAAGGAGA
66 AAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCATGAATTC-AT--C---AGGAGA
6293562 TAGATCAGCATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA-A-AAGAAGA
125 TAGAT---CA--A-CTTTTCC--AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGAAGAAGA
* *
6293625 AGTTCACAATGAGAAGAGCTTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATCAG
182 AATTCACAATGAGAAGAACTTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATCAG
* * * *
6293690 CATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATTTGAAGAAGAAATAAGAAGTTCA
247 CATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* *
6293755 TAATGAGAAGAACTTATTCAACCTTTTG
312 TAATGAGAAGAATTTGTTCAACCTTTTG
6293783 AATGACTCTA
Statistics
Matches: 614, Mismatches: 51, Indels: 44
0.87 0.07 0.06
Matches are distributed among these distances:
334 6 0.01
335 2 0.00
336 1 0.00
337 70 0.11
338 49 0.08
339 74 0.12
340 1 0.00
345 5 0.01
346 46 0.07
347 3 0.00
348 156 0.25
351 6 0.01
354 2 0.00
356 154 0.25
357 7 0.01
358 1 0.00
359 31 0.05
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (347 bp):
CATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCAAGAAGG
AAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCATGAATTCATCAGGAGATAGATC
AACTTTTCCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGAAGAAGAAATTCACAATGAGA
AGAACTTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATCAGCATCAACTTTTCCA
GAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATT
TGTTCAACCTTTTGTTTGAATT
Found at i:6294137 original size:3 final size:3
Alignment explanation
Indices: 6294131--6294195 Score: 80
Period size: 3 Copynumber: 21.7 Consensus size: 3
6294121 CTCCATTTTC
6294131 TAT TAT TAT TAT T-T TAT ATAT TAT TAT TAT TAT TAT T-T TATT TAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TA-T TAT
* *
6294176 TAT TAT TAA AAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
6294196 CAAACAGGCC
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 4 0.07
3 44 0.81
4 6 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:6294163 original size:24 final size:24
Alignment explanation
Indices: 6294131--6294183 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
6294121 CTCCATTTTC
6294131 TATTATTATTATTTTATATATTAT
1 TATTATTATTATTTTATATATTAT
*
6294155 TATTATTATTATTTTATTTATTAT
1 TATTATTATTATTTTATATATTAT
6294179 TATTA
1 TATTA
6294184 AAATTATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (24 bp):
TATTATTATTATTTTATATATTAT
Found at i:6295519 original size:3 final size:3
Alignment explanation
Indices: 6295505--6295537 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
6295495 TTATATGTTA
*
6295505 ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
6295538 TAACCATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:6295756 original size:20 final size:20
Alignment explanation
Indices: 6295731--6295773 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
6295721 TTATTTTATA
6295731 AATTATATATTAATTGTTTT
1 AATTATATATTAATTGTTTT
* * *
6295751 AATTATTTATTTATTTTTTT
1 AATTATATATTAATTGTTTT
6295771 AAT
1 AAT
6295774 ATCAAAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
AATTATATATTAATTGTTTT
Found at i:6297471 original size:2 final size:2
Alignment explanation
Indices: 6297466--6297514 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
6297456 CTCTCTTTTC
6297466 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6297508 AT AT AT A
1 AT AT AT A
6297515 CAGAAAGTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6307072 original size:21 final size:22
Alignment explanation
Indices: 6307013--6307062 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
6307003 ATTATTAACC
*
6307013 AATAGAATTA-TAATAAAATTT
1 AATATAATTATTAATAAAATTT
*
6307034 AATTTAATTATTAATAAAATTT
1 AATATAATTATTAATAAAATTT
6307056 AA-ATAAT
1 AATATAAT
6307063 ATTTACTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
AATATAATTATTAATAAAATTT
Found at i:6307903 original size:2 final size:2
Alignment explanation
Indices: 6307896--6307954 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
6307886 AATTTTGTAA
6307896 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6307938 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
6307955 ATTTTATGGA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6308171 original size:20 final size:20
Alignment explanation
Indices: 6308142--6308199 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
6308132 ATACTATTAT
* *
6308142 CTGATAATCTTACATTCTTA
1 CTGATTATCTTACATTCTCA
6308162 CTGATTATCTTACATTCTCA
1 CTGATTATCTTACATTCTCA
*
6308182 CTGATTATCTTATATTCT
1 CTGATTATCTTACATTCT
6308200 GTGAATCAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.48
Consensus pattern (20 bp):
CTGATTATCTTACATTCTCA
Found at i:6308559 original size:20 final size:21
Alignment explanation
Indices: 6308534--6308585 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
6308524 TTTTCCCAAT
*
6308534 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
6308554 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
6308575 TCGCAATGCGA
1 TCGCAATGCGA
6308586 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:6308598 original size:41 final size:41
Alignment explanation
Indices: 6308571--6308702 Score: 124
Period size: 41 Copynumber: 3.2 Consensus size: 41
6308561 GCGAATTGGG
* * * *
6308571 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTAACTATCGCAACGCGATAATAC
* *
6308612 AAAATCGCAACGAGATACTAACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGAGATACTAACTATCGCAACGCGATAAT-AC
** * * * *
6308654 --TTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTAACTATCGCAACGCGATAATAC
*
6308693 ATAATCGCAA
1 AAAATCGCAA
6308703 TGCGATTTTC
Statistics
Matches: 74, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 2 0.03
40 31 0.42
41 39 0.53
42 2 0.03
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTAACTATCGCAACGCGATAATAC
Found at i:6308599 original size:20 final size:20
Alignment explanation
Indices: 6308574--6308688 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
6308564 AATTGGGAAA
*
6308574 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
6308594 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
6308615 ATCGCAACGAGATACTAACT
1 ATCGCAACGCGATACTGACT
*
6308635 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
6308655 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
6308675 TTCGCAACGCGATA
1 ATCGCAACGCGATA
6308689 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:6308904 original size:22 final size:22
Alignment explanation
Indices: 6308876--6308919 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
6308866 CACTCTCTCA
6308876 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
6308898 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
6308920 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:6309169 original size:20 final size:20
Alignment explanation
Indices: 6309144--6309181 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6309134 CGCGAATCGC
6309144 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
6309164 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
6309182 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:6309372 original size:25 final size:24
Alignment explanation
Indices: 6309318--6309372 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
6309308 TGTTTATTAT
* *
6309318 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
6309342 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
6309368 TGTTT
1 TGTTT
6309373 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:6310521 original size:18 final size:18
Alignment explanation
Indices: 6310500--6310544 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
6310490 TCCACTTCGG
*
6310500 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
6310518 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
6310536 GAGCCATCA
1 GAGCCATCA
6310545 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:6311079 original size:20 final size:20
Alignment explanation
Indices: 6311054--6311099 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
6311044 TAGTTTACTT
6311054 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
6311074 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
6311094 TCGCAA
1 TCGCAA
6311100 TGCGAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:6311115 original size:19 final size:19
Alignment explanation
Indices: 6311093--6311175 Score: 97
Period size: 19 Copynumber: 4.6 Consensus size: 19
6311083 GGAAATGGCT
6311093 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATAAAA
6311112 ATCGCAA--C----TACAAA
1 ATCGCAATGCGAAATA-AAA
6311126 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATAAAA
* *
6311145 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATAAAA
6311164 ATCGCAATGCGA
1 ATCGCAATGCGA
6311176 TTTGTGTTTC
Statistics
Matches: 54, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
13 2 0.04
14 10 0.19
16 1 0.02
17 1 0.02
19 38 0.70
20 2 0.04
ACGTcount: A:0.48, C:0.20, G:0.17, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATAAAA
Found at i:6311187 original size:19 final size:19
Alignment explanation
Indices: 6311182--6311290 Score: 84
Period size: 19 Copynumber: 5.9 Consensus size: 19
6311172 GCGATTTGTG
*
6311182 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
6311201 TTTCGCATTGCGA-TTT--
1 TTTCGCATTGCGATTTTCA
*
6311217 TGTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
***
6311234 TTTCGCATTGCGATAGCCA
1 TTTCGCATTGCGATTTTCA
* **
6311253 TTTCTGCGTTGCGATAGTCA
1 TTTC-GCATTGCGATTTTCA
*
6311273 TTTTCGCGTTGCGATTTT
1 -TTTCGCATTGCGATTTT
6311291 AAGTTTCGTG
Statistics
Matches: 73, Mismatches: 10, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
14 6 0.08
15 3 0.04
16 4 0.05
17 4 0.05
18 3 0.04
19 25 0.34
20 24 0.33
21 4 0.05
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:6311297 original size:20 final size:19
Alignment explanation
Indices: 6311182--6311306 Score: 98
Period size: 20 Copynumber: 6.7 Consensus size: 19
6311172 GCGATTTGTG
6311182 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
6311201 TTTCGCATTGCGA-TTT--
1 TTTCGCGTTGCGATTTTCA
*
6311217 TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* ***
6311234 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGATTTTCA
**
6311253 TTTCTGCGTTGCGATAGTCA
1 TTTC-GCGTTGCGATTTTCA
*
6311273 TTTTCGCGTTGCGATTTTAA
1 -TTTCGCGTTGCGATTTTCA
*
6311293 GTTTCGTGTTGCGA
1 -TTTCGCGTTGCGA
6311307 AAGTAAACTA
Statistics
Matches: 84, Mismatches: 15, Indels: 13
0.75 0.13 0.12
Matches are distributed among these distances:
14 7 0.08
15 3 0.04
16 2 0.02
17 2 0.02
18 3 0.04
19 26 0.31
20 37 0.44
21 4 0.05
ACGTcount: A:0.14, C:0.19, G:0.23, T:0.44
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:6313173 original size:14 final size:14
Alignment explanation
Indices: 6313154--6313188 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
6313144 ATTGTTTAAT
6313154 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
6313168 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
6313182 TGATTTG
1 TGATTTG
6313189 CTTAATTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:6314445 original size:19 final size:19
Alignment explanation
Indices: 6314423--6314487 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
6314413 GGAAATTACT
6314423 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
6314442 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
6314456 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
6314475 ATCGCAACGCGAA
1 ATCGCAATGCGAA
6314488 TTTAGTTTCG
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:6314446 original size:39 final size:36
Alignment explanation
Indices: 6314403--6314485 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 36
6314393 CTTAATGTCT
*
6314403 ATCGCAACGCGGAAATTACTATCGCAATGCGAAATGAAA
1 ATCGCAACGCGGAAA-GA--ATCGCAATGCGAAATGAAA
*
6314442 ATCGCAA--C-GAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGCGGAAAGAATCGCAATGCGAAATGAAA
6314475 ATCGCAACGCG
1 ATCGCAACGCG
6314486 AATTTAGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
33 26 0.67
35 2 0.05
36 3 0.08
37 1 0.03
39 7 0.18
ACGTcount: A:0.41, C:0.22, G:0.23, T:0.14
Consensus pattern (36 bp):
ATCGCAACGCGGAAAGAATCGCAATGCGAAATGAAA
Found at i:6314505 original size:19 final size:19
Alignment explanation
Indices: 6314483--6314555 Score: 77
Period size: 19 Copynumber: 4.1 Consensus size: 19
6314473 AAATCGCAAC
*
6314483 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
6314502 GCGATTTTAGTTTCGTGTT
1 GCGATTTTAGTTTCGCGTT
6314521 GCGATTTTA---T--CGTT
1 GCGATTTTAGTTTCGCGTT
6314535 GCGATTTTCAG-TTCGCGTT
1 GCGATTTT-AGTTTCGCGTT
6314554 GC
1 GC
6314556 AATTCTCTCG
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 1 0.02
17 1 0.02
19 32 0.70
ACGTcount: A:0.12, C:0.16, G:0.26, T:0.45
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:6314540 original size:33 final size:34
Alignment explanation
Indices: 6314498--6314624 Score: 156
Period size: 33 Copynumber: 3.9 Consensus size: 34
6314488 TTTAGTTTCG
* *
6314498 CGTTGCGATTTT-AGTTTCGTGTTGCGATTTTAT
1 CGTTGCGATTTTCAGTTTCGTGTTGCGATTCTCT
* *
6314531 CGTTGCGATTTTCAG-TTCGCGTTGCAATTCTCT
1 CGTTGCGATTTTCAGTTTCGTGTTGCGATTCTCT
6314564 CGTTGCGATTTTCA-TTTCGCT-TTGCGATTCTCT
1 CGTTGCGATTTTCAGTTTCG-TGTTGCGATTCTCT
**
6314597 CGTTGCGATTTTCA-TTTCGCATTGCGAT
1 CGTTGCGATTTTCAGTTTCGTGTTGCGAT
6314625 AGTACTTTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
33 81 0.98
34 2 0.02
ACGTcount: A:0.12, C:0.20, G:0.21, T:0.46
Consensus pattern (34 bp):
CGTTGCGATTTTCAGTTTCGTGTTGCGATTCTCT
Found at i:6314575 original size:66 final size:66
Alignment explanation
Indices: 6314498--6314621 Score: 180
Period size: 66 Copynumber: 1.9 Consensus size: 66
6314488 TTTAGTTTCG
* *
6314498 CGTTGCGATTTT-AGTTTCG-TGTTGCGATTTTATCGTTGCGATTTTCAGTTCGCGTTGCAATTC
1 CGTTGCGATTTTCA-TTTCGCT-TTGCGATTCTATCGTTGCGATTTTCAGTTCGCATTGCAATTC
6314561 TCT
64 TCT
* *
6314564 CGTTGCGATTTTCATTTCGCTTTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 CGTTGCGATTTTCATTTCGCTTTGCGATTCTATCGTTGCGATTTTCAGTTCGCATTGC
6314622 GATAGTACTT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
66 50 0.96
67 2 0.04
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (66 bp):
CGTTGCGATTTTCATTTCGCTTTGCGATTCTATCGTTGCGATTTTCAGTTCGCATTGCAATTCTC
T
Found at i:6314590 original size:19 final size:18
Alignment explanation
Indices: 6314493--6314624 Score: 74
Period size: 19 Copynumber: 7.7 Consensus size: 18
6314483 GCGAATTTAG
6314493 TTTCGCGTTGCGATTTT-A
1 TTTCGC-TTGCGATTTTCA
*
6314511 GTTTCGTGTTGCGATTTT-A
1 -TTTCG-CTTGCGATTTTCA
6314530 --TCG-TTGCGATTTTCA
1 TTTCGCTTGCGATTTTCA
* *
6314545 GTTCGCGTTGC-A-ATTC-
1 TTTCGC-TTGCGATTTTCA
*
6314561 TCTCG-TTGCGATTTTCA
1 TTTCGCTTGCGATTTTCA
6314578 TTTCGCTTTGCGA--TTC-
1 TTTCGC-TTGCGATTTTCA
*
6314594 TCTCG-TTGCGATTTTCA
1 TTTCGCTTGCGATTTTCA
6314611 TTTCGCATTGCGAT
1 TTTCGC-TTGCGAT
6314625 AGTACTTTTT
Statistics
Matches: 89, Mismatches: 8, Indels: 32
0.69 0.06 0.25
Matches are distributed among these distances:
14 20 0.22
15 2 0.02
16 16 0.18
17 17 0.19
18 1 0.01
19 33 0.37
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.47
Consensus pattern (18 bp):
TTTCGCTTGCGATTTTCA
Found at i:6314604 original size:14 final size:14
Alignment explanation
Indices: 6314550--6314606 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
6314540 TTTCAGTTCG
*
6314550 CGTTGCAATTCTCT
1 CGTTGCGATTCTCT
*
6314564 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
6314581 CGCTTTGCGATTCTCT
1 CG--TTGCGATTCTCT
6314597 CGTTGCGATT
1 CGTTGCGATT
6314607 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 15 0.43
16 7 0.20
17 7 0.20
19 6 0.17
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:6314757 original size:14 final size:14
Alignment explanation
Indices: 6314740--6314766 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6314730 AACAAAACAA
6314740 CTTTTACAAATCAC
1 CTTTTACAAATCAC
6314754 CTTTTACAAATCA
1 CTTTTACAAATCA
6314767 ATTAAATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (14 bp):
CTTTTACAAATCAC
Found at i:6316183 original size:21 final size:21
Alignment explanation
Indices: 6316117--6316183 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
6316107 GTGAATCGGG
*
6316117 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
6316137 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
6316159 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
6316180 CTCT
1 CTCT
6316184 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:6316202 original size:42 final size:41
Alignment explanation
Indices: 6316117--6316239 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
6316107 GTGAATCGGG
* * * *
6316117 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
6316159 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
6316201 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
6316240 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:6316637 original size:91 final size:90
Alignment explanation
Indices: 6316458--6316642 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
6316448 ATTTCAAACT
*
6316458 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAATTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAATTTAGC
6316523 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
*
6316551 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAATTTAGCA
*
6316615 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
6316642 T
1 T
6316643 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 41 0.47
93 19 0.22
95 27 0.31
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAATTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:6318361 original size:20 final size:19
Alignment explanation
Indices: 6318330--6318485 Score: 120
Period size: 19 Copynumber: 8.6 Consensus size: 19
6318320 TCTTTTGGTT
6318330 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
6318349 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
6318370 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
6318389 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
6318403 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
6318422 G--A-G--AATCGCAACGCA
1 GAAATGAAAATCGCAACG-A
*
6318437 -AAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
6318455 GAAATGAAAATCGCAACGCA
1 GAAATGAAAATCGCAACG-A
6318475 -AAATGAAAATC
1 GAAATGAAAATC
6318486 ACAATGCGAT
Statistics
Matches: 110, Mismatches: 12, Indels: 30
0.72 0.08 0.20
Matches are distributed among these distances:
14 19 0.17
15 1 0.01
16 4 0.04
17 4 0.04
19 51 0.46
20 29 0.26
21 2 0.02
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:6318398 original size:14 final size:14
Alignment explanation
Indices: 6318379--6318434 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
6318369 GGAAATGACT
6318379 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
6318393 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
6318410 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
6318426 ATCGCAACG
1 ATCGCAACG
6318435 CAAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 6 0.17
19 7 0.20
ACGTcount: A:0.39, C:0.25, G:0.25, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:6318412 original size:33 final size:33
Alignment explanation
Indices: 6318355--6318453 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
6318345 ACGAGATAAT
6318355 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
6318389 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
* **
6318422 GAGAATCGCAACGCAAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
6318454 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
33 48 0.77
34 14 0.23
ACGTcount: A:0.41, C:0.23, G:0.24, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Done.