Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009611.1 Hibiscus syriacus cultivar Beakdansim tig00116997_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: 6671611
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 25 of 27
Found at i:6185450 original size:14 final size:14
Alignment explanation
Indices: 6185430--6185471 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
6185420 TTTTTGACTC
6185430 ATTATTATTTAAAA
1 ATTATTATTTAAAA
* *
6185444 TTTATTATTGAAAA
1 ATTATTATTTAAAA
*
6185458 AATATT-TTTAAAA
1 ATTATTATTTAAAA
6185471 A
1 A
6185472 CCTTAAATCA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
13 7 0.30
14 16 0.70
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
ATTATTATTTAAAA
Found at i:6186655 original size:16 final size:16
Alignment explanation
Indices: 6186634--6186666 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
6186624 GTGTATCGAT
6186634 GCACCTTAAGTGCATC
1 GCACCTTAAGTGCATC
6186650 GCACCTTAAGTGCATC
1 GCACCTTAAGTGCATC
6186666 G
1 G
6186667 ATGCACTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.24
Consensus pattern (16 bp):
GCACCTTAAGTGCATC
Found at i:6191537 original size:16 final size:16
Alignment explanation
Indices: 6191518--6191567 Score: 91
Period size: 16 Copynumber: 3.1 Consensus size: 16
6191508 TCGAGTATTG
6191518 CTGAGCTCGACTCGAA
1 CTGAGCTCGACTCGAA
*
6191534 CTGAGCTCGACTCAAA
1 CTGAGCTCGACTCGAA
6191550 CTGAGCTCGACTCGAA
1 CTGAGCTCGACTCGAA
6191566 CT
1 CT
6191568 TGAAAACTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.26, C:0.32, G:0.22, T:0.20
Consensus pattern (16 bp):
CTGAGCTCGACTCGAA
Found at i:6195792 original size:43 final size:42
Alignment explanation
Indices: 6195731--6195824 Score: 118
Period size: 43 Copynumber: 2.2 Consensus size: 42
6195721 TTCGTATGTC
*
6195731 TAAATTAGAGTTTCAATTATAAAGGTAGAAA-GTAAGATTGAAA
1 TAAATTAGAGTCTCAATTATAAAGGTA-AAATGTAAGATT-AAA
* * *
6195774 TAAATTAGGGTCTCAATTATAAATGTAAAATGTGAGATTAAA
1 TAAATTAGAGTCTCAATTATAAAGGTAAAATGTAAGATTAAA
*
6195816 AAAATTAGA
1 TAAATTAGA
6195825 AACCTCAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
42 13 0.30
43 31 0.70
ACGTcount: A:0.49, C:0.03, G:0.17, T:0.31
Consensus pattern (42 bp):
TAAATTAGAGTCTCAATTATAAAGGTAAAATGTAAGATTAAA
Found at i:6209559 original size:31 final size:31
Alignment explanation
Indices: 6209521--6209582 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
6209511 ATTATCATGA
6209521 ATTACTCATCTCCTTTCATTAACTCTCTTGT
1 ATTACTCATCTCCTTTCATTAACTCTCTTGT
6209552 ATTACTCATCTCCTTTCATTAACTCTCTTGT
1 ATTACTCATCTCCTTTCATTAACTCTCTTGT
6209583 GTCCTAACTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.19, C:0.29, G:0.03, T:0.48
Consensus pattern (31 bp):
ATTACTCATCTCCTTTCATTAACTCTCTTGT
Found at i:6209881 original size:12 final size:12
Alignment explanation
Indices: 6209864--6209888 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6209854 TTTTGAAATT
6209864 TAAAAAAAAAAG
1 TAAAAAAAAAAG
6209876 TAAAAAAAAAAG
1 TAAAAAAAAAAG
6209888 T
1 T
6209889 GAGTGAGTAT
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:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (12 bp):
TAAAAAAAAAAG
Found at i:6214373 original size:2 final size:2
Alignment explanation
Indices: 6214326--6214360 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6214316 CCTCAATTTC
6214326 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6214361 CTAGGAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6216652 original size:75 final size:74
Alignment explanation
Indices: 6216517--6216664 Score: 287
Period size: 75 Copynumber: 2.0 Consensus size: 74
6216507 ACAGTTCTGA
6216517 GTTAGTTGTGTCTTGTGTGTGTATTATTAGTAATGGTTGTAAGTGAAAGCGGTGAGAGGTTCATG
1 GTTAGTTGTGTCTTGTGTGTGTATTATTAGTAATGGTTGTAAGTGAAAGCGGTGAGAGGTTCATG
6216582 GTGATGAAT
66 GTGATGAAT
6216591 GTTAGTTGTGTCTTGTGTGTGTATTATTAGTTAATGGTTGTAAGTGAAAGCGGTGAGAGGTTCAT
1 GTTAGTTGTGTCTTGTGTGTGTATTATTAG-TAATGGTTGTAAGTGAAAGCGGTGAGAGGTTCAT
6216656 GGTGATGAA
65 GGTGATGAA
6216665 ACCTACTTTT
Statistics
Matches: 73, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
74 30 0.41
75 43 0.59
ACGTcount: A:0.23, C:0.04, G:0.34, T:0.39
Consensus pattern (74 bp):
GTTAGTTGTGTCTTGTGTGTGTATTATTAGTAATGGTTGTAAGTGAAAGCGGTGAGAGGTTCATG
GTGATGAAT
Found at i:6223956 original size:3 final size:3
Alignment explanation
Indices: 6223950--6224035 Score: 104
Period size: 3 Copynumber: 28.3 Consensus size: 3
6223940 TATGATGATG
6223950 ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA
* **
6223995 ATA ATA ATA ATAA ATA A-A AGA GGA ATA TATA ATA ATA ATA A
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA -ATA ATA ATA ATA A
6224036 AATCATTATA
Statistics
Matches: 75, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
2 4 0.05
3 62 0.83
4 9 0.12
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:6223998 original size:28 final size:30
Alignment explanation
Indices: 6223950--6224035 Score: 115
Period size: 28 Copynumber: 2.9 Consensus size: 30
6223940 TATGATGATG
*
6223950 ATAATAATATAATAATAATAATAATAAT-A
1 ATAATAAGATAATAATAATAATAATAATAA
6223979 ATAATAA-ATAATAATAATAATAATAATAA
1 ATAATAAGATAATAATAATAATAATAATAA
*
6224008 ATAA-AAGAGGAATATATAATAATAATAA
1 ATAATAAGA-TAATA-ATAATAATAATAA
6224036 AATCATTATA
Statistics
Matches: 52, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
28 22 0.42
29 13 0.25
30 4 0.08
31 13 0.25
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.30
Consensus pattern (30 bp):
ATAATAAGATAATAATAATAATAATAATAA
Found at i:6224026 original size:22 final size:22
Alignment explanation
Indices: 6223958--6224035 Score: 81
Period size: 22 Copynumber: 3.6 Consensus size: 22
6223948 TGATAATAAT
* *
6223958 ATAAT-AATAATAATAATAATA
1 ATAATAAATAATAAGAAGAATA
* *
6223979 ATAATAAATAATAATAATAATA
1 ATAATAAATAATAAGAAGAATA
*
6224001 ATAATAAATAA-AAGAGGAATA
1 ATAATAAATAATAAGAAGAATA
6224022 TATAAT-AATAATAA
1 -ATAATAAATAATAA
6224036 AATCATTATA
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
21 17 0.33
22 34 0.67
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (22 bp):
ATAATAAATAATAAGAAGAATA
Found at i:6230719 original size:21 final size:21
Alignment explanation
Indices: 6230703--6230826 Score: 117
Period size: 21 Copynumber: 6.0 Consensus size: 21
6230693 GCGTTGCATT
6230703 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
6230724 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
*
6230744 TCGCGTTGCTATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
6230765 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
*
6230785 TTGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
6230806 TCGCGTTGCGATAGTTAAAAA
1 TCGCGTTGCGATAGTTGAAAA
6230827 AAAGATTTTT
Statistics
Matches: 76, Mismatches: 25, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
20 28 0.37
21 48 0.63
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:6230744 original size:41 final size:41
Alignment explanation
Indices: 6230699--6230817 Score: 220
Period size: 41 Copynumber: 2.9 Consensus size: 41
6230689 ATTCGCGTTG
6230699 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
6230740 CATTTCGCGTTGCTATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
6230781 CATTTTGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
6230818 AGTTAAAAAA
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 75 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:6230749 original size:20 final size:20
Alignment explanation
Indices: 6230724--6230796 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
6230714 TAGTTGAAAA
6230724 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * ** **
6230744 TCGCGTTGCTATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
6230765 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
6230785 TTGCGTTGCGAT
1 TCGCGTTGCGAT
6230797 AGTTGAAAAT
Statistics
Matches: 39, Mismatches: 13, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
20 25 0.64
21 14 0.36
ACGTcount: A:0.15, C:0.21, G:0.23, T:0.41
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:6231424 original size:6 final size:6
Alignment explanation
Indices: 6231403--6231438 Score: 51
Period size: 5 Copynumber: 6.5 Consensus size: 6
6231393 TCTCGTCTCG
6231403 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT -GTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
6231439 AATACGTGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 15 0.52
6 14 0.48
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:6231434 original size:17 final size:16
Alignment explanation
Indices: 6231403--6231438 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
6231393 TCTCGTCTCG
6231403 GGTCGGGTCGGGTCGT
1 GGTCGGGTCGGGTCGT
*
6231419 GGTCGTGGTCGTGTCGT
1 GGTCG-GGTCGGGTCGT
6231436 GGT
1 GGT
6231439 AATACGTGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.31
Consensus pattern (16 bp):
GGTCGGGTCGGGTCGT
Found at i:6231612 original size:21 final size:20
Alignment explanation
Indices: 6231569--6231788 Score: 158
Period size: 20 Copynumber: 10.8 Consensus size: 20
6231559 ACTGTAGACT
*
6231569 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGGAAA
6231589 ATCGCAACGCGAAATGCGAAA
1 ATCGCAACGCGAAATG-GAAA
*
6231610 ATCGCAACGCGAAATGCGTAA
1 ATCGCAACGCGAAATG-GAAA
* *
6231631 ATCGCAA--AGAATTTGGAAA
1 ATCGCAACGCGAA-ATGGAAA
* **
6231650 ATCGCAACGAC-AACTGTAGACT
1 ATCGCAACG-CGAAATG--GAAA
*
6231672 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGGAAA
*** ** *
6231692 ATCGCAACGCGTTTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
** ** *
6231713 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
6231734 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGGAAA
*
6231754 ATCGCAACGCGAAACGGAAA
1 ATCGCAACGCGAAATGGAAA
6231774 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
6231789 ACAACGCGAA
Statistics
Matches: 165, Mismatches: 26, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
19 13 0.08
20 68 0.41
21 68 0.41
22 16 0.10
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:6231717 original size:82 final size:82
Alignment explanation
Indices: 6231569--6231784 Score: 201
Period size: 82 Copynumber: 2.6 Consensus size: 82
6231559 ACTGTAGACT
* * * *** *
6231569 ATCGCAACGCGAAATGAAAAATCGCAACGCGAAATGCGAAAATCGCAACGCGAAATGCGTAA--A
1 ATCGCAACGCGAACTGGAAAATCGCAACGCGAAACG-GAAAATCGCAACGCGTTTTTC--AACTA
*
6231632 TCGCAAAG-AATTTGGAA-A
63 TCGCAAAGCAATTTGCAACA
**
6231650 ATCGCAACGAC-AACTGTAGACTATCGCAACGCG-AACTGGAAAATCGCAACGCGTTTTTCAACT
1 ATCGCAACG-CGAACTG--GAAAATCGCAACGCGAAAC-GGAAAATCGCAACGCGTTTTTCAACT
* * * *
6231713 ATCGCAACGCGATTTTCAACT
62 ATCGCAAAGCAATTTGCAACA
6231734 ATCGCAACGCGAACTGGAAAATCGCAACGCGAAACGGAAAATCGCAACGCG
1 ATCGCAACGCGAACTGGAAAATCGCAACGCGAAACGGAAAATCGCAACGCG
6231785 AAATACAACG
Statistics
Matches: 109, Mismatches: 16, Indels: 19
0.76 0.11 0.13
Matches are distributed among these distances:
80 2 0.02
81 13 0.12
82 57 0.52
83 23 0.21
84 14 0.13
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.16
Consensus pattern (82 bp):
ATCGCAACGCGAACTGGAAAATCGCAACGCGAAACGGAAAATCGCAACGCGTTTTTCAACTATCG
CAAAGCAATTTGCAACA
Found at i:6236287 original size:14 final size:16
Alignment explanation
Indices: 6236268--6236300 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
6236258 TAAAATTATT
6236268 TTTAATAT-TTAA-TA
1 TTTAATATATTAATTA
6236282 TTTAATATATTAATTA
1 TTTAATATATTAATTA
6236298 TTT
1 TTT
6236301 TATAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 4 0.24
16 5 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTAATATATTAATTA
Found at i:6238793 original size:29 final size:29
Alignment explanation
Indices: 6238749--6238829 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
6238739 CTCACCTAAC
6238749 TAAATGAT-TAAGCAATGACATCATTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
6238777 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
6238806 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
6238830 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
28 8 0.16
29 41 0.84
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:6243502 original size:29 final size:29
Alignment explanation
Indices: 6243459--6243541 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
6243449 CTCACCTAAC
6243459 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
6243489 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
6243518 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
6243542 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:6259100 original size:38 final size:38
Alignment explanation
Indices: 6259043--6259118 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
6259033 TTAGATGATG
*
6259043 ACACTTGTAATCATCTGATTGGATAGAAATAAACAAAA
1 ACACGTGTAATCATCTGATTGGATAGAAATAAACAAAA
* *
6259081 ACACGTGTAATCATTTGATTGGATAGAAATTAACAAAA
1 ACACGTGTAATCATCTGATTGGATAGAAATAAACAAAA
6259119 GAAGAAGACT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (38 bp):
ACACGTGTAATCATCTGATTGGATAGAAATAAACAAAA
Found at i:6269671 original size:36 final size:35
Alignment explanation
Indices: 6269631--6269703 Score: 92
Period size: 36 Copynumber: 2.1 Consensus size: 35
6269621 AAAAATTTAA
* * * *
6269631 GAGCTCAATTGAAGCTCGAGACTCGAGCTCGATTTT
1 GAGCTCAATTCAAGCTCGA-ACTCAAACTCGAATTT
*
6269667 GAGCTCGATTCAAGCTCGAACTCAAACTCGAATTT
1 GAGCTCAATTCAAGCTCGAACTCAAACTCGAATTT
6269702 GA
1 GA
6269704 ACCTACAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
35 15 0.47
36 17 0.53
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (35 bp):
GAGCTCAATTCAAGCTCGAACTCAAACTCGAATTT
Found at i:6278805 original size:107 final size:107
Alignment explanation
Indices: 6278619--6278829 Score: 386
Period size: 107 Copynumber: 2.0 Consensus size: 107
6278609 TCTTAAAAAA
6278619 TCTTAAAAACCTCCTCTAAACTTTAAAAATCCTAAATCTAGTCCTATAACAATGCTCGTCACCCG
1 TCTTAAAAACCTCCTCTAAACTTTAAAAATCCTAAATCTAGTCCTATAACAATGCTCGTCACCCG
*
6278684 CCGTTGTCGTTGTCATTGATTGGACTTCCATCTGGTCACTTC
66 CCATTGTCGTTGTCATTGATTGGACTTCCATCTGGTCACTTC
* *
6278726 TCTTAAAAATCTCCTCTAAACTTTGAAAATCCTAAATCTAGTCCTATAACAATGCTCGTCACCCG
1 TCTTAAAAACCTCCTCTAAACTTTAAAAATCCTAAATCTAGTCCTATAACAATGCTCGTCACCCG
*
6278791 CTATTGTCGTTGTCATTGATTGGACTTCCATCTGGTCAC
66 CCATTGTCGTTGTCATTGATTGGACTTCCATCTGGTCAC
6278830 GCCTCAATCG
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
107 100 1.00
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.34
Consensus pattern (107 bp):
TCTTAAAAACCTCCTCTAAACTTTAAAAATCCTAAATCTAGTCCTATAACAATGCTCGTCACCCG
CCATTGTCGTTGTCATTGATTGGACTTCCATCTGGTCACTTC
Found at i:6281464 original size:119 final size:119
Alignment explanation
Indices: 6281317--6281554 Score: 311
Period size: 120 Copynumber: 2.0 Consensus size: 119
6281307 ATTTTAATCC
* * * * *
6281317 TGTTTTAATATTTATTTATTTTTCAATAT-TAAGAA-AGGGCAGTCTTAAAACAACTGGATGTCC
1 TGTTTTAATAATTATTTATTTTTCAATATCGAAGAATAGAGCAGTCTTAAAACAACTAGAAGTCC
*
6281380 ATTTTCTGATATTTTTAAATAAATAAATATCCTATTTTATAAAT-TATAAATTAAT
66 -TTTTCTGATATTTCTAAATAAATAAATATCCTA-TTTATAAATATATAAATTAAT
* * ** *
6281435 TGTTTTAATTAATTATTTATTTTTTAATATCGAAGAATAGAGCTGTCTTAAGGCACCTAGAAGTC
1 TGTTTTAA-TAATTATTTATTTTTCAATATCGAAGAATAGAGCAGTCTTAAAACAACTAGAAGTC
**
6281500 CTTTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATAAATTAAT
65 CTTTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATAAATTAAT
6281555 ATTTTTTTCA
Statistics
Matches: 103, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
118 8 0.08
119 28 0.27
120 46 0.45
121 21 0.20
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (119 bp):
TGTTTTAATAATTATTTATTTTTCAATATCGAAGAATAGAGCAGTCTTAAAACAACTAGAAGTCC
TTTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATAAATTAAT
Found at i:6281548 original size:27 final size:27
Alignment explanation
Indices: 6281518--6281572 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
6281508 ATATTTCTAA
6281518 ATAAATAAATATTTTATTT-ATAAATAT
1 ATAAATAAATATTTT-TTTCATAAATAT
* *
6281545 ATAAATTAATATTTTTTTCATAATTAT
1 ATAAATAAATATTTTTTTCATAAATAT
6281572 A
1 A
6281573 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 3 0.12
27 22 0.88
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (27 bp):
ATAAATAAATATTTTTTTCATAAATAT
Found at i:6281631 original size:47 final size:47
Alignment explanation
Indices: 6281544--6281634 Score: 112
Period size: 47 Copynumber: 1.9 Consensus size: 47
6281534 TTTATAAATA
* * * *
6281544 TATAAATTAATATTTTTTTCATAATTATAATTTTGAAATAATAGGAT
1 TATAAATTAATATATTTTTCAAAATTATAAATTTCAAATAATAGGAT
* *
6281591 TATAAATTAAATATATTTTTGAAAATT-TAAATTTCTAATAATAG
1 TATAAATT-AATATATTTTTCAAAATTATAAATTTCAAATAATAG
6281635 AGACAATTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
47 22 0.59
48 15 0.41
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.47
Consensus pattern (47 bp):
TATAAATTAATATATTTTTCAAAATTATAAATTTCAAATAATAGGAT
Found at i:6282080 original size:10 final size:10
Alignment explanation
Indices: 6282065--6282126 Score: 62
Period size: 8 Copynumber: 6.5 Consensus size: 10
6282055 TTTCTTTCAA
6282065 ATTTTTTATT
1 ATTTTTTATT
6282075 ATTTTTTA-T
1 ATTTTTTATT
*
6282084 -TTTTATA-T
1 ATTTTTTATT
6282092 A-TTTTTATT
1 ATTTTTTATT
6282101 A-TTTTTATT
1 ATTTTTTATT
6282110 ATTTTTTTACTT
1 A-TTTTTTA-TT
6282122 ATTTT
1 ATTTT
6282127 ATTCAAGTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
8 12 0.27
9 12 0.27
10 8 0.18
11 10 0.22
12 3 0.07
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (10 bp):
ATTTTTTATT
Found at i:6282123 original size:12 final size:11
Alignment explanation
Indices: 6282066--6282126 Score: 54
Period size: 12 Copynumber: 5.3 Consensus size: 11
6282056 TTCTTTCAAA
6282066 TTTTTTATTA-
1 TTTTTTATTAT
6282076 TTTTTTATT-T
1 TTTTTTATTAT
*
6282086 TTATATATTTTTAT
1 TT-T-T-TTATTAT
6282100 TATTTTTATTAT
1 T-TTTTTATTAT
6282112 TTTTTTACTTAT
1 TTTTTTA-TTAT
6282124 TTT
1 TTT
6282127 ATTCAAGTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
10 11 0.26
11 7 0.17
12 15 0.36
13 5 0.12
14 3 0.07
15 1 0.02
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTTATTAT
Found at i:6286555 original size:2 final size:2
Alignment explanation
Indices: 6286548--6286603 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
6286538 TTATCCTTTA
6286548 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
6286590 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
6286604 CCTTTGTTGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6286920 original size:26 final size:27
Alignment explanation
Indices: 6286890--6286943 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
6286880 TATTATACTC
* *
6286890 ATCCAGCAAAGAAA-GAAGAAAGAAAA
1 ATCCAACAAAGAAAGGAAAAAAGAAAA
6286916 ATCCAACAAAGAAAGGAAAAAAGAAAA
1 ATCCAACAAAGAAAGGAAAAAAGAAAA
6286943 A
1 A
6286944 GAGGAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 13 0.52
27 12 0.48
ACGTcount: A:0.69, C:0.11, G:0.17, T:0.04
Consensus pattern (27 bp):
ATCCAACAAAGAAAGGAAAAAAGAAAA
Found at i:6286943 original size:7 final size:7
Alignment explanation
Indices: 6286931--6287031 Score: 64
Period size: 7 Copynumber: 14.0 Consensus size: 7
6286921 ACAAAGAAAG
6286931 GAAAAAA
1 GAAAAAA
6286938 GAAAAAGA
1 GAAAAA-A
6286946 GGAAAAAA
1 -GAAAAAA
6286954 GAAAAAA
1 GAAAAAA
6286961 -AAACAAA
1 GAAA-AAA
*
6286968 -AAAACA
1 GAAAAAA
*
6286974 -AAAAAT
1 GAAAAAA
6286980 GAAATAAA
1 GAAA-AAA
6286988 TGAAAAAA
1 -GAAAAAA
*
6286996 AACAAAAA
1 GA-AAAAA
* *
6287004 CAAAAAG
1 GAAAAAA
*
6287011 GAAAAAG
1 GAAAAAA
*
6287018 GAAAAAG
1 GAAAAAA
6287025 GAAAAAA
1 GAAAAAA
6287032 AAAGGAAAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
6 9 0.12
7 46 0.59
8 13 0.17
9 10 0.13
ACGTcount: A:0.79, C:0.04, G:0.14, T:0.03
Consensus pattern (7 bp):
GAAAAAA
Found at i:6286950 original size:16 final size:16
Alignment explanation
Indices: 6286929--6286959 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
6286919 CAACAAAGAA
6286929 AGGAAAAAAGAAAAAG
1 AGGAAAAAAGAAAAAG
6286945 AGGAAAAAAGAAAAA
1 AGGAAAAAAGAAAAA
6286960 AAAACAAAAA
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:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AGGAAAAAAGAAAAAG
Found at i:6286977 original size:26 final size:26
Alignment explanation
Indices: 6286948--6287003 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
6286938 GAAAAAGAGG
6286948 AAAAAAGAAA-AAAAAACAAAAAAACA
1 AAAAAAGAAATAAAAAA-AAAAAAACA
* **
6286974 AAAAATGAAATAAATGAAAAAAAACA
1 AAAAAAGAAATAAAAAAAAAAAAACA
6287000 AAAA
1 AAAA
6287004 CAAAAAGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 22 0.85
27 4 0.15
ACGTcount: A:0.84, C:0.05, G:0.05, T:0.05
Consensus pattern (26 bp):
AAAAAAGAAATAAAAAAAAAAAAACA
Found at i:6287040 original size:7 final size:7
Alignment explanation
Indices: 6287005--6287041 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
6286995 AAACAAAAAC
6287005 AAAAAGG
1 AAAAAGG
6287012 AAAAAGG
1 AAAAAGG
6287019 AAAAAGG
1 AAAAAGG
6287026 -AAAA--
1 AAAAAGG
6287030 AAAAAGG
1 AAAAAGG
6287037 AAAAA
1 AAAAA
6287042 TTGAATCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
5 4 0.15
6 4 0.15
7 19 0.70
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (7 bp):
AAAAAGG
Found at i:6287041 original size:8 final size:8
Alignment explanation
Indices: 6286927--6287031 Score: 53
Period size: 8 Copynumber: 13.4 Consensus size: 8
6286917 TCCAACAAAG
6286927 AAAGGAAA
1 AAAGGAAA
6286935 AAA-GAAA
1 AAAGGAAA
6286942 AAGAGGAAA
1 AA-AGGAAA
*
6286951 AAAGAAAAA
1 AAAG-GAAA
**
6286960 AAAACAAA
1 AAAGGAAA
**
6286968 AAAACAAA
1 AAAGGAAA
*
6286976 AAATGAAA
1 AAAGGAAA
*
6286984 TAAATGAAA
1 -AAAGGAAA
6286993 AAA--AACA
1 AAAGGAA-A
6287000 AAA--ACAA
1 AAAGGA-AA
6287007 AAAGG-AA
1 AAAGGAAA
6287014 AAAGG-AA
1 AAAGGAAA
6287021 AAAGGAAA
1 AAAGGAAA
6287029 AAA
1 AAA
6287032 AAAGGAAAAA
Statistics
Matches: 83, Mismatches: 5, Indels: 18
0.78 0.05 0.17
Matches are distributed among these distances:
6 2 0.02
7 29 0.35
8 32 0.39
9 20 0.24
ACGTcount: A:0.79, C:0.04, G:0.14, T:0.03
Consensus pattern (8 bp):
AAAGGAAA
Found at i:6291635 original size:54 final size:54
Alignment explanation
Indices: 6291553--6291664 Score: 170
Period size: 54 Copynumber: 2.1 Consensus size: 54
6291543 CAATGATTGA
* *
6291553 GAACATCGGAGCAGAAACCACAAGAAAGGATGAATGTGTTGTCAAATATTTTAC
1 GAACATCGGAGCAGAAACCACAAGAAAGGATGAATGCGCTGTCAAATATTTTAC
* * * *
6291607 GAACATCTGAGCAGAAGCCACAGGAAAGGATGAATGCGCTGTCAAATGTTTTAC
1 GAACATCGGAGCAGAAACCACAAGAAAGGATGAATGCGCTGTCAAATATTTTAC
6291661 GAAC
1 GAAC
6291665 CTGCTATTCT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.21
Consensus pattern (54 bp):
GAACATCGGAGCAGAAACCACAAGAAAGGATGAATGCGCTGTCAAATATTTTAC
Found at i:6292062 original size:22 final size:22
Alignment explanation
Indices: 6292031--6292085 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
6292021 ATCTACACTC
*
6292031 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
6292053 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
6292075 TTCAAAGATGA
1 TTCAAAGATGA
6292086 AAGCTTTATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:6292648 original size:113 final size:113
Alignment explanation
Indices: 6292521--6292767 Score: 467
Period size: 113 Copynumber: 2.2 Consensus size: 113
6292511 ATTTCTGGAA
*
6292521 GAGTTCATAATGAGAAGAACTCATTTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
6292586 CAACTTTTCGCTTGAATTCATCATTCGATGGATCGGCATTACCAGGTC
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGTC
*
6292634 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
6292699 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGTC
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGTC
6292747 GAGTTCATAATGAGAAGAACT
1 GAGTTCATAATGAGAAGAACT
6292768 TGTTCAACTT
Statistics
Matches: 131, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 131 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (113 bp):
GAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGTC
Found at i:6292794 original size:73 final size:73
Alignment explanation
Indices: 6292675--6292840 Score: 314
Period size: 73 Copynumber: 2.3 Consensus size: 73
6292665 AGGAAGAAGA
* *
6292675 AGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTA
1 AGTTCATAATGAGAAGAACTTGTTCAACTTTTCACTTGAATTCATCATTCGATGGATCAACATTA
6292740 CCAGGTCG
66 CCAGGTCG
6292748 AGTTCATAATGAGAAGAACTTGTTCAACTTTTCACTTGAATTCATCATTCGATGGATCAACATTA
1 AGTTCATAATGAGAAGAACTTGTTCAACTTTTCACTTGAATTCATCATTCGATGGATCAACATTA
6292813 CCAGGTCG
66 CCAGGTCG
6292821 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
6292841 CATCTGAAGA
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 91 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (73 bp):
AGTTCATAATGAGAAGAACTTGTTCAACTTTTCACTTGAATTCATCATTCGATGGATCAACATTA
CCAGGTCG
Found at i:6292889 original size:186 final size:186
Alignment explanation
Indices: 6292562--6292948 Score: 702
Period size: 186 Copynumber: 2.1 Consensus size: 186
6292552 AAGAAGAAGA
* **
6292562 AGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCGGCATTA
1 AGTTCATAATGAGAAGAACTTGTTCAACTTTTCACTTGAATTCATCATTCGATGGATCAACATTA
6292627 CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
66 CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
* *
6292692 ACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGTCG
131 ACTTATTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGGCG
6292748 AGTTCATAATGAGAAGAACTTGTTCAACTTTTCACTTGAATTCATCATTCGATGGATCAACATTA
1 AGTTCATAATGAGAAGAACTTGTTCAACTTTTCACTTGAATTCATCATTCGATGGATCAACATTA
*
6292813 CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAATA
66 CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
* *
6292878 ACTTATTCAACTTTTCGCTTGAATTTATCATTCGATGGATCAGCATTGCCAGGGCG
131 ACTTATTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGGCG
6292934 AGTTCATAATGAGAA
1 AGTTCATAATGAGAA
6292949 AAAATCATCT
Statistics
Matches: 193, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
186 193 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30
Consensus pattern (186 bp):
AGTTCATAATGAGAAGAACTTGTTCAACTTTTCACTTGAATTCATCATTCGATGGATCAACATTA
CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
ACTTATTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGGCG
Found at i:6293059 original size:299 final size:298
Alignment explanation
Indices: 6292492--6293066 Score: 988
Period size: 299 Copynumber: 1.9 Consensus size: 298
6292482 AGTTCAAATC
* * *
6292492 CATCATTCAATGGATCAACATTTCTGGAAGAGTTCATAATGAGAAGAACTCATTTGAAGAAAGAA
1 CATCATTCAATGGATCAACATTCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAA
* *
6292557 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCGG
66 GAAGAAGTTCATAATGAGAAGAACTTATTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAG
* * * * *
6292622 CATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
131 CATTACCAGGGCGAGTTCATAATGAGAAAAAATCATCTGAAGAAAGAAAAAGAAGTTCATAATGA
6292687 GAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGTCGAGTT
196 GAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGTCGAGTT
6292752 CATAATGAGAAGAACTTGTTCAACTTTTCACTTGAATT
261 CATAATGAGAAGAACTTGTTCAACTTTTCACTTGAATT
* ** *
6292790 CATCATTCGATGGATCAACATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCAATGGATCAACATT-CCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
* *
6292855 AGAAGAAGTTCATAATGAGAATAACTTATTCAACTTTTCGCTTGAATTTATCATTCGATGGATCA
65 AGAAGAAGTTCATAATGAGAAGAACTTATTCAACTTTTCGCTTGAATTCATCATTCGATGGATCA
*
6292920 GCATTGCCAGGGCGAGTTCATAATGAGAAAAAATCATCTGAAGAAAGAAAAAGAAGTTCATAATG
130 GCATTACCAGGGCGAGTTCATAATGAGAAAAAATCATCTGAAGAAAGAAAAAGAAGTTCATAATG
6292985 AGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGTCGAGT
195 AGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGTCGAGT
6293050 TCATAATGAGAAGAACT
260 TCATAATGAGAAGAACT
6293067 CATCTGAAGA
Statistics
Matches: 259, Mismatches: 17, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
298 21 0.08
299 238 0.92
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (298 bp):
CATCATTCAATGGATCAACATTCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAA
GAAGAAGTTCATAATGAGAAGAACTTATTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAG
CATTACCAGGGCGAGTTCATAATGAGAAAAAATCATCTGAAGAAAGAAAAAGAAGTTCATAATGA
GAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGTCGAGTT
CATAATGAGAAGAACTTGTTCAACTTTTCACTTGAATT
Found at i:6293586 original size:113 final size:113
Alignment explanation
Indices: 6292748--6293571 Score: 1380
Period size: 113 Copynumber: 7.3 Consensus size: 113
6292738 TACCAGGTCG
* *
6292748 AGTTCATAATGAGAAGAACTTGTTCAACTTTTCACTTGAATTCATCATTCGATGGATCAACATTA
1 AGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTA
6292813 CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
66 CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * * *
6292861 AGTTCATAATGAGAATAACTTATTCAACTTTTCGCTTGAATTTATCATTCGATGGATCAGCATTG
1 AGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTA
* * * * *
6292926 CCAGGGCGAGTTCATAATGAGAAAAAATCATCTGAAGAAAGAAAAAGA
66 CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
6292974 AGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTA
1 AGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTA
6293039 CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
66 CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
*
6293087 AGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAACATTA
1 AGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTA
*
6293152 CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGA
66 CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
*
6293200 AGTTCATAATGAGAAGAACTTGTTCAACTTTTCACTTGAATTCATCATTCGATGGATCAGCATTA
1 AGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTA
6293265 CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
66 CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * *
6293313 AGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTTATCATTCGATGAATCAGCATTG
1 AGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTA
* * *
6293378 CCAGGGCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAAAAGA
66 CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * * * * *
6293426 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCGAATTCATCACTCGATGGATCAACTTTT
1 AGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTA
*
6293491 CCAGAG-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
66 CCAG-GTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
6293539 AGTTCATAATGAGAAGAACTTGTTCAATCTTTT
1 AGTTCATAATGAGAAGAACTTGTTCAA-CTTTT
6293572 GCATGATTCT
Statistics
Matches: 666, Mismatches: 43, Indels: 3
0.94 0.06 0.00
Matches are distributed among these distances:
113 660 0.99
114 6 0.01
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTA
CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
Found at i:6293921 original size:3 final size:3
Alignment explanation
Indices: 6293913--6294005 Score: 102
Period size: 3 Copynumber: 31.0 Consensus size: 3
6293903 ATTTGGTTTT
* *
6293913 TTA TTA TTA -TA TTTA TTA TTTA TTA -TA TTTA TTT TTA TTA CTA TTA
1 TTA TTA TTA TTA -TTA TTA -TTA TTA TTA -TTA TTA TTA TTA TTA TTA
* *
6293959 TTA TTA TTA TTA TTA ATA TTA TTA TTA TTA ATA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6294006 CAGATACAAC
Statistics
Matches: 76, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
2 6 0.08
3 63 0.83
4 7 0.09
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:6295487 original size:119 final size:118
Alignment explanation
Indices: 6295352--6295577 Score: 285
Period size: 120 Copynumber: 1.9 Consensus size: 118
6295342 ATTTTAATCC
* * * * *
6295352 TGTTTTAATATTTATTTATTTTTTAATAT-TAAG-AAAGGGCAGTCTTAAAACAACTGGATGTCC
1 TGTTTTAATATTTATTTATTTTTAAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCC
*
6295415 ATTTTCTAATATTTTTAAATAAATAAATATCCTATTTTATAAATTATATATTAAT
66 -TTTTCTAATATTTCTAAATAAATAAATATCCTA-TTTATAAATTATATATTAAT
* * ** *
6295470 TGTTTTAATTATTTATTTATTTTTAAATATCGAAGAAAATAGCTGTCTTAAGGCACCTAGAAGTC
1 TGTTTTAA-TATTTATTTATTTTTAAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTC
* **
6295535 CTTTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAAT
65 CTTTTCTAATATTTCTAAATAAATAAATATCCTATTTATAAAT
6295578 ATGTAAATTA
Statistics
Matches: 91, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
118 8 0.09
119 29 0.32
120 32 0.35
121 22 0.24
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.46
Consensus pattern (118 bp):
TGTTTTAATATTTATTTATTTTTAAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCC
TTTTCTAATATTTCTAAATAAATAAATATCCTATTTATAAATTATATATTAAT
Found at i:6300515 original size:3 final size:3
Alignment explanation
Indices: 6300507--6300541 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
6300497 ATAAATGAAC
*
6300507 ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
6300542 GTTTGATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:6307279 original size:145 final size:145
Alignment explanation
Indices: 6307016--6307439 Score: 770
Period size: 145 Copynumber: 3.0 Consensus size: 145
6307006 ACCCTACTAA
6307016 TTAGATGTGGATACCAGAGCTCGATAGCCTTGATTCGATTTCCATTTAACAATTACCAGGCAACA
1 TTAGATGTGGATACCAGAGCTCGATAGCCTTGATTCGATTTCCATTTAACAATTACCAGGCAACA
6307081 CCTACTCTGGTTGGCCATGATATTTTTAAGCATATTTTACTAATGTGGTGAATGCATTACCATAA
66 CCTACTCTGGTTGGCCATGATATTTTTAAGCATATTTTACTAATGTGGTGAATGCATTACCATAA
6307146 CCCTGCTTAATCAAT
131 CCCTGCTTAATCAAT
6307161 TTAGATGTGGATACCAGAGCTCGATAGCCTTGATTCGATTTCCATTTAACAATTACCAGGCAACA
1 TTAGATGTGGATACCAGAGCTCGATAGCCTTGATTCGATTTCCATTTAACAATTACCAGGCAACA
6307226 CCTACTCTGGTTGGCCATGATATTTTTAAGCATATTTTACTAATGTGGTGAATGCATTACCATAA
66 CCTACTCTGGTTGGCCATGATATTTTTAAGCATATTTTACTAATGTGGTGAATGCATTACCATAA
*
6307291 CCCTGCTTAGTCAAT
131 CCCTGCTTAATCAAT
*
6307306 TTAGATGTGGATACCAGAGCTCGATAGCCTGGATTCGATTTCCATTTAAC-A-T----GGCAACA
1 TTAGATGTGGATACCAGAGCTCGATAGCCTTGATTCGATTTCCATTTAACAATTACCAGGCAACA
*
6307365 CCTACTCTGGTTGGCCATGATATTTTTAAGCATATTTTACTAATGTGGTGAATGCATTTCCATAA
66 CCTACTCTGGTTGGCCATGATATTTTTAAGCATATTTTACTAATGTGGTGAATGCATTACCATAA
*
6307430 CCCTGTTTAA
131 CCCTGCTTAA
6307440 CCACACTTTT
Statistics
Matches: 274, Mismatches: 5, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
139 79 0.29
143 1 0.00
144 1 0.00
145 193 0.70
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (145 bp):
TTAGATGTGGATACCAGAGCTCGATAGCCTTGATTCGATTTCCATTTAACAATTACCAGGCAACA
CCTACTCTGGTTGGCCATGATATTTTTAAGCATATTTTACTAATGTGGTGAATGCATTACCATAA
CCCTGCTTAATCAAT
Found at i:6319068 original size:21 final size:21
Alignment explanation
Indices: 6319044--6319086 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
6319034 CTTGCTCCAG
*
6319044 CCTTTGC-TTGCGCTGCTTCTT
1 CCTTTGCTTTGCGCAGC-TCTT
6319065 CCTTTGCTTTGCGCAGCTCTT
1 CCTTTGCTTTGCGCAGCTCTT
6319086 C
1 C
6319087 ACAAGCCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.02, C:0.35, G:0.19, T:0.44
Consensus pattern (21 bp):
CCTTTGCTTTGCGCAGCTCTT
Found at i:6323753 original size:19 final size:17
Alignment explanation
Indices: 6323709--6323746 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
6323699 TTATATATCT
6323709 TAAATTAAATTCACATA
1 TAAATTAAATTCACATA
* *
6323726 TTAATTAAATTCACATC
1 TAAATTAAATTCACATA
6323743 TAAA
1 TAAA
6323747 CATTAAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (17 bp):
TAAATTAAATTCACATA
Found at i:6323959 original size:25 final size:26
Alignment explanation
Indices: 6323931--6323993 Score: 65
Period size: 31 Copynumber: 2.3 Consensus size: 26
6323921 ATTAATGTCA
6323931 ATATTTTT-AAATAAAAATAAAATAT
1 ATATTTTTAAAATAAAAATAAAATAT
*
6323956 ATATGTTAAGTTAAAAATAAGAATAAAATAT
1 ATAT-TT---TT-AAAATAAAAATAAAATAT
6323987 ATATTTT
1 ATATTTT
6323994 AATTTAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
25 4 0.13
26 2 0.06
27 1 0.03
29 2 0.06
30 2 0.06
31 20 0.65
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (26 bp):
ATATTTTTAAAATAAAAATAAAATAT
Found at i:6324005 original size:30 final size:30
Alignment explanation
Indices: 6323939--6324170 Score: 156
Period size: 30 Copynumber: 7.8 Consensus size: 30
6323929 CAATATTTTT
* *
6323939 AAATAAAAATAAAATATATATGTTAAGTTAA
1 AAATAAGAATAAAATATATATTTTAAGTT-A
*
6323970 AAATAAGAATAAAATATATATTTTAATTTA
1 AAATAAGAATAAAATATATATTTTAAGTTA
* * * *
6324000 AAATAAGGAT--AATTTATATTCAATAATTTA
1 AAATAAGAATAAAATATATATT--TTAAGTTA
* * * **
6324030 AGATAAGAATATAATATATGTAATAAGTTA
1 AAATAAGAATAAAATATATATTTTAAGTTA
* **
6324060 AAATAAAAATAAGCTATAT-TTTTAAAAGTTA
1 AAATAAGAATAAAATATATATTTT--AAGTTA
* *
6324091 AGATACA-AATAAAATATAT-TTTAAAGTTA
1 AAATA-AGAATAAAATATATATTTTAAGTTA
** *
6324120 TGATAAG-ATTAAA-ATATATTTTAAGTTA
1 AAATAAGAATAAAATATATATTTTAAGTTA
* *
6324148 AAATAAAAATAAAAAATAT-TTTT
1 AAATAAGAATAAAATATATATTTT
6324171 GATATAATAT
Statistics
Matches: 160, Mismatches: 30, Indels: 24
0.75 0.14 0.11
Matches are distributed among these distances:
27 4 0.03
28 28 0.17
29 21 0.13
30 50 0.31
31 49 0.31
32 8 0.05
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.37
Consensus pattern (30 bp):
AAATAAGAATAAAATATATATTTTAAGTTA
Found at i:6324272 original size:23 final size:23
Alignment explanation
Indices: 6324199--6324277 Score: 70
Period size: 28 Copynumber: 3.2 Consensus size: 23
6324189 TAAATTATTT
* *
6324199 AATATATTTTATAAGAT-ATATAA
1 AATATATTTTA-AAGTTAAGATAA
6324222 AATATATTTTAAAGTAAAATAAGAATAA
1 AATATATTTTAAAGT----TAAG-ATAA
6324250 AATATATTTTAAAGTTAAGATAA
1 AATATATTTTAAAGTTAAGATAA
6324273 GAATA
1 -AATA
6324278 AAAAATATAT
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
22 3 0.06
23 15 0.32
24 8 0.17
26 1 0.02
27 1 0.02
28 19 0.40
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.37
Consensus pattern (23 bp):
AATATATTTTAAAGTTAAGATAA
Found at i:6324285 original size:29 final size:29
Alignment explanation
Indices: 6324218--6324290 Score: 112
Period size: 28 Copynumber: 2.5 Consensus size: 29
6324208 TATAAGATAT
*
6324218 ATAAAATATATTTTAAAG-TAAAATAAGA
1 ATAAAATATATTTTAAAGTTAAGATAAGA
6324246 ATAAAATATATTTTAAAGTTAAGATAAGA
1 ATAAAATATATTTTAAAGTTAAGATAAGA
6324275 ATAAAAAATATATTTT
1 AT--AAAATATATTTT
6324291 TAATGTTTAG
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
28 18 0.44
29 11 0.27
31 12 0.29
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.36
Consensus pattern (29 bp):
ATAAAATATATTTTAAAGTTAAGATAAGA
Found at i:6324293 original size:60 final size:59
Alignment explanation
Indices: 6323939--6324290 Score: 179
Period size: 60 Copynumber: 5.9 Consensus size: 59
6323929 CAATATTTTT
* * * **
6323939 AAATAAAAATAAAATATATATGTT-AAGTTAAAAATAAGAATAAAATATATATTTTAATTTA
1 AAATAAGAATAAAATATAT-T-TTAAAGTT-AAGATAAGAATAAAAAATATATTTTAAAGTA
* ** ** * * * *
6324000 AAATAAGGATAATTTATATTCAATAATTTAAGATAAGAAT--ATAATATATGTAATAAGTTA
1 AAATAAGAATAAAATATATTTTA-AAGTTAAGATAAGAATAAAAAATATATTTTA-AAG-TA
* **
6324060 AAATAAAAATAAGCTATATTTTTAAAAGTTAAGATACA-AAT--AAAATATATTTTAAAGTTA
1 AAATAAGAATAAAATATA-TTTT-AAAGTTAAGATA-AGAATAAAAAATATATTTTAAAG-TA
** * * * *
6324120 TGATAAGATTAAAATATATTTT-AAGTTAAAATAAAAATAAAAAATAT-TTTTGATA-TA
1 AAATAAGAATAAAATATATTTTAAAGTTAAGATAAGAATAAAAAATATATTTT-AAAGTA
* *** * * *** *
6324177 ATATTTTTATTTTAAAT-TA-TTTAATA-TATTTTATAAGATATATAAAATATATTTTAAAGTA
1 A-AATAAGA-ATAAAATATATTTTAA-AGT-TAAGATAAGA-ATAAAAAATATATTTTAAAGTA
6324238 AAATAAGAATAAAATATATTTTAAAGTTAAGATAAGAATAAAAAATATATTTT
1 AAATAAGAATAAAATATATTTTAAAGTTAAGATAAGAATAAAAAATATATTTT
6324291 TAATGTTTAG
Statistics
Matches: 214, Mismatches: 55, Indels: 46
0.68 0.17 0.15
Matches are distributed among these distances:
56 1 0.00
57 18 0.08
58 19 0.09
59 47 0.22
60 70 0.33
61 57 0.27
62 2 0.01
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.39
Consensus pattern (59 bp):
AAATAAGAATAAAATATATTTTAAAGTTAAGATAAGAATAAAAAATATATTTTAAAGTA
Found at i:6324693 original size:21 final size:20
Alignment explanation
Indices: 6324666--6324764 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
6324656 AATCAGTTTC
6324666 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
6324687 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
6324708 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
6324728 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
6324749 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
6324765 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 16 0.26
21 45 0.74
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:6324793 original size:20 final size:20
Alignment explanation
Indices: 6324731--6324924 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
6324721 CGATTTTCCA
* ** *
6324731 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
6324751 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
6324771 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
6324791 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
6324811 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
6324831 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
6324851 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* ***
6324871 AAATCGCAACG-ATAATAAAT
1 AAATCGCAACGCGT-ATCCGT
6324891 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
6324912 AAATCGCAACGCG
1 AAATCGCAACGCG
6324925 ATATTTAAAG
Statistics
Matches: 144, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 125 0.87
21 16 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:6324815 original size:60 final size:60
Alignment explanation
Indices: 6324731--6324924 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
6324721 CGATTTTCCA
* ** * * *
6324731 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATAAATAAATCGCAACGCGTATCCGT
* * *** *
6324791 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATAAATAAATCGCAACGCGTATCCGT
* **
6324851 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATAAATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATAAAT-AAATCGCAACGCGTATCCGT
6324912 AAATCGCAACGCG
1 AAATCGCAACGCG
6324925 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATAAATAAATCGCAACGCGTATCCGT
Found at i:6325346 original size:33 final size:33
Alignment explanation
Indices: 6325307--6325377 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
6325297 TTCACTTAGA
*
6325307 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* * *
6325340 TTTCATTTCGCGTTGCTATTCTCTCGTTGTGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
6325373 TTTCA
1 TTTCA
6325378 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.21, G:0.18, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:6325501 original size:20 final size:20
Alignment explanation
Indices: 6325457--6325566 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
6325447 TGCAGAAGAG
*
6325457 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
6325478 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
6325498 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
6325519 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
6325533 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
6325552 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
6325567 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:6325514 original size:41 final size:38
Alignment explanation
Indices: 6325450--6325566 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
6325440 TTCAATTTGC
* *
6325450 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
6325488 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
6325529 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
6325562 AGAAT
1 AGAAT
6325567 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:6325536 original size:14 final size:14
Alignment explanation
Indices: 6325517--6325573 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
6325507 GAGAAATGAA
6325517 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
6325531 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
6325550 AATCGCAACGAGAG
1 AATCGCAACGAGAG
6325564 AATCGCAACG
1 AATCGCAACG
6325574 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:6325549 original size:33 final size:33
Alignment explanation
Indices: 6325509--6325589 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
6325499 CGCAACGAGA
6325509 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
6325542 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
6325575 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
6325590 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:6325607 original size:19 final size:19
Alignment explanation
Indices: 6325585--6325682 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
6325575 GAAACCAAAA
*
6325585 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
6325604 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
6325618 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
6325637 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
6325651 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
6325670 TCGCGTTGCGATT
1 TCGCGTTGCGATT
6325683 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:6325626 original size:14 final size:14
Alignment explanation
Indices: 6325607--6325696 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
6325597 TTTCATTTCG
6325607 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
6325621 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
6325640 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
6325654 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
6325673 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
6325687 CGTTGCGATT
1 CGTTGCGATT
6325697 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:6325632 original size:33 final size:33
Alignment explanation
Indices: 6325590--6325704 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
6325580 CAAAATCGCA
6325590 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
6325623 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
6325656 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
6325689 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
6325705 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:6327558 original size:93 final size:93
Alignment explanation
Indices: 6327399--6327867 Score: 922
Period size: 93 Copynumber: 5.1 Consensus size: 93
6327389 TAGATTGCTT
*
6327399 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
6327464 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
6327492 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
6327557 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
6327585 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
6327650 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
6327678 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
6327743 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
6327771 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
6327836 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
6327863 AGTAA
1 AGTAA
6327868 TGCAATCCAT
Statistics
Matches: 375, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
92 6 0.02
93 369 0.98
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:6327955 original size:19 final size:19
Alignment explanation
Indices: 6327915--6328013 Score: 109
Period size: 19 Copynumber: 5.4 Consensus size: 19
6327905 TAGTTTACTT
* *
6327915 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
6327935 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
6327954 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
6327973 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
6327987 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
6328006 TCGCAACG
1 TCGCAACG
6328014 AGAGAATCGC
Statistics
Matches: 67, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
14 9 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.58
20 13 0.19
ACGTcount: A:0.45, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:6327994 original size:33 final size:33
Alignment explanation
Indices: 6327952--6328044 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 33
6327942 GCGAAACCAA
6327952 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
** *
6327985 AATCGCAACGCGAAACCAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* **
6328018 AATCGCAATGCGTTATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
6328045 TGCGAAATGA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.44, C:0.24, G:0.20, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:6328041 original size:52 final size:52
Alignment explanation
Indices: 6327985--6328182 Score: 228
Period size: 52 Copynumber: 3.9 Consensus size: 52
6327975 GCAACGACAG
* ** **
6327985 AATCGCAACGCGAAACCAAAATCGCAACGAGAGAATCGCAATGCGTTATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
* ** * *
6328037 AATCGCAATGCGAAATGAAAATCGCATTATG-TTGAA-GGCAA----AAATGAC
1 AATCGCAATGCGAAATGAAAATCGCA--ACGAGAGAATCGCAATGCGAAATGAA
*
6328085 TATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
6328137 AATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCG
6328183 TTTATAATTT
Statistics
Matches: 120, Mismatches: 17, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
46 2 0.02
47 3 0.03
48 33 0.28
52 43 0.36
53 37 0.31
54 2 0.02
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.16
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:6328154 original size:20 final size:19
Alignment explanation
Indices: 6327931--6328164 Score: 129
Period size: 19 Copynumber: 12.5 Consensus size: 19
6327921 CACGAAACTT
* **
6327931 AAAATCGCAACGCGAAACC
1 AAAATCGCAATGCGAAATG
*
6327950 AAAATCGCAACGCGAAATG
1 AAAATCGCAATGCGAAATG
*
6327969 AAAATCGCAA--CGACA-G
1 AAAATCGCAATGCGAAATG
* **
6327985 --AATCGCAACGCGAAACC
1 AAAATCGCAATGCGAAATG
6328002 AAAATCGCAA--CG--A-G
1 AAAATCGCAATGCGAAATG
* **
6328016 AGAATCGCAATGCGTTATG
1 AAAATCGCAATGCGAAATG
6328035 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
*
6328054 AAAATCGCATTATGTTGAAGGCAAAAATG
1 AAAATCGCA--A---T----GC-GAAATG
**
6328083 ACTATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
6328102 AAAATCGCAA--CG--A-G
1 AAAATCGCAATGCGAAATG
*
6328116 AGAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
6328135 AAAATCGCAATGCGGAAATG
1 AAAATCGCAATGC-GAAATG
6328155 AAAATCGCAA
1 AAAATCGCAA
6328165 CGAGAGAATC
Statistics
Matches: 171, Mismatches: 18, Indels: 51
0.71 0.08 0.21
Matches are distributed among these distances:
14 27 0.16
15 2 0.01
16 9 0.05
17 8 0.05
18 2 0.01
19 87 0.51
20 18 0.11
21 1 0.01
24 2 0.01
27 1 0.01
28 2 0.01
29 12 0.07
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.14
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATG
Found at i:6328226 original size:33 final size:33
Alignment explanation
Indices: 6328189--6328420 Score: 285
Period size: 33 Copynumber: 6.9 Consensus size: 33
6328179 TGCGTTTATA
6328189 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
6328222 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
6328262 GTTGCG-ATTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
6328292 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
6328325 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
6328358 ATTTCCGCATTGCGATT-TCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTC
6328391 ATTTCGCATTGCGATTCTCTCGTTGCGATT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATT
6328421 GTAATTTCCG
Statistics
Matches: 171, Mismatches: 14, Indels: 28
0.80 0.07 0.13
Matches are distributed among these distances:
30 6 0.04
31 5 0.03
32 24 0.14
33 92 0.54
34 15 0.09
35 3 0.02
36 6 0.04
38 9 0.05
39 5 0.03
40 6 0.04
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:6328235 original size:19 final size:19
Alignment explanation
Indices: 6328211--6328406 Score: 193
Period size: 19 Copynumber: 11.4 Consensus size: 19
6328201 GATTCTCTCG
6328211 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
6328230 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
6328249 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
6328263 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
6328281 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
6328300 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
6328314 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
6328333 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
6328347 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
6328367 TTGCGA-TTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
6328380 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
6328399 TTGCGATT
1 TTGCGATT
6328407 CTCTCGTTGC
Statistics
Matches: 147, Mismatches: 8, Indels: 44
0.74 0.04 0.22
Matches are distributed among these distances:
13 5 0.03
14 23 0.16
15 4 0.03
16 23 0.16
17 17 0.12
18 8 0.05
19 61 0.41
20 6 0.04
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:6328246 original size:52 final size:52
Alignment explanation
Indices: 6328189--6328420 Score: 306
Period size: 52 Copynumber: 4.6 Consensus size: 52
6328179 TGCGTTTATA
6328189 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
6328241 ATTTCGCATTGCGATTCTCTCGTTGCGA-TTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
6328292 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT-T-TC
* * * *
6328346 GTTGCG-ATTTTC-ATT-TC-CGCATTGCGA-TTTCA--T-G--TTGGGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
6328391 ATTTCGCATTGCGATTCTCTCGTTGCGATT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATT
6328421 GTAATTTCCG
Statistics
Matches: 162, Mismatches: 7, Indels: 27
0.83 0.04 0.14
Matches are distributed among these distances:
45 9 0.06
46 11 0.07
47 10 0.06
48 2 0.01
49 1 0.01
50 1 0.01
51 53 0.33
52 55 0.34
53 11 0.07
54 9 0.06
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:6330718 original size:12 final size:12
Alignment explanation
Indices: 6330701--6330725 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6330691 TCTTCGGGGA
6330701 CTTTTTCTTCTT
1 CTTTTTCTTCTT
6330713 CTTTTTCTTCTT
1 CTTTTTCTTCTT
6330725 C
1 C
6330726 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:6330934 original size:24 final size:24
Alignment explanation
Indices: 6330900--6330946 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
6330890 CTGAAACATC
6330900 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
6330924 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
6330947 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:6331656 original size:20 final size:20
Alignment explanation
Indices: 6331628--6331857 Score: 228
Period size: 20 Copynumber: 11.5 Consensus size: 20
6331618 AAATTTCAGT
* * *
6331628 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
6331648 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
6331668 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
6331688 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
6331708 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
6331728 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * ** *
6331748 ATTGCAATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
6331768 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
6331788 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
6331808 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
6331828 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
6331848 GTTGCGATTT
1 GTTGCGATTT
6331858 TGGAAAATCG
Statistics
Matches: 180, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 179 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:6331874 original size:21 final size:21
Alignment explanation
Indices: 6331844--6331926 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
6331834 ATTTTCATAT
*
6331844 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
6331865 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
* *
6331886 TCGCATTACGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
6331907 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
6331927 CTGATTTGCG
Statistics
Matches: 45, Mismatches: 15, Indels: 4
0.70 0.23 0.06
Matches are distributed among these distances:
20 1 0.02
21 42 0.93
22 2 0.04
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:6332718 original size:25 final size:25
Alignment explanation
Indices: 6332685--6332743 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
6332675 CACCTTATCC
*
6332685 TAATCAAAAAAATATAAATAATTAT
1 TAATAAAAAAAATATAAATAATTAT
* *
6332710 TAATAAAAAATATATAATTAATTAT
1 TAATAAAAAAAATATAAATAATTAT
6332735 TAATAAAAA
1 TAATAAAAA
6332744 GTTAATATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (25 bp):
TAATAAAAAAAATATAAATAATTAT
Found at i:6333074 original size:27 final size:28
Alignment explanation
Indices: 6333011--6333074 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 28
6333001 TATCAATCAC
6333011 ATAATA-AAAAAATCAAACAATAATAAT
1 ATAATATAAAAAATCAAACAATAATAAT
* * * *
6333038 AAAATTTAAAAAAT-ATATAATAATAAT
1 ATAATATAAAAAATCAAACAATAATAAT
*
6333065 TTAATATAAA
1 ATAATATAAA
6333075 TATAAAGTCA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (28 bp):
ATAATATAAAAAATCAAACAATAATAAT
Found at i:6333075 original size:24 final size:21
Alignment explanation
Indices: 6333029--6333078 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
6333019 AAAATCAAAC
6333029 AATA-ATAATAAAATTTAAAA
1 AATATATAATAAAATTTAAAA
6333049 AATATATAATAATAATTTAATATA
1 AATATATAATAA-AATTTAA-A-A
6333073 AATATA
1 AATATA
6333079 AAGTCAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.15
21 7 0.27
22 7 0.27
23 1 0.04
24 7 0.27
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AATATATAATAAAATTTAAAA
Found at i:6333543 original size:41 final size:42
Alignment explanation
Indices: 6333498--6333579 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 42
6333488 CGCACTCGAA
* *
6333498 TTTGATTTACATGTGACAATAGTTTTT-CAGTAGTTTGATAC
1 TTTGATTTACAGGTGACAATAGTTTTTCCAATAGTTTGATAC
* *
6333539 TTTGATTTACGGGTGTCAATAGTTTTTCCAATAGTTTGATA
1 TTTGATTTACAGGTGACAATAGTTTTTCCAATAGTTTGATA
6333580 TACTTTTGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 24 0.67
42 12 0.33
ACGTcount: A:0.26, C:0.10, G:0.18, T:0.46
Consensus pattern (42 bp):
TTTGATTTACAGGTGACAATAGTTTTTCCAATAGTTTGATAC
Found at i:6342871 original size:21 final size:21
Alignment explanation
Indices: 6342845--6342898 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
6342835 TTACATATGC
6342845 TTTTAATTATGCGTCTGCATG
1 TTTTAATTATGCGTCTGCATG
*
6342866 TTTTAATTACGCGTCTGCATG
1 TTTTAATTATGCGTCTGCATG
6342887 TTTTAATTATGC
1 TTTTAATTATGC
6342899 TAACCCAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.48
Consensus pattern (21 bp):
TTTTAATTATGCGTCTGCATG
Found at i:6345426 original size:40 final size:41
Alignment explanation
Indices: 6345382--6345486 Score: 137
Period size: 40 Copynumber: 2.6 Consensus size: 41
6345372 TGTGATTTTC
* * *
6345382 CAAATTCACAACGCGAAT-CTGTAAAT-CGCAACACAGAAGT
1 CAAATTCGCAACGCGAATAGT-TAAATCCGCAACACAAAAGT
6345422 CAAATTCGCAACGCG-ATAGTTAAATCCGCAACACAAAAGT
1 CAAATTCGCAACGCGAATAGTTAAATCCGCAACACAAAAGT
*
6345462 CAAATTCGCAACGCGAA-AGTCAAAT
1 CAAATTCGCAACGCGAATAGTTAAAT
6345487 TTGCAACGCG
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
39 7 0.12
40 50 0.86
41 1 0.02
ACGTcount: A:0.43, C:0.25, G:0.15, T:0.17
Consensus pattern (41 bp):
CAAATTCGCAACGCGAATAGTTAAATCCGCAACACAAAAGT
Found at i:6345430 original size:20 final size:19
Alignment explanation
Indices: 6345407--6345598 Score: 154
Period size: 20 Copynumber: 9.6 Consensus size: 19
6345397 AATCTGTAAA
*
6345407 TCGCAACACAGAAGTCAAAT
1 TCGCAACGC-GAAGTCAAAT
*
6345427 TCGCAACGCGATAGTTAAAT
1 TCGCAACGCGA-AGTCAAAT
* * *
6345447 CCGCAACACAAAAGTCAAAT
1 TCGCAACGC-GAAGTCAAAT
6345467 TCGCAACGCGAAAGTCAAAT
1 TCGCAACGCG-AAGTCAAAT
*
6345487 TTGCAACGCGAATTTGT-AAA-
1 TCGCAACGCGAA---GTCAAAT
* *
6345507 TCGCAACACAAAAGTCAAAT
1 TCGCAACGC-GAAGTCAAAT
* *
6345527 TCGCAGCGCGATAGCCAAAT
1 TCGCAACGCGA-AGTCAAAT
* *
6345547 TCGCAACACAAAAGTCAAAT
1 TCGCAACGC-GAAGTCAAAT
*
6345567 TCGTAACGCGATAGTCAAAT
1 TCGCAACGCGA-AGTCAAAT
6345587 TCGCAACGCGAA
1 TCGCAACGCGAA
6345599 ACACAATATT
Statistics
Matches: 135, Mismatches: 25, Indels: 25
0.73 0.14 0.14
Matches are distributed among these distances:
18 2 0.01
19 10 0.07
20 114 0.84
21 7 0.05
22 2 0.01
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.18
Consensus pattern (19 bp):
TCGCAACGCGAAGTCAAAT
Found at i:6345482 original size:60 final size:58
Alignment explanation
Indices: 6345418--6345599 Score: 202
Period size: 60 Copynumber: 3.0 Consensus size: 58
6345408 CGCAACACAG
6345418 AAGTCAAATTCGCAACGCGATAGTTAAATCCGCAACACAAAAGTCAAATTCGCAACGCGA
1 AAGTCAAATTCGCAACGCGA-AGTTAAAT-CGCAACACAAAAGTCAAATTCGCAACGCGA
* * *
6345478 AAGTCAAATTTGCAACGCGAATTTGTAAATCGCAACACAAAAGTCAAATTCGCAGCGCGA
1 AAGTCAAATTCGCAACGCGAA-GT-TAAATCGCAACACAAAAGTCAAATTCGCAACGCGA
* * * * * * * * *
6345538 TAGCCAAATTCGCAACACAAAAGTCAAATTCGTAACGCGATAGTCAAATTCGCAACGCGA
1 AAGTCAAATTCGCAACGC-GAAGTTAAA-TCGCAACACAAAAGTCAAATTCGCAACGCGA
6345598 AA
1 AA
6345600 CACAATATTA
Statistics
Matches: 102, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
59 4 0.04
60 91 0.89
61 7 0.07
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.18
Consensus pattern (58 bp):
AAGTCAAATTCGCAACGCGAAGTTAAATCGCAACACAAAAGTCAAATTCGCAACGCGA
Found at i:6345493 original size:40 final size:40
Alignment explanation
Indices: 6345419--6345599 Score: 186
Period size: 40 Copynumber: 4.5 Consensus size: 40
6345409 GCAACACAGA
* * * * *
6345419 AGTCAAATTCGCAACGCGATAGTTAAATCCGCAACACAAA
1 AGTCAAATTCGCAACGCGAAAGTCAAATTCGCAACGCAAT
*
6345459 AGTCAAATTCGCAACGCGAAAGTCAAATTTGCAACGCGAATT
1 AGTCAAATTCGCAACGCGAAAGTCAAATTCGCAACGC-AA-T
* * * * *
6345501 TGT-AAA-TCGCAACACAAAAGTCAAATTCGCAGCGCGAT
1 AGTCAAATTCGCAACGCGAAAGTCAAATTCGCAACGCAAT
* * * * *
6345539 AGCCAAATTCGCAACACAAAAGTCAAATTCGTAACGCGAT
1 AGTCAAATTCGCAACGCGAAAGTCAAATTCGCAACGCAAT
6345579 AGTCAAATTCGCAACGCGAAA
1 AGTCAAATTCGCAACGCGAAA
6345600 CACAATATTA
Statistics
Matches: 118, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
38 2 0.02
39 4 0.03
40 105 0.89
41 5 0.04
42 2 0.02
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.18
Consensus pattern (40 bp):
AGTCAAATTCGCAACGCGAAAGTCAAATTCGCAACGCAAT
Found at i:6345505 original size:100 final size:100
Alignment explanation
Indices: 6345382--6345598 Score: 344
Period size: 100 Copynumber: 2.2 Consensus size: 100
6345372 TGTGATTTTC
* * **
6345382 CAAATTCACAACGCGAATCTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTTAAAT
1 CAAATTCGCAACGCGAATCTGTAAATCGCAACACAAAAGTCAAATTCGCAACGCGATAGCCAAAT
6345447 CCGCAACACAAAAGTCAAATTCGCAACGCGAAAGT
66 CCGCAACACAAAAGTCAAATTCGCAACGCGAAAGT
* * *
6345482 CAAATTTGCAACGCGAATTTGTAAATCGCAACACAAAAGTCAAATTCGCAGCGCGATAGCCAAAT
1 CAAATTCGCAACGCGAATCTGTAAATCGCAACACAAAAGTCAAATTCGCAACGCGATAGCCAAAT
* * *
6345547 TCGCAACACAAAAGTCAAATTCGTAACGCGATAGT
66 CCGCAACACAAAAGTCAAATTCGCAACGCGAAAGT
6345582 CAAATTCGCAACGCGAA
1 CAAATTCGCAACGCGAA
6345599 ACACAATATT
Statistics
Matches: 106, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 106 1.00
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.18
Consensus pattern (100 bp):
CAAATTCGCAACGCGAATCTGTAAATCGCAACACAAAAGTCAAATTCGCAACGCGATAGCCAAAT
CCGCAACACAAAAGTCAAATTCGCAACGCGAAAGT
Found at i:6345735 original size:22 final size:22
Alignment explanation
Indices: 6345709--6345759 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
6345699 CTACGGCGAC
*
6345709 ATCCGTCCCCATCTCTGACGAA
1 ATCCGTCCCCATCTCCGACGAA
6345731 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
6345753 ATCCGTC
1 ATCCGTC
6345760 TATCTCCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.22, C:0.43, G:0.14, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:6346188 original size:20 final size:20
Alignment explanation
Indices: 6346145--6346193 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
6346135 AAAATCGCAA
*
6346145 CGCGATTTT-AGTTTCGCGT
1 CGCGATTTTCAGTTTCACGT
*
6346164 CGCGATTTTCATTTTCACGT
1 CGCGATTTTCAGTTTCACGT
*
6346184 TGCGATTTTC
1 CGCGATTTTC
6346194 TCGTTGCGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.45
Consensus pattern (20 bp):
CGCGATTTTCAGTTTCACGT
Found at i:6348379 original size:24 final size:24
Alignment explanation
Indices: 6348347--6348400 Score: 78
Period size: 21 Copynumber: 2.4 Consensus size: 24
6348337 GCCCGATGCA
*
6348347 CCTATCATTATTCAAGAGTCGCTT
1 CCTATCATTATTCAAGAGGCGCTT
6348371 CCTATC---ATTCAAGAGGCGCTT
1 CCTATCATTATTCAAGAGGCGCTT
6348392 CCTATCATT
1 CCTATCATT
6348401 CAAGAGGCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 20 0.77
24 6 0.23
ACGTcount: A:0.24, C:0.28, G:0.13, T:0.35
Consensus pattern (24 bp):
CCTATCATTATTCAAGAGGCGCTT
Found at i:6348382 original size:21 final size:21
Alignment explanation
Indices: 6348356--6348408 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
6348346 ACCTATCATT
*
6348356 ATTCAAGAGTCGCTTCCTATC
1 ATTCAAGAGGCGCTTCCTATC
6348377 ATTCAAGAGGCGCTTCCTATC
1 ATTCAAGAGGCGCTTCCTATC
6348398 ATTCAAGAGGC
1 ATTCAAGAGGC
6348409 CCCTCTCATC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (21 bp):
ATTCAAGAGGCGCTTCCTATC
Found at i:6348419 original size:21 final size:21
Alignment explanation
Indices: 6348374--6348470 Score: 83
Period size: 21 Copynumber: 4.6 Consensus size: 21
6348364 GTCGCTTCCT
* *
6348374 ATCATTCAAGAGGCGCTTC-C
1 ATCATTCAAGAGGCCCCTCTC
6348394 TATCATTCAAGAGGCCCCTCTC
1 -ATCATTCAAGAGGCCCCTCTC
*
6348416 ATCA-TCGAAGAAGCCCCT-TCC
1 ATCATTC-AAGAGGCCCCTCT-C
* * *
6348437 ACCGTTCAAGAGGCCCCTGTC
1 ATCATTCAAGAGGCCCCTCTC
*
6348458 ATCGTTCAAGAGG
1 ATCATTCAAGAGG
6348471 TCCTGTCCGC
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
20 3 0.05
21 57 0.89
22 4 0.06
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.23
Consensus pattern (21 bp):
ATCATTCAAGAGGCCCCTCTC
Found at i:6348420 original size:42 final size:41
Alignment explanation
Indices: 6348374--6348470 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 41
6348364 GTCGCTTCCT
* *
6348374 ATCATTCAAGAGGCGCTTCCTATCATTCAAGAGGCCCCTCTC
1 ATCATTCAAGAGGCCCTTCC-ACCATTCAAGAGGCCCCTCTC
* * *
6348416 ATCA-TCGAAGAAGCCCCTTCCACCGTTCAAGAGGCCCCTGTC
1 ATCATTC-AAG-AGGCCCTTCCACCATTCAAGAGGCCCCTCTC
*
6348458 ATCGTTCAAGAGG
1 ATCATTCAAGAGG
6348471 TCCTGTCCGC
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
41 4 0.09
42 31 0.69
43 10 0.22
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.23
Consensus pattern (41 bp):
ATCATTCAAGAGGCCCTTCCACCATTCAAGAGGCCCCTCTC
Found at i:6348484 original size:21 final size:21
Alignment explanation
Indices: 6348399--6348487 Score: 67
Period size: 21 Copynumber: 4.2 Consensus size: 21
6348389 CTTCCTATCA
* *
6348399 TTCAAGAGGCCCCTCTCATC-
1 TTCAAGAGGCCCCTGTCACCG
* *
6348419 ATCGAAGAAGCCCCT-TCCACCG
1 TTC-AAGAGGCCCCTGT-CACCG
*
6348441 TTCAAGAGGCCCCTGTCATCG
1 TTCAAGAGGCCCCTGTCACCG
* *
6348462 TTCAAGAGG-TCCTGTCCGCCG
1 TTCAAGAGGCCCCTGT-CACCG
6348483 TTCAA
1 TTCAA
6348488 AAGCCCGATT
Statistics
Matches: 55, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
20 8 0.15
21 44 0.80
22 3 0.05
ACGTcount: A:0.21, C:0.36, G:0.20, T:0.22
Consensus pattern (21 bp):
TTCAAGAGGCCCCTGTCACCG
Found at i:6349947 original size:14 final size:14
Alignment explanation
Indices: 6349901--6349937 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
6349891 GCTTGTTTAA
*
6349901 TTGATTTATAAAAG
1 TTGATTTGTAAAAG
6349915 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
6349929 TTGATTTGT
1 TTGATTTGT
6349938 TTAATTTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:6349988 original size:80 final size:78
Alignment explanation
Indices: 6349847--6350016 Score: 295
Period size: 80 Copynumber: 2.2 Consensus size: 78
6349837 TTTTACATTG
*
6349847 AAAGTTGATTTTTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTATAA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTATAA
6349912 AAGTTGATTTGTA
66 AAGTTGATTTGTA
* *
6349925 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTAT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTA-TTTTTTGCTTGTTTAATTGATTTAT
6349990 AAAAGTTGATTTGTA
64 AAAAGTTGATTTGTA
6350005 AAAGTTGATTTG
1 AAAGTTGATTTG
6350017 GTTTGCGATT
Statistics
Matches: 87, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
78 16 0.18
79 19 0.22
80 52 0.60
ACGTcount: A:0.32, C:0.01, G:0.17, T:0.49
Consensus pattern (78 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTATAA
AAGTTGATTTGTA
Found at i:6350016 original size:14 final size:14
Alignment explanation
Indices: 6349981--6350016 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
6349971 GCTTGTTTAA
*
6349981 TTGATTTATAAAAG
1 TTGATTTGTAAAAG
6349995 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
6350009 TTGATTTG
1 TTGATTTG
6350017 GTTTGCGATT
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:0.33, C:0.00, G:0.19, T:0.47
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:6350363 original size:18 final size:18
Alignment explanation
Indices: 6350340--6350375 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
6350330 AAGCCGGTTG
*
6350340 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
6350358 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
6350376 CTTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:6352670 original size:24 final size:24
Alignment explanation
Indices: 6352636--6352689 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
6352626 CCATCACATC
6352636 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
6352660 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
6352684 ATCAAA
1 ATCAAA
6352690 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:6352703 original size:24 final size:24
Alignment explanation
Indices: 6352636--6352703 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
6352626 CCATCACATC
* * *
6352636 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
6352660 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
6352684 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
6352704 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:6354578 original size:29 final size:29
Alignment explanation
Indices: 6354537--6354613 Score: 136
Period size: 29 Copynumber: 2.7 Consensus size: 29
6354527 GAGGAGCAGG
*
6354537 AGGAGTGAATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
6354566 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
*
6354595 ATGAGTGCATGGCGACCTA
1 AGGAGTGCATGGCGACCTA
6354614 TGCTGGGAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.26, C:0.25, G:0.34, T:0.16
Consensus pattern (29 bp):
AGGAGTGCATGGCGACCTACAAGGTCGCC
Found at i:6358345 original size:37 final size:37
Alignment explanation
Indices: 6358303--6358411 Score: 170
Period size: 35 Copynumber: 3.0 Consensus size: 37
6358293 ATATTTCAAC
* *
6358303 AAACATCTATCAAACTTTGAAAAGCCATTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAAGCCATTTTTCAAAG
6358340 AAACATTTACCAAACTTTGAAAAG-CA-TTTTCAAAG
1 AAACATTTACCAAACTTTGAAAAGCCATTTTTCAAAG
6358375 AAACATTTACCAAACTTTGAAAA-CCATTTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAAGCCA-TTTTTCAAAG
6358412 TTTGTTGCCA
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
35 34 0.51
36 2 0.03
37 31 0.46
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.30
Consensus pattern (37 bp):
AAACATTTACCAAACTTTGAAAAGCCATTTTTCAAAG
Found at i:6358367 original size:21 final size:20
Alignment explanation
Indices: 6358340--6358403 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
6358330 TTTTTCAAAG
6358340 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
*
6358360 AAAGCATTT-TCAAA----G-
1 AAA-CATTTACCAAACTTTGA
6358375 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
6358395 AAACCATTT
1 AAA-CATTT
6358404 TTTCAAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 1 0.03
19 1 0.03
20 10 0.29
21 10 0.29
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.30
Consensus pattern (20 bp):
AAACATTTACCAAACTTTGA
Found at i:6369628 original size:30 final size:29
Alignment explanation
Indices: 6369594--6369668 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 29
6369584 TAAGGTACTT
**
6369594 AAATAATAAAAATAGATAGTTTAA-AGACTA
1 AAATAATAAAAATAGA-AAATTAAGA-ACTA
6369624 AAATAATAAAAAATAGAAAATTAAGTAACTA
1 AAATAAT-AAAAATAGAAAATTAAG-AACTA
6369655 AAATAATAAAAATA
1 AAATAATAAAAATA
6369669 TATAATAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
30 19 0.47
31 20 0.50
32 1 0.03
ACGTcount: A:0.67, C:0.03, G:0.07, T:0.24
Consensus pattern (29 bp):
AAATAATAAAAATAGAAAATTAAGAACTA
Found at i:6369710 original size:22 final size:22
Alignment explanation
Indices: 6369670--6369711 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
6369660 ATAAAAATAT
*
6369670 ATAATAAAAACTTTAATTTACA
1 ATAATAAAAACTTAAATTTACA
6369692 ATAATAAAAAC-TAACATTTA
1 ATAATAAAAACTTAA-ATTTA
6369712 AAAAAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (22 bp):
ATAATAAAAACTTAAATTTACA
Found at i:6371351 original size:25 final size:26
Alignment explanation
Indices: 6371309--6371369 Score: 81
Period size: 25 Copynumber: 2.3 Consensus size: 26
6371299 TAACATATAT
6371309 TAATAATAATAATAATATATATATTA
1 TAATAATAATAATAATATATATATTA
6371335 TAAT-ATAATACAT-ATATATATATTAA
1 TAATAATAATA-ATAATATATATATT-A
*
6371361 TACTAATAA
1 TAATAATAA
6371370 AAAATGGATG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
25 17 0.55
26 10 0.32
27 4 0.13
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (26 bp):
TAATAATAATAATAATATATATATTA
Found at i:6371702 original size:135 final size:135
Alignment explanation
Indices: 6371558--6371811 Score: 456
Period size: 135 Copynumber: 1.9 Consensus size: 135
6371548 CATTGAAAGA
6371558 CGTCACTGATTCGAAATG-TCGTGAACCAAGTGATAGGGCAAACAAGCTCTTCTCATTATGAACT
1 CGTCACTGATTCGAAATGCT-GTGAACCAAGTGATAGGGCAAACAAGCTCTTCTCATTATGAACT
6371622 TCTTCTTCCTCGTTAGATGAGTTCTTCTCATTATAAACTCTCCATTGAAAATGTTGATCCCTCAA
65 TCTTCTTCCTCGTTAGATGAGTTCTTCTCATTATAAACTCTCCATTGAAAATGTTGATCCCTCAA
6371687 GCGAGG
130 GCGAGG
* *
6371693 CGTCACTGATTCGAAATGCTGTGAATCAAGTGATAGGGCGAACAAGCTCTTCTCATTATGAACTT
1 CGTCACTGATTCGAAATGCTGTGAACCAAGTGATAGGGCAAACAAGCTCTTCTCATTATGAACTT
* *
6371758 CTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCATTGAAAATGTT
66 CTTCTTCCTCGTTAGATGAGTTCTTCTCATTATAAACTCTCCATTGAAAATGTT
6371812 AAGTCACCTC
Statistics
Matches: 114, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
135 113 0.99
136 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.33
Consensus pattern (135 bp):
CGTCACTGATTCGAAATGCTGTGAACCAAGTGATAGGGCAAACAAGCTCTTCTCATTATGAACTT
CTTCTTCCTCGTTAGATGAGTTCTTCTCATTATAAACTCTCCATTGAAAATGTTGATCCCTCAAG
CGAGG
Found at i:6371984 original size:247 final size:248
Alignment explanation
Indices: 6371481--6372056 Score: 763
Period size: 247 Copynumber: 2.3 Consensus size: 248
6371471 TTGTTGGATT
* * *
6371481 GAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTGTTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
* * *
6371546 TCCATTG-AAA-GACGTCACTGATTCGAAATGTCGTGAACCAAGTGATAGGGCAAACAAGCTCTT
66 TCCATTGAAAATGAAGTCACTCATTC---ATGTCGTGAACC-AGTGATAAGG-AAACAAGCTCTT
* *
6371609 CTCATTATGAACTTCTTCTTCCTCGTTAGATGAGTTCTTCTCATTATAAACTCTCCATTGAAAAT
126 CTCATTATGAACTTCTTCTCCCTCGTCAGATGAGTTCTTCTCATTATAAACTCTCCATTGAAAAT
** * *
6371674 GTTGATCCCTCAAGCGAGGCGTCACTGATTCGAAATGCTGTGAATCAAGTGATAGGGC
191 GTCAATCCCTCAAGAGAGGCATCACTGATTCGAAATGCTGTGAATCAAGTGATAGGGC
6371732 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
* * * * *
6371797 TCCATTGAAAATGTTAAGTCACCTCTTTC-TGTGGTGGA-C-TTGA-AAGG-AACAAGTTCTTCT
66 TCCATTGAAAATG--AAGTCA-CTCATTCATGTCGTGAACCAGTGATAAGGAAACAAGCTCTTCT
* * *
6371857 CATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATG
128 CATTATGAACTTCTTCTCCCTC-GTCAGATGAGTTCTTCTCATTATAAACTCTCCATTGAAAATG
** *
6371922 TCAATCCCTCAAGAGAGGCATCACTGATTCGAAATG-TCGTGAATTGAGTGATAGGTC
192 TCAATCCCTCAAGAGAGGCATCACTGATTCGAAATGCT-GTGAATCAAGTGATAGGGC
* *
6371979 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTC-GTTGGATGAGTTCTTCTCATTATGAACT
*
6372044 CTCCATTTAAAAT
65 CTCCATTGAAAAT
6372057 ACTGATGCGA
Statistics
Matches: 291, Mismatches: 26, Indels: 19
0.87 0.08 0.06
Matches are distributed among these distances:
246 34 0.12
247 121 0.42
248 42 0.14
249 3 0.01
251 70 0.24
252 10 0.03
253 1 0.00
255 5 0.02
256 5 0.02
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (248 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
TCCATTGAAAATGAAGTCACTCATTCATGTCGTGAACCAGTGATAAGGAAACAAGCTCTTCTCAT
TATGAACTTCTTCTCCCTCGTCAGATGAGTTCTTCTCATTATAAACTCTCCATTGAAAATGTCAA
TCCCTCAAGAGAGGCATCACTGATTCGAAATGCTGTGAATCAAGTGATAGGGC
Found at i:6372139 original size:91 final size:92
Alignment explanation
Indices: 6371974--6372147 Score: 278
Period size: 91 Copynumber: 1.9 Consensus size: 92
6371964 ATTGAGTGAT
* *
6371974 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
1 AGGTCAAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAATTCTTCTCATTAT
*
6372039 GAACTCTCCATTTAAAATACTGATGCG
66 GAACTCTCCATTGAAAATACTGATGCG
* * * *
6372066 AGGTCAAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTC-GTTGGATGAATTCTTCTCATTAT
1 AGGTCAAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAATTCTTCTCATTAT
6372130 GAACTCTCCATTGAAAAT
66 GAACTCTCCATTGAAAAT
6372148 GTTGATCCAC
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
91 38 0.51
92 37 0.49
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (92 bp):
AGGTCAAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAATTCTTCTCATTAT
GAACTCTCCATTGAAAATACTGATGCG
Found at i:6372203 original size:111 final size:105
Alignment explanation
Indices: 6372072--6372271 Score: 267
Period size: 105 Copynumber: 1.8 Consensus size: 105
6372062 TGCGAGGTCA
* * *
6372072 AACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCGTT-GGATGAATTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAAC--TTTC-TCCT--TTAAGACGAACTCTTCTCATTATGAACTC
6372136 TCCATTGAAAATGTTGATCCACCTCCTTTTGTGATGGACTCGAAAGG
61 TCC--TGAAAATGTTGATCCACCTCCTTTTGTGATGGACTCGAAAGG
* *
6372183 AACAAGTTCTTCTCATTATGAACTTTCTCCTTTAAGACGAGCTCTTCTCATTATGAACTCTTCTG
1 AACAAGTTCTTCTCATTATGAACTTTCTCCTTTAAGACGAACTCTTCTCATTATGAACTCTCCTG
**
6372248 GTAATGTTGATCCACCTCCTTTTG
66 AAAATGTTGATCCACCTCCTTTTG
6372272 CAGTGAATCT
Statistics
Matches: 81, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
105 24 0.30
106 2 0.02
107 24 0.30
108 4 0.05
109 4 0.05
111 23 0.28
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (105 bp):
AACAAGTTCTTCTCATTATGAACTTTCTCCTTTAAGACGAACTCTTCTCATTATGAACTCTCCTG
AAAATGTTGATCCACCTCCTTTTGTGATGGACTCGAAAGG
Found at i:6372245 original size:16 final size:16
Alignment explanation
Indices: 6372190--6372246 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
6372180 AGGAACAAGT
6372190 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
* *
6372206 T-TTCTCCTTTAAGACGAGC
1 TCTTCT-CATTATGA--A-C
6372225 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
6372241 TCTTCT
1 TCTTCT
6372247 GGTAATGTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 4 0.12
16 14 0.44
17 1 0.03
18 1 0.03
19 8 0.25
20 4 0.12
ACGTcount: A:0.21, C:0.26, G:0.09, T:0.44
Consensus pattern (16 bp):
TCTTCTCATTATGAAC
Found at i:6373149 original size:20 final size:19
Alignment explanation
Indices: 6373126--6373188 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
6373116 TCTCGAACCC
*
6373126 TTTTTTTTCTCTTCATTTT
1 TTTTTTTTCTCTTCTTTTT
*
6373145 TTTTTCTT-TCTT-TTTTT
1 TTTTTTTTCTCTTCTTTTT
*
6373162 TATTTTTTC-CTTCTTTTT
1 TTTTTTTTCTCTTCTTTTT
6373180 ATTTTTTTT
1 -TTTTTTTT
6373189 TCATTTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
17 13 0.36
18 9 0.25
19 14 0.39
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTTTTTTCTCTTCTTTTT
Found at i:6373162 original size:14 final size:16
Alignment explanation
Indices: 6373126--6373162 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
6373116 TCTCGAACCC
6373126 TTTTTTTTCTCTTCAT
1 TTTTTTTTCTCTTCAT
6373142 TTTTTTTTCT-TTC-T
1 TTTTTTTTCTCTTCAT
6373156 TTTTTTT
1 TTTTTTT
6373163 ATTTTTTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.38
15 3 0.14
16 10 0.48
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTTTCTCTTCAT
Found at i:6373189 original size:20 final size:20
Alignment explanation
Indices: 6373140--6373190 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
6373130 TTTTCTCTTC
*
6373140 ATTTTTTTTTCTTTCTTTTT
1 ATTTTTTTTTCCTTCTTTTT
6373160 -TTTATTTTTTCCTTCTTTTT
1 ATTT-TTTTTTCCTTCTTTTT
6373180 ATTTTTTTTTC
1 ATTTTTTTTTC
6373191 ATTTTTTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 3 0.11
20 22 0.79
21 3 0.11
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (20 bp):
ATTTTTTTTTCCTTCTTTTT
Found at i:6373195 original size:16 final size:17
Alignment explanation
Indices: 6373128--6373195 Score: 57
Period size: 17 Copynumber: 3.9 Consensus size: 17
6373118 TCGAACCCTT
*
6373128 TTTTTTCTCTTCATTTTT
1 TTTTTTC-CTTCATTTTA
* **
6373146 TTTTCTTTCTTTTTTTTA
1 TTTT-TTCCTTCATTTTA
*
6373164 TTTTTTCCTTCTTTTTA
1 TTTTTTCCTTCATTTTA
*
6373181 TTTTTT-TTTCATTTT
1 TTTTTTCCTTCATTTT
6373196 TTTCTTCAAG
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
16 7 0.17
17 17 0.41
18 15 0.37
19 2 0.05
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTTCCTTCATTTTA
Found at i:6373198 original size:20 final size:19
Alignment explanation
Indices: 6373140--6373198 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 19
6373130 TTTTCTCTTC
6373140 ATTTTTTTTTCTTTCTTTTT
1 ATTTTTTTTTCTTT-TTTTT
*
6373160 -TTTATTTTTTCCTTCTTTTT
1 ATTT-TTTTTT-CTTTTTTTT
*
6373180 ATTTTTTTTTCATTTTTTT
1 ATTTTTTTTTCTTTTTTTT
6373199 CTTCAAGCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 10 0.30
20 17 0.52
21 6 0.18
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (19 bp):
ATTTTTTTTTCTTTTTTTT
Found at i:6373203 original size:12 final size:11
Alignment explanation
Indices: 6373137--6373203 Score: 54
Period size: 10 Copynumber: 6.4 Consensus size: 11
6373127 TTTTTTTCTC
6373137 TTCATTTTTTT
1 TTCATTTTTTT
6373148 TTC-TTTCTTTT
1 TTCATTT-TTTT
*
6373159 TT--TTATTTT
1 TTCATTTTTTT
* *
6373168 TTC-CTTCTTT
1 TTCATTTTTTT
6373178 TT-ATTTTTTT
1 TTCATTTTTTT
6373188 TTCATTTTTTT
1 TTCATTTTTTT
6373199 CTTCA
1 -TTCA
6373204 AGCATAGTAC
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
9 6 0.13
10 18 0.40
11 17 0.38
12 4 0.09
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.79
Consensus pattern (11 bp):
TTCATTTTTTT
Found at i:6384933 original size:22 final size:22
Alignment explanation
Indices: 6384893--6384956 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
6384883 ATAAAAATAT
*
6384893 ATAATAAAAACTTTAATTTACA
1 ATAATAAAAACTTAAATTTACA
*
6384915 ATAATAAAAAC-TAACATTTAAAA
1 ATAATAAAAACTTAA-ATTT-ACA
*
6384938 AAAATAAAATA-TTAAATTT
1 ATAATAAAA-ACTTAAATTT
6384957 TAAATAAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
21 2 0.06
22 15 0.43
23 14 0.40
24 4 0.11
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (22 bp):
ATAATAAAAACTTAAATTTACA
Found at i:6386543 original size:3 final size:3
Alignment explanation
Indices: 6386537--6386627 Score: 71
Period size: 3 Copynumber: 30.0 Consensus size: 3
6386527 TAACATATAT
* * *
6386537 TAA TAA TAA TAA TAT TAT TAA TAA TAA TAG TAA TAA TAA TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
6386584 T-A TATA TTA TAA T-A TAA TACA TATA TATA TAT TAA TAC TAA TAA
1 TAA TA-A TAA TAA TAA TAA TA-A TA-A TA-A TAA TAA TAA TAA TAA
6386628 AAAATAGATG
Statistics
Matches: 72, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
2 6 0.08
3 54 0.75
4 12 0.17
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:6387513 original size:3 final size:3
Alignment explanation
Indices: 6387488--6387552 Score: 94
Period size: 3 Copynumber: 21.0 Consensus size: 3
6387478 TTGGGTTTTG
* *
6387488 TAA TAT TAA TAAA TAA TATA TAA TAA TAA TAA TAA TAA TAA TTA TAA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
6387535 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
6387553 ATTTAAATTT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
3 50 0.89
4 6 0.11
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Done.