Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168004.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_26, 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: 16099665
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 28 of 77
Found at i:5435378 original size:25 final size:25
Alignment explanation
Indices: 5435350--5435401 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
5435340 CACCTTAGTC
5435350 CTAACTCTAATCCAAACTCTAAAAT
1 CTAACTCTAATCCAAACTCTAAAAT
* *
5435375 CTAATTCTAATCCAAATTCTAAAAT
1 CTAACTCTAATCCAAACTCTAAAAT
5435400 CT
1 CT
5435402 TATCTTAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.42, C:0.25, G:0.00, T:0.33
Consensus pattern (25 bp):
CTAACTCTAATCCAAACTCTAAAAT
Found at i:5435414 original size:25 final size:25
Alignment explanation
Indices: 5435350--5435422 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 25
5435340 CACCTTAGTC
* * *
5435350 CTAACTCTAATCCAAACTCTAAAAT
1 CTAATTCTAACCCAAATTCTAAAAT
*
5435375 CTAATTCTAATCCAAATTCTAAAAT
1 CTAATTCTAACCCAAATTCTAAAAT
* *
5435400 CTTA-TCTTAACCCAAATTTTAAA
1 CTAATTC-TAACCCAAATTCTAAA
5435423 CCTAGGTCGA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
24 2 0.05
25 40 0.95
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.34
Consensus pattern (25 bp):
CTAATTCTAACCCAAATTCTAAAAT
Found at i:5438739 original size:43 final size:43
Alignment explanation
Indices: 5438642--5438779 Score: 217
Period size: 43 Copynumber: 3.2 Consensus size: 43
5438632 TATTAGTATC
* *
5438642 AAATTGCTCCTCTAAACAGAGGAACCACGAC-TTTG-GAAAGT
1 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAAGT
* *
5438683 AAATTGCTCCTCTAAATAGAGGCATCACGACTTTTGAAAAAGT
1 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAAGT
5438726 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAAAGT
1 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTTG-AAAAAGT
5438770 AAATTGCTCC
1 AAATTGCTCC
5438780 ATGACAATCA
Statistics
Matches: 88, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
41 28 0.32
42 4 0.05
43 39 0.44
44 17 0.19
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.25
Consensus pattern (43 bp):
AAATTGCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAAGT
Found at i:5439815 original size:15 final size:16
Alignment explanation
Indices: 5439792--5439903 Score: 133
Period size: 15 Copynumber: 7.1 Consensus size: 16
5439782 TCCTTTTTCA
*
5439792 TTCACTTTTTC-TTTT
1 TTCATTTTTTCATTTT
5439807 TTCA-TTTTTCATTTT
1 TTCATTTTTTCATTTT
5439822 TTCATTTTTTCATTTT
1 TTCATTTTTTCATTTT
5439838 TTCA-TTTTTCATTTT
1 TTCATTTTTTCATTTT
*
5439853 TTCATTTTTTTA-TTT
1 TTCATTTTTTCATTTT
*
5439868 TTCATTTTTATTATTTT
1 TTCATTTTT-TCATTTT
* *
5439885 TATTATTTTTTTATTTT
1 T-TCATTTTTTCATTTT
5439902 TT
1 TT
5439904 TCAAGCATAG
Statistics
Matches: 89, Mismatches: 2, Indels: 11
0.87 0.02 0.11
Matches are distributed among these distances:
14 6 0.07
15 39 0.44
16 25 0.28
17 12 0.13
18 7 0.08
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (16 bp):
TTCATTTTTTCATTTT
Found at i:5439829 original size:23 final size:24
Alignment explanation
Indices: 5439792--5439903 Score: 133
Period size: 23 Copynumber: 4.8 Consensus size: 24
5439782 TCCTTTTTCA
*
5439792 TTCACTTTTTC-TTTTTTCA-TTT
1 TTCATTTTTTCATTTTTTCATTTT
5439814 TTCATTTTTTCATTTTTTCATTTT
1 TTCATTTTTTCATTTTTTCATTTT
5439838 TTCA-TTTTTCATTTTTTCATTTT
1 TTCATTTTTTCATTTTTTCATTTT
* *
5439861 TTTA-TTTTTCATTTTTATTATTTT
1 TTCATTTTTTCATTTTT-TCATTTT
* *
5439885 TATTATTTTTTTATTTTTT
1 T-TCATTTTTTCATTTTTT
5439904 TCAAGCATAG
Statistics
Matches: 81, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.12
23 42 0.52
24 14 0.17
25 4 0.05
26 11 0.14
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (24 bp):
TTCATTTTTTCATTTTTTCATTTT
Found at i:5439904 original size:8 final size:8
Alignment explanation
Indices: 5439792--5439903 Score: 133
Period size: 8 Copynumber: 14.2 Consensus size: 8
5439782 TCCTTTTTCA
*
5439792 TTCACTTT
1 TTCATTTT
5439800 TTC-TTTT
1 TTCATTTT
5439807 TTCA-TTT
1 TTCATTTT
5439814 TTCATTTT
1 TTCATTTT
5439822 TTCATTTT
1 TTCATTTT
5439830 TTCATTTT
1 TTCATTTT
5439838 TTCA-TTT
1 TTCATTTT
5439845 TTCATTTT
1 TTCATTTT
5439853 TTCATTTT
1 TTCATTTT
*
5439861 TTTA-TTT
1 TTCATTTT
5439868 TTCATTTT
1 TTCATTTT
*
5439876 TATTATTTT
1 T-TCATTTT
*
5439885 TATTATTTT
1 T-TCATTTT
*
5439894 TTTATTTT
1 TTCATTTT
5439902 TT
1 TT
5439904 TCAAGCATAG
Statistics
Matches: 95, Mismatches: 4, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
7 26 0.27
8 53 0.56
9 16 0.17
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (8 bp):
TTCATTTT
Found at i:5457065 original size:2 final size:2
Alignment explanation
Indices: 5457058--5457087 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5457048 ACCCAAAAGT
5457058 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5457088 AGTGTTACCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5459729 original size:18 final size:18
Alignment explanation
Indices: 5459687--5459730 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
5459677 AACTACTCAA
* *
5459687 ATATATATGTACATGTAT
1 ATATACATGTACATGTAC
* *
5459705 GTTTACATGTACATGTAC
1 ATATACATGTACATGTAC
5459723 ATATACAT
1 ATATACAT
5459731 ATATATATGT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.41
Consensus pattern (18 bp):
ATATACATGTACATGTAC
Found at i:5464631 original size:25 final size:25
Alignment explanation
Indices: 5464603--5464667 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
5464593 AACCAAAGTC
5464603 TAATCCTAACCCTAAAACCTCACCT
1 TAATCCTAACCCTAAAACCTCACCT
* *
5464628 TAATTCTAACCCTAAAATCTCACCT
1 TAATCCTAACCCTAAAACCTCACCT
* *
5464653 TAGTCCTAACTCTAA
1 TAATCCTAACCCTAA
5464668 TCCAAACTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.35, C:0.34, G:0.02, T:0.29
Consensus pattern (25 bp):
TAATCCTAACCCTAAAACCTCACCT
Found at i:5464686 original size:25 final size:25
Alignment explanation
Indices: 5464658--5464709 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
5464648 CACCTTAGTC
5464658 CTAACTCTAATCCAAACTCTAAAAT
1 CTAACTCTAATCCAAACTCTAAAAT
* *
5464683 CTAATTCTAATCCAAATTCTAAAAT
1 CTAACTCTAATCCAAACTCTAAAAT
5464708 CT
1 CT
5464710 TATCTTAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.42, C:0.25, G:0.00, T:0.33
Consensus pattern (25 bp):
CTAACTCTAATCCAAACTCTAAAAT
Found at i:5464722 original size:25 final size:25
Alignment explanation
Indices: 5464658--5464730 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 25
5464648 CACCTTAGTC
* * *
5464658 CTAACTCTAATCCAAACTCTAAAAT
1 CTAATTCTAACCCAAATTCTAAAAT
*
5464683 CTAATTCTAATCCAAATTCTAAAAT
1 CTAATTCTAACCCAAATTCTAAAAT
* *
5464708 CTTA-TCTTAACCCAAATTTTAAA
1 CTAATTC-TAACCCAAATTCTAAA
5464731 CCTAGGTCGA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
24 2 0.05
25 40 0.95
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.34
Consensus pattern (25 bp):
CTAATTCTAACCCAAATTCTAAAAT
Found at i:5467745 original size:20 final size:20
Alignment explanation
Indices: 5467708--5467745 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5467698 TAATTTTTAC
* *
5467708 AAAAGTAAAAAAGAAAAATG
1 AAAAGCAAAAAAAAAAAATG
5467728 AAAAGCAAAAAAAAAAAA
1 AAAAGCAAAAAAAAAAAA
5467746 AAGAAATCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.82, C:0.03, G:0.11, T:0.05
Consensus pattern (20 bp):
AAAAGCAAAAAAAAAAAATG
Found at i:5467936 original size:40 final size:41
Alignment explanation
Indices: 5467881--5468004 Score: 178
Period size: 40 Copynumber: 3.0 Consensus size: 41
5467871 TATTAGTATC
5467881 AAATTGCTCCTCTAAACAGAGGCA-CACGACTTTGGAAAGT
1 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGT
* *
5467921 AAATTGCTCCTCTAAATAGAGGCATCCACGACTTTTGAAAAGT
1 AAATTGCTCCTCTAAACAGAGGCA-CCACGAC-TTTGGAAAGT
*
5467964 AAATTGCTCCCTCTAAACAGAGGCAACCACGACTTTTGAAA
1 AAATTGCT-CCTCTAAACAGAGGC-ACCACGACTTTGGAAA
5468005 AAAGTAATTG
Statistics
Matches: 74, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
40 23 0.31
42 6 0.08
43 23 0.31
44 21 0.28
45 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.24
Consensus pattern (41 bp):
AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGT
Found at i:5467988 original size:44 final size:42
Alignment explanation
Indices: 5467881--5468018 Score: 192
Period size: 44 Copynumber: 3.2 Consensus size: 42
5467871 TATTAGTATC
*
5467881 AAATTGCTCCTCTAAACAGAGGCA-CACGAC-TTTGGAAAGT
1 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGT
*
5467921 AAATTGCTCCTCTAAATAGAGGCATCCACGACTTTTGAAAAGT
1 AAATTGCTCCTCTAAACAGAGGCA-CCACGACTTTTGAAAAGT
5467964 AAATTGCTCCCTCTAAACAGAGGCAACCACGACTTTTGAAAAAAGT
1 AAATTGCT-CCTCTAAACAGAGGC-ACCACGACTTTTG--AAAAGT
5468010 -AATTGCTCC
1 AAATTGCTCC
5468019 ATGACAATCA
Statistics
Matches: 88, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
40 23 0.26
42 6 0.07
43 17 0.19
44 28 0.32
45 8 0.09
46 6 0.07
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.25
Consensus pattern (42 bp):
AAATTGCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGT
Found at i:5469052 original size:7 final size:7
Alignment explanation
Indices: 5469031--5469110 Score: 76
Period size: 7 Copynumber: 11.3 Consensus size: 7
5469021 TCCTTTTTCA
*
5469031 TTCACTT
1 TTCATTT
*
5469038 TTCTTTT
1 TTCATTT
5469045 TTCA-TT
1 TTCATTT
5469051 TTCATTT
1 TTCATTT
5469058 TTCATTTT
1 TTCA-TTT
5469066 TTCATTTT
1 TTCA-TTT
5469074 TTCATTTT
1 TTCA-TTT
5469082 TTCA-TT
1 TTCATTT
5469088 TTCATTT
1 TTCATTT
*
5469095 TT-TTATT
1 TTCAT-TT
5469102 TTCATTT
1 TTCATTT
5469109 TT
1 TT
5469111 ATTATTTTTA
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
6 13 0.21
7 26 0.41
8 24 0.38
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (7 bp):
TTCATTT
Found at i:5469058 original size:14 final size:14
Alignment explanation
Indices: 5469049--5469139 Score: 89
Period size: 14 Copynumber: 6.4 Consensus size: 14
5469039 TCTTTTTTCA
5469049 TTTTCATTTTTCATT
1 TTTTCA-TTTTCATT
5469064 TTTTCATTTTTTCATT
1 TTTTCA--TTTTCATT
5469080 TTTTCATTTTCATT
1 TTTTCATTTTCATT
*
5469094 TTTTTATTTTCATT
1 TTTTCATTTTCATT
* *
5469108 TTTATTATTTTTATT
1 TTT-TCATTTTCATT
*
5469123 ATTT--TTTT-ATT
1 TTTTCATTTTCATT
5469134 TTTTCA
1 TTTTCA
5469140 AGCATAGTAT
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
11 6 0.09
12 4 0.06
14 25 0.37
15 18 0.26
16 15 0.22
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTCATTTTCATT
Found at i:5469066 original size:8 final size:8
Alignment explanation
Indices: 5469036--5469139 Score: 98
Period size: 8 Copynumber: 13.8 Consensus size: 8
5469026 TTTCATTCAC
5469036 TTTTC-TT
1 TTTTCATT
5469043 TTTTCA--
1 TTTTCATT
5469049 TTTTCA-T
1 TTTTCATT
5469056 TTTTCATT
1 TTTTCATT
5469064 TTTTCATT
1 TTTTCATT
5469072 TTTTCATT
1 TTTTCATT
5469080 TTTTCA--
1 TTTTCATT
5469086 TTTTCATT
1 TTTTCATT
*
5469094 TTTT--TA
1 TTTTCATT
5469100 TTTTCATT
1 TTTTCATT
*
5469108 TTTATTATT
1 TTT-TCATT
*
5469117 TTTATTATT
1 TTT-TCATT
*
5469126 TTTTTATT
1 TTTTCATT
5469134 TTTTCA
1 TTTTCA
5469140 AGCATAGTAT
Statistics
Matches: 85, Mismatches: 4, Indels: 15
0.82 0.04 0.14
Matches are distributed among these distances:
6 17 0.20
7 11 0.13
8 41 0.48
9 16 0.19
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTCATT
Found at i:5469082 original size:37 final size:36
Alignment explanation
Indices: 5469036--5469119 Score: 118
Period size: 37 Copynumber: 2.3 Consensus size: 36
5469026 TTTCATTCAC
5469036 TTTTC-TTTTTTCATTTTCATTTTTCATT-TTTTCATT
1 TTTTCATTTTTTCATTTTCATTTTT--TTATTTTCATT
5469072 TTTTCATTTTTTCATTTTCATTTTTTTATTTTCATT
1 TTTTCATTTTTTCATTTTCATTTTTTTATTTTCATT
*
5469108 TTTATTATTTTT
1 TTT-TCATTTTT
5469120 ATTATTTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
35 2 0.05
36 16 0.36
37 26 0.59
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (36 bp):
TTTTCATTTTTTCATTTTCATTTTTTTATTTTCATT
Found at i:5469118 original size:20 final size:19
Alignment explanation
Indices: 5469041--5469137 Score: 78
Period size: 20 Copynumber: 5.2 Consensus size: 19
5469031 TTCACTTTTC
* *
5469041 TTTTTTCATTTTCATTTTT
1 TTTTTTCATTTTTATTATT
*
5469060 CATTTTTTCATTTTT-TCA--
1 --TTTTTTCATTTTTATTATT
* *
5469078 TTTTTTCATTTTCATTTTT
1 TTTTTTCATTTTTATTATT
5469097 TTATTTTCATTTTTATTATT
1 TT-TTTTCATTTTTATTATT
*
5469117 TTTATT-ATTTTT-TTATT
1 TTTTTTCATTTTTATTATT
5469134 TTTT
1 TTTT
5469138 CAAGCATAGT
Statistics
Matches: 62, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
16 12 0.19
17 9 0.15
18 6 0.10
19 5 0.08
20 18 0.29
21 12 0.19
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTTCATTTTTATTATT
Found at i:5473495 original size:20 final size:20
Alignment explanation
Indices: 5473466--5473574 Score: 62
Period size: 20 Copynumber: 5.0 Consensus size: 20
5473456 TATTTAAAGA
5473466 AAATAAAAT-AATAAAAAAT
1 AAATAAAATAAATAAAAAAT
5473485 AAATAAAAATAAATAAAAAGAAT
1 AAAT-AAAATAAAT-AAAA-AAT
*
5473508 ATTACATAAACCTAATCTAATAAATAAA-
1 A--A-AT-AA---AAT-AAATAAA-AAAT
*
5473536 AAATAAAATAAACAAAGAAAT
1 AAATAAAATAAATAAA-AAAT
5473557 AAATAAAA-AAATAAAAAA
1 AAATAAAATAAATAAAAAA
5473575 AAAAACCTGG
Statistics
Matches: 72, Mismatches: 5, Indels: 26
0.70 0.05 0.25
Matches are distributed among these distances:
19 7 0.10
20 19 0.26
21 14 0.19
22 4 0.06
23 4 0.06
24 2 0.03
25 3 0.04
26 6 0.08
28 1 0.01
29 8 0.11
30 4 0.06
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (20 bp):
AAATAAAATAAATAAAAAAT
Found at i:5473547 original size:16 final size:14
Alignment explanation
Indices: 5473526--5473579 Score: 51
Period size: 16 Copynumber: 3.8 Consensus size: 14
5473516 AACCTAATCT
5473526 AATAAATAAAAAATAA
1 AATAAA-AAAAAAT-A
5473542 AATAAACAAAGAAATA
1 AATAAA-AAA-AAATA
5473558 AAT--AAAAAAATA
1 AATAAAAAAAAATA
5473570 AA-AAAAAAAA
1 AATAAAAAAAA
5473580 CCTGGAGCGG
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
12 7 0.21
13 9 0.26
14 1 0.03
16 13 0.38
17 4 0.12
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.13
Consensus pattern (14 bp):
AATAAAAAAAAATA
Found at i:5473579 original size:12 final size:12
Alignment explanation
Indices: 5473529--5473579 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
5473519 CTAATCTAAT
*
5473529 AAATAAAAAATA
1 AAATAAAAAAAA
* *
5473541 AAATAAACAAAG
1 AAATAAAAAAAA
*
5473553 AAATAAATAAAA
1 AAATAAAAAAAA
5473565 AAATAAAAAAAA
1 AAATAAAAAAAA
5473577 AAA
1 AAA
5473580 CCTGGAGCGG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.84, C:0.02, G:0.02, T:0.12
Consensus pattern (12 bp):
AAATAAAAAAAA
Found at i:5473912 original size:19 final size:19
Alignment explanation
Indices: 5473884--5473927 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
5473874 AACACCGGTG
*
5473884 CCGGATTCTGGAAATTTCA
1 CCGGAATCTGGAAATTTCA
5473903 CCGGAATCTGGAAATTTCA
1 CCGGAATCTGGAAATTTCA
5473922 CCGGAA
1 CCGGAA
5473928 GTTGGCCGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (19 bp):
CCGGAATCTGGAAATTTCA
Found at i:5474832 original size:16 final size:15
Alignment explanation
Indices: 5474811--5474842 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
5474801 GTTTTAAGTG
5474811 TTTAATATTAATATAT
1 TTTAATATTAA-ATAT
5474827 TTTAATATTAAATAT
1 TTTAATATTAAATAT
5474842 T
1 T
5474843 ATTATTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTAATATTAAATAT
Found at i:5475235 original size:15 final size:15
Alignment explanation
Indices: 5475198--5475227 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5475188 CAAAAAATAT
5475198 AAATA-TTTTTGAAA
1 AAATATTTTTTGAAA
5475212 AAATATTTTTTGAAA
1 AAATATTTTTTGAAA
5475227 A
1 A
5475228 TTAATTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (15 bp):
AAATATTTTTTGAAA
Found at i:5476391 original size:20 final size:18
Alignment explanation
Indices: 5476361--5476417 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 18
5476351 TACATTTAAT
5476361 ATTTT-AAAAAATTAAAAA
1 ATTTTAAAAAAATT-AAAA
*
5476379 ATTTTCAAAAAAATTCAAA
1 ATTTT-AAAAAAATTAAAA
*
5476398 ATTTT-AAAAATTTAAAA
1 ATTTTAAAAAAATTAAAA
5476415 ATT
1 ATT
5476418 AAAATATCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
17 13 0.38
18 5 0.15
19 8 0.24
20 8 0.24
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (18 bp):
ATTTTAAAAAAATTAAAA
Found at i:5476443 original size:22 final size:22
Alignment explanation
Indices: 5476411--5476468 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
5476401 TTAAAAATTT
*
5476411 AAAAATTAAAATATCA-TTTTC
1 AAAAATTAAAATATCATTTTTA
*
5476432 AAAAATTCAAAATATGATTTTTA
1 AAAAATT-AAAATATCATTTTTA
5476455 AAAAATTAAAATAT
1 AAAAATTAAAATAT
5476469 TTAAAAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 7 0.21
22 15 0.45
23 11 0.33
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (22 bp):
AAAAATTAAAATATCATTTTTA
Found at i:5476483 original size:17 final size:17
Alignment explanation
Indices: 5476324--5476482 Score: 57
Period size: 17 Copynumber: 8.9 Consensus size: 17
5476314 AACTGATTTT
5476324 TATTT-AAAAATTAAAA
1 TATTTAAAAAATTAAAA
*
5476340 TA-TTAAAAAAGTACATTTAA
1 TATTTAAAAAATTA-A---AA
5476360 TATTTTAAAAAATTAAAA
1 TA-TTTAAAAAATTAAAA
*
5476378 AATTTTCAAAAAAATTCAAAA
1 TA-TTT--AAAAAATT-AAAA
*
5476399 T-TTTAAAAATTTAAAA
1 TATTTAAAAAATTAAAA
**
5476415 -A-TT--AAAA-TATCA
1 TATTTAAAAAATTAAAA
*
5476427 T-TTTCAAAAATTCAAAATA
1 TATTTAAAAAATT--AAA-A
5476446 TGATTTTTAAAAAATTAAAA
1 T-A--TTTAAAAAATTAAAA
5476466 TATTTAAAAATATTAAA
1 TATTTAAAAA-ATTAAA
5476483 TTAATATTTT
Statistics
Matches: 108, Mismatches: 11, Indels: 46
0.65 0.07 0.28
Matches are distributed among these distances:
12 3 0.03
13 5 0.05
15 8 0.07
16 14 0.13
17 16 0.15
18 14 0.13
19 6 0.06
20 14 0.13
21 8 0.07
22 10 0.09
23 10 0.09
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (17 bp):
TATTTAAAAAATTAAAA
Found at i:5476506 original size:23 final size:23
Alignment explanation
Indices: 5476456--5476507 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
5476446 TGATTTTTAA
5476456 AAAATTAAAATATTTAAAAATAT
1 AAAATTAAAATATTTAAAAATAT
* * *
5476479 TAAATTAATATTTTTCAAAAAT-T
1 AAAATTAAAATATTT-AAAAATAT
5476502 AAAATT
1 AAAATT
5476508 TCTAAAAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
AAAATTAAAATATTTAAAAATAT
Found at i:5476565 original size:25 final size:25
Alignment explanation
Indices: 5476524--5476588 Score: 87
Period size: 24 Copynumber: 2.6 Consensus size: 25
5476514 AGTTTTTTAG
* *
5476524 ATTTGATTTTTTCAAAAAAT-TAAA
1 ATTTGATTTTTTTAAAAAATAAAAA
5476548 ATTTGATTTTTTTAAAAAATAAAAA
1 ATTTGATTTTTTTAAAAAATAAAAA
*
5476573 ATATGATTTTTATTAA
1 ATTTGATTTTT-TTAA
5476589 TAATTGTACC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 19 0.53
25 13 0.36
26 4 0.11
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (25 bp):
ATTTGATTTTTTTAAAAAATAAAAA
Found at i:5478389 original size:9 final size:9
Alignment explanation
Indices: 5478375--5478420 Score: 83
Period size: 9 Copynumber: 5.1 Consensus size: 9
5478365 AATTATCCAA
5478375 AATTGAATT
1 AATTGAATT
5478384 AATTGAATT
1 AATTGAATT
5478393 AATTGAATT
1 AATTGAATT
*
5478402 AATTCAATT
1 AATTGAATT
5478411 AATTGAATT
1 AATTGAATT
5478420 A
1 A
5478421 TATTACTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (9 bp):
AATTGAATT
Found at i:5479045 original size:22 final size:22
Alignment explanation
Indices: 5479007--5479055 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
5478997 CTAATTTATT
*
5479007 AATTAATTATTCAATAATTGTA
1 AATTAATTATTCAATAATAGTA
*
5479029 AATTAATTATT-ATATAATAGTT
1 AATTAATTATTCA-ATAATAGTA
5479051 AATTA
1 AATTA
5479056 TTTAGTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (22 bp):
AATTAATTATTCAATAATAGTA
Found at i:5482349 original size:13 final size:12
Alignment explanation
Indices: 5482310--5482358 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
5482300 ATAATAATTT
5482310 AAAATATGATATA
1 AAAATAT-ATATA
*
5482323 ATAATATATCATA
1 AAAATATAT-ATA
5482336 AAAATAATATATA
1 AAAAT-ATATATA
*
5482349 AAAAGATATA
1 AAAATATATA
5482359 ATTTAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 7 0.23
13 20 0.65
14 4 0.13
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (12 bp):
AAAATATATATA
Found at i:5485004 original size:16 final size:15
Alignment explanation
Indices: 5484961--5484998 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
5484951 AATGGTTTCA
5484961 TTAAAAAA-AATTGATT
1 TTAAAAAATAA-T-ATT
5484977 TTAAAAAATAATATT
1 TTAAAAAATAATATT
5484992 TTAAAAA
1 TTAAAAA
5484999 TTTAATTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.48
16 9 0.43
17 2 0.10
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (15 bp):
TTAAAAAATAATATT
Found at i:5488937 original size:2 final size:2
Alignment explanation
Indices: 5488930--5488957 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5488920 TAAAATATTA
5488930 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
5488958 TGTTACTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5489122 original size:3 final size:3
Alignment explanation
Indices: 5489114--5489144 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5489104 TATTCCATTT
5489114 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
5489145 TATTATTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:5490849 original size:123 final size:123
Alignment explanation
Indices: 5490706--5490932 Score: 436
Period size: 123 Copynumber: 1.8 Consensus size: 123
5490696 ATATAAAAAA
5490706 AAGTTTACATGACAATTAACATATTCAAACGTAACAAAAATTAAGCTGACAGTATCAATGAATCA
1 AAGTTTACATGACAATTAACATATTCAAACGTAACAAAAATTAAGCTGACAGTATCAATGAATCA
5490771 CACTGATAAATGATATGGGATATATATATATATATATGTGTGTGTGTGTGTGTGTGTG
66 CACTGATAAATGATATGGGATATATATATATATATATGTGTGTGTGTGTGTGTGTGTG
* *
5490829 AAGTTTACATGACAATTAACATATTCAAACGTGACAAAAATTAAGTTGACAGTATCAATGAATCA
1 AAGTTTACATGACAATTAACATATTCAAACGTAACAAAAATTAAGCTGACAGTATCAATGAATCA
5490894 CACTGATAAATGATATGGGATATATATATATATATATGT
66 CACTGATAAATGATATGGGATATATATATATATATATGT
5490933 ATGTATATAT
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 102 1.00
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (123 bp):
AAGTTTACATGACAATTAACATATTCAAACGTAACAAAAATTAAGCTGACAGTATCAATGAATCA
CACTGATAAATGATATGGGATATATATATATATATATGTGTGTGTGTGTGTGTGTGTG
Found at i:5491733 original size:22 final size:22
Alignment explanation
Indices: 5491707--5491776 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 22
5491697 ATTAATTGAA
**
5491707 TAATTAATTATTATAAAATAAT
1 TAATTAAAAATTATAAAATAAT
* *
5491729 TAATTTACAATTACT-AAATAAT
1 TAATTAAAAATTA-TAAAATAAT
*
5491751 TAATTAACAAATTATAATATAAT
1 TAATTAA-AAATTATAAAATAAT
5491774 TAA
1 TAA
5491777 ACAACTAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
22 24 0.62
23 15 0.38
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (22 bp):
TAATTAAAAATTATAAAATAAT
Found at i:5493763 original size:22 final size:21
Alignment explanation
Indices: 5493738--5493800 Score: 92
Period size: 20 Copynumber: 2.9 Consensus size: 21
5493728 TATTTTTAAC
5493738 TATTTTAAGTTTTTAAAAATCA
1 TATTTTAA-TTTTTAAAAATCA
5493760 TATTTTTTAATTTTT-AAAATCA
1 TA--TTTTAATTTTTAAAAATCA
5493782 TATTTTAATTTTTAAAAAT
1 TATTTTAATTTTTAAAAAT
5493801 TTAATATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
20 11 0.29
21 5 0.13
22 11 0.29
23 5 0.13
24 6 0.16
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.56
Consensus pattern (21 bp):
TATTTTAATTTTTAAAAATCA
Found at i:5494111 original size:27 final size:26
Alignment explanation
Indices: 5494081--5494135 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 26
5494071 ATCTAGAAAA
*
5494081 TTTATA-AAAAAATTCAAATATTGAATT
1 TTTATACAAAAAATT-AAAT-TTAAATT
5494108 TTTATACTAAAAAATTAAATTTAAATT
1 TTTATAC-AAAAAATTAAATTTAAATT
5494135 T
1 T
5494136 CGTGTAAGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 13 0.52
28 4 0.16
29 8 0.32
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (26 bp):
TTTATACAAAAAATTAAATTTAAATT
Found at i:5495237 original size:14 final size:14
Alignment explanation
Indices: 5495220--5495249 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5495210 TGAAAATTAA
5495220 TTTTTAAAAAATAT
1 TTTTTAAAAAATAT
5495234 TTTTTAAAAAATAT
1 TTTTTAAAAAATAT
5495248 TT
1 TT
5495250 ACAATTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTTTAAAAAATAT
Found at i:5495431 original size:16 final size:17
Alignment explanation
Indices: 5495412--5495446 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5495402 TATTAAAGTT
*
5495412 ATTATA-TTTAACAATA
1 ATTATATTTTAAAAATA
5495428 ATTATATTTTAAAAATA
1 ATTATATTTTAAAAATA
5495445 AT
1 AT
5495447 GATTCACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTATATTTTAAAAATA
Found at i:5497598 original size:14 final size:14
Alignment explanation
Indices: 5497579--5497605 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5497569 ACAATAAAAA
5497579 TTATTATAATTATT
1 TTATTATAATTATT
5497593 TTATTATAATTAT
1 TTATTATAATTAT
5497606 CAAAATAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTATTATAATTATT
Found at i:5497694 original size:60 final size:60
Alignment explanation
Indices: 5497575--5497743 Score: 177
Period size: 60 Copynumber: 2.8 Consensus size: 60
5497565 ATAAACAATA
* * *
5497575 AAAATTATTATAATTATT-T-T-ATTATAATTATCAAAATAATT-TTTTATTATAGTTAATT
1 AAAATTATTATAA-TATTCTCTCATTATAATTATAAAAAT-ATTCTCTTATCATAGTTAATT
* * *
5497633 AAAATTTTTATAATATTCTCTCGTTATAATTATAAAAATATTCTCTTATCATCA-TTTATT
1 AAAATTATTATAATATTCTCTCATTATAATTATAAAAATATTCTCTTATCAT-AGTTAATT
* * * *
5497693 AAAATTATTATAATATTTTTTTATTATAATTACAAAAATATTTCTCTTATC
1 AAAATTATTATAATATTCTCTCATTATAATTATAAAAATA-TTCTCTTATC
5497744 TTATTAAAAT
Statistics
Matches: 93, Mismatches: 12, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
57 4 0.04
58 13 0.14
59 4 0.04
60 61 0.66
61 11 0.12
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.51
Consensus pattern (60 bp):
AAAATTATTATAATATTCTCTCATTATAATTATAAAAATATTCTCTTATCATAGTTAATT
Found at i:5504578 original size:16 final size:16
Alignment explanation
Indices: 5504541--5504592 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
5504531 TTTATATTTG
5504541 ATTTATTTAGTTATATT
1 ATTTATTT-GTTATATT
*
5504558 TTTTATTTGTTA-ATT
1 ATTTATTTGTTATATT
5504573 AATTTATTTGATTAT-TT
1 -ATTTATTTG-TTATATT
5504590 ATT
1 ATT
5504593 AAATTTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
15 3 0.10
16 15 0.50
17 12 0.40
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (16 bp):
ATTTATTTGTTATATT
Found at i:5504991 original size:19 final size:20
Alignment explanation
Indices: 5504969--5505006 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
5504959 ATATAAAAAT
*
5504969 AAAAAATACTAT-ATATTTA
1 AAAAAATAATATAATATTTA
*
5504988 AAAATATAATATAATATTT
1 AAAAAATAATATAATATTT
5505007 TATTTTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAAATAATATAATATTTA
Found at i:5506482 original size:9 final size:10
Alignment explanation
Indices: 5506459--5506484 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5506449 GAGTGTATAC
5506459 AAAAAATAAT
1 AAAAAATAAT
5506469 AAAAAATAAT
1 AAAAAATAAT
5506479 AAAAAA
1 AAAAAA
5506485 AAGTGTCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAATAAT
Found at i:5507533 original size:16 final size:16
Alignment explanation
Indices: 5507497--5507547 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
5507487 TTTATATTTG
5507497 ATTTATTTAGTTATATT
1 ATTTATTT-GTTATATT
5507514 -TTTATTTGTTA-ATT
1 ATTTATTTGTTATATT
5507528 AATTTATTTGATTAT-TT
1 -ATTTATTTG-TTATATT
5507545 ATT
1 ATT
5507548 AAATTTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
14 3 0.10
15 4 0.13
16 18 0.60
17 5 0.17
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (16 bp):
ATTTATTTGTTATATT
Found at i:5507946 original size:19 final size:20
Alignment explanation
Indices: 5507924--5507961 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
5507914 ATATAAAAAT
*
5507924 AAAAAATACTAT-ATATTTA
1 AAAAAATAATATAATATTTA
*
5507943 AAAATATAATATAATATTT
1 AAAAAATAATATAATATTT
5507962 TATTTTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAAATAATATAATATTTA
Found at i:5508162 original size:19 final size:21
Alignment explanation
Indices: 5508114--5508162 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 21
5508104 AAGTTCAAGT
5508114 TTAATTATGTTTTATTTGATTG
1 TTAATTATGTTTTATTT-ATTG
5508136 TCTAATTATGTTTTA-TT-TTG
1 T-TAATTATGTTTTATTTATTG
5508156 TTAATTA
1 TTAATTA
5508163 ATTATTCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 6 0.23
20 4 0.15
22 3 0.12
23 13 0.50
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.63
Consensus pattern (21 bp):
TTAATTATGTTTTATTTATTG
Found at i:5509438 original size:9 final size:10
Alignment explanation
Indices: 5509415--5509440 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5509405 AGTGTATCCC
5509415 AAAAAATAAT
1 AAAAAATAAT
5509425 AAAAAATAAT
1 AAAAAATAAT
5509435 AAAAAA
1 AAAAAA
5509441 AGTGTCTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAATAAT
Found at i:5512562 original size:18 final size:20
Alignment explanation
Indices: 5512526--5512563 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
5512516 ATATATAATT
5512526 TATATTATTAATAATATCTA
1 TATATTATTAATAATATCTA
*
5512546 TATATT-TTTATAA-ATCTA
1 TATATTATTAATAATATCTA
5512564 ATGATACTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 6 0.35
20 6 0.35
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (20 bp):
TATATTATTAATAATATCTA
Found at i:5514298 original size:2 final size:2
Alignment explanation
Indices: 5514293--5514329 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5514283 TGTGTGTGTG
5514293 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5514330 TGTGCAGTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5516510 original size:15 final size:16
Alignment explanation
Indices: 5516490--5516519 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5516480 ATTTATAATT
5516490 ATAAAAAA-TTCAAAA
1 ATAAAAAATTTCAAAA
5516505 ATAAAAAATTTCAAA
1 ATAAAAAATTTCAAA
5516520 TATTCAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (16 bp):
ATAAAAAATTTCAAAA
Found at i:5517092 original size:21 final size:21
Alignment explanation
Indices: 5517053--5517093 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5517043 AGGAAATAGA
* *
5517053 ACTTTGACAGATTAAGATTAC
1 ACTTTAACAGATCAAGATTAC
*
5517074 ACTTTAACAGATCATGATTA
1 ACTTTAACAGATCAAGATTA
5517094 TCATGATCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (21 bp):
ACTTTAACAGATCAAGATTAC
Found at i:5519318 original size:20 final size:21
Alignment explanation
Indices: 5519286--5519333 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 21
5519276 TCCGAAATTA
5519286 ATAAAATATTATTATTTTTAAAT
1 ATAAAATATTA-T-TTTTTAAAT
5519309 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTTAAAT
5519330 ATAA
1 ATAA
5519334 GTATTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 13 0.52
22 1 0.04
23 11 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAAATATTATTTTTTAAAT
Found at i:5520437 original size:83 final size:83
Alignment explanation
Indices: 5520345--5520515 Score: 326
Period size: 83 Copynumber: 2.1 Consensus size: 83
5520335 TTTTTCAAAA
5520345 ATTAA-TTTTTATATATTTATTTTTTAAAATTAATAAAAATTTATATTTAATCATTAATAAAATT
1 ATTAATTTTTTATATATTTATTTTTTAAAATTAATAAAAATTTATATTTAATCATTAATAAAATT
5520409 ACATCATTCAATTCATTT
66 ACATCATTCAATTCATTT
5520427 ATTAATTTTTTATATATTTATTTTTTAAAATTAATAAAAATTTATATTTAATCATTAATAAAATT
1 ATTAATTTTTTATATATTTATTTTTTAAAATTAATAAAAATTTATATTTAATCATTAATAAAATT
5520492 ACATCATTCAATTCATTT
66 ACATCATTCAATTCATTT
*
5520510 AATAAT
1 ATTAAT
5520516 ATACAAACTT
Statistics
Matches: 87, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
82 5 0.06
83 82 0.94
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (83 bp):
ATTAATTTTTTATATATTTATTTTTTAAAATTAATAAAAATTTATATTTAATCATTAATAAAATT
ACATCATTCAATTCATTT
Found at i:5524858 original size:19 final size:19
Alignment explanation
Indices: 5524819--5524855 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5524809 CAAAGCCAAA
*
5524819 ATTCTTTTATATTATTTTT
1 ATTCTCTTATATTATTTTT
5524838 ATTCTCTTAT-TTATTTTT
1 ATTCTCTTATATTATTTTT
5524856 TATAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (19 bp):
ATTCTCTTATATTATTTTT
Found at i:5525012 original size:24 final size:24
Alignment explanation
Indices: 5524963--5525006 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5524953 GCTTAACGTG
5524963 TCAAAAGATTAAAGTTTTCATAGA
1 TCAAAAGATTAAAGTTTTCATAGA
*
5524987 TCAAAATATT-AA-TTTTCATA
1 TCAAAAGATTAAAGTTTTCATA
5525007 AAGATCTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 2 0.11
24 9 0.47
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (24 bp):
TCAAAAGATTAAAGTTTTCATAGA
Found at i:5530020 original size:11 final size:11
Alignment explanation
Indices: 5530004--5530028 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5529994 AATTTTTTTG
5530004 TTTGGAAATTT
1 TTTGGAAATTT
5530015 TTTGGAAATTT
1 TTTGGAAATTT
5530026 TTT
1 TTT
5530029 AGATTCCGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (11 bp):
TTTGGAAATTT
Found at i:5530989 original size:191 final size:191
Alignment explanation
Indices: 5530649--5530996 Score: 422
Period size: 191 Copynumber: 1.8 Consensus size: 191
5530639 ATTATCCAAT
* * *
5530649 GATAAAATTTTTAGAAATTTTAAATGGTAAATTTTTATAAAATTCTTAGGTGAAAAATTTTATCT
1 GATAAAATTCTTAGAAATTTCAAATGGTAAATTTCTATAAAATTCTTAGGTGAAAAATTTTATCT
* * * * *
5530714 GAATTTATCCCAAATTGTGGAATAATTTAGATAAAGTTTCAATAACAATAATTAATATTTATTTT
66 AAATTTATCCCAAATGGTGGAAAAATTTAAATAAAGTTTCAATAAAAATAATTAATATTTATTTT
*
5530779 CAAACAAAAAAATAAAAAAATAAAAAATTTTTGGTTGAAAATATTTGATAAATTACCAAAG
131 CAAACAAAAAAACAAAAAAATAAAAAATTTTTGGTTGAAAATATTTGATAAATTACCAAAG
* * *
5530840 GATAAGATTCTTAGAAATTTCAAATGTTAAATTTCTA-AGAAA-TCTTTAGGTGAGAAATTTCT-
1 GATAAAATTCTTAGAAATTTCAAATGGTAAATTTCTATA-AAATTC-TTAGGTGAAAAATTT-TA
* *
5530902 T-TAAATTTGTCCCAAATGGTGGAAAAATTTAAATGAAA-TTTCAATAAAAAATAATT-TTCATA
63 TCTAAATTTATCCCAAATGGTGGAAAAATTTAAAT-AAAGTTTCAAT-AAAAATAATTAAT-AT-
*** *
5530964 TTATTTTCTTTC-CAAAAACAAAAAAATAAAAAA
124 TTATTTTCAAACAAAAAAACAAAAAAATAAAAAA
5530997 AGAGAGAATT
Statistics
Matches: 132, Mismatches: 18, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
190 39 0.30
191 83 0.63
192 10 0.08
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (191 bp):
GATAAAATTCTTAGAAATTTCAAATGGTAAATTTCTATAAAATTCTTAGGTGAAAAATTTTATCT
AAATTTATCCCAAATGGTGGAAAAATTTAAATAAAGTTTCAATAAAAATAATTAATATTTATTTT
CAAACAAAAAAACAAAAAAATAAAAAATTTTTGGTTGAAAATATTTGATAAATTACCAAAG
Found at i:5534978 original size:21 final size:22
Alignment explanation
Indices: 5534927--5534968 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
5534917 AAAAAATAAA
5534927 AAAGAGAAAAATGACAAAAGAG
1 AAAGAGAAAAATGACAAAAGAG
5534949 AAAGAGAAAATATGA-AAAAG
1 AAAGAGAAAA-ATGACAAAAG
5534969 TTAAAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.69, C:0.02, G:0.21, T:0.07
Consensus pattern (22 bp):
AAAGAGAAAAATGACAAAAGAG
Found at i:5534993 original size:10 final size:10
Alignment explanation
Indices: 5534971--5535004 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
5534961 TGAAAAAGTT
*
5534971 AAAAGAAAG-
1 AAAAAAAAGA
5534980 AAAAAAAAGA
1 AAAAAAAAGA
5534990 AAAAAAAAGA
1 AAAAAAAAGA
5535000 AAAAA
1 AAAAA
5535005 GATGAAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:5535012 original size:10 final size:9
Alignment explanation
Indices: 5534971--5535004 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
5534961 TGAAAAAGTT
*
5534971 AAAAGAAAG
1 AAAAAAAAG
5534980 AAAAAAAAG
1 AAAAAAAAG
5534989 AAAAAAAAAG
1 -AAAAAAAAG
5534999 AAAAAA
1 AAAAAA
5535005 GATGAAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:5536223 original size:24 final size:24
Alignment explanation
Indices: 5536184--5536241 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
5536174 TTTTTAGTCT
* *
5536184 TAAATGAGAATTTTTAAGAAATCC
1 TAAATAAGAATCTTTAAGAAATCC
*
5536208 TCAATAAGAATCTTTAAGAAATCC
1 TAAATAAGAATCTTTAAGAAATCC
*
5536232 TAAATGAGAA
1 TAAATAAGAA
5536242 CTGAGTCTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.29
Consensus pattern (24 bp):
TAAATAAGAATCTTTAAGAAATCC
Found at i:5536879 original size:43 final size:44
Alignment explanation
Indices: 5536832--5536920 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
5536822 TCCTTAAAAA
* *
5536832 AGCTTCATTTATTTTTTCAAAG-CATTGAGCCTCTGTTTAGAGG
1 AGCTTCATTTACTTTTTCAAAGTCATGGAGCCTCTGTTTAGAGG
** * *
5536875 AGCTTTGTTTACTTTTTCAAAGTCGTGGAGCTTCTGTTTAGAGG
1 AGCTTCATTTACTTTTTCAAAGTCATGGAGCCTCTGTTTAGAGG
5536919 AG
1 AG
5536921 TTTTATGTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
43 19 0.49
44 20 0.51
ACGTcount: A:0.21, C:0.15, G:0.22, T:0.42
Consensus pattern (44 bp):
AGCTTCATTTACTTTTTCAAAGTCATGGAGCCTCTGTTTAGAGG
Found at i:5543119 original size:21 final size:22
Alignment explanation
Indices: 5543059--5543184 Score: 116
Period size: 22 Copynumber: 5.8 Consensus size: 22
5543049 ATGATTAATA
*
5543059 ATTAAATTA-TAAGTTATTTACT
1 ATTAAATTATTAA-TGATTTACT
* *
5543081 ATTAATTTATTTATGATTTACT
1 ATTAAATTATTAATGATTTACT
*
5543103 ATTAAATT-GTAATGATTTACT
1 ATTAAATTATTAATGATTTACT
5543124 ATTAAATTATTAATGATTTA-T
1 ATTAAATTATTAATGATTTACT
* * * * *
5543145 TTCTAATTTATAAATGA-TTGCC
1 AT-TAAATTATTAATGATTTACT
*
5543167 ATTAAATTATGAATGATT
1 ATTAAATTATTAATGATT
5543185 CATCATTACG
Statistics
Matches: 84, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
21 35 0.42
22 47 0.56
23 2 0.02
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (22 bp):
ATTAAATTATTAATGATTTACT
Found at i:5543134 original size:43 final size:44
Alignment explanation
Indices: 5543059--5543184 Score: 132
Period size: 43 Copynumber: 2.9 Consensus size: 44
5543049 ATGATTAATA
* * *
5543059 ATTAAATTATAAGTTATTTACTATTAATTTATTTATGATTTACT
1 ATTAAATTATAAGTGATTTACTATTAAATTATTAATGATTTACT
*
5543103 ATTAAATTGTAA-TGATTTACTATTAAATTATTAATGATTTA-T
1 ATTAAATTATAAGTGATTTACTATTAAATTATTAATGATTTACT
* * * * * *
5543145 TTCTAATTTATAAATGA-TTGCCATTAAATTATGAATGATT
1 AT-TAAATTATAAGTGATTTACTATTAAATTATTAATGATT
5543185 CATCATTACG
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
42 2 0.03
43 54 0.77
44 14 0.20
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (44 bp):
ATTAAATTATAAGTGATTTACTATTAAATTATTAATGATTTACT
Found at i:5543419 original size:40 final size:42
Alignment explanation
Indices: 5543320--5543427 Score: 105
Period size: 40 Copynumber: 2.5 Consensus size: 42
5543310 GATTAACTAT
* * *
5543320 TTTACTTTTAAATTATCACTGATTTATAATTAAATTATTTATAC
1 TTTAC-TTTAAATTATTAATGA-TTATAATTAAATTAGTTATAC
* * *
5543364 TTTACTATTATATTATTAGTGATTATTATTAAATT-GTTA-A-
1 TTTACT-TTAAATTATTAATGATTATAATTAAATTAGTTATAC
5543404 TTTACTTCTAAATTATTAATGATT
1 TTTACTT-TAAATTATTAATGATT
5543428 TACTATTATA
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
39 1 0.02
40 20 0.36
41 1 0.02
42 3 0.05
43 13 0.24
44 17 0.31
ACGTcount: A:0.35, C:0.06, G:0.05, T:0.54
Consensus pattern (42 bp):
TTTACTTTAAATTATTAATGATTATAATTAAATTAGTTATAC
Found at i:5543596 original size:22 final size:21
Alignment explanation
Indices: 5543522--5543597 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 21
5543512 TATCACTAAA
* *
5543522 TTATCAATGATTCATTATAAAG
1 TTATC-ATGATTTATTATTAAG
* *
5543544 TTATTACTAATTTA-TATTAA-
1 TTATCA-TGATTTATTATTAAG
5543564 TTATACATGATTTATTATTAAG
1 TTAT-CATGATTTATTATTAAG
5543586 TTATCATTGATT
1 TTATCA-TGATT
5543598 AAACTATTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
20 10 0.23
21 15 0.35
22 18 0.42
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (21 bp):
TTATCATGATTTATTATTAAG
Found at i:5543689 original size:19 final size:19
Alignment explanation
Indices: 5543667--5543735 Score: 50
Period size: 19 Copynumber: 3.3 Consensus size: 19
5543657 AGAATTAACC
5543667 ACTAAATTATCAATTTTTT
1 ACTAAATTATCAATTTTTT
*
5543686 ACTACTAATTTATC-ATTAATATACT
1 ACTA--AA-TTATCAATT--T-T-TT
*
5543711 ACTAAATTATCAATTATTT
1 ACTAAATTATCAATTTTTT
5543730 ACTAAA
1 ACTAAA
5543736 ATTTATCATT
Statistics
Matches: 39, Mismatches: 3, Indels: 16
0.67 0.05 0.28
Matches are distributed among these distances:
19 11 0.28
20 1 0.03
21 5 0.13
22 10 0.26
23 6 0.15
24 1 0.03
25 5 0.13
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (19 bp):
ACTAAATTATCAATTTTTT
Found at i:5543692 original size:22 final size:22
Alignment explanation
Indices: 5543667--5543762 Score: 94
Period size: 22 Copynumber: 4.5 Consensus size: 22
5543657 AGAATTAACC
*
5543667 ACTAAATTATCAATTTTTTACT
1 ACTAAATTATCAATTATTTACT
* *
5543689 ACTAATTTATC-ATTAATATACT
1 ACTAAATTATCAATT-ATTTACT
5543711 ACTAAATTATCAATTATTTACT
1 ACTAAATTATCAATTATTTACT
5543733 A--AAATTTATC-ATTAATTT-CT
1 ACTAAA-TTATCAATT-ATTTACT
*
5543753 ACAAAATTAT
1 ACTAAATTAT
5543763 TTATGATTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
20 9 0.14
21 16 0.25
22 35 0.56
23 3 0.05
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (22 bp):
ACTAAATTATCAATTATTTACT
Found at i:5543715 original size:44 final size:42
Alignment explanation
Indices: 5543667--5543762 Score: 138
Period size: 44 Copynumber: 2.2 Consensus size: 42
5543657 AGAATTAACC
* *
5543667 ACTAAATTATCAATTTTTTACTACTAATTTATCATTAATATACT
1 ACTAAATTATCAATTATTTACTA-AAATTTATCATTAAT-TACT
*
5543711 ACTAAATTATCAATTATTTACTAAAATTTATCATTAATTTCT
1 ACTAAATTATCAATTATTTACTAAAATTTATCATTAATTACT
*
5543753 ACAAAATTAT
1 ACTAAATTAT
5543763 TTATGATTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 12 0.25
43 14 0.29
44 22 0.46
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (42 bp):
ACTAAATTATCAATTATTTACTAAAATTTATCATTAATTACT
Found at i:5543762 original size:21 final size:21
Alignment explanation
Indices: 5543695--5543762 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
5543685 TACTACTAAT
* *
5543695 TTATCATTAATATACTACTAAA
1 TTATCATTAAT-TTCTACAAAA
*
5543717 TTATCAATT-ATTTACTA-AAAT
1 TTATC-ATTAATTT-CTACAAAA
5543738 TTATCATTAATTTCTACAAAA
1 TTATCATTAATTTCTACAAAA
5543759 TTAT
1 TTAT
5543763 TTATGATTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
20 6 0.16
21 19 0.50
22 10 0.26
23 3 0.08
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.46
Consensus pattern (21 bp):
TTATCATTAATTTCTACAAAA
Found at i:5543813 original size:22 final size:22
Alignment explanation
Indices: 5543787--5543840 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
5543777 TCTCAATTAA
5543787 TTACTATTAAACTAAAACTAAT
1 TTACTATTAAACTAAAACTAAT
* ***
5543809 TTACTATTAAATTTTTACTAAT
1 TTACTATTAAACTAAAACTAAT
5543831 TTACTATTAA
1 TTACTATTAA
5543841 GTAGTCAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (22 bp):
TTACTATTAAACTAAAACTAAT
Found at i:5544081 original size:14 final size:14
Alignment explanation
Indices: 5544039--5544083 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
5544029 TTTAAAAAAA
5544039 TTATACATAATTTT
1 TTATACATAATTTT
5544053 TTA-A-A-AATTTCTT
1 TTATACATAA-TT-TT
5544066 TTATACATAATTTT
1 TTATACATAATTTT
5544080 TTAT
1 TTAT
5544084 TATATAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
11 2 0.08
12 3 0.12
13 6 0.23
14 10 0.38
15 3 0.12
16 2 0.08
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.58
Consensus pattern (14 bp):
TTATACATAATTTT
Found at i:5545146 original size:22 final size:22
Alignment explanation
Indices: 5545096--5545161 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
5545086 CTAATAACAA
*
5545096 AAAAAATT-TTAATTAA-ATTTAT
1 AAAAAATTACTAA-TAATATTT-T
5545118 AAAAAATTACTAATAATATTTT
1 AAAAAATTACTAATAATATTTT
* * **
5545140 AATAAATTGCTTTTAATATTTT
1 AAAAAATTACTAATAATATTTT
5545162 TAGAATTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 30 0.81
23 7 0.19
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (22 bp):
AAAAAATTACTAATAATATTTT
Found at i:5545236 original size:17 final size:18
Alignment explanation
Indices: 5545214--5545249 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
5545204 TAATTTTTTT
*
5545214 AGTCTAATTA-TAAAAAA
1 AGTCTAATAATTAAAAAA
5545231 AGTCTAATAATTAAAAAA
1 AGTCTAATAATTAAAAAA
5545249 A
1 A
5545250 TTATTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.28
Consensus pattern (18 bp):
AGTCTAATAATTAAAAAA
Found at i:5546970 original size:34 final size:34
Alignment explanation
Indices: 5546926--5546994 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
5546916 TATTAGAGGC
5546926 TTTTCTTTCTACTTGTTTCATTGTAATTTGCTTT
1 TTTTCTTTCTACTTGTTTCATTGTAATTTGCTTT
* *
5546960 TTTTTTTTCTACTTGTTTCATTGTAATTTTCTTT
1 TTTTCTTTCTACTTGTTTCATTGTAATTTGCTTT
5546994 T
1 T
5546995 CTGGTTTCGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.12, C:0.13, G:0.07, T:0.68
Consensus pattern (34 bp):
TTTTCTTTCTACTTGTTTCATTGTAATTTGCTTT
Found at i:5547112 original size:11 final size:10
Alignment explanation
Indices: 5547086--5547124 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
5547076 CTCACAACTT
*
5547086 AGAAAATAAA
1 AGAAAAAAAA
*
5547096 AGAAAAAACA
1 AGAAAAAAAA
5547106 AGAAAAAAAAA
1 AG-AAAAAAAA
5547117 AGAAAAAA
1 AGAAAAAA
5547125 GATGGAGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.85, C:0.03, G:0.10, T:0.03
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:5556246 original size:16 final size:16
Alignment explanation
Indices: 5556225--5556257 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5556215 ATAAAACATG
*
5556225 TGGTGATAACATTAAT
1 TGGTGAAAACATTAAT
5556241 TGGTGAAAACATTAAT
1 TGGTGAAAACATTAAT
5556257 T
1 T
5556258 AGTGGAGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.36
Consensus pattern (16 bp):
TGGTGAAAACATTAAT
Found at i:5559544 original size:2 final size:2
Alignment explanation
Indices: 5559537--5559569 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
5559527 CTTGGTAATG
5559537 TA TA TA TA TA TA TA TA TA TA T- TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5559570 TCTGGCTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:5562573 original size:11 final size:11
Alignment explanation
Indices: 5562559--5562585 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5562549 TAAAACTTTA
5562559 AAAAAAATAAT
1 AAAAAAATAAT
5562570 AAAAAAATAAT
1 AAAAAAATAAT
5562581 AAAAA
1 AAAAA
5562586 TACAATTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAAATAAT
Found at i:5568645 original size:2 final size:2
Alignment explanation
Indices: 5568638--5568664 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5568628 GCTAAGGATT
5568638 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5568665 TATGCGCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5571611 original size:3 final size:3
Alignment explanation
Indices: 5571603--5571631 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5571593 ATGTAGAAAG
5571603 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5571632 AAATTATGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5572600 original size:14 final size:14
Alignment explanation
Indices: 5572583--5572641 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
5572573 AGACACTAAA
5572583 AGCTTTATGTTTAT
1 AGCTTTATGTTTAT
*
5572597 AGCTTCA-GATTGTACT
1 AGCTTTATG-TT-TA-T
*
5572613 CG-TTTATGTTTAT
1 AGCTTTATGTTTAT
*
5572626 AGCTTTATCTTTAT
1 AGCTTTATGTTTAT
5572640 AG
1 AG
5572642 ATCATTGCAC
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
13 3 0.09
14 22 0.63
15 7 0.20
16 3 0.09
ACGTcount: A:0.22, C:0.12, G:0.15, T:0.51
Consensus pattern (14 bp):
AGCTTTATGTTTAT
Found at i:5574185 original size:14 final size:13
Alignment explanation
Indices: 5574162--5574208 Score: 60
Period size: 14 Copynumber: 3.6 Consensus size: 13
5574152 TAATAAGAGT
*
5574162 AAATAAAAATA-A
1 AAATAAAAAAATA
5574174 AAATAAAAAAATA
1 AAATAAAAAAATA
*
5574187 ACATAAATAAAATA
1 AAATAAA-AAAATA
5574201 AAATAAAA
1 AAATAAAA
5574209 GTCAAAACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
12 10 0.33
13 8 0.27
14 12 0.40
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (13 bp):
AAATAAAAAAATA
Found at i:5575136 original size:28 final size:28
Alignment explanation
Indices: 5575103--5575207 Score: 151
Period size: 28 Copynumber: 3.8 Consensus size: 28
5575093 TGATGAATAA
5575103 TTAGATGTGTGTTAGTGGTTTATGAAAG
1 TTAGATGTGTGTTAGTGGTTTATGAAAG
* *
5575131 TTAGATGTTTGTTAGTGGTTTATGGAAG
1 TTAGATGTGTGTTAGTGGTTTATGAAAG
*
5575159 TTAGATGTTTGTTAGTGGTTTATAGAAA-
1 TTAGATGTGTGTTAGTGGTTTAT-GAAAG
5575187 TTA-ATTGTGTGTTAGTGGTTT
1 TTAGA-TGTGTGTTAGTGGTTT
5575208 TCATTTACGG
Statistics
Matches: 71, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
27 1 0.01
28 67 0.94
29 3 0.04
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.48
Consensus pattern (28 bp):
TTAGATGTGTGTTAGTGGTTTATGAAAG
Found at i:5579495 original size:28 final size:28
Alignment explanation
Indices: 5579463--5579560 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
5579453 TGATGAACAA
*
5579463 TTAGATGTGTGTTAATGGTTTATGGAAG
1 TTAGATGTGTGTTAATGGTTTATGAAAG
* *
5579491 TTAGATGTTTGTTAGTGGTTTATGAAAG
1 TTAGATGTGTGTTAATGGTTTATGAAAG
* *
5579519 TTAGATGTGCGTTACTGGTTTATGAAAG
1 TTAGATGTGTGTTAATGGTTTATGAAAG
5579547 TTA-ATTGTGTGTTA
1 TTAGA-TGTGTGTTA
5579561 GTGATTTTCG
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
27 1 0.02
28 61 0.98
ACGTcount: A:0.24, C:0.02, G:0.29, T:0.45
Consensus pattern (28 bp):
TTAGATGTGTGTTAATGGTTTATGAAAG
Found at i:5581580 original size:14 final size:14
Alignment explanation
Indices: 5581563--5581621 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
5581553 AGACATTAAA
5581563 AGCTTTATGTTTAT
1 AGCTTTATGTTTAT
* *
5581577 AGCTTCA-GATTAT
1 AGCTTTATGTTTAT
*
5581590 ATTCGTTTATGTTTAT
1 A-GC-TTTATGTTTAT
5581606 AGCTTTATGTTTAT
1 AGCTTTATGTTTAT
5581620 AG
1 AG
5581622 ATCACTGCAC
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
13 6 0.17
14 20 0.56
15 4 0.11
16 6 0.17
ACGTcount: A:0.24, C:0.08, G:0.15, T:0.53
Consensus pattern (14 bp):
AGCTTTATGTTTAT
Found at i:5595884 original size:21 final size:21
Alignment explanation
Indices: 5595807--5595884 Score: 75
Period size: 24 Copynumber: 3.4 Consensus size: 21
5595797 TCTGCAGCCG
* *
5595807 TGGCGACAAAAGAGCCAACGA
1 TGGCTACAAAAGAGCTAACGA
5595828 TGGCGGCTACAAAAGAGCTAACGA
1 T---GGCTACAAAAGAGCTAACGA
5595852 TGGTGGCTACAAAAGAGCTAACGA
1 ---TGGCTACAAAAGAGCTAACGA
*
5595876 TGGCAACAA
1 TGGCTACAA
5595885 CAAATTGCAT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
21 9 0.19
24 38 0.79
27 1 0.02
ACGTcount: A:0.40, C:0.21, G:0.28, T:0.12
Consensus pattern (21 bp):
TGGCTACAAAAGAGCTAACGA
Found at i:5595888 original size:24 final size:24
Alignment explanation
Indices: 5595812--5595879 Score: 118
Period size: 24 Copynumber: 2.8 Consensus size: 24
5595802 AGCCGTGGCG
*
5595812 ACAAAAGAGCCAACGATGGCGGCT
1 ACAAAAGAGCTAACGATGGCGGCT
*
5595836 ACAAAAGAGCTAACGATGGTGGCT
1 ACAAAAGAGCTAACGATGGCGGCT
5595860 ACAAAAGAGCTAACGATGGC
1 ACAAAAGAGCTAACGATGGC
5595880 AACAACAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.40, C:0.21, G:0.28, T:0.12
Consensus pattern (24 bp):
ACAAAAGAGCTAACGATGGCGGCT
Found at i:5595937 original size:9 final size:8
Alignment explanation
Indices: 5595896--5595934 Score: 78
Period size: 8 Copynumber: 4.9 Consensus size: 8
5595886 AAATTGCATT
5595896 TTTTTTTC
1 TTTTTTTC
5595904 TTTTTTTC
1 TTTTTTTC
5595912 TTTTTTTC
1 TTTTTTTC
5595920 TTTTTTTC
1 TTTTTTTC
5595928 TTTTTTT
1 TTTTTTT
5595935 TCTAAGTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTTC
Found at i:5609731 original size:267 final size:267
Alignment explanation
Indices: 5609256--5609795 Score: 1008
Period size: 267 Copynumber: 2.0 Consensus size: 267
5609246 CTTTCCTATA
5609256 AATCATCTCAGTCTTTCTCAAGGATTCACAGTGGCATTTGGGGACTGTCAAGAGTTAACATTATC
1 AATCATCTCAGTCTTTCTCAAGGATTCACAGTGGCATTTGGGGACTGTCAAGAGTTAACATTATC
5609321 ACAAGTTCTAGGTGGTTTGTTACATTCGTCGATGATCATACTCAACTTACTTGATATTCCTTATG
66 ACAAGTTCTAGGTGGTTTGTTACATTCGTCGATGATCATACTCAACTTACTTGATATTCCTTATG
*
5609386 AAAGAAAAATCTGAGGTTGGCCAAATCTTTCAAAACTTCAATAACATACTACAAACCCAATTCCA
131 AAAGAAAAATCCGAGGTTGGCCAAATCTTTCAAAACTTCAATAACATACTACAAACCCAATTCCA
* *
5609451 AGCCAAAATCAAGTCTTAAAAACTGACAATGGGAGGGAATATTTCAAATCTATTCTCGGTCCTTA
196 AGCCAAAATCAAGTCTTAAAAACTGACAATGGAAGGGAATACTTCAAATCTATTCTCGGTCCTTA
5609516 CCTCACC
261 CCTCACC
* * *
5609523 AATCATCTCAGTCTTTCTCAAGGATTCACATTGGCATTTGGGTACTGTTAAGAGTTAACATTATC
1 AATCATCTCAGTCTTTCTCAAGGATTCACAGTGGCATTTGGGGACTGTCAAGAGTTAACATTATC
* *
5609588 ACAAGTTTTAGGTGGTTTGTTACATTCGTCGATGATCATACTCAACTTACTTGGTATTCCTTATG
66 ACAAGTTCTAGGTGGTTTGTTACATTCGTCGATGATCATACTCAACTTACTTGATATTCCTTATG
5609653 AAAGAAAAATCCGAGGTTGGCCAAATCTTTCAAAACTTCAATAACATACTACAAACCCAATTCCA
131 AAAGAAAAATCCGAGGTTGGCCAAATCTTTCAAAACTTCAATAACATACTACAAACCCAATTCCA
5609718 AGCCAAAATCAAGTCTTAAAAACTGACAATGGAAGGGAATACTTCAAATCTATTCTCGGTCCTTA
196 AGCCAAAATCAAGTCTTAAAAACTGACAATGGAAGGGAATACTTCAAATCTATTCTCGGTCCTTA
5609783 CCTCACC
261 CCTCACC
5609790 AATCAT
1 AATCAT
5609796 GGCTTTATCC
Statistics
Matches: 265, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
267 265 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (267 bp):
AATCATCTCAGTCTTTCTCAAGGATTCACAGTGGCATTTGGGGACTGTCAAGAGTTAACATTATC
ACAAGTTCTAGGTGGTTTGTTACATTCGTCGATGATCATACTCAACTTACTTGATATTCCTTATG
AAAGAAAAATCCGAGGTTGGCCAAATCTTTCAAAACTTCAATAACATACTACAAACCCAATTCCA
AGCCAAAATCAAGTCTTAAAAACTGACAATGGAAGGGAATACTTCAAATCTATTCTCGGTCCTTA
CCTCACC
Found at i:5616969 original size:28 final size:28
Alignment explanation
Indices: 5616929--5616982 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
5616919 GTTCCTGTCA
*
5616929 TATTACTTGATAGTAATGGAGGACAAAC
1 TATTACTTGATAGTAATAGAGGACAAAC
*
5616957 TATTACTTGATAGTGATAGAGGACAA
1 TATTACTTGATAGTAATAGAGGACAA
5616983 GTTTGTGGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (28 bp):
TATTACTTGATAGTAATAGAGGACAAAC
Found at i:5617648 original size:13 final size:13
Alignment explanation
Indices: 5617632--5617657 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5617622 ACCATGATAG
5617632 ATTAATGTGATCT
1 ATTAATGTGATCT
5617645 ATTAATGTGATCT
1 ATTAATGTGATCT
5617658 CAATGGTAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
ATTAATGTGATCT
Found at i:5619600 original size:25 final size:25
Alignment explanation
Indices: 5619572--5619631 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 25
5619562 TGGCAATTGT
*
5619572 TTTATATTTTAGTTTTT-TTATTTAA
1 TTTATATTTTACTTTTTCTT-TTTAA
*
5619597 TTTAT-TTTTTCTTTTTCTTTTTAA
1 TTTATATTTTACTTTTTCTTTTTAA
5619621 TTT-TAATTTTA
1 TTTAT-ATTTTA
5619632 ATTTATTGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
23 1 0.03
24 17 0.59
25 11 0.38
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.75
Consensus pattern (25 bp):
TTTATATTTTACTTTTTCTTTTTAA
Found at i:5624654 original size:13 final size:13
Alignment explanation
Indices: 5624632--5624670 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
5624622 GAAAATATTT
*
5624632 AAGGGTAAAAGAA
1 AAGGGAAAAAGAA
5624645 AAGGGAAAAAGAA
1 AAGGGAAAAAGAA
**
5624658 AACAGAAAAAGAA
1 AAGGGAAAAAGAA
5624671 GCTAAATAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.69, C:0.03, G:0.26, T:0.03
Consensus pattern (13 bp):
AAGGGAAAAAGAA
Found at i:5629758 original size:2 final size:2
Alignment explanation
Indices: 5629747--5629776 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5629737 TTTCTCCTTT
5629747 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5629777 TTTCTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:5629834 original size:2 final size:2
Alignment explanation
Indices: 5629827--5629853 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5629817 CCATGTCTTT
5629827 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5629854 TATTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5632435 original size:2 final size:2
Alignment explanation
Indices: 5632428--5632456 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5632418 AAAGAAGCAA
5632428 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5632457 CCTGGACTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5635396 original size:17 final size:19
Alignment explanation
Indices: 5635371--5635405 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5635361 AATTTTAAAA
5635371 TTTATTAA-TAAAATTGAT
1 TTTATTAATTAAAATTGAT
5635389 TTTA-TAATTAAAATTGA
1 TTTATTAATTAAAATTGA
5635406 ATTGCAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (19 bp):
TTTATTAATTAAAATTGAT
Found at i:5638236 original size:12 final size:11
Alignment explanation
Indices: 5638204--5638238 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
5638194 TAATCAAAAA
*
5638204 TTAAAATTTAT
1 TTAAAATTAAT
5638215 TTAAAATTAAT
1 TTAAAATTAAT
5638226 TTAATAATTAAT
1 TTAA-AATTAAT
5638238 T
1 T
5638239 AATTAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 14 0.64
12 8 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
TTAAAATTAAT
Found at i:5638623 original size:27 final size:26
Alignment explanation
Indices: 5638578--5638636 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
5638568 TTTTGAATTT
* * *
5638578 TATTATTTTATTTAGATAAGTTTTTA
1 TATTTTTTTATTTAAATAAATTTTTA
5638604 TATTTTTTATATTTAAATAAATTTTTA
1 TATTTTTT-TATTTAAATAAATTTTTA
*
5638631 AATTTT
1 TATTTT
5638637 AATTTGTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (26 bp):
TATTTTTTTATTTAAATAAATTTTTA
Found at i:5638718 original size:30 final size:29
Alignment explanation
Indices: 5638586--5638718 Score: 100
Period size: 30 Copynumber: 4.7 Consensus size: 29
5638576 TTTATTATTT
* *
5638586 TATTTAGATAAGTTTTTATA-TTTT--TTA
1 TATTTAAATAAATTTTTA-ACTTTTAATTA
* *
5638613 TATTTAAATAAATTTTTAAATTTTAATTTG
1 TATTTAAATAAATTTTTAACTTTTAA-TTA
* *
5638643 TATTTAAA-AAA-ATTTAACCTTTAATT-
1 TATTTAAATAAATTTTTAACTTTTAATTA
*
5638669 TATCTAAA-AAAGTTTTTAACTTTTAATTCA
1 TATTTAAATAAA-TTTTTAACTTTTAATT-A
* *
5638699 TATTTAAATAAGTTATTAAC
1 TATTTAAATAAATTTTTAAC
5638719 ATAATACATA
Statistics
Matches: 85, Mismatches: 12, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
26 11 0.13
27 22 0.26
28 23 0.27
29 3 0.04
30 24 0.28
31 2 0.02
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.52
Consensus pattern (29 bp):
TATTTAAATAAATTTTTAACTTTTAATTA
Found at i:5642192 original size:18 final size:17
Alignment explanation
Indices: 5642169--5642213 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
5642159 TCAATAATCG
*
5642169 ATCGATTAATTGAATTAA
1 ATCGATTAACTG-ATTAA
5642187 ATCGATTCAACTGATTAA
1 ATCGATT-AACTGATTAA
*
5642205 TTCGATTAA
1 ATCGATTAA
5642214 AATAAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 2 0.08
18 18 0.75
19 4 0.17
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (17 bp):
ATCGATTAACTGATTAA
Found at i:5642523 original size:30 final size:30
Alignment explanation
Indices: 5642482--5642583 Score: 96
Period size: 30 Copynumber: 3.4 Consensus size: 30
5642472 TATTTTTTTT
* *
5642482 ATATTTGAATAAATTTTTAATTTTTAATTA
1 ATATTTAAATAAATTTTTAACTTTTAATTA
* ** *
5642512 ATATTTAAATAAATTTTTGACCATTAATTT
1 ATATTTAAATAAATTTTTAACTTTTAATTA
* * * * *
5642542 TTATATGAATAAACTTTTAACTTTTAATTC
1 ATATTTAAATAAATTTTTAACTTTTAATTA
*
5642572 ATATCTAAATAA
1 ATATTTAAATAA
5642584 GCCATTAACA
Statistics
Matches: 55, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (30 bp):
ATATTTAAATAAATTTTTAACTTTTAATTA
Found at i:5646559 original size:27 final size:27
Alignment explanation
Indices: 5646529--5646728 Score: 115
Period size: 24 Copynumber: 7.1 Consensus size: 27
5646519 GTGACGATTC
5646529 TGATGATGACGAAGGTGGTGTTGGTGG
1 TGATGATGACGAAGGTGGTGTTGGTGG
* *
5646556 TGATGATGATTCTGATGATGAAGAAGGTGTTGTTGG
1 TGATGATGA--C-GA--A-G--G-TGGTGTTGGTGG
*
5646592 TGAGGATGATGACGAGGGTGGTGTTGGTGGCG
1 T---GATGATGACGAAGGTGGTGTTGGT-G-G
* *
5646624 ATGTTGATGACGAAAGTGGTGTTGGTGG
1 -TGATGATGACGAAGGTGGTGTTGGTGG
* * * *
5646652 CGATGATGATG-ACGT--TGGTGGTGG
1 TGATGATGACGAAGGTGGTGTTGGTGG
*
5646676 TGGTGATGACGAAGGT-G-G-TGGTGG
1 TGATGATGACGAAGGTGGTGTTGGTGG
* *
5646700 TGGTGATGACGAGGGTGGTGTTGGTGG
1 TGATGATGACGAAGGTGGTGTTGGTGG
5646727 TG
1 TG
5646729 GTGGTGATGG
Statistics
Matches: 135, Mismatches: 18, Indels: 40
0.70 0.09 0.21
Matches are distributed among these distances:
24 37 0.27
25 5 0.04
26 4 0.03
27 25 0.19
28 1 0.01
29 2 0.01
30 31 0.23
31 2 0.01
32 2 0.01
33 3 0.02
35 1 0.01
36 13 0.10
37 1 0.01
39 8 0.06
ACGTcount: A:0.18, C:0.04, G:0.47, T:0.30
Consensus pattern (27 bp):
TGATGATGACGAAGGTGGTGTTGGTGG
Found at i:5646563 original size:30 final size:30
Alignment explanation
Indices: 5646529--5646771 Score: 139
Period size: 30 Copynumber: 8.3 Consensus size: 30
5646519 GTGACGATTC
*
5646529 TGATGATGACGAAGGTGGTGTTGGTGGTGATGA
1 TGATGATGACGAAGGT-G-G-TGGTGGTGGTGA
* ** * *
5646562 TGATTCTGATGATGAAGAAGGTGTTGTTGGTGA
1 TGA---TGATGACGAAGGTGGTGGTGGTGGTGA
* * * *
5646595 GGATGATGACGAGGGTGGTGTTGGTGGCGA
1 TGATGATGACGAAGGTGGTGGTGGTGGTGA
* * * *
5646625 TGTTGATGACGAAAGTGGTGTTGGTGGCGA
1 TGATGATGACGAAGGTGGTGGTGGTGGTGA
5646655 TGATGATGAC----GT--TGGTGGTGGTG-
1 TGATGATGACGAAGGTGGTGGTGGTGGTGA
5646678 -G-TGATGACGAAGGTGGTGGTGGTGGTGA
1 TGATGATGACGAAGGTGGTGGTGGTGGTGA
* * ** ** *
5646706 TGACGAGGGTGGTGTTGGTGGTGGTGGTGA
1 TGATGATGACGAAGGTGGTGGTGGTGGTGA
* *
5646736 TGGTGATGATG-AGGT-GTGGTGGTGGTGA
1 TGATGATGACGAAGGTGGTGGTGGTGGTGA
*
5646764 TGGTGATG
1 TGATGATG
5646772 GTGATGATGA
Statistics
Matches: 165, Mismatches: 33, Indels: 29
0.73 0.15 0.13
Matches are distributed among these distances:
21 7 0.04
22 1 0.01
24 9 0.05
25 2 0.01
26 2 0.01
27 11 0.07
28 21 0.13
29 3 0.02
30 83 0.50
33 14 0.08
34 1 0.01
35 1 0.01
36 10 0.06
ACGTcount: A:0.17, C:0.04, G:0.49, T:0.30
Consensus pattern (30 bp):
TGATGATGACGAAGGTGGTGGTGGTGGTGA
Found at i:5646567 original size:39 final size:39
Alignment explanation
Indices: 5646514--5646603 Score: 128
Period size: 39 Copynumber: 2.3 Consensus size: 39
5646504 TAGATGGAGA
* * *
5646514 TGGTGGTGACGATTCTGATGATGACGAAGGTGGTGTTGG
1 TGGTGATGATGATTCTGATGATGAAGAAGGTGGTGTTGG
*
5646553 TGGTGATGATGATTCTGATGATGAAGAAGGTGTTGTTGG
1 TGGTGATGATGATTCTGATGATGAAGAAGGTGGTGTTGG
5646592 TGAG-GATGATGA
1 TG-GTGATGATGA
5646604 CGAGGGTGGT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 45 0.98
40 1 0.02
ACGTcount: A:0.22, C:0.04, G:0.41, T:0.32
Consensus pattern (39 bp):
TGGTGATGATGATTCTGATGATGAAGAAGGTGGTGTTGG
Found at i:5646669 original size:21 final size:21
Alignment explanation
Indices: 5646644--5646686 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5646634 CGAAAGTGGT
5646644 GTTGGTGGCGATGATGATGAC
1 GTTGGTGGCGATGATGATGAC
* * *
5646665 GTTGGTGGTGGTGGTGATGAC
1 GTTGGTGGCGATGATGATGAC
5646686 G
1 G
5646687 AAGGTGGTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.07, G:0.49, T:0.30
Consensus pattern (21 bp):
GTTGGTGGCGATGATGATGAC
Found at i:5646692 original size:21 final size:21
Alignment explanation
Indices: 5646658--5646725 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
5646648 GTGGCGATGA
**
5646658 TGATGACGTTGGTGGTGGTGG
1 TGATGACGAAGGTGGTGGTGG
5646679 TGATGACGAAGGTGGTGGTGGTGG
1 TGATGACGAA---GGTGGTGGTGG
* *
5646703 TGATGACGAGGGTGGTGTTGG
1 TGATGACGAAGGTGGTGGTGG
5646724 TG
1 TG
5646726 GTGGTGGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 20 0.50
24 20 0.50
ACGTcount: A:0.13, C:0.04, G:0.53, T:0.29
Consensus pattern (21 bp):
TGATGACGAAGGTGGTGGTGG
Found at i:5646695 original size:3 final size:3
Alignment explanation
Indices: 5646689--5646840 Score: 96
Period size: 3 Copynumber: 51.3 Consensus size: 3
5646679 TGATGACGAA
* ** *
5646689 GGT GGT GGT GGT GGT GAT GAC GAG- GGT GGT GTT GGT GGT GGT GGT
1 GGT GGT GGT GGT GGT GGT GGT G-GT GGT GGT GGT GGT GGT GGT GGT
* * * * * * * *
5646734 GAT GGT GAT GAT -GA GGT -GT GGT GGT GGT GAT GGT GAT GGT GAT GAT
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT
* * * * *
5646780 GAT GAT GAG- GGT GGT GGT GGT GGT GTT GGT GTT GGT GTT GGT GGT
1 GGT GGT G-GT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT
*
5646825 GGT GGT GGT GTT GGT G
1 GGT GGT GGT GGT GGT G
5646841 AAGAAGATAA
Statistics
Matches: 118, Mismatches: 25, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
2 4 0.03
3 114 0.97
ACGTcount: A:0.09, C:0.01, G:0.56, T:0.34
Consensus pattern (3 bp):
GGT
Found at i:5646729 original size:27 final size:27
Alignment explanation
Indices: 5646571--5646731 Score: 129
Period size: 27 Copynumber: 6.1 Consensus size: 27
5646561 ATGATTCTGA
* * *
5646571 TGATGAAGAAGGTGTTGTTGGTGAG-GA
1 TGATGACGAAGGTGGTGTTGGTG-GTGG
* *
5646598 TGATGACGAGGGTGGTGTTGGTGGCGATGT
1 TGATGACGAAGGTGGTGTTGGT-G-G-TGG
* * *
5646628 TGATGACGAAAGTGGTGTTGGTGGCGA
1 TGATGACGAAGGTGGTGTTGGTGGTGG
* * *
5646655 TGATGATG-ACGT--TGGTGGTGGTGG
1 TGATGACGAAGGTGGTGTTGGTGGTGG
5646679 TGATGACGAAGGT-G-G-TGGTGGTGG
1 TGATGACGAAGGTGGTGTTGGTGGTGG
*
5646703 TGATGACGAGGGTGGTGTTGGTGGTGG
1 TGATGACGAAGGTGGTGTTGGTGGTGG
5646730 TG
1 TG
5646732 GTGATGGTGA
Statistics
Matches: 109, Mismatches: 17, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
24 37 0.34
25 5 0.05
26 4 0.04
27 38 0.35
28 3 0.03
29 1 0.01
30 21 0.19
ACGTcount: A:0.17, C:0.04, G:0.50, T:0.29
Consensus pattern (27 bp):
TGATGACGAAGGTGGTGTTGGTGGTGG
Found at i:5646740 original size:24 final size:24
Alignment explanation
Indices: 5646665--5646840 Score: 95
Period size: 24 Copynumber: 7.0 Consensus size: 24
5646655 TGATGATGAC
*
5646665 GTTGGTGGTGGTGGTGATGACGAAGGT
1 GTTGGTGGTGGTGGTGATG--G-TGGT
* * *
5646692 GGTGGTGGTGGTGATGACGAGGGTGGT
1 GTTGGTGGTGGTG--G-TGATGGTGGT
*
5646719 GTTGGTGGTGGTGGTGATGGTGAT
1 GTTGGTGGTGGTGGTGATGGTGGT
* * *
5646743 GATGAG-GTGTGGTGGTGGTGATGGT
1 GTTG-GTG-GTGGTGGTGATGGTGGT
* * * *
5646768 GATGGTGATGATGATGATGAG-GGT
1 GTTGGTGGTGGTGGTGATG-GTGGT
* * * *
5646792 GGTGGTGGTGGTGTTGGTGTTGGT
1 GTTGGTGGTGGTGGTGATGGTGGT
* *
5646816 GTTGGTGGTGGTGGTGGTGTTGGT
1 GTTGGTGGTGGTGGTGATGGTGGT
5646840 G
1 G
5646841 AAGAAGATAA
Statistics
Matches: 116, Mismatches: 25, Indels: 19
0.73 0.16 0.12
Matches are distributed among these distances:
24 63 0.54
25 21 0.18
27 27 0.23
28 1 0.01
29 1 0.01
30 3 0.03
ACGTcount: A:0.10, C:0.01, G:0.55, T:0.34
Consensus pattern (24 bp):
GTTGGTGGTGGTGGTGATGGTGGT
Found at i:5668106 original size:26 final size:26
Alignment explanation
Indices: 5668070--5668126 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
5668060 ATCGATTTTG
5668070 ATGAGATTTTTGCTCCAGTTGTAAAA
1 ATGAGATTTTTGCTCCAGTTGTAAAA
5668096 ATGAGATTTTTGCTCCAGTTGTAAAA
1 ATGAGATTTTTGCTCCAGTTGTAAAA
5668122 ATGAG
1 ATGAG
5668127 TTCTATTCGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.37
Consensus pattern (26 bp):
ATGAGATTTTTGCTCCAGTTGTAAAA
Found at i:5673149 original size:32 final size:32
Alignment explanation
Indices: 5673108--5673203 Score: 147
Period size: 32 Copynumber: 3.0 Consensus size: 32
5673098 ACCAGTCCGC
5673108 AGTCATGGGAGTCATTAAGTGCTACACGGTGG
1 AGTCATGGGAGTCATTAAGTGCTACACGGTGG
*
5673140 AGTCATGGGAGTCATTAAGTGCTACATGGTGG
1 AGTCATGGGAGTCATTAAGTGCTACACGGTGG
* * * *
5673172 AGCCGTGGGAGTCACTAAATGCTACACGGTGG
1 AGTCATGGGAGTCATTAAGTGCTACACGGTGG
5673204 TCTGGTATGA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 58 1.00
ACGTcount: A:0.25, C:0.17, G:0.34, T:0.24
Consensus pattern (32 bp):
AGTCATGGGAGTCATTAAGTGCTACACGGTGG
Found at i:5677574 original size:21 final size:20
Alignment explanation
Indices: 5677550--5677588 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5677540 ATTTTGGATA
5677550 TTTAAGAAT-TAAATTAAATTT
1 TTTAA-AATATAAA-TAAATTT
5677571 TTTAAAATATAAATAAAT
1 TTTAAAATATAAATAAAT
5677589 AATATTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (20 bp):
TTTAAAATATAAATAAATTT
Found at i:5679593 original size:14 final size:14
Alignment explanation
Indices: 5679574--5679601 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5679564 ATTGAGACTG
5679574 TTAGATGCATCCTT
1 TTAGATGCATCCTT
5679588 TTAGATGCATCCTT
1 TTAGATGCATCCTT
5679602 ATTTTTTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.43
Consensus pattern (14 bp):
TTAGATGCATCCTT
Found at i:5679704 original size:15 final size:15
Alignment explanation
Indices: 5679684--5679744 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 15
5679674 AAGATTTTAT
5679684 AATTTTTCAAAAATA
1 AATTTTTCAAAAATA
*
5679699 AATTTTTAAAAAATCATA
1 AATTTTT-CAAAA--ATA
**
5679717 TAATTTTTTGAAAATA
1 -AATTTTTCAAAAATA
5679733 AA-TTTTCAAAAA
1 AATTTTTCAAAAA
5679745 ATTATAAACT
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
14 8 0.22
15 9 0.24
16 7 0.19
18 6 0.16
19 7 0.19
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (15 bp):
AATTTTTCAAAAATA
Done.