Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 87 of 226
Found at i:27434490 original size:16 final size:16
Alignment explanation
Indices: 27434469--27434503 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
27434459 TGGTAAATTA
27434469 TTAAATATTGTTATTG
1 TTAAATATTGTTATTG
27434485 TTAAATATTGTTATTG
1 TTAAATATTGTTATTG
27434501 TTA
1 TTA
27434504 TTTAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.57
Consensus pattern (16 bp):
TTAAATATTGTTATTG
Found at i:27434674 original size:16 final size:16
Alignment explanation
Indices: 27434637--27434678 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
27434627 TTAATCATAT
*
27434637 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
27434653 TT-AAATATATTATAA
1 TTAAAATATATTATAA
27434668 TTAAAATATAT
1 TTAAAATATAT
27434679 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:27434685 original size:14 final size:15
Alignment explanation
Indices: 27434646--27434687 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
27434636 TTTAAACATA
*
27434646 ATTATTATTAAATAT
1 ATTATAATTAAATAT
27434661 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
27434675 A-TATAATTTAATA
1 ATTATAATTAAATA
27434688 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:27434735 original size:54 final size:54
Alignment explanation
Indices: 27434677--27434855 Score: 146
Period size: 57 Copynumber: 3.1 Consensus size: 54
27434667 ATTAAAATAT
27434677 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATC
1 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATC
* * * * * * *
27434731 ATAATATATGATACTGTAAAA-TATAAATTAACATAATTATTATTAAAT-ATATTATAGTTAAAA
1 ATAAT-T-T-A-A---TAAAATTCTTAA-TAA-TTAA-TATTCTTATATGA-ATT-TA-CTCAAA
*
27434794 TAT
53 T-C
27434797 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATC
1 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATC
27434851 ATAAT
1 ATAAT
27434856 ATATGATACT
Statistics
Matches: 93, Mismatches: 16, Indels: 32
0.66 0.11 0.23
Matches are distributed among these distances:
54 10 0.11
55 6 0.06
56 3 0.03
57 13 0.14
58 5 0.05
59 8 0.09
60 8 0.09
61 8 0.09
62 5 0.05
63 13 0.14
64 3 0.03
65 6 0.06
66 5 0.05
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (54 bp):
ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATC
Found at i:27434737 original size:61 final size:61
Alignment explanation
Indices: 27434672--27434859 Score: 183
Period size: 61 Copynumber: 3.1 Consensus size: 61
27434662 TTATAATTAA
27434672 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * * *
27434733 AATATATGATACT-GTAAAA-T-AT-A-AATTAACATAATTATTAT-TAAATATA-TTATAGTTA
1 AATATATAAT-TTAATAAAATTCTTAATAATT-A-AT-ATTCTTATATGAATTTACTCA-AATCA
*
27434791 A
61 T
27434792 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
27434853 AATATAT
1 AATATAT
27434860 GATACTATAA
Statistics
Matches: 93, Mismatches: 22, Indels: 24
0.67 0.16 0.17
Matches are distributed among these distances:
57 4 0.04
58 5 0.05
59 26 0.28
60 16 0.17
61 33 0.35
62 5 0.05
63 4 0.04
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
Found at i:27434772 original size:120 final size:121
Alignment explanation
Indices: 27434635--27434932 Score: 496
Period size: 120 Copynumber: 2.5 Consensus size: 121
27434625 TTTTAATCAT
*
27434635 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
27434700 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAAT-ATAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTAT-AAATGA-AA
*
27434757 A-TT-AACATAATTATTATTAAATATATTATAGTTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
27434820 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
* * *
27434876 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
27434933 TAAAATAATT
Statistics
Matches: 167, Mismatches: 6, Indels: 8
0.92 0.03 0.04
Matches are distributed among these distances:
119 7 0.04
120 155 0.93
121 4 0.02
122 1 0.01
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (121 bp):
ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
Found at i:27435019 original size:24 final size:25
Alignment explanation
Indices: 27434973--27435020 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
27434963 TATGAATTTT
27434973 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
27434999 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
27435021 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:27438567 original size:21 final size:22
Alignment explanation
Indices: 27438517--27438567 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
27438507 CTTTTATAAC
*
27438517 ATTTTAA-ATTTAAATTTCTTT
1 ATTTTAATATTTAAATTTCTTG
**
27438538 ATTAAAATA-TTAAATTTCTTG
1 ATTTTAATATTTAAATTTCTTG
27438559 ATTTTAATA
1 ATTTTAATA
27438568 AAATATTAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (22 bp):
ATTTTAATATTTAAATTTCTTG
Found at i:27438600 original size:25 final size:25
Alignment explanation
Indices: 27438572--27438742 Score: 198
Period size: 25 Copynumber: 7.1 Consensus size: 25
27438562 TTAATAAAAT
27438572 ATTAAAGTCCTTATTTTAATTATTG
1 ATTAAAGTCCTTATTTTAATTATTG
* *
27438597 ATT--AGTCCTTATTTTAATAAAAT-
1 ATTAAAGTCCTTATTTTAAT-TATTG
27438620 ATTAAAGTCCTTATTTTAATTATTG
1 ATTAAAGTCCTTATTTTAATTATTG
* *
27438645 ATT--AGTCCTTATTTTAATAAAAT-
1 ATTAAAGTCCTTATTTTAAT-TATTG
27438668 ATTAAAGTCCTTATTTTAATTATTG
1 ATTAAAGTCCTTATTTTAATTATTG
* *
27438693 ATT--AGTCCTTATTTTAATAAAAT-
1 ATTAAAGTCCTTATTTTAAT-TATTG
27438716 ATTAAAGTCCTTATTTTAATTATTG
1 ATTAAAGTCCTTATTTTAATTATTG
27438741 AT
1 AT
27438743 GTAATTTTTA
Statistics
Matches: 122, Mismatches: 12, Indels: 24
0.77 0.08 0.15
Matches are distributed among these distances:
23 54 0.44
24 12 0.10
25 56 0.46
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.50
Consensus pattern (25 bp):
ATTAAAGTCCTTATTTTAATTATTG
Found at i:27438607 original size:23 final size:24
Alignment explanation
Indices: 27438576--27438742 Score: 184
Period size: 23 Copynumber: 7.0 Consensus size: 24
27438566 TAAAATATTA
27438576 AAGTCCTTATTTTAATTATTGATT
1 AAGTCCTTATTTTAATTATTGATT
* *
27438600 -AGTCCTTATTTTAATAAAAT-ATT
1 AAGTCCTTATTTTAAT-TATTGATT
27438623 AAAGTCCTTATTTTAATTATTGATT
1 -AAGTCCTTATTTTAATTATTGATT
* *
27438648 -AGTCCTTATTTTAATAAAAT-ATT
1 AAGTCCTTATTTTAAT-TATTGATT
27438671 AAAGTCCTTATTTTAATTATTGATT
1 -AAGTCCTTATTTTAATTATTGATT
* *
27438696 -AGTCCTTATTTTAATAAAAT-ATT
1 AAGTCCTTATTTTAAT-TATTGATT
27438719 AAAGTCCTTATTTTAATTATTGAT
1 -AAGTCCTTATTTTAATTATTGAT
27438743 GTAATTTTTA
Statistics
Matches: 119, Mismatches: 12, Indels: 23
0.77 0.08 0.15
Matches are distributed among these distances:
23 54 0.45
24 12 0.10
25 53 0.45
ACGTcount: A:0.35, C:0.08, G:0.07, T:0.50
Consensus pattern (24 bp):
AAGTCCTTATTTTAATTATTGATT
Found at i:27438611 original size:48 final size:48
Alignment explanation
Indices: 27438559--27438742 Score: 368
Period size: 48 Copynumber: 3.8 Consensus size: 48
27438549 AAATTTCTTG
27438559 ATTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTT
1 ATTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTT
27438607 ATTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTT
1 ATTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTT
27438655 ATTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTT
1 ATTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTT
27438703 ATTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGAT
1 ATTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGAT
27438743 GTAATTTTTA
Statistics
Matches: 136, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 136 1.00
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.50
Consensus pattern (48 bp):
ATTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTT
Found at i:27443250 original size:13 final size:13
Alignment explanation
Indices: 27443232--27443256 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27443222 TTTGACAATA
27443232 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
27443245 CTTTTGAAAAGT
1 CTTTTGAAAAGT
27443257 TGAAAAGTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:27444966 original size:32 final size:32
Alignment explanation
Indices: 27444925--27444993 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
27444915 TGATATTGCG
* *
27444925 ATGTTTTTGATATGTGAGGATGGGTGATTGTA
1 ATGTCTTTGATATGTGAGGATAGGTGATTGTA
27444957 ATGTCTTTGATATGTGAGGATAGGTGATTGTA
1 ATGTCTTTGATATGTGAGGATAGGTGATTGTA
27444989 ATGTC
1 ATGTC
27444994 AGTTTGGTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.23, C:0.03, G:0.32, T:0.42
Consensus pattern (32 bp):
ATGTCTTTGATATGTGAGGATAGGTGATTGTA
Found at i:27452428 original size:18 final size:18
Alignment explanation
Indices: 27452405--27452454 Score: 82
Period size: 18 Copynumber: 2.7 Consensus size: 18
27452395 CTAAGCAAAG
*
27452405 GAAACAATCAATTTTTAT
1 GAAACAATCAATTTTCAT
27452423 GAAACAATCAATTTTCAT
1 GAAACAATCAATTTTCAT
27452441 GAAACAATCTAATT
1 GAAACAATC-AATT
27452455 ACAATATTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 26 0.87
19 4 0.13
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (18 bp):
GAAACAATCAATTTTCAT
Found at i:27455724 original size:17 final size:17
Alignment explanation
Indices: 27455688--27455743 Score: 78
Period size: 16 Copynumber: 3.3 Consensus size: 17
27455678 TGAGATAACA
27455688 TAAATCAAAAATTAAA-
1 TAAATCAAAAATTAAAT
27455704 TAAATCAAAAATTAAAT
1 TAAATCAAAAATTAAAT
* *
27455721 TAAATTAGAAATTAAAT
1 TAAATCAAAAATTAAAT
27455738 TCAAAT
1 T-AAAT
27455744 TTTATAAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
16 16 0.44
17 16 0.44
18 4 0.11
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.30
Consensus pattern (17 bp):
TAAATCAAAAATTAAAT
Found at i:27457740 original size:12 final size:13
Alignment explanation
Indices: 27457715--27457745 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
27457705 TGCAAATGAA
27457715 TCATTTCTCATTT
1 TCATTTCTCATTT
27457728 TCATTTC-CATTT
1 TCATTTCTCATTT
27457740 TCATTT
1 TCATTT
27457746 TGAGAAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61
Consensus pattern (13 bp):
TCATTTCTCATTT
Found at i:27465461 original size:18 final size:19
Alignment explanation
Indices: 27465430--27465465 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
27465420 ACCCATTAGG
27465430 TTAATTTAGGTTAATTAAT
1 TTAATTTAGGTTAATTAAT
*
27465449 TTAA-TTAGTTTAATTAA
1 TTAATTTAGGTTAATTAA
27465466 AATATTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (19 bp):
TTAATTTAGGTTAATTAAT
Found at i:27470408 original size:5 final size:6
Alignment explanation
Indices: 27470387--27470418 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
27470377 TATATCCCAA
27470387 TTTTAT CTTTTAT TTTTAT TTTTAT TTTTAT T
1 TTTTAT -TTTTAT TTTTAT TTTTAT TTTTAT T
27470419 CGCATTTCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTAT
Found at i:27486037 original size:34 final size:34
Alignment explanation
Indices: 27485999--27486068 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
27485989 AAACATGAAA
27485999 TATTTGTT-AATCATTGGATAACCTAAGGAAGTGG
1 TATTT-TTCAATCATTGGATAACCTAAGGAAGTGG
* *
27486033 TATTTTTCTATCATTGGATAACCTAAGGTAGTGG
1 TATTTTTCAATCATTGGATAACCTAAGGAAGTGG
27486067 TA
1 TA
27486069 GTACCTTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 2 0.06
34 31 0.94
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (34 bp):
TATTTTTCAATCATTGGATAACCTAAGGAAGTGG
Found at i:27488872 original size:22 final size:22
Alignment explanation
Indices: 27488847--27488914 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
27488837 GGCCATTTTC
27488847 CGCGAAATCGCGTCCACGTCAG
1 CGCGAAATCGCGTCCACGTCAG
** * * *
27488869 CGCGATGTCAGGGTGCGCG-CA-
1 CGCGAAATC-GCGTCCACGTCAG
27488890 -G-GAAATCGCGTCCACGTCAG
1 CGCGAAATCGCGTCCACGTCAG
27488910 CGCGA
1 CGCGA
27488915 TTTGCTGACG
Statistics
Matches: 31, Mismatches: 10, Indels: 10
0.61 0.20 0.20
Matches are distributed among these distances:
18 6 0.19
19 6 0.19
20 1 0.03
21 1 0.03
22 11 0.35
23 6 0.19
ACGTcount: A:0.21, C:0.32, G:0.34, T:0.13
Consensus pattern (22 bp):
CGCGAAATCGCGTCCACGTCAG
Found at i:27489837 original size:30 final size:29
Alignment explanation
Indices: 27489770--27489837 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
27489760 GATTTCGCGG
*
27489770 AAAATGGCCCATTCCGGTAAATAATTAAA
1 AAAACGGCCCATTCCGGTAAATAATTAAA
* * *
27489799 AAACCGGCCCATTTCGGTAAAT-TTTGAAAA
1 AAAACGGCCCATTCCGGTAAATAATT--AAA
27489829 AAAACGGCC
1 AAAACGGCC
27489838 TTTTTTGGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
28 2 0.06
29 19 0.59
30 11 0.34
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (29 bp):
AAAACGGCCCATTCCGGTAAATAATTAAA
Found at i:27513214 original size:25 final size:25
Alignment explanation
Indices: 27513185--27513248 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
27513175 ATACATGTAT
*
27513185 GCTCATACGAGCT-A-TGAATCGGTAA
1 GCTCATACGAGCTGAGT-AA-CAGTAA
27513210 GCTCATACGAGCTGAGTAACAGTAA
1 GCTCATACGAGCTGAGTAACAGTAA
*
27513235 GCTCATTCGAGCTG
1 GCTCATACGAGCTG
27513249 TGTTGTGTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 31 0.89
26 3 0.09
27 1 0.03
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (25 bp):
GCTCATACGAGCTGAGTAACAGTAA
Found at i:27517292 original size:20 final size:20
Alignment explanation
Indices: 27517259--27517316 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
27517249 TAATTTTTGA
27517259 AGTTTATT-CAATTTAGTCT
1 AGTTTATTGCAATTTAGTCT
27517278 AGTTTATTGCAATTTAGTCT
1 AGTTTATTGCAATTTAGTCT
27517298 AGTTTATTGCAATTTAGTC
1 AGTTTATTGCAATTTAGTC
27517317 GCTGACCCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 8 0.21
20 30 0.79
ACGTcount: A:0.26, C:0.10, G:0.14, T:0.50
Consensus pattern (20 bp):
AGTTTATTGCAATTTAGTCT
Found at i:27517768 original size:20 final size:21
Alignment explanation
Indices: 27517743--27517781 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
27517733 ATGAAAGAAA
27517743 AACCT-AAACTAAAGCTTTCT
1 AACCTAAAACTAAAGCTTTCT
*
27517763 AACCTAAAACTACAGCTTT
1 AACCTAAAACTAAAGCTTT
27517782 TTTTTTCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.41, C:0.26, G:0.05, T:0.28
Consensus pattern (21 bp):
AACCTAAAACTAAAGCTTTCT
Found at i:27519743 original size:19 final size:19
Alignment explanation
Indices: 27519719--27519757 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
27519709 TTTTTTAACT
27519719 ATTTTAAAATTTCATTAGA
1 ATTTTAAAATTTCATTAGA
* *
27519738 ATTTTATAATTTTATTAGA
1 ATTTTAAAATTTCATTAGA
27519757 A
1 A
27519758 GAGGCAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (19 bp):
ATTTTAAAATTTCATTAGA
Found at i:27520752 original size:17 final size:18
Alignment explanation
Indices: 27520725--27520759 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
27520715 AATTCAGTTT
*
27520725 GAAATTAAATAATTAATA
1 GAAATTAAATAATAAATA
27520743 GAAA-TAAATAATAAATA
1 GAAATTAAATAATAAATA
27520760 TTATATATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (18 bp):
GAAATTAAATAATAAATA
Found at i:27523930 original size:42 final size:42
Alignment explanation
Indices: 27523871--27523955 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
27523861 CTTGATTAAT
27523871 TAGTGGAAGTGTCTTCTTGAAGGCACGTTGTTTGGTATTGGC
1 TAGTGGAAGTGTCTTCTTGAAGGCACGTTGTTTGGTATTGGC
27523913 TAGTGGAAGTGTCTTCTTGAAGGCACGTTGTTTGGTATTGGC
1 TAGTGGAAGTGTCTTCTTGAAGGCACGTTGTTTGGTATTGGC
27523955 T
1 T
27523956 CAGTTATTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.16, C:0.12, G:0.33, T:0.39
Consensus pattern (42 bp):
TAGTGGAAGTGTCTTCTTGAAGGCACGTTGTTTGGTATTGGC
Found at i:27531698 original size:42 final size:40
Alignment explanation
Indices: 27531651--27531733 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 40
27531641 TTTTGAGATG
* * *
27531651 TGATTTCACGTAAGACCATGTTTGGGACATTGGCATCGTATA
1 TGATTTCACGTAAGACC-TGTCTGAGACAGTGGCATCG-ATA
**
27531693 TGATTTCGTGTAAGACCTGTCTGAGACAGTGGCATCGATA
1 TGATTTCACGTAAGACCTGTCTGAGACAGTGGCATCGATA
27531733 T
1 T
27531734 CTTATAACAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
40 4 0.11
41 17 0.47
42 15 0.42
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (40 bp):
TGATTTCACGTAAGACCTGTCTGAGACAGTGGCATCGATA
Found at i:27532365 original size:25 final size:25
Alignment explanation
Indices: 27532329--27532415 Score: 81
Period size: 25 Copynumber: 3.5 Consensus size: 25
27532319 AAATTGGTGC
27532329 TTAATTGCTGTCCATTTTTTAGCATA
1 TTAA-TGCTGTCCATTTTTTAGCATA
* **
27532355 TTAATGCTGTCCAAATTAGT-GC-T-
1 TTAATGCTGTCC-ATTTTTTAGCATA
* *
27532378 TAAATGCTTTCCATTTTTTAGCATA
1 TTAATGCTGTCCATTTTTTAGCATA
*
27532403 TTAGTGCTGTCCA
1 TTAATGCTGTCCA
27532416 AATTAGTGCT
Statistics
Matches: 46, Mismatches: 11, Indels: 9
0.70 0.17 0.14
Matches are distributed among these distances:
22 4 0.09
23 12 0.26
24 2 0.04
25 20 0.43
26 8 0.17
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.45
Consensus pattern (25 bp):
TTAATGCTGTCCATTTTTTAGCATA
Found at i:27532383 original size:23 final size:23
Alignment explanation
Indices: 27532310--27532438 Score: 82
Period size: 23 Copynumber: 5.4 Consensus size: 23
27532300 TGATGATAAG
*
27532310 ATGCTGTCCAAATTGGTGCTTAA
1 ATGCTGTCCAAATTAGTGCTTAA
* * ** *
27532333 TTGCTGTCC-ATTTTTTAGCATATTA
1 ATGCTGTCCAAATTAGT-GC-T-TAA
27532358 ATGCTGTCCAAATTAGTGCTTAA
1 ATGCTGTCCAAATTAGTGCTTAA
* * ** *
27532381 ATGCTTTCC-ATTTTTTAGCATATTA
1 ATGCTGTCCAAATTAGT-GC-T-TAA
*
27532406 GTGCTGTCCAAATTAGTGCTTAA
1 ATGCTGTCCAAATTAGTGCTTAA
27532429 ATGCTGTCCA
1 ATGCTGTCCA
27532439 TTTTTTTTGA
Statistics
Matches: 76, Mismatches: 22, Indels: 16
0.67 0.19 0.14
Matches are distributed among these distances:
22 8 0.11
23 33 0.43
24 4 0.05
25 23 0.30
26 8 0.11
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (23 bp):
ATGCTGTCCAAATTAGTGCTTAA
Found at i:27532391 original size:48 final size:49
Alignment explanation
Indices: 27532310--27532538 Score: 309
Period size: 48 Copynumber: 4.7 Consensus size: 49
27532300 TGATGATAAG
* *
27532310 ATGCTGTCCAAATTGGTGCTTAATTGCTGTCCATTTTTT-AGCATATTA
1 ATGCTGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTGAGCATATTA
*
27532358 ATGCTGTCCAAATTAGTGCTTAAATGCTTTCCATTTTTT-AGCATATTA
1 ATGCTGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTGAGCATATTA
* *
27532406 GTGCTGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTTTGAGCACATTA
1 ATGCTGTCCAAATTAGTGCTTAAATGCTGTCCA--TTTTTTGAGCATATTA
* * * * *
27532457 ATGCTATCCAAATTAATGCTTAATTGCTATCCATTTTTTGAGTATATTA
1 ATGCTGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTGAGCATATTA
* * *
27532506 ATGCTGTCCAAATTGGTACTTAAATGTTGTCCA
1 ATGCTGTCCAAATTAGTGCTTAAATGCTGTCCA
27532539 AATATTTGTG
Statistics
Matches: 158, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
48 76 0.48
49 40 0.25
50 6 0.04
51 36 0.23
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (49 bp):
ATGCTGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTGAGCATATTA
Found at i:27532491 original size:99 final size:97
Alignment explanation
Indices: 27532310--27532538 Score: 325
Period size: 99 Copynumber: 2.3 Consensus size: 97
27532300 TGATGATAAG
* * * *
27532310 ATGCTGTCCAAATTGGTGCTTAATTGCTGTCCATTTTTTAGCATATTAATGCTGTCCAAATTAGT
1 ATGCTGTCCAAATTGGTGCTTAAATGCTGTCCATTTTTTAGCACATTAATGCTATCCAAATTAAT
*
27532375 GCTTAAATGCTTTCCATTTTTT-AGCATATTA
66 GCTTAAATGCTATCCATTTTTTGAGCATATTA
* *
27532406 GTGCTGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTTTGAGCACATTAATGCTATCCAAATT
1 ATGCTGTCCAAATTGGTGCTTAAATGCTGTCCA--TTTTTT-AGCACATTAATGCTATCCAAATT
* *
27532471 AATGCTTAATTGCTATCCATTTTTTGAGTATATTA
63 AATGCTTAAATGCTATCCATTTTTTGAGCATATTA
* *
27532506 ATGCTGTCCAAATTGGTACTTAAATGTTGTCCA
1 ATGCTGTCCAAATTGGTGCTTAAATGCTGTCCA
27532539 AATATTTGTG
Statistics
Matches: 116, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
96 30 0.26
98 6 0.05
99 43 0.37
100 37 0.32
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (97 bp):
ATGCTGTCCAAATTGGTGCTTAAATGCTGTCCATTTTTTAGCACATTAATGCTATCCAAATTAAT
GCTTAAATGCTATCCATTTTTTGAGCATATTA
Found at i:27540249 original size:48 final size:48
Alignment explanation
Indices: 27540172--27540394 Score: 286
Period size: 48 Copynumber: 4.6 Consensus size: 48
27540162 GATAAGATGT
* *
27540172 TGTCCAAATTGGTGCTTAATTGCTGTCCATTTTTTAGCATATTAATGC
1 TGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTAGCATATTAATGC
* * *
27540220 TGTCCAAATTAGTGCTTAAATGCTTTCCATTTTTTAGCATATTAGTGT
1 TGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTAGCATATTAATGC
*
27540268 TGTCCAAATTAGTGCTTAAATGTTGTCCATTTTTTTGAGCATATTAATGC
1 TGTCCAAATTAGTGCTTAAATGCTGTCCA-TTTTTT-AGCATATTAATGC
* * * *
27540318 TATCCAAATT-GATGCTTAATTGCTGTCCATTTTTGAGTATATTAATGC
1 TGTCCAAATTAG-TGCTTAAATGCTGTCCATTTTTTAGCATATTAATGC
* * * *
27540366 TGTCCAAATTGGTACGTAAATGTTGTCCA
1 TGTCCAAATTAGTGCTTAAATGCTGTCCA
27540395 AATATTTGTG
Statistics
Matches: 152, Mismatches: 19, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
48 104 0.68
49 13 0.09
50 35 0.23
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.43
Consensus pattern (48 bp):
TGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTAGCATATTAATGC
Found at i:27540336 original size:98 final size:96
Alignment explanation
Indices: 27540168--27540394 Score: 312
Period size: 98 Copynumber: 2.3 Consensus size: 96
27540158 TGATGATAAG
* * *
27540168 ATGTTGTCCAAATTGGTGCTTAATTGCTGTCCATTTTTTAGCATATTAATGCTGTCCAAATTAGT
1 ATGTTGTCCAAATTGGTGCTTAAATGTTGTCCATTTTTTAGCATATTAATGCTATCCAAATTAGT
* *
27540233 GCTTAAATGCTTTCCATTTTTTAGCATATTA
66 GCTTAAATGCTGTCCATTTTTGAGCATATTA
* *
27540264 GTGTTGTCCAAATTAGTGCTTAAATGTTGTCCATTTTTTTGAGCATATTAATGCTATCCAAATT-
1 ATGTTGTCCAAATTGGTGCTTAAATGTTGTCCA-TTTTTT-AGCATATTAATGCTATCCAAATTA
* *
27540328 GATGCTTAATTGCTGTCCATTTTTGAGTATATTA
64 G-TGCTTAAATGCTGTCCATTTTTGAGCATATTA
* * *
27540362 ATGCTGTCCAAATTGGTACGTAAATGTTGTCCA
1 ATGTTGTCCAAATTGGTGCTTAAATGTTGTCCA
27540395 AATATTTGTG
Statistics
Matches: 114, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
96 29 0.25
97 7 0.06
98 78 0.68
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.43
Consensus pattern (96 bp):
ATGTTGTCCAAATTGGTGCTTAAATGTTGTCCATTTTTTAGCATATTAATGCTATCCAAATTAGT
GCTTAAATGCTGTCCATTTTTGAGCATATTA
Found at i:27541515 original size:27 final size:27
Alignment explanation
Indices: 27541454--27541516 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
27541444 CTGAAAAATG
* *
27541454 AATCAA-TCCAAAAATAATAGAGACTC
1 AATCAATTCCAAAAAGAATAGAAACTC
* *
27541480 AATTC-ATTCGAAAAAGAATAGAAACTT
1 AA-TCAATTCCAAAAAGAATAGAAACTC
27541507 AATCAATTCC
1 AATCAATTCC
27541517 CAATGATTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
26 5 0.17
27 24 0.83
ACGTcount: A:0.51, C:0.17, G:0.08, T:0.24
Consensus pattern (27 bp):
AATCAATTCCAAAAAGAATAGAAACTC
Found at i:27555274 original size:25 final size:24
Alignment explanation
Indices: 27555246--27555303 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
27555236 TATTATCAAT
* *
27555246 AATTTTATGAAATTATATATTATTA
1 AATTATATGAAATAATA-ATTATTA
*
27555271 AATTATATGTAATAATAATTATTTTA
1 AATTATATGAAATAATAATTA--TTA
27555297 AATTATA
1 AATTATA
27555304 CAAATTCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 4 0.14
25 14 0.50
26 10 0.36
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (24 bp):
AATTATATGAAATAATAATTATTA
Found at i:27555370 original size:47 final size:49
Alignment explanation
Indices: 27555246--27555371 Score: 123
Period size: 47 Copynumber: 2.6 Consensus size: 49
27555236 TATTATCAAT
* *
27555246 AATTTTATGAAATTATATATTATTAAATTATATGTAATAATAATTATTTTA
1 AATTTTATCAAATCATATATT-TT-AATTATATGTAATAATAATTATTTTA
* *** * *
27555297 AATTATA-CAAATTCATATAAGATAATT-TAT-TAGTTATAATTATTTTA
1 AATTTTATCAAA-TCATATATTTTAATTATATGTAATAATAATTATTTTA
*
27555344 AATTTTATTAAATCATATATTTTAATTA
1 AATTTTATCAAATCATATATTTTAATTA
27555372 AAATATATTT
Statistics
Matches: 59, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
47 33 0.56
48 6 0.10
49 4 0.07
50 4 0.07
51 12 0.20
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.50
Consensus pattern (49 bp):
AATTTTATCAAATCATATATTTTAATTATATGTAATAATAATTATTTTA
Found at i:27555510 original size:25 final size:26
Alignment explanation
Indices: 27555478--27555532 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
27555468 TTATTAAATT
*
27555478 ATATATTTTAATTATAA-TATATTTA
1 ATATATTTTAATAATAATTATATTTA
*
27555503 ATATA-TTTAATAATAATTATGTTTA
1 ATATATTTTAATAATAATTATATTTA
27555528 A-ATAT
1 ATATAT
27555533 GATTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATATTTTAATAATAATTATATTTA
Found at i:27555699 original size:39 final size:40
Alignment explanation
Indices: 27555656--27555760 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 40
27555646 TTCTATTATG
27555656 CTATTACACCTCTATTCCATTCAACCAAACACAAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
* *** *
27555695 CTATTACGCCTCTATTTCATTACATTCAACCAAACAGTTGATTTG
1 CTATTACACCTCTA-TTC----CATTCAACCAAACACAAGATTTA
27555740 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
27555761 ACACCTCTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
39 13 0.24
40 7 0.13
44 19 0.35
45 15 0.28
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
Found at i:27555754 original size:45 final size:44
Alignment explanation
Indices: 27555654--27555763 Score: 122
Period size: 45 Copynumber: 2.6 Consensus size: 44
27555644 TTTTCTATTA
27555654 TGCTATTACACCTCTA-TTC----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTTCATTACATTCAACCAAACACAAGAT
* * ***
27555693 TACTATTACGCCTCTATTTCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTTCATTACATTCAACCAAACACAAGA-T
*
27555738 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTTCATTACA
27555764 CCTCTAATCC
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
39 14 0.25
40 3 0.05
44 16 0.28
45 24 0.42
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (44 bp):
TGCTATTACACCTCTATTTCATTACATTCAACCAAACACAAGAT
Found at i:27555763 original size:16 final size:16
Alignment explanation
Indices: 27555742--27555779 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
27555732 TTGATTTGCT
*
27555742 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
27555758 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
27555774 AATACA
1 ATTACA
27555780 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:27560625 original size:18 final size:19
Alignment explanation
Indices: 27560602--27560643 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
27560592 AAAAACTCAA
27560602 TTAAAACATT-TTTGA-AAT
1 TTAAAA-ATTATTTGAGAAT
27560620 TTAAAAATTATTTGAGAAT
1 TTAAAAATTATTTGAGAAT
27560639 TTAAA
1 TTAAA
27560644 TCATAATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.14
18 11 0.50
19 8 0.36
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (19 bp):
TTAAAAATTATTTGAGAAT
Found at i:27560654 original size:20 final size:18
Alignment explanation
Indices: 27560612--27560654 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
27560602 TTAAAACATT
*
27560612 TTTGAAATTTAAAAATTA
1 TTTGAAATTTAAAAATAA
*
27560630 TTTGAGAATTTAAATCATAA
1 TTTGA-AATTTAAA-AATAA
27560650 TTTGA
1 TTTGA
27560655 TGATTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 8 0.38
20 8 0.38
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (18 bp):
TTTGAAATTTAAAAATAA
Found at i:27581051 original size:9 final size:9
Alignment explanation
Indices: 27581034--27581079 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
27581024 TGAGTTTTAG
27581034 AATTCGAAT
1 AATTCGAAT
*
27581043 AACTCGAAT
1 AATTCGAAT
*
27581052 AATTTGAAT
1 AATTCGAAT
*
27581061 AATTTGAAT
1 AATTCGAAT
27581070 AATTCGAAT
1 AATTCGAAT
27581079 A
1 A
27581080 TCAAACTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.35
Consensus pattern (9 bp):
AATTCGAAT
Found at i:27588622 original size:27 final size:27
Alignment explanation
Indices: 27588592--27588650 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
27588582 TATCAAAGAA
*
27588592 ACCAAATCTCAAACATTAATAAACCAC
1 ACCAAACCTCAAACATTAATAAACCAC
27588619 ACCAAACCTCAAACATTAATAAACCAC
1 ACCAAACCTCAAACATTAATAAACCAC
27588646 ACCAA
1 ACCAA
27588651 CTTTATTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.53, C:0.32, G:0.00, T:0.15
Consensus pattern (27 bp):
ACCAAACCTCAAACATTAATAAACCAC
Found at i:27596867 original size:617 final size:617
Alignment explanation
Indices: 27595694--27596927 Score: 2378
Period size: 617 Copynumber: 2.0 Consensus size: 617
27595684 ATGTATTTCT
27595694 AAACATTTTACACACTACGTTTGTTCTGAGAAGCTCAAAAGAGCTTAACGGAAACCCGTTAAGGT
1 AAACATTTTACACACTACGTTTGTTCTGAGAAGCTCAAAAGAGCTTAACGGAAACCCGTTAAGGT
*
27595759 TAAACGAAAACTCATATGAGTTAACGGAAGCTCGTGAGAGCTAAACGAAAAGTAAATACGAAAGT
66 TAAACGAAAACTCATATGAGTTAACGGAAGCTCGTGAGAGCTAAACGAAAAGTAAATACAAAAGT
27595824 TCGCAACAAATGCCGAACCTCGATTTACTTGGGTAATTTGTCGTCAATTCCTCGTTTGCACTGAA
131 TCGCAACAAATGCCGAACCTCGATTTACTTGGGTAATTTGTCGTCAATTCCTCGTTTGCACTGAA
27595889 TGACTGTACTCAATCCCGCGTTCCGTTTGCTTCGAACGTTCAATTCAATTTCATAGCTTTAAAAA
196 TGACTGTACTCAATCCCGCGTTCCGTTTGCTTCGAACGTTCAATTCAATTTCATAGCTTTAAAAA
27595954 TAATTTTATTTTCAACAAATGATATGAATAAATACATAATACTATTCATCAATTTAACATATAAT
261 TAATTTTATTTTCAACAAATGATATGAATAAATACATAATACTATTCATCAATTTAACATATAAT
*
27596019 ATTAAATTTCAACCATTCAAATTTACCTGGATTAAATTGTAGAATTTGTAGTAGTTCAGGGACTA
326 ATTAAATTTCAACCATTCAAAATTACCTGGATTAAATTGTAGAATTTGTAGTAGTTCAGGGACTA
** *
27596084 TTCTGTTAATTTCCCTTTTTTATGATTATCTATGGGATCTTGATTTAAAATGTTTATGACTCGAT
391 TTCTGTTAATTTCCCTTTTTTATGATTATCTACAGGATCTTGATTTAAAATGTTTACGACTCGAT
27596149 TTATAAAATTGAGGTCTCGATACCTCATTTTGTAAACCACTTAGCATAATAATTTCTTACGACAC
456 TTATAAAATTGAGGTCTCGATACCTCATTTTGTAAACCACTTAGCATAATAATTTCTTACGACAC
27596214 ACAAATTAATACTTCAAAAATTCTCCTAAAATCACATTTAGATCGTAAGTACTAAATAATAAAAT
521 ACAAATTAATACTTCAAAAATTCTCCTAAAATCACATTTAGATCGTAAGTACTAAATAATAAAAT
27596279 TCACAAGCTCACTTGTCAGATTTGGTGGTCTC
586 TCACAAGCTCACTTGTCAGATTTGGTGGTCTC
* *
27596311 AAACATTTTACACACTACGTTTGTTCTGAGAAGCTCAAAAGAGCTTAATGGAAACCCGTTAGGGT
1 AAACATTTTACACACTACGTTTGTTCTGAGAAGCTCAAAAGAGCTTAACGGAAACCCGTTAAGGT
*
27596376 TAAACGAAAACTCATATGAGTTAACGGAAGCTCGTGAGAGCTAAACGGAAAGTAAATACAAAAGT
66 TAAACGAAAACTCATATGAGTTAACGGAAGCTCGTGAGAGCTAAACGAAAAGTAAATACAAAAGT
27596441 TCGCAACAAATGCCGAACCTCGATTTACTTGGGTAATTTGTCGTCAATTCCTCGTTTGCACTGAA
131 TCGCAACAAATGCCGAACCTCGATTTACTTGGGTAATTTGTCGTCAATTCCTCGTTTGCACTGAA
*
27596506 TGACTGTACTCAATCCCGCGTTCCGTTTGCTTCGAACGTTCAATTCAATTTCATAGCTTTAACAA
196 TGACTGTACTCAATCCCGCGTTCCGTTTGCTTCGAACGTTCAATTCAATTTCATAGCTTTAAAAA
27596571 TAATTTTATTTTCAACAAATGATATGAATAAATACATAATACTATTCATCAATTTAACATATAAT
261 TAATTTTATTTTCAACAAATGATATGAATAAATACATAATACTATTCATCAATTTAACATATAAT
27596636 ATTAAATTTCAACCATTCAAAATTACCTGGATTAAATTGTAGAATTTGTAGTAGTTCAGGGACTA
326 ATTAAATTTCAACCATTCAAAATTACCTGGATTAAATTGTAGAATTTGTAGTAGTTCAGGGACTA
27596701 TTCTGTTAATTTCCCTTTTTTATGATTATCTACAGGATCTTGATTTAAAATGTTTACGACTCGAT
391 TTCTGTTAATTTCCCTTTTTTATGATTATCTACAGGATCTTGATTTAAAATGTTTACGACTCGAT
*
27596766 TTATAAAATTGAGGTCTCGATACCTCATTTTGTAAACCACTTAGCTTAATAATTTCTTACGACAC
456 TTATAAAATTGAGGTCTCGATACCTCATTTTGTAAACCACTTAGCATAATAATTTCTTACGACAC
27596831 ACAAATTAATACTTCAAAAATTCTCCTAAAATCACATTTAGATCGTAAGTACTAAATAATAAAAT
521 ACAAATTAATACTTCAAAAATTCTCCTAAAATCACATTTAGATCGTAAGTACTAAATAATAAAAT
27596896 TCACAAGCTCACTTGTCAGATTTGGTGGTCTC
586 TCACAAGCTCACTTGTCAGATTTGGTGGTCTC
27596928 GAACCACTAT
Statistics
Matches: 607, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
617 607 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.34
Consensus pattern (617 bp):
AAACATTTTACACACTACGTTTGTTCTGAGAAGCTCAAAAGAGCTTAACGGAAACCCGTTAAGGT
TAAACGAAAACTCATATGAGTTAACGGAAGCTCGTGAGAGCTAAACGAAAAGTAAATACAAAAGT
TCGCAACAAATGCCGAACCTCGATTTACTTGGGTAATTTGTCGTCAATTCCTCGTTTGCACTGAA
TGACTGTACTCAATCCCGCGTTCCGTTTGCTTCGAACGTTCAATTCAATTTCATAGCTTTAAAAA
TAATTTTATTTTCAACAAATGATATGAATAAATACATAATACTATTCATCAATTTAACATATAAT
ATTAAATTTCAACCATTCAAAATTACCTGGATTAAATTGTAGAATTTGTAGTAGTTCAGGGACTA
TTCTGTTAATTTCCCTTTTTTATGATTATCTACAGGATCTTGATTTAAAATGTTTACGACTCGAT
TTATAAAATTGAGGTCTCGATACCTCATTTTGTAAACCACTTAGCATAATAATTTCTTACGACAC
ACAAATTAATACTTCAAAAATTCTCCTAAAATCACATTTAGATCGTAAGTACTAAATAATAAAAT
TCACAAGCTCACTTGTCAGATTTGGTGGTCTC
Found at i:27609947 original size:73 final size:73
Alignment explanation
Indices: 27609828--27609988 Score: 270
Period size: 73 Copynumber: 2.2 Consensus size: 73
27609818 TTCACAAGCC
* * *
27609828 AAAATAGTCGTAGAAAATAACTAAACTAAGCATAAGGAACAATTAAAGAGAAGAATAGAAGAAGA
1 AAAATAGTCGTAGAAAACAACTAAAATAAGCATAAGGAACAATTAAAGAGAAGAAGAGAAGAAG-
27609893 T-AACAACT
65 TGAACAACT
*
27609901 AAAATAGTCATAGAAAACAACTAAAATAAGCATAAGGAACAATTAAAGAGAAGAAGAGAAGAAGT
1 AAAATAGTCGTAGAAAACAACTAAAATAAGCATAAGGAACAATTAAAGAGAAGAAGAGAAGAAGT
27609966 GAACAACT
66 GAACAACT
27609974 AAAATAGTCGTAGAA
1 AAAATAGTCGTAGAA
27609989 GAAAACAAGC
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
72 1 0.01
73 81 0.99
ACGTcount: A:0.58, C:0.09, G:0.17, T:0.16
Consensus pattern (73 bp):
AAAATAGTCGTAGAAAACAACTAAAATAAGCATAAGGAACAATTAAAGAGAAGAAGAGAAGAAGT
GAACAACT
Found at i:27612681 original size:27 final size:26
Alignment explanation
Indices: 27612638--27612739 Score: 93
Period size: 27 Copynumber: 3.9 Consensus size: 26
27612628 TCTTACGGAG
* *
27612638 TTTGCCAGAAAGACATTCCTTTCATA
1 TTTGCCACAAAGGCATTCCTTTCATA
27612664 TTCTGCCACAAAGGCATT-CTTTCCATA
1 TT-TGCCACAAAGGCATTCCTTT-CATA
* *
27612691 TTGTGCCACAAA-GCTGTTCCTCTCATA
1 TT-TGCCACAAAGGC-ATTCCTTTCATA
* *
27612718 -TTGCCACAAAGGCTTTTCTTTC
1 TTTGCCACAAAGGCATTCCTTTC
27612740 CTAGCGTGTT
Statistics
Matches: 63, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
25 15 0.24
26 11 0.17
27 34 0.54
28 3 0.05
ACGTcount: A:0.25, C:0.27, G:0.13, T:0.35
Consensus pattern (26 bp):
TTTGCCACAAAGGCATTCCTTTCATA
Found at i:27617315 original size:28 final size:28
Alignment explanation
Indices: 27617251--27617316 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
27617241 TGGTTTATTG
* *
27617251 ATTTATTTTGTTTTTTTTATTTTTCCTT
1 ATTTATTTTATTTTTTTTATTTTTCCTA
27617279 ATTTA-TTTATTTATTTTTATTTCTT-C-A
1 ATTTATTTTATTT-TTTTTATTT-TTCCTA
27617306 ATTTATTTTAT
1 ATTTATTTTAT
27617317 GGTTTTTCGT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 11 0.33
28 20 0.61
29 2 0.06
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.74
Consensus pattern (28 bp):
ATTTATTTTATTTTTTTTATTTTTCCTA
Found at i:27617601 original size:13 final size:13
Alignment explanation
Indices: 27617583--27617611 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
27617573 AGGTTTCGAT
27617583 AATAAATTTTCAA
1 AATAAATTTTCAA
27617596 AATAAATTTTCAA
1 AATAAATTTTCAA
27617609 AAT
1 AAT
27617612 TAATAAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (13 bp):
AATAAATTTTCAA
Found at i:27621321 original size:20 final size:19
Alignment explanation
Indices: 27621296--27621350 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
27621286 ACCAAGCAGG
*
27621296 GGTATCGATAATTTTTGAAA
1 GGTATCGATACTTTTT-AAA
*
27621316 GGTATCGATACTTTGTTAAG
1 GGTATCGATACTTT-TTAAA
27621336 GGTATCGATACTTTT
1 GGTATCGATACTTTT
27621351 ATTTTTGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 1 0.03
20 29 0.91
21 2 0.06
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42
Consensus pattern (19 bp):
GGTATCGATACTTTTTAAA
Found at i:27621417 original size:72 final size:73
Alignment explanation
Indices: 27621336--27621474 Score: 185
Period size: 73 Copynumber: 1.9 Consensus size: 73
27621326 CTTTGTTAAG
*
27621336 GGTATCGATACTTTT-ATTTTTGT-T-TAATTTTCCAAAATATCGAAGCTCAAATTGGTATTGAT
1 GGTATCGATACTTTTGATTTTT-TCTATAATTTT-CAAAATATCGAAGCTCAAATTGGTATCGAT
27621398 ACCAGGTCAT
64 ACCAGGTCAT
* * * **
27621408 GGTATCGATACTTTTGATTTTTTCTATAGTTTTCAAAATTTTGAAGCTCATTTTGGTATCGATAC
1 GGTATCGATACTTTTGATTTTTTCTATAATTTTCAAAATATCGAAGCTCAAATTGGTATCGATAC
27621473 CA
66 CA
27621475 ATCATAGGTA
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
72 16 0.28
73 36 0.62
74 6 0.10
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (73 bp):
GGTATCGATACTTTTGATTTTTTCTATAATTTTCAAAATATCGAAGCTCAAATTGGTATCGATAC
CAGGTCAT
Found at i:27628905 original size:27 final size:27
Alignment explanation
Indices: 27628863--27629062 Score: 170
Period size: 27 Copynumber: 7.4 Consensus size: 27
27628853 GTAATGGGCC
* *
27628863 TAAAATGACCGAAATACCCCCAAAGGG
1 TAAAATGACTGAAATACCCCCGAAGGG
* *
27628890 TAAAATGACTGGAATACCCCCGAGGGG
1 TAAAATGACTGAAATACCCCCGAAGGG
* * **
27628917 TAAAATAACTTAAATACCGTCGAAGGG
1 TAAAATGACTGAAATACCCCCGAAGGG
** * **
27628944 TAAAATGACCAAAATATCCCTAAAGGG
1 TAAAATGACTGAAATACCCCCGAAGGG
* *
27628971 TAAAATGA-TAGAAATACCCCTGAGGGG
1 TAAAATGACT-GAAATACCCCCGAAGGG
* ** * *
27628998 TATAATGAAAGAAATACACTCGAAGGG
1 TAAAATGACTGAAATACCCCCGAAGGG
* *
27629025 TAAAATGACCGAAATACTCCC-ATAGGG
1 TAAAATGACTGAAATACCCCCGA-AGGG
27629052 TAAAATGACTG
1 TAAAATGACTG
27629063 TTATGCCCCT
Statistics
Matches: 135, Mismatches: 35, Indels: 6
0.77 0.20 0.03
Matches are distributed among these distances:
26 1 0.01
27 134 0.99
ACGTcount: A:0.43, C:0.18, G:0.21, T:0.18
Consensus pattern (27 bp):
TAAAATGACTGAAATACCCCCGAAGGG
Found at i:27629072 original size:81 final size:81
Alignment explanation
Indices: 27628863--27629062 Score: 264
Period size: 81 Copynumber: 2.5 Consensus size: 81
27628853 GTAATGGGCC
* * * **
27628863 TAAAATGACCGAAATACCCCCAAAGGGTAAAATGACTGGAATACCCCCGAGGGGTAAAATAACTT
1 TAAAATGACCGAAATACTCCCAAAGGGTAAAATGACTGAAATACCCCTGAGGGGTAAAATAACAG
27628928 AAATACCGTCGAAGGG
66 AAATACCGTCGAAGGG
* *
27628944 TAAAATGACCAAAATA-TCCCTAAAGGGTAAAATGA-TAGAAATACCCCTGAGGGGTATAATGAA
1 TAAAATGACCGAAATACTCCC-AAAGGGTAAAATGACT-GAAATACCCCTGAGGGGTAAAAT-AA
27629007 -AGAAATACAC-TCGAAGGG
63 CAGAAATAC-CGTCGAAGGG
*
27629025 TAAAATGACCGAAATACTCCCATAGGGTAAAATGACTG
1 TAAAATGACCGAAATACTCCCAAAGGGTAAAATGACTG
27629063 TTATGCCCCT
Statistics
Matches: 104, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
80 4 0.04
81 92 0.88
82 8 0.08
ACGTcount: A:0.43, C:0.18, G:0.21, T:0.18
Consensus pattern (81 bp):
TAAAATGACCGAAATACTCCCAAAGGGTAAAATGACTGAAATACCCCTGAGGGGTAAAATAACAG
AAATACCGTCGAAGGG
Found at i:27629264 original size:26 final size:26
Alignment explanation
Indices: 27629235--27629311 Score: 109
Period size: 26 Copynumber: 3.0 Consensus size: 26
27629225 TTGCCACATA
*
27629235 TACTGTTACTGGCAGCTTTACTGCGT
1 TACTGTTACTGGCAGCTTTACTGCAT
* *
27629261 TACTGTTACTAGCAGCTTTGCTGCAT
1 TACTGTTACTGGCAGCTTTACTGCAT
* *
27629287 CACTATTACTGGCAGCTTTACTGCA
1 TACTGTTACTGGCAGCTTTACTGCA
27629312 ATATTGGTGT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.36
Consensus pattern (26 bp):
TACTGTTACTGGCAGCTTTACTGCAT
Found at i:27629466 original size:28 final size:29
Alignment explanation
Indices: 27629417--27629473 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
27629407 ACTGCATTGT
* *
27629417 ATTGATTACTGTATTGGACTAAGGTCCAC
1 ATTGATTACTGTAATGGACTAAGGCCCAC
*
27629446 ATTG-TTACTGTAATGGGCTAAGGCCCAC
1 ATTGATTACTGTAATGGACTAAGGCCCAC
27629474 GCCGTACTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (29 bp):
ATTGATTACTGTAATGGACTAAGGCCCAC
Found at i:27636410 original size:27 final size:27
Alignment explanation
Indices: 27636372--27636483 Score: 136
Period size: 27 Copynumber: 4.1 Consensus size: 27
27636362 AATGGGCCTG
* *
27636372 AAATGACTGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCAAAGGGTA
* *
27636399 AAATGATCGAAATACCC-CTAAAAGGTA
1 AAATGACCGAAATACCCTC-AAAGGGTA
* *
27636426 AAATGACCGAAATACCCTTAAAGGATA
1 AAATGACCGAAATACCCTCAAAGGGTA
* *
27636453 AAATGACCAAAATACCCCCAAAGGGTA
1 AAATGACCGAAATACCCTCAAAGGGTA
27636480 AAAT
1 AAAT
27636484 AACTATTATA
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
26 1 0.01
27 70 0.99
ACGTcount: A:0.47, C:0.20, G:0.16, T:0.17
Consensus pattern (27 bp):
AAATGACCGAAATACCCTCAAAGGGTA
Found at i:27636455 original size:54 final size:54
Alignment explanation
Indices: 27636372--27636483 Score: 152
Period size: 54 Copynumber: 2.1 Consensus size: 54
27636362 AATGGGCCTG
* * * * * *
27636372 AAATGACTGAAATACCCTCGAAGGGTAAAATGATCGAAATACCCCTAAAAGGTA
1 AAATGACCGAAATACCCTCAAAGGATAAAATGACCAAAATACCCCCAAAAGGTA
* *
27636426 AAATGACCGAAATACCCTTAAAGGATAAAATGACCAAAATACCCCCAAAGGGTA
1 AAATGACCGAAATACCCTCAAAGGATAAAATGACCAAAATACCCCCAAAAGGTA
27636480 AAAT
1 AAAT
27636484 AACTATTATA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.47, C:0.20, G:0.16, T:0.17
Consensus pattern (54 bp):
AAATGACCGAAATACCCTCAAAGGATAAAATGACCAAAATACCCCCAAAAGGTA
Found at i:27636678 original size:27 final size:27
Alignment explanation
Indices: 27636633--27636707 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 27
27636623 ATAGGGGAAG
*
27636633 TATACTG-TACTGGTGGCTTTGCCACA
1 TATACTGTTACTGGTAGCTTTGCCACA
** *
27636659 TATACTGTTACTGGTAGCTTTGCTGCG
1 TATACTGTTACTGGTAGCTTTGCCACA
* *
27636686 T-TATTGTTATTGGTAGCTTTGC
1 TATACTGTTACTGGTAGCTTTGC
27636708 TGCATGACTA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 26 0.62
27 16 0.38
ACGTcount: A:0.16, C:0.17, G:0.24, T:0.43
Consensus pattern (27 bp):
TATACTGTTACTGGTAGCTTTGCCACA
Found at i:27654182 original size:84 final size:84
Alignment explanation
Indices: 27653717--27654376 Score: 541
Period size: 84 Copynumber: 7.9 Consensus size: 84
27653707 ACGAATATTA
* * *** *
27653717 AAATTAAATAAAATCTGTTTCAAGATTTACTCCCATCATTTAAC-AGATTTTATTCG-----ATT
1 AAATTAAATAAAATCTGTTTCAGGATTTATTCCTGCCGTTTAACAAGATTTTATTCGATTTTATT
*
27653776 TTGTTTCTAAATT---A--
66 TTGTTTCCAAATTAGAATT
* * * * * * ** *
27653790 AAAGTGAATAAAATTTGTTTCGGGATTTATTCCGGCCGTTCAATGA-ATTTTATTCCAATTTTGA
1 AAATTAAATAAAATCTGTTTCAGGATTTATTCCTGCCGTTTAACAAGATTTTATT-CGATTTT-A
* * *
27653854 TTTTATTTCCAAAATGAGTATT
64 TTTTGTTTCC-AAATTAGAATT
* * ** * * * **
27653876 AAAATTAAAATAAAAATCCGTTT-TGAGATTTATTCCTATCATTCAAC-GGATTTTATTCTTTTT
1 -AAATT-AAAT-AAAATCTGTTTCAG-GATTTATTCCTGCCGTTTAACAAGATTTTATTC-GATT
* *
27653939 TTATTTTATTTCCAAATGAGAAATT
61 TTATTTTGTTTCCAAATTAG-AATT
* ** * * *
27653964 AAAGTTAAATAAAATCTGTTTCGGGATTTATTCCCACTGTTCAAC-GGATTTTATTAC-ATTTTG
1 AAA-TTAAATAAAATCTGTTTCAGGATTTATTCCTGCCGTTTAACAAGATTTTATT-CGATTTT-
* **
27654027 ATTTTGTTGCCAAAACAAGAAATT
63 ATTTTGTTTCC-AAATTAG-AATT
* * * * *
27654051 AAAATTAAATAAAATCT-ATTCTGGATTTATTCCGGCCATTTAGCAAGATTTTATTCGATTTTAT
1 -AAATTAAATAAAATCTGTTTCAGGATTTATTCCTGCCGTTTAACAAGATTTTATTCGATTTTAT
**
27654115 TTTGTTTTTAAATTAGAATT
65 TTTGTTTCCAAATTAGAATT
27654135 AAATTAAATAAAATCTGTTTCAGGATTTATTCCTGCCGTTTAACAAGATTTTATTCGATTTTATT
1 AAATTAAATAAAATCTGTTTCAGGATTTATTCCTGCCGTTTAACAAGATTTTATTCGATTTTATT
27654200 TTGTTTCCAAATTAGAATT
66 TTGTTTCCAAATTAGAATT
* * * **
27654219 AAATTAAATAAAATTTGTTTC-GAGATTTATTCCCGTCGTTTAACAA-ATTTT-TTTTATTTTAT
1 AAATTAAATAAAATCTGTTTCAG-GATTTATTCCTGCCGTTTAACAAGATTTTATTCGATTTTAT
27654281 TTTGTTTCCAAATTAGAATT
65 TTTGTTTCCAAATTAGAATT
* * * *
27654301 AAATTAAATAAAATTTGTTTCAGGATTTATTACTGCCGTTTAACAAGATTTTATTCGATATTGTT
1 AAATTAAATAAAATCTGTTTCAGGATTTATTCCTGCCGTTTAACAAGATTTTATTCGATTTTATT
27654366 TTGTTTCCAAA
66 TTGTTTCCAAA
27654377 CAAAGACTTA
Statistics
Matches: 479, Mismatches: 74, Indels: 57
0.79 0.12 0.09
Matches are distributed among these distances:
73 40 0.08
74 2 0.00
80 9 0.02
81 4 0.01
82 70 0.15
83 28 0.06
84 125 0.26
85 9 0.02
86 74 0.15
87 57 0.12
88 24 0.05
89 37 0.08
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.45
Consensus pattern (84 bp):
AAATTAAATAAAATCTGTTTCAGGATTTATTCCTGCCGTTTAACAAGATTTTATTCGATTTTATT
TTGTTTCCAAATTAGAATT
Found at i:27654312 original size:166 final size:171
Alignment explanation
Indices: 27653713--27654444 Score: 652
Period size: 166 Copynumber: 4.4 Consensus size: 171
27653703 CTAAACGAAT
* * * * **
27653713 ATTAAAATTAAATAAAATCTGTTTCAAGATTTACTCCCATCATTTAAC--A---GATTTTATTCG
1 ATTAAAATTAAATAAAATCTGTTTCGAGATTTATTCCCGTCATTTAACAAATTTTATTTTATTTT
* * * * * *
27653773 ATTTTGTTTCTAAATT---A--AAAGTGAATAAAATTTGTTTCGGGATTTATTCCGGCCGTTCAA
66 ATTTTGTTTCCAAATTAGAATTAAATTAAATAAAATCTGTTTCAGGATTTATTCCTGCCGTTCAA
** * * * * *
27653833 TGA-ATTTTATTCCAATTTTGATTTTATTTCCAAAATGAGT
131 CAAGATTTTATTACGATTTTGATTTTGTTTCCAAAATAAGA
* * ** * ** *
27653873 ATTAAAATTAAAATAAAAATCCGTTTTGAGATTTATTCCTATCATTCAACGGATTTTATTCTTTT
1 ATTAAAATT-AAAT-AAAATCTGTTTCGAGATTTATTCCCGTCATTTAACAAATTTTATT-TTAT
* * * ** *
27653938 TTTATTTTATTTCCAAATGAGAAATTAAAGTTAAATAAAATCTGTTTCGGGATTTATTCCCACTG
63 TTTATTTTGTTTCCAAATTAG-AATTAAA-TTAAATAAAATCTGTTTCAGGATTTATTCCTGCCG
* * *
27654003 TTCAAC-GGATTTTATTAC-ATTTTGATTTTGTTGCCAAAACAAGAA
126 TTCAACAAGATTTTATTACGATTTTGATTTTGTTTCCAAAATAAG-A
* * * * **
27654048 ATTAAAATTAAATAAAATCT-ATTCTG-GATTTATTCCGGCCATTTAGCAAGATTTTATTCGATT
1 ATTAAAATTAAATAAAATCTGTTTC-GAGATTTATTCCCGTCATTTAACAA-ATTTTATTTTATT
** *
27654111 TTATTTTGTTTTTAAATTAGAATTAAATTAAATAAAATCTGTTTCAGGATTTATTCCTGCCGTTT
64 TTATTTTGTTTCCAAATTAGAATTAAATTAAATAAAATCTGTTTCAGGATTTATTCCTGCCGTTC
*
27654176 AACAAGATTTTATT-CGATTTT-ATTTTGTTTCC-AAATTAGA
129 AACAAGATTTTATTACGATTTTGATTTTGTTTCCAAAATAAGA
* *
27654216 ATT-AAATTAAATAAAATTTGTTTCGAGATTTATTCCCGTCGTTTAACAAATTTT-TTTTATTTT
1 ATTAAAATTAAATAAAATCTGTTTCGAGATTTATTCCCGTCATTTAACAAATTTTATTTTATTTT
* * *
27654279 ATTTTGTTTCCAAATTAGAATTAAATTAAATAAAATTTGTTTCAGGATTTATTACTGCCGTTTAA
66 ATTTTGTTTCCAAATTAGAATTAAATTAAATAAAATCTGTTTCAGGATTTATTCCTGCCGTTCAA
*
27654344 CAAGATTTTATT-CGATATTG-TTTTGTTTCCAAACA-AAGA
131 CAAGATTTTATTACGATTTTGATTTTGTTTCCAAA-ATAAGA
* * * * * * * *
27654383 CTT--AATCAAAT-AATTCTATTTTGGGATTTATTCCCGTCATTTAACAGATTCTATTTTGATTT
1 ATTAAAATTAAATAAAATCTGTTTCGAGATTTATTCCCGTCATTTAACAAATTTTATTTT-ATTT
27654445 AATTATATAA
Statistics
Matches: 467, Mismatches: 77, Indels: 49
0.79 0.13 0.08
Matches are distributed among these distances:
160 9 0.02
161 4 0.01
162 29 0.06
164 1 0.00
165 33 0.07
166 107 0.23
167 35 0.07
168 44 0.09
169 5 0.01
170 47 0.10
171 21 0.04
172 37 0.08
173 15 0.03
174 28 0.06
175 52 0.11
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.45
Consensus pattern (171 bp):
ATTAAAATTAAATAAAATCTGTTTCGAGATTTATTCCCGTCATTTAACAAATTTTATTTTATTTT
ATTTTGTTTCCAAATTAGAATTAAATTAAATAAAATCTGTTTCAGGATTTATTCCTGCCGTTCAA
CAAGATTTTATTACGATTTTGATTTTGTTTCCAAAATAAGA
Found at i:27654455 original size:59 final size:59
Alignment explanation
Indices: 27654392--27654503 Score: 136
Period size: 59 Copynumber: 1.9 Consensus size: 59
27654382 ACTTAATCAA
* * *
27654392 ATAATTCTATTTTGGGATTTATTCCCGTCATTTAACAGATTCT-ATTTTGATTTAATTAT
1 ATAATTCTATTTCGGGATTTAATCCCGTCATTTAACAAATT-TGATTTTGATTTAATTAT
* * * * *
27654451 ATAATTTTGTTTCGTGATTTAATCCTGTCGTTTAACAAATTTGATTTTGATTT
1 ATAATTCTATTTCGGGATTTAATCCCGTCATTTAACAAATTTGATTTTGATTT
27654504 TGTTTTAGAA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
58 1 0.02
59 43 0.98
ACGTcount: A:0.26, C:0.11, G:0.12, T:0.52
Consensus pattern (59 bp):
ATAATTCTATTTCGGGATTTAATCCCGTCATTTAACAAATTTGATTTTGATTTAATTAT
Found at i:27660941 original size:34 final size:35
Alignment explanation
Indices: 27660875--27660941 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
27660865 CAAACACCAG
*
27660875 AAAATATTTTCTAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCTAGTAAATCATTTTACAGAAAAGT
* *
27660910 AAAACATTTTCTAG-AAATTATTTTACGGAAAA
1 AAAACATTTTCTAGTAAATCATTTTACAGAAAA
27660942 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.36
Consensus pattern (35 bp):
AAAACATTTTCTAGTAAATCATTTTACAGAAAAGT
Found at i:27661896 original size:13 final size:13
Alignment explanation
Indices: 27661880--27661945 Score: 89
Period size: 13 Copynumber: 5.1 Consensus size: 13
27661870 TTTAAACTAA
27661880 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
27661893 ACTTCTCAAAAGT
1 ACTTTTCAAAAGC
*
27661906 ACTTTTCCATAA-C
1 ACTTTT-CAAAAGC
27661919 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
27661932 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
27661945 A
1 A
27661946 ATGAAGAACT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
12 4 0.09
13 37 0.82
14 4 0.09
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:27663956 original size:234 final size:234
Alignment explanation
Indices: 27663547--27663998 Score: 895
Period size: 234 Copynumber: 1.9 Consensus size: 234
27663537 AATCTGAACT
27663547 AAACGATTTATTCACTTGTGTCTTGATCCGTAGAAATCCCTAAATTATGTTAATATCTCTTTCGA
1 AAACGATTTATTCACTTGTGTCTTGATCCGTAGAAATCCCTAAATTATGTTAATATCTCTTTCGA
*
27663612 GAGTAAGAACAACTGACTCTAGGTTGATTAATTGAAATCTCTTTCTAGTTAAAACATCTATCGTT
66 GAGTAAGAACAACTGACTCTAGGTTGATTAATTGAAATCTCTTTCTAGTTAAAACATCTATCGTC
27663677 GCATTAACTCGATCTATGGATTCCCCTATTAGATTTGACTCTAATCCGGTAGATTTATGTCGTCC
131 GCATTAACTCGATCTATGGATTCCCCTATTAGATTTGACTCTAATCCGGTAGATTTATGTCGTCC
27663742 TATTTCCAGGATTGCACGCAACTCCACCTATTATTATGA
196 TATTTCCAGGATTGCACGCAACTCCACCTATTATTATGA
27663781 AAACGATTTATTCACTTGTGTCTTGATCCGTAGAAATCCCTAAATTATGTTAATATCTCTTTCGA
1 AAACGATTTATTCACTTGTGTCTTGATCCGTAGAAATCCCTAAATTATGTTAATATCTCTTTCGA
27663846 GAGTAAGAACAACTGACTCTAGGTTGATTAATTGAAATCTCTTTCTAGTTAAAACATCTATCGTC
66 GAGTAAGAACAACTGACTCTAGGTTGATTAATTGAAATCTCTTTCTAGTTAAAACATCTATCGTC
27663911 GCATTAACTCGATCTATGGATTCCCCTATTAGATTTGACTCTAATCCGGTAGATTTATGTCGTCC
131 GCATTAACTCGATCTATGGATTCCCCTATTAGATTTGACTCTAATCCGGTAGATTTATGTCGTCC
27663976 TATTTCCAGGATTGCACGCAACT
196 TATTTCCAGGATTGCACGCAACT
27663999 TCACTCAATT
Statistics
Matches: 217, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
234 217 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (234 bp):
AAACGATTTATTCACTTGTGTCTTGATCCGTAGAAATCCCTAAATTATGTTAATATCTCTTTCGA
GAGTAAGAACAACTGACTCTAGGTTGATTAATTGAAATCTCTTTCTAGTTAAAACATCTATCGTC
GCATTAACTCGATCTATGGATTCCCCTATTAGATTTGACTCTAATCCGGTAGATTTATGTCGTCC
TATTTCCAGGATTGCACGCAACTCCACCTATTATTATGA
Found at i:27669998 original size:15 final size:15
Alignment explanation
Indices: 27669980--27670010 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27669970 TGGTTTAAAT
27669980 TTATATATTATCATC
1 TTATATATTATCATC
*
27669995 TTATATATTATTATC
1 TTATATATTATCATC
27670010 T
1 T
27670011 ATGTTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATATATTATCATC
Found at i:27670316 original size:23 final size:23
Alignment explanation
Indices: 27670290--27670351 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
27670280 ACATACTTAT
*
27670290 ATATATTCTTTATATTCTCAAAA
1 ATATATTCTTTATATTCACAAAA
* * * *
27670313 ATATTTTTTTTATAATTCACATAC
1 ATATATTCTTTAT-ATTCACAAAA
27670337 ATATATTC-TTATATT
1 ATATATTCTTTATATT
27670352 ATTACAATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
22 3 0.10
23 15 0.48
24 13 0.42
ACGTcount: A:0.35, C:0.11, G:0.00, T:0.53
Consensus pattern (23 bp):
ATATATTCTTTATATTCACAAAA
Found at i:27670425 original size:24 final size:22
Alignment explanation
Indices: 27670382--27670425 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
27670372 ATACACGCAC
*
27670382 ATACTTACATTTTTATTTTATA
1 ATACTTACATTTTTAATTTATA
27670404 ATACTTACAGATTTTTAATTTA
1 ATACTTAC--ATTTTTAATTTA
27670426 ATATATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
24 11 0.58
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (22 bp):
ATACTTACATTTTTAATTTATA
Found at i:27671013 original size:107 final size:107
Alignment explanation
Indices: 27670735--27671141 Score: 574
Period size: 103 Copynumber: 3.9 Consensus size: 107
27670725 AGGTTTTTCT
27670735 AAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATT
1 AAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATT
*
27670800 TCTCGTTCGACCAAATAGCCAAATATCATTTTTAAACTTTTA
66 TCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAACTTTTA
*
27670842 AAAT----CAATATTTCGCGTTTGAAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATT
1 AAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATT
*
27670903 TCTCCTTCGACCAAATAGCCAAATATCCTTTTTAAACTTTTA
66 TCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAACTTTTA
* * * * * *
27670945 AAATAAGGCAATATTTAGCGTTTGGAAAATCAAGGAAACGTACCCTAACGTGTTGGGTTTCGACT
1 AAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATT
* **
27671010 TCTCGTTTGACCAAATAGCCAAATATCC-TTTTAAACTTTCG
66 TCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAACTTTTA
* * * * * * * * *
27671051 AAGTGAGGCAATATTT-GCATTTGGAAATTTGAGAGAACGTGCTCTAACGTGCTGGGTCTCAATT
1 AAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATT
*
27671115 TCTCGTTTGACCAAATAGCCAAATATC
66 TCTCGTTCGACCAAATAGCCAAATATC
27671142 TTCTTAACTT
Statistics
Matches: 268, Mismatches: 28, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
103 100 0.37
105 63 0.24
106 25 0.09
107 80 0.30
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (107 bp):
AAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATT
TCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAACTTTTA
Found at i:27675879 original size:41 final size:40
Alignment explanation
Indices: 27675774--27675881 Score: 99
Period size: 41 Copynumber: 2.6 Consensus size: 40
27675764 ACCGGCATGT
* ** * *
27675774 AGCCTACTAGGCCTGAAGCCTGATTTAGTTCACCGGCATAA
1 AGCCTACTAGGCATG-AGCCTGAAATAATTCACCAGCATAA
* * * * *
27675815 AGCCTGCTAGACATAAAGTCTGAAATAATTCACCAGCATTA
1 AGCCTACTAGGCAT-GAGCCTGAAATAATTCACCAGCATAA
27675856 AGCCTACTAGGCATCGAGCCTGAAAT
1 AGCCTACTAGGCAT-GAGCCTGAAAT
27675882 CACAGATACG
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.23
Consensus pattern (40 bp):
AGCCTACTAGGCATGAGCCTGAAATAATTCACCAGCATAA
Found at i:27702630 original size:29 final size:30
Alignment explanation
Indices: 27702571--27702628 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
27702561 TCCGAGCCTT
*
27702571 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
27702601 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
27702629 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:27702857 original size:13 final size:13
Alignment explanation
Indices: 27702839--27702870 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
27702829 TTTCCAGCAA
27702839 TTATGAATTTATT
1 TTATGAATTTATT
27702852 TTATGAATTTATT
1 TTATGAATTTATT
*
27702865 TGATGA
1 TTATGA
27702871 TGATCTAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:27703078 original size:50 final size:50
Alignment explanation
Indices: 27702965--27703162 Score: 252
Period size: 50 Copynumber: 3.8 Consensus size: 50
27702955 ATTTGGGTAA
* *
27702965 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAGA-C--G
* *
27703021 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
* * *
27703071 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
* * *
27703121 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
27703163 TGTTATTATC
Statistics
Matches: 130, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
50 85 0.65
52 1 0.01
53 3 0.02
55 2 0.02
56 39 0.30
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
Found at i:27703164 original size:106 final size:104
Alignment explanation
Indices: 27702965--27703155 Score: 300
Period size: 106 Copynumber: 1.9 Consensus size: 104
27702955 ATTTGGGTAA
27702965 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CCTT-AGATCATGAGAGGTCCC
*
27703030 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
64 CTATAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
27703071 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C-T-GA-GATGAGAGGTCCCCT
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCTTAGATCATGAGAGGTCCCCT
27703132 ATAAGACCATGTCTGGGACATGGC
66 ATAAGACCATGTCTGGGACATGGC
27703156 TTTGGCATGT
Statistics
Matches: 81, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
100 37 0.46
101 2 0.02
103 1 0.01
104 1 0.01
106 40 0.49
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (104 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCTTAGATCATGAGAGGTCCCCT
ATAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:27710169 original size:29 final size:30
Alignment explanation
Indices: 27710110--27710167 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
27710100 TCCGAGCCTT
*
27710110 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
27710140 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
27710168 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:27710397 original size:13 final size:13
Alignment explanation
Indices: 27710379--27710410 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
27710369 TTTCCAGCAA
27710379 TTATGAATTTATT
1 TTATGAATTTATT
27710392 TTATGAATTTATT
1 TTATGAATTTATT
*
27710405 TGATGA
1 TTATGA
27710411 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:27710618 original size:50 final size:50
Alignment explanation
Indices: 27710505--27710746 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
27710495 ATTTGGGTAA
* * *
27710505 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
27710561 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
27710611 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
27710661 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
27710711 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
27710747 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:27710694 original size:100 final size:103
Alignment explanation
Indices: 27710505--27710754 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
27710495 ATTTGGGTAA
27710505 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
27710570 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
27710611 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
27710673 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
27710711 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
27710755 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:27716625 original size:14 final size:15
Alignment explanation
Indices: 27716578--27716625 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 15
27716568 ATGTGTTAAA
*
27716578 ATATA-TATATTATT
1 ATATATTATAGTATT
27716592 ATTATATTATAGTA-T
1 A-TATATTATAGTATT
27716607 ATATATTATA-TATT
1 ATATATTATAGTATT
27716621 ATATA
1 ATATA
27716626 AATAAGTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 2 0.07
14 16 0.53
15 6 0.20
16 6 0.20
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATATTATAGTATT
Found at i:27717961 original size:18 final size:19
Alignment explanation
Indices: 27717938--27717976 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
27717928 ATATATAGAT
27717938 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
27717956 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
27717975 AT
1 AT
27717977 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:27718493 original size:18 final size:19
Alignment explanation
Indices: 27718472--27718512 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
27718462 AATGAAATGA
27718472 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
27718490 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
27718509 GAAA
1 GAAA
27718513 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:27719603 original size:26 final size:26
Alignment explanation
Indices: 27719574--27719678 Score: 128
Period size: 26 Copynumber: 4.2 Consensus size: 26
27719564 TGGTACAGAT
27719574 TGATAATGGGTTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
*
27719600 TGATAATGGATTAGGT-AATATT-CA
1 TGATAATGGGTTAGGTAAATATTCCA
*
27719624 TGATAAT-GGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
* * *
27719649 TGATAA-GGTTTAGGGTAAATGTTCCG
1 TGATAATGGGTTA-GGTAAATATTCCA
27719675 TGAT
1 TGAT
27719679 GGCATTTCAT
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
23 7 0.10
24 14 0.20
25 18 0.26
26 31 0.44
ACGTcount: A:0.32, C:0.07, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATATTCCA
Found at i:27721399 original size:52 final size:52
Alignment explanation
Indices: 27721286--27721424 Score: 190
Period size: 52 Copynumber: 2.6 Consensus size: 52
27721276 GGAAGCGTCT
*
27721286 TGGTGGCTATGCCACAAATTATTTGATCTGGTGGCTCTGCCACATATATCTGTTC
1 TGGTGGCTATG-CAC--ATTATCTGATCTGGTGGCTCTGCCACATATATCTGTTC
27721341 TGGTGGCTATGCACGATTATCTGATCTGGTGGCTCTG-CACATATATCTGTTC
1 TGGTGGCTATGCAC-ATTATCTGATCTGGTGGCTCTGCCACATATATCTGTTC
* *
27721393 TGGTGGCTCTGCAACAATATCTGTATCTGGTG
1 TGGTGGCTATGC-ACATTATCTG-ATCTGGTG
27721425 ACTTCGTCAC
Statistics
Matches: 78, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
52 33 0.42
53 31 0.40
54 3 0.04
55 11 0.14
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (52 bp):
TGGTGGCTATGCACATTATCTGATCTGGTGGCTCTGCCACATATATCTGTTC
Found at i:27721436 original size:27 final size:26
Alignment explanation
Indices: 27721311--27721442 Score: 146
Period size: 26 Copynumber: 5.0 Consensus size: 26
27721301 AAATTATTTG
27721311 ATCTGGTGGCTCTGCCACATATATCTGT
1 ATCTGGTGGCTCTG-CACA-ATATCTGT
* *
27721339 -TCTGGTGGCTATGCACGATTATCTG-
1 ATCTGGTGGCTCTGCAC-AATATCTGT
27721364 ATCTGGTGGCTCTGCACATATATCTGT
1 ATCTGGTGGCTCTGCACA-ATATCTGT
27721391 -TCTGGTGGCTCTGCAACAATATCTGT
1 ATCTGGTGGCTCTGC-ACAATATCTGT
*
27721417 ATCTGGTGACT-TCGTCACAATATCTG
1 ATCTGGTGGCTCT-G-CACAATATCTG
27721443 GCAGCCTCGC
Statistics
Matches: 91, Mismatches: 5, Indels: 17
0.81 0.04 0.15
Matches are distributed among these distances:
25 1 0.01
26 53 0.58
27 36 0.40
28 1 0.01
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.36
Consensus pattern (26 bp):
ATCTGGTGGCTCTGCACAATATCTGT
Found at i:27725558 original size:79 final size:79
Alignment explanation
Indices: 27725459--27725678 Score: 205
Period size: 79 Copynumber: 2.8 Consensus size: 79
27725449 CTCGTTCAAG
* * ** * *
27725459 TGCCTTCGGGACATAGCCCGGTCATAGTAACTCATTC-AATGCCTTCGGGACTTAACCCGGATTT
1 TGCCTTCGGGACATAACCCGG-AATAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGA-AT
*
27725523 TAA-AACTCGCACGAA
64 TAATAACTCGCACAAA
* * * *
27725538 TGCCTTCGGGACTTAACCCGGAATTGTATCTCGCACAAAGGCCTTCGGGACTTAACCCGGAATTA
1 TGCCTTCGGGACATAACCCGGAATAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGAATTA
27725603 ATAACTCGCACAAA
66 ATAACTCGCACAAA
* * ** * * *
27725617 TACCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGA-CATAACCCGGA-ATAGTAACTCA-CACAAAGGCCTTCGGGACTTAACCCGGA
27725679 CAGCATTCAA
Statistics
Matches: 116, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
78 16 0.14
79 68 0.59
80 26 0.22
81 6 0.05
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
TGCCTTCGGGACATAACCCGGAATAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGAATTA
ATAACTCGCACAAA
Found at i:27725638 original size:40 final size:40
Alignment explanation
Indices: 27725496--27725678 Score: 187
Period size: 40 Copynumber: 4.6 Consensus size: 40
27725486 TAACTCATTC
* *
27725496 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
27725536 AATGCCTTCGGGACTTAACCCGGAATT-GTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
27725575 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
27725615 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
27725656 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
27725679 CAGCATTCAA
Statistics
Matches: 120, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
39 41 0.34
40 68 0.57
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:27733456 original size:79 final size:80
Alignment explanation
Indices: 27733357--27733577 Score: 202
Period size: 80 Copynumber: 2.8 Consensus size: 80
27733347 CTCGTTCAAG
* * ** * *
27733357 TGCCTTCGGGACATAGCCCGGTCA-TAGTAACTCATTC-AATGCCTTCGGGACTTAACCCGGATT
1 TGCCTTCGGGACATAACCCGG-AATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGA-A
*
27733420 TTAA-AACTCGCACGAA
64 TTAATAACTCGCACAAA
* * *
27733436 TGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAGGCCTTCGGGACTTAACCCGGAATT
1 TGCCTTCGGGACATAACCCGGAATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGAATT
27733501 AATAACTCGCACAAA
66 AATAACTCGCACAAA
* * ** * * *
27733516 TACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGA-CATAACCCGGAAT-TAGTAACTCA-CACAAAGGCCTTCGGGACTTAACCCGGA
27733578 CAGCATTCAA
Statistics
Matches: 118, Mismatches: 18, Indels: 11
0.80 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 37 0.31
80 74 0.63
81 6 0.05
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
TGCCTTCGGGACATAACCCGGAATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGAATT
AATAACTCGCACAAA
Found at i:27733508 original size:80 final size:80
Alignment explanation
Indices: 27733397--27733577 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
27733387 CTCATTCAAT
* * *
27733397 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
27733460 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
27733476 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
27733540 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
27733557 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
27733578 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:27733537 original size:40 final size:40
Alignment explanation
Indices: 27733394--27733577 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
27733384 TAACTCATTC
* *
27733394 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
27733434 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
27733474 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
27733514 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
27733555 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
27733578 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:27744071 original size:19 final size:19
Alignment explanation
Indices: 27744043--27744079 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
27744033 TACTCTTCCT
*
27744043 ATCAATTAAAAAAAATTTG
1 ATCAACTAAAAAAAATTTG
*
27744062 ATCAACTAAAAATAATTT
1 ATCAACTAAAAAAAATTT
27744080 CACAAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.08, G:0.03, T:0.32
Consensus pattern (19 bp):
ATCAACTAAAAAAAATTTG
Found at i:27744472 original size:94 final size:100
Alignment explanation
Indices: 27744367--27744613 Score: 290
Period size: 110 Copynumber: 2.4 Consensus size: 100
27744357 TAAGATTTTT
* *
27744367 CAAAAACATTAATAAAATAAATTAATCAAACCTAATA-AAAC-A-C-A-ACAACAAAAATAA-TT
1 CAAAAATATTAATAAAACAAATTAATCAAACCTAATACAAACAACCAACACAACAAAAATAATTT
* *
27744426 TTTCCTTCAATACGAAAAACTAATATAAGATACCA
66 TTTCCTTAAATACAAAAAACTAATATAAGATACCA
*
27744461 CAAAAATATTAATAAAACAAATTAATAAAACCTTAATACAAACTTAAACCTAATAAAACACAACA
1 CAAAAATATTAATAAAACAAATTAATCAAACC-TAATACAAAC---AACC------AACACAACA
27744526 AAAATAATTTTTTCCTTAAATACAAAAAACTAATATAAGATACCA
56 AAAATAATTTTTTCCTTAAATACAAAAAACTAATATAAGATACCA
*
27744571 CAAAAATATTAATAAAACAAATTAATCATACCTTTAATACAAA
1 CAAAAATATTAATAAAACAAATTAATCAAACC--TAATACAAA
27744614 TCTAAAATTA
Statistics
Matches: 129, Mismatches: 7, Indels: 17
0.84 0.05 0.11
Matches are distributed among these distances:
94 29 0.22
95 5 0.04
96 4 0.03
100 1 0.01
101 1 0.01
108 1 0.01
109 13 0.10
110 65 0.50
111 10 0.08
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (100 bp):
CAAAAATATTAATAAAACAAATTAATCAAACCTAATACAAACAACCAACACAACAAAAATAATTT
TTTCCTTAAATACAAAAAACTAATATAAGATACCA
Found at i:27744558 original size:110 final size:111
Alignment explanation
Indices: 27744394--27744826 Score: 500
Period size: 113 Copynumber: 3.9 Consensus size: 111
27744384 TAAATTAATC
* *
27744394 AAACCTAATAAAACACAACAACAAAAATAATTTTTCCTTCAATACGAAAAACTAATATAAGATAC
1 AAACCTAATAAAACACAACAACAAAAAT-ATTTTTCCTTAAATACAAAAAACTAATATAAGATAC
* * *
27744459 CACAAAAATATTAATAAAACAAATTAATAAAACCTTAATACAAACTT
65 CACAAAAACATTAATAAAACAAATTAATCATACCTTAATACAAACTT
27744506 AAACCTAATAAAACACAACAA-AAATAAT-TTTTTCCTTAAATACAAAAAACTAATATAAGATAC
1 AAACCTAATAAAACACAACAACAAA-AATATTTTTCCTTAAATACAAAAAACTAATATAAGATAC
*
27744569 CACAAAAATATTAATAAAACAAATTAATCATACCTTTAATACAAA-TCT
65 CACAAAAACATTAATAAAACAAATTAATCATACC-TTAATACAAACT-T
** * ** * *
27744617 AAAATTAGTAAAACACAACAA-AAAAAT-TCCTTCCCCTTAAATACAAAAAAGTTGATATAAGAT
1 AAACCTAATAAAACACAACAACAAAAATAT--TTTTCCTTAAATACAAAAAA-CTAATATAAGAT
* * * *
27744680 ACAACAAAAGCATTAATAAAACAAACTAATCATACATTTAATACAAACTT
63 ACCACAAAAACATTAATAAAACAAATTAATCATAC-CTTAATACAAACTT
* * * ** *
27744730 AAATCTAATAAAACACAACAACAAAAA-ATCTTTCTTTTAAATACAAAAAACTGTTATAAGATAT
1 AAACCTAATAAAACACAACAACAAAAATATTTTTC-CTTAAATACAAAAAACTAATATAAGATAC
* * * *
27744794 CATAAAAACAATAGTAAAACAAATAAATCATAC
65 CACAAAAACATTAATAAAACAAATTAATCATAC
27744827 TTTTTTTTGT
Statistics
Matches: 277, Mismatches: 33, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
110 70 0.25
111 35 0.13
112 81 0.29
113 84 0.30
114 7 0.03
ACGTcount: A:0.56, C:0.16, G:0.03, T:0.25
Consensus pattern (111 bp):
AAACCTAATAAAACACAACAACAAAAATATTTTTCCTTAAATACAAAAAACTAATATAAGATACC
ACAAAAACATTAATAAAACAAATTAATCATACCTTAATACAAACTT
Found at i:27745512 original size:24 final size:24
Alignment explanation
Indices: 27745485--27745536 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
27745475 TCTCAAATAG
* *
27745485 ACAAGACCAATCAACCCCACTCGA
1 ACAACACCAATCAACCCCACTCAA
27745509 ACAACACCAATCAACCCCACTCAA
1 ACAACACCAATCAACCCCACTCAA
27745533 ACAA
1 ACAA
27745537 AATGAGTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.46, C:0.42, G:0.04, T:0.08
Consensus pattern (24 bp):
ACAACACCAATCAACCCCACTCAA
Found at i:27746798 original size:17 final size:18
Alignment explanation
Indices: 27746768--27746813 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
27746758 ATTTAAATTG
27746768 CGGTCGCGGTCGCGTTTT
1 CGGTCGCGGTCGCGTTTT
27746786 CGGTCGC-GTCGCG-TTT
1 CGGTCGCGGTCGCGTTTT
27746802 --GTCGCGGTCGCG
1 CGGTCGCGGTCGCG
27746814 GACATAACGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
16 3 0.11
17 6 0.22
18 7 0.26
ACGTcount: A:0.00, C:0.30, G:0.41, T:0.28
Consensus pattern (18 bp):
CGGTCGCGGTCGCGTTTT
Found at i:27754673 original size:30 final size:30
Alignment explanation
Indices: 27754637--27754694 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
27754627 GCATTTGTAC
27754637 AAGACCATAAGTACCAATTTGCTATGACAT
1 AAGACCATAAGTACCAATTTGCTATGACAT
27754667 AAGACCATAAGTACCAATTTGCTATGAC
1 AAGACCATAAGTACCAATTTGCTATGAC
27754695 TGGCATGGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.26
Consensus pattern (30 bp):
AAGACCATAAGTACCAATTTGCTATGACAT
Found at i:27755875 original size:14 final size:14
Alignment explanation
Indices: 27755853--27755892 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
27755843 ACAGAAAAGT
* *
27755853 AAAATATTTTCCAG
1 AAAACATTTTACAG
*
27755867 AAAACATTTTACGG
1 AAAACATTTTACAG
27755881 AAAACATTTTAC
1 AAAACATTTTAC
27755893 TGGCAATCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:27755884 original size:34 final size:35
Alignment explanation
Indices: 27755818--27755884 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
27755808 CAAACACCAG
*
27755818 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAAACATTTTACAGAAAAGT
*
27755853 AAAATATTTTCCAG-AAAACATTTTACGGAAAA
1 AAAATATTTTCCAGTAAAACATTTTACAGAAAA
27755885 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 16 0.53
35 14 0.47
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAAACATTTTACAGAAAAGT
Found at i:27758053 original size:27 final size:27
Alignment explanation
Indices: 27758022--27758079 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
27758012 TAAAATTATT
* *
27758022 ATTTAAAAGAAATACATTTTTAATAAA
1 ATTTAAAAGAAATACAATTCTAATAAA
* **
27758049 ATTTAAAATAAATTTAATTCTAATAAA
1 ATTTAAAAGAAATACAATTCTAATAAA
27758076 ATTT
1 ATTT
27758080 CTACTAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (27 bp):
ATTTAAAAGAAATACAATTCTAATAAA
Found at i:27766336 original size:33 final size:32
Alignment explanation
Indices: 27766264--27766339 Score: 80
Period size: 33 Copynumber: 2.3 Consensus size: 32
27766254 ATGTTTAAAT
* * *
27766264 GTAAGACCATAACTGGGCTATGACATTTTAAT
1 GTAAGACCATAACTGGGCTATGACACTTGAAC
* * *
27766296 GAAAAGACCATAACTGGGTTATGGCACCTTGAAC
1 G-TAAGACCATAACTGGGCTATGACA-CTTGAAC
27766330 GTAAGACCAT
1 GTAAGACCAT
27766340 GGTTGGACCA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
32 1 0.03
33 29 0.83
34 5 0.14
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (32 bp):
GTAAGACCATAACTGGGCTATGACACTTGAAC
Found at i:27766440 original size:33 final size:32
Alignment explanation
Indices: 27766368--27766444 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 32
27766358 TAGATATATG
* **
27766368 TGTAAGACCATAACTGGGCTATGGCATTCTGA
1 TGTAAGACCATAACTGGGCTATGGCATACAAA
* *
27766400 TGATAAGATCATAACTGGGTTATGGCACTACAAA
1 TG-TAAGACCATAACTGGGCTATGGCA-TACAAA
27766434 TGTAAGACCAT
1 TGTAAGACCAT
27766445 GGCAAGGCCA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
32 2 0.05
33 30 0.81
34 5 0.14
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (32 bp):
TGTAAGACCATAACTGGGCTATGGCATACAAA
Found at i:27766456 original size:105 final size:105
Alignment explanation
Indices: 27766263--27766456 Score: 266
Period size: 105 Copynumber: 1.8 Consensus size: 105
27766253 AATGTTTAAA
* **
27766263 TGTAAGACCATAACTGGGCTATGACATTTTAATGAAAAGACCATAACTGGGTTATGGCACCTTGA
1 TGTAAGACCATAACTGGGCTATGACATTCTAATGAAAAGACCATAACTGGGTTATGGCACCTCAA
**
27766328 ACGTAAGACCATGGTTGGACCATGGCATTATAGATATATG
66 ACGTAAGACCATGGAAGGACCATGGCATTATAGATATATG
* * * *
27766368 TGTAAGACCATAACTGGGCTATGGCATTCTGATGATAAGATCATAACTGGGTTATGGCA-CTACA
1 TGTAAGACCATAACTGGGCTATGACATTCTAATGAAAAGACCATAACTGGGTTATGGCACCT-CA
*
27766432 AATGTAAGACCATGGCAAGG-CCATG
65 AACGTAAGACCATGG-AAGGACCATG
27766457 ACAATGCATG
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
104 2 0.03
105 73 0.95
106 2 0.03
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (105 bp):
TGTAAGACCATAACTGGGCTATGACATTCTAATGAAAAGACCATAACTGGGTTATGGCACCTCAA
ACGTAAGACCATGGAAGGACCATGGCATTATAGATATATG
Found at i:27767652 original size:16 final size:17
Alignment explanation
Indices: 27767631--27767663 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
27767621 AAAGGGTCAG
27767631 AAAAAGA-AAAATTACA
1 AAAAAGACAAAATTACA
*
27767647 AAAAAGACCAAATTACA
1 AAAAAGACAAAATTACA
27767664 TAATGTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.70, C:0.12, G:0.06, T:0.12
Consensus pattern (17 bp):
AAAAAGACAAAATTACA
Found at i:27773350 original size:24 final size:23
Alignment explanation
Indices: 27773320--27773379 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
27773310 TTATATATAA
27773320 TAATTATTTTATAAAAAATAATT
1 TAATTATTTTATAAAAAATAATT
* *
27773343 TAATT-TATATATCAAAATATAATT
1 TAATTAT-TTTAT-AAAAAATAATT
*
27773367 TAATAATTTTATA
1 TAATTATTTTATA
27773380 TTTGAGTTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
22 1 0.03
23 10 0.33
24 18 0.60
25 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TAATTATTTTATAAAAAATAATT
Found at i:27778654 original size:13 final size:14
Alignment explanation
Indices: 27778634--27778673 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
27778624 GCCTTATTAT
27778634 TCGAATTATAAAGG
1 TCGAATTATAAAGG
*
27778648 T-GAATTAT-AATG
1 TCGAATTATAAAGG
27778660 TCGAATTATAAAGG
1 TCGAATTATAAAGG
27778674 CACTCCGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 4 0.18
13 14 0.64
14 4 0.18
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.33
Consensus pattern (14 bp):
TCGAATTATAAAGG
Found at i:27780869 original size:28 final size:28
Alignment explanation
Indices: 27780828--27780882 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
27780818 ATGACTGTAT
* *
27780828 AAAATTTTTTAATAAATAAAA-AATATAC
1 AAAATTATTAAAT-AATAAAATAATATAC
*
27780856 AAAATTATTAAATATTAAAATAATATA
1 AAAATTATTAAATAATAAAATAATATA
27780883 ATATAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (28 bp):
AAAATTATTAAATAATAAAATAATATAC
Found at i:27782014 original size:30 final size:31
Alignment explanation
Indices: 27781980--27782043 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
27781970 ATTTATTTTA
27781980 TTGTTAA-TTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTTGTTATTATTTTAAAGGCAT
* *
27782010 TTGTTAATTTTTTTTATTATTTTAGAGGCAT
1 TTGTTAATTTTTGTTATTATTTTAAAGGCAT
27782041 TTG
1 TTG
27782044 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 7 0.23
31 24 0.77
ACGTcount: A:0.23, C:0.03, G:0.14, T:0.59
Consensus pattern (31 bp):
TTGTTAATTTTTGTTATTATTTTAAAGGCAT
Found at i:27782327 original size:5 final size:5
Alignment explanation
Indices: 27782317--27782341 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
27782307 TAGTTGAGCT
27782317 CGACC CGACC CGACC CGACC CGACC
1 CGACC CGACC CGACC CGACC CGACC
27782342 TATGAGCACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.60, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:27782679 original size:34 final size:33
Alignment explanation
Indices: 27782635--27782748 Score: 126
Period size: 34 Copynumber: 3.5 Consensus size: 33
27782625 ACAATATTTA
*
27782635 AAAAAAACTAAATCCAAATTTAATTAATTTTCTT
1 AAAAACACTAAATCCAAATTTAATTAATTTT-TT
*
27782669 AAAAACACTAAAACCAAATTTAATTAATTTATTT
1 AAAAACACTAAATCCAAATTTAATTAATTT-TTT
* * * *
27782703 AAAATCCCTAAA-CCGTAATTTAATTAA--TTTA
1 AAAAACACTAAATCC-AAATTTAATTAATTTTTT
27782734 AAAAACACTAAATCC
1 AAAAACACTAAATCC
27782749 TGATTTATTT
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
31 12 0.17
32 3 0.04
33 2 0.03
34 51 0.74
35 1 0.01
ACGTcount: A:0.51, C:0.15, G:0.01, T:0.33
Consensus pattern (33 bp):
AAAAACACTAAATCCAAATTTAATTAATTTTTT
Found at i:27782869 original size:15 final size:15
Alignment explanation
Indices: 27782846--27782884 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
27782836 TTATTCTAAC
* * *
27782846 AAAATCCTAACCCTA
1 AAAACCCTAAACCAA
27782861 AAAACCCTAAACCAA
1 AAAACCCTAAACCAA
27782876 AAAACCCTA
1 AAAACCCTA
27782885 GGGACTAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.54, C:0.33, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAACCCTAAACCAA
Found at i:27791558 original size:17 final size:16
Alignment explanation
Indices: 27791524--27791573 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
27791514 TTGTAAAATA
27791524 AAAACAAATAACAA-A-
1 AAAACAAATAA-AACAT
*
27791539 AAATCAAATAAAACAT
1 AAAACAAATAAAACAT
*
27791555 AAAACTAAATAAAATAT
1 AAAAC-AAATAAAACAT
27791572 AA
1 AA
27791574 GTAATTCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 2 0.07
15 11 0.38
16 4 0.14
17 12 0.41
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAACAAATAAAACAT
Found at i:27791835 original size:30 final size:30
Alignment explanation
Indices: 27791801--27791861 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
27791791 TCCATGTGCT
* *
27791801 AAGCCATGTGAGCCATATGGCAGTGTGGCC
1 AAGCCATGTGAGCCACATGACAGTGTGGCC
*
27791831 AAGCCATGTGAGCCACATGACCGTGTGGCC
1 AAGCCATGTGAGCCACATGACAGTGTGGCC
27791861 A
1 A
27791862 GACCGTGTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.26, G:0.31, T:0.18
Consensus pattern (30 bp):
AAGCCATGTGAGCCACATGACAGTGTGGCC
Found at i:27792177 original size:13 final size:13
Alignment explanation
Indices: 27792159--27792201 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
27792149 GACACACCCA
*
27792159 TGTGTCCAAACCG
1 TGTGTCCAAGCCG
*
27792172 TGTGTCCAAGTCG
1 TGTGTCCAAGCCG
27792185 TGTGTCCAAGCCG
1 TGTGTCCAAGCCG
27792198 TGTG
1 TGTG
27792202 AATTCCTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (13 bp):
TGTGTCCAAGCCG
Found at i:27796387 original size:18 final size:19
Alignment explanation
Indices: 27796366--27796402 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
27796356 CACTGCTTGT
*
27796366 GTTAGAATTAC-TGAAAAG
1 GTTACAATTACATGAAAAG
27796384 GTTACAATTACATGAAAAG
1 GTTACAATTACATGAAAAG
27796403 ACACTCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.46, C:0.08, G:0.19, T:0.27
Consensus pattern (19 bp):
GTTACAATTACATGAAAAG
Found at i:27798938 original size:22 final size:22
Alignment explanation
Indices: 27798913--27798957 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
27798903 GCATTGAGAA
27798913 TGAGATTAAAATATGTTACTTT
1 TGAGATTAAAATATGTTACTTT
27798935 TGAGATTAAAATATGTTACTTT
1 TGAGATTAAAATATGTTACTTT
27798957 T
1 T
27798958 AGCACTTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (22 bp):
TGAGATTAAAATATGTTACTTT
Found at i:27815780 original size:20 final size:20
Alignment explanation
Indices: 27815755--27815801 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
27815745 AATATCCAAA
27815755 CAATAATAATAAAATAGTAG
1 CAATAATAATAAAATAGTAG
* *
27815775 CAATAATAGTAAAATTGTAG
1 CAATAATAATAAAATAGTAG
27815795 CAA-AATA
1 CAATAATA
27815802 GTGAGAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.57, C:0.06, G:0.11, T:0.26
Consensus pattern (20 bp):
CAATAATAATAAAATAGTAG
Found at i:27822181 original size:24 final size:24
Alignment explanation
Indices: 27822154--27822202 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
27822144 ATTTAAGCGC
27822154 TTAATTTTGATTTTGACTTTATGT
1 TTAATTTTGATTTTGACTTTATGT
27822178 TTAATTTTGATTTTGACTTTATGT
1 TTAATTTTGATTTTGACTTTATGT
27822202 T
1 T
27822203 GGGGGTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.04, G:0.12, T:0.63
Consensus pattern (24 bp):
TTAATTTTGATTTTGACTTTATGT
Found at i:27832770 original size:49 final size:49
Alignment explanation
Indices: 27832713--27832806 Score: 170
Period size: 49 Copynumber: 1.9 Consensus size: 49
27832703 ACAGAATCGT
*
27832713 AGGAAAGAAGAGGAAAAGAAAAATGGCAGGGAATAGAAAAACTAACAAA
1 AGGAAAGAAGAGGAAAAGAAAAATGGCAGGGAACAGAAAAACTAACAAA
*
27832762 AGGAAAGAAGAGGAAAAGAAAAATGGCAGGGAACAGAGAAACTAA
1 AGGAAAGAAGAGGAAAAGAAAAATGGCAGGGAACAGAAAAACTAA
27832807 TGCCAGATTG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.60, C:0.06, G:0.29, T:0.05
Consensus pattern (49 bp):
AGGAAAGAAGAGGAAAAGAAAAATGGCAGGGAACAGAAAAACTAACAAA
Found at i:27836482 original size:16 final size:16
Alignment explanation
Indices: 27836457--27836531 Score: 53
Period size: 16 Copynumber: 4.4 Consensus size: 16
27836447 AGCACTTGCG
*
27836457 TTTC-TTCTTTCTTTC
1 TTTCTTTCTTTTTTTC
* *
27836472 TTTTTTTCTTTATTTCC
1 TTTCTTTCTTT-TTTTC
27836489 TTTCTATTTCATTTTGTTTC
1 TTTC--TTTC-TTTT-TTTC
* *
27836509 TTTCTTTCTCTTTTTA
1 TTTCTTTCTTTTTTTC
27836525 TTTCTTT
1 TTTCTTT
27836532 TTCTTTTACT
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
15 3 0.06
16 16 0.34
17 9 0.19
18 4 0.09
19 5 0.11
20 10 0.21
ACGTcount: A:0.05, C:0.19, G:0.01, T:0.75
Consensus pattern (16 bp):
TTTCTTTCTTTTTTTC
Found at i:27836513 original size:20 final size:20
Alignment explanation
Indices: 27836480--27836531 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
27836470 TCTTTTTTTC
27836480 TTTATTTCCTTTCTATT-TCAT
1 TTTATTT-CTTTCT-TTCTCAT
* *
27836501 TTTGTTTCTTTCTTTCTCTT
1 TTTATTTCTTTCTTTCTCAT
27836521 TTTATTTCTTT
1 TTTATTTCTTT
27836532 TTCTTTTACT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.07
20 19 0.70
21 6 0.22
ACGTcount: A:0.08, C:0.17, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTATTTCTTTCTTTCTCAT
Found at i:27836599 original size:8 final size:8
Alignment explanation
Indices: 27836586--27836642 Score: 50
Period size: 8 Copynumber: 7.2 Consensus size: 8
27836576 TTTTAAGTTT
27836586 TAATATTA
1 TAATATTA
27836594 TAATATTA
1 TAATATTA
27836602 TAATA-TA
1 TAATATTA
*
27836609 T-ATATTT
1 TAATATTA
27836616 TAACT-TTA
1 TAA-TATTA
27836624 -AATATTTA
1 TAATA-TTA
27836632 TAATATATA
1 TAATAT-TA
27836641 TA
1 TA
27836643 CACTTATGCC
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
6 4 0.10
7 7 0.17
8 20 0.50
9 9 0.22
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (8 bp):
TAATATTA
Done.