Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168026.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_28, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 15507587
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 33 of 91
Found at i:5681737 original size:53 final size:53
Alignment explanation
Indices: 5681673--5681776 Score: 208
Period size: 53 Copynumber: 2.0 Consensus size: 53
5681663 CATGTAAAGG
5681673 AGAAGAAAAGGAGAGAGCATTCTAGATAGGTAGTAAAACAATTCTTAGGAAGA
1 AGAAGAAAAGGAGAGAGCATTCTAGATAGGTAGTAAAACAATTCTTAGGAAGA
5681726 AGAAGAAAAGGAGAGAGCATTCTAGATAGGTAGTAAAACAATTCTTAGGAA
1 AGAAGAAAAGGAGAGAGCATTCTAGATAGGTAGTAAAACAATTCTTAGGAA
5681777 AAATTAATTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.47, C:0.08, G:0.26, T:0.19
Consensus pattern (53 bp):
AGAAGAAAAGGAGAGAGCATTCTAGATAGGTAGTAAAACAATTCTTAGGAAGA
Found at i:5687505 original size:38 final size:38
Alignment explanation
Indices: 5687433--5687505 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
5687423 ATTATTTATT
*
5687433 TTCAAAAATATTTTCTAATATGTTAGTAAGATTTTCTG
1 TTCAAAAATATTTTCTAATATGTTAGTAAAATTTTCTG
5687471 TTCAAAAATATCTTTC-AATATGTT-GATAAAATTTT
1 TTCAAAAATAT-TTTCTAATATGTTAG-TAAAATTTT
5687506 ATGAAAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 1 0.03
38 27 0.84
39 4 0.12
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (38 bp):
TTCAAAAATATTTTCTAATATGTTAGTAAAATTTTCTG
Found at i:5687736 original size:29 final size:28
Alignment explanation
Indices: 5687704--5687787 Score: 73
Period size: 29 Copynumber: 3.0 Consensus size: 28
5687694 AAACTTTTTT
5687704 TAAAGTTTTCAAACCTTTCAATATGTTAG
1 TAAAGTTTTCAAACCTTTCAATATGTT-G
* ** * *
5687733 TAAAGCTTTT-TAATTTTTGAATCTG-TG
1 TAAAG-TTTTCAAACCTTTCAATATGTTG
* *
5687760 TAAAATTTTCAAACCTTCCAATATGTTG
1 TAAAGTTTTCAAACCTTTCAATATGTTG
5687788 GTTTTATTTT
Statistics
Matches: 40, Mismatches: 12, Indels: 7
0.68 0.20 0.12
Matches are distributed among these distances:
26 4 0.10
27 14 0.35
28 3 0.08
29 15 0.38
30 4 0.10
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (28 bp):
TAAAGTTTTCAAACCTTTCAATATGTTG
Found at i:5688270 original size:20 final size:20
Alignment explanation
Indices: 5688229--5688277 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 20
5688219 CATTGGAAAC
5688229 TTCAAAAATTAATCAAAAAA-
1 TTCAAAAATT-ATCAAAAAAT
5688249 TTCAAAAATT-TCCAAAATAAT
1 TTCAAAAATTAT-CAAAA-AAT
5688270 TTCAAAAA
1 TTCAAAAA
5688278 ATTTTCTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 1 0.04
19 5 0.19
20 12 0.46
21 8 0.31
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (20 bp):
TTCAAAAATTATCAAAAAAT
Found at i:5688272 original size:12 final size:10
Alignment explanation
Indices: 5688241--5688281 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
5688231 CAAAAATTAA
5688241 TCAAAAAA-T
1 TCAAAAAATT
5688250 TC-AAAAATT
1 TCAAAAAATT
5688259 TCCAAAATAATT
1 T-CAAAA-AATT
5688271 TCAAAAAATT
1 TCAAAAAATT
5688281 T
1 T
5688282 TCTTCAACCC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
8 5 0.18
9 4 0.14
10 6 0.21
11 8 0.29
12 5 0.18
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (10 bp):
TCAAAAAATT
Found at i:5688762 original size:21 final size:20
Alignment explanation
Indices: 5688699--5688784 Score: 79
Period size: 21 Copynumber: 4.2 Consensus size: 20
5688689 TTTTTATAAT
*
5688699 AATAATAATAATAAT-AAATA
1 AATAAAAATAA-AATAAAATA
* * *
5688719 AATAAAAAT-AAATGATATG
1 AATAAAAATAAAATAAAATA
5688738 AATAAAAAGTAAAATAAAATA
1 AATAAAAA-TAAAATAAAATA
5688759 AATAAATAATAAAA-ATAAATA
1 AATAAA-AATAAAATA-AAATA
5688780 AATAA
1 AATAA
5688785 GATAAAGATA
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
18 3 0.05
19 12 0.22
20 10 0.18
21 28 0.51
22 2 0.04
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.24
Consensus pattern (20 bp):
AATAAAAATAAAATAAAATA
Found at i:5688797 original size:15 final size:15
Alignment explanation
Indices: 5688777--5688865 Score: 57
Period size: 15 Copynumber: 5.9 Consensus size: 15
5688767 ATAAAAATAA
5688777 ATAAATAAGATAAAG
1 ATAAATAAGATAAAG
5688792 ATAAATAAGATACCTAAG
1 ATAAATAAGATA---AAG
5688810 ATAAAT--GAT-AAG
1 ATAAATAAGATAAAG
5688822 -TAAAATAA-AGTAAAG
1 AT-AAATAAGA-TAAAG
*
5688837 ATAAAATAA-ATAGAAA
1 AT-AAATAAGATA-AAG
5688853 ATAAATAAG-TAAA
1 ATAAATAAGATAAA
5688866 TAAATAAAGC
Statistics
Matches: 62, Mismatches: 1, Indels: 23
0.72 0.01 0.27
Matches are distributed among these distances:
11 1 0.02
12 7 0.11
13 1 0.02
14 3 0.05
15 25 0.40
16 16 0.26
18 9 0.15
ACGTcount: A:0.65, C:0.02, G:0.11, T:0.21
Consensus pattern (15 bp):
ATAAATAAGATAAAG
Found at i:5688798 original size:40 final size:41
Alignment explanation
Indices: 5688714--5688872 Score: 141
Period size: 40 Copynumber: 3.8 Consensus size: 41
5688704 TAATAATAAT
*
5688714 AAATAAATAAAAATAAATGATATGAATAAA-AAG-TAAA-ATA
1 AAATAAATAAAAATAAAT-A-ATAAATAAATAAGATAAAGATA
5688754 AAATAAATAAATAATAAA-AATAAATAAATAAGATAAAGAT-
1 AAATAAATAAA-AATAAATAATAAATAAATAAGATAAAGATA
* * *
5688794 AAATAAGATACCTAAGATAAATGATAAGTAAAATAA-AGTAAAGATA
1 AAATAA-ATA---AAAATAAATAATAAAT-AAATAAGA-TAAAGATA
5688840 AAATAAATAGAAAATAAATAAGTAAATAAATAA
1 AAATAAATA-AAAATAAATAA-TAAATAAATAA
5688873 AGCAGTGATA
Statistics
Matches: 98, Mismatches: 8, Indels: 23
0.76 0.06 0.18
Matches are distributed among these distances:
38 8 0.08
39 4 0.04
40 21 0.21
41 11 0.11
43 20 0.20
44 12 0.12
45 16 0.16
46 6 0.06
ACGTcount: A:0.69, C:0.01, G:0.08, T:0.22
Consensus pattern (41 bp):
AAATAAATAAAAATAAATAATAAATAAATAAGATAAAGATA
Found at i:5688888 original size:4 final size:4
Alignment explanation
Indices: 5688711--5688873 Score: 77
Period size: 4 Copynumber: 39.5 Consensus size: 4
5688701 TAATAATAAT
* * *
5688711 AATA AATA AAT- AA-A AATA AATGA TATG AATA AA-A AGTAA AATAA AATA
1 AATA AATA AATA AATA AATA AAT-A AATA AATA AATA AAT-A AAT-A AATA
* **
5688759 AATA AATA ATAAA AATA AATA AATA AGATAA AGATA AATA AGATA CCTA
1 AATA AATA A-ATA AATA AATA AATA A-AT-A A-ATA AATA A-ATA AATA
* * * * *
5688808 AGATA AAT- GATA AGTAA AATA AAGTA AAGA TA-A AATA AATA GA-A AATA
1 A-ATA AATA AATA AAT-A AATA AA-TA AATA AATA AATA AATA AATA AATA
*
5688856 AATA AGTA AATA AATA AA
1 AATA AATA AATA AATA AA
5688874 GCAGTGATAA
Statistics
Matches: 121, Mismatches: 23, Indels: 30
0.70 0.13 0.17
Matches are distributed among these distances:
3 12 0.10
4 73 0.60
5 31 0.26
6 5 0.04
ACGTcount: A:0.69, C:0.01, G:0.08, T:0.22
Consensus pattern (4 bp):
AATA
Found at i:5689166 original size:40 final size:40
Alignment explanation
Indices: 5689117--5689207 Score: 112
Period size: 39 Copynumber: 2.3 Consensus size: 40
5689107 GCACACAGCT
* * *
5689117 TTTAAAAATTAAGGGCTTTTCCAATATGGATGCACATAAC
1 TTTAAAAATTAAGGGCTCTTCCAAAATGGAGGCACATAAC
* * * *
5689157 TTTACAAATT-ATGGCTCTTCCAAAATGGCGGCACATTAC
1 TTTAAAAATTAAGGGCTCTTCCAAAATGGAGGCACATAAC
5689196 TTTAAAAATTAA
1 TTTAAAAATTAA
5689208 AGCCTTCTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
39 32 0.76
40 10 0.24
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.33
Consensus pattern (40 bp):
TTTAAAAATTAAGGGCTCTTCCAAAATGGAGGCACATAAC
Found at i:5694757 original size:61 final size:60
Alignment explanation
Indices: 5694609--5694818 Score: 174
Period size: 61 Copynumber: 3.4 Consensus size: 60
5694599 GTAGAATGGG
* * ** * * **
5694609 TATTATAGTAATTTT-AGCTAATTATGGTAAGAAAAATTTTTTGTAATTGTAGAATAAGGGA
1 TATTATAGTAATTTTGA-CCAATTATGGTAAGAAAAGTTTTTCATAATTATA-AAGAAGAAA
* * *
5694670 TATTATAGTAATTTTGATCAACTATGGTAAGAAAAGTATTTTCATAATTATATAGAAGAAA
1 TATTATAGTAATTTTGACCAATTATGGTAAGAAAAGT-TTTTCATAATTATAAAGAAGAAA
* * * * * *
5694731 TGTTATAGTAATTTT-AGCCATTTATGGTAGGAGAGGCTTTTTCATAATAATGGAAAGAA-AAA
1 TATTATAGTAATTTTGA-CCAATTATGGTAAGAAAAG-TTTTTCATAATTAT--AAAGAAGAAA
*
5694793 TATTATAGTAATTTTGACCATTTATG
1 TATTATAGTAATTTTGACCAATTATG
5694819 AGAGAATTGA
Statistics
Matches: 121, Mismatches: 21, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
60 1 0.01
61 75 0.62
62 39 0.32
63 6 0.05
ACGTcount: A:0.39, C:0.05, G:0.17, T:0.40
Consensus pattern (60 bp):
TATTATAGTAATTTTGACCAATTATGGTAAGAAAAGTTTTTCATAATTATAAAGAAGAAA
Found at i:5695700 original size:72 final size:74
Alignment explanation
Indices: 5695535--5695706 Score: 199
Period size: 72 Copynumber: 2.3 Consensus size: 74
5695525 AGTTATGATT
** * *
5695535 AAAAACACAATCTTTGTTGAAAAAATGAAAAAAAAAAATATTTTTCATAATTTAACAAAGACAAC
1 AAAAACATGATCTTTGTTG--AAAAT-ATAAAAAAAAATATTTTTCAGAATTTAACAAAGACAAC
5695600 TTTTCTAAGATA
63 TTTTCTAAGATA
* * *
5695612 AACAACATGATTTTTGTT-AAAATATAAAAAAAAATATTTTT-AGAATTTAACAAATACAACATT
1 AAAAACATGATCTTTGTTGAAAATATAAAAAAAAATATTTTTCAGAATTTAACAAAGACAAC-TT
5695675 TT-TAAGATA
65 TTCTAAGATA
*
5695684 AAAAATAT-AGTCTTTGTTGAAAA
1 AAAAACATGA-TCTTTGTTGAAAA
5695707 GACAACAATT
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
71 1 0.01
72 37 0.45
73 25 0.30
74 5 0.06
77 14 0.17
ACGTcount: A:0.52, C:0.08, G:0.07, T:0.33
Consensus pattern (74 bp):
AAAAACATGATCTTTGTTGAAAATATAAAAAAAAATATTTTTCAGAATTTAACAAAGACAACTTT
TCTAAGATA
Found at i:5695795 original size:114 final size:112
Alignment explanation
Indices: 5695639--5695930 Score: 315
Period size: 114 Copynumber: 2.6 Consensus size: 112
5695629 TAAAATATAA
* * * * * * * *
5695639 AAAAAAATATTTTT-AGAATTTAACAAATACAACATTTTTAAGATAAAAAATATAGTCTTTGTTG
1 AAAAAAATATTTTTCAGAATTTAATAAAAATAACGTTTCTAAGATAGAAAACATAGTTTTTGTTG
* * *
5695703 AAAAGACAACAAT-TTTGAAAGATAAAAATATAATCTTTGTTGTAAACAT
66 AAAA-AAAACAATGTTTGAAAGATAAAAACACAATCTTTGTTG-AAA-AT
* * * *
5695752 AAAAAAATATTTTTCAGAATTTAATAAAGATGAGGTTTCTAAGATAGAAAACGTAGTTTTTGTTG
1 AAAAAAATATTTTTCAGAATTTAATAAAAATAACGTTTCTAAGATAGAAAACATAGTTTTTGTTG
* ** *
5695817 AAAAAAAATAATGTTTTTAAGATAAAAACGCAATCTTTGTTGAAAAT
66 AAAAAAAACAATGTTTGAAAGATAAAAACACAATCTTTGTTGAAAAT
** *
5695864 ATAAAAAA-A--TTTCAGAATTCGATAAAAATAACGTTTCTAAAATAGAAAACATAGTTTTTGTT
1 A-AAAAAATATTTTTCAGAATTTAATAAAAATAACGTTTCTAAGATAGAAAACATAGTTTTTGTT
5695926 GAAAA
65 GAAAA
5695931 CATGAAAAAT
Statistics
Matches: 151, Mismatches: 25, Indels: 9
0.82 0.14 0.05
Matches are distributed among these distances:
110 51 0.34
112 4 0.03
113 29 0.19
114 67 0.44
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.34
Consensus pattern (112 bp):
AAAAAAATATTTTTCAGAATTTAATAAAAATAACGTTTCTAAGATAGAAAACATAGTTTTTGTTG
AAAAAAAACAATGTTTGAAAGATAAAAACACAATCTTTGTTGAAAAT
Found at i:5696007 original size:71 final size:73
Alignment explanation
Indices: 5695896--5696080 Score: 230
Period size: 74 Copynumber: 2.5 Consensus size: 73
5695886 TAAAAATAAC
*
5695896 GTTTCTAAAATAGAAAACATAGTTTTTGTTGAAAACATG-AAAAATATA-TTTTCAAAATTTAAT
1 GTTTCTAAAATA-AAAACATAGTTTTTGTTGAAAACATGAAAAAATATATTTTTCAAAATTCAAT
*
5695959 AAAGAGGGT
65 AAAGAGGAT
* * * * *
5695968 GTTTCTAAAATAAAAGCATAGTCTTTGTTGAACACATGAAAAAAATATATTTTTTAGAATTCAAT
1 GTTTCTAAAATAAAAACATAGTTTTTGTTGAAAACATG-AAAAAATATATTTTTCAAAATTCAAT
*
5696033 AAAGATGAT
65 AAAGAGGAT
* * * *
5696042 ATTTTTAAGATAAAAACATAGTTTTTGTTGAAAAAATGA
1 GTTTCTAAAATAAAAACATAGTTTTTGTTGAAAACATGA
5696081 CTTTTCTAAA
Statistics
Matches: 95, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
71 23 0.24
72 12 0.13
73 10 0.11
74 50 0.53
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (73 bp):
GTTTCTAAAATAAAAACATAGTTTTTGTTGAAAACATGAAAAAATATATTTTTCAAAATTCAATA
AAGAGGAT
Found at i:5703951 original size:18 final size:18
Alignment explanation
Indices: 5703928--5703964 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5703918 AAATCTTAAA
5703928 ATTTTAAGTTTAAATTCT
1 ATTTTAAGTTTAAATTCT
5703946 ATTTTAAGTTTAAATTCT
1 ATTTTAAGTTTAAATTCT
5703964 A
1 A
5703965 CTATGTCGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.54
Consensus pattern (18 bp):
ATTTTAAGTTTAAATTCT
Found at i:5704727 original size:16 final size:18
Alignment explanation
Indices: 5704683--5704727 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
5704673 ATTTGATAGG
5704683 TTAATTTAAATTTTTATAAT
1 TTAATTT-AA-TTTTATAAT
5704703 TTAATTTAATTTTAT-AT
1 TTAATTTAATTTTATAAT
5704720 TT-ATTTAA
1 TTAATTTAA
5704728 GATATTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.24
17 4 0.16
18 6 0.24
19 2 0.08
20 7 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTAATTTAATTTTATAAT
Found at i:5709665 original size:25 final size:23
Alignment explanation
Indices: 5709624--5709690 Score: 82
Period size: 25 Copynumber: 2.8 Consensus size: 23
5709614 AAAGCATAAA
*
5709624 AACAAAAGAAAATTGAAAAAAGG
1 AACAAAAGAAAAATGAAAAAAGG
5709647 AACAACAATGAAAAATGAAAAAAGGG
1 AACAA-AA-GAAAAATGAAAAAA-GG
*
5709673 AAAAAAAGAAAAA-GAAAA
1 AACAAAAGAAAAATGAAAA
5709691 TTCATTGGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
23 10 0.26
24 8 0.21
25 15 0.38
26 6 0.15
ACGTcount: A:0.73, C:0.04, G:0.16, T:0.06
Consensus pattern (23 bp):
AACAAAAGAAAAATGAAAAAAGG
Found at i:5710679 original size:29 final size:28
Alignment explanation
Indices: 5710619--5710683 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
5710609 TACACATAAA
* *
5710619 TAAAACTATTTTTATTAAACTAAAATAT
1 TAAAAATAATTTTATTAAACTAAAATAT
5710647 TAAATAATAATTTTATTAATA-TAATAATA-
1 TAAA-AATAATTTTATTAA-ACTAA-AATAT
5710676 TAAAAATA
1 TAAAAATA
5710684 TAAAATTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 8 0.25
29 19 0.59
30 5 0.16
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (28 bp):
TAAAAATAATTTTATTAAACTAAAATAT
Found at i:5711696 original size:26 final size:28
Alignment explanation
Indices: 5711667--5711731 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 28
5711657 TTGAAATAAT
*
5711667 AAAATCAAATAAAAAAAG-TAAATAGAA
1 AAAATCAAATAAAAAAAGAAAAATAGAA
*
5711694 AAAA--AAA-AGAAAAAAGAAAAATTGAA
1 AAAATCAAATA-AAAAAAGAAAAATAGAA
5711720 AAAATCAAATAA
1 AAAATCAAATAA
5711732 CTTGAAATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
24 1 0.03
25 10 0.32
26 11 0.35
27 4 0.13
28 4 0.13
29 1 0.03
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.12
Consensus pattern (28 bp):
AAAATCAAATAAAAAAAGAAAAATAGAA
Found at i:5711698 original size:18 final size:18
Alignment explanation
Indices: 5711677--5711714 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5711667 AAAATCAAAT
* *
5711677 AAAAAAAGTAAATAGAAA
1 AAAAAAAGAAAAAAGAAA
5711695 AAAAAAAGAAAAAAGAAA
1 AAAAAAAGAAAAAAGAAA
5711713 AA
1 AA
5711715 TTGAAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (18 bp):
AAAAAAAGAAAAAAGAAA
Found at i:5713506 original size:16 final size:16
Alignment explanation
Indices: 5713485--5713516 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5713475 GGCATATACA
*
5713485 CACATGTGTATACACG
1 CACATGTGCATACACG
5713501 CACATGTGCATACACG
1 CACATGTGCATACACG
5713517 TATATAATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (16 bp):
CACATGTGCATACACG
Found at i:5724810 original size:16 final size:16
Alignment explanation
Indices: 5724786--5724825 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
5724776 GAATGGATGT
*
5724786 AAAATAAAAAAAAAAA
1 AAAAGAAAAAAAAAAA
*
5724802 AAAAGAAAAAGAAAAA
1 AAAAGAAAAAAAAAAA
*
5724818 TAAAGAAA
1 AAAAGAAA
5724826 GAGATAGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.88, C:0.00, G:0.07, T:0.05
Consensus pattern (16 bp):
AAAAGAAAAAAAAAAA
Found at i:5725685 original size:22 final size:20
Alignment explanation
Indices: 5725644--5725703 Score: 57
Period size: 22 Copynumber: 2.9 Consensus size: 20
5725634 ATTGTTTTCT
* * *
5725644 TTTTTTTGATATATACAATTT
1 TTTTTTTAATAT-TAAAATTA
*
5725665 TTATTTTTATATTTTAAAATTA
1 TT-TTTTTA-ATATTAAAATTA
5725687 TTTTTTTAATATTAAAA
1 TTTTTTTAATATTAAAA
5725704 ATCTTGAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 8 0.25
21 8 0.25
22 13 0.41
23 3 0.09
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTTTTAATATTAAAATTA
Found at i:5726452 original size:22 final size:23
Alignment explanation
Indices: 5726427--5726481 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
5726417 CATACTAAAT
*
5726427 AAATTTAAATTTAAATTTT-TCA
1 AAATTTAAATATAAATTTTATCA
* *
5726449 AAATTTATATATAAATTTTATTA
1 AAATTTAAATATAAATTTTATCA
*
5726472 AATTTTAAAT
1 AAATTTAAAT
5726482 CATATTATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 17 0.63
23 10 0.37
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
AAATTTAAATATAAATTTTATCA
Found at i:5727361 original size:97 final size:98
Alignment explanation
Indices: 5727134--5727412 Score: 448
Period size: 97 Copynumber: 2.9 Consensus size: 98
5727124 AAAAATGATG
5727134 AACCTTGAAATGAAAATTTTTGCAGACGTTATCTTG--A-AA---T-GATGTTAGACATATTACT
1 AACCTTGAAATGAAAATTTTTGCAGACGTTATCTTGAAATAATGTTAGATGTTAGACATATTACT
* *
5727192 TAATTTTATTTGAAACGTGAATCACATTGGATG
66 TAATTTTAATTGAAACGTGAATCACATTGGATC
*
5727225 AACCTTGAAATGAAAATTTTTGCAGACGTTATCTTGAAATAATGTTAGATGTTAGACAAATTACT
1 AACCTTGAAATGAAAATTTTTGCAGACGTTATCTTGAAATAATGTTAGATGTTAGACATATTACT
5727290 TAATTTTAATTGAAACGTGAATCACA-TGGATC
66 TAATTTTAATTGAAACGTGAATCACATTGGATC
* * *
5727322 AACCTTGAGATGAAAATTTTGGCAGACGTTATCTTGAAATGATGTTAGATGTTAGACATATTACT
1 AACCTTGAAATGAAAATTTTTGCAGACGTTATCTTGAAATAATGTTAGATGTTAGACATATTACT
5727387 TAATTTTAATTGAAACGTGAATCACA
66 TAATTTTAATTGAAACGTGAATCACA
5727413 ATTTTCATGC
Statistics
Matches: 174, Mismatches: 7, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
91 36 0.21
93 1 0.01
94 2 0.01
97 93 0.53
98 42 0.24
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (98 bp):
AACCTTGAAATGAAAATTTTTGCAGACGTTATCTTGAAATAATGTTAGATGTTAGACATATTACT
TAATTTTAATTGAAACGTGAATCACATTGGATC
Found at i:5728379 original size:21 final size:21
Alignment explanation
Indices: 5728355--5728397 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
5728345 TATACTTGTT
5728355 TATTTTTATT-AAATTTATAAA
1 TATTTTTATTAAAATTT-TAAA
5728376 TATTTTTATTAAAATTTTAAA
1 TATTTTTATTAAAATTTTAAA
5728397 T
1 T
5728398 TATATTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TATTTTTATTAAAATTTTAAA
Found at i:5728405 original size:21 final size:22
Alignment explanation
Indices: 5728355--5728407 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
5728345 TATACTTGTT
*
5728355 TATTTTTATT-AAATTTATAAA
1 TATTATTATTAAAATTTATAAA
*
5728376 TATTTTTATTAAAATTT-TAAA
1 TATTATTATTAAAATTTATAAA
5728397 T-TATATTATTA
1 TAT-TATTATTA
5728408 GATAAATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 1 0.03
21 22 0.76
22 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TATTATTATTAAAATTTATAAA
Found at i:5729171 original size:14 final size:14
Alignment explanation
Indices: 5729140--5729169 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
5729130 TGATAAAATA
5729140 TTAAAATTTTAATT
1 TTAAAATTTTAATT
5729154 TTAATAATTTTAATT
1 TTAA-AATTTTAATT
5729169 T
1 T
5729170 AAATTCTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTAAAATTTTAATT
Found at i:5730935 original size:12 final size:12
Alignment explanation
Indices: 5730919--5730953 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
5730909 ACTAAGACTA
5730919 CAAAAAAAAAAG
1 CAAAAAAAAAAG
* *
5730931 TAAAAACAAAAG
1 CAAAAAAAAAAG
5730943 CAAAAAAAAAA
1 CAAAAAAAAAA
5730954 AAAACTTAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.83, C:0.09, G:0.06, T:0.03
Consensus pattern (12 bp):
CAAAAAAAAAAG
Found at i:5731561 original size:22 final size:22
Alignment explanation
Indices: 5731536--5731586 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
5731526 TTATATTTTG
5731536 ATTTTTTATTT-ATTAATTT-ATA
1 ATTTTTTATTTGA--AATTTAATA
*
5731558 ATTTTATATTTGAAATTTAATA
1 ATTTTTTATTTGAAATTTAATA
5731580 ATTTTTT
1 ATTTTTT
5731587 GTTGTTTTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 5 0.20
22 19 0.76
23 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
ATTTTTTATTTGAAATTTAATA
Found at i:5735819 original size:18 final size:18
Alignment explanation
Indices: 5735796--5735870 Score: 87
Period size: 18 Copynumber: 4.2 Consensus size: 18
5735786 TATAGTTATT
5735796 ATCCACCACAAATGTATC
1 ATCCACCACAAATGTATC
*
5735814 ATCCACCTCAAATGTATC
1 ATCCACCACAAATGTATC
**
5735832 ATTTACCACAAATGTATC
1 ATCCACCACAAATGTATC
** * *
5735850 CCCCACCATAAATTTATC
1 ATCCACCACAAATGTATC
5735868 ATC
1 ATC
5735871 ATCAAATATA
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.36, C:0.32, G:0.04, T:0.28
Consensus pattern (18 bp):
ATCCACCACAAATGTATC
Found at i:5735856 original size:36 final size:36
Alignment explanation
Indices: 5735800--5735869 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
5735790 GTTATTATCC
*
5735800 ACCACAAATGTATCATCCACC-TCAAATGTATCATTT
1 ACCACAAATGTATCACCCACCAT-AAATGTATCATTT
* *
5735836 ACCACAAATGTATCCCCCACCATAAATTTATCAT
1 ACCACAAATGTATCACCCACCATAAATGTATCAT
5735870 CATCAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 29 0.97
37 1 0.03
ACGTcount: A:0.37, C:0.30, G:0.04, T:0.29
Consensus pattern (36 bp):
ACCACAAATGTATCACCCACCATAAATGTATCATTT
Found at i:5738200 original size:14 final size:14
Alignment explanation
Indices: 5738177--5738220 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
5738167 ACGATATTAA
5738177 AAATTAAAAAATTT
1 AAATTAAAAAATTT
* *
5738191 AAATT-TAAAAGTT
1 AAATTAAAAAATTT
5738204 AAATTAAAAAATTT
1 AAATTAAAAAATTT
5738218 AAA
1 AAA
5738221 ACTAATAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (14 bp):
AAATTAAAAAATTT
Found at i:5746871 original size:77 final size:74
Alignment explanation
Indices: 5746747--5746895 Score: 174
Period size: 77 Copynumber: 2.0 Consensus size: 74
5746737 ACATTATCTG
* ** *
5746747 GTAAATTTACTGGTATTTCTTTGGAGTTTTTTACTAGTATTTGTTTCTTGATATTTTATTAGCGT
1 GTAAATTTACTGATATTTCTTT-GAGTTTTTTACTAAAATTTGTTTC-TAATATTTT-TTAGCGT
5746812 GATTGTAGGTCA
63 GATTGTAGGTCA
* * * *
5746824 GTAAATTTACTGATATTTCTTT-AGTTTTTTTGCTAAAATTTATTTTCTAATATTTTTTGGTGTG
1 GTAAATTTACTGATATTTCTTTGAG-TTTTTTACTAAAATTT-GTTTCTAATATTTTTTAGCGTG
5746888 ATTGTAGG
64 ATTGTAGG
5746896 GCATTGTTTG
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
75 16 0.26
76 21 0.34
77 25 0.40
ACGTcount: A:0.22, C:0.07, G:0.17, T:0.54
Consensus pattern (74 bp):
GTAAATTTACTGATATTTCTTTGAGTTTTTTACTAAAATTTGTTTCTAATATTTTTTAGCGTGAT
TGTAGGTCA
Found at i:5747453 original size:28 final size:27
Alignment explanation
Indices: 5747409--5747461 Score: 63
Period size: 28 Copynumber: 1.9 Consensus size: 27
5747399 ATATTCAACT
*
5747409 GGCAATTTGCAACTAGAAAGTAATCTGA
1 GGCAATTTGCAAATAG-AAGTAATCTGA
*
5747437 GGCAATTTG-ATAATAGAGGTAATCT
1 GGCAATTTGCA-AATAGAAGTAATCT
5747462 TATAACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (27 bp):
GGCAATTTGCAAATAGAAGTAATCTGA
Found at i:5748218 original size:24 final size:24
Alignment explanation
Indices: 5748180--5748249 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
5748170 ACTTTTGTTA
* * *
5748180 AAACTAGAATGGAAAGTGGATTCG
1 AAACTAGAGTTGAAAATGGATTCG
* * * *
5748204 AAGCTAGAGTTGAAATTGGAATGG
1 AAACTAGAGTTGAAAATGGATTCG
*
5748228 AAACTAGATTTGAAAATGGATT
1 AAACTAGAGTTGAAAATGGATT
5748250 TAGGGTTTGT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.41, C:0.06, G:0.27, T:0.26
Consensus pattern (24 bp):
AAACTAGAGTTGAAAATGGATTCG
Found at i:5750926 original size:42 final size:41
Alignment explanation
Indices: 5750880--5750973 Score: 100
Period size: 42 Copynumber: 2.3 Consensus size: 41
5750870 CAATTCTTAT
* * *
5750880 CCTTTCATTCCTTATTGCCTCACCTATATGTTGATTTTCTAC
1 CCTTTCATTCCTTATTACATCACCTACATGTTGA-TTTCTAC
* * *
5750922 CCTTTCATGT-TTTATTACATTAGCTACATGTTGATTTCTAC
1 CCTTTCAT-TCCTTATTACATCACCTACATGTTGATTTCTAC
*
5750963 CATTTCATTCC
1 CCTTTCATTCC
5750974 CTTCCACCTT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
40 1 0.02
41 14 0.33
42 26 0.62
43 1 0.02
ACGTcount: A:0.19, C:0.26, G:0.07, T:0.48
Consensus pattern (41 bp):
CCTTTCATTCCTTATTACATCACCTACATGTTGATTTCTAC
Found at i:5751564 original size:32 final size:32
Alignment explanation
Indices: 5751522--5751600 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
5751512 GTGCATGTCC
* * **
5751522 TTTACATTGTTATCTAA-TTTTTATTATAATTT
1 TTTACTTTGTTAT-AAATTTTTTATTATAAGCT
*
5751554 TTTACTTTGTTATAAATTTTTTGTTATAAGCT
1 TTTACTTTGTTATAAATTTTTTATTATAAGCT
5751586 TTTACTTTGTTATAA
1 TTTACTTTGTTATAA
5751601 CCAATGGTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
31 2 0.05
32 39 0.95
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (32 bp):
TTTACTTTGTTATAAATTTTTTATTATAAGCT
Found at i:5751568 original size:18 final size:16
Alignment explanation
Indices: 5751553--5751600 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 16
5751543 TATTATAATT
5751553 TTTTACTTTGTTATAA
1 TTTTACTTTGTTATAA
*
5751569 ATTT--TTTGTTATAA
1 TTTTACTTTGTTATAA
5751583 GCTTTTACTTTGTTATAA
1 --TTTTACTTTGTTATAA
5751601 CCAATGGTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 10 0.38
16 6 0.23
18 10 0.38
ACGTcount: A:0.25, C:0.06, G:0.08, T:0.60
Consensus pattern (16 bp):
TTTTACTTTGTTATAA
Found at i:5752878 original size:17 final size:17
Alignment explanation
Indices: 5752858--5752891 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5752848 TTTTATTGAA
5752858 ATTTCATTTAAATTCTT
1 ATTTCATTTAAATTCTT
*
5752875 ATTTTATTTAAATTCTT
1 ATTTCATTTAAATTCTT
5752892 CTACCATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTCATTTAAATTCTT
Found at i:5753210 original size:10 final size:10
Alignment explanation
Indices: 5753195--5753219 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5753185 ATTTAAAATA
5753195 TTTTTATATT
1 TTTTTATATT
5753205 TTTTTATATT
1 TTTTTATATT
5753215 TTTTT
1 TTTTT
5753220 CATTAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTATATT
Found at i:5754743 original size:44 final size:44
Alignment explanation
Indices: 5754695--5754987 Score: 292
Period size: 44 Copynumber: 6.7 Consensus size: 44
5754685 TCCCCTAAGC
* *
5754695 AGAGGCTC-ACAACTTTTGGAAAAATGAATATGGCTTCTTTAAAT
1 AGAGGCTCAACAAC-TTTGGAAAAATAAATATGGCTTCTCTAAAT
* * * *
5754739 AGAGGCTCAATAACTTTGAAAAAATAAATAAGGCTTCTCTAATT
1 AGAGGCTCAACAACTTTGGAAAAATAAATATGGCTTCTCTAAAT
* *
5754783 AGAGGCTCAACAATTTTGGAAAAATAAATATGGC-TCATTTAAAT
1 AGAGGCTCAACAACTTTGGAAAAATAAATATGGCTTC-TCTAAAT
* * * ** *
5754827 AAAGGCTTAACGACTTTGGAAAAATAAATAAAGCTCCTCTAAAT
1 AGAGGCTCAACAACTTTGGAAAAATAAATATGGCTTCTCTAAAT
* * *
5754871 AGAGACTTAACAACTTTGAAAAAATAAATATGGC-TCATCTAAAT
1 AGAGGCTCAACAACTTTGGAAAAATAAATATGGCTTC-TCTAAAT
* ** *
5754915 AAAGGCTCAACAACTTT-GAGAAAATAAATGCGGCTCCTCT-AAT
1 AGAGGCTCAACAACTTTGGA-AAAATAAATATGGCTTCTCTAAAT
* *
5754958 CAGAAGCTCAACAACTTT-AAAAAATAAATA
1 -AGAGGCTCAACAACTTTGGAAAAATAAATA
5754988 AAGCTCCTCG
Statistics
Matches: 204, Mismatches: 38, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
43 16 0.08
44 182 0.89
45 6 0.03
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.27
Consensus pattern (44 bp):
AGAGGCTCAACAACTTTGGAAAAATAAATATGGCTTCTCTAAAT
Found at i:5754813 original size:88 final size:88
Alignment explanation
Indices: 5754695--5754987 Score: 367
Period size: 88 Copynumber: 3.3 Consensus size: 88
5754685 TCCCCTAAGC
* * * *
5754695 AGAGGCTC-ACAACTTTTGGAAAAATGAATATGGCTTC-TTTAAATAGAGGCTCAATAACTTTGA
1 AGAGGCTCAACAAC-TTTGAAAAAATAAATATGGC-TCATTTAAATAAAGGCTCAACAACTTTGA
*
5754758 AAAAATAAATAAGGCTTCTCTAATT
64 AAAAATAAATAAGGCTCCTCTAATT
* * * * *
5754783 AGAGGCTCAACAATTTTGGAAAAATAAATATGGCTCATTTAAATAAAGGCTTAACGACTTTGGAA
1 AGAGGCTCAACAACTTTGAAAAAATAAATATGGCTCATTTAAATAAAGGCTCAACAACTTTGAAA
* *
5754848 AAATAAATAAAGCTCCTCTAAAT
66 AAATAAATAAGGCTCCTCTAATT
* * * *
5754871 AGAGACTTAACAACTTTGAAAAAATAAATATGGCTCATCTAAATAAAGGCTCAACAACTTTGAGA
1 AGAGGCTCAACAACTTTGAAAAAATAAATATGGCTCATTTAAATAAAGGCTCAACAACTTTGAAA
** *
5754936 AAATAAATGCGGCTCCTCTAATC
66 AAATAAATAAGGCTCCTCTAATT
*
5754959 AGAAGCTCAACAACTTT-AAAAAATAAATA
1 AGAGGCTCAACAACTTTGAAAAAATAAATA
5754988 AAGCTCCTCG
Statistics
Matches: 176, Mismatches: 27, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
87 14 0.08
88 158 0.90
89 4 0.02
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.27
Consensus pattern (88 bp):
AGAGGCTCAACAACTTTGAAAAAATAAATATGGCTCATTTAAATAAAGGCTCAACAACTTTGAAA
AAATAAATAAGGCTCCTCTAATT
Found at i:5754895 original size:132 final size:132
Alignment explanation
Indices: 5754709--5754996 Score: 334
Period size: 132 Copynumber: 2.2 Consensus size: 132
5754699 GCTCACAACT
* ** * * * *
5754709 TTTGGAAAAATGAATATGGCTTCTTTAAATAGAGGCTCAATAACTTTGAAAAAATAAATAAGGCT
1 TTTGGAAAAATAAATAAAGCTCCTCTAAATAGAGACTCAACAACTTTGAAAAAATAAATAAGGC-
* * * * * *
5754774 TC-TCTAATTAGAGGCTCAACAATTTTG-GAAAAATAAATATGGCTCATTTAAAT-A-AAGGCTT
65 TCATCTAAATAAAGGCTCAACAACTTTGAG-AAAATAAATACGGCTCATCT-AATCAGAA-GCTC
*
5754835 AACGAC
127 AACAAC
* *
5754841 TTTGGAAAAATAAATAAAGCTCCTCTAAATAGAGACTTAACAACTTTGAAAAAATAAATATGGCT
1 TTTGGAAAAATAAATAAAGCTCCTCTAAATAGAGACTCAACAACTTTGAAAAAATAAATAAGGCT
* *
5754906 CATCTAAATAAAGGCTCAACAACTTTGAGAAAATAAATGCGGCTCCTCTAATCAGAAGCTCAACA
66 CATCTAAATAAAGGCTCAACAACTTTGAGAAAATAAATACGGCTCATCTAATCAGAAGCTCAACA
5754971 AC
131 AC
*
5754973 TTT-AAAAAATAAATAAAGCTCCTC
1 TTTGGAAAAATAAATAAAGCTCCTC
5754997 GATAATCATG
Statistics
Matches: 133, Mismatches: 19, Indels: 9
0.83 0.12 0.06
Matches are distributed among these distances:
131 25 0.19
132 105 0.79
133 3 0.02
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.27
Consensus pattern (132 bp):
TTTGGAAAAATAAATAAAGCTCCTCTAAATAGAGACTCAACAACTTTGAAAAAATAAATAAGGCT
CATCTAAATAAAGGCTCAACAACTTTGAGAAAATAAATACGGCTCATCTAATCAGAAGCTCAACA
AC
Found at i:5755129 original size:19 final size:18
Alignment explanation
Indices: 5755094--5755143 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
5755084 CAATTCAAAG
5755094 ATTCACAAGAATTTTTAA
1 ATTCACAAGAATTTTTAA
* *
5755112 ATTCACAATAACTTTTTAG
1 ATTCACAAGAA-TTTTTAA
* *
5755131 CTTCGCAAGAATT
1 ATTCACAAGAATT
5755144 CACTAAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (18 bp):
ATTCACAAGAATTTTTAA
Found at i:5755199 original size:33 final size:33
Alignment explanation
Indices: 5755162--5755225 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
5755152 TTTGATTCCC
5755162 AAAATCTCA-ATTTGACAAGAATTAAAGATTCAT
1 AAAATCTCATATTTG-CAAGAATTAAAGATTCAT
* * *
5755195 AAAATTTCATATTTGCAAGATTTCAAGATTC
1 AAAATCTCATATTTGCAAGAATTAAAGATTC
5755226 GCATTTGTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 22 0.81
34 5 0.19
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.34
Consensus pattern (33 bp):
AAAATCTCATATTTGCAAGAATTAAAGATTCAT
Found at i:5755542 original size:42 final size:46
Alignment explanation
Indices: 5755477--5755569 Score: 131
Period size: 44 Copynumber: 2.1 Consensus size: 46
5755467 ACGATTCACG
* * *
5755477 TTCAATAAATCTTAGAGTTTCACAT-CTA-AGTTCAAAGGTTCTCA
1 TTCAATAAATCTTAGAGATTCACATCCAAGAGTTCAAAGCTTCTCA
5755521 TTCAA-AAAT-TTAGAGATTCACATCCAAGAGTTCAAAGCTTCTCA
1 TTCAATAAATCTTAGAGATTCACATCCAAGAGTTCAAAGCTTCTCA
5755565 TTCAA
1 TTCAA
5755570 GTTTGAAGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
42 13 0.30
43 6 0.14
44 25 0.57
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (46 bp):
TTCAATAAATCTTAGAGATTCACATCCAAGAGTTCAAAGCTTCTCA
Found at i:5755636 original size:44 final size:42
Alignment explanation
Indices: 5755571--5755652 Score: 119
Period size: 44 Copynumber: 1.9 Consensus size: 42
5755561 CTCATTCAAG
* *
5755571 TTTGAAGATTCACATTTGATAAATCTTAGAGTTTCACATCTAAA
1 TTTGAAGATTCACATTCGATAAATC-T-GAGATTCACATCTAAA
*
5755615 TTTGAAGGTTCACATTCGATAAATCTGAGATTCACATC
1 TTTGAAGATTCACATTCGATAAATCTGAGATTCACATC
5755653 CAAAAAGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
42 11 0.31
43 1 0.03
44 23 0.66
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (42 bp):
TTTGAAGATTCACATTCGATAAATCTGAGATTCACATCTAAA
Found at i:5755649 original size:22 final size:22
Alignment explanation
Indices: 5755576--5755651 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 22
5755566 TCAAGTTTGA
*
5755576 AGATTCACATTTGATAAATCTTAG
1 AGATTCACATTCGATAAATC-T-G
* *
5755600 AGTTTCACA-TC--TAAATTTG
1 AGATTCACATTCGATAAATCTG
*
5755619 AAGGTTCACATTCGATAAATCTG
1 -AGATTCACATTCGATAAATCTG
5755642 AGATTCACAT
1 AGATTCACAT
5755652 CCAAAAAGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
19 1 0.02
20 9 0.21
21 7 0.17
22 9 0.21
23 8 0.19
24 8 0.19
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (22 bp):
AGATTCACATTCGATAAATCTG
Found at i:5755753 original size:23 final size:23
Alignment explanation
Indices: 5755721--5755767 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
5755711 CAAAATTTTG
5755721 AAACTCAAAGATTCTCA-TTGAA
1 AAACTCAAAGATTCTCATTTGAA
*
5755743 AAACATCAAAGATTCTTATTTGAA
1 AAAC-TCAAAGATTCTCATTTGAA
5755767 A
1 A
5755768 CTCAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.18
23 12 0.55
24 6 0.27
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.30
Consensus pattern (23 bp):
AAACTCAAAGATTCTCATTTGAA
Found at i:5756333 original size:145 final size:145
Alignment explanation
Indices: 5756071--5756752 Score: 749
Period size: 145 Copynumber: 4.7 Consensus size: 145
5756061 GATTTTAAAA
* * * * *
5756071 CACCAAAACTCATGACATATTA-TAGAATTGAGATCTAAAAAGTTTCATGAAAATCCAAGCTT--
1 CACCAAAAATCATGAAATATTAGGA-AATTAAGATCTAAAAAGTTTCATGAAAATCTAAGCTTAG
* * * * * * *
5756133 GAGAGGTCAAATTACGAAAATACCATTGTAGGGGTATTATGGTAATTTCATACTTTTTTGGGTAC
65 GA-AAGTCAAATTACGAAAATACCCTTATAGGGGTATTTTGATAATTTCACACTTTTTGGGGTAC
*
5756198 TA-CTGTGATTTCAAATG
129 -AGCTATGATTTCAAATG
* *
5756215 CACCAAAAATCATGAAATATTAGGAAATTAAGATATGAAAAGTTTCATGAAAATCTAAG-TTCAG
1 CACCAAAAATCATGAAATATTAGGAAATTAAGATCTAAAAAGTTTCATGAAAATCTAAGCTT-AG
* * * * * *
5756279 GAATGTCAAATTACAAAAATACCCTTATAGGGGTATTTTGATAATTTCATACTTTTTCGGGCACT
65 GAAAGTCAAATTACGAAAATACCCTTATAGGGGTATTTTGATAATTTCACACTTTTTGGGGTACA
* *
5756344 GTTGTGATTTCAAATG
130 GCTATGATTTCAAATG
* * * *
5756360 CACCAAAAATCATGAAATATTAGGCAATTAAGATCTAAAAAGTTTTATGAAAATTTGAGCTTAGG
1 CACCAAAAATCATGAAATATTAGGAAATTAAGATCTAAAAAGTTTCATGAAAATCTAAGCTTAGG
* *
5756425 AAAGCCAAATTACGAAAATACCCTTATAGGAGTATTTTGATAATTTCACACTTTTTGGGGTACAG
66 AAAGTCAAATTACGAAAATACCCTTATAGGGGTATTTTGATAATTTCACACTTTTTGGGGTACAG
5756490 CTATGATTTCAAATG
131 CTATGATTTCAAATG
* * * * * * *
5756505 CATCC-AAAATTATGATATATTATGAAATTAAGATCTGAAAATTTTTATGAAAAT-TCGAGCTT-
1 CA-CCAAAAATCATGAAATATTAGGAAATTAAGATCTAAAAAGTTTCATGAAAATCT-AAGCTTA
* * * * *
5756567 GAAAAGGCTAAATTACCAAAATACCCTTATATGGGTATTTTGGTAATTTCACACTTTTTGGGGTA
64 GGAAAGTC-AAATTACGAAAATACCCTTATAGGGGTATTTTGATAATTTCACACTTTTTGGGGTA
*
5756632 CAGCTATGATTTGAAATG
128 CAGCTATGATTTCAAATG
* * *
5756650 TA-CAAACAATCATGAAATATTATGAAATTAAGATCTAAAGAGTTTCATGAAAAT-TCAAGCTT-
1 CACCAAA-AATCATGAAATATTAGGAAATTAAGATCTAAAAAGTTTCATGAAAATCT-AAGCTTA
* * *
5756712 GAAAAAG-CTAAATTACGAAAATATCCTTATAAGGGTATTTT
64 G-GAAAGTC-AAATTACGAAAATACCCTTATAGGGGTATTTT
5756753 AGTCATTTTA
Statistics
Matches: 469, Mismatches: 57, Indels: 23
0.85 0.10 0.04
Matches are distributed among these distances:
143 3 0.01
144 59 0.13
145 396 0.84
146 11 0.02
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (145 bp):
CACCAAAAATCATGAAATATTAGGAAATTAAGATCTAAAAAGTTTCATGAAAATCTAAGCTTAGG
AAAGTCAAATTACGAAAATACCCTTATAGGGGTATTTTGATAATTTCACACTTTTTGGGGTACAG
CTATGATTTCAAATG
Found at i:5760884 original size:17 final size:16
Alignment explanation
Indices: 5760847--5760895 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
5760837 AGGCATGTAA
* *
5760847 AAAAAAAAAAAAAAAG
1 AAAAAAAAAGAAAATG
5760863 AAAAAAAAAAGAGAAATG
1 -AAAAAAAAAGA-AAATG
*
5760881 AAAAGAAAAGAAAAT
1 AAAAAAAAAGAAAAT
5760896 TGGTTATGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 4 0.14
17 20 0.71
18 4 0.14
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (16 bp):
AAAAAAAAAGAAAATG
Found at i:5761385 original size:26 final size:24
Alignment explanation
Indices: 5761352--5761411 Score: 59
Period size: 27 Copynumber: 2.4 Consensus size: 24
5761342 GAAAGAACGC
*
5761352 AAAA-GAAAAAGTGAGAAAAAAAAA
1 AAAAGGAAAAAG-AAGAAAAAAAAA
*
5761376 AGAAAGGAAATAAAGAAGAAAAAAGAA
1 A-AAAGG-AA-AAAGAAGAAAAAAAAA
5761403 AAAAGGAAA
1 AAAAGGAAA
5761412 TATATGAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
24 2 0.07
25 5 0.17
26 6 0.20
27 13 0.43
28 4 0.13
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (24 bp):
AAAAGGAAAAAGAAGAAAAAAAAA
Found at i:5761800 original size:17 final size:17
Alignment explanation
Indices: 5761746--5761802 Score: 64
Period size: 17 Copynumber: 3.3 Consensus size: 17
5761736 TGCATGGTGT
5761746 AATAA-TAAAAAAGGTAAA
1 AATAAGTAAAAAA-G-AAA
*
5761764 AAAAAGTAAAAAAGAAA
1 AATAAGTAAAAAAGAAA
5761781 AATAAG-AAAGAAAGAAA
1 AATAAGTAAA-AAAGAAA
5761798 AATAA
1 AATAA
5761803 ATGAAAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
16 3 0.09
17 20 0.57
18 5 0.14
19 7 0.20
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.11
Consensus pattern (17 bp):
AATAAGTAAAAAAGAAA
Found at i:5762438 original size:22 final size:22
Alignment explanation
Indices: 5762413--5762482 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
5762403 AATGAAGATT
*
5762413 TAAGCCCAGATTAGCTAGCACA
1 TAAGCCCAGATTAGCTGGCACA
* *
5762435 TAAGCCCAGTTTAAC-GGCACA
1 TAAGCCCAGATTAGCTGGCACA
** *
5762456 TAAGCTAAGATTAGCTGGCATA
1 TAAGCCCAGATTAGCTGGCACA
5762478 TAAGC
1 TAAGC
5762483 TCGAATTAGT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
21 16 0.41
22 23 0.59
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (22 bp):
TAAGCCCAGATTAGCTGGCACA
Found at i:5762793 original size:97 final size:97
Alignment explanation
Indices: 5762689--5762990 Score: 408
Period size: 97 Copynumber: 3.1 Consensus size: 97
5762679 GGCACTAACA
* **
5762689 AAAGATTTAATCCCAGATTATCTGGCACATTATGAAAAGATTTTAAGCCCACCTTAGTTGGCACC
1 AAAGATTTAAGCCCAGATTATCTGGCACACCATGAAAAGATTTTAAGCCCACCTTAGTTGGCACC
*
5762754 TAAATTTAAGCCCAGTTTATTTGGCGCCAAAG
66 CAAATTTAAGCCCAGTTTATTTGGCGCCAAAG
* * * * *
5762786 AAAGATTTAAGCCTAGGTTATCTAGCACACCATGAAAAGATTTTAAGCCCAGCTTAGTTGACACC
1 AAAGATTTAAGCCCAGATTATCTGGCACACCATGAAAAGATTTTAAGCCCACCTTAGTTGGCACC
*
5762851 CAAATTTAAGCCCAGTTTATTTAGCGCCAAAG
66 CAAATTTAAGCCCAGTTTATTTGGCGCCAAAG
* * * * * *
5762883 AAAGATTTAAGCCCAAATTATTTGGCACACCATGAAAAGATTGTAAACCTAACC-TAGCTGGCAC
1 AAAGATTTAAGCCCAGATTATCTGGCACACCATGAAAAGATTTTAAGCC-CACCTTAGTTGGCAC
* * * *
5762947 CCAAATTTAATCCCAATTTAATTGGCACCAAAG
65 CCAAATTTAAGCCCAGTTTATTTGGCGCCAAAG
5762980 AAAGATTTAAG
1 AAAGATTTAAG
5762991 ATTAAATTAT
Statistics
Matches: 178, Mismatches: 26, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
97 176 0.99
98 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (97 bp):
AAAGATTTAAGCCCAGATTATCTGGCACACCATGAAAAGATTTTAAGCCCACCTTAGTTGGCACC
CAAATTTAAGCCCAGTTTATTTGGCGCCAAAG
Found at i:5762896 original size:33 final size:33
Alignment explanation
Indices: 5762757--5762897 Score: 105
Period size: 33 Copynumber: 4.3 Consensus size: 33
5762747 TGGCACCTAA
* *
5762757 ATTTAAGCCCAGTTTATTTGGCGCCAAAGAAAG
1 ATTTAAGCCCAGTTTATTTAGCACCAAAGAAAG
* * * * *
5762790 ATTTAAGCCTAGGTTATCTAGCACACCATGAAAAG
1 ATTTAAGCCCAGTTTATTTAGCAC-CAAAG-AAAG
* * *
5762825 ATTTTAAGCCCAGCTTAGTT-GACACC----CAA-
1 A-TTTAAGCCCAGTTTATTTAG-CACCAAAGAAAG
*
5762854 ATTTAAGCCCAGTTTATTTAGCGCCAAAGAAAG
1 ATTTAAGCCCAGTTTATTTAGCACCAAAGAAAG
5762887 ATTTAAGCCCA
1 ATTTAAGCCCA
5762898 AATTATTTGG
Statistics
Matches: 82, Mismatches: 16, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
28 19 0.23
29 2 0.02
30 2 0.02
32 2 0.02
33 30 0.37
34 3 0.04
35 7 0.09
36 17 0.21
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (33 bp):
ATTTAAGCCCAGTTTATTTAGCACCAAAGAAAG
Found at i:5763044 original size:97 final size:97
Alignment explanation
Indices: 5762689--5763056 Score: 405
Period size: 97 Copynumber: 3.8 Consensus size: 97
5762679 GGCACTAACA
* * * * ** *
5762689 AAAGATTTAATCCCAGATTATCTGGCACATTATGAAAAGATTTTAAGCCCACCTTAGTTGGCACC
1 AAAGATTTAAGCCTAAATTATTTGGCACACCATGAAAAGATTTTAAGCCCAACTTAGTTGGCACC
*
5762754 TAAATTTAAGCCCAGTTTATTTGGCGCCAAAG
66 CAAATTTAAGCCCAGTTTATTTGGCGCCAAAG
** * * * *
5762786 AAAGATTTAAGCCTAGGTTATCTAGCACACCATGAAAAGATTTTAAGCCCAGCTTAGTTGACACC
1 AAAGATTTAAGCCTAAATTATTTGGCACACCATGAAAAGATTTTAAGCCCAACTTAGTTGGCACC
*
5762851 CAAATTTAAGCCCAGTTTATTTAGCGCCAAAG
66 CAAATTTAAGCCCAGTTTATTTGGCGCCAAAG
* * * * * *
5762883 AAAGATTTAAGCCCAAATTATTTGGCACACCATGAAAAGATTGTAAACCTAACCTAGCTGGCACC
1 AAAGATTTAAGCCTAAATTATTTGGCACACCATGAAAAGATTTTAAGCCCAACTTAGTTGGCACC
* * * *
5762948 CAAATTTAATCCCAATTTAATTGGCACCAAAG
66 CAAATTTAAGCCCAGTTTATTTGGCGCCAAAG
** **** ** *
5762980 AAAGATTTAAGATTAAATTATTTGGCGTGTCATGAAAAGATTTTAAGCTTAACTTA-TCTAGCAC
1 AAAGATTTAAGCCTAAATTATTTGGCACACCATGAAAAGATTTTAAGCCCAACTTAGT-TGGCAC
5763044 CCTAAATTTAAGC
65 CC-AAATTTAAGC
5763057 TTAGATTATT
Statistics
Matches: 228, Mismatches: 41, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
97 219 0.96
98 9 0.04
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (97 bp):
AAAGATTTAAGCCTAAATTATTTGGCACACCATGAAAAGATTTTAAGCCCAACTTAGTTGGCACC
CAAATTTAAGCCCAGTTTATTTGGCGCCAAAG
Found at i:5763194 original size:33 final size:34
Alignment explanation
Indices: 5763077--5763199 Score: 126
Period size: 33 Copynumber: 3.6 Consensus size: 34
5763067 TAACATAAAA
* * *
5763077 GAAAATTTTAAGCCTAGTTTATTTTGCA-CTAAA
1 GAAAATTTTAAGCCCAGTTTATCTTGCACCTAAT
* * *
5763110 CAAAATTTTAAACCCAATTTA-CTTGACACCTAAT
1 GAAAATTTTAAGCCCAGTTTATCTTG-CACCTAAT
*
5763144 GAAAAGATTTTAAGCCCAGTTTATCTTGTACCTAAT
1 G-AAA-ATTTTAAGCCCAGTTTATCTTGCACCTAAT
*
5763180 GAAAA-TTTAAGCCCATTTTA
1 GAAAATTTTAAGCCCAGTTTA
5763200 GTTGGCACGT
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
32 3 0.04
33 33 0.45
34 5 0.07
35 6 0.08
36 23 0.31
37 4 0.05
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (34 bp):
GAAAATTTTAAGCCCAGTTTATCTTGCACCTAAT
Found at i:5763245 original size:22 final size:23
Alignment explanation
Indices: 5763197--5763245 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
5763187 TAAGCCCATT
* *
5763197 TTAGTTGGCACGTAAGCCTAAGA
1 TTAGTTGGCACATAAACCTAAGA
5763220 TTAGTTGGCACATAAACCT-AGA
1 TTAGTTGGCACATAAACCTAAGA
5763242 TTAG
1 TTAG
5763246 CAGTAAGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (23 bp):
TTAGTTGGCACATAAACCTAAGA
Found at i:5763447 original size:37 final size:37
Alignment explanation
Indices: 5763389--5763564 Score: 133
Period size: 37 Copynumber: 4.8 Consensus size: 37
5763379 TGTCTTGGTT
5763389 GTTCTTTAATTACTTGACTTGCAGTGTTATCCCGATC
1 GTTCTTTAATTACTTGACTTGCAGTGTTATCCCGATC
* * * * *
5763426 GTTCTTTAATTATTTGTCTTGCGGTGTTGTTCCGATC
1 GTTCTTTAATTACTTGACTTGCAGTGTTATCCCGATC
** * * **
5763463 GTTCTTT-ATTTTTTGACTTACTA-TGTTGTCCTAATC
1 GTTCTTTAATTACTTGACTTGC-AGTGTTATCCCGATC
* * * * * * ** *
5763499 GTTTTTTATTTTC-TGATTTACAATGTTATCCTAATT
1 GTTCTTTAATTACTTGACTTGCAGTGTTATCCCGATC
*
5763535 GTTCTTTAATTACTTGACTTGCAATGTTAT
1 GTTCTTTAATTACTTGACTTGCAGTGTTAT
5763565 TTAGTCATTC
Statistics
Matches: 112, Mismatches: 23, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
35 1 0.01
36 55 0.49
37 56 0.50
ACGTcount: A:0.18, C:0.16, G:0.14, T:0.52
Consensus pattern (37 bp):
GTTCTTTAATTACTTGACTTGCAGTGTTATCCCGATC
Found at i:5763500 original size:36 final size:36
Alignment explanation
Indices: 5763460--5763564 Score: 120
Period size: 36 Copynumber: 2.9 Consensus size: 36
5763450 TGTTGTTCCG
* * *
5763460 ATCGTTCTTTATTTTTTGACTTACTATGTTGTCCTA
1 ATCGTTCTTTATTTTCTGACTTACAATGTTATCCTA
* *
5763496 ATCGTTTTTTATTTTCTGATTTACAATGTTATCCTA
1 ATCGTTCTTTATTTTCTGACTTACAATGTTATCCTA
* * * *
5763532 ATTGTTCTTTAATTACTTGACTTGCAATGTTAT
1 ATCGTTCTTTATTTTC-TGACTTACAATGTTAT
5763565 TTAGTCATTC
Statistics
Matches: 57, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
36 43 0.75
37 14 0.25
ACGTcount: A:0.21, C:0.14, G:0.10, T:0.54
Consensus pattern (36 bp):
ATCGTTCTTTATTTTCTGACTTACAATGTTATCCTA
Found at i:5763636 original size:18 final size:18
Alignment explanation
Indices: 5763610--5763645 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5763600 CCCAAACCTT
5763610 AAAACCAAAAAAATAAAA
1 AAAACCAAAAAAATAAAA
*
5763628 AAAAGCAAAAAAATAAAA
1 AAAACCAAAAAAATAAAA
5763646 CTATTGAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.83, C:0.08, G:0.03, T:0.06
Consensus pattern (18 bp):
AAAACCAAAAAAATAAAA
Found at i:5765164 original size:27 final size:28
Alignment explanation
Indices: 5765112--5765165 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
5765102 TTTTTAATTT
*
5765112 TTTTATATATTATTTATTTCATTTTAAG
1 TTTTATATATTATTTATTGCATTTTAAG
*
5765140 TTTTAT-TGTTATTTA-TGCATATTTAA
1 TTTTATATATTATTTATTGCAT-TTTAA
5765166 AACTTATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 4 0.17
27 13 0.57
28 6 0.26
ACGTcount: A:0.28, C:0.04, G:0.06, T:0.63
Consensus pattern (28 bp):
TTTTATATATTATTTATTGCATTTTAAG
Found at i:5765238 original size:4 final size:4
Alignment explanation
Indices: 5765229--5765260 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
5765219 AATGAAAGCA
5765229 AAAT AAAT AAAT AAAT AAAT -AA- AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
5765261 TGAGTAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 4 0.15
4 22 0.85
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:5765256 original size:10 final size:10
Alignment explanation
Indices: 5765203--5765260 Score: 53
Period size: 10 Copynumber: 5.5 Consensus size: 10
5765193 TTGTTTTTAT
* *
5765203 AATAATAATT
1 AATAAAAATA
5765213 AATAAAAATGA
1 AATAAAAAT-A
**
5765224 AAGCAAAATA
1 AATAAAAATA
5765234 AATAAATAAATA
1 AAT-AA-AAATA
5765246 AATAAAAATA
1 AATAAAAATA
5765256 AATAA
1 AATAA
5765261 TGAGTAATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
10 21 0.54
11 10 0.26
12 8 0.21
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.22
Consensus pattern (10 bp):
AATAAAAATA
Found at i:5765812 original size:29 final size:30
Alignment explanation
Indices: 5765780--5765842 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
5765770 TAAATACTCA
*
5765780 AAACTTAAAATCCCAAAA-CCTAAAACCTT
1 AAACTCAAAATCCCAAAACCCTAAAACCTT
* * *
5765809 AAACTCGAAATCTCAAAACCCTAAAACTTT
1 AAACTCAAAATCCCAAAACCCTAAAACCTT
5765839 AAAC
1 AAAC
5765843 CCCAAAACTC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 15 0.52
30 14 0.48
ACGTcount: A:0.51, C:0.27, G:0.02, T:0.21
Consensus pattern (30 bp):
AAACTCAAAATCCCAAAACCCTAAAACCTT
Found at i:5765842 original size:15 final size:15
Alignment explanation
Indices: 5765824--5765881 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
5765814 CGAAATCTCA
5765824 AAACCCTAAAACTTT
1 AAACCCTAAAACTTT
* *
5765839 AAACCCCAAAACTCT
1 AAACCCTAAAACTTT
* * *
5765854 AAACCTCGAAACCTTA
1 AAACC-CTAAAACTTT
*
5765870 AAATCCTAAAAC
1 AAACCCTAAAAC
5765882 CCTTGAAACC
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
15 23 0.70
16 10 0.30
ACGTcount: A:0.48, C:0.31, G:0.02, T:0.19
Consensus pattern (15 bp):
AAACCCTAAAACTTT
Found at i:5765858 original size:30 final size:30
Alignment explanation
Indices: 5765793--5765871 Score: 81
Period size: 30 Copynumber: 2.7 Consensus size: 30
5765783 CTTAAAATCC
* * *
5765793 CAAAA-CCTAAAACCTTAAACTCGAAATCT
1 CAAAACCCTAAAACCTTAAACCCCAAAACT
*
5765822 CAAAACCCTAAAACTTTAAACCCCAAAACT
1 CAAAACCCTAAAACCTTAAACCCCAAAACT
* *
5765852 CTAAA-CCTCGAAACCTTAAA
1 CAAAACCCT-AAAACCTTAAA
5765872 ATCCTAAAAC
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
29 8 0.20
30 33 0.80
ACGTcount: A:0.48, C:0.30, G:0.03, T:0.19
Consensus pattern (30 bp):
CAAAACCCTAAAACCTTAAACCCCAAAACT
Found at i:5765872 original size:23 final size:23
Alignment explanation
Indices: 5765795--5765898 Score: 72
Period size: 23 Copynumber: 4.5 Consensus size: 23
5765785 TAAAATCCCA
5765795 AAACCT-AAAAC-CTTAAA-CTCG
1 AAACCTCAAAACTC-TAAACCTCG
* * * **
5765816 AAATCTCAAAACCCTAAAACTTT
1 AAACCTCAAAACTCTAAACCTCG
*
5765839 AAACCCCAAAACTCTAAACCTCG
1 AAACCTCAAAACTCTAAACCTCG
* *
5765862 AAACCTTAAAA-TCCTAAAACCCTTG
1 AAACCTCAAAACT-CT-AAA-CCTCG
5765887 AAACCTCAAAAC
1 AAACCTCAAAAC
5765899 CTTTCAATTT
Statistics
Matches: 63, Mismatches: 13, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
21 5 0.08
22 10 0.16
23 31 0.49
24 3 0.05
25 14 0.22
ACGTcount: A:0.47, C:0.31, G:0.03, T:0.19
Consensus pattern (23 bp):
AAACCTCAAAACTCTAAACCTCG
Found at i:5765940 original size:8 final size:8
Alignment explanation
Indices: 5765927--5766024 Score: 78
Period size: 8 Copynumber: 12.4 Consensus size: 8
5765917 TAAACCTTCC
5765927 AAACCCTA
1 AAACCCTA
5765935 AAACCCTTA
1 AAACCC-TA
* *
5765944 GAACCTTA
1 AAACCCTA
5765952 AAACCCTA
1 AAACCCTA
*
5765960 CAACCCTTA
1 AAACCC-TA
5765969 AAACCCTA
1 AAACCCTA
* *
5765977 AAACCTTG
1 AAACCCTA
*
5765985 AAA-TCTCA
1 AAACCCT-A
5765993 AAA-CC-A
1 AAACCCTA
5765999 AAACCCTA
1 AAACCCTA
*
5766007 AAATCC-A
1 AAACCCTA
5766014 AAACCCTA
1 AAACCCTA
5766022 AAA
1 AAA
5766025 TCTCAAAACC
Statistics
Matches: 70, Mismatches: 14, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
6 4 0.06
7 9 0.13
8 44 0.63
9 13 0.19
ACGTcount: A:0.49, C:0.33, G:0.02, T:0.16
Consensus pattern (8 bp):
AAACCCTA
Found at i:5765955 original size:25 final size:24
Alignment explanation
Indices: 5765914--5765981 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 24
5765904 AATTTCCAAA
*
5765914 CCTTAAACCTTCCAAACCCTAAAAC
1 CCTTAAACCTT-AAAACCCTAAAAC
*
5765939 CCTTAGAACCTTAAAACCCTACAAC
1 CCTTA-AACCTTAAAACCCTAAAAC
*
5765964 CCTTAAAACCCTAAAACC
1 CCTT-AAACCTTAAAACC
5765982 TTGAAATCTC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 31 0.82
26 7 0.18
ACGTcount: A:0.41, C:0.38, G:0.01, T:0.19
Consensus pattern (24 bp):
CCTTAAACCTTAAAACCCTAAAAC
Found at i:5765983 original size:16 final size:16
Alignment explanation
Indices: 5765927--5766040 Score: 85
Period size: 16 Copynumber: 7.2 Consensus size: 16
5765917 TAAACCTTCC
*
5765927 AAACCCTAAAACCCTTA
1 AAACCTTAAAACCC-TA
*
5765944 GAACCTTAAAACCCTA
1 AAACCTTAAAACCCTA
*
5765960 CAACCCTTAAAACCCTA
1 -AAACCTTAAAACCCTA
* *
5765977 AAACCTTGAAA-TCTCA
1 AAACCTTAAAACCCT-A
5765993 AAACC--AAAACCCTA
1 AAACCTTAAAACCCTA
5766007 AAATCC--AAAACCCTA
1 AAA-CCTTAAAACCCTA
* * *
5766022 AAATCTCAAAACCTTA
1 AAACCTTAAAACCCTA
5766038 AAA
1 AAA
5766041 TGAGACCCTA
Statistics
Matches: 80, Mismatches: 11, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
14 8 0.10
15 18 0.22
16 28 0.35
17 26 0.32
ACGTcount: A:0.49, C:0.32, G:0.02, T:0.18
Consensus pattern (16 bp):
AAACCTTAAAACCCTA
Found at i:5766017 original size:21 final size:22
Alignment explanation
Indices: 5765976--5766018 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5765966 TTAAAACCCT
* *
5765976 AAAACCTTGAAATCTCAAAACC
1 AAAACCCTAAAATCTCAAAACC
5765998 AAAACCCTAAAATC-CAAAACC
1 AAAACCCTAAAATCTCAAAACC
5766019 CTAAAATCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.53, C:0.30, G:0.02, T:0.14
Consensus pattern (22 bp):
AAAACCCTAAAATCTCAAAACC
Found at i:5766018 original size:37 final size:39
Alignment explanation
Indices: 5765927--5766034 Score: 112
Period size: 37 Copynumber: 2.7 Consensus size: 39
5765917 TAAACCTTCC
* * * *
5765927 AAACCCTAAAACCCTTAGAACCTTAAAACCCTACAACCCTTA
1 AAACCCTAAAACCC-TAAAATCTCAAAA-CC-AAAACCCTTA
* *
5765969 AAACCCTAAAACCTTGAAATCTCAAAACCAAAACCC-TA
1 AAACCCTAAAACCCTAAAATCTCAAAACCAAAACCCTTA
*
5766007 AAATCC-AAAACCCTAAAATCTCAAAACC
1 AAACCCTAAAACCCTAAAATCTCAAAACC
5766035 TTAAAATGAG
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
37 20 0.35
38 7 0.12
39 6 0.11
40 2 0.04
41 9 0.16
42 13 0.23
ACGTcount: A:0.48, C:0.33, G:0.02, T:0.17
Consensus pattern (39 bp):
AAACCCTAAAACCCTAAAATCTCAAAACCAAAACCCTTA
Found at i:5766040 original size:8 final size:8
Alignment explanation
Indices: 5765862--5766040 Score: 75
Period size: 8 Copynumber: 22.4 Consensus size: 8
5765852 CTAAACCTCG
5765862 AAACCTTA
1 AAACCTTA
5765870 AAATCC-TA
1 AAA-CCTTA
*
5765878 AAACCCTTG
1 AAA-CCTTA
*
5765887 AAACCTCA
1 AAACCTTA
*
5765895 AAACCTTT
1 AAACCTTA
* * *
5765903 CAA-TTTCC
1 AAACCTT-A
5765911 AAACCTT-
1 AAACCTTA
*
5765918 AAACCTTCC
1 AAACCTT-A
*
5765927 AAACCCTA
1 AAACCTTA
5765935 AAACCCTTA
1 AAA-CCTTA
*
5765944 GAACCTTA
1 AAACCTTA
*
5765952 AAACCCTA
1 AAACCTTA
*
5765960 CAACCCTTA
1 -AAACCTTA
*
5765969 AAACCCTA
1 AAACCTTA
*
5765977 AAACCTTG
1 AAACCTTA
* *
5765985 AAATCTCA
1 AAACCTTA
5765993 AAACC--A
1 AAACCTTA
*
5765999 AAACCCTA
1 AAACCTTA
5766007 AAATCC--A
1 AAA-CCTTA
*
5766014 AAACCCTA
1 AAACCTTA
* *
5766022 AAATCTCA
1 AAACCTTA
5766030 AAACCTTA
1 AAACCTTA
5766038 AAA
1 AAA
5766041 TGAGACCCTA
Statistics
Matches: 126, Mismatches: 32, Indels: 26
0.68 0.17 0.14
Matches are distributed among these distances:
6 8 0.06
7 13 0.10
8 77 0.61
9 28 0.22
ACGTcount: A:0.46, C:0.32, G:0.02, T:0.21
Consensus pattern (8 bp):
AAACCTTA
Found at i:5766041 original size:16 final size:15
Alignment explanation
Indices: 5765992--5766041 Score: 75
Period size: 15 Copynumber: 3.3 Consensus size: 15
5765982 TTGAAATCTC
5765992 AAAA-CCAAAACCCT
1 AAAATCCAAAACCCT
5766006 AAAATCCAAAACCCT
1 AAAATCCAAAACCCT
*
5766021 AAAATCTCAAAACCTT
1 AAAATC-CAAAACCCT
5766037 AAAAT
1 AAAAT
5766042 GAGACCCTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
14 4 0.12
15 16 0.48
16 13 0.39
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (15 bp):
AAAATCCAAAACCCT
Found at i:5767618 original size:20 final size:20
Alignment explanation
Indices: 5767593--5767630 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5767583 AGTAACTATT
5767593 TTCCTGAAAATGCCACTTGG
1 TTCCTGAAAATGCCACTTGG
*
5767613 TTCCTGAAGATGCCACTT
1 TTCCTGAAAATGCCACTT
5767631 AGGAAATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (20 bp):
TTCCTGAAAATGCCACTTGG
Found at i:5779111 original size:52 final size:52
Alignment explanation
Indices: 5779023--5779121 Score: 180
Period size: 52 Copynumber: 1.9 Consensus size: 52
5779013 GAAAATAGGC
*
5779023 TTTCATGTTTAAAGTTTTAATTTGATTAATAGCTTGAAAATTTTAGGATAGA
1 TTTCATGTTTAAAGTTTTAATTTGATTAATAACTTGAAAATTTTAGGATAGA
*
5779075 TTTCTTGTTTAAAGTTTTAATTTGATTAATAACTTGAAAATTTTAGG
1 TTTCATGTTTAAAGTTTTAATTTGATTAATAACTTGAAAATTTTAGG
5779122 GTAAATTATA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.33, C:0.04, G:0.14, T:0.48
Consensus pattern (52 bp):
TTTCATGTTTAAAGTTTTAATTTGATTAATAACTTGAAAATTTTAGGATAGA
Found at i:5779118 original size:26 final size:26
Alignment explanation
Indices: 5779037--5779119 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
5779027 ATGTTTAAAG
*
5779037 TTTTAATTTGATTAATAGCTTGAAAA
1 TTTTAATTTGATTAATAACTTGAAAA
* ** ** * *
5779063 TTTTAGGA-TAGATTTCT-TGTTTAAAG
1 TTTTA--ATTTGATTAATAACTTGAAAA
5779089 TTTTAATTTGATTAATAACTTGAAAA
1 TTTTAATTTGATTAATAACTTGAAAA
5779115 TTTTA
1 TTTTA
5779120 GGGTAAATTA
Statistics
Matches: 39, Mismatches: 14, Indels: 8
0.64 0.23 0.13
Matches are distributed among these distances:
24 1 0.03
25 6 0.15
26 25 0.64
27 6 0.15
28 1 0.03
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.49
Consensus pattern (26 bp):
TTTTAATTTGATTAATAACTTGAAAA
Found at i:5783584 original size:20 final size:20
Alignment explanation
Indices: 5783548--5783587 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5783538 TTCTTTTGAA
*
5783548 AAAAATTAATATCATTTTTT
1 AAAAATTAATATAATTTTTT
5783568 AAAAATT-ATATAAATTTTTT
1 AAAAATTAATAT-AATTTTTT
5783588 TATCGATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
AAAAATTAATATAATTTTTT
Found at i:5783585 original size:19 final size:20
Alignment explanation
Indices: 5783548--5783586 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
5783538 TTCTTTTGAA
* *
5783548 AAAAATTAATATCATTTTTT
1 AAAAATTAATATAAATTTTT
5783568 AAAAATT-ATATAAATTTTT
1 AAAAATTAATATAAATTTTT
5783587 TTATCGATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
AAAAATTAATATAAATTTTT
Found at i:5784048 original size:17 final size:17
Alignment explanation
Indices: 5784026--5784116 Score: 62
Period size: 18 Copynumber: 5.2 Consensus size: 17
5784016 TTCATTTTTA
5784026 AAAAAT-ATATTTCTATT
1 AAAAATAATATTT-TATT
5784043 AAAAATAATATTTTATT
1 AAAAATAATATTTTATT
* ** *
5784060 GATAAATAATATCATAAT
1 -AAAAATAATATTTTATT
*
5784078 AAAAATAAAAATTATT-TT
1 AAAAAT-AATATT-TTATT
*
5784096 AAATTATAATATTTTA-T
1 AAA-AATAATATTTTATT
5784113 AAAA
1 AAAA
5784117 TATTTTCGAA
Statistics
Matches: 56, Mismatches: 12, Indels: 13
0.69 0.15 0.16
Matches are distributed among these distances:
17 21 0.38
18 32 0.57
19 3 0.05
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (17 bp):
AAAAATAATATTTTATT
Found at i:5790111 original size:24 final size:24
Alignment explanation
Indices: 5790084--5790150 Score: 127
Period size: 24 Copynumber: 2.8 Consensus size: 24
5790074 GTAGTGAAAA
5790084 AATAAATTATTATACATTTTAATG
1 AATAAATTATTATACATTTTAATG
5790108 AATAAATTATTATACATTTTAATG
1 AATAAATTATTATACATTTTAATG
5790132 AATAAATTATTATAC-TTTT
1 AATAAATTATTATACATTTT
5790151 GGTAGTACAA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
23 4 0.09
24 39 0.91
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (24 bp):
AATAAATTATTATACATTTTAATG
Found at i:5793732 original size:218 final size:214
Alignment explanation
Indices: 5793347--5793979 Score: 723
Period size: 218 Copynumber: 2.9 Consensus size: 214
5793337 TATTTATTCA
* *
5793347 GATTATTGACTTTTGATTTTCTTGTATTCATTTT-TTT-AAACAATTATTTTTAAAATGAATTGA
1 GATTAATGACTTTTGATTTTCTTGTATTCATTTTATTTAAAACAATTATTTTTAAAATTAATTGA
* * * * *
5793410 TTAACCCTTTAGTTTGTAACATTTATATTTTTGACTTTTGATTTTCTTGTGACTTATGATCTTTT
66 TCAAACCTTTATTTTGTAACATTTATATTTTTTACTTTTGATTTTCTTGTGACTTATGGT-TTTT
* * * * * *
5793475 ATTTCTTTTAAGGGTAAAAGTTATATAAGTTTCTTTCATGTCTCTATTACACTTTTTTCTTCTAG
130 A-TT-TTTTAAAGGTGAGAGTTATATAAGTTTCTTTCATGTCTCTATTACACTTTTTTCTCCCAA
* ** * *
5793540 TTATTGTTTGTTATATTATTTT
193 TTATTATTTGCCATATTACTTG
* * * * *
5793562 GATTACTGACTTTTGAATTTCTTGTATTAATTTTATTTAAAACTATTATTTATTAAAATTTATTG
1 GATTAATGACTTTTGATTTTCTTGTATTCATTTTATTTAAAACAATTATTT-TTAAAATTAATTG
** * * * *
5793627 ATCAAACCTTTGATTTTGTAATGTTTATATTTTTTACTTTTGATTATCTTATAATTTATGGTTTT
65 ATCAAACCTTT-ATTTTGTAACATTTATATTTTTTACTTTTGATTTTCTTGTGACTTATGGTTTT
* * *
5793692 CTAGGTTTTTAAAGGTGAGAGTTATATAAATTTCTTTCATGTCTCTTTTACACTTTTTTCTCCCA
129 -TA-TTTTTTAAAGGTGAGAGTTATATAAGTTTCTTTCATGTCTCTATTACACTTTTTTCTCCCA
*
5793757 ATTCTTATTTGCCATATTACTTG
192 ATTATTATTTGCCATATTACTTG
* *
5793780 GATTAATGACTTTTGATTTTCTTGTATTCATTTTCA-TTAAAACCATTATCTGTTAAAATTAATT
1 GATTAATGACTTTTGATTTTCTTGTATTCATTTT-ATTTAAAACAATTAT-TTTTAAAATTAATT
* *
5793844 GATCAAATCTTTAGTTTTATAACATTTATATTTTTTACTTTTGATTTTCTTGTGACTTATGGTTT
64 GATCAAACCTTTA-TTTTGTAACATTTATATTTTTTACTTTTGATTTTCTTGTGACTTATGGTTT
* * * * * *
5793909 TTCATTTCTTTTAAGGATGAGAGATTGTATGAGTGTCTTTTATGTCTCTATTACACTTTCTTCTC
128 TT-ATTT-TTTAAAGG-TGAGAG-TTATATAAGTTTCTTTCATGTCTCTATTACACTTTTTTCTC
*
5793974 TCAATT
189 CCAATT
5793980 CTTGCTTGTC
Statistics
Matches: 349, Mismatches: 57, Indels: 19
0.82 0.13 0.04
Matches are distributed among these distances:
215 31 0.09
216 3 0.01
217 15 0.04
218 209 0.60
219 52 0.15
220 39 0.11
ACGTcount: A:0.25, C:0.11, G:0.10, T:0.54
Consensus pattern (214 bp):
GATTAATGACTTTTGATTTTCTTGTATTCATTTTATTTAAAACAATTATTTTTAAAATTAATTGA
TCAAACCTTTATTTTGTAACATTTATATTTTTTACTTTTGATTTTCTTGTGACTTATGGTTTTTA
TTTTTTAAAGGTGAGAGTTATATAAGTTTCTTTCATGTCTCTATTACACTTTTTTCTCCCAATTA
TTATTTGCCATATTACTTG
Found at i:5795512 original size:6 final size:6
Alignment explanation
Indices: 5795495--5795529 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
5795485 ATTTTTAATC
*
5795495 TGATTT TAATTT TGATTT TGATTT TGATTT T-ATTT
1 TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT
5795530 ATTAAGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.20, C:0.00, G:0.11, T:0.69
Consensus pattern (6 bp):
TGATTT
Found at i:5796245 original size:24 final size:24
Alignment explanation
Indices: 5796183--5796325 Score: 138
Period size: 24 Copynumber: 6.1 Consensus size: 24
5796173 AATATATTTG
**
5796183 TATTAATATATTTATTTGTGTGATT
1 TATTAATATATTTATTTGCATGA-T
5796208 TATT-A-ATA--TATTTGCATGAT
1 TATTAATATATTTATTTGCATGAT
*
5796228 TATTAATATATTTATTTGTATGAT
1 TATTAATATATTTATTTGCATGAT
* *
5796252 TA-T-ATTTAATTTGA-TTGCACGAT
1 TATTAATAT-ATTT-ATTTGCATGAT
* *
5796275 TATTAATATATTTAATTGCTTGAT
1 TATTAATATATTTATTTGCATGAT
*
5796299 TATTAATATATTTATTTGCTTGAT
1 TATTAATATATTTATTTGCATGAT
5796323 TAT
1 TAT
5796326 ATATTTAATT
Statistics
Matches: 99, Mismatches: 10, Indels: 19
0.77 0.08 0.15
Matches are distributed among these distances:
20 5 0.05
21 10 0.10
22 6 0.06
23 18 0.18
24 53 0.54
25 7 0.07
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.55
Consensus pattern (24 bp):
TATTAATATATTTATTTGCATGAT
Found at i:5796256 original size:20 final size:20
Alignment explanation
Indices: 5796188--5796256 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 20
5796178 ATTTGTATTA
*
5796188 ATATATTTATTTGTGTGATT
1 ATATATTTATTTGTATGATT
* *
5796208 -TATTAATATATTTGCATGATTATT
1 ATA-T-ATTTATTTG--T-ATGATT
5796232 AATATATTTATTTGTATGATT
1 -ATATATTTATTTGTATGATT
5796253 ATAT
1 ATAT
5796257 TTAATTTGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 14
0.66 0.09 0.25
Matches are distributed among these distances:
19 2 0.05
20 5 0.14
21 13 0.35
22 1 0.03
23 1 0.03
24 12 0.32
25 1 0.03
26 2 0.05
ACGTcount: A:0.32, C:0.01, G:0.10, T:0.57
Consensus pattern (20 bp):
ATATATTTATTTGTATGATT
Found at i:5796279 original size:47 final size:45
Alignment explanation
Indices: 5796183--5796311 Score: 158
Period size: 47 Copynumber: 2.8 Consensus size: 45
5796173 AATATATTTG
*
5796183 TATTAATATATTTATTTGTGTGATT-TATTAATATATTTGCATGAT
1 TATTAATATATTTATTTGT-TGATTATATTAATATATTTGCACGAT
*
5796228 TATTAATATATTTATTTGTATGATTATATTTAATTTGA-TTGCACGAT
1 TATTAATATATTTATTTGT-TGATTATA-TTAATAT-ATTTGCACGAT
*
5796275 TATTAATATATTTAATTGCTTGA-T-TATTAATATATTT
1 TATTAATATATTTATTTG-TTGATTATATTAATATATTT
5796312 ATTTGCTTGA
Statistics
Matches: 74, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
43 1 0.01
44 8 0.11
45 26 0.35
46 3 0.04
47 34 0.46
48 2 0.03
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.55
Consensus pattern (45 bp):
TATTAATATATTTATTTGTTGATTATATTAATATATTTGCACGAT
Found at i:5796329 original size:20 final size:20
Alignment explanation
Indices: 5796280--5796356 Score: 82
Period size: 20 Copynumber: 3.6 Consensus size: 20
5796270 ACGATTATTA
5796280 ATATATTTAATTGCTTGATTATT
1 ATATATTTAATTGCTTG---ATT
*
5796303 AATATATTTATTTGCTTGATT
1 -ATATATTTAATTGCTTGATT
* *
5796324 ATATATTTAATTACATGATT
1 ATATATTTAATTGCTTGATT
*
5796344 ATATGTTTAATTG
1 ATATATTTAATTG
5796357 TATGTTTTGC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 28 0.60
21 3 0.06
24 16 0.34
ACGTcount: A:0.32, C:0.04, G:0.09, T:0.55
Consensus pattern (20 bp):
ATATATTTAATTGCTTGATT
Found at i:5796390 original size:52 final size:52
Alignment explanation
Indices: 5796322--5796573 Score: 176
Period size: 55 Copynumber: 4.6 Consensus size: 52
5796312 ATTTGCTTGA
* *
5796322 TTATATA-T-TTAATTACATGATTATATGTTTAATTGTATGT-TTTGCATGGT
1 TTATATATTATTATTTACATGATTATATATTTAATT-TATGTATTTGCATGGT
** *
5796372 TTATATATTATTATTTACATGATTGCATGATTTATATATTAT-TATTTGCAT-GA
1 TTATATATTATTATTTACATGATTATAT-ATTTA-AT-TTATGTATTTGCATGGT
* * * *
5796425 TTATATATTTAATTGTATGTTTTGCATGGTTTATATATTATTATTTAAATG-A-TTGCATGAT
1 TTATATA-TT-A-T-TA---TTTACAT-GATTATATATT-TAATTT--ATGTATTTGCATGGT
* *
5796486 TTATATATTATTATTTGCATGATTATATATTTAATTGCATGTTTATTTGCATGGT
1 TTATATATTATTATTTACATGATTATATATTTAATT-TATG--TATTTGCATGGT
* *
5796541 TTATATATTACTATTTACATGATTATACATTTA
1 TTATATATTATTATTTACATGATTATATATTTA
5796574 GTTGCATATT
Statistics
Matches: 159, Mismatches: 19, Indels: 43
0.72 0.09 0.19
Matches are distributed among these distances:
50 7 0.04
51 4 0.03
52 19 0.12
53 23 0.14
54 22 0.14
55 40 0.25
56 1 0.01
57 4 0.03
58 1 0.01
59 3 0.02
60 19 0.12
61 16 0.10
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.54
Consensus pattern (52 bp):
TTATATATTATTATTTACATGATTATATATTTAATTTATGTATTTGCATGGT
Found at i:5796399 original size:31 final size:31
Alignment explanation
Indices: 5796363--5796509 Score: 145
Period size: 31 Copynumber: 5.1 Consensus size: 31
5796353 ATTGTATGTT
*
5796363 TTGCATGGTTTATATATTATTATTTACATGA
1 TTGCATGATTTATATATTATTATTTACATGA
*
5796394 TTGCATGATTTATATATTATTATTTGCATGA
1 TTGCATGATTTATATATTATTATTTACATGA
* *
5796425 TT--AT-ATATT-TA-ATT-GTATGT---T--
1 TTGCATGAT-TTATATATTATTATTTACATGA
* *
5796446 TTGCATGGTTTATATATTATTATTTAAATGA
1 TTGCATGATTTATATATTATTATTTACATGA
*
5796477 TTGCATGATTTATATATTATTATTTGCATGA
1 TTGCATGATTTATATATTATTATTTACATGA
5796508 TT
1 TT
5796510 ATATATTTAA
Statistics
Matches: 94, Mismatches: 10, Indels: 24
0.73 0.08 0.19
Matches are distributed among these distances:
21 2 0.02
23 5 0.05
24 3 0.03
25 3 0.03
26 8 0.09
27 3 0.03
28 4 0.04
29 5 0.05
31 61 0.65
ACGTcount: A:0.29, C:0.05, G:0.12, T:0.54
Consensus pattern (31 bp):
TTGCATGATTTATATATTATTATTTACATGA
Found at i:5796420 original size:23 final size:23
Alignment explanation
Indices: 5796394--5796470 Score: 75
Period size: 23 Copynumber: 3.1 Consensus size: 23
5796384 ATTTACATGA
5796394 TTGCATGATTTATATATTATTAT
1 TTGCATGATTTATATATTATTAT
5796417 TTGCATGA-TTATATATTTAATTGTATGTT
1 TTGCATGATTTATATA-TT-A-T-TA---T
*
5796446 TTGCATGGTTTATATATTATTAT
1 TTGCATGATTTATATATTATTAT
5796469 TT
1 TT
5796471 AAATGATTGC
Statistics
Matches: 45, Mismatches: 1, Indels: 16
0.73 0.02 0.26
Matches are distributed among these distances:
22 7 0.16
23 13 0.29
24 1 0.02
25 1 0.02
26 4 0.09
27 1 0.02
28 1 0.02
29 10 0.22
30 7 0.16
ACGTcount: A:0.27, C:0.04, G:0.12, T:0.57
Consensus pattern (23 bp):
TTGCATGATTTATATATTATTAT
Found at i:5796436 original size:83 final size:83
Alignment explanation
Indices: 5796337--5796564 Score: 393
Period size: 83 Copynumber: 2.7 Consensus size: 83
5796327 TATTTAATTA
*
5796337 CATGATTATATGTTTAATTGTATGTTTTGCATGGTTTATATATTATTATTTACATGATTGCATGA
1 CATGATTATATATTTAATTGTATGTTTTGCATGGTTTATATATTATTATTTACATGATTGCATGA
5796402 TTTATATATTATTATTTG
66 TTTATATATTATTATTTG
*
5796420 CATGATTATATATTTAATTGTATGTTTTGCATGGTTTATATATTATTATTTAAATGATTGCATGA
1 CATGATTATATATTTAATTGTATGTTTTGCATGGTTTATATATTATTATTTACATGATTGCATGA
5796485 TTTATATATTATTATTTG
66 TTTATATATTATTATTTG
* *
5796503 CATGATTATATATTTAATTGCATGTTTATTTGCATGGTTTATATATTACTATTTACATGATT
1 CATGATTATATATTTAATTGTATG--T-TTTGCATGGTTTATATATTATTATTTACATGATT
5796565 ATACATTTAG
Statistics
Matches: 137, Mismatches: 5, Indels: 3
0.94 0.03 0.02
Matches are distributed among these distances:
83 104 0.76
85 1 0.01
86 32 0.23
ACGTcount: A:0.29, C:0.05, G:0.12, T:0.54
Consensus pattern (83 bp):
CATGATTATATATTTAATTGTATGTTTTGCATGGTTTATATATTATTATTTACATGATTGCATGA
TTTATATATTATTATTTG
Found at i:5796523 original size:20 final size:22
Alignment explanation
Indices: 5796476--5796531 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 22
5796466 TATTTAAATG
5796476 ATTGCATGATTTATATATTATTA
1 ATTGCATGA-TTATATATTATTA
*
5796499 TTTGCATGATTATATA-T-TTA
1 ATTGCATGATTATATATTATTA
*
5796519 ATTGCATGTTTAT
1 ATTGCATGATTAT
5796532 TTGCATGGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 14 0.47
21 1 0.03
22 7 0.23
23 8 0.27
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.54
Consensus pattern (22 bp):
ATTGCATGATTATATATTATTA
Found at i:5797483 original size:58 final size:57
Alignment explanation
Indices: 5797297--5797632 Score: 340
Period size: 58 Copynumber: 5.7 Consensus size: 57
5797287 TTTTGTGCAG
* * * **
5797297 GAAAAATTGATACTTTCAACTTTTTCCTTGAAAATATTTTTGTTTTTGAAAACTTTAATTTCGA
1 GAAAAATTGATACTTTCAAC-TTTTCC--CAAAA-A-TATT-TTTTTGAAAA-TTTATTTTTAA
** * *** *
5797361 GGGAAATTGATACTTTCAACTTTTCTTC-AAAA-ATCCCTTTGAAAATTTATCTTTAA
1 GAAAAATTGATACTTTCAACTTTTC-CCAAAAATATTTTTTTGAAAATTTATTTTTAA
*
5797417 GAAAAATTGATATTTTCAACTTTTTCCCAAAAATATTTTTTTGAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAAC-TTTTCCCAAAAATATTTTTTTGAAAATTTATTTTTAA
* **
5797475 GAAAAATTGATACTTTCAACTTTTTCCCAAAAATA--TTTTTGAAAACTTTAATTTCGA
1 GAAAAATTGATACTTTCAAC-TTTTCCCAAAAATATTTTTTTGAAAA-TTTATTTTTAA
*
5797532 GAAAAATTGATACTTTCAACTTTTCTTCAAAAACCT-TTTTTTTGAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTC-CCAAAAA--TATTTTTTTGAAAATTTATTTTTAA
*
5797591 GAAAAATTGATACTTTCAACCTTTCCCTAAAAATATTTTTTT
1 GAAAAATTGATACTTTCAACTTTTCCC-AAAAATATTTTTTT
5797633 TTGGATTTTA
Statistics
Matches: 230, Mismatches: 30, Indels: 30
0.79 0.10 0.10
Matches are distributed among these distances:
56 40 0.17
57 52 0.23
58 63 0.27
59 38 0.17
60 11 0.05
61 3 0.01
63 5 0.02
64 18 0.08
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.45
Consensus pattern (57 bp):
GAAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTGAAAATTTATTTTTAA
Found at i:5797543 original size:57 final size:55
Alignment explanation
Indices: 5797339--5797630 Score: 316
Period size: 56 Copynumber: 5.1 Consensus size: 55
5797329 AATATTTTTG
** ** * *
5797339 TTTTTGAAAACTTTAATTTCGAGGGAAATTGATACTTTCAACTTTTCTTCAAAAATC
1 TTTTTGAAAA-TTTAATTTTAAGAAAAATTGATACTTTCAACTTTTC-CCAAAAATA
** *
5797396 CCTTTGAAAATTT-ATCTTTAAGAAAAATTGATATTTTCAACTTTTTCCCAAAAATA
1 TTTTTGAAAATTTAAT-TTTAAGAAAAATTGATACTTTCAAC-TTTTCCCAAAAATA
*
5797452 TTTTTTTGAAAATTTATTTTTAAGAAAAATTGATACTTTCAACTTTTTCCCAAAAATA
1 --TTTTTGAAAATTTAATTTTAAGAAAAATTGATACTTTCAAC-TTTTCCCAAAAATA
** * *
5797510 TTTTTGAAAACTTTAATTTCGAGAAAAATTGATACTTTCAACTTTTCTTCAAAAACCTTT
1 TTTTTGAAAA-TTTAATTTTAAGAAAAATTGATACTTTCAACTTTTC-CCAAAAA---TA
* *
5797570 TTTTTGAAAATTTATTTTTAAGAAAAATTGATACTTTCAACCTTTCCCTAAAAATA
1 TTTTTGAAAATTTAATTTTAAGAAAAATTGATACTTTCAACTTTTCCC-AAAAATA
5797626 TTTTT
1 TTTTT
5797631 TTTTGGATTT
Statistics
Matches: 200, Mismatches: 24, Indels: 23
0.81 0.10 0.09
Matches are distributed among these distances:
55 2 0.01
56 51 0.25
57 47 0.23
58 51 0.25
59 38 0.19
60 11 0.05
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (55 bp):
TTTTTGAAAATTTAATTTTAAGAAAAATTGATACTTTCAACTTTTCCCAAAAATA
Found at i:5797725 original size:36 final size:36
Alignment explanation
Indices: 5797646--5797748 Score: 104
Period size: 35 Copynumber: 2.8 Consensus size: 36
5797636 GATTTTATTT
* * **
5797646 AAAAAAAATAAAATAATAAAACA-AAATGAAAGTGA
1 AAAAAAAATAAAAAAATAAAAAATAAAAAAAAGTGA
*
5797681 AAATAAAATAAAAAAATAAAAAATAAAAAAAAGT-A
1 AAAAAAAATAAAAAAATAAAAAATAAAAAAAAGTGA
5797716 AAACAAAAATAAAAAAGA-AATAAAGATAAAAAA
1 AAA-AAAAATAAAAAA-ATAA-AAA-ATAAAAAA
5797749 CATTAAATAA
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
35 24 0.42
36 21 0.37
37 4 0.07
38 8 0.14
ACGTcount: A:0.80, C:0.02, G:0.06, T:0.13
Consensus pattern (36 bp):
AAAAAAAATAAAAAAATAAAAAATAAAAAAAAGTGA
Found at i:5797737 original size:52 final size:51
Alignment explanation
Indices: 5797648--5797748 Score: 125
Period size: 53 Copynumber: 2.0 Consensus size: 51
5797638 TTTTATTTAA
* * **
5797648 AAAAAATAAAATAATAAAACAAAATGAAAGTGAAAATAAA-ATAAAAAAAT
1 AAAAAATAAAAAAATAAAACAAAATAAAAAAGAAAATAAAGATAAAAAAAT
5797698 AAAAAATAAAAAAAAGTAAAACAAAAATAAAAAAG-AAATAAAGATAAAAAA
1 AAAAAAT-AAAAAAA-TAAAAC-AAAATAAAAAAGAAAATAAAGATAAAAAA
5797749 CATTAAATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
50 7 0.16
51 6 0.14
52 13 0.30
53 17 0.40
ACGTcount: A:0.79, C:0.02, G:0.06, T:0.13
Consensus pattern (51 bp):
AAAAAATAAAAAAATAAAACAAAATAAAAAAGAAAATAAAGATAAAAAAAT
Found at i:5797791 original size:17 final size:17
Alignment explanation
Indices: 5797681--5797799 Score: 61
Period size: 17 Copynumber: 6.9 Consensus size: 17
5797671 ATGAAAGTGA
5797681 AAATAAAATAAAA-AAAT
1 AAAT-AAATAAAATAAAT
*
5797698 AAA-AAATAAAAAAAAGT
1 AAATAAATAAAATAAA-T
*
5797715 AAA-ACA-AAAATAAA-
1 AAATAAATAAAATAAAT
* *
5797729 AAAGAAATAAAGATAAAA
1 AAATAAATAAA-ATAAAT
** *
5797747 AACATTAAATAATCCTAATT
1 AA-A-TAAATAA-AATAAAT
*
5797767 TAAT-AATAAAATAAAT
1 AAATAAATAAAATAAAT
5797783 AAATAAATAAATATAAA
1 AAATAAATAAA-ATAAA
5797800 AAAAAACCTG
Statistics
Matches: 78, Mismatches: 13, Indels: 21
0.70 0.12 0.19
Matches are distributed among these distances:
14 3 0.04
15 10 0.13
16 20 0.26
17 25 0.32
18 8 0.10
19 2 0.03
20 10 0.13
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (17 bp):
AAATAAATAAAATAAAT
Found at i:5798734 original size:3 final size:3
Alignment explanation
Indices: 5798721--5798767 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
5798711 TTACAAGATA
*
5798721 AAT AA- AAT AAT AAT AAT AAT AAT AAAT AAAT TAT AAT -AT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT AAT AAT AAT AAT AAT
5798766 AA
1 AA
5798768 ATATATAACT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 4 0.10
3 28 0.72
4 7 0.18
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5798750 original size:4 final size:4
Alignment explanation
Indices: 5798718--5798885 Score: 66
Period size: 4 Copynumber: 42.2 Consensus size: 4
5798708 ATATTACAAG
5798718 ATAA ATAA A-ATA AT-A AT-A AT-A AT-A ATAA ATAA ATTATA ATATA
1 ATAA ATAA ATA-A ATAA ATAA ATAA ATAA ATAA ATAA A-TA-A ATA-A
* * * * * *
5798761 AT-A ATAA ATAT ATAA CTAA ATAAA ATAC ATAT ATAA AT-A TTAA CAGAA
1 ATAA ATAA ATAA ATAA ATAA AT-AA ATAA ATAA ATAA ATAA ATAA -ATAA
* * * * * * *
5798809 AAAA ATAA ATAA ATAA ATAA AGAT ATAC ATAT ATTA ATAC ATAGTA AT-A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA--A ATAA
* *
5798858 ATAA ATAA ATAA AT-A GTAA ATAC ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
5798886 ATACAAAGGA
Statistics
Matches: 125, Mismatches: 26, Indels: 26
0.71 0.15 0.15
Matches are distributed among these distances:
3 23 0.18
4 84 0.67
5 14 0.11
6 4 0.03
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (4 bp):
ATAA
Found at i:5798781 original size:34 final size:31
Alignment explanation
Indices: 5798722--5798784 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 31
5798712 TACAAGATAA
5798722 ATAAAATAATAATAATAATAATAAATAAATT
1 ATAAAATAATAATAATAATAATAAATAAATT
*
5798753 ATAATATAATAATAAATATATAACTAAATAAA
1 ATAAAATAATAAT-AATA-ATAA-TAAATAAA
5798785 ATACATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 12 0.43
32 4 0.14
33 4 0.14
34 8 0.29
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (31 bp):
ATAAAATAATAATAATAATAATAAATAAATT
Found at i:5798782 original size:19 final size:18
Alignment explanation
Indices: 5798725--5798783 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
5798715 AAGATAAATA
5798725 AAATAAT-AATA-ATAAT
1 AAATAATAAATATATAAT
5798741 -AATAAATAAAT-TATAAT
1 AAAT-AATAAATATATAAT
5798758 ATAATAATAAATATATAACT
1 A-AATAATAAATATATAA-T
5798778 AAATAA
1 AAATAA
5798784 AATACATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
15 3 0.08
16 3 0.08
17 8 0.22
18 7 0.19
19 13 0.36
20 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATAATAAATATATAAT
Found at i:5798783 original size:22 final size:21
Alignment explanation
Indices: 5798729--5798796 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
5798719 TAAATAAAAT
5798729 AATA-ATAAT-AATAATAAATA
1 AATATATAATAAATAAT-AATA
5798749 AAT-TATAAT--ATAATAATA
1 AATATATAATAAATAATAATA
5798767 AATATATAACTAAATAA-AATA
1 AATATATAA-TAAATAATAATA
*
5798788 CATATATAA
1 AATATATAA
5798797 ATATTAACAG
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
18 7 0.17
19 10 0.24
20 9 0.21
21 12 0.29
22 4 0.10
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (21 bp):
AATATATAATAAATAATAATA
Found at i:5798814 original size:28 final size:29
Alignment explanation
Indices: 5798755--5798827 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 29
5798745 AATAAATTAT
*
5798755 AATATAAT-AATAAATATATAACTAAATAA
1 AATA-AATAAATAAATATATAACTAAAAAA
* *
5798784 AATACATATATAAATAT-TAAC-AGAAAAA
1 AATAAATAAATAAATATATAACTA-AAAAA
5798812 AATAAATAAATAAATA
1 AATAAATAAATAAATA
5798828 AAGATATACA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
27 1 0.03
28 24 0.65
29 12 0.32
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.27
Consensus pattern (29 bp):
AATAAATAAATAAATATATAACTAAAAAA
Found at i:5798877 original size:15 final size:15
Alignment explanation
Indices: 5798718--5798885 Score: 74
Period size: 15 Copynumber: 11.6 Consensus size: 15
5798708 ATATTACAAG
5798718 ATAAATAAAATAAT-A
1 ATAAAT-AAATAATAA
5798733 AT-AAT-AATAATAA
1 ATAAATAAATAATAA
*
5798746 ATAAAT-TATAATATA
1 ATAAATAAATAATA-A
5798761 AT-AATAAATATATAA
1 ATAAATAAATA-ATAA
* *
5798776 CTAAAT-AA-AATAC
1 ATAAATAAATAATAA
* *
5798789 ATATATAAATATTAA
1 ATAAATAAATAATAA
*
5798804 CA-GAA-AAA-AATAA
1 -ATAAATAAATAATAA
*
5798817 ATAAATAAATAA-AG
1 ATAAATAAATAATAA
* *
5798831 AT--ATACATATATTA
1 ATAAATAAATA-ATAA
*
5798845 ATACATAGTAATAATAA
1 ATAAATA--AATAATAA
*
5798862 ATAAATAAATAGTAA
1 ATAAATAAATAATAA
*
5798877 ATACATAAA
1 ATAAATAAA
5798886 ATACAAAGGA
Statistics
Matches: 114, Mismatches: 21, Indels: 36
0.67 0.12 0.21
Matches are distributed among these distances:
12 13 0.11
13 17 0.15
14 29 0.25
15 33 0.29
16 10 0.09
17 9 0.08
18 3 0.03
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (15 bp):
ATAAATAAATAATAA
Found at i:5798909 original size:22 final size:23
Alignment explanation
Indices: 5798881--5798942 Score: 83
Period size: 22 Copynumber: 2.8 Consensus size: 23
5798871 TAGTAAATAC
*
5798881 ATAAAATACAAAGGAAAAA-AAT
1 ATAAAATACAAAAGAAAAATAAT
*
5798903 ATAAAATA-AAAATAAAAATAAT
1 ATAAAATACAAAAGAAAAATAAT
*
5798925 ATAAAATACAAAATAAAA
1 ATAAAATACAAAAGAAAA
5798943 GCCAAATTGG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 8 0.22
22 19 0.53
23 9 0.25
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (23 bp):
ATAAAATACAAAAGAAAAATAAT
Found at i:5798928 original size:17 final size:16
Alignment explanation
Indices: 5798898--5798942 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
5798888 ACAAAGGAAA
5798898 AAAATATAAAATAAAAAT
1 AAAA-ATAAAAT-AAAAT
*
5798916 AAAAATAATATAAAAT
1 AAAAATAAAATAAAAT
5798932 ACAAAATAAAA
1 A-AAAATAAAA
5798943 GCCAAATTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 6 0.25
17 14 0.58
18 4 0.17
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (16 bp):
AAAAATAAAATAAAAT
Found at i:5799234 original size:41 final size:41
Alignment explanation
Indices: 5799133--5799387 Score: 357
Period size: 41 Copynumber: 6.1 Consensus size: 41
5799123 TTTGACTAAA
* * * * *
5799133 GCTCCTTTAAGCAGAGGCTCAACGACTTTGGAAAGATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAG-TAAATT
* * *
5799175 GCTCCTCTAAGCAAAGGCACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
5799216 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* *
5799257 GCTCCTCTAAACAGATGCACCACGACTTTGAAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-AAAAGTAAATT
*
5799299 GCTCCTCTAAACAAAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* * *
5799340 GCTCCTTTAAACAGAGGCACCACGACTTTGGAAAAATCAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATT
5799382 GCTCCT
1 GCTCCT
5799388 TGACAATCAT
Statistics
Matches: 195, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
41 110 0.56
42 85 0.44
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.24
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
Found at i:5799300 original size:83 final size:82
Alignment explanation
Indices: 5799133--5799387 Score: 366
Period size: 83 Copynumber: 3.1 Consensus size: 82
5799123 TTTGACTAAA
* * * * * * *
5799133 GCTCCTTTAAGCAGAGGCTCAACGACTTTGGAAAGATAAATTGCTCCTCTAAGCAAAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAG-TAAATTGCTCCTCTAAACAGAGGCACCAC
* *
5799198 GACTTTGGAAAGTAAATT
65 GACTTTGAAAAATAAATT
*
5799216 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGATGCACCACG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
5799281 ACTTTGAAAAAATAAATT
66 ACTTTG-AAAAATAAATT
* *
5799299 GCTCCTCTAAACAAAGGCACCACGACTTTGAAAAGTAAATTGCTCCTTTAAACAGAGGCACCACG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
*
5799364 ACTTTGGAAAAATCAATT
66 ACTTT-GAAAAATAAATT
5799382 GCTCCT
1 GCTCCT
5799388 TGACAATCAT
Statistics
Matches: 156, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
82 33 0.21
83 122 0.78
84 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.24
Consensus pattern (82 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
ACTTTGAAAAATAAATT
Found at i:5799353 original size:124 final size:125
Alignment explanation
Indices: 5799154--5799387 Score: 398
Period size: 124 Copynumber: 1.9 Consensus size: 125
5799144 CAGAGGCTCA
* * * *
5799154 ACGACTTTGGAAAGATAAATTGCTCCTCTAAGCAAAGGCACCACGACTTTGGAAAGTAAATTGCT
1 ACGACTTTGAAAAAATAAATTGCTCCTCTAAACAAAGGCACCACGACTTTGAAAAGTAAATTGCT
*
5799219 CCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATTGCTCCTCTAAACAGATGCACC
66 CCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGATGCACC
5799278 ACGACTTTGAAAAAATAAATTGCTCCTCTAAACAAAGGCACCACGACTTTGAAAAGTAAATTGCT
1 ACGACTTTGAAAAAATAAATTGCTCCTCTAAACAAAGGCACCACGACTTTGAAAAGTAAATTGCT
* *
5799343 CCTTTAAACAGAGGCACCACGACTTTGGAAAAATCAATTGCTCCT
66 CCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCT
5799388 TGACAATCAT
Statistics
Matches: 102, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
124 86 0.84
125 16 0.16
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.24
Consensus pattern (125 bp):
ACGACTTTGAAAAAATAAATTGCTCCTCTAAACAAAGGCACCACGACTTTGAAAAGTAAATTGCT
CCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGATGCACC
Found at i:5804754 original size:19 final size:19
Alignment explanation
Indices: 5804732--5804771 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
5804722 ATAATTTTCT
5804732 TAAAA-AAAGATAAATAAAA
1 TAAAATAAA-ATAAATAAAA
*
5804751 TAAAATAAAATATATAAAA
1 TAAAATAAAATAAATAAAA
5804770 TA
1 TA
5804772 TTTATAAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (19 bp):
TAAAATAAAATAAATAAAA
Found at i:5809165 original size:11 final size:11
Alignment explanation
Indices: 5809149--5809190 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
5809139 AAAAAAAGCC
5809149 TAAATAAATAA
1 TAAATAAATAA
5809160 TAAAT-AATGAA
1 TAAATAAAT-AA
5809171 TAAATAAATATA
1 TAAATAAATA-A
*
5809183 AAAATAAA
1 TAAATAAA
5809191 CAAAAAAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 3 0.11
11 13 0.48
12 11 0.41
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (11 bp):
TAAATAAATAA
Found at i:5810077 original size:96 final size:94
Alignment explanation
Indices: 5809914--5810105 Score: 305
Period size: 96 Copynumber: 2.0 Consensus size: 94
5809904 TCTGTGAAAC
*
5809914 AAGAAGTGTACAAAGATAAAAAACATTTTTTGTTCAAGTCAAGAAAAATAAAAAAGGCTTCCCTC
1 AAGAAGTATACAAAGATAAAAAACATTTTTTGTTCAAGTCAAGAAAAATAAAAAAGGCTTCCCTC
*
5809979 AACATAGGTTTTGAAACTTTAAAAATTTA
66 AACATAAGTTTTGAAACTTTAAAAATTTA
* * *
5810008 AAGAAGTATACAAAGATAAAAGACATCTATTTTGTTCAAGTCAAGAAAATTCAAAAAGGC-TCCC
1 AAGAAGTATACAAAGATAAAAAACAT-T-TTTTGTTCAAGTCAAGAAAAATAAAAAAGGCTTCCC
5810072 TTCAACATAAGTTTTGAAACTTTAAAAATTTA
64 -TCAACATAAGTTTTGAAACTTTAAAAATTTA
5810104 AA
1 AA
5810106 ATGCTTCGCT
Statistics
Matches: 90, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
94 24 0.27
95 5 0.06
96 61 0.68
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (94 bp):
AAGAAGTATACAAAGATAAAAAACATTTTTTGTTCAAGTCAAGAAAAATAAAAAAGGCTTCCCTC
AACATAAGTTTTGAAACTTTAAAAATTTA
Found at i:5810183 original size:41 final size:41
Alignment explanation
Indices: 5810088--5810184 Score: 108
Period size: 41 Copynumber: 2.3 Consensus size: 41
5810078 ATAAGTTTTG
* * * *
5810088 AAACTTTAAAAATTTAAAATGCTTCGCTTTCCAAAAGCTTTG
1 AAACTTTAAAAATTTAAAATGATTCCCCTT-CAAAAGCTTTA
*
5810130 AAACTTTGAAAATTTAAAAT-ATTCCCCTT-AACAGAGCTTTA
1 AAACTTTAAAAATTTAAAATGATTCCCCTTCAA-A-AGCTTTA
5810171 AAACTTTAAAAATT
1 AAACTTTAAAAATT
5810185 AAAGAGCTCC
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
39 2 0.04
40 1 0.02
41 25 0.53
42 19 0.40
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.35
Consensus pattern (41 bp):
AAACTTTAAAAATTTAAAATGATTCCCCTTCAAAAGCTTTA
Found at i:5810216 original size:41 final size:41
Alignment explanation
Indices: 5810171--5810305 Score: 137
Period size: 41 Copynumber: 3.3 Consensus size: 41
5810161 CAGAGCTTTA
* * *
5810171 AAACTTTAAAAATTAAAGAGCTCCTTTCAACGAGGGCTGTG
1 AAACTTTAAAAATTAAAGAGCTCCTCTCAACAAAGGCTGTG
* * * *
5810212 AAACTTTAAAAATTAATGAGTTCCTCTCATCAAAGGTTGTG
1 AAACTTTAAAAATTAAAGAGCTCCTCTCAACAAAGGCTGTG
* * * * *
5810253 AAACTTTAACAAATGAAAAAGCTTCTCTCATCAAAGGCTAT-
1 AAACTTTAA-AAATTAAAGAGCTCCTCTCAACAAAGGCTGTG
*
5810294 AAAATTTAAAAA
1 AAACTTTAAAAA
5810306 AAAAAAAATG
Statistics
Matches: 78, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
40 3 0.04
41 51 0.65
42 24 0.31
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (41 bp):
AAACTTTAAAAATTAAAGAGCTCCTCTCAACAAAGGCTGTG
Found at i:5810361 original size:48 final size:48
Alignment explanation
Indices: 5810258--5810361 Score: 120
Period size: 48 Copynumber: 2.1 Consensus size: 48
5810248 TTGTGAAACT
* *
5810258 TTAACAAATGAAAAAGCTTCTCTCATCAAAGGCTATAAAATTTAAAAAA
1 TTAA-AAATGAAAAAGCTTCTCTCACCAAAAGCTATAAAATTTAAAAAA
** * * *
5810307 AAAAAAATGAAAGAGCTTCTTTCACCAAAAGCTATGAAACTTT-AAAAA
1 TTAAAAATGAAAAAGCTTCTCTCACCAAAAGCTAT-AAAATTTAAAAAA
5810355 TTAAAAA
1 TTAAAAA
5810362 ACCTCTCTCA
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
48 37 0.82
49 8 0.18
ACGTcount: A:0.53, C:0.13, G:0.09, T:0.25
Consensus pattern (48 bp):
TTAAAAATGAAAAAGCTTCTCTCACCAAAAGCTATAAAATTTAAAAAA
Found at i:5810423 original size:43 final size:41
Alignment explanation
Indices: 5810308--5810437 Score: 152
Period size: 42 Copynumber: 3.1 Consensus size: 41
5810298 TTTAAAAAAA
* * *
5810308 AAAAAATGAAAGAGCTTCTTTCACCAAAAGCTATGAAACTTT
1 AAAAAATGAAAAAGC-TCTATCACCAAAGGCTATGAAACTTT
* * * * *
5810350 AAAAATTAAAAAACCTCTCTCACCAGAGGCTATGAAACTTTT
1 AAAAAATGAAAAAGCTCTATCACCAAAGGCTATGAAAC-TTT
*
5810392 AAAAAATGAAAAAGCTCATATCACTAAAGGCTATGAAACTTT
1 AAAAAATGAAAAAGCTC-TATCACCAAAGGCTATGAAACTTT
5810434 AAAA
1 AAAA
5810438 CTCATAACCA
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
41 20 0.27
42 35 0.48
43 18 0.25
ACGTcount: A:0.48, C:0.17, G:0.11, T:0.25
Consensus pattern (41 bp):
AAAAAATGAAAAAGCTCTATCACCAAAGGCTATGAAACTTT
Found at i:5810434 original size:84 final size:87
Alignment explanation
Indices: 5810308--5810487 Score: 215
Period size: 84 Copynumber: 2.1 Consensus size: 87
5810298 TTTAAAAAAA
* * *
5810308 AAAAAATGAAAGAGCTTCTTTCACCAAAAGCTATGAAACTTTAAAA-ATTA-AAAAACCTC-TCT
1 AAAAAATGAAAAAGCTTCTATCACCAAAAGCTATGAAACTTTAAAACATAACAAAAACCTCTTCT
*
5810370 CACCAGAGGCTATGAAACTTTT
66 CACCAGAAGCTATGAAACTTTT
* * *
5810392 AAAAAATGAAAAAGC-TCATATCACTAAAGGCTATGAAACTTTAAAACTCATAACCAAAAAGCTC
1 AAAAAATGAAAAAGCTTC-TATCACCAAAAGCTATGAAACTTTAAAA--CATAA-CAAAAACCTC
* *
5810456 TTTTCACCAGAAGCTGTGAAACTTTT
62 TTCTCACCAGAAGCTATGAAACTTTT
5810482 AAAAAA
1 AAAAAA
5810488 AATTTAAAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
83 2 0.03
84 39 0.49
87 3 0.04
89 8 0.10
90 28 0.35
ACGTcount: A:0.46, C:0.18, G:0.11, T:0.25
Consensus pattern (87 bp):
AAAAAATGAAAAAGCTTCTATCACCAAAAGCTATGAAACTTTAAAACATAACAAAAACCTCTTCT
CACCAGAAGCTATGAAACTTTT
Done.