Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167838.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_11, 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: 23775123
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 69000 characters in sequence are not A, C, G, or T
File 59 of 129
Found at i:11496041 original size:86 final size:87
Alignment explanation
Indices: 11495935--11496317 Score: 531
Period size: 88 Copynumber: 4.4 Consensus size: 87
11495925 TATTAAAATC
* * *
11495935 AAATA-TATCATCATGTTAT-AAAAAATTAAAACATATTCTTGAAGCATAGAAGTTCAAAGATAA
1 AAATATTAACATCATGTTATAAAAAAATTAAAACATATTCTTGAAGCATAGAAATTTAAAGATAA
11495998 CATGCTTATTTTAATATCACAA
66 CATGCTTATTTTAATATCACAA
* * *
11496020 AACTATTAACATCATGCTATAAAAAAAATTAAAACATATTCTTGAAGCATAGAAATTTATAGATA
1 AAATATTAACATCATGTTAT-AAAAAAATTAAAACATATTCTTGAAGCATAGAAATTTAAAGATA
11496085 ACATGCTTATTTTAATATCACAA
65 ACATGCTTATTTTAATATCACAA
* * * * *
11496108 AAAAATTAACATCTTGCTA-GAAAAAATTAAAACATATTCTTGAACCATAGAAATTTATAA-ATA
1 AAATATTAACATCATGTTATAAAAAAATTAAAACATATTCTTGAAGCATAGAAATTTA-AAGATA
11496171 ACATGCTTATTTTAATATCACAA
65 ACATGCTTATTTTAATATCACAA
* * * *
11496194 AAATATTAACATCATGTTATCAAGAAAATTAAAACATATTCTTGAAGCAAAAAAATTTATAGATA
1 AAATATTAACATCATGTTAT-AAAAAAATTAAAACATATTCTTGAAGCATAGAAATTTAAAGATA
*
11496259 ACATGCTTTTTTTAATATCACAA
65 ACATGCTTATTTTAATATCACAA
* * *
11496282 AAATATTAGCATCATATTATCAAAAAATTTAAAACA
1 AAATATTAACATCATGTTAT-AAAAAAATTAAAACA
11496318 CTAAAAGATT
Statistics
Matches: 265, Mismatches: 26, Indels: 11
0.88 0.09 0.04
Matches are distributed among these distances:
85 4 0.02
86 90 0.34
87 2 0.01
88 169 0.64
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.33
Consensus pattern (87 bp):
AAATATTAACATCATGTTATAAAAAAATTAAAACATATTCTTGAAGCATAGAAATTTAAAGATAA
CATGCTTATTTTAATATCACAA
Found at i:11496252 original size:174 final size:174
Alignment explanation
Indices: 11495954--11496294 Score: 558
Period size: 174 Copynumber: 2.0 Consensus size: 174
11495944 ATCATGTTAT
* *
11495954 AAAAAATTAAAACATATTCTTGAAGCATAGAAGTTCAAAGATAACATGCTTATTTTAATATCACA
1 AAAAAATTAAAACATATTCTTGAACCATAGAAATTCAAAGATAACATGCTTATTTTAATATCACA
* * *
11496019 AAACTATTAACATCATGCTATAAAAAAAATTAAAACATATTCTTGAAGCATAGAAATTTATAGAT
66 AAAATATTAACATCATGCTATAAAAAAAATTAAAACATATTCTTGAAGCAAAAAAATTTATAGAT
11496084 AACATGCTTATTTTAATATCACAAAAAAATTAACATCTTGCTAG
131 AACATGCTTATTTTAATATCACAAAAAAATTAACATCTTGCTAG
*
11496128 AAAAAATTAAAACATATTCTTGAACCATAGAAATTTATAA-ATAACATGCTTATTTTAATATCAC
1 AAAAAATTAAAACATATTCTTGAACCATAGAAATTCA-AAGATAACATGCTTATTTTAATATCAC
* * *
11496192 AAAAATATTAACATCATGTTATCAAGAAAATTAAAACATATTCTTGAAGCAAAAAAATTTATAGA
65 AAAAATATTAACATCATGCTATAAAAAAAATTAAAACATATTCTTGAAGCAAAAAAATTTATAGA
* * *
11496257 TAACATGCTTTTTTTAATATCACAAAAATATTAGCATC
130 TAACATGCTTATTTTAATATCACAAAAAAATTAACATC
11496295 ATATTATCAA
Statistics
Matches: 154, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
174 152 0.99
175 2 0.01
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33
Consensus pattern (174 bp):
AAAAAATTAAAACATATTCTTGAACCATAGAAATTCAAAGATAACATGCTTATTTTAATATCACA
AAAATATTAACATCATGCTATAAAAAAAATTAAAACATATTCTTGAAGCAAAAAAATTTATAGAT
AACATGCTTATTTTAATATCACAAAAAAATTAACATCTTGCTAG
Found at i:11498006 original size:2 final size:2
Alignment explanation
Indices: 11497999--11498026 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11497989 ACCTTCTGCC
11497999 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11498027 ACTTCTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11500938 original size:39 final size:39
Alignment explanation
Indices: 11500884--11500962 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
11500874 ACATAAGGGG
11500884 AGAAGAAATTACAGGTATTAAGATTCTAACCTCAAACCT
1 AGAAGAAATTACAGGTATTAAGATTCTAACCTCAAACCT
*
11500923 AGAAGAAATTACAGGTATTAAGATTTTAACCTCAAACCT
1 AGAAGAAATTACAGGTATTAAGATTCTAACCTCAAACCT
11500962 A
1 A
11500963 TTAGATATTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (39 bp):
AGAAGAAATTACAGGTATTAAGATTCTAACCTCAAACCT
Found at i:11502699 original size:20 final size:21
Alignment explanation
Indices: 11502661--11502703 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
11502651 TTTATTTCTT
*
11502661 TTTTAAATAAAAAATAAAAAA
1 TTTTAAATAAAAAACAAAAAA
*
11502682 TTTTAAA-AAAATACAAAAAA
1 TTTTAAATAAAAAACAAAAAA
11502702 TT
1 TT
11502704 AAAAATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
TTTTAAATAAAAAACAAAAAA
Found at i:11502705 original size:18 final size:18
Alignment explanation
Indices: 11502669--11502708 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
11502659 TTTTTTAAAT
*
11502669 AAAAAATAAAAAATTTTA
1 AAAAAATAAAAAATATTA
11502687 AAAAAATACAAAAA-ATTA
1 AAAAAATA-AAAAATATTA
11502705 AAAA
1 AAAA
11502709 TATTTTCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAAAATAAAAAATATTA
Found at i:11504743 original size:39 final size:37
Alignment explanation
Indices: 11504661--11504742 Score: 112
Period size: 37 Copynumber: 2.2 Consensus size: 37
11504651 ATAGCCAAGA
* *
11504661 TGAGAGAGGCTCATCCCTTCTTCATCGACGGTTGAGG
1 TGAGAGAGGCTCATCCCCTCTTCATCGACGGTCGAGG
* *
11504698 TGAGAGAGGCTCATCCCC-CTTTCATTGATGGTCGAGG
1 TGAGAGAGGCTCATCCCCTC-TTCATCGACGGTCGAGG
11504735 TGAGAGAG
1 TGAGAGAG
11504743 ACTAATCTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
36 1 0.03
37 39 0.98
ACGTcount: A:0.21, C:0.22, G:0.32, T:0.26
Consensus pattern (37 bp):
TGAGAGAGGCTCATCCCCTCTTCATCGACGGTCGAGG
Found at i:11511772 original size:43 final size:43
Alignment explanation
Indices: 11511711--11511799 Score: 124
Period size: 43 Copynumber: 2.1 Consensus size: 43
11511701 TAGAACGTAA
* *
11511711 AAGTTCATTCTAAAGCACAGACGTAATGAGCTAAACACATATT
1 AAGTTCATTCTAAAGCACAAACATAATGAGCTAAACACATATT
* * * *
11511754 AAGTTCATTTTAGAGCACAAATATGATGAGCTAAACACATATT
1 AAGTTCATTCTAAAGCACAAACATAATGAGCTAAACACATATT
11511797 AAG
1 AAG
11511800 GCAGTTTTCG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.27
Consensus pattern (43 bp):
AAGTTCATTCTAAAGCACAAACATAATGAGCTAAACACATATT
Found at i:11515471 original size:93 final size:93
Alignment explanation
Indices: 11515357--11515529 Score: 276
Period size: 93 Copynumber: 1.9 Consensus size: 93
11515347 AAACTATTGA
* *
11515357 AGGATTTAAATCTTAAATTAAATCTTACCAAACTATTGGAAGATTTAATAA-ATTTATAAAAGAA
1 AGGATTTAAATATTAAATTAAATCTTACCAAACTATTGAAAGATTTAATAATATTTATAAAA-AA
*
11515421 TAAAATTTTTAATCCTCCCAAATTATTAG
65 TAAAAATTTTAATCCTCCCAAATTATTAG
* * *
11515450 AGGATTTAAATATTAAGTTAAATCTTACTAAACTATTGAAAGATTTAATAATTTTTATAAAAAAT
1 AGGATTTAAATATTAAATTAAATCTTACCAAACTATTGAAAGATTTAATAATATTTATAAAAAAT
11515515 AAAAATTTTAATCCT
66 AAAAATTTTAATCCT
11515530 ATGAAATTAT
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
93 64 0.88
94 9 0.12
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.38
Consensus pattern (93 bp):
AGGATTTAAATATTAAATTAAATCTTACCAAACTATTGAAAGATTTAATAATATTTATAAAAAAT
AAAAATTTTAATCCTCCCAAATTATTAG
Found at i:11515537 original size:93 final size:93
Alignment explanation
Indices: 11515343--11515540 Score: 274
Period size: 93 Copynumber: 2.1 Consensus size: 93
11515333 GAATCATTCT
* * *
11515343 TACCAAACTATT-GAAGGATTTAAATCTTAAATTAAATCTTACCAAACTATTGGAAGATTTAATA
1 TACCAAATTATTAG-AGGATTTAAATATTAAATTAAATCTTACCAAACTATTGAAAGATTTAATA
*
11515407 AATTTATAAAAGAATAAAATTTTTAATCC
65 AATTTATAAAAGAATAAAAATTTTAATCC
* * *
11515436 TCCCAAATTATTAGAGGATTTAAATATTAAGTTAAATCTTACTAAACTATTGAAAGATTTAATAA
1 TACCAAATTATTAGAGGATTTAAATATTAAATTAAATCTTACCAAACTATTGAAAGATTTAATAA
*
11515501 TTTTTATAAAA-AATAAAAATTTTAATCC
66 -ATTTATAAAAGAATAAAAATTTTAATCC
**
11515529 TATGAAATTATT
1 TACCAAATTATT
11515541 GTAAAATGTG
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
93 82 0.89
94 10 0.11
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.38
Consensus pattern (93 bp):
TACCAAATTATTAGAGGATTTAAATATTAAATTAAATCTTACCAAACTATTGAAAGATTTAATAA
ATTTATAAAAGAATAAAAATTTTAATCC
Found at i:11518726 original size:21 final size:21
Alignment explanation
Indices: 11518682--11518726 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
11518672 TCTTTTGTTA
*
11518682 AATCATACCAAGGTAGCAATT
1 AATCATACCAAGGTAGCAACT
** *
11518703 AATCATACTGAGGTAGCACCT
1 AATCATACCAAGGTAGCAACT
11518724 AAT
1 AAT
11518727 GTCAATTCGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (21 bp):
AATCATACCAAGGTAGCAACT
Found at i:11520875 original size:13 final size:13
Alignment explanation
Indices: 11520857--11520893 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
11520847 GATATGATGC
11520857 ATTTTCATTTTTT
1 ATTTTCATTTTTT
*
11520870 ATTTTCATTCTTT
1 ATTTTCATTTTTT
*
11520883 ATTCTCATTTT
1 ATTTTCATTTT
11520894 CATACACCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70
Consensus pattern (13 bp):
ATTTTCATTTTTT
Found at i:11523796 original size:41 final size:41
Alignment explanation
Indices: 11523742--11523999 Score: 331
Period size: 41 Copynumber: 6.3 Consensus size: 41
11523732 TTAGAAAAAT
*
11523742 AAATAAAAGGCTCCTCTAAATAAAGGCTCAATGACTTTGAA
1 AAATAAAAGGCTCCTCTAAATAGAGGCTCAATGACTTTGAA
* *
11523783 AAATAAAAGGCTCCTCTAAGTAGAGGCTTAATGACTTTGAA
1 AAATAAAAGGCTCCTCTAAATAGAGGCTCAATGACTTTGAA
* **
11523824 AAATAAAATGCTCCTCT-AATAAGAGGCTCAATGACTTCAAA
1 AAATAAAAGGCTCCTCTAAAT-AGAGGCTCAATGACTTTGAA
* * *
11523865 AAATAAAAGGCTTCTCTAAACAGAGGCTCAACGACTTTGAA
1 AAATAAAAGGCTCCTCTAAATAGAGGCTCAATGACTTTGAA
* * * * *
11523906 AAATAAAAAGCTCATCT-AATCAGAGGCACGATAACTTTGAA
1 AAATAAAAGGCTCCTCTAAAT-AGAGGCTCAATGACTTTGAA
* **
11523947 AAATAAAAGGCTCCTCTAAATAGAGGCACAACAACTTTGAA
1 AAATAAAAGGCTCCTCTAAATAGAGGCTCAATGACTTTGAA
11523988 AAATAAAAGGCT
1 AAATAAAAGGCT
11524000 TATCGATAAT
Statistics
Matches: 187, Mismatches: 26, Indels: 8
0.85 0.12 0.04
Matches are distributed among these distances:
40 4 0.02
41 178 0.95
42 5 0.03
ACGTcount: A:0.44, C:0.17, G:0.16, T:0.23
Consensus pattern (41 bp):
AAATAAAAGGCTCCTCTAAATAGAGGCTCAATGACTTTGAA
Found at i:11524307 original size:20 final size:21
Alignment explanation
Indices: 11524232--11524307 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 21
11524222 TCCAACATTT
* * *
11524232 AAAGATTCTCATTCAAATTTT
1 AAAGATTCACATTCAAAGTTC
** *
11524253 GGAGATTCACATCCAAAAGTTC
1 AAAGATTCACATTC-AAAGTTC
* *
11524275 AAAGCTTCTCATTC-AAGTTC
1 AAAGATTCACATTCAAAGTTC
11524295 AAAGATTCACATT
1 AAAGATTCACATT
11524308 TAACAAATTT
Statistics
Matches: 41, Mismatches: 13, Indels: 3
0.72 0.23 0.05
Matches are distributed among these distances:
20 17 0.41
21 10 0.24
22 14 0.34
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.33
Consensus pattern (21 bp):
AAAGATTCACATTCAAAGTTC
Found at i:11524470 original size:21 final size:21
Alignment explanation
Indices: 11524446--11524524 Score: 104
Period size: 21 Copynumber: 3.8 Consensus size: 21
11524436 CATCTCAATG
*
11524446 ATTCTTATTTGAAACTCAAAT
1 ATTCTCATTTGAAACTCAAAT
* *
11524467 ATTCTCATTTGAGATTCAAAT
1 ATTCTCATTTGAAACTCAAAT
* *
11524488 ATTCTCATTTGAGACTCAAAG
1 ATTCTCATTTGAAACTCAAAT
*
11524509 ATTCTCATTTAAAACT
1 ATTCTCATTTGAAACT
11524525 TCATCAAAAG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (21 bp):
ATTCTCATTTGAAACTCAAAT
Found at i:11524633 original size:20 final size:20
Alignment explanation
Indices: 11524608--11524648 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
11524598 TCATGATTAG
11524608 TGATGCAAATGCTTTCTTAA
1 TGATGCAAATGCTTTCTTAA
11524628 TGATGCAAATGCTTTCTTAA
1 TGATGCAAATGCTTTCTTAA
11524648 T
1 T
11524649 AAATCAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (20 bp):
TGATGCAAATGCTTTCTTAA
Found at i:11524656 original size:20 final size:20
Alignment explanation
Indices: 11524610--11524659 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
11524600 ATGATTAGTG
*
11524610 ATGCAAATGCTTTCTTAATG
1 ATGCAAATGCTTTCTTAATA
11524630 ATGCAAATGCTTTCTTAATAA
1 ATGCAAATGCTTTCTTAAT-A
11524651 AT-CAAATGC
1 ATGCAAATGC
11524660 AACAAGCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 26 0.93
21 2 0.07
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (20 bp):
ATGCAAATGCTTTCTTAATA
Found at i:11525870 original size:8 final size:8
Alignment explanation
Indices: 11525859--11525951 Score: 87
Period size: 8 Copynumber: 10.9 Consensus size: 8
11525849 CTTTTTTTCC
11525859 ATTTTTTT
1 ATTTTTTT
11525867 ATTTTTTT
1 ATTTTTTT
11525875 ATTTTTTT
1 ATTTTTTT
11525883 ATTTTTTT
1 ATTTTTTT
11525891 ATTTTCTTT
1 ATTTT-TTT
*
11525900 TTTCCTTTTT
1 ATT--TTTTT
*
11525910 TTCTTTCTTT
1 AT-TTT-TTT
11525920 CATTTTTTT
1 -ATTTTTTT
* *
11525929 CTTTTTCT
1 ATTTTTTT
*
11525937 CTTTTTTT
1 ATTTTTTT
11525945 ATTTTTT
1 ATTTTTT
11525952 CATCCATTAG
Statistics
Matches: 73, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
8 48 0.66
9 10 0.14
10 11 0.15
11 4 0.05
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.83
Consensus pattern (8 bp):
ATTTTTTT
Found at i:11530073 original size:60 final size:59
Alignment explanation
Indices: 11530008--11530129 Score: 190
Period size: 60 Copynumber: 2.1 Consensus size: 59
11529998 AAATATTTTC
*
11530008 TCTTTTTGAATTTCTAAATTTTTCACCATTTAGGCCTATTTAGAAATATTTCTCTTTATT
1 TCTTTTTGAATTTCTAAATTTTCCACCATTTAGGCCTATTTAGAAATATTT-TCTTTATT
** * *
11530068 TCTTTTTTTATTTCTAAATTTTCCACCATTTGGGCCTATTTAGAAATATTTTTTTTATT
1 TCTTTTTGAATTTCTAAATTTTCCACCATTTAGGCCTATTTAGAAATATTTTCTTTATT
11530127 TCT
1 TCT
11530130 AAATTTTTCA
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
59 10 0.18
60 47 0.82
ACGTcount: A:0.23, C:0.15, G:0.07, T:0.56
Consensus pattern (59 bp):
TCTTTTTGAATTTCTAAATTTTCCACCATTTAGGCCTATTTAGAAATATTTTCTTTATT
Found at i:11530204 original size:52 final size:48
Alignment explanation
Indices: 11530070--11530221 Score: 218
Period size: 47 Copynumber: 3.1 Consensus size: 48
11530060 TCTTTATTTC
*
11530070 TTTTTTTATTTCTAAATTTTCCACCATTTGGGCCTATTTAGAAATA-T
1 TTTTTTTATTTCTAAATTTTTCACCATTTGGGCCTATTTAGAAATATT
**
11530117 TTTTTTTATTTCTAAATTTTTCACCATTTAAGCCTATTTAGAAATATT
1 TTTTTTTATTTCTAAATTTTTCACCATTTGGGCCTATTTAGAAATATT
*
11530165 TTTTTTTCAGAATTTCTAAATTTTTCACAATTTGGGCCTATTTAGAAAT-TT
1 TTTTTTT----ATTTCTAAATTTTTCACCATTTGGGCCTATTTAGAAATATT
11530216 TTTTTT
1 TTTTTT
11530222 CTTTTTTTTG
Statistics
Matches: 94, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
47 43 0.46
48 8 0.09
51 8 0.09
52 35 0.37
ACGTcount: A:0.26, C:0.12, G:0.07, T:0.54
Consensus pattern (48 bp):
TTTTTTTATTTCTAAATTTTTCACCATTTGGGCCTATTTAGAAATATT
Found at i:11530638 original size:13 final size:13
Alignment explanation
Indices: 11530620--11530644 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11530610 TTTTTATACT
11530620 TTTTTATTTTTTA
1 TTTTTATTTTTTA
11530633 TTTTTATTTTTT
1 TTTTTATTTTTT
11530645 CTAAAATTTA
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:11531520 original size:16 final size:16
Alignment explanation
Indices: 11531499--11531545 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
11531489 ATTATCAACT
*
11531499 AAAAATAAAATAAATA
1 AAAAATAAAATAAAAA
11531515 AAAAATCAAAATAAAAA
1 AAAAAT-AAAATAAAAA
*
11531532 AAAAAAAAAATAAA
1 AAAAATAAAATAAA
11531546 GCCTATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 14 0.50
17 14 0.50
ACGTcount: A:0.85, C:0.02, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAAATAAAATAAAAA
Found at i:11531528 original size:22 final size:22
Alignment explanation
Indices: 11531500--11531542 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
11531490 TTATCAACTA
* *
11531500 AAAATAAAATAAATAAAAAATC
1 AAAATAAAAAAAAAAAAAAATC
11531522 AAAATAAAAAAAAAAAAAAAT
1 AAAATAAAAAAAAAAAAAAAT
11531543 AAAGCCTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.84, C:0.02, G:0.00, T:0.14
Consensus pattern (22 bp):
AAAATAAAAAAAAAAAAAAATC
Found at i:11537486 original size:22 final size:22
Alignment explanation
Indices: 11537461--11537519 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
11537451 GAATATTTTG
*
11537461 ATGAGAATTTTTGAGAACTC-AA
1 ATGAGAATCTTTGAG-ACTCAAA
**
11537483 ATGAGAATCTTTGAGTTTCAAA
1 ATGAGAATCTTTGAGACTCAAA
11537505 ATGAGAATCTTTGAG
1 ATGAGAATCTTTGAG
11537520 GAGTGAAACC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 2 0.06
22 31 0.94
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.34
Consensus pattern (22 bp):
ATGAGAATCTTTGAGACTCAAA
Found at i:11537760 original size:42 final size:42
Alignment explanation
Indices: 11537701--11537784 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
11537691 TAAGCCTTTG
* *
11537701 AATTCAAATGAGAAGCTTT-GAATTTTGGATGTGAATCTCCAA
1 AATTCAAATGAAAAGCTTTAGAATTTTGGATATGAAT-TCCAA
* *
11537743 AATTCAAATGAAAAGCTTTAGATTTTTTGATATGAATTCCAA
1 AATTCAAATGAAAAGCTTTAGAATTTTGGATATGAATTCCAA
11537785 GTTTGCCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 23 0.62
43 14 0.38
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (42 bp):
AATTCAAATGAAAAGCTTTAGAATTTTGGATATGAATTCCAA
Found at i:11538242 original size:41 final size:41
Alignment explanation
Indices: 11538075--11538385 Score: 209
Period size: 41 Copynumber: 7.6 Consensus size: 41
11538065 ATGATTGTTA
* * * *
11538075 AGGAGTAATTTATTTTTCAAAGTCGTGGTTGCCTTTATTTAG
1 AGGAGCAATTTACTTTTCAAAGTTGTGG-TGCCTCTATTTAG
* *
11538117 AGGAGCAATTTACTTTTCAAAGTCATGAGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGT--TGTGGTGCCTCTATTTAG
* * * * *
11538160 AGGAGCAACTTACTTTCCAAAGTT-TCGTTGCCTTTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTTGT-GGTGCCTCTATTTAG
* *
11538201 AGGAGCAATTTACTTTTCAAAGTTGTGGTACCTCTACTTAG
1 AGGAGCAATTTACTTTTCAAAGTTGTGGTGCCTCTATTTAG
* * ** * * **
11538242 ATGAGC-ATTTACTTTT-GAAGTCATGGTGCATTTGCTTAG
1 AGGAGCAATTTACTTTTCAAAGTTGTGGTGCCTCTATTTAG
*** * * **
11538281 A-GATTTTATTTATTTTTCAAAGTTGTTGAACCTCTGA-TTAG
1 AGGA-GCAATTTACTTTTCAAAGTTGTGGTGCCTCT-ATTTAG
* * * * * *
11538322 AGGAGCCATTTATTTTTCAAAATTGTTGAGCCTCTAATTAG
1 AGGAGCAATTTACTTTTCAAAGTTGTGGTGCCTCTATTTAG
* *
11538363 AGGAGCCATTTATTTTTCAAAGT
1 AGGAGCAATTTACTTTTCAAAGT
11538386 CATTAAGCCT
Statistics
Matches: 215, Mismatches: 44, Indels: 21
0.77 0.16 0.08
Matches are distributed among these distances:
38 2 0.01
39 17 0.08
40 20 0.09
41 117 0.54
42 24 0.11
43 32 0.15
44 3 0.01
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.41
Consensus pattern (41 bp):
AGGAGCAATTTACTTTTCAAAGTTGTGGTGCCTCTATTTAG
Found at i:11538440 original size:42 final size:41
Alignment explanation
Indices: 11538288--11538451 Score: 220
Period size: 41 Copynumber: 4.0 Consensus size: 41
11538278 TAGAGATTTT
* *
11538288 ATTTATTTTTCAAAGTTGTTGAACCTCTGATTAGAGGAGCC
1 ATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCC
* * *
11538329 ATTTATTTTTCAAAATTGTTGAGCCTCTAATTAGAGGAGCC
1 ATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCC
* * * *
11538370 ATTTATTTTTCAAAGTCATTAAGCCTCTGACTAGATGAGCC
1 ATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCC
* *
11538411 ATTTATTTTTCAAAAGTCGTTGAGCCTCTGCTTAGAAGAGC
1 ATTTATTTTTC-AAAGTCGTTGAGCCTCTGATTAGAGGAGC
11538452 TTTGATCAAA
Statistics
Matches: 107, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
41 83 0.78
42 24 0.22
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (41 bp):
ATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCC
Found at i:11538601 original size:109 final size:106
Alignment explanation
Indices: 11538412--11538677 Score: 405
Period size: 106 Copynumber: 2.5 Consensus size: 106
11538402 AGATGAGCCA
*
11538412 TTTAT-TTT-TCAAAAGTCGTTGAGCCTCTGCTTAGAAGAGCTTTGATCAAAATTTAAAAATAAT
1 TTTATGTTTCTCAAAAGTCGTTGAGCCTCTGCTTAGAGGAGCTTTGATC-AAATTTAAAAAT-A-
*
11538475 AAAAAAAAAAAACAAAAAAAATTACCTCTATTTAGAGGAGTTTTG
63 AAAAAAAAAAAA-AAAAAAAATTACCTCTATTTAGAGGAGCTTTG
*
11538520 TTTATGTTTCT-TAAAGTCGTTGAGCCTCTGCTTAGAGGAGCTTTGATCAAATTTAAAAA-AAAA
1 TTTATGTTTCTCAAAAGTCGTTGAGCCTCTGCTTAGAGGAGCTTTGATCAAATTTAAAAATAAAA
*
11538583 ACAAAAAAAAATAAAAAAATTACCTTTATTTAGAGGAGCTTTG
66 A-AAAAAAAAA-AAAAAAATTACCTCTATTTAGAGGAGCTTTG
*
11538626 TTTATGTTTCTCAAAAGTCGTTGAGCCTCTACTTAGAGGAGCTTTGATCAAA
1 TTTATGTTTCTCAAAAGTCGTTGAGCCTCTGCTTAGAGGAGCTTTGATCAAA
11538678 ATTGTTTTCT
Statistics
Matches: 147, Mismatches: 6, Indels: 11
0.90 0.04 0.07
Matches are distributed among these distances:
105 5 0.03
106 49 0.33
107 38 0.26
108 16 0.11
109 38 0.26
110 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.33
Consensus pattern (106 bp):
TTTATGTTTCTCAAAAGTCGTTGAGCCTCTGCTTAGAGGAGCTTTGATCAAATTTAAAAATAAAA
AAAAAAAAAAAAAAAAATTACCTCTATTTAGAGGAGCTTTG
Found at i:11538665 original size:107 final size:109
Alignment explanation
Indices: 11538412--11538677 Score: 418
Period size: 107 Copynumber: 2.5 Consensus size: 109
11538402 AGATGAGCCA
*
11538412 TTTAT-TTT-TCAAAAGTCGTTGAGCCTCTGCTTAGAAGAGCTTTGATCAAAATTTAAAAATAAT
1 TTTATGTTTCTCAAAAGTCGTTGAGCCTCTGCTTAGAGGAGCTTTGATC-AAATTTAAAAATAAT
*
11538475 AAAAAAAAAAAACAAAAAAAATTACCTCTATTTAGAGGAGTTTTG
65 AAAAAAAAAAAACAAAAAAAATTACCTCTATTTAGAGGAGCTTTG
*
11538520 TTTATGTTTCT-TAAAGTCGTTGAGCCTCTGCTTAGAGGAGCTTTGATCAAATTTAAAAA-AA-A
1 TTTATGTTTCTCAAAAGTCGTTGAGCCTCTGCTTAGAGGAGCTTTGATCAAATTTAAAAATAATA
* *
11538582 AACAAAAAAAAA-TAAAAAAATTACCTTTATTTAGAGGAGCTTTG
66 AA-AAAAAAAAACAAAAAAAATTACCTCTATTTAGAGGAGCTTTG
*
11538626 TTTATGTTTCTCAAAAGTCGTTGAGCCTCTACTTAGAGGAGCTTTGATCAAA
1 TTTATGTTTCTCAAAAGTCGTTGAGCCTCTGCTTAGAGGAGCTTTGATCAAA
11538678 ATTGTTTTCT
Statistics
Matches: 147, Mismatches: 7, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
106 43 0.29
107 49 0.33
108 16 0.11
109 38 0.26
110 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.33
Consensus pattern (109 bp):
TTTATGTTTCTCAAAAGTCGTTGAGCCTCTGCTTAGAGGAGCTTTGATCAAATTTAAAAATAATA
AAAAAAAAAAACAAAAAAAATTACCTCTATTTAGAGGAGCTTTG
Found at i:11540771 original size:12 final size:11
Alignment explanation
Indices: 11540754--11540796 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
11540744 ACCTTCACTG
11540754 TTTATTTTTATT
1 TTTATTTTT-TT
11540766 TTTATTTTTTT
1 TTTATTTTTTT
* *
11540777 GTT-TTTTTTG
1 TTTATTTTTTT
11540787 TTTATTTTTT
1 TTTATTTTTT
11540797 GTAGTTCTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 8 0.30
11 10 0.37
12 9 0.33
ACGTcount: A:0.09, C:0.00, G:0.05, T:0.86
Consensus pattern (11 bp):
TTTATTTTTTT
Found at i:11540972 original size:58 final size:58
Alignment explanation
Indices: 11540888--11541292 Score: 580
Period size: 58 Copynumber: 6.9 Consensus size: 58
11540878 TAAAAAATAT
* * * *
11540888 AAAATAAAATTTTCGAGAATAATATTTTTGAGGAAAAGTTAAAAGTATCAATTTTCTTTG
1 AAAAT-AAATTTTCTA-AAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTG
11540948 AAAATAAATTTTCTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTG
1 AAAATAAATTTTCTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTG
* * * ** *
11541006 AAAAT-AAGTTTCCAAAAAATATTTTTGAGGAAAAGATGAAAGTATCAATTTTTTTTT
1 AAAATAAATTTTCTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTG
*
11541063 AAAATAAATTTTCTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAATTTCCTTG
1 AAAATAAATTTTCTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTG
** * * *
11541121 AAAATAAGCTTTCCAAAAACTATTTTTGATGAAAAGTTGAAAGTATCAATTTTCCTTG
1 AAAATAAATTTTCTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTG
* *
11541179 AAAATAAATTTTCTAAAAAATATTTTTGAGGAAAAGTTGGAAGTATCAATTTTCCTTA
1 AAAATAAATTTTCTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTG
* *
11541237 AAAATAAATTTCCAAAAAAAATATTTTTG-GAGAAAAGTTGAAAGTATCAATTTTCC
1 AAAATAAATTTTC-TAAAAAATATTTTTGAG-GAAAAGTTGAAAGTATCAATTTTCC
11541293 CTGCATAAAA
Statistics
Matches: 309, Mismatches: 33, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
57 51 0.17
58 206 0.67
59 47 0.15
60 5 0.02
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (58 bp):
AAAATAAATTTTCTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTG
Found at i:11541169 original size:116 final size:115
Alignment explanation
Indices: 11540908--11541291 Score: 626
Period size: 115 Copynumber: 3.3 Consensus size: 115
11540898 TTTCGAGAAT
*
11540908 AATATTTTTGAGGAAAAGTTAAAAGTATCAATTTTCTTTGAAAATAAATTTTCTAAAAAATATTT
1 AATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAATTTTCTAAAAAATATTT
11540973 TTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTCCAAAA
66 TTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTCCAAAA
* * *
11541023 AATATTTTTGAGGAAAAGATGAAAGTATCAATTTTTTTTTAAAATAAATTTTCTAAAAAATATTT
1 AATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAATTTTCTAAAAAATATTT
*
11541088 TTGAGGAAAAGTTGAAAGTATCAAATTTCCTTGAAAATAAGCTTTCCAAAA
66 TTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAG-TTTCCAAAA
* * *
11541139 ACTATTTTTGATGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTTCTAAAAAATATTT
1 AATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAATTTTCTAAAAAATATTT
* * *
11541204 TTGAGGAAAAGTTGGAAGTATCAATTTTCCTTAAAAATAAATTTCCAAAAAA
66 TTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTCC--AAAA
11541256 AATATTTTTG-GAGAAAAGTTGAAAGTATCAATTTTC
1 AATATTTTTGAG-GAAAAGTTGAAAGTATCAATTTTC
11541292 CCTGCATAAA
Statistics
Matches: 248, Mismatches: 17, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
115 106 0.43
116 105 0.42
117 37 0.15
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.37
Consensus pattern (115 bp):
AATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAATTTTCTAAAAAATATTT
TTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTCCAAAA
Found at i:11544235 original size:15 final size:15
Alignment explanation
Indices: 11544215--11544245 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11544205 ATCGAAGAAT
*
11544215 ATAAATAACATAAAA
1 ATAAATAAAATAAAA
11544230 ATAAATAAAATAAAA
1 ATAAATAAAATAAAA
11544245 A
1 A
11544246 CATACCGATA
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:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (15 bp):
ATAAATAAAATAAAA
Found at i:11546438 original size:17 final size:17
Alignment explanation
Indices: 11546416--11546449 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
11546406 ATTCAACCCC
11546416 CCATTTTTCATT-TTTTT
1 CCATTTTT-ATTATTTTT
11546433 CCATTTTTATTATTTTT
1 CCATTTTTATTATTTTT
11546450 AATAAAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (17 bp):
CCATTTTTATTATTTTT
Found at i:11546670 original size:42 final size:41
Alignment explanation
Indices: 11546610--11546948 Score: 284
Period size: 42 Copynumber: 8.1 Consensus size: 41
11546600 TTTGATTAAA
** *
11546610 GCTCCTCTAAGCAGAGGCTCAACGACTTTGAGAAACATAAA-T
1 GCTCCTCTAAATAGAGGC-CAACGACTTTGA-AAAAATAAATT
* *
11546652 ACTCCTCTAAATAGAGGCTCAACGACTTTG-AGAAATAAATT
1 GCTCCTCTAAATAGAGGC-CAACGACTTTGAAAAAATAAATT
* * * * * * *
11546693 GCTCATTTAAATAGAGACAACACTACTTTGGAAAGATAAATT
1 GCTCCTCTAAATAGAGGCCA-ACGACTTTGAAAAAATAAATT
* * *
11546735 GCTCCTCTAAATAGAGG-CAATAGAACATTGAAAAAATGAATT
1 GCTCCTCTAAATAGAGGCCAA-CG-ACTTTGAAAAAATAAATT
*
11546777 GCTCCTCTAAATAGAGG-CAACAAAACTTTGAAAAAATAAATT
1 GCTCCTCTAAATAGAGGCCAAC--GACTTTGAAAAAATAAATT
* * *
11546819 GCTCCTCTAAAAAGAGG-CAACAAAATTTTG-AAAAATAAATT
1 GCTCCTCTAAATAGAGGCCAAC--GACTTTGAAAAAATAAATT
* *
11546860 TCTCCTTTAAATAGAGG-CAACAGAACTTT-ACAAAAATAAATT
1 GCTCCTCTAAATAGAGGCCAAC-G-ACTTTGA-AAAAATAAATT
11546902 GCTCCTCTAAATAGAGG-CAACAGAACTTTG-AAAAATAAATT
1 GCTCCTCTAAATAGAGGCCAAC-G-ACTTTGAAAAAATAAATT
11546943 GCTCCT
1 GCTCCT
11546949 TGATAATCAT
Statistics
Matches: 250, Mismatches: 36, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
40 10 0.04
41 74 0.30
42 166 0.66
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (41 bp):
GCTCCTCTAAATAGAGGCCAACGACTTTGAAAAAATAAATT
Found at i:11546857 original size:125 final size:125
Alignment explanation
Indices: 11546653--11546948 Score: 391
Period size: 125 Copynumber: 2.4 Consensus size: 125
11546643 AACATAAATA
* * * * * * *
11546653 CTCCTCTAAATAGAGGC-TCAACGACTTTGAGAAATAAATTGCTCATTTAAATAGAGACAACACT
1 CTCCTCTAAATAGAGGCAACAA-AACTTTGAAAAATAAATTGCTCCTCTAAAAAGAGACAACACA
* * * *
11546717 ACTTTGGAAAGATAAATTGCTCCTCTAAATAGAGGCAATAGAACATTGA-AAAAATGAATTG
65 AATTTGGAAAAATAAATTGCTCCTCTAAATAGAGGCAACAGAAC-TTGACAAAAATAAATTG
*
11546778 CTCCTCTAAATAGAGGCAACAAAACTTTGAAAAAATAAATTGCTCCTCTAAAAAGAGGCAACA-A
1 CTCCTCTAAATAGAGGCAACAAAACTTTG-AAAAATAAATTGCTCCTCTAAAAAGAGACAACACA
* * * *
11546842 AATTTTGAAAAATAAATTTCTCCTTTAAATAGAGGCAACAGAACTTTACAAAAATAAATTG
65 AATTTGGAAAAATAAATTGCTCCTCTAAATAGAGGCAACAGAACTTGACAAAAATAAATTG
*
11546903 CTCCTCTAAATAGAGGCAACAGAACTTTGAAAAATAAATTGCTCCT
1 CTCCTCTAAATAGAGGCAACAAAACTTTGAAAAATAAATTGCTCCT
11546949 TGATAATCAT
Statistics
Matches: 151, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
124 20 0.13
125 100 0.66
126 31 0.21
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.26
Consensus pattern (125 bp):
CTCCTCTAAATAGAGGCAACAAAACTTTGAAAAATAAATTGCTCCTCTAAAAAGAGACAACACAA
ATTTGGAAAAATAAATTGCTCCTCTAAATAGAGGCAACAGAACTTGACAAAAATAAATTG
Found at i:11546895 original size:83 final size:82
Alignment explanation
Indices: 11546653--11546949 Score: 382
Period size: 83 Copynumber: 3.6 Consensus size: 82
11546643 AACATAAATA
* * * *
11546653 CTCCTCTAAATAGAGGCTCAAC-G-ACTTTGAGAAATAAATTGCTCATTTAAATAGAGACAACAC
1 CTCCTCTAAATAGAGG--CAACAGAACTTTGAAAAATAAATTGCTCCTTTAAATAGAGGCAACAA
* * *
11546716 TACTTTGGAAAGATAAATTG
64 AACTTT-AAAAAATAAATTG
* * * *
11546736 CTCCTCTAAATAGAGGCAATAGAACATTGAAAAAATGAATTGCTCCTCTAAATAGAGGCAACAAA
1 CTCCTCTAAATAGAGGCAACAGAACTTTG-AAAAATAAATTGCTCCTTTAAATAGAGGCAACAAA
11546801 ACTTTGAAAAAATAAATTG
65 ACTTT-AAAAAATAAATTG
* * * * *
11546820 CTCCTCTAAAAAGAGGCAACAAAATTTTGAAAAATAAATTTCTCCTTTAAATAGAGGCAACAGAA
1 CTCCTCTAAATAGAGGCAACAGAACTTTGAAAAATAAATTGCTCCTTTAAATAGAGGCAACAAAA
11546885 CTTTACAAAAATAAATTG
66 CTTTA-AAAAATAAATTG
11546903 CTCCTCTAAATAGAGGCAACAGAACTTTGAAAAATAAATTGCTCCTT
1 CTCCTCTAAATAGAGGCAACAGAACTTTGAAAAATAAATTGCTCCTT
11546950 GATAATCATG
Statistics
Matches: 186, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
81 3 0.02
82 2 0.01
83 112 0.60
84 69 0.37
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.26
Consensus pattern (82 bp):
CTCCTCTAAATAGAGGCAACAGAACTTTGAAAAATAAATTGCTCCTTTAAATAGAGGCAACAAAA
CTTTAAAAAATAAATTG
Found at i:11547357 original size:21 final size:21
Alignment explanation
Indices: 11547313--11547356 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
11547303 TTTTTTTTTG
11547313 AAATTCAAAGATTCTCATTCA
1 AAATTCAAAGATTCTCATTCA
11547334 AAATTCAAAGACTT-TCA-TCA
1 AAATTCAAAGA-TTCTCATTCA
11547354 AAA
1 AAA
11547357 AGTTCACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.27
21 14 0.64
22 2 0.09
ACGTcount: A:0.48, C:0.18, G:0.05, T:0.30
Consensus pattern (21 bp):
AAATTCAAAGATTCTCATTCA
Found at i:11548364 original size:26 final size:26
Alignment explanation
Indices: 11548335--11548388 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
11548325 AGTCTTTCCA
11548335 TTTTCGTTTTT-CATTTTTTTCATTTT
1 TTTTC-TTTTTACATTTTTTTCATTTT
* *
11548361 TTTTCTTTTTACTTTTTTTTCGTTTT
1 TTTTCTTTTTACATTTTTTTCATTTT
11548387 TT
1 TT
11548389 AAGCGTAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.06, C:0.11, G:0.04, T:0.80
Consensus pattern (26 bp):
TTTTCTTTTTACATTTTTTTCATTTT
Found at i:11551042 original size:20 final size:21
Alignment explanation
Indices: 11551004--11551042 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11550994 CTGTAGACAC
*
11551004 CCAATTGGGTCTAGGCCCAGA
1 CCAATTGGGCCTAGGCCCAGA
11551025 CCAATTGGGCCT-GGCCCA
1 CCAATTGGGCCTAGGCCCA
11551043 AATGGGGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.21, C:0.33, G:0.28, T:0.18
Consensus pattern (21 bp):
CCAATTGGGCCTAGGCCCAGA
Found at i:11551103 original size:13 final size:14
Alignment explanation
Indices: 11551085--11551114 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
11551075 ATTATTATTA
11551085 TTTTCTTTT-TTCT
1 TTTTCTTTTCTTCT
11551098 TTTTCTTTTCTTCT
1 TTTTCTTTTCTTCT
11551112 TTT
1 TTT
11551115 GTGTTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTCTTTTCTTCT
Found at i:11551187 original size:4 final size:4
Alignment explanation
Indices: 11551165--11551201 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
11551155 CATATGTATA
* *
11551165 TATT GATT TATT TAGT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT T
11551202 TGTTAATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.70
Consensus pattern (4 bp):
TATT
Found at i:11551187 original size:12 final size:12
Alignment explanation
Indices: 11551170--11551206 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
11551160 GTATATATTG
11551170 ATTTATTTAGTT
1 ATTTATTTAGTT
*
11551182 ATTTATTTATTT
1 ATTTATTTAGTT
*
11551194 ATTTATTTTGTT
1 ATTTATTTAGTT
11551206 A
1 A
11551207 ATATTTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.70
Consensus pattern (12 bp):
ATTTATTTAGTT
Found at i:11551712 original size:25 final size:24
Alignment explanation
Indices: 11551656--11551712 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
11551646 GTTCTGGGAG
*
11551656 TGAGAAAAAATTTTTAGAAATTTT
1 TGAGAAAAAATTTTTAGAAATTTC
* * *
11551680 TGGCGAAAAAGTTTTCTGGAAATTTC
1 T-GAGAAAAAATTTT-TAGAAATTTC
11551706 TGAGAAA
1 TGAGAAA
11551713 TTTCTAGATT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 1 0.04
25 16 0.62
26 9 0.35
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.35
Consensus pattern (24 bp):
TGAGAAAAAATTTTTAGAAATTTC
Found at i:11552251 original size:22 final size:21
Alignment explanation
Indices: 11552205--11552257 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
11552195 CCGCTCCAGG
11552205 TTTTTTT-TTTTTCTTTGAAT
1 TTTTTTTATTTTTCTTTGAAT
* * *
11552225 GTTTTTTATTTGTTTTTTTAAT
1 TTTTTTTATTT-TTCTTTGAAT
11552247 TTTTTTTATTT
1 TTTTTTTATTT
11552258 ATTATATTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 6 0.22
21 3 0.11
22 18 0.67
ACGTcount: A:0.11, C:0.02, G:0.06, T:0.81
Consensus pattern (21 bp):
TTTTTTTATTTTTCTTTGAAT
Found at i:11552337 original size:10 final size:10
Alignment explanation
Indices: 11552324--11552358 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
11552314 TTACTTTTCT
11552324 TTATTTTTTA
1 TTATTTTTTA
11552334 TTATTTATTTA
1 TTATTT-TTTA
11552345 -TATTTTTTA
1 TTATTTTTTA
11552354 TTATT
1 TTATT
11552359 CTATTTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 4 0.17
10 15 0.65
11 4 0.17
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (10 bp):
TTATTTTTTA
Found at i:11552348 original size:20 final size:21
Alignment explanation
Indices: 11552325--11552364 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
11552315 TACTTTTCTT
11552325 TATTTTTTATTATT-TATTTA
1 TATTTTTTATTATTCTATTTA
11552345 TATTTTTTATTATTCTATTT
1 TATTTTTTATTATTCTATTT
11552365 TCTTCAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (21 bp):
TATTTTTTATTATTCTATTTA
Found at i:11552463 original size:59 final size:58
Alignment explanation
Indices: 11552392--11552669 Score: 389
Period size: 59 Copynumber: 4.7 Consensus size: 58
11552382 AATTTTCCAA
*
11552392 AAAAAAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATACATTTTC
1 AAAAAAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
* *
11552450 AAAAAAGAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1 AAAAAA-ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
* * *
11552509 AAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAATAAAATTTC
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-AGAAATAAATTTTC
*
11552568 AAAAAAAGGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAATCGAAATTTTC
1 AAAAAAA--TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT--AAATTTTC
* *
11552630 AAAAAAATATTTTTGAGAAAAAGTTGAAAGTACCAATTTT
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
11552670 TCCTACACAA
Statistics
Matches: 197, Mismatches: 15, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
58 42 0.21
59 71 0.36
60 35 0.18
61 35 0.18
62 14 0.07
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (58 bp):
AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
Found at i:11556573 original size:8 final size:7
Alignment explanation
Indices: 11556546--11556600 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 7
11556536 AAAGATGATG
11556546 AAAA-AA
1 AAAAGAA
*
11556552 AAAAGAG
1 AAAAGAA
11556559 AAAA-AA
1 AAAAGAA
*
11556565 GAAAGAA
1 AAAAGAA
*
11556572 AGAAGAA
1 AAAAGAA
11556579 AAAATGAA
1 AAAA-GAA
11556587 AAAATGAA
1 AAAA-GAA
11556595 AAAAGA
1 AAAAGA
11556601 GATTCAAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
6 8 0.20
7 17 0.43
8 15 0.38
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (7 bp):
AAAAGAA
Found at i:11557892 original size:42 final size:42
Alignment explanation
Indices: 11557807--11557920 Score: 155
Period size: 40 Copynumber: 2.8 Consensus size: 42
11557797 GATTGTCAAA
* * *
11557807 GAGCAATTTACTTTT-CAAAGT-TTGTTGCCTCTGTTTAGAG
1 GAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAAAG
*
11557847 GAGCAATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAAAG
1 GAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAAAG
*
11557889 GAGCAATTTA--GTTCCAAAGTCGTGGTGCCTCT
1 GAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCT
11557921 AGCTTTGGTT
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
40 35 0.53
41 6 0.09
42 25 0.38
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (42 bp):
GAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAAAG
Found at i:11557964 original size:25 final size:25
Alignment explanation
Indices: 11557931--11557996 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 25
11557921 AGCTTTGGTT
*
11557931 AAAAAACAAAAAAATAATAAAAACA
1 AAAAAACAAAAAAATAAAAAAAACA
*
11557956 AAAAAACAAAAAAACAAAAAAAACA
1 AAAAAACAAAAAAATAAAAAAAACA
11557981 ACAAAAA-ATAAAAAAT
1 A-AAAAACA-AAAAAAT
11557997 GACAATGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
25 25 0.69
26 11 0.31
ACGTcount: A:0.85, C:0.09, G:0.00, T:0.06
Consensus pattern (25 bp):
AAAAAACAAAAAAATAAAAAAAACA
Found at i:11557978 original size:20 final size:21
Alignment explanation
Indices: 11557950--11557988 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
11557940 AAAAATAATA
11557950 AAAACAAAAAAACAAAAAAAC
1 AAAACAAAAAAACAAAAAAAC
*
11557971 AAAA-AAAACAACAAAAAA
1 AAAACAAAAAAACAAAAAA
11557989 TAAAAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (21 bp):
AAAACAAAAAAACAAAAAAAC
Found at i:11557993 original size:16 final size:14
Alignment explanation
Indices: 11557931--11557995 Score: 60
Period size: 14 Copynumber: 4.4 Consensus size: 14
11557921 AGCTTTGGTT
11557931 AAAAAACAAAAAAATA
1 AAAAAAC-AAAAAA-A
11557947 ATAAAAACAAAAAAA
1 A-AAAAACAAAAAAA
*
11557962 CAAAAAA-ACAAAAA
1 -AAAAAACAAAAAAA
*
11557976 AAACAACAAAAAATA
1 AAAAAACAAAAAA-A
11557991 AAAAA
1 AAAAA
11557996 TGACAATGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
13 5 0.12
14 11 0.27
15 11 0.27
16 8 0.20
17 6 0.15
ACGTcount: A:0.86, C:0.09, G:0.00, T:0.05
Consensus pattern (14 bp):
AAAAAACAAAAAAA
Found at i:11557993 original size:17 final size:17
Alignment explanation
Indices: 11557931--11557995 Score: 78
Period size: 17 Copynumber: 3.8 Consensus size: 17
11557921 AGCTTTGGTT
*
11557931 AAAAAACAAAAAAATAA
1 AAAAAACAAAAAAACAA
*
11557948 TAAAAACAAAAAAAC-A
1 AAAAAACAAAAAAACAA
11557964 AAAAAACAAAAAAAACAA
1 AAAAAAC-AAAAAAACAA
*
11557982 CAAAAAATAAAAAA
1 -AAAAAACAAAAAA
11557996 TGACAATGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
16 7 0.17
17 21 0.51
18 7 0.17
19 6 0.15
ACGTcount: A:0.86, C:0.09, G:0.00, T:0.05
Consensus pattern (17 bp):
AAAAAACAAAAAAACAA
Found at i:11557995 original size:8 final size:8
Alignment explanation
Indices: 11557931--11557987 Score: 78
Period size: 8 Copynumber: 6.8 Consensus size: 8
11557921 AGCTTTGGTT
11557931 AAAAAACA
1 AAAAAACA
*
11557939 AAAAAATA
1 AAAAAACA
11557947 ATAAAAACA
1 A-AAAAACA
11557956 AAAAAACA
1 AAAAAACA
11557964 AAAAAACAA
1 AAAAAAC-A
11557973 AAAAAACA
1 AAAAAACA
11557981 ACAAAAA
1 A-AAAAA
11557988 ATAAAAAATG
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
8 24 0.55
9 20 0.45
ACGTcount: A:0.86, C:0.11, G:0.00, T:0.04
Consensus pattern (8 bp):
AAAAAACA
Found at i:11558127 original size:20 final size:21
Alignment explanation
Indices: 11558089--11558129 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
11558079 CTGTAGACAC
11558089 CCAATTGGGTCCAGGCCCAAA
1 CCAATTGGGTCCAGGCCCAAA
*
11558110 CCAATTGGG-CCTGGCCCAAA
1 CCAATTGGGTCCAGGCCCAAA
11558130 GGGGGTAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.27, C:0.34, G:0.24, T:0.15
Consensus pattern (21 bp):
CCAATTGGGTCCAGGCCCAAA
Found at i:11558188 original size:13 final size:14
Alignment explanation
Indices: 11558170--11558199 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
11558160 ATTATTATTA
11558170 TTTTCTTTT-TTCT
1 TTTTCTTTTCTTCT
11558183 TTTTCTTTTCTTCT
1 TTTTCTTTTCTTCT
11558197 TTT
1 TTT
11558200 GTGTTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTCTTTTCTTCT
Found at i:11559285 original size:8 final size:8
Alignment explanation
Indices: 11559272--11559327 Score: 51
Period size: 8 Copynumber: 6.9 Consensus size: 8
11559262 TTGAATGTTT
11559272 TTTATTTG
1 TTTATTTG
11559280 TTTATTTG
1 TTTATTTG
* *
11559288 TTTTTTTA
1 TTTATTTG
*
11559296 TTTGTTT-
1 TTTATTTG
*
11559303 TTTATTTA
1 TTTATTTG
11559311 TTATATTTGG
1 TT-TATTT-G
11559321 TTTATTT
1 TTTATTT
11559328 AATATTCTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
7 6 0.15
8 22 0.55
9 10 0.25
10 2 0.05
ACGTcount: A:0.14, C:0.00, G:0.09, T:0.77
Consensus pattern (8 bp):
TTTATTTG
Found at i:11559292 original size:20 final size:20
Alignment explanation
Indices: 11559269--11559407 Score: 78
Period size: 20 Copynumber: 6.8 Consensus size: 20
11559259 TCTTTGAATG
*
11559269 TTTTTTATTTGTTTATTTGT
1 TTTTTTATTTGTTTATTTAT
11559289 TTTTTTATTTGTTT-TTTAT
1 TTTTTTATTTGTTTATTTAT
*
11559308 TTATTATATTTGGTTTATTTAAT
1 TT-TTTTATTT-GTTTATTT-AT
* * *
11559331 ATTCTT-TTTATCTTAGTTT-T
1 TTTTTTATTTGT-TTA-TTTAT
*
11559351 ATTTTTATTT-TTGT-TTTACT
1 TTTTTTATTTGTT-TATTTA-T
11559371 TTTCTTTATTT-TTTA-TTAT
1 TTT-TTTATTTGTTTATTTAT
11559390 TTATTTATATTT-TTTATT
1 TT-TTT-TATTTGTTTATT
11559408 ATTCTATTTT
Statistics
Matches: 96, Mismatches: 8, Indels: 29
0.72 0.06 0.22
Matches are distributed among these distances:
18 3 0.03
19 12 0.12
20 47 0.49
21 23 0.24
22 8 0.08
23 3 0.03
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.76
Consensus pattern (20 bp):
TTTTTTATTTGTTTATTTAT
Found at i:11559297 original size:12 final size:11
Alignment explanation
Indices: 11559267--11559309 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
11559257 TTTCTTTGAA
11559267 TGTTTTTTATT
1 TGTTTTTTATT
11559278 TG---TTTATT
1 TGTTTTTTATT
11559286 TGTTTTTTTATT
1 TG-TTTTTTATT
11559298 TGTTTTTTATT
1 TGTTTTTTATT
11559309 T
1 T
11559310 ATTATATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
8 8 0.29
11 12 0.43
12 8 0.29
ACGTcount: A:0.09, C:0.00, G:0.09, T:0.81
Consensus pattern (11 bp):
TGTTTTTTATT
Found at i:11559304 original size:31 final size:33
Alignment explanation
Indices: 11559267--11559328 Score: 92
Period size: 31 Copynumber: 1.9 Consensus size: 33
11559257 TTTCTTTGAA
* *
11559267 TGTTTTTTATTTGTT-TATTT-GTTTTTTTATT
1 TGTTTTTTATTTATTATATTTGGTTTATTTATT
11559298 TGTTTTTTATTTATTATATTTGGTTTATTTA
1 TGTTTTTTATTTATTATATTTGGTTTATTTA
11559329 ATATTCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 14 0.52
32 5 0.19
33 8 0.30
ACGTcount: A:0.15, C:0.00, G:0.10, T:0.76
Consensus pattern (33 bp):
TGTTTTTTATTTATTATATTTGGTTTATTTATT
Found at i:11559357 original size:17 final size:18
Alignment explanation
Indices: 11559334--11559373 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
11559324 ATTTAATATT
11559334 CTTTTTATCTTAGTTTTA
1 CTTTTTATCTTAGTTTTA
* *
11559352 -TTTTTATTTTTGTTTTA
1 CTTTTTATCTTAGTTTTA
11559369 CTTTT
1 CTTTT
11559374 CTTTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.75
Consensus pattern (18 bp):
CTTTTTATCTTAGTTTTA
Found at i:11559408 original size:20 final size:21
Alignment explanation
Indices: 11559377--11559416 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
11559367 TACTTTTCTT
11559377 TATTTTTTATTATT-TATTTA
1 TATTTTTTATTATTCTATTTA
11559397 TATTTTTTATTATTCTATTT
1 TATTTTTTATTATTCTATTT
11559417 TCTTCAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (21 bp):
TATTTTTTATTATTCTATTTA
Found at i:11559515 original size:59 final size:58
Alignment explanation
Indices: 11559444--11559721 Score: 380
Period size: 59 Copynumber: 4.7 Consensus size: 58
11559434 AATTTTCCAA
*
11559444 AAAAAAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATACATTTTC
1 AAAAAAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
* *
11559502 AAAAAAGAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1 AAAAAA-ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
* * *
11559561 AAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAATAAAATTTC
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-AGAAATAAATTTTC
* *
11559620 AAAAAAAGGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTT-GAAAATCAAAATTTTC
1 AAAAAAA--TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT--AAATTTTC
* *
11559682 AAAAAAATATTTTTGAGAAAAAGTTGAAAGTACCAATTTT
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
11559722 TCCTACACAA
Statistics
Matches: 196, Mismatches: 16, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
58 42 0.21
59 71 0.36
60 35 0.18
61 34 0.17
62 14 0.07
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.34
Consensus pattern (58 bp):
AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
Found at i:11565994 original size:53 final size:54
Alignment explanation
Indices: 11565937--11566074 Score: 152
Period size: 54 Copynumber: 2.6 Consensus size: 54
11565927 CTAATTATTC
* *
11565937 CACCATTTAGGCCAAATTAGAAATATTTTCTCT-CTTCAAATTTCTAAATTTTT
1 CACCATTTGGGCCAATTTAGAAATATTTTCTCTACTTCAAATTTCTAAATTTTT
** * * * * * ***
11565990 CACCATTTGGGCCTGTTTAGAATTTTTTTATTTATTTTTTATTTCTAAATTTTT
1 CACCATTTGGGCCAATTTAGAAATATTTTCTCTACTTCAAATTTCTAAATTTTT
*
11566044 CACCATTTGGGTCAATTTAGAAATATTTTCT
1 CACCATTTGGGCCAATTTAGAAATATTTTCT
11566075 TTTTTTTTTG
Statistics
Matches: 66, Mismatches: 18, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
53 25 0.38
54 41 0.62
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.49
Consensus pattern (54 bp):
CACCATTTGGGCCAATTTAGAAATATTTTCTCTACTTCAAATTTCTAAATTTTT
Found at i:11566063 original size:54 final size:54
Alignment explanation
Indices: 11565976--11566083 Score: 153
Period size: 54 Copynumber: 2.0 Consensus size: 54
11565966 CTCTCTTCAA
** * *
11565976 ATTTCTAAATTTTTCACCATTTGGGCCTGTTTAGAATTTTTTTATTTATTTTTT
1 ATTTCTAAATTTTTCACCATTTGGGCCAATTTAGAAATATTTTATTTATTTTTT
* * *
11566030 ATTTCTAAATTTTTCACCATTTGGGTCAATTTAGAAATATTTTCTTTTTTTTTT
1 ATTTCTAAATTTTTCACCATTTGGGCCAATTTAGAAATATTTTATTTATTTTTT
11566084 GGAAAGAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.22, C:0.11, G:0.08, T:0.58
Consensus pattern (54 bp):
ATTTCTAAATTTTTCACCATTTGGGCCAATTTAGAAATATTTTATTTATTTTTT
Found at i:11566705 original size:23 final size:23
Alignment explanation
Indices: 11566639--11566706 Score: 59
Period size: 25 Copynumber: 2.8 Consensus size: 23
11566629 TAATTTAATA
11566639 AAAAAATACCAAACGAATACATAAAT
1 AAAAAATACCAAAC-AA-A-ATAAAT
* *
11566665 -AAAAATACTTAAATAAAATAAAT
1 AAAAAATAC-CAAACAAAATAAAT
11566688 AAGAAAATACCAAA-AAAAT
1 AA-AAAATACCAAACAAAAT
11566707 TTGAAAACGG
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
23 11 0.31
24 5 0.14
25 17 0.47
26 3 0.08
ACGTcount: A:0.69, C:0.10, G:0.03, T:0.18
Consensus pattern (23 bp):
AAAAAATACCAAACAAAATAAAT
Found at i:11567659 original size:62 final size:61
Alignment explanation
Indices: 11567496--11567660 Score: 152
Period size: 62 Copynumber: 2.7 Consensus size: 61
11567486 CCCTTTTAAT
* * * *
11567496 TTTTTTAAAAAAAATTATTGAAGGTGTTTTTTTGTAGAAAACACCTTCAATAATCCCTTCTA
1 TTTTTTAAAGAAAATTATTGAAGGTG-TTTTTTGTAAAAAACACCTTCAATAATCCCATCCA
** ** * ** * **
11567558 -TTTTTATCTGAGGATTATTGGAGGCATTTTCTGTCAAAAAATGCCTTCAATAATCCCATCCA
1 TTTTTTA-AAGAAAATTATTGAAGGTGTTTTTTGT-AAAAAACACCTTCAATAATCCCATCCA
*
11567620 CTTTTTTAAAGAAAATTATTCAAGGTGTTTTTTGTAAAAAA
1 -TTTTTTAAAGAAAATTATTGAAGGTGTTTTTTGTAAAAAA
11567661 AAAAAAAAAT
Statistics
Matches: 76, Mismatches: 23, Indels: 8
0.71 0.21 0.07
Matches are distributed among these distances:
61 13 0.17
62 39 0.51
63 18 0.24
64 6 0.08
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (61 bp):
TTTTTTAAAGAAAATTATTGAAGGTGTTTTTTGTAAAAAACACCTTCAATAATCCCATCCA
Found at i:11567950 original size:64 final size:62
Alignment explanation
Indices: 11567875--11568520 Score: 354
Period size: 63 Copynumber: 10.2 Consensus size: 62
11567865 AAATGGAAGA
*
11567875 GATTATTGAAGGCATTTTCTACAAAAAATTACCTTCAATAATTTTCTTTAAAAAAATTAAAGGG
1 GATTATTGAAGGCATTTTCTACAAAAAAATACCTTCAATAATTTTCTTT-AAAAAATTAAA-GG
* * * * * *
11567939 GATTATTGAAGGCATTTT-TAGTTTAAAAAAGT--CTTCAATAATCTCCTTGTCAAAATTTAAAG
1 GATTATTGAAGGCATTTTCTA---CAAAAAAATACCTTCAATAATTTTCTT-TAAAAAATTAAAG
11568001 G
62 G
* * * * * ** *
11568002 GATTATTGAAGGTATTTT-TAGC-AGAAAATACCTTCAATAA-TCTC-TGATAAAATGGAAGA
1 GATTATTGAAGGCATTTTCTA-CAAAAAAATACCTTCAATAATTTTCTTTAAAAAATTAAAGG
* ** ** * * * *
11568061 GATTATTAAAGATATTTTCT-GTAAAAACTGCCTTCAGTAATTTTCTTTAAAAAATTAAAAAG
1 GATTATTGAAGGCATTTTCTACAAAAAAATACCTTCAATAATTTTCTTTAAAAAATT-AAAGG
* * * * * * *
11568123 GATTATTGAGGGGATTTTTTTATC--AAAAATGCCTTCCATAA-TCTCTTTGCCCAGAAAATTTA
1 GATTATTGAAGGCA-TTTTCTA-CAAAAAAATACCTTCAATAATTTTCTTT----A-AAAAATTA
11568185 AAGG
59 AAGG
* *
11568189 GATTATTGAAGGCATTTTCTAAAAAAAAAAATACCTTCAATAATTTTCTTTAAAAAATTGAAGG
1 GATTATTGAAGGCATTTTCT--ACAAAAAAATACCTTCAATAATTTTCTTTAAAAAATTAAAGG
* * * ** **
11568253 GAATTATTAAAGGCGTTTT-TGACAAAAAAATACCTTGAATAA-TCCCTTTATAAAAATGGAAGG
1 G-ATTATTGAAGGCATTTTCT-ACAAAAAAATACCTTCAATAATTTTCTTTA-AAAAATTAAAGG
* * * ** * * * *
11568316 GATTATTGAAGGTATTTTTTGCAAAAAAATGTCTTTAATAATTTCCTGTAAAAAATTAGAGG
1 GATTATTGAAGGCATTTTCTACAAAAAAATACCTTCAATAATTTTCTTTAAAAAATTAAAGG
* * ** * * *
11568378 AGATTATT-AACGGTATTTTTTTATCAAAAACGT--CTTCAATAATCTCCTCGTT-AAAATTTAA
1 -GATTATTGAA-GGCA-TTTTCTA-CAAAAAAATACCTTCAATAAT-T-TTCTTTAAAAAATTAA
11568439 AGG
60 AGG
* * * *
11568442 GATTATTGAAGGCGTTTTCTGCAAAAGAAAAAATGCCTTCAATAATTTTCTTTAAAAAATTGGAA
1 GATTATTGAAGGCATTTTCT---ACA-AAAAAATACCTTCAATAATTTTCTTTAAAAAATT-AAA
11568507 GG
61 GG
11568509 GATTATTGAAGG
1 GATTATTGAAGG
11568521 TGTTTTTTCC
Statistics
Matches: 443, Mismatches: 96, Indels: 83
0.71 0.15 0.13
Matches are distributed among these distances:
59 37 0.08
60 10 0.02
61 8 0.02
62 80 0.18
63 109 0.25
64 73 0.16
65 41 0.09
66 31 0.07
67 33 0.07
68 15 0.03
69 6 0.01
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (62 bp):
GATTATTGAAGGCATTTTCTACAAAAAAATACCTTCAATAATTTTCTTTAAAAAATTAAAGG
Found at i:11570200 original size:9 final size:8
Alignment explanation
Indices: 11570173--11570202 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
11570163 ATTGCATTCA
11570173 ATTTTATT
1 ATTTTATT
11570181 ATTTTATT
1 ATTTTATT
11570189 ATTTTGATT
1 ATTTT-ATT
11570198 ATTTT
1 ATTTT
11570203 TTGTATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (8 bp):
ATTTTATT
Found at i:11575530 original size:123 final size:122
Alignment explanation
Indices: 11575385--11575627 Score: 459
Period size: 123 Copynumber: 2.0 Consensus size: 122
11575375 ATAAATATAT
*
11575385 AAGATACATACATCTAATACAATTTAGATATCAGGGCTAATATTCAATTCTTCCAAACTTTATGC
1 AAGATACATACATCTAATACAATTTAGATATCAGGGCTAATATTCAATTCTTCCAAACCTTATGC
*
11575450 CTAGACAAAACTCCTTGGGTATCCATCAAAAAGCCACCCTTTCTCCTTAGCATCTTAA
66 CTAGACAAAACGCCTTGGGTATCCAT-AAAAAGCCACCCTTTCTCCTTAGCATCTTAA
11575508 AAGATACATACATCTAATACAATTTAGATATCAGGGCTAATATTCAATTCTTCCAAACCTTATGC
1 AAGATACATACATCTAATACAATTTAGATATCAGGGCTAATATTCAATTCTTCCAAACCTTATGC
11575573 CTAGACAAAACGCCTTGGGTATCCATAAAAAGCCACCCTTTCTCCTTAGCATCTT
66 CTAGACAAAACGCCTTGGGTATCCATAAAAAGCCACCCTTTCTCCTTAGCATCTT
11575628 TCCCTAAACT
Statistics
Matches: 118, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
122 29 0.25
123 89 0.75
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.30
Consensus pattern (122 bp):
AAGATACATACATCTAATACAATTTAGATATCAGGGCTAATATTCAATTCTTCCAAACCTTATGC
CTAGACAAAACGCCTTGGGTATCCATAAAAAGCCACCCTTTCTCCTTAGCATCTTAA
Found at i:11575722 original size:66 final size:66
Alignment explanation
Indices: 11575603--11575746 Score: 225
Period size: 66 Copynumber: 2.2 Consensus size: 66
11575593 ATCCATAAAA
* * *
11575603 AGCCACCCTTTCTCCTTAGCATCTTTCCCTAAACTTCTTAGCTATCGCATAAGATTACTTTCTCT
1 AGCCATCC-TTCTCCTTAACATCTTTCCCTAAACTTCTTAGCTATCACATAAGATTACTTTCTCT
11575668 TT
65 TT
* * *
11575670 AGTCATCCTTCTCGTTAACATCTTTCCCTAAACTTCTTAGCTATCACCTAAGATTACTTTCTCTT
1 AGCCATCCTTCTCCTTAACATCTTTCCCTAAACTTCTTAGCTATCACATAAGATTACTTTCTCTT
11575735 T
66 T
11575736 AGCCATCCTTC
1 AGCCATCCTTC
11575747 CACTAATGTG
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
66 64 0.91
67 6 0.09
ACGTcount: A:0.22, C:0.31, G:0.07, T:0.40
Consensus pattern (66 bp):
AGCCATCCTTCTCCTTAACATCTTTCCCTAAACTTCTTAGCTATCACATAAGATTACTTTCTCTT
T
Found at i:11580586 original size:66 final size:61
Alignment explanation
Indices: 11580504--11580742 Score: 241
Period size: 66 Copynumber: 3.8 Consensus size: 61
11580494 AATGCCTTTA
*
11580504 TTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATCCTTTTTTTTATTGAAATTTTATT
1 TTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATAT-CTTTTTTTT-TT--AATTTTA-A
11580569 T
61 T
* * *
11580570 TTCAAGAAAAACTGATACTTTCAACTTTTCCTC-AAAA-ATGTTTTTTTTTTAATTTTAAT
1 TTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATCTTTTTTTTTTAATTTTAAT
* * * * *
11580629 TTCAAGGAAAATTGATAGTTTCAACTTTTCCTTAAAAATATGTTTTTAAAATTTTTATTTTTTAT
1 TTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATCTTTTT----TTTTTA-ATTTTAA
11580694 T
61 T
* * * * *
11580695 TTTAAGGAAAATTAATACTTTTAACTTTTCTTTAAAAATAT-TTTTTTT
1 TTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATCTTTTTTT
11580743 GAAATTTTAT
Statistics
Matches: 151, Mismatches: 15, Indels: 19
0.82 0.08 0.10
Matches are distributed among these distances:
59 30 0.20
60 11 0.07
61 10 0.07
62 2 0.01
63 8 0.05
64 2 0.01
65 15 0.10
66 73 0.48
ACGTcount: A:0.33, C:0.10, G:0.06, T:0.50
Consensus pattern (61 bp):
TTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATCTTTTTTTTTTAATTTTAAT
Found at i:11580713 original size:125 final size:125
Alignment explanation
Indices: 11580504--11580765 Score: 309
Period size: 125 Copynumber: 2.1 Consensus size: 125
11580494 AATGCCTTTA
11580504 TTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATCCTTTTTTTTATTGAAATTTTATT
1 TTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATCCTTTTTTTTATTGAAATTTTATT
* * **
11580569 TTTCAAGAAAAACTGATACTTTCAACTTTTCCTCAAAAATGTTTTTTTTTTAATTTTAAT
66 TTTCAAGAAAAACTAATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAATTTTAAT
* * * **
11580629 TTCAAGGAAAATTGATAGTTTCAACTTTTCCTTAAAAATAT-GTTTTTAAAATTT-TT-ATTTTT
1 TTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATCCTTTTT----TTTATTGAAATTT
* * * * * *
11580691 TATTTTT-AAGGAAAATTAATACTTTTAACTTTTCTTTAAAAATATTTTTTTTGAAATTTTATT
62 TATTTTTCAAGAAAAACTAATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAATTTTAAT
*
11580754 TTTAA-GAAAATT
1 TTCAAGGAAAATT
11580766 ATTGAAAAAT
Statistics
Matches: 117, Mismatches: 16, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
124 12 0.10
125 89 0.76
126 11 0.09
127 2 0.02
128 3 0.03
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.50
Consensus pattern (125 bp):
TTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATCCTTTTTTTTATTGAAATTTTATT
TTTCAAGAAAAACTAATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAATTTTAAT
Found at i:11580829 original size:12 final size:12
Alignment explanation
Indices: 11580804--11580855 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
11580794 TTTAATCAAT
11580804 AAATAAATATATAA
1 AAAT-AATA-ATAA
11580818 AAATAATAATAA
1 AAATAATAATAA
*
11580830 TAATAATAATAA
1 AAATAATAATAA
*
11580842 ATAT-ATAAATAA
1 AAATAAT-AATAA
11580854 AA
1 AA
11580856 TGAAAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 2 0.06
12 23 0.70
13 4 0.12
14 4 0.12
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AAATAATAATAA
Found at i:11582126 original size:45 final size:45
Alignment explanation
Indices: 11582022--11582153 Score: 160
Period size: 45 Copynumber: 3.0 Consensus size: 45
11582012 ATTTTTTTAT
* *
11582022 TAAACAAAGCTTCTCTAAATAGAGACTCAACAA-TTTTC-AAAAA
1 TAAACAAAGCTTCTCTAAACAGAGACTCAACAACTTTACAAAAAA
* * *
11582065 TAAACAAAACTCCTCTAAACAGAGACTCAACAACTTTGCAAAAAA
1 TAAACAAAGCTTCTCTAAACAGAGACTCAACAACTTTACAAAAAA
* * * **
11582110 TAAATAAAGCTTCTCTAAACAAAGGCTCAATGACTTTACAAAAA
1 TAAACAAAGCTTCTCTAAACAGAGACTCAACAACTTTACAAAAA
11582154 CTGAAAGGCT
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
43 30 0.40
44 4 0.05
45 41 0.55
ACGTcount: A:0.49, C:0.20, G:0.08, T:0.23
Consensus pattern (45 bp):
TAAACAAAGCTTCTCTAAACAGAGACTCAACAACTTTACAAAAAA
Found at i:11582398 original size:22 final size:21
Alignment explanation
Indices: 11582337--11582398 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
11582327 GCAAGACTCA
* *
11582337 CATCCAACATTTAAATATTCT
1 CATCCAAAATTTAAAGATTCT
* * **
11582358 CATTCAAATTTTAGGGATTCT
1 CATCCAAAATTTAAAGATTCT
11582379 CATCCAAAAGTTTAAAGATT
1 CATCCAAAA-TTTAAAGATT
11582399 TTCGTTTGAA
Statistics
Matches: 30, Mismatches: 10, Indels: 1
0.73 0.24 0.02
Matches are distributed among these distances:
21 22 0.73
22 8 0.27
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (21 bp):
CATCCAAAATTTAAAGATTCT
Found at i:11582685 original size:25 final size:25
Alignment explanation
Indices: 11582601--11582898 Score: 261
Period size: 25 Copynumber: 12.6 Consensus size: 25
11582591 TTTACAACTC
* *
11582601 AAAGATTCTTATTTGAAAATATCTT
1 AAAGATTCTCATTTGAAAATGTCTT
* * *
11582626 AAAGGTTTTCATTT---AA-GACTT
1 AAAGATTCTCATTTGAAAATGTCTT
*
11582647 AAA-ATTCCTAATTTGAAAATGTCTT
1 AAAGATT-CTCATTTGAAAATGTCTT
* *
11582672 AAAGATTATCATTTGGAAATGTCTT
1 AAAGATTCTCATTTGAAAATGTCTT
*
11582697 AAAGATTCTTATTT-AAAA-GTC--
1 AAAGATTCTCATTTGAAAATGTCTT
*
11582718 AAATATTCTCATTTGAAAATGTCTT
1 AAAGATTCTCATTTGAAAATGTCTT
* *
11582743 AAAGATTCTCATTT---AA-GACTC
1 AAAGATTCTCATTTGAAAATGTCTT
*
11582764 AAATATTCTCATTTGAAAATGTCTT
1 AAAGATTCTCATTTGAAAATGTCTT
* * * *
11582789 AAAAATTTTCATTTGGAAACGTCTT
1 AAAGATTCTCATTTGAAAATGTCTT
*
11582814 AAAAATTCTCATTTGAAAATGTCTT
1 AAAGATTCTCATTTGAAAATGTCTT
* * *
11582839 AAAGATTATCATTT---AA-GACTC
1 AAAGATTCTCATTTGAAAATGTCTT
* *
11582860 AAAGATTCTCATTTGAGAACGTCTT
1 AAAGATTCTCATTTGAAAATGTCTT
11582885 AAAGATTCTCATTT
1 AAAGATTCTCATTT
11582899 AAGACTCAAA
Statistics
Matches: 218, Mismatches: 37, Indels: 36
0.75 0.13 0.12
Matches are distributed among these distances:
20 2 0.01
21 55 0.25
22 10 0.05
23 6 0.03
24 9 0.04
25 133 0.61
26 3 0.01
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (25 bp):
AAAGATTCTCATTTGAAAATGTCTT
Found at i:11582730 original size:46 final size:46
Alignment explanation
Indices: 11582672--11582925 Score: 330
Period size: 46 Copynumber: 5.4 Consensus size: 46
11582662 AAAATGTCTT
* * * * *
11582672 AAAGATTATCATTTGGAAATGTCTTAAAGATTCTTATTTAAAAGTC
1 AAAGATTCTCATTTGAAAATGTCTTAAAGATTCTCATTTAAGACTC
*
11582718 AAATATTCTCATTTGAAAATGTCTTAAAGATTCTCATTTAAGACTC
1 AAAGATTCTCATTTGAAAATGTCTTAAAGATTCTCATTTAAGACTC
* * *
11582764 AAATATTCTCATTTGAAAATGTCTTAAAAATTTTCATTTGGAA-ACGTC
1 AAAGATTCTCATTTGAAAATGTCTTAAAGATTCTCATTT--AAGAC-TC
* *
11582812 TTAAAAATTCTCATTTGAAAATGTCTTAAAGATTATCATTTAAGACTC
1 --AAAGATTCTCATTTGAAAATGTCTTAAAGATTCTCATTTAAGACTC
* *
11582860 AAAGATTCTCATTTGAGAACGTCTTAAAGATTCTCATTTAAGACTC
1 AAAGATTCTCATTTGAAAATGTCTTAAAGATTCTCATTTAAGACTC
*
11582906 AAAGATTTTCATTTGAAAAT
1 AAAGATTCTCATTTGAAAAT
11582926 TTAGGACTTC
Statistics
Matches: 184, Mismatches: 18, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
46 136 0.74
47 2 0.01
48 8 0.04
49 2 0.01
50 36 0.20
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.39
Consensus pattern (46 bp):
AAAGATTCTCATTTGAAAATGTCTTAAAGATTCTCATTTAAGACTC
Found at i:11582732 original size:71 final size:70
Alignment explanation
Indices: 11582601--11582898 Score: 280
Period size: 71 Copynumber: 4.2 Consensus size: 70
11582591 TTTACAACTC
* * * * * * * *
11582601 AAAGATTCTTATTTGAAAATATCTTAAAGGTTTTCATTTAAGACT-TAAAATTCCTAATTTGAAA
1 AAAGATTCTCATTTG-AAATGTCTTAAAGATTCTCATTTAAAAGTCAAAAATT-CTCATTTGAAA
*
11582665 ATGTCTT
64 ACGTCTT
* * *
11582672 AAAGATTATCATTTGGAAATGTCTTAAAGATTCTTATTTAAAAGTCAAATATTCTCATTTGAAAA
1 AAAGATTCTCATTT-GAAATGTCTTAAAGATTCTCATTTAAAAGTCAAAAATTCTCATTTGAAAA
*
11582737 TGTCTT
65 CGTCTT
* * * * *
11582743 AAAGATTCTCATTT--AA-GACTCAAATATTCTCATTTGAAAATGTCTTAAAAATTTTCATTTGG
1 AAAGATTCTCATTTGAAATGTCTTAAAGATTCTCATTT-AAAA-GTC--AAAAATTCTCATTTGA
11582805 AAACGTCTT
62 AAACGTCTT
* * * * * *
11582814 AAAAATTCTCATTTGAAAATGTCTTAAAGATTATCATTTAAGACTCAAAGATTCTCATTTGAGAA
1 AAAGATTCTCATTTG-AAATGTCTTAAAGATTCTCATTTAAAAGTCAAAAATTCTCATTTGAAAA
11582879 CGTCTT
65 CGTCTT
11582885 AAAGATTCTCATTT
1 AAAGATTCTCATTT
11582899 AAGACTCAAA
Statistics
Matches: 185, Mismatches: 32, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
67 15 0.08
68 6 0.03
69 3 0.02
71 133 0.72
72 6 0.03
73 2 0.01
74 5 0.03
75 15 0.08
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (70 bp):
AAAGATTCTCATTTGAAATGTCTTAAAGATTCTCATTTAAAAGTCAAAAATTCTCATTTGAAAAC
GTCTT
Found at i:11582805 original size:117 final size:118
Alignment explanation
Indices: 11582599--11582852 Score: 341
Period size: 117 Copynumber: 2.1 Consensus size: 118
11582589 GTTTTACAAC
* * * *
11582599 TCAAAGATTCTTATTTGAAAATATCTTAAAGGTTTTCATTTAAGACTTAAAATTCCTAATTTGAA
1 TCAAAGATTCTCATTTGAAAATATCTTAAAGATTCTCATTTAAGACTCAAAATTCCTAATTTGAA
* * * *
11582664 AATGTCTTAAAGATTATCATTTGGAAATGTCTTAAAGATTCTTATTT-AAAAG
66 AATGTCTTAAAAATTATCATTTGGAAACGTCTTAAAAATTCTCATTTGAAAAG
* * *
11582716 TCAAATATTCTCATTTGAAAATGTCTTAAAGATTCTCATTTAAGACTCAAATATT-CTCATTTGA
1 TCAAAGATTCTCATTTGAAAATATCTTAAAGATTCTCATTTAAGACTCAAA-ATTCCTAATTTGA
*
11582780 AAATGTCTTAAAAATTTTCATTTGGAAACGTCTTAAAAATTCTCATTTGAAAATG
65 AAATGTCTTAAAAATTATCATTTGGAAACGTCTTAAAAATTCTCATTTGAAAA-G
*
11582835 TCTTAAAGATTATCATTT
1 TC--AAAGATTCTCATTT
11582853 AAGACTCAAA
Statistics
Matches: 118, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
117 96 0.81
118 7 0.06
119 3 0.03
121 12 0.10
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (118 bp):
TCAAAGATTCTCATTTGAAAATATCTTAAAGATTCTCATTTAAGACTCAAAATTCCTAATTTGAA
AATGTCTTAAAAATTATCATTTGGAAACGTCTTAAAAATTCTCATTTGAAAAG
Found at i:11582830 original size:96 final size:92
Alignment explanation
Indices: 11582672--11582925 Score: 330
Period size: 96 Copynumber: 2.7 Consensus size: 92
11582662 AAAATGTCTT
* * *
11582672 AAAGATTATCATTTGGAAATGTCTTAAAGATTCTT-ATTTAAAAGTCAAATATTCTCATTTGAAA
1 AAAGATTCTCATTTGAAAATGTCTTAAAGATT-TTCATTTAAAAGTCAAAAATTCTCATTTGAAA
*
11582736 ATGTCTTAAAGATTCTCATTTAAGACTC
65 ATGTCTTAAAGATTATCATTTAAGACTC
* * *
11582764 AAATATTCTCATTTGAAAATGTCTTAAAAATTTTCATTTGGAAACGTCTTAAAAATTCTCATTTG
1 AAAGATTCTCATTTGAAAATGTCTTAAAGATTTTCATTT--AAAAGTC--AAAAATTCTCATTTG
11582829 AAAATGTCTTAAAGATTATCATTTAAGACTC
62 AAAATGTCTTAAAGATTATCATTTAAGACTC
* * * * * * *
11582860 AAAGATTCTCATTTGAGAACGTCTTAAAGATTCTCATTTAAGACTCAAAGATTTTCATTTGAAAA
1 AAAGATTCTCATTTGAAAATGTCTTAAAGATTTTCATTTAAAAGTCAAAAATTCTCATTTGAAAA
11582925 T
66 T
11582926 TTAGGACTTC
Statistics
Matches: 140, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
91 2 0.01
92 50 0.36
94 10 0.07
96 78 0.56
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.39
Consensus pattern (92 bp):
AAAGATTCTCATTTGAAAATGTCTTAAAGATTTTCATTTAAAAGTCAAAAATTCTCATTTGAAAA
TGTCTTAAAGATTATCATTTAAGACTC
Found at i:11582862 original size:142 final size:142
Alignment explanation
Indices: 11582657--11582925 Score: 412
Period size: 142 Copynumber: 1.9 Consensus size: 142
11582647 AAAATTCCTA
* * * * * * *
11582657 ATTTGAAAATGTCTTAAAGATTATCATTTGGAAATGTCTTAAAGATTCTTATTTAAAAGTCAAAT
1 ATTTGAAAACGTCTTAAAAATTATCATTTGAAAATGTCTTAAAGATTATCATTTAAAACTCAAAG
* *
11582722 ATTCTCATTTGAAAATGTCTTAAAGATTCTCATTTAAGACTCAAATATTCTCATTTGAAAATGTC
66 ATTCTCATTTGAAAACGTCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATGTC
11582787 TTAAAAATTTTC
131 TTAAAAATTTTC
* * *
11582799 ATTTGGAAACGTCTTAAAAATTCTCATTTGAAAATGTCTTAAAGATTATCATTTAAGACTCAAAG
1 ATTTGAAAACGTCTTAAAAATTATCATTTGAAAATGTCTTAAAGATTATCATTTAAAACTCAAAG
* *
11582864 ATTCTCATTTGAGAACGTCTTAAAGATTCTCATTTAAGACTCAAAGATTTTCATTTGAAAAT
66 ATTCTCATTTGAAAACGTCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAAT
11582926 TTAGGACTTC
Statistics
Matches: 113, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
142 113 1.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (142 bp):
ATTTGAAAACGTCTTAAAAATTATCATTTGAAAATGTCTTAAAGATTATCATTTAAAACTCAAAG
ATTCTCATTTGAAAACGTCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATGTC
TTAAAAATTTTC
Found at i:11584212 original size:1 final size:1
Alignment explanation
Indices: 11584208--11584269 Score: 61
Period size: 1 Copynumber: 62.0 Consensus size: 1
11584198 CCATTTTTCA
* * * ** * *
11584208 TTTTTTTTTTATTTTTTTCTTTCTTTTTTTTTTTTTTTTTTTTCCTTTTTTTCTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
11584270 CATCTTTTCC
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.02, C:0.10, G:0.00, T:0.89
Consensus pattern (1 bp):
T
Found at i:11584214 original size:10 final size:9
Alignment explanation
Indices: 11584201--11584270 Score: 72
Period size: 10 Copynumber: 7.7 Consensus size: 9
11584191 TTTTCTCCCA
11584201 TTTTTCATTT
1 TTTTTC-TTT
*
11584211 TTTTTTTATT
1 TTTTTCT-TT
11584221 TTTTTCTTT
1 TTTTTCTTT
*
11584230 CTTTT-TTT
1 TTTTTCTTT
11584238 TTTTT-TTT
1 TTTTTCTTT
*
11584246 TTTTTCCTT
1 TTTTTCTTT
11584255 TTTTTCTTCT
1 TTTTTCTT-T
11584265 TTTTTC
1 TTTTTC
11584271 ATCTTTTCCA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
8 15 0.29
9 16 0.31
10 20 0.39
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:11584224 original size:20 final size:19
Alignment explanation
Indices: 11584201--11584266 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
11584191 TTTTCTCCCA
11584201 TTTTTCATTT-TTTTTTTATT
1 TTTTTC-TTTCTTTTTTT-TT
11584221 TTTTTCTTTCTTTTTTTTT
1 TTTTTCTTTCTTTTTTTTT
*
11584240 TTTTT-TTT-TTTCCTTTTT
1 TTTTTCTTTCTTT-TTTTTT
*
11584258 TTCTTCTTT
1 TTTTTCTTT
11584267 TTTCATCTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
17 3 0.07
18 12 0.29
19 13 0.32
20 13 0.32
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (19 bp):
TTTTTCTTTCTTTTTTTTT
Found at i:11584234 original size:22 final size:22
Alignment explanation
Indices: 11584209--11584270 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
11584199 CATTTTTCAT
11584209 TTTTTTTTTATTTTTTTCTTT-C
1 TTTTTTTTT-TTTTTTTCTTTCC
*
11584231 TTTTTTTTTTTTTTTTTTTTCC
1 TTTTTTTTTTTTTTTTCTTTCC
*
11584253 TTTTTTTCTTCTTTTTTC
1 TTTTTTT-TTTTTTTTTC
11584271 ATCTTTTCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.29
22 17 0.49
23 8 0.23
ACGTcount: A:0.02, C:0.11, G:0.00, T:0.87
Consensus pattern (22 bp):
TTTTTTTTTTTTTTTTCTTTCC
Found at i:11588262 original size:66 final size:65
Alignment explanation
Indices: 11588184--11588307 Score: 203
Period size: 66 Copynumber: 1.9 Consensus size: 65
11588174 GCCTTTATTA
11588184 AAGGAAAATTGATACTTTCAACTTTTCCTTAAAAATATGTTTTTAAAATTTTTATTTTTTATTTT
1 AAGGAAAATTGATACTTTCAACTTTTCCTTAAAAATATGTTTTTAAAA-TTTTATTTTTTATTTT
11588249 C
65 C
* * * *
11588250 AAGGAAAATTGATACTTTCAACTTTTCTTTAAAAATTTTTTTTTGAAATTTTATTTTT
1 AAGGAAAATTGATACTTTCAACTTTTCCTTAAAAATATGTTTTTAAAATTTTATTTTT
11588308 AAGAAAATTA
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
65 10 0.19
66 44 0.81
ACGTcount: A:0.33, C:0.08, G:0.06, T:0.52
Consensus pattern (65 bp):
AAGGAAAATTGATACTTTCAACTTTTCCTTAAAAATATGTTTTTAAAATTTTATTTTTTATTTTC
Found at i:11588378 original size:3 final size:3
Alignment explanation
Indices: 11588370--11588404 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
11588360 AATAGACATA
* *
11588370 AAT AAT AAT ATT AAT AAT AAT AAT AAT AAC AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
11588405 ATATATAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:11588415 original size:18 final size:17
Alignment explanation
Indices: 11588356--11588416 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 17
11588346 TTAATCAATA
11588356 AATAAATAGAC-ATAAAT
1 AATAAATA-ACAATAAAT
*
11588373 AATAATATTAATAAT-AAT
1 AATAA-A-TAACAATAAAT
11588391 AAT-AATAACAATAAAT
1 AATAAATAACAATAAAT
11588407 ATATAAATAA
1 A-ATAAATAA
11588417 AATGAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
15 6 0.17
16 5 0.14
17 8 0.22
18 13 0.36
19 4 0.11
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.30
Consensus pattern (17 bp):
AATAAATAACAATAAAT
Found at i:11589312 original size:4 final size:4
Alignment explanation
Indices: 11589303--11589356 Score: 50
Period size: 4 Copynumber: 15.0 Consensus size: 4
11589293 TAATTAGCCA
11589303 AAAT AAAT AAAT AAA- ACAAT -AAT -AAT -AAT -AAT -AAT -AAT AAAT
1 AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
11589345 AAAT AAAT AAAT
1 AAAT AAAT AAAT
11589357 GACCAATTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
3 19 0.40
4 28 0.60
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:11593705 original size:19 final size:20
Alignment explanation
Indices: 11593674--11593733 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 20
11593664 CCAAAGTACC
11593674 AAAAATGATAAAATAAATAAA
1 AAAAATG-TAAAATAAATAAA
*
11593695 AAAAATG-AAAATAGAA-ACA
1 AAAAATGTAAAATA-AATAAA
11593714 AAAAATGTAACAA-AAATAAA
1 AAAAATGTAA-AATAAATAAA
11593734 TTTATTTACA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
19 17 0.52
20 7 0.21
21 9 0.27
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (20 bp):
AAAAATGTAAAATAAATAAA
Found at i:11594676 original size:30 final size:29
Alignment explanation
Indices: 11594610--11594677 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
11594600 TATAGTATAG
11594610 TATATTATATTATATTGTATATATCATTA
1 TATATTATATTATATTGTATATATCATTA
* *
11594639 TCATATTATATTATGTTATTATACTATCATTA
1 T-ATATTATATTATATT-GTATA-TATCATTA
11594671 T-TATTAT
1 TATATTAT
11594678 TTTTTTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 1 0.03
30 20 0.59
31 4 0.12
32 9 0.26
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (29 bp):
TATATTATATTATATTGTATATATCATTA
Found at i:11595524 original size:11 final size:11
Alignment explanation
Indices: 11595508--11595623 Score: 78
Period size: 11 Copynumber: 9.8 Consensus size: 11
11595498 GTTTTCTCTT
11595508 TTTTATTTTTA
1 TTTTATTTTTA
11595519 TTTTATTTTTGA
1 TTTTATTTTT-A
*
11595531 TTTCATTTTT-
1 TTTTATTTTTA
*
11595541 TTTCATATATTTA
1 TTT--TATTTTTA
11595554 TCTTATATTTTTA
1 T-TT-TATTTTTA
11595567 TTTT-TATTTTA
1 TTTTAT-TTTTA
11595578 TTTTTAGTTTTT-
1 -TTTTA-TTTTTA
11595590 TTTTATTTTACTA
1 TTTTATTTT--TA
11595603 GTTTTATTATTTA
1 -TTTTATT-TTTA
11595616 -TTTATTTT
1 TTTTATTTT
11595624 CCTTAAGTAA
Statistics
Matches: 87, Mismatches: 4, Indels: 29
0.73 0.03 0.24
Matches are distributed among these distances:
10 10 0.11
11 27 0.31
12 22 0.25
13 16 0.18
14 10 0.11
15 2 0.02
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.75
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:11600323 original size:12 final size:11
Alignment explanation
Indices: 11600281--11600311 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
11600271 AGAGGTATGC
11600281 AAAG-AAAAAA
1 AAAGTAAAAAA
11600291 AAAGTAAAAAA
1 AAAGTAAAAAA
11600302 AAAGTAAAAA
1 AAAGTAAAAA
11600312 GTAAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.06
Consensus pattern (11 bp):
AAAGTAAAAAA
Found at i:11600331 original size:11 final size:10
Alignment explanation
Indices: 11600281--11600332 Score: 52
Period size: 11 Copynumber: 4.9 Consensus size: 10
11600271 AGAGGTATGC
11600281 AAAGAAAAAA
1 AAAGAAAAAA
11600291 AAAGTAAAAAA
1 AAAG-AAAAAA
11600302 AAAGTAAAAAGTA
1 AAAG-AAAAA--A
11600315 AAA-AAAAAA
1 AAAGAAAAAA
*
11600324 AGAGAAAAA
1 AAAGAAAAA
11600333 TGAATACTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
9 3 0.08
10 9 0.24
11 21 0.57
13 4 0.11
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.06
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:11601502 original size:240 final size:240
Alignment explanation
Indices: 11601127--11601573 Score: 542
Period size: 240 Copynumber: 1.9 Consensus size: 240
11601117 TCAACTCTAC
* *
11601127 CTTGGTCACTTCTTTTCCTGACTCGTGATTTCATCCCAGTTATTCATTTTTGATCTTGACTTGGT
1 CTTGGTCACTTCATTTCCTGACTCGTGATTTCATCCCAGTTATTCATTTTTGATCTCGACTTGGT
* * ** *
11601192 TCTTGTTACTTTATCTTTTGGACTCATAATTTTATTTCGATCATTCGATCCCGACTTAGTCCAAA
66 TCTTGTTACTTTATCTTTTAGACTCACAATTTTATCCCGATCATTCGATCCCGACTCAGTCCAAA
* * * *** *
11601257 TCATTTTTCAGACTCACAGTTTCATCTTAGTCATCCGATCTTGGCTTA-TTTCAGATCATTTTCT
131 TCATTTTTCAGACTCACAATTTCATCCTAGTCATCCAATCTCAACTTAGTCT-AGATCATTTTCT
11601321 TGACTTATGATTTTATCTCATTTATTCATTTTGACATCGACTCAGT
195 TGACTTATGATTTTATCTCATTTATTCATTTTGACATCGACTCAGT
* * ** * *
11601367 CTTGGTCTCTTCATTTCTTGACTCGTGATTTTGTCCTAGTTATTCATTTTTTATCTCGACTTGG-
1 CTTGGTCACTTCATTTCCTGACTCGTGATTTCATCCCAGTTATTCATTTTTGATCTCGACTTGGT
** ** * *
11601431 TCTTGGTTGTTTTATCTTTTAGACTCACAATTTTATCCCTTTCA-TCTGAT-CTGAACTCAGTCT
66 TCTT-GTTACTTTATCTTTTAGACTCACAATTTTATCCCGATCATTC-GATCCCG-ACTCAGTCC
* * * * * *
11601494 AGATCATTTTTTAGACTTACAATTTCATCCTATTTATCCAATCTCAATTTAGTCTAGATCATTTT
128 AAATCATTTTTCAGACTCACAATTTCATCCTAGTCATCCAATCTCAACTTAGTCTAGATCATTTT
11601559 CTTGACTTATGATTT
193 CTTGACTTATGATTT
11601574 CATCCTGGTC
Statistics
Matches: 171, Mismatches: 32, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
239 8 0.05
240 161 0.94
241 2 0.01
ACGTcount: A:0.20, C:0.21, G:0.12, T:0.47
Consensus pattern (240 bp):
CTTGGTCACTTCATTTCCTGACTCGTGATTTCATCCCAGTTATTCATTTTTGATCTCGACTTGGT
TCTTGTTACTTTATCTTTTAGACTCACAATTTTATCCCGATCATTCGATCCCGACTCAGTCCAAA
TCATTTTTCAGACTCACAATTTCATCCTAGTCATCCAATCTCAACTTAGTCTAGATCATTTTCTT
GACTTATGATTTTATCTCATTTATTCATTTTGACATCGACTCAGT
Found at i:11602035 original size:5 final size:5
Alignment explanation
Indices: 11602011--11602068 Score: 55
Period size: 5 Copynumber: 11.6 Consensus size: 5
11602001 GTTTTATTGC
* * * *
11602011 TATAG TATAG TATAT TATAT TATAT TGTA- TATAT TATTAT CATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TA-TAT TATAT TATAT
*
11602061 TATGT TAT
1 TATAT TAT
11602069 TATACTCTCA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
4 3 0.07
5 38 0.84
6 4 0.09
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (5 bp):
TATAT
Found at i:11602486 original size:20 final size:20
Alignment explanation
Indices: 11602463--11602504 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
11602453 TGGGTTGGGT
*
11602463 TTGAATCTTCTAGGTCTAGA
1 TTGAAGCTTCTAGGTCTAGA
*
11602483 TTGAAGCTTCTAGGTTTAGA
1 TTGAAGCTTCTAGGTCTAGA
11602503 TT
1 TT
11602505 TAAATTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.12, G:0.21, T:0.43
Consensus pattern (20 bp):
TTGAAGCTTCTAGGTCTAGA
Found at i:11602980 original size:15 final size:16
Alignment explanation
Indices: 11602960--11602999 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
11602950 TTGATTTTTA
11602960 TTTTATTTT-TAGTTT
1 TTTTATTTTATAGTTT
11602975 TTTTATTTTACTAGTTT
1 TTTTATTTTA-TAGTTT
*
11602992 TATTATTT
1 TTTTATTT
11603000 ATTTATTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
17 13 0.59
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.75
Consensus pattern (16 bp):
TTTTATTTTATAGTTT
Found at i:11605064 original size:13 final size:13
Alignment explanation
Indices: 11605046--11605093 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
11605036 TAAAAGTATT
11605046 TAAAATAAATAAA
1 TAAAATAAATAAA
**
11605059 TAAAATAGGTAAA
1 TAAAATAAATAAA
* *
11605072 TAAAATAAACATA
1 TAAAATAAATAAA
11605085 TAAAATAAA
1 TAAAATAAA
11605094 AGTAAAAACA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (13 bp):
TAAAATAAATAAA
Found at i:11606417 original size:21 final size:21
Alignment explanation
Indices: 11606368--11606418 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
11606358 ATATATATAT
11606368 ATATTTAGAATTTATGTAAAAA
1 ATATTT-GAATTTATGTAAAAA
*
11606390 AGT-TTTGACATTTAT-TACAAA
1 A-TATTTGA-ATTTATGTAAAAA
11606411 ATATTTGA
1 ATATTTGA
11606419 GTTTTATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 1 0.04
21 13 0.52
22 10 0.40
23 1 0.04
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (21 bp):
ATATTTGAATTTATGTAAAAA
Found at i:11606774 original size:11 final size:11
Alignment explanation
Indices: 11606758--11606794 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
11606748 TTATATTAAA
11606758 AATTATTTTTT
1 AATTATTTTTT
11606769 AATTATTTTTT
1 AATTATTTTTT
*
11606780 --TAATTTTTT
1 AATTATTTTTT
11606789 AATTAT
1 AATTAT
11606795 ATGTAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 8 0.36
11 14 0.64
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
AATTATTTTTT
Found at i:11606829 original size:18 final size:20
Alignment explanation
Indices: 11606803--11606854 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 20
11606793 ATATGTAATT
11606803 ATATATTTATA-TTTAAAAA
1 ATATATTTATATTTTAAAAA
11606822 ATAT-TTTATATTTTAAAAAA
1 ATATATTTATATTTT-AAAAA
11606842 ATAATATTT-TATT
1 AT-ATATTTATATT
11606855 AATTTCAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 6 0.21
19 7 0.24
20 7 0.24
21 6 0.21
22 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATATATTTATATTTTAAAAA
Found at i:11606836 original size:19 final size:19
Alignment explanation
Indices: 11606803--11606854 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
11606793 ATATGTAATT
11606803 ATATATTTATATTTAAAAA
1 ATATATTTATATTTAAAAA
11606822 ATAT-TTTATATTTTAAAAAA
1 ATATATTTATA-TTT-AAAAA
11606842 ATAATATTT-TATT
1 AT-ATATTTATATT
11606855 AATTTCAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
18 6 0.21
19 7 0.24
20 9 0.31
21 4 0.14
22 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATATATTTATATTTAAAAA
Found at i:11609787 original size:20 final size:21
Alignment explanation
Indices: 11609764--11609803 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
11609754 ATAATTATTT
* *
11609764 TATATTTAAATTTAT-TTAAA
1 TATATTAAAAATTATATTAAA
11609784 TATATTAAAAATTATATTAA
1 TATATTAAAAATTATATTAA
11609804 GATAATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TATATTAAAAATTATATTAAA
Found at i:11617562 original size:2 final size:2
Alignment explanation
Indices: 11617557--11617584 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11617547 AGTGTGTGTC
11617557 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11617585 ATCATGCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11619209 original size:2 final size:2
Alignment explanation
Indices: 11619202--11619236 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
11619192 AGGGGCATTC
11619202 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11619237 AAGCTTTTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11620295 original size:2 final size:2
Alignment explanation
Indices: 11620251--11620277 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11620241 TTATTTAGGC
11620251 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
11620278 CATACACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11634019 original size:11 final size:11
Alignment explanation
Indices: 11634005--11634047 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
11633995 TGTTTACTGC
11634005 ATTTATTTTAA
1 ATTTATTTTAA
* *
11634016 ATTTGTTTCTAC
1 ATTTATTT-TAA
11634028 ATTTATTTTAA
1 ATTTATTTTAA
11634039 ATTTATTTT
1 ATTTATTTT
11634048 CTTTTTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (11 bp):
ATTTATTTTAA
Found at i:11634034 original size:23 final size:24
Alignment explanation
Indices: 11633992--11634042 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
11633982 TAAGTGTACT
*
11633992 ATTTGTTTACTGCATTTATTTTAA
1 ATTTGTTTACTACATTTATTTTAA
11634016 ATTTGTTT-CTACATTTATTTTAA
1 ATTTGTTTACTACATTTATTTTAA
11634039 ATTT
1 ATTT
11634043 ATTTTCTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 18 0.69
24 8 0.31
ACGTcount: A:0.25, C:0.08, G:0.06, T:0.61
Consensus pattern (24 bp):
ATTTGTTTACTACATTTATTTTAA
Found at i:11634917 original size:27 final size:27
Alignment explanation
Indices: 11634863--11634918 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
11634853 GAGATTGACT
* *
11634863 TTGGATATATTGAGACTAAGGCTGACA
1 TTGGATATAATGAGACTAAGGCTAACA
* * *
11634890 TTGGGTATAATGAGACTGAGGTTAACA
1 TTGGATATAATGAGACTAAGGCTAACA
11634917 TT
1 TT
11634919 AATCAAGAGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.32, C:0.09, G:0.27, T:0.32
Consensus pattern (27 bp):
TTGGATATAATGAGACTAAGGCTAACA
Found at i:11635977 original size:24 final size:24
Alignment explanation
Indices: 11635930--11636011 Score: 76
Period size: 24 Copynumber: 3.4 Consensus size: 24
11635920 GTCATATATG
* * * *
11635930 AATGACAAAAGTTGAATTAGTATA
1 AATGATAAAAATTAAATTTGTATA
**
11635954 AATGATAAATTTTAAAATTT-TATA
1 AATGATAAAAATT-AAATTTGTATA
* *
11635978 AATCAAAAAAATTAAATTTGTATA
1 AATGATAAAAATTAAATTTGTATA
11636002 AATGATAAAA
1 AATGATAAAA
11636012 TTTGGACTTG
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
23 6 0.13
24 35 0.78
25 4 0.09
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (24 bp):
AATGATAAAAATTAAATTTGTATA
Found at i:11636034 original size:48 final size:48
Alignment explanation
Indices: 11635930--11636065 Score: 121
Period size: 48 Copynumber: 2.8 Consensus size: 48
11635920 GTCATATATG
* * * * ** *
11635930 AATGACAAAAGTTGAATTAGTATAAATGATAAATTTTAAAATTTTATA
1 AATGAAAAAAATTGAATTTGTATAAATGATAAAATTTGGAATTGTATA
* * * *
11635978 AATCAAAAAAATTAAATTTGTATAAATGATAAAATTTGGACTTGTATT
1 AATGAAAAAAATTGAATTTGTATAAATGATAAAATTTGGAATTGTATA
** * *
11636026 AATGAAAAATTTTGAACTTGTATAAAT-AAAAATATTTGGA
1 AATGAAAAAAATTGAATTTGTATAAATGATAAA-ATTTGGA
11636066 GTTTTATACA
Statistics
Matches: 70, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
47 4 0.06
48 66 0.94
ACGTcount: A:0.49, C:0.03, G:0.11, T:0.37
Consensus pattern (48 bp):
AATGAAAAAAATTGAATTTGTATAAATGATAAAATTTGGAATTGTATA
Found at i:11636073 original size:24 final size:25
Alignment explanation
Indices: 11635995--11636065 Score: 94
Period size: 24 Copynumber: 3.0 Consensus size: 25
11635985 AAAATTAAAT
*
11635995 TTGTATAAATGATAAA-ATTTGGAC
1 TTGTATAAATGAAAAATATTTGGAC
* *
11636019 TTGTATTAATGAAAAAT-TTTGAAC
1 TTGTATAAATGAAAAATATTTGGAC
11636043 TTGTATAAAT-AAAAATATTTGGA
1 TTGTATAAATGAAAAATATTTGGA
11636066 GTTTTATACA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
23 6 0.15
24 34 0.85
ACGTcount: A:0.44, C:0.03, G:0.14, T:0.39
Consensus pattern (25 bp):
TTGTATAAATGAAAAATATTTGGAC
Found at i:11639130 original size:73 final size:73
Alignment explanation
Indices: 11639038--11639243 Score: 279
Period size: 72 Copynumber: 2.8 Consensus size: 73
11639028 GACAAGAACA
* *
11639038 ATATTCAAATATTATTATTTATATTGTTTTATAACATAAGAACAAAGGAGAAAATGATTTACAAT
1 ATATTCAAATACTATTATTTATATTGTTTCATAACATAAGAACAAAGGAGAAAATGATTTACAAT
*
11639103 AGTATAGT
66 ACTATAGT
** * ** * *
11639111 ATATTTGAATACTATTATTTACATAATTTCATAACATAAGAACAAAAGAG-AAATGTTTTACAAT
1 ATATTCAAATACTATTATTTATATTGTTTCATAACATAAGAACAAAGGAGAAAATGATTTACAAT
11639175 ACTATAGT
66 ACTATAGT
* * *
11639183 ATATTCAAATACTATTATTTATATTGTTTCGTAACATAAAAACAAAGGAGACAAATTATTT
1 ATATTCAAATACTATTATTTATATTGTTTCATAACATAAGAACAAAGGAGA-AAATGATTT
11639244 GTTATGTGAA
Statistics
Matches: 111, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
72 62 0.56
73 42 0.38
74 7 0.06
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.37
Consensus pattern (73 bp):
ATATTCAAATACTATTATTTATATTGTTTCATAACATAAGAACAAAGGAGAAAATGATTTACAAT
ACTATAGT
Found at i:11639807 original size:72 final size:72
Alignment explanation
Indices: 11639690--11639824 Score: 189
Period size: 72 Copynumber: 1.9 Consensus size: 72
11639680 AAACACTATG
* * *
11639690 TTTATTATCATAAAAACCTAGTGTTTGTTACAAACACAATGTTTATAAAACAACAATGTAGTGAT
1 TTTATTATCATAAAAACATAGTGTTTGTAACAAACACAATGTTTATAAAACAAAAATGTAGTGAT
11639755 TGCTGCA
66 TGCTGCA
* * * * * *
11639762 TTTATTGTCATAGAAACATTGTGTTTGTAACAAATACTATGTTTATATAACAAAAATGTAGTG
1 TTTATTATCATAAAAACATAGTGTTTGTAACAAACACAATGTTTATAAAACAAAAATGTAGTG
11639825 GTTGGGTCAA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 54 1.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (72 bp):
TTTATTATCATAAAAACATAGTGTTTGTAACAAACACAATGTTTATAAAACAAAAATGTAGTGAT
TGCTGCA
Found at i:11644443 original size:12 final size:12
Alignment explanation
Indices: 11644426--11644450 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11644416 TCTGGATTCA
11644426 TTTGGGTAACAT
1 TTTGGGTAACAT
11644438 TTTGGGTAACAT
1 TTTGGGTAACAT
11644450 T
1 T
11644451 CCATTAAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.44
Consensus pattern (12 bp):
TTTGGGTAACAT
Found at i:11653292 original size:2 final size:2
Alignment explanation
Indices: 11653285--11653322 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
11653275 TAGAAACTAC
*
11653285 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11653323 CGGCATCTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11655027 original size:6 final size:6
Alignment explanation
Indices: 11655016--11655040 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
11655006 TGGTTCCTAC
11655016 TTTATT TTTATT TTTATT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT T
11655041 CCATTATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Done.