Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, 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: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 70 of 147
Found at i:13298853 original size:14 final size:14
Alignment explanation
Indices: 13298834--13298867 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
13298824 AAAAATATAT
*
13298834 AATAATTGATAAAA
1 AATAATTAATAAAA
*
13298848 ATTAATTAATAAAA
1 AATAATTAATAAAA
13298862 AATAAT
1 AATAAT
13298868 AATTTAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (14 bp):
AATAATTAATAAAA
Found at i:13300489 original size:12 final size:11
Alignment explanation
Indices: 13300467--13300510 Score: 54
Period size: 12 Copynumber: 3.9 Consensus size: 11
13300457 GTGTGTAATA
*
13300467 AAAAAAAAAAC
1 AAAACAAAAAC
13300478 ACAAACAAAAAC
1 A-AAACAAAAAC
13300490 GAAAAC-AAAAC
1 -AAAACAAAAAC
13300501 AAAACAAAAA
1 AAAACAAAAA
13300511 AGACATTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
10 5 0.17
11 10 0.34
12 13 0.45
13 1 0.03
ACGTcount: A:0.82, C:0.16, G:0.02, T:0.00
Consensus pattern (11 bp):
AAAACAAAAAC
Found at i:13300510 original size:16 final size:17
Alignment explanation
Indices: 13300467--13300509 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
13300457 GTGTGTAATA
*
13300467 AAAAAAAAAACACAAAC
1 AAAAACAAAACACAAAC
13300484 AAAAACGAAAACA-AAAC
1 AAAAAC-AAAACACAAAC
13300501 -AAAACAAAA
1 AAAAACAAAA
13300510 AAGACATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 4 0.17
16 5 0.21
17 9 0.38
18 6 0.25
ACGTcount: A:0.81, C:0.16, G:0.02, T:0.00
Consensus pattern (17 bp):
AAAAACAAAACACAAAC
Found at i:13305044 original size:34 final size:34
Alignment explanation
Indices: 13305006--13305101 Score: 104
Period size: 35 Copynumber: 2.8 Consensus size: 34
13304996 TACATTAGCA
*
13305006 TTTTTGGAAAAGACATTTACATTTCATGTA-CATC
1 TTTTTAGAAAAGACATTTACATTTCATG-AGCATC
* * *
13305040 TTTTTAAGAAAAGATATTTTCATCTCATGAGCATC
1 TTTTT-AGAAAAGACATTTACATTTCATGAGCATC
* * *
13305075 ATTTAAGAAAAGACATTTGCATTTCAT
1 TTTTTAGAAAAGACATTTACATTTCAT
13305102 TTGCCTCATA
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
34 25 0.49
35 26 0.51
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (34 bp):
TTTTTAGAAAAGACATTTACATTTCATGAGCATC
Found at i:13305051 original size:35 final size:34
Alignment explanation
Indices: 13305012--13305101 Score: 110
Period size: 34 Copynumber: 2.6 Consensus size: 34
13305002 AGCATTTTTG
*
13305012 GAAAAGACATTTACATTTCATGTA-CATCTTTTTAA
1 GAAAAGACATTTACATTTCATG-AGCATC-ATTTAA
* * *
13305047 GAAAAGATATTTTCATCTCATGAGCATCATTTAA
1 GAAAAGACATTTACATTTCATGAGCATCATTTAA
*
13305081 GAAAAGACATTTGCATTTCAT
1 GAAAAGACATTTACATTTCAT
13305102 TTGCCTCATA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
34 24 0.51
35 23 0.49
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (34 bp):
GAAAAGACATTTACATTTCATGAGCATCATTTAA
Found at i:13305506 original size:40 final size:40
Alignment explanation
Indices: 13305428--13305507 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
13305418 TTGAATTGCA
* *
13305428 TTTTCTCAATGGTTATAGCCAAAGTCATTTGCCTTTTCTC
1 TTTTCTCAATGGTGATAGCCAAAGTCATTTGCCATTTCTC
* * *
13305468 TTTTCTCAGTGGTGATATCCGAAGTCATTTAG-CATTTCTC
1 TTTTCTCAATGGTGATAGCCAAAGTCATTT-GCCATTTCTC
13305508 GGTGGTGATA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
40 33 0.97
41 1 0.03
ACGTcount: A:0.20, C:0.21, G:0.15, T:0.44
Consensus pattern (40 bp):
TTTTCTCAATGGTGATAGCCAAAGTCATTTGCCATTTCTC
Found at i:13305556 original size:75 final size:74
Alignment explanation
Indices: 13305468--13306028 Score: 533
Period size: 75 Copynumber: 7.5 Consensus size: 74
13305458 GCCTTTTCTC
*
13305468 TTTTCTCAGTGGTGATATCCGAAGTCATTTAGCATTTCTCGGTGGTGATATCTGAGTGTCAAAGT
1 TTTTCTCAGTGGCGATATCCGAAGTCATTT-GCATTTCTCGGTGGTGATATCTGAGTGTCAAAGT
13305533 TTGAATTGCA
65 TTGAATTGCA
* * ** *
13305543 TTTTCTCAGTGGTGATATCCGAAGTCATTTGCATCTTTTTAGTGGTGATAATC-GAGTGTTAAAG
1 TTTTCTCAGTGGCGATATCCGAAGTCATTTGCAT-TTCTCGGTGGTGAT-ATCTGAGTGTCAAAG
***
13305607 TTTGAATCATA
64 TTTGAATTGCA
* * * * *
13305618 TTTTTTCGGTGACGATATCCAAAGTCATTTGCATTTTTCTCGGTGGTGATATCCGAGTGTGC-AA
1 TTTTCTCAGTGGCGATATCCGAAGTCATTTGCA--TTTCTCGGTGGTGATATCTGAGTGT-CAAA
13305682 GTTTGAATTGCA
63 GTTTGAATTGCA
* * * * *
13305694 TTTT-T-TGTGACGATATTCGAAGTCATTTGCATCTTCTTGGTGGTGATAACTGAGTGTCAAAGT
1 TTTTCTCAGTGGCGATATCCGAAGTCATTTGCAT-TTCTCGGTGGTGATATCTGAGTGTCAAAGT
*
13305757 TTGAATTACA
65 TTGAATTGCA
** * * * * * *
13305767 TTTTCTTGGTGGCAATATCTGAAGCCATTTGCATTTTCTTGGTGGTGATATCTAAGTGTCCAAGT
1 TTTTCTCAGTGGCGATATCCGAAGTCATTTGCA-TTTCTCGGTGGTGATATCTGAGTGTCAAAGT
*
13305832 TTGAATTGTA
65 TTGAATTGCA
* * * * ** * *
13305842 TTTTCT-TGATGGCGATATCCAAAGTCATTTGCCTTTTTTCAATGGTAATATCCT-AGTGTCCAA
1 TTTTCTCAG-TGGCGATATCCGAAGTCATTTG-CATTTCTCGGTGGTGATAT-CTGAGTGTCAAA
*
13305905 GTTTAAATTGCA
63 GTTTGAATTGCA
* * * *
13305917 TTTTCTCTGTAGTGATATCCGAAGTCATTTGCATTTTTCTCGGTAGTGATATCCT-AGTGTCAAA
1 TTTTCTCAGTGGCGATATCCGAAGTCATTTGCA--TTTCTCGGTGGTGATAT-CTGAGTGTCAAA
*
13305981 GTTTGAATTACA
63 GTTTGAATTGCA
* **
13305993 TTTTCTCAGTGGTGATATATGAAGTCATTTGCATTT
1 TTTTCTCAGTGGCGATATCCGAAGTCATTTGCATTT
13306029 TTTTTTATGG
Statistics
Matches: 403, Mismatches: 66, Indels: 35
0.80 0.13 0.07
Matches are distributed among these distances:
72 2 0.00
73 38 0.09
74 33 0.08
75 226 0.56
76 103 0.26
77 1 0.00
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.41
Consensus pattern (74 bp):
TTTTCTCAGTGGCGATATCCGAAGTCATTTGCATTTCTCGGTGGTGATATCTGAGTGTCAAAGTT
TGAATTGCA
Found at i:13305741 original size:224 final size:223
Alignment explanation
Indices: 13305481--13306031 Score: 709
Period size: 224 Copynumber: 2.4 Consensus size: 223
13305471 TCTCAGTGGT
*
13305481 GATATCCGAAGTCATTTAGCATTTCTCGGTGGTGATATCTGAGTGTCAAAGTTTGAATTGCATTT
1 GATATCCGAAGTCATTT-GCATTTCTCGGTGGTGATATCTGAGTGTCAAAGTTTGAATTACATTT
* * *
13305546 TCTCAGTGGTGATATCCGAAGTCATTTGCATCTTTTTAGTGGTGATAATC-GAGTGTTAAAGTTT
65 TCTCAGTGGTGATATCTGAAGTCATTTGCAT-TTTTTAGTGGTGAT-ATCTAAGTGTCAAAGTTT
* ** *
13305610 GAATCATATTTT-TTCGGTGACGATATCCAAAGTCATTTGCATTTTTCTCGGTGGTGATATCCGA
128 GAATCATATTTTCTT-GATGACGATATCCAAAGTCATTTGCATTTTT-TCAATGGTAATATCCGA
* *
13305674 GTGTGCAAGTTTGAATTGCATTTT-T-TGT-GAC
191 GTGTCCAAGTTTAAATTGCATTTTCTCTGTAG-C
* * *
13305705 GATATTCGAAGTCATTTGCATCTTCTTGGTGGTGATAACTGAGTGTCAAAGTTTGAATTACATTT
1 GATATCCGAAGTCATTTGCAT-TTCTCGGTGGTGATATCTGAGTGTCAAAGTTTGAATTACATTT
** ** * * *
13305770 TCTTGGTGGCAATATCTGAAGCCATTTGCATTTTCTTGGTGGTGATATCTAAGTGTCCAAGTTTG
65 TCTCAGTGGTGATATCTGAAGTCATTTGCATTTT-TTAGTGGTGATATCTAAGTGTCAAAGTTTG
** * * *
13305835 AATTGTATTTTCTTGATGGCGATATCCAAAGTCATTTGCCTTTTTTCAATGGTAATATCCTAGTG
129 AATCATATTTTCTTGATGACGATATCCAAAGTCATTTGCATTTTTTCAATGGTAATATCCGAGTG
*
13305900 TCCAAGTTTAAATTGCATTTTCTCTGTAGT
194 TCCAAGTTTAAATTGCATTTTCTCTGTAGC
*
13305930 GATATCCGAAGTCATTTGCATTTTTCTCGGTAGTGATATCCT-AGTGTCAAAGTTTGAATTACAT
1 GATATCCGAAGTCATTTGCA--TTTCTCGGTGGTGATAT-CTGAGTGTCAAAGTTTGAATTACAT
*
13305994 TTTCTCAGTGGTGATATATGAAGTCATTTGCATTTTTT
63 TTTCTCAGTGGTGATATCTGAAGTCATTTGCATTTTTT
13306032 TTTATGGTGA
Statistics
Matches: 281, Mismatches: 36, Indels: 19
0.84 0.11 0.06
Matches are distributed among these distances:
223 45 0.16
224 141 0.50
225 26 0.09
226 66 0.23
227 3 0.01
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (223 bp):
GATATCCGAAGTCATTTGCATTTCTCGGTGGTGATATCTGAGTGTCAAAGTTTGAATTACATTTT
CTCAGTGGTGATATCTGAAGTCATTTGCATTTTTTAGTGGTGATATCTAAGTGTCAAAGTTTGAA
TCATATTTTCTTGATGACGATATCCAAAGTCATTTGCATTTTTTCAATGGTAATATCCGAGTGTC
CAAGTTTAAATTGCATTTTCTCTGTAGC
Found at i:13305935 original size:42 final size:41
Alignment explanation
Indices: 13305889--13306010 Score: 98
Period size: 42 Copynumber: 3.1 Consensus size: 41
13305879 TTCAATGGTA
*
13305889 ATATCCTAGTGTCCAAGTTTAAATTGCATTTTCTCTGTAGTG
1 ATATCCTAGTGT-CAAGTTTAAATTGCATTTTCTCAGTAGTG
* * *
13305931 ATATCC----G--AAG--TCATTTGCATTTTTCTCGGTAGTG
1 ATATCCTAGTGTCAAGTTTAAATTGCA-TTTTCTCAGTAGTG
* * *
13305965 ATATCCTAGTGTCAAAGTTTGAATTACATTTTCTCAGTGGTG
1 ATATCCTAGTGTC-AAGTTTAAATTGCATTTTCTCAGTAGTG
13306007 ATAT
1 ATAT
13306011 ATGAAGTCAT
Statistics
Matches: 62, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
33 7 0.11
34 19 0.31
35 3 0.05
38 2 0.03
41 3 0.05
42 22 0.35
43 6 0.10
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.42
Consensus pattern (41 bp):
ATATCCTAGTGTCAAGTTTAAATTGCATTTTCTCAGTAGTG
Found at i:13306542 original size:5 final size:5
Alignment explanation
Indices: 13306532--13306556 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
13306522 GAAGACACTC
13306532 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
13306557 TTCTTCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:13306574 original size:6 final size:6
Alignment explanation
Indices: 13306565--13306611 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
13306555 TTTTCTTCAT
* * *
13306565 TTTTTC TTTTTC TTTCTC ATTTTC TTTTTC TTTTGC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
13306612 TGGTAACTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (6 bp):
TTTTTC
Found at i:13309411 original size:102 final size:102
Alignment explanation
Indices: 13309232--13309430 Score: 274
Period size: 102 Copynumber: 2.0 Consensus size: 102
13309222 ATAAAAAAAC
* * * *
13309232 TTTTCAATGCAAATAAGTCAATTCGTAATAGAGTCAATACATGAGTCAATATATGAGTTGCACCA
1 TTTTCAATGCAAATAAGTCAAATCATAATAGAATCAATACATGAGTCAAAATATGAGTTGCACCA
* * * *
13309297 GACCTGTTTTCTAAAATGGCGTTGTTTCAACCTGTTA
66 GAACTGTATTCTAAAAAGGCATTGTTTCAACCTGTTA
* * * *
13309334 TTTTCAATGCAAATAAGTCAAATCATGATAGAATCAATGCATGGGTCAAAATATGAGTTGCATCA
1 TTTTCAATGCAAATAAGTCAAATCATAATAGAATCAATACATGAGTCAAAATATGAGTTGCACCA
13309399 -AACTGGTATTCTAAAAAGGCATTGTTTCAACC
66 GAACT-GTATTCTAAAAAGGCATTGTTTCAACC
13309431 AATTACAAAA
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
101 3 0.04
102 81 0.96
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (102 bp):
TTTTCAATGCAAATAAGTCAAATCATAATAGAATCAATACATGAGTCAAAATATGAGTTGCACCA
GAACTGTATTCTAAAAAGGCATTGTTTCAACCTGTTA
Found at i:13309760 original size:19 final size:19
Alignment explanation
Indices: 13309718--13309757 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
13309708 TTATTTCTAA
*
13309718 TTGTTTTTGTTGGTTGTCT
1 TTGTTTTTGTTGGTTATCT
13309737 TTGTTTTTGTTGTGTTATCT
1 TTGTTTTTGTTG-GTTATCT
13309757 T
1 T
13309758 GTTGATTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.03, C:0.05, G:0.23, T:0.70
Consensus pattern (19 bp):
TTGTTTTTGTTGGTTATCT
Found at i:13309842 original size:7 final size:7
Alignment explanation
Indices: 13309830--13309874 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
13309820 TTTCATATTA
13309830 TTTCAAT
1 TTTCAAT
13309837 TTTCAAT
1 TTTCAAT
13309844 TTTCAAT
1 TTTCAAT
*
13309851 TTTCAAC
1 TTTCAAT
13309858 TTTCAAT
1 TTTCAAT
13309865 TTTCAAT
1 TTTCAAT
13309872 TTT
1 TTT
13309875 TGATTTTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.27, C:0.16, G:0.00, T:0.58
Consensus pattern (7 bp):
TTTCAAT
Found at i:13309886 original size:14 final size:14
Alignment explanation
Indices: 13309835--13309896 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
13309825 TATTATTTCA
*
13309835 ATTTTCAATTT-TCA
1 ATTTTCAATTTCT-G
*
13309849 ATTTTCAACTTTC-A
1 ATTTTCAA-TTTCTG
*
13309863 ATTTTCAATTTTTG
1 ATTTTCAATTTCTG
*
13309877 ATTTTGAATTTCTG
1 ATTTTCAATTTCTG
13309891 ATTTTC
1 ATTTTC
13309897 TTTTTTTTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
13 3 0.08
14 34 0.85
15 3 0.08
ACGTcount: A:0.24, C:0.13, G:0.05, T:0.58
Consensus pattern (14 bp):
ATTTTCAATTTCTG
Found at i:13309979 original size:19 final size:19
Alignment explanation
Indices: 13309948--13309989 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
13309938 CCAACTAAGC
13309948 AATAAAAATAAATAAAGAA
1 AATAAAAATAAATAAAGAA
*
13309967 AATAATAAA-AAATAAATAA
1 AATAA-AAATAAATAAAGAA
13309986 AATA
1 AATA
13309990 CTTTTGAGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (19 bp):
AATAAAAATAAATAAAGAA
Found at i:13310295 original size:12 final size:12
Alignment explanation
Indices: 13310279--13310322 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
13310269 AAATTAACAA
13310279 AAAAATCAAAAT
1 AAAAATCAAAAT
*
13310291 CAAAATCAAAAT
1 AAAAATCAAAAT
*
13310303 AAAAATAAATAAAT
1 AAAAAT-CA-AAAT
13310317 AAAAAT
1 AAAAAT
13310323 AAAGAAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 16 0.59
13 1 0.04
14 10 0.37
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (12 bp):
AAAAATCAAAAT
Found at i:13310318 original size:14 final size:14
Alignment explanation
Indices: 13310299--13310325 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13310289 ATCAAAATCA
13310299 AAATAAAAATAAAT
1 AAATAAAAATAAAT
13310313 AAATAAAAATAAA
1 AAATAAAAATAAA
13310326 GAAAAGACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAATAAAAATAAAT
Found at i:13323725 original size:23 final size:23
Alignment explanation
Indices: 13323698--13323744 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
13323688 CTTAAGCCAT
13323698 AATTCAGATCAGACCCTCCTGTC
1 AATTCAGATCAGACCCTCCTGTC
13323721 AATTCAGATCAGACCCTCCTGTC
1 AATTCAGATCAGACCCTCCTGTC
13323744 A
1 A
13323745 TGATGTCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.34, G:0.13, T:0.26
Consensus pattern (23 bp):
AATTCAGATCAGACCCTCCTGTC
Found at i:13327372 original size:20 final size:19
Alignment explanation
Indices: 13327343--13327405 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
13327333 AATAATTTTG
* *
13327343 AAAATAAAAATAAATTAAA
1 AAAATAAAAAAAAATGAAA
13327362 AAAACTAAAAAAAAATGAAA
1 AAAA-TAAAAAAAAATGAAA
* *
13327382 AATAA-AAAAAAGAATAAAA
1 AA-AATAAAAAAAAATGAAA
13327401 AAAAT
1 AAAAT
13327406 GAAGATATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
18 2 0.05
19 18 0.49
20 15 0.41
21 2 0.05
ACGTcount: A:0.81, C:0.02, G:0.03, T:0.14
Consensus pattern (19 bp):
AAAATAAAAAAAAATGAAA
Found at i:13327560 original size:2 final size:2
Alignment explanation
Indices: 13327553--13327582 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13327543 ATATGTTGTA
13327553 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13327583 GATTACTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13333149 original size:2 final size:2
Alignment explanation
Indices: 13333138--13333179 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
13333128 CTTTGTATGT
*
13333138 TA TA -A TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13333179 T
1 T
13333180 GATTACTCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13336535 original size:46 final size:46
Alignment explanation
Indices: 13336464--13336552 Score: 151
Period size: 46 Copynumber: 1.9 Consensus size: 46
13336454 GAACTTCCAA
* *
13336464 TTCCAGAGCACATGGATATCCATCATTTCACGGGGGAGATTGACAT
1 TTCCAGAGCACATGGATATCCATCATCTCACGAGGGAGATTGACAT
*
13336510 TTCCAGAGCACATGGATATCTATCATCTCACGAGGGAGATTGA
1 TTCCAGAGCACATGGATATCCATCATCTCACGAGGGAGATTGA
13336553 AGCTTCTGAC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (46 bp):
TTCCAGAGCACATGGATATCCATCATCTCACGAGGGAGATTGACAT
Found at i:13336737 original size:72 final size:72
Alignment explanation
Indices: 13336651--13336795 Score: 209
Period size: 72 Copynumber: 2.0 Consensus size: 72
13336641 AAAGCCGACG
* * * * **
13336651 TGACTTGGACCAGGTGATTGGATCTATTCACCTAAGCTTTGGGCCATTAGTTGTGTAAGGATTAT
1 TGACTTGGACCAGGTGATTGGATCCATTCACCTAAGCTTTGAGCCATTAGTTCTGTAAAGACCAT
13336716 TCCACCT
66 TCCACCT
* * *
13336723 TGACTTGGACCAGGTGGTTGGATCCATTCACCTAAGGTTTGAGCCGTTAGTTCTGTAAAGACCAT
1 TGACTTGGACCAGGTGATTGGATCCATTCACCTAAGCTTTGAGCCATTAGTTCTGTAAAGACCAT
13336788 TCCACCT
66 TCCACCT
13336795 T
1 T
13336796 TGGGCTTGTG
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 64 1.00
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.33
Consensus pattern (72 bp):
TGACTTGGACCAGGTGATTGGATCCATTCACCTAAGCTTTGAGCCATTAGTTCTGTAAAGACCAT
TCCACCT
Found at i:13337171 original size:163 final size:164
Alignment explanation
Indices: 13336883--13337189 Score: 474
Period size: 163 Copynumber: 1.9 Consensus size: 164
13336873 TTTGAATTAT
* *
13336883 TTTTAATTGTTGGTCGTGAAAATTTCAAAGGAAAATATGATTTAATAATTAAAGATTGTAAACAT
1 TTTTAATTGTTGATCATGAAAATTTCAAAGGAAAATATGATTTAATAATTAAAGATTGTAAACAT
* **
13336948 ATAGAAGTAAATAAAAATTCAACTAATAATGAAATTTTAAGAAAATTACGGGTCTCTAA-TTTTC
66 ATAGAAGTAAATAAAAATTCAACTAATAATAAAATTTTAAGAAAATTACGGAACTCTAATTTTTC
13337012 TTAAAAATTTTTAGGTGAGATAAATTTTTTATAA
131 TTAAAAATTTTTAGGTGAGATAAATTTTTTATAA
** *
13337046 TTTTAATTGTTGATCATGAAAATTTCAAAGGAAAATATGATTTAATAATTAATTATTGTAAATAT
1 TTTTAATTGTTGATCATGAAAATTTCAAAGGAAAATATGATTTAATAATTAAAGATTGTAAACAT
* * *
13337111 ATAGAAGTAAATACAAATTCAACTAATGATAAAATTTTAAGAAAGTTAC-GAACGTCTAATTTTT
66 ATAGAAGTAAATAAAAATTCAACTAATAATAAAATTTTAAGAAAATTACGGAAC-TCTAATTTTT
* *
13337175 TTTAAGAATTTTTAG
130 CTTAAAAATTTTTAG
13337190 ATGAAGAATT
Statistics
Matches: 129, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
162 2 0.02
163 110 0.85
164 17 0.13
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.39
Consensus pattern (164 bp):
TTTTAATTGTTGATCATGAAAATTTCAAAGGAAAATATGATTTAATAATTAAAGATTGTAAACAT
ATAGAAGTAAATAAAAATTCAACTAATAATAAAATTTTAAGAAAATTACGGAACTCTAATTTTTC
TTAAAAATTTTTAGGTGAGATAAATTTTTTATAA
Found at i:13339437 original size:145 final size:146
Alignment explanation
Indices: 13339218--13339508 Score: 521
Period size: 145 Copynumber: 2.0 Consensus size: 146
13339208 ATTATTTCAA
13339218 ATAGGCTCCAAACATCAAAATCACATAATTAGAGACAAAGAGGAGAAACTATTGTATATAAAATT
1 ATAGGCTCCAAACATCAAAATCACATAATTAGAGAC-AAGAGGAGAAACTATTGTATATAAAATT
* * *
13339283 GGAAAAGTGCATTAAGAAACAAGGTCACAGTTTGAACCACAATAACAAGGAGAAATAACAGAGTG
65 GAAAAAGTGCATTAAGAAACAAGGTCACAGTTTGAACCACAATAACAACGAGAAATAACAAAGTG
13339348 AAACAGAAAAGCTAGCG
130 AAACAGAAAAGCTAGCG
*
13339365 ATAGGCTCCAAACATCAAAATCACTTAATTAGAGAC-AGAGGAGAAACTATTGTATATAAAATTG
1 ATAGGCTCCAAACATCAAAATCACATAATTAGAGACAAGAGGAGAAACTATTGTATATAAAATTG
*
13339429 AAAAAGTGCATTAAGAAACAAGGTCACAGTTTTAACCACAATAACAACGAGAAATAACAAAGTGA
66 AAAAAGTGCATTAAGAAACAAGGTCACAGTTTGAACCACAATAACAACGAGAAATAACAAAGTGA
13339494 AACAGAAAAGCTAGC
131 AACAGAAAAGCTAGC
13339509 ATTTTGACAA
Statistics
Matches: 139, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
145 104 0.75
147 35 0.25
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.19
Consensus pattern (146 bp):
ATAGGCTCCAAACATCAAAATCACATAATTAGAGACAAGAGGAGAAACTATTGTATATAAAATTG
AAAAAGTGCATTAAGAAACAAGGTCACAGTTTGAACCACAATAACAACGAGAAATAACAAAGTGA
AACAGAAAAGCTAGCG
Found at i:13339607 original size:12 final size:12
Alignment explanation
Indices: 13339590--13339621 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
13339580 TTGTATATGC
13339590 CATCATCAAACT
1 CATCATCAAACT
13339602 CATCATCAAACT
1 CATCATCAAACT
*
13339614 CACCATCA
1 CATCATCA
13339622 TCATCGTCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.22
Consensus pattern (12 bp):
CATCATCAAACT
Found at i:13339631 original size:3 final size:3
Alignment explanation
Indices: 13339625--13339671 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
13339615 ACCATCATCA
* *
13339625 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCA TCG TCA TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
13339672 ATCATAATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.04, C:0.34, G:0.28, T:0.34
Consensus pattern (3 bp):
TCG
Found at i:13339672 original size:6 final size:6
Alignment explanation
Indices: 13339617--13339674 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
13339607 TCAAACTCAC
* * * * * *
13339617 CATCAT CATCGT CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT CATCGT
1 CATCGT CATCGT CATCGT CATCGT CATCGT CATCGT CATCGT CATCGT
13339665 CATCGT CATC
1 CATCGT CATC
13339675 ATAATAATCA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.10, C:0.34, G:0.22, T:0.33
Consensus pattern (6 bp):
CATCGT
Found at i:13339672 original size:12 final size:12
Alignment explanation
Indices: 13339622--13339674 Score: 79
Period size: 12 Copynumber: 4.4 Consensus size: 12
13339612 CTCACCATCA
13339622 TCATCGTCGTCG
1 TCATCGTCGTCG
*
13339634 TCGTCGTCGTCG
1 TCATCGTCGTCG
*
13339646 TCGTCGTCGTCG
1 TCATCGTCGTCG
*
13339658 TCATCGTCATCG
1 TCATCGTCGTCG
13339670 TCATC
1 TCATC
13339675 ATAATAATCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.08, C:0.34, G:0.25, T:0.34
Consensus pattern (12 bp):
TCATCGTCGTCG
Found at i:13339676 original size:3 final size:3
Alignment explanation
Indices: 13339658--13339725 Score: 50
Period size: 3 Copynumber: 22.7 Consensus size: 3
13339648 GTCGTCGTCG
* * * * *
13339658 TCA TCG TCA TCG TCA TCA TAA TAA TCA TCA TCCA -CA TCA -AA CTCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T-CA TCA TCA TCA -TCA
*
13339703 TCA TCA TAA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TC
13339726 CTTCACCATG
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
2 3 0.06
3 45 0.88
4 3 0.06
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.31
Consensus pattern (3 bp):
TCA
Found at i:13340529 original size:21 final size:22
Alignment explanation
Indices: 13340491--13340543 Score: 90
Period size: 21 Copynumber: 2.4 Consensus size: 22
13340481 TTCGAAATTA
13340491 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
13340513 ATAAAATATTA-TTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
13340534 ATAAATATAT
1 ATAAA-ATAT
13340544 AAATAATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 15 0.50
22 15 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:13341734 original size:14 final size:14
Alignment explanation
Indices: 13341717--13341784 Score: 66
Period size: 14 Copynumber: 4.7 Consensus size: 14
13341707 TACAATTAAT
*
13341717 TATTAATAATATCA
1 TATTAATAATATTA
13341731 TATTAATAATATTA
1 TATTAATAATATTA
* *
13341745 TTATT-ATCATTTTA
1 -TATTAATAATATTA
*
13341759 TATTAATCAATTATAA
1 TATTAAT-AA-TATTA
13341775 TATTAATAAT
1 TATTAATAAT
13341785 TTAAATTCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
13 4 0.09
14 23 0.52
15 7 0.16
16 10 0.23
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (14 bp):
TATTAATAATATTA
Found at i:13342356 original size:21 final size:21
Alignment explanation
Indices: 13342332--13342380 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
13342322 TGTTATTAAA
*
13342332 ATTAGATAGTGACATATTTGT
1 ATTAGATAGTGACAAATTTGT
* *
13342353 ATTATATATTGACAAATTTGT
1 ATTAGATAGTGACAAATTTGT
*
13342374 AATAGAT
1 ATTAGAT
13342381 TTTTAATAGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.04, G:0.14, T:0.43
Consensus pattern (21 bp):
ATTAGATAGTGACAAATTTGT
Found at i:13342591 original size:13 final size:13
Alignment explanation
Indices: 13342573--13342607 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
13342563 TAGGTTTTTC
* *
13342573 AATATTGTGATAG
1 AATATTATGAGAG
13342586 AATATTATGAGAG
1 AATATTATGAGAG
13342599 AATATTATG
1 AATATTATG
13342608 GTAATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (13 bp):
AATATTATGAGAG
Found at i:13342636 original size:16 final size:16
Alignment explanation
Indices: 13342610--13342667 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
13342600 ATATTATGGT
* *
13342610 AATTTTTAAAATTGAA
1 AATTTTAAAAATTAAA
*
13342626 TATTTTAAAAAATTAAA
1 AATTTT-AAAAATTAAA
13342643 AATTTCTAAAAATTCAAA
1 AATTT-TAAAAATT-AAA
13342661 ATATTTT
1 A-ATTTT
13342668 TTGTATTAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 5 0.15
17 19 0.56
18 6 0.18
19 4 0.12
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (16 bp):
AATTTTAAAAATTAAA
Found at i:13342738 original size:30 final size:30
Alignment explanation
Indices: 13342683--13342755 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
13342673 TTAGATAGAT
**
13342683 TAAATTTTAAATTTTGTGGAAGTATAAGGAC
1 TAAATTTTAAA-TCCGTGGAAGTATAAGGAC
* *
13342714 TAAATTTTAAATCCGTGTAAGTATAAGGAT
1 TAAATTTTAAATCCGTGGAAGTATAAGGAC
*
13342744 TAAATTTCAAAT
1 TAAATTTTAAAT
13342756 TTCGTATGAG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 26 0.70
31 11 0.30
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.38
Consensus pattern (30 bp):
TAAATTTTAAATCCGTGGAAGTATAAGGAC
Found at i:13348964 original size:9 final size:8
Alignment explanation
Indices: 13348947--13348976 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
13348937 AAATTAATTT
13348947 AATAAAAA
1 AATAAAAA
13348955 AATAAAAA
1 AATAAAAA
13348963 AAT-AAAA
1 AATAAAAA
13348970 AATAAAA
1 AATAAAA
13348977 TTATTGAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
AATAAAAA
Found at i:13351982 original size:52 final size:52
Alignment explanation
Indices: 13351830--13351986 Score: 194
Period size: 52 Copynumber: 3.0 Consensus size: 52
13351820 TATAACCATA
* * * **
13351830 CAAACTTGCCCATTAAGAATCC-CTCTCTTCTTAGAATTCTTCTCCTATAAGT
1 CAAACTTGCCTATTAAGAATCCTCTTTC-TCTTAGAATTCTTCTCTTGCAAGT
*
13351882 CAAACTTGCCTATTAAGAATCCT-TTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCTCTTT-CTCTTAGAATTCTTCTCTTGCAAGT
* *
13351934 CAAACTTACCTATTAAGAATCCTCTTTCTCTT-GAAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCTCTTTCTCTTAG-AATTCTTCTCTTGCAAGT
13351986 C
1 C
13351987 TTCTTGTCCA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
51 1 0.01
52 87 0.95
53 4 0.04
ACGTcount: A:0.26, C:0.25, G:0.08, T:0.40
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCTCTTTCTCTTAGAATTCTTCTCTTGCAAGT
Found at i:13365400 original size:3 final size:3
Alignment explanation
Indices: 13365394--13365423 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
13365384 ATCATCATCA
13365394 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
13365424 CCTCGACAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:13368322 original size:20 final size:22
Alignment explanation
Indices: 13368267--13368323 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 22
13368257 TGTATATATG
13368267 TATATGTATTATTACTTATGTTA
1 TATATGTATTATTAC-TATGTTA
*
13368290 GATCATG-ATTATTAC-ATG-TA
1 TAT-ATGTATTATTACTATGTTA
13368310 TATATGTATTATTA
1 TATATGTATTATTA
13368324 TTATTATTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
19 3 0.10
20 11 0.37
21 3 0.10
23 10 0.33
24 3 0.10
ACGTcount: A:0.33, C:0.05, G:0.11, T:0.51
Consensus pattern (22 bp):
TATATGTATTATTACTATGTTA
Found at i:13368352 original size:64 final size:67
Alignment explanation
Indices: 13368283--13368417 Score: 231
Period size: 64 Copynumber: 2.0 Consensus size: 67
13368273 TATTATTACT
13368283 TATGTTAGATCATGATTATTACATGTATAT-ATGTAT-TAT-TATTATTATTACATATATACATA
1 TATGTTAGATCATGATTATTACATGTATATAATGTATATATGTATTATTATTACATATATACATA
13368345 TA
66 TA
*
13368347 TATGTTAGATCATGATTATTACATGTATATCAATGTATATATGTATTATTATTACATGTATACAT
1 TATGTTAGATCATGATTATTACATGTATAT-AATGTATATATGTATTATTATTACATATATACAT
13368412 ATA
65 ATA
13368415 TAT
1 TAT
13368418 ATGTATACAT
Statistics
Matches: 66, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
64 30 0.45
66 6 0.09
67 3 0.05
68 27 0.41
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.47
Consensus pattern (67 bp):
TATGTTAGATCATGATTATTACATGTATATAATGTATATATGTATTATTATTACATATATACATA
TA
Found at i:13368392 original size:8 final size:8
Alignment explanation
Indices: 13368369--13368449 Score: 69
Period size: 8 Copynumber: 10.0 Consensus size: 8
13368359 TGATTATTAC
13368369 ATGTATAT
1 ATGTATAT
13368377 CAATGTATAT
1 --ATGTATAT
13368387 ATGTAT-T
1 ATGTATAT
*
13368394 AT-TATTAC
1 ATGTA-TAT
*
13368402 ATGTATAC
1 ATGTATAT
*
13368410 ATATATAT
1 ATGTATAT
*
13368418 ATGTATAC
1 ATGTATAT
13368426 ATGTATCA-
1 ATGTAT-AT
13368434 ATGTATAT
1 ATGTATAT
13368442 ATGTATAT
1 ATGTATAT
13368450 GTATCAATGT
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
6 2 0.03
7 5 0.08
8 43 0.70
9 3 0.05
10 8 0.13
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (8 bp):
ATGTATAT
Found at i:13368429 original size:24 final size:24
Alignment explanation
Indices: 13368369--13368448 Score: 85
Period size: 24 Copynumber: 3.3 Consensus size: 24
13368359 TGATTATTAC
*
13368369 ATGTATATCAATGTATATATGTAT-T
1 ATGTATA-C-ATGTATACATGTATAT
*
13368394 AT-TATTACATGTATACATATATAT
1 ATGTA-TACATGTATACATGTATAT
13368418 ATGTATACATGTAT-CAATGTATAT
1 ATGTATACATGTATAC-ATGTATAT
13368442 ATGTATA
1 ATGTATA
13368449 TGTATCAATG
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
23 13 0.27
24 29 0.60
25 6 0.12
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (24 bp):
ATGTATACATGTATACATGTATAT
Found at i:13368451 original size:22 final size:23
Alignment explanation
Indices: 13368413--13368461 Score: 82
Period size: 22 Copynumber: 2.1 Consensus size: 23
13368403 TGTATACATA
13368413 TATATATGTATACATGTATCAATG
1 TATATATGTATA-ATGTATCAATG
13368437 TATATATGTAT-ATGTATCAATG
1 TATATATGTATAATGTATCAATG
13368459 TAT
1 TAT
13368462 GTACAAAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 14 0.56
24 11 0.44
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (23 bp):
TATATATGTATAATGTATCAATG
Found at i:13368459 original size:8 final size:7
Alignment explanation
Indices: 13368378--13368461 Score: 55
Period size: 8 Copynumber: 11.0 Consensus size: 7
13368368 CATGTATATC
13368378 AATGTAT
1 AATGTAT
13368385 ATATGTAT
1 A-ATGTAT
*
13368393 TAT-TATT
1 AATGTA-T
13368400 ACATGTAT
1 A-ATGTAT
*
13368408 ACATATAT
1 A-ATGTAT
13368416 ATATGTAT
1 A-ATGTAT
13368424 ACATGTAT
1 A-ATGTAT
13368432 CAATGTAT
1 -AATGTAT
13368440 ATATGTAT
1 A-ATGTAT
13368448 -ATGTAT
1 AATGTAT
13368454 CAATGTAT
1 -AATGTAT
13368462 GTACAAAAAC
Statistics
Matches: 63, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
6 8 0.13
7 5 0.08
8 47 0.75
9 3 0.05
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (7 bp):
AATGTAT
Found at i:13368747 original size:17 final size:16
Alignment explanation
Indices: 13368721--13368752 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
13368711 AATATAATTT
13368721 TTATATTTATATATAA
1 TTATATTTATATATAA
13368737 TTATATGTTATATATA
1 TTATAT-TTATATATA
13368753 GTATATAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
TTATATTTATATATAA
Found at i:13368985 original size:44 final size:44
Alignment explanation
Indices: 13368918--13369002 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
13368908 AAATGAAAAA
* * *
13368918 AAAAATCATAGGTAATCACCTAATTG-GTCCTCAAAATTAAAGTG
1 AAAAATCATAGGTAATAACCTAA-TGACTACTCAAAATTAAAGTG
*
13368962 AAAAATCATAGGTAATAATCTAATGACTACTCAAAATTAAA
1 AAAAATCATAGGTAATAACCTAATGACTACTCAAAATTAAA
13369003 ACATAACCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
43 2 0.06
44 34 0.94
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (44 bp):
AAAAATCATAGGTAATAACCTAATGACTACTCAAAATTAAAGTG
Found at i:13369720 original size:19 final size:18
Alignment explanation
Indices: 13369698--13369744 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
13369688 ACATTGAGTC
13369698 TTCCTTTTTTATTCTTTTT
1 TTCCTTTTTTATT-TTTTT
* *
13369717 TTCCTTTTCTCTTTTTTT
1 TTCCTTTTTTATTTTTTT
*
13369735 TGCCTTTTTT
1 TTCCTTTTTT
13369745 TAAGCATAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (18 bp):
TTCCTTTTTTATTTTTTT
Found at i:13380264 original size:54 final size:55
Alignment explanation
Indices: 13380201--13380337 Score: 186
Period size: 55 Copynumber: 2.5 Consensus size: 55
13380191 GCTTTTATAT
* * *
13380201 AAGAAAAATTGATAATTTCAACTTTTCCT-TAAAGCATTTGGAAATTTTATTTTC
1 AAGAAAAATTGATACTTTCAACTTTTCCTAAAAAGCATTTGAAAATTTTATTTTC
* * * ** *
13380255 AGGAGAAATTGATACTTTCAACTTTTCATAAAAAGTTTTTGAAAATTTTATTTTT
1 AAGAAAAATTGATACTTTCAACTTTTCCTAAAAAGCATTTGAAAATTTTATTTTC
13380310 AAGAAAAATTGATACTTTCAACTTTTCC
1 AAGAAAAATTGATACTTTCAACTTTTCC
13380338 CCAAAATGTT
Statistics
Matches: 70, Mismatches: 12, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
54 25 0.36
55 45 0.64
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.42
Consensus pattern (55 bp):
AAGAAAAATTGATACTTTCAACTTTTCCTAAAAAGCATTTGAAAATTTTATTTTC
Found at i:13380421 original size:17 final size:17
Alignment explanation
Indices: 13380401--13380435 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
13380391 AAAAAATCAT
13380401 AAAATAAAAATAAAATA
1 AAAATAAAAATAAAATA
*
13380418 AAAATAAAGATAAAATA
1 AAAATAAAAATAAAATA
13380435 A
1 A
13380436 GGAATATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (17 bp):
AAAATAAAAATAAAATA
Found at i:13380435 original size:11 final size:11
Alignment explanation
Indices: 13380399--13380432 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
13380389 TAAAAAAATC
13380399 ATAAAATAAAA
1 ATAAAATAAAA
13380410 ATAAAATAAAA
1 ATAAAATAAAA
13380421 ATAAAGATAAAA
1 ATAAA-ATAAAA
13380433 TAAGGAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (11 bp):
ATAAAATAAAA
Found at i:13380792 original size:16 final size:16
Alignment explanation
Indices: 13380771--13380812 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
13380761 GATGCTTCTC
13380771 CCCTTCTCTCTCTCTT
1 CCCTTCTCTCTCTCTT
* *
13380787 CCCTTCTTTTTCTCTT
1 CCCTTCTCTCTCTCTT
13380803 CCC-TCTCTCT
1 CCCTTCTCTCT
13380813 ACTCGAACCT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (16 bp):
CCCTTCTCTCTCTCTT
Found at i:13381354 original size:24 final size:25
Alignment explanation
Indices: 13381237--13381354 Score: 122
Period size: 24 Copynumber: 4.9 Consensus size: 25
13381227 AGCAAAAAGA
*
13381237 AATAGATAAATAATAAATATATATAT
1 AATAGATAAATAATATATATATAT-T
* *
13381263 ACTA-ATAAATAATAGATA-ATAGTT
1 AATAGATAAATAATATATATATA-TT
* * *
13381287 AACA-ATAAA-AATTTATATACATT
1 AATAGATAAATAATATATATATATT
13381310 AATAGATAAATAATA-ATATATATT
1 AATAGATAAATAATATATATATATT
13381334 AATAGATAAA-AATATATATAT
1 AATAGATAAATAATATATATAT
13381355 TAATAAATAA
Statistics
Matches: 77, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
23 15 0.19
24 42 0.55
25 17 0.22
26 3 0.04
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.35
Consensus pattern (25 bp):
AATAGATAAATAATATATATATATT
Found at i:13381371 original size:48 final size:44
Alignment explanation
Indices: 13381245--13381372 Score: 127
Period size: 44 Copynumber: 2.9 Consensus size: 44
13381235 GAAATAGATA
* *
13381245 AATAATAAATATATATATACTAATAAATAATAGATAATAGTTAAC
1 AATAATAAATATATATATATTAATAAATAAT-GATAATAATTAAC
* * * *
13381290 AATAA-AAATTTATATACATTAATAGATAA--ATAATAATATATATT
1 AATAATAAATATATATATATTAATAAATAATGATAATAAT-TA-A-C
*
13381334 AATAGATAAAAATATATATATTAATAAATAATGATAATA
1 AATA-ATAAATATATATATATTAATAAATAATGATAATA
13381373 GCAATAAATA
Statistics
Matches: 66, Mismatches: 10, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
41 7 0.11
42 2 0.03
43 1 0.02
44 24 0.36
45 6 0.09
46 20 0.30
48 6 0.09
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (44 bp):
AATAATAAATATATATATATTAATAAATAATGATAATAATTAAC
Found at i:13381382 original size:4 final size:4
Alignment explanation
Indices: 13381375--13381419 Score: 58
Period size: 4 Copynumber: 11.5 Consensus size: 4
13381365 TGATAATAGC
*
13381375 AATA AATA AATA AATA AAT- AATA AATA AATA AGATA TA-A AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA A-ATA AATA AATA AA
13381420 AATATAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
3 5 0.14
4 28 0.78
5 3 0.08
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:13381382 original size:23 final size:20
Alignment explanation
Indices: 13381356--13381419 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 20
13381346 TATATATATT
13381356 AATAAATAATGATAATAGCAATA
1 AATAAATAA-GATAA-A-CAATA
*
13381379 AATAAATAA-ATAAATAATA
1 AATAAATAAGATAAACAATA
13381398 AATAAATAAGATATAA-AATA
1 AATAAATAAGATA-AACAATA
13381418 AA
1 AA
13381420 AATATAAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
19 13 0.34
20 10 0.26
21 6 0.16
23 9 0.24
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.25
Consensus pattern (20 bp):
AATAAATAAGATAAACAATA
Found at i:13381397 original size:15 final size:16
Alignment explanation
Indices: 13381379--13381419 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
13381369 AATAGCAATA
13381379 AATAAATAAATAA-AT
1 AATAAATAAATAAGAT
13381394 AATAAATAAATAAGAT
1 AATAAATAAATAAGAT
13381410 -ATAAAATAAA
1 AAT-AAATAAA
13381420 AATATAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (16 bp):
AATAAATAAATAAGAT
Found at i:13381738 original size:130 final size:127
Alignment explanation
Indices: 13381496--13382141 Score: 477
Period size: 130 Copynumber: 5.0 Consensus size: 127
13381486 CTACATTTAA
* * *
13381496 TATTACGAAAACTTATTTTATTTGCAATAAATTTTTAATG-CTGTTGTTTAATTTATTTTTTTAA
1 TATTACAAAAACTTATTTTATTTGCAATAAATTTTTAATGTC-ATTGCTTAATTTA-TTTTTTAA
* ** * * *
13381560 TATTTTATTTAA-CAGCAAAAAGTTATTAAGAAAATTTTTATCATATTTGTAACGATAAAAAATT
64 AATTTTATACAATGAG-AAAAAATTATT-A-AAAATTTTTATCATATTTGTAATGATAAAAAATT
13381624 AT
126 AT
* * ** * *
13381626 TGTTACAAAAACTTATTTTATTTACAA-CGATTTTTCAATGTTATTGCCTAATTTATTTTTTTAA
1 TATTACAAAAACTTATTTTATTTGCAATAAATTTTT-AATGTCATTGCTTAATTTA-TTTTTTAA
* * *
13381690 TATTTTATACAATGACGAAAAAATTATTAAAATTTTTTTATCACATTTGTAATGATAAAAAATTA
64 AATTTTATACAATGA-GAAAAAATTATTAAAA-ATTTTTATCATATTTGTAATGATAAAAAATTA
13381755 T
127 T
* * * *
13381756 TATTGC-AAAATTCTATTTTATTTGCAATAAATTTTTAATGTCGTTGTTTAATTTATTTTTTAAA
1 TATTACAAAAACT-TATTTTATTTGCAATAAATTTTTAATGTCATTGCTTAATTTATTTTTTAAA
* * * * *
13381820 AGTTTTATATAATGATAAAAAAGTTCTTATGAAAATTTTTATTATA-TTATAATGATAAAAAATT
65 A-TTTTATACAATGAGAAAAAA-TTATTA--AAAATTTTTATCATATTTGTAATGATAAAAAATT
13381884 AT
126 AT
* * * * *
13381886 TATT-CAAAAAACTTATTTTATTTGCAA-AGATTGTTATTCTCATTGCTTATTTTATTTTTTAAA
1 TATTAC-AAAAACTTATTTTATTTGCAATAAATTTTTAATGTCATTGCTTAATTTATTTTTTAAA
* ** * ** * * * * * *
13381949 ATTTTATACAATGATAAATTTTATCATTACGAATTCTTATTATATTCGTAA-CAAAAAAAATAAA
65 ATTTTATACAATGAGAAA--AAATTATTAAAAATTTTTATCATATTTGTAATGATAAAAAAT-TA
13382013 T
127 T
*** * * * * * * * *
13382014 TATTGTGAAAA-TT-TCTT-TTTGCAACAAATTTTCAATGCCTTTACTTAATTTAGTTTTTAATA
1 TATTACAAAAACTTATTTTATTTGCAATAAATTTTTAATGTCATTGCTTAATTTATTTTTTAAAA
* * * * **
13382076 TTTTATACAATGAAAAAATAATTGTTAAGAAAATTTTTTTAATATTTGTAACAATAAAAAATTAT
66 TTTTATACAATGAGAAAA-AATTATT-A-AAAATTTTTATCATATTTGTAATGATAAAAAATTAT
13382141 T
1 T
13382142 GTTGTAAAAT
Statistics
Matches: 410, Mismatches: 83, Indels: 49
0.76 0.15 0.09
Matches are distributed among these distances:
125 11 0.03
126 46 0.11
127 41 0.10
128 38 0.09
129 64 0.16
130 175 0.43
131 31 0.08
132 4 0.01
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (127 bp):
TATTACAAAAACTTATTTTATTTGCAATAAATTTTTAATGTCATTGCTTAATTTATTTTTTAAAA
TTTTATACAATGAGAAAAAATTATTAAAAATTTTTATCATATTTGTAATGATAAAAAATTAT
Found at i:13381902 original size:40 final size:40
Alignment explanation
Indices: 13381827--13381907 Score: 92
Period size: 40 Copynumber: 2.0 Consensus size: 40
13381817 AAAAGTTTTA
* * ***
13381827 TATAATGATAAAAAAGTTCTTATGAAAATTTTTATTATAT
1 TATAATGATAAAAAAGTTATTATCAAAAAACTTATTATAT
*
13381867 TATAATGATAAAAAA-TTATTATTCAAAAAACTTATTTTAT
1 TATAATGATAAAAAAGTTATTA-TCAAAAAACTTATTATAT
13381907 T
1 T
13381908 TGCAAAGATT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
39 5 0.15
40 29 0.85
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (40 bp):
TATAATGATAAAAAAGTTATTATCAAAAAACTTATTATAT
Found at i:13382166 original size:255 final size:257
Alignment explanation
Indices: 13381776--13382271 Score: 540
Period size: 255 Copynumber: 1.9 Consensus size: 257
13381766 TTCTATTTTA
* * * ** * *
13381776 TTTGCAATAAATTTTTAATGTCGTTGTTTAATTTATTTTTTAAAAGTTTTATATAATGATAAAAA
1 TTTGCAACAAATTTTCAATGCCGTTACTTAATTTAGTTTTTAAAAGTTTTATACAATGATAAAAA
* * ** * * *
13381841 AGTTCTTATGAAAATTTTTATTATATTATAATGATAAAAAATTATTATTCAAAAAACTTATTTTA
66 AATTCTTAAGAAAATTTTTATTATATTATAACAATAAAAAATTATTATTCAAAAAACGTATATCA
** * * * *
13381906 TTTGCAA-AGA-TTGTT-ATTCTCATTGCTTATTTTATTTTT-TAAA-ATTTTATACAATGATAA
131 TTTGCAATA-ACTT-TTGATAATCATTACTTAATTGATTTTTAAAAATATTTTATACAATGATAA
* * *
13381966 ATTTTATCATTACGAATTCTTATTATATTCGTAACAAAAAAAATAAATTATTGTGAAAATTTCTT
194 ATTTTATCATTACAAACTCTTATTATATTCATAACAAAAAAAA-AAATTATTGTGAAAATTTCTT
* *
13382031 TTTGCAACAAATTTTCAATGCCTTTACTTAATTTAGTTTTTAATA-TTTTATACAATGA-AAAAA
1 TTTGCAACAAATTTTCAATGCCGTTACTTAATTTAGTTTTTAAAAGTTTTATACAATGATAAAAA
* * * ** **
13382094 TAATTGTTAAGAAAATTTTT-TTAATATTTGTAACAATAAAAAATTATTGTTGTAAAATGGTATA
66 -AATTCTTAAGAAAATTTTTATT-ATA-TTATAACAATAAAAAATTATTATTCAAAAAACGTATA
**
13382158 TCATTTGCAATAACTTTTGATAATCATTACTTAATTGATTTTTAAAAATATTTTATGTAATGATA
128 TCATTTGCAATAACTTTTGATAATCATTACTTAATTGATTTTTAAAAATATTTTATACAATGATA
* * * *
13382223 ATTTTTATTATTGCAAACTCTTATTATATTCATAACAATAAAAAAAATT
193 AATTTTATCATTACAAACTCTTATTATATTCATAACAAAAAAAAAAATT
13382272 GCTGTAATAT
Statistics
Matches: 195, Mismatches: 38, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
253 7 0.04
254 31 0.16
255 76 0.39
256 22 0.11
257 8 0.04
258 51 0.26
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (257 bp):
TTTGCAACAAATTTTCAATGCCGTTACTTAATTTAGTTTTTAAAAGTTTTATACAATGATAAAAA
AATTCTTAAGAAAATTTTTATTATATTATAACAATAAAAAATTATTATTCAAAAAACGTATATCA
TTTGCAATAACTTTTGATAATCATTACTTAATTGATTTTTAAAAATATTTTATACAATGATAAAT
TTTATCATTACAAACTCTTATTATATTCATAACAAAAAAAAAAATTATTGTGAAAATTTCTT
Found at i:13385190 original size:15 final size:15
Alignment explanation
Indices: 13385170--13385199 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13385160 TTTTTTCAGT
13385170 ATTGAAACATAAAAG
1 ATTGAAACATAAAAG
*
13385185 ATTGAAGCATAAAAG
1 ATTGAAACATAAAAG
13385200 TGTTGGAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.17, T:0.20
Consensus pattern (15 bp):
ATTGAAACATAAAAG
Found at i:13389525 original size:30 final size:30
Alignment explanation
Indices: 13389489--13389561 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
13389479 TTTATCCAAT
*
13389489 TAAAAATTTAATTGAGTGAAAATAAATATA
1 TAAAAATTTAATTGAATGAAAATAAATATA
* *
13389519 TAAAAATTTAATTGAATTAAAATAAATATT
1 TAAAAATTTAATTGAATGAAAATAAATATA
13389549 TAAAAATTTAATT
1 TAAAAATTTAATT
13389562 AATTTTAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (30 bp):
TAAAAATTTAATTGAATGAAAATAAATATA
Found at i:13389587 original size:30 final size:30
Alignment explanation
Indices: 13389488--13389579 Score: 114
Period size: 30 Copynumber: 3.1 Consensus size: 30
13389478 TTTTATCCAA
* * *
13389488 TTAAAAATTTAATTGAGTGAAAATAAATAT
1 TTAAAAATTTAATTGAATTAAAATAAAAAT
* *
13389518 ATAAAAATTTAATTGAATTAAAATAAATAT
1 TTAAAAATTTAATTGAATTAAAATAAAAAT
*
13389548 TTAAAAATTTAATT-AATTTTAAATAAAAAT
1 TTAAAAATTTAATTGAA-TTAAAATAAAAAT
13389578 TT
1 TT
13389580 TGAAATTTGA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
29 2 0.04
30 53 0.96
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (30 bp):
TTAAAAATTTAATTGAATTAAAATAAAAAT
Found at i:13390028 original size:18 final size:17
Alignment explanation
Indices: 13389984--13390028 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
13389974 TTTTTATTTT
*
13389984 TTAAAAAAATTATAAAA
1 TTAAAAAAACTATAAAA
*
13390001 TATAACAAAACTATAAAAA
1 T-TAAAAAAACTAT-AAAA
13390020 TTAAAAAAA
1 TTAAAAAAA
13390029 AATTGAGTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 1 0.04
18 17 0.74
19 5 0.22
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (17 bp):
TTAAAAAAACTATAAAA
Found at i:13392786 original size:23 final size:23
Alignment explanation
Indices: 13392755--13392804 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
13392745 GATCGATAAG
* *
13392755 AAGATTTGTAGAAGAAGAATTCT
1 AAGACTTGTAGAAGAAGAATGCT
13392778 AAGACTTGTAGAAGAAGAATGCT
1 AAGACTTGTAGAAGAAGAATGCT
13392801 AAGA
1 AAGA
13392805 GAAAAAGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.46, C:0.06, G:0.24, T:0.24
Consensus pattern (23 bp):
AAGACTTGTAGAAGAAGAATGCT
Found at i:13393431 original size:31 final size:28
Alignment explanation
Indices: 13393362--13393432 Score: 88
Period size: 28 Copynumber: 2.4 Consensus size: 28
13393352 GGCTTTTTAG
* *
13393362 CCCAATAAATGGTATCAGAGTTGTGATT
1 CCCAACAAGTGGTATCAGAGTTGTGATT
*
13393390 CCTAACAAGTGGTATCAGAGTTGTGATGAT
1 CCCAACAAGTGGTATCAGAGTTGTGAT--T
13393420 CCCCAACAAGTGG
1 -CCCAACAAGTGG
13393433 CATTTGAGTC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 24 0.67
30 1 0.03
31 11 0.31
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (28 bp):
CCCAACAAGTGGTATCAGAGTTGTGATT
Found at i:13393610 original size:52 final size:52
Alignment explanation
Indices: 13393527--13393631 Score: 147
Period size: 52 Copynumber: 2.0 Consensus size: 52
13393517 TGGATAAGAA
* * *
13393527 GACTTGCAGAAGAAGAATTCTAAAAGAAAATGGATTCTTAATAGCCAAGTTT
1 GACTTGCAGAAAAAGAATTCTAAAAGAAAATGAATTCTTAATAGCAAAGTTT
* * * *
13393579 GACTTGCAGAAAAAGAATTTTAAGAGGAAATGAATTCTTAATAGGAAAGTTT
1 GACTTGCAGAAAAAGAATTCTAAAAGAAAATGAATTCTTAATAGCAAAGTTT
13393631 G
1 G
13393632 TATACTTATA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.28
Consensus pattern (52 bp):
GACTTGCAGAAAAAGAATTCTAAAAGAAAATGAATTCTTAATAGCAAAGTTT
Found at i:13393619 original size:18 final size:17
Alignment explanation
Indices: 13393593--13393626 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
13393583 TGCAGAAAAA
13393593 GAATTTTAAGAGGAAAT
1 GAATTTTAAGAGGAAAT
*
13393610 GAATTCTTAATAGGAAA
1 GAATT-TTAAGAGGAAA
13393627 GTTTGTATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.47, C:0.03, G:0.21, T:0.29
Consensus pattern (17 bp):
GAATTTTAAGAGGAAAT
Found at i:13396699 original size:22 final size:21
Alignment explanation
Indices: 13396659--13396699 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
13396649 AATGGTGTGG
* *
13396659 TAAAAATTTGATTGGTTTAAC
1 TAAAAATTTGAGTGATTTAAC
13396680 TAAAAAGTTTGAGTGATTTA
1 TAAAAA-TTTGAGTGATTTA
13396700 GAAGGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.39, C:0.02, G:0.17, T:0.41
Consensus pattern (21 bp):
TAAAAATTTGAGTGATTTAAC
Found at i:13398209 original size:210 final size:210
Alignment explanation
Indices: 13397603--13398660 Score: 1368
Period size: 210 Copynumber: 5.0 Consensus size: 210
13397593 TTCTAAGCAA
* *
13397603 GCTTAAACTTCTGAATTTAAGACGCTGCAAAAGTCTTAGGAGT-T-TTCCAACCAAAATAATTGG
1 GCTTAAACTTTTGAATTTAAGAGGCTGCAAAAGTCTTA-GA-TCTCTTCCAACC--AA-AATTGG
* * * * * *
13397666 AATGAAATCTCTTGAAGAATTAATTATTTC-GGATTGCTCAAAAT-TTGAAGGGTTTCCTGAGAT
61 AATGAAATCTCTTGACGAATTAATTCTTTCAGG-CTGCTC-AAATCTTCAAAGGTTTCCAGAGAT
* *
13397729 TGATGGGGAAATGAAATGTTTGCAGGAGCTTCATTTAGATGGAACAGGCATTGTAGAACTTCCCT
124 TGATGGCGAAATGAAATGTTTGCAGGAGCTTCATTTAGATGGAACAGGCATTGAAGAACTTCCCT
13397794 CTTCAATTGGACATCTCAGCGG
189 CTTCAATTGGACATCTCAGCGG
* *
13397816 GCTCAAGCTTTTGAATTTAAGAGGCTGCAAAAGTCTTAGGAGT-T-TTCCAACCAAAATAATTGG
1 GCTTAAACTTTTGAATTTAAGAGGCTGCAAAAGTCTTA-GA-TCTCTTCCAACC--AA-AATTGG
* * * *
13397879 AATGAAATCTCTTGAAC-AATTAATTCTTTCTGGTTGCTCAAATTTTGAAAGGCTTT-CAGAGAT
61 AATGAAATCTCTTG-ACGAATTAATTCTTTCAGGCTGCTCAAATCTTCAAAGG-TTTCCAGAGAT
** *
13397942 TGATGTTGCAATGAAATGTTTGCAGGAGCTTCATTTAGATGGAACAGGCATTGAAGAACTTCCCT
124 TGATGGCGAAATGAAATGTTTGCAGGAGCTTCATTTAGATGGAACAGGCATTGAAGAACTTCCCT
13398007 CTTCAATTGGACATCTCAGCGG
189 CTTCAATTGGACATCTCAGCGG
* * * *
13398029 GCTTAAAATTTTGAATTTAAGAGGCTGCAAAAATCTTATATCTCTTCCAACCAAAATTGGAATGG
1 GCTTAAACTTTTGAATTTAAGAGGCTGCAAAAGTCTTAGATCTCTTCCAACCAAAATTGGAATGA
* * * *
13398094 AATCGCTTTACGAATTAGTTCTTTCAGGCTGTTCAAATCTTCAAAGGTTTCCAGAGATTGATGGC
66 AATCTCTTGACGAATTAATTCTTTCAGGCTGCTCAAATCTTCAAAGGTTTCCAGAGATTGATGGC
* *
13398159 AAAATGGAATGTTTGCAGGAGCTTCATTTAGATGGAACAGGCATTGAAGAACTTCCCTCTTCAAT
131 GAAATGAAATGTTTGCAGGAGCTTCATTTAGATGGAACAGGCATTGAAGAACTTCCCTCTTCAAT
* *
13398224 TGGACAACTCGGCGG
196 TGGACATCTCAGCGG
*
13398239 GCTTAAATTTTTGAATTTAAGAGGCTGCAAAAGTCTTAGATCTCTTCCAACCAAAATTGGAATGA
1 GCTTAAACTTTTGAATTTAAGAGGCTGCAAAAGTCTTAGATCTCTTCCAACCAAAATTGGAATGA
* * *
13398304 AATCACTTGA--AACGTTAATTCTTTCAGACTGCTCAAATCTCCAAAGGTTTCCAGAGATTGATG
66 AATCTCTTGACGAA--TTAATTCTTTCAGGCTGCTCAAATCTTCAAAGGTTTCCAGAGATTGATG
* *
13398367 GCGAAATGAAATATTTGCAGGAGCTTCATGTAGATGGAACAGGCATTGAAGAAGACGAACTTCCC
129 GCGAAATGAAATGTTTGCAGGAGCTTCATTTAGATGGAACAGGCATT---G-A-A-GAACTTCCC
*
13398432 TCTT--ATTGGACATCTCAGCGA
188 TCTTCAATTGGACATCTCAGCGG
**
13398453 GCTTCGACTTTTGAATTTAAGAGGCTGCAAAAGTCTTAGATCTCTTCCAACCAAAATTGGAAATG
1 GCTTAAACTTTTGAATTTAAGAGGCTGCAAAAGTCTTAGATCTCTTCCAACCAAAATTGG-AATG
* * * * * *
13398518 GAATCTCTTTATGAATTAGTTCTTTTAGGCTGTTCAAATCTTCAAAGGTTTCCAGAGATTGATGG
65 AAATCTCTTGACGAATTAATTCTTTCAGGCTGCTCAAATCTTCAAAGGTTTCCAGAGATTGATGG
* ** *
13398583 CGAAATGAAATGTTTACAGCTGCTTCATTTAGATGGAACAGGCATTGAAGAACTTTCCTCTTCAA
130 CGAAATGAAATGTTTGCAGGAGCTTCATTTAGATGGAACAGGCATTGAAGAACTTCCCTCTTCAA
13398648 TTGG-CATCTCAGC
195 TTGGACATCTCAGC
13398661 CATCTTGTTT
Statistics
Matches: 757, Mismatches: 67, Indels: 45
0.87 0.08 0.05
Matches are distributed among these distances:
208 2 0.00
209 17 0.02
210 300 0.40
211 9 0.01
212 7 0.01
213 230 0.30
214 78 0.10
215 99 0.13
216 13 0.02
217 2 0.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (210 bp):
GCTTAAACTTTTGAATTTAAGAGGCTGCAAAAGTCTTAGATCTCTTCCAACCAAAATTGGAATGA
AATCTCTTGACGAATTAATTCTTTCAGGCTGCTCAAATCTTCAAAGGTTTCCAGAGATTGATGGC
GAAATGAAATGTTTGCAGGAGCTTCATTTAGATGGAACAGGCATTGAAGAACTTCCCTCTTCAAT
TGGACATCTCAGCGG
Found at i:13399648 original size:17 final size:17
Alignment explanation
Indices: 13399626--13399662 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
13399616 ATAGGTGGAA
13399626 GCCGTCGAAGGATATCT
1 GCCGTCGAAGGATATCT
13399643 GCCGTCGAAGGATATCT
1 GCCGTCGAAGGATATCT
13399660 GCC
1 GCC
13399663 ATCAAATGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.30, T:0.22
Consensus pattern (17 bp):
GCCGTCGAAGGATATCT
Found at i:13404286 original size:2 final size:2
Alignment explanation
Indices: 13404279--13404307 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13404269 ATGTACTTGA
13404279 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
13404308 CTTGAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:13406685 original size:59 final size:58
Alignment explanation
Indices: 13406619--13407077 Score: 589
Period size: 59 Copynumber: 7.7 Consensus size: 58
13406609 TCTTGTGCAG
* * * *
13406619 GGAAAATTGATACTTTCAACTTTTCCCTAAAGAAATTTTTTTTCAAATTTTAATTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAA-AAATTTTTTTTGAAATTTTATTTTTAA
* * * *
13406678 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATTTATTTTTTAAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAAATT-TTTTTTGAAATTTTATTTTTAA
* * *
13406737 GGAAAATTGATACTTTCAACTTTTCTCCAAAAATATATTTTTTTGAAACTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA-AT-TTTTTTTGAAA-TTTTATTTTTAA
* * * *
13406798 GGAAAATTGATACTTTCAAATTTTCCCC-AAAGACTCTTTTTGAAATTTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAAATTTTTTTTGAAATTTTATTTTTAA
13406855 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTGGAAAATTTTGATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA-A-TTTTTTTT-G-AAATTTT-ATTTTTAA
* * * * *
13406918 AGAAAATTGATACTTTCAACTTTTCCTC-AAAAATATTTTTTGAAACTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAAATTTTTTTTGAAA-TTTTATTTTTAA
* *
13406976 GGAAAATTGATACTTTCAACTTTTCCCCAAAAACCTTTTTTTCGAAATTTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA-ATTTTTTTTGAAATTTTATTTTTAA
13407035 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA-ATTTTTTTT
13407078 ATTCTTATTT
Statistics
Matches: 347, Mismatches: 40, Indels: 26
0.84 0.10 0.06
Matches are distributed among these distances:
57 37 0.11
58 53 0.15
59 138 0.40
60 36 0.10
61 38 0.11
62 11 0.03
63 34 0.10
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (58 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAAATTTTTTTTGAAATTTTATTTTTAA
Found at i:13406736 original size:14 final size:15
Alignment explanation
Indices: 13406706--13406734 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
13406696 ACTTTTCCTC
13406706 AAAAATTTATTTTTT
1 AAAAATTTATTTTTT
13406721 AAAAATTTATTTTT
1 AAAAATTTATTTTT
13406735 AAGGAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AAAAATTTATTTTTT
Found at i:13406848 original size:118 final size:116
Alignment explanation
Indices: 13406619--13407075 Score: 612
Period size: 120 Copynumber: 3.9 Consensus size: 116
13406609 TCTTGTGCAG
* * * *
13406619 GGAAAATTGATACTTTCAACTTTTCCCTAAAGAA-ATTTTTTTTCAAATTTTAATTTCAAGGAAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAA-AATATTTTTTTTGAAATTTGATTTTCAAGGAAA
* * *
13406683 ATTGATACTTTCAACTTTTCCTCAAAAATTTATTTTTTAAAAATTTATTTTTAA
65 ATTGATACTTTCAACTTTTCCCCAAAAA--TATTTTTTGAAATTTTATTTTTAA
*
13406737 GGAAAATTGATACTTTCAACTTTTCTCCAAAAATATATTTTTTTGAAACTTTGATTTTCAAGGAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATAT-TTTTTTTGAAA-TTTGATTTTCAAGGAA
* * *
13406802 AATTGATACTTTCAAATTTTCCCCAAAGACT-CTTTTTGAAATTTTATTTTTAA
64 AATTGATACTTTCAACTTTTCCCCAAA-AATATTTTTTGAAATTTTATTTTTAA
* *
13406855 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTGGAAAATTTTGATTTTTAAAG
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTTT-G-AAA-TTTGATTTTCAAGG
* * *
13406920 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAACTTTGATTTTCAA
62 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAA-TTTTATTTTTAA
** * * *
13406976 GGAAAATTGATACTTTCAACTTTTCCCCAAAAACCTTTTTTTCGAAATTTTATTTTTAAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTGATTTTCAAGGAAAA
13407041 TTGATACTTTCAACTTTTCCCCAAAAATATTTTTT
66 TTGATACTTTCAACTTTTCCCCAAAAATATTTTTT
13407076 TTATTCTTAT
Statistics
Matches: 303, Mismatches: 27, Indels: 19
0.87 0.08 0.05
Matches are distributed among these distances:
117 52 0.17
118 94 0.31
119 16 0.05
120 97 0.32
121 44 0.15
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.44
Consensus pattern (116 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTGATTTTCAAGGAAAA
TTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAATTTTATTTTTAA
Found at i:13407158 original size:33 final size:32
Alignment explanation
Indices: 13407088--13407176 Score: 94
Period size: 33 Copynumber: 2.8 Consensus size: 32
13407078 ATTCTTATTT
* * *
13407088 AAAGAAAATAAAATAATAAAA-CAA-AATAAA
1 AAAGAAAATAAAAAAATAAAATAAAGAAAAAA
**
13407118 AGTGAAAATAAAAAAATAAAATAAAGAAAAGAA
1 AAAGAAAATAAAAAAATAAAATAAAGAAAA-AA
13407151 AAAGAAAA-ATAAAAAATAAAATAAAG
1 AAAGAAAATA-AAAAAATAAAATAAAG
13407177 GTAAAAAGAA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
30 18 0.38
31 2 0.04
32 4 0.08
33 24 0.50
ACGTcount: A:0.79, C:0.01, G:0.08, T:0.12
Consensus pattern (32 bp):
AAAGAAAATAAAAAAATAAAATAAAGAAAAAA
Found at i:13407159 original size:21 final size:22
Alignment explanation
Indices: 13407121--13407163 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
13407111 AAATAAAAGT
*
13407121 GAAAATAAAAAAATAAAATAAA
1 GAAAAGAAAAAAATAAAATAAA
*
13407143 GAAAAGAAAAAGA-AAAATAAA
1 GAAAAGAAAAAAATAAAATAAA
13407164 AAATAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.09
Consensus pattern (22 bp):
GAAAAGAAAAAAATAAAATAAA
Found at i:13407332 original size:25 final size:24
Alignment explanation
Indices: 13407282--13407351 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 24
13407272 CAAGATAAAA
*
13407282 ATAATAATAATAAT-AA-ATAAATT
1 ATAAT-ATAATAATAAATATAAACT
13407305 ATAATATAATAATAAATATATAACT
1 ATAATATAATAATAAATATA-AACT
* *
13407330 ATATAAATAA-AATACATATAAA
1 ATA-ATATAATAATAAATATAAA
13407352 TATTAACAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
22 8 0.20
23 7 0.17
24 5 0.12
25 15 0.38
26 5 0.12
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (24 bp):
ATAATATAATAATAAATATAAACT
Found at i:13407333 original size:22 final size:22
Alignment explanation
Indices: 13407276--13407458 Score: 79
Period size: 22 Copynumber: 8.4 Consensus size: 22
13407266 TTATTACAAG
13407276 ATAAA-AATAATAATAATAATAA
1 ATAAATAATAAT-ATAATAATAA
*
13407298 ATAAATTATAATATAATAATAA
1 ATAAATAATAATATAATAATAA
*
13407320 ATATATAACT-ATAT-A-AATAAA
1 ATAAATAA-TAATATAATAAT-AA
* *
13407341 ATACAT-ATAAATATTAACAGA-AA
1 ATAAATAAT-AATA-TAATA-ATAA
13407364 A-AAATAACTAA-ATAA-AGATATA
1 ATAAATAA-TAATATAATA-ATA-A
*
13407386 CATATATTAATACATAGTAATAATAA
1 -ATA-AATAATA-ATA-TAATAATAA
* *
13407412 ATAAATAATAAAATAA-AAAAA
1 ATAAATAATAATATAATAATAA
*
13407433 ATAAA-AATAA-A-AATAATAC
1 ATAAATAATAATATAATAATAA
13407452 A-AAATAA
1 ATAAATAA
13407459 GAACCGAATT
Statistics
Matches: 128, Mismatches: 11, Indels: 47
0.69 0.06 0.25
Matches are distributed among these distances:
18 5 0.04
19 8 0.06
20 12 0.09
21 24 0.19
22 34 0.27
23 16 0.12
24 11 0.09
25 9 0.07
26 2 0.02
27 6 0.05
28 1 0.01
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (22 bp):
ATAAATAATAATATAATAATAA
Found at i:13407338 original size:28 final size:26
Alignment explanation
Indices: 13407280--13407353 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
13407270 TACAAGATAA
13407280 AAATAATAATAATAATAAATAAATTAT
1 AAAT-ATAATAATAATAAATAAATTAT
* *
13407307 -AATATAATAATAAATATATAACTATAT
1 AAATATAATAAT-AATAAATAAAT-TAT
*
13407334 AAATAAAATACAT-ATAAATA
1 AAATATAATA-ATAATAAATA
13407354 TTAACAGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
25 8 0.21
26 12 0.31
27 9 0.23
28 8 0.21
29 2 0.05
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (26 bp):
AAATATAATAATAATAAATAAATTAT
Found at i:13407434 original size:21 final size:22
Alignment explanation
Indices: 13407403--13407458 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
13407393 TAATACATAG
*
13407403 TAATAATAAATAAATAAT-AAAA
1 TAATAAAAAATAAA-AATAAAAA
13407425 TAA-AAAAAATAAAAATAAAAA
1 TAATAAAAAATAAAAATAAAAA
*
13407446 TAATACAAAATAA
1 TAATAAAAAATAA
13407459 GAACCGAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 3 0.10
21 16 0.53
22 11 0.37
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (22 bp):
TAATAAAAAATAAAAATAAAAA
Found at i:13407441 original size:15 final size:15
Alignment explanation
Indices: 13407407--13407458 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
13407397 ACATAGTAAT
13407407 AATAAATAAATAAT-AA
1 AATAAA-AAA-AATAAA
13407423 AATAAAAAAAATAAA
1 AATAAAAAAAATAAA
*
13407438 AATAAAAATAATACAA
1 AATAAAAAAAATA-AA
13407454 AATAA
1 AATAA
13407459 GAACCGAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
14 3 0.09
15 17 0.52
16 13 0.39
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (15 bp):
AATAAAAAAAATAAA
Found at i:13407625 original size:1 final size:1
Alignment explanation
Indices: 13407614--13407681 Score: 55
Period size: 1 Copynumber: 68.0 Consensus size: 1
13407604 AACATTTTCA
* * * * * * * * *
13407614 TTTTTTGTTTTTTTGTGTTTTTTTTTTTGTTTTTTGTTCTTTTTTTGTTTTTTTTTGTTTTTGTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
13407679 TTT
1 TTT
13407682 GACCAAAGCT
Statistics
Matches: 49, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.00, C:0.01, G:0.12, T:0.87
Consensus pattern (1 bp):
T
Found at i:13407637 original size:11 final size:10
Alignment explanation
Indices: 13407614--13407680 Score: 91
Period size: 10 Copynumber: 6.6 Consensus size: 10
13407604 AACATTTTCA
13407614 TTTTTTGTTT
1 TTTTTTGTTT
*
13407624 TTTTGTGTTT
1 TTTTTTGTTT
*
13407634 TTTTTT-TTG
1 TTTTTTGTTT
13407643 TTTTTTGTTCT
1 TTTTTTGTT-T
13407654 TTTTTTGTTT
1 TTTTTTGTTT
13407664 TTTTTTGTTT
1 TTTTTTGTTT
13407674 TTGTTTT
1 TT-TTTT
13407681 TGACCAAAGC
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
9 8 0.16
10 29 0.58
11 13 0.26
ACGTcount: A:0.00, C:0.01, G:0.12, T:0.87
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:13407640 original size:21 final size:20
Alignment explanation
Indices: 13407614--13407682 Score: 86
Period size: 21 Copynumber: 3.4 Consensus size: 20
13407604 AACATTTTCA
13407614 TTTTTTGTTTTTTTGTGTTTT
1 TTTTTTGTTTTTTT-TGTTTT
* *
13407635 TTTTTT-TGTTTTTTGTTCT
1 TTTTTTGTTTTTTTTGTTTT
13407654 TTTTTTGTTTTTTTTTGTTTT
1 TTTTTTG-TTTTTTTTGTTTT
13407675 TGTTTTTG
1 T-TTTTTG
13407683 ACCAAAGCTC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 11 0.27
20 6 0.15
21 18 0.44
22 6 0.15
ACGTcount: A:0.00, C:0.01, G:0.13, T:0.86
Consensus pattern (20 bp):
TTTTTTGTTTTTTTTGTTTT
Found at i:13407642 original size:22 final size:21
Alignment explanation
Indices: 13407614--13407682 Score: 81
Period size: 22 Copynumber: 3.3 Consensus size: 21
13407604 AACATTTTCA
13407614 TTTTTTGTTTTTTTGTGTTTTT
1 TTTTTTGTTTTTTT-TGTTTTT
*
13407636 TTTTTTG--TTTTTTG-TTCT
1 TTTTTTGTTTTTTTTGTTTTT
13407654 TTTTTTGTTTTTTTTTGTTTTT
1 TTTTTTG-TTTTTTTTGTTTTT
*
13407676 GTTTTTG
1 TTTTTTG
13407683 ACCAAAGCTC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 10 0.25
19 2 0.05
20 5 0.12
21 7 0.17
22 16 0.40
ACGTcount: A:0.00, C:0.01, G:0.13, T:0.86
Consensus pattern (21 bp):
TTTTTTGTTTTTTTTGTTTTT
Found at i:13407783 original size:41 final size:41
Alignment explanation
Indices: 13407689--13407994 Score: 362
Period size: 42 Copynumber: 7.1 Consensus size: 41
13407679 TTTGACCAAA
* * *
13407689 GCTCCTCTAAACAGAGGCTCAACGACTTTGAGAAACATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAA-GTAAATT
* * * *
13407732 GCTTCTCTAAACAAAAGCACCATGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
13407773 GCTCCTCTAAACAGAGGCACCACGACACCACGACTTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGA-G------G-CACCACGAC-TTTGAAAAGTAAATT
*
13407823 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAATTT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATT
13407865 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATT
* *
13407907 GCTCCTTTAAACAGAGGCACCACGACTTTGAAAATTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* * *
13407948 ACTCCTCTAAACAGAGGCCCCATGACTTT-AGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAAGTAAATT
13407989 GCTCCT
1 GCTCCT
13407995 TGACAATCAT
Statistics
Matches: 232, Mismatches: 21, Indels: 22
0.84 0.08 0.08
Matches are distributed among these distances:
40 1 0.00
41 72 0.31
42 93 0.40
43 26 0.11
48 1 0.00
49 9 0.04
50 30 0.13
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
Found at i:13409413 original size:19 final size:18
Alignment explanation
Indices: 13409393--13409493 Score: 71
Period size: 19 Copynumber: 5.3 Consensus size: 18
13409383 TTTGAATCTT
*
13409393 TTTTTTTC-ATTTTCTCA
1 TTTTTTTCTTTTTTCTCA
13409410 TTTTTCCTTCTTTTTTTCTCA
1 TTTTT--TTC-TTTTTTCTCA
**
13409431 TTTTTTTCTTTTTTTTCTTT
1 TTTTTTTC--TTTTTTCTCA
*
13409451 TTTTTTTCTTTTTTTTTCA
1 TTTTTTTC-TTTTTTCTCA
*
13409470 TCATCTTTT-TTTTTTCTCA
1 T--TTTTTTCTTTTTTCTCA
13409489 TTTTT
1 TTTTT
13409494 CATCCATTGT
Statistics
Matches: 68, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
17 8 0.12
19 25 0.37
20 17 0.25
21 18 0.26
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTTTCTTTTTTCTCA
Found at i:13409442 original size:29 final size:29
Alignment explanation
Indices: 13409389--13409493 Score: 83
Period size: 29 Copynumber: 3.6 Consensus size: 29
13409379 TCAATTTGAA
* *
13409389 TCTTTTTTTTTCA-TTTTCTCATTTTTCCT
1 TCTTTTTTTCTCATTTTTTTC-TTTTTCCT
*
13409418 TCTTTTTTTCTCATTTTTTTCTTTTT-TT
1 TCTTTTTTTCTCATTTTTTTCTTTTTCCT
* **
13409446 TCTTTTTTTTTTC-TTTTTTT-TTCATCATCT
1 TC-TTTTTTTCTCATTTTTTTCTTTTTC--CT
*
13409476 TTTTTTTTTCTCATTTTT
1 TCTTTTTTTCTCATTTTT
13409494 CATCCATTGT
Statistics
Matches: 61, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
27 3 0.05
28 10 0.16
29 35 0.57
30 13 0.21
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (29 bp):
TCTTTTTTTCTCATTTTTTTCTTTTTCCT
Found at i:13409443 original size:9 final size:9
Alignment explanation
Indices: 13409417--13409466 Score: 64
Period size: 9 Copynumber: 5.2 Consensus size: 9
13409407 TCATTTTTCC
13409417 TTCTTTTTT
1 TTCTTTTTT
*
13409426 TCTCATTTTT
1 T-TCTTTTTT
13409436 TTCTTTTTT
1 TTCTTTTTT
13409445 TTCTTTTTTTT
1 TTC--TTTTTT
13409456 TTCTTTTTT
1 TTCTTTTTT
13409465 TT
1 TT
13409467 TCATCATCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
9 19 0.53
10 8 0.22
11 9 0.25
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:13409454 original size:10 final size:10
Alignment explanation
Indices: 13409410--13409468 Score: 66
Period size: 11 Copynumber: 5.7 Consensus size: 10
13409400 CATTTTCTCA
*
13409410 TTTTTCCTTCT
1 TTTTTTCTT-T
*
13409421 TTTTTTCTCAT
1 TTTTTTCT-TT
13409432 TTTTTTC-TT
1 TTTTTTCTTT
13409441 TTTTTTCTTTT
1 TTTTTTC-TTT
13409452 TTTTTTCTTT
1 TTTTTTCTTT
13409462 TTTTTTC
1 TTTTTTC
13409469 ATCATCTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
9 8 0.19
10 10 0.24
11 24 0.57
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:13409463 original size:20 final size:20
Alignment explanation
Indices: 13409402--13409493 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 20
13409392 TTTTTTTTCA
13409402 TTTTCTCATTTTTCCTTC-TTT
1 TTTTCTCATTTTT--TTCTTTT
13409423 TTTTCTCATTTTTTTCTTTT
1 TTTTCTCATTTTTTTCTTTT
**
13409443 TTTTCTTTTTTTTTTCTTTT
1 TTTTCTCATTTTTTTCTTTT
** *
13409463 TTTT-TCATCATCTT-TTTT
1 TTTTCTCATTTTTTTCTTTT
13409481 TTTTCTCATTTTT
1 TTTTCTCATTTTT
13409494 CATCCATTGT
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
18 8 0.14
19 13 0.22
20 25 0.42
21 13 0.22
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTCTCATTTTTTTCTTTT
Found at i:13409489 original size:16 final size:16
Alignment explanation
Indices: 13409459--13409493 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
13409449 TTTTTTTTTC
13409459 TTTTTTTTTCATCATCT
1 TTTTTTTTTCATCAT-T
13409476 TTTTTTTTTC-TCATT
1 TTTTTTTTTCATCATT
13409491 TTT
1 TTT
13409494 CATCCATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 4 0.22
17 10 0.56
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTTTTTCATCATT
Found at i:13409492 original size:26 final size:27
Alignment explanation
Indices: 13409446--13409497 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
13409436 TTCTTTTTTT
**
13409446 TCTTTTTTTTTTCTTTTTTTTTCATCA
1 TCTTTTTTTTTTCTTCATTTTTCATCA
13409473 TCTTTTTTTTTTC-TCATTTTTCATC
1 TCTTTTTTTTTTCTTCATTTTTCATC
13409498 CATTGTTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (27 bp):
TCTTTTTTTTTTCTTCATTTTTCATCA
Found at i:13409493 original size:11 final size:11
Alignment explanation
Indices: 13409402--13409480 Score: 60
Period size: 11 Copynumber: 7.4 Consensus size: 11
13409392 TTTTTTTTCA
13409402 TTTTCTCA-TT
1 TTTTCTCATTT
*
13409412 TTTCCTTC-TTT
1 TTTTC-TCATTT
13409423 TTTTCTCATTT
1 TTTTCTCATTT
13409434 TTTTCT--TTT
1 TTTTCTCATTT
**
13409443 TTTTCTTTTTT
1 TTTTCTCATTT
*
13409454 TTTTCT-TTTT
1 TTTTCTCATTT
13409464 TTTTCATCATCTT
1 TTTTC-TCAT-TT
13409477 TTTT
1 TTTT
13409481 TTTTCTCATT
Statistics
Matches: 58, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
9 9 0.16
10 15 0.26
11 27 0.47
12 1 0.02
13 6 0.10
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTCTCATTT
Found at i:13413443 original size:14 final size:15
Alignment explanation
Indices: 13413413--13413441 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
13413403 ACTTTTTCTC
13413413 AAAAATTTATTTTTT
1 AAAAATTTATTTTTT
13413428 AAAAATTTATTTTT
1 AAAAATTTATTTTT
13413442 AAGGAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AAAAATTTATTTTTT
Found at i:13413517 original size:61 final size:60
Alignment explanation
Indices: 13413385--13413849 Score: 565
Period size: 59 Copynumber: 7.7 Consensus size: 60
13413375 TCTTGTGCAG
* * **
13413385 GGAAAATTGATACTTTCAACTTTTTCTCAAAAATTTATTTTTTAAAAATTT-ATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTTCCCAAAAATATATTTTTTTGAAATTTGATTTTTAA
*
13413444 GGAAAATTGATACTTTCAACTTTTTCCCAAAAATATATTTTTTTGAAACTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTTCCCAAAAATATATTTTTTTGAAA-TTTGATTTTTAA
* * * *
13413505 GGAAAATTGATACTTTCAAC-TTTTCCC-CAAAGA-CTTTTTTTGAAATTTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTTCCCAAAAATATATTTTTTTGAAATTTGATTTTTAA
* *
13413562 GGAAAATTGATACTTTCAACTTTTTCTCAAAAATAT-TTTTTTTGGAAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTTCCCAAAAATATATTTTTTT-G-AAA-TTTGATTTTTAA
* ** *
13413624 GGAAAATTGATACTTTCAAC-TTTTCCTCAAGAAAAACCTTTTTTTGAAATTTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTTCC-CAA-AAATATATTTTTTTGAAATTTGATTTTTAA
*
13413685 GGAAAATTGATACTTTCTTTCAAC-TTTTCCTC-AAAA-ATA-TTTTTTGAAACTTTGATTTTCA
1 GGAAAATTGATA----CTTTCAACTTTTTCC-CAAAAATATATTTTTTTGAAA-TTTGATTTTTA
13413746 A
60 A
** *
13413747 GGAAAATTGATACTTTCAACTTTTTCCCAAAAACCT-TTTTTTTGAAATTTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTTCCCAAAAATATATTTTTTTGAAATTTGATTTTTAA
*
13413806 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATATTTTTTT
1 GGAAAATTGATACTTTCAACTTTTTCCCAAAAATATATTTTTTT
13413850 ATTTTTATTT
Statistics
Matches: 355, Mismatches: 30, Indels: 41
0.83 0.07 0.10
Matches are distributed among these distances:
57 30 0.08
58 26 0.07
59 112 0.32
60 29 0.08
61 67 0.19
62 59 0.17
63 8 0.02
64 8 0.02
65 16 0.05
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.46
Consensus pattern (60 bp):
GGAAAATTGATACTTTCAACTTTTTCCCAAAAATATATTTTTTTGAAATTTGATTTTTAA
Found at i:13413872 original size:5 final size:5
Alignment explanation
Indices: 13413864--13413948 Score: 56
Period size: 5 Copynumber: 17.6 Consensus size: 5
13413854 TTATTTAAAG
* *
13413864 AAAAT AAAAT --AAT AAAAC AAAAT AAATGT GAAAAT AAAA- AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT -AAAAT AAAAT AAAAT AAAAT
* * *
13413913 AAAGA- AAAGT AAAAC AAAA- ATAA- AAAAT AAAAT AAA
1 AAA-AT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
13413949 GGTAAAAAGA
Statistics
Matches: 63, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
3 3 0.05
4 10 0.16
5 44 0.70
6 3 0.05
7 3 0.05
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:13413898 original size:30 final size:29
Alignment explanation
Indices: 13413863--13413949 Score: 90
Period size: 31 Copynumber: 3.0 Consensus size: 29
13413853 TTTATTTAAA
*
13413863 GAAAATAAAATAATAAAACAAAATAAATGT
1 GAAAATAAAATAATAAAATAAAATAAA-GT
*
13413893 GAAAATAAAAAAAATAAAATAAAGA-AAAGT
1 GAAAAT-AAAATAATAAAATAAA-ATAAAGT
*
13413923 -AAAACAAAAATAA-AAAATAAAATAAAG
1 GAAAA-TAAAATAATAAAATAAAATAAAG
13413950 GTAAAAAGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
27 1 0.02
28 12 0.24
29 10 0.20
30 8 0.16
31 17 0.35
32 1 0.02
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (29 bp):
GAAAATAAAATAATAAAATAAAATAAAGT
Found at i:13413997 original size:13 final size:13
Alignment explanation
Indices: 13413979--13414005 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13413969 AACCTAATCT
13413979 AATAAATAAAAAA
1 AATAAATAAAAAA
13413992 AATAAATAAAAAA
1 AATAAATAAAAAA
13414005 A
1 A
13414006 TTCAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AATAAATAAAAAA
Found at i:13414878 original size:19 final size:21
Alignment explanation
Indices: 13414835--13414933 Score: 69
Period size: 23 Copynumber: 4.6 Consensus size: 21
13414825 CAGAAAAAAT
*
13414835 AATAATAATAATAATAATCAGATA
1 AATAA-AA-AATAA-AATAAGATA
*
13414859 AATGAAAAA-AAAAT-AGATA
1 AATAAAAAATAAAATAAGATA
*
13414878 ATTAAAAAATAAAATAAGATA
1 AATAAAAAATAAAATAAGATA
** *
13414899 AATCCAAAAAATATTACAAGATA
1 AAT--AAAAAATAAAATAAGATA
13414922 AA-AAAATAATAA
1 AATAAAA-AATAA
13414934 TAAATAAATT
Statistics
Matches: 62, Mismatches: 8, Indels: 13
0.75 0.10 0.16
Matches are distributed among these distances:
19 12 0.19
20 12 0.19
21 13 0.21
22 2 0.03
23 19 0.31
24 4 0.06
ACGTcount: A:0.69, C:0.04, G:0.05, T:0.22
Consensus pattern (21 bp):
AATAAAAAATAAAATAAGATA
Found at i:13414907 original size:21 final size:19
Alignment explanation
Indices: 13414830--13414901 Score: 60
Period size: 19 Copynumber: 3.7 Consensus size: 19
13414820 AGCCCCAGAA
*
13414830 AAAATA-AT-AATAATAAT
1 AAAATAGATAAATAAAAAT
13414847 AATAATCAGATAAATGAAAAA-
1 AA-AAT-AGATAAAT-AAAAAT
*
13414868 AAAATAGATAATTAAAAAAT
1 AAAATAGATAAAT-AAAAAT
13414888 AAAATAAGATAAAT
1 AAAAT-AGATAAAT
13414902 CCAAAAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
17 2 0.05
18 3 0.07
19 13 0.30
20 10 0.23
21 12 0.27
22 4 0.09
ACGTcount: A:0.69, C:0.01, G:0.06, T:0.24
Consensus pattern (19 bp):
AAAATAGATAAATAAAAAT
Found at i:13414909 original size:40 final size:38
Alignment explanation
Indices: 13414828--13414942 Score: 94
Period size: 41 Copynumber: 2.9 Consensus size: 38
13414818 ACAGCCCCAG
* * *
13414828 AAAAAATAATAATAATAATAATAATCAGATAAATGAAA
1 AAAAAATAATAATAAAAATAATAATAAGATAAATCAAA
13414866 AAAAAATAGATAATTAAAAAATAA-AATAAGATAAATCCAAA
1 AAAAAATA-ATAA-T-AAAAATAATAATAAGATAAAT-CAAA
13414907 AAATATTACA-AGATAA-AAAAATAATAATAA-ATAAAT
1 AAA-A--A-ATA-ATAATAAAAATAATAATAAGATAAAT
13414943 TATAATATAA
Statistics
Matches: 65, Mismatches: 3, Indels: 15
0.78 0.04 0.18
Matches are distributed among these distances:
38 8 0.12
39 4 0.06
40 12 0.18
41 27 0.42
42 6 0.09
44 7 0.11
45 1 0.02
ACGTcount: A:0.70, C:0.03, G:0.04, T:0.23
Consensus pattern (38 bp):
AAAAAATAATAATAAAAATAATAATAAGATAAATCAAA
Found at i:13414940 original size:18 final size:18
Alignment explanation
Indices: 13414828--13414961 Score: 62
Period size: 18 Copynumber: 7.0 Consensus size: 18
13414818 ACAGCCCCAG
13414828 AAAAAATAATAAT-AATA
1 AAAAAATAATAATAAATA
* *
13414845 ATAATAATCAGATAAATGAA-A
1 A-AAAAAT-A-AT-AATAAATA
13414866 AAAAAATAGATAATTAAA-A
1 AAAAAATA-ATAA-TAAATA
* *
13414885 AATAAAATAA-GATAAATCC
1 AA-AAAATAATAATAAAT-A
* *
13414904 AAAAAATATTACA-AGATA
1 AAAAAATAATA-ATAAATA
13414922 AAAAAATAATAATAAATA
1 AAAAAATAATAATAAATA
13414940 AATTATAATATAATAATAAATA
1 AA--A-AA-ATAATAATAAATA
13414962 TATAACTATA
Statistics
Matches: 90, Mismatches: 11, Indels: 27
0.70 0.09 0.21
Matches are distributed among these distances:
17 6 0.07
18 30 0.33
19 17 0.19
20 15 0.17
21 7 0.08
22 15 0.17
ACGTcount: A:0.69, C:0.03, G:0.04, T:0.25
Consensus pattern (18 bp):
AAAAAATAATAATAAATA
Found at i:13414947 original size:11 final size:12
Alignment explanation
Indices: 13414927--13414963 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
13414917 AGATAAAAAA
13414927 ATAATAATAAAT
1 ATAATAATAAAT
*
13414939 A-AATTAT-AAT
1 ATAATAATAAAT
13414949 ATAATAATAAAT
1 ATAATAATAAAT
13414961 ATA
1 ATA
13414964 TAACTATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
10 4 0.19
11 10 0.48
12 7 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAATAATAAAT
Found at i:13414954 original size:19 final size:21
Alignment explanation
Indices: 13414930--13414979 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
13414920 TAAAAAAATA
13414930 ATAATAAATAAAT-TATAA-T
1 ATAATAAATAAATATATAACT
13414949 ATAAT-AATAAATATATAACT
1 ATAATAAATAAATATATAACT
13414969 AT-ATAAATAAA
1 ATAATAAATAAA
13414980 ATACATATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.25
19 12 0.43
20 9 0.32
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
ATAATAAATAAATATATAACT
Found at i:13414971 original size:25 final size:25
Alignment explanation
Indices: 13414925--13414990 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
13414915 CAAGATAAAA
13414925 AAATAATAAT-AA-ATAAA-T-TAT
1 AAATAATAATAAATATAAACTATAT
13414946 AATATAATAATAAATATATAACTATAT
1 AA-ATAATAATAAATATA-AACTATAT
*
13414973 AAATAA-AATACATATAAA
1 AAATAATAATAAATATAAA
13414991 TATTAACAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
21 2 0.05
22 8 0.21
23 2 0.05
24 5 0.13
25 11 0.29
26 5 0.13
27 5 0.13
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (25 bp):
AAATAATAATAAATATAAACTATAT
Found at i:13414972 original size:22 final size:22
Alignment explanation
Indices: 13414927--13414974 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
13414917 AGATAAAAAA
*
13414927 ATAATAATAAATAAATTATAAT
1 ATAATAATAAATAAATAATAAT
*
13414949 ATAATAATAAATATATAACT-AT
1 ATAATAATAAATAAATAA-TAAT
13414971 ATAA
1 ATAA
13414975 ATAAAATACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
ATAATAATAAATAAATAATAAT
Found at i:13415432 original size:20 final size:22
Alignment explanation
Indices: 13415403--13415444 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
13415393 GAAGGGCAGC
*
13415403 TTCTGTAAAAA-A-AAAAAAAA
1 TTCTGCAAAAACACAAAAAAAA
13415423 TTCTGCAAAAACACAAAAAAAA
1 TTCTGCAAAAACACAAAAAAAA
13415445 AACAACAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.67, C:0.12, G:0.05, T:0.17
Consensus pattern (22 bp):
TTCTGCAAAAACACAAAAAAAA
Found at i:13416045 original size:32 final size:32
Alignment explanation
Indices: 13415957--13416049 Score: 132
Period size: 32 Copynumber: 2.9 Consensus size: 32
13415947 CGGTCTGACT
*
13415957 AGACCGAACCGAACCGCCGGACCAAACCAACC
1 AGACCGAACCGAACCGCCGGACCGAACCAACC
* *
13415989 AGATCGAACTGAACCGCCGGACCGAACCAACC
1 AGACCGAACCGAACCGCCGGACCGAACCAACC
* * *
13416021 AGACCGAACCGAATCGTCGAACCGAACCA
1 AGACCGAACCGAACCGCCGGACCGAACCA
13416050 GGAGTTGACC
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.37, C:0.39, G:0.20, T:0.04
Consensus pattern (32 bp):
AGACCGAACCGAACCGCCGGACCGAACCAACC
Found at i:13416497 original size:19 final size:18
Alignment explanation
Indices: 13416457--13416500 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
13416447 TTTTAAAAAA
* *
13416457 TAATAAATAAAAATTGAT
1 TAATAAATAAAAATTAAC
*
13416475 TAATAAATTAAAATATAAC
1 TAATAAATAAAAAT-TAAC
13416494 TAATAAA
1 TAATAAA
13416501 AAATAAGAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (18 bp):
TAATAAATAAAAATTAAC
Found at i:13416599 original size:209 final size:210
Alignment explanation
Indices: 13416297--13416844 Score: 881
Period size: 209 Copynumber: 2.6 Consensus size: 210
13416287 AAAAAAATGA
*
13416297 AAGAA-AAAGGAAATTTTTATCCGACGATGAGATTCAAAGGTATTCCGAGTAGTGATGCCTACGA
1 AAGAAGAAAGGAAATTTTTATCCGATGATGAGATTCAAAGGTATTCCGAGTAGTGATGCCTACGA
13416361 AATCTCTAGGTGAGAAGATTTTTTTAAAATACTACCAGCGTATTGGAGTATTTATAAAAAATTTT
66 AATCTCTAGGTGAGAAGATTTTTTTAAAATACTACCAGCGTATTGGAGTATTTATAAAAAATTTT
* *
13416426 CAATACAGTAAAGATTTT-TTTTTT-TAAAAAATAATAAATAAAAATTGATTAATAAATTAAAAT
131 CAATACAGTAAAGATTTTCTTTTTTAAAAAAAATAATAAATAAAAATTGATTAATAAATTAAAAA
13416489 ATAACTAATAAAAAAT
196 ATAACTAAT-AAAAAT
*
13416505 AAG-AGAAGAGGAAATTTTTATCCGATGATGAGATACAAAGGTATTCCGAGTAGTGATGCCTACG
1 AAGAAGAA-AGGAAATTTTTATCCGATGATGAGATTCAAAGGTATTCCGAGTAGTGATGCCTACG
13416569 AAATCTCTAGGTGAGAAGATTTTTTTAAAATACTACCAGCGTATTGGAGTATTTATAAAAAATTT
65 AAATCTCTAGGTGAGAAGATTTTTTTAAAATACTACCAGCGTATTGGAGTATTTATAAAAAATTT
13416634 TCAATACAGTAAAGATTTTCTTTTTTAAAAAAAATAATAAATAAAAATTGATTAATAAATTAAAA
130 TCAATACAGTAAAGATTTTCTTTTTTAAAAAAAATAATAAATAAAAATTGATTAATAAATTAAAA
*
13416699 AATAAGTAATAAAAAT
195 AATAACTAATAAAAAT
* * * * * *
13416715 AGGAAGAAAAGAAA-TTTAATCCGATGATGAGATTCAAAGGTATTCCGAGTAGAGATGCTTTAAG
1 AAGAAGAAAGGAAATTTTTATCCGATGATGAGATTCAAAGGTATTCCGAGTAGTGATGC-CTACG
* * *
13416779 AAATCTCTAGGTGAGAAGATTTTTTTTGTAAAATATTACCAGCGTATTGGAATATTTATAGAAAA
65 AAATCTCTAGGTGAGAAGA--TTTTTT-TAAAATACTACCAGCGTATTGGAGTATTTATAAAAAA
13416844 T
127 T
13416845 CTCCAATATA
Statistics
Matches: 316, Mismatches: 15, Indels: 13
0.92 0.04 0.04
Matches are distributed among these distances:
207 1 0.00
208 5 0.02
209 179 0.57
210 41 0.13
211 49 0.16
212 6 0.02
213 35 0.11
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (210 bp):
AAGAAGAAAGGAAATTTTTATCCGATGATGAGATTCAAAGGTATTCCGAGTAGTGATGCCTACGA
AATCTCTAGGTGAGAAGATTTTTTTAAAATACTACCAGCGTATTGGAGTATTTATAAAAAATTTT
CAATACAGTAAAGATTTTCTTTTTTAAAAAAAATAATAAATAAAAATTGATTAATAAATTAAAAA
ATAACTAATAAAAAT
Found at i:13416913 original size:12 final size:12
Alignment explanation
Indices: 13416891--13416919 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
13416881 CAATTAAGAT
13416891 TAAAA-AATTAA
1 TAAAATAATTAA
13416902 TAAAATAATTAA
1 TAAAATAATTAA
13416914 TAAAAT
1 TAAAAT
13416920 TTTTGAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
TAAAATAATTAA
Found at i:13417332 original size:195 final size:196
Alignment explanation
Indices: 13416974--13417359 Score: 738
Period size: 195 Copynumber: 2.0 Consensus size: 196
13416964 GCATGGCATG
*
13416974 CATGACATAATTTCTTATGAAAAGTAAATTTAGACCTCCAAAGATGAGATTCTAAAAGTATTCCG
1 CATGACATAATTTCTTACGAAAAGTAAATTTAGACCTCCAAAGATGAGATTCTAAAAGTATTCCG
13417039 AGTAGAGATGCTTTAAAAAAATCTCTAGGTGAGAAAGAGTTCTTTTAATATTACCAACGTACTGG
66 AGTAGAGATGCTTTAAAAAAATCTCTAGGTGAGAAAGAGTTCTTTTAATATTACCAACGTACTGG
13417104 AACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAATTTTTTTAA
131 AACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAATTTTTTTAA
13417169 A
196 A
13417170 CATGACATAATTTCTTACGAAAAGTAAATTTAGACCTCCAAAGATGAGATTCTAAAAGTATTCCG
1 CATGACATAATTTCTTACGAAAAGTAAATTTAGACCTCCAAAGATGAGATTCTAAAAGTATTCCG
* *
13417235 AGTAGAGATGCTTT-AAGAAATCTCTAGGTGAGAAAGAGTTCTTTTAATGTTACCAACGTACTGG
66 AGTAGAGATGCTTTAAAAAAATCTCTAGGTGAGAAAGAGTTCTTTTAATATTACCAACGTACTGG
13417299 AACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAATTTTT
131 AACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAATTTTT
13417360 AATAAATAAA
Statistics
Matches: 187, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
195 109 0.58
196 78 0.42
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.36
Consensus pattern (196 bp):
CATGACATAATTTCTTACGAAAAGTAAATTTAGACCTCCAAAGATGAGATTCTAAAAGTATTCCG
AGTAGAGATGCTTTAAAAAAATCTCTAGGTGAGAAAGAGTTCTTTTAATATTACCAACGTACTGG
AACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAATTTTTTTAA
A
Found at i:13417726 original size:20 final size:22
Alignment explanation
Indices: 13417701--13417748 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
13417691 CAGTAATAAT
13417701 AAATAAATAAT-AAAATAA-A-A
1 AAATAAA-AATAAAAATAATACA
13417721 AAATAAAAATAAAAATAATACA
1 AAATAAAAATAAAAATAATACA
13417743 AAATAA
1 AAATAA
13417749 GAATCGAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.12
20 14 0.56
21 1 0.04
22 7 0.28
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (22 bp):
AAATAAAAATAAAAATAATACA
Found at i:13418317 original size:3 final size:3
Alignment explanation
Indices: 13418311--13418350 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
13418301 TCGTCGTTGC
* **
13418311 CAT CAT CAT CAT CAT CAT CAT CAT CGT CAT TGT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
13418351 TTCTTCTCCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.28, C:0.33, G:0.05, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:13419685 original size:21 final size:21
Alignment explanation
Indices: 13419661--13419727 Score: 93
Period size: 21 Copynumber: 3.2 Consensus size: 21
13419651 ATATTTATCA
13419661 TATTTATTAAAATATAAATAT
1 TATTTATTAAAATATAAATAT
13419682 TATTTATTAATAA-AT-AATAAT
1 TATTTATTAA-AATATAAAT-AT
*
13419703 TATTTATTAAAATGTAAATAT
1 TATTTATTAAAATATAAATAT
13419724 TATT
1 TATT
13419728 ATGTATTATA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
20 5 0.12
21 31 0.76
22 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (21 bp):
TATTTATTAAAATATAAATAT
Found at i:13419721 original size:42 final size:43
Alignment explanation
Indices: 13419636--13419727 Score: 141
Period size: 42 Copynumber: 2.1 Consensus size: 43
13419626 ATTATTTATA
* *
13419636 ATTATTTATTAATAAATATTTATCATATTTATTAAAATATAAAT
1 ATTATTTATTAATAAATAATAAT-ATATTTATTAAAATATAAAT
*
13419680 ATTATTTATTAATAAATAATAAT-TATTTATTAAAATGTAAAT
1 ATTATTTATTAATAAATAATAATATATTTATTAAAATATAAAT
13419722 ATTATT
1 ATTATT
13419728 ATGTATTATA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
42 24 0.53
44 21 0.47
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (43 bp):
ATTATTTATTAATAAATAATAATATATTTATTAAAATATAAAT
Found at i:13419728 original size:24 final size:23
Alignment explanation
Indices: 13419636--13419741 Score: 68
Period size: 21 Copynumber: 4.7 Consensus size: 23
13419626 ATTATTTATA
13419636 ATTATTTATT--AA-TAAATATTT
1 ATTATTTATTAAAATTAAATA-TT
13419657 ATCATATTTATTAAAA-TATAA-A-T
1 AT--TATTTATTAAAATTA-AATATT
*
13419680 ATTATTTATT--AA-TAAATAATA
1 ATTATTTATTAAAATTAAAT-ATT
13419701 ATTATTTATTAAAATGTAAATATT
1 ATTATTTATTAAAAT-TAAATATT
* *
13419725 ATTATGTATTATAATTA
1 ATTATTTATTAAAATTA
13419742 TTATATATTA
Statistics
Matches: 69, Mismatches: 4, Indels: 22
0.73 0.04 0.23
Matches are distributed among these distances:
18 2 0.03
19 4 0.06
20 1 0.01
21 20 0.29
23 15 0.22
24 15 0.22
25 10 0.14
26 2 0.03
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (23 bp):
ATTATTTATTAAAATTAAATATT
Done.