Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, 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: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 98 of 105
Found at i:17665619 original size:22 final size:22
Alignment explanation
Indices: 17665507--17665625 Score: 89
Period size: 22 Copynumber: 5.5 Consensus size: 22
17665497 AACAAATTAG
*
17665507 TAGTAAATCAATT-ATAAATTAA
1 TAGTAAATC-ATTGATAACTTAA
* * * *
17665529 AAGTAAATAATTGATAATTTAG
1 TAGTAAATCATTGATAACTTAA
* * *
17665551 TAGTTAACCATTGAAAACTTAA
1 TAGTAAATCATTGATAACTTAA
* * * *
17665573 AAGAAAATCAAT-ATAACTTAG
1 TAGTAAATCATTGATAACTTAA
*
17665594 TAGTAAATCATTGATAACATAA
1 TAGTAAATCATTGATAACTTAA
*
17665616 TAGTTAATCA
1 TAGTAAATCA
17665626 AGTTATCAAT
Statistics
Matches: 71, Mismatches: 24, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
21 19 0.27
22 52 0.73
ACGTcount: A:0.50, C:0.08, G:0.09, T:0.33
Consensus pattern (22 bp):
TAGTAAATCATTGATAACTTAA
Found at i:17665625 original size:43 final size:45
Alignment explanation
Indices: 17665503--17665626 Score: 123
Period size: 43 Copynumber: 2.8 Consensus size: 45
17665493 TATAAACAAA
*
17665503 TTAGTAGTAAATCAATT-ATAA-ATTAAAAGTAAAT-AATTGATAAT
1 TTAGTAGTAAATC-ATTGATAACA-TAAAAGTAAATCAATTGATAAC
* * * * *
17665547 TTAGTAGTTAACCATTGAAAACTTAAAAGAAAATCAA-T-ATAAC
1 TTAGTAGTAAATCATTGATAACATAAAAGTAAATCAATTGATAAC
* *
17665590 TTAGTAGTAAATCATTGATAACATAATAGTTAATCAA
1 TTAGTAGTAAATCATTGATAACATAAAAGTAAATCAA
17665627 GTTATCAATG
Statistics
Matches: 64, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
43 37 0.58
44 25 0.39
45 2 0.03
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (45 bp):
TTAGTAGTAAATCATTGATAACATAAAAGTAAATCAATTGATAAC
Found at i:17665656 original size:52 final size:50
Alignment explanation
Indices: 17665579--17665677 Score: 128
Period size: 52 Copynumber: 1.9 Consensus size: 50
17665569 TTAAAAGAAA
* *
17665579 ATCAATATAACTTAGTAGTAAATCATTG-ATAACATAATAGTTAATCAAGTT
1 ATCAATACAACTTAATAGTAAATCA-TGCATAACATAATA-TTAATCAAGTT
**
17665630 ATCAATGACAACTTAATAGTAAATCATGCATAATTTAATATTAATCAA
1 ATCAAT-ACAACTTAATAGTAAATCATGCATAACATAATATTAATCAA
17665678 TAATAATTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
51 16 0.38
52 26 0.62
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.34
Consensus pattern (50 bp):
ATCAATACAACTTAATAGTAAATCATGCATAACATAATATTAATCAAGTT
Found at i:17665667 original size:22 final size:21
Alignment explanation
Indices: 17665642--17665909 Score: 87
Period size: 22 Copynumber: 12.4 Consensus size: 21
17665632 CAATGACAAC
17665642 TTAATAGTAAATCATGCATAAT
1 TTAATAGTAAATCATG-ATAAT
* *
17665664 TTAATA-TTAATCAATAATAAT
1 TTAATAGTAAATC-ATGATAAT
* *
17665685 TTGATAGTGAATCATAGATAAT
1 TTAATAGTAAATCAT-GATAAT
*
17665707 TTAAT-GATAAATTGATGATAAT
1 TTAATAG-TAAA-TCATGATAAT
** * * * * *
17665729 TTTGTAATAAATAATTAAAAA
1 TTAATAGTAAATCATGATAAT
* * *
17665750 TTAAGTAGCAAATTAATGATAAC
1 TTAA-TAGTAAA-TCATGATAAT
* * * *
17665773 ATAATACTAAATACATAAAAAT
1 TTAATAGTAAAT-CATGATAAT
*
17665795 ATAATA-TAAAATCATTGATAAT
1 TTAATAGT-AAATCA-TGATAAT
* * *
17665817 TTAGTAGTAAAT--TAATAAC
1 TTAATAGTAAATCATGATAAT
* * *
17665836 TTAGTAGTAAATCATTAATAAC
1 TTAATAGTAAATCA-TGATAAT
* * *
17665858 GTAGTAGTAAATCATTAATAAT
1 TTAATAGTAAATCA-TGATAAT
* * *
17665880 TTAGTTGTAAACCAATGATAAT
1 TTAATAGTAAATC-ATGATAAT
*
17665902 TTAGTAGT
1 TTAATAGT
17665910 TAATTAGTTA
Statistics
Matches: 188, Mismatches: 42, Indels: 32
0.72 0.16 0.12
Matches are distributed among these distances:
19 17 0.09
21 30 0.16
22 126 0.67
23 15 0.08
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.37
Consensus pattern (21 bp):
TTAATAGTAAATCATGATAAT
Found at i:17665678 original size:43 final size:43
Alignment explanation
Indices: 17665630--17665711 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
17665620 TAATCAAGTT
*
17665630 ATCAATGACAACTTAATAGTAAATCAT-GCATAATTTAATATTA
1 ATCAATAACAACTTAATAGTAAATCATAG-ATAATTTAATATTA
* * * *
17665673 ATCAATAATAATTTGATAGTGAATCATAGATAATTTAAT
1 ATCAATAACAACTTAATAGTAAATCATAGATAATTTAAT
17665712 GATAAATTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
43 32 0.97
44 1 0.03
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (43 bp):
ATCAATAACAACTTAATAGTAAATCATAGATAATTTAATATTA
Found at i:17665884 original size:44 final size:44
Alignment explanation
Indices: 17665803--17666117 Score: 219
Period size: 44 Copynumber: 7.0 Consensus size: 44
17665793 ATATAATATA
* *
17665803 AAATCATTGATAATTTAGTAGT-AA--ATTAATAACTTAGTAGT
1 AAATCATTAATAATTTAGTAGTAAATCATTAATAATTTAGTAGT
** *
17665844 AAATCATTAATAACGTAGTAGTAAATCATTAATAATTTAGTTGT
1 AAATCATTAATAATTTAGTAGTAAATCATTAATAATTTAGTAGT
* * * * *
17665888 AAACCAATGATAATTTAGTAGTTAATTAGTTAATTACTGATAACTTT-TTAGT
1 AAATCATTAATAATTTAGTAG-TAA--A--TCATTA---ATAA-TTTAGTAGT
* * * * *
17665940 AAATTATTGATAAATTAGTAGTAAATAGATT-ATAACTTTA-TAAT
1 AAATCATTAATAATTTAGTAGTAAAT-CATTAATAA-TTTAGTAGT
* * ** * *
17665984 AAATAATCAATAATTTAGTAGTAAATCGCTAATAATTTAATGGT
1 AAATCATTAATAATTTAGTAGTAAATCATTAATAATTTAGTAGT
* * * * * *
17666028 AAATCATTCATAACTTAGTTGCAAATCATTCATAAATTAGTAGT
1 AAATCATTAATAATTTAGTAGTAAATCATTAATAATTTAGTAGT
* * *
17666072 AAATCATTAATAATTTAGTAATAAATCATTTATAACTTAGTAGT
1 AAATCATTAATAATTTAGTAGTAAATCATTAATAATTTAGTAGT
17666116 AA
1 AA
17666118 GTAACTGATA
Statistics
Matches: 211, Mismatches: 47, Indels: 29
0.74 0.16 0.10
Matches are distributed among these distances:
41 19 0.09
42 2 0.01
43 5 0.02
44 141 0.67
45 3 0.01
47 2 0.01
48 3 0.01
49 6 0.03
51 3 0.01
52 24 0.11
53 3 0.01
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (44 bp):
AAATCATTAATAATTTAGTAGTAAATCATTAATAATTTAGTAGT
Found at i:17665961 original size:22 final size:22
Alignment explanation
Indices: 17665936--17666117 Score: 152
Period size: 22 Copynumber: 8.3 Consensus size: 22
17665926 GATAACTTTT
* * *
17665936 TAGTAAATTATTGATAAATTAG
1 TAGTAAATCATTAATAATTTAG
*
17665958 TAGTAAATAGATT-ATAACTTTA-
1 TAGTAAAT-CATTAATAA-TTTAG
* * *
17665980 TAATAAATAATCAATAATTTAG
1 TAGTAAATCATTAATAATTTAG
** *
17666002 TAGTAAATCGCTAATAATTTAA
1 TAGTAAATCATTAATAATTTAG
* * *
17666024 TGGTAAATCATTCATAACTTAG
1 TAGTAAATCATTAATAATTTAG
* * * *
17666046 TTGCAAATCATTCATAAATTAG
1 TAGTAAATCATTAATAATTTAG
17666068 TAGTAAATCATTAATAATTTAG
1 TAGTAAATCATTAATAATTTAG
* * *
17666090 TAATAAATCATTTATAACTTAG
1 TAGTAAATCATTAATAATTTAG
17666112 TAGTAA
1 TAGTAA
17666118 GTAACTGATA
Statistics
Matches: 128, Mismatches: 28, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
21 6 0.05
22 116 0.91
23 6 0.05
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.38
Consensus pattern (22 bp):
TAGTAAATCATTAATAATTTAG
Found at i:17666471 original size:22 final size:22
Alignment explanation
Indices: 17666446--17666487 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
17666436 AGTTAATAAT
*
17666446 TGATGACTTAATAACAAATTAA
1 TGATAACTTAATAACAAATTAA
* *
17666468 TGATAATTTAATAATAAATT
1 TGATAACTTAATAACAAATT
17666488 GGTTATAATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (22 bp):
TGATAACTTAATAACAAATTAA
Found at i:17666495 original size:22 final size:22
Alignment explanation
Indices: 17666453--17666527 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 22
17666443 AATTGATGAC
* * *
17666453 TTAATAACAAATTAATGATAAT
1 TTAATAATAAATTAGTTATAAT
*
17666475 TTAATAATAAATTGGTTATAAT
1 TTAATAATAAATTAGTTATAAT
* * *
17666497 GTAATAGTGAATTAGTT-TCAAT
1 TTAATAATAAATTAGTTAT-AAT
17666519 TTAATAATA
1 TTAATAATA
17666528 GTTAATTGAT
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
21 1 0.02
22 40 0.98
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (22 bp):
TTAATAATAAATTAGTTATAAT
Found at i:17666658 original size:22 final size:22
Alignment explanation
Indices: 17666632--17666682 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 22
17666622 TATAATTTAG
17666632 TAATAGTTAATC-ATCAATAACT
1 TAATAGTTAATCGAT-AATAACT
17666654 TAATAGTTAATCGATAATAACT
1 TAATAGTTAATCGATAATAACT
17666676 TAATAGT
1 TAATAGT
17666683 AAATTATGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 26 0.93
23 2 0.07
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (22 bp):
TAATAGTTAATCGATAATAACT
Found at i:17666695 original size:22 final size:21
Alignment explanation
Indices: 17666648--17666862 Score: 103
Period size: 22 Copynumber: 9.9 Consensus size: 21
17666638 TTAATCATCA
* * *
17666648 ATAACTTAATAGTTAATCGATA
1 ATAACTTAATAGTAAAT-TATG
17666670 ATAACTTAATAGTAAATTATGG
1 ATAACTTAATAGTAAATTAT-G
* * *
17666692 ATAATTTAATA-TAAATTGGTT
1 ATAACTTAATAGTAAATT-ATG
* * *
17666713 ATAACTTGATAATGAATTATG
1 ATAACTTAATAGTAAATTATG
* * * *
17666734 GTTACTTTAGTAATAAATCTATG
1 ATAAC-TTAATAGTAAAT-TATG
* *
17666757 ATAACTT--TAGTAAATAATAA
1 ATAACTTAATAGTAAATTAT-G
* * *
17666777 AAAAATTAAGTAGTAAATCAATG
1 ATAACTTAA-TAGTAAAT-TATG
* *
17666800 ATAACATAATAGTAAATTACTA
1 ATAACTTAATAGTAAATTA-TG
* * *
17666822 ATAACTTAGTTGTAAATCAATG
1 ATAACTTAATAGTAAAT-TATG
*
17666844 ATAAATTAATAGTAAATTA
1 ATAACTTAATAGTAAATTA
17666863 ATTAATCATT
Statistics
Matches: 143, Mismatches: 38, Indels: 25
0.69 0.18 0.12
Matches are distributed among these distances:
19 2 0.01
20 12 0.08
21 23 0.16
22 81 0.57
23 22 0.15
24 3 0.02
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (21 bp):
ATAACTTAATAGTAAATTATG
Found at i:17666859 original size:11 final size:11
Alignment explanation
Indices: 17666779--17666864 Score: 52
Period size: 11 Copynumber: 7.7 Consensus size: 11
17666769 AATAATAAAA
17666779 AAATTAAGTAGT
1 AAATTAA-TAGT
*
17666791 AAATCAAT-GAT
1 AAATTAATAG-T
17666802 AACA-TAATAGT
1 AA-ATTAATAGT
* *
17666813 AAATTACTAAT
1 AAATTAATAGT
* * *
17666824 AACTTAGTTGT
1 AAATTAATAGT
*
17666835 AAATCAAT-GAT
1 AAATTAATAG-T
17666846 AAATTAATAGT
1 AAATTAATAGT
17666857 AAATTAAT
1 AAATTAAT
17666865 TAATCATTGA
Statistics
Matches: 56, Mismatches: 12, Indels: 13
0.69 0.15 0.16
Matches are distributed among these distances:
10 3 0.05
11 44 0.79
12 9 0.16
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (11 bp):
AAATTAATAGT
Found at i:17666870 original size:30 final size:30
Alignment explanation
Indices: 17666836--17666892 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
17666826 CTTAGTTGTA
17666836 AATCAATGATAAATTAATAGTAAATTAATT
1 AATCAATGATAAATTAATAGTAAATTAATT
* * **
17666866 AATCATTGATAACTTTGTAGTAAATTA
1 AATCAATGATAAATTAATAGTAAATTA
17666893 TCGATAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.39
Consensus pattern (30 bp):
AATCAATGATAAATTAATAGTAAATTAATT
Found at i:17667042 original size:44 final size:44
Alignment explanation
Indices: 17666967--17667143 Score: 119
Period size: 44 Copynumber: 4.0 Consensus size: 44
17666957 CATCAACAAT
* * *
17666967 TTAGTAG-AAATCACT-TATAAATTAGTGATAAATTATTCATAAA
1 TTAGTAGTAAATCAATGT-TAAATTAGTAATAAATTATTAATAAA
* * *
17667010 TTAGTAGTAAATCAATGTTAATTTAGTAATAAATCATTAATAAT
1 TTAGTAGTAAATCAATGTTAAATTAGTAATAAATTATTAATAAA
* * * * * * *
17667054 TTAGCT-GTATATTATTGATGACTTAGTAATAAATTATTGAT-AA
1 TTAG-TAGTAAATCAATGTTAAATTAGTAATAAATTATTAATAAA
* ** * * * *
17667097 TATAATAGTAAATCAATAATAACTTAATTATCAATTATTAATAAA
1 T-TAGTAGTAAATCAATGTTAAATTAGTAATAAATTATTAATAAA
17667142 TT
1 TT
17667144 TTTTATATTT
Statistics
Matches: 103, Mismatches: 25, Indels: 11
0.74 0.18 0.08
Matches are distributed among these distances:
43 10 0.10
44 88 0.85
45 5 0.05
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (44 bp):
TTAGTAGTAAATCAATGTTAAATTAGTAATAAATTATTAATAAA
Found at i:17667053 original size:22 final size:22
Alignment explanation
Indices: 17666908--17667057 Score: 92
Period size: 22 Copynumber: 6.9 Consensus size: 22
17666898 AAATTAATAG
17666908 TAAATCAATT-ATAACTTTA-TAA
1 TAAATC-ATTAATAA-TTTAGTAA
* * * * *
17666930 CAAATTATTAGTAATTTAATAG
1 TAAATCATTAATAATTTAGTAA
* *
17666952 TAAATCATCAACAATTTAGT-A
1 TAAATCATTAATAATTTAGTAA
* * *
17666973 GAAATCACTT-ATAAATTAGTGA
1 TAAATCA-TTAATAATTTAGTAA
* * * *
17666995 TAAATTATTCATAAATTAGTAG
1 TAAATCATTAATAATTTAGTAA
* **
17667017 TAAATCAATGTTAATTTAGTAA
1 TAAATCATTAATAATTTAGTAA
17667039 TAAATCATTAATAATTTAG
1 TAAATCATTAATAATTTAG
17667058 CTGTATATTA
Statistics
Matches: 95, Mismatches: 28, Indels: 10
0.71 0.21 0.08
Matches are distributed among these distances:
21 23 0.24
22 72 0.76
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.39
Consensus pattern (22 bp):
TAAATCATTAATAATTTAGTAA
Found at i:17667477 original size:42 final size:42
Alignment explanation
Indices: 17667422--17667559 Score: 147
Period size: 42 Copynumber: 3.3 Consensus size: 42
17667412 TAGTTACCAA
*
17667422 AAAATTA-CTAAAATTATATCAAAAGATTACTAAAATTTTGTC
1 AAAATTATC-AAAATTATATCAAAAGATTACTAAAATTTTATC
* * *
17667464 AAAATTATCAAAATTGTAT-AAATGATTACCAAAATTTTATC
1 AAAATTATCAAAATTATATCAAAAGATTACTAAAATTTTATC
** * * *
17667505 AATGGTTATCAAAATTATATCATAAG-TTACTAAAAATATATC
1 AA-AATTATCAAAATTATATCAAAAGATTACTAAAATTTTATC
*
17667547 AAAATTACCAAAA
1 AAAATTATCAAAA
17667560 ATGAATCGAA
Statistics
Matches: 78, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
41 29 0.37
42 45 0.58
43 4 0.05
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.34
Consensus pattern (42 bp):
AAAATTATCAAAATTATATCAAAAGATTACTAAAATTTTATC
Found at i:17667560 original size:21 final size:20
Alignment explanation
Indices: 17667531--17667580 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
17667521 ATATCATAAG
*
17667531 TTACTAAAAAT-ATATCAAAA
1 TTACCAAAAATGA-ATCAAAA
* *
17667551 TTACCAAAAATGAATCGAAG
1 TTACCAAAAATGAATCAAAA
17667571 TTACCAAAAA
1 TTACCAAAAA
17667581 ATTTTCAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.56, C:0.14, G:0.06, T:0.24
Consensus pattern (20 bp):
TTACCAAAAATGAATCAAAA
Found at i:17667561 original size:20 final size:20
Alignment explanation
Indices: 17667422--17667559 Score: 98
Period size: 21 Copynumber: 6.7 Consensus size: 20
17667412 TAGTTACCAA
*
17667422 AAAATTACTAAAATTATATC
1 AAAATTACCAAAATTATATC
* * *
17667442 AAAAGATTACTAAAATTTTGTC
1 -AAA-ATTACCAAAATTATATC
* *
17667464 AAAATTATCAAAATTGTAT-
1 AAAATTACCAAAATTATATC
*
17667483 AAATGATTACCAAAATTTTATC
1 AAA--ATTACCAAAATTATATC
** *
17667505 AATGGTTATCAAAATTATATC
1 AA-AATTACCAAAATTATATC
* * *
17667526 ATAAGTTACTAAAAATATATC
1 A-AAATTACCAAAATTATATC
17667547 AAAATTACCAAAA
1 AAAATTACCAAAA
17667560 ATGAATCGAA
Statistics
Matches: 93, Mismatches: 18, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
19 3 0.03
20 22 0.24
21 50 0.54
22 18 0.19
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.34
Consensus pattern (20 bp):
AAAATTACCAAAATTATATC
Found at i:17667574 original size:20 final size:20
Alignment explanation
Indices: 17667489--17667580 Score: 78
Period size: 21 Copynumber: 4.5 Consensus size: 20
17667479 GTATAAATGA
* * *
17667489 TTACCAAAATTTTATCAATGG
1 TTACCAAAAATATATCAA-AG
* *
17667510 TTATCAAAATTATATCATAAG
1 TTACCAAAAATATATCA-AAG
* *
17667531 TTACTAAAAATATATCAAAA
1 TTACCAAAAATATATCAAAG
*
17667551 TTACCAAAAATGA-ATCGAAG
1 TTACCAAAAAT-ATATCAAAG
17667571 TTACCAAAAA
1 TTACCAAAAA
17667581 ATTTTCAAAG
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
20 27 0.46
21 31 0.53
22 1 0.02
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (20 bp):
TTACCAAAAATATATCAAAG
Found at i:17673856 original size:11 final size:11
Alignment explanation
Indices: 17673836--17673869 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
17673826 AAGAAGAAGG
17673836 AAAA-AGAAAA
1 AAAATAGAAAA
17673846 AAAATAGAAAA
1 AAAATAGAAAA
17673857 AAAATA-AAAA
1 AAAATAGAAAA
17673867 AAA
1 AAA
17673870 TAAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 11 0.48
11 12 0.52
ACGTcount: A:0.88, C:0.00, G:0.06, T:0.06
Consensus pattern (11 bp):
AAAATAGAAAA
Found at i:17673865 original size:9 final size:9
Alignment explanation
Indices: 17673836--17673905 Score: 59
Period size: 9 Copynumber: 7.4 Consensus size: 9
17673826 AAGAAGAAGG
*
17673836 AAAAAGAAA
1 AAAAATAAA
17673845 AAAAATAGAAA
1 AAAAAT--AAA
17673856 AAAAATAAA
1 AAAAATAAA
17673865 AAAAATAAA
1 AAAAATAAA
* *
17673874 TAATAATAAT
1 -AAAAATAAA
* *
17673884 AATAATAAT
1 AAAAATAAA
*
17673893 AACAATAAA
1 AAAAATAAA
17673902 AAAA
1 AAAA
17673906 TGATGTTTAC
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
9 36 0.69
10 7 0.13
11 9 0.17
ACGTcount: A:0.80, C:0.01, G:0.03, T:0.16
Consensus pattern (9 bp):
AAAAATAAA
Found at i:17674266 original size:49 final size:48
Alignment explanation
Indices: 17674079--17674399 Score: 237
Period size: 49 Copynumber: 6.8 Consensus size: 48
17674069 TCATATGAGC
* * * * * **
17674079 AGAGACTCAACAACTTTAAAA--TTCTCTTGAAAAAGCTCCTCCCAAC
1 AGAGGCTCAACAACTTTAAAATCTTATCTTGAAAAAACTCATCTCAGT
* * * * * *
17674125 AGAGGCTTAACAACTTTTAAATTCTCATCTTG-GAAAA-GC-T-T-AAT
1 AGAGGCTCAACAAC-TTTAAAATCTTATCTTGAAAAAACTCATCTCAGT
* * * *
17674169 AGAGGTTCAACAACTTTAAAAAAATCTTATCTTGGAAAAGCTCCTCTCAGT
1 AGAGGCTCAACAACTTT---AAAATCTTATCTTGAAAAAACTCATCTCAGT
* * *
17674220 AGAGGCTCAATAACTTTAAGAATCTCATCTTGAAAAAACTTATCTCAGT
1 AGAGGCTCAACAACTTTAA-AATCTTATCTTGAAAAAACTCATCTCAGT
* * * * *
17674269 AGAGACTCAACAACTTTAAACT-TTATCTTGAAAAAGCTTATCTCAGC
1 AGAGGCTCAACAACTTTAAAATCTTATCTTGAAAAAACTCATCTCAGT
* * * * *
17674316 ATAGGCTTAACAACTTTAAGAATCTCATCTTGAAAAAACTCCTCTCAGC
1 AGAGGCTCAACAACTTTAA-AATCTTATCTTGAAAAAACTCATCTCAGT
* *
17674365 AGAGGCTTAACAACTTTAAACT-TTATCTTGAAAAA
1 AGAGGCTCAACAACTTTAAAATCTTATCTTGAAAAA
17674400 TTGATTTTTC
Statistics
Matches: 219, Mismatches: 42, Indels: 27
0.76 0.15 0.09
Matches are distributed among these distances:
43 3 0.01
44 14 0.06
46 25 0.11
47 60 0.27
48 12 0.05
49 87 0.40
50 1 0.00
51 17 0.08
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.30
Consensus pattern (48 bp):
AGAGGCTCAACAACTTTAAAATCTTATCTTGAAAAAACTCATCTCAGT
Found at i:17674322 original size:96 final size:96
Alignment explanation
Indices: 17674079--17674399 Score: 350
Period size: 96 Copynumber: 3.4 Consensus size: 96
17674069 TCATATGAGC
* * * *
17674079 AGAGACTCAACAACTTTAAA-ATTCTCTTGAAAAAGCTCCTCCCAACAGAGGCTTAACAACTTTT
1 AGAGACTCAACAACTTTAAACTTTATCTTGAAAAAGCTCCTCTCAGCAGAGGCTTAACAAC-TTT
* * *
17674143 AA-ATTCTCATCTTGGAAAAGCTTA----A-T
65 AAGAATCTCATCTTGAAAAAACTTATCTCAGT
** * * * * *
17674169 AGAGGTTCAACAACTTTAAAAAAATCTTATCTTGGAAAAGCTCCTCTCAGTAGAGGCTCAATAAC
1 AGAGACTCAACAACTTT---AAACT-TTATCTTGAAAAAGCTCCTCTCAGCAGAGGCTTAACAAC
17674234 TTTAAGAATCTCATCTTGAAAAAACTTATCTCAGT
62 TTTAAGAATCTCATCTTGAAAAAACTTATCTCAGT
** *
17674269 AGAGACTCAACAACTTTAAACTTTATCTTGAAAAAGCTTATCTCAGCATAGGCTTAACAACTTTA
1 AGAGACTCAACAACTTTAAACTTTATCTTGAAAAAGCTCCTCTCAGCAGAGGCTTAACAACTTTA
** *
17674334 AGAATCTCATCTTGAAAAAACTCCTCTCAGC
66 AGAATCTCATCTTGAAAAAACTTATCTCAGT
* *
17674365 AGAGGCTTAACAACTTTAAACTTTATCTTGAAAAA
1 AGAGACTCAACAACTTTAAACTTTATCTTGAAAAA
17674400 TTGATTTTTC
Statistics
Matches: 192, Mismatches: 28, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
90 15 0.08
93 3 0.02
94 5 0.03
95 51 0.27
96 97 0.51
97 4 0.02
99 1 0.01
100 16 0.08
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.30
Consensus pattern (96 bp):
AGAGACTCAACAACTTTAAACTTTATCTTGAAAAAGCTCCTCTCAGCAGAGGCTTAACAACTTTA
AGAATCTCATCTTGAAAAAACTTATCTCAGT
Found at i:17687653 original size:11 final size:11
Alignment explanation
Indices: 17687637--17687682 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
17687627 AAGGAAGAAG
17687637 AAAAAGAAAAA
1 AAAAAGAAAAA
*
17687648 AAAAAGAAGAA
1 AAAAAGAAAAA
*
17687659 AGAAAG--AAA
1 AAAAAGAAAAA
17687668 AAAAAGAAAAA
1 AAAAAGAAAAA
17687679 AAAA
1 AAAA
17687683 TAATAACAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
9 7 0.24
11 22 0.76
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:17687656 original size:20 final size:19
Alignment explanation
Indices: 17687631--17687682 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
17687621 CTGGATAAGG
17687631 AAGAAGAAAAAGAAAAAAAA
1 AAGAAGAAAAA-AAAAAAAA
*
17687651 AAGAAGAAAGAAAGAAAAAA
1 AAGAAGAAA-AAAAAAAAAA
17687671 AAGAA-AAAAAAA
1 AAGAAGAAAAAAA
17687683 TAATAACAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 3 0.10
19 3 0.10
20 21 0.72
21 2 0.07
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (19 bp):
AAGAAGAAAAAAAAAAAAA
Found at i:17687668 original size:17 final size:18
Alignment explanation
Indices: 17687634--17687682 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
17687624 GATAAGGAAG
17687634 AAGAA-AAAGAAAAAAAA
1 AAGAAGAAAGAAAAAAAA
*
17687651 AAGAAGAAAGAAAGAAAA
1 AAGAAGAAAGAAAAAAAA
17687669 AA-AAGAAA-AAAAAA
1 AAGAAGAAAGAAAAAA
17687683 TAATAACAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 5 0.17
17 11 0.38
18 13 0.45
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (18 bp):
AAGAAGAAAGAAAAAAAA
Found at i:17688261 original size:123 final size:120
Alignment explanation
Indices: 17687995--17688351 Score: 378
Period size: 123 Copynumber: 2.9 Consensus size: 120
17687985 AAATATAAAT
* * * *
17687995 AGATTATTTAAAGTGTTTTTGAACCAAAAATACCTTAAATAATCTCTAATATTTTTTTAAAAGTG
1 AGATTATTTAAGGTATTTTTG-ATCAAAAATACCTTAAATAATCTCTAATA-TTTTTT-AAAGGG
* * * * * *
17688060 ATTA-TTTA-ATATATTTTTAGCAAAAACACTTTAAATAATACTCTTTAATTTTTTGAAGG
63 ATTATTTTAGGT-TTTTTTTATCAAAAATACCTTAAATAAT-CTC-TTAATTTTTTAAAGG
* * * *
17688119 ATATTATTTAAGGTATTTTTGATTAAAAATACCTTAAATAATTTTTAATATTTTTTAAAGGGATT
1 AGATTATTTAAGGTATTTTTGATCAAAAATACCTTAAATAATCTCTAATATTTTTTAAAGGGATT
*
17688184 ATTTTAGGTTTTTTTTATTAAAAATACCTTAAATAATCTC-TAATTTTTTTAAAGG
66 ATTTTAGGTTTTTTTTATCAAAAATACCTTAAATAATCTCTTAA-TTTTTTAAAGG
* * * *
17688239 AGATTATTTAAGACTTTTTTTTTTATCAAAAATACTTTAAATAATCTCTAATATTTTTTAAAGGA
1 AGATTATTTAAG---GTATTTTTGATCAAAAATACCTTAAATAATCTCTAATATTTTTTAAAGG-
* * * * *
17688304 GATTATTTAAGGTTTTTTTTGTCAAAAATATCTTGAATAATCTTTTAA
62 GATTATTTTAGGTTTTTTTTATCAAAAATACCTTAAATAATCTCTTAA
17688352 AAAATATTAA
Statistics
Matches: 196, Mismatches: 29, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
119 3 0.02
120 21 0.11
121 12 0.06
122 33 0.17
123 68 0.35
124 56 0.29
125 3 0.02
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (120 bp):
AGATTATTTAAGGTATTTTTGATCAAAAATACCTTAAATAATCTCTAATATTTTTTAAAGGGATT
ATTTTAGGTTTTTTTTATCAAAAATACCTTAAATAATCTCTTAATTTTTTAAAGG
Found at i:17688320 original size:63 final size:61
Alignment explanation
Indices: 17687995--17688346 Score: 372
Period size: 61 Copynumber: 5.7 Consensus size: 61
17687985 AAATATAAAT
* ** * *
17687995 AGATTATTTAAAGTGTTTTTGAACCAAAAATACCTTAAATAATCTCTAATATTTTTTTAAAAG
1 AGATTATTTAAGGT-TTTTTTTATCAAAAATACCTTAAATAATCTCTAATA-TTTTTTAAAGG
* * * * * * *
17688058 TGATTATTTAA--TATATTTTTAGCAAAAACACTTTAAATAATACTCT-TTAATTTTTTGAAGG
1 AGATTATTTAAGGT-TTTTTTTATCAAAAATACCTTAAATAAT-CTCTAAT-ATTTTTTAAAGG
* * * * * *
17688119 ATATTATTTAAGGTATTTTTGATTAAAAATACCTTAAATAATTTTTAATATTTTTTAAAGG
1 AGATTATTTAAGGTTTTTTTTATCAAAAATACCTTAAATAATCTCTAATATTTTTTAAAGG
* *
17688180 -GATTATTTTAGGTTTTTTTTATTAAAAATACCTTAAATAATCTCTAAT-TTTTTTAAAGG
1 AGATTATTTAAGGTTTTTTTTATCAAAAATACCTTAAATAATCTCTAATATTTTTTAAAGG
* *
17688239 AGATTATTTAAGACTTTTTTTTTTATCAAAAATACTTTAAATAATCTCTAATATTTTTTAAAGG
1 AGATTATTTAAG---GTTTTTTTTATCAAAAATACCTTAAATAATCTCTAATATTTTTTAAAGG
* * *
17688303 AGATTATTTAAGGTTTTTTTTGTCAAAAATATCTTGAATAATCT
1 AGATTATTTAAGGTTTTTTTTATCAAAAATACCTTAAATAATCT
17688347 TTTAAAAAAT
Statistics
Matches: 240, Mismatches: 39, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
59 11 0.05
60 52 0.22
61 82 0.34
62 27 0.11
63 45 0.19
64 23 0.10
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (61 bp):
AGATTATTTAAGGTTTTTTTTATCAAAAATACCTTAAATAATCTCTAATATTTTTTAAAGG
Found at i:17695152 original size:125 final size:125
Alignment explanation
Indices: 17694930--17695179 Score: 437
Period size: 125 Copynumber: 2.0 Consensus size: 125
17694920 AATATTTAGG
*
17694930 ATGAATGGTAATTACAAATATTTCTTTTACTGGTTTGACGCAGGAATTTCTTGCTTTGCCAAGGG
1 ATGAATGGTAATTACAAATATTTATTTTACTGGTTTGACGCAGGAATTTCTTGCTTTGCCAAGGG
*
17694995 CTGATGCAATTCATCTCCTTGCACAATACAATGGAAATGCTGAGACAGTAATCCAGCAAA
66 CTGATGCAATCCATCTCCTTGCACAATACAATGGAAATGCTGAGACAGTAATCCAGCAAA
* *
17695055 ATGAATGGTAATTACAAATATTTATTTTGCTGGTTTGACGCAGGAATTTCTTGCTTTGCCGAGGG
1 ATGAATGGTAATTACAAATATTTATTTTACTGGTTTGACGCAGGAATTTCTTGCTTTGCCAAGGG
* * *
17695120 CTGATGCAATCCATCTTCTTGCATAATACAATGGAAATGTTGAGACAGTAATCCAGCAAA
66 CTGATGCAATCCATCTCCTTGCACAATACAATGGAAATGCTGAGACAGTAATCCAGCAAA
17695180 TATTTTCAAA
Statistics
Matches: 118, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
125 118 1.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (125 bp):
ATGAATGGTAATTACAAATATTTATTTTACTGGTTTGACGCAGGAATTTCTTGCTTTGCCAAGGG
CTGATGCAATCCATCTCCTTGCACAATACAATGGAAATGCTGAGACAGTAATCCAGCAAA
Found at i:17698280 original size:21 final size:22
Alignment explanation
Indices: 17698243--17698286 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
17698233 CGTGTTTGGT
*
17698243 AGAACAGAAAAATAAAAA-AAA
1 AGAAAAGAAAAATAAAAAGAAA
17698264 AGAAAAGAAAAGA-AAAAAGAAA
1 AGAAAAGAAAA-ATAAAAAGAAA
17698286 A
1 A
17698287 AATTATTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.82, C:0.02, G:0.14, T:0.02
Consensus pattern (22 bp):
AGAAAAGAAAAATAAAAAGAAA
Found at i:17701848 original size:2 final size:2
Alignment explanation
Indices: 17701836--17701865 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
17701826 TGAAACCTTA
*
17701836 AT AT AT GT 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
17701866 TAAATATGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17711004 original size:2 final size:2
Alignment explanation
Indices: 17710991--17711033 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
17710981 CCACCCCCAG
* *
17710991 GA GA GT GA GA GA GA GG GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
17711033 G
1 G
17711034 TCAAACCTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.44, C:0.00, G:0.53, T:0.02
Consensus pattern (2 bp):
GA
Found at i:17714818 original size:273 final size:273
Alignment explanation
Indices: 17714331--17714872 Score: 985
Period size: 273 Copynumber: 2.0 Consensus size: 273
17714321 AAGCAGCCGC
17714331 AATCTTTGAAGGGAAGATTCCCATGGAATCTTGTATCCTCACCGTTTACTTGCAAAGATTCCTCG
1 AATCTTTGAAGGGAAGATTCCCATGGAATCTTGTATCCTCACCGTTTACTTGCAAAGATTCCTCG
* *
17714396 CAAAGAAATCAATAATAAATGTTATCATACGTTCTTAACCACTTTTGTCCTATGGTATGGGGCAT
66 CAAAGAAATCAATAATAAATGATATCATACGTCCTTAACCACTTTTGTCCTATGGTATGGGGCAT
* *
17714461 CTGACAAGTTGTCAGAAGCCAAAAAATGGAATCCCCAGGCCGGTGCCCCAACCTGCCAGTGTTAC
131 CTGACAAATTGTCAGAAGACAAAAAATGGAATCCCCAGGCCGGTGCCCCAACCTGCCAGTGTTAC
*
17714526 AAAACCTTTAATAATCGGTCAAAAACTTTTCCATGTGCGATCATTTTGGGCTTTTAGCAGTAAGT
196 AAAACCTTTAATAATCGGTCAAAAACTTTTCCATGTGCGATCATTTTAGGCTTTTAGCAGTAAGT
17714591 ACACTTTAAAGGG
261 ACACTTTAAAGGG
* * *
17714604 AATCTTTGAAGGGAGGATTCCCATGGAATCTTTTATCCTCACCGTTTATTTGCAAAGATTCCTCG
1 AATCTTTGAAGGGAAGATTCCCATGGAATCTTGTATCCTCACCGTTTACTTGCAAAGATTCCTCG
* *
17714669 CAAAGAAATCAATAATAAATGATATCGTACGTCCTTAAGCACTTTTGTCCTATGGTATGGGGCAT
66 CAAAGAAATCAATAATAAATGATATCATACGTCCTTAACCACTTTTGTCCTATGGTATGGGGCAT
17714734 CTGACAAATTGTCAGAAGACAAAAAATGGAATCCCCAGGCCGGTGCCCCAACCTGCCAGTGTTAC
131 CTGACAAATTGTCAGAAGACAAAAAATGGAATCCCCAGGCCGGTGCCCCAACCTGCCAGTGTTAC
*
17714799 AAAACCTTTAATAATCGGTCAAAAACTTTTGCATGTGCGATCATTTTAGGCTTTTAGCAGTAAGT
196 AAAACCTTTAATAATCGGTCAAAAACTTTTCCATGTGCGATCATTTTAGGCTTTTAGCAGTAAGT
17714864 ACACTTTAA
261 ACACTTTAA
17714873 CAACTGTGGT
Statistics
Matches: 258, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
273 258 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (273 bp):
AATCTTTGAAGGGAAGATTCCCATGGAATCTTGTATCCTCACCGTTTACTTGCAAAGATTCCTCG
CAAAGAAATCAATAATAAATGATATCATACGTCCTTAACCACTTTTGTCCTATGGTATGGGGCAT
CTGACAAATTGTCAGAAGACAAAAAATGGAATCCCCAGGCCGGTGCCCCAACCTGCCAGTGTTAC
AAAACCTTTAATAATCGGTCAAAAACTTTTCCATGTGCGATCATTTTAGGCTTTTAGCAGTAAGT
ACACTTTAAAGGG
Found at i:17715617 original size:33 final size:33
Alignment explanation
Indices: 17715552--17715617 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
17715542 ATGAATGCAT
* *
17715552 TAGGTTCTTCCTTGATACTTGAGACTTGAAAAA
1 TAGGTTCTTCCTTGATACTTGAGACATAAAAAA
*
17715585 TAGGTTCTTCCTTGATATTTGAGACATAAAAAA
1 TAGGTTCTTCCTTGATACTTGAGACATAAAAAA
17715618 ATGCCTGGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (33 bp):
TAGGTTCTTCCTTGATACTTGAGACATAAAAAA
Found at i:17716227 original size:100 final size:102
Alignment explanation
Indices: 17716054--17716250 Score: 283
Period size: 100 Copynumber: 2.0 Consensus size: 102
17716044 CACCAAAAAA
* **
17716054 TATAAGGGTGATTTTGCACTATATCACTCTTTAAATGTTAAGGAGAGACGAAAAGGAAATTAAAT
1 TATAAGGGTGATTTTGCACTATATCACTCTTTAAAAGTTAAAAAGAGACGAAAAGGAAATTAAAT
*
17716119 ACATAATGAA-A-TTGCATGGCCCACGCAAAGCACTG
66 AAATAATGAACAGTTGCATGGCCCACGCAAAGCACTG
* * **
17716154 TATAAGGGTGATTTTGCAGC-ATATCATTCTTTAAAAGTTAAAAAGAGACGTAAAGGGGATTAAA
1 TATAAGGGTGATTTTGCA-CTATATCACTCTTTAAAAGTTAAAAAGAGACGAAAAGGAAATTAAA
*
17716218 TAAATAATGAACAGTTGCATGGCCCATGCAAAG
65 TAAATAATGAACAGTTGCATGGCCCACGCAAAG
17716251 TACTATTGTG
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
100 65 0.76
101 2 0.02
102 18 0.21
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (102 bp):
TATAAGGGTGATTTTGCACTATATCACTCTTTAAAAGTTAAAAAGAGACGAAAAGGAAATTAAAT
AAATAATGAACAGTTGCATGGCCCACGCAAAGCACTG
Found at i:17718659 original size:50 final size:50
Alignment explanation
Indices: 17718602--17718705 Score: 190
Period size: 50 Copynumber: 2.1 Consensus size: 50
17718592 AATATCACAT
* *
17718602 ATTATAAGTAATTGCACAAAATTAATTTATTTAAATCTCGAATTTAAGTA
1 ATTATAAGTAATTGCACAAAATTAATTTAGTCAAATCTCGAATTTAAGTA
17718652 ATTATAAGTAATTGCACAAAATTAATTTAGTCAAATCTCGAATTTAAGTA
1 ATTATAAGTAATTGCACAAAATTAATTTAGTCAAATCTCGAATTTAAGTA
17718702 ATTA
1 ATTA
17718706 ACCACTTTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (50 bp):
ATTATAAGTAATTGCACAAAATTAATTTAGTCAAATCTCGAATTTAAGTA
Found at i:17722632 original size:17 final size:17
Alignment explanation
Indices: 17722596--17722633 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
17722586 CTGGTTTCAG
*
17722596 TTTTCAATATTATTTTC
1 TTTTCAATATTATTTCC
17722613 TTTTCAATAATT-TTTCC
1 TTTTCAAT-ATTATTTCC
17722630 TTTT
1 TTTT
17722634 TTGATCGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.21, C:0.13, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTCAATATTATTTCC
Found at i:17723580 original size:52 final size:52
Alignment explanation
Indices: 17723494--17723650 Score: 199
Period size: 52 Copynumber: 3.0 Consensus size: 52
17723484 TATAACCATA
* * * * *
17723494 CAAACTTGCCCATTAAAAAT-TTCTCTCCTCTTAGAATTCTTCTCTTATAAGT
1 CAAACTTACCTATTAAAAATCTTAT-TTCTCTTAGAATTCTTCTCTTACAAGT
* * * * *
17723546 CAAACTTGCCTATTAAGAATCTTTTTTCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTACCTATTAAAAATCTTATTTCTCTTAGAATTCTTCTCTTACAAGT
*
17723598 CAAACTTACCTATTAAAAATCTTATTTCTCTTAGAATTCTTCTTTTACAAGT
1 CAAACTTACCTATTAAAAATCTTATTTCTCTTAGAATTCTTCTCTTACAAGT
17723650 C
1 C
17723651 TTCTTGTCTA
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
52 88 0.97
53 3 0.03
ACGTcount: A:0.29, C:0.22, G:0.06, T:0.43
Consensus pattern (52 bp):
CAAACTTACCTATTAAAAATCTTATTTCTCTTAGAATTCTTCTCTTACAAGT
Found at i:17723693 original size:11 final size:11
Alignment explanation
Indices: 17723675--17723713 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
17723665 GCAATATCTG
17723675 ACAAATCTCAA
1 ACAAATCTCAA
* *
17723686 ATAAATCTCTA
1 ACAAATCTCAA
17723697 ACAAATCTCAA
1 ACAAATCTCAA
17723708 ACAAAT
1 ACAAAT
17723714 ATCTTATGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:17724012 original size:24 final size:24
Alignment explanation
Indices: 17723979--17724057 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 24
17723969 AACCTTTAGT
17723979 TCTTTCCACATCTCGAACTTTCAAC
1 TCTTT-CACATCTCGAACTTTCAAC
* * **
17724004 TCTTTCACATATCGAACCTTCGGC
1 TCTTTCACATCTCGAACTTTCAAC
* *
17724028 TCTTTTCATATCTTGAA-TCTTCAAC
1 TC-TTTCACATCTCGAACT-TTCAAC
17724053 TCTTT
1 TCTTT
17724058 TCATGTTTCG
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
24 20 0.48
25 22 0.52
ACGTcount: A:0.22, C:0.30, G:0.06, T:0.42
Consensus pattern (24 bp):
TCTTTCACATCTCGAACTTTCAAC
Found at i:17724032 original size:49 final size:50
Alignment explanation
Indices: 17723969--17724080 Score: 120
Period size: 49 Copynumber: 2.3 Consensus size: 50
17723959 CCACATCTTA
* *
17723969 AACCTTTAGTTCTTTCCACATCTCGAA-CTTTCAACTC-TTTCACATATCG
1 AACCTTCAGCTCTTTCCACATCTCGAATC-TTCAACTCTTTTCACATATCG
* * * * ** *
17724018 AACCTTCGGCTCTTTTCATATCTTGAATCTTCAACTCTTTTCATGTTTCG
1 AACCTTCAGCTCTTTCCACATCTCGAATCTTCAACTCTTTTCACATATCG
17724068 AACCTTCAGCTCT
1 AACCTTCAGCTCT
17724081 GATACCACTT
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
49 29 0.57
50 22 0.43
ACGTcount: A:0.21, C:0.29, G:0.08, T:0.41
Consensus pattern (50 bp):
AACCTTCAGCTCTTTCCACATCTCGAATCTTCAACTCTTTTCACATATCG
Found at i:17724074 original size:25 final size:25
Alignment explanation
Indices: 17723991--17724080 Score: 85
Period size: 25 Copynumber: 3.6 Consensus size: 25
17723981 TTTCCACATC
* * *
17723991 TCGAACTTTCAACTC-TTTCACATA
1 TCGAACCTTCAACTCTTTTCATATT
**
17724015 TCGAACCTTCGGCTCTTTTCATATCT
1 TCGAACCTTCAACTCTTTTCATAT-T
* *
17724041 T-GAATCTTCAACTCTTTTCATGTT
1 TCGAACCTTCAACTCTTTTCATATT
*
17724065 TCGAACCTTCAGCTCT
1 TCGAACCTTCAACTCT
17724081 GATACCACTT
Statistics
Matches: 52, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
24 14 0.27
25 37 0.71
26 1 0.02
ACGTcount: A:0.21, C:0.29, G:0.09, T:0.41
Consensus pattern (25 bp):
TCGAACCTTCAACTCTTTTCATATT
Found at i:17724602 original size:68 final size:69
Alignment explanation
Indices: 17724481--17724618 Score: 201
Period size: 68 Copynumber: 2.0 Consensus size: 69
17724471 CCTATGTGGA
*
17724481 CCCTCTAAGTCTCTTCTAGTCCACTCACAAACAAACATGCACACCTATAAGACGTAGAG-CCTCA
1 CCCTCTAAGTCTCTTCTAGTCCACTCACAAACAAACATACACACCTATAAGACGTAGAGCCCT-A
17724545 ATACT
65 ATACT
* * *
17724550 CCCTCTCAGTCTCTTCTAGT-CACTTACAAACAAACATATACA-CTCATAAGACGTAGAGCCCTA
1 CCCTCTAAGTCTCTTCTAGTCCACTCACAAACAAACATACACACCT-ATAAGACGTAGAGCCCTA
17724613 ATACT
65 ATACT
17724618 C
1 C
17724619 TTATGAGGTG
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
67 2 0.03
68 39 0.62
69 22 0.35
ACGTcount: A:0.33, C:0.33, G:0.09, T:0.25
Consensus pattern (69 bp):
CCCTCTAAGTCTCTTCTAGTCCACTCACAAACAAACATACACACCTATAAGACGTAGAGCCCTAA
TACT
Found at i:17724804 original size:52 final size:52
Alignment explanation
Indices: 17724713--17724869 Score: 199
Period size: 52 Copynumber: 3.0 Consensus size: 52
17724703 TATAACCATA
* * *
17724713 CAAACTTACCCATTAAGAATC-TCTCTCCTCTTAAAATTCTTCTCTTGTAAGT
1 CAAACTTACCTATTAAGAATCATCT-TTCTCTTAGAATTCTTCTCTTGTAAGT
* * * * *
17724765 CAAATTTATCTATTAAGAATCATTTTTCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTACCTATTAAGAATCATCTTTCTCTTAGAATTCTTCTCTTGTAAGT
* * *
17724817 CAAACTTACCTATTAAGAATCCTCTTTCTCTTAGAATTCTTTTTTTGTAAGT
1 CAAACTTACCTATTAAGAATCATCTTTCTCTTAGAATTCTTCTCTTGTAAGT
17724869 C
1 C
17724870 TTCTTGTCTA
Statistics
Matches: 88, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
52 86 0.98
53 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.07, T:0.44
Consensus pattern (52 bp):
CAAACTTACCTATTAAGAATCATCTTTCTCTTAGAATTCTTCTCTTGTAAGT
Found at i:17724910 original size:11 final size:11
Alignment explanation
Indices: 17724894--17724935 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
17724884 GTAATATTTG
17724894 ACAAATCTCAA
1 ACAAATCTCAA
**
17724905 ACAAATCTTTA
1 ACAAATCTCAA
17724916 ACAAATCTCAA
1 ACAAATCTCAA
17724927 ACAAATCTC
1 ACAAATCTC
17724936 TTATAGTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:17727956 original size:39 final size:38
Alignment explanation
Indices: 17727891--17727966 Score: 91
Period size: 39 Copynumber: 2.0 Consensus size: 38
17727881 TTTGTATAAA
17727891 TTTTTTAAAAATAAAATTTGTAAATTTGAACTTTAAAAC
1 TTTTTTAAAAATAAAATTTGTAAATTTGAA-TTTAAAAC
* * * *
17727930 TTTTTTAAAAA-ATATTTTTTACAATTTTAATTTAAAA
1 TTTTTTAAAAATAAAATTTGTA-AATTTGAATTTAAAA
17727967 AATAATAGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
38 14 0.44
39 18 0.56
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.49
Consensus pattern (38 bp):
TTTTTTAAAAATAAAATTTGTAAATTTGAATTTAAAAC
Found at i:17734296 original size:19 final size:20
Alignment explanation
Indices: 17734260--17734307 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
17734250 TGCAACAAAA
17734260 AATTTTAATTTATTAATTTT
1 AATTTTAATTTATTAATTTT
* *
17734280 GATTTTGATTT-TTAATTTT
1 AATTTTAATTTATTAATTTT
17734299 AA-TTTAATT
1 AATTTTAATT
17734308 GTTTCTACTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 6 0.25
19 9 0.38
20 9 0.38
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (20 bp):
AATTTTAATTTATTAATTTT
Found at i:17749299 original size:30 final size:30
Alignment explanation
Indices: 17749263--17749324 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
17749253 TAAGTCCCTA
17749263 AGCCTTTGATCTAGTGGCTAAAGGCGTTTG
1 AGCCTTTGATCTAGTGGCTAAAGGCGTTTG
*
17749293 AGCCTTTGGTCTAGTGGCTAAAGGCGTTTG
1 AGCCTTTGATCTAGTGGCTAAAGGCGTTTG
17749323 AG
1 AG
17749325 GGGACATCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.19, C:0.16, G:0.32, T:0.32
Consensus pattern (30 bp):
AGCCTTTGATCTAGTGGCTAAAGGCGTTTG
Found at i:17749812 original size:2 final size:2
Alignment explanation
Indices: 17749805--17749833 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17749795 CAAATAAAAG
17749805 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 A
17749834 AAGCTTTTCC
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17752036 original size:26 final size:26
Alignment explanation
Indices: 17752006--17752077 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 26
17751996 ATTTTATATA
*
17752006 TTATTAATGAATAAAATGATATCATT
1 TTATTAATGAATAAAATGATATCACT
17752032 TTATTAATGAAGTGAATCAAATGATATCACT
1 TTATTAATGAA-T--A--AAATGATATCACT
*
17752063 TTATTAATAAATAAA
1 TTATTAATGAATAAA
17752078 TTTTTTAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
26 13 0.33
27 1 0.03
28 1 0.03
29 1 0.03
30 1 0.03
31 22 0.56
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (26 bp):
TTATTAATGAATAAAATGATATCACT
Found at i:17752576 original size:2 final size:2
Alignment explanation
Indices: 17752569--17752597 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17752559 TCTGTTTGAG
17752569 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 A
17752598 GAGAGAGAGA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17752602 original size:2 final size:2
Alignment explanation
Indices: 17752597--17752635 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
17752587 ATATATATAT
17752597 AG AG AG AG AG 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 AG AG AG AG AG A
17752636 AAGTCCTAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17761203 original size:38 final size:39
Alignment explanation
Indices: 17761116--17761207 Score: 134
Period size: 38 Copynumber: 2.4 Consensus size: 39
17761106 GATTGGATGG
*
17761116 GGTGGGGAGGGATTGGGTGTGGTGAGGCATTAGGGGGAA
1 GGTGGGGAGGGATTGAGTGTGGTGAGGCATTAGGGGGAA
*
17761155 GGTGGGGAGGGATTGAGTGTGGTG-GG-ATGTTGGGGGAA
1 GGTGGGGAGGGATTGAGTGTGGTGAGGCAT-TAGGGGGAA
*
17761193 GGTGGAGAGGGATTG
1 GGTGGGGAGGGATTG
17761208 GATAGAGGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
37 2 0.04
38 24 0.49
39 23 0.47
ACGTcount: A:0.17, C:0.01, G:0.60, T:0.22
Consensus pattern (39 bp):
GGTGGGGAGGGATTGAGTGTGGTGAGGCATTAGGGGGAA
Found at i:17761759 original size:26 final size:26
Alignment explanation
Indices: 17761731--17761779 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
17761721 TAAAAAATAA
*
17761731 AAAATATAGGTTTGAAAA-TTTTATT
1 AAAATATAAGTTTGAAAACTTTTATT
17761756 AAAATATAAGTTTGAAAACTTTTA
1 AAAATATAAGTTTGAAAACTTTTA
17761780 ATTTTTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (26 bp):
AAAATATAAGTTTGAAAACTTTTATT
Found at i:17763152 original size:13 final size:15
Alignment explanation
Indices: 17763117--17763146 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
17763107 AAAATCATCG
17763117 TAAATCATCATTATCA
1 TAAATCATCATTAT-A
17763133 TAAATCATCATTAT
1 TAAATCATCATTAT
17763147 TAATCAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAATCATCATTATA
Found at i:17765698 original size:5 final size:5
Alignment explanation
Indices: 17765682--17765733 Score: 68
Period size: 5 Copynumber: 9.8 Consensus size: 5
17765672 CAGCGTTATG
*
17765682 ATAAA GATAAA ATAAA ATAATA TTATAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA -ATAAA ATAAA ATAA-A ATA-AA ATAAA ATAAA ATAAA ATAAA
17765730 ATAA
1 ATAA
17765734 TTTTATTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
5 30 0.71
6 11 0.26
7 1 0.02
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (5 bp):
ATAAA
Found at i:17765827 original size:13 final size:13
Alignment explanation
Indices: 17765781--17765827 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
17765771 AATAATTTAT
*
17765781 TTATTAATTAAAA
1 TTATTAATTTAAA
*
17765794 TTATT-TTTTAAA
1 TTATTAATTTAAA
*
17765806 ATATATAATTTAAA
1 TTAT-TAATTTAAA
17765820 TTATTAAT
1 TTATTAAT
17765828 ATAATTTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
12 8 0.30
13 10 0.37
14 9 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTATTAATTTAAA
Found at i:17765835 original size:35 final size:37
Alignment explanation
Indices: 17765763--17765845 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 37
17765753 ATATAATGAA
* *
17765763 TAAAATATAATAATTTATTTATTAATTAAAATTATTTTT
1 TAAAATAT-ATAATTTA-TAATTAATTAAAATAATTTTT
*
17765802 TAAAATATATAATTTA-AATT-ATTAATATAATTTTT
1 TAAAATATATAATTTATAATTAATTAAAATAATTTTT
*
17765837 AAAAATATA
1 TAAAATATA
17765846 ATAAAACATA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
35 21 0.52
36 3 0.08
38 8 0.20
39 8 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (37 bp):
TAAAATATATAATTTATAATTAATTAAAATAATTTTT
Found at i:17767122 original size:22 final size:26
Alignment explanation
Indices: 17767097--17767150 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
17767087 ATTTTTAAAA
17767097 TTTATT-AAA-TTT-AT-ATATAATT
1 TTTATTAAAATTTTAATAATATAATT
17767119 TTTATTAAAATTTTAAATAATATAATT
1 TTTATTAAAATTTT-AATAATATAATT
17767146 TTTAT
1 TTTAT
17767151 ATTATATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 6 0.22
23 3 0.11
24 3 0.11
26 2 0.07
27 13 0.48
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
TTTATTAAAATTTTAATAATATAATT
Found at i:17767186 original size:25 final size:24
Alignment explanation
Indices: 17767145--17767191 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
17767135 ATAATATAAT
*
17767145 TTTTATATTATATTATCGTATTATA
1 TTTTATAATATATTATC-TATTATA
17767170 TTTTATAATATCA-TATCTATTA
1 TTTTATAATAT-ATTATCTATTA
17767192 CAAGTGCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 5 0.25
25 14 0.70
26 1 0.05
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.57
Consensus pattern (24 bp):
TTTTATAATATATTATCTATTATA
Found at i:17768446 original size:16 final size:16
Alignment explanation
Indices: 17768420--17768452 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
17768410 CAAAACCATC
17768420 TAACAAAAATATTTAAA
1 TAACAAAAATA-TTAAA
17768437 TAAC-AAAATATTAAA
1 TAACAAAAATATTAAA
17768452 T
1 T
17768453 TAAAATCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 6 0.38
17 4 0.25
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (16 bp):
TAACAAAAATATTAAA
Found at i:17773837 original size:8 final size:8
Alignment explanation
Indices: 17773824--17773943 Score: 95
Period size: 8 Copynumber: 14.9 Consensus size: 8
17773814 TAATAATGGG
*
17773824 TGAAAGAA
1 TGAAAAAA
17773832 TGAAAGAAA
1 TGAAA-AAA
*
17773841 -GGAA-AA
1 TGAAAAAA
17773847 TGAAAAAA
1 TGAAAAAA
17773855 TGAAAAAA
1 TGAAAAAA
17773863 TGAAAAAA
1 TGAAAAAA
*
17773871 TAAAAAAA
1 TGAAAAAA
*
17773879 TAAAAAAA
1 TGAAAAAA
*
17773887 TAAAAAAA
1 TGAAAAAA
17773895 TAGAGAAAAA
1 T-GA-AAAAA
*
17773905 AG-AAAAA
1 TGAAAAAA
17773912 T-AAAAAA
1 TGAAAAAA
*
17773919 TAAAAAAAA
1 T-GAAAAAA
*
17773928 TAGAAAAGA
1 T-GAAAAAA
17773937 TGAAAAA
1 TGAAAAA
17773944 GAGTAAAAAA
Statistics
Matches: 94, Mismatches: 10, Indels: 16
0.78 0.08 0.13
Matches are distributed among these distances:
6 2 0.02
7 14 0.15
8 55 0.59
9 18 0.19
10 5 0.05
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.11
Consensus pattern (8 bp):
TGAAAAAA
Found at i:17773856 original size:23 final size:22
Alignment explanation
Indices: 17773824--17773926 Score: 63
Period size: 23 Copynumber: 4.7 Consensus size: 22
17773814 TAATAATGGG
*
17773824 TGAAAGAATGAAAGAAAGGAAAA
1 TGAAAAAATGAAA-AAAGGAAAA
*
17773847 TGAAAAAATGAAAAAATGAAAAAA
1 TGAAAAAATGAAAAAA-G-GAAAA
* **
17773871 TAAAAAAAT-AAAAAAATAAAA
1 TGAAAAAATGAAAAAAGGAAAA
* *
17773892 --AAATAGA-GAAAAAAGAAAAA
1 TGAAA-AAATGAAAAAAGGAAAA
*
17773912 T-AAAAAATAAAAAAA
1 TGAAAAAATGAAAAAA
17773927 ATAGAAAAGA
Statistics
Matches: 64, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
19 3 0.05
20 14 0.22
21 13 0.20
22 3 0.05
23 19 0.30
24 12 0.19
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.11
Consensus pattern (22 bp):
TGAAAAAATGAAAAAAGGAAAA
Found at i:17773864 original size:16 final size:16
Alignment explanation
Indices: 17773843--17773926 Score: 109
Period size: 16 Copynumber: 5.2 Consensus size: 16
17773833 GAAAGAAAGG
*
17773843 AAAATGAAAAAATGAA
1 AAAATGAAAAAATAAA
17773859 AAAATGAAAAAATAAA
1 AAAATGAAAAAATAAA
*
17773875 AAAATAAAAAAATAAA
1 AAAATGAAAAAATAAA
*
17773891 AAAATAGAGAAAAA-AGA
1 AAAAT-GA-AAAAATAAA
17773908 AAAAT-AAAAAATAAA
1 AAAATGAAAAAATAAA
17773923 AAAA
1 AAAA
17773927 ATAGAAAAGA
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
14 5 0.08
15 7 0.12
16 35 0.58
17 8 0.13
18 5 0.08
ACGTcount: A:0.82, C:0.00, G:0.07, T:0.11
Consensus pattern (16 bp):
AAAATGAAAAAATAAA
Found at i:17773876 original size:24 final size:24
Alignment explanation
Indices: 17773843--17773953 Score: 109
Period size: 24 Copynumber: 4.5 Consensus size: 24
17773833 GAAAGAAAGG
*
17773843 AAAATGAAAAAATGAAAAAATGAA
1 AAAATAAAAAAATGAAAAAATGAA
* *
17773867 AAAATAAAAAAATAAAAAAATAAA
1 AAAATAAAAAAATGAAAAAATGAA
*
17773891 AAAATAGAGAAAAAAG-AAAAAT-AA
1 AAAATA-A-AAAAATGAAAAAATGAA
*
17773915 AAAATAAAAAAAATAGAAAAGATGAA
1 AAAAT-AAAAAAAT-GAAAAAATGAA
17773941 AAAGAGTAAAAAA
1 AAA-A-TAAAAAA
17773954 GAAGACTTAA
Statistics
Matches: 72, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
23 5 0.07
24 36 0.50
25 13 0.18
26 10 0.14
27 7 0.10
28 1 0.01
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.11
Consensus pattern (24 bp):
AAAATAAAAAAATGAAAAAATGAA
Found at i:17773956 original size:24 final size:22
Alignment explanation
Indices: 17773833--17773956 Score: 76
Period size: 24 Copynumber: 5.5 Consensus size: 22
17773823 GTGAAAGAAT
*
17773833 GAAAGAAAGGAAAATGAAAAAATGA
1 GAAA-AAAGAAAAAT-AAAAAA-GA
*
17773858 -AAAAATGAAAAAATAAAAAA-A
1 GAAAAAAG-AAAAATAAAAAAGA
* * *
17773879 TAAAAAA-ATAAA-AAAATAGA
1 GAAAAAAGAAAAATAAAAAAGA
*
17773899 GAAAAAAGAAAAATAAAAAATAA
1 GAAAAAAGAAAAATAAAAAA-GA
* *
17773922 AAAAAATAGAAAAGATGAAAAAGA
1 GAAAAA-AGAAAA-ATAAAAAAGA
17773946 GTAAAAAAGAA
1 G-AAAAAAGAA
17773957 GACTTAAATT
Statistics
Matches: 77, Mismatches: 13, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
19 5 0.06
20 11 0.14
21 5 0.06
22 10 0.13
23 15 0.19
24 19 0.25
25 12 0.16
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (22 bp):
GAAAAAAGAAAAATAAAAAAGA
Found at i:17775213 original size:46 final size:46
Alignment explanation
Indices: 17775155--17775398 Score: 284
Period size: 46 Copynumber: 5.4 Consensus size: 46
17775145 AAGTCCTGAG
*
17775155 TTTTCAAATGAGAATCTTTGAGTCTTAAATGAAAATCTTTAAGACA
1 TTTTCAAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGACA
* * * * * * *
17775201 TTTTCAAGTGAGAATATTTGAATTTTAAATGAGAATTTTTAATATA
1 TTTTCAAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGACA
* * *
17775247 TTTTCAAATAAGAATCTTTAAGTCTTAAACGAGAATCTTTAAGACA
1 TTTTCAAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGACA
* * *
17775293 TTTTCAAATGAGAA-CTTTTAAGTCTTAAATGAAAATCTTTAAGATA
1 TTTTCAAATGAGAATC-TTTGAGTCTTAAATGAGAATCTTTAAGACA
*
17775339 TTTT----TGAGAACCTTTGAGTCTTAAATGAGAATCTTTAAGA-A
1 TTTTCAAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGACA
*
17775380 GTTTTTAAATGAGAATCTT
1 -TTTTCAAATGAGAATCTT
17775399 AAGACATTTT
Statistics
Matches: 166, Mismatches: 25, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
41 1 0.01
42 36 0.22
43 1 0.01
45 1 0.01
46 127 0.77
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.40
Consensus pattern (46 bp):
TTTTCAAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGACA
Found at i:17775466 original size:25 final size:24
Alignment explanation
Indices: 17775155--17775469 Score: 201
Period size: 21 Copynumber: 13.8 Consensus size: 24
17775145 AAGTCCTGAG
*
17775155 TTTTCAAATGAGAATCTTT--GAG
1 TTTTCAAATGAGAATCTTTAAGAA
* *
17775177 TCTT-AAATGAAAATCTTTAAGACA
1 TTTTCAAATGAGAATCTTTAAGA-A
* *
17775201 TTTTCAAGTGAGAATATTT--GAA
1 TTTTCAAATGAGAATCTTTAAGAA
* *
17775223 TTTT-AAATGAGAATTTTTAATATA
1 TTTTCAAATGAGAATCTTTAAGA-A
*
17775247 TTTTCAAATAAGAATCTTTAAG--
1 TTTTCAAATGAGAATCTTTAAGAA
* *
17775269 TCTT-AAACGAGAATCTTTAAGACA
1 TTTTCAAATGAGAATCTTTAAGA-A
17775293 TTTTCAAATGAGAA-CTTTTAAG--
1 TTTTCAAATGAGAATC-TTTAAGAA
* *
17775315 TCTT-AAATGAAAATCTTTAAGATA
1 TTTTCAAATGAGAATCTTTAAGA-A
* *
17775339 TTTT----TGAGAACCTTT--GAG
1 TTTTCAAATGAGAATCTTTAAGAA
*
17775357 TCTT-AAATGAGAATCTTTAAGAA
1 TTTTCAAATGAGAATCTTTAAGAA
*
17775380 GTTTTTAAATGAGAATC-TTAAGACA
1 -TTTTCAAATGAGAATCTTTAAGA-A
* * *
17775405 TTTTCAAATAAAAACCTTTAAG--
1 TTTTCAAATGAGAATCTTTAAGAA
*
17775427 TCTT-AAATGAGAATCTTTAAGACA
1 TTTTCAAATGAGAATCTTTAAGA-A
*
17775451 TTTTCAAATGAAAATCTTT
1 TTTTCAAATGAGAATCTTT
17775470 GAGTTTTGAG
Statistics
Matches: 225, Mismatches: 38, Indels: 57
0.70 0.12 0.18
Matches are distributed among these distances:
18 3 0.01
19 2 0.01
21 87 0.39
22 18 0.08
23 7 0.03
24 39 0.17
25 69 0.31
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.39
Consensus pattern (24 bp):
TTTTCAAATGAGAATCTTTAAGAA
Found at i:17776004 original size:42 final size:42
Alignment explanation
Indices: 17775920--17776070 Score: 216
Period size: 42 Copynumber: 3.6 Consensus size: 42
17775910 ATGATTATCA
*
17775920 AGGAGCCTTTTATTTTTCAAAA-TTGTGGTGCCTCTGTTTAG
1 AGGAGCATTTTATTTTTCAAAAGTTGTGGTGCCTCTGTTTAG
* *
17775961 AGGAGCATTTTATTTTTCAAAAGTTATGGTGCCTCTTTTTAG
1 AGGAGCATTTTATTTTTCAAAAGTTGTGGTGCCTCTGTTTAG
* * *
17776003 AGGAGCAATTTATTTTTCAAGAGTTGTGGTACCTCTGTTTAG
1 AGGAGCATTTTATTTTTCAAAAGTTGTGGTGCCTCTGTTTAG
* *
17776045 AAGAACATTTTATTTTTC-AAAGTTGT
1 AGGAGCATTTTATTTTTCAAAAGTTGT
17776071 TGAGCTTCTA
Statistics
Matches: 97, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
41 28 0.29
42 69 0.71
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.44
Consensus pattern (42 bp):
AGGAGCATTTTATTTTTCAAAAGTTGTGGTGCCTCTGTTTAG
Found at i:17776085 original size:41 final size:41
Alignment explanation
Indices: 17775920--17776087 Score: 194
Period size: 42 Copynumber: 4.0 Consensus size: 41
17775910 ATGATTATCA
* * *
17775920 AGGAGCCTTTTATTTTTCAAAATTGTGGTGCCTCTGTTTAG
1 AGGAGCATTTTATTTTTCAAAGTTGTGGAGCCTCTGTTTAG
* * *
17775961 AGGAGCATTTTATTTTTCAAAAGTTATGGTGCCTCTTTTTAG
1 AGGAGCATTTTATTTTTC-AAAGTTGTGGAGCCTCTGTTTAG
*
17776003 AGGAGCAATTTATTTTTCAAGAGTTGTGGTA-CCTCTGTTTAG
1 AGGAGCATTTTATTTTTCAA-AGTTGTGG-AGCCTCTGTTTAG
* * * * *
17776045 AAGAACATTTTATTTTTCAAAGTTGTTGAGCTTCTATTTAG
1 AGGAGCATTTTATTTTTCAAAGTTGTGGAGCCTCTGTTTAG
17776086 AG
1 AG
17776088 AAGCTTTGTT
Statistics
Matches: 108, Mismatches: 15, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
40 1 0.01
41 36 0.33
42 71 0.66
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.43
Consensus pattern (41 bp):
AGGAGCATTTTATTTTTCAAAGTTGTGGAGCCTCTGTTTAG
Found at i:17776262 original size:8 final size:8
Alignment explanation
Indices: 17776249--17776278 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
17776239 TTGTTAATAA
17776249 AAAAAAAT
1 AAAAAAAT
17776257 AAAAAAAT
1 AAAAAAAT
17776265 -AAAAAAT
1 AAAAAAAT
17776272 AAAAAAA
1 AAAAAAA
17776279 AAGTAGTTGA
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:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:17776267 original size:18 final size:18
Alignment explanation
Indices: 17776244--17776280 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
17776234 TAATTTTGTT
17776244 AATAAAAAA-AAATAAAAA
1 AATAAAAAATAAA-AAAAA
17776262 AATAAAAAATAAAAAAAA
1 AATAAAAAATAAAAAAAA
17776280 A
1 A
17776281 GTAGTTGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (18 bp):
AATAAAAAATAAAAAAAA
Found at i:17776270 original size:15 final size:15
Alignment explanation
Indices: 17776250--17776278 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17776240 TGTTAATAAA
17776250 AAAAAATAAAAAAAT
1 AAAAAATAAAAAAAT
17776265 AAAAAATAAAAAAA
1 AAAAAATAAAAAAA
17776279 AAGTAGTTGA
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:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAAAATAAAAAAAT
Found at i:17776678 original size:10 final size:10
Alignment explanation
Indices: 17776663--17776696 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
17776653 CGTTTCATTT
17776663 TTTTTTGGTA
1 TTTTTTGGTA
17776673 TTTTTT-GTA
1 TTTTTTGGTA
17776682 -TTTTTGGTA
1 TTTTTTGGTA
17776691 TTTTTT
1 TTTTTT
17776697 ATGTGTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 5 0.23
9 6 0.27
10 11 0.50
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.76
Consensus pattern (10 bp):
TTTTTTGGTA
Found at i:17776682 original size:9 final size:9
Alignment explanation
Indices: 17776663--17776696 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
17776653 CGTTTCATTT
17776663 TTTTTTGGTA
1 TTTTTT-GTA
17776673 TTTTTTGTA
1 TTTTTTGTA
*
17776682 TTTTTGGTA
1 TTTTTTGTA
17776691 TTTTTT
1 TTTTTT
17776697 ATGTGTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 16 0.73
10 6 0.27
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.76
Consensus pattern (9 bp):
TTTTTTGTA
Found at i:17776746 original size:9 final size:8
Alignment explanation
Indices: 17776731--17776756 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
17776721 TGATTAAATT
17776731 TAAAAAAA
1 TAAAAAAA
17776739 TAAAAAAA
1 TAAAAAAA
17776747 TAAAAAAA
1 TAAAAAAA
17776755 TA
1 TA
17776757 TTTTTGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (8 bp):
TAAAAAAA
Found at i:17777047 original size:181 final size:170
Alignment explanation
Indices: 17776799--17777257 Score: 415
Period size: 170 Copynumber: 2.6 Consensus size: 170
17776789 AAATTTATAG
* * *
17776799 AAATTTCAAATGGTAAATTTTTATA-AAAT-TCTTAGGTGAGGAAAATTTTATCCTAAATTTATC
1 AAATTTCAAATGATAAA-TTTTA-AGAAATCTC-TAGGTGA-G-AAATTTTATTCTAAATTTGTC
17776862 CCAAATGGTGAAATAATTTAAGAT-AAAGTTTCAATAACAATAATTAATATT-TATTTTCAAACA
61 CCAAATGGTGAAATAATTTAAGATGAAA-TTTCAATAA-AATAATT-ATATTCT-TTTTC--A-A
*
17776925 ATAAAA-AAT-A-TAAAAAT-TTTGGAATTAAATATAAATTACCCAAGGATGAGATTCTTAA
119 ATAAAATAATGATTAAAAATATTT-G-A--AAAT-T--A-T--CCAAGGATGAAATTCTTAA
*
17776983 AAATTTCAAATGATAAATTTCTAAGAAATCTCTA-GTGAGAAATTTTTTTCTAAATTTGTCCCAA
1 AAATTTCAAATGATAAATTT-TAAGAAATCTCTAGGTGAGAAATTTTATTCTAAATTTGTCCC-A
* * * **
17777047 AAT-GTGGAAT-ATTTTAGATGAAATTTCAATAAAATTAATTGTATTCTTTTTCAAATAAAATTT
64 AATGGTGAAATAATTTAAGATGAAATTTCAATAAAA-TAATTATATTCTTTTTCAAATAAAATAA
*
17777110 TGATTAAAAATATTTGAAAATTATCCAATGATGAAATTCTTAA
128 TGATTAAAAATATTTGAAAATTATCCAAGGATGAAATTCTTAA
* * * * *
17777153 AAATTTCAAATGAAAAAATTTTGAGAAATCTCTAGGTGAGAAATTTTCTT-TAAATTTGTTCTAA
1 AAATTTCAAATG-ATAAATTTTAAGAAATCTCTAGGTGAGAAATTTTATTCTAAATTTGTCCCAA
17777217 ATGGTGGAAA-AATTTAA-ATGAAATTTCAATTAAAAATAATT
65 ATGGT-GAAATAATTTAAGATGAAATTTCAA-T-AAAATAATT
17777258 GTCATATTAT
Statistics
Matches: 239, Mismatches: 18, Indels: 49
0.78 0.06 0.16
Matches are distributed among these distances:
169 4 0.02
170 65 0.27
171 35 0.15
172 5 0.02
173 1 0.00
175 1 0.00
176 11 0.05
177 2 0.01
178 2 0.01
179 19 0.08
180 26 0.11
181 29 0.12
182 5 0.02
183 8 0.03
184 24 0.10
185 2 0.01
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (170 bp):
AAATTTCAAATGATAAATTTTAAGAAATCTCTAGGTGAGAAATTTTATTCTAAATTTGTCCCAAA
TGGTGAAATAATTTAAGATGAAATTTCAATAAAATAATTATATTCTTTTTCAAATAAAATAATGA
TTAAAAATATTTGAAAATTATCCAAGGATGAAATTCTTAA
Found at i:17777406 original size:4 final size:4
Alignment explanation
Indices: 17777397--17777429 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
17777387 TAGAAATAAA
17777397 AATT AATT AATT AATT AATT AATT AATT GAATT
1 AATT AATT AATT AATT AATT AATT AATT -AATT
17777430 TCTAAATAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:17778653 original size:23 final size:20
Alignment explanation
Indices: 17778627--17778677 Score: 50
Period size: 22 Copynumber: 2.5 Consensus size: 20
17778617 GATCTATACT
17778627 TATTTAATAGTAAAAATTATCAA
1 TATTTAATAGTAAAAA-TAT--A
* *
17778650 TATTT-TTATTAAAAATATA
1 TATTTAATAGTAAAAATATA
17778669 TATTTAATA
1 TATTTAATA
17778678 AATATATCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
19 6 0.25
20 2 0.08
21 3 0.12
22 8 0.33
23 5 0.21
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (20 bp):
TATTTAATAGTAAAAATATA
Found at i:17778996 original size:2 final size:2
Alignment explanation
Indices: 17778989--17779018 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
17778979 CCAGCCCCAG
*
17778989 GA GA GA GA GA GA GA GA GA GA GG GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
17779019 ACCAAACCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:17783668 original size:35 final size:35
Alignment explanation
Indices: 17783626--17783693 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
17783616 GTACTTGCAC
** *
17783626 TAGTTGATATTTTAGGCAATTTCGTATTCTTTTAG
1 TAGTTGATATCGTAGGCAATTTCGTACTCTTTTAG
17783661 TAGTTGATATCGTAGGCAATTTCGTACTCTTTT
1 TAGTTGATATCGTAGGCAATTTCGTACTCTTTT
17783694 CATTTTTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.49
Consensus pattern (35 bp):
TAGTTGATATCGTAGGCAATTTCGTACTCTTTTAG
Found at i:17793384 original size:13 final size:15
Alignment explanation
Indices: 17793347--17793387 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
17793337 AACCAGTTTG
17793347 TATTATTATTATTATT
1 TATTATTATT-TTATT
17793363 TATTATTATTTTATT
1 TATTATTATTTTATT
17793378 T-TT-TTATTTT
1 TATTATTATTTT
17793388 TTGTTGATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.28
14 2 0.08
15 6 0.24
16 10 0.40
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TATTATTATTTTATT
Found at i:17793794 original size:20 final size:20
Alignment explanation
Indices: 17793756--17793796 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
17793746 TGAAAAATTC
* *
17793756 CCAGATTTTGACAATATTTT
1 CCAGATTTCGACAAAATTTT
*
17793776 CCAGATTTCGATAAAATTTT
1 CCAGATTTCGACAAAATTTT
17793796 C
1 C
17793797 AGCGTCAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (20 bp):
CCAGATTTCGACAAAATTTT
Found at i:17794440 original size:24 final size:26
Alignment explanation
Indices: 17794391--17794442 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
17794381 AATAAATAAT
* *
17794391 AATTATCAAATGATGAAATTTTTATA
1 AATTATCAAAAGATGAAATTTCTATA
17794417 AATT-TCAAAAGAT-AAATTTCTATA
1 AATTATCAAAAGATGAAATTTCTATA
17794441 AA
1 AA
17794443 ATTTTTAGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 12 0.50
25 8 0.33
26 4 0.17
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (26 bp):
AATTATCAAAAGATGAAATTTCTATA
Found at i:17794444 original size:25 final size:26
Alignment explanation
Indices: 17794386--17794446 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 26
17794376 TTAAGAATAA
* *
17794386 ATAATAATTATCAAATGATGAAATTTTT
1 ATAA-AATT-TCAAAAGATGAAATTTCT
17794414 AT-AAATTTCAAAAGAT-AAATTTCT
1 ATAAAATTTCAAAAGATGAAATTTCT
17794438 ATAAAATTT
1 ATAAAATTT
17794447 TTAGGTGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 9 0.30
25 14 0.47
26 4 0.13
27 1 0.03
28 2 0.07
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (26 bp):
ATAAAATTTCAAAAGATGAAATTTCT
Found at i:17799262 original size:20 final size:21
Alignment explanation
Indices: 17799237--17799277 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17799227 CAAAAACATA
*
17799237 TTTTATT-TTGTTTTATATTT
1 TTTTATTATTGTTTTAAATTT
*
17799257 TTTTATTATTTTTTTAAATTT
1 TTTTATTATTGTTTTAAATTT
17799278 AATCATGCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (21 bp):
TTTTATTATTGTTTTAAATTT
Found at i:17799307 original size:4 final size:4
Alignment explanation
Indices: 17799298--17799345 Score: 53
Period size: 4 Copynumber: 11.8 Consensus size: 4
17799288 AAATACTTAA
* *
17799298 AAAT AAAT AACT AAAT AAAT GAAT AAAT AAA- ATAAT AAAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT -AAAT AAAT AAA
17799346 AATACCAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
3 1 0.03
4 32 0.86
5 3 0.08
6 1 0.03
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:17799315 original size:12 final size:11
Alignment explanation
Indices: 17799298--17799349 Score: 61
Period size: 12 Copynumber: 4.5 Consensus size: 11
17799288 AAATACTTAA
17799298 AAATAAATAACT
1 AAATAAATAA-T
17799310 AAATAAATGAAT
1 AAATAAAT-AAT
17799322 AAATAAAATAAT
1 AAAT-AAATAAT
17799334 AAAATAAATAA-
1 -AAATAAATAAT
17799345 AAATA
1 AAATA
17799350 CCAAAATAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
10 5 0.14
12 22 0.59
13 10 0.27
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:17800175 original size:21 final size:20
Alignment explanation
Indices: 17800136--17800181 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
17800126 GAGTTTTTCC
* *
17800136 TATTTTTTTGTTTTTATTAT
1 TATTTATTTATTTTTATTAT
17800156 TATTTATTTATTTTTCATTAT
1 TATTTATTTATTTTT-ATTAT
17800177 TATTT
1 TATTT
17800182 TTAATTAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (20 bp):
TATTTATTTATTTTTATTAT
Found at i:17808686 original size:17 final size:16
Alignment explanation
Indices: 17808655--17808698 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
17808645 TAAAAATTAG
** *
17808655 AAATAAATAGTCAAAT
1 AAATAAATAAACAAAC
17808671 AAATAAAATAAACAAAC
1 AAAT-AAATAAACAAAC
17808688 AAATAAATAAA
1 AAATAAATAAA
17808699 TAAAAGATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.73, C:0.07, G:0.02, T:0.18
Consensus pattern (16 bp):
AAATAAATAAACAAAC
Found at i:17808929 original size:13 final size:14
Alignment explanation
Indices: 17808911--17808943 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
17808901 AATTTCTTTG
17808911 CTTTTTTT-TTAAT
1 CTTTTTTTCTTAAT
17808924 CTTTTTTTCTTAAT
1 CTTTTTTTCTTAAT
17808938 -TTTTTT
1 CTTTTTT
17808944 AATTGATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (14 bp):
CTTTTTTTCTTAAT
Found at i:17812329 original size:182 final size:182
Alignment explanation
Indices: 17812022--17812386 Score: 703
Period size: 182 Copynumber: 2.0 Consensus size: 182
17812012 GGATTTGGGT
17812022 GTTTCATATTTAGTGTAATCTTAGAAAAATATGAACATTTTCTTACTACACAGAAGGAATTTGTA
1 GTTTCATATTTAGTGTAATCTTAGAAAAATATGAACATTTTCTTACTACACAGAAGGAATTTGTA
*
17812087 TTAGTCTATGCATATATGTACTGCGCAATACTCTGAACAATGAACCTAGACTCAGATATGTGAAG
66 TTAGTCTATGCATATATGTACTGCACAATACTCTGAACAATGAACCTAGACTCAGATATGTGAAG
17812152 TATTGCAGTACCAGGAACAGTTATTAGGAATCAAAAGATCATATGCATGAGA
131 TATTGCAGTACCAGGAACAGTTATTAGGAATCAAAAGATCATATGCATGAGA
17812204 GTTTCATATTTAGTGTAATCTTAGAAAAATATGAACATTTTCTTACTACACAGAAGGAATTTGTA
1 GTTTCATATTTAGTGTAATCTTAGAAAAATATGAACATTTTCTTACTACACAGAAGGAATTTGTA
* *
17812269 TTATTCTATGCATATATGTACTGCACAATACTCTGTACAATGAACCTAGACTCAGATATGTGAAG
66 TTAGTCTATGCATATATGTACTGCACAATACTCTGAACAATGAACCTAGACTCAGATATGTGAAG
17812334 TATTGCAGTACCAGGAACAGTTATTAGGAATCAAAAGATCATATGCATGAGA
131 TATTGCAGTACCAGGAACAGTTATTAGGAATCAAAAGATCATATGCATGAGA
17812386 G
1 G
17812387 ATTCCTTCGG
Statistics
Matches: 180, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
182 180 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (182 bp):
GTTTCATATTTAGTGTAATCTTAGAAAAATATGAACATTTTCTTACTACACAGAAGGAATTTGTA
TTAGTCTATGCATATATGTACTGCACAATACTCTGAACAATGAACCTAGACTCAGATATGTGAAG
TATTGCAGTACCAGGAACAGTTATTAGGAATCAAAAGATCATATGCATGAGA
Found at i:17828176 original size:2 final size:2
Alignment explanation
Indices: 17828171--17828207 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
17828161 ATATATATAT
17828171 AG AG AG AG 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 AG AG AG AG A
17828208 ACGCCCTAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17833019 original size:17 final size:17
Alignment explanation
Indices: 17832971--17833020 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
17832961 ACTTATCATG
17832971 CATAAATATAAAAAATA
1 CATAAATATAAAAAATA
*
17832988 CTTAAA-ATAACAAAAATA
1 CATAAATAT-A-AAAAATA
17833006 -ATAATATATAAAAAA
1 CATAA-ATATAAAAAA
17833021 ATTAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
16 2 0.07
17 14 0.52
18 9 0.33
19 2 0.07
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
CATAAATATAAAAAATA
Found at i:17846580 original size:18 final size:19
Alignment explanation
Indices: 17846559--17846594 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
17846549 CAAAAAAAAT
*
17846559 TTAAAAATCA-AAATTTAC
1 TTAAAAAACATAAATTTAC
17846577 TTAAAAAACATAAATTTA
1 TTAAAAAACATAAATTTA
17846595 ACAAGTAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (19 bp):
TTAAAAAACATAAATTTAC
Found at i:17853153 original size:2 final size:2
Alignment explanation
Indices: 17853146--17853175 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
17853136 CATATTTTAC
*
17853146 AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17853176 TTAGTAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17853548 original size:12 final size:11
Alignment explanation
Indices: 17853526--17853555 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
17853516 TACTCATTTT
17853526 TATATTTTATA
1 TATATTTTATA
17853537 TATATATTTATA
1 TATAT-TTTATA
17853549 TATATTT
1 TATATTT
17853556 AGTAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TATATTTTATA
Found at i:17858860 original size:23 final size:22
Alignment explanation
Indices: 17858804--17858862 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 22
17858794 AGGCTTTTTG
*
17858804 TTTAGGGTTTTGGCTTGGGGAT
1 TTTAAGGTTTTGGCTTGGGGAT
* *
17858826 TTTAAGATTTTTGGACTT-TGGAT
1 TTTAAG-GTTTTGG-CTTGGGGAT
17858849 TTTAAAGGTTTTGG
1 TTT-AAGGTTTTGG
17858863 GAATTGGCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
22 5 0.17
23 19 0.63
24 6 0.20
ACGTcount: A:0.17, C:0.03, G:0.31, T:0.49
Consensus pattern (22 bp):
TTTAAGGTTTTGGCTTGGGGAT
Found at i:17858982 original size:29 final size:28
Alignment explanation
Indices: 17858902--17859054 Score: 121
Period size: 29 Copynumber: 5.3 Consensus size: 28
17858892 CTTTTGATTC
*
17858902 TAGGGTTTCGATTTTAAGGTTTGAGG-TT
1 TAGGGTTTTGATTTT-AGGTTTGAGGTTT
* * **
17858930 TGGGGTTTTGATCTTAAGACTTGAGGTTT
1 TAGGGTTTTGAT-TTTAGGTTTGAGGTTT
17858959 TAGGGTTTTGATTTTAGGATTTGAGGTTT
1 TAGGGTTTTGATTTTAGG-TTTGAGGTTT
** *
17858988 TCA-GGTTTCAATTTTAAGGTTTGAGGGTT
1 T-AGGGTTTTGATTTT-AGGTTTGAGGTTT
* * * *
17859017 TAGGATTTTAATTTCGAGGTTTAGAGGTTC
1 TAGGGTTTTGATTT-TAGGTTT-GAGGTTT
17859047 TAGGGTTT
1 TAGGGTTT
17859055 AAAGCATTTA
Statistics
Matches: 99, Mismatches: 18, Indels: 14
0.76 0.14 0.11
Matches are distributed among these distances:
28 23 0.23
29 60 0.61
30 16 0.16
ACGTcount: A:0.19, C:0.05, G:0.30, T:0.46
Consensus pattern (28 bp):
TAGGGTTTTGATTTTAGGTTTGAGGTTT
Found at i:17859151 original size:59 final size:57
Alignment explanation
Indices: 17859047--17859241 Score: 194
Period size: 59 Copynumber: 3.3 Consensus size: 57
17859037 TTAGAGGTTC
* ** * * * *
17859047 TAGGGTTTAAAGCATTTAGGGTTTCAATTTTAGGGTTTAAAGGTTTAAGGGTATCGTTT
1 TAGGGTTTAGAGGGTTTAGGGTTTC-GTTTTAGGGTTTAAGGGTTT-AGAGTATCATTT
* * *
17859106 TAAGGTTTAGAGGGTTTAGGGTTTCGTTTTAAGGTTTGGAGGGTTTAGAG-ATTCAATTT
1 TAGGGTTTAGAGGGTTTAGGGTTTCGTTTTAGGGTTT-AAGGGTTTAGAGTA-TC-ATTT
* * * * *
17859165 CAGGGTTTAGAGGTTTTAAGGTATCGTTTTAGGGTTTAAAGGGTTTAGAGTTTCATTT
1 TAGGGTTTAGAGGGTTTAGGGTTTCGTTTTAGGGTTT-AAGGGTTTAGAGTATCATTT
17859223 TAGGGTTTAGAGGGTTTAG
1 TAGGGTTTAGAGGGTTTAG
17859242 AGATTTTAGG
Statistics
Matches: 110, Mismatches: 22, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
57 1 0.01
58 35 0.32
59 74 0.67
ACGTcount: A:0.23, C:0.04, G:0.31, T:0.42
Consensus pattern (57 bp):
TAGGGTTTAGAGGGTTTAGGGTTTCGTTTTAGGGTTTAAGGGTTTAGAGTATCATTT
Found at i:17859161 original size:88 final size:88
Alignment explanation
Indices: 17859069--17859246 Score: 268
Period size: 88 Copynumber: 2.0 Consensus size: 88
17859059 CATTTAGGGT
* * * *
17859069 TTCAATTTTAGGGTTTAAAGG-TTTAAGGGTATCGTTTTAAGGTTTAGAGGGTTTAGGGTTTCGT
1 TTCAATTTCAGGGTTTAAAGGTTTTAA-GGTATCGTTTTAAGGTTTAAAGGGTTTAGAGTTTCAT
*
17859133 TTTAAGGTTTGGAGGGTTTAGAGA
65 TTTAAGGTTTAGAGGGTTTAGAGA
* *
17859157 TTCAATTTCAGGGTTTAGAGGTTTTAAGGTATCGTTTTAGGGTTTAAAGGGTTTAGAGTTTCATT
1 TTCAATTTCAGGGTTTAAAGGTTTTAAGGTATCGTTTTAAGGTTTAAAGGGTTTAGAGTTTCATT
*
17859222 TTAGGGTTTAGAGGGTTTAGAGA
66 TTAAGGTTTAGAGGGTTTAGAGA
17859245 TT
1 TT
17859247 TTAGGGTTTA
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
88 76 0.94
89 5 0.06
ACGTcount: A:0.23, C:0.04, G:0.30, T:0.43
Consensus pattern (88 bp):
TTCAATTTCAGGGTTTAAAGGTTTTAAGGTATCGTTTTAAGGTTTAAAGGGTTTAGAGTTTCATT
TTAAGGTTTAGAGGGTTTAGAGA
Found at i:17859242 original size:29 final size:29
Alignment explanation
Indices: 17859047--17859257 Score: 173
Period size: 29 Copynumber: 7.3 Consensus size: 29
17859037 TTAGAGGTTC
* ** *
17859047 TAGGGTTTAAAGCATTTAGGGTTTCAATTT
1 TAGGGTTTAGAGGGTTTAGAGTTTC-ATTT
* * * *
17859077 TAGGGTTTA-AAGGTTTAAGGGTATCGTTT
1 TAGGGTTTAGAGGGTTT-AGAGTTTCATTT
* * *
17859106 TAAGGTTTAGAGGGTTTAGGGTTTCGTTT
1 TAGGGTTTAGAGGGTTTAGAGTTTCATTT
* * *
17859135 TAAGGTTTGGAGGGTTTAGAGATTCAATTT
1 TAGGGTTTAGAGGGTTTAGAGTTTC-ATTT
* * * *
17859165 CAGGGTTTAGAGGTTTTA-AGGTATCGTTT
1 TAGGGTTTAGAGGGTTTAGA-GTTTCATTT
*
17859194 TAGGGTTTAAAGGGTTTAGAGTTTCATTT
1 TAGGGTTTAGAGGGTTTAGAGTTTCATTT
17859223 TAGGGTTTAGAGGGTTTAGAG----ATTT
1 TAGGGTTTAGAGGGTTTAGAGTTTCATTT
17859248 TAGGGTTTAG
1 TAGGGTTTAG
17859258 TTTATTGTTA
Statistics
Matches: 151, Mismatches: 25, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
25 14 0.09
29 94 0.62
30 43 0.28
ACGTcount: A:0.23, C:0.04, G:0.31, T:0.42
Consensus pattern (29 bp):
TAGGGTTTAGAGGGTTTAGAGTTTCATTT
Found at i:17859751 original size:7 final size:7
Alignment explanation
Indices: 17859741--17859787 Score: 94
Period size: 7 Copynumber: 6.7 Consensus size: 7
17859731 TAAAAAAGGT
17859741 AAAAATG
1 AAAAATG
17859748 AAAAATG
1 AAAAATG
17859755 AAAAATG
1 AAAAATG
17859762 AAAAATG
1 AAAAATG
17859769 AAAAATG
1 AAAAATG
17859776 AAAAATG
1 AAAAATG
17859783 AAAAA
1 AAAAA
17859788 ATGATAAAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (7 bp):
AAAAATG
Found at i:17859758 original size:21 final size:21
Alignment explanation
Indices: 17859741--17859796 Score: 94
Period size: 21 Copynumber: 2.6 Consensus size: 21
17859731 TAAAAAAGGT
17859741 AAAAATGAAAAATGAAAAATG
1 AAAAATGAAAAATGAAAAATG
17859762 AAAAATGAAAAATGAAAAATG
1 AAAAATGAAAAATGAAAAATG
17859783 AAAAAATGATAAAA
1 -AAAAATGA-AAAA
17859797 CAATTACATG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 8 0.24
23 4 0.12
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.14
Consensus pattern (21 bp):
AAAAATGAAAAATGAAAAATG
Found at i:17860800 original size:3 final size:3
Alignment explanation
Indices: 17860792--17860847 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
17860782 TAATTAAATC
17860792 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17860840 ATT ATT AT
1 ATT ATT AT
17860848 ACAAAAATTG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:17863290 original size:23 final size:21
Alignment explanation
Indices: 17863268--17863308 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
17863258 AATATTAATA
*
17863268 ATATGAAATTAATATAAAAAAT
1 ATATGAAAATAA-ATAAAAAAT
*
17863290 ATATTAAAATAAATAAAAA
1 ATATGAAAATAAATAAAAA
17863309 TTCATTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (21 bp):
ATATGAAAATAAATAAAAAAT
Found at i:17872232 original size:236 final size:236
Alignment explanation
Indices: 17871812--17872269 Score: 736
Period size: 236 Copynumber: 1.9 Consensus size: 236
17871802 CACGTTGTAT
* * * *
17871812 TTTATATTAAAATTACGTGTCACAATTTATAAGGTTATAAATGAACCAAATATAAATGAATGACC
1 TTTATATTAAAATTACATGTCACAATTTATAAGATTATAAACGAACCAAATATAAATGAACGACC
* **
17871877 GTATGTTTGTGGTTTGTTTGTTTATTTTTAAAGATGTTCATGTTTGATTCATGTTCACTAACAAA
66 GTATGTTTGTGGTTTGTTCGTTTATTTTTAAAGATGTTCATGTTCAATTCATGTTCACTAACAAA
* * *
17871942 ATTGCTTTGTTCGTTCATGTTTTGTTCATTTAAATAGTAGGTTATTTGTGTTCGATTCAATTAAG
131 ATTGCTTTATTCATTCATGTTTTGTTCATTTAAATAGTAAGTTATTTGTGTTCGATTCAATTAAG
*
17872007 TTAAACGAGATTGTTCATAAACATTAAACGAACATGTTATG
196 TTAAACGAGATCGTTCATAAACATTAAACGAACATGTTATG
*
17872048 TTTATATTAAAATTACATGTCACAATTTATAAGATTGTAAACGAACCAAATATAAATGAACGACC
1 TTTATATTAAAATTACATGTCACAATTTATAAGATTATAAACGAACCAAATATAAATGAACGACC
* * *
17872113 GTATGTTTGTGGTTTGTTCGTTTATTTTTAAAGATTTTCGTGTTCAATTCATGTTCACTAAGAAA
66 GTATGTTTGTGGTTTGTTCGTTTATTTTTAAAGATGTTCATGTTCAATTCATGTTCACTAACAAA
* * *
17872178 ATTGCTTTATTCATTCATGTTTTGTTCGTTTAAATAGTAAGTTCTTTTTGTTCGATTCAATTAAG
131 ATTGCTTTATTCATTCATGTTTTGTTCATTTAAATAGTAAGTTATTTGTGTTCGATTCAATTAAG
* *
17872243 TTAAATGAGCTCGTTCATAAACATTAA
196 TTAAACGAGATCGTTCATAAACATTAA
17872270 GTGAACATAT
Statistics
Matches: 202, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
236 202 1.00
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.43
Consensus pattern (236 bp):
TTTATATTAAAATTACATGTCACAATTTATAAGATTATAAACGAACCAAATATAAATGAACGACC
GTATGTTTGTGGTTTGTTCGTTTATTTTTAAAGATGTTCATGTTCAATTCATGTTCACTAACAAA
ATTGCTTTATTCATTCATGTTTTGTTCATTTAAATAGTAAGTTATTTGTGTTCGATTCAATTAAG
TTAAACGAGATCGTTCATAAACATTAAACGAACATGTTATG
Found at i:17878614 original size:25 final size:25
Alignment explanation
Indices: 17878580--17878631 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
17878570 GGTTTGGGAT
*
17878580 ATCTACTCGTGATGTAACGAGAATG
1 ATCTACTCGTCATGTAACGAGAATG
* * *
17878605 ATCTTCTCGTCATGTGACGTGAATG
1 ATCTACTCGTCATGTAACGAGAATG
17878630 AT
1 AT
17878632 GAGTCAAAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (25 bp):
ATCTACTCGTCATGTAACGAGAATG
Found at i:17881380 original size:23 final size:22
Alignment explanation
Indices: 17881328--17881380 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
17881318 AATAATTTAT
* *
17881328 ATAAATAATCTTTGGAGTAAAA
1 ATAAAAAATATTTGGAGTAAAA
* *
17881350 TTACAAAAATATTTTGAGTGAAAA
1 ATA-AAAAATATTTGGAGT-AAAA
17881374 ATAAAAA
1 ATAAAAA
17881381 GCAATGGAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 2 0.08
23 16 0.67
24 6 0.25
ACGTcount: A:0.55, C:0.04, G:0.11, T:0.30
Consensus pattern (22 bp):
ATAAAAAATATTTGGAGTAAAA
Found at i:17882792 original size:10 final size:10
Alignment explanation
Indices: 17882762--17882794 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
17882752 ATTTTTCATT
17882762 TACATATATA
1 TACATATATA
17882772 T--ATATATA
1 TACATATATA
17882780 TACATATATA
1 TACATATATA
17882790 TACAT
1 TACAT
17882795 GAATGTATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.38
10 13 0.62
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.42
Consensus pattern (10 bp):
TACATATATA
Found at i:17892365 original size:24 final size:22
Alignment explanation
Indices: 17892316--17892357 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
17892306 TTATGTTACT
* * *
17892316 TTTTTAATTATAAATATTCAAA
1 TTTTGAATTATAAAAATGCAAA
17892338 TTTTGAATTATAAAAATGCA
1 TTTTGAATTATAAAAATGCA
17892358 TACATTTTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (22 bp):
TTTTGAATTATAAAAATGCAAA
Found at i:17892973 original size:23 final size:23
Alignment explanation
Indices: 17892930--17892973 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
17892920 ATATACATTT
*
17892930 TGTATTAAAATTTAAATATATTA
1 TGTATTAAAATTTAAAAATATTA
*
17892953 TGTATT-ATATTTAATAAATAT
1 TGTATTAAAATTTAA-AAATAT
17892974 GATATTTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (23 bp):
TGTATTAAAATTTAAAAATATTA
Found at i:17894182 original size:22 final size:23
Alignment explanation
Indices: 17894132--17894192 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 23
17894122 TCTGTCTTGG
* *
17894132 TATTTTACAT-ATATATATATAT
1 TATTTTAAATAATATAAATATAT
*
17894154 T-TATTAAATAATATAAAT-TAT
1 TATTTTAAATAATATAAATATAT
17894175 TATTTTAAATTAAT-TAAA
1 TATTTTAAA-TAATATAAA
17894193 ATTAATATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
21 10 0.31
22 18 0.56
23 4 0.12
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTTTAAATAATATAAATATAT
Found at i:17894337 original size:36 final size:34
Alignment explanation
Indices: 17894303--17894387 Score: 89
Period size: 37 Copynumber: 2.3 Consensus size: 34
17894293 GAGGTTATGG
* *
17894303 ATAAAAAAATTATTTATATTTATTAAATATTTATGAAA
1 ATAAAAAAAAT-TTTAAATTTA--AAATATTTATG-AA
17894341 ATAAAAAAAATTTTAAATTTAAAATATTTATTGAA
1 ATAAAAAAAATTTTAAATTTAAAATATTTA-TGAA
17894376 TATAAATAAAAA
1 -ATAAA-AAAAA
17894388 ATAAATATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
35 11 0.26
36 7 0.17
37 14 0.33
38 10 0.24
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (34 bp):
ATAAAAAAAATTTTAAATTTAAAATATTTATGAA
Found at i:17894393 original size:35 final size:34
Alignment explanation
Indices: 17894327--17894393 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 34
17894317 TATATTTATT
*
17894327 AAATATTTATGAAAATAAAAAAAATTTTAAATTTA
1 AAATATTTATGAAAATAAAAAAAA-TATAAATTTA
*
17894362 AAATATTTATTGAATATAAATAAAAA-ATAAAT
1 AAATATTTA-TGAAAATAAA-AAAAATATAAAT
17894394 ATAATATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
35 14 0.50
36 9 0.32
37 5 0.18
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (34 bp):
AAATATTTATGAAAATAAAAAAAATATAAATTTA
Found at i:17895490 original size:3 final size:3
Alignment explanation
Indices: 17895482--17895511 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
17895472 AACCTAAATT
17895482 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
17895512 GAAAAACGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:17896087 original size:33 final size:33
Alignment explanation
Indices: 17896045--17896212 Score: 180
Period size: 33 Copynumber: 4.8 Consensus size: 33
17896035 CTTACATAAG
17896045 CATCTAGATGGTCTGCATTTGCTCTCATTTGTT
1 CATCTAGATGGTCTGCATTTGCTCTCATTTGTT
* *
17896078 CATCTAGATGGTCT-CATCTAG--ATCATTTGCTCT
1 CATCTAGATGGTCTGCAT-TTGCTCTCATTTG-T-T
17896111 CATCTAGATGGTCTGCATTTGCTCTCATTTGTT
1 CATCTAGATGGTCTGCATTTGCTCTCATTTGTT
*
17896144 CATCTAGATGCTCTCATCTAGATCATTTGCTCTCATTTGTT
1 CATCTAGATG-----GTCT-G--CATTTGCTCTCATTTGTT
*
17896185 CATCTAGATGGTCTGCATTTGTTCTCAT
1 CATCTAGATGGTCTGCATTTGCTCTCAT
17896213 GTAACTAGAA
Statistics
Matches: 114, Mismatches: 7, Indels: 28
0.77 0.05 0.19
Matches are distributed among these distances:
31 7 0.06
32 4 0.04
33 56 0.49
34 4 0.04
35 8 0.07
36 3 0.03
38 3 0.03
39 1 0.01
41 28 0.25
ACGTcount: A:0.18, C:0.23, G:0.16, T:0.43
Consensus pattern (33 bp):
CATCTAGATGGTCTGCATTTGCTCTCATTTGTT
Found at i:17896113 original size:19 final size:19
Alignment explanation
Indices: 17896089--17896179 Score: 67
Period size: 19 Copynumber: 4.3 Consensus size: 19
17896079 ATCTAGATGG
17896089 TCTCATCTAGATCATTTGC
1 TCTCATCTAGATCATTTGC
17896108 TCTCATCTAGATGGTCTGCATTTGC
1 TCTCATCTAGA-----T-CATTTGC
* *
17896133 TCTCAT-TTGTTCATCTAGATGC
1 TCTCATCTAGATCAT-T---TGC
17896155 TCTCATCTAGATCATTTGC
1 TCTCATCTAGATCATTTGC
17896174 TCTCAT
1 TCTCAT
17896180 TTGTTCATCT
Statistics
Matches: 57, Mismatches: 4, Indels: 22
0.69 0.05 0.27
Matches are distributed among these distances:
18 3 0.05
19 22 0.39
22 10 0.18
23 6 0.11
24 3 0.05
25 13 0.23
ACGTcount: A:0.19, C:0.25, G:0.13, T:0.43
Consensus pattern (19 bp):
TCTCATCTAGATCATTTGC
Found at i:17896151 original size:66 final size:66
Alignment explanation
Indices: 17896045--17896179 Score: 261
Period size: 66 Copynumber: 2.0 Consensus size: 66
17896035 CTTACATAAG
*
17896045 CATCTAGATGGTCTGCATTTGCTCTCATTTGTTCATCTAGATGGTCTCATCTAGATCATTTGCTC
1 CATCTAGATGGTCTGCATTTGCTCTCATTTGTTCATCTAGATGCTCTCATCTAGATCATTTGCTC
17896110 T
66 T
17896111 CATCTAGATGGTCTGCATTTGCTCTCATTTGTTCATCTAGATGCTCTCATCTAGATCATTTGCTC
1 CATCTAGATGGTCTGCATTTGCTCTCATTTGTTCATCTAGATGCTCTCATCTAGATCATTTGCTC
17896176 T
66 T
17896177 CAT
1 CAT
17896180 TTGTTCATCT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.19, C:0.24, G:0.16, T:0.42
Consensus pattern (66 bp):
CATCTAGATGGTCTGCATTTGCTCTCATTTGTTCATCTAGATGCTCTCATCTAGATCATTTGCTC
T
Found at i:17898473 original size:81 final size:81
Alignment explanation
Indices: 17898388--17898633 Score: 186
Period size: 81 Copynumber: 3.0 Consensus size: 81
17898378 AATATGCACC
*
17898388 TAATTGATTTTATAATTTGAAATTAAAAATTTTCAGTAAAAATGTAATAATTAATTAATAATATT
1 TAATTGATTTTATAATTTGAAATTAAAATTTTTCAGTAAAAATGTAATAATTAATTAATAATATT
17898453 TTATATTTTTCATTTT
66 TTATATTTTTCATTTT
* * * * ** * * *
17898469 TAATTAATTATT-TGAA-GTCAATATTTATTTTTTTGAAGT--TAATGTAA-AATATTATTAATA
1 TAATTGATT-TTAT-AATTTGAA-ATTAAAATTTTT-CAGTAAAAATGTAATAAT-TAATTAATA
* ** * *
17898529 GA-ATTTGA-AAGTAT-ATGTATC
61 -ATATTTTATATTTTTCAT-T-TT
*
17898550 TAATTGATTTTATAATTTGGAATTAAAATTTTTCAAG-AAAAATGTAATAATTAATTAATATAAT
1 TAATTGATTTTATAATTTGAAATTAAAATTTTTC-AGTAAAAATGTAATAATTAATT-A-ATAAT
17898614 ATTTTATATTTTTCATTTT
63 ATTTTATATTTTTCATTTT
17898633 T
1 T
17898634 GGTTAATTAT
Statistics
Matches: 116, Mismatches: 30, Indels: 36
0.64 0.16 0.20
Matches are distributed among these distances:
79 2 0.02
80 22 0.19
81 55 0.47
82 18 0.16
83 13 0.11
84 4 0.03
85 2 0.02
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (81 bp):
TAATTGATTTTATAATTTGAAATTAAAATTTTTCAGTAAAAATGTAATAATTAATTAATAATATT
TTATATTTTTCATTTT
Done.