Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167849.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_12, 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: 22966848
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 129000 characters in sequence are not A, C, G, or T
File 101 of 129
Found at i:16710876 original size:2 final size:2
Alignment explanation
Indices: 16710869--16710893 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16710859 GTCATGCATT
16710869 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
16710894 CTGTGTACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16710992 original size:2 final size:2
Alignment explanation
Indices: 16710985--16711013 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16710975 ACTTATATGC
16710985 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
16711014 CACACACAAA
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:16715101 original size:2 final size:2
Alignment explanation
Indices: 16715094--16715130 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
16715084 AGCGTTGGTT
*
16715094 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16715131 GTTGTGTGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16722840 original size:2 final size:2
Alignment explanation
Indices: 16722833--16722876 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
16722823 CAAGCATACA
16722833 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
16722875 TC
1 TC
16722877 ATTCTTATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:16727655 original size:3 final size:3
Alignment explanation
Indices: 16727647--16727676 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
16727637 CTTCAGAGGA
*
16727647 TTC TTC TTC TTC TTT TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
16727677 AAAGGAAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:16729908 original size:25 final size:25
Alignment explanation
Indices: 16729874--16729924 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
16729864 TAGCGTTTTT
* * *
16729874 AATTATAAATGTCATTAAATTAAAA
1 AATTAAAAATGCCACTAAATTAAAA
16729899 AATTAAAAATGCCACTAAATTAAAA
1 AATTAAAAATGCCACTAAATTAAAA
16729924 A
1 A
16729925 TTTTACTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.59, C:0.08, G:0.04, T:0.29
Consensus pattern (25 bp):
AATTAAAAATGCCACTAAATTAAAA
Found at i:16740044 original size:24 final size:23
Alignment explanation
Indices: 16740008--16740060 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
16739998 TTTTTTAAGT
*
16740008 AATAAA-AGTTTTAGTATAAA-AA
1 AATAAATAGTTTTA-AATAAATAA
16740030 AATAAATATGTTTTAAATAAATAA
1 AATAAATA-GTTTTAAATAAATAA
16740054 AATAAAT
1 AATAAAT
16740061 TTATTAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 6 0.22
23 6 0.22
24 15 0.56
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (23 bp):
AATAAATAGTTTTAAATAAATAA
Found at i:16741787 original size:24 final size:24
Alignment explanation
Indices: 16741755--16741801 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
16741745 GTTAAAGCAG
* *
16741755 GATAATAATGTTTGATACACTAAA
1 GATAATAATATTTAATACACTAAA
16741779 GATAATAATATTTAATACACTAA
1 GATAATAATATTTAATACACTAA
16741802 CAATATATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.34
Consensus pattern (24 bp):
GATAATAATATTTAATACACTAAA
Found at i:16741831 original size:3 final size:3
Alignment explanation
Indices: 16741823--16741864 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
16741813 ATATAAACTC
*
16741823 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AAA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16741865 GTATATGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:16747027 original size:28 final size:28
Alignment explanation
Indices: 16746996--16747051 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
16746986 AAGGATACCG
16746996 ATTTAGTTTTCTTTT-AATTTTTCAAAGC
1 ATTT-GTTTTCTTTTAAATTTTTCAAAGC
* *
16747024 ATTTTTTTTTTTTTAAATTTTTCAAAGC
1 ATTTGTTTTCTTTTAAATTTTTCAAAGC
16747052 CTTCCAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 8 0.32
28 17 0.68
ACGTcount: A:0.25, C:0.09, G:0.05, T:0.61
Consensus pattern (28 bp):
ATTTGTTTTCTTTTAAATTTTTCAAAGC
Found at i:16752442 original size:11 final size:11
Alignment explanation
Indices: 16752426--16752495 Score: 54
Period size: 10 Copynumber: 5.8 Consensus size: 11
16752416 CATTTTTTTT
16752426 AAATAAAATAA
1 AAATAAAATAA
16752437 AAAT-AAATAA
1 AAATAAAATAA
16752447 AAATAAAATGGGTTAA
1 AAATAAAA-----TAA
16752463 AAATAAAATTAA
1 AAATAAAA-TAA
16752475 ATCAA-AAAATAA
1 A--AATAAAATAA
16752487 AAATAAAAT
1 AAATAAAAT
16752496 TGAAGAAAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 18
0.74 0.00 0.26
Matches are distributed among these distances:
10 12 0.24
11 12 0.24
12 9 0.18
13 4 0.08
14 2 0.04
16 11 0.22
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.21
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:16752445 original size:15 final size:16
Alignment explanation
Indices: 16752425--16752493 Score: 61
Period size: 18 Copynumber: 4.2 Consensus size: 16
16752415 ACATTTTTTT
16752425 TAAAT-AAAATAAAAA
1 TAAATAAAAATAAAAA
16752440 TAAATAAAAAT-AAAA
1 TAAATAAAAATAAAAA
*** *
16752455 TGGGTTAAAAATAAAAT
1 T-AAATAAAAATAAAAA
16752472 TAAATCAAAAAATAAAAA
1 TAAAT--AAAAATAAAAA
16752490 TAAA
1 TAAA
16752494 ATTGAAGAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
15 10 0.24
16 13 0.32
17 4 0.10
18 14 0.34
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.22
Consensus pattern (16 bp):
TAAATAAAAATAAAAA
Found at i:16752851 original size:20 final size:21
Alignment explanation
Indices: 16752826--16752864 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
16752816 TAGAAAAATC
16752826 TAGATTT-TTTCAAATTTTTT
1 TAGATTTCTTTCAAATTTTTT
16752846 TAGATTTCTTTCAAATTTT
1 TAGATTTCTTTCAAATTTT
16752865 GTCTTAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.62
Consensus pattern (21 bp):
TAGATTTCTTTCAAATTTTTT
Found at i:16753277 original size:3 final size:3
Alignment explanation
Indices: 16753271--16753322 Score: 52
Period size: 3 Copynumber: 16.7 Consensus size: 3
16753261 TAGAAGAAAT
* *
16753271 ATA ATA ATA ATA ATA ATA ATA ATT ATA TATA CATTA GTA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -A-TA ATA ATA ATA ATA
16753318 ATA AT
1 ATA AT
16753323 GACATTAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
2 2 0.05
3 33 0.80
4 4 0.10
5 2 0.05
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:16753327 original size:23 final size:24
Alignment explanation
Indices: 16753284--16753329 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
16753274 ATAATAATAA
*
16753284 TAATAATAATTATATATACATTAG
1 TAATAATAATAATATATACATTAG
16753308 TAAT-ATAATAATA-ATGACATTA
1 TAATAATAATAATATAT-ACATTA
16753330 AAATGGTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 2 0.10
23 14 0.70
24 4 0.20
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (24 bp):
TAATAATAATAATATATACATTAG
Found at i:16753738 original size:114 final size:116
Alignment explanation
Indices: 16753620--16753904 Score: 321
Period size: 115 Copynumber: 2.5 Consensus size: 116
16753610 TAAATTATAT
* ** *
16753620 GAAATGATTTGAATCGAGTCAAGATCAAGTGATTAGAATGAAATCACTAGTTAAAATAAAA-CGC
1 GAAATGATTTGAATTGAGTCAAGATCAAGTGATTAGAATGAAATCAAGAGTCAAAATAAAAGCGC
* * *
16753684 TTAAGA-T-AAGTCG-AGGTTGAAAATGACCT-AGACGAAATCACGAATAATGA
66 TCAAGATTGAA-T-GAAAGTCGAAAATGA-CTGAGACGAAATCACGAATAATGA
* * * * *
16753734 GAAATGATTTGGATTGAGTTAAGATCAAGTGA-TCGGATGAAATCAAGAGTCAAAATAAAAGCGG
1 GAAATGATTTGAATTGAGTCAAGATCAAGTGATTAGAATGAAATCAAGAGTCAAAATAAAAGCGC
* * *
16753798 TCAAGATTGAATGAAAGTCGAAAATGATTGAGATGAAATCACGAATCATGA
66 TCAAGATTGAATGAAAGTCGAAAATGACTGAGACGAAATCACGAATAATGA
* * * * *
16753849 GAAATTATTTGAATTAAGTCAAGATCAAGTGATCAGAACGAAATCATGAGTCAAAA
1 GAAATGATTTGAATTGAGTCAAGATCAAGTGATTAGAATGAAATCAAGAGTCAAAA
16753905 AATGAAGTAA
Statistics
Matches: 141, Mismatches: 24, Indels: 10
0.81 0.14 0.06
Matches are distributed among these distances:
113 23 0.16
114 38 0.27
115 60 0.43
116 20 0.14
ACGTcount: A:0.45, C:0.10, G:0.21, T:0.24
Consensus pattern (116 bp):
GAAATGATTTGAATTGAGTCAAGATCAAGTGATTAGAATGAAATCAAGAGTCAAAATAAAAGCGC
TCAAGATTGAATGAAAGTCGAAAATGACTGAGACGAAATCACGAATAATGA
Found at i:16753962 original size:116 final size:116
Alignment explanation
Indices: 16753534--16754110 Score: 434
Period size: 114 Copynumber: 5.0 Consensus size: 116
16753524 GAATATCAGA
* * *
16753534 TGATCGAGATAAAATCATAAGTC--AAAATGAAGCAA-CAAAGA-CTGAGTCGAGAG-CGAAAAT
1 TGATCG-GATGAAATCATGAGTCAAAAAATGAAGCAATC-AAGATC-GAGTCAAG-GTCGAAAAT
* * ** * * *
16753594 AATCGAGATAAAATCATAAATTAT-ATGAAATGATTTGAATCGAGTCAAGATCAAG
62 GATCGAGATGAAATCACGAATCATGA-GAAATGATTTGGATTGAGTCAAGATCAAG
* * * * * * *
16753649 TGATTAGAATGAAATCACT-AGTTAAAATAA--AACGC--TTAAGAT-AAGTCGAGGTTGAAAAT
1 TGA-TCGGATGAAATCA-TGAGTCAAAA-AATGAA-GCAATCAAGATCGAGTCAAGGTCGAAAAT
* * * * *
16753708 GACCTAGACGAAATCACGAATAATGAGAAATGATTTGGATTGAGTTAAGATCAAG
62 GATCGAGATGAAATCACGAATCATGAGAAATGATTTGGATTGAGTCAAGATCAAG
* ** * * * *
16753763 TGATCGGATGAAATCAAGAGTCAAAATAA--AAGCGGTCAAGATTGAATGAAAGTCGAAAATGAT
1 TGATCGGATGAAATCATGAGTCAAAA-AATGAAGCAATCAAGATCGAGTCAAGGTCGAAAATGAT
* * * *
16753826 TGAGATGAAATCACGAATCATGAGAAATTATTTGAATTAAGTCAAGATCAAG
65 CGAGATGAAATCACGAATCATGAGAAATGATTTGGATTGAGTCAAGATCAAG
* * * * *
16753878 TGATCAGAACGAAATCATGAGTCAAAAAATGAAGTAATCAACATCGAGTCAAGGTCGAAAATGAA
1 TGATC-GGATGAAATCATGAGTCAAAAAATGAAGCAATCAAGATCGAGTCAAGGTCGAAAATGAT
* * * * * *
16753943 CGAGATG-AATCATGAATCATAAAAAATGATCTGGATTGAGCCAAGATCAAA
65 CGAGATGAAATCACGAATCATGAGAAATGATTTGGATTGAGTCAAGATCAAG
* * ** * **
16753994 TGATCTGGATGAAATCATGAGT--TAAAATGAAGCAATCAAGA-CAAGTTGAGATAAAAAATGAT
1 TGATC-GGATGAAATCATGAGTCAAAAAATGAAGCAATCAAGATCGAGTCAAGGTCGAAAATGAT
* * *
16754056 CAAGATGAAATCACGAATTATGAGAAATGATTTGGATTGAGTCAAAATCAAG
65 CGAGATGAAATCACGAATCATGAGAAATGATTTGGATTGAGTCAAGATCAAG
16754108 TGA
1 TGA
16754111 ATGATGTAAA
Statistics
Matches: 362, Mismatches: 82, Indels: 37
0.75 0.17 0.08
Matches are distributed among these distances:
112 2 0.01
113 44 0.12
114 119 0.33
115 83 0.23
116 77 0.21
117 35 0.10
118 2 0.01
ACGTcount: A:0.46, C:0.11, G:0.21, T:0.23
Consensus pattern (116 bp):
TGATCGGATGAAATCATGAGTCAAAAAATGAAGCAATCAAGATCGAGTCAAGGTCGAAAATGATC
GAGATGAAATCACGAATCATGAGAAATGATTTGGATTGAGTCAAGATCAAG
Found at i:16754864 original size:43 final size:44
Alignment explanation
Indices: 16754736--16754910 Score: 180
Period size: 43 Copynumber: 4.0 Consensus size: 44
16754726 TTTCATTTAA
* * *
16754736 TTCATGTTGCC-TTTCAAGGTTTTCAACTTGAACTTTTTTATTTG
1 TTCAAGTTGCCTTTTCGA-GTTTTCAACTTGAACTTTTTTTTTTG
* * *
16754780 AATCCAAGTCGCCTTTTCGAGTTTTCAACTTGAAC--CTTTTTTTG
1 --TTCAAGTTGCCTTTTCGAGTTTTCAACTTGAACTTTTTTTTTTG
*
16754824 TTCAAGTTGTCC-TTTCGA-TTTTCAACTCGAACTTTTTTTTTTG
1 TTCAAGTTG-CCTTTTCGAGTTTTCAACTTGAACTTTTTTTTTTG
* * *
16754867 TTCAAGTTACCTTTTCGAGTTTTCAATTTAAACTTTTCTTTTTT
1 TTCAAGTTGCCTTTTCGAGTTTTCAACTTGAACTTTT-TTTTTT
16754911 TAGAATCAAG
Statistics
Matches: 108, Mismatches: 14, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
41 13 0.12
42 15 0.14
43 24 0.22
44 22 0.20
45 6 0.06
46 23 0.21
47 5 0.05
ACGTcount: A:0.19, C:0.18, G:0.11, T:0.51
Consensus pattern (44 bp):
TTCAAGTTGCCTTTTCGAGTTTTCAACTTGAACTTTTTTTTTTG
Found at i:16761566 original size:3 final size:3
Alignment explanation
Indices: 16761552--16761581 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
16761542 TTAAATATAT
*
16761552 TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
16761582 ATATTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:16761593 original size:16 final size:16
Alignment explanation
Indices: 16761559--16761607 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
16761549 TATTAATACT
16761559 AATA-ATAATAA-TAA
1 AATATATAATAATTAA
*
16761573 TAATA-ATAAATATTTAA
1 -AATATAT-AATAATTAA
16761590 AATATATAATAATTAA
1 AATATATAATAATTAA
16761606 AA
1 AA
16761608 AATTAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 6 0.21
16 18 0.62
17 5 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATATATAATAATTAA
Found at i:16761628 original size:22 final size:22
Alignment explanation
Indices: 16761600--16761645 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
16761590 AATATATAAT
16761600 AATTAAAAAATTAAA-AAAATTA
1 AATT-AAAAATTAAATAAAATTA
*
16761622 AATTAAAAATTAAATTAAATTA
1 AATTAAAAATTAAATAAAATTA
16761644 AA
1 AA
16761646 AAAAGAAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTAAAAATTAAATAAAATTA
Found at i:16761631 original size:12 final size:12
Alignment explanation
Indices: 16761614--16761640 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
16761604 AAAAAATTAA
16761614 AAAAATTAAATT
1 AAAAATTAAATT
16761626 AAAAATTAAATT
1 AAAAATTAAATT
16761638 AAA
1 AAA
16761641 TTAAAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAAAATTAAATT
Found at i:16762671 original size:26 final size:26
Alignment explanation
Indices: 16762627--16762709 Score: 78
Period size: 26 Copynumber: 3.2 Consensus size: 26
16762617 TTGGTCACCT
* * *
16762627 GAATCGTTGAACCGGTCAGATCGCCC
1 GAATCGTCGAACTGATCAGATCGCCC
** *
16762653 GAA-CAGTCGAACTGATCAGATCTTCT
1 GAATC-GTCGAACTGATCAGATCGCCC
* *
16762679 GAATCGTCGAACTGGTTAGATCGCCC
1 GAATCGTCGAACTGATCAGATCGCCC
16762705 GAATC
1 GAATC
16762710 AACGTTGATC
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
25 1 0.02
26 42 0.95
27 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.23
Consensus pattern (26 bp):
GAATCGTCGAACTGATCAGATCGCCC
Found at i:16762792 original size:17 final size:17
Alignment explanation
Indices: 16762772--16762805 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
16762762 TCTAAATTTA
*
16762772 TTTTATGTTATTATTAT
1 TTTTATGTTATAATTAT
*
16762789 TTTTATTTTATAATTAT
1 TTTTATGTTATAATTAT
16762806 GTATGATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTATGTTATAATTAT
Found at i:16762883 original size:24 final size:23
Alignment explanation
Indices: 16762856--16762900 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
16762846 TGTTATTAAT
*
16762856 AATAATAAAATAAAAATAATATAA
1 AATAAAAAAATAAAAA-AATATAA
16762880 AATAAAAAAATAAAAAAATAT
1 AATAAAAAAATAAAAAAATAT
16762901 GTTGAAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (23 bp):
AATAAAAAAATAAAAAAATATAA
Found at i:16762891 original size:8 final size:8
Alignment explanation
Indices: 16762856--16762899 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
16762846 TGTTATTAAT
*
16762856 AATAATAA
1 AATAAAAA
16762864 AATAAAAA
1 AATAAAAA
*
16762872 TAAT-ATAA
1 -AATAAAAA
16762880 AATAAAAA
1 AATAAAAA
16762888 AATAAAAA
1 AATAAAAA
16762896 AATA
1 AATA
16762900 TGTTGAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
7 3 0.10
8 25 0.81
9 3 0.10
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (8 bp):
AATAAAAA
Found at i:16762897 original size:16 final size:17
Alignment explanation
Indices: 16762853--16762899 Score: 71
Period size: 16 Copynumber: 2.9 Consensus size: 17
16762843 AATTGTTATT
16762853 AATAATAATAAAATAAA
1 AATAATAATAAAATAAA
16762870 AATAAT-ATAAAATAAA
1 AATAATAATAAAATAAA
*
16762886 AA-AATAAAAAAATA
1 AATAATAATAAAATA
16762900 TGTTGAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 3 0.11
16 19 0.68
17 6 0.21
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (17 bp):
AATAATAATAAAATAAA
Found at i:16763023 original size:19 final size:19
Alignment explanation
Indices: 16762999--16763037 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
16762989 TCAAACAAAT
16762999 AATTTCGCCTAGATGTTGA
1 AATTTCGCCTAGATGTTGA
16763018 AATTTCGCCTAGATGTTGA
1 AATTTCGCCTAGATGTTGA
16763037 A
1 A
16763038 GGGAATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (19 bp):
AATTTCGCCTAGATGTTGA
Found at i:16763030 original size:68 final size:68
Alignment explanation
Indices: 16762957--16763084 Score: 206
Period size: 68 Copynumber: 1.9 Consensus size: 68
16762947 ATTTTCCCTA
*
16762957 CCTAGATATT-AGAGGGAATAAAAAATATTTTTTCAAACAAATAATT-TCGCCTAGATGTTGAAA
1 CCTAGATATTGA-AGGGAATAAAAAATATTTTTTCAAACAAATAATTCTC-CCTAGAGGTTGAAA
16763020 TTTCG
64 TTTCG
*
16763025 CCTAGATGTTGAAGGGAATAAAAAATATTTTTTCAAACAAATAATTCTCCCTAGAGGTTG
1 CCTAGATATTGAAGGGAATAAAAAATATTTTTTCAAACAAATAATTCTCCCTAGAGGTTG
16763085 GAGAATTATT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
68 53 0.95
69 3 0.05
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (68 bp):
CCTAGATATTGAAGGGAATAAAAAATATTTTTTCAAACAAATAATTCTCCCTAGAGGTTGAAATT
TCG
Found at i:16770491 original size:19 final size:20
Alignment explanation
Indices: 16770451--16770491 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
16770441 AGCCTACAGC
* *
16770451 TGCTGATAAAAAAAATGTAA
1 TGCTGAAAAAAAAAAAGTAA
16770471 TGCTGAAAAAAAAAAAG-AA
1 TGCTGAAAAAAAAAAAGTAA
16770490 TG
1 TG
16770492 GCATGCCTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.59, C:0.05, G:0.17, T:0.20
Consensus pattern (20 bp):
TGCTGAAAAAAAAAAAGTAA
Found at i:16774441 original size:11 final size:10
Alignment explanation
Indices: 16774402--16774470 Score: 54
Period size: 10 Copynumber: 6.8 Consensus size: 10
16774392 ATTTTACCTT
*
16774402 AAAAAAAAAG
1 AAAAAAAATG
*
16774412 AAAAAATAT-
1 AAAAAAAATG
16774421 ACAAAAAAATG
1 A-AAAAAAATG
16774432 AAAAATAAAT-
1 AAAAA-AAATG
*
16774442 AAAAAATAA-A
1 AAAAAA-AATG
16774452 AACAAAAAATG
1 AA-AAAAAATG
16774463 AAAAAAAA
1 AAAAAAAA
16774471 ATGAGAAAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
9 2 0.04
10 35 0.73
11 11 0.23
ACGTcount: A:0.83, C:0.03, G:0.04, T:0.10
Consensus pattern (10 bp):
AAAAAAAATG
Found at i:16774445 original size:19 final size:20
Alignment explanation
Indices: 16774403--16774447 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
16774393 TTTTACCTTA
*
16774403 AAAAAAAAGAAAAAATATAC
1 AAAAAAAAGAAAAAATAAAC
* *
16774423 AAAAAAATG-AAAAATAAAT
1 AAAAAAAAGAAAAAATAAAC
16774442 AAAAAA
1 AAAAAA
16774448 TAAAAACAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.82, C:0.02, G:0.04, T:0.11
Consensus pattern (20 bp):
AAAAAAAAGAAAAAATAAAC
Found at i:16774446 original size:20 final size:19
Alignment explanation
Indices: 16774401--16774471 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 19
16774391 TATTTTACCT
*
16774401 TAAAAAAAAAGAAAAAATA
1 TAAAAAAAAAGAAAAAAAA
*
16774420 TACAAAAAAATGAAAAATAAA
1 TA-AAAAAAAAGAAAAA-AAA
16774441 TAAAAAATAAA-AACAAAAAA
1 TAAAAAA-AAAGAA-AAAAAA
16774461 TGAAAAAAAAA
1 T-AAAAAAAAA
16774472 TGAGAAAAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
19 2 0.05
20 27 0.61
21 15 0.34
ACGTcount: A:0.82, C:0.03, G:0.04, T:0.11
Consensus pattern (19 bp):
TAAAAAAAAAGAAAAAAAA
Found at i:16774471 original size:11 final size:11
Alignment explanation
Indices: 16774402--16774479 Score: 60
Period size: 11 Copynumber: 7.5 Consensus size: 11
16774392 ATTTTACCTT
16774402 AAAAAAAAA-G
1 AAAAAAAAATG
*
16774412 -AAAAAATAT-
1 AAAAAAAAATG
*
16774421 ACAAAAAAATG
1 AAAAAAAAATG
*
16774432 AAAAATAAAT-
1 AAAAAAAAATG
16774442 AAAAAATAAA--
1 AAAAAA-AAATG
*
16774452 AACAAAAAATG
1 AAAAAAAAATG
16774463 AAAAAAAAATG
1 AAAAAAAAATG
16774474 AGAAAA
1 A-AAAA
16774480 GAAGTGATTC
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
9 10 0.19
10 17 0.32
11 22 0.42
12 4 0.08
ACGTcount: A:0.81, C:0.03, G:0.06, T:0.10
Consensus pattern (11 bp):
AAAAAAAAATG
Found at i:16775605 original size:69 final size:69
Alignment explanation
Indices: 16775513--16775750 Score: 248
Period size: 69 Copynumber: 3.4 Consensus size: 69
16775503 GTTCAATCTT
* *
16775513 AATCATCTTTAACCTTTGGCTCGTGGTTTAATCCTGATCATTTCATTTTCTGACTTGCAGTTCAA
1 AATCATCTTTAATCTTTGACTCGTGGTTTAATCCTGATCATTTCATTTTCTGACTTGCAGTTCAA
16775578 TTCC
66 TTCC
* * *
16775582 AATCATCTTTAATCTCTGACTCGTGGTTTAATCCCGATCATTTCATTAATTGTCTGACTTG-TGA
1 AATCATCTTTAATCTTTGACTCGTGGTTTAATCCTGATCATTTCA-T--TT-TCTGACTTGCAG-
*
16775646 TTC-AGTCC
61 TTCAATTCC
* * * * *
16775654 AGTCATCTTTAATCTTTGACTCGTGGTTTGAT-CTCGATCATTTCATTCTCTGACTTACGGTTCA
1 AATCATCTTTAATCTTTGACTCGTGGTTTAATCCT-GATCATTTCATTTTCTGACTTGCAGTTCA
* *
16775718 GTCCC
65 ATTCC
** * *
16775723 TGTCATTTTTAATCTTTGACTTGTGGTT
1 AATCATCTTTAATCTTTGACTCGTGGTT
16775751 CAGTTTCAAT
Statistics
Matches: 142, Mismatches: 19, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
68 11 0.08
69 70 0.49
70 1 0.01
71 2 0.01
72 46 0.32
73 12 0.08
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.44
Consensus pattern (69 bp):
AATCATCTTTAATCTTTGACTCGTGGTTTAATCCTGATCATTTCATTTTCTGACTTGCAGTTCAA
TTCC
Found at i:16775638 original size:38 final size:38
Alignment explanation
Indices: 16775532--16775700 Score: 101
Period size: 35 Copynumber: 4.7 Consensus size: 38
16775522 TAACCTTTGG
*
16775532 CTCGTGGTTTAATCCTGATCATTTCA-T--T-TTCTGA
1 CTCGTGGTTTAATCCCGATCATTTCATTAATCTTCTGA
* ** * * * *
16775566 CTTGCAGTTCAATTCCAATCA--TCTTTAATC-TCTGA
1 CTCGTGGTTTAATCCCGATCATTTCATTAATCTTCTGA
16775601 CTCGTGGTTTAATCCCGATCATTTCATTAAT-TGTCTGA
1 CTCGTGGTTTAATCCCGATCATTTCATTAATCT-TCTGA
* * * * * *
16775639 CTTGTGATTCAGTCCAG-TCA--TCTTTAATCTT-TGA
1 CTCGTGGTTTAATCCCGATCATTTCATTAATCTTCTGA
* *
16775673 CTCGTGGTTTGATCTCGATCATTTCATT
1 CTCGTGGTTTAATCCCGATCATTTCATT
16775701 CTCTGACTTA
Statistics
Matches: 94, Mismatches: 29, Indels: 21
0.65 0.20 0.15
Matches are distributed among these distances:
32 2 0.02
33 1 0.01
34 27 0.29
35 32 0.34
36 1 0.01
37 14 0.15
38 17 0.18
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.44
Consensus pattern (38 bp):
CTCGTGGTTTAATCCCGATCATTTCATTAATCTTCTGA
Found at i:16775769 original size:35 final size:35
Alignment explanation
Indices: 16775580--16775776 Score: 123
Period size: 35 Copynumber: 5.6 Consensus size: 35
16775570 CAGTTCAATT
* * * *
16775580 CCAATCATCTTTAATCTCTGACTCGTGGTTTAATC
1 CCAATCATCTTTAATCTTTGACTTGTGGTTCAGTC
* * *
16775615 CCGATCATTTCATTAAT-TGTCTGACTTGTGATTCAGT-
1 CCAATCA--TCTTTAATCT-T-TGACTTGTGGTTCAGTC
* * *
16775652 CCAGTCATCTTTAATCTTTGACTCGTGGTT-TGATC
1 CCAATCATCTTTAATCTTTGACTTGTGGTTCAG-TC
* * * * * **
16775687 TCGATCAT-TTCATTCTCTGACTTACGGTTCAGTC
1 CCAATCATCTTTAATCTTTGACTTGTGGTTCAGTC
** * *
16775721 CCTGTCATTTTTAATCTTTGACTTGTGGTTCAGTT
1 CCAATCATCTTTAATCTTTGACTTGTGGTTCAGTC
*
16775756 TCAATCATCTTTAATCTTTGA
1 CCAATCATCTTTAATCTTTGA
16775777 TTTCGTTAAT
Statistics
Matches: 117, Mismatches: 36, Indels: 18
0.68 0.21 0.11
Matches are distributed among these distances:
33 1 0.01
34 33 0.28
35 57 0.49
36 2 0.02
37 12 0.10
38 12 0.10
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.44
Consensus pattern (35 bp):
CCAATCATCTTTAATCTTTGACTTGTGGTTCAGTC
Found at i:16776041 original size:73 final size:73
Alignment explanation
Indices: 16775776--16777050 Score: 1136
Period size: 73 Copynumber: 18.0 Consensus size: 73
16775766 TTAATCTTTG
* * ** * * * **
16775776 ATTTCGTTAATTCTTTGACTTATGATTCAGCCCCAGTCATCTTTAATCTTTGGCTCG-CATTTAA
1 ATTTCATTAATTCTCTGACTTGCGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTGGTTTAA
16775840 TCCCGATC
66 TCCCGATC
* * *
16775848 ATTTCATTAATTGC-CTGACTTGTGGTTCAGTCCCAGTCATCTTTAATCTCTGACTCGTAGTTTA
1 ATTTCATTAATT-CTCTGACTTGCGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTGGTTTA
*
16775912 ATCTCGATC
65 ATCCCGATC
* *
16775921 ATTTCATT--CT-TC-GACTTGTGGTTCAGTCCCAGTCATCTTT-ATCCTTTGACTCGTGGTTTA
1 ATTTCATTAATTCTCTGACTTGCGGTTCAGTCCCAGTCATCTTTAAT-CTTTGACTCGTGGTTTA
* *
16775981 ATCTCGATT
65 ATCCCGATC
* * * *
16775990 ATTTCATTAATTGTCTGACTTGCGATTCAGTCCCAGTCGTCTTTAATCTTTGACTCATGGTTTAA
1 ATTTCATTAATTCTCTGACTTGCGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTGGTTTAA
*
16776055 TCTCGATC
66 TCCCGATC
* * * *
16776063 ATTTC----ATTCCCTGACTTGTGATTCAGTCCC-GATCATCTTTAATCTTTGACTCGTGATTTA
1 ATTTCATTAATTCTCTGACTTGCGGTTCAGTCCCAG-TCATCTTTAATCTTTGACTCGTGGTTTA
16776123 ATCCCGATC
65 ATCCCGATC
** * * *
16776132 ATTTCATTAATTGC-CCAACTTACGATTCAGTCCCAGTCATCTTTAATCTCTGACTCGTGGTTTA
1 ATTTCATTAATT-CTCTGACTTGCGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTGGTTTA
16776196 ATCCCGATC
65 ATCCCGATC
* * * ** * *
16776205 ATTTC----ATTCTTTGGCTTACGGTTCAGTCCCAACCATCTATAATATTTGACTCGTGGTTTAA
1 ATTTCATTAATTCTCTGACTTGCGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTGGTTTAA
*
16776266 TCCTGATC
66 TCCCGATC
* ** *
16776274 ATTTCATTAATTGCTC-GACTTGCGATTCAGTTTCAATCATCTTTAATCTTTGACTCGTGGTTTA
1 ATTTCATTAATT-CTCTGACTTGCGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTGGTTTA
* *
16776338 ATCTCGATT
65 ATCCCGATC
* * * *
16776347 ATTTC----ATTCTCTGACTTGCGGTTCAGTCCCAATCATCTTTAACCTTTGGCTCGTGATTTAA
1 ATTTCATTAATTCTCTGACTTGCGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTGGTTTAA
16776408 TCCCGATC
66 TCCCGATC
* * * *
16776416 ATTTCATTAATTCTCTGACTTACGGTTCAGTCCCAGTCATCTTTAACCTTTGGCTCATGGTTTAA
1 ATTTCATTAATTCTCTGACTTGCGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTGGTTTAA
*
16776481 TCCCGGTC
66 TCCCGATC
* * * * * * ** *
16776489 ATTTCATTAATTTTTTGATTTGTGGTTCAGTCTCAGTCATCTTTAGTCTTTGGTTCGTGATTTAA
1 ATTTCATTAATTCTCTGACTTGCGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTGGTTTAA
*
16776554 TCCCAATC
66 TCCCGATC
* *
16776562 ATTTC----ATTCTCTGACTTGCGGTTCAG-CCTCAGTAATCTTT-ATCTTTTAACTCGTGGTTT
1 ATTTCATTAATTCTCTGACTTGCGGTTCAGTCC-CAGTCATCTTTAATC-TTTGACTCGTGGTTT
16776621 AATCCCGATC
64 AATCCCGATC
* ** * * * **
16776631 ATTTCATTAATTGC-CTGACTAGCAATTCAGTCTCAGTCATCTTTAATATTTAACTTATGGTTTA
1 ATTTCATTAATT-CTCTGACTTGCGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTGGTTTA
*
16776695 ATCTCGATC
65 ATCCCGATC
* * ** * * *
16776704 ATTTC----ATTCTCTGACTTACGGTTCAATTTCAGTCATTTTTAATCTCTGACTCGTGGTTTGA
1 ATTTCATTAATTCTCTGACTTGCGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTGGTTTAA
*
16776765 TCCTGATC
66 TCCCGATC
* * *
16776773 ATTTCATT--TT-T-TGACTTGCGGTTCAGTCCCAATCACCTTT-ATCCTTTAACTCGTGGTTTA
1 ATTTCATTAATTCTCTGACTTGCGGTTCAGTCCCAGTCATCTTTAAT-CTTTGACTCGTGGTTTA
*
16776833 ATCTCGATC
65 ATCCCGATC
* * * *
16776842 ATTTCGTTCATTACTC-GACTTGCGGTTCAGTCTCAGGCATCTTTAATCTTTGACTC--------
1 ATTTCATTAATT-CTCTGACTTGCGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTGGTTTA
*
16776898 A-CCCGACC
65 ATCCCGATC
* * * * *
16776906 ATTTCATTAATTCCCTCGACTTGCGGTTCAG-CTCAATCATCTTTAATCTTTGACTCGCGATTTA
1 ATTTCATTAATTCTCT-GACTTGCGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTGGTTTA
* *
16776970 ATCTCGGTC
65 ATCCCGATC
* * * * * * * *
16776979 ATTTCATTAATTCCCTCGACTTACGGTTCAGTCTCAGTCATCTTTAACCCTTGACTCGCGGTGTC
1 ATTTCATTAATTCTCT-GACTTGCGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTGGTTTA
16777044 ATCCCGA
65 ATCCCGA
16777051 CACTTTCTTT
Statistics
Matches: 989, Mismatches: 155, Indels: 116
0.78 0.12 0.09
Matches are distributed among these distances:
63 2 0.00
64 38 0.04
65 15 0.02
68 13 0.01
69 386 0.39
70 2 0.00
71 6 0.01
72 51 0.05
73 432 0.44
74 44 0.04
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.41
Consensus pattern (73 bp):
ATTTCATTAATTCTCTGACTTGCGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTGGTTTAA
TCCCGATC
Found at i:16776044 original size:142 final size:141
Alignment explanation
Indices: 16775801--16777050 Score: 1076
Period size: 142 Copynumber: 8.8 Consensus size: 141
16775791 TGACTTATGA
* * * *
16775801 TTCAGCCCCAGTCATCTTTAATCTTTGGCTCG-CATTTAATCCCGATCATTTCATTAATTGCCTG
1 TTCAGTCCCAGTCATCTTT-ATCTTTGACTCGTGATTTAATCCCGATCATTTCATTAATTGTCTG
* * * *
16775865 ACTTGTGGTTCAGTCCCAGTCATCTTTAATCTCTGACTCGTAGTTTAATCTCGATCATTTCATTC
65 ACTTGCGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTGGTTTAATCCCGATCATTTCATTC
*
16775930 TTCGACTTGTGG
130 TTCGACTTGCGG
* * *
16775942 TTCAGTCCCAGTCATCTTTATCCTTTGACTCGTGGTTTAATCTCGATTATTTCATTAATTGTCTG
1 TTCAGTCCCAGTCATCTTTAT-CTTTGACTCGTGATTTAATCCCGATCATTTCATTAATTGTCTG
* * * *
16776007 ACTTGCGATTCAGTCCCAGTCGTCTTTAATCTTTGACTCATGGTTTAATCTCGATCATTTCATTC
65 ACTTGCGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTGGTTTAATCCCGATCATTTCATTC
* * *
16776072 -CCTGACTTGTGA
130 TTC-GACTTGCGG
* *
16776084 TTCAGTCCC-GATCATCTTTAATCTTTGACTCGTGATTTAATCCCGATCATTTCATTAATTGCCC
1 TTCAGTCCCAG-TCATCTTT-ATCTTTGACTCGTGATTTAATCCCGATCATTTCATTAATTGTCT
* * * *
16776148 AACTTACGATTCAGTCCCAGTCATCTTTAATCTCTGACTCGTGGTTTAATCCCGATCATTTCATT
64 GACTTGCGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTGGTTTAATCCCGATCATTTCATT
* * *
16776213 CTTTGGCTTACGG
129 CTTCGACTTGCGG
** * * * *
16776226 TTCAGTCCCAACCATCTATAATATTTGACTCGTGGTTTAATCCTGATCATTTCATTAATTG-CTC
1 TTCAGTCCCAGTCATCT-TTATCTTTGACTCGTGATTTAATCCCGATCATTTCATTAATTGTCT-
* ** * * *
16776290 GACTTGCGATTCAGTTTCAATCATCTTTAATCTTTGACTCGTGGTTTAATCTCGATTATTTCATT
64 GACTTGCGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTGGTTTAATCCCGATCATTTCATT
16776355 C-TCTGACTTGCGG
129 CTTC-GACTTGCGG
* * * *
16776368 TTCAGTCCCAATCATCTTTAACCTTTGGCTCGTGATTTAATCCCGATCATTTCATTAATTCTCTG
1 TTCAGTCCCAGTCATCTTT-ATCTTTGACTCGTGATTTAATCCCGATCATTTCATTAATTGTCTG
* * * * *
16776433 ACTTACGGTTCAGTCCCAGTCATCTTTAACCTTTGGCTCATGGTTTAATCCCGGTCATTTCATTA
65 ACTTGCGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTGGTTTAATCCCGATCATTTC----
* * * *
16776498 ATTTTTTGATTTGTGG
126 ATTCTTCGACTTGCGG
* ** * *
16776514 TTCAGTCTCAGTCATCTTTAGTCTTTGGTTCGTGATTTAATCCCAATCATTTC----ATTCTCTG
1 TTCAGTCCCAGTCATCTTTA-TCTTTGACTCGTGATTTAATCCCGATCATTTCATTAATTGTCTG
* *
16776575 ACTTGCGGTTCAG-CCTCAGTAATCTTT-ATCTTTTAACTCGTGGTTTAATCCCGATCATTTCAT
65 ACTTGCGGTTCAGTCC-CAGTCATCTTTAATC-TTTGACTCGTGGTTTAATCCCGATCATTTCAT
* * **
16776638 TAATTGCCTGACTAGCAA
128 T-CTT--C-GACTTGCGG
* * * ** * * *
16776656 TTCAGTCTCAGTCATCTTTAATATTTAACTTATGGTTTAATCTCGATCATTTC----ATTCTCTG
1 TTCAGTCCCAGTCATCTTT-ATCTTTGACTCGTGATTTAATCCCGATCATTTCATTAATTGTCTG
* * ** * * * * *
16776717 ACTTACGGTTCAATTTCAGTCATTTTTAATCTCTGACTCGTGGTTTGATCCTGATCATTTCATTT
65 ACTTGCGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTGGTTTAATCCCGATCATTTCATTC
*
16776782 TTTGACTTGCGG
130 TTCGACTTGCGG
* * * * * * * *
16776794 TTCAGTCCCAATCACCTTTATCCTTTAACTCGTGGTTTAATCTCGATCATTTCGTTCATT-ACTC
1 TTCAGTCCCAGTCATCTTTAT-CTTTGACTCGTGATTTAATCCCGATCATTTCATTAATTGTCT-
* * *
16776858 GACTTGCGGTTCAGTCTCAGGCATCTTTAATCTTTGACTC--------A-CCCGACCATTTCATT
64 GACTTGCGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTGGTTTAATCCCGATCATTTC---
*
16776914 AATTCCCTCGACTTGCGG
126 -ATT-CTTCGACTTGCGG
* * * * * **
16776932 TTCAG-CTCAATCATCTTTAATCTTTGACTCGCGATTTAATCTCGGTCATTTCATTAATTCCCTC
1 TTCAGTCCCAGTCATCTTT-ATCTTTGACTCGTGATTTAATCCCGATCATTTCATTAATTGTCT-
* * * * * * *
16776996 GACTTACGGTTCAGTCTCAGTCATCTTTAACCCTTGACTCGCGGTGTCATCCCGA
64 GACTTGCGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTGGTTTAATCCCGA
16777051 CACTTTCTTT
Statistics
Matches: 913, Mismatches: 147, Indels: 92
0.79 0.13 0.08
Matches are distributed among these distances:
133 10 0.01
134 1 0.00
137 48 0.05
138 109 0.12
139 2 0.00
140 2 0.00
141 40 0.04
142 628 0.69
143 9 0.01
145 1 0.00
146 57 0.06
147 6 0.01
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.41
Consensus pattern (141 bp):
TTCAGTCCCAGTCATCTTTATCTTTGACTCGTGATTTAATCCCGATCATTTCATTAATTGTCTGA
CTTGCGGTTCAGTCCCAGTCATCTTTAATCTTTGACTCGTGGTTTAATCCCGATCATTTCATTCT
TCGACTTGCGG
Found at i:16776344 original size:284 final size:284
Alignment explanation
Indices: 16775799--16777025 Score: 1274
Period size: 284 Copynumber: 4.3 Consensus size: 284
16775789 TTTGACTTAT
* * * *
16775799 GATTCAGCCCCAGTCATCTTTAATCTTTGGCTCG-CATTTAATCCCGATCATTTCATTAATTGCC
1 GATTCAGTCCCAATCATCTTTAATCTTTGACTCGTGATTTAATCCCGATCATTTCATTAATTGCC
* ** * *
16775863 TGACTTGTGGTTCAGTCCCAGTCATCTTTAATCTCTGACTCGTAGTTTAATCTCGATCATTTCAT
66 CGACTTACGGTTCAGTCCCAGTCATCTTTAATCTCTGACTCGTGGTTTAATCCCGATCATTTCAT
* * * * *
16775928 TCTTCGACTTGTGGTTCAGTCCCAGTCATCTTTATCCTTTGACTCGTGGTTTAATCTCGATTATT
131 TCTTTGACTTGCGGTTCAGTCCCAATCATCTTAATCCTTTGACTCGTGGTTTAATCTCGATCATT
* * *
16775993 TCATTAATTG-TCTGACTTGCGATTCAGTCCCAGTCGTCTTTAATCTTTGACTCATGGTTTAATC
196 TCATTAATTGCTC-GACTTGCGATTCAGTCTCAGTCATCTTTAATCTTTGACTCGTGGTTTAATC
*
16776057 TCGATCATTTCATTCCCTGACTTGT
260 TCGATCATTTCATTCCCTGACTTGC
*
16776082 GATTCAGTCCCGATCATCTTTAATCTTTGACTCGTGATTTAATCCCGATCATTTCATTAATTGCC
1 GATTCAGTCCCAATCATCTTTAATCTTTGACTCGTGATTTAATCCCGATCATTTCATTAATTGCC
* *
16776147 CAACTTACGATTCAGTCCCAGTCATCTTTAATCTCTGACTCGTGGTTTAATCCCGATCATTTCAT
66 CGACTTACGGTTCAGTCCCAGTCATCTTTAATCTCTGACTCGTGGTTTAATCCCGATCATTTCAT
* * * *
16776212 TCTTTGGCTTACGGTTCAGTCCCAACCATCTATAAT-ATTTGACTCGTGGTTTAATC-CTGATCA
131 TCTTTGACTTGCGGTTCAGTCCCAATCATCT-TAATCCTTTGACTCGTGGTTTAATCTC-GATCA
* *
16776275 TTTCATTAATTGCTCGACTTGCGATTCAGTTTCAATCATCTTTAATCTTTGACTCGTGGTTTAAT
194 TTTCATTAATTGCTCGACTTGCGATTCAGTCTCAGTCATCTTTAATCTTTGACTCGTGGTTTAAT
* *
16776340 CTCGATTATTTCATTCTCTGACTTGC
259 CTCGATCATTTCATTCCCTGACTTGC
* * *
16776366 GGTTCAGTCCCAATCATCTTTAACCTTTGGCTCGTGATTTAATCCCGATCATTTCATTAATT-CT
1 GATTCAGTCCCAATCATCTTTAATCTTTGACTCGTGATTTAATCCCGATCATTTCATTAATTGC-
* * * * * *
16776430 CTGACTTACGGTTCAGTCCCAGTCATCTTTAACCTTTGGCTCATGGTTTAATCCCGGTCATTTCA
65 CCGACTTACGGTTCAGTCCCAGTCATCTTTAATCTCTGACTCGTGGTTTAATCCCGATCATTTC-
* * * * * * ** * * *
16776495 TTAATTTTTTGATTTGTGGTTCAGTCTCAGTCATCTTTAGT-CTTTGGTTCGTGATTTAATCCCA
129 ---ATTCTTTGACTTGCGGTTCAGTCCCAATCATC-TTAATCCTTTGACTCGTGGTTTAATCTCG
* * * * *
16776559 ATCATTTCATT--CT-CT-GACTTGCGGTTCAGCCTCAGTAATCTTT-ATCTTTTAACTCGTGGT
190 ATCATTTCATTAATTGCTCGACTTGCGATTCAGTCTCAGTCATCTTTAATC-TTTGACTCGTGGT
* * *
16776619 TTAATCCCGATCATTTCATTAATTGCCTGACTAGC
254 TTAATCTCGATCATTTC----ATTCCCTGACTTGC
* * * * * ** * * *
16776654 AATTCAGTCTCAGTCATCTTTAATATTTAACTTATGGTTTAATCTCGATCATTTCATT--CT--C
1 GATTCAGTCCCAATCATCTTTAATCTTTGACTCGTGATTTAATCCCGATCATTTCATTAATTGCC
* * ** * * *
16776715 TGACTTACGGTTCAATTTCAGTCATTTTTAATCTCTGACTCGTGGTTTGATCCTGATCATTTCAT
66 CGACTTACGGTTCAGTCCCAGTCATCTTTAATCTCTGACTCGTGGTTTAATCCCGATCATTTCAT
* * * *
16776780 TTTTTGACTTGCGGTTCAGTCCCAATCACCTTTATCCTTTAACTCGTGGTTTAATCTCGATCATT
131 TCTTTGACTTGCGGTTCAGTCCCAATCATCTTAATCCTTTGACTCGTGGTTTAATCTCGATCATT
* * * * * *** ***
16776845 TCGTTCATTACTCGACTTGCGGTTCAGTCTCAGGCATCTTTAATCTTTGACTCACCCG-ACCAT-
196 TCATTAATTGCTCGACTTGCGATTCAGTCTCAGTCATCTTTAATCTTTGACTC-GTGGTTTAATC
*
16776908 T---TCA-TTAATTCCCTCGACTTGC
260 TCGATCATTTCATTCCCT-GACTTGC
* * * * * *
16776930 GGTTCAG-CTCAATCATCTTTAATCTTTGACTCGCGATTTAATCTCGGTCATTTCATTAATTCCC
1 GATTCAGTCCCAATCATCTTTAATCTTTGACTCGTGATTTAATCCCGATCATTTCATTAATTGCC
*
16776994 TCGACTTACGGTTCAGTCTCAGTCATCTTTAA
66 -CGACTTACGGTTCAGTCCCAGTCATCTTTAA
16777026 CCCTTGACTC
Statistics
Matches: 780, Mismatches: 135, Indels: 61
0.80 0.14 0.06
Matches are distributed among these distances:
275 48 0.06
276 11 0.01
277 1 0.00
279 6 0.01
280 84 0.11
282 1 0.00
283 37 0.05
284 466 0.60
285 11 0.01
286 2 0.00
288 111 0.14
289 2 0.00
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.41
Consensus pattern (284 bp):
GATTCAGTCCCAATCATCTTTAATCTTTGACTCGTGATTTAATCCCGATCATTTCATTAATTGCC
CGACTTACGGTTCAGTCCCAGTCATCTTTAATCTCTGACTCGTGGTTTAATCCCGATCATTTCAT
TCTTTGACTTGCGGTTCAGTCCCAATCATCTTAATCCTTTGACTCGTGGTTTAATCTCGATCATT
TCATTAATTGCTCGACTTGCGATTCAGTCTCAGTCATCTTTAATCTTTGACTCGTGGTTTAATCT
CGATCATTTCATTCCCTGACTTGC
Found at i:16776913 original size:138 final size:138
Alignment explanation
Indices: 16776785--16777035 Score: 353
Period size: 138 Copynumber: 1.8 Consensus size: 138
16776775 TTCATTTTTT
* * *
16776785 GACTTGCGGTTCAGTCCCAATCACCTTT-ATCCTTTAACTCGTGGTTTAATCTCGATCATTTCGT
1 GACTTGCGGTTCAG-CCCAATCACCTTTAAT-CTTTAACTCGCGATTTAATCTCGATCATTTCAT
* * * *
16776849 TCATT-ACTCGACTTGCGGTTCAGTCTCAGGCATCTTTAATCTTTGACTCACCCGACCATTTCAT
64 TAATTCACTCGACTTACGGTTCAGTCTCAGGCATCTTTAACCCTTGACTCACCCGACCATTTCAT
16776913 TAATTCCCTC
129 TAATTCCCTC
* * * *
16776923 GACTTGCGGTTCAGCTCAATCATCTTTAATCTTTGACTCGCGATTTAATCTCGGTCATTTCATTA
1 GACTTGCGGTTCAGCCCAATCACCTTTAATCTTTAACTCGCGATTTAATCTCGATCATTTCATTA
* *
16776988 ATTCCCTCGACTTACGGTTCAGTCTCAGTCATCTTTAACCCTTGACTC
66 ATTCACTCGACTTACGGTTCAGTCTCAGGCATCTTTAACCCTTGACTC
16777036 GCGGTGTCAT
Statistics
Matches: 98, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
137 43 0.44
138 55 0.56
ACGTcount: A:0.20, C:0.28, G:0.14, T:0.38
Consensus pattern (138 bp):
GACTTGCGGTTCAGCCCAATCACCTTTAATCTTTAACTCGCGATTTAATCTCGATCATTTCATTA
ATTCACTCGACTTACGGTTCAGTCTCAGGCATCTTTAACCCTTGACTCACCCGACCATTTCATTA
ATTCCCTC
Found at i:16777019 original size:39 final size:39
Alignment explanation
Indices: 16776905--16777019 Score: 105
Period size: 39 Copynumber: 3.1 Consensus size: 39
16776895 CTCACCCGAC
*
16776905 CATTTCATTAATTCCCTCGACTTGCGGTTCAG-CTCAAT
1 CATTTCATTAATTCCCTCGACTTGCGGTTCAGTCTCAGT
* * * * * * * *
16776943 CA--TCTTTAA-T-CTTTGACTCGCGATTTAATCTCGGT
1 CATTTCATTAATTCCCTCGACTTGCGGTTCAGTCTCAGT
*
16776978 CATTTCATTAATTCCCTCGACTTACGGTTCAGTCTCAGT
1 CATTTCATTAATTCCCTCGACTTGCGGTTCAGTCTCAGT
16777017 CAT
1 CAT
16777020 CTTTAACCCT
Statistics
Matches: 54, Mismatches: 18, Indels: 9
0.67 0.22 0.11
Matches are distributed among these distances:
34 12 0.22
35 7 0.13
36 6 0.11
37 6 0.11
38 3 0.06
39 20 0.37
ACGTcount: A:0.21, C:0.27, G:0.13, T:0.39
Consensus pattern (39 bp):
CATTTCATTAATTCCCTCGACTTGCGGTTCAGTCTCAGT
Found at i:16777295 original size:3 final size:3
Alignment explanation
Indices: 16777276--16777333 Score: 55
Period size: 3 Copynumber: 18.7 Consensus size: 3
16777266 TTTCATTTTA
* *
16777276 AAT ATT AAT ACT AAT AAT AAT AAT AAT AAT AAAT ATAT AA- AAT ATAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT A-AT AAT AAT A-AT
*
16777323 AAT AAT TAT AA
1 AAT AAT AAT AA
16777334 AATTAAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 2 0.04
3 34 0.76
4 9 0.20
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:16777333 original size:26 final size:23
Alignment explanation
Indices: 16777291--16777341 Score: 66
Period size: 26 Copynumber: 2.1 Consensus size: 23
16777281 TAATACTAAT
16777291 AATAATAATAATAATAAATATATAA
1 AATAATAATAATAATAAA-AT-TAA
*
16777316 AATATATAATAATTATAAAATTAA
1 AATA-ATAATAATAATAAAATTAA
16777340 AA
1 AA
16777342 AAATTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 5 0.21
25 6 0.25
26 13 0.54
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
AATAATAATAATAATAAAATTAA
Found at i:16777352 original size:26 final size:27
Alignment explanation
Indices: 16777314--16777370 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
16777304 ATAAATATAT
* *
16777314 AAAATATATAAT-AATTATAAAATTAAA
1 AAAATATAAAATAAATTATAAAA-AAAA
*
16777341 AAAAT-TAAAATAAATTTTAAAAAAAA
1 AAAATATAAAATAAATTATAAAAAAAA
16777367 AAAA
1 AAAA
16777371 GAAAAAGAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (27 bp):
AAAATATAAAATAAATTATAAAAAAAA
Found at i:16777453 original size:23 final size:23
Alignment explanation
Indices: 16777424--16777475 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
16777414 GTCGCTGTCG
*
16777424 CCCCTGTCAGCCTCCCGACCAAC
1 CCCCTGTCAACCTCCCGACCAAC
* *
16777447 CCCCTGTCAACCTCCTGACCAGC
1 CCCCTGTCAACCTCCCGACCAAC
16777470 CCCCTG
1 CCCCTG
16777476 ACCAACTCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.15, C:0.56, G:0.13, T:0.15
Consensus pattern (23 bp):
CCCCTGTCAACCTCCCGACCAAC
Found at i:16777484 original size:23 final size:23
Alignment explanation
Indices: 16777424--16777485 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
16777414 GTCGCTGTCG
* *
16777424 CCCCTGTCAGCCTCCCGACCAAC
1 CCCCTGCCAACCTCCCGACCAAC
* * *
16777447 CCCCTGTCAACCTCCTGACCAGC
1 CCCCTGCCAACCTCCCGACCAAC
16777470 CCCCTGACCAA-CTCCC
1 CCCCTG-CCAACCTCCC
16777486 TTTCAGCCCA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
23 30 0.91
24 3 0.09
ACGTcount: A:0.18, C:0.56, G:0.11, T:0.15
Consensus pattern (23 bp):
CCCCTGCCAACCTCCCGACCAAC
Found at i:16777486 original size:12 final size:12
Alignment explanation
Indices: 16777440--16777486 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
16777430 TCAGCCTCCC
16777440 GACCAACCCCCT
1 GACCAACCCCCT
* *
16777452 G-TCAACCTCCT
1 GACCAACCCCCT
*
16777463 GACCAGCCCCCT
1 GACCAACCCCCT
*
16777475 GACCAACTCCCT
1 GACCAACCCCCT
16777487 TTCAGCCCAC
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.21, C:0.53, G:0.11, T:0.15
Consensus pattern (12 bp):
GACCAACCCCCT
Found at i:16778582 original size:16 final size:17
Alignment explanation
Indices: 16778556--16778587 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
16778546 AATTGTTATT
16778556 AATAATAATAAAATAAA
1 AATAATAATAAAATAAA
16778573 AATAAT-ATAAAATAA
1 AATAATAATAAAATAA
16778588 TAAAATATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
AATAATAATAAAATAAA
Found at i:16782961 original size:37 final size:37
Alignment explanation
Indices: 16782854--16782964 Score: 100
Period size: 37 Copynumber: 2.9 Consensus size: 37
16782844 TATATATAAT
* *
16782854 AAATAGATAATTAAGCAAATATAAGCAATGAATAAAAAGA
1 AAATAAATAATAAAGCAAATATAAGCAATG---AAAAAGA
* * **
16782894 AAGACAAATAA-ATAAGTAGGTATACA-CAATGAAAAAGA
1 AA-ATAAATAATA-AAGCAAATATA-AGCAATGAAAAAGA
16782932 AAATAAATAATAAAGCAAATATAAGCAATGAAA
1 AAATAAATAATAAAGCAAATATAAGCAATGAAA
16782965 GGGAATAAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
36 1 0.02
37 23 0.41
38 10 0.18
40 2 0.04
41 19 0.34
42 1 0.02
ACGTcount: A:0.63, C:0.06, G:0.13, T:0.18
Consensus pattern (37 bp):
AAATAAATAATAAAGCAAATATAAGCAATGAAAAAGA
Found at i:16784390 original size:18 final size:17
Alignment explanation
Indices: 16784367--16784412 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
16784357 AAAATGGGTT
*
16784367 AAAAATAAAATCAAATCA
1 AAAAATAAAATAAAAT-A
16784385 AAAAATAAAAATAAAATA
1 AAAAAT-AAAATAAAATA
*
16784403 AAAAAGAAAA
1 AAAAATAAAA
16784413 AATTTGTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.16
18 12 0.48
19 9 0.36
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.13
Consensus pattern (17 bp):
AAAAATAAAATAAAATA
Found at i:16784412 original size:24 final size:24
Alignment explanation
Indices: 16784366--16784415 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
16784356 TAAAATGGGT
**
16784366 TAAAAATAAAATCAAATCAAAAAA
1 TAAAAATAAAATCAAAAAAAAAAA
*
16784390 TAAAAATAAAATAAAAAAGAAAAAA
1 TAAAAATAAAATCAAAAA-AAAAAA
16784415 T
1 T
16784416 TTGTGATCGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.16
Consensus pattern (24 bp):
TAAAAATAAAATCAAAAAAAAAAA
Found at i:16784414 original size:19 final size:19
Alignment explanation
Indices: 16784367--16784415 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
16784357 AAAATGGGTT
* *
16784367 AAAAATAAAATCAAATCAA
1 AAAAAAAAAATAAAATCAA
*
16784386 AAAATAAAAATAAAAT-AA
1 AAAAAAAAAATAAAATCAA
16784404 AAAAGAAAAAAT
1 AAAA-AAAAAAT
16784416 TTGTGATCGG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.14
Consensus pattern (19 bp):
AAAAAAAAAATAAAATCAA
Found at i:16794835 original size:12 final size:12
Alignment explanation
Indices: 16794820--16794847 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
16794810 GCAACCTTGC
16794820 CTACCCTTTTGA
1 CTACCCTTTTGA
16794832 CTACCCTTTTGA
1 CTACCCTTTTGA
16794844 CTAC
1 CTAC
16794848 TCGAAAAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.36, G:0.07, T:0.39
Consensus pattern (12 bp):
CTACCCTTTTGA
Found at i:16796971 original size:3 final size:3
Alignment explanation
Indices: 16796963--16797025 Score: 117
Period size: 3 Copynumber: 21.0 Consensus size: 3
16796953 ATCCTAGCCC
*
16796963 AAT AAT AAT AAA AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16797011 AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT
16797026 TATTATTATT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:16797030 original size:3 final size:3
Alignment explanation
Indices: 16797024--16797058 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
16797014 AATAATAATA
16797024 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
16797059 ATTTTTGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:16797781 original size:20 final size:20
Alignment explanation
Indices: 16797749--16797785 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
16797739 ATTTTTAAAT
16797749 TTTAGTGAATTTTTCAATAG
1 TTTAGTGAATTTTTCAATAG
16797769 TTTA-TGAATTTTTCAAT
1 TTTAGTGAATTTTTCAAT
16797786 GACATTCTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTAGTGAATTTTTCAATAG
Found at i:16798243 original size:33 final size:32
Alignment explanation
Indices: 16798175--16798242 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
16798165 TATTTTGGTA
*
16798175 TTTGTTGTATGTTTTATAGTTTATTTATTTATT
1 TTTGTTGTATGTTTTATA-TTTATTTATTCATT
* *
16798208 TTTGTTTTATGTTATTAT-TTTCTTTATTCATT
1 TTTGTTGTATGTT-TTATATTTATTTATTCATT
16798240 TTT
1 TTT
16798243 TAAAAATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 15 0.48
33 12 0.39
34 4 0.13
ACGTcount: A:0.16, C:0.03, G:0.09, T:0.72
Consensus pattern (32 bp):
TTTGTTGTATGTTTTATATTTATTTATTCATT
Found at i:16798644 original size:187 final size:181
Alignment explanation
Indices: 16798306--16798655 Score: 427
Period size: 187 Copynumber: 1.9 Consensus size: 181
16798296 GAAAAAATAT
* * *
16798306 AAAAAAAATTTTAATAAAATTTTGAGAATAAATAATAATTATCTAATGATAAAATTTTAAAAATT
1 AAAAAAAAATTTAATAAAATTTTGAGAATAAATAATAATTATCCAATAATAAAATTTTAAAAATT
* * * * * *
16798371 ATAAATGGTAAATTTTTAAAAAAAATTTAGGTGAGAATTTTTCTAAATTTGACCTAAATAAAGGA
66 ATAAATGATAAATTTTTAAAAAAAATTTAGATAAGAATTTCTCTAAACTTAACCTAAAT-AAGGA
16798436 AAATTTTAGATAAAATTTTAATAATAA-TAATTAATATTTATTTTCAATTCTA
130 AAATTTTAGATAAAATTTTAATAA-AAGTAATTAATATTTATTTTCAATTCTA
* * *
16798488 AAAAAATAAATTTAATAAAATTTTGGGAATGAATTAATAATTATCCAATAATGAAATTCTTAAAA
1 AAAAAA-AAATTTAATAAAATTTTGAGAAT-AAATAATAATTATCCAATAATAAAATT-TTAAAA
* ** *
16798553 ATT-TCAAATGATAAATTTTTTAAGAAATCTTTAGATAAGAAATTTCTCTAAACTTAACTTAAAT
63 ATTAT-AAATGATAAA-TTTTTAAAAAAAATTTAGATAAG-AATTTCTCTAAACTTAACCTAAAT
* *
16798617 -TGTAAAATAATTTAGATAAAATTTTAATAAAAGTAATTA
125 AAGGAAAAT--TTTAGATAAAATTTTAATAAAAGTAATTA
16798656 CATTCCTTCT
Statistics
Matches: 141, Mismatches: 18, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
182 6 0.04
183 21 0.15
184 24 0.17
185 24 0.17
186 20 0.14
187 46 0.33
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (181 bp):
AAAAAAAAATTTAATAAAATTTTGAGAATAAATAATAATTATCCAATAATAAAATTTTAAAAATT
ATAAATGATAAATTTTTAAAAAAAATTTAGATAAGAATTTCTCTAAACTTAACCTAAATAAGGAA
AATTTTAGATAAAATTTTAATAAAAGTAATTAATATTTATTTTCAATTCTA
Found at i:16798970 original size:53 final size:51
Alignment explanation
Indices: 16798908--16799018 Score: 127
Period size: 53 Copynumber: 2.1 Consensus size: 51
16798898 TAAATTTTAA
*
16798908 GAAAATATTTCTAAAGTT-GGCTCAAAT-TGTGAAAAGTTTAAAAATGAAACTT
1 GAAAATATTTCTAAA-TTAGGCCCAAATATG-GAAAA-TTTAAAAATGAAACTT
* *
16798960 GAAAGATATTTCTAAATTAGGCCCAAATAATGGGAAATTTAGAAATGAAACTT
1 GAAA-ATATTTCTAAATTAGGCCCAAAT-ATGGAAAATTTAAAAATGAAACTT
16799013 GTAAAA
1 G-AAAA
16799019 CAAAAAAATA
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
52 6 0.12
53 36 0.71
54 7 0.14
55 2 0.04
ACGTcount: A:0.46, C:0.08, G:0.16, T:0.30
Consensus pattern (51 bp):
GAAAATATTTCTAAATTAGGCCCAAATATGGAAAATTTAAAAATGAAACTT
Found at i:16801991 original size:20 final size:19
Alignment explanation
Indices: 16801957--16801999 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
16801947 GAAAAGATTG
*
16801957 TTTTATTTGTTTTTATTAT
1 TTTTATTTGTTTTTACTAT
*
16801976 TTTTATTATTTTTTTACTAT
1 TTTTATT-TGTTTTTACTAT
16801996 TTTT
1 TTTT
16802000 GGAAAGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTATTTGTTTTTACTAT
Found at i:16802112 original size:20 final size:20
Alignment explanation
Indices: 16802089--16802127 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16802079 AAATAAAATG
16802089 AATAAAATAAAAAAACTGAA
1 AATAAAATAAAAAAACTGAA
* *
16802109 AATAACATTAAAAAACTGA
1 AATAAAATAAAAAAACTGA
16802128 TTATATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.69, C:0.08, G:0.05, T:0.18
Consensus pattern (20 bp):
AATAAAATAAAAAAACTGAA
Found at i:16802135 original size:22 final size:20
Alignment explanation
Indices: 16802092--16802175 Score: 66
Period size: 18 Copynumber: 4.2 Consensus size: 20
16802082 TAAAATGAAT
16802092 AAAATAAAAAAACTGAAAATA
1 AAAAT-AAAAAACTGAAAATA
* * *
16802113 ACATTAAAAAACTGATTATATA
1 AAAATAAAAAACTGA--AAATA
* *
16802135 AAAATAAAAAA-TAAAAAAA
1 AAAATAAAAAACTGAAAATA
*
16802154 AAAAT-AAAAA-TAAAAATA
1 AAAATAAAAAACTGAAAATA
16802172 AAAA
1 AAAA
16802176 ATTTACGATC
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
18 16 0.31
19 8 0.15
20 10 0.19
21 5 0.10
22 13 0.25
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (20 bp):
AAAATAAAAAACTGAAAATA
Found at i:16802177 original size:7 final size:6
Alignment explanation
Indices: 16802132--16802175 Score: 70
Period size: 6 Copynumber: 7.2 Consensus size: 6
16802122 AACTGATTAT
*
16802132 ATAAAA ATAAAAA ATAAAA AAAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA AT-AAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA A
16802176 ATTTACGATC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 29 0.83
7 6 0.17
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
ATAAAA
Found at i:16802994 original size:3 final size:3
Alignment explanation
Indices: 16802986--16803052 Score: 68
Period size: 3 Copynumber: 23.3 Consensus size: 3
16802976 GAAAATAAAA
* * * * *
16802986 AAT AAT AAT AAA AAT AAT AAT AAC AAT GAT GAT GAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16803033 AAT AAT -AT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
16803053 TATTATAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 6 0.11
3 49 0.89
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:16803036 original size:11 final size:11
Alignment explanation
Indices: 16802986--16803047 Score: 65
Period size: 11 Copynumber: 5.6 Consensus size: 11
16802976 GAAAATAAAA
16802986 AATAATAATA-
1 AATAATAATAT
16802996 AA-AATAATAAT
1 AATAATAAT-AT
* *
16803007 AACAATGATGAT
1 AATAATAAT-AT
*
16803019 GATAATAATAT
1 AATAATAATAT
16803030 AATAATAATAT
1 AATAATAATAT
16803041 AATAATA
1 AATAATA
16803048 TAATATATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
9 6 0.14
10 3 0.07
11 21 0.49
12 13 0.30
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.31
Consensus pattern (11 bp):
AATAATAATAT
Found at i:16803482 original size:63 final size:63
Alignment explanation
Indices: 16803383--16803538 Score: 285
Period size: 63 Copynumber: 2.5 Consensus size: 63
16803373 GGTCCGTTTC
* *
16803383 TCTTTTAAATATTCTATAATGATAAAATGACTGTTTTATTTTTTTAATAATATTTCTCACATT
1 TCTTTTAAATATTCTGTAATGATAAAATGACTGTTTTATTTTCTTAATAATATTTCTCACATT
16803446 TCTTTTAAATATTCTGTAATGATAAAATGACTGTTTTATTTTCTTAATAATATTTCTCACATT
1 TCTTTTAAATATTCTGTAATGATAAAATGACTGTTTTATTTTCTTAATAATATTTCTCACATT
*
16803509 TCTTTTAAATAATCTGTAATGATAAAATGA
1 TCTTTTAAATATTCTGTAATGATAAAATGA
16803539 TGGTGATTCG
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 90 1.00
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.49
Consensus pattern (63 bp):
TCTTTTAAATATTCTGTAATGATAAAATGACTGTTTTATTTTCTTAATAATATTTCTCACATT
Found at i:16805350 original size:7 final size:6
Alignment explanation
Indices: 16805324--16805372 Score: 64
Period size: 6 Copynumber: 8.0 Consensus size: 6
16805314 ATAAAATGGG
*
16805324 TTAAAA ATAAAA TT-AAA TTAAAAA TTAAAA TTAAAA TTAAAA TTGAAAA
1 TTAAAA TTAAAA TTAAAA TT-AAAA TTAAAA TTAAAA TTAAAA TT-AAAA
16805373 AAGAAAACAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
5 5 0.13
6 24 0.63
7 9 0.24
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (6 bp):
TTAAAA
Found at i:16805786 original size:21 final size:20
Alignment explanation
Indices: 16805748--16805786 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
16805738 TAGAAAAATC
16805748 TAGATTTCTTCAAATTTTTT
1 TAGATTTCTTCAAATTTTTT
16805768 TAGATTTCTTTC-AATTTTT
1 TAGATTTC-TTCAAATTTTT
16805787 GTCTTAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.23, C:0.10, G:0.05, T:0.62
Consensus pattern (20 bp):
TAGATTTCTTCAAATTTTTT
Found at i:16806240 original size:11 final size:11
Alignment explanation
Indices: 16806209--16806259 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
16806199 ATGGGAATAA
*
16806209 TAATAATAATAA
1 TAATAAT-ATAG
*
16806221 TAATAATATAT
1 TAATAATATAG
*
16806232 TAATCATATAG
1 TAATAATATAG
16806243 TAATAATA-A-
1 TAATAATATAG
16806252 TAATAATA
1 TAATAATA
16806260 GTGACATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
9 8 0.23
10 1 0.03
11 19 0.54
12 7 0.20
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (11 bp):
TAATAATATAG
Found at i:16806273 original size:3 final size:3
Alignment explanation
Indices: 16806204--16806259 Score: 71
Period size: 3 Copynumber: 19.3 Consensus size: 3
16806194 AAAGAATGGG
* * *
16806204 AAT AAT AAT AAT AAT AAT AAT AAT -AT ATT AAT CAT -AT AGT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16806250 AAT AAT AAT A
1 AAT AAT AAT A
16806260 GTGACATTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
2 4 0.09
3 42 0.91
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:16806885 original size:114 final size:113
Alignment explanation
Indices: 16806569--16806904 Score: 361
Period size: 114 Copynumber: 2.9 Consensus size: 113
16806559 TAAATTATAT
* * * * * * *
16806569 GAAATGATCTGAATCGAGTCAAGATCAAGCGATTAAAATGAAATCACGAGTTAAAATAAAGCGAT
1 GAAATGATCTGAATTGAGTTAAGATCAAGTGATCAGAATGAAATCAAGAGTCAAAATAAAGCGAT
* *
16806634 TAGGATCAAGTTGAGGTTGAAAATGATCTGGACGAAATCACGAATAATGA
66 T-GGATCGAG-TGAGGTCGAAAATGATCTGGACGAAATCACGAATAATGA
* * *
16806684 GAAATGATTTGGATTGAGTTAAGATCAAGTGATC-GGATGAAATCAAGAGTCAAAATAAAGCGAT
1 GAAATGATCTGAATTGAGTTAAGATCAAGTGATCAGAATGAAATCAAGAGTCAAAATAAAGCGAT
** * * * * *
16806748 CAAGATTGAATGAAAGTCGAAAATGAT-TGAGATGAAATCACGAATCATGA
66 -TGGATCGAGTG-AGGTCGAAAATGATCTG-GACGAAATCACGAATAATGA
* * * * *
16806798 GAAATTATCTGAATTAAGTTAAGATCAAGTGATCAGAACGAAATCATGAGTCAAAATGAAGCGAT
1 GAAATGATCTGAATTGAGTTAAGATCAAGTGATCAGAATGAAATCAAGAGTCAAAATAAAGCGAT
* * *
16806863 TGGATCGAGTCGAGGTCAAAAATGATCAGGACGAAATTACGA
66 TGGATCGAGT-GAGGTCGAAAATGATCTGGACGAAATCACGA
16806905 GTTAAAAAAT
Statistics
Matches: 179, Mismatches: 36, Indels: 13
0.79 0.16 0.06
Matches are distributed among these distances:
113 4 0.02
114 119 0.66
115 56 0.31
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (113 bp):
GAAATGATCTGAATTGAGTTAAGATCAAGTGATCAGAATGAAATCAAGAGTCAAAATAAAGCGAT
TGGATCGAGTGAGGTCGAAAATGATCTGGACGAAATCACGAATAATGA
Found at i:16807053 original size:115 final size:115
Alignment explanation
Indices: 16806926--16807138 Score: 273
Period size: 115 Copynumber: 1.9 Consensus size: 115
16806916 GAGCAACCAA
** ** * * *
16806926 GATCGAGTCGAGGTTGAAAATGATCGGGATAAAATCATGTATCATAAGAAATGATCTAGATTGAG
1 GATCGAGTCGAGGTAAAAAATGATAAGGATAAAACCATGAATCATAAGAAATGATCTAGATTAAG
* *
16806991 CTAAGATCAAATGATCGAGAGGAAATCACGAGTCAAAATAAAGTGTCCAG
66 CCAAGATCAAATGATCGAGACGAAATCACGAGTCAAAATAAAGTGTCCAG
* * * * * *
16807041 GATCGAGTCGAGGTAAAAAATGATAAGGATGAAACCATGAATCATGATAAGTGATTTGGATTAAG
1 GATCGAGTCGAGGTAAAAAATGATAAGGATAAAACCATGAATCATAAGAAATGATCTAGATTAAG
* *
16807106 CCAAGATTAAATGATCGGGACGAAATCACGAGT
66 CCAAGATCAAATGATCGAGACGAAATCACGAGT
16807139 TAAGATCGGG
Statistics
Matches: 81, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
115 81 1.00
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.23
Consensus pattern (115 bp):
GATCGAGTCGAGGTAAAAAATGATAAGGATAAAACCATGAATCATAAGAAATGATCTAGATTAAG
CCAAGATCAAATGATCGAGACGAAATCACGAGTCAAAATAAAGTGTCCAG
Found at i:16807167 original size:24 final size:24
Alignment explanation
Indices: 16807118--16807169 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
16807108 AAGATTAAAT
* * *
16807118 GATCGGGACGAAATCACGAGTTAA
1 GATCGGGACGAAACCACGAATCAA
*
16807142 GATCGGGACGAAACCATGAATCAA
1 GATCGGGACGAAACCACGAATCAA
16807166 GATC
1 GATC
16807170 AAGTTGAGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.19, G:0.27, T:0.15
Consensus pattern (24 bp):
GATCGGGACGAAACCACGAATCAA
Found at i:16808200 original size:43 final size:43
Alignment explanation
Indices: 16808065--16808218 Score: 147
Period size: 42 Copynumber: 3.6 Consensus size: 43
16808055 GCCTTTCAAG
* *
16808065 GTTTTCAACTTGAACTTTTTTATTTGAATCCAAGTCGC-CTTTTTGA
1 GTTTTCAACTTGAACTTTTTT-TTTG--TTCAAGTTGCTC-TTTTGA
* **
16808111 ATTTTCAACTTGAA-TTTTTTTTTGTTCAAG-T-CATCCTTCCGA
1 GTTTTCAACTTGAACTTTTTTTTTGTTCAAGTTGC-T-CTTTTGA
*
16808153 -TTTTCAACTCGAACTTTTTTTTTGTTCAAGTTGCTCTTTTGA
1 GTTTTCAACTTGAACTTTTTTTTTGTTCAAGTTGCTCTTTTGA
* *
16808195 GTTTTCAATTTAAACTTTTTTTTT
1 GTTTTCAACTTGAACTTTTTTTTT
16808219 TTTAGAATCA
Statistics
Matches: 90, Mismatches: 11, Indels: 17
0.76 0.09 0.14
Matches are distributed among these distances:
40 1 0.01
41 12 0.13
42 30 0.33
43 23 0.26
44 5 0.06
45 6 0.07
46 13 0.14
ACGTcount: A:0.20, C:0.16, G:0.10, T:0.53
Consensus pattern (43 bp):
GTTTTCAACTTGAACTTTTTTTTTGTTCAAGTTGCTCTTTTGA
Found at i:16814784 original size:23 final size:25
Alignment explanation
Indices: 16814745--16814793 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 25
16814735 GTTTCCATTT
16814745 TAAATATATTAATAATA-ATAAATAA
1 TAAATATATTAATAATATAT-AATAA
16814770 TAAATAT-TTAA-AATATATAATAA
1 TAAATATATTAATAATATATAATAA
16814793 T
1 T
16814794 TAAAAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 10 0.43
24 6 0.26
25 7 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
TAAATATATTAATAATATATAATAA
Found at i:16814785 original size:34 final size:33
Alignment explanation
Indices: 16814741--16814839 Score: 93
Period size: 34 Copynumber: 3.0 Consensus size: 33
16814731 TACTGTTTCC
* *
16814741 ATTTTAAATATATTAATAA-TAATAAA-TAATAAA
1 ATTTAAAATATA-TAATAATTAAAAAATTAA-AAA
16814774 TATTTAAAATATATAATAATTAAAAAATTAAAAA
1 -ATTTAAAATATATAATAATTAAAAAATTAAAAA
16814808 ATTT-AAAT-TA-AA-AATTAAATTAAATTAAAAA
1 ATTTAAAATATATAATAATTAAA--AAATTAAAAA
16814839 A
1 A
16814840 AAAAAGGAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
29 7 0.12
30 2 0.03
31 13 0.22
32 4 0.07
33 10 0.17
34 20 0.34
35 3 0.05
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (33 bp):
ATTTAAAATATATAATAATTAAAAAATTAAAAA
Found at i:16814791 original size:16 final size:16
Alignment explanation
Indices: 16814746--16814798 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
16814736 TTTCCATTTT
*
16814746 AAATATATTAATAATAA
1 AAATATA-TAATAATTA
*
16814763 TAAATA-ATAAATATTTA
1 -AAATATAT-AATAATTA
16814780 AAATATATAATAATTA
1 AAATATATAATAATTA
16814796 AAA
1 AAA
16814799 AATTAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 16 0.53
17 9 0.30
18 5 0.17
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATATATAATAATTA
Found at i:16814825 original size:12 final size:13
Alignment explanation
Indices: 16814798--16814831 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
16814788 AATAATTAAA
16814798 AAATTAAAAAATTT
1 AAATT-AAAAATTT
16814812 AAATTAAAAA-TT
1 AAATTAAAAATTT
16814824 AAATTAAA
1 AAATTAAA
16814832 TTAAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.50
13 5 0.25
14 5 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATTAAAAATTT
Found at i:16816045 original size:17 final size:17
Alignment explanation
Indices: 16816025--16816071 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
16816015 AATTGTTATT
16816025 AATAATAATAAAATAAA
1 AATAATAATAAAATAAA
16816042 AATAAT-ATAAAATAAA
1 AATAATAATAAAATAAA
16816058 AA-AATTAA-AAAATA
1 AATAA-TAATAAAATA
16816072 TGTTGAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 2 0.07
16 19 0.68
17 7 0.25
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (17 bp):
AATAATAATAAAATAAA
Found at i:16816055 original size:24 final size:23
Alignment explanation
Indices: 16816028--16816072 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
16816018 TGTTATTAAT
*
16816028 AATAATAAAATAAAAATAATATAA
1 AATAAAAAAATAAAAA-AATATAA
*
16816052 AATAAAAAAATTAAAAAATAT
1 AATAAAAAAATAAAAAAATAT
16816073 GTTGAAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (23 bp):
AATAAAAAAATAAAAAAATATAA
Found at i:16816181 original size:49 final size:49
Alignment explanation
Indices: 16816128--16816223 Score: 183
Period size: 49 Copynumber: 2.0 Consensus size: 49
16816118 TATTTTTCCT
16816128 GCCTAGATATTGGAGGGAATAAAAAATATTTTTTCAAACAAATAATTTC
1 GCCTAGATATTGGAGGGAATAAAAAATATTTTTTCAAACAAATAATTTC
*
16816177 GCCTAGATGTTGGAGGGAATAAAAAATATTTTTTCAAACAAATAATT
1 GCCTAGATATTGGAGGGAATAAAAAATATTTTTTCAAACAAATAATT
16816224 CTGCTTAGAG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.32
Consensus pattern (49 bp):
GCCTAGATATTGGAGGGAATAAAAAATATTTTTTCAAACAAATAATTTC
Found at i:16816238 original size:49 final size:49
Alignment explanation
Indices: 16816128--16816240 Score: 174
Period size: 49 Copynumber: 2.3 Consensus size: 49
16816118 TATTTTTCCT
**
16816128 GCCTAGATATTGGAGGGAATAAAAAATATTTTTTCAAACAAATAATTTC
1 GCCTAGAGGTTGGAGGGAATAAAAAATATTTTTTCAAACAAATAATTTC
*
16816177 GCCTAGATGTTGGAGGGAATAAAAAATATTTTTTCAAACAAATAA-TTC
1 GCCTAGAGGTTGGAGGGAATAAAAAATATTTTTTCAAACAAATAATTTC
*
16816225 TGCTTAGAGGTTGGAG
1 -GCCTAGAGGTTGGAG
16816241 AATTATTATG
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
48 3 0.05
49 57 0.95
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (49 bp):
GCCTAGAGGTTGGAGGGAATAAAAAATATTTTTTCAAACAAATAATTTC
Found at i:16824315 original size:3 final size:3
Alignment explanation
Indices: 16824307--16824347 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
16824297 GGGTCTACTT
* *
16824307 TAA TAA TAA TAT TAA TAA TAA TAA TAA TATA TAA AAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA T
16824348 TATTAATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:16824376 original size:8 final size:8
Alignment explanation
Indices: 16824360--16824405 Score: 74
Period size: 8 Copynumber: 5.8 Consensus size: 8
16824350 TTAATTATAT
*
16824360 AAAATATA
1 AAAAAATA
16824368 AAAAAATA
1 AAAAAATA
16824376 AAAAAATA
1 AAAAAATA
16824384 AAAAAATA
1 AAAAAATA
*
16824392 AAAAGATA
1 AAAAAATA
16824400 AAAAAA
1 AAAAAA
16824406 GACACAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 35 1.00
ACGTcount: A:0.85, C:0.00, G:0.02, T:0.13
Consensus pattern (8 bp):
AAAAAATA
Found at i:16824512 original size:13 final size:13
Alignment explanation
Indices: 16824488--16824558 Score: 106
Period size: 13 Copynumber: 5.5 Consensus size: 13
16824478 AGCCACCCTA
*
16824488 CAGCCATATCTAC
1 CAGCCCTATCTAC
* *
16824501 CAGTCCTATCTAT
1 CAGCCCTATCTAC
16824514 CAGCCCTATCTAC
1 CAGCCCTATCTAC
*
16824527 CAGTCCTATCTAC
1 CAGCCCTATCTAC
16824540 CAGCCCTATCTAC
1 CAGCCCTATCTAC
16824553 CAGCCC
1 CAGCCC
16824559 CGACCAACCA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 51 1.00
ACGTcount: A:0.24, C:0.42, G:0.08, T:0.25
Consensus pattern (13 bp):
CAGCCCTATCTAC
Found at i:16824518 original size:26 final size:26
Alignment explanation
Indices: 16824488--16824555 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
16824478 AGCCACCCTA
* *
16824488 CAGCCATATCTACCAGTCCTATCTAT
1 CAGCCCTATCTACCAGTCCTATCTAC
16824514 CAGCCCTATCTACCAGTCCTATCTAC
1 CAGCCCTATCTACCAGTCCTATCTAC
16824540 CAGCCCTATCTACCAG
1 CAGCCCTATCTACCAG
16824556 CCCCGACCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.25, C:0.40, G:0.09, T:0.26
Consensus pattern (26 bp):
CAGCCCTATCTACCAGTCCTATCTAC
Found at i:16824824 original size:14 final size:14
Alignment explanation
Indices: 16824776--16824826 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
16824766 AACAGCAATC
16824776 CAAAAA-ACAGAAA
1 CAAAAACACAGAAA
* * *
16824789 CAGAAACGCAAAAAA
1 CAAAAACAC-AGAAA
16824804 CCAAAAACACAGAAA
1 -CAAAAACACAGAAA
16824819 CAAAAACA
1 CAAAAACA
16824827 AAAAAAAAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
13 5 0.17
14 9 0.31
15 8 0.28
16 7 0.24
ACGTcount: A:0.71, C:0.22, G:0.08, T:0.00
Consensus pattern (14 bp):
CAAAAACACAGAAA
Found at i:16824832 original size:30 final size:29
Alignment explanation
Indices: 16824775--16824833 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
16824765 AAACAGCAAT
* **
16824775 CCAAAAAACAGAAACAGAAACGCAAAAAA
1 CCAAAAAACAGAAACAAAAACAAAAAAAA
16824804 CCAAAAACACAGAAACAAAAACAAAAAAAA
1 CCAAAAA-ACAGAAACAAAAACAAAAAAAA
16824834 AGTCAAACAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.73, C:0.20, G:0.07, T:0.00
Consensus pattern (29 bp):
CCAAAAAACAGAAACAAAAACAAAAAAAA
Found at i:16825964 original size:33 final size:32
Alignment explanation
Indices: 16825938--16826005 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 32
16825928 ATCCTAGGAT
16825938 TCTAAAACCCCTAAAAATCCAAAATCCATTAAA
1 TCTAAAACCCCTAAAAATCCAAAATCCA-TAAA
16825971 TCTAAAACCCCTAAAAATCCAAAATCCATTAAA
1 TCTAAAACCCCTAAAAATCCAAAATCCA-TAAA
16826004 TC
1 TC
16826006 CAAAGTCCCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (32 bp):
TCTAAAACCCCTAAAAATCCAAAATCCATAAA
Found at i:16825977 original size:16 final size:16
Alignment explanation
Indices: 16825952--16826042 Score: 76
Period size: 16 Copynumber: 5.6 Consensus size: 16
16825942 AAACCCCTAA
16825952 AAATCCAAAATCCATT
1 AAATCCAAAATCCATT
* * * *
16825968 AAATCTAAAACCCCTAA
1 AAATCCAAAATCCAT-T
16825985 AAATCCAAAATCCATT
1 AAATCCAAAATCCATT
* ***
16826001 AAATCCAAAGTCCCCCG
1 AAATCCAAAAT-CCATT
16826018 AAATCCAAAATCC-TT
1 AAATCCAAAATCCATT
16826033 GAAATCCAAA
1 -AAATCCAAA
16826043 GTCCTAAAAA
Statistics
Matches: 57, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
16 33 0.58
17 24 0.42
ACGTcount: A:0.48, C:0.29, G:0.03, T:0.20
Consensus pattern (16 bp):
AAATCCAAAATCCATT
Found at i:16826022 original size:33 final size:34
Alignment explanation
Indices: 16825945--16826046 Score: 138
Period size: 33 Copynumber: 3.1 Consensus size: 34
16825935 GATTCTAAAA
* *
16825945 CCCCTAAAAATCCAAAATCCATTAAATCTAAA-A
1 CCCCTAAAAATCCAAAATCCATTAAATCCAAAGT
16825978 CCCCTAAAAATCCAAAATCCATTAAATCCAAAGT
1 CCCCTAAAAATCCAAAATCCATTAAATCCAAAGT
**
16826012 CCCC-CGAAATCCAAAATCC-TTGAAATCCAAAGT
1 CCCCTAAAAATCCAAAATCCATT-AAATCCAAAGT
16826045 CC
1 CC
16826047 TAAAAAAAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
32 2 0.03
33 57 0.90
34 4 0.06
ACGTcount: A:0.45, C:0.31, G:0.04, T:0.20
Consensus pattern (34 bp):
CCCCTAAAAATCCAAAATCCATTAAATCCAAAGT
Found at i:16833508 original size:8 final size:8
Alignment explanation
Indices: 16833495--16833545 Score: 54
Period size: 8 Copynumber: 6.8 Consensus size: 8
16833485 AGGATGGGGC
16833495 ATAAAAAA
1 ATAAAAAA
16833503 ATAAAAAA
1 ATAAAAAA
*
16833511 AT--ATAA
1 ATAAAAAA
*
16833517 ATAAAAAT
1 ATAAAAAA
16833525 A-AAAAAA
1 ATAAAAAA
*
16833532 AGAAAAAA
1 ATAAAAAA
16833540 ATAAAA
1 ATAAAA
16833546 GGGACATATT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
6 5 0.14
7 6 0.17
8 24 0.69
ACGTcount: A:0.84, C:0.00, G:0.02, T:0.14
Consensus pattern (8 bp):
ATAAAAAA
Found at i:16833516 original size:10 final size:9
Alignment explanation
Indices: 16833497--16833545 Score: 64
Period size: 9 Copynumber: 5.3 Consensus size: 9
16833487 GATGGGGCAT
16833497 AAAAAAATA
1 AAAAAAATA
16833506 AAAAAATATA
1 AAAAAA-ATA
16833516 AATAAAAATA
1 AA-AAAAATA
*
16833526 AAAAAAA-G
1 AAAAAAATA
16833534 AAAAAAATA
1 AAAAAAATA
16833543 AAA
1 AAA
16833546 GGGACATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 7 0.20
9 14 0.40
10 10 0.29
11 4 0.11
ACGTcount: A:0.86, C:0.00, G:0.02, T:0.12
Consensus pattern (9 bp):
AAAAAAATA
Found at i:16835300 original size:41 final size:41
Alignment explanation
Indices: 16835241--16835345 Score: 115
Period size: 41 Copynumber: 2.6 Consensus size: 41
16835231 GCATGTTTTT
* *
16835241 AAAATTTT-AAAGTCTCTGTTTAAGAGAAACC-GTTCTCAATC
1 AAAATTTTAAAACT-TCTGTTTAAGAGAAACCAATT-TCAATC
* *
16835282 AAAATTTTAAAACTTCTGTTGAAGAGGAACCAATTTCAATC
1 AAAATTTTAAAACTTCTGTTTAAGAGAAACCAATTTCAATC
* * *
16835323 AAGATTTTAAAGCCTCTGTTTAA
1 AAAATTTTAAAACTTCTGTTTAA
16835346 AGGGGAACCT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
41 48 0.89
42 6 0.11
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.34
Consensus pattern (41 bp):
AAAATTTTAAAACTTCTGTTTAAGAGAAACCAATTTCAATC
Found at i:16835508 original size:23 final size:22
Alignment explanation
Indices: 16835478--16835668 Score: 158
Period size: 23 Copynumber: 8.7 Consensus size: 22
16835468 AAGATTTTGA
*
16835478 GATTCTGTAAGACCTCCGGACAT
1 GATT-TGTAAGACCTCCGGGCAT
16835501 GATTCTGTAAGACCTCCGGGCAT
1 GATT-TGTAAGACCTCCGGGCAT
* * *
16835524 GATTTTTAAGACCTTCAGG--T
1 GATTTGTAAGACCTCCGGGCAT
* ** *
16835544 AATTCTGTAAGATATTCGGGCAT
1 GATT-TGTAAGACCTCCGGGCAT
*
16835567 GATTT-TAAGACCTCTGGG--T
1 GATTTGTAAGACCTCCGGGCAT
* *
16835586 AATTTTGTAAGACCTCTGGGCAT
1 GA-TTTGTAAGACCTCCGGGCAT
16835609 GATTCTGTAAGACCTCCGGGCAT
1 GATT-TGTAAGACCTCCGGGCAT
* * * *
16835632 AATTTCTAAGACTTTCGGGCAT
1 GATTTGTAAGACCTCCGGGCAT
*
16835654 GATTTTTAAGACCTC
1 GATTTGTAAGACCTC
16835669 TAGGCATAAA
Statistics
Matches: 135, Mismatches: 25, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
19 2 0.01
20 7 0.05
21 33 0.24
22 41 0.30
23 52 0.39
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (22 bp):
GATTTGTAAGACCTCCGGGCAT
Found at i:16835587 original size:42 final size:43
Alignment explanation
Indices: 16835502--16835669 Score: 166
Period size: 42 Copynumber: 3.9 Consensus size: 43
16835492 TCCGGACATG
* * *
16835502 ATTCTGTAAGACCTCCGGGCATGATTTTTAAGACCT-TCAGGTA
1 ATTCTGTAAGATCTTCGGGCATGATTTTTAAGACCTCT-GGGTA
*
16835545 ATTCTGTAAGATATTCGGGCATGA-TTTTAAGACCTCTGGGTA
1 ATTCTGTAAGATCTTCGGGCATGATTTTTAAGACCTCTGGGTA
* * * *
16835587 ATTTTGTAAGA-CCTCTGGGCATGATTCTGTAAGACCTCCGGGCATA
1 ATTCTGTAAGATCTTC-GGGCATGATT-TTTAAGACCTCTGGG--TA
*
16835633 ATT-TCTAAGA-CTTTCGGGCATGATTTTTAAGACCTCT
1 ATTCTGTAAGATC-TTCGGGCATGATTTTTAAGACCTCT
16835670 AGGCATAAAT
Statistics
Matches: 105, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
41 2 0.02
42 33 0.31
43 23 0.22
44 23 0.22
45 17 0.16
46 7 0.07
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (43 bp):
ATTCTGTAAGATCTTCGGGCATGATTTTTAAGACCTCTGGGTA
Found at i:16835767 original size:22 final size:22
Alignment explanation
Indices: 16835742--16835904 Score: 114
Period size: 22 Copynumber: 7.4 Consensus size: 22
16835732 GTCAATTCTG
* *
16835742 TAAGACCTCCGGGTATAATTTT
1 TAAGACCTCCGGGCATGATTTT
* * *
16835764 TAAGACTTTC-GG-ATAATTTT
1 TAAGACCTCCGGGCATGATTTT
* *
16835784 GTAAGACCTACGAGCATGATTTT
1 -TAAGACCTCCGGGCATGATTTT
* * * * * *
16835807 GTAAAACTTTCAGGCATGATGTC
1 -TAAGACCTCCGGGCATGATTTT
* *
16835830 TAAGACCTCTGGGCATGATTCTG
1 TAAGACCTCCGGGCATGATT-TT
* * *
16835853 TAAGACCTCCGGACATGACTTC
1 TAAGACCTCCGGGCATGATTTT
*
16835875 TAAGACCTCCGGGTATGATTTT
1 TAAGACCTCCGGGCATGATTTT
16835897 TAAGACCT
1 TAAGACCT
16835905 TCGGATAATT
Statistics
Matches: 109, Mismatches: 28, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
20 8 0.07
21 10 0.09
22 50 0.46
23 41 0.38
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (22 bp):
TAAGACCTCCGGGCATGATTTT
Found at i:16835870 original size:45 final size:44
Alignment explanation
Indices: 16835785--16835909 Score: 119
Period size: 45 Copynumber: 2.8 Consensus size: 44
16835775 GATAATTTTG
* * * * *
16835785 TAAGACCTACGAGCATGATTTTGTAAAACTTTCAGG-CATGA-TGTC
1 TAAGACCTCCGGGCATGA-TTTGTAAGAC-CTCCGGACATGACT-TC
*
16835830 TAAGACCTCTGGGCATGATTCTGTAAGACCTCCGGACATGACTTC
1 TAAGACCTCCGGGCATGATT-TGTAAGACCTCCGGACATGACTTC
* * *
16835875 TAAGACCTCCGGGTATGATTTTTAAGACCTTCGGA
1 TAAGACCTCCGGGCATGATTTGTAAGACCTCCGGA
16835910 TAATTCTGTA
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
44 19 0.28
45 47 0.70
46 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (44 bp):
TAAGACCTCCGGGCATGATTTGTAAGACCTCCGGACATGACTTC
Found at i:16836207 original size:47 final size:47
Alignment explanation
Indices: 16836133--16836582 Score: 445
Period size: 47 Copynumber: 9.3 Consensus size: 47
16836123 AATTTGAAAA
* *
16836133 AGATGAGAATTTTTAAAGTTGTGGAGCCTCTACTGAGAGGAGCTTTTTC
1 AGATGAG-A-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
*
16836182 AGATGAGATTTTAAAGTTGTTGAGCCTCTACTGAGAGCAGAAAAGCTTTTTC
1 AGATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAG--G---AGCTTTTTC
* * *
16836234 AAGATGAGAATTTTAAAGTT-TTGGAGCTTCTGTTGAGAGGAGCTTTTTTA
1 -AGATGAG-ATTTTAAAGTTGTT-GAGCCTCTGCTGAGAGGAGC-TTTTTC
* * *
16836284 AGAAGAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCC
1 AGATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
* * * * * *
16836331 AAGATGAAAATTTTAAAATTGTGGAGCCTATGTTGAGAGGAGCTTTTCC
1 -AGATG-AGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
* * *
16836380 AGATGAGATTTTAAAGTTGTTGAGCCTTTGATGAGAGGAGCTTTTCC
1 AGATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
* * * *
16836427 AAGATGAGAATTTTAAAGTTGTGGAGCCTATGTTGAGATGAGCTTTTTC
1 -AGATGAG-ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
* * * *
16836476 AGATGAGATTTTAAAGTTGTTGAGCCTTTACCGAGATGAGC-TTTTC
1 AGATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
* * * * *
16836522 TATATGAGATTTTTAAAGTTGTTGAGCCTTTGTTGAGATGAGCCTTTTC
1 -AGATGAGA-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
*
16836571 AAATGAGATTTT
1 AGATGAGATTTT
16836583 CATATGAGAT
Statistics
Matches: 348, Mismatches: 36, Indels: 36
0.83 0.09 0.09
Matches are distributed among these distances:
46 5 0.01
47 109 0.31
48 90 0.26
49 96 0.28
50 5 0.01
52 10 0.03
53 9 0.03
54 24 0.07
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.36
Consensus pattern (47 bp):
AGATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
Found at i:16836422 original size:96 final size:96
Alignment explanation
Indices: 16836132--16836582 Score: 557
Period size: 96 Copynumber: 4.6 Consensus size: 96
16836122 AAATTTGAAA
* **
16836132 AAGATGAGAATTTTTAAAGTTGTGGAGCCTCTACTGAGAGGAGCTTTTTCAGATGAGATTTTAAA
1 AAGATGAGAA-TTTTAAAGTTGTGGAGCCTATGTTGAGAGGAGCTTTTTCAGATGAGATTTTAAA
* *
16836197 GTTGTTGAGCCTCTACTGA-GAGCAGAAAAGCTTTTTC
65 GTTGTTGAGCCT-T--TGATGAG-AG--GAGCTTTTCC
* * * * * *
16836234 AAGATGAGAATTTTAAAGTTTTGGAGCTTCTGTTGAGAGGAGCTTTTTTAAGAAGAAATTTTAAA
1 AAGATGAGAATTTTAAAGTTGTGGAGCCTATGTTGAGAGGAGC-TTTTTCAGATGAGATTTTAAA
* *
16836299 GTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCC
65 GTTGTTGAGCCTTTGATGAGAGGAGCTTTTCC
* * *
16836331 AAGATGAAAATTTTAAAATTGTGGAGCCTATGTTGAGAGGAGCTTTTCCAGATGAGATTTTAAAG
1 AAGATGAGAATTTTAAAGTTGTGGAGCCTATGTTGAGAGGAGCTTTTTCAGATGAGATTTTAAAG
16836396 TTGTTGAGCCTTTGATGAGAGGAGCTTTTCC
66 TTGTTGAGCCTTTGATGAGAGGAGCTTTTCC
*
16836427 AAGATGAGAATTTTAAAGTTGTGGAGCCTATGTTGAGATGAGCTTTTTCAGATGAGATTTTAAAG
1 AAGATGAGAATTTTAAAGTTGTGGAGCCTATGTTGAGAGGAGCTTTTTCAGATGAGATTTTAAAG
* *
16836492 TTGTTGAGCCTTT-ACCGAGATGAGCTTTT-C
66 TTGTTGAGCCTTTGA-TGAGAGGAGCTTTTCC
* * * * * * * *
16836522 TATATGAGATTTTTAAAGTTGTTGAGCCTTTGTTGAGATGAGCCTTTTCAAATGAGATTTT
1 AAGATGAGAATTTTAAAGTTGTGGAGCCTATGTTGAGAGGAGCTTTTTCAGATGAGATTTT
16836583 CATATGAGAT
Statistics
Matches: 311, Mismatches: 35, Indels: 13
0.87 0.10 0.04
Matches are distributed among these distances:
95 56 0.18
96 133 0.43
97 46 0.15
99 4 0.01
100 3 0.01
101 29 0.09
102 40 0.13
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.36
Consensus pattern (96 bp):
AAGATGAGAATTTTAAAGTTGTGGAGCCTATGTTGAGAGGAGCTTTTTCAGATGAGATTTTAAAG
TTGTTGAGCCTTTGATGAGAGGAGCTTTTCC
Found at i:16836584 original size:13 final size:13
Alignment explanation
Indices: 16836566--16836595 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
16836556 GAGATGAGCC
16836566 TTTTCAAATGAGA
1 TTTTCAAATGAGA
*
16836579 TTTTCATATGAGA
1 TTTTCAAATGAGA
16836592 TTTT
1 TTTT
16836596 AAAGTTGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (13 bp):
TTTTCAAATGAGA
Found at i:16836603 original size:60 final size:62
Alignment explanation
Indices: 16836511--16836633 Score: 187
Period size: 60 Copynumber: 2.0 Consensus size: 62
16836501 CTTTACCGAG
* * ** *
16836511 ATGAGCTTTTCTATATGAGATTTTTAAAGTTGTTGAGCCTTTGTTGAGATGAGCCTTTTCAA
1 ATGAGATTTTCTATATGAGATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCCTTTTCAA
16836573 ATGAGATTTTC-ATATGAGA-TTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCCTTTTCAA
1 ATGAGATTTTCTATATGAGATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCCTTTTCAA
16836633 A
1 A
16836634 AAAAATAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
60 38 0.68
61 8 0.14
62 10 0.18
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (62 bp):
ATGAGATTTTCTATATGAGATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCCTTTTCAA
Found at i:16837074 original size:21 final size:21
Alignment explanation
Indices: 16837023--16837074 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
16837013 AAAAAAGAAG
16837023 AAGCC-CTCTCGAACCCCCTT
1 AAGCCTCTCTCGAACCCCCTT
16837043 AAGGCCT-TCTCGAACCCCCTT
1 AA-GCCTCTCTCGAACCCCCTT
16837064 CAA-CCTCTCTC
1 -AAGCCTCTCTC
16837075 TCGGAGATCC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
20 5 0.18
21 21 0.75
22 2 0.07
ACGTcount: A:0.19, C:0.48, G:0.10, T:0.23
Consensus pattern (21 bp):
AAGCCTCTCTCGAACCCCCTT
Found at i:16840389 original size:3 final size:3
Alignment explanation
Indices: 16840381--16840417 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
16840371 CTTAAATATT
16840381 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
16840418 TTCATGAGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:16841974 original size:2 final size:2
Alignment explanation
Indices: 16841967--16842002 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
16841957 AAATTTATGC
* *
16841967 AT AT AT AT GT AC 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 AT AT AT
16842003 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:16842296 original size:16 final size:16
Alignment explanation
Indices: 16842272--16842302 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16842262 GAATTATTTG
*
16842272 AATTTAAATAATTTTA
1 AATTCAAATAATTTTA
16842288 AATTCAAATAATTTT
1 AATTCAAATAATTTT
16842303 TGATTTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTCAAATAATTTTA
Found at i:16842717 original size:14 final size:14
Alignment explanation
Indices: 16842698--16842725 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16842688 TTGGATTTAA
16842698 AAAAAAAAAATTTG
1 AAAAAAAAAATTTG
16842712 AAAAAAAAAATTTG
1 AAAAAAAAAATTTG
16842726 CTACGTGGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (14 bp):
AAAAAAAAAATTTG
Found at i:16842717 original size:16 final size:15
Alignment explanation
Indices: 16842692--16842721 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
16842682 TATAAATTGG
16842692 ATTTAAAAAAAAAAA
1 ATTTAAAAAAAAAAA
16842707 ATTTGAAAAAAAAAA
1 ATTT-AAAAAAAAAA
16842722 TTTGCTACGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (15 bp):
ATTTAAAAAAAAAAA
Found at i:16843128 original size:16 final size:17
Alignment explanation
Indices: 16843087--16843129 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
16843077 ATTAATTGAT
16843087 TTTATGAATATTATATA
1 TTTATGAATATTATATA
*
16843104 TTCATGAATACTTA-A-A
1 TTTATGAATA-TTATATA
16843120 TTTATGAATA
1 TTTATGAATA
16843130 ATCAAAGTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 10 0.43
17 10 0.43
18 3 0.13
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (17 bp):
TTTATGAATATTATATA
Found at i:16844220 original size:19 final size:19
Alignment explanation
Indices: 16844198--16844240 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
16844188 AATTTTTATG
16844198 AAATTAT-TT-TTTATATATA
1 AAATTATATTATTTA-AT-TA
16844217 AAATTATATTATTTAATTA
1 AAATTATATTATTTAATTA
16844236 AAATT
1 AAATT
16844241 CTAAATGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 14 0.64
20 4 0.18
21 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AAATTATATTATTTAATTA
Found at i:16847502 original size:18 final size:18
Alignment explanation
Indices: 16847461--16847502 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
16847451 TATATGATTT
* *
16847461 AAAATTTTAATAAAAATT
1 AAAAATTTAATAAAAATA
*
16847479 ATAAATTTAATAAAAATA
1 AAAAATTTAATAAAAATA
16847497 AAAAAT
1 AAAAAT
16847503 ATATTTTTAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAATTTAATAAAAATA
Found at i:16848682 original size:12 final size:12
Alignment explanation
Indices: 16848665--16848690 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16848655 TATATGTAAC
16848665 ATATAAATTTTT
1 ATATAAATTTTT
16848677 ATATAAATTTTT
1 ATATAAATTTTT
16848689 AT
1 AT
16848691 TTTGATTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATATAAATTTTT
Found at i:16852386 original size:2 final size:2
Alignment explanation
Indices: 16852379--16852404 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16852369 AAGGTCTAAT
16852379 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
16852405 TTCGTGGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:16867371 original size:2 final size:2
Alignment explanation
Indices: 16867364--16867393 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16867354 GTTACCAATC
16867364 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
16867394 TACAACATAC
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:16869913 original size:9 final size:9
Alignment explanation
Indices: 16869893--16869942 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
16869883 TATCAAGATT
16869893 TTTTATTTTA
1 TTTTA-TTTA
16869903 TTTTATTTA
1 TTTTATTTA
16869912 -TTTATTTA
1 TTTTATTTA
*
16869920 TTTTTTATTA
1 TTTTAT-TTA
16869930 TTATTA-TTA
1 TT-TTATTTA
16869939 TTTT
1 TTTT
16869943 TAAATTAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
8 10 0.29
9 13 0.37
10 10 0.29
11 2 0.06
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTATTTA
Found at i:16869917 original size:18 final size:18
Alignment explanation
Indices: 16869890--16869942 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 18
16869880 TCGTATCAAG
16869890 ATTT-TTTATTTTATTTT
1 ATTTATTTATTTTATTTT
16869907 ATTTATTTA-TTTATTTT
1 ATTTATTTATTTTATTTT
*
16869924 TTATTA-TTATTATTATTTT
1 AT-TTATTTATT-TTATTTT
16869943 TAAATTAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 16 0.52
18 8 0.26
19 7 0.23
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (18 bp):
ATTTATTTATTTTATTTT
Found at i:16870103 original size:59 final size:60
Alignment explanation
Indices: 16870021--16870387 Score: 266
Period size: 62 Copynumber: 6.2 Consensus size: 60
16870011 TGATTTTCCT
* * *
16870021 AAAATAAAGTTTCAAAAAA-ATATTTTTGAGGAAAAA-TTGAAAGCATCAATTTTTCTTG
1 AAAATAAAATTTTAAAAAATATATTTTTGAGGAAAAAGTTGAAAGTATCAATTTTTCTTG
*
16870079 AAAATAAAATTTTAAAAAATATATTTTTGAAGG--AAAGTTGAATA-TATCAA-TTTCCTTTG
1 AAAATAAAATTTTAAAAAATATATTTTTG-AGGAAAAAGTTGAA-AGTATCAATTTTTC-TTG
* * * *
16870138 AACACAAAA--TTAAAAAATACATTTTT-A-AAAGAAAGTTGAAAGTATCAATTTTTCTTG
1 AAAATAAAATTTTAAAAAATATATTTTTGAGGAA-AAAGTTGAAAGTATCAATTTTTCTTG
* * *
16870195 AAAATAAAAATGTTTAAAAAATATATATTTTCAGGAAAAAGTTGAAAGTATAAATTTTTCTCG
1 AAAAT-AAAAT-TTTAAAAAATATAT-TTTTGAGGAAAAAGTTGAAAGTATCAATTTTTCTTG
* * * ** * *
16870258 AAATTAAAATTTCAGAAAAA-AAATATTTCAAGG-AAAAGTT-AGAAGTA-CTAATTTTCCTTA
1 AAAATAAAATTTTA-AAAAATATAT-TTTTGAGGAAAAAGTTGA-AAGTATC-AATTTTTCTTG
* * * *
16870318 AAAATAAAAAACTTATCAAGAAAA-ACA-TTTTAAGGAAAAA-TTGAAAGTATCAATTTTCCTT-
1 AAAAT--AAAA-TT-TTAA-AAAATATATTTTTGAGGAAAAAGTTGAAAGTATCAATTTTTCTTG
16870379 AAAATAAAA
1 AAAATAAAA
16870388 ATCTCCAAAT
Statistics
Matches: 254, Mismatches: 27, Indels: 55
0.76 0.08 0.16
Matches are distributed among these distances:
55 1 0.00
56 1 0.00
57 37 0.15
58 32 0.13
59 34 0.13
60 28 0.11
61 30 0.12
62 42 0.17
63 38 0.15
64 11 0.04
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (60 bp):
AAAATAAAATTTTAAAAAATATATTTTTGAGGAAAAAGTTGAAAGTATCAATTTTTCTTG
Found at i:16870411 original size:54 final size:54
Alignment explanation
Indices: 16870346--16870486 Score: 228
Period size: 54 Copynumber: 2.6 Consensus size: 54
16870336 AGAAAAACAT
* *
16870346 TTTAAGGAAAAATTGAAAGTATCAATTTTCCTTAAAATAAAAATCTCCAAATGC
1 TTTAAGAAAAAATTGAAAGTATCAATTTTCCTTAAAATAAAAACCTCCAAATGC
* * * *
16870400 TTTAAGTAAAAATTGAAAATATTAATTTTTCTTAAAATAAAAACCTCCAAATGC
1 TTTAAGAAAAAATTGAAAGTATCAATTTTCCTTAAAATAAAAACCTCCAAATGC
16870454 TTTAAGAAAAAATTGAAAGTATCAATTTTCCTT
1 TTTAAGAAAAAATTGAAAGTATCAATTTTCCTT
16870487 GTACAAAAGC
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 78 1.00
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.35
Consensus pattern (54 bp):
TTTAAGAAAAAATTGAAAGTATCAATTTTCCTTAAAATAAAAACCTCCAAATGC
Found at i:16874341 original size:11 final size:10
Alignment explanation
Indices: 16874317--16874369 Score: 58
Period size: 9 Copynumber: 5.4 Consensus size: 10
16874307 AGAAAAAAAG
16874317 AAAA-AAGAA
1 AAAATAAGAA
16874326 AAAATAAGAGA
1 AAAATAAGA-A
16874337 AAAATAA-AA
1 AAAATAAGAA
*
16874346 AAAA-ATGAA
1 AAAATAAGAA
16874355 AAAATAAGAGA
1 AAAATAAGA-A
16874366 AAAA
1 AAAA
16874370 AGATGAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
8 1 0.03
9 15 0.41
10 8 0.22
11 13 0.35
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (10 bp):
AAAATAAGAA
Done.