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 80 of 129
Found at i:12739990 original size:14 final size:14
Alignment explanation
Indices: 12739964--12740010 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
12739954 GTTTATATAC
12739964 ATTTAAGATTTATTT
1 ATTTAA-ATTTATTT
12739979 ATTTAAATTTATTT
1 ATTTAAATTTATTT
*
12739993 GA-TTATAATTTGTTT
1 -ATTTA-AATTTATTT
12740008 ATT
1 ATT
12740011 ATTCATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 12 0.43
15 16 0.57
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (14 bp):
ATTTAAATTTATTT
Found at i:12740011 original size:14 final size:15
Alignment explanation
Indices: 12739971--12740012 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
12739961 TACATTTAAG
12739971 ATTTATTTATT-TAA
1 ATTTATTTATTATAA
12739985 ATTTATTTGATTAT-A
1 ATTTATTT-ATTATAA
*
12740000 ATTTGTTTATTAT
1 ATTTATTTATTAT
12740013 TCATAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 13 0.52
15 11 0.44
16 1 0.04
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (15 bp):
ATTTATTTATTATAA
Found at i:12741533 original size:16 final size:16
Alignment explanation
Indices: 12741512--12741544 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
12741502 AGAGTTATTG
12741512 TTCCAATAGCGCCATC
1 TTCCAATAGCGCCATC
12741528 TTCCAATAGCGCCATC
1 TTCCAATAGCGCCATC
12741544 T
1 T
12741545 GAATTCAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.36, G:0.12, T:0.27
Consensus pattern (16 bp):
TTCCAATAGCGCCATC
Found at i:12751674 original size:62 final size:61
Alignment explanation
Indices: 12751608--12751726 Score: 139
Period size: 62 Copynumber: 1.9 Consensus size: 61
12751598 TTATTTTATT
* * * * *
12751608 AAAATAATTTATTAAAAATTTGAATCTTTCAATATGTTGGTAAAATTTATTTTTATTTGAAA
1 AAAATAATTTATTAAAAATTTGAACCCTCCAATATGTTGAT-AAAGTTATTTTTATTTGAAA
* * ** *
12751670 AAAATATTTTTTTAGCAATTTGAACCCTCCAATATGTTGATAAAGTTCTTTTTATTT
1 AAAATAATTTATTAAAAATTTGAACCCTCCAATATGTTGATAAAGTTATTTTTATTT
12751727 TATTTAAATT
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
61 14 0.30
62 33 0.70
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (61 bp):
AAAATAATTTATTAAAAATTTGAACCCTCCAATATGTTGATAAAGTTATTTTTATTTGAAA
Found at i:12751773 original size:4 final size:4
Alignment explanation
Indices: 12751754--12751866 Score: 54
Period size: 4 Copynumber: 28.2 Consensus size: 4
12751744 ATATTTATAG
* ** * *
12751754 ATAA ATGA AT-A ATAA ATAA AT-A ACCA ATAA ATAA AAAA ATAA ATGA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
* * * * * *
12751800 A-AA ACAA CTAA ACAA ACAA CTAA ATAA TTAGA CATAA ATAAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA-A -ATAA AT-AA ATAA ATAA
*
12751850 ATAGA AAAA AT-A ATAA A
1 ATA-A ATAA ATAA ATAA A
12751867 AATAACAAGA
Statistics
Matches: 82, Mismatches: 19, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
3 10 0.12
4 61 0.74
5 9 0.11
6 2 0.02
ACGTcount: A:0.70, C:0.07, G:0.04, T:0.19
Consensus pattern (4 bp):
ATAA
Found at i:12751811 original size:27 final size:25
Alignment explanation
Indices: 12751764--12751868 Score: 81
Period size: 27 Copynumber: 4.0 Consensus size: 25
12751754 ATAAATGAAT
12751764 AATAAATAAATAACCAATAAATAAAAA
1 AATAAATAAA-AA-CAATAAATAAAAA
* *
12751791 AATAAATGAAAAACAACTAAACAAACA
1 AATAAAT-AAAAACAA-TAAATAAAAA
* *
12751818 ACTAAATAATTAGAC-ATAAATAAAATA
1 AATAAATAA--AAACAATAAATAAAA-A
12751845 AATAAATAGAAAA-AAT-AATAAAAA
1 AATAAATA-AAAACAATAAATAAAAA
12751869 TAACAAGAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
24 1 0.02
25 7 0.11
26 16 0.25
27 32 0.51
28 7 0.11
ACGTcount: A:0.71, C:0.08, G:0.03, T:0.18
Consensus pattern (25 bp):
AATAAATAAAAACAATAAATAAAAA
Found at i:12751851 original size:13 final size:12
Alignment explanation
Indices: 12751764--12751868 Score: 68
Period size: 14 Copynumber: 8.0 Consensus size: 12
12751754 ATAAATGAAT
12751764 AATAAATAAATAA
1 AATAAATAAA-AA
12751777 CCAATAAATAAAAA
1 --AATAAATAAAAA
12751791 AATAAATGAAAAA
1 AATAAAT-AAAAA
* *
12751804 CAACTAAACAAACA
1 -AA-TAAATAAAAA
* *
12751818 ACTAAATAATTAGA
1 AATAAATAA--AAA
*
12751832 CATAAATAAAATA
1 AATAAATAAAA-A
12751845 AATAAATAGAAAA
1 AATAAATA-AAAA
12751858 AAT-AATAAAAA
1 AATAAATAAAAA
12751869 TAACAAGAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 18
0.73 0.09 0.18
Matches are distributed among these distances:
11 4 0.05
12 18 0.24
13 18 0.24
14 20 0.27
15 14 0.19
ACGTcount: A:0.71, C:0.08, G:0.03, T:0.18
Consensus pattern (12 bp):
AATAAATAAAAA
Found at i:12751869 original size:22 final size:22
Alignment explanation
Indices: 12751820--12751879 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
12751810 AACAAACAAC
* *
12751820 TAAATAATTAGACATAAATAAAA
1 TAAATAAATAGA-AAAAATAAAA
12751843 TAAATAAATAGAAAAAATAATAA
1 TAAATAAATAGAAAAAATAA-AA
12751866 -AAATAACA-AGAAAA
1 TAAATAA-ATAGAAAA
12751880 TGGCTCAGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
22 19 0.58
23 14 0.42
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.20
Consensus pattern (22 bp):
TAAATAAATAGAAAAAATAAAA
Found at i:12752691 original size:11 final size:10
Alignment explanation
Indices: 12752671--12752695 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12752661 GCGTCTCTTA
12752671 TTTTTCTTTT
1 TTTTTCTTTT
12752681 TTTTTCTTTT
1 TTTTTCTTTT
12752691 TTTTT
1 TTTTT
12752696 ACAATTTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:12754400 original size:30 final size:30
Alignment explanation
Indices: 12754305--12754400 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
12754295 ATTAATTTAT
* * * *
12754305 ATTAAAAATTTATTCATATACAAATTAAAA
1 ATTAATAATTTATTTAGATAAAAATTAAAA
* * *
12754335 ATTAAAAATTTATTTAGATACAGATTAAAA
1 ATTAATAATTTATTTAGATAAAAATTAAAA
*
12754365 ATTAATGATTTATTT-GAGTAAAAATTAAAA
1 ATTAATAATTTATTTAGA-TAAAAATTAAAA
12754395 ATTAAT
1 ATTAAT
12754401 TAATATGTTA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
29 2 0.03
30 56 0.97
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (30 bp):
ATTAATAATTTATTTAGATAAAAATTAAAA
Found at i:12754613 original size:25 final size:25
Alignment explanation
Indices: 12754576--12754629 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
12754566 ATTCATATAT
12754576 TTATATATTAATTTATA-TA-AAAA
1 TTATATATTAATTTATATTATAAAA
*
12754599 TTATATATTAGAATTTGTATTATAAAA
1 TTATATATT--AATTTATATTATAAAA
12754626 TTAT
1 TTAT
12754630 GACAAACGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 9 0.35
25 7 0.27
26 2 0.08
27 8 0.31
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (25 bp):
TTATATATTAATTTATATTATAAAA
Found at i:12755048 original size:16 final size:17
Alignment explanation
Indices: 12755027--12755058 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
12755017 ATATCACATA
12755027 TATATAAAA-TAAAAAT
1 TATATAAAAGTAAAAAT
12755043 TATATAAAAGTAAAAA
1 TATATAAAAGTAAAAA
12755059 CTAAGTTTAA
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:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (17 bp):
TATATAAAAGTAAAAAT
Found at i:12755048 original size:18 final size:17
Alignment explanation
Indices: 12755025--12755058 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12755015 GGATATCACA
12755025 TATATATAAAATAAAAAT
1 TATATA-AAAATAAAAAT
*
12755043 TATATAAAAGTAAAAA
1 TATATAAAAATAAAAA
12755059 CTAAGTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
TATATAAAAATAAAAAT
Found at i:12755340 original size:12 final size:12
Alignment explanation
Indices: 12755325--12755349 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12755315 AAAATTATTT
12755325 TTTAATTAATTA
1 TTTAATTAATTA
12755337 TTTAATTAATTA
1 TTTAATTAATTA
12755349 T
1 T
12755350 ATATATTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTAATTAATTA
Found at i:12755385 original size:30 final size:31
Alignment explanation
Indices: 12755335--12755406 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 31
12755325 TTTAATTAAT
* * * *
12755335 TATTTAATTAATTATATATATTTATATAATGA
1 TATTT-ATTAAATATATATATTTAAAAAATAA
*
12755367 TATTT-TTAAATATTTATATTTAAAAAATAA
1 TATTTATTAAATATATATATTTAAAAAATAA
12755397 TATTTATTAA
1 TATTTATTAA
12755407 TTTCGGGTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 25 0.74
31 4 0.12
32 5 0.15
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (31 bp):
TATTTATTAAATATATATATTTAAAAAATAA
Found at i:12756306 original size:28 final size:27
Alignment explanation
Indices: 12756257--12756324 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
12756247 TATCATATTA
* *
12756257 ATTAATAAATTTATAATTTAAATATCAC
1 ATTAA-AAATTTTTAATCTAAATATCAC
* *
12756285 ATTAAAAATTTTTAAATCTAAATATTAT
1 ATTAAAAATTTTT-AATCTAAATATCAC
*
12756313 ATTAAATATTTT
1 ATTAAAAATTTT
12756325 ATTATAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 7 0.21
28 27 0.79
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (27 bp):
ATTAAAAATTTTTAATCTAAATATCAC
Found at i:12756730 original size:18 final size:18
Alignment explanation
Indices: 12756707--12756820 Score: 90
Period size: 18 Copynumber: 7.0 Consensus size: 18
12756697 AATTTTACTT
12756707 ATAAATAATATTATATTA
1 ATAAATAATATTATATTA
12756725 ATAAAT-A-A-TATATTA
1 ATAAATAATATTATATTA
*
12756740 ATAAATATTATTATA--A
1 ATAAATAATATTATATTA
*
12756756 AT--A-AATATTATACTA
1 ATAAATAATATTATATTA
* *
12756771 AT--AT-AT-TAATTTTA
1 ATAAATAATATTATATTA
12756785 ATAAATAATATTATATTA
1 ATAAATAATATTATATTA
* *
12756803 ATAAATAAAATCATATTA
1 ATAAATAATATTATATTA
12756821 TAGTAATAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
13 8 0.10
14 8 0.10
15 19 0.25
16 6 0.08
17 4 0.05
18 32 0.42
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAAATAATATTATATTA
Found at i:12756736 original size:15 final size:15
Alignment explanation
Indices: 12756713--12756859 Score: 90
Period size: 15 Copynumber: 9.6 Consensus size: 15
12756703 ACTTATAAAT
*
12756713 AATATTATATTAATA
1 AATAATATATTAATA
12756728 AATAATATATTAATA
1 AATAATATATTAATA
* *
12756743 AATATTATTATAAATA
1 AATAATA-TATTAATA
* *
12756759 AATATTATACTAATA
1 AATAATATATTAATA
*
12756774 TATTAAT-T-TTAATA
1 -AATAATATATTAATA
12756788 AATAATATTATATTAATA
1 AAT-A-A-TATATTAATA
12756806 AATAAAATCATATT-AT-
1 AAT--AAT-ATATTAATA
* *
12756822 AGTAATA-A-AAATA
1 AATAATATATTAATA
*
12756835 TTATAATATATTAATA
1 -AATAATATATTAATA
12756851 AATAATATA
1 AATAATATA
12756860 AAGAATAAGA
Statistics
Matches: 103, Mismatches: 15, Indels: 28
0.71 0.10 0.19
Matches are distributed among these distances:
12 3 0.03
13 3 0.03
14 14 0.14
15 37 0.36
16 25 0.24
17 4 0.04
18 15 0.15
19 2 0.02
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (15 bp):
AATAATATATTAATA
Found at i:12756749 original size:10 final size:11
Alignment explanation
Indices: 12756728--12756851 Score: 50
Period size: 11 Copynumber: 11.5 Consensus size: 11
12756718 TATATTAATA
12756728 AATAATATATT
1 AATAATATATT
12756739 AATAA-ATATT
1 AATAATATATT
12756749 -AT--TATA--
1 AATAATATATT
12756755 AATAA-ATATT
1 AATAATATATT
12756765 ATACTAATATATT
1 A-A-TAATATATT
*
12756778 AATTTTAATA-AAT
1 AA---TAATATATT
*
12756791 AATATTATATT
1 AATAATATATT
* *
12756802 AATAAATAAAAT
1 AAT-AATATATT
* * *
12756814 CATATTATAGT
1 AATAATATATT
*
12756825 AATAAAAATATT
1 AAT-AATATATT
12756837 -ATAATATATT
1 AATAATATATT
12756847 AATAA
1 AATAA
12756852 ATAATATAAA
Statistics
Matches: 82, Mismatches: 16, Indels: 30
0.64 0.12 0.23
Matches are distributed among these distances:
7 2 0.02
8 6 0.07
9 2 0.02
10 17 0.21
11 24 0.29
12 16 0.20
13 10 0.12
14 5 0.06
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.42
Consensus pattern (11 bp):
AATAATATATT
Found at i:12756818 original size:23 final size:23
Alignment explanation
Indices: 12756709--12756860 Score: 103
Period size: 23 Copynumber: 6.3 Consensus size: 23
12756699 TTTTACTTAT
12756709 AAATAATATTATATTAATAAATA
1 AAATAATATTATATTAATAAATA
*
12756732 ATATATTAATA-AATATTATTATAAATA
1 A-A-A-TAATATTATATTA--ATAAATA
* *
12756759 AATATTATACTAATATATTAATTTTAAT-
1 AA-A-TA-A-TATTATATTAA--TAAATA
12756787 AAATAATATTATATTAATAAATA
1 AAATAATATTATATTAATAAATA
* *
12756810 AAATCATATTATAGTAATAAA-A
1 AAATAATATTATATTAATAAATA
* * *
12756832 ATATTATAATATATTAATAAATA
1 AAATAATATTATATTAATAAATA
*
12756855 ATATAA
1 AAATAA
12756861 AGAATAAGAA
Statistics
Matches: 105, Mismatches: 12, Indels: 24
0.74 0.09 0.17
Matches are distributed among these distances:
22 22 0.21
23 26 0.25
24 11 0.10
25 8 0.08
26 13 0.12
27 11 0.10
28 4 0.04
29 10 0.10
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (23 bp):
AAATAATATTATATTAATAAATA
Found at i:12756917 original size:19 final size:18
Alignment explanation
Indices: 12756890--12756933 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
12756880 TTTTAAGTAT
*
12756890 TTTTTATATTAACATAATA
1 TTTTAATATTAA-ATAATA
*
12756909 TTTTAATATTAAATATTA
1 TTTTAATATTAAATAATA
12756927 TTATTAA
1 TT-TTAA
12756934 AATATTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTTAATATTAAATAATA
Found at i:12756941 original size:11 final size:13
Alignment explanation
Indices: 12756915--12756945 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
12756905 AATATTTTAA
12756915 TATTAAATATTAT
1 TATTAAATATTAT
12756928 TATTAAAATATTAT
1 TATT-AAATATTAT
12756942 TATT
1 TATT
12756946 TTTTAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATTAAATATTAT
Found at i:12756964 original size:16 final size:16
Alignment explanation
Indices: 12756888--12756980 Score: 51
Period size: 16 Copynumber: 5.3 Consensus size: 16
12756878 TATTTTAAGT
*
12756888 ATTTTTTATATTAACATA
1 ATTTTTAATATT-A-ATA
12756906 ATATTTTAATATTAAATA
1 AT-TTTTAATATT-AATA
* *
12756924 TTATTATTAAAATATTATTA
1 --ATT-TT-TAATATTAATA
*
12756944 TTTTTTAATATTAATA
1 ATTTTTAATATTAATA
* * *
12756960 ATTTTAAAAATAAATA
1 ATTTTTAATATTAATA
12756976 ATTTT
1 ATTTT
12756981 ATTATATTTT
Statistics
Matches: 60, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
16 26 0.43
17 2 0.03
18 7 0.12
19 12 0.20
20 7 0.12
21 6 0.10
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTTTTAATATTAATA
Found at i:12764932 original size:22 final size:20
Alignment explanation
Indices: 12764900--12764939 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
12764890 ATTAAATTCA
*
12764900 ATAATTTTAAATATGATACT
1 ATAATTTTAAAAATGATACT
12764920 ATAATTTAATAAAAATGATA
1 ATAATTT--TAAAAATGATA
12764940 TAAAAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
22 10 0.59
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (20 bp):
ATAATTTTAAAAATGATACT
Found at i:12767722 original size:23 final size:24
Alignment explanation
Indices: 12767661--12767783 Score: 105
Period size: 23 Copynumber: 5.0 Consensus size: 24
12767651 CTCAATTTAT
12767661 TATTAATAATATAATAATATTTATTAATA
1 TATTAATAATATAATAATA--TA-T--TA
*
12767690 TATTATTAATA-AATAATATATTA
1 TATTAATAATATAATAATATATTA
12767713 TATTAATAATATAATACAT-TATT-
1 TATTAATAATATAATA-ATATATTA
* *
12767736 TATTAATTGATATAATATTAT-TTA
1 TATTAA-TAATATAATAATATATTA
12767760 TA-TAATAAATATAATAATA-ATTA
1 TATTAAT-AATATAATAATATATTA
12767783 T
1 T
12767784 CCATATATTA
Statistics
Matches: 81, Mismatches: 6, Indels: 20
0.76 0.06 0.19
Matches are distributed among these distances:
22 1 0.01
23 38 0.47
24 20 0.25
25 3 0.04
26 2 0.02
28 7 0.09
29 10 0.12
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (24 bp):
TATTAATAATATAATAATATATTA
Found at i:12767781 original size:38 final size:37
Alignment explanation
Indices: 12767664--12767844 Score: 124
Period size: 38 Copynumber: 4.8 Consensus size: 37
12767654 AATTTATTAT
* * *
12767664 TAATAATATAATAATATTTATTAATATATTATTAATAAA
1 TAATTATATAATATTATTTATTAATATAATA-TAAT-AA
* * * * * * *
12767703 TAA-TATATTATATTAATAATATAATACATTAT-TTAT
1 TAATTATATAATATTATTTAT-TAATATAATATAATAA
12767739 TAATTGATATAATATTATTTATATAATA-AATATAATAA
1 TAATT-ATATAATATTATTTAT-TAATATAATATAATAA
*
12767777 TAATTATCCAT-ATATTATTTATTAATATAATAT-TTATA
1 TAATTAT--ATAATATTATTTATTAATATAATATAATA-A
*
12767815 TAA-TA-AAAATATTATTTTATTAATATAATA
1 TAATTATATAATATTA-TTTATTAATATAATA
12767845 ATTGTAACAT
Statistics
Matches: 116, Mismatches: 16, Indels: 23
0.75 0.10 0.15
Matches are distributed among these distances:
34 1 0.01
35 6 0.05
36 19 0.16
37 17 0.15
38 59 0.51
39 14 0.12
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.48
Consensus pattern (37 bp):
TAATTATATAATATTATTTATTAATATAATATAATAA
Found at i:12767804 original size:96 final size:96
Alignment explanation
Indices: 12767660--12767838 Score: 222
Period size: 96 Copynumber: 1.9 Consensus size: 96
12767650 ACTCAATTTA
* * *
12767660 TTATTAATAATATAATAATATTTATTAATATATTATTAATAAATAATATATTATATTA-ATAATA
1 TTATTAATAATATAATAATAATTATCAATATATTATT-ATAAATAATATAATAT-TTATATAATA
*
12767724 TAATACATTA-TTTATTAATTGATATAATATTAT
64 -AAAACATTATTTTATTAATTGATATAATATTAT
* *
12767757 TTATATAATAAATATAATAATAATTATCCATATATTATT-T-ATTAATATAATATTTATATAATA
1 TTAT-TAAT-AATATAATAATAATTATCAATATATTATTATAAATAATATAATATTTATATAATA
*
12767820 AAAATATTATTTTATTAAT
64 AAAACATTATTTTATTAAT
12767839 ATAATAATTG
Statistics
Matches: 71, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
95 10 0.14
96 26 0.37
97 5 0.07
98 4 0.06
99 26 0.37
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.49
Consensus pattern (96 bp):
TTATTAATAATATAATAATAATTATCAATATATTATTATAAATAATATAATATTTATATAATAAA
AACATTATTTTATTAATTGATATAATATTAT
Found at i:12777484 original size:2 final size:2
Alignment explanation
Indices: 12777472--12777517 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
12777462 GAGCATTTGT
*
12777472 AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12777514 AG AG
1 AG AG
12777518 GTTCTCTGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12781710 original size:163 final size:161
Alignment explanation
Indices: 12781429--12781753 Score: 553
Period size: 163 Copynumber: 2.0 Consensus size: 161
12781419 TTGCTTCTTT
*
12781429 ATAGTTTTTTGGTTCATTTCTCATTTTTCTCTCTTTCTGAATACGCTCCCCCACCCCCACCTTGA
1 ATAGTTTTTTGGTTCATTTCTCATTTTTCTCTCTTTCTGAATACGCT-CCCCACCACCACCTTGA
* *
12781494 CCGTCACTGACATGACACGTACGATATTGTCAGTTTTGCCATTATCACCATCTAGACTCTTTCCA
65 CCATCACTGACATGACACCTACGATATTGTCAGTTTTGCCATTATCACCATCTAGACTCTTTCCA
12781559 GCCACCATAGTTTGTTTCCCTGCTTGATTGTA
130 GCCACCATAGTTTGTTTCCCTGCTTGATTGTA
* * *
12781591 ATAGTTTTTTTTGTTCATTTCTCATTTTTCTCTCTCTTTCTGAATACGCT-TCCACCACCAGCTT
1 ATAG-TTTTTTGGTTCATTTCTCA-TTTT-TCTCTCTTTCTGAATACGCTCCCCACCACCACCTT
12781655 GACCATCACTGACATGACACCTACGATATTGTCAGTTTTGCCATTATCACCATCTAGACTCTTTC
63 GACCATCACTGACATGACACCTACGATATTGTCAGTTTTGCCATTATCACCATCTAGACTCTTTC
12781720 CAGCCACCATAGTTTGTTTCCCTGCTTGATTGTA
128 CAGCCACCATAGTTTGTTTCCCTGCTTGATTGTA
12781754 CCTCCCACCA
Statistics
Matches: 154, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
162 4 0.03
163 126 0.82
164 4 0.03
165 20 0.13
ACGTcount: A:0.20, C:0.29, G:0.12, T:0.39
Consensus pattern (161 bp):
ATAGTTTTTTGGTTCATTTCTCATTTTTCTCTCTTTCTGAATACGCTCCCCACCACCACCTTGAC
CATCACTGACATGACACCTACGATATTGTCAGTTTTGCCATTATCACCATCTAGACTCTTTCCAG
CCACCATAGTTTGTTTCCCTGCTTGATTGTA
Found at i:12783047 original size:26 final size:26
Alignment explanation
Indices: 12783007--12783069 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
12782997 ATTGAAATCA
* * *
12783007 ATAATAAAAATTATTGTAGTTGCGAT
1 ATAAAAAAAAATATTATAGTTGCGAT
*
12783033 ATAAAAAAAAATATTATAGTTGTGAT
1 ATAAAAAAAAATATTATAGTTGCGAT
12783059 -TGAAAAAAAAA
1 AT-AAAAAAAAA
12783070 AATAAAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 1 0.03
26 31 0.97
ACGTcount: A:0.54, C:0.02, G:0.13, T:0.32
Consensus pattern (26 bp):
ATAAAAAAAAATATTATAGTTGCGAT
Found at i:12783487 original size:16 final size:16
Alignment explanation
Indices: 12783468--12783509 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
12783458 AAAAAATTTG
12783468 AATTTAAAATAA-TCTA
1 AATTTAAAATAATTC-A
12783484 AATTTAAAATAATTCA
1 AATTTAAAATAATTCA
*
12783500 AACTTAAAAT
1 AATTTAAAAT
12783510 TACTTTATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 22 0.92
17 2 0.08
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (16 bp):
AATTTAAAATAATTCA
Found at i:12784063 original size:14 final size:15
Alignment explanation
Indices: 12784044--12784073 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
12784034 ATATCAAATT
12784044 TAAATAATT-ATAAA
1 TAAATAATTAATAAA
12784058 TAAATAATTAATAAA
1 TAAATAATTAATAAA
12784073 T
1 T
12784074 TTAAATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATAATTAATAAA
Found at i:12784428 original size:19 final size:18
Alignment explanation
Indices: 12784363--12784425 Score: 53
Period size: 18 Copynumber: 3.6 Consensus size: 18
12784353 GAATTCATAT
*
12784363 ATTTAAATAAATAGTACTT-
1 ATTTAAAT-AATAATA-TTA
12784382 ATTTAAAT-A-AAT-TTA
1 ATTTAAATAATAATATTA
*
12784397 GATTTAGATAATAATATTA
1 -ATTTAAATAATAATATTA
12784416 ATTTAAATAA
1 ATTTAAATAA
12784426 ATATTTAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
14 2 0.06
16 9 0.25
17 2 0.06
18 12 0.33
19 11 0.31
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.43
Consensus pattern (18 bp):
ATTTAAATAATAATATTA
Found at i:12784452 original size:27 final size:26
Alignment explanation
Indices: 12784422--12784473 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
12784412 ATTAATTTAA
*
12784422 ATAAATATTTAAATAAATTTAAATATT
1 ATAAATA-TTAAACAAATTTAAATATT
* *
12784449 ATAAGTATTAAACGAATTTAAATAT
1 ATAAATATTAAACAAATTTAAATAT
12784474 ATTTATTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (26 bp):
ATAAATATTAAACAAATTTAAATATT
Found at i:12785484 original size:32 final size:32
Alignment explanation
Indices: 12785419--12785485 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
12785409 AGATTTGGTG
*
12785419 ATTTATATATTTTTATTATATAAAATATTAAA
1 ATTTATATATTTTTATTATATAAAATATAAAA
***
12785451 ATTTATAT-TTTTATATTATATTTTATATAAAA
1 ATTTATATATTTT-TATTATATAAAATATAAAA
12785483 ATT
1 ATT
12785486 ATACGTCGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 4 0.13
32 26 0.87
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (32 bp):
ATTTATATATTTTTATTATATAAAATATAAAA
Found at i:12785858 original size:28 final size:28
Alignment explanation
Indices: 12785796--12785859 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
12785786 CACATTCAAA
* *
12785796 AATAAAAATTTAAATTAATTGAATTTAT
1 AATAAAAAATTAAATTAATTGAAATTAT
12785824 AATAAAAAATTAAATTAATT-AAATTA-
1 AATAAAAAATTAAATTAATTGAAATTAT
*
12785850 AATTAAAAAT
1 AATAAAAAAT
12785860 ATTTTAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 9 0.27
27 5 0.15
28 19 0.58
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (28 bp):
AATAAAAAATTAAATTAATTGAAATTAT
Found at i:12786723 original size:17 final size:18
Alignment explanation
Indices: 12786684--12786730 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
12786674 CTCGACCCGA
12786684 AATTAATA-AAATATTAT
1 AATTAATATAAATATTAT
**
12786701 TTTTAATATAAATA-TAT
1 AATTAATATAAATATTAT
12786718 AATTAAATATAAA
1 AATT-AATATAAA
12786731 ATTTAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTAATATAAATATTAT
Found at i:12786740 original size:19 final size:18
Alignment explanation
Indices: 12786705--12786744 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
12786695 TATTATTTTT
*
12786705 AATATAAATATATAATTA
1 AATATAAATATAAAATTA
*
12786723 AATATAAAATTTAAAATTA
1 AATAT-AAATATAAAATTA
12786742 AAT
1 AAT
12786745 TAATTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATATAAATATAAAATTA
Found at i:12787910 original size:16 final size:17
Alignment explanation
Indices: 12787889--12787951 Score: 58
Period size: 18 Copynumber: 3.8 Consensus size: 17
12787879 ATAATAACTG
*
12787889 TTTTTAATTTTA-ATAA
1 TTTTAAATTTTATATAA
* *
12787905 TTTT-TAGTTTATATAA
1 TTTTAAATTTTATATAA
**
12787921 TTAAAAATATTTATATAA
1 TTTTAAAT-TTTATATAA
12787939 TTTTAAATTTTAT
1 TTTTAAATTTTAT
12787952 TTATTATTGG
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
15 5 0.14
16 10 0.28
17 6 0.17
18 15 0.42
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
TTTTAAATTTTATATAA
Found at i:12791764 original size:34 final size:35
Alignment explanation
Indices: 12791726--12791792 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
12791716 GTTTTTTTTA
*
12791726 AAAAAAGTATA-TATTTTAATTTTTAAAATTTTCC
1 AAAAAAGTATAGTATTTTAATTTTCAAAATTTTCC
* * * *
12791760 AAAAAATTTTAGTTTTTTTATTTTCAAAATTTT
1 AAAAAAGTATAGTATTTTAATTTTCAAAATTTT
12791793 AAATTTTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 9 0.33
35 18 0.67
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.52
Consensus pattern (35 bp):
AAAAAAGTATAGTATTTTAATTTTCAAAATTTTCC
Found at i:12791852 original size:40 final size:39
Alignment explanation
Indices: 12791806--12791889 Score: 118
Period size: 38 Copynumber: 2.2 Consensus size: 39
12791796 TTTTTTTGTG
*
12791806 AATTTTTTTTAATTTTAAGAA-AATTAT-ATTTTTATTAA
1 AATTTTTTTTAATATT-AGAATAATTATAATTTTTATTAA
*
12791844 AATTTTTTTTAATATTAGAATAATTTTGAATTTTTATTAA
1 AATTTTTTTTAATATTAGAATAATTAT-AATTTTTATTAA
12791884 AATTTT
1 AATTTT
12791890 GAGATTTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
37 4 0.10
38 20 0.49
40 17 0.41
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (39 bp):
AATTTTTTTTAATATTAGAATAATTATAATTTTTATTAA
Found at i:12791910 original size:27 final size:27
Alignment explanation
Indices: 12791844--12791938 Score: 79
Period size: 27 Copynumber: 3.5 Consensus size: 27
12791834 TTTTTATTAA
** * *
12791844 AATTTTTTTTAATATTAGAATAATTTTG
1 AATTTTTTAAAATGTTAG-ATATTTTTG
*
12791872 AATTTTTATTAAAATTTTGAGAT-TTTTTG
1 AA-TTTT-TTAAAATGTT-AGATATTTTTG
*
12791901 AATTTTTTAAAATGTTATATATTTTT-
1 AATTTTTTAAAATGTTAGATATTTTTG
12791927 AA-TTTTTAAAAT
1 AATTTTTTAAAAT
12791939 ATTTCATATA
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
25 10 0.18
26 5 0.09
27 14 0.25
28 6 0.11
29 11 0.19
30 9 0.16
31 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (27 bp):
AATTTTTTAAAATGTTAGATATTTTTG
Found at i:12792039 original size:21 final size:20
Alignment explanation
Indices: 12791992--12792053 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 20
12791982 TCAAAATATT
12791992 TTAAATTTTAAATTTTTTTAA
1 TTAAATTTTAAA-TTTTTTAA
**
12792013 AAAAATTTTAAATTTTTTAGA
1 TTAAATTTTAAATTTTTTA-A
*
12792034 TTAAATGTTTTCAATTTTTT
1 TTAAA--TTTTAAATTTTTT
12792054 TCTTTAATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
20 7 0.21
21 14 0.42
23 12 0.36
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (20 bp):
TTAAATTTTAAATTTTTTAA
Found at i:12813174 original size:15 final size:15
Alignment explanation
Indices: 12813156--12813208 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
12813146 TATAATTATG
12813156 ATTAAAAAAATTTTT
1 ATTAAAAAAATTTTT
*
12813171 ATTAATGAAAATTTTAT
1 ATTAA-AAAAATTTT-T
* *
12813188 ATTGAATAAA-TTTT
1 ATTAAAAAAATTTTT
12813202 ATTAAAA
1 ATTAAAA
12813209 TTAATATTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
14 6 0.20
15 8 0.27
16 11 0.37
17 5 0.17
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (15 bp):
ATTAAAAAAATTTTT
Found at i:12813334 original size:26 final size:28
Alignment explanation
Indices: 12813263--12813334 Score: 66
Period size: 28 Copynumber: 2.7 Consensus size: 28
12813253 TACACTAAAA
*
12813263 ATATT-ATAAAATAGA-ATTATTATTTG
1 ATATTAATTAAATAGATATTATTATTTG
12813289 ATAATTTAATTTAAA-A-ATATTA-TATTT-
1 AT-A-TTAA-TTAAATAGATATTATTATTTG
12813316 ATATTAATTAAATAGATAT
1 ATATTAATTAAATAGATAT
12813335 GATTTCTATT
Statistics
Matches: 38, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
24 5 0.13
25 5 0.13
26 7 0.18
27 3 0.08
28 8 0.21
29 6 0.16
30 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (28 bp):
ATATTAATTAAATAGATATTATTATTTG
Found at i:12813695 original size:2 final size:2
Alignment explanation
Indices: 12813683--12813722 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
12813673 GAGCATTTGT
*
12813683 AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12813723 TTCTCTGAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12815619 original size:12 final size:11
Alignment explanation
Indices: 12815602--12815671 Score: 61
Period size: 12 Copynumber: 6.0 Consensus size: 11
12815592 AATATAAGTA
12815602 TTAAATTTAAGT
1 TTAAATTTAA-T
*
12815614 TTAAATTTATTT
1 TTAAATTTA-AT
12815626 TTAAATTTGAGACT
1 TTAAATTT-A-A-T
* *
12815640 TAAAATTTGAT
1 TTAAATTTAAT
12815651 TTAAATTTAA-
1 TTAAATTTAAT
12815661 TTAAATTTAAT
1 TTAAATTTAAT
12815672 ATTTTTTGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
10 10 0.21
11 9 0.19
12 19 0.40
13 1 0.02
14 8 0.17
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.51
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:12818016 original size:163 final size:161
Alignment explanation
Indices: 12817735--12818059 Score: 553
Period size: 163 Copynumber: 2.0 Consensus size: 161
12817725 TTGCTTCTTT
12817735 ATAGTTTTTTGGTTCATTCCTCATTTTTCTCTCTTTCTGAATACGCTCCCCCACCCCCACCTTGA
1 ATAGTTTTTTGGTTCATTCCTCATTTTTCTCTCTTTCTGAATACGCT-CCCCACCCCCACCTTGA
* *
12817800 CCGTCACTGACATGACACGTACGATATTGTCAGTTTTGCCATTATCACCATCTAGACTCTTTCCA
65 CCATCACTGACATGACACCTACGATATTGTCAGTTTTGCCATTATCACCATCTAGACTCTTTCCA
12817865 GCCACCATAGTTTGTTTCCCTGCTTGATTGTA
130 GCCACCATAGTTTGTTTCCCTGCTTGATTGTA
* * * *
12817897 ATAGTTTTTTTTGTTCATTTCTCATTTTTCTCTCTCTTTCTGAATACGCT-TCCACCCCCAGCTT
1 ATAG-TTTTTTGGTTCATTCCTCA-TTTT-TCTCTCTTTCTGAATACGCTCCCCACCCCCACCTT
12817961 GACCATCACTGACATGACACCTACGATATTGTCAGTTTTGCCATTATCACCATCTAGACTCTTTC
63 GACCATCACTGACATGACACCTACGATATTGTCAGTTTTGCCATTATCACCATCTAGACTCTTTC
12818026 CAGCCACCATAGTTTGTTTCCCTGCTTGATTGTA
128 CAGCCACCATAGTTTGTTTCCCTGCTTGATTGTA
12818060 CCTCCCACCA
Statistics
Matches: 154, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
162 4 0.03
163 126 0.82
164 4 0.03
165 20 0.13
ACGTcount: A:0.19, C:0.29, G:0.12, T:0.39
Consensus pattern (161 bp):
ATAGTTTTTTGGTTCATTCCTCATTTTTCTCTCTTTCTGAATACGCTCCCCACCCCCACCTTGAC
CATCACTGACATGACACCTACGATATTGTCAGTTTTGCCATTATCACCATCTAGACTCTTTCCAG
CCACCATAGTTTGTTTCCCTGCTTGATTGTA
Found at i:12819756 original size:16 final size:16
Alignment explanation
Indices: 12819737--12819778 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
12819727 AAAAAATTTG
12819737 AATTTAAAATAA-TCTA
1 AATTTAAAATAATTC-A
12819753 AATTTAAAATAATTCA
1 AATTTAAAATAATTCA
*
12819769 AACTTAAAAT
1 AATTTAAAAT
12819779 TACTTTATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 22 0.92
17 2 0.08
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (16 bp):
AATTTAAAATAATTCA
Found at i:12820330 original size:14 final size:15
Alignment explanation
Indices: 12820311--12820340 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
12820301 ATATCAAATT
12820311 TAAATAATT-ATAAA
1 TAAATAATTAATAAA
12820325 TAAATAATTAATAAA
1 TAAATAATTAATAAA
12820340 T
1 T
12820341 TTAAATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATAATTAATAAA
Found at i:12820654 original size:19 final size:19
Alignment explanation
Indices: 12820630--12820696 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 19
12820620 TGAATTCAGA
12820630 TATTTAAATAAATAATACT
1 TATTTAAATAAATAATACT
* *
12820649 TATTTAAACAAAT--T-CA
1 TATTTAAATAAATAATACT
* *
12820665 GATTTAGAT-AATAATACT
1 TATTTAAATAAATAATACT
*
12820683 AATTTAAATAAATA
1 TATTTAAATAAATA
12820697 TTTAAATAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
15 3 0.08
16 7 0.19
17 2 0.06
18 8 0.22
19 16 0.44
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (19 bp):
TATTTAAATAAATAATACT
Found at i:12820688 original size:34 final size:36
Alignment explanation
Indices: 12820598--12820695 Score: 98
Period size: 34 Copynumber: 2.8 Consensus size: 36
12820588 TGATAAAAAT
* **
12820598 TTTAAATAAATAA-A-T-ATTTTAATGAATTCAGATA
1 TTTAAATAAATAATACTAATTTAAACAAATTCAGA-A
*
12820632 TTTAAATAAATAATACTTATTTAAACAAATTCAG-A
1 TTTAAATAAATAATACTAATTTAAACAAATTCAGAA
* *
12820667 TTTAGAT-AATAATACTAATTTAAATAAAT
1 TTTAAATAAATAATACTAATTTAAACAAAT
12820696 ATTTAAATAA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
34 33 0.60
35 8 0.15
36 1 0.02
37 13 0.24
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (36 bp):
TTTAAATAAATAATACTAATTTAAACAAATTCAGAA
Found at i:12824372 original size:28 final size:28
Alignment explanation
Indices: 12824313--12824396 Score: 70
Period size: 28 Copynumber: 3.1 Consensus size: 28
12824303 ATTCAAAAAT
**
12824313 AAAAAATTAAATTAATTGAATTTATAA-T-
1 AAAAAATTAAATTAATT-AAAATA-AATTA
12824341 AAAAAATTAAATTAATTAAAATAAATTA
1 AAAAAATTAAATTAATTAAAATAAATTA
* *
12824369 AAAATATT---TTAATTAAAAAAAACTTA
1 AAAAAATTAAATTAATTAAAATAAA-TTA
12824395 AA
1 AA
12824397 TATCTTAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
25 13 0.27
26 7 0.14
27 5 0.10
28 24 0.49
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (28 bp):
AAAAAATTAAATTAATTAAAATAAATTA
Found at i:12824404 original size:24 final size:24
Alignment explanation
Indices: 12824352--12824404 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
12824342 AAAAATTAAA
* *
12824352 TTAATTAAAATAAATTAAAAATATT
1 TTAATTAAAAAAAATT-AAAATATC
12824377 TTAATTAAAAAAAACTT-AAATATC
1 TTAATTAAAAAAAA-TTAAAATATC
12824401 TTAA
1 TTAA
12824405 ATTTAGCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 10 0.40
25 13 0.52
26 2 0.08
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (24 bp):
TTAATTAAAAAAAATTAAAATATC
Found at i:12825574 original size:21 final size:22
Alignment explanation
Indices: 12825529--12825574 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
12825519 AAATGTGATA
*
12825529 TTTGTAATTTAATCAAAAGTAT
1 TTTGTAATTTAATCAAAAATAT
* *
12825551 TTTGTTATTTAA-CAAAAATTT
1 TTTGTAATTTAATCAAAAATAT
12825572 TTT
1 TTT
12825575 ATTCAAGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (22 bp):
TTTGTAATTTAATCAAAAATAT
Found at i:12826021 original size:18 final size:17
Alignment explanation
Indices: 12825987--12826026 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
12825977 TAAATTTTAG
12825987 TTTATATAATTAAAAAT
1 TTTATATAATTAAAAAT
**
12826004 ATTTATATAATTTCAAAT
1 -TTTATATAATTAAAAAT
12826022 TTTAT
1 TTTAT
12826027 TTATTATTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTATATAATTAAAAAT
Found at i:12835696 original size:12 final size:12
Alignment explanation
Indices: 12835679--12835703 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12835669 AAAAATAATA
12835679 ATAATTATTATT
1 ATAATTATTATT
12835691 ATAATTATTATT
1 ATAATTATTATT
12835703 A
1 A
12835704 AAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATAATTATTATT
Found at i:12836206 original size:2 final size:2
Alignment explanation
Indices: 12836199--12836241 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
12836189 GTAGGGAGGA
12836199 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12836241 A
1 A
12836242 TAATTTTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12837840 original size:6 final size:6
Alignment explanation
Indices: 12837829--12837895 Score: 50
Period size: 6 Copynumber: 11.3 Consensus size: 6
12837819 CAATATAATA
** * * *
12837829 TTAAAT TTAAAT TTAAAT TTATTT TTAAAT TTGAGAT TTAAAAC TT-GAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TT-AAAT TT-AAAT TTAAAT
12837878 TTAAAT TT-AA- TTAAAT TT
1 TTAAAT TTAAAT TTAAAT TT
12837896 TATATTTTTT
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
4 2 0.04
5 7 0.15
6 28 0.61
7 9 0.20
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (6 bp):
TTAAAT
Found at i:12840324 original size:163 final size:161
Alignment explanation
Indices: 12840043--12840367 Score: 562
Period size: 163 Copynumber: 2.0 Consensus size: 161
12840033 TTGCTTCTTT
12840043 ATAGTTTTTTGGTTCATTTCTCATTTTTCTCTCTTTCTGAATACGCTCCCCCACCCCCACCTTGA
1 ATAGTTTTTTGGTTCATTTCTCATTTTTCTCTCTTTCTGAATACGCT-CCCCACCCCCACCTTGA
* *
12840108 CCGTCACTGACATGACACGTACGATATTGTCAGTTTTGCCATTATCACCATCTAGACTCTTTCCA
65 CCATCACTGACATGACACCTACGATATTGTCAGTTTTGCCATTATCACCATCTAGACTCTTTCCA
12840173 GCCACCATAGTTTGTTTCCCTGCTTGATTGTA
130 GCCACCATAGTTTGTTTCCCTGCTTGATTGTA
* * *
12840205 ATAGTTTTTTTTGTTCATTTCTCATTTTTCTCTCTCTTTCTGAATACGCT-TCCACCCCCAGCTT
1 ATAG-TTTTTTGGTTCATTTCTCA-TTTT-TCTCTCTTTCTGAATACGCTCCCCACCCCCACCTT
12840269 GACCATCACTGACATGACACCTACGATATTGTCAGTTTTGCCATTATCACCATCTAGACTCTTTC
63 GACCATCACTGACATGACACCTACGATATTGTCAGTTTTGCCATTATCACCATCTAGACTCTTTC
12840334 CAGCCACCATAGTTTGTTTCCCTGCTTGATTGTA
128 CAGCCACCATAGTTTGTTTCCCTGCTTGATTGTA
12840368 CCTCCCACCA
Statistics
Matches: 155, Mismatches: 5, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
162 4 0.03
163 127 0.82
164 4 0.03
165 20 0.13
ACGTcount: A:0.19, C:0.29, G:0.12, T:0.39
Consensus pattern (161 bp):
ATAGTTTTTTGGTTCATTTCTCATTTTTCTCTCTTTCTGAATACGCTCCCCACCCCCACCTTGAC
CATCACTGACATGACACCTACGATATTGTCAGTTTTGCCATTATCACCATCTAGACTCTTTCCAG
CCACCATAGTTTGTTTCCCTGCTTGATTGTA
Found at i:12841665 original size:26 final size:26
Alignment explanation
Indices: 12841625--12841689 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
12841615 ATTGAAATCA
* * *
12841625 ATAATAAAAATTATTGTAGTTGCGAT
1 ATAAAAAAAAATATTATAGTTGCGAT
*
12841651 ATAAAAAAAAATATTATAGTTGTGAT
1 ATAAAAAAAAATATTATAGTTGCGAT
12841677 -TGAAAAAAAAATA
1 AT-AAAAAAAAATA
12841690 ATAAAAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 1 0.03
26 33 0.97
ACGTcount: A:0.54, C:0.02, G:0.12, T:0.32
Consensus pattern (26 bp):
ATAAAAAAAAATATTATAGTTGCGAT
Found at i:12842719 original size:14 final size:15
Alignment explanation
Indices: 12842700--12842729 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
12842690 ATATCGAATT
12842700 TAAATAATT-ATAAA
1 TAAATAATTAATAAA
12842714 TAAATAATTAATAAA
1 TAAATAATTAATAAA
12842729 T
1 T
12842730 TTAAATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATAATTAATAAA
Found at i:12843131 original size:46 final size:45
Alignment explanation
Indices: 12843036--12843133 Score: 110
Period size: 46 Copynumber: 2.1 Consensus size: 45
12843026 AAATAGTGCT
* * *
12843036 TATTTAAATGAATTTAGATTTAGATAATAATACTAATTTAAATAAA
1 TATTTAAATGAATTTAAATTTAAATAATAATACGAATTTAAAT-AA
*
12843082 TATTTAAATGAATTTAAATATTATAAGTATTAA-ACGAATTTAAAT-A
1 TATTTAAATGAATTTAAAT-TTA-AA-TAATAATACGAATTTAAATAA
12843128 TATTTA
1 TATTTA
12843134 TTTAAATTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
46 25 0.56
47 3 0.07
48 12 0.27
49 5 0.11
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (45 bp):
TATTTAAATGAATTTAAATTTAAATAATAATACGAATTTAAATAA
Found at i:12844138 original size:32 final size:32
Alignment explanation
Indices: 12844073--12844139 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
12844063 AGATTTGGTG
*
12844073 ATTTATATATTTTTATTATATAAAATATTAAA
1 ATTTATATATTTTTATTATATAAAATATAAAA
***
12844105 ATTTATAT-TTTTATATTATATTTTATATAAAA
1 ATTTATATATTTT-TATTATATAAAATATAAAA
12844137 ATT
1 ATT
12844140 ATACGTCGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 4 0.13
32 26 0.87
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (32 bp):
ATTTATATATTTTTATTATATAAAATATAAAA
Found at i:12844505 original size:28 final size:27
Alignment explanation
Indices: 12844452--12844516 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 27
12844442 CACATTCAAA
* **
12844452 AATAAAAATTTAAATTAATTGAATTTAT
1 AATAAAAAATTAAATTAATAAAATTT-T
12844480 AATAAAAAATTAAATTAA-AAATATTTT
1 AATAAAAAATTAAATTAATAAA-ATTTT
12844507 AATTAAAAAA
1 AA-TAAAAAA
12844517 ACTTAAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 4 0.12
28 28 0.88
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (27 bp):
AATAAAAAATTAAATTAATAAAATTTT
Found at i:12845365 original size:17 final size:18
Alignment explanation
Indices: 12845326--12845372 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
12845316 CTCGACCCGA
12845326 AATTAATA-AAATATTAT
1 AATTAATATAAATATTAT
**
12845343 TTTTAATATAAATA-TAT
1 AATTAATATAAATATTAT
12845360 AATTAAATATAAA
1 AATT-AATATAAA
12845373 ATTTAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTAATATAAATATTAT
Found at i:12846550 original size:16 final size:17
Alignment explanation
Indices: 12846529--12846591 Score: 58
Period size: 18 Copynumber: 3.8 Consensus size: 17
12846519 ATAATAACTG
*
12846529 TTTTTAATTTTA-ATAA
1 TTTTAAATTTTATATAA
* *
12846545 TTTT-TAGTTTATATAA
1 TTTTAAATTTTATATAA
**
12846561 TTAAAAATATTTATATAA
1 TTTTAAAT-TTTATATAA
12846579 TTTTAAATTTTAT
1 TTTTAAATTTTAT
12846592 TTATTATTGG
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
15 5 0.14
16 10 0.28
17 6 0.17
18 15 0.42
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
TTTTAAATTTTATATAA
Found at i:12850489 original size:38 final size:39
Alignment explanation
Indices: 12850447--12850527 Score: 112
Period size: 38 Copynumber: 2.1 Consensus size: 39
12850437 TTTTTGTGAA
*
12850447 TTTTTTTAATTTTAAGAA-AATTAT-ATTTTTATTAAAAT
1 TTTTTTTAATATT-AGAATAATTATAATTTTTATTAAAAT
*
12850485 TTTTTTTAATATTAGAATAATTTTGAATTTTTATTAAAAT
1 TTTTTTTAATATTAGAATAATTAT-AATTTTTATTAAAAT
12850525 TTT
1 TTT
12850528 GAGATTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
37 4 0.11
38 17 0.45
40 17 0.45
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (39 bp):
TTTTTTTAATATTAGAATAATTATAATTTTTATTAAAAT
Found at i:12850548 original size:27 final size:27
Alignment explanation
Indices: 12850482--12850576 Score: 79
Period size: 27 Copynumber: 3.5 Consensus size: 27
12850472 TTTTTATTAA
** * *
12850482 AATTTTTTTTAATATTAGAATAATTTTG
1 AATTTTTTAAAATGTTAG-ATATTTTTG
*
12850510 AATTTTTATTAAAATTTTGAGAT-TTTTTG
1 AA-TTTT-TTAAAATGTT-AGATATTTTTG
*
12850539 AATTTTTTAAAATGTTATATATTTTT-
1 AATTTTTTAAAATGTTAGATATTTTTG
12850565 AA-TTTTTAAAAT
1 AATTTTTTAAAAT
12850577 ATTTCATATA
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
25 10 0.18
26 5 0.09
27 14 0.25
28 6 0.11
29 11 0.19
30 9 0.16
31 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (27 bp):
AATTTTTTAAAATGTTAGATATTTTTG
Found at i:12850643 original size:37 final size:37
Alignment explanation
Indices: 12850559--12850645 Score: 106
Period size: 37 Copynumber: 2.4 Consensus size: 37
12850549 AATGTTATAT
* *
12850559 ATTTTTAATTTTTAAAATATTTCATATATATATTTAT
1 ATTTTTAATTTTTAAAATATTTCATAAATATATTTAA
*
12850596 TTTTTTAATTTTTAAAAAATATTTCA-AAATAT-TTTAA
1 ATTTTTAATTTTT--AAAATATTTCATAAATATATTTAA
*
12850633 ATTTTAAATTTTT
1 ATTTTTAATTTTT
12850646 TTAAAAAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
37 27 0.63
38 5 0.12
39 11 0.26
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (37 bp):
ATTTTTAATTTTTAAAATATTTCATAAATATATTTAA
Found at i:12850676 original size:21 final size:20
Alignment explanation
Indices: 12850629--12850690 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 20
12850619 TCAAAATATT
12850629 TTAAATTTTAAATTTTTTTAA
1 TTAAATTTTAAA-TTTTTTAA
**
12850650 AAAAATTTTAAATTTTTTAGA
1 TTAAATTTTAAATTTTTTA-A
*
12850671 TTAAATGTTTTCAATTTTTT
1 TTAAA--TTTTAAATTTTTT
12850691 TCTTTAATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
20 7 0.21
21 14 0.42
23 12 0.36
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (20 bp):
TTAAATTTTAAATTTTTTAA
Found at i:12862433 original size:2 final size:2
Alignment explanation
Indices: 12862426--12862451 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12862416 GTTATAGTCC
12862426 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
12862452 TCATCCGTTA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:12867464 original size:12 final size:12
Alignment explanation
Indices: 12867438--12867470 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12867428 TCCTTACATC
*
12867438 TTTTGTTTT-TA
1 TTTTATTTTATA
12867449 TTTTATTTTATA
1 TTTTATTTTATA
12867461 TTTTATTTTA
1 TTTTATTTTA
12867471 CCCTTTAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (12 bp):
TTTTATTTTATA
Found at i:12867688 original size:17 final size:17
Alignment explanation
Indices: 12867666--12867700 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
12867656 AAATTTTAAA
*
12867666 TTTTTATTTTCTATCAT
1 TTTTTATATTCTATCAT
*
12867683 TTTTTATATTGTATCAT
1 TTTTTATATTCTATCAT
12867700 T
1 T
12867701 ATATAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.09, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTTTATATTCTATCAT
Found at i:12870008 original size:121 final size:121
Alignment explanation
Indices: 12869793--12870028 Score: 373
Period size: 121 Copynumber: 2.0 Consensus size: 121
12869783 ATTGCTTCTC
* *
12869793 AGAAGTTACAGCAGAGCATCCAAATTTTCCCTGAGAACTAACAGTTGAAAAGTGTTAAAGTGGTG
1 AGAAGTTACAGCAGAGCATCCAAATTTTCCATGAGAACTAACAGATGAAAAGTGTTAAAGTGGTG
* *
12869858 TTATGACGTCTAATAAATATCTAACTTTTAAAATCTTATATTCAAATTAGTCCCTT
66 TTATAACATCTAATAAATATCTAACTTTTAAAATCTTATATTCAAATTAGTCCCTT
* * *
12869914 AGAAGTTATAGCAGAGCATCCAAATTTTCCATGAGAACTAATAGATGAAAAGTGTTAAAGTGTTG
1 AGAAGTTACAGCAGAGCATCCAAATTTTCCATGAGAACTAACAGATGAAAAGTGTTAAAGTGGTG
* * * *
12869979 TTATAACATTTAATAAATATCTAATTTTTATAATTTTATATTCAAATTAG
66 TTATAACATCTAATAAATATCTAACTTTTAAAATCTTATATTCAAATTAG
12870029 ATCCTTTAAC
Statistics
Matches: 104, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
121 104 1.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (121 bp):
AGAAGTTACAGCAGAGCATCCAAATTTTCCATGAGAACTAACAGATGAAAAGTGTTAAAGTGGTG
TTATAACATCTAATAAATATCTAACTTTTAAAATCTTATATTCAAATTAGTCCCTT
Found at i:12871415 original size:20 final size:20
Alignment explanation
Indices: 12871390--12871428 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
12871380 AAGTGAGACC
12871390 GCAGAATTCTATCATATAGA
1 GCAGAATTCTATCATATAGA
12871410 GCAGAATTCTATCATATAG
1 GCAGAATTCTATCATATAG
12871429 CCATTGTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (20 bp):
GCAGAATTCTATCATATAGA
Found at i:12873064 original size:2 final size:2
Alignment explanation
Indices: 12873057--12873083 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12873047 TAAGTAAAGA
12873057 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
12873084 GAAAATAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12886062 original size:43 final size:43
Alignment explanation
Indices: 12885979--12886141 Score: 114
Period size: 43 Copynumber: 3.7 Consensus size: 43
12885969 TTTTATTACG
* ** * *
12885979 AATTTTAAATTTTCAATGCCTTTGGTTAGAATGAG-CTTTTTAA
1 AATTTTAAAATTTCAAAACCTTTGGTTA-AAAGAGTTTTTTTAA
*
12886022 AATTTTAAAATTTCAAAACCTTTTGTTAAAAGAGTTTTTTTTTGTTACA
1 AATTTTAAAATTTCAAAACCTTTGGTTAAAAGAG----TTTTT-TTA-A
* * * * * *
12886071 TATTTTAAAGTTTCAATACCTTTAGTTAGAGGAGTTTTTTTCAA
1 AATTTTAAAATTTCAAAACCTTTGGTTAAAAGAGTTTTTTT-AA
* *
12886115 AATTTT-AAATTTTATAACCTTTGGTTA
1 AATTTTAAAATTTCAAAACCTTTGGTTA
12886142 GATGATCATT
Statistics
Matches: 94, Mismatches: 18, Indels: 16
0.73 0.14 0.12
Matches are distributed among these distances:
42 5 0.05
43 40 0.43
44 8 0.09
45 6 0.06
47 3 0.03
48 3 0.03
49 29 0.31
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.48
Consensus pattern (43 bp):
AATTTTAAAATTTCAAAACCTTTGGTTAAAAGAGTTTTTTTAA
Found at i:12886125 original size:92 final size:92
Alignment explanation
Indices: 12885966--12886141 Score: 223
Period size: 92 Copynumber: 1.9 Consensus size: 92
12885956 CAAGGTCTAG
* * * *
12885966 TTTTTTTATTACGAATTTTAAATTTTCAATGCCTTTGGTTAGAATGAGCTTTTTAAAATTTTAAA
1 TTTTTTTATTACGAATTTTAAAGTTTCAATACCTTTAGTTAGAAGGAGCTTTTTAAAATTTTAAA
*
12886031 ATTTCAAAACCTTTTGTTAAAAGAGTT
66 ATTTCAAAACCTTTGGTTAAAAGAGTT
* *
12886058 TTTTTTTGTTAC-ATATTTTAAAGTTTCAATACCTTTAGTTAG-AGGAGTTTTTTTCAAAATTTT
1 TTTTTTTATTACGA-ATTTTAAAGTTTCAATACCTTTAGTTAGAAGGAG-CTTTTT-AAAATTTT
* *
12886121 -AAATTTTATAACCTTTGGTTA
63 AAAATTTCAAAACCTTTGGTTA
12886142 GATGATCATT
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
91 5 0.07
92 59 0.82
93 8 0.11
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.50
Consensus pattern (92 bp):
TTTTTTTATTACGAATTTTAAAGTTTCAATACCTTTAGTTAGAAGGAGCTTTTTAAAATTTTAAA
ATTTCAAAACCTTTGGTTAAAAGAGTT
Found at i:12886574 original size:48 final size:48
Alignment explanation
Indices: 12886461--12886579 Score: 132
Period size: 48 Copynumber: 2.4 Consensus size: 48
12886451 AACGCTTCAG
* *
12886461 TTGAAGAGGAGCTTTTCAATTTTAAAATTTTTAAGTTTTAACACATCTA
1 TTGAAGA-GAGCTTTTCAATTTTAAAATTTTTAAGTTTCAAAACATCTA
** * * *
12886510 TTGTGGATGAGTTTTTCAATTTT-GAATTTTTAAGTTTCAAAACCTCTA
1 TTGAAGA-GAGCTTTTCAATTTTAAAATTTTTAAGTTTCAAAACATCTA
*
12886558 TTGAAGAGAAACTTTTCAATTT
1 TTGAAGAG-AGCTTTTCAATTT
12886580 CAAATTTCTA
Statistics
Matches: 57, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
47 1 0.02
48 37 0.65
49 19 0.33
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (48 bp):
TTGAAGAGAGCTTTTCAATTTTAAAATTTTTAAGTTTCAAAACATCTA
Found at i:12889229 original size:21 final size:22
Alignment explanation
Indices: 12889187--12889239 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
12889177 AAATTTATTT
12889187 AATTTTATATTTATTTAAAAATAA
1 AATTTTATATTTA--TAAAAATAA
*
12889211 TATTTTATATTTA-AAAAATAA
1 AATTTTATATTTATAAAAATAA
12889232 AATTTTAT
1 AATTTTAT
12889240 TAATTTCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 15 0.56
24 12 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATTTTATATTTATAAAAATAA
Found at i:12889988 original size:19 final size:19
Alignment explanation
Indices: 12889966--12890006 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
12889956 TTTACATTAA
*
12889966 ATAAA-AAATTTAATTATTT
1 ATAAATAAAATTAATT-TTT
12889985 ATAAATAAAATTAATTTTT
1 ATAAATAAAATTAATTTTT
12890004 ATA
1 ATA
12890007 TTTAATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATAAATAAAATTAATTTTT
Found at i:12890060 original size:38 final size:42
Alignment explanation
Indices: 12890018--12890111 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 42
12890008 TTAATTTTAT
*
12890018 TTATATTTTAAATAAT-T-A-TATTTGAATAAAAAT-AATTA
1 TTATATTATAAATAATATAACTATTTGAATAAAAATAAATTA
* *
12890056 TTATATAATAAATAATAATAACTATTTGAATATAAATAAATTA
1 TTATATTATAAATAAT-ATAACTATTTGAATAAAAATAAATTA
12890099 TTAT-TTATAAATA
1 TTATATTATAAATA
12890112 TTACGACTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
38 14 0.30
40 1 0.02
41 1 0.02
42 22 0.47
43 9 0.19
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (42 bp):
TTATATTATAAATAATATAACTATTTGAATAAAAATAAATTA
Found at i:12890504 original size:18 final size:18
Alignment explanation
Indices: 12890469--12890505 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12890459 TTATATAAGT
* *
12890469 ACACATTTAATATGTTTA
1 ACACATTTAACATATTTA
12890487 ACACATTTAACATATTTA
1 ACACATTTAACATATTTA
12890505 A
1 A
12890506 GATGTTTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.41
Consensus pattern (18 bp):
ACACATTTAACATATTTA
Found at i:12896828 original size:17 final size:17
Alignment explanation
Indices: 12896806--12896840 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
12896796 CCAATTTTTG
*
12896806 CCTTATTCCTATACTAA
1 CCTTATTCATATACTAA
12896823 CCTTATTCATATACTAA
1 CCTTATTCATATACTAA
12896840 C
1 C
12896841 ATTCTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.29, G:0.00, T:0.40
Consensus pattern (17 bp):
CCTTATTCATATACTAA
Found at i:12910665 original size:41 final size:42
Alignment explanation
Indices: 12910620--12910725 Score: 132
Period size: 41 Copynumber: 2.6 Consensus size: 42
12910610 AAATATTTTT
*
12910620 ATTATTTATTTAAT-TTTATATTT-ATATA-TTATATTAATAAA
1 ATTATTTATTTAATATTTA-ATTTAAGATATTTAT-TTAATAAA
12910661 ATTA-TTATTTAATATTTAATTTAAGATATTTATTTAATAAA
1 ATTATTTATTTAATATTTAATTTAAGATATTTATTTAATAAA
*
12910702 ATTATTATATTT-ATATATAATTTA
1 ATTATT-TATTTAATATTTAATTTA
12910726 TATTAAAAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
40 13 0.22
41 24 0.41
42 16 0.28
43 5 0.09
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (42 bp):
ATTATTTATTTAATATTTAATTTAAGATATTTATTTAATAAA
Found at i:12910677 original size:47 final size:45
Alignment explanation
Indices: 12910626--12910729 Score: 126
Period size: 42 Copynumber: 2.3 Consensus size: 45
12910616 TTTTATTATT
*
12910626 TATTTAATTTTATATTTATATATTATATTAATAAAATTATTAT-TTAA
1 TATTTAA-TTTATATTGATAT-TTAT-TTAATAAAATTATTATATTAA
*
12910673 TATTTAATTTA-A--GATATTTATTTAATAAAATTATTATATTTA
1 TATTTAATTTATATTGATATTTATTTAATAAAATTATTATATTAA
*
12910715 TATATAATTTATATT
1 TATTTAATTTATATT
12910730 AAAAAATATT
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
41 16 0.32
42 17 0.34
43 5 0.10
45 1 0.02
46 4 0.08
47 7 0.14
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (45 bp):
TATTTAATTTATATTGATATTTATTTAATAAAATTATTATATTAA
Found at i:12910714 original size:22 final size:22
Alignment explanation
Indices: 12910641--12910715 Score: 61
Period size: 22 Copynumber: 3.5 Consensus size: 22
12910631 AATTTTATAT
12910641 TTATATATTATATTAATAAAATTA
1 TTATAT-TTAT-TTAATAAAATTA
12910665 TTAT-TTAATATTTAAT----TTA
1 TTATATT--TATTTAATAAAATTA
**
12910684 AGATATTTATTTAATAAAATTA
1 TTATATTTATTTAATAAAATTA
12910706 TTATATTTAT
1 TTATATTTAT
12910716 ATATAATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 16
0.67 0.07 0.27
Matches are distributed among these distances:
18 8 0.20
19 5 0.12
20 2 0.05
22 12 0.30
23 6 0.15
24 7 0.17
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (22 bp):
TTATATTTATTTAATAAAATTA
Found at i:12910754 original size:16 final size:16
Alignment explanation
Indices: 12910723--12910768 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
12910713 TATATATAAT
*
12910723 TTATATTAAAA-AATA
1 TTATATTAAAATTATA
*
12910738 TTTTA-TAAATATTATA
1 TTATATTAAA-ATTATA
12910754 TTATATTAAAATTAT
1 TTATATTAAAATTAT
12910769 TAAATTTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
14 4 0.16
15 5 0.20
16 12 0.48
17 4 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTATATTAAAATTATA
Found at i:12911392 original size:27 final size:27
Alignment explanation
Indices: 12911354--12911408 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
12911344 TTATATGTAA
12911354 TAATAATAAGAAAATATAATTTAAATT
1 TAATAATAAGAAAATATAATTTAAATT
*
12911381 TAATAATAAGAAAATGTAATTTAAATT
1 TAATAATAAGAAAATATAATTTAAATT
12911408 T
1 T
12911409 TATATGTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (27 bp):
TAATAATAAGAAAATATAATTTAAATT
Found at i:12911632 original size:63 final size:66
Alignment explanation
Indices: 12911510--12911632 Score: 153
Period size: 63 Copynumber: 1.9 Consensus size: 66
12911500 AATCCTTTTT
* * ** * *
12911510 TTTTAACATTCACTATATTTTTTTTATCTTAAAAATGTGATCTTTATTAAAATTTTAAAAATATA
1 TTTTAACATTCACTATATTGTTTTTATCTTAAAAAGGCAATATTTATTAAAATTGTAAAAATATA
12911575 G
66 G
* *
12911576 TTTTAACATTCA-T-TA-TGTTTTTATTTTAAAAAGGCAATATTTGTTAAAATTGTAAAA
1 TTTTAACATTCACTATATTGTTTTTATCTTAAAAAGGCAATATTTATTAAAATTGTAAAA
12911633 TTTTAAAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
63 34 0.69
64 2 0.04
65 1 0.02
66 12 0.24
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.49
Consensus pattern (66 bp):
TTTTAACATTCACTATATTGTTTTTATCTTAAAAAGGCAATATTTATTAAAATTGTAAAAATATA
G
Found at i:12911785 original size:72 final size:71
Alignment explanation
Indices: 12911615--12911920 Score: 255
Period size: 72 Copynumber: 4.3 Consensus size: 71
12911605 AAAGGCAATA
* * * *
12911615 TTTGTTAAAATTGTAAAATTTTAAAAATATAGTTTCAACAACTACTACA-TTTTATTTTGAAAAT
1 TTTGTTAAAATT-TTAAATTTTAAAAATATAATTTCAACAACTACTACATTTTTATCTTAAAAAT
12911679 -TG-TGGTT
65 ATGAT--TT
* * * *
12911686 TTTGTTAAAATTTCAAATTTTCAAAAATATAATTTCAACATCTATTATATTTTTATCTTAAAAAT
1 TTTGTTAAAATTTTAAATTTT-AAAAATATAATTTCAACAACTACTACATTTTTATCTTAAAAAT
12911751 ATGATTT
65 ATGATTT
* * * *
12911758 TTTGTTAAAATTTTAGAATTTTGAAAATAAAATTTCAATATCTACTACATTTTTTATCTTAAAAA
1 TTTGTTAAAATTTTA-AATTTTAAAAATATAATTTCAACAACTACTACA-TTTTTATCTTAAAAA
** *
12911823 CGT-AATT
64 TATGATTT
* * * * **
12911830 TTTGTT-AAATTTTCAAAAATTCAAAAGTATAATTTCAACAACCACTATGTTTTTTTATCTTAAA
1 TTTGTTAAAATTTT--AAATTTTAAAAATATAATTTCAACAACTACTA--CATTTTTATCTTAAA
* *
12911894 AATAT-AATA
62 AATATGATTT
* *
12911903 TTTGTTGAAATTATAAAT
1 TTTGTTAAAATTTTAAAT
12911921 AATAAAAGCT
Statistics
Matches: 193, Mismatches: 31, Indels: 21
0.79 0.13 0.09
Matches are distributed among these distances:
70 8 0.04
71 42 0.22
72 86 0.45
73 50 0.26
74 7 0.04
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (71 bp):
TTTGTTAAAATTTTAAATTTTAAAAATATAATTTCAACAACTACTACATTTTTATCTTAAAAATA
TGATTT
Found at i:12911884 original size:73 final size:73
Alignment explanation
Indices: 12911559--12911914 Score: 266
Period size: 71 Copynumber: 5.0 Consensus size: 73
12911549 ATCTTTATTA
* * * * * *** *
12911559 AAATTTTAAAAATATAGTTTTAACAT-T-C-ATTATGTTTTTATTTTAAAAAGGCAATATTTGTT
1 AAATTTTCAAAATATAATTTCAACATCTACTA-TATTTTTTTATCTTAAAAATATAATTTTTGTT
* *
12911621 AAAATTGTA
65 AAAATTTTC
* * * * * * * * **
12911630 AAATTTTAAAAATATAGTTTCAACAACTACTACATTTTATT-T-TGAAAATTGTGGTTTTTGTTA
1 AAATTTTCAAAATATAATTTCAACATCTACTATATTTTTTTATCTTAAAAATATAATTTTTGTTA
12911693 AAA-TTTC
66 AAATTTTC
* *
12911700 AAATTTTCAAAAATATAATTTCAACATCTA-T-TATATTTTTATCTTAAAAATATGATTTTTTGT
1 AAATTTTC-AAAATATAATTTCAACATCTACTATATTTTTTTATCTTAAAAATAT-AATTTTTGT
12911763 TAAAATTTT-
64 TAAAATTTTC
* * * * **
12911772 AGAATTTTGAAAATAAAATTTCAATATCTACTACA-TTTTTTATCTTAAAAACGTAATTTTTGTT
1 A-AATTTTCAAAATATAATTTCAACATCTACTATATTTTTTTATCTTAAAAATATAATTTTTGTT
12911836 -AAATTTTC
65 AAAATTTTC
** * * * *
12911844 AAAAATTCAAAAGTATAATTTCAACAACCACTATGTTTTTTTATCTTAAAAATATAATATTTGTT
1 AAATTTTCAAAA-TATAATTTCAACATCTACTATATTTTTTTATCTTAAAAATATAATTTTTGTT
*
12911909 GAAATT
65 AAAATT
12911915 ATAAATAATA
Statistics
Matches: 225, Mismatches: 45, Indels: 27
0.76 0.15 0.09
Matches are distributed among these distances:
69 6 0.03
70 11 0.05
71 82 0.36
72 60 0.27
73 59 0.26
74 7 0.03
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (73 bp):
AAATTTTCAAAATATAATTTCAACATCTACTATATTTTTTTATCTTAAAAATATAATTTTTGTTA
AAATTTTC
Found at i:12912393 original size:23 final size:23
Alignment explanation
Indices: 12912344--12912391 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
12912334 ATTTTATCGG
*
12912344 TTTAATTTAATTTATTTATAGAT
1 TTTAATTTAATTTATTTATAAAT
12912367 TTTAATTTTAATTT-TTT-TAAAT
1 TTTAA-TTTAATTTATTTATAAAT
12912389 TTT
1 TTT
12912392 TATATATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 7 0.30
23 8 0.35
24 8 0.35
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTAATTTAATTTATTTATAAAT
Found at i:12913442 original size:14 final size:13
Alignment explanation
Indices: 12913422--12913465 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
12913412 TAAATATTAA
12913422 TTTTAATAAAATT
1 TTTTAATAAAATT
12913435 TATTTAATATAAATT
1 T-TTTAATA-AAATT
*
12913450 TTTT-ATTAAATT
1 TTTTAATAAAATT
12913462 TTTT
1 TTTT
12913466 TTCAATCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 9 0.32
13 3 0.11
14 10 0.36
15 6 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTTAATAAAATT
Found at i:12913461 original size:12 final size:14
Alignment explanation
Indices: 12913422--12913465 Score: 58
Period size: 12 Copynumber: 3.3 Consensus size: 14
12913412 TAAATATTAA
12913422 TTTTAATA-AAATT
1 TTTTAATATAAATT
12913435 TATTTAATATAAATT
1 T-TTTAATATAAATT
12913450 TTTT-AT-TAAATT
1 TTTTAATATAAATT
12913462 TTTT
1 TTTT
12913466 TTCAATCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 10 0.34
13 3 0.10
14 10 0.34
15 6 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTTAATATAAATT
Found at i:12914225 original size:2 final size:2
Alignment explanation
Indices: 12914218--12914252 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12914208 ATTTTTCCAG
12914218 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12914253 AAAGATTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12914504 original size:12 final size:14
Alignment explanation
Indices: 12914486--12914523 Score: 53
Period size: 12 Copynumber: 2.8 Consensus size: 14
12914476 GACCTTTGGT
12914486 TGGTGGAATATC-G
1 TGGTGGAATATCGG
12914499 -GGTGGAACTATCGG
1 TGGTGGAA-TATCGG
12914513 TGGTGGAATAT
1 TGGTGGAATAT
12914524 TTGGAGGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 4 0.18
15 7 0.32
ACGTcount: A:0.24, C:0.08, G:0.39, T:0.29
Consensus pattern (14 bp):
TGGTGGAATATCGG
Found at i:12915526 original size:23 final size:23
Alignment explanation
Indices: 12915499--12915542 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
12915489 ATTTAATATT
12915499 ATTATTTTTA-TATTAAAATAATA
1 ATTATTTTTAGT-TTAAAATAATA
12915522 ATTATTTTTAGTTTAAAATAA
1 ATTATTTTTAGTTTAAAATAA
12915543 AGTTTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
ATTATTTTTAGTTTAAAATAATA
Found at i:12916824 original size:31 final size:31
Alignment explanation
Indices: 12916755--12916824 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
12916745 TCTTTATTGG
*
12916755 TTTAAAAAATTAAGTAAAAACTCCATATCAT
1 TTTAAAATATTAAGTAAAAACTCCATATCAT
* * *
12916786 TTTAAAATATTAGGTAAAAATTTTCATATCA-
1 TTTAAAATATTAAGTAAAAA-CTCCATATCAT
12916817 TTTAAAAT
1 TTTAAAAT
12916825 TTTGATTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 26 0.76
32 8 0.24
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.39
Consensus pattern (31 bp):
TTTAAAATATTAAGTAAAAACTCCATATCAT
Found at i:12918520 original size:17 final size:16
Alignment explanation
Indices: 12918477--12918532 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
12918467 TTTTTCCTAC
*
12918477 ATTTTT-TATTAGTTT
1 ATTTTTATATTAATTT
* *
12918492 AGTATTATTATTAAATTT
1 ATTTTTA-TATT-AATTT
*
12918510 ATTTTTATATTATTTT
1 ATTTTTATATTAATTT
12918526 ATTTTTA
1 ATTTTTA
12918533 AAGTTTATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
15 4 0.12
16 11 0.34
17 8 0.25
18 9 0.28
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.68
Consensus pattern (16 bp):
ATTTTTATATTAATTT
Found at i:12919258 original size:20 final size:19
Alignment explanation
Indices: 12919233--12919278 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
12919223 AAACTATAGA
**
12919233 TTTTTTTGTATTCTGACTCT
1 TTTTTTTGTAAACTGACT-T
*
12919253 TTTTTTTTTAAACTGACTT
1 TTTTTTTGTAAACTGACTT
12919272 TTTTTTT
1 TTTTTTT
12919279 TTGTGCATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.13, C:0.11, G:0.07, T:0.70
Consensus pattern (19 bp):
TTTTTTTGTAAACTGACTT
Found at i:12926481 original size:16 final size:15
Alignment explanation
Indices: 12926460--12926501 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
12926450 TAAATTAAAT
12926460 TTATATTTAAAATATA
1 TTATATTTAAAAT-TA
* *
12926476 TTATA-TTAATATTT
1 TTATATTTAAAATTA
12926490 TTATATTTAAAA
1 TTATATTTAAAA
12926502 ATAATTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 6 0.27
15 11 0.50
16 5 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATATTTAAAATTA
Found at i:12927545 original size:20 final size:20
Alignment explanation
Indices: 12927516--12927561 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
12927506 AAAATTAAGA
12927516 AAATAATATTTTTAAAATAT
1 AAATAATATTTTTAAAATAT
* *
12927536 AAATATTATTTTTTAAATAT
1 AAATAATATTTTTAAAATAT
12927556 AAATAA
1 AAATAA
12927562 AAAATTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AAATAATATTTTTAAAATAT
Found at i:12927589 original size:16 final size:16
Alignment explanation
Indices: 12927568--12927617 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
12927558 ATAAAAAATT
12927568 AAATATATATAATATA
1 AAATATATATAATATA
12927584 AAATATATATAAT-T-
1 AAATATATATAATATA
*
12927598 AAATA-A-ATAATAAA
1 AAATATATATAATATA
12927612 AAATAT
1 AAATAT
12927618 TTTATATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 5 0.17
13 1 0.03
14 10 0.33
15 1 0.03
16 13 0.43
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAATATATATAATATA
Found at i:12927591 original size:14 final size:14
Alignment explanation
Indices: 12927567--12927617 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
12927557 AATAAAAAAT
12927567 TAAATATATATAATA
1 TAAA-ATATATAATA
12927582 TAAAATATAT-ATAA
1 TAAAATATATAAT-A
* *
12927596 TTAAATAAATAATA
1 TAAAATATATAATA
*
12927610 AAAAATAT
1 TAAAATAT
12927618 TTTATATATA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
13 2 0.07
14 21 0.72
15 6 0.21
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAAAATATATAATA
Found at i:12927605 original size:18 final size:17
Alignment explanation
Indices: 12927549--12927606 Score: 64
Period size: 18 Copynumber: 3.4 Consensus size: 17
12927539 TATTATTTTT
* *
12927549 TAAATATAAATAAAAAA
1 TAAATATATATAATAAA
*
12927566 TTAAATATATATAATATA
1 -TAAATATATATAATAAA
12927584 -AAATATATATAATTAAA
1 TAAATATATATAA-TAAA
12927601 TAAATA
1 TAAATA
12927607 ATAAAAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
16 12 0.35
17 3 0.09
18 19 0.56
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAATATATATAATAAA
Found at i:12927733 original size:41 final size:40
Alignment explanation
Indices: 12927687--12927780 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 40
12927677 TTTAAAATTT
12927687 AATTAGACTCAAAATTCAAT-TTAAAAAATATGAT-TTTATAA
1 AATTAGA-TCAAAATT-AATCTTAAAAAATAT-ATATTTATAA
* *
12927728 AATTAGATCTAGATTAATCTTAAAAAATATATACTTTATAA
1 AATTAGATCAAAATTAATCTTAAAAAATATATA-TTTATAA
*
12927769 AATTAAATCAAA
1 AATTAGATCAAA
12927781 TCAAAATATC
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
39 5 0.11
40 17 0.38
41 23 0.51
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.36
Consensus pattern (40 bp):
AATTAGATCAAAATTAATCTTAAAAAATATATATTTATAA
Found at i:12928717 original size:28 final size:26
Alignment explanation
Indices: 12928650--12928705 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
12928640 ATCATAAAAC
* *
12928650 AAAATTTAATTAAATAAATTTAATAT
1 AAAATTAAACTAAATAAATTTAATAT
*
12928676 AAAATTATACTAAACTAACATTTAATAT
1 AAAATTAAACTAAA-TAA-ATTTAATAT
12928704 AA
1 AA
12928706 CTTAAATCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 11 0.44
27 3 0.12
28 11 0.44
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (26 bp):
AAAATTAAACTAAATAAATTTAATAT
Found at i:12934600 original size:26 final size:27
Alignment explanation
Indices: 12934566--12934623 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
12934556 TTTTATTTTA
*
12934566 TTTTATTTTTGAA-TTATTTTTAGTTAC
1 TTTTATTTTT-AAGTTATTTTTAATTAC
12934593 -TTT-TTTTTAAGTTTATTTTTAATTAC
1 TTTTATTTTTAAG-TTATTTTTAATTAC
12934619 TTTTA
1 TTTTA
12934624 ATTACCAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
24 2 0.08
25 5 0.19
26 16 0.62
27 3 0.12
ACGTcount: A:0.22, C:0.03, G:0.05, T:0.69
Consensus pattern (27 bp):
TTTTATTTTTAAGTTATTTTTAATTAC
Found at i:12940438 original size:17 final size:17
Alignment explanation
Indices: 12940418--12940451 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12940408 AATGAAAAAA
12940418 AAAAAAAAAAAAAAAGG
1 AAAAAAAAAAAAAAAGG
* *
12940435 AAAAAGAAAAGAAAAGG
1 AAAAAAAAAAAAAAAGG
12940452 TGACAATAAA
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:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAAAAGG
Found at i:12941641 original size:15 final size:16
Alignment explanation
Indices: 12941621--12941653 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
12941611 TAAAAATATG
*
12941621 TTTAATTT-TTTATTT
1 TTTAATTTGATTATTT
12941636 TTTAATTTGATTATTT
1 TTTAATTTGATTATTT
12941652 TT
1 TT
12941654 AAAAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTAATTTGATTATTT
Found at i:12943745 original size:11 final size:11
Alignment explanation
Indices: 12943729--12943767 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
12943719 CGATAATACG
12943729 ATATAAAAATA
1 ATATAAAAATA
12943740 ATATAAATAA-A
1 ATATAAA-AATA
12943751 ATATAAAAATA
1 ATATAAAAATA
12943762 ATATAA
1 ATATAA
12943768 TTTAAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 2 0.08
11 22 0.85
12 2 0.08
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
ATATAAAAATA
Found at i:12944405 original size:2 final size:2
Alignment explanation
Indices: 12944398--12944427 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
12944388 TTCAATCTTA
12944398 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12944428 AAAGATTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12945294 original size:27 final size:28
Alignment explanation
Indices: 12945255--12945323 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 28
12945245 TATCACATTA
*
12945255 ATTAATAAATTTTT-AGTTTATA-TATCAT
1 ATTAA-AAATTTTTAAATTTA-AGTATCAT
12945283 ATTAAAAATTTTTAAAATTTAAGTATCAT
1 ATTAAAAATTTTT-AAATTTAAGTATCAT
*
12945312 ATTAAATATTTT
1 ATTAAAAATTTT
12945324 ATAATAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
27 8 0.22
28 6 0.17
29 22 0.61
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (28 bp):
ATTAAAAATTTTTAAATTTAAGTATCAT
Found at i:12945311 original size:29 final size:31
Alignment explanation
Indices: 12945277--12945335 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 31
12945267 TTAGTTTATA
12945277 TATCATATTAAAAATTTT-TAA-AATTTAAG
1 TATCATATTAAAAATTTTATAATAATTTAAG
*
12945306 TATCATATTAAATATTTTATAATAATTTAA
1 TATCATATTAAAAATTTTATAATAATTTAA
12945336 TGATCATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 17 0.63
30 3 0.11
31 7 0.26
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (31 bp):
TATCATATTAAAAATTTTATAATAATTTAAG
Found at i:12945963 original size:2 final size:2
Alignment explanation
Indices: 12945956--12945980 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12945946 CATTAACATA
12945956 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 A
12945981 AAAGATTATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12946077 original size:21 final size:22
Alignment explanation
Indices: 12946036--12946086 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 22
12946026 ATTAGTAAAT
* *
12946036 TGAAT-AATACTACTTTATTAA
1 TGAATAAATATTAATTTATTAA
12946057 TGAATAAATATTAATTT-TTAA
1 TGAATAAATATTAATTTATTAA
12946078 --AATAAATAT
1 TGAATAAATAT
12946087 ACAAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 9 0.33
21 9 0.33
22 9 0.33
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (22 bp):
TGAATAAATATTAATTTATTAA
Found at i:12946612 original size:32 final size:32
Alignment explanation
Indices: 12946571--12946633 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
12946561 TTAAATAAAA
12946571 CAAGCTATGGGACTTTAGGATATAATTAGGTG
1 CAAGCTATGGGACTTTAGGATATAATTAGGTG
12946603 CAAGCTATGGGACTTTAGGATATAATTAGGT
1 CAAGCTATGGGACTTTAGGATATAATTAGGT
12946634 TTATGGAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.32, C:0.10, G:0.27, T:0.32
Consensus pattern (32 bp):
CAAGCTATGGGACTTTAGGATATAATTAGGTG
Found at i:12954656 original size:30 final size:30
Alignment explanation
Indices: 12954585--12954659 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 30
12954575 TTATAATTGT
* *
12954585 TATTTTTATTTAAATGAATTTTTATATTTC
1 TATTTATATTTAAATAAATTTTTATATTTC
*
12954615 TA-TTATATTTAAATAAATTTTTATGTTT-
1 TATTTATATTTAAATAAATTTTTATATTTC
*
12954643 TAATTTGTATTTAAATA
1 T-ATTTATATTTAAATA
12954660 TGGTTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 1 0.03
29 24 0.62
30 14 0.36
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60
Consensus pattern (30 bp):
TATTTATATTTAAATAAATTTTTATATTTC
Done.