Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold43
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: 2559314
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 13088 characters in sequence are not A, C, G, or T
File 16 of 19
Found at i:1852060 original size:24 final size:27
Alignment explanation
Indices: 1852026--1852084 Score: 79
Period size: 24 Copynumber: 2.3 Consensus size: 27
1852016 ATATTTAAAA
*
1852026 TAATATAAATTTTAATA-ATT-TATAT
1 TAATATTAATTTTAATATATTATATAT
1852051 T-ATATTAATTTTAATATATTAATATAT
1 TAATATTAATTTTAATATATT-ATATAT
1852078 TAATATT
1 TAATATT
1852085 TTATTTTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 14 0.48
25 4 0.14
27 6 0.21
28 5 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TAATATTAATTTTAATATATTATATAT
Found at i:1852070 original size:14 final size:14
Alignment explanation
Indices: 1852041--1852093 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
1852031 TAAATTTTAA
*
1852041 TAATTTATATTATAT
1 TAATTT-TAATATAT
1852056 TAATTTTAATATAT
1 TAATTTTAATATAT
*
1852070 TAATATATTAATATTT
1 TAAT-T-TTAATATAT
*
1852086 TATTTTTA
1 TAATTTTA
1852094 TTATTTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
14 14 0.42
15 8 0.24
16 11 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TAATTTTAATATAT
Found at i:1852100 original size:8 final size:8
Alignment explanation
Indices: 1852034--1852110 Score: 52
Period size: 8 Copynumber: 9.6 Consensus size: 8
1852024 AATAATATAA
1852034 ATTTTAAT
1 ATTTTAAT
*
1852042 AATTT-AT
1 ATTTTAAT
* *
1852049 ATTATATT
1 ATTTTAAT
1852057 AATTTTAAT
1 -ATTTTAAT
*
1852066 ATATTAAT
1 ATTTTAAT
*
1852074 ATATTAAT
1 ATTTTAAT
1852082 ATTTT-AT
1 ATTTTAAT
*
1852089 -TTTTATT
1 ATTTTAAT
1852096 ATTTTTAAAT
1 A-TTTT-AAT
1852106 ATTTT
1 ATTTT
1852111 TTTATTATAT
Statistics
Matches: 53, Mismatches: 10, Indels: 11
0.72 0.14 0.15
Matches are distributed among these distances:
6 4 0.08
7 8 0.15
8 24 0.45
9 14 0.26
10 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATTTTAAT
Found at i:1852106 original size:24 final size:23
Alignment explanation
Indices: 1852079--1852123 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
1852069 TTAATATATT
1852079 AATATTTTATTT-TTATTATTTTTA
1 AATATTTT-TTTATTA-TATTTTTA
1852103 AATATTTTTTTATTATATTTT
1 AATATTTTTTTATTATATTTT
1852124 ATTTTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (23 bp):
AATATTTTTTTATTATATTTTTA
Found at i:1852126 original size:18 final size:18
Alignment explanation
Indices: 1852075--1852140 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
1852065 TATATTAATA
1852075 TATTAATATTTTATTTTTAT
1 TATT-ATATTTTATTTTT-T
*
1852095 TATT-T-TTAAATATTTTTT
1 TATTATATT--TTATTTTTT
*
1852113 TATTATATTTTATTTTAT
1 TATTATATTTTATTTTTT
*
1852131 AATTATATTT
1 TATTATATTT
1852141 CATCTAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
17 2 0.05
18 22 0.58
19 8 0.21
20 6 0.16
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TATTATATTTTATTTTTT
Found at i:1852907 original size:21 final size:19
Alignment explanation
Indices: 1852883--1852927 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1852873 TTGAAGGTTA
1852883 ATATTACATTTAATAATTTAT
1 ATATT-CATTTAAT-ATTTAT
* *
1852904 ATATTTATTTTATATTTAT
1 ATATTCATTTAATATTTAT
1852923 ATATT
1 ATATT
1852928 TTAATTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 11 0.50
20 6 0.27
21 5 0.23
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
ATATTCATTTAATATTTAT
Found at i:1852934 original size:6 final size:7
Alignment explanation
Indices: 1852899--1852970 Score: 53
Period size: 8 Copynumber: 10.4 Consensus size: 7
1852889 CATTTAATAA
1852899 TTTATAT
1 TTTATAT
*
1852906 ATT-TAT
1 TTTATAT
1852912 TTTATAT
1 TTTATAT
1852919 TTATATAT
1 TT-TATAT
1852927 TTTA-AT
1 TTTATAT
1852933 TTTATTAT
1 TTTA-TAT
1852941 TTT-T-T
1 TTTATAT
* *
1852946 ATAATAT
1 TTTATAT
*
1852953 TTAATAT
1 TTTATAT
1852960 TTTAATAT
1 TTT-ATAT
1852968 TTT
1 TTT
1852971 TTATGTCATA
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
5 2 0.04
6 13 0.25
7 18 0.35
8 19 0.37
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
TTTATAT
Found at i:1852934 original size:33 final size:33
Alignment explanation
Indices: 1852899--1852974 Score: 93
Period size: 34 Copynumber: 2.2 Consensus size: 33
1852889 CATTTAATAA
1852899 TTTATATATTTATTT-T-ATATTTATATATTTTAAT
1 TTTAT-TATTT-TTTATAATATTTA-ATATTTTAAT
1852933 TTTATTATTTTTTATAATATTTAATATTTTAAT
1 TTTATTATTTTTTATAATATTTAATATTTTAAT
*
1852966 ATTTTTTAT
1 -TTTATTAT
1852975 GTCATATTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
32 3 0.08
33 16 0.42
34 19 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (33 bp):
TTTATTATTTTTTATAATATTTAATATTTTAAT
Found at i:1852946 original size:25 final size:27
Alignment explanation
Indices: 1852918--1852974 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
1852908 TTATTTTATA
* *
1852918 TTTAT-ATATTTTA-ATTTTATTATTT
1 TTTATAATATTTAATATTTTAATATTT
1852943 TTTATAATATTTAATATTTTAATATTT
1 TTTATAATATTTAATATTTTAATATTT
1852970 TTTAT
1 TTTAT
1852975 GTCATATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 5 0.18
26 7 0.25
27 16 0.57
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (27 bp):
TTTATAATATTTAATATTTTAATATTT
Found at i:1852965 original size:15 final size:16
Alignment explanation
Indices: 1852909--1852969 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 16
1852899 TTTATATATT
1852909 TATTTT-ATATTTATA
1 TATTTTAATATTTATA
1852924 TATTTTAAT-TTTATTA
1 TATTTTAATATTTA-TA
*
1852940 TTTTTTATAATATTTA-A
1 -TATTT-TAATATTTATA
1852957 TATTTTAATATTT
1 TATTTTAATATTT
1852970 TTTATGTCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
15 18 0.46
16 8 0.21
17 5 0.13
18 4 0.10
19 4 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTTTAATATTTATA
Found at i:1854456 original size:18 final size:18
Alignment explanation
Indices: 1854399--1854458 Score: 56
Period size: 16 Copynumber: 3.6 Consensus size: 18
1854389 ATATAAATAA
* *
1854399 ATATATATATTAAAATTT
1 ATATAAATATTAAATTTT
* *
1854417 ATAT-AATA-TGAATTAT
1 ATATAAATATTAAATTTT
1854433 -TA-AAATATTAAATTTT
1 ATATAAATATTAAATTTT
1854449 ATATAAATAT
1 ATATAAATAT
1854459 AAAAAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
15 6 0.19
16 11 0.34
17 5 0.16
18 10 0.31
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
ATATAAATATTAAATTTT
Found at i:1856506 original size:66 final size:65
Alignment explanation
Indices: 1856421--1856595 Score: 199
Period size: 66 Copynumber: 2.6 Consensus size: 65
1856411 TCCTAGCCCT
* * * *
1856421 CCCGGAGAGGGACACAAGTTAACCGACAGCTCAACTCTTGGTGGTATAGAGGACTCCGGTCCAAG
1 CCCGGTGAGGGACACAAGTTAACCGACAGCTC-ACTCTTGGTGGTATAAAAGACTCCGCTCCAAG
1856486 C
65 C
* * **
1856487 CCCGGTGAGGGACACAAGTTAATCGATAGCTCGACTCTTGGTGGTATAAAAGACTCCGCTCTGAG
1 CCCGGTGAGGGACACAAGTTAACCGACAGCTC-ACTCTTGGTGGTATAAAAGACTCCGCTCCAAG
1856552 C
65 C
* * * *
1856553 CCTGGTGTCGGGA-ACAAGTTTACCGACAGCATCACTCTAGGTG
1 CCCGGTG-AGGGACACAAGTTAACCGACAGC-TCACTCTTGGTG
1856596 ACATTAAGAA
Statistics
Matches: 92, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
66 86 0.93
67 6 0.07
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.21
Consensus pattern (65 bp):
CCCGGTGAGGGACACAAGTTAACCGACAGCTCACTCTTGGTGGTATAAAAGACTCCGCTCCAAGC
Found at i:1857335 original size:28 final size:29
Alignment explanation
Indices: 1857303--1857367 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 29
1857293 ACTTAATATG
*
1857303 AATATATTTAATTTTGTA-AAATATTTAA
1 AATATATTTAATTTTATATAAATATTTAA
* **
1857331 AATAT-TATAATTTTATATTTATATTTAA
1 AATATATTTAATTTTATATAAATATTTAA
1857359 ATATATATT
1 A-ATATATT
1857368 AAATATAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 10 0.34
28 14 0.48
29 4 0.14
30 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (29 bp):
AATATATTTAATTTTATATAAATATTTAA
Found at i:1858257 original size:13 final size:15
Alignment explanation
Indices: 1858239--1858279 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
1858229 TTCGAGTTGA
1858239 ATTTAATTT-TTTT-
1 ATTTAATTTATTTTC
1858252 ATTTAATTTATTTTC
1 ATTTAATTTATTTTC
*
1858267 ATTTAAATTATTT
1 ATTTAATTTATTT
1858280 AATAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 9 0.36
14 4 0.16
15 12 0.48
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTAATTTATTTTC
Found at i:1858301 original size:21 final size:20
Alignment explanation
Indices: 1858275--1858317 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1858265 TCATTTAAAT
1858275 TATTTAATAAATAAAATAATA
1 TATTTAAT-AATAAAATAATA
* *
1858296 TATTTAATTATAAAATTATA
1 TATTTAATAATAAAATAATA
1858316 TA
1 TA
1858318 AATATTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TATTTAATAATAAAATAATA
Found at i:1858310 original size:20 final size:20
Alignment explanation
Indices: 1858275--1858336 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
1858265 TCATTTAAAT
*
1858275 TATTTAATAAATAAAATAATA
1 TATTTAAT-TATAAAATAATA
1858296 TATTTAATTATAAAATTATATA
1 TATTTAATTATAAAA-TA-ATA
*
1858318 AATATTAATTA-AAAATAAT
1 TAT-TTAATTATAAAATAAT
1858337 TTTGTATATT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
20 8 0.22
21 12 0.33
22 9 0.25
23 7 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TATTTAATTATAAAATAATA
Found at i:1858832 original size:5 final size:5
Alignment explanation
Indices: 1858811--1858880 Score: 60
Period size: 5 Copynumber: 14.4 Consensus size: 5
1858801 TATTTAAAAT
* *
1858811 ATTAA AATAA TTTAA ATTAA ATTTAA ATTAA A--AA ATT-- ATTAA A-TAA
1 ATTAA ATTAA ATTAA ATTAA A-TTAA ATTAA ATTAA ATTAA ATTAA ATTAA
1858857 ATAATAA ATTAA ATTAA ATTAA AT
1 AT--TAA ATTAA ATTAA ATTAA AT
1858881 AATTTTAATA
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
3 6 0.11
4 4 0.08
5 33 0.62
6 5 0.09
7 5 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATTAA
Found at i:1858835 original size:11 final size:11
Alignment explanation
Indices: 1858819--1858880 Score: 50
Period size: 11 Copynumber: 6.3 Consensus size: 11
1858809 ATATTAAAAT
1858819 AATTTAAATTA
1 AATTTAAATTA
1858830 AATTTAAATTA
1 AATTTAAATTA
1858841 AA---AAATT-
1 AATTTAAATTA
1858848 -A-TTAAA-TA
1 AATTTAAATTA
*
1858856 AATAATAAATTA
1 AAT-TTAAATTA
1858868 AA-TTAAATTA
1 AATTTAAATTA
1858878 AAT
1 AAT
1858881 AATTTTAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 16
0.69 0.03 0.27
Matches are distributed among these distances:
6 1 0.02
7 1 0.02
8 8 0.20
9 1 0.02
10 9 0.22
11 17 0.41
12 4 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AATTTAAATTA
Found at i:1858844 original size:27 final size:27
Alignment explanation
Indices: 1858811--1858882 Score: 69
Period size: 26 Copynumber: 2.7 Consensus size: 27
1858801 TATTTAAAAT
* *
1858811 ATTAAAATAAT-TTAAATTAAAT-TTAA
1 ATTAAAAAAATATTAAA-TAAATAATAA
*
1858837 ATTAAAAAATTATTAAATAAATAATAA
1 ATTAAAAAAATATTAAATAAATAATAA
**
1858864 ATTAAATTAA-ATTAAATAA
1 ATTAAAAAAATATTAAATAA
1858883 TTTTAATAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
26 23 0.61
27 15 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (27 bp):
ATTAAAAAAATATTAAATAAATAATAA
Found at i:1858851 original size:37 final size:36
Alignment explanation
Indices: 1858806--1858896 Score: 100
Period size: 37 Copynumber: 2.5 Consensus size: 36
1858796 TTCATTATTT
1858806 AAAA-TATTAAAATAATTTAAATTAAATTTAAATTAA
1 AAAATTATTAAAATAATTTAAATTAAA-TTAAATTAA
*
1858842 AAAATTATT-AAATAAATAATAAATTAAATTAAATTAA
1 AAAATTATTAAAAT-AAT-TTAAATTAAATTAAATTAA
*
1858879 ATAATT-TTAATAA-AATTT
1 AAAATTATTAA-AATAATTT
1858897 TTTTATGTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
35 1 0.02
36 13 0.28
37 22 0.47
38 11 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (36 bp):
AAAATTATTAAAATAATTTAAATTAAATTAAATTAA
Found at i:1858852 original size:16 final size:17
Alignment explanation
Indices: 1858828--1858874 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
1858818 TAATTTAAAT
1858828 TAAATTTAAATTAAAAAA
1 TAAA-TTAAATTAAAAAA
* *
1858846 T-TATTAAA-TAAATAA
1 TAAATTAAATTAAAAAA
1858861 TAAATTAAATTAAA
1 TAAATTAAATTAAA
1858875 TTAAATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
15 7 0.29
16 11 0.46
17 5 0.21
18 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAATTAAATTAAAAAA
Found at i:1865592 original size:3 final size:3
Alignment explanation
Indices: 1865586--1865649 Score: 60
Period size: 3 Copynumber: 20.7 Consensus size: 3
1865576 AAAAACAAAT
* *
1865586 ATA ATA ATA ATA ATA ATA ATA ATA ATA TATGA A-A ATA TTA A-A ATTT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -AT-A ATA ATA ATA ATA A-TA
1865632 ATA TATA ATA ATA ATA AT
1 ATA -ATA ATA ATA ATA AT
1865650 TGTGAACTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
2 4 0.08
3 39 0.76
4 7 0.14
5 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:1865644 original size:22 final size:22
Alignment explanation
Indices: 1865586--1865649 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
1865576 AAAAACAAAT
1865586 ATAATA-ATAATAATAATAATA
1 ATAATATATAATAATAATAATA
*
1865607 ATAATATATGAA-AATATTAA-A
1 ATAATATAT-AATAATAATAATA
*
1865628 ATTTATATATAATAATAATAAT
1 A-TAATATATAATAATAATAAT
1865650 TGTGAACTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
21 10 0.29
22 23 0.66
23 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
ATAATATATAATAATAATAATA
Found at i:1865781 original size:15 final size:16
Alignment explanation
Indices: 1865763--1865795 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1865753 AATATCTAAA
*
1865763 TAAAAATATT-AATTT
1 TAAAAAAATTAAATTT
1865778 TAAAAAAATTAAATTT
1 TAAAAAAATTAAATTT
1865794 TA
1 TA
1865796 TTTTAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAAAAAATTAAATTT
Found at i:1865835 original size:20 final size:22
Alignment explanation
Indices: 1865797--1865845 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 22
1865787 TAAATTTTAT
*
1865797 TTTAATTTTAACATTTAAA-A-
1 TTTAAATTTAACATTTAAATAC
1865817 TTTAAATTTAAC-TTATAAATAC
1 TTTAAATTTAACATT-TAAATAC
1865839 TTTAAAT
1 TTTAAAT
1865846 AATTTGATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 2 0.08
20 15 0.60
21 1 0.04
22 7 0.28
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTAAATTTAACATTTAAATAC
Found at i:1868747 original size:13 final size:13
Alignment explanation
Indices: 1868730--1868762 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1868720 TTATTTATTT
1868730 ATTAAATTTTAAA
1 ATTAAATTTTAAA
*
1868743 TTTAAATTTTAAA
1 ATTAAATTTTAAA
1868756 ATTAAAT
1 ATTAAAT
1868763 AATTTAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTAAATTTTAAA
Found at i:1869084 original size:23 final size:23
Alignment explanation
Indices: 1869058--1869101 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1869048 AATTATTTAT
1869058 TAAATA-TTATATGTAATAATTAA
1 TAAATATTTAT-TGTAATAATTAA
*
1869081 TAAATATTTATTTTAATAATT
1 TAAATATTTATTGTAATAATT
1869102 TATTGTCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TAAATATTTATTGTAATAATTAA
Found at i:1869799 original size:26 final size:23
Alignment explanation
Indices: 1869761--1869822 Score: 70
Period size: 26 Copynumber: 2.5 Consensus size: 23
1869751 AAAATTAAAG
*
1869761 TAATTTAATTTAATTTAAAATATTT
1 TAATTTAAATTAATTT--AATATTT
1869786 TAATTTAAAATTAATTTAATATTT
1 TAATTT-AAATTAATTTAATATTT
1869810 TAAAATTTAAATT
1 T--AATTTAAATT
1869823 TCAATACATC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 8 0.24
25 11 0.33
26 14 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TAATTTAAATTAATTTAATATTT
Found at i:1877119 original size:37 final size:36
Alignment explanation
Indices: 1877073--1877187 Score: 104
Period size: 37 Copynumber: 3.4 Consensus size: 36
1877063 TTTAAACTTC
*
1877073 AAATCAATTAAATTTTATATTTTAAAAATAATTATAT
1 AAATTAATTAAATTTTATATTTT-AAAATAATTATAT
* *
1877110 AAATTAATTAAA--TTAAAATTT---A-AA-T-T-T
1 AAATTAATTAAATTTTATATTTTAAAATAATTATAT
* *
1877137 AAATTAATTTAATATTATATTTTTAAAATAATTATAT
1 AAATTAATTAAATTTTATA-TTTTAAAATAATTATAT
1877174 AAATTAATTAAATT
1 AAATTAATTAAATT
1877188 AAAATTCATA
Statistics
Matches: 60, Mismatches: 8, Indels: 20
0.68 0.09 0.23
Matches are distributed among these distances:
27 12 0.20
28 1 0.02
29 5 0.08
30 5 0.08
31 1 0.02
33 1 0.02
34 2 0.03
35 8 0.13
36 1 0.02
37 24 0.40
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (36 bp):
AAATTAATTAAATTTTATATTTTAAAATAATTATAT
Found at i:1877166 original size:64 final size:65
Alignment explanation
Indices: 1877062--1877193 Score: 212
Period size: 64 Copynumber: 2.0 Consensus size: 65
1877052 GAACGTGAAG
*
1877062 ATTTAAACTTCAAATCAATTAAATTTTATATTTTAAAAATAATTATATAAATTAATTAAATTAAA
1 ATTTAAACTTCAAATCAATTAAATATTATATTTTAAAAATAATTATATAAATTAATTAAATTAAA
* * * *
1877127 ATTTAAA-TTTAAATTAATTTAATATTATATTTTTAAAATAATTATATAAATTAATTAAATTAAA
1 ATTTAAACTTCAAATCAATTAAATATTATATTTTAAAAATAATTATATAAATTAATTAAATTAAA
1877191 ATT
1 ATT
1877194 CATATTTTTT
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
64 55 0.89
65 7 0.11
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (65 bp):
ATTTAAACTTCAAATCAATTAAATATTATATTTTAAAAATAATTATATAAATTAATTAAATTAAA
Found at i:1877749 original size:13 final size:13
Alignment explanation
Indices: 1877731--1877757 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1877721 AAATGTAAAT
1877731 ATATTTATATTTA
1 ATATTTATATTTA
1877744 ATATTTATATTTA
1 ATATTTATATTTA
1877757 A
1 A
1877758 ATAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATATTTATATTTA
Found at i:1878309 original size:19 final size:19
Alignment explanation
Indices: 1878272--1878309 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1878262 TTGATACAAA
*
1878272 TTAAATGATAAAAACTTAT
1 TTAAATGATAAAAAATTAT
1878291 TTAAAT-ATAATAAAATTAT
1 TTAAATGATAA-AAAATTAT
1878310 AAAGTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (19 bp):
TTAAATGATAAAAAATTAT
Found at i:1881605 original size:4 final size:4
Alignment explanation
Indices: 1881596--1881628 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
1881586 GAAAAATTAA
1881596 AAAT AAAT -AAT AAAT -AAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1881629 AGAGAGACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 6 0.22
4 21 0.78
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1881607 original size:7 final size:7
Alignment explanation
Indices: 1881593--1881627 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
1881583 AATGAAAAAT
1881593 TAAA-AA
1 TAAATAA
1881599 TAAATAA
1 TAAATAA
1881606 TAAATAA
1 TAAATAA
1881613 TAAATAAA
1 TAAAT-AA
1881621 TAAATAA
1 TAAATAA
1881628 AAGAGAGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 4 0.15
7 16 0.59
8 7 0.26
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
TAAATAA
Found at i:1881913 original size:20 final size:20
Alignment explanation
Indices: 1881888--1881928 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1881878 TATTATTTTT
1881888 TATTAT-AATTATATTTAAAA
1 TATTATCAATT-TATTTAAAA
*
1881908 TATTATCTATTTATTTAAAA
1 TATTATCAATTTATTTAAAA
1881928 T
1 T
1881929 TTAAGGTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTATCAATTTATTTAAAA
Found at i:1882058 original size:43 final size:44
Alignment explanation
Indices: 1881947--1882060 Score: 119
Period size: 43 Copynumber: 2.6 Consensus size: 44
1881937 TTAATAATTT
* * * *
1881947 TTATATAATTTTATTATATTGTTTTATTTATATTAAATAAAATAA
1 TTATATAATTTTAATATATTATTTTA-ATATAATAAATAAAATAA
* *
1881992 TTA-ATAACTTT-ATTTATTAATTTTAATATAATAAAT-AAA-AA
1 TTATATAATTTTAATATATT-ATTTTAATATAATAAATAAAATAA
1882033 TTATATTAATTTTAATATATTATTTTAA
1 TTATA-TAATTTTAATATATTATTTTAA
1882061 AATCACTTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
41 5 0.09
42 4 0.07
43 27 0.47
44 18 0.32
45 3 0.05
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.54
Consensus pattern (44 bp):
TTATATAATTTTAATATATTATTTTAATATAATAAATAAAATAA
Found at i:1882063 original size:30 final size:30
Alignment explanation
Indices: 1882006--1882101 Score: 84
Period size: 30 Copynumber: 3.0 Consensus size: 30
1881996 TAACTTTATT
* ** *
1882006 TATTAATTTTAATATAATAAATAAAAATTA
1 TATTAATTTTAATATATTATTTTAAAATTA
*
1882036 TATTAATTTTAATATATTATTTTAAAATCA
1 TATTAATTTTAATATATTATTTTAAAATTA
* *
1882066 CTTTTGATATTTTACTTATATTATATTTAAAATTA
1 -TATT-A-ATTTTA-ATATATTAT-TTTAAAATTA
1882101 T
1 T
1882102 TAGTTTTAGT
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
30 25 0.47
31 3 0.06
32 1 0.02
33 6 0.11
34 9 0.17
35 9 0.17
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (30 bp):
TATTAATTTTAATATATTATTTTAAAATTA
Found at i:1882939 original size:23 final size:21
Alignment explanation
Indices: 1882897--1882947 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 21
1882887 AAAATATTTT
*
1882897 ATTTTAATATTAATT-TTAAA
1 ATTTTAATATTAATTATAAAA
1882917 ATTTTAATAATTTATATTATAAAA
1 ATTTTAAT-A-TTA-ATTATAAAA
1882941 ATTTTAA
1 ATTTTAA
1882948 AAATATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 8 0.31
21 1 0.04
22 3 0.12
23 3 0.12
24 11 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTTAATATTAATTATAAAA
Found at i:1882951 original size:60 final size:63
Alignment explanation
Indices: 1882860--1882976 Score: 150
Period size: 60 Copynumber: 1.9 Consensus size: 63
1882850 TTATTGTTAT
* * * * *
1882860 ATAATTTATGATAATATAAATATTTTTAAAATATTTTATTTTAATATTA-ATTTTAAAATTTTA
1 ATAATTTATGAT-ATATAAAAATTTTAAAAATATATTAATATAATATTATATTTTAAAATTTTA
*
1882923 ATAATTTAT-AT-TATAAAAATTTTAAAAATATATTAATATCATATTATATTTTAA
1 ATAATTTATGATATATAAAAATTTTAAAAATATATTAATATAATATTATATTTTAA
1882977 TTATTTTATT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
60 29 0.62
61 7 0.15
62 2 0.04
63 9 0.19
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (63 bp):
ATAATTTATGATATATAAAAATTTTAAAAATATATTAATATAATATTATATTTTAAAATTTTA
Found at i:1882967 original size:33 final size:32
Alignment explanation
Indices: 1882908--1882970 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
1882898 TTTTAATATT
* * *
1882908 AATTTTAAAATTTTAATAATTTATATTATAAA
1 AATTTTAAAAATATAATAATTCATATTATAAA
*
1882940 AATTTTAAAAATATATTAATATCATATTATA
1 AATTTTAAAAATATAATAAT-TCATATTATA
1882971 TTTTAATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 17 0.65
33 9 0.35
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (32 bp):
AATTTTAAAAATATAATAATTCATATTATAAA
Found at i:1883009 original size:23 final size:23
Alignment explanation
Indices: 1882966--1883010 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1882956 TAATATCATA
* *
1882966 TTATATTTTAATTATTTTATTTT
1 TTATATTTTAATAATTATATTTT
1882989 TTATA-TTTATATAATTATATTT
1 TTATATTTTA-ATAATTATATTT
1883011 AATATTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (23 bp):
TTATATTTTAATAATTATATTTT
Found at i:1883020 original size:15 final size:15
Alignment explanation
Indices: 1882989--1883028 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1882979 ATTTTATTTT
1882989 TTATATTT-ATATAA
1 TTATATTTAATATAA
*
1883003 TTATATTTAATATTA
1 TTATATTTAATATAA
*
1883018 TTAAATTTAAT
1 TTATATTTAAT
1883029 TCACACTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATATTTAATATAA
Found at i:1883362 original size:14 final size:14
Alignment explanation
Indices: 1883345--1883384 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
1883335 TTGTAGTTTT
1883345 TTAATTAAAATAAA
1 TTAATTAAAATAAA
1883359 TTAATTGAAAA-AAA
1 TTAATT-AAAATAAA
1883373 TTAA--AAAATAAA
1 TTAATTAAAATAAA
1883385 AGATAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 4 0.17
12 3 0.12
14 13 0.54
15 4 0.17
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (14 bp):
TTAATTAAAATAAA
Found at i:1884302 original size:13 final size:14
Alignment explanation
Indices: 1884271--1884303 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1884261 ATACATATTT
*
1884271 TTTAAAAAATAATA
1 TTTAATAAATAATA
1884285 TTTAATAAATAA-A
1 TTTAATAAATAATA
1884298 TTTAAT
1 TTTAAT
1884304 GAGAGTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTTAATAAATAATA
Found at i:1884691 original size:25 final size:25
Alignment explanation
Indices: 1884648--1884710 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 25
1884638 GTAACTTGAA
1884648 AATAAA-AAATAATATATATTTATTATAT
1 AATAAATAAA-AA-ATAT-TTTA-TATAT
*
1884676 AATAATTAAAAAATATTTTATATAT
1 AATAAATAAAAAATATTTTATATAT
*
1884701 TATAAATAAA
1 AATAAATAAA
1884711 GTTTTTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 13 0.42
26 4 0.13
27 4 0.13
28 7 0.23
29 3 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATAAATAAAAAATATTTTATATAT
Found at i:1884698 original size:32 final size:29
Alignment explanation
Indices: 1884650--1884709 Score: 75
Period size: 32 Copynumber: 2.0 Consensus size: 29
1884640 AACTTGAAAA
1884650 TAAAAAATAATATATATTTATTATATAATAAT
1 TAAAAAATAATATATA--TATTATA-AATAAT
* *
1884682 TAAAAAATATTTTATATATTATAAATAA
1 TAAAAAATAATATATATATTATAAATAA
1884710 AGTTTTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 5 0.19
30 7 0.27
32 14 0.54
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (29 bp):
TAAAAAATAATATATATATTATAAATAAT
Found at i:1885931 original size:16 final size:16
Alignment explanation
Indices: 1885910--1886052 Score: 70
Period size: 16 Copynumber: 8.8 Consensus size: 16
1885900 TCATTAATAA
1885910 ATTTAATAATTTATAT
1 ATTTAATAATTTATAT
1885926 ATTT-A-AA-TTATAT
1 ATTTAATAATTTATAT
1885939 -TTTGAAT-ATATTATAT
1 ATTT-AATAAT-TTATAT
1885955 ATTTATATAAAATTTCATAT
1 ATTTA-AT--AATTT-ATAT
1885975 A-TTAATAATTTATATT
1 ATTTAATAATTTATA-T
* *
1885991 ATATAA-ATTTTAATAT
1 ATTTAATAATTT-ATAT
*
1886007 ATTT-ATATTTTTATTAT
1 ATTTAATA-ATTTA-TAT
*
1886024 ATTTATATTATATTATAT
1 ATTTA-ATAAT-TTATAT
*
1886042 -TTTAATTATTT
1 ATTTAATAATTT
1886053 TTTATCATAT
Statistics
Matches: 102, Mismatches: 5, Indels: 41
0.69 0.03 0.28
Matches are distributed among these distances:
12 3 0.03
13 6 0.06
14 4 0.04
15 7 0.07
16 33 0.32
17 26 0.25
18 6 0.06
19 10 0.10
20 7 0.07
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.58
Consensus pattern (16 bp):
ATTTAATAATTTATAT
Found at i:1885940 original size:27 final size:27
Alignment explanation
Indices: 1885910--1886015 Score: 78
Period size: 29 Copynumber: 3.9 Consensus size: 27
1885900 TCATTAATAA
*
1885910 ATTTAATAATTTATATATTTAAATTAT
1 ATTTAATAATTTATATATTTATATTAT
* *
1885937 ATTTTGAAT-ATATTATATATTTATATAAA
1 A-TTT-AATAAT-TTATATATTTATATTAT
* *
1885966 ATTTCATATATTAATA-ATTTATATTAT
1 ATTTAATA-ATTTATATATTTATATTAT
*
1885993 A--TAA-ATTTTAATATATTTATATT
1 ATTTAATAATTT-ATATATTTATATT
1886016 TTTATTATAT
Statistics
Matches: 62, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
23 2 0.03
24 4 0.06
25 11 0.18
27 13 0.21
28 12 0.19
29 20 0.32
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (27 bp):
ATTTAATAATTTATATATTTATATTAT
Found at i:1885992 original size:56 final size:56
Alignment explanation
Indices: 1885908--1886050 Score: 132
Period size: 58 Copynumber: 2.5 Consensus size: 56
1885898 CATCATTAAT
*
1885908 AAATTTAATAATTTATATATTTAAATTATAT-TTTGAATATATTATATATTTATATA
1 AAATTTAATAATTAATATATTTAAATTATATATTTGAATATATT-TATATTTATATA
* * * * *
1885964 AAATTTCATATATTAATA-ATTTATATTATATAAATTTTAATATATTTATATTTTTATT
1 AAATTTAATA-ATTAATATATTTAAATTATAT--ATTTGAATATATTTATATTTATATA
* *
1886022 ATATTT-AT-ATTATATTATATTTTAATTAT
1 AAATTTAATAATTA-A-TATATTTAAATTAT
1886051 TTTTTATCAT
Statistics
Matches: 71, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
55 4 0.06
56 22 0.31
57 10 0.14
58 24 0.34
59 11 0.15
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.57
Consensus pattern (56 bp):
AAATTTAATAATTAATATATTTAAATTATATATTTGAATATATTTATATTTATATA
Found at i:1886015 original size:6 final size:6
Alignment explanation
Indices: 1886004--1886043 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
1885994 TAAATTTTAA
*
1886004 TATATT TATATT TTTA-T TATATT TATA-T TATA-T TATATT T
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT T
1886044 TAATTATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 14 0.47
6 16 0.53
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATATT
Found at i:1886018 original size:17 final size:17
Alignment explanation
Indices: 1885998--1886032 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1885988 ATTATATAAA
1885998 TTTTAATATATTTATAT
1 TTTTAATATATTTATAT
*
1886015 TTTTATTATATTTATAT
1 TTTTAATATATTTATAT
1886032 T
1 T
1886033 ATATTATATT
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:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTAATATATTTATAT
Found at i:1886025 original size:11 final size:11
Alignment explanation
Indices: 1885972--1886042 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
1885962 TAAAATTTCA
1885972 TATATTAATAATT
1 TATATT-AT-ATT
*
1885985 TATATTATATA
1 TATATTATATT
* * *
1885996 AATTTTA-ATA
1 TATATTATATT
1886006 TAT-TTATATT
1 TATATTATATT
*
1886016 TTTATTATATT
1 TATATTATATT
1886027 TATATTATA-T
1 TATATTATATT
1886037 TATATT
1 TATATT
1886043 TTAATTATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
9 3 0.06
10 16 0.33
11 22 0.45
12 2 0.04
13 6 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TATATTATATT
Found at i:1886672 original size:2 final size:2
Alignment explanation
Indices: 1886665--1886689 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1886655 TTAACTCATA
1886665 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
1886690 CACACACACG
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:1888001 original size:17 final size:17
Alignment explanation
Indices: 1887979--1888013 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1887969 CTAAGTATAA
*
1887979 TATTTTATAATTTGAAT
1 TATTTTATAATTTAAAT
1887996 TATTTTATAATTTAAAT
1 TATTTTATAATTTAAAT
1888013 T
1 T
1888014 TGATTTAAAT
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:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (17 bp):
TATTTTATAATTTAAAT
Found at i:1888026 original size:23 final size:24
Alignment explanation
Indices: 1887982--1888035 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
1887972 AGTATAATAT
**
1887982 TTTATAATTTGAATTATTTTATAA
1 TTTATAATTTGAATTAAATTATAA
* *
1888006 TTTA-AATTTGATTTAAATTATTA
1 TTTATAATTTGAATTAAATTATAA
1888029 TTTATAA
1 TTTATAA
1888036 AATAAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (24 bp):
TTTATAATTTGAATTAAATTATAA
Found at i:1888118 original size:14 final size:14
Alignment explanation
Indices: 1888085--1888123 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1888075 TTTAATATTT
*
1888085 TAATATATTT-AAA
1 TAATAAATTTAAAA
1888098 TAATAAATTTAAAA
1 TAATAAATTTAAAA
*
1888112 TATTAAATTTAA
1 TAATAAATTTAA
1888124 TTTAATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TAATAAATTTAAAA
Found at i:1888123 original size:6 final size:6
Alignment explanation
Indices: 1888091--1888149 Score: 50
Period size: 6 Copynumber: 9.7 Consensus size: 6
1888081 ATTTTAATAT
* *
1888091 ATTTAA ATAATAA ATTTAAA ATATTAA ATTT-A ATTT-A ATTTAA TTTTAA
1 ATTTAA AT-TTAA ATTT-AA AT-TTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
1888140 ACTTAA ATTT
1 ATTTAA ATTT
1888150 TACATTTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
5 10 0.23
6 18 0.42
7 13 0.30
8 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (6 bp):
ATTTAA
Found at i:1889384 original size:20 final size:22
Alignment explanation
Indices: 1889359--1889402 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
1889349 AATTTGAGTT
1889359 TAATT-AATTT-TTTTATTAAA
1 TAATTAAATTTATTTTATTAAA
1889379 TAATTAAAATTTATTTTATTAAA
1 TAATT-AAATTTATTTTATTAAA
1889402 T
1 T
1889403 TTATTTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.24
22 5 0.24
23 11 0.52
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TAATTAAATTTATTTTATTAAA
Found at i:1889415 original size:13 final size:14
Alignment explanation
Indices: 1889383--1889415 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1889373 ATTAAATAAT
1889383 TAAAATTTATTTTA
1 TAAAATTTATTTTA
*
1889397 TTAAATTTA-TTTA
1 TAAAATTTATTTTA
1889410 TAAAAT
1 TAAAAT
1889416 AAAAAGTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TAAAATTTATTTTA
Found at i:1889497 original size:26 final size:26
Alignment explanation
Indices: 1889447--1889502 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
1889437 CATTCATATC
*
1889447 AAATTTAATTATTTATATTTAAATTT
1 AAATTTAATTATTTATATTTAAATTA
*
1889473 AAATTTAAATT-TTT-TATTATTAATTA
1 AAATTT-AATTATTTATATT-TAAATTA
1889499 AAAT
1 AAAT
1889503 AATAAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 4 0.15
26 18 0.69
27 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
AAATTTAATTATTTATATTTAAATTA
Found at i:1892066 original size:21 final size:21
Alignment explanation
Indices: 1892036--1892103 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
1892026 CATTCATTTT
1892036 TTTA-AATTTAAATTTTAATA
1 TTTATAATTTAAATTTTAATA
** *
1892056 TTTATAATTTATTTTTTTATCA
1 TTTATAATTTAAATTTTAAT-A
*
1892078 -ATATAATTTAAATTTTAA-A
1 TTTATAATTTAAATTTTAATA
1892097 TTT-TAAT
1 TTTATAAT
1892104 ATCTGAACCA
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
19 5 0.14
20 5 0.14
21 26 0.70
22 1 0.03
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTATAATTTAAATTTTAATA
Found at i:1896854 original size:26 final size:25
Alignment explanation
Indices: 1896803--1896873 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 25
1896793 AATTTTGCTC
1896803 AATTTAA-TTATAAAAATATTAAAAT
1 AATTTAATTTATAAAAATATT-AAAT
1896828 AATTTAATTTATATTAAAATATT-AAT
1 AATTTAATTTATA--AAAATATTAAAT
*
1896854 ATTTTAATTTATAAATAATA
1 AATTTAATTTATAAA-AATA
1896874 AAAATTTAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
24 2 0.05
25 11 0.27
26 20 0.49
28 8 0.20
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
AATTTAATTTATAAAAATATTAAAT
Found at i:1896857 original size:20 final size:20
Alignment explanation
Indices: 1896818--1896857 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1896808 AATTATAAAA
*
1896818 ATATTAAAATAATTTAATTT
1 ATATTAAAATAATTAAATTT
1896838 ATATTAAAAT-ATTAATATTT
1 ATATTAAAATAATTAA-ATTT
1896858 TAATTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTAAAATAATTAAATTT
Found at i:1899008 original size:20 final size:18
Alignment explanation
Indices: 1898968--1899032 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 18
1898958 TTTATTATAA
1898968 TTATATTTA-A-AAATAT
1 TTATATTTATATAAATAT
1898984 TTATATTTATATAAATA-
1 TTATATTTATATAAATAT
*
1899001 TTA-ATATAT-TAATATAT
1 TTATATTTATATAA-ATAT
*
1899018 TTTTA-TTATATAAAT
1 TTATATTTATATAAAT
1899033 TTCAAAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
15 3 0.08
16 17 0.43
17 11 0.28
18 9 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATATTTATATAAATAT
Found at i:1899096 original size:15 final size:16
Alignment explanation
Indices: 1899072--1899110 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
1899062 TTTATTTTAT
1899072 AATATTAATATAATTA
1 AATATTAATATAATTA
*
1899088 AAT-TTAATATTATTA
1 AATATTAATATAATTA
1899103 AATATTAA
1 AATATTAA
1899111 AGAATCTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AATATTAATATAATTA
Found at i:1915223 original size:16 final size:17
Alignment explanation
Indices: 1915197--1915232 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
1915187 TTAATAATTG
1915197 AATATTTATATTATATA
1 AATATTTATATTATATA
1915214 AATA-TTATATTATATA
1 AATATTTATATTATATA
1915230 AAT
1 AAT
1915233 TTTGTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AATATTTATATTATATA
Found at i:1916208 original size:213 final size:219
Alignment explanation
Indices: 1915764--1916173 Score: 476
Period size: 223 Copynumber: 1.9 Consensus size: 219
1915754 ATTTATATTG
1915764 TGGTTA-GTTCCTACAGAAAAAAATGTATTTACTCAAAATGTATTTTGTTTGATTTGAAAACTTT
1 TGGTTAGGTTCCTACAGAAAAAAATGTATTTACTCAAAATG-ATTTTGTTTGATTTGAAAACTTT
* **
1915828 TTAAAGTGTTTAAAAATTTATATAAAATAGTTAAAATTTAATATTTTTTTATAGTACTTTTTTAT
65 TTAAAGTATTTAAAAATTTATATAAAATAGTTAAAA-TTAATATTTTTTTATAGTAAATTTTTAT
* *
1915893 ATGTTTTTTAATAACATTTAAATAAAAATATTTTTAATTAATGAAATAATACTTTAAAGTCAGAG
129 ATATTTTTTAATAAAATTTAAATAAAAATATTTTTAATTAAT-AAATAATACTTTAAAGTCAGAG
* * *
1915958 TTAATTAGCATCTGTTCTCTTTAGCTT
193 TGAATTAGAATCTGTGCTCTTTAGCTT
* * * * *
1915985 TGGTTTAGGTTCCTATATAACAAAATTTAATTTATTCAAAAT-AGTTTTG-TTGATTTTGAAAAC
1 TGG-TTAGGTTCCTACAGAAAAAAATGT-ATTTACTCAAAATGA-TTTTGTTTGA-TTTGAAAAC
* *
1916048 TTTTT-TATTATTT-AAAATTTAT-TAAAATA-TT-AAA-TAATA-TTTTTTATA-TAAATTTTT
62 TTTTTAAAGTATTTAAAAATTTATATAAAATAGTTAAAATTAATATTTTTTTATAGTAAATTTTT
1916105 A-ATATTTTTTAATAAAATTTAAGATAAAAATATTTTGTTAATT-AT-AATAATACTTT-AA-TC
127 ATATATTTTTTAATAAAATTTAA-ATAAAAATA-TTT-TTAATTAATAAATAATACTTTAAAGTC
1916165 AGA-TGAATT
189 AGAGTGAATT
1916174 TTGAATCTAG
Statistics
Matches: 168, Mismatches: 13, Indels: 27
0.81 0.06 0.13
Matches are distributed among these distances:
210 5 0.03
211 5 0.03
212 2 0.01
213 30 0.18
214 17 0.10
215 14 0.08
216 11 0.07
218 3 0.02
219 2 0.01
220 7 0.04
221 12 0.07
222 13 0.08
223 35 0.21
224 12 0.07
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (219 bp):
TGGTTAGGTTCCTACAGAAAAAAATGTATTTACTCAAAATGATTTTGTTTGATTTGAAAACTTTT
TAAAGTATTTAAAAATTTATATAAAATAGTTAAAATTAATATTTTTTTATAGTAAATTTTTATAT
ATTTTTTAATAAAATTTAAATAAAAATATTTTTAATTAATAAATAATACTTTAAAGTCAGAGTGA
ATTAGAATCTGTGCTCTTTAGCTT
Found at i:1925924 original size:14 final size:13
Alignment explanation
Indices: 1925900--1925977 Score: 54
Period size: 14 Copynumber: 5.8 Consensus size: 13
1925890 CTTGCCCTCC
1925900 TCCTCTTGCCCCGG
1 TCCT-TTGCCCCGG
*
1925914 TCCTTTGGCCCCCG
1 TCCTTT-GCCCCGG
**
1925928 TGCC--TGCGTCGG
1 T-CCTTTGCCCCGG
1925940 TCCTTTGCCACCGG
1 TCCTTTGCC-CCGG
*
1925954 TCCTTGGCACCCGG
1 TCCTTTGC-CCCGG
1925968 -CCTTTGCCCC
1 TCCTTTGCCCC
1925978 AGTACTTGAT
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
11 2 0.04
12 8 0.16
13 12 0.24
14 25 0.50
15 3 0.06
ACGTcount: A:0.03, C:0.46, G:0.24, T:0.27
Consensus pattern (13 bp):
TCCTTTGCCCCGG
Found at i:1933127 original size:19 final size:19
Alignment explanation
Indices: 1933105--1933155 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1933095 TGTTGTTTCA
*
1933105 TTAATTTTATTTATGTTTT
1 TTAATTTTATTTATATTTT
**
1933124 TTAAAATTATTTATATTTT
1 TTAATTTTATTTATATTTT
*
1933143 TTTATATTTATTT
1 TTAAT-TTTATTT
1933156 GAATATATAT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (19 bp):
TTAATTTTATTTATATTTT
Found at i:1933153 original size:20 final size:19
Alignment explanation
Indices: 1933105--1933155 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
1933095 TGTTGTTTCA
*
1933105 TTAATTTTATTTATGTTTT
1 TTAAATTTATTTATGTTTT
* *
1933124 TTAAAATTATTTATATTTTT
1 TTAAATTTATTTAT-GTTTT
*
1933144 TTATATTTATTT
1 TTAAATTTATTT
1933156 GAATATATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (19 bp):
TTAAATTTATTTATGTTTT
Found at i:1936248 original size:15 final size:14
Alignment explanation
Indices: 1936201--1936276 Score: 58
Period size: 13 Copynumber: 5.8 Consensus size: 14
1936191 ATTAAAGTTC
*
1936201 ATTAAATTTAAGT-
1 ATTAAATTTAATTA
*
1936214 AGTAATATTTAATTA
1 ATTAA-ATTTAATTA
1936229 ATTAAA-TT--TT-
1 ATTAAATTTAATTA
*
1936239 ATT-AATTTAAAT-
1 ATTAAATTTAATTA
1936251 ATTAAATTTAATTA
1 ATTAAATTTAATTA
1936265 ATTTAAATTTAA
1 A-TTAAATTTAA
1936277 AATAATTCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
9 2 0.04
10 5 0.10
11 2 0.04
12 4 0.08
13 14 0.28
14 9 0.18
15 14 0.28
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (14 bp):
ATTAAATTTAATTA
Found at i:1936279 original size:22 final size:22
Alignment explanation
Indices: 1936220--1936277 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
1936210 AAGTAGTAAT
* *
1936220 ATTTAATTAATTAAATTTTATTA
1 ATTTAAAT-ATTAAATTTAATTA
1936243 ATTTAAATATTAAATTTAATTA
1 ATTTAAATATTAAATTTAATTA
1936265 ATTTAAAT-TTAAA
1 ATTTAAATATTAAA
1936278 ATAATTCAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 5 0.15
22 21 0.64
23 7 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTTAAATATTAAATTTAATTA
Found at i:1937816 original size:1 final size:1
Alignment explanation
Indices: 1937812--1937917 Score: 140
Period size: 1 Copynumber: 106.0 Consensus size: 1
1937802 TTATTTTTAC
* * * * **
1937812 AAAAAAAATAAAAATATAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAATTAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
1937877 AAATAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1937918 TATATTAAGT
Statistics
Matches: 91, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
1 91 1.00
ACGTcount: A:0.92, C:0.00, G:0.01, T:0.07
Consensus pattern (1 bp):
A
Found at i:1937873 original size:54 final size:54
Alignment explanation
Indices: 1937812--1937918 Score: 180
Period size: 54 Copynumber: 2.0 Consensus size: 54
1937802 TTATTTTTAC
* *
1937812 AAAAAAAATAAAAATATAAAAAAAAAAAAAAAA-AAAATAAAAAAAAAAAAAATT
1 AAAAAAAAAAAAAATA-AAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAATT
1937866 AAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAT
1 AAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAT
1937919 ATATTAAGTT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
53 16 0.32
54 34 0.68
ACGTcount: A:0.92, C:0.00, G:0.01, T:0.07
Consensus pattern (54 bp):
AAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAATT
Found at i:1954124 original size:15 final size:15
Alignment explanation
Indices: 1954097--1954146 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
1954087 ATTTATTAAA
*
1954097 ATAA-AATATAAAAT
1 ATAATAATAAAAAAT
1954111 ATAATAATAAAAAAT
1 ATAATAATAAAAAAT
1954126 A-AATAAATATAAATAAT
1 ATAAT-AATA-AAA-AAT
1954143 ATAA
1 ATAA
1954147 AGTTAAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
14 7 0.23
15 14 0.47
16 3 0.10
17 4 0.13
18 2 0.07
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
ATAATAATAAAAAAT
Found at i:1954137 original size:17 final size:17
Alignment explanation
Indices: 1954093--1954143 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
1954083 TTTTATTTAT
*
1954093 TAAA-ATAAAATATAAAA
1 TAAATATAAAAAAT-AAA
1954110 TATAATAATAAAAAATAAA
1 TA-AAT-ATAAAAAATAAA
*
1954129 TAAATATAAATAATA
1 TAAATATAAAAAATA
1954144 TAAAGTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 11 0.38
18 5 0.17
19 5 0.17
20 8 0.28
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAATATAAAAAATAAA
Found at i:1954137 original size:20 final size:20
Alignment explanation
Indices: 1954096--1954134 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1954086 TATTTATTAA
* *
1954096 AATAAAATATAAAATATAAT
1 AATAAAAAATAAAAAATAAT
1954116 AATAAAAAATAAATAAATA
1 AATAAAAAATAAA-AAATA
1954135 TAAATAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
AATAAAAAATAAAAAATAAT
Found at i:1959548 original size:19 final size:19
Alignment explanation
Indices: 1959508--1959549 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1959498 ATTAATGTAA
*
1959508 AAATAATATTTAAATATTT
1 AAATAATATTTAAATATAT
*
1959527 AAATATTATTATAAATA-AT
1 AAATAATATT-TAAATATAT
1959546 AAAT
1 AAAT
1959550 TAAATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATAATATTTAAATATAT
Found at i:1963656 original size:2 final size:2
Alignment explanation
Indices: 1963649--1963691 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1963639 AATTCTTGCA
*
1963649 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA 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
1963691 A
1 A
1963692 AAGAATGGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1964652 original size:14 final size:14
Alignment explanation
Indices: 1964597--1964695 Score: 87
Period size: 14 Copynumber: 7.1 Consensus size: 14
1964587 TGTTAGGTAA
1964597 CTGTGTCAAAAGTAC
1 CTGTGTC-AAAGTAC
* *
1964612 CTGTG-CTAAAATGC
1 CTGTGTC-AAAGTAC
* *
1964626 CTATATC-AAGTAC
1 CTGTGTCAAAGTAC
*
1964639 CTATGTCAAAGTAC
1 CTGTGTCAAAGTAC
* *
1964653 TTGTGTCAAAGTGC
1 CTGTGTCAAAGTAC
*
1964667 CTGTG-CCAAGTAC
1 CTGTGTCAAAGTAC
1964680 CTGTGTCAAAGTAC
1 CTGTGTCAAAGTAC
1964694 CT
1 CT
1964696 ACGCCAGGCA
Statistics
Matches: 66, Mismatches: 15, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
13 21 0.32
14 39 0.59
15 6 0.09
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (14 bp):
CTGTGTCAAAGTAC
Found at i:1964661 original size:27 final size:27
Alignment explanation
Indices: 1964597--1964696 Score: 85
Period size: 27 Copynumber: 3.6 Consensus size: 27
1964587 TGTTAGGTAA
* * *
1964597 CTGTGTCAAAAGTACCTGTGCTAAAATGC
1 CTGTGTC-AAAGTACCTATGC-AAAGTAC
* *
1964626 CTATATC-AAGTACCTATGTCAAAGTAC
1 CTGTGTCAAAGTACCTATG-CAAAGTAC
* * * *
1964653 TTGTGTCAAAGTGCCTGTGCCAAGTAC
1 CTGTGTCAAAGTACCTATGCAAAGTAC
1964680 CTGTGTCAAAGTACCTA
1 CTGTGTCAAAGTACCTA
1964697 CGCCAGGCAC
Statistics
Matches: 55, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
27 40 0.73
28 10 0.18
29 5 0.09
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (27 bp):
CTGTGTCAAAGTACCTATGCAAAGTAC
Found at i:1964668 original size:41 final size:41
Alignment explanation
Indices: 1964600--1964695 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
1964590 TAGGTAACTG
*
1964600 TGTCAAAAGTACCTGTGCTAAAATGCCTATATCAAGTACCTA
1 TGTC-AAAGTACCTGTGCTAAAATGCCTATACCAAGTACCTA
* * * * *
1964642 TGTCAAAGTACTTGTG-TCAAAGTGCCTGTGCCAAGTACCTG
1 TGTCAAAGTACCTGTGCT-AAAATGCCTATACCAAGTACCTA
1964683 TGTCAAAGTACCT
1 TGTCAAAGTACCT
1964696 ACGCCAGGCA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
40 1 0.02
41 41 0.89
42 4 0.09
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (41 bp):
TGTCAAAGTACCTGTGCTAAAATGCCTATACCAAGTACCTA
Found at i:1964701 original size:27 final size:27
Alignment explanation
Indices: 1964633--1964729 Score: 104
Period size: 27 Copynumber: 3.6 Consensus size: 27
1964623 TGCCTATATC
*
1964633 AAGTACCTATGTCAAAGTACTTGTGTCA
1 AAGTACCTATG-CCAAGTACTTGTGTCA
* * *
1964661 AAGTGCCTGTGCCAAGTACCTGTGTCA
1 AAGTACCTATGCCAAGTACTTGTGTCA
* * * *
1964688 AAGTACCTACGCCAGGCACTTGTGCCA
1 AAGTACCTATGCCAAGTACTTGTGTCA
*
1964715 AAGTACCTGTGCCAA
1 AAGTACCTATGCCAA
1964730 AGAGTATTAT
Statistics
Matches: 55, Mismatches: 14, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
27 46 0.84
28 9 0.16
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.25
Consensus pattern (27 bp):
AAGTACCTATGCCAAGTACTTGTGTCA
Found at i:1964727 original size:14 final size:14
Alignment explanation
Indices: 1964633--1964731 Score: 85
Period size: 14 Copynumber: 7.2 Consensus size: 14
1964623 TGCCTATATC
* *
1964633 AAGTACCTATGTCA
1 AAGTACCTGTGCCA
* *
1964647 AAGTACTTGTGTCA
1 AAGTACCTGTGCCA
*
1964661 AAGTGCCTGTGCC-
1 AAGTACCTGTGCCA
*
1964674 AAGTACCTGTGTCA
1 AAGTACCTGTGCCA
**
1964688 AAGTACCTACGCC-
1 AAGTACCTGTGCCA
* * *
1964701 AGGCACTTGTGCCA
1 AAGTACCTGTGCCA
1964715 AAGTACCTGTGCCA
1 AAGTACCTGTGCCA
1964729 AAG
1 AAG
1964732 AGTATTATGG
Statistics
Matches: 65, Mismatches: 18, Indels: 4
0.75 0.21 0.05
Matches are distributed among these distances:
13 19 0.29
14 46 0.71
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.24
Consensus pattern (14 bp):
AAGTACCTGTGCCA
Found at i:1965306 original size:14 final size:14
Alignment explanation
Indices: 1965289--1965327 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 14
1965279 CCCACGAGGC
1965289 ATTATCCGTAAGGT
1 ATTATCCGTAAGGT
1965303 ATTATTCACTGTAAGGT
1 ATTA-TC-C-GTAAGGT
1965320 ATTATCCG
1 ATTATCCG
1965328 CGAGATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 5 0.23
15 3 0.14
16 3 0.14
17 11 0.50
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (14 bp):
ATTATCCGTAAGGT
Found at i:1965582 original size:16 final size:17
Alignment explanation
Indices: 1965561--1965595 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1965551 TTTTTTTTTA
1965561 AACTT-ATAAAATATAT
1 AACTTAATAAAATATAT
1965577 AACTTAAATAAAATATAT
1 AACTT-AATAAAATATAT
1965595 A
1 A
1965596 TATAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
18 12 0.71
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (17 bp):
AACTTAATAAAATATAT
Found at i:1973388 original size:2 final size:2
Alignment explanation
Indices: 1973381--1973408 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1973371 TAGTTAATGC
1973381 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
1973409 GAGAAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1974162 original size:19 final size:19
Alignment explanation
Indices: 1974119--1974165 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
1974109 ATTTTATTTA
1974119 AATTTT-AT-TAAAAATAT
1 AATTTTAATATAAAAATAT
** *
1974136 AAAATTAATATAAAGATAT
1 AATTTTAATATAAAAATAT
1974155 AATTTTAATAT
1 AATTTTAATAT
1974166 TTTAATAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
17 4 0.17
18 2 0.09
19 17 0.74
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
AATTTTAATATAAAAATAT
Found at i:1974326 original size:25 final size:28
Alignment explanation
Indices: 1974295--1974345 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
1974285 ATTTAAAGTA
1974295 TTATTT-AA-TTAATTAAAAA-ATATTT
1 TTATTTAAATTTAATTAAAAACATATTT
*
1974320 TTATTTAAATTTTATTAAAAACATAT
1 TTATTTAAATTTAATTAAAAACATAT
1974346 AAAAATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 6 0.27
26 2 0.09
27 10 0.45
28 4 0.18
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (28 bp):
TTATTTAAATTTAATTAAAAACATATTT
Found at i:1974403 original size:19 final size:19
Alignment explanation
Indices: 1974351--1974409 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 19
1974341 CATATAAAAA
*
1974351 TTTATATAA-AAAATATAAT
1 TTTAAATAATAAAATA-AAT
* **
1974370 TTT-AATATTTTAATAAAT
1 TTTAAATAATAAAATAAAT
*
1974388 TTTAAATAATAAAATAAGT
1 TTTAAATAATAAAATAAAT
1974407 TTT
1 TTT
1974410 CAAAATCAAC
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
18 9 0.30
19 21 0.70
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
TTTAAATAATAAAATAAAT
Found at i:1974618 original size:211 final size:210
Alignment explanation
Indices: 1974061--1974691 Score: 1072
Period size: 212 Copynumber: 3.0 Consensus size: 210
1974051 AAAATATTTT
* * * * *
1974061 AGATTCAAATTACTTTGATTTAAATTATTATTTAATTAATAAAATATAATTTTATTTAAATTTTA
1 AGATTCAAATTAATCTGATTTAAAGTATTATTTAATTAATAAAAAATATTTTTATTTAAATTTTA
*
1974126 TT-AAAA-ATAT-AAAATTAATAT-AAAGATATAATTTTAATATTTTAATAAATTTTAAACAATA
66 TTAAAAACATATAAAAATTAATATAAAAAATATAATTTTAATATTTTAATAAATTTTAAACAATA
* *
1974187 AAATAAGTTTTCAAAATCAACAAACATTTTGAATATATACATTTTTTTTATATAAGAACCTAACC
131 AAATAAGTTTTCAAAATCAACAAACATTTTGAATAAATACA-TTTTTTTATATAGGAACCTAACC
*
1974252 AAATATAAATATAACT
195 AAATATAAATATAACC
1974268 AGATTCAAATTAATCTGATTTAAAGTATTATTTAATTAATTAAAAAATATTTTTATTTAAATTTT
1 AGATTCAAATTAATCTGATTTAAAGTATTATTTAATTAA-TAAAAAATATTTTTATTTAAATTTT
* *
1974333 ATTAAAAACATATAAAAATTTATATAAAAAATATAATTTTAATATTTTAATAAATTTTAAATAAT
65 ATTAAAAACATATAAAAATTAATATAAAAAATATAATTTTAATATTTTAATAAATTTTAAACAAT
1974398 AAAATAAGTTTTCAAAATCAACAAAACATTTTGAATAAATACATTTTTTTATATAGGAACCTAAC
130 AAAATAAGTTTTCAAAATCAAC-AAACATTTTGAATAAATACATTTTTTTATATAGGAACCTAAC
1974463 CAAATATAAATATAACC
194 CAAATATAAATATAACC
*
1974480 AGATTCTAATTAATCTGATTTAAAGTATTATTTAATTAATAAAAAATATTTTTATTTAAATTTTA
1 AGATTCAAATTAATCTGATTTAAAGTATTATTTAATTAATAAAAAATATTTTTATTTAAATTTTA
1974545 TTAAAAACATATAAAAATTAATATAAAAAATATAATTTTAATATTTTAATAAATTTTAAACAATA
66 TTAAAAACATATAAAAATTAATATAAAAAATATAATTTTAATATTTTAATAAATTTTAAACAATA
* * *
1974610 AAATAAGTTTTCAAAATCAACAAACATTTTGAGTAAATACATTTTTTTCTGTAGGAACCTAACCA
131 AAATAAGTTTTCAAAATCAACAAACATTTTGAATAAATACATTTTTTTATATAGGAACCTAACCA
1974675 AATATAAATATAACC
196 AATATAAATATAACC
1974690 AG
1 AG
1974692 TAATGCTACC
Statistics
Matches: 401, Mismatches: 17, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
207 36 0.09
208 26 0.06
209 4 0.01
210 62 0.15
211 120 0.30
212 134 0.33
213 19 0.05
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (210 bp):
AGATTCAAATTAATCTGATTTAAAGTATTATTTAATTAATAAAAAATATTTTTATTTAAATTTTA
TTAAAAACATATAAAAATTAATATAAAAAATATAATTTTAATATTTTAATAAATTTTAAACAATA
AAATAAGTTTTCAAAATCAACAAACATTTTGAATAAATACATTTTTTTATATAGGAACCTAACCA
AATATAAATATAACC
Found at i:1975144 original size:24 final size:27
Alignment explanation
Indices: 1975087--1975144 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 27
1975077 ATTAAATTTG
1975087 ATAATAT--TAAAAATAATTATAACAT
1 ATAATATAATAAAAATAATTATAACAT
1975112 AT-ATAATAATAAAAA-AATTA-AA-AT
1 ATAAT-ATAATAAAAATAATTATAACAT
1975136 ATAATATAA
1 ATAATATAA
1975145 GATAAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
24 10 0.34
25 8 0.28
26 5 0.17
27 6 0.21
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (27 bp):
ATAATATAATAAAAATAATTATAACAT
Found at i:1975150 original size:26 final size:27
Alignment explanation
Indices: 1975087--1975144 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
1975077 ATTAAATTTG
* *
1975087 ATAATATTAAAAATAATTATAACATAT
1 ATAATAATAAAAATAATTAAAACATAT
*
1975114 ATAATAATAAAAA-AATTAAAATATAAT
1 ATAATAATAAAAATAATTAAAACAT-AT
1975141 ATAA
1 ATAA
1975145 GATAAATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
27 18 0.67
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (27 bp):
ATAATAATAAAAATAATTAAAACATAT
Found at i:1975151 original size:22 final size:24
Alignment explanation
Indices: 1975112--1975161 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
1975102 ATTATAACAT
1975112 ATATAATAATAAAAAAAT-TA-AA
1 ATATAATAATAAAAAAATATATAA
*
1975134 ATATAAT-ATAAGATAAATATATAA
1 ATATAATAATAA-AAAAATATATAA
1975158 ATAT
1 ATAT
1975162 TTTAAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 4 0.17
22 12 0.50
23 2 0.08
24 6 0.25
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (24 bp):
ATATAATAATAAAAAAATATATAA
Found at i:1975246 original size:29 final size:29
Alignment explanation
Indices: 1975139--1975246 Score: 72
Period size: 29 Copynumber: 3.9 Consensus size: 29
1975129 TTAAAATATA
*
1975139 ATATAAGATAAATATATAAA-TA-T-TTT
1 ATATAATATAAATATATAAATTATTATTT
*
1975165 A-A-AAT-TAAATAATATTAATTATTAATTT
1 ATATAATATAAAT-ATATAAATTATT-ATTT
* **
1975193 -TACAA-A-ATTTATATAAATATAATTATTT
1 ATATAATATAAATATATAAAT-T-ATTATTT
1975221 ATATAATATAAATATATAAATTATTA
1 ATATAATATAAATATATAAATTATTA
1975247 AATTAAAATA
Statistics
Matches: 61, Mismatches: 8, Indels: 23
0.66 0.09 0.25
Matches are distributed among these distances:
23 5 0.08
24 8 0.13
25 3 0.05
26 2 0.03
27 7 0.11
28 11 0.18
29 13 0.21
30 2 0.03
31 10 0.16
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (29 bp):
ATATAATATAAATATATAAATTATTATTT
Found at i:1975784 original size:24 final size:22
Alignment explanation
Indices: 1975732--1975802 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 22
1975722 AATTTTTTTA
1975732 AATT-TATATAATATT-AATAT
1 AATTATATATAATATTAAATAT
1975752 ATATATATATATAATATTTTAAATAT
1 A-AT-TATATATAATA--TTAAATAT
*
1975778 AATTATATTATATACATTAAATAT
1 AATTATA-TATA-ATATTAAATAT
1975802 A
1 A
1975803 TGAATTATAA
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
20 1 0.02
21 2 0.05
22 1 0.02
23 9 0.21
24 13 0.31
25 8 0.19
26 8 0.19
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (22 bp):
AATTATATATAATATTAAATAT
Found at i:1976046 original size:17 final size:16
Alignment explanation
Indices: 1976021--1976116 Score: 61
Period size: 17 Copynumber: 5.8 Consensus size: 16
1976011 ATAAGTATTA
*
1976021 AAATTATTATTAGTTTT
1 AAATAATTATTA-TTTT
*
1976038 AAATAATTAATTCTTTT
1 AAATAATT-ATTATTTT
*
1976055 CAAATACTTATTTATTTT
1 -AAATAATTA-TTATTTT
1976073 AAA-AATTTATTA-TTT
1 AAATAA-TTATTATTTT
* **
1976088 AAATATTTAATTATGAT
1 AAATAATT-ATTATTTT
*
1976105 AAAAAATTATTA
1 AAATAATTATTA
1976117 AAATATTTAA
Statistics
Matches: 62, Mismatches: 10, Indels: 15
0.71 0.11 0.17
Matches are distributed among these distances:
15 8 0.13
16 13 0.21
17 25 0.40
18 16 0.26
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (16 bp):
AAATAATTATTATTTT
Found at i:1976128 original size:16 final size:16
Alignment explanation
Indices: 1976063--1976129 Score: 51
Period size: 13 Copynumber: 4.6 Consensus size: 16
1976053 TTCAAATACT
1976063 TATTT-ATT-TTAAAA
1 TATTTAATTATTAAAA
*
1976077 -ATTT-ATTATTTAAA
1 TATTTAATTATTAAAA
*
1976091 TATTTAATTATGATAAA
1 TATTTAATTATTA-AAA
1976108 -A---AATTATTAAAA
1 TATTTAATTATTAAAA
1976120 TATTTAATTA
1 TATTTAATTA
1976130 AAAAAACATA
Statistics
Matches: 41, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
12 3 0.07
13 15 0.37
14 5 0.12
15 4 0.10
16 11 0.27
17 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (16 bp):
TATTTAATTATTAAAA
Found at i:1976631 original size:23 final size:24
Alignment explanation
Indices: 1976591--1976636 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
1976581 ATAATAAAAG
*
1976591 ATATATATTAAAATTTAA-ATTTT
1 ATATATATTAAAAGTTAATATTTT
* *
1976614 ATATATGTTGAAAGTTAATATTT
1 ATATATATTAAAAGTTAATATTT
1976637 AAAAAGATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (24 bp):
ATATATATTAAAAGTTAATATTTT
Found at i:1977682 original size:34 final size:32
Alignment explanation
Indices: 1977624--1977690 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 32
1977614 TAAAACGAAA
*
1977624 TTTAAAAATATAATTCAATTAATTTATATAATTT
1 TTTAAAAATATAATTCAATGAATTTA-A-AATTT
1977658 TTTAAAAATAT-ATTCAATAGAATTTAAAATTT
1 TTTAAAAATATAATTCAAT-GAATTTAAAATTT
1977690 T
1 T
1977691 AATTATATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 6 0.19
33 8 0.26
34 17 0.55
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (32 bp):
TTTAAAAATATAATTCAATGAATTTAAAATTT
Found at i:1978183 original size:23 final size:23
Alignment explanation
Indices: 1978149--1978197 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
1978139 TAAAGTTAAT
*
1978149 TAATATATTATTTA-TAATAATAA
1 TAATATATTATTAAGTAAT-ATAA
1978172 TAATAT-TATATTAAGTAATATAA
1 TAATATAT-TATTAAGTAATATAA
1978195 TAA
1 TAA
1978198 CTTTATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 1 0.04
23 18 0.78
24 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TAATATATTATTAAGTAATATAA
Found at i:1979415 original size:28 final size:27
Alignment explanation
Indices: 1979375--1979452 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 27
1979365 AATCTTAAAA
*
1979375 TTTA-AATATTTATATTTTATTTATATAT
1 TTTATAATA-TTATATTATATTTA-ATAT
*
1979403 TTTATAATATTATAATCATATTTAATAT
1 TTTATAATATTAT-ATTATATTTAATAT
1979431 TTTAATAAT-TTATATTATATTT
1 TTT-ATAATATTATATTATATTT
1979453 TTTTAATGTA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
27 8 0.18
28 19 0.43
29 17 0.39
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (27 bp):
TTTATAATATTATATTATATTTAATAT
Found at i:1979428 original size:18 final size:16
Alignment explanation
Indices: 1979407--1979449 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
1979397 ATATATTTTA
1979407 TAATATTATAATCATATT
1 TAATATTATAAT-A-ATT
*
1979425 TAATATTTTAATAATT
1 TAATATTATAATAATT
1979441 T-ATATTATA
1 TAATATTATA
1979450 TTTTTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 7 0.30
16 4 0.17
17 1 0.04
18 11 0.48
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
TAATATTATAATAATT
Found at i:1979438 original size:21 final size:19
Alignment explanation
Indices: 1979380--1979475 Score: 68
Period size: 20 Copynumber: 4.8 Consensus size: 19
1979370 TAAAATTTAA
* *
1979380 ATATTTATATTTTATTTAT
1 ATATTTATATTTTAATAAT
*
1979399 ATATTTTATAATATT-ATAAT
1 ATA-TTTAT-ATTTTAATAAT
1979419 CATATTTAATATTTTAATAAT
1 -ATATTT-ATATTTTAATAAT
* **
1979440 TTATATTATATTTTTTTAAT
1 ATAT-TTATATTTTAATAAT
*
1979460 GTATTTATATATTTAA
1 ATATTTATAT-TTTAA
1979476 ACTGTATTAT
Statistics
Matches: 60, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
19 9 0.15
20 35 0.58
21 16 0.27
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (19 bp):
ATATTTATATTTTAATAAT
Found at i:1982549 original size:18 final size:19
Alignment explanation
Indices: 1982531--1982583 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
1982521 TTTTAATATT
1982531 ATTTTAAATAATAAAATTA
1 ATTTTAAATAATAAAATTA
1982550 ATTTTTAAAT--T-AAATTA
1 A-TTTTAAATAATAAAATTA
*
1982567 AATTTAAATAA-AAAATT
1 ATTTTAAATAATAAAATT
1982584 CATAAATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
16 7 0.24
17 7 0.24
18 6 0.21
19 1 0.03
20 8 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATTTTAAATAATAAAATTA
Found at i:1983116 original size:30 final size:29
Alignment explanation
Indices: 1983070--1983127 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
1983060 TCCACAATTC
*
1983070 TATATTTATATATTTTAT-TATTATATAAT
1 TATATTTAAATATTTTATAT-TTATATAAT
1983099 TATATTTAAATTATTTTATATTTATATAA
1 TATATTTAAA-TATTTTATATTTATATAA
1983128 AATTTGATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 9 0.35
30 16 0.62
31 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (29 bp):
TATATTTAAATATTTTATATTTATATAAT
Found at i:1983118 original size:22 final size:21
Alignment explanation
Indices: 1983078--1983125 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
1983068 TCTATATTTA
*
1983078 TATATTTTATTATTATATAAT
1 TATATTTAATTATTATATAAT
* *
1983099 TATATTTAAATTATTTTATATT
1 TATATTT-AATTATTATATAAT
1983121 TATAT
1 TATAT
1983126 AAAATTTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATATTTAATTATTATATAAT
Found at i:1983165 original size:16 final size:15
Alignment explanation
Indices: 1983065--1983165 Score: 57
Period size: 16 Copynumber: 6.5 Consensus size: 15
1983055 ACAATTCCAC
*
1983065 AATTCTATATT-TAT
1 AATTTTATATTATAT
1983079 ATATTTTATTATTATAT
1 A-ATTTTA-TATTATAT
* *
1983096 AATTATAT-TTAAAT
1 AATTTTATATTATAT
*
1983110 TATTTTATATTTATAT
1 AATTTTATA-TTATAT
*
1983126 AAAATTTGATAGGTTA-AT
1 --AATTTTATA--TTATAT
1983144 AA-TTTATATTATAT
1 AATTTTATATTATAT
1983158 AAATTTTA
1 -AATTTTA
1983166 AAATATATAT
Statistics
Matches: 66, Mismatches: 10, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
13 3 0.05
14 14 0.21
15 13 0.20
16 20 0.30
17 4 0.06
18 9 0.14
19 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (15 bp):
AATTTTATATTATAT
Found at i:1983199 original size:2 final size:2
Alignment explanation
Indices: 1983192--1983225 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
1983182 TTTATTATTT
*
1983192 TA TA TA TA TA TA TA TA TA TA TA TCA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA T
1983226 TTAATATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1985530 original size:2 final size:2
Alignment explanation
Indices: 1985523--1985557 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1985513 TGAAATAATT
1985523 TA TA TA TA TA 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 TA TA TA TA TA T
1985558 TTGATTTTAA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1985987 original size:17 final size:18
Alignment explanation
Indices: 1985946--1985989 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
1985936 TTATATTTTT
1985946 AAAATTATAGTAAATAAA
1 AAAATTATAGTAAATAAA
1985964 AATAATTA-A-TAATATAAA
1 AA-AATTATAGTAA-ATAAA
1985982 AAAATTAT
1 AAAATTAT
1985990 TTAAATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 8 0.35
18 10 0.43
19 5 0.22
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (18 bp):
AAAATTATAGTAAATAAA
Found at i:1986005 original size:21 final size:21
Alignment explanation
Indices: 1985958--1986005 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
1985948 AATTATAGTA
1985958 AATAAAAATAATTAATAATAT
1 AATAAAAATAATTAATAATAT
* *
1985979 AA-AAAAATTATTTA-AATATT
1 AATAAAAATAATTAATAATA-T
1985999 AATAAAA
1 AATAAAA
1986006 TATTGAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 4 0.17
20 13 0.57
21 6 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AATAAAAATAATTAATAATAT
Found at i:1986105 original size:18 final size:18
Alignment explanation
Indices: 1986082--1986116 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1986072 GTTTGTATCT
1986082 TTTTGTATAATATAAAAA
1 TTTTGTATAATATAAAAA
*
1986100 TTTTGTATCATATAAAA
1 TTTTGTATAATATAAAA
1986117 CATTAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (18 bp):
TTTTGTATAATATAAAAA
Found at i:1986209 original size:14 final size:14
Alignment explanation
Indices: 1986190--1986239 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
1986180 TGTAATTTTA
1986190 AAAATATAAATATT
1 AAAATATAAATATT
*
1986204 AAAATATTAAATTTT
1 AAAATA-TAAATATT
*
1986219 ATAATATATAA-ATT
1 AAAATATA-AATATT
1986233 AAAATAT
1 AAAATAT
1986240 CTCATTTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 16 0.53
15 14 0.47
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AAAATATAAATATT
Found at i:1986233 original size:29 final size:30
Alignment explanation
Indices: 1986183--1986239 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
1986173 TATTTAGTGT
1986183 AATTTTAAAAATATAAATATTAAAATATTA
1 AATTTTAAAAATATAAATATTAAAATATTA
*
1986213 AATTTT-ATAATATATAA-ATTAAAATAT
1 AATTTTAAAAATATA-AATATTAAAATAT
1986240 CTCATTTACT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (30 bp):
AATTTTAAAAATATAAATATTAAAATATTA
Found at i:1986552 original size:15 final size:15
Alignment explanation
Indices: 1986532--1986561 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1986522 GATTTATTTT
1986532 TTAATTATATAATTA
1 TTAATTATATAATTA
*
1986547 TTAATTTTATAATTA
1 TTAATTATATAATTA
1986562 AATTTAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTAATTATATAATTA
Found at i:1988124 original size:12 final size:12
Alignment explanation
Indices: 1988104--1988146 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
1988094 GATTTTGATT
* *
1988104 TTATCATATTTA
1 TTATAATATTAA
1988116 TTATAATA-TAA
1 TTATAATATTAA
*
1988127 TTATAAAATTAA
1 TTATAATATTAA
1988139 TTATAATA
1 TTATAATA
1988147 AATAGTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (12 bp):
TTATAATATTAA
Found at i:1988159 original size:28 final size:27
Alignment explanation
Indices: 1988120--1988176 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
1988110 TATTTATTAT
*
1988120 AATATAATTATAAA-ATTAATTATAATA
1 AATATAATTATAAATATTAA-TAAAATA
1988147 AATAGTAATTATAAATATTAATAAAATA
1 AATA-TAATTATAAATATTAATAAAATA
1988175 AA
1 AA
1988177 AAAAATCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 4 0.15
28 18 0.67
29 5 0.19
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (27 bp):
AATATAATTATAAATATTAATAAAATA
Found at i:1988162 original size:13 final size:13
Alignment explanation
Indices: 1988109--1988168 Score: 54
Period size: 13 Copynumber: 4.6 Consensus size: 13
1988099 TGATTTTATC
*
1988109 ATATTTATTAT-A
1 ATATTAATTATAA
1988121 ATA-TAATTATAA
1 ATATTAATTATAA
1988133 A-ATTAATTATAATAA
1 ATATTAA-T-T-ATAA
*
1988148 ATAGTAATTATAA
1 ATATTAATTATAA
1988161 ATATTAAT
1 ATATTAAT
1988169 AAAATAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
11 7 0.18
12 8 0.21
13 12 0.31
14 2 0.05
15 6 0.15
16 4 0.10
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (13 bp):
ATATTAATTATAA
Found at i:1988428 original size:20 final size:20
Alignment explanation
Indices: 1988395--1988433 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
1988385 TTTTATGATT
*
1988395 ATTTTTTTTATAAT-TTTAA
1 ATTTTTATTATAATATTTAA
1988414 ATTTTTATTATTAATATTTA
1 ATTTTTATTA-TAATATTTA
1988434 TTATAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 4 0.24
21 4 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTTTTATTATAATATTTAA
Done.