Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 94 of 105
Found at i:16686566 original size:28 final size:28
Alignment explanation
Indices: 16686508--16686560 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
16686498 ATAGAATTCG
*
16686508 AATTTTTTAAAGTAAAATTTTAATTTTA
1 AATTTTATAAAGTAAAATTTTAATTTTA
16686536 AATTTTATAAA-TAAAA-TTTAATTTT
1 AATTTTATAAAGTAAAATTTTAATTTT
16686561 TTAAATAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 9 0.38
27 5 0.21
28 10 0.42
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (28 bp):
AATTTTATAAAGTAAAATTTTAATTTTA
Found at i:16687343 original size:30 final size:30
Alignment explanation
Indices: 16687267--16687352 Score: 79
Period size: 30 Copynumber: 2.9 Consensus size: 30
16687257 TTGTTGTTGA
* *
16687267 ATTTAAATAAAATTTT-ATAATTTTA-TTGC
1 ATTTAAATAAAATTTTAAT-ATTTAATTTAC
* * *
16687296 ATTTAAGT-AAGTCTTTAATATTTAATTTAT
1 ATTTAAATAAAAT-TTTAATATTTAATTTAC
*
16687326 ATTTAAATAAAATTTTAATTTTTAATT
1 ATTTAAATAAAATTTTAATATTTAATT
16687353 AGTATCCAGT
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
28 3 0.07
29 15 0.33
30 24 0.53
31 3 0.07
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (30 bp):
ATTTAAATAAAATTTTAATATTTAATTTAC
Found at i:16687506 original size:28 final size:28
Alignment explanation
Indices: 16687449--16687506 Score: 64
Period size: 29 Copynumber: 2.1 Consensus size: 28
16687439 GTATAAAAGT
* * *
16687449 TAAAGTATAAAAATTTATTTGGATATAA
1 TAAAGTACAAAAATTTATTTGAAGATAA
*
16687477 TAAAGATACAAAAATTTATTTTAAGA-AA
1 TAAAG-TACAAAAATTTATTTGAAGATAA
16687505 TA
1 TA
16687507 GAATAGTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (28 bp):
TAAAGTACAAAAATTTATTTGAAGATAA
Found at i:16696734 original size:26 final size:26
Alignment explanation
Indices: 16696661--16696724 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 26
16696651 AATTTTGATA
*
16696661 AAATTAAAAATAATAATTATTATTATTAT
1 AAATT-AAAA-AA-AATTATTATAATTAT
16696690 AAATTAAAAAAAATTATTATAATTAT
1 AAATTAAAAAAAATTATTATAATTAT
16696716 -AATTAAAAA
1 AAATTAAAAA
16696725 TTTTATATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
25 9 0.26
26 14 0.41
27 2 0.06
28 4 0.12
29 5 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (26 bp):
AAATTAAAAAAAATTATTATAATTAT
Found at i:16696898 original size:2 final size:2
Alignment explanation
Indices: 16696891--16696925 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
16696881 CAAAGGAATA
16696891 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
16696926 CTTGGCATGA
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:16699139 original size:16 final size:18
Alignment explanation
Indices: 16699119--16699158 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
16699109 TCATATTTTA
16699119 ATTATATTATATT-ATTT
1 ATTATATTATATTAATTT
*
16699136 -TTATATTGTATTAATTT
1 ATTATATTATATTAATTT
16699153 ATTATA
1 ATTATA
16699159 ATTTAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 11 0.55
17 4 0.20
18 5 0.25
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
ATTATATTATATTAATTT
Found at i:16700409 original size:30 final size:30
Alignment explanation
Indices: 16700301--16700410 Score: 129
Period size: 31 Copynumber: 3.6 Consensus size: 30
16700291 TGAAATTTTA
16700301 TTATATTCAAATAAA-TATT-TGATCTTTAAT
1 TTATATTCAAATAAATTATTAT-AT-TTTAAT
*
16700331 TTACA-TCAAAATAAATTATTATATTTTAAT
1 TTATATTC-AAATAAATTATTATATTTTAAT
*
16700361 TTGTATTCAAATTAAATTATTATATTTTAAT
1 TTATATTCAAA-TAAATTATTATATTTTAAT
16700392 TTATATAT-AAATAAATTAT
1 TTATAT-TCAAATAAATTAT
16700411 AAATATAAAT
Statistics
Matches: 70, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
29 2 0.03
30 31 0.44
31 35 0.50
32 2 0.03
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.50
Consensus pattern (30 bp):
TTATATTCAAATAAATTATTATATTTTAAT
Found at i:16700767 original size:10 final size:10
Alignment explanation
Indices: 16700752--16700847 Score: 54
Period size: 10 Copynumber: 9.2 Consensus size: 10
16700742 AATGAGTAAA
16700752 TTTATTTTAT
1 TTTATTTTAT
16700762 TTTATTTTAT
1 TTTATTTTAT
*
16700772 TTTGTTTTAT
1 TTTATTTTAT
*
16700782 AATATATTTATAT
1 --TTTATTT-TAT
*
16700795 TTT-TTGTATT
1 TTTATTTTA-T
16700805 TTTATATTTA-
1 TTTAT-TTTAT
16700815 -TTATTTATAT
1 TTTATTT-TAT
*
16700825 ATATATTTTAT
1 -TTTATTTTAT
* *
16700836 TATAATTTAT
1 TTTATTTTAT
16700846 TT
1 TT
16700848 GTTAATATAT
Statistics
Matches: 67, Mismatches: 9, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
8 2 0.03
9 8 0.12
10 35 0.52
11 6 0.09
12 13 0.19
13 3 0.04
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (10 bp):
TTTATTTTAT
Found at i:16700772 original size:15 final size:15
Alignment explanation
Indices: 16700752--16700847 Score: 54
Period size: 15 Copynumber: 6.1 Consensus size: 15
16700742 AATGAGTAAA
16700752 TTTATTTTATTTTAT
1 TTTATTTTATTTTAT
*
16700767 TTTATTTTGTTTTAT
1 TTTATTTTATTTTAT
*
16700782 AATATATTTATATTTT-T
1 --TTTATTT-TATTTTAT
*
16700799 TGTATTTTTATATTTA-
1 TTTA-TTTTAT-TTTAT
*
16700815 -TTATTTATATATATAT
1 TTTATTT-TAT-TTTAT
* *
16700831 TTTATTATAATTTAT
1 TTTATTTTATTTTAT
16700846 TT
1 TT
16700848 GTTAATATAT
Statistics
Matches: 63, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
14 3 0.05
15 35 0.56
16 8 0.13
17 12 0.19
18 5 0.08
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTATTTTATTTTAT
Found at i:16700886 original size:69 final size:74
Alignment explanation
Indices: 16700754--16700888 Score: 163
Period size: 74 Copynumber: 1.9 Consensus size: 74
16700744 TGAGTAAATT
* * * * * * * *
16700754 TATTTTATTTTATTTTATTTTGTTTTATAATATATTTATATTTTTTGTATTTTTATATTTATTAT
1 TATTTTATTATAATTTATTTTGTTTAATAATATATATATACTTTATGTATTATTATATCTATTAT
16700819 TTATATATA
66 TTATATATA
16700828 TATTTTATTATAATTTA-TTTG-TTAAT-ATATATATATACTTTAT-TATTATT-TATCTATTAT
1 TATTTTATTATAATTTATTTTGTTTAATAATATATATATACTTTATGTATTATTATATCTATTAT
16700888 T
66 T
16700889 ATTACTATTT
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
69 10 0.19
70 6 0.11
71 14 0.26
72 4 0.08
73 4 0.08
74 15 0.28
ACGTcount: A:0.30, C:0.01, G:0.02, T:0.67
Consensus pattern (74 bp):
TATTTTATTATAATTTATTTTGTTTAATAATATATATATACTTTATGTATTATTATATCTATTAT
TTATATATA
Found at i:16700892 original size:20 final size:20
Alignment explanation
Indices: 16700867--16700931 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
16700857 TATATATACT
16700867 TTATTATTATTTATCTATTA
1 TTATTATTATTTATCTATTA
*
16700887 TTATTACTATTTATCTATTA
1 TTATTATTATTTATCTATTA
*
16700907 --ATTAATATATTATCT-TTA
1 TTATTATTAT-TTATCTATTA
16700925 TT-TTATT
1 TTATTATT
16700932 TTATTTTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 10 0.26
19 10 0.26
20 19 0.49
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (20 bp):
TTATTATTATTTATCTATTA
Found at i:16700899 original size:55 final size:52
Alignment explanation
Indices: 16700807--16700932 Score: 132
Period size: 55 Copynumber: 2.3 Consensus size: 52
16700797 TTTGTATTTT
* * *
16700807 TATA-TTTATTATTTATATATATATTTTATTATAATTTATTTGTTAATATATATA
1 TATACTTTATTA-TTATTTATATATTTTATTATAATTTATCTATTAAT-TA-ATA
*
16700861 TATACTTTATTATTATTTATCTATTATTATTACT-ATTTATCTATTAATTAATA
1 TATACTTTATTATTATTTATATATT-TTATTA-TAATTTATCTATTAATTAATA
16700914 TATTATCTTTATT-TTATTT
1 TA-TA-CTTTATTATTATTT
16700933 TATTTTATTT
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
53 5 0.08
54 25 0.40
55 32 0.51
56 1 0.02
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (52 bp):
TATACTTTATTATTATTTATATATTTTATTATAATTTATCTATTAATTAATA
Found at i:16703612 original size:3 final size:3
Alignment explanation
Indices: 16703604--16703646 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
16703594 TGTCCAGATC
*
16703604 TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA -AA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
16703647 TATATTTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:16704039 original size:5 final size:6
Alignment explanation
Indices: 16704022--16704046 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
16704012 AAACAGAAAC
16704022 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
16704047 AATAATAGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:16705178 original size:17 final size:17
Alignment explanation
Indices: 16705158--16705221 Score: 78
Period size: 17 Copynumber: 3.9 Consensus size: 17
16705148 TTCTAAAACT
*
16705158 CCTAAAATTCAAAATCC
1 CCTAAAATCCAAAATCC
*
16705175 CCTAAAATCTAAAAT--
1 CCTAAAATCCAAAATCC
* *
16705190 CCTAAAAGCCAAAACCC
1 CCTAAAATCCAAAATCC
16705207 CCTAAAATCCAAAAT
1 CCTAAAATCCAAAAT
16705222 TTTAAAATTC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
15 12 0.32
17 26 0.68
ACGTcount: A:0.50, C:0.30, G:0.02, T:0.19
Consensus pattern (17 bp):
CCTAAAATCCAAAATCC
Found at i:16705193 original size:32 final size:32
Alignment explanation
Indices: 16705149--16705236 Score: 113
Period size: 32 Copynumber: 2.7 Consensus size: 32
16705139 ATCCTAGGTT
16705149 TCTAAAACTCCTAAAATTCAAAATCCCCTAAAA
1 TCTAAAA-TCCTAAAATTCAAAATCCCCTAAAA
** *
16705182 TCTAAAATCCTAAAAGCCAAAACCCCCTAAAA
1 TCTAAAATCCTAAAATTCAAAATCCCCTAAAA
* **
16705214 TCCAAAATTTTAAAATTCAAAAT
1 TCTAAAATCCTAAAATTCAAAAT
16705237 TTTAAAACCG
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
32 39 0.85
33 7 0.15
ACGTcount: A:0.50, C:0.25, G:0.01, T:0.24
Consensus pattern (32 bp):
TCTAAAATCCTAAAATTCAAAATCCCCTAAAA
Found at i:16705229 original size:15 final size:15
Alignment explanation
Indices: 16705209--16705243 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
16705199 CAAAACCCCC
16705209 TAAAATCCAAAATTT
1 TAAAATCCAAAATTT
*
16705224 TAAAATTCAAAATTT
1 TAAAATCCAAAATTT
16705239 TAAAA
1 TAAAA
16705244 CCGAAACCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (15 bp):
TAAAATCCAAAATTT
Found at i:16713811 original size:22 final size:22
Alignment explanation
Indices: 16713772--16713840 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
16713762 TTGAGATTTG
* * *
16713772 TAAGTCCTTCGGGTATAATCTT
1 TAAGACCTCCGGGCATAATCTT
* *
16713794 TAAGATCTCTGGGCATAAT-TT
1 TAAGACCTCCGGGCATAATCTT
16713815 TCAAGACCTCCGGGCATAATCTT
1 T-AAGACCTCCGGGCATAATCTT
16713838 TAA
1 TAA
16713841 AGCCTTTATG
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 3 0.08
22 32 0.84
23 3 0.08
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (22 bp):
TAAGACCTCCGGGCATAATCTT
Found at i:16714182 original size:22 final size:22
Alignment explanation
Indices: 16714157--16714198 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
16714147 TCGATTCTGC
*
16714157 AAGACCTCCGAACATGATTTCT
1 AAGACCTCCGAACATAATTTCT
*
16714179 AAGACCTCCGAGCATAATTT
1 AAGACCTCCGAACATAATTT
16714199 TGATTCGCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.26
Consensus pattern (22 bp):
AAGACCTCCGAACATAATTTCT
Found at i:16714258 original size:110 final size:109
Alignment explanation
Indices: 16714062--16714369 Score: 354
Period size: 110 Copynumber: 2.8 Consensus size: 109
16714052 TCAAAGATGA
* * * ** * * * *
16714062 GATTTTTAAGACTTCCGAGCATATTTTCGATTTGTAATGTTATCTCGATCGATTCCTTATCTTTC
1 GATTTCTAAGACCTCCGAGCATATTTT-GATTCGCGATGTTATCCCGATCGATTTCTTATTTTTT
*
16714127 GACTTGTGGTGTTATCTCAGTCGATTCTGCAAGACCTCCGAACAT
65 GACTTGTGGTGTTATCACAGTCGATTCTGCAAGACCTCCGAACAT
16714172 GATTTCTAAGACCTCCGAGCATAATTTTGATTCGCGATGTTATCCCGATCGATTTCTTATTTTTT
1 GATTTCTAAGACCTCCGAGCAT-ATTTTGATTCGCGATGTTATCCCGATCGATTTCTTATTTTTT
** * * * *
16714237 GACTTACGGTGTTATCCCAGTCGATTCTGTAAGACCTTCGGACAT
65 GACTTGTGGTGTTATCACAGTCGATTCTGCAAGACCTCCGAACAT
* ** * * * *
16714282 AATTTCTAAGACCTCCGAGC--A-TTCAATTCACGGTGTTATCCC-ATTCAATTTTTTATTTTTT
1 GATTTCTAAGACCTCCGAGCATATTTTGATTCGCGATGTTATCCCGA-TCGATTTCTTATTTTTT
16714343 GACTTGTGGTGTTATCACAGTCGATTC
65 GACTTGTGGTGTTATCACAGTCGATTC
16714370 CGTAAGACTT
Statistics
Matches: 171, Mismatches: 25, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
105 1 0.01
106 56 0.33
107 1 0.01
110 108 0.63
111 5 0.03
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.40
Consensus pattern (109 bp):
GATTTCTAAGACCTCCGAGCATATTTTGATTCGCGATGTTATCCCGATCGATTTCTTATTTTTTG
ACTTGTGGTGTTATCACAGTCGATTCTGCAAGACCTCCGAACAT
Found at i:16714617 original size:110 final size:108
Alignment explanation
Indices: 16714383--16714708 Score: 338
Period size: 109 Copynumber: 3.0 Consensus size: 108
16714373 AAGACTTCTG
* * * * *
16714383 GGCATAATTTTGATTCGCGATGTTATCCCGATCGATTCTTCATTTTTTGACTTATGA-GATTTGT
1 GGCATAAATTCGATTCGCGGTGTTATCTCGATCGATTCTT-ATTTTTTGACTTACGATG--TTGT
* * * *
16714447 CCCAGTCGATTCTGTAAGACCTCCGGGCATGATTTCTAAGACCTCT
63 CTCAATCGATTCTGTAAGACCTCCGGACATGATTTCTAAGACCTCA
* * *
16714493 GAGAAT-AATTCGATTCGCGGTATTATCTCGATTGATTCTTGATTTTTTGACTTACGATGTTGTC
1 G-GCATAAATTCGATTCGCGGTGTTATCTCGATCGATTCTT-ATTTTTTGACTTACGATGTTGTC
** *
16714557 TCAATCGATTCTGTAAGATTTTCGGACATGATTTCTAAGACCTCCA
64 TCAATCGATTCTGTAAGACCTCCGGACATGATTTCTAAGACCT-CA
* * * *
16714603 GGCATAAATTCGATTCGCAGTGTTGTCTCGATCGATTCATTA-TTTTTGACTTACGGTGTTATCT
1 GGCATAAATTCGATTCGCGGTGTTATCTCGATCGATTC-TTATTTTTTGACTTACGATGTTGTCT
** *
16714667 TGATCGATTCTATAAGACCTCC-GAGCATGA-TTCTTAAGACCT
65 CAATCGATTCTGTAAGACCTCCGGA-CATGATTTC-TAAGACCT
16714709 TCGAACATGA
Statistics
Matches: 180, Mismatches: 29, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
108 5 0.03
109 94 0.52
110 75 0.42
111 6 0.03
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.39
Consensus pattern (108 bp):
GGCATAAATTCGATTCGCGGTGTTATCTCGATCGATTCTTATTTTTTGACTTACGATGTTGTCTC
AATCGATTCTGTAAGACCTCCGGACATGATTTCTAAGACCTCA
Found at i:16714706 original size:22 final size:22
Alignment explanation
Indices: 16714672--16714738 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
16714662 TATCTTGATC
*
16714672 GATTCTATAAGACCTCCGAGCAT
1 GATTCT-TAAGACCTCCGAACAT
*
16714695 GATTCTTAAGACCTTCGAACAT
1 GATTCTTAAGACCTCCGAACAT
* * *
16714717 GATTTTTAAGATCTCCGGACAT
1 GATTCTTAAGACCTCCGAACAT
16714739 AAATTTAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
22 32 0.84
23 6 0.16
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.31
Consensus pattern (22 bp):
GATTCTTAAGACCTCCGAACAT
Found at i:16715976 original size:14 final size:14
Alignment explanation
Indices: 16715954--16715985 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
16715944 AAAAAATTTT
*
16715954 TTTTCTTTTTTAAA
1 TTTTATTTTTTAAA
16715968 TTTTATTTTTTAAA
1 TTTTATTTTTTAAA
16715982 TTTT
1 TTTT
16715986 TTATATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTATTTTTTAAA
Found at i:16716454 original size:17 final size:15
Alignment explanation
Indices: 16716428--16716479 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
16716418 CTAGGTTTTT
16716428 AAAATCCCTAAAATCC
1 AAAAT-CCTAAAATCC
*
16716444 AAAATTTCCTAAAATCT
1 AAAA--TCCTAAAATCC
*
16716461 AAAATCCTAAAATTC
1 AAAATCCTAAAATCC
16716476 AAAA
1 AAAA
16716480 ATTTAAAACC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 13 0.42
16 4 0.13
17 13 0.42
18 1 0.03
ACGTcount: A:0.54, C:0.21, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAATCCTAAAATCC
Found at i:16716472 original size:8 final size:8
Alignment explanation
Indices: 16716427--16716473 Score: 53
Period size: 7 Copynumber: 5.8 Consensus size: 8
16716417 CCTAGGTTTT
16716427 TAAAATCCC
1 TAAAAT-CC
16716436 TAAAATCC
1 TAAAATCC
16716444 -AAAATTTCC
1 TAAAA--TCC
16716453 TAAAAT-C
1 TAAAATCC
16716460 TAAAATCC
1 TAAAATCC
16716468 TAAAAT
1 TAAAAT
16716474 TCAAAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
7 11 0.32
8 10 0.29
9 9 0.26
10 4 0.12
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (8 bp):
TAAAATCC
Found at i:16716554 original size:29 final size:29
Alignment explanation
Indices: 16716477--16716590 Score: 106
Period size: 30 Copynumber: 3.8 Consensus size: 29
16716467 CTAAAATTCA
* * *
16716477 AAAATTTAAAACCGAAACCTTAAAATCTTC
1 AAAACTTAAAACC-AAACCCTAAAACCTTC
*
16716507 -AAACTCTAAAATCAAAACCCT-AAACCTTC
1 AAAACT-TAAAA-CCAAACCCTAAAACCTTC
* *
16716536 CATACATTAAAACCAAACCCTAAAACCTTC
1 AAAAC-TTAAAACCAAACCCTAAAACCTTC
*
16716566 AAAACTTAAATCCAAACCCTTAAAA
1 AAAACTTAAAACCAAACCC-TAAAA
16716591 TCTAAATCTT
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
29 32 0.46
30 35 0.51
31 2 0.03
ACGTcount: A:0.50, C:0.27, G:0.01, T:0.22
Consensus pattern (29 bp):
AAAACTTAAAACCAAACCCTAAAACCTTC
Found at i:16718066 original size:28 final size:29
Alignment explanation
Indices: 16718021--16718091 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
16718011 TTATATCTAA
*
16718021 TAAATTATAAATATAAAT-GAAAAATTTATT
1 TAAA-TAT-AATAAAAATAGAAAAATTTATT
*
16718051 TAAATATAATAAAAATATAAAAATTTATT
1 TAAATATAATAAAAATAGAAAAATTTATT
*
16718080 TAAACA-AATAAA
1 TAAATATAATAAA
16718092 TACTTTAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 14 0.38
29 19 0.51
30 4 0.11
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (29 bp):
TAAATATAATAAAAATAGAAAAATTTATT
Found at i:16718485 original size:23 final size:25
Alignment explanation
Indices: 16718454--16718508 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 25
16718444 ACAAATAAAT
*
16718454 TAAATAAATTTT-AAATTT-AAAAA
1 TAAAAAAATTTTCAAATTTGAAAAA
* *
16718477 TAAAAAAATTTTCAATTTTGAAACA
1 TAAAAAAATTTTCAAATTTGAAAAA
16718502 TAAAAAA
1 TAAAAAA
16718509 GAGGTGAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 11 0.41
24 5 0.19
25 11 0.41
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (25 bp):
TAAAAAAATTTTCAAATTTGAAAAA
Found at i:16719665 original size:166 final size:158
Alignment explanation
Indices: 16719400--16719722 Score: 522
Period size: 166 Copynumber: 2.0 Consensus size: 158
16719390 CAATTTCTTT
16719400 AAATACTCACATAAAATAATTATTTATAATAATAATTTTTTTCTTAAAATATATTAATAATATAT
1 AAATACTCACATAAAATAATTATTTATAATAATAATTTTTTTCTTAAAATATATTAATAATATAT
*
16719465 AAAAAAGATTTTTAGGTGTAATATATAAAAACAAAATTCACAATTATAATAAG-AAAAAATGTTA
66 AAAAAAGATTTTTAGGTGTAATAGATAAAAACAAAATTCACAATTATAATAAGAAAAAAATGTTA
16719529 TAATAAGAACATATAACATATAATAAGC
131 TAATAAGAACATATAACATATAATAAGC
*
16719557 AAATACTCATATAAAATAATTATTTATAATAATAATTTTTTTCTTAAAATATATAAAATATATTA
1 AAATACTCACATAAAATAATTATTTATAATAATAATTTTTTTCTT-AAA-ATAT---AT-TA--A
16719622 CTAATATATAAAAAAGATTTTTAGGTGTAATAGATAAAAACAAAATTCACAATTATAATAAGAAA
58 -TAATATATAAAAAAGATTTTTAGGTGTAATAGATAAAAACAAAATTCACAATTATAATAAGAAA
* *
16719687 AAAATGTTATAATAAGAACGTGTAACATATAATAAG
122 AAAATGTTATAATAAGAACATATAACATATAATAAG
16719723 AAAAAATATT
Statistics
Matches: 152, Mismatches: 4, Indels: 10
0.92 0.02 0.06
Matches are distributed among these distances:
157 44 0.29
158 3 0.02
159 4 0.03
162 2 0.01
163 2 0.01
165 1 0.01
166 60 0.39
167 36 0.24
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (158 bp):
AAATACTCACATAAAATAATTATTTATAATAATAATTTTTTTCTTAAAATATATTAATAATATAT
AAAAAAGATTTTTAGGTGTAATAGATAAAAACAAAATTCACAATTATAATAAGAAAAAAATGTTA
TAATAAGAACATATAACATATAATAAGC
Found at i:16719861 original size:17 final size:15
Alignment explanation
Indices: 16719821--16719851 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
16719811 AAATACTCAC
16719821 ATAAAATAATTTTTT
1 ATAAAATAATTTTTT
16719836 ATAACAATAATTTTTT
1 ATAA-AATAATTTTTT
16719852 TCTTAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (15 bp):
ATAAAATAATTTTTT
Found at i:16719921 original size:15 final size:17
Alignment explanation
Indices: 16719903--16719936 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
16719893 AATAAAATTT
16719903 AAAA-TTATAATAAGAA
1 AAAAGTTATAATAAGAA
16719919 AAAATGTTATAATAAGAA
1 AAAA-GTTATAATAAGAA
16719937 CATTTAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
18 12 0.75
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (17 bp):
AAAAGTTATAATAAGAA
Found at i:16720055 original size:9 final size:9
Alignment explanation
Indices: 16720028--16720061 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
16720018 CTAAATTTTT
16720028 TTTTATATA
1 TTTTATATA
16720037 TTATTAATATA
1 TT-TT-ATATA
16720048 TTTTATATA
1 TTTTATATA
16720057 TTTTA
1 TTTTA
16720062 AGAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 12 0.52
10 4 0.17
11 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTTATATA
Found at i:16720566 original size:128 final size:128
Alignment explanation
Indices: 16720415--16720669 Score: 393
Period size: 128 Copynumber: 2.0 Consensus size: 128
16720405 ATATAATTAT
*
16720415 ATGAAAGAGAGAATACCTCTTCTTTTAATTTTAAAAGATACTAATTGTACCAAGTTTCGAGCTGA
1 ATGAAAGAGAGAATACCTCTTCTTCTAATTTTAAAAGATACTAATTGTACCAAGTTTCGAGCTGA
* * * * ** *
16720480 GAGTTTTCCTATCCTAATGCCAAGGGTCAATTCGGCTCCTTTAGGTACGTACCAAGCTTATAG
66 AAATTCTCCTATCCTAATGCCAAGGGTCAATTCGACTCCTCCAGCTACGTACCAAGCTTATAG
* * *
16720543 ATGAAAGAGAGAATATCTCTTCTTCTAATTTTAAAAGATACTAATTGTGCCGAGTTTCGAGCTGA
1 ATGAAAGAGAGAATACCTCTTCTTCTAATTTTAAAAGATACTAATTGTACCAAGTTTCGAGCTGA
* *
16720608 AAATTCTCCTGTCCTAATGCCAAGGGTCAGTTCGACTCCTCCAGCTACGTACCAAGCTTATA
66 AAATTCTCCTATCCTAATGCCAAGGGTCAATTCGACTCCTCCAGCTACGTACCAAGCTTATA
16720670 TCGTCAACCA
Statistics
Matches: 114, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
128 114 1.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (128 bp):
ATGAAAGAGAGAATACCTCTTCTTCTAATTTTAAAAGATACTAATTGTACCAAGTTTCGAGCTGA
AAATTCTCCTATCCTAATGCCAAGGGTCAATTCGACTCCTCCAGCTACGTACCAAGCTTATAG
Found at i:16725348 original size:2 final size:2
Alignment explanation
Indices: 16725341--16725370 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16725331 AAGTGTCAAC
16725341 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16725371 GAATGTGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16726802 original size:21 final size:22
Alignment explanation
Indices: 16726766--16726807 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
16726756 CTTTTCATTT
16726766 TATTTTGAATAAAAATAATTAA
1 TATTTTGAATAAAAATAATTAA
*
16726788 TATTTT-AATATAAATAATTA
1 TATTTTGAATAAAAATAATTA
16726808 TTATCAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TATTTTGAATAAAAATAATTAA
Found at i:16726826 original size:24 final size:25
Alignment explanation
Indices: 16726767--16726835 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 25
16726757 TTTTCATTTT
16726767 ATTTTGAATAAAAATAATTA--AT--
1 ATTTT-AATAAAAATAATTATTATCA
*
16726789 ATTTTAATATAAATAATTATTATCA
1 ATTTTAATAAAAATAATTATTATCA
* *
16726814 ATTTTAA-AAAAATCATTTTTAT
1 ATTTTAATAAAAATAATTATTAT
16726836 ATATTGTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 13 0.33
22 5 0.13
23 2 0.05
24 12 0.31
25 7 0.18
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46
Consensus pattern (25 bp):
ATTTTAATAAAAATAATTATTATCA
Found at i:16727100 original size:21 final size:20
Alignment explanation
Indices: 16727067--16727111 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
16727057 ATTTCATCAC
*
16727067 TAAT-TTTAATTTACTGTTA
1 TAATATTTAATTTACTATTA
*
16727086 TAATATTTAATTTTATTATTA
1 TAATATTTAA-TTTACTATTA
16727107 TAATA
1 TAATA
16727112 ACTAATCTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 5 0.23
21 13 0.59
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (20 bp):
TAATATTTAATTTACTATTA
Found at i:16728713 original size:29 final size:29
Alignment explanation
Indices: 16728681--16728740 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
16728671 TGTCAATAAG
16728681 CACTCCCTTTATTGTGATTATAAAACTTA
1 CACTCCCTTTATTGTGATTATAAAACTTA
16728710 CACTCCCTTTATTGTGATTATAAAACTTA
1 CACTCCCTTTATTGTGATTATAAAACTTA
16728739 CA
1 CA
16728741 TTTTACTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.40
Consensus pattern (29 bp):
CACTCCCTTTATTGTGATTATAAAACTTA
Found at i:16729460 original size:23 final size:23
Alignment explanation
Indices: 16729434--16729479 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
16729424 ATATTATCCA
16729434 AAAAAAGTATAA-TTATTTATAAT
1 AAAAAAGTATAACTT-TTTATAAT
* *
16729457 AAAAAATTTTAACTTTTTATAAT
1 AAAAAAGTATAACTTTTTATAAT
16729480 GCGATGATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
AAAAAAGTATAACTTTTTATAAT
Found at i:16742165 original size:15 final size:15
Alignment explanation
Indices: 16742147--16742177 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
16742137 TATTAGTTTT
*
16742147 ATTCTCGTTCTTATA
1 ATTCTCATTCTTATA
16742162 ATTCTCATTCTTATA
1 ATTCTCATTCTTATA
16742177 A
1 A
16742178 CTGCGGAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.19, G:0.03, T:0.52
Consensus pattern (15 bp):
ATTCTCATTCTTATA
Found at i:16743112 original size:36 final size:36
Alignment explanation
Indices: 16743072--16743145 Score: 112
Period size: 36 Copynumber: 2.1 Consensus size: 36
16743062 AAAGATAACA
* *
16743072 AACTTTAGCTGATTGACAAACCTCAACACATAACGC
1 AACTTTAGCTGATTAACAAACCTCAACACATAAAGC
* *
16743108 AACTTTAGCTGATTAAGAAACCTCAACGCATAAAGC
1 AACTTTAGCTGATTAACAAACCTCAACACATAAAGC
16743144 AA
1 AA
16743146 TTGGAAGACC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.42, C:0.24, G:0.12, T:0.22
Consensus pattern (36 bp):
AACTTTAGCTGATTAACAAACCTCAACACATAAAGC
Found at i:16746898 original size:61 final size:57
Alignment explanation
Indices: 16746826--16746941 Score: 151
Period size: 61 Copynumber: 2.0 Consensus size: 57
16746816 AATTTCAAAG
* * *
16746826 AAAATTAATACTTTTAACTTTTTCTCAAAAAGAAACCTTTTTTTTTAATTTATTTTTAAGA
1 AAAATTAATACTTTCAACTTTTCCTCAAAAA-AAA--TTTTTTTTGAATTT-TTTTTAAGA
* *
16746887 AAAATTGATACTTTCAACTTTTCCTCAAAAATAATTTTTTTTGAATTTTTTTTAA
1 AAAATTAATACTTTCAACTTTTCCTCAAAAAAAATTTTTTTTGAATTTTTTTTAA
16746942 AAATAAAATA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
57 7 0.14
58 13 0.26
60 2 0.04
61 28 0.56
ACGTcount: A:0.36, C:0.10, G:0.03, T:0.50
Consensus pattern (57 bp):
AAAATTAATACTTTCAACTTTTCCTCAAAAAAAATTTTTTTTGAATTTTTTTTAAGA
Found at i:16746957 original size:13 final size:13
Alignment explanation
Indices: 16746941--16746965 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16746931 ATTTTTTTTA
16746941 AAAATAAAATAAT
1 AAAATAAAATAAT
16746954 AAAATAAAATAA
1 AAAATAAAATAA
16746966 ACAAAGTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATAAAATAAT
Found at i:16747074 original size:22 final size:23
Alignment explanation
Indices: 16747032--16747080 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
16747022 AAACAATTCT
16747032 AATATAATAATAATAACAAAAAA
1 AATATAATAATAATAACAAAAAA
16747055 AATA-AATAAATAATGAA-AAAAAA
1 AATATAAT-AATAAT-AACAAAAAA
16747078 AAT
1 AAT
16747081 CTAGGAACGG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 3 0.12
23 19 0.79
24 2 0.08
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (23 bp):
AATATAATAATAATAACAAAAAA
Found at i:16747364 original size:21 final size:22
Alignment explanation
Indices: 16747329--16747372 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
16747319 TTCAGTAGAA
*
16747329 CCCTTCCTCTCTTCTCTCTCTT
1 CCCTTCCTCTCTTCTCTCCCTT
*
16747351 CCCTT-CTTTCTTCTCTCCCTT
1 CCCTTCCTCTCTTCTCTCCCTT
16747372 C
1 C
16747373 TCTCTAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (22 bp):
CCCTTCCTCTCTTCTCTCCCTT
Found at i:16747619 original size:11 final size:11
Alignment explanation
Indices: 16747605--16747634 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
16747595 ATTTTCAAAA
16747605 AAAAAATTCGT
1 AAAAAATTCGT
16747616 -AAAAATTCGT
1 AAAAAATTCGT
16747626 AAAAAATTC
1 AAAAAATTC
16747635 TTACCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.27
Consensus pattern (11 bp):
AAAAAATTCGT
Found at i:16747931 original size:12 final size:13
Alignment explanation
Indices: 16747910--16747961 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 13
16747900 AAGAAAGAAG
* *
16747910 AAAAGAAAAAAAT
1 AAAATAAAATAAT
16747923 AAAATAAAATAA-
1 AAAATAAAATAAT
*
16747935 ATAATAAAATAAT
1 AAAATAAAATAAT
*
16747948 AAAA-AAGATAAT
1 AAAATAAAATAAT
16747960 AA
1 AA
16747962 TAAGGATAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
12 20 0.61
13 13 0.39
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (13 bp):
AAAATAAAATAAT
Found at i:16747969 original size:12 final size:11
Alignment explanation
Indices: 16747921--16748022 Score: 50
Period size: 12 Copynumber: 8.8 Consensus size: 11
16747911 AAAGAAAAAA
*
16747921 ATAA-AATAAA
1 ATAATAATAAG
*
16747931 ATAAATAATAAA
1 AT-AATAATAAG
*
16747943 ATAATAAAAAAG
1 ATAAT-AATAAG
16747955 ATAATAATAAGG
1 ATAATAATAA-G
16747967 ATAATATATTAA-
1 ATAATA-A-TAAG
*
16747979 TTAATAGATAA-
1 ATAATA-ATAAG
*
16747990 ATAATAATATAT
1 ATAATAATA-AG
16748002 ATAAATAGATAA-
1 AT-AATA-ATAAG
16748014 ATAATAATA
1 ATAATAATA
16748023 CATATATCTA
Statistics
Matches: 76, Mismatches: 6, Indels: 20
0.75 0.06 0.20
Matches are distributed among these distances:
10 8 0.11
11 22 0.29
12 34 0.45
13 6 0.08
14 6 0.08
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (11 bp):
ATAATAATAAG
Found at i:16747993 original size:4 final size:4
Alignment explanation
Indices: 16747981--16748140 Score: 55
Period size: 4 Copynumber: 40.0 Consensus size: 4
16747971 TATATTAATT
* * * *
16747981 AATA GATA AAT- AATA ATATA TATA AATA GATA AAT- AAT- AATA CATA
1 AATA AATA AATA AATA A-ATA AATA AATA AATA AATA AATA AATA AATA
* * * * * * * * *
16748027 TATC TATC AATA GATA AAT- AATA AAAA TAATAA AATA AATA TATA TATT
1 AATA AATA AATA AATA AATA AATA AATA -AAT-A AATA AATA AATA AATA
* * *
16748076 AATA AATA GTAAT- AATA AATA AATG AAT- AATA AATA CATAA AATA CA-A
1 AATA AATA --AATA AATA AATA AATA AATA AATA AATA AAT-A AATA AATA
*
16748124 AATA AAGTA AAAA AATA
1 AATA AA-TA AATA AATA
16748141 TAAGAGATAC
Statistics
Matches: 117, Mismatches: 26, Indels: 26
0.69 0.15 0.15
Matches are distributed among these distances:
3 20 0.17
4 78 0.67
5 15 0.13
6 4 0.03
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (4 bp):
AATA
Found at i:16748018 original size:47 final size:43
Alignment explanation
Indices: 16747930--16748111 Score: 120
Period size: 47 Copynumber: 3.8 Consensus size: 43
16747920 AATAAAATAA
*
16747930 AATAAATA-ATAAAATAATAAAAAAGATAATAATAAGGATAATATATT
1 AATAAATAGAT-AAATAAT-AAATA-ATAATAATAA--ATAATATATT
*
16747977 AATTAATAGATAAATAATAATATATATAAATAGATAAATAATAATACATAT
1 AATAAATAGATAAATAATAA-ATA-AT-AATA-ATAAATAAT-AT--AT-T
*
16748028 ATCTATCAATAGATAAATAATAAA-AATAATAAAATAAATATATATATT
1 A---ATAAATAGATAAATAATAAATAATAAT--AATAAATA-ATATATT
16748076 AATAAATAG-T-AATAATAAATAAATGAATAATAAATA
1 AATAAATAGATAAATAATAAAT-AAT-AATAATAAATA
16748112 CATAAAATAC
Statistics
Matches: 113, Mismatches: 5, Indels: 37
0.73 0.03 0.24
Matches are distributed among these distances:
43 9 0.08
44 9 0.08
45 10 0.09
46 5 0.04
47 23 0.20
48 10 0.09
49 6 0.05
50 5 0.04
51 13 0.12
52 4 0.04
53 1 0.01
54 18 0.16
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (43 bp):
AATAAATAGATAAATAATAAATAATAATAATAAATAATATATT
Found at i:16748047 original size:30 final size:24
Alignment explanation
Indices: 16747967--16748028 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 24
16747957 AATAATAAGG
*
16747967 ATAATATATTAATTAATAGATAAATA
1 ATAATATA-T-ATAAATAGATAAATA
16747993 ATAATATATATAAATAGATAAATA
1 ATAATATATATAAATAGATAAATA
*
16748017 ATAATACATATA
1 ATAATATATATA
16748029 TCTATCAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 25 0.74
25 1 0.03
26 8 0.24
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (24 bp):
ATAATATATATAAATAGATAAATA
Found at i:16748096 original size:41 final size:42
Alignment explanation
Indices: 16748002--16748111 Score: 71
Period size: 45 Copynumber: 2.5 Consensus size: 42
16747992 AATAATATAT
* * * *
16748002 ATAAATAGAT-AAATAATAATACATATATCTATCAATAGATAAATA
1 ATAAATA-ATAAAAT-A-AATATATATATCAATAAATAAAT-AATA
* *
16748047 ATAAAAATAATAAAATAAATATATATATTAATAAAT-AGTAATA
1 AT--AAATAATAAAATAAATATATATATCAATAAATAAATAATA
16748090 ATAAATAAATGAATAATAAATA
1 ATAAAT-AAT-AA-AATAAATA
16748112 CATAAAATAC
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
41 4 0.08
42 3 0.06
43 8 0.15
44 9 0.17
45 17 0.32
46 3 0.06
47 9 0.17
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.31
Consensus pattern (42 bp):
ATAAATAATAAAATAAATATATATATCAATAAATAAATAATA
Found at i:16748511 original size:42 final size:42
Alignment explanation
Indices: 16748449--16748858 Score: 286
Period size: 41 Copynumber: 10.0 Consensus size: 42
16748439 TTGATCAAAA
* * *
16748449 CTCCTCTAAACAGAGACTCAACGACTTTTGAAAAATAAATGG
1 CTCCTCTAATCAGAGGCTCAACGACTTTAGAAAAATAAATGG
* *
16748491 CTCCTATAATCAGAGGCTCAACGACTTT-GAAAAATAAATTG
1 CTCCTCTAATCAGAGGCTCAACGACTTTAGAAAAATAAATGG
* *
16748532 TTCCTTTAATCAGAGGCTCAACGACTTTAGAAAAATAAATGG
1 CTCCTCTAATCAGAGGCTCAACGACTTTAGAAAAATAAATGG
16748574 CTCCTCTAATCAGAGGCTCAACGACTTTAGAAAAATAAATGG
1 CTCCTCTAATCAGAGGCTCAACGACTTTAGAAAAATAAATGG
* * * * * *
16748616 CTCCTCCAATTAGAGGCT-TA--ACTTTTGAAAAGTAAATTG
1 CTCCTCTAATCAGAGGCTCAACGACTTTAGAAAAATAAATGG
* ** * * ** * *
16748655 TTAATCTAAAT-AGAGGCACCATAACTTT-GAAAAGTAAATTG
1 CTCCTCT-AATCAGAGGCTCAACGACTTTAGAAAAATAAATGG
* * * ** * *
16748696 TTCCTCTAAAT-AGAGGCACCATAACTTT-GAAAAGTAAATTG
1 CTCCTCT-AATCAGAGGCTCAACGACTTTAGAAAAATAAATGG
* * * ** * * *
16748737 CTCCTCTAAACAGAGGCACCATAACTTTTGAAAAGTAAATTG
1 CTCCTCTAATCAGAGGCTCAACGACTTTAGAAAAATAAATGG
* * * * *
16748779 CTCCTCTAAAT-AGAGGCACCACAACTTTA-AAAAGTAAATTG
1 CTCCTCT-AATCAGAGGCTCAACGACTTTAGAAAAATAAATGG
* * * *
16748820 CTCCTCTAAAT-AAAGGCACCACAACTTT-GAAAAATAAAT
1 CTCCTCT-AATCAGAGGCTCAACGACTTTAGAAAAATAAAT
16748859 TACCCCTTGA
Statistics
Matches: 329, Mismatches: 30, Indels: 19
0.87 0.08 0.05
Matches are distributed among these distances:
39 25 0.08
40 6 0.02
41 162 0.49
42 134 0.41
43 2 0.01
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (42 bp):
CTCCTCTAATCAGAGGCTCAACGACTTTAGAAAAATAAATGG
Found at i:16748598 original size:83 final size:82
Alignment explanation
Indices: 16748449--16748859 Score: 350
Period size: 83 Copynumber: 5.0 Consensus size: 82
16748439 TTGATCAAAA
* * * * * * * * * *
16748449 CTCCTCTAAACAGAGACTCAACGACTTTTGAAAAATAAATGGCTCCTATAATCAGAGGCTCAACG
1 CTCCT-TAAATAGAGGCTCAACAACTTTAGAAAAGTAAATTGCTCCTCTAATCAGAGGCACCACA
16748514 ACTTTGAAAAATAAATTG
65 ACTTTGAAAAATAAATTG
* * * * * * * *
16748532 TTCCTTTAATCAGAGGCTCAACGACTTTAGAAAAATAAATGGCTCCTCTAATCAGAGGCTCAACG
1 CTCCTTAAAT-AGAGGCTCAACAACTTTAGAAAAGTAAATTGCTCCTCTAATCAGAGGCACCACA
*
16748597 ACTTTAGAAAAATAAATGG
65 ACTTT-GAAAAATAAATTG
* * * * * ** *
16748616 CTCCTCCAATTAGAGGCT---TAACTTTTGAAAAGTAAATTGTTAATCTAAAT-AGAGGCACCAT
1 CTCCT-TAAATAGAGGCTCAACAACTTTAGAAAAGTAAATTGCTCCTCT-AATCAGAGGCACCAC
*
16748677 AACTTTGAAAAGTAAATTG
64 AACTTTGAAAAATAAATTG
* * * * * *
16748696 TTCCTCTAAATAGAGGCACCATAACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGGCACCATA
1 CTCCT-TAAATAGAGGCTCAACAACTTTAGAAAAGTAAATTGCTCCTCTAATCAGAGGCACCACA
*
16748760 ACTTTTGAAAAGTAAATTG
65 AC-TTTGAAAAATAAATTG
* * *
16748779 CTCCTCTAAATAGAGGCACCACAACTTTA-AAAAGTAAATTGCTCCTCTAAAT-AAAGGCACCAC
1 CTCCT-TAAATAGAGGCTCAACAACTTTAGAAAAGTAAATTGCTCCTCT-AATCAGAGGCACCAC
16748842 AACTTTGAAAAATAAATT
64 AACTTTGAAAAATAAATT
16748860 ACCCCTTGAC
Statistics
Matches: 278, Mismatches: 39, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
80 25 0.09
81 35 0.13
82 51 0.18
83 140 0.50
84 25 0.09
85 2 0.01
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (82 bp):
CTCCTTAAATAGAGGCTCAACAACTTTAGAAAAGTAAATTGCTCCTCTAATCAGAGGCACCACAA
CTTTGAAAAATAAATTG
Found at i:16748790 original size:124 final size:124
Alignment explanation
Indices: 16748475--16748859 Score: 377
Period size: 124 Copynumber: 3.1 Consensus size: 124
16748465 CTCAACGACT
* * * * * ** * * **
16748475 TTTGAAAAATAAATGGCTCCTATAATCAGAGGCTCAACGAC-TTTGAAAAATAAATTGTTCCT-T
1 TTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCATAACTTTTGAAAAGTAAATTGCTAATCT
* * * * * * * * * *
16748538 TAATCAGAGGCTCAACGACTTTAGAAAAATAAATGGCTCCTCT-AATCAGAGGCTCAACGAC
66 AAAT-AGAGGCACCACAACTTTA-AAAAGTAAATTGCTCCTCTAAAT-AAAGGCACCACAAC
* * ** * *
16748599 TTTAGAAAAATAAATGGCTCCTCCAATTAGAGG---CTTAACTTTTGAAAAGTAAATTGTTAATC
1 TTT-GAAAAATAAATTGCTCCTCTAAACAGAGGCACCATAACTTTTGAAAAGTAAATTGCTAATC
* * * * *
16748661 TAAATAGAGGCACCATAACTTTGAAAAGTAAATTGTTCCTCTAAATAGAGGCACCATAAC
65 TAAATAGAGGCACCACAACTTTAAAAAGTAAATTGCTCCTCTAAATAAAGGCACCACAAC
* **
16748721 TTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCATAACTTTTGAAAAGTAAATTGCTCCTCT
1 TTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCATAACTTTTGAAAAGTAAATTGCTAATCT
16748786 AAATAGAGGCACCACAACTTTAAAAAGTAAATTGCTCCTCTAAATAAAGGCACCACAAC
66 AAATAGAGGCACCACAACTTTAAAAAGTAAATTGCTCCTCTAAATAAAGGCACCACAAC
16748845 TTTGAAAAATAAATT
1 TTTGAAAAATAAATT
16748860 ACCCCTTGAC
Statistics
Matches: 216, Mismatches: 38, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
121 24 0.11
122 31 0.14
123 34 0.16
124 101 0.47
125 26 0.12
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (124 bp):
TTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCATAACTTTTGAAAAGTAAATTGCTAATCT
AAATAGAGGCACCACAACTTTAAAAAGTAAATTGCTCCTCTAAATAAAGGCACCACAAC
Found at i:16750923 original size:11 final size:11
Alignment explanation
Indices: 16750907--16750931 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16750897 GACATTTATT
16750907 TTTTCTTTTTC
1 TTTTCTTTTTC
16750918 TTTTCTTTTTC
1 TTTTCTTTTTC
16750929 TTT
1 TTT
16750932 CCATCTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:16754724 original size:58 final size:58
Alignment explanation
Indices: 16754487--16754761 Score: 299
Period size: 59 Copynumber: 4.7 Consensus size: 58
16754477 TTGTACAGGA
* ** *
16754487 GAAAATTGATACTTTCAAC-TTTTCTCCCAAAATTTTTTTTTGAAAACTTTAATTTCAAG
1 GAAAATTGATACTTTCAACTTTTTCT-CAAAAATAATTTTTT-AAAAATTTAATTTCAAG
* * * * *
16754546 GAAAATTGATACTTTCAACTTTTTCTCAAAAAGAAACCTTTTTT--TAATTTATTTTTAAA
1 GAAAATTGATACTTTCAACTTTTTCTCAAAAA-TAA--TTTTTTAAAAATTTAATTTCAAG
* * * *
16754605 GAAAATTGATACTTTCAAC-TTTTCTCCAAAAAT-ATTTTTTGAAACTTTAATTTCGAT
1 GAAAATTGATACTTTCAACTTTTTCT-CAAAAATAATTTTTTAAAAATTTAATTTCAAG
* **
16754662 GAAAATTGATACTTTCAACTTTTTCTCAAAAATAATTTTTTAAAAATTTATTTTTGAG
1 GAAAATTGATACTTTCAACTTTTTCTCAAAAATAATTTTTTAAAAATTTAATTTCAAG
*
16754720 GAAAATTGATACTTTCAACTTTTCCTCAAAAATAAATTTTTT
1 GAAAATTGATACTTTCAACTTTTTCTCAAAAAT-AATTTTTT
16754762 TGAATTTTTT
Statistics
Matches: 184, Mismatches: 22, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
55 6 0.03
57 36 0.20
58 63 0.34
59 67 0.36
60 6 0.03
62 6 0.03
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (58 bp):
GAAAATTGATACTTTCAACTTTTTCTCAAAAATAATTTTTTAAAAATTTAATTTCAAG
Found at i:16754760 original size:116 final size:116
Alignment explanation
Indices: 16754486--16754753 Score: 391
Period size: 115 Copynumber: 2.3 Consensus size: 116
16754476 TTTGTACAGG
* *
16754486 AGAAAATTGATACTTTCAACTTTTCTCCCAAAATTTTTTTTTGAAAACTTTAATTTCAAGGAAAA
1 AGAAAATTGATACTTTCAACTTTTCT-CCAAAAATATTTTTTGAAAACTTTAATTTCAAGGAAAA
*
16754551 TTGATACTTTCAACTTTTTCTCAAAAAGAAACCTTTTTTTAATTTATTTTTAA
65 TTGATACTTTCAACTTTTTCTCAAAAAGAAA-CTTTTTTAAATTTATTTTTAA
* *
16754604 AGAAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTG-AAACTTTAATTTCGATGAAAAT
1 AGAAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTGAAAACTTTAATTTCAAGGAAAAT
* *
16754668 TGATACTTTCAACTTTTTCTCAAAAA-TAA-TTTTTTAAAAATTTATTTTTGA
66 TGATACTTTCAACTTTTTCTCAAAAAGAAACTTTTTT--AAATTTATTTTTAA
*
16754719 GGAAAATTGATACTTTCAACTTTTC-CTCAAAAATA
1 AGAAAATTGATACTTTCAACTTTTCTC-CAAAAATA
16754754 AATTTTTTTG
Statistics
Matches: 139, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
113 6 0.04
114 1 0.01
115 46 0.33
116 46 0.33
117 14 0.10
118 26 0.19
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (116 bp):
AGAAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTGAAAACTTTAATTTCAAGGAAAAT
TGATACTTTCAACTTTTTCTCAAAAAGAAACTTTTTTAAATTTATTTTTAA
Found at i:16754812 original size:16 final size:16
Alignment explanation
Indices: 16754791--16754824 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
16754781 AAAATAAACA
16754791 AAGTAAAAATGA-AAAT
1 AAGTAAAAA-GATAAAT
16754807 AAGTAAAAAGATAAAT
1 AAGTAAAAAGATAAAT
16754823 AA
1 AA
16754825 AAATAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 15 0.88
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.18
Consensus pattern (16 bp):
AAGTAAAAAGATAAAT
Found at i:16754830 original size:6 final size:6
Alignment explanation
Indices: 16754775--16754841 Score: 50
Period size: 6 Copynumber: 11.2 Consensus size: 6
16754765 ATTTTTTTTA
* * * *
16754775 AAAAAT -AAAAT AAACAAAGT AAAAAT GAAAAT --AAGT AAAAAG ATAAAT
1 AAAAAT AAAAAT -AA-AAA-T AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
16754823 AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT A
16754842 TTAAACAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
4 3 0.06
5 5 0.10
6 30 0.62
7 4 0.08
8 5 0.10
9 1 0.02
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:16755455 original size:11 final size:11
Alignment explanation
Indices: 16755441--16755470 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
16755431 ATTTCTAGAA
16755441 AAAAAATTCAC
1 AAAAAATTCAC
16755452 -AAAAATTCAC
1 AAAAAATTCAC
16755462 AAAAAATTC
1 AAAAAATTC
16755471 CTACCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.63, C:0.17, G:0.00, T:0.20
Consensus pattern (11 bp):
AAAAAATTCAC
Found at i:16755766 original size:13 final size:14
Alignment explanation
Indices: 16755750--16755970 Score: 67
Period size: 14 Copynumber: 14.5 Consensus size: 14
16755740 AGAAGAAAAG
16755750 AAAAAAATAA-AAT
1 AAAAAAATAATAAT
16755763 AAAATAAATAATAA-
1 AAAA-AAATAATAAT
*
16755777 AAAATAATAATAAT
1 AAAAAAATAATAAT
*
16755791 AAAGATAATATATTAATT
1 AAA-A-AA-ATAATAA-T
16755809 AATAGATAAATAATAAT
1 AA-A-A-AAATAATAAT
*
16755826 ATATATAAATAGATAAAT
1 A-A-AAAAATA-AT-AAT
*
16755844 AATAATACATATATATAT
1 AA-AA-AAATA-ATA-AT
* * *
16755862 CAATAGATAAATAAT
1 AAAAAAAT-AATAAT
16755877 AAAAATAATAA-AAT
1 AAAAA-AATAATAAT
*
16755891 AAAATAAATATATATT
1 AAAA-AAATA-ATAAT
*
16755907 AATAAATAGTAATAAT
1 AA-AAA-AATAATAAT
*
16755923 AAATAAATGAATAAT
1 AAAAAAAT-AATAAT
* *
16755938 AAATACATAA-AAT
1 AAAAAAATAATAAT
*
16755951 -ACAAAATAA-AAGT
1 AAAAAAATAATAA-T
16755964 AAAAAAA
1 AAAAAAA
16755971 ATAAGAAATA
Statistics
Matches: 161, Mismatches: 24, Indels: 45
0.70 0.10 0.20
Matches are distributed among these distances:
12 8 0.05
13 16 0.10
14 33 0.20
15 27 0.17
16 25 0.16
17 21 0.13
18 25 0.16
19 6 0.04
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (14 bp):
AAAAAAATAATAAT
Found at i:16755768 original size:10 final size:11
Alignment explanation
Indices: 16755755--16755974 Score: 77
Period size: 12 Copynumber: 18.9 Consensus size: 11
16755745 AAAAGAAAAA
16755755 AATAAAATAA-
1 AATAAAATAAT
16755765 AAT-AAATAAT
1 AATAAAATAAT
*
16755775 AAAAAATAATAAT
1 -AATAA-AATAAT
16755788 AATAAAGATAAT
1 AATAAA-ATAAT
* *
16755800 ATATTAATTAAT
1 A-ATAAAATAAT
16755812 AGAT-AAATAAT
1 A-ATAAAATAAT
*
16755823 AATATATATAAAT
1 AATA-AAAT-AAT
16755836 AGAT-AAATAAT
1 A-ATAAAATAAT
16755847 AATACATATATATAT
1 AATA-A-A-ATA-AT
*
16755862 CAAT-AGATAAAT
1 -AATAAAAT-AAT
16755874 AAT-AAA-AAT
1 AATAAAATAAT
16755883 AATAAAATAA-
1 AATAAAATAAT
16755893 AATAAATATATATT
1 AATAAA-ATA-A-T
16755907 AATAAATAGTAAT
1 AATAAA-A-TAAT
16755920 AAT-AAATAAAT
1 AATAAAAT-AAT
*
16755931 GAATAATA-AAT
1 -AATAAAATAAT
*
16755942 ACATAAAATACAA
1 A-ATAAAATA-AT
16755955 AATAAAAGTAA-
1 AATAAAA-TAAT
16755966 AA-AAAATAA
1 AATAAAATAA
16755975 GAAATACAAA
Statistics
Matches: 166, Mismatches: 13, Indels: 63
0.69 0.05 0.26
Matches are distributed among these distances:
9 15 0.09
10 22 0.13
11 38 0.23
12 43 0.26
13 26 0.16
14 15 0.09
15 4 0.02
16 3 0.02
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:16755773 original size:4 final size:4
Alignment explanation
Indices: 16755754--16755948 Score: 70
Period size: 4 Copynumber: 48.8 Consensus size: 4
16755744 GAAAAGAAAA
*
16755754 AAAT AAAAT AAAAT AAAT -AAT AAA- AAAT -AAT -AAT -AAT AAAG ATAAT
1 AAAT -AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT
* * * * * *
16755800 ATAT TAAT TAAT AGAT AAAT -AAT AATAT ATAT AAAT AGAT AAAT -AAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT
* * * * * *
16755847 -AAT ACAT ATAT ATAT CAAT AGAT AAAT -AAT AAAA ATAAT AAAAT AAAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT -AAAT -AAAT
* *
16755896 AAAT ATATAT TAAT AAAT AGTAAT -AAT AAAT AAAT GAAT -AAT AAAT
1 AAAT A-A-AT AAAT AAAT A--AAT AAAT AAAT AAAT AAAT AAAT AAAT
*
16755942 ACAT AAA
1 AAAT AAA
16755949 ATACAAAATA
Statistics
Matches: 148, Mismatches: 26, Indels: 33
0.71 0.13 0.16
Matches are distributed among these distances:
3 33 0.22
4 82 0.55
5 27 0.18
6 6 0.04
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.30
Consensus pattern (4 bp):
AAAT
Found at i:16755904 original size:102 final size:99
Alignment explanation
Indices: 16755766--16755947 Score: 246
Period size: 102 Copynumber: 1.8 Consensus size: 99
16755756 ATAAAATAAA
* *
16755766 ATAAATAATAAAAAATAATAATAATAAAGATAATATATTAATTAATAGATAAATAATAATATATA
1 ATAAATAATAAAAAATAATAATAATAAAGATAATATATTAATAAATAG-T-AATAATAA-ATAAA
16755831 TAAATAGATAAATA-ATAATACATATATATATCAATAG
63 TAAATA-ATAAATACATAATACATATATATATCAATAG
16755868 ATAAATAAT-AAAAATAATAA-AATAAA-ATAAATATATATTAATAAATAGTAATAATAAATAAA
1 ATAAATAATAAAAAATAATAATAATAAAGAT--A-ATATATTAATAAATAGTAATAATAAATAAA
*
16755930 TGAATAATAAATACATAA
63 TAAATAATAAATACATAA
16755948 AATACAAAAT
Statistics
Matches: 73, Mismatches: 3, Indels: 11
0.84 0.03 0.13
Matches are distributed among these distances:
98 7 0.10
99 15 0.21
100 14 0.19
101 13 0.18
102 24 0.33
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (99 bp):
ATAAATAATAAAAAATAATAATAATAAAGATAATATATTAATAAATAGTAATAATAAATAAATAA
ATAATAAATACATAATACATATATATATCAATAG
Found at i:16755910 original size:60 final size:59
Alignment explanation
Indices: 16755760--16755960 Score: 162
Period size: 60 Copynumber: 3.3 Consensus size: 59
16755750 AAAAAAATAA
* * * *
16755760 AATAAAATAAATAATAAA-AAATAATAAT-AATA-AAGATAATATATTAATTAATAGATAAAT
1 AATAAAAT-AA-AATAAATAAATAATAATAAATAGTA-ATAATAAATAAATGAATA-ATAAAT
* *
16755820 AATAATATATATAAATAGATAAATAATAATACATATA-TATATCAATAGATAAAT-AATAA-AAA
1 AATAA-A-ATA-AAATAAATAAATAATAATA-A-ATAGTA-AT-AATAAATAAATGAATAATAAA
16755882 T
59 T
* *
16755883 AATAAAATAAAATAAATATATATTAATAAATAGTAATAATAAATAAATGAATAATAAAT
1 AATAAAATAAAATAAATAAATAATAATAAATAGTAATAATAAATAAATGAATAATAAAT
16755942 ACATAAAATACAAAATAAA
1 A-ATAAAAT--AAAATAAA
16755961 AGTAAAAAAA
Statistics
Matches: 118, Mismatches: 9, Indels: 26
0.77 0.06 0.17
Matches are distributed among these distances:
57 10 0.08
58 10 0.08
59 8 0.07
60 28 0.24
61 10 0.08
62 22 0.19
63 9 0.08
64 2 0.02
65 10 0.08
66 9 0.08
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (59 bp):
AATAAAATAAAATAAATAAATAATAATAAATAGTAATAATAAATAAATGAATAATAAAT
Found at i:16755936 original size:44 final size:45
Alignment explanation
Indices: 16755814--16755939 Score: 125
Period size: 46 Copynumber: 2.8 Consensus size: 45
16755804 TAATTAATAG
* *
16755814 ATAAATA-ATAATATATATAAATAGATAAATAATAATACATATATAT
1 ATAAATAGATAA-ATA-ATAAATAAATAAATAATAATAAATATATAT
* *
16755860 ATCAATAGATAAATAATAAAAATAATAAAATAA-AATAAATATATATT
1 ATAAATAGATAAATAATAAATA-AAT-AAATAATAATAAATATATA-T
*
16755907 AATAAATAG-T-AATAATAAATAAATGAATAATAA
1 -ATAAATAGATAAATAATAAATAAATAAATAATAA
16755940 ATACATAAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
44 5 0.07
45 11 0.16
46 32 0.48
47 12 0.18
48 7 0.10
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (45 bp):
ATAAATAGATAAATAATAAATAAATAAATAATAATAAATATATAT
Found at i:16761809 original size:22 final size:22
Alignment explanation
Indices: 16761739--16761810 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 22
16761729 TTAAATCAAT
* *
16761739 CTAGAATATTACTAAAATATTA
1 CTAGAATATTACCATAATATTA
* * * *
16761761 TTAGAATAATATCATCA-ATT-
1 CTAGAATATTACCATAATATTA
16761781 -TAGAATATTACCATAATATTA
1 CTAGAATATTACCATAATATTA
16761802 CTAGAATAT
1 CTAGAATAT
16761811 CATTGATAGG
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 13 0.34
20 3 0.08
21 3 0.08
22 19 0.50
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.38
Consensus pattern (22 bp):
CTAGAATATTACCATAATATTA
Found at i:16761810 original size:38 final size:39
Alignment explanation
Indices: 16761733--16761813 Score: 101
Period size: 41 Copynumber: 2.1 Consensus size: 39
16761723 TTAATATTAA
* *
16761733 ATCAATCTAGAATATTACTAAAATATTATTAGAATAATATC
1 ATCAATCTAGAATATTACCAAAATATTACTAG-A-AATATC
* *
16761774 ATCAATTTAGAATATTACCATAATATTACTAG-AATATC
1 ATCAATCTAGAATATTACCAAAATATTACTAGAAATATC
16761812 AT
1 AT
16761814 TGATAGGATA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 8 0.22
41 28 0.78
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (39 bp):
ATCAATCTAGAATATTACCAAAATATTACTAGAAATATC
Found at i:16763144 original size:17 final size:18
Alignment explanation
Indices: 16763124--16763168 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
16763114 TATTAATATT
16763124 TTTATTAAAAATATC-AA
1 TTTATTAAAAATATCAAA
* *
16763141 TTTAATAAATATATCAAAA
1 TTTATTAAAAATATC-AAA
16763160 TTTATTAAA
1 TTTATTAAA
16763169 TTTTTTTCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 13 0.57
19 10 0.43
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
TTTATTAAAAATATCAAA
Found at i:16763236 original size:13 final size:13
Alignment explanation
Indices: 16763217--16763248 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
16763207 ATTTATCAAT
16763217 CTTTTAATTTTAA
1 CTTTTAATTTTAA
*
16763230 TTTTTAATTTTAA
1 CTTTTAATTTTAA
16763243 CTTTTA
1 CTTTTA
16763249 TTTACTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (13 bp):
CTTTTAATTTTAA
Found at i:16763311 original size:22 final size:22
Alignment explanation
Indices: 16763283--16763326 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
16763273 TTATTAACTC
16763283 CATTTATTAAACTTCAAGTAAA
1 CATTTATTAAACTTCAAGTAAA
16763305 CATTTATTAAACTTCAAGTAAA
1 CATTTATTAAACTTCAAGTAAA
16763327 TTTTTCCCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (22 bp):
CATTTATTAAACTTCAAGTAAA
Found at i:16763765 original size:170 final size:171
Alignment explanation
Indices: 16763545--16763885 Score: 555
Period size: 170 Copynumber: 2.0 Consensus size: 171
16763535 ATTAAAAGAG
*
16763545 TTAGATAACTCATATAATTTGGCACTTTAATTAAGTTGTAAGTATCAATACCTTACTCGATT-TT
1 TTAGATAACTCATATAATTTGGCACTTTAATTAAGTTATAAGTATCAATACCTTACTCGATTCTT
*
16763609 TGGTCTTATATATAGAGAATGGATAAACTTACAT-AAAAA-TTTTTTTATATTTT-TTAATTATT
66 TGGTC-T-TATATAGAGAATGGATAAACTAACATAAAAAACTTTTTTTATATTTTGTTAATTATT
*
16763671 GATTTTAATAGATCTATGATTGAGAATAAAAAAATTATATATAT
129 AATTTTAATAGATCTATGATTGAGAAT-AAAAAATTATATATAT
* *
16763715 TTAGATAACTCATATAATTTGGTACTTTAATTAAGTTATAAGTTTCAATACCTTACTCGATTCTT
1 TTAGATAACTCATATAATTTGGCACTTTAATTAAGTTATAAGTATCAATACCTTACTCGATTCTT
* * *
16763780 TGGTCTTATATAGAGAATGGATCAACTAATATAAAAAACTTTTTTTTTATTTTGTTAATTATTAA
66 TGGTCTTATATAGAGAATGGATAAACTAACATAAAAAACTTTTTTTATATTTTGTTAATTATTAA
16763845 TTTTAATAGATCTATGATTGAGAATAAAAAATTATATATAT
131 TTTTAATAGATCTATGATTGAGAATAAAAAATTATATATAT
16763886 ATATATATAT
Statistics
Matches: 159, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
169 23 0.14
170 65 0.41
171 36 0.23
172 35 0.22
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (171 bp):
TTAGATAACTCATATAATTTGGCACTTTAATTAAGTTATAAGTATCAATACCTTACTCGATTCTT
TGGTCTTATATAGAGAATGGATAAACTAACATAAAAAACTTTTTTTATATTTTGTTAATTATTAA
TTTTAATAGATCTATGATTGAGAATAAAAAATTATATATAT
Found at i:16763882 original size:2 final size:2
Alignment explanation
Indices: 16763877--16763903 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16763867 AATAAAAAAT
16763877 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 T
16763904 GCTTTGAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16765638 original size:2 final size:2
Alignment explanation
Indices: 16765631--16765698 Score: 73
Period size: 2 Copynumber: 34.0 Consensus size: 2
16765621 GATACTTGAC
* * * * *
16765631 AT AT AT AT AT AT AT AT AT AT GT AT GT GT GT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
16765673 AT AT AT AT GT AT AT AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
16765699 CTAAGGAACA
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.47
Consensus pattern (2 bp):
AT
Found at i:16769219 original size:25 final size:25
Alignment explanation
Indices: 16769170--16769219 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
16769160 ATTGAAAAAA
*
16769170 ATTTAAATTATTTCATGTTTTGATT
1 ATTTAAATTATTTCATGTTTAGATT
16769195 ATTTAAATT-TTAATCAT-TTTAGATT
1 ATTTAAATTATT--TCATGTTTAGATT
16769220 TGATTTTGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 2 0.09
25 16 0.73
26 4 0.18
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.58
Consensus pattern (25 bp):
ATTTAAATTATTTCATGTTTAGATT
Found at i:16769732 original size:19 final size:19
Alignment explanation
Indices: 16769705--16769760 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
16769695 ATATAATAAT
*
16769705 ATAATAATTTAAAATTTTA
1 ATAAAAATTTAAAATTTTA
*
16769724 ATAAAAATTATAAATAAATTTA
1 ATAAAAATT-T-AA-AATTTTA
16769746 AT-AAAA-TTAAAATTT
1 ATAAAAATTTAAAATTT
16769761 ATATTTTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
17 4 0.13
18 2 0.06
19 9 0.29
20 2 0.06
21 6 0.19
22 8 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATAAAAATTTAAAATTTTA
Found at i:16770043 original size:9 final size:9
Alignment explanation
Indices: 16769998--16770044 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
16769988 AAATATCAAA
*
16769998 TTTTGAATA
1 TTTTGAATT
16770007 TTTTGAATAT
1 TTTTGAAT-T
*
16770017 TTTTAAATT
1 TTTTGAATT
*
16770026 TTTTAAATT
1 TTTTGAATT
16770035 TTTTGAATT
1 TTTTGAATT
16770044 T
1 T
16770045 GACAGGTCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
9 27 0.79
10 7 0.21
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (9 bp):
TTTTGAATT
Found at i:16770043 original size:18 final size:19
Alignment explanation
Indices: 16769998--16770044 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
16769988 AAATATCAAA
* *
16769998 TTTTGAATATTTTGAATAT
1 TTTTGAATTTTTTAAATAT
*
16770017 TTTTAAATTTTTTAAAT-T
1 TTTTGAATTTTTTAAATAT
16770035 TTTTGAATTT
1 TTTTGAATTT
16770045 GACAGGTCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (19 bp):
TTTTGAATTTTTTAAATAT
Found at i:16770315 original size:29 final size:29
Alignment explanation
Indices: 16770274--16770342 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
16770264 AGTCATTTTT
16770274 AATTATAATAAAATAGTTAATATAATATTTA
1 AATTAT-A-AAAATAGTTAATATAATATTTA
* ** *
16770305 AATTTTAAAAATTTTTAATATAATATTTT
1 AATTATAAAAATAGTTAATATAATATTTA
16770334 AATTATAAA
1 AATTATAAA
16770343 TTTATTAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 27 0.82
30 1 0.03
31 5 0.15
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (29 bp):
AATTATAAAAATAGTTAATATAATATTTA
Found at i:16770355 original size:29 final size:28
Alignment explanation
Indices: 16770290--16770355 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
16770280 AATAAAATAG
16770290 TTAATATAATATTTAAATTTTAAAAATTT
1 TTAATATAATATTTAAA-TTTAAAAATTT
* *
16770319 TTAATATAATATTTTAA-TTATAAATTT
1 TTAATATAATATTTAAATTTAAAAATTT
16770346 ATTAAATATA
1 -TT-AATATA
16770356 TTAAAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 9 0.27
28 2 0.06
29 22 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
TTAATATAATATTTAAATTTAAAAATTT
Found at i:16770809 original size:3 final size:3
Alignment explanation
Indices: 16770803--16770829 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
16770793 AGTAATAATA
16770803 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
16770830 CAAATCTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:16777045 original size:13 final size:13
Alignment explanation
Indices: 16777027--16777064 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
16777017 TATATAATAT
16777027 TTATATTATATTA
1 TTATATTATATTA
16777040 TTATATTATATT-
1 TTATATTATATTA
*
16777052 TTAAATTAT-TTA
1 TTATATTATATTA
16777064 T
1 T
16777065 GAAATAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 2 0.09
12 9 0.39
13 12 0.52
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTATATTATATTA
Found at i:16777064 original size:24 final size:24
Alignment explanation
Indices: 16777010--16777082 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
16777000 ATGATATTCG
* *
16777010 TATTTTTTATATAATA-TTTATAT
1 TATTTATTATATAATATTTTAAAT
*
16777033 TATATTATTATATTATATTTTAAAT
1 TAT-TTATTATATAATATTTTAAAT
* * *
16777058 TATTTATGAAATAATGTTTTAAAT
1 TATTTATTATATAATATTTTAAAT
16777082 T
1 T
16777083 TTAATATGAA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
23 3 0.07
24 29 0.71
25 9 0.22
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (24 bp):
TATTTATTATATAATATTTTAAAT
Found at i:16777423 original size:26 final size:26
Alignment explanation
Indices: 16777374--16777423 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
16777364 CGCAACTCTC
* *
16777374 TTTCTTTTTTTAATTTATTTTTTTCT
1 TTTCTATTTTTAATGTATTTTTTTCT
16777400 TTTCTATTTTTAA-GTATTTATTTT
1 TTTCTATTTTTAATGTATTT-TTTT
16777424 AGGTAAAGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.76
Consensus pattern (26 bp):
TTTCTATTTTTAATGTATTTTTTTCT
Found at i:16785396 original size:25 final size:25
Alignment explanation
Indices: 16785368--16785428 Score: 122
Period size: 25 Copynumber: 2.4 Consensus size: 25
16785358 TTATGTGATA
16785368 AGATTTAAATGAAAATTACATACTG
1 AGATTTAAATGAAAATTACATACTG
16785393 AGATTTAAATGAAAATTACATACTG
1 AGATTTAAATGAAAATTACATACTG
16785418 AGATTTAAATG
1 AGATTTAAATG
16785429 GTCATTTAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.48, C:0.07, G:0.13, T:0.33
Consensus pattern (25 bp):
AGATTTAAATGAAAATTACATACTG
Found at i:16786033 original size:29 final size:29
Alignment explanation
Indices: 16785991--16786074 Score: 100
Period size: 29 Copynumber: 2.8 Consensus size: 29
16785981 GATTATTATT
16785991 AATTAATAAATTTAATATTTAATAAAATA
1 AATTAATAAATTTAATATTTAATAAAATA
16786020 AATTAATAAATTTAAT-TTTAATATAAAATA
1 AATTAATAAATTTAATATTT-A-ATAAAATA
*
16786050 AATATAA-AATTTTAAATAATTTAAT
1 AAT-TAATAAATTT-AAT-ATTTAAT
16786075 GTAATCATTT
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
28 3 0.06
29 17 0.35
30 16 0.33
31 8 0.17
32 1 0.02
33 3 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (29 bp):
AATTAATAAATTTAATATTTAATAAAATA
Found at i:16786036 original size:13 final size:13
Alignment explanation
Indices: 16785989--16786036 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
16785979 TGGATTATTA
16785989 TTAATTAATAAAT
1 TTAATTAATAAAT
*
16786002 TTAATATTTAATAAAA
1 TT-A-A-TTAATAAAT
*
16786018 TAAATTAATAAAT
1 TTAATTAATAAAT
16786031 TTAATT
1 TTAATT
16786037 TTAATATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
13 15 0.54
14 2 0.07
15 2 0.07
16 9 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAATTAATAAAT
Found at i:16795830 original size:40 final size:40
Alignment explanation
Indices: 16795786--16795861 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
16795776 TTTTTTTAAT
*
16795786 TTTTATATTATA-TCAT-TTTTGTATTTATATTTAATAAAAA
1 TTTTA-ATTATATTCATATTTT-TATTGATATTTAATAAAAA
*
16795826 TTTTAATTATATTTATATTTTTATTGATATTTAATA
1 TTTTAATTATATTCATATTTTTATTGATATTTAATA
16795862 GATATGAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
39 6 0.19
40 22 0.69
41 4 0.12
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.61
Consensus pattern (40 bp):
TTTTAATTATATTCATATTTTTATTGATATTTAATAAAAA
Found at i:16796040 original size:23 final size:24
Alignment explanation
Indices: 16795987--16796041 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
16795977 ATATACTTGT
* *
16795987 TTTAATAAAAATATATTAATTTTA
1 TTTAATTAAAATATATTAATATTA
* *
16796011 ATTAATTAAAATA-ATTTATATTA
1 TTTAATTAAAATATATTAATATTA
16796034 TTTAATTA
1 TTTAATTA
16796042 TTTATTTACT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTTAATTAAAATATATTAATATTA
Found at i:16803130 original size:56 final size:56
Alignment explanation
Indices: 16803044--16803156 Score: 199
Period size: 56 Copynumber: 2.0 Consensus size: 56
16803034 AAAAAAAAAA
* * *
16803044 AAGCAAATGAAGTTAAAAAGTAAGGCTTAGAAATCAATACCATTTTGGAAGAAACC
1 AAGCAAATGAAGTTAAAAAGCAAGGCTTAGAAATCAATACAAGTTTGGAAGAAACC
16803100 AAGCAAATGAAGTTAAAAAGCAAGGCTTAGAAATCAATACAAGTTTGGAAGAAACC
1 AAGCAAATGAAGTTAAAAAGCAAGGCTTAGAAATCAATACAAGTTTGGAAGAAACC
16803156 A
1 A
16803157 TGCATTATTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.50, C:0.12, G:0.19, T:0.19
Consensus pattern (56 bp):
AAGCAAATGAAGTTAAAAAGCAAGGCTTAGAAATCAATACAAGTTTGGAAGAAACC
Found at i:16803991 original size:22 final size:23
Alignment explanation
Indices: 16803948--16803991 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
16803938 AATTATAATC
*
16803948 AATGAAGCTGTCGTTTTTTGAGAG
1 AATGAAGCTGTC-TATTTTGAGAG
16803972 AATGAAGCTGT-TATTTTGAG
1 AATGAAGCTGTCTATTTTGAG
16803992 GCAAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
24 11 0.58
ACGTcount: A:0.27, C:0.07, G:0.27, T:0.39
Consensus pattern (23 bp):
AATGAAGCTGTCTATTTTGAGAG
Found at i:16804196 original size:43 final size:40
Alignment explanation
Indices: 16804103--16804203 Score: 109
Period size: 40 Copynumber: 2.5 Consensus size: 40
16804093 TTAATTTATA
* **
16804103 TATTTATTTAGATTTGATTTAAATAAATAAAATTTTAAATT
1 TATTTA-TTAAATTTGATTTAAATAAATAAAATAATAAATT
16804144 T-TTTA--AAATTTGATTTAAATTACAATAAAAATAATAAATT
1 TATTTATTAAATTTGATTTAAA-TA-AAT-AAAATAATAAATT
*
16804184 TATTTATTAAATTTAATTTA
1 TATTTATTAAATTTGATTTA
16804204 TGTAATAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
37 13 0.26
38 2 0.04
39 3 0.06
40 16 0.32
41 5 0.10
43 11 0.22
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.50
Consensus pattern (40 bp):
TATTTATTAAATTTGATTTAAATAAATAAAATAATAAATT
Found at i:16804269 original size:24 final size:23
Alignment explanation
Indices: 16804217--16804270 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
16804207 AATAAAAAAT
16804217 TAAAAAATAATTAAATTAAT-T-
1 TAAAAAATAATTAAATTAATATA
*
16804238 TAATAAAATTATATTAAATTCATATA
1 TAA-AAAA-TA-ATTAAATTAATATA
16804264 TAAAAAA
1 TAAAAAA
16804271 AATAAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 3 0.11
22 4 0.15
23 2 0.07
24 10 0.37
25 5 0.19
26 3 0.11
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
TAAAAAATAATTAAATTAATATA
Found at i:16808764 original size:14 final size:14
Alignment explanation
Indices: 16808745--16808774 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
16808735 CCCATTCTAT
16808745 AAAAAAATATATAAA
1 AAAAAAATA-ATAAA
16808760 AAAAAAATAATAAA
1 AAAAAAATAATAAA
16808774 A
1 A
16808775 TCACTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAAAAATAATAAA
Found at i:16810482 original size:11 final size:10
Alignment explanation
Indices: 16810453--16810479 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
16810443 TTAAGTATAC
16810453 AAAATTTGAA
1 AAAATTTGAA
16810463 AAAATTTGAA
1 AAAATTTGAA
16810473 AAAATTT
1 AAAATTT
16810480 TGATATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.33
Consensus pattern (10 bp):
AAAATTTGAA
Found at i:16812261 original size:36 final size:36
Alignment explanation
Indices: 16812220--16812296 Score: 88
Period size: 36 Copynumber: 2.1 Consensus size: 36
16812210 ATTTCGTTAT
16812220 ATAAA-TTAAATATGTAAATTTTTTAAA-AAA-ATTTTA
1 ATAAATTTAAATA--TAAA-TTTTTAAATAAATATTTTA
* *
16812256 ATAAATTTTAATATACATTTTTAAATAAATATTTTA
1 ATAAATTTAAATATAAATTTTTAAATAAATATTTTA
16812292 ATAAA
1 ATAAA
16812297 AATATTAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
34 8 0.22
35 6 0.17
36 16 0.44
37 6 0.17
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (36 bp):
ATAAATTTAAATATAAATTTTTAAATAAATATTTTA
Found at i:16812294 original size:12 final size:12
Alignment explanation
Indices: 16812234--16812296 Score: 53
Period size: 11 Copynumber: 5.3 Consensus size: 12
16812224 ATTAAATATG
*
16812234 TAAATTTTTTAA
1 TAAATATTTTAA
*
16812246 -AAAAATTTTAA
1 TAAATATTTTAA
16812257 T-AA-ATTTTAA
1 TAAATATTTTAA
16812267 TATACAT-TTTTAAA
1 TA-A-ATATTTT-AA
16812281 TAAATATTTTAA
1 TAAATATTTTAA
16812293 TAAA
1 TAAA
16812297 AATATTAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
10 8 0.19
11 11 0.26
12 9 0.21
13 10 0.24
14 4 0.10
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (12 bp):
TAAATATTTTAA
Found at i:16812299 original size:14 final size:14
Alignment explanation
Indices: 16812260--16812302 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
16812250 ATTTTAATAA
*
16812260 ATTTTAATATACAT
1 ATTTTAATATAAAT
16812274 -TTTTAA-ATAAAT
1 ATTTTAATATAAAT
*
16812286 ATTTTAATAAAAAT
1 ATTTTAATATAAAT
16812300 ATT
1 ATT
16812303 AACAAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 5 0.20
13 12 0.48
14 8 0.32
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTTTAATATAAAT
Found at i:16813536 original size:21 final size:20
Alignment explanation
Indices: 16813491--16813538 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
16813481 TTTAACTTGC
16813491 AAAT-TATTTAATTAAATTA
1 AAATATATTTAATTAAATTA
*
16813510 ATATATATTT-ATATAATATTA
1 AAATATATTTAAT-TAA-ATTA
16813531 AAATATAT
1 AAATATAT
16813539 ATATCAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 5 0.21
20 8 0.33
21 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AAATATATTTAATTAAATTA
Found at i:16814217 original size:20 final size:19
Alignment explanation
Indices: 16814166--16814217 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
16814156 ATTATAATAC
16814166 ATAAT-TTTTATATAAAAT
1 ATAATATTTTATATAAAAT
** *
16814184 ATAATATAAATATATAAATT
1 ATAATAT-TTTATATAAAAT
16814204 ATTAATATTTTATA
1 A-TAATATTTTATA
16814218 CGATACAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 5 0.19
19 1 0.04
20 14 0.54
21 6 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATAATATTTTATATAAAAT
Found at i:16816633 original size:2 final size:2
Alignment explanation
Indices: 16816628--16816661 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
16816618 ATGCTAAAAA
*
16816628 AC AC AC AC AC AC AC AC AC AC CC AC AC -C AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
16816662 GAAAGACAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.53, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:16823996 original size:12 final size:12
Alignment explanation
Indices: 16823979--16824017 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
16823969 TTTACATTTG
16823979 AATTTGGTTTAA
1 AATTTGGTTTAA
16823991 AATTTGAGATTTAA
1 AATTTG-G-TTTAA
*
16824005 AATTTGATTTAA
1 AATTTGGTTTAA
16824017 A
1 A
16824018 CATAATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 12 0.50
13 1 0.04
14 11 0.46
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (12 bp):
AATTTGGTTTAA
Found at i:16824228 original size:15 final size:16
Alignment explanation
Indices: 16824198--16824228 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
16824188 TAATTAAAAT
16824198 AATAAAAATATATTAA
1 AATAAAAATATATTAA
16824214 AATAAAAATAT-TTAA
1 AATAAAAATATATTAA
16824229 TTAGATTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AATAAAAATATATTAA
Found at i:16824267 original size:21 final size:21
Alignment explanation
Indices: 16824209--16824273 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
16824199 ATAAAAATAT
16824209 ATTAAA-ATAAAAATATTT-A
1 ATTAAATATAAAAATATTTAA
* * * *
16824228 ATTAGATTTACGAATTATTTAA
1 ATTAAATATA-AAAATATTTAA
16824250 ATTAAATATAAAAATATTTAA
1 ATTAAATATAAAAATATTTAA
16824271 ATT
1 ATT
16824274 TGATTTGATC
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
19 5 0.14
20 2 0.06
21 19 0.54
22 9 0.26
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.42
Consensus pattern (21 bp):
ATTAAATATAAAAATATTTAA
Found at i:16827441 original size:13 final size:13
Alignment explanation
Indices: 16827396--16827455 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 13
16827386 CAACTTTCGA
*
16827396 AAAAATTTTA-AT
1 AAAATTTTTAGAT
16827408 -AAATTTTATAGAT
1 AAAATTTT-TAGAT
*
16827421 AAATATTTTTAGTT
1 AAA-ATTTTTAGAT
16827435 AAAA-TTTT-GAT
1 AAAATTTTTAGAT
16827446 AAAATTTTTA
1 AAAATTTTTA
16827456 TTGTTGAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
11 12 0.31
12 10 0.26
13 3 0.08
14 9 0.23
15 5 0.13
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (13 bp):
AAAATTTTTAGAT
Found at i:16829980 original size:20 final size:21
Alignment explanation
Indices: 16829952--16829991 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16829942 AATTTAGATC
*
16829952 AATTCTTTT-TAAATAAATTT
1 AATTCTTTTATAAAAAAATTT
*
16829972 AATTTTTTTATAAAAAAATT
1 AATTCTTTTATAAAAAAATT
16829992 ACTTTAGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
AATTCTTTTATAAAAAAATTT
Found at i:16832915 original size:22 final size:22
Alignment explanation
Indices: 16832879--16832922 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
16832869 TAAATTTAGA
* *
16832879 TGCTTTCCCATGCAAAAGCAAT
1 TGCTTTCCCAAGCAAAAACAAT
*
16832901 TGCTTTGCCAAGCAAAAACAAT
1 TGCTTTCCCAAGCAAAAACAAT
16832923 ATGCCAATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (22 bp):
TGCTTTCCCAAGCAAAAACAAT
Found at i:16834294 original size:3 final size:3
Alignment explanation
Indices: 16834288--16834326 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
16834278 CAACATCATC
16834288 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16834327 TTTAGAGATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:16840363 original size:133 final size:132
Alignment explanation
Indices: 16840121--16840387 Score: 435
Period size: 133 Copynumber: 2.0 Consensus size: 132
16840111 TGCAGTTTCT
16840121 AGTGGAACACCAAGGGCAACTGGTTCCAAAAAACCAATTTCAAGGTTAGTTATTACATATATTCT
1 AGTGGAACACCAAGGGCAACTGGTTCCAAAAAACCAATTTCAAGGTTAGTTATTACATATATTCT
* * *
16840186 TATATCATATTGAACTTACTTTTAGTAGAACTTGGGCATTTGAGTGCCCAGATAGTAAAACATGA
66 TATATCATATTGAAATTACTTTTAGTAGAACTTAGGCATATGAGTGCCCAGATAGTAAAACATGA
16840251 AA
131 AA
* *
16840253 AGTGGAACACCAAGGGCAACTGGTTCCAGAAAACCAATTTTCAAGGTTATTTATTACATATATTC
1 AGTGGAACACCAAGGGCAACTGGTTCCAAAAAACCAA-TTTCAAGGTTAGTTATTACATATATTC
* * * * *
16840318 TTATATCATATTGAAATTAGTTTTAGTTGAACTTAGGTATATGAGTGCCCAGATATTAAAGCATG
65 TTATATCATATTGAAATTACTTTTAGTAGAACTTAGGCATATGAGTGCCCAGATAGTAAAACATG
16840383 AAA
130 AAA
16840386 AG
1 AG
16840388 AGCAGAAGGC
Statistics
Matches: 124, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
132 36 0.29
133 88 0.71
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (132 bp):
AGTGGAACACCAAGGGCAACTGGTTCCAAAAAACCAATTTCAAGGTTAGTTATTACATATATTCT
TATATCATATTGAAATTACTTTTAGTAGAACTTAGGCATATGAGTGCCCAGATAGTAAAACATGA
AA
Found at i:16845116 original size:14 final size:14
Alignment explanation
Indices: 16845097--16845126 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
16845087 TGAATATTAT
16845097 AATATATTCTCAAA
1 AATATATTCTCAAA
*
16845111 AATATATTTTCAAA
1 AATATATTCTCAAA
16845125 AA
1 AA
16845127 AATAATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (14 bp):
AATATATTCTCAAA
Found at i:16845160 original size:33 final size:33
Alignment explanation
Indices: 16845095--16845160 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 33
16845085 TTTGAATATT
* *
16845095 ATAATATATTCTCAAAAATATATTTTCAAAAAA
1 ATAATATATTCTCAAAAATAGATTATCAAAAAA
*
16845128 ATAATATAATTCTTAAAAATAGATTATCAAAAA
1 ATAATAT-ATTCTCAAAAATAGATTATCAAAAA
16845161 TAAAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 7 0.24
34 22 0.76
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.35
Consensus pattern (33 bp):
ATAATATATTCTCAAAAATAGATTATCAAAAAA
Found at i:16845869 original size:34 final size:34
Alignment explanation
Indices: 16845831--16845903 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
16845821 ATAAATATCC
* * * *
16845831 AAAAATTCTTAAAATTTATCAAATATTTATTTTT
1 AAAAAATCTTAAAATTAATCAAATATTCATTTCT
* * *
16845865 AAAAAATCTTATAGTTAATCGAATATTCATTTCT
1 AAAAAATCTTAAAATTAATCAAATATTCATTTCT
16845899 AAAAA
1 AAAAA
16845904 GCTCAATTTC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (34 bp):
AAAAAATCTTAAAATTAATCAAATATTCATTTCT
Found at i:16846318 original size:23 final size:25
Alignment explanation
Indices: 16846292--16846344 Score: 83
Period size: 23 Copynumber: 2.2 Consensus size: 25
16846282 CTTTTAGATG
16846292 TTTTATCAATTGT-CATTTT-TTTT
1 TTTTATCAATTGTGCATTTTCTTTT
*
16846315 TTTTATCAATTTTGCATTTTCTTTT
1 TTTTATCAATTGTGCATTTTCTTTT
16846340 TTTTA
1 TTTTA
16846345 AGAAAATGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 12 0.44
24 6 0.22
25 9 0.33
ACGTcount: A:0.17, C:0.09, G:0.04, T:0.70
Consensus pattern (25 bp):
TTTTATCAATTGTGCATTTTCTTTT
Found at i:16846756 original size:15 final size:15
Alignment explanation
Indices: 16846726--16846755 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
16846716 TATAAAACAT
16846726 AGATTCAGCACAAAA
1 AGATTCAGCACAAAA
16846741 AGATTCA-CACAAAA
1 AGATTCAGCACAAAA
16846755 A
1 A
16846756 AAAAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.57, C:0.20, G:0.10, T:0.13
Consensus pattern (15 bp):
AGATTCAGCACAAAA
Found at i:16849866 original size:19 final size:20
Alignment explanation
Indices: 16849840--16849892 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
16849830 TTAATCAAAT
*
16849840 AAATATATATTAATGATTTA
1 AAATATATATTAATAATTTA
* *
16849860 AGA-ATATATTAAAAATTTA
1 AAATATATATTAATAATTTA
16849879 AAATATATATTAAT
1 AAATATATATTAAT
16849893 CAACAATTGC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (20 bp):
AAATATATATTAATAATTTA
Found at i:16849940 original size:15 final size:18
Alignment explanation
Indices: 16849906--16849938 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
16849896 CAATTGCTTA
16849906 AATTGTTGATAGATTTTT
1 AATTGTTGATAGATTTTT
16849924 AATT-TTGATA-ATTTT
1 AATTGTTGATAGATTTT
16849939 AAGTATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (18 bp):
AATTGTTGATAGATTTTT
Found at i:16850134 original size:25 final size:23
Alignment explanation
Indices: 16850091--16850137 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
16850081 TTTAAATCTT
16850091 AAATTTATTAAATATATTTTTTA
1 AAATTTATTAAATATATTTTTTA
16850114 AAATATTATATAAACTA-ATTTTTT
1 AAAT-TTAT-TAAA-TATATTTTTT
16850138 TCCATGAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 4 0.19
25 11 0.52
26 2 0.10
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
AAATTTATTAAATATATTTTTTA
Found at i:16860292 original size:3 final size:3
Alignment explanation
Indices: 16860284--16860311 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
16860274 ATTTTTACTA
16860284 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
16860312 TTGTTTTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:16863600 original size:2 final size:2
Alignment explanation
Indices: 16863593--16863627 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
16863583 CAGTTGGTTT
16863593 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
16863628 TGGGAGAGTA
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:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.