Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015020.1 Kokia drynarioides strain JFW-HI SEQ_130064, 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: 1341705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 344 characters in sequence are not A, C, G, or T
File 1 of 5
Found at i:4560 original size:29 final size:30
Alignment explanation
Indices: 4528--4636 Score: 91
Period size: 29 Copynumber: 3.7 Consensus size: 30
4518 AGGCGAAAAT
4528 TTTTTTTACCAACTTTTAAGGGGTCC-CAA
1 TTTTTTTACCAACTTTTAAGGGGTCCACAA
** * *
4557 TTTTTTT-TTAGCTTTTAA-AGGTCCAACAA
1 TTTTTTTACCAACTTTTAAGGGGTCC-ACAA
* * * *
4586 TTTTTTTACTAA-TTTTAAAGGGACCTAAAA
1 TTTTTTTACCAACTTTTAAGGGGTCC-ACAA
*
4616 TTTTTTTTCCAACTTTTAAGG
1 TTTTTTTACCAACTTTTAAGG
4637 AACCTAAAAC
Statistics
Matches: 62, Mismatches: 13, Indels: 8
0.75 0.16 0.10
Matches are distributed among these distances:
27 5 0.08
28 8 0.13
29 23 0.37
30 19 0.31
31 7 0.11
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.47
Consensus pattern (30 bp):
TTTTTTTACCAACTTTTAAGGGGTCCACAA
Found at i:4561 original size:30 final size:30
Alignment explanation
Indices: 4525--4636 Score: 97
Period size: 30 Copynumber: 3.8 Consensus size: 30
4515 TGAAGGCGAA
4525 AATTTTTTTTACCAACTTTTAAGGGGTCC-C
1 AATTTTTTTT-CCAACTTTTAAGGGGTCCAC
* * *
4555 AATTTTTTTT-TAGCTTTTAA-AGGTCCAAC
1 AATTTTTTTTCCAACTTTTAAGGGGTCC-AC
* * * * *
4584 AATTTTTTTACTAA-TTTTAAAGGGACCTAA
1 AATTTTTTTTCCAACTTTTAAGGGGTCC-AC
4614 AATTTTTTTTCCAACTTTTAAGG
1 AATTTTTTTTCCAACTTTTAAGG
4637 AACCTAAAAC
Statistics
Matches: 65, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
27 5 0.08
28 8 0.12
29 16 0.25
30 29 0.45
31 7 0.11
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (30 bp):
AATTTTTTTTCCAACTTTTAAGGGGTCCAC
Found at i:4642 original size:30 final size:30
Alignment explanation
Indices: 4584--4645 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
4574 AAGGTCCAAC
* *
4584 AATTTTTTTACTAATTTTAAAGGGACCTAA
1 AATTTTTTTACCAATTTTAAAGGAACCTAA
*
4614 AATTTTTTTTCCAACTTTT-AAGGAACCTAA
1 AATTTTTTTACCAA-TTTTAAAGGAACCTAA
4644 AA
1 AA
4646 CCTCATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (30 bp):
AATTTTTTTACCAATTTTAAAGGAACCTAA
Found at i:23860 original size:21 final size:21
Alignment explanation
Indices: 23836--23878 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
23826 AATGTCAGTC
*
23836 CTATAAATAATGAAATCAAAT
1 CTATAAACAATGAAATCAAAT
*
23857 CTATAAACAATGAAATCTAAT
1 CTATAAACAATGAAATCAAAT
23878 C
1 C
23879 ATGAACATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.28
Consensus pattern (21 bp):
CTATAAACAATGAAATCAAAT
Found at i:25762 original size:22 final size:22
Alignment explanation
Indices: 25737--25779 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
25727 AAAATTTTAA
* *
25737 TTTAATCTTTTAAAAATTACAT
1 TTTAATATTGTAAAAATTACAT
*
25759 TTTACTATTGTAAAAATTACA
1 TTTAATATTGTAAAAATTACA
25780 ATCTCTAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (22 bp):
TTTAATATTGTAAAAATTACAT
Found at i:30171 original size:17 final size:17
Alignment explanation
Indices: 30136--30170 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
30126 AAAGTAATAT
*
30136 ATAATTATATTTTAAAA
1 ATAATTATATTCTAAAA
30153 ATAATATATATTCTAAAA
1 ATAAT-TATATTCTAAAA
30171 TTAGAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAATTATATTCTAAAA
Found at i:33007 original size:12 final size:12
Alignment explanation
Indices: 32990--33014 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32980 TGTTAATATG
32990 ATGAATGCTATT
1 ATGAATGCTATT
33002 ATGAATGCTATT
1 ATGAATGCTATT
33014 A
1 A
33015 ATTATTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:35568 original size:21 final size:21
Alignment explanation
Indices: 35538--35587 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
35528 ACTTTGCCAA
* * *
35538 AACCAAAACTTGTTTTACCAG
1 AACCAGAACTAGTTTCACCAG
35559 AACCAGAACTAGTTTCACCAG
1 AACCAGAACTAGTTTCACCAG
*
35580 AACTAGAA
1 AACCAGAA
35588 GTGATGAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.42, C:0.24, G:0.12, T:0.22
Consensus pattern (21 bp):
AACCAGAACTAGTTTCACCAG
Found at i:41666 original size:32 final size:31
Alignment explanation
Indices: 41604--41712 Score: 155
Period size: 31 Copynumber: 3.5 Consensus size: 31
41594 AAAAATGGGA
* *
41604 GGGTTTGAACAAAAATATAGACCCAAAAAAT
1 GGGTTTGGACAAAAATATAGGCCCAAAAAAT
41635 GGGTTTGGACAAAAATAATAGGCCCAAAAAAT
1 GGGTTTGGACAAAAAT-ATAGGCCCAAAAAAT
* *
41667 GGGTTTAGACAAAAATATAGGCCCGAAAAAT
1 GGGTTTGGACAAAAATATAGGCCCAAAAAAT
**
41698 GGACTTGGACAAAAA
1 GGGTTTGGACAAAAA
41713 GTGAGGCTCA
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
31 41 0.59
32 29 0.41
ACGTcount: A:0.48, C:0.13, G:0.21, T:0.18
Consensus pattern (31 bp):
GGGTTTGGACAAAAATATAGGCCCAAAAAAT
Found at i:41857 original size:22 final size:21
Alignment explanation
Indices: 41832--41914 Score: 78
Period size: 22 Copynumber: 3.7 Consensus size: 21
41822 TATATTGTTG
41832 TTTTGGTGCTATTTTTTTT-CTA
1 TTTTGGTG-T-TTTTTTTTACTA
*
41854 TTTTGGTGTTGTTGTTTTTTACTG
1 TTTTGGTG-T-TT-TTTTTTACTA
*
41878 TTTTAGTGTTTTTTTTTACTA
1 TTTTGGTGTTTTTTTTTACTA
*
41899 TTTTGGTTGTTGTTTT
1 TTTTGG-TGTTTTTTT
41915 AGTGATGTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
21 14 0.27
22 21 0.41
23 7 0.14
24 9 0.18
ACGTcount: A:0.07, C:0.05, G:0.18, T:0.70
Consensus pattern (21 bp):
TTTTGGTGTTTTTTTTTACTA
Found at i:41887 original size:21 final size:22
Alignment explanation
Indices: 41861--41914 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
41851 CTATTTTGGT
*
41861 GTTGTTGTTTTTTACTGTTTTA
1 GTTGTTGTTTTTTACTATTTTA
* *
41883 G-TGTTTTTTTTTACTATTTTG
1 GTTGTTGTTTTTTACTATTTTA
41904 GTTGTTGTTTT
1 GTTGTTGTTTT
41915 AGTGATGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.07, C:0.04, G:0.19, T:0.70
Consensus pattern (22 bp):
GTTGTTGTTTTTTACTATTTTA
Found at i:41955 original size:12 final size:12
Alignment explanation
Indices: 41934--42009 Score: 82
Period size: 12 Copynumber: 6.4 Consensus size: 12
41924 ATTTTTACTA
*
41934 TTTTGATGTTAT
1 TTTTGTTGTTAT
41946 TTTTGTTGTTAT
1 TTTTGTTGTTAT
**
41958 TTTTGTTACTAT
1 TTTTGTTGTTAT
*
41970 TTTTGCTGTTAT
1 TTTTGTTGTTAT
*
41982 TTTTGTTGTT-G
1 TTTTGTTGTTAT
* *
41993 TTTTGCTATTAT
1 TTTTGTTGTTAT
42005 TTTTG
1 TTTTG
42010 CTACGGTTTT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
11 8 0.15
12 44 0.85
ACGTcount: A:0.11, C:0.04, G:0.16, T:0.70
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:41997 original size:35 final size:35
Alignment explanation
Indices: 41884--42011 Score: 118
Period size: 35 Copynumber: 3.7 Consensus size: 35
41874 ACTGTTTTAG
* * * * *
41884 TGTT-TTTTTTTACTATTTTGGTTGTTGTTTTAG-
1 TGTTGTTTTGTTACTATTTTTGCTGTTATTTTTGT
* * *
41917 TGATGTTATTTTTACTA-TTTTGATGTTATTTTTGT
1 TGTTGTT-TTGTTACTATTTTTGCTGTTATTTTTGT
*
41952 TGTTATTTTTGTTACTATTTTTGCTGTTATTTTTGT
1 TGTT-GTTTTGTTACTATTTTTGCTGTTATTTTTGT
* *
41988 TGTTGTTTTGCTATTATTTTTGCT
1 TGTTGTTTTGTTACTATTTTTGCT
42012 ACGGTTTTGG
Statistics
Matches: 78, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
33 3 0.04
34 15 0.19
35 37 0.47
36 23 0.29
ACGTcount: A:0.12, C:0.05, G:0.16, T:0.68
Consensus pattern (35 bp):
TGTTGTTTTGTTACTATTTTTGCTGTTATTTTTGT
Found at i:42235 original size:21 final size:21
Alignment explanation
Indices: 42193--42236 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
42183 ATTTATTTAT
* *
42193 TTTTTAATGTTTGTTTTAATG
1 TTTTTAATGTTTATTTGAATG
42214 TTTTTAA-GTTTATTTGATATG
1 TTTTTAATGTTTATTTGA-ATG
42235 TT
1 TT
42237 ATATATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.20, C:0.00, G:0.14, T:0.66
Consensus pattern (21 bp):
TTTTTAATGTTTATTTGAATG
Found at i:42248 original size:38 final size:38
Alignment explanation
Indices: 42166--42249 Score: 91
Period size: 38 Copynumber: 2.2 Consensus size: 38
42156 ATATAAAGAA
* * *
42166 TTTTTAATGTATTTTAAATTTATTTATTTTTTAATGTT
1 TTTTTAATGTATTTTAAATTTATTTATATGTTAATGAT
*
42204 TGTTTTAATGT-TTTTAAGTTTATTTGATATGTTATAT-AT
1 T-TTTTAATGTATTTTAAATTTATTT-ATATGTTA-ATGAT
42243 TTTTTAA
1 TTTTTAA
42250 ATTTGTTGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
38 20 0.51
39 17 0.44
40 2 0.05
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.65
Consensus pattern (38 bp):
TTTTTAATGTATTTTAAATTTATTTATATGTTAATGAT
Found at i:46543 original size:12 final size:12
Alignment explanation
Indices: 46526--46550 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
46516 TGTTAATATG
46526 ATGAATGCTATT
1 ATGAATGCTATT
46538 ATGAATGCTATT
1 ATGAATGCTATT
46550 A
1 A
46551 ATTATTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:64997 original size:22 final size:22
Alignment explanation
Indices: 64948--64998 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
64938 ATATTATTTT
64948 TAATTTTAAAAAAATATTTATA
1 TAATTTTAAAAAAATATTTATA
* **
64970 TTATTTTAATTAAATATTTA-A
1 TAATTTTAAAAAAATATTTATA
*
64991 TAAATTTA
1 TAATTTTA
64999 TATTTTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TAATTTTAAAAAAATATTTATA
Found at i:72010 original size:83 final size:83
Alignment explanation
Indices: 71865--72039 Score: 269
Period size: 83 Copynumber: 2.1 Consensus size: 83
71855 TGTCCTCTAT
* *
71865 TATTGCTATGTTTTGAAACATATAAACTTGGATGACTACTTTTCCTCAAACTAAGACCCGAAAAT
1 TATTG-TATGTTCTAAAACATATAAACTTGGATGACTACTTTTCCTCAAACTAAGACCCGAAAAT
* * * *
71930 AGCGATTTGGTTTGGAAAA
65 AGCAACTTGGTTCGAAAAA
*
71949 TATTGTATGTTCTAAAACATATAAACTTGGATGACTACTTTTCCTCAAACTAAGACTCGAAAATA
1 TATTGTATGTTCTAAAACATATAAACTTGGATGACTACTTTTCCTCAAACTAAGACCCGAAAATA
72014 GCAACTTGGTTCGAAAAA
66 GCAACTTGGTTCGAAAAA
*
72032 TGTTGTAT
1 TATTGTAT
72040 AATAAAGCAT
Statistics
Matches: 83, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
83 78 0.94
84 5 0.06
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (83 bp):
TATTGTATGTTCTAAAACATATAAACTTGGATGACTACTTTTCCTCAAACTAAGACCCGAAAATA
GCAACTTGGTTCGAAAAA
Found at i:74338 original size:21 final size:21
Alignment explanation
Indices: 74312--74383 Score: 108
Period size: 21 Copynumber: 3.4 Consensus size: 21
74302 ACAAAACATT
74312 ATGTTTGTAACTCTCCTCATA
1 ATGTTTGTAACTCTCCTCATA
*
74333 ATGTTTATAACTCTCCTCATA
1 ATGTTTGTAACTCTCCTCATA
* *
74354 ATGTTTTGTAACTCCCCTCATT
1 ATG-TTTGTAACTCTCCTCATA
74376 ATGTTTGT
1 ATGTTTGT
74384 TTTAAATTTC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
21 28 0.61
22 18 0.39
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.46
Consensus pattern (21 bp):
ATGTTTGTAACTCTCCTCATA
Found at i:74372 original size:22 final size:22
Alignment explanation
Indices: 74315--74381 Score: 100
Period size: 22 Copynumber: 3.1 Consensus size: 22
74305 AAACATTATG
74315 TTTGTAACTCTCCTCATAATG-
1 TTTGTAACTCTCCTCATAATGT
*
74336 TTTATAACTCTCCTCATAATGT
1 TTTGTAACTCTCCTCATAATGT
* *
74358 TTTGTAACTCCCCTCATTATGT
1 TTTGTAACTCTCCTCATAATGT
74380 TT
1 TT
74382 GTTTTAAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
21 20 0.49
22 21 0.51
ACGTcount: A:0.22, C:0.24, G:0.07, T:0.46
Consensus pattern (22 bp):
TTTGTAACTCTCCTCATAATGT
Found at i:79806 original size:29 final size:29
Alignment explanation
Indices: 79766--79824 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
79756 TTGTAGAAGA
* * *
79766 GGTGGAGAACTTGTTCGTTGAGAGTTCGT
1 GGTGAAGAACTTGTTCGTAGAGAATTCGT
*
79795 GGTGAAGAACTTGTTTGTAGAGAATTCGT
1 GGTGAAGAACTTGTTCGTAGAGAATTCGT
79824 G
1 G
79825 TCAAGGTAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.22, C:0.08, G:0.36, T:0.34
Consensus pattern (29 bp):
GGTGAAGAACTTGTTCGTAGAGAATTCGT
Found at i:88283 original size:21 final size:21
Alignment explanation
Indices: 88257--88306 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
88247 ACAAAACATT
88257 ATGTTTGTAACTCTCCTCATA
1 ATGTTTGTAACTCTCCTCATA
*
88278 ATGTTTGTAACTCTCCTCATT
1 ATGTTTGTAACTCTCCTCATA
88299 ATGTTTGT
1 ATGTTTGT
88307 TTTAAATTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.20, G:0.12, T:0.48
Consensus pattern (21 bp):
ATGTTTGTAACTCTCCTCATA
Found at i:88988 original size:16 final size:17
Alignment explanation
Indices: 88950--88994 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
88940 TTGTATGAAA
*
88950 ATATATTTATTTACTTTT
1 ATAT-TTTAATTACTTTT
*
88968 CTATTTTAATTAC-TTT
1 ATATTTTAATTACTTTT
88984 ATATTTTAATT
1 ATATTTTAATT
88995 TTCTTATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 13 0.54
17 8 0.33
18 3 0.12
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (17 bp):
ATATTTTAATTACTTTT
Found at i:91918 original size:6 final size:6
Alignment explanation
Indices: 91907--91937 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
91897 TCTAATGGAA
*
91907 TCTCAT TCTCAT TTTCAT TCTCAT TCTCAT T
1 TCTCAT TCTCAT TCTCAT TCTCAT TCTCAT T
91938 TGAAGAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.16, C:0.29, G:0.00, T:0.55
Consensus pattern (6 bp):
TCTCAT
Found at i:95689 original size:18 final size:18
Alignment explanation
Indices: 95643--95691 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
95633 CACATAGTCA
**
95643 ATTGCAACCACAATCGGG
1 ATTGCAACCACAATCAAG
* *
95661 ATTACAGCCACAATCAAG
1 ATTGCAACCACAATCAAG
*
95679 TTTGCAACCACAA
1 ATTGCAACCACAA
95692 ATGCAAGGAC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.39, C:0.29, G:0.14, T:0.18
Consensus pattern (18 bp):
ATTGCAACCACAATCAAG
Found at i:101891 original size:12 final size:12
Alignment explanation
Indices: 101871--101900 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
101861 GAACAAGAGA
*
101871 ATGAAGCGAAGG
1 ATGACGCGAAGG
101883 ATGACGCGAAGG
1 ATGACGCGAAGG
101895 ATGACG
1 ATGACG
101901 AACACATTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.40, T:0.10
Consensus pattern (12 bp):
ATGACGCGAAGG
Found at i:102367 original size:17 final size:17
Alignment explanation
Indices: 102327--102359 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
102317 AGTTAGCATT
102327 CTTACA-TTTTATTGTC
1 CTTACATTTTTATTGTC
102343 CTTACATTTTTATTGTC
1 CTTACATTTTTATTGTC
102360 ACTGCATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.18, C:0.18, G:0.06, T:0.58
Consensus pattern (17 bp):
CTTACATTTTTATTGTC
Found at i:107287 original size:17 final size:17
Alignment explanation
Indices: 107278--107313 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
107268 TAAATATATT
107278 TATTATATAAAATAATA
1 TATTATATAAAATAATA
*
107295 TATTATA-ACAATAATA
1 TATTATATAAAATAATA
107311 TAT
1 TAT
107314 AAGTGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TATTATATAAAATAATA
Found at i:129711 original size:45 final size:45
Alignment explanation
Indices: 129662--129763 Score: 168
Period size: 45 Copynumber: 2.3 Consensus size: 45
129652 GTCTTTCTGT
129662 TATGGTCTTACTCACTTCTATCATGATGCCATAACATCTTTCAAC
1 TATGGTCTTACTCACTTCTATCATGATGCCATAACATCTTTCAAC
* * * *
129707 TATGGTTTTACTCACTTTTATCATGATGTCATAACATCTTTCAGC
1 TATGGTCTTACTCACTTCTATCATGATGCCATAACATCTTTCAAC
129752 TATGGTCTTACT
1 TATGGTCTTACT
129764 TATTTTTTGG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.42
Consensus pattern (45 bp):
TATGGTCTTACTCACTTCTATCATGATGCCATAACATCTTTCAAC
Found at i:139792 original size:48 final size:46
Alignment explanation
Indices: 139740--139860 Score: 172
Period size: 48 Copynumber: 2.5 Consensus size: 46
139730 ATACATTTGA
139740 AAATTTATTATTTT-TTCATTGTTTAACTGAATTTATTTTATATCTATT
1 AAATTTA-TATTTTATT-ATT-TTTAACTGAATTTATTTTATATCTATT
139788 AAATTTATATTTTACATTATTTTTAACTGAATTTATTTTATATCTATT
1 AAATTTATATTTT--ATTATTTTTAACTGAATTTATTTTATATCTATT
139836 AAATTTATATTTTACATTATTTTTA
1 AAATTTATATTTT--ATTATTTTTA
139861 CATATATTAC
Statistics
Matches: 70, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
47 6 0.09
48 59 0.84
49 3 0.04
50 2 0.03
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (46 bp):
AAATTTATATTTTATTATTTTTAACTGAATTTATTTTATATCTATT
Found at i:139807 original size:27 final size:27
Alignment explanation
Indices: 139777--139855 Score: 80
Period size: 27 Copynumber: 3.1 Consensus size: 27
139767 TGAATTTATT
139777 TTATATCTATTAAATTTATATTTTACA
1 TTATATCTATTAAATTTATATTTTACA
* * **
139804 TTAT-T-T-TT-AACTGA-A-TTTATT
1 TTATATCTATTAAATTTATATTTTACA
139825 TTATATCTATTAAATTTATATTTTACA
1 TTATATCTATTAAATTTATATTTTACA
139852 TTAT
1 TTAT
139856 TTTTACATAT
Statistics
Matches: 38, Mismatches: 8, Indels: 12
0.66 0.14 0.21
Matches are distributed among these distances:
21 8 0.21
22 2 0.05
23 5 0.13
24 4 0.11
25 5 0.13
26 2 0.05
27 12 0.32
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.58
Consensus pattern (27 bp):
TTATATCTATTAAATTTATATTTTACA
Found at i:142035 original size:34 final size:35
Alignment explanation
Indices: 141997--142076 Score: 83
Period size: 35 Copynumber: 2.3 Consensus size: 35
141987 TGTATATCTG
* * *
141997 ACTAGTGTTGGGCACACAT-TCGTTGGTTTATTCA
1 ACTAGAGTTGGGCACAAATATCGTTGGTTTATCCA
* * *
142031 ACTAGCA-TTGAGCACAAATATTGTTGGTTTCTCCA
1 ACTAG-AGTTGGGCACAAATATCGTTGGTTTATCCA
142066 ACTAGAGTTGG
1 ACTAGAGTTGG
142077 AATCACTATT
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
34 16 0.44
35 20 0.56
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (35 bp):
ACTAGAGTTGGGCACAAATATCGTTGGTTTATCCA
Found at i:146841 original size:37 final size:36
Alignment explanation
Indices: 146800--146947 Score: 161
Period size: 37 Copynumber: 4.0 Consensus size: 36
146790 AGCCCGATTT
* * * *
146800 CACCGGCACGAAGTCTACTAGGCACATAGTCCGAATA
1 CACCGACAC-AAGCCTACTAGGCACATAGCCCAAATA
* * *
146837 CACCGACACAAACCTGCTAGGCACATAGCCCGAATA
1 CACCGACACAAGCCTACTAGGCACATAGCCCAAATA
* * * *
146873 CATCGGCACAATGCCTGCTAGGCAAATAGCCCAAATA
1 CACCGACACAA-GCCTACTAGGCACATAGCCCAAATA
*
146910 CACCAACACGAAGCCTACTAGGCACATAGCCCAAATA
1 CACCGACAC-AAGCCTACTAGGCACATAGCCCAAATA
146947 C
1 C
146948 TCAAATGCAA
Statistics
Matches: 94, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
36 32 0.34
37 60 0.64
38 2 0.02
ACGTcount: A:0.36, C:0.33, G:0.18, T:0.14
Consensus pattern (36 bp):
CACCGACACAAGCCTACTAGGCACATAGCCCAAATA
Found at i:146860 original size:36 final size:36
Alignment explanation
Indices: 146817--146947 Score: 163
Period size: 37 Copynumber: 3.6 Consensus size: 36
146807 ACGAAGTCTA
* * *
146817 CTAGGCACATAGTCCGAATACACCGACACAAACCTG
1 CTAGGCACATAGCCCAAATACACCGACACAAGCCTG
* * *
146853 CTAGGCACATAGCCCGAATACATCGGCACAATGCCTG
1 CTAGGCACATAGCCCAAATACACCGACACAA-GCCTG
* * *
146890 CTAGGCAAATAGCCCAAATACACCAACACGAAGCCTA
1 CTAGGCACATAGCCCAAATACACCGACAC-AAGCCTG
146927 CTAGGCACATAGCCCAAATAC
1 CTAGGCACATAGCCCAAATAC
146948 TCAAATGCAA
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
36 28 0.34
37 52 0.63
38 2 0.02
ACGTcount: A:0.37, C:0.33, G:0.17, T:0.14
Consensus pattern (36 bp):
CTAGGCACATAGCCCAAATACACCGACACAAGCCTG
Found at i:146867 original size:73 final size:74
Alignment explanation
Indices: 146778--146947 Score: 191
Period size: 73 Copynumber: 2.3 Consensus size: 74
146768 CACAAAGGCA
* * * * * * * * *
146778 TGCTAGGCATAAAGCCCGATTTCACCGGCACGAA-GTCTACTAGGCACATAGTCCGAATACACCG
1 TGCTAGGCACATAGCCCGAATACACCGGCAC-AATGCCTACTAGGCAAATAGCCCAAATACACCA
146842 ACAC-AAACC
65 ACACGAAACC
* *
146851 TGCTAGGCACATAGCCCGAATACATCGGCACAATGCCTGCTAGGCAAATAGCCCAAATACACCAA
1 TGCTAGGCACATAGCCCGAATACACCGGCACAATGCCTACTAGGCAAATAGCCCAAATACACCAA
*
146916 CACGAAGCC
66 CACGAAACC
* *
146925 TACTAGGCACATAGCCCAAATAC
1 TGCTAGGCACATAGCCCGAATAC
146948 TCAAATGCAA
Statistics
Matches: 81, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
72 2 0.02
73 54 0.67
74 25 0.31
ACGTcount: A:0.35, C:0.32, G:0.18, T:0.15
Consensus pattern (74 bp):
TGCTAGGCACATAGCCCGAATACACCGGCACAATGCCTACTAGGCAAATAGCCCAAATACACCAA
CACGAAACC
Found at i:148874 original size:37 final size:36
Alignment explanation
Indices: 148818--149033 Score: 225
Period size: 37 Copynumber: 5.8 Consensus size: 36
148808 GTTATTAGAT
* *
148818 CACCGGCACAAAGCTTGCTAGGCACATAGCCTGAATA
1 CACCGGCA-TAAGCCTGCTAGGCACATAGCCTGAATA
* *
148855 CACCGGCATGAAGCCTGCTAGGCACACAGCCTTAATA
1 CACCGGCAT-AAGCCTGCTAGGCACATAGCCTGAATA
** * *
148892 CACAAGCACAAGGCCTGCTAGGCACACAGCCTGAATA
1 CACCGGCATAA-GCCTGCTAGGCACATAGCCTGAATA
* ** * **
148929 CACTGGCACTAAAACTACTAGGCACATAGCCCAAATA
1 CACCGGCA-TAAGCCTGCTAGGCACATAGCCTGAATA
* *
148966 CACCGACACAAAGCCTGCTAGGCACATAGCCTGAATA
1 CACCGGCA-TAAGCCTGCTAGGCACATAGCCTGAATA
*
149003 CACCAGCACTAAGCCTGCTAGGCACATAGCC
1 CACCGGCA-TAAGCCTGCTAGGCACATAGCC
149034 CGAGTATTGT
Statistics
Matches: 148, Mismatches: 28, Indels: 6
0.81 0.15 0.03
Matches are distributed among these distances:
36 2 0.01
37 144 0.97
38 2 0.01
ACGTcount: A:0.34, C:0.32, G:0.19, T:0.14
Consensus pattern (36 bp):
CACCGGCATAAGCCTGCTAGGCACATAGCCTGAATA
Found at i:148950 original size:74 final size:73
Alignment explanation
Indices: 148823--149034 Score: 282
Period size: 74 Copynumber: 2.9 Consensus size: 73
148813 TAGATCACCG
* * *
148823 GCACAAAGCTTGCTAGGCACATAGCCTGAATACACCGGCA-TGAAGCCTGCTAGGCACACAGCCT
1 GCACAAAGCCTGCTAGGCACATAGCCTGAATACACCGGCACT-AAGCCTGCTAGGCACATAGCCC
*
148887 TAATACACAA
65 AAATACAC-A
* * * ** *
148897 GCACAAGGCCTGCTAGGCACACAGCCTGAATACACTGGCACTAAAACTACTAGGCACATAGCCCA
1 GCACAAAGCCTGCTAGGCACATAGCCTGAATACACCGGCACTAAGCCTGCTAGGCACATAGCCCA
*
148962 AATACACC
66 AATACACA
*
148970 GACACAAAGCCTGCTAGGCACATAGCCTGAATACACCAGCACTAAGCCTGCTAGGCACATAGCCC
1 G-CACAAAGCCTGCTAGGCACATAGCCTGAATACACCGGCACTAAGCCTGCTAGGCACATAGCCC
149035 GAGTATTGTG
Statistics
Matches: 118, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
73 1 0.01
74 116 0.98
75 1 0.01
ACGTcount: A:0.34, C:0.32, G:0.19, T:0.15
Consensus pattern (73 bp):
GCACAAAGCCTGCTAGGCACATAGCCTGAATACACCGGCACTAAGCCTGCTAGGCACATAGCCCA
AATACACA
Found at i:156090 original size:37 final size:37
Alignment explanation
Indices: 156037--156255 Score: 242
Period size: 37 Copynumber: 5.9 Consensus size: 37
156027 ATTGGATCAT
*
156037 CGGCACAAAGCCTGCTAGGCATATAGCCTGAATACAC
1 CGGCACAAAGCCTGCTAGGCACATAGCCTGAATACAC
* * *
156074 CGGCACAAAGCTTGCTAGGCACACAACCTGAATACAC
1 CGGCACAAAGCCTGCTAGGCACATAGCCTGAATACAC
** * * *
156111 CAACACAAGGCCTGTTAGGCAC-TCAGCCTGAATACAT
1 CGGCACAAAGCCTGCTAGGCACAT-AGCCTGAATACAC
* **
156148 CGGCACTAAGCCTGCTAGGCACATAGCCCAAATACAC
1 CGGCACAAAGCCTGCTAGGCACATAGCCTGAATACAC
* * * *
156185 CGGCATAAAGCCTGCTAGGCACATAGCTTAAACACAC
1 CGGCACAAAGCCTGCTAGGCACATAGCCTGAATACAC
* * * *
156222 CGACACTAAGCTTGCTAGGCACATAGCCCGAATA
1 CGGCACAAAGCCTGCTAGGCACATAGCCTGAATA
156256 TTGTGGAAGC
Statistics
Matches: 147, Mismatches: 33, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
37 146 0.99
38 1 0.01
ACGTcount: A:0.33, C:0.31, G:0.20, T:0.16
Consensus pattern (37 bp):
CGGCACAAAGCCTGCTAGGCACATAGCCTGAATACAC
Found at i:156241 original size:111 final size:111
Alignment explanation
Indices: 156034--156243 Score: 278
Period size: 111 Copynumber: 1.9 Consensus size: 111
156024 GTTATTGGAT
* ** *
156034 CATCGGCACAAAGCCTGCTAGGCATATAGCCTGAATACACCGGCACAAAGCTTGCTAGGCACACA
1 CATCGGCACAAAGCCTGCTAGGCACATAGCCCAAATACACCGGCACAAAGCCTGCTAGGCACACA
* * *
156099 ACCTGAATACACCAACACAAGGCCTGTTAGGCACTCAGCCTGAATA
66 ACCTAAACACACCAACACAAGGCCTGCTAGGCACTCAGCCTGAATA
* * *
156145 CATCGGCACTAAGCCTGCTAGGCACATAGCCCAAATACACCGGCATAAAGCCTGCTAGGCACATA
1 CATCGGCACAAAGCCTGCTAGGCACATAGCCCAAATACACCGGCACAAAGCCTGCTAGGCACACA
* * * *
156210 GCTTAAACACACCGACACTAA-GCTTGCTAGGCAC
66 ACCTAAACACACCAACAC-AAGGCCTGCTAGGCAC
156244 ATAGCCCGAA
Statistics
Matches: 84, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
111 82 0.98
112 2 0.02
ACGTcount: A:0.33, C:0.31, G:0.20, T:0.16
Consensus pattern (111 bp):
CATCGGCACAAAGCCTGCTAGGCACATAGCCCAAATACACCGGCACAAAGCCTGCTAGGCACACA
ACCTAAACACACCAACACAAGGCCTGCTAGGCACTCAGCCTGAATA
Found at i:157001 original size:4 final size:4
Alignment explanation
Indices: 156994--157040 Score: 62
Period size: 4 Copynumber: 11.8 Consensus size: 4
156984 TTCTTCCTTC
156994 TTCT TTCT TTCT TTCT TTCT TTCTT TATCT TT-T TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTCT TTCT TTC-T T-TCT TTCT TTCT TTCT TTCT TTC
157041 CTTAATTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
3 6 0.15
4 27 0.69
5 4 0.10
6 2 0.05
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:157011 original size:12 final size:11
Alignment explanation
Indices: 156994--157040 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
156984 TTCTTCCTTC
156994 TTCTTTCTTTCT
1 TTCTTTCTTT-T
*
157006 TTCTTTCTTTC
1 TTCTTTCTTTT
*
157017 TT-TATCTTTT
1 TTCTTTCTTTT
157027 TTCTTTCTTTT
1 TTCTTTCTTTT
157038 TTC
1 TTC
157041 CTTAATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
10 8 0.27
11 12 0.40
12 10 0.33
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (11 bp):
TTCTTTCTTTT
Found at i:157407 original size:10 final size:9
Alignment explanation
Indices: 157390--157416 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
157380 TTTTAAATAT
157390 ATAAAAAAA
1 ATAAAAAAA
157399 ATAAAAAAA
1 ATAAAAAAA
157408 ATAAAAAAA
1 ATAAAAAAA
157417 CACGTGTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:157798 original size:20 final size:20
Alignment explanation
Indices: 157739--157799 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
157729 ATAAATGTCT
*
157739 TATAAATAAATATTAATAAT
1 TATAAATAAATATTAATAAA
**
157759 TATATTTAAATA-TAATTAAA
1 TATAAATAAATATTAA-TAAA
* *
157779 TATAGATAAATATTAGTAAA
1 TATAAATAAATATTAATAAA
157799 T
1 T
157800 CTCGAATTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 3 0.09
20 28 0.85
21 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (20 bp):
TATAAATAAATATTAATAAA
Found at i:157877 original size:14 final size:14
Alignment explanation
Indices: 157836--157885 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
157826 TTTGAATTCA
*
157836 AAATTTAAA-ATTT
1 AAATTTAAAGTTTT
157849 AAAGTTTAAAGTTTT
1 AAA-TTTAAAGTTTT
*
157864 AAATTTAGAGTTTT
1 AAATTTAAAGTTTT
157878 AATATTTA
1 AA-ATTTA
157886 TTTATGTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 3 0.09
14 18 0.56
15 11 0.34
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (14 bp):
AAATTTAAAGTTTT
Found at i:157885 original size:21 final size:22
Alignment explanation
Indices: 157838--157885 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
157828 TGAATTCAAA
157838 ATTTAAAATTTAAAGTTTAAAGT
1 ATTT-AAATTTAAAGTTTAAAGT
* *
157861 -TTTAAATTTAGAGTTTTAA-T
1 ATTTAAATTTAAAGTTTAAAGT
157881 ATTTA
1 ATTTA
157886 TTTATGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.05
21 18 0.82
22 3 0.14
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (22 bp):
ATTTAAATTTAAAGTTTAAAGT
Found at i:165491 original size:15 final size:16
Alignment explanation
Indices: 165471--165500 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
165461 ATCATAATTT
165471 TTTTCTT-CTTTTTCA
1 TTTTCTTCCTTTTTCA
165486 TTTTCTTCCTTTTTC
1 TTTTCTTCCTTTTTC
165501 TCATTTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTCTTCCTTTTTCA
Found at i:165512 original size:15 final size:16
Alignment explanation
Indices: 165469--165515 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
165459 TTATCATAAT
*
165469 TTTTTTCTTCTTTTTCA
1 TTTTTTCTT-TTTCTCA
165486 TTTTCTTCCTTTTTCTCA
1 TTTT-TT-CTTTTTCTCA
165504 -TTTTTCTTTTTC
1 TTTTTTCTTTTTC
165516 GAGTGACTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 7 0.26
16 2 0.07
17 7 0.26
18 8 0.30
19 3 0.11
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTCTTTTTCTCA
Found at i:185937 original size:24 final size:24
Alignment explanation
Indices: 185910--185963 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
185900 GTAGGTATTG
*
185910 GTAGTTCTGCTCATAGAAGTATCA
1 GTAGTTCTACTCATAGAAGTATCA
*
185934 GTAGTTCTACTCATAGAAGTATCG
1 GTAGTTCTACTCATAGAAGTATCA
185958 GTAGTT
1 GTAGTT
185964 TATGTACTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (24 bp):
GTAGTTCTACTCATAGAAGTATCA
Found at i:186389 original size:36 final size:36
Alignment explanation
Indices: 186341--186436 Score: 156
Period size: 36 Copynumber: 2.7 Consensus size: 36
186331 TTCGGGTGTT
*
186341 ACATGAAGAACATATCCACATATTTTCTATCACATG
1 ACATGAAGAACATACCCACATATTTTCTATCACATG
* *
186377 GCATGAAGAACATACCCACATATTTTCTGTCACATG
1 ACATGAAGAACATACCCACATATTTTCTATCACATG
*
186413 ACACGAAGAACATACCCACATATT
1 ACATGAAGAACATACCCACATATT
186437 CACTTTCACA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.39, C:0.25, G:0.10, T:0.26
Consensus pattern (36 bp):
ACATGAAGAACATACCCACATATTTTCTATCACATG
Found at i:186551 original size:23 final size:23
Alignment explanation
Indices: 186520--186937 Score: 452
Period size: 23 Copynumber: 18.3 Consensus size: 23
186510 TAATTCTTTT
186520 AGCATAAATCACATTAATATTTA
1 AGCATAAATCACATTAATATTTA
* *
186543 ATCATAAATCATATTAATATTT-
1 AGCATAAATCACATTAATATTTA
*
186565 AGCAAAAATCACATTAATATTTA
1 AGCATAAATCACATTAATATTTA
* * * * *
186588 AACATATATTATATTAATATTTG
1 AGCATAAATCACATTAATATTTA
* *
186611 AGCACAAATCATATTAATATTTA
1 AGCATAAATCACATTAATATTTA
* * *
186634 GGCACAAATCATATTAATATTTA
1 AGCATAAATCACATTAATATTTA
* * *
186657 AGTACAAATCACATTAATA-TTG
1 AGCATAAATCACATTAATATTTA
* *
186679 AGTACT-AATCACATTAATATTTC
1 AGCA-TAAATCACATTAATATTTA
* *
186702 AGAATAAATCATATTAATATTTA
1 AGCATAAATCACATTAATATTTA
*
186725 AGCATAAATCACATTAATATTCA
1 AGCATAAATCACATTAATATTTA
*
186748 AGCATAAATCACATTAATATTTG
1 AGCATAAATCACATTAATATTTA
*
186771 AGCACAAATCACATTAATATTTA
1 AGCATAAATCACATTAATATTTA
** * *
186794 AATATAGATCACATTAATATTTG
1 AGCATAAATCACATTAATATTTA
*
186817 AGCACAAATCACATTAATATTTA
1 AGCATAAATCACATTAATATTTA
*
186840 AGCATAAATCATATTAATATTTGA
1 AGCATAAATCACATTAATATTT-A
*
186864 GAGC--AAATCATATTAATATTTA
1 -AGCATAAATCACATTAATATTTA
* *
186886 AGCAGAAATCGA-ATTAATATTTG
1 AGCATAAATC-ACATTAATATTTA
* *
186909 AGAAAAAATCACATTAATATTTA
1 AGCATAAATCACATTAATATTTA
186932 AGCATA
1 AGCATA
186938 GATATAAGAA
Statistics
Matches: 334, Mismatches: 51, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
21 3 0.01
22 41 0.12
23 285 0.85
24 2 0.01
25 3 0.01
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (23 bp):
AGCATAAATCACATTAATATTTA
Found at i:190204 original size:36 final size:36
Alignment explanation
Indices: 190154--190293 Score: 208
Period size: 36 Copynumber: 3.9 Consensus size: 36
190144 AATATAATTA
* * *
190154 GTCACATGGTATGAAGAATACACCCACATATTTTCT
1 GTCACATGGCATGAAGAACATACCCACATATTTTCT
* ** *
190190 GTCACATGCCATGAAGAACATATTCACATATTTTCA
1 GTCACATGGCATGAAGAACATACCCACATATTTTCT
*
190226 GTCACATGGCATGAAAAACATACCCACATATTTTCT
1 GTCACATGGCATGAAGAACATACCCACATATTTTCT
190262 GTCACATGGCATGAAGAACATACCCACATATT
1 GTCACATGGCATGAAGAACATACCCACATATT
190294 CACTTTTACT
Statistics
Matches: 91, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 91 1.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.28
Consensus pattern (36 bp):
GTCACATGGCATGAAGAACATACCCACATATTTTCT
Found at i:190423 original size:23 final size:23
Alignment explanation
Indices: 190373--190795 Score: 542
Period size: 23 Copynumber: 18.3 Consensus size: 23
190363 ATCTTAATTC
190373 TTTAAGCACAAATCACATTAAATA
1 TTTAAGCACAAATCACATT-AATA
* * *
190397 TTTAATCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
190420 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
190443 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
190466 TTTAAGTACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
190489 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
190512 TTTAAGCACAAACCGCATAAATA
1 TTTAAGCACAAATCACATTAATA
* *
190535 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* * **
190558 TTTAAGCACAAACCGCACAAATA
1 TTTAAGCACAAATCACATTAATA
* *
190581 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
190604 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
190627 TTTGAGTACAAATGACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
190650 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
190673 TGTT-AGCACAAATCACATTAATA
1 T-TTAAGCACAAATCACATTAATA
* * *
190696 TTTTAGCACAAATCATATTAATG
1 TTTAAGCACAAATCACATTAATA
* *
190719 TTTAAACATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
190742 TTTAAGCAGAAATCGCATTAATA
1 TTTAAGCACAAATCACATTAATA
*
190765 TTTGAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
190788 TTTAAGCA
1 TTTAAGCA
190796 TAGATATAAT
Statistics
Matches: 337, Mismatches: 60, Indels: 5
0.84 0.15 0.01
Matches are distributed among these distances:
22 2 0.01
23 317 0.94
24 18 0.05
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.32
Consensus pattern (23 bp):
TTTAAGCACAAATCACATTAATA
Found at i:192727 original size:23 final size:23
Alignment explanation
Indices: 192696--192739 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
192686 ACACCAATGA
192696 ATTGTGTT-GTTGGAATTAGATTGG
1 ATTGTGTTGGTT-GAATT-GATTGG
192720 ATTG-GTTGGTTGAATTGATT
1 ATTGTGTTGGTTGAATTGATT
192740 AGATCGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.21
23 8 0.42
24 7 0.37
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.48
Consensus pattern (23 bp):
ATTGTGTTGGTTGAATTGATTGG
Found at i:197888 original size:12 final size:12
Alignment explanation
Indices: 197849--197888 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
197839 TCAAGTAGAG
197849 ATGAATATATAT
1 ATGAATATATAT
197861 AT-ATATATATAT
1 ATGA-ATATATAT
*
197873 ATGAATATATAC
1 ATGAATATATAT
197885 ATGA
1 ATGA
197889 TGTAATGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 1 0.04
12 23 0.92
13 1 0.04
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (12 bp):
ATGAATATATAT
Found at i:198585 original size:25 final size:25
Alignment explanation
Indices: 198557--198611 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
198547 CTTTATGCCA
* * *
198557 TATTCTTAATGATGCCCTTGTGGCG
1 TATTCTGAAGGATGCCCATGTGGCG
*
198582 TATTCTGAAGGATGCCCATGTGGTG
1 TATTCTGAAGGATGCCCATGTGGCG
198607 TATTC
1 TATTC
198612 AAATTGGCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (25 bp):
TATTCTGAAGGATGCCCATGTGGCG
Found at i:202752 original size:13 final size:13
Alignment explanation
Indices: 202734--202771 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
202724 GTTAACAAGG
202734 TGAAGGTTCACAT
1 TGAAGGTTCACAT
202747 TGAAGGTTCACAT
1 TGAAGGTTCACAT
202760 TGAAGGTTCACA
1 TGAAGGTTCACA
202772 CTTCGGTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Consensus pattern (13 bp):
TGAAGGTTCACAT
Found at i:205327 original size:16 final size:15
Alignment explanation
Indices: 205293--205332 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
205283 TATTAAAAAG
*
205293 AAAGAAAAA-TGTTA
1 AAAGAAAAATTGTAA
205307 AAAGAAAAATTTGTAA
1 AAAGAAAAA-TTGTAA
205323 AAAGAAAAAT
1 AAAGAAAAAT
205333 ATTTTTTAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 9 0.39
15 1 0.04
16 13 0.57
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.20
Consensus pattern (15 bp):
AAAGAAAAATTGTAA
Found at i:210917 original size:6 final size:6
Alignment explanation
Indices: 210906--210933 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
210896 TAAAGTCACT
210906 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
210934 TCTTCCTCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:212066 original size:8 final size:9
Alignment explanation
Indices: 212044--212068 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
212034 TAAAAGACAC
212044 CTTTTTACA
1 CTTTTTACA
212053 CTTTTTACA
1 CTTTTTACA
212062 CTTTTTA
1 CTTTTTA
212069 TTCCCTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (9 bp):
CTTTTTACA
Found at i:217217 original size:17 final size:17
Alignment explanation
Indices: 217175--217217 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
217165 AAATGAACTA
*
217175 ACAAGTAAAATGCAACG
1 ACAACTAAAATGCAACG
* *
217192 AAAACTAAAATGCAATG
1 ACAACTAAAATGCAACG
*
217209 ACAATTAAA
1 ACAACTAAA
217218 TGGGATGCAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.58, C:0.14, G:0.12, T:0.16
Consensus pattern (17 bp):
ACAACTAAAATGCAACG
Found at i:261285 original size:12 final size:11
Alignment explanation
Indices: 261268--261306 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
261258 TAAATAGCAC
261268 AAAATAAAAGA
1 AAAATAAAAGA
*
261279 TAAAATAAAATA
1 -AAAATAAAAGA
261291 GAAAATAAAAGA
1 -AAAATAAAAGA
261303 AAAA
1 AAAA
261307 GTTTGAGATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 4 0.17
12 20 0.83
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (11 bp):
AAAATAAAAGA
Found at i:261290 original size:17 final size:17
Alignment explanation
Indices: 261268--261305 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
261258 TAAATAGCAC
*
261268 AAAATA-AAAGATAAAAT
1 AAAATAGAAA-ATAAAAG
261285 AAAATAGAAAATAAAAG
1 AAAATAGAAAATAAAAG
261302 AAAA
1 AAAA
261306 AGTTTGAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (17 bp):
AAAATAGAAAATAAAAG
Found at i:270112 original size:34 final size:34
Alignment explanation
Indices: 270074--270146 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
270064 AGTAAACAAC
* * *
270074 ATTTGGGTAAGGTAAAAGATAAAATATTAGAAAT
1 ATTTGGGTAAGATAAAAGATAAAAAATTAAAAAT
*
270108 ATTTGGGTAAGATAAAAGGTAAAAAATTAAAAAT
1 ATTTGGGTAAGATAAAAGATAAAAAATTAAAAAT
270142 ATTTG
1 ATTTG
270147 AGTTTAGTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.30
Consensus pattern (34 bp):
ATTTGGGTAAGATAAAAGATAAAAAATTAAAAAT
Found at i:270410 original size:23 final size:23
Alignment explanation
Indices: 270366--270411 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
270356 AAAAAAAGTT
* **
270366 TAACTCGATTCGTTTAACTCGAA
1 TAACTCAATTCGAATAACTCGAA
*
270389 TAACTCAATTCGAATAATTCGAA
1 TAACTCAATTCGAATAACTCGAA
270412 GTTTGAAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.33
Consensus pattern (23 bp):
TAACTCAATTCGAATAACTCGAA
Found at i:272908 original size:24 final size:24
Alignment explanation
Indices: 272875--272921 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
272865 GTTAAGAGTA
*
272875 AAAATTGTCAATGCAAATGTAATAT
1 AAAATTGTCAAAGCAAAT-TAATAT
272900 AAAA-TGTCAAAGCAAATTAATA
1 AAAATTGTCAAAGCAAATTAATA
272922 AAAGATGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 12 0.57
25 4 0.19
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.28
Consensus pattern (24 bp):
AAAATTGTCAAAGCAAATTAATAT
Found at i:277317 original size:2 final size:2
Alignment explanation
Indices: 277310--277334 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
277300 TTTATTAATC
277310 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
277335 GTATGCATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:278455 original size:18 final size:18
Alignment explanation
Indices: 278432--278473 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
278422 TCGCTACAAA
278432 TTCTTCTTATTT-TTCTC
1 TTCTTCTTATTTCTTCTC
*
278449 TTTCTTCTTCTTTCTTCTC
1 -TTCTTCTTATTTCTTCTC
278468 TTCTTC
1 TTCTTC
278474 CTCCACTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (18 bp):
TTCTTCTTATTTCTTCTC
Found at i:283309 original size:16 final size:17
Alignment explanation
Indices: 283268--283310 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
283258 GTTACTTGAA
283268 AAAAAAAATGAGAAAAAG
1 AAAAAAAAT-AGAAAAAG
* *
283286 GAAGAAAAT-GAAAAAG
1 AAAAAAAATAGAAAAAG
283302 AAAAAAAAT
1 AAAAAAAAT
283311 TAAATGCTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 14 0.67
18 7 0.33
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (17 bp):
AAAAAAAATAGAAAAAG
Found at i:288331 original size:13 final size:14
Alignment explanation
Indices: 288301--288331 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
288291 TTTAAATACA
288301 TTGACATTTAACCT
1 TTGACATTTAACCT
288315 TTGACATTTAA-CT
1 TTGACATTTAACCT
288328 TTGA
1 TTGA
288332 TTGCGATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.45
Consensus pattern (14 bp):
TTGACATTTAACCT
Found at i:293824 original size:20 final size:21
Alignment explanation
Indices: 293788--293826 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
293778 CATTTTTTTA
*
293788 TTTACTTTTATTTGTTTCACT
1 TTTACTTTTAGTTGTTTCACT
293809 TTTACTTTT-GTTGTTTCA
1 TTTACTTTTAGTTGTTTCA
293827 AATTCATTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTACTTTTAGTTGTTTCACT
Found at i:308782 original size:20 final size:21
Alignment explanation
Indices: 308743--308782 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
308733 AATTCAACAT
*
308743 TTGAAACATTACTGGCTTGAG
1 TTGAAACATTACTAGCTTGAG
*
308764 TTGAAA-ATTCCTAGCTTGA
1 TTGAAACATTACTAGCTTGA
308783 ATTGTTGGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (21 bp):
TTGAAACATTACTAGCTTGAG
Found at i:318895 original size:25 final size:29
Alignment explanation
Indices: 318861--318918 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 29
318851 TATATTTATA
*
318861 TATTGCAATAT-ATAAATA-ATTA-TAAT
1 TATTGCAATATAAAAAATATATTACTAAT
318887 TATT-CAATATAAAAAATATATTACTAAT
1 TATTGCAATATAAAAAATATATTACTAAT
318915 TATT
1 TATT
318919 TCTTTAAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 6 0.21
26 10 0.36
27 4 0.14
28 8 0.29
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (29 bp):
TATTGCAATATAAAAAATATATTACTAAT
Found at i:319998 original size:112 final size:112
Alignment explanation
Indices: 319801--320025 Score: 450
Period size: 112 Copynumber: 2.0 Consensus size: 112
319791 GACCAAATTT
319801 AGTTAAAAAATAAGTACCAAATTGATAAAAATGCAAATAATAAGGGCTTAATTTTTCATTATGTC
1 AGTTAAAAAATAAGTACCAAATTGATAAAAATGCAAATAATAAGGGCTTAATTTTTCATTATGTC
319866 AAAATTAAACTAATGGTTGGGATATGTCCATAAATTTCCCCCTAAAA
66 AAAATTAAACTAATGGTTGGGATATGTCCATAAATTTCCCCCTAAAA
319913 AGTTAAAAAATAAGTACCAAATTGATAAAAATGCAAATAATAAGGGCTTAATTTTTCATTATGTC
1 AGTTAAAAAATAAGTACCAAATTGATAAAAATGCAAATAATAAGGGCTTAATTTTTCATTATGTC
319978 AAAATTAAACTAATGGTTGGGATATGTCCATAAATTTCCCCCTAAAA
66 AAAATTAAACTAATGGTTGGGATATGTCCATAAATTTCCCCCTAAAA
320025 A
1 A
320026 AATCACAAAC
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 113 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (112 bp):
AGTTAAAAAATAAGTACCAAATTGATAAAAATGCAAATAATAAGGGCTTAATTTTTCATTATGTC
AAAATTAAACTAATGGTTGGGATATGTCCATAAATTTCCCCCTAAAA
Found at i:321926 original size:18 final size:18
Alignment explanation
Indices: 321903--321938 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
321893 TTTACATACA
321903 AAAATAATAATTATATTT
1 AAAATAATAATTATATTT
* *
321921 AAAATAATTATTTTATTT
1 AAAATAATAATTATATTT
321939 TATAATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAAATAATAATTATATTT
Found at i:322621 original size:29 final size:30
Alignment explanation
Indices: 322579--322648 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 30
322569 TGCGCTTTTC
** *
322579 TTCAAAATCGATCTATTTCTCTAAAT-AAT
1 TTCAAAATCGATCTAAATATCTAAATAAAT
*
322608 TTCAAAATCGATCTAAATATTTAAATAAAT
1 TTCAAAATCGATCTAAATATCTAAATAAAT
322638 TTCAAAATCGA
1 TTCAAAATCGA
322649 AATATATTCC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 22 0.61
30 14 0.39
ACGTcount: A:0.44, C:0.14, G:0.04, T:0.37
Consensus pattern (30 bp):
TTCAAAATCGATCTAAATATCTAAATAAAT
Found at i:349470 original size:16 final size:16
Alignment explanation
Indices: 349446--349476 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
349436 ACCGAAATTA
*
349446 AATTTTAATTTTTATT
1 AATTATAATTTTTATT
349462 AATTATAATTTTTAT
1 AATTATAATTTTTAT
349477 GGTAATAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
AATTATAATTTTTATT
Found at i:349561 original size:16 final size:17
Alignment explanation
Indices: 349536--349568 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
349526 GTAATTTTAT
*
349536 TTTTATTAA-TTTAAAA
1 TTTTAATAATTTTAAAA
349552 TTTTAATAATTTTAAAA
1 TTTTAATAATTTTAAAA
349569 GACTTAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTAATAATTTTAAAA
Found at i:351300 original size:32 final size:32
Alignment explanation
Indices: 351263--351324 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
351253 AAGAGATTTT
*
351263 AAATCAATTTGAATAG-AATCAAATCAAATTAA
1 AAATCAATTTG-ATAGAAATAAAATCAAATTAA
*
351295 AAATCAATTTGATTGAAATAAAATCAAATT
1 AAATCAATTTGATAGAAATAAAATCAAATT
351325 GAGATATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 3 0.11
32 24 0.89
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.31
Consensus pattern (32 bp):
AAATCAATTTGATAGAAATAAAATCAAATTAA
Found at i:354784 original size:29 final size:29
Alignment explanation
Indices: 354742--354798 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
354732 TAAACCTAAT
*
354742 ACAGTTACAATTACAGATGCAGACATGAC
1 ACAGATACAATTACAGATGCAGACATGAC
*
354771 ACAGATACAGTTACAGATGCAGACATGA
1 ACAGATACAATTACAGATGCAGACATGA
354799 TACCCCTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (29 bp):
ACAGATACAATTACAGATGCAGACATGAC
Found at i:355660 original size:465 final size:467
Alignment explanation
Indices: 354785--355719 Score: 1491
Period size: 465 Copynumber: 2.0 Consensus size: 467
354775 ATACAGTTAC
* * * *
354785 AGATGCAGACATGATACCCCTATCAACTATAAACCATCTCCGTCCAACCTAACACACCAATATCC
1 AGATGCAGACATGATACCCCCATCAACTATAAACCATCTCCATCCAACCCAACACACAAATATCC
* * * * ** * *
354850 AACCCTAGACACCATATAGTGTTGGTATGGCACGTTGCAGTGTTCATAGTTTCACAGCTAGATAA
66 AACCCTACACACCATATAGTATCGGTATGACACGACGCAGTGTTCACAGTTTCACAGCCAGATAA
*
354915 GATAATCTCAAGTGGATTAACCACTAAAACAGTTCAGATAACTTCCTTCAAAACACAATTTCCAA
131 GATAATCTCAAGTGGATTAACCACT--AACAGTTCAAATAACTTCCTTCAAAACACAATTTCCAA
* * *
354980 CCCATGTAGATGTACAGAACGTATGACAGATATGTATAACTACCAATAGATGTGACCATACAATC
194 CCCATGTAGATGTACAGAACGTATGAAAAATATGTATAACTACCAATAGACGTGACCATACAATC
* *
355045 CTAATATAACAGTATGCTGAGAATATTCCTAATAATTTCGTACAGTTATCTAGATACCACATATC
259 CTAATATAACAATATGCTGAGAATATTCCTAATAATTTCGTACAGTTATCTAAATACCACATATC
* *
355110 CTTAATCAAAATAGTAACATAGAAGCGTACCTGTATGCTGAACAAAATATGAATAGTACCTGAAC
324 CTTAATCAAAATAGTAACACAGAAGCGTACCTGTATGCTGAACAAAATACGAATAGTACCTGAAC
* *
355175 AGAATACATACTTTAATGCATCCAAATAAATTCACATTACACATTATCGAGTCAATATTAATTTT
389 AGAATACATACTTTAATGCATCCAAACAAATTCACATTACACATTATCGAGCCAATATTAATTTT
355240 TTTATATTCGTATA
454 TTTATATTCGTATA
*
355254 AGATGCAGACATGATACCCCCATCAACTATACACCATCTCCATCCAACCCAACACACAAATATCC
1 AGATGCAGACATGATACCCCCATCAACTATAAACCATCTCCATCCAACCCAACACACAAATATCC
* * *
355319 AACCTTACACACCATATAGTATCGGTATGACACGACGCAGTGTTCACAGTTTCATAGCCAGATCA
66 AACCCTACACACCATATAGTATCGGTATGACACGACGCAGTGTTCACAGTTTCACAGCCAGATAA
* *
355384 GATAATCTCAAGTGGGTTAACCA-T-ACAGTTCAAATAACTTCCTTCAAATCACAATTTCCAACC
131 GATAATCTCAAGTGGATTAACCACTAACAGTTCAAATAACTTCCTTCAAAACACAATTTCCAACC
* *
355447 CATGTAGATGTACAGAACGTATGAAAAATATGTATAATTACCAATAGACGTGATCATACAATCCT
196 CATGTAGATGTACAGAACGTATGAAAAATATGTATAACTACCAATAGACGTGACCATACAATCCT
* * *
355512 AGTATAACAATGTGCTGAGAATATTCCTAATCAA-TTCGTACAGTTATAC-AAATACCATATATC
261 AATATAACAATATGCTGAGAATATTCCTAAT-AATTTCGTACAGTTAT-CTAAATACCACATATC
*
355575 CTTAATCAAAATAGTAACACAGAAGCGTACCTGTATGCTTAACAAAATACGAATAGTACCTGAAC
324 CTTAATCAAAATAGTAACACAGAAGCGTACCTGTATGCTGAACAAAATACGAATAGTACCTGAAC
*
355640 ATAATACATACTTTAATGCATCCAAACAAATTCACATTACACATTATCGAGCCAATATTAATTTT
389 AGAATACATACTTTAATGCATCCAAACAAATTCACATTACACATTATCGAGCCAATATTAATTTT
355705 TTTATATTCGTATA
454 TTTATATTCGTATA
355719 A
1 A
355720 CATACGTATA
Statistics
Matches: 429, Mismatches: 35, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
465 289 0.67
466 3 0.01
468 1 0.00
469 136 0.32
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (467 bp):
AGATGCAGACATGATACCCCCATCAACTATAAACCATCTCCATCCAACCCAACACACAAATATCC
AACCCTACACACCATATAGTATCGGTATGACACGACGCAGTGTTCACAGTTTCACAGCCAGATAA
GATAATCTCAAGTGGATTAACCACTAACAGTTCAAATAACTTCCTTCAAAACACAATTTCCAACC
CATGTAGATGTACAGAACGTATGAAAAATATGTATAACTACCAATAGACGTGACCATACAATCCT
AATATAACAATATGCTGAGAATATTCCTAATAATTTCGTACAGTTATCTAAATACCACATATCCT
TAATCAAAATAGTAACACAGAAGCGTACCTGTATGCTGAACAAAATACGAATAGTACCTGAACAG
AATACATACTTTAATGCATCCAAACAAATTCACATTACACATTATCGAGCCAATATTAATTTTTT
TATATTCGTATA
Found at i:356074 original size:55 final size:53
Alignment explanation
Indices: 356002--356117 Score: 160
Period size: 55 Copynumber: 2.2 Consensus size: 53
355992 CACACACACA
* *
356002 CCCGTGTGTTAGCCCGTGTGCCACAAAACAATATACACACACCCTCTGGCACATG
1 CCCGTGTGTCAGCCCGTGTGCCACAAAACAATATACACACA-CCT-TGACACATG
* * * *
356057 CCCGTGTGTCAGGCCGTGTGCCTCAAAATAGTATACACACACCTTGACACATG
1 CCCGTGTGTCAGCCCGTGTGCCACAAAACAATATACACACACCTTGACACATG
356110 CCCGTGTG
1 CCCGTGTG
356118 CTTCAAAATA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
53 16 0.29
54 3 0.05
55 36 0.65
ACGTcount: A:0.25, C:0.33, G:0.21, T:0.22
Consensus pattern (53 bp):
CCCGTGTGTCAGCCCGTGTGCCACAAAACAATATACACACACCTTGACACATG
Found at i:357725 original size:29 final size:29
Alignment explanation
Indices: 357654--357747 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 29
357644 AAATATATAT
*
357654 ATAATACAGTTATAGTTACAGATGCACAC
1 ATAATACAGTTACAGTTACAGATGCACAC
* * * * *
357683 ATTATAAAGATACATTTACAGATTCA-AGC
1 ATAATACAGTTACAGTTACAGATGCACA-C
* *
357712 ATAATACAGTTACAGTTATAGATGCAGAC
1 ATAATACAGTTACAGTTACAGATGCACAC
*
357741 ATGATAC
1 ATAATAC
357748 CCCCATCCAC
Statistics
Matches: 50, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
28 1 0.02
29 48 0.96
30 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.29
Consensus pattern (29 bp):
ATAATACAGTTACAGTTACAGATGCACAC
Found at i:358611 original size:108 final size:110
Alignment explanation
Indices: 358473--358691 Score: 253
Period size: 108 Copynumber: 2.0 Consensus size: 110
358463 CCTTAAATAA
* * * * * *
358473 AAAATAGTATACAAACACACACCCTAACACACGCTCATGTGTCAGACCGTATGCCTCAAACCAGT
1 AAAACAGTATAC-AACACACACCCTAACACACGCCCATGTATCAGACCATATACCTCAAAACAGT
* * * * *
358538 ATATACACATCCTAACATACGCCCATGTGTC-AGCCCGTGTGCCTC
65 ATACACACAACATAACACACGCCCATGTATCTAGCCCGTGTGCCTC
* * * * *
358583 AAAACAGTATAC-ACACACACCCTGACACATGCCCATGTATCAGCCCATGTACTTCAAAACAGTA
1 AAAACAGTATACAACACACACCCTAACACACGCCCATGTATCAGACCATATACCTCAAAACAGTA
* *
358647 TACACACAACATGACACACGCCCATGTATCTTGCCCGTGTGCCTC
66 TACACACAACATAACACACGCCCATGTATCTAGCCCGTGTGCCTC
358692 TTGCAACTTA
Statistics
Matches: 90, Mismatches: 18, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
108 66 0.73
109 13 0.14
110 11 0.12
ACGTcount: A:0.33, C:0.33, G:0.13, T:0.21
Consensus pattern (110 bp):
AAAACAGTATACAACACACACCCTAACACACGCCCATGTATCAGACCATATACCTCAAAACAGTA
TACACACAACATAACACACGCCCATGTATCTAGCCCGTGTGCCTC
Found at i:358626 original size:55 final size:55
Alignment explanation
Indices: 358473--358691 Score: 221
Period size: 53 Copynumber: 4.0 Consensus size: 55
358463 CCTTAAATAA
* * * * *
358473 AAAATAGTATACAAACACACACCCTAACACACGCTCATGTGTCAGACCGTATGCCTC
1 AAAACAGTATAC--ACACACACCCTAACACACGCCCATGTATCAGCCCGTGTGCCTC
* * * * *
358530 AAACCAGTAT--ATACACATCCTAACATACGCCCATGTGTCAGCCCGTGTGCCTC
1 AAAACAGTATACACACACACCCTAACACACGCCCATGTATCAGCCCGTGTGCCTC
* * * * *
358583 AAAACAGTATACACACACACCCTGACACATGCCCATGTATCAGCCCATGTACTTC
1 AAAACAGTATACACACACACCCTAACACACGCCCATGTATCAGCCCGTGTGCCTC
* * *
358638 AAAACAGTATACACACA-A-CATGACACACGCCCATGTATCTTGCCCGTGTGCCTC
1 AAAACAGTATACACACACACCCTAACACACGCCCATGTATC-AGCCCGTGTGCCTC
358692 TTGCAACTTA
Statistics
Matches: 135, Mismatches: 24, Indels: 9
0.80 0.14 0.05
Matches are distributed among these distances:
53 65 0.48
54 11 0.08
55 51 0.38
57 8 0.06
ACGTcount: A:0.33, C:0.33, G:0.13, T:0.21
Consensus pattern (55 bp):
AAAACAGTATACACACACACCCTAACACACGCCCATGTATCAGCCCGTGTGCCTC
Found at i:360751 original size:55 final size:54
Alignment explanation
Indices: 360662--360849 Score: 175
Period size: 55 Copynumber: 3.4 Consensus size: 54
360652 GCATCAAACC
* * * *
360662 AGTATACACACAC-TC-TGACACACGTCCGTGTGTCAGCCCATGTGCCTTAAAAT
1 AGTATACACACACACCTTGACACATGCCCGTGTGTCA-CCCATGTGACTTAAAAT
* * * * *
360715 AGTATACACACACACCTTGACACATGCCCGTATGTCACCTCATGCGTCTCAAAAC
1 AGTATACACACACACCTTGACACATGCCCGTGTGTCACC-CATGTGACTTAAAAT
* * * * *
360770 AATATACACACACACCCTAACACATGCCCATGTGTCAACC-TGTGTACTTCCAAAAT
1 AGTATACACACACACCTTGACACATGCCCGTGTGTCACCCATGTG-ACTT--AAAAT
*
360826 AGTATAAACACACACCTTGACACA
1 AGTATACACACACACCTTGACACA
360850 CGTTCGTGTG
Statistics
Matches: 107, Mismatches: 22, Indels: 9
0.78 0.16 0.07
Matches are distributed among these distances:
53 16 0.15
54 6 0.06
55 61 0.57
56 24 0.22
ACGTcount: A:0.34, C:0.32, G:0.12, T:0.22
Consensus pattern (54 bp):
AGTATACACACACACCTTGACACATGCCCGTGTGTCACCCATGTGACTTAAAAT
Found at i:363632 original size:36 final size:36
Alignment explanation
Indices: 363592--363712 Score: 109
Period size: 36 Copynumber: 3.4 Consensus size: 36
363582 ATTGCATACG
* * *
363592 TCTCGATTAGAGCGTATTACTACGAAAGTGCTTACA
1 TCTCGATTAGAGCGTAATACTAAGAAACTGCTTACA
* * *
363628 TCTCGATTAAAGCGTAATGCTAAGGAACTGCTTACA
1 TCTCGATTAGAGCGTAATACTAAGAAACTGCTTACA
* * * * **
363664 TCTC-AGTTAGAGCGTTATGCTAAGGAAGTGCTTATG
1 TCTCGA-TTAGAGCGTAATACTAAGAAACTGCTTACA
*
363700 TCTCGGTTAGAGC
1 TCTCGATTAGAGC
363713 ATAAGGCCAT
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
35 1 0.01
36 70 0.99
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (36 bp):
TCTCGATTAGAGCGTAATACTAAGAAACTGCTTACA
Found at i:365903 original size:24 final size:24
Alignment explanation
Indices: 365871--365919 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
365861 TGTTTAGAAG
*
365871 TAATTAAGAAAAGTTCGTAACAAA
1 TAATTAAGAAAAGTTCGCAACAAA
365895 TAATTAAGAAAAGTTCGCAACAAA
1 TAATTAAGAAAAGTTCGCAACAAA
365919 T
1 T
365920 GAAACTAGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.10, G:0.12, T:0.24
Consensus pattern (24 bp):
TAATTAAGAAAAGTTCGCAACAAA
Found at i:372028 original size:7 final size:7
Alignment explanation
Indices: 372016--372049 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
372006 ATTATAATGC
372016 TATTTTT
1 TATTTTT
372023 TATTTTT
1 TATTTTT
372030 TATTTTT
1 TATTTTT
372037 TATTTTT
1 TATTTTT
*
372044 AATTTT
1 TATTTT
372050 GTAAGTTGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (7 bp):
TATTTTT
Found at i:372144 original size:53 final size:53
Alignment explanation
Indices: 372084--372189 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
372074 CAAGCACTTC
*
372084 TATTTATTATACATGAAATTAAAATCAAATGAGTGAAAGGTTAGAAAGTTTTT
1 TATTTATTATACATGAAATTAAAATCAAATGAGAGAAAGGTTAGAAAGTTTTT
*
372137 TATTTATTATACATGAAGTTAAAATCAAATGAGAGAAAGGTTAGAAAGTTTTT
1 TATTTATTATACATGAAATTAAAATCAAATGAGAGAAAGGTTAGAAAGTTTTT
372190 AAAAAAATTA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (53 bp):
TATTTATTATACATGAAATTAAAATCAAATGAGAGAAAGGTTAGAAAGTTTTT
Found at i:374885 original size:10 final size:10
Alignment explanation
Indices: 374870--374894 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
374860 ATTAAACAAG
374870 AGAAAGGTTC
1 AGAAAGGTTC
374880 AGAAAGGTTC
1 AGAAAGGTTC
374890 AGAAA
1 AGAAA
374895 TGGATACATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.08, G:0.28, T:0.16
Consensus pattern (10 bp):
AGAAAGGTTC
Found at i:375081 original size:23 final size:23
Alignment explanation
Indices: 375049--375093 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
375039 AAAGAACAAA
* *
375049 GAAAACAAAACTATTTAGAAACT
1 GAAAACAAAACTAATTAAAAACT
*
375072 GAAAATAAAACTAATTAAAAAC
1 GAAAACAAAACTAATTAAAAAC
375094 CTAAATCTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.62, C:0.11, G:0.07, T:0.20
Consensus pattern (23 bp):
GAAAACAAAACTAATTAAAAACT
Found at i:375735 original size:31 final size:31
Alignment explanation
Indices: 375697--375758 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
375687 TCATTCATGG
375697 AGTGATTTACATAAATCTTGAGTTAGTCACT
1 AGTGATTTACATAAATCTTGAGTTAGTCACT
375728 AGTGATTTACATAAATCTTGAGTTAGTCACT
1 AGTGATTTACATAAATCTTGAGTTAGTCACT
375759 GACCATGCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (31 bp):
AGTGATTTACATAAATCTTGAGTTAGTCACT
Found at i:381227 original size:19 final size:19
Alignment explanation
Indices: 381203--381243 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
381193 TGCAATCTAA
381203 TATTGCTCAT-ACAAGCCAG
1 TATTGCTC-TGACAAGCCAG
*
381222 TATTGCTCTGACGAGCCAG
1 TATTGCTCTGACAAGCCAG
381241 TAT
1 TAT
381244 GCTTGAACGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (19 bp):
TATTGCTCTGACAAGCCAG
Found at i:381253 original size:18 final size:19
Alignment explanation
Indices: 381216--381282 Score: 86
Period size: 18 Copynumber: 3.6 Consensus size: 19
381206 TGCTCATACA
381216 AGCCAGTATTGCTCTG-ACG
1 AGCCAGTA-TGCTCTGAACG
381235 AGCCAGTATGCT-TGAACG
1 AGCCAGTATGCTCTGAACG
*
381253 AGCCAGCATGCTCT-AACG
1 AGCCAGTATGCTCTGAACG
*
381271 AGCCAATATGCT
1 AGCCAGTATGCT
381283 ATTTCTTCCG
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
17 2 0.05
18 32 0.74
19 9 0.21
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (19 bp):
AGCCAGTATGCTCTGAACG
Found at i:384135 original size:15 final size:14
Alignment explanation
Indices: 384115--384146 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
384105 TTCCTTAAAT
384115 CAAGGGAGTTATAGA
1 CAAGGGAGTTATA-A
384130 CAAGGGAGTTATAA
1 CAAGGGAGTTATAA
384144 CAA
1 CAA
384147 CCAACAATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (14 bp):
CAAGGGAGTTATAA
Found at i:406291 original size:220 final size:220
Alignment explanation
Indices: 405909--406337 Score: 822
Period size: 220 Copynumber: 1.9 Consensus size: 220
405899 GAAAAATCAT
*
405909 CTATAAGAGTTAGCATATAATTAGCTCCACCTCTCGAAGGCACTCTAGATGGTCCCCAAAGATCA
1 CTATAAGAGTTAGCATATAATTAGCTCCACCTCTCGAAGGCACTCTAGATGGTCCCCAAAGATAA
*
405974 GAATGAATATAATCCAATGTTCCGTTCGTATTATGGATTCCTTTGGTGAATCGAACTCTCTTTTG
66 GAATGAATATAATCCAATGTTCCGTTCGTATTATGGATTCCTCTGGTGAATCGAACTCTCTTTTG
406039 CTTCCCAAAAATGCAATGCTCACAGGACTTTAGTTTGCTAATGCCTTGCCTATCAAGAAGTCCTC
131 CTTCCCAAAAATGCAATGCTCACAGGACTTTAGTTTGCTAATGCCTTGCCTATCAAGAAGTCCTC
*
406104 ATTTACTCAATTCTCTCATGGATTC
196 ATTTACTAAATTCTCTCATGGATTC
*
406129 CTATAAGAGTTAGCATATAATTAGTTCCACCTCTCGAAGGCACTCTAGATGGTCCCCAAAGATAA
1 CTATAAGAGTTAGCATATAATTAGCTCCACCTCTCGAAGGCACTCTAGATGGTCCCCAAAGATAA
406194 GAATGAATATAATCCAATGTTCCGTTCGTATTATGGATTCCTCTGGTGAATCGAACTCTCTTTTG
66 GAATGAATATAATCCAATGTTCCGTTCGTATTATGGATTCCTCTGGTGAATCGAACTCTCTTTTG
406259 CTTCCCAAAAATGCAATGCTCACAGGACTTTAGTTTGCTAATGCCTTGCCTATCAAGAAGTCCTC
131 CTTCCCAAAAATGCAATGCTCACAGGACTTTAGTTTGCTAATGCCTTGCCTATCAAGAAGTCCTC
406324 ATTTACTAAATTCT
196 ATTTACTAAATTCT
406338 TCCATGTCGG
Statistics
Matches: 205, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
220 205 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (220 bp):
CTATAAGAGTTAGCATATAATTAGCTCCACCTCTCGAAGGCACTCTAGATGGTCCCCAAAGATAA
GAATGAATATAATCCAATGTTCCGTTCGTATTATGGATTCCTCTGGTGAATCGAACTCTCTTTTG
CTTCCCAAAAATGCAATGCTCACAGGACTTTAGTTTGCTAATGCCTTGCCTATCAAGAAGTCCTC
ATTTACTAAATTCTCTCATGGATTC
Found at i:419750 original size:27 final size:27
Alignment explanation
Indices: 419720--419778 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
419710 CAAGGACAAC
* *
419720 ATCATCAACATCAATAGCAGTAATTTA
1 ATCAACAACATCAATAGCAGCAATTTA
*
419747 ATCAACAACATCAATAGCTGCAATTTA
1 ATCAACAACATCAATAGCAGCAATTTA
419774 ATCAA
1 ATCAA
419779 TCTAAGGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.46, C:0.20, G:0.07, T:0.27
Consensus pattern (27 bp):
ATCAACAACATCAATAGCAGCAATTTA
Found at i:433962 original size:17 final size:17
Alignment explanation
Indices: 433937--433974 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
433927 ATGCATCTCA
433937 TTTAATTGTCATTGCAT
1 TTTAATTGTCATTGCAT
*
433954 TTTAGTTGTCATTGCAT
1 TTTAATTGTCATTGCAT
433971 TTTA
1 TTTA
433975 CCTGTTAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.21, C:0.11, G:0.13, T:0.55
Consensus pattern (17 bp):
TTTAATTGTCATTGCAT
Found at i:439708 original size:21 final size:21
Alignment explanation
Indices: 439661--439718 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
439651 AATAATGCAG
*
439661 ACTTCTACCGATACAAATGAT
1 ACTTCTACCGATACAAATAAT
* *
439682 AGTTCTACCGATACAAGTAACT
1 ACTTCTACCGATACAAATAA-T
*
439704 -CTTCTACCGAAACAA
1 ACTTCTACCGATACAA
439719 TTCTTTCTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.38, C:0.26, G:0.10, T:0.26
Consensus pattern (21 bp):
ACTTCTACCGATACAAATAAT
Found at i:441663 original size:18 final size:17
Alignment explanation
Indices: 441638--441671 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
441628 TATTCCTTTT
441638 CTAACTTTTATTGATTA
1 CTAACTTTTATTGATTA
*
441655 CTAATCTTTTGTTGATT
1 CTAA-CTTTTATTGATT
441672 TTCTTTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.56
Consensus pattern (17 bp):
CTAACTTTTATTGATTA
Found at i:453914 original size:19 final size:19
Alignment explanation
Indices: 453858--453908 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
453848 GATGATGACA
* *
453858 AAATAAAAAT-ACATATAT
1 AAATAAAAATAAAATAAAT
*
453876 GAATAAAAATAAAATAAAT
1 AAATAAAAATAAAATAAAT
453895 AAATAAAAATAAAA
1 AAATAAAAATAAAA
453909 GTAATATCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (19 bp):
AAATAAAAATAAAATAAAT
Found at i:454067 original size:11 final size:11
Alignment explanation
Indices: 454053--454095 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
454043 AAAATTTTAA
454053 AAAAATAAAAT
1 AAAAATAAAAT
454064 AAAAATAAAGAT
1 AAAAATAAA-AT
454076 -AAAAT-AAAT
1 AAAAATAAAAT
454085 AAATAATAAAA
1 AAA-AATAAAA
454096 GGGACTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
9 2 0.07
10 4 0.14
11 17 0.61
12 5 0.18
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:455403 original size:17 final size:18
Alignment explanation
Indices: 455381--455421 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
455371 TGGGTTTATG
455381 TATTT-TGGACTTT-AATT
1 TATTTCTGGA-TTTCAATT
455398 TATTTTCTGGATTTCAATT
1 TA-TTTCTGGATTTCAATT
455417 TATTT
1 TATTT
455422 ATAAAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.10
18 9 0.43
19 10 0.48
ACGTcount: A:0.22, C:0.07, G:0.10, T:0.61
Consensus pattern (18 bp):
TATTTCTGGATTTCAATT
Found at i:456178 original size:102 final size:101
Alignment explanation
Indices: 456013--456399 Score: 418
Period size: 102 Copynumber: 3.8 Consensus size: 101
456003 TTTGCTTCTG
* * **
456013 TAGTTTTAATCTGATCC-TTGCAACTTCACAATTATAGGATTTGGTG-TGTAACTTCACTCCATT
1 TAGTTTTAATCTGATCCACTACAACTTCAGGA-TATAGGATTTGGTGTTGTAACTTCACTCCATT
* *
456076 CCACAAAAACTTCAAGGAGATTGAGATCCGCTACTGT
65 CCACTAAAACTTCAGGGAGATTGAGATCCGCTACTGT
* * * * ** * *
456113 TAGTTTTATTTTGATCCATTACAAATTCATGGATATAGGATTTTATGTTGAAACTTCATTCCATT
1 TAGTTTTAATCTGATCCACTACAACTTCA-GGATATAGGATTTGGTGTTGTAACTTCACTCCATT
** * *
456178 CCACTGTAACTTCAGGGAGATTAAAATCCGCTACTGT
65 CCACTAAAACTTCAGGGAGATTGAGATCCGCTACTGT
* * * *
456215 TAGTTTTAATCTGATTCACTGCAACTTCAACGATATAAGATTTGGTGTTGTAACTTCACTCCATT
1 TAGTTTTAATCTGATCCACTACAACTTC-AGGATATAGGATTTGGTGTTGTAACTTCACTCCATT
* * * **
456280 TCACTACAACTTTAGGGAGATTGAGATTTGCTACTGT
65 CCACTAAAACTTCAGGGAGATTGAGATCCGCTACTGT
* * * * *
456317 TAGTTTTAATCTAATCCACTAGAACTTTAGTGATATAGGATTTTGTGTTGTAACGTCACTCCATT
1 TAGTTTTAATCTGATCCACTACAACTTCAG-GATATAGGATTTGGTGTTGTAACTTCACTCCATT
* *
456382 CCACTACAACTTTAGGGA
65 CCACTAAAACTTCAGGGA
456400 TATAGGATTT
Statistics
Matches: 236, Mismatches: 46, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
100 15 0.06
101 22 0.09
102 198 0.84
103 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (101 bp):
TAGTTTTAATCTGATCCACTACAACTTCAGGATATAGGATTTGGTGTTGTAACTTCACTCCATTC
CACTAAAACTTCAGGGAGATTGAGATCCGCTACTGT
Found at i:456290 original size:50 final size:50
Alignment explanation
Indices: 456246--456561 Score: 211
Period size: 50 Copynumber: 6.2 Consensus size: 50
456236 CAACTTCAAC
*
456246 GATATAAGATTTGGTGTTGTAACTTCACTCCATTTCACTACAACTTTAGG
1 GATATAAGATTTGGTGTTGTAACTTCACTCCATTCCACTACAACTTTAGG
* * * ** ** * * * * * *
456296 GAGATTGAGATTTGCTACTGTTAGTTTTAATCTAATCCACTAGAACTTTAGT
1 GATA-TAAGATTTGGTGTTG-TAACTTCACTCCATTCCACTACAACTTTAGG
* * *
456348 GATATAGGATTTTGTGTTGTAACGTCACTCCATTCCACTACAACTTTAGG
1 GATATAAGATTTGGTGTTGTAACTTCACTCCATTCCACTACAACTTTAGG
* * *
456398 GATATAGGATTTGGTGTTGTAACTTCACTCCATTCCACTGCAACTTCAGG
1 GATATAAGATTTGGTGTTGTAACTTCACTCCATTCCACTACAACTTTAGG
* * ** * * ** * * * * * *
456448 GAGATTGAGATCCGCTACTAT-TAGTTTTAATCTAATCCACTACAACTTCAGA
1 GATA-TAAGATTTGGT-GT-TGTAACTTCACTCCATTCCACTACAACTTTAGG
* * ** *
456500 GATATAGGATTTGGTGTTGTAACTTCACTCTATTCCACTGTAACTTCAGG
1 GATATAAGATTTGGTGTTGTAACTTCACTCCATTCCACTACAACTTTAGG
*
456550 GAGATTAAGATT
1 GATA-TAAGATT
456562 CGCTACTATT
Statistics
Matches: 193, Mismatches: 66, Indels: 13
0.71 0.24 0.05
Matches are distributed among these distances:
49 1 0.01
50 101 0.52
51 38 0.20
52 52 0.27
53 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (50 bp):
GATATAAGATTTGGTGTTGTAACTTCACTCCATTCCACTACAACTTTAGG
Found at i:456382 original size:204 final size:202
Alignment explanation
Indices: 456013--456386 Score: 502
Period size: 204 Copynumber: 1.8 Consensus size: 202
456003 TTTGCTTCTG
*
456013 TAGTTTTAATCTGATCCTTGCAACTTCACAATTATAGGATTTGGTGTGTAACTTCACTCCATTCC
1 TAGTTTTAATCTGATCCTTGCAACTTCACAATTATAAGATTTGGTGTGTAACTTCACTCCATTCC
* * * *
456078 ACAAAAACTTCAAGGAGATTGAGATCCGCTACTGTTAGTTTTATTTTGATCCATTACAAATTCAT
66 ACAAAAACTTCAAGGAGATTGAGATCCGCTACTGTTAGTTTTAATCTAATCCACTACAAATTCAT
* *
456143 GGATATAGGATTTTATGTTGAAACTTCATTCCATTCCACTGTAACTTCAGGGAGATTAAAATCCG
131 GGATATAGGATTTTATGTTGAAACGTCACTCCATTCCACTGTAACTTCAGGGAGATTAAAATCCG
456208 CTACTGT
196 CTACTGT
*
456215 TAGTTTTAATCTGATTCAC-TGCAACTTCAACGA-TATAAGATTTGGTGTTGTAACTTCACTCCA
1 TAGTTTTAATCTGA-TC-CTTGCAACTTC-ACAATTATAAGATTTGGTG-TGTAACTTCACTCCA
* * * * * ** * *
456278 TTTCACTACAACTTTAGGGAGATTGAGATTTGCTACTGTTAGTTTTAATCTAATCCACTAGAACT
62 TTCCACAAAAACTTCAAGGAGATTGAGATCCGCTACTGTTAGTTTTAATCTAATCCACTACAAAT
* * *
456343 TTA-GTGATATAGGATTTTGTGTTGTAACGTCACTCCATTCCACT
127 TCATG-GATATAGGATTTTATGTTGAAACGTCACTCCATTCCACT
456387 ACAACTTTAG
Statistics
Matches: 147, Mismatches: 20, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
202 14 0.10
203 25 0.17
204 108 0.73
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (202 bp):
TAGTTTTAATCTGATCCTTGCAACTTCACAATTATAAGATTTGGTGTGTAACTTCACTCCATTCC
ACAAAAACTTCAAGGAGATTGAGATCCGCTACTGTTAGTTTTAATCTAATCCACTACAAATTCAT
GGATATAGGATTTTATGTTGAAACGTCACTCCATTCCACTGTAACTTCAGGGAGATTAAAATCCG
CTACTGT
Found at i:456488 original size:102 final size:102
Alignment explanation
Indices: 456381--456711 Score: 448
Period size: 102 Copynumber: 3.3 Consensus size: 102
456371 GTCACTCCAT
* * *
456381 TCCACTACAACTTTAGGGATATAGGATTTGGTGTTGTAACTTCACTCCATTCCACTGCAACTTCA
1 TCCACTACAACTTCAGGGATATAGGATTTGGTGTTGTAACTTCACTCTATTCCACTGTAACTTCA
456446 GGGAGATTGAGATCCGCTACTATTAGTTTTAATCTAA
66 GGGAGATTGAGATCCGCTACTATTAGTTTTAATCTAA
*
456483 TCCACTACAACTTCAGAGATATAGGATTTGGTGTTGTAACTTCACTCTATTCCACTGTAACTTCA
1 TCCACTACAACTTCAGGGATATAGGATTTGGTGTTGTAACTTCACTCTATTCCACTGTAACTTCA
* * * * **
456548 GGGAGATTAAGATTCGCTACTATTAGTTTTGATTTGG
66 GGGAGATTGAGATCCGCTACTATTAGTTTTAATCTAA
* * * *
456585 TCTATTGCAACTTCAAGGATATAGGATTTGGTGTTGTAACTTCACTCTATTCCACTGTAACTTCA
1 TCCACTACAACTTCAGGGATATAGGATTTGGTGTTGTAACTTCACTCTATTCCACTGTAACTTCA
* * * ** * * *
456650 AGGAGATTGAGATCCACTATTGCTA-TTTTACTCCAT
66 GGGAGATTGAGATCCGCTACTATTAGTTTTAATCTAA
*
456686 TTCACTACAACTTCAGGGATATAGGA
1 TCCACTACAACTTCAGGGATATAGGA
456712 GTTGTCGTTT
Statistics
Matches: 196, Mismatches: 33, Indels: 1
0.85 0.14 0.00
Matches are distributed among these distances:
101 26 0.13
102 170 0.87
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (102 bp):
TCCACTACAACTTCAGGGATATAGGATTTGGTGTTGTAACTTCACTCTATTCCACTGTAACTTCA
GGGAGATTGAGATCCGCTACTATTAGTTTTAATCTAA
Found at i:456517 original size:152 final size:152
Alignment explanation
Indices: 456246--456561 Score: 470
Period size: 152 Copynumber: 2.1 Consensus size: 152
456236 CAACTTCAAC
* * **
456246 GATATAAGATTTGGTGTTGTAACTTCACTCCATTTCACTACAACTTTAGGGAGATTGAGATTTGC
1 GATATAAGATTTGGTGTTGTAACTTCACTCCATTCCACTACAACTTCAGGGAGATTGAGATCCGC
* * * * *
456311 TACTGTTAGTTTTAATCTAATCCACTAGAACTTTAGTGATATAGGATTTTGTGTTGTAACGTCAC
66 TACTATTAGTTTTAATCTAATCCACTACAACTTCAGAGATATAGGATTTGGTGTTGTAACGTCAC
456376 TCCATTCCACTACAACTTTAGG
131 TCCATTCCACTACAACTTTAGG
* *
456398 GATATAGGATTTGGTGTTGTAACTTCACTCCATTCCACTGCAACTTCAGGGAGATTGAGATCCGC
1 GATATAAGATTTGGTGTTGTAACTTCACTCCATTCCACTACAACTTCAGGGAGATTGAGATCCGC
*
456463 TACTATTAGTTTTAATCTAATCCACTACAACTTCAGAGATATAGGATTTGGTGTTGTAACTTCAC
66 TACTATTAGTTTTAATCTAATCCACTACAACTTCAGAGATATAGGATTTGGTGTTGTAACGTCAC
* ** *
456528 TCTATTCCACTGTAACTTCAGG
131 TCCATTCCACTACAACTTTAGG
*
456550 GAGATTAAGATT
1 GATA-TAAGATT
456562 CGCTACTATT
Statistics
Matches: 145, Mismatches: 18, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
152 139 0.96
153 6 0.04
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (152 bp):
GATATAAGATTTGGTGTTGTAACTTCACTCCATTCCACTACAACTTCAGGGAGATTGAGATCCGC
TACTATTAGTTTTAATCTAATCCACTACAACTTCAGAGATATAGGATTTGGTGTTGTAACGTCAC
TCCATTCCACTACAACTTTAGG
Found at i:456608 original size:254 final size:254
Alignment explanation
Indices: 456143--456640 Score: 678
Period size: 254 Copynumber: 2.0 Consensus size: 254
456133 ACAAATTCAT
* * *
456143 GGATATAGGATTTTATGTTGAAACTTCATTCCATTCCACTGTAACTTCAGGGAGATTAAAATCCG
1 GGATATAGGATTTGATGTTGAAACTTCACTCCATTCCACTGCAACTTCAGGGAGATTAAAATCCG
* * * *
456208 CTACTGTTAGTTTTAATCTGATTCACTGCAACTTCAACGATATAAGATTTGGTGTTGTAACTTCA
66 CTACTATTAGTTTTAATCTAATCCACTACAACTTCAACGATATAAGATTTGGTGTTGTAACTTCA
* * * * *
456273 CTCCATTTCACTACAACTTTAGGGAGATTGAGATTTGCTACTGTTAGTTTTAATCTAATCCACTA
131 CTCCATTCCACTACAACTTCAGGGAGATTAAGATTCGCTACTATTAGTTTTAATCTAATCCACTA
* *
456338 GAACTTTAGTGATATAGGATTTTGTGTTGTAACGTCACTCCATTCCACTACAACTTTAG
196 GAACTTAAGTGATATAGGATTTGGTGTTGTAACGTCACTCCATTCCACTACAACTTTAG
* * * *
456397 GGATATAGGATTTGGTGTTGTAACTTCACTCCATTCCACTGCAACTTCAGGGAGATTGAGATCCG
1 GGATATAGGATTTGATGTTGAAACTTCACTCCATTCCACTGCAACTTCAGGGAGATTAAAATCCG
*
456462 CTACTATTAGTTTTAATCTAATCCACTACAACTTCAGA-GATATAGGATTTGGTGTTGTAACTTC
66 CTACTATTAGTTTTAATCTAATCCACTACAACTTCA-ACGATATAAGATTTGGTGTTGTAACTTC
* ** * * ** *
456526 ACTCTATTCCACTGTAACTTCAGGGAGATTAAGATTCGCTACTATTAGTTTTGATTTGGTCTA-T
130 ACTCCATTCCACTACAACTTCAGGGAGATTAAGATTCGCTACTATTAGTTTTAATCTAATCCACT
* * *
456590 TGCAACTTCAAG-GATATAGGATTTGGTGTTGTAACTTCACTCTATTCCACT
195 AG-AACTT-AAGTGATATAGGATTTGGTGTTGTAACGTCACTCCATTCCACT
456641 GTAACTTCAA
Statistics
Matches: 211, Mismatches: 30, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
253 2 0.01
254 206 0.98
255 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.37
Consensus pattern (254 bp):
GGATATAGGATTTGATGTTGAAACTTCACTCCATTCCACTGCAACTTCAGGGAGATTAAAATCCG
CTACTATTAGTTTTAATCTAATCCACTACAACTTCAACGATATAAGATTTGGTGTTGTAACTTCA
CTCCATTCCACTACAACTTCAGGGAGATTAAGATTCGCTACTATTAGTTTTAATCTAATCCACTA
GAACTTAAGTGATATAGGATTTGGTGTTGTAACGTCACTCCATTCCACTACAACTTTAG
Found at i:458066 original size:25 final size:25
Alignment explanation
Indices: 458038--458119 Score: 76
Period size: 25 Copynumber: 3.1 Consensus size: 25
458028 GGGGGTGAAT
458038 TAAATAAAGGATTAAATTAAAACTATAAA
1 TAAATAAAGGATTAAATTAAAAC----AA
* *
458067 CAAATTAAAGGCTTAAATTAAAA-AA
1 TAAA-TAAAGGATTAAATTAAAACAA
*
458092 TAGAATAAAGAATTAAATTAAAACAA
1 TA-AATAAAGGATTAAATTAAAACAA
458118 TA
1 TA
458120 TAAAAAATGC
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
25 19 0.42
26 6 0.13
29 3 0.07
30 17 0.38
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.26
Consensus pattern (25 bp):
TAAATAAAGGATTAAATTAAAACAA
Found at i:458279 original size:16 final size:16
Alignment explanation
Indices: 458227--458271 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
458217 ATTAAGGGGA
*
458227 AAAATT-AAAATGAATT
1 AAAATTAAAAAAGAA-T
458243 AAAATTAAAAAAGAAT
1 AAAATTAAAAAAGAAT
*
458259 GAAATTAAAAAAG
1 AAAATTAAAAAAG
458272 GAAAAAATGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 19 0.73
17 7 0.27
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.22
Consensus pattern (16 bp):
AAAATTAAAAAAGAAT
Found at i:459034 original size:90 final size:90
Alignment explanation
Indices: 458881--459049 Score: 313
Period size: 90 Copynumber: 1.9 Consensus size: 90
458871 ATTTTTTACT
458881 TGTGTATATTTTTCTTTACTTTCGAAACTAAAAAAATCAAAAAATAGTAATCCCTTTACATTCGA
1 TGTGTATATTTTTCTTTACTTTCGAAACTAAAAAAATCAAAAAATAGTAATCCCTTTACATTCGA
458946 TTCTTTGGGGTTTTACGTATATAGA
66 TTCTTTGGGGTTTTACGTATATAGA
*
458971 TGTGTATATATTTT-TTTACTTTCGAAACTAAAAAAATCAGAAAATAGTAATCCCTTTACATTCG
1 TGTGTATAT-TTTTCTTTACTTTCGAAACTAAAAAAATCAAAAAATAGTAATCCCTTTACATTCG
459035 ATTCTTTGGGGTTTT
65 ATTCTTTGGGGTTTT
459050 TATAACCTGG
Statistics
Matches: 77, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
90 73 0.95
91 4 0.05
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (90 bp):
TGTGTATATTTTTCTTTACTTTCGAAACTAAAAAAATCAAAAAATAGTAATCCCTTTACATTCGA
TTCTTTGGGGTTTTACGTATATAGA
Found at i:464672 original size:34 final size:34
Alignment explanation
Indices: 464633--464699 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
464623 CCACGCAGCG
464633 GAAAAATTGAAGCCTTTAATTTTATAGGAAAAAA
1 GAAAAATTGAAGCCTTTAATTTTATAGGAAAAAA
464667 GAAAAATTGAAGCCTTTAATTTTATAGGAAAAA
1 GAAAAATTGAAGCCTTTAATTTTATAGGAAAAA
464700 CAAAGTCTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.49, C:0.06, G:0.15, T:0.30
Consensus pattern (34 bp):
GAAAAATTGAAGCCTTTAATTTTATAGGAAAAAA
Found at i:467691 original size:67 final size:67
Alignment explanation
Indices: 467604--467735 Score: 219
Period size: 67 Copynumber: 2.0 Consensus size: 67
467594 ATGCAATAGG
* * *
467604 ATCACAAGCACAATGTAATGCACCTAATCACCTATACACCAACGCAATGGAGAAGGTTCCTCAGA
1 ATCACAAGCACAATGCAATGCACCCAATCACCTATACACCAACACAATGGAGAAGGTTCCTCAGA
467669 GA
66 GA
* *
467671 ATCACAAGCACAATGCAATGCACCCAATCACCTATACACCAACATAGTGGAGAAGGTTCCTCAGA
1 ATCACAAGCACAATGCAATGCACCCAATCACCTATACACCAACACAATGGAGAAGGTTCCTCAGA
467736 ACCCCTCCTC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.39, C:0.28, G:0.16, T:0.17
Consensus pattern (67 bp):
ATCACAAGCACAATGCAATGCACCCAATCACCTATACACCAACACAATGGAGAAGGTTCCTCAGA
GA
Found at i:468480 original size:22 final size:21
Alignment explanation
Indices: 468449--468517 Score: 58
Period size: 22 Copynumber: 3.4 Consensus size: 21
468439 AAGTTGTATG
468449 AAAGCTCAACTTTAGTCAAAGTC
1 AAAG-TCAAC-TTAGTCAAAGTC
*
468472 AAAGTCAAC-TA-T--GA-TC
1 AAAGTCAACTTAGTCAAAGTC
*
468488 AAAGTCAACCTTGGTCAAAGTC
1 AAAGTCAA-CTTAGTCAAAGTC
468510 AAAGTCAA
1 AAAGTCAA
468518 GGGGTCAGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 13
0.70 0.06 0.25
Matches are distributed among these distances:
16 10 0.27
17 2 0.05
18 1 0.03
19 2 0.05
20 2 0.05
21 1 0.03
22 15 0.41
23 4 0.11
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.23
Consensus pattern (21 bp):
AAAGTCAACTTAGTCAAAGTC
Found at i:468489 original size:16 final size:16
Alignment explanation
Indices: 468470--468511 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
468460 TTAGTCAAAG
468470 TCAAAGTCAA-CTATGA
1 TCAAAGTCAACCT-TGA
*
468486 TCAAAGTCAACCTTGG
1 TCAAAGTCAACCTTGA
468502 TCAAAGTCAA
1 TCAAAGTCAA
468512 AGTCAAGGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 22 0.92
17 2 0.08
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.24
Consensus pattern (16 bp):
TCAAAGTCAACCTTGA
Found at i:468570 original size:7 final size:7
Alignment explanation
Indices: 468560--468584 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
468550 CGGTCAGTGG
468560 TCAATGA
1 TCAATGA
468567 TCAATGA
1 TCAATGA
468574 TCAATGA
1 TCAATGA
468581 TCAA
1 TCAA
468585 ATCGATTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (7 bp):
TCAATGA
Found at i:478854 original size:16 final size:16
Alignment explanation
Indices: 478833--478872 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
478823 GTTGTCTAAA
478833 AAAGTCAA-CTCTGGTC
1 AAAGTCAACCT-TGGTC
478849 AAAGTCAACCTTGGTC
1 AAAGTCAACCTTGGTC
*
478865 AAACTCAA
1 AAAGTCAA
478873 AGTCAACAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 20 0.91
17 2 0.09
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.23
Consensus pattern (16 bp):
AAAGTCAACCTTGGTC
Found at i:480392 original size:20 final size:18
Alignment explanation
Indices: 480368--480419 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
480358 AATAGTATTT
*
480368 TATTAATTTAATATTGAAG
1 TATTAATTTAATATT-AAA
480387 TGATT-ATCTTAATATTAAA
1 T-ATTAAT-TTAATATTAAA
480406 T-TTAATTTAATATT
1 TATTAATTTAATATT
480420 TTTCTTGTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
17 10 0.34
18 2 0.07
19 6 0.21
20 11 0.38
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (18 bp):
TATTAATTTAATATTAAA
Found at i:480506 original size:56 final size:60
Alignment explanation
Indices: 480395--480508 Score: 137
Period size: 56 Copynumber: 1.9 Consensus size: 60
480385 AGTGATTATC
* * * * *
480395 TTAATATTAAATTTAATTTAATATTTTTCTTGTAGATAAACATTCTATTATTTTAATAATAT
1 TTAATATTAAATTTAATATAATATTTATC-T-AAGATAAACATTATATTAATTTAATAATAT
480457 TTAATATTAAA-TTAATATAATATTTATC-AAGAT-AA-ATTATATTAATTTAATA
1 TTAATATTAAATTTAATATAATATTTATCTAAGATAAACATTATATTAATTTAATA
480509 TTAAAATGAT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
56 15 0.32
57 2 0.04
58 4 0.09
61 15 0.32
62 11 0.23
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.50
Consensus pattern (60 bp):
TTAATATTAAATTTAATATAATATTTATCTAAGATAAACATTATATTAATTTAATAATAT
Done.