Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008217.1 Hibiscus syriacus cultivar Beakdansim tig00110847_pilon, 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: 2417150
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 14
Found at i:418303 original size:14 final size:12
Alignment explanation
Indices: 418270--418316 Score: 51
Period size: 14 Copynumber: 3.8 Consensus size: 12
418260 TTTTAAATAT
*
418270 TTATCAATTTAA
1 TTATTAATTTAA
418282 TT-TTAATTTAA
1 TTATTAATTTAA
418293 TATATTAAATTTAA
1 T-TATT-AATTTAA
418307 TTATTTAATT
1 TTA-TTAATT
418317 AGATTGTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
11 9 0.30
12 3 0.10
13 8 0.27
14 10 0.33
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (12 bp):
TTATTAATTTAA
Found at i:431691 original size:22 final size:22
Alignment explanation
Indices: 431663--431707 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
431653 TTAACCAATG
431663 GTTGGGAGAGGAGTTCTCCCCA
1 GTTGGGAGAGGAGTTCTCCCCA
431685 GTTGGGAGAGGAGTTCTCCCCA
1 GTTGGGAGAGGAGTTCTCCCCA
431707 G
1 G
431708 AATACGCCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.22, G:0.38, T:0.22
Consensus pattern (22 bp):
GTTGGGAGAGGAGTTCTCCCCA
Found at i:438663 original size:31 final size:31
Alignment explanation
Indices: 438628--438694 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
438618 AAAAAAAACA
** *
438628 TAAGACATGGTTACTTTTGTTTTTATTTAAT
1 TAAGACATGGCCACTTTCGTTTTTATTTAAT
*
438659 TAAGATATGGCCACTTTCGTTTTTATTTAAT
1 TAAGACATGGCCACTTTCGTTTTTATTTAAT
438690 TAAGA
1 TAAGA
438695 TGTGGTCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.28, C:0.09, G:0.13, T:0.49
Consensus pattern (31 bp):
TAAGACATGGCCACTTTCGTTTTTATTTAAT
Found at i:438879 original size:25 final size:26
Alignment explanation
Indices: 438830--438883 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
438820 AAAATAAAAA
*
438830 AAAATATTTTTAAATTAAGTTAATAAT
1 AAAATATATTTAAATTAAGTTAAT-AT
438857 AAAATATATTT-AA-TAAGTTAATAT
1 AAAATATATTTAAATTAAGTTAATAT
438881 AAA
1 AAA
438884 TTTTTTAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 9 0.35
26 2 0.08
27 10 0.38
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (26 bp):
AAAATATATTTAAATTAAGTTAATAT
Found at i:438890 original size:22 final size:25
Alignment explanation
Indices: 438830--438896 Score: 68
Period size: 27 Copynumber: 2.6 Consensus size: 25
438820 AAAATAAAAA
438830 AAAATATTTTTAAATTAAGTTAATAAT
1 AAAAT-TTTTT-AATTAAGTTAATAAT
*
438857 AAAATATATTTAA-TAAGTTAAT-AT
1 AAAAT-TTTTTAATTAAGTTAATAAT
438881 -AAATTTTTTAAGTTAA
1 AAAATTTTTTAA-TTAA
438897 CATATATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
22 6 0.17
23 4 0.11
24 5 0.14
25 9 0.25
26 2 0.06
27 10 0.28
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (25 bp):
AAAATTTTTTAATTAAGTTAATAAT
Found at i:441332 original size:6 final size:6
Alignment explanation
Indices: 441321--441387 Score: 57
Period size: 6 Copynumber: 10.8 Consensus size: 6
441311 GGTAAAAAAT
* * *
441321 AATAAA AATAAA TAATAAT AATAAT AATAAT AATAAA CAA-AAA GAGA-AAA
1 AATAAA AATAAA -AATAAA AATAAA AATAAA AATAAA -AATAAA -A-ATAAA
441371 AATAAA AATAAA AATAA
1 AATAAA AATAAA AATAA
441388 GAAAATATTA
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
5 1 0.02
6 42 0.78
7 11 0.20
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.19
Consensus pattern (6 bp):
AATAAA
Found at i:441337 original size:3 final size:3
Alignment explanation
Indices: 441318--441356 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
441308 AAGGGTAAAA
*
441318 AAT AAT AAA AAT AAAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AA
441357 ACAAAAAGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:441463 original size:29 final size:29
Alignment explanation
Indices: 441404--441470 Score: 82
Period size: 32 Copynumber: 2.2 Consensus size: 29
441394 ATTAAAATTT
*
441404 AAAAAACGAAAAAAATGTTAAATTTTGAAAGG
1 AAAAAAAGAAAAAAATGTTAAA---TGAAAGG
441436 AAAAAAAGAAAAAAATGTTAAGA-GAAAGG
1 AAAAAAAGAAAAAAATGTTAA-ATGAAAGG
441465 AAAAAA
1 AAAAAA
441471 TGTTAATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
29 12 0.36
32 20 0.61
33 1 0.03
ACGTcount: A:0.67, C:0.01, G:0.16, T:0.15
Consensus pattern (29 bp):
AAAAAAAGAAAAAAATGTTAAATGAAAGG
Found at i:442218 original size:158 final size:158
Alignment explanation
Indices: 441930--442248 Score: 532
Period size: 158 Copynumber: 2.0 Consensus size: 158
441920 CCAAAATGTT
* *
441930 CTTCCCAACCCAGTGAGCCCGAATCTGAGGCTAAATCCCACAAAAAAGCCCATAAAAGTGTATAT
1 CTTCCCAACCCAGTGAGCCCGAATCCGAGGCTAAATCCCACAAAAAAGCCCAGAAAAGTGTATAT
* * * *
441995 TTACGCCCAAAGTTTCGGGGTTTTACCTCTACCGATGGTGACTTTCCAACTTTTTGGTAGTTGTT
66 CTACGCCCAAAGTTTCGGGGTTTTACCTCTACCAATGATGACTTTCCAACTTTCTGGTAGTTGTT
442060 CCTCATTTGATCCAACGCCAGTGTTCAC
131 CCTCATTTGATCCAACGCCAGTGTTCAC
*
442088 CTTCCCAACCTAGTGAGCCCGAATCCGAGGCTAAATCCCACAAAAAAGCCCAGAAAAGTGTATAT
1 CTTCCCAACCCAGTGAGCCCGAATCCGAGGCTAAATCCCACAAAAAAGCCCAGAAAAGTGTATAT
*
442153 CTACGCCCAAAGTTTCGGGTTTTTACCTCTACCAATGATGA-TTTCCTAACTTTCTGGTAGTTGT
66 CTACGCCCAAAGTTTCGGGGTTTTACCTCTACCAATGATGACTTTCC-AACTTTCTGGTAGTTGT
* *
442217 TCCTCCTTTGATCCAACGCTAGTGTTCAC
130 TCCTCATTTGATCCAACGCCAGTGTTCAC
442246 CTT
1 CTT
442249 GCTTTTTCCG
Statistics
Matches: 150, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
157 5 0.03
158 145 0.97
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (158 bp):
CTTCCCAACCCAGTGAGCCCGAATCCGAGGCTAAATCCCACAAAAAAGCCCAGAAAAGTGTATAT
CTACGCCCAAAGTTTCGGGGTTTTACCTCTACCAATGATGACTTTCCAACTTTCTGGTAGTTGTT
CCTCATTTGATCCAACGCCAGTGTTCAC
Found at i:442757 original size:4 final size:4
Alignment explanation
Indices: 442748--442783 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
442738 AGAAAACATA
442748 AAAT AAAT AAAT AAAT -AAT AAAT AAAT -AAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
442784 TGTTAATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 6 0.20
4 24 0.80
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:442769 original size:11 final size:11
Alignment explanation
Indices: 442748--442783 Score: 63
Period size: 11 Copynumber: 3.2 Consensus size: 11
442738 AGAAAACATA
442748 AAATAAATAAAT
1 AAAT-AATAAAT
442760 AAATAATAAAT
1 AAATAATAAAT
442771 AAATAATAAAT
1 AAATAATAAAT
442782 AA
1 AA
442784 TGTTAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 20 0.83
12 4 0.17
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (11 bp):
AAATAATAAAT
Found at i:442926 original size:39 final size:38
Alignment explanation
Indices: 442870--443063 Score: 172
Period size: 38 Copynumber: 5.2 Consensus size: 38
442860 AAAACAAACA
* * *
442870 TTTTTAAAACTATATAATATATATATTTTTCAAAAATTA
1 TTTTCAAAACTAAATAATATATATA-TTTTCAAAAATTG
* *
442909 TTTTCGAAATTAAATAATATATATATTTTCAAAAATTG
1 TTTTCAAAACTAAATAATATATATATTTTCAAAAATTG
*
442947 TTTTCAAAACTATATAATATACT-TATTTTCAAAAAATTG
1 TTTTCAAAACTAAATAATATA-TATATTTTC-AAAAATTG
* *
442986 TTTTCAAAAC----T-ATGTATATATTTTCAAAAATCG
1 TTTTCAAAACTAAATAATATATATATTTTCAAAAATTG
* * * * *
443019 TTTTCTAAAATTATAT-AT-TATATTTTTTTAAAAA-TA
1 TTTTC-AAAACTAAATAATATATATATTTTCAAAAATTG
443055 TTTTCAAAA
1 TTTTCAAAA
443064 ACTATACTAT
Statistics
Matches: 132, Mismatches: 15, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
33 13 0.10
34 15 0.11
35 5 0.04
36 5 0.04
37 14 0.11
38 40 0.30
39 40 0.30
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (38 bp):
TTTTCAAAACTAAATAATATATATATTTTCAAAAATTG
Found at i:443013 original size:34 final size:33
Alignment explanation
Indices: 442886--443075 Score: 148
Period size: 36 Copynumber: 5.2 Consensus size: 33
442876 AAACTATATA
* *
442886 ATATATATATTTTTCAAAAATTATTTTCGAAATTAAAT
1 ATATATATA-TTTTCAAAAATTGTTTTC--AA--AACT
442924 AATATATATATTTTCAAAAATTGTTTTCAAAACTAT
1 -ATATATATATTTTCAAAAATTGTTTTCAAAAC--T
442960 ATAATATACTTATTTTCAAAAAATTGTTTTCAAAACT
1 AT-ATATA--TATTTTC-AAAAATTGTTTTCAAAACT
* * *
442997 ATGTATATATTTTCAAAAATCGTTTTCTAAAATT
1 ATATATATATTTTCAAAAATTGTTTTC-AAAACT
* *
443031 ATATATTATATTTTTTTAAAAA-TATTTTCAAAAACT
1 ATATA-TATA--TTTTCAAAAATTGTTTTC-AAAACT
443067 ATACTATAT
1 ATA-TATAT
443076 TAATTTATAT
Statistics
Matches: 129, Mismatches: 11, Indels: 25
0.78 0.07 0.15
Matches are distributed among these distances:
33 12 0.09
34 18 0.14
35 6 0.05
36 28 0.22
37 14 0.11
38 24 0.19
39 27 0.21
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (33 bp):
ATATATATATTTTCAAAAATTGTTTTCAAAACT
Found at i:443927 original size:8 final size:10
Alignment explanation
Indices: 443903--443931 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
443893 TCACACTAAA
443903 TTCTCTCAAC
1 TTCTCTCAAC
443913 TTCTCTCAAC
1 TTCTCTCAAC
443923 TTCTCTCAA
1 TTCTCTCAA
443932 ATACTCTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.00, T:0.41
Consensus pattern (10 bp):
TTCTCTCAAC
Found at i:443938 original size:10 final size:10
Alignment explanation
Indices: 443900--443938 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
443890 TCATCACACT
443900 AAATTCTCTC
1 AAATTCTCTC
*
443910 AACTTCTCTC
1 AAATTCTCTC
*
443920 AACTTCTCTC
1 AAATTCTCTC
*
443930 AAATACTCT
1 AAATTCTCT
443939 TATAATCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.28, C:0.33, G:0.00, T:0.38
Consensus pattern (10 bp):
AAATTCTCTC
Found at i:443997 original size:9 final size:9
Alignment explanation
Indices: 443985--444035 Score: 70
Period size: 9 Copynumber: 5.9 Consensus size: 9
443975 TAATATTTTG
443985 TATTTAATT
1 TATTTAATT
*
443994 TATTTAA-G
1 TATTTAATT
444002 TATTTAATT
1 TATTTAATT
*
444011 TATTTAA-G
1 TATTTAATT
444019 TATTTAATT
1 TATTTAATT
444028 TATTTAAT
1 TATTTAAT
444036 ATTTTACTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
8 14 0.39
9 22 0.61
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (9 bp):
TATTTAATT
Found at i:444041 original size:17 final size:17
Alignment explanation
Indices: 443984--444039 Score: 105
Period size: 17 Copynumber: 3.4 Consensus size: 17
443974 TTAATATTTT
443984 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
444001 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
444018 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
444035 -TATTT
1 GTATTT
444040 TACTTAATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
16 5 0.13
17 34 0.87
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:446131 original size:25 final size:25
Alignment explanation
Indices: 446096--446169 Score: 82
Period size: 26 Copynumber: 3.0 Consensus size: 25
446086 CATCAACAAA
446096 ATTTTTATTATATTTGTATTTATTAC
1 ATTTTTATTATATTTGT-TTTATTAC
*
446122 -TTTTTATTATAGTTG-TTTATTGAAC
1 ATTTTTATTATATTTGTTTTATT--AC
*
446147 ATTTTTATTGTATTT-TTTTATTA
1 ATTTTTATTATATTTGTTTTATTA
446170 TTTATCATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
23 6 0.15
24 1 0.02
25 16 0.39
26 18 0.44
ACGTcount: A:0.24, C:0.03, G:0.07, T:0.66
Consensus pattern (25 bp):
ATTTTTATTATATTTGTTTTATTAC
Found at i:446868 original size:25 final size:25
Alignment explanation
Indices: 446840--446894 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
446830 CTATTTAACT
446840 GCGCTATACTCCTAGGTGGCCTAAG
1 GCGCTATACTCCTAGGTGGCCTAAG
446865 GCGCTATACTCCTAGGTGGCCTAAG
1 GCGCTATACTCCTAGGTGGCCTAAG
446890 GCGCT
1 GCGCT
446895 CCCTCGGGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.18, C:0.29, G:0.29, T:0.24
Consensus pattern (25 bp):
GCGCTATACTCCTAGGTGGCCTAAG
Found at i:447287 original size:19 final size:19
Alignment explanation
Indices: 447265--447304 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
447255 TATCAATTAC
447265 ATAGATGGAATCAAATTTA
1 ATAGATGGAATCAAATTTA
*
447284 ATAGATGGAGTCAAATTTA
1 ATAGATGGAATCAAATTTA
447303 AT
1 AT
447305 CATGAAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.17, T:0.33
Consensus pattern (19 bp):
ATAGATGGAATCAAATTTA
Found at i:450851 original size:53 final size:53
Alignment explanation
Indices: 450788--450896 Score: 218
Period size: 53 Copynumber: 2.1 Consensus size: 53
450778 TGGGCATAGC
450788 GGGTGCTATTGCGGTGATTGCGGGTGTTGCAGTCAAATAATAGCGTTTTCAGA
1 GGGTGCTATTGCGGTGATTGCGGGTGTTGCAGTCAAATAATAGCGTTTTCAGA
450841 GGGTGCTATTGCGGTGATTGCGGGTGTTGCAGTCAAATAATAGCGTTTTCAGA
1 GGGTGCTATTGCGGTGATTGCGGGTGTTGCAGTCAAATAATAGCGTTTTCAGA
450894 GGG
1 GGG
450897 CATCACTACC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.20, C:0.13, G:0.36, T:0.31
Consensus pattern (53 bp):
GGGTGCTATTGCGGTGATTGCGGGTGTTGCAGTCAAATAATAGCGTTTTCAGA
Found at i:453968 original size:16 final size:17
Alignment explanation
Indices: 453937--453969 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
453927 TCTTACTTAA
453937 AGAAAGATAGAAGAAGAG
1 AGAAAGATA-AAGAAGAG
453955 AGAAAGAT-AAGAAGA
1 AGAAAGATAAAGAAGA
453970 TAGGAAGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.64, C:0.00, G:0.30, T:0.06
Consensus pattern (17 bp):
AGAAAGATAAAGAAGAG
Found at i:459913 original size:2 final size:2
Alignment explanation
Indices: 459908--459945 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
459898 TAACTCTTCA
459908 AT AT AT AT 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 AT AT AT AT
459946 CCTATTCCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:463026 original size:40 final size:40
Alignment explanation
Indices: 462971--463046 Score: 152
Period size: 40 Copynumber: 1.9 Consensus size: 40
462961 CCGGAAGGAA
462971 AGGATGTGCATAAGTTCCAGGGATGGACCGTGGGGGTAAC
1 AGGATGTGCATAAGTTCCAGGGATGGACCGTGGGGGTAAC
463011 AGGATGTGCATAAGTTCCAGGGATGGACCGTGGGGG
1 AGGATGTGCATAAGTTCCAGGGATGGACCGTGGGGG
463047 CATGTTACCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.24, C:0.14, G:0.42, T:0.20
Consensus pattern (40 bp):
AGGATGTGCATAAGTTCCAGGGATGGACCGTGGGGGTAAC
Found at i:463933 original size:56 final size:55
Alignment explanation
Indices: 463846--463998 Score: 173
Period size: 56 Copynumber: 2.8 Consensus size: 55
463836 TTTTGGGATA
* * ** *
463846 CCTATTTTATGATTTTTAATGGCAACAACTGATAAATATACTCGATTTC-GGGACC
1 CCTATTTTATGCTTATTAATAACAATAACTGATAAATATACTCGATTTCAGGG-CC
* * * *
463901 CCTATTTTTATGCTTCTTAATAATAATAACTGATAGATATATTCGATTTCAGGGCC
1 CCTA-TTTTATGCTTATTAATAACAATAACTGATAAATATACTCGATTTCAGGGCC
* * *
463957 TCTATTTTATGCTTATTAATGACAATAATTGATAAATATACT
1 CCTATTTTATGCTTATTAATAACAATAACTGATAAATATACT
463999 TTTTTTTCAA
Statistics
Matches: 81, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
55 36 0.44
56 42 0.52
57 3 0.04
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.41
Consensus pattern (55 bp):
CCTATTTTATGCTTATTAATAACAATAACTGATAAATATACTCGATTTCAGGGCC
Found at i:464991 original size:60 final size:60
Alignment explanation
Indices: 464898--465029 Score: 167
Period size: 60 Copynumber: 2.2 Consensus size: 60
464888 TGAAAATGAA
* * * * * *
464898 CTAAAAGTTCAATGACTGTATTGCATGTTTTAAAAGTTTGG-TGACCAAAATGCAAGCGTC
1 CTAAAAGTTTAGTGAATGTATTGCATGTTTTAAAAG-CTGGATGACCAAAATACAAGCGCC
* *
464958 CTAAAAGTTTAGTGAATGTATTGCATGTTTTAAAAGCTGGATGACCATAATACGAGCGCC
1 CTAAAAGTTTAGTGAATGTATTGCATGTTTTAAAAGCTGGATGACCAAAATACAAGCGCC
*
465018 CTAAACGTTTAG
1 CTAAAAGTTTAG
465030 GGACTATTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 3 0.05
60 59 0.95
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.31
Consensus pattern (60 bp):
CTAAAAGTTTAGTGAATGTATTGCATGTTTTAAAAGCTGGATGACCAAAATACAAGCGCC
Found at i:469854 original size:240 final size:235
Alignment explanation
Indices: 469430--469992 Score: 807
Period size: 240 Copynumber: 2.4 Consensus size: 235
469420 ATGGAATCAC
* * * *
469430 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTCGGATGAGTTTTTCTCATTA
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCATCGGATGAGTTATTCTCATTA
* * *
469495 TGAACTCTCAACTGGAAATGTTGATCCACCTCCTTCTGTTATGATTGAGCCAAGGTGATGCTGAT
66 TGAACTCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATGATTGAGCCAAGGTAATGCTGAT
*
469560 CCAACTCCTTATGTGAGGGACTTGCGAAATGATTATGCTGATCCAACTCCTTATGTGATGGACAA
131 CCAACTCCTTATGTGAGGGACTAGCGAAATGATTATGCTGATCCAACTCCTTATGTGATGGACAA
**
469625 GCAAAAGTCGGTGATGTTCCATTTCCTTATGCGATGGAAACAA
196 GCAAAAGTCGGTGATGTTCCAACTCCTTATGCGAT-G-AA-AA
* *
469668 GCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCGGATGAGTTCTTCTCAT
1 -C-AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCATCGGATGAGTTATTCTCAT
* * * *
469733 TATTAACTCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATGATTGATCTAAGGTAATGTTG
64 TATGAACTCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATGATTGAGCCAAGGTAATGCTG
* *
469798 ATCCATCTCCTTATGTGAGGGACTAGCTAAATGATTATGCTGATCCAACTCCTTATGTGATGGAC
129 ATCCAACTCCTTATGTGAGGGACTAGCGAAATGATTATGCTGATCCAACTCCTTATGTGATGGAC
* **
469863 GAGCAAAAGTCGGTTTTGTTCCAACTCCTTATGCGATGAAAA
194 AAGCAAAAGTCGGTGATGTTCCAACTCCTTATGCGATGAAAA
*
469905 CAA-GCT-AA-AA-TTCTTCTCATTATGAACTTCGTT-TCCCTT-ATCGGATGAGTTATTCTCAT
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTC-TTCT-CCTTCATCGGATGAGTTATTCTCAT
469964 TATGAACTCTCCACTGGAAA-GATTGATCC
64 TATGAACTCTCCACTGGAAATG-TTGATCC
469993 CTCGAGTGAG
Statistics
Matches: 297, Mismatches: 23, Indels: 16
0.88 0.07 0.05
Matches are distributed among these distances:
230 1 0.00
231 65 0.22
232 8 0.03
233 2 0.01
234 2 0.01
235 2 0.01
236 1 0.00
237 2 0.01
238 2 0.01
239 2 0.01
240 210 0.71
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (235 bp):
CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCATCGGATGAGTTATTCTCATTA
TGAACTCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATGATTGAGCCAAGGTAATGCTGAT
CCAACTCCTTATGTGAGGGACTAGCGAAATGATTATGCTGATCCAACTCCTTATGTGATGGACAA
GCAAAAGTCGGTGATGTTCCAACTCCTTATGCGATGAAAA
Found at i:470261 original size:136 final size:136
Alignment explanation
Indices: 469915--470404 Score: 684
Period size: 139 Copynumber: 3.6 Consensus size: 136
469905 CAAGCTAAAA
* *
469915 TTCTTCTCATTATGAACTTCGTT-TCCCTTATCGGATGAGTTATTCTCATTATGAACTCTCCACT
1 TTCTTCTCATTATGAACTTC-TTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCACT
*
469979 GGAAA-GATTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGTGACGAATCGAGCTAA
65 GGAAATG-TTGATCCCTCGAGTGAGGTGTTGCTGATTCAA---CATATGTGATGAATCGAGCTAA
470043 GGTTGAACAAG
126 GGTTGAACAAG
470054 TTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCACTG
1 TTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCACTG
* ** ** * * * * *
470119 GAAATGTTGATCCCTCGAGTGAAGCATCACTGATTCGA-A-ATGTCATAAATCGAG-TGATTGAT
66 GAAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACATATGTGATGAATCGAGCT-A-AGGT
*
470181 CGAACAAG
129 TGAACAAG
*
470189 CTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACTCTCCACT
1 TTCTTCTCATTATGAACTTCTTCTCCCTC-ATCGGATGAGTTCTTCTCATTATGAACTCTCCACT
*
470254 GGAAATGTTGATCCCTCGAGTGAGGTGTTGCTAATTCAACTCCATATGTGATGAATCGAGCTAAG
65 GGAAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAA---CATATGTGATGAATCGAGCTAAG
470319 GTTGAACAAG
127 GTTGAACAAG
* *
470329 TTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCATTT
1 TTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCACTG
470394 GAAATGTTGAT
66 GAAATGTTGAT
470405 TGGTTCATCT
Statistics
Matches: 310, Mismatches: 30, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
133 1 0.00
134 13 0.04
135 38 0.12
136 67 0.22
138 2 0.01
139 135 0.44
140 39 0.13
141 14 0.05
142 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (136 bp):
TTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCACTG
GAAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACATATGTGATGAATCGAGCTAAGGTTG
AACAAG
Found at i:470998 original size:18 final size:18
Alignment explanation
Indices: 470977--471023 Score: 78
Period size: 18 Copynumber: 2.6 Consensus size: 18
470967 GCGAGAGCAA
470977 TCTTCATTGC-TAGATCAG
1 TCTTCATT-CTTAGATCAG
470995 TCTTCATTCTTAGATCAG
1 TCTTCATTCTTAGATCAG
471013 TCTTCATTCTT
1 TCTTCATTCTT
471024 TTCCTGGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 1 0.04
18 27 0.96
ACGTcount: A:0.19, C:0.23, G:0.11, T:0.47
Consensus pattern (18 bp):
TCTTCATTCTTAGATCAG
Found at i:471224 original size:52 final size:53
Alignment explanation
Indices: 471164--471304 Score: 169
Period size: 54 Copynumber: 2.7 Consensus size: 53
471154 ATTTACAGTT
*
471164 ATCAAGAAACCCCT-AAAATTAGGCTTAACTTCTCTCAAAAATTCA-AAAAAAA
1 ATCAAGAAACCCCTAAAAATTAGGCTTAATTTCT-TCAAAAATTCATAAAAAAA
* ** ** ** *
471216 ATCAAGAAACCCCTGAAAACCAGGCTTAATTTCTTTGAAAATTCATTTGAAAAC
1 ATCAAGAAACCCCTAAAAATTAGGCTTAATTTCTTCAAAAATTCA-TAAAAAAA
471270 ATCAAGAAACCCCTAAAAATTAGGCTTAATTTCTT
1 ATCAAGAAACCCCTAAAAATTAGGCTTAATTTCTT
471305 TGAACGTTCA
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
52 23 0.31
53 16 0.21
54 36 0.48
ACGTcount: A:0.44, C:0.21, G:0.09, T:0.27
Consensus pattern (53 bp):
ATCAAGAAACCCCTAAAAATTAGGCTTAATTTCTTCAAAAATTCATAAAAAAA
Found at i:471281 original size:54 final size:54
Alignment explanation
Indices: 471211--471745 Score: 519
Period size: 54 Copynumber: 9.9 Consensus size: 54
471201 AAAATTCAAA
* ** * * * *
471211 AAAAAATCAAGAAACCCCTGAAAACCAGGCTTAATTTCTTTGAAAATTCATTTG
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAATTCATTTG
** * * * * * **
471265 AAAACATCAAGAAACCCCTAAAAATTAGGCTTAATTTCTTTGAACGTTCATTTG
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAATTCATTTG
* *
471319 AGAAAAATCAAGAAACTT-TCGAAAATCAGACTTAATTTCTTTAAAACA--CATTTG
1 A-AAACATCAAGAAACTTCT-GAAAATCAGACTTAGTTTCTTTAAAA-ATTCATTTG
* * *
471373 AAAAGCGTCAAGAAACTTCTAAAAATCAGACTTAGTTTCTTTAAAAACTCATTTG
1 AAAA-CATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAATTCATTTG
* * * * *
471428 AAATCATCATGAAACTTCTAAAAATCAGACTTAGTTTCGTTGAAAACTT-ATTTG
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTC-TTTAAAAATTCATTTG
* * * *
471482 AAATCATCAAGAAACTTTTGAAAATCAGACTTAGTTTCTTTAAAAACTCACTTG
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAATTCATTTG
* * *
471536 AAAATCATCATGAAACTTCTGAAAATCAGACTTAGTTTCATTGAAAACTT-ATTTG
1 AAAA-CATCAAGAAACTTCTGAAAATCAGACTTAGTTTC-TTTAAAAATTCATTTG
* * *
471591 AAATCATCAAGAAACTTCTGAAAATAAGACTTAGTTTCTTTAAAAAACTCATTT-
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTT-AAAAATTCATTTG
* * * * *
471645 AAAATGATCAAGAAACTT-TCGAAAATCGGAATTAGTTTC-TAAAAAACTCATTTG
1 AAAA-CATCAAGAAACTTCT-GAAAATCAGACTTAGTTTCTTTAAAAATTCATTTG
* * *
471699 AAAATCGTCAAGAAACTTATGAAAATTAGACTTAGTTTCTTTAAAAA
1 AAAA-CATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAA
471746 CTAATAAAAA
Statistics
Matches: 406, Mismatches: 57, Indels: 35
0.82 0.11 0.07
Matches are distributed among these distances:
53 25 0.06
54 245 0.60
55 129 0.32
56 7 0.02
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.32
Consensus pattern (54 bp):
AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAATTCATTTG
Found at i:471355 original size:109 final size:108
Alignment explanation
Indices: 471211--471747 Score: 548
Period size: 109 Copynumber: 4.9 Consensus size: 108
471201 AAAATTCAAA
** * * *
471211 AAAAAATCAAGAAACCCCTGAAAACCAGGCTTAATTTCTTTGAAAATTCATTTGAAAACATCAAG
1 AAAAAATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAATTCATTTGAAAACATCAAG
** * * * * ***
471276 AAACCCCTAAAAATTAGGCTTAATTTCTTTGAACGTTCATTTG
66 AAACTTCTAAAAATCAGACTTAGTTTCTTTAAAAACTCATTTG
* ** *
471319 AGAAAAATCAAGAAACTT-TCGAAAATCAGACTTAATTTCTTT-AAAACACATTTGAAAAGCGTC
1 A-AAAAATCAAGAAACTTCT-GAAAATCAGACTTAGTTTCTTTGAAAATTCATTTGAAAA-CATC
471382 AAGAAACTTCTAAAAATCAGACTTAGTTTCTTTAAAAACTCATTTG
63 AAGAAACTTCTAAAAATCAGACTTAGTTTCTTTAAAAACTCATTTG
** * * * *
471428 AAATCATCATGAAACTTCTAAAAATCAGACTTAGTTTCGTTGAAAACTT-ATTTGAAATCATCAA
1 AAAAAATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAA-TTCATTTGAAAACATCAA
* * *
471492 GAAACTTTTGAAAATCAGACTTAGTTTCTTTAAAAACTCACTTG
65 GAAACTTCTAAAAATCAGACTTAGTTTCTTTAAAAACTCATTTG
* * * *
471536 AAAATCATCATGAAACTTCTGAAAATCAGACTTAGTTTCATTGAAAACTT-ATTTGAAATCATCA
1 AAAA-AATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAA-TTCATTTGAAAACATCA
* *
471600 AGAAACTTCTGAAAATAAGACTTAGTTTCTTTAAAAAACTCATTT-
64 AGAAACTTCTAAAAATCAGACTTAGTTTCTTT-AAAAACTCATTTG
* * * ** * *
471645 AAAATGATCAAGAAACTT-TCGAAAATCGGAATTAGTTTC-TAAAAAACTCATTTGAAAATCGTC
1 AAAA-AATCAAGAAACTTCT-GAAAATCAGACTTAGTTTCTTTGAAAATTCATTTGAAAA-CATC
* * *
471708 AAGAAACTTATGAAAATTAGACTTAGTTTCTTTAAAAACT
63 AAGAAACTTCTAAAAATCAGACTTAGTTTCTTTAAAAACT
471748 AATAAAAAAT
Statistics
Matches: 372, Mismatches: 46, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
107 1 0.00
108 118 0.32
109 242 0.65
110 11 0.03
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.32
Consensus pattern (108 bp):
AAAAAATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAATTCATTTGAAAACATCAAG
AAACTTCTAAAAATCAGACTTAGTTTCTTTAAAAACTCATTTG
Found at i:471539 original size:163 final size:163
Alignment explanation
Indices: 471217--471747 Score: 647
Period size: 163 Copynumber: 3.3 Consensus size: 163
471207 CAAAAAAAAA
** * * * * * * **
471217 TCAAGAAACCCCTGAAAACCAGGCTTAATTTCTTTGAAAATTCATTTGAAAACATCAAGAAACCC
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTGAAATCATCAAGAAACTT
* * * *
471282 CTAAAAATTAGGCTTAATTTCTTTG--AACGTTCATTTGAGAAAAATCAAGAAACTTTCGAAAAT
66 CTAAAAATAAGACTTAGTTTCTTTGAAAAC-TT-ATTTGA-AATAATCAAGAAACTTTCGAAAAT
* * *
471345 CAGACTTAATTTCTTT-AAAACACATTTGAAAAGCG
128 CAGACTTAGTTTCTTTAAAAACTCATTTGAAAATCG
* *
471380 TCAAGAAACTTCTAAAAATCAGACTTAGTTTCTTTAAAAACTCATTTGAAATCATCATGAAACTT
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTGAAATCATCAAGAAACTT
* * * *
471445 CTAAAAATCAGACTTAGTTTCGTTGAAAACTTATTTGAAATCATCAAGAAACTTTTGAAAATCAG
66 CTAAAAATAAGACTTAGTTTCTTTGAAAACTTATTTGAAATAATCAAGAAACTTTCGAAAATCAG
* *
471510 ACTTAGTTTCTTTAAAAACTCACTTGAAAATCA
131 ACTTAGTTTCTTTAAAAACTCATTTGAAAATCG
* * * *
471543 TCATGAAACTTCTGAAAATCAGACTTAGTTTCATTGAAAACTTATTTGAAATCATCAAGAAACTT
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTGAAATCATCAAGAAACTT
* * * * * *
471608 CTGAAAATAAGACTTAGTTTCTTTAAAAAACTCATTTAAAATGATCAAGAAACTTTCGAAAATCG
66 CTAAAAATAAGACTTAGTTTCTTT-GAAAACTTATTTGAAATAATCAAGAAACTTTCGAAAATCA
* *
471673 GAATTAGTTTC-TAAAAAACTCATTTGAAAATCG
130 GACTTAGTTTCTTTAAAAACTCATTTGAAAATCG
* *
471706 TCAAGAAACTTATGAAAATTAGACTTAGTTTCTTTAAAAACT
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACT
471748 AATAAAAAAT
Statistics
Matches: 316, Mismatches: 48, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
162 36 0.11
163 231 0.73
164 46 0.15
165 3 0.01
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (163 bp):
TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTGAAATCATCAAGAAACTT
CTAAAAATAAGACTTAGTTTCTTTGAAAACTTATTTGAAATAATCAAGAAACTTTCGAAAATCAG
ACTTAGTTTCTTTAAAAACTCATTTGAAAATCG
Found at i:471757 original size:54 final size:54
Alignment explanation
Indices: 471325--471793 Score: 498
Period size: 54 Copynumber: 8.6 Consensus size: 54
471315 TTTGAGAAAA
* *
471325 ATCAAGAAACTT-TCGAAAATCAGACTTAATTTCTTT-AAAAC-ACATTTGAAAAGC
1 ATCAAGAAACTTCT-GAAAATCAGACTTAGTTTCTTTAAAAACTA-ATTT-AAAATC
* * * *
471379 GTCAAGAAACTTCTAAAAATCAGACTTAGTTTCTTTAAAAACTCATTTGAAATC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTAATTTAAAATC
* * * * * *
471433 ATCATGAAACTTCTAAAAATCAGACTTAGTTTCGTTGAAAACTTATTTGAAATC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTAATTTAAAATC
* * *
471487 ATCAAGAAACTTTTGAAAATCAGACTTAGTTTCTTTAAAAACTCACTTGAAAATC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACT-AATTTAAAATC
* * * * *
471542 ATCATGAAACTTCTGAAAATCAGACTTAGTTTCATTGAAAACTTATTTGAAATC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTAATTTAAAATC
* * *
471596 ATCAAGAAACTTCTGAAAATAAGACTTAGTTTCTTTAAAAAACTCATTTAAAATG
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTT-AAAAACTAATTTAAAATC
* * * *
471651 ATCAAGAAACTT-TCGAAAATCGGAATTAGTTTC-TAAAAAACTCATTTGAAAATC
1 ATCAAGAAACTTCT-GAAAATCAGACTTAGTTTCTTTAAAAACTAATTT-AAAATC
* * * **
471705 GTCAAGAAACTTATGAAAATTAGACTTAGTTTCTTTAAAAACTAATAAAAAATACC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTAATTTAAAAT--C
* *
471761 ATGTCAAGAAACCTCTGAAAATCAGACGTAGTT
1 A--TCAAGAAACTTCTGAAAATCAGACTTAGTT
471794 CCTAAAAACA
Statistics
Matches: 349, Mismatches: 53, Indels: 22
0.82 0.12 0.05
Matches are distributed among these distances:
53 12 0.03
54 201 0.58
55 109 0.31
56 1 0.00
58 26 0.07
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.32
Consensus pattern (54 bp):
ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTAATTTAAAATC
Found at i:473725 original size:17 final size:17
Alignment explanation
Indices: 473685--473727 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
473675 GTTGGATCTG
*
473685 TCTATTTCTTTTTTTAA
1 TCTATTTTTTTTTTTAA
**
473702 TCT-TTTTTTTTTTTCT
1 TCTATTTTTTTTTTTAA
473718 TCTATTTTTT
1 TCTATTTTTT
473728 CTCTTTCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (17 bp):
TCTATTTTTTTTTTTAA
Found at i:473725 original size:27 final size:27
Alignment explanation
Indices: 473690--473745 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
473680 ATCTGTCTAT
* * *
473690 TTCTTTTTTTAATCTTTTTTTTTTTTC
1 TTCTATTTTTAATCTTTCTTTTTTCTC
**
473717 TTCTATTTTTTCTCTTTCTTTTTTCTC
1 TTCTATTTTTAATCTTTCTTTTTTCTC
473744 TT
1 TT
473746 TTTTCTATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (27 bp):
TTCTATTTTTAATCTTTCTTTTTTCTC
Found at i:473745 original size:9 final size:9
Alignment explanation
Indices: 473733--473795 Score: 65
Period size: 9 Copynumber: 6.9 Consensus size: 9
473723 TTTTTCTCTT
473733 TCTTTTTTC
1 TCTTTTTTC
473742 TCTTTTTTC
1 TCTTTTTTC
*
473751 TATTTTTT-
1 TCTTTTTTC
*
473759 TCTGTGTTTC
1 TCT-TTTTTC
*
473769 TCTTTTTTT
1 TCTTTTTTC
*
473778 TCCTTTTTTT
1 T-CTTTTTTC
473788 TCTTTTTT
1 TCTTTTTT
473796 TTTTTGTGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
8 2 0.04
9 32 0.70
10 12 0.26
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.79
Consensus pattern (9 bp):
TCTTTTTTC
Found at i:473778 original size:39 final size:40
Alignment explanation
Indices: 473725--473806 Score: 121
Period size: 39 Copynumber: 2.1 Consensus size: 40
473715 TCTTCTATTT
*
473725 TTTCTCTTTCTTTTTTCTCTTTTTTCTATTTTTTTCTGTG
1 TTTCTCTTTCTTTTTCCTCTTTTTTCTATTTTTTTCTGTG
* * *
473765 TTTCTCTTT-TTTTTCCTTTTTTTTCTTTTTTTTTTTGTG
1 TTTCTCTTTCTTTTTCCTCTTTTTTCTATTTTTTTCTGTG
473804 TTT
1 TTT
473807 TTTATATATC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
39 29 0.76
40 9 0.24
ACGTcount: A:0.01, C:0.15, G:0.05, T:0.79
Consensus pattern (40 bp):
TTTCTCTTTCTTTTTCCTCTTTTTTCTATTTTTTTCTGTG
Found at i:473796 original size:9 final size:9
Alignment explanation
Indices: 473689--473797 Score: 87
Period size: 10 Copynumber: 11.3 Consensus size: 9
473679 GATCTGTCTA
473689 TTTCTTTTT
1 TTTCTTTTT
473698 TTAATC-TTTT
1 TT--TCTTTTT
473708 TTT-TTTTT
1 TTTCTTTTT
*
473716 CTTCTATTTT
1 TTTCT-TTTT
473726 TTCTCTTTCTTT
1 TT-TC-TT-TTT
*
473738 TTTCTCTTT
1 TTTCTTTTT
473747 TTTCTATTTT
1 TTTCT-TTTT
*
473757 TTTCTGTGTT
1 TTTCT-TTTT
*
473767 TCTCTTTTT
1 TTTCTTTTT
473776 TTTCCTTTTT
1 TTT-CTTTTT
473786 TTTCTTTTT
1 TTTCTTTTT
473795 TTT
1 TTT
473798 TTTGTGTTTT
Statistics
Matches: 81, Mismatches: 9, Indels: 20
0.74 0.08 0.18
Matches are distributed among these distances:
8 7 0.09
9 25 0.31
10 36 0.44
11 7 0.09
12 6 0.07
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.80
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:493698 original size:82 final size:80
Alignment explanation
Indices: 493583--493738 Score: 176
Period size: 82 Copynumber: 1.9 Consensus size: 80
493573 CCCGAATATA
* *
493583 TTAAGTAAGCATTAAAAGAATGTAATTTAGATTACAACTCTTTTAATTGATATATATAA-TTCAG
1 TTAAATAAACATTAAAAGAATGTAATTTAGATTACAACTC-TTTAA-TG-TATATATAAGTT--G
493647 AA-TAATTAAATAAGTTTTT
61 AATTAATTAAATAAGTTTTT
* * * *
493666 TTAAATAAACATT-AAAGATTGTAATTCT-GATTATAAGTCTTTAATGTATATTTAAGTTGAATT
1 TTAAATAAACATTAAAAGAATGTAATT-TAGATTACAACTCTTTAATGTATATATAAGTTGAATT
493729 AATTAAATAA
65 AATTAAATAA
493739 TATTTTATTT
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
78 3 0.05
79 19 0.30
80 4 0.06
81 5 0.08
82 21 0.33
83 12 0.19
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.42
Consensus pattern (80 bp):
TTAAATAAACATTAAAAGAATGTAATTTAGATTACAACTCTTTAATGTATATATAAGTTGAATTA
ATTAAATAAGTTTTT
Found at i:498045 original size:31 final size:31
Alignment explanation
Indices: 498010--498089 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 31
498000 AGTCATGCTT
* * *
498010 GCATTAAGATAATGCATAGTATGTCAGGTTC
1 GCATTAAGACAATGCACAATATGTCAGGTTC
* * *
498041 GCATTCAGACAATGCACAATATGTCATGTTT
1 GCATTAAGACAATGCACAATATGTCAGGTTC
* *
498072 GCATTAAGAGAATACACA
1 GCATTAAGACAATGCACA
498090 GGAGCATCAG
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (31 bp):
GCATTAAGACAATGCACAATATGTCAGGTTC
Found at i:500501 original size:17 final size:17
Alignment explanation
Indices: 500479--500516 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
500469 AGACCCGATC
500479 TAAAATAATATATTTAT
1 TAAAATAATATATTTAT
* *
500496 TAAAATATTATTTTTAT
1 TAAAATAATATATTTAT
500513 TAAA
1 TAAA
500517 TAGAAATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAAATAATATATTTAT
Found at i:504185 original size:3 final size:3
Alignment explanation
Indices: 504177--504203 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
504167 TGTTCAAATG
504177 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
504204 CAGTTCATAG
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:509947 original size:36 final size:35
Alignment explanation
Indices: 509861--509986 Score: 83
Period size: 36 Copynumber: 3.8 Consensus size: 35
509851 AATACGAAAT
*
509861 AAATAAACAAC--ATAA-AAAATAAAAAAATGATA
1 AAATAAACAACAAAAAACAAAATAAAAAAATGATA
* * ** * *
509893 AAGTAAAGAGTAATAAACAAAATAAATAGAATGATA
1 AAATAAACAACAAAAAACAAAATAAA-AAAATGATA
*
509929 AAATAAACAACAAAAAAC---ATAAAAAAA--AGA
1 AAATAAACAACAAAAAACAAAATAAAAAAATGATA
*
509959 AAATAATA-AAC-AAAAACAGAATAAAAAA
1 AAATAA-ACAACAAAAAACAAAATAAAAAA
509987 CAAAGGAAAA
Statistics
Matches: 72, Mismatches: 14, Indels: 16
0.71 0.14 0.16
Matches are distributed among these distances:
29 6 0.08
30 11 0.15
31 1 0.01
32 18 0.25
33 5 0.07
34 2 0.03
35 8 0.11
36 21 0.29
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.13
Consensus pattern (35 bp):
AAATAAACAACAAAAAACAAAATAAAAAAATGATA
Found at i:509973 original size:18 final size:17
Alignment explanation
Indices: 509930--509990 Score: 54
Period size: 18 Copynumber: 3.6 Consensus size: 17
509920 AGAATGATAA
*
509930 AATAAACAACAAAAAA-
1 AATAAACAAAAAAAAAT
*
509946 CATAAA-AAAAAGAAAAT
1 AATAAACAAAAA-AAAAT
*
509963 AATAAACAAAAACAGAAT
1 AATAAACAAAAA-AAAAT
*
509981 AAAAAACAAA
1 AATAAACAAA
509991 GGAAAAAGTA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
15 4 0.11
16 9 0.25
17 5 0.14
18 18 0.50
ACGTcount: A:0.79, C:0.10, G:0.03, T:0.08
Consensus pattern (17 bp):
AATAAACAAAAAAAAAT
Found at i:509985 original size:30 final size:30
Alignment explanation
Indices: 509928--509986 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
509918 ATAGAATGAT
*
509928 AAAATAAACAACAAAAAACATAAAAAAAAG
1 AAAATAAACAACAAAAAACAGAAAAAAAAG
509958 AAAATAATA-AAC-AAAAACAGAATAAAAAA
1 AAAATAA-ACAACAAAAAACAGAA-AAAAAA
509987 CAAAGGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 9 0.35
30 16 0.62
31 1 0.04
ACGTcount: A:0.80, C:0.08, G:0.03, T:0.08
Consensus pattern (30 bp):
AAAATAAACAACAAAAAACAGAAAAAAAAG
Found at i:510176 original size:23 final size:21
Alignment explanation
Indices: 510150--510206 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 21
510140 ATAGAAGAAC
*
510150 AAATAATAAAAAAACCAAAATGA
1 AAATAATAAAAAAA-AAAAAT-A
*
510173 AAATAGTAAAATAAAAAAAATA
1 AAATAATAAAA-AAAAAAAATA
510195 AAATAA-AAAAAA
1 AAATAATAAAAAA
510207 TATATACATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 2 0.07
21 4 0.13
22 6 0.20
23 15 0.50
24 3 0.10
ACGTcount: A:0.79, C:0.04, G:0.04, T:0.14
Consensus pattern (21 bp):
AAATAATAAAAAAAAAAAATA
Found at i:510206 original size:14 final size:14
Alignment explanation
Indices: 510154--510208 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
510144 AAGAACAAAT
**
510154 AATAAAAAAACCAA
1 AATAAAAAAAATAA
* * *
510168 AATGAAAATAGTAA
1 AATAAAAAAAATAA
510182 AATAAAAAAAATAA
1 AATAAAAAAAATAA
510196 AATAAAAAAAATA
1 AATAAAAAAAATA
510209 TATACATAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.15
Consensus pattern (14 bp):
AATAAAAAAAATAA
Found at i:510307 original size:15 final size:16
Alignment explanation
Indices: 510269--510309 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
510259 TAACATTAAT
*
510269 AAAAC-AAACAAAAGT
1 AAAACAAAACAAAAGC
*
510284 AAAATAAAACAAAA-C
1 AAAACAAAACAAAAGC
510299 AAAACAAAACA
1 AAAACAAAACA
510310 TATAAAAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.78, C:0.15, G:0.02, T:0.05
Consensus pattern (16 bp):
AAAACAAAACAAAAGC
Found at i:510307 original size:20 final size:20
Alignment explanation
Indices: 510266--510307 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
510256 ACATAACATT
*
510266 AATAAAACAAACAAAAGTAA
1 AATAAAACAAACAAAAGCAA
510286 AATAAAACAAAACAAAA-CAA
1 AATAAAAC-AAACAAAAGCAA
510306 AA
1 AA
510308 CATATAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.79, C:0.12, G:0.02, T:0.07
Consensus pattern (20 bp):
AATAAAACAAACAAAAGCAA
Found at i:511337 original size:19 final size:18
Alignment explanation
Indices: 511313--511370 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
511303 TGACGACTGA
511313 TGCTTCTGGCCGTTGAAAT
1 TGCTTCTGGCCGTTG-AAT
** *
511332 TGCTTCTGGATGTTGACT
1 TGCTTCTGGCCGTTGAAT
*
511350 TGCTTTCTGGCCGTTGGAT
1 TGC-TTCTGGCCGTTGAAT
511369 TG
1 TG
511371 GGTCAGATCC
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
18 5 0.16
19 26 0.84
ACGTcount: A:0.10, C:0.19, G:0.29, T:0.41
Consensus pattern (18 bp):
TGCTTCTGGCCGTTGAAT
Found at i:511556 original size:15 final size:14
Alignment explanation
Indices: 511524--511552 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
511514 TGAAAAAAAC
511524 ATAAAAAGAAAATA
1 ATAAAAAGAAAATA
511538 ATAAAAAGAAAATA
1 ATAAAAAGAAAATA
511552 A
1 A
511553 ATAATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (14 bp):
ATAAAAAGAAAATA
Found at i:511629 original size:32 final size:32
Alignment explanation
Indices: 511592--511869 Score: 138
Period size: 36 Copynumber: 8.1 Consensus size: 32
511582 ATATAATACA
*
511592 TATATTTCAAAAATATTTTTTAAACTATATAT
1 TATATTTCAAAAATATTTTTAAAACTATATAT
*
511624 TATATTT-AAAAA-AGTTTTCAAAACTATAT-T
1 TATATTTCAAAAATA-TTTTTAAAACTATATAT
* *
511654 ATATAGTTTTC-AAAAT-GTTTTAAAAATATTATAT
1 -TATA--TTTCAAAAATATTTTTAAAACTA-TATAT
* *
511688 AAGT-TTTAAAAAATATTTTTAAAACTATATACT
1 TA-TATTTCAAAAATATTTTTAAAACTATATA-T
*
511721 ATATAATTTATTCAAAAATGTTTTTAAAACTATATAT
1 -TAT-A--T-TTCAAAAATATTTTTAAAACTATATAT
**
511758 TATATAAGGTTTTAAAATGA-TTTTAAAACTATATGTTAT
1 TATAT----TTCAAAAAT-ATTTTTAAAACTATA---TAT
* * * *
511797 ATATATTTTCTAAAATGTTTTAAAAACTATATGTT
1 -TATA-TTTCAAAAATATTTTTAAAACTATAT-AT
*
511832 ATATAGTTTTCAAAAATATTTTAAAAAACTATATAT
1 -TATA--TTTCAAAAATATTTT-TAAAACTATATAT
511868 TA
1 TA
511870 CCCATATTTT
Statistics
Matches: 192, Mismatches: 23, Indels: 59
0.70 0.08 0.22
Matches are distributed among these distances:
30 2 0.01
31 25 0.13
32 25 0.13
33 24 0.12
34 4 0.02
35 9 0.05
36 38 0.20
37 33 0.17
38 24 0.12
39 3 0.02
40 4 0.02
41 1 0.01
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (32 bp):
TATATTTCAAAAATATTTTTAAAACTATATAT
Found at i:511635 original size:31 final size:31
Alignment explanation
Indices: 511592--511762 Score: 116
Period size: 31 Copynumber: 5.2 Consensus size: 31
511582 ATATAATACA
*
511592 TATATTTCAAAAATATTTTTTAAACTATATAT
1 TATATTT-AAAAATATTTTTAAAACTATATAT
*
511624 TATATTTAAAAA-AGTTTTCAAAACTATAT-T
1 TATATTTAAAAATA-TTTTTAAAACTATATAT
* * *
511654 ATATAGTTTTCAAAAT-GTTTTAAAAATATTATAT
1 -TATA--TTTAAAAATATTTTTAAAACTA-TATAT
*
511688 AAGT-TTTAAAAAATATTTTTAAAACTATATACT
1 TA-TATTT-AAAAATATTTTTAAAACTATATA-T
*
511721 ATATAATTTATTCAAAAATGTTTTTAAAACTATATAT
1 -TAT-A--T-TT-AAAAATATTTTTAAAACTATATAT
511758 TATAT
1 TATAT
511763 AAGGTTTTAA
Statistics
Matches: 109, Mismatches: 13, Indels: 33
0.70 0.08 0.21
Matches are distributed among these distances:
30 2 0.02
31 25 0.23
32 25 0.23
33 24 0.22
34 3 0.03
35 1 0.01
36 3 0.03
37 2 0.02
38 24 0.22
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (31 bp):
TATATTTAAAAATATTTTTAAAACTATATAT
Found at i:511706 original size:96 final size:104
Alignment explanation
Indices: 511600--511869 Score: 256
Period size: 111 Copynumber: 2.6 Consensus size: 104
511590 CATATATTTC
*
511600 AAAAATATTTTTTAAACTATATA-T-TAT-ATTTA-AAAAA-GTTTTCAAAAC-TATATTATAT-
1 AAAAATATTTTTAAAACTATATACTATATAATTTATAAAAATGTTTTCAAAACATATATTATATA
511658 A-GTTTTCAAAATG-TTTTAAAAATATTATATAAGTTTTA
66 AGGTTTT-AAAATGATTTTAAAAATATTATATAAGTTTTA
*
511696 AAAAATATTTTTAAAACTATATACTATATAATTTATTCAAAAATGTTTTTAAAACTATATATTAT
1 AAAAATATTTTTAAAACTATATACTATATAATTTA-T-AAAAATGTTTTCAAAAC-ATATATTAT
*
511761 ATAAGGTTTTAAAATGATTTTAAAACTATATGTTATATATA-TTTTC
63 ATAAGGTTTTAAAATGATTTTAAAA--ATA--TTATATA-AGTTTTA
* * * ** * * *
511807 TAAAATGTTTTAAAAACTATATGTTATATAGTTT-TCAAAAATATTTTAAAAAACTATATATTA
1 AAAAATATTTTTAAAACTATATACTATATAATTTAT-AAAAATGTTTT-CAAAAC-ATATATTA
511870 CCCATATTTT
Statistics
Matches: 145, Mismatches: 11, Indels: 22
0.81 0.06 0.12
Matches are distributed among these distances:
96 22 0.15
97 1 0.01
98 3 0.02
99 5 0.03
102 5 0.03
103 10 0.07
105 10 0.07
106 7 0.05
107 13 0.09
109 15 0.10
110 14 0.10
111 39 0.27
112 1 0.01
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (104 bp):
AAAAATATTTTTAAAACTATATACTATATAATTTATAAAAATGTTTTCAAAACATATATTATATA
AGGTTTTAAAATGATTTTAAAAATATTATATAAGTTTTA
Found at i:511812 original size:37 final size:36
Alignment explanation
Indices: 511638--511857 Score: 207
Period size: 36 Copynumber: 6.2 Consensus size: 36
511628 TTTAAAAAAG
511638 TTTTCAAAACTATA-TTATAT-AGTTTTC-AAAATG-
1 TTTT-AAAACTATATTTATATAAGTTTTCAAAAATGA
*
511671 TTTTAAAA--ATA-TTATATAAGTTTTAAAAAAT-A
1 TTTTAAAACTATATTTATATAAGTTTTCAAAAATGA
* * *
511703 TTTTTAAAACTATATACTATATAATTTATTCAAAAATGT
1 -TTTTAAAACTATAT-TTATATAAGTT-TTCAAAAATGA
511742 TTTTAAAACTATATATTATATAAGGTTTT--AAAATGA
1 TTTTAAAACTATAT-TTATATAA-GTTTTCAAAAATGA
*
511778 TTTTAAAACTATATGTTATATATA-TTTTCTAAAATG-
1 TTTTAAAACTATAT-TTATATA-AGTTTTCAAAAATGA
511814 TTTTAAAAACTATATGTTATAT-AGTTTTCAAAAAT-A
1 TTTT-AAAACTATAT-TTATATAAGTTTTCAAAAATGA
511850 TTTTAAAA
1 TTTTAAAA
511858 AACTATATAT
Statistics
Matches: 160, Mismatches: 10, Indels: 32
0.79 0.05 0.16
Matches are distributed among these distances:
30 9 0.06
31 6 0.04
32 9 0.06
33 12 0.08
35 12 0.08
36 45 0.28
37 33 0.21
38 32 0.20
39 2 0.01
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (36 bp):
TTTTAAAACTATATTTATATAAGTTTTCAAAAATGA
Found at i:511885 original size:37 final size:35
Alignment explanation
Indices: 511581--511890 Score: 182
Period size: 37 Copynumber: 8.8 Consensus size: 35
511571 TAATATAAAT
* * **
511581 TATATAATACATATATTTCAAAAATATTTTTTAAAC
1 TATATATTACATAT-TTTCAAAAATGTTTTAAAAAC
* *
511617 TATATATT--ATA-TTT-AAAAAAGTTTTCAAAAC
1 TATATATTACATATTTTCAAAAATGTTTTAAAAAC
*
511648 --TATATTATATAGTTTTC-AAAATGTTTTAAAAA-
1 TATATATTACATA-TTTTCAAAAATGTTTTAAAAAC
* * * *
511680 TAT-TATATA-A-GTTTTAAAAAATATTTTTAAAAC
1 TATATAT-TACATATTTTCAAAAATGTTTTAAAAAC
* * *
511713 TATATACTATATAATTTATTCAAAAATGTTTTTAAAAC
1 TATATATTACAT-A-TT-TTCAAAAATGTTTTAAAAAC
*
511751 TATATATTATATAAGGTTTT--AAAATGATTTT-AAAAC
1 TATATATTACAT-A--TTTTCAAAAATG-TTTTAAAAAC
* * *
511787 TATATGTTATATATATTTTCTAAAATGTTTTAAAAAC
1 TATAT-AT-TACATATTTTCAAAAATGTTTTAAAAAC
* * *
511824 TATATGTTATATAGTTTTCAAAAATATTTTAAAAAAC
1 TATATATTACATA-TTTTCAAAAATGTTTT-AAAAAC
511861 TATATATTACCCATATTTTC-AAAATGTTTT
1 TATATATTA--CATATTTTCAAAAATGTTTT
511891 CTTTTTAAAA
Statistics
Matches: 223, Mismatches: 24, Indels: 53
0.74 0.08 0.18
Matches are distributed among these distances:
29 6 0.03
31 20 0.09
32 16 0.07
33 25 0.11
34 9 0.04
35 10 0.04
36 42 0.19
37 47 0.21
38 43 0.19
39 5 0.02
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.45
Consensus pattern (35 bp):
TATATATTACATATTTTCAAAAATGTTTTAAAAAC
Found at i:512746 original size:85 final size:83
Alignment explanation
Indices: 512594--513382 Score: 899
Period size: 85 Copynumber: 9.5 Consensus size: 83
512584 GAGTCTTTGG
* * * * *
512594 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCATATAATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAA
*
512659 CTCAAAGGTCTTTTGGTCA
66 CTCAAAGGTC-TTTGGTGA
* * * * * * *
512678 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGAAGCTGAGCGTAGTCGA
* * *
512743 ACTCGAAGGTCTTTTGTTGG
65 ACTCAAAGGTC-TTTGGTGA
* * * *
512763 CAGACAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAAGCTGAGCGTAGTCGA
* *
512828 ACTCGAGGGTCTTT-G-G-
65 ACTCAAAGGTCTTTGGTGA
* * * *
512844 CAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAA
512909 CTCAAAGGTCTTTGGTGA
66 CTCAAAGGTCTTTGGTGA
* * * * * * * *
512927 CAAATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGAAGCTGAGCGTAGTCGA
* * * *
512992 ACTTAAGGGTCTTTAGTTGG
65 ACTCAAAGGTCTTT-GGTGA
*
513012 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAA
* *
513077 CTCAAAGGTCTTTTGTTA
66 CTCAAAGGTCTTTGGTGA
* * *
513095 GCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCG
1 -CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAAGCTGAGCGTAGTCG
* *
513160 AACTCGAGGGTCTTT-G-G-
64 AACTCAAAGGTCTTTGGTGA
* * *
513177 CAGATAACCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAA
513242 CTCAAAGGTCTTTGGTGA
66 CTCAAAGGTCTTTGGTGA
* * * * * * *
513260 CA-ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGAAGCTGAGCGTAGTCGA
* * * *
513324 ACTTAAGGGTCTTTAGTTGG
65 ACTCAAAGGTCTTT-GGTGA
513344 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
513383 TTGTTTAAAA
Statistics
Matches: 591, Mismatches: 99, Indels: 29
0.82 0.14 0.04
Matches are distributed among these distances:
80 56 0.09
81 86 0.15
82 35 0.06
83 67 0.11
84 152 0.26
85 195 0.33
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (83 bp):
CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAA
CTCAAAGGTCTTTGGTGA
Found at i:513033 original size:249 final size:247
Alignment explanation
Indices: 512536--513382 Score: 1035
Period size: 249 Copynumber: 3.4 Consensus size: 247
512526 TCGCCATGAA
* * * * * * * *
512536 TTATGTTGTAAATGATATGACCTCGAAGTTGAGTGTAATCGAACTC-GGGAGTC-TTTGGCAGAT
1 TTATGCTGCAAATGATGTG-CCTTGAAGCTGAGCGTAGTCGAACTCAAGG-GTCTTTTGGCAGAT
* * *
512599 AGCCCTTCTCGACTTAAGCTATGCTGCATATAATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAA
64 AACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAA
*
512664 AGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAG
129 AGGTC-TTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAG
*
512729 CTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAG
193 CTGAGTGTAATCGAACTC-AAGGTC-TTTGTTGGCAGATAACCCTTCTAGACTTAAG
* * *
512786 TTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGAGGGTC-TTTGGCAGATA
1 TTATGCTGCAAATGATGTGCCTT-GAAGCTGAGCGTAGTCGAACTCAAGGGTCTTTTGGCAGATA
* *
512850 GCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAA
65 ACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAA
*
512915 GGTCTTTGGTGACAAATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCT
130 GGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCT
* *
512980 GAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTCGACTTAAG
195 GAGTGTAATCGAACTCAA-GGTCTTT-GTTGGCAGATAACCCTTCTAGACTTAAG
* *
513035 TTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGA
1 TTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACTCAAGGGTCTTTTG---GCAGA
* * * * *
513100 TAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTC
63 TAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT-GGAGCTGAGCGTAGTCGAACTC
* * * * * * * * * *
513165 GAGGGTCTTT-G-G-CAGATAACCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG-CCTTGGA
127 AAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAA
* * * * * *
513226 GCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGACA-ATAACCCTTCTAGCCTTGAG
192 GCTGAGTGTAATCGAACTC-AAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAG
* * * * *
513282 TTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAG
1 TTATGCTGCAAATGATGTG-CCTTGAAGCTGAGCGTAGTCGAACTCAAGGGTC-TT--TTGGCAG
*
513347 ATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
62 ATAACCCTTCTCGACTTAAGCTATGCTGCAAATGAT
513383 TTGTTTAAAA
Statistics
Matches: 526, Mismatches: 57, Indels: 30
0.86 0.09 0.05
Matches are distributed among these distances:
247 34 0.06
248 101 0.19
249 164 0.31
250 149 0.28
251 6 0.01
252 44 0.08
253 28 0.05
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (247 bp):
TTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACTCAAGGGTCTTTTGGCAGATAA
CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAG
GTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTG
AGTGTAATCGAACTCAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAG
Found at i:513087 original size:333 final size:333
Alignment explanation
Indices: 512636--513382 Score: 1280
Period size: 333 Copynumber: 2.2 Consensus size: 333
512626 ATATAATGTG
* * * * * * * ** * * *
512636 CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
1 CCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTCGACTTAAG
* * * *
512701 TTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAG
66 TTATGCTGCAAATGATATGCCCTTGAAGCTGAGCGTAATCGAACTCAAAGGTCTTTTGTTAGCAG
512766 ACAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACT
131 ACAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACT
*
512831 CGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCT
196 CGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCT
512896 GAGCGTAGTCGAACTCAAAGGTCTTTGGTGACAAATAACCCTTCTAGCCTTGAGTTATGCTGTAA
261 GAGCGTAGTCGAACTCAAAGGTCTTTGGTGAC-AATAACCCTTCTAGCCTTGAGTTATGCTGTAA
512961 ATGATATGC
325 ATGATATGC
512970 CCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTCGACTTAAG
1 CCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTCGACTTAAG
* * *
513035 TTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAGCAG
66 TTATGCTGCAAATGATATGCCCTTGAAGCTGAGCGTAATCGAACTCAAAGGTCTTTTGTTAGCAG
* *
513099 ATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACT
131 ACAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACT
513164 CGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCT
196 CGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCT
513229 GAGCGTAGTCGAACTCAAAGGTCTTTGGTGACAATAACCCTTCTAGCCTTGAGTTATGCTGTAAA
261 GAGCGTAGTCGAACTCAAAGGTCTTTGGTGACAATAACCCTTCTAGCCTTGAGTTATGCTGTAAA
513294 TGATATGC
326 TGATATGC
513302 CCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTCGACTTAAG
1 CCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTCGACTTAAG
513367 TTATGCTGCAAATGAT
66 TTATGCTGCAAATGAT
513383 TTGTTTAAAA
Statistics
Matches: 391, Mismatches: 22, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
332 122 0.31
333 199 0.51
334 70 0.18
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (333 bp):
CCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTCGACTTAAG
TTATGCTGCAAATGATATGCCCTTGAAGCTGAGCGTAATCGAACTCAAAGGTCTTTTGTTAGCAG
ACAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACT
CGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCT
GAGCGTAGTCGAACTCAAAGGTCTTTGGTGACAATAACCCTTCTAGCCTTGAGTTATGCTGTAAA
TGATATGC
Found at i:516764 original size:18 final size:19
Alignment explanation
Indices: 516723--516767 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
516713 AGTTAATGTG
516723 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
516742 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
516760 AATGCAAA
1 AATGCAAA
516768 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:518684 original size:36 final size:35
Alignment explanation
Indices: 518598--518704 Score: 85
Period size: 36 Copynumber: 3.1 Consensus size: 35
518588 AATACGAAAT
*
518598 AAATAAACAAC--ATAA-AAAATAAAAAAATGATA
1 AAATAAACAACAAAAAACAAAATAAAAAAATGATA
* * ** * *
518630 AAGTAAAGAGTAATAAACAAAATAAATAGAATGATA
1 AAATAAACAACAAAAAACAAAATAAA-AAAATGATA
* *
518666 AAATAAACAACAAAAAACATAAAAAAAGAAAATAATA
1 AAATAAACAACAAAAAACA-AAATAAA-AAAATGATA
518703 AA
1 AA
518705 CAAAAACAGA
Statistics
Matches: 54, Mismatches: 16, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
32 7 0.13
34 2 0.04
35 8 0.15
36 22 0.41
37 15 0.28
ACGTcount: A:0.73, C:0.06, G:0.07, T:0.15
Consensus pattern (35 bp):
AAATAAACAACAAAAAACAAAATAAAAAAATGATA
Found at i:518720 original size:29 final size:29
Alignment explanation
Indices: 518665--518721 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
518655 ATAGAATGAT
*
518665 AAAATAAACAACAAAAAACATAAAAAAAG
1 AAAATAAACAACAAAAAACAGAAAAAAAG
518694 AAAATAATA-AAC-AAAAACAGAATAAAAA
1 AAAATAA-ACAACAAAAAACAGAA-AAAAA
518722 ACAAAGGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 9 0.36
29 15 0.60
30 1 0.04
ACGTcount: A:0.79, C:0.09, G:0.04, T:0.09
Consensus pattern (29 bp):
AAAATAAACAACAAAAAACAGAAAAAAAG
Found at i:519031 original size:16 final size:15
Alignment explanation
Indices: 519005--519034 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
518995 ATAACATTAA
519005 TAAAAAAAACAAAAG
1 TAAAAAAAACAAAAG
519020 TAAAATAAAACAAAA
1 TAAAA-AAAACAAAA
519035 CAAAACAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.80, C:0.07, G:0.03, T:0.10
Consensus pattern (15 bp):
TAAAAAAAACAAAAG
Found at i:519039 original size:15 final size:14
Alignment explanation
Indices: 519003--519046 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
518993 ACATAACATT
519003 AATAAAAAAAACAA
1 AATAAAAAAAACAA
519017 AAGTAAAATAAAACAA
1 AA-TAAAA-AAAACAA
*
519033 AACAAAACAAAACA
1 AATAAAA-AAAACA
519047 TATAAAAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 2 0.08
15 15 0.58
16 9 0.35
ACGTcount: A:0.80, C:0.11, G:0.02, T:0.07
Consensus pattern (14 bp):
AATAAAAAAAACAA
Found at i:519044 original size:20 final size:20
Alignment explanation
Indices: 519003--519044 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
518993 ACATAACATT
*
519003 AATAAAAAAAACAAAAGTAA
1 AATAAAAAAAACAAAAGCAA
519023 AATAAAACAAAACAAAA-CAA
1 AATAAAA-AAAACAAAAGCAA
519043 AA
1 AA
519045 CATATAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.81, C:0.10, G:0.02, T:0.07
Consensus pattern (20 bp):
AATAAAAAAAACAAAAGCAA
Found at i:520064 original size:19 final size:18
Alignment explanation
Indices: 520040--520097 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
520030 TGACGACTGA
520040 TGCTTCTGGCCGTTGAAAT
1 TGCTTCTGGCCGTTG-AAT
** *
520059 TGCTTCTGGATGTTGACT
1 TGCTTCTGGCCGTTGAAT
*
520077 TGCTTTCTGGCCGTTGGAT
1 TGC-TTCTGGCCGTTGAAT
520096 TG
1 TG
520098 GGTCAGATCC
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
18 5 0.16
19 26 0.84
ACGTcount: A:0.10, C:0.19, G:0.29, T:0.41
Consensus pattern (18 bp):
TGCTTCTGGCCGTTGAAT
Found at i:520283 original size:15 final size:14
Alignment explanation
Indices: 520251--520279 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
520241 TGAAAAAAAC
520251 ATAAAAAGAAAATA
1 ATAAAAAGAAAATA
520265 ATAAAAAGAAAATA
1 ATAAAAAGAAAATA
520279 A
1 A
520280 ATAATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (14 bp):
ATAAAAAGAAAATA
Found at i:520362 original size:31 final size:32
Alignment explanation
Indices: 520319--520379 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
520309 ATATAATACA
**
520319 TATATTTCAAAAATA-TTTTTTAAACTATATAT
1 TATATTTCAAAAA-AGTTTTCAAAACTATATAT
520351 TATATTT-AAAAAAGTTTTCAAAACTATAT
1 TATATTTCAAAAAAGTTTTCAAAACTATAT
520380 TATATAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 1 0.04
31 18 0.69
32 7 0.27
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (32 bp):
TATATTTCAAAAAAGTTTTCAAAACTATATAT
Found at i:520489 original size:36 final size:36
Alignment explanation
Indices: 520397--520576 Score: 165
Period size: 36 Copynumber: 4.9 Consensus size: 36
520387 TTTTCAAAAT
*
520397 GTTTTAAAAAAT-ATTTTTAAAACTATATACTATATAA
1 GTTTT-AAAAATGA-TTTTAAAACTATATATTATATAA
* *
520434 TTTATTCAAAAATGTTTTTAAAACTATATATTATATAA
1 GTT-TT-AAAAATGATTTTAAAACTATATATTATATAA
*
520472 GGTTTT-AAAATGATTTTAAAACTATATGTTATATATA
1 -GTTTTAAAAATGATTTTAAAACTATATATTATATA-A
* *
520509 -TTTTCTAAAATG-TTTTAAAAACTATATGTTATAT-A
1 GTTTT-AAAAATGATTTT-AAAACTATATATTATATAA
520544 GTTTTCAAAAAT-ATTTTAAAAAACTATATATTA
1 GTTTT-AAAAATGATTTT--AAAACTATATATTA
520577 CCCATATTTT
Statistics
Matches: 124, Mismatches: 9, Indels: 20
0.81 0.06 0.13
Matches are distributed among these distances:
35 5 0.04
36 45 0.36
37 40 0.32
38 32 0.26
39 2 0.02
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (36 bp):
GTTTTAAAAATGATTTTAAAACTATATATTATATAA
Found at i:520530 original size:37 final size:36
Alignment explanation
Indices: 520398--520597 Score: 185
Period size: 37 Copynumber: 5.4 Consensus size: 36
520388 TTTCAAAATG
* * * *
520398 TTTTAAAAAATATTTTTAAAACTATATACTATATAA
1 TTTTCAAAAATGTTTTAAAAACTATATATTATATAA
*
520434 TTTATTCAAAAATGTTTTTAAAACTATATATTATATAA
1 -TT-TTCAAAAATGTTTTAAAAACTATATATTATATAA
*
520472 GGTTTT--AAAATGATTTT-AAAACTATATGTTATATATA
1 --TTTTCAAAAATG-TTTTAAAAACTATATATTATATA-A
* * *
520509 TTTTCTAAAATGTTTTAAAAACTATATGTTATATAG
1 TTTTCAAAAATGTTTTAAAAACTATATATTATATAA
* *
520545 TTTTCAAAAATATTTTAAAAAACTATATATTACCCAT-A
1 TTTTCAAAAATGTTTT-AAAAACTATATATTA--TATAA
520583 TTTTC-AAAATGTTTT
1 TTTTCAAAAATGTTTT
520598 CTTTTTAAAA
Statistics
Matches: 141, Mismatches: 12, Indels: 20
0.82 0.07 0.12
Matches are distributed among these distances:
35 4 0.03
36 41 0.29
37 54 0.38
38 38 0.27
39 4 0.03
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (36 bp):
TTTTCAAAAATGTTTTAAAAACTATATATTATATAA
Found at i:520541 original size:73 final size:70
Alignment explanation
Indices: 520397--520597 Score: 217
Period size: 74 Copynumber: 2.7 Consensus size: 70
520387 TTTTCAAAAT
* *
520397 GTTTTAAAAAATATTTTTAAAACTATATACTATATA-ATTTATTCAAAAATGTTTTTAAAACTAT
1 GTTTT-AAAAATA-TTTTAAAACTATATATTATATATA-TT-TTC-AAAATGTTTTAAAAACTAT
520461 ATATTATATAA
61 ATATTATAT-A
*
520472 GGTTTT-AAAATGATTTTAAAACTATATGTTATATATATTTTCTAAAATGTTTTAAAAACTATAT
1 -GTTTTAAAAAT-ATTTTAAAACTATATATTATATATATTTTC-AAAATGTTTTAAAAACTATAT
*
520536 GTTATATA
63 ATTATATA
***
520544 GTTTTCAAAAATATTTTAAAAAACTATATATTACCCATATTTTCAAAATGTTTT
1 GTTTT-AAAAATATTTT--AAAACTATATATTATATATATTTTCAAAATGTTTT
520598 CTTTTTAAAA
Statistics
Matches: 110, Mismatches: 9, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
71 5 0.05
72 6 0.05
73 44 0.40
74 48 0.44
75 2 0.02
76 5 0.05
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (70 bp):
GTTTTAAAAATATTTTAAAACTATATATTATATATATTTTCAAAATGTTTTAAAAACTATATATT
ATATA
Found at i:521313 original size:17 final size:17
Alignment explanation
Indices: 521293--521344 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
521283 TATAATGACG
521293 TTAAAATTATGATTATT
1 TTAAAATTATGATTATT
* *
521310 TTAATATTATGA--A-G
1 TTAAAATTATGATTATT
*
521324 TTAAAATCATGATTATT
1 TTAAAATTATGATTATT
521341 TTAA
1 TTAA
521345 TATAACGGCG
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
14 10 0.37
15 1 0.04
16 1 0.04
17 15 0.56
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (17 bp):
TTAAAATTATGATTATT
Found at i:521316 original size:31 final size:31
Alignment explanation
Indices: 521281--521358 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
521271 TTTTAGTAAA
*
521281 AATATAATGACGTTAAAATTATGATTATTTT
1 AATATAATGACGTTAAAATCATGATTATTTT
* *
521312 AATATTATGAAGTTAAAATCATGATTATTTT
1 AATATAATGACGTTAAAATCATGATTATTTT
* *
521343 AATATAACGGCGTTAA
1 AATATAATGACGTTAA
521359 GCTTTTTTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.41
Consensus pattern (31 bp):
AATATAATGACGTTAAAATCATGATTATTTT
Found at i:529743 original size:16 final size:16
Alignment explanation
Indices: 529712--529754 Score: 68
Period size: 16 Copynumber: 2.6 Consensus size: 16
529702 TTAAATAATG
*
529712 TCGGAAATGTGAGTTTA
1 TCGGAAAT-AGAGTTTA
529729 TCGGAAATAGAGTTTA
1 TCGGAAATAGAGTTTA
529745 TCGGAAATAG
1 TCGGAAATAG
529755 GTTATTGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 17 0.68
17 8 0.32
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (16 bp):
TCGGAAATAGAGTTTA
Found at i:530236 original size:60 final size:57
Alignment explanation
Indices: 530162--530312 Score: 169
Period size: 60 Copynumber: 2.6 Consensus size: 57
530152 TTTGAATCTG
*
530162 GTCCTTAAAATTTTGAATATTCCAATTTCATCCTCAAACTATGAATCTTATTCTAAACCA
1 GTCCTTAAACTTTTGAATATTCCAATTTCATCC-CAAACTATGAATC-T-TTCTAAACCA
* * * * * ***
530222 GTCCTTAAACTTTTGAACAATCTAATTTTATCCCTAAACTATGACTCTTTCTAAATTG
1 GTCCTTAAACTTTTGAATATTCCAATTTCATCCC-AAACTATGAATCTTTCTAAACCA
*
530280 GTCCCT-AACTTTTGAATATTCCAATTTCATCCC
1 GTCCTTAAACTTTTGAATATTCCAATTTCATCCC
530313 CAAATTCATT
Statistics
Matches: 76, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
57 23 0.30
58 12 0.16
59 2 0.03
60 39 0.51
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.40
Consensus pattern (57 bp):
GTCCTTAAACTTTTGAATATTCCAATTTCATCCCAAACTATGAATCTTTCTAAACCA
Found at i:532851 original size:15 final size:15
Alignment explanation
Indices: 532831--532861 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
532821 GAGAACTTTG
532831 CTTCAAGGTCGACAA
1 CTTCAAGGTCGACAA
*
532846 CTTCAAGGTCGGCAA
1 CTTCAAGGTCGACAA
532861 C
1 C
532862 AACAAGCAGG
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:0.29, C:0.29, G:0.23, T:0.19
Consensus pattern (15 bp):
CTTCAAGGTCGACAA
Found at i:532881 original size:54 final size:54
Alignment explanation
Indices: 532817--532923 Score: 178
Period size: 54 Copynumber: 2.0 Consensus size: 54
532807 TGAAGGCTCC
532817 GTCCGAGAACTTTGCTTCAAGGTCGACAACTTCAAGGTCGGCAACAACAAGCAG
1 GTCCGAGAACTTTGCTTCAAGGTCGACAACTTCAAGGTCGGCAACAACAAGCAG
* * * *
532871 GTCCGAGAACTTTTCTTCAAGGTCGACTACTTCAAGGTTGGCAGCAACAAGCA
1 GTCCGAGAACTTTGCTTCAAGGTCGACAACTTCAAGGTCGGCAACAACAAGCA
532924 AATTACAGTT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.21
Consensus pattern (54 bp):
GTCCGAGAACTTTGCTTCAAGGTCGACAACTTCAAGGTCGGCAACAACAAGCAG
Found at i:534038 original size:22 final size:22
Alignment explanation
Indices: 534013--534057 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
534003 TTCCCATGAA
*
534013 TTTGTAAATCCTCCGGGTCATT
1 TTTGTAAAACCTCCGGGTCATT
534035 TTTGTAAAACCTCCGGGTCATT
1 TTTGTAAAACCTCCGGGTCATT
534057 T
1 T
534058 GTAAAAGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.40
Consensus pattern (22 bp):
TTTGTAAAACCTCCGGGTCATT
Found at i:534060 original size:20 final size:20
Alignment explanation
Indices: 534012--534197 Score: 122
Period size: 20 Copynumber: 9.1 Consensus size: 20
534002 TTTCCCATGA
* *
534012 ATTTGTAAATCCTCCGGGTC
1 ATTTGTAAAACCTTCGGGTC
*
534032 ATTTTTGTAAAACCTCCGGGTC
1 A--TTTGTAAAACCTTCGGGTC
* *
534054 ATTTGTAAAAGCTTCGGGTA
1 ATTTGTAAAACCTTCGGGTC
* *
534074 ATTTGTAAATCCTTCAGGTC
1 ATTTGTAAAACCTTCGGGTC
* * * ** * *
534094 ATCTATCAGTCTTTCGAG-C
1 ATTTGTAAAACCTTCGGGTC
* * *
534113 ATGATGTGTAAAACATCCAGGTC
1 AT--T-TGTAAAACCTTCGGGTC
*
534136 ATTTGTAAAACCTTCGAGTC
1 ATTTGTAAAACCTTCGGGTC
* *
534156 ATTTGTAAAATCTTCGGGTA
1 ATTTGTAAAACCTTCGGGTC
* *
534176 ATTTGTAAATCTTTCGGGTC
1 ATTTGTAAAACCTTCGGGTC
534196 AT
1 AT
534198 CTGTCAGTCT
Statistics
Matches: 125, Mismatches: 35, Indels: 12
0.73 0.20 0.07
Matches are distributed among these distances:
19 3 0.02
20 92 0.74
21 1 0.01
22 26 0.21
23 3 0.02
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (20 bp):
ATTTGTAAAACCTTCGGGTC
Found at i:534189 original size:82 final size:82
Alignment explanation
Indices: 534037--534191 Score: 195
Period size: 82 Copynumber: 1.9 Consensus size: 82
534027 GGGTCATTTT
* * * * * *
534037 TGTAAAACCTCCGGGTCATTTGTAAAAGCTTCGGGTAATTTGTAAATCCTTCAGGTCATCTATCA
1 TGTAAAACATCCAGGTCATTTGTAAAACCTTCGAGTAATTTGTAAATCCTTCAGGTAATCTATAA
*
534102 GTCTTTCGAGCATGATG
66 ATCTTTCGAGCATGATG
* * * *
534119 TGTAAAACATCCAGGTCATTTGTAAAACCTTCGAGTCATTTGTAAAAT-CTTCGGGTAATTTGTA
1 TGTAAAACATCCAGGTCATTTGTAAAACCTTCGAGTAATTTGT-AAATCCTTCAGGTAATCTATA
534183 AATCTTTCG
65 AATCTTTCG
534192 GGTCATCTGT
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
82 57 0.93
83 4 0.07
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (82 bp):
TGTAAAACATCCAGGTCATTTGTAAAACCTTCGAGTAATTTGTAAATCCTTCAGGTAATCTATAA
ATCTTTCGAGCATGATG
Found at i:534238 original size:102 final size:102
Alignment explanation
Indices: 534015--534239 Score: 326
Period size: 102 Copynumber: 2.2 Consensus size: 102
534005 CCCATGAATT
*
534015 TGTAAATCCTCCGGGTCATTTTTGTAAAACCTCCGGGTCATTTGTAAAAGCTTCGGGTAATTTGT
1 TGTAAATCCTCCGGGTCA--TTTGTAAAACCTCCGAGTCATTTGTAAAAGCTTCGGGTAATTTGT
534080 AAATCCTTCAGGTCATCTATCAGTCTTTCGAGCATGATG
64 AAATCCTTCAGGTCATCTATCAGTCTTTCGAGCATGATG
* * * * *
534119 TGTAAAACATCCAGGTCATTTGTAAAACCTTCGAGTCATTTGTAAAATCTTCGGGTAATTTGTAA
1 TGTAAATCCTCCGGGTCATTTGTAAAACCTCCGAGTCATTTGTAAAAGCTTCGGGTAATTTGTAA
* * *
534184 ATCTTTCGGGTCATCTGTCAGTCTTTCGAGCATGATG
66 ATCCTTCAGGTCATCTATCAGTCTTTCGAGCATGATG
*
534221 CT-TAAATCCTTCGGGTCAT
1 -TGTAAATCCTCCGGGTCAT
534240 CTGTTAGTCT
Statistics
Matches: 107, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
102 91 0.85
103 1 0.01
104 15 0.14
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.36
Consensus pattern (102 bp):
TGTAAATCCTCCGGGTCATTTGTAAAACCTCCGAGTCATTTGTAAAAGCTTCGGGTAATTTGTAA
ATCCTTCAGGTCATCTATCAGTCTTTCGAGCATGATG
Found at i:534464 original size:36 final size:36
Alignment explanation
Indices: 534373--534646 Score: 321
Period size: 36 Copynumber: 7.7 Consensus size: 36
534363 TTCAGTGTAA
534373 TTCAACCTTCACGGAAGAGTAGTGAAGT-AATACAAAGT
1 TTCAACCTTCACGGAAGAGTAGTGAAGTAAAT-C-AA-T
* * *
534411 TT-GATCTTCACGGAAGAGTAGCGAAGTAAATCAAT
1 TTCAACCTTCACGGAAGAGTAGTGAAGTAAATCAAT
* * *
534446 TTCAACATTCACGGAAGAGTAGTGAAGTAATTCAAA
1 TTCAACCTTCACGGAAGAGTAGTGAAGTAAATCAAT
*
534482 TTCAGCCTTCACGGAAGAGTAGTGAAGTAAATC-AT
1 TTCAACCTTCACGGAAGAGTAGTGAAGTAAATCAAT
534517 TCTCAACCTTCACGGAAGAGTAGTGAAGT-AATGC-AT
1 T-TCAACCTTCACGGAAGAGTAGTGAAGTAAAT-CAAT
*
534553 CTC-ACCTTCACGGAAGAGTAGTGAAGT-AATGC-AT
1 TTCAACCTTCACGGAAGAGTAGTGAAGTAAAT-CAAT
* * *
534587 CTCAACCTTCACGGAAGAGTAGTGAAGTAATTCAAA
1 TTCAACCTTCACGGAAGAGTAGTGAAGTAAATCAAT
* *
534623 TTCAGCATTCACGGAAGAGTAGTG
1 TTCAACCTTCACGGAAGAGTAGTG
534647 GAACGAATTT
Statistics
Matches: 209, Mismatches: 20, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
34 34 0.16
35 35 0.17
36 112 0.54
37 23 0.11
38 5 0.02
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.24
Consensus pattern (36 bp):
TTCAACCTTCACGGAAGAGTAGTGAAGTAAATCAAT
Found at i:534523 original size:72 final size:72
Alignment explanation
Indices: 534374--534646 Score: 389
Period size: 72 Copynumber: 3.8 Consensus size: 72
534364 TCAGTGTAAT
* * * *
534374 TCAACCTTCACGGAAGAGTAGTGAAGTAATACAAAGTT-TGATCTTCACGGAAGAGTAGCGAAGT
1 TCAACCTTCACGGAAGAGTAGTGAAGTAATTCAAA-TTCAG-CCTTCACGGAAGAGTAGTGAAGT
534438 AAATCAATT-
64 AAATC-ATTC
*
534447 TCAACATTCACGGAAGAGTAGTGAAGTAATTCAAATTCAGCCTTCACGGAAGAGTAGTGAAGTAA
1 TCAACCTTCACGGAAGAGTAGTGAAGTAATTCAAATTCAGCCTTCACGGAAGAGTAGTGAAGTAA
534512 ATCATTC
66 ATCATTC
*
534519 TCAACCTTCACGGAAGAGTAGTGAAGTAATGC--ATCTCA-CCTTCACGGAAGAGTAGTGAAGT-
1 TCAACCTTCACGGAAGAGTAGTGAAGTAATTCAAAT-TCAGCCTTCACGGAAGAGTAGTGAAGTA
534580 AATGCA-TC
65 AAT-CATTC
*
534588 TCAACCTTCACGGAAGAGTAGTGAAGTAATTCAAATTCAGCATTCACGGAAGAGTAGTG
1 TCAACCTTCACGGAAGAGTAGTGAAGTAATTCAAATTCAGCCTTCACGGAAGAGTAGTG
534647 GAACGAATTT
Statistics
Matches: 184, Mismatches: 9, Indels: 16
0.88 0.04 0.08
Matches are distributed among these distances:
69 36 0.20
70 30 0.16
71 26 0.14
72 58 0.32
73 34 0.18
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.24
Consensus pattern (72 bp):
TCAACCTTCACGGAAGAGTAGTGAAGTAATTCAAATTCAGCCTTCACGGAAGAGTAGTGAAGTAA
ATCATTC
Found at i:534634 original size:141 final size:144
Alignment explanation
Indices: 534374--534646 Score: 428
Period size: 141 Copynumber: 1.9 Consensus size: 144
534364 TCAGTGTAAT
* * *
534374 TCAACCTTCACGGAAGAGTAGTGAAGTAATACAAAGTTTGATCTTCACGGAAGAGTAGCGAAGTA
1 TCAACCTTCACGGAAGAGTAGTGAAGTAATAC-AAGTCTCACCTTCACGGAAGAGTAGCGAAGTA
* *
534439 AATCAATTTCAACATTCACGGAAGAGTAGTGAAGTAATTCAAATTCAGCCTTCACGGAAGAGTAG
65 AATCAATCTCAACATTCACGGAAGAGTAGTGAAGTAATTCAAATTCAGCATTCACGGAAGAGTAG
534504 TGAAGTAAATCATTC
130 TGAAGTAAATCATTC
* *
534519 TCAACCTTCACGGAAGAGTAGTGAAGTAATGC-A-TCTCACCTTCACGGAAGAGTAGTGAAGT-A
1 TCAACCTTCACGGAAGAGTAGTGAAGTAATACAAGTCTCACCTTCACGGAAGAGTAGCGAAGTAA
*
534581 ATGC-ATCTCAACCTTCACGGAAGAGTAGTGAAGTAATTCAAATTCAGCATTCACGGAAGAGTAG
66 AT-CAATCTCAACATTCACGGAAGAGTAGTGAAGTAATTCAAATTCAGCATTCACGGAAGAGTAG
534645 TG
130 TG
534647 GAACGAATTT
Statistics
Matches: 119, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
141 62 0.52
142 25 0.21
143 1 0.01
145 31 0.26
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.24
Consensus pattern (144 bp):
TCAACCTTCACGGAAGAGTAGTGAAGTAATACAAGTCTCACCTTCACGGAAGAGTAGCGAAGTAA
ATCAATCTCAACATTCACGGAAGAGTAGTGAAGTAATTCAAATTCAGCATTCACGGAAGAGTAGT
GAAGTAAATCATTC
Found at i:537139 original size:161 final size:160
Alignment explanation
Indices: 536894--537351 Score: 590
Period size: 161 Copynumber: 2.9 Consensus size: 160
536884 TTTAAACACT
* * *
536894 CTCCTAAACCATAGTAGAATATATGTGTACTTTATATTCCTCTTTTAGATAACAAATTTTTTATT
1 CTCCTAAACCATAGTAGAATACATGTGTATTTTA-ATTCCTCTTTTTGATAACAAATTTTTTATT
*
536959 TTTCAATTTAGTCCTTCAATTTTTCATAATCTCCTTAGTTCTTCAATTCGTCATTTATTTTAAGT
65 TTTCAATTTAGTCCTTCAATTTTTCATAATCTCCTTA-TTCTTCAATTCGTAATTTATTTTAAGT
*
537024 CCCTTTTTTTTTTTACCAAATTTGAGCCATATG
129 -CCTTTTTTTTTTTACCAAATTTGAGCCACATG
* * * * *
537057 CTCCTAAAACATATTAGAATACATGTGTATTTTCAATTCATCTTTTTGATAA-AAAATGTTT-TT
1 CTCCTAAACCATAGTAGAATACATGTGTATTTT-AATTCCTCTTTTTGATAACAAATTTTTTATT
* * * *
537120 TTTCAATTTAGTCCTTCAATTTTTCACAATTTCCTTATTTCTTCAATTCTTTATTTATTTTAAGT
65 TTTCAATTTAGTCCTTCAATTTTTCATAATCTCCTTA-TTCTTCAATTCGTAATTTATTTTAAGT
* *
537185 CC-----GTTTTTACCGAATTTGAGCCACATG
129 CCTTTTTTTTTTTACCAAATTTGAGCCACATG
**
537212 CTCCTAAACCATAGTAGAGCACATGTGTACTTTTAATTCCTCTTTTTTGATAACAAATTTTTTAT
1 CTCCTAAACCATAGTAGAATACATGTGTA-TTTTAATTCCTC-TTTTTGATAACAAATTTTTTAT
* * * *
537277 TTTTCAATGTAGT-CTTCAATTTTTCATAATCTCTTTATTCCTTCAATTTGTAATTTATTTCAAG
64 TTTTCAATTTAGTCCTTCAATTTTTCATAATCTCCTTATT-CTTCAATTCGTAATTTATTTTAAG
537341 TCCTTTTTTTT
128 TCCTTTTTTTT
537352 ATCAAATTTG
Statistics
Matches: 252, Mismatches: 32, Indels: 23
0.82 0.10 0.07
Matches are distributed among these distances:
155 54 0.21
156 16 0.06
157 51 0.20
158 13 0.05
160 2 0.01
161 62 0.25
162 9 0.04
163 44 0.17
164 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.49
Consensus pattern (160 bp):
CTCCTAAACCATAGTAGAATACATGTGTATTTTAATTCCTCTTTTTGATAACAAATTTTTTATTT
TTCAATTTAGTCCTTCAATTTTTCATAATCTCCTTATTCTTCAATTCGTAATTTATTTTAAGTCC
TTTTTTTTTTTACCAAATTTGAGCCACATG
Found at i:537415 original size:157 final size:158
Alignment explanation
Indices: 536894--537416 Score: 533
Period size: 161 Copynumber: 3.3 Consensus size: 158
536884 TTTAAACACT
* * * * * * *
536894 CTCCTAAACCATAGTAGAATATATGTGT-ACTTTATATTCCTCTTTTAGATAACAAATTTTTTAT
1 CTCCTAAACCATAATAGAAAACATGTGTAACTTCA-ATTCTTTTTTTTGATAACAAATTTTTTAT
* *
536958 TTTTCAATTTAGTCCTTCAATTTTTCATAATCTCCTTAGTTCTTCAATTCGTCATTTATTTTAAG
65 TTTTCAATTTAGTCCTTCAATTTTTCATAATCTCCTTA-TTCTTCAATTTGTAATTTATTTTAAG
*
537023 TCCCTTTTTTTTTTTACCAAATTTGAGCCATATG
129 T-CC---TTTTTTTTACCAAATTTGAGCCACATG
* * * ** * * * *
537057 CTCCTAAAACATATTAGAATACATGTGTATTTTCAATTCATCTTTTTGATAA-AAAATGTTT-TT
1 CTCCTAAACCATAATAGAAAACATGTGTAACTTCAATTCTTTTTTTTGATAACAAATTTTTTATT
* * *
537120 TTTCAATTTAGTCCTTCAATTTTTCACAATTTCCTTATTTCTTCAATTCT-TTATTTATTTTAAG
66 TTTCAATTTAGTCCTTCAATTTTTCATAATCTCCTTA-TTCTTCAATT-TGTAATTTATTTTAAG
* *
537184 TCC--GTTTTTACCGAATTTGAGCCACATG
129 TCCTTTTTTTTACCAAATTTGAGCCACATG
* ** * *
537212 CTCCTAAACCATAGTAGAGCACATGTGT-ACTTTTAATTCCTCTTTTTTGATAACAAATTTTTTA
1 CTCCTAAACCATAATAGAAAACATGTGTAAC-TTCAATT-CTTTTTTTTGATAACAAATTTTTTA
* * *
537276 TTTTTCAATGTAGT-CTTCAATTTTTCATAATCTCTTTATTCCTTCAATTTGTAATTTATTTCAA
64 TTTTTCAATTTAGTCCTTCAATTTTTCATAATCTCCTTATT-CTTCAATTTGTAATTTATTTTAA
* * *
537340 GTCCTTTTTTTTATCAAATTTGAACCACGTG
128 GTCCTTTTTTTTACCAAATTTGAGCCACATG
* * * *
537371 CTCATATACCACAATAGAAAACATATGTAACTTCAATT-TTTTTTTT
1 CTCCTAAACCATAATAGAAAACATGTGTAACTTCAATTCTTTTTTTT
537417 ACTAAAGATG
Statistics
Matches: 299, Mismatches: 50, Indels: 28
0.79 0.13 0.07
Matches are distributed among these distances:
155 52 0.17
156 14 0.05
157 58 0.19
158 13 0.04
159 47 0.16
160 4 0.01
161 61 0.20
162 7 0.02
163 40 0.13
164 3 0.01
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.47
Consensus pattern (158 bp):
CTCCTAAACCATAATAGAAAACATGTGTAACTTCAATTCTTTTTTTTGATAACAAATTTTTTATT
TTTCAATTTAGTCCTTCAATTTTTCATAATCTCCTTATTCTTCAATTTGTAATTTATTTTAAGTC
CTTTTTTTTACCAAATTTGAGCCACATG
Found at i:539634 original size:23 final size:23
Alignment explanation
Indices: 539568--539676 Score: 83
Period size: 23 Copynumber: 4.7 Consensus size: 23
539558 TATTCGACTT
**
539568 GTTTAACGTTTATGAACGCATTC
1 GTTTAACGTTTATGAACATATTC
* * ** * * *
539591 ATTTAACATTTACAAATATGTTT
1 GTTTAACGTTTATGAACATATTC
*
539614 GTTTAACGTTTATGAACATGTTC
1 GTTTAACGTTTATGAACATATTC
* **
539637 GTTTATCGTTCGTGAACATATTC
1 GTTTAACGTTTATGAACATATTC
* *
539660 GCTTAACGTTTGTGAAC
1 GTTTAACGTTTATGAAC
539677 CTTAAAATAG
Statistics
Matches: 64, Mismatches: 22, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 64 1.00
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.42
Consensus pattern (23 bp):
GTTTAACGTTTATGAACATATTC
Found at i:539700 original size:13 final size:13
Alignment explanation
Indices: 539682--539706 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
539672 TGAACCTTAA
539682 AATAGAAAAAGAT
1 AATAGAAAAAGAT
539695 AATAGAAAAAGA
1 AATAGAAAAAGA
539707 AGAACCAAAC
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:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (13 bp):
AATAGAAAAAGAT
Found at i:542550 original size:23 final size:22
Alignment explanation
Indices: 542520--542576 Score: 89
Period size: 23 Copynumber: 2.6 Consensus size: 22
542510 ACTCTTATTA
542520 GAGTATCGATACTGGGACCTTGG
1 GAGTATCGATACTGGGACCTT-G
*
542543 GAGTATCGATATTGGGACCTTG
1 GAGTATCGATACTGGGACCTTG
542565 G-GTATCGATACT
1 GAGTATCGATACT
542577 CCCTTGAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 10 0.31
22 2 0.06
23 20 0.62
ACGTcount: A:0.23, C:0.16, G:0.32, T:0.30
Consensus pattern (22 bp):
GAGTATCGATACTGGGACCTTG
Found at i:545553 original size:19 final size:19
Alignment explanation
Indices: 545531--545568 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
545521 ATGGCCTTAC
545531 AGTAT-GATACCCTATATGT
1 AGTATCGATACCCTA-ATGT
545550 AGTATCGATACCCTAATGT
1 AGTATCGATACCCTAATGT
545569 TGAATTACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (19 bp):
AGTATCGATACCCTAATGT
Found at i:547168 original size:28 final size:29
Alignment explanation
Indices: 547137--547218 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 29
547127 ATAAAAGTAC
*
547137 TATATATTAATATTATTTATAGTATATTTATAT
1 TATATATTAATATTATTTATA--ATA--TATTT
* *
547170 TATATATTAATATGTA--AACAATATATTT
1 TATATATTAATAT-TATTTATAATATATTT
547198 TATATATTAATATTATTTATA
1 TATATATTAATATTATTTATA
547219 TTGTAAATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
27 2 0.05
28 17 0.41
29 2 0.05
30 3 0.07
32 2 0.05
33 13 0.32
34 2 0.05
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (29 bp):
TATATATTAATATTATTTATAATATATTT
Found at i:548182 original size:22 final size:22
Alignment explanation
Indices: 548150--548192 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
548140 TCAACCATTT
548150 GATAATAAATGTTTAAATATTA
1 GATAATAAATGTTTAAATATTA
*
548172 GATAATGAATGTTTAAATATT
1 GATAATAAATGTTTAAATATT
548193 TTGTAGTCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.42
Consensus pattern (22 bp):
GATAATAAATGTTTAAATATTA
Found at i:548958 original size:23 final size:23
Alignment explanation
Indices: 548931--548987 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
548921 TATTCGGTTT
* *
548931 GTTTAACGTTTACGAACACATTC
1 GTTTAACGTTTACAAACACATCC
* * * *
548954 GTTTAACATTCACAAATATATCC
1 GTTTAACGTTTACAAACACATCC
548977 GTTTAACGTTT
1 GTTTAACGTTT
548988 GTAAACATGT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.39
Consensus pattern (23 bp):
GTTTAACGTTTACAAACACATCC
Found at i:554048 original size:23 final size:23
Alignment explanation
Indices: 553982--554050 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
553972 CACCACAGCT
* * *
553982 CGTATAAATGCACCTAAGTGACA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
554005 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
554028 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
554051 TATAAGGTTG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:555705 original size:24 final size:22
Alignment explanation
Indices: 555653--555707 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 22
555643 TCCCCTTGAA
*
555653 GTGCATCGATGCATCCTACCGT
1 GTGCATCGATGCATCCTAACGT
555675 GT--ATCGATGCATCCCTTAACGT
1 GTGCATCGATGCAT-CC-TAACGT
555697 GTGCATCGATG
1 GTGCATCGATG
555708 AACTCCTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 10 0.36
21 2 0.07
22 9 0.32
24 7 0.25
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.29
Consensus pattern (22 bp):
GTGCATCGATGCATCCTAACGT
Found at i:559065 original size:23 final size:23
Alignment explanation
Indices: 558999--559067 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
558989 CACCACAGCT
* * *
558999 CGTATAAATGCACCTAAGTGACA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
559022 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
559045 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
559068 TATAAGGTTG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:559553 original size:2 final size:2
Alignment explanation
Indices: 559546--559570 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
559536 TTCATCTTCC
559546 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
559571 CATCTTTCTT
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:560738 original size:24 final size:22
Alignment explanation
Indices: 560686--560743 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
560676 TCCCCTTGAA
*
560686 GTGCATCGATGCATCCTACCGT
1 GTGCATCGATGCATCCTAACGT
560708 GT--ATCGATGCATCCTTTAACGT
1 GTGCATCGATGCATCC--TAACGT
560730 GTGCATCGATGCAT
1 GTGCATCGATGCAT
560744 TAATTGCATT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 12 0.39
22 9 0.29
24 10 0.32
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.31
Consensus pattern (22 bp):
GTGCATCGATGCATCCTAACGT
Found at i:565465 original size:24 final size:23
Alignment explanation
Indices: 565416--565465 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
565406 ACCGTATCAT
* * *
565416 TAACTATTTAAGTGTTGATAATA
1 TAACTATTTAAGGGCTGATAAGA
565439 TAACTATTTAACGGGCTGATAAGA
1 TAACTATTTAA-GGGCTGATAAGA
565463 TAA
1 TAA
565466 TTTAAATGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (23 bp):
TAACTATTTAAGGGCTGATAAGA
Found at i:565742 original size:2 final size:2
Alignment explanation
Indices: 565726--565783 Score: 102
Period size: 2 Copynumber: 30.0 Consensus size: 2
565716 AAAGAGCATG
565726 TA TA -A TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
565766 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
565784 ATTTTAGTAT
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 52 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:567773 original size:19 final size:19
Alignment explanation
Indices: 567749--567790 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
567739 TCTTTAAATT
*
567749 TTAAATTTTTATAAATTAA
1 TTAAATTTATATAAATTAA
567768 TTAAATTTATATAAATTAA
1 TTAAATTTATATAAATTAA
567787 TTAA
1 TTAA
567791 TGGTGTTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAAATTTATATAAATTAA
Found at i:568049 original size:14 final size:14
Alignment explanation
Indices: 568032--568071 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
568022 AACGAACATA
*
568032 AACGAACACGAACG
1 AACGAACACAAACG
*
568046 AACGAACATAAACG
1 AACGAACACAAACG
568060 AAC-AACACAAAC
1 AACGAACACAAAC
568072 ACAAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.57, C:0.28, G:0.12, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:568354 original size:24 final size:26
Alignment explanation
Indices: 568325--568376 Score: 81
Period size: 24 Copynumber: 2.1 Consensus size: 26
568315 GCCCTCTGTT
*
568325 CGAACATAAATGAACATA-AAT-GAA
1 CGAACATAAACGAACATATAATCGAA
568349 CGAACATAAACGAACATATAATCGAA
1 CGAACATAAACGAACATATAATCGAA
568375 CG
1 CG
568377 TTCACGAACG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 17 0.68
25 3 0.12
26 5 0.20
ACGTcount: A:0.54, C:0.17, G:0.13, T:0.15
Consensus pattern (26 bp):
CGAACATAAACGAACATATAATCGAA
Found at i:569104 original size:2 final size:2
Alignment explanation
Indices: 569097--569131 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
569087 TTTGGTCATC
569097 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
569132 CTTTTTAACA
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:569293 original size:2 final size:2
Alignment explanation
Indices: 569286--569328 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
569276 CGTTTGGTTC
569286 AT AT AT AT AT AT 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 AT AT AT AT AT AT
569328 A
1 A
569329 ATTGGAATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:571465 original size:60 final size:60
Alignment explanation
Indices: 571365--571498 Score: 164
Period size: 60 Copynumber: 2.2 Consensus size: 60
571355 TTCATTGGGT
* * * * *
571365 AAAGTATAC-AAATGGTCTTTCGACTATAGGATGTTGCTTTGTTGAGTCCTTCGACTACTA
1 AAAGT-TACAAAATGGTCTTTCGACTATAAGATATTACTTTGTTGAGTCCCTCAACTACTA
* *
571425 AAAGTTACAAAATGGT-TTCTTGACTATAAGATATTACTTTGTTGAGTCCCTCAACTATTA
1 AAAGTTACAAAATGGTCTT-TCGACTATAAGATATTACTTTGTTGAGTCCCTCAACTACTA
*
571485 AAAGCTACAAAATG
1 AAAGTTACAAAATG
571499 ATAATCGGAC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
59 5 0.08
60 59 0.92
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (60 bp):
AAAGTTACAAAATGGTCTTTCGACTATAAGATATTACTTTGTTGAGTCCCTCAACTACTA
Found at i:571510 original size:60 final size:60
Alignment explanation
Indices: 571386--571511 Score: 146
Period size: 60 Copynumber: 2.1 Consensus size: 60
571376 ATGGTCTTTC
* * * * * * * * *
571386 GACTATAGGATGTTGCTTTGTTGAGTCCTTCGACTACTAAAAGTTACAAAATGGTTTCTT
1 GACTATAAGATATTACTTTGTTGAGTCCCTCAACTACTAAAAGCTACAAAATGATATCTG
*
571446 GACTATAAGATATTACTTTGTTGAGTCCCTCAACTATTAAAAGCTACAAAATGATAATC-G
1 GACTATAAGATATTACTTTGTTGAGTCCCTCAACTACTAAAAGCTACAAAATGAT-ATCTG
571506 GACTAT
1 GACTAT
571512 TCATTATGTT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 53 0.96
61 2 0.04
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Consensus pattern (60 bp):
GACTATAAGATATTACTTTGTTGAGTCCCTCAACTACTAAAAGCTACAAAATGATATCTG
Found at i:582163 original size:6 final size:6
Alignment explanation
Indices: 582154--582181 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
582144 TTGCGAAAAT
582154 GACCAC GACCAC GACCAC GACCAC GACC
1 GACCAC GACCAC GACCAC GACCAC GACC
582182 CGAGACGAGA
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:0.32, C:0.50, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:587728 original size:6 final size:6
Alignment explanation
Indices: 587717--587752 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
587707 TCTCGTCTCG
587717 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
587753 ACGTGTCTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:587944 original size:21 final size:21
Alignment explanation
Indices: 587881--587944 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
587871 ACAACTGTAG
* *
587881 ACTATCACAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
587902 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
587922 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
587943 AC
1 AC
587945 GCGAATTTGC
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.39, C:0.27, G:0.17, T:0.17
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:590120 original size:18 final size:17
Alignment explanation
Indices: 590066--590114 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
590056 TTGGACCCTT
* *
590066 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
590084 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
590102 AGTGCATTCGATG
1 AGTGCA-TCGATG
590115 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:590225 original size:65 final size:64
Alignment explanation
Indices: 590062--590246 Score: 223
Period size: 65 Copynumber: 2.9 Consensus size: 64
590052 ACCGTTGGAC
* * *
590062 CCTTAGTGCATCGGTGCACTAAG-AGTGCATCGATGCATCAAGTGCATTCGATGTT-TCAAAATA
1 CCTTAGTGCATCGGTGCA-T-GGTGGTGCATCGATGCATCAAATGCATTCGATGTTCTCAAAATA
*
590125 G
64 A
** * *
590126 CCAGAGTGCATCGATGCATGGATGGTGCATCGATGCATCAAATGTATTCGATGTTCTCATAAA-A
1 CCTTAGTGCATCGGTGCATGG-TGGTGCATCGATGCATCAAATGCATTCGATGTTCTCA-AAATA
590190 A
64 A
*
590191 CCTTAGTGCATCGGTGCATGGTGTGTGCATCGATGCATGAAATGCATTCGATGTTC
1 CCTTAGTGCATCGGTGCATGGTG-GTGCATCGATGCATCAAATGCATTCGATGTTC
590247 AATTTAATTC
Statistics
Matches: 103, Mismatches: 13, Indels: 9
0.82 0.10 0.07
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 46 0.45
65 52 0.50
66 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.29
Consensus pattern (64 bp):
CCTTAGTGCATCGGTGCATGGTGGTGCATCGATGCATCAAATGCATTCGATGTTCTCAAAATAA
Found at i:590285 original size:65 final size:64
Alignment explanation
Indices: 590087--590285 Score: 206
Period size: 65 Copynumber: 3.1 Consensus size: 64
590077 GCACTAAGAG
* * *
590087 TGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT-AGCCA-GAGTGCATCGATGCATGGATG
1 TGCATCGATGCATCAAATGCATTCGATG-TTCAATATAAACCATG-GTGCATCGATGCATGGATG
*
590150 G
64 T
* * * * * *
590151 TGCATCGATGCATCAAATGTATTCGATGTTCTCATAAAAACCTTAGTGCATCGGTGCATGG-TGT
1 TGCATCGATGCATCAAATGCATTCGATGTTC-AATATAAACCATGGTGCATCGATGCATGGATGT
* * **
590215 GTGCATCGATGCATGAAATGCATTCGATGTTCAATTTAATTCATGGTGCATCGATGCATGGATTG
1 -TGCATCGATGCATCAAATGCATTCGATGTTCAATATAAACCATGGTGCATCGATGCATGGA-TG
590280 T
64 T
590281 TGCAT
1 TGCAT
590286 AACTCTGAAA
Statistics
Matches: 109, Mismatches: 20, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
63 3 0.03
64 51 0.47
65 52 0.48
66 3 0.03
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.32
Consensus pattern (64 bp):
TGCATCGATGCATCAAATGCATTCGATGTTCAATATAAACCATGGTGCATCGATGCATGGATGT
Found at i:591408 original size:21 final size:21
Alignment explanation
Indices: 591384--591427 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
591374 GAGCTGGAGG
* *
591384 AGGAGGAGCACGAGAGGAGCT
1 AGGAGCAGCACGAGAGGAACT
* *
591405 AGGAGCAGCTCGTGAGGAACT
1 AGGAGCAGCACGAGAGGAACT
591426 AG
1 AG
591428 CTCCCGAAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.43, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAGGAACT
Found at i:596907 original size:22 final size:21
Alignment explanation
Indices: 596865--596904 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
596855 GAGCTTATTT
*
596865 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
596886 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
596905 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:598890 original size:18 final size:17
Alignment explanation
Indices: 598836--598884 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
598826 TTGGACCCTT
* *
598836 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
598854 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
598872 AGTGCATTCGATG
1 AGTGCA-TCGATG
598885 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:598991 original size:65 final size:64
Alignment explanation
Indices: 598832--599016 Score: 223
Period size: 65 Copynumber: 2.9 Consensus size: 64
598822 ACCGTTGGAC
* * * *
598832 CCTTAGTGCATCGGTGCACTAAG-AGTGCATCGATGCATCAAGTGCATTCGATGTT-TCAAAATA
1 CCTTAGTGCATCGGTGCA-T-GGTGGTGCATCGATGCATGAAATGCATTCGATGTTCTCAAAATA
*
598895 G
64 A
** * *
598896 CCAGAGTGCATCGATGCATGGCTGGTGCATCGGTGCATGAAATGCATTCGATGTTCTCATAAA-A
1 CCTTAGTGCATCGGTGCATGG-TGGTGCATCGATGCATGAAATGCATTCGATGTTCTCA-AAATA
598960 A
64 A
598961 CCTTAGTGCATCGGTGCATGGTGTGTGCATCGATGCATGAAATGCATTCGATGTTC
1 CCTTAGTGCATCGGTGCATGGTG-GTGCATCGATGCATGAAATGCATTCGATGTTC
599017 AATTTAATTC
Statistics
Matches: 103, Mismatches: 13, Indels: 9
0.82 0.10 0.07
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 45 0.44
65 53 0.51
66 3 0.03
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (64 bp):
CCTTAGTGCATCGGTGCATGGTGGTGCATCGATGCATGAAATGCATTCGATGTTCTCAAAATAA
Found at i:600638 original size:20 final size:20
Alignment explanation
Indices: 600615--600667 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
600605 CTTCTTACAA
600615 TATCAATACCCT-CTCTATA-G
1 TATCAATACCCTACTC-A-AGG
*
600635 TATCGATACCCTACTCAAGG
1 TATCAATACCCTACTCAAGG
600655 TATCAATACCCTA
1 TATCAATACCCTA
600668 ATGATAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.03
20 25 0.86
21 3 0.10
ACGTcount: A:0.32, C:0.30, G:0.08, T:0.30
Consensus pattern (20 bp):
TATCAATACCCTACTCAAGG
Found at i:600767 original size:21 final size:23
Alignment explanation
Indices: 600715--600770 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
600705 TACTCTTATC
*
600715 GGAGTATCGATACTGGGACCTTG
1 GGAGTATCGATACTAGGACCTTG
600738 GGAGTATCGATACTAGGACCTT-
1 GGAGTATCGATACTAGGACCTTG
600760 GG-GTATCGATA
1 GGAGTATCGATA
600771 ATCCCTTGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 9 0.28
22 2 0.06
23 21 0.66
ACGTcount: A:0.25, C:0.16, G:0.32, T:0.27
Consensus pattern (23 bp):
GGAGTATCGATACTAGGACCTTG
Done.