Multiple sequence alignment - TraesCS3B01G311200

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G311200 chr3B 100.000 2596 0 0 1 2596 499807128 499804533 0.000000e+00 4795.0
1 TraesCS3B01G311200 chr3D 91.898 1728 65 30 524 2217 384568278 384566592 0.000000e+00 2346.0
2 TraesCS3B01G311200 chr3D 94.101 356 13 5 138 490 384568629 384568279 3.800000e-148 534.0
3 TraesCS3B01G311200 chr3D 90.769 65 6 0 488 552 384568249 384568185 1.280000e-13 87.9
4 TraesCS3B01G311200 chr3A 88.889 1584 65 43 650 2196 507121252 507119743 0.000000e+00 1847.0
5 TraesCS3B01G311200 chr3A 90.909 396 15 9 38 423 507126217 507125833 1.780000e-141 512.0
6 TraesCS3B01G311200 chr3A 86.994 346 30 10 2262 2596 507119688 507119347 2.440000e-100 375.0
7 TraesCS3B01G311200 chr1B 98.361 122 2 0 998 1119 585680431 585680310 5.630000e-52 215.0
8 TraesCS3B01G311200 chr1B 83.117 154 26 0 1216 1369 585680201 585680048 9.690000e-30 141.0
9 TraesCS3B01G311200 chr1D 96.825 126 4 0 994 1119 433464228 433464103 7.280000e-51 211.0
10 TraesCS3B01G311200 chr1D 84.247 146 23 0 1216 1361 433463990 433463845 2.690000e-30 143.0
11 TraesCS3B01G311200 chr1A 96.825 126 4 0 994 1119 531986748 531986623 7.280000e-51 211.0
12 TraesCS3B01G311200 chr1A 89.928 139 14 0 1458 1596 531986238 531986100 2.050000e-41 180.0
13 TraesCS3B01G311200 chr1A 82.468 154 27 0 1216 1369 531986507 531986354 4.510000e-28 135.0
14 TraesCS3B01G311200 chr7D 86.331 139 16 3 983 1119 60700008 60700145 5.790000e-32 148.0
15 TraesCS3B01G311200 chr7B 86.331 139 16 3 983 1119 3336849 3336986 5.790000e-32 148.0
16 TraesCS3B01G311200 chr7A 86.331 139 16 3 983 1119 65005995 65006132 5.790000e-32 148.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G311200 chr3B 499804533 499807128 2595 True 4795.0 4795 100.0000 1 2596 1 chr3B.!!$R1 2595
1 TraesCS3B01G311200 chr3D 384566592 384568629 2037 True 989.3 2346 92.2560 138 2217 3 chr3D.!!$R1 2079
2 TraesCS3B01G311200 chr3A 507119347 507121252 1905 True 1111.0 1847 87.9415 650 2596 2 chr3A.!!$R2 1946

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
234 235 0.036164 TACGAATTGCAGGCCAGTGT 59.964 50.0 5.01 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1683 1757 0.041047 CACAATCCCATATGCGTGCG 60.041 55.0 0.0 0.0 0.0 5.34 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 6.484364 TTCTCATGTATCAGGCTACAATCA 57.516 37.500 0.00 0.00 35.37 2.57
24 25 5.847304 TCTCATGTATCAGGCTACAATCAC 58.153 41.667 0.00 0.00 35.37 3.06
25 26 5.363580 TCTCATGTATCAGGCTACAATCACA 59.636 40.000 0.00 0.00 35.37 3.58
26 27 5.988287 TCATGTATCAGGCTACAATCACAA 58.012 37.500 0.00 0.00 35.37 3.33
27 28 6.594744 TCATGTATCAGGCTACAATCACAAT 58.405 36.000 0.00 0.00 35.37 2.71
28 29 7.734942 TCATGTATCAGGCTACAATCACAATA 58.265 34.615 0.00 0.00 35.37 1.90
29 30 8.210265 TCATGTATCAGGCTACAATCACAATAA 58.790 33.333 0.00 0.00 35.37 1.40
30 31 8.839343 CATGTATCAGGCTACAATCACAATAAA 58.161 33.333 0.00 0.00 35.37 1.40
31 32 8.978874 TGTATCAGGCTACAATCACAATAAAT 57.021 30.769 0.00 0.00 0.00 1.40
32 33 8.839343 TGTATCAGGCTACAATCACAATAAATG 58.161 33.333 0.00 0.00 0.00 2.32
33 34 9.056005 GTATCAGGCTACAATCACAATAAATGA 57.944 33.333 0.00 0.00 0.00 2.57
34 35 7.558161 TCAGGCTACAATCACAATAAATGAG 57.442 36.000 0.00 0.00 0.00 2.90
35 36 7.337938 TCAGGCTACAATCACAATAAATGAGA 58.662 34.615 0.00 0.00 33.01 3.27
36 37 7.828717 TCAGGCTACAATCACAATAAATGAGAA 59.171 33.333 0.00 0.00 32.20 2.87
37 38 8.627403 CAGGCTACAATCACAATAAATGAGAAT 58.373 33.333 0.00 0.00 32.20 2.40
38 39 9.193806 AGGCTACAATCACAATAAATGAGAATT 57.806 29.630 0.00 0.00 32.20 2.17
39 40 9.241317 GGCTACAATCACAATAAATGAGAATTG 57.759 33.333 0.00 0.00 38.71 2.32
40 41 9.793252 GCTACAATCACAATAAATGAGAATTGT 57.207 29.630 0.00 0.00 44.94 2.71
49 50 8.028938 ACAATAAATGAGAATTGTGGTTGTAGC 58.971 33.333 0.20 0.00 43.01 3.58
50 51 5.391312 AAATGAGAATTGTGGTTGTAGCC 57.609 39.130 0.00 0.00 0.00 3.93
51 52 3.788227 TGAGAATTGTGGTTGTAGCCT 57.212 42.857 0.00 0.00 0.00 4.58
52 53 3.411446 TGAGAATTGTGGTTGTAGCCTG 58.589 45.455 0.00 0.00 0.00 4.85
53 54 3.181445 TGAGAATTGTGGTTGTAGCCTGT 60.181 43.478 0.00 0.00 0.00 4.00
54 55 3.149196 AGAATTGTGGTTGTAGCCTGTG 58.851 45.455 0.00 0.00 0.00 3.66
55 56 2.656947 ATTGTGGTTGTAGCCTGTGT 57.343 45.000 0.00 0.00 0.00 3.72
56 57 3.780804 ATTGTGGTTGTAGCCTGTGTA 57.219 42.857 0.00 0.00 0.00 2.90
57 58 2.831685 TGTGGTTGTAGCCTGTGTAG 57.168 50.000 0.00 0.00 0.00 2.74
58 59 2.321719 TGTGGTTGTAGCCTGTGTAGA 58.678 47.619 0.00 0.00 0.00 2.59
59 60 2.701423 TGTGGTTGTAGCCTGTGTAGAA 59.299 45.455 0.00 0.00 0.00 2.10
60 61 3.244078 TGTGGTTGTAGCCTGTGTAGAAG 60.244 47.826 0.00 0.00 0.00 2.85
61 62 2.969950 TGGTTGTAGCCTGTGTAGAAGT 59.030 45.455 0.00 0.00 0.00 3.01
62 63 3.389983 TGGTTGTAGCCTGTGTAGAAGTT 59.610 43.478 0.00 0.00 0.00 2.66
63 64 4.589798 TGGTTGTAGCCTGTGTAGAAGTTA 59.410 41.667 0.00 0.00 0.00 2.24
64 65 5.070714 TGGTTGTAGCCTGTGTAGAAGTTAA 59.929 40.000 0.00 0.00 0.00 2.01
65 66 5.638234 GGTTGTAGCCTGTGTAGAAGTTAAG 59.362 44.000 0.00 0.00 0.00 1.85
66 67 6.221659 GTTGTAGCCTGTGTAGAAGTTAAGT 58.778 40.000 0.00 0.00 0.00 2.24
67 68 7.373493 GTTGTAGCCTGTGTAGAAGTTAAGTA 58.627 38.462 0.00 0.00 0.00 2.24
68 69 7.713734 TGTAGCCTGTGTAGAAGTTAAGTAT 57.286 36.000 0.00 0.00 0.00 2.12
69 70 7.544622 TGTAGCCTGTGTAGAAGTTAAGTATG 58.455 38.462 0.00 0.00 0.00 2.39
70 71 5.978814 AGCCTGTGTAGAAGTTAAGTATGG 58.021 41.667 0.00 0.00 0.00 2.74
71 72 5.104900 AGCCTGTGTAGAAGTTAAGTATGGG 60.105 44.000 0.00 0.00 0.00 4.00
72 73 5.338137 GCCTGTGTAGAAGTTAAGTATGGGT 60.338 44.000 0.00 0.00 0.00 4.51
73 74 6.708285 CCTGTGTAGAAGTTAAGTATGGGTT 58.292 40.000 0.00 0.00 0.00 4.11
74 75 6.594159 CCTGTGTAGAAGTTAAGTATGGGTTG 59.406 42.308 0.00 0.00 0.00 3.77
75 76 7.069877 TGTGTAGAAGTTAAGTATGGGTTGT 57.930 36.000 0.00 0.00 0.00 3.32
76 77 8.192743 TGTGTAGAAGTTAAGTATGGGTTGTA 57.807 34.615 0.00 0.00 0.00 2.41
77 78 8.308931 TGTGTAGAAGTTAAGTATGGGTTGTAG 58.691 37.037 0.00 0.00 0.00 2.74
78 79 7.277319 GTGTAGAAGTTAAGTATGGGTTGTAGC 59.723 40.741 0.00 0.00 0.00 3.58
79 80 5.742063 AGAAGTTAAGTATGGGTTGTAGCC 58.258 41.667 0.00 0.00 36.00 3.93
80 81 5.487845 AGAAGTTAAGTATGGGTTGTAGCCT 59.512 40.000 0.00 0.00 36.53 4.58
81 82 5.099042 AGTTAAGTATGGGTTGTAGCCTG 57.901 43.478 0.00 0.00 36.53 4.85
82 83 4.534897 AGTTAAGTATGGGTTGTAGCCTGT 59.465 41.667 0.00 0.00 36.53 4.00
83 84 3.350219 AAGTATGGGTTGTAGCCTGTG 57.650 47.619 0.00 0.00 36.53 3.66
84 85 2.266279 AGTATGGGTTGTAGCCTGTGT 58.734 47.619 0.00 0.00 36.53 3.72
85 86 3.446968 AGTATGGGTTGTAGCCTGTGTA 58.553 45.455 0.00 0.00 36.53 2.90
86 87 3.841845 AGTATGGGTTGTAGCCTGTGTAA 59.158 43.478 0.00 0.00 36.53 2.41
87 88 3.799432 ATGGGTTGTAGCCTGTGTAAA 57.201 42.857 0.00 0.00 36.53 2.01
88 89 3.579534 TGGGTTGTAGCCTGTGTAAAA 57.420 42.857 0.00 0.00 36.53 1.52
89 90 3.482436 TGGGTTGTAGCCTGTGTAAAAG 58.518 45.455 0.00 0.00 36.53 2.27
90 91 3.136809 TGGGTTGTAGCCTGTGTAAAAGA 59.863 43.478 0.00 0.00 36.53 2.52
91 92 4.202524 TGGGTTGTAGCCTGTGTAAAAGAT 60.203 41.667 0.00 0.00 36.53 2.40
92 93 4.156008 GGGTTGTAGCCTGTGTAAAAGATG 59.844 45.833 0.00 0.00 31.81 2.90
93 94 4.379499 GGTTGTAGCCTGTGTAAAAGATGC 60.379 45.833 0.00 0.00 0.00 3.91
94 95 4.014569 TGTAGCCTGTGTAAAAGATGCA 57.985 40.909 0.00 0.00 0.00 3.96
95 96 4.393834 TGTAGCCTGTGTAAAAGATGCAA 58.606 39.130 0.00 0.00 0.00 4.08
96 97 5.009631 TGTAGCCTGTGTAAAAGATGCAAT 58.990 37.500 0.00 0.00 0.00 3.56
97 98 6.176896 TGTAGCCTGTGTAAAAGATGCAATA 58.823 36.000 0.00 0.00 0.00 1.90
98 99 6.657117 TGTAGCCTGTGTAAAAGATGCAATAA 59.343 34.615 0.00 0.00 0.00 1.40
99 100 6.199937 AGCCTGTGTAAAAGATGCAATAAG 57.800 37.500 0.00 0.00 0.00 1.73
100 101 5.711976 AGCCTGTGTAAAAGATGCAATAAGT 59.288 36.000 0.00 0.00 0.00 2.24
101 102 6.884295 AGCCTGTGTAAAAGATGCAATAAGTA 59.116 34.615 0.00 0.00 0.00 2.24
102 103 7.557719 AGCCTGTGTAAAAGATGCAATAAGTAT 59.442 33.333 0.00 0.00 0.00 2.12
103 104 7.645340 GCCTGTGTAAAAGATGCAATAAGTATG 59.355 37.037 0.00 0.00 0.00 2.39
104 105 8.131100 CCTGTGTAAAAGATGCAATAAGTATGG 58.869 37.037 0.00 0.00 0.00 2.74
105 106 7.995289 TGTGTAAAAGATGCAATAAGTATGGG 58.005 34.615 0.00 0.00 0.00 4.00
106 107 7.613801 TGTGTAAAAGATGCAATAAGTATGGGT 59.386 33.333 0.00 0.00 0.00 4.51
107 108 8.466798 GTGTAAAAGATGCAATAAGTATGGGTT 58.533 33.333 0.00 0.00 0.00 4.11
108 109 9.030452 TGTAAAAGATGCAATAAGTATGGGTTT 57.970 29.630 0.00 0.00 0.00 3.27
109 110 9.301153 GTAAAAGATGCAATAAGTATGGGTTTG 57.699 33.333 0.00 0.00 0.00 2.93
110 111 7.480760 AAAGATGCAATAAGTATGGGTTTGT 57.519 32.000 0.00 0.00 0.00 2.83
111 112 8.588290 AAAGATGCAATAAGTATGGGTTTGTA 57.412 30.769 0.00 0.00 0.00 2.41
112 113 7.568199 AGATGCAATAAGTATGGGTTTGTAC 57.432 36.000 0.00 0.00 0.00 2.90
113 114 7.346471 AGATGCAATAAGTATGGGTTTGTACT 58.654 34.615 0.00 0.00 32.75 2.73
114 115 6.995511 TGCAATAAGTATGGGTTTGTACTC 57.004 37.500 0.00 0.00 31.10 2.59
115 116 6.477253 TGCAATAAGTATGGGTTTGTACTCA 58.523 36.000 0.00 0.00 39.58 3.41
116 117 6.943146 TGCAATAAGTATGGGTTTGTACTCAA 59.057 34.615 0.00 0.00 38.51 3.02
117 118 7.448777 TGCAATAAGTATGGGTTTGTACTCAAA 59.551 33.333 0.00 0.00 38.51 2.69
118 119 8.301002 GCAATAAGTATGGGTTTGTACTCAAAA 58.699 33.333 0.00 0.00 43.78 2.44
125 126 9.581099 GTATGGGTTTGTACTCAAAATTTATGG 57.419 33.333 0.00 0.00 43.78 2.74
126 127 6.998802 TGGGTTTGTACTCAAAATTTATGGG 58.001 36.000 0.00 0.00 43.78 4.00
127 128 5.872617 GGGTTTGTACTCAAAATTTATGGGC 59.127 40.000 0.00 0.00 43.78 5.36
128 129 6.295632 GGGTTTGTACTCAAAATTTATGGGCT 60.296 38.462 0.00 0.00 43.78 5.19
129 130 7.158697 GGTTTGTACTCAAAATTTATGGGCTT 58.841 34.615 0.00 0.00 43.78 4.35
130 131 7.117667 GGTTTGTACTCAAAATTTATGGGCTTG 59.882 37.037 0.00 0.00 43.78 4.01
131 132 6.279513 TGTACTCAAAATTTATGGGCTTGG 57.720 37.500 0.00 0.00 0.00 3.61
132 133 6.013379 TGTACTCAAAATTTATGGGCTTGGA 58.987 36.000 0.00 0.00 0.00 3.53
133 134 6.495181 TGTACTCAAAATTTATGGGCTTGGAA 59.505 34.615 0.00 0.00 0.00 3.53
134 135 6.041423 ACTCAAAATTTATGGGCTTGGAAG 57.959 37.500 0.00 0.00 0.00 3.46
230 231 4.312052 GGTACGAATTGCAGGCCA 57.688 55.556 5.01 0.00 0.00 5.36
231 232 2.098293 GGTACGAATTGCAGGCCAG 58.902 57.895 5.01 0.00 0.00 4.85
232 233 0.676782 GGTACGAATTGCAGGCCAGT 60.677 55.000 5.01 0.00 0.00 4.00
233 234 0.447801 GTACGAATTGCAGGCCAGTG 59.552 55.000 5.01 0.00 0.00 3.66
234 235 0.036164 TACGAATTGCAGGCCAGTGT 59.964 50.000 5.01 0.00 0.00 3.55
272 276 0.550914 TCAACTCACTGGCTTGGGTT 59.449 50.000 0.00 0.00 41.07 4.11
301 305 8.404000 CACCTTACTCATCACGTTATTACTAGT 58.596 37.037 0.00 0.00 0.00 2.57
373 377 2.763448 TGCCCATGCTTATTGTAAACCC 59.237 45.455 0.00 0.00 38.71 4.11
381 385 7.545615 CCATGCTTATTGTAAACCCTTTTCTTC 59.454 37.037 0.00 0.00 0.00 2.87
398 402 3.646715 CCAAGGGTTCGGGCCAGA 61.647 66.667 4.39 1.93 0.00 3.86
414 418 4.989279 GCCAGATCTTTTGATGGCTTAA 57.011 40.909 12.82 0.00 46.07 1.85
470 474 4.582701 AGTCGCCTCTCTCATTCATTAG 57.417 45.455 0.00 0.00 0.00 1.73
558 593 9.654663 TTTTTAAACTAGAGAGAGGCAGATAAC 57.345 33.333 0.00 0.00 0.00 1.89
559 594 5.862678 AAACTAGAGAGAGGCAGATAACC 57.137 43.478 0.00 0.00 0.00 2.85
560 595 4.528076 ACTAGAGAGAGGCAGATAACCA 57.472 45.455 0.00 0.00 0.00 3.67
561 596 4.873010 ACTAGAGAGAGGCAGATAACCAA 58.127 43.478 0.00 0.00 0.00 3.67
562 597 5.463154 ACTAGAGAGAGGCAGATAACCAAT 58.537 41.667 0.00 0.00 0.00 3.16
563 598 5.902431 ACTAGAGAGAGGCAGATAACCAATT 59.098 40.000 0.00 0.00 0.00 2.32
564 599 5.707066 AGAGAGAGGCAGATAACCAATTT 57.293 39.130 0.00 0.00 0.00 1.82
565 600 6.814954 AGAGAGAGGCAGATAACCAATTTA 57.185 37.500 0.00 0.00 0.00 1.40
566 601 6.825610 AGAGAGAGGCAGATAACCAATTTAG 58.174 40.000 0.00 0.00 0.00 1.85
567 602 6.613271 AGAGAGAGGCAGATAACCAATTTAGA 59.387 38.462 0.00 0.00 0.00 2.10
568 603 7.126421 AGAGAGAGGCAGATAACCAATTTAGAA 59.874 37.037 0.00 0.00 0.00 2.10
569 604 7.278875 AGAGAGGCAGATAACCAATTTAGAAG 58.721 38.462 0.00 0.00 0.00 2.85
570 605 7.126421 AGAGAGGCAGATAACCAATTTAGAAGA 59.874 37.037 0.00 0.00 0.00 2.87
571 606 7.051000 AGAGGCAGATAACCAATTTAGAAGAC 58.949 38.462 0.00 0.00 0.00 3.01
572 607 6.963322 AGGCAGATAACCAATTTAGAAGACT 58.037 36.000 0.00 0.00 0.00 3.24
573 608 7.051000 AGGCAGATAACCAATTTAGAAGACTC 58.949 38.462 0.00 0.00 0.00 3.36
574 609 6.823689 GGCAGATAACCAATTTAGAAGACTCA 59.176 38.462 0.00 0.00 0.00 3.41
575 610 7.336931 GGCAGATAACCAATTTAGAAGACTCAA 59.663 37.037 0.00 0.00 0.00 3.02
576 611 8.178313 GCAGATAACCAATTTAGAAGACTCAAC 58.822 37.037 0.00 0.00 0.00 3.18
577 612 9.219603 CAGATAACCAATTTAGAAGACTCAACA 57.780 33.333 0.00 0.00 0.00 3.33
578 613 9.793259 AGATAACCAATTTAGAAGACTCAACAA 57.207 29.630 0.00 0.00 0.00 2.83
626 661 3.636153 AGAGAGAGGCGGCTTATTTTT 57.364 42.857 14.76 0.00 0.00 1.94
647 690 2.445682 ACTACAAAACTGGCCCAACA 57.554 45.000 0.00 0.00 0.00 3.33
684 727 0.679640 AAATTGCGGCCGAATCCAGA 60.680 50.000 33.48 1.88 0.00 3.86
837 888 1.282382 CCTTTTTCCCCGTCCTCCTA 58.718 55.000 0.00 0.00 0.00 2.94
838 889 1.631898 CCTTTTTCCCCGTCCTCCTAA 59.368 52.381 0.00 0.00 0.00 2.69
944 998 3.968568 CAACAAGCCGCAGCAGCA 61.969 61.111 2.79 0.00 43.56 4.41
1132 1186 2.203972 CTTCCCGTCGGTGCGTAAGA 62.204 60.000 11.06 0.00 43.02 2.10
1133 1187 1.597797 TTCCCGTCGGTGCGTAAGAT 61.598 55.000 11.06 0.00 43.02 2.40
1137 1191 1.064505 CCGTCGGTGCGTAAGATAAGA 59.935 52.381 2.08 0.00 43.02 2.10
1144 1198 3.877508 GGTGCGTAAGATAAGAAATGGCT 59.122 43.478 0.00 0.00 43.02 4.75
1151 1205 7.041372 GCGTAAGATAAGAAATGGCTAATCCAA 60.041 37.037 0.00 0.00 45.84 3.53
1168 1222 2.560542 TCCAATTGTTGCTATTTGGCGT 59.439 40.909 4.43 0.00 38.78 5.68
1169 1223 2.667481 CCAATTGTTGCTATTTGGCGTG 59.333 45.455 4.43 0.00 32.88 5.34
1175 1229 1.743996 TGCTATTTGGCGTGTGCATA 58.256 45.000 0.00 0.00 45.35 3.14
1181 1235 4.536687 GGCGTGTGCATAAGCCGC 62.537 66.667 23.08 15.46 44.55 6.53
1182 1236 4.536687 GCGTGTGCATAAGCCGCC 62.537 66.667 10.16 0.00 41.17 6.13
1183 1237 2.819595 CGTGTGCATAAGCCGCCT 60.820 61.111 0.00 0.00 41.13 5.52
1184 1238 2.813179 CGTGTGCATAAGCCGCCTC 61.813 63.158 0.00 0.00 41.13 4.70
1185 1239 2.124736 TGTGCATAAGCCGCCTCC 60.125 61.111 0.00 0.00 41.13 4.30
1186 1240 2.124736 GTGCATAAGCCGCCTCCA 60.125 61.111 0.00 0.00 41.13 3.86
1377 1440 0.389426 GTAACCATGCACGTCGGACT 60.389 55.000 6.57 0.00 0.00 3.85
1667 1741 0.452184 CACAGTAGATCTCCACGCGT 59.548 55.000 5.58 5.58 0.00 6.01
1668 1742 1.135373 CACAGTAGATCTCCACGCGTT 60.135 52.381 10.22 0.00 0.00 4.84
1669 1743 1.544691 ACAGTAGATCTCCACGCGTTT 59.455 47.619 10.22 0.00 0.00 3.60
1670 1744 2.029290 ACAGTAGATCTCCACGCGTTTT 60.029 45.455 10.22 0.00 0.00 2.43
1671 1745 2.993899 CAGTAGATCTCCACGCGTTTTT 59.006 45.455 10.22 0.00 0.00 1.94
1728 1802 2.151502 TTTCTCTCGCATCCTCCTCT 57.848 50.000 0.00 0.00 0.00 3.69
1729 1803 1.686355 TTCTCTCGCATCCTCCTCTC 58.314 55.000 0.00 0.00 0.00 3.20
1730 1804 0.548510 TCTCTCGCATCCTCCTCTCA 59.451 55.000 0.00 0.00 0.00 3.27
1731 1805 1.144708 TCTCTCGCATCCTCCTCTCAT 59.855 52.381 0.00 0.00 0.00 2.90
1735 1809 3.571828 TCTCGCATCCTCCTCTCATTAAG 59.428 47.826 0.00 0.00 0.00 1.85
1762 1836 1.218316 CCTGTCCCGGCAACTACTC 59.782 63.158 0.00 0.00 0.00 2.59
1854 1928 6.520447 CGTTCGTTTCGGCTAATAATTTTGAA 59.480 34.615 0.00 0.00 0.00 2.69
2038 2118 6.058183 GGTCTGCTTCAACTCCATATACATT 58.942 40.000 0.00 0.00 0.00 2.71
2046 2126 8.958119 TTCAACTCCATATACATTGTTCCTAC 57.042 34.615 0.00 0.00 0.00 3.18
2112 2195 4.477302 TTTCGCGGTTAAGGAAGAAAAG 57.523 40.909 6.13 0.00 0.00 2.27
2116 2199 4.575645 TCGCGGTTAAGGAAGAAAAGAAAA 59.424 37.500 6.13 0.00 0.00 2.29
2119 2202 6.129194 CGCGGTTAAGGAAGAAAAGAAAAATG 60.129 38.462 0.00 0.00 0.00 2.32
2120 2203 6.921307 GCGGTTAAGGAAGAAAAGAAAAATGA 59.079 34.615 0.00 0.00 0.00 2.57
2121 2204 7.096189 GCGGTTAAGGAAGAAAAGAAAAATGAC 60.096 37.037 0.00 0.00 0.00 3.06
2122 2205 7.918562 CGGTTAAGGAAGAAAAGAAAAATGACA 59.081 33.333 0.00 0.00 0.00 3.58
2123 2206 9.764363 GGTTAAGGAAGAAAAGAAAAATGACAT 57.236 29.630 0.00 0.00 0.00 3.06
2127 2210 8.877808 AGGAAGAAAAGAAAAATGACATTCAC 57.122 30.769 0.05 0.00 0.00 3.18
2128 2211 7.928167 AGGAAGAAAAGAAAAATGACATTCACC 59.072 33.333 0.05 0.00 0.00 4.02
2129 2212 7.710475 GGAAGAAAAGAAAAATGACATTCACCA 59.290 33.333 0.05 0.00 0.00 4.17
2160 2243 5.521010 CCACTCAAATTTGATGCGCATAAAT 59.479 36.000 25.40 22.93 36.46 1.40
2171 2254 9.970243 TTTGATGCGCATAAATTCTTTATTTTG 57.030 25.926 25.40 0.00 37.60 2.44
2217 2303 0.328926 TTGGACCCCAATACCGAACC 59.671 55.000 0.00 0.00 38.75 3.62
2218 2304 1.153309 GGACCCCAATACCGAACCG 60.153 63.158 0.00 0.00 0.00 4.44
2219 2305 1.598517 GACCCCAATACCGAACCGT 59.401 57.895 0.00 0.00 0.00 4.83
2220 2306 0.036105 GACCCCAATACCGAACCGTT 60.036 55.000 0.00 0.00 0.00 4.44
2221 2307 0.036105 ACCCCAATACCGAACCGTTC 60.036 55.000 0.76 0.76 0.00 3.95
2232 2318 3.546714 AACCGTTCGGGGCAAGGAG 62.547 63.158 15.66 0.00 41.60 3.69
2233 2319 4.016706 CCGTTCGGGGCAAGGAGT 62.017 66.667 3.04 0.00 0.00 3.85
2234 2320 2.032071 CGTTCGGGGCAAGGAGTT 59.968 61.111 0.00 0.00 0.00 3.01
2235 2321 2.033194 CGTTCGGGGCAAGGAGTTC 61.033 63.158 0.00 0.00 0.00 3.01
2238 2324 2.359975 CGGGGCAAGGAGTTCACC 60.360 66.667 0.00 0.00 0.00 4.02
2239 2325 2.035783 GGGGCAAGGAGTTCACCC 59.964 66.667 0.00 0.00 40.05 4.61
2240 2326 2.035783 GGGCAAGGAGTTCACCCC 59.964 66.667 0.00 0.00 34.23 4.95
2241 2327 2.359975 GGCAAGGAGTTCACCCCG 60.360 66.667 0.00 0.00 0.00 5.73
2242 2328 3.056328 GCAAGGAGTTCACCCCGC 61.056 66.667 0.00 0.00 0.00 6.13
2244 2330 1.966451 CAAGGAGTTCACCCCGCAC 60.966 63.158 0.00 0.00 0.00 5.34
2245 2331 3.530910 AAGGAGTTCACCCCGCACG 62.531 63.158 0.00 0.00 0.00 5.34
2258 2344 2.707039 GCACGCGCGAACCATAAT 59.293 55.556 39.36 8.45 0.00 1.28
2259 2345 1.928653 GCACGCGCGAACCATAATA 59.071 52.632 39.36 0.00 0.00 0.98
2260 2346 0.511221 GCACGCGCGAACCATAATAT 59.489 50.000 39.36 6.60 0.00 1.28
2264 2350 3.366724 CACGCGCGAACCATAATATATGT 59.633 43.478 39.36 4.34 0.00 2.29
2268 2354 4.322934 CGCGAACCATAATATATGTTGCG 58.677 43.478 0.00 7.68 34.56 4.85
2308 2395 0.034756 GCCCAAAACGCAATTCCCTT 59.965 50.000 0.00 0.00 0.00 3.95
2318 2405 3.573967 ACGCAATTCCCTTGAAGAATGTT 59.426 39.130 0.00 0.00 36.97 2.71
2321 2408 5.801947 CGCAATTCCCTTGAAGAATGTTAAG 59.198 40.000 0.00 0.00 36.97 1.85
2385 2472 3.441572 CCTGCCTCAACCAACAAATAGAG 59.558 47.826 0.00 0.00 0.00 2.43
2394 2481 7.712797 TCAACCAACAAATAGAGAAAAAGACC 58.287 34.615 0.00 0.00 0.00 3.85
2411 2498 6.819397 AAAGACCTAAAAATGCACTAGACC 57.181 37.500 0.00 0.00 0.00 3.85
2443 2532 5.131142 ACTCCCTGAAAATAATCGAGGACAT 59.869 40.000 0.00 0.00 0.00 3.06
2445 2534 7.016661 ACTCCCTGAAAATAATCGAGGACATAT 59.983 37.037 0.00 0.00 0.00 1.78
2478 2567 9.903682 AAATCTTTAGTTGTCATGACATGAAAG 57.096 29.630 29.73 29.73 41.69 2.62
2479 2568 6.902341 TCTTTAGTTGTCATGACATGAAAGC 58.098 36.000 30.21 16.12 41.69 3.51
2540 2637 6.942532 AAGAGCTACAAAGTTTGACATTGA 57.057 33.333 22.23 0.00 31.86 2.57
2541 2638 6.942532 AGAGCTACAAAGTTTGACATTGAA 57.057 33.333 22.23 0.00 31.86 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.127083 TGTGATTGTAGCCTGATACATGAGAA 60.127 38.462 0.00 0.00 35.65 2.87
1 2 5.363580 TGTGATTGTAGCCTGATACATGAGA 59.636 40.000 0.00 0.00 35.65 3.27
2 3 5.604565 TGTGATTGTAGCCTGATACATGAG 58.395 41.667 0.00 0.00 35.65 2.90
3 4 5.612725 TGTGATTGTAGCCTGATACATGA 57.387 39.130 0.00 0.00 35.65 3.07
4 5 6.872628 ATTGTGATTGTAGCCTGATACATG 57.127 37.500 0.00 0.00 35.65 3.21
5 6 8.978874 TTTATTGTGATTGTAGCCTGATACAT 57.021 30.769 0.00 0.00 35.65 2.29
6 7 8.839343 CATTTATTGTGATTGTAGCCTGATACA 58.161 33.333 0.00 0.00 33.88 2.29
7 8 9.056005 TCATTTATTGTGATTGTAGCCTGATAC 57.944 33.333 0.00 0.00 0.00 2.24
8 9 9.276590 CTCATTTATTGTGATTGTAGCCTGATA 57.723 33.333 0.00 0.00 0.00 2.15
9 10 7.994911 TCTCATTTATTGTGATTGTAGCCTGAT 59.005 33.333 0.00 0.00 0.00 2.90
10 11 7.337938 TCTCATTTATTGTGATTGTAGCCTGA 58.662 34.615 0.00 0.00 0.00 3.86
11 12 7.558161 TCTCATTTATTGTGATTGTAGCCTG 57.442 36.000 0.00 0.00 0.00 4.85
12 13 8.757982 ATTCTCATTTATTGTGATTGTAGCCT 57.242 30.769 0.00 0.00 0.00 4.58
13 14 9.241317 CAATTCTCATTTATTGTGATTGTAGCC 57.759 33.333 0.00 0.00 0.00 3.93
14 15 9.793252 ACAATTCTCATTTATTGTGATTGTAGC 57.207 29.630 0.00 0.00 41.90 3.58
23 24 8.028938 GCTACAACCACAATTCTCATTTATTGT 58.971 33.333 0.00 0.00 43.70 2.71
24 25 7.489113 GGCTACAACCACAATTCTCATTTATTG 59.511 37.037 0.00 0.00 37.67 1.90
25 26 7.397192 AGGCTACAACCACAATTCTCATTTATT 59.603 33.333 0.00 0.00 0.00 1.40
26 27 6.891908 AGGCTACAACCACAATTCTCATTTAT 59.108 34.615 0.00 0.00 0.00 1.40
27 28 6.150976 CAGGCTACAACCACAATTCTCATTTA 59.849 38.462 0.00 0.00 0.00 1.40
28 29 5.047802 CAGGCTACAACCACAATTCTCATTT 60.048 40.000 0.00 0.00 0.00 2.32
29 30 4.460382 CAGGCTACAACCACAATTCTCATT 59.540 41.667 0.00 0.00 0.00 2.57
30 31 4.012374 CAGGCTACAACCACAATTCTCAT 58.988 43.478 0.00 0.00 0.00 2.90
31 32 3.181445 ACAGGCTACAACCACAATTCTCA 60.181 43.478 0.00 0.00 0.00 3.27
32 33 3.189287 CACAGGCTACAACCACAATTCTC 59.811 47.826 0.00 0.00 0.00 2.87
33 34 3.149196 CACAGGCTACAACCACAATTCT 58.851 45.455 0.00 0.00 0.00 2.40
34 35 2.884639 ACACAGGCTACAACCACAATTC 59.115 45.455 0.00 0.00 0.00 2.17
35 36 2.944129 ACACAGGCTACAACCACAATT 58.056 42.857 0.00 0.00 0.00 2.32
36 37 2.656947 ACACAGGCTACAACCACAAT 57.343 45.000 0.00 0.00 0.00 2.71
37 38 2.701423 TCTACACAGGCTACAACCACAA 59.299 45.455 0.00 0.00 0.00 3.33
38 39 2.321719 TCTACACAGGCTACAACCACA 58.678 47.619 0.00 0.00 0.00 4.17
39 40 3.244112 ACTTCTACACAGGCTACAACCAC 60.244 47.826 0.00 0.00 0.00 4.16
40 41 2.969950 ACTTCTACACAGGCTACAACCA 59.030 45.455 0.00 0.00 0.00 3.67
41 42 3.679824 ACTTCTACACAGGCTACAACC 57.320 47.619 0.00 0.00 0.00 3.77
42 43 6.221659 ACTTAACTTCTACACAGGCTACAAC 58.778 40.000 0.00 0.00 0.00 3.32
43 44 6.415206 ACTTAACTTCTACACAGGCTACAA 57.585 37.500 0.00 0.00 0.00 2.41
44 45 7.363530 CCATACTTAACTTCTACACAGGCTACA 60.364 40.741 0.00 0.00 0.00 2.74
45 46 6.979238 CCATACTTAACTTCTACACAGGCTAC 59.021 42.308 0.00 0.00 0.00 3.58
46 47 6.097839 CCCATACTTAACTTCTACACAGGCTA 59.902 42.308 0.00 0.00 0.00 3.93
47 48 5.104900 CCCATACTTAACTTCTACACAGGCT 60.105 44.000 0.00 0.00 0.00 4.58
48 49 5.116882 CCCATACTTAACTTCTACACAGGC 58.883 45.833 0.00 0.00 0.00 4.85
49 50 6.295719 ACCCATACTTAACTTCTACACAGG 57.704 41.667 0.00 0.00 0.00 4.00
50 51 7.159372 ACAACCCATACTTAACTTCTACACAG 58.841 38.462 0.00 0.00 0.00 3.66
51 52 7.069877 ACAACCCATACTTAACTTCTACACA 57.930 36.000 0.00 0.00 0.00 3.72
52 53 7.277319 GCTACAACCCATACTTAACTTCTACAC 59.723 40.741 0.00 0.00 0.00 2.90
53 54 7.325694 GCTACAACCCATACTTAACTTCTACA 58.674 38.462 0.00 0.00 0.00 2.74
54 55 6.760298 GGCTACAACCCATACTTAACTTCTAC 59.240 42.308 0.00 0.00 0.00 2.59
55 56 6.670902 AGGCTACAACCCATACTTAACTTCTA 59.329 38.462 0.00 0.00 0.00 2.10
56 57 5.487845 AGGCTACAACCCATACTTAACTTCT 59.512 40.000 0.00 0.00 0.00 2.85
57 58 5.585047 CAGGCTACAACCCATACTTAACTTC 59.415 44.000 0.00 0.00 0.00 3.01
58 59 5.013808 ACAGGCTACAACCCATACTTAACTT 59.986 40.000 0.00 0.00 0.00 2.66
59 60 4.534897 ACAGGCTACAACCCATACTTAACT 59.465 41.667 0.00 0.00 0.00 2.24
60 61 4.634443 CACAGGCTACAACCCATACTTAAC 59.366 45.833 0.00 0.00 0.00 2.01
61 62 4.287585 ACACAGGCTACAACCCATACTTAA 59.712 41.667 0.00 0.00 0.00 1.85
62 63 3.841845 ACACAGGCTACAACCCATACTTA 59.158 43.478 0.00 0.00 0.00 2.24
63 64 2.642807 ACACAGGCTACAACCCATACTT 59.357 45.455 0.00 0.00 0.00 2.24
64 65 2.266279 ACACAGGCTACAACCCATACT 58.734 47.619 0.00 0.00 0.00 2.12
65 66 2.781681 ACACAGGCTACAACCCATAC 57.218 50.000 0.00 0.00 0.00 2.39
66 67 4.912317 TTTACACAGGCTACAACCCATA 57.088 40.909 0.00 0.00 0.00 2.74
67 68 3.799432 TTTACACAGGCTACAACCCAT 57.201 42.857 0.00 0.00 0.00 4.00
68 69 3.136809 TCTTTTACACAGGCTACAACCCA 59.863 43.478 0.00 0.00 0.00 4.51
69 70 3.746940 TCTTTTACACAGGCTACAACCC 58.253 45.455 0.00 0.00 0.00 4.11
70 71 4.379499 GCATCTTTTACACAGGCTACAACC 60.379 45.833 0.00 0.00 0.00 3.77
71 72 4.215399 TGCATCTTTTACACAGGCTACAAC 59.785 41.667 0.00 0.00 0.00 3.32
72 73 4.393834 TGCATCTTTTACACAGGCTACAA 58.606 39.130 0.00 0.00 0.00 2.41
73 74 4.014569 TGCATCTTTTACACAGGCTACA 57.985 40.909 0.00 0.00 0.00 2.74
74 75 5.567138 ATTGCATCTTTTACACAGGCTAC 57.433 39.130 0.00 0.00 0.00 3.58
75 76 6.884295 ACTTATTGCATCTTTTACACAGGCTA 59.116 34.615 0.00 0.00 0.00 3.93
76 77 5.711976 ACTTATTGCATCTTTTACACAGGCT 59.288 36.000 0.00 0.00 0.00 4.58
77 78 5.954335 ACTTATTGCATCTTTTACACAGGC 58.046 37.500 0.00 0.00 0.00 4.85
78 79 8.131100 CCATACTTATTGCATCTTTTACACAGG 58.869 37.037 0.00 0.00 0.00 4.00
79 80 8.131100 CCCATACTTATTGCATCTTTTACACAG 58.869 37.037 0.00 0.00 0.00 3.66
80 81 7.613801 ACCCATACTTATTGCATCTTTTACACA 59.386 33.333 0.00 0.00 0.00 3.72
81 82 7.996385 ACCCATACTTATTGCATCTTTTACAC 58.004 34.615 0.00 0.00 0.00 2.90
82 83 8.588290 AACCCATACTTATTGCATCTTTTACA 57.412 30.769 0.00 0.00 0.00 2.41
83 84 9.301153 CAAACCCATACTTATTGCATCTTTTAC 57.699 33.333 0.00 0.00 0.00 2.01
84 85 9.030452 ACAAACCCATACTTATTGCATCTTTTA 57.970 29.630 0.00 0.00 0.00 1.52
85 86 7.906327 ACAAACCCATACTTATTGCATCTTTT 58.094 30.769 0.00 0.00 0.00 2.27
86 87 7.480760 ACAAACCCATACTTATTGCATCTTT 57.519 32.000 0.00 0.00 0.00 2.52
87 88 7.834181 AGTACAAACCCATACTTATTGCATCTT 59.166 33.333 0.00 0.00 0.00 2.40
88 89 7.346471 AGTACAAACCCATACTTATTGCATCT 58.654 34.615 0.00 0.00 0.00 2.90
89 90 7.282224 TGAGTACAAACCCATACTTATTGCATC 59.718 37.037 0.00 0.00 31.69 3.91
90 91 7.116075 TGAGTACAAACCCATACTTATTGCAT 58.884 34.615 0.00 0.00 31.69 3.96
91 92 6.477253 TGAGTACAAACCCATACTTATTGCA 58.523 36.000 0.00 0.00 31.69 4.08
92 93 6.995511 TGAGTACAAACCCATACTTATTGC 57.004 37.500 0.00 0.00 31.69 3.56
99 100 9.581099 CCATAAATTTTGAGTACAAACCCATAC 57.419 33.333 0.00 0.00 44.22 2.39
100 101 8.754080 CCCATAAATTTTGAGTACAAACCCATA 58.246 33.333 0.00 0.00 44.22 2.74
101 102 7.619965 CCCATAAATTTTGAGTACAAACCCAT 58.380 34.615 0.00 0.00 44.22 4.00
102 103 6.519213 GCCCATAAATTTTGAGTACAAACCCA 60.519 38.462 0.00 0.00 44.22 4.51
103 104 5.872617 GCCCATAAATTTTGAGTACAAACCC 59.127 40.000 0.00 0.00 44.22 4.11
104 105 6.697395 AGCCCATAAATTTTGAGTACAAACC 58.303 36.000 0.00 0.00 44.22 3.27
105 106 7.117667 CCAAGCCCATAAATTTTGAGTACAAAC 59.882 37.037 0.00 0.00 44.22 2.93
106 107 7.015682 TCCAAGCCCATAAATTTTGAGTACAAA 59.984 33.333 0.00 0.00 43.10 2.83
107 108 6.495181 TCCAAGCCCATAAATTTTGAGTACAA 59.505 34.615 0.00 0.00 0.00 2.41
108 109 6.013379 TCCAAGCCCATAAATTTTGAGTACA 58.987 36.000 0.00 0.00 0.00 2.90
109 110 6.524101 TCCAAGCCCATAAATTTTGAGTAC 57.476 37.500 0.00 0.00 0.00 2.73
110 111 6.350949 GCTTCCAAGCCCATAAATTTTGAGTA 60.351 38.462 0.00 0.00 46.20 2.59
111 112 5.569428 GCTTCCAAGCCCATAAATTTTGAGT 60.569 40.000 0.00 0.00 46.20 3.41
112 113 4.872124 GCTTCCAAGCCCATAAATTTTGAG 59.128 41.667 0.00 0.00 46.20 3.02
113 114 4.831107 GCTTCCAAGCCCATAAATTTTGA 58.169 39.130 0.00 0.00 46.20 2.69
126 127 5.876087 AAGTTGTTCTTGCGCTTCCAAGC 62.876 47.826 9.73 0.83 41.47 4.01
127 128 1.334869 AGTTGTTCTTGCGCTTCCAAG 59.665 47.619 9.73 3.55 42.73 3.61
128 129 1.388547 AGTTGTTCTTGCGCTTCCAA 58.611 45.000 9.73 1.59 0.00 3.53
129 130 1.065401 CAAGTTGTTCTTGCGCTTCCA 59.935 47.619 9.73 0.00 45.37 3.53
130 131 1.758783 CAAGTTGTTCTTGCGCTTCC 58.241 50.000 9.73 0.00 45.37 3.46
233 234 2.924290 GAGAGTCAGCAACGTTGGATAC 59.076 50.000 28.33 12.51 0.00 2.24
234 235 2.560981 TGAGAGTCAGCAACGTTGGATA 59.439 45.455 28.33 0.00 0.00 2.59
272 276 5.654603 ATAACGTGATGAGTAAGGTGTGA 57.345 39.130 0.00 0.00 0.00 3.58
332 336 7.925993 TGGGCATAATCGTAAATCTTTGTAAG 58.074 34.615 0.00 0.00 0.00 2.34
373 377 1.886542 CCCGAACCCTTGGAAGAAAAG 59.113 52.381 0.00 0.00 0.00 2.27
381 385 2.893682 GATCTGGCCCGAACCCTTGG 62.894 65.000 0.00 0.00 0.00 3.61
388 392 2.368439 CATCAAAAGATCTGGCCCGAA 58.632 47.619 0.00 0.00 0.00 4.30
441 445 5.543507 ATGAGAGAGGCGACTTATGAAAT 57.456 39.130 0.00 0.00 44.43 2.17
442 446 5.105351 TGAATGAGAGAGGCGACTTATGAAA 60.105 40.000 0.00 0.00 44.43 2.69
443 447 4.402474 TGAATGAGAGAGGCGACTTATGAA 59.598 41.667 0.00 0.00 44.43 2.57
444 448 3.954258 TGAATGAGAGAGGCGACTTATGA 59.046 43.478 0.00 0.00 44.43 2.15
450 454 4.545610 CTCTAATGAATGAGAGAGGCGAC 58.454 47.826 0.00 0.00 41.55 5.19
452 456 3.005684 AGCTCTAATGAATGAGAGAGGCG 59.994 47.826 8.64 0.00 41.55 5.52
486 490 8.383175 TGTTGAGTCTTCTAAATTGGTTATCCT 58.617 33.333 0.00 0.00 34.23 3.24
532 567 9.654663 GTTATCTGCCTCTCTCTAGTTTAAAAA 57.345 33.333 0.00 0.00 0.00 1.94
533 568 8.258708 GGTTATCTGCCTCTCTCTAGTTTAAAA 58.741 37.037 0.00 0.00 0.00 1.52
534 569 7.399191 TGGTTATCTGCCTCTCTCTAGTTTAAA 59.601 37.037 0.00 0.00 0.00 1.52
535 570 6.895756 TGGTTATCTGCCTCTCTCTAGTTTAA 59.104 38.462 0.00 0.00 0.00 1.52
536 571 6.432581 TGGTTATCTGCCTCTCTCTAGTTTA 58.567 40.000 0.00 0.00 0.00 2.01
537 572 5.273208 TGGTTATCTGCCTCTCTCTAGTTT 58.727 41.667 0.00 0.00 0.00 2.66
538 573 4.873010 TGGTTATCTGCCTCTCTCTAGTT 58.127 43.478 0.00 0.00 0.00 2.24
539 574 4.528076 TGGTTATCTGCCTCTCTCTAGT 57.472 45.455 0.00 0.00 0.00 2.57
540 575 6.418057 AATTGGTTATCTGCCTCTCTCTAG 57.582 41.667 0.00 0.00 0.00 2.43
541 576 6.814954 AAATTGGTTATCTGCCTCTCTCTA 57.185 37.500 0.00 0.00 0.00 2.43
542 577 5.707066 AAATTGGTTATCTGCCTCTCTCT 57.293 39.130 0.00 0.00 0.00 3.10
543 578 6.821388 TCTAAATTGGTTATCTGCCTCTCTC 58.179 40.000 0.00 0.00 0.00 3.20
544 579 6.814954 TCTAAATTGGTTATCTGCCTCTCT 57.185 37.500 0.00 0.00 0.00 3.10
545 580 7.225734 GTCTTCTAAATTGGTTATCTGCCTCTC 59.774 40.741 0.00 0.00 0.00 3.20
546 581 7.051000 GTCTTCTAAATTGGTTATCTGCCTCT 58.949 38.462 0.00 0.00 0.00 3.69
547 582 7.051000 AGTCTTCTAAATTGGTTATCTGCCTC 58.949 38.462 0.00 0.00 0.00 4.70
548 583 6.963322 AGTCTTCTAAATTGGTTATCTGCCT 58.037 36.000 0.00 0.00 0.00 4.75
549 584 6.823689 TGAGTCTTCTAAATTGGTTATCTGCC 59.176 38.462 0.00 0.00 0.00 4.85
550 585 7.849804 TGAGTCTTCTAAATTGGTTATCTGC 57.150 36.000 0.00 0.00 0.00 4.26
551 586 9.219603 TGTTGAGTCTTCTAAATTGGTTATCTG 57.780 33.333 0.00 0.00 0.00 2.90
552 587 9.793259 TTGTTGAGTCTTCTAAATTGGTTATCT 57.207 29.630 0.00 0.00 0.00 1.98
602 637 2.438800 TAAGCCGCCTCTCTCTAACT 57.561 50.000 0.00 0.00 0.00 2.24
604 639 4.755266 AAAATAAGCCGCCTCTCTCTAA 57.245 40.909 0.00 0.00 0.00 2.10
626 661 3.899726 TGTTGGGCCAGTTTTGTAGTAA 58.100 40.909 6.23 0.00 0.00 2.24
629 664 3.453424 GTTTGTTGGGCCAGTTTTGTAG 58.547 45.455 6.23 0.00 0.00 2.74
630 665 2.168728 GGTTTGTTGGGCCAGTTTTGTA 59.831 45.455 6.23 0.00 0.00 2.41
631 666 1.065782 GGTTTGTTGGGCCAGTTTTGT 60.066 47.619 6.23 0.00 0.00 2.83
632 667 1.065854 TGGTTTGTTGGGCCAGTTTTG 60.066 47.619 6.23 0.00 0.00 2.44
684 727 2.050714 CGTACGTCGCACACACCT 60.051 61.111 7.22 0.00 0.00 4.00
837 888 0.621862 GGGTGGGAGTGGAGAGGATT 60.622 60.000 0.00 0.00 0.00 3.01
838 889 1.003573 GGGTGGGAGTGGAGAGGAT 59.996 63.158 0.00 0.00 0.00 3.24
944 998 2.762234 GGTCGATCGGTCTGTCGCT 61.762 63.158 16.41 0.00 37.74 4.93
949 1003 2.221906 AAACGGGGTCGATCGGTCTG 62.222 60.000 16.41 12.11 40.11 3.51
1125 1179 6.426937 TGGATTAGCCATTTCTTATCTTACGC 59.573 38.462 0.00 0.00 43.33 4.42
1144 1198 5.105554 ACGCCAAATAGCAACAATTGGATTA 60.106 36.000 10.83 0.00 44.01 1.75
1151 1205 2.926159 GCACACGCCAAATAGCAACAAT 60.926 45.455 0.00 0.00 0.00 2.71
1168 1222 2.124736 GGAGGCGGCTTATGCACA 60.125 61.111 14.76 0.00 41.91 4.57
1169 1223 1.748879 TTGGAGGCGGCTTATGCAC 60.749 57.895 14.76 0.00 41.91 4.57
1175 1229 2.125106 GATCGTTGGAGGCGGCTT 60.125 61.111 14.76 0.00 0.00 4.35
1180 1234 0.532573 TGTCAGAGATCGTTGGAGGC 59.467 55.000 0.59 0.00 0.00 4.70
1181 1235 2.167281 ACATGTCAGAGATCGTTGGAGG 59.833 50.000 0.00 0.00 0.00 4.30
1182 1236 3.516981 ACATGTCAGAGATCGTTGGAG 57.483 47.619 0.00 0.00 0.00 3.86
1183 1237 3.961480 AACATGTCAGAGATCGTTGGA 57.039 42.857 0.00 0.00 0.00 3.53
1184 1238 3.425359 GCAAACATGTCAGAGATCGTTGG 60.425 47.826 0.00 0.06 0.00 3.77
1185 1239 3.187022 TGCAAACATGTCAGAGATCGTTG 59.813 43.478 0.00 0.00 0.00 4.10
1186 1240 3.402110 TGCAAACATGTCAGAGATCGTT 58.598 40.909 0.00 0.00 0.00 3.85
1302 1361 1.299541 GATGACCATGTACTTGGCGG 58.700 55.000 23.97 5.08 40.68 6.13
1377 1440 2.106566 GTGAGGGCAGAGATGAGAAGA 58.893 52.381 0.00 0.00 0.00 2.87
1442 1509 1.078759 CCTGCGATCACAGACGGAAC 61.079 60.000 12.38 0.00 40.25 3.62
1668 1742 3.795342 GCGCGGCGGCTAGAAAAA 61.795 61.111 25.03 0.00 36.88 1.94
1681 1755 2.606961 AATCCCATATGCGTGCGCG 61.607 57.895 16.86 16.86 45.51 6.86
1682 1756 1.081906 CAATCCCATATGCGTGCGC 60.082 57.895 9.85 9.85 42.35 6.09
1683 1757 0.041047 CACAATCCCATATGCGTGCG 60.041 55.000 0.00 0.00 0.00 5.34
1684 1758 0.311790 CCACAATCCCATATGCGTGC 59.688 55.000 0.00 0.00 0.00 5.34
1728 1802 3.034635 GACAGGGAGAGAGGCTTAATGA 58.965 50.000 0.00 0.00 0.00 2.57
1729 1803 2.103941 GGACAGGGAGAGAGGCTTAATG 59.896 54.545 0.00 0.00 0.00 1.90
1730 1804 2.403561 GGACAGGGAGAGAGGCTTAAT 58.596 52.381 0.00 0.00 0.00 1.40
1731 1805 1.622725 GGGACAGGGAGAGAGGCTTAA 60.623 57.143 0.00 0.00 0.00 1.85
1735 1809 3.151022 CGGGACAGGGAGAGAGGC 61.151 72.222 0.00 0.00 0.00 4.70
1762 1836 3.456105 GAGGGGTGGTAATCGGCGG 62.456 68.421 7.21 0.00 0.00 6.13
1859 1933 6.349243 TGACCAAAACGATAGGTAGAAGAA 57.651 37.500 0.00 0.00 43.77 2.52
1863 1937 5.878116 CCAAATGACCAAAACGATAGGTAGA 59.122 40.000 0.00 0.00 43.77 2.59
1867 1941 3.761752 ACCCAAATGACCAAAACGATAGG 59.238 43.478 0.00 0.00 43.77 2.57
1868 1942 5.160641 CAACCCAAATGACCAAAACGATAG 58.839 41.667 0.00 0.00 46.19 2.08
1998 2078 3.130633 CAGACCACACGATCAGTTCAAA 58.869 45.455 0.00 0.00 0.00 2.69
1999 2079 2.754472 CAGACCACACGATCAGTTCAA 58.246 47.619 0.00 0.00 0.00 2.69
2000 2080 1.605457 GCAGACCACACGATCAGTTCA 60.605 52.381 0.00 0.00 0.00 3.18
2001 2081 1.071605 GCAGACCACACGATCAGTTC 58.928 55.000 0.00 0.00 0.00 3.01
2002 2082 0.681733 AGCAGACCACACGATCAGTT 59.318 50.000 0.00 0.00 0.00 3.16
2003 2083 0.681733 AAGCAGACCACACGATCAGT 59.318 50.000 0.00 0.00 0.00 3.41
2038 2118 0.898320 GCAGGAGCAGAGTAGGAACA 59.102 55.000 0.00 0.00 41.58 3.18
2094 2177 4.477302 TTTCTTTTCTTCCTTAACCGCG 57.523 40.909 0.00 0.00 0.00 6.46
2102 2185 7.928167 GGTGAATGTCATTTTTCTTTTCTTCCT 59.072 33.333 0.00 0.00 0.00 3.36
2104 2187 8.647143 TGGTGAATGTCATTTTTCTTTTCTTC 57.353 30.769 0.00 0.00 0.00 2.87
2112 2195 7.656948 TGGATTCTTTGGTGAATGTCATTTTTC 59.343 33.333 0.00 0.00 36.86 2.29
2116 2199 5.776716 AGTGGATTCTTTGGTGAATGTCATT 59.223 36.000 0.00 0.00 36.86 2.57
2119 2202 4.761739 TGAGTGGATTCTTTGGTGAATGTC 59.238 41.667 0.00 0.00 36.86 3.06
2120 2203 4.728772 TGAGTGGATTCTTTGGTGAATGT 58.271 39.130 0.00 0.00 36.86 2.71
2121 2204 5.710513 TTGAGTGGATTCTTTGGTGAATG 57.289 39.130 0.00 0.00 36.86 2.67
2122 2205 6.923199 ATTTGAGTGGATTCTTTGGTGAAT 57.077 33.333 0.00 0.00 39.14 2.57
2123 2206 6.729690 AATTTGAGTGGATTCTTTGGTGAA 57.270 33.333 0.00 0.00 0.00 3.18
2124 2207 6.323482 TCAAATTTGAGTGGATTCTTTGGTGA 59.677 34.615 16.91 0.00 32.50 4.02
2126 2209 6.729690 TCAAATTTGAGTGGATTCTTTGGT 57.270 33.333 16.91 0.00 32.50 3.67
2127 2210 6.091713 GCATCAAATTTGAGTGGATTCTTTGG 59.908 38.462 24.17 2.81 41.08 3.28
2128 2211 6.183360 CGCATCAAATTTGAGTGGATTCTTTG 60.183 38.462 24.17 14.72 41.08 2.77
2129 2212 5.865552 CGCATCAAATTTGAGTGGATTCTTT 59.134 36.000 24.17 2.71 41.08 2.52
2181 2267 3.954258 GTCCAACTAAAATGGCTATGGCT 59.046 43.478 0.00 0.00 37.88 4.75
2196 2282 1.003928 GTTCGGTATTGGGGTCCAACT 59.996 52.381 1.05 0.00 46.95 3.16
2217 2303 2.032071 AACTCCTTGCCCCGAACG 59.968 61.111 0.00 0.00 0.00 3.95
2218 2304 1.072505 TGAACTCCTTGCCCCGAAC 59.927 57.895 0.00 0.00 0.00 3.95
2219 2305 1.072505 GTGAACTCCTTGCCCCGAA 59.927 57.895 0.00 0.00 0.00 4.30
2220 2306 2.747686 GTGAACTCCTTGCCCCGA 59.252 61.111 0.00 0.00 0.00 5.14
2221 2307 2.359975 GGTGAACTCCTTGCCCCG 60.360 66.667 0.00 0.00 0.00 5.73
2222 2308 2.035783 GGGTGAACTCCTTGCCCC 59.964 66.667 0.00 0.00 33.40 5.80
2223 2309 2.035783 GGGGTGAACTCCTTGCCC 59.964 66.667 0.00 0.00 38.61 5.36
2224 2310 2.359975 CGGGGTGAACTCCTTGCC 60.360 66.667 0.00 0.00 0.00 4.52
2225 2311 3.056328 GCGGGGTGAACTCCTTGC 61.056 66.667 0.00 0.00 0.00 4.01
2226 2312 1.966451 GTGCGGGGTGAACTCCTTG 60.966 63.158 0.00 0.00 0.00 3.61
2227 2313 2.430367 GTGCGGGGTGAACTCCTT 59.570 61.111 0.00 0.00 0.00 3.36
2228 2314 4.003788 CGTGCGGGGTGAACTCCT 62.004 66.667 0.00 0.00 0.00 3.69
2241 2327 0.511221 ATATTATGGTTCGCGCGTGC 59.489 50.000 30.98 22.17 37.91 5.34
2242 2328 3.366724 ACATATATTATGGTTCGCGCGTG 59.633 43.478 30.98 14.79 0.00 5.34
2244 2330 4.322934 CAACATATATTATGGTTCGCGCG 58.677 43.478 26.76 26.76 0.00 6.86
2245 2331 4.088648 GCAACATATATTATGGTTCGCGC 58.911 43.478 0.00 0.00 0.00 6.86
2247 2333 4.088648 GCGCAACATATATTATGGTTCGC 58.911 43.478 12.35 12.35 34.96 4.70
2248 2334 4.090786 TCGCGCAACATATATTATGGTTCG 59.909 41.667 8.75 1.14 0.00 3.95
2249 2335 5.524511 TCGCGCAACATATATTATGGTTC 57.475 39.130 8.75 0.00 0.00 3.62
2250 2336 5.163764 CCATCGCGCAACATATATTATGGTT 60.164 40.000 8.75 0.00 0.00 3.67
2251 2337 4.332543 CCATCGCGCAACATATATTATGGT 59.667 41.667 8.75 0.00 0.00 3.55
2252 2338 4.786292 GCCATCGCGCAACATATATTATGG 60.786 45.833 8.75 5.92 35.52 2.74
2253 2339 4.274069 GCCATCGCGCAACATATATTATG 58.726 43.478 8.75 0.00 0.00 1.90
2254 2340 3.312421 GGCCATCGCGCAACATATATTAT 59.688 43.478 8.75 0.00 35.02 1.28
2255 2341 2.675844 GGCCATCGCGCAACATATATTA 59.324 45.455 8.75 0.00 35.02 0.98
2256 2342 1.468520 GGCCATCGCGCAACATATATT 59.531 47.619 8.75 0.00 35.02 1.28
2257 2343 1.086696 GGCCATCGCGCAACATATAT 58.913 50.000 8.75 0.00 35.02 0.86
2258 2344 0.034756 AGGCCATCGCGCAACATATA 59.965 50.000 8.75 0.00 35.02 0.86
2259 2345 1.227943 AGGCCATCGCGCAACATAT 60.228 52.632 8.75 0.00 35.02 1.78
2260 2346 1.887242 GAGGCCATCGCGCAACATA 60.887 57.895 8.75 0.00 35.02 2.29
2327 2414 3.261390 CCCACAACATTGGAATCCATGTT 59.739 43.478 18.02 18.02 39.24 2.71
2328 2415 2.833338 CCCACAACATTGGAATCCATGT 59.167 45.455 1.39 7.15 39.24 3.21
2333 2420 0.536724 GGGCCCACAACATTGGAATC 59.463 55.000 19.95 0.00 39.24 2.52
2337 2424 0.471617 TTTTGGGCCCACAACATTGG 59.528 50.000 28.70 0.00 36.26 3.16
2358 2445 0.610232 GTTGGTTGAGGCAGGAGCAT 60.610 55.000 0.00 0.00 44.61 3.79
2365 2452 4.365514 TCTCTATTTGTTGGTTGAGGCA 57.634 40.909 0.00 0.00 0.00 4.75
2371 2458 7.898014 AGGTCTTTTTCTCTATTTGTTGGTT 57.102 32.000 0.00 0.00 0.00 3.67
2372 2459 8.990163 TTAGGTCTTTTTCTCTATTTGTTGGT 57.010 30.769 0.00 0.00 0.00 3.67
2385 2472 7.808381 GGTCTAGTGCATTTTTAGGTCTTTTTC 59.192 37.037 0.00 0.00 0.00 2.29
2507 2600 8.999431 CAAACTTTGTAGCTCTTTGTCCTATTA 58.001 33.333 0.00 0.00 0.00 0.98
2513 2606 6.119144 TGTCAAACTTTGTAGCTCTTTGTC 57.881 37.500 0.00 0.00 0.00 3.18
2519 2612 6.959361 TCTTCAATGTCAAACTTTGTAGCTC 58.041 36.000 0.00 0.00 35.51 4.09


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.