Multiple sequence alignment - TraesCS6D01G302300

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 TraesCS6D01G302300 chr6D 100.000 4475 0 0 1 4475 411618915 411614441 0.000000e+00 8264.0
1 TraesCS6D01G302300 chr6D 85.294 136 17 3 1111 1245 295143179 295143046 2.170000e-28 137.0
2 TraesCS6D01G302300 chr6D 78.212 179 27 10 2536 2710 438802637 438802467 2.200000e-18 104.0
3 TraesCS6D01G302300 chr6A 90.842 2457 133 31 1381 3801 556533562 556531162 0.000000e+00 3206.0
4 TraesCS6D01G302300 chr6A 90.244 697 49 15 3793 4475 556531108 556530417 0.000000e+00 893.0
5 TraesCS6D01G302300 chr6A 83.150 546 61 23 565 1086 556534407 556533869 1.880000e-128 470.0
6 TraesCS6D01G302300 chr6A 88.489 139 16 0 1230 1368 556533837 556533699 7.700000e-38 169.0
7 TraesCS6D01G302300 chr6A 85.950 121 15 2 1111 1231 60987464 60987346 1.310000e-25 128.0
8 TraesCS6D01G302300 chr6A 87.179 117 9 2 392 508 556534646 556534536 1.310000e-25 128.0
9 TraesCS6D01G302300 chr6A 91.892 74 6 0 1921 1994 64260717 64260790 2.200000e-18 104.0
10 TraesCS6D01G302300 chr6A 91.026 78 5 2 246 321 556536475 556536398 2.200000e-18 104.0
11 TraesCS6D01G302300 chr6B 89.909 1209 50 19 1396 2599 618944586 618943445 0.000000e+00 1491.0
12 TraesCS6D01G302300 chr6B 92.998 1014 61 7 2610 3617 618943385 618942376 0.000000e+00 1471.0
13 TraesCS6D01G302300 chr6B 89.396 613 38 13 515 1113 618945302 618944703 0.000000e+00 747.0
14 TraesCS6D01G302300 chr6B 93.095 420 24 4 4057 4475 618940464 618940049 1.060000e-170 610.0
15 TraesCS6D01G302300 chr6B 83.503 394 46 12 4 388 618946210 618945827 2.560000e-92 350.0
16 TraesCS6D01G302300 chr6B 90.625 256 8 7 3793 4037 618942019 618941769 4.320000e-85 326.0
17 TraesCS6D01G302300 chr6B 93.296 179 11 1 3615 3792 618942263 618942085 3.430000e-66 263.0
18 TraesCS6D01G302300 chr6B 92.233 103 6 1 1230 1330 618944689 618944587 1.300000e-30 145.0
19 TraesCS6D01G302300 chr6B 86.029 136 12 3 390 524 618945503 618945374 6.040000e-29 139.0
20 TraesCS6D01G302300 chr6B 91.892 74 6 0 1921 1994 512188517 512188590 2.200000e-18 104.0
21 TraesCS6D01G302300 chr2D 86.300 781 96 8 2802 3580 396670381 396669610 0.000000e+00 839.0
22 TraesCS6D01G302300 chr2D 81.157 605 78 17 3829 4410 396669282 396668691 1.900000e-123 453.0
23 TraesCS6D01G302300 chr2D 79.898 393 65 11 1991 2377 396670946 396670562 4.410000e-70 276.0
24 TraesCS6D01G302300 chr2D 85.714 224 22 5 1489 1711 396671477 396671263 1.250000e-55 228.0
25 TraesCS6D01G302300 chr2D 90.683 161 15 0 1709 1869 396671141 396670981 9.750000e-52 215.0
26 TraesCS6D01G302300 chr2D 83.007 153 23 3 2552 2702 326206914 326206763 7.810000e-28 135.0
27 TraesCS6D01G302300 chr2D 90.566 53 5 0 3744 3796 396669541 396669489 2.230000e-08 71.3
28 TraesCS6D01G302300 chr2D 88.889 54 6 0 2500 2553 140348645 140348698 2.890000e-07 67.6
29 TraesCS6D01G302300 chr2A 86.189 782 97 8 2801 3580 534632541 534631769 0.000000e+00 835.0
30 TraesCS6D01G302300 chr2A 81.157 605 78 17 3829 4410 534631438 534630847 1.900000e-123 453.0
31 TraesCS6D01G302300 chr2A 81.269 331 57 5 2054 2381 534633045 534632717 3.430000e-66 263.0
32 TraesCS6D01G302300 chr2A 89.840 187 16 2 1526 1711 534633606 534633422 2.080000e-58 237.0
33 TraesCS6D01G302300 chr2A 90.683 161 15 0 1709 1869 534633300 534633140 9.750000e-52 215.0
34 TraesCS6D01G302300 chr2A 84.314 153 21 3 2552 2702 391901710 391901861 3.610000e-31 147.0
35 TraesCS6D01G302300 chr2A 92.453 53 4 0 3744 3796 534631700 534631648 4.800000e-10 76.8
36 TraesCS6D01G302300 chr2B 87.064 688 86 2 2805 3492 470066562 470065878 0.000000e+00 774.0
37 TraesCS6D01G302300 chr2B 81.952 543 62 20 3829 4346 470065485 470064954 1.150000e-115 427.0
38 TraesCS6D01G302300 chr2B 79.747 395 69 10 1991 2381 470067131 470066744 4.410000e-70 276.0
39 TraesCS6D01G302300 chr2B 89.305 187 17 2 1526 1711 470067633 470067449 9.680000e-57 231.0
40 TraesCS6D01G302300 chr2B 89.441 161 17 0 1709 1869 470067326 470067166 2.110000e-48 204.0
41 TraesCS6D01G302300 chr2B 84.028 144 20 3 2561 2702 395532872 395532730 7.810000e-28 135.0
42 TraesCS6D01G302300 chr2B 91.667 72 6 0 1921 1992 754008463 754008534 2.850000e-17 100.0
43 TraesCS6D01G302300 chr2B 87.500 72 6 2 3725 3796 470065765 470065697 3.710000e-11 80.5
44 TraesCS6D01G302300 chr7B 87.023 131 13 4 1117 1245 627977368 627977240 1.300000e-30 145.0
45 TraesCS6D01G302300 chr1D 86.029 136 17 2 1111 1245 95876311 95876445 1.300000e-30 145.0
46 TraesCS6D01G302300 chr1D 87.603 121 14 1 1111 1231 437905814 437905695 6.040000e-29 139.0
47 TraesCS6D01G302300 chr1D 85.401 137 17 3 1110 1245 470591752 470591618 6.040000e-29 139.0
48 TraesCS6D01G302300 chr1D 92.958 71 5 0 1921 1991 320590018 320589948 2.200000e-18 104.0
49 TraesCS6D01G302300 chr1D 87.805 82 9 1 1923 2003 319515818 319515737 1.330000e-15 95.3
50 TraesCS6D01G302300 chr7D 86.400 125 15 2 1107 1231 591456899 591456777 7.810000e-28 135.0
51 TraesCS6D01G302300 chr7D 83.942 137 17 4 1111 1245 562201650 562201783 4.700000e-25 126.0
52 TraesCS6D01G302300 chr7D 79.769 173 26 7 2552 2719 550977022 550977190 2.830000e-22 117.0
53 TraesCS6D01G302300 chr1B 83.824 136 19 3 1111 1245 634251274 634251407 4.700000e-25 126.0
54 TraesCS6D01G302300 chr5A 80.795 151 26 3 2553 2701 110379744 110379595 1.020000e-21 115.0
55 TraesCS6D01G302300 chr5B 81.119 143 26 1 2563 2704 648746401 648746543 3.660000e-21 113.0
56 TraesCS6D01G302300 chr4D 90.278 72 7 0 1921 1992 230473093 230473164 1.330000e-15 95.3
57 TraesCS6D01G302300 chr4A 90.278 72 7 0 1923 1994 567678325 567678254 1.330000e-15 95.3


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 TraesCS6D01G302300 chr6D 411614441 411618915 4474 True 8264.000000 8264 100.000000 1 4475 1 chr6D.!!$R2 4474
1 TraesCS6D01G302300 chr6A 556530417 556536475 6058 True 828.333333 3206 88.488333 246 4475 6 chr6A.!!$R2 4229
2 TraesCS6D01G302300 chr6B 618940049 618946210 6161 True 615.777778 1491 90.120444 4 4475 9 chr6B.!!$R1 4471
3 TraesCS6D01G302300 chr2D 396668691 396671477 2786 True 347.050000 839 85.719667 1489 4410 6 chr2D.!!$R2 2921
4 TraesCS6D01G302300 chr2A 534630847 534633606 2759 True 346.633333 835 86.931833 1526 4410 6 chr2A.!!$R1 2884
5 TraesCS6D01G302300 chr2B 470064954 470067633 2679 True 332.083333 774 85.834833 1526 4346 6 chr2B.!!$R2 2820

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
511 2198 0.028242 CGAGGAATCCACTCTCGTCG 59.972 60.0 0.61 0.0 43.51 5.12 F
585 2384 0.096976 CGCCCAACATAAGTCGCAAG 59.903 55.0 0.00 0.0 0.00 4.01 F
586 2385 0.179163 GCCCAACATAAGTCGCAAGC 60.179 55.0 0.00 0.0 37.18 4.01 F
596 2395 0.251354 AGTCGCAAGCCATCACTCAT 59.749 50.0 0.00 0.0 37.18 2.90 F
622 2421 0.533032 GACTCAGACCTACAGCACCC 59.467 60.0 0.00 0.0 0.00 4.61 F
1346 3207 0.586319 TTTTGCTGCTTTCCTCGTCG 59.414 50.0 0.00 0.0 0.00 5.12 F
3105 5321 0.036010 AGGCATCAGACTCAAACCCG 60.036 55.0 0.00 0.0 0.00 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1332 3193 0.241213 TGAGTCGACGAGGAAAGCAG 59.759 55.000 10.46 0.0 0.00 4.24 R
1706 3709 0.613777 CAGGAGTGTCCTTGTACCCC 59.386 60.000 0.00 0.0 46.91 4.95 R
2183 4319 0.879765 CTGAAAAGCTGCACAGGGAG 59.120 55.000 1.02 0.0 35.23 4.30 R
2398 4534 0.881118 GCGCAAAATGTCAGAAGGGA 59.119 50.000 0.30 0.0 0.00 4.20 R
2402 4538 1.603456 TGGAGCGCAAAATGTCAGAA 58.397 45.000 11.47 0.0 0.00 3.02 R
3195 5411 0.319555 GCGGGGTTTCAAGCTTTTCC 60.320 55.000 0.00 0.0 0.00 3.13 R
4086 7920 2.095110 TCATTCCAAAGCGTGATTGCAG 60.095 45.455 0.00 0.0 37.31 4.41 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
24 25 7.703058 GGAGATGGAAAACAATTAGGAGAAA 57.297 36.000 0.00 0.00 0.00 2.52
32 33 5.443230 AACAATTAGGAGAAAGAGAGGGG 57.557 43.478 0.00 0.00 0.00 4.79
34 35 2.642171 TTAGGAGAAAGAGAGGGGCA 57.358 50.000 0.00 0.00 0.00 5.36
40 41 0.951040 GAAAGAGAGGGGCACGTGTG 60.951 60.000 18.38 0.00 0.00 3.82
81 83 5.478679 CGATGATAAGGAGGAGAGGTACAAT 59.521 44.000 0.00 0.00 0.00 2.71
97 99 2.996631 ACAATCTCCTCTTGGATGTGC 58.003 47.619 0.00 0.00 42.29 4.57
107 109 4.515361 CTCTTGGATGTGCAAAGAGAGAT 58.485 43.478 16.74 0.00 46.46 2.75
117 119 7.750229 TGTGCAAAGAGAGATGATAAAGTTT 57.250 32.000 0.00 0.00 0.00 2.66
121 123 9.017509 TGCAAAGAGAGATGATAAAGTTTGATT 57.982 29.630 0.00 0.00 0.00 2.57
149 152 6.540438 AAAAGTACGGAGAGGTTCATGATA 57.460 37.500 0.00 0.00 0.00 2.15
150 153 5.776173 AAGTACGGAGAGGTTCATGATAG 57.224 43.478 0.00 0.00 0.00 2.08
160 163 6.537355 AGAGGTTCATGATAGAGAGAGAGAG 58.463 44.000 0.00 0.00 0.00 3.20
162 165 6.537355 AGGTTCATGATAGAGAGAGAGAGAG 58.463 44.000 0.00 0.00 0.00 3.20
163 166 6.329986 AGGTTCATGATAGAGAGAGAGAGAGA 59.670 42.308 0.00 0.00 0.00 3.10
166 169 7.237209 TCATGATAGAGAGAGAGAGAGAGAG 57.763 44.000 0.00 0.00 0.00 3.20
170 173 7.244558 TGATAGAGAGAGAGAGAGAGAGAGAT 58.755 42.308 0.00 0.00 0.00 2.75
171 174 5.804944 AGAGAGAGAGAGAGAGAGAGATG 57.195 47.826 0.00 0.00 0.00 2.90
181 184 4.493547 AGAGAGAGAGATGTGAAAAAGCG 58.506 43.478 0.00 0.00 0.00 4.68
198 201 9.180678 TGAAAAAGCGAGAGAAATATGAAAAAC 57.819 29.630 0.00 0.00 0.00 2.43
201 204 7.440523 AAGCGAGAGAAATATGAAAAACAGT 57.559 32.000 0.00 0.00 0.00 3.55
228 231 3.005684 TGAAAAGGCGAAGACAATGCAAT 59.994 39.130 0.00 0.00 39.87 3.56
229 232 4.217334 TGAAAAGGCGAAGACAATGCAATA 59.783 37.500 0.00 0.00 39.87 1.90
230 233 4.782019 AAAGGCGAAGACAATGCAATAA 57.218 36.364 0.00 0.00 39.87 1.40
231 234 4.782019 AAGGCGAAGACAATGCAATAAA 57.218 36.364 0.00 0.00 39.87 1.40
232 235 4.989279 AGGCGAAGACAATGCAATAAAT 57.011 36.364 0.00 0.00 39.87 1.40
233 236 5.329035 AGGCGAAGACAATGCAATAAATT 57.671 34.783 0.00 0.00 39.87 1.82
234 237 5.104374 AGGCGAAGACAATGCAATAAATTG 58.896 37.500 0.00 0.00 39.87 2.32
235 238 5.101628 GGCGAAGACAATGCAATAAATTGA 58.898 37.500 6.87 0.00 38.21 2.57
236 239 5.576384 GGCGAAGACAATGCAATAAATTGAA 59.424 36.000 6.87 0.00 38.21 2.69
237 240 6.454186 GGCGAAGACAATGCAATAAATTGAAC 60.454 38.462 6.87 0.00 38.21 3.18
238 241 6.308766 GCGAAGACAATGCAATAAATTGAACT 59.691 34.615 6.87 1.15 40.14 3.01
243 246 7.119699 AGACAATGCAATAAATTGAACTCGAGA 59.880 33.333 21.68 0.00 40.14 4.04
244 247 7.246311 ACAATGCAATAAATTGAACTCGAGAG 58.754 34.615 21.68 0.00 40.14 3.20
358 526 0.233848 CACGAGTGTTAAACCCACGC 59.766 55.000 0.00 0.00 37.88 5.34
359 527 0.179078 ACGAGTGTTAAACCCACGCA 60.179 50.000 0.00 0.00 37.88 5.24
385 558 3.195698 GTGGCGGAATCTGGCGAC 61.196 66.667 11.10 6.78 34.03 5.19
474 2161 4.740822 GCCCGGCCCAACACTGAT 62.741 66.667 0.00 0.00 0.00 2.90
511 2198 0.028242 CGAGGAATCCACTCTCGTCG 59.972 60.000 0.61 0.00 43.51 5.12
513 2200 1.743958 GAGGAATCCACTCTCGTCGAA 59.256 52.381 0.61 0.00 32.28 3.71
585 2384 0.096976 CGCCCAACATAAGTCGCAAG 59.903 55.000 0.00 0.00 0.00 4.01
586 2385 0.179163 GCCCAACATAAGTCGCAAGC 60.179 55.000 0.00 0.00 37.18 4.01
588 2387 1.164411 CCAACATAAGTCGCAAGCCA 58.836 50.000 0.00 0.00 37.18 4.75
589 2388 1.745087 CCAACATAAGTCGCAAGCCAT 59.255 47.619 0.00 0.00 37.18 4.40
590 2389 2.223340 CCAACATAAGTCGCAAGCCATC 60.223 50.000 0.00 0.00 37.18 3.51
592 2391 2.009774 ACATAAGTCGCAAGCCATCAC 58.990 47.619 0.00 0.00 37.18 3.06
593 2392 2.283298 CATAAGTCGCAAGCCATCACT 58.717 47.619 0.00 0.00 37.18 3.41
596 2395 0.251354 AGTCGCAAGCCATCACTCAT 59.749 50.000 0.00 0.00 37.18 2.90
622 2421 0.533032 GACTCAGACCTACAGCACCC 59.467 60.000 0.00 0.00 0.00 4.61
690 2490 1.726853 ATGCAGAGCGTTAGTGGTTC 58.273 50.000 0.00 0.00 0.00 3.62
693 2493 1.997669 CAGAGCGTTAGTGGTTCTCC 58.002 55.000 0.00 0.00 0.00 3.71
706 2506 4.819761 TCTCCGTGCTGCATCGGC 62.820 66.667 27.32 8.05 45.44 5.54
766 2567 2.498726 CCGCTGGCCTTCTCTCTC 59.501 66.667 3.32 0.00 0.00 3.20
767 2568 2.057408 CCGCTGGCCTTCTCTCTCT 61.057 63.158 3.32 0.00 0.00 3.10
768 2569 1.437160 CGCTGGCCTTCTCTCTCTC 59.563 63.158 3.32 0.00 0.00 3.20
769 2570 1.037030 CGCTGGCCTTCTCTCTCTCT 61.037 60.000 3.32 0.00 0.00 3.10
770 2571 0.746659 GCTGGCCTTCTCTCTCTCTC 59.253 60.000 3.32 0.00 0.00 3.20
771 2572 1.686115 GCTGGCCTTCTCTCTCTCTCT 60.686 57.143 3.32 0.00 0.00 3.10
772 2573 2.301346 CTGGCCTTCTCTCTCTCTCTC 58.699 57.143 3.32 0.00 0.00 3.20
773 2574 1.922447 TGGCCTTCTCTCTCTCTCTCT 59.078 52.381 3.32 0.00 0.00 3.10
774 2575 2.092429 TGGCCTTCTCTCTCTCTCTCTC 60.092 54.545 3.32 0.00 0.00 3.20
775 2576 2.173569 GGCCTTCTCTCTCTCTCTCTCT 59.826 54.545 0.00 0.00 0.00 3.10
776 2577 3.471680 GCCTTCTCTCTCTCTCTCTCTC 58.528 54.545 0.00 0.00 0.00 3.20
789 2590 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
790 2591 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
893 2738 3.943671 TTGACTTTGGTTTCTCTCCCA 57.056 42.857 0.00 0.00 0.00 4.37
906 2751 6.289064 GTTTCTCTCCCAAGTTCTTACAAGA 58.711 40.000 0.00 0.00 0.00 3.02
919 2764 2.656947 TACAAGAAGGGCAGCTTTGT 57.343 45.000 3.42 3.42 0.00 2.83
927 2772 1.557832 AGGGCAGCTTTGTCGGTATAA 59.442 47.619 0.00 0.00 0.00 0.98
1103 2962 1.137825 CGCCCAGTCTCTCTCGTTC 59.862 63.158 0.00 0.00 0.00 3.95
1113 2972 3.510753 GTCTCTCTCGTTCCCCTTTTACT 59.489 47.826 0.00 0.00 0.00 2.24
1114 2973 3.762823 TCTCTCTCGTTCCCCTTTTACTC 59.237 47.826 0.00 0.00 0.00 2.59
1115 2974 2.490903 TCTCTCGTTCCCCTTTTACTCG 59.509 50.000 0.00 0.00 0.00 4.18
1116 2975 1.067354 TCTCGTTCCCCTTTTACTCGC 60.067 52.381 0.00 0.00 0.00 5.03
1117 2976 0.971386 TCGTTCCCCTTTTACTCGCT 59.029 50.000 0.00 0.00 0.00 4.93
1118 2977 1.067354 TCGTTCCCCTTTTACTCGCTC 60.067 52.381 0.00 0.00 0.00 5.03
1119 2978 1.735386 GTTCCCCTTTTACTCGCTCC 58.265 55.000 0.00 0.00 0.00 4.70
1121 2980 0.901580 TCCCCTTTTACTCGCTCCGT 60.902 55.000 0.00 0.00 0.00 4.69
1124 2983 1.730612 CCCTTTTACTCGCTCCGTTTC 59.269 52.381 0.00 0.00 0.00 2.78
1126 2985 3.367703 CCCTTTTACTCGCTCCGTTTCTA 60.368 47.826 0.00 0.00 0.00 2.10
1127 2986 4.240096 CCTTTTACTCGCTCCGTTTCTAA 58.760 43.478 0.00 0.00 0.00 2.10
1128 2987 4.687483 CCTTTTACTCGCTCCGTTTCTAAA 59.313 41.667 0.00 0.00 0.00 1.85
1129 2988 5.350640 CCTTTTACTCGCTCCGTTTCTAAAT 59.649 40.000 0.00 0.00 0.00 1.40
1130 2989 6.532657 CCTTTTACTCGCTCCGTTTCTAAATA 59.467 38.462 0.00 0.00 0.00 1.40
1131 2990 7.224167 CCTTTTACTCGCTCCGTTTCTAAATAT 59.776 37.037 0.00 0.00 0.00 1.28
1132 2991 9.241317 CTTTTACTCGCTCCGTTTCTAAATATA 57.759 33.333 0.00 0.00 0.00 0.86
1133 2992 9.585099 TTTTACTCGCTCCGTTTCTAAATATAA 57.415 29.630 0.00 0.00 0.00 0.98
1134 2993 8.792831 TTACTCGCTCCGTTTCTAAATATAAG 57.207 34.615 0.00 0.00 0.00 1.73
1135 2994 6.803642 ACTCGCTCCGTTTCTAAATATAAGT 58.196 36.000 0.00 0.00 0.00 2.24
1136 2995 6.916932 ACTCGCTCCGTTTCTAAATATAAGTC 59.083 38.462 0.00 0.00 0.00 3.01
1137 2996 6.798482 TCGCTCCGTTTCTAAATATAAGTCA 58.202 36.000 0.00 0.00 0.00 3.41
1138 2997 7.431249 TCGCTCCGTTTCTAAATATAAGTCAT 58.569 34.615 0.00 0.00 0.00 3.06
1139 2998 7.924412 TCGCTCCGTTTCTAAATATAAGTCATT 59.076 33.333 0.00 0.00 0.00 2.57
1140 2999 8.548721 CGCTCCGTTTCTAAATATAAGTCATTT 58.451 33.333 0.00 0.00 0.00 2.32
1192 3051 9.567848 ACGGAATAAAATGAATGAAATGTACAC 57.432 29.630 0.00 0.00 0.00 2.90
1193 3052 9.787532 CGGAATAAAATGAATGAAATGTACACT 57.212 29.630 0.00 0.00 0.00 3.55
1237 3096 7.817962 ACATTTGTATGTAGTCTGTACTGAACC 59.182 37.037 3.77 0.00 43.12 3.62
1264 3125 0.843309 TTCAACTCAGTTGGGCTGGA 59.157 50.000 17.71 0.00 45.08 3.86
1274 3135 2.045926 GGGCTGGACTGTCGCAAT 60.046 61.111 9.37 0.00 0.00 3.56
1332 3193 6.703165 AGAGATGTTTCAATCCAAAGTTTTGC 59.297 34.615 0.00 0.00 36.86 3.68
1335 3196 4.332268 TGTTTCAATCCAAAGTTTTGCTGC 59.668 37.500 0.00 0.00 36.86 5.25
1346 3207 0.586319 TTTTGCTGCTTTCCTCGTCG 59.414 50.000 0.00 0.00 0.00 5.12
1356 3217 3.575630 CTTTCCTCGTCGACTCAAATCA 58.424 45.455 14.70 0.00 0.00 2.57
1361 3222 2.530177 TCGTCGACTCAAATCATCTGC 58.470 47.619 14.70 0.00 0.00 4.26
1368 3229 3.362706 ACTCAAATCATCTGCCATTGCT 58.637 40.909 0.00 0.00 38.71 3.91
1369 3230 3.380637 ACTCAAATCATCTGCCATTGCTC 59.619 43.478 0.00 0.00 38.71 4.26
1370 3231 3.358118 TCAAATCATCTGCCATTGCTCA 58.642 40.909 0.00 0.00 38.71 4.26
1371 3232 3.129813 TCAAATCATCTGCCATTGCTCAC 59.870 43.478 0.00 0.00 38.71 3.51
1372 3233 2.430248 ATCATCTGCCATTGCTCACA 57.570 45.000 0.00 0.00 38.71 3.58
1373 3234 2.203470 TCATCTGCCATTGCTCACAA 57.797 45.000 0.00 0.00 40.87 3.33
1375 3236 1.816835 CATCTGCCATTGCTCACAACT 59.183 47.619 0.00 0.00 38.99 3.16
1376 3237 1.985473 TCTGCCATTGCTCACAACTT 58.015 45.000 0.00 0.00 38.99 2.66
1377 3238 1.881973 TCTGCCATTGCTCACAACTTC 59.118 47.619 0.00 0.00 38.99 3.01
1378 3239 1.884579 CTGCCATTGCTCACAACTTCT 59.115 47.619 0.00 0.00 38.99 2.85
1379 3240 1.881973 TGCCATTGCTCACAACTTCTC 59.118 47.619 0.00 0.00 38.99 2.87
1384 3369 4.629200 CCATTGCTCACAACTTCTCTAGAC 59.371 45.833 0.00 0.00 38.99 2.59
1390 3375 5.968848 GCTCACAACTTCTCTAGACGATTAG 59.031 44.000 0.00 0.00 0.00 1.73
1515 3502 5.640189 ATGAATTCTGCCACTCTTCTTTG 57.360 39.130 7.05 0.00 0.00 2.77
1622 3625 3.562635 GGAAACGTTCCTCAGCCG 58.437 61.111 0.00 0.00 46.57 5.52
1706 3709 2.224137 TGGAGTTTCAGACACTGCTCAG 60.224 50.000 9.39 0.00 33.90 3.35
1839 3967 5.604758 TGTAGGAAGAGTCTCCAATCATG 57.395 43.478 10.19 0.00 38.02 3.07
1869 3997 7.332182 AGTTTACTAACTCTGACATAAGCTTGC 59.668 37.037 9.86 0.00 40.60 4.01
1889 4017 6.127619 GCTTGCCCTCAAACTAAACTTGATAT 60.128 38.462 0.00 0.00 32.53 1.63
1921 4052 8.803397 AATTACTACCTCTGTACCAAAAATCC 57.197 34.615 0.00 0.00 0.00 3.01
1922 4053 5.836024 ACTACCTCTGTACCAAAAATCCA 57.164 39.130 0.00 0.00 0.00 3.41
1989 4120 1.734163 ACATTTTTCTACGGAGGGCG 58.266 50.000 0.00 0.00 0.00 6.13
2012 4144 0.603707 TCACAAGCAAGAAGGCCTCG 60.604 55.000 5.23 0.00 0.00 4.63
2022 4154 5.885912 AGCAAGAAGGCCTCGAATTTATTTA 59.114 36.000 5.23 0.00 0.00 1.40
2075 4208 7.821595 TTACATTCTGTACAATTACTCACCG 57.178 36.000 0.00 0.00 31.69 4.94
2166 4302 8.338259 CACTCCAATAATCCTGTTTCTATTTCG 58.662 37.037 0.00 0.00 0.00 3.46
2183 4319 3.781341 TTCGCTAACACATGTTCGTTC 57.219 42.857 4.93 0.00 39.31 3.95
2394 4530 6.017934 CCGGTAAGTTCCAATATTCTGACATG 60.018 42.308 0.00 0.00 0.00 3.21
2395 4531 6.761242 CGGTAAGTTCCAATATTCTGACATGA 59.239 38.462 0.00 0.00 0.00 3.07
2396 4532 7.042456 CGGTAAGTTCCAATATTCTGACATGAG 60.042 40.741 0.00 0.00 0.00 2.90
2398 4534 9.553064 GTAAGTTCCAATATTCTGACATGAGAT 57.447 33.333 0.00 0.00 0.00 2.75
2402 4538 5.848369 TCCAATATTCTGACATGAGATCCCT 59.152 40.000 0.00 0.00 0.00 4.20
2403 4539 6.331042 TCCAATATTCTGACATGAGATCCCTT 59.669 38.462 0.00 0.00 0.00 3.95
2738 4946 7.690454 TGAAAATGGATGGAGTATTAGGAGA 57.310 36.000 0.00 0.00 0.00 3.71
2750 4958 9.177608 TGGAGTATTAGGAGAAAAATCAACATG 57.822 33.333 0.00 0.00 0.00 3.21
2795 5011 5.004448 TGTCAAGTGTCTAACAACCAACAA 58.996 37.500 0.00 0.00 0.00 2.83
2796 5012 5.123186 TGTCAAGTGTCTAACAACCAACAAG 59.877 40.000 0.00 0.00 0.00 3.16
2797 5013 5.123344 GTCAAGTGTCTAACAACCAACAAGT 59.877 40.000 0.00 0.00 0.00 3.16
2847 5063 5.011227 GTCTTGACTACTCCTGAAGGAAAGT 59.989 44.000 11.87 11.87 44.91 2.66
2907 5123 3.192922 GGCGTCGAAATCCACGGG 61.193 66.667 0.00 0.00 36.50 5.28
3042 5258 2.289002 CGTAGCTGATGAAATTGGAGCC 59.711 50.000 0.00 0.00 0.00 4.70
3084 5300 2.858745 TCACCCTTTGCAAGTTACTCC 58.141 47.619 0.00 0.00 0.00 3.85
3105 5321 0.036010 AGGCATCAGACTCAAACCCG 60.036 55.000 0.00 0.00 0.00 5.28
3351 5567 2.288518 TGGGCGCTTGTTTTTATCCAAC 60.289 45.455 7.64 0.00 0.00 3.77
3471 5687 1.401552 CCGTTTCTACCGTCCGATGTA 59.598 52.381 0.00 0.00 0.00 2.29
3535 5751 8.916654 CATCAGATCATTTACCTTACGTATCAC 58.083 37.037 0.00 0.00 0.00 3.06
3545 5763 8.692110 TTACCTTACGTATCACAACTATGTTG 57.308 34.615 8.66 8.66 37.82 3.33
3577 5795 5.874093 AGGTCATTGATTTCTTCTCACTGT 58.126 37.500 0.00 0.00 0.00 3.55
3578 5796 5.704515 AGGTCATTGATTTCTTCTCACTGTG 59.295 40.000 0.17 0.17 0.00 3.66
3600 5818 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3607 5825 0.167908 GTGTGTGTGTGTGTGTGTGG 59.832 55.000 0.00 0.00 0.00 4.17
3640 5973 4.937620 TGCTGGATCAACACTTTGTATCTC 59.062 41.667 0.00 0.00 34.02 2.75
3694 6027 0.817634 CAGCCTTTGGGTTGACACGA 60.818 55.000 0.00 0.00 45.06 4.35
3712 6045 4.330894 ACACGAATTGCATCTGTGATGTAG 59.669 41.667 13.62 0.00 34.72 2.74
3793 6139 7.305474 CCACACACTCAATACTTAAATTGGTC 58.695 38.462 1.08 0.00 37.44 4.02
3818 6231 8.729756 TCCACATAATCAGTACAAGTTTGATTG 58.270 33.333 14.37 5.36 40.63 2.67
3965 6505 7.849804 TTAGATCTAAATTTCACTGGTCAGC 57.150 36.000 12.87 0.00 0.00 4.26
4037 6584 8.424133 ACTTTGCTGTCCTTCAAATTCTTTAAT 58.576 29.630 0.00 0.00 32.51 1.40
4038 6585 9.264719 CTTTGCTGTCCTTCAAATTCTTTAATT 57.735 29.630 0.00 0.00 36.87 1.40
4041 6588 8.641541 TGCTGTCCTTCAAATTCTTTAATTCTT 58.358 29.630 0.00 0.00 34.12 2.52
4079 7913 5.873164 GGGACTCTCAAGCTTATCGTAAAAA 59.127 40.000 0.00 0.00 0.00 1.94
4152 7986 3.674997 TGTCTCAAGTAAATGTCAGGCC 58.325 45.455 0.00 0.00 0.00 5.19
4157 7991 3.091545 CAAGTAAATGTCAGGCCCACAT 58.908 45.455 11.46 11.46 35.94 3.21
4158 7992 2.726821 AGTAAATGTCAGGCCCACATG 58.273 47.619 16.82 0.94 34.59 3.21
4164 7998 1.354031 TGTCAGGCCCACATGTTACAT 59.646 47.619 0.00 0.00 0.00 2.29
4372 8219 8.542132 CGAATTATCGCCATCAAATTCATTTTT 58.458 29.630 7.25 0.00 42.96 1.94
4401 8248 8.627208 ACAATGTATCATGTTCAAAGAAGAGT 57.373 30.769 0.00 0.00 0.00 3.24
4451 8298 6.856895 ACAAAGCCTAATAGCTGATCAAAAC 58.143 36.000 0.00 0.00 44.11 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.567285 TCTTTCTCCTAATTGTTTTCCATCTC 57.433 34.615 0.00 0.00 0.00 2.75
2 3 8.386264 TCTCTTTCTCCTAATTGTTTTCCATCT 58.614 33.333 0.00 0.00 0.00 2.90
4 5 7.613411 CCTCTCTTTCTCCTAATTGTTTTCCAT 59.387 37.037 0.00 0.00 0.00 3.41
5 6 6.942576 CCTCTCTTTCTCCTAATTGTTTTCCA 59.057 38.462 0.00 0.00 0.00 3.53
6 7 6.375736 CCCTCTCTTTCTCCTAATTGTTTTCC 59.624 42.308 0.00 0.00 0.00 3.13
7 8 6.375736 CCCCTCTCTTTCTCCTAATTGTTTTC 59.624 42.308 0.00 0.00 0.00 2.29
9 10 5.808050 GCCCCTCTCTTTCTCCTAATTGTTT 60.808 44.000 0.00 0.00 0.00 2.83
13 14 3.201045 GTGCCCCTCTCTTTCTCCTAATT 59.799 47.826 0.00 0.00 0.00 1.40
14 15 2.774809 GTGCCCCTCTCTTTCTCCTAAT 59.225 50.000 0.00 0.00 0.00 1.73
15 16 2.188817 GTGCCCCTCTCTTTCTCCTAA 58.811 52.381 0.00 0.00 0.00 2.69
16 17 1.867363 GTGCCCCTCTCTTTCTCCTA 58.133 55.000 0.00 0.00 0.00 2.94
17 18 1.261238 CGTGCCCCTCTCTTTCTCCT 61.261 60.000 0.00 0.00 0.00 3.69
18 19 1.219393 CGTGCCCCTCTCTTTCTCC 59.781 63.158 0.00 0.00 0.00 3.71
24 25 2.203640 TCACACGTGCCCCTCTCT 60.204 61.111 17.22 0.00 0.00 3.10
32 33 0.306533 AAAATGTCCGTCACACGTGC 59.693 50.000 17.22 0.00 40.58 5.34
54 55 2.560542 CCTCTCCTCCTTATCATCGGTG 59.439 54.545 0.00 0.00 0.00 4.94
55 56 2.178106 ACCTCTCCTCCTTATCATCGGT 59.822 50.000 0.00 0.00 0.00 4.69
56 57 2.883026 ACCTCTCCTCCTTATCATCGG 58.117 52.381 0.00 0.00 0.00 4.18
58 59 6.723977 AGATTGTACCTCTCCTCCTTATCATC 59.276 42.308 0.00 0.00 0.00 2.92
60 61 6.031964 AGATTGTACCTCTCCTCCTTATCA 57.968 41.667 0.00 0.00 0.00 2.15
85 87 3.935315 TCTCTCTTTGCACATCCAAGAG 58.065 45.455 15.90 15.90 0.00 2.85
129 131 5.050126 TCTATCATGAACCTCTCCGTACT 57.950 43.478 0.00 0.00 0.00 2.73
149 152 5.070180 CACATCTCTCTCTCTCTCTCTCTCT 59.930 48.000 0.00 0.00 0.00 3.10
150 153 5.069648 TCACATCTCTCTCTCTCTCTCTCTC 59.930 48.000 0.00 0.00 0.00 3.20
160 163 4.489810 TCGCTTTTTCACATCTCTCTCTC 58.510 43.478 0.00 0.00 0.00 3.20
162 165 4.489810 TCTCGCTTTTTCACATCTCTCTC 58.510 43.478 0.00 0.00 0.00 3.20
163 166 4.219507 TCTCTCGCTTTTTCACATCTCTCT 59.780 41.667 0.00 0.00 0.00 3.10
166 169 5.597813 TTTCTCTCGCTTTTTCACATCTC 57.402 39.130 0.00 0.00 0.00 2.75
170 173 7.433708 TTCATATTTCTCTCGCTTTTTCACA 57.566 32.000 0.00 0.00 0.00 3.58
171 174 8.728088 TTTTCATATTTCTCTCGCTTTTTCAC 57.272 30.769 0.00 0.00 0.00 3.18
198 201 5.757886 TGTCTTCGCCTTTTCAATTTACTG 58.242 37.500 0.00 0.00 0.00 2.74
201 204 5.633182 GCATTGTCTTCGCCTTTTCAATTTA 59.367 36.000 0.00 0.00 0.00 1.40
228 231 5.856986 CGTGTTCTCTCTCGAGTTCAATTTA 59.143 40.000 13.13 0.00 38.45 1.40
229 232 4.681942 CGTGTTCTCTCTCGAGTTCAATTT 59.318 41.667 13.13 0.00 38.45 1.82
230 233 4.023107 TCGTGTTCTCTCTCGAGTTCAATT 60.023 41.667 13.13 0.00 38.45 2.32
231 234 3.502595 TCGTGTTCTCTCTCGAGTTCAAT 59.497 43.478 13.13 0.00 38.45 2.57
232 235 2.876550 TCGTGTTCTCTCTCGAGTTCAA 59.123 45.455 13.13 0.00 38.45 2.69
233 236 2.223611 GTCGTGTTCTCTCTCGAGTTCA 59.776 50.000 13.13 1.63 38.45 3.18
234 237 2.722403 CGTCGTGTTCTCTCTCGAGTTC 60.722 54.545 13.13 0.00 38.45 3.01
235 238 1.194997 CGTCGTGTTCTCTCTCGAGTT 59.805 52.381 13.13 0.00 38.45 3.01
236 239 0.791422 CGTCGTGTTCTCTCTCGAGT 59.209 55.000 13.13 0.00 38.45 4.18
237 240 0.519586 GCGTCGTGTTCTCTCTCGAG 60.520 60.000 5.93 5.93 38.67 4.04
238 241 0.949588 AGCGTCGTGTTCTCTCTCGA 60.950 55.000 0.00 0.00 0.00 4.04
243 246 0.961358 AGGCTAGCGTCGTGTTCTCT 60.961 55.000 9.00 0.00 0.00 3.10
244 247 0.109226 AAGGCTAGCGTCGTGTTCTC 60.109 55.000 10.89 0.00 0.00 2.87
358 526 1.455786 GATTCCGCCACGATCGTATTG 59.544 52.381 22.26 13.39 0.00 1.90
359 527 1.340248 AGATTCCGCCACGATCGTATT 59.660 47.619 22.26 0.97 0.00 1.89
425 2111 2.344203 CGGGCCACTCTTCGTCTCT 61.344 63.158 4.39 0.00 0.00 3.10
427 2113 4.070552 GCGGGCCACTCTTCGTCT 62.071 66.667 4.39 0.00 0.00 4.18
461 2148 0.802494 CACGTTATCAGTGTTGGGCC 59.198 55.000 0.00 0.00 35.08 5.80
462 2149 1.803334 TCACGTTATCAGTGTTGGGC 58.197 50.000 0.00 0.00 40.28 5.36
463 2150 3.363575 CGTTTCACGTTATCAGTGTTGGG 60.364 47.826 0.00 0.00 40.28 4.12
464 2151 3.491639 TCGTTTCACGTTATCAGTGTTGG 59.508 43.478 0.00 0.00 43.14 3.77
465 2152 4.443063 TCTCGTTTCACGTTATCAGTGTTG 59.557 41.667 0.00 0.00 43.14 3.33
474 2161 1.959747 CGAGCTCTCGTTTCACGTTA 58.040 50.000 12.85 0.00 46.99 3.18
511 2198 1.519455 CATCCTCTGTCGCCGGTTC 60.519 63.158 1.90 0.00 0.00 3.62
513 2200 1.739338 GATCATCCTCTGTCGCCGGT 61.739 60.000 1.90 0.00 0.00 5.28
585 2384 3.341823 AGTCAAGTGAATGAGTGATGGC 58.658 45.455 0.00 0.00 31.82 4.40
586 2385 4.572909 TGAGTCAAGTGAATGAGTGATGG 58.427 43.478 0.00 0.00 33.17 3.51
588 2387 5.477510 GTCTGAGTCAAGTGAATGAGTGAT 58.522 41.667 0.00 0.00 33.17 3.06
589 2388 4.262207 GGTCTGAGTCAAGTGAATGAGTGA 60.262 45.833 0.00 0.00 33.17 3.41
590 2389 3.993081 GGTCTGAGTCAAGTGAATGAGTG 59.007 47.826 0.00 0.00 33.17 3.51
592 2391 4.533919 AGGTCTGAGTCAAGTGAATGAG 57.466 45.455 0.00 0.00 0.00 2.90
593 2392 4.832823 TGTAGGTCTGAGTCAAGTGAATGA 59.167 41.667 0.00 0.00 0.00 2.57
596 2395 3.005897 GCTGTAGGTCTGAGTCAAGTGAA 59.994 47.826 0.00 0.00 0.00 3.18
766 2567 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
767 2568 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
768 2569 4.023279 CGAGAGAGAGAGAGAGAGAGAGAG 60.023 54.167 0.00 0.00 0.00 3.20
769 2570 3.885901 CGAGAGAGAGAGAGAGAGAGAGA 59.114 52.174 0.00 0.00 0.00 3.10
770 2571 3.634448 ACGAGAGAGAGAGAGAGAGAGAG 59.366 52.174 0.00 0.00 0.00 3.20
771 2572 3.381590 CACGAGAGAGAGAGAGAGAGAGA 59.618 52.174 0.00 0.00 0.00 3.10
772 2573 3.381590 TCACGAGAGAGAGAGAGAGAGAG 59.618 52.174 0.00 0.00 0.00 3.20
773 2574 3.361786 TCACGAGAGAGAGAGAGAGAGA 58.638 50.000 0.00 0.00 0.00 3.10
774 2575 3.801114 TCACGAGAGAGAGAGAGAGAG 57.199 52.381 0.00 0.00 0.00 3.20
775 2576 4.753516 AATCACGAGAGAGAGAGAGAGA 57.246 45.455 0.00 0.00 33.27 3.10
776 2577 5.353956 TCAAAATCACGAGAGAGAGAGAGAG 59.646 44.000 0.00 0.00 33.27 3.20
789 2590 6.873605 ACTGTACATGATTCTCAAAATCACGA 59.126 34.615 0.00 0.00 39.22 4.35
790 2591 7.065216 ACTGTACATGATTCTCAAAATCACG 57.935 36.000 0.00 0.00 39.22 4.35
866 2711 6.350194 GGAGAGAAACCAAAGTCAAAACTTGT 60.350 38.462 0.00 0.00 45.07 3.16
893 2738 3.149981 GCTGCCCTTCTTGTAAGAACTT 58.850 45.455 3.05 0.00 39.95 2.66
906 2751 0.328258 ATACCGACAAAGCTGCCCTT 59.672 50.000 0.00 0.00 34.51 3.95
919 2764 3.128349 GCGCTCCTCATTTTTATACCGA 58.872 45.455 0.00 0.00 0.00 4.69
927 2772 1.586154 CGTTGGGCGCTCCTCATTTT 61.586 55.000 3.94 0.00 36.20 1.82
1103 2962 0.036671 AACGGAGCGAGTAAAAGGGG 60.037 55.000 0.00 0.00 0.00 4.79
1113 2972 6.798482 TGACTTATATTTAGAAACGGAGCGA 58.202 36.000 0.00 0.00 0.00 4.93
1114 2973 7.639162 ATGACTTATATTTAGAAACGGAGCG 57.361 36.000 0.00 0.00 0.00 5.03
1166 3025 9.567848 GTGTACATTTCATTCATTTTATTCCGT 57.432 29.630 0.00 0.00 0.00 4.69
1167 3026 9.787532 AGTGTACATTTCATTCATTTTATTCCG 57.212 29.630 0.00 0.00 0.00 4.30
1210 3069 9.850628 GTTCAGTACAGACTACATACAAATGTA 57.149 33.333 0.00 0.00 45.66 2.29
1212 3071 8.035394 AGGTTCAGTACAGACTACATACAAATG 58.965 37.037 0.00 0.00 34.67 2.32
1213 3072 8.135382 AGGTTCAGTACAGACTACATACAAAT 57.865 34.615 0.00 0.00 33.32 2.32
1214 3073 7.450634 AGAGGTTCAGTACAGACTACATACAAA 59.549 37.037 0.00 0.00 33.32 2.83
1215 3074 6.946583 AGAGGTTCAGTACAGACTACATACAA 59.053 38.462 0.00 0.00 33.32 2.41
1216 3075 6.482524 AGAGGTTCAGTACAGACTACATACA 58.517 40.000 0.00 0.00 33.32 2.29
1217 3076 8.503458 TTAGAGGTTCAGTACAGACTACATAC 57.497 38.462 0.00 0.00 33.32 2.39
1218 3077 9.524496 TTTTAGAGGTTCAGTACAGACTACATA 57.476 33.333 0.00 0.00 33.32 2.29
1219 3078 8.418597 TTTTAGAGGTTCAGTACAGACTACAT 57.581 34.615 0.00 0.00 33.32 2.29
1220 3079 7.828508 TTTTAGAGGTTCAGTACAGACTACA 57.171 36.000 0.00 0.00 33.32 2.74
1221 3080 9.356433 GAATTTTAGAGGTTCAGTACAGACTAC 57.644 37.037 0.00 0.00 33.32 2.73
1222 3081 9.085645 TGAATTTTAGAGGTTCAGTACAGACTA 57.914 33.333 0.00 0.00 33.32 2.59
1223 3082 7.963532 TGAATTTTAGAGGTTCAGTACAGACT 58.036 34.615 0.00 0.00 35.80 3.24
1224 3083 8.496751 GTTGAATTTTAGAGGTTCAGTACAGAC 58.503 37.037 0.00 0.00 33.82 3.51
1225 3084 8.429641 AGTTGAATTTTAGAGGTTCAGTACAGA 58.570 33.333 0.00 0.00 33.82 3.41
1226 3085 8.608844 AGTTGAATTTTAGAGGTTCAGTACAG 57.391 34.615 0.00 0.00 33.82 2.74
1227 3086 8.208224 TGAGTTGAATTTTAGAGGTTCAGTACA 58.792 33.333 0.00 0.00 33.82 2.90
1228 3087 8.603242 TGAGTTGAATTTTAGAGGTTCAGTAC 57.397 34.615 0.00 0.00 33.82 2.73
1237 3096 5.474876 AGCCCAACTGAGTTGAATTTTAGAG 59.525 40.000 25.75 6.22 45.28 2.43
1274 3135 6.205853 ACGTAATGCAGGTAAATTTTCACTGA 59.794 34.615 16.08 6.12 0.00 3.41
1332 3193 0.241213 TGAGTCGACGAGGAAAGCAG 59.759 55.000 10.46 0.00 0.00 4.24
1335 3196 3.575630 TGATTTGAGTCGACGAGGAAAG 58.424 45.455 10.46 0.00 0.00 2.62
1346 3207 3.380637 AGCAATGGCAGATGATTTGAGTC 59.619 43.478 7.21 0.00 44.61 3.36
1356 3217 2.211250 AGTTGTGAGCAATGGCAGAT 57.789 45.000 0.00 0.00 44.61 2.90
1361 3222 4.629200 GTCTAGAGAAGTTGTGAGCAATGG 59.371 45.833 0.00 0.00 36.92 3.16
1368 3229 6.653740 TCACTAATCGTCTAGAGAAGTTGTGA 59.346 38.462 11.96 11.96 0.00 3.58
1369 3230 6.843208 TCACTAATCGTCTAGAGAAGTTGTG 58.157 40.000 0.00 1.63 0.00 3.33
1370 3231 7.040617 TGTTCACTAATCGTCTAGAGAAGTTGT 60.041 37.037 0.00 0.00 31.71 3.32
1371 3232 7.306213 TGTTCACTAATCGTCTAGAGAAGTTG 58.694 38.462 0.00 0.00 31.71 3.16
1372 3233 7.450124 TGTTCACTAATCGTCTAGAGAAGTT 57.550 36.000 0.00 0.00 31.71 2.66
1373 3234 7.450124 TTGTTCACTAATCGTCTAGAGAAGT 57.550 36.000 0.00 0.00 31.71 3.01
1486 3473 1.812571 GTGGCAGAATTCATTGGACGT 59.187 47.619 8.44 0.00 0.00 4.34
1515 3502 2.012673 GTGGGTCATCACTCATCAAGC 58.987 52.381 0.00 0.00 34.66 4.01
1622 3625 3.123621 GCTGATAATACAGTACGGCATGC 59.876 47.826 9.90 9.90 39.73 4.06
1629 3632 6.078202 TGCTCTCTGCTGATAATACAGTAC 57.922 41.667 0.00 0.00 43.37 2.73
1706 3709 0.613777 CAGGAGTGTCCTTGTACCCC 59.386 60.000 0.00 0.00 46.91 4.95
1839 3967 9.085250 GCTTATGTCAGAGTTAGTAAACTTACC 57.915 37.037 0.00 0.00 46.09 2.85
1869 3997 9.449719 ACTACAATATCAAGTTTAGTTTGAGGG 57.550 33.333 0.00 0.00 37.91 4.30
1989 4120 3.084786 AGGCCTTCTTGCTTGTGAATAC 58.915 45.455 0.00 0.00 0.00 1.89
2069 4202 1.164411 TGCTGCCATAAAACGGTGAG 58.836 50.000 0.00 0.00 0.00 3.51
2075 4208 3.428045 GGTGACTCATGCTGCCATAAAAC 60.428 47.826 0.00 0.00 0.00 2.43
2166 4302 2.415512 GGGAGAACGAACATGTGTTAGC 59.584 50.000 0.00 0.00 38.56 3.09
2183 4319 0.879765 CTGAAAAGCTGCACAGGGAG 59.120 55.000 1.02 0.00 35.23 4.30
2280 4416 1.676014 CGCCTAGGGGTTGAGACTTTG 60.676 57.143 17.58 0.00 34.45 2.77
2305 4441 2.939103 CCAACGGGATTTCATCAGTCTC 59.061 50.000 0.00 0.00 35.59 3.36
2394 4530 3.064545 CGCAAAATGTCAGAAGGGATCTC 59.935 47.826 0.00 0.00 35.73 2.75
2395 4531 3.012518 CGCAAAATGTCAGAAGGGATCT 58.987 45.455 0.00 0.00 39.68 2.75
2396 4532 2.478539 GCGCAAAATGTCAGAAGGGATC 60.479 50.000 0.30 0.00 0.00 3.36
2398 4534 0.881118 GCGCAAAATGTCAGAAGGGA 59.119 50.000 0.30 0.00 0.00 4.20
2402 4538 1.603456 TGGAGCGCAAAATGTCAGAA 58.397 45.000 11.47 0.00 0.00 3.02
2403 4539 1.603456 TTGGAGCGCAAAATGTCAGA 58.397 45.000 11.47 0.00 0.00 3.27
2720 4928 8.101309 TGATTTTTCTCCTAATACTCCATCCA 57.899 34.615 0.00 0.00 0.00 3.41
2724 4932 9.177608 CATGTTGATTTTTCTCCTAATACTCCA 57.822 33.333 0.00 0.00 0.00 3.86
2732 4940 6.267471 ACCTTTGCATGTTGATTTTTCTCCTA 59.733 34.615 0.00 0.00 0.00 2.94
2738 4946 6.347696 TGAGAACCTTTGCATGTTGATTTTT 58.652 32.000 0.00 0.00 0.00 1.94
2750 4958 4.682860 CACAACATTCATGAGAACCTTTGC 59.317 41.667 0.00 0.00 36.39 3.68
2797 5013 8.618677 CGATGTTGAATAACTCAGTAGGTACTA 58.381 37.037 0.00 0.00 37.54 1.82
2847 5063 4.158394 GCAAGGCATTGAGGTTAGAAATCA 59.842 41.667 16.56 0.00 38.83 2.57
2879 5095 1.368641 TTCGACGCCATCAAATCCTG 58.631 50.000 0.00 0.00 0.00 3.86
2907 5123 3.251004 GGTCGATCAAATAACCATGAGCC 59.749 47.826 0.00 0.00 0.00 4.70
3042 5258 2.851195 AGCCTTATGCCAACCTTATCG 58.149 47.619 0.00 0.00 42.71 2.92
3084 5300 1.363744 GGTTTGAGTCTGATGCCTCG 58.636 55.000 0.00 0.00 0.00 4.63
3105 5321 1.424638 TGTATAGGCCCAGAGCTTCC 58.575 55.000 0.00 0.00 43.05 3.46
3195 5411 0.319555 GCGGGGTTTCAAGCTTTTCC 60.320 55.000 0.00 0.00 0.00 3.13
3378 5594 3.260884 TGTACTTGTTGAGAGGACCATCC 59.739 47.826 0.00 0.00 36.58 3.51
3453 5669 4.297299 TCATACATCGGACGGTAGAAAC 57.703 45.455 0.00 0.00 0.00 2.78
3535 5751 7.921786 TGACCTTATTCCTTCAACATAGTTG 57.078 36.000 3.58 3.58 0.00 3.16
3545 5763 9.183368 AGAAGAAATCAATGACCTTATTCCTTC 57.817 33.333 9.36 0.00 0.00 3.46
3577 5795 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3578 5796 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3600 5818 3.623060 CCAGCATACATAAGACCACACAC 59.377 47.826 0.00 0.00 0.00 3.82
3607 5825 6.051717 AGTGTTGATCCAGCATACATAAGAC 58.948 40.000 0.00 0.00 0.00 3.01
3761 6107 2.978156 ATTGAGTGTGTGGGATTGGT 57.022 45.000 0.00 0.00 0.00 3.67
3793 6139 8.729756 TCAATCAAACTTGTACTGATTATGTGG 58.270 33.333 6.89 0.00 37.63 4.17
3818 6231 7.438160 GTGGGCTAGGTGCAAAATAAATAAATC 59.562 37.037 0.00 0.00 45.15 2.17
4054 7873 2.741145 ACGATAAGCTTGAGAGTCCCT 58.259 47.619 9.86 0.00 0.00 4.20
4079 7913 4.379813 CCAAAGCGTGATTGCAGAATTACT 60.380 41.667 0.00 0.00 37.31 2.24
4086 7920 2.095110 TCATTCCAAAGCGTGATTGCAG 60.095 45.455 0.00 0.00 37.31 4.41
4188 8022 7.231519 TCACTATTCTGTAGGTGGTGATATCAG 59.768 40.741 5.42 0.00 0.00 2.90
4251 8085 4.032960 TGCTGAAGGAACCATAACACAT 57.967 40.909 0.00 0.00 0.00 3.21
4372 8219 7.757941 TCTTTGAACATGATACATTGTCCAA 57.242 32.000 0.00 0.00 0.00 3.53
4432 8279 5.734855 TTCGTTTTGATCAGCTATTAGGC 57.265 39.130 0.00 0.00 0.00 3.93


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

AutoCloner maintained by Alex Coulton.