Multiple sequence alignment - TraesCS6D01G224600

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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 TraesCS6D01G224600 chr6D 100.000 4707 0 0 1 4707 316430780 316426074 0.000000e+00 8693.0
1 TraesCS6D01G224600 chr6D 85.100 698 89 8 2903 3587 467878702 467879397 0.000000e+00 699.0
2 TraesCS6D01G224600 chr6D 87.725 611 57 7 960 1557 467876980 467877585 0.000000e+00 697.0
3 TraesCS6D01G224600 chr6A 94.729 1309 35 9 2873 4168 454386970 454385683 0.000000e+00 2004.0
4 TraesCS6D01G224600 chr6A 92.069 1223 56 20 749 1960 454390917 454389725 0.000000e+00 1683.0
5 TraesCS6D01G224600 chr6A 95.155 743 33 2 1 740 454392198 454391456 0.000000e+00 1170.0
6 TraesCS6D01G224600 chr6A 85.828 501 28 15 2335 2819 454387788 454387315 4.230000e-135 492.0
7 TraesCS6D01G224600 chr6A 94.340 318 13 1 4132 4444 454385680 454385363 2.550000e-132 483.0
8 TraesCS6D01G224600 chr6A 95.135 185 9 0 4395 4579 454385379 454385195 4.610000e-75 292.0
9 TraesCS6D01G224600 chr6A 92.073 164 12 1 4545 4707 454385199 454385036 3.660000e-56 230.0
10 TraesCS6D01G224600 chr6A 92.308 78 4 2 2126 2201 454387961 454387884 4.980000e-20 110.0
11 TraesCS6D01G224600 chr6A 94.737 57 2 1 2070 2125 454388038 454387982 2.330000e-13 87.9
12 TraesCS6D01G224600 chr6B 96.296 783 25 3 2880 3661 508172982 508173761 0.000000e+00 1282.0
13 TraesCS6D01G224600 chr6B 86.379 1182 99 34 953 2101 508168633 508169785 0.000000e+00 1234.0
14 TraesCS6D01G224600 chr6B 86.888 633 71 11 2903 3523 713563717 713564349 0.000000e+00 699.0
15 TraesCS6D01G224600 chr6B 86.888 633 71 7 2903 3523 713883225 713883857 0.000000e+00 699.0
16 TraesCS6D01G224600 chr6B 89.184 564 52 8 177 739 508160383 508160938 0.000000e+00 695.0
17 TraesCS6D01G224600 chr6B 86.414 633 74 5 2903 3523 713331468 713332100 0.000000e+00 682.0
18 TraesCS6D01G224600 chr6B 89.421 501 41 5 1067 1557 713329510 713330008 5.170000e-174 621.0
19 TraesCS6D01G224600 chr6B 84.702 621 56 13 949 1557 713881297 713881890 6.790000e-163 584.0
20 TraesCS6D01G224600 chr6B 87.780 491 45 9 1055 1535 713557217 713557702 1.140000e-155 560.0
21 TraesCS6D01G224600 chr6B 91.694 301 21 3 3979 4278 508176127 508176424 9.420000e-112 414.0
22 TraesCS6D01G224600 chr6B 97.183 71 2 0 1 71 508155265 508155335 2.300000e-23 121.0
23 TraesCS6D01G224600 chr6B 90.123 81 7 1 3677 3757 508175237 508175316 2.320000e-18 104.0
24 TraesCS6D01G224600 chr6B 93.220 59 3 1 3979 4037 711369671 711369614 8.390000e-13 86.1
25 TraesCS6D01G224600 chr3D 75.744 672 121 29 1 647 477838360 477837706 2.750000e-77 300.0
26 TraesCS6D01G224600 chr1B 88.333 240 24 3 4471 4707 31562390 31562628 7.710000e-73 285.0
27 TraesCS6D01G224600 chr1B 92.308 104 6 2 2184 2286 539573359 539573257 3.800000e-31 147.0
28 TraesCS6D01G224600 chr1B 91.176 102 9 0 2190 2291 133188847 133188948 6.350000e-29 139.0
29 TraesCS6D01G224600 chr5A 80.000 355 58 12 76 421 326687231 326687581 2.810000e-62 250.0
30 TraesCS6D01G224600 chr5A 92.784 97 7 0 2194 2290 309680267 309680171 1.770000e-29 141.0
31 TraesCS6D01G224600 chr4D 83.182 220 22 8 3727 3942 442156554 442156346 2.240000e-43 187.0
32 TraesCS6D01G224600 chr5D 94.737 95 5 0 2192 2286 496216250 496216344 1.060000e-31 148.0
33 TraesCS6D01G224600 chr5D 95.455 88 4 0 2197 2284 276292431 276292518 1.770000e-29 141.0
34 TraesCS6D01G224600 chr1A 93.814 97 5 1 2191 2287 96040641 96040546 1.370000e-30 145.0
35 TraesCS6D01G224600 chr2B 92.000 100 8 0 2199 2298 214312028 214312127 1.770000e-29 141.0
36 TraesCS6D01G224600 chr7A 91.919 99 6 2 2196 2293 608993358 608993261 2.280000e-28 137.0
37 TraesCS6D01G224600 chr7A 91.000 100 9 0 2188 2287 78133314 78133413 8.220000e-28 135.0
38 TraesCS6D01G224600 chr3A 84.211 133 20 1 515 646 423674292 423674160 1.370000e-25 128.0


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 TraesCS6D01G224600 chr6D 316426074 316430780 4706 True 8693.000000 8693 100.000000 1 4707 1 chr6D.!!$R1 4706
1 TraesCS6D01G224600 chr6D 467876980 467879397 2417 False 698.000000 699 86.412500 960 3587 2 chr6D.!!$F1 2627
2 TraesCS6D01G224600 chr6A 454385036 454392198 7162 True 727.988889 2004 92.930444 1 4707 9 chr6A.!!$R1 4706
3 TraesCS6D01G224600 chr6B 508168633 508176424 7791 False 758.500000 1282 91.123000 953 4278 4 chr6B.!!$F5 3325
4 TraesCS6D01G224600 chr6B 713563717 713564349 632 False 699.000000 699 86.888000 2903 3523 1 chr6B.!!$F4 620
5 TraesCS6D01G224600 chr6B 508160383 508160938 555 False 695.000000 695 89.184000 177 739 1 chr6B.!!$F2 562
6 TraesCS6D01G224600 chr6B 713329510 713332100 2590 False 651.500000 682 87.917500 1067 3523 2 chr6B.!!$F6 2456
7 TraesCS6D01G224600 chr6B 713881297 713883857 2560 False 641.500000 699 85.795000 949 3523 2 chr6B.!!$F7 2574
8 TraesCS6D01G224600 chr3D 477837706 477838360 654 True 300.000000 300 75.744000 1 647 1 chr3D.!!$R1 646

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
392 402 0.178301 CCTTTCGAGGCTAGGGTTCC 59.822 60.0 0.0 0.0 0.0 3.62 F
1571 2176 0.179179 GCGCACCAGCTTCTGATTTC 60.179 55.0 0.3 0.0 39.1 2.17 F
2703 7949 0.038251 TCATGTGAGTGAGTGACGGC 60.038 55.0 0.0 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1799 2645 0.553819 TGTAAACCAGGCAACACCCT 59.446 50.0 0.00 0.00 40.58 4.34 R
2866 8765 0.247460 CGGTCAGCCATCAGTCAGAA 59.753 55.0 0.00 0.00 34.09 3.02 R
4497 12631 0.753479 TCCAAAACCCACATGTGCGT 60.753 50.0 20.81 15.54 0.00 5.24 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
118 121 5.989477 TGGGGATTTAATATCCTATCTGCG 58.011 41.667 13.15 0.00 38.26 5.18
392 402 0.178301 CCTTTCGAGGCTAGGGTTCC 59.822 60.000 0.00 0.00 0.00 3.62
433 443 6.712276 TCTGGCTTCTCTATATCTCGTATCA 58.288 40.000 0.00 0.00 0.00 2.15
473 483 1.103803 TCACATAGTCGACCAGGAGC 58.896 55.000 13.01 0.00 0.00 4.70
496 509 1.217244 GGCGACGGTGGTTATGACT 59.783 57.895 0.00 0.00 0.00 3.41
529 551 2.257207 TGTTTTCTCCTCTGGATCCGT 58.743 47.619 7.39 0.00 0.00 4.69
530 552 2.233922 TGTTTTCTCCTCTGGATCCGTC 59.766 50.000 7.39 0.00 0.00 4.79
531 553 1.103803 TTTCTCCTCTGGATCCGTCG 58.896 55.000 7.39 0.00 0.00 5.12
585 607 4.452455 GCTTCATATGGTTGGTTCCTATCG 59.548 45.833 2.13 0.00 0.00 2.92
593 615 4.171754 GGTTGGTTCCTATCGCGTATATC 58.828 47.826 5.77 0.00 0.00 1.63
619 641 5.212194 CGCGATTTTTACCCCATATTCTTG 58.788 41.667 0.00 0.00 0.00 3.02
680 702 2.553685 ATCCTGAAGATGTGCACAAGCA 60.554 45.455 25.72 17.20 40.64 3.91
720 742 9.787435 ACAAAACCTAAGTCTATGACACAAATA 57.213 29.630 0.46 0.00 34.60 1.40
747 769 9.453572 TCGAAGTAAAAAGTAGTACTCCTATGA 57.546 33.333 2.58 0.00 30.18 2.15
767 1319 5.437289 TGATGTTGCTAAAACTGACCAAG 57.563 39.130 0.00 0.00 0.00 3.61
791 1343 7.506971 AGTAATGAGCTAGGGTAACATAAACC 58.493 38.462 0.00 0.00 39.74 3.27
795 1349 5.834742 TGAGCTAGGGTAACATAAACCGATA 59.165 40.000 0.00 0.00 37.93 2.92
801 1355 7.576861 AGGGTAACATAAACCGATATTTTGG 57.423 36.000 0.00 0.00 37.93 3.28
828 1382 2.736670 AAGCTTTGACAAGGTGGACT 57.263 45.000 0.00 0.00 39.96 3.85
829 1383 2.736670 AGCTTTGACAAGGTGGACTT 57.263 45.000 0.00 0.00 39.36 3.01
955 1509 9.856488 GTCGTATTTACACCATCATACTATCAT 57.144 33.333 0.00 0.00 0.00 2.45
1004 1561 0.464870 CCTCTGCTCCAGACATCCAG 59.535 60.000 0.00 0.00 35.39 3.86
1016 1573 4.141846 CCAGACATCCAGCAAGTAGTACAT 60.142 45.833 2.52 0.00 0.00 2.29
1138 1698 3.188786 GGTGCACATCGAGTCCGC 61.189 66.667 20.43 0.00 35.37 5.54
1405 1997 3.129502 CGACGCCGGAGTGAGGTA 61.130 66.667 18.14 0.00 0.00 3.08
1571 2176 0.179179 GCGCACCAGCTTCTGATTTC 60.179 55.000 0.30 0.00 39.10 2.17
1575 2180 2.413371 GCACCAGCTTCTGATTTCGTTC 60.413 50.000 0.00 0.00 37.91 3.95
1707 2386 7.980099 ACACGTTATTTGGATTTACAAAAACCA 59.020 29.630 0.00 0.00 42.91 3.67
1783 2629 2.143876 AGGCCACAGAAACAAGTTGT 57.856 45.000 5.01 1.64 0.00 3.32
1799 2645 4.431416 AGTTGTGTACAATCCAGAACCA 57.569 40.909 0.00 0.00 36.92 3.67
1805 2651 1.149101 ACAATCCAGAACCAGGGTGT 58.851 50.000 0.00 0.00 0.00 4.16
1983 4211 5.827326 AGCTTCTTTTACCTAGACCAACT 57.173 39.130 0.00 0.00 0.00 3.16
1997 4230 1.271217 ACCAACTAAGAACCCTTCGGC 60.271 52.381 0.00 0.00 33.94 5.54
2061 4297 7.009631 CAGTATAAATAGCGATATGACACCAGC 59.990 40.741 0.00 0.00 0.00 4.85
2126 4783 8.390921 CCATTTATTTACCCACCCTACATCTAT 58.609 37.037 0.00 0.00 0.00 1.98
2127 4784 9.449719 CATTTATTTACCCACCCTACATCTATC 57.550 37.037 0.00 0.00 0.00 2.08
2130 4787 3.993658 ACCCACCCTACATCTATCTGA 57.006 47.619 0.00 0.00 0.00 3.27
2140 4818 7.126421 ACCCTACATCTATCTGAGTTCATGTTT 59.874 37.037 0.00 0.00 0.00 2.83
2169 4847 2.737180 CGGTGTCTGACTGGCTGT 59.263 61.111 9.51 0.00 0.00 4.40
2198 5710 8.322091 GGCTAACCAGTCAAATCCATATATACT 58.678 37.037 0.00 0.00 35.26 2.12
2203 5715 9.036980 ACCAGTCAAATCCATATATACTACTCC 57.963 37.037 0.00 0.00 0.00 3.85
2204 5716 8.478877 CCAGTCAAATCCATATATACTACTCCC 58.521 40.741 0.00 0.00 0.00 4.30
2205 5717 9.261035 CAGTCAAATCCATATATACTACTCCCT 57.739 37.037 0.00 0.00 0.00 4.20
2206 5718 9.482175 AGTCAAATCCATATATACTACTCCCTC 57.518 37.037 0.00 0.00 0.00 4.30
2207 5719 8.697292 GTCAAATCCATATATACTACTCCCTCC 58.303 40.741 0.00 0.00 0.00 4.30
2208 5720 7.560262 TCAAATCCATATATACTACTCCCTCCG 59.440 40.741 0.00 0.00 0.00 4.63
2209 5721 6.593759 ATCCATATATACTACTCCCTCCGT 57.406 41.667 0.00 0.00 0.00 4.69
2210 5722 6.398655 TCCATATATACTACTCCCTCCGTT 57.601 41.667 0.00 0.00 0.00 4.44
2211 5723 6.797707 TCCATATATACTACTCCCTCCGTTT 58.202 40.000 0.00 0.00 0.00 3.60
2212 5724 6.888632 TCCATATATACTACTCCCTCCGTTTC 59.111 42.308 0.00 0.00 0.00 2.78
2213 5725 6.662234 CCATATATACTACTCCCTCCGTTTCA 59.338 42.308 0.00 0.00 0.00 2.69
2214 5726 7.342284 CCATATATACTACTCCCTCCGTTTCAT 59.658 40.741 0.00 0.00 0.00 2.57
2215 5727 9.404848 CATATATACTACTCCCTCCGTTTCATA 57.595 37.037 0.00 0.00 0.00 2.15
2217 5729 8.896722 ATATACTACTCCCTCCGTTTCATATT 57.103 34.615 0.00 0.00 0.00 1.28
2218 5730 9.986157 ATATACTACTCCCTCCGTTTCATATTA 57.014 33.333 0.00 0.00 0.00 0.98
2219 5731 6.402456 ACTACTCCCTCCGTTTCATATTAC 57.598 41.667 0.00 0.00 0.00 1.89
2220 5732 6.134754 ACTACTCCCTCCGTTTCATATTACT 58.865 40.000 0.00 0.00 0.00 2.24
2221 5733 5.532664 ACTCCCTCCGTTTCATATTACTC 57.467 43.478 0.00 0.00 0.00 2.59
2222 5734 4.960469 ACTCCCTCCGTTTCATATTACTCA 59.040 41.667 0.00 0.00 0.00 3.41
2223 5735 5.602978 ACTCCCTCCGTTTCATATTACTCAT 59.397 40.000 0.00 0.00 0.00 2.90
2224 5736 6.097915 TCCCTCCGTTTCATATTACTCATC 57.902 41.667 0.00 0.00 0.00 2.92
2225 5737 5.600898 TCCCTCCGTTTCATATTACTCATCA 59.399 40.000 0.00 0.00 0.00 3.07
2226 5738 5.696724 CCCTCCGTTTCATATTACTCATCAC 59.303 44.000 0.00 0.00 0.00 3.06
2227 5739 6.463049 CCCTCCGTTTCATATTACTCATCACT 60.463 42.308 0.00 0.00 0.00 3.41
2228 5740 6.422100 CCTCCGTTTCATATTACTCATCACTG 59.578 42.308 0.00 0.00 0.00 3.66
2229 5741 7.107639 TCCGTTTCATATTACTCATCACTGA 57.892 36.000 0.00 0.00 0.00 3.41
2230 5742 7.726216 TCCGTTTCATATTACTCATCACTGAT 58.274 34.615 0.00 0.00 0.00 2.90
2231 5743 8.204160 TCCGTTTCATATTACTCATCACTGATT 58.796 33.333 0.00 0.00 0.00 2.57
2232 5744 8.830580 CCGTTTCATATTACTCATCACTGATTT 58.169 33.333 0.00 0.00 0.00 2.17
2259 5771 9.298774 AGTACAAAGTTATACTAAATCAGCGAC 57.701 33.333 0.00 0.00 29.70 5.19
2260 5772 7.218145 ACAAAGTTATACTAAATCAGCGACG 57.782 36.000 0.00 0.00 0.00 5.12
2261 5773 7.031372 ACAAAGTTATACTAAATCAGCGACGA 58.969 34.615 0.00 0.00 0.00 4.20
2262 5774 7.220300 ACAAAGTTATACTAAATCAGCGACGAG 59.780 37.037 0.00 0.00 0.00 4.18
2263 5775 6.374565 AGTTATACTAAATCAGCGACGAGT 57.625 37.500 0.00 0.00 0.00 4.18
2264 5776 7.488187 AGTTATACTAAATCAGCGACGAGTA 57.512 36.000 0.00 0.00 0.00 2.59
2265 5777 7.923888 AGTTATACTAAATCAGCGACGAGTAA 58.076 34.615 0.00 0.00 0.00 2.24
2266 5778 8.566260 AGTTATACTAAATCAGCGACGAGTAAT 58.434 33.333 0.00 0.00 0.00 1.89
2267 5779 9.817365 GTTATACTAAATCAGCGACGAGTAATA 57.183 33.333 0.00 0.00 0.00 0.98
2269 5781 8.897457 ATACTAAATCAGCGACGAGTAATATG 57.103 34.615 0.00 0.00 0.00 1.78
2270 5782 6.150318 ACTAAATCAGCGACGAGTAATATGG 58.850 40.000 0.00 0.00 0.00 2.74
2271 5783 4.848562 AATCAGCGACGAGTAATATGGA 57.151 40.909 0.00 0.00 0.00 3.41
2272 5784 4.848562 ATCAGCGACGAGTAATATGGAA 57.151 40.909 0.00 0.00 0.00 3.53
2273 5785 3.961182 TCAGCGACGAGTAATATGGAAC 58.039 45.455 0.00 0.00 0.00 3.62
2274 5786 2.719556 CAGCGACGAGTAATATGGAACG 59.280 50.000 0.00 0.00 0.00 3.95
2275 5787 2.049228 GCGACGAGTAATATGGAACGG 58.951 52.381 0.00 0.00 0.00 4.44
2276 5788 2.287188 GCGACGAGTAATATGGAACGGA 60.287 50.000 0.00 0.00 0.00 4.69
2277 5789 3.552541 CGACGAGTAATATGGAACGGAG 58.447 50.000 0.00 0.00 0.00 4.63
2278 5790 3.608707 CGACGAGTAATATGGAACGGAGG 60.609 52.174 0.00 0.00 0.00 4.30
2279 5791 2.626743 ACGAGTAATATGGAACGGAGGG 59.373 50.000 0.00 0.00 0.00 4.30
2280 5792 2.889045 CGAGTAATATGGAACGGAGGGA 59.111 50.000 0.00 0.00 0.00 4.20
2281 5793 3.057456 CGAGTAATATGGAACGGAGGGAG 60.057 52.174 0.00 0.00 0.00 4.30
2282 5794 3.896272 GAGTAATATGGAACGGAGGGAGT 59.104 47.826 0.00 0.00 0.00 3.85
2283 5795 5.070823 AGTAATATGGAACGGAGGGAGTA 57.929 43.478 0.00 0.00 0.00 2.59
2284 5796 4.831710 AGTAATATGGAACGGAGGGAGTAC 59.168 45.833 0.00 0.00 0.00 2.73
2296 5808 5.163163 ACGGAGGGAGTACTACATATGTGTA 60.163 44.000 18.81 14.53 39.77 2.90
2297 5809 5.180868 CGGAGGGAGTACTACATATGTGTAC 59.819 48.000 25.31 25.31 39.77 2.90
2298 5810 6.305411 GGAGGGAGTACTACATATGTGTACT 58.695 44.000 30.31 30.31 41.22 2.73
2299 5811 6.430616 GGAGGGAGTACTACATATGTGTACTC 59.569 46.154 35.50 35.50 45.61 2.59
2302 5814 6.238610 GAGTACTACATATGTGTACTCCGG 57.761 45.833 34.64 16.75 43.69 5.14
2305 5817 1.789523 ACATATGTGTACTCCGGCCT 58.210 50.000 7.78 0.00 36.63 5.19
2306 5818 2.953453 ACATATGTGTACTCCGGCCTA 58.047 47.619 7.78 0.00 36.63 3.93
2378 7242 3.775261 AGTAGTACCTCGATCCTCCTC 57.225 52.381 0.00 0.00 0.00 3.71
2389 7253 1.414181 GATCCTCCTCGCTGGAAATGA 59.586 52.381 0.00 0.00 45.63 2.57
2392 7256 2.158900 TCCTCCTCGCTGGAAATGATTC 60.159 50.000 0.00 0.00 45.63 2.52
2427 7291 1.587946 GTTGCACGCTTGGTTCTTTTG 59.412 47.619 0.00 0.00 0.00 2.44
2443 7307 6.544197 GGTTCTTTTGGGGCAAGAAAATAAAA 59.456 34.615 0.00 0.00 40.99 1.52
2451 7315 5.102313 GGGCAAGAAAATAAAATGGTCTCG 58.898 41.667 0.00 0.00 0.00 4.04
2453 7317 5.160641 GCAAGAAAATAAAATGGTCTCGCA 58.839 37.500 0.00 0.00 0.00 5.10
2454 7318 5.633182 GCAAGAAAATAAAATGGTCTCGCAA 59.367 36.000 0.00 0.00 0.00 4.85
2455 7319 6.145371 GCAAGAAAATAAAATGGTCTCGCAAA 59.855 34.615 0.00 0.00 0.00 3.68
2456 7320 7.148590 GCAAGAAAATAAAATGGTCTCGCAAAT 60.149 33.333 0.00 0.00 0.00 2.32
2457 7321 9.352784 CAAGAAAATAAAATGGTCTCGCAAATA 57.647 29.630 0.00 0.00 0.00 1.40
2458 7322 9.573133 AAGAAAATAAAATGGTCTCGCAAATAG 57.427 29.630 0.00 0.00 0.00 1.73
2463 7327 2.973694 TGGTCTCGCAAATAGGTACC 57.026 50.000 2.73 2.73 0.00 3.34
2533 7734 0.912006 GCTCCCTGACCTCCTCCTTT 60.912 60.000 0.00 0.00 0.00 3.11
2550 7751 3.017442 CCTTTCCTAGCTAAAACCAGCC 58.983 50.000 0.00 0.00 42.84 4.85
2555 7756 4.875389 TCCTAGCTAAAACCAGCCTACTA 58.125 43.478 0.00 0.00 42.84 1.82
2556 7757 4.648307 TCCTAGCTAAAACCAGCCTACTAC 59.352 45.833 0.00 0.00 42.84 2.73
2557 7758 4.650131 CCTAGCTAAAACCAGCCTACTACT 59.350 45.833 0.00 0.00 42.84 2.57
2558 7759 4.739587 AGCTAAAACCAGCCTACTACTC 57.260 45.455 0.00 0.00 42.84 2.59
2559 7760 4.094476 AGCTAAAACCAGCCTACTACTCA 58.906 43.478 0.00 0.00 42.84 3.41
2560 7761 4.081586 AGCTAAAACCAGCCTACTACTCAC 60.082 45.833 0.00 0.00 42.84 3.51
2632 7878 2.667481 CGTCGCCGACCAAGTTAAATAA 59.333 45.455 12.26 0.00 35.63 1.40
2634 7880 3.681417 GTCGCCGACCAAGTTAAATAAGT 59.319 43.478 5.81 0.00 0.00 2.24
2635 7881 4.864247 GTCGCCGACCAAGTTAAATAAGTA 59.136 41.667 5.81 0.00 0.00 2.24
2636 7882 4.864247 TCGCCGACCAAGTTAAATAAGTAC 59.136 41.667 0.00 0.00 0.00 2.73
2637 7883 4.866486 CGCCGACCAAGTTAAATAAGTACT 59.134 41.667 0.00 0.00 0.00 2.73
2638 7884 6.035843 CGCCGACCAAGTTAAATAAGTACTA 58.964 40.000 0.00 0.00 0.00 1.82
2641 7887 6.473455 CCGACCAAGTTAAATAAGTACTACCG 59.527 42.308 0.00 0.00 0.00 4.02
2642 7888 6.020360 CGACCAAGTTAAATAAGTACTACCGC 60.020 42.308 0.00 0.00 0.00 5.68
2643 7889 6.939622 ACCAAGTTAAATAAGTACTACCGCT 58.060 36.000 0.00 0.00 0.00 5.52
2644 7890 8.066612 ACCAAGTTAAATAAGTACTACCGCTA 57.933 34.615 0.00 0.00 0.00 4.26
2645 7891 7.976175 ACCAAGTTAAATAAGTACTACCGCTAC 59.024 37.037 0.00 0.00 0.00 3.58
2646 7892 7.436376 CCAAGTTAAATAAGTACTACCGCTACC 59.564 40.741 0.00 0.00 0.00 3.18
2647 7893 7.645058 AGTTAAATAAGTACTACCGCTACCA 57.355 36.000 0.00 0.00 0.00 3.25
2648 7894 7.710896 AGTTAAATAAGTACTACCGCTACCAG 58.289 38.462 0.00 0.00 0.00 4.00
2649 7895 4.581077 AATAAGTACTACCGCTACCAGC 57.419 45.455 0.00 0.00 38.02 4.85
2656 7902 0.970640 TACCGCTACCAGCAAACAGA 59.029 50.000 0.00 0.00 42.58 3.41
2696 7942 1.004595 CCGTGCATCATGTGAGTGAG 58.995 55.000 0.00 0.00 0.00 3.51
2697 7943 1.673923 CCGTGCATCATGTGAGTGAGT 60.674 52.381 0.00 0.00 0.00 3.41
2698 7944 1.392510 CGTGCATCATGTGAGTGAGTG 59.607 52.381 0.00 0.00 0.00 3.51
2699 7945 2.691927 GTGCATCATGTGAGTGAGTGA 58.308 47.619 0.00 0.00 0.00 3.41
2700 7946 2.414481 GTGCATCATGTGAGTGAGTGAC 59.586 50.000 0.00 0.00 0.00 3.67
2701 7947 1.657594 GCATCATGTGAGTGAGTGACG 59.342 52.381 0.00 0.00 0.00 4.35
2702 7948 2.265683 CATCATGTGAGTGAGTGACGG 58.734 52.381 0.00 0.00 0.00 4.79
2703 7949 0.038251 TCATGTGAGTGAGTGACGGC 60.038 55.000 0.00 0.00 0.00 5.68
2716 7962 3.415650 GACGGCCGGGGAATGGAAT 62.416 63.158 31.76 3.06 0.00 3.01
2819 8073 4.314440 GAGCGACACAGTGGGCCA 62.314 66.667 0.00 0.00 0.00 5.36
2823 8077 3.570212 GACACAGTGGGCCACCCT 61.570 66.667 32.30 15.41 45.70 4.34
2824 8078 3.850098 GACACAGTGGGCCACCCTG 62.850 68.421 32.30 27.11 45.70 4.45
2838 8737 4.321527 GGCCACCCTGTAGTCGTAATATAC 60.322 50.000 0.00 0.00 0.00 1.47
2839 8738 4.522022 GCCACCCTGTAGTCGTAATATACT 59.478 45.833 0.00 0.00 0.00 2.12
2841 8740 6.207417 GCCACCCTGTAGTCGTAATATACTTA 59.793 42.308 0.00 0.00 0.00 2.24
2842 8741 7.094032 GCCACCCTGTAGTCGTAATATACTTAT 60.094 40.741 0.00 0.00 0.00 1.73
2844 8743 9.837525 CACCCTGTAGTCGTAATATACTTATTC 57.162 37.037 0.00 0.00 30.64 1.75
2845 8744 9.578576 ACCCTGTAGTCGTAATATACTTATTCA 57.421 33.333 0.00 0.00 30.64 2.57
2873 8772 8.880991 TTCAAAGTAGTACTCCTATTCTGACT 57.119 34.615 2.58 0.00 0.00 3.41
2874 8773 8.282455 TCAAAGTAGTACTCCTATTCTGACTG 57.718 38.462 2.58 0.00 0.00 3.51
2875 8774 8.107729 TCAAAGTAGTACTCCTATTCTGACTGA 58.892 37.037 2.58 0.00 0.00 3.41
2878 8777 7.001674 AGTAGTACTCCTATTCTGACTGATGG 58.998 42.308 0.00 0.00 0.00 3.51
2879 8778 4.586841 AGTACTCCTATTCTGACTGATGGC 59.413 45.833 0.00 0.00 0.00 4.40
2883 8782 3.386078 TCCTATTCTGACTGATGGCTGAC 59.614 47.826 0.00 0.00 0.00 3.51
2891 8842 2.303549 CTGATGGCTGACCGACCTCC 62.304 65.000 0.00 0.00 39.70 4.30
3412 9375 1.044611 GGAGCTGACTATCAGGGACC 58.955 60.000 7.89 0.00 44.43 4.46
3510 9473 1.002624 TTTCCTCATCACGGCCACC 60.003 57.895 2.24 0.00 0.00 4.61
3587 9550 2.101415 GGGGACTCAAATAAGCCAATGC 59.899 50.000 0.00 0.00 37.95 3.56
3609 9572 4.083802 GCTAGCCATCGATATCCACAAAAC 60.084 45.833 2.29 0.00 0.00 2.43
3616 9579 6.073058 CCATCGATATCCACAAAACCTATGTG 60.073 42.308 0.00 0.00 46.05 3.21
3617 9580 5.984725 TCGATATCCACAAAACCTATGTGT 58.015 37.500 5.99 0.00 45.23 3.72
3672 9635 2.151360 CGAATTTCTCGTAGCGAATCCG 59.849 50.000 0.00 0.00 42.89 4.18
3679 11101 3.550275 TCTCGTAGCGAATCCGATTTTTG 59.450 43.478 0.00 0.00 38.22 2.44
3692 11114 8.918961 AATCCGATTTTTGTTTGCGAAATATA 57.081 26.923 0.00 0.00 0.00 0.86
3761 11191 5.878669 GTCGAAAGTGTATACAAATTCCCCT 59.121 40.000 18.89 5.53 0.00 4.79
3777 11207 7.855784 AATTCCCCTCAAAAAGAAAGTGTAT 57.144 32.000 0.00 0.00 0.00 2.29
3781 11211 7.291566 TCCCCTCAAAAAGAAAGTGTATACAA 58.708 34.615 7.25 0.00 0.00 2.41
3947 11717 8.995220 GTGACATTAGATTAGTACACACCAAAA 58.005 33.333 0.00 0.00 0.00 2.44
3982 11752 3.746492 ACACGCTTGAGGTTGTTCTTATC 59.254 43.478 0.00 0.00 0.00 1.75
4152 12248 7.087409 TGATTGACCATGTGCTTTTACTATG 57.913 36.000 0.00 0.00 0.00 2.23
4242 12343 9.773328 CATAACTATTAAAACCACACATCACTG 57.227 33.333 0.00 0.00 0.00 3.66
4280 12381 4.330620 CCGGTGCTTGTACGTTTGTATAAT 59.669 41.667 0.00 0.00 32.22 1.28
4286 12387 7.960738 GTGCTTGTACGTTTGTATAATTGTGAT 59.039 33.333 0.00 0.00 32.22 3.06
4334 12435 3.540314 AAGCTTAGCTCCAGAGACATG 57.460 47.619 7.36 0.00 38.25 3.21
4370 12471 4.412199 ACCTATATGGGCTTATGTGTGTGT 59.588 41.667 4.76 0.00 41.11 3.72
4374 12475 3.153369 TGGGCTTATGTGTGTGTGAAT 57.847 42.857 0.00 0.00 0.00 2.57
4398 12499 9.685276 AATGATTGTTAACAACATCCTCTGATA 57.315 29.630 22.78 1.83 41.79 2.15
4454 12588 5.831525 TCTTTCTAAGGCATATGACCGAGTA 59.168 40.000 4.47 0.00 0.00 2.59
4531 12665 1.155889 TTGGATGATGTCGTGTGTGC 58.844 50.000 0.00 0.00 0.00 4.57
4538 12672 2.658593 GTCGTGTGTGCGCTCAGT 60.659 61.111 13.23 0.00 0.00 3.41
4546 12680 2.094026 TGTGTGCGCTCAGTGAGATATT 60.094 45.455 24.55 0.00 0.00 1.28
4567 12701 9.178758 GATATTCAGTGAAGTTTAATGGGAAGT 57.821 33.333 11.91 0.00 0.00 3.01
4570 12704 5.468746 TCAGTGAAGTTTAATGGGAAGTTCG 59.531 40.000 0.00 0.00 38.62 3.95
4622 12787 3.305676 CGTCAAGGCGATCCATTATCTCT 60.306 47.826 0.00 0.00 31.87 3.10
4637 12802 8.786898 TCCATTATCTCTGTTTTTGTTTCTCTG 58.213 33.333 0.00 0.00 0.00 3.35
4640 12805 5.235305 TCTCTGTTTTTGTTTCTCTGTGC 57.765 39.130 0.00 0.00 0.00 4.57
4643 12808 1.852280 GTTTTTGTTTCTCTGTGCGGC 59.148 47.619 0.00 0.00 0.00 6.53
4651 12816 1.744368 CTCTGTGCGGCTGATGCTT 60.744 57.895 0.00 0.00 39.59 3.91
4663 12828 3.005554 GCTGATGCTTTGTCTGCTCTTA 58.994 45.455 0.00 0.00 37.51 2.10
4665 12830 4.260702 GCTGATGCTTTGTCTGCTCTTATC 60.261 45.833 0.00 0.00 37.51 1.75
4683 12848 8.342634 GCTCTTATCAATAAAGCAATTACGGAA 58.657 33.333 0.00 0.00 33.21 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 121 6.183360 TGCCCTAGTATGTATAGGTGTTGAAC 60.183 42.308 0.00 0.00 38.54 3.18
392 402 3.626670 GCCAGAAACTCCATCAGATCAAG 59.373 47.826 0.00 0.00 0.00 3.02
433 443 1.686325 CCCCATGTCTTCGGATCGGT 61.686 60.000 0.00 0.00 0.00 4.69
473 483 0.108329 ATAACCACCGTCGCCTTCTG 60.108 55.000 0.00 0.00 0.00 3.02
482 492 0.973632 TGAGCAGTCATAACCACCGT 59.026 50.000 0.00 0.00 0.00 4.83
496 509 4.225942 AGGAGAAAACATCTGGTATGAGCA 59.774 41.667 0.00 0.00 38.96 4.26
529 551 1.336517 CGAGGAAAACCTACTGCACGA 60.337 52.381 0.00 0.00 0.00 4.35
530 552 1.068474 CGAGGAAAACCTACTGCACG 58.932 55.000 0.00 0.00 0.00 5.34
531 553 1.798813 CACGAGGAAAACCTACTGCAC 59.201 52.381 0.00 0.00 0.00 4.57
593 615 1.011333 ATGGGGTAAAAATCGCGTCG 58.989 50.000 5.77 0.00 0.00 5.12
598 620 8.446599 AGTACAAGAATATGGGGTAAAAATCG 57.553 34.615 0.00 0.00 0.00 3.34
619 641 7.175119 AGTTTTGAGGCATTAGAAGGAAAGTAC 59.825 37.037 0.00 0.00 0.00 2.73
680 702 4.383173 AGGTTTTGTCGGAACTTTATCGT 58.617 39.130 0.00 0.00 0.00 3.73
740 762 5.880332 GGTCAGTTTTAGCAACATCATAGGA 59.120 40.000 0.00 0.00 0.00 2.94
741 763 5.647658 TGGTCAGTTTTAGCAACATCATAGG 59.352 40.000 0.00 0.00 0.00 2.57
742 764 6.741992 TGGTCAGTTTTAGCAACATCATAG 57.258 37.500 0.00 0.00 0.00 2.23
743 765 6.714810 ACTTGGTCAGTTTTAGCAACATCATA 59.285 34.615 0.00 0.00 27.32 2.15
744 766 5.536161 ACTTGGTCAGTTTTAGCAACATCAT 59.464 36.000 0.00 0.00 27.32 2.45
746 768 5.438761 ACTTGGTCAGTTTTAGCAACATC 57.561 39.130 0.00 0.00 27.32 3.06
747 769 6.952773 TTACTTGGTCAGTTTTAGCAACAT 57.047 33.333 0.00 0.00 36.88 2.71
767 1319 6.423001 CGGTTTATGTTACCCTAGCTCATTAC 59.577 42.308 0.00 0.00 31.75 1.89
819 1373 1.152546 GCCAACCCAAGTCCACCTT 60.153 57.895 0.00 0.00 0.00 3.50
828 1382 3.070302 GTGTTTGGATTTAGCCAACCCAA 59.930 43.478 0.00 0.00 46.99 4.12
829 1383 2.630580 GTGTTTGGATTTAGCCAACCCA 59.369 45.455 0.00 0.00 46.99 4.51
830 1384 2.630580 TGTGTTTGGATTTAGCCAACCC 59.369 45.455 0.00 0.00 46.99 4.11
831 1385 3.554129 GGTGTGTTTGGATTTAGCCAACC 60.554 47.826 0.00 0.00 46.99 3.77
832 1386 3.649073 GGTGTGTTTGGATTTAGCCAAC 58.351 45.455 0.00 0.00 46.99 3.77
849 1403 0.818040 GGCAAGAACTTCCACGGTGT 60.818 55.000 7.45 0.00 0.00 4.16
955 1509 5.708230 CCCTATTTATACGGGCTTTGCATTA 59.292 40.000 0.00 0.00 0.00 1.90
958 1512 3.482436 CCCTATTTATACGGGCTTTGCA 58.518 45.455 0.00 0.00 0.00 4.08
991 1548 2.499289 ACTACTTGCTGGATGTCTGGAG 59.501 50.000 0.00 0.00 0.00 3.86
1118 1678 2.103042 GGACTCGATGTGCACCTGC 61.103 63.158 15.69 2.33 42.50 4.85
1571 2176 5.861787 AGAAAATGGCCGAAATTTAAGAACG 59.138 36.000 0.00 0.00 0.00 3.95
1575 2180 6.868339 AGTTCAGAAAATGGCCGAAATTTAAG 59.132 34.615 0.00 0.00 0.00 1.85
1657 2336 2.825205 AGTTTGGCAAGATGTTTGTGC 58.175 42.857 0.00 0.00 37.55 4.57
1672 2351 4.355437 TCCAAATAACGTGTGCAAGTTTG 58.645 39.130 8.59 2.49 34.91 2.93
1676 2355 6.146216 TGTAAATCCAAATAACGTGTGCAAG 58.854 36.000 0.00 0.00 0.00 4.01
1761 2607 3.260632 ACAACTTGTTTCTGTGGCCTTTT 59.739 39.130 3.32 0.00 0.00 2.27
1762 2608 2.831526 ACAACTTGTTTCTGTGGCCTTT 59.168 40.909 3.32 0.00 0.00 3.11
1765 2611 1.476488 ACACAACTTGTTTCTGTGGCC 59.524 47.619 0.00 0.00 43.81 5.36
1783 2629 2.039746 CACCCTGGTTCTGGATTGTACA 59.960 50.000 0.00 0.00 0.00 2.90
1799 2645 0.553819 TGTAAACCAGGCAACACCCT 59.446 50.000 0.00 0.00 40.58 4.34
1870 2720 4.780815 TCAGTTGCACTATATCAAAGGGG 58.219 43.478 0.00 0.00 0.00 4.79
1924 2955 4.245054 CCGAACGGTCACTGTCAG 57.755 61.111 0.00 0.00 0.00 3.51
1970 4198 5.280998 AGGGTTCTTAGTTGGTCTAGGTA 57.719 43.478 0.00 0.00 0.00 3.08
2096 4753 2.432874 GGGTGGGTAAATAAATGGGTGC 59.567 50.000 0.00 0.00 0.00 5.01
2126 4783 6.839124 ATAAATGCCAAACATGAACTCAGA 57.161 33.333 0.00 0.00 39.60 3.27
2127 4784 6.694411 GCTATAAATGCCAAACATGAACTCAG 59.306 38.462 0.00 0.00 39.60 3.35
2130 4787 5.450412 CCGCTATAAATGCCAAACATGAACT 60.450 40.000 0.00 0.00 39.60 3.01
2140 4818 2.169561 TCAGACACCGCTATAAATGCCA 59.830 45.455 0.00 0.00 0.00 4.92
2169 4847 2.109128 TGGATTTGACTGGTTAGCCCAA 59.891 45.455 0.00 0.00 44.65 4.12
2198 5710 6.131264 TGAGTAATATGAAACGGAGGGAGTA 58.869 40.000 0.00 0.00 0.00 2.59
2199 5711 4.960469 TGAGTAATATGAAACGGAGGGAGT 59.040 41.667 0.00 0.00 0.00 3.85
2200 5712 5.531122 TGAGTAATATGAAACGGAGGGAG 57.469 43.478 0.00 0.00 0.00 4.30
2201 5713 5.600898 TGATGAGTAATATGAAACGGAGGGA 59.399 40.000 0.00 0.00 0.00 4.20
2202 5714 5.696724 GTGATGAGTAATATGAAACGGAGGG 59.303 44.000 0.00 0.00 0.00 4.30
2203 5715 6.422100 CAGTGATGAGTAATATGAAACGGAGG 59.578 42.308 0.00 0.00 0.00 4.30
2204 5716 7.203218 TCAGTGATGAGTAATATGAAACGGAG 58.797 38.462 0.00 0.00 0.00 4.63
2205 5717 7.107639 TCAGTGATGAGTAATATGAAACGGA 57.892 36.000 0.00 0.00 0.00 4.69
2206 5718 7.953158 ATCAGTGATGAGTAATATGAAACGG 57.047 36.000 4.39 0.00 0.00 4.44
2233 5745 9.298774 GTCGCTGATTTAGTATAACTTTGTACT 57.701 33.333 4.13 4.13 38.43 2.73
2234 5746 8.257841 CGTCGCTGATTTAGTATAACTTTGTAC 58.742 37.037 0.00 0.00 0.00 2.90
2235 5747 8.183536 TCGTCGCTGATTTAGTATAACTTTGTA 58.816 33.333 0.00 0.00 0.00 2.41
2236 5748 7.031372 TCGTCGCTGATTTAGTATAACTTTGT 58.969 34.615 0.00 0.00 0.00 2.83
2237 5749 7.220300 ACTCGTCGCTGATTTAGTATAACTTTG 59.780 37.037 0.00 0.00 0.00 2.77
2238 5750 7.256286 ACTCGTCGCTGATTTAGTATAACTTT 58.744 34.615 0.00 0.00 0.00 2.66
2239 5751 6.793349 ACTCGTCGCTGATTTAGTATAACTT 58.207 36.000 0.00 0.00 0.00 2.66
2240 5752 6.374565 ACTCGTCGCTGATTTAGTATAACT 57.625 37.500 0.00 0.00 0.00 2.24
2241 5753 8.725212 ATTACTCGTCGCTGATTTAGTATAAC 57.275 34.615 0.00 0.00 0.00 1.89
2243 5755 9.983804 CATATTACTCGTCGCTGATTTAGTATA 57.016 33.333 0.00 0.00 0.00 1.47
2244 5756 7.968956 CCATATTACTCGTCGCTGATTTAGTAT 59.031 37.037 0.00 0.00 0.00 2.12
2245 5757 7.173735 TCCATATTACTCGTCGCTGATTTAGTA 59.826 37.037 0.00 0.00 0.00 1.82
2246 5758 6.016527 TCCATATTACTCGTCGCTGATTTAGT 60.017 38.462 0.00 0.00 0.00 2.24
2247 5759 6.379386 TCCATATTACTCGTCGCTGATTTAG 58.621 40.000 0.00 0.00 0.00 1.85
2248 5760 6.321848 TCCATATTACTCGTCGCTGATTTA 57.678 37.500 0.00 0.00 0.00 1.40
2249 5761 5.196341 TCCATATTACTCGTCGCTGATTT 57.804 39.130 0.00 0.00 0.00 2.17
2250 5762 4.848562 TCCATATTACTCGTCGCTGATT 57.151 40.909 0.00 0.00 0.00 2.57
2251 5763 4.547532 GTTCCATATTACTCGTCGCTGAT 58.452 43.478 0.00 0.00 0.00 2.90
2252 5764 3.547413 CGTTCCATATTACTCGTCGCTGA 60.547 47.826 0.00 0.00 0.00 4.26
2253 5765 2.719556 CGTTCCATATTACTCGTCGCTG 59.280 50.000 0.00 0.00 0.00 5.18
2254 5766 2.287427 CCGTTCCATATTACTCGTCGCT 60.287 50.000 0.00 0.00 0.00 4.93
2255 5767 2.049228 CCGTTCCATATTACTCGTCGC 58.951 52.381 0.00 0.00 0.00 5.19
2256 5768 3.552541 CTCCGTTCCATATTACTCGTCG 58.447 50.000 0.00 0.00 0.00 5.12
2257 5769 3.305199 CCCTCCGTTCCATATTACTCGTC 60.305 52.174 0.00 0.00 0.00 4.20
2258 5770 2.626743 CCCTCCGTTCCATATTACTCGT 59.373 50.000 0.00 0.00 0.00 4.18
2259 5771 2.889045 TCCCTCCGTTCCATATTACTCG 59.111 50.000 0.00 0.00 0.00 4.18
2260 5772 3.896272 ACTCCCTCCGTTCCATATTACTC 59.104 47.826 0.00 0.00 0.00 2.59
2261 5773 3.924922 ACTCCCTCCGTTCCATATTACT 58.075 45.455 0.00 0.00 0.00 2.24
2262 5774 4.831710 AGTACTCCCTCCGTTCCATATTAC 59.168 45.833 0.00 0.00 0.00 1.89
2263 5775 5.070823 AGTACTCCCTCCGTTCCATATTA 57.929 43.478 0.00 0.00 0.00 0.98
2264 5776 3.924922 AGTACTCCCTCCGTTCCATATT 58.075 45.455 0.00 0.00 0.00 1.28
2265 5777 3.614568 AGTACTCCCTCCGTTCCATAT 57.385 47.619 0.00 0.00 0.00 1.78
2266 5778 3.202818 TGTAGTACTCCCTCCGTTCCATA 59.797 47.826 0.00 0.00 0.00 2.74
2267 5779 2.024655 TGTAGTACTCCCTCCGTTCCAT 60.025 50.000 0.00 0.00 0.00 3.41
2268 5780 1.355381 TGTAGTACTCCCTCCGTTCCA 59.645 52.381 0.00 0.00 0.00 3.53
2269 5781 2.134789 TGTAGTACTCCCTCCGTTCC 57.865 55.000 0.00 0.00 0.00 3.62
2270 5782 4.826183 ACATATGTAGTACTCCCTCCGTTC 59.174 45.833 6.56 0.00 0.00 3.95
2271 5783 4.583489 CACATATGTAGTACTCCCTCCGTT 59.417 45.833 8.32 0.00 0.00 4.44
2272 5784 4.142790 CACATATGTAGTACTCCCTCCGT 58.857 47.826 8.32 0.00 0.00 4.69
2273 5785 4.142790 ACACATATGTAGTACTCCCTCCG 58.857 47.826 8.32 0.00 37.26 4.63
2274 5786 6.305411 AGTACACATATGTAGTACTCCCTCC 58.695 44.000 27.50 13.42 43.50 4.30
2281 5793 4.320788 GGCCGGAGTACACATATGTAGTAC 60.321 50.000 25.31 25.31 43.69 2.73
2282 5794 3.822735 GGCCGGAGTACACATATGTAGTA 59.177 47.826 5.05 10.46 43.69 1.82
2283 5795 2.626743 GGCCGGAGTACACATATGTAGT 59.373 50.000 5.05 11.41 45.86 2.73
2284 5796 2.891580 AGGCCGGAGTACACATATGTAG 59.108 50.000 5.05 5.94 42.06 2.74
2296 5808 1.948391 AGTTAGGTTTAGGCCGGAGT 58.052 50.000 5.05 0.00 0.00 3.85
2297 5809 2.102084 GGTAGTTAGGTTTAGGCCGGAG 59.898 54.545 5.05 0.00 0.00 4.63
2298 5810 2.110578 GGTAGTTAGGTTTAGGCCGGA 58.889 52.381 5.05 0.00 0.00 5.14
2299 5811 1.832998 TGGTAGTTAGGTTTAGGCCGG 59.167 52.381 0.00 0.00 0.00 6.13
2300 5812 3.615224 TTGGTAGTTAGGTTTAGGCCG 57.385 47.619 0.00 0.00 0.00 6.13
2301 5813 6.209986 ACATTTTTGGTAGTTAGGTTTAGGCC 59.790 38.462 0.00 0.00 0.00 5.19
2302 5814 7.223260 ACATTTTTGGTAGTTAGGTTTAGGC 57.777 36.000 0.00 0.00 0.00 3.93
2305 5817 8.449251 ACGAACATTTTTGGTAGTTAGGTTTA 57.551 30.769 0.00 0.00 0.00 2.01
2306 5818 7.283807 AGACGAACATTTTTGGTAGTTAGGTTT 59.716 33.333 0.00 0.00 0.00 3.27
2378 7242 2.002586 ACTGACGAATCATTTCCAGCG 58.997 47.619 0.00 0.00 33.22 5.18
2389 7253 3.372206 GCAACTGCATCTAACTGACGAAT 59.628 43.478 0.00 0.00 41.59 3.34
2392 7256 2.795121 GCAACTGCATCTAACTGACG 57.205 50.000 0.00 0.00 41.59 4.35
2427 7291 5.419542 GAGACCATTTTATTTTCTTGCCCC 58.580 41.667 0.00 0.00 0.00 5.80
2443 7307 2.223971 CGGTACCTATTTGCGAGACCAT 60.224 50.000 10.90 0.00 0.00 3.55
2451 7315 4.497300 TGTCAACTACGGTACCTATTTGC 58.503 43.478 10.90 8.72 0.00 3.68
2453 7317 6.350629 ACTTGTCAACTACGGTACCTATTT 57.649 37.500 10.90 0.00 0.00 1.40
2454 7318 5.990120 ACTTGTCAACTACGGTACCTATT 57.010 39.130 10.90 0.00 0.00 1.73
2455 7319 5.990120 AACTTGTCAACTACGGTACCTAT 57.010 39.130 10.90 0.04 0.00 2.57
2456 7320 5.068987 ACAAACTTGTCAACTACGGTACCTA 59.931 40.000 10.90 0.74 36.50 3.08
2457 7321 4.141869 ACAAACTTGTCAACTACGGTACCT 60.142 41.667 10.90 0.00 36.50 3.08
2458 7322 4.122046 ACAAACTTGTCAACTACGGTACC 58.878 43.478 0.16 0.16 36.50 3.34
2463 7327 5.192496 CGGTTAACAAACTTGTCAACTACG 58.808 41.667 8.10 1.99 38.92 3.51
2533 7734 3.721021 AGTAGGCTGGTTTTAGCTAGGA 58.279 45.455 0.00 0.00 43.22 2.94
2550 7751 2.292016 CTCGGCCATGAGTGAGTAGTAG 59.708 54.545 2.24 0.00 0.00 2.57
2560 7761 1.067821 GGTCTAAGACTCGGCCATGAG 59.932 57.143 2.24 4.59 41.86 2.90
2632 7878 1.843368 TTGCTGGTAGCGGTAGTACT 58.157 50.000 0.00 0.00 46.26 2.73
2634 7880 1.894466 TGTTTGCTGGTAGCGGTAGTA 59.106 47.619 2.14 0.00 46.26 1.82
2635 7881 0.682852 TGTTTGCTGGTAGCGGTAGT 59.317 50.000 2.14 0.00 46.26 2.73
2636 7882 1.067142 TCTGTTTGCTGGTAGCGGTAG 60.067 52.381 2.14 0.00 46.26 3.18
2637 7883 0.970640 TCTGTTTGCTGGTAGCGGTA 59.029 50.000 2.14 0.00 46.26 4.02
2638 7884 0.320771 CTCTGTTTGCTGGTAGCGGT 60.321 55.000 2.14 0.00 46.26 5.68
2641 7887 2.169832 TGTCTCTGTTTGCTGGTAGC 57.830 50.000 0.00 0.00 42.82 3.58
2642 7888 2.926200 CGATGTCTCTGTTTGCTGGTAG 59.074 50.000 0.00 0.00 0.00 3.18
2643 7889 2.353704 CCGATGTCTCTGTTTGCTGGTA 60.354 50.000 0.00 0.00 0.00 3.25
2644 7890 1.609061 CCGATGTCTCTGTTTGCTGGT 60.609 52.381 0.00 0.00 0.00 4.00
2645 7891 1.081892 CCGATGTCTCTGTTTGCTGG 58.918 55.000 0.00 0.00 0.00 4.85
2646 7892 0.445436 GCCGATGTCTCTGTTTGCTG 59.555 55.000 0.00 0.00 0.00 4.41
2647 7893 0.674895 GGCCGATGTCTCTGTTTGCT 60.675 55.000 0.00 0.00 0.00 3.91
2648 7894 1.796796 GGCCGATGTCTCTGTTTGC 59.203 57.895 0.00 0.00 0.00 3.68
2649 7895 1.970917 GCGGCCGATGTCTCTGTTTG 61.971 60.000 33.48 0.00 0.00 2.93
2679 7925 2.414481 GTCACTCACTCACATGATGCAC 59.586 50.000 0.00 0.00 0.00 4.57
2698 7944 3.415650 ATTCCATTCCCCGGCCGTC 62.416 63.158 26.12 0.00 0.00 4.79
2699 7945 3.415650 GATTCCATTCCCCGGCCGT 62.416 63.158 26.12 0.65 0.00 5.68
2700 7946 2.594592 GATTCCATTCCCCGGCCG 60.595 66.667 21.04 21.04 0.00 6.13
2701 7947 2.203494 GGATTCCATTCCCCGGCC 60.203 66.667 0.00 0.00 0.00 6.13
2702 7948 1.153756 ATGGATTCCATTCCCCGGC 59.846 57.895 12.62 0.00 42.23 6.13
2819 8073 9.578576 TGAATAAGTATATTACGACTACAGGGT 57.421 33.333 0.00 0.00 31.83 4.34
2848 8747 8.740906 CAGTCAGAATAGGAGTACTACTTTGAA 58.259 37.037 14.24 0.00 33.70 2.69
2849 8748 8.107729 TCAGTCAGAATAGGAGTACTACTTTGA 58.892 37.037 14.24 9.68 33.70 2.69
2851 8750 8.908903 CATCAGTCAGAATAGGAGTACTACTTT 58.091 37.037 14.24 1.84 33.70 2.66
2854 8753 6.294286 GCCATCAGTCAGAATAGGAGTACTAC 60.294 46.154 0.00 0.00 33.70 2.73
2857 8756 4.586841 AGCCATCAGTCAGAATAGGAGTAC 59.413 45.833 0.00 0.00 0.00 2.73
2860 8759 3.640498 TCAGCCATCAGTCAGAATAGGAG 59.360 47.826 0.00 0.00 0.00 3.69
2861 8760 3.386078 GTCAGCCATCAGTCAGAATAGGA 59.614 47.826 0.00 0.00 0.00 2.94
2863 8762 3.726607 GGTCAGCCATCAGTCAGAATAG 58.273 50.000 0.00 0.00 34.09 1.73
2864 8763 2.101415 CGGTCAGCCATCAGTCAGAATA 59.899 50.000 0.00 0.00 34.09 1.75
2866 8765 0.247460 CGGTCAGCCATCAGTCAGAA 59.753 55.000 0.00 0.00 34.09 3.02
2867 8766 0.611896 TCGGTCAGCCATCAGTCAGA 60.612 55.000 0.00 0.00 34.09 3.27
2868 8767 0.459237 GTCGGTCAGCCATCAGTCAG 60.459 60.000 0.00 0.00 34.09 3.51
2869 8768 1.591703 GTCGGTCAGCCATCAGTCA 59.408 57.895 0.00 0.00 34.09 3.41
2870 8769 1.153549 GGTCGGTCAGCCATCAGTC 60.154 63.158 0.00 0.00 34.09 3.51
2872 8771 1.142748 GAGGTCGGTCAGCCATCAG 59.857 63.158 0.00 0.00 34.09 2.90
2873 8772 2.359169 GGAGGTCGGTCAGCCATCA 61.359 63.158 0.00 0.00 34.09 3.07
2874 8773 2.060980 AGGAGGTCGGTCAGCCATC 61.061 63.158 0.00 0.00 34.09 3.51
2875 8774 2.039624 AGGAGGTCGGTCAGCCAT 59.960 61.111 0.00 0.00 34.09 4.40
2878 8777 2.262915 CACAGGAGGTCGGTCAGC 59.737 66.667 0.00 0.00 0.00 4.26
2879 8778 1.892819 ATGCACAGGAGGTCGGTCAG 61.893 60.000 0.00 0.00 0.00 3.51
2883 8782 2.821366 GCATGCACAGGAGGTCGG 60.821 66.667 14.21 0.00 0.00 4.79
3412 9375 1.915614 GACACATGCACGGGCTTGAG 61.916 60.000 29.91 24.20 45.33 3.02
3510 9473 1.012486 GCCGTGTCTACTTGGGAACG 61.012 60.000 0.00 0.00 0.00 3.95
3516 9479 2.148916 TGTCTTGCCGTGTCTACTTG 57.851 50.000 0.00 0.00 0.00 3.16
3587 9550 4.452455 GGTTTTGTGGATATCGATGGCTAG 59.548 45.833 8.54 0.00 0.00 3.42
3982 11752 8.034215 TGCCTTCATAAACCAATTTAACATCAG 58.966 33.333 0.00 0.00 33.98 2.90
4130 12187 7.701539 TTCATAGTAAAAGCACATGGTCAAT 57.298 32.000 0.00 0.00 0.00 2.57
4169 12265 7.910441 AAATTTGGCTCAAGTATTTTCATGG 57.090 32.000 0.00 0.00 0.00 3.66
4222 12323 9.508642 TTCATACAGTGATGTGTGGTTTTAATA 57.491 29.630 0.00 0.00 36.54 0.98
4242 12343 3.315191 AGCACCGGCACAAATATTCATAC 59.685 43.478 0.00 0.00 44.61 2.39
4322 12423 3.843422 AGGAGGATACATGTCTCTGGAG 58.157 50.000 0.00 0.00 41.41 3.86
4334 12435 5.599242 GCCCATATAGGTTCTAGGAGGATAC 59.401 48.000 0.00 0.00 34.66 2.24
4370 12471 7.665145 TCAGAGGATGTTGTTAACAATCATTCA 59.335 33.333 26.59 19.93 45.86 2.57
4374 12475 9.685276 AATATCAGAGGATGTTGTTAACAATCA 57.315 29.630 23.11 20.73 45.86 2.57
4454 12588 4.323409 GCCTTCTCCAGAAACTCTCAATCT 60.323 45.833 0.00 0.00 33.07 2.40
4497 12631 0.753479 TCCAAAACCCACATGTGCGT 60.753 50.000 20.81 15.54 0.00 5.24
4504 12638 2.158559 CGACATCATCCAAAACCCACA 58.841 47.619 0.00 0.00 0.00 4.17
4531 12665 4.298744 TCACTGAATATCTCACTGAGCG 57.701 45.455 0.62 0.00 0.00 5.03
4538 12672 8.548025 TCCCATTAAACTTCACTGAATATCTCA 58.452 33.333 0.00 0.00 0.00 3.27
4546 12680 5.468746 CGAACTTCCCATTAAACTTCACTGA 59.531 40.000 0.00 0.00 0.00 3.41
4570 12704 3.484229 CGTGATGGCGAGAAAGAATTCAC 60.484 47.826 8.44 0.00 38.06 3.18
4600 12765 2.989840 GAGATAATGGATCGCCTTGACG 59.010 50.000 0.00 0.00 39.80 4.35
4608 12773 8.454106 AGAAACAAAAACAGAGATAATGGATCG 58.546 33.333 0.00 0.00 39.80 3.69
4622 12787 2.733858 GCCGCACAGAGAAACAAAAACA 60.734 45.455 0.00 0.00 0.00 2.83
4637 12802 1.154150 GACAAAGCATCAGCCGCAC 60.154 57.895 0.00 0.00 43.56 5.34
4640 12805 1.136147 GCAGACAAAGCATCAGCCG 59.864 57.895 0.00 0.00 43.56 5.52
4643 12808 4.874396 TGATAAGAGCAGACAAAGCATCAG 59.126 41.667 0.00 0.00 0.00 2.90
4651 12816 7.686438 TTGCTTTATTGATAAGAGCAGACAA 57.314 32.000 14.34 0.00 37.51 3.18
4663 12828 7.770897 ACTCTCTTCCGTAATTGCTTTATTGAT 59.229 33.333 0.00 0.00 0.00 2.57
4665 12830 7.308782 ACTCTCTTCCGTAATTGCTTTATTG 57.691 36.000 0.00 0.00 0.00 1.90
4683 12848 2.103153 TCACACCCTCCAAACTCTCT 57.897 50.000 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.