Multiple sequence alignment - TraesCS5D01G036000

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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 TraesCS5D01G036000 chr5D 100.000 3386 0 0 1 3386 35305229 35308614 0.000000e+00 6253.0
1 TraesCS5D01G036000 chr5D 89.660 1973 178 14 1012 2981 202685717 202683768 0.000000e+00 2490.0
2 TraesCS5D01G036000 chr5D 93.829 713 40 2 1 712 35551395 35550686 0.000000e+00 1070.0
3 TraesCS5D01G036000 chr5D 88.646 458 42 5 2931 3384 202683767 202683316 1.780000e-152 549.0
4 TraesCS5D01G036000 chr5D 83.850 452 53 12 1 448 35531688 35532123 2.430000e-111 412.0
5 TraesCS5D01G036000 chr5D 88.657 335 30 3 1 334 35294310 35294637 5.260000e-108 401.0
6 TraesCS5D01G036000 chr5D 80.392 459 67 17 1 448 35534208 35534654 9.060000e-86 327.0
7 TraesCS5D01G036000 chr5D 91.892 74 5 1 841 913 535591519 535591592 5.980000e-18 102.0
8 TraesCS5D01G036000 chr2D 87.053 2379 278 17 1017 3386 414414260 414411903 0.000000e+00 2660.0
9 TraesCS5D01G036000 chr3A 78.577 2404 434 49 1017 3385 579230578 579228221 0.000000e+00 1511.0
10 TraesCS5D01G036000 chr5A 88.187 728 42 16 1 722 24182658 24181969 0.000000e+00 828.0
11 TraesCS5D01G036000 chr5A 90.333 600 38 6 1 599 23933822 23934402 0.000000e+00 769.0
12 TraesCS5D01G036000 chr5A 81.278 454 60 16 6 448 24177138 24177577 9.000000e-91 344.0
13 TraesCS5D01G036000 chr3D 81.788 895 140 13 2082 2971 582185697 582184821 0.000000e+00 728.0
14 TraesCS5D01G036000 chr3D 87.861 346 41 1 1290 1634 582186039 582185694 4.070000e-109 405.0
15 TraesCS5D01G036000 chr3D 79.061 554 97 13 2837 3385 338617215 338616676 2.480000e-96 363.0
16 TraesCS5D01G036000 chr3D 79.826 461 83 8 2931 3384 582184810 582184353 9.060000e-86 327.0
17 TraesCS5D01G036000 chrUn 86.686 676 49 10 1 676 298147082 298146448 0.000000e+00 712.0
18 TraesCS5D01G036000 chrUn 86.232 552 50 9 1 551 340388846 340388320 2.930000e-160 575.0
19 TraesCS5D01G036000 chrUn 93.151 365 20 2 228 588 349553675 349553312 6.430000e-147 531.0
20 TraesCS5D01G036000 chrUn 84.361 454 39 16 1 451 340491751 340491327 1.880000e-112 416.0
21 TraesCS5D01G036000 chrUn 80.088 452 68 18 1 447 288040934 288040500 1.960000e-82 316.0
22 TraesCS5D01G036000 chrUn 79.529 425 58 12 36 439 316546033 316545617 3.330000e-70 276.0
23 TraesCS5D01G036000 chr4D 92.199 141 9 2 841 979 29657672 29657812 7.410000e-47 198.0
24 TraesCS5D01G036000 chr1D 93.798 129 6 1 851 979 421438948 421439074 3.450000e-45 193.0
25 TraesCS5D01G036000 chr1D 92.308 130 7 2 849 977 39998307 39998434 7.460000e-42 182.0
26 TraesCS5D01G036000 chr3B 80.625 160 27 4 1388 1545 417289980 417290137 1.650000e-23 121.0
27 TraesCS5D01G036000 chr1B 86.207 87 12 0 1441 1527 649231418 649231332 1.000000e-15 95.3
28 TraesCS5D01G036000 chr7B 79.070 129 23 4 1419 1545 133735985 133736111 6.020000e-13 86.1
29 TraesCS5D01G036000 chr6A 81.333 75 12 2 1400 1473 52930673 52930746 3.650000e-05 60.2


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 TraesCS5D01G036000 chr5D 35305229 35308614 3385 False 6253.000000 6253 100.000000 1 3386 1 chr5D.!!$F2 3385
1 TraesCS5D01G036000 chr5D 202683316 202685717 2401 True 1519.500000 2490 89.153000 1012 3384 2 chr5D.!!$R2 2372
2 TraesCS5D01G036000 chr5D 35550686 35551395 709 True 1070.000000 1070 93.829000 1 712 1 chr5D.!!$R1 711
3 TraesCS5D01G036000 chr5D 35531688 35534654 2966 False 369.500000 412 82.121000 1 448 2 chr5D.!!$F4 447
4 TraesCS5D01G036000 chr2D 414411903 414414260 2357 True 2660.000000 2660 87.053000 1017 3386 1 chr2D.!!$R1 2369
5 TraesCS5D01G036000 chr3A 579228221 579230578 2357 True 1511.000000 1511 78.577000 1017 3385 1 chr3A.!!$R1 2368
6 TraesCS5D01G036000 chr5A 24181969 24182658 689 True 828.000000 828 88.187000 1 722 1 chr5A.!!$R1 721
7 TraesCS5D01G036000 chr5A 23933822 23934402 580 False 769.000000 769 90.333000 1 599 1 chr5A.!!$F1 598
8 TraesCS5D01G036000 chr3D 582184353 582186039 1686 True 486.666667 728 83.158333 1290 3384 3 chr3D.!!$R2 2094
9 TraesCS5D01G036000 chr3D 338616676 338617215 539 True 363.000000 363 79.061000 2837 3385 1 chr3D.!!$R1 548
10 TraesCS5D01G036000 chrUn 298146448 298147082 634 True 712.000000 712 86.686000 1 676 1 chrUn.!!$R2 675
11 TraesCS5D01G036000 chrUn 340388320 340388846 526 True 575.000000 575 86.232000 1 551 1 chrUn.!!$R4 550

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
712 2223 0.108377 TGCGTAGGTCGTCATGCATT 60.108 50.0 0.0 0.0 42.13 3.56 F
1140 2913 0.393448 TCGTTCGACATGGGTTCCAA 59.607 50.0 0.0 0.0 36.95 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2028 3812 0.108186 TGAATCTCGAATGCACCGCT 60.108 50.0 5.55 0.0 0.00 5.52 R
2623 4410 0.393077 CCTGACCGACAACTGTCCTT 59.607 55.0 4.30 0.0 41.86 3.36 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
17 18 2.046988 CCACCGTGCTGCTGATCA 60.047 61.111 0.00 0.00 0.00 2.92
208 215 1.239296 CGACCACGGTGTACTCCTCA 61.239 60.000 11.98 0.00 35.72 3.86
580 2050 0.570734 CGAAATGCGGCGTAGTACAG 59.429 55.000 9.37 0.00 36.03 2.74
590 2060 1.679680 GCGTAGTACAGGGCATGTCTA 59.320 52.381 8.59 7.66 42.70 2.59
593 2063 3.380637 CGTAGTACAGGGCATGTCTAGTT 59.619 47.826 8.59 0.00 42.70 2.24
659 2168 3.689649 GTGGCAGAAGAAATGTTCCGTAT 59.310 43.478 0.00 0.00 0.00 3.06
672 2183 1.523711 CCGTATGAAGCCGCCATGT 60.524 57.895 0.00 0.00 0.00 3.21
712 2223 0.108377 TGCGTAGGTCGTCATGCATT 60.108 50.000 0.00 0.00 42.13 3.56
726 2237 2.507547 CATTGGCATGTGCGGCAC 60.508 61.111 25.55 25.55 41.78 5.01
734 2245 3.970721 TGTGCGGCACAAGAGATG 58.029 55.556 31.72 0.00 41.69 2.90
735 2246 1.071299 TGTGCGGCACAAGAGATGT 59.929 52.632 31.72 0.00 41.69 3.06
738 2249 1.804151 GTGCGGCACAAGAGATGTAAA 59.196 47.619 27.10 0.00 41.46 2.01
740 2251 3.081061 TGCGGCACAAGAGATGTAAATT 58.919 40.909 0.00 0.00 41.46 1.82
741 2252 3.126858 TGCGGCACAAGAGATGTAAATTC 59.873 43.478 0.00 0.00 41.46 2.17
742 2253 3.126858 GCGGCACAAGAGATGTAAATTCA 59.873 43.478 0.00 0.00 41.46 2.57
743 2254 4.201950 GCGGCACAAGAGATGTAAATTCAT 60.202 41.667 0.00 0.00 41.46 2.57
744 2255 5.268544 CGGCACAAGAGATGTAAATTCATG 58.731 41.667 0.00 0.00 41.46 3.07
745 2256 5.065090 CGGCACAAGAGATGTAAATTCATGA 59.935 40.000 0.00 0.00 41.46 3.07
748 2259 7.977853 GGCACAAGAGATGTAAATTCATGAAAT 59.022 33.333 13.09 0.02 41.46 2.17
791 2302 7.643569 TTTTTGATTAGGAGCTTGCATATCA 57.356 32.000 0.00 0.00 0.00 2.15
792 2303 7.643569 TTTTGATTAGGAGCTTGCATATCAA 57.356 32.000 0.00 0.00 0.00 2.57
793 2304 7.828508 TTTGATTAGGAGCTTGCATATCAAT 57.171 32.000 10.80 0.00 33.57 2.57
794 2305 7.828508 TTGATTAGGAGCTTGCATATCAATT 57.171 32.000 0.00 0.00 33.57 2.32
795 2306 7.444629 TGATTAGGAGCTTGCATATCAATTC 57.555 36.000 0.00 0.00 33.57 2.17
796 2307 6.999871 TGATTAGGAGCTTGCATATCAATTCA 59.000 34.615 0.00 0.00 33.57 2.57
797 2308 7.503230 TGATTAGGAGCTTGCATATCAATTCAA 59.497 33.333 0.00 0.00 33.57 2.69
798 2309 7.828508 TTAGGAGCTTGCATATCAATTCAAT 57.171 32.000 0.00 0.00 33.57 2.57
799 2310 6.726490 AGGAGCTTGCATATCAATTCAATT 57.274 33.333 0.00 0.00 33.57 2.32
800 2311 7.828508 AGGAGCTTGCATATCAATTCAATTA 57.171 32.000 0.00 0.00 33.57 1.40
801 2312 8.418597 AGGAGCTTGCATATCAATTCAATTAT 57.581 30.769 0.00 0.00 33.57 1.28
802 2313 8.304596 AGGAGCTTGCATATCAATTCAATTATG 58.695 33.333 0.00 0.00 33.57 1.90
803 2314 7.544566 GGAGCTTGCATATCAATTCAATTATGG 59.455 37.037 0.00 0.00 33.57 2.74
804 2315 7.959175 AGCTTGCATATCAATTCAATTATGGT 58.041 30.769 0.00 0.00 33.57 3.55
805 2316 8.086522 AGCTTGCATATCAATTCAATTATGGTC 58.913 33.333 0.00 0.00 33.57 4.02
806 2317 7.330208 GCTTGCATATCAATTCAATTATGGTCC 59.670 37.037 0.00 0.00 33.57 4.46
807 2318 6.912082 TGCATATCAATTCAATTATGGTCCG 58.088 36.000 0.00 0.00 0.00 4.79
808 2319 6.072008 TGCATATCAATTCAATTATGGTCCGG 60.072 38.462 0.00 0.00 0.00 5.14
809 2320 4.853924 ATCAATTCAATTATGGTCCGGC 57.146 40.909 0.00 0.00 0.00 6.13
810 2321 3.897239 TCAATTCAATTATGGTCCGGCT 58.103 40.909 0.00 0.00 0.00 5.52
811 2322 5.042463 TCAATTCAATTATGGTCCGGCTA 57.958 39.130 0.00 0.00 0.00 3.93
812 2323 5.630121 TCAATTCAATTATGGTCCGGCTAT 58.370 37.500 0.00 0.00 0.00 2.97
813 2324 6.068010 TCAATTCAATTATGGTCCGGCTATT 58.932 36.000 0.00 0.00 0.00 1.73
814 2325 7.227873 TCAATTCAATTATGGTCCGGCTATTA 58.772 34.615 0.00 0.00 0.00 0.98
815 2326 7.174253 TCAATTCAATTATGGTCCGGCTATTAC 59.826 37.037 0.00 0.00 0.00 1.89
816 2327 4.901868 TCAATTATGGTCCGGCTATTACC 58.098 43.478 0.00 0.00 0.00 2.85
817 2328 4.595781 TCAATTATGGTCCGGCTATTACCT 59.404 41.667 10.37 0.00 34.23 3.08
818 2329 5.072600 TCAATTATGGTCCGGCTATTACCTT 59.927 40.000 10.37 6.82 34.23 3.50
819 2330 2.930826 ATGGTCCGGCTATTACCTTG 57.069 50.000 10.37 0.00 34.23 3.61
820 2331 1.868713 TGGTCCGGCTATTACCTTGA 58.131 50.000 10.37 0.00 34.23 3.02
821 2332 2.404559 TGGTCCGGCTATTACCTTGAT 58.595 47.619 10.37 0.00 34.23 2.57
822 2333 2.775384 TGGTCCGGCTATTACCTTGATT 59.225 45.455 10.37 0.00 34.23 2.57
823 2334 3.181458 TGGTCCGGCTATTACCTTGATTC 60.181 47.826 10.37 0.00 34.23 2.52
824 2335 3.071167 GGTCCGGCTATTACCTTGATTCT 59.929 47.826 0.00 0.00 0.00 2.40
825 2336 4.444449 GGTCCGGCTATTACCTTGATTCTT 60.444 45.833 0.00 0.00 0.00 2.52
826 2337 5.221581 GGTCCGGCTATTACCTTGATTCTTA 60.222 44.000 0.00 0.00 0.00 2.10
827 2338 5.927115 GTCCGGCTATTACCTTGATTCTTAG 59.073 44.000 0.00 0.00 0.00 2.18
828 2339 5.836898 TCCGGCTATTACCTTGATTCTTAGA 59.163 40.000 0.00 0.00 0.00 2.10
829 2340 6.325545 TCCGGCTATTACCTTGATTCTTAGAA 59.674 38.462 0.00 0.00 0.00 2.10
830 2341 7.016268 TCCGGCTATTACCTTGATTCTTAGAAT 59.984 37.037 7.23 7.23 0.00 2.40
831 2342 7.332182 CCGGCTATTACCTTGATTCTTAGAATC 59.668 40.741 23.69 23.69 0.00 2.52
832 2343 7.332182 CGGCTATTACCTTGATTCTTAGAATCC 59.668 40.741 26.29 12.86 0.00 3.01
833 2344 8.379331 GGCTATTACCTTGATTCTTAGAATCCT 58.621 37.037 26.29 12.40 0.00 3.24
834 2345 9.430623 GCTATTACCTTGATTCTTAGAATCCTC 57.569 37.037 26.29 9.31 0.00 3.71
844 2355 9.612879 TGATTCTTAGAATCCTCATATTCTCCT 57.387 33.333 26.29 0.00 43.52 3.69
847 2358 8.588290 TCTTAGAATCCTCATATTCTCCTAGC 57.412 38.462 2.53 0.00 43.52 3.42
848 2359 7.617723 TCTTAGAATCCTCATATTCTCCTAGCC 59.382 40.741 2.53 0.00 43.52 3.93
849 2360 5.029474 AGAATCCTCATATTCTCCTAGCCC 58.971 45.833 0.00 0.00 41.34 5.19
850 2361 3.923273 TCCTCATATTCTCCTAGCCCA 57.077 47.619 0.00 0.00 0.00 5.36
851 2362 3.784178 TCCTCATATTCTCCTAGCCCAG 58.216 50.000 0.00 0.00 0.00 4.45
852 2363 3.142977 TCCTCATATTCTCCTAGCCCAGT 59.857 47.826 0.00 0.00 0.00 4.00
853 2364 3.260380 CCTCATATTCTCCTAGCCCAGTG 59.740 52.174 0.00 0.00 0.00 3.66
854 2365 3.242867 TCATATTCTCCTAGCCCAGTGG 58.757 50.000 0.63 0.63 0.00 4.00
874 2385 4.057428 AGCGAGCCGGTGTGTCTC 62.057 66.667 1.90 0.00 35.85 3.36
876 2387 4.039357 CGAGCCGGTGTGTCTCGT 62.039 66.667 17.20 0.00 43.16 4.18
877 2388 2.430921 GAGCCGGTGTGTCTCGTG 60.431 66.667 1.90 0.00 0.00 4.35
878 2389 3.916392 GAGCCGGTGTGTCTCGTGG 62.916 68.421 1.90 0.00 0.00 4.94
882 2393 3.986006 GGTGTGTCTCGTGGCCGA 61.986 66.667 0.00 0.00 41.73 5.54
883 2394 2.733593 GTGTGTCTCGTGGCCGAC 60.734 66.667 0.00 0.00 38.40 4.79
897 2408 4.717629 CGACGCAGGTTCGAGCCA 62.718 66.667 21.22 0.00 0.00 4.75
898 2409 3.112709 GACGCAGGTTCGAGCCAC 61.113 66.667 21.22 10.94 0.00 5.01
917 2428 4.427661 GCTCGGACGCTGCTGTCT 62.428 66.667 18.75 0.00 38.91 3.41
918 2429 2.202544 CTCGGACGCTGCTGTCTC 60.203 66.667 18.75 11.22 38.91 3.36
919 2430 2.982744 CTCGGACGCTGCTGTCTCA 61.983 63.158 18.75 8.97 38.91 3.27
920 2431 2.807045 CGGACGCTGCTGTCTCAC 60.807 66.667 18.75 6.84 38.91 3.51
921 2432 2.340078 GGACGCTGCTGTCTCACA 59.660 61.111 18.75 0.00 38.91 3.58
922 2433 1.079543 GGACGCTGCTGTCTCACAT 60.080 57.895 18.75 0.00 38.91 3.21
923 2434 0.671781 GGACGCTGCTGTCTCACATT 60.672 55.000 18.75 0.00 38.91 2.71
924 2435 1.151668 GACGCTGCTGTCTCACATTT 58.848 50.000 14.37 0.00 35.95 2.32
925 2436 1.127582 GACGCTGCTGTCTCACATTTC 59.872 52.381 14.37 0.00 35.95 2.17
926 2437 1.270518 ACGCTGCTGTCTCACATTTCT 60.271 47.619 0.00 0.00 0.00 2.52
927 2438 1.802960 CGCTGCTGTCTCACATTTCTT 59.197 47.619 0.00 0.00 0.00 2.52
928 2439 2.159734 CGCTGCTGTCTCACATTTCTTC 60.160 50.000 0.00 0.00 0.00 2.87
929 2440 3.072944 GCTGCTGTCTCACATTTCTTCT 58.927 45.455 0.00 0.00 0.00 2.85
930 2441 3.124976 GCTGCTGTCTCACATTTCTTCTC 59.875 47.826 0.00 0.00 0.00 2.87
931 2442 4.567971 CTGCTGTCTCACATTTCTTCTCT 58.432 43.478 0.00 0.00 0.00 3.10
932 2443 4.965814 TGCTGTCTCACATTTCTTCTCTT 58.034 39.130 0.00 0.00 0.00 2.85
933 2444 6.101650 TGCTGTCTCACATTTCTTCTCTTA 57.898 37.500 0.00 0.00 0.00 2.10
934 2445 6.524734 TGCTGTCTCACATTTCTTCTCTTAA 58.475 36.000 0.00 0.00 0.00 1.85
937 2448 9.155975 GCTGTCTCACATTTCTTCTCTTAATAA 57.844 33.333 0.00 0.00 0.00 1.40
961 2472 2.095604 ATCAGTAGGGGCTTCTCCTC 57.904 55.000 0.00 0.00 35.92 3.71
963 2474 2.215093 TCAGTAGGGGCTTCTCCTCTA 58.785 52.381 0.00 0.00 46.31 2.43
969 2480 2.176148 AGGGGCTTCTCCTCTACTAGTC 59.824 54.545 0.00 0.00 46.31 2.59
970 2481 2.176148 GGGGCTTCTCCTCTACTAGTCT 59.824 54.545 0.00 0.00 34.39 3.24
971 2482 3.395273 GGGGCTTCTCCTCTACTAGTCTA 59.605 52.174 0.00 0.00 34.39 2.59
972 2483 4.506095 GGGGCTTCTCCTCTACTAGTCTAG 60.506 54.167 0.00 5.27 34.39 2.43
973 2484 4.103627 GGGCTTCTCCTCTACTAGTCTAGT 59.896 50.000 16.65 16.65 37.65 2.57
974 2485 5.398239 GGGCTTCTCCTCTACTAGTCTAGTT 60.398 48.000 17.59 2.97 36.24 2.24
975 2486 6.124340 GGCTTCTCCTCTACTAGTCTAGTTT 58.876 44.000 17.59 0.00 40.14 2.66
977 2488 7.123098 GGCTTCTCCTCTACTAGTCTAGTTTTT 59.877 40.741 17.59 0.00 40.14 1.94
1010 2521 8.008922 AGATCATTAACAATCAATGGGAATCCT 58.991 33.333 0.00 0.00 34.73 3.24
1028 2800 2.678934 CCCTTCCTCCCGTCGTCA 60.679 66.667 0.00 0.00 0.00 4.35
1041 2813 3.449227 CGTCAGCTACTCCGGCCA 61.449 66.667 2.24 0.00 0.00 5.36
1140 2913 0.393448 TCGTTCGACATGGGTTCCAA 59.607 50.000 0.00 0.00 36.95 3.53
1156 2929 3.494254 AACCCCCGCTTGGTGACA 61.494 61.111 0.00 0.00 35.88 3.58
1171 2944 2.363795 ACATCCTCCTTCCGCCGA 60.364 61.111 0.00 0.00 0.00 5.54
1202 2975 4.636435 CGGTGGTTTCGGGCCTGT 62.636 66.667 12.43 0.00 0.00 4.00
1328 3107 2.324014 AAGGAACTGTGGCGTCAGCA 62.324 55.000 0.00 0.00 42.95 4.41
1386 3165 2.026879 GAGCGCCACGAGATCTCC 59.973 66.667 17.13 1.97 0.00 3.71
1475 3254 0.955428 ATCGTGTGCTTCCGTTGCAT 60.955 50.000 0.00 0.00 42.69 3.96
1500 3279 0.549950 CTGGCCATGTCTCCAAGGAT 59.450 55.000 5.51 0.00 30.80 3.24
1742 3526 3.562635 GCCTAACGACCTGTGCAC 58.437 61.111 10.75 10.75 0.00 4.57
1833 3617 1.300971 GCGCAAACAGAGGCATCTCA 61.301 55.000 0.30 0.00 42.34 3.27
1897 3681 1.071471 CCAGAGTGGCTGTCGGTTT 59.929 57.895 0.00 0.00 43.33 3.27
1902 3686 1.125711 AGTGGCTGTCGGTTTACCCT 61.126 55.000 0.00 0.00 0.00 4.34
1939 3723 1.525995 CTTGTGGTGTTCGGCAGGT 60.526 57.895 0.00 0.00 0.00 4.00
2124 3908 1.973812 GGTGGAAGACCTGCTTGGC 60.974 63.158 0.00 0.00 42.25 4.52
2126 3910 1.073722 TGGAAGACCTGCTTGGCTG 59.926 57.895 0.00 0.00 40.22 4.85
2174 3958 2.729862 GTCAAGCTCGCGTCGTGT 60.730 61.111 5.77 0.00 0.00 4.49
2182 3966 0.720027 CTCGCGTCGTGTTCTCTCTA 59.280 55.000 5.77 0.00 0.00 2.43
2189 3973 4.534168 CGTCGTGTTCTCTCTACTTTCAA 58.466 43.478 0.00 0.00 0.00 2.69
2197 3981 4.072839 TCTCTCTACTTTCAAGCTCACGA 58.927 43.478 0.00 0.00 0.00 4.35
2259 4043 4.302622 GCTATCCCTGAGCCTGGA 57.697 61.111 0.00 0.00 33.60 3.86
2300 4084 2.100991 GGCGCTGCTGCAATACAC 59.899 61.111 16.29 0.00 39.64 2.90
2301 4085 2.689785 GGCGCTGCTGCAATACACA 61.690 57.895 16.29 0.00 39.64 3.72
2316 4100 6.604396 TGCAATACACAAGATTCTCATCCATT 59.396 34.615 0.00 0.00 0.00 3.16
2370 4155 2.833957 GTGGTTCTTGACGGGGGT 59.166 61.111 0.00 0.00 0.00 4.95
2373 4158 2.826003 GGTTCTTGACGGGGGTGGT 61.826 63.158 0.00 0.00 0.00 4.16
2402 4187 1.334384 TAGTGGGCAGAGCGGCATTA 61.334 55.000 1.45 0.00 43.60 1.90
2474 4259 4.254709 AGCGTGCCTGGCAGTTCA 62.255 61.111 24.10 8.15 40.08 3.18
2500 4285 4.008933 GACTCCCGTGCTGGCAGT 62.009 66.667 17.16 0.00 35.87 4.40
2708 4496 6.555463 ATGCCTTCTGGAATTCAAAATCAT 57.445 33.333 7.93 0.00 34.57 2.45
2734 4522 0.323816 TCGATGGAGAGAGGTGCAGT 60.324 55.000 0.00 0.00 0.00 4.40
2798 4587 2.510238 GCACTGCGAGCGGATCTT 60.510 61.111 11.27 0.00 0.00 2.40
2804 4593 2.287909 ACTGCGAGCGGATCTTCTATTC 60.288 50.000 11.27 0.00 0.00 1.75
2831 4620 2.491152 CGCTTCCGCCAATTGCAT 59.509 55.556 0.00 0.00 41.33 3.96
3234 5130 0.970937 CGGTGGTAGCTCTTCCTGGA 60.971 60.000 0.00 0.00 0.00 3.86
3252 5160 0.170561 GACATGCACGTACGGAGACT 59.829 55.000 21.06 0.00 0.00 3.24
3258 5166 2.353889 TGCACGTACGGAGACTATTCTC 59.646 50.000 21.06 1.50 46.90 2.87
3270 5178 6.861065 GAGACTATTCTCGACTCTGATCTT 57.139 41.667 0.00 0.00 39.13 2.40
3346 5254 0.104671 GCAAAGGGCTCTTGCAACAA 59.895 50.000 0.00 0.00 41.91 2.83
3361 5269 0.255890 AACAATCACGGAGGGGATGG 59.744 55.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 4.393155 AAGTGCGGCGATGGAGCA 62.393 61.111 12.98 0.00 39.27 4.26
28 29 2.507102 ATGACGAGAAGTGCGGCG 60.507 61.111 0.51 0.51 40.33 6.46
34 35 2.818751 AGAGGGAGATGACGAGAAGT 57.181 50.000 0.00 0.00 0.00 3.01
121 122 2.254350 CCGAGCTCGACGTCAACA 59.746 61.111 36.59 0.00 43.02 3.33
251 261 4.651008 GTCACCGTCGGCCGACAA 62.651 66.667 46.26 30.27 44.77 3.18
580 2050 1.653151 GGTTCGAACTAGACATGCCC 58.347 55.000 26.32 3.34 0.00 5.36
590 2060 0.598065 GCAGCATTTGGGTTCGAACT 59.402 50.000 26.32 4.67 0.00 3.01
593 2063 2.331893 CGGCAGCATTTGGGTTCGA 61.332 57.895 0.00 0.00 0.00 3.71
659 2168 0.815213 GAGCATACATGGCGGCTTCA 60.815 55.000 11.43 0.00 36.59 3.02
712 2223 3.672447 CTTGTGCCGCACATGCCA 61.672 61.111 26.22 10.99 44.16 4.92
723 2234 8.922058 ATTTCATGAATTTACATCTCTTGTGC 57.078 30.769 9.40 0.00 39.48 4.57
767 2278 7.643569 TGATATGCAAGCTCCTAATCAAAAA 57.356 32.000 0.00 0.00 0.00 1.94
769 2280 7.828508 ATTGATATGCAAGCTCCTAATCAAA 57.171 32.000 12.54 0.00 40.42 2.69
770 2281 7.503230 TGAATTGATATGCAAGCTCCTAATCAA 59.497 33.333 11.49 11.49 40.42 2.57
771 2282 6.999871 TGAATTGATATGCAAGCTCCTAATCA 59.000 34.615 0.00 0.00 40.42 2.57
772 2283 7.444629 TGAATTGATATGCAAGCTCCTAATC 57.555 36.000 0.00 0.00 40.42 1.75
773 2284 7.828508 TTGAATTGATATGCAAGCTCCTAAT 57.171 32.000 0.00 0.00 40.42 1.73
774 2285 7.828508 ATTGAATTGATATGCAAGCTCCTAA 57.171 32.000 0.00 0.00 40.42 2.69
775 2286 7.828508 AATTGAATTGATATGCAAGCTCCTA 57.171 32.000 0.00 0.00 40.42 2.94
776 2287 6.726490 AATTGAATTGATATGCAAGCTCCT 57.274 33.333 0.00 0.00 40.42 3.69
777 2288 7.544566 CCATAATTGAATTGATATGCAAGCTCC 59.455 37.037 0.00 0.00 40.42 4.70
778 2289 8.086522 ACCATAATTGAATTGATATGCAAGCTC 58.913 33.333 0.00 0.00 40.42 4.09
780 2291 7.330208 GGACCATAATTGAATTGATATGCAAGC 59.670 37.037 0.00 0.00 40.42 4.01
781 2292 7.539710 CGGACCATAATTGAATTGATATGCAAG 59.460 37.037 0.00 0.00 40.42 4.01
782 2293 7.369607 CGGACCATAATTGAATTGATATGCAA 58.630 34.615 0.00 0.00 41.53 4.08
783 2294 6.072008 CCGGACCATAATTGAATTGATATGCA 60.072 38.462 0.00 0.00 0.00 3.96
786 2297 6.248433 AGCCGGACCATAATTGAATTGATAT 58.752 36.000 5.05 0.00 0.00 1.63
787 2298 5.630121 AGCCGGACCATAATTGAATTGATA 58.370 37.500 5.05 0.00 0.00 2.15
788 2299 4.473444 AGCCGGACCATAATTGAATTGAT 58.527 39.130 5.05 0.00 0.00 2.57
790 2301 5.964958 ATAGCCGGACCATAATTGAATTG 57.035 39.130 5.05 0.00 0.00 2.32
791 2302 6.433093 GGTAATAGCCGGACCATAATTGAATT 59.567 38.462 5.05 0.00 33.16 2.17
792 2303 5.944007 GGTAATAGCCGGACCATAATTGAAT 59.056 40.000 5.05 0.00 33.16 2.57
793 2304 5.072600 AGGTAATAGCCGGACCATAATTGAA 59.927 40.000 5.05 0.00 35.56 2.69
794 2305 4.595781 AGGTAATAGCCGGACCATAATTGA 59.404 41.667 5.05 0.00 35.56 2.57
795 2306 4.906618 AGGTAATAGCCGGACCATAATTG 58.093 43.478 5.05 0.00 35.56 2.32
796 2307 5.072600 TCAAGGTAATAGCCGGACCATAATT 59.927 40.000 5.05 0.00 35.56 1.40
797 2308 4.595781 TCAAGGTAATAGCCGGACCATAAT 59.404 41.667 5.05 0.00 35.56 1.28
798 2309 3.968649 TCAAGGTAATAGCCGGACCATAA 59.031 43.478 5.05 0.00 35.56 1.90
799 2310 3.578978 TCAAGGTAATAGCCGGACCATA 58.421 45.455 5.05 0.00 35.56 2.74
800 2311 2.404559 TCAAGGTAATAGCCGGACCAT 58.595 47.619 5.05 0.00 35.56 3.55
801 2312 1.868713 TCAAGGTAATAGCCGGACCA 58.131 50.000 5.05 0.00 35.56 4.02
802 2313 3.071167 AGAATCAAGGTAATAGCCGGACC 59.929 47.826 5.05 2.55 0.00 4.46
803 2314 4.338379 AGAATCAAGGTAATAGCCGGAC 57.662 45.455 5.05 0.00 0.00 4.79
804 2315 5.836898 TCTAAGAATCAAGGTAATAGCCGGA 59.163 40.000 5.05 0.00 0.00 5.14
805 2316 6.097915 TCTAAGAATCAAGGTAATAGCCGG 57.902 41.667 0.00 0.00 0.00 6.13
806 2317 7.332182 GGATTCTAAGAATCAAGGTAATAGCCG 59.668 40.741 0.20 0.00 0.00 5.52
807 2318 8.379331 AGGATTCTAAGAATCAAGGTAATAGCC 58.621 37.037 0.20 0.00 0.00 3.93
808 2319 9.430623 GAGGATTCTAAGAATCAAGGTAATAGC 57.569 37.037 0.20 0.00 0.00 2.97
818 2329 9.612879 AGGAGAATATGAGGATTCTAAGAATCA 57.387 33.333 0.20 0.62 44.46 2.57
821 2332 9.030452 GCTAGGAGAATATGAGGATTCTAAGAA 57.970 37.037 0.00 0.00 44.46 2.52
822 2333 7.617723 GGCTAGGAGAATATGAGGATTCTAAGA 59.382 40.741 0.00 0.00 44.46 2.10
823 2334 7.147742 GGGCTAGGAGAATATGAGGATTCTAAG 60.148 44.444 0.00 0.28 44.46 2.18
824 2335 6.670027 GGGCTAGGAGAATATGAGGATTCTAA 59.330 42.308 0.00 0.00 44.46 2.10
825 2336 6.198639 GGGCTAGGAGAATATGAGGATTCTA 58.801 44.000 0.00 0.00 44.46 2.10
826 2337 5.029474 GGGCTAGGAGAATATGAGGATTCT 58.971 45.833 0.00 0.00 46.57 2.40
827 2338 4.780021 TGGGCTAGGAGAATATGAGGATTC 59.220 45.833 0.00 0.00 36.28 2.52
828 2339 4.767908 TGGGCTAGGAGAATATGAGGATT 58.232 43.478 0.00 0.00 0.00 3.01
829 2340 4.202879 ACTGGGCTAGGAGAATATGAGGAT 60.203 45.833 2.02 0.00 0.00 3.24
830 2341 3.142977 ACTGGGCTAGGAGAATATGAGGA 59.857 47.826 2.02 0.00 0.00 3.71
831 2342 3.260380 CACTGGGCTAGGAGAATATGAGG 59.740 52.174 2.02 0.00 0.00 3.86
832 2343 3.260380 CCACTGGGCTAGGAGAATATGAG 59.740 52.174 2.02 0.00 0.00 2.90
833 2344 3.242867 CCACTGGGCTAGGAGAATATGA 58.757 50.000 2.02 0.00 0.00 2.15
834 2345 3.692257 CCACTGGGCTAGGAGAATATG 57.308 52.381 2.02 0.00 0.00 1.78
856 2367 4.363990 AGACACACCGGCTCGCTG 62.364 66.667 0.00 0.00 0.00 5.18
857 2368 4.057428 GAGACACACCGGCTCGCT 62.057 66.667 0.00 0.00 0.00 4.93
860 2371 2.430921 CACGAGACACACCGGCTC 60.431 66.667 0.00 0.00 0.00 4.70
861 2372 3.991051 CCACGAGACACACCGGCT 61.991 66.667 0.00 0.00 0.00 5.52
865 2376 3.986006 TCGGCCACGAGACACACC 61.986 66.667 2.24 0.00 45.59 4.16
880 2391 4.717629 TGGCTCGAACCTGCGTCG 62.718 66.667 6.39 0.00 0.00 5.12
881 2392 3.112709 GTGGCTCGAACCTGCGTC 61.113 66.667 6.39 0.00 0.00 5.19
900 2411 4.427661 AGACAGCAGCGTCCGAGC 62.428 66.667 12.07 0.00 36.52 5.03
901 2412 2.202544 GAGACAGCAGCGTCCGAG 60.203 66.667 12.07 0.00 36.52 4.63
902 2413 2.983592 TGAGACAGCAGCGTCCGA 60.984 61.111 12.07 0.00 36.52 4.55
903 2414 2.807045 GTGAGACAGCAGCGTCCG 60.807 66.667 12.07 0.00 36.52 4.79
904 2415 0.671781 AATGTGAGACAGCAGCGTCC 60.672 55.000 12.07 6.42 36.52 4.79
905 2416 1.127582 GAAATGTGAGACAGCAGCGTC 59.872 52.381 8.75 8.75 36.08 5.19
906 2417 1.151668 GAAATGTGAGACAGCAGCGT 58.848 50.000 0.00 0.00 0.00 5.07
907 2418 1.436600 AGAAATGTGAGACAGCAGCG 58.563 50.000 0.00 0.00 0.00 5.18
908 2419 3.072944 AGAAGAAATGTGAGACAGCAGC 58.927 45.455 0.00 0.00 0.00 5.25
909 2420 4.567971 AGAGAAGAAATGTGAGACAGCAG 58.432 43.478 0.00 0.00 0.00 4.24
910 2421 4.613925 AGAGAAGAAATGTGAGACAGCA 57.386 40.909 0.00 0.00 0.00 4.41
911 2422 7.608308 ATTAAGAGAAGAAATGTGAGACAGC 57.392 36.000 0.00 0.00 0.00 4.40
939 2450 3.193782 AGGAGAAGCCCCTACTGATTTT 58.806 45.455 0.00 0.00 37.37 1.82
940 2451 2.774809 GAGGAGAAGCCCCTACTGATTT 59.225 50.000 0.00 0.00 37.37 2.17
945 2456 2.219571 AGTAGAGGAGAAGCCCCTACT 58.780 52.381 0.00 0.00 36.43 2.57
947 2458 3.395273 GACTAGTAGAGGAGAAGCCCCTA 59.605 52.174 3.59 0.00 37.37 3.53
951 2462 5.300411 ACTAGACTAGTAGAGGAGAAGCC 57.700 47.826 13.63 0.00 37.23 4.35
952 2463 7.634671 AAAACTAGACTAGTAGAGGAGAAGC 57.365 40.000 15.51 0.00 38.26 3.86
978 2489 9.234827 CCCATTGATTGTTAATGATCTATAGCA 57.765 33.333 0.00 0.00 37.65 3.49
979 2490 9.453572 TCCCATTGATTGTTAATGATCTATAGC 57.546 33.333 0.00 0.00 37.65 2.97
983 2494 9.300681 GGATTCCCATTGATTGTTAATGATCTA 57.699 33.333 0.00 0.00 37.65 1.98
984 2495 8.008922 AGGATTCCCATTGATTGTTAATGATCT 58.991 33.333 0.00 0.00 37.65 2.75
986 2497 7.234166 GGAGGATTCCCATTGATTGTTAATGAT 59.766 37.037 0.00 0.00 37.53 2.45
987 2498 6.550854 GGAGGATTCCCATTGATTGTTAATGA 59.449 38.462 0.00 0.00 37.53 2.57
989 2500 6.983906 GGAGGATTCCCATTGATTGTTAAT 57.016 37.500 0.00 0.00 37.53 1.40
1003 2514 1.411651 CGGGAGGAAGGGAGGATTCC 61.412 65.000 0.00 0.00 45.56 3.01
1006 2517 1.075151 GACGGGAGGAAGGGAGGAT 60.075 63.158 0.00 0.00 0.00 3.24
1008 2519 3.148279 CGACGGGAGGAAGGGAGG 61.148 72.222 0.00 0.00 0.00 4.30
1010 2521 2.362120 GACGACGGGAGGAAGGGA 60.362 66.667 0.00 0.00 0.00 4.20
1140 2913 3.256960 ATGTCACCAAGCGGGGGT 61.257 61.111 0.00 0.00 42.53 4.95
1156 2929 2.128507 GTCTCGGCGGAAGGAGGAT 61.129 63.158 7.21 0.00 0.00 3.24
1376 3155 3.332395 TCTCCGGGGAGATCTCGT 58.668 61.111 16.46 0.00 45.26 4.18
1475 3254 1.274703 GGAGACATGGCCAGGAAGGA 61.275 60.000 26.87 0.00 41.22 3.36
1500 3279 2.032528 CTCCTGGGTCGCTTGCAA 59.967 61.111 0.00 0.00 0.00 4.08
1833 3617 1.366366 CTCCAACACGAACTCCGGT 59.634 57.895 0.00 0.00 43.93 5.28
1897 3681 0.410663 TCCTCTGGACGGAAAGGGTA 59.589 55.000 0.00 0.00 0.00 3.69
1939 3723 1.137675 CATGAGATTCCTGTGCTCCGA 59.862 52.381 0.00 0.00 0.00 4.55
2028 3812 0.108186 TGAATCTCGAATGCACCGCT 60.108 50.000 5.55 0.00 0.00 5.52
2124 3908 1.608055 TGTCCACCATGCAAGAACAG 58.392 50.000 0.00 0.00 0.00 3.16
2126 3910 2.642139 CATGTCCACCATGCAAGAAC 57.358 50.000 0.00 0.00 44.21 3.01
2174 3958 4.519350 TCGTGAGCTTGAAAGTAGAGAGAA 59.481 41.667 0.00 0.00 0.00 2.87
2182 3966 1.209128 CACGTCGTGAGCTTGAAAGT 58.791 50.000 20.75 0.00 35.23 2.66
2189 3973 4.039357 CCGTCCACGTCGTGAGCT 62.039 66.667 26.53 0.00 35.23 4.09
2233 4017 2.042762 AGGGATAGCCAGCCACCA 59.957 61.111 0.00 0.00 35.15 4.17
2300 4084 7.068348 ACTGATTCCAAATGGATGAGAATCTTG 59.932 37.037 2.38 3.87 44.98 3.02
2301 4085 7.068348 CACTGATTCCAAATGGATGAGAATCTT 59.932 37.037 2.38 0.00 44.98 2.40
2316 4100 1.808411 GAAGTCGGCACTGATTCCAA 58.192 50.000 0.00 0.00 31.06 3.53
2370 4155 0.686441 CCCACTATCGGAGGACACCA 60.686 60.000 0.00 0.00 0.00 4.17
2373 4158 1.001120 TGCCCACTATCGGAGGACA 59.999 57.895 0.00 0.00 0.00 4.02
2621 4408 1.341531 CTGACCGACAACTGTCCTTCT 59.658 52.381 4.30 0.00 41.86 2.85
2623 4410 0.393077 CCTGACCGACAACTGTCCTT 59.607 55.000 4.30 0.00 41.86 3.36
2685 4473 6.555463 ATGATTTTGAATTCCAGAAGGCAT 57.445 33.333 2.27 1.70 33.74 4.40
2708 4496 2.093075 ACCTCTCTCCATCGAGTCGTTA 60.093 50.000 13.12 0.00 37.40 3.18
2734 4522 1.842920 TCCTGGACTGCAAGCTGGA 60.843 57.895 0.00 0.00 37.60 3.86
2740 4528 0.813610 CACGTTGTCCTGGACTGCAA 60.814 55.000 26.03 10.90 33.15 4.08
2831 4620 2.038975 AGGCGCCAACTCCCTAGA 59.961 61.111 31.54 0.00 0.00 2.43
2973 4864 0.880278 CGGCAGGTTGGTCATATCCG 60.880 60.000 0.00 0.00 0.00 4.18
2977 4868 2.270850 GCCGGCAGGTTGGTCATA 59.729 61.111 24.80 0.00 40.50 2.15
3234 5130 1.456296 TAGTCTCCGTACGTGCATGT 58.544 50.000 17.19 17.19 0.00 3.21
3252 5160 6.378564 AGTTGGAAAGATCAGAGTCGAGAATA 59.621 38.462 0.00 0.00 0.00 1.75
3258 5166 3.681897 CCAAGTTGGAAAGATCAGAGTCG 59.318 47.826 17.60 0.00 40.96 4.18
3270 5178 1.531365 CAGGGCAGCCAAGTTGGAA 60.531 57.895 26.52 0.00 40.96 3.53
3346 5254 1.771746 ATGCCATCCCCTCCGTGAT 60.772 57.895 0.00 0.00 0.00 3.06
3361 5269 1.542915 TGCCAAAGCTTCTTGAGATGC 59.457 47.619 0.00 10.03 43.17 3.91


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

AutoCloner maintained by Alex Coulton.