Multiple sequence alignment - TraesCS7A01G195800

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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 TraesCS7A01G195800 chr7A 100.000 3314 0 0 1 3314 155647689 155644376 0.000000e+00 6120.0
1 TraesCS7A01G195800 chr7B 89.983 2915 137 62 1 2840 115562143 115559309 0.000000e+00 3622.0
2 TraesCS7A01G195800 chr7B 93.970 398 14 5 2926 3314 115526260 115525864 7.920000e-166 593.0
3 TraesCS7A01G195800 chr7B 84.545 110 12 2 1773 1877 619071990 619072099 1.630000e-18 104.0
4 TraesCS7A01G195800 chr7D 90.692 2009 96 31 856 2835 153774122 153772176 0.000000e+00 2590.0
5 TraesCS7A01G195800 chr7D 91.854 712 31 8 1 711 153774876 153774191 0.000000e+00 968.0
6 TraesCS7A01G195800 chr7D 94.315 387 17 3 2928 3314 153769272 153768891 3.680000e-164 588.0
7 TraesCS7A01G195800 chr7D 84.211 95 13 1 1443 1537 30175013 30175105 1.270000e-14 91.6
8 TraesCS7A01G195800 chr6B 80.499 882 133 25 1171 2022 599685658 599686530 1.000000e-179 640.0
9 TraesCS7A01G195800 chr6D 80.298 873 142 18 1171 2022 400648390 400649253 1.680000e-177 632.0
10 TraesCS7A01G195800 chr6A 79.435 885 143 20 1171 2022 546596371 546597249 1.020000e-164 590.0
11 TraesCS7A01G195800 chr5D 77.880 217 33 5 1337 1540 247346648 247346862 1.620000e-23 121.0


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 TraesCS7A01G195800 chr7A 155644376 155647689 3313 True 6120 6120 100.000 1 3314 1 chr7A.!!$R1 3313
1 TraesCS7A01G195800 chr7B 115559309 115562143 2834 True 3622 3622 89.983 1 2840 1 chr7B.!!$R2 2839
2 TraesCS7A01G195800 chr7D 153768891 153774876 5985 True 1382 2590 92.287 1 3314 3 chr7D.!!$R1 3313
3 TraesCS7A01G195800 chr6B 599685658 599686530 872 False 640 640 80.499 1171 2022 1 chr6B.!!$F1 851
4 TraesCS7A01G195800 chr6D 400648390 400649253 863 False 632 632 80.298 1171 2022 1 chr6D.!!$F1 851
5 TraesCS7A01G195800 chr6A 546596371 546597249 878 False 590 590 79.435 1171 2022 1 chr6A.!!$F1 851

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
524 551 0.110373 CCGTTGGTTTCTTGCTACGC 60.11 55.0 0.0 0.0 0.0 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2369 2453 0.045419 GCGAAAAACAACAACGCACG 60.045 50.0 0.0 0.0 46.75 5.34 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 7.740346 GGCACATCGTTCGATAAGTTTATTATG 59.260 37.037 7.38 0.00 0.00 1.90
49 50 8.484799 GCACATCGTTCGATAAGTTTATTATGA 58.515 33.333 7.38 0.00 0.00 2.15
131 132 8.996271 CATTATGAGAAGCATGCTGACTTTATA 58.004 33.333 23.48 19.65 37.87 0.98
132 133 9.736414 ATTATGAGAAGCATGCTGACTTTATAT 57.264 29.630 23.48 16.53 37.87 0.86
186 187 1.213926 GATGCTCTCCCTCCAAATGGT 59.786 52.381 0.00 0.00 36.34 3.55
189 190 1.680249 GCTCTCCCTCCAAATGGTCAC 60.680 57.143 0.00 0.00 36.34 3.67
193 194 0.323725 CCCTCCAAATGGTCACCCAG 60.324 60.000 0.00 0.00 46.15 4.45
214 215 1.201647 TGGGAGACGACGATTGTTCTC 59.798 52.381 0.00 2.62 0.00 2.87
215 216 1.201647 GGGAGACGACGATTGTTCTCA 59.798 52.381 14.21 0.00 0.00 3.27
454 481 3.403038 TGAGCTAAAGTCTTCAACTGCC 58.597 45.455 0.00 0.00 38.58 4.85
489 516 7.990886 ACTTAGAAATAAGTTGTCCTTGTCACA 59.009 33.333 0.00 0.00 36.98 3.58
524 551 0.110373 CCGTTGGTTTCTTGCTACGC 60.110 55.000 0.00 0.00 0.00 4.42
551 578 7.713942 AGTTAAACACGGTTGAGAGAAACTATT 59.286 33.333 0.00 0.00 0.00 1.73
557 584 7.072030 CACGGTTGAGAGAAACTATTTTTCTG 58.928 38.462 4.02 0.00 38.73 3.02
573 600 7.704789 ATTTTTCTGATCTGACAAGCAAAAC 57.295 32.000 1.16 0.00 0.00 2.43
583 610 5.041951 TGACAAGCAAAACGGACATTATC 57.958 39.130 0.00 0.00 0.00 1.75
584 611 4.078363 ACAAGCAAAACGGACATTATCG 57.922 40.909 0.00 0.00 0.00 2.92
677 705 3.048600 AGGCCAGCATTAGACTATTCCA 58.951 45.455 5.01 0.00 0.00 3.53
684 712 4.058817 GCATTAGACTATTCCAACCGAGG 58.941 47.826 0.00 0.00 0.00 4.63
713 741 2.012236 ACTTCTCCCCTCCTACCTTCT 58.988 52.381 0.00 0.00 0.00 2.85
714 742 2.387510 ACTTCTCCCCTCCTACCTTCTT 59.612 50.000 0.00 0.00 0.00 2.52
715 743 2.850695 TCTCCCCTCCTACCTTCTTC 57.149 55.000 0.00 0.00 0.00 2.87
735 763 0.249676 CCACAGAGCAGATGCAGAGT 59.750 55.000 7.68 0.00 45.16 3.24
824 856 7.958053 AACGGCAAGTTATACTATTATCCAC 57.042 36.000 0.00 0.00 42.14 4.02
825 857 7.058023 ACGGCAAGTTATACTATTATCCACA 57.942 36.000 0.00 0.00 0.00 4.17
826 858 7.152645 ACGGCAAGTTATACTATTATCCACAG 58.847 38.462 0.00 0.00 0.00 3.66
829 861 9.420551 GGCAAGTTATACTATTATCCACAGTAC 57.579 37.037 0.00 0.00 0.00 2.73
833 865 8.853126 AGTTATACTATTATCCACAGTACGCAA 58.147 33.333 0.00 0.00 0.00 4.85
834 866 9.635520 GTTATACTATTATCCACAGTACGCAAT 57.364 33.333 0.00 0.00 0.00 3.56
842 874 8.719560 TTATCCACAGTACGCAATAATTTGTA 57.280 30.769 0.00 0.00 35.17 2.41
846 878 7.982919 TCCACAGTACGCAATAATTTGTATACT 59.017 33.333 4.17 0.00 36.70 2.12
847 879 8.061857 CCACAGTACGCAATAATTTGTATACTG 58.938 37.037 19.08 19.08 46.08 2.74
850 882 8.974408 CAGTACGCAATAATTTGTATACTGCTA 58.026 33.333 4.17 0.00 41.33 3.49
852 884 8.975439 GTACGCAATAATTTGTATACTGCTACT 58.025 33.333 4.17 0.00 35.17 2.57
854 886 9.193133 ACGCAATAATTTGTATACTGCTACTAG 57.807 33.333 4.17 0.00 35.17 2.57
914 952 2.679716 CCTGCTTCCTTCCCCCTG 59.320 66.667 0.00 0.00 0.00 4.45
915 953 2.044551 CTGCTTCCTTCCCCCTGC 60.045 66.667 0.00 0.00 0.00 4.85
916 954 3.651980 CTGCTTCCTTCCCCCTGCC 62.652 68.421 0.00 0.00 0.00 4.85
917 955 4.448976 GCTTCCTTCCCCCTGCCC 62.449 72.222 0.00 0.00 0.00 5.36
918 956 2.615288 CTTCCTTCCCCCTGCCCT 60.615 66.667 0.00 0.00 0.00 5.19
919 957 1.307866 CTTCCTTCCCCCTGCCCTA 60.308 63.158 0.00 0.00 0.00 3.53
920 958 1.618447 TTCCTTCCCCCTGCCCTAC 60.618 63.158 0.00 0.00 0.00 3.18
921 959 3.097162 CCTTCCCCCTGCCCTACC 61.097 72.222 0.00 0.00 0.00 3.18
975 1013 2.284417 CGTCAAGCTTTATAACCCGAGC 59.716 50.000 0.00 0.00 35.42 5.03
986 1024 1.449726 AACCCGAGCCGGTTTTGTTC 61.450 55.000 1.90 0.00 43.88 3.18
1012 1050 2.813354 GCCTCATTCATCCACCCATCTC 60.813 54.545 0.00 0.00 0.00 2.75
1031 1069 1.889573 GCCGAGAGCTACAATGGCC 60.890 63.158 0.00 0.00 38.99 5.36
1032 1070 1.592669 CCGAGAGCTACAATGGCCG 60.593 63.158 0.00 0.00 0.00 6.13
1033 1071 2.240500 CGAGAGCTACAATGGCCGC 61.241 63.158 0.00 0.00 0.00 6.53
1036 1074 2.438434 AGCTACAATGGCCGCCAC 60.438 61.111 16.16 0.00 35.80 5.01
1038 1076 2.045438 CTACAATGGCCGCCACCA 60.045 61.111 16.16 0.00 45.82 4.17
1049 1087 1.372087 CCGCCACCATCAGAAGAAGC 61.372 60.000 0.00 0.00 0.00 3.86
1058 1096 1.219393 CAGAAGAAGCGTCTCCCCC 59.781 63.158 1.62 0.00 30.70 5.40
1352 1396 0.673644 CCTACCAGCACAACTTCGGG 60.674 60.000 0.00 0.00 0.00 5.14
1565 1636 1.725557 CCACCGAGACGACCATCGAT 61.726 60.000 5.04 0.00 43.74 3.59
1757 1828 4.162690 GCCTTCTCGCCCACCGAT 62.163 66.667 0.00 0.00 46.31 4.18
2000 2071 3.771160 CTCTACGGCGGCAACCCT 61.771 66.667 13.24 0.00 0.00 4.34
2216 2300 5.594317 ACTTTGCTCTAGGATTTGTGTTGTT 59.406 36.000 0.00 0.00 0.00 2.83
2217 2301 5.437289 TTGCTCTAGGATTTGTGTTGTTG 57.563 39.130 0.00 0.00 0.00 3.33
2218 2302 4.460263 TGCTCTAGGATTTGTGTTGTTGT 58.540 39.130 0.00 0.00 0.00 3.32
2220 2304 6.237901 TGCTCTAGGATTTGTGTTGTTGTAT 58.762 36.000 0.00 0.00 0.00 2.29
2221 2305 7.390823 TGCTCTAGGATTTGTGTTGTTGTATA 58.609 34.615 0.00 0.00 0.00 1.47
2223 2307 8.726988 GCTCTAGGATTTGTGTTGTTGTATAAA 58.273 33.333 0.00 0.00 0.00 1.40
2225 2309 9.562408 TCTAGGATTTGTGTTGTTGTATAAACA 57.438 29.630 0.00 0.00 34.01 2.83
2266 2350 6.039382 TGTGCAAGATAGTGTAGATACGTGAT 59.961 38.462 0.00 0.00 0.00 3.06
2268 2352 6.918022 TGCAAGATAGTGTAGATACGTGATTG 59.082 38.462 0.00 0.00 0.00 2.67
2270 2354 7.435488 GCAAGATAGTGTAGATACGTGATTGTT 59.565 37.037 0.00 0.00 0.00 2.83
2271 2355 9.946165 CAAGATAGTGTAGATACGTGATTGTTA 57.054 33.333 0.00 0.00 0.00 2.41
2276 2360 5.803461 GTGTAGATACGTGATTGTTAGTGCA 59.197 40.000 0.00 0.00 0.00 4.57
2285 2369 6.697455 ACGTGATTGTTAGTGCATGTATAGAG 59.303 38.462 0.00 0.00 0.00 2.43
2288 2372 3.977427 TGTTAGTGCATGTATAGAGCGG 58.023 45.455 0.00 0.00 0.00 5.52
2298 2382 6.015940 TGCATGTATAGAGCGGATCATATAGG 60.016 42.308 0.00 0.00 0.00 2.57
2299 2383 6.207614 GCATGTATAGAGCGGATCATATAGGA 59.792 42.308 0.00 0.00 0.00 2.94
2300 2384 7.589395 CATGTATAGAGCGGATCATATAGGAC 58.411 42.308 0.00 0.00 0.00 3.85
2301 2385 6.659824 TGTATAGAGCGGATCATATAGGACA 58.340 40.000 0.00 0.00 0.00 4.02
2302 2386 7.290813 TGTATAGAGCGGATCATATAGGACAT 58.709 38.462 0.00 0.00 0.00 3.06
2303 2387 6.892658 ATAGAGCGGATCATATAGGACATC 57.107 41.667 0.00 0.00 0.00 3.06
2304 2388 4.865905 AGAGCGGATCATATAGGACATCT 58.134 43.478 0.00 0.00 0.00 2.90
2305 2389 4.644234 AGAGCGGATCATATAGGACATCTG 59.356 45.833 0.00 0.00 0.00 2.90
2306 2390 4.348486 AGCGGATCATATAGGACATCTGT 58.652 43.478 0.00 0.00 0.00 3.41
2307 2391 4.774726 AGCGGATCATATAGGACATCTGTT 59.225 41.667 0.00 0.00 0.00 3.16
2308 2392 5.952347 AGCGGATCATATAGGACATCTGTTA 59.048 40.000 0.00 0.00 0.00 2.41
2309 2393 6.437477 AGCGGATCATATAGGACATCTGTTAA 59.563 38.462 0.00 0.00 0.00 2.01
2310 2394 7.039011 AGCGGATCATATAGGACATCTGTTAAA 60.039 37.037 0.00 0.00 0.00 1.52
2311 2395 7.602644 GCGGATCATATAGGACATCTGTTAAAA 59.397 37.037 0.00 0.00 0.00 1.52
2312 2396 9.489084 CGGATCATATAGGACATCTGTTAAAAA 57.511 33.333 0.00 0.00 0.00 1.94
2369 2453 7.148255 TGTGGTATCATATGAGTTTTGCAGAAC 60.148 37.037 12.01 12.01 0.00 3.01
2381 2465 1.061887 GCAGAACGTGCGTTGTTGT 59.938 52.632 14.89 0.00 43.99 3.32
2382 2466 0.522495 GCAGAACGTGCGTTGTTGTT 60.522 50.000 14.89 0.00 43.99 2.83
2385 2469 2.659279 CAGAACGTGCGTTGTTGTTTTT 59.341 40.909 14.89 0.00 38.60 1.94
2386 2470 2.912345 AGAACGTGCGTTGTTGTTTTTC 59.088 40.909 14.89 0.00 38.60 2.29
2387 2471 1.252235 ACGTGCGTTGTTGTTTTTCG 58.748 45.000 0.00 0.00 0.00 3.46
2388 2472 0.045419 CGTGCGTTGTTGTTTTTCGC 60.045 50.000 0.00 0.00 45.70 4.70
2390 2474 3.752831 GCGTTGTTGTTTTTCGCAC 57.247 47.368 0.00 0.00 45.01 5.34
2392 2476 2.442424 GCGTTGTTGTTTTTCGCACTA 58.558 42.857 0.00 0.00 45.01 2.74
2393 2477 2.462565 GCGTTGTTGTTTTTCGCACTAG 59.537 45.455 0.00 0.00 45.01 2.57
2394 2478 3.033185 CGTTGTTGTTTTTCGCACTAGG 58.967 45.455 0.00 0.00 0.00 3.02
2398 2482 3.942748 TGTTGTTTTTCGCACTAGGAGTT 59.057 39.130 0.00 0.00 0.00 3.01
2399 2483 4.034742 TGTTGTTTTTCGCACTAGGAGTTC 59.965 41.667 0.00 0.00 0.00 3.01
2400 2484 3.799366 TGTTTTTCGCACTAGGAGTTCA 58.201 40.909 0.00 0.00 0.00 3.18
2401 2485 3.558418 TGTTTTTCGCACTAGGAGTTCAC 59.442 43.478 0.00 0.00 0.00 3.18
2402 2486 3.746045 TTTTCGCACTAGGAGTTCACT 57.254 42.857 0.00 0.00 0.00 3.41
2403 2487 4.859304 TTTTCGCACTAGGAGTTCACTA 57.141 40.909 0.00 0.00 0.00 2.74
2404 2488 3.844577 TTCGCACTAGGAGTTCACTAC 57.155 47.619 0.00 0.00 0.00 2.73
2405 2489 1.736126 TCGCACTAGGAGTTCACTACG 59.264 52.381 0.00 0.00 0.00 3.51
2406 2490 1.736126 CGCACTAGGAGTTCACTACGA 59.264 52.381 0.00 0.00 0.00 3.43
2407 2491 2.161012 CGCACTAGGAGTTCACTACGAA 59.839 50.000 0.00 0.00 0.00 3.85
2408 2492 3.728268 CGCACTAGGAGTTCACTACGAAG 60.728 52.174 0.00 0.00 33.09 3.79
2409 2493 3.760537 CACTAGGAGTTCACTACGAAGC 58.239 50.000 0.00 0.00 33.09 3.86
2410 2494 3.440872 CACTAGGAGTTCACTACGAAGCT 59.559 47.826 0.00 0.00 33.09 3.74
2411 2495 4.634883 CACTAGGAGTTCACTACGAAGCTA 59.365 45.833 0.00 0.00 33.09 3.32
2412 2496 4.877251 ACTAGGAGTTCACTACGAAGCTAG 59.123 45.833 0.00 0.00 33.09 3.42
2472 2562 1.597797 ATGTGGCATTTGGACGGCAG 61.598 55.000 0.00 0.00 38.50 4.85
2572 2669 4.082136 GTCTTGACCCGTTTAGAGTCTGAT 60.082 45.833 1.86 0.00 0.00 2.90
2573 2670 3.868757 TGACCCGTTTAGAGTCTGATG 57.131 47.619 1.86 0.00 0.00 3.07
2575 2672 3.444034 TGACCCGTTTAGAGTCTGATGAG 59.556 47.826 1.86 0.00 0.00 2.90
2576 2673 3.432378 ACCCGTTTAGAGTCTGATGAGT 58.568 45.455 1.86 0.00 0.00 3.41
2577 2674 3.444388 ACCCGTTTAGAGTCTGATGAGTC 59.556 47.826 1.86 0.00 41.68 3.36
2611 2709 1.394618 TCAGAACCAAAAACACGGGG 58.605 50.000 0.00 0.00 0.00 5.73
2628 2726 2.855370 CGGGGAAAGAAACAAAAACACG 59.145 45.455 0.00 0.00 0.00 4.49
2649 2752 3.188460 CGGGAACAGAAAATGTGGTACAG 59.812 47.826 0.00 0.00 43.00 2.74
2659 2762 5.607119 AAATGTGGTACAGAAATGTCGTC 57.393 39.130 0.00 0.00 41.80 4.20
2693 2809 7.433680 ACATGATTTGTAGACCCAAGAAAAAC 58.566 34.615 0.00 0.00 36.57 2.43
2839 3555 6.190346 TCTCTATAGAGTAGTCCCTTGGTC 57.810 45.833 25.54 0.00 42.60 4.02
2847 3563 5.046231 AGAGTAGTCCCTTGGTCTGAAATTC 60.046 44.000 0.00 0.00 0.00 2.17
2853 3569 2.229784 CCTTGGTCTGAAATTCCTGTGC 59.770 50.000 0.00 0.00 0.00 4.57
2854 3570 2.655090 TGGTCTGAAATTCCTGTGCA 57.345 45.000 0.00 0.00 0.00 4.57
2855 3571 3.159213 TGGTCTGAAATTCCTGTGCAT 57.841 42.857 0.00 0.00 0.00 3.96
2856 3572 4.299586 TGGTCTGAAATTCCTGTGCATA 57.700 40.909 0.00 0.00 0.00 3.14
2857 3573 4.858850 TGGTCTGAAATTCCTGTGCATAT 58.141 39.130 0.00 0.00 0.00 1.78
2861 3733 5.587844 GTCTGAAATTCCTGTGCATATCAGT 59.412 40.000 8.69 0.00 35.66 3.41
2868 3740 4.323417 TCCTGTGCATATCAGTTTCGTTT 58.677 39.130 0.00 0.00 0.00 3.60
2869 3741 5.483811 TCCTGTGCATATCAGTTTCGTTTA 58.516 37.500 0.00 0.00 0.00 2.01
2875 3747 8.941977 TGTGCATATCAGTTTCGTTTACTAAAT 58.058 29.630 0.00 0.00 0.00 1.40
2876 3748 9.769093 GTGCATATCAGTTTCGTTTACTAAATT 57.231 29.630 0.00 0.00 0.00 1.82
2877 3749 9.767684 TGCATATCAGTTTCGTTTACTAAATTG 57.232 29.630 0.00 0.00 0.00 2.32
2878 3750 9.221775 GCATATCAGTTTCGTTTACTAAATTGG 57.778 33.333 3.68 0.00 0.00 3.16
2895 5480 0.681887 TGGTGCTCTTCCCATGCATG 60.682 55.000 20.19 20.19 39.00 4.06
2910 5495 2.733956 TGCATGGAATTTGTACCTCCC 58.266 47.619 0.00 0.00 0.00 4.30
2911 5496 1.676006 GCATGGAATTTGTACCTCCCG 59.324 52.381 0.00 0.00 0.00 5.14
2913 5498 0.391927 TGGAATTTGTACCTCCCGCG 60.392 55.000 0.00 0.00 0.00 6.46
2914 5499 1.093496 GGAATTTGTACCTCCCGCGG 61.093 60.000 21.04 21.04 0.00 6.46
2915 5500 1.712018 GAATTTGTACCTCCCGCGGC 61.712 60.000 22.85 5.24 0.00 6.53
2916 5501 3.692370 ATTTGTACCTCCCGCGGCC 62.692 63.158 22.85 2.81 0.00 6.13
2942 5871 2.022129 CGGACGAGTTGTGTGAGGC 61.022 63.158 0.00 0.00 0.00 4.70
3071 6000 2.504032 GATCCGATCACCCCGCAA 59.496 61.111 3.33 0.00 0.00 4.85
3074 6003 2.869503 ATCCGATCACCCCGCAACAC 62.870 60.000 0.00 0.00 0.00 3.32
3076 6005 1.963855 CGATCACCCCGCAACACAA 60.964 57.895 0.00 0.00 0.00 3.33
3085 6014 1.226831 CGCAACACAACCACCAACC 60.227 57.895 0.00 0.00 0.00 3.77
3088 6017 1.181786 CAACACAACCACCAACCAGT 58.818 50.000 0.00 0.00 0.00 4.00
3089 6018 1.134175 CAACACAACCACCAACCAGTC 59.866 52.381 0.00 0.00 0.00 3.51
3090 6019 0.746563 ACACAACCACCAACCAGTCG 60.747 55.000 0.00 0.00 0.00 4.18
3091 6020 1.822186 ACAACCACCAACCAGTCGC 60.822 57.895 0.00 0.00 0.00 5.19
3127 6056 4.247380 GCCCCCAGCTCAGATCCG 62.247 72.222 0.00 0.00 38.99 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 3.242804 GCATGCTTGAGCTCTGAAGAATC 60.243 47.826 16.19 2.66 42.66 2.52
49 50 2.683867 GCATGCTTGAGCTCTGAAGAAT 59.316 45.455 16.19 8.33 42.66 2.40
50 51 2.082231 GCATGCTTGAGCTCTGAAGAA 58.918 47.619 16.19 6.09 42.66 2.52
131 132 6.942005 TCTTTTGATCATTGTGTGTCTACCAT 59.058 34.615 0.00 0.00 0.00 3.55
132 133 6.295249 TCTTTTGATCATTGTGTGTCTACCA 58.705 36.000 0.00 0.00 0.00 3.25
186 187 1.906824 GTCGTCTCCCACTGGGTGA 60.907 63.158 14.25 14.10 44.74 4.02
189 190 1.605058 AATCGTCGTCTCCCACTGGG 61.605 60.000 7.97 7.97 46.11 4.45
193 194 1.067776 AGAACAATCGTCGTCTCCCAC 60.068 52.381 0.00 0.00 0.00 4.61
197 198 3.181539 GCTTTGAGAACAATCGTCGTCTC 60.182 47.826 3.52 3.52 35.85 3.36
214 215 7.917505 GTGGTAGATTAATCCTTTCATGCTTTG 59.082 37.037 11.92 0.00 0.00 2.77
215 216 7.068716 GGTGGTAGATTAATCCTTTCATGCTTT 59.931 37.037 11.92 0.00 0.00 3.51
402 404 4.834496 AGTATTATACATTTCCCCGTCCGA 59.166 41.667 5.11 0.00 0.00 4.55
403 405 4.927425 CAGTATTATACATTTCCCCGTCCG 59.073 45.833 5.11 0.00 0.00 4.79
406 408 5.298989 TGCAGTATTATACATTTCCCCGT 57.701 39.130 5.11 0.00 0.00 5.28
411 438 9.604626 GCTCAATCTTGCAGTATTATACATTTC 57.395 33.333 5.11 0.00 0.00 2.17
489 516 3.403038 CAACGGGAAGAGTCATTCAAGT 58.597 45.455 0.00 0.00 0.00 3.16
524 551 5.293569 AGTTTCTCTCAACCGTGTTTAACTG 59.706 40.000 0.00 0.00 0.00 3.16
551 578 5.273170 CGTTTTGCTTGTCAGATCAGAAAA 58.727 37.500 0.00 0.00 0.00 2.29
557 584 2.548057 TGTCCGTTTTGCTTGTCAGATC 59.452 45.455 0.00 0.00 0.00 2.75
573 600 2.161808 AGCGAGGATACGATAATGTCCG 59.838 50.000 0.00 0.00 46.39 4.79
583 610 2.222508 CGTGTTGAAAAGCGAGGATACG 60.223 50.000 0.00 0.00 46.39 3.06
584 611 2.735134 ACGTGTTGAAAAGCGAGGATAC 59.265 45.455 0.00 0.00 0.00 2.24
677 705 1.624312 GAAGTTTCCCTCTCCTCGGTT 59.376 52.381 0.00 0.00 0.00 4.44
713 741 0.035725 CTGCATCTGCTCTGTGGGAA 60.036 55.000 3.53 0.00 42.66 3.97
714 742 0.906282 TCTGCATCTGCTCTGTGGGA 60.906 55.000 3.53 0.00 42.66 4.37
715 743 0.462225 CTCTGCATCTGCTCTGTGGG 60.462 60.000 3.53 0.00 42.66 4.61
735 763 0.900182 ATGGTCGTCAGCAGTCTGGA 60.900 55.000 1.14 0.00 40.69 3.86
814 846 9.811655 CAAATTATTGCGTACTGTGGATAATAG 57.188 33.333 0.00 0.00 0.00 1.73
818 850 8.896320 ATACAAATTATTGCGTACTGTGGATA 57.104 30.769 0.00 0.00 40.34 2.59
819 851 7.801716 ATACAAATTATTGCGTACTGTGGAT 57.198 32.000 0.00 0.00 40.34 3.41
820 852 7.982919 AGTATACAAATTATTGCGTACTGTGGA 59.017 33.333 5.50 0.00 40.34 4.02
821 853 8.061857 CAGTATACAAATTATTGCGTACTGTGG 58.938 37.037 17.14 0.00 43.72 4.17
822 854 7.582679 GCAGTATACAAATTATTGCGTACTGTG 59.417 37.037 21.66 9.77 46.47 3.66
823 855 7.494625 AGCAGTATACAAATTATTGCGTACTGT 59.505 33.333 21.66 13.23 46.47 3.55
824 856 7.851508 AGCAGTATACAAATTATTGCGTACTG 58.148 34.615 19.17 19.17 46.89 2.74
825 857 8.975439 GTAGCAGTATACAAATTATTGCGTACT 58.025 33.333 5.50 0.00 40.34 2.73
826 858 8.975439 AGTAGCAGTATACAAATTATTGCGTAC 58.025 33.333 5.50 8.41 40.34 3.67
829 861 9.406828 TCTAGTAGCAGTATACAAATTATTGCG 57.593 33.333 5.50 0.00 40.34 4.85
842 874 7.069986 TGGATCTTTCCTTCTAGTAGCAGTAT 58.930 38.462 0.00 0.00 43.07 2.12
846 878 6.620877 TTTGGATCTTTCCTTCTAGTAGCA 57.379 37.500 0.00 0.00 43.07 3.49
847 879 6.708502 GGATTTGGATCTTTCCTTCTAGTAGC 59.291 42.308 0.00 0.00 43.07 3.58
850 882 6.642733 TGGATTTGGATCTTTCCTTCTAGT 57.357 37.500 0.00 0.00 43.07 2.57
852 884 5.888161 GCTTGGATTTGGATCTTTCCTTCTA 59.112 40.000 0.00 0.00 43.07 2.10
854 886 4.439289 CGCTTGGATTTGGATCTTTCCTTC 60.439 45.833 0.00 0.00 43.07 3.46
861 899 2.489329 CAACACGCTTGGATTTGGATCT 59.511 45.455 0.00 0.00 32.66 2.75
897 935 2.679716 CAGGGGGAAGGAAGCAGG 59.320 66.667 0.00 0.00 0.00 4.85
904 942 3.097162 GGTAGGGCAGGGGGAAGG 61.097 72.222 0.00 0.00 0.00 3.46
975 1013 0.037734 AGGCTAGGGAACAAAACCGG 59.962 55.000 0.00 0.00 0.00 5.28
986 1024 1.072965 GGTGGATGAATGAGGCTAGGG 59.927 57.143 0.00 0.00 0.00 3.53
1031 1069 1.699656 CGCTTCTTCTGATGGTGGCG 61.700 60.000 0.00 0.00 35.75 5.69
1032 1070 0.674895 ACGCTTCTTCTGATGGTGGC 60.675 55.000 0.00 0.00 0.00 5.01
1033 1071 1.066573 AGACGCTTCTTCTGATGGTGG 60.067 52.381 0.00 0.00 0.00 4.61
1036 1074 1.472376 GGGAGACGCTTCTTCTGATGG 60.472 57.143 0.00 0.00 29.47 3.51
1038 1076 0.827368 GGGGAGACGCTTCTTCTGAT 59.173 55.000 0.00 0.00 40.76 2.90
1039 1077 1.258445 GGGGGAGACGCTTCTTCTGA 61.258 60.000 0.00 0.00 44.03 3.27
1040 1078 1.219393 GGGGGAGACGCTTCTTCTG 59.781 63.158 0.00 0.00 44.03 3.02
1041 1079 3.715015 GGGGGAGACGCTTCTTCT 58.285 61.111 0.00 0.00 44.03 2.85
1058 1096 4.567385 GCGAGCAGAGCGAGGAGG 62.567 72.222 0.00 0.00 0.00 4.30
2000 2071 3.204505 CGTGACGCCCTTGAAGTTA 57.795 52.632 0.00 0.00 0.00 2.24
2117 2197 3.305403 CCAAGAAGAACTAGCACGACAGA 60.305 47.826 0.00 0.00 0.00 3.41
2118 2198 2.989840 CCAAGAAGAACTAGCACGACAG 59.010 50.000 0.00 0.00 0.00 3.51
2216 2300 9.607988 CACCCAATGACTACTAATGTTTATACA 57.392 33.333 0.00 0.00 38.95 2.29
2217 2301 9.609346 ACACCCAATGACTACTAATGTTTATAC 57.391 33.333 0.00 0.00 0.00 1.47
2218 2302 9.607988 CACACCCAATGACTACTAATGTTTATA 57.392 33.333 0.00 0.00 0.00 0.98
2220 2304 6.373216 GCACACCCAATGACTACTAATGTTTA 59.627 38.462 0.00 0.00 0.00 2.01
2221 2305 5.183140 GCACACCCAATGACTACTAATGTTT 59.817 40.000 0.00 0.00 0.00 2.83
2223 2307 4.261801 GCACACCCAATGACTACTAATGT 58.738 43.478 0.00 0.00 0.00 2.71
2224 2308 4.260985 TGCACACCCAATGACTACTAATG 58.739 43.478 0.00 0.00 0.00 1.90
2225 2309 4.568072 TGCACACCCAATGACTACTAAT 57.432 40.909 0.00 0.00 0.00 1.73
2226 2310 4.041075 TCTTGCACACCCAATGACTACTAA 59.959 41.667 0.00 0.00 0.00 2.24
2227 2311 3.580895 TCTTGCACACCCAATGACTACTA 59.419 43.478 0.00 0.00 0.00 1.82
2228 2312 2.371841 TCTTGCACACCCAATGACTACT 59.628 45.455 0.00 0.00 0.00 2.57
2229 2313 2.778299 TCTTGCACACCCAATGACTAC 58.222 47.619 0.00 0.00 0.00 2.73
2236 2320 2.949177 ACACTATCTTGCACACCCAA 57.051 45.000 0.00 0.00 0.00 4.12
2266 2350 4.098807 TCCGCTCTATACATGCACTAACAA 59.901 41.667 0.00 0.00 0.00 2.83
2268 2352 4.238761 TCCGCTCTATACATGCACTAAC 57.761 45.455 0.00 0.00 0.00 2.34
2270 2354 4.079253 TGATCCGCTCTATACATGCACTA 58.921 43.478 0.00 0.00 0.00 2.74
2271 2355 2.893489 TGATCCGCTCTATACATGCACT 59.107 45.455 0.00 0.00 0.00 4.40
2272 2356 3.303881 TGATCCGCTCTATACATGCAC 57.696 47.619 0.00 0.00 0.00 4.57
2276 2360 7.290813 TGTCCTATATGATCCGCTCTATACAT 58.709 38.462 0.00 0.00 0.00 2.29
2285 2369 4.727507 ACAGATGTCCTATATGATCCGC 57.272 45.455 0.00 0.00 0.00 5.54
2309 2393 3.427193 GCGCACCATTTTCGTGTATTTTT 59.573 39.130 0.30 0.00 33.61 1.94
2310 2394 2.983803 GCGCACCATTTTCGTGTATTTT 59.016 40.909 0.30 0.00 33.61 1.82
2311 2395 2.591133 GCGCACCATTTTCGTGTATTT 58.409 42.857 0.30 0.00 33.61 1.40
2312 2396 1.135517 GGCGCACCATTTTCGTGTATT 60.136 47.619 10.83 0.00 35.26 1.89
2313 2397 0.450184 GGCGCACCATTTTCGTGTAT 59.550 50.000 10.83 0.00 35.26 2.29
2314 2398 1.579084 GGGCGCACCATTTTCGTGTA 61.579 55.000 10.83 0.00 39.85 2.90
2315 2399 2.642700 GGCGCACCATTTTCGTGT 59.357 55.556 10.83 0.00 35.26 4.49
2316 2400 2.126502 GGGCGCACCATTTTCGTG 60.127 61.111 10.83 0.00 39.85 4.35
2347 2431 6.901887 CACGTTCTGCAAAACTCATATGATAC 59.098 38.462 5.72 0.00 0.00 2.24
2369 2453 0.045419 GCGAAAAACAACAACGCACG 60.045 50.000 0.00 0.00 46.75 5.34
2374 2458 4.201881 ACTCCTAGTGCGAAAAACAACAAC 60.202 41.667 0.00 0.00 0.00 3.32
2375 2459 3.942748 ACTCCTAGTGCGAAAAACAACAA 59.057 39.130 0.00 0.00 0.00 2.83
2377 2461 4.034742 TGAACTCCTAGTGCGAAAAACAAC 59.965 41.667 0.00 0.00 0.00 3.32
2378 2462 4.034742 GTGAACTCCTAGTGCGAAAAACAA 59.965 41.667 0.00 0.00 0.00 2.83
2381 2465 4.067972 AGTGAACTCCTAGTGCGAAAAA 57.932 40.909 0.00 0.00 0.00 1.94
2382 2466 3.746045 AGTGAACTCCTAGTGCGAAAA 57.254 42.857 0.00 0.00 0.00 2.29
2385 2469 1.736126 CGTAGTGAACTCCTAGTGCGA 59.264 52.381 0.00 0.00 0.00 5.10
2386 2470 1.736126 TCGTAGTGAACTCCTAGTGCG 59.264 52.381 0.00 0.00 0.00 5.34
2387 2471 3.760537 CTTCGTAGTGAACTCCTAGTGC 58.239 50.000 0.00 0.00 31.87 4.40
2388 2472 3.440872 AGCTTCGTAGTGAACTCCTAGTG 59.559 47.826 0.00 0.00 31.87 2.74
2389 2473 3.688235 AGCTTCGTAGTGAACTCCTAGT 58.312 45.455 0.00 0.00 31.87 2.57
2390 2474 4.260866 GCTAGCTTCGTAGTGAACTCCTAG 60.261 50.000 7.70 0.00 32.81 3.02
2392 2476 2.424246 GCTAGCTTCGTAGTGAACTCCT 59.576 50.000 7.70 0.00 31.87 3.69
2393 2477 2.791849 CGCTAGCTTCGTAGTGAACTCC 60.792 54.545 13.93 0.00 33.09 3.85
2394 2478 2.442424 CGCTAGCTTCGTAGTGAACTC 58.558 52.381 13.93 0.00 33.09 3.01
2398 2482 1.015109 CTCCGCTAGCTTCGTAGTGA 58.985 55.000 13.93 0.00 33.09 3.41
2399 2483 3.535691 CTCCGCTAGCTTCGTAGTG 57.464 57.895 13.93 0.00 0.00 2.74
2409 2493 2.775856 TTCTCGCCTGCTCCGCTAG 61.776 63.158 0.00 0.00 0.00 3.42
2410 2494 2.754254 TTCTCGCCTGCTCCGCTA 60.754 61.111 0.00 0.00 0.00 4.26
2411 2495 4.443266 GTTCTCGCCTGCTCCGCT 62.443 66.667 0.00 0.00 0.00 5.52
2572 2669 1.106944 TGAGTGGCACGACAGACTCA 61.107 55.000 12.71 5.67 41.93 3.41
2573 2670 0.244994 ATGAGTGGCACGACAGACTC 59.755 55.000 20.51 9.53 36.23 3.36
2575 2672 0.038251 TGATGAGTGGCACGACAGAC 60.038 55.000 20.51 17.24 0.00 3.51
2576 2673 0.244721 CTGATGAGTGGCACGACAGA 59.755 55.000 21.71 12.83 31.60 3.41
2577 2674 0.244721 TCTGATGAGTGGCACGACAG 59.755 55.000 20.51 20.70 0.00 3.51
2611 2709 4.924462 TGTTCCCGTGTTTTTGTTTCTTTC 59.076 37.500 0.00 0.00 0.00 2.62
2628 2726 4.394729 TCTGTACCACATTTTCTGTTCCC 58.605 43.478 0.00 0.00 35.29 3.97
2649 2752 5.985530 TCATGTATCATCCAGACGACATTTC 59.014 40.000 0.00 0.00 35.18 2.17
2659 2762 6.652481 GGGTCTACAAATCATGTATCATCCAG 59.348 42.308 0.00 0.00 43.42 3.86
2739 2855 5.278604 GTTTGTATGGAACGGGCAATTATC 58.721 41.667 0.00 0.00 0.00 1.75
2811 2929 9.589461 CCAAGGGACTACTCTATAGAGAAATTA 57.411 37.037 31.91 15.16 41.15 1.40
2829 2947 3.084786 CAGGAATTTCAGACCAAGGGAC 58.915 50.000 0.00 0.00 0.00 4.46
2836 3552 4.883585 TGATATGCACAGGAATTTCAGACC 59.116 41.667 0.00 0.00 0.00 3.85
2839 3555 6.446781 AACTGATATGCACAGGAATTTCAG 57.553 37.500 7.62 5.04 41.44 3.02
2847 3563 4.685169 AAACGAAACTGATATGCACAGG 57.315 40.909 7.62 0.00 39.38 4.00
2855 3571 8.231837 GCACCAATTTAGTAAACGAAACTGATA 58.768 33.333 0.00 0.00 0.00 2.15
2856 3572 7.040686 AGCACCAATTTAGTAAACGAAACTGAT 60.041 33.333 0.00 0.00 0.00 2.90
2857 3573 6.261381 AGCACCAATTTAGTAAACGAAACTGA 59.739 34.615 0.00 0.00 0.00 3.41
2861 3733 6.870971 AGAGCACCAATTTAGTAAACGAAA 57.129 33.333 0.00 0.00 0.00 3.46
2868 3740 4.919774 TGGGAAGAGCACCAATTTAGTA 57.080 40.909 0.00 0.00 32.89 1.82
2869 3741 3.806949 TGGGAAGAGCACCAATTTAGT 57.193 42.857 0.00 0.00 32.89 2.24
2875 3747 0.040058 ATGCATGGGAAGAGCACCAA 59.960 50.000 0.00 0.00 41.60 3.67
2876 3748 0.681887 CATGCATGGGAAGAGCACCA 60.682 55.000 19.40 0.00 41.60 4.17
2877 3749 1.389609 CCATGCATGGGAAGAGCACC 61.390 60.000 34.31 0.00 44.31 5.01
2878 3750 2.112898 CCATGCATGGGAAGAGCAC 58.887 57.895 34.31 0.00 44.31 4.40
2895 5480 1.093496 CCGCGGGAGGTACAAATTCC 61.093 60.000 20.10 0.00 0.00 3.01
2917 5502 2.126580 CAACTCGTCCGGTCGTCC 60.127 66.667 20.21 0.00 0.00 4.79
2918 5503 1.728426 CACAACTCGTCCGGTCGTC 60.728 63.158 20.21 0.21 0.00 4.20
2919 5504 2.333938 CACAACTCGTCCGGTCGT 59.666 61.111 20.21 0.00 0.00 4.34
2920 5505 2.014554 CACACAACTCGTCCGGTCG 61.015 63.158 15.22 15.22 0.00 4.79
2921 5506 0.663568 CTCACACAACTCGTCCGGTC 60.664 60.000 0.00 0.00 0.00 4.79
2922 5507 1.362717 CTCACACAACTCGTCCGGT 59.637 57.895 0.00 0.00 0.00 5.28
2923 5508 1.372997 CCTCACACAACTCGTCCGG 60.373 63.158 0.00 0.00 0.00 5.14
2924 5509 2.022129 GCCTCACACAACTCGTCCG 61.022 63.158 0.00 0.00 0.00 4.79
2925 5510 2.022129 CGCCTCACACAACTCGTCC 61.022 63.158 0.00 0.00 0.00 4.79
2926 5511 1.007734 TCGCCTCACACAACTCGTC 60.008 57.895 0.00 0.00 0.00 4.20
2931 5860 1.548973 CTGTCGTCGCCTCACACAAC 61.549 60.000 0.00 0.00 0.00 3.32
2942 5871 0.732880 GGGATGTGTCACTGTCGTCG 60.733 60.000 4.27 0.00 0.00 5.12
3071 6000 0.746563 CGACTGGTTGGTGGTTGTGT 60.747 55.000 0.00 0.00 0.00 3.72
3074 6003 1.507141 GAGCGACTGGTTGGTGGTTG 61.507 60.000 0.00 0.00 0.00 3.77
3076 6005 2.426023 GAGCGACTGGTTGGTGGT 59.574 61.111 0.00 0.00 0.00 4.16
3267 6196 4.699522 GGAGGTGACGGTGGTGCC 62.700 72.222 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.