Multiple sequence alignment - TraesCS5D01G274000

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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 TraesCS5D01G274000 chr5D 100.000 2540 0 0 1 2540 377263182 377260643 0.000000e+00 4691
1 TraesCS5D01G274000 chr5A 92.431 1810 89 30 1 1798 477716669 477714896 0.000000e+00 2540
2 TraesCS5D01G274000 chr5B 91.031 1784 83 30 47 1798 450513285 450511547 0.000000e+00 2337
3 TraesCS5D01G274000 chr5B 84.161 644 90 11 1808 2446 668107792 668107156 4.640000e-172 614
4 TraesCS5D01G274000 chr5B 96.825 63 0 2 1 62 450513804 450513743 1.240000e-18 104
5 TraesCS5D01G274000 chr2A 85.388 657 88 8 1796 2447 2741745 2742398 0.000000e+00 675
6 TraesCS5D01G274000 chr6A 84.356 652 92 10 1800 2446 608655993 608656639 4.610000e-177 630
7 TraesCS5D01G274000 chr1D 84.360 633 89 8 1811 2440 272535892 272536517 1.670000e-171 612
8 TraesCS5D01G274000 chr1D 83.463 641 95 10 1811 2447 444844592 444845225 1.010000e-163 586
9 TraesCS5D01G274000 chr3A 83.409 657 96 11 1800 2447 373354507 373355159 4.680000e-167 597
10 TraesCS5D01G274000 chr3D 83.155 653 102 8 1800 2446 15890728 15891378 7.830000e-165 590
11 TraesCS5D01G274000 chr7D 82.927 656 106 6 1793 2445 635663686 635663034 1.010000e-163 586
12 TraesCS5D01G274000 chr1B 83.053 655 99 10 1800 2449 26425110 26425757 3.640000e-163 584


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 TraesCS5D01G274000 chr5D 377260643 377263182 2539 True 4691.0 4691 100.000 1 2540 1 chr5D.!!$R1 2539
1 TraesCS5D01G274000 chr5A 477714896 477716669 1773 True 2540.0 2540 92.431 1 1798 1 chr5A.!!$R1 1797
2 TraesCS5D01G274000 chr5B 450511547 450513804 2257 True 1220.5 2337 93.928 1 1798 2 chr5B.!!$R2 1797
3 TraesCS5D01G274000 chr5B 668107156 668107792 636 True 614.0 614 84.161 1808 2446 1 chr5B.!!$R1 638
4 TraesCS5D01G274000 chr2A 2741745 2742398 653 False 675.0 675 85.388 1796 2447 1 chr2A.!!$F1 651
5 TraesCS5D01G274000 chr6A 608655993 608656639 646 False 630.0 630 84.356 1800 2446 1 chr6A.!!$F1 646
6 TraesCS5D01G274000 chr1D 272535892 272536517 625 False 612.0 612 84.360 1811 2440 1 chr1D.!!$F1 629
7 TraesCS5D01G274000 chr1D 444844592 444845225 633 False 586.0 586 83.463 1811 2447 1 chr1D.!!$F2 636
8 TraesCS5D01G274000 chr3A 373354507 373355159 652 False 597.0 597 83.409 1800 2447 1 chr3A.!!$F1 647
9 TraesCS5D01G274000 chr3D 15890728 15891378 650 False 590.0 590 83.155 1800 2446 1 chr3D.!!$F1 646
10 TraesCS5D01G274000 chr7D 635663034 635663686 652 True 586.0 586 82.927 1793 2445 1 chr7D.!!$R1 652
11 TraesCS5D01G274000 chr1B 26425110 26425757 647 False 584.0 584 83.053 1800 2449 1 chr1B.!!$F1 649

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
130 603 0.033642 GGGCGGTATAGCAACTCCTC 59.966 60.000 2.37 0.0 39.27 3.71 F
456 930 1.073923 TCCAAGAGAGGGGAGTTTTGC 59.926 52.381 0.00 0.0 0.00 3.68 F
1267 1771 1.600916 GGACGGCCACAGAAGCTTT 60.601 57.895 0.00 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1267 1771 0.039888 TCATCGACGTCGTGCTTGAA 60.040 50.0 34.4 16.3 40.8 2.69 R
1371 1875 0.178915 TCTTCTTCCCTCCGTTCCCA 60.179 55.0 0.0 0.0 0.0 4.37 R
2451 2980 0.468648 GGTGGATAGGGCTAAGCGTT 59.531 55.0 0.0 0.0 0.0 4.84 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
124 597 0.107831 GTCCATGGGCGGTATAGCAA 59.892 55.000 13.02 0.00 39.27 3.91
125 598 0.107831 TCCATGGGCGGTATAGCAAC 59.892 55.000 13.02 0.00 39.27 4.17
126 599 0.108585 CCATGGGCGGTATAGCAACT 59.891 55.000 2.85 0.00 39.27 3.16
127 600 1.512926 CATGGGCGGTATAGCAACTC 58.487 55.000 2.37 0.00 39.27 3.01
128 601 0.396811 ATGGGCGGTATAGCAACTCC 59.603 55.000 2.37 0.00 39.27 3.85
129 602 0.689745 TGGGCGGTATAGCAACTCCT 60.690 55.000 2.37 0.00 39.27 3.69
130 603 0.033642 GGGCGGTATAGCAACTCCTC 59.966 60.000 2.37 0.00 39.27 3.71
137 610 4.725490 GGTATAGCAACTCCTCTCTCTCT 58.275 47.826 0.00 0.00 0.00 3.10
285 759 1.565759 TCTGCTGCCCATAGTCCATTT 59.434 47.619 0.00 0.00 0.00 2.32
367 841 3.512680 CGTAGATCAGTCCAGACAAACC 58.487 50.000 0.00 0.00 0.00 3.27
369 843 4.382040 CGTAGATCAGTCCAGACAAACCAT 60.382 45.833 0.00 0.00 0.00 3.55
375 849 4.952957 TCAGTCCAGACAAACCATCAAAAA 59.047 37.500 0.00 0.00 0.00 1.94
376 850 5.067674 TCAGTCCAGACAAACCATCAAAAAG 59.932 40.000 0.00 0.00 0.00 2.27
377 851 4.342092 AGTCCAGACAAACCATCAAAAAGG 59.658 41.667 0.00 0.00 0.00 3.11
456 930 1.073923 TCCAAGAGAGGGGAGTTTTGC 59.926 52.381 0.00 0.00 0.00 3.68
562 1036 6.884472 TCTGTTAATCAATCCCTAGTTGGA 57.116 37.500 0.00 0.00 39.18 3.53
635 1114 3.028366 GCTCGCGGTTCTTGCCTTC 62.028 63.158 6.13 0.00 0.00 3.46
702 1181 2.501723 TGTAGCTGGTTCTCCTTGGATC 59.498 50.000 0.00 0.00 34.23 3.36
743 1231 2.170166 TCATTCCCACCTGAAATGTGC 58.830 47.619 0.00 0.00 30.52 4.57
835 1332 5.793030 TTTGTGTATTTTACCCCCAACAG 57.207 39.130 0.00 0.00 0.00 3.16
884 1381 2.226912 GACATCGTTAGATAGCCGAGCT 59.773 50.000 3.87 3.87 43.41 4.09
986 1490 2.447244 ACCGTCTTCTGCTCTCTTTG 57.553 50.000 0.00 0.00 0.00 2.77
1043 1547 7.508977 AGTTATTTGGTTGATTCTTTCCAAGGA 59.491 33.333 0.00 0.00 40.34 3.36
1116 1620 2.992543 CTCTGCGATTAGAGCTATTGGC 59.007 50.000 0.00 0.00 37.93 4.52
1206 1710 3.533691 GCGAAGAACGAGGACGCG 61.534 66.667 3.53 3.53 45.77 6.01
1267 1771 1.600916 GGACGGCCACAGAAGCTTT 60.601 57.895 0.00 0.00 0.00 3.51
1296 1800 1.950909 GACGTCGATGAGGAAGAGGAT 59.049 52.381 12.58 0.00 0.00 3.24
1297 1801 1.678627 ACGTCGATGAGGAAGAGGATG 59.321 52.381 12.58 0.00 0.00 3.51
1298 1802 1.678627 CGTCGATGAGGAAGAGGATGT 59.321 52.381 0.00 0.00 0.00 3.06
1398 1902 3.771160 GGGAAGAAGAGGCGGCGA 61.771 66.667 12.98 0.00 0.00 5.54
1566 2070 4.402474 TCTGAAGACTGAAGAAGTGTGTGA 59.598 41.667 0.00 0.00 40.07 3.58
1567 2071 4.433615 TGAAGACTGAAGAAGTGTGTGAC 58.566 43.478 0.00 0.00 40.07 3.67
1568 2072 3.085443 AGACTGAAGAAGTGTGTGACG 57.915 47.619 0.00 0.00 40.07 4.35
1569 2073 2.427453 AGACTGAAGAAGTGTGTGACGT 59.573 45.455 0.00 0.00 40.07 4.34
1570 2074 3.630769 AGACTGAAGAAGTGTGTGACGTA 59.369 43.478 0.00 0.00 40.07 3.57
1571 2075 4.097437 AGACTGAAGAAGTGTGTGACGTAA 59.903 41.667 0.00 0.00 40.07 3.18
1572 2076 4.945246 ACTGAAGAAGTGTGTGACGTAAT 58.055 39.130 0.00 0.00 37.88 1.89
1573 2077 4.745125 ACTGAAGAAGTGTGTGACGTAATG 59.255 41.667 0.00 0.00 37.88 1.90
1574 2078 4.939271 TGAAGAAGTGTGTGACGTAATGA 58.061 39.130 0.00 0.00 0.00 2.57
1575 2079 4.982295 TGAAGAAGTGTGTGACGTAATGAG 59.018 41.667 0.00 0.00 0.00 2.90
1576 2080 3.914312 AGAAGTGTGTGACGTAATGAGG 58.086 45.455 0.00 0.00 0.00 3.86
1577 2081 3.572682 AGAAGTGTGTGACGTAATGAGGA 59.427 43.478 0.00 0.00 0.00 3.71
1578 2082 4.038763 AGAAGTGTGTGACGTAATGAGGAA 59.961 41.667 0.00 0.00 0.00 3.36
1579 2083 3.650139 AGTGTGTGACGTAATGAGGAAC 58.350 45.455 0.00 0.00 0.00 3.62
1581 2085 3.428870 GTGTGTGACGTAATGAGGAACTG 59.571 47.826 0.00 0.00 41.55 3.16
1582 2086 2.412089 GTGTGACGTAATGAGGAACTGC 59.588 50.000 0.00 0.00 41.55 4.40
1583 2087 2.036604 TGTGACGTAATGAGGAACTGCA 59.963 45.455 0.00 0.00 41.55 4.41
1584 2088 3.064207 GTGACGTAATGAGGAACTGCAA 58.936 45.455 0.00 0.00 41.55 4.08
1585 2089 3.496884 GTGACGTAATGAGGAACTGCAAA 59.503 43.478 0.00 0.00 41.55 3.68
1586 2090 4.154195 GTGACGTAATGAGGAACTGCAAAT 59.846 41.667 0.00 0.00 41.55 2.32
1587 2091 4.154015 TGACGTAATGAGGAACTGCAAATG 59.846 41.667 0.00 0.00 41.55 2.32
1588 2092 4.072131 ACGTAATGAGGAACTGCAAATGT 58.928 39.130 0.00 0.00 41.55 2.71
1589 2093 4.083324 ACGTAATGAGGAACTGCAAATGTG 60.083 41.667 0.00 0.00 41.55 3.21
1596 2100 3.250040 AGGAACTGCAAATGTGACGTAAC 59.750 43.478 0.00 0.00 37.18 2.50
1607 2111 0.669619 TGACGTAACGAGGAACTGCA 59.330 50.000 0.00 0.00 41.55 4.41
1726 2241 7.996644 GGGGTTTATGTCAGTTAATTCTATGGA 59.003 37.037 0.00 0.00 0.00 3.41
1735 2250 7.436673 GTCAGTTAATTCTATGGACAGTGCTAG 59.563 40.741 0.00 0.00 0.00 3.42
1738 2253 5.939764 AATTCTATGGACAGTGCTAGTGA 57.060 39.130 0.00 0.00 0.00 3.41
1768 2283 9.113838 GCATATGGATTAAAACTTTCTGAGAGA 57.886 33.333 4.56 0.00 0.00 3.10
1783 2298 6.672266 TCTGAGAGAAACTCCATTTACAGT 57.328 37.500 0.00 0.00 44.34 3.55
1786 2301 4.973168 AGAGAAACTCCATTTACAGTGCA 58.027 39.130 0.00 0.00 0.00 4.57
1893 2408 6.827586 ATTACAACCATGTTCGTTAACCAT 57.172 33.333 0.00 0.00 41.05 3.55
1918 2433 2.925306 GCGACGACTACAAACACTGGAT 60.925 50.000 0.00 0.00 0.00 3.41
1924 2439 2.563179 ACTACAAACACTGGATCGAGCT 59.437 45.455 4.41 0.00 0.00 4.09
1929 2444 1.550327 ACACTGGATCGAGCTGAAGA 58.450 50.000 4.41 0.00 0.00 2.87
1932 2447 0.453793 CTGGATCGAGCTGAAGACGT 59.546 55.000 0.00 0.00 0.00 4.34
1945 2460 3.792401 TGAAGACGTGTTGTTGTCATCT 58.208 40.909 1.19 0.00 37.58 2.90
1951 2466 2.810400 CGTGTTGTTGTCATCTCCCCTT 60.810 50.000 0.00 0.00 0.00 3.95
1953 2468 2.076863 GTTGTTGTCATCTCCCCTTCG 58.923 52.381 0.00 0.00 0.00 3.79
1999 2515 5.368256 TTGTAGTAGTCAGTCGGAAAGTC 57.632 43.478 0.00 0.00 0.00 3.01
2039 2555 1.079819 GACCAGCGCACTAGAGCAA 60.080 57.895 11.47 0.00 43.61 3.91
2047 2563 1.806542 CGCACTAGAGCAACAACCATT 59.193 47.619 12.77 0.00 0.00 3.16
2062 2578 2.094675 ACCATTGCCGATGAAGAAAGG 58.905 47.619 0.00 0.00 38.03 3.11
2068 2584 1.571919 CCGATGAAGAAAGGCGTAGG 58.428 55.000 0.00 0.00 0.00 3.18
2122 2638 2.100197 AGATGAACGAAGACCGGATGA 58.900 47.619 9.46 0.00 43.93 2.92
2173 2689 1.179174 AATCCCGCGAGATCCGATGA 61.179 55.000 8.23 1.66 41.76 2.92
2184 2701 4.508662 GAGATCCGATGAAGAAACACCTT 58.491 43.478 0.00 0.00 0.00 3.50
2185 2702 4.911390 AGATCCGATGAAGAAACACCTTT 58.089 39.130 0.00 0.00 0.00 3.11
2190 2707 4.755123 CCGATGAAGAAACACCTTTACACT 59.245 41.667 0.00 0.00 0.00 3.55
2196 2713 3.974642 AGAAACACCTTTACACTCCCTCT 59.025 43.478 0.00 0.00 0.00 3.69
2225 2742 1.213013 GACGCACCATCGAGACAGT 59.787 57.895 0.00 0.00 0.00 3.55
2243 2760 3.131223 ACAGTGATAGAACGTGGGAGATG 59.869 47.826 0.00 0.00 0.00 2.90
2258 2775 6.040616 CGTGGGAGATGTTATTCCTACTAAGT 59.959 42.308 5.66 0.00 41.33 2.24
2269 2787 1.607628 CCTACTAAGTACATCGCCGCT 59.392 52.381 0.00 0.00 0.00 5.52
2296 2816 3.879295 CACAACTCAACCAAGACACTGAT 59.121 43.478 0.00 0.00 0.00 2.90
2365 2890 0.747283 CTCTGCACCTCCATGGCTTC 60.747 60.000 6.96 0.00 40.22 3.86
2440 2969 2.816672 GCTTTTCTTGTGGAGGAGGAAG 59.183 50.000 0.00 0.00 0.00 3.46
2447 2976 3.033659 TGTGGAGGAGGAAGGAGATAC 57.966 52.381 0.00 0.00 0.00 2.24
2448 2977 2.314852 TGTGGAGGAGGAAGGAGATACA 59.685 50.000 0.00 0.00 0.00 2.29
2450 2979 3.133183 GTGGAGGAGGAAGGAGATACAAC 59.867 52.174 0.00 0.00 0.00 3.32
2451 2980 3.245984 TGGAGGAGGAAGGAGATACAACA 60.246 47.826 0.00 0.00 0.00 3.33
2452 2981 3.775316 GGAGGAGGAAGGAGATACAACAA 59.225 47.826 0.00 0.00 0.00 2.83
2453 2982 4.383226 GGAGGAGGAAGGAGATACAACAAC 60.383 50.000 0.00 0.00 0.00 3.32
2454 2983 3.195825 AGGAGGAAGGAGATACAACAACG 59.804 47.826 0.00 0.00 0.00 4.10
2455 2984 2.930682 GAGGAAGGAGATACAACAACGC 59.069 50.000 0.00 0.00 0.00 4.84
2456 2985 2.567615 AGGAAGGAGATACAACAACGCT 59.432 45.455 0.00 0.00 0.00 5.07
2457 2986 3.008049 AGGAAGGAGATACAACAACGCTT 59.992 43.478 0.00 0.00 0.00 4.68
2458 2987 4.222145 AGGAAGGAGATACAACAACGCTTA 59.778 41.667 0.00 0.00 0.00 3.09
2459 2988 4.567159 GGAAGGAGATACAACAACGCTTAG 59.433 45.833 0.00 0.00 0.00 2.18
2460 2989 3.522553 AGGAGATACAACAACGCTTAGC 58.477 45.455 0.00 0.00 0.00 3.09
2461 2990 2.608090 GGAGATACAACAACGCTTAGCC 59.392 50.000 0.00 0.00 0.00 3.93
2462 2991 2.608090 GAGATACAACAACGCTTAGCCC 59.392 50.000 0.00 0.00 0.00 5.19
2463 2992 2.236395 AGATACAACAACGCTTAGCCCT 59.764 45.455 0.00 0.00 0.00 5.19
2464 2993 3.449737 AGATACAACAACGCTTAGCCCTA 59.550 43.478 0.00 0.00 0.00 3.53
2465 2994 2.781681 ACAACAACGCTTAGCCCTAT 57.218 45.000 0.00 0.00 0.00 2.57
2466 2995 2.629051 ACAACAACGCTTAGCCCTATC 58.371 47.619 0.00 0.00 0.00 2.08
2467 2996 1.940613 CAACAACGCTTAGCCCTATCC 59.059 52.381 0.00 0.00 0.00 2.59
2468 2997 1.200519 ACAACGCTTAGCCCTATCCA 58.799 50.000 0.00 0.00 0.00 3.41
2469 2998 1.134491 ACAACGCTTAGCCCTATCCAC 60.134 52.381 0.00 0.00 0.00 4.02
2470 2999 0.468648 AACGCTTAGCCCTATCCACC 59.531 55.000 0.00 0.00 0.00 4.61
2471 3000 1.006102 CGCTTAGCCCTATCCACCG 60.006 63.158 0.00 0.00 0.00 4.94
2472 3001 1.745320 CGCTTAGCCCTATCCACCGT 61.745 60.000 0.00 0.00 0.00 4.83
2473 3002 1.335145 GCTTAGCCCTATCCACCGTA 58.665 55.000 0.00 0.00 0.00 4.02
2474 3003 1.000618 GCTTAGCCCTATCCACCGTAC 59.999 57.143 0.00 0.00 0.00 3.67
2475 3004 2.595238 CTTAGCCCTATCCACCGTACT 58.405 52.381 0.00 0.00 0.00 2.73
2476 3005 3.759581 CTTAGCCCTATCCACCGTACTA 58.240 50.000 0.00 0.00 0.00 1.82
2477 3006 2.994957 AGCCCTATCCACCGTACTAT 57.005 50.000 0.00 0.00 0.00 2.12
2478 3007 2.526432 AGCCCTATCCACCGTACTATG 58.474 52.381 0.00 0.00 0.00 2.23
2479 3008 1.067071 GCCCTATCCACCGTACTATGC 60.067 57.143 0.00 0.00 0.00 3.14
2480 3009 2.526432 CCCTATCCACCGTACTATGCT 58.474 52.381 0.00 0.00 0.00 3.79
2481 3010 2.897969 CCCTATCCACCGTACTATGCTT 59.102 50.000 0.00 0.00 0.00 3.91
2482 3011 3.323979 CCCTATCCACCGTACTATGCTTT 59.676 47.826 0.00 0.00 0.00 3.51
2483 3012 4.557205 CCTATCCACCGTACTATGCTTTC 58.443 47.826 0.00 0.00 0.00 2.62
2484 3013 2.973694 TCCACCGTACTATGCTTTCC 57.026 50.000 0.00 0.00 0.00 3.13
2485 3014 2.463752 TCCACCGTACTATGCTTTCCT 58.536 47.619 0.00 0.00 0.00 3.36
2486 3015 2.167693 TCCACCGTACTATGCTTTCCTG 59.832 50.000 0.00 0.00 0.00 3.86
2487 3016 2.093658 CCACCGTACTATGCTTTCCTGT 60.094 50.000 0.00 0.00 0.00 4.00
2488 3017 3.596214 CACCGTACTATGCTTTCCTGTT 58.404 45.455 0.00 0.00 0.00 3.16
2489 3018 3.617263 CACCGTACTATGCTTTCCTGTTC 59.383 47.826 0.00 0.00 0.00 3.18
2490 3019 3.259876 ACCGTACTATGCTTTCCTGTTCA 59.740 43.478 0.00 0.00 0.00 3.18
2491 3020 4.081087 ACCGTACTATGCTTTCCTGTTCAT 60.081 41.667 0.00 0.00 0.00 2.57
2492 3021 4.271049 CCGTACTATGCTTTCCTGTTCATG 59.729 45.833 0.00 0.00 0.00 3.07
2493 3022 5.109210 CGTACTATGCTTTCCTGTTCATGA 58.891 41.667 0.00 0.00 0.00 3.07
2494 3023 5.005779 CGTACTATGCTTTCCTGTTCATGAC 59.994 44.000 0.00 0.00 0.00 3.06
2495 3024 4.910195 ACTATGCTTTCCTGTTCATGACA 58.090 39.130 0.00 0.00 36.65 3.58
2496 3025 5.503927 ACTATGCTTTCCTGTTCATGACAT 58.496 37.500 0.00 0.00 37.69 3.06
2497 3026 4.713824 ATGCTTTCCTGTTCATGACATG 57.286 40.909 9.28 9.28 37.69 3.21
2498 3027 2.229543 TGCTTTCCTGTTCATGACATGC 59.770 45.455 10.76 0.00 37.69 4.06
2499 3028 2.416431 GCTTTCCTGTTCATGACATGCC 60.416 50.000 10.76 4.47 37.69 4.40
2500 3029 2.885135 TTCCTGTTCATGACATGCCT 57.115 45.000 10.76 0.00 37.69 4.75
2501 3030 2.118313 TCCTGTTCATGACATGCCTG 57.882 50.000 10.76 7.50 37.69 4.85
2502 3031 1.629861 TCCTGTTCATGACATGCCTGA 59.370 47.619 10.76 0.51 37.69 3.86
2503 3032 1.741706 CCTGTTCATGACATGCCTGAC 59.258 52.381 10.76 7.21 37.69 3.51
2504 3033 2.617276 CCTGTTCATGACATGCCTGACT 60.617 50.000 10.76 0.00 37.69 3.41
2505 3034 3.369787 CCTGTTCATGACATGCCTGACTA 60.370 47.826 10.76 0.00 37.69 2.59
2506 3035 4.256110 CTGTTCATGACATGCCTGACTAA 58.744 43.478 10.76 0.00 37.69 2.24
2507 3036 4.650734 TGTTCATGACATGCCTGACTAAA 58.349 39.130 10.76 0.00 32.00 1.85
2508 3037 4.455533 TGTTCATGACATGCCTGACTAAAC 59.544 41.667 10.76 7.78 32.00 2.01
2509 3038 4.558226 TCATGACATGCCTGACTAAACT 57.442 40.909 10.76 0.00 0.00 2.66
2510 3039 5.675684 TCATGACATGCCTGACTAAACTA 57.324 39.130 10.76 0.00 0.00 2.24
2511 3040 5.664457 TCATGACATGCCTGACTAAACTAG 58.336 41.667 10.76 0.00 0.00 2.57
2512 3041 3.861840 TGACATGCCTGACTAAACTAGC 58.138 45.455 0.00 0.00 0.00 3.42
2513 3042 3.260632 TGACATGCCTGACTAAACTAGCA 59.739 43.478 0.00 0.00 34.28 3.49
2514 3043 4.253685 GACATGCCTGACTAAACTAGCAA 58.746 43.478 0.00 0.00 33.35 3.91
2515 3044 4.848357 ACATGCCTGACTAAACTAGCAAT 58.152 39.130 0.00 0.00 33.35 3.56
2516 3045 5.256474 ACATGCCTGACTAAACTAGCAATT 58.744 37.500 0.00 0.00 33.35 2.32
2517 3046 6.414732 ACATGCCTGACTAAACTAGCAATTA 58.585 36.000 0.00 0.00 33.35 1.40
2518 3047 6.316390 ACATGCCTGACTAAACTAGCAATTAC 59.684 38.462 0.00 0.00 33.35 1.89
2519 3048 5.800296 TGCCTGACTAAACTAGCAATTACA 58.200 37.500 0.00 0.00 0.00 2.41
2520 3049 5.874810 TGCCTGACTAAACTAGCAATTACAG 59.125 40.000 0.00 0.00 0.00 2.74
2521 3050 5.875359 GCCTGACTAAACTAGCAATTACAGT 59.125 40.000 0.00 0.00 0.00 3.55
2522 3051 6.371825 GCCTGACTAAACTAGCAATTACAGTT 59.628 38.462 0.00 0.00 34.03 3.16
2523 3052 7.094762 GCCTGACTAAACTAGCAATTACAGTTT 60.095 37.037 12.93 12.93 43.16 2.66
2524 3053 8.784043 CCTGACTAAACTAGCAATTACAGTTTT 58.216 33.333 13.36 1.68 41.46 2.43
2525 3054 9.599322 CTGACTAAACTAGCAATTACAGTTTTG 57.401 33.333 13.36 13.43 41.46 2.44
2526 3055 9.116067 TGACTAAACTAGCAATTACAGTTTTGT 57.884 29.630 17.40 17.40 44.81 2.83
2527 3056 9.946165 GACTAAACTAGCAATTACAGTTTTGTT 57.054 29.630 17.95 9.06 43.37 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
124 597 3.964031 GAGAGAGAGAGAGAGAGAGGAGT 59.036 52.174 0.00 0.00 0.00 3.85
125 598 4.222336 AGAGAGAGAGAGAGAGAGAGGAG 58.778 52.174 0.00 0.00 0.00 3.69
126 599 4.078922 AGAGAGAGAGAGAGAGAGAGAGGA 60.079 50.000 0.00 0.00 0.00 3.71
127 600 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
128 601 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
129 602 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
130 603 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
137 610 4.892345 CAGAGAGAGAGAGAGAGAGAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
285 759 2.283101 GGGTGATGCTGTTGGGCA 60.283 61.111 0.00 0.00 46.63 5.36
367 841 5.009410 GGACTGATCTATGGCCTTTTTGATG 59.991 44.000 3.32 0.00 0.00 3.07
369 843 4.018506 TGGACTGATCTATGGCCTTTTTGA 60.019 41.667 3.32 0.00 0.00 2.69
375 849 2.324541 GTCTGGACTGATCTATGGCCT 58.675 52.381 3.32 0.00 0.00 5.19
376 850 2.042464 TGTCTGGACTGATCTATGGCC 58.958 52.381 0.00 0.00 0.00 5.36
377 851 3.827008 TTGTCTGGACTGATCTATGGC 57.173 47.619 2.38 0.00 0.00 4.40
456 930 1.986378 CAGGCGACGAACTTGTTCTAG 59.014 52.381 11.11 4.33 0.00 2.43
562 1036 1.285962 CTCCAAATCATCACCCCAGGT 59.714 52.381 0.00 0.00 35.62 4.00
635 1114 7.171337 CCATCTAAATCCAACAACCAAAAACAG 59.829 37.037 0.00 0.00 0.00 3.16
702 1181 3.053828 CTTGCTTGCTTGGTGGGG 58.946 61.111 0.00 0.00 0.00 4.96
743 1231 0.462759 GGAGCATCAAAGGACTCCGG 60.463 60.000 0.00 0.00 39.40 5.14
857 1354 3.574826 GGCTATCTAACGATGTCTCCCTT 59.425 47.826 0.00 0.00 0.00 3.95
863 1360 2.226912 AGCTCGGCTATCTAACGATGTC 59.773 50.000 0.00 0.00 36.99 3.06
884 1381 6.922957 CAGATTAAGCAGCTGTTGGTTTAAAA 59.077 34.615 16.64 3.78 44.75 1.52
1012 1516 8.306761 GGAAAGAATCAACCAAATAACTGATGT 58.693 33.333 0.00 0.00 0.00 3.06
1043 1547 1.065854 CATCTTTCCTCTCGGTGCCTT 60.066 52.381 0.00 0.00 0.00 4.35
1218 1722 1.690633 GGCTGGGATCACCTCCTCA 60.691 63.158 0.00 0.00 44.28 3.86
1267 1771 0.039888 TCATCGACGTCGTGCTTGAA 60.040 50.000 34.40 16.30 40.80 2.69
1280 1784 1.950216 CGACATCCTCTTCCTCATCGA 59.050 52.381 0.00 0.00 0.00 3.59
1296 1800 0.878523 CGTCTTCAACCTTGGCGACA 60.879 55.000 0.00 0.00 39.83 4.35
1297 1801 0.599204 TCGTCTTCAACCTTGGCGAC 60.599 55.000 0.00 0.00 0.00 5.19
1298 1802 0.599204 GTCGTCTTCAACCTTGGCGA 60.599 55.000 0.00 0.00 0.00 5.54
1371 1875 0.178915 TCTTCTTCCCTCCGTTCCCA 60.179 55.000 0.00 0.00 0.00 4.37
1566 2070 4.072131 ACATTTGCAGTTCCTCATTACGT 58.928 39.130 0.00 0.00 0.00 3.57
1567 2071 4.154015 TCACATTTGCAGTTCCTCATTACG 59.846 41.667 0.00 0.00 0.00 3.18
1568 2072 5.393962 GTCACATTTGCAGTTCCTCATTAC 58.606 41.667 0.00 0.00 0.00 1.89
1569 2073 4.154015 CGTCACATTTGCAGTTCCTCATTA 59.846 41.667 0.00 0.00 0.00 1.90
1570 2074 3.058016 CGTCACATTTGCAGTTCCTCATT 60.058 43.478 0.00 0.00 0.00 2.57
1571 2075 2.485426 CGTCACATTTGCAGTTCCTCAT 59.515 45.455 0.00 0.00 0.00 2.90
1572 2076 1.872952 CGTCACATTTGCAGTTCCTCA 59.127 47.619 0.00 0.00 0.00 3.86
1573 2077 1.873591 ACGTCACATTTGCAGTTCCTC 59.126 47.619 0.00 0.00 0.00 3.71
1574 2078 1.967319 ACGTCACATTTGCAGTTCCT 58.033 45.000 0.00 0.00 0.00 3.36
1575 2079 3.551551 GTTACGTCACATTTGCAGTTCC 58.448 45.455 0.00 0.00 0.00 3.62
1576 2080 3.060138 TCGTTACGTCACATTTGCAGTTC 60.060 43.478 4.24 0.00 0.00 3.01
1577 2081 2.867368 TCGTTACGTCACATTTGCAGTT 59.133 40.909 4.24 0.00 0.00 3.16
1578 2082 2.475111 CTCGTTACGTCACATTTGCAGT 59.525 45.455 4.24 0.00 0.00 4.40
1579 2083 2.159841 CCTCGTTACGTCACATTTGCAG 60.160 50.000 4.24 0.00 0.00 4.41
1580 2084 1.795872 CCTCGTTACGTCACATTTGCA 59.204 47.619 4.24 0.00 0.00 4.08
1581 2085 2.063266 TCCTCGTTACGTCACATTTGC 58.937 47.619 4.24 0.00 0.00 3.68
1582 2086 3.739300 AGTTCCTCGTTACGTCACATTTG 59.261 43.478 4.24 0.00 0.00 2.32
1583 2087 3.739300 CAGTTCCTCGTTACGTCACATTT 59.261 43.478 4.24 0.00 0.00 2.32
1584 2088 3.314553 CAGTTCCTCGTTACGTCACATT 58.685 45.455 4.24 0.00 0.00 2.71
1585 2089 2.925306 GCAGTTCCTCGTTACGTCACAT 60.925 50.000 4.24 0.00 0.00 3.21
1586 2090 1.601162 GCAGTTCCTCGTTACGTCACA 60.601 52.381 4.24 0.00 0.00 3.58
1587 2091 1.058404 GCAGTTCCTCGTTACGTCAC 58.942 55.000 4.24 0.00 0.00 3.67
1588 2092 0.669619 TGCAGTTCCTCGTTACGTCA 59.330 50.000 4.24 0.00 0.00 4.35
1589 2093 1.992170 ATGCAGTTCCTCGTTACGTC 58.008 50.000 4.24 0.00 0.00 4.34
1617 2121 9.953565 ATTTTCAAGCTAGTACATAACAACCTA 57.046 29.630 0.00 0.00 0.00 3.08
1619 2123 9.341899 CAATTTTCAAGCTAGTACATAACAACC 57.658 33.333 0.00 0.00 0.00 3.77
1622 2126 8.020819 GTGCAATTTTCAAGCTAGTACATAACA 58.979 33.333 0.00 0.00 0.00 2.41
1726 2241 0.979665 ATGCCAGTCACTAGCACTGT 59.020 50.000 17.22 1.48 39.84 3.55
1735 2250 6.699575 AGTTTTAATCCATATGCCAGTCAC 57.300 37.500 0.00 0.00 0.00 3.67
1738 2253 7.615365 TCAGAAAGTTTTAATCCATATGCCAGT 59.385 33.333 0.00 0.00 0.00 4.00
1768 2283 7.370383 CAATTAGTGCACTGTAAATGGAGTTT 58.630 34.615 29.57 3.21 0.00 2.66
1805 2320 9.917887 AAGATGAATAGATTGGAAGTTTCTCAT 57.082 29.630 0.00 0.00 0.00 2.90
1887 2402 3.534554 TGTAGTCGTCGCTAGATGGTTA 58.465 45.455 0.00 0.00 34.23 2.85
1893 2408 2.810274 AGTGTTTGTAGTCGTCGCTAGA 59.190 45.455 0.00 0.00 0.00 2.43
1918 2433 0.384309 ACAACACGTCTTCAGCTCGA 59.616 50.000 0.00 0.00 0.00 4.04
1924 2439 3.792401 AGATGACAACAACACGTCTTCA 58.208 40.909 0.00 0.00 38.26 3.02
1929 2444 1.542547 GGGGAGATGACAACAACACGT 60.543 52.381 0.00 0.00 0.00 4.49
1932 2447 2.549992 CGAAGGGGAGATGACAACAACA 60.550 50.000 0.00 0.00 0.00 3.33
1945 2460 2.283529 GCTCCAGTGACGAAGGGGA 61.284 63.158 0.00 0.00 0.00 4.81
1951 2466 3.371063 GTCCGGCTCCAGTGACGA 61.371 66.667 0.00 0.00 0.00 4.20
1953 2468 1.070786 TTTGTCCGGCTCCAGTGAC 59.929 57.895 0.00 0.00 0.00 3.67
1999 2515 2.202756 GGAGCCTTAGCACGACGG 60.203 66.667 0.00 0.00 43.56 4.79
2039 2555 2.198827 TCTTCATCGGCAATGGTTGT 57.801 45.000 0.00 0.00 35.94 3.32
2047 2563 0.248012 TACGCCTTTCTTCATCGGCA 59.752 50.000 0.00 0.00 42.59 5.69
2062 2578 2.930682 GTTTGATCCTTCTGACCTACGC 59.069 50.000 0.00 0.00 0.00 4.42
2068 2584 7.041098 AGTGTTTACATGTTTGATCCTTCTGAC 60.041 37.037 2.30 0.00 0.00 3.51
2122 2638 2.105821 TGGTCTTCGGTGGATCTGTTTT 59.894 45.455 0.00 0.00 0.00 2.43
2173 2689 4.412528 AGAGGGAGTGTAAAGGTGTTTCTT 59.587 41.667 0.00 0.00 0.00 2.52
2184 2701 1.476891 GCATCGTCAGAGGGAGTGTAA 59.523 52.381 0.00 0.00 0.00 2.41
2185 2702 1.103803 GCATCGTCAGAGGGAGTGTA 58.896 55.000 0.00 0.00 0.00 2.90
2190 2707 1.681538 GTCTAGCATCGTCAGAGGGA 58.318 55.000 0.00 0.00 0.00 4.20
2225 2742 6.462487 GGAATAACATCTCCCACGTTCTATCA 60.462 42.308 0.00 0.00 0.00 2.15
2243 2760 5.855395 CGGCGATGTACTTAGTAGGAATAAC 59.145 44.000 0.00 0.00 0.00 1.89
2258 2775 4.075854 TGTGGCAGCGGCGATGTA 62.076 61.111 26.78 13.37 42.47 2.29
2269 2787 1.102154 CTTGGTTGAGTTGTGTGGCA 58.898 50.000 0.00 0.00 0.00 4.92
2296 2816 3.068590 ACCCGTTCTCGTTCTTGTTAGAA 59.931 43.478 0.00 0.00 38.06 2.10
2365 2890 0.894141 CCCTATCTCTGATGGCCTCG 59.106 60.000 3.32 0.00 0.00 4.63
2407 2934 3.234353 CAAGAAAAGCCCCTTCTCCTTT 58.766 45.455 0.00 0.00 31.85 3.11
2408 2935 2.177888 ACAAGAAAAGCCCCTTCTCCTT 59.822 45.455 0.00 0.00 31.85 3.36
2440 2969 2.608090 GGCTAAGCGTTGTTGTATCTCC 59.392 50.000 0.00 0.00 0.00 3.71
2447 2976 1.940613 GGATAGGGCTAAGCGTTGTTG 59.059 52.381 0.00 0.00 0.00 3.33
2448 2977 1.557832 TGGATAGGGCTAAGCGTTGTT 59.442 47.619 0.00 0.00 0.00 2.83
2450 2979 1.583054 GTGGATAGGGCTAAGCGTTG 58.417 55.000 0.00 0.00 0.00 4.10
2451 2980 0.468648 GGTGGATAGGGCTAAGCGTT 59.531 55.000 0.00 0.00 0.00 4.84
2452 2981 1.745320 CGGTGGATAGGGCTAAGCGT 61.745 60.000 0.00 0.00 0.00 5.07
2453 2982 1.006102 CGGTGGATAGGGCTAAGCG 60.006 63.158 0.00 0.00 0.00 4.68
2454 2983 1.000618 GTACGGTGGATAGGGCTAAGC 59.999 57.143 0.00 0.00 0.00 3.09
2455 2984 2.595238 AGTACGGTGGATAGGGCTAAG 58.405 52.381 0.00 0.00 0.00 2.18
2456 2985 2.761786 AGTACGGTGGATAGGGCTAA 57.238 50.000 0.00 0.00 0.00 3.09
2457 2986 3.693807 CATAGTACGGTGGATAGGGCTA 58.306 50.000 0.00 0.00 0.00 3.93
2458 2987 2.526432 CATAGTACGGTGGATAGGGCT 58.474 52.381 0.00 0.00 0.00 5.19
2459 2988 1.067071 GCATAGTACGGTGGATAGGGC 60.067 57.143 0.00 0.00 0.00 5.19
2460 2989 2.526432 AGCATAGTACGGTGGATAGGG 58.474 52.381 0.00 0.00 0.00 3.53
2461 2990 4.557205 GAAAGCATAGTACGGTGGATAGG 58.443 47.826 0.00 0.00 0.00 2.57
2462 2991 4.281182 AGGAAAGCATAGTACGGTGGATAG 59.719 45.833 0.00 0.00 0.00 2.08
2463 2992 4.038763 CAGGAAAGCATAGTACGGTGGATA 59.961 45.833 0.00 0.00 0.00 2.59
2464 2993 3.039011 AGGAAAGCATAGTACGGTGGAT 58.961 45.455 0.00 0.00 0.00 3.41
2465 2994 2.167693 CAGGAAAGCATAGTACGGTGGA 59.832 50.000 0.00 0.00 0.00 4.02
2466 2995 2.093658 ACAGGAAAGCATAGTACGGTGG 60.094 50.000 0.00 0.00 0.00 4.61
2467 2996 3.247006 ACAGGAAAGCATAGTACGGTG 57.753 47.619 0.00 0.00 0.00 4.94
2468 2997 3.259876 TGAACAGGAAAGCATAGTACGGT 59.740 43.478 0.00 0.00 0.00 4.83
2469 2998 3.857052 TGAACAGGAAAGCATAGTACGG 58.143 45.455 0.00 0.00 0.00 4.02
2470 2999 5.005779 GTCATGAACAGGAAAGCATAGTACG 59.994 44.000 0.00 0.00 0.00 3.67
2471 3000 5.874810 TGTCATGAACAGGAAAGCATAGTAC 59.125 40.000 0.00 0.00 32.81 2.73
2472 3001 6.048732 TGTCATGAACAGGAAAGCATAGTA 57.951 37.500 0.00 0.00 32.81 1.82
2473 3002 4.910195 TGTCATGAACAGGAAAGCATAGT 58.090 39.130 0.00 0.00 32.81 2.12
2474 3003 5.732528 GCATGTCATGAACAGGAAAGCATAG 60.733 44.000 17.24 0.75 42.26 2.23
2475 3004 4.096833 GCATGTCATGAACAGGAAAGCATA 59.903 41.667 17.24 0.00 42.26 3.14
2476 3005 3.119245 GCATGTCATGAACAGGAAAGCAT 60.119 43.478 17.24 0.24 42.26 3.79
2477 3006 2.229543 GCATGTCATGAACAGGAAAGCA 59.770 45.455 17.24 0.00 42.26 3.91
2478 3007 2.416431 GGCATGTCATGAACAGGAAAGC 60.416 50.000 17.24 0.00 42.26 3.51
2479 3008 3.087031 AGGCATGTCATGAACAGGAAAG 58.913 45.455 17.24 0.00 42.26 2.62
2480 3009 2.821378 CAGGCATGTCATGAACAGGAAA 59.179 45.455 17.24 0.00 42.26 3.13
2481 3010 2.040145 TCAGGCATGTCATGAACAGGAA 59.960 45.455 17.24 0.00 42.26 3.36
2482 3011 1.629861 TCAGGCATGTCATGAACAGGA 59.370 47.619 17.24 7.42 42.26 3.86
2483 3012 1.741706 GTCAGGCATGTCATGAACAGG 59.258 52.381 17.24 1.17 42.37 4.00
2484 3013 2.708051 AGTCAGGCATGTCATGAACAG 58.292 47.619 17.24 5.64 42.37 3.16
2485 3014 2.865119 AGTCAGGCATGTCATGAACA 57.135 45.000 17.24 0.00 43.51 3.18
2486 3015 4.697352 AGTTTAGTCAGGCATGTCATGAAC 59.303 41.667 17.24 8.94 37.23 3.18
2487 3016 4.910195 AGTTTAGTCAGGCATGTCATGAA 58.090 39.130 17.24 0.00 37.23 2.57
2488 3017 4.558226 AGTTTAGTCAGGCATGTCATGA 57.442 40.909 17.24 0.00 32.41 3.07
2489 3018 4.272018 GCTAGTTTAGTCAGGCATGTCATG 59.728 45.833 8.56 8.56 0.00 3.07
2490 3019 4.080919 TGCTAGTTTAGTCAGGCATGTCAT 60.081 41.667 0.00 0.00 0.00 3.06
2491 3020 3.260632 TGCTAGTTTAGTCAGGCATGTCA 59.739 43.478 0.00 0.00 0.00 3.58
2492 3021 3.861840 TGCTAGTTTAGTCAGGCATGTC 58.138 45.455 0.00 0.00 0.00 3.06
2493 3022 3.981071 TGCTAGTTTAGTCAGGCATGT 57.019 42.857 0.00 0.00 0.00 3.21
2494 3023 5.824904 AATTGCTAGTTTAGTCAGGCATG 57.175 39.130 0.00 0.00 0.00 4.06
2495 3024 6.414732 TGTAATTGCTAGTTTAGTCAGGCAT 58.585 36.000 0.00 0.00 0.00 4.40
2496 3025 5.800296 TGTAATTGCTAGTTTAGTCAGGCA 58.200 37.500 0.00 0.00 0.00 4.75
2497 3026 5.875359 ACTGTAATTGCTAGTTTAGTCAGGC 59.125 40.000 0.00 0.00 0.00 4.85
2498 3027 7.907214 AACTGTAATTGCTAGTTTAGTCAGG 57.093 36.000 0.00 0.00 30.98 3.86
2499 3028 9.599322 CAAAACTGTAATTGCTAGTTTAGTCAG 57.401 33.333 17.45 0.00 42.11 3.51
2500 3029 9.116067 ACAAAACTGTAATTGCTAGTTTAGTCA 57.884 29.630 17.45 0.00 42.11 3.41
2501 3030 9.946165 AACAAAACTGTAATTGCTAGTTTAGTC 57.054 29.630 17.45 0.00 42.11 2.59


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

AutoCloner maintained by Alex Coulton.