Multiple sequence alignment - TraesCS7D01G074700

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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 TraesCS7D01G074700 chr7D 100.000 3545 0 0 1 3545 44301269 44297725 0.000000e+00 6547.0
1 TraesCS7D01G074700 chr4A 90.966 2557 149 31 313 2807 655261336 655258800 0.000000e+00 3367.0
2 TraesCS7D01G074700 chr4A 79.328 774 91 43 2805 3545 655258833 655258096 2.480000e-131 479.0
3 TraesCS7D01G074700 chr4A 93.174 293 9 5 1 285 655261619 655261330 1.520000e-113 420.0
4 TraesCS7D01G074700 chr7A 93.301 836 48 5 2068 2895 46721381 46720546 0.000000e+00 1227.0
5 TraesCS7D01G074700 chr7A 86.325 702 47 27 975 1642 46722723 46722037 0.000000e+00 719.0
6 TraesCS7D01G074700 chr7A 86.515 482 24 6 3068 3545 46716185 46715741 3.180000e-135 492.0
7 TraesCS7D01G074700 chr7A 77.576 825 105 45 16 800 46724047 46723263 3.270000e-115 425.0
8 TraesCS7D01G074700 chr7A 95.359 237 9 2 708 944 46723254 46723020 3.340000e-100 375.0
9 TraesCS7D01G074700 chr7A 78.354 656 86 22 1436 2066 46722041 46721417 1.200000e-99 374.0
10 TraesCS7D01G074700 chr7A 95.181 166 8 0 2894 3059 46720463 46720298 2.710000e-66 263.0
11 TraesCS7D01G074700 chr5B 87.395 119 13 2 940 1057 640805271 640805154 6.170000e-28 135.0
12 TraesCS7D01G074700 chr2A 80.851 94 13 4 3278 3367 657520743 657520835 6.350000e-08 69.4
13 TraesCS7D01G074700 chr6D 95.122 41 2 0 3338 3378 88882961 88882921 8.210000e-07 65.8
14 TraesCS7D01G074700 chr5A 80.000 90 16 2 3278 3366 622430777 622430865 8.210000e-07 65.8
15 TraesCS7D01G074700 chr4B 91.667 48 0 4 3338 3382 586929477 586929523 2.950000e-06 63.9
16 TraesCS7D01G074700 chr3D 92.683 41 3 0 3326 3366 157099405 157099445 3.820000e-05 60.2
17 TraesCS7D01G074700 chr3A 88.000 50 6 0 3326 3375 171176867 171176818 3.820000e-05 60.2
18 TraesCS7D01G074700 chr6A 87.273 55 2 5 3325 3377 85753685 85753736 1.370000e-04 58.4


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 TraesCS7D01G074700 chr7D 44297725 44301269 3544 True 6547.000000 6547 100.000000 1 3545 1 chr7D.!!$R1 3544
1 TraesCS7D01G074700 chr4A 655258096 655261619 3523 True 1422.000000 3367 87.822667 1 3545 3 chr4A.!!$R1 3544
2 TraesCS7D01G074700 chr7A 46720298 46724047 3749 True 563.833333 1227 87.682667 16 3059 6 chr7A.!!$R2 3043


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
777 902 0.178992 CAGGTCTTGAAGCCCACCAA 60.179 55.0 0.00 0.0 0.00 3.67 F
1285 1703 0.459078 GGTAGTACCAACCGAGCTCC 59.541 60.0 14.82 0.0 38.42 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1644 2280 0.386478 GCAAGCAGAAGTCAAAGCCG 60.386 55.0 0.00 0.0 0.0 5.52 R
3227 4044 0.331278 TTGGCCATTTCCGAGGTGAT 59.669 50.0 6.09 0.0 0.0 3.06 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
34 35 2.476854 GCTGAACCATCATTTGAGCGAC 60.477 50.000 0.00 0.00 34.37 5.19
187 204 4.309933 TCATGTGTGACTCAACTTGCTAG 58.690 43.478 0.00 0.00 0.00 3.42
188 205 3.819564 TGTGTGACTCAACTTGCTAGT 57.180 42.857 0.00 0.00 35.68 2.57
189 206 4.929819 TGTGTGACTCAACTTGCTAGTA 57.070 40.909 0.00 0.00 33.17 1.82
213 230 2.618241 TGTTACAGTTGCAGGCAAGAAG 59.382 45.455 6.99 3.12 36.52 2.85
266 288 4.758688 TGTGAACTCTGCCATGTATGTAG 58.241 43.478 0.00 0.00 0.00 2.74
309 335 1.072159 GCAGTGGCTCAGAAGGTGT 59.928 57.895 0.00 0.00 36.96 4.16
311 337 0.683973 CAGTGGCTCAGAAGGTGTCT 59.316 55.000 0.00 0.00 36.88 3.41
376 402 2.360165 ACTGTTTAGAACACTCGGACGT 59.640 45.455 0.00 0.00 36.25 4.34
395 421 3.175152 CGTTGCTGCAAAACTGTTTGTA 58.825 40.909 17.80 0.72 45.06 2.41
438 464 6.628856 GCATCGTGCATTGTAAACTGTAATAG 59.371 38.462 0.00 0.00 44.26 1.73
443 470 7.312899 GTGCATTGTAAACTGTAATAGCCTTT 58.687 34.615 0.00 0.00 0.00 3.11
470 499 5.586243 TGAGAAGCAAGTCCATTGTAATAGC 59.414 40.000 0.00 0.00 41.29 2.97
477 506 5.847111 AGTCCATTGTAATAGCTGTCGTA 57.153 39.130 0.00 0.00 0.00 3.43
570 599 3.620966 GCCTGAGATTCTTGGCACTTACT 60.621 47.826 20.02 0.00 44.34 2.24
601 630 1.173913 CTGTCGGGATGGGGTTTTTC 58.826 55.000 0.00 0.00 0.00 2.29
602 631 0.774908 TGTCGGGATGGGGTTTTTCT 59.225 50.000 0.00 0.00 0.00 2.52
605 634 2.230508 GTCGGGATGGGGTTTTTCTTTC 59.769 50.000 0.00 0.00 0.00 2.62
606 635 1.201414 CGGGATGGGGTTTTTCTTTCG 59.799 52.381 0.00 0.00 0.00 3.46
607 636 2.521126 GGGATGGGGTTTTTCTTTCGA 58.479 47.619 0.00 0.00 0.00 3.71
609 638 3.418047 GGATGGGGTTTTTCTTTCGAGA 58.582 45.455 0.00 0.00 0.00 4.04
659 688 6.555463 AGCATCTTCAATGGGAAATCAATT 57.445 33.333 0.00 0.00 34.44 2.32
664 693 9.309516 CATCTTCAATGGGAAATCAATTAGTTG 57.690 33.333 0.00 0.00 34.44 3.16
672 708 5.639082 GGGAAATCAATTAGTTGTTGCCAAG 59.361 40.000 6.88 0.00 34.22 3.61
757 882 1.828979 TACATTCCGAGGCCCAAAAC 58.171 50.000 0.00 0.00 0.00 2.43
762 887 2.115266 CGAGGCCCAAAACCAGGT 59.885 61.111 0.00 0.00 0.00 4.00
777 902 0.178992 CAGGTCTTGAAGCCCACCAA 60.179 55.000 0.00 0.00 0.00 3.67
788 913 2.198426 CCACCAACAGGCCCACTT 59.802 61.111 0.00 0.00 0.00 3.16
789 914 1.458486 CCACCAACAGGCCCACTTA 59.542 57.895 0.00 0.00 0.00 2.24
1278 1696 1.001181 TGCGTCAAGGTAGTACCAACC 59.999 52.381 21.49 6.86 41.95 3.77
1285 1703 0.459078 GGTAGTACCAACCGAGCTCC 59.541 60.000 14.82 0.00 38.42 4.70
1286 1704 1.472188 GTAGTACCAACCGAGCTCCT 58.528 55.000 8.47 0.00 0.00 3.69
1288 1706 0.971447 AGTACCAACCGAGCTCCTCC 60.971 60.000 8.47 0.00 0.00 4.30
1290 1708 2.164332 TACCAACCGAGCTCCTCCCT 62.164 60.000 8.47 0.00 0.00 4.20
1291 1709 2.294078 CCAACCGAGCTCCTCCCTT 61.294 63.158 8.47 0.00 0.00 3.95
1292 1710 1.219393 CAACCGAGCTCCTCCCTTC 59.781 63.158 8.47 0.00 0.00 3.46
1293 1711 1.079438 AACCGAGCTCCTCCCTTCT 59.921 57.895 8.47 0.00 0.00 2.85
1294 1712 1.261238 AACCGAGCTCCTCCCTTCTG 61.261 60.000 8.47 0.00 0.00 3.02
1296 1714 2.057408 CGAGCTCCTCCCTTCTGCT 61.057 63.158 8.47 0.00 36.63 4.24
1297 1715 0.753479 CGAGCTCCTCCCTTCTGCTA 60.753 60.000 8.47 0.00 33.83 3.49
1298 1716 1.039856 GAGCTCCTCCCTTCTGCTAG 58.960 60.000 0.87 0.00 33.83 3.42
1317 1747 7.290014 TCTGCTAGTCCCTTGATAATGTTCATA 59.710 37.037 0.00 0.00 0.00 2.15
1389 1824 9.856488 TTATTAAACTAAACCATTTTATGCGCA 57.144 25.926 14.96 14.96 0.00 6.09
1431 1866 8.586273 GTGATTGAATGAACGAATGTTTTATGG 58.414 33.333 0.00 0.00 38.78 2.74
1434 1869 5.047731 TGAATGAACGAATGTTTTATGGCCA 60.048 36.000 8.56 8.56 38.78 5.36
1435 1870 4.855715 TGAACGAATGTTTTATGGCCAA 57.144 36.364 10.96 0.00 38.78 4.52
1443 1878 5.697082 ATGTTTTATGGCCAACATGGATT 57.303 34.783 17.98 0.00 41.18 3.01
1455 1890 4.563993 CCAACATGGATTGAATGCTTTGGT 60.564 41.667 13.24 2.40 40.96 3.67
1457 1892 3.119388 ACATGGATTGAATGCTTTGGTCG 60.119 43.478 0.00 0.00 0.00 4.79
1459 1894 3.680490 TGGATTGAATGCTTTGGTCGTA 58.320 40.909 0.00 0.00 0.00 3.43
1465 1900 6.811253 TTGAATGCTTTGGTCGTACTTAAT 57.189 33.333 0.00 0.00 0.00 1.40
1502 1937 3.648982 TGGCGTGTGCTTGAAGCG 61.649 61.111 13.05 0.00 46.26 4.68
1569 2004 4.374702 GCGTGGTCTTGCTGCGTG 62.375 66.667 0.00 0.00 0.00 5.34
1582 2017 1.382522 CTGCGTGTCTGCCCATTATT 58.617 50.000 0.00 0.00 0.00 1.40
1584 2019 3.141398 CTGCGTGTCTGCCCATTATTAT 58.859 45.455 0.00 0.00 0.00 1.28
1585 2020 3.550820 TGCGTGTCTGCCCATTATTATT 58.449 40.909 0.00 0.00 0.00 1.40
1644 2280 5.675538 AGTAATTTCTGAGCTACCATGACC 58.324 41.667 0.00 0.00 0.00 4.02
1664 2300 0.038801 GGCTTTGACTTCTGCTTGCC 60.039 55.000 0.00 0.00 0.00 4.52
1670 2306 0.877743 GACTTCTGCTTGCCCTTCAC 59.122 55.000 0.00 0.00 0.00 3.18
1723 2359 3.754965 TCAGTACAAGCAGCTTTTGGAT 58.245 40.909 4.38 0.00 0.00 3.41
1741 2377 1.181098 ATGTGTTCTGGGCAAGCCAC 61.181 55.000 13.87 2.87 37.98 5.01
1805 2441 7.702348 GCAACCAATATAGGTGATTGACTTTTC 59.298 37.037 0.00 0.00 42.25 2.29
1819 2456 9.482627 TGATTGACTTTTCTTTCTCTAGACTTC 57.517 33.333 0.00 0.00 0.00 3.01
1837 2474 6.760291 AGACTTCTTTTCCGTCAGTAAATCT 58.240 36.000 0.00 0.00 0.00 2.40
1842 2479 6.628185 TCTTTTCCGTCAGTAAATCTACTCC 58.372 40.000 0.00 0.00 36.14 3.85
1846 2483 5.962433 TCCGTCAGTAAATCTACTCCTTTG 58.038 41.667 0.00 0.00 36.14 2.77
2038 2695 3.914966 GTGCATAGCAGTAGTATAGCACG 59.085 47.826 0.00 0.00 40.08 5.34
2110 2801 3.668191 CCGTCATTTTCACAAATGGAACG 59.332 43.478 11.86 11.86 46.57 3.95
2146 2837 3.181445 TGGCTGCTCTTACCAAAGAAAGA 60.181 43.478 0.00 0.00 41.19 2.52
2200 2891 1.780309 ACAAAGATCCAACCACTGGGA 59.220 47.619 0.00 0.00 46.44 4.37
2212 2903 2.582636 ACCACTGGGAGCATTTTATCCT 59.417 45.455 0.00 0.00 38.05 3.24
2234 2925 3.265791 GCTGAACCAGAACATCAGGTAG 58.734 50.000 4.39 0.00 35.01 3.18
2270 2961 0.318441 TCTTCCTTGTGAGACCTGCG 59.682 55.000 0.00 0.00 0.00 5.18
2282 2973 1.660560 GACCTGCGATGCAAATGGCT 61.661 55.000 0.00 0.00 45.15 4.75
2289 2980 2.355756 GCGATGCAAATGGCTTTCTAGA 59.644 45.455 0.00 0.00 45.15 2.43
2291 2982 4.675146 GCGATGCAAATGGCTTTCTAGAAA 60.675 41.667 16.85 16.85 45.15 2.52
2324 3018 9.466497 TCCTCTTTATGCATCTTGTTTTCTTAT 57.534 29.630 0.19 0.00 0.00 1.73
2330 3024 9.624697 TTATGCATCTTGTTTTCTTATGTGAAC 57.375 29.630 0.19 0.00 0.00 3.18
2333 3027 7.013178 TGCATCTTGTTTTCTTATGTGAACTCA 59.987 33.333 0.00 0.00 0.00 3.41
2352 3046 9.985730 TGAACTCAATTTTCATGCTAGAAATTT 57.014 25.926 0.00 0.00 37.35 1.82
2430 3124 0.837691 TCCTGTCATCCACACTGGCT 60.838 55.000 0.00 0.00 37.47 4.75
2473 3167 1.077858 GAGCTCTGCCCTCCAAAGG 60.078 63.158 6.43 0.00 42.95 3.11
2534 3228 1.005450 GAAAGGTTGGCCCATCCTACA 59.995 52.381 13.80 0.00 41.52 2.74
2751 3459 2.710377 TCAATCATCTGTCGGTTTGGG 58.290 47.619 0.00 0.00 0.00 4.12
2793 3501 5.189736 TGCTGTACCCATGTTTATCTCTTCT 59.810 40.000 0.00 0.00 0.00 2.85
2819 3527 5.449177 GGCTTGCTGTACTCATGTTTTATCC 60.449 44.000 0.00 0.00 0.00 2.59
2843 3555 0.035152 CTGGGCTTGCTGGACATGTA 60.035 55.000 0.00 0.00 0.00 2.29
2871 3583 8.962679 TGAAGTTGTAAGATGTAACTTTTGGTT 58.037 29.630 0.00 0.00 42.75 3.67
2884 3596 8.253810 TGTAACTTTTGGTTGATTCAATTGTGA 58.746 29.630 5.13 0.00 38.75 3.58
3017 3834 9.416794 GAATATGTACAGATGGAGATAACACTG 57.583 37.037 3.26 0.00 0.00 3.66
3043 3860 4.820173 ACTCCCTACAAAGTTGCACTAAAC 59.180 41.667 0.00 0.00 0.00 2.01
3054 3871 4.082571 AGTTGCACTAAACCAGCATCAATC 60.083 41.667 0.00 0.00 38.19 2.67
3060 3877 6.639686 GCACTAAACCAGCATCAATCAATATG 59.360 38.462 0.00 0.00 0.00 1.78
3064 3881 9.234827 CTAAACCAGCATCAATCAATATGGATA 57.765 33.333 0.00 0.00 0.00 2.59
3066 3883 6.185511 ACCAGCATCAATCAATATGGATAGG 58.814 40.000 0.00 0.00 0.00 2.57
3067 3884 6.012245 ACCAGCATCAATCAATATGGATAGGA 60.012 38.462 0.00 0.00 0.00 2.94
3068 3885 6.542735 CCAGCATCAATCAATATGGATAGGAG 59.457 42.308 0.00 0.00 0.00 3.69
3069 3886 6.542735 CAGCATCAATCAATATGGATAGGAGG 59.457 42.308 0.00 0.00 0.00 4.30
3070 3887 5.826737 GCATCAATCAATATGGATAGGAGGG 59.173 44.000 0.00 0.00 0.00 4.30
3071 3888 6.353342 GCATCAATCAATATGGATAGGAGGGA 60.353 42.308 0.00 0.00 0.00 4.20
3072 3889 6.881067 TCAATCAATATGGATAGGAGGGAG 57.119 41.667 0.00 0.00 0.00 4.30
3073 3890 6.334296 TCAATCAATATGGATAGGAGGGAGT 58.666 40.000 0.00 0.00 0.00 3.85
3074 3891 7.487338 TCAATCAATATGGATAGGAGGGAGTA 58.513 38.462 0.00 0.00 0.00 2.59
3075 3892 7.400339 TCAATCAATATGGATAGGAGGGAGTAC 59.600 40.741 0.00 0.00 0.00 2.73
3076 3893 6.485388 TCAATATGGATAGGAGGGAGTACT 57.515 41.667 0.00 0.00 0.00 2.73
3077 3894 7.599353 TCAATATGGATAGGAGGGAGTACTA 57.401 40.000 0.00 0.00 0.00 1.82
3078 3895 7.644062 TCAATATGGATAGGAGGGAGTACTAG 58.356 42.308 0.00 0.00 0.00 2.57
3079 3896 7.242101 TCAATATGGATAGGAGGGAGTACTAGT 59.758 40.741 0.00 0.00 0.00 2.57
3080 3897 8.558312 CAATATGGATAGGAGGGAGTACTAGTA 58.442 40.741 0.00 0.00 0.00 1.82
3081 3898 5.839517 TGGATAGGAGGGAGTACTAGTAC 57.160 47.826 23.03 23.03 36.35 2.73
3082 3899 5.229966 TGGATAGGAGGGAGTACTAGTACA 58.770 45.833 29.87 11.08 38.48 2.90
3083 3900 5.856160 TGGATAGGAGGGAGTACTAGTACAT 59.144 44.000 29.87 17.38 38.48 2.29
3084 3901 6.012683 TGGATAGGAGGGAGTACTAGTACATC 60.013 46.154 29.87 22.85 38.48 3.06
3085 3902 6.216046 GGATAGGAGGGAGTACTAGTACATCT 59.784 46.154 29.87 22.87 38.48 2.90
3118 3935 7.794041 TGCATAATAATTCTCATTTTTGCCCT 58.206 30.769 0.00 0.00 0.00 5.19
3131 3948 4.470334 TTTTGCCCTTGCTGATTATTCC 57.530 40.909 0.00 0.00 38.71 3.01
3132 3949 2.824689 TGCCCTTGCTGATTATTCCA 57.175 45.000 0.00 0.00 38.71 3.53
3150 3967 8.713708 TTATTCCATTGAGGTTCCTTTTGTTA 57.286 30.769 0.00 0.00 39.02 2.41
3179 3996 5.357742 AATTAAATGGCATCCCTGGTTTC 57.642 39.130 0.00 0.00 0.00 2.78
3180 3997 2.323999 AAATGGCATCCCTGGTTTCA 57.676 45.000 0.00 0.00 0.00 2.69
3181 3998 2.555732 AATGGCATCCCTGGTTTCAT 57.444 45.000 0.00 0.00 0.00 2.57
3186 4003 1.952296 GCATCCCTGGTTTCATGCTAG 59.048 52.381 8.93 0.00 38.89 3.42
3202 4019 1.404035 GCTAGCCCCCACAAATAAACG 59.596 52.381 2.29 0.00 0.00 3.60
3207 4024 1.401800 CCCCCACAAATAAACGCGAAC 60.402 52.381 15.93 0.00 0.00 3.95
3220 4037 2.078392 ACGCGAACGGGAACAAAATAT 58.922 42.857 15.93 0.00 46.04 1.28
3227 4044 5.106634 CGAACGGGAACAAAATATTGGTGTA 60.107 40.000 5.67 0.00 36.33 2.90
3252 4069 0.323360 TCGGAAATGGCCAAAGGAGG 60.323 55.000 10.96 0.00 0.00 4.30
3264 4081 2.689983 CCAAAGGAGGCCATATCACAAC 59.310 50.000 5.01 0.00 0.00 3.32
3268 4085 3.559069 AGGAGGCCATATCACAACAATG 58.441 45.455 5.01 0.00 0.00 2.82
3284 4101 2.040412 ACAATGTGTTCTCTCCTTCCCC 59.960 50.000 0.00 0.00 0.00 4.81
3295 4113 4.225267 TCTCTCCTTCCCCAAATAAGTGTC 59.775 45.833 0.00 0.00 0.00 3.67
3305 4123 6.490721 TCCCCAAATAAGTGTCGTTGTTTTAT 59.509 34.615 0.00 0.00 0.00 1.40
3336 4154 9.705290 AATTGTGACTTTCAAACTAAAACAACT 57.295 25.926 0.00 0.00 0.00 3.16
3356 4174 4.828829 ACTACACTTATTTTGGGACGGAG 58.171 43.478 0.00 0.00 0.00 4.63
3360 4178 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
3367 4185 1.502039 TGGGACGGAGGGAGTACATAT 59.498 52.381 0.00 0.00 0.00 1.78
3368 4186 2.090943 TGGGACGGAGGGAGTACATATT 60.091 50.000 0.00 0.00 0.00 1.28
3369 4187 2.970640 GGGACGGAGGGAGTACATATTT 59.029 50.000 0.00 0.00 0.00 1.40
3370 4188 4.154942 GGGACGGAGGGAGTACATATTTA 58.845 47.826 0.00 0.00 0.00 1.40
3371 4189 4.590222 GGGACGGAGGGAGTACATATTTAA 59.410 45.833 0.00 0.00 0.00 1.52
3372 4190 5.070847 GGGACGGAGGGAGTACATATTTAAA 59.929 44.000 0.00 0.00 0.00 1.52
3373 4191 6.408434 GGGACGGAGGGAGTACATATTTAAAA 60.408 42.308 0.00 0.00 0.00 1.52
3374 4192 7.222161 GGACGGAGGGAGTACATATTTAAAAT 58.778 38.462 0.00 0.00 0.00 1.82
3404 4222 9.723601 AAATACCACATTTCTACAATGCAAAAT 57.276 25.926 0.00 0.00 0.00 1.82
3452 4275 9.955208 CATGTAGAAATGCATGTATAACACATT 57.045 29.630 0.00 0.00 46.01 2.71
3473 4298 8.207252 CACATTCGTGAACATTTTCATAACAAC 58.793 33.333 0.00 0.00 46.80 3.32
3494 4319 9.528018 AACAACATATTTTCACACTACAAAAGG 57.472 29.630 0.00 0.00 0.00 3.11
3531 4363 8.250332 ACATACATGAAAACGAGCCATATTTTT 58.750 29.630 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 2.594303 TGAAGCAGGGCAACACGG 60.594 61.111 0.00 0.00 39.74 4.94
142 159 4.342092 ACCTTCCACAATCCAAGACAAAAG 59.658 41.667 0.00 0.00 0.00 2.27
187 204 4.497473 TGCCTGCAACTGTAACAAATAC 57.503 40.909 0.00 0.00 34.92 1.89
188 205 4.824537 TCTTGCCTGCAACTGTAACAAATA 59.175 37.500 0.00 0.00 0.00 1.40
189 206 3.636300 TCTTGCCTGCAACTGTAACAAAT 59.364 39.130 0.00 0.00 0.00 2.32
309 335 3.117322 TCCCATTCCAACACCAAAAGAGA 60.117 43.478 0.00 0.00 0.00 3.10
311 337 3.230134 CTCCCATTCCAACACCAAAAGA 58.770 45.455 0.00 0.00 0.00 2.52
376 402 3.923461 GTGTACAAACAGTTTTGCAGCAA 59.077 39.130 2.83 2.83 45.32 3.91
395 421 1.230635 GCATCGGCTCAACTGTGTGT 61.231 55.000 0.00 0.00 36.96 3.72
443 470 6.707440 TTACAATGGACTTGCTTCTCAAAA 57.293 33.333 0.00 0.00 38.50 2.44
470 499 6.412362 CAGATTCTTTCATACGAGTACGACAG 59.588 42.308 0.00 0.00 42.66 3.51
477 506 4.398358 TCGTCCAGATTCTTTCATACGAGT 59.602 41.667 0.00 0.00 33.15 4.18
570 599 1.621317 TCCCGACAGTTTGCATCTACA 59.379 47.619 0.00 0.00 0.00 2.74
619 648 5.625150 AGATGCTTATAACTCATCCCAACC 58.375 41.667 14.65 0.00 37.82 3.77
664 693 5.444663 AAAGAGAGTTCATTCTTGGCAAC 57.555 39.130 0.00 0.00 34.09 4.17
694 730 7.309621 CCCAACAATCAGAGTTCATTCTCAAAT 60.310 37.037 0.00 0.00 36.97 2.32
738 863 1.614850 GGTTTTGGGCCTCGGAATGTA 60.615 52.381 4.53 0.00 0.00 2.29
757 882 1.303643 GGTGGGCTTCAAGACCTGG 60.304 63.158 11.75 0.00 46.32 4.45
762 887 0.178992 CCTGTTGGTGGGCTTCAAGA 60.179 55.000 0.00 0.00 0.00 3.02
777 902 1.072505 CCGTGTTAAGTGGGCCTGT 59.927 57.895 4.53 0.00 0.00 4.00
788 913 4.382320 GCTGTCCGGCCCGTGTTA 62.382 66.667 0.85 0.00 0.00 2.41
970 1095 2.692741 GAGGGGAGGGAAGGTGGG 60.693 72.222 0.00 0.00 0.00 4.61
973 1098 2.125225 GTGGAGGGGAGGGAAGGT 59.875 66.667 0.00 0.00 0.00 3.50
975 1100 3.787001 GCGTGGAGGGGAGGGAAG 61.787 72.222 0.00 0.00 0.00 3.46
1137 1555 3.655810 CTCGGAGCGCCAGAAGCTT 62.656 63.158 7.44 0.00 46.13 3.74
1160 1578 3.691342 CGTGGAGGCACCCGAAGA 61.691 66.667 0.00 0.00 38.00 2.87
1278 1696 0.753479 TAGCAGAAGGGAGGAGCTCG 60.753 60.000 7.83 0.00 36.80 5.03
1285 1703 1.484240 CAAGGGACTAGCAGAAGGGAG 59.516 57.143 0.00 0.00 38.49 4.30
1286 1704 1.078823 TCAAGGGACTAGCAGAAGGGA 59.921 52.381 0.00 0.00 38.49 4.20
1288 1706 5.163258 ACATTATCAAGGGACTAGCAGAAGG 60.163 44.000 0.00 0.00 38.49 3.46
1290 1708 5.957771 ACATTATCAAGGGACTAGCAGAA 57.042 39.130 0.00 0.00 38.49 3.02
1291 1709 5.425217 TGAACATTATCAAGGGACTAGCAGA 59.575 40.000 0.00 0.00 38.49 4.26
1292 1710 5.674525 TGAACATTATCAAGGGACTAGCAG 58.325 41.667 0.00 0.00 38.49 4.24
1293 1711 5.692115 TGAACATTATCAAGGGACTAGCA 57.308 39.130 0.00 0.00 38.49 3.49
1294 1712 8.725148 CAATATGAACATTATCAAGGGACTAGC 58.275 37.037 0.00 0.00 38.49 3.42
1296 1714 9.778741 GACAATATGAACATTATCAAGGGACTA 57.221 33.333 0.00 0.00 38.49 2.59
1298 1716 7.576236 CGACAATATGAACATTATCAAGGGAC 58.424 38.462 0.00 0.00 32.06 4.46
1339 1770 3.834489 AGCACAGAGAACAGGATATGG 57.166 47.619 0.00 0.00 0.00 2.74
1340 1771 3.875727 CCAAGCACAGAGAACAGGATATG 59.124 47.826 0.00 0.00 0.00 1.78
1344 1775 1.131638 ACCAAGCACAGAGAACAGGA 58.868 50.000 0.00 0.00 0.00 3.86
1389 1824 8.509690 CATTCAATCACTGATAGTTTCACTTGT 58.490 33.333 0.00 0.00 32.78 3.16
1402 1837 6.558771 AACATTCGTTCATTCAATCACTGA 57.441 33.333 0.00 0.00 0.00 3.41
1431 1866 2.973694 AGCATTCAATCCATGTTGGC 57.026 45.000 0.00 0.00 37.47 4.52
1434 1869 4.618927 CGACCAAAGCATTCAATCCATGTT 60.619 41.667 0.00 0.00 0.00 2.71
1435 1870 3.119388 CGACCAAAGCATTCAATCCATGT 60.119 43.478 0.00 0.00 0.00 3.21
1443 1878 7.466725 GCATATTAAGTACGACCAAAGCATTCA 60.467 37.037 0.00 0.00 0.00 2.57
1455 1890 6.288294 AGCAAATCAGGCATATTAAGTACGA 58.712 36.000 0.00 0.00 0.00 3.43
1457 1892 6.638468 GCAAGCAAATCAGGCATATTAAGTAC 59.362 38.462 0.00 0.00 0.00 2.73
1459 1894 5.361857 AGCAAGCAAATCAGGCATATTAAGT 59.638 36.000 0.00 0.00 0.00 2.24
1465 1900 2.164827 CACAGCAAGCAAATCAGGCATA 59.835 45.455 0.00 0.00 0.00 3.14
1502 1937 3.907894 TCTAAACAAACACGCCCAATC 57.092 42.857 0.00 0.00 0.00 2.67
1543 1978 4.988598 AGACCACGCGCACCAAGG 62.989 66.667 5.73 3.42 0.00 3.61
1557 1992 2.553268 GCAGACACGCAGCAAGAC 59.447 61.111 0.00 0.00 0.00 3.01
1644 2280 0.386478 GCAAGCAGAAGTCAAAGCCG 60.386 55.000 0.00 0.00 0.00 5.52
1664 2300 1.374252 CGACCTGAACGGGTGAAGG 60.374 63.158 10.24 0.00 40.06 3.46
1670 2306 2.882927 TCATATTCGACCTGAACGGG 57.117 50.000 0.00 0.00 40.00 5.28
1723 2359 1.827789 GTGGCTTGCCCAGAACACA 60.828 57.895 9.35 0.00 46.54 3.72
1741 2377 1.437986 GAAGACCTCCCGTGGATCG 59.562 63.158 0.00 0.00 39.52 3.69
1805 2441 6.448006 TGACGGAAAAGAAGTCTAGAGAAAG 58.552 40.000 0.00 0.00 36.01 2.62
1819 2456 6.631962 AGGAGTAGATTTACTGACGGAAAAG 58.368 40.000 0.00 0.00 40.21 2.27
1837 2474 7.472522 GATGATCATCACATCCTCAAAGGAGTA 60.473 40.741 27.30 0.00 41.59 2.59
1842 2479 6.056236 ACAGATGATCATCACATCCTCAAAG 58.944 40.000 31.99 12.22 43.30 2.77
1846 2483 5.277876 GCAAACAGATGATCATCACATCCTC 60.278 44.000 31.99 14.63 43.30 3.71
1913 2570 2.103941 GGGGAAAATGTTGGCTTTGTCA 59.896 45.455 0.00 0.00 0.00 3.58
1914 2571 2.368548 AGGGGAAAATGTTGGCTTTGTC 59.631 45.455 0.00 0.00 0.00 3.18
1990 2647 4.018960 AGAGGATAGTGAGGCAAATGTGTT 60.019 41.667 0.00 0.00 0.00 3.32
2079 2770 4.578871 TGTGAAAATGACGGATCTGTGAT 58.421 39.130 13.13 6.32 0.00 3.06
2110 2801 0.599728 CAGCCAATCTAGCCTCGAGC 60.600 60.000 6.99 2.54 44.25 5.03
2146 2837 1.600916 GCGGTCCTTGGCTTGTTCT 60.601 57.895 0.00 0.00 0.00 3.01
2212 2903 1.421268 ACCTGATGTTCTGGTTCAGCA 59.579 47.619 0.69 0.00 44.87 4.41
2234 2925 8.844244 ACAAGGAAGAATAATGAATGACATAGC 58.156 33.333 0.00 0.00 38.38 2.97
2270 2961 7.838771 ATTTTTCTAGAAAGCCATTTGCATC 57.161 32.000 17.05 0.00 44.83 3.91
2309 3003 9.903682 ATTGAGTTCACATAAGAAAACAAGATG 57.096 29.630 0.00 0.00 32.60 2.90
2317 3011 9.195411 GCATGAAAATTGAGTTCACATAAGAAA 57.805 29.630 0.00 0.00 37.80 2.52
2318 3012 8.579006 AGCATGAAAATTGAGTTCACATAAGAA 58.421 29.630 0.00 0.00 37.80 2.52
2319 3013 8.114331 AGCATGAAAATTGAGTTCACATAAGA 57.886 30.769 0.00 0.00 37.80 2.10
2324 3018 7.509141 TTCTAGCATGAAAATTGAGTTCACA 57.491 32.000 0.00 0.00 37.80 3.58
2333 3027 8.308931 TCAGCTCAAATTTCTAGCATGAAAATT 58.691 29.630 19.26 0.05 39.08 1.82
2336 3030 6.822667 TCAGCTCAAATTTCTAGCATGAAA 57.177 33.333 19.26 6.60 38.75 2.69
2338 3032 5.163683 GCTTCAGCTCAAATTTCTAGCATGA 60.164 40.000 19.26 16.27 38.75 3.07
2339 3033 5.035443 GCTTCAGCTCAAATTTCTAGCATG 58.965 41.667 19.26 14.87 38.75 4.06
2352 3046 3.052082 GGCTTGCGCTTCAGCTCA 61.052 61.111 21.04 0.00 39.32 4.26
2430 3124 0.652071 CATACGCATTCAGCTTCGCA 59.348 50.000 0.00 0.00 42.61 5.10
2473 3167 2.171448 TGGAGCTTATCTTCTTCTGGGC 59.829 50.000 0.00 0.00 0.00 5.36
2534 3228 3.134804 AGAATGGGCTAGCTAAATGTCGT 59.865 43.478 15.72 0.00 0.00 4.34
2680 3388 3.253188 CCGTGACCAAGTGAACAATGAAT 59.747 43.478 0.00 0.00 0.00 2.57
2751 3459 1.598676 GCAAACGGACGGAGAAAAACC 60.599 52.381 0.00 0.00 0.00 3.27
2793 3501 0.692476 ACATGAGTACAGCAAGCCCA 59.308 50.000 0.00 0.00 0.00 5.36
2819 3527 1.073722 TCCAGCAAGCCCAGAACAG 59.926 57.895 0.00 0.00 0.00 3.16
2843 3555 8.621286 CCAAAAGTTACATCTTACAACTTCACT 58.379 33.333 0.00 0.00 40.63 3.41
2915 3712 1.372683 GGTCAGCTCAGCACTTGGA 59.627 57.895 0.00 0.00 0.00 3.53
3017 3834 2.742589 GTGCAACTTTGTAGGGAGTAGC 59.257 50.000 0.00 0.00 0.00 3.58
3043 3860 6.420638 TCCTATCCATATTGATTGATGCTGG 58.579 40.000 0.00 0.00 0.00 4.85
3054 3871 7.415086 ACTAGTACTCCCTCCTATCCATATTG 58.585 42.308 0.00 0.00 0.00 1.90
3060 3877 5.839517 TGTACTAGTACTCCCTCCTATCC 57.160 47.826 28.56 3.45 37.00 2.59
3064 3881 5.998128 AAGATGTACTAGTACTCCCTCCT 57.002 43.478 28.56 15.34 37.00 3.69
3066 3883 6.127423 TGCAAAAGATGTACTAGTACTCCCTC 60.127 42.308 28.56 19.88 37.00 4.30
3067 3884 5.720041 TGCAAAAGATGTACTAGTACTCCCT 59.280 40.000 28.56 20.10 37.00 4.20
3068 3885 5.974108 TGCAAAAGATGTACTAGTACTCCC 58.026 41.667 28.56 18.56 37.00 4.30
3069 3886 7.466050 GCATTGCAAAAGATGTACTAGTACTCC 60.466 40.741 28.56 20.59 37.00 3.85
3070 3887 7.064609 TGCATTGCAAAAGATGTACTAGTACTC 59.935 37.037 28.56 22.51 34.76 2.59
3071 3888 6.878923 TGCATTGCAAAAGATGTACTAGTACT 59.121 34.615 28.56 16.82 34.76 2.73
3072 3889 7.072177 TGCATTGCAAAAGATGTACTAGTAC 57.928 36.000 23.58 23.58 34.76 2.73
3073 3890 7.864108 ATGCATTGCAAAAGATGTACTAGTA 57.136 32.000 16.46 0.00 43.62 1.82
3074 3891 6.764308 ATGCATTGCAAAAGATGTACTAGT 57.236 33.333 16.46 0.00 43.62 2.57
3080 3897 9.826574 AGAATTATTATGCATTGCAAAAGATGT 57.173 25.926 16.46 0.00 43.62 3.06
3118 3935 5.360714 GGAACCTCAATGGAATAATCAGCAA 59.639 40.000 0.00 0.00 39.71 3.91
3158 3975 4.360889 TGAAACCAGGGATGCCATTTAAT 58.639 39.130 5.86 0.00 0.00 1.40
3164 3981 0.971959 GCATGAAACCAGGGATGCCA 60.972 55.000 5.86 0.00 36.08 4.92
3179 3996 2.363306 TATTTGTGGGGGCTAGCATG 57.637 50.000 18.24 0.00 0.00 4.06
3180 3997 3.031013 GTTTATTTGTGGGGGCTAGCAT 58.969 45.455 18.24 0.84 0.00 3.79
3181 3998 2.452505 GTTTATTTGTGGGGGCTAGCA 58.547 47.619 18.24 0.00 0.00 3.49
3186 4003 1.153920 CGCGTTTATTTGTGGGGGC 60.154 57.895 0.00 0.00 0.00 5.80
3202 4019 3.175929 CCAATATTTTGTTCCCGTTCGC 58.824 45.455 0.00 0.00 0.00 4.70
3207 4024 6.262601 GTGATACACCAATATTTTGTTCCCG 58.737 40.000 5.07 0.00 0.00 5.14
3227 4044 0.331278 TTGGCCATTTCCGAGGTGAT 59.669 50.000 6.09 0.00 0.00 3.06
3234 4051 1.948721 GCCTCCTTTGGCCATTTCCG 61.949 60.000 6.09 0.00 46.82 4.30
3235 4052 1.900351 GCCTCCTTTGGCCATTTCC 59.100 57.895 6.09 0.00 46.82 3.13
3264 4081 2.040278 TGGGGAAGGAGAGAACACATTG 59.960 50.000 0.00 0.00 0.00 2.82
3268 4085 2.951229 TTTGGGGAAGGAGAGAACAC 57.049 50.000 0.00 0.00 0.00 3.32
3270 4087 4.944317 CACTTATTTGGGGAAGGAGAGAAC 59.056 45.833 0.00 0.00 0.00 3.01
3271 4088 4.601857 ACACTTATTTGGGGAAGGAGAGAA 59.398 41.667 0.00 0.00 0.00 2.87
3279 4096 3.822940 ACAACGACACTTATTTGGGGAA 58.177 40.909 0.00 0.00 0.00 3.97
3280 4097 3.495434 ACAACGACACTTATTTGGGGA 57.505 42.857 0.00 0.00 0.00 4.81
3310 4128 9.705290 AGTTGTTTTAGTTTGAAAGTCACAATT 57.295 25.926 7.78 3.16 0.00 2.32
3313 4131 8.784994 TGTAGTTGTTTTAGTTTGAAAGTCACA 58.215 29.630 0.00 0.00 0.00 3.58
3314 4132 9.058424 GTGTAGTTGTTTTAGTTTGAAAGTCAC 57.942 33.333 0.00 0.00 0.00 3.67
3315 4133 9.005777 AGTGTAGTTGTTTTAGTTTGAAAGTCA 57.994 29.630 0.00 0.00 0.00 3.41
3316 4134 9.836076 AAGTGTAGTTGTTTTAGTTTGAAAGTC 57.164 29.630 0.00 0.00 0.00 3.01
3329 4147 6.238814 CCGTCCCAAAATAAGTGTAGTTGTTT 60.239 38.462 0.00 0.00 0.00 2.83
3336 4154 3.054948 CCCTCCGTCCCAAAATAAGTGTA 60.055 47.826 0.00 0.00 0.00 2.90
3346 4164 0.042131 ATGTACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
3347 4165 0.928505 TATGTACTCCCTCCGTCCCA 59.071 55.000 0.00 0.00 0.00 4.37
3349 4167 5.796424 TTAAATATGTACTCCCTCCGTCC 57.204 43.478 0.00 0.00 0.00 4.79
3446 4269 7.421599 TGTTATGAAAATGTTCACGAATGTGT 58.578 30.769 0.00 0.00 46.40 3.72
3447 4270 7.850268 TGTTATGAAAATGTTCACGAATGTG 57.150 32.000 0.00 0.00 46.40 3.21
3499 4331 6.150307 TGGCTCGTTTTCATGTATGTATTTGT 59.850 34.615 0.00 0.00 0.00 2.83
3500 4332 6.550843 TGGCTCGTTTTCATGTATGTATTTG 58.449 36.000 0.00 0.00 0.00 2.32



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

AutoCloner maintained by Alex Coulton.