Multiple sequence alignment - TraesCS7B01G483000

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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 TraesCS7B01G483000 chr7B 100.000 5462 0 0 1 5462 741247098 741241637 0.000000e+00 10087.0
1 TraesCS7B01G483000 chr7B 80.410 536 66 18 2866 3389 739642875 739643383 6.680000e-99 372.0
2 TraesCS7B01G483000 chr7D 89.537 2313 117 40 570 2805 635395087 635397351 0.000000e+00 2815.0
3 TraesCS7B01G483000 chr7D 92.194 1960 104 22 2818 4766 634892170 634890249 0.000000e+00 2726.0
4 TraesCS7B01G483000 chr7D 93.790 1256 50 17 2852 4102 635397846 635399078 0.000000e+00 1862.0
5 TraesCS7B01G483000 chr7D 89.114 1332 67 28 573 1846 634894796 634893485 0.000000e+00 1585.0
6 TraesCS7B01G483000 chr7D 96.386 913 22 3 1901 2805 634893473 634892564 0.000000e+00 1493.0
7 TraesCS7B01G483000 chr7D 87.565 965 42 21 4217 5145 635399105 635400027 0.000000e+00 1046.0
8 TraesCS7B01G483000 chr7D 91.433 677 43 7 4794 5462 634890253 634889584 0.000000e+00 915.0
9 TraesCS7B01G483000 chr7D 94.231 572 32 1 1 572 635393582 635394152 0.000000e+00 872.0
10 TraesCS7B01G483000 chr7D 84.832 567 74 11 13 572 634895494 634894933 1.330000e-155 560.0
11 TraesCS7B01G483000 chr7D 92.614 352 22 1 5111 5462 635400217 635400564 2.270000e-138 503.0
12 TraesCS7B01G483000 chr7D 93.889 180 7 4 2570 2746 636665209 636665031 9.020000e-68 268.0
13 TraesCS7B01G483000 chr7D 89.655 116 12 0 13 128 634894405 634894290 1.230000e-31 148.0
14 TraesCS7B01G483000 chr7D 90.090 111 8 1 4062 4172 236821642 236821535 2.050000e-29 141.0
15 TraesCS7B01G483000 chr7D 87.603 121 13 2 929 1049 635393595 635393713 7.380000e-29 139.0
16 TraesCS7B01G483000 chr7D 86.508 126 15 2 1 125 635395479 635395603 2.650000e-28 137.0
17 TraesCS7B01G483000 chr7D 84.892 139 14 5 4052 4188 550233532 550233665 3.430000e-27 134.0
18 TraesCS7B01G483000 chr7A 92.931 1160 50 6 1672 2822 730712926 730711790 0.000000e+00 1659.0
19 TraesCS7B01G483000 chr7A 95.400 1000 39 4 3090 4084 730711228 730710231 0.000000e+00 1585.0
20 TraesCS7B01G483000 chr7A 87.560 828 40 20 4217 5016 730710189 730709397 0.000000e+00 900.0
21 TraesCS7B01G483000 chr7A 86.513 304 26 10 5160 5462 730709403 730709114 2.450000e-83 320.0
22 TraesCS7B01G483000 chr7A 88.077 260 15 7 1389 1640 730713173 730712922 1.490000e-75 294.0
23 TraesCS7B01G483000 chr7A 81.351 370 23 21 810 1160 730713607 730713265 5.430000e-65 259.0
24 TraesCS7B01G483000 chr7A 90.323 186 11 6 2570 2752 729612601 729612782 2.540000e-58 237.0
25 TraesCS7B01G483000 chr7A 90.323 186 11 6 2570 2752 729638005 729638186 2.540000e-58 237.0
26 TraesCS7B01G483000 chr7A 94.964 139 5 2 2855 2992 730711366 730711229 3.310000e-52 217.0
27 TraesCS7B01G483000 chr7A 90.741 108 7 1 4065 4172 252178501 252178397 2.050000e-29 141.0
28 TraesCS7B01G483000 chr7A 91.753 97 4 4 1186 1280 730713268 730713174 1.230000e-26 132.0
29 TraesCS7B01G483000 chr7A 94.030 67 4 0 25 91 730713461 730713395 9.680000e-18 102.0
30 TraesCS7B01G483000 chrUn 81.056 549 65 18 2866 3402 373778130 373778651 8.520000e-108 401.0
31 TraesCS7B01G483000 chrUn 80.874 549 66 17 2866 3402 159048888 159048367 3.960000e-106 396.0
32 TraesCS7B01G483000 chrUn 80.410 536 66 18 2866 3389 287874100 287874608 6.680000e-99 372.0
33 TraesCS7B01G483000 chrUn 80.410 536 66 18 2866 3389 307004160 307004668 6.680000e-99 372.0
34 TraesCS7B01G483000 chrUn 83.578 341 43 7 2866 3194 391122724 391123063 1.910000e-79 307.0
35 TraesCS7B01G483000 chrUn 82.065 368 19 16 4565 4899 50447813 50448166 2.510000e-68 270.0
36 TraesCS7B01G483000 chr4A 82.016 367 20 16 4565 4899 708069002 708069354 2.510000e-68 270.0
37 TraesCS7B01G483000 chr4A 94.167 120 7 0 4780 4899 708091890 708092009 3.360000e-42 183.0
38 TraesCS7B01G483000 chr6B 91.228 114 7 1 4062 4175 507471549 507471659 9.480000e-33 152.0
39 TraesCS7B01G483000 chr5B 75.068 365 70 14 129 474 462713389 462713027 3.410000e-32 150.0
40 TraesCS7B01G483000 chr5B 75.191 262 53 9 129 384 309030700 309030955 4.470000e-21 113.0
41 TraesCS7B01G483000 chr6D 90.351 114 9 1 4062 4175 317078892 317078781 1.230000e-31 148.0
42 TraesCS7B01G483000 chr5D 89.167 120 9 3 4053 4171 448453698 448453582 4.410000e-31 147.0
43 TraesCS7B01G483000 chr4B 89.474 114 11 1 4062 4175 479155508 479155620 5.700000e-30 143.0
44 TraesCS7B01G483000 chr3B 87.302 126 11 3 4050 4174 8054650 8054771 7.380000e-29 139.0
45 TraesCS7B01G483000 chr3B 73.780 164 37 4 140 297 818938393 818938556 5.910000e-05 60.2
46 TraesCS7B01G483000 chr2B 79.856 139 27 1 141 278 789858039 789858177 3.480000e-17 100.0
47 TraesCS7B01G483000 chr3A 80.645 93 16 2 129 221 741632763 741632853 2.730000e-08 71.3
48 TraesCS7B01G483000 chr5A 84.058 69 7 4 141 208 635781155 635781090 4.570000e-06 63.9
49 TraesCS7B01G483000 chr4D 100.000 30 0 0 150 179 6782110 6782139 7.640000e-04 56.5


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 TraesCS7B01G483000 chr7B 741241637 741247098 5461 True 10087.000000 10087 100.000000 1 5462 1 chr7B.!!$R1 5461
1 TraesCS7B01G483000 chr7B 739642875 739643383 508 False 372.000000 372 80.410000 2866 3389 1 chr7B.!!$F1 523
2 TraesCS7B01G483000 chr7D 634889584 634895494 5910 True 1237.833333 2726 90.602333 13 5462 6 chr7D.!!$R3 5449
3 TraesCS7B01G483000 chr7D 635393582 635400564 6982 False 1053.428571 2815 90.264000 1 5462 7 chr7D.!!$F2 5461
4 TraesCS7B01G483000 chr7A 730709114 730713607 4493 True 607.555556 1659 90.286556 25 5462 9 chr7A.!!$R2 5437
5 TraesCS7B01G483000 chrUn 373778130 373778651 521 False 401.000000 401 81.056000 2866 3402 1 chrUn.!!$F4 536
6 TraesCS7B01G483000 chrUn 159048367 159048888 521 True 396.000000 396 80.874000 2866 3402 1 chrUn.!!$R1 536
7 TraesCS7B01G483000 chrUn 287874100 287874608 508 False 372.000000 372 80.410000 2866 3389 1 chrUn.!!$F2 523
8 TraesCS7B01G483000 chrUn 307004160 307004668 508 False 372.000000 372 80.410000 2866 3389 1 chrUn.!!$F3 523

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
360 367 0.039798 TCTTCGTGCGTGTGTCTACC 60.040 55.000 0.00 0.0 0.00 3.18 F
1176 2199 0.043334 TCCCTCCCTCTCTTTCCCAG 59.957 60.000 0.00 0.0 0.00 4.45 F
2158 3216 0.250124 AGACGTTGTGCCCATCGAAA 60.250 50.000 6.65 0.0 37.26 3.46 F
2403 3461 0.462759 CTTCCTTGACTGGATCCCGC 60.463 60.000 9.90 0.0 35.83 6.13 F
3548 5085 1.070134 TCCTCTGTCCAGGTTTTGTCG 59.930 52.381 0.00 0.0 34.76 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1696 2751 0.179174 GCCGGTCAAAGTAAATGCCG 60.179 55.000 1.9 0.0 37.28 5.69 R
2160 3218 1.115467 CCAGGAATCTAGACCGTGCT 58.885 55.000 0.0 0.0 0.00 4.40 R
3402 4939 1.014564 GCCTGTACTTGTGTCGAGGC 61.015 60.000 0.0 0.0 40.92 4.70 R
4202 5746 1.003118 TGCATGACGGAAGCTACCTTT 59.997 47.619 0.0 0.0 0.00 3.11 R
5307 7161 1.142870 TCAACAACCTCCTCACCCTTG 59.857 52.381 0.0 0.0 0.00 3.61 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
153 160 6.921307 GGTGTTTTATGTGAGTTTGTTTAGGG 59.079 38.462 0.00 0.00 0.00 3.53
259 266 2.278013 CTAGCGTCGTCGAAGGGC 60.278 66.667 6.17 8.02 39.71 5.19
310 317 1.216977 CATTCCGTCGGTGCTGGTA 59.783 57.895 11.88 0.00 0.00 3.25
314 321 1.216977 CCGTCGGTGCTGGTATTCA 59.783 57.895 2.08 0.00 0.00 2.57
340 347 4.458397 GATCTGCTTGGATCCAATCTTCA 58.542 43.478 27.20 19.33 36.91 3.02
360 367 0.039798 TCTTCGTGCGTGTGTCTACC 60.040 55.000 0.00 0.00 0.00 3.18
402 409 5.906113 ATACTTCTCTTCATCAGTGACGT 57.094 39.130 0.00 0.00 33.41 4.34
403 410 4.592485 ACTTCTCTTCATCAGTGACGTT 57.408 40.909 0.00 0.00 33.11 3.99
413 420 1.066071 TCAGTGACGTTGGTTGTTCCA 60.066 47.619 0.00 0.00 45.60 3.53
433 440 0.855598 ATGATGTGGGGCCTTAGCAT 59.144 50.000 0.84 2.31 42.56 3.79
525 532 7.168804 GTGCTTATAGTCGTTATTAGGTGGTTC 59.831 40.741 0.00 0.00 0.00 3.62
730 1708 4.693566 TGTGTAATTTTGAGACGGATGGAC 59.306 41.667 0.00 0.00 0.00 4.02
769 1748 2.099431 GGTGAAGCAGAGCAGAGCG 61.099 63.158 0.00 0.00 35.48 5.03
786 1768 5.275788 GCAGAGCGAAAACAATACTACTACG 60.276 44.000 0.00 0.00 0.00 3.51
973 1996 4.899239 CGGGCGCCAGGCTCTAAG 62.899 72.222 30.85 3.27 41.25 2.18
1031 2054 4.129737 TGTGCCGCTCTACTCCGC 62.130 66.667 0.00 0.00 0.00 5.54
1149 2172 0.682852 CCAACTCCGTGGTAACCTCA 59.317 55.000 0.00 0.00 33.63 3.86
1176 2199 0.043334 TCCCTCCCTCTCTTTCCCAG 59.957 60.000 0.00 0.00 0.00 4.45
1260 2295 2.665000 CCCGGAGCAGAGCAAGAA 59.335 61.111 0.73 0.00 0.00 2.52
1326 2363 3.620300 CTGCGCGGTGGTTCGACTA 62.620 63.158 8.83 0.00 0.00 2.59
1327 2364 2.879462 GCGCGGTGGTTCGACTAG 60.879 66.667 8.83 0.00 0.00 2.57
1328 2365 2.202570 CGCGGTGGTTCGACTAGG 60.203 66.667 0.00 0.00 0.00 3.02
1329 2366 2.693762 CGCGGTGGTTCGACTAGGA 61.694 63.158 0.00 0.00 0.00 2.94
1372 2409 4.398598 GCGGCGCATTTTGTCGGT 62.399 61.111 29.21 0.00 0.00 4.69
1413 2463 2.742372 GGCCGTGTGGTGCTACAG 60.742 66.667 0.00 0.00 37.67 2.74
1458 2509 5.998454 TTGCCATTTTTACCATGTGTTTG 57.002 34.783 0.00 0.00 0.00 2.93
1490 2541 2.916716 GCATTGTGTGAACCTAAATGCG 59.083 45.455 3.24 0.00 42.40 4.73
1550 2602 6.991485 CATTTACTTCGAAAAATGCTGTGT 57.009 33.333 17.74 4.69 36.57 3.72
1634 2689 2.183555 GGCGGTAGGGAAGTGTCG 59.816 66.667 0.00 0.00 0.00 4.35
1640 2695 1.534163 GGTAGGGAAGTGTCGTTTTGC 59.466 52.381 0.00 0.00 0.00 3.68
1657 2712 1.172175 TGCGCAATGGAAATGCTGTA 58.828 45.000 8.16 0.00 41.64 2.74
1696 2751 6.790285 TTGTATTTTTCAAGGTAGACCGTC 57.210 37.500 0.00 0.00 42.08 4.79
1768 2823 9.209297 GTTTTGTGAAATTAAAACATTCTGTGC 57.791 29.630 8.69 0.00 43.02 4.57
1820 2876 2.056577 GTTACTTGTTCGACCGACCAG 58.943 52.381 0.00 0.00 0.00 4.00
1846 2902 4.088634 TGGATGCATTTCCTTTTAGTGCT 58.911 39.130 0.00 0.00 36.68 4.40
1847 2903 5.260424 TGGATGCATTTCCTTTTAGTGCTA 58.740 37.500 0.00 0.00 36.68 3.49
1881 2937 5.773575 TGCTTCTTGTAACAAAACACAACA 58.226 33.333 0.00 0.00 31.61 3.33
1882 2938 6.393990 TGCTTCTTGTAACAAAACACAACAT 58.606 32.000 0.00 0.00 31.61 2.71
1883 2939 6.529829 TGCTTCTTGTAACAAAACACAACATC 59.470 34.615 0.00 0.00 31.61 3.06
1884 2940 6.529829 GCTTCTTGTAACAAAACACAACATCA 59.470 34.615 0.00 0.00 31.61 3.07
1885 2941 7.462724 GCTTCTTGTAACAAAACACAACATCAC 60.463 37.037 0.00 0.00 31.61 3.06
1886 2942 6.914259 TCTTGTAACAAAACACAACATCACA 58.086 32.000 0.00 0.00 31.61 3.58
1887 2943 7.371159 TCTTGTAACAAAACACAACATCACAA 58.629 30.769 0.00 0.00 31.61 3.33
1888 2944 6.936222 TGTAACAAAACACAACATCACAAC 57.064 33.333 0.00 0.00 0.00 3.32
1889 2945 5.864474 TGTAACAAAACACAACATCACAACC 59.136 36.000 0.00 0.00 0.00 3.77
1890 2946 4.527509 ACAAAACACAACATCACAACCA 57.472 36.364 0.00 0.00 0.00 3.67
1891 2947 4.241681 ACAAAACACAACATCACAACCAC 58.758 39.130 0.00 0.00 0.00 4.16
1892 2948 4.240888 CAAAACACAACATCACAACCACA 58.759 39.130 0.00 0.00 0.00 4.17
1893 2949 3.781079 AACACAACATCACAACCACAG 57.219 42.857 0.00 0.00 0.00 3.66
1894 2950 1.405105 ACACAACATCACAACCACAGC 59.595 47.619 0.00 0.00 0.00 4.40
1895 2951 0.662619 ACAACATCACAACCACAGCG 59.337 50.000 0.00 0.00 0.00 5.18
1896 2952 0.943673 CAACATCACAACCACAGCGA 59.056 50.000 0.00 0.00 0.00 4.93
1897 2953 0.944386 AACATCACAACCACAGCGAC 59.056 50.000 0.00 0.00 0.00 5.19
2142 3200 3.194968 TGATTCCCCTCTTCGTTACAGAC 59.805 47.826 0.00 0.00 0.00 3.51
2158 3216 0.250124 AGACGTTGTGCCCATCGAAA 60.250 50.000 6.65 0.00 37.26 3.46
2160 3218 2.004017 GACGTTGTGCCCATCGAAATA 58.996 47.619 6.65 0.00 37.26 1.40
2403 3461 0.462759 CTTCCTTGACTGGATCCCGC 60.463 60.000 9.90 0.00 35.83 6.13
2421 3479 1.379527 GCGAGAAAACTATGGGGGTG 58.620 55.000 0.00 0.00 0.00 4.61
2454 3512 1.669760 CGGCGGCTTGTACAGGAAA 60.670 57.895 9.51 0.00 0.00 3.13
2503 3564 6.540189 AGGTATGATGATTAGTGAACAGCAAC 59.460 38.462 0.00 0.00 33.86 4.17
2564 3630 3.131223 TCATCCGAGTCTCCTTTGATGTC 59.869 47.826 12.42 0.00 33.80 3.06
2761 3827 7.110155 GGTATTTTCTCTGATTCACCCTGTAA 58.890 38.462 0.00 0.00 0.00 2.41
2772 3838 4.301072 TCACCCTGTAATTCCTTCCTTG 57.699 45.455 0.00 0.00 0.00 3.61
2853 4336 5.645929 TGTTTTGAACTTGCAGAGTCTGTAA 59.354 36.000 20.61 20.61 37.72 2.41
2959 4482 1.264288 CAGACTCCGTTCCTTTGTTGC 59.736 52.381 0.00 0.00 0.00 4.17
2973 4496 4.450053 CTTTGTTGCCATTTCCTTGGAAA 58.550 39.130 16.03 16.03 39.25 3.13
3075 4611 3.340034 TCAACAGGGCTTAATTGTACCG 58.660 45.455 0.00 0.00 0.00 4.02
3087 4623 4.946784 AATTGTACCGATCTGCAAAGTC 57.053 40.909 0.00 0.00 0.00 3.01
3088 4624 2.380084 TGTACCGATCTGCAAAGTCC 57.620 50.000 0.00 0.00 0.00 3.85
3135 4671 6.126863 AGAAATTGACTGTATTCCTGTCCA 57.873 37.500 0.00 0.00 40.31 4.02
3137 4673 6.431234 AGAAATTGACTGTATTCCTGTCCAAC 59.569 38.462 0.00 0.00 40.31 3.77
3141 4677 2.290323 ACTGTATTCCTGTCCAACTGCC 60.290 50.000 0.00 0.00 0.00 4.85
3169 4705 9.996554 TCAATATAGGATGAATTATGAACACGT 57.003 29.630 0.00 0.00 0.00 4.49
3267 4804 3.208747 TCCTCACTTTCCACTTTGACC 57.791 47.619 0.00 0.00 0.00 4.02
3362 4899 3.064207 TCAAAAGATTGACCGGTCGAAG 58.936 45.455 28.11 13.47 40.59 3.79
3369 4906 1.608055 TGACCGGTCGAAGTGAAGTA 58.392 50.000 28.70 4.91 0.00 2.24
3548 5085 1.070134 TCCTCTGTCCAGGTTTTGTCG 59.930 52.381 0.00 0.00 34.76 4.35
3842 5384 2.928757 CACTTTCTCGATCAAGCAGAGG 59.071 50.000 4.10 0.00 33.16 3.69
3952 5494 1.277557 CAGCACCAGGCCTATCTATCC 59.722 57.143 3.98 0.00 46.50 2.59
3983 5525 1.236616 TTCCATGCAAGCTGGACACG 61.237 55.000 7.03 0.00 42.43 4.49
4043 5587 6.885376 TGAATCTTTATTTAGTACCGGCCAAA 59.115 34.615 0.00 0.00 0.00 3.28
4046 5590 6.655930 TCTTTATTTAGTACCGGCCAAATCT 58.344 36.000 0.00 0.00 0.00 2.40
4084 5628 8.233349 AGTACTCCCTCTGATCCATATTACTA 57.767 38.462 0.00 0.00 0.00 1.82
4085 5629 8.110908 AGTACTCCCTCTGATCCATATTACTAC 58.889 40.741 0.00 0.00 0.00 2.73
4086 5630 7.109901 ACTCCCTCTGATCCATATTACTACT 57.890 40.000 0.00 0.00 0.00 2.57
4094 5638 7.928167 TCTGATCCATATTACTACTTGTTGCTG 59.072 37.037 0.00 0.00 0.00 4.41
4104 5648 5.072741 ACTACTTGTTGCTGAAATGGATGT 58.927 37.500 0.00 0.00 0.00 3.06
4107 5651 6.199937 ACTTGTTGCTGAAATGGATGTATC 57.800 37.500 0.00 0.00 0.00 2.24
4112 5656 7.512130 TGTTGCTGAAATGGATGTATCTAGAT 58.488 34.615 10.73 10.73 0.00 1.98
4116 5660 8.309656 TGCTGAAATGGATGTATCTAGATGTAG 58.690 37.037 15.79 0.00 0.00 2.74
4135 5679 6.392625 TGTAGTTCAGTGCTAGATACATCC 57.607 41.667 0.00 0.00 0.00 3.51
4141 5685 4.401202 TCAGTGCTAGATACATCCGTTTGA 59.599 41.667 0.00 0.00 0.00 2.69
4181 5725 4.346730 TCGGAGGGAGTAGTATCAAAACA 58.653 43.478 0.00 0.00 0.00 2.83
4189 5733 8.497745 AGGGAGTAGTATCAAAACATTCATCAT 58.502 33.333 0.00 0.00 0.00 2.45
4207 5751 6.070656 TCATCATGTTCAGGAAAGAAAAGGT 58.929 36.000 0.00 0.00 0.00 3.50
4209 5753 7.391554 TCATCATGTTCAGGAAAGAAAAGGTAG 59.608 37.037 0.00 0.00 0.00 3.18
4214 5758 4.652822 TCAGGAAAGAAAAGGTAGCTTCC 58.347 43.478 7.80 0.07 0.00 3.46
4215 5759 3.437049 CAGGAAAGAAAAGGTAGCTTCCG 59.563 47.826 7.80 0.00 0.00 4.30
4256 5800 2.186243 AGTCATCCTGTCTGTCTGCAT 58.814 47.619 0.00 0.00 0.00 3.96
4455 6015 1.229496 TGGCACCAAGAGGCTAGGA 60.229 57.895 7.08 0.00 39.06 2.94
4467 6027 2.627699 GAGGCTAGGAATCTGACTGAGG 59.372 54.545 0.00 0.00 0.00 3.86
4468 6028 2.246067 AGGCTAGGAATCTGACTGAGGA 59.754 50.000 0.00 0.00 0.00 3.71
4470 6030 3.645687 GGCTAGGAATCTGACTGAGGAAT 59.354 47.826 0.00 0.00 0.00 3.01
4471 6031 4.102367 GGCTAGGAATCTGACTGAGGAATT 59.898 45.833 0.00 0.00 0.00 2.17
4472 6032 5.397334 GGCTAGGAATCTGACTGAGGAATTT 60.397 44.000 0.00 0.00 0.00 1.82
4473 6033 6.118852 GCTAGGAATCTGACTGAGGAATTTT 58.881 40.000 0.00 0.00 0.00 1.82
4474 6034 6.038050 GCTAGGAATCTGACTGAGGAATTTTG 59.962 42.308 0.00 0.00 0.00 2.44
4475 6035 5.885465 AGGAATCTGACTGAGGAATTTTGT 58.115 37.500 0.00 0.00 0.00 2.83
4476 6036 5.942826 AGGAATCTGACTGAGGAATTTTGTC 59.057 40.000 0.00 0.00 0.00 3.18
4477 6037 5.163814 GGAATCTGACTGAGGAATTTTGTCG 60.164 44.000 0.00 0.00 0.00 4.35
4478 6038 3.067106 TCTGACTGAGGAATTTTGTCGC 58.933 45.455 0.00 0.00 0.00 5.19
4479 6039 2.807967 CTGACTGAGGAATTTTGTCGCA 59.192 45.455 0.00 0.00 0.00 5.10
4480 6040 2.807967 TGACTGAGGAATTTTGTCGCAG 59.192 45.455 0.00 0.00 0.00 5.18
4481 6041 2.808543 GACTGAGGAATTTTGTCGCAGT 59.191 45.455 0.00 0.00 36.87 4.40
4482 6042 3.214328 ACTGAGGAATTTTGTCGCAGTT 58.786 40.909 0.00 0.00 32.93 3.16
4483 6043 3.251004 ACTGAGGAATTTTGTCGCAGTTC 59.749 43.478 0.00 0.00 32.93 3.01
4660 6227 4.040047 TGGATGTGACTCCCTCATGTATT 58.960 43.478 0.00 0.00 34.12 1.89
4662 6229 5.070446 TGGATGTGACTCCCTCATGTATTAC 59.930 44.000 0.00 0.00 34.12 1.89
4663 6230 5.070446 GGATGTGACTCCCTCATGTATTACA 59.930 44.000 0.00 0.00 0.00 2.41
4696 6263 6.574350 ACTGTTGTGCCTTACTATGATCTAC 58.426 40.000 0.00 0.00 0.00 2.59
4697 6264 6.381420 ACTGTTGTGCCTTACTATGATCTACT 59.619 38.462 0.00 0.00 0.00 2.57
4698 6265 7.560262 ACTGTTGTGCCTTACTATGATCTACTA 59.440 37.037 0.00 0.00 0.00 1.82
4769 6383 3.247006 AGTCAGCATACAGTTTACGGG 57.753 47.619 0.00 0.00 0.00 5.28
4797 6411 3.590720 GCCATTTGCTTGTTTTGTGTC 57.409 42.857 0.00 0.00 36.87 3.67
4925 6548 9.480861 TGGTCTTATATTGGAGATAGAATCGAT 57.519 33.333 0.00 0.00 0.00 3.59
4969 6593 9.773328 TCACTTATTTCTTCAGCAAAATATTCG 57.227 29.630 0.00 0.00 29.90 3.34
5080 6704 1.388547 TGAAACTGCAACACTGGACC 58.611 50.000 0.00 0.00 0.00 4.46
5242 7096 2.936032 AGTGCCCTCAACCCCTCC 60.936 66.667 0.00 0.00 0.00 4.30
5307 7161 2.266554 CAGGTGATCTGCTTTCTCGAC 58.733 52.381 0.00 0.00 36.60 4.20
5321 7175 0.900647 CTCGACAAGGGTGAGGAGGT 60.901 60.000 0.00 0.00 0.00 3.85
5335 7189 1.664965 GAGGTTGTTGACGCGCTCT 60.665 57.895 5.73 0.00 0.00 4.09
5377 7231 2.172293 GCCCATCATCTCAAAGGACTCT 59.828 50.000 0.00 0.00 0.00 3.24
5381 7235 4.502950 CCATCATCTCAAAGGACTCTAGGC 60.503 50.000 0.00 0.00 0.00 3.93
5382 7236 3.034635 TCATCTCAAAGGACTCTAGGCC 58.965 50.000 0.00 0.00 0.00 5.19
5383 7237 1.475403 TCTCAAAGGACTCTAGGCCG 58.525 55.000 0.00 0.00 0.00 6.13
5384 7238 0.461961 CTCAAAGGACTCTAGGCCGG 59.538 60.000 0.00 0.00 0.00 6.13
5430 7284 3.077556 GGGAAGGAGAGGCAGCGA 61.078 66.667 0.00 0.00 0.00 4.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 1.589414 AGCTGGGTTTAGAGCCTGAT 58.411 50.000 11.87 3.10 42.91 2.90
135 142 6.603997 ACACAAACCCTAAACAAACTCACATA 59.396 34.615 0.00 0.00 0.00 2.29
136 143 5.420739 ACACAAACCCTAAACAAACTCACAT 59.579 36.000 0.00 0.00 0.00 3.21
153 160 5.747197 TCGTCTTTCTGAGTAGAACACAAAC 59.253 40.000 0.00 0.00 42.41 2.93
259 266 3.406361 GAGACGCACCTGCACACG 61.406 66.667 0.00 0.00 42.21 4.49
340 347 1.402456 GGTAGACACACGCACGAAGAT 60.402 52.381 0.00 0.00 0.00 2.40
360 367 8.798748 AAGTATAGATCGAAAGTATTCAACCG 57.201 34.615 0.00 0.00 35.15 4.44
413 420 0.630673 TGCTAAGGCCCCACATCATT 59.369 50.000 0.00 0.00 37.74 2.57
433 440 3.324846 AGTGGACAGTCAGCAAGTTATCA 59.675 43.478 2.17 0.00 0.00 2.15
497 504 6.862090 CCACCTAATAACGACTATAAGCACTC 59.138 42.308 0.00 0.00 0.00 3.51
638 1599 9.838339 ACATAGGATAAGTATTTGAGACAAAGG 57.162 33.333 0.00 0.00 0.00 3.11
704 1668 6.537301 TCCATCCGTCTCAAAATTACACATAC 59.463 38.462 0.00 0.00 0.00 2.39
706 1670 5.354234 GTCCATCCGTCTCAAAATTACACAT 59.646 40.000 0.00 0.00 0.00 3.21
730 1708 1.123928 AAAGGCATACTCCTCCTCCG 58.876 55.000 0.00 0.00 34.82 4.63
769 1748 6.750963 AGTAGCAGCGTAGTAGTATTGTTTTC 59.249 38.462 0.00 0.00 0.00 2.29
786 1768 0.960861 GGGTTTGGTGGAGTAGCAGC 60.961 60.000 0.00 0.00 38.18 5.25
849 1845 1.828224 GGGAATGGATTGCGGGGAC 60.828 63.158 0.00 0.00 0.00 4.46
855 1851 1.450531 CCGAGCTGGGAATGGATTGC 61.451 60.000 9.58 0.00 0.00 3.56
1161 2184 1.616628 GGCCTGGGAAAGAGAGGGA 60.617 63.158 0.00 0.00 0.00 4.20
1257 2292 5.239525 GTGCTCACTAAGGTTGAAACATTCT 59.760 40.000 0.00 0.00 34.45 2.40
1260 2295 3.821033 GGTGCTCACTAAGGTTGAAACAT 59.179 43.478 0.00 0.00 0.00 2.71
1326 2363 2.913617 CCTGGTAACTTCCTTCCTTCCT 59.086 50.000 0.00 0.00 37.61 3.36
1327 2364 2.618302 GCCTGGTAACTTCCTTCCTTCC 60.618 54.545 0.00 0.00 37.61 3.46
1328 2365 2.306219 AGCCTGGTAACTTCCTTCCTTC 59.694 50.000 0.00 0.00 37.61 3.46
1329 2366 2.349445 AGCCTGGTAACTTCCTTCCTT 58.651 47.619 0.00 0.00 37.61 3.36
1361 2398 2.738135 GGACCAAACACCGACAAAATG 58.262 47.619 0.00 0.00 0.00 2.32
1370 2407 2.617274 GCTGCTCGGACCAAACACC 61.617 63.158 0.00 0.00 0.00 4.16
1371 2408 1.598130 AGCTGCTCGGACCAAACAC 60.598 57.895 0.00 0.00 0.00 3.32
1372 2409 1.597854 CAGCTGCTCGGACCAAACA 60.598 57.895 0.00 0.00 0.00 2.83
1399 2449 2.742372 GGCCTGTAGCACCACACG 60.742 66.667 0.00 0.00 46.50 4.49
1404 2454 0.967380 AAAGCATGGCCTGTAGCACC 60.967 55.000 3.32 0.00 46.50 5.01
1413 2463 2.825532 TCCTAACAAGAAAAGCATGGCC 59.174 45.455 0.00 0.00 0.00 5.36
1634 2689 1.799994 AGCATTTCCATTGCGCAAAAC 59.200 42.857 28.81 10.07 44.82 2.43
1640 2695 8.746922 AATTAATATACAGCATTTCCATTGCG 57.253 30.769 0.00 0.00 44.82 4.85
1670 2725 7.998580 ACGGTCTACCTTGAAAAATACAAAAA 58.001 30.769 0.00 0.00 0.00 1.94
1696 2751 0.179174 GCCGGTCAAAGTAAATGCCG 60.179 55.000 1.90 0.00 37.28 5.69
1807 2863 1.076332 CCATTTCTGGTCGGTCGAAC 58.924 55.000 0.95 0.95 37.79 3.95
1808 2864 0.970640 TCCATTTCTGGTCGGTCGAA 59.029 50.000 0.00 0.00 43.61 3.71
1809 2865 1.134818 CATCCATTTCTGGTCGGTCGA 60.135 52.381 0.00 0.00 43.61 4.20
1846 2902 4.137116 ACAAGAAGCATGCTATTCGGTA 57.863 40.909 23.00 0.00 0.00 4.02
1847 2903 2.991250 ACAAGAAGCATGCTATTCGGT 58.009 42.857 23.00 15.78 0.00 4.69
1860 2916 7.540400 TGTGATGTTGTGTTTTGTTACAAGAAG 59.460 33.333 0.00 0.00 37.46 2.85
1881 2937 0.944311 GACGTCGCTGTGGTTGTGAT 60.944 55.000 0.00 0.00 0.00 3.06
1882 2938 1.590525 GACGTCGCTGTGGTTGTGA 60.591 57.895 0.00 0.00 0.00 3.58
1883 2939 1.221466 ATGACGTCGCTGTGGTTGTG 61.221 55.000 11.62 0.00 0.00 3.33
1884 2940 1.069090 ATGACGTCGCTGTGGTTGT 59.931 52.632 11.62 0.00 0.00 3.32
1885 2941 1.492873 CATGACGTCGCTGTGGTTG 59.507 57.895 11.62 0.00 0.00 3.77
1886 2942 1.667830 CCATGACGTCGCTGTGGTT 60.668 57.895 11.62 0.00 0.00 3.67
1887 2943 2.048222 CCATGACGTCGCTGTGGT 60.048 61.111 11.62 0.00 0.00 4.16
1888 2944 1.227999 AAACCATGACGTCGCTGTGG 61.228 55.000 20.59 20.59 36.06 4.17
1889 2945 0.586319 AAAACCATGACGTCGCTGTG 59.414 50.000 11.62 7.04 0.00 3.66
1890 2946 0.586319 CAAAACCATGACGTCGCTGT 59.414 50.000 11.62 4.44 0.00 4.40
1891 2947 0.865111 TCAAAACCATGACGTCGCTG 59.135 50.000 11.62 10.79 0.00 5.18
1892 2948 1.148310 CTCAAAACCATGACGTCGCT 58.852 50.000 11.62 0.00 0.00 4.93
1893 2949 0.865769 ACTCAAAACCATGACGTCGC 59.134 50.000 11.62 0.00 0.00 5.19
1894 2950 1.864711 ACACTCAAAACCATGACGTCG 59.135 47.619 11.62 0.00 0.00 5.12
1895 2951 3.963383 AACACTCAAAACCATGACGTC 57.037 42.857 9.11 9.11 0.00 4.34
1896 2952 4.035909 GGTTAACACTCAAAACCATGACGT 59.964 41.667 8.10 0.00 41.89 4.34
1897 2953 4.533222 GGTTAACACTCAAAACCATGACG 58.467 43.478 8.10 0.00 41.89 4.35
2063 3119 5.334105 CGGATGAATTTCGAAGAGTTGTTGT 60.334 40.000 0.00 0.00 38.43 3.32
2064 3120 5.082059 CGGATGAATTTCGAAGAGTTGTTG 58.918 41.667 0.00 0.00 38.43 3.33
2065 3121 4.154195 CCGGATGAATTTCGAAGAGTTGTT 59.846 41.667 0.00 0.00 38.43 2.83
2142 3200 1.268032 GCTATTTCGATGGGCACAACG 60.268 52.381 13.04 13.04 43.28 4.10
2158 3216 2.894126 CCAGGAATCTAGACCGTGCTAT 59.106 50.000 0.00 0.00 0.00 2.97
2160 3218 1.115467 CCAGGAATCTAGACCGTGCT 58.885 55.000 0.00 0.00 0.00 4.40
2403 3461 2.017113 GCCACCCCCATAGTTTTCTCG 61.017 57.143 0.00 0.00 0.00 4.04
2454 3512 2.838637 TGGGAAACTTTTGGGTCAGT 57.161 45.000 0.00 0.00 0.00 3.41
2503 3564 1.302383 TGGGCGCGACCAAATACAAG 61.302 55.000 36.27 0.00 42.05 3.16
2761 3827 2.880443 ACACATGCACAAGGAAGGAAT 58.120 42.857 0.00 0.00 0.00 3.01
2772 3838 2.159254 AGTGAACAACCAACACATGCAC 60.159 45.455 0.00 0.00 37.05 4.57
2826 4309 5.863397 CAGACTCTGCAAGTTCAAAACAAAA 59.137 36.000 0.00 0.00 38.74 2.44
2827 4310 5.048083 ACAGACTCTGCAAGTTCAAAACAAA 60.048 36.000 5.92 0.00 38.74 2.83
2853 4336 8.291032 CGAGAGACGATGGTTTATAGTAAGAAT 58.709 37.037 0.00 0.00 45.77 2.40
3075 4611 3.366781 GCAAGGAAAGGACTTTGCAGATC 60.367 47.826 16.74 0.00 46.81 2.75
3137 4673 9.676861 TCATAATTCATCCTATATTGAAGGCAG 57.323 33.333 0.00 0.00 35.47 4.85
3165 4701 2.802816 AGCAAACTTCTGAAGCTACGTG 59.197 45.455 17.00 9.07 33.06 4.49
3329 4866 5.176223 GTCAATCTTTTGAACCTGCACATTG 59.824 40.000 0.00 0.00 43.29 2.82
3362 4899 5.877012 TCTCTTGATGAAATGGCTACTTCAC 59.123 40.000 0.00 0.00 34.52 3.18
3369 4906 7.707624 TTTGTAATCTCTTGATGAAATGGCT 57.292 32.000 0.00 0.00 32.44 4.75
3402 4939 1.014564 GCCTGTACTTGTGTCGAGGC 61.015 60.000 0.00 0.00 40.92 4.70
3548 5085 3.181456 CCAATGGAGAAGTCTCATCCTCC 60.181 52.174 10.39 0.00 44.60 4.30
3618 5155 5.891451 TGTCATTAGTCAGAACAGGTATCG 58.109 41.667 0.00 0.00 0.00 2.92
3842 5384 3.005684 TGGTTTTGCTGGATGTTGTCATC 59.994 43.478 0.22 0.22 46.82 2.92
3941 5483 1.490574 AGATGCGGGGATAGATAGGC 58.509 55.000 0.00 0.00 0.00 3.93
3952 5494 1.271001 TGCATGGAAGATAGATGCGGG 60.271 52.381 0.00 0.00 44.52 6.13
4043 5587 6.732862 AGGGAGTACTATATTTGGCATGAGAT 59.267 38.462 0.00 0.00 0.00 2.75
4046 5590 6.014242 CAGAGGGAGTACTATATTTGGCATGA 60.014 42.308 0.00 0.00 0.00 3.07
4084 5628 5.948162 AGATACATCCATTTCAGCAACAAGT 59.052 36.000 0.00 0.00 0.00 3.16
4085 5629 6.446781 AGATACATCCATTTCAGCAACAAG 57.553 37.500 0.00 0.00 0.00 3.16
4086 5630 7.337938 TCTAGATACATCCATTTCAGCAACAA 58.662 34.615 0.00 0.00 0.00 2.83
4107 5651 8.384607 TGTATCTAGCACTGAACTACATCTAG 57.615 38.462 0.00 0.00 0.00 2.43
4112 5656 5.008712 CGGATGTATCTAGCACTGAACTACA 59.991 44.000 0.00 0.00 0.00 2.74
4116 5660 4.308899 ACGGATGTATCTAGCACTGAAC 57.691 45.455 0.00 0.00 0.00 3.18
4119 5663 4.682787 TCAAACGGATGTATCTAGCACTG 58.317 43.478 0.00 0.00 0.00 3.66
4135 5679 7.461546 CGATCCATATTACTTATCGCTCAAACG 60.462 40.741 0.00 0.00 33.84 3.60
4141 5685 5.067936 CCTCCGATCCATATTACTTATCGCT 59.932 44.000 0.00 0.00 38.43 4.93
4181 5725 7.234166 ACCTTTTCTTTCCTGAACATGATGAAT 59.766 33.333 0.00 0.00 0.00 2.57
4189 5733 5.048846 AGCTACCTTTTCTTTCCTGAACA 57.951 39.130 0.00 0.00 0.00 3.18
4194 5738 3.072622 ACGGAAGCTACCTTTTCTTTCCT 59.927 43.478 0.00 0.00 0.00 3.36
4202 5746 1.003118 TGCATGACGGAAGCTACCTTT 59.997 47.619 0.00 0.00 0.00 3.11
4207 5751 3.819564 ATTACTGCATGACGGAAGCTA 57.180 42.857 0.00 0.00 0.00 3.32
4209 5753 3.871594 ACTAATTACTGCATGACGGAAGC 59.128 43.478 0.00 0.00 0.00 3.86
4214 5758 4.598406 TGCAACTAATTACTGCATGACG 57.402 40.909 11.68 0.00 41.01 4.35
4215 5759 5.942872 ACTTGCAACTAATTACTGCATGAC 58.057 37.500 23.84 0.00 44.99 3.06
4256 5800 4.215185 TGTTCAGCTGTCGAAATAATGCAA 59.785 37.500 14.67 0.00 0.00 4.08
4294 5854 8.437742 CAGTGCACCTGATTTGAAAATTAAATC 58.562 33.333 14.63 5.55 44.49 2.17
4295 5855 7.933033 ACAGTGCACCTGATTTGAAAATTAAAT 59.067 29.630 14.63 0.00 44.49 1.40
4302 5862 6.183360 ACAATAACAGTGCACCTGATTTGAAA 60.183 34.615 14.63 0.00 44.49 2.69
4401 5961 3.322254 ACTTGGATGTCGCCCTTAGATAG 59.678 47.826 0.00 0.00 0.00 2.08
4455 6015 4.154918 GCGACAAAATTCCTCAGTCAGATT 59.845 41.667 0.00 0.00 0.00 2.40
4467 6027 7.061752 ACTATGTAGAACTGCGACAAAATTC 57.938 36.000 0.00 0.00 35.71 2.17
4468 6028 7.435068 AACTATGTAGAACTGCGACAAAATT 57.565 32.000 0.00 0.00 35.71 1.82
4470 6030 7.117236 CCTTAACTATGTAGAACTGCGACAAAA 59.883 37.037 0.00 0.00 35.71 2.44
4471 6031 6.588756 CCTTAACTATGTAGAACTGCGACAAA 59.411 38.462 0.00 0.00 35.71 2.83
4472 6032 6.071784 TCCTTAACTATGTAGAACTGCGACAA 60.072 38.462 0.00 0.00 35.71 3.18
4473 6033 5.416639 TCCTTAACTATGTAGAACTGCGACA 59.583 40.000 0.00 0.00 36.54 4.35
4474 6034 5.888105 TCCTTAACTATGTAGAACTGCGAC 58.112 41.667 0.00 0.00 0.00 5.19
4475 6035 6.519679 TTCCTTAACTATGTAGAACTGCGA 57.480 37.500 0.00 0.00 0.00 5.10
4476 6036 7.772332 AATTCCTTAACTATGTAGAACTGCG 57.228 36.000 0.00 0.00 0.00 5.18
4477 6037 9.774742 CAAAATTCCTTAACTATGTAGAACTGC 57.225 33.333 0.00 0.00 0.00 4.40
4480 6040 9.968743 CGACAAAATTCCTTAACTATGTAGAAC 57.031 33.333 0.00 0.00 0.00 3.01
4481 6041 8.662141 GCGACAAAATTCCTTAACTATGTAGAA 58.338 33.333 0.00 0.00 0.00 2.10
4482 6042 7.820386 TGCGACAAAATTCCTTAACTATGTAGA 59.180 33.333 0.00 0.00 0.00 2.59
4483 6043 7.970384 TGCGACAAAATTCCTTAACTATGTAG 58.030 34.615 0.00 0.00 0.00 2.74
4660 6227 4.884744 AGGCACAACAGTTAACAACATGTA 59.115 37.500 8.61 0.00 0.00 2.29
4662 6229 4.305989 AGGCACAACAGTTAACAACATG 57.694 40.909 8.61 4.00 0.00 3.21
4663 6230 5.592688 AGTAAGGCACAACAGTTAACAACAT 59.407 36.000 8.61 0.00 0.00 2.71
4797 6411 7.420002 TGAATATGCAAAATTCCTCTCGATTG 58.580 34.615 17.72 0.00 33.28 2.67
4969 6593 6.220201 TGGCTTCAAGTTAATTTGGTAAAGC 58.780 36.000 19.10 19.10 0.00 3.51
5080 6704 4.083164 TGAGTATGCTGCACTTTGATTGTG 60.083 41.667 3.57 0.00 38.36 3.33
5153 7007 2.688446 AGTTGCATGAGATGGCTTCATG 59.312 45.455 17.17 17.17 42.79 3.07
5307 7161 1.142870 TCAACAACCTCCTCACCCTTG 59.857 52.381 0.00 0.00 0.00 3.61
5346 7200 1.768275 AGATGATGGGCATGGACGTTA 59.232 47.619 0.00 0.00 37.34 3.18
5381 7235 4.778143 CGGTGGAAGAAGGCCCGG 62.778 72.222 0.00 0.00 35.11 5.73


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

AutoCloner maintained by Alex Coulton.