Multiple sequence alignment - TraesCS7A01G404700

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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 TraesCS7A01G404700 chr7A 100.000 3465 0 0 1 3465 586694688 586691224 0.000000e+00 6399.0
1 TraesCS7A01G404700 chr7A 96.158 1718 56 1 758 2465 588740674 588738957 0.000000e+00 2798.0
2 TraesCS7A01G404700 chr7A 96.448 1492 29 5 980 2465 587518477 587519950 0.000000e+00 2440.0
3 TraesCS7A01G404700 chr7A 77.933 571 87 23 4 562 588748602 588748059 1.550000e-83 320.0
4 TraesCS7A01G404700 chr7A 90.977 133 10 1 1 131 586933927 586933795 9.880000e-41 178.0
5 TraesCS7A01G404700 chr7B 92.334 2009 109 22 737 2720 544880888 544882876 0.000000e+00 2815.0
6 TraesCS7A01G404700 chr7B 92.413 1898 101 29 610 2470 544981828 544983719 0.000000e+00 2667.0
7 TraesCS7A01G404700 chr7B 93.508 1756 89 19 738 2470 545975538 545973785 0.000000e+00 2588.0
8 TraesCS7A01G404700 chr7B 88.533 750 59 12 1 750 544880150 544880872 0.000000e+00 883.0
9 TraesCS7A01G404700 chr7B 89.846 325 31 2 2810 3134 544885178 544885500 1.920000e-112 416.0
10 TraesCS7A01G404700 chr7B 80.224 536 84 18 51 573 544869997 544870523 1.950000e-102 383.0
11 TraesCS7A01G404700 chr7B 83.659 410 56 10 2893 3300 545968721 545968321 3.260000e-100 375.0
12 TraesCS7A01G404700 chr7B 89.785 186 16 3 3128 3311 544885661 544885845 5.780000e-58 235.0
13 TraesCS7A01G404700 chr7B 93.478 46 3 0 2524 2569 545973774 545973729 6.210000e-08 69.4
14 TraesCS7A01G404700 chr7D 94.137 1859 73 17 620 2465 514091991 514093826 0.000000e+00 2796.0
15 TraesCS7A01G404700 chr7D 92.921 1907 83 23 737 2621 513311699 513313575 0.000000e+00 2726.0
16 TraesCS7A01G404700 chr7D 93.019 1189 52 16 479 1661 515238497 515237334 0.000000e+00 1707.0
17 TraesCS7A01G404700 chr7D 92.935 1189 53 16 479 1661 515222291 515221128 0.000000e+00 1701.0
18 TraesCS7A01G404700 chr7D 95.926 810 29 1 1660 2465 515237029 515236220 0.000000e+00 1310.0
19 TraesCS7A01G404700 chr7D 95.802 810 30 1 1660 2465 515220823 515220014 0.000000e+00 1304.0
20 TraesCS7A01G404700 chr7D 90.704 753 44 10 1 750 513310954 513311683 0.000000e+00 979.0
21 TraesCS7A01G404700 chr7D 93.651 189 10 2 2630 2817 513313651 513313838 7.320000e-72 281.0
22 TraesCS7A01G404700 chr7D 100.000 28 0 0 535 562 510303352 510303325 6.000000e-03 52.8


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 TraesCS7A01G404700 chr7A 586691224 586694688 3464 True 6399.000000 6399 100.000000 1 3465 1 chr7A.!!$R1 3464
1 TraesCS7A01G404700 chr7A 588738957 588740674 1717 True 2798.000000 2798 96.158000 758 2465 1 chr7A.!!$R3 1707
2 TraesCS7A01G404700 chr7A 587518477 587519950 1473 False 2440.000000 2440 96.448000 980 2465 1 chr7A.!!$F1 1485
3 TraesCS7A01G404700 chr7A 588748059 588748602 543 True 320.000000 320 77.933000 4 562 1 chr7A.!!$R4 558
4 TraesCS7A01G404700 chr7B 544981828 544983719 1891 False 2667.000000 2667 92.413000 610 2470 1 chr7B.!!$F2 1860
5 TraesCS7A01G404700 chr7B 545973729 545975538 1809 True 1328.700000 2588 93.493000 738 2569 2 chr7B.!!$R2 1831
6 TraesCS7A01G404700 chr7B 544880150 544885845 5695 False 1087.250000 2815 90.124500 1 3311 4 chr7B.!!$F3 3310
7 TraesCS7A01G404700 chr7B 544869997 544870523 526 False 383.000000 383 80.224000 51 573 1 chr7B.!!$F1 522
8 TraesCS7A01G404700 chr7D 514091991 514093826 1835 False 2796.000000 2796 94.137000 620 2465 1 chr7D.!!$F1 1845
9 TraesCS7A01G404700 chr7D 515236220 515238497 2277 True 1508.500000 1707 94.472500 479 2465 2 chr7D.!!$R3 1986
10 TraesCS7A01G404700 chr7D 515220014 515222291 2277 True 1502.500000 1701 94.368500 479 2465 2 chr7D.!!$R2 1986
11 TraesCS7A01G404700 chr7D 513310954 513313838 2884 False 1328.666667 2726 92.425333 1 2817 3 chr7D.!!$F2 2816

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
963 1070 1.229304 TCTGAAGCTCCTGGCCTGA 60.229 57.895 11.88 3.09 43.05 3.86 F
2383 2841 1.471119 AGATCGAGTACTCCGGCAAA 58.529 50.000 17.23 0.00 0.00 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2404 2862 1.668151 GACCTTGACGTGGGAGCAC 60.668 63.158 0.0 0.0 0.00 4.4 R
3432 6341 0.180406 ACAAAGCGGTTCAGACAGGT 59.820 50.000 0.0 0.0 33.09 4.0 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
161 166 9.738832 TCATAAATGCATGAATGACTGTTTATG 57.261 29.630 16.41 14.40 38.59 1.90
392 405 5.760193 TTGATGCACGATTTACATTTTGC 57.240 34.783 0.00 0.00 0.00 3.68
557 594 8.751302 AAAATACGCGATGAACCTTTTTAAAT 57.249 26.923 15.93 0.00 0.00 1.40
690 727 4.448537 TTTTCATTTTCCCATGCCTACG 57.551 40.909 0.00 0.00 0.00 3.51
730 767 3.825908 ATGTTGGGGAGGTGTTGTATT 57.174 42.857 0.00 0.00 0.00 1.89
750 827 1.957177 TCCATGTACGAGATGGAGCTC 59.043 52.381 4.71 4.71 43.71 4.09
852 958 1.481901 TAGCCGGCAACCACAACCTA 61.482 55.000 31.54 4.70 0.00 3.08
876 982 4.665833 AATAGCAAATGAGCATGCATGT 57.334 36.364 26.79 14.24 44.95 3.21
914 1020 7.360607 CGAATAATTAAACCGAACACTTGTCCT 60.361 37.037 0.00 0.00 0.00 3.85
963 1070 1.229304 TCTGAAGCTCCTGGCCTGA 60.229 57.895 11.88 3.09 43.05 3.86
2287 2745 1.686355 TCAAAAACATCACCGGCACT 58.314 45.000 0.00 0.00 0.00 4.40
2383 2841 1.471119 AGATCGAGTACTCCGGCAAA 58.529 50.000 17.23 0.00 0.00 3.68
2404 2862 1.321474 ACAACAAGACCATGGCTGTG 58.679 50.000 13.04 9.64 0.00 3.66
2408 2866 0.892358 CAAGACCATGGCTGTGTGCT 60.892 55.000 13.04 0.00 42.39 4.40
2511 2970 0.886490 CAAGACCGCAAGAGGCACTT 60.886 55.000 0.00 0.00 45.17 3.16
2518 2977 1.879796 CGCAAGAGGCACTTTCCTTCT 60.880 52.381 0.00 0.00 45.17 2.85
2521 2980 4.013050 GCAAGAGGCACTTTCCTTCTATT 58.987 43.478 0.00 0.00 41.55 1.73
2559 3018 6.642683 TTCTTTTCTCGGTATGTCGATTTC 57.357 37.500 0.00 0.00 38.55 2.17
2608 3067 6.503560 TTAGTTTTCTTCCTAGGTTGACCA 57.496 37.500 9.08 0.00 38.89 4.02
2621 3080 7.847848 TCCTAGGTTGACCACTTACCTTTATAT 59.152 37.037 9.08 0.00 42.18 0.86
2622 3081 9.151177 CCTAGGTTGACCACTTACCTTTATATA 57.849 37.037 0.00 0.00 42.18 0.86
2662 3188 0.239082 TATATGTACGTGCCGGCTCG 59.761 55.000 40.17 40.17 38.64 5.03
2697 3223 8.128582 TGATCCATATACTTTTGACGATTTTGC 58.871 33.333 0.00 0.00 0.00 3.68
2702 3228 8.586273 CATATACTTTTGACGATTTTGCCTTTG 58.414 33.333 0.00 0.00 0.00 2.77
2758 4766 5.041287 GGTCAGTACCAACAAAGCTTTTTC 58.959 41.667 9.53 0.00 45.98 2.29
2860 5600 5.066893 TGCAGAAATAGGCATGAATTGAGTC 59.933 40.000 0.00 0.00 34.58 3.36
2863 5603 6.037500 CAGAAATAGGCATGAATTGAGTCGAA 59.962 38.462 0.00 0.00 0.00 3.71
2865 5605 3.340814 AGGCATGAATTGAGTCGAAGT 57.659 42.857 0.00 0.00 0.00 3.01
2871 5611 2.104111 TGAATTGAGTCGAAGTGGTGGT 59.896 45.455 0.00 0.00 0.00 4.16
2885 5625 7.762615 TCGAAGTGGTGGTATCAAAATTAGTAG 59.237 37.037 0.00 0.00 0.00 2.57
2889 5629 7.120726 AGTGGTGGTATCAAAATTAGTAGTTGC 59.879 37.037 0.00 0.00 0.00 4.17
2891 5631 8.322828 TGGTGGTATCAAAATTAGTAGTTGCTA 58.677 33.333 0.00 0.00 0.00 3.49
2912 5652 9.534565 TTGCTACTTATGAGATAATTCACAGAC 57.465 33.333 0.00 0.00 0.00 3.51
2918 5658 9.421806 CTTATGAGATAATTCACAGACTGGATC 57.578 37.037 7.51 0.43 0.00 3.36
2923 5663 7.271511 AGATAATTCACAGACTGGATCAAGAC 58.728 38.462 3.42 0.00 0.00 3.01
2937 5677 7.667219 ACTGGATCAAGACATAATGAGTTTGTT 59.333 33.333 3.42 0.00 0.00 2.83
2947 5687 6.549364 ACATAATGAGTTTGTTCCCAAGACAA 59.451 34.615 0.00 0.00 35.36 3.18
2949 5689 5.930837 ATGAGTTTGTTCCCAAGACAAAA 57.069 34.783 4.22 0.00 45.43 2.44
2957 5697 4.582656 TGTTCCCAAGACAAAATCGTCAAT 59.417 37.500 0.00 0.00 38.43 2.57
2973 5713 4.764823 TCGTCAATGCCTAGGACAAAATTT 59.235 37.500 14.75 0.00 0.00 1.82
2985 5725 9.921637 CCTAGGACAAAATTTAGTGCAAAATTA 57.078 29.630 1.05 0.00 37.93 1.40
3018 5758 1.712977 CGCATGCAAGGCTTCTCCTC 61.713 60.000 19.57 0.00 46.94 3.71
3024 5764 2.624838 TGCAAGGCTTCTCCTCAAAAAG 59.375 45.455 0.00 0.00 46.94 2.27
3027 5767 2.868899 AGGCTTCTCCTCAAAAAGGTG 58.131 47.619 0.00 0.00 43.20 4.00
3031 5771 2.951229 TCTCCTCAAAAAGGTGGACC 57.049 50.000 0.00 0.00 46.32 4.46
3075 5815 8.988934 TGAGAGTAGAACATGTTAATGTGAAAC 58.011 33.333 11.95 1.65 46.58 2.78
3091 5831 4.024133 TGTGAAACAGAACAATGATGTCGG 60.024 41.667 0.00 0.00 45.67 4.79
3096 5836 5.964958 ACAGAACAATGATGTCGGAAAAT 57.035 34.783 0.00 0.00 39.40 1.82
3109 5849 3.813166 GTCGGAAAATTCTTCCACACTCA 59.187 43.478 15.30 0.00 38.49 3.41
3126 5866 6.294787 CCACACTCATAAGTAGTTGAGACAGT 60.295 42.308 6.91 0.72 41.53 3.55
3134 5874 8.683615 CATAAGTAGTTGAGACAGTGTGGTATA 58.316 37.037 0.00 0.00 0.00 1.47
3135 5875 7.719871 AAGTAGTTGAGACAGTGTGGTATAT 57.280 36.000 0.00 0.00 0.00 0.86
3136 5876 7.719871 AGTAGTTGAGACAGTGTGGTATATT 57.280 36.000 0.00 0.00 0.00 1.28
3137 5877 8.135382 AGTAGTTGAGACAGTGTGGTATATTT 57.865 34.615 0.00 0.00 0.00 1.40
3138 5878 8.594550 AGTAGTTGAGACAGTGTGGTATATTTT 58.405 33.333 0.00 0.00 0.00 1.82
3139 5879 9.216117 GTAGTTGAGACAGTGTGGTATATTTTT 57.784 33.333 0.00 0.00 0.00 1.94
3140 5880 8.324163 AGTTGAGACAGTGTGGTATATTTTTC 57.676 34.615 0.00 0.00 0.00 2.29
3141 5881 7.390718 AGTTGAGACAGTGTGGTATATTTTTCC 59.609 37.037 0.00 0.00 0.00 3.13
3148 6055 8.646900 ACAGTGTGGTATATTTTTCCATTGTTT 58.353 29.630 0.00 0.00 33.68 2.83
3149 6056 8.924691 CAGTGTGGTATATTTTTCCATTGTTTG 58.075 33.333 0.00 0.00 33.68 2.93
3177 6084 0.752743 TGGGTGGATATGCTTGCAGC 60.753 55.000 0.87 1.70 42.82 5.25
3178 6085 0.466922 GGGTGGATATGCTTGCAGCT 60.467 55.000 0.87 0.00 42.97 4.24
3199 6106 7.524698 GCAGCTATTACTAAGTGAGCTAAGGAT 60.525 40.741 0.00 0.00 41.48 3.24
3206 6113 2.716217 AGTGAGCTAAGGATTGTTGGC 58.284 47.619 0.00 0.00 34.28 4.52
3209 6116 2.019984 GAGCTAAGGATTGTTGGCCAG 58.980 52.381 5.11 0.00 34.59 4.85
3210 6117 1.635487 AGCTAAGGATTGTTGGCCAGA 59.365 47.619 5.11 0.00 34.59 3.86
3211 6118 2.243221 AGCTAAGGATTGTTGGCCAGAT 59.757 45.455 5.11 1.19 34.59 2.90
3213 6120 3.067320 GCTAAGGATTGTTGGCCAGATTC 59.933 47.826 5.11 0.37 0.00 2.52
3214 6121 2.905415 AGGATTGTTGGCCAGATTCA 57.095 45.000 5.11 1.47 0.00 2.57
3215 6122 3.393426 AGGATTGTTGGCCAGATTCAT 57.607 42.857 5.11 0.00 0.00 2.57
3244 6153 2.236893 ACCCCATTTGATTTGTGATGGC 59.763 45.455 0.00 0.00 38.14 4.40
3285 6194 6.570672 ATGCAGATGATATTGTGGTCATTC 57.429 37.500 0.00 0.00 35.33 2.67
3298 6207 6.827586 TGTGGTCATTCTGGGTTAAAATAC 57.172 37.500 0.00 0.00 0.00 1.89
3319 6228 8.425577 AATACAAATCAATAGTTGAGACTCGG 57.574 34.615 0.00 0.00 43.98 4.63
3320 6229 5.794894 ACAAATCAATAGTTGAGACTCGGT 58.205 37.500 0.00 0.00 43.98 4.69
3321 6230 6.931838 ACAAATCAATAGTTGAGACTCGGTA 58.068 36.000 0.00 0.00 43.98 4.02
3322 6231 7.383687 ACAAATCAATAGTTGAGACTCGGTAA 58.616 34.615 0.00 0.00 43.98 2.85
3323 6232 8.041323 ACAAATCAATAGTTGAGACTCGGTAAT 58.959 33.333 0.00 0.00 43.98 1.89
3324 6233 8.883731 CAAATCAATAGTTGAGACTCGGTAATT 58.116 33.333 0.00 0.00 43.98 1.40
3325 6234 9.449719 AAATCAATAGTTGAGACTCGGTAATTT 57.550 29.630 0.00 0.00 43.98 1.82
3326 6235 9.449719 AATCAATAGTTGAGACTCGGTAATTTT 57.550 29.630 0.00 0.00 43.98 1.82
3327 6236 8.842358 TCAATAGTTGAGACTCGGTAATTTTT 57.158 30.769 0.00 0.00 37.33 1.94
3328 6237 9.932207 TCAATAGTTGAGACTCGGTAATTTTTA 57.068 29.630 0.00 0.00 37.33 1.52
3330 6239 6.723131 AGTTGAGACTCGGTAATTTTTAGC 57.277 37.500 0.00 0.00 0.00 3.09
3331 6240 6.228258 AGTTGAGACTCGGTAATTTTTAGCA 58.772 36.000 0.00 0.00 0.00 3.49
3332 6241 6.708949 AGTTGAGACTCGGTAATTTTTAGCAA 59.291 34.615 0.00 0.00 0.00 3.91
3333 6242 7.390718 AGTTGAGACTCGGTAATTTTTAGCAAT 59.609 33.333 0.00 0.00 0.00 3.56
3334 6243 7.681939 TGAGACTCGGTAATTTTTAGCAATT 57.318 32.000 0.00 0.00 0.00 2.32
3335 6244 8.780846 TGAGACTCGGTAATTTTTAGCAATTA 57.219 30.769 0.00 0.00 0.00 1.40
3336 6245 9.391006 TGAGACTCGGTAATTTTTAGCAATTAT 57.609 29.630 0.00 0.00 32.49 1.28
3339 6248 9.783256 GACTCGGTAATTTTTAGCAATTATTGT 57.217 29.630 6.81 0.00 32.49 2.71
3413 6322 8.922058 AATTAGCAAGATTTGTTAATGAGCAG 57.078 30.769 10.34 0.00 43.36 4.24
3414 6323 5.972107 AGCAAGATTTGTTAATGAGCAGT 57.028 34.783 0.00 0.00 0.00 4.40
3415 6324 6.336842 AGCAAGATTTGTTAATGAGCAGTT 57.663 33.333 0.00 0.00 0.00 3.16
3416 6325 6.154445 AGCAAGATTTGTTAATGAGCAGTTG 58.846 36.000 0.00 0.00 0.00 3.16
3417 6326 6.016024 AGCAAGATTTGTTAATGAGCAGTTGA 60.016 34.615 0.00 0.00 0.00 3.18
3418 6327 6.642131 GCAAGATTTGTTAATGAGCAGTTGAA 59.358 34.615 0.00 0.00 0.00 2.69
3419 6328 7.148853 GCAAGATTTGTTAATGAGCAGTTGAAG 60.149 37.037 0.00 0.00 0.00 3.02
3420 6329 7.750229 AGATTTGTTAATGAGCAGTTGAAGA 57.250 32.000 0.00 0.00 0.00 2.87
3421 6330 8.169977 AGATTTGTTAATGAGCAGTTGAAGAA 57.830 30.769 0.00 0.00 0.00 2.52
3422 6331 8.800332 AGATTTGTTAATGAGCAGTTGAAGAAT 58.200 29.630 0.00 0.00 0.00 2.40
3423 6332 9.415544 GATTTGTTAATGAGCAGTTGAAGAATT 57.584 29.630 0.00 0.00 0.00 2.17
3424 6333 9.768662 ATTTGTTAATGAGCAGTTGAAGAATTT 57.231 25.926 0.00 0.00 0.00 1.82
3429 6338 9.859427 TTAATGAGCAGTTGAAGAATTTAATGG 57.141 29.630 0.00 0.00 0.00 3.16
3430 6339 5.713025 TGAGCAGTTGAAGAATTTAATGGC 58.287 37.500 0.00 0.00 0.00 4.40
3431 6340 5.243507 TGAGCAGTTGAAGAATTTAATGGCA 59.756 36.000 0.00 0.00 31.32 4.92
3432 6341 6.100404 AGCAGTTGAAGAATTTAATGGCAA 57.900 33.333 0.00 0.00 31.32 4.52
3433 6342 5.928264 AGCAGTTGAAGAATTTAATGGCAAC 59.072 36.000 0.00 0.00 31.32 4.17
3434 6343 5.120674 GCAGTTGAAGAATTTAATGGCAACC 59.879 40.000 0.00 0.00 35.90 3.77
3435 6344 6.458210 CAGTTGAAGAATTTAATGGCAACCT 58.542 36.000 0.00 0.00 35.90 3.50
3436 6345 6.366877 CAGTTGAAGAATTTAATGGCAACCTG 59.633 38.462 0.00 0.00 35.90 4.00
3437 6346 6.041979 AGTTGAAGAATTTAATGGCAACCTGT 59.958 34.615 0.00 0.00 35.90 4.00
3438 6347 6.024552 TGAAGAATTTAATGGCAACCTGTC 57.975 37.500 0.00 0.00 0.00 3.51
3439 6348 5.774690 TGAAGAATTTAATGGCAACCTGTCT 59.225 36.000 0.00 0.00 0.00 3.41
3440 6349 5.649782 AGAATTTAATGGCAACCTGTCTG 57.350 39.130 0.00 0.00 0.00 3.51
3441 6350 5.324409 AGAATTTAATGGCAACCTGTCTGA 58.676 37.500 0.00 0.00 0.00 3.27
3442 6351 5.774690 AGAATTTAATGGCAACCTGTCTGAA 59.225 36.000 0.00 0.00 0.00 3.02
3443 6352 4.846779 TTTAATGGCAACCTGTCTGAAC 57.153 40.909 0.00 0.00 0.00 3.18
3444 6353 1.620822 AATGGCAACCTGTCTGAACC 58.379 50.000 0.00 0.00 0.00 3.62
3445 6354 0.606401 ATGGCAACCTGTCTGAACCG 60.606 55.000 0.00 0.00 0.00 4.44
3446 6355 2.617274 GGCAACCTGTCTGAACCGC 61.617 63.158 0.00 0.00 0.00 5.68
3447 6356 1.598130 GCAACCTGTCTGAACCGCT 60.598 57.895 0.00 0.00 0.00 5.52
3448 6357 1.166531 GCAACCTGTCTGAACCGCTT 61.167 55.000 0.00 0.00 0.00 4.68
3449 6358 1.308998 CAACCTGTCTGAACCGCTTT 58.691 50.000 0.00 0.00 0.00 3.51
3450 6359 1.002468 CAACCTGTCTGAACCGCTTTG 60.002 52.381 0.00 0.00 0.00 2.77
3451 6360 0.180406 ACCTGTCTGAACCGCTTTGT 59.820 50.000 0.00 0.00 0.00 2.83
3452 6361 1.308998 CCTGTCTGAACCGCTTTGTT 58.691 50.000 0.00 0.00 0.00 2.83
3453 6362 1.264288 CCTGTCTGAACCGCTTTGTTC 59.736 52.381 0.00 0.00 43.90 3.18
3454 6363 2.213499 CTGTCTGAACCGCTTTGTTCT 58.787 47.619 10.63 0.00 43.96 3.01
3455 6364 3.390135 CTGTCTGAACCGCTTTGTTCTA 58.610 45.455 10.63 0.00 43.96 2.10
3456 6365 3.799366 TGTCTGAACCGCTTTGTTCTAA 58.201 40.909 10.63 0.00 43.96 2.10
3457 6366 4.385825 TGTCTGAACCGCTTTGTTCTAAT 58.614 39.130 10.63 0.00 43.96 1.73
3458 6367 5.543714 TGTCTGAACCGCTTTGTTCTAATA 58.456 37.500 10.63 0.00 43.96 0.98
3459 6368 6.170506 TGTCTGAACCGCTTTGTTCTAATAT 58.829 36.000 10.63 0.00 43.96 1.28
3460 6369 6.653320 TGTCTGAACCGCTTTGTTCTAATATT 59.347 34.615 10.63 0.00 43.96 1.28
3461 6370 6.961554 GTCTGAACCGCTTTGTTCTAATATTG 59.038 38.462 0.00 0.00 43.96 1.90
3462 6371 5.636837 TGAACCGCTTTGTTCTAATATTGC 58.363 37.500 0.00 0.00 43.96 3.56
3463 6372 4.632538 ACCGCTTTGTTCTAATATTGCC 57.367 40.909 0.00 0.00 0.00 4.52
3464 6373 4.013728 ACCGCTTTGTTCTAATATTGCCA 58.986 39.130 0.00 0.00 0.00 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
131 135 9.661563 AACAGTCATTCATGCATTTATGAAAAT 57.338 25.926 17.66 8.11 46.63 1.82
149 153 8.846943 TGTTCAACATCTACATAAACAGTCAT 57.153 30.769 0.00 0.00 0.00 3.06
150 154 8.846943 ATGTTCAACATCTACATAAACAGTCA 57.153 30.769 0.00 0.00 32.38 3.41
161 166 9.760660 GTATGTTTCAGAATGTTCAACATCTAC 57.239 33.333 2.74 0.00 37.97 2.59
208 215 4.329256 GCCGGTACTTCAAAGAATACTCAC 59.671 45.833 1.90 0.00 0.00 3.51
217 226 3.915437 AAATGTGCCGGTACTTCAAAG 57.085 42.857 23.67 0.00 0.00 2.77
268 278 6.689669 ACATAACAAAACAAGTTTAGCGTGAC 59.310 34.615 0.00 0.00 31.63 3.67
690 727 6.530019 ACATTTCATCCCAAATAAGGTGTC 57.470 37.500 0.00 0.00 0.00 3.67
730 767 1.957177 GAGCTCCATCTCGTACATGGA 59.043 52.381 11.73 11.73 46.39 3.41
750 827 4.085107 GCTTGTGTGTGAAAATTTAAGGCG 60.085 41.667 0.00 0.00 0.00 5.52
752 829 6.312426 TGTTGCTTGTGTGTGAAAATTTAAGG 59.688 34.615 0.00 0.00 0.00 2.69
756 862 5.064962 CCATGTTGCTTGTGTGTGAAAATTT 59.935 36.000 0.00 0.00 0.00 1.82
852 958 5.878116 ACATGCATGCTCATTTGCTATTTTT 59.122 32.000 26.53 0.00 39.60 1.94
876 982 7.360017 CGGTTTAATTATTCGCTATGCTCATGA 60.360 37.037 0.00 0.00 0.00 3.07
914 1020 3.992943 AAATACACATCGGTTCAGGGA 57.007 42.857 0.00 0.00 0.00 4.20
963 1070 4.471386 TCCTTCTCGATCCTTGATCCTTTT 59.529 41.667 0.00 0.00 35.83 2.27
1128 1254 4.019513 TCCCCACCCGGACCAGAT 62.020 66.667 0.73 0.00 0.00 2.90
1131 1257 3.603080 TACTCCCCACCCGGACCA 61.603 66.667 0.73 0.00 0.00 4.02
1135 1261 3.455469 GTCGTACTCCCCACCCGG 61.455 72.222 0.00 0.00 0.00 5.73
1136 1262 2.012902 GATGTCGTACTCCCCACCCG 62.013 65.000 0.00 0.00 0.00 5.28
1140 1266 0.251877 TGGTGATGTCGTACTCCCCA 60.252 55.000 0.00 0.00 0.00 4.96
1373 1499 3.674906 CGGCCCCGTGAAATTCAA 58.325 55.556 0.00 0.00 34.35 2.69
1993 2451 2.411701 CTGCCAATGCTGATGCCG 59.588 61.111 0.00 0.00 38.61 5.69
2185 2643 3.318275 GGCAGTACTTCTGGTCGATGATA 59.682 47.826 0.00 0.00 43.78 2.15
2383 2841 2.101249 CACAGCCATGGTCTTGTTGTTT 59.899 45.455 14.67 0.00 0.00 2.83
2404 2862 1.668151 GACCTTGACGTGGGAGCAC 60.668 63.158 0.00 0.00 0.00 4.40
2408 2866 2.863346 CGGTGACCTTGACGTGGGA 61.863 63.158 0.00 0.00 0.00 4.37
2470 2928 4.174762 GTTATCTCTTCAACCGTGGAGTC 58.825 47.826 0.00 0.00 31.46 3.36
2511 2970 2.418692 TGTCGCGCAAAATAGAAGGAA 58.581 42.857 8.75 0.00 0.00 3.36
2518 2977 4.614555 AGAAATCATGTCGCGCAAAATA 57.385 36.364 8.75 0.00 0.00 1.40
2521 2980 2.987413 AAGAAATCATGTCGCGCAAA 57.013 40.000 8.75 0.00 0.00 3.68
2559 3018 2.032860 ATCTCCTGGCGTGGATTCGG 62.033 60.000 0.00 0.00 35.30 4.30
2662 3188 4.899352 AGTATATGGATCAAGTGGCTCC 57.101 45.455 0.00 0.00 0.00 4.70
2697 3223 9.493206 CACAAAAATCAAAAGACAAATCAAAGG 57.507 29.630 0.00 0.00 0.00 3.11
2702 3228 6.128729 CGGCACAAAAATCAAAAGACAAATC 58.871 36.000 0.00 0.00 0.00 2.17
2776 4784 6.032956 ACACGTGAAACCAGATACTCAATA 57.967 37.500 25.01 0.00 0.00 1.90
2860 5600 6.737254 ACTAATTTTGATACCACCACTTCG 57.263 37.500 0.00 0.00 0.00 3.79
2863 5603 7.120726 GCAACTACTAATTTTGATACCACCACT 59.879 37.037 0.00 0.00 0.00 4.00
2865 5605 7.172342 AGCAACTACTAATTTTGATACCACCA 58.828 34.615 0.00 0.00 0.00 4.17
2885 5625 9.534565 TCTGTGAATTATCTCATAAGTAGCAAC 57.465 33.333 0.00 0.00 0.00 4.17
2889 5629 9.689976 CCAGTCTGTGAATTATCTCATAAGTAG 57.310 37.037 0.00 0.00 0.00 2.57
2891 5631 8.311395 TCCAGTCTGTGAATTATCTCATAAGT 57.689 34.615 0.00 0.00 0.00 2.24
2908 5648 6.580788 ACTCATTATGTCTTGATCCAGTCTG 58.419 40.000 0.00 0.00 0.00 3.51
2912 5652 7.621428 ACAAACTCATTATGTCTTGATCCAG 57.379 36.000 9.37 0.00 0.00 3.86
2918 5658 6.573664 TGGGAACAAACTCATTATGTCTTG 57.426 37.500 0.00 0.00 37.44 3.02
2937 5677 3.057596 GCATTGACGATTTTGTCTTGGGA 60.058 43.478 0.00 0.00 39.64 4.37
2947 5687 3.627395 TGTCCTAGGCATTGACGATTT 57.373 42.857 2.96 0.00 0.00 2.17
2949 5689 3.627395 TTTGTCCTAGGCATTGACGAT 57.373 42.857 2.96 0.00 0.00 3.73
2957 5697 4.402829 TGCACTAAATTTTGTCCTAGGCA 58.597 39.130 2.96 9.50 0.00 4.75
2973 5713 9.734620 GCATTGTTCATAGATAATTTTGCACTA 57.265 29.630 0.00 0.00 0.00 2.74
2985 5725 2.619646 TGCATGCGCATTGTTCATAGAT 59.380 40.909 22.81 0.00 45.36 1.98
3018 5758 3.230134 TGAATCCAGGTCCACCTTTTTG 58.770 45.455 0.00 0.00 46.09 2.44
3044 5784 9.950496 ACATTAACATGTTCTACTCTCAGAAAT 57.050 29.630 15.85 1.71 41.16 2.17
3052 5792 8.988934 TCTGTTTCACATTAACATGTTCTACTC 58.011 33.333 15.85 0.00 41.16 2.59
3075 5815 6.615088 AGAATTTTCCGACATCATTGTTCTG 58.385 36.000 0.00 0.00 35.79 3.02
3076 5816 6.824305 AGAATTTTCCGACATCATTGTTCT 57.176 33.333 0.00 0.00 35.79 3.01
3088 5828 4.079980 TGAGTGTGGAAGAATTTTCCGA 57.920 40.909 12.04 2.78 41.43 4.55
3089 5829 6.149474 ACTTATGAGTGTGGAAGAATTTTCCG 59.851 38.462 12.04 0.00 36.70 4.30
3091 5831 9.220767 ACTACTTATGAGTGTGGAAGAATTTTC 57.779 33.333 0.00 0.00 36.60 2.29
3096 5836 7.232737 TCTCAACTACTTATGAGTGTGGAAGAA 59.767 37.037 0.00 0.00 42.86 2.52
3109 5849 7.719871 ATACCACACTGTCTCAACTACTTAT 57.280 36.000 0.00 0.00 0.00 1.73
3134 5874 9.054922 CCAGATGTTAACAAACAATGGAAAAAT 57.945 29.630 13.23 0.00 41.97 1.82
3135 5875 7.497249 CCCAGATGTTAACAAACAATGGAAAAA 59.503 33.333 13.23 0.00 41.97 1.94
3136 5876 6.989169 CCCAGATGTTAACAAACAATGGAAAA 59.011 34.615 13.23 0.00 41.97 2.29
3137 5877 6.098982 ACCCAGATGTTAACAAACAATGGAAA 59.901 34.615 13.23 0.00 41.97 3.13
3138 5878 5.600484 ACCCAGATGTTAACAAACAATGGAA 59.400 36.000 13.23 0.00 41.97 3.53
3139 5879 5.010516 CACCCAGATGTTAACAAACAATGGA 59.989 40.000 13.23 0.00 41.97 3.41
3140 5880 5.229423 CACCCAGATGTTAACAAACAATGG 58.771 41.667 13.23 14.71 40.46 3.16
3141 5881 5.010516 TCCACCCAGATGTTAACAAACAATG 59.989 40.000 13.23 7.18 36.12 2.82
3148 6055 4.165950 AGCATATCCACCCAGATGTTAACA 59.834 41.667 11.41 11.41 0.00 2.41
3149 6056 4.718961 AGCATATCCACCCAGATGTTAAC 58.281 43.478 0.00 0.00 0.00 2.01
3178 6085 9.817809 CAACAATCCTTAGCTCACTTAGTAATA 57.182 33.333 0.00 0.00 0.00 0.98
3199 6106 1.203162 ACCCATGAATCTGGCCAACAA 60.203 47.619 7.01 0.00 34.77 2.83
3203 6110 0.928505 ATGACCCATGAATCTGGCCA 59.071 50.000 4.71 4.71 34.77 5.36
3237 6146 2.455674 GGAACCAAAAAGGCCATCAC 57.544 50.000 5.01 0.00 43.14 3.06
3298 6207 7.827819 TTACCGAGTCTCAACTATTGATTTG 57.172 36.000 0.00 0.00 39.30 2.32
3313 6222 9.783256 ACAATAATTGCTAAAAATTACCGAGTC 57.217 29.630 0.00 0.00 35.42 3.36
3387 6296 9.362539 CTGCTCATTAACAAATCTTGCTAATTT 57.637 29.630 0.00 0.00 31.50 1.82
3388 6297 8.526147 ACTGCTCATTAACAAATCTTGCTAATT 58.474 29.630 0.00 0.00 31.50 1.40
3389 6298 8.059798 ACTGCTCATTAACAAATCTTGCTAAT 57.940 30.769 0.00 0.00 33.48 1.73
3390 6299 7.452880 ACTGCTCATTAACAAATCTTGCTAA 57.547 32.000 0.00 0.00 0.00 3.09
3391 6300 7.174772 TCAACTGCTCATTAACAAATCTTGCTA 59.825 33.333 0.00 0.00 0.00 3.49
3392 6301 5.972107 ACTGCTCATTAACAAATCTTGCT 57.028 34.783 0.00 0.00 0.00 3.91
3393 6302 6.151691 TCAACTGCTCATTAACAAATCTTGC 58.848 36.000 0.00 0.00 0.00 4.01
3394 6303 8.077991 TCTTCAACTGCTCATTAACAAATCTTG 58.922 33.333 0.00 0.00 0.00 3.02
3395 6304 8.169977 TCTTCAACTGCTCATTAACAAATCTT 57.830 30.769 0.00 0.00 0.00 2.40
3396 6305 7.750229 TCTTCAACTGCTCATTAACAAATCT 57.250 32.000 0.00 0.00 0.00 2.40
3397 6306 8.976986 ATTCTTCAACTGCTCATTAACAAATC 57.023 30.769 0.00 0.00 0.00 2.17
3398 6307 9.768662 AAATTCTTCAACTGCTCATTAACAAAT 57.231 25.926 0.00 0.00 0.00 2.32
3403 6312 9.859427 CCATTAAATTCTTCAACTGCTCATTAA 57.141 29.630 0.00 0.00 0.00 1.40
3404 6313 7.975616 GCCATTAAATTCTTCAACTGCTCATTA 59.024 33.333 0.00 0.00 0.00 1.90
3405 6314 6.815142 GCCATTAAATTCTTCAACTGCTCATT 59.185 34.615 0.00 0.00 0.00 2.57
3406 6315 6.071221 TGCCATTAAATTCTTCAACTGCTCAT 60.071 34.615 0.00 0.00 0.00 2.90
3407 6316 5.243507 TGCCATTAAATTCTTCAACTGCTCA 59.756 36.000 0.00 0.00 0.00 4.26
3408 6317 5.713025 TGCCATTAAATTCTTCAACTGCTC 58.287 37.500 0.00 0.00 0.00 4.26
3409 6318 5.726980 TGCCATTAAATTCTTCAACTGCT 57.273 34.783 0.00 0.00 0.00 4.24
3410 6319 5.120674 GGTTGCCATTAAATTCTTCAACTGC 59.879 40.000 0.00 0.00 34.49 4.40
3411 6320 6.366877 CAGGTTGCCATTAAATTCTTCAACTG 59.633 38.462 0.00 0.00 34.49 3.16
3412 6321 6.041979 ACAGGTTGCCATTAAATTCTTCAACT 59.958 34.615 0.00 0.00 34.49 3.16
3413 6322 6.223120 ACAGGTTGCCATTAAATTCTTCAAC 58.777 36.000 0.00 0.00 33.61 3.18
3414 6323 6.267471 AGACAGGTTGCCATTAAATTCTTCAA 59.733 34.615 0.00 0.00 0.00 2.69
3415 6324 5.774690 AGACAGGTTGCCATTAAATTCTTCA 59.225 36.000 0.00 0.00 0.00 3.02
3416 6325 6.071952 TCAGACAGGTTGCCATTAAATTCTTC 60.072 38.462 0.00 0.00 0.00 2.87
3417 6326 5.774690 TCAGACAGGTTGCCATTAAATTCTT 59.225 36.000 0.00 0.00 0.00 2.52
3418 6327 5.324409 TCAGACAGGTTGCCATTAAATTCT 58.676 37.500 0.00 0.00 0.00 2.40
3419 6328 5.643379 TCAGACAGGTTGCCATTAAATTC 57.357 39.130 0.00 0.00 0.00 2.17
3420 6329 5.279456 GGTTCAGACAGGTTGCCATTAAATT 60.279 40.000 0.00 0.00 0.00 1.82
3421 6330 4.220602 GGTTCAGACAGGTTGCCATTAAAT 59.779 41.667 0.00 0.00 0.00 1.40
3422 6331 3.572255 GGTTCAGACAGGTTGCCATTAAA 59.428 43.478 0.00 0.00 0.00 1.52
3423 6332 3.153919 GGTTCAGACAGGTTGCCATTAA 58.846 45.455 0.00 0.00 0.00 1.40
3424 6333 2.790433 GGTTCAGACAGGTTGCCATTA 58.210 47.619 0.00 0.00 0.00 1.90
3425 6334 1.620822 GGTTCAGACAGGTTGCCATT 58.379 50.000 0.00 0.00 0.00 3.16
3426 6335 0.606401 CGGTTCAGACAGGTTGCCAT 60.606 55.000 0.00 0.00 0.00 4.40
3427 6336 1.227823 CGGTTCAGACAGGTTGCCA 60.228 57.895 0.00 0.00 0.00 4.92
3428 6337 2.617274 GCGGTTCAGACAGGTTGCC 61.617 63.158 0.00 0.00 0.00 4.52
3429 6338 1.166531 AAGCGGTTCAGACAGGTTGC 61.167 55.000 0.00 0.00 39.58 4.17
3430 6339 1.002468 CAAAGCGGTTCAGACAGGTTG 60.002 52.381 0.00 0.00 40.03 3.77
3431 6340 1.308998 CAAAGCGGTTCAGACAGGTT 58.691 50.000 0.00 0.00 42.13 3.50
3432 6341 0.180406 ACAAAGCGGTTCAGACAGGT 59.820 50.000 0.00 0.00 33.09 4.00
3433 6342 1.264288 GAACAAAGCGGTTCAGACAGG 59.736 52.381 0.00 0.00 45.07 4.00
3434 6343 2.670401 GAACAAAGCGGTTCAGACAG 57.330 50.000 0.00 0.00 45.07 3.51
3440 6349 5.034797 GGCAATATTAGAACAAAGCGGTTC 58.965 41.667 0.00 9.90 45.87 3.62
3441 6350 4.461081 TGGCAATATTAGAACAAAGCGGTT 59.539 37.500 0.00 0.00 0.00 4.44
3442 6351 4.013728 TGGCAATATTAGAACAAAGCGGT 58.986 39.130 0.00 0.00 0.00 5.68
3443 6352 4.630894 TGGCAATATTAGAACAAAGCGG 57.369 40.909 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.