Multiple sequence alignment - TraesCS2B01G150700

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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 TraesCS2B01G150700 chr2B 100.000 6433 0 0 1 6433 117865165 117871597 0.000000e+00 11880.0
1 TraesCS2B01G150700 chr2B 77.907 344 55 18 2683 3010 775156095 775156433 1.830000e-45 195.0
2 TraesCS2B01G150700 chr2D 94.924 5693 224 27 1 5663 76612264 76617921 0.000000e+00 8852.0
3 TraesCS2B01G150700 chr2D 87.129 505 59 2 5918 6421 76632940 76633439 9.360000e-158 568.0
4 TraesCS2B01G150700 chr2D 84.915 411 57 5 6021 6428 309090783 309090375 1.670000e-110 411.0
5 TraesCS2B01G150700 chr2D 88.433 268 20 3 5655 5922 76631088 76631344 4.840000e-81 313.0
6 TraesCS2B01G150700 chr2A 90.941 5619 413 53 871 6426 77155184 77160769 0.000000e+00 7468.0
7 TraesCS2B01G150700 chr2A 86.859 624 66 8 252 871 77154513 77155124 0.000000e+00 684.0
8 TraesCS2B01G150700 chr2A 80.272 294 44 11 2729 3010 682637489 682637780 6.540000e-50 209.0
9 TraesCS2B01G150700 chr1B 85.504 407 51 6 6029 6433 112693665 112693265 9.980000e-113 418.0
10 TraesCS2B01G150700 chr1B 84.428 411 54 6 6023 6430 387937954 387938357 4.670000e-106 396.0
11 TraesCS2B01G150700 chr4D 84.951 412 55 4 6023 6433 122210640 122210235 1.670000e-110 411.0
12 TraesCS2B01G150700 chr7B 84.804 408 58 3 6022 6428 60510242 60510646 2.160000e-109 407.0
13 TraesCS2B01G150700 chr6D 84.672 411 53 9 6023 6428 49847193 49846788 1.000000e-107 401.0
14 TraesCS2B01G150700 chr7A 84.559 408 55 6 6021 6427 534465424 534465024 1.300000e-106 398.0
15 TraesCS2B01G150700 chr3B 77.093 454 77 13 2673 3104 637010040 637010488 3.000000e-58 237.0
16 TraesCS2B01G150700 chr3B 77.014 422 69 22 2694 3098 466620350 466620760 3.910000e-52 217.0
17 TraesCS2B01G150700 chr3B 74.194 403 80 22 2679 3062 769705276 769705673 5.200000e-31 147.0
18 TraesCS2B01G150700 chr6A 78.824 340 56 14 2684 3010 828888 829224 1.400000e-51 215.0
19 TraesCS2B01G150700 chr3D 79.257 323 48 15 2699 3007 540230643 540230326 2.350000e-49 207.0
20 TraesCS2B01G150700 chr6B 76.080 301 63 8 2707 3001 689061983 689062280 1.450000e-31 148.0
21 TraesCS2B01G150700 chr5D 76.221 307 42 24 2669 2959 297986673 297986382 4.050000e-27 134.0
22 TraesCS2B01G150700 chr3A 95.238 42 2 0 3043 3084 685337442 685337483 4.160000e-07 67.6


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 TraesCS2B01G150700 chr2B 117865165 117871597 6432 False 11880.0 11880 100.000 1 6433 1 chr2B.!!$F1 6432
1 TraesCS2B01G150700 chr2D 76612264 76617921 5657 False 8852.0 8852 94.924 1 5663 1 chr2D.!!$F1 5662
2 TraesCS2B01G150700 chr2D 76631088 76633439 2351 False 440.5 568 87.781 5655 6421 2 chr2D.!!$F2 766
3 TraesCS2B01G150700 chr2A 77154513 77160769 6256 False 4076.0 7468 88.900 252 6426 2 chr2A.!!$F2 6174

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
237 238 0.257039 ATGAAGGCCCAGCTAACCAG 59.743 55.000 0.00 0.0 0.00 4.00 F
250 251 0.889994 TAACCAGCGAGCTCCGTTTA 59.110 50.000 8.47 0.0 41.15 2.01 F
270 271 0.969409 GGCTCATGGAAAAGCAGCCT 60.969 55.000 11.14 0.0 45.40 4.58 F
458 461 0.976073 TTAGGGCCAGGAGACTTCGG 60.976 60.000 6.18 0.0 40.21 4.30 F
486 489 1.168714 CTTCTCCTTTCCCTTTGCCG 58.831 55.000 0.00 0.0 0.00 5.69 F
657 661 2.159014 ACATGCATGGAACAATGGCATC 60.159 45.455 29.41 0.0 46.31 3.91 F
661 665 2.582272 TGGAACAATGGCATCTGGC 58.418 52.632 0.00 0.0 37.25 4.85 F
1453 1522 2.633488 GCCACAGTAGGAAACCTCATC 58.367 52.381 0.00 0.0 34.61 2.92 F
1755 1844 4.505039 GGAGAGAAGGGAACTAGCAACAAA 60.505 45.833 0.00 0.0 42.68 2.83 F
2812 2906 4.142403 TGAACTTCAAACTTTGCTGGACAG 60.142 41.667 0.00 0.0 0.00 3.51 F
3693 3822 1.312815 GAGATGGCCGGAAATCAAGG 58.687 55.000 5.05 0.0 0.00 3.61 F
4569 4718 0.908910 TGCTACATCCCCACGATTGT 59.091 50.000 0.00 0.0 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1727 1816 1.405243 AGTTCCCTTCTCTCCCCCTA 58.595 55.000 0.00 0.00 0.00 3.53 R
1885 1974 2.032054 GCTATTAGCAAACGAGCATGCA 59.968 45.455 21.98 0.00 44.95 3.96 R
2039 2129 5.636123 ACTACAAATATGGTTTGGTGGTGA 58.364 37.500 9.36 0.00 33.92 4.02 R
2425 2516 1.354942 AAACACCTGTAACCCGGGGT 61.355 55.000 27.92 24.02 44.78 4.95 R
2429 2520 3.053831 AGATGAAACACCTGTAACCCG 57.946 47.619 0.00 0.00 0.00 5.28 R
2588 2679 7.461749 CCACCACCATATCTATATCAAAGGTT 58.538 38.462 0.00 0.00 0.00 3.50 R
2665 2756 2.041081 TCCACCACAACTTTCCCTATGG 59.959 50.000 0.00 0.00 0.00 2.74 R
2729 2820 1.552348 GACTGCACGGATAGCGATGC 61.552 60.000 0.00 0.00 38.59 3.91 R
3041 3156 2.229784 CCCTCCAACATTGCTTTGAGAC 59.770 50.000 0.00 0.00 0.00 3.36 R
4151 4282 1.401552 CAATCCATGTTGTAGCACCCG 59.598 52.381 0.00 0.00 0.00 5.28 R
4806 4959 1.522580 CCGCTCCTAGCTTCTTGCC 60.523 63.158 0.00 0.00 44.23 4.52 R
6186 7949 0.240945 GGCAGTTTGTGGGATCGTTG 59.759 55.000 0.00 0.00 0.00 4.10 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
30 31 0.315251 CAGATCGAGGGAGCGCAATA 59.685 55.000 11.47 0.00 32.66 1.90
60 61 2.029838 AATAGGAGCGGAACAAGCAG 57.970 50.000 0.00 0.00 37.01 4.24
84 85 2.549754 CAGTCAGCCAATCTTCGTGTTT 59.450 45.455 0.00 0.00 0.00 2.83
95 96 2.037511 TCTTCGTGTTTAATGGACGGGT 59.962 45.455 0.00 0.00 33.88 5.28
154 155 2.866028 GCAGAGAGCGCCAAACAG 59.134 61.111 2.29 0.00 0.00 3.16
181 182 3.347216 CCTTGGATGGACTTACACAAGG 58.653 50.000 6.84 6.84 45.97 3.61
231 232 1.000396 GGTTGATGAAGGCCCAGCT 60.000 57.895 0.00 0.00 0.00 4.24
237 238 0.257039 ATGAAGGCCCAGCTAACCAG 59.743 55.000 0.00 0.00 0.00 4.00
246 247 2.583593 GCTAACCAGCGAGCTCCG 60.584 66.667 8.47 4.62 38.22 4.63
250 251 0.889994 TAACCAGCGAGCTCCGTTTA 59.110 50.000 8.47 0.00 41.15 2.01
254 255 2.184579 GCGAGCTCCGTTTAGGCT 59.815 61.111 8.47 0.00 40.77 4.58
267 268 3.426695 CGTTTAGGCTCATGGAAAAGCAG 60.427 47.826 6.47 0.00 40.36 4.24
270 271 0.969409 GGCTCATGGAAAAGCAGCCT 60.969 55.000 11.14 0.00 45.40 4.58
290 291 0.976641 CTTAGGACAGCTGACCCACA 59.023 55.000 28.18 13.50 0.00 4.17
299 300 1.745890 CTGACCCACAGTTCGGACA 59.254 57.895 0.00 0.00 41.30 4.02
305 306 2.140717 CCCACAGTTCGGACAACTTAC 58.859 52.381 0.00 0.00 0.00 2.34
314 315 1.792006 GGACAACTTACGACACCCAG 58.208 55.000 0.00 0.00 0.00 4.45
328 329 3.763897 GACACCCAGGCACAAAAATAGAT 59.236 43.478 0.00 0.00 0.00 1.98
341 342 7.429340 GCACAAAAATAGATGGATAGAAACACG 59.571 37.037 0.00 0.00 0.00 4.49
342 343 8.450964 CACAAAAATAGATGGATAGAAACACGT 58.549 33.333 0.00 0.00 0.00 4.49
346 347 6.650427 ATAGATGGATAGAAACACGTAGCA 57.350 37.500 0.00 0.00 0.00 3.49
382 383 4.388485 GGAAAGGGTTCGGTTTTACTGTA 58.612 43.478 0.00 0.00 34.28 2.74
455 458 1.566231 CCAATTAGGGCCAGGAGACTT 59.434 52.381 6.18 0.00 40.21 3.01
458 461 0.976073 TTAGGGCCAGGAGACTTCGG 60.976 60.000 6.18 0.00 40.21 4.30
482 485 2.753168 GCACCACTTCTCCTTTCCCTTT 60.753 50.000 0.00 0.00 0.00 3.11
486 489 1.168714 CTTCTCCTTTCCCTTTGCCG 58.831 55.000 0.00 0.00 0.00 5.69
496 499 4.256090 CTTTGCCGGCTATGCGGC 62.256 66.667 29.70 16.06 44.07 6.53
532 536 6.770785 TCCACCCTTCATACTATTACAAATGC 59.229 38.462 0.00 0.00 0.00 3.56
613 617 8.921353 TGGGTTGTACATTTAAAGCTTTAGTA 57.079 30.769 17.91 14.03 0.00 1.82
657 661 2.159014 ACATGCATGGAACAATGGCATC 60.159 45.455 29.41 0.00 46.31 3.91
661 665 2.582272 TGGAACAATGGCATCTGGC 58.418 52.632 0.00 0.00 37.25 4.85
1017 1081 4.022589 CACCCTATGTGTACCTACCATACG 60.023 50.000 0.00 0.00 40.26 3.06
1120 1186 9.908152 AACTTAGTTTATTCCTACAAACAATGC 57.092 29.630 0.00 0.00 37.16 3.56
1236 1302 6.092670 TCATAGAACTTTATGTGCTTGTGAGC 59.907 38.462 0.00 0.00 38.21 4.26
1398 1467 8.736751 TCGACAAGGAACTAAAATTTTAATGC 57.263 30.769 11.62 8.86 38.49 3.56
1399 1468 8.353684 TCGACAAGGAACTAAAATTTTAATGCA 58.646 29.630 11.62 0.00 38.49 3.96
1419 1488 3.624861 GCATCATATAGGTGCTACCATGC 59.375 47.826 7.86 8.47 41.95 4.06
1453 1522 2.633488 GCCACAGTAGGAAACCTCATC 58.367 52.381 0.00 0.00 34.61 2.92
1755 1844 4.505039 GGAGAGAAGGGAACTAGCAACAAA 60.505 45.833 0.00 0.00 42.68 2.83
1885 1974 5.256806 AGTTGGCTCCTTTAACCACTATT 57.743 39.130 0.00 0.00 31.83 1.73
2013 2102 8.641498 AAGGAACTAGATGTGAAATGATTTGT 57.359 30.769 0.00 0.00 38.49 2.83
2139 2229 7.602644 TGTAGAACCTTCATTAGTTCATGACAC 59.397 37.037 0.00 0.00 43.89 3.67
2584 2675 8.415950 TGACAAGATTTGTAAATAACCCACAT 57.584 30.769 0.00 0.00 45.52 3.21
2665 2756 7.065803 TGCATCTTTATGTACTTCCTTGCTAAC 59.934 37.037 0.00 0.00 35.38 2.34
2729 2820 4.823989 CCTTATCTAGCCACCCATTTTCTG 59.176 45.833 0.00 0.00 0.00 3.02
2812 2906 4.142403 TGAACTTCAAACTTTGCTGGACAG 60.142 41.667 0.00 0.00 0.00 3.51
3041 3156 8.893727 AGTAATAAATTAGTTGGCTAGCACAAG 58.106 33.333 18.24 0.00 0.00 3.16
3424 3553 2.281484 GTGGCGAAGGGCTGAACA 60.281 61.111 0.00 0.00 42.94 3.18
3425 3554 2.281484 TGGCGAAGGGCTGAACAC 60.281 61.111 0.00 0.00 42.94 3.32
3594 3723 5.417811 CCTGATGCTAGCTACTATGGATTG 58.582 45.833 17.23 0.00 0.00 2.67
3616 3745 3.663025 CATGTCACCACTGATGTGTACA 58.337 45.455 0.00 0.00 42.34 2.90
3684 3813 2.124983 CACAGTGGAGATGGCCGG 60.125 66.667 0.00 0.00 0.00 6.13
3693 3822 1.312815 GAGATGGCCGGAAATCAAGG 58.687 55.000 5.05 0.00 0.00 3.61
3754 3883 9.965902 AACTTCTTTATTCACATGAGTTCCTAT 57.034 29.630 0.00 0.00 0.00 2.57
3792 3921 5.941948 AACTGTTTTAGACCTCAAATCGG 57.058 39.130 0.00 0.00 0.00 4.18
3870 4000 9.826574 TTGTCAAACTATAAAGAACACTACTGT 57.173 29.630 0.00 0.00 0.00 3.55
4083 4214 4.942483 CCAGGAAATGATCTGCCTATGATC 59.058 45.833 0.00 0.00 40.34 2.92
4104 4235 8.965986 TGATCGTAAGCTTACATACATATGTC 57.034 34.615 30.63 16.18 41.77 3.06
4151 4282 4.709397 CAGAGGGATGGATATGAGAGTACC 59.291 50.000 0.00 0.00 0.00 3.34
4410 4555 6.755141 TGTAACACAATCTTCTAGGCGTATTC 59.245 38.462 0.00 0.00 0.00 1.75
4444 4593 4.024387 TGGAATGTTCTACTCGTTGTTTGC 60.024 41.667 0.00 0.00 0.00 3.68
4468 4617 8.846211 TGCAGTAAAAGCTAGACTTAAACAAAT 58.154 29.630 0.00 0.00 37.75 2.32
4565 4714 1.685765 AGCTGCTACATCCCCACGA 60.686 57.895 0.00 0.00 0.00 4.35
4569 4718 0.908910 TGCTACATCCCCACGATTGT 59.091 50.000 0.00 0.00 0.00 2.71
4626 4775 2.095364 CGAAGTAGCTTACTCCACACGT 60.095 50.000 0.00 0.00 38.26 4.49
4627 4776 3.243336 GAAGTAGCTTACTCCACACGTG 58.757 50.000 15.48 15.48 38.26 4.49
4628 4777 2.236766 AGTAGCTTACTCCACACGTGT 58.763 47.619 17.22 17.22 32.47 4.49
4631 4780 2.914059 AGCTTACTCCACACGTGTTTT 58.086 42.857 20.79 5.90 0.00 2.43
4632 4781 3.275999 AGCTTACTCCACACGTGTTTTT 58.724 40.909 20.79 6.27 0.00 1.94
4717 4870 7.035004 ACAACCCATTCAAAATTATCATGTCG 58.965 34.615 0.00 0.00 0.00 4.35
4806 4959 2.190325 ACGACTTCCGATCTTAAGCG 57.810 50.000 0.00 13.65 41.76 4.68
4873 5026 5.181748 ACTTCTCGATTGATTTCCCTTCAG 58.818 41.667 0.00 0.00 0.00 3.02
5238 5396 2.035442 GCGCTTCCAACTCCTCCAC 61.035 63.158 0.00 0.00 0.00 4.02
5307 5465 1.741706 CTGACTTGCGCCTCATTGAAT 59.258 47.619 4.18 0.00 0.00 2.57
5605 5766 9.483916 TCGAGAAACAAGTTTATCATAGAAACA 57.516 29.630 17.31 0.00 39.88 2.83
5627 5788 6.215845 ACAACAAATGCACTAGAAATTGACC 58.784 36.000 0.00 0.00 0.00 4.02
5675 5836 8.607441 TGCATACTAGGAATTATCACATTGAC 57.393 34.615 0.00 0.00 0.00 3.18
5759 5920 3.737172 GCCACATGTCGCACCACC 61.737 66.667 10.82 0.00 0.00 4.61
5788 5950 8.514594 GGATGTATACAATATCATGGGTTGTTG 58.485 37.037 10.14 7.51 37.30 3.33
5790 5952 8.815565 TGTATACAATATCATGGGTTGTTGTT 57.184 30.769 2.20 5.71 37.30 2.83
5791 5953 9.907229 TGTATACAATATCATGGGTTGTTGTTA 57.093 29.630 2.20 1.15 37.30 2.41
5794 5956 7.346751 ACAATATCATGGGTTGTTGTTATCC 57.653 36.000 0.00 0.00 32.53 2.59
5795 5957 6.894654 ACAATATCATGGGTTGTTGTTATCCA 59.105 34.615 0.00 0.00 32.53 3.41
5796 5958 6.959639 ATATCATGGGTTGTTGTTATCCAC 57.040 37.500 0.00 0.00 0.00 4.02
5797 5959 4.105754 TCATGGGTTGTTGTTATCCACA 57.894 40.909 0.00 0.00 0.00 4.17
5798 5960 4.474394 TCATGGGTTGTTGTTATCCACAA 58.526 39.130 0.00 0.00 43.55 3.33
5830 5992 6.015856 CCAAGGGTTGTAATGTTTATGTCACA 60.016 38.462 0.00 0.00 0.00 3.58
5839 6001 9.210329 TGTAATGTTTATGTCACACGTATTCTT 57.790 29.630 0.00 0.00 0.00 2.52
5858 6020 6.579666 TTCTTAGTCGTTGTTTAGCCTCTA 57.420 37.500 0.00 0.00 0.00 2.43
5867 6029 7.330208 GTCGTTGTTTAGCCTCTAATCTTTACA 59.670 37.037 0.00 0.00 0.00 2.41
5928 7690 3.939066 ACTTGAAAGGTGCTTATACGCT 58.061 40.909 2.63 0.00 0.00 5.07
5945 7707 1.682740 GCTAGGAGGACGAAGCTAGT 58.317 55.000 0.00 0.00 32.34 2.57
5983 7745 2.096268 CGCAACTTGTGTGTCGATTGAT 60.096 45.455 0.00 0.00 32.74 2.57
6006 7768 1.080498 AGAACCCCATGAGTCCACCTA 59.920 52.381 0.00 0.00 0.00 3.08
6026 7788 6.926826 CACCTATAAGCGTGTATAATGTTGGA 59.073 38.462 0.00 0.00 0.00 3.53
6046 7808 9.575783 TGTTGGAAAACATAGTAGAAAACAAAC 57.424 29.630 0.00 0.00 0.00 2.93
6047 7809 9.575783 GTTGGAAAACATAGTAGAAAACAAACA 57.424 29.630 0.00 0.00 0.00 2.83
6144 7907 2.530177 CGAGTTGCAGCGAAAGAGATA 58.470 47.619 0.00 0.00 0.00 1.98
6149 7912 3.592898 TGCAGCGAAAGAGATAAGTCA 57.407 42.857 0.00 0.00 0.00 3.41
6166 7929 4.966965 AGTCAGTGTAGATCGTACTTGG 57.033 45.455 0.00 0.00 0.00 3.61
6169 7932 3.377485 TCAGTGTAGATCGTACTTGGAGC 59.623 47.826 0.00 0.00 0.00 4.70
6180 7943 3.665675 CTTGGAGCCCCTCGAACCG 62.666 68.421 0.00 0.00 0.00 4.44
6186 7949 1.108132 AGCCCCTCGAACCGTAGATC 61.108 60.000 0.00 0.00 0.00 2.75
6198 7961 1.407618 CCGTAGATCAACGATCCCACA 59.592 52.381 0.00 0.00 45.68 4.17
6202 7965 3.703001 AGATCAACGATCCCACAAACT 57.297 42.857 0.00 0.00 39.66 2.66
6208 7971 0.893270 CGATCCCACAAACTGCCCAA 60.893 55.000 0.00 0.00 0.00 4.12
6267 8030 1.538512 TCTACGAGTTGCAAGCGTACT 59.461 47.619 23.04 8.78 39.24 2.73
6280 8043 4.389077 GCAAGCGTACTGTCTTAACAATCT 59.611 41.667 0.00 0.00 34.24 2.40
6281 8044 5.575606 GCAAGCGTACTGTCTTAACAATCTA 59.424 40.000 0.00 0.00 34.24 1.98
6294 8057 1.066573 ACAATCTAGCAGCGCTTCACT 60.067 47.619 7.50 8.56 40.44 3.41
6312 8075 5.209818 TCACTGTCCAGAACTAATCGTTT 57.790 39.130 0.40 0.00 35.56 3.60
6314 8077 5.010719 TCACTGTCCAGAACTAATCGTTTCT 59.989 40.000 0.40 0.00 35.56 2.52
6315 8078 6.208007 TCACTGTCCAGAACTAATCGTTTCTA 59.792 38.462 0.40 0.00 35.56 2.10
6316 8079 6.528423 CACTGTCCAGAACTAATCGTTTCTAG 59.472 42.308 0.40 0.00 35.56 2.43
6328 8091 9.411189 ACTAATCGTTTCTAGAGAATTAGAGGT 57.589 33.333 20.66 7.27 31.97 3.85
6349 8112 5.780793 AGGTAGAAGATTAGAACCACACTGT 59.219 40.000 0.00 0.00 32.43 3.55
6362 8125 7.620880 AGAACCACACTGTGCTTCTAATTATA 58.379 34.615 15.36 0.00 36.90 0.98
6406 8169 8.802267 GTCTAGCTCTAATTGATCAACTAGGAT 58.198 37.037 20.57 13.63 0.00 3.24
6427 8190 8.974060 AGGATCAACTAGAACTAGAACTAGAG 57.026 38.462 23.59 17.77 39.25 2.43
6428 8191 8.774183 AGGATCAACTAGAACTAGAACTAGAGA 58.226 37.037 23.59 20.52 39.25 3.10
6429 8192 9.398538 GGATCAACTAGAACTAGAACTAGAGAA 57.601 37.037 23.59 13.70 39.25 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.145225 CGATTATTGCGCTCCCTCG 58.855 57.895 9.73 7.25 0.00 4.63
41 42 1.555075 TCTGCTTGTTCCGCTCCTATT 59.445 47.619 0.00 0.00 0.00 1.73
60 61 2.158449 CACGAAGATTGGCTGACTGTTC 59.842 50.000 0.00 0.00 0.00 3.18
95 96 3.567478 ATGCGTGACGTGAAGCGGA 62.567 57.895 6.91 1.71 46.52 5.54
120 121 1.196354 CTGCACAACTTAGCACTGCTC 59.804 52.381 6.86 0.00 40.44 4.26
128 129 0.718343 GCGCTCTCTGCACAACTTAG 59.282 55.000 0.00 0.00 43.06 2.18
146 147 2.118294 AAGGGCCTCCTGTTTGGC 59.882 61.111 6.46 0.00 44.07 4.52
154 155 1.575447 AAGTCCATCCAAGGGCCTCC 61.575 60.000 6.46 0.00 32.23 4.30
159 160 3.347216 CTTGTGTAAGTCCATCCAAGGG 58.653 50.000 0.00 0.00 0.00 3.95
181 182 5.299531 GCCCATTTAACTGAATAGACTTCCC 59.700 44.000 0.00 0.00 0.00 3.97
231 232 0.889994 TAAACGGAGCTCGCTGGTTA 59.110 50.000 7.83 6.64 43.89 2.85
237 238 1.878975 GAGCCTAAACGGAGCTCGC 60.879 63.158 7.83 3.37 43.18 5.03
246 247 3.674410 GCTGCTTTTCCATGAGCCTAAAC 60.674 47.826 0.00 0.00 38.11 2.01
250 251 0.969409 GGCTGCTTTTCCATGAGCCT 60.969 55.000 11.14 0.00 44.94 4.58
254 255 2.592102 AAGAGGCTGCTTTTCCATGA 57.408 45.000 0.00 0.00 0.00 3.07
267 268 0.176910 GGTCAGCTGTCCTAAGAGGC 59.823 60.000 21.09 0.00 34.61 4.70
270 271 1.267121 GTGGGTCAGCTGTCCTAAGA 58.733 55.000 25.95 8.32 0.00 2.10
290 291 2.544486 GGTGTCGTAAGTTGTCCGAACT 60.544 50.000 0.00 0.00 39.48 3.01
295 296 1.607251 CCTGGGTGTCGTAAGTTGTCC 60.607 57.143 0.00 0.00 39.48 4.02
299 300 0.250166 GTGCCTGGGTGTCGTAAGTT 60.250 55.000 0.00 0.00 39.48 2.66
305 306 0.673437 ATTTTTGTGCCTGGGTGTCG 59.327 50.000 0.00 0.00 0.00 4.35
314 315 7.702348 GTGTTTCTATCCATCTATTTTTGTGCC 59.298 37.037 0.00 0.00 0.00 5.01
328 329 2.871133 CGTGCTACGTGTTTCTATCCA 58.129 47.619 0.00 0.00 36.74 3.41
341 342 1.226435 CTCTCCGCTCACGTGCTAC 60.226 63.158 11.67 1.15 37.70 3.58
342 343 2.407428 CCTCTCCGCTCACGTGCTA 61.407 63.158 11.67 0.00 37.70 3.49
344 345 4.803426 CCCTCTCCGCTCACGTGC 62.803 72.222 11.67 0.00 37.70 5.34
346 347 1.878656 CTTTCCCTCTCCGCTCACGT 61.879 60.000 0.00 0.00 37.70 4.49
455 458 2.649034 GAGAAGTGGTGCGACCGA 59.351 61.111 0.00 0.00 42.58 4.69
458 461 1.149148 GAAAGGAGAAGTGGTGCGAC 58.851 55.000 0.00 0.00 0.00 5.19
486 489 3.044305 GATCACCGCCGCATAGCC 61.044 66.667 0.00 0.00 0.00 3.93
501 504 3.715648 AGTATGAAGGGTGGAGAGGAT 57.284 47.619 0.00 0.00 0.00 3.24
575 579 4.746115 TGTACAACCCAAATCGATATACGC 59.254 41.667 0.00 0.00 42.26 4.42
657 661 4.745125 CACAATTATAGTAGTGGACGCCAG 59.255 45.833 0.00 0.00 32.34 4.85
661 665 6.387041 TCCTCACAATTATAGTAGTGGACG 57.613 41.667 0.00 0.00 33.01 4.79
971 1035 9.668497 GGTGTCCTTAATGAAGATTTAGTAGTT 57.332 33.333 0.00 0.00 34.25 2.24
1017 1081 7.256119 CCCCCTATATATAGATCTGATGTGTGC 60.256 44.444 19.51 0.00 32.05 4.57
1236 1302 2.070783 ACGCCACCAGTAATAACAACG 58.929 47.619 0.00 0.00 0.00 4.10
1398 1467 4.874396 CAGCATGGTAGCACCTATATGATG 59.126 45.833 0.00 0.00 39.58 3.07
1399 1468 4.533707 ACAGCATGGTAGCACCTATATGAT 59.466 41.667 0.00 0.00 43.62 2.45
1419 1488 2.115910 TGGCCAGGGAAGCAACAG 59.884 61.111 0.00 0.00 0.00 3.16
1504 1592 6.323739 GGGAAATATAGGAACCAAAGAATGCA 59.676 38.462 0.00 0.00 0.00 3.96
1727 1816 1.405243 AGTTCCCTTCTCTCCCCCTA 58.595 55.000 0.00 0.00 0.00 3.53
1763 1852 5.046087 ACCAAGGGTAACTATGTACTTGACC 60.046 44.000 0.00 0.00 37.98 4.02
1885 1974 2.032054 GCTATTAGCAAACGAGCATGCA 59.968 45.455 21.98 0.00 44.95 3.96
2039 2129 5.636123 ACTACAAATATGGTTTGGTGGTGA 58.364 37.500 9.36 0.00 33.92 4.02
2197 2288 9.205719 CATGAAAATTTTGATGTTGATGGTGTA 57.794 29.630 18.79 0.00 28.95 2.90
2308 2399 2.893489 GGAATTTGACTTCAGGCTTGGT 59.107 45.455 0.00 0.00 0.00 3.67
2425 2516 1.354942 AAACACCTGTAACCCGGGGT 61.355 55.000 27.92 24.02 44.78 4.95
2429 2520 3.053831 AGATGAAACACCTGTAACCCG 57.946 47.619 0.00 0.00 0.00 5.28
2588 2679 7.461749 CCACCACCATATCTATATCAAAGGTT 58.538 38.462 0.00 0.00 0.00 3.50
2665 2756 2.041081 TCCACCACAACTTTCCCTATGG 59.959 50.000 0.00 0.00 0.00 2.74
2729 2820 1.552348 GACTGCACGGATAGCGATGC 61.552 60.000 0.00 0.00 38.59 3.91
2812 2906 9.472361 TCCTATATTGTAGTTAGATCGTTTTGC 57.528 33.333 0.00 0.00 0.00 3.68
2924 3024 9.921637 AACTTTAATGTGTGAAAAACTTTCAGA 57.078 25.926 2.13 0.00 0.00 3.27
2926 3026 9.921637 AGAACTTTAATGTGTGAAAAACTTTCA 57.078 25.926 0.00 0.00 0.00 2.69
3041 3156 2.229784 CCCTCCAACATTGCTTTGAGAC 59.770 50.000 0.00 0.00 0.00 3.36
3159 3274 9.086336 ACAAACAACAAAACTCACATTCTTATG 57.914 29.630 0.00 0.00 37.79 1.90
3227 3343 6.264292 AGGAGTAACATGTGTGTTTGCATTTA 59.736 34.615 0.00 0.00 46.07 1.40
3425 3554 7.041098 AGCTAAGAAACAACACTTCCATAGTTG 60.041 37.037 0.00 0.00 45.97 3.16
3476 3605 3.844577 AACAGAGCAAACATGCATCTC 57.155 42.857 0.00 0.00 37.25 2.75
3681 3810 5.621193 ACTCCATTATACCTTGATTTCCGG 58.379 41.667 0.00 0.00 0.00 5.14
3684 3813 9.614792 ACACTAACTCCATTATACCTTGATTTC 57.385 33.333 0.00 0.00 0.00 2.17
3693 3822 6.204882 GCCATCCAACACTAACTCCATTATAC 59.795 42.308 0.00 0.00 0.00 1.47
3761 3890 9.616156 TTGAGGTCTAAAACAGTTATAAACACA 57.384 29.630 0.00 0.00 0.00 3.72
3791 3920 1.689813 GCTAGCTTTCTAGGGAGTCCC 59.310 57.143 21.81 21.81 45.90 4.46
3792 3921 2.673258 AGCTAGCTTTCTAGGGAGTCC 58.327 52.381 12.68 0.00 42.00 3.85
3882 4012 7.560626 GGTGTACCATAAACAACCCCATAAATA 59.439 37.037 0.00 0.00 35.64 1.40
3899 4029 7.292319 AGTAACAAAAAGTAAGGGTGTACCAT 58.708 34.615 3.11 0.00 43.89 3.55
4083 4214 5.060569 GCGGACATATGTATGTAAGCTTACG 59.939 44.000 27.07 14.95 46.20 3.18
4151 4282 1.401552 CAATCCATGTTGTAGCACCCG 59.598 52.381 0.00 0.00 0.00 5.28
4565 4714 3.243068 GCTTCGTTTTGTCAGGACACAAT 60.243 43.478 0.77 0.00 41.67 2.71
4569 4718 2.325583 AGCTTCGTTTTGTCAGGACA 57.674 45.000 0.00 0.00 39.98 4.02
4639 4792 6.817765 TTTAACACATGGTCTTGGATTCTC 57.182 37.500 0.00 0.00 0.00 2.87
4717 4870 7.658167 AGAAACTTTAAGCAAGAGTAAGAGACC 59.342 37.037 0.00 0.00 36.21 3.85
4787 4940 2.190325 CGCTTAAGATCGGAAGTCGT 57.810 50.000 6.67 0.00 40.32 4.34
4796 4949 2.284190 AGCTTCTTGCCGCTTAAGATC 58.716 47.619 6.67 0.00 44.23 2.75
4806 4959 1.522580 CCGCTCCTAGCTTCTTGCC 60.523 63.158 0.00 0.00 44.23 4.52
4873 5026 9.936759 CCTAGATCCAAATTAGAACCTATCTTC 57.063 37.037 0.00 0.00 39.71 2.87
4991 5145 7.226325 TCCATGCCTCATAAAACAAAACAAAAG 59.774 33.333 0.00 0.00 0.00 2.27
5148 5306 5.652518 TGCCATGTATGTGAACAATGATTG 58.347 37.500 3.16 3.16 32.02 2.67
5150 5308 5.918426 TTGCCATGTATGTGAACAATGAT 57.082 34.783 0.00 0.00 32.02 2.45
5238 5396 4.335647 AAGGACGCCACTGCCCAG 62.336 66.667 0.00 0.00 0.00 4.45
5307 5465 2.683465 GGCTGCTCCTTCCATCCCA 61.683 63.158 0.00 0.00 0.00 4.37
5579 5740 9.483916 TGTTTCTATGATAAACTTGTTTCTCGA 57.516 29.630 1.72 0.00 37.64 4.04
5599 5760 8.196771 TCAATTTCTAGTGCATTTGTTGTTTCT 58.803 29.630 0.00 0.00 0.00 2.52
5605 5766 6.403866 TGGTCAATTTCTAGTGCATTTGTT 57.596 33.333 0.00 0.00 0.00 2.83
5627 5788 2.743636 TAGACAGCCTTCGGAGTTTG 57.256 50.000 0.00 0.00 0.00 2.93
5759 5920 8.733458 CAACCCATGATATTGTATACATCCTTG 58.267 37.037 6.36 2.92 0.00 3.61
5788 5950 3.610911 CTTGGTCCTCCTTGTGGATAAC 58.389 50.000 0.00 0.00 42.29 1.89
5790 5952 2.196595 CCTTGGTCCTCCTTGTGGATA 58.803 52.381 0.00 0.00 42.29 2.59
5791 5953 0.995024 CCTTGGTCCTCCTTGTGGAT 59.005 55.000 0.00 0.00 42.29 3.41
5792 5954 1.133809 CCCTTGGTCCTCCTTGTGGA 61.134 60.000 0.00 0.00 40.69 4.02
5793 5955 1.380302 CCCTTGGTCCTCCTTGTGG 59.620 63.158 0.00 0.00 34.23 4.17
5794 5956 0.478507 AACCCTTGGTCCTCCTTGTG 59.521 55.000 0.00 0.00 33.12 3.33
5795 5957 0.478507 CAACCCTTGGTCCTCCTTGT 59.521 55.000 0.00 0.00 33.12 3.16
5796 5958 0.478507 ACAACCCTTGGTCCTCCTTG 59.521 55.000 0.00 0.00 33.12 3.61
5797 5959 2.127651 TACAACCCTTGGTCCTCCTT 57.872 50.000 0.00 0.00 33.12 3.36
5798 5960 2.127651 TTACAACCCTTGGTCCTCCT 57.872 50.000 0.00 0.00 33.12 3.69
5830 5992 5.574443 GGCTAAACAACGACTAAGAATACGT 59.426 40.000 0.00 0.00 40.64 3.57
5839 6001 6.770746 AGATTAGAGGCTAAACAACGACTA 57.229 37.500 0.00 0.00 0.00 2.59
5858 6020 5.415701 ACGCCTCAACATGATTGTAAAGATT 59.584 36.000 0.00 0.00 34.06 2.40
5867 6029 1.812571 GGACAACGCCTCAACATGATT 59.187 47.619 0.00 0.00 0.00 2.57
5894 6056 5.939883 CACCTTTCAAGTATCTGATGGTCAA 59.060 40.000 0.00 0.00 33.15 3.18
5928 7690 2.776536 ACCTACTAGCTTCGTCCTCCTA 59.223 50.000 0.00 0.00 0.00 2.94
5965 7727 5.056480 TCTTCATCAATCGACACACAAGTT 58.944 37.500 0.00 0.00 0.00 2.66
5975 7737 3.199727 TCATGGGGTTCTTCATCAATCGA 59.800 43.478 0.00 0.00 0.00 3.59
5983 7745 1.351017 GTGGACTCATGGGGTTCTTCA 59.649 52.381 0.00 0.00 0.00 3.02
6006 7768 8.046294 TGTTTTCCAACATTATACACGCTTAT 57.954 30.769 0.00 0.00 38.03 1.73
6144 7907 5.008331 TCCAAGTACGATCTACACTGACTT 58.992 41.667 0.00 0.00 0.00 3.01
6149 7912 2.688958 GGCTCCAAGTACGATCTACACT 59.311 50.000 0.00 0.00 0.00 3.55
6166 7929 1.108132 ATCTACGGTTCGAGGGGCTC 61.108 60.000 0.00 0.00 0.00 4.70
6169 7932 1.108776 TTGATCTACGGTTCGAGGGG 58.891 55.000 0.00 0.00 0.00 4.79
6180 7943 4.330074 CAGTTTGTGGGATCGTTGATCTAC 59.670 45.833 6.74 0.00 38.91 2.59
6186 7949 0.240945 GGCAGTTTGTGGGATCGTTG 59.759 55.000 0.00 0.00 0.00 4.10
6198 7961 1.484653 GGGACTGTTTTTGGGCAGTTT 59.515 47.619 0.00 0.00 44.89 2.66
6202 7965 0.821711 CGAGGGACTGTTTTTGGGCA 60.822 55.000 0.00 0.00 41.55 5.36
6208 7971 0.754472 TCCGTTCGAGGGACTGTTTT 59.246 50.000 3.37 0.00 41.55 2.43
6267 8030 2.930040 GCGCTGCTAGATTGTTAAGACA 59.070 45.455 0.00 0.00 0.00 3.41
6280 8043 1.079819 GGACAGTGAAGCGCTGCTA 60.080 57.895 18.27 0.00 44.75 3.49
6281 8044 2.358003 GGACAGTGAAGCGCTGCT 60.358 61.111 18.27 10.25 44.75 4.24
6294 8057 6.657966 TCTCTAGAAACGATTAGTTCTGGACA 59.342 38.462 0.00 0.00 43.37 4.02
6328 8091 5.246203 AGCACAGTGTGGTTCTAATCTTCTA 59.754 40.000 21.94 0.00 41.72 2.10
6362 8125 6.277044 AGCTAGACCTAGATCCTCTAATCCTT 59.723 42.308 8.16 0.00 35.21 3.36


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

AutoCloner maintained by Alex Coulton.