Multiple sequence alignment - TraesCS2B01G016900

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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 TraesCS2B01G016900 chr2B 100.000 2929 0 0 1 2929 7836463 7839391 0.000000e+00 5409
1 TraesCS2B01G016900 chr2B 96.496 1855 61 2 1 1852 7761240 7763093 0.000000e+00 3062
2 TraesCS2B01G016900 chr2B 90.614 2035 164 16 631 2652 8227629 8225609 0.000000e+00 2675
3 TraesCS2B01G016900 chr2B 90.570 2036 164 17 631 2652 8071875 8069854 0.000000e+00 2671
4 TraesCS2B01G016900 chr2B 90.435 1976 155 19 620 2586 7902667 7900717 0.000000e+00 2571
5 TraesCS2B01G016900 chr2B 93.654 914 51 4 1892 2804 7763090 7763997 0.000000e+00 1360
6 TraesCS2B01G016900 chr2B 100.000 141 0 0 3417 3557 7839879 7840019 9.790000e-66 261
7 TraesCS2B01G016900 chr2A 94.071 2277 112 7 532 2804 2725681 2727938 0.000000e+00 3435
8 TraesCS2B01G016900 chr2A 95.749 494 21 0 39 532 2724858 2725351 0.000000e+00 797
9 TraesCS2B01G016900 chr2A 84.375 160 22 3 425 583 441997830 441997673 1.710000e-33 154
10 TraesCS2B01G016900 chr2D 93.428 2176 101 26 420 2562 2949281 2947115 0.000000e+00 3188
11 TraesCS2B01G016900 chr2D 91.686 421 34 1 1 421 2949814 2949395 1.840000e-162 582
12 TraesCS2B01G016900 chr3D 79.349 1535 232 52 1031 2542 606940928 606942400 0.000000e+00 1000
13 TraesCS2B01G016900 chr5D 77.600 1250 232 29 1200 2431 371862258 371863477 0.000000e+00 713
14 TraesCS2B01G016900 chr5A 77.102 1249 240 28 1200 2431 475294991 475296210 0.000000e+00 680
15 TraesCS2B01G016900 chr5B 76.389 720 126 26 1728 2431 441745515 441746206 7.310000e-92 348
16 TraesCS2B01G016900 chr7A 74.830 588 136 9 1195 1776 518524557 518523976 4.560000e-64 255
17 TraesCS2B01G016900 chr7D 74.411 594 128 20 1195 1776 477855753 477856334 2.140000e-57 233


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 TraesCS2B01G016900 chr2B 7836463 7840019 3556 False 2835 5409 100.000 1 3557 2 chr2B.!!$F2 3556
1 TraesCS2B01G016900 chr2B 8225609 8227629 2020 True 2675 2675 90.614 631 2652 1 chr2B.!!$R3 2021
2 TraesCS2B01G016900 chr2B 8069854 8071875 2021 True 2671 2671 90.570 631 2652 1 chr2B.!!$R2 2021
3 TraesCS2B01G016900 chr2B 7900717 7902667 1950 True 2571 2571 90.435 620 2586 1 chr2B.!!$R1 1966
4 TraesCS2B01G016900 chr2B 7761240 7763997 2757 False 2211 3062 95.075 1 2804 2 chr2B.!!$F1 2803
5 TraesCS2B01G016900 chr2A 2724858 2727938 3080 False 2116 3435 94.910 39 2804 2 chr2A.!!$F1 2765
6 TraesCS2B01G016900 chr2D 2947115 2949814 2699 True 1885 3188 92.557 1 2562 2 chr2D.!!$R1 2561
7 TraesCS2B01G016900 chr3D 606940928 606942400 1472 False 1000 1000 79.349 1031 2542 1 chr3D.!!$F1 1511
8 TraesCS2B01G016900 chr5D 371862258 371863477 1219 False 713 713 77.600 1200 2431 1 chr5D.!!$F1 1231
9 TraesCS2B01G016900 chr5A 475294991 475296210 1219 False 680 680 77.102 1200 2431 1 chr5A.!!$F1 1231
10 TraesCS2B01G016900 chr5B 441745515 441746206 691 False 348 348 76.389 1728 2431 1 chr5B.!!$F1 703
11 TraesCS2B01G016900 chr7A 518523976 518524557 581 True 255 255 74.830 1195 1776 1 chr7A.!!$R1 581
12 TraesCS2B01G016900 chr7D 477855753 477856334 581 False 233 233 74.411 1195 1776 1 chr7D.!!$F1 581

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
181 182 1.256812 GGCTATGCCTTGTGTTTGGT 58.743 50.0 0.73 0.0 46.69 3.67 F
1689 2170 0.106708 GCGATGTCTTCTGGGCCATA 59.893 55.0 6.72 0.0 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1966 2447 1.431036 GGCTCAAATTCAGCTCCGC 59.569 57.895 8.77 0.0 37.05 5.54 R
2848 3369 0.478072 TCCCACATGTTGCAGTCCTT 59.522 50.000 0.00 0.0 0.00 3.36 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
48 49 1.268625 ACGTGCTAGTTCGTGTGATGA 59.731 47.619 12.04 0.00 38.85 2.92
93 94 6.883756 TGTGATCATGGTTGCAGTAATTTCTA 59.116 34.615 0.00 0.00 0.00 2.10
181 182 1.256812 GGCTATGCCTTGTGTTTGGT 58.743 50.000 0.73 0.00 46.69 3.67
236 237 5.896073 AATATTTGTTTTCCCCCACACAA 57.104 34.783 0.00 0.00 0.00 3.33
241 242 2.564947 TGTTTTCCCCCACACAATATGC 59.435 45.455 0.00 0.00 0.00 3.14
824 1301 7.634671 TTAGATATGCATTGGGATTGCTATG 57.365 36.000 3.54 0.00 40.77 2.23
827 1304 2.309613 TGCATTGGGATTGCTATGTCC 58.690 47.619 0.00 0.00 40.77 4.02
909 1386 7.095187 CCGGGTAATCTTAGTAAGCATTGATTC 60.095 40.741 4.93 0.00 0.00 2.52
1308 1789 0.826062 GCGGTAGCCTAAACAGGGTA 59.174 55.000 0.00 0.00 40.54 3.69
1370 1851 2.918345 CGTACCGGTCCGTGGACAA 61.918 63.158 12.40 0.52 46.20 3.18
1626 2107 2.665649 ACGTCATTGATGCCGAGTTA 57.334 45.000 5.77 0.00 32.91 2.24
1659 2140 1.475034 GGCACACTCCTGAACAAGACA 60.475 52.381 0.00 0.00 0.00 3.41
1689 2170 0.106708 GCGATGTCTTCTGGGCCATA 59.893 55.000 6.72 0.00 0.00 2.74
1883 2364 2.249413 ATCAGGGCGCTTGTCCAGAG 62.249 60.000 7.64 0.00 41.02 3.35
2314 2823 2.264480 CGGTGGATTCGGCAGACA 59.736 61.111 0.00 0.00 0.00 3.41
2376 2888 4.508128 ATGGCGCCGTACGTGAGG 62.508 66.667 22.45 1.94 46.11 3.86
2386 2898 1.820906 TACGTGAGGTCCGGATCCG 60.821 63.158 27.65 27.65 39.44 4.18
2467 2979 5.517770 CCGAAATACTTCAAGGGTAACTACG 59.482 44.000 0.00 0.00 0.00 3.51
2567 3083 3.313526 CGAGCATCTTAATTGTTCCCCTG 59.686 47.826 0.00 0.00 0.00 4.45
2586 3102 4.038042 CCCTGTTTTCTCCTCCTTTTGAAC 59.962 45.833 0.00 0.00 0.00 3.18
2611 3127 7.500559 ACCAGCTGCAAAATATTTTGGTTAAAA 59.499 29.630 31.89 0.00 45.73 1.52
2629 3149 6.419710 GGTTAAAACATCTTACTTGTTGTGGC 59.580 38.462 0.00 0.00 37.38 5.01
2652 3172 3.468770 TGCAAGCCTTCGTTTTACTACA 58.531 40.909 0.00 0.00 0.00 2.74
2653 3173 4.069304 TGCAAGCCTTCGTTTTACTACAT 58.931 39.130 0.00 0.00 0.00 2.29
2654 3174 5.239351 TGCAAGCCTTCGTTTTACTACATA 58.761 37.500 0.00 0.00 0.00 2.29
2655 3175 5.121142 TGCAAGCCTTCGTTTTACTACATAC 59.879 40.000 0.00 0.00 0.00 2.39
2671 3191 5.839063 ACTACATACATGCATGGTAGGTACT 59.161 40.000 29.39 18.10 46.37 2.73
2672 3192 4.960938 ACATACATGCATGGTAGGTACTG 58.039 43.478 29.41 15.69 41.52 2.74
2688 3208 9.730705 GGTAGGTACTGTATATCTACATGTACA 57.269 37.037 19.97 0.00 40.12 2.90
2811 3332 9.918630 ATGTCACTTCTTGAAATAATTGAAAGG 57.081 29.630 0.00 0.00 35.39 3.11
2812 3333 7.867403 TGTCACTTCTTGAAATAATTGAAAGGC 59.133 33.333 0.00 0.00 35.39 4.35
2813 3334 8.084684 GTCACTTCTTGAAATAATTGAAAGGCT 58.915 33.333 0.00 0.00 35.39 4.58
2814 3335 8.084073 TCACTTCTTGAAATAATTGAAAGGCTG 58.916 33.333 0.00 0.00 0.00 4.85
2815 3336 8.084073 CACTTCTTGAAATAATTGAAAGGCTGA 58.916 33.333 0.00 0.00 0.00 4.26
2816 3337 8.641541 ACTTCTTGAAATAATTGAAAGGCTGAA 58.358 29.630 0.00 0.00 0.00 3.02
2817 3338 9.480053 CTTCTTGAAATAATTGAAAGGCTGAAA 57.520 29.630 0.00 0.00 0.00 2.69
2819 3340 9.643693 TCTTGAAATAATTGAAAGGCTGAAATC 57.356 29.630 0.00 0.00 0.00 2.17
2820 3341 9.426837 CTTGAAATAATTGAAAGGCTGAAATCA 57.573 29.630 0.00 0.00 0.00 2.57
2821 3342 8.761575 TGAAATAATTGAAAGGCTGAAATCAC 57.238 30.769 0.00 0.00 0.00 3.06
2822 3343 8.587608 TGAAATAATTGAAAGGCTGAAATCACT 58.412 29.630 0.00 0.00 0.00 3.41
2823 3344 9.428097 GAAATAATTGAAAGGCTGAAATCACTT 57.572 29.630 0.00 0.00 0.00 3.16
2824 3345 9.783081 AAATAATTGAAAGGCTGAAATCACTTT 57.217 25.926 0.00 0.00 35.99 2.66
2856 3377 9.807649 AAATCATGATATTTTTGTAAGGACTGC 57.192 29.630 9.04 0.00 0.00 4.40
2857 3378 7.936496 TCATGATATTTTTGTAAGGACTGCA 57.064 32.000 0.00 0.00 0.00 4.41
2858 3379 8.347004 TCATGATATTTTTGTAAGGACTGCAA 57.653 30.769 0.00 0.00 0.00 4.08
2859 3380 8.243426 TCATGATATTTTTGTAAGGACTGCAAC 58.757 33.333 0.00 0.00 0.00 4.17
2860 3381 7.517614 TGATATTTTTGTAAGGACTGCAACA 57.482 32.000 0.00 0.00 0.00 3.33
2861 3382 8.121305 TGATATTTTTGTAAGGACTGCAACAT 57.879 30.769 0.00 0.00 0.00 2.71
2862 3383 8.028354 TGATATTTTTGTAAGGACTGCAACATG 58.972 33.333 0.00 0.00 0.00 3.21
2863 3384 5.590530 TTTTTGTAAGGACTGCAACATGT 57.409 34.783 0.00 0.00 0.00 3.21
2864 3385 4.566545 TTTGTAAGGACTGCAACATGTG 57.433 40.909 0.00 0.00 0.00 3.21
2865 3386 2.503331 TGTAAGGACTGCAACATGTGG 58.497 47.619 0.00 0.00 0.00 4.17
2866 3387 1.812571 GTAAGGACTGCAACATGTGGG 59.187 52.381 0.00 0.00 0.00 4.61
2867 3388 0.478072 AAGGACTGCAACATGTGGGA 59.522 50.000 0.00 0.00 0.00 4.37
2868 3389 0.478072 AGGACTGCAACATGTGGGAA 59.522 50.000 0.00 0.00 0.00 3.97
2869 3390 0.883833 GGACTGCAACATGTGGGAAG 59.116 55.000 0.00 1.19 0.00 3.46
2870 3391 1.609208 GACTGCAACATGTGGGAAGT 58.391 50.000 10.44 10.44 0.00 3.01
2871 3392 2.552155 GGACTGCAACATGTGGGAAGTA 60.552 50.000 10.58 0.00 0.00 2.24
2872 3393 3.146066 GACTGCAACATGTGGGAAGTAA 58.854 45.455 10.58 0.00 0.00 2.24
2873 3394 3.758554 GACTGCAACATGTGGGAAGTAAT 59.241 43.478 10.58 0.00 0.00 1.89
2874 3395 4.151883 ACTGCAACATGTGGGAAGTAATT 58.848 39.130 9.18 0.00 0.00 1.40
2875 3396 4.022068 ACTGCAACATGTGGGAAGTAATTG 60.022 41.667 9.18 0.00 0.00 2.32
2876 3397 4.148079 TGCAACATGTGGGAAGTAATTGA 58.852 39.130 0.00 0.00 0.00 2.57
2877 3398 4.586421 TGCAACATGTGGGAAGTAATTGAA 59.414 37.500 0.00 0.00 0.00 2.69
2878 3399 5.069648 TGCAACATGTGGGAAGTAATTGAAA 59.930 36.000 0.00 0.00 0.00 2.69
2879 3400 6.165577 GCAACATGTGGGAAGTAATTGAAAT 58.834 36.000 0.00 0.00 0.00 2.17
2880 3401 6.311200 GCAACATGTGGGAAGTAATTGAAATC 59.689 38.462 0.00 0.00 0.00 2.17
2881 3402 6.194796 ACATGTGGGAAGTAATTGAAATCG 57.805 37.500 0.00 0.00 0.00 3.34
2882 3403 4.695217 TGTGGGAAGTAATTGAAATCGC 57.305 40.909 0.00 0.00 0.00 4.58
2883 3404 4.331968 TGTGGGAAGTAATTGAAATCGCT 58.668 39.130 0.00 0.00 0.00 4.93
2884 3405 4.764823 TGTGGGAAGTAATTGAAATCGCTT 59.235 37.500 0.00 0.00 0.00 4.68
2885 3406 5.242838 TGTGGGAAGTAATTGAAATCGCTTT 59.757 36.000 0.00 0.00 0.00 3.51
2886 3407 6.156519 GTGGGAAGTAATTGAAATCGCTTTT 58.843 36.000 0.00 0.00 0.00 2.27
2887 3408 6.645003 GTGGGAAGTAATTGAAATCGCTTTTT 59.355 34.615 0.00 0.00 0.00 1.94
2888 3409 7.810759 GTGGGAAGTAATTGAAATCGCTTTTTA 59.189 33.333 0.00 0.00 0.00 1.52
2889 3410 8.026607 TGGGAAGTAATTGAAATCGCTTTTTAG 58.973 33.333 0.00 0.00 0.00 1.85
2890 3411 8.241367 GGGAAGTAATTGAAATCGCTTTTTAGA 58.759 33.333 0.00 0.00 0.00 2.10
2891 3412 9.620660 GGAAGTAATTGAAATCGCTTTTTAGAA 57.379 29.630 0.00 0.00 0.00 2.10
2893 3414 9.959749 AAGTAATTGAAATCGCTTTTTAGAACA 57.040 25.926 0.00 0.00 0.00 3.18
2897 3418 9.474920 AATTGAAATCGCTTTTTAGAACATTGA 57.525 25.926 0.00 0.00 0.00 2.57
2898 3419 8.864069 TTGAAATCGCTTTTTAGAACATTGAA 57.136 26.923 0.00 0.00 0.00 2.69
2899 3420 8.864069 TGAAATCGCTTTTTAGAACATTGAAA 57.136 26.923 0.00 0.00 0.00 2.69
2900 3421 9.307121 TGAAATCGCTTTTTAGAACATTGAAAA 57.693 25.926 0.00 0.00 0.00 2.29
2901 3422 9.567917 GAAATCGCTTTTTAGAACATTGAAAAC 57.432 29.630 0.00 0.00 0.00 2.43
2902 3423 8.871686 AATCGCTTTTTAGAACATTGAAAACT 57.128 26.923 0.00 0.00 0.00 2.66
2903 3424 8.871686 ATCGCTTTTTAGAACATTGAAAACTT 57.128 26.923 0.00 0.00 0.00 2.66
2904 3425 8.696410 TCGCTTTTTAGAACATTGAAAACTTT 57.304 26.923 0.00 0.00 0.00 2.66
2905 3426 9.145865 TCGCTTTTTAGAACATTGAAAACTTTT 57.854 25.926 0.00 0.00 0.00 2.27
3436 3957 1.850441 CACGCTTACCGAGAAATACCG 59.150 52.381 0.00 0.00 41.02 4.02
3437 3958 1.745087 ACGCTTACCGAGAAATACCGA 59.255 47.619 0.00 0.00 41.02 4.69
3438 3959 2.164219 ACGCTTACCGAGAAATACCGAA 59.836 45.455 0.00 0.00 41.02 4.30
3439 3960 2.533129 CGCTTACCGAGAAATACCGAAC 59.467 50.000 0.00 0.00 40.02 3.95
3440 3961 3.514645 GCTTACCGAGAAATACCGAACA 58.485 45.455 0.00 0.00 0.00 3.18
3441 3962 4.117685 GCTTACCGAGAAATACCGAACAT 58.882 43.478 0.00 0.00 0.00 2.71
3442 3963 5.284079 GCTTACCGAGAAATACCGAACATA 58.716 41.667 0.00 0.00 0.00 2.29
3443 3964 5.924825 GCTTACCGAGAAATACCGAACATAT 59.075 40.000 0.00 0.00 0.00 1.78
3444 3965 6.423001 GCTTACCGAGAAATACCGAACATATT 59.577 38.462 0.00 0.00 0.00 1.28
3445 3966 7.042254 GCTTACCGAGAAATACCGAACATATTT 60.042 37.037 0.00 0.00 35.43 1.40
3446 3967 8.721019 TTACCGAGAAATACCGAACATATTTT 57.279 30.769 0.00 0.00 33.39 1.82
3447 3968 7.242914 ACCGAGAAATACCGAACATATTTTC 57.757 36.000 0.00 0.00 33.39 2.29
3448 3969 6.019318 ACCGAGAAATACCGAACATATTTTCG 60.019 38.462 15.46 15.46 46.46 3.46
3512 4033 9.290988 TGACTAGATATAGATGAGACTTGAACC 57.709 37.037 0.33 0.00 0.00 3.62
3513 4034 8.330466 ACTAGATATAGATGAGACTTGAACCG 57.670 38.462 0.33 0.00 0.00 4.44
3514 4035 7.940137 ACTAGATATAGATGAGACTTGAACCGT 59.060 37.037 0.33 0.00 0.00 4.83
3515 4036 9.438228 CTAGATATAGATGAGACTTGAACCGTA 57.562 37.037 0.00 0.00 0.00 4.02
3516 4037 8.693120 AGATATAGATGAGACTTGAACCGTAA 57.307 34.615 0.00 0.00 0.00 3.18
3517 4038 9.132923 AGATATAGATGAGACTTGAACCGTAAA 57.867 33.333 0.00 0.00 0.00 2.01
3518 4039 9.915629 GATATAGATGAGACTTGAACCGTAAAT 57.084 33.333 0.00 0.00 0.00 1.40
3522 4043 8.252964 AGATGAGACTTGAACCGTAAATTAAC 57.747 34.615 0.00 0.00 0.00 2.01
3523 4044 7.876068 AGATGAGACTTGAACCGTAAATTAACA 59.124 33.333 0.00 0.00 0.00 2.41
3524 4045 7.416154 TGAGACTTGAACCGTAAATTAACAG 57.584 36.000 0.00 0.00 0.00 3.16
3525 4046 7.211573 TGAGACTTGAACCGTAAATTAACAGA 58.788 34.615 0.00 0.00 0.00 3.41
3526 4047 7.711772 TGAGACTTGAACCGTAAATTAACAGAA 59.288 33.333 0.00 0.00 0.00 3.02
3527 4048 8.441312 AGACTTGAACCGTAAATTAACAGAAA 57.559 30.769 0.00 0.00 0.00 2.52
3528 4049 8.895737 AGACTTGAACCGTAAATTAACAGAAAA 58.104 29.630 0.00 0.00 0.00 2.29
3529 4050 9.166126 GACTTGAACCGTAAATTAACAGAAAAG 57.834 33.333 0.00 0.00 0.00 2.27
3530 4051 8.680001 ACTTGAACCGTAAATTAACAGAAAAGT 58.320 29.630 0.00 0.00 0.00 2.66
3531 4052 8.844441 TTGAACCGTAAATTAACAGAAAAGTG 57.156 30.769 0.00 0.00 0.00 3.16
3532 4053 8.211116 TGAACCGTAAATTAACAGAAAAGTGA 57.789 30.769 0.00 0.00 0.00 3.41
3533 4054 8.842280 TGAACCGTAAATTAACAGAAAAGTGAT 58.158 29.630 0.00 0.00 0.00 3.06
3534 4055 9.113876 GAACCGTAAATTAACAGAAAAGTGATG 57.886 33.333 0.00 0.00 0.00 3.07
3535 4056 7.590279 ACCGTAAATTAACAGAAAAGTGATGG 58.410 34.615 0.00 0.00 0.00 3.51
3536 4057 7.229907 ACCGTAAATTAACAGAAAAGTGATGGT 59.770 33.333 0.00 0.00 0.00 3.55
3537 4058 8.723311 CCGTAAATTAACAGAAAAGTGATGGTA 58.277 33.333 0.00 0.00 0.00 3.25
3542 4063 9.965902 AATTAACAGAAAAGTGATGGTATCTCT 57.034 29.630 0.00 0.00 34.83 3.10
3543 4064 8.777865 TTAACAGAAAAGTGATGGTATCTCTG 57.222 34.615 0.00 0.00 33.75 3.35
3544 4065 6.365970 ACAGAAAAGTGATGGTATCTCTGT 57.634 37.500 0.00 0.00 37.91 3.41
3545 4066 6.169094 ACAGAAAAGTGATGGTATCTCTGTG 58.831 40.000 8.80 2.74 40.44 3.66
3546 4067 5.583854 CAGAAAAGTGATGGTATCTCTGTGG 59.416 44.000 0.00 0.00 33.75 4.17
3547 4068 5.485353 AGAAAAGTGATGGTATCTCTGTGGA 59.515 40.000 0.00 0.00 33.75 4.02
3548 4069 5.762179 AAAGTGATGGTATCTCTGTGGAA 57.238 39.130 0.00 0.00 33.75 3.53
3549 4070 5.762179 AAGTGATGGTATCTCTGTGGAAA 57.238 39.130 0.00 0.00 33.75 3.13
3550 4071 5.091261 AGTGATGGTATCTCTGTGGAAAC 57.909 43.478 0.00 0.00 32.37 2.78
3551 4072 4.780021 AGTGATGGTATCTCTGTGGAAACT 59.220 41.667 0.00 0.00 32.37 2.66
3552 4073 5.105146 AGTGATGGTATCTCTGTGGAAACTC 60.105 44.000 0.00 0.00 32.37 3.01
3553 4074 5.026121 TGATGGTATCTCTGTGGAAACTCT 58.974 41.667 0.00 0.00 0.00 3.24
3554 4075 4.808414 TGGTATCTCTGTGGAAACTCTG 57.192 45.455 0.00 0.00 0.00 3.35
3555 4076 3.055819 TGGTATCTCTGTGGAAACTCTGC 60.056 47.826 0.00 0.00 0.00 4.26
3556 4077 3.055819 GGTATCTCTGTGGAAACTCTGCA 60.056 47.826 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 3.752222 ACACGAGACTCAGTTAGTTCGAT 59.248 43.478 2.82 2.70 39.07 3.59
93 94 5.024118 CCTTATCCCAATCTAGTCCGGTAT 58.976 45.833 0.00 0.00 0.00 2.73
181 182 5.912149 ATGAGGGTATCCAAGCATTTAGA 57.088 39.130 0.00 0.00 34.83 2.10
261 262 5.809562 CGCATTATTTTTGGCCAAACATCTA 59.190 36.000 30.43 19.54 0.00 1.98
263 264 4.727448 GCGCATTATTTTTGGCCAAACATC 60.727 41.667 30.43 15.48 0.00 3.06
264 265 3.126686 GCGCATTATTTTTGGCCAAACAT 59.873 39.130 30.43 29.05 0.00 2.71
270 271 5.064579 AGTTTAATGCGCATTATTTTTGGCC 59.935 36.000 36.01 19.70 33.71 5.36
1644 2125 3.480470 CATGGTTGTCTTGTTCAGGAGT 58.520 45.455 0.00 0.00 0.00 3.85
1716 2197 3.519973 CTGCCACCTCAGCACGACA 62.520 63.158 0.00 0.00 36.01 4.35
1883 2364 3.195698 GGAAGACGGCCATGTCGC 61.196 66.667 2.24 0.99 43.70 5.19
1966 2447 1.431036 GGCTCAAATTCAGCTCCGC 59.569 57.895 8.77 0.00 37.05 5.54
2148 2647 5.163468 CCTGAGCTGCTTGTAGAAGATCTTA 60.163 44.000 8.25 0.00 37.21 2.10
2267 2770 3.401033 TGTACAACTGCATGCTGTACT 57.599 42.857 31.88 22.29 44.30 2.73
2327 2839 1.911766 TCCCTCACCCACTTCGTCC 60.912 63.158 0.00 0.00 0.00 4.79
2331 2843 0.693049 ACATGTCCCTCACCCACTTC 59.307 55.000 0.00 0.00 0.00 3.01
2376 2888 2.107141 CTTGGCTCGGATCCGGAC 59.893 66.667 32.79 25.01 40.25 4.79
2386 2898 1.275421 AAGTAGGCTCCCCTTGGCTC 61.275 60.000 0.00 0.00 42.87 4.70
2467 2979 2.270527 GGCCTTGGTGAGCCTCTC 59.729 66.667 0.00 0.00 46.14 3.20
2567 3083 4.499865 GCTGGTTCAAAAGGAGGAGAAAAC 60.500 45.833 0.00 0.00 0.00 2.43
2586 3102 7.432350 TTTAACCAAAATATTTTGCAGCTGG 57.568 32.000 28.17 19.69 44.62 4.85
2611 3127 3.149196 CAGGCCACAACAAGTAAGATGT 58.851 45.455 5.01 0.00 0.00 3.06
2619 3139 1.300388 GCTTGCAGGCCACAACAAG 60.300 57.895 10.18 17.75 41.89 3.16
2629 3149 1.880027 AGTAAAACGAAGGCTTGCAGG 59.120 47.619 3.46 0.00 0.00 4.85
2652 3172 6.935240 ATACAGTACCTACCATGCATGTAT 57.065 37.500 24.58 14.92 0.00 2.29
2653 3173 7.893833 AGATATACAGTACCTACCATGCATGTA 59.106 37.037 24.58 15.31 0.00 2.29
2654 3174 6.726299 AGATATACAGTACCTACCATGCATGT 59.274 38.462 24.58 15.01 0.00 3.21
2655 3175 7.175347 AGATATACAGTACCTACCATGCATG 57.825 40.000 20.19 20.19 0.00 4.06
2787 3308 8.084684 AGCCTTTCAATTATTTCAAGAAGTGAC 58.915 33.333 0.00 0.00 34.52 3.67
2796 3317 8.587608 AGTGATTTCAGCCTTTCAATTATTTCA 58.412 29.630 0.00 0.00 0.00 2.69
2797 3318 8.992835 AGTGATTTCAGCCTTTCAATTATTTC 57.007 30.769 0.00 0.00 0.00 2.17
2830 3351 9.807649 GCAGTCCTTACAAAAATATCATGATTT 57.192 29.630 14.65 2.68 0.00 2.17
2831 3352 8.970020 TGCAGTCCTTACAAAAATATCATGATT 58.030 29.630 14.65 0.00 0.00 2.57
2832 3353 8.523915 TGCAGTCCTTACAAAAATATCATGAT 57.476 30.769 13.81 13.81 0.00 2.45
2833 3354 7.936496 TGCAGTCCTTACAAAAATATCATGA 57.064 32.000 0.00 0.00 0.00 3.07
2834 3355 8.028354 TGTTGCAGTCCTTACAAAAATATCATG 58.972 33.333 0.00 0.00 0.00 3.07
2835 3356 8.121305 TGTTGCAGTCCTTACAAAAATATCAT 57.879 30.769 0.00 0.00 0.00 2.45
2836 3357 7.517614 TGTTGCAGTCCTTACAAAAATATCA 57.482 32.000 0.00 0.00 0.00 2.15
2837 3358 8.028938 ACATGTTGCAGTCCTTACAAAAATATC 58.971 33.333 0.00 0.00 0.00 1.63
2838 3359 7.814107 CACATGTTGCAGTCCTTACAAAAATAT 59.186 33.333 0.00 0.00 0.00 1.28
2839 3360 7.144661 CACATGTTGCAGTCCTTACAAAAATA 58.855 34.615 0.00 0.00 0.00 1.40
2840 3361 5.984926 CACATGTTGCAGTCCTTACAAAAAT 59.015 36.000 0.00 0.00 0.00 1.82
2841 3362 5.347342 CACATGTTGCAGTCCTTACAAAAA 58.653 37.500 0.00 0.00 0.00 1.94
2842 3363 4.202101 CCACATGTTGCAGTCCTTACAAAA 60.202 41.667 0.00 0.00 0.00 2.44
2843 3364 3.317711 CCACATGTTGCAGTCCTTACAAA 59.682 43.478 0.00 0.00 0.00 2.83
2844 3365 2.884012 CCACATGTTGCAGTCCTTACAA 59.116 45.455 0.00 0.00 0.00 2.41
2845 3366 2.503331 CCACATGTTGCAGTCCTTACA 58.497 47.619 0.00 0.00 0.00 2.41
2846 3367 1.812571 CCCACATGTTGCAGTCCTTAC 59.187 52.381 0.00 0.00 0.00 2.34
2847 3368 1.702401 TCCCACATGTTGCAGTCCTTA 59.298 47.619 0.00 0.00 0.00 2.69
2848 3369 0.478072 TCCCACATGTTGCAGTCCTT 59.522 50.000 0.00 0.00 0.00 3.36
2849 3370 0.478072 TTCCCACATGTTGCAGTCCT 59.522 50.000 0.00 0.00 0.00 3.85
2850 3371 0.883833 CTTCCCACATGTTGCAGTCC 59.116 55.000 0.00 0.00 0.00 3.85
2851 3372 1.609208 ACTTCCCACATGTTGCAGTC 58.391 50.000 0.00 0.00 0.00 3.51
2852 3373 2.949177 TACTTCCCACATGTTGCAGT 57.051 45.000 0.00 0.00 0.00 4.40
2853 3374 4.218200 TCAATTACTTCCCACATGTTGCAG 59.782 41.667 0.00 0.00 0.00 4.41
2854 3375 4.148079 TCAATTACTTCCCACATGTTGCA 58.852 39.130 0.00 0.00 0.00 4.08
2855 3376 4.782019 TCAATTACTTCCCACATGTTGC 57.218 40.909 0.00 0.00 0.00 4.17
2856 3377 6.527722 CGATTTCAATTACTTCCCACATGTTG 59.472 38.462 0.00 0.00 0.00 3.33
2857 3378 6.620678 CGATTTCAATTACTTCCCACATGTT 58.379 36.000 0.00 0.00 0.00 2.71
2858 3379 5.393027 GCGATTTCAATTACTTCCCACATGT 60.393 40.000 0.00 0.00 0.00 3.21
2859 3380 5.036737 GCGATTTCAATTACTTCCCACATG 58.963 41.667 0.00 0.00 0.00 3.21
2860 3381 4.949856 AGCGATTTCAATTACTTCCCACAT 59.050 37.500 0.00 0.00 0.00 3.21
2861 3382 4.331968 AGCGATTTCAATTACTTCCCACA 58.668 39.130 0.00 0.00 0.00 4.17
2862 3383 4.965119 AGCGATTTCAATTACTTCCCAC 57.035 40.909 0.00 0.00 0.00 4.61
2863 3384 5.975693 AAAGCGATTTCAATTACTTCCCA 57.024 34.783 0.00 0.00 0.00 4.37
2864 3385 8.241367 TCTAAAAAGCGATTTCAATTACTTCCC 58.759 33.333 0.00 0.00 0.00 3.97
2865 3386 9.620660 TTCTAAAAAGCGATTTCAATTACTTCC 57.379 29.630 0.00 0.00 0.00 3.46
2867 3388 9.959749 TGTTCTAAAAAGCGATTTCAATTACTT 57.040 25.926 0.00 0.00 0.00 2.24
2871 3392 9.474920 TCAATGTTCTAAAAAGCGATTTCAATT 57.525 25.926 0.00 0.00 0.00 2.32
2872 3393 9.474920 TTCAATGTTCTAAAAAGCGATTTCAAT 57.525 25.926 0.00 0.00 0.00 2.57
2873 3394 8.864069 TTCAATGTTCTAAAAAGCGATTTCAA 57.136 26.923 0.00 0.00 0.00 2.69
2874 3395 8.864069 TTTCAATGTTCTAAAAAGCGATTTCA 57.136 26.923 0.00 0.00 0.00 2.69
2875 3396 9.567917 GTTTTCAATGTTCTAAAAAGCGATTTC 57.432 29.630 0.00 0.00 0.00 2.17
2876 3397 9.313118 AGTTTTCAATGTTCTAAAAAGCGATTT 57.687 25.926 0.00 0.00 0.00 2.17
2877 3398 8.871686 AGTTTTCAATGTTCTAAAAAGCGATT 57.128 26.923 0.00 0.00 0.00 3.34
2878 3399 8.871686 AAGTTTTCAATGTTCTAAAAAGCGAT 57.128 26.923 0.00 0.00 0.00 4.58
2879 3400 8.696410 AAAGTTTTCAATGTTCTAAAAAGCGA 57.304 26.923 0.00 0.00 0.00 4.93
3416 3937 1.850441 CGGTATTTCTCGGTAAGCGTG 59.150 52.381 0.00 0.00 0.00 5.34
3417 3938 1.745087 TCGGTATTTCTCGGTAAGCGT 59.255 47.619 0.00 0.00 33.20 5.07
3418 3939 2.480224 TCGGTATTTCTCGGTAAGCG 57.520 50.000 0.00 0.00 0.00 4.68
3419 3940 3.514645 TGTTCGGTATTTCTCGGTAAGC 58.485 45.455 0.00 0.00 0.00 3.09
3420 3941 7.941795 AATATGTTCGGTATTTCTCGGTAAG 57.058 36.000 0.00 0.00 0.00 2.34
3421 3942 8.721019 AAAATATGTTCGGTATTTCTCGGTAA 57.279 30.769 0.00 0.00 32.21 2.85
3422 3943 7.167968 CGAAAATATGTTCGGTATTTCTCGGTA 59.832 37.037 18.58 0.00 45.21 4.02
3423 3944 6.019318 CGAAAATATGTTCGGTATTTCTCGGT 60.019 38.462 18.58 0.00 45.21 4.69
3424 3945 6.352526 CGAAAATATGTTCGGTATTTCTCGG 58.647 40.000 18.58 0.00 45.21 4.63
3486 4007 9.290988 GGTTCAAGTCTCATCTATATCTAGTCA 57.709 37.037 0.00 0.00 0.00 3.41
3487 4008 8.447833 CGGTTCAAGTCTCATCTATATCTAGTC 58.552 40.741 0.00 0.00 0.00 2.59
3488 4009 7.940137 ACGGTTCAAGTCTCATCTATATCTAGT 59.060 37.037 0.00 0.00 0.00 2.57
3489 4010 8.330466 ACGGTTCAAGTCTCATCTATATCTAG 57.670 38.462 0.00 0.00 0.00 2.43
3490 4011 9.788889 TTACGGTTCAAGTCTCATCTATATCTA 57.211 33.333 0.00 0.00 0.00 1.98
3491 4012 8.693120 TTACGGTTCAAGTCTCATCTATATCT 57.307 34.615 0.00 0.00 0.00 1.98
3492 4013 9.915629 ATTTACGGTTCAAGTCTCATCTATATC 57.084 33.333 0.00 0.00 0.00 1.63
3496 4017 9.362539 GTTAATTTACGGTTCAAGTCTCATCTA 57.637 33.333 0.00 0.00 0.00 1.98
3497 4018 7.876068 TGTTAATTTACGGTTCAAGTCTCATCT 59.124 33.333 0.00 0.00 0.00 2.90
3498 4019 8.025243 TGTTAATTTACGGTTCAAGTCTCATC 57.975 34.615 0.00 0.00 0.00 2.92
3499 4020 7.876068 TCTGTTAATTTACGGTTCAAGTCTCAT 59.124 33.333 3.51 0.00 0.00 2.90
3500 4021 7.211573 TCTGTTAATTTACGGTTCAAGTCTCA 58.788 34.615 3.51 0.00 0.00 3.27
3501 4022 7.647907 TCTGTTAATTTACGGTTCAAGTCTC 57.352 36.000 3.51 0.00 0.00 3.36
3502 4023 8.441312 TTTCTGTTAATTTACGGTTCAAGTCT 57.559 30.769 3.51 0.00 0.00 3.24
3503 4024 9.166126 CTTTTCTGTTAATTTACGGTTCAAGTC 57.834 33.333 3.51 0.00 0.00 3.01
3504 4025 8.680001 ACTTTTCTGTTAATTTACGGTTCAAGT 58.320 29.630 3.51 7.30 0.00 3.16
3505 4026 8.953990 CACTTTTCTGTTAATTTACGGTTCAAG 58.046 33.333 3.51 6.81 0.00 3.02
3506 4027 8.675504 TCACTTTTCTGTTAATTTACGGTTCAA 58.324 29.630 3.51 0.00 0.00 2.69
3507 4028 8.211116 TCACTTTTCTGTTAATTTACGGTTCA 57.789 30.769 3.51 0.00 0.00 3.18
3508 4029 9.113876 CATCACTTTTCTGTTAATTTACGGTTC 57.886 33.333 3.51 0.00 0.00 3.62
3509 4030 8.079809 CCATCACTTTTCTGTTAATTTACGGTT 58.920 33.333 3.51 0.00 0.00 4.44
3510 4031 7.229907 ACCATCACTTTTCTGTTAATTTACGGT 59.770 33.333 3.51 0.00 0.00 4.83
3511 4032 7.590279 ACCATCACTTTTCTGTTAATTTACGG 58.410 34.615 0.00 0.00 0.00 4.02
3516 4037 9.965902 AGAGATACCATCACTTTTCTGTTAATT 57.034 29.630 0.00 0.00 0.00 1.40
3517 4038 9.388506 CAGAGATACCATCACTTTTCTGTTAAT 57.611 33.333 0.00 0.00 0.00 1.40
3518 4039 8.375506 ACAGAGATACCATCACTTTTCTGTTAA 58.624 33.333 0.00 0.00 36.82 2.01
3519 4040 7.819415 CACAGAGATACCATCACTTTTCTGTTA 59.181 37.037 1.41 0.00 37.57 2.41
3520 4041 6.652481 CACAGAGATACCATCACTTTTCTGTT 59.348 38.462 1.41 0.00 37.57 3.16
3521 4042 6.169094 CACAGAGATACCATCACTTTTCTGT 58.831 40.000 0.00 0.00 39.14 3.41
3522 4043 5.583854 CCACAGAGATACCATCACTTTTCTG 59.416 44.000 0.00 0.00 34.56 3.02
3523 4044 5.485353 TCCACAGAGATACCATCACTTTTCT 59.515 40.000 0.00 0.00 0.00 2.52
3524 4045 5.734720 TCCACAGAGATACCATCACTTTTC 58.265 41.667 0.00 0.00 0.00 2.29
3525 4046 5.762179 TCCACAGAGATACCATCACTTTT 57.238 39.130 0.00 0.00 0.00 2.27
3526 4047 5.762179 TTCCACAGAGATACCATCACTTT 57.238 39.130 0.00 0.00 0.00 2.66
3527 4048 5.249393 AGTTTCCACAGAGATACCATCACTT 59.751 40.000 0.00 0.00 0.00 3.16
3528 4049 4.780021 AGTTTCCACAGAGATACCATCACT 59.220 41.667 0.00 0.00 0.00 3.41
3529 4050 5.091261 AGTTTCCACAGAGATACCATCAC 57.909 43.478 0.00 0.00 0.00 3.06
3530 4051 5.026121 AGAGTTTCCACAGAGATACCATCA 58.974 41.667 0.00 0.00 0.00 3.07
3531 4052 5.355596 CAGAGTTTCCACAGAGATACCATC 58.644 45.833 0.00 0.00 0.00 3.51
3532 4053 4.383552 GCAGAGTTTCCACAGAGATACCAT 60.384 45.833 0.00 0.00 0.00 3.55
3533 4054 3.055819 GCAGAGTTTCCACAGAGATACCA 60.056 47.826 0.00 0.00 0.00 3.25
3534 4055 3.055819 TGCAGAGTTTCCACAGAGATACC 60.056 47.826 0.00 0.00 0.00 2.73
3535 4056 4.193826 TGCAGAGTTTCCACAGAGATAC 57.806 45.455 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.