Multiple sequence alignment - TraesCS4A01G221800

Loading Multiple Alignment...

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 TraesCS4A01G221800 chr4A 100.000 2977 0 0 1 2977 527577790 527574814 0.000000e+00 5498.0
1 TraesCS4A01G221800 chr4A 96.262 107 4 0 780 886 527576949 527576843 3.050000e-40 176.0
2 TraesCS4A01G221800 chr4A 96.262 107 4 0 842 948 527577011 527576905 3.050000e-40 176.0
3 TraesCS4A01G221800 chr4A 93.333 45 3 0 780 824 527576887 527576843 1.920000e-07 67.6
4 TraesCS4A01G221800 chr4A 93.333 45 3 0 904 948 527577011 527576967 1.920000e-07 67.6
5 TraesCS4A01G221800 chr2D 94.213 1175 64 2 915 2085 348076644 348075470 0.000000e+00 1790.0
6 TraesCS4A01G221800 chr2D 97.123 730 18 2 1 730 348077526 348076800 0.000000e+00 1229.0
7 TraesCS4A01G221800 chr2D 84.858 634 68 16 2258 2886 348075382 348074772 5.450000e-172 614.0
8 TraesCS4A01G221800 chr3A 93.713 1177 52 5 912 2085 323385441 323386598 0.000000e+00 1744.0
9 TraesCS4A01G221800 chr3A 96.164 730 27 1 1 730 323384550 323385278 0.000000e+00 1192.0
10 TraesCS4A01G221800 chr3A 96.429 56 2 0 674 729 323385282 323385337 3.160000e-15 93.5
11 TraesCS4A01G221800 chr3D 92.438 1177 59 6 912 2085 75767465 75766316 0.000000e+00 1653.0
12 TraesCS4A01G221800 chr3D 96.301 730 26 1 1 730 75768356 75767628 0.000000e+00 1197.0
13 TraesCS4A01G221800 chr3D 83.696 644 80 13 2249 2886 75766240 75765616 4.280000e-163 584.0
14 TraesCS4A01G221800 chr3D 94.643 56 3 0 674 729 75767624 75767569 1.470000e-13 87.9
15 TraesCS4A01G221800 chr1A 95.175 912 41 1 913 1821 41412468 41413379 0.000000e+00 1437.0
16 TraesCS4A01G221800 chr1A 95.066 912 42 1 913 1821 41319856 41318945 0.000000e+00 1432.0
17 TraesCS4A01G221800 chr1A 88.230 1130 99 21 965 2084 330762582 330761477 0.000000e+00 1319.0
18 TraesCS4A01G221800 chr1A 96.438 730 25 1 1 730 41320748 41320020 0.000000e+00 1203.0
19 TraesCS4A01G221800 chr1A 96.301 730 26 1 1 730 41411576 41412304 0.000000e+00 1197.0
20 TraesCS4A01G221800 chr1A 92.074 757 43 7 1 741 330763513 330762758 0.000000e+00 1050.0
21 TraesCS4A01G221800 chr1A 96.429 56 2 0 674 729 41320016 41319961 3.160000e-15 93.5
22 TraesCS4A01G221800 chr1A 96.429 56 2 0 674 729 41412308 41412363 3.160000e-15 93.5
23 TraesCS4A01G221800 chr5D 96.576 847 27 2 2036 2882 51196211 51195367 0.000000e+00 1402.0
24 TraesCS4A01G221800 chr5D 96.240 851 27 2 2036 2882 51156720 51155871 0.000000e+00 1389.0
25 TraesCS4A01G221800 chr5D 95.887 851 30 2 2036 2882 51119301 51118452 0.000000e+00 1373.0
26 TraesCS4A01G221800 chr5D 95.566 857 27 2 2036 2882 51177224 51176369 0.000000e+00 1362.0
27 TraesCS4A01G221800 chr5D 84.009 863 103 23 2036 2882 240171092 240171935 0.000000e+00 797.0
28 TraesCS4A01G221800 chr2B 88.930 1093 94 16 966 2049 516099481 516100555 0.000000e+00 1323.0
29 TraesCS4A01G221800 chr2B 93.067 851 31 9 2036 2886 592573110 592573932 0.000000e+00 1219.0
30 TraesCS4A01G221800 chr2B 90.886 779 49 12 1 758 516098528 516099305 0.000000e+00 1026.0
31 TraesCS4A01G221800 chr2B 96.167 600 20 1 1489 2085 592572595 592573194 0.000000e+00 977.0
32 TraesCS4A01G221800 chr2B 91.496 635 48 2 1419 2047 198522323 198521689 0.000000e+00 869.0
33 TraesCS4A01G221800 chr2B 85.797 521 49 15 2038 2553 516100508 516101008 2.030000e-146 529.0
34 TraesCS4A01G221800 chr2B 95.977 174 7 0 1 174 198531467 198531294 1.750000e-72 283.0
35 TraesCS4A01G221800 chr1B 93.617 846 28 6 2037 2882 188444406 188445225 0.000000e+00 1240.0
36 TraesCS4A01G221800 chr1B 98.333 60 1 0 815 874 188444156 188444215 4.060000e-19 106.0
37 TraesCS4A01G221800 chr1B 100.000 33 0 0 780 812 188444183 188444215 8.910000e-06 62.1
38 TraesCS4A01G221800 chrUn 96.798 687 22 0 2196 2882 415626134 415625448 0.000000e+00 1147.0
39 TraesCS4A01G221800 chrUn 87.873 503 51 7 2387 2886 79709274 79709769 1.540000e-162 582.0
40 TraesCS4A01G221800 chr7A 90.594 808 50 19 1 785 219381488 219380684 0.000000e+00 1048.0
41 TraesCS4A01G221800 chr7A 86.301 949 88 21 1419 2356 219379897 219378980 0.000000e+00 994.0
42 TraesCS4A01G221800 chr7A 91.106 416 34 2 963 1375 219380408 219379993 7.210000e-156 560.0
43 TraesCS4A01G221800 chr6B 90.447 806 56 9 1 785 578015612 578016417 0.000000e+00 1042.0
44 TraesCS4A01G221800 chr6B 90.045 673 55 5 1419 2085 578017126 578017792 0.000000e+00 861.0
45 TraesCS4A01G221800 chr6B 90.376 426 37 3 963 1388 578016585 578017006 9.320000e-155 556.0
46 TraesCS4A01G221800 chr3B 91.085 673 48 5 1419 2085 52856605 52855939 0.000000e+00 900.0
47 TraesCS4A01G221800 chr4B 90.845 426 35 3 963 1388 369780769 369780348 4.310000e-158 568.0
48 TraesCS4A01G221800 chr5B 87.375 499 54 7 2387 2883 60976625 60977116 5.570000e-157 564.0


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 TraesCS4A01G221800 chr4A 527574814 527577790 2976 True 1197.040000 5498 95.838000 1 2977 5 chr4A.!!$R1 2976
1 TraesCS4A01G221800 chr2D 348074772 348077526 2754 True 1211.000000 1790 92.064667 1 2886 3 chr2D.!!$R1 2885
2 TraesCS4A01G221800 chr3A 323384550 323386598 2048 False 1009.833333 1744 95.435333 1 2085 3 chr3A.!!$F1 2084
3 TraesCS4A01G221800 chr3D 75765616 75768356 2740 True 880.475000 1653 91.769500 1 2886 4 chr3D.!!$R1 2885
4 TraesCS4A01G221800 chr1A 330761477 330763513 2036 True 1184.500000 1319 90.152000 1 2084 2 chr1A.!!$R2 2083
5 TraesCS4A01G221800 chr1A 41318945 41320748 1803 True 909.500000 1432 95.977667 1 1821 3 chr1A.!!$R1 1820
6 TraesCS4A01G221800 chr1A 41411576 41413379 1803 False 909.166667 1437 95.968333 1 1821 3 chr1A.!!$F1 1820
7 TraesCS4A01G221800 chr5D 51195367 51196211 844 True 1402.000000 1402 96.576000 2036 2882 1 chr5D.!!$R4 846
8 TraesCS4A01G221800 chr5D 51155871 51156720 849 True 1389.000000 1389 96.240000 2036 2882 1 chr5D.!!$R2 846
9 TraesCS4A01G221800 chr5D 51118452 51119301 849 True 1373.000000 1373 95.887000 2036 2882 1 chr5D.!!$R1 846
10 TraesCS4A01G221800 chr5D 51176369 51177224 855 True 1362.000000 1362 95.566000 2036 2882 1 chr5D.!!$R3 846
11 TraesCS4A01G221800 chr5D 240171092 240171935 843 False 797.000000 797 84.009000 2036 2882 1 chr5D.!!$F1 846
12 TraesCS4A01G221800 chr2B 592572595 592573932 1337 False 1098.000000 1219 94.617000 1489 2886 2 chr2B.!!$F2 1397
13 TraesCS4A01G221800 chr2B 516098528 516101008 2480 False 959.333333 1323 88.537667 1 2553 3 chr2B.!!$F1 2552
14 TraesCS4A01G221800 chr2B 198521689 198522323 634 True 869.000000 869 91.496000 1419 2047 1 chr2B.!!$R1 628
15 TraesCS4A01G221800 chr1B 188444156 188445225 1069 False 469.366667 1240 97.316667 780 2882 3 chr1B.!!$F1 2102
16 TraesCS4A01G221800 chrUn 415625448 415626134 686 True 1147.000000 1147 96.798000 2196 2882 1 chrUn.!!$R1 686
17 TraesCS4A01G221800 chr7A 219378980 219381488 2508 True 867.333333 1048 89.333667 1 2356 3 chr7A.!!$R1 2355
18 TraesCS4A01G221800 chr6B 578015612 578017792 2180 False 819.666667 1042 90.289333 1 2085 3 chr6B.!!$F1 2084
19 TraesCS4A01G221800 chr3B 52855939 52856605 666 True 900.000000 900 91.085000 1419 2085 1 chr3B.!!$R1 666

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
464 480 0.044855 AGCCTCACCACCCTTATCCT 59.955 55.0 0.0 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2036 2433 0.321653 GCACGGACACTCCATCCTTT 60.322 55.0 0.0 0.0 35.91 3.11 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
168 169 3.055385 GTCCCTGCAGGTATTAGTGAACA 60.055 47.826 30.63 0.00 36.75 3.18
205 221 6.417191 TTTGATCGTTTCATAACTACTGGC 57.583 37.500 0.00 0.00 33.34 4.85
297 313 3.555966 CCAGGGTTTCTTCCACCATATC 58.444 50.000 0.00 0.00 35.80 1.63
405 421 2.907897 GATCACGGTTGAGAGGGCGG 62.908 65.000 0.00 0.00 34.35 6.13
423 439 1.334869 CGGTTGCAGCTTTCAAGAACT 59.665 47.619 0.00 0.00 0.00 3.01
464 480 0.044855 AGCCTCACCACCCTTATCCT 59.955 55.000 0.00 0.00 0.00 3.24
567 583 2.887152 GAGCACACTTGGACTGGAAATT 59.113 45.455 0.00 0.00 0.00 1.82
759 815 9.203421 TGTAATGCACTATAAATAATCCTGTCG 57.797 33.333 0.00 0.00 0.00 4.35
771 827 0.605319 TCCTGTCGTGTGCCCAAATC 60.605 55.000 0.00 0.00 0.00 2.17
800 856 8.165239 ACATTTATGTTGCTGTTTAGACTTGA 57.835 30.769 0.00 0.00 37.90 3.02
801 857 8.796475 ACATTTATGTTGCTGTTTAGACTTGAT 58.204 29.630 0.00 0.00 37.90 2.57
857 913 9.781633 TTTTACTACCTTATGTTGCTGTTTAGA 57.218 29.630 0.00 0.00 0.00 2.10
860 916 7.450903 ACTACCTTATGTTGCTGTTTAGACTT 58.549 34.615 0.00 0.00 0.00 3.01
861 917 6.560253 ACCTTATGTTGCTGTTTAGACTTG 57.440 37.500 0.00 0.00 0.00 3.16
864 920 8.100791 ACCTTATGTTGCTGTTTAGACTTGATA 58.899 33.333 0.00 0.00 0.00 2.15
1017 1268 3.405093 GATGGCGGCTGATGGTGGA 62.405 63.158 11.43 0.00 0.00 4.02
1340 1594 4.534647 TGGGCCATATCAAGGTTTGTAT 57.465 40.909 0.00 0.00 0.00 2.29
1343 1597 5.830991 TGGGCCATATCAAGGTTTGTATTAC 59.169 40.000 0.00 0.00 0.00 1.89
1625 2014 6.314896 GTGGTTTTGAATTTGTTGTTGATGGA 59.685 34.615 0.00 0.00 0.00 3.41
1638 2027 4.478203 TGTTGATGGAAATGAACCTGGAA 58.522 39.130 0.00 0.00 0.00 3.53
1975 2372 1.077123 GAGACTCGTCGCACTCACTA 58.923 55.000 0.00 0.00 34.09 2.74
2212 2650 7.147320 CCATGCCCCTATATATGTGAAGGAATA 60.147 40.741 1.39 0.00 0.00 1.75
2592 3075 9.973450 TTCAATCAGCAAAGATATCTAGTCTAC 57.027 33.333 5.46 0.00 0.00 2.59
2601 3086 6.832520 AGATATCTAGTCTACAGTGCATGG 57.167 41.667 2.53 0.00 0.00 3.66
2759 3244 4.363991 AAATCTGAGTTGAGCCTGTCTT 57.636 40.909 0.00 0.00 0.00 3.01
2799 3284 6.313411 ACCAAACACACATTTCAACTCATTTG 59.687 34.615 0.00 0.00 36.42 2.32
2867 3353 0.253894 CATGACAGATGCACCCAGGA 59.746 55.000 0.00 0.00 0.00 3.86
2886 3372 0.601057 AAACCAAACACGCCCATAGC 59.399 50.000 0.00 0.00 38.52 2.97
2895 3381 4.225497 GCCCATAGCGCTTCTGTT 57.775 55.556 18.68 0.00 0.00 3.16
2896 3382 1.723870 GCCCATAGCGCTTCTGTTG 59.276 57.895 18.68 8.48 0.00 3.33
2897 3383 1.718757 GCCCATAGCGCTTCTGTTGG 61.719 60.000 18.68 14.92 32.33 3.77
2898 3384 0.107703 CCCATAGCGCTTCTGTTGGA 60.108 55.000 18.68 0.00 33.59 3.53
2899 3385 1.293924 CCATAGCGCTTCTGTTGGAG 58.706 55.000 18.68 0.00 33.59 3.86
2900 3386 1.134699 CCATAGCGCTTCTGTTGGAGA 60.135 52.381 18.68 0.00 33.59 3.71
2901 3387 2.484417 CCATAGCGCTTCTGTTGGAGAT 60.484 50.000 18.68 0.00 33.59 2.75
2902 3388 2.299993 TAGCGCTTCTGTTGGAGATG 57.700 50.000 18.68 0.00 0.00 2.90
2903 3389 1.023513 AGCGCTTCTGTTGGAGATGC 61.024 55.000 2.64 0.00 44.71 3.91
2904 3390 1.023513 GCGCTTCTGTTGGAGATGCT 61.024 55.000 0.00 0.00 45.55 3.79
2905 3391 1.005340 CGCTTCTGTTGGAGATGCTC 58.995 55.000 0.00 0.00 45.55 4.26
2906 3392 1.405256 CGCTTCTGTTGGAGATGCTCT 60.405 52.381 0.00 0.00 45.55 4.09
2907 3393 2.008329 GCTTCTGTTGGAGATGCTCTG 58.992 52.381 0.00 0.00 44.73 3.35
2908 3394 2.354503 GCTTCTGTTGGAGATGCTCTGA 60.355 50.000 0.00 0.00 44.73 3.27
2909 3395 3.523547 CTTCTGTTGGAGATGCTCTGAG 58.476 50.000 0.00 0.00 0.00 3.35
2910 3396 1.829849 TCTGTTGGAGATGCTCTGAGG 59.170 52.381 6.83 0.00 0.00 3.86
2911 3397 0.251354 TGTTGGAGATGCTCTGAGGC 59.749 55.000 6.83 0.00 0.00 4.70
2912 3398 0.463474 GTTGGAGATGCTCTGAGGCC 60.463 60.000 6.83 0.00 0.00 5.19
2913 3399 1.964608 TTGGAGATGCTCTGAGGCCG 61.965 60.000 6.83 0.00 0.00 6.13
2914 3400 2.130426 GGAGATGCTCTGAGGCCGA 61.130 63.158 6.83 0.00 0.00 5.54
2915 3401 1.067250 GAGATGCTCTGAGGCCGAC 59.933 63.158 6.83 0.00 0.00 4.79
2916 3402 2.279120 GATGCTCTGAGGCCGACG 60.279 66.667 6.83 0.00 0.00 5.12
2917 3403 3.069980 GATGCTCTGAGGCCGACGT 62.070 63.158 6.83 0.00 0.00 4.34
2918 3404 2.564553 GATGCTCTGAGGCCGACGTT 62.565 60.000 6.83 0.00 0.00 3.99
2919 3405 2.811317 GCTCTGAGGCCGACGTTG 60.811 66.667 6.83 0.00 0.00 4.10
2920 3406 2.125912 CTCTGAGGCCGACGTTGG 60.126 66.667 18.24 18.24 0.00 3.77
2921 3407 2.915659 TCTGAGGCCGACGTTGGT 60.916 61.111 22.97 3.97 0.00 3.67
2922 3408 2.738521 CTGAGGCCGACGTTGGTG 60.739 66.667 22.97 5.31 0.00 4.17
2923 3409 4.980805 TGAGGCCGACGTTGGTGC 62.981 66.667 22.97 12.73 0.00 5.01
2924 3410 4.980805 GAGGCCGACGTTGGTGCA 62.981 66.667 22.97 0.00 0.00 4.57
2925 3411 4.329545 AGGCCGACGTTGGTGCAT 62.330 61.111 22.97 4.50 0.00 3.96
2926 3412 4.101790 GGCCGACGTTGGTGCATG 62.102 66.667 22.97 0.00 0.00 4.06
2927 3413 3.047280 GCCGACGTTGGTGCATGA 61.047 61.111 22.97 0.00 0.00 3.07
2928 3414 2.398554 GCCGACGTTGGTGCATGAT 61.399 57.895 22.97 0.00 0.00 2.45
2929 3415 1.087202 GCCGACGTTGGTGCATGATA 61.087 55.000 22.97 0.00 0.00 2.15
2930 3416 0.930310 CCGACGTTGGTGCATGATAG 59.070 55.000 14.24 0.00 0.00 2.08
2931 3417 1.470805 CCGACGTTGGTGCATGATAGA 60.471 52.381 14.24 0.00 0.00 1.98
2932 3418 1.854743 CGACGTTGGTGCATGATAGAG 59.145 52.381 0.00 0.00 0.00 2.43
2933 3419 2.479560 CGACGTTGGTGCATGATAGAGA 60.480 50.000 0.00 0.00 0.00 3.10
2934 3420 3.722147 GACGTTGGTGCATGATAGAGAT 58.278 45.455 0.00 0.00 0.00 2.75
2935 3421 3.461061 ACGTTGGTGCATGATAGAGATG 58.539 45.455 0.00 0.00 0.00 2.90
2936 3422 2.804527 CGTTGGTGCATGATAGAGATGG 59.195 50.000 0.00 0.00 0.00 3.51
2937 3423 2.551459 GTTGGTGCATGATAGAGATGGC 59.449 50.000 0.00 0.00 0.00 4.40
2938 3424 1.072806 TGGTGCATGATAGAGATGGCC 59.927 52.381 0.00 0.00 0.00 5.36
2939 3425 1.072806 GGTGCATGATAGAGATGGCCA 59.927 52.381 8.56 8.56 0.00 5.36
2940 3426 2.424557 GTGCATGATAGAGATGGCCAG 58.575 52.381 13.05 0.00 0.00 4.85
2941 3427 1.350019 TGCATGATAGAGATGGCCAGG 59.650 52.381 13.05 0.00 0.00 4.45
2942 3428 1.627329 GCATGATAGAGATGGCCAGGA 59.373 52.381 13.05 0.00 0.00 3.86
2943 3429 2.354906 GCATGATAGAGATGGCCAGGAG 60.355 54.545 13.05 0.00 0.00 3.69
2944 3430 3.171528 CATGATAGAGATGGCCAGGAGA 58.828 50.000 13.05 0.00 0.00 3.71
2945 3431 2.603021 TGATAGAGATGGCCAGGAGAC 58.397 52.381 13.05 0.55 0.00 3.36
2946 3432 2.091111 TGATAGAGATGGCCAGGAGACA 60.091 50.000 13.05 2.60 0.00 3.41
2947 3433 2.783379 TAGAGATGGCCAGGAGACAT 57.217 50.000 13.05 0.00 0.00 3.06
2948 3434 1.129917 AGAGATGGCCAGGAGACATG 58.870 55.000 13.05 0.00 0.00 3.21
2949 3435 0.534652 GAGATGGCCAGGAGACATGC 60.535 60.000 13.05 0.00 0.00 4.06
2950 3436 1.890979 GATGGCCAGGAGACATGCG 60.891 63.158 13.05 0.00 0.00 4.73
2951 3437 2.599645 GATGGCCAGGAGACATGCGT 62.600 60.000 13.05 0.00 0.00 5.24
2952 3438 2.512515 GGCCAGGAGACATGCGTC 60.513 66.667 0.00 0.00 42.95 5.19
2953 3439 2.512515 GCCAGGAGACATGCGTCC 60.513 66.667 5.90 5.90 43.73 4.79
2954 3440 2.981302 CCAGGAGACATGCGTCCA 59.019 61.111 14.76 0.00 43.73 4.02
2955 3441 1.524002 CCAGGAGACATGCGTCCAT 59.476 57.895 14.76 0.00 43.73 3.41
2956 3442 0.752658 CCAGGAGACATGCGTCCATA 59.247 55.000 14.76 0.00 43.73 2.74
2957 3443 1.269988 CCAGGAGACATGCGTCCATAG 60.270 57.143 14.76 5.69 43.73 2.23
2958 3444 1.683385 CAGGAGACATGCGTCCATAGA 59.317 52.381 14.76 0.00 43.73 1.98
2959 3445 1.959985 AGGAGACATGCGTCCATAGAG 59.040 52.381 14.76 0.00 43.73 2.43
2960 3446 1.604185 GGAGACATGCGTCCATAGAGC 60.604 57.143 8.73 0.00 43.73 4.09
2961 3447 0.390860 AGACATGCGTCCATAGAGCC 59.609 55.000 0.00 0.00 43.73 4.70
2962 3448 0.390860 GACATGCGTCCATAGAGCCT 59.609 55.000 0.00 0.00 36.02 4.58
2963 3449 0.105593 ACATGCGTCCATAGAGCCTG 59.894 55.000 0.00 0.00 33.73 4.85
2964 3450 1.070445 ATGCGTCCATAGAGCCTGC 59.930 57.895 0.00 0.00 0.00 4.85
2965 3451 2.280457 GCGTCCATAGAGCCTGCC 60.280 66.667 0.00 0.00 0.00 4.85
2966 3452 2.423446 CGTCCATAGAGCCTGCCC 59.577 66.667 0.00 0.00 0.00 5.36
2967 3453 2.423446 GTCCATAGAGCCTGCCCG 59.577 66.667 0.00 0.00 0.00 6.13
2968 3454 2.041922 TCCATAGAGCCTGCCCGT 60.042 61.111 0.00 0.00 0.00 5.28
2969 3455 1.689233 TCCATAGAGCCTGCCCGTT 60.689 57.895 0.00 0.00 0.00 4.44
2970 3456 1.224592 CCATAGAGCCTGCCCGTTT 59.775 57.895 0.00 0.00 0.00 3.60
2971 3457 0.394352 CCATAGAGCCTGCCCGTTTT 60.394 55.000 0.00 0.00 0.00 2.43
2972 3458 1.134220 CCATAGAGCCTGCCCGTTTTA 60.134 52.381 0.00 0.00 0.00 1.52
2973 3459 1.940613 CATAGAGCCTGCCCGTTTTAC 59.059 52.381 0.00 0.00 0.00 2.01
2974 3460 1.272807 TAGAGCCTGCCCGTTTTACT 58.727 50.000 0.00 0.00 0.00 2.24
2975 3461 0.036294 AGAGCCTGCCCGTTTTACTC 60.036 55.000 0.00 0.00 0.00 2.59
2976 3462 0.321298 GAGCCTGCCCGTTTTACTCA 60.321 55.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
168 169 7.708752 TGAAACGATCAAAAGCCACTAAAAATT 59.291 29.630 0.00 0.00 34.30 1.82
205 221 4.380531 AGAGGTCATGTGTTGTGTTACTG 58.619 43.478 0.00 0.00 0.00 2.74
405 421 2.099756 ACCAGTTCTTGAAAGCTGCAAC 59.900 45.455 1.02 0.00 0.00 4.17
423 439 2.092158 TGTTGTCCACAATTCTCCACCA 60.092 45.455 0.00 0.00 38.24 4.17
464 480 4.451096 GCTAGGACGATTTTGACTTGTGAA 59.549 41.667 0.00 0.00 0.00 3.18
567 583 0.832626 ATCACACCATCCGATGCTGA 59.167 50.000 10.14 7.21 0.00 4.26
654 670 1.670811 CACACGTGAATTGCCCCTATC 59.329 52.381 25.01 0.00 0.00 2.08
742 798 5.408604 GGGCACACGACAGGATTATTTATAG 59.591 44.000 0.00 0.00 0.00 1.31
746 802 2.290641 TGGGCACACGACAGGATTATTT 60.291 45.455 0.00 0.00 0.00 1.40
753 809 1.875963 GATTTGGGCACACGACAGG 59.124 57.895 0.00 0.00 0.00 4.00
759 815 2.723124 ATGTTTCGATTTGGGCACAC 57.277 45.000 0.00 0.00 0.00 3.82
895 1063 8.591072 AGTCTAAACAGCAACATAAGGTAGTAA 58.409 33.333 0.00 0.00 0.00 2.24
897 1065 7.005709 AGTCTAAACAGCAACATAAGGTAGT 57.994 36.000 0.00 0.00 0.00 2.73
898 1066 7.602644 TCAAGTCTAAACAGCAACATAAGGTAG 59.397 37.037 0.00 0.00 0.00 3.18
900 1068 6.296026 TCAAGTCTAAACAGCAACATAAGGT 58.704 36.000 0.00 0.00 0.00 3.50
951 1173 8.977412 AGAACAAACAAAAGGAAAGGAGAAATA 58.023 29.630 0.00 0.00 0.00 1.40
958 1180 6.626302 TGTACAGAACAAACAAAAGGAAAGG 58.374 36.000 0.00 0.00 34.29 3.11
1017 1268 1.378514 GTGATTCCCACCGCCATGT 60.379 57.895 0.00 0.00 39.86 3.21
1230 1484 4.698575 GGAGCTTACTTATCTTCACCCAG 58.301 47.826 0.00 0.00 0.00 4.45
1340 1594 5.499004 ACTGATCAGCCACTAAAAGGTAA 57.501 39.130 22.83 0.00 0.00 2.85
1343 1597 3.873952 GCTACTGATCAGCCACTAAAAGG 59.126 47.826 22.83 0.00 32.68 3.11
1415 1786 2.565841 GGATGGTCCTACATGAAGCAC 58.434 52.381 0.00 0.00 32.53 4.40
1416 1787 1.490490 GGGATGGTCCTACATGAAGCA 59.510 52.381 0.00 0.00 36.57 3.91
1606 1995 8.610896 GTTCATTTCCATCAACAACAAATTCAA 58.389 29.630 0.00 0.00 0.00 2.69
1625 2014 3.771216 AGCACTCATTCCAGGTTCATTT 58.229 40.909 0.00 0.00 0.00 2.32
1638 2027 0.743701 GCAGCAGCAGTAGCACTCAT 60.744 55.000 0.00 0.00 45.49 2.90
1975 2372 1.557269 GGAGAGGTGGTGCATGACCT 61.557 60.000 17.23 17.23 46.32 3.85
2036 2433 0.321653 GCACGGACACTCCATCCTTT 60.322 55.000 0.00 0.00 35.91 3.11
2144 2559 4.701956 AAAATATGGTCAGCTTCGTTGG 57.298 40.909 0.00 0.00 0.00 3.77
2463 2914 9.494479 CATCTTTGCTGTTTGTACAAGTATATG 57.506 33.333 8.56 1.91 32.92 1.78
2523 2976 6.335471 TCACATGTCTTCAAAATTGCAGAT 57.665 33.333 0.00 0.00 33.28 2.90
2646 3131 9.942850 TTGTATGATGTGAAATTTGACTCTAGA 57.057 29.630 9.24 0.00 0.00 2.43
2759 3244 3.138304 GTTTGGTGTACTGCATGAGACA 58.862 45.455 0.00 0.00 0.00 3.41
2799 3284 1.930908 GCCTGGTTGAGCTCATGCAC 61.931 60.000 19.04 12.94 42.74 4.57
2867 3353 0.601057 GCTATGGGCGTGTTTGGTTT 59.399 50.000 0.00 0.00 0.00 3.27
2899 3385 2.279120 CGTCGGCCTCAGAGCATC 60.279 66.667 0.00 0.00 0.00 3.91
2900 3386 2.650116 AACGTCGGCCTCAGAGCAT 61.650 57.895 0.00 0.00 0.00 3.79
2901 3387 3.303135 AACGTCGGCCTCAGAGCA 61.303 61.111 0.00 0.00 0.00 4.26
2902 3388 2.811317 CAACGTCGGCCTCAGAGC 60.811 66.667 0.00 0.00 0.00 4.09
2903 3389 2.125912 CCAACGTCGGCCTCAGAG 60.126 66.667 0.00 0.00 0.00 3.35
2904 3390 2.915659 ACCAACGTCGGCCTCAGA 60.916 61.111 0.00 0.00 0.00 3.27
2905 3391 2.738521 CACCAACGTCGGCCTCAG 60.739 66.667 0.00 0.00 0.00 3.35
2906 3392 4.980805 GCACCAACGTCGGCCTCA 62.981 66.667 0.00 0.00 0.00 3.86
2907 3393 4.980805 TGCACCAACGTCGGCCTC 62.981 66.667 0.00 0.00 0.00 4.70
2908 3394 4.329545 ATGCACCAACGTCGGCCT 62.330 61.111 0.00 0.00 0.00 5.19
2909 3395 4.101790 CATGCACCAACGTCGGCC 62.102 66.667 0.00 0.00 0.00 6.13
2910 3396 1.087202 TATCATGCACCAACGTCGGC 61.087 55.000 0.00 0.00 0.00 5.54
2911 3397 0.930310 CTATCATGCACCAACGTCGG 59.070 55.000 0.00 0.00 0.00 4.79
2912 3398 1.854743 CTCTATCATGCACCAACGTCG 59.145 52.381 0.00 0.00 0.00 5.12
2913 3399 3.165058 TCTCTATCATGCACCAACGTC 57.835 47.619 0.00 0.00 0.00 4.34
2914 3400 3.461061 CATCTCTATCATGCACCAACGT 58.539 45.455 0.00 0.00 0.00 3.99
2915 3401 2.804527 CCATCTCTATCATGCACCAACG 59.195 50.000 0.00 0.00 0.00 4.10
2916 3402 2.551459 GCCATCTCTATCATGCACCAAC 59.449 50.000 0.00 0.00 0.00 3.77
2917 3403 2.487805 GGCCATCTCTATCATGCACCAA 60.488 50.000 0.00 0.00 0.00 3.67
2918 3404 1.072806 GGCCATCTCTATCATGCACCA 59.927 52.381 0.00 0.00 0.00 4.17
2919 3405 1.072806 TGGCCATCTCTATCATGCACC 59.927 52.381 0.00 0.00 0.00 5.01
2920 3406 2.424557 CTGGCCATCTCTATCATGCAC 58.575 52.381 5.51 0.00 0.00 4.57
2921 3407 1.350019 CCTGGCCATCTCTATCATGCA 59.650 52.381 5.51 0.00 0.00 3.96
2922 3408 1.627329 TCCTGGCCATCTCTATCATGC 59.373 52.381 5.51 0.00 0.00 4.06
2923 3409 3.055963 GTCTCCTGGCCATCTCTATCATG 60.056 52.174 5.51 0.00 0.00 3.07
2924 3410 3.172339 GTCTCCTGGCCATCTCTATCAT 58.828 50.000 5.51 0.00 0.00 2.45
2925 3411 2.091111 TGTCTCCTGGCCATCTCTATCA 60.091 50.000 5.51 0.00 0.00 2.15
2926 3412 2.603021 TGTCTCCTGGCCATCTCTATC 58.397 52.381 5.51 0.00 0.00 2.08
2927 3413 2.783379 TGTCTCCTGGCCATCTCTAT 57.217 50.000 5.51 0.00 0.00 1.98
2928 3414 2.323599 CATGTCTCCTGGCCATCTCTA 58.676 52.381 5.51 0.00 0.00 2.43
2929 3415 1.129917 CATGTCTCCTGGCCATCTCT 58.870 55.000 5.51 0.00 0.00 3.10
2930 3416 0.534652 GCATGTCTCCTGGCCATCTC 60.535 60.000 5.51 0.00 0.00 2.75
2931 3417 1.530771 GCATGTCTCCTGGCCATCT 59.469 57.895 5.51 0.00 0.00 2.90
2932 3418 1.890979 CGCATGTCTCCTGGCCATC 60.891 63.158 5.51 0.00 0.00 3.51
2933 3419 2.191375 CGCATGTCTCCTGGCCAT 59.809 61.111 5.51 0.00 0.00 4.40
2934 3420 3.315142 GACGCATGTCTCCTGGCCA 62.315 63.158 4.71 4.71 42.08 5.36
2935 3421 2.512515 GACGCATGTCTCCTGGCC 60.513 66.667 0.00 0.00 42.08 5.36
2936 3422 2.512515 GGACGCATGTCTCCTGGC 60.513 66.667 0.00 0.00 44.83 4.85
2937 3423 0.752658 TATGGACGCATGTCTCCTGG 59.247 55.000 10.96 0.00 44.83 4.45
2938 3424 1.683385 TCTATGGACGCATGTCTCCTG 59.317 52.381 10.96 3.79 44.83 3.86
2939 3425 1.959985 CTCTATGGACGCATGTCTCCT 59.040 52.381 10.96 2.02 44.83 3.69
2940 3426 1.604185 GCTCTATGGACGCATGTCTCC 60.604 57.143 0.00 0.00 44.83 3.71
2941 3427 1.604185 GGCTCTATGGACGCATGTCTC 60.604 57.143 0.00 0.00 44.83 3.36
2942 3428 0.390860 GGCTCTATGGACGCATGTCT 59.609 55.000 0.00 0.00 44.83 3.41
2943 3429 0.390860 AGGCTCTATGGACGCATGTC 59.609 55.000 0.00 0.00 44.72 3.06
2944 3430 0.105593 CAGGCTCTATGGACGCATGT 59.894 55.000 0.00 0.00 31.54 3.21
2945 3431 1.226686 GCAGGCTCTATGGACGCATG 61.227 60.000 9.57 9.57 38.36 4.06
2946 3432 1.070445 GCAGGCTCTATGGACGCAT 59.930 57.895 0.00 0.00 0.00 4.73
2947 3433 2.501128 GCAGGCTCTATGGACGCA 59.499 61.111 0.00 0.00 0.00 5.24
2948 3434 2.280457 GGCAGGCTCTATGGACGC 60.280 66.667 0.00 0.00 0.00 5.19
2949 3435 2.423446 GGGCAGGCTCTATGGACG 59.577 66.667 0.00 0.00 0.00 4.79
2950 3436 1.972660 AACGGGCAGGCTCTATGGAC 61.973 60.000 0.00 0.00 0.00 4.02
2951 3437 1.271840 AAACGGGCAGGCTCTATGGA 61.272 55.000 0.00 0.00 0.00 3.41
2952 3438 0.394352 AAAACGGGCAGGCTCTATGG 60.394 55.000 0.00 0.00 0.00 2.74
2953 3439 1.940613 GTAAAACGGGCAGGCTCTATG 59.059 52.381 0.00 0.00 0.00 2.23
2954 3440 1.838077 AGTAAAACGGGCAGGCTCTAT 59.162 47.619 0.00 0.00 0.00 1.98
2955 3441 1.206371 GAGTAAAACGGGCAGGCTCTA 59.794 52.381 0.00 0.00 0.00 2.43
2956 3442 0.036294 GAGTAAAACGGGCAGGCTCT 60.036 55.000 0.00 0.00 0.00 4.09
2957 3443 0.321298 TGAGTAAAACGGGCAGGCTC 60.321 55.000 0.00 0.00 0.00 4.70
2958 3444 1.758592 TGAGTAAAACGGGCAGGCT 59.241 52.632 0.00 0.00 0.00 4.58
2959 3445 4.390048 TGAGTAAAACGGGCAGGC 57.610 55.556 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.