Multiple sequence alignment - TraesCS7A01G394900

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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 TraesCS7A01G394900 chr7A 100.000 3873 0 0 1 3873 573129543 573125671 0.000000e+00 7153.0
1 TraesCS7A01G394900 chr7A 95.858 507 5 7 3382 3873 85440743 85440238 0.000000e+00 806.0
2 TraesCS7A01G394900 chr7A 78.679 863 161 20 1274 2132 194324647 194323804 1.570000e-153 553.0
3 TraesCS7A01G394900 chr7A 88.845 251 19 3 3381 3622 85439888 85440138 2.260000e-77 300.0
4 TraesCS7A01G394900 chr7A 87.854 247 25 5 3380 3622 573125326 573125571 6.330000e-73 285.0
5 TraesCS7A01G394900 chr7B 90.809 1643 73 35 792 2385 533615122 533613509 0.000000e+00 2126.0
6 TraesCS7A01G394900 chr7B 92.105 950 53 9 2433 3382 533613362 533612435 0.000000e+00 1319.0
7 TraesCS7A01G394900 chr7B 77.984 863 167 20 1274 2132 334322217 334323060 1.590000e-143 520.0
8 TraesCS7A01G394900 chr7B 80.251 638 40 40 1 590 533616032 533615433 6.030000e-108 401.0
9 TraesCS7A01G394900 chr7B 84.375 160 10 7 637 791 533615302 533615153 4.030000e-30 143.0
10 TraesCS7A01G394900 chr7D 90.753 1633 55 31 792 2385 505616994 505615419 0.000000e+00 2091.0
11 TraesCS7A01G394900 chr7D 94.013 952 43 8 2433 3382 505615272 505614333 0.000000e+00 1430.0
12 TraesCS7A01G394900 chr7D 77.868 863 168 20 1274 2132 189430232 189431075 7.420000e-142 514.0
13 TraesCS7A01G394900 chr7D 78.413 857 63 39 1 791 505617827 505617027 2.750000e-121 446.0
14 TraesCS7A01G394900 chr6A 94.757 515 5 7 3381 3873 4877664 4878178 0.000000e+00 782.0
15 TraesCS7A01G394900 chr6A 79.838 863 148 21 1274 2132 504624711 504623871 1.190000e-169 606.0
16 TraesCS7A01G394900 chr6A 79.545 396 33 21 3382 3762 26785969 26786331 5.000000e-59 239.0
17 TraesCS7A01G394900 chr5A 94.747 514 5 8 3382 3873 597492556 597493069 0.000000e+00 780.0
18 TraesCS7A01G394900 chr5A 92.289 415 9 9 3382 3773 622221702 622222116 5.620000e-158 568.0
19 TraesCS7A01G394900 chr5A 100.000 109 0 0 3765 3873 622222270 622222378 6.560000e-48 202.0
20 TraesCS7A01G394900 chr5A 84.524 84 7 4 1052 1130 563100903 563100985 1.150000e-10 78.7
21 TraesCS7A01G394900 chr5A 84.524 84 7 4 1052 1130 563164782 563164864 1.150000e-10 78.7
22 TraesCS7A01G394900 chr6D 79.538 865 147 24 1274 2132 363597028 363596188 1.200000e-164 590.0
23 TraesCS7A01G394900 chr6B 78.844 865 153 24 1274 2132 548384260 548383420 1.220000e-154 556.0
24 TraesCS7A01G394900 chr6B 87.500 120 7 1 3762 3873 665585540 665585659 8.730000e-27 132.0
25 TraesCS7A01G394900 chr5B 84.426 244 29 6 3381 3622 532888354 532888590 8.370000e-57 231.0
26 TraesCS7A01G394900 chr1B 90.000 160 14 1 3381 3538 28035473 28035314 5.070000e-49 206.0
27 TraesCS7A01G394900 chr2D 86.325 117 8 5 3765 3873 532435936 532436052 1.890000e-23 121.0


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 TraesCS7A01G394900 chr7A 573125671 573129543 3872 True 7153.000000 7153 100.000000 1 3873 1 chr7A.!!$R3 3872
1 TraesCS7A01G394900 chr7A 85440238 85440743 505 True 806.000000 806 95.858000 3382 3873 1 chr7A.!!$R1 491
2 TraesCS7A01G394900 chr7A 194323804 194324647 843 True 553.000000 553 78.679000 1274 2132 1 chr7A.!!$R2 858
3 TraesCS7A01G394900 chr7B 533612435 533616032 3597 True 997.250000 2126 86.885000 1 3382 4 chr7B.!!$R1 3381
4 TraesCS7A01G394900 chr7B 334322217 334323060 843 False 520.000000 520 77.984000 1274 2132 1 chr7B.!!$F1 858
5 TraesCS7A01G394900 chr7D 505614333 505617827 3494 True 1322.333333 2091 87.726333 1 3382 3 chr7D.!!$R1 3381
6 TraesCS7A01G394900 chr7D 189430232 189431075 843 False 514.000000 514 77.868000 1274 2132 1 chr7D.!!$F1 858
7 TraesCS7A01G394900 chr6A 4877664 4878178 514 False 782.000000 782 94.757000 3381 3873 1 chr6A.!!$F1 492
8 TraesCS7A01G394900 chr6A 504623871 504624711 840 True 606.000000 606 79.838000 1274 2132 1 chr6A.!!$R1 858
9 TraesCS7A01G394900 chr5A 597492556 597493069 513 False 780.000000 780 94.747000 3382 3873 1 chr5A.!!$F3 491
10 TraesCS7A01G394900 chr5A 622221702 622222378 676 False 385.000000 568 96.144500 3382 3873 2 chr5A.!!$F4 491
11 TraesCS7A01G394900 chr6D 363596188 363597028 840 True 590.000000 590 79.538000 1274 2132 1 chr6D.!!$R1 858
12 TraesCS7A01G394900 chr6B 548383420 548384260 840 True 556.000000 556 78.844000 1274 2132 1 chr6B.!!$R1 858

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
74 75 0.037046 GCTCACCCTTTTTGCCCATG 60.037 55.0 0.0 0.0 0.0 3.66 F
679 820 0.040058 ATTGATGAACCAGCCCAGCA 59.960 50.0 0.0 0.0 0.0 4.41 F
2193 2437 0.249868 TGACCGTTTCCTGCACAGAG 60.250 55.0 0.0 0.0 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1219 1457 0.179097 GAGGAGGATGCGTTGGAGTC 60.179 60.000 0.0 0.0 0.0 3.36 R
2510 2859 2.798976 TGTCTGCAAAAATGGTGAGC 57.201 45.000 0.0 0.0 0.0 4.26 R
3083 3433 1.542915 CCTTTGCAGATTGACACCAGG 59.457 52.381 0.0 0.0 0.0 4.45 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
62 63 1.429148 CGCCACTTATTCGCTCACCC 61.429 60.000 0.00 0.00 0.00 4.61
65 66 2.711542 CCACTTATTCGCTCACCCTTT 58.288 47.619 0.00 0.00 0.00 3.11
67 68 3.506067 CCACTTATTCGCTCACCCTTTTT 59.494 43.478 0.00 0.00 0.00 1.94
68 69 4.475944 CACTTATTCGCTCACCCTTTTTG 58.524 43.478 0.00 0.00 0.00 2.44
74 75 0.037046 GCTCACCCTTTTTGCCCATG 60.037 55.000 0.00 0.00 0.00 3.66
209 248 0.439985 GTCTCGTACTCGTACACGCA 59.560 55.000 7.86 0.00 38.05 5.24
210 249 0.439985 TCTCGTACTCGTACACGCAC 59.560 55.000 7.86 0.00 38.05 5.34
218 257 1.933041 CGTACACGCACGATCGGAG 60.933 63.158 20.98 12.64 44.69 4.63
418 474 2.153401 TTGGATGGATAGGGCCGGG 61.153 63.158 2.18 0.00 0.00 5.73
459 515 1.532868 GCACAGTGATTGATATCCGCC 59.467 52.381 4.15 0.00 0.00 6.13
467 523 4.024048 GTGATTGATATCCGCCGTGAATTT 60.024 41.667 0.00 0.00 0.00 1.82
481 537 5.626211 CCGTGAATTTGCACTTTTTGTTTT 58.374 33.333 0.00 0.00 36.65 2.43
482 538 6.673316 GCCGTGAATTTGCACTTTTTGTTTTA 60.673 34.615 0.00 0.00 36.65 1.52
483 539 7.405769 CCGTGAATTTGCACTTTTTGTTTTAT 58.594 30.769 0.00 0.00 36.65 1.40
484 540 8.543774 CCGTGAATTTGCACTTTTTGTTTTATA 58.456 29.630 0.00 0.00 36.65 0.98
485 541 9.566624 CGTGAATTTGCACTTTTTGTTTTATAG 57.433 29.630 0.00 0.00 36.65 1.31
516 572 4.200092 AGAGATTCGTTAATTGGGGCTTC 58.800 43.478 0.00 0.00 0.00 3.86
560 617 2.048222 CGGCAAGCACGAGAAGGA 60.048 61.111 0.00 0.00 0.00 3.36
566 623 0.174617 AAGCACGAGAAGGAGCTAGC 59.825 55.000 6.62 6.62 34.89 3.42
567 624 0.967887 AGCACGAGAAGGAGCTAGCA 60.968 55.000 18.83 0.00 34.35 3.49
568 625 0.804156 GCACGAGAAGGAGCTAGCAC 60.804 60.000 18.83 11.05 0.00 4.40
569 626 0.179124 CACGAGAAGGAGCTAGCACC 60.179 60.000 22.31 22.31 0.00 5.01
575 632 2.202810 GGAGCTAGCACCACGAGC 60.203 66.667 24.45 0.00 46.50 5.03
598 667 3.763897 ACCCAACAAAATGTCCTAGCATC 59.236 43.478 0.00 0.00 0.00 3.91
646 787 0.885150 AGAGCGACAGACAGTGACGA 60.885 55.000 0.00 0.00 45.67 4.20
658 799 2.031333 ACAGTGACGAACTCGAGGTTAC 60.031 50.000 18.41 11.70 43.02 2.50
679 820 0.040058 ATTGATGAACCAGCCCAGCA 59.960 50.000 0.00 0.00 0.00 4.41
680 821 0.040058 TTGATGAACCAGCCCAGCAT 59.960 50.000 0.00 0.00 0.00 3.79
742 892 5.175859 TGCAGTAGTAGCATGTTTCTTACC 58.824 41.667 0.00 0.00 37.02 2.85
745 895 5.288712 CAGTAGTAGCATGTTTCTTACCGTG 59.711 44.000 0.00 0.00 0.00 4.94
782 932 4.126437 CCACCCAGAAACATTCCAAAAAC 58.874 43.478 0.00 0.00 0.00 2.43
785 935 4.343814 ACCCAGAAACATTCCAAAAACGAT 59.656 37.500 0.00 0.00 0.00 3.73
791 941 4.425577 ACATTCCAAAAACGATGAGAGC 57.574 40.909 0.00 0.00 0.00 4.09
792 942 3.820467 ACATTCCAAAAACGATGAGAGCA 59.180 39.130 0.00 0.00 0.00 4.26
793 943 4.083110 ACATTCCAAAAACGATGAGAGCAG 60.083 41.667 0.00 0.00 0.00 4.24
869 1061 3.337358 CCATCAATTCCTGCCAAAAACC 58.663 45.455 0.00 0.00 0.00 3.27
876 1068 3.322191 TCCTGCCAAAAACCTTTACCT 57.678 42.857 0.00 0.00 0.00 3.08
891 1083 1.094073 TACCTCGCGTACTCTCTGCC 61.094 60.000 5.77 0.00 0.00 4.85
896 1088 1.063811 GCGTACTCTCTGCCGTACC 59.936 63.158 0.00 0.00 34.05 3.34
934 1148 3.330853 GCGTAATCCTCAGCGCCG 61.331 66.667 2.29 0.00 43.52 6.46
953 1167 2.997315 TGCTCCCACACTCCCTCG 60.997 66.667 0.00 0.00 0.00 4.63
975 1189 2.124193 CATTGCTCCCCATCCGCA 60.124 61.111 0.00 0.00 0.00 5.69
1153 1376 3.897681 TACCACTCCCTGCTCGCCA 62.898 63.158 0.00 0.00 0.00 5.69
1229 1467 2.811317 CAGCTCCGACTCCAACGC 60.811 66.667 0.00 0.00 0.00 4.84
1230 1468 3.303135 AGCTCCGACTCCAACGCA 61.303 61.111 0.00 0.00 0.00 5.24
1231 1469 2.125512 GCTCCGACTCCAACGCAT 60.126 61.111 0.00 0.00 0.00 4.73
1253 1491 4.116328 CTCGTCGCCGAAGCAGGA 62.116 66.667 0.00 0.00 43.69 3.86
1254 1492 4.116328 TCGTCGCCGAAGCAGGAG 62.116 66.667 0.00 0.00 40.86 3.69
1573 1817 1.618640 GAACTGCACCTTCTCGACGC 61.619 60.000 0.00 0.00 0.00 5.19
2193 2437 0.249868 TGACCGTTTCCTGCACAGAG 60.250 55.000 0.00 0.00 0.00 3.35
2203 2447 2.878406 TCCTGCACAGAGTTTGTTTAGC 59.122 45.455 0.00 0.00 38.16 3.09
2214 2458 6.260050 CAGAGTTTGTTTAGCTTAGTGGACAA 59.740 38.462 0.00 0.00 0.00 3.18
2229 2473 8.528044 TTAGTGGACAAATGTTACTCCTTTTT 57.472 30.769 7.42 0.00 31.43 1.94
2238 2482 3.695060 TGTTACTCCTTTTTCGCAAACCA 59.305 39.130 0.00 0.00 0.00 3.67
2239 2483 4.158025 TGTTACTCCTTTTTCGCAAACCAA 59.842 37.500 0.00 0.00 0.00 3.67
2240 2484 3.878160 ACTCCTTTTTCGCAAACCAAA 57.122 38.095 0.00 0.00 0.00 3.28
2278 2523 4.038883 TGAATTTGGCATGTTGATGTGACA 59.961 37.500 0.00 0.00 31.50 3.58
2279 2524 4.811969 ATTTGGCATGTTGATGTGACAT 57.188 36.364 0.00 0.00 38.21 3.06
2280 2525 4.603989 TTTGGCATGTTGATGTGACATT 57.396 36.364 0.00 0.00 35.64 2.71
2310 2555 6.187682 CACTGGAATTACCCAATTAGGAACT 58.812 40.000 0.00 0.00 41.22 3.01
2352 2597 3.365969 CGACTAAAAGTGCCCATTTGGTC 60.366 47.826 3.88 3.88 41.10 4.02
2357 2602 5.760484 AAAAGTGCCCATTTGGTCATAAT 57.240 34.783 0.00 0.00 36.04 1.28
2371 2616 7.994425 TTGGTCATAATGTTGCTTCTAAAGA 57.006 32.000 0.00 0.00 0.00 2.52
2377 2622 7.768582 TCATAATGTTGCTTCTAAAGATTCCGA 59.231 33.333 0.00 0.00 0.00 4.55
2385 2630 5.502544 GCTTCTAAAGATTCCGAATTCGTGG 60.503 44.000 25.10 11.97 37.74 4.94
2386 2631 5.080969 TCTAAAGATTCCGAATTCGTGGT 57.919 39.130 25.10 10.97 37.74 4.16
2389 2634 7.944061 TCTAAAGATTCCGAATTCGTGGTATA 58.056 34.615 25.10 9.27 37.74 1.47
2390 2635 8.582437 TCTAAAGATTCCGAATTCGTGGTATAT 58.418 33.333 25.10 9.94 37.74 0.86
2392 2637 6.591750 AGATTCCGAATTCGTGGTATATCT 57.408 37.500 25.10 17.89 37.74 1.98
2393 2638 6.390721 AGATTCCGAATTCGTGGTATATCTG 58.609 40.000 25.10 7.04 37.74 2.90
2395 2640 5.777850 TCCGAATTCGTGGTATATCTGAA 57.222 39.130 25.10 0.00 37.74 3.02
2396 2641 6.151663 TCCGAATTCGTGGTATATCTGAAA 57.848 37.500 25.10 0.00 37.74 2.69
2397 2642 6.755206 TCCGAATTCGTGGTATATCTGAAAT 58.245 36.000 25.10 0.00 37.74 2.17
2398 2643 6.645003 TCCGAATTCGTGGTATATCTGAAATG 59.355 38.462 25.10 4.97 37.74 2.32
2399 2644 6.423905 CCGAATTCGTGGTATATCTGAAATGT 59.576 38.462 25.10 0.00 37.74 2.71
2401 2646 8.425491 CGAATTCGTGGTATATCTGAAATGTAC 58.575 37.037 19.67 0.00 34.11 2.90
2403 2648 6.718522 TCGTGGTATATCTGAAATGTACCA 57.281 37.500 8.94 8.94 41.44 3.25
2406 2651 6.718522 TGGTATATCTGAAATGTACCACGA 57.281 37.500 8.94 0.00 39.69 4.35
2409 2654 8.208224 TGGTATATCTGAAATGTACCACGAATT 58.792 33.333 8.94 0.00 39.69 2.17
2411 2656 9.864034 GTATATCTGAAATGTACCACGAATTTG 57.136 33.333 0.00 0.00 0.00 2.32
2412 2657 8.731275 ATATCTGAAATGTACCACGAATTTGA 57.269 30.769 0.00 0.00 0.00 2.69
2414 2659 5.995282 TCTGAAATGTACCACGAATTTGAGT 59.005 36.000 0.00 0.00 29.86 3.41
2415 2660 5.996219 TGAAATGTACCACGAATTTGAGTG 58.004 37.500 0.00 1.40 38.05 3.51
2416 2661 5.529430 TGAAATGTACCACGAATTTGAGTGT 59.471 36.000 0.00 0.00 36.69 3.55
2417 2662 6.038825 TGAAATGTACCACGAATTTGAGTGTT 59.961 34.615 0.00 0.00 36.69 3.32
2419 2664 4.699637 TGTACCACGAATTTGAGTGTTCT 58.300 39.130 0.00 0.00 36.69 3.01
2420 2665 5.120399 TGTACCACGAATTTGAGTGTTCTT 58.880 37.500 0.00 0.00 36.69 2.52
2421 2666 4.552166 ACCACGAATTTGAGTGTTCTTG 57.448 40.909 0.00 0.00 36.69 3.02
2434 2698 6.337356 TGAGTGTTCTTGGTTTTCATTTTCC 58.663 36.000 0.00 0.00 0.00 3.13
2435 2699 6.071108 TGAGTGTTCTTGGTTTTCATTTTCCA 60.071 34.615 0.00 0.00 0.00 3.53
2451 2800 2.768253 TCCATGCAGTCCTAGTTGTG 57.232 50.000 0.00 0.00 0.00 3.33
2458 2807 4.377021 TGCAGTCCTAGTTGTGTTACTTG 58.623 43.478 0.00 0.00 0.00 3.16
2473 2822 8.903570 TGTGTTACTTGTTTTACATTTGTCAG 57.096 30.769 0.00 0.00 0.00 3.51
2474 2823 8.731605 TGTGTTACTTGTTTTACATTTGTCAGA 58.268 29.630 0.00 0.00 0.00 3.27
2475 2824 9.562583 GTGTTACTTGTTTTACATTTGTCAGAA 57.437 29.630 0.00 0.00 0.00 3.02
2478 2827 7.698836 ACTTGTTTTACATTTGTCAGAATGC 57.301 32.000 7.32 0.00 39.97 3.56
2479 2828 7.264221 ACTTGTTTTACATTTGTCAGAATGCA 58.736 30.769 0.00 0.00 39.97 3.96
2480 2829 7.927629 ACTTGTTTTACATTTGTCAGAATGCAT 59.072 29.630 0.00 0.00 39.97 3.96
2481 2830 7.640616 TGTTTTACATTTGTCAGAATGCATG 57.359 32.000 0.00 0.00 39.97 4.06
2482 2831 6.645827 TGTTTTACATTTGTCAGAATGCATGG 59.354 34.615 0.00 0.00 39.97 3.66
2483 2832 5.981088 TTACATTTGTCAGAATGCATGGT 57.019 34.783 0.00 0.00 39.97 3.55
2490 2839 6.622833 TTGTCAGAATGCATGGTGTATATG 57.377 37.500 0.00 0.00 34.76 1.78
2510 2859 4.327982 TGTGAAAGACTGACTCCTCTTG 57.672 45.455 0.00 0.00 0.00 3.02
2795 3144 1.516423 GAGAAGACGCCCTGGTACC 59.484 63.158 4.43 4.43 0.00 3.34
2864 3213 2.173519 AGAGAACCATTGGCAATGTGG 58.826 47.619 31.88 24.50 37.18 4.17
2924 3273 3.454371 ACGGACTGGTGTATAGCATTC 57.546 47.619 1.14 1.14 34.40 2.67
2970 3319 2.496942 GGGCATCCCTCATGTTGTG 58.503 57.895 0.00 0.00 41.34 3.33
2971 3320 0.034186 GGGCATCCCTCATGTTGTGA 60.034 55.000 0.00 0.00 41.34 3.58
2972 3321 1.616725 GGGCATCCCTCATGTTGTGAA 60.617 52.381 0.00 0.00 41.34 3.18
3013 3362 3.349927 TCATGATTTGGAGCTTGTGAGG 58.650 45.455 0.00 0.00 0.00 3.86
3164 3515 7.040755 TCCGTGTAAATCTCATTGTTGAATTGT 60.041 33.333 0.00 0.00 0.00 2.71
3175 3526 8.620116 TCATTGTTGAATTGTTCTCAGTCATA 57.380 30.769 0.00 0.00 0.00 2.15
3193 3544 8.139350 TCAGTCATAATTCATTGCATTCCATTC 58.861 33.333 0.00 0.00 0.00 2.67
3203 3555 2.491298 TGCATTCCATTCGCTTAAAGCA 59.509 40.909 0.00 0.00 42.58 3.91
3214 3566 3.058293 TCGCTTAAAGCACCAAGTTGATG 60.058 43.478 3.87 0.00 42.58 3.07
3251 3603 7.748847 CATCGATGATGATGATGCATTTCTAA 58.251 34.615 21.02 0.00 46.98 2.10
3274 3626 9.728021 CTAAGATTAGATTGTTGCACCTTGCGG 62.728 44.444 0.00 0.00 38.45 5.69
3301 3653 4.143115 CCTTTGTTGACTATATATGCCGCG 60.143 45.833 0.00 0.00 0.00 6.46
3330 3682 4.367039 AAACTGTTCTAGCAGCCCTAAA 57.633 40.909 0.00 0.00 39.96 1.85
3344 3696 3.119137 AGCCCTAAATTTTGTTGGATCGC 60.119 43.478 0.00 0.00 0.00 4.58
3364 3716 3.612479 CGCCAAGTTCATGCTTAAAGCTT 60.612 43.478 0.00 0.00 42.97 3.74
3369 3721 6.446318 CAAGTTCATGCTTAAAGCTTACCAA 58.554 36.000 0.00 0.00 42.97 3.67
3503 3856 4.367023 GGCGACACGTGGCACCTA 62.367 66.667 21.44 0.00 35.94 3.08
3623 3983 3.717294 CGCCTTAGGTGGTGGCCT 61.717 66.667 3.32 0.00 43.42 5.19
3624 3984 2.763902 GCCTTAGGTGGTGGCCTT 59.236 61.111 3.32 0.00 40.71 4.35
3626 3986 0.107165 GCCTTAGGTGGTGGCCTTAG 60.107 60.000 3.32 0.00 40.71 2.18
3627 3987 0.546598 CCTTAGGTGGTGGCCTTAGG 59.453 60.000 3.32 0.00 45.43 2.69
3628 3988 1.286248 CTTAGGTGGTGGCCTTAGGT 58.714 55.000 3.32 0.00 39.94 3.08
3629 3989 0.988832 TTAGGTGGTGGCCTTAGGTG 59.011 55.000 3.32 0.00 39.94 4.00
3630 3990 0.912487 TAGGTGGTGGCCTTAGGTGG 60.912 60.000 3.32 0.00 39.94 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.176045 TCCAAGCGTAATCAGACTCCA 58.824 47.619 0.00 0.00 0.00 3.86
47 48 3.057526 GCAAAAAGGGTGAGCGAATAAGT 60.058 43.478 0.00 0.00 0.00 2.24
50 51 1.816224 GGCAAAAAGGGTGAGCGAATA 59.184 47.619 0.00 0.00 0.00 1.75
130 156 4.699522 GGTCACCACGTCCCAGGC 62.700 72.222 0.00 0.00 0.00 4.85
192 231 0.850794 CGTGCGTGTACGAGTACGAG 60.851 60.000 20.20 6.31 46.46 4.18
200 239 1.933041 CTCCGATCGTGCGTGTACG 60.933 63.158 15.09 4.03 44.98 3.67
201 240 1.585521 CCTCCGATCGTGCGTGTAC 60.586 63.158 15.09 0.00 0.00 2.90
202 241 2.795973 CCTCCGATCGTGCGTGTA 59.204 61.111 15.09 0.00 0.00 2.90
203 242 4.796231 GCCTCCGATCGTGCGTGT 62.796 66.667 15.09 0.00 0.00 4.49
306 351 0.250727 AGGTGTCACCATGGGAAACG 60.251 55.000 24.02 0.00 41.95 3.60
376 421 0.100682 CGTATCCCTCTGACACCACG 59.899 60.000 0.00 0.00 0.00 4.94
459 515 9.566624 CTATAAAACAAAAAGTGCAAATTCACG 57.433 29.630 0.00 0.00 41.61 4.35
467 523 7.001674 TCCCTCTCTATAAAACAAAAAGTGCA 58.998 34.615 0.00 0.00 0.00 4.57
481 537 6.442541 AACGAATCTCTCTCCCTCTCTATA 57.557 41.667 0.00 0.00 0.00 1.31
482 538 4.993705 ACGAATCTCTCTCCCTCTCTAT 57.006 45.455 0.00 0.00 0.00 1.98
483 539 4.781775 AACGAATCTCTCTCCCTCTCTA 57.218 45.455 0.00 0.00 0.00 2.43
484 540 3.662759 AACGAATCTCTCTCCCTCTCT 57.337 47.619 0.00 0.00 0.00 3.10
485 541 6.212955 CAATTAACGAATCTCTCTCCCTCTC 58.787 44.000 0.00 0.00 0.00 3.20
533 589 4.410743 GCTTGCCGAACCTGCTGC 62.411 66.667 0.00 0.00 0.00 5.25
534 590 2.979676 TGCTTGCCGAACCTGCTG 60.980 61.111 0.00 0.00 0.00 4.41
535 591 2.980233 GTGCTTGCCGAACCTGCT 60.980 61.111 0.00 0.00 0.00 4.24
560 617 2.262915 GTGCTCGTGGTGCTAGCT 59.737 61.111 17.23 0.00 36.90 3.32
566 623 1.380403 TTTGTTGGGTGCTCGTGGTG 61.380 55.000 0.00 0.00 0.00 4.17
567 624 0.681564 TTTTGTTGGGTGCTCGTGGT 60.682 50.000 0.00 0.00 0.00 4.16
568 625 0.673437 ATTTTGTTGGGTGCTCGTGG 59.327 50.000 0.00 0.00 0.00 4.94
569 626 1.066908 ACATTTTGTTGGGTGCTCGTG 59.933 47.619 0.00 0.00 0.00 4.35
575 632 2.890311 TGCTAGGACATTTTGTTGGGTG 59.110 45.455 0.00 0.00 0.00 4.61
634 775 1.400371 CCTCGAGTTCGTCACTGTCTG 60.400 57.143 12.31 0.00 40.80 3.51
635 776 0.875728 CCTCGAGTTCGTCACTGTCT 59.124 55.000 12.31 0.00 40.80 3.41
646 787 6.070995 TGGTTCATCAATAGTAACCTCGAGTT 60.071 38.462 12.31 8.43 41.60 3.01
658 799 1.952296 GCTGGGCTGGTTCATCAATAG 59.048 52.381 0.00 0.00 0.00 1.73
679 820 0.957395 CGGTGTGCTTGAGGCTCAAT 60.957 55.000 28.67 0.00 44.42 2.57
680 821 1.597854 CGGTGTGCTTGAGGCTCAA 60.598 57.895 27.01 27.01 44.42 3.02
713 854 0.387202 ATGCTACTACTGCAGCTCCG 59.613 55.000 15.27 1.91 44.04 4.63
718 859 5.292101 GGTAAGAAACATGCTACTACTGCAG 59.708 44.000 13.48 13.48 44.04 4.41
721 862 5.288712 CACGGTAAGAAACATGCTACTACTG 59.711 44.000 0.00 0.00 0.00 2.74
731 878 1.073284 ACTGGCCACGGTAAGAAACAT 59.927 47.619 0.00 0.00 33.46 2.71
742 892 2.388232 GCCTCGTTTACTGGCCACG 61.388 63.158 0.00 3.20 40.71 4.94
827 1010 0.739813 GTCACCGTATCCTGTGTGCC 60.740 60.000 0.00 0.00 34.14 5.01
869 1061 2.791849 GCAGAGAGTACGCGAGGTAAAG 60.792 54.545 15.93 0.00 31.61 1.85
876 1068 1.448365 TACGGCAGAGAGTACGCGA 60.448 57.895 15.93 0.00 0.00 5.87
896 1088 0.036671 AGGCGAGACCCCTTTTTACG 60.037 55.000 0.00 0.00 40.58 3.18
934 1148 3.322318 GAGGGAGTGTGGGAGCAGC 62.322 68.421 0.00 0.00 0.00 5.25
1153 1376 3.003763 GCAGAGGGAGAACGGGGT 61.004 66.667 0.00 0.00 0.00 4.95
1219 1457 0.179097 GAGGAGGATGCGTTGGAGTC 60.179 60.000 0.00 0.00 0.00 3.36
1220 1458 1.901085 GAGGAGGATGCGTTGGAGT 59.099 57.895 0.00 0.00 0.00 3.85
1253 1491 4.035102 GCCTGGACCTTTCCCGCT 62.035 66.667 0.00 0.00 42.01 5.52
1256 1494 2.231380 TCAGGCCTGGACCTTTCCC 61.231 63.158 32.23 0.00 42.01 3.97
1264 1502 3.319198 GTTCGGGTCAGGCCTGGA 61.319 66.667 32.23 18.56 43.94 3.86
1651 1895 4.200283 CTCCTCCAGCGCCTCGAC 62.200 72.222 2.29 0.00 0.00 4.20
2193 2437 7.200455 ACATTTGTCCACTAAGCTAAACAAAC 58.800 34.615 0.00 0.00 38.84 2.93
2203 2447 7.745620 AAAGGAGTAACATTTGTCCACTAAG 57.254 36.000 0.00 0.00 31.17 2.18
2214 2458 5.163499 TGGTTTGCGAAAAAGGAGTAACATT 60.163 36.000 0.00 0.00 0.00 2.71
2238 2482 5.927954 AATTCAAACGATGCAGCAATTTT 57.072 30.435 1.53 0.00 0.00 1.82
2239 2483 5.334260 CCAAATTCAAACGATGCAGCAATTT 60.334 36.000 1.53 3.46 0.00 1.82
2240 2484 4.152759 CCAAATTCAAACGATGCAGCAATT 59.847 37.500 1.53 0.00 0.00 2.32
2280 2525 5.559148 ATTGGGTAATTCCAGTGCAAAAA 57.441 34.783 0.00 0.00 38.17 1.94
2286 2531 6.187682 AGTTCCTAATTGGGTAATTCCAGTG 58.812 40.000 7.83 0.00 37.64 3.66
2310 2555 5.473162 AGTCGATGGAAAATGACACATGAAA 59.527 36.000 0.00 0.00 33.83 2.69
2352 2597 7.919690 TCGGAATCTTTAGAAGCAACATTATG 58.080 34.615 0.00 0.00 0.00 1.90
2357 2602 6.402118 CGAATTCGGAATCTTTAGAAGCAACA 60.402 38.462 20.16 0.00 35.37 3.33
2371 2616 6.340962 TCAGATATACCACGAATTCGGAAT 57.659 37.500 29.79 18.64 44.95 3.01
2377 2622 8.208224 TGGTACATTTCAGATATACCACGAATT 58.792 33.333 0.00 0.00 40.24 2.17
2385 2630 9.864034 CAAATTCGTGGTACATTTCAGATATAC 57.136 33.333 0.00 0.00 44.52 1.47
2386 2631 9.825109 TCAAATTCGTGGTACATTTCAGATATA 57.175 29.630 0.00 0.00 44.52 0.86
2389 2634 6.655003 ACTCAAATTCGTGGTACATTTCAGAT 59.345 34.615 0.00 0.00 44.52 2.90
2390 2635 5.995282 ACTCAAATTCGTGGTACATTTCAGA 59.005 36.000 0.00 0.00 44.52 3.27
2392 2637 5.529430 ACACTCAAATTCGTGGTACATTTCA 59.471 36.000 0.00 0.00 44.52 2.69
2393 2638 5.997385 ACACTCAAATTCGTGGTACATTTC 58.003 37.500 0.00 0.00 44.52 2.17
2395 2640 5.763204 AGAACACTCAAATTCGTGGTACATT 59.237 36.000 0.00 0.00 44.52 2.71
2396 2641 5.305585 AGAACACTCAAATTCGTGGTACAT 58.694 37.500 0.00 0.00 44.52 2.29
2397 2642 4.699637 AGAACACTCAAATTCGTGGTACA 58.300 39.130 0.00 0.00 35.51 2.90
2398 2643 5.440685 CAAGAACACTCAAATTCGTGGTAC 58.559 41.667 7.22 0.00 35.51 3.34
2399 2644 4.513692 CCAAGAACACTCAAATTCGTGGTA 59.486 41.667 9.82 0.00 44.59 3.25
2401 2646 3.888934 CCAAGAACACTCAAATTCGTGG 58.111 45.455 4.87 4.87 44.38 4.94
2403 2648 5.576447 AAACCAAGAACACTCAAATTCGT 57.424 34.783 0.00 0.00 0.00 3.85
2404 2649 6.033341 TGAAAACCAAGAACACTCAAATTCG 58.967 36.000 0.00 0.00 0.00 3.34
2405 2650 8.424274 AATGAAAACCAAGAACACTCAAATTC 57.576 30.769 0.00 0.00 0.00 2.17
2406 2651 8.791327 AAATGAAAACCAAGAACACTCAAATT 57.209 26.923 0.00 0.00 0.00 1.82
2409 2654 6.816140 GGAAAATGAAAACCAAGAACACTCAA 59.184 34.615 0.00 0.00 0.00 3.02
2411 2656 6.337356 TGGAAAATGAAAACCAAGAACACTC 58.663 36.000 0.00 0.00 0.00 3.51
2412 2657 6.293004 TGGAAAATGAAAACCAAGAACACT 57.707 33.333 0.00 0.00 0.00 3.55
2414 2659 5.526846 GCATGGAAAATGAAAACCAAGAACA 59.473 36.000 0.00 0.00 36.00 3.18
2415 2660 5.526846 TGCATGGAAAATGAAAACCAAGAAC 59.473 36.000 0.00 0.00 36.00 3.01
2416 2661 5.678583 TGCATGGAAAATGAAAACCAAGAA 58.321 33.333 0.00 0.00 36.00 2.52
2417 2662 5.163322 ACTGCATGGAAAATGAAAACCAAGA 60.163 36.000 0.00 0.00 36.00 3.02
2419 2664 5.033589 ACTGCATGGAAAATGAAAACCAA 57.966 34.783 0.00 0.00 36.00 3.67
2420 2665 4.502950 GGACTGCATGGAAAATGAAAACCA 60.503 41.667 0.00 0.00 36.83 3.67
2421 2666 3.996363 GGACTGCATGGAAAATGAAAACC 59.004 43.478 0.00 0.00 0.00 3.27
2434 2698 4.569943 AGTAACACAACTAGGACTGCATG 58.430 43.478 0.00 0.00 0.00 4.06
2435 2699 4.891992 AGTAACACAACTAGGACTGCAT 57.108 40.909 0.00 0.00 0.00 3.96
2458 2807 6.646240 ACCATGCATTCTGACAAATGTAAAAC 59.354 34.615 0.00 0.00 38.60 2.43
2473 2822 7.012704 AGTCTTTCACATATACACCATGCATTC 59.987 37.037 0.00 0.00 0.00 2.67
2474 2823 6.830324 AGTCTTTCACATATACACCATGCATT 59.170 34.615 0.00 0.00 0.00 3.56
2475 2824 6.261603 CAGTCTTTCACATATACACCATGCAT 59.738 38.462 0.00 0.00 0.00 3.96
2476 2825 5.585844 CAGTCTTTCACATATACACCATGCA 59.414 40.000 0.00 0.00 0.00 3.96
2477 2826 5.817296 TCAGTCTTTCACATATACACCATGC 59.183 40.000 0.00 0.00 0.00 4.06
2478 2827 7.044181 AGTCAGTCTTTCACATATACACCATG 58.956 38.462 0.00 0.00 0.00 3.66
2479 2828 7.187824 AGTCAGTCTTTCACATATACACCAT 57.812 36.000 0.00 0.00 0.00 3.55
2480 2829 6.351033 GGAGTCAGTCTTTCACATATACACCA 60.351 42.308 0.00 0.00 0.00 4.17
2481 2830 6.043411 GGAGTCAGTCTTTCACATATACACC 58.957 44.000 0.00 0.00 0.00 4.16
2482 2831 6.868622 AGGAGTCAGTCTTTCACATATACAC 58.131 40.000 0.00 0.00 0.00 2.90
2483 2832 6.892456 AGAGGAGTCAGTCTTTCACATATACA 59.108 38.462 0.00 0.00 0.00 2.29
2490 2839 3.063485 GCAAGAGGAGTCAGTCTTTCAC 58.937 50.000 4.61 0.00 30.31 3.18
2510 2859 2.798976 TGTCTGCAAAAATGGTGAGC 57.201 45.000 0.00 0.00 0.00 4.26
2769 3118 2.649034 GCGTCTTCTCGGACCACA 59.351 61.111 0.00 0.00 33.07 4.17
2795 3144 1.417592 GCTTCATGCTGTCGTCGTG 59.582 57.895 0.00 0.00 38.95 4.35
2864 3213 2.033801 GCTCATGCCATATTCACACACC 59.966 50.000 0.00 0.00 0.00 4.16
2967 3316 5.449862 GCTGTTTGTTAGGTTCACATTCACA 60.450 40.000 0.00 0.00 0.00 3.58
2968 3317 4.976116 GCTGTTTGTTAGGTTCACATTCAC 59.024 41.667 0.00 0.00 0.00 3.18
2969 3318 4.887071 AGCTGTTTGTTAGGTTCACATTCA 59.113 37.500 0.00 0.00 0.00 2.57
2970 3319 5.008613 TGAGCTGTTTGTTAGGTTCACATTC 59.991 40.000 0.00 0.00 0.00 2.67
2971 3320 4.887071 TGAGCTGTTTGTTAGGTTCACATT 59.113 37.500 0.00 0.00 0.00 2.71
2972 3321 4.460263 TGAGCTGTTTGTTAGGTTCACAT 58.540 39.130 0.00 0.00 0.00 3.21
3013 3362 3.553922 CGCTTTCCTCCCATCTCTATCAC 60.554 52.174 0.00 0.00 0.00 3.06
3048 3398 1.750399 ACAATCTGCCATGCCGTCC 60.750 57.895 0.00 0.00 0.00 4.79
3083 3433 1.542915 CCTTTGCAGATTGACACCAGG 59.457 52.381 0.00 0.00 0.00 4.45
3134 3485 6.313658 TCAACAATGAGATTTACACGGATGAG 59.686 38.462 0.00 0.00 0.00 2.90
3164 3515 7.339976 TGGAATGCAATGAATTATGACTGAGAA 59.660 33.333 0.00 0.00 0.00 2.87
3175 3526 4.395959 AGCGAATGGAATGCAATGAATT 57.604 36.364 0.00 0.00 0.00 2.17
3193 3544 3.058293 TCATCAACTTGGTGCTTTAAGCG 60.058 43.478 12.54 0.00 46.26 4.68
3203 3555 4.207891 ACGAAGCTATCATCAACTTGGT 57.792 40.909 0.00 0.00 0.00 3.67
3251 3603 3.127548 CGCAAGGTGCAACAATCTAATCT 59.872 43.478 3.64 0.00 45.36 2.40
3274 3626 6.347725 CGGCATATATAGTCAACAAAGGAAGC 60.348 42.308 0.00 0.00 0.00 3.86
3330 3682 3.320541 TGAACTTGGCGATCCAACAAAAT 59.679 39.130 0.00 0.00 46.89 1.82
3344 3696 5.048083 TGGTAAGCTTTAAGCATGAACTTGG 60.048 40.000 19.63 0.00 45.56 3.61
3351 3703 5.627499 TCAGTTGGTAAGCTTTAAGCATG 57.373 39.130 19.63 0.00 45.56 4.06
3369 3721 9.672086 TTTCGACAAAAATTCGATTTATTCAGT 57.328 25.926 0.00 0.00 44.59 3.41
3622 3982 2.040544 CCAAGCGGCACCACCTAAG 61.041 63.158 1.45 0.00 35.61 2.18
3623 3983 2.033448 CCAAGCGGCACCACCTAA 59.967 61.111 1.45 0.00 35.61 2.69
3624 3984 2.925706 TCCAAGCGGCACCACCTA 60.926 61.111 1.45 0.00 35.61 3.08


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

AutoCloner maintained by Alex Coulton.