Multiple sequence alignment - TraesCS4B01G336400

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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 TraesCS4B01G336400 chr4B 100.000 3646 0 0 1 3646 628659074 628662719 0.000000e+00 6734.0
1 TraesCS4B01G336400 chr4B 88.197 466 52 3 2199 2662 604532731 604532267 1.480000e-153 553.0
2 TraesCS4B01G336400 chr4B 89.831 295 27 3 1132 1423 604533163 604532869 3.440000e-100 375.0
3 TraesCS4B01G336400 chr4B 88.028 142 11 2 2766 2901 628675574 628675433 2.910000e-36 163.0
4 TraesCS4B01G336400 chr4D 83.838 1652 127 54 540 2116 489740482 489742068 0.000000e+00 1443.0
5 TraesCS4B01G336400 chr4D 93.235 680 25 3 2110 2768 489742238 489742917 0.000000e+00 981.0
6 TraesCS4B01G336400 chr4D 89.755 449 42 4 1 447 489739496 489739942 4.080000e-159 571.0
7 TraesCS4B01G336400 chr4D 87.983 466 53 3 2199 2662 478231101 478230637 6.880000e-152 547.0
8 TraesCS4B01G336400 chr4D 90.031 321 26 3 1111 1425 478231547 478231227 9.420000e-111 411.0
9 TraesCS4B01G336400 chr4D 76.471 187 31 5 3135 3308 116146466 116146280 5.010000e-14 89.8
10 TraesCS4B01G336400 chr5A 87.621 1236 89 39 540 1740 671190476 671191682 0.000000e+00 1376.0
11 TraesCS4B01G336400 chr5A 87.137 241 17 5 1877 2116 671192282 671192509 1.000000e-65 261.0
12 TraesCS4B01G336400 chr5A 89.130 92 8 2 1765 1856 671191736 671191825 2.980000e-21 113.0
13 TraesCS4B01G336400 chr5A 92.857 70 4 1 477 545 671190332 671190401 2.320000e-17 100.0
14 TraesCS4B01G336400 chr7B 95.827 623 26 0 2925 3547 684442428 684443050 0.000000e+00 1007.0
15 TraesCS4B01G336400 chr7B 90.726 496 40 4 2184 2675 582655198 582655691 0.000000e+00 656.0
16 TraesCS4B01G336400 chr7B 84.158 505 65 15 27 528 619601154 619600662 3.290000e-130 475.0
17 TraesCS4B01G336400 chr7B 95.172 290 14 0 1129 1418 582653179 582653468 3.320000e-125 459.0
18 TraesCS4B01G336400 chr7B 92.683 164 7 1 2773 2931 684440836 684440999 7.870000e-57 231.0
19 TraesCS4B01G336400 chr7B 97.196 107 2 1 3540 3646 684443141 684443246 2.890000e-41 180.0
20 TraesCS4B01G336400 chr7B 92.500 80 5 1 2773 2852 684456883 684456805 2.980000e-21 113.0
21 TraesCS4B01G336400 chr7D 94.224 554 25 3 2773 3319 613375514 613376067 0.000000e+00 839.0
22 TraesCS4B01G336400 chr7D 92.058 554 22 5 2773 3319 541507205 541506667 0.000000e+00 760.0
23 TraesCS4B01G336400 chr7D 87.652 575 55 8 2111 2675 539764345 539764913 0.000000e+00 654.0
24 TraesCS4B01G336400 chr7D 94.562 331 16 2 3314 3642 613376133 613376463 9.030000e-141 510.0
25 TraesCS4B01G336400 chr7D 95.548 292 13 0 1127 1418 539761151 539761442 5.510000e-128 468.0
26 TraesCS4B01G336400 chr7D 96.552 232 8 0 3314 3545 541506601 541506370 5.710000e-103 385.0
27 TraesCS4B01G336400 chr7D 91.791 134 6 1 2773 2901 541504376 541504509 8.040000e-42 182.0
28 TraesCS4B01G336400 chr7D 92.248 129 4 2 2778 2901 613383220 613383093 1.040000e-40 178.0
29 TraesCS4B01G336400 chr7A 91.494 482 37 2 2188 2665 620934763 620935244 0.000000e+00 660.0
30 TraesCS4B01G336400 chr7A 95.517 290 13 0 1129 1418 620932430 620932719 7.130000e-127 464.0
31 TraesCS4B01G336400 chr7A 83.086 337 46 6 3319 3646 596676208 596675874 2.750000e-76 296.0
32 TraesCS4B01G336400 chr4A 88.553 463 51 2 2198 2658 684899729 684899267 8.840000e-156 560.0
33 TraesCS4B01G336400 chr4A 89.180 305 30 2 1125 1426 684900120 684899816 9.560000e-101 377.0
34 TraesCS4B01G336400 chr2A 96.407 334 12 0 3313 3646 668532994 668533327 5.320000e-153 551.0
35 TraesCS4B01G336400 chr2A 92.795 347 23 2 2845 3189 668532404 668532750 5.440000e-138 501.0
36 TraesCS4B01G336400 chr2A 94.505 182 6 3 3142 3319 668532748 668532929 9.970000e-71 278.0
37 TraesCS4B01G336400 chr2A 93.333 135 4 1 2772 2901 668538013 668537879 1.030000e-45 195.0
38 TraesCS4B01G336400 chr2B 85.329 334 38 7 3319 3644 61495170 61495500 5.830000e-88 335.0
39 TraesCS4B01G336400 chr2B 90.196 102 7 1 3545 3646 709849930 709850028 2.950000e-26 130.0
40 TraesCS4B01G336400 chr2B 76.471 187 30 7 3135 3308 709849238 709849423 5.010000e-14 89.8
41 TraesCS4B01G336400 chr1B 83.728 338 44 6 3318 3646 112877479 112877814 3.540000e-80 309.0
42 TraesCS4B01G336400 chr1B 92.593 135 5 1 2772 2901 28558370 28558504 4.810000e-44 189.0
43 TraesCS4B01G336400 chr1D 83.881 335 39 7 3319 3645 71647868 71648195 4.570000e-79 305.0
44 TraesCS4B01G336400 chr1D 77.540 187 29 5 3135 3308 476215634 476215448 2.320000e-17 100.0
45 TraesCS4B01G336400 chr1A 83.136 338 44 8 3318 3645 71775657 71775991 2.750000e-76 296.0
46 TraesCS4B01G336400 chr1A 82.196 337 49 6 3319 3646 221796761 221797095 2.770000e-71 279.0
47 TraesCS4B01G336400 chr6D 75.269 372 60 20 2958 3308 471339793 471340153 8.160000e-32 148.0
48 TraesCS4B01G336400 chr3B 90.196 102 7 1 3545 3646 248613880 248613782 2.950000e-26 130.0
49 TraesCS4B01G336400 chr3B 77.778 198 31 5 3135 3319 248614568 248614371 3.850000e-20 110.0


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 TraesCS4B01G336400 chr4B 628659074 628662719 3645 False 6734.000000 6734 100.000000 1 3646 1 chr4B.!!$F1 3645
1 TraesCS4B01G336400 chr4B 604532267 604533163 896 True 464.000000 553 89.014000 1132 2662 2 chr4B.!!$R2 1530
2 TraesCS4B01G336400 chr4D 489739496 489742917 3421 False 998.333333 1443 88.942667 1 2768 3 chr4D.!!$F1 2767
3 TraesCS4B01G336400 chr4D 478230637 478231547 910 True 479.000000 547 89.007000 1111 2662 2 chr4D.!!$R2 1551
4 TraesCS4B01G336400 chr5A 671190332 671192509 2177 False 462.500000 1376 89.186250 477 2116 4 chr5A.!!$F1 1639
5 TraesCS4B01G336400 chr7B 582653179 582655691 2512 False 557.500000 656 92.949000 1129 2675 2 chr7B.!!$F1 1546
6 TraesCS4B01G336400 chr7B 684440836 684443246 2410 False 472.666667 1007 95.235333 2773 3646 3 chr7B.!!$F2 873
7 TraesCS4B01G336400 chr7D 613375514 613376463 949 False 674.500000 839 94.393000 2773 3642 2 chr7D.!!$F3 869
8 TraesCS4B01G336400 chr7D 541506370 541507205 835 True 572.500000 760 94.305000 2773 3545 2 chr7D.!!$R2 772
9 TraesCS4B01G336400 chr7D 539761151 539764913 3762 False 561.000000 654 91.600000 1127 2675 2 chr7D.!!$F2 1548
10 TraesCS4B01G336400 chr7A 620932430 620935244 2814 False 562.000000 660 93.505500 1129 2665 2 chr7A.!!$F1 1536
11 TraesCS4B01G336400 chr4A 684899267 684900120 853 True 468.500000 560 88.866500 1125 2658 2 chr4A.!!$R1 1533
12 TraesCS4B01G336400 chr2A 668532404 668533327 923 False 443.333333 551 94.569000 2845 3646 3 chr2A.!!$F1 801

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
379 381 0.249155 GACCGTGTCAGTGAAACCGA 60.249 55.0 7.9 0.0 37.8 4.69 F
977 1479 0.321122 CCGTCTCTGCTCCTTTTGCT 60.321 55.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1403 1927 1.130373 GGTACGTACCGTCGAACATGA 59.870 52.381 28.0 0.0 41.54 3.07 R
2716 6954 0.984109 CAAATCGCACGCAACATTCC 59.016 50.000 0.0 0.0 0.00 3.01 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 9.515226 TTAAAGCAAAAGGAGTACTGAATATGT 57.485 29.630 0.00 0.00 0.00 2.29
36 37 4.433615 AGGAGTACTGAATATGTTGCACG 58.566 43.478 0.00 0.00 0.00 5.34
40 41 5.419542 AGTACTGAATATGTTGCACGTCAT 58.580 37.500 0.00 0.00 0.00 3.06
55 56 4.630069 GCACGTCATGAAGGTTATACTTGT 59.370 41.667 13.36 0.00 0.00 3.16
79 80 8.081633 TGTGATTACAAATGATTTGAACACCTC 58.918 33.333 23.37 11.16 43.26 3.85
87 88 9.048446 CAAATGATTTGAACACCTCTTTGAAAT 57.952 29.630 12.37 0.00 43.26 2.17
102 103 7.042797 TCTTTGAAATGGAAAGAACAAGAGG 57.957 36.000 0.00 0.00 36.67 3.69
103 104 4.853924 TGAAATGGAAAGAACAAGAGGC 57.146 40.909 0.00 0.00 0.00 4.70
152 153 4.463186 ACAACTAAGAGAAGGCTACACGAT 59.537 41.667 0.00 0.00 0.00 3.73
161 162 6.266558 AGAGAAGGCTACACGATATGAGAAAT 59.733 38.462 0.00 0.00 0.00 2.17
167 168 5.107298 GCTACACGATATGAGAAATGAAGGC 60.107 44.000 0.00 0.00 0.00 4.35
185 186 4.439253 AGGCTGGGAAGATATGTTTACC 57.561 45.455 0.00 1.66 0.00 2.85
186 187 3.785887 AGGCTGGGAAGATATGTTTACCA 59.214 43.478 8.88 8.88 0.00 3.25
194 195 9.403583 TGGGAAGATATGTTTACCAAAGTTATC 57.596 33.333 7.29 0.00 0.00 1.75
207 208 5.240623 ACCAAAGTTATCGAGTTTTGCATCA 59.759 36.000 0.00 0.00 31.03 3.07
210 211 7.358352 CCAAAGTTATCGAGTTTTGCATCAAAC 60.358 37.037 5.97 5.97 32.79 2.93
215 216 5.375417 TCGAGTTTTGCATCAAACATGAT 57.625 34.783 14.70 0.00 32.79 2.45
229 230 8.464404 CATCAAACATGATATTTCACTTCCAGT 58.536 33.333 0.00 0.00 33.85 4.00
231 232 8.298854 TCAAACATGATATTTCACTTCCAGTTG 58.701 33.333 0.00 0.00 33.85 3.16
253 254 2.755064 TGCCATGCATGTTCCCCG 60.755 61.111 24.58 9.73 31.71 5.73
265 266 1.278127 TGTTCCCCGAGGATCAAAGTC 59.722 52.381 0.00 0.00 43.54 3.01
266 267 1.555533 GTTCCCCGAGGATCAAAGTCT 59.444 52.381 0.00 0.00 43.54 3.24
274 275 4.363999 CGAGGATCAAAGTCTAAGCGAAT 58.636 43.478 0.00 0.00 33.17 3.34
281 282 5.741011 TCAAAGTCTAAGCGAATAACCCAT 58.259 37.500 0.00 0.00 0.00 4.00
282 283 5.584649 TCAAAGTCTAAGCGAATAACCCATG 59.415 40.000 0.00 0.00 0.00 3.66
315 317 2.299582 TCAAACGAGGATTACCACCGAA 59.700 45.455 0.00 0.00 37.71 4.30
327 329 5.918426 TTACCACCGAAGTGTCATGTATA 57.082 39.130 0.00 0.00 42.88 1.47
328 330 4.119442 ACCACCGAAGTGTCATGTATAC 57.881 45.455 0.00 0.00 42.88 1.47
330 332 4.951715 ACCACCGAAGTGTCATGTATACTA 59.048 41.667 4.17 0.00 42.88 1.82
361 363 1.003928 AGTGCATGTGGAGCTTCATGA 59.996 47.619 22.51 5.61 42.52 3.07
363 365 0.737219 GCATGTGGAGCTTCATGACC 59.263 55.000 22.51 5.93 42.52 4.02
367 369 0.320771 GTGGAGCTTCATGACCGTGT 60.321 55.000 0.00 0.00 0.00 4.49
378 380 0.528901 TGACCGTGTCAGTGAAACCG 60.529 55.000 7.90 4.13 37.67 4.44
379 381 0.249155 GACCGTGTCAGTGAAACCGA 60.249 55.000 7.90 0.00 37.80 4.69
380 382 0.529119 ACCGTGTCAGTGAAACCGAC 60.529 55.000 7.90 0.00 37.80 4.79
395 397 1.692519 ACCGACACTACCTTGCTTCTT 59.307 47.619 0.00 0.00 0.00 2.52
399 401 3.740115 GACACTACCTTGCTTCTTGGAA 58.260 45.455 0.00 0.00 0.00 3.53
421 423 2.171003 GGGTTGTTTGGATCCTTCAGG 58.829 52.381 14.23 0.00 0.00 3.86
423 425 3.245122 GGGTTGTTTGGATCCTTCAGGTA 60.245 47.826 14.23 0.00 36.34 3.08
424 426 3.756963 GGTTGTTTGGATCCTTCAGGTAC 59.243 47.826 14.23 5.06 36.34 3.34
432 434 4.844085 TGGATCCTTCAGGTACTTTCTCAA 59.156 41.667 14.23 0.00 34.60 3.02
433 435 5.309543 TGGATCCTTCAGGTACTTTCTCAAA 59.690 40.000 14.23 0.00 34.60 2.69
447 449 7.410120 ACTTTCTCAAAACTTTGACAAGGAT 57.590 32.000 16.59 0.00 41.88 3.24
448 450 7.840931 ACTTTCTCAAAACTTTGACAAGGATT 58.159 30.769 16.59 0.00 41.88 3.01
449 451 8.314021 ACTTTCTCAAAACTTTGACAAGGATTT 58.686 29.630 16.59 2.07 41.88 2.17
450 452 9.154847 CTTTCTCAAAACTTTGACAAGGATTTT 57.845 29.630 4.05 4.92 41.88 1.82
451 453 9.500785 TTTCTCAAAACTTTGACAAGGATTTTT 57.499 25.926 4.05 0.00 41.88 1.94
477 480 2.691526 TGGCCGTGACTCGTTTATATCT 59.308 45.455 0.00 0.00 37.94 1.98
478 481 3.243301 TGGCCGTGACTCGTTTATATCTC 60.243 47.826 0.00 0.00 37.94 2.75
480 483 3.303593 GCCGTGACTCGTTTATATCTCGA 60.304 47.826 0.00 0.00 37.94 4.04
524 527 5.497474 AGGTCGAATAACTTAGTTGCCAAT 58.503 37.500 8.00 0.00 0.00 3.16
538 906 8.810652 TTAGTTGCCAATTTGATAACTTTGTC 57.189 30.769 17.41 0.00 33.93 3.18
546 914 7.254252 CCAATTTGATAACTTTGTCGCAAACAA 60.254 33.333 0.00 0.00 46.11 2.83
564 1016 3.288092 ACAACCTTTCTCTGGTGTTTCC 58.712 45.455 0.00 0.00 37.93 3.13
568 1020 4.610333 ACCTTTCTCTGGTGTTTCCTTTT 58.390 39.130 0.00 0.00 36.30 2.27
574 1026 5.694995 TCTCTGGTGTTTCCTTTTCTGAAT 58.305 37.500 0.00 0.00 37.07 2.57
578 1030 6.936900 TCTGGTGTTTCCTTTTCTGAATCTAG 59.063 38.462 0.00 0.00 37.07 2.43
629 1089 4.699257 GGTTGAGAGAGCATTTTCTGTGAT 59.301 41.667 0.00 0.00 0.00 3.06
651 1111 6.693113 TGATATATATCAAGTCTGATTCGCGC 59.307 38.462 20.75 0.00 39.36 6.86
663 1123 0.881118 ATTCGCGCAACAGAATTGGT 59.119 45.000 8.75 0.00 33.73 3.67
664 1124 1.514003 TTCGCGCAACAGAATTGGTA 58.486 45.000 8.75 0.00 0.00 3.25
666 1126 1.195900 TCGCGCAACAGAATTGGTAAC 59.804 47.619 8.75 0.00 0.00 2.50
669 1129 2.350007 GCGCAACAGAATTGGTAACGAA 60.350 45.455 0.30 0.00 42.51 3.85
682 1142 9.594478 GAATTGGTAACGAATTTTTATCCCATT 57.406 29.630 0.00 0.00 42.51 3.16
701 1161 8.877864 TCCCATTGTTTGATTACTATTTCAGT 57.122 30.769 0.00 0.00 41.62 3.41
703 1163 7.910162 CCCATTGTTTGATTACTATTTCAGTCG 59.090 37.037 0.00 0.00 38.80 4.18
704 1164 8.664798 CCATTGTTTGATTACTATTTCAGTCGA 58.335 33.333 0.00 0.00 38.80 4.20
717 1181 5.733620 TTTCAGTCGATTACTACCAAGGT 57.266 39.130 0.00 0.00 35.76 3.50
719 1183 4.338012 TCAGTCGATTACTACCAAGGTCA 58.662 43.478 0.00 0.00 35.76 4.02
720 1184 4.157289 TCAGTCGATTACTACCAAGGTCAC 59.843 45.833 0.00 0.00 35.76 3.67
812 1310 2.738846 CCGTGACGTACTACTGTACTGT 59.261 50.000 10.46 10.46 44.97 3.55
889 1389 2.795329 AGCTTGACCCCACATAGTTTG 58.205 47.619 0.00 0.00 0.00 2.93
890 1390 2.375174 AGCTTGACCCCACATAGTTTGA 59.625 45.455 0.00 0.00 0.00 2.69
891 1391 2.749621 GCTTGACCCCACATAGTTTGAG 59.250 50.000 0.00 0.00 0.00 3.02
892 1392 3.810743 GCTTGACCCCACATAGTTTGAGT 60.811 47.826 0.00 0.00 0.00 3.41
893 1393 3.695830 TGACCCCACATAGTTTGAGTC 57.304 47.619 0.00 0.00 0.00 3.36
895 1395 2.572104 GACCCCACATAGTTTGAGTCCT 59.428 50.000 0.00 0.00 0.00 3.85
915 1417 4.536687 GCCGCCGTTGTGCATAGC 62.537 66.667 0.00 0.00 0.00 2.97
973 1475 2.294078 CCCCCGTCTCTGCTCCTTT 61.294 63.158 0.00 0.00 0.00 3.11
975 1477 0.674895 CCCCGTCTCTGCTCCTTTTG 60.675 60.000 0.00 0.00 0.00 2.44
976 1478 1.301677 CCCGTCTCTGCTCCTTTTGC 61.302 60.000 0.00 0.00 0.00 3.68
977 1479 0.321122 CCGTCTCTGCTCCTTTTGCT 60.321 55.000 0.00 0.00 0.00 3.91
978 1480 1.066858 CCGTCTCTGCTCCTTTTGCTA 60.067 52.381 0.00 0.00 0.00 3.49
997 1506 0.894184 ACGAGCTTCTCTCCCACGAA 60.894 55.000 0.00 0.00 38.62 3.85
1051 1560 7.479603 CGTTGAAAATTCGAGATATATGCATGG 59.520 37.037 10.16 0.00 0.00 3.66
1052 1561 7.984422 TGAAAATTCGAGATATATGCATGGT 57.016 32.000 10.16 0.04 0.00 3.55
1056 1565 4.471904 TCGAGATATATGCATGGTTCCC 57.528 45.455 10.16 0.00 0.00 3.97
1137 1655 4.498520 CTGCTGGACGTCGCCGAT 62.499 66.667 9.92 0.00 37.88 4.18
1403 1927 3.394836 GCTCTTCCAGCTCCCCGT 61.395 66.667 0.00 0.00 45.83 5.28
1457 1986 2.594592 GTCACGCCCCTGCTTTGT 60.595 61.111 0.00 0.00 34.43 2.83
1471 2000 4.500205 CCTGCTTTGTTGCTGAAATTCTGA 60.500 41.667 4.00 0.00 34.47 3.27
1473 2002 4.098349 TGCTTTGTTGCTGAAATTCTGACT 59.902 37.500 4.00 0.00 0.00 3.41
1547 2076 1.521457 CCGCTGCGATCTTGGCTTA 60.521 57.895 25.45 0.00 0.00 3.09
1552 2081 3.604772 CGCTGCGATCTTGGCTTAATTAC 60.605 47.826 18.66 0.00 0.00 1.89
1561 2090 9.639601 CGATCTTGGCTTAATTACTGTATATCA 57.360 33.333 0.00 0.00 0.00 2.15
1634 2608 5.110940 GACATCCCTGTCGAGATTAGTAC 57.889 47.826 0.00 0.00 42.24 2.73
1653 2633 8.700722 TTAGTACGTAACAAAGTTGAGACAAA 57.299 30.769 0.00 0.00 0.00 2.83
1682 2662 3.058224 GCTTGTGCCAAAAGTATCGTTCT 60.058 43.478 0.00 0.00 0.00 3.01
1759 2772 7.389803 TCTTTGAACTTCATGACAAACTCAA 57.610 32.000 0.00 0.00 30.60 3.02
1797 2938 5.512082 CGTCATCTGAAAACCTACTCGTAAG 59.488 44.000 0.00 0.00 0.00 2.34
1802 2943 6.808829 TCTGAAAACCTACTCGTAAGTTTGA 58.191 36.000 4.97 0.00 36.92 2.69
1830 3088 9.132521 GTATTTTTACTTATGATGATGCATGGC 57.867 33.333 2.46 0.00 0.00 4.40
1887 3780 1.414538 GGGAGGTGATATCAGGGGTGA 60.415 57.143 5.42 0.00 0.00 4.02
1969 5661 6.721208 ACATTTTCCATGACTTCATACTGGTT 59.279 34.615 0.00 0.00 34.26 3.67
1974 5666 6.640518 TCCATGACTTCATACTGGTTAAGAC 58.359 40.000 0.00 0.00 34.26 3.01
2027 5736 2.135933 GTCCAATCGGATCGTCCATTC 58.864 52.381 0.00 0.00 45.33 2.67
2068 5781 6.404734 CCCCTTTGCTAGTGTCATTTGAATAC 60.405 42.308 0.00 0.00 0.00 1.89
2079 5792 5.163804 TGTCATTTGAATACCACGTGCATAC 60.164 40.000 10.91 0.62 0.00 2.39
2080 5793 4.938226 TCATTTGAATACCACGTGCATACA 59.062 37.500 10.91 3.39 0.00 2.29
2081 5794 5.588246 TCATTTGAATACCACGTGCATACAT 59.412 36.000 10.91 0.00 0.00 2.29
2082 5795 6.763610 TCATTTGAATACCACGTGCATACATA 59.236 34.615 10.91 2.30 0.00 2.29
2096 5809 4.812626 TGCATACATAATGTCAGCTGTCAG 59.187 41.667 18.30 7.89 37.93 3.51
2100 5813 5.405935 ACATAATGTCAGCTGTCAGTGTA 57.594 39.130 21.28 12.44 0.00 2.90
2101 5814 5.171476 ACATAATGTCAGCTGTCAGTGTAC 58.829 41.667 21.28 8.17 0.00 2.90
2210 6423 2.447572 TGTGGTGCTCCAGGGACA 60.448 61.111 7.99 0.00 45.24 4.02
2264 6477 1.302511 GGGCAAGAAGCTCACGGAA 60.303 57.895 0.00 0.00 45.63 4.30
2531 6744 1.153765 CGTGAAGCAGATCCAGCGA 60.154 57.895 2.47 0.00 37.01 4.93
2695 6933 0.108804 CGACCTTTGCTTAGCTCGGA 60.109 55.000 5.60 0.00 0.00 4.55
2696 6934 1.671850 CGACCTTTGCTTAGCTCGGAA 60.672 52.381 5.60 0.00 0.00 4.30
2761 6999 7.415877 GGTGGAGTAAATTACGCAAAACCATAT 60.416 37.037 15.30 0.00 32.42 1.78
2776 7014 9.338622 GCAAAACCATATACCATATATAGGACC 57.661 37.037 0.00 0.00 0.00 4.46
2816 7054 4.141965 TGCGACCATCCGTGCGAT 62.142 61.111 0.00 0.00 0.00 4.58
2903 7146 7.554959 AATACAGACCATAATACCGATTCCT 57.445 36.000 0.00 0.00 0.00 3.36
2937 8615 6.281405 ACTCTCGTCATTAAAACTGAACACT 58.719 36.000 0.00 0.00 0.00 3.55
2942 8620 5.907391 CGTCATTAAAACTGAACACTGAACC 59.093 40.000 0.00 0.00 0.00 3.62
2949 8627 4.170468 ACTGAACACTGAACCAAAGGAT 57.830 40.909 0.00 0.00 0.00 3.24
2990 8668 4.641954 GAAACAGATGCACAGAATACACG 58.358 43.478 0.00 0.00 0.00 4.49
3203 8934 5.784750 TCAATCTGACGCATCAAAAGTAG 57.215 39.130 0.00 0.00 33.30 2.57
3215 8946 7.387948 ACGCATCAAAAGTAGTAAATCTCACTT 59.612 33.333 0.00 0.00 32.73 3.16
3346 9152 5.339990 CCTTGTGGAACTTGTACAACAAAG 58.660 41.667 3.59 7.68 34.70 2.77
3361 9167 1.003118 ACAAAGCGTGGCCAGAATCTA 59.997 47.619 5.11 0.00 0.00 1.98
3379 9185 2.560981 TCTACAGATCCAAACAGCGACA 59.439 45.455 0.00 0.00 0.00 4.35
3492 9298 6.041423 TGTAGCATCTCTGATTTCAGTTCA 57.959 37.500 7.42 0.00 44.12 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.994432 CATATTCAGTACTCCTTTTGCTTTAAG 57.006 33.333 0.00 0.00 0.00 1.85
21 22 4.863152 TCATGACGTGCAACATATTCAG 57.137 40.909 0.00 0.00 35.74 3.02
30 31 4.827692 AGTATAACCTTCATGACGTGCAA 58.172 39.130 0.00 0.00 0.00 4.08
36 37 9.378551 TGTAATCACAAGTATAACCTTCATGAC 57.621 33.333 0.00 0.00 0.00 3.06
55 56 8.408043 AGAGGTGTTCAAATCATTTGTAATCA 57.592 30.769 9.98 3.34 41.36 2.57
64 65 7.015487 TCCATTTCAAAGAGGTGTTCAAATCAT 59.985 33.333 0.00 0.00 0.00 2.45
79 80 5.693555 GCCTCTTGTTCTTTCCATTTCAAAG 59.306 40.000 0.00 0.00 32.89 2.77
87 88 2.172505 TGACAGCCTCTTGTTCTTTCCA 59.827 45.455 0.00 0.00 0.00 3.53
102 103 6.529125 CCAAGATATGAAACAACATTGACAGC 59.471 38.462 0.00 0.00 0.00 4.40
103 104 7.596494 ACCAAGATATGAAACAACATTGACAG 58.404 34.615 0.00 0.00 0.00 3.51
152 153 4.474651 TCTTCCCAGCCTTCATTTCTCATA 59.525 41.667 0.00 0.00 0.00 2.15
161 162 4.591321 AAACATATCTTCCCAGCCTTCA 57.409 40.909 0.00 0.00 0.00 3.02
167 168 7.703058 AACTTTGGTAAACATATCTTCCCAG 57.297 36.000 0.00 0.00 0.00 4.45
185 186 7.167302 TGTTTGATGCAAAACTCGATAACTTTG 59.833 33.333 13.62 0.00 40.11 2.77
186 187 7.199766 TGTTTGATGCAAAACTCGATAACTTT 58.800 30.769 13.62 0.00 40.11 2.66
194 195 7.745022 AATATCATGTTTGATGCAAAACTCG 57.255 32.000 13.62 6.33 42.60 4.18
253 254 6.201234 GGTTATTCGCTTAGACTTTGATCCTC 59.799 42.308 0.00 0.00 0.00 3.71
265 266 5.277974 CCATCAACATGGGTTATTCGCTTAG 60.278 44.000 0.00 0.00 45.63 2.18
266 267 4.578516 CCATCAACATGGGTTATTCGCTTA 59.421 41.667 0.00 0.00 45.63 3.09
281 282 3.627123 CCTCGTTTGATATGCCATCAACA 59.373 43.478 9.65 1.50 37.71 3.33
282 283 3.876914 TCCTCGTTTGATATGCCATCAAC 59.123 43.478 9.65 5.84 37.71 3.18
299 301 1.922570 CACTTCGGTGGTAATCCTCG 58.077 55.000 0.00 0.00 41.88 4.63
315 317 8.187913 AGCTCAATGATAGTATACATGACACT 57.812 34.615 5.50 1.68 0.00 3.55
328 330 4.451435 CCACATGCACTAGCTCAATGATAG 59.549 45.833 0.00 0.00 42.74 2.08
330 332 3.118149 TCCACATGCACTAGCTCAATGAT 60.118 43.478 0.00 0.00 42.74 2.45
361 363 1.817881 TCGGTTTCACTGACACGGT 59.182 52.632 3.60 0.00 0.00 4.83
367 369 2.313317 AGGTAGTGTCGGTTTCACTGA 58.687 47.619 8.54 0.00 44.41 3.41
378 380 3.402628 TCCAAGAAGCAAGGTAGTGTC 57.597 47.619 0.00 0.00 0.00 3.67
379 381 3.857157 TTCCAAGAAGCAAGGTAGTGT 57.143 42.857 0.00 0.00 0.00 3.55
380 382 3.441572 CCATTCCAAGAAGCAAGGTAGTG 59.558 47.826 0.00 0.00 0.00 2.74
395 397 2.111613 AGGATCCAAACAACCCATTCCA 59.888 45.455 15.82 0.00 0.00 3.53
399 401 3.434309 CTGAAGGATCCAAACAACCCAT 58.566 45.455 15.82 0.00 0.00 4.00
421 423 7.758495 TCCTTGTCAAAGTTTTGAGAAAGTAC 58.242 34.615 15.25 2.37 45.76 2.73
423 425 6.834168 TCCTTGTCAAAGTTTTGAGAAAGT 57.166 33.333 15.25 0.00 45.76 2.66
424 426 8.707938 AAATCCTTGTCAAAGTTTTGAGAAAG 57.292 30.769 15.25 15.69 45.76 2.62
477 480 5.060506 TGCTTTCACTAACAAAATCCTCGA 58.939 37.500 0.00 0.00 0.00 4.04
478 481 5.356882 TGCTTTCACTAACAAAATCCTCG 57.643 39.130 0.00 0.00 0.00 4.63
480 483 5.598417 ACCTTGCTTTCACTAACAAAATCCT 59.402 36.000 0.00 0.00 0.00 3.24
481 484 5.842907 ACCTTGCTTTCACTAACAAAATCC 58.157 37.500 0.00 0.00 0.00 3.01
538 906 1.676006 ACCAGAGAAAGGTTGTTTGCG 59.324 47.619 0.00 0.00 35.33 4.85
546 914 3.953542 AAGGAAACACCAGAGAAAGGT 57.046 42.857 0.00 0.00 42.04 3.50
551 1002 4.771114 TCAGAAAAGGAAACACCAGAGA 57.229 40.909 0.00 0.00 42.04 3.10
568 1020 6.832384 ACCGTAGAACCAATACTAGATTCAGA 59.168 38.462 0.00 0.00 0.00 3.27
574 1026 3.313526 GCGACCGTAGAACCAATACTAGA 59.686 47.826 0.00 0.00 0.00 2.43
578 1030 1.564207 GGCGACCGTAGAACCAATAC 58.436 55.000 0.00 0.00 0.00 1.89
598 1055 1.905922 GCTCTCTCAACCGTTGCAGC 61.906 60.000 6.37 7.33 0.00 5.25
600 1057 0.035317 ATGCTCTCTCAACCGTTGCA 59.965 50.000 6.37 0.37 0.00 4.08
605 1062 3.070018 ACAGAAAATGCTCTCTCAACCG 58.930 45.455 0.00 0.00 0.00 4.44
629 1089 5.949735 TGCGCGAATCAGACTTGATATATA 58.050 37.500 12.10 0.00 43.20 0.86
647 1107 1.602191 GTTACCAATTCTGTTGCGCG 58.398 50.000 0.00 0.00 0.00 6.86
664 1124 9.500785 AATCAAACAATGGGATAAAAATTCGTT 57.499 25.926 0.00 0.00 0.00 3.85
691 1151 7.123847 ACCTTGGTAGTAATCGACTGAAATAGT 59.876 37.037 0.00 0.00 44.02 2.12
692 1152 7.490000 ACCTTGGTAGTAATCGACTGAAATAG 58.510 38.462 0.00 0.00 39.39 1.73
694 1154 6.070995 TGACCTTGGTAGTAATCGACTGAAAT 60.071 38.462 0.00 0.00 39.39 2.17
695 1155 5.244402 TGACCTTGGTAGTAATCGACTGAAA 59.756 40.000 0.00 0.00 39.39 2.69
697 1157 4.157289 GTGACCTTGGTAGTAATCGACTGA 59.843 45.833 0.00 0.00 39.39 3.41
698 1158 4.421948 GTGACCTTGGTAGTAATCGACTG 58.578 47.826 0.00 0.00 39.39 3.51
700 1160 3.194116 TGGTGACCTTGGTAGTAATCGAC 59.806 47.826 2.11 0.00 0.00 4.20
701 1161 3.433343 TGGTGACCTTGGTAGTAATCGA 58.567 45.455 2.11 0.00 0.00 3.59
703 1163 3.877508 GCATGGTGACCTTGGTAGTAATC 59.122 47.826 17.82 0.00 0.00 1.75
704 1164 3.265737 TGCATGGTGACCTTGGTAGTAAT 59.734 43.478 17.82 0.00 0.00 1.89
705 1165 2.640332 TGCATGGTGACCTTGGTAGTAA 59.360 45.455 17.82 0.00 0.00 2.24
707 1167 1.064003 TGCATGGTGACCTTGGTAGT 58.936 50.000 17.82 0.00 0.00 2.73
708 1168 2.425143 ATGCATGGTGACCTTGGTAG 57.575 50.000 17.82 0.00 0.00 3.18
717 1181 5.830799 ATCTTGATAGGTATGCATGGTGA 57.169 39.130 10.16 0.00 0.00 4.02
719 1183 7.062322 TGAAAATCTTGATAGGTATGCATGGT 58.938 34.615 10.16 0.00 0.00 3.55
720 1184 7.514784 TGAAAATCTTGATAGGTATGCATGG 57.485 36.000 10.16 0.00 0.00 3.66
915 1417 0.680921 AATGGGAATGGCGTCCTGTG 60.681 55.000 6.95 0.00 37.85 3.66
919 1421 0.682855 TGGAAATGGGAATGGCGTCC 60.683 55.000 0.00 0.00 36.90 4.79
920 1422 0.455815 GTGGAAATGGGAATGGCGTC 59.544 55.000 0.00 0.00 0.00 5.19
921 1423 0.970427 GGTGGAAATGGGAATGGCGT 60.970 55.000 0.00 0.00 0.00 5.68
922 1424 1.675720 GGGTGGAAATGGGAATGGCG 61.676 60.000 0.00 0.00 0.00 5.69
923 1425 1.675720 CGGGTGGAAATGGGAATGGC 61.676 60.000 0.00 0.00 0.00 4.40
959 1461 1.996191 GTAGCAAAAGGAGCAGAGACG 59.004 52.381 0.00 0.00 0.00 4.18
973 1475 0.818296 GGGAGAGAAGCTCGTAGCAA 59.182 55.000 9.09 0.00 45.56 3.91
975 1477 0.101579 GTGGGAGAGAAGCTCGTAGC 59.898 60.000 0.00 0.00 44.91 3.58
976 1478 0.378962 CGTGGGAGAGAAGCTCGTAG 59.621 60.000 0.00 0.00 44.91 3.51
977 1479 0.035725 TCGTGGGAGAGAAGCTCGTA 60.036 55.000 0.00 0.00 44.91 3.43
978 1480 0.894184 TTCGTGGGAGAGAAGCTCGT 60.894 55.000 0.00 0.00 44.91 4.18
997 1506 1.220206 CTGAAGCTGAGCCCATCGT 59.780 57.895 0.00 0.00 0.00 3.73
1027 1536 8.394971 ACCATGCATATATCTCGAATTTTCAA 57.605 30.769 0.00 0.00 0.00 2.69
1028 1537 7.984422 ACCATGCATATATCTCGAATTTTCA 57.016 32.000 0.00 0.00 0.00 2.69
1051 1560 2.737376 GCGACTGGACGTGGGAAC 60.737 66.667 0.00 0.00 35.59 3.62
1052 1561 3.228017 TGCGACTGGACGTGGGAA 61.228 61.111 0.00 0.00 35.59 3.97
1403 1927 1.130373 GGTACGTACCGTCGAACATGA 59.870 52.381 28.00 0.00 41.54 3.07
1428 1952 1.137513 GGCGTGACTGTGTACAGAAC 58.862 55.000 18.18 13.65 46.59 3.01
1433 1957 1.374252 CAGGGGCGTGACTGTGTAC 60.374 63.158 0.00 0.00 0.00 2.90
1471 2000 3.942829 TCCGAGCATTTCAATTCTGAGT 58.057 40.909 0.00 0.00 31.69 3.41
1473 2002 4.096833 CCAATCCGAGCATTTCAATTCTGA 59.903 41.667 0.00 0.00 0.00 3.27
1552 2081 8.816894 ACCATGGACTAATTACCTGATATACAG 58.183 37.037 21.47 0.00 45.36 2.74
1624 2598 8.848528 GTCTCAACTTTGTTACGTACTAATCTC 58.151 37.037 0.00 0.00 0.00 2.75
1629 2603 7.758980 TGTTTGTCTCAACTTTGTTACGTACTA 59.241 33.333 0.00 0.00 0.00 1.82
1634 2608 6.102006 TCTGTTTGTCTCAACTTTGTTACG 57.898 37.500 0.00 0.00 0.00 3.18
1682 2662 4.080919 CCACTACTGGAATCTGGAATCACA 60.081 45.833 0.00 0.00 40.55 3.58
1759 2772 6.479972 TCAGATGACGTAGGATTATGGTTT 57.520 37.500 0.00 0.00 0.00 3.27
1875 3557 5.314039 TCAATGGATCAATCACCCCTGATAT 59.686 40.000 0.00 0.00 35.96 1.63
1887 3780 6.625740 CGGCTTAACTTTGTCAATGGATCAAT 60.626 38.462 0.00 0.00 0.00 2.57
2068 5781 3.303329 GCTGACATTATGTATGCACGTGG 60.303 47.826 18.88 0.00 37.81 4.94
2079 5792 4.568359 GGTACACTGACAGCTGACATTATG 59.432 45.833 23.35 19.46 0.00 1.90
2080 5793 4.678044 CGGTACACTGACAGCTGACATTAT 60.678 45.833 23.35 6.64 0.00 1.28
2081 5794 3.366985 CGGTACACTGACAGCTGACATTA 60.367 47.826 23.35 9.21 0.00 1.90
2082 5795 2.610479 CGGTACACTGACAGCTGACATT 60.610 50.000 23.35 12.32 0.00 2.71
2096 5809 3.949842 AAAAGTCTACCTCCGGTACAC 57.050 47.619 0.00 0.00 37.09 2.90
2100 5813 4.401837 GTCATCTAAAAGTCTACCTCCGGT 59.598 45.833 0.00 0.00 40.16 5.28
2101 5814 4.645588 AGTCATCTAAAAGTCTACCTCCGG 59.354 45.833 0.00 0.00 0.00 5.14
2119 6319 4.879197 TCAGAGTTCACATGTCAGTCAT 57.121 40.909 0.00 0.00 37.22 3.06
2531 6744 3.374402 CAGACCAGGTCGGCGACT 61.374 66.667 35.42 19.06 39.03 4.18
2695 6933 1.226888 GCCGTAGCGAGTCCGAATT 60.227 57.895 0.00 0.00 38.22 2.17
2696 6934 2.412112 GCCGTAGCGAGTCCGAAT 59.588 61.111 0.00 0.00 38.22 3.34
2716 6954 0.984109 CAAATCGCACGCAACATTCC 59.016 50.000 0.00 0.00 0.00 3.01
2761 6999 4.028131 CAAGCCCGGTCCTATATATGGTA 58.972 47.826 0.00 0.00 0.00 3.25
2768 7006 1.074775 AGGCAAGCCCGGTCCTATA 60.075 57.895 7.62 0.00 39.21 1.31
2769 7007 2.366972 AGGCAAGCCCGGTCCTAT 60.367 61.111 7.62 0.00 39.21 2.57
2770 7008 3.399181 CAGGCAAGCCCGGTCCTA 61.399 66.667 7.62 0.00 39.21 2.94
2937 8615 8.902806 GTGATTGTGATTATATCCTTTGGTTCA 58.097 33.333 0.00 0.00 0.00 3.18
2942 8620 6.568462 GCGGGTGATTGTGATTATATCCTTTG 60.568 42.308 0.00 0.00 0.00 2.77
2949 8627 3.737032 TCGCGGGTGATTGTGATTATA 57.263 42.857 6.13 0.00 0.00 0.98
2990 8668 1.555741 TTGCATTTTGGCGCGCTTTC 61.556 50.000 32.29 15.45 36.28 2.62
3203 8934 8.834749 ACCTTGAAGAACTAAGTGAGATTTAC 57.165 34.615 0.00 0.00 0.00 2.01
3310 9045 0.527565 CACAAGGGTGCATGGTAAGC 59.472 55.000 0.00 0.00 38.37 3.09
3346 9152 0.175760 TCTGTAGATTCTGGCCACGC 59.824 55.000 0.00 0.00 0.00 5.34
3361 9167 1.344438 TCTGTCGCTGTTTGGATCTGT 59.656 47.619 0.00 0.00 0.00 3.41
3492 9298 8.827279 ACAAAAACTGTAGTGGATGCTTTCCAT 61.827 37.037 11.42 4.94 46.40 3.41


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

AutoCloner maintained by Alex Coulton.