Multiple sequence alignment - TraesCS6A01G047600

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 TraesCS6A01G047600 chr6A 100.000 3230 0 0 1 3230 24047620 24050849 0.000000e+00 5965.0
1 TraesCS6A01G047600 chr6A 84.432 1471 152 44 767 2230 24031659 24030259 0.000000e+00 1376.0
2 TraesCS6A01G047600 chr6A 82.554 1347 154 44 886 2228 23963284 23962015 0.000000e+00 1110.0
3 TraesCS6A01G047600 chr6A 86.102 885 107 12 1378 2252 23952052 23951174 0.000000e+00 939.0
4 TraesCS6A01G047600 chr6A 80.338 829 102 43 443 1225 23897373 23896560 3.620000e-159 571.0
5 TraesCS6A01G047600 chr6A 84.964 552 55 17 748 1280 23952643 23952101 4.740000e-148 534.0
6 TraesCS6A01G047600 chr6A 95.000 60 3 0 3171 3230 563382212 563382153 9.540000e-16 95.3
7 TraesCS6A01G047600 chr6A 100.000 31 0 0 2318 2348 24030182 24030152 1.250000e-04 58.4
8 TraesCS6A01G047600 chr6D 92.801 1153 45 12 472 1601 25914425 25915562 0.000000e+00 1635.0
9 TraesCS6A01G047600 chr6D 90.807 1251 72 12 1593 2841 25915585 25916794 0.000000e+00 1633.0
10 TraesCS6A01G047600 chr6D 80.040 1989 247 100 453 2369 25805661 25803751 0.000000e+00 1336.0
11 TraesCS6A01G047600 chr6D 88.194 864 85 12 1375 2233 25879793 25878942 0.000000e+00 1014.0
12 TraesCS6A01G047600 chr6D 85.396 897 107 18 1369 2252 25827289 25826404 0.000000e+00 909.0
13 TraesCS6A01G047600 chr6D 84.252 889 114 19 1369 2252 25852310 25851443 0.000000e+00 843.0
14 TraesCS6A01G047600 chr6D 82.277 694 78 29 604 1280 25827992 25827327 2.810000e-155 558.0
15 TraesCS6A01G047600 chr6D 85.192 520 60 10 763 1278 25880334 25879828 4.780000e-143 518.0
16 TraesCS6A01G047600 chr6D 87.059 340 26 11 2848 3171 25916773 25917110 5.090000e-98 368.0
17 TraesCS6A01G047600 chr6B 85.747 1298 143 23 6 1270 42392025 42393313 0.000000e+00 1334.0
18 TraesCS6A01G047600 chr6B 80.717 1841 230 71 450 2238 42006315 42004548 0.000000e+00 1317.0
19 TraesCS6A01G047600 chr6B 88.761 872 82 10 1369 2233 42318447 42317585 0.000000e+00 1053.0
20 TraesCS6A01G047600 chr6B 85.913 1008 107 21 1339 2336 42393342 42394324 0.000000e+00 1042.0
21 TraesCS6A01G047600 chr6B 86.000 900 104 16 1369 2252 42211680 42210787 0.000000e+00 944.0
22 TraesCS6A01G047600 chr6B 85.586 555 55 16 732 1270 42212263 42211718 2.810000e-155 558.0
23 TraesCS6A01G047600 chr6B 85.463 454 54 7 2381 2830 42394543 42394988 2.270000e-126 462.0
24 TraesCS6A01G047600 chr6B 87.311 331 30 10 2849 3169 42394978 42395306 5.090000e-98 368.0
25 TraesCS6A01G047600 chr6B 82.308 390 60 6 2 386 34441922 34442307 2.400000e-86 329.0
26 TraesCS6A01G047600 chr7D 80.962 998 148 36 1376 2349 579100024 579099045 0.000000e+00 752.0
27 TraesCS6A01G047600 chr7B 80.864 1019 140 41 1373 2349 643292475 643291470 0.000000e+00 750.0
28 TraesCS6A01G047600 chr7B 82.488 868 129 19 1376 2232 643462571 643463426 0.000000e+00 739.0
29 TraesCS6A01G047600 chr7B 84.775 578 84 4 1657 2232 643295740 643295165 7.770000e-161 577.0
30 TraesCS6A01G047600 chr7A 82.529 870 136 13 1373 2232 670946926 670946063 0.000000e+00 750.0
31 TraesCS6A01G047600 chr7A 98.276 58 1 0 3173 3230 667200316 667200259 5.700000e-18 102.0
32 TraesCS6A01G047600 chr7A 96.552 58 2 0 3173 3230 127763179 127763122 2.650000e-16 97.1
33 TraesCS6A01G047600 chr1D 81.614 446 77 5 4 447 199828342 199827900 6.590000e-97 364.0
34 TraesCS6A01G047600 chr2A 81.114 413 69 8 12 419 758305408 758305000 4.020000e-84 322.0
35 TraesCS6A01G047600 chr3B 81.538 390 67 4 4 392 11621129 11620744 1.870000e-82 316.0
36 TraesCS6A01G047600 chr3B 80.186 429 75 10 2 427 241931122 241931543 2.420000e-81 313.0
37 TraesCS6A01G047600 chr3B 83.636 330 51 3 5 332 313820290 313820618 1.130000e-79 307.0
38 TraesCS6A01G047600 chr3B 96.552 58 2 0 3173 3230 28193582 28193525 2.650000e-16 97.1
39 TraesCS6A01G047600 chr4D 79.955 449 72 17 8 447 44050348 44049909 6.730000e-82 315.0
40 TraesCS6A01G047600 chr2D 83.030 330 51 5 3 330 67573166 67572840 8.760000e-76 294.0
41 TraesCS6A01G047600 chr5B 83.193 119 15 5 3052 3170 256945884 256945771 1.590000e-18 104.0
42 TraesCS6A01G047600 chr5B 96.552 58 2 0 3173 3230 477558030 477557973 2.650000e-16 97.1
43 TraesCS6A01G047600 chr5B 88.525 61 6 1 2601 2660 593472758 593472818 4.470000e-09 73.1
44 TraesCS6A01G047600 chr5B 86.885 61 7 1 2601 2660 593556768 593556828 2.080000e-07 67.6
45 TraesCS6A01G047600 chr5D 98.246 57 1 0 3174 3230 63154985 63154929 2.050000e-17 100.0
46 TraesCS6A01G047600 chr4A 95.161 62 3 0 3169 3230 139718060 139717999 7.370000e-17 99.0
47 TraesCS6A01G047600 chr5A 96.552 58 2 0 3173 3230 428152030 428152087 2.650000e-16 97.1
48 TraesCS6A01G047600 chr5A 90.278 72 4 3 3160 3230 33127497 33127566 1.230000e-14 91.6
49 TraesCS6A01G047600 chr5A 86.885 61 6 1 2602 2660 603790505 603790565 2.080000e-07 67.6


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G047600 chr6A 24047620 24050849 3229 False 5965.0 5965 100.000000 1 3230 1 chr6A.!!$F1 3229
1 TraesCS6A01G047600 chr6A 23962015 23963284 1269 True 1110.0 1110 82.554000 886 2228 1 chr6A.!!$R2 1342
2 TraesCS6A01G047600 chr6A 23951174 23952643 1469 True 736.5 939 85.533000 748 2252 2 chr6A.!!$R4 1504
3 TraesCS6A01G047600 chr6A 24030152 24031659 1507 True 717.2 1376 92.216000 767 2348 2 chr6A.!!$R5 1581
4 TraesCS6A01G047600 chr6A 23896560 23897373 813 True 571.0 571 80.338000 443 1225 1 chr6A.!!$R1 782
5 TraesCS6A01G047600 chr6D 25803751 25805661 1910 True 1336.0 1336 80.040000 453 2369 1 chr6D.!!$R1 1916
6 TraesCS6A01G047600 chr6D 25914425 25917110 2685 False 1212.0 1635 90.222333 472 3171 3 chr6D.!!$F1 2699
7 TraesCS6A01G047600 chr6D 25851443 25852310 867 True 843.0 843 84.252000 1369 2252 1 chr6D.!!$R2 883
8 TraesCS6A01G047600 chr6D 25878942 25880334 1392 True 766.0 1014 86.693000 763 2233 2 chr6D.!!$R4 1470
9 TraesCS6A01G047600 chr6D 25826404 25827992 1588 True 733.5 909 83.836500 604 2252 2 chr6D.!!$R3 1648
10 TraesCS6A01G047600 chr6B 42004548 42006315 1767 True 1317.0 1317 80.717000 450 2238 1 chr6B.!!$R1 1788
11 TraesCS6A01G047600 chr6B 42317585 42318447 862 True 1053.0 1053 88.761000 1369 2233 1 chr6B.!!$R2 864
12 TraesCS6A01G047600 chr6B 42392025 42395306 3281 False 801.5 1334 86.108500 6 3169 4 chr6B.!!$F2 3163
13 TraesCS6A01G047600 chr6B 42210787 42212263 1476 True 751.0 944 85.793000 732 2252 2 chr6B.!!$R3 1520
14 TraesCS6A01G047600 chr7D 579099045 579100024 979 True 752.0 752 80.962000 1376 2349 1 chr7D.!!$R1 973
15 TraesCS6A01G047600 chr7B 643462571 643463426 855 False 739.0 739 82.488000 1376 2232 1 chr7B.!!$F1 856
16 TraesCS6A01G047600 chr7B 643291470 643295740 4270 True 663.5 750 82.819500 1373 2349 2 chr7B.!!$R1 976
17 TraesCS6A01G047600 chr7A 670946063 670946926 863 True 750.0 750 82.529000 1373 2232 1 chr7A.!!$R3 859

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
372 375 0.459585 GGGATTGAACTACTGCGCGA 60.460 55.0 12.10 0.00 0.00 5.87 F
1421 3319 0.606604 ATGACGTGGGTAGCTTCGTT 59.393 50.0 13.65 0.59 36.67 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1772 3767 0.179179 GAACGCTTTGATGAGCTGGC 60.179 55.0 0.00 0.0 40.52 4.85 R
3186 5436 0.103937 CCTTCATGGAGCTCGGTCTC 59.896 60.0 7.83 0.0 38.35 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
21 22 4.864704 TCCGCTTTTTATTTTGGCTTCT 57.135 36.364 0.00 0.00 0.00 2.85
99 100 2.542020 TTCATGCTTCTCGTGACCAA 57.458 45.000 0.00 0.00 40.23 3.67
101 102 1.069978 TCATGCTTCTCGTGACCAACA 59.930 47.619 0.00 0.00 35.87 3.33
184 185 9.136952 GTTTCAATGTTGATACTTAGTACGAGT 57.863 33.333 9.42 9.42 36.58 4.18
185 186 8.683550 TTCAATGTTGATACTTAGTACGAGTG 57.316 34.615 13.21 0.00 37.00 3.51
187 188 8.683615 TCAATGTTGATACTTAGTACGAGTGAT 58.316 33.333 13.21 5.26 31.01 3.06
220 222 6.978343 TCAATTATTTTGTGTCTAGGACCG 57.022 37.500 0.00 0.00 0.00 4.79
222 224 7.335627 TCAATTATTTTGTGTCTAGGACCGAT 58.664 34.615 0.00 0.00 0.00 4.18
223 225 7.279981 TCAATTATTTTGTGTCTAGGACCGATG 59.720 37.037 0.00 0.00 0.00 3.84
232 235 6.110707 GTGTCTAGGACCGATGGAAAAATTA 58.889 40.000 0.00 0.00 0.00 1.40
272 275 9.918630 ATCTAAAATTGATTGAAACTTGACTGG 57.081 29.630 0.00 0.00 0.00 4.00
289 292 7.284489 ACTTGACTGGTTTAGATGCAAAAACTA 59.716 33.333 17.13 12.67 36.17 2.24
290 293 7.759489 TGACTGGTTTAGATGCAAAAACTAT 57.241 32.000 17.13 7.58 36.17 2.12
324 327 8.440059 GTTGTGGAAACTTAAAACTTTTTGAGG 58.560 33.333 10.09 0.00 37.88 3.86
349 352 6.377146 GGATTTTCTATTTTACTGTGCCCTCA 59.623 38.462 0.00 0.00 0.00 3.86
352 355 5.435686 TCTATTTTACTGTGCCCTCATGT 57.564 39.130 0.00 0.00 0.00 3.21
370 373 0.727398 GTGGGATTGAACTACTGCGC 59.273 55.000 0.00 0.00 0.00 6.09
372 375 0.459585 GGGATTGAACTACTGCGCGA 60.460 55.000 12.10 0.00 0.00 5.87
467 471 3.386726 TCCGTTACCTCCCACTATGAATG 59.613 47.826 0.00 0.00 0.00 2.67
481 485 4.697352 ACTATGAATGCACTTGGAACACTC 59.303 41.667 0.00 0.00 39.29 3.51
559 570 6.293845 GGAATAGTTGCCATCATGACTTGATC 60.294 42.308 0.00 0.00 43.40 2.92
759 797 5.413833 ACAGATCAGTTTTTGGCATCTACAG 59.586 40.000 0.00 0.00 0.00 2.74
849 906 2.351706 AACGGCCTAACTTTGACCAA 57.648 45.000 0.00 0.00 0.00 3.67
1015 1081 2.119655 GCCATGGCTTCCAGCTCTG 61.120 63.158 29.98 0.00 41.99 3.35
1282 1375 9.996554 TCGAATTGATTTACCATCATATACAGT 57.003 29.630 0.00 0.00 0.00 3.55
1330 1423 3.377172 GTGAACACGCTTAATTAGGCCAT 59.623 43.478 13.40 0.02 0.00 4.40
1331 1424 4.013728 TGAACACGCTTAATTAGGCCATT 58.986 39.130 13.40 0.00 0.00 3.16
1332 1425 4.095782 TGAACACGCTTAATTAGGCCATTC 59.904 41.667 13.40 13.58 0.00 2.67
1334 1427 3.877508 ACACGCTTAATTAGGCCATTCTC 59.122 43.478 13.40 0.00 0.00 2.87
1335 1428 4.130118 CACGCTTAATTAGGCCATTCTCT 58.870 43.478 13.40 0.00 0.00 3.10
1336 1429 4.576463 CACGCTTAATTAGGCCATTCTCTT 59.424 41.667 13.40 0.00 0.00 2.85
1421 3319 0.606604 ATGACGTGGGTAGCTTCGTT 59.393 50.000 13.65 0.59 36.67 3.85
1604 3544 4.640771 ACTACAATCAATGGACAGTGGT 57.359 40.909 0.00 0.00 0.00 4.16
1785 3780 1.000521 CCTGGGCCAGCTCATCAAA 60.001 57.895 28.51 0.00 0.00 2.69
2223 4218 1.237285 GCAACTGCAGGGTCGTCAAT 61.237 55.000 19.93 0.00 41.59 2.57
2271 4297 8.621286 GCCATATGTGTTACAAATATATAGGCC 58.379 37.037 17.73 0.00 30.47 5.19
2449 4680 0.040336 CGCTCCGACGTATACATGCT 60.040 55.000 3.32 0.00 0.00 3.79
2477 4708 3.775261 AAAGGAAACCAAGCATGCATT 57.225 38.095 21.98 8.51 0.00 3.56
2480 4711 2.369532 AGGAAACCAAGCATGCATTGTT 59.630 40.909 21.98 13.60 0.00 2.83
2515 4746 4.759693 ACTGGAGTGATATTTGCGACAAAA 59.240 37.500 8.65 0.00 0.00 2.44
2516 4747 5.041951 TGGAGTGATATTTGCGACAAAAC 57.958 39.130 8.65 3.86 0.00 2.43
2517 4748 4.759693 TGGAGTGATATTTGCGACAAAACT 59.240 37.500 8.65 7.70 0.00 2.66
2518 4749 5.088739 GGAGTGATATTTGCGACAAAACTG 58.911 41.667 8.65 0.00 0.00 3.16
2519 4750 5.334879 GGAGTGATATTTGCGACAAAACTGT 60.335 40.000 8.65 0.00 0.00 3.55
2520 4751 5.451908 AGTGATATTTGCGACAAAACTGTG 58.548 37.500 8.65 0.00 0.00 3.66
2541 4772 4.972440 GTGACTGTGAGAGAAAACAAATGC 59.028 41.667 0.00 0.00 0.00 3.56
2547 4778 5.065859 TGTGAGAGAAAACAAATGCGAAGAA 59.934 36.000 0.00 0.00 0.00 2.52
2548 4779 5.622856 GTGAGAGAAAACAAATGCGAAGAAG 59.377 40.000 0.00 0.00 0.00 2.85
2579 4811 9.503427 TTTTTCGATCTTTCTTTTCTTTGAGTC 57.497 29.630 0.00 0.00 0.00 3.36
2580 4812 7.786178 TTCGATCTTTCTTTTCTTTGAGTCA 57.214 32.000 0.00 0.00 0.00 3.41
2671 4904 3.311322 TCAACATCAGTTTTGTCCGACAC 59.689 43.478 0.00 0.00 35.28 3.67
2686 4919 2.536365 CGACACATACCTTACACGCAT 58.464 47.619 0.00 0.00 0.00 4.73
2747 4980 3.945523 ACGGGTAGGGGAAGGTAAATAT 58.054 45.455 0.00 0.00 0.00 1.28
2750 4983 4.103627 CGGGTAGGGGAAGGTAAATATTGT 59.896 45.833 0.00 0.00 0.00 2.71
2752 4985 5.133153 GGGTAGGGGAAGGTAAATATTGTGA 59.867 44.000 0.00 0.00 0.00 3.58
2764 4998 8.512138 AGGTAAATATTGTGAAGAGAAAAACGG 58.488 33.333 0.00 0.00 0.00 4.44
2788 5022 2.283388 AGGTGAGGCGAACCGGTA 60.283 61.111 8.00 0.00 42.89 4.02
2792 5026 1.607178 TGAGGCGAACCGGTAGGAA 60.607 57.895 8.00 0.00 42.76 3.36
2793 5027 1.153686 GAGGCGAACCGGTAGGAAC 60.154 63.158 8.00 0.00 42.76 3.62
2795 5029 1.004679 GGCGAACCGGTAGGAACAA 60.005 57.895 8.00 0.00 41.02 2.83
2800 5034 1.794701 GAACCGGTAGGAACAAACGTC 59.205 52.381 8.00 0.00 41.02 4.34
2803 5037 0.788391 CGGTAGGAACAAACGTCTGC 59.212 55.000 0.00 0.00 0.00 4.26
2804 5038 1.870580 CGGTAGGAACAAACGTCTGCA 60.871 52.381 0.00 0.00 0.00 4.41
2810 5044 5.705609 AGGAACAAACGTCTGCAATAAAT 57.294 34.783 0.00 0.00 0.00 1.40
2820 5054 4.097741 CGTCTGCAATAAATGGGGATTGAA 59.902 41.667 0.00 0.00 35.46 2.69
2828 5062 0.255890 ATGGGGATTGAACGGAGTGG 59.744 55.000 0.00 0.00 45.00 4.00
2829 5063 0.838554 TGGGGATTGAACGGAGTGGA 60.839 55.000 0.00 0.00 45.00 4.02
2830 5064 0.326927 GGGGATTGAACGGAGTGGAA 59.673 55.000 0.00 0.00 45.00 3.53
2831 5065 1.679032 GGGGATTGAACGGAGTGGAAG 60.679 57.143 0.00 0.00 45.00 3.46
2832 5066 1.087501 GGATTGAACGGAGTGGAAGC 58.912 55.000 0.00 0.00 45.00 3.86
2833 5067 0.721718 GATTGAACGGAGTGGAAGCG 59.278 55.000 0.00 0.00 45.00 4.68
2834 5068 0.320374 ATTGAACGGAGTGGAAGCGA 59.680 50.000 0.00 0.00 45.00 4.93
2835 5069 0.320374 TTGAACGGAGTGGAAGCGAT 59.680 50.000 0.00 0.00 45.00 4.58
2836 5070 0.389817 TGAACGGAGTGGAAGCGATG 60.390 55.000 0.00 0.00 45.00 3.84
2837 5071 1.696832 GAACGGAGTGGAAGCGATGC 61.697 60.000 0.00 0.00 45.00 3.91
2838 5072 2.125552 CGGAGTGGAAGCGATGCA 60.126 61.111 0.00 0.00 0.00 3.96
2839 5073 1.741401 CGGAGTGGAAGCGATGCAA 60.741 57.895 0.00 0.00 0.00 4.08
2840 5074 1.298157 CGGAGTGGAAGCGATGCAAA 61.298 55.000 0.00 0.00 0.00 3.68
2841 5075 0.881118 GGAGTGGAAGCGATGCAAAA 59.119 50.000 0.00 0.00 0.00 2.44
2842 5076 1.269448 GGAGTGGAAGCGATGCAAAAA 59.731 47.619 0.00 0.00 0.00 1.94
2865 5099 4.988716 ACCGGAGTGGAGGCGACA 62.989 66.667 9.46 0.00 42.00 4.35
2870 5104 0.534203 GGAGTGGAGGCGACAAAACA 60.534 55.000 0.00 0.00 0.00 2.83
2897 5131 8.798975 ACTCCCCAATAATAGAGATTAAGACA 57.201 34.615 0.00 0.00 31.28 3.41
2898 5132 8.875168 ACTCCCCAATAATAGAGATTAAGACAG 58.125 37.037 0.00 0.00 31.28 3.51
2902 5136 7.821846 CCCAATAATAGAGATTAAGACAGGAGC 59.178 40.741 0.00 0.00 31.28 4.70
2922 5156 1.168714 GTACTGAAGCAAGCCCCTTG 58.831 55.000 0.74 0.74 43.57 3.61
2962 5196 2.158608 ACCAATAGCAGCCAAGGATACC 60.159 50.000 0.00 0.00 37.17 2.73
2976 5210 5.242393 CCAAGGATACCAGAAATAGCCAATG 59.758 44.000 0.00 0.00 30.06 2.82
2978 5212 4.751028 AGGATACCAGAAATAGCCAATGGC 60.751 45.833 18.04 18.04 44.87 4.40
2994 5233 2.367202 GGCTCTCGGGTCCCATTGA 61.367 63.158 9.12 1.53 0.00 2.57
3004 5243 2.460669 GGTCCCATTGAGCCTGATTTT 58.539 47.619 0.00 0.00 35.38 1.82
3005 5244 2.428530 GGTCCCATTGAGCCTGATTTTC 59.571 50.000 0.00 0.00 35.38 2.29
3007 5246 3.511146 GTCCCATTGAGCCTGATTTTCAA 59.489 43.478 0.00 0.00 35.52 2.69
3009 5248 4.778958 TCCCATTGAGCCTGATTTTCAAAT 59.221 37.500 0.00 0.00 34.80 2.32
3010 5249 5.957168 TCCCATTGAGCCTGATTTTCAAATA 59.043 36.000 0.00 0.00 34.80 1.40
3075 5324 6.313519 TCTTGGAAGCAAGAATGGTATAGT 57.686 37.500 0.00 0.00 38.15 2.12
3076 5325 6.115446 TCTTGGAAGCAAGAATGGTATAGTG 58.885 40.000 0.00 0.00 38.15 2.74
3085 5334 8.082852 AGCAAGAATGGTATAGTGTTATACTCG 58.917 37.037 5.10 0.00 40.87 4.18
3146 5396 6.467677 TCTGGGACAAAAACAAACAAATTGA 58.532 32.000 0.00 0.00 38.78 2.57
3179 5429 9.372541 CAAAAGTGTCAATTGTAATGAAAATGC 57.627 29.630 5.13 0.00 0.00 3.56
3180 5430 7.656707 AAGTGTCAATTGTAATGAAAATGCC 57.343 32.000 5.13 0.00 0.00 4.40
3181 5431 6.757237 AGTGTCAATTGTAATGAAAATGCCA 58.243 32.000 5.13 0.00 0.00 4.92
3182 5432 7.215789 AGTGTCAATTGTAATGAAAATGCCAA 58.784 30.769 5.13 0.00 0.00 4.52
3183 5433 7.714377 AGTGTCAATTGTAATGAAAATGCCAAA 59.286 29.630 5.13 0.00 0.00 3.28
3184 5434 7.798052 GTGTCAATTGTAATGAAAATGCCAAAC 59.202 33.333 5.13 0.00 0.00 2.93
3185 5435 7.008859 GTCAATTGTAATGAAAATGCCAAACG 58.991 34.615 5.13 0.00 0.00 3.60
3186 5436 6.146837 TCAATTGTAATGAAAATGCCAAACGG 59.853 34.615 5.13 0.00 0.00 4.44
3187 5437 4.855715 TGTAATGAAAATGCCAAACGGA 57.144 36.364 0.00 0.00 0.00 4.69
3188 5438 4.804108 TGTAATGAAAATGCCAAACGGAG 58.196 39.130 0.00 0.00 0.00 4.63
3189 5439 4.520874 TGTAATGAAAATGCCAAACGGAGA 59.479 37.500 0.00 0.00 0.00 3.71
3190 5440 3.575965 ATGAAAATGCCAAACGGAGAC 57.424 42.857 0.00 0.00 0.00 3.36
3191 5441 1.611491 TGAAAATGCCAAACGGAGACC 59.389 47.619 0.00 0.00 0.00 3.85
3204 5454 3.657956 GAGACCGAGCTCCATGAAG 57.342 57.895 8.47 0.00 0.00 3.02
3205 5455 0.103937 GAGACCGAGCTCCATGAAGG 59.896 60.000 8.47 4.75 39.47 3.46
3206 5456 1.522580 GACCGAGCTCCATGAAGGC 60.523 63.158 8.47 0.00 37.29 4.35
3207 5457 2.203126 CCGAGCTCCATGAAGGCC 60.203 66.667 8.47 0.00 37.29 5.19
3208 5458 2.739996 CCGAGCTCCATGAAGGCCT 61.740 63.158 8.47 0.00 37.29 5.19
3209 5459 1.222936 CGAGCTCCATGAAGGCCTT 59.777 57.895 20.65 20.65 37.29 4.35
3210 5460 0.393537 CGAGCTCCATGAAGGCCTTT 60.394 55.000 21.54 0.44 37.29 3.11
3211 5461 1.134401 CGAGCTCCATGAAGGCCTTTA 60.134 52.381 21.54 17.17 37.29 1.85
3212 5462 2.486191 CGAGCTCCATGAAGGCCTTTAT 60.486 50.000 21.54 18.94 37.29 1.40
3213 5463 3.560105 GAGCTCCATGAAGGCCTTTATT 58.440 45.455 21.54 5.18 37.29 1.40
3214 5464 3.956848 GAGCTCCATGAAGGCCTTTATTT 59.043 43.478 21.54 0.00 37.29 1.40
3215 5465 3.703052 AGCTCCATGAAGGCCTTTATTTG 59.297 43.478 21.54 14.05 37.29 2.32
3216 5466 3.701040 GCTCCATGAAGGCCTTTATTTGA 59.299 43.478 21.54 17.32 37.29 2.69
3217 5467 4.160252 GCTCCATGAAGGCCTTTATTTGAA 59.840 41.667 21.54 5.11 37.29 2.69
3218 5468 5.337491 GCTCCATGAAGGCCTTTATTTGAAA 60.337 40.000 21.54 3.38 37.29 2.69
3219 5469 6.678568 TCCATGAAGGCCTTTATTTGAAAA 57.321 33.333 21.54 0.00 37.29 2.29
3220 5470 6.463360 TCCATGAAGGCCTTTATTTGAAAAC 58.537 36.000 21.54 2.76 37.29 2.43
3221 5471 6.269769 TCCATGAAGGCCTTTATTTGAAAACT 59.730 34.615 21.54 0.00 37.29 2.66
3222 5472 6.936335 CCATGAAGGCCTTTATTTGAAAACTT 59.064 34.615 21.54 0.00 0.00 2.66
3223 5473 7.445096 CCATGAAGGCCTTTATTTGAAAACTTT 59.555 33.333 21.54 0.00 0.00 2.66
3224 5474 8.839343 CATGAAGGCCTTTATTTGAAAACTTTT 58.161 29.630 21.54 0.00 0.00 2.27
3226 5476 9.892130 TGAAGGCCTTTATTTGAAAACTTTTAA 57.108 25.926 21.54 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.555262 TCAGAAGCCAAAATAAAAAGCGG 58.445 39.130 0.00 0.00 0.00 5.52
49 50 9.936759 AAAACAGAACTTAGTTTGGAATTTTCA 57.063 25.926 0.00 0.00 37.94 2.69
173 174 9.447040 TGATTTTTATCGATCACTCGTACTAAG 57.553 33.333 0.00 0.00 45.25 2.18
215 217 5.890424 TCAAGTAATTTTTCCATCGGTCC 57.110 39.130 0.00 0.00 0.00 4.46
256 259 6.803807 GCATCTAAACCAGTCAAGTTTCAATC 59.196 38.462 0.00 0.00 38.37 2.67
257 260 6.265196 TGCATCTAAACCAGTCAAGTTTCAAT 59.735 34.615 0.00 0.00 38.37 2.57
297 300 8.888579 TCAAAAAGTTTTAAGTTTCCACAACA 57.111 26.923 0.24 0.00 31.47 3.33
300 303 7.038941 TCCCTCAAAAAGTTTTAAGTTTCCACA 60.039 33.333 0.24 0.00 31.47 4.17
301 304 7.324935 TCCCTCAAAAAGTTTTAAGTTTCCAC 58.675 34.615 0.24 0.00 31.47 4.02
303 306 8.958119 AATCCCTCAAAAAGTTTTAAGTTTCC 57.042 30.769 0.24 0.00 31.47 3.13
324 327 6.377146 TGAGGGCACAGTAAAATAGAAAATCC 59.623 38.462 0.00 0.00 0.00 3.01
333 336 3.091545 CCACATGAGGGCACAGTAAAAT 58.908 45.455 0.00 0.00 0.00 1.82
335 338 1.271871 CCCACATGAGGGCACAGTAAA 60.272 52.381 15.85 0.00 43.10 2.01
336 339 0.327924 CCCACATGAGGGCACAGTAA 59.672 55.000 15.85 0.00 43.10 2.24
349 352 2.632377 CGCAGTAGTTCAATCCCACAT 58.368 47.619 0.00 0.00 0.00 3.21
352 355 0.739462 CGCGCAGTAGTTCAATCCCA 60.739 55.000 8.75 0.00 0.00 4.37
370 373 4.174129 GGTTTGCCCCGCGATTCG 62.174 66.667 8.23 0.62 38.08 3.34
390 393 2.125106 CCAAGTCCTACTGCCCGC 60.125 66.667 0.00 0.00 0.00 6.13
392 395 1.078143 CTGCCAAGTCCTACTGCCC 60.078 63.158 0.00 0.00 0.00 5.36
398 401 0.976641 CACTCACCTGCCAAGTCCTA 59.023 55.000 0.00 0.00 0.00 2.94
444 448 3.104519 TCATAGTGGGAGGTAACGGAA 57.895 47.619 0.00 0.00 46.39 4.30
467 471 1.070758 TCAGAGGAGTGTTCCAAGTGC 59.929 52.381 0.00 0.00 46.64 4.40
559 570 1.344763 GGGACCGGAGAAGGATATGTG 59.655 57.143 9.46 0.00 34.73 3.21
701 739 8.999220 ATATATATGTTGCTCATCTGTCACTG 57.001 34.615 0.00 0.00 37.91 3.66
759 797 3.112580 GACTAAGAGCAACGCATCTCTC 58.887 50.000 2.09 0.00 38.62 3.20
1233 1303 6.359480 ACATAAGTATCTTTTGCTAACGGC 57.641 37.500 0.00 0.00 42.22 5.68
1330 1423 5.732331 ATCCCACCATTAATCCAAGAGAA 57.268 39.130 0.00 0.00 0.00 2.87
1331 1424 5.732331 AATCCCACCATTAATCCAAGAGA 57.268 39.130 0.00 0.00 0.00 3.10
1332 1425 5.470098 CGTAATCCCACCATTAATCCAAGAG 59.530 44.000 0.00 0.00 0.00 2.85
1334 1427 5.130350 ACGTAATCCCACCATTAATCCAAG 58.870 41.667 0.00 0.00 0.00 3.61
1335 1428 5.118729 ACGTAATCCCACCATTAATCCAA 57.881 39.130 0.00 0.00 0.00 3.53
1336 1429 4.781775 ACGTAATCCCACCATTAATCCA 57.218 40.909 0.00 0.00 0.00 3.41
1421 3319 2.781595 GAAAGGCCGTCTTCTCGCCA 62.782 60.000 0.00 0.00 33.94 5.69
1604 3544 4.157656 AGCAACAAGAAAAGTGCAGTGTAA 59.842 37.500 0.00 0.00 0.00 2.41
1653 3646 1.073216 CTAGCTGCAGGAACGACGTG 61.073 60.000 17.12 0.00 37.43 4.49
1772 3767 0.179179 GAACGCTTTGATGAGCTGGC 60.179 55.000 0.00 0.00 40.52 4.85
1785 3780 1.560860 GCTGCTTCTTGTCGAACGCT 61.561 55.000 0.00 0.00 31.40 5.07
2449 4680 4.402829 TGCTTGGTTTCCTTTATAGCACA 58.597 39.130 0.00 0.00 32.73 4.57
2480 4711 8.877864 AATATCACTCCAGTGTTCCATAAAAA 57.122 30.769 6.61 0.00 45.76 1.94
2488 4719 3.932710 TCGCAAATATCACTCCAGTGTTC 59.067 43.478 6.61 0.00 45.76 3.18
2495 4726 5.088739 CAGTTTTGTCGCAAATATCACTCC 58.911 41.667 5.97 0.00 0.00 3.85
2502 4733 4.334203 ACAGTCACAGTTTTGTCGCAAATA 59.666 37.500 5.97 0.00 34.62 1.40
2515 4746 4.471904 TGTTTTCTCTCACAGTCACAGT 57.528 40.909 0.00 0.00 0.00 3.55
2516 4747 5.801350 TTTGTTTTCTCTCACAGTCACAG 57.199 39.130 0.00 0.00 0.00 3.66
2517 4748 5.449041 GCATTTGTTTTCTCTCACAGTCACA 60.449 40.000 0.00 0.00 0.00 3.58
2518 4749 4.972440 GCATTTGTTTTCTCTCACAGTCAC 59.028 41.667 0.00 0.00 0.00 3.67
2519 4750 4.260743 CGCATTTGTTTTCTCTCACAGTCA 60.261 41.667 0.00 0.00 0.00 3.41
2520 4751 4.024893 TCGCATTTGTTTTCTCTCACAGTC 60.025 41.667 0.00 0.00 0.00 3.51
2575 4807 9.880064 GTAAAATTAAACCAAAGAGTCTGACTC 57.120 33.333 26.43 26.43 45.38 3.36
2579 4811 9.827411 GCTAGTAAAATTAAACCAAAGAGTCTG 57.173 33.333 0.00 0.00 0.00 3.51
2580 4812 9.794719 AGCTAGTAAAATTAAACCAAAGAGTCT 57.205 29.630 0.00 0.00 0.00 3.24
2613 4845 2.791347 TACCCCGTTGCAACATATGT 57.209 45.000 28.01 19.74 0.00 2.29
2618 4850 2.791347 ATGTATACCCCGTTGCAACA 57.209 45.000 28.01 9.66 0.00 3.33
2671 4904 8.757164 TTAGAATATGATGCGTGTAAGGTATG 57.243 34.615 0.00 0.00 0.00 2.39
2717 4950 4.202295 CCTTCCCCTACCCGTACTTAAATC 60.202 50.000 0.00 0.00 0.00 2.17
2723 4956 1.308877 TACCTTCCCCTACCCGTACT 58.691 55.000 0.00 0.00 0.00 2.73
2727 4960 4.103627 ACAATATTTACCTTCCCCTACCCG 59.896 45.833 0.00 0.00 0.00 5.28
2747 4980 2.370349 TGCCCGTTTTTCTCTTCACAA 58.630 42.857 0.00 0.00 0.00 3.33
2750 4983 1.953686 CCTTGCCCGTTTTTCTCTTCA 59.046 47.619 0.00 0.00 0.00 3.02
2752 4985 2.230660 CTCCTTGCCCGTTTTTCTCTT 58.769 47.619 0.00 0.00 0.00 2.85
2764 4998 3.254024 TTCGCCTCACCTCCTTGCC 62.254 63.158 0.00 0.00 0.00 4.52
2788 5022 5.460646 CATTTATTGCAGACGTTTGTTCCT 58.539 37.500 8.00 0.00 0.00 3.36
2792 5026 3.056891 CCCCATTTATTGCAGACGTTTGT 60.057 43.478 8.00 0.00 0.00 2.83
2793 5027 3.192422 TCCCCATTTATTGCAGACGTTTG 59.808 43.478 0.86 0.86 0.00 2.93
2795 5029 3.080300 TCCCCATTTATTGCAGACGTT 57.920 42.857 0.00 0.00 0.00 3.99
2800 5034 4.362279 CGTTCAATCCCCATTTATTGCAG 58.638 43.478 0.00 0.00 33.91 4.41
2803 5037 4.644685 ACTCCGTTCAATCCCCATTTATTG 59.355 41.667 0.00 0.00 34.96 1.90
2804 5038 4.644685 CACTCCGTTCAATCCCCATTTATT 59.355 41.667 0.00 0.00 0.00 1.40
2810 5044 0.838554 TCCACTCCGTTCAATCCCCA 60.839 55.000 0.00 0.00 0.00 4.96
2820 5054 2.125512 GCATCGCTTCCACTCCGT 60.126 61.111 0.00 0.00 0.00 4.69
2844 5078 1.599797 CGCCTCCACTCCGGTTTTT 60.600 57.895 0.00 0.00 35.57 1.94
2845 5079 2.032071 CGCCTCCACTCCGGTTTT 59.968 61.111 0.00 0.00 35.57 2.43
2846 5080 2.920912 TCGCCTCCACTCCGGTTT 60.921 61.111 0.00 0.00 35.57 3.27
2847 5081 3.692406 GTCGCCTCCACTCCGGTT 61.692 66.667 0.00 0.00 35.57 4.44
2848 5082 4.988716 TGTCGCCTCCACTCCGGT 62.989 66.667 0.00 0.00 35.57 5.28
2849 5083 2.725203 TTTTGTCGCCTCCACTCCGG 62.725 60.000 0.00 0.00 0.00 5.14
2850 5084 1.301401 TTTTGTCGCCTCCACTCCG 60.301 57.895 0.00 0.00 0.00 4.63
2851 5085 0.534203 TGTTTTGTCGCCTCCACTCC 60.534 55.000 0.00 0.00 0.00 3.85
2852 5086 1.305201 TTGTTTTGTCGCCTCCACTC 58.695 50.000 0.00 0.00 0.00 3.51
2853 5087 1.404035 GTTTGTTTTGTCGCCTCCACT 59.596 47.619 0.00 0.00 0.00 4.00
2854 5088 1.404035 AGTTTGTTTTGTCGCCTCCAC 59.596 47.619 0.00 0.00 0.00 4.02
2855 5089 1.673920 GAGTTTGTTTTGTCGCCTCCA 59.326 47.619 0.00 0.00 0.00 3.86
2856 5090 1.001706 GGAGTTTGTTTTGTCGCCTCC 60.002 52.381 0.00 0.00 0.00 4.30
2865 5099 9.547279 AATCTCTATTATTGGGGAGTTTGTTTT 57.453 29.630 0.00 0.00 0.00 2.43
2897 5131 0.390472 GCTTGCTTCAGTACGCTCCT 60.390 55.000 0.00 0.00 0.00 3.69
2898 5132 1.362406 GGCTTGCTTCAGTACGCTCC 61.362 60.000 0.00 0.00 0.00 4.70
2902 5136 0.321653 AAGGGGCTTGCTTCAGTACG 60.322 55.000 0.00 0.00 0.00 3.67
2976 5210 2.190578 CAATGGGACCCGAGAGCC 59.809 66.667 5.91 0.00 0.00 4.70
2978 5212 1.144936 GCTCAATGGGACCCGAGAG 59.855 63.158 15.94 16.96 0.00 3.20
3035 5284 9.655769 GCTTCCAAGATTTTTCAGAAAATTTTC 57.344 29.630 21.00 21.00 43.61 2.29
3036 5285 9.176460 TGCTTCCAAGATTTTTCAGAAAATTTT 57.824 25.926 9.19 2.28 43.61 1.82
3060 5309 7.866393 ACGAGTATAACACTATACCATTCTTGC 59.134 37.037 0.00 0.00 40.54 4.01
3085 5334 8.008279 GTCACTCCTTCGTGAAACTTTTTATAC 58.992 37.037 0.00 0.00 44.73 1.47
3115 5364 1.602377 GTTTTTGTCCCAGAGTCCACG 59.398 52.381 0.00 0.00 0.00 4.94
3162 5412 6.146837 TCCGTTTGGCATTTTCATTACAATTG 59.853 34.615 3.24 3.24 34.14 2.32
3171 5421 1.611491 GGTCTCCGTTTGGCATTTTCA 59.389 47.619 0.00 0.00 34.14 2.69
3172 5422 1.401018 CGGTCTCCGTTTGGCATTTTC 60.401 52.381 0.00 0.00 42.73 2.29
3173 5423 0.596082 CGGTCTCCGTTTGGCATTTT 59.404 50.000 0.00 0.00 42.73 1.82
3174 5424 2.253513 CGGTCTCCGTTTGGCATTT 58.746 52.632 0.00 0.00 42.73 2.32
3175 5425 3.981308 CGGTCTCCGTTTGGCATT 58.019 55.556 0.00 0.00 42.73 3.56
3186 5436 0.103937 CCTTCATGGAGCTCGGTCTC 59.896 60.000 7.83 0.00 38.35 3.36
3187 5437 1.965754 GCCTTCATGGAGCTCGGTCT 61.966 60.000 7.83 0.00 38.35 3.85
3188 5438 1.522580 GCCTTCATGGAGCTCGGTC 60.523 63.158 7.83 0.00 38.35 4.79
3189 5439 2.586792 GCCTTCATGGAGCTCGGT 59.413 61.111 7.83 0.00 38.35 4.69
3190 5440 2.203126 GGCCTTCATGGAGCTCGG 60.203 66.667 7.83 2.99 38.35 4.63
3191 5441 0.393537 AAAGGCCTTCATGGAGCTCG 60.394 55.000 20.79 0.00 38.35 5.03
3192 5442 2.717639 TAAAGGCCTTCATGGAGCTC 57.282 50.000 20.79 4.71 38.35 4.09
3193 5443 3.677156 AATAAAGGCCTTCATGGAGCT 57.323 42.857 20.79 2.41 38.35 4.09
3194 5444 3.701040 TCAAATAAAGGCCTTCATGGAGC 59.299 43.478 20.79 0.00 38.35 4.70
3195 5445 5.920193 TTCAAATAAAGGCCTTCATGGAG 57.080 39.130 20.79 7.92 38.35 3.86
3196 5446 6.269769 AGTTTTCAAATAAAGGCCTTCATGGA 59.730 34.615 20.79 8.83 38.35 3.41
3197 5447 6.466812 AGTTTTCAAATAAAGGCCTTCATGG 58.533 36.000 20.79 6.33 39.35 3.66
3198 5448 7.967890 AAGTTTTCAAATAAAGGCCTTCATG 57.032 32.000 20.79 14.99 0.00 3.07
3199 5449 8.978874 AAAAGTTTTCAAATAAAGGCCTTCAT 57.021 26.923 20.79 6.96 0.00 2.57
3200 5450 9.892130 TTAAAAGTTTTCAAATAAAGGCCTTCA 57.108 25.926 20.79 3.87 0.00 3.02


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

AutoCloner maintained by Alex Coulton.