Multiple sequence alignment - TraesCS2D01G416500

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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 TraesCS2D01G416500 chr2D 100.000 8334 0 0 1 8334 530265928 530257595 0.000000e+00 15391.0
1 TraesCS2D01G416500 chr2D 91.892 1036 53 6 5906 6938 531264048 531263041 0.000000e+00 1419.0
2 TraesCS2D01G416500 chr2D 81.299 1524 181 50 2473 3939 531267448 531265972 0.000000e+00 1140.0
3 TraesCS2D01G416500 chr2D 78.571 1050 189 30 5895 6929 531349075 531348047 0.000000e+00 660.0
4 TraesCS2D01G416500 chr2D 95.664 369 15 1 2103 2470 531267786 531267418 7.200000e-165 592.0
5 TraesCS2D01G416500 chr2D 81.008 595 67 21 7721 8290 531259966 531259393 1.660000e-116 431.0
6 TraesCS2D01G416500 chr2D 80.508 590 74 23 3259 3830 531267786 531267220 1.670000e-111 414.0
7 TraesCS2D01G416500 chr2D 81.795 390 49 9 2101 2470 530262672 530262285 2.920000e-79 307.0
8 TraesCS2D01G416500 chr2D 81.795 390 49 9 3257 3644 530263828 530263459 2.920000e-79 307.0
9 TraesCS2D01G416500 chr2D 73.858 876 180 35 4242 5088 531265767 531264912 3.780000e-78 303.0
10 TraesCS2D01G416500 chr2D 87.190 242 28 2 1840 2078 531268024 531267783 1.070000e-68 272.0
11 TraesCS2D01G416500 chr2D 88.800 125 7 6 7100 7218 530258790 530258667 6.740000e-31 147.0
12 TraesCS2D01G416500 chr2D 88.800 125 7 6 7139 7262 530258829 530258711 6.740000e-31 147.0
13 TraesCS2D01G416500 chr2D 82.550 149 24 2 1918 2064 531266992 531266844 6.790000e-26 130.0
14 TraesCS2D01G416500 chr2D 90.588 85 4 3 7179 7262 531262827 531262746 8.840000e-20 110.0
15 TraesCS2D01G416500 chr2D 91.250 80 2 4 7492 7567 615384208 615384286 4.110000e-18 104.0
16 TraesCS2D01G416500 chr2D 100.000 32 0 0 2472 2503 530263490 530263459 9.030000e-05 60.2
17 TraesCS2D01G416500 chr2D 100.000 31 0 0 151 181 47285126 47285096 3.250000e-04 58.4
18 TraesCS2D01G416500 chr2A 97.283 6367 111 18 894 7218 675086153 675079807 0.000000e+00 10743.0
19 TraesCS2D01G416500 chr2A 94.214 1037 54 4 5905 6938 675747930 675746897 0.000000e+00 1578.0
20 TraesCS2D01G416500 chr2A 81.484 1523 182 49 2473 3939 675751340 675749862 0.000000e+00 1158.0
21 TraesCS2D01G416500 chr2A 94.315 686 16 4 7649 8334 675079514 675078852 0.000000e+00 1029.0
22 TraesCS2D01G416500 chr2A 78.896 1033 186 26 5910 6929 675897503 675896490 0.000000e+00 671.0
23 TraesCS2D01G416500 chr2A 84.438 649 52 23 37 642 675088812 675088170 2.000000e-165 593.0
24 TraesCS2D01G416500 chr2A 94.087 389 11 4 7139 7525 675079931 675079553 1.560000e-161 580.0
25 TraesCS2D01G416500 chr2A 95.304 362 16 1 2110 2470 675751671 675751310 2.610000e-159 573.0
26 TraesCS2D01G416500 chr2A 81.513 595 64 21 7721 8290 675745908 675745335 1.650000e-121 448.0
27 TraesCS2D01G416500 chr2A 80.756 582 71 23 3267 3830 675751670 675751112 4.650000e-112 416.0
28 TraesCS2D01G416500 chr2A 81.795 390 49 9 3257 3644 675084925 675084556 2.920000e-79 307.0
29 TraesCS2D01G416500 chr2A 72.993 1059 213 51 4242 5251 675749658 675748624 3.780000e-78 303.0
30 TraesCS2D01G416500 chr2A 84.158 202 20 9 7375 7567 745392777 745392975 1.430000e-42 185.0
31 TraesCS2D01G416500 chr2A 82.550 149 24 2 1918 2064 675750884 675750736 6.790000e-26 130.0
32 TraesCS2D01G416500 chr2A 100.000 34 0 0 2470 2503 675084589 675084556 6.980000e-06 63.9
33 TraesCS2D01G416500 chr2B 94.407 3558 104 22 449 3958 630142327 630138817 0.000000e+00 5380.0
34 TraesCS2D01G416500 chr2B 94.583 3249 142 8 3982 7218 630138824 630135598 0.000000e+00 4994.0
35 TraesCS2D01G416500 chr2B 77.174 2909 471 122 2471 5270 631106358 631103534 0.000000e+00 1515.0
36 TraesCS2D01G416500 chr2B 89.591 1028 99 8 5906 6929 631102872 631101849 0.000000e+00 1299.0
37 TraesCS2D01G416500 chr2B 92.566 834 20 8 7138 7965 630135722 630134925 0.000000e+00 1158.0
38 TraesCS2D01G416500 chr2B 79.258 1051 180 30 5895 6929 631203831 631202803 0.000000e+00 699.0
39 TraesCS2D01G416500 chr2B 95.957 371 15 0 7964 8334 630134812 630134442 3.330000e-168 603.0
40 TraesCS2D01G416500 chr2B 94.475 362 16 2 2110 2470 631106684 631106326 9.450000e-154 555.0
41 TraesCS2D01G416500 chr2B 86.304 460 55 6 1 457 630143612 630143158 2.090000e-135 494.0
42 TraesCS2D01G416500 chr2B 79.840 625 63 25 7721 8317 631101047 631100458 1.690000e-106 398.0
43 TraesCS2D01G416500 chr2B 81.128 514 68 13 3334 3830 631106631 631106130 1.310000e-102 385.0
44 TraesCS2D01G416500 chr2B 81.282 390 51 7 2101 2470 630139518 630139131 6.320000e-76 296.0
45 TraesCS2D01G416500 chr2B 86.911 191 23 2 151 339 74728523 74728713 6.550000e-51 213.0
46 TraesCS2D01G416500 chr2B 82.843 204 23 8 7375 7567 749803202 749803404 1.110000e-38 172.0
47 TraesCS2D01G416500 chr2B 83.448 145 22 2 1922 2064 631105899 631105755 5.250000e-27 134.0
48 TraesCS2D01G416500 chr2B 89.412 85 5 3 7179 7262 631101631 631101550 4.110000e-18 104.0
49 TraesCS2D01G416500 chr2B 100.000 34 0 0 2470 2503 630140340 630140307 6.980000e-06 63.9
50 TraesCS2D01G416500 chr4D 97.089 1271 36 1 2913 4183 410440054 410438785 0.000000e+00 2141.0
51 TraesCS2D01G416500 chr4D 85.809 451 48 8 7708 8154 47288641 47289079 1.640000e-126 464.0
52 TraesCS2D01G416500 chr4D 80.000 390 56 8 2101 2470 410439710 410439323 1.380000e-67 268.0
53 TraesCS2D01G416500 chr3D 97.941 923 19 0 2914 3836 554513152 554514074 0.000000e+00 1600.0
54 TraesCS2D01G416500 chr3D 95.455 330 12 3 3855 4183 554514061 554514388 2.670000e-144 523.0
55 TraesCS2D01G416500 chr3D 80.874 366 48 9 2101 2446 554513495 554513858 1.380000e-67 268.0
56 TraesCS2D01G416500 chr4A 86.253 451 47 8 7708 8154 551215467 551215028 7.570000e-130 475.0
57 TraesCS2D01G416500 chr4B 84.583 240 25 7 7919 8158 68670434 68670661 2.340000e-55 228.0
58 TraesCS2D01G416500 chr4B 87.838 148 14 4 3681 3826 58060771 58060626 4.000000e-38 171.0
59 TraesCS2D01G416500 chr4B 92.424 66 4 1 2614 2679 58060690 58060626 8.910000e-15 93.5
60 TraesCS2D01G416500 chr3B 89.286 112 5 3 6711 6816 732058711 732058601 5.250000e-27 134.0


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 TraesCS2D01G416500 chr2D 530257595 530265928 8333 True 15391.000000 15391 100.000000 1 8334 1 chr2D.!!$R2 8333
1 TraesCS2D01G416500 chr2D 531348047 531349075 1028 True 660.000000 660 78.571000 5895 6929 1 chr2D.!!$R3 1034
2 TraesCS2D01G416500 chr2D 531259393 531268024 8631 True 534.555556 1419 84.950778 1840 8290 9 chr2D.!!$R5 6450
3 TraesCS2D01G416500 chr2A 675078852 675088812 9960 True 2219.316667 10743 91.986333 37 8334 6 chr2A.!!$R2 8297
4 TraesCS2D01G416500 chr2A 675896490 675897503 1013 True 671.000000 671 78.896000 5910 6929 1 chr2A.!!$R1 1019
5 TraesCS2D01G416500 chr2A 675745335 675751671 6336 True 658.000000 1578 84.116286 1918 8290 7 chr2A.!!$R3 6372
6 TraesCS2D01G416500 chr2B 630134442 630143612 9170 True 1855.557143 5380 92.157000 1 8334 7 chr2B.!!$R2 8333
7 TraesCS2D01G416500 chr2B 631202803 631203831 1028 True 699.000000 699 79.258000 5895 6929 1 chr2B.!!$R1 1034
8 TraesCS2D01G416500 chr2B 631100458 631106684 6226 True 627.142857 1515 85.009714 1922 8317 7 chr2B.!!$R3 6395
9 TraesCS2D01G416500 chr4D 410438785 410440054 1269 True 1204.500000 2141 88.544500 2101 4183 2 chr4D.!!$R1 2082
10 TraesCS2D01G416500 chr3D 554513152 554514388 1236 False 797.000000 1600 91.423333 2101 4183 3 chr3D.!!$F1 2082

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
263 265 0.179073 CATGGTTAGGCTCAGGTCCG 60.179 60.000 0.00 0.0 0.00 4.79 F
705 1594 0.729116 CGATGGCAAGCACACTTAGG 59.271 55.000 0.00 0.0 33.74 2.69 F
1444 4237 1.003051 AAGATACCAGAGCCCCGGT 59.997 57.895 0.00 0.0 39.41 5.28 F
1784 4607 2.675844 CGTTCCCTGATTTACATGCGAA 59.324 45.455 0.00 0.0 0.00 4.70 F
2643 5495 3.181493 GCTATTGTTTGGAGTCAGCATGG 60.181 47.826 0.00 0.0 36.16 3.66 F
4281 7175 3.072211 TGCTCAACTCTTGAAGATGCTG 58.928 45.455 0.00 0.0 39.58 4.41 F
5613 8600 0.980423 GCAGAGGAGGAAACAGAGGT 59.020 55.000 0.00 0.0 0.00 3.85 F
7112 10283 0.182537 AAGGCCTGCTGTGTTGTGTA 59.817 50.000 5.69 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1706 4529 0.541863 TTGGAGGGGATCTTCTTCGC 59.458 55.000 0.00 0.00 0.00 4.70 R
1784 4607 1.980765 TCATGCCAGAGTTCAGAAGGT 59.019 47.619 0.00 0.00 0.00 3.50 R
2643 5495 3.243873 CCAAAAGGCCCAAAGTTCTTCTC 60.244 47.826 0.00 0.00 0.00 2.87 R
3230 6095 8.331022 CAGATAACTTTCATTCCTATTCACGTG 58.669 37.037 9.94 9.94 0.00 4.49 R
4378 7275 1.451387 CATTGTAGGCCCGTGACCC 60.451 63.158 0.00 0.00 0.00 4.46 R
5679 8666 2.438021 AGAGTCACCCAGTTTTAGCACA 59.562 45.455 0.00 0.00 0.00 4.57 R
7125 10296 0.040958 CACAGCAAAGCCGAGTCAAC 60.041 55.000 0.00 0.00 0.00 3.18 R
8201 13808 1.110442 TGGCCACAACTTTGGTCTTG 58.890 50.000 0.00 0.00 42.29 3.02 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
56 58 6.659824 ACTAAACTCCCTCTTCTTTTTGACA 58.340 36.000 0.00 0.00 0.00 3.58
62 64 4.834496 TCCCTCTTCTTTTTGACAATGCAT 59.166 37.500 0.00 0.00 0.00 3.96
69 71 6.017400 TCTTTTTGACAATGCATTCTCTCC 57.983 37.500 9.53 0.00 0.00 3.71
71 73 3.333029 TTGACAATGCATTCTCTCCGA 57.667 42.857 9.53 0.00 0.00 4.55
96 98 2.743636 AAGAAATCGGCGAGTCTTCA 57.256 45.000 24.74 0.00 0.00 3.02
136 138 2.817258 CAAGGGCGATTAGGACAAACAA 59.183 45.455 0.00 0.00 0.00 2.83
144 146 4.154015 CGATTAGGACAAACAATGACTGCA 59.846 41.667 0.00 0.00 0.00 4.41
145 147 5.334802 CGATTAGGACAAACAATGACTGCAA 60.335 40.000 0.00 0.00 0.00 4.08
179 181 7.955324 CGTGTAATTTGTATTACTCACACCAAG 59.045 37.037 8.87 0.00 44.20 3.61
186 188 3.738830 TTACTCACACCAAGCGTACTT 57.261 42.857 0.00 0.00 36.19 2.24
210 212 4.380841 AATTGTGCTAGTGATGCAATGG 57.619 40.909 0.00 0.00 42.41 3.16
233 235 1.693627 CGTATGGTAGGAGTGAGCCT 58.306 55.000 0.00 0.00 42.15 4.58
238 240 3.689872 TGGTAGGAGTGAGCCTAGAAT 57.310 47.619 0.00 0.00 41.05 2.40
240 242 3.706594 TGGTAGGAGTGAGCCTAGAATTG 59.293 47.826 0.00 0.00 41.05 2.32
244 246 1.939255 GAGTGAGCCTAGAATTGCAGC 59.061 52.381 0.00 0.00 0.00 5.25
263 265 0.179073 CATGGTTAGGCTCAGGTCCG 60.179 60.000 0.00 0.00 0.00 4.79
264 266 1.338136 ATGGTTAGGCTCAGGTCCGG 61.338 60.000 0.00 0.00 0.00 5.14
274 277 2.350522 CTCAGGTCCGGATTCTTGTTG 58.649 52.381 7.81 0.00 0.00 3.33
279 282 2.552373 GGTCCGGATTCTTGTTGGAACT 60.552 50.000 7.81 0.00 33.57 3.01
288 291 7.433680 GGATTCTTGTTGGAACTTTGTAACAT 58.566 34.615 0.00 0.00 33.56 2.71
293 296 7.990886 TCTTGTTGGAACTTTGTAACATAGACT 59.009 33.333 0.00 0.00 33.56 3.24
302 305 7.680730 ACTTTGTAACATAGACTGAGATGGTT 58.319 34.615 0.00 0.00 0.00 3.67
315 319 5.707298 ACTGAGATGGTTTGGTTGAGTAATG 59.293 40.000 0.00 0.00 0.00 1.90
318 322 4.832266 AGATGGTTTGGTTGAGTAATGCAA 59.168 37.500 0.00 0.00 0.00 4.08
322 326 5.757320 TGGTTTGGTTGAGTAATGCAAATTG 59.243 36.000 0.00 0.00 0.00 2.32
327 331 6.815089 TGGTTGAGTAATGCAAATTGTTCTT 58.185 32.000 0.00 0.00 0.00 2.52
368 372 3.120304 GGAGCACGGTGTCTTAAACAATC 60.120 47.826 10.24 0.00 40.31 2.67
370 374 4.890088 AGCACGGTGTCTTAAACAATCTA 58.110 39.130 10.24 0.00 40.31 1.98
451 466 8.842280 TGTAACCTTATGTACTTGTTCCTTTTG 58.158 33.333 0.00 0.00 0.00 2.44
493 1347 4.751098 ACAATTCTCTTACGCGTTACCAAA 59.249 37.500 20.78 3.67 0.00 3.28
642 1531 9.559732 TGTTGATTAGCAAATACATATACAGCT 57.440 29.630 0.00 0.00 38.44 4.24
664 1553 7.641411 CAGCTTACAGCAATGACATAATAACAC 59.359 37.037 0.00 0.00 45.56 3.32
705 1594 0.729116 CGATGGCAAGCACACTTAGG 59.271 55.000 0.00 0.00 33.74 2.69
706 1595 1.675714 CGATGGCAAGCACACTTAGGA 60.676 52.381 0.00 0.00 33.74 2.94
707 1596 2.012673 GATGGCAAGCACACTTAGGAG 58.987 52.381 0.00 0.00 33.74 3.69
746 1635 7.282585 TCGATGATGATCTTGAGGGTTATTTT 58.717 34.615 0.00 0.00 0.00 1.82
747 1636 7.775093 TCGATGATGATCTTGAGGGTTATTTTT 59.225 33.333 0.00 0.00 0.00 1.94
778 1667 5.958321 ACAAGGGAAAAGAAAGAAGAGGAT 58.042 37.500 0.00 0.00 0.00 3.24
779 1668 5.772169 ACAAGGGAAAAGAAAGAAGAGGATG 59.228 40.000 0.00 0.00 0.00 3.51
780 1669 5.590976 AGGGAAAAGAAAGAAGAGGATGT 57.409 39.130 0.00 0.00 0.00 3.06
781 1670 5.958321 AGGGAAAAGAAAGAAGAGGATGTT 58.042 37.500 0.00 0.00 0.00 2.71
782 1671 5.772169 AGGGAAAAGAAAGAAGAGGATGTTG 59.228 40.000 0.00 0.00 0.00 3.33
783 1672 5.770162 GGGAAAAGAAAGAAGAGGATGTTGA 59.230 40.000 0.00 0.00 0.00 3.18
784 1673 6.294231 GGGAAAAGAAAGAAGAGGATGTTGAC 60.294 42.308 0.00 0.00 0.00 3.18
808 1697 6.217693 ACTCTTGAGGGGTAAGATGGTAAAAT 59.782 38.462 2.55 0.00 33.99 1.82
1444 4237 1.003051 AAGATACCAGAGCCCCGGT 59.997 57.895 0.00 0.00 39.41 5.28
1501 4294 4.324991 GGGCGTGGTTCGGGAAGT 62.325 66.667 0.00 0.00 40.26 3.01
1784 4607 2.675844 CGTTCCCTGATTTACATGCGAA 59.324 45.455 0.00 0.00 0.00 4.70
2003 4828 8.230486 GTGTGATCTCAGATTGTTTCGTATTTT 58.770 33.333 0.00 0.00 0.00 1.82
2090 4915 8.113173 ACTCCAGGTTTATAGATCGAGATAAC 57.887 38.462 0.00 0.00 0.00 1.89
2643 5495 3.181493 GCTATTGTTTGGAGTCAGCATGG 60.181 47.826 0.00 0.00 36.16 3.66
3230 6095 4.395231 GTGTGCTCCAAGGTTTATAGGTTC 59.605 45.833 0.00 0.00 0.00 3.62
4055 6948 6.151312 TGTTACTGCTTTCCTTGTGTAAAACA 59.849 34.615 0.00 0.00 36.85 2.83
4281 7175 3.072211 TGCTCAACTCTTGAAGATGCTG 58.928 45.455 0.00 0.00 39.58 4.41
4287 7181 3.748083 ACTCTTGAAGATGCTGCAGAAA 58.252 40.909 20.43 4.69 0.00 2.52
4378 7275 0.987294 ATCCCTCCCTGTGTCAGTTG 59.013 55.000 0.00 0.00 0.00 3.16
4747 7653 1.541588 ACCTTAACGTCCGTAGTCCAC 59.458 52.381 0.00 0.00 0.00 4.02
4755 7661 2.563702 GTCCGTAGTCCACCTCTAGAG 58.436 57.143 13.18 13.18 0.00 2.43
4835 7741 3.850752 ACCAGAAGAAGTCCTCTGAAGA 58.149 45.455 8.25 0.00 33.37 2.87
4876 7782 4.573201 CAGTTCGGAAGTACAAGGTTCAAA 59.427 41.667 0.00 0.00 33.41 2.69
4899 7805 1.159285 TGACGGCTGAAAATGCTGAG 58.841 50.000 0.00 0.00 39.85 3.35
5221 8149 2.548920 GCGCCCTTCTACTTCTGCATAT 60.549 50.000 0.00 0.00 0.00 1.78
5290 8218 7.721286 ATATCACACTATTTACTTGCTGCTC 57.279 36.000 0.00 0.00 0.00 4.26
5342 8270 8.718102 TTGCTAGAGGTTCAATACAATAGTTC 57.282 34.615 0.00 0.00 0.00 3.01
5447 8431 6.418057 TTTTTCAATTCACTGCCCACTTAT 57.582 33.333 0.00 0.00 0.00 1.73
5613 8600 0.980423 GCAGAGGAGGAAACAGAGGT 59.020 55.000 0.00 0.00 0.00 3.85
5836 8862 5.105567 TCGTTTCAGGGATGCCTTTATTA 57.894 39.130 1.40 0.00 0.00 0.98
6555 9584 3.900855 GAGGACGACTACTCGCCA 58.099 61.111 0.00 0.00 44.33 5.69
6778 9813 4.699522 AGAACGGGCACGGCTTCC 62.700 66.667 15.46 0.00 46.48 3.46
7108 10279 1.656441 GTGAAGGCCTGCTGTGTTG 59.344 57.895 13.40 0.00 0.00 3.33
7109 10280 1.103398 GTGAAGGCCTGCTGTGTTGT 61.103 55.000 13.40 0.00 0.00 3.32
7110 10281 1.102809 TGAAGGCCTGCTGTGTTGTG 61.103 55.000 13.40 0.00 0.00 3.33
7111 10282 1.076777 AAGGCCTGCTGTGTTGTGT 60.077 52.632 5.69 0.00 0.00 3.72
7112 10283 0.182537 AAGGCCTGCTGTGTTGTGTA 59.817 50.000 5.69 0.00 0.00 2.90
7113 10284 0.535102 AGGCCTGCTGTGTTGTGTAC 60.535 55.000 3.11 0.00 0.00 2.90
7114 10285 0.817634 GGCCTGCTGTGTTGTGTACA 60.818 55.000 0.00 0.00 0.00 2.90
7115 10286 1.238439 GCCTGCTGTGTTGTGTACAT 58.762 50.000 0.00 0.00 39.39 2.29
7116 10287 1.069022 GCCTGCTGTGTTGTGTACATG 60.069 52.381 0.00 0.00 39.39 3.21
7117 10288 1.069022 CCTGCTGTGTTGTGTACATGC 60.069 52.381 0.00 0.00 39.39 4.06
7118 10289 1.875514 CTGCTGTGTTGTGTACATGCT 59.124 47.619 0.00 0.00 39.39 3.79
7119 10290 1.872952 TGCTGTGTTGTGTACATGCTC 59.127 47.619 0.00 0.00 39.39 4.26
7120 10291 1.136252 GCTGTGTTGTGTACATGCTCG 60.136 52.381 0.00 0.00 39.39 5.03
7121 10292 2.135139 CTGTGTTGTGTACATGCTCGT 58.865 47.619 0.00 0.00 39.39 4.18
7122 10293 2.131972 TGTGTTGTGTACATGCTCGTC 58.868 47.619 0.00 0.00 39.39 4.20
7123 10294 2.131972 GTGTTGTGTACATGCTCGTCA 58.868 47.619 0.00 0.00 39.39 4.35
7124 10295 2.542178 GTGTTGTGTACATGCTCGTCAA 59.458 45.455 0.00 0.00 39.39 3.18
7125 10296 2.799978 TGTTGTGTACATGCTCGTCAAG 59.200 45.455 0.00 0.00 0.00 3.02
7126 10297 2.800544 GTTGTGTACATGCTCGTCAAGT 59.199 45.455 0.00 0.00 0.00 3.16
7127 10298 3.106242 TGTGTACATGCTCGTCAAGTT 57.894 42.857 0.00 0.00 0.00 2.66
7128 10299 2.799978 TGTGTACATGCTCGTCAAGTTG 59.200 45.455 0.00 0.00 0.00 3.16
7129 10300 3.057019 GTGTACATGCTCGTCAAGTTGA 58.943 45.455 0.08 0.08 0.00 3.18
7130 10301 3.057019 TGTACATGCTCGTCAAGTTGAC 58.943 45.455 23.53 23.53 43.65 3.18
7131 10302 2.533266 ACATGCTCGTCAAGTTGACT 57.467 45.000 28.53 11.02 44.85 3.41
7132 10303 2.408050 ACATGCTCGTCAAGTTGACTC 58.592 47.619 28.53 18.98 44.85 3.36
7133 10304 1.388093 CATGCTCGTCAAGTTGACTCG 59.612 52.381 28.53 20.71 44.85 4.18
7134 10305 0.318699 TGCTCGTCAAGTTGACTCGG 60.319 55.000 28.53 19.67 44.85 4.63
7135 10306 1.618640 GCTCGTCAAGTTGACTCGGC 61.619 60.000 28.53 23.94 44.85 5.54
7136 10307 0.039074 CTCGTCAAGTTGACTCGGCT 60.039 55.000 28.53 0.00 44.85 5.52
7137 10308 0.387929 TCGTCAAGTTGACTCGGCTT 59.612 50.000 28.53 0.00 44.85 4.35
7138 10309 1.202486 TCGTCAAGTTGACTCGGCTTT 60.202 47.619 28.53 0.00 44.85 3.51
7139 10310 1.070577 CGTCAAGTTGACTCGGCTTTG 60.071 52.381 28.53 10.78 44.85 2.77
7140 10311 0.944386 TCAAGTTGACTCGGCTTTGC 59.056 50.000 0.08 0.00 0.00 3.68
7141 10312 0.947244 CAAGTTGACTCGGCTTTGCT 59.053 50.000 0.00 0.00 0.00 3.91
7142 10313 0.947244 AAGTTGACTCGGCTTTGCTG 59.053 50.000 0.00 0.00 36.06 4.41
7143 10314 0.179045 AGTTGACTCGGCTTTGCTGT 60.179 50.000 0.00 0.00 36.18 4.40
7144 10315 0.040958 GTTGACTCGGCTTTGCTGTG 60.041 55.000 0.00 0.00 36.18 3.66
7145 10316 0.463654 TTGACTCGGCTTTGCTGTGT 60.464 50.000 5.89 5.89 43.03 3.72
7146 10317 0.463654 TGACTCGGCTTTGCTGTGTT 60.464 50.000 7.38 0.00 40.91 3.32
7147 10318 0.235926 GACTCGGCTTTGCTGTGTTC 59.764 55.000 7.38 0.00 40.91 3.18
7167 10338 1.286501 GTACATGCTCGCCGAATTGA 58.713 50.000 0.00 0.00 0.00 2.57
7676 13138 2.429494 TGCGGTCAGGCAATCACA 59.571 55.556 0.00 0.00 40.59 3.58
8201 13808 1.617357 ACGAAGGTTCTGTGAGGTACC 59.383 52.381 2.73 2.73 0.00 3.34
8271 13881 4.757149 AGAGAAGCTAAACCACATTCACAC 59.243 41.667 0.00 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.753867 GAGGTAACAGGCTAGCCTCC 59.246 60.000 33.94 28.92 46.28 4.30
56 58 3.634397 TCCTTTCGGAGAGAATGCATT 57.366 42.857 12.83 12.83 38.86 3.56
69 71 1.730064 TCGCCGATTTCTTTCCTTTCG 59.270 47.619 0.00 0.00 0.00 3.46
71 73 2.742589 GACTCGCCGATTTCTTTCCTTT 59.257 45.455 0.00 0.00 0.00 3.11
84 86 1.126846 GATGTTGTTGAAGACTCGCCG 59.873 52.381 0.00 0.00 0.00 6.46
96 98 1.165270 GCGGGCACTAAGATGTTGTT 58.835 50.000 0.00 0.00 0.00 2.83
127 129 4.211794 CCATTTTGCAGTCATTGTTTGTCC 59.788 41.667 0.00 0.00 0.00 4.02
136 138 3.084039 ACACGATCCATTTTGCAGTCAT 58.916 40.909 0.00 0.00 0.00 3.06
179 181 4.151689 TCACTAGCACAATTTCAAGTACGC 59.848 41.667 0.00 0.00 0.00 4.42
186 188 5.404096 CATTGCATCACTAGCACAATTTCA 58.596 37.500 0.00 0.00 42.54 2.69
187 189 4.802039 CCATTGCATCACTAGCACAATTTC 59.198 41.667 0.00 0.00 42.54 2.17
188 190 4.751060 CCATTGCATCACTAGCACAATTT 58.249 39.130 0.00 0.00 42.54 1.82
213 215 0.674534 GGCTCACTCCTACCATACGG 59.325 60.000 0.00 0.00 38.77 4.02
233 235 2.951642 GCCTAACCATGCTGCAATTCTA 59.048 45.455 6.36 0.00 0.00 2.10
238 240 0.038021 TGAGCCTAACCATGCTGCAA 59.962 50.000 6.36 0.00 38.11 4.08
240 242 1.099879 CCTGAGCCTAACCATGCTGC 61.100 60.000 0.00 0.00 38.11 5.25
244 246 0.179073 CGGACCTGAGCCTAACCATG 60.179 60.000 0.00 0.00 0.00 3.66
263 265 6.801575 TGTTACAAAGTTCCAACAAGAATCC 58.198 36.000 0.00 0.00 0.00 3.01
264 266 9.612620 CTATGTTACAAAGTTCCAACAAGAATC 57.387 33.333 0.00 0.00 34.79 2.52
274 277 7.278868 CCATCTCAGTCTATGTTACAAAGTTCC 59.721 40.741 0.00 0.00 0.00 3.62
279 282 7.390440 CCAAACCATCTCAGTCTATGTTACAAA 59.610 37.037 0.00 0.00 0.00 2.83
288 291 4.593206 ACTCAACCAAACCATCTCAGTCTA 59.407 41.667 0.00 0.00 0.00 2.59
293 296 4.458989 GCATTACTCAACCAAACCATCTCA 59.541 41.667 0.00 0.00 0.00 3.27
302 305 6.815089 AGAACAATTTGCATTACTCAACCAA 58.185 32.000 0.00 0.00 0.00 3.67
315 319 4.528531 TTTTTGCGGAAGAACAATTTGC 57.471 36.364 0.00 0.00 0.00 3.68
343 347 2.812011 GTTTAAGACACCGTGCTCCATT 59.188 45.455 0.00 0.00 0.00 3.16
344 348 2.224426 TGTTTAAGACACCGTGCTCCAT 60.224 45.455 0.00 0.00 32.00 3.41
345 349 1.139256 TGTTTAAGACACCGTGCTCCA 59.861 47.619 0.00 0.00 32.00 3.86
352 356 6.780706 ACACTTAGATTGTTTAAGACACCG 57.219 37.500 0.00 0.00 38.18 4.94
368 372 6.757010 GTGAACATCCACACCTATACACTTAG 59.243 42.308 0.00 0.00 37.04 2.18
370 374 5.488341 GTGAACATCCACACCTATACACTT 58.512 41.667 0.00 0.00 37.04 3.16
446 461 4.853743 GCCTCGCTTCATTAAGAACAAAAG 59.146 41.667 0.00 0.00 34.37 2.27
451 466 2.742053 TGTGCCTCGCTTCATTAAGAAC 59.258 45.455 0.00 0.00 34.37 3.01
493 1347 5.701224 TGGTCTTCAGAATACCCTGTTTTT 58.299 37.500 13.79 0.00 35.71 1.94
641 1530 7.905126 TCGTGTTATTATGTCATTGCTGTAAG 58.095 34.615 0.00 0.00 0.00 2.34
642 1531 7.835634 TCGTGTTATTATGTCATTGCTGTAA 57.164 32.000 0.00 0.00 0.00 2.41
643 1532 7.835634 TTCGTGTTATTATGTCATTGCTGTA 57.164 32.000 0.00 0.00 0.00 2.74
644 1533 6.735678 TTCGTGTTATTATGTCATTGCTGT 57.264 33.333 0.00 0.00 0.00 4.40
645 1534 7.020602 TGTTTCGTGTTATTATGTCATTGCTG 58.979 34.615 0.00 0.00 0.00 4.41
646 1535 7.094805 ACTGTTTCGTGTTATTATGTCATTGCT 60.095 33.333 0.00 0.00 0.00 3.91
647 1536 7.007367 CACTGTTTCGTGTTATTATGTCATTGC 59.993 37.037 0.00 0.00 0.00 3.56
664 1553 6.359545 TCGTTGAATAATTGTCACTGTTTCG 58.640 36.000 0.00 0.00 0.00 3.46
705 1594 4.748892 TCATCGATGGACTTCTTTCACTC 58.251 43.478 24.61 0.00 0.00 3.51
706 1595 4.808414 TCATCGATGGACTTCTTTCACT 57.192 40.909 24.61 0.00 0.00 3.41
707 1596 5.111989 TCATCATCGATGGACTTCTTTCAC 58.888 41.667 24.61 0.00 40.15 3.18
747 1636 9.816354 CTTCTTTCTTTTCCCTTGTCAAAATAA 57.184 29.630 0.00 0.00 0.00 1.40
748 1637 9.196139 TCTTCTTTCTTTTCCCTTGTCAAAATA 57.804 29.630 0.00 0.00 0.00 1.40
750 1639 7.363793 CCTCTTCTTTCTTTTCCCTTGTCAAAA 60.364 37.037 0.00 0.00 0.00 2.44
751 1640 6.096846 CCTCTTCTTTCTTTTCCCTTGTCAAA 59.903 38.462 0.00 0.00 0.00 2.69
752 1641 5.594317 CCTCTTCTTTCTTTTCCCTTGTCAA 59.406 40.000 0.00 0.00 0.00 3.18
753 1642 5.104109 TCCTCTTCTTTCTTTTCCCTTGTCA 60.104 40.000 0.00 0.00 0.00 3.58
760 1649 6.488344 AGTCAACATCCTCTTCTTTCTTTTCC 59.512 38.462 0.00 0.00 0.00 3.13
778 1667 3.583228 TCTTACCCCTCAAGAGTCAACA 58.417 45.455 0.00 0.00 0.00 3.33
779 1668 4.508662 CATCTTACCCCTCAAGAGTCAAC 58.491 47.826 0.00 0.00 35.57 3.18
780 1669 3.519510 CCATCTTACCCCTCAAGAGTCAA 59.480 47.826 0.00 0.00 35.57 3.18
781 1670 3.107601 CCATCTTACCCCTCAAGAGTCA 58.892 50.000 0.00 0.00 35.57 3.41
782 1671 3.108376 ACCATCTTACCCCTCAAGAGTC 58.892 50.000 0.00 0.00 35.57 3.36
783 1672 3.207044 ACCATCTTACCCCTCAAGAGT 57.793 47.619 0.00 0.00 35.57 3.24
784 1673 5.693769 TTTACCATCTTACCCCTCAAGAG 57.306 43.478 0.00 0.00 35.57 2.85
808 1697 2.253051 TCGCGTACACACAGACCGA 61.253 57.895 5.77 0.00 0.00 4.69
843 1732 2.972144 TTTCGACGCCCATTTGCCG 61.972 57.895 0.00 0.00 0.00 5.69
855 1744 0.666577 AGCACGCTACCAGTTTCGAC 60.667 55.000 0.00 0.00 0.00 4.20
1024 3817 2.486370 GGTGGAATTGGGTTGGGTTTTG 60.486 50.000 0.00 0.00 0.00 2.44
1131 3924 1.472878 TCTTGTCACCGGAATCTCTCG 59.527 52.381 9.46 0.00 0.00 4.04
1501 4294 4.386591 GGGTCCCGAGGTCCATTA 57.613 61.111 0.00 0.00 32.60 1.90
1597 4411 3.070159 GCCATCTGCTTGGATAGTAGTCA 59.930 47.826 5.26 0.00 39.25 3.41
1706 4529 0.541863 TTGGAGGGGATCTTCTTCGC 59.458 55.000 0.00 0.00 0.00 4.70
1784 4607 1.980765 TCATGCCAGAGTTCAGAAGGT 59.019 47.619 0.00 0.00 0.00 3.50
2003 4828 2.677836 GCGTAATCATGGAGCAGAAACA 59.322 45.455 0.00 0.00 0.00 2.83
2090 4915 5.728471 ACAGATAGATAATCGCCAATCCTG 58.272 41.667 0.00 0.00 39.79 3.86
2284 5110 4.124970 ACAACCGTTTAGGAGTTCAGTTC 58.875 43.478 0.00 0.00 45.00 3.01
2643 5495 3.243873 CCAAAAGGCCCAAAGTTCTTCTC 60.244 47.826 0.00 0.00 0.00 2.87
3230 6095 8.331022 CAGATAACTTTCATTCCTATTCACGTG 58.669 37.037 9.94 9.94 0.00 4.49
4055 6948 7.706607 GGAAAAAGAACAGTTAGAAACAGCAAT 59.293 33.333 0.00 0.00 0.00 3.56
4100 6994 3.736094 TCTACCTCTTCAATGGGACCAT 58.264 45.455 0.00 0.00 38.46 3.55
4281 7175 6.690194 ACTAATGAATGTGGAGATTTCTGC 57.310 37.500 0.00 0.00 34.66 4.26
4287 7181 6.318144 CAGAAGCAACTAATGAATGTGGAGAT 59.682 38.462 0.00 0.00 0.00 2.75
4378 7275 1.451387 CATTGTAGGCCCGTGACCC 60.451 63.158 0.00 0.00 0.00 4.46
4735 7641 2.170187 TCTCTAGAGGTGGACTACGGAC 59.830 54.545 19.67 0.00 0.00 4.79
4747 7653 3.053245 TCCCACTCTTCCTTCTCTAGAGG 60.053 52.174 19.67 5.01 39.73 3.69
4755 7661 7.112779 TCTTCAAATATTCCCACTCTTCCTTC 58.887 38.462 0.00 0.00 0.00 3.46
4876 7782 1.956477 AGCATTTTCAGCCGTCAAGTT 59.044 42.857 0.00 0.00 0.00 2.66
4899 7805 4.579869 TGAACTCCTTGAAGGTTATCTGC 58.420 43.478 11.60 0.00 36.53 4.26
5348 8277 8.015658 GCTGTAAAGGTATTGTTTACACAGAAG 58.984 37.037 4.67 0.00 42.64 2.85
5349 8278 7.499563 TGCTGTAAAGGTATTGTTTACACAGAA 59.500 33.333 4.67 0.00 42.64 3.02
5368 8297 3.802866 TCACACACATGTTCTGCTGTAA 58.197 40.909 0.00 0.00 36.72 2.41
5613 8600 6.593268 TCCAATGAAATCTTGAATTGCTCA 57.407 33.333 0.00 0.00 0.00 4.26
5679 8666 2.438021 AGAGTCACCCAGTTTTAGCACA 59.562 45.455 0.00 0.00 0.00 4.57
5836 8862 2.689471 TGCACTTGCTGACAATCTTTGT 59.311 40.909 2.33 0.00 44.05 2.83
6555 9584 1.497991 CCACGACAACTGTGATCGTT 58.502 50.000 14.67 1.64 46.38 3.85
6778 9813 2.047844 CTGCAGGTCCACGGACTG 60.048 66.667 15.62 12.28 44.04 3.51
6861 9896 2.268298 GTGATGTCGGCGTACTTGATT 58.732 47.619 6.85 0.00 0.00 2.57
6943 9978 2.182030 GAACTCGACGGCCTGGAG 59.818 66.667 0.00 7.11 0.00 3.86
7108 10279 3.057019 TCAACTTGACGAGCATGTACAC 58.943 45.455 0.00 0.00 34.14 2.90
7109 10280 3.057019 GTCAACTTGACGAGCATGTACA 58.943 45.455 6.16 0.00 37.67 2.90
7110 10281 3.706994 GTCAACTTGACGAGCATGTAC 57.293 47.619 6.16 0.00 37.67 2.90
7121 10292 0.944386 GCAAAGCCGAGTCAACTTGA 59.056 50.000 0.00 0.00 0.00 3.02
7122 10293 0.947244 AGCAAAGCCGAGTCAACTTG 59.053 50.000 0.00 0.00 0.00 3.16
7123 10294 0.947244 CAGCAAAGCCGAGTCAACTT 59.053 50.000 0.00 0.00 0.00 2.66
7124 10295 0.179045 ACAGCAAAGCCGAGTCAACT 60.179 50.000 0.00 0.00 0.00 3.16
7125 10296 0.040958 CACAGCAAAGCCGAGTCAAC 60.041 55.000 0.00 0.00 0.00 3.18
7126 10297 0.463654 ACACAGCAAAGCCGAGTCAA 60.464 50.000 0.00 0.00 0.00 3.18
7127 10298 0.463654 AACACAGCAAAGCCGAGTCA 60.464 50.000 0.00 0.00 0.00 3.41
7128 10299 0.235926 GAACACAGCAAAGCCGAGTC 59.764 55.000 0.00 0.00 0.00 3.36
7129 10300 1.498865 CGAACACAGCAAAGCCGAGT 61.499 55.000 0.00 0.00 0.00 4.18
7130 10301 1.205064 CGAACACAGCAAAGCCGAG 59.795 57.895 0.00 0.00 0.00 4.63
7131 10302 0.249531 TACGAACACAGCAAAGCCGA 60.250 50.000 0.00 0.00 0.00 5.54
7132 10303 0.110823 GTACGAACACAGCAAAGCCG 60.111 55.000 0.00 0.00 0.00 5.52
7133 10304 0.941542 TGTACGAACACAGCAAAGCC 59.058 50.000 0.00 0.00 0.00 4.35
7134 10305 2.574322 CATGTACGAACACAGCAAAGC 58.426 47.619 0.00 0.00 38.78 3.51
7135 10306 2.224079 AGCATGTACGAACACAGCAAAG 59.776 45.455 0.00 0.00 40.59 2.77
7136 10307 2.217750 AGCATGTACGAACACAGCAAA 58.782 42.857 0.00 0.00 40.59 3.68
7137 10308 1.798223 GAGCATGTACGAACACAGCAA 59.202 47.619 0.00 0.00 40.59 3.91
7138 10309 1.428448 GAGCATGTACGAACACAGCA 58.572 50.000 0.00 0.00 40.59 4.41
7139 10310 0.366871 CGAGCATGTACGAACACAGC 59.633 55.000 7.66 0.00 38.78 4.40
7140 10311 0.366871 GCGAGCATGTACGAACACAG 59.633 55.000 15.37 0.00 38.78 3.66
7141 10312 1.011968 GGCGAGCATGTACGAACACA 61.012 55.000 15.37 0.00 38.78 3.72
7142 10313 1.708027 GGCGAGCATGTACGAACAC 59.292 57.895 15.37 0.88 38.78 3.32
7143 10314 1.803922 CGGCGAGCATGTACGAACA 60.804 57.895 0.00 0.00 40.69 3.18
7144 10315 1.074319 TTCGGCGAGCATGTACGAAC 61.074 55.000 10.46 7.81 38.46 3.95
7145 10316 0.179121 ATTCGGCGAGCATGTACGAA 60.179 50.000 10.46 13.54 45.83 3.85
7146 10317 0.179121 AATTCGGCGAGCATGTACGA 60.179 50.000 10.46 6.56 0.00 3.43
7147 10318 0.043053 CAATTCGGCGAGCATGTACG 60.043 55.000 10.46 8.77 0.00 3.67
7167 10338 2.504367 ACACAGCAAAGCCGTAAGAAT 58.496 42.857 0.00 0.00 43.02 2.40
7286 10461 3.771479 ACAGTGATCAGCAGTATCTCCAA 59.229 43.478 0.00 0.00 0.00 3.53
7524 10810 4.575885 GTTCAGTGTAATGCCCTGAGTTA 58.424 43.478 0.00 0.00 36.64 2.24
7525 10811 3.412386 GTTCAGTGTAATGCCCTGAGTT 58.588 45.455 0.00 0.00 36.64 3.01
7676 13138 6.547141 TGTGTATACCACTACGGCTATTACTT 59.453 38.462 0.00 0.00 44.81 2.24
7705 13167 8.853077 TTTTCTCTGATGTATGACTTCACATT 57.147 30.769 0.00 0.00 35.55 2.71
7716 13178 5.440610 GGTGTGGGATTTTCTCTGATGTAT 58.559 41.667 0.00 0.00 0.00 2.29
7777 13239 1.342975 TGGAGACGAATCCCCAGATCA 60.343 52.381 7.96 0.00 38.72 2.92
8178 13785 1.971357 ACCTCACAGAACCTTCGTGAT 59.029 47.619 10.85 0.05 38.76 3.06
8201 13808 1.110442 TGGCCACAACTTTGGTCTTG 58.890 50.000 0.00 0.00 42.29 3.02
8271 13881 3.804036 TCCTAGTATTTTCATGTGGCCG 58.196 45.455 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.