Multiple sequence alignment - TraesCS2B01G335600

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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 TraesCS2B01G335600 chr2B 100.000 3128 0 0 1 3128 479545947 479549074 0.000000e+00 5777.0
1 TraesCS2B01G335600 chr2B 84.932 73 9 1 2456 2528 419556219 419556149 4.330000e-09 73.1
2 TraesCS2B01G335600 chr2B 94.737 38 2 0 1393 1430 141156523 141156486 3.370000e-05 60.2
3 TraesCS2B01G335600 chr2D 90.765 1646 74 33 963 2538 404888927 404890564 0.000000e+00 2126.0
4 TraesCS2B01G335600 chr2D 92.439 939 54 5 11 946 404887192 404888116 0.000000e+00 1325.0
5 TraesCS2B01G335600 chr2D 80.000 560 69 16 2538 3058 139462079 139462634 1.060000e-99 374.0
6 TraesCS2B01G335600 chr2D 82.251 231 30 7 645 866 43458744 43458516 4.120000e-44 189.0
7 TraesCS2B01G335600 chr2D 84.343 198 24 6 2539 2732 111572648 111572842 1.480000e-43 187.0
8 TraesCS2B01G335600 chr2A 95.062 1215 52 3 963 2169 542759893 542761107 0.000000e+00 1905.0
9 TraesCS2B01G335600 chr2A 90.069 433 42 1 1 432 542741942 542742374 7.580000e-156 560.0
10 TraesCS2B01G335600 chr2A 88.636 308 31 3 440 746 542745019 542745323 3.810000e-99 372.0
11 TraesCS2B01G335600 chr2A 80.224 536 66 20 2542 3040 31815176 31815708 1.770000e-97 366.0
12 TraesCS2B01G335600 chr2A 88.889 207 20 2 741 946 542755009 542755213 5.180000e-63 252.0
13 TraesCS2B01G335600 chr4D 81.982 555 59 16 2541 3058 365405249 365405799 1.720000e-117 433.0
14 TraesCS2B01G335600 chr4A 81.314 487 70 13 2545 3017 100127880 100127401 2.950000e-100 375.0
15 TraesCS2B01G335600 chr4A 79.783 277 44 6 638 908 256430678 256430408 1.150000e-44 191.0
16 TraesCS2B01G335600 chr3A 78.947 532 74 20 2545 3040 711543907 711543378 8.360000e-86 327.0
17 TraesCS2B01G335600 chr3B 73.561 938 192 39 1189 2113 127852454 127853348 1.090000e-79 307.0
18 TraesCS2B01G335600 chr3B 86.957 253 29 4 2794 3043 553724224 553724475 6.600000e-72 281.0
19 TraesCS2B01G335600 chr3B 87.273 220 23 3 2536 2750 553604451 553604670 2.410000e-61 246.0
20 TraesCS2B01G335600 chr3B 79.114 316 53 6 638 946 673298558 673298867 4.090000e-49 206.0
21 TraesCS2B01G335600 chr3B 80.505 277 42 6 638 908 415464646 415464376 5.290000e-48 202.0
22 TraesCS2B01G335600 chr3B 81.385 231 32 6 645 866 175773293 175773521 8.910000e-41 178.0
23 TraesCS2B01G335600 chr3B 81.385 231 32 6 645 866 175774608 175774836 8.910000e-41 178.0
24 TraesCS2B01G335600 chr6B 78.627 510 68 20 2538 3010 697808293 697807788 1.820000e-77 300.0
25 TraesCS2B01G335600 chr6B 86.154 65 6 3 2468 2530 672098569 672098632 2.010000e-07 67.6
26 TraesCS2B01G335600 chr1D 85.619 299 28 13 616 908 311929937 311929648 1.820000e-77 300.0
27 TraesCS2B01G335600 chr1D 75.952 499 75 24 2551 3010 470952064 470951572 6.790000e-52 215.0
28 TraesCS2B01G335600 chr1B 83.471 242 40 0 2799 3040 657194933 657195174 3.140000e-55 226.0
29 TraesCS2B01G335600 chr1B 75.686 510 82 23 2546 3017 6186906 6186401 1.890000e-52 217.0
30 TraesCS2B01G335600 chr5A 76.389 288 50 15 1391 1669 457086533 457086811 4.210000e-29 139.0
31 TraesCS2B01G335600 chr5A 77.778 198 42 2 1383 1579 457797653 457797849 1.520000e-23 121.0
32 TraesCS2B01G335600 chr5A 98.039 51 1 0 2343 2393 345152014 345151964 4.300000e-14 89.8
33 TraesCS2B01G335600 chr5A 97.143 35 0 1 2468 2501 522359369 522359335 1.210000e-04 58.4
34 TraesCS2B01G335600 chr3D 78.605 215 40 6 2799 3010 416987763 416987552 1.510000e-28 137.0
35 TraesCS2B01G335600 chr5D 80.899 178 26 5 1391 1564 354941547 354941720 1.960000e-27 134.0
36 TraesCS2B01G335600 chr5D 92.063 63 3 2 2548 2610 8711208 8711148 1.550000e-13 87.9
37 TraesCS2B01G335600 chr5B 86.885 61 7 1 2468 2527 597297319 597297379 2.010000e-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 TraesCS2B01G335600 chr2B 479545947 479549074 3127 False 5777.0 5777 100.0000 1 3128 1 chr2B.!!$F1 3127
1 TraesCS2B01G335600 chr2D 404887192 404890564 3372 False 1725.5 2126 91.6020 11 2538 2 chr2D.!!$F3 2527
2 TraesCS2B01G335600 chr2D 139462079 139462634 555 False 374.0 374 80.0000 2538 3058 1 chr2D.!!$F2 520
3 TraesCS2B01G335600 chr2A 542759893 542761107 1214 False 1905.0 1905 95.0620 963 2169 1 chr2A.!!$F3 1206
4 TraesCS2B01G335600 chr2A 542741942 542745323 3381 False 466.0 560 89.3525 1 746 2 chr2A.!!$F4 745
5 TraesCS2B01G335600 chr2A 31815176 31815708 532 False 366.0 366 80.2240 2542 3040 1 chr2A.!!$F1 498
6 TraesCS2B01G335600 chr4D 365405249 365405799 550 False 433.0 433 81.9820 2541 3058 1 chr4D.!!$F1 517
7 TraesCS2B01G335600 chr3A 711543378 711543907 529 True 327.0 327 78.9470 2545 3040 1 chr3A.!!$R1 495
8 TraesCS2B01G335600 chr3B 127852454 127853348 894 False 307.0 307 73.5610 1189 2113 1 chr3B.!!$F1 924
9 TraesCS2B01G335600 chr6B 697807788 697808293 505 True 300.0 300 78.6270 2538 3010 1 chr6B.!!$R1 472
10 TraesCS2B01G335600 chr1B 6186401 6186906 505 True 217.0 217 75.6860 2546 3017 1 chr1B.!!$R1 471

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
53 54 0.31179 CTCGTGCATTGCAACAAGGT 59.688 50.000 13.94 0.0 41.47 3.50 F
160 161 1.06406 GACATTGTTGGGTAGCATCGC 59.936 52.381 0.00 0.0 0.00 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1623 5059 0.175760 CGAGGAAAATGCGGGAGAGA 59.824 55.0 0.0 0.0 0.00 3.10 R
2140 5593 0.032952 TCGTTTCCGTTCAGTCCAGG 59.967 55.0 0.0 0.0 35.01 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
33 34 8.884124 TGTCCCTTAACTAAACTAGCTAACTA 57.116 34.615 0.00 0.00 0.00 2.24
53 54 0.311790 CTCGTGCATTGCAACAAGGT 59.688 50.000 13.94 0.00 41.47 3.50
103 104 2.240279 ACGAGTGCCTTAAGAGTGACT 58.760 47.619 3.36 0.00 0.00 3.41
105 106 3.069729 ACGAGTGCCTTAAGAGTGACTTT 59.930 43.478 3.36 0.00 39.72 2.66
108 109 2.226674 GTGCCTTAAGAGTGACTTTGCC 59.773 50.000 3.36 0.00 39.72 4.52
125 126 3.708563 TGCCAGTGCTTTTTGTCTAAC 57.291 42.857 0.00 0.00 38.71 2.34
148 149 1.438651 CGTCCCACATCGACATTGTT 58.561 50.000 0.00 0.00 0.00 2.83
155 156 2.095853 CACATCGACATTGTTGGGTAGC 59.904 50.000 4.20 0.00 0.00 3.58
160 161 1.064060 GACATTGTTGGGTAGCATCGC 59.936 52.381 0.00 0.00 0.00 4.58
262 263 6.978343 TTAAGGTGATTATCGTTTGAGGTG 57.022 37.500 0.00 0.00 0.00 4.00
277 278 4.260139 TGAGGTGTTTAATCGCACTACA 57.740 40.909 0.00 0.00 36.03 2.74
306 307 4.703093 AGTGAAAACCGGAAAAGAGTGAAA 59.297 37.500 9.46 0.00 0.00 2.69
310 311 6.754675 TGAAAACCGGAAAAGAGTGAAATTTC 59.245 34.615 9.46 11.41 33.38 2.17
374 377 6.405278 AGGACAAGGAAATAAAAGTGTTGG 57.595 37.500 0.00 0.00 0.00 3.77
384 387 7.982919 GGAAATAAAAGTGTTGGTTTGGTTAGT 59.017 33.333 0.00 0.00 0.00 2.24
433 436 9.836076 CATTAGTTTTTACTAGTAAACTTGCCC 57.164 33.333 24.39 10.76 40.64 5.36
456 3096 4.060205 GTGCATTGCAACTGGAGAAAAAT 58.940 39.130 13.94 0.00 41.47 1.82
566 3207 7.011016 GGTGTTTATTCAAGGTGTTTTCCAAAG 59.989 37.037 0.00 0.00 0.00 2.77
568 3209 8.314751 TGTTTATTCAAGGTGTTTTCCAAAGAA 58.685 29.630 0.00 0.00 0.00 2.52
610 3251 7.561021 TGCGCAAAAACATAAAGATAGGATA 57.439 32.000 8.16 0.00 0.00 2.59
612 3253 8.462811 TGCGCAAAAACATAAAGATAGGATAAA 58.537 29.630 8.16 0.00 0.00 1.40
642 3283 4.145052 ACTGAAGGTGTTTCCAGAAATCC 58.855 43.478 0.00 3.26 39.02 3.01
746 3387 8.435430 GTGTACATCATCGTATATGATTGGTTG 58.565 37.037 4.61 3.91 36.69 3.77
756 3397 8.145122 TCGTATATGATTGGTTGTTATGCACTA 58.855 33.333 0.00 0.00 0.00 2.74
783 3424 8.029522 TGCGAAATAGAGAGGATGATTATGTAC 58.970 37.037 0.00 0.00 0.00 2.90
831 3472 1.850345 TGGTAGGAATCAACATCCCCC 59.150 52.381 0.00 0.00 37.71 5.40
867 3508 6.690194 ATTTGTGAGAGCATCAAACTATCC 57.310 37.500 0.00 0.00 40.43 2.59
1059 4495 1.834856 CTCTGCTCTGCCACTCCCAA 61.835 60.000 0.00 0.00 0.00 4.12
1171 4607 1.615392 GGCTGACAATGGCAAAGAACT 59.385 47.619 0.00 0.00 0.00 3.01
1362 4798 2.044555 CGTGCGTCTCTACCTCCCA 61.045 63.158 0.00 0.00 0.00 4.37
1440 4876 2.356780 GGGGTTCGTGATCGGGTCT 61.357 63.158 0.00 0.00 37.69 3.85
1591 5027 1.483595 CCTCAAGTGGGTGCTCTCCA 61.484 60.000 0.00 0.00 0.00 3.86
1680 5116 1.870055 GCAACATCTGCCACCACCTG 61.870 60.000 0.00 0.00 46.13 4.00
1703 5139 1.480212 ATGCACCACGACTTGAGGGA 61.480 55.000 0.00 0.00 31.66 4.20
1962 5415 1.582610 GGGATTTCTTGCGTTGGCGA 61.583 55.000 0.00 0.00 44.10 5.54
2060 5513 0.949105 GGGCACGTGTTCTACCTGTG 60.949 60.000 18.38 0.00 0.00 3.66
2061 5514 0.949105 GGCACGTGTTCTACCTGTGG 60.949 60.000 18.38 0.00 0.00 4.17
2172 5640 1.465856 GGAAACGATGAAAGAAGGCGC 60.466 52.381 0.00 0.00 0.00 6.53
2174 5642 1.234821 AACGATGAAAGAAGGCGCAA 58.765 45.000 10.83 0.00 0.00 4.85
2175 5643 0.798776 ACGATGAAAGAAGGCGCAAG 59.201 50.000 10.83 0.00 43.44 4.01
2221 5690 6.537301 AGACGTTTCAAGTGTGTATTTTCTGA 59.463 34.615 0.00 0.00 0.00 3.27
2222 5691 6.715464 ACGTTTCAAGTGTGTATTTTCTGAG 58.285 36.000 0.00 0.00 0.00 3.35
2225 5694 5.560722 TCAAGTGTGTATTTTCTGAGGGA 57.439 39.130 0.00 0.00 0.00 4.20
2226 5695 5.935945 TCAAGTGTGTATTTTCTGAGGGAA 58.064 37.500 0.00 0.00 0.00 3.97
2267 5747 3.924610 GAAACGGACGCATGTTTCTATC 58.075 45.455 15.59 0.00 46.49 2.08
2270 5750 2.128035 CGGACGCATGTTTCTATCCTC 58.872 52.381 0.00 0.00 0.00 3.71
2291 5771 1.372087 GAGCTCAAATGTGCTCGGGG 61.372 60.000 18.29 0.00 46.94 5.73
2306 5786 3.007635 CTCGGGGTGAACAGTAAAATCC 58.992 50.000 0.00 0.00 0.00 3.01
2311 5791 4.320714 GGGGTGAACAGTAAAATCCGTTTC 60.321 45.833 0.00 0.00 0.00 2.78
2315 5795 6.017357 GGTGAACAGTAAAATCCGTTTCTTCT 60.017 38.462 0.00 0.00 0.00 2.85
2373 5860 9.332301 CAAATATTGACAAATGTTTTCAATGCC 57.668 29.630 10.98 0.00 39.68 4.40
2376 5863 3.808726 TGACAAATGTTTTCAATGCCTGC 59.191 39.130 0.00 0.00 0.00 4.85
2380 5867 5.209240 CAAATGTTTTCAATGCCTGCAAAG 58.791 37.500 0.00 0.00 0.00 2.77
2384 5871 4.699257 TGTTTTCAATGCCTGCAAAGTTTT 59.301 33.333 0.00 0.00 0.00 2.43
2388 5875 5.465532 TCAATGCCTGCAAAGTTTTATCA 57.534 34.783 0.00 0.00 0.00 2.15
2395 5882 7.609960 TGCCTGCAAAGTTTTATCATGAATTA 58.390 30.769 0.00 0.00 0.00 1.40
2396 5883 8.259411 TGCCTGCAAAGTTTTATCATGAATTAT 58.741 29.630 0.00 0.00 0.00 1.28
2397 5884 9.101655 GCCTGCAAAGTTTTATCATGAATTATT 57.898 29.630 0.00 0.00 0.00 1.40
2424 5934 5.680594 TGCTCCCAAAATGCTGAAAATAT 57.319 34.783 0.00 0.00 0.00 1.28
2437 5947 7.621832 TGCTGAAAATATTTGTCAAAGTTCG 57.378 32.000 0.39 3.90 0.00 3.95
2453 5966 7.321509 GTCAAAGTTCGCTAAAAATCTCAGAAC 59.678 37.037 0.00 0.00 37.39 3.01
2459 5972 9.659830 GTTCGCTAAAAATCTCAGAACTTTTTA 57.340 29.630 6.01 6.01 34.76 1.52
2509 6029 4.507710 TCATGAGCTCAAATAAACTCGCT 58.492 39.130 22.50 0.00 31.64 4.93
2512 6032 3.865745 TGAGCTCAAATAAACTCGCTAGC 59.134 43.478 15.67 4.06 31.64 3.42
2533 6053 4.125703 GCAGAAGATGACTTTCGGATGAT 58.874 43.478 0.00 0.00 36.39 2.45
2538 6058 7.818446 CAGAAGATGACTTTCGGATGATGATAT 59.182 37.037 0.00 0.00 36.39 1.63
2539 6059 8.373981 AGAAGATGACTTTCGGATGATGATATT 58.626 33.333 0.00 0.00 36.39 1.28
2540 6060 9.645059 GAAGATGACTTTCGGATGATGATATTA 57.355 33.333 0.00 0.00 36.39 0.98
2617 6138 8.752187 ACAATCATTCATTACAAAACTAGCCAT 58.248 29.630 0.00 0.00 0.00 4.40
2647 6169 5.141568 CGGAACACTTTACATAAAACACCG 58.858 41.667 0.00 0.00 0.00 4.94
2671 6193 4.580995 TCGGACCTGCTATCAAAACAAAAA 59.419 37.500 0.00 0.00 0.00 1.94
2685 6210 8.586570 TCAAAACAAAAATTAATCTCATGCGT 57.413 26.923 0.00 0.00 0.00 5.24
2688 6213 8.761575 AAACAAAAATTAATCTCATGCGTCAT 57.238 26.923 0.00 0.00 0.00 3.06
2698 6223 3.829026 TCTCATGCGTCATCCTATTAGCT 59.171 43.478 0.00 0.00 0.00 3.32
2705 6230 3.243873 CGTCATCCTATTAGCTTGCCTGA 60.244 47.826 0.00 0.00 0.00 3.86
2728 6253 8.400184 TGACAATCTTCACAATCTTGAAATCT 57.600 30.769 0.00 0.00 35.07 2.40
2795 6328 4.487948 ACATGTCAATGGATTCTTTTGCG 58.512 39.130 0.00 0.00 38.19 4.85
2797 6330 2.295629 TGTCAATGGATTCTTTTGCGCA 59.704 40.909 5.66 5.66 0.00 6.09
2806 6364 1.821336 TCTTTTGCGCACAGTTTTCG 58.179 45.000 11.12 0.00 0.00 3.46
2821 6379 5.147162 CAGTTTTCGAAATAACTGGTCTGC 58.853 41.667 25.22 3.35 44.65 4.26
2904 6462 2.505819 AGTGCAGGACCGGATAAAATCT 59.494 45.455 9.46 0.00 0.00 2.40
2918 6476 7.698130 CCGGATAAAATCTCATGAAGAAAACAC 59.302 37.037 0.00 0.00 37.61 3.32
2923 6481 5.852738 ATCTCATGAAGAAAACACGACTG 57.147 39.130 0.00 0.00 37.61 3.51
2928 6486 1.092921 AAGAAAACACGACTGCGCCA 61.093 50.000 4.18 0.00 42.48 5.69
2954 6512 3.074390 TGATTCCTGGCAATAATCCCGAT 59.926 43.478 15.17 0.00 0.00 4.18
3045 6603 3.282021 CTCCCAATCATGACGACCATTT 58.718 45.455 0.00 0.00 31.94 2.32
3052 6610 1.735018 CATGACGACCATTTGCGGTTA 59.265 47.619 0.00 0.00 40.22 2.85
3054 6612 1.001068 TGACGACCATTTGCGGTTAGA 59.999 47.619 0.00 0.00 40.22 2.10
3055 6613 2.277084 GACGACCATTTGCGGTTAGAT 58.723 47.619 0.00 0.00 40.22 1.98
3056 6614 3.119065 TGACGACCATTTGCGGTTAGATA 60.119 43.478 0.00 0.00 40.22 1.98
3058 6616 4.448210 ACGACCATTTGCGGTTAGATAAT 58.552 39.130 0.00 0.00 40.22 1.28
3059 6617 4.879545 ACGACCATTTGCGGTTAGATAATT 59.120 37.500 0.00 0.00 40.22 1.40
3060 6618 5.204833 CGACCATTTGCGGTTAGATAATTG 58.795 41.667 0.00 0.00 40.22 2.32
3061 6619 5.514274 ACCATTTGCGGTTAGATAATTGG 57.486 39.130 0.00 0.00 34.91 3.16
3062 6620 5.197451 ACCATTTGCGGTTAGATAATTGGA 58.803 37.500 0.00 0.00 34.91 3.53
3063 6621 5.299279 ACCATTTGCGGTTAGATAATTGGAG 59.701 40.000 0.00 0.00 34.91 3.86
3064 6622 5.278463 CCATTTGCGGTTAGATAATTGGAGG 60.278 44.000 0.00 0.00 0.00 4.30
3065 6623 4.764050 TTGCGGTTAGATAATTGGAGGA 57.236 40.909 0.00 0.00 0.00 3.71
3066 6624 4.974645 TGCGGTTAGATAATTGGAGGAT 57.025 40.909 0.00 0.00 0.00 3.24
3067 6625 4.641396 TGCGGTTAGATAATTGGAGGATG 58.359 43.478 0.00 0.00 0.00 3.51
3068 6626 4.346709 TGCGGTTAGATAATTGGAGGATGA 59.653 41.667 0.00 0.00 0.00 2.92
3069 6627 5.163248 TGCGGTTAGATAATTGGAGGATGAA 60.163 40.000 0.00 0.00 0.00 2.57
3070 6628 5.409826 GCGGTTAGATAATTGGAGGATGAAG 59.590 44.000 0.00 0.00 0.00 3.02
3071 6629 6.741521 GCGGTTAGATAATTGGAGGATGAAGA 60.742 42.308 0.00 0.00 0.00 2.87
3072 6630 7.390027 CGGTTAGATAATTGGAGGATGAAGAT 58.610 38.462 0.00 0.00 0.00 2.40
3073 6631 8.531982 CGGTTAGATAATTGGAGGATGAAGATA 58.468 37.037 0.00 0.00 0.00 1.98
3074 6632 9.660180 GGTTAGATAATTGGAGGATGAAGATAC 57.340 37.037 0.00 0.00 0.00 2.24
3085 6643 8.673711 TGGAGGATGAAGATACATTTTAAAACG 58.326 33.333 1.97 0.00 0.00 3.60
3086 6644 8.674607 GGAGGATGAAGATACATTTTAAAACGT 58.325 33.333 4.90 4.90 0.00 3.99
3088 6646 9.840427 AGGATGAAGATACATTTTAAAACGTTG 57.160 29.630 4.83 1.93 0.00 4.10
3089 6647 8.583765 GGATGAAGATACATTTTAAAACGTTGC 58.416 33.333 4.83 0.00 0.00 4.17
3090 6648 7.541743 TGAAGATACATTTTAAAACGTTGCG 57.458 32.000 4.83 0.00 0.00 4.85
3091 6649 7.133513 TGAAGATACATTTTAAAACGTTGCGT 58.866 30.769 4.83 0.00 43.97 5.24
3100 6658 3.552384 ACGTTGCGTTCCTGGGGA 61.552 61.111 0.00 0.00 36.35 4.81
3101 6659 2.742372 CGTTGCGTTCCTGGGGAG 60.742 66.667 0.00 0.00 31.21 4.30
3102 6660 2.359975 GTTGCGTTCCTGGGGAGG 60.360 66.667 0.00 0.00 31.21 4.30
3103 6661 2.852075 TTGCGTTCCTGGGGAGGT 60.852 61.111 0.00 0.00 31.21 3.85
3104 6662 1.536907 TTGCGTTCCTGGGGAGGTA 60.537 57.895 0.00 0.00 31.21 3.08
3105 6663 1.550130 TTGCGTTCCTGGGGAGGTAG 61.550 60.000 0.00 0.00 31.21 3.18
3106 6664 1.988406 GCGTTCCTGGGGAGGTAGT 60.988 63.158 0.00 0.00 31.21 2.73
3107 6665 1.898154 CGTTCCTGGGGAGGTAGTG 59.102 63.158 0.00 0.00 31.21 2.74
3108 6666 0.903454 CGTTCCTGGGGAGGTAGTGT 60.903 60.000 0.00 0.00 31.21 3.55
3109 6667 1.359168 GTTCCTGGGGAGGTAGTGTT 58.641 55.000 0.00 0.00 31.21 3.32
3110 6668 1.278413 GTTCCTGGGGAGGTAGTGTTC 59.722 57.143 0.00 0.00 31.21 3.18
3111 6669 0.490017 TCCTGGGGAGGTAGTGTTCA 59.510 55.000 0.00 0.00 0.00 3.18
3112 6670 0.905357 CCTGGGGAGGTAGTGTTCAG 59.095 60.000 0.00 0.00 0.00 3.02
3113 6671 1.645710 CTGGGGAGGTAGTGTTCAGT 58.354 55.000 0.00 0.00 0.00 3.41
3114 6672 1.276421 CTGGGGAGGTAGTGTTCAGTG 59.724 57.143 0.00 0.00 0.00 3.66
3115 6673 0.036294 GGGGAGGTAGTGTTCAGTGC 60.036 60.000 0.00 0.00 0.00 4.40
3116 6674 0.977395 GGGAGGTAGTGTTCAGTGCT 59.023 55.000 0.00 0.00 0.00 4.40
3117 6675 1.338200 GGGAGGTAGTGTTCAGTGCTG 60.338 57.143 0.00 0.00 0.00 4.41
3118 6676 1.433534 GAGGTAGTGTTCAGTGCTGC 58.566 55.000 0.00 0.00 0.00 5.25
3119 6677 0.758734 AGGTAGTGTTCAGTGCTGCA 59.241 50.000 0.00 0.00 0.00 4.41
3120 6678 1.349026 AGGTAGTGTTCAGTGCTGCAT 59.651 47.619 5.27 0.00 0.00 3.96
3121 6679 2.154462 GGTAGTGTTCAGTGCTGCATT 58.846 47.619 5.27 0.00 0.00 3.56
3122 6680 2.095567 GGTAGTGTTCAGTGCTGCATTG 60.096 50.000 17.87 17.87 0.00 2.82
3123 6681 0.313043 AGTGTTCAGTGCTGCATTGC 59.687 50.000 18.97 7.86 0.00 3.56
3124 6682 0.665369 GTGTTCAGTGCTGCATTGCC 60.665 55.000 18.97 12.52 0.00 4.52
3125 6683 1.443194 GTTCAGTGCTGCATTGCCG 60.443 57.895 18.97 0.16 0.00 5.69
3126 6684 3.271706 TTCAGTGCTGCATTGCCGC 62.272 57.895 18.97 16.99 39.16 6.53
3127 6685 4.789075 CAGTGCTGCATTGCCGCC 62.789 66.667 20.27 12.46 37.97 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 8.965819 AGTAGTTAGCTAGTTTAGTTAAGGGAC 58.034 37.037 0.00 0.00 33.13 4.46
15 16 7.119699 TGCACGAGTAGTTAGCTAGTTTAGTTA 59.880 37.037 0.00 0.00 31.38 2.24
33 34 0.311790 CCTTGTTGCAATGCACGAGT 59.688 50.000 7.72 0.00 38.71 4.18
103 104 4.429108 GTTAGACAAAAAGCACTGGCAAA 58.571 39.130 0.00 0.00 44.61 3.68
105 106 2.032799 CGTTAGACAAAAAGCACTGGCA 59.967 45.455 0.00 0.00 44.61 4.92
108 109 2.604614 GGGCGTTAGACAAAAAGCACTG 60.605 50.000 0.00 0.00 34.85 3.66
148 149 3.365291 GACCACGCGATGCTACCCA 62.365 63.158 15.93 0.00 0.00 4.51
155 156 2.803670 ACGTTCGACCACGCGATG 60.804 61.111 15.93 7.49 44.37 3.84
160 161 2.251869 TATCTTCACGTTCGACCACG 57.748 50.000 8.05 8.05 46.04 4.94
253 254 4.483476 AGTGCGATTAAACACCTCAAAC 57.517 40.909 0.00 0.00 37.51 2.93
262 263 7.932643 CACTAAATGTGTAGTGCGATTAAAC 57.067 36.000 0.00 0.00 43.27 2.01
277 278 6.320418 ACTCTTTTCCGGTTTTCACTAAATGT 59.680 34.615 0.00 0.00 0.00 2.71
306 307 9.974980 AAAAACAACATTCATTACTACGGAAAT 57.025 25.926 0.00 0.00 0.00 2.17
417 420 2.963432 GCACGGGCAAGTTTACTAGTA 58.037 47.619 3.77 0.00 40.72 1.82
432 435 1.210931 CTCCAGTTGCAATGCACGG 59.789 57.895 7.72 9.36 38.71 4.94
433 436 0.592637 TTCTCCAGTTGCAATGCACG 59.407 50.000 7.72 0.00 38.71 5.34
456 3096 2.301870 GAGTGTGTGTATGAGGGTGGAA 59.698 50.000 0.00 0.00 0.00 3.53
566 3207 6.912051 TGCGCAATATCACTTATCATGTTTTC 59.088 34.615 8.16 0.00 0.00 2.29
568 3209 6.375945 TGCGCAATATCACTTATCATGTTT 57.624 33.333 8.16 0.00 0.00 2.83
610 3251 5.531287 GGAAACACCTTCAGTACACTCATTT 59.469 40.000 0.00 0.00 35.55 2.32
612 3253 4.102524 TGGAAACACCTTCAGTACACTCAT 59.897 41.667 0.00 0.00 39.86 2.90
623 3264 6.127619 CCATAAGGATTTCTGGAAACACCTTC 60.128 42.308 24.67 10.36 43.03 3.46
642 3283 9.225201 CATATTGTTTGAAATCGTGTCCATAAG 57.775 33.333 0.00 0.00 0.00 1.73
684 3325 9.208022 TGATATGAGCTATATGTAAACAAGTGC 57.792 33.333 0.00 0.00 32.09 4.40
718 3359 9.020731 ACCAATCATATACGATGATGTACACTA 57.979 33.333 0.00 0.00 38.62 2.74
746 3387 6.090088 CCTCTCTATTTCGCATAGTGCATAAC 59.910 42.308 2.63 0.00 45.36 1.89
756 3397 7.619050 ACATAATCATCCTCTCTATTTCGCAT 58.381 34.615 0.00 0.00 0.00 4.73
787 3428 8.531982 CCAGCTACCATATGCTAAAGATTACTA 58.468 37.037 0.00 0.00 37.81 1.82
789 3430 7.162082 ACCAGCTACCATATGCTAAAGATTAC 58.838 38.462 0.00 0.00 37.81 1.89
889 3530 5.830991 GGCTTGTTATATATGTTTCCCACCA 59.169 40.000 0.00 0.00 0.00 4.17
908 3549 4.824479 ATGGGTATTTTGGAAAGGCTTG 57.176 40.909 0.00 0.00 0.00 4.01
910 3551 8.065007 TCTTTATATGGGTATTTTGGAAAGGCT 58.935 33.333 0.00 0.00 0.00 4.58
946 3588 6.557253 TGGTAGGAGTGGCTTGTTATATATGT 59.443 38.462 0.00 0.00 0.00 2.29
958 3689 2.292918 TGGTAGATTGGTAGGAGTGGCT 60.293 50.000 0.00 0.00 0.00 4.75
960 3691 2.434702 GGTGGTAGATTGGTAGGAGTGG 59.565 54.545 0.00 0.00 0.00 4.00
961 3692 2.434702 GGGTGGTAGATTGGTAGGAGTG 59.565 54.545 0.00 0.00 0.00 3.51
1059 4495 1.264020 CCGTATTTGTAGCGCATGCAT 59.736 47.619 19.57 8.14 46.23 3.96
1153 4589 2.886523 TGGAGTTCTTTGCCATTGTCAG 59.113 45.455 0.00 0.00 0.00 3.51
1154 4590 2.622942 GTGGAGTTCTTTGCCATTGTCA 59.377 45.455 0.00 0.00 33.66 3.58
1389 4825 2.603776 ACGAGGACGGGGAGCTTT 60.604 61.111 0.00 0.00 44.46 3.51
1623 5059 0.175760 CGAGGAAAATGCGGGAGAGA 59.824 55.000 0.00 0.00 0.00 3.10
1680 5116 2.672996 AAGTCGTGGTGCATGGCC 60.673 61.111 0.00 0.00 0.00 5.36
1722 5158 1.690219 GGTGGATCAGGACGATGCCT 61.690 60.000 0.00 0.00 41.59 4.75
1854 5307 1.400530 GGTTCATCCGGGGATCGTCT 61.401 60.000 0.00 0.00 37.11 4.18
1947 5400 2.903547 GCCTCGCCAACGCAAGAAA 61.904 57.895 0.00 0.00 43.62 2.52
2043 5496 0.949105 CCCACAGGTAGAACACGTGC 60.949 60.000 17.22 0.00 45.05 5.34
2060 5513 3.254024 TTCTCCGTTGCAGGCTCCC 62.254 63.158 0.00 0.00 0.00 4.30
2061 5514 1.743252 CTTCTCCGTTGCAGGCTCC 60.743 63.158 0.00 0.00 0.00 4.70
2140 5593 0.032952 TCGTTTCCGTTCAGTCCAGG 59.967 55.000 0.00 0.00 35.01 4.45
2142 5595 1.341852 TCATCGTTTCCGTTCAGTCCA 59.658 47.619 0.00 0.00 35.01 4.02
2144 5597 3.739300 TCTTTCATCGTTTCCGTTCAGTC 59.261 43.478 0.00 0.00 35.01 3.51
2145 5598 3.724374 TCTTTCATCGTTTCCGTTCAGT 58.276 40.909 0.00 0.00 35.01 3.41
2170 5638 5.443763 GTCGTCGTTTATTTTGATACTTGCG 59.556 40.000 0.00 0.00 0.00 4.85
2172 5640 9.069078 TCTAGTCGTCGTTTATTTTGATACTTG 57.931 33.333 0.00 0.00 0.00 3.16
2174 5642 7.427606 CGTCTAGTCGTCGTTTATTTTGATACT 59.572 37.037 0.93 0.00 0.00 2.12
2175 5643 7.217070 ACGTCTAGTCGTCGTTTATTTTGATAC 59.783 37.037 9.27 0.00 40.04 2.24
2221 5690 6.400096 AATCTTCATCCTCTTTTCTTCCCT 57.600 37.500 0.00 0.00 0.00 4.20
2222 5691 6.660949 TCAAATCTTCATCCTCTTTTCTTCCC 59.339 38.462 0.00 0.00 0.00 3.97
2225 5694 8.078596 CGTTTCAAATCTTCATCCTCTTTTCTT 58.921 33.333 0.00 0.00 0.00 2.52
2226 5695 7.308830 CCGTTTCAAATCTTCATCCTCTTTTCT 60.309 37.037 0.00 0.00 0.00 2.52
2266 5746 1.627329 AGCACATTTGAGCTCTGAGGA 59.373 47.619 16.19 0.00 37.40 3.71
2267 5747 2.110901 AGCACATTTGAGCTCTGAGG 57.889 50.000 16.19 7.61 37.40 3.86
2291 5771 6.956047 AGAAGAAACGGATTTTACTGTTCAC 58.044 36.000 0.00 0.00 38.25 3.18
2342 5822 8.886719 TGAAAACATTTGTCAATATTTGCAACA 58.113 25.926 0.00 0.00 23.46 3.33
2343 5823 9.713740 TTGAAAACATTTGTCAATATTTGCAAC 57.286 25.926 0.00 0.00 31.76 4.17
2346 5826 8.842777 GCATTGAAAACATTTGTCAATATTTGC 58.157 29.630 4.37 2.75 39.40 3.68
2347 5827 9.332301 GGCATTGAAAACATTTGTCAATATTTG 57.668 29.630 4.37 0.00 39.40 2.32
2348 5828 9.287373 AGGCATTGAAAACATTTGTCAATATTT 57.713 25.926 4.37 0.00 39.40 1.40
2349 5829 8.723311 CAGGCATTGAAAACATTTGTCAATATT 58.277 29.630 4.37 0.00 39.40 1.28
2370 5857 5.465532 TTCATGATAAAACTTTGCAGGCA 57.534 34.783 0.00 0.00 0.00 4.75
2398 5885 3.834489 TCAGCATTTTGGGAGCAAAAA 57.166 38.095 0.00 0.00 37.55 1.94
2401 5888 3.834489 TTTTCAGCATTTTGGGAGCAA 57.166 38.095 0.00 0.00 0.00 3.91
2402 5889 5.680594 ATATTTTCAGCATTTTGGGAGCA 57.319 34.783 0.00 0.00 0.00 4.26
2403 5890 6.372381 ACAAATATTTTCAGCATTTTGGGAGC 59.628 34.615 0.00 0.00 0.00 4.70
2404 5891 7.603404 TGACAAATATTTTCAGCATTTTGGGAG 59.397 33.333 0.00 0.00 0.00 4.30
2405 5892 7.448420 TGACAAATATTTTCAGCATTTTGGGA 58.552 30.769 0.00 0.00 0.00 4.37
2406 5893 7.670009 TGACAAATATTTTCAGCATTTTGGG 57.330 32.000 0.00 0.00 0.00 4.12
2424 5934 7.476667 TGAGATTTTTAGCGAACTTTGACAAA 58.523 30.769 0.00 0.00 0.00 2.83
2482 6002 6.904011 CGAGTTTATTTGAGCTCATGATGAAC 59.096 38.462 25.08 25.08 0.00 3.18
2490 6010 3.865745 GCTAGCGAGTTTATTTGAGCTCA 59.134 43.478 13.74 13.74 36.30 4.26
2491 6011 3.865745 TGCTAGCGAGTTTATTTGAGCTC 59.134 43.478 10.77 6.82 36.30 4.09
2509 6029 4.402474 TCATCCGAAAGTCATCTTCTGCTA 59.598 41.667 0.00 0.00 32.90 3.49
2512 6032 5.354767 TCATCATCCGAAAGTCATCTTCTG 58.645 41.667 0.00 0.00 32.90 3.02
2617 6138 0.887387 GTAAAGTGTTCCGCCCTGCA 60.887 55.000 0.00 0.00 0.00 4.41
2647 6169 2.695359 TGTTTTGATAGCAGGTCCGAC 58.305 47.619 0.00 0.00 0.00 4.79
2671 6193 7.493971 GCTAATAGGATGACGCATGAGATTAAT 59.506 37.037 2.50 0.00 0.00 1.40
2685 6210 3.711190 TGTCAGGCAAGCTAATAGGATGA 59.289 43.478 0.00 0.00 0.00 2.92
2688 6213 4.708177 GATTGTCAGGCAAGCTAATAGGA 58.292 43.478 0.00 0.00 40.11 2.94
2698 6223 4.401022 AGATTGTGAAGATTGTCAGGCAA 58.599 39.130 0.00 0.00 41.89 4.52
2728 6253 6.732896 AGGAGTGTCTCAAAACTCTCTAAA 57.267 37.500 3.11 0.00 42.07 1.85
2732 6257 6.316390 TGAAAAAGGAGTGTCTCAAAACTCTC 59.684 38.462 3.11 0.00 42.07 3.20
2733 6258 6.180472 TGAAAAAGGAGTGTCTCAAAACTCT 58.820 36.000 3.11 0.00 42.07 3.24
2806 6364 4.246458 ACTCTTCGCAGACCAGTTATTTC 58.754 43.478 0.00 0.00 34.32 2.17
2818 6376 8.700644 GTTATACATTGGTATTACTCTTCGCAG 58.299 37.037 0.00 0.00 40.61 5.18
2821 6379 9.193133 CAGGTTATACATTGGTATTACTCTTCG 57.807 37.037 0.00 0.00 40.61 3.79
2856 6414 6.260050 GTGTGGATGAAGTGAAAGTTCTTACA 59.740 38.462 0.00 0.00 46.43 2.41
2858 6416 6.353323 TGTGTGGATGAAGTGAAAGTTCTTA 58.647 36.000 0.00 0.00 46.43 2.10
2860 6418 4.780815 TGTGTGGATGAAGTGAAAGTTCT 58.219 39.130 0.00 0.00 46.43 3.01
2864 6422 4.790766 GCACTTGTGTGGATGAAGTGAAAG 60.791 45.833 13.82 0.00 46.31 2.62
2869 6427 2.224606 CTGCACTTGTGTGGATGAAGT 58.775 47.619 2.61 0.00 43.39 3.01
2904 6462 2.220824 CGCAGTCGTGTTTTCTTCATGA 59.779 45.455 0.00 0.00 0.00 3.07
2918 6476 1.970917 GAATCACCTTGGCGCAGTCG 61.971 60.000 10.83 0.00 39.07 4.18
3017 6575 2.093500 CGTCATGATTGGGAGGTTCAGA 60.093 50.000 0.00 0.00 0.00 3.27
3019 6577 1.905894 TCGTCATGATTGGGAGGTTCA 59.094 47.619 0.00 0.00 0.00 3.18
3021 6579 1.065418 GGTCGTCATGATTGGGAGGTT 60.065 52.381 0.00 0.00 0.00 3.50
3022 6580 0.541863 GGTCGTCATGATTGGGAGGT 59.458 55.000 0.00 0.00 0.00 3.85
3023 6581 0.541392 TGGTCGTCATGATTGGGAGG 59.459 55.000 0.00 0.00 0.00 4.30
3045 6603 4.346709 TCATCCTCCAATTATCTAACCGCA 59.653 41.667 0.00 0.00 0.00 5.69
3059 6617 8.673711 CGTTTTAAAATGTATCTTCATCCTCCA 58.326 33.333 11.34 0.00 0.00 3.86
3060 6618 8.674607 ACGTTTTAAAATGTATCTTCATCCTCC 58.325 33.333 21.47 0.00 36.43 4.30
3062 6620 9.840427 CAACGTTTTAAAATGTATCTTCATCCT 57.160 29.630 22.72 4.09 37.16 3.24
3063 6621 8.583765 GCAACGTTTTAAAATGTATCTTCATCC 58.416 33.333 22.72 0.00 37.16 3.51
3064 6622 8.304138 CGCAACGTTTTAAAATGTATCTTCATC 58.696 33.333 22.72 7.97 37.16 2.92
3065 6623 7.806014 ACGCAACGTTTTAAAATGTATCTTCAT 59.194 29.630 22.72 6.01 36.35 2.57
3066 6624 7.133513 ACGCAACGTTTTAAAATGTATCTTCA 58.866 30.769 22.72 0.00 36.35 3.02
3067 6625 7.543127 ACGCAACGTTTTAAAATGTATCTTC 57.457 32.000 22.72 11.18 36.35 2.87
3083 6641 3.530910 CTCCCCAGGAACGCAACGT 62.531 63.158 0.00 0.00 43.97 3.99
3084 6642 2.742372 CTCCCCAGGAACGCAACG 60.742 66.667 0.00 0.00 0.00 4.10
3085 6643 1.833787 TACCTCCCCAGGAACGCAAC 61.834 60.000 0.00 0.00 43.65 4.17
3086 6644 1.536907 TACCTCCCCAGGAACGCAA 60.537 57.895 0.00 0.00 43.65 4.85
3087 6645 1.987855 CTACCTCCCCAGGAACGCA 60.988 63.158 0.00 0.00 43.65 5.24
3088 6646 1.988406 ACTACCTCCCCAGGAACGC 60.988 63.158 0.00 0.00 43.65 4.84
3089 6647 0.903454 ACACTACCTCCCCAGGAACG 60.903 60.000 0.00 0.00 43.65 3.95
3090 6648 1.278413 GAACACTACCTCCCCAGGAAC 59.722 57.143 0.00 0.00 43.65 3.62
3091 6649 1.132657 TGAACACTACCTCCCCAGGAA 60.133 52.381 0.00 0.00 43.65 3.36
3092 6650 0.490017 TGAACACTACCTCCCCAGGA 59.510 55.000 0.00 0.00 43.65 3.86
3093 6651 0.905357 CTGAACACTACCTCCCCAGG 59.095 60.000 0.00 0.00 46.87 4.45
3094 6652 1.276421 CACTGAACACTACCTCCCCAG 59.724 57.143 0.00 0.00 0.00 4.45
3095 6653 1.348064 CACTGAACACTACCTCCCCA 58.652 55.000 0.00 0.00 0.00 4.96
3096 6654 0.036294 GCACTGAACACTACCTCCCC 60.036 60.000 0.00 0.00 0.00 4.81
3097 6655 0.977395 AGCACTGAACACTACCTCCC 59.023 55.000 0.00 0.00 0.00 4.30
3098 6656 1.941668 GCAGCACTGAACACTACCTCC 60.942 57.143 0.81 0.00 0.00 4.30
3099 6657 1.270305 TGCAGCACTGAACACTACCTC 60.270 52.381 0.81 0.00 0.00 3.85
3100 6658 0.758734 TGCAGCACTGAACACTACCT 59.241 50.000 0.81 0.00 0.00 3.08
3101 6659 1.813513 ATGCAGCACTGAACACTACC 58.186 50.000 0.00 0.00 0.00 3.18
3102 6660 2.666619 GCAATGCAGCACTGAACACTAC 60.667 50.000 8.35 0.00 0.00 2.73
3103 6661 1.536766 GCAATGCAGCACTGAACACTA 59.463 47.619 8.35 0.00 0.00 2.74
3104 6662 0.313043 GCAATGCAGCACTGAACACT 59.687 50.000 8.35 0.00 0.00 3.55
3105 6663 0.665369 GGCAATGCAGCACTGAACAC 60.665 55.000 8.35 0.00 35.83 3.32
3106 6664 1.661480 GGCAATGCAGCACTGAACA 59.339 52.632 8.35 0.00 35.83 3.18
3107 6665 1.443194 CGGCAATGCAGCACTGAAC 60.443 57.895 8.35 0.00 35.83 3.18
3108 6666 2.956194 CGGCAATGCAGCACTGAA 59.044 55.556 8.35 0.00 35.83 3.02


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

AutoCloner maintained by Alex Coulton.