Multiple sequence alignment - TraesCS3D01G273300

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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 TraesCS3D01G273300 chr3D 100.000 2650 0 0 1 2650 378933474 378930825 0.000000e+00 4894.0
1 TraesCS3D01G273300 chr3D 100.000 2301 0 0 2993 5293 378930482 378928182 0.000000e+00 4250.0
2 TraesCS3D01G273300 chr3D 97.872 564 12 0 2993 3556 405310873 405310310 0.000000e+00 976.0
3 TraesCS3D01G273300 chr3D 79.890 363 41 27 109 446 301762351 301761996 2.460000e-58 237.0
4 TraesCS3D01G273300 chr3D 79.618 314 52 11 142 446 313296502 313296812 1.150000e-51 215.0
5 TraesCS3D01G273300 chr3A 90.476 1953 107 32 1 1905 502844041 502842120 0.000000e+00 2503.0
6 TraesCS3D01G273300 chr3A 94.466 759 28 3 3550 4305 502842128 502841381 0.000000e+00 1157.0
7 TraesCS3D01G273300 chr3A 89.262 894 80 11 4394 5278 502841196 502840310 0.000000e+00 1105.0
8 TraesCS3D01G273300 chr3A 90.286 350 30 3 98 446 502910200 502909854 6.250000e-124 455.0
9 TraesCS3D01G273300 chr3A 82.906 117 19 1 495 610 88204315 88204199 2.610000e-18 104.0
10 TraesCS3D01G273300 chr1D 99.733 749 1 1 1903 2650 391737650 391736902 0.000000e+00 1371.0
11 TraesCS3D01G273300 chr1D 99.118 567 4 1 2993 3559 391736775 391736210 0.000000e+00 1018.0
12 TraesCS3D01G273300 chr1D 97.683 561 13 0 2993 3553 62937810 62937250 0.000000e+00 965.0
13 TraesCS3D01G273300 chr7D 97.864 749 13 3 1903 2650 266018215 266018961 0.000000e+00 1291.0
14 TraesCS3D01G273300 chr7D 96.950 754 18 5 1899 2650 615763976 615764726 0.000000e+00 1260.0
15 TraesCS3D01G273300 chr7D 98.205 557 10 0 2993 3549 266019090 266019646 0.000000e+00 974.0
16 TraesCS3D01G273300 chr3B 91.237 970 37 20 3558 4511 494076624 494075687 0.000000e+00 1277.0
17 TraesCS3D01G273300 chr3B 87.645 777 77 11 4507 5278 494075586 494074824 0.000000e+00 885.0
18 TraesCS3D01G273300 chr3B 86.253 742 54 22 487 1208 494078061 494077348 0.000000e+00 761.0
19 TraesCS3D01G273300 chr3B 85.755 709 36 19 1226 1904 494077296 494076623 0.000000e+00 689.0
20 TraesCS3D01G273300 chr3B 78.571 378 54 25 87 446 769216062 769216430 1.920000e-54 224.0
21 TraesCS3D01G273300 chr6D 97.340 752 17 3 1901 2650 324815765 324816515 0.000000e+00 1275.0
22 TraesCS3D01G273300 chr6D 97.456 747 14 5 1906 2650 453648799 453649542 0.000000e+00 1269.0
23 TraesCS3D01G273300 chr6D 98.923 557 6 0 2993 3549 453649670 453650226 0.000000e+00 996.0
24 TraesCS3D01G273300 chr6D 85.057 87 13 0 499 585 453284075 453283989 7.300000e-14 89.8
25 TraesCS3D01G273300 chr2D 97.340 752 15 5 1903 2650 3028152 3028902 0.000000e+00 1273.0
26 TraesCS3D01G273300 chr2D 98.025 557 11 0 2993 3549 3029030 3029586 0.000000e+00 968.0
27 TraesCS3D01G273300 chr5D 97.067 750 19 3 1903 2650 560416643 560417391 0.000000e+00 1260.0
28 TraesCS3D01G273300 chr5D 97.059 748 18 4 1905 2650 47084748 47084003 0.000000e+00 1256.0
29 TraesCS3D01G273300 chr5D 98.743 557 7 0 2993 3549 499746241 499745685 0.000000e+00 990.0
30 TraesCS3D01G273300 chr5D 98.029 558 11 0 2993 3550 560417518 560418075 0.000000e+00 970.0
31 TraesCS3D01G273300 chr4D 97.059 748 17 5 1905 2650 111583774 111583030 0.000000e+00 1254.0
32 TraesCS3D01G273300 chr4D 97.849 558 11 1 2993 3550 111582903 111582347 0.000000e+00 963.0
33 TraesCS3D01G273300 chr5A 79.294 425 61 16 43 446 350812255 350812673 6.750000e-69 272.0
34 TraesCS3D01G273300 chr5A 78.868 265 42 10 43 301 350807923 350807667 3.280000e-37 167.0
35 TraesCS3D01G273300 chr1B 87.892 223 22 5 226 446 168625642 168625423 1.890000e-64 257.0
36 TraesCS3D01G273300 chr1B 78.417 278 38 17 93 363 577956930 577956668 1.530000e-35 161.0
37 TraesCS3D01G273300 chr1B 89.796 49 5 0 532 580 642926747 642926795 4.430000e-06 63.9
38 TraesCS3D01G273300 chr7A 79.240 342 60 10 111 446 617033852 617034188 1.480000e-55 228.0
39 TraesCS3D01G273300 chr7A 88.235 68 6 2 517 584 80988067 80988002 4.390000e-11 80.5
40 TraesCS3D01G273300 chr6B 77.534 365 60 19 98 447 561696047 561696404 3.230000e-47 200.0
41 TraesCS3D01G273300 chr6B 78.761 113 23 1 500 611 448350876 448350988 2.040000e-09 75.0
42 TraesCS3D01G273300 chr7B 76.536 358 65 16 101 446 25637904 25638254 1.510000e-40 178.0


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 TraesCS3D01G273300 chr3D 378928182 378933474 5292 True 4572.000000 4894 100.000000 1 5293 2 chr3D.!!$R3 5292
1 TraesCS3D01G273300 chr3D 405310310 405310873 563 True 976.000000 976 97.872000 2993 3556 1 chr3D.!!$R2 563
2 TraesCS3D01G273300 chr3A 502840310 502844041 3731 True 1588.333333 2503 91.401333 1 5278 3 chr3A.!!$R3 5277
3 TraesCS3D01G273300 chr1D 391736210 391737650 1440 True 1194.500000 1371 99.425500 1903 3559 2 chr1D.!!$R2 1656
4 TraesCS3D01G273300 chr1D 62937250 62937810 560 True 965.000000 965 97.683000 2993 3553 1 chr1D.!!$R1 560
5 TraesCS3D01G273300 chr7D 615763976 615764726 750 False 1260.000000 1260 96.950000 1899 2650 1 chr7D.!!$F1 751
6 TraesCS3D01G273300 chr7D 266018215 266019646 1431 False 1132.500000 1291 98.034500 1903 3549 2 chr7D.!!$F2 1646
7 TraesCS3D01G273300 chr3B 494074824 494078061 3237 True 903.000000 1277 87.722500 487 5278 4 chr3B.!!$R1 4791
8 TraesCS3D01G273300 chr6D 324815765 324816515 750 False 1275.000000 1275 97.340000 1901 2650 1 chr6D.!!$F1 749
9 TraesCS3D01G273300 chr6D 453648799 453650226 1427 False 1132.500000 1269 98.189500 1906 3549 2 chr6D.!!$F2 1643
10 TraesCS3D01G273300 chr2D 3028152 3029586 1434 False 1120.500000 1273 97.682500 1903 3549 2 chr2D.!!$F1 1646
11 TraesCS3D01G273300 chr5D 47084003 47084748 745 True 1256.000000 1256 97.059000 1905 2650 1 chr5D.!!$R1 745
12 TraesCS3D01G273300 chr5D 560416643 560418075 1432 False 1115.000000 1260 97.548000 1903 3550 2 chr5D.!!$F1 1647
13 TraesCS3D01G273300 chr5D 499745685 499746241 556 True 990.000000 990 98.743000 2993 3549 1 chr5D.!!$R2 556
14 TraesCS3D01G273300 chr4D 111582347 111583774 1427 True 1108.500000 1254 97.454000 1905 3550 2 chr4D.!!$R1 1645

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
962 974 0.390866 CAGCTCGTGGTGATCAAGCT 60.391 55.000 12.15 12.15 43.76 3.74 F
1612 1679 0.038801 GGCAGTTCCAGCAGAAAAGC 60.039 55.000 0.00 0.00 35.85 3.51 F
1768 1856 4.258702 AGCATATTCGCCTACTAACCAG 57.741 45.455 0.00 0.00 0.00 4.00 F
3384 3495 3.012518 GAGGTTGTCTGTGCATGCTAAT 58.987 45.455 20.33 0.00 0.00 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1809 1908 5.086104 AGTAGGCGAATATGACAAGTTGT 57.914 39.130 8.61 8.61 0.00 3.32 R
3384 3495 2.086094 TGATGTAGCACCGTAGTTCGA 58.914 47.619 0.00 0.00 42.86 3.71 R
3730 3841 0.965363 AGGCAGCCATTAAACGTGGG 60.965 55.000 15.80 0.00 37.22 4.61 R
4729 5059 0.100861 GGACGACTTCGAGGTGGATC 59.899 60.000 16.37 9.51 43.02 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
47 48 1.423921 TGGGAGGGGAAAAGTTCTGTC 59.576 52.381 0.00 0.00 0.00 3.51
64 65 5.988310 TCTGTCATTTCTTTACTACCCGA 57.012 39.130 0.00 0.00 0.00 5.14
84 85 5.175859 CCGAAACATCTAAGCCTAGAACAA 58.824 41.667 0.00 0.00 37.70 2.83
216 218 2.357517 GACGGTGAGTGGGCAGTG 60.358 66.667 0.00 0.00 0.00 3.66
238 240 1.576421 GCAAAGCTTCCCGTCACTG 59.424 57.895 0.00 0.00 0.00 3.66
240 242 0.886490 CAAAGCTTCCCGTCACTGCT 60.886 55.000 0.00 0.00 35.30 4.24
269 271 4.730949 CCTAGATCGGTAGGTTTTGTCA 57.269 45.455 0.00 0.00 35.67 3.58
276 278 1.144298 GGTAGGTTTTGTCAGTGGGGT 59.856 52.381 0.00 0.00 0.00 4.95
278 280 1.775385 AGGTTTTGTCAGTGGGGTTG 58.225 50.000 0.00 0.00 0.00 3.77
305 307 0.594602 CACGACCAACCTCGTAGTGA 59.405 55.000 0.00 0.00 45.09 3.41
314 316 3.064987 CTCGTAGTGAGTGCCCCGG 62.065 68.421 0.00 0.00 40.03 5.73
341 343 3.006967 CACCTCTTTATATAGCCCAGCGT 59.993 47.826 0.00 0.00 0.00 5.07
344 346 4.238514 CTCTTTATATAGCCCAGCGTGAC 58.761 47.826 0.00 0.00 0.00 3.67
363 365 2.124445 GGGGCCCGTCAACCATAC 60.124 66.667 17.79 0.00 0.00 2.39
377 379 4.123545 ATACTGGGTTGGGCGCCC 62.124 66.667 39.40 39.40 46.26 6.13
448 450 4.518249 GGGAGGAGATCAACCTAACAAAG 58.482 47.826 10.71 0.00 37.93 2.77
458 460 3.964411 AACCTAACAAAGGGTGCTATCC 58.036 45.455 0.00 0.00 46.78 2.59
459 461 3.332485 AACCTAACAAAGGGTGCTATCCA 59.668 43.478 0.00 0.00 46.78 3.41
469 471 7.512746 ACAAAGGGTGCTATCCAGATAATACTA 59.487 37.037 0.00 0.00 0.00 1.82
470 472 8.543774 CAAAGGGTGCTATCCAGATAATACTAT 58.456 37.037 0.00 0.00 0.00 2.12
471 473 7.906199 AGGGTGCTATCCAGATAATACTATC 57.094 40.000 0.00 0.00 35.10 2.08
472 474 7.422512 AGGGTGCTATCCAGATAATACTATCA 58.577 38.462 0.00 0.00 37.05 2.15
473 475 8.070604 AGGGTGCTATCCAGATAATACTATCAT 58.929 37.037 0.00 0.00 37.05 2.45
474 476 9.368416 GGGTGCTATCCAGATAATACTATCATA 57.632 37.037 0.00 0.00 37.05 2.15
476 478 9.885934 GTGCTATCCAGATAATACTATCATACG 57.114 37.037 0.00 0.00 37.05 3.06
477 479 9.628500 TGCTATCCAGATAATACTATCATACGT 57.372 33.333 0.00 0.00 37.05 3.57
497 499 3.666374 CGTATCATACGCTCCGAACTACC 60.666 52.174 3.82 0.00 45.81 3.18
502 504 2.356780 CGCTCCGAACTACCCCCTT 61.357 63.158 0.00 0.00 0.00 3.95
545 547 9.850628 TCGGGAAAATAAATATATCTAGACGTG 57.149 33.333 0.00 0.00 0.00 4.49
565 567 9.701098 AGACGTGTTTTAGTTCTAAATACATCA 57.299 29.630 0.00 6.87 30.05 3.07
594 596 4.111375 TCCATTTCTGCGACTAGTCTTC 57.889 45.455 20.34 12.24 0.00 2.87
617 619 5.244402 TCCACACGAAGGAAGTATTTGTCTA 59.756 40.000 0.00 0.00 30.71 2.59
619 621 6.157211 CACACGAAGGAAGTATTTGTCTAGT 58.843 40.000 0.00 0.00 0.00 2.57
620 622 6.308282 CACACGAAGGAAGTATTTGTCTAGTC 59.692 42.308 0.00 0.00 0.00 2.59
733 735 0.609131 CCAACAACCCGGCTTCATCT 60.609 55.000 0.00 0.00 0.00 2.90
835 838 2.978824 CCCATTCTCCACGTCCGT 59.021 61.111 0.00 0.00 0.00 4.69
940 952 1.728971 GCACAGAGAAAGGATCACACG 59.271 52.381 0.00 0.00 0.00 4.49
962 974 0.390866 CAGCTCGTGGTGATCAAGCT 60.391 55.000 12.15 12.15 43.76 3.74
978 990 2.178890 GCTGCCAGCCAAGAGATCG 61.179 63.158 5.06 0.00 34.48 3.69
983 995 0.392193 CCAGCCAAGAGATCGCAAGT 60.392 55.000 0.00 0.00 39.48 3.16
1071 1093 2.041928 AGCTTCCTGGAGGAGGGG 59.958 66.667 10.38 0.00 46.36 4.79
1113 1135 3.720566 GACGACAACGACGACGAG 58.279 61.111 15.32 8.51 42.66 4.18
1114 1136 1.791283 GACGACAACGACGACGAGG 60.791 63.158 15.32 7.78 42.66 4.63
1115 1137 2.162921 GACGACAACGACGACGAGGA 62.163 60.000 15.32 0.00 42.66 3.71
1116 1138 1.509370 CGACAACGACGACGAGGAG 60.509 63.158 15.32 3.15 42.66 3.69
1191 1213 2.320587 GCACTCCCAGCTTCACGTG 61.321 63.158 9.94 9.94 0.00 4.49
1210 1232 1.000506 TGAGTTTTCCTCCTCCGTTCG 59.999 52.381 0.00 0.00 39.65 3.95
1219 1241 1.186917 TCCTCCGTTCGGTAGCCAAA 61.187 55.000 11.04 0.00 0.00 3.28
1224 1280 0.643820 CGTTCGGTAGCCAAATCGTC 59.356 55.000 0.00 0.00 0.00 4.20
1251 1307 2.766400 CGAGAGTCCTGACGGGAGC 61.766 68.421 2.22 0.00 46.10 4.70
1265 1321 2.125912 GAGCGACGCCATGTCTGT 60.126 61.111 17.79 0.00 45.87 3.41
1481 1543 3.496309 CTGCAGGTCCAAGTGGGCA 62.496 63.158 5.57 1.76 42.93 5.36
1490 1552 3.637273 AAGTGGGCACGGTCCCTC 61.637 66.667 14.25 11.00 46.67 4.30
1565 1627 0.818296 AGCTAATCTTCAGACGGCGT 59.182 50.000 14.65 14.65 0.00 5.68
1566 1628 2.022195 AGCTAATCTTCAGACGGCGTA 58.978 47.619 14.74 0.00 0.00 4.42
1567 1629 2.426024 AGCTAATCTTCAGACGGCGTAA 59.574 45.455 14.74 2.38 0.00 3.18
1568 1630 3.068307 AGCTAATCTTCAGACGGCGTAAT 59.932 43.478 14.74 0.82 0.00 1.89
1569 1631 4.277672 AGCTAATCTTCAGACGGCGTAATA 59.722 41.667 14.74 0.00 0.00 0.98
1570 1632 4.980434 GCTAATCTTCAGACGGCGTAATAA 59.020 41.667 14.74 6.38 0.00 1.40
1578 1640 8.971321 TCTTCAGACGGCGTAATAATAATTAAC 58.029 33.333 14.74 0.00 29.41 2.01
1612 1679 0.038801 GGCAGTTCCAGCAGAAAAGC 60.039 55.000 0.00 0.00 35.85 3.51
1738 1826 5.237127 TGTTGTGCTGTTTAGAGTTGATGAG 59.763 40.000 0.00 0.00 0.00 2.90
1741 1829 6.935167 TGTGCTGTTTAGAGTTGATGAGATA 58.065 36.000 0.00 0.00 0.00 1.98
1744 1832 6.070824 TGCTGTTTAGAGTTGATGAGATACCA 60.071 38.462 0.00 0.00 0.00 3.25
1768 1856 4.258702 AGCATATTCGCCTACTAACCAG 57.741 45.455 0.00 0.00 0.00 4.00
1784 1875 7.784470 ACTAACCAGAGTAGAACTTCTCATT 57.216 36.000 10.18 5.19 33.63 2.57
1803 1902 8.617290 TCTCATTAGAAGTGGGTAAGAAAAAC 57.383 34.615 0.00 0.00 0.00 2.43
3384 3495 3.012518 GAGGTTGTCTGTGCATGCTAAT 58.987 45.455 20.33 0.00 0.00 1.73
3629 3740 4.317488 ACGGACGCTTCCAAGTAAATTAA 58.683 39.130 10.24 0.00 43.00 1.40
3693 3804 3.382855 GTGACATGAACTTGCATTGCAA 58.617 40.909 21.97 21.97 46.80 4.08
3730 3841 4.142004 ACCAGTCGACCAGATGTTATTACC 60.142 45.833 13.01 0.00 0.00 2.85
3747 3858 1.248101 ACCCCACGTTTAATGGCTGC 61.248 55.000 0.00 0.00 35.74 5.25
3809 3920 2.050639 AAACCGAAAACCGCACGTCC 62.051 55.000 0.00 0.00 36.84 4.79
4118 4229 0.540365 AGAACAACATGCACCTGGGG 60.540 55.000 0.00 0.00 0.00 4.96
4163 4274 4.680237 TCCAAGTGGCTCGGCACG 62.680 66.667 16.41 5.01 45.26 5.34
4305 4419 3.801971 CGTGATGCGTGCATGGCA 61.802 61.111 12.81 16.32 45.71 4.92
4306 4420 2.101575 GTGATGCGTGCATGGCAG 59.898 61.111 12.81 0.00 44.71 4.85
4307 4421 2.046120 TGATGCGTGCATGGCAGA 60.046 55.556 12.81 7.18 44.71 4.26
4308 4422 2.400962 TGATGCGTGCATGGCAGAC 61.401 57.895 12.81 14.96 44.71 3.51
4309 4423 2.360225 ATGCGTGCATGGCAGACA 60.360 55.556 18.37 3.90 44.71 3.41
4321 4435 1.762370 TGGCAGACAGACAACAAGAGA 59.238 47.619 0.00 0.00 26.55 3.10
4323 4437 3.206150 GGCAGACAGACAACAAGAGAAA 58.794 45.455 0.00 0.00 0.00 2.52
4343 4457 3.870538 ATATGATGCCATGGTGTCACT 57.129 42.857 19.25 12.73 34.31 3.41
4344 4458 1.758936 ATGATGCCATGGTGTCACTG 58.241 50.000 19.25 0.00 0.00 3.66
4345 4459 0.401356 TGATGCCATGGTGTCACTGT 59.599 50.000 14.67 0.00 0.00 3.55
4346 4460 1.089920 GATGCCATGGTGTCACTGTC 58.910 55.000 14.67 0.00 0.00 3.51
4348 4462 0.534877 TGCCATGGTGTCACTGTCAC 60.535 55.000 14.67 0.00 35.36 3.67
4389 4522 0.537828 GGGCGCTCTAGTAGGCTAGT 60.538 60.000 7.64 7.12 43.86 2.57
4392 4610 1.465777 GCGCTCTAGTAGGCTAGTAGC 59.534 57.143 25.28 18.82 43.86 3.58
4444 4662 1.204941 AGGTTGTGCGTAGTCAGGATC 59.795 52.381 0.00 0.00 0.00 3.36
4491 4712 3.878778 AGAAGAGAAATCCGTTGATGGG 58.121 45.455 0.00 0.00 0.00 4.00
4494 4715 2.092914 AGAGAAATCCGTTGATGGGGAC 60.093 50.000 0.00 0.00 34.58 4.46
4527 4856 6.668323 AGTTATCCAGTTTTCACAAATCACG 58.332 36.000 0.00 0.00 0.00 4.35
4548 4877 5.126384 CACGGGCTAATTTTCATCCCTTAAA 59.874 40.000 0.00 0.00 34.84 1.52
4602 4931 1.204146 GCACATCCCCTCAACCTCTA 58.796 55.000 0.00 0.00 0.00 2.43
4606 4935 2.225908 ACATCCCCTCAACCTCTACCTT 60.226 50.000 0.00 0.00 0.00 3.50
4627 4956 3.315142 GCTCCGGCAGATGGTGACA 62.315 63.158 0.00 0.00 41.33 3.58
4640 4969 3.005539 TGACAGGGAGGCAGCTCC 61.006 66.667 0.54 0.54 42.62 4.70
4652 4981 0.249826 GCAGCTCCAGCCAGTAGATC 60.250 60.000 0.00 0.00 43.38 2.75
4709 5039 1.202973 GATGACGGAGCATCGTGTCG 61.203 60.000 9.01 0.00 43.96 4.35
4729 5059 0.035056 AAATGGTCTTCCTGCCTCCG 60.035 55.000 0.00 0.00 34.23 4.63
4742 5074 1.736586 CCTCCGATCCACCTCGAAG 59.263 63.158 0.00 0.00 41.12 3.79
4774 5106 1.801913 CAAAGACGACCGAGCTCCG 60.802 63.158 8.47 8.78 38.18 4.63
4775 5107 1.970114 AAAGACGACCGAGCTCCGA 60.970 57.895 16.27 0.00 41.76 4.55
4799 5131 7.565190 ACATAGATCCATGTCATTACCTCAT 57.435 36.000 0.44 0.00 33.89 2.90
4801 5133 7.236225 ACATAGATCCATGTCATTACCTCATGA 59.764 37.037 0.44 0.00 40.64 3.07
4809 5141 4.161377 TGTCATTACCTCATGATGGTCGAA 59.839 41.667 16.95 9.80 38.88 3.71
4832 5164 2.521105 AGGGTTACTTGTCGTGTGTC 57.479 50.000 0.00 0.00 0.00 3.67
4841 5173 3.961197 TCGTGTGTCTGCGCGAGT 61.961 61.111 12.10 0.00 44.84 4.18
4849 5181 0.658368 GTCTGCGCGAGTGAGATCTA 59.342 55.000 12.10 0.00 0.00 1.98
4852 5184 1.867865 CTGCGCGAGTGAGATCTAGTA 59.132 52.381 12.10 0.00 0.00 1.82
4853 5185 1.867865 TGCGCGAGTGAGATCTAGTAG 59.132 52.381 12.10 0.00 0.00 2.57
4854 5186 1.868498 GCGCGAGTGAGATCTAGTAGT 59.132 52.381 12.10 0.00 0.00 2.73
4855 5187 2.349060 GCGCGAGTGAGATCTAGTAGTG 60.349 54.545 12.10 0.00 0.00 2.74
4856 5188 2.867368 CGCGAGTGAGATCTAGTAGTGT 59.133 50.000 0.00 0.00 0.00 3.55
4857 5189 3.310227 CGCGAGTGAGATCTAGTAGTGTT 59.690 47.826 0.00 0.00 0.00 3.32
4858 5190 4.507021 CGCGAGTGAGATCTAGTAGTGTTA 59.493 45.833 0.00 0.00 0.00 2.41
4859 5191 5.006455 CGCGAGTGAGATCTAGTAGTGTTAA 59.994 44.000 0.00 0.00 0.00 2.01
4891 5223 4.588106 TGCAGATTGATTCAAGGGTTCAAA 59.412 37.500 5.21 0.00 33.45 2.69
4914 5246 4.038080 CAACAACGGCTTCGGGGC 62.038 66.667 0.00 0.00 38.38 5.80
4933 5265 1.228245 GCCTGTCTTCAAGGGCACA 60.228 57.895 0.00 0.00 43.59 4.57
4973 5306 3.826524 TGTCATCAACAAGGTTAAGCCA 58.173 40.909 0.00 0.00 34.16 4.75
4983 5316 0.461516 GGTTAAGCCAGCTCCGGTAC 60.462 60.000 0.00 0.00 37.17 3.34
5018 5351 4.391405 ACGACATGTCATTAGCTCATCA 57.609 40.909 24.93 0.00 0.00 3.07
5020 5353 6.089249 ACGACATGTCATTAGCTCATCATA 57.911 37.500 24.93 0.00 0.00 2.15
5044 5378 0.178955 TGACGGTAGTGGTCAGGGAA 60.179 55.000 0.00 0.00 39.36 3.97
5048 5382 0.531200 GGTAGTGGTCAGGGAACTCG 59.469 60.000 0.00 0.00 40.21 4.18
5049 5383 1.542492 GTAGTGGTCAGGGAACTCGA 58.458 55.000 0.00 0.00 40.21 4.04
5089 5423 4.150897 TGGGGTGTATTCATACTTCTGC 57.849 45.455 0.00 0.00 34.41 4.26
5091 5425 4.966168 TGGGGTGTATTCATACTTCTGCTA 59.034 41.667 0.00 0.00 34.41 3.49
5094 5428 6.260271 GGGGTGTATTCATACTTCTGCTAAAC 59.740 42.308 0.00 0.00 34.41 2.01
5214 5548 9.832445 AGAAAGACATCAAGTTAACTACAAGAA 57.168 29.630 8.92 0.00 0.00 2.52
5243 5577 8.668353 TCATGATTAAAGAAAAGACTGGAATCG 58.332 33.333 0.00 0.00 30.80 3.34
5248 5582 6.555812 AAAGAAAAGACTGGAATCGTAACC 57.444 37.500 0.00 0.00 0.00 2.85
5253 5587 3.733236 CTGGAATCGTAACCAGCGA 57.267 52.632 0.00 0.00 45.30 4.93
5275 5609 5.872617 CGAGTATCACACCCATTTTAGTGAA 59.127 40.000 0.00 0.00 43.38 3.18
5278 5612 7.633789 AGTATCACACCCATTTTAGTGAAGAT 58.366 34.615 0.00 0.00 43.38 2.40
5279 5613 8.109634 AGTATCACACCCATTTTAGTGAAGATT 58.890 33.333 0.00 0.00 43.38 2.40
5280 5614 7.781324 ATCACACCCATTTTAGTGAAGATTT 57.219 32.000 0.00 0.00 43.38 2.17
5281 5615 7.214467 TCACACCCATTTTAGTGAAGATTTC 57.786 36.000 0.00 0.00 37.99 2.17
5282 5616 6.072728 TCACACCCATTTTAGTGAAGATTTCG 60.073 38.462 0.00 0.00 37.99 3.46
5283 5617 5.768164 ACACCCATTTTAGTGAAGATTTCGT 59.232 36.000 0.00 0.00 37.43 3.85
5284 5618 6.264518 ACACCCATTTTAGTGAAGATTTCGTT 59.735 34.615 0.00 0.00 37.43 3.85
5285 5619 6.582295 CACCCATTTTAGTGAAGATTTCGTTG 59.418 38.462 0.00 0.00 36.01 4.10
5286 5620 6.264518 ACCCATTTTAGTGAAGATTTCGTTGT 59.735 34.615 0.00 0.00 0.00 3.32
5287 5621 7.145323 CCCATTTTAGTGAAGATTTCGTTGTT 58.855 34.615 0.00 0.00 0.00 2.83
5288 5622 8.293867 CCCATTTTAGTGAAGATTTCGTTGTTA 58.706 33.333 0.00 0.00 0.00 2.41
5289 5623 9.672086 CCATTTTAGTGAAGATTTCGTTGTTAA 57.328 29.630 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 7.611213 AGATGTTTCGGGTAGTAAAGAAATG 57.389 36.000 0.00 0.00 35.45 2.32
64 65 6.876257 CAGAGTTGTTCTAGGCTTAGATGTTT 59.124 38.462 6.37 0.00 35.88 2.83
84 85 4.780021 AGAACCTATCAATGGTGTCAGAGT 59.220 41.667 0.00 0.00 37.93 3.24
223 225 1.302033 CAGCAGTGACGGGAAGCTT 60.302 57.895 0.00 0.00 32.35 3.74
226 228 2.046892 CCCAGCAGTGACGGGAAG 60.047 66.667 11.06 0.00 43.21 3.46
238 240 0.318762 CCGATCTAGGTTAGCCCAGC 59.681 60.000 0.00 0.00 34.66 4.85
240 242 2.490351 CCTACCGATCTAGGTTAGCCCA 60.490 54.545 0.00 0.00 43.00 5.36
292 294 0.389948 GGGCACTCACTACGAGGTTG 60.390 60.000 0.00 0.00 46.98 3.77
314 316 3.055021 GGGCTATATAAAGAGGTGAGGGC 60.055 52.174 0.00 0.00 0.00 5.19
318 320 3.258372 CGCTGGGCTATATAAAGAGGTGA 59.742 47.826 0.00 0.00 0.00 4.02
320 322 3.006967 CACGCTGGGCTATATAAAGAGGT 59.993 47.826 0.00 0.00 0.00 3.85
344 346 2.675242 TATGGTTGACGGGCCCCTG 61.675 63.158 18.66 5.47 0.00 4.45
385 387 2.125326 GGCCCTTAAATCCGTGCCC 61.125 63.158 0.00 0.00 32.74 5.36
390 392 1.822186 CACCGGGCCCTTAAATCCG 60.822 63.158 22.43 3.11 41.90 4.18
430 432 4.010349 CACCCTTTGTTAGGTTGATCTCC 58.990 47.826 0.00 0.00 38.68 3.71
448 450 7.661536 TGATAGTATTATCTGGATAGCACCC 57.338 40.000 6.78 0.00 37.23 4.61
476 478 3.365767 GGGTAGTTCGGAGCGTATGATAC 60.366 52.174 0.00 0.00 0.00 2.24
477 479 2.816087 GGGTAGTTCGGAGCGTATGATA 59.184 50.000 0.00 0.00 0.00 2.15
478 480 1.612463 GGGTAGTTCGGAGCGTATGAT 59.388 52.381 0.00 0.00 0.00 2.45
479 481 1.027357 GGGTAGTTCGGAGCGTATGA 58.973 55.000 0.00 0.00 0.00 2.15
483 485 3.073101 GGGGGTAGTTCGGAGCGT 61.073 66.667 0.00 0.00 0.00 5.07
497 499 3.692593 ACAAATATTTTCGGACGAAGGGG 59.307 43.478 7.25 0.00 35.38 4.79
565 567 8.281212 ACTAGTCGCAGAAATGGATAAAAATT 57.719 30.769 0.00 0.00 39.69 1.82
594 596 4.315803 AGACAAATACTTCCTTCGTGTGG 58.684 43.478 0.00 0.00 0.00 4.17
617 619 0.944311 CGTAACGCTTGCCACAGACT 60.944 55.000 0.00 0.00 0.00 3.24
619 621 0.249531 TTCGTAACGCTTGCCACAGA 60.250 50.000 0.00 0.00 0.00 3.41
620 622 0.584396 TTTCGTAACGCTTGCCACAG 59.416 50.000 0.00 0.00 0.00 3.66
733 735 1.385347 ACGGGATAATGGGGCCTGA 60.385 57.895 0.84 0.00 0.00 3.86
940 952 2.512515 GATCACCACGAGCTGGGC 60.513 66.667 0.00 0.00 45.78 5.36
953 965 0.963856 CTTGGCTGGCAGCTTGATCA 60.964 55.000 35.73 23.13 41.99 2.92
962 974 2.124983 GCGATCTCTTGGCTGGCA 60.125 61.111 0.00 0.00 0.00 4.92
978 990 2.163412 TGTCTGTGTGTTTTGGACTTGC 59.837 45.455 0.00 0.00 0.00 4.01
983 995 3.360867 ACCATTGTCTGTGTGTTTTGGA 58.639 40.909 0.00 0.00 0.00 3.53
1071 1093 2.851071 CGGCCATCTCTCCGTCTCC 61.851 68.421 2.24 0.00 40.72 3.71
1101 1123 1.134901 CTCCTCCTCGTCGTCGTTG 59.865 63.158 1.33 0.00 38.33 4.10
1102 1124 2.039405 CCTCCTCCTCGTCGTCGTT 61.039 63.158 1.33 0.00 38.33 3.85
1113 1135 1.841103 GCTGGATCCCTCCTCCTCC 60.841 68.421 9.90 0.00 42.59 4.30
1114 1136 2.206536 CGCTGGATCCCTCCTCCTC 61.207 68.421 9.90 0.00 42.59 3.71
1115 1137 2.123077 CGCTGGATCCCTCCTCCT 60.123 66.667 9.90 0.00 42.59 3.69
1116 1138 3.237741 CCGCTGGATCCCTCCTCC 61.238 72.222 9.90 0.00 42.59 4.30
1191 1213 1.672145 CCGAACGGAGGAGGAAAACTC 60.672 57.143 7.53 0.00 40.77 3.01
1210 1232 2.128035 CGATCAGACGATTTGGCTACC 58.872 52.381 0.00 0.00 35.09 3.18
1219 1241 0.306228 CTCTCGTGCGATCAGACGAT 59.694 55.000 14.60 0.00 43.26 3.73
1224 1280 0.248417 CAGGACTCTCGTGCGATCAG 60.248 60.000 0.00 0.00 36.49 2.90
1235 1291 2.752238 CGCTCCCGTCAGGACTCT 60.752 66.667 0.00 0.00 40.93 3.24
1265 1321 2.118076 CCCAAGGCCTCCTGCAAA 59.882 61.111 5.23 0.00 43.89 3.68
1326 1382 1.078143 GCATCTTCTCCACGGCCTT 60.078 57.895 0.00 0.00 0.00 4.35
1481 1543 1.228800 GGGGATATCGAGGGACCGT 60.229 63.158 0.00 0.00 0.00 4.83
1490 1552 3.583086 ACCAATTACCTGAGGGGATATCG 59.417 47.826 2.38 0.00 38.76 2.92
1570 1632 9.189156 TGCCAGCTCTTTCATTAAGTTAATTAT 57.811 29.630 5.34 0.00 35.28 1.28
1578 1640 4.142513 GGAACTGCCAGCTCTTTCATTAAG 60.143 45.833 0.00 0.00 36.34 1.85
1582 1644 1.074405 TGGAACTGCCAGCTCTTTCAT 59.926 47.619 0.00 0.00 43.33 2.57
1738 1826 3.931578 AGGCGAATATGCTTCTGGTATC 58.068 45.455 0.00 0.00 34.52 2.24
1741 1829 2.700897 AGTAGGCGAATATGCTTCTGGT 59.299 45.455 0.00 0.00 34.52 4.00
1744 1832 4.344102 TGGTTAGTAGGCGAATATGCTTCT 59.656 41.667 0.00 0.00 34.52 2.85
1777 1868 9.063615 GTTTTTCTTACCCACTTCTAATGAGAA 57.936 33.333 0.00 0.00 39.47 2.87
1778 1869 8.437575 AGTTTTTCTTACCCACTTCTAATGAGA 58.562 33.333 0.00 0.00 0.00 3.27
1781 1872 9.503399 ACTAGTTTTTCTTACCCACTTCTAATG 57.497 33.333 0.00 0.00 0.00 1.90
1784 1875 9.987272 GTTACTAGTTTTTCTTACCCACTTCTA 57.013 33.333 0.00 0.00 0.00 2.10
1803 1902 6.757010 AGGCGAATATGACAAGTTGTTACTAG 59.243 38.462 10.45 0.85 33.17 2.57
1809 1908 5.086104 AGTAGGCGAATATGACAAGTTGT 57.914 39.130 8.61 8.61 0.00 3.32
3384 3495 2.086094 TGATGTAGCACCGTAGTTCGA 58.914 47.619 0.00 0.00 42.86 3.71
3629 3740 2.347490 GTGACGGGTGCCTGACAT 59.653 61.111 3.74 0.00 30.73 3.06
3693 3804 1.682684 CTGGTCTGGTCGGGCTAGT 60.683 63.158 0.00 0.00 0.00 2.57
3730 3841 0.965363 AGGCAGCCATTAAACGTGGG 60.965 55.000 15.80 0.00 37.22 4.61
3747 3858 3.443976 CGGTTTTGGAAGTGTTTTGAGG 58.556 45.455 0.00 0.00 0.00 3.86
3809 3920 4.741676 CACCAAACTTTTTGCTTAGCAGAG 59.258 41.667 7.08 9.55 40.61 3.35
4118 4229 1.676967 CTTGTGCTTCCTCCAGGGC 60.677 63.158 0.00 0.00 35.41 5.19
4305 4419 7.065563 GCATCATATTTCTCTTGTTGTCTGTCT 59.934 37.037 0.00 0.00 0.00 3.41
4306 4420 7.185453 GCATCATATTTCTCTTGTTGTCTGTC 58.815 38.462 0.00 0.00 0.00 3.51
4307 4421 6.094603 GGCATCATATTTCTCTTGTTGTCTGT 59.905 38.462 0.00 0.00 0.00 3.41
4308 4422 6.094464 TGGCATCATATTTCTCTTGTTGTCTG 59.906 38.462 0.00 0.00 0.00 3.51
4309 4423 6.182627 TGGCATCATATTTCTCTTGTTGTCT 58.817 36.000 0.00 0.00 0.00 3.41
4321 4435 4.340097 CAGTGACACCATGGCATCATATTT 59.660 41.667 18.79 5.83 37.93 1.40
4323 4437 3.117776 ACAGTGACACCATGGCATCATAT 60.118 43.478 18.79 10.12 37.93 1.78
4343 4457 1.915952 CATACGGCATACACGTGACA 58.084 50.000 25.01 9.98 45.20 3.58
4344 4458 0.575390 GCATACGGCATACACGTGAC 59.425 55.000 25.01 8.29 45.20 3.67
4345 4459 2.966324 GCATACGGCATACACGTGA 58.034 52.632 25.01 6.34 45.20 4.35
4389 4522 7.365741 GTTACACACTCTACTAACAAGTGCTA 58.634 38.462 1.85 0.00 43.30 3.49
4392 4610 5.628193 CCGTTACACACTCTACTAACAAGTG 59.372 44.000 0.00 0.00 44.68 3.16
4444 4662 8.037382 TCAAGAGCAGATTCAAGAAATTACAG 57.963 34.615 0.00 0.00 0.00 2.74
4491 4712 7.511959 AAACTGGATAACTTTTCTCTTGTCC 57.488 36.000 0.00 0.00 0.00 4.02
4494 4715 8.405531 TGTGAAAACTGGATAACTTTTCTCTTG 58.594 33.333 0.00 0.00 35.70 3.02
4527 4856 9.764363 CTAAATTTAAGGGATGAAAATTAGCCC 57.236 33.333 0.00 0.00 39.12 5.19
4548 4877 4.407296 TGCCTGGTTTGTTTGGTTCTAAAT 59.593 37.500 0.00 0.00 0.00 1.40
4580 4909 0.548682 AGGTTGAGGGGATGTGCTCT 60.549 55.000 0.00 0.00 0.00 4.09
4619 4948 2.976490 GCTGCCTCCCTGTCACCAT 61.976 63.158 0.00 0.00 0.00 3.55
4640 4969 1.341531 CCCTAACCGATCTACTGGCTG 59.658 57.143 0.00 0.00 0.00 4.85
4644 4973 4.213513 ACCTAACCCTAACCGATCTACTG 58.786 47.826 0.00 0.00 0.00 2.74
4652 4981 1.470458 GCGAAGACCTAACCCTAACCG 60.470 57.143 0.00 0.00 0.00 4.44
4709 5039 1.756430 GGAGGCAGGAAGACCATTTC 58.244 55.000 0.00 0.00 38.94 2.17
4729 5059 0.100861 GGACGACTTCGAGGTGGATC 59.899 60.000 16.37 9.51 43.02 3.36
4762 5094 1.158484 TCTATGTCGGAGCTCGGTCG 61.158 60.000 19.51 12.26 39.77 4.79
4775 5107 7.236225 TCATGAGGTAATGACATGGATCTATGT 59.764 37.037 23.16 23.16 43.61 2.29
4799 5131 4.091549 AGTAACCCTAACTTCGACCATCA 58.908 43.478 0.00 0.00 0.00 3.07
4801 5133 4.285260 ACAAGTAACCCTAACTTCGACCAT 59.715 41.667 0.00 0.00 34.99 3.55
4809 5141 3.385755 ACACACGACAAGTAACCCTAACT 59.614 43.478 0.00 0.00 0.00 2.24
4832 5164 0.660488 ACTAGATCTCACTCGCGCAG 59.340 55.000 8.75 6.77 0.00 5.18
4849 5181 7.713734 TCTGCAGTACCTAATTAACACTACT 57.286 36.000 14.67 0.00 0.00 2.57
4852 5184 7.620880 TCAATCTGCAGTACCTAATTAACACT 58.379 34.615 14.67 0.00 0.00 3.55
4853 5185 7.843490 TCAATCTGCAGTACCTAATTAACAC 57.157 36.000 14.67 0.00 0.00 3.32
4854 5186 9.109393 GAATCAATCTGCAGTACCTAATTAACA 57.891 33.333 14.67 0.00 0.00 2.41
4855 5187 9.109393 TGAATCAATCTGCAGTACCTAATTAAC 57.891 33.333 14.67 0.00 0.00 2.01
4856 5188 9.679661 TTGAATCAATCTGCAGTACCTAATTAA 57.320 29.630 14.67 0.00 0.00 1.40
4857 5189 9.330063 CTTGAATCAATCTGCAGTACCTAATTA 57.670 33.333 14.67 0.00 0.00 1.40
4858 5190 7.284034 CCTTGAATCAATCTGCAGTACCTAATT 59.716 37.037 14.67 7.45 0.00 1.40
4859 5191 6.769822 CCTTGAATCAATCTGCAGTACCTAAT 59.230 38.462 14.67 0.00 0.00 1.73
4891 5223 2.123897 AAGCCGTTGTTGCCACCT 60.124 55.556 0.00 0.00 0.00 4.00
4921 5253 0.674581 TCGAGCATGTGCCCTTGAAG 60.675 55.000 0.57 0.00 43.38 3.02
4922 5254 0.250684 TTCGAGCATGTGCCCTTGAA 60.251 50.000 0.57 0.00 43.38 2.69
4965 5298 0.804933 CGTACCGGAGCTGGCTTAAC 60.805 60.000 9.46 0.00 0.00 2.01
4983 5316 0.247735 TGTCGTTTTCGTTGTTGCCG 60.248 50.000 0.00 0.00 44.46 5.69
5018 5351 2.097825 GACCACTACCGTCACCACTAT 58.902 52.381 0.00 0.00 0.00 2.12
5020 5353 0.468585 TGACCACTACCGTCACCACT 60.469 55.000 0.00 0.00 35.35 4.00
5065 5399 5.066505 GCAGAAGTATGAATACACCCCAAAG 59.933 44.000 3.43 0.00 35.74 2.77
5068 5402 3.780294 AGCAGAAGTATGAATACACCCCA 59.220 43.478 3.43 0.00 35.74 4.96
5069 5403 4.423625 AGCAGAAGTATGAATACACCCC 57.576 45.455 3.43 0.00 35.74 4.95
5109 5443 6.526325 CGTGTTCTTTTTGTGAAAATGACTCA 59.474 34.615 0.00 0.00 35.21 3.41
5110 5444 6.526674 ACGTGTTCTTTTTGTGAAAATGACTC 59.473 34.615 0.00 0.00 35.21 3.36
5115 5449 5.395642 ACGACGTGTTCTTTTTGTGAAAAT 58.604 33.333 0.00 0.00 34.45 1.82
5237 5571 2.857592 TACTCGCTGGTTACGATTCC 57.142 50.000 0.00 0.00 39.12 3.01
5243 5577 2.537401 GGTGTGATACTCGCTGGTTAC 58.463 52.381 0.00 0.00 0.00 2.50
5248 5582 2.315925 AATGGGTGTGATACTCGCTG 57.684 50.000 0.00 0.00 29.93 5.18
5253 5587 7.016153 TCTTCACTAAAATGGGTGTGATACT 57.984 36.000 0.00 0.00 38.89 2.12


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

AutoCloner maintained by Alex Coulton.