Multiple sequence alignment - TraesCS6B01G231200

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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 TraesCS6B01G231200 chr6B 100.000 5166 0 0 1 5166 378962035 378956870 0.000000e+00 9540.0
1 TraesCS6B01G231200 chr6B 98.221 1012 17 1 4156 5166 641399308 641400319 0.000000e+00 1768.0
2 TraesCS6B01G231200 chr6B 97.532 1013 23 2 4156 5166 12871539 12872551 0.000000e+00 1731.0
3 TraesCS6B01G231200 chr6B 89.474 76 6 2 723 797 378961236 378961310 1.530000e-15 95.3
4 TraesCS6B01G231200 chr6B 83.908 87 7 5 730 811 122793825 122793741 5.550000e-10 76.8
5 TraesCS6B01G231200 chr6B 81.915 94 10 7 723 811 717149024 717148933 7.180000e-09 73.1
6 TraesCS6B01G231200 chr6A 93.234 3015 126 48 174 3149 264829925 264832900 0.000000e+00 4366.0
7 TraesCS6B01G231200 chr6A 91.707 820 34 11 3194 4001 264833577 264834374 0.000000e+00 1107.0
8 TraesCS6B01G231200 chr6A 90.411 73 6 1 4081 4153 264834390 264834461 1.530000e-15 95.3
9 TraesCS6B01G231200 chr6D 95.361 2393 59 36 784 3149 226788913 226786546 0.000000e+00 3757.0
10 TraesCS6B01G231200 chr6D 92.471 943 39 12 3175 4107 226781059 226780139 0.000000e+00 1319.0
11 TraesCS6B01G231200 chr6D 86.305 701 57 15 3 689 226795587 226794912 0.000000e+00 726.0
12 TraesCS6B01G231200 chr5B 97.727 1012 22 1 4156 5166 576253888 576254899 0.000000e+00 1740.0
13 TraesCS6B01G231200 chr5B 88.494 956 104 2 4212 5166 571884010 571883060 0.000000e+00 1151.0
14 TraesCS6B01G231200 chr5B 92.771 166 12 0 177 342 357175268 357175103 1.860000e-59 241.0
15 TraesCS6B01G231200 chr5B 78.912 294 55 5 1609 1897 102162334 102162625 5.280000e-45 193.0
16 TraesCS6B01G231200 chr2A 96.044 1011 39 1 4156 5165 654433943 654434953 0.000000e+00 1644.0
17 TraesCS6B01G231200 chr2A 93.939 66 4 0 4156 4221 510288466 510288531 3.290000e-17 100.0
18 TraesCS6B01G231200 chr2A 95.238 63 2 1 4156 4218 4530262 4530323 1.180000e-16 99.0
19 TraesCS6B01G231200 chr1A 85.700 1014 139 5 4156 5165 30881890 30882901 0.000000e+00 1064.0
20 TraesCS6B01G231200 chr1A 90.643 171 16 0 180 350 237013106 237013276 1.450000e-55 228.0
21 TraesCS6B01G231200 chr4D 88.288 777 88 3 4156 4930 471203071 471203846 0.000000e+00 928.0
22 TraesCS6B01G231200 chr4D 83.162 291 47 2 1609 1898 173572944 173573233 1.100000e-66 265.0
23 TraesCS6B01G231200 chr4D 90.116 172 17 0 177 348 223037550 223037379 1.870000e-54 224.0
24 TraesCS6B01G231200 chr4D 82.418 91 11 4 24 114 220095197 220095112 2.000000e-09 75.0
25 TraesCS6B01G231200 chr4D 80.198 101 19 1 393 493 455436931 455436832 2.000000e-09 75.0
26 TraesCS6B01G231200 chr2D 81.906 934 162 6 4234 5163 534431865 534432795 0.000000e+00 782.0
27 TraesCS6B01G231200 chr1D 80.655 1008 184 10 4156 5157 192870647 192871649 0.000000e+00 771.0
28 TraesCS6B01G231200 chr1D 88.770 187 21 0 165 351 159606021 159606207 4.020000e-56 230.0
29 TraesCS6B01G231200 chr1D 83.333 138 17 2 3 140 239313112 239312981 7.020000e-24 122.0
30 TraesCS6B01G231200 chr1D 83.654 104 17 0 393 496 487961928 487961825 1.180000e-16 99.0
31 TraesCS6B01G231200 chr4A 83.162 291 47 2 1609 1898 227093921 227093632 1.100000e-66 265.0
32 TraesCS6B01G231200 chr4A 80.142 141 24 4 362 501 66155869 66155732 9.150000e-18 102.0
33 TraesCS6B01G231200 chr4B 82.818 291 48 2 1609 1898 246319268 246318979 5.130000e-65 259.0
34 TraesCS6B01G231200 chr7D 90.643 171 16 0 180 350 530357459 530357629 1.450000e-55 228.0
35 TraesCS6B01G231200 chr7D 100.000 30 0 0 85 114 486301530 486301559 7.230000e-04 56.5
36 TraesCS6B01G231200 chr2B 90.698 172 15 1 169 339 393599901 393600072 1.450000e-55 228.0
37 TraesCS6B01G231200 chr2B 84.615 104 9 5 714 812 257534763 257534864 4.260000e-16 97.1
38 TraesCS6B01G231200 chr2B 82.979 94 9 6 723 811 725734899 725734808 1.540000e-10 78.7
39 TraesCS6B01G231200 chr2B 81.522 92 12 5 723 810 410266437 410266527 2.580000e-08 71.3
40 TraesCS6B01G231200 chr3B 90.361 166 16 0 177 342 299564912 299564747 8.710000e-53 219.0
41 TraesCS6B01G231200 chr3D 89.349 169 18 0 177 345 292239082 292238914 4.050000e-51 213.0
42 TraesCS6B01G231200 chr3D 83.962 106 17 0 393 498 444193433 444193538 9.150000e-18 102.0
43 TraesCS6B01G231200 chr5D 79.252 294 54 4 1609 1897 95273981 95274272 1.130000e-46 198.0
44 TraesCS6B01G231200 chr5D 82.796 93 9 6 723 810 549469903 549469813 5.550000e-10 76.8
45 TraesCS6B01G231200 chr5D 77.273 132 22 5 32 160 184737681 184737555 2.580000e-08 71.3
46 TraesCS6B01G231200 chr5A 79.392 296 50 8 1609 1897 89978199 89978490 1.130000e-46 198.0
47 TraesCS6B01G231200 chr7B 77.586 290 60 4 1573 1858 601327340 601327052 2.470000e-38 171.0
48 TraesCS6B01G231200 chr3A 81.988 161 21 4 5 162 204394858 204394703 4.200000e-26 130.0
49 TraesCS6B01G231200 chr7A 79.605 152 31 0 351 502 271344007 271344158 5.470000e-20 110.0
50 TraesCS6B01G231200 chr1B 77.439 164 28 4 3 162 95838138 95837980 7.120000e-14 89.8
51 TraesCS6B01G231200 chr1B 81.915 94 9 7 723 811 416583021 416582931 7.180000e-09 73.1


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 TraesCS6B01G231200 chr6B 378956870 378962035 5165 True 9540.0 9540 100.000 1 5166 1 chr6B.!!$R2 5165
1 TraesCS6B01G231200 chr6B 641399308 641400319 1011 False 1768.0 1768 98.221 4156 5166 1 chr6B.!!$F3 1010
2 TraesCS6B01G231200 chr6B 12871539 12872551 1012 False 1731.0 1731 97.532 4156 5166 1 chr6B.!!$F1 1010
3 TraesCS6B01G231200 chr6A 264829925 264834461 4536 False 1856.1 4366 91.784 174 4153 3 chr6A.!!$F1 3979
4 TraesCS6B01G231200 chr6D 226786546 226788913 2367 True 3757.0 3757 95.361 784 3149 1 chr6D.!!$R2 2365
5 TraesCS6B01G231200 chr6D 226780139 226781059 920 True 1319.0 1319 92.471 3175 4107 1 chr6D.!!$R1 932
6 TraesCS6B01G231200 chr6D 226794912 226795587 675 True 726.0 726 86.305 3 689 1 chr6D.!!$R3 686
7 TraesCS6B01G231200 chr5B 576253888 576254899 1011 False 1740.0 1740 97.727 4156 5166 1 chr5B.!!$F2 1010
8 TraesCS6B01G231200 chr5B 571883060 571884010 950 True 1151.0 1151 88.494 4212 5166 1 chr5B.!!$R2 954
9 TraesCS6B01G231200 chr2A 654433943 654434953 1010 False 1644.0 1644 96.044 4156 5165 1 chr2A.!!$F3 1009
10 TraesCS6B01G231200 chr1A 30881890 30882901 1011 False 1064.0 1064 85.700 4156 5165 1 chr1A.!!$F1 1009
11 TraesCS6B01G231200 chr4D 471203071 471203846 775 False 928.0 928 88.288 4156 4930 1 chr4D.!!$F2 774
12 TraesCS6B01G231200 chr2D 534431865 534432795 930 False 782.0 782 81.906 4234 5163 1 chr2D.!!$F1 929
13 TraesCS6B01G231200 chr1D 192870647 192871649 1002 False 771.0 771 80.655 4156 5157 1 chr1D.!!$F2 1001

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
576 591 0.106519 AATTTCGAGGGGATGCCCTG 60.107 55.0 32.28 21.03 44.66 4.45 F
1999 2014 0.109086 ACCTGCTCATCGACGACAAG 60.109 55.0 0.00 1.46 0.00 3.16 F
2283 2363 0.179084 ACTTGTGTGAGTGTCCGTGG 60.179 55.0 0.00 0.00 0.00 4.94 F
3714 4440 0.028505 GCTGATGGTGTGCTAATGCG 59.971 55.0 0.00 0.00 43.34 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2280 2360 0.037326 TGCTCAATCTCCGTGACCAC 60.037 55.000 0.00 0.0 0.00 4.16 R
3669 4392 0.235665 CAAAGAATGTGTCGCGCTGT 59.764 50.000 5.56 0.0 0.00 4.40 R
3957 4697 0.250338 GGTCGCCTATGGTTCCATCC 60.250 60.000 7.67 0.0 0.00 3.51 R
4988 5735 2.040606 AGGTGGTAGCCGATGGGT 59.959 61.111 0.00 0.0 37.19 4.51 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
60 61 5.431420 TTGCACACAATTCGTCTTATTGT 57.569 34.783 0.00 0.00 44.69 2.71
62 63 5.448438 TGCACACAATTCGTCTTATTGTTC 58.552 37.500 0.00 0.00 42.02 3.18
72 73 7.424227 TTCGTCTTATTGTTCACGGTTTTAT 57.576 32.000 0.00 0.00 33.02 1.40
78 79 9.064706 TCTTATTGTTCACGGTTTTATTACCAA 57.935 29.630 0.00 0.00 38.12 3.67
79 80 9.680315 CTTATTGTTCACGGTTTTATTACCAAA 57.320 29.630 0.00 0.00 38.12 3.28
80 81 7.933728 ATTGTTCACGGTTTTATTACCAAAC 57.066 32.000 0.00 0.00 38.12 2.93
81 82 5.829829 TGTTCACGGTTTTATTACCAAACC 58.170 37.500 4.73 4.73 46.78 3.27
105 106 2.159531 ACCGTTTGTGATTCATGCATCG 60.160 45.455 0.00 0.00 0.00 3.84
114 115 0.798159 TTCATGCATCGCACACAGTC 59.202 50.000 0.00 0.00 43.04 3.51
129 130 3.259374 ACACAGTCTCATCGATTGGTCTT 59.741 43.478 0.00 0.00 33.97 3.01
150 153 4.968812 TCGATACATGTTCGTTAGGACA 57.031 40.909 21.46 6.18 37.82 4.02
166 169 2.292267 GGACAATCCTGCAGTACATGG 58.708 52.381 13.81 1.75 32.53 3.66
167 170 2.356125 GGACAATCCTGCAGTACATGGT 60.356 50.000 13.81 5.15 32.53 3.55
168 171 3.118408 GGACAATCCTGCAGTACATGGTA 60.118 47.826 13.81 0.00 32.53 3.25
169 172 4.444876 GGACAATCCTGCAGTACATGGTAT 60.445 45.833 13.81 0.00 32.53 2.73
170 173 4.454678 ACAATCCTGCAGTACATGGTATG 58.545 43.478 13.81 3.71 0.00 2.39
171 174 4.080356 ACAATCCTGCAGTACATGGTATGT 60.080 41.667 13.81 4.30 46.92 2.29
172 175 4.778213 ATCCTGCAGTACATGGTATGTT 57.222 40.909 13.81 0.00 41.63 2.71
173 176 3.872696 TCCTGCAGTACATGGTATGTTG 58.127 45.455 13.81 0.00 41.63 3.33
174 177 3.263170 TCCTGCAGTACATGGTATGTTGT 59.737 43.478 13.81 0.00 41.63 3.32
175 178 4.468153 TCCTGCAGTACATGGTATGTTGTA 59.532 41.667 13.81 0.00 41.63 2.41
220 223 4.461431 TGACGAGTGTAAGCCTTTATCTGA 59.539 41.667 0.00 0.00 0.00 3.27
297 300 3.854809 GTCTTCGATATGCGCTTCTATCC 59.145 47.826 9.73 0.00 40.61 2.59
310 313 2.981859 TCTATCCTTTGCGGGACTTC 57.018 50.000 0.00 0.00 38.30 3.01
342 345 2.301870 GGTGATAGGACCGCATATTGGA 59.698 50.000 0.00 0.00 0.00 3.53
372 375 2.032549 GATGCAATCGTTGATCCGAAGG 60.033 50.000 0.00 0.00 42.04 3.46
391 394 1.518572 TTCGAAATCGGGCTCTCGC 60.519 57.895 0.00 0.00 40.29 5.03
412 415 2.510411 CACACAGTGGGACCTGCA 59.490 61.111 0.00 0.00 35.83 4.41
459 462 2.735237 CGGATCTCGGGTAAGGGC 59.265 66.667 0.00 0.00 34.75 5.19
461 464 2.517798 GGATCTCGGGTAAGGGCCC 61.518 68.421 16.46 16.46 45.21 5.80
462 465 2.447959 ATCTCGGGTAAGGGCCCC 60.448 66.667 21.43 2.17 45.91 5.80
496 499 8.087136 GTGATCTGAGCTAGATGATAACATGAA 58.913 37.037 0.00 0.00 46.12 2.57
497 500 8.305317 TGATCTGAGCTAGATGATAACATGAAG 58.695 37.037 0.00 0.00 46.12 3.02
498 501 7.830099 TCTGAGCTAGATGATAACATGAAGA 57.170 36.000 0.00 0.00 36.82 2.87
518 521 8.519799 TGAAGAAAAATACTGTATTGGGGATC 57.480 34.615 13.42 10.16 0.00 3.36
526 529 4.497516 ACTGTATTGGGGATCTGCTAGAT 58.502 43.478 0.00 0.00 37.73 1.98
528 531 4.492646 TGTATTGGGGATCTGCTAGATGA 58.507 43.478 0.00 0.00 34.53 2.92
529 532 5.096521 TGTATTGGGGATCTGCTAGATGAT 58.903 41.667 0.00 0.00 34.53 2.45
532 547 5.489792 TTGGGGATCTGCTAGATGATAAC 57.510 43.478 0.00 0.00 34.53 1.89
535 550 5.046087 TGGGGATCTGCTAGATGATAACATG 60.046 44.000 0.00 0.00 34.53 3.21
569 584 9.908747 TTACTTTCAAATATAATTTCGAGGGGA 57.091 29.630 0.00 0.00 0.00 4.81
576 591 0.106519 AATTTCGAGGGGATGCCCTG 60.107 55.000 32.28 21.03 44.66 4.45
615 630 3.629398 GGTTAGCTCAAATGGATCCACAG 59.371 47.826 18.99 11.72 0.00 3.66
622 637 3.258872 TCAAATGGATCCACAGGCAAAAG 59.741 43.478 18.99 0.00 0.00 2.27
634 649 5.347342 CACAGGCAAAAGTTGTTTATCACA 58.653 37.500 0.00 0.00 0.00 3.58
637 652 6.042143 CAGGCAAAAGTTGTTTATCACAGTT 58.958 36.000 0.00 0.00 36.48 3.16
648 663 6.336566 TGTTTATCACAGTTGCACAAAACAT 58.663 32.000 0.00 0.00 32.40 2.71
675 690 6.224420 AGTTTTAGAGTACGTGACATTTGC 57.776 37.500 0.00 0.00 0.00 3.68
713 728 4.402056 TGCAACTACCTTATCTACAGGC 57.598 45.455 0.00 0.00 34.32 4.85
718 733 6.183360 GCAACTACCTTATCTACAGGCTACTT 60.183 42.308 0.00 0.00 34.32 2.24
719 734 7.427214 CAACTACCTTATCTACAGGCTACTTC 58.573 42.308 0.00 0.00 34.32 3.01
720 735 6.670617 ACTACCTTATCTACAGGCTACTTCA 58.329 40.000 0.00 0.00 34.32 3.02
721 736 6.773685 ACTACCTTATCTACAGGCTACTTCAG 59.226 42.308 0.00 0.00 34.32 3.02
736 751 5.220491 GCTACTTCAGCCGTCTCAAAATAAG 60.220 44.000 0.00 0.00 45.23 1.73
740 755 5.142061 TCAGCCGTCTCAAAATAAGTGTA 57.858 39.130 0.00 0.00 0.00 2.90
815 830 6.672266 TGAGATGGAGGGAGTATTTGATAC 57.328 41.667 0.00 0.00 35.99 2.24
821 836 4.202367 GGAGGGAGTATTTGATACAGTGGG 60.202 50.000 0.00 0.00 38.21 4.61
940 955 0.525761 GGTGGCATGCACGTTACAAT 59.474 50.000 21.36 0.00 0.00 2.71
1376 1391 2.860972 GAAGAAGGCTCCGGTGCTCC 62.861 65.000 26.25 15.63 0.00 4.70
1999 2014 0.109086 ACCTGCTCATCGACGACAAG 60.109 55.000 0.00 1.46 0.00 3.16
2200 2215 1.454479 CGGAAAGCCCATCATGCCT 60.454 57.895 0.00 0.00 34.14 4.75
2281 2361 3.362581 CACTTGTGTGAGTGTCCGT 57.637 52.632 0.00 0.00 46.55 4.69
2282 2362 0.930310 CACTTGTGTGAGTGTCCGTG 59.070 55.000 0.00 0.00 46.55 4.94
2283 2363 0.179084 ACTTGTGTGAGTGTCCGTGG 60.179 55.000 0.00 0.00 0.00 4.94
2284 2364 0.179084 CTTGTGTGAGTGTCCGTGGT 60.179 55.000 0.00 0.00 0.00 4.16
2285 2365 0.179094 TTGTGTGAGTGTCCGTGGTC 60.179 55.000 0.00 0.00 0.00 4.02
2286 2366 1.324005 TGTGTGAGTGTCCGTGGTCA 61.324 55.000 0.00 0.00 0.00 4.02
2287 2367 0.874607 GTGTGAGTGTCCGTGGTCAC 60.875 60.000 8.02 8.02 39.85 3.67
2471 2551 4.996434 GTGGACACGCTGCTGGCT 62.996 66.667 0.00 0.00 39.13 4.75
2624 2704 8.902540 AACCACCCATTTTATCTTTCTTTTTC 57.097 30.769 0.00 0.00 0.00 2.29
2626 2706 9.374711 ACCACCCATTTTATCTTTCTTTTTCTA 57.625 29.630 0.00 0.00 0.00 2.10
2669 2750 7.258022 CAAATTAGGTTTGGTTTTCCTTTGG 57.742 36.000 0.00 0.00 42.79 3.28
2826 2911 4.308458 CCTTGGCGTGTGACCCGA 62.308 66.667 0.00 0.00 0.00 5.14
2950 3035 2.402640 ACGACGTGACTTTGACTCTC 57.597 50.000 0.00 0.00 0.00 3.20
2952 3037 2.358267 ACGACGTGACTTTGACTCTCTT 59.642 45.455 0.00 0.00 0.00 2.85
2953 3038 2.974536 CGACGTGACTTTGACTCTCTTC 59.025 50.000 0.00 0.00 0.00 2.87
3115 3200 8.699130 ACTTCATTTCATTTCTTAATCCCATCC 58.301 33.333 0.00 0.00 0.00 3.51
3155 3272 4.794241 GACGTGCGCGCCATGTTC 62.794 66.667 30.77 13.82 43.58 3.18
3168 3285 4.554723 GCGCCATGTTCATGTTTCTATACC 60.555 45.833 11.13 0.00 0.00 2.73
3170 3287 5.277490 CGCCATGTTCATGTTTCTATACCTG 60.277 44.000 11.13 0.00 0.00 4.00
3171 3288 5.822519 GCCATGTTCATGTTTCTATACCTGA 59.177 40.000 11.13 0.00 0.00 3.86
3603 4326 0.257328 TCCCTGCCAACAAAGACACA 59.743 50.000 0.00 0.00 0.00 3.72
3614 4337 0.251922 AAAGACACAGCCATGCCCAT 60.252 50.000 0.00 0.00 0.00 4.00
3669 4392 4.578871 TCTGTCTAATTTTGCTGCTGCTA 58.421 39.130 17.00 6.36 40.48 3.49
3694 4420 2.286125 CGCGACACATTCTTTGACACAA 60.286 45.455 0.00 0.00 0.00 3.33
3706 4432 1.596603 TGACACAAGCTGATGGTGTG 58.403 50.000 11.35 14.30 45.09 3.82
3707 4433 0.239347 GACACAAGCTGATGGTGTGC 59.761 55.000 11.35 0.00 45.09 4.57
3708 4434 0.179009 ACACAAGCTGATGGTGTGCT 60.179 50.000 14.03 1.31 43.58 4.40
3709 4435 1.072173 ACACAAGCTGATGGTGTGCTA 59.928 47.619 14.03 0.00 43.58 3.49
3710 4436 2.153645 CACAAGCTGATGGTGTGCTAA 58.846 47.619 2.70 0.00 35.85 3.09
3711 4437 2.751259 CACAAGCTGATGGTGTGCTAAT 59.249 45.455 2.70 0.00 35.85 1.73
3712 4438 2.751259 ACAAGCTGATGGTGTGCTAATG 59.249 45.455 0.00 0.00 35.85 1.90
3713 4439 1.386533 AGCTGATGGTGTGCTAATGC 58.613 50.000 0.00 0.00 35.05 3.56
3714 4440 0.028505 GCTGATGGTGTGCTAATGCG 59.971 55.000 0.00 0.00 43.34 4.73
3739 4465 2.093181 TGTGATTCATCAGGGTTACGGG 60.093 50.000 0.00 0.00 37.51 5.28
3804 4530 0.902531 GGAGGGAACATGGACGAGAA 59.097 55.000 0.00 0.00 0.00 2.87
3897 4637 2.420022 GCAGCGGTAGAAAATGACATGT 59.580 45.455 0.00 0.00 0.00 3.21
3898 4638 3.119849 GCAGCGGTAGAAAATGACATGTT 60.120 43.478 0.00 0.00 0.00 2.71
3899 4639 4.094294 GCAGCGGTAGAAAATGACATGTTA 59.906 41.667 0.00 0.00 0.00 2.41
3900 4640 5.727791 GCAGCGGTAGAAAATGACATGTTAG 60.728 44.000 0.00 0.00 0.00 2.34
3901 4641 5.580691 CAGCGGTAGAAAATGACATGTTAGA 59.419 40.000 0.00 0.00 0.00 2.10
3902 4642 5.812642 AGCGGTAGAAAATGACATGTTAGAG 59.187 40.000 0.00 0.00 0.00 2.43
3903 4643 5.006746 GCGGTAGAAAATGACATGTTAGAGG 59.993 44.000 0.00 0.00 0.00 3.69
3904 4644 5.523916 CGGTAGAAAATGACATGTTAGAGGG 59.476 44.000 0.00 0.00 0.00 4.30
3905 4645 6.415573 GGTAGAAAATGACATGTTAGAGGGT 58.584 40.000 0.00 0.00 0.00 4.34
3956 4696 1.609208 GTGCACAGAAACACCTCCAT 58.391 50.000 13.17 0.00 0.00 3.41
3957 4697 1.267806 GTGCACAGAAACACCTCCATG 59.732 52.381 13.17 0.00 0.00 3.66
3958 4698 0.883833 GCACAGAAACACCTCCATGG 59.116 55.000 4.97 4.97 42.93 3.66
3959 4699 1.545428 GCACAGAAACACCTCCATGGA 60.545 52.381 15.27 15.27 39.71 3.41
3960 4700 2.881403 GCACAGAAACACCTCCATGGAT 60.881 50.000 16.63 0.00 39.71 3.41
3961 4701 2.751259 CACAGAAACACCTCCATGGATG 59.249 50.000 16.63 15.64 39.71 3.51
3977 4717 0.468226 GATGGAACCATAGGCGACCA 59.532 55.000 6.31 0.00 36.70 4.02
4045 4786 4.736896 GGTGCCACGTCCCGAGAC 62.737 72.222 0.00 0.00 39.83 3.36
4055 4796 0.321996 GTCCCGAGACTCAGGCTTTT 59.678 55.000 2.82 0.00 40.10 2.27
4096 4837 1.741732 CGGAGCAGAGTTGGAAGGATG 60.742 57.143 0.00 0.00 0.00 3.51
4134 4875 0.902531 ATGAGACTTGTACACCGGGG 59.097 55.000 0.00 0.00 0.00 5.73
4135 4876 0.470456 TGAGACTTGTACACCGGGGT 60.470 55.000 16.91 16.91 0.00 4.95
4140 4881 1.767681 ACTTGTACACCGGGGTTGTAA 59.232 47.619 18.35 7.34 0.00 2.41
4141 4882 2.172293 ACTTGTACACCGGGGTTGTAAA 59.828 45.455 18.35 1.18 0.00 2.01
4452 5197 2.988010 TGCGATGTTTCCATAGCTCT 57.012 45.000 8.78 0.00 46.30 4.09
4463 5208 3.378512 TCCATAGCTCTCACAAGACCAT 58.621 45.455 0.00 0.00 0.00 3.55
4549 5294 2.169789 CCAAGCTCATCGTCGCTGG 61.170 63.158 0.00 0.00 36.45 4.85
4988 5735 1.216977 CGATGTCCAACGCCCACTA 59.783 57.895 0.00 0.00 0.00 2.74
5107 5854 1.340405 CCAACCATCTGTCTTCCCAGG 60.340 57.143 0.00 0.00 33.14 4.45
5147 5894 4.070716 CTCCTTGCATTGACTCTCAAAGT 58.929 43.478 0.00 0.00 40.12 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.537793 ACGATTCGAAAAAGAGTTGGC 57.462 42.857 13.95 0.00 0.00 4.52
1 2 7.295201 TCAAATACGATTCGAAAAAGAGTTGG 58.705 34.615 13.95 0.00 0.00 3.77
13 14 3.181530 GCGGATCCATCAAATACGATTCG 60.182 47.826 13.41 4.14 36.91 3.34
82 83 3.822594 TGCATGAATCACAAACGGTAC 57.177 42.857 0.00 0.00 0.00 3.34
105 106 1.662629 CCAATCGATGAGACTGTGTGC 59.337 52.381 0.00 0.00 0.00 4.57
129 130 4.968812 TGTCCTAACGAACATGTATCGA 57.031 40.909 26.23 11.82 42.76 3.59
150 153 4.778213 ACATACCATGTACTGCAGGATT 57.222 40.909 19.93 0.00 42.78 3.01
175 178 8.551205 CGTCACAAGCTATAACATGAATACATT 58.449 33.333 0.00 0.00 34.15 2.71
189 192 3.512680 GCTTACACTCGTCACAAGCTAT 58.487 45.455 0.00 0.00 38.80 2.97
199 202 5.599999 ATCAGATAAAGGCTTACACTCGT 57.400 39.130 0.00 0.00 0.00 4.18
297 300 1.266989 GAACTTGGAAGTCCCGCAAAG 59.733 52.381 0.00 0.00 38.57 2.77
322 325 3.326747 GTCCAATATGCGGTCCTATCAC 58.673 50.000 0.00 0.00 0.00 3.06
356 359 2.268298 CGAACCTTCGGATCAACGATT 58.732 47.619 0.00 0.00 46.30 3.34
372 375 2.288969 CGAGAGCCCGATTTCGAAC 58.711 57.895 0.00 0.00 43.02 3.95
397 400 1.676635 CCATGCAGGTCCCACTGTG 60.677 63.158 0.00 0.00 40.59 3.66
412 415 1.414919 GCATTGACATTGATGGCCCAT 59.585 47.619 0.00 0.00 33.92 4.00
452 455 4.176752 CAGCTCGGGGGCCCTTAC 62.177 72.222 24.38 11.77 0.00 2.34
459 462 2.765807 AGATCACCAGCTCGGGGG 60.766 66.667 4.84 0.00 39.52 5.40
461 464 1.440893 CTCAGATCACCAGCTCGGG 59.559 63.158 0.00 0.00 40.22 5.14
462 465 1.227205 GCTCAGATCACCAGCTCGG 60.227 63.158 0.00 1.16 42.50 4.63
496 499 6.547510 GCAGATCCCCAATACAGTATTTTTCT 59.452 38.462 2.77 0.13 0.00 2.52
497 500 6.547510 AGCAGATCCCCAATACAGTATTTTTC 59.452 38.462 2.77 0.00 0.00 2.29
498 501 6.435164 AGCAGATCCCCAATACAGTATTTTT 58.565 36.000 2.77 0.00 0.00 1.94
507 510 5.690464 ATCATCTAGCAGATCCCCAATAC 57.310 43.478 0.00 0.00 31.32 1.89
569 584 2.158564 CCCATTACATGTCTCAGGGCAT 60.159 50.000 0.00 0.00 0.00 4.40
576 591 2.981859 ACCGTCCCATTACATGTCTC 57.018 50.000 0.00 0.00 0.00 3.36
593 608 3.620488 TGTGGATCCATTTGAGCTAACC 58.380 45.455 19.62 0.27 0.00 2.85
615 630 5.276820 GCAACTGTGATAAACAACTTTTGCC 60.277 40.000 0.00 0.00 38.67 4.52
622 637 6.090088 TGTTTTGTGCAACTGTGATAAACAAC 59.910 34.615 0.00 0.00 38.67 3.32
693 708 4.674281 AGCCTGTAGATAAGGTAGTTGC 57.326 45.455 0.00 0.00 37.13 4.17
713 728 5.869888 ACTTATTTTGAGACGGCTGAAGTAG 59.130 40.000 0.00 0.00 0.00 2.57
718 733 4.002906 ACACTTATTTTGAGACGGCTGA 57.997 40.909 0.00 0.00 0.00 4.26
719 734 5.580691 TGATACACTTATTTTGAGACGGCTG 59.419 40.000 0.00 0.00 0.00 4.85
720 735 5.730550 TGATACACTTATTTTGAGACGGCT 58.269 37.500 0.00 0.00 0.00 5.52
721 736 6.092259 AGTTGATACACTTATTTTGAGACGGC 59.908 38.462 0.00 0.00 0.00 5.68
722 737 7.596749 AGTTGATACACTTATTTTGAGACGG 57.403 36.000 0.00 0.00 0.00 4.79
776 791 8.616076 CCTCCATCTCAAAATAAGTGTATCAAC 58.384 37.037 0.00 0.00 0.00 3.18
781 796 6.443849 ACTCCCTCCATCTCAAAATAAGTGTA 59.556 38.462 0.00 0.00 0.00 2.90
797 812 4.408921 CCACTGTATCAAATACTCCCTCCA 59.591 45.833 0.00 0.00 36.70 3.86
815 830 2.672651 TTGACATGCCGCCCACTG 60.673 61.111 0.00 0.00 0.00 3.66
821 836 1.026182 TCATCTGGTTGACATGCCGC 61.026 55.000 0.00 0.00 0.00 6.53
1376 1391 0.241213 TTGTTGAGAGAGGCGACGAG 59.759 55.000 0.00 0.00 0.00 4.18
1447 1462 2.515523 GCTGCATCATGGTCGCCT 60.516 61.111 0.00 0.00 0.00 5.52
1594 1609 1.550524 CCGATCTTGTCCAACCTCTCA 59.449 52.381 0.00 0.00 0.00 3.27
1999 2014 3.567797 GCGATCTTGAGCACGCCC 61.568 66.667 0.00 0.00 44.27 6.13
2200 2215 0.406750 TAGGAACCTCGGTCTGTCCA 59.593 55.000 7.78 0.00 35.57 4.02
2280 2360 0.037326 TGCTCAATCTCCGTGACCAC 60.037 55.000 0.00 0.00 0.00 4.16
2281 2361 0.247460 CTGCTCAATCTCCGTGACCA 59.753 55.000 0.00 0.00 0.00 4.02
2282 2362 1.086634 GCTGCTCAATCTCCGTGACC 61.087 60.000 0.00 0.00 0.00 4.02
2283 2363 0.108424 AGCTGCTCAATCTCCGTGAC 60.108 55.000 0.00 0.00 0.00 3.67
2284 2364 0.108472 CAGCTGCTCAATCTCCGTGA 60.108 55.000 0.00 0.00 0.00 4.35
2285 2365 1.703438 GCAGCTGCTCAATCTCCGTG 61.703 60.000 31.33 0.00 38.21 4.94
2286 2366 1.449246 GCAGCTGCTCAATCTCCGT 60.449 57.895 31.33 0.00 38.21 4.69
2287 2367 1.449070 TGCAGCTGCTCAATCTCCG 60.449 57.895 36.61 0.00 42.66 4.63
2288 2368 0.675837 TGTGCAGCTGCTCAATCTCC 60.676 55.000 34.40 15.34 40.94 3.71
2289 2369 1.162698 TTGTGCAGCTGCTCAATCTC 58.837 50.000 38.61 21.21 45.77 2.75
2471 2551 1.759299 CCGGTGGGAGGGTTCGATA 60.759 63.158 0.00 0.00 34.06 2.92
2508 2588 2.159085 GGCTACTTACTTGGCTGTCGAT 60.159 50.000 0.00 0.00 0.00 3.59
2553 2633 0.596577 ACAAGTTGATGCTGCTGCTG 59.403 50.000 17.00 7.12 40.48 4.41
2554 2634 1.808945 GTACAAGTTGATGCTGCTGCT 59.191 47.619 17.00 2.26 40.48 4.24
2555 2635 1.135575 GGTACAAGTTGATGCTGCTGC 60.136 52.381 10.54 8.89 40.20 5.25
2592 2672 2.209690 AAAATGGGTGGTTCTACGGG 57.790 50.000 0.00 0.00 0.00 5.28
2674 2755 6.157123 TGGGTTCTGTAGAATTTTTGGGTTTT 59.843 34.615 0.00 0.00 36.33 2.43
2675 2756 5.663556 TGGGTTCTGTAGAATTTTTGGGTTT 59.336 36.000 0.00 0.00 36.33 3.27
2676 2757 5.069914 GTGGGTTCTGTAGAATTTTTGGGTT 59.930 40.000 0.00 0.00 36.33 4.11
2677 2758 4.587262 GTGGGTTCTGTAGAATTTTTGGGT 59.413 41.667 0.00 0.00 36.33 4.51
2678 2759 4.832823 AGTGGGTTCTGTAGAATTTTTGGG 59.167 41.667 0.00 0.00 36.33 4.12
2679 2760 5.770162 AGAGTGGGTTCTGTAGAATTTTTGG 59.230 40.000 0.00 0.00 36.33 3.28
2680 2761 6.884280 AGAGTGGGTTCTGTAGAATTTTTG 57.116 37.500 0.00 0.00 36.33 2.44
2810 2895 3.041940 GTCGGGTCACACGCCAAG 61.042 66.667 0.00 0.00 0.00 3.61
2826 2911 1.003718 GGTACTTGGGCAAGCTCGT 60.004 57.895 0.00 0.00 41.99 4.18
2926 3011 5.287226 AGAGTCAAAGTCACGTCGTAATTT 58.713 37.500 0.00 0.00 0.00 1.82
3106 3191 1.087417 GGATGGGATGGGATGGGATT 58.913 55.000 0.00 0.00 0.00 3.01
3107 3192 0.852683 GGGATGGGATGGGATGGGAT 60.853 60.000 0.00 0.00 0.00 3.85
3108 3193 1.465986 GGGATGGGATGGGATGGGA 60.466 63.158 0.00 0.00 0.00 4.37
3109 3194 1.466788 AGGGATGGGATGGGATGGG 60.467 63.158 0.00 0.00 0.00 4.00
3110 3195 0.773305 TGAGGGATGGGATGGGATGG 60.773 60.000 0.00 0.00 0.00 3.51
3115 3200 1.350351 GAGACATGAGGGATGGGATGG 59.650 57.143 0.00 0.00 36.23 3.51
3206 3929 8.413229 GCCTCCTCTGCAAACATAAATAAATAA 58.587 33.333 0.00 0.00 0.00 1.40
3207 3930 7.559533 TGCCTCCTCTGCAAACATAAATAAATA 59.440 33.333 0.00 0.00 35.40 1.40
3459 4182 2.341101 CGTGGCGTAGGACCTCTGT 61.341 63.158 0.00 0.00 0.00 3.41
3669 4392 0.235665 CAAAGAATGTGTCGCGCTGT 59.764 50.000 5.56 0.00 0.00 4.40
3679 4405 4.022589 CCATCAGCTTGTGTCAAAGAATGT 60.023 41.667 0.00 0.00 0.00 2.71
3694 4420 1.386533 GCATTAGCACACCATCAGCT 58.613 50.000 0.00 0.00 41.58 4.24
3706 4432 3.485947 TGAATCACAAACCGCATTAGC 57.514 42.857 0.00 0.00 37.42 3.09
3707 4433 5.233957 TGATGAATCACAAACCGCATTAG 57.766 39.130 0.00 0.00 0.00 1.73
3708 4434 4.096231 CCTGATGAATCACAAACCGCATTA 59.904 41.667 0.00 0.00 32.50 1.90
3709 4435 3.119388 CCTGATGAATCACAAACCGCATT 60.119 43.478 0.00 0.00 32.50 3.56
3710 4436 2.424601 CCTGATGAATCACAAACCGCAT 59.575 45.455 0.00 0.00 32.50 4.73
3711 4437 1.811965 CCTGATGAATCACAAACCGCA 59.188 47.619 0.00 0.00 32.50 5.69
3712 4438 1.133025 CCCTGATGAATCACAAACCGC 59.867 52.381 0.00 0.00 32.50 5.68
3713 4439 2.436417 ACCCTGATGAATCACAAACCG 58.564 47.619 0.00 0.00 32.50 4.44
3714 4440 4.142687 CGTAACCCTGATGAATCACAAACC 60.143 45.833 0.00 0.00 32.50 3.27
3783 4509 1.229368 TCGTCCATGTTCCCTCCCA 60.229 57.895 0.00 0.00 0.00 4.37
3902 4642 1.222936 CTGGCAGTGAGGATGACCC 59.777 63.158 6.28 0.00 36.73 4.46
3903 4643 0.835941 ATCTGGCAGTGAGGATGACC 59.164 55.000 15.27 0.00 0.00 4.02
3904 4644 1.537776 CGATCTGGCAGTGAGGATGAC 60.538 57.143 15.27 0.00 0.00 3.06
3905 4645 0.749049 CGATCTGGCAGTGAGGATGA 59.251 55.000 15.27 0.00 0.00 2.92
3915 4655 2.895680 GACAGGCTCGATCTGGCA 59.104 61.111 14.60 0.00 39.92 4.92
3956 4696 0.468226 GTCGCCTATGGTTCCATCCA 59.532 55.000 7.67 0.00 42.01 3.41
3957 4697 0.250338 GGTCGCCTATGGTTCCATCC 60.250 60.000 7.67 0.00 0.00 3.51
3958 4698 0.468226 TGGTCGCCTATGGTTCCATC 59.532 55.000 7.67 0.00 0.00 3.51
3959 4699 0.469917 CTGGTCGCCTATGGTTCCAT 59.530 55.000 9.37 9.37 0.00 3.41
3960 4700 1.904771 CTGGTCGCCTATGGTTCCA 59.095 57.895 0.00 0.00 0.00 3.53
3961 4701 1.523938 GCTGGTCGCCTATGGTTCC 60.524 63.158 0.00 0.00 0.00 3.62
3962 4702 0.811616 CTGCTGGTCGCCTATGGTTC 60.812 60.000 0.00 0.00 38.05 3.62
3963 4703 1.221840 CTGCTGGTCGCCTATGGTT 59.778 57.895 0.00 0.00 38.05 3.67
3964 4704 2.735772 CCTGCTGGTCGCCTATGGT 61.736 63.158 0.51 0.00 38.05 3.55
3977 4717 2.185350 CGCGTTGGAGATCCTGCT 59.815 61.111 0.00 0.00 36.82 4.24
4045 4786 4.015084 ACATGGATCAAGAAAAGCCTGAG 58.985 43.478 0.00 0.00 0.00 3.35
4055 4796 8.414003 GCTCCGTATTATATACATGGATCAAGA 58.586 37.037 0.00 0.00 0.00 3.02
4078 4819 1.377536 GCATCCTTCCAACTCTGCTC 58.622 55.000 0.00 0.00 0.00 4.26
4096 4837 0.893727 TTTCCCTTGAGGCTTTCCGC 60.894 55.000 0.00 0.00 37.47 5.54
4324 5069 1.620822 CTGTTCAAAGGGAGGTTGGG 58.379 55.000 0.00 0.00 0.00 4.12
4463 5208 8.271458 ACAAGGACATACATACCATGTTATTGA 58.729 33.333 14.92 0.00 41.63 2.57
4549 5294 3.802852 AAACTGGTTGGGGGCCGAC 62.803 63.158 0.00 0.00 37.19 4.79
4988 5735 2.040606 AGGTGGTAGCCGATGGGT 59.959 61.111 0.00 0.00 37.19 4.51


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

AutoCloner maintained by Alex Coulton.