Multiple sequence alignment - TraesCS2B01G093400

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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 TraesCS2B01G093400 chr2B 100.000 5277 0 0 1 5277 53703135 53697859 0.000000e+00 9745.0
1 TraesCS2B01G093400 chr2B 82.443 393 67 2 1908 2299 549308764 549308373 5.060000e-90 342.0
2 TraesCS2B01G093400 chrUn 96.033 4033 104 19 567 4572 24920201 24916198 0.000000e+00 6510.0
3 TraesCS2B01G093400 chrUn 94.400 625 27 6 4519 5138 24916205 24915584 0.000000e+00 953.0
4 TraesCS2B01G093400 chrUn 91.152 486 27 9 1 476 24921489 24921010 0.000000e+00 645.0
5 TraesCS2B01G093400 chrUn 98.925 93 1 0 476 568 24920423 24920331 3.270000e-37 167.0
6 TraesCS2B01G093400 chr6D 83.257 2174 262 58 1600 3720 310396137 310398261 0.000000e+00 1905.0
7 TraesCS2B01G093400 chr6D 90.047 422 41 1 3852 4272 310398298 310398719 3.590000e-151 545.0
8 TraesCS2B01G093400 chr6D 93.220 59 4 0 4214 4272 310398802 310398860 2.620000e-13 87.9
9 TraesCS2B01G093400 chr6B 83.095 2165 264 60 1600 3720 478466320 478468426 0.000000e+00 1877.0
10 TraesCS2B01G093400 chr6B 81.317 744 102 17 2852 3592 53602152 53602861 2.130000e-158 569.0
11 TraesCS2B01G093400 chr6B 90.047 422 41 1 3852 4272 478468463 478468884 3.590000e-151 545.0
12 TraesCS2B01G093400 chr6B 81.667 180 28 4 4275 4454 478469076 478469250 1.530000e-30 145.0
13 TraesCS2B01G093400 chr6B 91.525 59 5 0 4214 4272 478468928 478468986 1.220000e-11 82.4
14 TraesCS2B01G093400 chr6A 81.511 1628 216 52 1600 3186 446779149 446780732 0.000000e+00 1260.0
15 TraesCS2B01G093400 chr6A 87.216 485 45 6 3237 3720 446780739 446781207 2.160000e-148 536.0
16 TraesCS2B01G093400 chr6A 88.679 424 43 5 3852 4272 446781244 446781665 3.640000e-141 512.0
17 TraesCS2B01G093400 chr7D 82.930 744 94 16 2852 3592 564574736 564574023 1.600000e-179 640.0
18 TraesCS2B01G093400 chr7B 82.527 744 98 15 2852 3592 285344732 285344018 4.490000e-175 625.0
19 TraesCS2B01G093400 chr3D 82.927 615 87 13 2926 3537 554225782 554225183 6.010000e-149 538.0
20 TraesCS2B01G093400 chr3D 82.085 614 93 12 2926 3537 554179574 554178976 4.710000e-140 508.0
21 TraesCS2B01G093400 chr7A 80.971 515 68 18 3081 3592 595995354 595995841 1.070000e-101 381.0
22 TraesCS2B01G093400 chr2A 80.814 516 69 17 3080 3592 745304753 745304265 1.390000e-100 377.0
23 TraesCS2B01G093400 chr2A 81.955 399 70 2 1902 2299 612084813 612084416 2.350000e-88 337.0
24 TraesCS2B01G093400 chr2D 83.208 399 65 2 1902 2299 470389372 470388975 1.080000e-96 364.0
25 TraesCS2B01G093400 chr3B 88.889 72 8 0 3719 3790 188181675 188181604 7.280000e-14 89.8
26 TraesCS2B01G093400 chr3A 100.000 30 0 0 3718 3747 416128437 416128466 7.380000e-04 56.5


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 TraesCS2B01G093400 chr2B 53697859 53703135 5276 True 9745.000000 9745 100.000000 1 5277 1 chr2B.!!$R1 5276
1 TraesCS2B01G093400 chrUn 24915584 24921489 5905 True 2068.750000 6510 95.127500 1 5138 4 chrUn.!!$R1 5137
2 TraesCS2B01G093400 chr6D 310396137 310398860 2723 False 845.966667 1905 88.841333 1600 4272 3 chr6D.!!$F1 2672
3 TraesCS2B01G093400 chr6B 478466320 478469250 2930 False 662.350000 1877 86.583500 1600 4454 4 chr6B.!!$F2 2854
4 TraesCS2B01G093400 chr6B 53602152 53602861 709 False 569.000000 569 81.317000 2852 3592 1 chr6B.!!$F1 740
5 TraesCS2B01G093400 chr6A 446779149 446781665 2516 False 769.333333 1260 85.802000 1600 4272 3 chr6A.!!$F1 2672
6 TraesCS2B01G093400 chr7D 564574023 564574736 713 True 640.000000 640 82.930000 2852 3592 1 chr7D.!!$R1 740
7 TraesCS2B01G093400 chr7B 285344018 285344732 714 True 625.000000 625 82.527000 2852 3592 1 chr7B.!!$R1 740
8 TraesCS2B01G093400 chr3D 554225183 554225782 599 True 538.000000 538 82.927000 2926 3537 1 chr3D.!!$R2 611
9 TraesCS2B01G093400 chr3D 554178976 554179574 598 True 508.000000 508 82.085000 2926 3537 1 chr3D.!!$R1 611

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
707 1436 0.106967 CTTCCCTAGCAAAGCTCCCC 60.107 60.000 0.00 0.0 40.44 4.81 F
738 1467 0.387929 TCTCGGTCTGTTGCGAAACT 59.612 50.000 8.00 0.0 0.00 2.66 F
1160 1899 1.089920 GTGAGGCTGGCACACTATTG 58.910 55.000 21.16 0.0 36.31 1.90 F
1777 2520 1.572689 TACTCCCTCTCCTGCTCGGT 61.573 60.000 0.00 0.0 0.00 4.69 F
2919 3711 2.225467 GATGCTGGCAATAGGAAGGTC 58.775 52.381 0.00 0.0 0.00 3.85 F
3729 4529 2.309755 TGGTCTTTAGTACTCCCTCCGA 59.690 50.000 0.00 0.0 0.00 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2675 3453 0.248215 GCGTCCATTGATTTGCTCCG 60.248 55.000 0.00 0.00 0.00 4.63 R
2847 3639 6.765512 GCTTTATATTGATCTCAGCCCTATCC 59.234 42.308 0.00 0.00 0.00 2.59 R
2970 3762 1.487976 AGCTCTTGCCTTATAGCTGCA 59.512 47.619 1.02 0.00 43.46 4.41 R
3646 4446 3.229697 TCCTAGCTGCTAGATAGTGCA 57.770 47.619 32.56 8.78 36.26 4.57 R
4064 4865 0.321996 AACTTCTTCTCCCTGCCGAC 59.678 55.000 0.00 0.00 0.00 4.79 R
5145 6184 0.112412 GTTGGCCTTGGGAGGAAGAA 59.888 55.000 3.32 0.00 46.74 2.52 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
49 50 2.769652 ATCGCACAGGGCCAACACAT 62.770 55.000 6.18 0.00 40.31 3.21
56 57 1.481772 CAGGGCCAACACATTAATGGG 59.518 52.381 16.31 16.31 37.19 4.00
104 106 9.588096 AATTCTAGAAGGTTTTGGTCAAGTATT 57.412 29.630 11.53 0.00 0.00 1.89
197 199 9.050601 TGTTTTTCATAATGGTCCAATTGAAAC 57.949 29.630 19.16 13.56 34.03 2.78
211 213 7.066887 GTCCAATTGAAACAATCCCAAAACTTT 59.933 33.333 7.12 0.00 0.00 2.66
462 473 3.979101 TGCATCACTCAGTCCATAACA 57.021 42.857 0.00 0.00 0.00 2.41
634 1363 4.938832 GGGTTTCCGAAATTAAAATTGGGG 59.061 41.667 0.00 3.53 0.00 4.96
652 1381 1.066143 GGGAAAACCTCAGCTCGATCA 60.066 52.381 0.00 0.00 35.85 2.92
657 1386 2.593346 ACCTCAGCTCGATCATCAAC 57.407 50.000 0.00 0.00 0.00 3.18
704 1433 1.134250 CCCTCTTCCCTAGCAAAGCTC 60.134 57.143 0.00 0.00 40.44 4.09
705 1434 1.134250 CCTCTTCCCTAGCAAAGCTCC 60.134 57.143 0.00 0.00 40.44 4.70
706 1435 0.912486 TCTTCCCTAGCAAAGCTCCC 59.088 55.000 0.00 0.00 40.44 4.30
707 1436 0.106967 CTTCCCTAGCAAAGCTCCCC 60.107 60.000 0.00 0.00 40.44 4.81
708 1437 1.571773 TTCCCTAGCAAAGCTCCCCC 61.572 60.000 0.00 0.00 40.44 5.40
709 1438 2.190578 CCTAGCAAAGCTCCCCCG 59.809 66.667 0.00 0.00 40.44 5.73
718 1447 3.735097 GCTCCCCCGCCCCTTTTA 61.735 66.667 0.00 0.00 0.00 1.52
738 1467 0.387929 TCTCGGTCTGTTGCGAAACT 59.612 50.000 8.00 0.00 0.00 2.66
768 1497 1.956170 ACACGTGAGCCAGCGAAAG 60.956 57.895 25.01 0.00 0.00 2.62
818 1548 2.879907 GCTACACGAGCCCACGTA 59.120 61.111 0.00 0.00 46.41 3.57
856 1586 2.799540 GCGATCGGCGTTCTGTTCC 61.800 63.158 18.30 0.00 43.41 3.62
1160 1899 1.089920 GTGAGGCTGGCACACTATTG 58.910 55.000 21.16 0.00 36.31 1.90
1163 1902 2.162681 GAGGCTGGCACACTATTGTTT 58.837 47.619 3.38 0.00 31.66 2.83
1199 1938 5.372343 TGATGTTTACTGCCATCTGGTAT 57.628 39.130 0.00 0.00 38.59 2.73
1241 1980 7.257003 TGGATTTTGTTGTCATACATGTATGC 58.743 34.615 32.32 26.99 41.92 3.14
1366 2105 9.243637 TGTTTTTCTGTTTTCATATACACTTGC 57.756 29.630 0.00 0.00 0.00 4.01
1388 2127 9.791820 CTTGCTATGAAATGTCATTTTACATGA 57.208 29.630 12.04 0.19 42.03 3.07
1419 2158 5.437060 TCTGGAGAATGTATTTTACAGGGC 58.563 41.667 7.33 0.00 42.77 5.19
1420 2159 5.191722 TCTGGAGAATGTATTTTACAGGGCT 59.808 40.000 7.33 0.00 42.77 5.19
1421 2160 5.192927 TGGAGAATGTATTTTACAGGGCTG 58.807 41.667 0.00 0.00 42.77 4.85
1422 2161 5.045213 TGGAGAATGTATTTTACAGGGCTGA 60.045 40.000 0.00 0.00 42.77 4.26
1423 2162 6.064717 GGAGAATGTATTTTACAGGGCTGAT 58.935 40.000 0.00 0.00 42.77 2.90
1424 2163 6.547510 GGAGAATGTATTTTACAGGGCTGATT 59.452 38.462 0.00 0.00 42.77 2.57
1425 2164 7.255277 GGAGAATGTATTTTACAGGGCTGATTC 60.255 40.741 0.00 0.00 42.77 2.52
1426 2165 7.118723 AGAATGTATTTTACAGGGCTGATTCA 58.881 34.615 0.00 0.00 42.77 2.57
1427 2166 7.781693 AGAATGTATTTTACAGGGCTGATTCAT 59.218 33.333 0.00 0.00 42.77 2.57
1428 2167 6.698008 TGTATTTTACAGGGCTGATTCATG 57.302 37.500 0.00 0.00 34.06 3.07
1429 2168 4.660789 ATTTTACAGGGCTGATTCATGC 57.339 40.909 0.00 0.00 0.00 4.06
1521 2263 6.260271 GCAACATTTTCACCTAGTAGGATACC 59.740 42.308 23.50 0.00 44.47 2.73
1559 2301 5.625311 CAGCCATTTTAACTTTCGACTTGTC 59.375 40.000 0.00 0.00 0.00 3.18
1562 2304 7.015877 GCCATTTTAACTTTCGACTTGTCTAG 58.984 38.462 0.00 0.00 0.00 2.43
1567 2309 2.231721 ACTTTCGACTTGTCTAGAGCCC 59.768 50.000 0.00 0.00 0.00 5.19
1633 2375 5.627499 TGTTGCGAAAATATCAGCTTTCT 57.373 34.783 0.00 0.00 30.80 2.52
1777 2520 1.572689 TACTCCCTCTCCTGCTCGGT 61.573 60.000 0.00 0.00 0.00 4.69
2361 3119 3.071479 GTTCTGTGCGTTCCTATTTCCA 58.929 45.455 0.00 0.00 0.00 3.53
2675 3453 5.741388 AAATCCGATGTTCTGATGCTAAC 57.259 39.130 0.00 0.00 0.00 2.34
2847 3639 2.713976 CGCTTAAACTGACTTTTGTGCG 59.286 45.455 0.00 0.00 36.20 5.34
2919 3711 2.225467 GATGCTGGCAATAGGAAGGTC 58.775 52.381 0.00 0.00 0.00 3.85
2970 3762 2.358258 TGGAAAGGGAATCCAGAGGTT 58.642 47.619 0.09 0.00 41.98 3.50
3186 3981 8.082852 TCGTATAATGCTTCTAATCCTTCTGAC 58.917 37.037 0.00 0.00 0.00 3.51
3646 4446 7.665559 TCTCACAAGAAAAAGGTATGTTATGCT 59.334 33.333 0.00 0.00 0.00 3.79
3671 4471 5.622007 GCACTATCTAGCAGCTAGGAATGAG 60.622 48.000 26.28 17.94 35.03 2.90
3726 4526 5.046520 ACACATTGGTCTTTAGTACTCCCTC 60.047 44.000 0.00 0.00 0.00 4.30
3727 4527 4.470304 ACATTGGTCTTTAGTACTCCCTCC 59.530 45.833 0.00 0.00 0.00 4.30
3729 4529 2.309755 TGGTCTTTAGTACTCCCTCCGA 59.690 50.000 0.00 0.00 0.00 4.55
3733 4533 3.203710 TCTTTAGTACTCCCTCCGATCCA 59.796 47.826 0.00 0.00 0.00 3.41
3738 4538 4.753186 AGTACTCCCTCCGATCCATATTT 58.247 43.478 0.00 0.00 0.00 1.40
3845 4645 3.254903 TCCCGTGGATTCGATAGTATGTG 59.745 47.826 0.00 0.00 37.40 3.21
3846 4646 3.005472 CCCGTGGATTCGATAGTATGTGT 59.995 47.826 0.00 0.00 37.40 3.72
4114 4915 3.087031 CTCCATGGTGAAGTCTGCAAAT 58.913 45.455 12.58 0.00 0.00 2.32
4247 5213 2.305927 TCAAAGCCCGAGGAGAGAAATT 59.694 45.455 0.00 0.00 0.00 1.82
4263 5253 4.085009 AGAAATTCTTCAAAGCCTGAGGG 58.915 43.478 0.00 0.00 34.81 4.30
4290 5280 1.821061 CGCTGACAACTCCCTGGTCT 61.821 60.000 0.00 0.00 32.84 3.85
4322 5312 2.744202 CCCGAGGACATGCATATAAAGC 59.256 50.000 0.00 0.00 0.00 3.51
4390 5380 7.859325 GGTGATACCAACAGCTTCTAATTTA 57.141 36.000 0.00 0.00 38.42 1.40
4463 5453 3.169099 CCTGATCTCCCTCCGTTCATAT 58.831 50.000 0.00 0.00 0.00 1.78
4467 5457 5.144832 TGATCTCCCTCCGTTCATATGTTA 58.855 41.667 1.90 0.00 0.00 2.41
4477 5467 9.104965 CCTCCGTTCATATGTTATCAGTTTTTA 57.895 33.333 1.90 0.00 0.00 1.52
4587 5622 2.028203 TCTGGATTGATCGACTGCAACA 60.028 45.455 0.00 0.00 0.00 3.33
4629 5664 2.762887 TGACATGCAACCCACTTTGAAA 59.237 40.909 0.00 0.00 0.00 2.69
4873 5908 6.773976 TGAAACTTTTCACAAGGATGACTT 57.226 33.333 0.07 0.00 41.88 3.01
4882 5917 1.747444 AAGGATGACTTGGTGAGGGT 58.253 50.000 0.00 0.00 38.21 4.34
4886 5921 3.200825 AGGATGACTTGGTGAGGGTAATG 59.799 47.826 0.00 0.00 0.00 1.90
4887 5922 3.199946 GGATGACTTGGTGAGGGTAATGA 59.800 47.826 0.00 0.00 0.00 2.57
4891 5926 3.769844 GACTTGGTGAGGGTAATGAGAGA 59.230 47.826 0.00 0.00 0.00 3.10
4894 5929 5.964477 ACTTGGTGAGGGTAATGAGAGATTA 59.036 40.000 0.00 0.00 0.00 1.75
4919 5954 4.725556 TTGACAACGTTGTAGCAGATTC 57.274 40.909 32.39 17.98 42.43 2.52
4926 5961 4.632153 ACGTTGTAGCAGATTCAAGAACT 58.368 39.130 0.00 0.00 0.00 3.01
4963 5998 0.677731 TTCATTTCTGCCAGGCTCCG 60.678 55.000 14.15 1.01 0.00 4.63
5007 6042 5.183713 CAGTCTTGGCCACAAATTCAAGATA 59.816 40.000 3.88 0.00 44.61 1.98
5034 6069 3.261897 TCCTAAAGAACTGCTCCCTTCAG 59.738 47.826 0.00 0.00 37.56 3.02
5037 6072 4.379302 AAAGAACTGCTCCCTTCAGATT 57.621 40.909 0.00 0.00 35.61 2.40
5038 6073 3.347077 AGAACTGCTCCCTTCAGATTG 57.653 47.619 0.00 0.00 35.61 2.67
5047 6082 4.035675 GCTCCCTTCAGATTGGAATAAACG 59.964 45.833 0.00 0.00 0.00 3.60
5093 6128 7.177568 TCCCAAATTTAGCTAGCAAAACATGTA 59.822 33.333 18.83 0.00 0.00 2.29
5101 6140 7.864108 AGCTAGCAAAACATGTATATTCACA 57.136 32.000 18.83 0.00 0.00 3.58
5138 6177 9.872757 TTAGAAACTTCATTCAACAACGAATAC 57.127 29.630 0.00 0.00 33.82 1.89
5139 6178 8.154649 AGAAACTTCATTCAACAACGAATACT 57.845 30.769 0.00 0.00 33.82 2.12
5140 6179 8.621286 AGAAACTTCATTCAACAACGAATACTT 58.379 29.630 0.00 0.00 33.82 2.24
5141 6180 8.782533 AAACTTCATTCAACAACGAATACTTC 57.217 30.769 0.00 0.00 33.82 3.01
5142 6181 7.730364 ACTTCATTCAACAACGAATACTTCT 57.270 32.000 0.00 0.00 33.82 2.85
5143 6182 8.154649 ACTTCATTCAACAACGAATACTTCTT 57.845 30.769 0.00 0.00 33.82 2.52
5144 6183 8.283291 ACTTCATTCAACAACGAATACTTCTTC 58.717 33.333 0.00 0.00 33.82 2.87
5145 6184 7.962964 TCATTCAACAACGAATACTTCTTCT 57.037 32.000 0.00 0.00 33.82 2.85
5146 6185 8.378172 TCATTCAACAACGAATACTTCTTCTT 57.622 30.769 0.00 0.00 33.82 2.52
5147 6186 8.495949 TCATTCAACAACGAATACTTCTTCTTC 58.504 33.333 0.00 0.00 33.82 2.87
5148 6187 8.499162 CATTCAACAACGAATACTTCTTCTTCT 58.501 33.333 0.00 0.00 33.82 2.85
5149 6188 8.433421 TTCAACAACGAATACTTCTTCTTCTT 57.567 30.769 0.00 0.00 0.00 2.52
5150 6189 8.073355 TCAACAACGAATACTTCTTCTTCTTC 57.927 34.615 0.00 0.00 0.00 2.87
5151 6190 7.170998 TCAACAACGAATACTTCTTCTTCTTCC 59.829 37.037 0.00 0.00 0.00 3.46
5152 6191 6.760291 ACAACGAATACTTCTTCTTCTTCCT 58.240 36.000 0.00 0.00 0.00 3.36
5153 6192 6.869388 ACAACGAATACTTCTTCTTCTTCCTC 59.131 38.462 0.00 0.00 0.00 3.71
5154 6193 5.968254 ACGAATACTTCTTCTTCTTCCTCC 58.032 41.667 0.00 0.00 0.00 4.30
5155 6194 5.105269 ACGAATACTTCTTCTTCTTCCTCCC 60.105 44.000 0.00 0.00 0.00 4.30
5156 6195 5.105310 CGAATACTTCTTCTTCTTCCTCCCA 60.105 44.000 0.00 0.00 0.00 4.37
5157 6196 6.574465 CGAATACTTCTTCTTCTTCCTCCCAA 60.574 42.308 0.00 0.00 0.00 4.12
5158 6197 4.632327 ACTTCTTCTTCTTCCTCCCAAG 57.368 45.455 0.00 0.00 0.00 3.61
5159 6198 3.329225 ACTTCTTCTTCTTCCTCCCAAGG 59.671 47.826 0.00 0.00 44.89 3.61
5160 6199 1.630878 TCTTCTTCTTCCTCCCAAGGC 59.369 52.381 0.00 0.00 43.02 4.35
5161 6200 0.698818 TTCTTCTTCCTCCCAAGGCC 59.301 55.000 0.00 0.00 43.02 5.19
5162 6201 0.475632 TCTTCTTCCTCCCAAGGCCA 60.476 55.000 5.01 0.00 43.02 5.36
5163 6202 0.405585 CTTCTTCCTCCCAAGGCCAA 59.594 55.000 5.01 0.00 43.02 4.52
5164 6203 0.112412 TTCTTCCTCCCAAGGCCAAC 59.888 55.000 5.01 0.00 43.02 3.77
5165 6204 1.675641 CTTCCTCCCAAGGCCAACG 60.676 63.158 5.01 0.00 43.02 4.10
5166 6205 3.860930 TTCCTCCCAAGGCCAACGC 62.861 63.158 5.01 0.00 43.02 4.84
5167 6206 4.659172 CCTCCCAAGGCCAACGCA 62.659 66.667 5.01 0.00 35.37 5.24
5168 6207 3.365265 CTCCCAAGGCCAACGCAC 61.365 66.667 5.01 0.00 36.38 5.34
5254 6293 4.101448 CTGCCCTCCCCGGAACTG 62.101 72.222 0.73 0.00 33.16 3.16
5257 6296 3.787001 CCCTCCCCGGAACTGCTC 61.787 72.222 0.73 0.00 33.16 4.26
5258 6297 3.787001 CCTCCCCGGAACTGCTCC 61.787 72.222 0.73 0.00 41.40 4.70
5259 6298 3.787001 CTCCCCGGAACTGCTCCC 61.787 72.222 0.73 0.00 41.87 4.30
5262 6301 4.410400 CCCGGAACTGCTCCCCAC 62.410 72.222 0.73 0.00 41.87 4.61
5263 6302 3.636231 CCGGAACTGCTCCCCACA 61.636 66.667 0.00 0.00 41.87 4.17
5264 6303 2.046892 CGGAACTGCTCCCCACAG 60.047 66.667 0.00 0.00 41.87 3.66
5265 6304 2.360475 GGAACTGCTCCCCACAGC 60.360 66.667 0.00 0.00 38.44 4.40
5266 6305 2.360475 GAACTGCTCCCCACAGCC 60.360 66.667 0.00 0.00 38.80 4.85
5267 6306 4.335647 AACTGCTCCCCACAGCCG 62.336 66.667 0.00 0.00 38.80 5.52
5272 6311 3.322466 CTCCCCACAGCCGGTCTT 61.322 66.667 1.90 0.00 0.00 3.01
5273 6312 3.612247 CTCCCCACAGCCGGTCTTG 62.612 68.421 1.90 1.89 0.00 3.02
5276 6315 4.641645 CCACAGCCGGTCTTGCCA 62.642 66.667 1.90 0.00 36.97 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.035439 AATGCGACGAATTGGACCCT 60.035 50.000 0.00 0.00 0.00 4.34
56 57 2.257409 TAGCAGCTAGTTGGGCCAGC 62.257 60.000 13.09 13.09 35.49 4.85
57 58 0.462759 GTAGCAGCTAGTTGGGCCAG 60.463 60.000 6.23 0.00 0.00 4.85
153 155 9.467796 TGAAAAACATAAAAACCCAGGAAAAAT 57.532 25.926 0.00 0.00 0.00 1.82
462 473 2.398554 CGCCGCATTGGTACTGCTT 61.399 57.895 4.32 0.00 41.21 3.91
568 1166 2.099405 CCTAAAACGCCCAATCATGGT 58.901 47.619 0.00 0.00 46.01 3.55
634 1363 3.525537 TGATGATCGAGCTGAGGTTTTC 58.474 45.455 0.90 0.00 0.00 2.29
704 1433 1.150764 GAGATAAAAGGGGCGGGGG 59.849 63.158 0.00 0.00 0.00 5.40
705 1434 1.227853 CGAGATAAAAGGGGCGGGG 60.228 63.158 0.00 0.00 0.00 5.73
706 1435 1.227853 CCGAGATAAAAGGGGCGGG 60.228 63.158 0.00 0.00 35.42 6.13
707 1436 0.532196 GACCGAGATAAAAGGGGCGG 60.532 60.000 0.00 0.00 43.95 6.13
708 1437 0.464452 AGACCGAGATAAAAGGGGCG 59.536 55.000 0.00 0.00 30.95 6.13
709 1438 1.209747 ACAGACCGAGATAAAAGGGGC 59.790 52.381 0.00 0.00 0.00 5.80
718 1447 1.000955 AGTTTCGCAACAGACCGAGAT 59.999 47.619 0.00 0.00 35.05 2.75
738 1467 4.988716 ACGTGTGAGGCGGAGGGA 62.989 66.667 0.00 0.00 0.00 4.20
768 1497 3.426568 GCGGTCAGAGCAGGTTGC 61.427 66.667 0.00 0.00 45.46 4.17
773 1502 4.803426 GGGACGCGGTCAGAGCAG 62.803 72.222 12.47 0.00 33.68 4.24
793 1522 3.778000 CTCGTGTAGCTGCTGCAG 58.222 61.111 24.80 24.80 42.74 4.41
813 1543 2.049802 AAGGCGTCCACGTACGTG 60.050 61.111 35.57 35.57 44.64 4.49
814 1544 2.192608 GAGAAGGCGTCCACGTACGT 62.193 60.000 16.72 16.72 44.64 3.57
815 1545 1.513586 GAGAAGGCGTCCACGTACG 60.514 63.158 15.01 15.01 45.58 3.67
816 1546 1.153881 GGAGAAGGCGTCCACGTAC 60.154 63.158 0.36 0.00 42.22 3.67
817 1547 1.303888 AGGAGAAGGCGTCCACGTA 60.304 57.895 0.36 0.00 42.22 3.57
818 1548 2.600769 AGGAGAAGGCGTCCACGT 60.601 61.111 0.36 0.00 42.22 4.49
856 1586 2.956964 GATCGTCGCCGCAGAAGG 60.957 66.667 0.00 0.00 0.00 3.46
1025 1764 1.828768 CCAGATCTGCTCCACCTCC 59.171 63.158 17.76 0.00 0.00 4.30
1034 1773 4.148825 ACGGACCGCCAGATCTGC 62.149 66.667 17.76 11.60 0.00 4.26
1199 1938 7.888021 ACAAAATCCATGTTGGTAAGATCAGTA 59.112 33.333 0.00 0.00 39.03 2.74
1241 1980 3.441222 TGTCTGCCAAATTAGTCTGCATG 59.559 43.478 0.00 0.00 0.00 4.06
1304 2043 8.049117 AGATCAAGCAAATAAGAATGGTGAGTA 58.951 33.333 0.00 0.00 0.00 2.59
1404 2143 6.239120 GCATGAATCAGCCCTGTAAAATACAT 60.239 38.462 0.00 0.00 38.15 2.29
1559 2301 5.941555 TTTCTCCTTTTCTAGGGCTCTAG 57.058 43.478 15.01 15.01 44.86 2.43
1562 2304 6.209589 ACAAAATTTCTCCTTTTCTAGGGCTC 59.790 38.462 0.00 0.00 44.86 4.70
1594 2336 8.819152 TTCGCAACAAATTTGAAATTCTTTTC 57.181 26.923 24.64 0.63 41.39 2.29
1625 2367 6.166279 TGTGAGTATTCCTGTTAGAAAGCTG 58.834 40.000 0.00 0.00 0.00 4.24
1633 2375 5.305902 TCTGTGGTTGTGAGTATTCCTGTTA 59.694 40.000 0.00 0.00 0.00 2.41
2349 3106 5.016831 ACCCAGATGTTTGGAAATAGGAAC 58.983 41.667 0.00 0.00 40.87 3.62
2399 3157 5.901276 AGGTGATGATTTAATGCTGGGATTT 59.099 36.000 0.00 0.00 0.00 2.17
2400 3158 5.303589 CAGGTGATGATTTAATGCTGGGATT 59.696 40.000 0.00 0.00 0.00 3.01
2401 3159 4.831155 CAGGTGATGATTTAATGCTGGGAT 59.169 41.667 0.00 0.00 0.00 3.85
2675 3453 0.248215 GCGTCCATTGATTTGCTCCG 60.248 55.000 0.00 0.00 0.00 4.63
2847 3639 6.765512 GCTTTATATTGATCTCAGCCCTATCC 59.234 42.308 0.00 0.00 0.00 2.59
2919 3711 7.470424 GCATAAGGCTCTCTATCTATCCATCTG 60.470 44.444 0.00 0.00 40.25 2.90
2970 3762 1.487976 AGCTCTTGCCTTATAGCTGCA 59.512 47.619 1.02 0.00 43.46 4.41
3169 3964 5.091261 TCAAGGTCAGAAGGATTAGAAGC 57.909 43.478 0.00 0.00 0.00 3.86
3646 4446 3.229697 TCCTAGCTGCTAGATAGTGCA 57.770 47.619 32.56 8.78 36.26 4.57
3726 4526 6.918892 TTGGCGATAATAAATATGGATCGG 57.081 37.500 14.69 3.62 39.74 4.18
3780 4580 8.375493 TCTACTTCCTCCAACACATATTAACT 57.625 34.615 0.00 0.00 0.00 2.24
3790 4590 9.832445 GTATGATATTTTCTACTTCCTCCAACA 57.168 33.333 0.00 0.00 0.00 3.33
3955 4756 6.370442 CCGTTAAGAGGTGAAACATGTAATCA 59.630 38.462 0.00 4.32 39.98 2.57
4064 4865 0.321996 AACTTCTTCTCCCTGCCGAC 59.678 55.000 0.00 0.00 0.00 4.79
4066 4867 2.762535 TAAACTTCTTCTCCCTGCCG 57.237 50.000 0.00 0.00 0.00 5.69
4114 4915 3.529341 ATTGCACGGACCAGCGACA 62.529 57.895 0.00 0.00 0.00 4.35
4174 4975 5.468540 TCATCGACTTTTCTTTCCTCTGA 57.531 39.130 0.00 0.00 0.00 3.27
4247 5213 1.279271 GCTACCCTCAGGCTTTGAAGA 59.721 52.381 0.00 0.00 34.81 2.87
4322 5312 9.125026 ACCATGAATCCTAAATAGCTTAACAAG 57.875 33.333 0.00 0.00 0.00 3.16
4390 5380 8.039603 TCTAGATGTTACGCAATTGAACAATT 57.960 30.769 10.34 6.91 41.33 2.32
4477 5467 8.164070 ACTTCTCCAACTAAAATAACAGATGGT 58.836 33.333 0.00 0.00 36.42 3.55
4587 5622 7.161404 TGTCACAAGTAGATGTAAAGAATGCT 58.839 34.615 0.00 0.00 30.84 3.79
4629 5664 7.781324 ACATCCCAACTCTTTTATGTCATTT 57.219 32.000 0.00 0.00 0.00 2.32
4825 5860 6.696411 TGGAAGTTTTTCTCTTTTGCTGAAA 58.304 32.000 0.00 0.00 33.68 2.69
4873 5908 4.654262 GGTAATCTCTCATTACCCTCACCA 59.346 45.833 11.14 0.00 44.73 4.17
4882 5917 7.383687 ACGTTGTCAAAGGTAATCTCTCATTA 58.616 34.615 3.52 0.00 32.76 1.90
4886 5921 5.465724 ACAACGTTGTCAAAGGTAATCTCTC 59.534 40.000 27.70 0.00 36.50 3.20
4887 5922 5.365619 ACAACGTTGTCAAAGGTAATCTCT 58.634 37.500 27.70 0.00 36.50 3.10
4891 5926 4.817464 TGCTACAACGTTGTCAAAGGTAAT 59.183 37.500 35.40 11.29 42.35 1.89
4894 5929 2.612212 CTGCTACAACGTTGTCAAAGGT 59.388 45.455 35.40 13.52 42.35 3.50
4919 5954 3.817647 CCTTCAAGTCTCCCAAGTTCTTG 59.182 47.826 5.66 5.66 37.14 3.02
4926 5961 3.045634 TGAACTCCTTCAAGTCTCCCAA 58.954 45.455 0.00 0.00 33.20 4.12
4963 5998 5.186198 ACTGGACACATATTTAAGACCTGC 58.814 41.667 0.00 0.00 0.00 4.85
5007 6042 3.549794 GGAGCAGTTCTTTAGGATGCAT 58.450 45.455 0.00 0.00 39.34 3.96
5069 6104 8.931385 ATACATGTTTTGCTAGCTAAATTTGG 57.069 30.769 23.72 16.48 0.00 3.28
5138 6177 3.871851 GCCTTGGGAGGAAGAAGAAGAAG 60.872 52.174 0.00 0.00 46.74 2.85
5139 6178 2.040412 GCCTTGGGAGGAAGAAGAAGAA 59.960 50.000 0.00 0.00 46.74 2.52
5140 6179 1.630878 GCCTTGGGAGGAAGAAGAAGA 59.369 52.381 0.00 0.00 46.74 2.87
5141 6180 1.340502 GGCCTTGGGAGGAAGAAGAAG 60.341 57.143 0.00 0.00 46.74 2.85
5142 6181 0.698818 GGCCTTGGGAGGAAGAAGAA 59.301 55.000 0.00 0.00 46.74 2.52
5143 6182 0.475632 TGGCCTTGGGAGGAAGAAGA 60.476 55.000 3.32 0.00 46.74 2.87
5144 6183 0.405585 TTGGCCTTGGGAGGAAGAAG 59.594 55.000 3.32 0.00 46.74 2.85
5145 6184 0.112412 GTTGGCCTTGGGAGGAAGAA 59.888 55.000 3.32 0.00 46.74 2.52
5146 6185 1.767692 GTTGGCCTTGGGAGGAAGA 59.232 57.895 3.32 0.00 46.74 2.87
5147 6186 1.675641 CGTTGGCCTTGGGAGGAAG 60.676 63.158 3.32 0.00 46.74 3.46
5148 6187 2.434331 CGTTGGCCTTGGGAGGAA 59.566 61.111 3.32 0.00 46.74 3.36
5149 6188 4.344865 GCGTTGGCCTTGGGAGGA 62.345 66.667 3.32 0.00 46.74 3.71
5150 6189 4.659172 TGCGTTGGCCTTGGGAGG 62.659 66.667 3.32 0.00 46.50 4.30
5151 6190 3.365265 GTGCGTTGGCCTTGGGAG 61.365 66.667 3.32 0.00 38.85 4.30
5237 6276 4.101448 CAGTTCCGGGGAGGGCAG 62.101 72.222 0.00 0.00 41.52 4.85
5240 6279 3.787001 GAGCAGTTCCGGGGAGGG 61.787 72.222 0.00 0.00 41.52 4.30
5241 6280 3.787001 GGAGCAGTTCCGGGGAGG 61.787 72.222 0.00 0.00 42.97 4.30
5248 6287 2.360475 GCTGTGGGGAGCAGTTCC 60.360 66.667 0.00 0.00 46.00 3.62
5249 6288 2.360475 GGCTGTGGGGAGCAGTTC 60.360 66.667 0.00 0.00 41.08 3.01
5250 6289 4.335647 CGGCTGTGGGGAGCAGTT 62.336 66.667 0.00 0.00 41.08 3.16
5255 6294 3.322466 AAGACCGGCTGTGGGGAG 61.322 66.667 0.00 0.00 0.00 4.30
5256 6295 3.636231 CAAGACCGGCTGTGGGGA 61.636 66.667 0.00 0.00 0.00 4.81
5259 6298 4.641645 TGGCAAGACCGGCTGTGG 62.642 66.667 0.00 0.00 43.94 4.17


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

AutoCloner maintained by Alex Coulton.