Multiple sequence alignment - TraesCS3D01G345700

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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 TraesCS3D01G345700 chr3D 100.000 6189 0 0 1 6189 457090724 457096912 0.000000e+00 11430.0
1 TraesCS3D01G345700 chr3A 94.306 5093 204 40 654 5698 600004120 600009174 0.000000e+00 7720.0
2 TraesCS3D01G345700 chr3A 88.594 377 35 2 5813 6189 600009286 600009654 9.460000e-123 451.0
3 TraesCS3D01G345700 chr3A 90.164 183 18 0 1 183 600003607 600003789 8.020000e-59 239.0
4 TraesCS3D01G345700 chr3A 100.000 31 0 0 529 559 708095182 708095212 2.410000e-04 58.4
5 TraesCS3D01G345700 chr3B 91.858 3230 187 42 653 3833 603855741 603858943 0.000000e+00 4438.0
6 TraesCS3D01G345700 chr3B 95.147 1875 82 8 3826 5695 603859121 603860991 0.000000e+00 2950.0
7 TraesCS3D01G345700 chr3B 89.952 418 34 1 5771 6188 603861011 603861420 3.280000e-147 532.0
8 TraesCS3D01G345700 chr3B 79.097 421 62 11 5775 6186 78706126 78705723 3.680000e-67 267.0
9 TraesCS3D01G345700 chr5B 89.507 934 77 15 1 924 700911518 700910596 0.000000e+00 1162.0
10 TraesCS3D01G345700 chr4B 77.712 507 70 27 5699 6189 605403075 605403554 2.840000e-68 270.0
11 TraesCS3D01G345700 chr7A 76.667 240 35 11 5957 6178 45069683 45069919 5.070000e-21 113.0
12 TraesCS3D01G345700 chr7A 76.250 240 36 11 5957 6178 45022865 45023101 2.360000e-19 108.0
13 TraesCS3D01G345700 chr7A 83.486 109 14 3 6072 6178 44899878 44899984 1.420000e-16 99.0


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 TraesCS3D01G345700 chr3D 457090724 457096912 6188 False 11430.000000 11430 100.000000 1 6189 1 chr3D.!!$F1 6188
1 TraesCS3D01G345700 chr3A 600003607 600009654 6047 False 2803.333333 7720 91.021333 1 6189 3 chr3A.!!$F2 6188
2 TraesCS3D01G345700 chr3B 603855741 603861420 5679 False 2640.000000 4438 92.319000 653 6188 3 chr3B.!!$F1 5535
3 TraesCS3D01G345700 chr5B 700910596 700911518 922 True 1162.000000 1162 89.507000 1 924 1 chr5B.!!$R1 923

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
820 921 0.395862 CGCCTCCTCCTTCTCCAGTA 60.396 60.000 0.0 0.0 0.00 2.74 F
1665 1794 0.811616 CAGGGCTGCTGAATCCGTAC 60.812 60.000 0.0 0.0 0.00 3.67 F
2151 2292 0.238289 CCGTGCTTGAGTGCGATTTT 59.762 50.000 0.0 0.0 35.36 1.82 F
2153 2294 1.195448 CGTGCTTGAGTGCGATTTTCT 59.805 47.619 0.0 0.0 35.36 2.52 F
3171 3336 1.486310 ACTGAATATCTTGGCTCGGCA 59.514 47.619 0.0 0.0 0.00 5.69 F
5149 5512 0.398318 GGAAGAGACCAACAGCCAGT 59.602 55.000 0.0 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 2046 0.801872 CATTTCCGGCGTGTTCATGA 59.198 50.000 6.01 0.0 0.00 3.07 R
2667 2830 1.068610 TGCAAGACGGTAAGCATTTGC 60.069 47.619 0.00 0.0 40.81 3.68 R
3171 3336 1.251251 GGACAACCTTGCTGAATGCT 58.749 50.000 0.00 0.0 43.37 3.79 R
4085 4443 9.784531 CTTGATAAGGATATTCTCTGGCTTTAA 57.215 33.333 0.00 0.0 0.00 1.52 R
5155 5518 0.905357 AAAGCCACGGATGCTCTAGT 59.095 50.000 0.00 0.0 38.34 2.57 R
6056 6463 4.597004 AGATTGATGCCAAGATGTTGAGT 58.403 39.130 3.74 0.0 35.46 3.41 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
41 42 6.872547 TGCATGCTTTTGTTATATGCTTCAAA 59.127 30.769 20.33 0.00 43.29 2.69
184 185 5.907866 CCCGTGGGTGAATAGTAAATTTT 57.092 39.130 0.00 0.00 0.00 1.82
185 186 6.275494 CCCGTGGGTGAATAGTAAATTTTT 57.725 37.500 0.00 0.00 0.00 1.94
252 254 4.470462 GAAGATGTTTGAGTGTGTGATGC 58.530 43.478 0.00 0.00 0.00 3.91
253 255 2.816087 AGATGTTTGAGTGTGTGATGCC 59.184 45.455 0.00 0.00 0.00 4.40
254 256 1.317613 TGTTTGAGTGTGTGATGCCC 58.682 50.000 0.00 0.00 0.00 5.36
270 272 1.135257 TGCCCGTGCCAAATTTTATCG 60.135 47.619 0.00 0.00 36.33 2.92
273 275 2.094957 CCCGTGCCAAATTTTATCGTGT 60.095 45.455 0.00 0.00 0.00 4.49
291 293 3.364964 CGTGTTTGGACATTTGAGTAGCC 60.365 47.826 0.00 0.00 38.23 3.93
292 294 3.821033 GTGTTTGGACATTTGAGTAGCCT 59.179 43.478 0.00 0.00 38.23 4.58
325 327 8.383175 AGAAAGATAAATTTAGGGTGTGTGAGA 58.617 33.333 3.94 0.00 0.00 3.27
333 335 8.706322 AATTTAGGGTGTGTGAGAAAGTTTAT 57.294 30.769 0.00 0.00 0.00 1.40
352 356 2.758770 TAGTGCGCACTGTTCGGACC 62.759 60.000 44.69 15.88 46.98 4.46
359 363 1.136057 GCACTGTTCGGACCGATTTTC 60.136 52.381 19.12 9.37 35.23 2.29
370 375 4.378459 CGGACCGATTTTCTCTTTTTCCAG 60.378 45.833 8.64 0.00 0.00 3.86
403 410 6.420306 TGATGTCCGAACACATTGAAATTTTG 59.580 34.615 0.00 0.00 37.11 2.44
526 534 6.060788 GCCTGGACTCAGAATTGAATATTCT 58.939 40.000 16.24 0.00 43.49 2.40
565 573 2.020836 GACAAGATTACCGCGTGCCG 62.021 60.000 4.92 0.00 0.00 5.69
602 614 7.778853 TCTCTCTCCGTCCCATAATATAATACC 59.221 40.741 0.00 0.00 0.00 2.73
633 645 8.782533 ATTTTTGACAGAAACGTTCTTACATC 57.217 30.769 0.00 0.00 38.11 3.06
640 652 5.586243 CAGAAACGTTCTTACATCATGGGAT 59.414 40.000 0.00 0.00 38.11 3.85
644 656 5.496556 ACGTTCTTACATCATGGGATTGAA 58.503 37.500 0.00 0.00 0.00 2.69
661 760 8.167392 TGGGATTGAAAGAGTAGTCCAAATTAA 58.833 33.333 0.00 0.00 0.00 1.40
668 767 5.411781 AGAGTAGTCCAAATTAAGTGAGCG 58.588 41.667 0.00 0.00 0.00 5.03
675 774 3.425193 CCAAATTAAGTGAGCGTTTGTGC 59.575 43.478 0.00 0.00 0.00 4.57
676 775 3.980646 AATTAAGTGAGCGTTTGTGCA 57.019 38.095 0.00 0.00 37.31 4.57
677 776 3.980646 ATTAAGTGAGCGTTTGTGCAA 57.019 38.095 0.00 0.00 37.31 4.08
678 777 3.980646 TTAAGTGAGCGTTTGTGCAAT 57.019 38.095 0.00 0.00 37.31 3.56
680 779 5.621197 TTAAGTGAGCGTTTGTGCAATAT 57.379 34.783 0.00 0.00 37.31 1.28
681 780 3.747099 AGTGAGCGTTTGTGCAATATC 57.253 42.857 0.00 0.00 37.31 1.63
682 781 2.094258 AGTGAGCGTTTGTGCAATATCG 59.906 45.455 0.00 0.00 37.31 2.92
685 784 1.401552 AGCGTTTGTGCAATATCGCAT 59.598 42.857 22.36 10.21 45.26 4.73
686 785 1.775208 GCGTTTGTGCAATATCGCATC 59.225 47.619 17.93 0.00 45.26 3.91
687 786 2.790812 GCGTTTGTGCAATATCGCATCA 60.791 45.455 17.93 0.00 45.26 3.07
688 787 3.031126 CGTTTGTGCAATATCGCATCAG 58.969 45.455 0.00 0.00 45.26 2.90
692 792 1.538512 GTGCAATATCGCATCAGCCAT 59.461 47.619 0.00 0.00 45.26 4.40
718 818 3.578688 GCTGAAACACAATTAAGGCAGG 58.421 45.455 0.00 0.00 0.00 4.85
816 917 2.776913 CGTCGCCTCCTCCTTCTCC 61.777 68.421 0.00 0.00 0.00 3.71
817 918 1.682684 GTCGCCTCCTCCTTCTCCA 60.683 63.158 0.00 0.00 0.00 3.86
818 919 1.380515 TCGCCTCCTCCTTCTCCAG 60.381 63.158 0.00 0.00 0.00 3.86
819 920 1.684049 CGCCTCCTCCTTCTCCAGT 60.684 63.158 0.00 0.00 0.00 4.00
820 921 0.395862 CGCCTCCTCCTTCTCCAGTA 60.396 60.000 0.00 0.00 0.00 2.74
821 922 1.408969 GCCTCCTCCTTCTCCAGTAG 58.591 60.000 0.00 0.00 0.00 2.57
920 1040 2.680913 AATGGCGACGCAACTGCTC 61.681 57.895 23.09 2.35 39.32 4.26
1139 1263 2.738521 CGCCGCATTAGATCCCCG 60.739 66.667 0.00 0.00 0.00 5.73
1325 1449 3.952799 AACCCCTCCTCCTCCTGGC 62.953 68.421 0.00 0.00 0.00 4.85
1342 1466 3.728373 CCCCCTCCCTGTTTCCGG 61.728 72.222 0.00 0.00 0.00 5.14
1467 1592 7.364522 TCTTCTTGGACGATTTTCATACTTG 57.635 36.000 0.00 0.00 0.00 3.16
1469 1594 4.394920 TCTTGGACGATTTTCATACTTGCC 59.605 41.667 0.00 0.00 0.00 4.52
1470 1595 3.680490 TGGACGATTTTCATACTTGCCA 58.320 40.909 0.00 0.00 0.00 4.92
1553 1678 2.988493 CCAATGCCTGTCACAAAATTCG 59.012 45.455 0.00 0.00 0.00 3.34
1555 1683 3.559238 ATGCCTGTCACAAAATTCGAC 57.441 42.857 0.00 0.00 0.00 4.20
1561 1689 2.105821 TGTCACAAAATTCGACCTCCCT 59.894 45.455 0.00 0.00 0.00 4.20
1567 1695 0.831307 AATTCGACCTCCCTGCCTAC 59.169 55.000 0.00 0.00 0.00 3.18
1586 1714 0.884514 CTCGAGTGCTCTGTTCTCCA 59.115 55.000 3.62 0.00 0.00 3.86
1620 1748 8.787852 GGAGATTTTATCATAATTCTGACCCAC 58.212 37.037 0.00 0.00 0.00 4.61
1650 1779 4.144297 TGTTTCTGTTTCTTGGATCAGGG 58.856 43.478 0.00 0.00 0.00 4.45
1662 1791 0.883814 GATCAGGGCTGCTGAATCCG 60.884 60.000 0.00 0.00 34.26 4.18
1665 1794 0.811616 CAGGGCTGCTGAATCCGTAC 60.812 60.000 0.00 0.00 0.00 3.67
1743 1872 1.446099 CACAGCACGCCAGTACGAT 60.446 57.895 0.00 0.00 36.70 3.73
1809 1938 0.912487 TCTTCCATACCAAGCCGGGT 60.912 55.000 0.00 0.00 45.10 5.28
1884 2025 1.204312 GGCAGAAACGTTCGTGCTC 59.796 57.895 25.45 16.14 35.54 4.26
1920 2061 2.431771 CGTCATGAACACGCCGGA 60.432 61.111 5.05 0.00 0.00 5.14
1941 2082 3.626924 GACGGCTGTGAGGGGTGT 61.627 66.667 0.80 0.00 0.00 4.16
1955 2096 1.374252 GGTGTGCCGAGGTGTACAG 60.374 63.158 0.00 0.00 0.00 2.74
1975 2116 4.724602 GCTCGTCACCGCTCTGCA 62.725 66.667 0.00 0.00 0.00 4.41
2001 2142 2.046217 GCCGGGGGACTCAAGAAC 60.046 66.667 2.18 0.00 0.00 3.01
2065 2206 5.070446 GTGTATGGGAGGTACAAGATCATGA 59.930 44.000 4.68 0.00 34.15 3.07
2131 2272 1.767681 AGATGAAGCAGAGTGGGGATC 59.232 52.381 0.00 0.00 0.00 3.36
2133 2274 1.274703 TGAAGCAGAGTGGGGATCCC 61.275 60.000 23.95 23.95 45.71 3.85
2151 2292 0.238289 CCGTGCTTGAGTGCGATTTT 59.762 50.000 0.00 0.00 35.36 1.82
2153 2294 1.195448 CGTGCTTGAGTGCGATTTTCT 59.805 47.619 0.00 0.00 35.36 2.52
2158 2299 3.666374 GCTTGAGTGCGATTTTCTGACAG 60.666 47.826 0.00 0.00 0.00 3.51
2178 2319 2.428890 AGATTCTGGGCAAGTAGACGAG 59.571 50.000 0.00 0.00 31.20 4.18
2181 2322 2.886124 GGGCAAGTAGACGAGCGC 60.886 66.667 0.00 0.00 0.00 5.92
2182 2323 2.182030 GGCAAGTAGACGAGCGCT 59.818 61.111 11.27 11.27 0.00 5.92
2387 2535 4.484912 GATCTAATGTAGAGGGGGAGTGT 58.515 47.826 0.00 0.00 38.38 3.55
2488 2636 5.006941 GCCATTTTGCAAATATACAAGGCAG 59.993 40.000 17.72 1.81 35.69 4.85
2540 2700 6.103997 ACCATTTTCAGAGCTGCAAATAATG 58.896 36.000 1.02 4.17 34.97 1.90
2655 2818 3.149436 TCACTTGCTTGCTGTTTGTTC 57.851 42.857 0.00 0.00 0.00 3.18
2667 2830 4.226761 GCTGTTTGTTCCGGTTCTAATTG 58.773 43.478 0.00 0.00 0.00 2.32
2735 2898 5.934625 GTCACTGACAATGTAGAGTTGGATT 59.065 40.000 4.17 0.00 32.09 3.01
2769 2932 2.295349 ACAATCTGAAAAGCAGCAGTGG 59.705 45.455 0.00 0.00 44.52 4.00
2899 3062 4.686554 CGGAAATCTGCTACACTTATAGCC 59.313 45.833 2.51 0.00 45.95 3.93
3171 3336 1.486310 ACTGAATATCTTGGCTCGGCA 59.514 47.619 0.00 0.00 0.00 5.69
3445 3613 6.039616 TGCAAACTACTTGATTGTTTGGAAC 58.960 36.000 16.16 4.35 45.92 3.62
3792 3963 3.703556 TCTCTGAGAATCCCTTAGTGCAG 59.296 47.826 4.57 0.00 31.08 4.41
4085 4443 7.616935 ACCATTTAAGGATCATTCATTGTGACT 59.383 33.333 0.00 0.00 0.00 3.41
4189 4547 4.194640 CAGACAGCTTATGCCTGTATGTT 58.805 43.478 14.16 0.00 40.80 2.71
4325 4683 7.897575 AGTAGTTCTTTTGCTGAGTTGATAG 57.102 36.000 0.00 0.00 0.00 2.08
4611 4972 5.424252 TGGAGGACGTGGATAGTCTTTTATT 59.576 40.000 0.00 0.00 38.58 1.40
4614 4975 7.336176 GGAGGACGTGGATAGTCTTTTATTTTT 59.664 37.037 0.00 0.00 38.58 1.94
4898 5259 6.833041 TGAGGTACACTTCATTTCCTGTTTA 58.167 36.000 0.00 0.00 0.00 2.01
4901 5262 7.970102 AGGTACACTTCATTTCCTGTTTACTA 58.030 34.615 0.00 0.00 0.00 1.82
4914 5275 4.705023 CCTGTTTACTATTTCAACCCCCTG 59.295 45.833 0.00 0.00 0.00 4.45
4927 5288 1.135094 CCCCCTGTCAGTCATATGCT 58.865 55.000 0.00 0.00 0.00 3.79
4928 5289 2.329267 CCCCCTGTCAGTCATATGCTA 58.671 52.381 0.00 0.00 0.00 3.49
5080 5443 1.718757 GACATCACTTGCGATGCCCC 61.719 60.000 0.92 0.00 45.56 5.80
5083 5446 3.499737 CACTTGCGATGCCCCGAC 61.500 66.667 0.00 0.00 0.00 4.79
5107 5470 4.662145 CGCAGTTTGTGGATTTTCTATCC 58.338 43.478 0.00 0.00 38.66 2.59
5149 5512 0.398318 GGAAGAGACCAACAGCCAGT 59.602 55.000 0.00 0.00 0.00 4.00
5155 5518 0.819259 GACCAACAGCCAGTGAAGCA 60.819 55.000 0.00 0.00 0.00 3.91
5205 5568 1.925285 TAATCTGGGGCCAGCCACTG 61.925 60.000 13.07 12.14 43.31 3.66
5282 5645 4.339530 ACTCCTTTTGTGAAGCCTTCTTTC 59.660 41.667 5.96 0.00 31.48 2.62
5293 5656 7.033185 GTGAAGCCTTCTTTCAAAAACTTGTA 58.967 34.615 5.96 0.00 31.48 2.41
5326 5690 4.214332 GTGGTTTTCTGAGAGTTCCATGTC 59.786 45.833 5.26 0.00 0.00 3.06
5490 5856 6.754193 TCATGCGTGTATGTAAATATGAGGA 58.246 36.000 5.68 0.00 0.00 3.71
5494 5860 8.445275 TGCGTGTATGTAAATATGAGGAAAAT 57.555 30.769 0.00 0.00 0.00 1.82
5604 5971 5.582665 GTCCAGTGTTTGATAAGGACATCTC 59.417 44.000 0.00 0.00 43.74 2.75
5624 5991 0.109827 CAACGCCGTGCATCAAATCA 60.110 50.000 0.00 0.00 0.00 2.57
5626 5993 1.584483 CGCCGTGCATCAAATCAGC 60.584 57.895 0.00 0.00 0.00 4.26
5630 5997 0.179156 CGTGCATCAAATCAGCCACC 60.179 55.000 0.00 0.00 0.00 4.61
5646 6013 2.360600 CCCCAAACATCGGCGGAA 60.361 61.111 7.21 0.00 0.00 4.30
5674 6041 2.514824 GAGCCGGCCATCAACCTC 60.515 66.667 26.15 7.69 0.00 3.85
5683 6050 0.888736 CCATCAACCTCGTGCACCAA 60.889 55.000 12.15 0.00 0.00 3.67
5684 6051 0.950836 CATCAACCTCGTGCACCAAA 59.049 50.000 12.15 0.00 0.00 3.28
5685 6052 1.541147 CATCAACCTCGTGCACCAAAT 59.459 47.619 12.15 0.00 0.00 2.32
5686 6053 0.950836 TCAACCTCGTGCACCAAATG 59.049 50.000 12.15 4.67 0.00 2.32
5687 6054 0.667993 CAACCTCGTGCACCAAATGT 59.332 50.000 12.15 0.00 0.00 2.71
5688 6055 0.951558 AACCTCGTGCACCAAATGTC 59.048 50.000 12.15 0.00 0.00 3.06
5689 6056 0.889186 ACCTCGTGCACCAAATGTCC 60.889 55.000 12.15 0.00 0.00 4.02
5690 6057 1.497278 CTCGTGCACCAAATGTCCG 59.503 57.895 12.15 0.00 0.00 4.79
5691 6058 2.126888 CGTGCACCAAATGTCCGC 60.127 61.111 12.15 0.00 0.00 5.54
5692 6059 2.616330 CGTGCACCAAATGTCCGCT 61.616 57.895 12.15 0.00 0.00 5.52
5693 6060 1.210155 GTGCACCAAATGTCCGCTC 59.790 57.895 5.22 0.00 0.00 5.03
5694 6061 1.971167 TGCACCAAATGTCCGCTCC 60.971 57.895 0.00 0.00 0.00 4.70
5695 6062 3.039202 GCACCAAATGTCCGCTCCG 62.039 63.158 0.00 0.00 0.00 4.63
5707 6074 4.115199 GCTCCGGGCCATCAACCT 62.115 66.667 4.39 0.00 34.27 3.50
5708 6075 2.190578 CTCCGGGCCATCAACCTC 59.809 66.667 4.39 0.00 0.00 3.85
5709 6076 3.740128 CTCCGGGCCATCAACCTCG 62.740 68.421 4.39 0.00 0.00 4.63
5710 6077 4.096003 CCGGGCCATCAACCTCGT 62.096 66.667 4.39 0.00 0.00 4.18
5711 6078 2.819595 CGGGCCATCAACCTCGTG 60.820 66.667 4.39 0.00 0.00 4.35
5712 6079 3.134127 GGGCCATCAACCTCGTGC 61.134 66.667 4.39 0.00 0.00 5.34
5713 6080 2.359850 GGCCATCAACCTCGTGCA 60.360 61.111 0.00 0.00 0.00 4.57
5714 6081 2.690778 GGCCATCAACCTCGTGCAC 61.691 63.158 6.82 6.82 0.00 4.57
5715 6082 2.690778 GCCATCAACCTCGTGCACC 61.691 63.158 12.15 0.00 0.00 5.01
5716 6083 1.302431 CCATCAACCTCGTGCACCA 60.302 57.895 12.15 0.00 0.00 4.17
5723 6090 0.108585 ACCTCGTGCACCAAATGTCT 59.891 50.000 12.15 0.00 0.00 3.41
5756 6123 1.289160 CCTCCTCCACCTCCATTTGA 58.711 55.000 0.00 0.00 0.00 2.69
5757 6124 1.065126 CCTCCTCCACCTCCATTTGAC 60.065 57.143 0.00 0.00 0.00 3.18
5758 6125 1.630369 CTCCTCCACCTCCATTTGACA 59.370 52.381 0.00 0.00 0.00 3.58
5759 6126 2.240667 CTCCTCCACCTCCATTTGACAT 59.759 50.000 0.00 0.00 0.00 3.06
5760 6127 2.025981 TCCTCCACCTCCATTTGACATG 60.026 50.000 0.00 0.00 0.00 3.21
5761 6128 2.025981 CCTCCACCTCCATTTGACATGA 60.026 50.000 0.00 0.00 0.00 3.07
5762 6129 3.372349 CCTCCACCTCCATTTGACATGAT 60.372 47.826 0.00 0.00 0.00 2.45
5763 6130 4.141413 CCTCCACCTCCATTTGACATGATA 60.141 45.833 0.00 0.00 0.00 2.15
5764 6131 4.780815 TCCACCTCCATTTGACATGATAC 58.219 43.478 0.00 0.00 0.00 2.24
5829 6236 6.387041 AGATGCAAACATATCCAATCACAG 57.613 37.500 0.00 0.00 36.35 3.66
5841 6248 5.314923 TCCAATCACAGCTAAAAAGCATC 57.685 39.130 0.00 0.00 37.25 3.91
5919 6326 4.901868 ACGTCAATTTTTGCCTCCTAGTA 58.098 39.130 0.00 0.00 0.00 1.82
5920 6327 5.310451 ACGTCAATTTTTGCCTCCTAGTAA 58.690 37.500 0.00 0.00 0.00 2.24
5929 6336 1.831736 GCCTCCTAGTAAAGCTGTCCA 59.168 52.381 0.00 0.00 0.00 4.02
5931 6338 3.118223 GCCTCCTAGTAAAGCTGTCCATT 60.118 47.826 0.00 0.00 0.00 3.16
5951 6358 5.412594 CCATTTCAAATTCTTCACTCCTCGA 59.587 40.000 0.00 0.00 0.00 4.04
6036 6443 1.528824 CCGCATGGGATCCAAGTCT 59.471 57.895 15.23 0.00 36.95 3.24
6055 6462 4.040829 AGTCTGACATCTTCATGGTCAACA 59.959 41.667 10.88 0.00 33.82 3.33
6056 6463 4.756642 GTCTGACATCTTCATGGTCAACAA 59.243 41.667 2.24 0.00 33.82 2.83
6057 6464 4.756642 TCTGACATCTTCATGGTCAACAAC 59.243 41.667 3.79 0.00 33.82 3.32
6058 6465 4.717877 TGACATCTTCATGGTCAACAACT 58.282 39.130 0.00 0.00 33.82 3.16
6059 6466 4.756642 TGACATCTTCATGGTCAACAACTC 59.243 41.667 0.00 0.00 33.82 3.01
6060 6467 4.717877 ACATCTTCATGGTCAACAACTCA 58.282 39.130 0.00 0.00 33.82 3.41
6061 6468 5.132502 ACATCTTCATGGTCAACAACTCAA 58.867 37.500 0.00 0.00 33.82 3.02
6062 6469 5.009010 ACATCTTCATGGTCAACAACTCAAC 59.991 40.000 0.00 0.00 33.82 3.18
6104 6511 4.829968 TCTCTTGGAGCTTGATCTTCTTG 58.170 43.478 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 95 6.918022 GGTGCTATGTGAAAATTATAACTGCC 59.082 38.462 0.00 0.00 0.00 4.85
219 221 3.320541 TCAAACATCTTCCGTGCCATTTT 59.679 39.130 0.00 0.00 0.00 1.82
220 222 2.890311 TCAAACATCTTCCGTGCCATTT 59.110 40.909 0.00 0.00 0.00 2.32
221 223 2.489329 CTCAAACATCTTCCGTGCCATT 59.511 45.455 0.00 0.00 0.00 3.16
222 224 2.086869 CTCAAACATCTTCCGTGCCAT 58.913 47.619 0.00 0.00 0.00 4.40
252 254 2.094957 ACACGATAAAATTTGGCACGGG 60.095 45.455 0.00 0.00 0.00 5.28
253 255 3.210358 ACACGATAAAATTTGGCACGG 57.790 42.857 0.00 0.00 0.00 4.94
254 256 4.143431 CCAAACACGATAAAATTTGGCACG 60.143 41.667 1.91 0.00 43.29 5.34
270 272 3.821033 AGGCTACTCAAATGTCCAAACAC 59.179 43.478 0.00 0.00 38.48 3.32
273 275 6.303839 ACTAAAGGCTACTCAAATGTCCAAA 58.696 36.000 0.00 0.00 0.00 3.28
309 311 9.449719 CTATAAACTTTCTCACACACCCTAAAT 57.550 33.333 0.00 0.00 0.00 1.40
325 327 4.377022 CGAACAGTGCGCACTATAAACTTT 60.377 41.667 40.17 23.05 40.20 2.66
333 335 1.372499 GTCCGAACAGTGCGCACTA 60.372 57.895 40.17 22.83 40.20 2.74
352 356 5.855395 CAGCTTCTGGAAAAAGAGAAAATCG 59.145 40.000 0.00 0.00 0.00 3.34
359 363 3.144506 TCAGCAGCTTCTGGAAAAAGAG 58.855 45.455 13.60 0.00 34.91 2.85
370 375 0.723981 GTTCGGACATCAGCAGCTTC 59.276 55.000 0.00 0.00 0.00 3.86
403 410 1.820519 TCAAATGCTTGATGTCCAGGC 59.179 47.619 0.00 0.00 46.78 4.85
546 554 1.713830 GGCACGCGGTAATCTTGTC 59.286 57.895 12.47 0.00 0.00 3.18
602 614 7.145323 AGAACGTTTCTGTCAAAAATATTGGG 58.855 34.615 0.46 0.00 38.91 4.12
614 626 5.163854 CCCATGATGTAAGAACGTTTCTGTC 60.164 44.000 0.46 0.00 40.59 3.51
618 630 6.093495 TCAATCCCATGATGTAAGAACGTTTC 59.907 38.462 0.46 0.00 0.00 2.78
633 645 5.102953 TGGACTACTCTTTCAATCCCATG 57.897 43.478 0.00 0.00 0.00 3.66
640 652 9.273016 CTCACTTAATTTGGACTACTCTTTCAA 57.727 33.333 0.00 0.00 0.00 2.69
644 656 5.869888 CGCTCACTTAATTTGGACTACTCTT 59.130 40.000 0.00 0.00 0.00 2.85
661 760 2.094258 CGATATTGCACAAACGCTCACT 59.906 45.455 0.00 0.00 0.00 3.41
675 774 2.941064 CCCTATGGCTGATGCGATATTG 59.059 50.000 0.00 0.00 38.76 1.90
676 775 2.092753 CCCCTATGGCTGATGCGATATT 60.093 50.000 0.00 0.00 38.76 1.28
677 776 1.487976 CCCCTATGGCTGATGCGATAT 59.512 52.381 0.00 0.00 38.76 1.63
678 777 0.904649 CCCCTATGGCTGATGCGATA 59.095 55.000 0.00 0.00 38.55 2.92
680 779 3.150949 CCCCTATGGCTGATGCGA 58.849 61.111 0.00 0.00 40.82 5.10
692 792 4.340617 CCTTAATTGTGTTTCAGCCCCTA 58.659 43.478 0.00 0.00 0.00 3.53
816 917 0.681564 AGGCGAGGACTGGACTACTG 60.682 60.000 0.00 0.00 0.00 2.74
817 918 0.394625 GAGGCGAGGACTGGACTACT 60.395 60.000 0.00 0.00 0.00 2.57
818 919 1.385756 GGAGGCGAGGACTGGACTAC 61.386 65.000 0.00 0.00 0.00 2.73
819 920 1.076923 GGAGGCGAGGACTGGACTA 60.077 63.158 0.00 0.00 0.00 2.59
820 921 2.363147 GGAGGCGAGGACTGGACT 60.363 66.667 0.00 0.00 0.00 3.85
821 922 2.363147 AGGAGGCGAGGACTGGAC 60.363 66.667 0.00 0.00 0.00 4.02
1325 1449 3.728373 CCGGAAACAGGGAGGGGG 61.728 72.222 0.00 0.00 0.00 5.40
1357 1481 1.880186 GAGATTTCGCGGGGCAAAA 59.120 52.632 6.13 0.00 0.00 2.44
1467 1592 7.011109 CAGGATCAATTTCAATTCTTTGATGGC 59.989 37.037 2.03 0.00 41.38 4.40
1469 1594 7.494625 CCCAGGATCAATTTCAATTCTTTGATG 59.505 37.037 2.03 0.00 41.38 3.07
1470 1595 7.365295 CCCCAGGATCAATTTCAATTCTTTGAT 60.365 37.037 0.00 0.00 41.38 2.57
1553 1678 1.076923 TCGAGTAGGCAGGGAGGTC 60.077 63.158 0.00 0.00 0.00 3.85
1555 1683 1.076632 ACTCGAGTAGGCAGGGAGG 60.077 63.158 18.46 0.00 0.00 4.30
1561 1689 0.609406 ACAGAGCACTCGAGTAGGCA 60.609 55.000 24.67 0.00 34.09 4.75
1567 1695 0.884514 TGGAGAACAGAGCACTCGAG 59.115 55.000 11.84 11.84 34.09 4.04
1620 1748 8.597662 ATCCAAGAAACAGAAACATCAAATTG 57.402 30.769 0.00 0.00 0.00 2.32
1650 1779 2.526120 GCCGTACGGATTCAGCAGC 61.526 63.158 37.62 14.80 37.50 5.25
1662 1791 2.802414 GACGACCACACGCCGTAC 60.802 66.667 0.00 0.00 36.60 3.67
1743 1872 1.203087 TGGAAGAAGAGGTCGGTGGTA 60.203 52.381 0.00 0.00 0.00 3.25
1809 1938 1.429299 TCCTCCTCCTTGTCTCTGTCA 59.571 52.381 0.00 0.00 0.00 3.58
1884 2025 4.514577 CAGTAGTCGCCAGGGCCG 62.515 72.222 4.42 0.26 37.98 6.13
1905 2046 0.801872 CATTTCCGGCGTGTTCATGA 59.198 50.000 6.01 0.00 0.00 3.07
1920 2061 1.002134 CCCCTCACAGCCGTCATTT 60.002 57.895 0.00 0.00 0.00 2.32
1941 2082 2.656646 CAGCTGTACACCTCGGCA 59.343 61.111 5.25 0.00 39.38 5.69
2013 2154 2.418746 GCTAGAATTTCGGACCAGCTCA 60.419 50.000 0.00 0.00 0.00 4.26
2065 2206 4.614475 TCCAGTATCTCTGTCTGGTCATT 58.386 43.478 9.71 0.00 46.04 2.57
2131 2272 1.577328 AAATCGCACTCAAGCACGGG 61.577 55.000 0.00 0.00 0.00 5.28
2133 2274 1.195448 AGAAAATCGCACTCAAGCACG 59.805 47.619 0.00 0.00 0.00 5.34
2151 2292 1.980765 ACTTGCCCAGAATCTGTCAGA 59.019 47.619 9.63 4.68 0.00 3.27
2153 2294 3.055819 GTCTACTTGCCCAGAATCTGTCA 60.056 47.826 9.63 4.08 0.00 3.58
2158 2299 2.815478 CTCGTCTACTTGCCCAGAATC 58.185 52.381 0.00 0.00 0.00 2.52
2181 2322 2.486982 CTCCACAACATTCAGCTCCAAG 59.513 50.000 0.00 0.00 0.00 3.61
2182 2323 2.106338 TCTCCACAACATTCAGCTCCAA 59.894 45.455 0.00 0.00 0.00 3.53
2254 2395 5.127194 TGGAGTACTGATACTTACTTGCAGG 59.873 44.000 0.00 0.00 41.98 4.85
2516 2664 5.726980 TTATTTGCAGCTCTGAAAATGGT 57.273 34.783 20.68 3.86 45.72 3.55
2581 2741 2.470821 GCACTACATGACCCATACGTC 58.529 52.381 0.00 0.00 0.00 4.34
2636 2799 2.195922 GGAACAAACAGCAAGCAAGTG 58.804 47.619 0.00 0.00 0.00 3.16
2637 2800 1.202290 CGGAACAAACAGCAAGCAAGT 60.202 47.619 0.00 0.00 0.00 3.16
2655 2818 3.508744 AGCATTTGCAATTAGAACCGG 57.491 42.857 0.00 0.00 45.16 5.28
2667 2830 1.068610 TGCAAGACGGTAAGCATTTGC 60.069 47.619 0.00 0.00 40.81 3.68
2899 3062 4.710423 TGACTCTGGATCTTCTTTCTCG 57.290 45.455 0.00 0.00 0.00 4.04
3019 3184 8.541133 TTTCTTTAACAACAACCAAAGAAAGG 57.459 30.769 14.00 0.00 45.22 3.11
3047 3212 8.993121 GGATGCATACCATATAAGCATATGTAC 58.007 37.037 0.00 0.00 45.08 2.90
3171 3336 1.251251 GGACAACCTTGCTGAATGCT 58.749 50.000 0.00 0.00 43.37 3.79
3445 3613 9.853177 ACCAAGTCCCTTAAATATCTTCTTATG 57.147 33.333 0.00 0.00 0.00 1.90
4085 4443 9.784531 CTTGATAAGGATATTCTCTGGCTTTAA 57.215 33.333 0.00 0.00 0.00 1.52
4189 4547 2.747989 AGCTCGATAAGAACGTGACTGA 59.252 45.455 0.00 0.00 0.00 3.41
4527 4887 5.412904 GGTTGGAGCTATATATTTCCACAGC 59.587 44.000 12.55 4.38 39.32 4.40
4530 4890 6.769512 TCTGGTTGGAGCTATATATTTCCAC 58.230 40.000 12.55 9.20 39.32 4.02
4611 4972 8.740906 TGTTTGTGTGAGTTGAGGTTATAAAAA 58.259 29.630 0.00 0.00 0.00 1.94
4614 4975 6.824196 TGTGTTTGTGTGAGTTGAGGTTATAA 59.176 34.615 0.00 0.00 0.00 0.98
4791 5152 7.861629 TCTAACATTTCCATGTCTATTGGACT 58.138 34.615 1.69 0.00 43.34 3.85
4898 5259 2.986728 ACTGACAGGGGGTTGAAATAGT 59.013 45.455 7.51 0.00 0.00 2.12
4901 5262 1.780309 TGACTGACAGGGGGTTGAAAT 59.220 47.619 7.51 0.00 0.00 2.17
4908 5269 1.135094 AGCATATGACTGACAGGGGG 58.865 55.000 6.97 0.00 0.00 5.40
4914 5275 9.497030 CGAATACTCTTATAGCATATGACTGAC 57.503 37.037 6.97 0.00 0.00 3.51
4927 5288 8.837788 TCGAGTGGTTATCGAATACTCTTATA 57.162 34.615 12.68 0.00 45.52 0.98
4928 5289 7.741027 TCGAGTGGTTATCGAATACTCTTAT 57.259 36.000 12.68 0.00 45.52 1.73
4988 5351 7.130099 TGGATACAGATAAGGAAGGTAAGTCA 58.870 38.462 0.00 0.00 46.17 3.41
5080 5443 1.234615 AATCCACAAACTGCGGGTCG 61.235 55.000 0.00 0.00 0.00 4.79
5083 5446 1.613437 AGAAAATCCACAAACTGCGGG 59.387 47.619 0.00 0.00 0.00 6.13
5107 5470 3.953612 TGGGGTTTATTTGCAGCAGATAG 59.046 43.478 5.81 0.00 0.00 2.08
5149 5512 1.134995 CACGGATGCTCTAGTGCTTCA 60.135 52.381 25.12 6.43 38.40 3.02
5155 5518 0.905357 AAAGCCACGGATGCTCTAGT 59.095 50.000 0.00 0.00 38.34 2.57
5205 5568 1.172175 CCCCTGAAGCAGAAGAAAGC 58.828 55.000 0.00 0.00 32.44 3.51
5326 5690 1.476074 AAACAGCAACGTTTCATGCG 58.524 45.000 0.00 0.00 46.98 4.73
5351 5715 2.372852 GGCAAGACCCTCTACACCA 58.627 57.895 0.00 0.00 0.00 4.17
5383 5748 0.963962 ACAGGCCAGTTCAGCAAATG 59.036 50.000 5.01 0.00 0.00 2.32
5407 5772 1.746220 CCGACACCAACAAAGAAACCA 59.254 47.619 0.00 0.00 0.00 3.67
5490 5856 7.106439 TGTACAGACACACATGGAAAATTTT 57.894 32.000 2.28 2.28 0.00 1.82
5494 5860 3.563808 GCTGTACAGACACACATGGAAAA 59.436 43.478 27.08 0.00 0.00 2.29
5604 5971 0.798009 GATTTGATGCACGGCGTTGG 60.798 55.000 11.19 0.05 0.00 3.77
5624 5991 2.035626 CCGATGTTTGGGGTGGCT 59.964 61.111 0.00 0.00 0.00 4.75
5626 5993 3.439540 CGCCGATGTTTGGGGTGG 61.440 66.667 0.00 0.00 34.90 4.61
5630 5997 1.241315 ACTTTCCGCCGATGTTTGGG 61.241 55.000 0.00 0.00 0.00 4.12
5646 6013 2.955881 GCCGGCTCCACTACCACTT 61.956 63.158 22.15 0.00 0.00 3.16
5674 6041 2.126888 GCGGACATTTGGTGCACG 60.127 61.111 11.45 0.00 37.78 5.34
5690 6057 4.115199 AGGTTGATGGCCCGGAGC 62.115 66.667 0.73 4.32 42.60 4.70
5691 6058 2.190578 GAGGTTGATGGCCCGGAG 59.809 66.667 0.73 0.00 0.00 4.63
5692 6059 3.781307 CGAGGTTGATGGCCCGGA 61.781 66.667 0.73 0.00 0.00 5.14
5693 6060 4.096003 ACGAGGTTGATGGCCCGG 62.096 66.667 0.00 0.00 0.00 5.73
5694 6061 2.819595 CACGAGGTTGATGGCCCG 60.820 66.667 0.00 0.00 0.00 6.13
5695 6062 3.134127 GCACGAGGTTGATGGCCC 61.134 66.667 0.00 0.00 0.00 5.80
5696 6063 2.359850 TGCACGAGGTTGATGGCC 60.360 61.111 0.00 0.00 0.00 5.36
5697 6064 2.690778 GGTGCACGAGGTTGATGGC 61.691 63.158 11.45 0.00 0.00 4.40
5698 6065 0.888736 TTGGTGCACGAGGTTGATGG 60.889 55.000 11.45 0.00 0.00 3.51
5699 6066 0.950836 TTTGGTGCACGAGGTTGATG 59.049 50.000 11.45 0.00 0.00 3.07
5700 6067 1.541147 CATTTGGTGCACGAGGTTGAT 59.459 47.619 11.45 0.00 0.00 2.57
5701 6068 0.950836 CATTTGGTGCACGAGGTTGA 59.049 50.000 11.45 0.00 0.00 3.18
5702 6069 0.667993 ACATTTGGTGCACGAGGTTG 59.332 50.000 11.45 8.29 0.00 3.77
5703 6070 0.951558 GACATTTGGTGCACGAGGTT 59.048 50.000 11.45 0.00 0.00 3.50
5704 6071 0.108585 AGACATTTGGTGCACGAGGT 59.891 50.000 11.45 7.13 0.00 3.85
5705 6072 0.518636 CAGACATTTGGTGCACGAGG 59.481 55.000 11.45 3.69 0.00 4.63
5706 6073 0.110056 GCAGACATTTGGTGCACGAG 60.110 55.000 11.45 0.00 37.16 4.18
5707 6074 0.534877 AGCAGACATTTGGTGCACGA 60.535 50.000 11.45 3.44 39.80 4.35
5708 6075 0.110056 GAGCAGACATTTGGTGCACG 60.110 55.000 11.45 0.00 39.80 5.34
5709 6076 0.242017 GGAGCAGACATTTGGTGCAC 59.758 55.000 8.80 8.80 39.80 4.57
5710 6077 0.178995 TGGAGCAGACATTTGGTGCA 60.179 50.000 9.11 0.00 43.16 4.57
5711 6078 0.524862 CTGGAGCAGACATTTGGTGC 59.475 55.000 0.00 0.28 37.41 5.01
5712 6079 1.171308 CCTGGAGCAGACATTTGGTG 58.829 55.000 0.00 0.00 32.44 4.17
5713 6080 0.773644 ACCTGGAGCAGACATTTGGT 59.226 50.000 0.00 0.00 32.44 3.67
5714 6081 1.457346 GACCTGGAGCAGACATTTGG 58.543 55.000 0.00 0.00 32.44 3.28
5715 6082 1.457346 GGACCTGGAGCAGACATTTG 58.543 55.000 0.00 0.00 32.44 2.32
5716 6083 0.036010 CGGACCTGGAGCAGACATTT 60.036 55.000 0.00 0.00 32.44 2.32
5756 6123 9.901172 ATTGATCTATGTATGCATGTATCATGT 57.099 29.630 10.16 10.58 37.39 3.21
5759 6126 9.538508 GCTATTGATCTATGTATGCATGTATCA 57.461 33.333 10.16 14.59 36.58 2.15
5760 6127 9.538508 TGCTATTGATCTATGTATGCATGTATC 57.461 33.333 10.16 9.33 36.58 2.24
5761 6128 9.895138 TTGCTATTGATCTATGTATGCATGTAT 57.105 29.630 10.16 6.11 36.58 2.29
5762 6129 9.895138 ATTGCTATTGATCTATGTATGCATGTA 57.105 29.630 10.16 0.00 36.58 2.29
5763 6130 8.803397 ATTGCTATTGATCTATGTATGCATGT 57.197 30.769 10.16 0.00 36.58 3.21
5792 6159 7.806409 TGTTTGCATCTTGCTATACATATGT 57.194 32.000 13.93 13.93 45.31 2.29
5795 6162 9.166173 GGATATGTTTGCATCTTGCTATACATA 57.834 33.333 16.41 16.41 45.31 2.29
5803 6170 5.461078 GTGATTGGATATGTTTGCATCTTGC 59.539 40.000 0.00 0.00 45.29 4.01
5805 6172 6.682113 GCTGTGATTGGATATGTTTGCATCTT 60.682 38.462 0.00 0.00 36.58 2.40
5810 6177 4.644103 AGCTGTGATTGGATATGTTTGC 57.356 40.909 0.00 0.00 0.00 3.68
5820 6227 4.100529 CGATGCTTTTTAGCTGTGATTGG 58.899 43.478 0.00 0.00 35.49 3.16
5829 6236 4.355543 TGTTGATCCGATGCTTTTTAGC 57.644 40.909 0.00 0.00 0.00 3.09
5841 6248 6.007936 TGGATGTAAAAACTTGTTGATCCG 57.992 37.500 0.00 0.00 32.34 4.18
5919 6326 6.703165 GTGAAGAATTTGAAATGGACAGCTTT 59.297 34.615 0.00 0.00 0.00 3.51
5920 6327 6.041296 AGTGAAGAATTTGAAATGGACAGCTT 59.959 34.615 0.00 0.00 0.00 3.74
5929 6336 5.412904 GGTCGAGGAGTGAAGAATTTGAAAT 59.587 40.000 0.00 0.00 0.00 2.17
5931 6338 4.315803 GGTCGAGGAGTGAAGAATTTGAA 58.684 43.478 0.00 0.00 0.00 2.69
6036 6443 4.717877 AGTTGTTGACCATGAAGATGTCA 58.282 39.130 0.00 0.00 41.67 3.58
6055 6462 5.014858 AGATTGATGCCAAGATGTTGAGTT 58.985 37.500 3.74 0.00 35.46 3.01
6056 6463 4.597004 AGATTGATGCCAAGATGTTGAGT 58.403 39.130 3.74 0.00 35.46 3.41
6057 6464 5.357314 AGAAGATTGATGCCAAGATGTTGAG 59.643 40.000 3.74 0.00 35.46 3.02
6058 6465 5.258841 AGAAGATTGATGCCAAGATGTTGA 58.741 37.500 3.74 0.00 35.46 3.18
6059 6466 5.578005 AGAAGATTGATGCCAAGATGTTG 57.422 39.130 0.00 0.00 35.48 3.33
6060 6467 5.950549 AGAAGAAGATTGATGCCAAGATGTT 59.049 36.000 0.00 0.00 35.48 2.71
6061 6468 5.507637 AGAAGAAGATTGATGCCAAGATGT 58.492 37.500 0.00 0.00 35.48 3.06
6062 6469 5.823570 AGAGAAGAAGATTGATGCCAAGATG 59.176 40.000 0.00 0.00 35.48 2.90


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

AutoCloner maintained by Alex Coulton.