Multiple sequence alignment - TraesCS7D01G485500

Loading Multiple Alignment...

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 TraesCS7D01G485500 chr7D 100.000 8748 0 0 1 8748 595731826 595723079 0.000000e+00 16155.0
1 TraesCS7D01G485500 chr7D 80.192 833 104 22 7787 8594 595578345 595577549 1.270000e-157 568.0
2 TraesCS7D01G485500 chr7D 76.739 920 110 47 6460 7306 595606505 595605617 1.360000e-112 418.0
3 TraesCS7D01G485500 chr7D 81.935 310 34 7 6419 6720 595581364 595581069 8.770000e-60 243.0
4 TraesCS7D01G485500 chr7D 80.386 311 43 10 7353 7649 595605119 595604813 4.110000e-53 220.0
5 TraesCS7D01G485500 chr7D 83.550 231 19 4 8368 8596 595613161 595612948 1.930000e-46 198.0
6 TraesCS7D01G485500 chr7D 80.216 278 34 4 7534 7790 595666651 595666374 1.160000e-43 189.0
7 TraesCS7D01G485500 chr7D 86.061 165 16 4 8368 8527 595665557 595665395 4.200000e-38 171.0
8 TraesCS7D01G485500 chr7D 86.395 147 12 5 7164 7308 595531917 595531777 4.230000e-33 154.0
9 TraesCS7D01G485500 chr7D 89.873 79 5 2 6770 6847 595580493 595580417 2.010000e-16 99.0
10 TraesCS7D01G485500 chr7D 100.000 39 0 0 8556 8594 595723234 595723196 1.220000e-08 73.1
11 TraesCS7D01G485500 chr7D 100.000 39 0 0 8593 8631 595723271 595723233 1.220000e-08 73.1
12 TraesCS7D01G485500 chr7A 96.462 5285 157 15 3331 8594 688690572 688685297 0.000000e+00 8696.0
13 TraesCS7D01G485500 chr7A 94.824 2608 101 21 1 2582 688694184 688691585 0.000000e+00 4037.0
14 TraesCS7D01G485500 chr7A 97.486 716 16 1 2581 3296 688691284 688690571 0.000000e+00 1221.0
15 TraesCS7D01G485500 chr7A 80.872 826 105 20 7785 8594 688457232 688456444 1.260000e-167 601.0
16 TraesCS7D01G485500 chr7A 80.233 516 61 23 7302 7788 688457817 688457314 5.030000e-92 350.0
17 TraesCS7D01G485500 chr7A 85.088 228 26 5 8368 8592 688626899 688626677 8.840000e-55 226.0
18 TraesCS7D01G485500 chr7A 82.510 263 22 7 6419 6674 688459549 688459304 8.900000e-50 209.0
19 TraesCS7D01G485500 chr7A 89.697 165 10 4 8368 8527 688662654 688662492 4.140000e-48 204.0
20 TraesCS7D01G485500 chr7A 92.647 136 6 2 8593 8724 688685335 688685200 8.960000e-45 193.0
21 TraesCS7D01G485500 chr7B 96.308 5228 130 28 2767 7977 673310066 673304885 0.000000e+00 8527.0
22 TraesCS7D01G485500 chr7B 94.610 2690 111 11 2 2658 673312749 673310061 0.000000e+00 4133.0
23 TraesCS7D01G485500 chr7B 94.502 582 23 4 8007 8583 673304885 673304308 0.000000e+00 889.0
24 TraesCS7D01G485500 chr7B 83.134 836 102 14 7785 8594 672915088 672914266 0.000000e+00 726.0
25 TraesCS7D01G485500 chr7B 80.606 825 101 25 7787 8594 672841824 672841042 4.550000e-162 582.0
26 TraesCS7D01G485500 chr7B 78.462 520 64 25 7302 7788 672842411 672841907 6.640000e-76 296.0
27 TraesCS7D01G485500 chr7B 83.746 283 26 12 6566 6840 672843771 672843501 5.240000e-62 250.0
28 TraesCS7D01G485500 chr7B 93.125 160 7 2 8593 8748 673304335 673304176 1.900000e-56 231.0
29 TraesCS7D01G485500 chr7B 85.455 165 17 4 8368 8527 673136533 673136371 1.950000e-36 165.0
30 TraesCS7D01G485500 chr2A 82.057 457 61 14 1898 2353 714211858 714211422 3.860000e-98 370.0
31 TraesCS7D01G485500 chr2B 81.222 442 62 14 1905 2345 692167317 692166896 3.910000e-88 337.0
32 TraesCS7D01G485500 chr2D 89.655 261 26 1 2080 2340 576195691 576195432 1.820000e-86 331.0
33 TraesCS7D01G485500 chr1D 100.000 29 0 0 3729 3757 439568584 439568612 4.000000e-03 54.7


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 TraesCS7D01G485500 chr7D 595723079 595731826 8747 True 16155.000000 16155 100.00000 1 8748 1 chr7D.!!$R3 8747
1 TraesCS7D01G485500 chr7D 595604813 595606505 1692 True 319.000000 418 78.56250 6460 7649 2 chr7D.!!$R5 1189
2 TraesCS7D01G485500 chr7D 595577549 595581364 3815 True 303.333333 568 84.00000 6419 8594 3 chr7D.!!$R4 2175
3 TraesCS7D01G485500 chr7A 688685200 688694184 8984 True 3536.750000 8696 95.35475 1 8724 4 chr7A.!!$R4 8723
4 TraesCS7D01G485500 chr7A 688456444 688459549 3105 True 386.666667 601 81.20500 6419 8594 3 chr7A.!!$R3 2175
5 TraesCS7D01G485500 chr7B 673304176 673312749 8573 True 3445.000000 8527 94.63625 2 8748 4 chr7B.!!$R4 8746
6 TraesCS7D01G485500 chr7B 672914266 672915088 822 True 726.000000 726 83.13400 7785 8594 1 chr7B.!!$R1 809
7 TraesCS7D01G485500 chr7B 672841042 672843771 2729 True 376.000000 582 80.93800 6566 8594 3 chr7B.!!$R3 2028

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
495 506 0.593128 CTGTCCCTTTTTCACTGCCG 59.407 55.000 0.00 0.00 0.00 5.69 F
617 634 1.109609 TTTGTTGCCACAGTCATGCA 58.890 45.000 0.00 0.00 33.22 3.96 F
1157 1212 1.303561 GGGATGCACACCAGAAGCA 60.304 57.895 12.79 0.00 43.14 3.91 F
2016 2071 2.434884 CACCATGCCTTCGTCGCT 60.435 61.111 0.00 0.00 0.00 4.93 F
2568 2624 0.603975 AGGAACCAGTCGCTTCTTGC 60.604 55.000 0.00 0.00 38.57 4.01 F
2927 3285 2.553602 CTGGTTTGCATCTTGTAGCACA 59.446 45.455 0.00 0.00 41.05 4.57 F
3610 3968 2.614829 AACACGTACTCCAAACTGCT 57.385 45.000 0.00 0.00 0.00 4.24 F
3646 4004 3.657727 AGAAGGAATTGACCCTTGAAGGA 59.342 43.478 13.97 0.00 43.59 3.36 F
3901 4259 5.415077 AGCAGGAGAGATCTTTGTCAATTTG 59.585 40.000 0.00 0.00 0.00 2.32 F
5440 5799 4.084693 GCATGCAAAGCTCTTGAAGAAAAC 60.085 41.667 14.21 0.00 0.00 2.43 F
6075 6435 2.319025 TCACTAGTCACCATGGTCCA 57.681 50.000 16.53 0.77 0.00 4.02 F
6915 8276 2.170607 GGGAAATACTAGCACCTCAGCA 59.829 50.000 0.00 0.00 36.85 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 1882 3.495193 CATCATGTGCCTTCTTTGAACG 58.505 45.455 0.00 0.00 0.00 3.95 R
2511 2567 0.242017 GCAGTGCCACTGGATGAAAC 59.758 55.000 25.24 3.90 46.01 2.78 R
2545 2601 2.450609 GAAGCGACTGGTTCCTACAA 57.549 50.000 0.00 0.00 44.83 2.41 R
3734 4092 0.323178 GACTCTGGGTCCGGTACAGA 60.323 60.000 19.12 19.12 38.93 3.41 R
4335 4693 0.750249 TCTTCACGACTGGAGCAACA 59.250 50.000 0.00 0.00 0.00 3.33 R
4405 4763 1.266989 GAAGCCAAACAACTTCTCCCG 59.733 52.381 0.00 0.00 39.36 5.14 R
4595 4954 4.274459 GCTTGCATATACCTCTTGAACAGG 59.726 45.833 0.00 0.00 37.03 4.00 R
5440 5799 7.264373 ACACTTGGATTTCTTGTTAAGTGAG 57.736 36.000 18.37 0.00 44.59 3.51 R
5838 6197 4.946772 TGAAGTGGTGTGTTCATGAAAAGA 59.053 37.500 10.35 0.00 0.00 2.52 R
6327 6687 3.989817 CCAACAGCCAGTATTTTCAAAGC 59.010 43.478 0.00 0.00 0.00 3.51 R
7513 9421 4.953940 AAAAGAGCTCTCTGTCTGTCTT 57.046 40.909 18.55 0.68 40.36 3.01 R
8611 10986 0.178964 CCTTGCCCCAAACCTGAAGA 60.179 55.000 0.00 0.00 0.00 2.87 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
29 30 2.813908 GGCATTCCGTCGAACGCT 60.814 61.111 0.00 0.00 40.91 5.07
59 60 2.412089 GTGTTGCGATTTCGTAGAGCTT 59.588 45.455 1.55 0.00 42.22 3.74
74 75 2.747855 CTTCTGGGCTTCGGGTGC 60.748 66.667 0.00 0.00 0.00 5.01
76 77 1.899437 CTTCTGGGCTTCGGGTGCTA 61.899 60.000 0.00 0.00 0.00 3.49
77 78 1.899437 TTCTGGGCTTCGGGTGCTAG 61.899 60.000 0.00 0.00 0.00 3.42
116 118 2.636299 CCGTTTGATCGGGTGGTTT 58.364 52.632 0.00 0.00 45.88 3.27
273 275 4.094739 GCTGTTGCTTTGGTGATTGTTTTT 59.905 37.500 0.00 0.00 36.03 1.94
274 276 5.542616 TGTTGCTTTGGTGATTGTTTTTG 57.457 34.783 0.00 0.00 0.00 2.44
276 278 3.871485 TGCTTTGGTGATTGTTTTTGCT 58.129 36.364 0.00 0.00 0.00 3.91
291 294 4.607293 TTTTGCTTGTGCTCTCTCTAGA 57.393 40.909 0.00 0.00 40.48 2.43
337 348 4.678287 GGCATATGCTTCATTCGATTTGTG 59.322 41.667 26.12 0.00 41.70 3.33
474 485 5.918011 CCAGTCGTAGAATCTTAGATTCAGC 59.082 44.000 29.48 21.37 39.69 4.26
475 486 5.623264 CAGTCGTAGAATCTTAGATTCAGCG 59.377 44.000 29.48 28.58 39.69 5.18
476 487 4.380382 GTCGTAGAATCTTAGATTCAGCGC 59.620 45.833 29.48 22.67 39.69 5.92
480 491 4.367450 AGAATCTTAGATTCAGCGCTGTC 58.633 43.478 34.70 25.85 0.00 3.51
495 506 0.593128 CTGTCCCTTTTTCACTGCCG 59.407 55.000 0.00 0.00 0.00 5.69
616 633 2.129607 CTTTTGTTGCCACAGTCATGC 58.870 47.619 0.00 0.00 33.22 4.06
617 634 1.109609 TTTGTTGCCACAGTCATGCA 58.890 45.000 0.00 0.00 33.22 3.96
653 670 2.164422 CCCTGAAAGCGGAATTCCTTTC 59.836 50.000 23.13 23.13 44.39 2.62
675 692 4.083003 TCGGCATTTTCGCTACAGAATTTT 60.083 37.500 0.00 0.00 0.00 1.82
681 698 7.537306 GCATTTTCGCTACAGAATTTTACTTGA 59.463 33.333 0.00 0.00 0.00 3.02
705 722 9.223099 TGAATATGCATTACCTGTTGATCATAG 57.777 33.333 3.54 0.00 0.00 2.23
714 731 5.564550 ACCTGTTGATCATAGTTTGCTCTT 58.435 37.500 0.00 0.00 0.00 2.85
740 757 2.181954 AGCTTGTTTCTCCAGCAGAG 57.818 50.000 0.00 0.00 44.75 3.35
789 806 4.082081 TCAGCTATTGCCAAATTTGACCAG 60.082 41.667 19.86 9.61 40.80 4.00
790 807 2.931969 GCTATTGCCAAATTTGACCAGC 59.068 45.455 19.86 13.99 0.00 4.85
916 971 4.406326 TGGTGGACACAAGAGTTAGTTACA 59.594 41.667 4.69 0.00 0.00 2.41
1157 1212 1.303561 GGGATGCACACCAGAAGCA 60.304 57.895 12.79 0.00 43.14 3.91
1827 1882 3.941483 ACTTGCTATGTACACAAGATGCC 59.059 43.478 23.93 4.36 42.71 4.40
1986 2041 9.079833 CACTTGCTGATGAGGTAATTTAATTTG 57.920 33.333 0.00 0.00 0.00 2.32
2016 2071 2.434884 CACCATGCCTTCGTCGCT 60.435 61.111 0.00 0.00 0.00 4.93
2038 2093 6.036517 CGCTGACTTTTCTGCTTCATATACTT 59.963 38.462 2.62 0.00 42.91 2.24
2044 2099 9.066892 ACTTTTCTGCTTCATATACTTTTCACA 57.933 29.630 0.00 0.00 0.00 3.58
2049 2104 5.586243 TGCTTCATATACTTTTCACAGCTCC 59.414 40.000 0.00 0.00 0.00 4.70
2148 2203 4.878968 TGTCAGGTGAGGGTATAGATGAA 58.121 43.478 0.00 0.00 0.00 2.57
2208 2263 7.760340 GGTATACCAACTAAGAGAGAGTTTGTG 59.240 40.741 17.44 0.00 34.63 3.33
2511 2567 8.125448 GCCTAGAACTGCATACTAAAATTTCTG 58.875 37.037 0.00 0.00 0.00 3.02
2545 2601 2.678336 GCACTGCGCCTATTTCTAACTT 59.322 45.455 4.18 0.00 32.94 2.66
2568 2624 0.603975 AGGAACCAGTCGCTTCTTGC 60.604 55.000 0.00 0.00 38.57 4.01
2679 3037 4.657055 CGAAAACGATATTGTGCATTGGA 58.343 39.130 0.00 0.00 0.00 3.53
2738 3096 8.160765 TGAGAGTAGTTTTCACATTAAATGGGA 58.839 33.333 0.00 0.00 41.87 4.37
2926 3284 2.554032 ACTGGTTTGCATCTTGTAGCAC 59.446 45.455 0.00 0.00 41.05 4.40
2927 3285 2.553602 CTGGTTTGCATCTTGTAGCACA 59.446 45.455 0.00 0.00 41.05 4.57
2933 3291 4.743057 TGCATCTTGTAGCACAGTCTAT 57.257 40.909 0.00 0.00 35.51 1.98
3316 3674 2.729194 ACACAGCAACACCCACTAAAA 58.271 42.857 0.00 0.00 0.00 1.52
3365 3723 4.141287 TCAATTCCCACTGTGTTACTTGG 58.859 43.478 7.08 0.00 0.00 3.61
3441 3799 6.418057 TGCTCCAAACAATTATCCAAAACT 57.582 33.333 0.00 0.00 0.00 2.66
3477 3835 9.666626 TTTCATTTGGTGTTATAGTTGTTAACG 57.333 29.630 0.26 0.00 33.23 3.18
3610 3968 2.614829 AACACGTACTCCAAACTGCT 57.385 45.000 0.00 0.00 0.00 4.24
3646 4004 3.657727 AGAAGGAATTGACCCTTGAAGGA 59.342 43.478 13.97 0.00 43.59 3.36
3901 4259 5.415077 AGCAGGAGAGATCTTTGTCAATTTG 59.585 40.000 0.00 0.00 0.00 2.32
4020 4378 6.126863 TCTGACCAATTTAATCAGGTGAGT 57.873 37.500 12.72 0.00 40.28 3.41
4034 4392 6.139679 TCAGGTGAGTTTCCATTTCCTATT 57.860 37.500 0.00 0.00 0.00 1.73
4335 4693 5.934625 AGAAACTGTGATAAAGATGCTTCGT 59.065 36.000 0.00 0.00 0.00 3.85
4405 4763 6.524101 TGAAAATTTTAGGGAGTACCATGC 57.476 37.500 2.75 0.00 43.89 4.06
4524 4882 8.752005 TTTCAAGGGGAAACATATAATCTCAG 57.248 34.615 0.00 0.00 40.51 3.35
4838 5197 8.685838 AAGCAGGTTCACAGTAACTTAATAAA 57.314 30.769 0.00 0.00 0.00 1.40
4844 5203 9.620660 GGTTCACAGTAACTTAATAAATTGTGG 57.379 33.333 0.00 0.00 36.31 4.17
5440 5799 4.084693 GCATGCAAAGCTCTTGAAGAAAAC 60.085 41.667 14.21 0.00 0.00 2.43
5653 6012 7.304735 TGATGGTATGACAAACAAAATTCTCG 58.695 34.615 0.00 0.00 0.00 4.04
5667 6026 8.492673 ACAAAATTCTCGATTGTCTATGCTAA 57.507 30.769 0.00 0.00 32.02 3.09
5803 6162 6.863126 CACTTAAAGGATGCCAAGTTTACAAG 59.137 38.462 0.00 0.00 0.00 3.16
5805 6164 7.451566 ACTTAAAGGATGCCAAGTTTACAAGAT 59.548 33.333 0.00 0.00 0.00 2.40
5811 6170 9.474313 AGGATGCCAAGTTTACAAGATAAATAA 57.526 29.630 0.00 0.00 0.00 1.40
5965 6325 8.956426 GGTTACTCCAATAATTGATTGAGTTGA 58.044 33.333 7.52 0.00 46.94 3.18
6075 6435 2.319025 TCACTAGTCACCATGGTCCA 57.681 50.000 16.53 0.77 0.00 4.02
6326 6686 4.079253 ACAAGCCACTAAATTGATCCGTT 58.921 39.130 0.00 0.00 0.00 4.44
6327 6687 4.082787 ACAAGCCACTAAATTGATCCGTTG 60.083 41.667 0.00 0.00 0.00 4.10
6542 6909 5.930405 TCATGATTGTCTGTTTTGTGATCG 58.070 37.500 0.00 0.00 0.00 3.69
6599 6968 5.240623 TGCGTAGTGGAGAAAAACATTCATT 59.759 36.000 0.00 0.00 0.00 2.57
6915 8276 2.170607 GGGAAATACTAGCACCTCAGCA 59.829 50.000 0.00 0.00 36.85 4.41
7133 8553 2.673775 TGGGATTTCTTTGTGGCTCA 57.326 45.000 0.00 0.00 0.00 4.26
7459 9342 9.743057 CAGTGTTTTCTTGTAAATGTTATTCCA 57.257 29.630 0.00 0.00 0.00 3.53
7513 9421 7.233962 TGTTAGTGTGTCTTCCTTACTATTGGA 59.766 37.037 0.00 0.00 0.00 3.53
7840 10154 5.992829 ACAAACCGTTGTATGTCTGTAATGA 59.007 36.000 0.00 0.00 46.33 2.57
7880 10198 2.440517 ATGCTGTGGATAACATGGCA 57.559 45.000 0.00 0.00 41.22 4.92
7991 10309 5.954335 TCGGATCATGCTATATATATGCGG 58.046 41.667 5.44 4.55 0.00 5.69
8099 10417 6.877611 TTTGTCACTAAGAAAGAACATCCC 57.122 37.500 0.00 0.00 0.00 3.85
8137 10455 3.412386 GGATGCCCGCAGTAAATTCTAT 58.588 45.455 0.00 0.00 0.00 1.98
8149 10467 6.127897 GCAGTAAATTCTATGTTGGAGCACTT 60.128 38.462 0.00 0.00 0.00 3.16
8226 10557 1.498865 CGCGGAATGATCTTTCCCCG 61.499 60.000 26.51 25.46 41.87 5.73
8518 10879 0.033920 TGGTGTCACTAGCAGCAGTG 59.966 55.000 15.18 15.18 46.04 3.66
8524 10885 3.944476 ACTAGCAGCAGTGAAAGGG 57.056 52.632 0.00 0.00 0.00 3.95
8527 10888 2.803155 TAGCAGCAGTGAAAGGGGCG 62.803 60.000 0.00 0.00 0.00 6.13
8528 10889 2.281761 CAGCAGTGAAAGGGGCGT 60.282 61.111 0.00 0.00 0.00 5.68
8589 10964 0.969149 CCTTTCTTCAGGTTTGGGGC 59.031 55.000 0.00 0.00 0.00 5.80
8590 10965 1.703411 CTTTCTTCAGGTTTGGGGCA 58.297 50.000 0.00 0.00 0.00 5.36
8591 10966 2.038659 CTTTCTTCAGGTTTGGGGCAA 58.961 47.619 0.00 0.00 0.00 4.52
8592 10967 1.703411 TTCTTCAGGTTTGGGGCAAG 58.297 50.000 0.00 0.00 0.00 4.01
8593 10968 0.178964 TCTTCAGGTTTGGGGCAAGG 60.179 55.000 0.00 0.00 0.00 3.61
8594 10969 0.178964 CTTCAGGTTTGGGGCAAGGA 60.179 55.000 0.00 0.00 0.00 3.36
8595 10970 0.486879 TTCAGGTTTGGGGCAAGGAT 59.513 50.000 0.00 0.00 0.00 3.24
8596 10971 1.377690 TCAGGTTTGGGGCAAGGATA 58.622 50.000 0.00 0.00 0.00 2.59
8597 10972 1.713647 TCAGGTTTGGGGCAAGGATAA 59.286 47.619 0.00 0.00 0.00 1.75
8598 10973 2.314549 TCAGGTTTGGGGCAAGGATAAT 59.685 45.455 0.00 0.00 0.00 1.28
8599 10974 2.431782 CAGGTTTGGGGCAAGGATAATG 59.568 50.000 0.00 0.00 0.00 1.90
8600 10975 1.138859 GGTTTGGGGCAAGGATAATGC 59.861 52.381 0.00 0.00 43.08 3.56
8601 10976 2.110578 GTTTGGGGCAAGGATAATGCT 58.889 47.619 0.00 0.00 43.34 3.79
8602 10977 2.071778 TTGGGGCAAGGATAATGCTC 57.928 50.000 0.00 0.00 43.70 4.26
8605 10980 1.902938 GGGCAAGGATAATGCTCCTC 58.097 55.000 0.00 0.00 45.15 3.71
8606 10981 1.546548 GGGCAAGGATAATGCTCCTCC 60.547 57.143 0.00 0.00 45.15 4.30
8607 10982 1.546548 GGCAAGGATAATGCTCCTCCC 60.547 57.143 0.00 0.00 45.15 4.30
8608 10983 1.546548 GCAAGGATAATGCTCCTCCCC 60.547 57.143 0.00 0.00 45.15 4.81
8609 10984 2.061061 CAAGGATAATGCTCCTCCCCT 58.939 52.381 0.00 0.00 45.15 4.79
8610 10985 2.444766 CAAGGATAATGCTCCTCCCCTT 59.555 50.000 0.00 0.00 45.15 3.95
8611 10986 2.794286 AGGATAATGCTCCTCCCCTTT 58.206 47.619 0.00 0.00 42.12 3.11
8612 10987 2.713708 AGGATAATGCTCCTCCCCTTTC 59.286 50.000 0.00 0.00 42.12 2.62
8613 10988 2.713708 GGATAATGCTCCTCCCCTTTCT 59.286 50.000 0.00 0.00 32.18 2.52
8614 10989 3.139211 GGATAATGCTCCTCCCCTTTCTT 59.861 47.826 0.00 0.00 32.18 2.52
8615 10990 2.816777 AATGCTCCTCCCCTTTCTTC 57.183 50.000 0.00 0.00 0.00 2.87
8616 10991 1.673767 ATGCTCCTCCCCTTTCTTCA 58.326 50.000 0.00 0.00 0.00 3.02
8617 10992 0.987294 TGCTCCTCCCCTTTCTTCAG 59.013 55.000 0.00 0.00 0.00 3.02
8618 10993 0.254462 GCTCCTCCCCTTTCTTCAGG 59.746 60.000 0.00 0.00 0.00 3.86
8619 10994 1.662686 CTCCTCCCCTTTCTTCAGGT 58.337 55.000 0.00 0.00 30.96 4.00
8620 10995 1.988846 CTCCTCCCCTTTCTTCAGGTT 59.011 52.381 0.00 0.00 30.96 3.50
8621 10996 2.376855 CTCCTCCCCTTTCTTCAGGTTT 59.623 50.000 0.00 0.00 30.96 3.27
8622 10997 2.108250 TCCTCCCCTTTCTTCAGGTTTG 59.892 50.000 0.00 0.00 30.96 2.93
8623 10998 2.519013 CTCCCCTTTCTTCAGGTTTGG 58.481 52.381 0.00 0.00 30.96 3.28
8624 10999 1.146982 TCCCCTTTCTTCAGGTTTGGG 59.853 52.381 0.00 0.00 30.96 4.12
8625 11000 1.632589 CCCTTTCTTCAGGTTTGGGG 58.367 55.000 0.00 0.00 30.96 4.96
8626 11001 0.969149 CCTTTCTTCAGGTTTGGGGC 59.031 55.000 0.00 0.00 0.00 5.80
8691 11070 1.003839 CAAGGGCTGCCGTGAGTTA 60.004 57.895 15.47 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.776322 CGACGGAATGCCTGGCCA 62.776 66.667 17.53 4.71 0.00 5.36
9 10 2.452813 CGTTCGACGGAATGCCTGG 61.453 63.158 0.00 0.00 38.08 4.45
59 60 2.284331 TAGCACCCGAAGCCCAGA 60.284 61.111 0.00 0.00 0.00 3.86
116 118 1.632018 ATCAAATCCCCGGCCTCGAA 61.632 55.000 0.00 0.00 39.00 3.71
245 247 5.418524 ACAATCACCAAAGCAACAGCATATA 59.581 36.000 0.00 0.00 0.00 0.86
246 248 4.221262 ACAATCACCAAAGCAACAGCATAT 59.779 37.500 0.00 0.00 0.00 1.78
247 249 3.573538 ACAATCACCAAAGCAACAGCATA 59.426 39.130 0.00 0.00 0.00 3.14
273 275 3.056962 CAGTTCTAGAGAGAGCACAAGCA 60.057 47.826 0.00 0.00 45.49 3.91
274 276 3.192422 TCAGTTCTAGAGAGAGCACAAGC 59.808 47.826 0.00 0.00 35.46 4.01
291 294 5.471456 CCTCATAAAGTCAAACAGCTCAGTT 59.529 40.000 0.00 0.00 0.00 3.16
337 348 0.107459 GGATCAGAGGCCAAGTCACC 60.107 60.000 5.01 0.00 0.00 4.02
474 485 0.040067 GCAGTGAAAAAGGGACAGCG 60.040 55.000 0.00 0.00 0.00 5.18
475 486 0.315251 GGCAGTGAAAAAGGGACAGC 59.685 55.000 0.00 0.00 0.00 4.40
476 487 0.593128 CGGCAGTGAAAAAGGGACAG 59.407 55.000 0.00 0.00 0.00 3.51
480 491 1.524008 GGGACGGCAGTGAAAAAGGG 61.524 60.000 0.00 0.00 0.00 3.95
495 506 2.291741 GAGCATTTTCGGATCATGGGAC 59.708 50.000 0.00 0.00 0.00 4.46
653 670 3.405170 AATTCTGTAGCGAAAATGCCG 57.595 42.857 0.00 0.00 34.65 5.69
675 692 8.978874 ATCAACAGGTAATGCATATTCAAGTA 57.021 30.769 0.00 0.00 0.00 2.24
681 698 9.578576 AACTATGATCAACAGGTAATGCATATT 57.421 29.630 0.00 0.00 0.00 1.28
714 731 0.889186 GGAGAAACAAGCTTGCCGGA 60.889 55.000 26.27 0.00 0.00 5.14
740 757 4.822026 ACTGAATTGCACAGTACTAGGAC 58.178 43.478 6.66 0.00 45.10 3.85
916 971 2.885266 TCTGAGAACAGCAAGTCGTAGT 59.115 45.455 0.00 0.00 43.17 2.73
972 1027 1.225855 CGGCTCTTGCTTACACACAA 58.774 50.000 0.00 0.00 39.59 3.33
1071 1126 1.027357 GGTACTCGTCGCCCATCTTA 58.973 55.000 0.00 0.00 0.00 2.10
1157 1212 6.790232 TTCCAAGTTTCTCCATTTTGAACT 57.210 33.333 0.00 0.00 0.00 3.01
1186 1241 3.371898 TCAACATCATTGAGTGCATCGTC 59.628 43.478 0.00 0.00 0.00 4.20
1827 1882 3.495193 CATCATGTGCCTTCTTTGAACG 58.505 45.455 0.00 0.00 0.00 3.95
2016 2071 9.283768 TGAAAAGTATATGAAGCAGAAAAGTCA 57.716 29.630 0.00 0.00 0.00 3.41
2038 2093 5.755409 TTTATAGAGTGGGAGCTGTGAAA 57.245 39.130 0.00 0.00 0.00 2.69
2044 2099 6.963322 AGTCAAAATTTATAGAGTGGGAGCT 58.037 36.000 0.00 0.00 0.00 4.09
2148 2203 6.332976 ACCTCCCTCTTGACATTATTCATT 57.667 37.500 0.00 0.00 0.00 2.57
2511 2567 0.242017 GCAGTGCCACTGGATGAAAC 59.758 55.000 25.24 3.90 46.01 2.78
2545 2601 2.450609 GAAGCGACTGGTTCCTACAA 57.549 50.000 0.00 0.00 44.83 2.41
2679 3037 3.228188 TGCAATCCTCACAAGAAGGTT 57.772 42.857 0.00 0.00 0.00 3.50
2766 3124 6.799512 AGGAACAAAATATAGAACAGCATGC 58.200 36.000 10.51 10.51 42.53 4.06
3295 3653 2.428544 TTAGTGGGTGTTGCTGTGTT 57.571 45.000 0.00 0.00 0.00 3.32
3302 3660 7.214467 ACATTATGTCTTTTAGTGGGTGTTG 57.786 36.000 0.00 0.00 0.00 3.33
3441 3799 3.118482 ACACCAAATGAAATGCACCAACA 60.118 39.130 0.00 0.00 0.00 3.33
3477 3835 6.651225 AGTGTCTTAGGCACAAAGAGAAATAC 59.349 38.462 19.53 0.00 39.17 1.89
3610 3968 1.904537 TCCTTCTTCAGAGATGCAGCA 59.095 47.619 4.07 0.00 0.00 4.41
3734 4092 0.323178 GACTCTGGGTCCGGTACAGA 60.323 60.000 19.12 19.12 38.93 3.41
3901 4259 6.445357 TCATTTTAAGTAAGCGAAATCCCC 57.555 37.500 0.00 0.00 0.00 4.81
4020 4378 8.429237 TGCTTTAGGAAAATAGGAAATGGAAA 57.571 30.769 0.00 0.00 0.00 3.13
4034 4392 4.316025 AAGGCTGGTATGCTTTAGGAAA 57.684 40.909 0.00 0.00 30.43 3.13
4335 4693 0.750249 TCTTCACGACTGGAGCAACA 59.250 50.000 0.00 0.00 0.00 3.33
4405 4763 1.266989 GAAGCCAAACAACTTCTCCCG 59.733 52.381 0.00 0.00 39.36 5.14
4523 4881 7.950124 TGAGAAAAGGAGATAAAACAAATCCCT 59.050 33.333 0.00 0.00 0.00 4.20
4524 4882 8.122472 TGAGAAAAGGAGATAAAACAAATCCC 57.878 34.615 0.00 0.00 0.00 3.85
4595 4954 4.274459 GCTTGCATATACCTCTTGAACAGG 59.726 45.833 0.00 0.00 37.03 4.00
5440 5799 7.264373 ACACTTGGATTTCTTGTTAAGTGAG 57.736 36.000 18.37 0.00 44.59 3.51
5554 5913 9.151471 CCGTTATTTACTATGTCTATTCCATGG 57.849 37.037 4.97 4.97 0.00 3.66
5653 6012 6.163159 GCTAGCATGTTAGCATAGACAATC 57.837 41.667 29.96 2.88 44.30 2.67
5667 6026 5.711976 AGAAACCAAACTAATGCTAGCATGT 59.288 36.000 30.19 21.17 36.68 3.21
5834 6193 5.360714 AGTGGTGTGTTCATGAAAAGAATGT 59.639 36.000 10.35 0.00 0.00 2.71
5838 6197 4.946772 TGAAGTGGTGTGTTCATGAAAAGA 59.053 37.500 10.35 0.00 0.00 2.52
5932 6291 3.375647 TTATTGGAGTAACCCTTGCCC 57.624 47.619 0.00 0.00 38.00 5.36
5965 6325 2.838736 AGAACAAGTCACGCAATGAGT 58.161 42.857 0.00 0.00 43.29 3.41
5974 6334 4.439057 TGGAACACACTAGAACAAGTCAC 58.561 43.478 0.00 0.00 0.00 3.67
6028 6388 1.017387 GCAAGGAGGGCAACTAATCG 58.983 55.000 0.00 0.00 0.00 3.34
6075 6435 8.926710 GCTACGCTATCAAACAATATCAATACT 58.073 33.333 0.00 0.00 0.00 2.12
6153 6513 7.118825 CGCCAGTAATGATATCACAAGATGATT 59.881 37.037 7.78 0.00 46.54 2.57
6219 6579 3.996480 AGAGCAGAAGAAACACTACCAC 58.004 45.455 0.00 0.00 0.00 4.16
6226 6586 4.572389 GTCAACAGAAGAGCAGAAGAAACA 59.428 41.667 0.00 0.00 0.00 2.83
6326 6686 4.501229 CCAACAGCCAGTATTTTCAAAGCA 60.501 41.667 0.00 0.00 0.00 3.91
6327 6687 3.989817 CCAACAGCCAGTATTTTCAAAGC 59.010 43.478 0.00 0.00 0.00 3.51
6859 7912 6.715264 GGAGAGGAAAAAGAAAATGACCTACA 59.285 38.462 0.00 0.00 0.00 2.74
7513 9421 4.953940 AAAAGAGCTCTCTGTCTGTCTT 57.046 40.909 18.55 0.68 40.36 3.01
7630 9543 6.330250 GGATAAGATATATACAGGGGTGGCAT 59.670 42.308 0.00 0.00 0.00 4.40
7666 9595 5.655090 TGAAGCTACTGGCAGTAATACAGTA 59.345 40.000 26.12 5.60 43.13 2.74
7840 10154 9.107177 CAGCATTCACTAAGATAAGAAACAGAT 57.893 33.333 0.00 0.00 0.00 2.90
7880 10198 7.669427 TCAAAGTCATTGCATAAAAGGTCATT 58.331 30.769 0.00 0.00 38.98 2.57
8069 10387 9.698309 TGTTCTTTCTTAGTGACAAATCTCTAG 57.302 33.333 0.00 0.00 33.57 2.43
8137 10455 3.485394 TGCTTTATGAAGTGCTCCAACA 58.515 40.909 0.00 0.00 35.25 3.33
8226 10557 4.082081 TGCTTTGATCCAACACAATGATCC 60.082 41.667 0.00 0.00 35.18 3.36
8518 10879 2.335712 CCTTCAGCACGCCCCTTTC 61.336 63.158 0.00 0.00 0.00 2.62
8527 10888 1.003233 GTCAGGTCCCCTTCAGCAC 60.003 63.158 0.00 0.00 0.00 4.40
8528 10889 1.059584 TTGTCAGGTCCCCTTCAGCA 61.060 55.000 0.00 0.00 0.00 4.41
8592 10967 2.713708 AGAAAGGGGAGGAGCATTATCC 59.286 50.000 0.00 0.00 39.89 2.59
8593 10968 4.141390 TGAAGAAAGGGGAGGAGCATTATC 60.141 45.833 0.00 0.00 0.00 1.75
8594 10969 3.788142 TGAAGAAAGGGGAGGAGCATTAT 59.212 43.478 0.00 0.00 0.00 1.28
8595 10970 3.189606 TGAAGAAAGGGGAGGAGCATTA 58.810 45.455 0.00 0.00 0.00 1.90
8596 10971 1.995542 TGAAGAAAGGGGAGGAGCATT 59.004 47.619 0.00 0.00 0.00 3.56
8597 10972 1.563410 CTGAAGAAAGGGGAGGAGCAT 59.437 52.381 0.00 0.00 0.00 3.79
8598 10973 0.987294 CTGAAGAAAGGGGAGGAGCA 59.013 55.000 0.00 0.00 0.00 4.26
8599 10974 0.254462 CCTGAAGAAAGGGGAGGAGC 59.746 60.000 0.00 0.00 33.28 4.70
8600 10975 1.662686 ACCTGAAGAAAGGGGAGGAG 58.337 55.000 0.00 0.00 42.11 3.69
8601 10976 2.108250 CAAACCTGAAGAAAGGGGAGGA 59.892 50.000 0.00 0.00 42.11 3.71
8602 10977 2.519013 CAAACCTGAAGAAAGGGGAGG 58.481 52.381 0.00 0.00 42.11 4.30
8603 10978 2.519013 CCAAACCTGAAGAAAGGGGAG 58.481 52.381 0.00 0.00 42.11 4.30
8604 10979 1.146982 CCCAAACCTGAAGAAAGGGGA 59.853 52.381 0.00 0.00 42.11 4.81
8605 10980 1.632589 CCCAAACCTGAAGAAAGGGG 58.367 55.000 0.00 0.00 42.11 4.79
8606 10981 1.632589 CCCCAAACCTGAAGAAAGGG 58.367 55.000 0.00 0.00 42.11 3.95
8607 10982 0.969149 GCCCCAAACCTGAAGAAAGG 59.031 55.000 0.00 0.00 43.57 3.11
8608 10983 1.703411 TGCCCCAAACCTGAAGAAAG 58.297 50.000 0.00 0.00 0.00 2.62
8609 10984 2.038659 CTTGCCCCAAACCTGAAGAAA 58.961 47.619 0.00 0.00 0.00 2.52
8610 10985 1.703411 CTTGCCCCAAACCTGAAGAA 58.297 50.000 0.00 0.00 0.00 2.52
8611 10986 0.178964 CCTTGCCCCAAACCTGAAGA 60.179 55.000 0.00 0.00 0.00 2.87
8612 10987 1.187567 CCCTTGCCCCAAACCTGAAG 61.188 60.000 0.00 0.00 0.00 3.02
8613 10988 1.152355 CCCTTGCCCCAAACCTGAA 60.152 57.895 0.00 0.00 0.00 3.02
8614 10989 2.525592 CCCTTGCCCCAAACCTGA 59.474 61.111 0.00 0.00 0.00 3.86
8615 10990 2.604382 CCCCTTGCCCCAAACCTG 60.604 66.667 0.00 0.00 0.00 4.00
8616 10991 2.264494 AAACCCCTTGCCCCAAACCT 62.264 55.000 0.00 0.00 0.00 3.50
8617 10992 1.349542 AAAACCCCTTGCCCCAAACC 61.350 55.000 0.00 0.00 0.00 3.27
8618 10993 0.548989 AAAAACCCCTTGCCCCAAAC 59.451 50.000 0.00 0.00 0.00 2.93
8619 10994 0.840617 GAAAAACCCCTTGCCCCAAA 59.159 50.000 0.00 0.00 0.00 3.28
8620 10995 1.057275 GGAAAAACCCCTTGCCCCAA 61.057 55.000 0.00 0.00 0.00 4.12
8621 10996 1.460497 GGAAAAACCCCTTGCCCCA 60.460 57.895 0.00 0.00 0.00 4.96
8622 10997 1.152118 AGGAAAAACCCCTTGCCCC 60.152 57.895 0.00 0.00 40.05 5.80
8623 10998 1.480212 CCAGGAAAAACCCCTTGCCC 61.480 60.000 0.00 0.00 40.05 5.36
8624 10999 1.480212 CCCAGGAAAAACCCCTTGCC 61.480 60.000 0.00 0.00 40.05 4.52
8625 11000 0.471022 TCCCAGGAAAAACCCCTTGC 60.471 55.000 0.00 0.00 40.05 4.01
8626 11001 1.970640 CTTCCCAGGAAAAACCCCTTG 59.029 52.381 0.00 0.00 40.05 3.61
8658 11033 1.155042 CCTTGTGCTCAACTGCTCTC 58.845 55.000 0.00 0.00 0.00 3.20


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

AutoCloner maintained by Alex Coulton.