Multiple sequence alignment - TraesCS3B01G369300

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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 TraesCS3B01G369300 chr3B 100.000 7832 0 0 1 7832 581342244 581334413 0.000000e+00 14464
1 TraesCS3B01G369300 chr3B 100.000 113 0 0 1451 1563 581344418 581344530 7.960000e-50 209
2 TraesCS3B01G369300 chr4D 96.893 7305 171 20 182 7472 349007112 349014374 0.000000e+00 12181
3 TraesCS3B01G369300 chr4D 93.301 209 11 3 7498 7704 302343251 302343044 9.870000e-79 305
4 TraesCS3B01G369300 chr4D 95.699 186 8 0 1 186 349004869 349005054 4.590000e-77 300
5 TraesCS3B01G369300 chr4A 97.019 3959 99 11 3518 7466 115915522 115911573 0.000000e+00 6639
6 TraesCS3B01G369300 chr4A 95.785 1281 38 6 1117 2396 115918121 115916856 0.000000e+00 2052
7 TraesCS3B01G369300 chr4A 96.844 1109 30 5 2394 3500 115916615 115915510 0.000000e+00 1849
8 TraesCS3B01G369300 chr4A 96.186 1075 37 2 1 1074 115919604 115918533 0.000000e+00 1755
9 TraesCS3B01G369300 chr6A 95.816 3705 129 16 2164 5853 466340674 466336981 0.000000e+00 5960
10 TraesCS3B01G369300 chr6A 95.118 2745 99 5 1 2715 466330971 466328232 0.000000e+00 4294
11 TraesCS3B01G369300 chr6A 96.654 2570 65 8 4932 7498 466325242 466322691 0.000000e+00 4250
12 TraesCS3B01G369300 chr6A 95.317 1922 90 0 1 1922 466345379 466343458 0.000000e+00 3051
13 TraesCS3B01G369300 chr6A 95.021 1928 90 3 1 1922 466363405 466361478 0.000000e+00 3024
14 TraesCS3B01G369300 chr6A 93.757 1922 94 13 1 1922 466350192 466348297 0.000000e+00 2861
15 TraesCS3B01G369300 chr6A 92.564 1950 92 26 1 1922 466358584 466356660 0.000000e+00 2748
16 TraesCS3B01G369300 chr6A 96.602 1295 30 7 2748 4033 466328233 466326944 0.000000e+00 2135
17 TraesCS3B01G369300 chr6A 98.182 880 14 2 4043 4922 466326516 466325639 0.000000e+00 1535
18 TraesCS3B01G369300 chr6A 94.656 131 5 1 7704 7832 108072995 108072865 1.330000e-47 202
19 TraesCS3B01G369300 chr4B 96.741 3160 94 6 1 3155 429091943 429095098 0.000000e+00 5256
20 TraesCS3B01G369300 chr4B 96.778 3073 66 8 4597 7649 429095100 429098159 0.000000e+00 5096
21 TraesCS3B01G369300 chr4B 94.660 206 8 3 7501 7704 593592924 593592720 4.560000e-82 316
22 TraesCS3B01G369300 chr4B 95.161 124 6 0 7704 7827 565485100 565485223 6.200000e-46 196
23 TraesCS3B01G369300 chr4B 93.893 131 6 1 7704 7832 593592771 593592641 6.200000e-46 196
24 TraesCS3B01G369300 chr7D 94.203 207 10 2 7500 7704 293961616 293961822 1.640000e-81 315
25 TraesCS3B01G369300 chr7D 94.203 207 10 2 7500 7704 294114630 294114424 1.640000e-81 315
26 TraesCS3B01G369300 chr5B 94.175 206 9 3 7501 7704 278205665 278205461 2.120000e-80 311
27 TraesCS3B01G369300 chr5B 94.175 206 9 3 7501 7704 387152413 387152209 2.120000e-80 311
28 TraesCS3B01G369300 chr5B 93.750 208 10 3 7499 7704 418314664 418314870 7.630000e-80 309
29 TraesCS3B01G369300 chr2B 94.175 206 9 3 7501 7704 725997559 725997763 2.120000e-80 311
30 TraesCS3B01G369300 chr2B 94.656 131 5 1 7704 7832 590332658 590332528 1.330000e-47 202
31 TraesCS3B01G369300 chr6B 93.893 131 6 1 7704 7832 500564279 500564149 6.200000e-46 196
32 TraesCS3B01G369300 chr1D 93.893 131 6 1 7704 7832 88372444 88372314 6.200000e-46 196
33 TraesCS3B01G369300 chr1B 93.893 131 6 1 7704 7832 373130192 373130062 6.200000e-46 196
34 TraesCS3B01G369300 chr1B 93.893 131 6 1 7704 7832 475477027 475476897 6.200000e-46 196
35 TraesCS3B01G369300 chr1B 93.893 131 6 2 7704 7832 574352974 574353104 6.200000e-46 196


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 TraesCS3B01G369300 chr3B 581334413 581342244 7831 True 14464.000000 14464 100.000000 1 7832 1 chr3B.!!$R1 7831
1 TraesCS3B01G369300 chr4D 349004869 349014374 9505 False 6240.500000 12181 96.296000 1 7472 2 chr4D.!!$F1 7471
2 TraesCS3B01G369300 chr4A 115911573 115919604 8031 True 3073.750000 6639 96.458500 1 7466 4 chr4A.!!$R1 7465
3 TraesCS3B01G369300 chr6A 466336981 466350192 13211 True 3957.333333 5960 94.963333 1 5853 3 chr6A.!!$R3 5852
4 TraesCS3B01G369300 chr6A 466322691 466330971 8280 True 3053.500000 4294 96.639000 1 7498 4 chr6A.!!$R2 7497
5 TraesCS3B01G369300 chr6A 466356660 466363405 6745 True 2886.000000 3024 93.792500 1 1922 2 chr6A.!!$R4 1921
6 TraesCS3B01G369300 chr4B 429091943 429098159 6216 False 5176.000000 5256 96.759500 1 7649 2 chr4B.!!$F2 7648

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
782 7661 1.022982 TTGAGCATGCAGGAGAAGCG 61.023 55.000 21.98 0.0 33.85 4.68 F
1997 14075 0.734889 CGATGATGCCCAAACCTGTC 59.265 55.000 0.00 0.0 0.00 3.51 F
2971 17876 1.029681 TATCTCTTTAGCTGCGCCGA 58.970 50.000 4.18 0.0 0.00 5.54 F
3018 17923 4.215109 ACAGTTTTACATCAAGGCCAAGT 58.785 39.130 5.01 0.0 0.00 3.16 F
4427 19798 6.412362 AGGGTGATAATGATAGTGTCTGAC 57.588 41.667 0.00 0.0 0.00 3.51 F
5127 20891 0.673985 GGCCCAACTGTTTGAGGAAC 59.326 55.000 0.00 0.0 38.78 3.62 F
5678 21442 2.433868 TGCACAGGTAGAAACGACTC 57.566 50.000 0.00 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2543 17411 1.276622 AAATGAGCTACCAGGACCGT 58.723 50.000 0.0 0.0 0.00 4.83 R
3194 18099 2.554462 TCGATCAGTAGCTGGATGTAGC 59.446 50.000 0.0 0.0 44.01 3.58 R
4427 19798 4.022416 GGAGTGTATCTATCTGCTGTGGAG 60.022 50.000 0.0 0.0 0.00 3.86 R
4972 20732 7.121463 GGATCTAAAGAGAAGTGAGACTGTACA 59.879 40.741 0.0 0.0 34.61 2.90 R
5645 21409 0.325933 TGTGCATGAGTTCCTCCCAG 59.674 55.000 0.0 0.0 0.00 4.45 R
5953 21717 1.008538 CAAAGCTCAACACCGCACC 60.009 57.895 0.0 0.0 0.00 5.01 R
7446 23224 1.581934 CAAGAAACAGACACCAGCGA 58.418 50.000 0.0 0.0 0.00 4.93 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
32 33 2.501723 ACTGATACTGGGAGCGATGTTT 59.498 45.455 0.00 0.00 0.00 2.83
77 79 8.652290 ACCTGTATTTTTGGCAATTTACCTTTA 58.348 29.630 0.00 0.00 0.00 1.85
104 106 7.505585 TGTTCTTATCACCAGAAATCCTTTTGT 59.494 33.333 0.00 0.00 31.98 2.83
109 111 4.037923 TCACCAGAAATCCTTTTGTCAAGC 59.962 41.667 0.00 0.00 0.00 4.01
121 123 5.403897 TTTTGTCAAGCTGAAAGTACTCG 57.596 39.130 0.00 0.00 35.30 4.18
235 7114 5.914898 AACTTGCAAGTTTTACTCCACTT 57.085 34.783 33.85 12.06 46.52 3.16
523 7402 6.484977 GGTTGAAGATGAATTCTATCAGGTCC 59.515 42.308 7.05 6.38 33.05 4.46
559 7438 3.284617 ACCACATAATTCCCCTTAACGC 58.715 45.455 0.00 0.00 0.00 4.84
607 7486 1.104630 GTTCTCCCTACAGGTCCGAG 58.895 60.000 0.00 0.00 36.75 4.63
624 7503 2.226437 CCGAGCAGTTGCATGTAAAACT 59.774 45.455 6.90 1.40 45.16 2.66
782 7661 1.022982 TTGAGCATGCAGGAGAAGCG 61.023 55.000 21.98 0.00 33.85 4.68
834 7713 7.932120 AATGTATCTCGTGTAAGTTAGATGC 57.068 36.000 0.00 0.00 33.33 3.91
865 7744 9.908152 ATTGGTTCTTTATTTGTAGTTAACTGC 57.092 29.630 18.56 17.20 0.00 4.40
986 7865 5.500234 CAAAATCCTAGGGTCAGTGAATCA 58.500 41.667 9.46 0.00 0.00 2.57
1036 7915 3.264193 ACTTGATGGTCTCATTGCAGGTA 59.736 43.478 0.00 0.00 32.72 3.08
1301 8549 5.542779 ACTCTTTTCTTCTATGTTGCGACT 58.457 37.500 5.50 0.00 0.00 4.18
1597 8849 7.721842 TGTACCCATGTTCTTATTTTCTGTCAA 59.278 33.333 0.00 0.00 0.00 3.18
1609 8861 9.869844 CTTATTTTCTGTCAATCGTATGGAATC 57.130 33.333 0.00 0.00 0.00 2.52
1629 8881 8.860780 GGAATCTGAGAATATTCCAAGCTATT 57.139 34.615 11.92 6.70 46.95 1.73
1692 8945 7.223971 CAGGCTGCTAAGTAATTTGTAACGATA 59.776 37.037 0.00 0.00 0.00 2.92
1790 13840 9.219603 CAGTTTGATTTAGGACAACTGAATCTA 57.780 33.333 11.46 3.63 46.69 1.98
1997 14075 0.734889 CGATGATGCCCAAACCTGTC 59.265 55.000 0.00 0.00 0.00 3.51
2008 14086 3.636300 CCCAAACCTGTCACAAAAGATGA 59.364 43.478 0.00 0.00 0.00 2.92
2075 14153 5.523059 AGTTCGGACTTTTGGGTGAACCA 62.523 47.826 1.16 0.00 39.57 3.67
2234 16854 9.793259 AGACCGGAAAATGTATAATGTCATTAT 57.207 29.630 19.48 19.48 38.83 1.28
2282 16903 8.021973 ACTTGTCTACAACATTTAGAGACTACG 58.978 37.037 0.00 0.00 37.82 3.51
2339 16960 3.570912 AGGTTTCGTGAGGGAAAGAAA 57.429 42.857 0.00 0.00 36.64 2.52
2346 16967 7.983484 GGTTTCGTGAGGGAAAGAAATATACTA 59.017 37.037 0.00 0.00 36.64 1.82
2426 17290 4.134563 ACCACAGTTTGAGACCACAATAC 58.865 43.478 0.00 0.00 0.00 1.89
2543 17411 6.486320 TGATCACTGTTAGCAGATTGTTTGAA 59.514 34.615 14.09 0.00 45.28 2.69
2679 17547 3.256136 ACTTGAGTTCTACAACGAGAGGG 59.744 47.826 0.00 0.00 37.61 4.30
2914 17816 4.023707 CAGAGTGTTCCATTTCTCCAACAC 60.024 45.833 5.79 5.79 45.96 3.32
2971 17876 1.029681 TATCTCTTTAGCTGCGCCGA 58.970 50.000 4.18 0.00 0.00 5.54
3018 17923 4.215109 ACAGTTTTACATCAAGGCCAAGT 58.785 39.130 5.01 0.00 0.00 3.16
3194 18099 8.534333 AACATATCTATTACATAGGTTGCACG 57.466 34.615 0.00 0.00 31.29 5.34
3425 18334 6.493115 TCTTGTCCATTCAAACACATGGTTAT 59.507 34.615 0.00 0.00 40.90 1.89
4427 19798 6.412362 AGGGTGATAATGATAGTGTCTGAC 57.588 41.667 0.00 0.00 0.00 3.51
4972 20732 5.046376 TGAGATGGTGTGTTCAGTATGTGAT 60.046 40.000 0.00 0.00 37.40 3.06
5127 20891 0.673985 GGCCCAACTGTTTGAGGAAC 59.326 55.000 0.00 0.00 38.78 3.62
5166 20930 9.480053 ACAATGTGGTGAAAAGAATTTGAATAG 57.520 29.630 0.00 0.00 39.02 1.73
5260 21024 6.932960 ACTTGTTTTTATGCGTAGGTAGAGTT 59.067 34.615 0.00 0.00 0.00 3.01
5500 21264 3.681593 TTTTCACATGCAATTCCCCTG 57.318 42.857 0.00 0.00 0.00 4.45
5678 21442 2.433868 TGCACAGGTAGAAACGACTC 57.566 50.000 0.00 0.00 0.00 3.36
5801 21565 8.035984 GCAGTATAGGAGAAGTTCAAAGTACTT 58.964 37.037 1.12 1.12 38.49 2.24
5916 21680 9.552114 CTTTATTGTAGAACATGCAAAGAAGAG 57.448 33.333 0.00 0.00 37.05 2.85
5953 21717 6.373774 AGCTGTAAATTCTTCTGGATCAACTG 59.626 38.462 0.00 0.00 0.00 3.16
6055 21819 1.250154 TTCTCATGCTTTTGGCCCCG 61.250 55.000 0.00 0.00 40.92 5.73
6443 22207 0.179045 GTGCTGCAAGTCCGGGATAT 60.179 55.000 2.77 0.00 35.30 1.63
6828 22592 2.485038 GCAAAGGCAATGGTTGAAATGG 59.515 45.455 0.00 0.00 40.72 3.16
6901 22665 5.460646 CACCATTGTGTTCTAACATCAACC 58.539 41.667 0.00 0.00 41.59 3.77
6979 22743 8.268850 AGTTTCATATGATTAGTTGTGTCACC 57.731 34.615 6.17 0.00 0.00 4.02
7027 22792 9.914131 ATTAGTTGTTTTCTTTAAGAATGGAGC 57.086 29.630 8.31 0.00 33.67 4.70
7028 22793 6.749139 AGTTGTTTTCTTTAAGAATGGAGCC 58.251 36.000 8.31 0.00 33.67 4.70
7153 22919 5.452777 GGTAAGCAAGAACAAAGCAGTTAG 58.547 41.667 0.00 0.00 0.00 2.34
7324 23092 4.082841 TGTGCATGTATGATTTGTGTGTCC 60.083 41.667 0.00 0.00 0.00 4.02
7446 23224 6.035866 TGTGTGTTTACGTTTGTCGAAAGTAT 59.964 34.615 0.00 0.00 42.86 2.12
7492 23273 3.608008 CGCTGTGGCTTCTTTTCTTCTTC 60.608 47.826 0.00 0.00 36.09 2.87
7532 23314 4.440112 CCTTTCGGTTTATGGGCTCAAATC 60.440 45.833 0.00 0.00 0.00 2.17
7534 23316 3.541632 TCGGTTTATGGGCTCAAATCTC 58.458 45.455 0.00 0.00 0.00 2.75
7583 23365 5.241949 GTGAGTGGAGGAATGTATCTCGTAT 59.758 44.000 0.00 0.00 0.00 3.06
7656 23439 2.635714 CATGCATGCTTGGTCACTAGA 58.364 47.619 22.49 0.00 0.00 2.43
7657 23440 3.211865 CATGCATGCTTGGTCACTAGAT 58.788 45.455 22.49 0.00 0.00 1.98
7658 23441 2.635714 TGCATGCTTGGTCACTAGATG 58.364 47.619 20.33 0.00 0.00 2.90
7659 23442 2.236893 TGCATGCTTGGTCACTAGATGA 59.763 45.455 20.33 0.00 33.79 2.92
7660 23443 2.871022 GCATGCTTGGTCACTAGATGAG 59.129 50.000 11.37 0.00 38.28 2.90
7661 23444 3.681034 GCATGCTTGGTCACTAGATGAGT 60.681 47.826 11.37 0.00 38.28 3.41
7662 23445 4.442052 GCATGCTTGGTCACTAGATGAGTA 60.442 45.833 11.37 0.00 38.28 2.59
7663 23446 4.991153 TGCTTGGTCACTAGATGAGTAG 57.009 45.455 0.00 0.00 38.28 2.57
7664 23447 3.701542 TGCTTGGTCACTAGATGAGTAGG 59.298 47.826 0.00 0.00 38.28 3.18
7665 23448 3.954904 GCTTGGTCACTAGATGAGTAGGA 59.045 47.826 0.00 0.00 38.28 2.94
7666 23449 4.402793 GCTTGGTCACTAGATGAGTAGGAA 59.597 45.833 0.00 0.00 38.28 3.36
7667 23450 5.680151 GCTTGGTCACTAGATGAGTAGGAAC 60.680 48.000 0.00 0.00 38.28 3.62
7668 23451 4.930696 TGGTCACTAGATGAGTAGGAACA 58.069 43.478 0.00 0.00 38.28 3.18
7669 23452 5.519808 TGGTCACTAGATGAGTAGGAACAT 58.480 41.667 0.00 0.00 38.28 2.71
7670 23453 5.958380 TGGTCACTAGATGAGTAGGAACATT 59.042 40.000 0.00 0.00 38.28 2.71
7671 23454 7.123383 TGGTCACTAGATGAGTAGGAACATTA 58.877 38.462 0.00 0.00 38.28 1.90
7672 23455 7.785028 TGGTCACTAGATGAGTAGGAACATTAT 59.215 37.037 0.00 0.00 38.28 1.28
7673 23456 9.298250 GGTCACTAGATGAGTAGGAACATTATA 57.702 37.037 0.00 0.00 38.28 0.98
7676 23459 9.579768 CACTAGATGAGTAGGAACATTATATGC 57.420 37.037 0.00 0.00 35.64 3.14
7677 23460 9.314133 ACTAGATGAGTAGGAACATTATATGCA 57.686 33.333 0.00 0.00 36.27 3.96
7682 23465 8.978874 TGAGTAGGAACATTATATGCATTTGT 57.021 30.769 3.54 1.34 0.00 2.83
7683 23466 8.839343 TGAGTAGGAACATTATATGCATTTGTG 58.161 33.333 3.54 3.76 0.00 3.33
7684 23467 8.752005 AGTAGGAACATTATATGCATTTGTGT 57.248 30.769 3.54 4.41 0.00 3.72
7685 23468 8.623903 AGTAGGAACATTATATGCATTTGTGTG 58.376 33.333 3.54 0.84 0.00 3.82
7686 23469 7.408756 AGGAACATTATATGCATTTGTGTGT 57.591 32.000 3.54 1.51 0.00 3.72
7687 23470 7.839907 AGGAACATTATATGCATTTGTGTGTT 58.160 30.769 3.54 10.34 0.00 3.32
7688 23471 7.975616 AGGAACATTATATGCATTTGTGTGTTC 59.024 33.333 22.68 22.68 41.08 3.18
7689 23472 7.975616 GGAACATTATATGCATTTGTGTGTTCT 59.024 33.333 25.97 9.77 41.37 3.01
7690 23473 9.357652 GAACATTATATGCATTTGTGTGTTCTT 57.642 29.630 23.07 7.39 39.60 2.52
7691 23474 9.709495 AACATTATATGCATTTGTGTGTTCTTT 57.291 25.926 3.54 0.00 0.00 2.52
7692 23475 9.709495 ACATTATATGCATTTGTGTGTTCTTTT 57.291 25.926 3.54 0.00 0.00 2.27
7718 23501 9.601217 TTTAATTCTTGCTAGATGAGTAGGAAC 57.399 33.333 0.00 0.00 38.41 3.62
7719 23502 6.798427 ATTCTTGCTAGATGAGTAGGAACA 57.202 37.500 0.00 0.00 38.41 3.18
7720 23503 6.798427 TTCTTGCTAGATGAGTAGGAACAT 57.202 37.500 0.00 0.00 32.14 2.71
7721 23504 6.798427 TCTTGCTAGATGAGTAGGAACATT 57.202 37.500 0.00 0.00 0.00 2.71
7722 23505 7.898014 TCTTGCTAGATGAGTAGGAACATTA 57.102 36.000 0.00 0.00 0.00 1.90
7723 23506 7.717568 TCTTGCTAGATGAGTAGGAACATTAC 58.282 38.462 0.00 0.00 0.00 1.89
7724 23507 7.342026 TCTTGCTAGATGAGTAGGAACATTACA 59.658 37.037 0.00 0.00 0.00 2.41
7725 23508 7.603180 TGCTAGATGAGTAGGAACATTACAT 57.397 36.000 0.00 0.00 0.00 2.29
7726 23509 7.436933 TGCTAGATGAGTAGGAACATTACATG 58.563 38.462 0.00 0.00 0.00 3.21
7727 23510 6.367422 GCTAGATGAGTAGGAACATTACATGC 59.633 42.308 0.00 0.00 0.00 4.06
7728 23511 6.239217 AGATGAGTAGGAACATTACATGCA 57.761 37.500 0.00 0.00 0.00 3.96
7729 23512 6.835174 AGATGAGTAGGAACATTACATGCAT 58.165 36.000 0.00 0.00 0.00 3.96
7730 23513 7.285566 AGATGAGTAGGAACATTACATGCATT 58.714 34.615 0.00 0.00 0.00 3.56
7731 23514 7.776969 AGATGAGTAGGAACATTACATGCATTT 59.223 33.333 0.00 0.00 0.00 2.32
7732 23515 7.087409 TGAGTAGGAACATTACATGCATTTG 57.913 36.000 0.00 0.00 0.00 2.32
7733 23516 6.658816 TGAGTAGGAACATTACATGCATTTGT 59.341 34.615 0.00 0.00 0.00 2.83
7734 23517 6.855836 AGTAGGAACATTACATGCATTTGTG 58.144 36.000 0.00 0.00 0.00 3.33
7735 23518 5.726980 AGGAACATTACATGCATTTGTGT 57.273 34.783 0.00 0.00 0.00 3.72
7736 23519 5.472148 AGGAACATTACATGCATTTGTGTG 58.528 37.500 0.00 1.46 0.00 3.82
7737 23520 5.010922 AGGAACATTACATGCATTTGTGTGT 59.989 36.000 0.00 2.11 33.79 3.72
7738 23521 5.695816 GGAACATTACATGCATTTGTGTGTT 59.304 36.000 18.17 18.17 39.90 3.32
7739 23522 6.128849 GGAACATTACATGCATTTGTGTGTTC 60.129 38.462 25.93 25.93 44.75 3.18
7740 23523 6.088016 ACATTACATGCATTTGTGTGTTCT 57.912 33.333 0.00 0.00 30.49 3.01
7741 23524 6.514947 ACATTACATGCATTTGTGTGTTCTT 58.485 32.000 0.00 0.00 30.49 2.52
7742 23525 6.985645 ACATTACATGCATTTGTGTGTTCTTT 59.014 30.769 0.00 0.00 30.49 2.52
7743 23526 7.495279 ACATTACATGCATTTGTGTGTTCTTTT 59.505 29.630 0.00 0.00 30.49 2.27
7744 23527 7.840342 TTACATGCATTTGTGTGTTCTTTTT 57.160 28.000 0.00 0.00 0.00 1.94
7772 23555 7.739022 TTCTTGCATGCAAAGATTTAATACG 57.261 32.000 31.37 16.32 35.33 3.06
7773 23556 5.743398 TCTTGCATGCAAAGATTTAATACGC 59.257 36.000 31.37 0.00 35.33 4.42
7774 23557 4.991472 TGCATGCAAAGATTTAATACGCA 58.009 34.783 20.30 0.00 0.00 5.24
7775 23558 5.590145 TGCATGCAAAGATTTAATACGCAT 58.410 33.333 20.30 0.00 39.07 4.73
7776 23559 6.041511 TGCATGCAAAGATTTAATACGCATT 58.958 32.000 20.30 0.00 36.53 3.56
7777 23560 6.019720 TGCATGCAAAGATTTAATACGCATTG 60.020 34.615 20.30 0.00 36.53 2.82
7778 23561 6.198778 GCATGCAAAGATTTAATACGCATTGA 59.801 34.615 14.21 0.00 36.53 2.57
7779 23562 7.254050 GCATGCAAAGATTTAATACGCATTGAA 60.254 33.333 14.21 0.00 36.53 2.69
7780 23563 8.593842 CATGCAAAGATTTAATACGCATTGAAA 58.406 29.630 0.00 0.00 36.53 2.69
7781 23564 8.526218 TGCAAAGATTTAATACGCATTGAAAA 57.474 26.923 0.00 0.00 0.00 2.29
7782 23565 8.431593 TGCAAAGATTTAATACGCATTGAAAAC 58.568 29.630 0.00 0.00 0.00 2.43
7783 23566 8.647226 GCAAAGATTTAATACGCATTGAAAACT 58.353 29.630 0.00 0.00 0.00 2.66
7793 23576 9.906660 AATACGCATTGAAAACTAAAAATGAGA 57.093 25.926 5.23 0.00 34.93 3.27
7796 23579 9.559958 ACGCATTGAAAACTAAAAATGAGATAG 57.440 29.630 5.23 0.00 34.93 2.08
7797 23580 9.773328 CGCATTGAAAACTAAAAATGAGATAGA 57.227 29.630 0.00 0.00 33.34 1.98
7805 23588 8.900983 AACTAAAAATGAGATAGAGATGAGCC 57.099 34.615 0.00 0.00 0.00 4.70
7806 23589 7.449247 ACTAAAAATGAGATAGAGATGAGCCC 58.551 38.462 0.00 0.00 0.00 5.19
7807 23590 6.512514 AAAAATGAGATAGAGATGAGCCCT 57.487 37.500 0.00 0.00 0.00 5.19
7808 23591 5.743636 AAATGAGATAGAGATGAGCCCTC 57.256 43.478 0.00 0.00 0.00 4.30
7809 23592 4.680278 ATGAGATAGAGATGAGCCCTCT 57.320 45.455 0.00 0.00 42.97 3.69
7810 23593 5.794767 ATGAGATAGAGATGAGCCCTCTA 57.205 43.478 0.00 0.00 44.50 2.43
7811 23594 5.590976 TGAGATAGAGATGAGCCCTCTAA 57.409 43.478 0.00 0.00 43.85 2.10
7812 23595 5.958321 TGAGATAGAGATGAGCCCTCTAAA 58.042 41.667 0.00 0.00 43.85 1.85
7813 23596 6.560361 TGAGATAGAGATGAGCCCTCTAAAT 58.440 40.000 0.00 0.00 43.85 1.40
7814 23597 7.015680 TGAGATAGAGATGAGCCCTCTAAATT 58.984 38.462 0.00 0.00 43.85 1.82
7815 23598 7.039152 TGAGATAGAGATGAGCCCTCTAAATTG 60.039 40.741 0.00 0.00 43.85 2.32
7816 23599 7.015680 AGATAGAGATGAGCCCTCTAAATTGA 58.984 38.462 0.00 0.00 43.85 2.57
7817 23600 5.965033 AGAGATGAGCCCTCTAAATTGAA 57.035 39.130 0.00 0.00 39.07 2.69
7818 23601 6.319048 AGAGATGAGCCCTCTAAATTGAAA 57.681 37.500 0.00 0.00 39.07 2.69
7819 23602 6.725364 AGAGATGAGCCCTCTAAATTGAAAA 58.275 36.000 0.00 0.00 39.07 2.29
7820 23603 7.177878 AGAGATGAGCCCTCTAAATTGAAAAA 58.822 34.615 0.00 0.00 39.07 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 64 9.249053 TGATAAGAACATAAAGGTAAATTGCCA 57.751 29.630 2.39 0.00 0.00 4.92
77 79 8.526147 CAAAAGGATTTCTGGTGATAAGAACAT 58.474 33.333 0.00 0.00 37.28 2.71
104 106 2.866460 GCCACGAGTACTTTCAGCTTGA 60.866 50.000 0.00 0.00 0.00 3.02
109 111 3.745975 TCATTTGCCACGAGTACTTTCAG 59.254 43.478 0.00 0.00 0.00 3.02
121 123 6.985188 TCAGTAGTAAATCTCATTTGCCAC 57.015 37.500 0.00 0.00 35.77 5.01
235 7114 7.165485 ACAAAGCAGTTATCATTACAGTGGTA 58.835 34.615 0.00 0.00 0.00 3.25
313 7192 7.149569 TGAATGCTTCAATTCTTACTTCTGG 57.850 36.000 0.00 0.00 37.44 3.86
523 7402 8.833231 AATTATGTGGTATAAGAGAATGACCG 57.167 34.615 0.00 0.00 32.55 4.79
559 7438 4.577834 ACAATAAACAAAAGACACGGGG 57.422 40.909 0.00 0.00 0.00 5.73
607 7486 3.568538 CCAGAGTTTTACATGCAACTGC 58.431 45.455 9.62 0.00 42.50 4.40
624 7503 0.607489 GCTTTGCAAGAGCTCCCAGA 60.607 55.000 19.77 0.00 42.74 3.86
782 7661 6.558771 TGATAATTAGTACCATGTGCATGC 57.441 37.500 11.82 11.82 37.49 4.06
966 7845 3.135530 GCTGATTCACTGACCCTAGGATT 59.864 47.826 11.48 0.00 0.00 3.01
986 7865 9.696917 CAGATTTAAACATTTGAAGTTTAGGCT 57.303 29.630 0.00 0.00 41.06 4.58
1036 7915 4.166144 ACATACCTCCGGATTTTTCTCCAT 59.834 41.667 3.57 0.00 34.78 3.41
1145 8393 6.003950 AGGCTTTGTGTTACATTGACTACAT 58.996 36.000 0.00 0.00 0.00 2.29
1465 8714 5.276536 GCAGCAATTCTGAAAGTGAAAACAC 60.277 40.000 8.22 0.00 45.72 3.32
1609 8861 9.566432 AAGGTTAATAGCTTGGAATATTCTCAG 57.434 33.333 14.95 11.58 40.43 3.35
1692 8945 3.053917 ACAGTTGGGGTTGTGTAGACTTT 60.054 43.478 0.00 0.00 0.00 2.66
1701 8954 4.724279 AGAAATCTACAGTTGGGGTTGT 57.276 40.909 0.00 0.00 0.00 3.32
1997 14075 5.939883 TCAACAGGAGGTATCATCTTTTGTG 59.060 40.000 0.00 0.00 0.00 3.33
2008 14086 5.602978 CCAGGTATACTTCAACAGGAGGTAT 59.397 44.000 2.25 4.80 46.78 2.73
2234 16854 8.935844 CAAGTGTTAGATATCAGCAAACAACTA 58.064 33.333 5.32 0.00 32.32 2.24
2346 16967 6.078456 TGGGAATACATTCTCAAATGAGGT 57.922 37.500 10.37 3.77 43.82 3.85
2382 17003 8.175716 GTGGTTTTAGTCTTACATTGATAGCAC 58.824 37.037 0.00 0.00 0.00 4.40
2543 17411 1.276622 AAATGAGCTACCAGGACCGT 58.723 50.000 0.00 0.00 0.00 4.83
2585 17453 7.565029 TGGTGTGATGCCTGCTATACTATATAT 59.435 37.037 0.00 0.00 0.00 0.86
2588 17456 5.083821 TGGTGTGATGCCTGCTATACTATA 58.916 41.667 0.00 0.00 0.00 1.31
2590 17458 3.304829 TGGTGTGATGCCTGCTATACTA 58.695 45.455 0.00 0.00 0.00 1.82
2679 17547 4.217550 TGTTTCCATGCTAAACTGTAAGCC 59.782 41.667 17.58 0.00 37.60 4.35
2914 17816 7.119262 ACGACAACCCAAATAAAGAAGATACAG 59.881 37.037 0.00 0.00 0.00 2.74
2989 17894 6.145534 GGCCTTGATGTAAAACTGTAAAAAGC 59.854 38.462 0.00 0.00 0.00 3.51
3018 17923 7.094162 TGACCATATCCTCGCAAATTTTTGTTA 60.094 33.333 5.05 0.00 40.24 2.41
3194 18099 2.554462 TCGATCAGTAGCTGGATGTAGC 59.446 50.000 0.00 0.00 44.01 3.58
3842 18794 6.586344 TCCTTTTGATGCAAACAATGGTTTA 58.414 32.000 18.57 0.00 45.18 2.01
4014 18966 4.996434 ACCCTGCTGTGACGCTGC 62.996 66.667 10.63 10.63 41.65 5.25
4427 19798 4.022416 GGAGTGTATCTATCTGCTGTGGAG 60.022 50.000 0.00 0.00 0.00 3.86
4972 20732 7.121463 GGATCTAAAGAGAAGTGAGACTGTACA 59.879 40.741 0.00 0.00 34.61 2.90
5127 20891 3.173599 CCACATTGTTTGCTTATGCTCG 58.826 45.455 1.96 0.00 40.48 5.03
5166 20930 7.404671 AAATATGGTTGGTCAGTGGAATTAC 57.595 36.000 0.00 0.00 0.00 1.89
5211 20975 6.647895 GTCCGAAGTCCTTGTATGTTAAGAAA 59.352 38.462 0.00 0.00 0.00 2.52
5500 21264 1.398390 GCACACGAGATCATCCCAAAC 59.602 52.381 0.00 0.00 0.00 2.93
5645 21409 0.325933 TGTGCATGAGTTCCTCCCAG 59.674 55.000 0.00 0.00 0.00 4.45
5678 21442 7.857569 TCATCTAAGTACTTGGTTGTTTTTCG 58.142 34.615 22.15 3.57 0.00 3.46
5801 21565 8.701908 ACGGAATATAGTAAGTCATACCTCAA 57.298 34.615 0.00 0.00 34.89 3.02
5916 21680 7.793927 AGAATTTACAGCTAAGCTATTGACC 57.206 36.000 0.00 0.00 36.40 4.02
5953 21717 1.008538 CAAAGCTCAACACCGCACC 60.009 57.895 0.00 0.00 0.00 5.01
6055 21819 6.558009 TCTCAAGCAAAATATCAAGTGATGC 58.442 36.000 4.00 0.24 36.05 3.91
6828 22592 1.806542 CTTGGTGCACATGACCACTAC 59.193 52.381 20.43 0.00 43.37 2.73
6901 22665 4.377431 GCTTTCGCATATTACTTGATCCCG 60.377 45.833 0.00 0.00 35.78 5.14
6931 22695 7.813331 ACTCCTCATTAGTCACTACTGGTATA 58.187 38.462 2.53 0.00 36.36 1.47
7027 22792 3.763360 TGGTCACATGCCATAGAAAAAGG 59.237 43.478 0.00 0.00 0.00 3.11
7028 22793 4.701651 TCTGGTCACATGCCATAGAAAAAG 59.298 41.667 0.00 0.00 35.19 2.27
7138 22904 2.143925 GTCGGCTAACTGCTTTGTTCT 58.856 47.619 0.00 0.00 42.39 3.01
7153 22919 1.732259 CAACACATCTTAGTGGTCGGC 59.268 52.381 0.00 0.00 43.72 5.54
7446 23224 1.581934 CAAGAAACAGACACCAGCGA 58.418 50.000 0.00 0.00 0.00 4.93
7492 23273 6.604735 CGAAAGGGATGGAGTATTTTGTAG 57.395 41.667 0.00 0.00 0.00 2.74
7532 23314 3.760151 TGCCTTGGTTGATGAGATTTGAG 59.240 43.478 0.00 0.00 0.00 3.02
7534 23316 4.730949 ATGCCTTGGTTGATGAGATTTG 57.269 40.909 0.00 0.00 0.00 2.32
7650 23433 9.579768 GCATATAATGTTCCTACTCATCTAGTG 57.420 37.037 0.00 0.00 39.39 2.74
7651 23434 9.314133 TGCATATAATGTTCCTACTCATCTAGT 57.686 33.333 0.00 0.00 42.62 2.57
7656 23439 9.578576 ACAAATGCATATAATGTTCCTACTCAT 57.421 29.630 0.00 0.00 0.00 2.90
7657 23440 8.839343 CACAAATGCATATAATGTTCCTACTCA 58.161 33.333 0.00 0.00 0.00 3.41
7658 23441 8.840321 ACACAAATGCATATAATGTTCCTACTC 58.160 33.333 0.00 0.00 0.00 2.59
7659 23442 8.623903 CACACAAATGCATATAATGTTCCTACT 58.376 33.333 0.00 0.00 0.00 2.57
7660 23443 8.405531 ACACACAAATGCATATAATGTTCCTAC 58.594 33.333 0.00 0.00 0.00 3.18
7661 23444 8.518430 ACACACAAATGCATATAATGTTCCTA 57.482 30.769 0.00 0.00 0.00 2.94
7662 23445 7.408756 ACACACAAATGCATATAATGTTCCT 57.591 32.000 0.00 0.00 0.00 3.36
7663 23446 7.975616 AGAACACACAAATGCATATAATGTTCC 59.024 33.333 25.02 15.29 42.69 3.62
7664 23447 8.915871 AGAACACACAAATGCATATAATGTTC 57.084 30.769 23.12 23.12 42.25 3.18
7665 23448 9.709495 AAAGAACACACAAATGCATATAATGTT 57.291 25.926 0.00 7.75 0.00 2.71
7666 23449 9.709495 AAAAGAACACACAAATGCATATAATGT 57.291 25.926 0.00 0.29 0.00 2.71
7692 23475 9.601217 GTTCCTACTCATCTAGCAAGAATTAAA 57.399 33.333 0.00 0.00 34.73 1.52
7693 23476 8.758829 TGTTCCTACTCATCTAGCAAGAATTAA 58.241 33.333 0.00 0.00 34.73 1.40
7694 23477 8.306313 TGTTCCTACTCATCTAGCAAGAATTA 57.694 34.615 0.00 0.00 34.73 1.40
7695 23478 7.187824 TGTTCCTACTCATCTAGCAAGAATT 57.812 36.000 0.00 0.00 34.73 2.17
7696 23479 6.798427 TGTTCCTACTCATCTAGCAAGAAT 57.202 37.500 0.00 0.00 34.73 2.40
7697 23480 6.798427 ATGTTCCTACTCATCTAGCAAGAA 57.202 37.500 0.00 0.00 34.73 2.52
7698 23481 6.798427 AATGTTCCTACTCATCTAGCAAGA 57.202 37.500 0.00 0.00 35.80 3.02
7699 23482 7.492524 TGTAATGTTCCTACTCATCTAGCAAG 58.507 38.462 0.00 0.00 0.00 4.01
7700 23483 7.418337 TGTAATGTTCCTACTCATCTAGCAA 57.582 36.000 0.00 0.00 0.00 3.91
7701 23484 7.436933 CATGTAATGTTCCTACTCATCTAGCA 58.563 38.462 0.00 0.00 40.20 3.49
7702 23485 7.881643 CATGTAATGTTCCTACTCATCTAGC 57.118 40.000 0.00 0.00 40.20 3.42
7719 23502 8.436046 AAAAAGAACACACAAATGCATGTAAT 57.564 26.923 0.00 0.00 30.84 1.89
7720 23503 7.840342 AAAAAGAACACACAAATGCATGTAA 57.160 28.000 0.00 0.00 30.84 2.41
7746 23529 8.810427 CGTATTAAATCTTTGCATGCAAGAATT 58.190 29.630 30.25 27.20 37.24 2.17
7747 23530 7.043192 GCGTATTAAATCTTTGCATGCAAGAAT 60.043 33.333 30.25 23.78 37.24 2.40
7748 23531 6.253298 GCGTATTAAATCTTTGCATGCAAGAA 59.747 34.615 30.25 22.73 37.24 2.52
7749 23532 5.743398 GCGTATTAAATCTTTGCATGCAAGA 59.257 36.000 30.25 27.10 37.24 3.02
7750 23533 5.515982 TGCGTATTAAATCTTTGCATGCAAG 59.484 36.000 30.25 23.49 37.24 4.01
7751 23534 5.405797 TGCGTATTAAATCTTTGCATGCAA 58.594 33.333 28.80 28.80 0.00 4.08
7752 23535 4.991472 TGCGTATTAAATCTTTGCATGCA 58.009 34.783 18.46 18.46 0.00 3.96
7753 23536 6.198778 TCAATGCGTATTAAATCTTTGCATGC 59.801 34.615 11.82 11.82 40.38 4.06
7754 23537 7.682593 TCAATGCGTATTAAATCTTTGCATG 57.317 32.000 0.00 0.00 40.38 4.06
7755 23538 8.700722 TTTCAATGCGTATTAAATCTTTGCAT 57.299 26.923 0.00 0.00 42.83 3.96
7756 23539 8.431593 GTTTTCAATGCGTATTAAATCTTTGCA 58.568 29.630 0.00 0.00 35.10 4.08
7757 23540 8.647226 AGTTTTCAATGCGTATTAAATCTTTGC 58.353 29.630 0.00 0.00 0.00 3.68
7767 23550 9.906660 TCTCATTTTTAGTTTTCAATGCGTATT 57.093 25.926 0.00 0.00 0.00 1.89
7770 23553 9.559958 CTATCTCATTTTTAGTTTTCAATGCGT 57.440 29.630 0.00 0.00 0.00 5.24
7771 23554 9.773328 TCTATCTCATTTTTAGTTTTCAATGCG 57.227 29.630 0.00 0.00 0.00 4.73
7779 23562 9.336171 GGCTCATCTCTATCTCATTTTTAGTTT 57.664 33.333 0.00 0.00 0.00 2.66
7780 23563 7.936301 GGGCTCATCTCTATCTCATTTTTAGTT 59.064 37.037 0.00 0.00 0.00 2.24
7781 23564 7.292120 AGGGCTCATCTCTATCTCATTTTTAGT 59.708 37.037 0.00 0.00 0.00 2.24
7782 23565 7.678837 AGGGCTCATCTCTATCTCATTTTTAG 58.321 38.462 0.00 0.00 0.00 1.85
7783 23566 7.512058 AGAGGGCTCATCTCTATCTCATTTTTA 59.488 37.037 0.00 0.00 39.57 1.52
7784 23567 6.329723 AGAGGGCTCATCTCTATCTCATTTTT 59.670 38.462 0.00 0.00 39.57 1.94
7785 23568 5.845614 AGAGGGCTCATCTCTATCTCATTTT 59.154 40.000 0.00 0.00 39.57 1.82
7786 23569 5.405279 AGAGGGCTCATCTCTATCTCATTT 58.595 41.667 0.00 0.00 39.57 2.32
7787 23570 5.014534 AGAGGGCTCATCTCTATCTCATT 57.985 43.478 0.00 0.00 39.57 2.57
7788 23571 4.680278 AGAGGGCTCATCTCTATCTCAT 57.320 45.455 0.00 0.00 39.57 2.90
7789 23572 5.590976 TTAGAGGGCTCATCTCTATCTCA 57.409 43.478 0.00 0.00 41.69 3.27
7790 23573 7.178274 TCAATTTAGAGGGCTCATCTCTATCTC 59.822 40.741 0.00 0.00 41.69 2.75
7791 23574 7.015680 TCAATTTAGAGGGCTCATCTCTATCT 58.984 38.462 0.00 0.00 41.69 1.98
7792 23575 7.238486 TCAATTTAGAGGGCTCATCTCTATC 57.762 40.000 0.00 0.00 41.69 2.08
7793 23576 7.623999 TTCAATTTAGAGGGCTCATCTCTAT 57.376 36.000 0.00 0.00 41.69 1.98
7794 23577 7.437713 TTTCAATTTAGAGGGCTCATCTCTA 57.562 36.000 0.00 0.00 41.37 2.43
7795 23578 5.965033 TTCAATTTAGAGGGCTCATCTCT 57.035 39.130 0.00 0.00 43.31 3.10
7796 23579 7.396540 TTTTTCAATTTAGAGGGCTCATCTC 57.603 36.000 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.