Multiple sequence alignment - TraesCS1B01G028100

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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 TraesCS1B01G028100 chr1B 100.000 2412 0 0 1 2412 13505602 13503191 0.000000e+00 4455
1 TraesCS1B01G028100 chr1B 88.265 2156 192 29 1 2113 13018174 13016037 0.000000e+00 2523
2 TraesCS1B01G028100 chr1B 89.980 1507 113 14 400 1877 12764966 12763469 0.000000e+00 1912
3 TraesCS1B01G028100 chr1B 89.510 572 51 5 757 1322 12357597 12358165 0.000000e+00 715
4 TraesCS1B01G028100 chr1B 89.750 400 39 2 3 401 12777114 12776716 5.950000e-141 510
5 TraesCS1B01G028100 chr1B 87.179 195 25 0 1118 1312 13560069 13559875 3.120000e-54 222
6 TraesCS1B01G028100 chr1B 91.111 90 6 2 1371 1460 12368672 12368759 1.170000e-23 121
7 TraesCS1B01G028100 chr1A 83.413 1049 103 30 1393 2387 10714363 10713332 0.000000e+00 907
8 TraesCS1B01G028100 chr1A 86.237 574 57 9 757 1325 10716300 10715744 9.540000e-169 603
9 TraesCS1B01G028100 chr1D 88.438 640 44 18 1106 1731 9434779 9434156 0.000000e+00 745
10 TraesCS1B01G028100 chr1D 88.735 506 48 6 819 1322 9420830 9420332 5.700000e-171 610
11 TraesCS1B01G028100 chr1D 79.443 574 66 29 1323 1877 9420292 9419752 2.280000e-95 359
12 TraesCS1B01G028100 chr1D 85.423 343 41 5 975 1309 9426032 9426373 4.940000e-92 348
13 TraesCS1B01G028100 chr1D 81.707 164 24 5 2228 2388 9433638 9433478 5.410000e-27 132
14 TraesCS1B01G028100 chr2D 77.043 257 54 5 232 485 34013668 34013922 2.500000e-30 143
15 TraesCS1B01G028100 chr7D 88.119 101 12 0 381 481 590865483 590865383 1.170000e-23 121
16 TraesCS1B01G028100 chr7B 82.707 133 21 2 340 471 105829486 105829617 1.520000e-22 117


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 TraesCS1B01G028100 chr1B 13503191 13505602 2411 True 4455.0 4455 100.0000 1 2412 1 chr1B.!!$R4 2411
1 TraesCS1B01G028100 chr1B 13016037 13018174 2137 True 2523.0 2523 88.2650 1 2113 1 chr1B.!!$R3 2112
2 TraesCS1B01G028100 chr1B 12763469 12764966 1497 True 1912.0 1912 89.9800 400 1877 1 chr1B.!!$R1 1477
3 TraesCS1B01G028100 chr1B 12357597 12358165 568 False 715.0 715 89.5100 757 1322 1 chr1B.!!$F1 565
4 TraesCS1B01G028100 chr1A 10713332 10716300 2968 True 755.0 907 84.8250 757 2387 2 chr1A.!!$R1 1630
5 TraesCS1B01G028100 chr1D 9419752 9420830 1078 True 484.5 610 84.0890 819 1877 2 chr1D.!!$R1 1058
6 TraesCS1B01G028100 chr1D 9433478 9434779 1301 True 438.5 745 85.0725 1106 2388 2 chr1D.!!$R2 1282

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
237 239 0.320421 TGGAGCCGTTAACTGCAGAC 60.32 55.0 23.35 7.41 31.32 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1470 2838 1.234821 TTTGACTTGGTGATGGCGAC 58.765 50.0 0.0 0.0 0.0 5.19 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
96 98 8.959734 AAAATAGTGAATAAACCGTAAGCAAC 57.040 30.769 0.00 0.00 0.00 4.17
113 115 2.914838 GCAACGAAATTAAAAGGCGGAG 59.085 45.455 0.00 0.00 0.00 4.63
115 117 4.403453 CAACGAAATTAAAAGGCGGAGAG 58.597 43.478 0.00 0.00 0.00 3.20
214 216 3.372730 GCAAATGCGGACTGGCCA 61.373 61.111 4.71 4.71 35.94 5.36
218 220 0.396139 AAATGCGGACTGGCCATCAT 60.396 50.000 5.51 2.22 35.94 2.45
220 222 2.903855 GCGGACTGGCCATCATGG 60.904 66.667 5.51 0.00 41.55 3.66
227 229 2.124151 GGCCATCATGGAGCCGTT 60.124 61.111 8.30 0.00 40.96 4.44
233 235 1.331756 CATCATGGAGCCGTTAACTGC 59.668 52.381 13.54 13.54 0.00 4.40
237 239 0.320421 TGGAGCCGTTAACTGCAGAC 60.320 55.000 23.35 7.41 31.32 3.51
269 271 1.053424 TGGCTCGTCTTTACTGGGTT 58.947 50.000 0.00 0.00 0.00 4.11
270 272 1.418637 TGGCTCGTCTTTACTGGGTTT 59.581 47.619 0.00 0.00 0.00 3.27
271 273 1.804748 GGCTCGTCTTTACTGGGTTTG 59.195 52.381 0.00 0.00 0.00 2.93
272 274 1.804748 GCTCGTCTTTACTGGGTTTGG 59.195 52.381 0.00 0.00 0.00 3.28
279 281 0.402504 TTACTGGGTTTGGCATCCGT 59.597 50.000 0.00 0.00 0.00 4.69
285 287 0.734889 GGTTTGGCATCCGTGATCTG 59.265 55.000 0.00 0.00 0.00 2.90
303 305 6.661377 GTGATCTGGGCATACTCTCTATAAGA 59.339 42.308 0.00 0.00 0.00 2.10
311 313 6.428771 GGCATACTCTCTATAAGACGAGTTCT 59.571 42.308 11.57 0.00 35.69 3.01
318 320 7.536855 TCTCTATAAGACGAGTTCTTTTGTCC 58.463 38.462 0.00 0.00 42.37 4.02
321 323 8.145767 TCTATAAGACGAGTTCTTTTGTCCAAA 58.854 33.333 0.00 0.00 42.37 3.28
327 329 3.617284 AGTTCTTTTGTCCAAACCGAGT 58.383 40.909 0.00 0.00 0.00 4.18
330 332 3.349022 TCTTTTGTCCAAACCGAGTGTT 58.651 40.909 0.00 0.00 39.43 3.32
367 369 4.561938 CGGTAAATTCTCCCATATGCCGTA 60.562 45.833 0.00 0.00 0.00 4.02
368 370 4.694037 GGTAAATTCTCCCATATGCCGTAC 59.306 45.833 0.00 0.00 0.00 3.67
369 371 4.431416 AAATTCTCCCATATGCCGTACA 57.569 40.909 0.00 0.00 0.00 2.90
387 391 0.388649 CACTAGTGTGTGCCGAGACC 60.389 60.000 15.06 0.00 39.24 3.85
389 393 1.532078 TAGTGTGTGCCGAGACCCA 60.532 57.895 0.00 0.00 0.00 4.51
404 408 4.333690 GAGACCCATACTCGGCTTAGATA 58.666 47.826 0.00 0.00 0.00 1.98
405 409 4.936802 AGACCCATACTCGGCTTAGATAT 58.063 43.478 0.00 0.00 0.00 1.63
415 419 2.096218 CGGCTTAGATATCTTTTGCCGC 60.096 50.000 32.39 18.46 44.09 6.53
451 455 2.616842 GGACTCGGCAAAGACAAAAGAA 59.383 45.455 0.00 0.00 0.00 2.52
462 466 6.725246 CAAAGACAAAAGAACTCGGTAACAT 58.275 36.000 0.00 0.00 0.00 2.71
464 468 5.607477 AGACAAAAGAACTCGGTAACATCA 58.393 37.500 0.00 0.00 0.00 3.07
467 471 7.228706 AGACAAAAGAACTCGGTAACATCAATT 59.771 33.333 0.00 0.00 0.00 2.32
475 479 5.054390 TCGGTAACATCAATTTTTCCAGC 57.946 39.130 0.00 0.00 0.00 4.85
504 508 4.336433 GCTATGCAGCCAACATCTTAAAGA 59.664 41.667 0.00 0.00 42.37 2.52
528 532 4.518249 TGTGTGTATATTTCCGGCATTGA 58.482 39.130 0.00 0.00 0.00 2.57
598 602 7.930325 TGGTTATGCATTGTTTGAGAAAAATCA 59.070 29.630 3.54 0.00 0.00 2.57
607 611 8.506140 TTGTTTGAGAAAAATCATTTCTAGCG 57.494 30.769 3.60 0.00 38.73 4.26
609 613 7.803189 TGTTTGAGAAAAATCATTTCTAGCGAC 59.197 33.333 3.60 2.73 38.73 5.19
672 677 9.533253 GAAATATCATGGAAAATGTTAAGGGTG 57.467 33.333 0.00 0.00 0.00 4.61
673 678 5.937975 ATCATGGAAAATGTTAAGGGTGG 57.062 39.130 0.00 0.00 0.00 4.61
681 686 1.394618 TGTTAAGGGTGGTGTGCAAC 58.605 50.000 0.00 0.00 37.35 4.17
707 712 4.038633 GGACTGGAAAGGGTAGAATAGGT 58.961 47.826 0.00 0.00 0.00 3.08
722 727 9.110502 GGTAGAATAGGTAGGAAAAATGAGTTG 57.889 37.037 0.00 0.00 0.00 3.16
726 731 3.826729 AGGTAGGAAAAATGAGTTGGTGC 59.173 43.478 0.00 0.00 0.00 5.01
728 733 1.613437 AGGAAAAATGAGTTGGTGCGG 59.387 47.619 0.00 0.00 0.00 5.69
729 734 1.336795 GGAAAAATGAGTTGGTGCGGG 60.337 52.381 0.00 0.00 0.00 6.13
739 744 0.600557 TTGGTGCGGGCTTTGTATTG 59.399 50.000 0.00 0.00 0.00 1.90
767 772 2.838202 AGGATATACCCCTAATGTGCCG 59.162 50.000 0.00 0.00 40.05 5.69
780 785 4.434713 AATGTGCCGTAACCATCTTTTC 57.565 40.909 0.00 0.00 0.00 2.29
886 891 6.741992 ATTTTGTGAGCAAACGATCTATCA 57.258 33.333 0.00 0.00 43.47 2.15
966 975 6.311935 TGCATGCTAAATGAATCTCTTTTTGC 59.688 34.615 20.33 11.64 40.13 3.68
970 980 5.290400 GCTAAATGAATCTCTTTTTGCTGCC 59.710 40.000 0.00 0.00 38.34 4.85
1128 1146 2.852075 TCCTGGCCGGAGTTGGTT 60.852 61.111 15.09 0.00 36.69 3.67
1273 1291 4.486887 TCGACCCACGAGACAAGA 57.513 55.556 0.00 0.00 46.45 3.02
1371 2733 4.727507 GTGGCGATCACATATCTAGGAT 57.272 45.455 4.75 0.00 45.39 3.24
1372 2734 4.428209 GTGGCGATCACATATCTAGGATG 58.572 47.826 4.75 4.53 45.39 3.51
1373 2735 4.081972 GTGGCGATCACATATCTAGGATGT 60.082 45.833 5.61 5.61 45.39 3.06
1374 2736 5.125578 GTGGCGATCACATATCTAGGATGTA 59.874 44.000 9.91 2.45 45.39 2.29
1386 2754 4.378774 TCTAGGATGTAGCTACTCGTGTC 58.621 47.826 23.84 13.30 0.00 3.67
1387 2755 3.000684 AGGATGTAGCTACTCGTGTCA 57.999 47.619 23.84 2.92 0.00 3.58
1391 2759 5.105310 AGGATGTAGCTACTCGTGTCATTTT 60.105 40.000 23.84 0.00 0.00 1.82
1565 2954 4.326504 AGGCACATTTGGAAAGAAACAG 57.673 40.909 0.00 0.00 0.00 3.16
1632 3037 2.414559 GCTTGCGTGTAATCACATTGCT 60.415 45.455 0.00 0.00 44.02 3.91
1643 3048 1.071542 TCACATTGCTTCCTGACGGAA 59.928 47.619 0.00 0.00 46.90 4.30
1664 3069 2.954989 AGCGAGAGAGTAATCTGCATCA 59.045 45.455 0.00 0.00 0.00 3.07
1692 3097 3.689649 CCCAAGGATGTACAACTTGTAGC 59.310 47.826 27.71 5.25 39.85 3.58
1740 3184 6.266131 TGGATTCAGCTGTTATATTCCCTT 57.734 37.500 14.67 0.00 0.00 3.95
1785 3229 5.000591 TCACTGGTTAATTTGCTCGATCAA 58.999 37.500 0.00 0.00 0.00 2.57
1855 3302 6.774354 TCGTTAGTCAACTTAATTGTCACC 57.226 37.500 0.00 0.00 39.54 4.02
1862 3309 5.407387 GTCAACTTAATTGTCACCGAGCTAA 59.593 40.000 0.00 0.00 39.54 3.09
1873 3320 2.932614 CACCGAGCTAAGATTGGAAGTG 59.067 50.000 0.00 0.00 0.00 3.16
1941 3406 9.762933 TTTTTATTAACTAACTGACACTACCGT 57.237 29.630 0.00 0.00 0.00 4.83
1978 3443 9.884636 ACGATCGATCCATATAATCCATTAAAA 57.115 29.630 24.34 0.00 0.00 1.52
2040 3506 4.077822 AGTTCAAGAGCAAAGAAGATGGG 58.922 43.478 0.00 0.00 0.00 4.00
2052 3518 2.092049 AGAAGATGGGAAGATGCATGCA 60.092 45.455 25.04 25.04 0.00 3.96
2088 3554 4.530857 GTCGCCATGGTCCTCGGG 62.531 72.222 14.67 0.00 0.00 5.14
2114 3580 2.437359 GCTGCTTCAGTCCCGCAT 60.437 61.111 0.00 0.00 33.43 4.73
2115 3581 2.758089 GCTGCTTCAGTCCCGCATG 61.758 63.158 0.00 0.00 33.43 4.06
2116 3582 2.046023 TGCTTCAGTCCCGCATGG 60.046 61.111 0.00 0.00 0.00 3.66
2117 3583 2.268920 GCTTCAGTCCCGCATGGA 59.731 61.111 0.00 0.00 42.41 3.41
2125 3591 2.295904 TCCCGCATGGACAATCTCA 58.704 52.632 0.00 0.00 38.61 3.27
2126 3592 0.617935 TCCCGCATGGACAATCTCAA 59.382 50.000 0.00 0.00 38.61 3.02
2127 3593 1.019673 CCCGCATGGACAATCTCAAG 58.980 55.000 0.00 0.00 37.49 3.02
2128 3594 1.019673 CCGCATGGACAATCTCAAGG 58.980 55.000 0.00 0.00 37.49 3.61
2129 3595 1.679944 CCGCATGGACAATCTCAAGGT 60.680 52.381 0.00 0.00 37.49 3.50
2130 3596 2.419990 CCGCATGGACAATCTCAAGGTA 60.420 50.000 0.00 0.00 37.49 3.08
2131 3597 2.868583 CGCATGGACAATCTCAAGGTAG 59.131 50.000 0.00 0.00 0.00 3.18
2132 3598 3.679917 CGCATGGACAATCTCAAGGTAGT 60.680 47.826 0.00 0.00 0.00 2.73
2133 3599 4.441495 CGCATGGACAATCTCAAGGTAGTA 60.441 45.833 0.00 0.00 0.00 1.82
2134 3600 5.428253 GCATGGACAATCTCAAGGTAGTAA 58.572 41.667 0.00 0.00 0.00 2.24
2135 3601 6.058183 GCATGGACAATCTCAAGGTAGTAAT 58.942 40.000 0.00 0.00 0.00 1.89
2136 3602 7.217200 GCATGGACAATCTCAAGGTAGTAATA 58.783 38.462 0.00 0.00 0.00 0.98
2137 3603 7.715249 GCATGGACAATCTCAAGGTAGTAATAA 59.285 37.037 0.00 0.00 0.00 1.40
2138 3604 9.613428 CATGGACAATCTCAAGGTAGTAATAAA 57.387 33.333 0.00 0.00 0.00 1.40
2139 3605 9.838339 ATGGACAATCTCAAGGTAGTAATAAAG 57.162 33.333 0.00 0.00 0.00 1.85
2140 3606 7.769044 TGGACAATCTCAAGGTAGTAATAAAGC 59.231 37.037 0.00 0.00 0.00 3.51
2141 3607 7.769044 GGACAATCTCAAGGTAGTAATAAAGCA 59.231 37.037 0.00 0.00 0.00 3.91
2142 3608 8.723942 ACAATCTCAAGGTAGTAATAAAGCAG 57.276 34.615 0.00 0.00 0.00 4.24
2143 3609 7.281100 ACAATCTCAAGGTAGTAATAAAGCAGC 59.719 37.037 0.00 0.00 0.00 5.25
2144 3610 5.671493 TCTCAAGGTAGTAATAAAGCAGCC 58.329 41.667 0.00 0.00 0.00 4.85
2145 3611 5.188948 TCTCAAGGTAGTAATAAAGCAGCCA 59.811 40.000 0.00 0.00 0.00 4.75
2146 3612 6.001449 TCAAGGTAGTAATAAAGCAGCCAT 57.999 37.500 0.00 0.00 0.00 4.40
2147 3613 6.423182 TCAAGGTAGTAATAAAGCAGCCATT 58.577 36.000 0.00 0.00 0.00 3.16
2148 3614 6.889722 TCAAGGTAGTAATAAAGCAGCCATTT 59.110 34.615 0.00 0.00 0.00 2.32
2149 3615 7.396055 TCAAGGTAGTAATAAAGCAGCCATTTT 59.604 33.333 0.00 0.00 0.00 1.82
2150 3616 7.334844 AGGTAGTAATAAAGCAGCCATTTTC 57.665 36.000 0.00 0.00 0.00 2.29
2151 3617 6.038271 AGGTAGTAATAAAGCAGCCATTTTCG 59.962 38.462 0.00 0.00 0.00 3.46
2152 3618 6.037830 GGTAGTAATAAAGCAGCCATTTTCGA 59.962 38.462 0.00 0.00 0.00 3.71
2153 3619 6.509418 AGTAATAAAGCAGCCATTTTCGAA 57.491 33.333 0.00 0.00 0.00 3.71
2154 3620 6.919721 AGTAATAAAGCAGCCATTTTCGAAA 58.080 32.000 6.47 6.47 0.00 3.46
2155 3621 7.375053 AGTAATAAAGCAGCCATTTTCGAAAA 58.625 30.769 24.43 24.43 0.00 2.29
2156 3622 7.870445 AGTAATAAAGCAGCCATTTTCGAAAAA 59.130 29.630 25.77 10.76 0.00 1.94
2190 3656 7.285566 TCTCAAGGTATACTAACACTATCGGT 58.714 38.462 2.25 0.00 0.00 4.69
2218 3736 3.053896 GCGTAACCTTGGCGGCTT 61.054 61.111 11.43 0.00 35.61 4.35
2242 3761 4.707768 ATGGGTCGACGGGGGACA 62.708 66.667 9.92 2.04 36.12 4.02
2254 3773 2.683933 GGGACAAGGCGAGGGAGA 60.684 66.667 0.00 0.00 0.00 3.71
2257 3776 1.045911 GGACAAGGCGAGGGAGAGAT 61.046 60.000 0.00 0.00 0.00 2.75
2258 3777 1.693627 GACAAGGCGAGGGAGAGATA 58.306 55.000 0.00 0.00 0.00 1.98
2275 3794 4.700692 AGAGATATACCTAGATTTGCGCGA 59.299 41.667 12.10 0.00 0.00 5.87
2278 3797 1.552226 TACCTAGATTTGCGCGAACG 58.448 50.000 13.41 1.64 44.07 3.95
2282 3801 0.671163 TAGATTTGCGCGAACGGGTT 60.671 50.000 13.41 0.00 40.57 4.11
2293 3812 2.459202 GAACGGGTTGACGGTGGGAT 62.459 60.000 0.00 0.00 38.39 3.85
2313 3832 0.753479 GAGGAGAGGGCGAGACATGA 60.753 60.000 0.00 0.00 0.00 3.07
2317 3836 0.753479 AGAGGGCGAGACATGACGAT 60.753 55.000 0.00 0.00 0.00 3.73
2320 3839 0.032678 GGGCGAGACATGACGATGAT 59.967 55.000 0.00 0.00 33.36 2.45
2326 3845 2.101415 GAGACATGACGATGATGGGACA 59.899 50.000 0.00 0.00 36.26 4.02
2329 3848 2.501316 ACATGACGATGATGGGACAAGA 59.499 45.455 0.00 0.00 35.65 3.02
2346 3865 5.279156 GGACAAGAGATTTGCCATTTTGAGT 60.279 40.000 0.00 0.00 0.00 3.41
2350 3869 5.958955 AGAGATTTGCCATTTTGAGTAAGC 58.041 37.500 0.00 0.00 0.00 3.09
2357 3876 1.135402 CATTTTGAGTAAGCGTGGGCC 60.135 52.381 0.00 0.00 41.24 5.80
2362 3881 1.173913 GAGTAAGCGTGGGCCAAAAT 58.826 50.000 8.40 0.00 41.24 1.82
2388 3907 0.036306 ATTTGTCCGTCTGGGTGTCC 59.964 55.000 0.00 0.00 37.00 4.02
2389 3908 2.372040 TTTGTCCGTCTGGGTGTCCG 62.372 60.000 0.00 0.00 37.00 4.79
2390 3909 4.065281 GTCCGTCTGGGTGTCCGG 62.065 72.222 0.00 0.00 41.75 5.14
2394 3913 3.948719 GTCTGGGTGTCCGGGCAA 61.949 66.667 12.16 0.00 43.45 4.52
2395 3914 2.933287 TCTGGGTGTCCGGGCAAT 60.933 61.111 12.16 0.00 39.90 3.56
2396 3915 2.751436 CTGGGTGTCCGGGCAATG 60.751 66.667 12.16 0.00 35.76 2.82
2399 3918 2.988684 GGTGTCCGGGCAATGCAA 60.989 61.111 12.16 0.00 0.00 4.08
2400 3919 2.569354 GGTGTCCGGGCAATGCAAA 61.569 57.895 12.16 0.00 0.00 3.68
2401 3920 1.365633 GTGTCCGGGCAATGCAAAA 59.634 52.632 12.16 0.00 0.00 2.44
2402 3921 0.943835 GTGTCCGGGCAATGCAAAAC 60.944 55.000 12.16 0.00 0.00 2.43
2403 3922 1.112315 TGTCCGGGCAATGCAAAACT 61.112 50.000 6.10 0.00 0.00 2.66
2404 3923 0.388520 GTCCGGGCAATGCAAAACTC 60.389 55.000 7.79 0.00 0.00 3.01
2405 3924 1.079888 CCGGGCAATGCAAAACTCC 60.080 57.895 7.79 0.00 0.00 3.85
2406 3925 1.079888 CGGGCAATGCAAAACTCCC 60.080 57.895 7.79 0.00 0.00 4.30
2407 3926 1.079888 GGGCAATGCAAAACTCCCG 60.080 57.895 7.79 0.00 0.00 5.14
2408 3927 1.737735 GGCAATGCAAAACTCCCGC 60.738 57.895 7.79 0.00 0.00 6.13
2409 3928 1.737735 GCAATGCAAAACTCCCGCC 60.738 57.895 0.00 0.00 0.00 6.13
2410 3929 1.664873 CAATGCAAAACTCCCGCCA 59.335 52.632 0.00 0.00 0.00 5.69
2411 3930 0.667184 CAATGCAAAACTCCCGCCAC 60.667 55.000 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 76 6.340537 CGTTGCTTACGGTTTATTCACTAT 57.659 37.500 4.34 0.00 46.42 2.12
75 77 5.766702 CGTTGCTTACGGTTTATTCACTA 57.233 39.130 4.34 0.00 46.42 2.74
93 95 4.403453 CTCTCCGCCTTTTAATTTCGTTG 58.597 43.478 0.00 0.00 0.00 4.10
96 98 2.418628 TGCTCTCCGCCTTTTAATTTCG 59.581 45.455 0.00 0.00 38.05 3.46
109 111 2.808523 TGCTCAATATCTGCTCTCCG 57.191 50.000 0.00 0.00 0.00 4.63
113 115 4.343811 GCATGATGCTCAATATCTGCTC 57.656 45.455 10.72 0.00 40.96 4.26
205 207 1.527844 GCTCCATGATGGCCAGTCC 60.528 63.158 13.05 3.33 37.47 3.85
212 214 1.942657 CAGTTAACGGCTCCATGATGG 59.057 52.381 4.74 4.74 39.43 3.51
214 216 1.065491 TGCAGTTAACGGCTCCATGAT 60.065 47.619 27.10 0.00 37.92 2.45
218 220 0.320421 GTCTGCAGTTAACGGCTCCA 60.320 55.000 27.10 10.08 37.92 3.86
220 222 2.070861 CGTCTGCAGTTAACGGCTC 58.929 57.895 27.10 17.35 37.92 4.70
227 229 1.671054 GCAAGGCCGTCTGCAGTTA 60.671 57.895 14.67 0.00 43.89 2.24
264 266 0.679640 GATCACGGATGCCAAACCCA 60.680 55.000 0.00 0.00 0.00 4.51
269 271 1.224315 CCCAGATCACGGATGCCAA 59.776 57.895 2.83 0.00 0.00 4.52
270 272 2.910360 CCCAGATCACGGATGCCA 59.090 61.111 2.83 0.00 0.00 4.92
271 273 2.592861 GCCCAGATCACGGATGCC 60.593 66.667 2.83 0.00 0.00 4.40
272 274 0.035317 TATGCCCAGATCACGGATGC 59.965 55.000 2.83 0.12 0.00 3.91
279 281 6.661377 GTCTTATAGAGAGTATGCCCAGATCA 59.339 42.308 0.00 0.00 34.31 2.92
285 287 5.005094 ACTCGTCTTATAGAGAGTATGCCC 58.995 45.833 0.00 0.00 41.57 5.36
303 305 2.353579 CGGTTTGGACAAAAGAACTCGT 59.646 45.455 0.00 0.00 31.33 4.18
311 313 3.377798 GGTAACACTCGGTTTGGACAAAA 59.622 43.478 0.00 0.00 40.96 2.44
314 316 1.764134 AGGTAACACTCGGTTTGGACA 59.236 47.619 0.00 0.00 40.96 4.02
318 320 2.806244 CCTCAAGGTAACACTCGGTTTG 59.194 50.000 0.00 0.00 40.96 2.93
321 323 0.974383 CCCTCAAGGTAACACTCGGT 59.026 55.000 0.00 0.00 41.41 4.69
327 329 1.550130 CCGAGCCCCTCAAGGTAACA 61.550 60.000 0.00 0.00 41.41 2.41
330 332 0.041535 TTACCGAGCCCCTCAAGGTA 59.958 55.000 0.00 0.00 36.49 3.08
369 371 1.533469 GGGTCTCGGCACACACTAGT 61.533 60.000 0.00 0.00 0.00 2.57
387 391 6.091441 GCAAAAGATATCTAAGCCGAGTATGG 59.909 42.308 5.46 0.00 0.00 2.74
389 393 6.166982 GGCAAAAGATATCTAAGCCGAGTAT 58.833 40.000 20.55 0.00 31.13 2.12
404 408 2.180204 CGGGATCGCGGCAAAAGAT 61.180 57.895 23.27 0.00 0.00 2.40
405 409 2.817834 CGGGATCGCGGCAAAAGA 60.818 61.111 23.27 0.00 0.00 2.52
431 435 3.312697 AGTTCTTTTGTCTTTGCCGAGTC 59.687 43.478 0.00 0.00 0.00 3.36
451 455 5.335661 GCTGGAAAAATTGATGTTACCGAGT 60.336 40.000 0.00 0.00 0.00 4.18
462 466 3.648339 GCTCACTGCTGGAAAAATTGA 57.352 42.857 0.00 0.00 38.95 2.57
504 508 5.592282 TCAATGCCGGAAATATACACACAAT 59.408 36.000 5.05 0.00 0.00 2.71
528 532 1.818674 GCAAAATCCAGAACCATCCGT 59.181 47.619 0.00 0.00 0.00 4.69
534 538 7.573968 ATTATACAGAGCAAAATCCAGAACC 57.426 36.000 0.00 0.00 0.00 3.62
572 576 7.930325 TGATTTTTCTCAAACAATGCATAACCA 59.070 29.630 0.00 0.00 0.00 3.67
581 585 9.132521 CGCTAGAAATGATTTTTCTCAAACAAT 57.867 29.630 4.00 0.00 39.30 2.71
582 586 8.349245 TCGCTAGAAATGATTTTTCTCAAACAA 58.651 29.630 4.00 0.00 39.30 2.83
598 602 7.462571 AAAAAGGTAAATGGTCGCTAGAAAT 57.537 32.000 0.00 0.00 0.00 2.17
662 667 1.341089 TGTTGCACACCACCCTTAACA 60.341 47.619 0.00 0.00 0.00 2.41
665 670 0.179004 CCTGTTGCACACCACCCTTA 60.179 55.000 0.00 0.00 0.00 2.69
672 677 1.898574 CAGTCCCCTGTTGCACACC 60.899 63.158 0.00 0.00 33.80 4.16
673 678 1.898574 CCAGTCCCCTGTTGCACAC 60.899 63.158 0.00 0.00 36.95 3.82
681 686 0.912486 CTACCCTTTCCAGTCCCCTG 59.088 60.000 0.00 0.00 38.50 4.45
686 691 5.304871 CCTACCTATTCTACCCTTTCCAGTC 59.695 48.000 0.00 0.00 0.00 3.51
698 703 8.832735 ACCAACTCATTTTTCCTACCTATTCTA 58.167 33.333 0.00 0.00 0.00 2.10
707 712 2.817258 CCGCACCAACTCATTTTTCCTA 59.183 45.455 0.00 0.00 0.00 2.94
722 727 1.131693 GTACAATACAAAGCCCGCACC 59.868 52.381 0.00 0.00 0.00 5.01
726 731 4.098960 TCCTCTAGTACAATACAAAGCCCG 59.901 45.833 0.00 0.00 0.00 6.13
728 733 9.857957 GTATATCCTCTAGTACAATACAAAGCC 57.142 37.037 0.00 0.00 0.00 4.35
729 734 9.857957 GGTATATCCTCTAGTACAATACAAAGC 57.142 37.037 0.00 0.00 0.00 3.51
886 891 6.676456 GCTTCGATGTTATCACTGCATTTCTT 60.676 38.462 0.00 0.00 0.00 2.52
939 944 8.328146 CAAAAAGAGATTCATTTAGCATGCATG 58.672 33.333 22.70 22.70 0.00 4.06
953 958 1.812571 TCCGGCAGCAAAAAGAGATTC 59.187 47.619 0.00 0.00 0.00 2.52
956 961 1.541147 CATTCCGGCAGCAAAAAGAGA 59.459 47.619 0.00 0.00 0.00 3.10
959 964 0.037975 AGCATTCCGGCAGCAAAAAG 60.038 50.000 13.71 0.00 35.83 2.27
962 971 1.252175 TTTAGCATTCCGGCAGCAAA 58.748 45.000 13.71 9.48 35.83 3.68
966 975 3.254166 AGCATTATTTAGCATTCCGGCAG 59.746 43.478 0.00 0.00 35.83 4.85
970 980 5.682862 GTGTCAAGCATTATTTAGCATTCCG 59.317 40.000 0.00 0.00 0.00 4.30
1146 1164 2.932614 GCTGTTAATCGTCATCACTGCT 59.067 45.455 0.00 0.00 31.62 4.24
1300 1318 3.710209 AGAAACACTGAGCTAGCCAAT 57.290 42.857 12.13 0.00 0.00 3.16
1360 2722 6.596106 ACACGAGTAGCTACATCCTAGATATG 59.404 42.308 25.28 10.49 0.00 1.78
1365 2727 4.127907 TGACACGAGTAGCTACATCCTAG 58.872 47.826 25.28 12.00 0.00 3.02
1368 2730 3.992260 ATGACACGAGTAGCTACATCC 57.008 47.619 25.28 12.70 0.00 3.51
1369 2731 6.648725 AAAAATGACACGAGTAGCTACATC 57.351 37.500 25.28 17.25 0.00 3.06
1370 2732 9.245962 GTATAAAAATGACACGAGTAGCTACAT 57.754 33.333 25.28 10.75 0.00 2.29
1371 2733 8.245491 TGTATAAAAATGACACGAGTAGCTACA 58.755 33.333 25.28 3.50 0.00 2.74
1372 2734 8.624701 TGTATAAAAATGACACGAGTAGCTAC 57.375 34.615 16.43 16.43 0.00 3.58
1373 2735 9.811995 AATGTATAAAAATGACACGAGTAGCTA 57.188 29.630 0.00 0.00 0.00 3.32
1374 2736 8.718102 AATGTATAAAAATGACACGAGTAGCT 57.282 30.769 0.00 0.00 0.00 3.32
1470 2838 1.234821 TTTGACTTGGTGATGGCGAC 58.765 50.000 0.00 0.00 0.00 5.19
1565 2954 3.796844 GCAGTTGCCCTCAAGAGTTTTTC 60.797 47.826 0.00 0.00 31.93 2.29
1643 3048 2.954989 TGATGCAGATTACTCTCTCGCT 59.045 45.455 0.00 0.00 0.00 4.93
1664 3069 5.193099 AGTTGTACATCCTTGGGCTTATT 57.807 39.130 0.00 0.00 0.00 1.40
1692 3097 5.007039 GCTTGCAGAAGGAAAAAGGAAAAAG 59.993 40.000 0.00 0.00 0.00 2.27
1765 3209 6.260936 ACCTATTGATCGAGCAAATTAACCAG 59.739 38.462 21.22 8.53 0.00 4.00
1775 3219 6.628175 GCCTATTCATACCTATTGATCGAGCA 60.628 42.308 0.00 0.00 0.00 4.26
1785 3229 5.069914 TGACAACGTGCCTATTCATACCTAT 59.930 40.000 0.00 0.00 0.00 2.57
1855 3302 3.614616 GTGTCACTTCCAATCTTAGCTCG 59.385 47.826 0.00 0.00 0.00 5.03
1862 3309 6.169094 CACTAATCAGTGTCACTTCCAATCT 58.831 40.000 1.67 0.00 46.03 2.40
1920 3385 8.115490 ACTTACGGTAGTGTCAGTTAGTTAAT 57.885 34.615 0.00 0.00 0.00 1.40
1928 3393 5.725110 CGTATACTTACGGTAGTGTCAGT 57.275 43.478 0.56 0.00 45.86 3.41
1940 3405 4.087265 GGATCGATCGTGCGTATACTTAC 58.913 47.826 18.81 0.00 0.00 2.34
1941 3406 3.747529 TGGATCGATCGTGCGTATACTTA 59.252 43.478 18.81 0.00 0.00 2.24
1942 3407 2.551032 TGGATCGATCGTGCGTATACTT 59.449 45.455 18.81 0.00 0.00 2.24
1943 3408 2.148768 TGGATCGATCGTGCGTATACT 58.851 47.619 18.81 0.00 0.00 2.12
1952 3417 9.884636 TTTTAATGGATTATATGGATCGATCGT 57.115 29.630 18.81 12.44 0.00 3.73
1986 3451 3.433173 CCATCTCCTGCACTCATTCATGA 60.433 47.826 0.00 0.00 35.16 3.07
1991 3456 3.378512 TCTACCATCTCCTGCACTCATT 58.621 45.455 0.00 0.00 0.00 2.57
2114 3580 7.769044 GCTTTATTACTACCTTGAGATTGTCCA 59.231 37.037 0.00 0.00 0.00 4.02
2115 3581 7.769044 TGCTTTATTACTACCTTGAGATTGTCC 59.231 37.037 0.00 0.00 0.00 4.02
2116 3582 8.718102 TGCTTTATTACTACCTTGAGATTGTC 57.282 34.615 0.00 0.00 0.00 3.18
2117 3583 7.281100 GCTGCTTTATTACTACCTTGAGATTGT 59.719 37.037 0.00 0.00 0.00 2.71
2118 3584 7.254932 GGCTGCTTTATTACTACCTTGAGATTG 60.255 40.741 0.00 0.00 0.00 2.67
2119 3585 6.768381 GGCTGCTTTATTACTACCTTGAGATT 59.232 38.462 0.00 0.00 0.00 2.40
2120 3586 6.126768 TGGCTGCTTTATTACTACCTTGAGAT 60.127 38.462 0.00 0.00 0.00 2.75
2121 3587 5.188948 TGGCTGCTTTATTACTACCTTGAGA 59.811 40.000 0.00 0.00 0.00 3.27
2122 3588 5.428253 TGGCTGCTTTATTACTACCTTGAG 58.572 41.667 0.00 0.00 0.00 3.02
2123 3589 5.429681 TGGCTGCTTTATTACTACCTTGA 57.570 39.130 0.00 0.00 0.00 3.02
2124 3590 6.699575 AATGGCTGCTTTATTACTACCTTG 57.300 37.500 0.00 0.00 0.00 3.61
2125 3591 7.415206 CGAAAATGGCTGCTTTATTACTACCTT 60.415 37.037 0.00 0.00 0.00 3.50
2126 3592 6.038271 CGAAAATGGCTGCTTTATTACTACCT 59.962 38.462 0.00 0.00 0.00 3.08
2127 3593 6.037830 TCGAAAATGGCTGCTTTATTACTACC 59.962 38.462 0.00 0.00 0.00 3.18
2128 3594 7.011828 TCGAAAATGGCTGCTTTATTACTAC 57.988 36.000 0.00 0.00 0.00 2.73
2129 3595 7.618502 TTCGAAAATGGCTGCTTTATTACTA 57.381 32.000 0.00 0.00 0.00 1.82
2130 3596 6.509418 TTCGAAAATGGCTGCTTTATTACT 57.491 33.333 0.00 0.00 0.00 2.24
2131 3597 7.575332 TTTTCGAAAATGGCTGCTTTATTAC 57.425 32.000 19.08 0.00 0.00 1.89
2155 3621 9.614792 GTTAGTATACCTTGAGATTGTCCATTT 57.385 33.333 0.00 0.00 0.00 2.32
2156 3622 8.768397 TGTTAGTATACCTTGAGATTGTCCATT 58.232 33.333 0.00 0.00 0.00 3.16
2157 3623 8.204836 GTGTTAGTATACCTTGAGATTGTCCAT 58.795 37.037 0.00 0.00 0.00 3.41
2158 3624 7.399191 AGTGTTAGTATACCTTGAGATTGTCCA 59.601 37.037 0.00 0.00 0.00 4.02
2201 3667 3.035576 GAAGCCGCCAAGGTTACGC 62.036 63.158 0.00 0.00 43.70 4.42
2226 3744 4.938074 TTGTCCCCCGTCGACCCA 62.938 66.667 10.58 0.00 0.00 4.51
2242 3761 2.380590 AGGTATATCTCTCCCTCGCCTT 59.619 50.000 0.00 0.00 0.00 4.35
2254 3773 5.162075 GTTCGCGCAAATCTAGGTATATCT 58.838 41.667 8.75 0.00 0.00 1.98
2257 3776 3.302555 CGTTCGCGCAAATCTAGGTATA 58.697 45.455 8.75 0.00 0.00 1.47
2258 3777 2.124903 CGTTCGCGCAAATCTAGGTAT 58.875 47.619 8.75 0.00 0.00 2.73
2275 3794 2.522367 ATCCCACCGTCAACCCGTT 61.522 57.895 0.00 0.00 0.00 4.44
2278 3797 1.078426 CTCATCCCACCGTCAACCC 60.078 63.158 0.00 0.00 0.00 4.11
2282 3801 0.684479 CTCTCCTCATCCCACCGTCA 60.684 60.000 0.00 0.00 0.00 4.35
2293 3812 1.039785 CATGTCTCGCCCTCTCCTCA 61.040 60.000 0.00 0.00 0.00 3.86
2313 3832 4.194640 CAAATCTCTTGTCCCATCATCGT 58.805 43.478 0.00 0.00 0.00 3.73
2317 3836 2.041485 TGGCAAATCTCTTGTCCCATCA 59.959 45.455 0.00 0.00 0.00 3.07
2320 3839 2.905415 ATGGCAAATCTCTTGTCCCA 57.095 45.000 0.00 0.00 0.00 4.37
2326 3845 6.393171 GCTTACTCAAAATGGCAAATCTCTT 58.607 36.000 0.00 0.00 0.00 2.85
2329 3848 4.218417 ACGCTTACTCAAAATGGCAAATCT 59.782 37.500 0.00 0.00 0.00 2.40
2346 3865 0.037790 GCAATTTTGGCCCACGCTTA 60.038 50.000 0.00 0.00 34.44 3.09
2350 3869 0.033228 TTGAGCAATTTTGGCCCACG 59.967 50.000 0.00 0.00 0.00 4.94
2357 3876 4.984161 AGACGGACAAATTGAGCAATTTTG 59.016 37.500 16.21 13.96 45.67 2.44
2362 3881 1.879380 CCAGACGGACAAATTGAGCAA 59.121 47.619 0.00 0.00 0.00 3.91
2388 3907 1.079888 GGGAGTTTTGCATTGCCCG 60.080 57.895 6.12 0.00 0.00 6.13
2389 3908 1.079888 CGGGAGTTTTGCATTGCCC 60.080 57.895 6.12 0.00 0.00 5.36
2390 3909 1.737735 GCGGGAGTTTTGCATTGCC 60.738 57.895 6.12 0.00 0.00 4.52
2391 3910 1.737735 GGCGGGAGTTTTGCATTGC 60.738 57.895 0.46 0.46 0.00 3.56
2392 3911 0.667184 GTGGCGGGAGTTTTGCATTG 60.667 55.000 0.00 0.00 0.00 2.82
2393 3912 1.665442 GTGGCGGGAGTTTTGCATT 59.335 52.632 0.00 0.00 0.00 3.56
2394 3913 3.365535 GTGGCGGGAGTTTTGCAT 58.634 55.556 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.