Multiple sequence alignment - TraesCS1D01G423000

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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 TraesCS1D01G423000 chr1D 100.000 4909 0 0 1 4909 478230059 478225151 0.000000e+00 9066
1 TraesCS1D01G423000 chr1D 91.791 134 11 0 568 701 356929218 356929085 2.330000e-43 187
2 TraesCS1D01G423000 chr1A 95.788 4036 71 29 932 4909 574475298 574471304 0.000000e+00 6420
3 TraesCS1D01G423000 chr1A 92.857 308 8 5 1 301 574476188 574475888 7.550000e-118 435
4 TraesCS1D01G423000 chr1A 96.714 213 3 1 734 946 574475738 574475530 7.820000e-93 351
5 TraesCS1D01G423000 chr1A 93.793 145 7 1 424 566 574475881 574475737 2.980000e-52 217
6 TraesCS1D01G423000 chr1A 87.838 148 15 2 568 714 146960676 146960531 2.350000e-38 171
7 TraesCS1D01G423000 chr1B 96.261 3905 73 30 696 4556 665798399 665794524 0.000000e+00 6335
8 TraesCS1D01G423000 chr1B 96.319 326 7 2 1 326 665798867 665798547 9.360000e-147 531
9 TraesCS1D01G423000 chr1B 93.208 265 18 0 4645 4909 665497166 665496902 1.660000e-104 390
10 TraesCS1D01G423000 chr1B 95.425 153 6 1 418 569 665798547 665798395 4.910000e-60 243
11 TraesCS1D01G423000 chr6D 79.534 1803 310 45 2125 3910 315246704 315248464 0.000000e+00 1230
12 TraesCS1D01G423000 chr6D 80.920 1478 233 35 2446 3908 315192360 315190917 0.000000e+00 1122
13 TraesCS1D01G423000 chr6D 83.068 691 98 13 973 1653 315193841 315193160 1.170000e-170 610
14 TraesCS1D01G423000 chr6D 81.804 643 87 25 1030 1653 315245682 315246313 3.390000e-141 512
15 TraesCS1D01G423000 chr6A 81.033 1471 241 27 2446 3908 452265688 452264248 0.000000e+00 1136
16 TraesCS1D01G423000 chr6A 82.590 695 99 17 973 1653 452267175 452266489 1.180000e-165 593
17 TraesCS1D01G423000 chr6A 80.840 381 53 10 1966 2345 452266122 452265761 1.040000e-71 281
18 TraesCS1D01G423000 chr6B 80.621 1481 244 31 2446 3915 512217552 512219000 0.000000e+00 1105
19 TraesCS1D01G423000 chr5B 93.382 136 9 0 566 701 445765202 445765337 8.330000e-48 202
20 TraesCS1D01G423000 chr5B 88.312 154 14 4 566 716 674272364 674272212 1.090000e-41 182
21 TraesCS1D01G423000 chr5D 92.593 135 10 0 565 699 491658853 491658719 1.390000e-45 195
22 TraesCS1D01G423000 chr7B 91.912 136 11 0 569 704 708467900 708467765 1.800000e-44 191
23 TraesCS1D01G423000 chr7B 91.667 108 7 2 323 430 637751259 637751364 1.100000e-31 148
24 TraesCS1D01G423000 chr7B 91.509 106 9 0 321 426 217312361 217312256 3.960000e-31 147
25 TraesCS1D01G423000 chr7A 92.248 129 10 0 569 697 686137816 686137688 3.020000e-42 183
26 TraesCS1D01G423000 chr7A 90.299 134 13 0 566 699 612595916 612595783 5.050000e-40 176
27 TraesCS1D01G423000 chr7D 90.977 133 12 0 565 697 226697753 226697885 3.900000e-41 180
28 TraesCS1D01G423000 chr7D 94.845 97 5 0 323 419 271458331 271458235 8.510000e-33 152
29 TraesCS1D01G423000 chr7D 88.889 117 9 4 323 438 30953113 30953226 1.840000e-29 141
30 TraesCS1D01G423000 chr2B 94.000 100 6 0 322 421 730560959 730560860 8.510000e-33 152
31 TraesCS1D01G423000 chr2A 92.233 103 8 0 317 419 186403673 186403775 3.960000e-31 147
32 TraesCS1D01G423000 chr2A 92.929 99 7 0 322 420 419654482 419654384 1.420000e-30 145
33 TraesCS1D01G423000 chr3D 92.929 99 7 0 321 419 603946159 603946257 1.420000e-30 145
34 TraesCS1D01G423000 chr3D 89.381 113 8 4 323 434 19269814 19269705 6.630000e-29 139


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 TraesCS1D01G423000 chr1D 478225151 478230059 4908 True 9066.000000 9066 100.000000 1 4909 1 chr1D.!!$R2 4908
1 TraesCS1D01G423000 chr1A 574471304 574476188 4884 True 1855.750000 6420 94.788000 1 4909 4 chr1A.!!$R2 4908
2 TraesCS1D01G423000 chr1B 665794524 665798867 4343 True 2369.666667 6335 96.001667 1 4556 3 chr1B.!!$R2 4555
3 TraesCS1D01G423000 chr6D 315245682 315248464 2782 False 871.000000 1230 80.669000 1030 3910 2 chr6D.!!$F1 2880
4 TraesCS1D01G423000 chr6D 315190917 315193841 2924 True 866.000000 1122 81.994000 973 3908 2 chr6D.!!$R1 2935
5 TraesCS1D01G423000 chr6A 452264248 452267175 2927 True 670.000000 1136 81.487667 973 3908 3 chr6A.!!$R1 2935
6 TraesCS1D01G423000 chr6B 512217552 512219000 1448 False 1105.000000 1105 80.621000 2446 3915 1 chr6B.!!$F1 1469

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
579 590 0.105039 CTAGCTTAGGCCCAGTTCGG 59.895 60.000 0.00 0.00 39.73 4.30 F
1660 1951 0.175073 CCTTAGACAGGTACGGTGCC 59.825 60.000 7.22 7.22 36.51 5.01 F
2347 2906 1.464997 GCCTGGAAGCAGACGTAAAAG 59.535 52.381 0.00 0.00 0.00 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2407 2993 0.590195 GAAAGTCTGCTGCACACCAG 59.410 55.000 4.36 0.00 44.67 4.00 R
2673 3259 3.742640 CGGAAAATGCCACCAAGGAAAAA 60.743 43.478 0.00 0.00 41.22 1.94 R
4287 4881 4.572389 ACTTATGTGCAAAGTGATCGGATC 59.428 41.667 11.07 11.07 35.87 3.36 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
125 127 8.768501 ATCCATAGTCAAACTACTCATAGTCA 57.231 34.615 0.00 0.00 41.00 3.41
126 128 8.768501 TCCATAGTCAAACTACTCATAGTCAT 57.231 34.615 0.00 0.00 41.00 3.06
127 129 9.862149 TCCATAGTCAAACTACTCATAGTCATA 57.138 33.333 0.00 0.00 41.00 2.15
227 235 5.405935 ACCAGATGTTAAAGAATTTGGGC 57.594 39.130 7.91 0.00 39.63 5.36
307 315 6.897413 ACACTAGAAAAATGATAGGGGCAATT 59.103 34.615 0.00 0.00 0.00 2.32
331 339 8.480133 TTCTCTAATTGACTTATACTCCCTCC 57.520 38.462 0.00 0.00 0.00 4.30
332 340 6.715718 TCTCTAATTGACTTATACTCCCTCCG 59.284 42.308 0.00 0.00 0.00 4.63
333 341 6.371278 TCTAATTGACTTATACTCCCTCCGT 58.629 40.000 0.00 0.00 0.00 4.69
334 342 5.952347 AATTGACTTATACTCCCTCCGTT 57.048 39.130 0.00 0.00 0.00 4.44
335 343 4.996788 TTGACTTATACTCCCTCCGTTC 57.003 45.455 0.00 0.00 0.00 3.95
336 344 3.294214 TGACTTATACTCCCTCCGTTCC 58.706 50.000 0.00 0.00 0.00 3.62
337 345 3.294214 GACTTATACTCCCTCCGTTCCA 58.706 50.000 0.00 0.00 0.00 3.53
338 346 3.703052 GACTTATACTCCCTCCGTTCCAA 59.297 47.826 0.00 0.00 0.00 3.53
339 347 4.098894 ACTTATACTCCCTCCGTTCCAAA 58.901 43.478 0.00 0.00 0.00 3.28
340 348 4.533311 ACTTATACTCCCTCCGTTCCAAAA 59.467 41.667 0.00 0.00 0.00 2.44
341 349 5.191124 ACTTATACTCCCTCCGTTCCAAAAT 59.809 40.000 0.00 0.00 0.00 1.82
342 350 6.384886 ACTTATACTCCCTCCGTTCCAAAATA 59.615 38.462 0.00 0.00 0.00 1.40
343 351 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
344 352 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
345 353 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
346 354 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
347 355 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
348 356 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
349 357 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
350 358 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
351 359 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
352 360 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
353 361 6.414732 TCCGTTCCAAAATAGATGACTCAAT 58.585 36.000 0.00 0.00 0.00 2.57
354 362 6.884295 TCCGTTCCAAAATAGATGACTCAATT 59.116 34.615 0.00 0.00 0.00 2.32
355 363 7.393234 TCCGTTCCAAAATAGATGACTCAATTT 59.607 33.333 0.00 0.00 0.00 1.82
356 364 8.028938 CCGTTCCAAAATAGATGACTCAATTTT 58.971 33.333 0.00 0.00 33.07 1.82
395 403 7.648039 ACAAAGTTAATACAAAGTTGGGTCA 57.352 32.000 0.00 0.00 0.00 4.02
396 404 8.245195 ACAAAGTTAATACAAAGTTGGGTCAT 57.755 30.769 0.00 0.00 0.00 3.06
397 405 8.357402 ACAAAGTTAATACAAAGTTGGGTCATC 58.643 33.333 0.00 0.00 0.00 2.92
398 406 8.576442 CAAAGTTAATACAAAGTTGGGTCATCT 58.424 33.333 0.00 0.00 0.00 2.90
399 407 9.802039 AAAGTTAATACAAAGTTGGGTCATCTA 57.198 29.630 0.00 0.00 0.00 1.98
400 408 9.975218 AAGTTAATACAAAGTTGGGTCATCTAT 57.025 29.630 0.00 0.00 0.00 1.98
401 409 9.975218 AGTTAATACAAAGTTGGGTCATCTATT 57.025 29.630 0.00 0.00 0.00 1.73
405 413 8.877864 ATACAAAGTTGGGTCATCTATTTTGA 57.122 30.769 0.00 0.00 0.00 2.69
406 414 7.595819 ACAAAGTTGGGTCATCTATTTTGAA 57.404 32.000 0.00 0.00 0.00 2.69
407 415 8.017418 ACAAAGTTGGGTCATCTATTTTGAAA 57.983 30.769 0.00 0.00 0.00 2.69
408 416 7.926018 ACAAAGTTGGGTCATCTATTTTGAAAC 59.074 33.333 0.00 0.00 0.00 2.78
409 417 6.254281 AGTTGGGTCATCTATTTTGAAACG 57.746 37.500 0.00 0.00 0.00 3.60
410 418 5.183140 AGTTGGGTCATCTATTTTGAAACGG 59.817 40.000 0.00 0.00 0.00 4.44
411 419 4.912586 TGGGTCATCTATTTTGAAACGGA 58.087 39.130 0.00 0.00 0.00 4.69
412 420 4.941263 TGGGTCATCTATTTTGAAACGGAG 59.059 41.667 0.00 0.00 0.00 4.63
413 421 4.335594 GGGTCATCTATTTTGAAACGGAGG 59.664 45.833 0.00 0.00 0.00 4.30
414 422 5.183228 GGTCATCTATTTTGAAACGGAGGA 58.817 41.667 0.00 0.00 0.00 3.71
415 423 5.646360 GGTCATCTATTTTGAAACGGAGGAA 59.354 40.000 0.00 0.00 0.00 3.36
416 424 6.183360 GGTCATCTATTTTGAAACGGAGGAAG 60.183 42.308 0.00 0.00 0.00 3.46
417 425 6.371825 GTCATCTATTTTGAAACGGAGGAAGT 59.628 38.462 0.00 0.00 0.00 3.01
418 426 7.548075 GTCATCTATTTTGAAACGGAGGAAGTA 59.452 37.037 0.00 0.00 0.00 2.24
419 427 7.548075 TCATCTATTTTGAAACGGAGGAAGTAC 59.452 37.037 0.00 0.00 0.00 2.73
420 428 7.001099 TCTATTTTGAAACGGAGGAAGTACT 57.999 36.000 0.00 0.00 0.00 2.73
421 429 8.125978 TCTATTTTGAAACGGAGGAAGTACTA 57.874 34.615 0.00 0.00 0.00 1.82
422 430 8.587608 TCTATTTTGAAACGGAGGAAGTACTAA 58.412 33.333 0.00 0.00 0.00 2.24
507 517 2.627945 TCGGCAATCACTAACATCACC 58.372 47.619 0.00 0.00 0.00 4.02
565 576 3.635510 CTTCCCCGGAAGCTAGCT 58.364 61.111 12.68 12.68 43.95 3.32
566 577 1.908483 CTTCCCCGGAAGCTAGCTT 59.092 57.895 29.71 29.71 43.95 3.74
567 578 1.120530 CTTCCCCGGAAGCTAGCTTA 58.879 55.000 29.39 10.62 43.95 3.09
568 579 1.069358 CTTCCCCGGAAGCTAGCTTAG 59.931 57.143 29.39 23.84 43.95 2.18
569 580 0.759436 TCCCCGGAAGCTAGCTTAGG 60.759 60.000 30.32 30.32 36.26 2.69
570 581 1.069935 CCCGGAAGCTAGCTTAGGC 59.930 63.158 31.22 20.65 36.26 3.93
571 582 1.069935 CCGGAAGCTAGCTTAGGCC 59.930 63.158 29.39 23.60 39.73 5.19
572 583 1.069935 CGGAAGCTAGCTTAGGCCC 59.930 63.158 29.39 23.26 39.73 5.80
573 584 1.686325 CGGAAGCTAGCTTAGGCCCA 61.686 60.000 29.39 0.00 39.73 5.36
574 585 0.107643 GGAAGCTAGCTTAGGCCCAG 59.892 60.000 29.39 0.00 39.73 4.45
575 586 0.833949 GAAGCTAGCTTAGGCCCAGT 59.166 55.000 29.39 4.55 39.73 4.00
576 587 1.210722 GAAGCTAGCTTAGGCCCAGTT 59.789 52.381 29.39 3.71 39.73 3.16
577 588 0.833949 AGCTAGCTTAGGCCCAGTTC 59.166 55.000 12.68 0.00 39.73 3.01
578 589 0.530870 GCTAGCTTAGGCCCAGTTCG 60.531 60.000 7.70 0.00 39.73 3.95
579 590 0.105039 CTAGCTTAGGCCCAGTTCGG 59.895 60.000 0.00 0.00 39.73 4.30
587 598 2.485122 CCCAGTTCGGCAAATCGC 59.515 61.111 0.00 0.00 41.28 4.58
628 639 2.270527 GCCTTCCAGCCACTCCTC 59.729 66.667 0.00 0.00 0.00 3.71
629 640 2.596851 GCCTTCCAGCCACTCCTCA 61.597 63.158 0.00 0.00 0.00 3.86
630 641 2.069776 CCTTCCAGCCACTCCTCAA 58.930 57.895 0.00 0.00 0.00 3.02
631 642 0.401738 CCTTCCAGCCACTCCTCAAA 59.598 55.000 0.00 0.00 0.00 2.69
632 643 1.005215 CCTTCCAGCCACTCCTCAAAT 59.995 52.381 0.00 0.00 0.00 2.32
633 644 2.556114 CCTTCCAGCCACTCCTCAAATT 60.556 50.000 0.00 0.00 0.00 1.82
634 645 3.308402 CCTTCCAGCCACTCCTCAAATTA 60.308 47.826 0.00 0.00 0.00 1.40
635 646 4.335416 CTTCCAGCCACTCCTCAAATTAA 58.665 43.478 0.00 0.00 0.00 1.40
636 647 4.380843 TCCAGCCACTCCTCAAATTAAA 57.619 40.909 0.00 0.00 0.00 1.52
637 648 4.735369 TCCAGCCACTCCTCAAATTAAAA 58.265 39.130 0.00 0.00 0.00 1.52
638 649 4.522789 TCCAGCCACTCCTCAAATTAAAAC 59.477 41.667 0.00 0.00 0.00 2.43
639 650 4.524328 CCAGCCACTCCTCAAATTAAAACT 59.476 41.667 0.00 0.00 0.00 2.66
640 651 5.710099 CCAGCCACTCCTCAAATTAAAACTA 59.290 40.000 0.00 0.00 0.00 2.24
641 652 6.127897 CCAGCCACTCCTCAAATTAAAACTAG 60.128 42.308 0.00 0.00 0.00 2.57
642 653 6.655003 CAGCCACTCCTCAAATTAAAACTAGA 59.345 38.462 0.00 0.00 0.00 2.43
643 654 7.337942 CAGCCACTCCTCAAATTAAAACTAGAT 59.662 37.037 0.00 0.00 0.00 1.98
644 655 7.554476 AGCCACTCCTCAAATTAAAACTAGATC 59.446 37.037 0.00 0.00 0.00 2.75
645 656 7.201741 GCCACTCCTCAAATTAAAACTAGATCC 60.202 40.741 0.00 0.00 0.00 3.36
646 657 8.049721 CCACTCCTCAAATTAAAACTAGATCCT 58.950 37.037 0.00 0.00 0.00 3.24
647 658 8.887717 CACTCCTCAAATTAAAACTAGATCCTG 58.112 37.037 0.00 0.00 0.00 3.86
648 659 7.554476 ACTCCTCAAATTAAAACTAGATCCTGC 59.446 37.037 0.00 0.00 0.00 4.85
649 660 7.633789 TCCTCAAATTAAAACTAGATCCTGCT 58.366 34.615 0.00 0.00 0.00 4.24
650 661 7.770897 TCCTCAAATTAAAACTAGATCCTGCTC 59.229 37.037 0.00 0.00 0.00 4.26
651 662 7.012799 CCTCAAATTAAAACTAGATCCTGCTCC 59.987 40.741 0.00 0.00 0.00 4.70
652 663 6.538742 TCAAATTAAAACTAGATCCTGCTCCG 59.461 38.462 0.00 0.00 0.00 4.63
653 664 2.317530 AAAACTAGATCCTGCTCCGC 57.682 50.000 0.00 0.00 0.00 5.54
654 665 1.490574 AAACTAGATCCTGCTCCGCT 58.509 50.000 0.00 0.00 0.00 5.52
655 666 1.036707 AACTAGATCCTGCTCCGCTC 58.963 55.000 0.00 0.00 0.00 5.03
656 667 0.825840 ACTAGATCCTGCTCCGCTCC 60.826 60.000 0.00 0.00 0.00 4.70
657 668 1.861542 CTAGATCCTGCTCCGCTCCG 61.862 65.000 0.00 0.00 0.00 4.63
671 682 3.691342 TCCGGCGTGGAGTTGGAG 61.691 66.667 6.01 0.00 43.74 3.86
672 683 3.691342 CCGGCGTGGAGTTGGAGA 61.691 66.667 6.01 0.00 42.00 3.71
673 684 2.125912 CGGCGTGGAGTTGGAGAG 60.126 66.667 0.00 0.00 0.00 3.20
674 685 2.932234 CGGCGTGGAGTTGGAGAGT 61.932 63.158 0.00 0.00 0.00 3.24
675 686 1.374758 GGCGTGGAGTTGGAGAGTG 60.375 63.158 0.00 0.00 0.00 3.51
676 687 1.374758 GCGTGGAGTTGGAGAGTGG 60.375 63.158 0.00 0.00 0.00 4.00
677 688 1.816863 GCGTGGAGTTGGAGAGTGGA 61.817 60.000 0.00 0.00 0.00 4.02
678 689 0.244994 CGTGGAGTTGGAGAGTGGAG 59.755 60.000 0.00 0.00 0.00 3.86
679 690 1.633774 GTGGAGTTGGAGAGTGGAGA 58.366 55.000 0.00 0.00 0.00 3.71
680 691 1.548269 GTGGAGTTGGAGAGTGGAGAG 59.452 57.143 0.00 0.00 0.00 3.20
681 692 1.429299 TGGAGTTGGAGAGTGGAGAGA 59.571 52.381 0.00 0.00 0.00 3.10
682 693 1.822371 GGAGTTGGAGAGTGGAGAGAC 59.178 57.143 0.00 0.00 0.00 3.36
683 694 2.556559 GGAGTTGGAGAGTGGAGAGACT 60.557 54.545 0.00 0.00 0.00 3.24
684 695 2.752903 GAGTTGGAGAGTGGAGAGACTC 59.247 54.545 0.00 0.00 42.45 3.36
694 705 1.604915 GAGAGACTCCAAAGGGCCC 59.395 63.158 16.46 16.46 0.00 5.80
718 729 3.436577 AGTCTCGAGTGTTTCTCCCTA 57.563 47.619 13.13 0.00 39.84 3.53
719 730 3.349022 AGTCTCGAGTGTTTCTCCCTAG 58.651 50.000 13.13 0.00 39.84 3.02
720 731 2.093106 TCTCGAGTGTTTCTCCCTAGC 58.907 52.381 13.13 0.00 39.84 3.42
721 732 2.096248 CTCGAGTGTTTCTCCCTAGCT 58.904 52.381 3.62 0.00 39.84 3.32
725 736 3.330267 GAGTGTTTCTCCCTAGCTGTTG 58.670 50.000 0.00 0.00 37.22 3.33
892 909 1.626654 CGAAATTCGTGTCGCCAGCT 61.627 55.000 7.29 0.00 34.72 4.24
893 910 0.517316 GAAATTCGTGTCGCCAGCTT 59.483 50.000 0.00 0.00 0.00 3.74
894 911 1.730064 GAAATTCGTGTCGCCAGCTTA 59.270 47.619 0.00 0.00 0.00 3.09
895 912 2.024176 AATTCGTGTCGCCAGCTTAT 57.976 45.000 0.00 0.00 0.00 1.73
1428 1716 5.826737 GCCATGTCTTCCTACTAGTACAGTA 59.173 44.000 0.00 0.56 38.80 2.74
1656 1947 1.856629 TTCCCCTTAGACAGGTACGG 58.143 55.000 0.00 0.00 42.02 4.02
1658 1949 0.822164 CCCCTTAGACAGGTACGGTG 59.178 60.000 0.00 0.00 42.02 4.94
1660 1951 0.175073 CCTTAGACAGGTACGGTGCC 59.825 60.000 7.22 7.22 36.51 5.01
1662 1953 1.549170 CTTAGACAGGTACGGTGCCTT 59.451 52.381 15.59 7.29 36.51 4.35
1715 2242 5.679734 ACAGATTTGAGTGTGCTTAACAG 57.320 39.130 0.00 0.00 40.26 3.16
1716 2243 5.368145 ACAGATTTGAGTGTGCTTAACAGA 58.632 37.500 0.00 0.00 40.26 3.41
1718 2245 5.468072 CAGATTTGAGTGTGCTTAACAGAGT 59.532 40.000 0.00 0.00 40.26 3.24
1789 2332 6.890558 TGCTAGGATTAACGTACACAAAAAC 58.109 36.000 0.00 0.00 0.00 2.43
1963 2513 8.564574 TGGTCTTTGTCACTAAATATGAAACAC 58.435 33.333 0.00 0.00 0.00 3.32
2278 2837 3.380479 TTCTTCCAGTGGTTCTACACG 57.620 47.619 9.54 0.00 45.80 4.49
2347 2906 1.464997 GCCTGGAAGCAGACGTAAAAG 59.535 52.381 0.00 0.00 0.00 2.27
2407 2993 4.946784 ACGCTATGTTTTGTCAGATTCC 57.053 40.909 0.00 0.00 0.00 3.01
4024 4618 5.687828 CCGTTTAACTTTATTTGCACCGTA 58.312 37.500 0.00 0.00 0.00 4.02
4332 4927 1.702957 TCCTTACAAACTGGAGTGGGG 59.297 52.381 0.00 0.00 0.00 4.96
4481 5079 7.337942 ACATTTCATAGACTTTCATGTTCCTCC 59.662 37.037 0.00 0.00 0.00 4.30
4514 5112 2.606213 TCTGATGCGGTGGGTCCA 60.606 61.111 0.00 0.00 35.57 4.02
4578 5183 2.697751 CCGATGAGGAGAAGACTTCCAT 59.302 50.000 11.67 7.83 45.00 3.41
4583 5188 3.006247 GAGGAGAAGACTTCCATGTTGC 58.994 50.000 11.67 0.00 0.00 4.17
4622 5227 2.849162 GATGGATGAGGGCGGGGA 60.849 66.667 0.00 0.00 0.00 4.81
4626 5231 2.227036 GGATGAGGGCGGGGATGAT 61.227 63.158 0.00 0.00 0.00 2.45
4737 5351 2.359975 AAGGAGAAAAGGCGGCCG 60.360 61.111 24.05 24.05 0.00 6.13
4801 5415 4.442753 CCTCCCTAGATCTTGACTTCTTGC 60.443 50.000 0.00 0.00 0.00 4.01
4808 5422 6.889301 AGATCTTGACTTCTTGCATTTTCA 57.111 33.333 0.00 0.00 0.00 2.69
4814 5428 4.275689 TGACTTCTTGCATTTTCATGACGT 59.724 37.500 0.00 0.00 31.07 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.903547 CGGTTGTTGGGACTTGGCG 61.904 63.158 0.00 0.00 0.00 5.69
15 16 1.388837 AACGGTTGTTGGGACTTGGC 61.389 55.000 0.00 0.00 36.81 4.52
227 235 0.537188 ACCGCCCAAGTACAGATGAG 59.463 55.000 0.00 0.00 0.00 2.90
286 294 7.586349 AGAGAATTGCCCCTATCATTTTTCTA 58.414 34.615 0.00 0.00 0.00 2.10
307 315 6.715718 CGGAGGGAGTATAAGTCAATTAGAGA 59.284 42.308 0.00 0.00 0.00 3.10
317 325 3.393426 TGGAACGGAGGGAGTATAAGT 57.607 47.619 0.00 0.00 0.00 2.24
326 334 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
328 336 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
329 337 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
330 338 6.683974 ATTGAGTCATCTATTTTGGAACGG 57.316 37.500 0.00 0.00 0.00 4.44
331 339 8.970691 AAAATTGAGTCATCTATTTTGGAACG 57.029 30.769 11.47 0.00 44.08 3.95
369 377 9.357161 TGACCCAACTTTGTATTAACTTTGTAT 57.643 29.630 0.00 0.00 0.00 2.29
370 378 8.749026 TGACCCAACTTTGTATTAACTTTGTA 57.251 30.769 0.00 0.00 0.00 2.41
371 379 7.648039 TGACCCAACTTTGTATTAACTTTGT 57.352 32.000 0.00 0.00 0.00 2.83
372 380 8.576442 AGATGACCCAACTTTGTATTAACTTTG 58.424 33.333 0.00 0.00 0.00 2.77
373 381 8.706322 AGATGACCCAACTTTGTATTAACTTT 57.294 30.769 0.00 0.00 0.00 2.66
374 382 9.975218 ATAGATGACCCAACTTTGTATTAACTT 57.025 29.630 0.00 0.00 0.00 2.66
375 383 9.975218 AATAGATGACCCAACTTTGTATTAACT 57.025 29.630 0.00 0.00 0.00 2.24
379 387 9.308000 TCAAAATAGATGACCCAACTTTGTATT 57.692 29.630 0.00 0.00 0.00 1.89
380 388 8.877864 TCAAAATAGATGACCCAACTTTGTAT 57.122 30.769 0.00 0.00 0.00 2.29
381 389 8.698973 TTCAAAATAGATGACCCAACTTTGTA 57.301 30.769 0.00 0.00 0.00 2.41
382 390 7.595819 TTCAAAATAGATGACCCAACTTTGT 57.404 32.000 0.00 0.00 0.00 2.83
383 391 7.114811 CGTTTCAAAATAGATGACCCAACTTTG 59.885 37.037 0.00 0.00 0.00 2.77
384 392 7.145323 CGTTTCAAAATAGATGACCCAACTTT 58.855 34.615 0.00 0.00 0.00 2.66
385 393 6.294508 CCGTTTCAAAATAGATGACCCAACTT 60.295 38.462 0.00 0.00 0.00 2.66
386 394 5.183140 CCGTTTCAAAATAGATGACCCAACT 59.817 40.000 0.00 0.00 0.00 3.16
387 395 5.182380 TCCGTTTCAAAATAGATGACCCAAC 59.818 40.000 0.00 0.00 0.00 3.77
388 396 5.317808 TCCGTTTCAAAATAGATGACCCAA 58.682 37.500 0.00 0.00 0.00 4.12
389 397 4.912586 TCCGTTTCAAAATAGATGACCCA 58.087 39.130 0.00 0.00 0.00 4.51
390 398 4.335594 CCTCCGTTTCAAAATAGATGACCC 59.664 45.833 0.00 0.00 0.00 4.46
391 399 5.183228 TCCTCCGTTTCAAAATAGATGACC 58.817 41.667 0.00 0.00 0.00 4.02
392 400 6.371825 ACTTCCTCCGTTTCAAAATAGATGAC 59.628 38.462 0.00 0.00 0.00 3.06
393 401 6.472887 ACTTCCTCCGTTTCAAAATAGATGA 58.527 36.000 0.00 0.00 0.00 2.92
394 402 6.743575 ACTTCCTCCGTTTCAAAATAGATG 57.256 37.500 0.00 0.00 0.00 2.90
395 403 7.621796 AGTACTTCCTCCGTTTCAAAATAGAT 58.378 34.615 0.00 0.00 0.00 1.98
396 404 7.001099 AGTACTTCCTCCGTTTCAAAATAGA 57.999 36.000 0.00 0.00 0.00 1.98
397 405 8.654215 GTTAGTACTTCCTCCGTTTCAAAATAG 58.346 37.037 0.00 0.00 0.00 1.73
398 406 8.370182 AGTTAGTACTTCCTCCGTTTCAAAATA 58.630 33.333 0.00 0.00 0.00 1.40
399 407 7.222161 AGTTAGTACTTCCTCCGTTTCAAAAT 58.778 34.615 0.00 0.00 0.00 1.82
400 408 6.585416 AGTTAGTACTTCCTCCGTTTCAAAA 58.415 36.000 0.00 0.00 0.00 2.44
401 409 6.165700 AGTTAGTACTTCCTCCGTTTCAAA 57.834 37.500 0.00 0.00 0.00 2.69
402 410 5.796424 AGTTAGTACTTCCTCCGTTTCAA 57.204 39.130 0.00 0.00 0.00 2.69
403 411 6.240894 TCTAGTTAGTACTTCCTCCGTTTCA 58.759 40.000 0.00 0.00 35.78 2.69
404 412 6.749923 TCTAGTTAGTACTTCCTCCGTTTC 57.250 41.667 0.00 0.00 35.78 2.78
405 413 8.993404 ATATCTAGTTAGTACTTCCTCCGTTT 57.007 34.615 0.00 0.00 35.78 3.60
407 415 9.723601 CTTATATCTAGTTAGTACTTCCTCCGT 57.276 37.037 0.00 0.00 35.78 4.69
408 416 9.941325 TCTTATATCTAGTTAGTACTTCCTCCG 57.059 37.037 0.00 0.00 35.78 4.63
507 517 0.841961 TCCAAGCTGGGGATGAGATG 59.158 55.000 7.48 0.00 38.32 2.90
570 581 2.485122 GCGATTTGCCGAACTGGG 59.515 61.111 0.00 0.00 38.63 4.45
590 601 4.441695 TTCGCAGGCTCCGCTCTG 62.442 66.667 0.00 0.00 32.70 3.35
591 602 4.140599 CTTCGCAGGCTCCGCTCT 62.141 66.667 0.00 0.00 0.00 4.09
612 623 0.401738 TTTGAGGAGTGGCTGGAAGG 59.598 55.000 0.00 0.00 0.00 3.46
613 624 2.503895 ATTTGAGGAGTGGCTGGAAG 57.496 50.000 0.00 0.00 0.00 3.46
614 625 2.978156 AATTTGAGGAGTGGCTGGAA 57.022 45.000 0.00 0.00 0.00 3.53
615 626 4.380843 TTTAATTTGAGGAGTGGCTGGA 57.619 40.909 0.00 0.00 0.00 3.86
616 627 4.524328 AGTTTTAATTTGAGGAGTGGCTGG 59.476 41.667 0.00 0.00 0.00 4.85
617 628 5.712152 AGTTTTAATTTGAGGAGTGGCTG 57.288 39.130 0.00 0.00 0.00 4.85
618 629 6.779860 TCTAGTTTTAATTTGAGGAGTGGCT 58.220 36.000 0.00 0.00 0.00 4.75
619 630 7.201741 GGATCTAGTTTTAATTTGAGGAGTGGC 60.202 40.741 0.00 0.00 0.00 5.01
620 631 8.049721 AGGATCTAGTTTTAATTTGAGGAGTGG 58.950 37.037 0.00 0.00 0.00 4.00
621 632 8.887717 CAGGATCTAGTTTTAATTTGAGGAGTG 58.112 37.037 0.00 0.00 0.00 3.51
622 633 7.554476 GCAGGATCTAGTTTTAATTTGAGGAGT 59.446 37.037 0.00 0.00 0.00 3.85
623 634 7.772757 AGCAGGATCTAGTTTTAATTTGAGGAG 59.227 37.037 0.00 0.00 0.00 3.69
624 635 7.633789 AGCAGGATCTAGTTTTAATTTGAGGA 58.366 34.615 0.00 0.00 0.00 3.71
625 636 7.012799 GGAGCAGGATCTAGTTTTAATTTGAGG 59.987 40.741 0.00 0.00 0.00 3.86
626 637 7.254590 CGGAGCAGGATCTAGTTTTAATTTGAG 60.255 40.741 0.00 0.00 0.00 3.02
627 638 6.538742 CGGAGCAGGATCTAGTTTTAATTTGA 59.461 38.462 0.00 0.00 0.00 2.69
628 639 6.719365 CGGAGCAGGATCTAGTTTTAATTTG 58.281 40.000 0.00 0.00 0.00 2.32
629 640 6.927294 CGGAGCAGGATCTAGTTTTAATTT 57.073 37.500 0.00 0.00 0.00 1.82
654 665 3.691342 CTCCAACTCCACGCCGGA 61.691 66.667 5.05 0.00 43.61 5.14
655 666 3.649277 CTCTCCAACTCCACGCCGG 62.649 68.421 0.00 0.00 0.00 6.13
656 667 2.125912 CTCTCCAACTCCACGCCG 60.126 66.667 0.00 0.00 0.00 6.46
657 668 1.374758 CACTCTCCAACTCCACGCC 60.375 63.158 0.00 0.00 0.00 5.68
658 669 1.374758 CCACTCTCCAACTCCACGC 60.375 63.158 0.00 0.00 0.00 5.34
659 670 0.244994 CTCCACTCTCCAACTCCACG 59.755 60.000 0.00 0.00 0.00 4.94
660 671 1.548269 CTCTCCACTCTCCAACTCCAC 59.452 57.143 0.00 0.00 0.00 4.02
661 672 1.429299 TCTCTCCACTCTCCAACTCCA 59.571 52.381 0.00 0.00 0.00 3.86
662 673 1.822371 GTCTCTCCACTCTCCAACTCC 59.178 57.143 0.00 0.00 0.00 3.85
663 674 2.752903 GAGTCTCTCCACTCTCCAACTC 59.247 54.545 0.00 0.00 39.91 3.01
664 675 2.802719 GAGTCTCTCCACTCTCCAACT 58.197 52.381 0.00 0.00 39.91 3.16
676 687 1.604915 GGGCCCTTTGGAGTCTCTC 59.395 63.158 17.04 0.00 0.00 3.20
677 688 1.925972 GGGGCCCTTTGGAGTCTCT 60.926 63.158 24.38 0.00 0.00 3.10
678 689 1.501654 AAGGGGCCCTTTGGAGTCTC 61.502 60.000 32.48 0.00 41.69 3.36
679 690 0.178843 TAAGGGGCCCTTTGGAGTCT 60.179 55.000 40.98 18.66 41.69 3.24
680 691 0.256177 CTAAGGGGCCCTTTGGAGTC 59.744 60.000 40.98 5.79 41.69 3.36
681 692 0.477795 ACTAAGGGGCCCTTTGGAGT 60.478 55.000 40.98 33.03 41.69 3.85
682 693 0.256177 GACTAAGGGGCCCTTTGGAG 59.744 60.000 40.98 32.37 41.69 3.86
683 694 0.178843 AGACTAAGGGGCCCTTTGGA 60.179 55.000 40.98 23.53 41.69 3.53
684 695 0.256177 GAGACTAAGGGGCCCTTTGG 59.744 60.000 40.98 32.30 41.69 3.28
685 696 0.107654 CGAGACTAAGGGGCCCTTTG 60.108 60.000 40.98 37.92 41.69 2.77
686 697 0.252558 TCGAGACTAAGGGGCCCTTT 60.253 55.000 40.98 25.93 41.69 3.11
687 698 0.688087 CTCGAGACTAAGGGGCCCTT 60.688 60.000 38.28 38.28 46.63 3.95
688 699 1.075896 CTCGAGACTAAGGGGCCCT 60.076 63.158 22.67 22.67 33.87 5.19
689 700 1.381463 ACTCGAGACTAAGGGGCCC 60.381 63.158 21.68 17.12 0.00 5.80
690 701 0.971447 ACACTCGAGACTAAGGGGCC 60.971 60.000 21.68 0.00 0.00 5.80
691 702 0.896226 AACACTCGAGACTAAGGGGC 59.104 55.000 21.68 0.00 0.00 5.80
692 703 2.826725 AGAAACACTCGAGACTAAGGGG 59.173 50.000 21.68 0.00 0.00 4.79
693 704 3.119424 GGAGAAACACTCGAGACTAAGGG 60.119 52.174 21.68 0.00 45.76 3.95
694 705 3.119424 GGGAGAAACACTCGAGACTAAGG 60.119 52.174 21.68 3.60 45.76 2.69
721 732 0.599991 CCGACTAGTGCTGCACAACA 60.600 55.000 31.90 16.67 36.74 3.33
725 736 2.815647 GGCCGACTAGTGCTGCAC 60.816 66.667 24.59 24.59 34.10 4.57
894 911 9.975218 ATTGGTCAGTACAAATTCCTACTAAAT 57.025 29.630 0.00 0.00 0.00 1.40
895 912 9.802039 AATTGGTCAGTACAAATTCCTACTAAA 57.198 29.630 0.00 0.00 34.70 1.85
1036 1303 0.377554 TCGTCTTTCTCGATCTCCGC 59.622 55.000 0.00 0.00 38.37 5.54
1428 1716 5.187967 AGGTAGTGCAAAGCTAGTAACTGAT 59.812 40.000 0.40 0.00 0.00 2.90
1658 1949 2.155279 AGAAAAGAAGAAGCGGAAGGC 58.845 47.619 0.00 0.00 44.05 4.35
1660 1951 7.584987 TCAATTTAGAAAAGAAGAAGCGGAAG 58.415 34.615 0.00 0.00 0.00 3.46
1662 1953 7.504924 TTCAATTTAGAAAAGAAGAAGCGGA 57.495 32.000 0.00 0.00 0.00 5.54
1837 2381 1.276421 GAGCAGCAGAGGTTCCAACTA 59.724 52.381 0.00 0.00 0.00 2.24
1937 2487 8.564574 GTGTTTCATATTTAGTGACAAAGACCA 58.435 33.333 0.00 0.00 0.00 4.02
1963 2513 3.756434 ACGACCAATACCTGAAAACATGG 59.244 43.478 0.00 0.00 0.00 3.66
2347 2906 1.402852 GGAACAGAATTGCGAAAGGGC 60.403 52.381 0.00 0.00 0.00 5.19
2407 2993 0.590195 GAAAGTCTGCTGCACACCAG 59.410 55.000 4.36 0.00 44.67 4.00
2673 3259 3.742640 CGGAAAATGCCACCAAGGAAAAA 60.743 43.478 0.00 0.00 41.22 1.94
2860 3453 7.978975 GCTGTCCTCACCTCTATTATTGATATC 59.021 40.741 0.00 0.00 0.00 1.63
4117 4711 6.798427 ATTCAGTAGACACATACACCATCT 57.202 37.500 0.00 0.00 0.00 2.90
4287 4881 4.572389 ACTTATGTGCAAAGTGATCGGATC 59.428 41.667 11.07 11.07 35.87 3.36
4351 4946 1.648467 GACCATTGGCCTCGCTCAAC 61.648 60.000 3.32 0.00 0.00 3.18
4481 5079 5.220624 CGCATCAGAGAAAGAAATTCCTGAG 60.221 44.000 0.00 0.00 42.91 3.35
4569 5167 1.142688 AGGGGGCAACATGGAAGTCT 61.143 55.000 0.00 0.00 39.74 3.24
4605 5210 2.227036 ATCCCCGCCCTCATCCATC 61.227 63.158 0.00 0.00 0.00 3.51
4668 5282 2.522193 CTCTCTACGGAGGGCCCC 60.522 72.222 21.43 10.33 39.86 5.80
4737 5351 0.539518 GAGAGAAGGTCCAAGCCCTC 59.460 60.000 0.00 0.00 0.00 4.30
4743 5357 0.471211 ACCGTGGAGAGAAGGTCCAA 60.471 55.000 0.00 0.00 45.85 3.53
4745 5359 0.898789 TCACCGTGGAGAGAAGGTCC 60.899 60.000 0.00 0.00 34.25 4.46
4748 5362 0.969894 AACTCACCGTGGAGAGAAGG 59.030 55.000 18.46 0.00 38.30 3.46
4814 5428 3.055385 AGCCCTACGAAAAGCATGACTAA 60.055 43.478 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.