Multiple sequence alignment - TraesCS5B01G302700

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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 TraesCS5B01G302700 chr5B 100.000 3592 0 0 1 3592 487250434 487246843 0.000000e+00 6634.0
1 TraesCS5B01G302700 chr5B 100.000 84 0 0 786 869 487249615 487249532 4.800000e-34 156.0
2 TraesCS5B01G302700 chr5B 100.000 84 0 0 820 903 487249649 487249566 4.800000e-34 156.0
3 TraesCS5B01G302700 chr5B 100.000 50 0 0 786 835 487249581 487249532 3.820000e-15 93.5
4 TraesCS5B01G302700 chr5B 100.000 50 0 0 854 903 487249649 487249600 3.820000e-15 93.5
5 TraesCS5B01G302700 chr5A 92.456 2757 132 22 854 3592 511964798 511962100 0.000000e+00 3869.0
6 TraesCS5B01G302700 chr5A 89.032 155 16 1 1 154 512037130 512036976 1.320000e-44 191.0
7 TraesCS5B01G302700 chr5A 97.980 99 2 0 723 821 511964861 511964763 4.770000e-39 172.0
8 TraesCS5B01G302700 chr5A 88.660 97 5 2 691 787 512024652 512024562 2.930000e-21 113.0
9 TraesCS5B01G302700 chr5A 90.244 82 5 2 889 967 511964879 511964798 1.760000e-18 104.0
10 TraesCS5B01G302700 chr5A 100.000 36 0 0 820 855 511964798 511964763 2.310000e-07 67.6
11 TraesCS5B01G302700 chr5D 96.580 2105 66 5 854 2953 406352120 406350017 0.000000e+00 3483.0
12 TraesCS5B01G302700 chr5D 89.740 653 58 5 2945 3592 406346291 406345643 0.000000e+00 826.0
13 TraesCS5B01G302700 chr5D 88.182 440 40 7 398 835 406352499 406352070 6.880000e-142 514.0
14 TraesCS5B01G302700 chr5D 87.688 398 41 6 8 402 406352934 406352542 1.180000e-124 457.0
15 TraesCS5B01G302700 chr5D 79.793 193 25 9 3411 3592 423223837 423223648 1.050000e-25 128.0
16 TraesCS5B01G302700 chr5D 79.085 153 25 7 395 543 563904361 563904510 8.210000e-17 99.0
17 TraesCS5B01G302700 chr2A 85.258 1723 201 26 893 2583 21191505 21193206 0.000000e+00 1725.0
18 TraesCS5B01G302700 chr2A 85.194 1675 194 24 963 2592 21006723 21005058 0.000000e+00 1670.0
19 TraesCS5B01G302700 chr2A 84.316 1696 219 18 935 2593 21177283 21178968 0.000000e+00 1615.0
20 TraesCS5B01G302700 chr2A 85.183 1586 196 14 1035 2593 21148240 21149813 0.000000e+00 1591.0
21 TraesCS5B01G302700 chr2A 83.427 531 82 3 2063 2593 21180368 21180892 4.170000e-134 488.0
22 TraesCS5B01G302700 chr2A 86.813 182 20 2 2542 2722 10550276 10550454 2.190000e-47 200.0
23 TraesCS5B01G302700 chr2A 87.640 89 11 0 434 522 77201407 77201495 1.760000e-18 104.0
24 TraesCS5B01G302700 chr2B 85.767 1637 189 20 996 2599 33728328 33729953 0.000000e+00 1692.0
25 TraesCS5B01G302700 chr2B 84.360 1688 219 18 936 2588 33662956 33664633 0.000000e+00 1613.0
26 TraesCS5B01G302700 chr2B 85.874 538 69 3 2063 2599 33578994 33578463 1.870000e-157 566.0
27 TraesCS5B01G302700 chr2D 84.229 1674 214 18 958 2593 20324794 20323133 0.000000e+00 1583.0
28 TraesCS5B01G302700 chr2D 87.349 1328 129 14 1337 2632 10313566 10314886 0.000000e+00 1485.0
29 TraesCS5B01G302700 chr2D 86.988 1099 139 3 963 2058 20381027 20382124 0.000000e+00 1234.0
30 TraesCS5B01G302700 chr2D 85.299 551 72 5 2050 2599 20382145 20382687 8.710000e-156 560.0
31 TraesCS5B01G302700 chr2D 85.932 526 68 1 2063 2588 20315438 20314919 1.130000e-154 556.0
32 TraesCS5B01G302700 chr3D 83.243 185 28 3 401 583 536888293 536888110 2.220000e-37 167.0
33 TraesCS5B01G302700 chr3D 80.226 177 24 5 3395 3565 497513283 497513454 4.870000e-24 122.0
34 TraesCS5B01G302700 chr4B 80.233 172 24 5 399 568 637347465 637347628 1.750000e-23 121.0
35 TraesCS5B01G302700 chr7B 76.847 203 44 3 3061 3260 728629363 728629161 1.050000e-20 111.0
36 TraesCS5B01G302700 chr7D 71.935 310 69 13 3061 3363 627354260 627354558 1.380000e-09 75.0
37 TraesCS5B01G302700 chr1A 92.683 41 3 0 455 495 554879408 554879448 3.870000e-05 60.2
38 TraesCS5B01G302700 chr6B 80.519 77 12 3 493 567 213835648 213835573 5.010000e-04 56.5


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 TraesCS5B01G302700 chr5B 487246843 487250434 3591 True 1426.60 6634 100.0000 1 3592 5 chr5B.!!$R1 3591
1 TraesCS5B01G302700 chr5A 511962100 511964879 2779 True 1053.15 3869 95.1700 723 3592 4 chr5A.!!$R3 2869
2 TraesCS5B01G302700 chr5D 406345643 406352934 7291 True 1320.00 3483 90.5475 8 3592 4 chr5D.!!$R2 3584
3 TraesCS5B01G302700 chr2A 21191505 21193206 1701 False 1725.00 1725 85.2580 893 2583 1 chr2A.!!$F3 1690
4 TraesCS5B01G302700 chr2A 21005058 21006723 1665 True 1670.00 1670 85.1940 963 2592 1 chr2A.!!$R1 1629
5 TraesCS5B01G302700 chr2A 21148240 21149813 1573 False 1591.00 1591 85.1830 1035 2593 1 chr2A.!!$F2 1558
6 TraesCS5B01G302700 chr2A 21177283 21180892 3609 False 1051.50 1615 83.8715 935 2593 2 chr2A.!!$F5 1658
7 TraesCS5B01G302700 chr2B 33728328 33729953 1625 False 1692.00 1692 85.7670 996 2599 1 chr2B.!!$F2 1603
8 TraesCS5B01G302700 chr2B 33662956 33664633 1677 False 1613.00 1613 84.3600 936 2588 1 chr2B.!!$F1 1652
9 TraesCS5B01G302700 chr2B 33578463 33578994 531 True 566.00 566 85.8740 2063 2599 1 chr2B.!!$R1 536
10 TraesCS5B01G302700 chr2D 20323133 20324794 1661 True 1583.00 1583 84.2290 958 2593 1 chr2D.!!$R2 1635
11 TraesCS5B01G302700 chr2D 10313566 10314886 1320 False 1485.00 1485 87.3490 1337 2632 1 chr2D.!!$F1 1295
12 TraesCS5B01G302700 chr2D 20381027 20382687 1660 False 897.00 1234 86.1435 963 2599 2 chr2D.!!$F2 1636
13 TraesCS5B01G302700 chr2D 20314919 20315438 519 True 556.00 556 85.9320 2063 2588 1 chr2D.!!$R1 525

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
427 477 0.115349 AGAGACTGGGCCAGTGTAGT 59.885 55.0 42.11 25.55 45.44 2.73 F
491 541 0.246910 GGAAACGTCTCCTCCCACTC 59.753 60.0 0.00 0.00 32.21 3.51 F
497 547 0.966920 GTCTCCTCCCACTCAACGAA 59.033 55.0 0.00 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2115 2243 0.034896 TCGTTGGTGAGGGCTTTCTC 59.965 55.000 0.0 0.0 0.00 2.87 R
2447 2576 0.107831 TGCCACTTTGGTAGCTCGTT 59.892 50.000 0.0 0.0 40.46 3.85 R
2745 2877 8.348285 TGAAAACAGAAATCATTAGTTAGGGG 57.652 34.615 0.0 0.0 0.00 4.79 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
27 28 8.348983 AGTCGAAAATAAACTATGTGTATCGG 57.651 34.615 0.00 0.00 0.00 4.18
37 38 2.902705 TGTGTATCGGCCTACCAATC 57.097 50.000 0.00 0.00 34.57 2.67
68 70 7.296628 AGGAGTAGAGACATCAATGGTTATC 57.703 40.000 0.00 0.00 0.00 1.75
83 85 9.884636 TCAATGGTTATCGAGAAAAATCTTCTA 57.115 29.630 0.00 0.00 0.00 2.10
92 94 8.703604 TCGAGAAAAATCTTCTATGTGTAAGG 57.296 34.615 0.00 0.00 0.00 2.69
150 152 4.283978 AGTGATTGAATTCAATTGGCACCA 59.716 37.500 29.57 21.76 45.72 4.17
201 204 0.614294 TTGGGCGAACCGATCCTTTA 59.386 50.000 0.00 0.00 44.64 1.85
206 209 3.878699 GGGCGAACCGATCCTTTATTTAA 59.121 43.478 0.00 0.00 36.48 1.52
209 212 5.237779 GGCGAACCGATCCTTTATTTAATGA 59.762 40.000 0.00 0.00 0.00 2.57
233 236 2.951229 AAAAACATCACGGAGGAGGT 57.049 45.000 0.00 0.00 32.39 3.85
262 265 7.127032 TGGGATGTGGAGGCAAAAATAAATTAT 59.873 33.333 0.00 0.00 0.00 1.28
268 271 9.822185 GTGGAGGCAAAAATAAATTATGAAGAT 57.178 29.630 0.00 0.00 0.00 2.40
286 289 4.164822 AGATGAAAATGAACCAAGCGTG 57.835 40.909 0.00 0.00 0.00 5.34
303 306 3.400054 GCCGGCCTACCAACTCCT 61.400 66.667 18.11 0.00 34.57 3.69
308 311 1.003233 CGGCCTACCAACTCCTCTTTT 59.997 52.381 0.00 0.00 34.57 2.27
309 312 2.437413 GGCCTACCAACTCCTCTTTTG 58.563 52.381 0.00 0.00 35.26 2.44
406 456 4.584743 TCATTCACATATACGAGCACCTCT 59.415 41.667 0.00 0.00 0.00 3.69
409 459 3.565902 TCACATATACGAGCACCTCTGAG 59.434 47.826 0.00 0.00 0.00 3.35
416 466 0.817013 GAGCACCTCTGAGAGACTGG 59.183 60.000 11.82 0.00 0.00 4.00
419 469 1.305718 ACCTCTGAGAGACTGGGCC 60.306 63.158 11.82 0.00 0.00 5.80
420 470 1.305633 CCTCTGAGAGACTGGGCCA 60.306 63.158 11.82 5.85 0.00 5.36
421 471 1.329171 CCTCTGAGAGACTGGGCCAG 61.329 65.000 31.62 31.62 37.52 4.85
423 473 0.902048 TCTGAGAGACTGGGCCAGTG 60.902 60.000 42.11 26.06 45.44 3.66
427 477 0.115349 AGAGACTGGGCCAGTGTAGT 59.885 55.000 42.11 25.55 45.44 2.73
433 483 4.345257 AGACTGGGCCAGTGTAGTATATTG 59.655 45.833 42.11 11.59 45.44 1.90
439 489 6.101150 TGGGCCAGTGTAGTATATTGAGATTT 59.899 38.462 0.00 0.00 0.00 2.17
443 493 9.542462 GCCAGTGTAGTATATTGAGATTTTACA 57.458 33.333 0.00 0.00 0.00 2.41
456 506 9.778741 ATTGAGATTTTACAAAGTCACTACAGA 57.221 29.630 0.86 0.00 0.00 3.41
474 524 2.180769 CGCCTCACAATCGACGGA 59.819 61.111 0.00 0.00 0.00 4.69
477 527 0.442699 GCCTCACAATCGACGGAAAC 59.557 55.000 0.00 0.00 0.00 2.78
491 541 0.246910 GGAAACGTCTCCTCCCACTC 59.753 60.000 0.00 0.00 32.21 3.51
497 547 0.966920 GTCTCCTCCCACTCAACGAA 59.033 55.000 0.00 0.00 0.00 3.85
524 574 2.806244 CCGGAAGCCTGGAATAAATACG 59.194 50.000 0.00 0.00 41.53 3.06
527 577 4.065789 GGAAGCCTGGAATAAATACGAGG 58.934 47.826 0.00 0.00 35.60 4.63
535 585 6.878923 CCTGGAATAAATACGAGGATAATGCA 59.121 38.462 0.00 0.00 34.68 3.96
537 587 8.862325 TGGAATAAATACGAGGATAATGCAAT 57.138 30.769 0.00 0.00 0.00 3.56
541 591 6.560253 AAATACGAGGATAATGCAATCACC 57.440 37.500 0.00 0.00 0.00 4.02
543 593 3.884895 ACGAGGATAATGCAATCACCAA 58.115 40.909 0.00 0.00 0.00 3.67
555 605 6.698008 TGCAATCACCAATGTAAATCTAGG 57.302 37.500 0.00 0.00 0.00 3.02
556 606 6.422333 TGCAATCACCAATGTAAATCTAGGA 58.578 36.000 0.00 0.00 0.00 2.94
557 607 6.318648 TGCAATCACCAATGTAAATCTAGGAC 59.681 38.462 0.00 0.00 0.00 3.85
558 608 6.543831 GCAATCACCAATGTAAATCTAGGACT 59.456 38.462 0.00 0.00 0.00 3.85
559 609 7.067494 GCAATCACCAATGTAAATCTAGGACTT 59.933 37.037 0.00 0.00 0.00 3.01
560 610 8.400947 CAATCACCAATGTAAATCTAGGACTTG 58.599 37.037 0.00 0.00 0.00 3.16
568 618 7.801893 TGTAAATCTAGGACTTGAACCCTAA 57.198 36.000 0.00 0.00 34.86 2.69
570 620 9.496710 TGTAAATCTAGGACTTGAACCCTAATA 57.503 33.333 0.00 0.00 34.86 0.98
576 626 4.783227 AGGACTTGAACCCTAATAAGCTGA 59.217 41.667 0.00 0.00 0.00 4.26
577 627 5.250774 AGGACTTGAACCCTAATAAGCTGAA 59.749 40.000 0.00 0.00 0.00 3.02
582 632 8.718656 ACTTGAACCCTAATAAGCTGAAGATAT 58.281 33.333 0.00 0.00 0.00 1.63
600 650 9.552695 TGAAGATATATGACATTGTCCTCCTAT 57.447 33.333 14.05 8.37 0.00 2.57
603 653 5.667539 ATATGACATTGTCCTCCTATCCG 57.332 43.478 14.05 0.00 0.00 4.18
604 654 2.039418 TGACATTGTCCTCCTATCCGG 58.961 52.381 14.05 0.00 0.00 5.14
612 662 0.987294 CCTCCTATCCGGCCAATCAT 59.013 55.000 2.24 0.00 0.00 2.45
629 679 6.373774 GCCAATCATATTCATCTCCTACTTGG 59.626 42.308 0.00 0.00 33.17 3.61
645 695 5.362717 CCTACTTGGTTTGGGAAGAAACTTT 59.637 40.000 0.00 0.00 36.30 2.66
725 775 4.518970 GGTGAATTAGAACAAGCACCAAGA 59.481 41.667 0.00 0.00 43.87 3.02
745 795 7.178274 ACCAAGAAACTTCCATGCATGTAATTA 59.822 33.333 24.58 4.86 0.00 1.40
825 875 3.464111 TTTTCGAAACGGACTTCTCCT 57.536 42.857 10.79 0.00 33.79 3.69
826 876 4.589216 TTTTCGAAACGGACTTCTCCTA 57.411 40.909 10.79 0.00 33.79 2.94
827 877 3.565905 TTCGAAACGGACTTCTCCTAC 57.434 47.619 0.00 0.00 33.79 3.18
828 878 2.787994 TCGAAACGGACTTCTCCTACT 58.212 47.619 0.00 0.00 33.79 2.57
829 879 3.152341 TCGAAACGGACTTCTCCTACTT 58.848 45.455 0.00 0.00 33.79 2.24
830 880 3.057736 TCGAAACGGACTTCTCCTACTTG 60.058 47.826 0.00 0.00 33.79 3.16
831 881 3.057736 CGAAACGGACTTCTCCTACTTGA 60.058 47.826 0.00 0.00 33.79 3.02
832 882 4.380655 CGAAACGGACTTCTCCTACTTGAT 60.381 45.833 0.00 0.00 33.79 2.57
833 883 5.480205 GAAACGGACTTCTCCTACTTGATT 58.520 41.667 0.00 0.00 33.79 2.57
834 884 5.485209 AACGGACTTCTCCTACTTGATTT 57.515 39.130 0.00 0.00 33.79 2.17
835 885 5.485209 ACGGACTTCTCCTACTTGATTTT 57.515 39.130 0.00 0.00 33.79 1.82
836 886 6.600882 ACGGACTTCTCCTACTTGATTTTA 57.399 37.500 0.00 0.00 33.79 1.52
837 887 7.184067 ACGGACTTCTCCTACTTGATTTTAT 57.816 36.000 0.00 0.00 33.79 1.40
838 888 7.621796 ACGGACTTCTCCTACTTGATTTTATT 58.378 34.615 0.00 0.00 33.79 1.40
839 889 8.101419 ACGGACTTCTCCTACTTGATTTTATTT 58.899 33.333 0.00 0.00 33.79 1.40
840 890 8.947115 CGGACTTCTCCTACTTGATTTTATTTT 58.053 33.333 0.00 0.00 33.79 1.82
859 909 3.464111 TTTTCGAAACGGACTTCTCCT 57.536 42.857 10.79 0.00 33.79 3.69
860 910 4.589216 TTTTCGAAACGGACTTCTCCTA 57.411 40.909 10.79 0.00 33.79 2.94
861 911 3.565905 TTCGAAACGGACTTCTCCTAC 57.434 47.619 0.00 0.00 33.79 3.18
862 912 2.787994 TCGAAACGGACTTCTCCTACT 58.212 47.619 0.00 0.00 33.79 2.57
863 913 3.152341 TCGAAACGGACTTCTCCTACTT 58.848 45.455 0.00 0.00 33.79 2.24
864 914 3.057736 TCGAAACGGACTTCTCCTACTTG 60.058 47.826 0.00 0.00 33.79 3.16
865 915 3.057736 CGAAACGGACTTCTCCTACTTGA 60.058 47.826 0.00 0.00 33.79 3.02
866 916 4.380655 CGAAACGGACTTCTCCTACTTGAT 60.381 45.833 0.00 0.00 33.79 2.57
867 917 5.480205 GAAACGGACTTCTCCTACTTGATT 58.520 41.667 0.00 0.00 33.79 2.57
868 918 5.485209 AACGGACTTCTCCTACTTGATTT 57.515 39.130 0.00 0.00 33.79 2.17
869 919 5.485209 ACGGACTTCTCCTACTTGATTTT 57.515 39.130 0.00 0.00 33.79 1.82
870 920 6.600882 ACGGACTTCTCCTACTTGATTTTA 57.399 37.500 0.00 0.00 33.79 1.52
871 921 7.184067 ACGGACTTCTCCTACTTGATTTTAT 57.816 36.000 0.00 0.00 33.79 1.40
872 922 7.621796 ACGGACTTCTCCTACTTGATTTTATT 58.378 34.615 0.00 0.00 33.79 1.40
873 923 8.101419 ACGGACTTCTCCTACTTGATTTTATTT 58.899 33.333 0.00 0.00 33.79 1.40
874 924 8.947115 CGGACTTCTCCTACTTGATTTTATTTT 58.053 33.333 0.00 0.00 33.79 1.82
1073 1139 4.764172 TCATGGTTTGTTTCTTGGGTTTG 58.236 39.130 0.00 0.00 0.00 2.93
1077 1143 4.284746 TGGTTTGTTTCTTGGGTTTGTTCT 59.715 37.500 0.00 0.00 0.00 3.01
1110 1179 1.006102 CTTGCGTCGACCTCCAACT 60.006 57.895 10.58 0.00 0.00 3.16
1122 1191 1.402456 CCTCCAACTACACCGACTTCG 60.402 57.143 0.00 0.00 39.44 3.79
1264 1333 1.520120 CACCGCTCTGCATCGTGAT 60.520 57.895 0.00 0.00 0.00 3.06
1376 1445 2.043248 GGCCTCTCCTACCGGTCA 60.043 66.667 12.40 0.00 0.00 4.02
1668 1743 1.814527 GACGCCTACGGGAATCTGT 59.185 57.895 0.00 0.00 46.04 3.41
1915 2013 1.659098 CGTAGAAAATCGTCAGGCCAC 59.341 52.381 5.01 0.00 0.00 5.01
2283 2412 3.179830 CTCTACAACATCCAGTACGTGC 58.820 50.000 0.00 0.00 0.00 5.34
2745 2877 2.159379 GCCAACATAGCTGCAAAGGTAC 60.159 50.000 1.02 0.00 0.00 3.34
2996 6862 2.723273 TCTCGATCTTGGTAGCACAGA 58.277 47.619 0.00 1.74 0.00 3.41
3003 6869 4.302559 TCTTGGTAGCACAGACTCTCTA 57.697 45.455 0.00 0.00 0.00 2.43
3008 6874 3.510360 GGTAGCACAGACTCTCTAAACCA 59.490 47.826 0.00 0.00 0.00 3.67
3044 6910 2.758207 TTTCTTCCCCACACCGCCA 61.758 57.895 0.00 0.00 0.00 5.69
3099 6965 1.038681 TGTCGGCGGCAAGGATAGTA 61.039 55.000 13.70 0.00 0.00 1.82
3107 6973 1.694693 GGCAAGGATAGTAGGGACCCA 60.695 57.143 14.60 0.00 0.00 4.51
3142 7013 2.039348 TCTCCCTAGGTTTTGTTTCCCG 59.961 50.000 8.29 0.00 0.00 5.14
3145 7016 2.039348 CCCTAGGTTTTGTTTCCCGAGA 59.961 50.000 8.29 0.00 0.00 4.04
3148 7019 3.570912 AGGTTTTGTTTCCCGAGAGAA 57.429 42.857 0.00 0.00 0.00 2.87
3203 7074 2.617840 TAAGGTCCCTTCGGTCTCTT 57.382 50.000 0.89 0.00 37.47 2.85
3207 7078 1.341778 GGTCCCTTCGGTCTCTTCCTA 60.342 57.143 0.00 0.00 0.00 2.94
3222 7093 3.875727 TCTTCCTACCTCTACGATGTTCG 59.124 47.826 0.00 0.00 46.93 3.95
3227 7098 1.955080 ACCTCTACGATGTTCGATCCC 59.045 52.381 3.62 0.00 43.74 3.85
3271 7142 7.121463 GTGAGAGTTTGTGTCTCTAGATCCTAA 59.879 40.741 0.00 0.00 41.58 2.69
3300 7171 7.905604 ATTGACACGTTTCAGATCTTGATAA 57.094 32.000 4.36 0.00 35.27 1.75
3327 7198 1.960689 TGCCCTTTACAAAGAGCAACC 59.039 47.619 8.26 0.00 45.01 3.77
3371 7242 5.833406 TTTCAACATCTTCTGCAACTTGA 57.167 34.783 0.00 0.00 0.00 3.02
3409 7280 3.562176 CCTCTGCCTAAACCTGGACATTT 60.562 47.826 0.00 0.00 0.00 2.32
3415 7287 3.192633 CCTAAACCTGGACATTTTTCGGG 59.807 47.826 0.00 0.00 0.00 5.14
3416 7288 0.966179 AACCTGGACATTTTTCGGGC 59.034 50.000 0.00 0.00 0.00 6.13
3417 7289 0.898326 ACCTGGACATTTTTCGGGCC 60.898 55.000 0.00 0.00 0.00 5.80
3482 7829 0.607620 CCGGCCCAAAACACATGAAT 59.392 50.000 0.00 0.00 0.00 2.57
3484 7831 2.430332 CCGGCCCAAAACACATGAATAT 59.570 45.455 0.00 0.00 0.00 1.28
3585 8072 4.192317 CCATATTAGGGCTTATCTTCGGC 58.808 47.826 0.00 0.00 0.00 5.54
3586 8073 4.080863 CCATATTAGGGCTTATCTTCGGCT 60.081 45.833 0.00 0.00 0.00 5.52
3589 8076 2.333688 AGGGCTTATCTTCGGCTTTC 57.666 50.000 0.00 0.00 0.00 2.62
3590 8077 0.938008 GGGCTTATCTTCGGCTTTCG 59.062 55.000 0.00 0.00 40.90 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.477709 CCGATACACATAGTTTATTTTCGACTC 58.522 37.037 0.00 0.00 0.00 3.36
6 7 7.492352 AGGCCGATACACATAGTTTATTTTC 57.508 36.000 0.00 0.00 0.00 2.29
11 12 4.894705 TGGTAGGCCGATACACATAGTTTA 59.105 41.667 0.00 0.00 37.67 2.01
24 25 1.580059 AAAGAGGATTGGTAGGCCGA 58.420 50.000 0.00 0.00 37.67 5.54
55 57 9.443283 GAAGATTTTTCTCGATAACCATTGATG 57.557 33.333 0.00 0.00 0.00 3.07
68 70 8.383619 CACCTTACACATAGAAGATTTTTCTCG 58.616 37.037 0.00 0.00 0.00 4.04
83 85 8.641541 AGAATTTGAAAATCACACCTTACACAT 58.358 29.630 0.00 0.00 0.00 3.21
85 87 8.871686 AAGAATTTGAAAATCACACCTTACAC 57.128 30.769 0.00 0.00 0.00 2.90
130 132 4.812626 GGATGGTGCCAATTGAATTCAATC 59.187 41.667 29.08 19.05 45.06 2.67
139 141 4.497300 CTTAGTTTGGATGGTGCCAATTG 58.503 43.478 0.00 0.00 46.59 2.32
181 183 0.034477 AAAGGATCGGTTCGCCCAAT 60.034 50.000 0.00 0.00 0.00 3.16
183 185 0.834612 ATAAAGGATCGGTTCGCCCA 59.165 50.000 0.00 0.00 0.00 5.36
221 224 1.685765 CCCATCACCTCCTCCGTGA 60.686 63.158 0.00 0.00 44.00 4.35
222 225 1.050988 ATCCCATCACCTCCTCCGTG 61.051 60.000 0.00 0.00 0.00 4.94
223 226 1.050988 CATCCCATCACCTCCTCCGT 61.051 60.000 0.00 0.00 0.00 4.69
224 227 1.050988 ACATCCCATCACCTCCTCCG 61.051 60.000 0.00 0.00 0.00 4.63
230 233 1.639635 GCCTCCACATCCCATCACCT 61.640 60.000 0.00 0.00 0.00 4.00
232 235 0.034186 TTGCCTCCACATCCCATCAC 60.034 55.000 0.00 0.00 0.00 3.06
233 236 0.703488 TTTGCCTCCACATCCCATCA 59.297 50.000 0.00 0.00 0.00 3.07
235 238 2.323999 TTTTTGCCTCCACATCCCAT 57.676 45.000 0.00 0.00 0.00 4.00
262 265 4.278170 ACGCTTGGTTCATTTTCATCTTCA 59.722 37.500 0.00 0.00 0.00 3.02
268 271 1.269517 GGCACGCTTGGTTCATTTTCA 60.270 47.619 0.00 0.00 0.00 2.69
286 289 3.387225 GAGGAGTTGGTAGGCCGGC 62.387 68.421 21.18 21.18 37.67 6.13
385 388 4.584743 TCAGAGGTGCTCGTATATGTGAAT 59.415 41.667 0.00 0.00 35.36 2.57
394 397 1.279558 AGTCTCTCAGAGGTGCTCGTA 59.720 52.381 0.57 0.00 35.36 3.43
406 456 0.114364 TACACTGGCCCAGTCTCTCA 59.886 55.000 15.03 0.00 43.43 3.27
409 459 1.848652 TACTACACTGGCCCAGTCTC 58.151 55.000 15.03 0.00 43.43 3.36
416 466 8.989980 GTAAAATCTCAATATACTACACTGGCC 58.010 37.037 0.00 0.00 0.00 5.36
433 483 7.619571 GCGTCTGTAGTGACTTTGTAAAATCTC 60.620 40.741 0.00 0.00 35.00 2.75
439 489 3.319972 AGGCGTCTGTAGTGACTTTGTAA 59.680 43.478 0.00 0.00 35.00 2.41
443 493 1.961394 TGAGGCGTCTGTAGTGACTTT 59.039 47.619 8.06 0.00 35.00 2.66
447 497 1.324383 TTGTGAGGCGTCTGTAGTGA 58.676 50.000 8.06 0.00 0.00 3.41
451 501 1.135489 GTCGATTGTGAGGCGTCTGTA 60.135 52.381 8.06 0.00 0.00 2.74
456 506 2.126071 CCGTCGATTGTGAGGCGT 60.126 61.111 0.00 0.00 33.10 5.68
474 524 1.070289 GTTGAGTGGGAGGAGACGTTT 59.930 52.381 0.00 0.00 0.00 3.60
477 527 1.213013 CGTTGAGTGGGAGGAGACG 59.787 63.158 0.00 0.00 0.00 4.18
491 541 1.419922 CTTCCGGCGATGTTCGTTG 59.580 57.895 9.30 0.00 42.81 4.10
497 547 4.473520 CCAGGCTTCCGGCGATGT 62.474 66.667 9.30 0.00 42.94 3.06
524 574 5.779529 ACATTGGTGATTGCATTATCCTC 57.220 39.130 0.00 0.00 0.00 3.71
535 585 8.328758 TCAAGTCCTAGATTTACATTGGTGATT 58.671 33.333 0.00 0.00 0.00 2.57
537 587 7.252612 TCAAGTCCTAGATTTACATTGGTGA 57.747 36.000 0.00 0.00 0.00 4.02
541 591 7.112779 AGGGTTCAAGTCCTAGATTTACATTG 58.887 38.462 0.00 0.00 0.00 2.82
543 593 6.893020 AGGGTTCAAGTCCTAGATTTACAT 57.107 37.500 0.00 0.00 0.00 2.29
555 605 6.407202 TCTTCAGCTTATTAGGGTTCAAGTC 58.593 40.000 0.00 0.00 0.00 3.01
556 606 6.374417 TCTTCAGCTTATTAGGGTTCAAGT 57.626 37.500 0.00 0.00 0.00 3.16
568 618 9.664332 GGACAATGTCATATATCTTCAGCTTAT 57.336 33.333 15.86 0.00 33.68 1.73
570 620 7.743749 AGGACAATGTCATATATCTTCAGCTT 58.256 34.615 15.86 0.00 33.68 3.74
572 622 6.593382 GGAGGACAATGTCATATATCTTCAGC 59.407 42.308 15.86 0.00 33.68 4.26
576 626 8.986991 GGATAGGAGGACAATGTCATATATCTT 58.013 37.037 21.38 10.11 31.65 2.40
577 627 7.286546 CGGATAGGAGGACAATGTCATATATCT 59.713 40.741 21.38 9.06 31.65 1.98
582 632 3.832490 CCGGATAGGAGGACAATGTCATA 59.168 47.826 15.86 2.89 45.00 2.15
583 633 2.634940 CCGGATAGGAGGACAATGTCAT 59.365 50.000 15.86 8.19 45.00 3.06
584 634 2.039418 CCGGATAGGAGGACAATGTCA 58.961 52.381 15.86 0.00 45.00 3.58
585 635 1.270358 GCCGGATAGGAGGACAATGTC 60.270 57.143 5.05 4.51 45.00 3.06
586 636 0.759346 GCCGGATAGGAGGACAATGT 59.241 55.000 5.05 0.00 45.00 2.71
589 639 1.002403 TGGCCGGATAGGAGGACAA 59.998 57.895 5.05 0.00 43.72 3.18
600 650 3.307691 GGAGATGAATATGATTGGCCGGA 60.308 47.826 5.05 0.00 0.00 5.14
603 653 6.059787 AGTAGGAGATGAATATGATTGGCC 57.940 41.667 0.00 0.00 0.00 5.36
604 654 6.373774 CCAAGTAGGAGATGAATATGATTGGC 59.626 42.308 0.00 0.00 41.22 4.52
612 662 5.729229 TCCCAAACCAAGTAGGAGATGAATA 59.271 40.000 0.00 0.00 41.22 1.75
629 679 4.692228 TGCATGAAAGTTTCTTCCCAAAC 58.308 39.130 16.33 0.00 36.64 2.93
645 695 2.621055 GGCCGGTTAATTACATGCATGA 59.379 45.455 32.75 12.33 0.00 3.07
725 775 7.238486 TGGTTAATTACATGCATGGAAGTTT 57.762 32.000 27.96 20.18 33.38 2.66
1101 1167 1.617357 GAAGTCGGTGTAGTTGGAGGT 59.383 52.381 0.00 0.00 0.00 3.85
1122 1191 2.887568 CGTGGAGATGCAGCGGAC 60.888 66.667 0.00 0.00 0.00 4.79
1247 1316 1.520120 CATCACGATGCAGAGCGGT 60.520 57.895 10.49 0.00 34.48 5.68
1376 1445 3.241530 TCGCTGTTGGGGCAGACT 61.242 61.111 0.00 0.00 38.70 3.24
1406 1475 1.153549 GAGCTTGGCGAGGTCGATT 60.154 57.895 17.52 0.00 42.45 3.34
1668 1743 2.282180 GGCCTTCTTGTCCGCCAA 60.282 61.111 0.00 0.00 41.25 4.52
1730 1828 0.168788 ACAGCACGATGCCGAAATTG 59.831 50.000 6.39 1.22 46.52 2.32
1915 2013 0.175989 GAGGTACAGGGCTTCGAAGG 59.824 60.000 25.77 11.96 0.00 3.46
2115 2243 0.034896 TCGTTGGTGAGGGCTTTCTC 59.965 55.000 0.00 0.00 0.00 2.87
2283 2412 1.283793 CTTTGCCGTTCCAGTGCTG 59.716 57.895 0.00 0.00 0.00 4.41
2447 2576 0.107831 TGCCACTTTGGTAGCTCGTT 59.892 50.000 0.00 0.00 40.46 3.85
2745 2877 8.348285 TGAAAACAGAAATCATTAGTTAGGGG 57.652 34.615 0.00 0.00 0.00 4.79
2850 2982 3.431673 TGGCTATTGTCATCACCAACA 57.568 42.857 0.00 0.00 0.00 3.33
2996 6862 1.207329 GACGGCCATGGTTTAGAGAGT 59.793 52.381 14.67 2.18 0.00 3.24
3003 6869 2.740826 CGACGACGGCCATGGTTT 60.741 61.111 14.67 0.00 35.72 3.27
3044 6910 3.069318 GAGAAGGGGGAGCGACGT 61.069 66.667 0.00 0.00 0.00 4.34
3099 6965 1.698874 AAAAGGATGGATGGGTCCCT 58.301 50.000 10.00 0.00 44.41 4.20
3126 6997 4.267349 TCTCTCGGGAAACAAAACCTAG 57.733 45.455 0.00 0.00 0.00 3.02
3142 7013 3.181485 CCACCACCTAGTCGATTTCTCTC 60.181 52.174 0.00 0.00 0.00 3.20
3145 7016 1.207329 GCCACCACCTAGTCGATTTCT 59.793 52.381 0.00 0.00 0.00 2.52
3148 7019 1.515954 CGCCACCACCTAGTCGATT 59.484 57.895 0.00 0.00 0.00 3.34
3271 7142 5.794894 AGATCTGAAACGTGTCAATAGGTT 58.205 37.500 10.22 0.00 0.00 3.50
3300 7171 3.571590 TCTTTGTAAAGGGCACACCAAT 58.428 40.909 4.67 0.00 43.89 3.16
3327 7198 2.179018 CGCTTCAATGGCCAACCG 59.821 61.111 10.96 0.21 39.70 4.44
3565 8052 5.763876 AAGCCGAAGATAAGCCCTAATAT 57.236 39.130 0.00 0.00 0.00 1.28


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

AutoCloner maintained by Alex Coulton.