Multiple sequence alignment - TraesCS5B01G366000

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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 TraesCS5B01G366000 chr5B 100.000 4202 0 0 1 4202 544607877 544612078 0.000000e+00 7760.0
1 TraesCS5B01G366000 chr5B 91.209 273 22 2 1659 1929 663246446 663246174 1.850000e-98 370.0
2 TraesCS5B01G366000 chr5A 91.152 2769 188 30 766 3489 564495581 564498337 0.000000e+00 3703.0
3 TraesCS5B01G366000 chr5A 97.514 724 8 5 3489 4202 663161987 663161264 0.000000e+00 1229.0
4 TraesCS5B01G366000 chr5A 97.376 724 9 4 3489 4202 675470889 675471612 0.000000e+00 1223.0
5 TraesCS5B01G366000 chr5A 90.997 311 25 3 1650 1957 149694669 149694359 2.340000e-112 416.0
6 TraesCS5B01G366000 chr5A 90.415 313 27 3 1648 1957 522676122 522675810 3.910000e-110 409.0
7 TraesCS5B01G366000 chr5D 91.282 1904 118 19 1 1868 446517608 446519499 0.000000e+00 2553.0
8 TraesCS5B01G366000 chr5D 91.778 1350 97 7 2142 3489 446519703 446521040 0.000000e+00 1866.0
9 TraesCS5B01G366000 chr5D 91.429 210 17 1 1897 2105 446519492 446519701 1.910000e-73 287.0
10 TraesCS5B01G366000 chr5D 88.571 70 7 1 72 141 469517131 469517063 2.690000e-12 84.2
11 TraesCS5B01G366000 chr1A 97.652 724 7 5 3489 4202 6929764 6930487 0.000000e+00 1234.0
12 TraesCS5B01G366000 chr1A 88.350 103 12 0 2601 2703 492806193 492806091 1.590000e-24 124.0
13 TraesCS5B01G366000 chrUn 97.514 724 8 4 3489 4202 83555239 83555962 0.000000e+00 1229.0
14 TraesCS5B01G366000 chr6A 97.376 724 9 4 3489 4202 560547706 560546983 0.000000e+00 1223.0
15 TraesCS5B01G366000 chr6A 87.898 314 34 4 1648 1957 391628233 391627920 2.390000e-97 366.0
16 TraesCS5B01G366000 chr4A 97.376 724 9 5 3489 4202 210938919 210939642 0.000000e+00 1223.0
17 TraesCS5B01G366000 chr4A 86.765 68 6 2 72 137 695108472 695108538 5.830000e-09 73.1
18 TraesCS5B01G366000 chr2B 97.376 724 9 5 3489 4202 161427304 161426581 0.000000e+00 1223.0
19 TraesCS5B01G366000 chr2B 97.376 724 9 5 3489 4202 774205819 774205096 0.000000e+00 1223.0
20 TraesCS5B01G366000 chr7B 97.376 724 8 8 3489 4202 484611698 484612420 0.000000e+00 1221.0
21 TraesCS5B01G366000 chr7B 91.753 97 8 0 2598 2694 539218379 539218283 7.330000e-28 135.0
22 TraesCS5B01G366000 chr6B 91.209 273 22 2 1659 1929 49680604 49680332 1.850000e-98 370.0
23 TraesCS5B01G366000 chr6B 90.476 273 24 2 1659 1929 522435340 522435068 3.990000e-95 359.0
24 TraesCS5B01G366000 chr1B 90.842 273 23 2 1659 1929 37921144 37920872 8.590000e-97 364.0
25 TraesCS5B01G366000 chr2A 90.775 271 23 2 1659 1927 761133149 761133419 1.110000e-95 361.0
26 TraesCS5B01G366000 chr7A 91.753 97 8 0 2598 2694 581374345 581374249 7.330000e-28 135.0
27 TraesCS5B01G366000 chr7A 90.909 66 5 1 72 137 725736768 725736704 2.080000e-13 87.9
28 TraesCS5B01G366000 chr3B 88.991 109 12 0 2589 2697 752373323 752373431 7.330000e-28 135.0
29 TraesCS5B01G366000 chr3D 90.099 101 10 0 2598 2698 305448565 305448665 9.480000e-27 132.0
30 TraesCS5B01G366000 chr1D 90.722 97 9 0 2598 2694 392556581 392556677 3.410000e-26 130.0
31 TraesCS5B01G366000 chr6D 88.235 102 12 0 2598 2699 41640809 41640910 5.710000e-24 122.0
32 TraesCS5B01G366000 chr4B 87.255 102 13 0 2598 2699 642195553 642195654 2.650000e-22 117.0


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 TraesCS5B01G366000 chr5B 544607877 544612078 4201 False 7760.000000 7760 100.000000 1 4202 1 chr5B.!!$F1 4201
1 TraesCS5B01G366000 chr5A 564495581 564498337 2756 False 3703.000000 3703 91.152000 766 3489 1 chr5A.!!$F1 2723
2 TraesCS5B01G366000 chr5A 663161264 663161987 723 True 1229.000000 1229 97.514000 3489 4202 1 chr5A.!!$R3 713
3 TraesCS5B01G366000 chr5A 675470889 675471612 723 False 1223.000000 1223 97.376000 3489 4202 1 chr5A.!!$F2 713
4 TraesCS5B01G366000 chr5D 446517608 446521040 3432 False 1568.666667 2553 91.496333 1 3489 3 chr5D.!!$F1 3488
5 TraesCS5B01G366000 chr1A 6929764 6930487 723 False 1234.000000 1234 97.652000 3489 4202 1 chr1A.!!$F1 713
6 TraesCS5B01G366000 chrUn 83555239 83555962 723 False 1229.000000 1229 97.514000 3489 4202 1 chrUn.!!$F1 713
7 TraesCS5B01G366000 chr6A 560546983 560547706 723 True 1223.000000 1223 97.376000 3489 4202 1 chr6A.!!$R2 713
8 TraesCS5B01G366000 chr4A 210938919 210939642 723 False 1223.000000 1223 97.376000 3489 4202 1 chr4A.!!$F1 713
9 TraesCS5B01G366000 chr2B 161426581 161427304 723 True 1223.000000 1223 97.376000 3489 4202 1 chr2B.!!$R1 713
10 TraesCS5B01G366000 chr2B 774205096 774205819 723 True 1223.000000 1223 97.376000 3489 4202 1 chr2B.!!$R2 713
11 TraesCS5B01G366000 chr7B 484611698 484612420 722 False 1221.000000 1221 97.376000 3489 4202 1 chr7B.!!$F1 713

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
948 977 0.182775 AGGGTCCTCGTTGCAAAACT 59.817 50.0 0.00 0.0 0.00 2.66 F
2189 2241 0.257328 TGAGTTGGCCACAAACCTGA 59.743 50.0 3.88 0.0 38.54 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2861 2937 1.197721 GCGTTGCTGCACAAGAGTATT 59.802 47.619 0.0 0.0 39.50 1.89 R
3211 3287 0.110486 ACATCCACACACAAGGGGAC 59.890 55.000 0.0 0.0 31.04 4.46 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
100 117 6.905736 TGAAAACAGGATATAATAGCACCCA 58.094 36.000 0.00 0.00 0.00 4.51
101 118 6.998074 TGAAAACAGGATATAATAGCACCCAG 59.002 38.462 0.00 0.00 0.00 4.45
141 159 4.006989 CCGTTTTCATCCCTACATGAACA 58.993 43.478 0.00 0.00 41.52 3.18
190 208 5.601583 ATGATGATGTTGCAAATGCCTAA 57.398 34.783 0.00 0.00 41.18 2.69
196 214 6.900189 TGATGTTGCAAATGCCTAATTTTTG 58.100 32.000 0.00 0.00 36.28 2.44
198 216 6.057627 TGTTGCAAATGCCTAATTTTTGTG 57.942 33.333 0.00 0.00 36.28 3.33
199 217 5.819379 TGTTGCAAATGCCTAATTTTTGTGA 59.181 32.000 0.00 0.00 36.28 3.58
200 218 6.485984 TGTTGCAAATGCCTAATTTTTGTGAT 59.514 30.769 0.00 0.00 36.28 3.06
201 219 7.658982 TGTTGCAAATGCCTAATTTTTGTGATA 59.341 29.630 0.00 0.00 36.28 2.15
202 220 7.830940 TGCAAATGCCTAATTTTTGTGATAG 57.169 32.000 2.46 0.00 36.28 2.08
353 373 7.488792 TGCTACAATATGATTTTTGTGTCATGC 59.511 33.333 4.35 0.00 36.75 4.06
367 387 7.692460 TTGTGTCATGCTTATCTGATTTTCT 57.308 32.000 0.00 0.00 0.00 2.52
379 399 9.971922 CTTATCTGATTTTCTGACTTTTGGTTT 57.028 29.630 0.00 0.00 0.00 3.27
396 416 3.133542 TGGTTTGACATGTGCATTTTGGA 59.866 39.130 1.15 0.00 0.00 3.53
402 422 3.666274 ACATGTGCATTTTGGATGTTGG 58.334 40.909 0.00 0.00 0.00 3.77
420 440 8.186821 GGATGTTGGAATAAGTCAGAATTTCAG 58.813 37.037 0.00 0.00 0.00 3.02
456 476 3.008923 TCTGCTTGGGACATATTGTGACA 59.991 43.478 0.00 0.00 39.30 3.58
460 480 4.496341 GCTTGGGACATATTGTGACATTCG 60.496 45.833 0.00 0.00 39.30 3.34
470 490 5.695851 ATTGTGACATTCGCTTCTTTCTT 57.304 34.783 0.00 0.00 0.00 2.52
476 496 6.087291 GTGACATTCGCTTCTTTCTTGATTTG 59.913 38.462 0.00 0.00 0.00 2.32
533 553 0.243636 GTGCCCACATAGTTTGGTGC 59.756 55.000 0.00 0.00 33.72 5.01
536 556 1.312371 CCCACATAGTTTGGTGCGGG 61.312 60.000 0.00 0.00 33.72 6.13
552 572 1.270839 GCGGGCTGGCTAATTATCTGA 60.271 52.381 0.00 0.00 0.00 3.27
554 574 3.679389 CGGGCTGGCTAATTATCTGATT 58.321 45.455 0.00 0.00 0.00 2.57
555 575 3.438087 CGGGCTGGCTAATTATCTGATTG 59.562 47.826 0.00 0.00 0.00 2.67
579 599 6.978659 TGACTTCCGATACATGTTAGATGTTC 59.021 38.462 2.30 0.00 33.76 3.18
630 650 1.472728 CCAAGAATCGGGTTACGGGAG 60.473 57.143 0.00 0.00 44.45 4.30
632 652 2.428171 CAAGAATCGGGTTACGGGAGTA 59.572 50.000 0.00 0.00 46.17 2.59
682 702 1.004745 GGGCCTCATGGAGAAACAAGA 59.995 52.381 0.84 0.00 34.57 3.02
693 713 3.057946 GGAGAAACAAGAAGACCATGCAC 60.058 47.826 0.00 0.00 0.00 4.57
694 714 3.554934 AGAAACAAGAAGACCATGCACA 58.445 40.909 0.00 0.00 0.00 4.57
695 715 3.316308 AGAAACAAGAAGACCATGCACAC 59.684 43.478 0.00 0.00 0.00 3.82
696 716 2.645838 ACAAGAAGACCATGCACACT 57.354 45.000 0.00 0.00 0.00 3.55
697 717 2.498167 ACAAGAAGACCATGCACACTC 58.502 47.619 0.00 0.00 0.00 3.51
698 718 2.105477 ACAAGAAGACCATGCACACTCT 59.895 45.455 0.00 0.00 0.00 3.24
705 725 0.926155 CCATGCACACTCTTCGATCG 59.074 55.000 9.36 9.36 0.00 3.69
709 729 0.368227 GCACACTCTTCGATCGCTTG 59.632 55.000 11.09 5.08 0.00 4.01
740 760 5.932303 GGCCTCGTCATAGAGCATAAAAATA 59.068 40.000 0.00 0.00 36.95 1.40
741 761 6.595716 GGCCTCGTCATAGAGCATAAAAATAT 59.404 38.462 0.00 0.00 36.95 1.28
747 767 8.113062 CGTCATAGAGCATAAAAATATAGCAGC 58.887 37.037 0.00 0.00 0.00 5.25
758 778 7.559590 AAAAATATAGCAGCGAGAGTTGAAT 57.440 32.000 0.00 0.00 46.01 2.57
764 784 5.119931 AGCAGCGAGAGTTGAATAGATAG 57.880 43.478 0.00 0.00 46.01 2.08
771 791 7.174253 AGCGAGAGTTGAATAGATAGTTAGAGG 59.826 40.741 0.00 0.00 0.00 3.69
839 860 7.643579 ACAGTCTTAATTCTCTTTTGCAACTC 58.356 34.615 0.00 0.00 0.00 3.01
858 880 3.383505 ACTCCAAAAGCCAAAGTTACCAC 59.616 43.478 0.00 0.00 0.00 4.16
879 901 5.424757 CACGGAGGTTAAATTGGAGTATGA 58.575 41.667 0.00 0.00 0.00 2.15
919 948 7.373617 TGTATGAAGGGATGCAGTAATTAGA 57.626 36.000 0.00 0.00 0.00 2.10
924 953 3.709653 AGGGATGCAGTAATTAGAACGGA 59.290 43.478 0.00 0.00 0.00 4.69
925 954 3.808174 GGGATGCAGTAATTAGAACGGAC 59.192 47.826 0.00 0.00 0.00 4.79
948 977 0.182775 AGGGTCCTCGTTGCAAAACT 59.817 50.000 0.00 0.00 0.00 2.66
1033 1069 0.546122 CCCCGATCTGGTTGAATCCA 59.454 55.000 2.19 0.00 35.15 3.41
1408 1447 3.243737 GGAAATTTTTGGCGGAAGTGTCT 60.244 43.478 0.00 0.00 0.00 3.41
1491 1530 2.305928 TGTGGAAGTGGTGTCCAAATG 58.694 47.619 0.00 0.00 46.66 2.32
1492 1531 2.306847 GTGGAAGTGGTGTCCAAATGT 58.693 47.619 0.00 0.00 46.66 2.71
1505 1544 4.142038 GTCCAAATGTTAGGTGGTTCTGT 58.858 43.478 0.00 0.00 33.88 3.41
1537 1576 1.848652 AGCTGCAGAAATGGATGCTT 58.151 45.000 20.43 0.00 42.98 3.91
1604 1644 6.261118 GCTACGAATGCATTCTTCTGAATTT 58.739 36.000 31.12 10.71 40.61 1.82
1606 1646 7.910162 GCTACGAATGCATTCTTCTGAATTTTA 59.090 33.333 31.12 8.14 40.61 1.52
1613 1653 6.097270 TGCATTCTTCTGAATTTTAGGATGGG 59.903 38.462 0.00 0.00 40.61 4.00
1625 1665 8.551682 AATTTTAGGATGGGATGCAAATCTTA 57.448 30.769 0.00 0.00 0.00 2.10
1639 1679 4.201666 GCAAATCTTACTCTTCTGTCTGCG 60.202 45.833 0.00 0.00 0.00 5.18
1684 1724 7.905604 TGTATTGTGTTGAACTCTAGAATGG 57.094 36.000 0.00 0.00 0.00 3.16
1716 1756 6.169557 TGTATGGAACTTTGTACACAGAGT 57.830 37.500 15.81 7.83 42.26 3.24
1717 1757 5.989168 TGTATGGAACTTTGTACACAGAGTG 59.011 40.000 15.81 0.00 39.96 3.51
1733 1773 3.058432 CAGAGTGTGATTGCTGGTCTTTG 60.058 47.826 0.00 0.00 0.00 2.77
1735 1775 3.290710 AGTGTGATTGCTGGTCTTTGTT 58.709 40.909 0.00 0.00 0.00 2.83
1761 1801 2.485814 GCTAGACAAACTTCCAGCCAAG 59.514 50.000 0.00 0.00 0.00 3.61
1868 1908 6.309737 CAGAGCAATGTTTCCTTTATTTGAGC 59.690 38.462 0.00 0.00 0.00 4.26
1888 1928 4.751060 AGCCTTGTATCAATGCATTGTTG 58.249 39.130 32.67 14.94 38.84 3.33
1900 1940 2.533266 GCATTGTTGCCAGCAATACTC 58.467 47.619 8.52 0.00 43.38 2.59
1901 1941 2.165030 GCATTGTTGCCAGCAATACTCT 59.835 45.455 8.52 0.00 43.38 3.24
1903 1943 4.497006 GCATTGTTGCCAGCAATACTCTAG 60.497 45.833 8.52 0.00 43.38 2.43
1908 1948 4.760530 TGCCAGCAATACTCTAGAATGT 57.239 40.909 0.00 0.00 0.00 2.71
1965 2006 1.529226 TACTTTGGGCATTCACCACG 58.471 50.000 0.00 0.00 37.82 4.94
1982 2023 1.978617 CGCAGCATTTTGTCCCCCT 60.979 57.895 0.00 0.00 0.00 4.79
1990 2039 1.822425 TTTTGTCCCCCTGGTACTGA 58.178 50.000 0.00 0.00 0.00 3.41
2022 2071 4.559862 AGTGGCACCTATTCCATATAGC 57.440 45.455 15.27 0.00 34.47 2.97
2063 2112 5.489792 TCAGATCTTTTACAGGCTTCACT 57.510 39.130 0.00 0.00 0.00 3.41
2118 2167 7.389884 GTGGATCATGCACAAGATACAATCTAT 59.610 37.037 4.06 0.00 36.87 1.98
2189 2241 0.257328 TGAGTTGGCCACAAACCTGA 59.743 50.000 3.88 0.00 38.54 3.86
2207 2259 9.150348 CAAACCTGATTGTTAAACTTGTCTTTT 57.850 29.630 0.00 0.00 0.00 2.27
2232 2284 4.258702 AGACGTTCTTTGCATAGACTGT 57.741 40.909 6.34 8.09 0.00 3.55
2244 2296 6.036577 TGCATAGACTGTTAGATGTGTTGA 57.963 37.500 0.00 0.00 0.00 3.18
2248 2300 5.745312 AGACTGTTAGATGTGTTGATGGA 57.255 39.130 0.00 0.00 0.00 3.41
2315 2367 8.986929 TGTTTCAAAACAAAATATGGGGAAAT 57.013 26.923 5.86 0.00 45.17 2.17
2337 2389 9.823098 GAAATAATGAGCAGCTTGTTATATCAG 57.177 33.333 11.54 0.00 0.00 2.90
2346 2398 7.230108 AGCAGCTTGTTATATCAGTATTGCATT 59.770 33.333 0.00 0.00 0.00 3.56
2347 2399 8.506437 GCAGCTTGTTATATCAGTATTGCATTA 58.494 33.333 0.00 0.00 0.00 1.90
2357 2409 6.915544 TCAGTATTGCATTAGAGCTTTGAG 57.084 37.500 0.00 0.00 34.99 3.02
2416 2469 5.772393 ATCTGGTTTTCCTGGTGTATGTA 57.228 39.130 0.00 0.00 41.38 2.29
2449 2502 5.324409 TGATTTTCCTGCTAGATGTGGTTT 58.676 37.500 0.00 0.00 0.00 3.27
2453 2506 4.574674 TCCTGCTAGATGTGGTTTTGAT 57.425 40.909 0.00 0.00 0.00 2.57
2624 2677 5.659525 TCCCTCCTATTCGACTTAATTGACA 59.340 40.000 0.00 0.00 0.00 3.58
2667 2741 5.984233 TTTTACATTGTATAGAGGCTGCG 57.016 39.130 0.00 0.00 0.00 5.18
2696 2770 7.664552 TTAATTTGGATCGGAGGAAGTACTA 57.335 36.000 0.00 0.00 0.00 1.82
2733 2808 6.927294 TTCTCCTTCTGTTTTTCTTCTGAC 57.073 37.500 0.00 0.00 0.00 3.51
2741 2816 6.620678 TCTGTTTTTCTTCTGACTGGTTTTG 58.379 36.000 0.00 0.00 0.00 2.44
2777 2853 3.503363 TCATTTGGAAGACATGTCAGCAC 59.497 43.478 27.02 14.31 0.00 4.40
2778 2854 2.636647 TTGGAAGACATGTCAGCACA 57.363 45.000 27.02 16.55 36.78 4.57
2788 2864 2.772568 TGTCAGCACAACAATTTCCG 57.227 45.000 0.00 0.00 0.00 4.30
2834 2910 6.805713 ACTGACCCAATTTAGTTTTCTGTTG 58.194 36.000 0.00 0.00 0.00 3.33
2838 2914 8.750298 TGACCCAATTTAGTTTTCTGTTGTTTA 58.250 29.630 0.00 0.00 0.00 2.01
2861 2937 5.576447 TGTAAGAGCTGACGAATGTGATA 57.424 39.130 0.00 0.00 0.00 2.15
2926 3002 0.680618 CATCCCAGCTTTGGTGCAAA 59.319 50.000 0.00 0.00 34.99 3.68
2944 3020 3.938334 GCAAAAACTTTGGCAAGAAGGAA 59.062 39.130 0.00 0.00 37.08 3.36
2969 3045 2.151202 GAAGGATGTGCCGACTTTCAA 58.849 47.619 0.00 0.00 43.43 2.69
2973 3049 1.464997 GATGTGCCGACTTTCAAGGAC 59.535 52.381 0.00 0.00 0.00 3.85
2978 3054 1.335051 GCCGACTTTCAAGGACAAAGC 60.335 52.381 0.00 0.00 34.67 3.51
2980 3056 1.266989 CGACTTTCAAGGACAAAGCCC 59.733 52.381 0.00 0.00 34.67 5.19
2982 3058 2.294512 GACTTTCAAGGACAAAGCCCTG 59.705 50.000 0.00 0.00 34.67 4.45
2983 3059 2.310538 CTTTCAAGGACAAAGCCCTGT 58.689 47.619 0.00 0.00 33.55 4.00
2992 3068 3.386726 GGACAAAGCCCTGTTTTTACCTT 59.613 43.478 0.00 0.00 0.00 3.50
2993 3069 4.141801 GGACAAAGCCCTGTTTTTACCTTT 60.142 41.667 0.00 0.00 0.00 3.11
2994 3070 4.765273 ACAAAGCCCTGTTTTTACCTTTG 58.235 39.130 8.79 8.79 42.72 2.77
3034 3110 2.556459 CCGGTCCTCAGCGATCGAT 61.556 63.158 21.57 10.64 46.86 3.59
3105 3181 8.023021 TCTTATTATCACATACAAGGAGTGCT 57.977 34.615 0.00 0.00 33.44 4.40
3161 3237 2.163509 GAGCGCCTCTATGGATCTACA 58.836 52.381 2.29 0.00 38.35 2.74
3211 3287 3.202906 TCGTCTGTTCTCCTTTTTGGTG 58.797 45.455 0.00 0.00 37.07 4.17
3292 3368 3.118075 TGGGTTCATCTCAAATATCCGCA 60.118 43.478 0.00 0.00 0.00 5.69
3352 3429 3.044235 TGTGATGTCAGCCTGTAACTG 57.956 47.619 0.00 0.00 36.44 3.16
3436 3513 2.638480 TTTACTTGTGAGCTGCAGGT 57.362 45.000 20.31 20.31 0.00 4.00
3475 3552 9.829507 TGGTGTTTTCTTTTGATACAAAATGAT 57.170 25.926 9.52 0.00 0.00 2.45
3658 3735 6.798427 TTCTCTTCTACATGCTATTGGAGT 57.202 37.500 0.00 0.00 0.00 3.85
3906 3993 1.685491 CGGTGTCTCCTAACCCTAGCT 60.685 57.143 0.00 0.00 32.44 3.32
4145 4232 2.508891 GCGTCGCCTTCGTCATCAG 61.509 63.158 5.75 0.00 36.96 2.90
4151 4238 1.089920 GCCTTCGTCATCAGCATGTT 58.910 50.000 0.00 0.00 37.40 2.71
4186 4273 4.508128 CCGCCGCCGAGAAAGCTA 62.508 66.667 0.00 0.00 36.29 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 8.744011 GCATATACTACTAGAAACAAACACGAG 58.256 37.037 0.00 0.00 0.00 4.18
42 43 6.518208 TTGAAACCACGGAAATAAATAGGG 57.482 37.500 0.00 0.00 0.00 3.53
84 101 6.115448 ACAGAACTGGGTGCTATTATATCC 57.885 41.667 6.76 0.00 34.19 2.59
85 102 6.807230 CGTACAGAACTGGGTGCTATTATATC 59.193 42.308 6.76 0.00 34.19 1.63
90 107 2.565834 ACGTACAGAACTGGGTGCTATT 59.434 45.455 6.76 0.00 34.19 1.73
100 117 2.401351 GGAGCGAAAACGTACAGAACT 58.599 47.619 0.00 0.00 0.00 3.01
101 118 1.123756 CGGAGCGAAAACGTACAGAAC 59.876 52.381 0.00 0.00 0.00 3.01
169 187 5.601583 ATTAGGCATTTGCAACATCATCA 57.398 34.783 0.00 0.00 44.36 3.07
209 228 9.708222 GCAACATCTACATATTGTCAAAGTAAG 57.292 33.333 0.00 0.00 0.00 2.34
212 231 7.627088 GCAGCAACATCTACATATTGTCAAAGT 60.627 37.037 0.00 0.00 0.00 2.66
323 342 8.243289 ACACAAAAATCATATTGTAGCAAAGC 57.757 30.769 0.00 0.00 37.66 3.51
353 373 9.971922 AAACCAAAAGTCAGAAAATCAGATAAG 57.028 29.630 0.00 0.00 0.00 1.73
367 387 3.194329 TGCACATGTCAAACCAAAAGTCA 59.806 39.130 0.00 0.00 0.00 3.41
379 399 4.308265 CAACATCCAAAATGCACATGTCA 58.692 39.130 0.00 0.00 0.00 3.58
396 416 8.641498 ACTGAAATTCTGACTTATTCCAACAT 57.359 30.769 6.87 0.00 0.00 2.71
402 422 9.736023 AAACACAACTGAAATTCTGACTTATTC 57.264 29.630 6.87 0.00 0.00 1.75
420 440 6.019075 GTCCCAAGCAGAATTTTAAACACAAC 60.019 38.462 0.00 0.00 0.00 3.32
456 476 4.219288 AGGCAAATCAAGAAAGAAGCGAAT 59.781 37.500 0.00 0.00 0.00 3.34
460 480 3.496155 CGAGGCAAATCAAGAAAGAAGC 58.504 45.455 0.00 0.00 0.00 3.86
470 490 1.305219 CCGCTTTCCGAGGCAAATCA 61.305 55.000 0.00 0.00 40.02 2.57
533 553 2.839486 TCAGATAATTAGCCAGCCCG 57.161 50.000 0.00 0.00 0.00 6.13
536 556 6.072783 GGAAGTCAATCAGATAATTAGCCAGC 60.073 42.308 0.00 0.00 0.00 4.85
541 561 9.914131 TGTATCGGAAGTCAATCAGATAATTAG 57.086 33.333 0.00 0.00 37.93 1.73
552 572 7.500992 ACATCTAACATGTATCGGAAGTCAAT 58.499 34.615 0.00 0.00 0.00 2.57
554 574 6.465439 ACATCTAACATGTATCGGAAGTCA 57.535 37.500 0.00 0.00 0.00 3.41
555 575 6.421202 GGAACATCTAACATGTATCGGAAGTC 59.579 42.308 0.00 0.00 0.00 3.01
600 620 3.711704 ACCCGATTCTTGGTCTCATGTAT 59.288 43.478 0.00 0.00 0.00 2.29
630 650 6.715264 TCTTCTTCCTTCATTTTCAACCCTAC 59.285 38.462 0.00 0.00 0.00 3.18
632 652 5.705400 TCTTCTTCCTTCATTTTCAACCCT 58.295 37.500 0.00 0.00 0.00 4.34
636 656 8.737175 CATCATCTCTTCTTCCTTCATTTTCAA 58.263 33.333 0.00 0.00 0.00 2.69
639 659 6.606395 CCCATCATCTCTTCTTCCTTCATTTT 59.394 38.462 0.00 0.00 0.00 1.82
682 702 1.344438 TCGAAGAGTGTGCATGGTCTT 59.656 47.619 7.01 7.01 31.85 3.01
693 713 0.644331 CAGCAAGCGATCGAAGAGTG 59.356 55.000 21.57 9.24 43.63 3.51
694 714 0.528017 TCAGCAAGCGATCGAAGAGT 59.472 50.000 21.57 0.00 43.63 3.24
695 715 1.198767 CTCAGCAAGCGATCGAAGAG 58.801 55.000 21.57 11.26 43.63 2.85
696 716 0.528017 ACTCAGCAAGCGATCGAAGA 59.472 50.000 21.57 5.44 45.75 2.87
697 717 0.644331 CACTCAGCAAGCGATCGAAG 59.356 55.000 21.57 8.43 0.00 3.79
698 718 0.737367 CCACTCAGCAAGCGATCGAA 60.737 55.000 21.57 0.00 0.00 3.71
705 725 3.123620 CGAGGCCACTCAGCAAGC 61.124 66.667 5.01 0.00 44.17 4.01
709 729 0.249238 CTATGACGAGGCCACTCAGC 60.249 60.000 5.01 0.00 44.17 4.26
740 760 5.720371 ATCTATTCAACTCTCGCTGCTAT 57.280 39.130 0.00 0.00 0.00 2.97
741 761 5.765677 ACTATCTATTCAACTCTCGCTGCTA 59.234 40.000 0.00 0.00 0.00 3.49
747 767 8.610248 TCCTCTAACTATCTATTCAACTCTCG 57.390 38.462 0.00 0.00 0.00 4.04
764 784 9.771534 AATGAGATGCTAAAGTATTCCTCTAAC 57.228 33.333 0.00 0.00 0.00 2.34
771 791 9.937175 GGTTGTAAATGAGATGCTAAAGTATTC 57.063 33.333 0.00 0.00 0.00 1.75
777 797 7.994425 TCAAGGTTGTAAATGAGATGCTAAA 57.006 32.000 0.00 0.00 0.00 1.85
839 860 2.544903 CCGTGGTAACTTTGGCTTTTGG 60.545 50.000 0.00 0.00 37.61 3.28
858 880 6.995511 TTTCATACTCCAATTTAACCTCCG 57.004 37.500 0.00 0.00 0.00 4.63
924 953 2.743718 CAACGAGGACCCTGCTGT 59.256 61.111 0.00 0.00 0.00 4.40
925 954 2.743928 GCAACGAGGACCCTGCTG 60.744 66.667 0.00 0.00 0.00 4.41
948 977 2.776526 AGAGTGTGGGGGTTGGCA 60.777 61.111 0.00 0.00 0.00 4.92
1033 1069 1.134280 CGAGTGCTCCTTGGATTGGAT 60.134 52.381 0.00 0.00 32.56 3.41
1253 1289 2.935481 CAGGGCAGGGGGAGACAA 60.935 66.667 0.00 0.00 0.00 3.18
1440 1479 2.515523 CTGCCAGCGCTGCCTTAT 60.516 61.111 31.96 0.00 35.36 1.73
1491 1530 3.995048 GCAGTAGAACAGAACCACCTAAC 59.005 47.826 0.00 0.00 0.00 2.34
1492 1531 3.644265 TGCAGTAGAACAGAACCACCTAA 59.356 43.478 0.00 0.00 0.00 2.69
1537 1576 1.163420 ATCAAACCACGCGCACTCAA 61.163 50.000 5.73 0.00 0.00 3.02
1604 1644 6.101734 AGAGTAAGATTTGCATCCCATCCTAA 59.898 38.462 0.00 0.00 0.00 2.69
1606 1646 4.414846 AGAGTAAGATTTGCATCCCATCCT 59.585 41.667 0.00 0.00 0.00 3.24
1613 1653 6.456718 GCAGACAGAAGAGTAAGATTTGCATC 60.457 42.308 0.00 0.00 0.00 3.91
1625 1665 1.291588 CTGCCGCAGACAGAAGAGT 59.708 57.895 15.74 0.00 37.32 3.24
1639 1679 1.210155 CTAAACAAGCACGGCTGCC 59.790 57.895 9.11 9.11 45.53 4.85
1684 1724 5.723295 ACAAAGTTCCATACATTTGCATCC 58.277 37.500 0.00 0.00 36.36 3.51
1716 1756 2.223782 GCAACAAAGACCAGCAATCACA 60.224 45.455 0.00 0.00 0.00 3.58
1717 1757 2.035066 AGCAACAAAGACCAGCAATCAC 59.965 45.455 0.00 0.00 0.00 3.06
1733 1773 3.315191 TGGAAGTTTGTCTAGCAAGCAAC 59.685 43.478 13.24 5.03 40.21 4.17
1735 1775 3.141398 CTGGAAGTTTGTCTAGCAAGCA 58.859 45.455 13.24 0.00 40.21 3.91
1761 1801 8.995220 TGTTTTATACAAGTAACATGGACAGTC 58.005 33.333 0.00 0.00 32.64 3.51
1888 1928 4.446371 ACACATTCTAGAGTATTGCTGGC 58.554 43.478 0.00 0.00 0.00 4.85
1965 2006 1.593265 CAGGGGGACAAAATGCTGC 59.407 57.895 0.00 0.00 0.00 5.25
1982 2023 4.645136 CCACTAGTAGCAGAATCAGTACCA 59.355 45.833 0.00 0.00 0.00 3.25
1990 2039 2.472029 AGGTGCCACTAGTAGCAGAAT 58.528 47.619 16.61 2.80 40.28 2.40
2022 2071 8.530311 AGATCTGATTCTATTATGCAGGTACAG 58.470 37.037 0.00 0.00 0.00 2.74
2063 2112 3.610637 GCAAAAAGCAGATGCCCAA 57.389 47.368 0.14 0.00 44.79 4.12
2138 2190 9.829507 GGAGCATTAGCAATATCTCATAACTAT 57.170 33.333 0.00 0.00 45.49 2.12
2152 2204 4.081406 ACTCAAACATGGAGCATTAGCAA 58.919 39.130 0.00 0.00 45.49 3.91
2207 2259 5.177511 CAGTCTATGCAAAGAACGTCTTGAA 59.822 40.000 8.66 0.00 36.71 2.69
2212 2264 4.992381 AACAGTCTATGCAAAGAACGTC 57.008 40.909 0.00 0.00 0.00 4.34
2232 2284 4.256110 CAGCTGTCCATCAACACATCTAA 58.744 43.478 5.25 0.00 0.00 2.10
2244 2296 2.992576 ATGGCAGGCAGCTGTCCAT 61.993 57.895 23.46 21.22 44.79 3.41
2248 2300 2.547640 CTACCATGGCAGGCAGCTGT 62.548 60.000 16.64 2.02 44.79 4.40
2301 2353 6.556116 AGCTGCTCATTATTTCCCCATATTTT 59.444 34.615 0.00 0.00 0.00 1.82
2306 2358 3.607490 AGCTGCTCATTATTTCCCCAT 57.393 42.857 0.00 0.00 0.00 4.00
2316 2368 8.781196 CAATACTGATATAACAAGCTGCTCATT 58.219 33.333 1.00 2.96 0.00 2.57
2319 2371 6.203530 TGCAATACTGATATAACAAGCTGCTC 59.796 38.462 1.00 0.00 0.00 4.26
2337 2389 7.553881 TTACCTCAAAGCTCTAATGCAATAC 57.446 36.000 0.00 0.00 34.99 1.89
2384 2437 6.152831 ACCAGGAAAACCAGATATTTAGTTGC 59.847 38.462 0.00 0.00 0.00 4.17
2424 2477 3.881688 CCACATCTAGCAGGAAAATCAGG 59.118 47.826 0.00 0.00 0.00 3.86
2493 2546 9.515020 TTGTCAGTTAATTTTGTTCTGAACATC 57.485 29.630 22.60 8.57 41.79 3.06
2610 2663 3.258372 AGAGGCTGTGTCAATTAAGTCGA 59.742 43.478 0.00 0.00 0.00 4.20
2614 2667 8.554528 CATTGTATAGAGGCTGTGTCAATTAAG 58.445 37.037 0.00 0.00 0.00 1.85
2624 2677 9.765795 GTAAAATAGACATTGTATAGAGGCTGT 57.234 33.333 0.00 0.00 0.00 4.40
2667 2741 6.318900 ACTTCCTCCGATCCAAATTAATTGAC 59.681 38.462 0.39 0.00 41.85 3.18
2707 2781 8.244113 GTCAGAAGAAAAACAGAAGGAGAAAAA 58.756 33.333 0.00 0.00 0.00 1.94
2733 2808 5.649395 TGAAGATTGAGATAGGCAAAACCAG 59.351 40.000 0.00 0.00 43.14 4.00
2741 2816 6.949352 TTCCAAATGAAGATTGAGATAGGC 57.051 37.500 0.00 0.00 0.00 3.93
2773 2849 2.159382 CCCTACGGAAATTGTTGTGCT 58.841 47.619 0.00 0.00 0.00 4.40
2774 2850 1.402325 GCCCTACGGAAATTGTTGTGC 60.402 52.381 0.00 0.00 0.00 4.57
2777 2853 2.943033 CCTAGCCCTACGGAAATTGTTG 59.057 50.000 0.00 0.00 0.00 3.33
2778 2854 2.574824 ACCTAGCCCTACGGAAATTGTT 59.425 45.455 0.00 0.00 0.00 2.83
2788 2864 8.057623 TCAGTATATACCATAACCTAGCCCTAC 58.942 40.741 9.32 0.00 0.00 3.18
2793 2869 6.666546 TGGGTCAGTATATACCATAACCTAGC 59.333 42.308 9.32 1.84 37.51 3.42
2834 2910 6.310467 TCACATTCGTCAGCTCTTACATAAAC 59.690 38.462 0.00 0.00 0.00 2.01
2838 2914 4.456280 TCACATTCGTCAGCTCTTACAT 57.544 40.909 0.00 0.00 0.00 2.29
2845 2921 6.398234 AGAGTATTATCACATTCGTCAGCT 57.602 37.500 0.00 0.00 0.00 4.24
2861 2937 1.197721 GCGTTGCTGCACAAGAGTATT 59.802 47.619 0.00 0.00 39.50 1.89
2926 3002 5.833131 TCAGTATTCCTTCTTGCCAAAGTTT 59.167 36.000 0.00 0.00 34.78 2.66
2944 3020 2.111384 AGTCGGCACATCCTTCAGTAT 58.889 47.619 0.00 0.00 0.00 2.12
2969 3045 2.963101 GGTAAAAACAGGGCTTTGTCCT 59.037 45.455 0.00 0.00 38.72 3.85
2973 3049 4.765273 ACAAAGGTAAAAACAGGGCTTTG 58.235 39.130 0.00 0.00 36.83 2.77
2978 3054 3.868661 GCACAACAAAGGTAAAAACAGGG 59.131 43.478 0.00 0.00 0.00 4.45
2980 3056 4.754322 AGGCACAACAAAGGTAAAAACAG 58.246 39.130 0.00 0.00 0.00 3.16
2982 3058 5.416083 AGAAGGCACAACAAAGGTAAAAAC 58.584 37.500 0.00 0.00 0.00 2.43
2983 3059 5.669164 AGAAGGCACAACAAAGGTAAAAA 57.331 34.783 0.00 0.00 0.00 1.94
2992 3068 4.734398 ATGACAAAAGAAGGCACAACAA 57.266 36.364 0.00 0.00 0.00 2.83
2993 3069 5.451242 GGTTATGACAAAAGAAGGCACAACA 60.451 40.000 0.00 0.00 0.00 3.33
2994 3070 4.982295 GGTTATGACAAAAGAAGGCACAAC 59.018 41.667 0.00 0.00 0.00 3.32
3034 3110 1.203994 GGTAGCGTACTTCTTCCAGCA 59.796 52.381 0.00 0.00 0.00 4.41
3179 3255 4.142138 GGAGAACAGACGATGTCCATAACT 60.142 45.833 0.00 0.00 43.00 2.24
3185 3261 3.320673 AAAGGAGAACAGACGATGTCC 57.679 47.619 0.00 0.00 43.00 4.02
3211 3287 0.110486 ACATCCACACACAAGGGGAC 59.890 55.000 0.00 0.00 31.04 4.46
3292 3368 0.546122 TCTTCCACACAACACAGCCT 59.454 50.000 0.00 0.00 0.00 4.58
3295 3371 4.898829 TTTCATCTTCCACACAACACAG 57.101 40.909 0.00 0.00 0.00 3.66
3302 3378 5.123979 GGAGGTACATTTTCATCTTCCACAC 59.876 44.000 0.00 0.00 0.00 3.82
3304 3380 5.355350 CAGGAGGTACATTTTCATCTTCCAC 59.645 44.000 0.00 0.00 0.00 4.02
3352 3429 2.442236 TTCAAAGGATGGCAGGGATC 57.558 50.000 0.00 0.00 0.00 3.36
3384 3461 4.630940 CAGAAGGCAGAACAAAAAGCAAAA 59.369 37.500 0.00 0.00 0.00 2.44
3385 3462 4.183101 CAGAAGGCAGAACAAAAAGCAAA 58.817 39.130 0.00 0.00 0.00 3.68
3386 3463 3.195396 ACAGAAGGCAGAACAAAAAGCAA 59.805 39.130 0.00 0.00 0.00 3.91
3398 3475 3.655276 AAAGCAAATGACAGAAGGCAG 57.345 42.857 0.00 0.00 0.00 4.85
3436 3513 1.978455 AACACCAACCAGGCACGAGA 61.978 55.000 0.00 0.00 43.14 4.04
3475 3552 0.531753 TCAGCAACAGTAAGTGCGCA 60.532 50.000 5.66 5.66 33.17 6.09
3658 3735 2.569404 GAGGGCCTCTTCTCTTCTCAAA 59.431 50.000 26.44 0.00 0.00 2.69
3906 3993 1.276138 AGATGTGATCTGTTCGTGGCA 59.724 47.619 0.00 0.00 38.44 4.92
4145 4232 4.147322 CGGCGTCGGTGAACATGC 62.147 66.667 0.00 0.00 0.00 4.06


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

AutoCloner maintained by Alex Coulton.