Multiple sequence alignment - TraesCS1D01G388400

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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 TraesCS1D01G388400 chr1D 100.000 3039 0 0 1 3039 460656453 460659491 0.000000e+00 5613
1 TraesCS1D01G388400 chr1D 88.571 770 79 7 2273 3037 305746922 305747687 0.000000e+00 926
2 TraesCS1D01G388400 chr1D 91.329 173 14 1 491 662 338937373 338937201 5.070000e-58 235
3 TraesCS1D01G388400 chr1A 96.281 726 27 0 650 1375 551822933 551823658 0.000000e+00 1192
4 TraesCS1D01G388400 chr1A 94.792 384 11 6 27 406 551822355 551822733 9.380000e-165 590
5 TraesCS1D01G388400 chr1A 96.629 89 3 0 404 492 551822846 551822934 6.790000e-32 148
6 TraesCS1D01G388400 chrUn 87.658 948 54 22 1357 2273 8073296 8074211 0.000000e+00 1044
7 TraesCS1D01G388400 chrUn 91.405 477 35 5 709 1183 8051621 8052093 0.000000e+00 649
8 TraesCS1D01G388400 chrUn 90.879 307 20 5 1 301 8044873 8045177 3.650000e-109 405
9 TraesCS1D01G388400 chrUn 90.879 307 20 5 1 301 8045954 8046258 3.650000e-109 405
10 TraesCS1D01G388400 chrUn 90.228 307 22 5 1 301 8044315 8044619 7.900000e-106 394
11 TraesCS1D01G388400 chrUn 90.228 307 22 5 1 301 8045431 8045735 7.900000e-106 394
12 TraesCS1D01G388400 chrUn 90.503 179 13 4 488 663 141680911 141680734 1.820000e-57 233
13 TraesCS1D01G388400 chrUn 97.959 98 2 0 395 492 8051484 8051581 1.450000e-38 171
14 TraesCS1D01G388400 chr6D 90.298 773 66 4 2273 3039 452198267 452197498 0.000000e+00 1003
15 TraesCS1D01G388400 chr6D 89.243 753 78 2 2288 3037 37315535 37316287 0.000000e+00 939
16 TraesCS1D01G388400 chr2D 89.870 770 68 5 2274 3037 131482903 131483668 0.000000e+00 981
17 TraesCS1D01G388400 chr2D 89.351 770 70 9 2274 3039 341152530 341151769 0.000000e+00 957
18 TraesCS1D01G388400 chr2D 88.787 767 76 6 2274 3037 590123329 590122570 0.000000e+00 931
19 TraesCS1D01G388400 chr2D 93.252 163 10 1 491 652 362930808 362930970 3.920000e-59 239
20 TraesCS1D01G388400 chr4D 89.453 768 77 3 2273 3037 405378886 405379652 0.000000e+00 966
21 TraesCS1D01G388400 chr3D 89.323 768 70 9 2274 3037 491086915 491087674 0.000000e+00 953
22 TraesCS1D01G388400 chr7D 89.032 775 73 9 2269 3037 440081720 440082488 0.000000e+00 950
23 TraesCS1D01G388400 chr7D 88.516 775 82 5 2269 3039 128768034 128768805 0.000000e+00 931
24 TraesCS1D01G388400 chr4A 91.667 180 13 2 483 661 517406463 517406641 6.510000e-62 248
25 TraesCS1D01G388400 chr5B 93.252 163 10 1 491 652 82456817 82456979 3.920000e-59 239
26 TraesCS1D01G388400 chr7B 92.727 165 11 1 488 651 650608928 650609092 1.410000e-58 237
27 TraesCS1D01G388400 chr7B 91.329 173 12 3 488 659 11441307 11441137 1.820000e-57 233
28 TraesCS1D01G388400 chr2B 90.395 177 15 2 476 651 66994819 66994644 6.550000e-57 231
29 TraesCS1D01G388400 chr4B 91.176 170 14 1 488 656 344463295 344463464 2.360000e-56 230


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 TraesCS1D01G388400 chr1D 460656453 460659491 3038 False 5613.000000 5613 100.000000 1 3039 1 chr1D.!!$F2 3038
1 TraesCS1D01G388400 chr1D 305746922 305747687 765 False 926.000000 926 88.571000 2273 3037 1 chr1D.!!$F1 764
2 TraesCS1D01G388400 chr1A 551822355 551823658 1303 False 643.333333 1192 95.900667 27 1375 3 chr1A.!!$F1 1348
3 TraesCS1D01G388400 chrUn 8073296 8074211 915 False 1044.000000 1044 87.658000 1357 2273 1 chrUn.!!$F1 916
4 TraesCS1D01G388400 chrUn 8051484 8052093 609 False 410.000000 649 94.682000 395 1183 2 chrUn.!!$F3 788
5 TraesCS1D01G388400 chrUn 8044315 8046258 1943 False 399.500000 405 90.553500 1 301 4 chrUn.!!$F2 300
6 TraesCS1D01G388400 chr6D 452197498 452198267 769 True 1003.000000 1003 90.298000 2273 3039 1 chr6D.!!$R1 766
7 TraesCS1D01G388400 chr6D 37315535 37316287 752 False 939.000000 939 89.243000 2288 3037 1 chr6D.!!$F1 749
8 TraesCS1D01G388400 chr2D 131482903 131483668 765 False 981.000000 981 89.870000 2274 3037 1 chr2D.!!$F1 763
9 TraesCS1D01G388400 chr2D 341151769 341152530 761 True 957.000000 957 89.351000 2274 3039 1 chr2D.!!$R1 765
10 TraesCS1D01G388400 chr2D 590122570 590123329 759 True 931.000000 931 88.787000 2274 3037 1 chr2D.!!$R2 763
11 TraesCS1D01G388400 chr4D 405378886 405379652 766 False 966.000000 966 89.453000 2273 3037 1 chr4D.!!$F1 764
12 TraesCS1D01G388400 chr3D 491086915 491087674 759 False 953.000000 953 89.323000 2274 3037 1 chr3D.!!$F1 763
13 TraesCS1D01G388400 chr7D 440081720 440082488 768 False 950.000000 950 89.032000 2269 3037 1 chr7D.!!$F2 768
14 TraesCS1D01G388400 chr7D 128768034 128768805 771 False 931.000000 931 88.516000 2269 3039 1 chr7D.!!$F1 770

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
339 1461 0.972883 CCTCCCTCTACTATGCCAGC 59.027 60.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2289 3580 0.045008 TGCCTATGACCCTACCCCAA 59.955 55.0 0.0 0.0 0.0 4.12 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
45 50 2.052690 GTCGCTAGACAGCCCAGGA 61.053 63.158 0.00 0.00 45.64 3.86
81 644 4.821589 GCGAGTCCCCAGCGAAGG 62.822 72.222 0.00 0.00 0.00 3.46
339 1461 0.972883 CCTCCCTCTACTATGCCAGC 59.027 60.000 0.00 0.00 0.00 4.85
490 1728 7.229306 CCACTTTATCACATGGCACTGTTATAT 59.771 37.037 0.00 0.00 0.00 0.86
491 1729 9.271828 CACTTTATCACATGGCACTGTTATATA 57.728 33.333 0.00 0.00 0.00 0.86
492 1730 9.273016 ACTTTATCACATGGCACTGTTATATAC 57.727 33.333 0.00 0.00 0.00 1.47
493 1731 9.494271 CTTTATCACATGGCACTGTTATATACT 57.506 33.333 0.00 0.00 0.00 2.12
495 1733 5.853936 TCACATGGCACTGTTATATACTCC 58.146 41.667 0.00 0.00 0.00 3.85
496 1734 4.997395 CACATGGCACTGTTATATACTCCC 59.003 45.833 0.00 0.00 0.00 4.30
497 1735 4.907875 ACATGGCACTGTTATATACTCCCT 59.092 41.667 0.00 0.00 0.00 4.20
499 1737 3.901844 TGGCACTGTTATATACTCCCTCC 59.098 47.826 0.00 0.00 0.00 4.30
500 1738 3.056749 GGCACTGTTATATACTCCCTCCG 60.057 52.174 0.00 0.00 0.00 4.63
501 1739 3.573110 GCACTGTTATATACTCCCTCCGT 59.427 47.826 0.00 0.00 0.00 4.69
503 1741 5.770417 CACTGTTATATACTCCCTCCGTTC 58.230 45.833 0.00 0.00 0.00 3.95
505 1743 5.070823 TGTTATATACTCCCTCCGTTCCT 57.929 43.478 0.00 0.00 0.00 3.36
506 1744 6.183361 ACTGTTATATACTCCCTCCGTTCCTA 60.183 42.308 0.00 0.00 0.00 2.94
507 1745 6.613699 TGTTATATACTCCCTCCGTTCCTAA 58.386 40.000 0.00 0.00 0.00 2.69
508 1746 7.068702 TGTTATATACTCCCTCCGTTCCTAAA 58.931 38.462 0.00 0.00 0.00 1.85
509 1747 7.731688 TGTTATATACTCCCTCCGTTCCTAAAT 59.268 37.037 0.00 0.00 0.00 1.40
510 1748 9.247861 GTTATATACTCCCTCCGTTCCTAAATA 57.752 37.037 0.00 0.00 0.00 1.40
514 1752 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
516 1754 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
521 1759 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
536 1774 6.824305 AGTCTTTTTAGACATTCCACCATG 57.176 37.500 7.92 0.00 41.02 3.66
537 1775 5.711976 AGTCTTTTTAGACATTCCACCATGG 59.288 40.000 11.19 11.19 41.02 3.66
538 1776 5.710099 GTCTTTTTAGACATTCCACCATGGA 59.290 40.000 21.47 0.00 40.55 3.41
539 1777 6.349363 GTCTTTTTAGACATTCCACCATGGAC 60.349 42.308 21.47 0.00 41.28 4.02
540 1778 8.444146 GTCTTTTTAGACATTCCACCATGGACT 61.444 40.741 21.47 0.00 41.28 3.85
548 1786 3.021177 TCCACCATGGACTACATACGA 57.979 47.619 21.47 0.00 42.67 3.43
549 1787 3.367321 TCCACCATGGACTACATACGAA 58.633 45.455 21.47 0.00 42.67 3.85
550 1788 3.383505 TCCACCATGGACTACATACGAAG 59.616 47.826 21.47 0.00 42.67 3.79
551 1789 3.123804 CACCATGGACTACATACGAAGC 58.876 50.000 21.47 0.00 37.84 3.86
552 1790 2.764010 ACCATGGACTACATACGAAGCA 59.236 45.455 21.47 0.00 37.84 3.91
553 1791 3.196901 ACCATGGACTACATACGAAGCAA 59.803 43.478 21.47 0.00 37.84 3.91
554 1792 4.188462 CCATGGACTACATACGAAGCAAA 58.812 43.478 5.56 0.00 37.84 3.68
555 1793 4.634004 CCATGGACTACATACGAAGCAAAA 59.366 41.667 5.56 0.00 37.84 2.44
556 1794 5.296780 CCATGGACTACATACGAAGCAAAAT 59.703 40.000 5.56 0.00 37.84 1.82
557 1795 6.481976 CCATGGACTACATACGAAGCAAAATA 59.518 38.462 5.56 0.00 37.84 1.40
558 1796 7.011950 CCATGGACTACATACGAAGCAAAATAA 59.988 37.037 5.56 0.00 37.84 1.40
559 1797 7.534085 TGGACTACATACGAAGCAAAATAAG 57.466 36.000 0.00 0.00 0.00 1.73
560 1798 7.101054 TGGACTACATACGAAGCAAAATAAGT 58.899 34.615 0.00 0.00 0.00 2.24
561 1799 7.064134 TGGACTACATACGAAGCAAAATAAGTG 59.936 37.037 0.00 0.00 0.00 3.16
562 1800 7.277098 GGACTACATACGAAGCAAAATAAGTGA 59.723 37.037 0.00 0.00 0.00 3.41
563 1801 8.542497 ACTACATACGAAGCAAAATAAGTGAA 57.458 30.769 0.00 0.00 0.00 3.18
564 1802 9.162764 ACTACATACGAAGCAAAATAAGTGAAT 57.837 29.630 0.00 0.00 0.00 2.57
565 1803 9.638300 CTACATACGAAGCAAAATAAGTGAATC 57.362 33.333 0.00 0.00 0.00 2.52
566 1804 8.268850 ACATACGAAGCAAAATAAGTGAATCT 57.731 30.769 0.00 0.00 0.00 2.40
567 1805 9.378551 ACATACGAAGCAAAATAAGTGAATCTA 57.621 29.630 0.00 0.00 0.00 1.98
568 1806 9.638300 CATACGAAGCAAAATAAGTGAATCTAC 57.362 33.333 0.00 0.00 0.00 2.59
569 1807 7.667043 ACGAAGCAAAATAAGTGAATCTACA 57.333 32.000 0.00 0.00 0.00 2.74
570 1808 7.519002 ACGAAGCAAAATAAGTGAATCTACAC 58.481 34.615 0.00 0.00 40.60 2.90
602 1840 8.783833 AATGTCTATATACATCCGTACGTAGT 57.216 34.615 15.21 11.60 41.42 2.73
603 1841 8.783833 ATGTCTATATACATCCGTACGTAGTT 57.216 34.615 15.21 0.00 37.47 2.24
604 1842 8.607441 TGTCTATATACATCCGTACGTAGTTT 57.393 34.615 15.21 7.24 37.78 2.66
605 1843 8.712363 TGTCTATATACATCCGTACGTAGTTTC 58.288 37.037 15.21 3.67 37.78 2.78
606 1844 8.930760 GTCTATATACATCCGTACGTAGTTTCT 58.069 37.037 15.21 1.06 37.78 2.52
609 1847 8.839310 ATATACATCCGTACGTAGTTTCTAGT 57.161 34.615 15.21 2.39 37.78 2.57
610 1848 5.227238 ACATCCGTACGTAGTTTCTAGTG 57.773 43.478 15.21 0.00 37.78 2.74
611 1849 4.937620 ACATCCGTACGTAGTTTCTAGTGA 59.062 41.667 15.21 0.00 37.78 3.41
612 1850 5.412594 ACATCCGTACGTAGTTTCTAGTGAA 59.587 40.000 15.21 0.00 37.78 3.18
613 1851 5.940192 TCCGTACGTAGTTTCTAGTGAAA 57.060 39.130 15.21 0.00 37.78 2.69
614 1852 6.500684 TCCGTACGTAGTTTCTAGTGAAAT 57.499 37.500 15.21 0.00 37.78 2.17
615 1853 6.546395 TCCGTACGTAGTTTCTAGTGAAATC 58.454 40.000 15.21 0.00 37.78 2.17
616 1854 6.372659 TCCGTACGTAGTTTCTAGTGAAATCT 59.627 38.462 15.21 0.00 37.78 2.40
617 1855 7.025963 CCGTACGTAGTTTCTAGTGAAATCTT 58.974 38.462 15.21 0.00 37.78 2.40
618 1856 7.540055 CCGTACGTAGTTTCTAGTGAAATCTTT 59.460 37.037 15.21 0.00 37.78 2.52
619 1857 9.546909 CGTACGTAGTTTCTAGTGAAATCTTTA 57.453 33.333 7.22 0.00 37.78 1.85
645 1883 8.959705 AAAAGACTAATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
646 1884 7.909485 AAGACTAATATTTAGGAACGGAGGA 57.091 36.000 0.00 0.00 0.00 3.71
647 1885 7.909485 AGACTAATATTTAGGAACGGAGGAA 57.091 36.000 0.00 0.00 0.00 3.36
648 1886 7.953752 AGACTAATATTTAGGAACGGAGGAAG 58.046 38.462 0.00 0.00 0.00 3.46
856 2116 5.278660 GCTTCCTATATTTGGGCATCAGTTG 60.279 44.000 0.00 0.00 0.00 3.16
911 2171 6.402550 CCATAGAACAGACAACATAACTGTGC 60.403 42.308 0.00 0.00 42.81 4.57
954 2214 4.286297 TGAACCATTCTCGAGTTCCATT 57.714 40.909 13.13 3.10 39.30 3.16
1096 2356 7.396907 ACATCATGAACAATCCCTCAAAATACA 59.603 33.333 0.00 0.00 0.00 2.29
1124 2384 6.403636 CCTCTGGAGTTTGTGCACAAATATAC 60.404 42.308 39.08 31.32 46.12 1.47
1191 2451 9.851686 AAAATCCAAAAGAAGCCTTATTTTCTT 57.148 25.926 6.82 0.07 43.49 2.52
1239 2499 1.216710 CTCCACACGGCTCCTCTTC 59.783 63.158 0.00 0.00 0.00 2.87
1253 2513 2.886523 TCCTCTTCTTTGTGTTGCCATG 59.113 45.455 0.00 0.00 0.00 3.66
1265 2525 5.366460 TGTGTTGCCATGTCATTGAAATTT 58.634 33.333 0.00 0.00 0.00 1.82
1278 2538 8.092068 TGTCATTGAAATTTTCATCATCTTGCT 58.908 29.630 12.39 0.00 39.84 3.91
1287 2547 1.546923 CATCATCTTGCTTGTTGCCCA 59.453 47.619 0.00 0.00 42.00 5.36
1375 2635 1.693103 CCACCTCCCTAACCCTCCC 60.693 68.421 0.00 0.00 0.00 4.30
1389 2649 4.628661 ACCCTCCCACTAGAACTAGAAT 57.371 45.455 14.64 0.00 36.97 2.40
1396 2656 7.070571 CCTCCCACTAGAACTAGAATGAGAAAT 59.929 40.741 14.64 0.00 36.97 2.17
1444 2704 8.031864 AGTTCATAGCCATCTTATATGACTTCG 58.968 37.037 0.00 0.00 36.05 3.79
1452 2712 7.044181 CCATCTTATATGACTTCGCACCATAT 58.956 38.462 0.00 0.00 37.31 1.78
1530 2802 9.590451 GATTTCCATCATTTGCTTAATCTTCAA 57.410 29.630 0.00 0.00 0.00 2.69
1576 2850 6.070824 TGGATAATGCGATATATGTGTGTCCT 60.071 38.462 0.00 0.00 0.00 3.85
1582 2856 8.621532 ATGCGATATATGTGTGTCCTTTTATT 57.378 30.769 0.00 0.00 0.00 1.40
1617 2891 6.655003 TGTTTCTTGAAAGATATGTGTCTCCC 59.345 38.462 0.00 0.00 34.49 4.30
1618 2892 6.627087 TTCTTGAAAGATATGTGTCTCCCT 57.373 37.500 0.00 0.00 34.49 4.20
1619 2893 6.627087 TCTTGAAAGATATGTGTCTCCCTT 57.373 37.500 0.00 0.00 0.00 3.95
1620 2894 7.020827 TCTTGAAAGATATGTGTCTCCCTTT 57.979 36.000 0.00 0.00 0.00 3.11
1621 2895 7.461749 TCTTGAAAGATATGTGTCTCCCTTTT 58.538 34.615 0.00 0.00 0.00 2.27
1623 2897 6.180472 TGAAAGATATGTGTCTCCCTTTTCC 58.820 40.000 0.00 0.00 0.00 3.13
1624 2898 6.012508 TGAAAGATATGTGTCTCCCTTTTCCT 60.013 38.462 0.00 0.00 0.00 3.36
1625 2899 6.394345 AAGATATGTGTCTCCCTTTTCCTT 57.606 37.500 0.00 0.00 0.00 3.36
1626 2900 6.394345 AGATATGTGTCTCCCTTTTCCTTT 57.606 37.500 0.00 0.00 0.00 3.11
1627 2901 6.418946 AGATATGTGTCTCCCTTTTCCTTTC 58.581 40.000 0.00 0.00 0.00 2.62
1628 2902 2.846193 TGTGTCTCCCTTTTCCTTTCG 58.154 47.619 0.00 0.00 0.00 3.46
1629 2903 2.152016 GTGTCTCCCTTTTCCTTTCGG 58.848 52.381 0.00 0.00 0.00 4.30
1630 2904 2.051692 TGTCTCCCTTTTCCTTTCGGA 58.948 47.619 0.00 0.00 37.60 4.55
1653 2927 3.393089 AACATGTGTCTCTCCACTCAC 57.607 47.619 0.00 0.00 36.30 3.51
1674 2949 8.709308 ACTCACTAAAAAGTCCATAGCATAGAT 58.291 33.333 0.00 0.00 0.00 1.98
1768 3043 4.139786 ACAGAGTTACTCGTGGTTGACTA 58.860 43.478 6.73 0.00 35.36 2.59
1795 3070 7.581213 TGTCACACCAAAATTCACTTTATCT 57.419 32.000 0.00 0.00 0.00 1.98
1816 3091 5.547465 TCTTTTTATGCAGAGAACCGAGAA 58.453 37.500 0.00 0.00 0.00 2.87
1864 3139 3.126001 TGTGTAGAGAAACAAGGGCTG 57.874 47.619 0.00 0.00 0.00 4.85
1930 3205 6.366061 GCAAGGATTTTAAAGGACAATGTGTC 59.634 38.462 0.00 0.00 46.23 3.67
1941 3216 3.198068 GACAATGTGTCATAGGCGTGAT 58.802 45.455 3.52 0.00 46.22 3.06
1947 3222 2.535984 GTGTCATAGGCGTGATCGAAAG 59.464 50.000 0.00 0.00 39.71 2.62
1959 3234 4.435554 CGTGATCGAAAGCAATTGCATAAG 59.564 41.667 30.89 18.87 40.77 1.73
2051 3326 8.388103 CCAATCTTTGTTAGATAACGTTTCGAT 58.612 33.333 5.91 0.00 42.90 3.59
2071 3346 5.303333 TCGATGCATACATGTTCCTAGGTAA 59.697 40.000 9.08 0.00 36.35 2.85
2153 3440 2.830370 GCGAGCCCCTTCCCATTG 60.830 66.667 0.00 0.00 0.00 2.82
2175 3462 7.490962 TTGGTTACTCAACAGAAATACACTG 57.509 36.000 0.00 0.00 40.68 3.66
2180 3467 5.930135 ACTCAACAGAAATACACTGGTTCT 58.070 37.500 0.00 0.00 39.38 3.01
2216 3507 7.065204 GGAGAGATTCTGAGTTGGAAAATACAC 59.935 40.741 0.00 0.00 0.00 2.90
2242 3533 6.646267 ACTGTAGTAGGAAACTTGTTGTGAA 58.354 36.000 0.00 0.00 43.67 3.18
2250 3541 6.068010 AGGAAACTTGTTGTGAATCACCATA 58.932 36.000 11.24 0.00 37.44 2.74
2261 3552 9.289303 GTTGTGAATCACCATATATTGAAACAC 57.711 33.333 11.24 14.01 34.92 3.32
2289 3580 4.678256 ACGGGGTGATGATGATATAGACT 58.322 43.478 0.00 0.00 0.00 3.24
2329 3620 3.468071 TGACCTATACGCCCTATCCAT 57.532 47.619 0.00 0.00 0.00 3.41
2330 3621 4.596354 TGACCTATACGCCCTATCCATA 57.404 45.455 0.00 0.00 0.00 2.74
2342 3633 4.647399 GCCCTATCCATAGTCACTATCCTC 59.353 50.000 0.00 0.00 0.00 3.71
2354 3645 5.105146 AGTCACTATCCTCGAAGCAAAGAAT 60.105 40.000 0.00 0.00 0.00 2.40
2433 3725 0.702902 AGTTACTCGGAGACCCCTCA 59.297 55.000 12.86 0.00 41.20 3.86
2435 3727 1.682323 GTTACTCGGAGACCCCTCATC 59.318 57.143 12.86 0.00 41.20 2.92
2457 3749 1.079405 GAAGTCGCCCGACCAATCA 60.079 57.895 16.31 0.00 45.59 2.57
2471 3763 1.739466 CCAATCAACCACTCGACCATG 59.261 52.381 0.00 0.00 0.00 3.66
2481 3773 0.933097 CTCGACCATGCAAGAATCCG 59.067 55.000 0.00 0.00 0.00 4.18
2498 3790 2.307768 TCCGCTCGACCTATTGAAGAT 58.692 47.619 0.00 0.00 0.00 2.40
2521 3813 7.508636 AGATCAGGAGTCATCTAGAATAGCAAA 59.491 37.037 0.00 0.00 38.99 3.68
2526 3818 6.168270 AGTCATCTAGAATAGCAAAGGACC 57.832 41.667 0.00 0.00 38.99 4.46
2537 3829 1.308998 CAAAGGACCAGCGTTCACTT 58.691 50.000 0.00 0.00 0.00 3.16
2618 3910 1.529226 TGTACATTGAACCCTTGGCG 58.471 50.000 0.00 0.00 0.00 5.69
2644 3936 3.007920 CTGGCTGAGGTCCTGGCT 61.008 66.667 0.00 0.00 39.49 4.75
2692 3984 2.594592 GCACAAGGGTTCGCACCT 60.595 61.111 3.73 0.00 43.65 4.00
2704 3996 0.973632 TCGCACCTCCTGTAACACAT 59.026 50.000 0.00 0.00 0.00 3.21
2751 4049 0.940833 GTACCGAGACGTAGGGCTAC 59.059 60.000 8.73 0.00 0.00 3.58
2770 4068 1.304713 TACTTCCTCCGCGAAGGGT 60.305 57.895 12.95 4.82 43.01 4.34
2954 4256 1.391577 CATCATCATGGTTTCCGGCA 58.608 50.000 0.00 0.00 0.00 5.69
2995 4297 4.760047 ATCCGTCTTGGCGCGCTT 62.760 61.111 32.29 1.74 37.80 4.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 50 2.597805 CCGATCCTCGATCCGGGT 60.598 66.667 0.00 0.00 43.74 5.28
490 1728 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
491 1729 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
492 1730 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
493 1731 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
495 1733 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
510 1748 8.960591 CATGGTGGAATGTCTAAAAAGACTTAT 58.039 33.333 7.04 0.00 39.41 1.73
511 1749 7.393234 CCATGGTGGAATGTCTAAAAAGACTTA 59.607 37.037 2.57 0.00 40.96 2.24
512 1750 6.209391 CCATGGTGGAATGTCTAAAAAGACTT 59.791 38.462 2.57 0.00 40.96 3.01
513 1751 5.711976 CCATGGTGGAATGTCTAAAAAGACT 59.288 40.000 2.57 0.00 40.96 3.24
514 1752 5.710099 TCCATGGTGGAATGTCTAAAAAGAC 59.290 40.000 12.58 0.00 45.00 3.01
528 1766 3.021177 TCGTATGTAGTCCATGGTGGA 57.979 47.619 12.58 0.00 45.98 4.02
529 1767 3.717707 CTTCGTATGTAGTCCATGGTGG 58.282 50.000 12.58 0.00 39.43 4.61
530 1768 3.123804 GCTTCGTATGTAGTCCATGGTG 58.876 50.000 12.58 0.00 34.86 4.17
531 1769 2.764010 TGCTTCGTATGTAGTCCATGGT 59.236 45.455 12.58 0.00 34.86 3.55
532 1770 3.452755 TGCTTCGTATGTAGTCCATGG 57.547 47.619 4.97 4.97 34.86 3.66
533 1771 5.794687 TTTTGCTTCGTATGTAGTCCATG 57.205 39.130 0.00 0.00 34.86 3.66
534 1772 7.769044 ACTTATTTTGCTTCGTATGTAGTCCAT 59.231 33.333 0.00 0.00 37.58 3.41
535 1773 7.064134 CACTTATTTTGCTTCGTATGTAGTCCA 59.936 37.037 0.00 0.00 0.00 4.02
536 1774 7.277098 TCACTTATTTTGCTTCGTATGTAGTCC 59.723 37.037 0.00 0.00 0.00 3.85
537 1775 8.181487 TCACTTATTTTGCTTCGTATGTAGTC 57.819 34.615 0.00 0.00 0.00 2.59
538 1776 8.542497 TTCACTTATTTTGCTTCGTATGTAGT 57.458 30.769 0.00 0.00 0.00 2.73
539 1777 9.638300 GATTCACTTATTTTGCTTCGTATGTAG 57.362 33.333 0.00 0.00 0.00 2.74
540 1778 9.378551 AGATTCACTTATTTTGCTTCGTATGTA 57.621 29.630 0.00 0.00 0.00 2.29
541 1779 8.268850 AGATTCACTTATTTTGCTTCGTATGT 57.731 30.769 0.00 0.00 0.00 2.29
542 1780 9.638300 GTAGATTCACTTATTTTGCTTCGTATG 57.362 33.333 0.00 0.00 0.00 2.39
543 1781 9.378551 TGTAGATTCACTTATTTTGCTTCGTAT 57.621 29.630 0.00 0.00 0.00 3.06
544 1782 8.653338 GTGTAGATTCACTTATTTTGCTTCGTA 58.347 33.333 0.00 0.00 35.68 3.43
545 1783 7.387948 AGTGTAGATTCACTTATTTTGCTTCGT 59.612 33.333 0.00 0.00 44.92 3.85
546 1784 7.743104 AGTGTAGATTCACTTATTTTGCTTCG 58.257 34.615 0.00 0.00 44.92 3.79
547 1785 8.940952 AGAGTGTAGATTCACTTATTTTGCTTC 58.059 33.333 0.98 0.00 46.81 3.86
548 1786 8.854614 AGAGTGTAGATTCACTTATTTTGCTT 57.145 30.769 0.98 0.00 46.81 3.91
549 1787 9.944376 TTAGAGTGTAGATTCACTTATTTTGCT 57.056 29.630 0.98 0.00 46.81 3.91
576 1814 9.224267 ACTACGTACGGATGTATATAGACATTT 57.776 33.333 21.06 5.24 40.18 2.32
577 1815 8.783833 ACTACGTACGGATGTATATAGACATT 57.216 34.615 21.06 1.88 40.18 2.71
578 1816 8.783833 AACTACGTACGGATGTATATAGACAT 57.216 34.615 21.06 12.70 42.82 3.06
579 1817 8.607441 AAACTACGTACGGATGTATATAGACA 57.393 34.615 21.06 2.07 32.11 3.41
580 1818 8.930760 AGAAACTACGTACGGATGTATATAGAC 58.069 37.037 21.06 6.90 32.11 2.59
583 1821 9.929180 ACTAGAAACTACGTACGGATGTATATA 57.071 33.333 21.06 0.00 32.11 0.86
584 1822 8.715998 CACTAGAAACTACGTACGGATGTATAT 58.284 37.037 21.06 0.00 32.11 0.86
585 1823 7.926018 TCACTAGAAACTACGTACGGATGTATA 59.074 37.037 21.06 0.30 32.11 1.47
586 1824 6.763135 TCACTAGAAACTACGTACGGATGTAT 59.237 38.462 21.06 0.00 32.11 2.29
587 1825 6.106003 TCACTAGAAACTACGTACGGATGTA 58.894 40.000 21.06 0.00 0.00 2.29
588 1826 4.937620 TCACTAGAAACTACGTACGGATGT 59.062 41.667 21.06 11.85 0.00 3.06
589 1827 5.475273 TCACTAGAAACTACGTACGGATG 57.525 43.478 21.06 11.20 0.00 3.51
590 1828 6.500684 TTTCACTAGAAACTACGTACGGAT 57.499 37.500 21.06 1.34 38.76 4.18
591 1829 5.940192 TTTCACTAGAAACTACGTACGGA 57.060 39.130 21.06 10.81 38.76 4.69
592 1830 6.549952 AGATTTCACTAGAAACTACGTACGG 58.450 40.000 21.06 5.00 45.79 4.02
593 1831 8.445193 AAAGATTTCACTAGAAACTACGTACG 57.555 34.615 15.01 15.01 45.79 3.67
619 1857 9.392259 CCTCCGTTCCTAAATATTAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
620 1858 8.765517 TCCTCCGTTCCTAAATATTAGTCTTTT 58.234 33.333 0.00 0.00 0.00 2.27
621 1859 8.315220 TCCTCCGTTCCTAAATATTAGTCTTT 57.685 34.615 0.00 0.00 0.00 2.52
622 1860 7.909485 TCCTCCGTTCCTAAATATTAGTCTT 57.091 36.000 0.00 0.00 0.00 3.01
623 1861 7.564292 ACTTCCTCCGTTCCTAAATATTAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
624 1862 7.724287 ACTTCCTCCGTTCCTAAATATTAGTC 58.276 38.462 0.00 0.00 0.00 2.59
625 1863 7.672122 ACTTCCTCCGTTCCTAAATATTAGT 57.328 36.000 0.00 0.00 0.00 2.24
626 1864 7.813627 GCTACTTCCTCCGTTCCTAAATATTAG 59.186 40.741 0.00 0.00 0.00 1.73
627 1865 7.288389 TGCTACTTCCTCCGTTCCTAAATATTA 59.712 37.037 0.00 0.00 0.00 0.98
628 1866 6.099269 TGCTACTTCCTCCGTTCCTAAATATT 59.901 38.462 0.00 0.00 0.00 1.28
629 1867 5.601313 TGCTACTTCCTCCGTTCCTAAATAT 59.399 40.000 0.00 0.00 0.00 1.28
630 1868 4.957954 TGCTACTTCCTCCGTTCCTAAATA 59.042 41.667 0.00 0.00 0.00 1.40
631 1869 3.773119 TGCTACTTCCTCCGTTCCTAAAT 59.227 43.478 0.00 0.00 0.00 1.40
632 1870 3.167485 TGCTACTTCCTCCGTTCCTAAA 58.833 45.455 0.00 0.00 0.00 1.85
633 1871 2.811410 TGCTACTTCCTCCGTTCCTAA 58.189 47.619 0.00 0.00 0.00 2.69
634 1872 2.519771 TGCTACTTCCTCCGTTCCTA 57.480 50.000 0.00 0.00 0.00 2.94
635 1873 1.867363 ATGCTACTTCCTCCGTTCCT 58.133 50.000 0.00 0.00 0.00 3.36
636 1874 2.280628 CAATGCTACTTCCTCCGTTCC 58.719 52.381 0.00 0.00 0.00 3.62
637 1875 2.973945 ACAATGCTACTTCCTCCGTTC 58.026 47.619 0.00 0.00 0.00 3.95
638 1876 3.074412 CAACAATGCTACTTCCTCCGTT 58.926 45.455 0.00 0.00 0.00 4.44
639 1877 2.038557 ACAACAATGCTACTTCCTCCGT 59.961 45.455 0.00 0.00 0.00 4.69
640 1878 2.673368 GACAACAATGCTACTTCCTCCG 59.327 50.000 0.00 0.00 0.00 4.63
641 1879 3.010420 GGACAACAATGCTACTTCCTCC 58.990 50.000 0.00 0.00 0.00 4.30
642 1880 3.944087 AGGACAACAATGCTACTTCCTC 58.056 45.455 0.00 0.00 0.00 3.71
643 1881 4.373156 AAGGACAACAATGCTACTTCCT 57.627 40.909 0.00 0.00 30.53 3.36
644 1882 4.321230 CCAAAGGACAACAATGCTACTTCC 60.321 45.833 0.00 0.00 0.00 3.46
645 1883 4.321230 CCCAAAGGACAACAATGCTACTTC 60.321 45.833 0.00 0.00 33.47 3.01
646 1884 3.573967 CCCAAAGGACAACAATGCTACTT 59.426 43.478 0.00 0.00 33.47 2.24
647 1885 3.157087 CCCAAAGGACAACAATGCTACT 58.843 45.455 0.00 0.00 33.47 2.57
648 1886 2.890945 ACCCAAAGGACAACAATGCTAC 59.109 45.455 0.00 0.00 36.73 3.58
856 2116 7.432252 GCACATAGATTTGTAAACTGGTATTGC 59.568 37.037 0.00 0.00 0.00 3.56
937 2197 7.710907 TGTAAGATAAATGGAACTCGAGAATGG 59.289 37.037 21.68 0.00 0.00 3.16
1017 2277 3.771577 AGGACGACCACAGAAAGATTT 57.228 42.857 6.71 0.00 38.94 2.17
1025 2285 4.985538 AGTAAGATAAGGACGACCACAG 57.014 45.455 6.71 0.00 38.94 3.66
1064 2324 5.440610 AGGGATTGTTCATGATGTTAGACC 58.559 41.667 0.00 0.00 0.00 3.85
1096 2356 0.111061 TGCACAAACTCCAGAGGCAT 59.889 50.000 0.00 0.00 0.00 4.40
1165 2425 9.851686 AAGAAAATAAGGCTTCTTTTGGATTTT 57.148 25.926 22.99 17.39 38.45 1.82
1212 2472 3.490759 CGTGTGGAGCGGCATGTC 61.491 66.667 1.45 0.00 0.00 3.06
1253 2513 8.475331 AGCAAGATGATGAAAATTTCAATGAC 57.525 30.769 12.75 5.57 43.95 3.06
1278 2538 3.763360 CAGAGAATGGTATTGGGCAACAA 59.237 43.478 0.00 0.00 44.54 2.83
1287 2547 2.590821 GCCATGGCAGAGAATGGTATT 58.409 47.619 32.08 0.00 44.45 1.89
1311 2571 5.390991 GCAAGAATAGGAGAAGAAAACACCG 60.391 44.000 0.00 0.00 0.00 4.94
1426 2686 3.433615 GGTGCGAAGTCATATAAGATGGC 59.566 47.826 0.00 0.00 0.00 4.40
1438 2698 4.521130 TCCTATCATATGGTGCGAAGTC 57.479 45.455 2.13 0.00 0.00 3.01
1444 2704 6.552445 AACTAGGATCCTATCATATGGTGC 57.448 41.667 21.95 0.00 0.00 5.01
1503 2774 8.751242 TGAAGATTAAGCAAATGATGGAAATCA 58.249 29.630 0.00 0.00 34.73 2.57
1602 2876 6.394345 AAGGAAAAGGGAGACACATATCTT 57.606 37.500 0.00 0.00 0.00 2.40
1605 2879 5.186198 CGAAAGGAAAAGGGAGACACATAT 58.814 41.667 0.00 0.00 0.00 1.78
1606 2880 4.575885 CGAAAGGAAAAGGGAGACACATA 58.424 43.478 0.00 0.00 0.00 2.29
1608 2882 2.846193 CGAAAGGAAAAGGGAGACACA 58.154 47.619 0.00 0.00 0.00 3.72
1623 2897 5.424121 AGAGACACATGTTTTTCCGAAAG 57.576 39.130 0.00 0.00 0.00 2.62
1624 2898 4.274950 GGAGAGACACATGTTTTTCCGAAA 59.725 41.667 0.00 0.00 0.00 3.46
1625 2899 3.813166 GGAGAGACACATGTTTTTCCGAA 59.187 43.478 0.00 0.00 0.00 4.30
1626 2900 3.181459 TGGAGAGACACATGTTTTTCCGA 60.181 43.478 0.00 0.00 0.00 4.55
1627 2901 3.058914 GTGGAGAGACACATGTTTTTCCG 60.059 47.826 0.00 0.00 40.99 4.30
1628 2902 4.137543 AGTGGAGAGACACATGTTTTTCC 58.862 43.478 0.00 5.44 43.72 3.13
1629 2903 4.816385 TGAGTGGAGAGACACATGTTTTTC 59.184 41.667 0.00 0.00 43.72 2.29
1630 2904 4.576463 GTGAGTGGAGAGACACATGTTTTT 59.424 41.667 0.00 0.00 43.72 1.94
1633 2907 2.968574 AGTGAGTGGAGAGACACATGTT 59.031 45.455 0.00 0.00 43.72 2.71
1635 2909 4.790765 TTAGTGAGTGGAGAGACACATG 57.209 45.455 0.00 0.00 43.72 3.21
1640 2914 5.221461 TGGACTTTTTAGTGAGTGGAGAGAC 60.221 44.000 0.00 0.00 0.00 3.36
1768 3043 9.260002 GATAAAGTGAATTTTGGTGTGACAAAT 57.740 29.630 0.00 0.00 39.80 2.32
1795 3070 4.154195 GCTTCTCGGTTCTCTGCATAAAAA 59.846 41.667 0.00 0.00 0.00 1.94
1816 3091 1.447838 CGTAGCCACATGAACCGCT 60.448 57.895 0.00 2.75 35.34 5.52
1864 3139 1.604278 GGCGGAATATCTTCTTGTGCC 59.396 52.381 0.00 0.00 32.56 5.01
1930 3205 1.570813 TGCTTTCGATCACGCCTATG 58.429 50.000 0.00 0.00 39.58 2.23
1932 3207 2.309528 ATTGCTTTCGATCACGCCTA 57.690 45.000 0.00 0.00 39.58 3.93
1936 3211 2.245795 TGCAATTGCTTTCGATCACG 57.754 45.000 29.37 0.00 42.66 4.35
1941 3216 4.455533 AGACACTTATGCAATTGCTTTCGA 59.544 37.500 29.37 10.86 42.66 3.71
1959 3234 2.328099 CCTTCGGCCTTGCAGACAC 61.328 63.158 0.00 0.00 31.79 3.67
1991 3266 1.740297 TTACACACGCCAACACACTT 58.260 45.000 0.00 0.00 0.00 3.16
2071 3346 5.874897 ATGCACACATGGGCTTTATTTAT 57.125 34.783 7.77 0.00 46.62 1.40
2102 3383 9.398170 ACAAAACGAACATCTTCATTGAAATAG 57.602 29.630 0.01 0.00 0.00 1.73
2144 3431 4.651778 TCTGTTGAGTAACCAATGGGAAG 58.348 43.478 3.55 0.00 35.92 3.46
2147 3434 5.982890 ATTTCTGTTGAGTAACCAATGGG 57.017 39.130 3.55 0.00 35.92 4.00
2153 3440 5.995897 ACCAGTGTATTTCTGTTGAGTAACC 59.004 40.000 0.00 0.00 35.92 2.85
2175 3462 1.882623 CTCTCCCTGTTTGCAAGAACC 59.117 52.381 0.00 0.00 0.00 3.62
2180 3467 3.072915 TCAGAATCTCTCCCTGTTTGCAA 59.927 43.478 0.00 0.00 0.00 4.08
2216 3507 7.431249 TCACAACAAGTTTCCTACTACAGTAG 58.569 38.462 6.00 6.00 45.68 2.57
2250 3541 5.646360 CACCCCGTAAAGAGTGTTTCAATAT 59.354 40.000 0.00 0.00 0.00 1.28
2261 3552 3.819564 TCATCATCACCCCGTAAAGAG 57.180 47.619 0.00 0.00 0.00 2.85
2289 3580 0.045008 TGCCTATGACCCTACCCCAA 59.955 55.000 0.00 0.00 0.00 4.12
2329 3620 4.948004 TCTTTGCTTCGAGGATAGTGACTA 59.052 41.667 0.00 0.00 0.00 2.59
2330 3621 3.764434 TCTTTGCTTCGAGGATAGTGACT 59.236 43.478 0.00 0.00 0.00 3.41
2342 3633 4.687948 TGTCTCTTGAGATTCTTTGCTTCG 59.312 41.667 3.50 0.00 0.00 3.79
2354 3645 2.251818 CCTCCCTGTTGTCTCTTGAGA 58.748 52.381 0.00 0.00 0.00 3.27
2433 3725 2.363795 TCGGGCGACTTCAGGGAT 60.364 61.111 0.00 0.00 0.00 3.85
2435 3727 4.452733 GGTCGGGCGACTTCAGGG 62.453 72.222 0.00 0.00 44.04 4.45
2457 3749 0.396435 TCTTGCATGGTCGAGTGGTT 59.604 50.000 0.00 0.00 0.00 3.67
2471 3763 0.102481 TAGGTCGAGCGGATTCTTGC 59.898 55.000 9.28 0.00 0.00 4.01
2481 3773 3.319405 TCCTGATCTTCAATAGGTCGAGC 59.681 47.826 6.48 6.48 36.75 5.03
2498 3790 6.041409 CCTTTGCTATTCTAGATGACTCCTGA 59.959 42.308 0.00 0.00 0.00 3.86
2521 3813 0.180406 ACAAAGTGAACGCTGGTCCT 59.820 50.000 0.00 0.00 0.00 3.85
2526 3818 4.795970 AAAGACTACAAAGTGAACGCTG 57.204 40.909 0.00 0.00 35.56 5.18
2583 3875 3.857052 TGTACATAAAGAGGAGGCGTTG 58.143 45.455 0.00 0.00 0.00 4.10
2618 3910 1.294780 CCTCAGCCAGTCCACTGTC 59.705 63.158 5.99 0.00 42.27 3.51
2634 3926 3.913370 ATATAGAGTGAGCCAGGACCT 57.087 47.619 0.00 0.00 0.00 3.85
2644 3936 3.517612 GGGGGTGGCTTATATAGAGTGA 58.482 50.000 0.00 0.00 0.00 3.41
2692 3984 9.154632 ACTGGATTATATGTATGTGTTACAGGA 57.845 33.333 0.00 0.00 43.87 3.86
2704 3996 4.591498 AGGCGGTCAACTGGATTATATGTA 59.409 41.667 0.00 0.00 0.00 2.29
2733 4031 0.833287 AGTAGCCCTACGTCTCGGTA 59.167 55.000 0.00 0.00 40.80 4.02
2751 4049 1.321074 ACCCTTCGCGGAGGAAGTAG 61.321 60.000 35.60 19.66 41.44 2.57
2770 4068 4.039703 CACACGAGTTTTACGAGTTCAGA 58.960 43.478 0.00 0.00 33.07 3.27
2852 4152 3.463944 CCAACTGTCGTGGTTCTAAGTT 58.536 45.455 0.00 0.00 0.00 2.66
2853 4153 2.805657 GCCAACTGTCGTGGTTCTAAGT 60.806 50.000 0.84 0.00 0.00 2.24
2954 4256 2.679716 GCCCTCAGCCAATCCACT 59.320 61.111 0.00 0.00 34.35 4.00


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

AutoCloner maintained by Alex Coulton.