Multiple sequence alignment - TraesCS5B01G001900

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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 TraesCS5B01G001900 chr5B 100.000 3397 0 0 1 3397 2615406 2612010 0.000000e+00 6274.0
1 TraesCS5B01G001900 chr5B 85.119 1391 132 34 969 2315 2883453 2884812 0.000000e+00 1352.0
2 TraesCS5B01G001900 chr5B 82.555 1284 128 48 1095 2328 2805580 2806817 0.000000e+00 1042.0
3 TraesCS5B01G001900 chr5B 88.235 68 6 2 789 854 697184919 697184986 2.810000e-11 80.5
4 TraesCS5B01G001900 chr5B 85.000 80 6 5 803 881 476462271 476462345 3.630000e-10 76.8
5 TraesCS5B01G001900 chr5D 84.891 1701 160 60 853 2493 3012300 3013963 0.000000e+00 1628.0
6 TraesCS5B01G001900 chr5D 86.232 1380 138 33 969 2315 3070498 3071858 0.000000e+00 1448.0
7 TraesCS5B01G001900 chr5D 92.552 913 58 7 2486 3395 3016340 3017245 0.000000e+00 1301.0
8 TraesCS5B01G001900 chr5D 88.808 822 56 12 1 805 3011500 3012302 0.000000e+00 976.0
9 TraesCS5B01G001900 chr5D 85.208 818 67 29 1543 2318 2797719 2798524 0.000000e+00 791.0
10 TraesCS5B01G001900 chr5D 87.547 265 31 2 2615 2877 2798723 2798987 4.260000e-79 305.0
11 TraesCS5B01G001900 chr5D 100.000 43 0 0 2389 2431 2798566 2798608 2.810000e-11 80.5
12 TraesCS5B01G001900 chr5A 86.338 1442 127 35 970 2376 1759616 1758210 0.000000e+00 1507.0
13 TraesCS5B01G001900 chr5A 81.018 1533 166 64 969 2428 1834965 1833485 0.000000e+00 1103.0
14 TraesCS5B01G001900 chr5A 86.521 779 79 10 1050 1825 1714393 1713638 0.000000e+00 833.0
15 TraesCS5B01G001900 chr5A 82.780 813 86 30 1 804 1804624 1803857 0.000000e+00 676.0
16 TraesCS5B01G001900 chr5A 89.056 466 42 5 1856 2315 1713547 1713085 1.370000e-158 569.0
17 TraesCS5B01G001900 chr5A 85.630 508 33 7 2363 2855 1757927 1757445 6.550000e-137 497.0
18 TraesCS5B01G001900 chr5A 89.426 331 24 7 1989 2318 1803115 1802795 1.130000e-109 407.0
19 TraesCS5B01G001900 chr5A 86.325 351 45 3 3047 3397 1752092 1751745 2.470000e-101 379.0
20 TraesCS5B01G001900 chr5A 89.236 288 23 3 1053 1337 1336371 1336653 1.500000e-93 353.0
21 TraesCS5B01G001900 chr5A 89.344 244 21 3 2619 2860 1833148 1832908 5.510000e-78 302.0
22 TraesCS5B01G001900 chr5A 83.884 242 25 5 2361 2588 1802661 1802420 5.710000e-53 219.0
23 TraesCS5B01G001900 chr5A 91.150 113 10 0 2860 2972 1752495 1752383 1.630000e-33 154.0
24 TraesCS5B01G001900 chr5A 89.394 66 4 2 803 868 645135337 645135275 2.810000e-11 80.5
25 TraesCS5B01G001900 chr5A 88.710 62 3 2 973 1033 1714433 1714375 4.700000e-09 73.1
26 TraesCS5B01G001900 chr7D 74.406 379 67 16 199 569 3789200 3788844 5.910000e-28 135.0
27 TraesCS5B01G001900 chr7B 92.063 63 3 2 793 854 715085598 715085537 1.680000e-13 87.9
28 TraesCS5B01G001900 chr7B 89.394 66 4 2 803 868 857133 857195 2.810000e-11 80.5
29 TraesCS5B01G001900 chr7B 85.000 80 6 5 803 881 708469481 708469555 3.630000e-10 76.8
30 TraesCS5B01G001900 chr2D 96.226 53 2 0 802 854 526936485 526936537 1.680000e-13 87.9
31 TraesCS5B01G001900 chr6D 86.250 80 5 5 803 881 450292086 450292012 7.810000e-12 82.4
32 TraesCS5B01G001900 chr3A 85.000 80 6 5 803 881 492042427 492042501 3.630000e-10 76.8


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 TraesCS5B01G001900 chr5B 2612010 2615406 3396 True 6274.000000 6274 100.000000 1 3397 1 chr5B.!!$R1 3396
1 TraesCS5B01G001900 chr5B 2883453 2884812 1359 False 1352.000000 1352 85.119000 969 2315 1 chr5B.!!$F2 1346
2 TraesCS5B01G001900 chr5B 2805580 2806817 1237 False 1042.000000 1042 82.555000 1095 2328 1 chr5B.!!$F1 1233
3 TraesCS5B01G001900 chr5D 3070498 3071858 1360 False 1448.000000 1448 86.232000 969 2315 1 chr5D.!!$F1 1346
4 TraesCS5B01G001900 chr5D 3011500 3017245 5745 False 1301.666667 1628 88.750333 1 3395 3 chr5D.!!$F3 3394
5 TraesCS5B01G001900 chr5D 2797719 2798987 1268 False 392.166667 791 90.918333 1543 2877 3 chr5D.!!$F2 1334
6 TraesCS5B01G001900 chr5A 1757445 1759616 2171 True 1002.000000 1507 85.984000 970 2855 2 chr5A.!!$R4 1885
7 TraesCS5B01G001900 chr5A 1832908 1834965 2057 True 702.500000 1103 85.181000 969 2860 2 chr5A.!!$R6 1891
8 TraesCS5B01G001900 chr5A 1713085 1714433 1348 True 491.700000 833 88.095667 973 2315 3 chr5A.!!$R2 1342
9 TraesCS5B01G001900 chr5A 1802420 1804624 2204 True 434.000000 676 85.363333 1 2588 3 chr5A.!!$R5 2587
10 TraesCS5B01G001900 chr5A 1751745 1752495 750 True 266.500000 379 88.737500 2860 3397 2 chr5A.!!$R3 537

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
818 844 0.038744 AGTTACTCCCTCCGTTCGGA 59.961 55.0 13.34 13.34 0.00 4.55 F
1455 2154 0.324091 ACCAGACCGAGGATACCGTT 60.324 55.0 0.00 0.00 37.17 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2320 3187 0.037232 GCTAGCCCGTGTTGAAGACT 60.037 55.0 2.29 0.0 0.0 3.24 R
3294 7330 0.035820 TGCCGCCCGATTAGAAGTTT 60.036 50.0 0.00 0.0 0.0 2.66 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
52 61 2.687200 TCAGGTGCGGGCAGGTAT 60.687 61.111 0.00 0.00 0.00 2.73
111 120 0.412244 TAGGGATACGATGGAGGGGG 59.588 60.000 0.00 0.00 37.60 5.40
152 161 6.213677 CACTACTTGCTCAGTTGTTGTACTA 58.786 40.000 0.00 0.00 39.20 1.82
155 164 4.101119 ACTTGCTCAGTTGTTGTACTAGGT 59.899 41.667 0.00 0.00 27.32 3.08
287 296 1.217244 GGCTATCGGTGGTCGTGTT 59.783 57.895 0.00 0.00 40.32 3.32
323 332 2.230750 GGTCTTGTAGTGCTTACTCCGT 59.769 50.000 0.00 0.00 33.23 4.69
331 340 0.956633 TGCTTACTCCGTCGTTGTCT 59.043 50.000 0.00 0.00 0.00 3.41
357 366 1.425066 ACCTTTCCTCTGTGGATTGCA 59.575 47.619 0.00 0.00 45.68 4.08
358 367 2.042162 ACCTTTCCTCTGTGGATTGCAT 59.958 45.455 0.00 0.00 45.68 3.96
359 368 2.686915 CCTTTCCTCTGTGGATTGCATC 59.313 50.000 0.00 0.00 45.68 3.91
371 382 0.331278 ATTGCATCGGGGAGGTTTCA 59.669 50.000 0.00 0.00 0.00 2.69
382 393 2.359975 GGTTTCAGTCGGCCCCAG 60.360 66.667 0.00 0.00 0.00 4.45
421 432 4.440112 GCCTATGTAATTTGCTTGGTGGTC 60.440 45.833 0.00 0.00 0.00 4.02
437 448 2.202053 TCGTGGGGGTGGTGTAGT 59.798 61.111 0.00 0.00 0.00 2.73
456 473 6.877322 GTGTAGTGGTGACCTATGTATTTTGT 59.123 38.462 2.11 0.00 0.00 2.83
472 489 1.458398 TTGTCTTGGGTGTGTGTGTG 58.542 50.000 0.00 0.00 0.00 3.82
473 490 0.326595 TGTCTTGGGTGTGTGTGTGT 59.673 50.000 0.00 0.00 0.00 3.72
474 491 0.732571 GTCTTGGGTGTGTGTGTGTG 59.267 55.000 0.00 0.00 0.00 3.82
475 492 0.326595 TCTTGGGTGTGTGTGTGTGT 59.673 50.000 0.00 0.00 0.00 3.72
476 493 0.451383 CTTGGGTGTGTGTGTGTGTG 59.549 55.000 0.00 0.00 0.00 3.82
477 494 0.250945 TTGGGTGTGTGTGTGTGTGT 60.251 50.000 0.00 0.00 0.00 3.72
478 495 0.957888 TGGGTGTGTGTGTGTGTGTG 60.958 55.000 0.00 0.00 0.00 3.82
479 496 0.958382 GGGTGTGTGTGTGTGTGTGT 60.958 55.000 0.00 0.00 0.00 3.72
495 512 2.030717 GTGTGTTGTGTGTGGTGTTTCA 60.031 45.455 0.00 0.00 0.00 2.69
512 529 4.035792 TGTTTCACATGAGTTTGTAACGGG 59.964 41.667 0.00 0.00 36.23 5.28
543 568 9.725019 TTGATGGTTGGTGCTTTATATATAGAG 57.275 33.333 6.02 6.02 0.00 2.43
544 569 7.824289 TGATGGTTGGTGCTTTATATATAGAGC 59.176 37.037 22.42 22.42 39.97 4.09
545 570 7.073457 TGGTTGGTGCTTTATATATAGAGCA 57.927 36.000 26.14 26.14 44.91 4.26
546 571 7.161404 TGGTTGGTGCTTTATATATAGAGCAG 58.839 38.462 28.97 10.58 46.79 4.24
605 630 3.438087 CCATCTGGTGTGAACTTTGCTAG 59.562 47.826 0.00 0.00 0.00 3.42
654 680 2.467566 TTCAGTTCCCGGAAAGTAGC 57.532 50.000 0.73 0.00 0.00 3.58
667 693 3.259064 GAAAGTAGCATGTAGGCGACAA 58.741 45.455 4.12 0.00 42.78 3.18
732 758 4.445385 GTGGAAACAGCAAATAAAGCACAG 59.555 41.667 0.00 0.00 44.46 3.66
764 790 1.065636 TCTTGAGCTGAAGATGCCCTG 60.066 52.381 11.93 0.00 0.00 4.45
765 791 0.679002 TTGAGCTGAAGATGCCCTGC 60.679 55.000 0.00 0.00 0.00 4.85
766 792 1.823041 GAGCTGAAGATGCCCTGCC 60.823 63.158 0.00 0.00 0.00 4.85
801 827 2.238144 CTGTCTCCCATTGACATCCAGT 59.762 50.000 0.00 0.00 42.57 4.00
805 831 4.080863 GTCTCCCATTGACATCCAGTTACT 60.081 45.833 0.00 0.00 34.80 2.24
806 832 4.162320 TCTCCCATTGACATCCAGTTACTC 59.838 45.833 0.00 0.00 0.00 2.59
807 833 3.199946 TCCCATTGACATCCAGTTACTCC 59.800 47.826 0.00 0.00 0.00 3.85
808 834 3.545703 CCATTGACATCCAGTTACTCCC 58.454 50.000 0.00 0.00 0.00 4.30
810 836 4.446371 CATTGACATCCAGTTACTCCCTC 58.554 47.826 0.00 0.00 0.00 4.30
811 837 2.467880 TGACATCCAGTTACTCCCTCC 58.532 52.381 0.00 0.00 0.00 4.30
812 838 1.409427 GACATCCAGTTACTCCCTCCG 59.591 57.143 0.00 0.00 0.00 4.63
814 840 1.831736 CATCCAGTTACTCCCTCCGTT 59.168 52.381 0.00 0.00 0.00 4.44
815 841 1.553706 TCCAGTTACTCCCTCCGTTC 58.446 55.000 0.00 0.00 0.00 3.95
816 842 0.172803 CCAGTTACTCCCTCCGTTCG 59.827 60.000 0.00 0.00 0.00 3.95
817 843 0.172803 CAGTTACTCCCTCCGTTCGG 59.827 60.000 4.74 4.74 0.00 4.30
818 844 0.038744 AGTTACTCCCTCCGTTCGGA 59.961 55.000 13.34 13.34 0.00 4.55
819 845 0.890683 GTTACTCCCTCCGTTCGGAA 59.109 55.000 14.79 0.04 33.41 4.30
820 846 1.479730 GTTACTCCCTCCGTTCGGAAT 59.520 52.381 14.79 2.09 33.41 3.01
821 847 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
822 848 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
823 849 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
824 850 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
825 851 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
826 852 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
827 853 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
828 854 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
829 855 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
830 856 2.030007 TCCGTTCGGAATTACTTGTCGT 60.030 45.455 11.66 0.00 0.00 4.34
831 857 2.091588 CCGTTCGGAATTACTTGTCGTG 59.908 50.000 5.19 0.00 0.00 4.35
832 858 2.091588 CGTTCGGAATTACTTGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
833 859 3.319755 GTTCGGAATTACTTGTCGTGGA 58.680 45.455 0.00 0.00 0.00 4.02
834 860 3.663995 TCGGAATTACTTGTCGTGGAA 57.336 42.857 0.00 0.00 0.00 3.53
835 861 3.992643 TCGGAATTACTTGTCGTGGAAA 58.007 40.909 0.00 0.00 0.00 3.13
836 862 4.571919 TCGGAATTACTTGTCGTGGAAAT 58.428 39.130 0.00 0.00 0.00 2.17
837 863 5.722263 TCGGAATTACTTGTCGTGGAAATA 58.278 37.500 0.00 0.00 0.00 1.40
838 864 6.164876 TCGGAATTACTTGTCGTGGAAATAA 58.835 36.000 0.00 0.00 0.00 1.40
839 865 6.649973 TCGGAATTACTTGTCGTGGAAATAAA 59.350 34.615 0.00 0.00 0.00 1.40
840 866 7.334921 TCGGAATTACTTGTCGTGGAAATAAAT 59.665 33.333 0.00 0.00 0.00 1.40
841 867 7.428183 CGGAATTACTTGTCGTGGAAATAAATG 59.572 37.037 0.00 0.00 0.00 2.32
842 868 8.241367 GGAATTACTTGTCGTGGAAATAAATGT 58.759 33.333 0.00 0.00 0.00 2.71
846 872 9.661563 TTACTTGTCGTGGAAATAAATGTATCT 57.338 29.630 0.00 0.00 0.00 1.98
848 874 9.314321 ACTTGTCGTGGAAATAAATGTATCTAG 57.686 33.333 0.00 0.00 0.00 2.43
849 875 9.529325 CTTGTCGTGGAAATAAATGTATCTAGA 57.471 33.333 0.00 0.00 0.00 2.43
850 876 8.867112 TGTCGTGGAAATAAATGTATCTAGAC 57.133 34.615 0.00 0.00 0.00 2.59
944 970 9.666626 CTTGTATTGCAGACATACTAGTAGTAC 57.333 37.037 12.25 0.59 32.84 2.73
949 1553 8.659925 TTGCAGACATACTAGTAGTACTACTC 57.340 38.462 33.47 19.79 44.58 2.59
950 1554 7.215789 TGCAGACATACTAGTAGTACTACTCC 58.784 42.308 33.47 16.83 44.58 3.85
987 1591 5.061179 CCAACTATAAATACCCTCCCAACG 58.939 45.833 0.00 0.00 0.00 4.10
988 1592 4.968971 ACTATAAATACCCTCCCAACGG 57.031 45.455 0.00 0.00 0.00 4.44
989 1593 4.559726 ACTATAAATACCCTCCCAACGGA 58.440 43.478 0.00 0.00 36.45 4.69
1021 1629 3.257873 CACCTCACTCATCTCACTCACTT 59.742 47.826 0.00 0.00 0.00 3.16
1034 1670 2.797156 CACTCACTTCTTCTCCAACACG 59.203 50.000 0.00 0.00 0.00 4.49
1036 1672 3.053455 CTCACTTCTTCTCCAACACGAC 58.947 50.000 0.00 0.00 0.00 4.34
1037 1673 2.135933 CACTTCTTCTCCAACACGACC 58.864 52.381 0.00 0.00 0.00 4.79
1038 1674 1.760613 ACTTCTTCTCCAACACGACCA 59.239 47.619 0.00 0.00 0.00 4.02
1039 1675 2.224066 ACTTCTTCTCCAACACGACCAG 60.224 50.000 0.00 0.00 0.00 4.00
1069 1718 2.842496 TCTCACTCATTCCTCCAGCAAT 59.158 45.455 0.00 0.00 0.00 3.56
1080 1729 2.481854 CTCCAGCAATCTTCATCTCCG 58.518 52.381 0.00 0.00 0.00 4.63
1081 1730 1.833630 TCCAGCAATCTTCATCTCCGT 59.166 47.619 0.00 0.00 0.00 4.69
1082 1731 1.938577 CCAGCAATCTTCATCTCCGTG 59.061 52.381 0.00 0.00 0.00 4.94
1099 1748 2.964389 GCCTTCGGCTGCGATCTC 60.964 66.667 0.00 0.00 46.69 2.75
1147 1801 3.442167 TGTGCCATGTCATGCCGC 61.442 61.111 7.35 3.76 0.00 6.53
1148 1802 4.197498 GTGCCATGTCATGCCGCC 62.197 66.667 7.35 0.00 0.00 6.13
1171 1825 3.558099 CTGGACGTCGCTGCTCACA 62.558 63.158 9.92 0.00 0.00 3.58
1267 1960 3.858868 GACGTCTGCGCCACCAAGA 62.859 63.158 8.70 0.00 42.83 3.02
1405 2098 1.575576 CGACGACTTCCTCGACCTGT 61.576 60.000 0.00 0.00 46.14 4.00
1411 2104 1.186200 CTTCCTCGACCTGTCATCCA 58.814 55.000 0.00 0.00 0.00 3.41
1455 2154 0.324091 ACCAGACCGAGGATACCGTT 60.324 55.000 0.00 0.00 37.17 4.44
1456 2155 1.064463 ACCAGACCGAGGATACCGTTA 60.064 52.381 0.00 0.00 37.17 3.18
1514 2231 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1519 2236 3.024356 AGGAGGAGGAGGAGGCGA 61.024 66.667 0.00 0.00 0.00 5.54
1520 2237 2.200092 GGAGGAGGAGGAGGCGAT 59.800 66.667 0.00 0.00 0.00 4.58
1521 2238 2.206536 GGAGGAGGAGGAGGCGATG 61.207 68.421 0.00 0.00 0.00 3.84
1527 2244 3.237741 GAGGAGGCGATGGGGGAG 61.238 72.222 0.00 0.00 0.00 4.30
1528 2245 4.888325 AGGAGGCGATGGGGGAGG 62.888 72.222 0.00 0.00 0.00 4.30
1752 2469 2.064762 CTCAAGCTCTGTTTCGTGGAG 58.935 52.381 0.00 0.00 0.00 3.86
1780 2569 1.330655 TGCCTCGGGATCTGTTCTCC 61.331 60.000 0.00 0.00 0.00 3.71
1845 2685 0.656785 ATAGCGTCGACGAGGAAGAC 59.343 55.000 39.74 20.48 43.02 3.01
2024 2888 1.374758 GCTGCTGCAGAACTACCGT 60.375 57.895 32.30 0.00 39.41 4.83
2160 3024 1.297456 ACGAGGAAGAGGTCGACGAC 61.297 60.000 19.70 19.70 39.53 4.34
2170 3037 3.175724 TCGACGACGAGGAGAAGC 58.824 61.111 5.75 0.00 43.81 3.86
2171 3038 2.276743 CGACGACGAGGAGAAGCG 60.277 66.667 0.00 0.00 42.66 4.68
2226 3093 2.530151 AGGGAGGAGCTGGTGCAA 60.530 61.111 0.00 0.00 42.74 4.08
2300 3167 2.375014 TACTCCATCATCGCCACCTA 57.625 50.000 0.00 0.00 0.00 3.08
2303 3170 2.439507 ACTCCATCATCGCCACCTAATT 59.560 45.455 0.00 0.00 0.00 1.40
2318 3185 7.042254 CGCCACCTAATTATTACTCCAAACTAC 60.042 40.741 0.00 0.00 0.00 2.73
2340 3214 1.080093 TCTTCAACACGGGCTAGCG 60.080 57.895 9.00 0.00 0.00 4.26
2506 6321 6.813152 ACAACAATTTTATTCAGGTAGCATGC 59.187 34.615 10.51 10.51 0.00 4.06
2537 6352 6.921857 CCTGGCAAATGAGATATGTGAATTTC 59.078 38.462 0.00 0.00 0.00 2.17
2571 6388 7.987458 CCATAGAGTGCACTTTATTAAGGAGAA 59.013 37.037 23.46 0.00 35.61 2.87
2642 6460 4.286808 TGGTCTCCAAATCATGTCTCTGAA 59.713 41.667 0.00 0.00 0.00 3.02
2653 6471 4.336713 TCATGTCTCTGAACTCTATGACCG 59.663 45.833 0.00 0.00 0.00 4.79
2792 6612 0.038526 GAACCTGTGACGATCGTGGT 60.039 55.000 28.12 22.89 0.00 4.16
2880 6700 0.036875 GTTGACTTGCAGGGGTAGCT 59.963 55.000 0.00 0.00 0.00 3.32
2881 6701 0.771127 TTGACTTGCAGGGGTAGCTT 59.229 50.000 0.00 0.00 0.00 3.74
2883 6703 1.555075 TGACTTGCAGGGGTAGCTTAG 59.445 52.381 0.00 0.00 0.00 2.18
3022 6842 6.263842 CACCCTATCATGTACTAGGTCGTTAA 59.736 42.308 13.83 0.00 33.93 2.01
3101 7137 1.337118 TTTTGACACCCCTGATTGGC 58.663 50.000 0.00 0.00 0.00 4.52
3280 7316 0.179048 CATCGGTTGGGCAGCTATCA 60.179 55.000 0.00 0.00 0.00 2.15
3294 7330 2.511218 AGCTATCATTTGAGGGGCTTGA 59.489 45.455 0.00 0.00 0.00 3.02
3301 7337 3.312736 TTTGAGGGGCTTGAAACTTCT 57.687 42.857 0.00 0.00 0.00 2.85
3306 7342 3.610911 AGGGGCTTGAAACTTCTAATCG 58.389 45.455 0.00 0.00 0.00 3.34
3315 7351 0.743345 ACTTCTAATCGGGCGGCAAC 60.743 55.000 12.47 0.00 0.00 4.17
3391 7427 1.065418 GTCGATGGTTCCCTTGTGGAT 60.065 52.381 0.00 0.00 44.66 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 120 2.433318 GCACTCCGGCTCTCACAC 60.433 66.667 0.00 0.00 0.00 3.82
152 161 1.403687 GGATTCCGCTGCCTCTACCT 61.404 60.000 0.00 0.00 0.00 3.08
155 164 3.129300 CGGATTCCGCTGCCTCTA 58.871 61.111 12.95 0.00 41.17 2.43
262 271 0.980754 ACCACCGATAGCCATCACCA 60.981 55.000 0.00 0.00 0.00 4.17
287 296 0.976641 AGACCGTGCATCCAAGAAGA 59.023 50.000 0.00 0.00 0.00 2.87
323 332 2.223971 GGAAAGGTGAGACAGACAACGA 60.224 50.000 0.00 0.00 0.00 3.85
331 340 1.694150 CCACAGAGGAAAGGTGAGACA 59.306 52.381 0.00 0.00 41.22 3.41
357 366 1.614241 CCGACTGAAACCTCCCCGAT 61.614 60.000 0.00 0.00 0.00 4.18
358 367 2.280552 CCGACTGAAACCTCCCCGA 61.281 63.158 0.00 0.00 0.00 5.14
359 368 2.264794 CCGACTGAAACCTCCCCG 59.735 66.667 0.00 0.00 0.00 5.73
382 393 2.563427 GCGCCAAGAAGAACTGCC 59.437 61.111 0.00 0.00 0.00 4.85
385 396 1.279271 ACATAGGCGCCAAGAAGAACT 59.721 47.619 31.54 6.76 0.00 3.01
421 432 2.345991 CACTACACCACCCCCACG 59.654 66.667 0.00 0.00 0.00 4.94
437 448 5.943416 CCAAGACAAAATACATAGGTCACCA 59.057 40.000 0.00 0.00 0.00 4.17
456 473 0.326595 ACACACACACACACCCAAGA 59.673 50.000 0.00 0.00 0.00 3.02
472 489 0.878416 ACACCACACACAACACACAC 59.122 50.000 0.00 0.00 0.00 3.82
473 490 1.610363 AACACCACACACAACACACA 58.390 45.000 0.00 0.00 0.00 3.72
474 491 2.030717 TGAAACACCACACACAACACAC 60.031 45.455 0.00 0.00 0.00 3.82
475 492 2.030717 GTGAAACACCACACACAACACA 60.031 45.455 0.00 0.00 37.04 3.72
476 493 2.030717 TGTGAAACACCACACACAACAC 60.031 45.455 0.00 0.00 45.67 3.32
477 494 2.230660 TGTGAAACACCACACACAACA 58.769 42.857 0.00 0.00 45.67 3.33
478 495 2.999507 TGTGAAACACCACACACAAC 57.000 45.000 0.00 0.00 45.67 3.32
495 512 3.547746 ACAACCCGTTACAAACTCATGT 58.452 40.909 0.00 0.00 37.32 3.21
512 529 2.888834 AGCACCAACCATCAAACAAC 57.111 45.000 0.00 0.00 0.00 3.32
583 608 2.233271 AGCAAAGTTCACACCAGATGG 58.767 47.619 0.00 0.00 42.17 3.51
620 646 6.045955 GGGAACTGAAAAACATTTGCACTTA 58.954 36.000 0.00 0.00 32.83 2.24
732 758 3.056250 TCAGCTCAAGAATCTCACTGTCC 60.056 47.826 0.00 0.00 0.00 4.02
764 790 4.457257 GGAGACAGCAATGAATATAAGGGC 59.543 45.833 0.00 0.00 0.00 5.19
765 791 5.006386 GGGAGACAGCAATGAATATAAGGG 58.994 45.833 0.00 0.00 0.00 3.95
766 792 5.624159 TGGGAGACAGCAATGAATATAAGG 58.376 41.667 0.00 0.00 0.00 2.69
801 827 1.856629 ATTCCGAACGGAGGGAGTAA 58.143 50.000 15.34 0.34 46.06 2.24
805 831 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
806 832 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
807 833 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
808 834 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
810 836 2.091588 CACGACAAGTAATTCCGAACGG 59.908 50.000 6.94 6.94 0.00 4.44
811 837 2.091588 CCACGACAAGTAATTCCGAACG 59.908 50.000 0.00 0.00 0.00 3.95
812 838 3.319755 TCCACGACAAGTAATTCCGAAC 58.680 45.455 0.00 0.00 0.00 3.95
814 840 3.663995 TTCCACGACAAGTAATTCCGA 57.336 42.857 0.00 0.00 0.00 4.55
815 841 4.939509 ATTTCCACGACAAGTAATTCCG 57.060 40.909 0.00 0.00 0.00 4.30
816 842 8.241367 ACATTTATTTCCACGACAAGTAATTCC 58.759 33.333 0.00 0.00 0.00 3.01
820 846 9.661563 AGATACATTTATTTCCACGACAAGTAA 57.338 29.630 0.00 0.00 0.00 2.24
822 848 9.314321 CTAGATACATTTATTTCCACGACAAGT 57.686 33.333 0.00 0.00 0.00 3.16
823 849 9.529325 TCTAGATACATTTATTTCCACGACAAG 57.471 33.333 0.00 0.00 0.00 3.16
824 850 9.309516 GTCTAGATACATTTATTTCCACGACAA 57.690 33.333 0.00 0.00 0.00 3.18
825 851 7.646526 CGTCTAGATACATTTATTTCCACGACA 59.353 37.037 0.00 0.00 0.00 4.35
826 852 7.646922 ACGTCTAGATACATTTATTTCCACGAC 59.353 37.037 0.00 0.00 0.00 4.34
827 853 7.709947 ACGTCTAGATACATTTATTTCCACGA 58.290 34.615 0.00 0.00 0.00 4.35
828 854 7.925703 ACGTCTAGATACATTTATTTCCACG 57.074 36.000 0.00 0.00 0.00 4.94
829 855 9.962783 AGTACGTCTAGATACATTTATTTCCAC 57.037 33.333 0.00 0.00 0.00 4.02
901 927 8.031277 GCAATACAAGAAAGAACATTCCATTCT 58.969 33.333 5.05 5.05 38.05 2.40
902 928 7.814107 TGCAATACAAGAAAGAACATTCCATTC 59.186 33.333 0.00 1.41 0.00 2.67
903 929 7.669427 TGCAATACAAGAAAGAACATTCCATT 58.331 30.769 0.00 0.00 0.00 3.16
944 970 3.517901 TGGGGTTTGTGATGTAGGAGTAG 59.482 47.826 0.00 0.00 0.00 2.57
949 1553 3.154827 AGTTGGGGTTTGTGATGTAGG 57.845 47.619 0.00 0.00 0.00 3.18
950 1554 7.931578 TTTATAGTTGGGGTTTGTGATGTAG 57.068 36.000 0.00 0.00 0.00 2.74
987 1591 3.009714 GAGGTGGTGAGGGGGTCC 61.010 72.222 0.00 0.00 0.00 4.46
988 1592 2.203938 TGAGGTGGTGAGGGGGTC 60.204 66.667 0.00 0.00 0.00 4.46
989 1593 2.529389 GTGAGGTGGTGAGGGGGT 60.529 66.667 0.00 0.00 0.00 4.95
1021 1629 1.613925 CTCTGGTCGTGTTGGAGAAGA 59.386 52.381 0.00 0.00 0.00 2.87
1034 1670 2.360801 GAGTGAGATGGCTACTCTGGTC 59.639 54.545 11.31 4.07 38.20 4.02
1036 1672 2.382882 TGAGTGAGATGGCTACTCTGG 58.617 52.381 0.00 0.00 41.01 3.86
1037 1673 4.501229 GGAATGAGTGAGATGGCTACTCTG 60.501 50.000 0.00 0.00 41.01 3.35
1038 1674 3.640967 GGAATGAGTGAGATGGCTACTCT 59.359 47.826 0.00 0.00 41.01 3.24
1039 1675 3.640967 AGGAATGAGTGAGATGGCTACTC 59.359 47.826 0.00 0.00 40.85 2.59
1069 1718 0.173481 CGAAGGCACGGAGATGAAGA 59.827 55.000 0.00 0.00 0.00 2.87
1099 1748 2.545946 TCATCTCGCACGATCTACAGAG 59.454 50.000 0.00 0.00 0.00 3.35
1165 1819 0.668706 ATGCGAGTGTGAGTGTGAGC 60.669 55.000 0.00 0.00 0.00 4.26
1171 1825 2.433145 CGGCATGCGAGTGTGAGT 60.433 61.111 12.44 0.00 0.00 3.41
1208 1871 2.046988 TCCACATGTCCAGCTGCG 60.047 61.111 8.66 1.56 0.00 5.18
1248 1941 4.980805 TTGGTGGCGCAGACGTCC 62.981 66.667 13.01 0.00 41.59 4.79
1253 1946 4.329545 GGGTCTTGGTGGCGCAGA 62.330 66.667 10.83 0.00 33.08 4.26
1405 2098 1.040646 GGTGCGTAGAGGATGGATGA 58.959 55.000 0.00 0.00 0.00 2.92
1411 2104 2.758327 TGGCGGTGCGTAGAGGAT 60.758 61.111 0.00 0.00 0.00 3.24
1432 2131 0.686769 GTATCCTCGGTCTGGTGGGT 60.687 60.000 0.00 0.00 0.00 4.51
1455 2154 1.318158 GCGAGAAGAAGTCCCCGGTA 61.318 60.000 0.00 0.00 0.00 4.02
1456 2155 2.647158 GCGAGAAGAAGTCCCCGGT 61.647 63.158 0.00 0.00 0.00 5.28
1587 2304 2.885113 CGAGACATGGACGGCAGA 59.115 61.111 0.00 0.00 0.00 4.26
1780 2569 0.322277 ATGCTCTGCTTCTGGTGGTG 60.322 55.000 0.00 0.00 0.00 4.17
1854 2700 1.525077 CTCGTCCTCCTCCTCCTCG 60.525 68.421 0.00 0.00 0.00 4.63
2024 2888 1.065273 GGAGCGGCTAATTCGTCGA 59.935 57.895 8.29 0.00 32.97 4.20
2160 3024 3.816524 ACGCTCCGCTTCTCCTCG 61.817 66.667 0.00 0.00 0.00 4.63
2177 3044 4.908687 ACGTGAACAGCAGCGGCA 62.909 61.111 12.44 0.00 44.61 5.69
2255 3122 2.279784 CGATGAAGAGCGGCCTCC 60.280 66.667 0.00 0.00 38.96 4.30
2318 3185 2.735762 GCTAGCCCGTGTTGAAGACTAG 60.736 54.545 2.29 0.00 0.00 2.57
2320 3187 0.037232 GCTAGCCCGTGTTGAAGACT 60.037 55.000 2.29 0.00 0.00 3.24
2321 3188 1.352156 CGCTAGCCCGTGTTGAAGAC 61.352 60.000 9.66 0.00 0.00 3.01
2340 3214 8.755696 TTAACATACAAAATTGGCATTCTCAC 57.244 30.769 0.00 0.00 0.00 3.51
2497 6312 4.489771 AGGGCGTGGCATGCTACC 62.490 66.667 28.98 22.40 0.00 3.18
2498 6313 3.204827 CAGGGCGTGGCATGCTAC 61.205 66.667 28.98 23.11 0.00 3.58
2537 6352 9.601217 AATAAAGTGCACTCTATGGTTAGTTAG 57.399 33.333 21.95 0.00 0.00 2.34
2571 6388 9.739276 TGTAAGATGAAGGAAAACATACTTGAT 57.261 29.630 0.00 0.00 0.00 2.57
2642 6460 6.595716 CCTCTTCAAATTTTCGGTCATAGAGT 59.404 38.462 0.00 0.00 0.00 3.24
2653 6471 5.176406 GTGCTGCTTTCCTCTTCAAATTTTC 59.824 40.000 0.00 0.00 0.00 2.29
2716 6534 8.692710 TGAGGTGTTCTAAACAATAGATCGTAT 58.307 33.333 0.00 0.00 44.16 3.06
2718 6536 6.931838 TGAGGTGTTCTAAACAATAGATCGT 58.068 36.000 0.00 0.00 44.16 3.73
2773 6591 0.038526 ACCACGATCGTCACAGGTTC 60.039 55.000 19.84 0.00 0.00 3.62
2779 6599 0.999406 CCAATGACCACGATCGTCAC 59.001 55.000 19.84 12.79 42.75 3.67
2792 6612 1.252215 TACGCCTCGGTGTCCAATGA 61.252 55.000 5.27 0.00 39.72 2.57
2880 6700 4.476846 TCCATGGCATTCCTAAACTCCTAA 59.523 41.667 6.96 0.00 0.00 2.69
2881 6701 4.044308 TCCATGGCATTCCTAAACTCCTA 58.956 43.478 6.96 0.00 0.00 2.94
2883 6703 3.297134 TCCATGGCATTCCTAAACTCC 57.703 47.619 6.96 0.00 0.00 3.85
2946 6766 1.841556 TGTTGAGGGAGGCGAAGGT 60.842 57.895 0.00 0.00 0.00 3.50
3022 6842 2.066999 GGCCCTCTCCCGTCAGATT 61.067 63.158 0.00 0.00 0.00 2.40
3264 7300 1.066002 CAAATGATAGCTGCCCAACCG 59.934 52.381 0.00 0.00 0.00 4.44
3276 7312 4.934356 AGTTTCAAGCCCCTCAAATGATA 58.066 39.130 0.00 0.00 0.00 2.15
3280 7316 3.849527 AGAAGTTTCAAGCCCCTCAAAT 58.150 40.909 0.00 0.00 0.00 2.32
3294 7330 0.035820 TGCCGCCCGATTAGAAGTTT 60.036 50.000 0.00 0.00 0.00 2.66
3301 7337 2.236223 TTACCGTTGCCGCCCGATTA 62.236 55.000 1.45 0.00 0.00 1.75
3306 7342 2.748647 ACATTACCGTTGCCGCCC 60.749 61.111 0.00 0.00 0.00 6.13
3315 7351 1.338674 TGACTTGGGCTGACATTACCG 60.339 52.381 0.00 0.00 0.00 4.02
3319 7355 3.087031 CAATCTGACTTGGGCTGACATT 58.913 45.455 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.