Multiple sequence alignment - TraesCS5A01G534500

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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 TraesCS5A01G534500 chr5A 100.000 3689 0 0 1 3689 691791949 691795637 0.000000e+00 6813.0
1 TraesCS5A01G534500 chr5A 89.141 838 57 20 1 807 675534767 675535601 0.000000e+00 1013.0
2 TraesCS5A01G534500 chr5A 85.730 911 74 23 904 1804 692832889 692832025 0.000000e+00 911.0
3 TraesCS5A01G534500 chr5A 83.082 928 83 45 893 1768 692783311 692782406 0.000000e+00 776.0
4 TraesCS5A01G534500 chr5A 82.394 852 80 48 972 1768 692847703 692846867 0.000000e+00 678.0
5 TraesCS5A01G534500 chr5A 97.695 347 5 3 2864 3209 691735377 691735721 8.820000e-166 593.0
6 TraesCS5A01G534500 chr5A 89.640 444 31 7 2778 3209 691735718 691736158 5.380000e-153 551.0
7 TraesCS5A01G534500 chr5A 84.462 251 33 4 1813 2063 692831980 692831736 3.680000e-60 243.0
8 TraesCS5A01G534500 chr5A 99.065 107 1 0 2086 2192 692830533 692830427 3.760000e-45 193.0
9 TraesCS5A01G534500 chr5A 85.455 165 18 4 1846 2009 692846411 692846252 2.280000e-37 167.0
10 TraesCS5A01G534500 chr5A 96.842 95 2 1 2908 3002 692392469 692392376 1.370000e-34 158.0
11 TraesCS5A01G534500 chr5A 96.591 88 1 2 2778 2863 691736155 691736242 1.070000e-30 145.0
12 TraesCS5A01G534500 chr4B 92.017 927 51 10 888 1805 654089392 654090304 0.000000e+00 1280.0
13 TraesCS5A01G534500 chr4B 88.504 548 60 2 2187 2731 654090894 654091441 0.000000e+00 660.0
14 TraesCS5A01G534500 chr4B 82.727 770 75 33 1054 1768 656262555 656263321 1.870000e-177 632.0
15 TraesCS5A01G534500 chr4B 88.235 442 48 3 2243 2681 656302489 656302929 3.260000e-145 525.0
16 TraesCS5A01G534500 chr4B 88.235 442 48 3 2243 2681 656353905 656354345 3.260000e-145 525.0
17 TraesCS5A01G534500 chr4B 93.009 329 16 6 2911 3236 654091543 654091867 1.200000e-129 473.0
18 TraesCS5A01G534500 chr4B 86.981 361 33 5 1831 2191 654090464 654090810 9.600000e-106 394.0
19 TraesCS5A01G534500 chr4B 85.286 367 35 9 3330 3689 654092217 654092571 9.740000e-96 361.0
20 TraesCS5A01G534500 chr4B 96.842 95 2 1 2907 3001 656304558 656304651 1.370000e-34 158.0
21 TraesCS5A01G534500 chr4B 92.593 54 4 0 2693 2746 135215421 135215368 1.100000e-10 78.7
22 TraesCS5A01G534500 chr2D 89.707 923 67 16 1 895 297179791 297180713 0.000000e+00 1153.0
23 TraesCS5A01G534500 chr2D 88.973 925 72 16 1 896 634076283 634075360 0.000000e+00 1116.0
24 TraesCS5A01G534500 chr2D 95.349 43 2 0 2702 2744 306465278 306465236 6.610000e-08 69.4
25 TraesCS5A01G534500 chr4D 89.621 896 29 9 1972 2863 507480728 507479893 0.000000e+00 1081.0
26 TraesCS5A01G534500 chr4D 86.839 813 84 21 972 1768 507689157 507688352 0.000000e+00 887.0
27 TraesCS5A01G534500 chr4D 94.081 321 15 4 2911 3229 507479910 507479592 5.540000e-133 484.0
28 TraesCS5A01G534500 chr4D 82.425 569 73 21 1056 1611 507716968 507716414 4.310000e-129 472.0
29 TraesCS5A01G534500 chr4D 86.098 410 38 11 971 1368 507675651 507675249 1.220000e-114 424.0
30 TraesCS5A01G534500 chr4D 94.465 271 11 3 898 1167 507484160 507483893 7.370000e-112 414.0
31 TraesCS5A01G534500 chr4D 88.955 335 37 0 2246 2580 507673385 507673051 7.370000e-112 414.0
32 TraesCS5A01G534500 chr4D 87.845 362 25 7 3332 3689 507479427 507479081 1.230000e-109 407.0
33 TraesCS5A01G534500 chr4D 82.265 468 72 9 1045 1502 507724462 507723996 9.600000e-106 394.0
34 TraesCS5A01G534500 chr4D 86.447 273 19 8 1921 2191 507673773 507673517 2.170000e-72 283.0
35 TraesCS5A01G534500 chr4D 95.238 63 3 0 3259 3321 507479533 507479471 2.340000e-17 100.0
36 TraesCS5A01G534500 chrUn 87.634 930 77 22 1 896 77775261 77774336 0.000000e+00 1046.0
37 TraesCS5A01G534500 chrUn 88.009 442 49 3 2243 2681 60659660 60660100 1.520000e-143 520.0
38 TraesCS5A01G534500 chrUn 88.155 439 48 3 2246 2681 231862306 231861869 1.520000e-143 520.0
39 TraesCS5A01G534500 chrUn 87.783 442 50 3 2243 2681 60717146 60717586 7.060000e-142 514.0
40 TraesCS5A01G534500 chrUn 87.783 442 50 3 2243 2681 256882099 256882539 7.060000e-142 514.0
41 TraesCS5A01G534500 chrUn 87.927 439 49 3 2246 2681 329542120 329541683 7.060000e-142 514.0
42 TraesCS5A01G534500 chr3A 87.177 928 84 16 1 894 568244886 568243960 0.000000e+00 1022.0
43 TraesCS5A01G534500 chr1D 85.824 910 110 12 1 904 107544301 107545197 0.000000e+00 948.0
44 TraesCS5A01G534500 chr2A 85.498 924 98 20 1 891 19923645 19922725 0.000000e+00 931.0
45 TraesCS5A01G534500 chr2A 90.083 121 3 7 2905 3021 42482211 42482096 8.250000e-32 148.0
46 TraesCS5A01G534500 chr5B 85.812 881 89 20 1 848 690172091 690171214 0.000000e+00 902.0
47 TraesCS5A01G534500 chr5B 84.008 494 48 15 4 466 344284150 344283657 2.610000e-121 446.0
48 TraesCS5A01G534500 chr7B 84.731 930 102 17 1 892 729232424 729231497 0.000000e+00 894.0
49 TraesCS5A01G534500 chr7B 96.842 95 2 1 2910 3004 480326917 480326824 1.370000e-34 158.0
50 TraesCS5A01G534500 chr7B 97.727 44 1 0 2697 2740 690298233 690298276 3.950000e-10 76.8
51 TraesCS5A01G534500 chr7B 93.617 47 3 0 2694 2740 64133546 64133592 1.840000e-08 71.3
52 TraesCS5A01G534500 chr6B 87.211 649 80 2 248 894 716582237 716582884 0.000000e+00 736.0
53 TraesCS5A01G534500 chr6B 97.727 44 1 0 2697 2740 474189248 474189205 3.950000e-10 76.8
54 TraesCS5A01G534500 chr6A 78.058 556 82 26 1070 1611 133807542 133807013 7.690000e-82 315.0
55 TraesCS5A01G534500 chr6A 96.842 95 1 2 2911 3003 22187290 22187384 1.370000e-34 158.0
56 TraesCS5A01G534500 chr2B 83.478 230 32 1 1234 1457 571924655 571924884 3.730000e-50 209.0
57 TraesCS5A01G534500 chr2B 83.043 230 33 2 1234 1457 789278524 789278753 1.740000e-48 204.0
58 TraesCS5A01G534500 chr2B 76.190 378 62 19 1234 1597 220520560 220520923 1.360000e-39 174.0
59 TraesCS5A01G534500 chr2B 93.750 48 3 0 2697 2744 442308978 442308931 5.110000e-09 73.1
60 TraesCS5A01G534500 chr1A 87.692 65 4 4 2678 2740 432969286 432969348 5.110000e-09 73.1


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 TraesCS5A01G534500 chr5A 691791949 691795637 3688 False 6813.000000 6813 100.000000 1 3689 1 chr5A.!!$F2 3688
1 TraesCS5A01G534500 chr5A 675534767 675535601 834 False 1013.000000 1013 89.141000 1 807 1 chr5A.!!$F1 806
2 TraesCS5A01G534500 chr5A 692782406 692783311 905 True 776.000000 776 83.082000 893 1768 1 chr5A.!!$R2 875
3 TraesCS5A01G534500 chr5A 692830427 692832889 2462 True 449.000000 911 89.752333 904 2192 3 chr5A.!!$R3 1288
4 TraesCS5A01G534500 chr5A 691735377 691736242 865 False 429.666667 593 94.642000 2778 3209 3 chr5A.!!$F3 431
5 TraesCS5A01G534500 chr5A 692846252 692847703 1451 True 422.500000 678 83.924500 972 2009 2 chr5A.!!$R4 1037
6 TraesCS5A01G534500 chr4B 654089392 654092571 3179 False 633.600000 1280 89.159400 888 3689 5 chr4B.!!$F3 2801
7 TraesCS5A01G534500 chr4B 656262555 656263321 766 False 632.000000 632 82.727000 1054 1768 1 chr4B.!!$F1 714
8 TraesCS5A01G534500 chr4B 656302489 656304651 2162 False 341.500000 525 92.538500 2243 3001 2 chr4B.!!$F4 758
9 TraesCS5A01G534500 chr2D 297179791 297180713 922 False 1153.000000 1153 89.707000 1 895 1 chr2D.!!$F1 894
10 TraesCS5A01G534500 chr2D 634075360 634076283 923 True 1116.000000 1116 88.973000 1 896 1 chr2D.!!$R2 895
11 TraesCS5A01G534500 chr4D 507688352 507689157 805 True 887.000000 887 86.839000 972 1768 1 chr4D.!!$R1 796
12 TraesCS5A01G534500 chr4D 507479081 507484160 5079 True 497.200000 1081 92.250000 898 3689 5 chr4D.!!$R4 2791
13 TraesCS5A01G534500 chr4D 507716414 507716968 554 True 472.000000 472 82.425000 1056 1611 1 chr4D.!!$R2 555
14 TraesCS5A01G534500 chr4D 507673051 507675651 2600 True 373.666667 424 87.166667 971 2580 3 chr4D.!!$R5 1609
15 TraesCS5A01G534500 chrUn 77774336 77775261 925 True 1046.000000 1046 87.634000 1 896 1 chrUn.!!$R1 895
16 TraesCS5A01G534500 chr3A 568243960 568244886 926 True 1022.000000 1022 87.177000 1 894 1 chr3A.!!$R1 893
17 TraesCS5A01G534500 chr1D 107544301 107545197 896 False 948.000000 948 85.824000 1 904 1 chr1D.!!$F1 903
18 TraesCS5A01G534500 chr2A 19922725 19923645 920 True 931.000000 931 85.498000 1 891 1 chr2A.!!$R1 890
19 TraesCS5A01G534500 chr5B 690171214 690172091 877 True 902.000000 902 85.812000 1 848 1 chr5B.!!$R2 847
20 TraesCS5A01G534500 chr7B 729231497 729232424 927 True 894.000000 894 84.731000 1 892 1 chr7B.!!$R2 891
21 TraesCS5A01G534500 chr6B 716582237 716582884 647 False 736.000000 736 87.211000 248 894 1 chr6B.!!$F1 646
22 TraesCS5A01G534500 chr6A 133807013 133807542 529 True 315.000000 315 78.058000 1070 1611 1 chr6A.!!$R1 541

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
835 882 0.458260 GCTTTTTGTGTTGGACCCGT 59.542 50.0 0.00 0.0 0.0 5.28 F
1654 5651 0.038526 AGTGGTCGGCGAAGTTACTG 60.039 55.0 12.92 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1951 6771 0.614294 AGTGCTGCTCTGCATCTTCT 59.386 50.0 3.04 0.0 45.23 2.85 R
2891 10597 0.324943 TCCTTGGCCTGCTTAGTCAC 59.675 55.0 3.32 0.0 0.00 3.67 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
111 112 3.628942 CGTTCACCATGATGGATGACAAT 59.371 43.478 20.11 0.00 40.96 2.71
143 144 1.683790 GATGTACACACGCCGACTGC 61.684 60.000 0.00 0.00 0.00 4.40
186 187 4.206375 AGGACAACATGACACAACATTGA 58.794 39.130 0.00 0.00 0.00 2.57
191 192 5.532032 ACAACATGACACAACATTGATCAGA 59.468 36.000 0.00 0.00 33.03 3.27
243 246 7.416777 GGGTATTCCAAGCATAAGAAGGAAAAG 60.417 40.741 0.00 0.00 41.27 2.27
246 249 5.010282 TCCAAGCATAAGAAGGAAAAGGAC 58.990 41.667 0.00 0.00 0.00 3.85
333 369 9.965902 ACAATTAGGAATGAGAACTAAAGATGT 57.034 29.630 0.00 0.00 31.25 3.06
429 465 5.994250 AGTGGCTAGAATTAGAAGATGCAA 58.006 37.500 0.00 0.00 0.00 4.08
518 554 5.477510 GTGGAGCATATTGATGACTAGGAG 58.522 45.833 0.00 0.00 34.73 3.69
525 563 6.933521 GCATATTGATGACTAGGAGTGTTCAT 59.066 38.462 0.00 0.00 34.73 2.57
538 576 6.170506 AGGAGTGTTCATATTTTAACTCGCA 58.829 36.000 0.00 0.00 35.89 5.10
559 597 3.378911 TCTGACGTCAGTGTGCATTTA 57.621 42.857 37.21 17.72 44.12 1.40
641 682 7.235804 ACAATATGTGTTAGGTTAACCCACTT 58.764 34.615 24.19 21.20 37.01 3.16
643 684 7.696992 ATATGTGTTAGGTTAACCCACTTTG 57.303 36.000 24.19 0.00 37.88 2.77
751 792 3.093278 GCGAGAAATGTCCCGCTG 58.907 61.111 4.28 0.00 43.75 5.18
767 808 0.598065 GCTGCAATGGAAAACCGAGT 59.402 50.000 0.00 0.00 0.00 4.18
807 852 3.744940 AGAAAAGGGGAAGATGCATCA 57.255 42.857 27.81 0.00 0.00 3.07
835 882 0.458260 GCTTTTTGTGTTGGACCCGT 59.542 50.000 0.00 0.00 0.00 5.28
848 895 5.413213 TGTTGGACCCGTATGTTGAAAATAG 59.587 40.000 0.00 0.00 0.00 1.73
849 896 5.168647 TGGACCCGTATGTTGAAAATAGT 57.831 39.130 0.00 0.00 0.00 2.12
855 902 7.794041 ACCCGTATGTTGAAAATAGTATGGTA 58.206 34.615 0.00 0.00 0.00 3.25
867 914 8.426569 AAAATAGTATGGTAGATAGCCCGTAA 57.573 34.615 0.00 0.00 0.00 3.18
991 1039 1.386533 AAATGGGCAGCTCGATCAAG 58.613 50.000 0.00 0.00 0.00 3.02
1197 4419 2.584608 GGCACCTGGCTGTACGAT 59.415 61.111 0.00 0.00 44.01 3.73
1199 4421 1.815421 GCACCTGGCTGTACGATGG 60.815 63.158 0.00 0.00 40.25 3.51
1272 4506 2.852075 TCCCTCCGCACCAACCTT 60.852 61.111 0.00 0.00 0.00 3.50
1386 4681 2.678934 TACCTCCAGGCGTTCGCT 60.679 61.111 16.40 0.74 39.32 4.93
1625 5622 2.291465 CCGGTAAGCTAGTATGCACGTA 59.709 50.000 0.00 0.00 34.99 3.57
1642 5639 1.202043 CGTAGTACTGCTCAGTGGTCG 60.202 57.143 12.43 8.09 42.52 4.79
1644 5641 1.446272 GTACTGCTCAGTGGTCGGC 60.446 63.158 12.43 0.00 42.52 5.54
1654 5651 0.038526 AGTGGTCGGCGAAGTTACTG 60.039 55.000 12.92 0.00 0.00 2.74
1669 5667 7.806014 GCGAAGTTACTGGTAAAATTTTCATGA 59.194 33.333 6.72 0.00 0.00 3.07
1768 6095 1.966451 CCAGTTCCACGGCCAAGTC 60.966 63.158 2.24 0.00 0.00 3.01
1782 6468 3.643792 GGCCAAGTCAGTAGTATCATCCT 59.356 47.826 0.00 0.00 0.00 3.24
1783 6469 4.502259 GGCCAAGTCAGTAGTATCATCCTG 60.502 50.000 0.00 0.00 0.00 3.86
1786 6472 6.276847 CCAAGTCAGTAGTATCATCCTGAAC 58.723 44.000 0.00 0.00 35.85 3.18
1787 6473 5.759506 AGTCAGTAGTATCATCCTGAACG 57.240 43.478 0.00 0.00 35.85 3.95
1809 6498 9.419297 GAACGGCCTTAATTTCTTCTTAATTTT 57.581 29.630 0.00 0.00 0.00 1.82
1810 6499 8.757164 ACGGCCTTAATTTCTTCTTAATTTTG 57.243 30.769 0.00 0.00 0.00 2.44
1855 6675 2.902705 TCATATTGGTAGGTCGTGGC 57.097 50.000 0.00 0.00 0.00 5.01
1856 6676 1.414919 TCATATTGGTAGGTCGTGGCC 59.585 52.381 0.00 0.00 0.00 5.36
1892 6712 1.689243 CCAGCGGGATGGACATCTCA 61.689 60.000 12.29 0.00 43.57 3.27
1905 6725 0.178767 CATCTCAAGGGACATCGCCA 59.821 55.000 0.00 0.00 0.00 5.69
2034 6854 3.120199 CCAACTGGTGCTAGAAAATGTCG 60.120 47.826 0.00 0.00 0.00 4.35
2077 8082 4.546674 TCCTCTAATCACATGGAGCTACA 58.453 43.478 0.00 0.00 0.00 2.74
2078 8083 5.150715 TCCTCTAATCACATGGAGCTACAT 58.849 41.667 5.29 5.29 0.00 2.29
2079 8084 5.604231 TCCTCTAATCACATGGAGCTACATT 59.396 40.000 9.33 0.00 0.00 2.71
2080 8085 6.100279 TCCTCTAATCACATGGAGCTACATTT 59.900 38.462 9.33 0.00 0.00 2.32
2081 8086 6.769822 CCTCTAATCACATGGAGCTACATTTT 59.230 38.462 9.33 3.69 0.00 1.82
2196 8318 2.615493 GCACTGCACTGGGTACAAGTAT 60.615 50.000 0.00 0.00 0.00 2.12
2400 8525 0.323999 TTCTGTCGGGGAGGATCGAA 60.324 55.000 0.00 0.00 37.14 3.71
2484 8609 2.391724 GACGCCCCAAGAGGTTCACA 62.392 60.000 0.00 0.00 0.00 3.58
2640 8765 2.758737 GACGAGTGGGACGGGGAT 60.759 66.667 0.00 0.00 34.93 3.85
2668 8793 2.954753 CTGGAACAAGCGCACCGTC 61.955 63.158 11.47 0.79 38.70 4.79
2687 8814 2.950309 GTCATCTCGCCAAGTACCTCTA 59.050 50.000 0.00 0.00 0.00 2.43
2695 8822 4.647853 TCGCCAAGTACCTCTAATGTACAT 59.352 41.667 1.41 1.41 40.79 2.29
2743 8872 3.985019 TTTGTTTACGGAGGGAGCATA 57.015 42.857 0.00 0.00 0.00 3.14
2767 8896 3.526931 TTCTTCGATCTTCTCCGCAAT 57.473 42.857 0.00 0.00 0.00 3.56
2846 10552 6.460123 GCAGAAATAGGACACACAAATATGGG 60.460 42.308 0.00 0.00 35.48 4.00
2848 10554 7.339212 CAGAAATAGGACACACAAATATGGGAA 59.661 37.037 0.00 0.00 32.82 3.97
2849 10555 7.893302 AGAAATAGGACACACAAATATGGGAAA 59.107 33.333 0.00 0.00 32.82 3.13
2850 10556 8.429237 AAATAGGACACACAAATATGGGAAAA 57.571 30.769 0.00 0.00 32.82 2.29
2851 10557 8.429237 AATAGGACACACAAATATGGGAAAAA 57.571 30.769 0.00 0.00 32.82 1.94
2906 10612 2.656947 AAAAGTGACTAAGCAGGCCA 57.343 45.000 5.01 0.00 0.00 5.36
2907 10613 2.656947 AAAGTGACTAAGCAGGCCAA 57.343 45.000 5.01 0.00 0.00 4.52
2908 10614 2.191128 AAGTGACTAAGCAGGCCAAG 57.809 50.000 5.01 0.00 0.00 3.61
3001 10778 2.224305 ACTAGACCACTGGTGCTTTGAC 60.224 50.000 5.10 0.00 36.51 3.18
3117 10894 4.989279 ACATCCTTCAACACATTATGCC 57.011 40.909 0.00 0.00 0.00 4.40
3222 11091 6.291269 GCATTTGTTTTTCACTTCTCTTCGTG 60.291 38.462 0.00 0.00 0.00 4.35
3229 11098 2.766263 TCACTTCTCTTCGTGGCCATAT 59.234 45.455 9.72 0.00 0.00 1.78
3236 11105 3.990092 TCTTCGTGGCCATATACATCAC 58.010 45.455 9.72 0.00 0.00 3.06
3237 11106 3.641436 TCTTCGTGGCCATATACATCACT 59.359 43.478 9.72 0.00 0.00 3.41
3238 11107 4.100963 TCTTCGTGGCCATATACATCACTT 59.899 41.667 9.72 0.00 0.00 3.16
3239 11108 3.990092 TCGTGGCCATATACATCACTTC 58.010 45.455 9.72 0.00 0.00 3.01
3240 11109 3.641436 TCGTGGCCATATACATCACTTCT 59.359 43.478 9.72 0.00 0.00 2.85
3241 11110 3.990469 CGTGGCCATATACATCACTTCTC 59.010 47.826 9.72 0.00 0.00 2.87
3242 11111 4.262207 CGTGGCCATATACATCACTTCTCT 60.262 45.833 9.72 0.00 0.00 3.10
3243 11112 4.993584 GTGGCCATATACATCACTTCTCTG 59.006 45.833 9.72 0.00 0.00 3.35
3244 11113 4.655649 TGGCCATATACATCACTTCTCTGT 59.344 41.667 0.00 0.00 0.00 3.41
3245 11114 5.221521 TGGCCATATACATCACTTCTCTGTC 60.222 44.000 0.00 0.00 0.00 3.51
3246 11115 5.221521 GGCCATATACATCACTTCTCTGTCA 60.222 44.000 0.00 0.00 0.00 3.58
3247 11116 6.283694 GCCATATACATCACTTCTCTGTCAA 58.716 40.000 0.00 0.00 0.00 3.18
3248 11117 6.933521 GCCATATACATCACTTCTCTGTCAAT 59.066 38.462 0.00 0.00 0.00 2.57
3249 11118 7.443575 GCCATATACATCACTTCTCTGTCAATT 59.556 37.037 0.00 0.00 0.00 2.32
3321 11227 1.025041 TCTGTGCTCGCATCGTAGAT 58.975 50.000 0.00 0.00 45.12 1.98
3322 11228 2.218603 TCTGTGCTCGCATCGTAGATA 58.781 47.619 0.00 0.00 45.12 1.98
3323 11229 2.814336 TCTGTGCTCGCATCGTAGATAT 59.186 45.455 0.00 0.00 45.12 1.63
3324 11230 2.913590 CTGTGCTCGCATCGTAGATATG 59.086 50.000 0.00 0.00 45.12 1.78
3325 11231 2.254459 GTGCTCGCATCGTAGATATGG 58.746 52.381 0.00 0.00 45.12 2.74
3326 11232 1.886542 TGCTCGCATCGTAGATATGGT 59.113 47.619 0.00 0.00 45.12 3.55
3329 11235 3.686128 CTCGCATCGTAGATATGGTAGC 58.314 50.000 0.00 0.00 45.12 3.58
3330 11236 3.344515 TCGCATCGTAGATATGGTAGCT 58.655 45.455 0.00 0.00 45.12 3.32
3337 11376 6.063496 TCGTAGATATGGTAGCTATCCTGT 57.937 41.667 0.44 0.00 0.00 4.00
3345 11388 9.409918 GATATGGTAGCTATCCTGTAGACATAA 57.590 37.037 0.44 0.00 0.00 1.90
3354 11397 7.255977 GCTATCCTGTAGACATAATTCTGTCCA 60.256 40.741 17.63 10.29 45.41 4.02
3398 11443 1.419387 AGATAGCTGGTTGAGGATGCC 59.581 52.381 0.00 0.00 0.00 4.40
3449 11494 9.319143 TGTAACAAATTCATTTCGATTTTGGTT 57.681 25.926 11.78 0.00 40.36 3.67
3466 11511 9.803315 GATTTTGGTTCTAGTTTCACTTTTTCT 57.197 29.630 0.00 0.00 0.00 2.52
3525 11570 8.208718 GGCAACTATATACATCACAAAAGTGA 57.791 34.615 0.33 0.33 37.79 3.41
3604 11651 9.730420 ACAATATATAAGACATTTTTGCGAACC 57.270 29.630 0.00 0.00 0.00 3.62
3621 11668 2.969628 ACCAGATCTTGCTTACTCCG 57.030 50.000 0.00 0.00 0.00 4.63
3636 11683 5.629435 GCTTACTCCGTTCAAAATCAAAAGG 59.371 40.000 0.00 0.00 0.00 3.11
3637 11684 4.584327 ACTCCGTTCAAAATCAAAAGGG 57.416 40.909 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.027751 GTCCTCGGCTATGTCGCC 59.972 66.667 0.00 0.00 46.68 5.54
52 53 0.098200 CGAGCTCATCGTGGTCGTTA 59.902 55.000 15.40 0.00 46.62 3.18
111 112 5.449999 CGTGTGTACATCCTGTAGAGCATAA 60.450 44.000 0.00 0.00 32.84 1.90
143 144 1.011333 ACCCACGAACGTTTCAACAG 58.989 50.000 0.46 0.00 0.00 3.16
191 192 9.347240 CCTCTTTTCTACAATATCATGAACCAT 57.653 33.333 0.00 0.00 0.00 3.55
243 246 3.250280 GGAACACCTTTTCTTTCTCGTCC 59.750 47.826 0.00 0.00 0.00 4.79
246 249 4.574828 TCTTGGAACACCTTTTCTTTCTCG 59.425 41.667 0.00 0.00 39.29 4.04
333 369 7.683578 TCATCTTCTTCTTTCTCATTCCTTGA 58.316 34.615 0.00 0.00 0.00 3.02
429 465 3.768878 TCTTCTCTTTCTCGTCCTTCCT 58.231 45.455 0.00 0.00 0.00 3.36
490 526 2.037641 TCATCAATATGCTCCACCTCCG 59.962 50.000 0.00 0.00 32.76 4.63
518 554 7.636359 GTCAGATGCGAGTTAAAATATGAACAC 59.364 37.037 0.00 0.00 0.00 3.32
525 563 5.404096 TGACGTCAGATGCGAGTTAAAATA 58.596 37.500 15.76 0.00 0.00 1.40
538 576 2.462456 AATGCACACTGACGTCAGAT 57.538 45.000 43.55 30.14 46.59 2.90
559 597 5.200483 TCTCAAAGGTCCATTCAACTTTGT 58.800 37.500 13.59 0.00 45.97 2.83
751 792 0.243636 CCCACTCGGTTTTCCATTGC 59.756 55.000 0.00 0.00 40.70 3.56
767 808 1.368374 ATCGAAACCTTCCCTTCCCA 58.632 50.000 0.00 0.00 0.00 4.37
807 852 3.007182 CCAACACAAAAAGCTCATCCCAT 59.993 43.478 0.00 0.00 0.00 4.00
815 860 0.744281 CGGGTCCAACACAAAAAGCT 59.256 50.000 0.00 0.00 0.00 3.74
817 862 3.316868 ACATACGGGTCCAACACAAAAAG 59.683 43.478 0.00 0.00 0.00 2.27
848 895 5.225642 GTTGTTACGGGCTATCTACCATAC 58.774 45.833 0.00 0.00 0.00 2.39
849 896 4.022935 CGTTGTTACGGGCTATCTACCATA 60.023 45.833 0.00 0.00 43.94 2.74
867 914 1.296056 GCAGAATACCCGTGCGTTGT 61.296 55.000 0.00 0.00 0.00 3.32
923 971 1.068954 CCGCCTCTTTGTTTTCAGAGC 60.069 52.381 0.00 0.00 32.85 4.09
991 1039 0.242017 GCTTTGTCCATGTGGAGCAC 59.758 55.000 1.07 0.00 46.49 4.40
1386 4681 4.426971 TGGAGATCGAACCACCGA 57.573 55.556 5.46 0.00 43.16 4.69
1390 4685 3.014085 GCCCGTGGAGATCGAACCA 62.014 63.158 5.46 5.46 0.00 3.67
1466 5045 1.579932 CTCCTGCAGTACGACACGT 59.420 57.895 13.81 1.91 44.35 4.49
1510 5304 2.125350 CTCCTCCTGCAGTTCGCC 60.125 66.667 13.81 0.00 41.33 5.54
1511 5305 2.125350 CCTCCTCCTGCAGTTCGC 60.125 66.667 13.81 0.00 42.89 4.70
1512 5306 1.515020 CTCCTCCTCCTGCAGTTCG 59.485 63.158 13.81 0.00 0.00 3.95
1518 5312 2.364842 TGCTCCTCCTCCTCCTGC 60.365 66.667 0.00 0.00 0.00 4.85
1601 5564 0.031721 GCATACTAGCTTACCGGCGT 59.968 55.000 6.01 0.00 37.29 5.68
1625 5622 1.878656 GCCGACCACTGAGCAGTACT 61.879 60.000 2.36 0.00 40.20 2.73
1642 5639 6.440436 TGAAAATTTTACCAGTAACTTCGCC 58.560 36.000 2.75 0.00 0.00 5.54
1644 5641 9.113876 GTCATGAAAATTTTACCAGTAACTTCG 57.886 33.333 2.75 0.00 0.00 3.79
1654 5651 5.285798 TCGACCGTCATGAAAATTTTACC 57.714 39.130 2.75 0.00 0.00 2.85
1669 5667 0.744874 ATCGTTCATGGATCGACCGT 59.255 50.000 9.16 0.00 42.61 4.83
1782 6468 7.696992 ATTAAGAAGAAATTAAGGCCGTTCA 57.303 32.000 0.00 0.00 0.00 3.18
1783 6469 8.981724 AAATTAAGAAGAAATTAAGGCCGTTC 57.018 30.769 0.00 0.00 0.00 3.95
1786 6472 8.647226 CACAAAATTAAGAAGAAATTAAGGCCG 58.353 33.333 0.00 0.00 0.00 6.13
1787 6473 9.705290 TCACAAAATTAAGAAGAAATTAAGGCC 57.295 29.630 0.00 0.00 0.00 5.19
1809 6498 3.382855 GCATGTTGCAAAGTTCATCACA 58.617 40.909 0.00 0.00 44.26 3.58
1838 6563 1.502690 TGGCCACGACCTACCAATAT 58.497 50.000 0.00 0.00 0.00 1.28
1842 6567 1.502690 ATTATGGCCACGACCTACCA 58.497 50.000 8.16 0.00 36.43 3.25
1844 6569 2.895404 TCCTATTATGGCCACGACCTAC 59.105 50.000 8.16 0.00 0.00 3.18
1855 6675 4.589908 GCTGGGGTTGTATCCTATTATGG 58.410 47.826 0.00 0.00 0.00 2.74
1856 6676 4.253685 CGCTGGGGTTGTATCCTATTATG 58.746 47.826 0.00 0.00 0.00 1.90
1892 6712 3.706373 ACGCTGGCGATGTCCCTT 61.706 61.111 21.77 0.00 42.83 3.95
1905 6725 4.021925 GACCTCCTTGGCCACGCT 62.022 66.667 3.88 0.00 40.22 5.07
1951 6771 0.614294 AGTGCTGCTCTGCATCTTCT 59.386 50.000 3.04 0.00 45.23 2.85
1952 6772 0.727970 CAGTGCTGCTCTGCATCTTC 59.272 55.000 17.48 0.00 45.23 2.87
1953 6773 2.855887 CAGTGCTGCTCTGCATCTT 58.144 52.632 17.48 0.00 45.23 2.40
2034 6854 1.300233 GGATCTGGGCGTGATCGAC 60.300 63.158 10.69 0.00 45.48 4.20
2048 6868 6.119240 TCCATGTGATTAGAGGATTGGATC 57.881 41.667 0.00 0.00 0.00 3.36
2407 8532 1.958205 GCATCATCTCCTTCGGCGG 60.958 63.158 7.21 0.00 0.00 6.13
2413 8538 1.134580 CACGTCCTGCATCATCTCCTT 60.135 52.381 0.00 0.00 0.00 3.36
2484 8609 2.434884 CTTGCGCCGAGGTCATGT 60.435 61.111 4.18 0.00 0.00 3.21
2503 8628 4.392921 ACCAATCCTCATACTCGAACAG 57.607 45.455 0.00 0.00 0.00 3.16
2616 8741 1.378882 CGTCCCACTCGTCCCGATAA 61.379 60.000 0.00 0.00 34.61 1.75
2636 8761 2.757099 CCAGCAGTTGGGCATCCC 60.757 66.667 0.00 0.00 43.75 3.85
2668 8793 4.202161 ACATTAGAGGTACTTGGCGAGATG 60.202 45.833 9.20 1.62 41.55 2.90
2695 8822 9.982651 ATAAGAGCGCTTAGATCACTATTTTAA 57.017 29.630 13.26 0.00 39.79 1.52
2743 8872 3.068732 TGCGGAGAAGATCGAAGAATCAT 59.931 43.478 0.00 0.00 43.58 2.45
2886 10592 2.944129 TGGCCTGCTTAGTCACTTTTT 58.056 42.857 3.32 0.00 0.00 1.94
2887 10593 2.656947 TGGCCTGCTTAGTCACTTTT 57.343 45.000 3.32 0.00 0.00 2.27
2888 10594 2.508526 CTTGGCCTGCTTAGTCACTTT 58.491 47.619 3.32 0.00 0.00 2.66
2889 10595 1.271597 CCTTGGCCTGCTTAGTCACTT 60.272 52.381 3.32 0.00 0.00 3.16
2890 10596 0.326264 CCTTGGCCTGCTTAGTCACT 59.674 55.000 3.32 0.00 0.00 3.41
2891 10597 0.324943 TCCTTGGCCTGCTTAGTCAC 59.675 55.000 3.32 0.00 0.00 3.67
2892 10598 1.064003 TTCCTTGGCCTGCTTAGTCA 58.936 50.000 3.32 0.00 0.00 3.41
2893 10599 2.200373 TTTCCTTGGCCTGCTTAGTC 57.800 50.000 3.32 0.00 0.00 2.59
2894 10600 2.675658 TTTTCCTTGGCCTGCTTAGT 57.324 45.000 3.32 0.00 0.00 2.24
3001 10778 6.258160 GTGGGATGTTCAAATAAATCACTCG 58.742 40.000 0.00 0.00 0.00 4.18
3117 10894 3.127721 GGATCCTTTTCTTCTTTCTGGCG 59.872 47.826 3.84 0.00 0.00 5.69
3222 11091 5.220710 ACAGAGAAGTGATGTATATGGCC 57.779 43.478 0.00 0.00 0.00 5.36
3229 11098 9.554395 TTTTGTAATTGACAGAGAAGTGATGTA 57.446 29.630 0.00 0.00 39.88 2.29
3236 11105 9.844790 TGCATAATTTTGTAATTGACAGAGAAG 57.155 29.630 0.00 0.00 39.88 2.85
3241 11110 9.467258 CCCTATGCATAATTTTGTAATTGACAG 57.533 33.333 8.00 0.00 39.88 3.51
3242 11111 9.194972 TCCCTATGCATAATTTTGTAATTGACA 57.805 29.630 8.00 0.00 35.61 3.58
3243 11112 9.463443 GTCCCTATGCATAATTTTGTAATTGAC 57.537 33.333 8.00 0.00 35.61 3.18
3244 11113 9.194972 TGTCCCTATGCATAATTTTGTAATTGA 57.805 29.630 8.00 0.00 35.61 2.57
3245 11114 9.467258 CTGTCCCTATGCATAATTTTGTAATTG 57.533 33.333 8.00 0.00 35.61 2.32
3246 11115 9.420118 TCTGTCCCTATGCATAATTTTGTAATT 57.580 29.630 8.00 0.00 37.68 1.40
3247 11116 8.995027 TCTGTCCCTATGCATAATTTTGTAAT 57.005 30.769 8.00 0.00 0.00 1.89
3248 11117 8.815565 TTCTGTCCCTATGCATAATTTTGTAA 57.184 30.769 8.00 0.00 0.00 2.41
3249 11118 8.271458 TCTTCTGTCCCTATGCATAATTTTGTA 58.729 33.333 8.00 0.00 0.00 2.41
3251 11120 7.572523 TCTTCTGTCCCTATGCATAATTTTG 57.427 36.000 8.00 0.00 0.00 2.44
3252 11121 8.593945 TTTCTTCTGTCCCTATGCATAATTTT 57.406 30.769 8.00 0.00 0.00 1.82
3253 11122 8.470002 GTTTTCTTCTGTCCCTATGCATAATTT 58.530 33.333 8.00 0.00 0.00 1.82
3321 11227 9.769677 AATTATGTCTACAGGATAGCTACCATA 57.230 33.333 12.89 5.97 0.00 2.74
3322 11228 8.671987 AATTATGTCTACAGGATAGCTACCAT 57.328 34.615 12.89 0.00 0.00 3.55
3323 11229 7.950684 AGAATTATGTCTACAGGATAGCTACCA 59.049 37.037 12.89 0.00 0.00 3.25
3324 11230 8.247562 CAGAATTATGTCTACAGGATAGCTACC 58.752 40.741 0.00 0.00 0.00 3.18
3325 11231 8.798402 ACAGAATTATGTCTACAGGATAGCTAC 58.202 37.037 0.00 0.00 0.00 3.58
3326 11232 8.941995 ACAGAATTATGTCTACAGGATAGCTA 57.058 34.615 0.00 0.00 0.00 3.32
3354 11397 1.978580 GAATCTATGTCCCCCATCCGT 59.021 52.381 0.00 0.00 34.86 4.69
3365 11408 4.830046 ACCAGCTATCTGTCGAATCTATGT 59.170 41.667 0.00 0.00 38.66 2.29
3398 11443 1.801771 CAAGCATTGCACCCATGTTTG 59.198 47.619 11.91 10.71 40.39 2.93
3431 11476 9.626045 GAAACTAGAACCAAAATCGAAATGAAT 57.374 29.630 0.00 0.00 0.00 2.57
3486 11531 9.783256 GTATATAGTTGCCTTCGTTTTTCATTT 57.217 29.630 0.00 0.00 0.00 2.32
3491 11536 8.395633 GTGATGTATATAGTTGCCTTCGTTTTT 58.604 33.333 0.00 0.00 0.00 1.94
3495 11540 6.156748 TGTGATGTATATAGTTGCCTTCGT 57.843 37.500 0.00 0.00 0.00 3.85
3497 11542 8.893727 ACTTTTGTGATGTATATAGTTGCCTTC 58.106 33.333 0.00 0.00 0.00 3.46
3588 11635 4.074970 AGATCTGGTTCGCAAAAATGTCT 58.925 39.130 0.00 0.00 0.00 3.41
3590 11637 4.549458 CAAGATCTGGTTCGCAAAAATGT 58.451 39.130 0.00 0.00 0.00 2.71
3594 11641 2.229792 AGCAAGATCTGGTTCGCAAAA 58.770 42.857 0.00 0.00 28.96 2.44
3604 11651 3.849911 TGAACGGAGTAAGCAAGATCTG 58.150 45.455 0.00 0.00 45.00 2.90
3621 11668 7.784633 TGTTCAATCCCTTTTGATTTTGAAC 57.215 32.000 15.67 15.67 40.08 3.18
3636 11683 9.638239 TTATTTCTATTGCTGTTTGTTCAATCC 57.362 29.630 0.00 0.00 33.13 3.01


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

AutoCloner maintained by Alex Coulton.