Multiple sequence alignment - TraesCS3A01G309000

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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 TraesCS3A01G309000 chr3A 100.000 2890 0 0 1 2890 547235954 547233065 0.000000e+00 5337.0
1 TraesCS3A01G309000 chr3A 95.288 1231 31 9 915 2120 547254627 547255855 0.000000e+00 1927.0
2 TraesCS3A01G309000 chr3A 84.177 158 13 6 746 892 547254480 547254636 3.000000e-30 143.0
3 TraesCS3A01G309000 chr3B 89.901 2218 98 55 1 2148 144068827 144070988 0.000000e+00 2739.0
4 TraesCS3A01G309000 chr3B 90.452 1571 58 45 646 2151 144058527 144056984 0.000000e+00 1986.0
5 TraesCS3A01G309000 chr3B 94.600 463 20 3 2165 2627 23380639 23380182 0.000000e+00 712.0
6 TraesCS3A01G309000 chr3B 89.655 377 33 4 2165 2541 187556789 187557159 2.610000e-130 475.0
7 TraesCS3A01G309000 chr3B 91.549 284 23 1 2607 2890 187557256 187557538 9.710000e-105 390.0
8 TraesCS3A01G309000 chr3B 87.745 204 8 10 1934 2120 144074600 144074803 3.750000e-54 222.0
9 TraesCS3A01G309000 chr3B 97.015 67 2 0 2824 2890 23380129 23380063 2.350000e-21 113.0
10 TraesCS3A01G309000 chr3B 96.667 60 1 1 2572 2630 23380183 23380124 6.590000e-17 99.0
11 TraesCS3A01G309000 chr3D 89.742 1472 68 43 646 2074 92750972 92749541 0.000000e+00 1805.0
12 TraesCS3A01G309000 chr3D 91.736 1210 45 25 916 2073 92783246 92784452 0.000000e+00 1629.0
13 TraesCS3A01G309000 chr3D 93.005 386 22 4 1 383 92781385 92781768 2.520000e-155 558.0
14 TraesCS3A01G309000 chr3D 82.800 250 35 7 2165 2413 204745259 204745501 1.740000e-52 217.0
15 TraesCS3A01G309000 chr3D 89.583 144 11 4 653 795 92781794 92781934 2.290000e-41 180.0
16 TraesCS3A01G309000 chr3D 92.929 99 3 2 2069 2167 92787394 92787488 1.080000e-29 141.0
17 TraesCS3A01G309000 chr3D 90.526 95 4 2 2071 2165 92749299 92749210 1.410000e-23 121.0
18 TraesCS3A01G309000 chr3D 97.059 34 1 0 264 297 92781022 92781055 1.120000e-04 58.4
19 TraesCS3A01G309000 chr4B 92.151 1274 51 24 837 2090 50443145 50444389 0.000000e+00 1753.0
20 TraesCS3A01G309000 chr4B 90.600 1351 66 38 837 2167 50400485 50399176 0.000000e+00 1735.0
21 TraesCS3A01G309000 chr4B 88.599 307 26 1 1 307 50402202 50401905 5.890000e-97 364.0
22 TraesCS3A01G309000 chr4B 89.573 211 9 6 646 849 50442833 50443037 3.700000e-64 255.0
23 TraesCS3A01G309000 chr4B 89.796 147 10 3 646 788 50400817 50400672 1.770000e-42 183.0
24 TraesCS3A01G309000 chr4B 100.000 39 0 0 2130 2168 50453593 50453631 3.990000e-09 73.1
25 TraesCS3A01G309000 chr4B 87.500 56 2 1 794 849 50400643 50400593 3.110000e-05 60.2
26 TraesCS3A01G309000 chr4B 97.059 34 1 0 264 297 50402482 50402449 1.120000e-04 58.4
27 TraesCS3A01G309000 chr7B 96.976 463 10 2 2165 2627 446671574 446672032 0.000000e+00 774.0
28 TraesCS3A01G309000 chr7B 99.060 319 3 0 2572 2890 446672031 446672349 8.980000e-160 573.0
29 TraesCS3A01G309000 chr7B 96.970 33 1 0 2574 2606 446672066 446672098 4.020000e-04 56.5
30 TraesCS3A01G309000 chr2A 93.856 472 22 4 2160 2630 54205642 54205177 0.000000e+00 704.0
31 TraesCS3A01G309000 chr2A 97.015 67 2 0 2824 2890 54205182 54205116 2.350000e-21 113.0
32 TraesCS3A01G309000 chr6A 93.978 465 23 3 2163 2627 2867225 2866766 0.000000e+00 699.0
33 TraesCS3A01G309000 chr5A 93.952 463 23 3 2165 2627 632240317 632240774 0.000000e+00 695.0
34 TraesCS3A01G309000 chr5A 97.015 67 2 0 2824 2890 632240881 632240947 2.350000e-21 113.0
35 TraesCS3A01G309000 chr5A 95.000 60 2 1 2572 2630 632240827 632240886 3.070000e-15 93.5
36 TraesCS3A01G309000 chr2B 91.135 282 25 0 2609 2890 51191008 51191289 1.620000e-102 383.0
37 TraesCS3A01G309000 chr5B 80.973 473 79 7 1397 1868 588156413 588155951 5.890000e-97 364.0
38 TraesCS3A01G309000 chr5D 80.127 473 83 7 1397 1868 480154987 480154525 2.760000e-90 342.0
39 TraesCS3A01G309000 chr1B 80.882 136 25 1 993 1128 101591803 101591669 3.940000e-19 106.0
40 TraesCS3A01G309000 chr1B 87.952 83 10 0 2609 2691 628627306 628627388 6.590000e-17 99.0
41 TraesCS3A01G309000 chr1D 80.451 133 25 1 997 1128 63543578 63543710 1.830000e-17 100.0


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 TraesCS3A01G309000 chr3A 547233065 547235954 2889 True 5337.000000 5337 100.000000 1 2890 1 chr3A.!!$R1 2889
1 TraesCS3A01G309000 chr3A 547254480 547255855 1375 False 1035.000000 1927 89.732500 746 2120 2 chr3A.!!$F1 1374
2 TraesCS3A01G309000 chr3B 144056984 144058527 1543 True 1986.000000 1986 90.452000 646 2151 1 chr3B.!!$R1 1505
3 TraesCS3A01G309000 chr3B 144068827 144074803 5976 False 1480.500000 2739 88.823000 1 2148 2 chr3B.!!$F1 2147
4 TraesCS3A01G309000 chr3B 187556789 187557538 749 False 432.500000 475 90.602000 2165 2890 2 chr3B.!!$F2 725
5 TraesCS3A01G309000 chr3B 23380063 23380639 576 True 308.000000 712 96.094000 2165 2890 3 chr3B.!!$R2 725
6 TraesCS3A01G309000 chr3D 92749210 92750972 1762 True 963.000000 1805 90.134000 646 2165 2 chr3D.!!$R1 1519
7 TraesCS3A01G309000 chr3D 92781022 92787488 6466 False 513.280000 1629 92.862400 1 2167 5 chr3D.!!$F2 2166
8 TraesCS3A01G309000 chr4B 50442833 50444389 1556 False 1004.000000 1753 90.862000 646 2090 2 chr4B.!!$F2 1444
9 TraesCS3A01G309000 chr4B 50399176 50402482 3306 True 480.120000 1735 90.710800 1 2167 5 chr4B.!!$R1 2166
10 TraesCS3A01G309000 chr7B 446671574 446672349 775 False 467.833333 774 97.668667 2165 2890 3 chr7B.!!$F1 725
11 TraesCS3A01G309000 chr2A 54205116 54205642 526 True 408.500000 704 95.435500 2160 2890 2 chr2A.!!$R1 730
12 TraesCS3A01G309000 chr5A 632240317 632240947 630 False 300.500000 695 95.322333 2165 2890 3 chr5A.!!$F1 725

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
899 3292 0.167908 CCACACACACACACACACAC 59.832 55.0 0.0 0.0 0.0 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2685 8240 0.033228 CTGGGGAGAATAGAGCGCAG 59.967 60.0 11.47 0.0 0.0 5.18 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
32 398 3.390135 CCTTAGTGTTTTCGAGACAGCA 58.610 45.455 4.19 0.00 0.00 4.41
48 414 1.509923 GCAAGAGGGCACATTGCTC 59.490 57.895 18.60 0.00 46.33 4.26
88 454 5.620206 TCTCAAGCCTCAAATAAGTTGTGA 58.380 37.500 0.00 0.00 38.47 3.58
125 491 1.425267 CGCGTTGGAATATCGTGGCA 61.425 55.000 0.00 0.00 0.00 4.92
151 517 2.034053 AGAGCTAGCGAAGAATCTTCCG 59.966 50.000 16.49 12.51 0.00 4.30
152 518 0.855995 GCTAGCGAAGAATCTTCCGC 59.144 55.000 22.57 22.57 47.00 5.54
266 632 3.181510 CGCCTACCACTTGCTAAATCAAC 60.182 47.826 0.00 0.00 0.00 3.18
325 691 8.439993 TGATTTACAGTGTTTTGCTACAGTAA 57.560 30.769 0.00 0.00 30.69 2.24
362 730 9.682465 TCTTCATTTTAGACTAGCTGACTACTA 57.318 33.333 0.00 0.00 0.00 1.82
383 751 5.965091 ACTATAGCTTACCTGACTTCCCTTT 59.035 40.000 0.00 0.00 0.00 3.11
406 774 2.159085 CCACGTTAGAGGATCCAGTTCC 60.159 54.545 15.82 0.00 33.66 3.62
410 778 1.776662 TAGAGGATCCAGTTCCGGTG 58.223 55.000 15.82 0.00 40.94 4.94
419 1247 0.602905 CAGTTCCGGTGTTGAGACCC 60.603 60.000 0.00 0.00 31.57 4.46
436 1264 4.570663 CCGACGATGGGAGGCGAC 62.571 72.222 0.00 0.00 0.00 5.19
479 1307 8.547894 CGATCGATGTGGAGTAATTTGAATTTA 58.452 33.333 10.26 0.00 0.00 1.40
560 1388 6.642707 AATTGGTTCCGTGATCTACAAAAA 57.357 33.333 0.00 0.00 0.00 1.94
565 1393 6.084277 GGTTCCGTGATCTACAAAAATGAAC 58.916 40.000 0.00 0.00 0.00 3.18
579 1407 3.889520 AATGAACGGAGGGAGTAGTTC 57.110 47.619 0.77 0.77 42.19 3.01
586 1414 3.245336 ACGGAGGGAGTAGTTCTTTCTCT 60.245 47.826 0.00 0.00 0.00 3.10
695 1815 7.690952 AGATGATTACTTACTCTATCCGGTC 57.309 40.000 0.00 0.00 0.00 4.79
892 3285 0.689412 TCTCCTCCCACACACACACA 60.689 55.000 0.00 0.00 0.00 3.72
894 3287 1.223211 CCTCCCACACACACACACA 59.777 57.895 0.00 0.00 0.00 3.72
895 3288 1.095228 CCTCCCACACACACACACAC 61.095 60.000 0.00 0.00 0.00 3.82
896 3289 0.392327 CTCCCACACACACACACACA 60.392 55.000 0.00 0.00 0.00 3.72
897 3290 0.675208 TCCCACACACACACACACAC 60.675 55.000 0.00 0.00 0.00 3.82
898 3291 0.957888 CCCACACACACACACACACA 60.958 55.000 0.00 0.00 0.00 3.72
899 3292 0.167908 CCACACACACACACACACAC 59.832 55.000 0.00 0.00 0.00 3.82
900 3293 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
901 3294 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
902 3295 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
903 3296 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
904 3297 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
905 3298 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
906 3299 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
907 3300 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
908 3301 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
909 3302 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
910 3303 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
911 3304 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
912 3305 1.155889 CACACACACACACACACACT 58.844 50.000 0.00 0.00 0.00 3.55
913 3306 1.136000 CACACACACACACACACACTG 60.136 52.381 0.00 0.00 0.00 3.66
914 3307 1.270571 ACACACACACACACACACTGA 60.271 47.619 0.00 0.00 0.00 3.41
915 3308 1.128507 CACACACACACACACACTGAC 59.871 52.381 0.00 0.00 0.00 3.51
916 3309 1.270571 ACACACACACACACACTGACA 60.271 47.619 0.00 0.00 0.00 3.58
917 3310 1.128507 CACACACACACACACTGACAC 59.871 52.381 0.00 0.00 0.00 3.67
918 3311 1.270571 ACACACACACACACTGACACA 60.271 47.619 0.00 0.00 0.00 3.72
919 3312 1.128507 CACACACACACACTGACACAC 59.871 52.381 0.00 0.00 0.00 3.82
920 3313 1.270571 ACACACACACACTGACACACA 60.271 47.619 0.00 0.00 0.00 3.72
921 3314 1.128507 CACACACACACTGACACACAC 59.871 52.381 0.00 0.00 0.00 3.82
922 3315 1.270571 ACACACACACTGACACACACA 60.271 47.619 0.00 0.00 0.00 3.72
923 3316 1.128507 CACACACACTGACACACACAC 59.871 52.381 0.00 0.00 0.00 3.82
924 3317 1.270571 ACACACACTGACACACACACA 60.271 47.619 0.00 0.00 0.00 3.72
925 3318 1.128507 CACACACTGACACACACACAC 59.871 52.381 0.00 0.00 0.00 3.82
926 3319 0.369931 CACACTGACACACACACACG 59.630 55.000 0.00 0.00 0.00 4.49
927 3320 1.348250 CACTGACACACACACACGC 59.652 57.895 0.00 0.00 0.00 5.34
928 3321 1.079474 ACTGACACACACACACGCA 60.079 52.632 0.00 0.00 0.00 5.24
929 3322 1.348250 CTGACACACACACACGCAC 59.652 57.895 0.00 0.00 0.00 5.34
930 3323 1.357991 CTGACACACACACACGCACA 61.358 55.000 0.00 0.00 0.00 4.57
931 3324 1.060308 GACACACACACACGCACAC 59.940 57.895 0.00 0.00 0.00 3.82
933 3326 3.860125 ACACACACACGCACACGC 61.860 61.111 0.00 0.00 45.53 5.34
934 3327 3.563088 CACACACACGCACACGCT 61.563 61.111 0.00 0.00 45.53 5.07
935 3328 2.105328 ACACACACGCACACGCTA 59.895 55.556 0.00 0.00 45.53 4.26
984 3395 2.623416 CCTGTAGAGCATCCATCACGTA 59.377 50.000 0.00 0.00 33.66 3.57
985 3396 3.551046 CCTGTAGAGCATCCATCACGTAC 60.551 52.174 0.00 0.00 33.66 3.67
1026 3438 1.303317 GGTGAAGGTGTTCGGGCAT 60.303 57.895 0.00 0.00 35.17 4.40
1129 3541 4.379243 CCGGCGAGCACAAGAGGT 62.379 66.667 9.30 0.00 0.00 3.85
1245 3658 0.951558 TTTCTTCCTTGCAGCCGTTC 59.048 50.000 0.00 0.00 0.00 3.95
1494 3928 3.060003 CAGCGGAATCGAAGAATTAGCAG 60.060 47.826 0.00 0.00 43.58 4.24
1894 4328 1.405821 AGGTGCGCAGTACTAGATGTC 59.594 52.381 12.22 0.00 44.37 3.06
1956 4415 0.323908 AGAGAAGAGACCTCCCGTGG 60.324 60.000 0.00 0.00 0.00 4.94
1957 4416 1.950973 GAGAAGAGACCTCCCGTGGC 61.951 65.000 0.00 0.00 0.00 5.01
1993 4462 3.748083 TGCCCGTCTAGTTCGAGTATAT 58.252 45.455 10.52 0.00 0.00 0.86
2012 4481 0.308684 TGCTTTCAGTTTCAGCAGCG 59.691 50.000 0.00 0.00 38.65 5.18
2014 4483 0.308684 CTTTCAGTTTCAGCAGCGCA 59.691 50.000 11.47 0.00 0.00 6.09
2019 4490 0.819259 AGTTTCAGCAGCGCAAGGAA 60.819 50.000 11.47 4.84 38.28 3.36
2113 7542 3.181455 TGGTCAATGCTGCTAATCCGTAT 60.181 43.478 0.00 0.00 0.00 3.06
2127 7561 9.334947 TGCTAATCCGTATGTCCTATATAGTAC 57.665 37.037 8.92 3.83 0.00 2.73
2128 7562 9.558396 GCTAATCCGTATGTCCTATATAGTACT 57.442 37.037 8.92 0.00 0.00 2.73
2245 7681 7.962964 TTTACTATCCTTGTTTGAGTGACAG 57.037 36.000 0.00 0.00 0.00 3.51
2321 7757 3.011818 TGTTCTAGCACGTCCGAATCTA 58.988 45.455 0.00 0.00 0.00 1.98
2374 7810 6.591834 GTGTCAGTTGACTGCTATTCAATAGT 59.408 38.462 12.97 0.00 44.99 2.12
2375 7811 7.759886 GTGTCAGTTGACTGCTATTCAATAGTA 59.240 37.037 12.97 0.57 44.99 1.82
2376 7812 7.976175 TGTCAGTTGACTGCTATTCAATAGTAG 59.024 37.037 18.23 18.23 46.82 2.57
2382 7818 6.268617 TGACTGCTATTCAATAGTAGATGGCT 59.731 38.462 24.66 6.01 45.07 4.75
2503 7939 1.423845 CAACCCAGCAATACGTCGC 59.576 57.895 0.00 0.00 0.00 5.19
2576 8131 2.659897 GCTGCGTCCTATCCTGCG 60.660 66.667 0.00 0.00 0.00 5.18
2634 8189 3.461773 GTCGCTGGCCAGGCTCTA 61.462 66.667 33.46 6.94 0.00 2.43
2635 8190 3.150335 TCGCTGGCCAGGCTCTAG 61.150 66.667 33.46 8.32 0.00 2.43
2636 8191 4.906792 CGCTGGCCAGGCTCTAGC 62.907 72.222 33.46 17.47 41.14 3.42
2638 8193 4.232878 CTGGCCAGGCTCTAGCGG 62.233 72.222 26.14 0.00 43.26 5.52
2642 8197 4.232878 CCAGGCTCTAGCGGCAGG 62.233 72.222 9.14 6.18 43.26 4.85
2643 8198 4.906792 CAGGCTCTAGCGGCAGGC 62.907 72.222 9.14 3.24 43.26 4.85
2646 8201 4.168291 GCTCTAGCGGCAGGCCTT 62.168 66.667 0.00 0.00 45.17 4.35
2648 8203 3.453070 CTCTAGCGGCAGGCCTTCC 62.453 68.421 12.07 12.07 45.17 3.46
2653 8208 2.983592 CGGCAGGCCTTCCGTTTT 60.984 61.111 32.63 0.00 40.72 2.43
2657 8212 1.587043 GCAGGCCTTCCGTTTTCCTC 61.587 60.000 0.00 0.00 37.47 3.71
2659 8214 1.074248 GGCCTTCCGTTTTCCTCCA 59.926 57.895 0.00 0.00 0.00 3.86
2661 8216 1.587043 GCCTTCCGTTTTCCTCCAGC 61.587 60.000 0.00 0.00 0.00 4.85
2662 8217 1.298859 CCTTCCGTTTTCCTCCAGCG 61.299 60.000 0.00 0.00 0.00 5.18
2663 8218 0.320421 CTTCCGTTTTCCTCCAGCGA 60.320 55.000 0.00 0.00 0.00 4.93
2676 8231 4.686695 AGCGAGGCTGAGATGGTA 57.313 55.556 0.00 0.00 37.57 3.25
2677 8232 2.424474 AGCGAGGCTGAGATGGTAG 58.576 57.895 0.00 0.00 37.57 3.18
2679 8234 2.021068 GCGAGGCTGAGATGGTAGCA 62.021 60.000 0.00 0.00 41.63 3.49
2680 8235 0.678395 CGAGGCTGAGATGGTAGCAT 59.322 55.000 7.23 7.23 41.63 3.79
2681 8236 1.604947 CGAGGCTGAGATGGTAGCATG 60.605 57.143 13.10 0.00 41.63 4.06
2682 8237 0.763652 AGGCTGAGATGGTAGCATGG 59.236 55.000 13.10 1.21 41.63 3.66
2683 8238 0.888285 GGCTGAGATGGTAGCATGGC 60.888 60.000 13.10 6.46 41.63 4.40
2684 8239 1.226686 GCTGAGATGGTAGCATGGCG 61.227 60.000 13.10 0.00 39.67 5.69
2685 8240 1.226686 CTGAGATGGTAGCATGGCGC 61.227 60.000 13.10 0.00 42.91 6.53
2700 8255 3.929389 CGCTGCGCTCTATTCTCC 58.071 61.111 9.88 0.00 0.00 3.71
2701 8256 1.663074 CGCTGCGCTCTATTCTCCC 60.663 63.158 9.88 0.00 0.00 4.30
2702 8257 1.301322 GCTGCGCTCTATTCTCCCC 60.301 63.158 9.73 0.00 0.00 4.81
2703 8258 2.032860 GCTGCGCTCTATTCTCCCCA 62.033 60.000 9.73 0.00 0.00 4.96
2704 8259 0.033228 CTGCGCTCTATTCTCCCCAG 59.967 60.000 9.73 0.00 0.00 4.45
2707 8262 1.118356 CGCTCTATTCTCCCCAGCCT 61.118 60.000 0.00 0.00 0.00 4.58
2708 8263 0.396060 GCTCTATTCTCCCCAGCCTG 59.604 60.000 0.00 0.00 0.00 4.85
2709 8264 1.055040 CTCTATTCTCCCCAGCCTGG 58.945 60.000 2.91 2.91 37.25 4.45
2710 8265 0.343372 TCTATTCTCCCCAGCCTGGT 59.657 55.000 10.47 0.00 35.17 4.00
2711 8266 0.761802 CTATTCTCCCCAGCCTGGTC 59.238 60.000 10.47 0.00 35.17 4.02
2712 8267 1.048724 TATTCTCCCCAGCCTGGTCG 61.049 60.000 10.47 0.00 35.17 4.79
2738 8293 3.046870 CCTCTAGCGCTAGGCCAG 58.953 66.667 37.05 27.91 45.17 4.85
2746 8301 3.174265 GCTAGGCCAGCCCCATCT 61.174 66.667 5.01 0.00 45.23 2.90
2750 8305 4.529731 GGCCAGCCCCATCTTCCC 62.530 72.222 0.00 0.00 0.00 3.97
2752 8307 3.023116 CCAGCCCCATCTTCCCCA 61.023 66.667 0.00 0.00 0.00 4.96
2753 8308 2.625460 CCAGCCCCATCTTCCCCAA 61.625 63.158 0.00 0.00 0.00 4.12
2754 8309 1.380380 CAGCCCCATCTTCCCCAAC 60.380 63.158 0.00 0.00 0.00 3.77
2756 8311 3.087065 CCCCATCTTCCCCAACGT 58.913 61.111 0.00 0.00 0.00 3.99
2757 8312 1.378514 CCCCATCTTCCCCAACGTG 60.379 63.158 0.00 0.00 0.00 4.49
2758 8313 1.378514 CCCATCTTCCCCAACGTGG 60.379 63.158 0.00 0.00 37.25 4.94
2759 8314 1.378762 CCATCTTCCCCAACGTGGT 59.621 57.895 0.00 0.00 35.17 4.16
2760 8315 0.676782 CCATCTTCCCCAACGTGGTC 60.677 60.000 0.00 0.00 35.17 4.02
2761 8316 0.036164 CATCTTCCCCAACGTGGTCA 59.964 55.000 0.00 0.00 35.17 4.02
2762 8317 0.036306 ATCTTCCCCAACGTGGTCAC 59.964 55.000 0.00 0.00 35.17 3.67
2765 8320 2.281484 CCCCAACGTGGTCACTGG 60.281 66.667 0.00 0.00 35.17 4.00
2766 8321 2.978010 CCCAACGTGGTCACTGGC 60.978 66.667 0.00 0.00 35.17 4.85
2767 8322 2.978010 CCAACGTGGTCACTGGCC 60.978 66.667 0.00 0.00 31.35 5.36
2769 8324 2.111043 AACGTGGTCACTGGCCAG 59.889 61.111 31.60 31.60 36.57 4.85
2770 8325 4.626081 ACGTGGTCACTGGCCAGC 62.626 66.667 33.06 16.73 36.57 4.85
2774 8329 4.416738 GGTCACTGGCCAGCCCTC 62.417 72.222 33.06 19.12 34.56 4.30
2775 8330 3.640407 GTCACTGGCCAGCCCTCA 61.640 66.667 33.06 9.14 34.56 3.86
2776 8331 3.324930 TCACTGGCCAGCCCTCAG 61.325 66.667 33.06 15.10 34.56 3.35
2794 8349 3.431725 CGCAAGGCCCTCCGTTTC 61.432 66.667 0.00 0.00 37.47 2.78
2795 8350 3.062466 GCAAGGCCCTCCGTTTCC 61.062 66.667 0.00 0.00 37.47 3.13
2796 8351 2.757077 CAAGGCCCTCCGTTTCCT 59.243 61.111 0.00 0.00 37.47 3.36
2797 8352 1.377333 CAAGGCCCTCCGTTTCCTC 60.377 63.158 0.00 0.00 37.47 3.71
2800 8355 1.377333 GGCCCTCCGTTTCCTCTTG 60.377 63.158 0.00 0.00 0.00 3.02
2801 8356 1.377333 GCCCTCCGTTTCCTCTTGG 60.377 63.158 0.00 0.00 0.00 3.61
2802 8357 1.377333 CCCTCCGTTTCCTCTTGGC 60.377 63.158 0.00 0.00 0.00 4.52
2803 8358 1.374947 CCTCCGTTTCCTCTTGGCA 59.625 57.895 0.00 0.00 0.00 4.92
2805 8360 1.089920 CTCCGTTTCCTCTTGGCATG 58.910 55.000 0.00 0.00 0.00 4.06
2806 8361 0.322456 TCCGTTTCCTCTTGGCATGG 60.322 55.000 0.00 0.00 0.00 3.66
2817 8372 4.175337 GGCATGGCCGAGGTGCTA 62.175 66.667 8.35 0.00 39.62 3.49
2818 8373 2.590007 GCATGGCCGAGGTGCTAG 60.590 66.667 13.09 0.00 36.02 3.42
2819 8374 2.109799 CATGGCCGAGGTGCTAGG 59.890 66.667 0.00 0.00 0.00 3.02
2820 8375 3.164269 ATGGCCGAGGTGCTAGGG 61.164 66.667 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 398 0.392193 CGAGAGCAATGTGCCCTCTT 60.392 55.000 9.63 0.00 44.72 2.85
48 414 1.606668 GAGAGAGATGGTAGCACCGAG 59.393 57.143 0.00 0.00 42.58 4.63
88 454 2.289072 CGCGGGAAGATAATCATGTCCT 60.289 50.000 0.00 0.00 0.00 3.85
125 491 4.148838 AGATTCTTCGCTAGCTCTACCAT 58.851 43.478 13.93 0.00 0.00 3.55
151 517 0.179156 CTGCCGACATGTTCCAATGC 60.179 55.000 0.00 0.00 0.00 3.56
152 518 0.179156 GCTGCCGACATGTTCCAATG 60.179 55.000 0.00 0.00 0.00 2.82
153 519 0.322816 AGCTGCCGACATGTTCCAAT 60.323 50.000 0.00 0.00 0.00 3.16
160 526 1.226686 GCTATCCAGCTGCCGACATG 61.227 60.000 8.66 0.00 44.93 3.21
266 632 4.451150 TCGCTAGCAGTTGGCCCG 62.451 66.667 16.45 0.00 46.50 6.13
362 730 5.339282 GGAAAAGGGAAGTCAGGTAAGCTAT 60.339 44.000 0.00 0.00 0.00 2.97
383 751 2.816411 ACTGGATCCTCTAACGTGGAA 58.184 47.619 14.23 0.00 36.48 3.53
410 778 1.153628 CCATCGTCGGGGTCTCAAC 60.154 63.158 0.00 0.00 0.00 3.18
419 1247 4.570663 GTCGCCTCCCATCGTCGG 62.571 72.222 0.00 0.00 0.00 4.79
434 1262 4.144703 GTCCTTCCTCCCCGCGTC 62.145 72.222 4.92 0.00 0.00 5.19
439 1267 3.153270 GATCGCGTCCTTCCTCCCC 62.153 68.421 5.77 0.00 0.00 4.81
440 1268 2.417936 GATCGCGTCCTTCCTCCC 59.582 66.667 5.77 0.00 0.00 4.30
441 1269 1.797211 ATCGATCGCGTCCTTCCTCC 61.797 60.000 11.09 0.00 38.98 4.30
442 1270 0.661780 CATCGATCGCGTCCTTCCTC 60.662 60.000 11.09 0.00 38.98 3.71
443 1271 1.360551 CATCGATCGCGTCCTTCCT 59.639 57.895 11.09 0.00 38.98 3.36
445 1273 1.209275 CCACATCGATCGCGTCCTTC 61.209 60.000 11.09 0.00 38.98 3.46
449 1277 0.306840 TACTCCACATCGATCGCGTC 59.693 55.000 11.09 1.94 38.98 5.19
512 1340 1.349688 ACAGCCCTCAAAACATCGGTA 59.650 47.619 0.00 0.00 0.00 4.02
523 1351 0.322456 CCAATTTCCGACAGCCCTCA 60.322 55.000 0.00 0.00 0.00 3.86
525 1353 0.112412 AACCAATTTCCGACAGCCCT 59.888 50.000 0.00 0.00 0.00 5.19
548 1376 4.941263 CCCTCCGTTCATTTTTGTAGATCA 59.059 41.667 0.00 0.00 0.00 2.92
560 1388 3.103080 AGAACTACTCCCTCCGTTCAT 57.897 47.619 0.00 0.00 38.50 2.57
565 1393 3.358118 AGAGAAAGAACTACTCCCTCCG 58.642 50.000 0.00 0.00 31.76 4.63
685 1805 8.088981 GCTCTTAAATCATTTAGACCGGATAGA 58.911 37.037 9.46 0.00 0.00 1.98
686 1806 8.091449 AGCTCTTAAATCATTTAGACCGGATAG 58.909 37.037 9.46 0.00 0.00 2.08
687 1807 7.963532 AGCTCTTAAATCATTTAGACCGGATA 58.036 34.615 9.46 0.00 0.00 2.59
688 1808 6.831976 AGCTCTTAAATCATTTAGACCGGAT 58.168 36.000 9.46 0.00 0.00 4.18
689 1809 6.127168 TGAGCTCTTAAATCATTTAGACCGGA 60.127 38.462 16.19 0.00 0.00 5.14
695 1815 8.192774 TGCCAAATGAGCTCTTAAATCATTTAG 58.807 33.333 16.19 5.92 46.58 1.85
770 1907 6.971184 GCTACATCGACTTTTTAGCTAGTGTA 59.029 38.462 0.00 0.00 33.74 2.90
873 3241 0.689412 TGTGTGTGTGTGGGAGGAGA 60.689 55.000 0.00 0.00 0.00 3.71
892 3285 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
894 3287 1.155889 CAGTGTGTGTGTGTGTGTGT 58.844 50.000 0.00 0.00 0.00 3.72
895 3288 1.128507 GTCAGTGTGTGTGTGTGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
896 3289 1.270571 TGTCAGTGTGTGTGTGTGTGT 60.271 47.619 0.00 0.00 0.00 3.72
897 3290 1.128507 GTGTCAGTGTGTGTGTGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
898 3291 1.270571 TGTGTCAGTGTGTGTGTGTGT 60.271 47.619 0.00 0.00 0.00 3.72
899 3292 1.128507 GTGTGTCAGTGTGTGTGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
900 3293 1.270571 TGTGTGTCAGTGTGTGTGTGT 60.271 47.619 0.00 0.00 0.00 3.72
901 3294 1.128507 GTGTGTGTCAGTGTGTGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
902 3295 1.270571 TGTGTGTGTCAGTGTGTGTGT 60.271 47.619 0.00 0.00 0.00 3.72
903 3296 1.128507 GTGTGTGTGTCAGTGTGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
904 3297 1.270571 TGTGTGTGTGTCAGTGTGTGT 60.271 47.619 0.00 0.00 0.00 3.72
905 3298 1.128507 GTGTGTGTGTGTCAGTGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
906 3299 1.438651 GTGTGTGTGTGTCAGTGTGT 58.561 50.000 0.00 0.00 0.00 3.72
907 3300 0.369931 CGTGTGTGTGTGTCAGTGTG 59.630 55.000 0.00 0.00 0.00 3.82
908 3301 1.358725 GCGTGTGTGTGTGTCAGTGT 61.359 55.000 0.00 0.00 0.00 3.55
909 3302 1.348250 GCGTGTGTGTGTGTCAGTG 59.652 57.895 0.00 0.00 0.00 3.66
910 3303 1.079474 TGCGTGTGTGTGTGTCAGT 60.079 52.632 0.00 0.00 0.00 3.41
911 3304 1.348250 GTGCGTGTGTGTGTGTCAG 59.652 57.895 0.00 0.00 0.00 3.51
912 3305 1.374758 TGTGCGTGTGTGTGTGTCA 60.375 52.632 0.00 0.00 0.00 3.58
913 3306 1.060308 GTGTGCGTGTGTGTGTGTC 59.940 57.895 0.00 0.00 0.00 3.67
914 3307 2.735677 CGTGTGCGTGTGTGTGTGT 61.736 57.895 0.00 0.00 0.00 3.72
915 3308 2.021243 CGTGTGCGTGTGTGTGTG 59.979 61.111 0.00 0.00 0.00 3.82
916 3309 3.860125 GCGTGTGCGTGTGTGTGT 61.860 61.111 0.00 0.00 40.81 3.72
955 3348 1.759445 GATGCTCTACAGGCAGGAGAA 59.241 52.381 0.00 0.00 43.15 2.87
956 3349 1.407936 GATGCTCTACAGGCAGGAGA 58.592 55.000 0.00 0.00 43.15 3.71
957 3350 0.392336 GGATGCTCTACAGGCAGGAG 59.608 60.000 0.00 0.00 43.15 3.69
958 3351 0.325577 TGGATGCTCTACAGGCAGGA 60.326 55.000 0.00 0.00 43.15 3.86
984 3395 1.595794 GACATGTTTGTCCGTGAACGT 59.404 47.619 0.00 0.00 45.45 3.99
985 3396 2.294479 GACATGTTTGTCCGTGAACG 57.706 50.000 0.00 0.00 45.45 3.95
1026 3438 1.133407 CGACGTTTGTCAACATCGGA 58.867 50.000 0.00 0.00 43.28 4.55
1129 3541 0.759959 TTTAGCTGGACGTGTTGGGA 59.240 50.000 0.00 0.00 0.00 4.37
1245 3658 2.436646 AACCCAGGCATCTTCGCG 60.437 61.111 0.00 0.00 0.00 5.87
1494 3928 1.671054 CCGTCCACATGTCCACCAC 60.671 63.158 0.00 0.00 0.00 4.16
1956 4415 1.099879 GGCAGATGATCACCCACAGC 61.100 60.000 0.00 0.00 0.00 4.40
1957 4416 0.465097 GGGCAGATGATCACCCACAG 60.465 60.000 16.17 0.00 42.33 3.66
1993 4462 0.308684 CGCTGCTGAAACTGAAAGCA 59.691 50.000 0.00 0.00 44.36 3.91
2113 7542 7.809238 AGTGGTGTACAGTACTATATAGGACA 58.191 38.462 24.17 10.51 39.68 4.02
2127 7561 6.460814 CCATTCTGATCTCTAGTGGTGTACAG 60.461 46.154 0.00 0.00 0.00 2.74
2128 7562 5.360999 CCATTCTGATCTCTAGTGGTGTACA 59.639 44.000 0.00 0.00 0.00 2.90
2222 7658 6.464222 CCTGTCACTCAAACAAGGATAGTAA 58.536 40.000 0.00 0.00 0.00 2.24
2223 7659 5.568825 GCCTGTCACTCAAACAAGGATAGTA 60.569 44.000 0.00 0.00 0.00 1.82
2227 7663 2.158623 TGCCTGTCACTCAAACAAGGAT 60.159 45.455 0.00 0.00 0.00 3.24
2245 7681 1.839424 AGAAAACCAGCCTGTATGCC 58.161 50.000 0.00 0.00 0.00 4.40
2503 7939 2.232298 GAAGGACAGGAGACAGCGGG 62.232 65.000 0.00 0.00 0.00 6.13
2625 8180 4.232878 CCTGCCGCTAGAGCCTGG 62.233 72.222 0.00 0.00 37.91 4.45
2626 8181 4.906792 GCCTGCCGCTAGAGCCTG 62.907 72.222 0.00 0.00 37.91 4.85
2629 8184 4.168291 AAGGCCTGCCGCTAGAGC 62.168 66.667 5.69 0.00 41.95 4.09
2630 8185 2.107953 GAAGGCCTGCCGCTAGAG 59.892 66.667 5.69 0.00 41.95 2.43
2631 8186 3.470888 GGAAGGCCTGCCGCTAGA 61.471 66.667 16.27 0.00 41.95 2.43
2638 8193 1.587043 GAGGAAAACGGAAGGCCTGC 61.587 60.000 5.69 2.81 0.00 4.85
2640 8195 1.379146 GGAGGAAAACGGAAGGCCT 59.621 57.895 0.00 0.00 0.00 5.19
2642 8197 1.587043 GCTGGAGGAAAACGGAAGGC 61.587 60.000 0.00 0.00 0.00 4.35
2643 8198 1.298859 CGCTGGAGGAAAACGGAAGG 61.299 60.000 0.00 0.00 0.00 3.46
2644 8199 0.320421 TCGCTGGAGGAAAACGGAAG 60.320 55.000 0.00 0.00 0.00 3.46
2645 8200 0.320421 CTCGCTGGAGGAAAACGGAA 60.320 55.000 0.00 0.00 36.61 4.30
2646 8201 1.292223 CTCGCTGGAGGAAAACGGA 59.708 57.895 0.00 0.00 36.61 4.69
2659 8214 1.743321 GCTACCATCTCAGCCTCGCT 61.743 60.000 0.00 0.00 40.77 4.93
2661 8216 0.678395 ATGCTACCATCTCAGCCTCG 59.322 55.000 0.00 0.00 36.95 4.63
2662 8217 1.270732 CCATGCTACCATCTCAGCCTC 60.271 57.143 0.00 0.00 36.95 4.70
2663 8218 0.763652 CCATGCTACCATCTCAGCCT 59.236 55.000 0.00 0.00 36.95 4.58
2665 8220 1.226686 CGCCATGCTACCATCTCAGC 61.227 60.000 0.00 0.00 38.31 4.26
2666 8221 1.226686 GCGCCATGCTACCATCTCAG 61.227 60.000 0.00 0.00 41.73 3.35
2667 8222 1.227645 GCGCCATGCTACCATCTCA 60.228 57.895 0.00 0.00 41.73 3.27
2668 8223 3.647824 GCGCCATGCTACCATCTC 58.352 61.111 0.00 0.00 41.73 2.75
2685 8240 0.033228 CTGGGGAGAATAGAGCGCAG 59.967 60.000 11.47 0.00 0.00 5.18
2686 8241 2.032860 GCTGGGGAGAATAGAGCGCA 62.033 60.000 11.47 0.00 0.00 6.09
2688 8243 1.118356 AGGCTGGGGAGAATAGAGCG 61.118 60.000 0.00 0.00 0.00 5.03
2689 8244 0.396060 CAGGCTGGGGAGAATAGAGC 59.604 60.000 6.61 0.00 0.00 4.09
2691 8246 0.343372 ACCAGGCTGGGGAGAATAGA 59.657 55.000 35.34 0.00 43.37 1.98
2692 8247 0.761802 GACCAGGCTGGGGAGAATAG 59.238 60.000 35.34 9.19 43.37 1.73
2694 8249 2.370445 CGACCAGGCTGGGGAGAAT 61.370 63.158 35.34 15.24 43.37 2.40
2695 8250 3.003173 CGACCAGGCTGGGGAGAA 61.003 66.667 35.34 0.00 43.37 2.87
2716 8271 2.338257 CTAGCGCTAGAGGCTGCC 59.662 66.667 35.85 11.65 41.69 4.85
2717 8272 2.338257 CCTAGCGCTAGAGGCTGC 59.662 66.667 39.42 0.00 41.69 5.25
2731 8286 2.078665 GGAAGATGGGGCTGGCCTA 61.079 63.158 20.47 15.19 36.10 3.93
2734 8289 4.529731 GGGGAAGATGGGGCTGGC 62.530 72.222 0.00 0.00 0.00 4.85
2735 8290 2.625460 TTGGGGAAGATGGGGCTGG 61.625 63.158 0.00 0.00 0.00 4.85
2736 8291 1.380380 GTTGGGGAAGATGGGGCTG 60.380 63.158 0.00 0.00 0.00 4.85
2737 8292 2.983879 CGTTGGGGAAGATGGGGCT 61.984 63.158 0.00 0.00 0.00 5.19
2738 8293 2.440247 CGTTGGGGAAGATGGGGC 60.440 66.667 0.00 0.00 0.00 5.80
2739 8294 1.378514 CACGTTGGGGAAGATGGGG 60.379 63.158 0.00 0.00 0.00 4.96
2741 8296 0.676782 GACCACGTTGGGGAAGATGG 60.677 60.000 8.57 0.00 43.37 3.51
2742 8297 0.036164 TGACCACGTTGGGGAAGATG 59.964 55.000 8.57 0.00 43.37 2.90
2743 8298 0.036306 GTGACCACGTTGGGGAAGAT 59.964 55.000 8.57 0.00 43.37 2.40
2744 8299 1.052124 AGTGACCACGTTGGGGAAGA 61.052 55.000 8.57 0.00 43.37 2.87
2745 8300 0.884704 CAGTGACCACGTTGGGGAAG 60.885 60.000 8.57 0.00 43.37 3.46
2746 8301 1.147376 CAGTGACCACGTTGGGGAA 59.853 57.895 8.57 0.00 43.37 3.97
2750 8305 2.978010 GGCCAGTGACCACGTTGG 60.978 66.667 0.00 0.00 45.02 3.77
2752 8307 2.111043 CTGGCCAGTGACCACGTT 59.889 61.111 25.53 0.00 36.20 3.99
2753 8308 4.626081 GCTGGCCAGTGACCACGT 62.626 66.667 32.81 0.00 36.20 4.49
2757 8312 4.416738 GAGGGCTGGCCAGTGACC 62.417 72.222 32.81 29.05 37.98 4.02
2758 8313 3.618780 CTGAGGGCTGGCCAGTGAC 62.619 68.421 32.81 22.36 37.98 3.67
2759 8314 3.324930 CTGAGGGCTGGCCAGTGA 61.325 66.667 32.81 7.76 37.98 3.41
2778 8333 3.062466 GGAAACGGAGGGCCTTGC 61.062 66.667 7.89 0.00 0.00 4.01
2779 8334 1.377333 GAGGAAACGGAGGGCCTTG 60.377 63.158 7.89 6.31 0.00 3.61
2780 8335 1.134438 AAGAGGAAACGGAGGGCCTT 61.134 55.000 7.89 0.00 0.00 4.35
2781 8336 1.539124 AAGAGGAAACGGAGGGCCT 60.539 57.895 5.25 5.25 0.00 5.19
2782 8337 1.377333 CAAGAGGAAACGGAGGGCC 60.377 63.158 0.00 0.00 0.00 5.80
2783 8338 1.377333 CCAAGAGGAAACGGAGGGC 60.377 63.158 0.00 0.00 36.89 5.19
2784 8339 1.377333 GCCAAGAGGAAACGGAGGG 60.377 63.158 0.00 0.00 36.89 4.30
2785 8340 0.035056 ATGCCAAGAGGAAACGGAGG 60.035 55.000 0.00 0.00 36.89 4.30
2786 8341 1.089920 CATGCCAAGAGGAAACGGAG 58.910 55.000 0.00 0.00 36.89 4.63
2788 8343 1.937546 GCCATGCCAAGAGGAAACGG 61.938 60.000 0.00 0.00 36.89 4.44
2789 8344 1.508088 GCCATGCCAAGAGGAAACG 59.492 57.895 0.00 0.00 36.89 3.60
2800 8355 4.175337 TAGCACCTCGGCCATGCC 62.175 66.667 2.24 0.00 46.75 4.40
2801 8356 2.590007 CTAGCACCTCGGCCATGC 60.590 66.667 2.24 6.88 39.74 4.06
2802 8357 2.109799 CCTAGCACCTCGGCCATG 59.890 66.667 2.24 0.00 0.00 3.66
2803 8358 3.164269 CCCTAGCACCTCGGCCAT 61.164 66.667 2.24 0.00 0.00 4.40
2815 8370 1.561542 AGAATTCCCTGTGTGCCCTAG 59.438 52.381 0.65 0.00 0.00 3.02
2816 8371 1.559682 GAGAATTCCCTGTGTGCCCTA 59.440 52.381 0.65 0.00 0.00 3.53
2817 8372 0.329596 GAGAATTCCCTGTGTGCCCT 59.670 55.000 0.65 0.00 0.00 5.19
2818 8373 1.026718 CGAGAATTCCCTGTGTGCCC 61.027 60.000 0.65 0.00 0.00 5.36
2819 8374 1.648467 GCGAGAATTCCCTGTGTGCC 61.648 60.000 0.65 0.00 0.00 5.01
2820 8375 0.955428 TGCGAGAATTCCCTGTGTGC 60.955 55.000 0.65 0.00 0.00 4.57
2821 8376 0.798776 GTGCGAGAATTCCCTGTGTG 59.201 55.000 0.65 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.