Multiple sequence alignment - TraesCS6A01G061200

Loading Multiple Alignment...

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 TraesCS6A01G061200 chr6A 100.000 4696 0 0 400 5095 32901424 32896729 0.000000e+00 8672.0
1 TraesCS6A01G061200 chr6A 100.000 141 0 0 1 141 32901823 32901683 1.410000e-65 261.0
2 TraesCS6A01G061200 chr6A 87.500 48 4 2 9 55 521882310 521882264 3.000000e-03 54.7
3 TraesCS6A01G061200 chr6D 94.512 4009 144 23 402 4376 29768388 29772354 0.000000e+00 6115.0
4 TraesCS6A01G061200 chr6D 92.180 665 51 1 4429 5093 29772355 29773018 0.000000e+00 939.0
5 TraesCS6A01G061200 chr6D 79.798 990 185 12 3099 4080 468096619 468095637 0.000000e+00 706.0
6 TraesCS6A01G061200 chr6D 78.253 538 110 6 4559 5092 451626661 451627195 6.320000e-89 339.0
7 TraesCS6A01G061200 chr6D 82.840 169 25 3 1082 1248 468060679 468060513 1.140000e-31 148.0
8 TraesCS6A01G061200 chr6D 86.111 108 13 2 33 140 29768248 29768353 1.160000e-21 115.0
9 TraesCS6A01G061200 chr5B 84.016 1026 156 7 3065 4087 629897834 629898854 0.000000e+00 979.0
10 TraesCS6A01G061200 chr5B 83.821 1026 158 7 3065 4087 623171877 623172897 0.000000e+00 968.0
11 TraesCS6A01G061200 chr5B 83.723 1026 159 7 3065 4087 626842844 626843864 0.000000e+00 963.0
12 TraesCS6A01G061200 chr5B 83.626 1026 160 7 3065 4087 625117658 625118678 0.000000e+00 957.0
13 TraesCS6A01G061200 chr5B 83.431 1026 162 7 3065 4087 628697207 628698227 0.000000e+00 946.0
14 TraesCS6A01G061200 chr5B 83.431 1020 159 9 3065 4082 633176327 633175316 0.000000e+00 939.0
15 TraesCS6A01G061200 chr5B 76.582 1375 210 68 1000 2329 626838040 626839347 0.000000e+00 652.0
16 TraesCS6A01G061200 chr5B 76.582 1375 210 69 1000 2329 628694452 628695759 0.000000e+00 652.0
17 TraesCS6A01G061200 chr5B 76.436 1375 212 69 1000 2329 625114903 625116210 4.300000e-180 641.0
18 TraesCS6A01G061200 chr5B 76.201 1374 225 62 1000 2329 623167064 623168379 2.590000e-177 632.0
19 TraesCS6A01G061200 chr5B 76.204 1370 212 67 1006 2329 629895666 629896967 2.020000e-173 619.0
20 TraesCS6A01G061200 chr5B 76.117 1365 222 64 1000 2329 633179349 633178054 2.020000e-173 619.0
21 TraesCS6A01G061200 chr5B 79.762 84 17 0 4994 5077 466702262 466702179 1.530000e-05 62.1
22 TraesCS6A01G061200 chr5A 83.013 1042 165 11 3065 4101 625733542 625732508 0.000000e+00 933.0
23 TraesCS6A01G061200 chr5A 76.909 1074 166 48 1000 2053 625738764 625737753 7.510000e-148 534.0
24 TraesCS6A01G061200 chr2D 80.029 696 116 10 4399 5090 579402595 579403271 1.270000e-135 494.0
25 TraesCS6A01G061200 chr2D 80.952 294 50 3 4802 5090 640173030 640173322 1.430000e-55 228.0
26 TraesCS6A01G061200 chr7D 79.310 696 140 4 4399 5092 626537701 626538394 7.670000e-133 484.0
27 TraesCS6A01G061200 chr7D 78.603 673 123 17 4430 5091 26555189 26555851 4.710000e-115 425.0
28 TraesCS6A01G061200 chr4A 78.282 617 124 9 4430 5044 710673407 710674015 6.190000e-104 388.0
29 TraesCS6A01G061200 chr2B 78.908 531 110 2 4564 5092 775109056 775109586 4.850000e-95 359.0
30 TraesCS6A01G061200 chr2B 73.571 700 174 7 4399 5092 754778167 754778861 1.820000e-64 257.0
31 TraesCS6A01G061200 chr1D 78.850 539 101 10 4399 4929 361878484 361877951 8.120000e-93 351.0
32 TraesCS6A01G061200 chr1D 78.307 378 77 5 4585 4960 361853273 361853647 6.590000e-59 239.0
33 TraesCS6A01G061200 chr2A 77.778 477 101 5 4446 4919 578672960 578672486 6.450000e-74 289.0
34 TraesCS6A01G061200 chr4D 76.772 508 109 1 4401 4908 315514133 315513635 5.020000e-70 276.0
35 TraesCS6A01G061200 chr7A 88.889 72 8 0 5021 5092 7138625 7138696 7.030000e-14 89.8


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 TraesCS6A01G061200 chr6A 32896729 32901823 5094 True 4466.500000 8672 100.000000 1 5095 2 chr6A.!!$R2 5094
1 TraesCS6A01G061200 chr6D 29768248 29773018 4770 False 2389.666667 6115 90.934333 33 5093 3 chr6D.!!$F2 5060
2 TraesCS6A01G061200 chr6D 468095637 468096619 982 True 706.000000 706 79.798000 3099 4080 1 chr6D.!!$R2 981
3 TraesCS6A01G061200 chr6D 451626661 451627195 534 False 339.000000 339 78.253000 4559 5092 1 chr6D.!!$F1 533
4 TraesCS6A01G061200 chr5B 626838040 626843864 5824 False 807.500000 963 80.152500 1000 4087 2 chr5B.!!$F3 3087
5 TraesCS6A01G061200 chr5B 623167064 623172897 5833 False 800.000000 968 80.011000 1000 4087 2 chr5B.!!$F1 3087
6 TraesCS6A01G061200 chr5B 625114903 625118678 3775 False 799.000000 957 80.031000 1000 4087 2 chr5B.!!$F2 3087
7 TraesCS6A01G061200 chr5B 628694452 628698227 3775 False 799.000000 946 80.006500 1000 4087 2 chr5B.!!$F4 3087
8 TraesCS6A01G061200 chr5B 629895666 629898854 3188 False 799.000000 979 80.110000 1006 4087 2 chr5B.!!$F5 3081
9 TraesCS6A01G061200 chr5B 633175316 633179349 4033 True 779.000000 939 79.774000 1000 4082 2 chr5B.!!$R2 3082
10 TraesCS6A01G061200 chr5A 625732508 625733542 1034 True 933.000000 933 83.013000 3065 4101 1 chr5A.!!$R1 1036
11 TraesCS6A01G061200 chr5A 625737753 625738764 1011 True 534.000000 534 76.909000 1000 2053 1 chr5A.!!$R2 1053
12 TraesCS6A01G061200 chr2D 579402595 579403271 676 False 494.000000 494 80.029000 4399 5090 1 chr2D.!!$F1 691
13 TraesCS6A01G061200 chr7D 626537701 626538394 693 False 484.000000 484 79.310000 4399 5092 1 chr7D.!!$F2 693
14 TraesCS6A01G061200 chr7D 26555189 26555851 662 False 425.000000 425 78.603000 4430 5091 1 chr7D.!!$F1 661
15 TraesCS6A01G061200 chr4A 710673407 710674015 608 False 388.000000 388 78.282000 4430 5044 1 chr4A.!!$F1 614
16 TraesCS6A01G061200 chr2B 775109056 775109586 530 False 359.000000 359 78.908000 4564 5092 1 chr2B.!!$F2 528
17 TraesCS6A01G061200 chr2B 754778167 754778861 694 False 257.000000 257 73.571000 4399 5092 1 chr2B.!!$F1 693
18 TraesCS6A01G061200 chr1D 361877951 361878484 533 True 351.000000 351 78.850000 4399 4929 1 chr1D.!!$R1 530

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
31 32 0.037046 GAAGGCAATTGGGCAGTTGG 60.037 55.000 7.72 0.00 46.44 3.77 F
455 456 0.251341 AAACCATGGCTCGCTTCCTT 60.251 50.000 13.04 0.00 0.00 3.36 F
1267 1304 0.306228 CATGACAACCGCAACGAACA 59.694 50.000 0.00 0.00 0.00 3.18 F
1446 1486 0.234884 GCAGCACCAACGTTACTCAC 59.765 55.000 0.00 0.00 0.00 3.51 F
1544 1610 0.320421 GGCTGGAGTGTTAGCGTCAA 60.320 55.000 0.00 0.00 40.78 3.18 F
1841 1928 0.674895 CTGCCGAAGAAGTTCCCCAG 60.675 60.000 0.00 0.00 0.00 4.45 F
1845 1932 1.000771 GAAGAAGTTCCCCAGGGGC 60.001 63.158 21.90 6.88 43.94 5.80 F
3341 7402 2.101917 GGGCATCCTTGGTGATGAATTG 59.898 50.000 5.26 0.00 43.94 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1260 1297 0.249699 TGAGCGTGATGGTGTTCGTT 60.250 50.000 0.00 0.00 0.00 3.85 R
1327 1367 0.321034 GTGTTGGGGAACGAGTACCC 60.321 60.000 4.35 4.35 44.94 3.69 R
2795 3091 0.458669 CAAATGTGCAGGCCATCCTC 59.541 55.000 5.01 0.00 41.93 3.71 R
3364 7425 3.378512 TCATTCTCCAGCAGACTACCAT 58.621 45.455 0.00 0.00 0.00 3.55 R
3458 7519 3.624707 GCAATGGGGTATCAACTTCCAGA 60.625 47.826 0.00 0.00 34.26 3.86 R
3680 7741 1.159285 CGAAGTCTGCAATCTTGGCA 58.841 50.000 7.61 0.00 39.32 4.92 R
3893 7954 7.418368 CCTCTTCTATGAGCTCCAATGAAACTA 60.418 40.741 12.15 0.00 33.02 2.24 R
4389 8451 0.250295 GCCGATTAGCCCATAGTGCA 60.250 55.000 0.00 0.00 0.00 4.57 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
25 26 1.741528 CCAAATGAAGGCAATTGGGC 58.258 50.000 7.72 0.45 46.66 5.36
26 27 1.003349 CCAAATGAAGGCAATTGGGCA 59.997 47.619 7.72 0.00 46.66 5.36
27 28 2.352388 CAAATGAAGGCAATTGGGCAG 58.648 47.619 7.72 0.00 46.44 4.85
28 29 1.648116 AATGAAGGCAATTGGGCAGT 58.352 45.000 7.72 0.00 46.44 4.40
29 30 1.648116 ATGAAGGCAATTGGGCAGTT 58.352 45.000 7.72 0.00 46.44 3.16
30 31 0.680618 TGAAGGCAATTGGGCAGTTG 59.319 50.000 7.72 0.00 46.44 3.16
31 32 0.037046 GAAGGCAATTGGGCAGTTGG 60.037 55.000 7.72 0.00 46.44 3.77
32 33 2.046988 GGCAATTGGGCAGTTGGC 60.047 61.111 7.72 0.00 43.77 4.52
33 34 2.432972 GCAATTGGGCAGTTGGCG 60.433 61.111 7.72 0.00 46.16 5.69
55 56 1.802508 GCGGCTGCCATTTTTACATCC 60.803 52.381 20.29 0.00 33.98 3.51
62 63 2.752903 GCCATTTTTACATCCCGAGTGT 59.247 45.455 0.00 0.00 0.00 3.55
68 69 4.665833 TTTACATCCCGAGTGTATGGAG 57.334 45.455 0.00 0.00 32.56 3.86
107 108 5.642063 CGTGAGGTGTGGTATTTTACATCTT 59.358 40.000 0.00 0.00 38.32 2.40
109 110 5.872617 TGAGGTGTGGTATTTTACATCTTCG 59.127 40.000 0.00 0.00 38.32 3.79
110 111 5.183228 AGGTGTGGTATTTTACATCTTCGG 58.817 41.667 0.00 0.00 34.76 4.30
114 115 7.241376 GTGTGGTATTTTACATCTTCGGAAAG 58.759 38.462 0.00 0.00 0.00 2.62
118 119 2.754946 TTACATCTTCGGAAAGCGGT 57.245 45.000 0.00 0.00 32.18 5.68
121 122 0.721718 CATCTTCGGAAAGCGGTGAC 59.278 55.000 0.00 0.00 32.18 3.67
450 451 2.034687 AGCAAACCATGGCTCGCT 59.965 55.556 13.04 14.12 34.76 4.93
451 452 1.589716 GAGCAAACCATGGCTCGCTT 61.590 55.000 19.91 1.55 46.01 4.68
452 453 1.153958 GCAAACCATGGCTCGCTTC 60.154 57.895 13.04 0.00 0.00 3.86
453 454 1.508088 CAAACCATGGCTCGCTTCC 59.492 57.895 13.04 0.00 0.00 3.46
454 455 0.962356 CAAACCATGGCTCGCTTCCT 60.962 55.000 13.04 0.00 0.00 3.36
455 456 0.251341 AAACCATGGCTCGCTTCCTT 60.251 50.000 13.04 0.00 0.00 3.36
456 457 0.618458 AACCATGGCTCGCTTCCTTA 59.382 50.000 13.04 0.00 0.00 2.69
478 479 2.417719 CGGCTTAACCATCCTATCAGC 58.582 52.381 0.00 0.00 39.03 4.26
508 509 2.741878 CGACGGCTTGAACCATCCTATT 60.742 50.000 0.00 0.00 0.00 1.73
577 578 3.228188 TCCCCATTTCATCAGCCATAC 57.772 47.619 0.00 0.00 0.00 2.39
781 797 7.396540 AAAAGATATCAGTCCCATTGTCAAC 57.603 36.000 5.32 0.00 0.00 3.18
782 798 5.965033 AGATATCAGTCCCATTGTCAACT 57.035 39.130 5.32 0.00 0.00 3.16
783 799 7.437713 AAGATATCAGTCCCATTGTCAACTA 57.562 36.000 5.32 0.00 0.00 2.24
784 800 6.821388 AGATATCAGTCCCATTGTCAACTAC 58.179 40.000 5.32 0.00 0.00 2.73
785 801 4.908601 ATCAGTCCCATTGTCAACTACA 57.091 40.909 0.00 0.00 35.88 2.74
786 802 4.271696 TCAGTCCCATTGTCAACTACAG 57.728 45.455 0.00 0.00 39.87 2.74
787 803 3.646162 TCAGTCCCATTGTCAACTACAGT 59.354 43.478 0.00 0.00 39.87 3.55
788 804 4.836175 TCAGTCCCATTGTCAACTACAGTA 59.164 41.667 0.00 0.00 39.87 2.74
789 805 5.305902 TCAGTCCCATTGTCAACTACAGTAA 59.694 40.000 0.00 0.00 39.87 2.24
833 849 5.844004 AGGTTTGAGCTATATAACGTGGAG 58.156 41.667 0.00 0.00 0.00 3.86
845 861 2.733593 GTGGAGTCACGTCGGCAC 60.734 66.667 0.00 0.00 33.87 5.01
945 961 4.755411 TCGATCAGTTGACCCTTGATTAC 58.245 43.478 0.00 0.00 32.03 1.89
957 973 5.615289 ACCCTTGATTACATACAGAGCATC 58.385 41.667 0.00 0.00 0.00 3.91
959 975 4.999950 CCTTGATTACATACAGAGCATCCC 59.000 45.833 0.00 0.00 33.66 3.85
968 993 1.255882 CAGAGCATCCCGAGCTATCT 58.744 55.000 0.00 0.00 43.58 1.98
1051 1079 1.115467 ATTGCCAGTCCTCCTACTCG 58.885 55.000 0.00 0.00 0.00 4.18
1056 1084 1.746220 CCAGTCCTCCTACTCGTTCTG 59.254 57.143 0.00 0.00 0.00 3.02
1076 1104 2.116772 AGGTGCAGCAGCCATTGT 59.883 55.556 21.07 0.00 41.13 2.71
1077 1105 1.532316 AGGTGCAGCAGCCATTGTT 60.532 52.632 21.07 0.00 41.13 2.83
1110 1147 3.857854 CAGCAGCCGATCACGCAC 61.858 66.667 4.72 0.00 38.29 5.34
1128 1165 2.046285 CCCGGGATGCCAAGACAAC 61.046 63.158 18.48 0.00 0.00 3.32
1257 1294 4.120331 GGCAGCGGCATGACAACC 62.120 66.667 11.88 0.00 43.71 3.77
1267 1304 0.306228 CATGACAACCGCAACGAACA 59.694 50.000 0.00 0.00 0.00 3.18
1268 1305 0.306533 ATGACAACCGCAACGAACAC 59.693 50.000 0.00 0.00 0.00 3.32
1280 1317 0.667487 ACGAACACCATCACGCTCAG 60.667 55.000 0.00 0.00 0.00 3.35
1292 1329 2.202544 GCTCAGCGAGTCCGACAG 60.203 66.667 0.40 0.00 38.22 3.51
1339 1379 2.582978 GCCTGGGGTACTCGTTCC 59.417 66.667 0.00 0.00 0.00 3.62
1352 1392 1.666872 CGTTCCCCAACACCTCGAC 60.667 63.158 0.00 0.00 32.14 4.20
1358 1398 2.743718 CAACACCTCGACCTGGCT 59.256 61.111 0.00 0.00 0.00 4.75
1440 1480 3.952675 CGCTGCAGCACCAACGTT 61.953 61.111 36.03 0.00 42.21 3.99
1443 1483 1.507141 GCTGCAGCACCAACGTTACT 61.507 55.000 33.36 0.00 41.59 2.24
1446 1486 0.234884 GCAGCACCAACGTTACTCAC 59.765 55.000 0.00 0.00 0.00 3.51
1448 1488 2.210116 CAGCACCAACGTTACTCACTT 58.790 47.619 0.00 0.00 0.00 3.16
1462 1502 6.563010 CGTTACTCACTTCAAGCTCAAAGAAG 60.563 42.308 13.39 13.40 43.27 2.85
1472 1512 2.015587 GCTCAAAGAAGAGGCCATGAG 58.984 52.381 5.01 7.90 37.83 2.90
1473 1513 2.617532 GCTCAAAGAAGAGGCCATGAGT 60.618 50.000 5.01 0.00 37.27 3.41
1533 1596 4.148825 GTCGGCATCGGCTGGAGT 62.149 66.667 0.00 0.00 46.76 3.85
1536 1599 2.045926 GGCATCGGCTGGAGTGTT 60.046 61.111 0.00 0.00 40.87 3.32
1537 1600 1.220749 GGCATCGGCTGGAGTGTTA 59.779 57.895 0.00 0.00 40.87 2.41
1544 1610 0.320421 GGCTGGAGTGTTAGCGTCAA 60.320 55.000 0.00 0.00 40.78 3.18
1549 1615 1.000506 GGAGTGTTAGCGTCAAGGACA 59.999 52.381 0.00 0.00 32.09 4.02
1555 1621 2.543687 TAGCGTCAAGGACAGCTCGC 62.544 60.000 15.22 4.19 40.54 5.03
1620 1689 4.521062 AGCCATCTCGAGCACGCC 62.521 66.667 7.81 0.00 39.58 5.68
1624 1693 3.842923 ATCTCGAGCACGCCAGGG 61.843 66.667 7.81 0.00 39.58 4.45
1684 1753 3.461773 GCTCGGAGCCCAGCTACA 61.462 66.667 19.20 0.00 39.98 2.74
1688 1757 2.124942 GGAGCCCAGCTACAGCAC 60.125 66.667 3.70 0.00 39.71 4.40
1692 1761 2.125512 CCCAGCTACAGCACCGTC 60.126 66.667 3.70 0.00 45.16 4.79
1693 1762 2.507102 CCAGCTACAGCACCGTCG 60.507 66.667 3.70 0.00 45.16 5.12
1694 1763 3.181967 CAGCTACAGCACCGTCGC 61.182 66.667 3.70 0.00 45.16 5.19
1695 1764 3.374402 AGCTACAGCACCGTCGCT 61.374 61.111 3.70 0.00 45.21 4.93
1799 1874 1.507174 GCTACACCTTCTCGACGCT 59.493 57.895 0.00 0.00 0.00 5.07
1840 1927 1.374947 CTGCCGAAGAAGTTCCCCA 59.625 57.895 0.00 0.00 0.00 4.96
1841 1928 0.674895 CTGCCGAAGAAGTTCCCCAG 60.675 60.000 0.00 0.00 0.00 4.45
1842 1929 1.377333 GCCGAAGAAGTTCCCCAGG 60.377 63.158 0.00 0.00 0.00 4.45
1843 1930 1.299976 CCGAAGAAGTTCCCCAGGG 59.700 63.158 0.00 0.00 0.00 4.45
1844 1931 1.299976 CGAAGAAGTTCCCCAGGGG 59.700 63.158 20.55 20.55 46.11 4.79
1845 1932 1.000771 GAAGAAGTTCCCCAGGGGC 60.001 63.158 21.90 6.88 43.94 5.80
1846 1933 2.821679 GAAGAAGTTCCCCAGGGGCG 62.822 65.000 21.90 0.00 43.94 6.13
2073 2160 6.438763 AGGTTTGTCGAAATGTTTTGATCTC 58.561 36.000 0.00 0.00 33.43 2.75
2080 2167 4.488879 GAAATGTTTTGATCTCCACAGGC 58.511 43.478 0.00 0.00 0.00 4.85
2187 2305 6.252599 TGAGTGCAAGTTCCCAGATATATT 57.747 37.500 0.00 0.00 0.00 1.28
2335 2453 3.692101 CGATTGTGGGTAAGTAAATGGCA 59.308 43.478 0.00 0.00 0.00 4.92
2551 2669 4.890088 TCCTCATTTTATTACCGGATCCG 58.110 43.478 27.65 27.65 39.44 4.18
2559 2677 6.653526 TTTATTACCGGATCCGTTCTATGA 57.346 37.500 31.22 13.35 37.81 2.15
2795 3091 5.373812 AAATTGGGGTCACCTAGTATGAG 57.626 43.478 0.00 0.00 41.11 2.90
3341 7402 2.101917 GGGCATCCTTGGTGATGAATTG 59.898 50.000 5.26 0.00 43.94 2.32
3350 7411 4.620589 TGGTGATGAATTGGTTGCAATT 57.379 36.364 0.59 0.00 37.47 2.32
3364 7425 7.441890 TGGTTGCAATTAAGAAGACGATTAA 57.558 32.000 0.59 0.00 0.00 1.40
3458 7519 2.371841 TGTCAGGCTCATAGGTTGTTGT 59.628 45.455 0.00 0.00 0.00 3.32
3533 7594 2.414559 CCATGACATTCTTCACGGCAAC 60.415 50.000 0.00 0.00 0.00 4.17
3680 7741 9.920946 AATATACTGTTGGATGATAGGTTTGTT 57.079 29.630 0.00 0.00 0.00 2.83
3893 7954 7.332926 CACTCTGATAACAACAGCTTAGTCAAT 59.667 37.037 0.00 0.00 35.61 2.57
3913 7974 7.714377 AGTCAATAGTTTCATTGGAGCTCATAG 59.286 37.037 17.19 2.11 36.69 2.23
4245 8306 9.426837 TGTCCATCAATTTCATGAAATTTCTTC 57.573 29.630 33.67 23.25 45.67 2.87
4349 8411 6.925610 AATGTATGTATTGTGCTACACTGG 57.074 37.500 0.00 0.00 34.59 4.00
4380 8442 6.765403 GGTACCCAATAGTGCAGTATAATGA 58.235 40.000 14.42 0.00 0.00 2.57
4381 8443 7.221450 GGTACCCAATAGTGCAGTATAATGAA 58.779 38.462 14.42 0.00 0.00 2.57
4382 8444 7.387948 GGTACCCAATAGTGCAGTATAATGAAG 59.612 40.741 14.42 7.74 0.00 3.02
4383 8445 7.136822 ACCCAATAGTGCAGTATAATGAAGA 57.863 36.000 14.42 0.00 0.00 2.87
4384 8446 7.573710 ACCCAATAGTGCAGTATAATGAAGAA 58.426 34.615 14.42 0.00 0.00 2.52
4385 8447 8.220559 ACCCAATAGTGCAGTATAATGAAGAAT 58.779 33.333 14.42 0.00 0.00 2.40
4386 8448 9.725019 CCCAATAGTGCAGTATAATGAAGAATA 57.275 33.333 14.42 0.00 0.00 1.75
4392 8454 9.123902 AGTGCAGTATAATGAAGAATAATTGCA 57.876 29.630 3.96 0.00 32.49 4.08
4393 8455 9.173939 GTGCAGTATAATGAAGAATAATTGCAC 57.826 33.333 3.96 6.68 40.39 4.57
4394 8456 9.123902 TGCAGTATAATGAAGAATAATTGCACT 57.876 29.630 3.96 0.00 31.16 4.40
4423 8485 3.890674 GGCCGACGATTTTCAGCT 58.109 55.556 0.00 0.00 0.00 4.24
4426 8488 1.009829 GCCGACGATTTTCAGCTCAT 58.990 50.000 0.00 0.00 0.00 2.90
4654 8726 0.105658 ATCTCCTTGTAGGCGGCCTA 60.106 55.000 24.51 24.51 34.61 3.93
4683 8756 2.429610 ACCTGACATTAGCGATACCGTT 59.570 45.455 0.00 0.00 38.24 4.44
4730 8803 3.048941 GCGTTAGGAGTCGAGCGGT 62.049 63.158 0.00 0.00 0.00 5.68
4763 8841 3.071206 AGGTCTGCGTCCGATGCT 61.071 61.111 13.67 0.00 0.00 3.79
4773 8852 0.250467 GTCCGATGCTATGGCCATGT 60.250 55.000 29.04 11.30 37.74 3.21
4799 8878 1.004440 GAGTTGCTCCTCCGCTTGT 60.004 57.895 0.00 0.00 0.00 3.16
4960 9043 1.228583 TGACACCAGCTCGTCCTCT 60.229 57.895 5.28 0.00 0.00 3.69
5006 9097 2.032528 CCTTTGTCTGCCTGCCGA 59.967 61.111 0.00 0.00 0.00 5.54
5027 9118 1.457267 TGCCAACCCACAGCAATGT 60.457 52.632 0.00 0.00 32.56 2.71
5093 9184 1.019278 TTTAAAGCGCGAGGAGGCTG 61.019 55.000 12.10 0.00 39.93 4.85
5094 9185 2.167398 TTAAAGCGCGAGGAGGCTGT 62.167 55.000 12.10 0.00 39.93 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.289819 ACTGCCCAATTGCCTTCATTTG 60.290 45.455 0.00 0.00 34.84 2.32
8 9 1.980036 ACTGCCCAATTGCCTTCATTT 59.020 42.857 0.00 0.00 0.00 2.32
9 10 1.648116 ACTGCCCAATTGCCTTCATT 58.352 45.000 0.00 0.00 0.00 2.57
10 11 1.276989 CAACTGCCCAATTGCCTTCAT 59.723 47.619 0.00 0.00 0.00 2.57
11 12 0.680618 CAACTGCCCAATTGCCTTCA 59.319 50.000 0.00 0.00 0.00 3.02
12 13 0.037046 CCAACTGCCCAATTGCCTTC 60.037 55.000 0.00 0.00 0.00 3.46
13 14 2.060370 CCAACTGCCCAATTGCCTT 58.940 52.632 0.00 0.00 0.00 4.35
14 15 2.586293 GCCAACTGCCCAATTGCCT 61.586 57.895 0.00 0.00 0.00 4.75
15 16 2.046988 GCCAACTGCCCAATTGCC 60.047 61.111 0.00 0.00 0.00 4.52
16 17 2.432972 CGCCAACTGCCCAATTGC 60.433 61.111 0.00 0.00 36.24 3.56
17 18 2.432972 GCGCCAACTGCCCAATTG 60.433 61.111 0.00 0.00 36.24 2.32
18 19 4.054825 CGCGCCAACTGCCCAATT 62.055 61.111 0.00 0.00 36.24 2.32
32 33 3.675482 TAAAAATGGCAGCCGCGCG 62.675 57.895 25.67 25.67 39.92 6.86
33 34 2.158330 GTAAAAATGGCAGCCGCGC 61.158 57.895 7.03 0.00 39.92 6.86
34 35 0.179140 ATGTAAAAATGGCAGCCGCG 60.179 50.000 7.03 0.00 39.92 6.46
35 36 1.559831 GATGTAAAAATGGCAGCCGC 58.440 50.000 7.03 0.00 37.44 6.53
36 37 1.202405 GGGATGTAAAAATGGCAGCCG 60.202 52.381 7.03 0.00 39.36 5.52
37 38 1.202405 CGGGATGTAAAAATGGCAGCC 60.202 52.381 3.66 3.66 37.90 4.85
38 39 1.748493 TCGGGATGTAAAAATGGCAGC 59.252 47.619 0.00 0.00 0.00 5.25
39 40 3.016736 ACTCGGGATGTAAAAATGGCAG 58.983 45.455 0.00 0.00 0.00 4.85
40 41 2.752354 CACTCGGGATGTAAAAATGGCA 59.248 45.455 0.00 0.00 0.00 4.92
41 42 2.752903 ACACTCGGGATGTAAAAATGGC 59.247 45.455 0.00 0.00 0.00 4.40
42 43 5.008613 CCATACACTCGGGATGTAAAAATGG 59.991 44.000 0.00 0.00 36.19 3.16
55 56 2.602257 TTGCATCTCCATACACTCGG 57.398 50.000 0.00 0.00 0.00 4.63
62 63 6.765512 TCACGATGTAAATTTGCATCTCCATA 59.234 34.615 32.67 18.32 44.72 2.74
68 69 5.030295 CACCTCACGATGTAAATTTGCATC 58.970 41.667 29.09 29.09 43.86 3.91
107 108 0.244450 ATTACGTCACCGCTTTCCGA 59.756 50.000 0.00 0.00 40.02 4.55
109 110 3.547649 AAAATTACGTCACCGCTTTCC 57.452 42.857 0.00 0.00 37.70 3.13
399 400 5.730296 ATCCCCAATAGAAGATGTAGACG 57.270 43.478 0.00 0.00 0.00 4.18
400 401 7.233757 ACAGTATCCCCAATAGAAGATGTAGAC 59.766 40.741 0.00 0.00 0.00 2.59
401 402 7.233553 CACAGTATCCCCAATAGAAGATGTAGA 59.766 40.741 0.00 0.00 0.00 2.59
402 403 7.233553 TCACAGTATCCCCAATAGAAGATGTAG 59.766 40.741 0.00 0.00 0.00 2.74
403 404 7.073208 TCACAGTATCCCCAATAGAAGATGTA 58.927 38.462 0.00 0.00 0.00 2.29
404 405 5.905331 TCACAGTATCCCCAATAGAAGATGT 59.095 40.000 0.00 0.00 0.00 3.06
405 406 6.268617 TCTCACAGTATCCCCAATAGAAGATG 59.731 42.308 0.00 0.00 0.00 2.90
406 407 6.385443 TCTCACAGTATCCCCAATAGAAGAT 58.615 40.000 0.00 0.00 0.00 2.40
407 408 5.777449 TCTCACAGTATCCCCAATAGAAGA 58.223 41.667 0.00 0.00 0.00 2.87
408 409 5.011533 CCTCTCACAGTATCCCCAATAGAAG 59.988 48.000 0.00 0.00 0.00 2.85
418 419 3.526534 GTTTGCTCCTCTCACAGTATCC 58.473 50.000 0.00 0.00 0.00 2.59
450 451 2.420967 GGATGGTTAAGCCGCTAAGGAA 60.421 50.000 1.51 0.00 45.00 3.36
451 452 1.140252 GGATGGTTAAGCCGCTAAGGA 59.860 52.381 1.51 0.00 45.00 3.36
452 453 1.141053 AGGATGGTTAAGCCGCTAAGG 59.859 52.381 1.51 0.00 44.97 2.69
453 454 2.622064 AGGATGGTTAAGCCGCTAAG 57.378 50.000 1.51 0.00 41.21 2.18
454 455 3.644265 TGATAGGATGGTTAAGCCGCTAA 59.356 43.478 1.51 0.00 41.21 3.09
455 456 3.236047 TGATAGGATGGTTAAGCCGCTA 58.764 45.455 1.51 0.00 41.21 4.26
456 457 2.037772 CTGATAGGATGGTTAAGCCGCT 59.962 50.000 1.51 0.00 41.21 5.52
460 461 3.492102 TGGCTGATAGGATGGTTAAGC 57.508 47.619 0.00 0.00 0.00 3.09
508 509 0.875908 GCATGTCGAGGCGATGCTTA 60.876 55.000 7.83 0.00 38.38 3.09
577 578 1.411394 TTTCGTCGAACTACAAGGCG 58.589 50.000 7.29 0.00 0.00 5.52
688 702 7.101652 ACTCTTCATCTTGTATACATCGTGT 57.898 36.000 6.36 0.00 0.00 4.49
759 773 6.319048 AGTTGACAATGGGACTGATATCTT 57.681 37.500 3.98 0.00 0.00 2.40
845 861 4.269603 CACAAAGTAAGCTGATCTCATCGG 59.730 45.833 0.00 0.00 38.71 4.18
851 867 6.525629 ACTGTTACACAAAGTAAGCTGATCT 58.474 36.000 0.00 0.00 43.06 2.75
884 900 1.374125 CGCCATGGTCAAGTCGTCA 60.374 57.895 14.67 0.00 0.00 4.35
945 961 0.678395 AGCTCGGGATGCTCTGTATG 59.322 55.000 0.00 0.00 35.67 2.39
957 973 0.465705 TCTGCCAAAGATAGCTCGGG 59.534 55.000 0.00 0.00 0.00 5.14
959 975 2.606725 CTGTTCTGCCAAAGATAGCTCG 59.393 50.000 0.00 0.00 33.93 5.03
968 993 1.398692 GTGGGTTCTGTTCTGCCAAA 58.601 50.000 0.00 0.00 0.00 3.28
1051 1079 2.595463 TGCTGCACCTGCCAGAAC 60.595 61.111 0.00 0.00 41.18 3.01
1076 1104 1.003476 TGCTCATCTTGCTCGCCAA 60.003 52.632 0.00 0.00 0.00 4.52
1077 1105 1.449070 CTGCTCATCTTGCTCGCCA 60.449 57.895 0.00 0.00 0.00 5.69
1080 1108 2.007549 CTGCTGCTCATCTTGCTCG 58.992 57.895 0.00 0.00 0.00 5.03
1110 1147 2.046285 GTTGTCTTGGCATCCCGGG 61.046 63.158 16.85 16.85 0.00 5.73
1116 1153 2.629656 GCCGCAGTTGTCTTGGCAT 61.630 57.895 0.00 0.00 40.39 4.40
1121 1158 0.311790 CATGTTGCCGCAGTTGTCTT 59.688 50.000 0.00 0.00 0.00 3.01
1122 1159 0.534877 TCATGTTGCCGCAGTTGTCT 60.535 50.000 0.00 0.00 0.00 3.41
1128 1165 1.063649 GATGCTCATGTTGCCGCAG 59.936 57.895 10.03 0.00 35.66 5.18
1247 1284 0.996727 GTTCGTTGCGGTTGTCATGC 60.997 55.000 0.00 0.00 0.00 4.06
1249 1286 0.306533 GTGTTCGTTGCGGTTGTCAT 59.693 50.000 0.00 0.00 0.00 3.06
1250 1287 1.707239 GGTGTTCGTTGCGGTTGTCA 61.707 55.000 0.00 0.00 0.00 3.58
1251 1288 1.010462 GGTGTTCGTTGCGGTTGTC 60.010 57.895 0.00 0.00 0.00 3.18
1252 1289 1.098712 ATGGTGTTCGTTGCGGTTGT 61.099 50.000 0.00 0.00 0.00 3.32
1253 1290 0.385473 GATGGTGTTCGTTGCGGTTG 60.385 55.000 0.00 0.00 0.00 3.77
1254 1291 0.816018 TGATGGTGTTCGTTGCGGTT 60.816 50.000 0.00 0.00 0.00 4.44
1257 1294 1.154672 CGTGATGGTGTTCGTTGCG 60.155 57.895 0.00 0.00 0.00 4.85
1258 1295 1.440353 GCGTGATGGTGTTCGTTGC 60.440 57.895 0.00 0.00 0.00 4.17
1260 1297 0.249699 TGAGCGTGATGGTGTTCGTT 60.250 50.000 0.00 0.00 0.00 3.85
1300 1337 0.824182 AGATAGGGGGCGTCGAAGAG 60.824 60.000 1.37 0.00 36.95 2.85
1304 1341 2.520982 CCAGATAGGGGGCGTCGA 60.521 66.667 0.00 0.00 0.00 4.20
1323 1363 3.306379 GGGAACGAGTACCCCAGG 58.694 66.667 8.23 0.00 40.19 4.45
1327 1367 0.321034 GTGTTGGGGAACGAGTACCC 60.321 60.000 4.35 4.35 44.94 3.69
1328 1368 0.321034 GGTGTTGGGGAACGAGTACC 60.321 60.000 0.00 0.00 0.00 3.34
1329 1369 0.683412 AGGTGTTGGGGAACGAGTAC 59.317 55.000 0.00 0.00 0.00 2.73
1339 1379 2.347490 CCAGGTCGAGGTGTTGGG 59.653 66.667 0.00 0.00 0.00 4.12
1358 1398 1.977009 ACGTCCATGAGCTCGACCA 60.977 57.895 9.64 0.00 0.00 4.02
1404 1444 2.803817 GGACGTGATGGGGCCGTAT 61.804 63.158 0.00 0.00 34.51 3.06
1438 1478 6.480320 TCTTCTTTGAGCTTGAAGTGAGTAAC 59.520 38.462 14.70 0.00 38.52 2.50
1440 1480 6.161855 TCTTCTTTGAGCTTGAAGTGAGTA 57.838 37.500 14.70 0.04 38.52 2.59
1443 1483 4.384056 CCTCTTCTTTGAGCTTGAAGTGA 58.616 43.478 16.15 11.82 38.52 3.41
1446 1486 2.487372 GGCCTCTTCTTTGAGCTTGAAG 59.513 50.000 0.00 11.13 38.69 3.02
1448 1488 1.421268 TGGCCTCTTCTTTGAGCTTGA 59.579 47.619 3.32 0.00 33.02 3.02
1522 1585 1.141881 CGCTAACACTCCAGCCGAT 59.858 57.895 0.00 0.00 34.15 4.18
1533 1596 0.679505 AGCTGTCCTTGACGCTAACA 59.320 50.000 10.34 0.00 39.26 2.41
1536 1599 1.506718 CGAGCTGTCCTTGACGCTA 59.493 57.895 11.50 0.00 40.34 4.26
1537 1600 2.259818 CGAGCTGTCCTTGACGCT 59.740 61.111 11.40 11.40 41.84 5.07
1555 1621 2.202440 CGTCGTGTAGGTGGAGCG 60.202 66.667 0.00 0.00 0.00 5.03
1678 1747 3.374402 AGCGACGGTGCTGTAGCT 61.374 61.111 11.97 11.97 45.28 3.32
1761 1836 2.223502 GCGTGACTTCTCGATCACCATA 60.224 50.000 10.47 0.00 41.87 2.74
1799 1874 2.149803 CTTGTCGCCGTACAGGTCCA 62.150 60.000 0.00 0.00 43.70 4.02
1857 1944 1.136984 GACGATGGCGAAGTCGAGT 59.863 57.895 4.59 0.00 43.02 4.18
2073 2160 5.388654 AGGATGGAAATTATTAGCCTGTGG 58.611 41.667 0.00 0.00 0.00 4.17
2146 2264 5.167121 CACTCATCGATGTCTTCAGAAGTT 58.833 41.667 24.09 1.57 0.00 2.66
2153 2271 3.257393 ACTTGCACTCATCGATGTCTTC 58.743 45.455 24.09 12.90 0.00 2.87
2536 2654 6.653526 TCATAGAACGGATCCGGTAATAAA 57.346 37.500 35.87 14.87 40.58 1.40
2545 2663 9.503399 AATAAAGGTATTTCATAGAACGGATCC 57.497 33.333 0.00 0.00 0.00 3.36
2795 3091 0.458669 CAAATGTGCAGGCCATCCTC 59.541 55.000 5.01 0.00 41.93 3.71
2913 5922 8.928733 GGATGACAACTTAAGAAACAACGTATA 58.071 33.333 10.09 0.00 0.00 1.47
2916 5925 5.820947 AGGATGACAACTTAAGAAACAACGT 59.179 36.000 10.09 2.33 0.00 3.99
3341 7402 7.432252 CCATTAATCGTCTTCTTAATTGCAACC 59.568 37.037 0.00 0.00 0.00 3.77
3350 7411 7.068348 AGCAGACTACCATTAATCGTCTTCTTA 59.932 37.037 0.00 0.00 33.02 2.10
3364 7425 3.378512 TCATTCTCCAGCAGACTACCAT 58.621 45.455 0.00 0.00 0.00 3.55
3458 7519 3.624707 GCAATGGGGTATCAACTTCCAGA 60.625 47.826 0.00 0.00 34.26 3.86
3533 7594 3.857093 CCAAGTTCAAAGGTTTGTTGTCG 59.143 43.478 2.49 0.00 39.18 4.35
3680 7741 1.159285 CGAAGTCTGCAATCTTGGCA 58.841 50.000 7.61 0.00 39.32 4.92
3893 7954 7.418368 CCTCTTCTATGAGCTCCAATGAAACTA 60.418 40.741 12.15 0.00 33.02 2.24
3913 7974 1.604915 GTTGCCCTCTCCCCTCTTC 59.395 63.158 0.00 0.00 0.00 2.87
4337 8399 1.271325 CCCATGTTCCAGTGTAGCACA 60.271 52.381 2.01 0.00 36.74 4.57
4376 8438 6.552350 AGCCCATAGTGCAATTATTCTTCATT 59.448 34.615 0.00 0.00 0.00 2.57
4377 8439 6.073314 AGCCCATAGTGCAATTATTCTTCAT 58.927 36.000 0.00 0.00 0.00 2.57
4378 8440 5.448654 AGCCCATAGTGCAATTATTCTTCA 58.551 37.500 0.00 0.00 0.00 3.02
4379 8441 7.510549 TTAGCCCATAGTGCAATTATTCTTC 57.489 36.000 0.00 0.00 0.00 2.87
4380 8442 7.094634 CGATTAGCCCATAGTGCAATTATTCTT 60.095 37.037 0.00 0.00 0.00 2.52
4381 8443 6.372659 CGATTAGCCCATAGTGCAATTATTCT 59.627 38.462 0.00 0.00 0.00 2.40
4382 8444 6.403636 CCGATTAGCCCATAGTGCAATTATTC 60.404 42.308 0.00 0.00 0.00 1.75
4383 8445 5.415701 CCGATTAGCCCATAGTGCAATTATT 59.584 40.000 0.00 0.00 0.00 1.40
4384 8446 4.943705 CCGATTAGCCCATAGTGCAATTAT 59.056 41.667 0.00 0.00 0.00 1.28
4385 8447 4.323417 CCGATTAGCCCATAGTGCAATTA 58.677 43.478 0.00 0.00 0.00 1.40
4386 8448 3.149196 CCGATTAGCCCATAGTGCAATT 58.851 45.455 0.00 0.00 0.00 2.32
4387 8449 2.783135 CCGATTAGCCCATAGTGCAAT 58.217 47.619 0.00 0.00 0.00 3.56
4388 8450 1.813862 GCCGATTAGCCCATAGTGCAA 60.814 52.381 0.00 0.00 0.00 4.08
4389 8451 0.250295 GCCGATTAGCCCATAGTGCA 60.250 55.000 0.00 0.00 0.00 4.57
4390 8452 2.544726 GCCGATTAGCCCATAGTGC 58.455 57.895 0.00 0.00 0.00 4.40
4423 8485 1.538047 GTTGAAGCCAAGCTGGATGA 58.462 50.000 6.40 0.00 40.96 2.92
4426 8488 1.600636 CCGTTGAAGCCAAGCTGGA 60.601 57.895 6.40 0.00 40.96 3.86
4527 8596 1.238439 CACGAAGTTGGCAAGTCCAT 58.762 50.000 8.24 0.00 46.04 3.41
4533 8602 0.950836 CATGACCACGAAGTTGGCAA 59.049 50.000 0.00 0.00 46.95 4.52
4654 8726 7.387948 GGTATCGCTAATGTCAGGTGAAATTAT 59.612 37.037 3.53 0.00 34.66 1.28
4683 8756 2.319011 GACATCCGTCGCGTCTGCTA 62.319 60.000 5.77 0.00 39.65 3.49
4763 8841 4.442401 ACTCATCATTGACATGGCCATA 57.558 40.909 20.30 2.40 0.00 2.74
4773 8852 2.419159 CGGAGGAGCAACTCATCATTGA 60.419 50.000 10.95 0.00 42.21 2.57
4799 8878 1.066152 CATCTCCTCGACGAGCATCAA 59.934 52.381 19.55 3.03 33.17 2.57
4986 9069 1.228245 GGCAGGCAGACAAAGGTCA 60.228 57.895 0.00 0.00 46.80 4.02
5006 9097 2.661574 ATTGCTGTGGGTTGGCAGGT 62.662 55.000 0.00 0.00 37.28 4.00
5027 9118 0.826715 CAGAAGAAGGAGATGGCCGA 59.173 55.000 0.00 0.00 0.00 5.54
5077 9168 4.008933 ACAGCCTCCTCGCGCTTT 62.009 61.111 5.56 0.00 31.40 3.51


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

AutoCloner maintained by Alex Coulton.