Multiple sequence alignment - TraesCS4A01G077200

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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 TraesCS4A01G077200 chr4A 100.000 7866 0 0 975 8840 76414777 76422642 0.000000e+00 14526.0
1 TraesCS4A01G077200 chr4A 100.000 475 0 0 1 475 76413803 76414277 0.000000e+00 878.0
2 TraesCS4A01G077200 chr4A 91.824 159 5 1 2306 2464 76416033 76416183 1.930000e-51 215.0
3 TraesCS4A01G077200 chr4A 91.824 159 5 1 2231 2381 76416108 76416266 1.930000e-51 215.0
4 TraesCS4A01G077200 chr4A 85.714 84 4 1 2381 2464 76416033 76416108 2.050000e-11 82.4
5 TraesCS4A01G077200 chr4A 85.714 84 4 1 2231 2306 76416183 76416266 2.050000e-11 82.4
6 TraesCS4A01G077200 chr4D 96.037 7519 188 43 994 8483 394846401 394853838 0.000000e+00 12133.0
7 TraesCS4A01G077200 chr4D 89.855 345 17 9 8505 8832 394853832 394854175 2.280000e-115 427.0
8 TraesCS4A01G077200 chr4D 89.262 298 13 6 179 475 394845724 394846003 1.090000e-93 355.0
9 TraesCS4A01G077200 chr4D 92.357 157 10 1 1 157 394845290 394845444 1.160000e-53 222.0
10 TraesCS4A01G077200 chr4D 96.825 126 4 0 2231 2356 394847719 394847844 2.500000e-50 211.0
11 TraesCS4A01G077200 chr4D 90.566 159 7 1 2306 2464 394847644 394847794 4.180000e-48 204.0
12 TraesCS4A01G077200 chr4D 95.652 46 2 0 147 192 394845661 394845706 3.420000e-09 75.0
13 TraesCS4A01G077200 chr4B 95.815 6643 187 33 2231 8832 485548018 485554610 0.000000e+00 10643.0
14 TraesCS4A01G077200 chr4B 95.607 865 33 4 2249 3109 485544790 485545653 0.000000e+00 1382.0
15 TraesCS4A01G077200 chr4B 95.216 857 24 3 1608 2464 485547329 485548168 0.000000e+00 1339.0
16 TraesCS4A01G077200 chr4B 92.976 840 40 6 975 1811 485546505 485547328 0.000000e+00 1206.0
17 TraesCS4A01G077200 chr4B 88.000 300 14 8 179 475 485546148 485546428 1.420000e-87 335.0
18 TraesCS4A01G077200 chr4B 92.357 157 9 3 1 157 485545715 485545868 4.150000e-53 220.0
19 TraesCS4A01G077200 chr4B 91.195 159 6 1 2306 2464 485547943 485548093 8.990000e-50 209.0
20 TraesCS4A01G077200 chr4B 90.566 159 7 5 2231 2381 485548093 485548251 4.180000e-48 204.0
21 TraesCS4A01G077200 chr4B 88.050 159 11 5 2231 2381 485544847 485545005 1.960000e-41 182.0
22 TraesCS4A01G077200 chr4B 89.362 141 7 1 2324 2464 485544790 485544922 4.240000e-38 171.0


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 TraesCS4A01G077200 chr4A 76413803 76422642 8839 False 7702.00 14526 100.000000 1 8840 2 chr4A.!!$F1 8839
1 TraesCS4A01G077200 chr4D 394845290 394853838 8548 False 3196.25 12133 93.327000 1 8483 4 chr4D.!!$F2 8482
2 TraesCS4A01G077200 chr4B 485544790 485554610 9820 False 1743.00 10643 92.064222 1 8832 9 chr4B.!!$F2 8831

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
240 1425 0.179040 GTGTTCCACGAGGACCCAAA 60.179 55.0 0.00 0.00 45.73 3.28 F
351 1538 0.316204 AACCAGTAGAACGGACCGTG 59.684 55.0 22.53 8.59 39.99 4.94 F
1790 3185 0.667792 GAGTCGTCTCGCAAAGGCTT 60.668 55.0 0.00 0.00 38.10 4.35 F
2469 3940 0.109132 GCTGTAAATGTGCTGGTGCC 60.109 55.0 0.00 0.00 38.71 5.01 F
3162 4637 0.323999 ATCATGCATGTGGCTGTGGT 60.324 50.0 25.43 0.00 45.15 4.16 F
4001 5478 0.320050 TCTGTGTTGCGGACTATGCA 59.680 50.0 0.00 0.00 41.38 3.96 F
4022 5499 0.321564 TTCAATGCGAGGTCAGGGTG 60.322 55.0 0.00 0.00 0.00 4.61 F
4948 6426 0.782384 GTGTAACACGCCAGTTCTCG 59.218 55.0 0.00 0.00 36.32 4.04 F
6493 7980 0.761187 ATCAGCCATATGGACAGCGT 59.239 50.0 26.47 2.59 37.39 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1767 3162 0.994995 CTTTGCGAGACGACTCCATG 59.005 55.000 9.30 0.0 39.76 3.66 R
1878 3273 6.071108 TGACAGAATTTTGTTTTCCCAACTCA 60.071 34.615 2.77 0.0 0.00 3.41 R
3731 5206 0.706729 CGGTCGACAGTAAAACTCGC 59.293 55.000 18.91 0.0 0.00 5.03 R
4001 5478 1.004745 ACCCTGACCTCGCATTGAAAT 59.995 47.619 0.00 0.0 0.00 2.17 R
4568 6046 1.627329 GGCATCATCCTCCTGCTCATA 59.373 52.381 0.00 0.0 36.18 2.15 R
5300 6787 0.741221 CGGCGCCTTCTCTAAAAGCT 60.741 55.000 26.68 0.0 0.00 3.74 R
6011 7498 0.107066 TCCATTGATCGCCACTGCAT 60.107 50.000 0.00 0.0 37.32 3.96 R
6784 8271 1.295792 TTCCTGCACACGTCTCAAAC 58.704 50.000 0.00 0.0 0.00 2.93 R
7949 9438 0.109597 ATAACGCTGCTTGTGCTTGC 60.110 50.000 0.00 0.0 40.48 4.01 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
78 1004 9.927668 AAAAGGATGTAAACTATTTCCATGTTG 57.072 29.630 0.00 0.00 0.00 3.33
82 1008 8.184192 GGATGTAAACTATTTCCATGTTGTCTG 58.816 37.037 0.00 0.00 0.00 3.51
86 1012 4.848357 ACTATTTCCATGTTGTCTGGGAG 58.152 43.478 0.00 0.00 34.36 4.30
91 1017 3.486383 TCCATGTTGTCTGGGAGTTTTC 58.514 45.455 0.00 0.00 34.36 2.29
141 1067 1.097547 GCTGAATGGGGGATGACACG 61.098 60.000 0.00 0.00 0.00 4.49
147 1073 2.662596 GGGGATGACACGCTCACA 59.337 61.111 0.00 0.00 0.00 3.58
205 1390 1.362768 CATGTGACACCCATCGACTG 58.637 55.000 2.45 0.00 0.00 3.51
223 1408 1.196808 CTGTGAAACGGGAATTCGGTG 59.803 52.381 0.00 0.00 42.39 4.94
240 1425 0.179040 GTGTTCCACGAGGACCCAAA 60.179 55.000 0.00 0.00 45.73 3.28
243 1428 1.003233 GTTCCACGAGGACCCAAAGAT 59.997 52.381 0.00 0.00 45.73 2.40
252 1437 4.378046 CGAGGACCCAAAGATAAAAACACG 60.378 45.833 0.00 0.00 0.00 4.49
255 1440 4.460505 GACCCAAAGATAAAAACACGTCG 58.539 43.478 0.00 0.00 0.00 5.12
349 1536 1.706443 GAAACCAGTAGAACGGACCG 58.294 55.000 13.61 13.61 0.00 4.79
350 1537 1.000171 GAAACCAGTAGAACGGACCGT 60.000 52.381 15.37 15.37 43.97 4.83
351 1538 0.316204 AACCAGTAGAACGGACCGTG 59.684 55.000 22.53 8.59 39.99 4.94
353 1540 1.445582 CAGTAGAACGGACCGTGGC 60.446 63.158 22.53 15.90 39.99 5.01
379 1566 2.922740 AAAACCAGTAGAACGCCTGA 57.077 45.000 0.00 0.00 0.00 3.86
380 1567 2.922740 AAACCAGTAGAACGCCTGAA 57.077 45.000 0.00 0.00 0.00 3.02
381 1568 2.165319 AACCAGTAGAACGCCTGAAC 57.835 50.000 0.00 0.00 0.00 3.18
1254 2442 4.496670 CCTCCAGAAGGTAACGCG 57.503 61.111 3.53 3.53 40.67 6.01
1550 2741 9.753674 TTATGGTTCTTAGATTCAACAGGATTT 57.246 29.630 0.00 0.00 0.00 2.17
1602 2793 6.385766 ACTAGTACTAGTTACTCTGTGGGT 57.614 41.667 26.61 3.55 43.35 4.51
1606 2797 3.363627 ACTAGTTACTCTGTGGGTAGCC 58.636 50.000 3.29 3.29 0.00 3.93
1767 3162 2.814336 GGTTGAATTGGAGTGGTCAGTC 59.186 50.000 0.00 0.00 0.00 3.51
1790 3185 0.667792 GAGTCGTCTCGCAAAGGCTT 60.668 55.000 0.00 0.00 38.10 4.35
1842 3237 4.662468 TCTTCCTGATTCGAGAAGGATG 57.338 45.455 12.09 13.56 39.80 3.51
2055 3451 6.787085 ACTTTACATCTTTCACTTCCTTCG 57.213 37.500 0.00 0.00 0.00 3.79
2060 3456 5.738909 ACATCTTTCACTTCCTTCGATGAT 58.261 37.500 0.00 0.00 33.10 2.45
2061 3457 6.878317 ACATCTTTCACTTCCTTCGATGATA 58.122 36.000 0.00 0.00 33.10 2.15
2062 3458 6.983307 ACATCTTTCACTTCCTTCGATGATAG 59.017 38.462 0.00 0.00 33.10 2.08
2365 3761 4.043200 GCACTCCGCCTTGGTTGC 62.043 66.667 0.00 0.00 39.52 4.17
2403 3874 4.758165 TCAATTTTCCGTTACAACTCTCCC 59.242 41.667 0.00 0.00 0.00 4.30
2417 3888 2.203788 TCCCGAGGCACCTTGACT 60.204 61.111 5.43 0.00 39.41 3.41
2421 3892 1.237285 CCGAGGCACCTTGACTTTGG 61.237 60.000 5.43 0.00 34.53 3.28
2434 3905 3.240606 CTTTGGTGCACTCCGCGTG 62.241 63.158 17.98 0.00 46.97 5.34
2456 3927 0.605319 CGCCTTGGTTGGAGCTGTAA 60.605 55.000 0.00 0.00 0.00 2.41
2469 3940 0.109132 GCTGTAAATGTGCTGGTGCC 60.109 55.000 0.00 0.00 38.71 5.01
2530 4001 1.165270 AGATTTTTCTTGTCCCCGCG 58.835 50.000 0.00 0.00 0.00 6.46
2680 4151 6.966534 AACTTGTTTCAGTTCTGGAATGAT 57.033 33.333 0.00 0.00 30.76 2.45
3011 4482 6.677913 AGTGTAAACAATTGTGCCATAACTC 58.322 36.000 12.82 5.72 0.00 3.01
3054 4525 3.942829 TCTCTGCATTGGTGAACTAAGG 58.057 45.455 0.00 0.00 0.00 2.69
3162 4637 0.323999 ATCATGCATGTGGCTGTGGT 60.324 50.000 25.43 0.00 45.15 4.16
3263 4738 3.436704 AGGTATTTGACAATGCACGACTG 59.563 43.478 0.00 0.00 0.00 3.51
3546 5021 3.686726 AGAGGCTTTTCGTTTCATGCTAG 59.313 43.478 0.00 0.00 0.00 3.42
3557 5032 7.485418 TCGTTTCATGCTAGTTCAAGTTAAA 57.515 32.000 0.00 0.00 0.00 1.52
3587 5062 9.436957 CATAAAACACTACTCATTGAACTAGGT 57.563 33.333 0.00 0.00 0.00 3.08
3639 5114 4.262635 CCGAACTCTGCTTATATCCACCAT 60.263 45.833 0.00 0.00 0.00 3.55
3752 5227 2.860062 CGAGTTTTACTGTCGACCGAT 58.140 47.619 14.12 0.46 35.70 4.18
3824 5301 8.165239 TGCTGACATTTGTTAGTATTTTCTGT 57.835 30.769 4.66 0.00 34.54 3.41
3825 5302 9.278978 TGCTGACATTTGTTAGTATTTTCTGTA 57.721 29.630 4.66 0.00 34.54 2.74
3852 5329 7.762159 AGCTGCTAATAGAAGAGTTAACAGTTC 59.238 37.037 8.61 9.75 30.52 3.01
3853 5330 7.545965 GCTGCTAATAGAAGAGTTAACAGTTCA 59.454 37.037 17.47 7.94 30.52 3.18
4001 5478 0.320050 TCTGTGTTGCGGACTATGCA 59.680 50.000 0.00 0.00 41.38 3.96
4021 5498 0.400213 TTTCAATGCGAGGTCAGGGT 59.600 50.000 0.00 0.00 0.00 4.34
4022 5499 0.321564 TTCAATGCGAGGTCAGGGTG 60.322 55.000 0.00 0.00 0.00 4.61
4023 5500 1.191489 TCAATGCGAGGTCAGGGTGA 61.191 55.000 0.00 0.00 0.00 4.02
4024 5501 1.021390 CAATGCGAGGTCAGGGTGAC 61.021 60.000 0.00 0.00 46.23 3.67
4065 5542 5.120399 CCATGCATTAAATTGAGTGGCATT 58.880 37.500 0.00 0.00 38.34 3.56
4077 5555 6.418057 TTGAGTGGCATTTGGTTAGAATTT 57.582 33.333 0.00 0.00 0.00 1.82
4215 5693 2.912295 TGGGACAGATGAAGGACAATCA 59.088 45.455 0.00 0.00 0.00 2.57
4281 5759 5.655532 CCAAAGAAGTGGGATTGATCTTGAT 59.344 40.000 0.00 0.00 34.77 2.57
4314 5792 8.900983 AAGATTATTTCATAACTCTGAGAGCC 57.099 34.615 12.44 0.00 32.04 4.70
4648 6126 0.966875 ATCCGCAGAAGCATGCCAAA 60.967 50.000 15.66 0.00 43.49 3.28
4754 6232 4.705507 TCGAGAGTTATTGGAAGCAGTACT 59.294 41.667 0.00 0.00 0.00 2.73
4879 6357 4.808364 CCAGCTTACTAGTTGATCTTCAGC 59.192 45.833 0.00 0.00 34.82 4.26
4901 6379 7.615365 TCAGCAAGATACATTATTCCTTGGTTT 59.385 33.333 0.00 0.00 41.70 3.27
4938 6416 6.074676 GGAAACTACAGTAACAGTGTAACACG 60.075 42.308 0.00 0.00 41.43 4.49
4947 6425 1.792949 CAGTGTAACACGCCAGTTCTC 59.207 52.381 0.00 0.00 41.43 2.87
4948 6426 0.782384 GTGTAACACGCCAGTTCTCG 59.218 55.000 0.00 0.00 36.32 4.04
4960 6442 4.357142 GCCAGTTCTCGTTATTCGTGATA 58.643 43.478 0.00 0.00 40.76 2.15
5072 6554 5.049060 TGTTTTGAGGTGATTGATACGTTGG 60.049 40.000 0.00 0.00 0.00 3.77
5139 6625 6.653740 ACTTTAGTTGCTACTTGGGTTGATAC 59.346 38.462 6.03 0.00 35.78 2.24
5221 6708 1.433534 GACTGTAGTCACCAGCAAGC 58.566 55.000 7.14 0.00 44.18 4.01
5225 6712 2.816087 CTGTAGTCACCAGCAAGCATTT 59.184 45.455 0.00 0.00 0.00 2.32
5239 6726 4.866486 GCAAGCATTTAGGATTTGTTGAGG 59.134 41.667 0.00 0.00 0.00 3.86
5300 6787 8.257306 ACTAAATTTTCTTTGCAGGTTGAGAAA 58.743 29.630 0.00 7.00 36.61 2.52
5318 6805 1.454201 AAGCTTTTAGAGAAGGCGCC 58.546 50.000 21.89 21.89 0.00 6.53
5811 7298 4.025061 CCACGCTGAGATTGAATCTTCATC 60.025 45.833 9.35 4.28 40.38 2.92
5920 7407 2.598589 CAGCAATCAAAACCATCACGG 58.401 47.619 0.00 0.00 42.50 4.94
5980 7467 4.872691 CACTCCTCTTGTTGGTATGATGAC 59.127 45.833 0.00 0.00 0.00 3.06
6011 7498 7.568349 AGATGAATCTAGAAGTGTTGGCAATA 58.432 34.615 1.92 0.00 34.85 1.90
6429 7916 1.991121 ACAGGACGTGAACCACTAGA 58.009 50.000 0.00 0.00 31.34 2.43
6433 7920 1.342174 GGACGTGAACCACTAGACCAA 59.658 52.381 0.00 0.00 31.34 3.67
6490 7977 3.766068 ACAGATCAGCCATATGGACAG 57.234 47.619 26.47 13.40 37.39 3.51
6493 7980 0.761187 ATCAGCCATATGGACAGCGT 59.239 50.000 26.47 2.59 37.39 5.07
6682 8169 1.137086 AGCAGTGTGACGTCTTTGAGT 59.863 47.619 17.92 0.00 0.00 3.41
6715 8202 4.924462 CCAGAATCATCATCATCTGACTCG 59.076 45.833 3.34 0.00 41.38 4.18
6784 8271 3.951979 AGAACTGCTTCACGTTCTTTG 57.048 42.857 0.00 0.00 45.42 2.77
7145 8632 3.067106 GAGCAAATTCTCAAGACACCGA 58.933 45.455 0.00 0.00 33.41 4.69
7387 8874 3.010420 GTCACCCAAAGATGGTAAGAGC 58.990 50.000 0.00 0.00 46.01 4.09
7777 9265 6.911250 AAACGAGGTAAATTTCCAATTCCT 57.089 33.333 0.00 0.00 0.00 3.36
7778 9266 6.911250 AACGAGGTAAATTTCCAATTCCTT 57.089 33.333 0.00 0.00 0.00 3.36
7779 9267 6.911250 ACGAGGTAAATTTCCAATTCCTTT 57.089 33.333 0.00 0.00 0.00 3.11
7780 9268 7.297936 ACGAGGTAAATTTCCAATTCCTTTT 57.702 32.000 0.00 0.00 0.00 2.27
7781 9269 7.732025 ACGAGGTAAATTTCCAATTCCTTTTT 58.268 30.769 0.00 0.00 0.00 1.94
7782 9270 7.870954 ACGAGGTAAATTTCCAATTCCTTTTTC 59.129 33.333 0.00 0.00 0.00 2.29
7783 9271 7.061789 CGAGGTAAATTTCCAATTCCTTTTTCG 59.938 37.037 0.00 0.00 0.00 3.46
7784 9272 7.732025 AGGTAAATTTCCAATTCCTTTTTCGT 58.268 30.769 0.00 0.00 0.00 3.85
7785 9273 8.208224 AGGTAAATTTCCAATTCCTTTTTCGTT 58.792 29.630 0.00 0.00 0.00 3.85
7786 9274 8.492748 GGTAAATTTCCAATTCCTTTTTCGTTC 58.507 33.333 0.00 0.00 0.00 3.95
7787 9275 9.256477 GTAAATTTCCAATTCCTTTTTCGTTCT 57.744 29.630 0.00 0.00 0.00 3.01
7788 9276 7.713764 AATTTCCAATTCCTTTTTCGTTCTG 57.286 32.000 0.00 0.00 0.00 3.02
7789 9277 4.237349 TCCAATTCCTTTTTCGTTCTGC 57.763 40.909 0.00 0.00 0.00 4.26
7790 9278 3.888930 TCCAATTCCTTTTTCGTTCTGCT 59.111 39.130 0.00 0.00 0.00 4.24
7808 9296 4.750098 TCTGCTTCAGTAGTTCCTTTTTCG 59.250 41.667 0.00 0.00 32.61 3.46
7818 9306 3.888930 AGTTCCTTTTTCGGAATGCTGAA 59.111 39.130 0.00 0.00 44.34 3.02
7900 9388 9.159470 GCTGTTTTTATCATCGCTTACTTATTC 57.841 33.333 0.00 0.00 0.00 1.75
7905 9393 8.607441 TTTATCATCGCTTACTTATTCTGCAT 57.393 30.769 0.00 0.00 0.00 3.96
7920 9409 0.328926 TGCATGGGATGAACTGCTGA 59.671 50.000 0.00 0.00 35.66 4.26
7953 9442 3.165606 GGTGATCACCTGGAGCAAG 57.834 57.895 33.47 0.00 44.79 4.01
7954 9443 1.028868 GGTGATCACCTGGAGCAAGC 61.029 60.000 33.47 6.64 44.79 4.01
7955 9444 0.321919 GTGATCACCTGGAGCAAGCA 60.322 55.000 15.31 0.00 44.79 3.91
7956 9445 0.321919 TGATCACCTGGAGCAAGCAC 60.322 55.000 0.00 0.00 39.36 4.40
7957 9446 0.321919 GATCACCTGGAGCAAGCACA 60.322 55.000 0.00 0.00 0.00 4.57
8020 9533 3.495753 CGAGCTAAAACCAACTAAACGGT 59.504 43.478 0.00 0.00 36.98 4.83
8039 9552 1.130561 GTCCTGCGGTGCTGTTTATTC 59.869 52.381 0.00 0.00 0.00 1.75
8095 9608 6.316640 TGACCTTAGAGAAGTCGTTAGATCAG 59.683 42.308 0.00 0.00 0.00 2.90
8158 9674 2.451693 TGTGGCGCAGAAACGTATC 58.548 52.632 10.83 0.00 34.88 2.24
8222 9738 3.070590 GGTTCTAGATTAGCCCCGCTTTA 59.929 47.826 0.00 0.00 40.44 1.85
8312 9828 4.620982 CAAAGGGGAAAGCTAACAACAAG 58.379 43.478 0.00 0.00 0.00 3.16
8322 9838 5.006153 AGCTAACAACAAGAAAAACCACC 57.994 39.130 0.00 0.00 0.00 4.61
8348 9864 3.997021 AGCATCCAAGAGTAGTCAAAACG 59.003 43.478 0.00 0.00 0.00 3.60
8376 9892 0.806868 AGCTTGAATGGTGATGCACG 59.193 50.000 0.00 0.00 34.83 5.34
8417 9933 1.432251 GTCATGGCAGATGCAGCAC 59.568 57.895 4.07 0.00 44.36 4.40
8446 9962 2.231964 CACAACCAATCATCACAAGGGG 59.768 50.000 0.00 0.00 0.00 4.79
8447 9963 2.158325 ACAACCAATCATCACAAGGGGT 60.158 45.455 0.00 0.00 0.00 4.95
8448 9964 2.899256 CAACCAATCATCACAAGGGGTT 59.101 45.455 0.00 0.00 37.62 4.11
8449 9965 2.528564 ACCAATCATCACAAGGGGTTG 58.471 47.619 0.00 0.00 0.00 3.77
8450 9966 2.109834 ACCAATCATCACAAGGGGTTGA 59.890 45.455 0.00 0.00 0.00 3.18
8479 9995 4.404073 AGATCATGGTGTCTAGAACAGGAC 59.596 45.833 9.07 5.32 38.97 3.85
8522 10038 1.764854 GGAACCCTATCCCCTCGCA 60.765 63.158 0.00 0.00 33.05 5.10
8533 10049 2.176273 CCCTCGCATTGGCTCGAAG 61.176 63.158 0.00 0.00 38.10 3.79
8538 10054 2.436646 CATTGGCTCGAAGGGCGT 60.437 61.111 0.00 0.00 41.80 5.68
8539 10055 2.125106 ATTGGCTCGAAGGGCGTC 60.125 61.111 0.00 0.00 41.80 5.19
8544 10060 3.048941 GCTCGAAGGGCGTCGTACT 62.049 63.158 8.75 0.00 41.80 2.73
8545 10061 1.226323 CTCGAAGGGCGTCGTACTG 60.226 63.158 8.75 0.00 41.80 2.74
8560 10076 5.276773 CGTCGTACTGTTGGAGTATAGAGAC 60.277 48.000 0.00 0.00 39.44 3.36
8568 10084 2.172930 TGGAGTATAGAGACGCTCACCT 59.827 50.000 9.09 0.47 32.06 4.00
8572 10088 2.719531 ATAGAGACGCTCACCTGAGA 57.280 50.000 6.49 0.00 44.74 3.27
8599 10115 0.613012 GGATGCCAACCTCAAAGCCT 60.613 55.000 0.00 0.00 0.00 4.58
8637 10153 1.811266 CTCGATTCGGGCACACCTG 60.811 63.158 6.18 0.00 44.63 4.00
8717 10233 0.108615 ATTGTCGTCGAAGGAGGCAG 60.109 55.000 0.00 0.00 0.00 4.85
8771 10287 2.358322 ACCGACCACAATGGAAAACT 57.642 45.000 0.84 0.00 40.96 2.66
8832 10348 0.472898 GGAACCCTATTCCCTTCCGG 59.527 60.000 0.00 0.00 32.48 5.14
8833 10349 0.179026 GAACCCTATTCCCTTCCGGC 60.179 60.000 0.00 0.00 0.00 6.13
8834 10350 0.623617 AACCCTATTCCCTTCCGGCT 60.624 55.000 0.00 0.00 0.00 5.52
8835 10351 0.623617 ACCCTATTCCCTTCCGGCTT 60.624 55.000 0.00 0.00 0.00 4.35
8836 10352 0.108774 CCCTATTCCCTTCCGGCTTC 59.891 60.000 0.00 0.00 0.00 3.86
8837 10353 1.132500 CCTATTCCCTTCCGGCTTCT 58.868 55.000 0.00 0.00 0.00 2.85
8838 10354 1.202698 CCTATTCCCTTCCGGCTTCTG 60.203 57.143 0.00 0.00 0.00 3.02
8839 10355 0.180406 TATTCCCTTCCGGCTTCTGC 59.820 55.000 0.00 0.00 38.76 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 1004 1.602377 CAACGTGGAAAACTCCCAGAC 59.398 52.381 0.00 0.00 33.75 3.51
82 1008 2.294979 AGAACAACGTGGAAAACTCCC 58.705 47.619 0.00 0.00 0.00 4.30
86 1012 4.870221 ACACTAGAACAACGTGGAAAAC 57.130 40.909 0.00 0.00 33.13 2.43
91 1017 5.004440 CGATTCATACACTAGAACAACGTGG 59.996 44.000 0.00 0.00 33.13 4.94
123 1049 1.097547 GCGTGTCATCCCCCATTCAG 61.098 60.000 0.00 0.00 0.00 3.02
205 1390 1.232119 ACACCGAATTCCCGTTTCAC 58.768 50.000 0.00 0.00 0.00 3.18
240 1425 2.222445 GTGGTGCGACGTGTTTTTATCT 59.778 45.455 0.00 0.00 0.00 1.98
243 1428 1.062294 GTGTGGTGCGACGTGTTTTTA 59.938 47.619 0.00 0.00 0.00 1.52
252 1437 0.517316 GAAATCTGGTGTGGTGCGAC 59.483 55.000 0.00 0.00 0.00 5.19
255 1440 1.069227 GTTCGAAATCTGGTGTGGTGC 60.069 52.381 0.00 0.00 0.00 5.01
360 1547 2.876550 GTTCAGGCGTTCTACTGGTTTT 59.123 45.455 0.00 0.00 35.47 2.43
362 1549 1.414919 TGTTCAGGCGTTCTACTGGTT 59.585 47.619 0.00 0.00 35.47 3.67
364 1551 2.163818 TTGTTCAGGCGTTCTACTGG 57.836 50.000 0.00 0.00 35.47 4.00
365 1552 2.345641 CGATTGTTCAGGCGTTCTACTG 59.654 50.000 0.00 0.00 36.07 2.74
366 1553 2.230508 TCGATTGTTCAGGCGTTCTACT 59.769 45.455 0.00 0.00 0.00 2.57
367 1554 2.602878 TCGATTGTTCAGGCGTTCTAC 58.397 47.619 0.00 0.00 0.00 2.59
368 1555 2.991190 GTTCGATTGTTCAGGCGTTCTA 59.009 45.455 0.00 0.00 0.00 2.10
369 1556 1.798813 GTTCGATTGTTCAGGCGTTCT 59.201 47.619 0.00 0.00 0.00 3.01
370 1557 1.136057 GGTTCGATTGTTCAGGCGTTC 60.136 52.381 0.00 0.00 0.00 3.95
371 1558 0.872388 GGTTCGATTGTTCAGGCGTT 59.128 50.000 0.00 0.00 0.00 4.84
372 1559 1.289109 CGGTTCGATTGTTCAGGCGT 61.289 55.000 0.00 0.00 0.00 5.68
373 1560 1.419922 CGGTTCGATTGTTCAGGCG 59.580 57.895 0.00 0.00 0.00 5.52
374 1561 1.134694 GCGGTTCGATTGTTCAGGC 59.865 57.895 0.00 0.00 0.00 4.85
375 1562 1.419922 CGCGGTTCGATTGTTCAGG 59.580 57.895 0.00 0.00 41.67 3.86
376 1563 1.225745 GCGCGGTTCGATTGTTCAG 60.226 57.895 8.83 0.00 41.67 3.02
377 1564 2.857448 GCGCGGTTCGATTGTTCA 59.143 55.556 8.83 0.00 41.67 3.18
378 1565 2.275812 CGCGCGGTTCGATTGTTC 60.276 61.111 24.84 0.00 41.67 3.18
379 1566 3.784412 CCGCGCGGTTCGATTGTT 61.784 61.111 39.71 0.00 41.67 2.83
1470 2660 1.345089 GCTAAGCTTAGTAGGGAGGGC 59.655 57.143 29.42 12.89 33.32 5.19
1550 2741 3.716195 CGTCAGGGGCACATGGGA 61.716 66.667 0.00 0.00 0.00 4.37
1602 2793 4.334552 TCAAAGTCAATGCAATCTGGCTA 58.665 39.130 0.00 0.00 34.04 3.93
1606 2797 4.921515 CCAACTCAAAGTCAATGCAATCTG 59.078 41.667 0.00 0.00 0.00 2.90
1767 3162 0.994995 CTTTGCGAGACGACTCCATG 59.005 55.000 9.30 0.00 39.76 3.66
1790 3185 6.174720 ACCAGTTCTAAATCAAGTGTCTCA 57.825 37.500 0.00 0.00 0.00 3.27
1842 3237 6.563422 TGACATGCCAGAATTATTGCTTTAC 58.437 36.000 0.00 0.00 0.00 2.01
1878 3273 6.071108 TGACAGAATTTTGTTTTCCCAACTCA 60.071 34.615 2.77 0.00 0.00 3.41
2060 3456 7.121463 GCTTGCTAGCTTATCATCCTACTACTA 59.879 40.741 17.23 0.00 44.27 1.82
2061 3457 6.071616 GCTTGCTAGCTTATCATCCTACTACT 60.072 42.308 17.23 0.00 44.27 2.57
2062 3458 6.096695 GCTTGCTAGCTTATCATCCTACTAC 58.903 44.000 17.23 0.00 44.27 2.73
2365 3761 5.346822 GGAAAATTGAGCACATTTACAGCTG 59.653 40.000 13.48 13.48 39.02 4.24
2403 3874 0.535102 ACCAAAGTCAAGGTGCCTCG 60.535 55.000 0.00 0.00 36.60 4.63
2417 3888 3.276091 CACGCGGAGTGCACCAAA 61.276 61.111 14.63 0.00 46.97 3.28
2434 3905 3.056328 GCTCCAACCAAGGCGGAC 61.056 66.667 0.00 0.00 38.63 4.79
2456 3927 0.673644 GAGTACGGCACCAGCACATT 60.674 55.000 0.00 0.00 44.61 2.71
2469 3940 8.655970 TCAATCATGATTTTACACAAGAGTACG 58.344 33.333 18.41 1.99 0.00 3.67
2514 3985 1.104630 AAACGCGGGGACAAGAAAAA 58.895 45.000 12.47 0.00 0.00 1.94
2783 4254 5.336150 TGCAGTGACTTGAAATTTTCCAA 57.664 34.783 6.68 0.00 0.00 3.53
3011 4482 9.840427 AGAGAACAAAATAAAATATGAACCACG 57.160 29.630 0.00 0.00 0.00 4.94
3042 4513 8.141298 TCATAGTTATCAACCTTAGTTCACCA 57.859 34.615 0.00 0.00 32.45 4.17
3263 4738 3.372514 GCATTTCTCGTTCCCTTTCTCTC 59.627 47.826 0.00 0.00 0.00 3.20
3557 5032 9.561069 AGTTCAATGAGTAGTGTTTTATGTCTT 57.439 29.630 0.00 0.00 0.00 3.01
3576 5051 7.763071 GTCCGTAAGTTGAATACCTAGTTCAAT 59.237 37.037 9.46 0.04 44.56 2.57
3587 5062 9.491675 TCAGTTATTTTGTCCGTAAGTTGAATA 57.508 29.630 0.00 0.00 0.00 1.75
3639 5114 3.578282 TGTTCTCTAGTGCATCTTCCACA 59.422 43.478 0.00 0.00 35.69 4.17
3708 5183 6.321435 CGCCAGGATCTTACCATATCTATACA 59.679 42.308 0.00 0.00 0.00 2.29
3731 5206 0.706729 CGGTCGACAGTAAAACTCGC 59.293 55.000 18.91 0.00 0.00 5.03
3752 5227 3.448301 CCAGCAGGCTTAAATGGAATCAA 59.552 43.478 0.00 0.00 32.55 2.57
3824 5301 8.750298 ACTGTTAACTCTTCTATTAGCAGCTTA 58.250 33.333 0.00 0.00 41.01 3.09
3825 5302 7.616313 ACTGTTAACTCTTCTATTAGCAGCTT 58.384 34.615 0.00 0.00 41.01 3.74
4001 5478 1.004745 ACCCTGACCTCGCATTGAAAT 59.995 47.619 0.00 0.00 0.00 2.17
4021 5498 3.244215 GGTCAACATTGAGGAGTCAGTCA 60.244 47.826 0.00 0.00 37.98 3.41
4022 5499 3.244215 TGGTCAACATTGAGGAGTCAGTC 60.244 47.826 0.00 0.00 37.98 3.51
4023 5500 2.705658 TGGTCAACATTGAGGAGTCAGT 59.294 45.455 0.00 0.00 37.98 3.41
4024 5501 3.407424 TGGTCAACATTGAGGAGTCAG 57.593 47.619 0.00 0.00 37.98 3.51
4215 5693 7.415429 CCAACATTTTCAAAGCCAAAAACATCT 60.415 33.333 0.00 0.00 0.00 2.90
4314 5792 2.587194 CGGCCATCGAGCTTCCAG 60.587 66.667 2.24 0.00 42.43 3.86
4529 6007 9.401058 AGTATTACAAATGCTCTCAATTAAGCT 57.599 29.630 7.81 0.00 39.31 3.74
4568 6046 1.627329 GGCATCATCCTCCTGCTCATA 59.373 52.381 0.00 0.00 36.18 2.15
4648 6126 3.795688 TCTCTTGCCAATTCAGGACTT 57.204 42.857 0.00 0.00 0.00 3.01
4754 6232 9.955208 GTGCAATCAGAATCATTCATTATACAA 57.045 29.630 0.00 0.00 0.00 2.41
4822 6300 6.877322 GCTAAGACACCTTAATTTGGTAGACA 59.123 38.462 3.01 0.00 35.80 3.41
4901 6379 9.485206 GTTACTGTAGTTTCCTTGTAAGATTGA 57.515 33.333 0.00 0.00 0.00 2.57
4938 6416 2.602878 TCACGAATAACGAGAACTGGC 58.397 47.619 0.00 0.00 45.77 4.85
4948 6426 9.953697 ACTAGAAGTCTTCATATCACGAATAAC 57.046 33.333 14.97 0.00 0.00 1.89
4960 6442 6.437477 TGACATACACCACTAGAAGTCTTCAT 59.563 38.462 14.97 3.06 0.00 2.57
5019 6501 7.420002 CATTGATCAACAGAAAGAGAACACAA 58.580 34.615 11.07 0.00 0.00 3.33
5111 6596 6.378848 TCAACCCAAGTAGCAACTAAAGTTTT 59.621 34.615 0.00 0.00 35.83 2.43
5122 6608 6.909550 AAAAATGTATCAACCCAAGTAGCA 57.090 33.333 0.00 0.00 0.00 3.49
5183 6669 3.774766 AGTCACACCAATAGTATGGCAGA 59.225 43.478 0.00 0.00 44.75 4.26
5220 6707 8.686334 TCTAATTCCTCAACAAATCCTAAATGC 58.314 33.333 0.00 0.00 0.00 3.56
5225 6712 7.918076 AGTGTCTAATTCCTCAACAAATCCTA 58.082 34.615 0.00 0.00 0.00 2.94
5239 6726 6.341316 TGCTTGGAGTATGAGTGTCTAATTC 58.659 40.000 0.00 0.00 0.00 2.17
5281 6768 3.701040 AGCTTTCTCAACCTGCAAAGAAA 59.299 39.130 0.00 0.00 36.57 2.52
5300 6787 0.741221 CGGCGCCTTCTCTAAAAGCT 60.741 55.000 26.68 0.00 0.00 3.74
5318 6805 0.879400 TTTGTGCATTTTGCTGGGCG 60.879 50.000 0.00 0.00 45.31 6.13
5920 7407 5.641636 GTCCTTTCTCAACCTCAGATTTCTC 59.358 44.000 0.00 0.00 0.00 2.87
5980 7467 2.294791 ACTTCTAGATTCATCTCGGCCG 59.705 50.000 22.12 22.12 38.32 6.13
6011 7498 0.107066 TCCATTGATCGCCACTGCAT 60.107 50.000 0.00 0.00 37.32 3.96
6429 7916 1.494721 TGGACCTTTCAGAAGCTTGGT 59.505 47.619 2.10 3.07 0.00 3.67
6433 7920 2.050144 TCAGTGGACCTTTCAGAAGCT 58.950 47.619 0.00 0.00 0.00 3.74
6490 7977 2.421424 AGCAGATTGATTTTCCTCACGC 59.579 45.455 0.00 0.00 0.00 5.34
6493 7980 5.771666 AGAACAAGCAGATTGATTTTCCTCA 59.228 36.000 5.14 0.00 41.83 3.86
6682 8169 5.306160 TGATGATGATTCTGGAGTATGAGCA 59.694 40.000 0.00 0.00 0.00 4.26
6715 8202 2.621526 GACTCTCTCCGAAGATTCCTCC 59.378 54.545 0.00 0.00 0.00 4.30
6784 8271 1.295792 TTCCTGCACACGTCTCAAAC 58.704 50.000 0.00 0.00 0.00 2.93
7145 8632 0.035630 GGCATGACTCTGAAGCTGGT 60.036 55.000 0.00 0.00 0.00 4.00
7387 8874 1.030488 TCCTTGCTACCGACTCTCCG 61.030 60.000 0.00 0.00 0.00 4.63
7444 8931 3.513662 CTTCACATCTGTCTGCTCTCTG 58.486 50.000 0.00 0.00 0.00 3.35
7776 9264 5.659048 ACTACTGAAGCAGAACGAAAAAG 57.341 39.130 0.82 0.00 35.18 2.27
7777 9265 5.007332 GGAACTACTGAAGCAGAACGAAAAA 59.993 40.000 0.82 0.00 35.18 1.94
7778 9266 4.510340 GGAACTACTGAAGCAGAACGAAAA 59.490 41.667 0.82 0.00 35.18 2.29
7779 9267 4.056050 GGAACTACTGAAGCAGAACGAAA 58.944 43.478 0.82 0.00 35.18 3.46
7780 9268 3.321111 AGGAACTACTGAAGCAGAACGAA 59.679 43.478 0.82 0.00 36.02 3.85
7781 9269 2.891580 AGGAACTACTGAAGCAGAACGA 59.108 45.455 0.82 0.00 36.02 3.85
7782 9270 3.305398 AGGAACTACTGAAGCAGAACG 57.695 47.619 0.82 0.00 36.02 3.95
7783 9271 6.378710 AAAAAGGAACTACTGAAGCAGAAC 57.621 37.500 0.82 0.00 38.49 3.01
7784 9272 5.236478 CGAAAAAGGAACTACTGAAGCAGAA 59.764 40.000 0.82 0.00 38.49 3.02
7785 9273 4.750098 CGAAAAAGGAACTACTGAAGCAGA 59.250 41.667 0.82 0.00 38.49 4.26
7786 9274 4.083802 CCGAAAAAGGAACTACTGAAGCAG 60.084 45.833 0.00 0.00 38.49 4.24
7787 9275 3.813166 CCGAAAAAGGAACTACTGAAGCA 59.187 43.478 0.00 0.00 38.49 3.91
7788 9276 4.062991 TCCGAAAAAGGAACTACTGAAGC 58.937 43.478 0.00 0.00 38.49 3.86
7808 9296 2.089980 ACATGACAGCTTCAGCATTCC 58.910 47.619 0.00 0.00 45.16 3.01
7818 9306 3.079578 CCAACTCATTCACATGACAGCT 58.920 45.455 0.00 0.00 34.22 4.24
7882 9370 6.591448 CCATGCAGAATAAGTAAGCGATGATA 59.409 38.462 0.00 0.00 0.00 2.15
7900 9388 0.738975 CAGCAGTTCATCCCATGCAG 59.261 55.000 0.00 0.00 41.14 4.41
7905 9393 1.191489 TCGGTCAGCAGTTCATCCCA 61.191 55.000 0.00 0.00 0.00 4.37
7949 9438 0.109597 ATAACGCTGCTTGTGCTTGC 60.110 50.000 0.00 0.00 40.48 4.01
7952 9441 2.009774 CCTAATAACGCTGCTTGTGCT 58.990 47.619 0.00 0.00 40.48 4.40
7953 9442 1.064060 CCCTAATAACGCTGCTTGTGC 59.936 52.381 0.00 0.00 40.20 4.57
7954 9443 2.627945 TCCCTAATAACGCTGCTTGTG 58.372 47.619 0.00 0.00 0.00 3.33
7955 9444 3.206150 CATCCCTAATAACGCTGCTTGT 58.794 45.455 0.00 0.00 0.00 3.16
7956 9445 3.206150 ACATCCCTAATAACGCTGCTTG 58.794 45.455 0.00 0.00 0.00 4.01
7957 9446 3.560636 ACATCCCTAATAACGCTGCTT 57.439 42.857 0.00 0.00 0.00 3.91
8039 9552 1.880027 GCTTAGGGATGTAAATGGCGG 59.120 52.381 0.00 0.00 0.00 6.13
8158 9674 2.857575 TAGCATGGTGTGAGCAGCGG 62.858 60.000 7.89 0.00 45.36 5.52
8222 9738 4.082245 CCAGGTTGATGGCTTCGTTAAATT 60.082 41.667 0.00 0.00 32.48 1.82
8312 9828 1.068541 GGATGCTCGTGGTGGTTTTTC 60.069 52.381 0.00 0.00 0.00 2.29
8322 9838 2.164422 TGACTACTCTTGGATGCTCGTG 59.836 50.000 0.00 0.00 0.00 4.35
8348 9864 3.003275 TCACCATTCAAGCTTTGTTCGTC 59.997 43.478 0.00 0.00 0.00 4.20
8391 9907 3.282021 GCATCTGCCATGACCTTCTTTA 58.718 45.455 0.00 0.00 34.31 1.85
8442 9958 4.264532 ACCATGATCTTCAAATCAACCCCT 60.265 41.667 0.00 0.00 39.04 4.79
8446 9962 6.506500 AGACACCATGATCTTCAAATCAAC 57.493 37.500 0.00 0.00 39.04 3.18
8447 9963 7.623630 TCTAGACACCATGATCTTCAAATCAA 58.376 34.615 0.00 0.00 39.04 2.57
8448 9964 7.186570 TCTAGACACCATGATCTTCAAATCA 57.813 36.000 0.00 0.00 39.85 2.57
8449 9965 7.550551 TGTTCTAGACACCATGATCTTCAAATC 59.449 37.037 0.00 0.00 32.00 2.17
8450 9966 7.397221 TGTTCTAGACACCATGATCTTCAAAT 58.603 34.615 0.00 0.00 32.00 2.32
8479 9995 4.873746 TCAGTGTTAGAGAAGGAAGGTG 57.126 45.455 0.00 0.00 0.00 4.00
8510 10026 0.321122 GAGCCAATGCGAGGGGATAG 60.321 60.000 0.00 0.00 44.33 2.08
8520 10036 3.880846 CGCCCTTCGAGCCAATGC 61.881 66.667 0.00 0.00 41.67 3.56
8522 10038 2.125106 GACGCCCTTCGAGCCAAT 60.125 61.111 0.00 0.00 41.67 3.16
8533 10049 1.445582 CTCCAACAGTACGACGCCC 60.446 63.158 0.00 0.00 0.00 6.13
8538 10054 4.807834 CGTCTCTATACTCCAACAGTACGA 59.192 45.833 0.00 0.00 40.60 3.43
8539 10055 4.552378 GCGTCTCTATACTCCAACAGTACG 60.552 50.000 0.00 0.00 40.60 3.67
8544 10060 3.377485 GTGAGCGTCTCTATACTCCAACA 59.623 47.826 8.07 0.00 0.00 3.33
8545 10061 3.243134 GGTGAGCGTCTCTATACTCCAAC 60.243 52.174 8.07 0.00 0.00 3.77
8568 10084 0.986527 TGGCATCCTTCTTGCTCTCA 59.013 50.000 0.00 0.00 40.03 3.27
8572 10088 0.407139 AGGTTGGCATCCTTCTTGCT 59.593 50.000 11.39 0.00 40.03 3.91
8599 10115 2.263852 CGCTCTGAGGCTGCTTCA 59.736 61.111 14.02 14.02 0.00 3.02
8717 10233 4.329545 TTCACCTCGGTGCCCTGC 62.330 66.667 11.21 0.00 45.04 4.85


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

AutoCloner maintained by Alex Coulton.