Multiple sequence alignment - TraesCS5D01G368900

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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 TraesCS5D01G368900 chr5D 100.000 4221 0 0 1 4221 444709659 444713879 0.000000e+00 7795.0
1 TraesCS5D01G368900 chr5D 84.468 1204 158 18 2137 3331 484427827 484426644 0.000000e+00 1160.0
2 TraesCS5D01G368900 chr5D 84.815 540 70 10 884 1421 484428966 484428437 2.230000e-147 532.0
3 TraesCS5D01G368900 chr5D 73.952 334 71 11 3901 4221 134455609 134455279 2.060000e-23 121.0
4 TraesCS5D01G368900 chr5B 91.440 2430 140 36 1823 4221 541499149 541501541 0.000000e+00 3273.0
5 TraesCS5D01G368900 chr5B 91.055 2437 154 30 1823 4221 541528052 541530462 0.000000e+00 3234.0
6 TraesCS5D01G368900 chr5B 95.006 1682 74 7 1 1677 541497474 541499150 0.000000e+00 2632.0
7 TraesCS5D01G368900 chr5B 96.371 1295 42 2 1 1292 541526267 541527559 0.000000e+00 2126.0
8 TraesCS5D01G368900 chr5B 84.577 1193 151 21 2148 3331 595632200 595631032 0.000000e+00 1153.0
9 TraesCS5D01G368900 chr5B 82.836 1206 174 23 2137 3331 595645628 595644445 0.000000e+00 1050.0
10 TraesCS5D01G368900 chr5B 84.787 539 72 5 884 1421 595633353 595632824 2.230000e-147 532.0
11 TraesCS5D01G368900 chr5B 95.023 221 10 1 1457 1677 541527834 541528053 3.120000e-91 346.0
12 TraesCS5D01G368900 chr5A 94.271 1536 66 10 2165 3697 561554064 561555580 0.000000e+00 2329.0
13 TraesCS5D01G368900 chr5A 94.662 1049 46 6 690 1728 561553016 561554064 0.000000e+00 1618.0
14 TraesCS5D01G368900 chr5A 83.181 1207 170 19 2137 3331 606059491 606058306 0.000000e+00 1074.0
15 TraesCS5D01G368900 chr5A 95.710 303 13 0 497 799 561552715 561553017 4.910000e-134 488.0
16 TraesCS5D01G368900 chr5A 93.525 139 9 0 319 457 561552576 561552714 1.540000e-49 207.0
17 TraesCS5D01G368900 chr5A 89.216 102 11 0 425 526 395300611 395300510 1.230000e-25 128.0
18 TraesCS5D01G368900 chr4D 80.074 813 140 14 2430 3234 52469010 52469808 6.080000e-163 584.0
19 TraesCS5D01G368900 chr4B 78.923 873 151 21 2430 3288 76814940 76815793 2.850000e-156 562.0
20 TraesCS5D01G368900 chr4B 94.643 56 2 1 1 56 327529793 327529739 7.520000e-13 86.1
21 TraesCS5D01G368900 chr7A 80.591 474 76 13 957 1417 126865011 126865481 6.710000e-93 351.0
22 TraesCS5D01G368900 chr7A 86.842 114 13 2 415 526 339753277 339753164 4.430000e-25 126.0
23 TraesCS5D01G368900 chr7A 78.571 140 26 4 4079 4218 7210282 7210417 5.810000e-14 89.8
24 TraesCS5D01G368900 chr2D 78.963 347 47 8 3896 4221 18298404 18298063 3.310000e-51 213.0
25 TraesCS5D01G368900 chr2D 80.339 295 41 7 3935 4221 619435154 619434869 1.540000e-49 207.0
26 TraesCS5D01G368900 chr2D 87.273 110 14 0 425 534 192181586 192181477 4.430000e-25 126.0
27 TraesCS5D01G368900 chr2D 85.321 109 16 0 425 533 480566681 480566573 3.450000e-21 113.0
28 TraesCS5D01G368900 chr2D 94.444 54 3 0 3 56 208540136 208540189 2.700000e-12 84.2
29 TraesCS5D01G368900 chr1A 78.710 310 45 9 3933 4221 303798738 303799047 2.000000e-43 187.0
30 TraesCS5D01G368900 chr3B 93.137 102 7 0 425 526 581966093 581965992 2.630000e-32 150.0
31 TraesCS5D01G368900 chr3B 85.455 110 16 0 424 533 665451208 665451099 9.590000e-22 115.0
32 TraesCS5D01G368900 chr3D 75.841 327 60 11 3901 4221 612309808 612310121 9.460000e-32 148.0
33 TraesCS5D01G368900 chr3D 89.091 110 12 0 424 533 281089345 281089454 2.050000e-28 137.0
34 TraesCS5D01G368900 chr3D 92.857 56 4 0 1 56 455952342 455952397 9.730000e-12 82.4
35 TraesCS5D01G368900 chr2A 91.089 101 9 0 425 525 469789681 469789781 2.050000e-28 137.0
36 TraesCS5D01G368900 chr2A 88.462 104 12 0 423 526 35967424 35967321 4.430000e-25 126.0
37 TraesCS5D01G368900 chr2B 77.833 203 33 6 4030 4221 424509870 424509669 9.590000e-22 115.0
38 TraesCS5D01G368900 chr2B 94.444 54 3 0 3 56 262903635 262903688 2.700000e-12 84.2
39 TraesCS5D01G368900 chr7D 87.000 100 12 1 436 534 301996983 301997082 1.240000e-20 111.0
40 TraesCS5D01G368900 chr1B 85.714 105 15 0 428 532 58802753 58802649 1.240000e-20 111.0
41 TraesCS5D01G368900 chr6D 78.378 148 27 5 4075 4221 134244097 134243954 1.620000e-14 91.6
42 TraesCS5D01G368900 chr6B 98.039 51 1 0 6 56 13827521 13827571 5.810000e-14 89.8
43 TraesCS5D01G368900 chr4A 98.039 51 1 0 6 56 127224726 127224676 5.810000e-14 89.8
44 TraesCS5D01G368900 chr3A 82.353 102 18 0 425 526 91026950 91027051 5.810000e-14 89.8
45 TraesCS5D01G368900 chr1D 98.000 50 1 0 7 56 111518776 111518825 2.090000e-13 87.9


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 TraesCS5D01G368900 chr5D 444709659 444713879 4220 False 7795.0 7795 100.000000 1 4221 1 chr5D.!!$F1 4220
1 TraesCS5D01G368900 chr5D 484426644 484428966 2322 True 846.0 1160 84.641500 884 3331 2 chr5D.!!$R2 2447
2 TraesCS5D01G368900 chr5B 541497474 541501541 4067 False 2952.5 3273 93.223000 1 4221 2 chr5B.!!$F1 4220
3 TraesCS5D01G368900 chr5B 541526267 541530462 4195 False 1902.0 3234 94.149667 1 4221 3 chr5B.!!$F2 4220
4 TraesCS5D01G368900 chr5B 595644445 595645628 1183 True 1050.0 1050 82.836000 2137 3331 1 chr5B.!!$R1 1194
5 TraesCS5D01G368900 chr5B 595631032 595633353 2321 True 842.5 1153 84.682000 884 3331 2 chr5B.!!$R2 2447
6 TraesCS5D01G368900 chr5A 561552576 561555580 3004 False 1160.5 2329 94.542000 319 3697 4 chr5A.!!$F1 3378
7 TraesCS5D01G368900 chr5A 606058306 606059491 1185 True 1074.0 1074 83.181000 2137 3331 1 chr5A.!!$R2 1194
8 TraesCS5D01G368900 chr4D 52469010 52469808 798 False 584.0 584 80.074000 2430 3234 1 chr4D.!!$F1 804
9 TraesCS5D01G368900 chr4B 76814940 76815793 853 False 562.0 562 78.923000 2430 3288 1 chr4B.!!$F1 858

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
181 182 1.065701 CGGGACACTTAGTGATCTCCG 59.934 57.143 20.07 19.02 36.96 4.63 F
867 978 1.135199 GTCACAATGCAGATGCTTGGG 60.135 52.381 16.12 13.64 42.66 4.12 F
1861 2208 0.396435 TCACACCTGCGACCTTGAAT 59.604 50.000 0.00 0.00 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1833 2180 1.002366 CGCAGGTGTGAACTATGCTC 58.998 55.000 0.00 0.0 34.75 4.26 R
2858 3230 2.024080 TGGGGAGCTTGAATTGCCTAAT 60.024 45.455 0.00 0.0 0.00 1.73 R
3273 3649 0.547075 TGACGGTTGAAACCCTTCCA 59.453 50.000 6.64 0.0 46.53 3.53 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
135 136 7.815549 TGTGTGATCTTAAGAAAACGCTATACA 59.184 33.333 23.81 15.51 0.00 2.29
163 164 5.432885 AATGAACAACTAAAAGGTCACGG 57.567 39.130 0.00 0.00 0.00 4.94
169 170 2.044758 ACTAAAAGGTCACGGGACACT 58.955 47.619 21.40 11.55 46.17 3.55
181 182 1.065701 CGGGACACTTAGTGATCTCCG 59.934 57.143 20.07 19.02 36.96 4.63
198 199 5.890424 TCTCCGAATAAATTGGTTGTTCC 57.110 39.130 0.00 0.00 34.69 3.62
433 434 4.660771 AGCTTGGCATTTAGTACTCCCTAT 59.339 41.667 0.00 0.00 0.00 2.57
460 461 5.414144 TCCATATTTGTTGTCGCTCAAATGA 59.586 36.000 11.66 1.15 42.01 2.57
526 527 5.279006 GCGACAACTAATATGGATCAGAGGA 60.279 44.000 0.00 0.00 0.00 3.71
695 698 3.527665 CCCGGGATAGGATGGGATATTTT 59.472 47.826 18.48 0.00 44.88 1.82
696 699 4.017499 CCCGGGATAGGATGGGATATTTTT 60.017 45.833 18.48 0.00 44.88 1.94
788 791 4.369182 ACGAGAGACAACAAACCACTTAG 58.631 43.478 0.00 0.00 0.00 2.18
865 976 1.542472 TGGTCACAATGCAGATGCTTG 59.458 47.619 6.35 10.12 42.66 4.01
867 978 1.135199 GTCACAATGCAGATGCTTGGG 60.135 52.381 16.12 13.64 42.66 4.12
1546 1777 2.040544 AGCCGCCTGTACATGTTGC 61.041 57.895 2.30 1.31 0.00 4.17
1584 1815 4.157656 ACTCAAAGTGCTTGTTTTGTGCTA 59.842 37.500 0.00 0.00 36.09 3.49
1620 1881 9.201989 AGAGGTCTGTATCAATCTTATACACAA 57.798 33.333 0.00 0.00 35.44 3.33
1689 1951 5.698545 CACTAGAAGCTTTAGCACTGTTTCT 59.301 40.000 0.00 6.48 45.16 2.52
1728 1990 6.614160 ACATACGTTTAGTATTTTGGTTGGC 58.386 36.000 0.00 0.00 43.12 4.52
1730 1992 5.777850 ACGTTTAGTATTTTGGTTGGCTT 57.222 34.783 0.00 0.00 0.00 4.35
1742 2004 7.555306 TTTTGGTTGGCTTGGTAAAATAAAC 57.445 32.000 0.00 0.00 0.00 2.01
1743 2005 5.871396 TGGTTGGCTTGGTAAAATAAACA 57.129 34.783 0.00 0.00 0.00 2.83
1744 2006 5.848406 TGGTTGGCTTGGTAAAATAAACAG 58.152 37.500 0.00 0.00 0.00 3.16
1747 2009 5.975693 TGGCTTGGTAAAATAAACAGGAG 57.024 39.130 0.00 0.00 0.00 3.69
1750 2012 5.393135 GGCTTGGTAAAATAAACAGGAGCTC 60.393 44.000 4.71 4.71 0.00 4.09
1752 2014 6.071896 GCTTGGTAAAATAAACAGGAGCTCTT 60.072 38.462 14.64 2.08 0.00 2.85
1754 2016 7.214467 TGGTAAAATAAACAGGAGCTCTTTG 57.786 36.000 14.64 14.59 0.00 2.77
1756 2018 7.040686 TGGTAAAATAAACAGGAGCTCTTTGAC 60.041 37.037 20.60 11.76 0.00 3.18
1757 2019 6.959639 AAAATAAACAGGAGCTCTTTGACA 57.040 33.333 20.60 8.91 0.00 3.58
1758 2020 6.566197 AAATAAACAGGAGCTCTTTGACAG 57.434 37.500 20.60 2.72 0.00 3.51
1759 2021 2.557920 AACAGGAGCTCTTTGACAGG 57.442 50.000 20.60 2.06 0.00 4.00
1761 2023 2.050144 ACAGGAGCTCTTTGACAGGAA 58.950 47.619 20.60 0.00 0.00 3.36
1763 2025 1.349357 AGGAGCTCTTTGACAGGAACC 59.651 52.381 14.64 0.00 0.00 3.62
1764 2026 1.433534 GAGCTCTTTGACAGGAACCG 58.566 55.000 6.43 0.00 0.00 4.44
1771 2104 5.063564 GCTCTTTGACAGGAACCGTTATTAG 59.936 44.000 0.00 0.00 0.00 1.73
1779 2112 2.941064 GGAACCGTTATTAGTCCCTTGC 59.059 50.000 0.00 0.00 0.00 4.01
1787 2120 6.053005 CGTTATTAGTCCCTTGCCATTTCTA 58.947 40.000 0.00 0.00 0.00 2.10
1792 2139 4.530875 AGTCCCTTGCCATTTCTATGAAG 58.469 43.478 0.00 0.00 33.37 3.02
1803 2150 7.880713 TGCCATTTCTATGAAGTGTAGTTGTTA 59.119 33.333 0.00 0.00 33.37 2.41
1808 2155 9.653287 TTTCTATGAAGTGTAGTTGTTATCCTG 57.347 33.333 0.00 0.00 0.00 3.86
1809 2156 8.362464 TCTATGAAGTGTAGTTGTTATCCTGT 57.638 34.615 0.00 0.00 0.00 4.00
1810 2157 8.812972 TCTATGAAGTGTAGTTGTTATCCTGTT 58.187 33.333 0.00 0.00 0.00 3.16
1813 2160 7.959175 TGAAGTGTAGTTGTTATCCTGTTAGT 58.041 34.615 0.00 0.00 0.00 2.24
1814 2161 8.086522 TGAAGTGTAGTTGTTATCCTGTTAGTC 58.913 37.037 0.00 0.00 0.00 2.59
1815 2162 6.618811 AGTGTAGTTGTTATCCTGTTAGTCG 58.381 40.000 0.00 0.00 0.00 4.18
1816 2163 5.803967 GTGTAGTTGTTATCCTGTTAGTCGG 59.196 44.000 0.00 0.00 0.00 4.79
1817 2164 3.858247 AGTTGTTATCCTGTTAGTCGGC 58.142 45.455 0.00 0.00 0.00 5.54
1818 2165 3.259876 AGTTGTTATCCTGTTAGTCGGCA 59.740 43.478 0.00 0.00 0.00 5.69
1819 2166 4.081087 AGTTGTTATCCTGTTAGTCGGCAT 60.081 41.667 0.00 0.00 0.00 4.40
1820 2167 3.792401 TGTTATCCTGTTAGTCGGCATG 58.208 45.455 0.00 0.00 0.00 4.06
1821 2168 3.449377 TGTTATCCTGTTAGTCGGCATGA 59.551 43.478 0.00 0.00 0.00 3.07
1833 2180 1.811965 TCGGCATGATTCACCTTTGTG 59.188 47.619 0.00 0.00 44.18 3.33
1861 2208 0.396435 TCACACCTGCGACCTTGAAT 59.604 50.000 0.00 0.00 0.00 2.57
1933 2280 8.754080 ACTAGTCTGTTACTTTTCTGAGCATAT 58.246 33.333 0.00 0.00 39.80 1.78
1948 2296 7.780064 TCTGAGCATATCTAATCTTATGGAGC 58.220 38.462 0.00 0.00 0.00 4.70
2000 2348 0.906282 AAGGCTGGGGAATTTGCTGG 60.906 55.000 0.00 0.00 0.00 4.85
2007 2355 1.416030 GGGGAATTTGCTGGTGTGTTT 59.584 47.619 0.00 0.00 0.00 2.83
2076 2428 3.816580 GGAGTCTTTGTCTCCGACC 57.183 57.895 0.00 0.00 41.36 4.79
2156 2509 7.759489 AAAAGTATTTCATAGTGGTGCTTCA 57.241 32.000 0.00 0.00 37.28 3.02
2203 2560 9.793252 AAGTTTGTATGCTCATATGAATTGTTC 57.207 29.630 6.90 0.00 0.00 3.18
2309 2673 2.512885 CTGCTTTGCATTCTTAGCACG 58.487 47.619 0.00 0.00 42.54 5.34
2319 2683 8.880878 TTGCATTCTTAGCACGACTATTATAA 57.119 30.769 0.00 0.00 42.54 0.98
2393 2760 6.700020 CAGCAGTACTGTCAATCTATTTTCG 58.300 40.000 23.44 0.00 41.86 3.46
2423 2792 7.480542 CGTAATTGACCTTTGTTTATTTCTCCG 59.519 37.037 0.00 0.00 0.00 4.63
2495 2864 1.005037 ACAAGCGGTCGCATCAAGA 60.005 52.632 17.71 0.00 44.88 3.02
2858 3230 1.531365 CCAAGGCAGAGGGTTGCAA 60.531 57.895 0.00 0.00 45.86 4.08
3249 3624 0.927537 TCTGAAAGTGCGTGTTGTCG 59.072 50.000 0.00 0.00 33.76 4.35
3273 3649 4.169059 TGCCTCAGCCATTACATGTAAT 57.831 40.909 22.70 22.70 38.69 1.89
3302 3678 2.779755 TCAACCGTCAGCCATGTTAT 57.220 45.000 0.00 0.00 0.00 1.89
3345 3721 4.574674 TGGTTCTGCTAAGACATCCAAT 57.425 40.909 0.00 0.00 30.12 3.16
3346 3722 5.692115 TGGTTCTGCTAAGACATCCAATA 57.308 39.130 0.00 0.00 30.12 1.90
3347 3723 6.252599 TGGTTCTGCTAAGACATCCAATAT 57.747 37.500 0.00 0.00 30.12 1.28
3348 3724 7.373617 TGGTTCTGCTAAGACATCCAATATA 57.626 36.000 0.00 0.00 30.12 0.86
3381 3758 7.622048 GCCTTTTAATAATGACTTGCTTGTTGC 60.622 37.037 0.00 0.00 43.25 4.17
3392 3769 0.854705 GCTTGTTGCGCAAAGGAAAG 59.145 50.000 26.87 23.79 36.53 2.62
3425 3811 5.348451 ACTGTTTTTCATTAATCATTGCGGC 59.652 36.000 0.00 0.00 0.00 6.53
3426 3812 4.325741 TGTTTTTCATTAATCATTGCGGCG 59.674 37.500 0.51 0.51 0.00 6.46
3439 3825 4.228097 CGGCGCTGCGGATTTCTG 62.228 66.667 24.61 7.60 0.00 3.02
3470 3857 3.261643 ACCTCATGCCAAAAGGAAAATCC 59.738 43.478 4.48 0.00 36.58 3.01
3569 3958 3.704100 GCCAATGGCCACTTTTTGT 57.296 47.368 14.47 0.00 44.06 2.83
3603 3992 7.432350 TGCTCTTCAATTTCTCTTCTTCTTC 57.568 36.000 0.00 0.00 0.00 2.87
3604 3993 7.222872 TGCTCTTCAATTTCTCTTCTTCTTCT 58.777 34.615 0.00 0.00 0.00 2.85
3605 3994 7.718753 TGCTCTTCAATTTCTCTTCTTCTTCTT 59.281 33.333 0.00 0.00 0.00 2.52
3743 4134 2.907897 CTACCCTCTTCCTTGCCGCG 62.908 65.000 0.00 0.00 0.00 6.46
3794 4185 5.349270 CGAGAATCTATTCCGACGTAGAGAT 59.651 44.000 0.00 0.00 37.51 2.75
3848 4239 1.102978 GCTTTCTCGCTCTCCTCTCT 58.897 55.000 0.00 0.00 0.00 3.10
3862 4253 1.692121 CCTCTCTGATTCCCTGCCTCT 60.692 57.143 0.00 0.00 0.00 3.69
3880 4271 2.030371 TCTGAGCATCTACAGCCTCAG 58.970 52.381 9.57 9.57 37.98 3.35
3887 4278 1.153745 CTACAGCCTCAGACACGGC 60.154 63.158 0.00 0.00 46.65 5.68
3912 4313 3.619038 GTCCTCCGATCACTTCACAAATC 59.381 47.826 0.00 0.00 0.00 2.17
3913 4314 3.260632 TCCTCCGATCACTTCACAAATCA 59.739 43.478 0.00 0.00 0.00 2.57
3916 4317 4.578871 TCCGATCACTTCACAAATCATGT 58.421 39.130 0.00 0.00 45.34 3.21
3918 4319 4.493057 CCGATCACTTCACAAATCATGTCG 60.493 45.833 0.00 0.00 41.46 4.35
3921 4322 4.376146 TCACTTCACAAATCATGTCGTCA 58.624 39.130 0.00 0.00 41.46 4.35
3930 4331 5.146460 CAAATCATGTCGTCAACATTCGTT 58.854 37.500 0.00 0.00 46.73 3.85
3931 4332 4.584029 ATCATGTCGTCAACATTCGTTC 57.416 40.909 0.00 0.00 46.73 3.95
3934 4335 4.091365 TCATGTCGTCAACATTCGTTCATC 59.909 41.667 0.00 0.00 46.73 2.92
3942 4343 6.346120 CGTCAACATTCGTTCATCTCATATCC 60.346 42.308 0.00 0.00 31.13 2.59
3948 4349 5.966742 TCGTTCATCTCATATCCGATCTT 57.033 39.130 0.00 0.00 0.00 2.40
3951 4352 5.799435 CGTTCATCTCATATCCGATCTTCTG 59.201 44.000 0.00 0.00 0.00 3.02
3966 4367 7.039923 TCCGATCTTCTGTATCCATACTAAACC 60.040 40.741 0.00 0.00 34.41 3.27
3974 4375 8.520351 TCTGTATCCATACTAAACCATACATCG 58.480 37.037 0.00 0.00 34.41 3.84
3991 4392 7.221259 CCATACATCGTTGATCAAACTACGTAA 59.779 37.037 10.35 0.00 39.23 3.18
4009 4410 9.261180 ACTACGTAAATCATCAAATGGACATAG 57.739 33.333 0.00 0.00 0.00 2.23
4039 4440 7.119997 GCACTATACGTTCATCAAAAGATCAC 58.880 38.462 0.00 0.00 0.00 3.06
4044 4445 4.578516 ACGTTCATCAAAAGATCACCAACA 59.421 37.500 0.00 0.00 0.00 3.33
4059 4460 5.436175 TCACCAACAGATCTTCAAAAGACA 58.564 37.500 0.00 0.00 41.01 3.41
4064 4465 4.660168 ACAGATCTTCAAAAGACAGCCAT 58.340 39.130 0.00 0.00 41.01 4.40
4090 4491 8.054152 AGTTCACATAATGCACATAAATGACA 57.946 30.769 11.01 0.00 0.00 3.58
4095 4496 7.642586 CACATAATGCACATAAATGACAGACAG 59.357 37.037 11.01 0.00 0.00 3.51
4109 4510 8.451908 AATGACAGACAGCTTTAAACTAAACT 57.548 30.769 0.00 0.00 0.00 2.66
4112 4513 8.823818 TGACAGACAGCTTTAAACTAAACTTAC 58.176 33.333 0.00 0.00 0.00 2.34
4114 4515 9.169592 ACAGACAGCTTTAAACTAAACTTACAA 57.830 29.630 0.00 0.00 0.00 2.41
4139 4557 5.774498 AAAGTGAACAAAGTGGATCTTCC 57.226 39.130 0.00 0.00 35.02 3.46
4149 4567 3.525862 AGTGGATCTTCCTCACTTCCTT 58.474 45.455 0.00 0.00 38.44 3.36
4162 4580 3.140073 TTCCTTGCCGGCCCTTTCA 62.140 57.895 26.77 0.00 0.00 2.69
4164 4582 3.373565 CTTGCCGGCCCTTTCACC 61.374 66.667 26.77 0.00 0.00 4.02
4167 4585 3.062466 GCCGGCCCTTTCACCTTC 61.062 66.667 18.11 0.00 0.00 3.46
4168 4586 2.757077 CCGGCCCTTTCACCTTCT 59.243 61.111 0.00 0.00 0.00 2.85
4170 4588 1.374947 CGGCCCTTTCACCTTCTGA 59.625 57.895 0.00 0.00 0.00 3.27
4174 4592 1.339151 GCCCTTTCACCTTCTGATCGT 60.339 52.381 0.00 0.00 0.00 3.73
4178 4596 1.541379 TTCACCTTCTGATCGTCGGA 58.459 50.000 0.00 0.00 0.00 4.55
4191 4609 1.292223 GTCGGAACAGCTGTAGGCA 59.708 57.895 22.01 1.74 44.79 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 164 4.657436 ATTCGGAGATCACTAAGTGTCC 57.343 45.455 0.00 0.00 35.04 4.02
169 170 7.827236 ACAACCAATTTATTCGGAGATCACTAA 59.173 33.333 0.00 0.00 35.04 2.24
198 199 4.342092 ACACTTTTCATCACTTTTCCCCTG 59.658 41.667 0.00 0.00 0.00 4.45
433 434 4.512484 TGAGCGACAACAAATATGGATCA 58.488 39.130 0.00 0.00 0.00 2.92
638 639 4.537135 TTCAGTCTTATCTTTCCGCACT 57.463 40.909 0.00 0.00 0.00 4.40
788 791 4.355543 TCAATTGCGTCATAAAGGAAGC 57.644 40.909 0.00 0.00 41.73 3.86
865 976 1.974543 CCCATTGTGCAAAGGTCCC 59.025 57.895 5.62 0.00 0.00 4.46
867 978 0.609662 ATGCCCATTGTGCAAAGGTC 59.390 50.000 0.00 0.00 42.92 3.85
1245 1360 1.367840 GAGCACGAACTGGACCACT 59.632 57.895 0.00 0.00 0.00 4.00
1546 1777 1.179152 TGAGTGAAGCAATGGCATGG 58.821 50.000 0.00 0.00 44.61 3.66
1664 1926 3.330267 ACAGTGCTAAAGCTTCTAGTGC 58.670 45.455 0.00 0.82 42.66 4.40
1728 1990 7.454260 AAGAGCTCCTGTTTATTTTACCAAG 57.546 36.000 10.93 0.00 0.00 3.61
1730 1992 7.001674 TCAAAGAGCTCCTGTTTATTTTACCA 58.998 34.615 10.93 0.00 0.00 3.25
1742 2004 2.421619 GTTCCTGTCAAAGAGCTCCTG 58.578 52.381 10.93 8.65 0.00 3.86
1743 2005 1.349357 GGTTCCTGTCAAAGAGCTCCT 59.651 52.381 10.93 0.00 0.00 3.69
1744 2006 1.814793 GGTTCCTGTCAAAGAGCTCC 58.185 55.000 10.93 0.00 0.00 4.70
1747 2009 1.594331 AACGGTTCCTGTCAAAGAGC 58.406 50.000 0.00 0.00 0.00 4.09
1750 2012 5.350640 GGACTAATAACGGTTCCTGTCAAAG 59.649 44.000 0.00 0.00 0.00 2.77
1752 2014 4.322953 GGGACTAATAACGGTTCCTGTCAA 60.323 45.833 0.00 0.00 0.00 3.18
1754 2016 3.450096 AGGGACTAATAACGGTTCCTGTC 59.550 47.826 0.00 2.57 39.76 3.51
1756 2018 4.189231 CAAGGGACTAATAACGGTTCCTG 58.811 47.826 0.00 0.00 40.30 3.86
1757 2019 3.370209 GCAAGGGACTAATAACGGTTCCT 60.370 47.826 0.00 0.00 42.80 3.36
1758 2020 2.941064 GCAAGGGACTAATAACGGTTCC 59.059 50.000 0.00 0.00 38.49 3.62
1759 2021 2.941064 GGCAAGGGACTAATAACGGTTC 59.059 50.000 0.00 0.00 38.49 3.62
1761 2023 1.910671 TGGCAAGGGACTAATAACGGT 59.089 47.619 0.00 0.00 38.49 4.83
1763 2025 4.881850 AGAAATGGCAAGGGACTAATAACG 59.118 41.667 0.00 0.00 38.49 3.18
1764 2026 7.719633 TCATAGAAATGGCAAGGGACTAATAAC 59.280 37.037 0.00 0.00 32.75 1.89
1771 2104 4.096984 CACTTCATAGAAATGGCAAGGGAC 59.903 45.833 0.00 0.00 33.61 4.46
1787 2120 8.594550 ACTAACAGGATAACAACTACACTTCAT 58.405 33.333 0.00 0.00 0.00 2.57
1792 2139 5.803967 CCGACTAACAGGATAACAACTACAC 59.196 44.000 0.00 0.00 0.00 2.90
1803 2150 3.134623 TGAATCATGCCGACTAACAGGAT 59.865 43.478 0.00 0.00 38.84 3.24
1805 2152 2.609459 GTGAATCATGCCGACTAACAGG 59.391 50.000 0.00 0.00 0.00 4.00
1807 2154 2.236146 AGGTGAATCATGCCGACTAACA 59.764 45.455 0.00 0.00 0.00 2.41
1808 2155 2.906354 AGGTGAATCATGCCGACTAAC 58.094 47.619 0.00 0.00 0.00 2.34
1809 2156 3.627395 AAGGTGAATCATGCCGACTAA 57.373 42.857 0.00 0.00 0.00 2.24
1810 2157 3.270027 CAAAGGTGAATCATGCCGACTA 58.730 45.455 0.00 0.00 0.00 2.59
1811 2158 2.086869 CAAAGGTGAATCATGCCGACT 58.913 47.619 0.00 0.00 0.00 4.18
1812 2159 1.812571 ACAAAGGTGAATCATGCCGAC 59.187 47.619 0.00 0.00 0.00 4.79
1813 2160 2.198827 ACAAAGGTGAATCATGCCGA 57.801 45.000 0.00 0.00 0.00 5.54
1833 2180 1.002366 CGCAGGTGTGAACTATGCTC 58.998 55.000 0.00 0.00 34.75 4.26
1861 2208 7.230849 ACAGGATAAGCAAAATCATTCACAA 57.769 32.000 0.00 0.00 0.00 3.33
1933 2280 8.178313 TGAGAATTACGCTCCATAAGATTAGA 57.822 34.615 0.00 0.00 0.00 2.10
1942 2289 5.292765 CACAGTATGAGAATTACGCTCCAT 58.707 41.667 0.00 0.00 39.69 3.41
1948 2296 7.115520 CCAAGATAGCACAGTATGAGAATTACG 59.884 40.741 0.00 0.00 39.69 3.18
2000 2348 6.039781 TGAAGAGCGTAAAGTAAAACACAC 57.960 37.500 0.00 0.00 0.00 3.82
2141 2494 4.558226 ACATCTTGAAGCACCACTATGA 57.442 40.909 0.00 0.00 0.00 2.15
2156 2509 7.765695 ACTTAAATGGTCATCACAACATCTT 57.234 32.000 0.00 0.00 0.00 2.40
2203 2560 2.065993 ACAACGACGGATGACAGAAG 57.934 50.000 9.51 0.00 0.00 2.85
2669 3041 6.238211 CCATCAGAAGACGAAATGTATTGGTC 60.238 42.308 0.00 0.00 30.67 4.02
2670 3042 5.586243 CCATCAGAAGACGAAATGTATTGGT 59.414 40.000 0.00 0.00 30.67 3.67
2858 3230 2.024080 TGGGGAGCTTGAATTGCCTAAT 60.024 45.455 0.00 0.00 0.00 1.73
2926 3298 2.044551 GGAAGCTGGAGGCCCAAG 60.045 66.667 0.00 0.00 42.98 3.61
3240 3615 1.831389 CTGAGGCAACCGACAACACG 61.831 60.000 0.00 0.00 37.17 4.49
3249 3624 1.406539 CATGTAATGGCTGAGGCAACC 59.593 52.381 14.16 4.39 41.79 3.77
3273 3649 0.547075 TGACGGTTGAAACCCTTCCA 59.453 50.000 6.64 0.00 46.53 3.53
3285 3661 1.280710 TGGATAACATGGCTGACGGTT 59.719 47.619 0.00 0.00 0.00 4.44
3381 3758 1.000731 TCCAATTGGCTTTCCTTTGCG 59.999 47.619 20.33 0.00 34.44 4.85
3392 3769 7.387397 TGATTAATGAAAAACAGTCCAATTGGC 59.613 33.333 20.33 14.47 34.44 4.52
3425 3811 0.740868 TCTTCCAGAAATCCGCAGCG 60.741 55.000 8.18 8.18 0.00 5.18
3426 3812 1.131315 GTTCTTCCAGAAATCCGCAGC 59.869 52.381 0.00 0.00 35.75 5.25
3439 3825 3.350219 TTGGCATGAGGTAGTTCTTCC 57.650 47.619 0.00 0.00 0.00 3.46
3486 3873 8.414003 TGAGATTCATGTTGGATAGTACAGTAC 58.586 37.037 2.05 2.05 0.00 2.73
3487 3874 8.533569 TGAGATTCATGTTGGATAGTACAGTA 57.466 34.615 0.00 0.00 0.00 2.74
3488 3875 7.423844 TGAGATTCATGTTGGATAGTACAGT 57.576 36.000 0.00 0.00 0.00 3.55
3489 3876 7.328005 CGATGAGATTCATGTTGGATAGTACAG 59.672 40.741 0.00 0.00 37.20 2.74
3490 3877 7.147976 CGATGAGATTCATGTTGGATAGTACA 58.852 38.462 0.00 0.00 37.20 2.90
3604 3993 7.924412 AGATAAGCGAGGATATGAAAAACGTAA 59.076 33.333 0.00 0.00 0.00 3.18
3605 3994 7.431249 AGATAAGCGAGGATATGAAAAACGTA 58.569 34.615 0.00 0.00 0.00 3.57
3667 4058 4.487948 CAAATCGATCAACACAATTGGCT 58.512 39.130 10.83 0.00 0.00 4.75
3671 4062 4.865925 CCATGCAAATCGATCAACACAATT 59.134 37.500 0.00 0.00 0.00 2.32
3743 4134 3.133901 GGAGAGAAACTGAGGAAGGATCC 59.866 52.174 2.48 2.48 46.98 3.36
3794 4185 2.662866 ACTATAGTGCTGGAGGCGTTA 58.337 47.619 4.10 0.00 45.43 3.18
3848 4239 0.911045 TGCTCAGAGGCAGGGAATCA 60.911 55.000 0.00 0.00 37.29 2.57
3862 4253 1.753649 GTCTGAGGCTGTAGATGCTCA 59.246 52.381 0.00 0.00 0.00 4.26
3887 4278 1.586564 GAAGTGATCGGAGGACGCG 60.587 63.158 3.53 3.53 43.86 6.01
3889 4280 0.526211 TGTGAAGTGATCGGAGGACG 59.474 55.000 0.00 0.00 46.11 4.79
3893 4284 4.633126 ACATGATTTGTGAAGTGATCGGAG 59.367 41.667 0.00 0.00 37.11 4.63
3894 4285 4.578871 ACATGATTTGTGAAGTGATCGGA 58.421 39.130 0.00 0.00 37.11 4.55
3898 4299 4.996758 TGACGACATGATTTGTGAAGTGAT 59.003 37.500 0.00 0.00 39.18 3.06
3916 4317 3.908213 TGAGATGAACGAATGTTGACGA 58.092 40.909 0.00 0.00 38.78 4.20
3918 4319 6.346120 CGGATATGAGATGAACGAATGTTGAC 60.346 42.308 0.00 0.00 38.78 3.18
3921 4322 5.842907 TCGGATATGAGATGAACGAATGTT 58.157 37.500 0.00 0.00 42.23 2.71
3930 4331 7.284261 GGATACAGAAGATCGGATATGAGATGA 59.716 40.741 0.00 0.00 0.00 2.92
3931 4332 7.067981 TGGATACAGAAGATCGGATATGAGATG 59.932 40.741 0.00 0.00 46.17 2.90
3934 4335 6.765915 TGGATACAGAAGATCGGATATGAG 57.234 41.667 0.00 0.00 46.17 2.90
3951 4352 8.922676 CAACGATGTATGGTTTAGTATGGATAC 58.077 37.037 0.00 0.00 0.00 2.24
3966 4367 6.569228 ACGTAGTTTGATCAACGATGTATG 57.431 37.500 21.12 10.49 37.78 2.39
3969 4370 7.329962 TGATTTACGTAGTTTGATCAACGATGT 59.670 33.333 21.12 17.52 37.78 3.06
3972 4373 7.542824 TGATGATTTACGTAGTTTGATCAACGA 59.457 33.333 21.12 0.22 37.78 3.85
3974 4375 9.820229 TTTGATGATTTACGTAGTTTGATCAAC 57.180 29.630 7.89 3.85 37.78 3.18
3991 4392 7.924412 GTGCATTTCTATGTCCATTTGATGATT 59.076 33.333 0.00 0.00 34.12 2.57
4001 4402 6.156748 ACGTATAGTGCATTTCTATGTCCA 57.843 37.500 5.76 0.00 34.12 4.02
4039 4440 4.320788 GGCTGTCTTTTGAAGATCTGTTGG 60.321 45.833 0.00 0.00 40.18 3.77
4044 4445 6.059787 ACTATGGCTGTCTTTTGAAGATCT 57.940 37.500 0.00 0.00 40.18 2.75
4052 4453 7.629222 GCATTATGTGAACTATGGCTGTCTTTT 60.629 37.037 0.00 0.00 0.00 2.27
4056 4457 4.576053 TGCATTATGTGAACTATGGCTGTC 59.424 41.667 0.00 0.00 0.00 3.51
4059 4460 4.525996 TGTGCATTATGTGAACTATGGCT 58.474 39.130 0.00 0.00 37.27 4.75
4064 4465 9.171877 TGTCATTTATGTGCATTATGTGAACTA 57.828 29.630 0.00 0.00 37.27 2.24
4106 4507 9.581099 CCACTTTGTTCACTTTAATTGTAAGTT 57.419 29.630 5.36 0.00 33.73 2.66
4108 4509 9.965824 ATCCACTTTGTTCACTTTAATTGTAAG 57.034 29.630 0.00 0.00 0.00 2.34
4109 4510 9.959749 GATCCACTTTGTTCACTTTAATTGTAA 57.040 29.630 0.00 0.00 0.00 2.41
4112 4513 9.185192 GAAGATCCACTTTGTTCACTTTAATTG 57.815 33.333 0.00 0.00 39.13 2.32
4114 4515 7.725844 AGGAAGATCCACTTTGTTCACTTTAAT 59.274 33.333 0.00 0.00 39.61 1.40
4115 4516 7.060421 AGGAAGATCCACTTTGTTCACTTTAA 58.940 34.615 0.00 0.00 39.61 1.52
4116 4517 6.601332 AGGAAGATCCACTTTGTTCACTTTA 58.399 36.000 0.00 0.00 39.61 1.85
4117 4518 5.449553 AGGAAGATCCACTTTGTTCACTTT 58.550 37.500 0.00 0.00 39.61 2.66
4118 4519 5.053978 AGGAAGATCCACTTTGTTCACTT 57.946 39.130 0.00 0.00 39.61 3.16
4119 4520 4.103153 TGAGGAAGATCCACTTTGTTCACT 59.897 41.667 0.00 0.00 39.61 3.41
4120 4521 4.214332 GTGAGGAAGATCCACTTTGTTCAC 59.786 45.833 0.00 0.00 39.61 3.18
4121 4522 4.103153 AGTGAGGAAGATCCACTTTGTTCA 59.897 41.667 0.00 0.00 39.61 3.18
4122 4523 4.646572 AGTGAGGAAGATCCACTTTGTTC 58.353 43.478 0.00 0.00 39.61 3.18
4130 4548 2.026822 GCAAGGAAGTGAGGAAGATCCA 60.027 50.000 0.00 0.00 39.61 3.41
4139 4557 2.747855 GGCCGGCAAGGAAGTGAG 60.748 66.667 30.85 0.00 45.00 3.51
4149 4567 3.860930 GAAGGTGAAAGGGCCGGCA 62.861 63.158 30.85 2.40 0.00 5.69
4162 4580 1.202582 CTGTTCCGACGATCAGAAGGT 59.797 52.381 0.00 0.00 37.84 3.50
4164 4582 1.135257 AGCTGTTCCGACGATCAGAAG 60.135 52.381 14.51 0.00 37.84 2.85
4167 4585 0.109086 ACAGCTGTTCCGACGATCAG 60.109 55.000 15.25 3.08 38.40 2.90
4168 4586 1.132453 CTACAGCTGTTCCGACGATCA 59.868 52.381 27.06 1.01 0.00 2.92
4170 4588 0.456221 CCTACAGCTGTTCCGACGAT 59.544 55.000 27.06 0.00 0.00 3.73
4174 4592 0.175760 GATGCCTACAGCTGTTCCGA 59.824 55.000 27.06 5.67 44.23 4.55
4178 4596 1.450312 GCCGATGCCTACAGCTGTT 60.450 57.895 27.06 6.10 44.23 3.16


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

AutoCloner maintained by Alex Coulton.