Multiple sequence alignment - TraesCS6D01G015700

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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 TraesCS6D01G015700 chr6D 100.000 5178 0 0 1 5178 6369050 6374227 0.000000e+00 9563.0
1 TraesCS6D01G015700 chr6D 89.447 2587 229 22 2527 5091 6426508 6429072 0.000000e+00 3225.0
2 TraesCS6D01G015700 chr6D 88.622 2127 235 5 2269 4389 6352914 6355039 0.000000e+00 2580.0
3 TraesCS6D01G015700 chr6D 86.642 2141 267 11 2043 4168 6497207 6499343 0.000000e+00 2351.0
4 TraesCS6D01G015700 chr6D 91.445 1204 61 16 1 1168 6350257 6351454 0.000000e+00 1615.0
5 TraesCS6D01G015700 chr6D 89.077 1062 114 2 3059 4119 6465693 6466753 0.000000e+00 1317.0
6 TraesCS6D01G015700 chr6D 84.615 845 90 17 1192 2014 6496275 6497101 0.000000e+00 804.0
7 TraesCS6D01G015700 chr6D 84.643 827 103 14 1207 2013 6425187 6426009 0.000000e+00 802.0
8 TraesCS6D01G015700 chr6D 89.100 633 66 2 2269 2898 6443012 6443644 0.000000e+00 784.0
9 TraesCS6D01G015700 chr6D 83.354 823 104 19 1210 2009 6441821 6442633 0.000000e+00 730.0
10 TraesCS6D01G015700 chr6D 84.418 507 59 9 1192 1681 6351602 6352105 1.010000e-131 481.0
11 TraesCS6D01G015700 chr6D 91.011 356 31 1 2016 2370 6442687 6443042 3.630000e-131 479.0
12 TraesCS6D01G015700 chr6D 87.724 391 48 0 1624 2014 6352120 6352510 1.700000e-124 457.0
13 TraesCS6D01G015700 chr6D 87.725 334 41 0 2029 2362 6426072 6426405 1.750000e-104 390.0
14 TraesCS6D01G015700 chr6D 85.827 254 28 3 4409 4662 6467520 6467765 3.980000e-66 263.0
15 TraesCS6D01G015700 chr6D 83.453 278 46 0 2269 2546 6426456 6426733 5.140000e-65 259.0
16 TraesCS6D01G015700 chr6D 88.679 212 22 2 4450 4661 6507756 6507965 1.850000e-64 257.0
17 TraesCS6D01G015700 chr6D 82.745 255 39 5 4163 4416 6466768 6467018 6.750000e-54 222.0
18 TraesCS6D01G015700 chr6D 93.878 49 1 1 4673 4719 6507949 6507997 7.190000e-09 73.1
19 TraesCS6D01G015700 chr6A 89.902 2664 241 19 2527 5178 5940875 5943522 0.000000e+00 3404.0
20 TraesCS6D01G015700 chr6A 87.877 2153 253 6 2269 4416 5917642 5919791 0.000000e+00 2523.0
21 TraesCS6D01G015700 chr6A 87.526 1892 228 5 2531 4416 5901924 5903813 0.000000e+00 2180.0
22 TraesCS6D01G015700 chr6A 81.206 1559 284 7 2548 4100 6699821 6701376 0.000000e+00 1247.0
23 TraesCS6D01G015700 chr6A 84.994 813 98 14 1207 1999 5939554 5940362 0.000000e+00 804.0
24 TraesCS6D01G015700 chr6A 84.107 862 94 11 1192 2013 5900708 5901566 0.000000e+00 793.0
25 TraesCS6D01G015700 chr6A 87.719 684 67 9 4409 5091 5904322 5904989 0.000000e+00 782.0
26 TraesCS6D01G015700 chr6A 90.863 591 40 11 160 747 5881908 5882487 0.000000e+00 780.0
27 TraesCS6D01G015700 chr6A 86.667 540 63 6 2016 2546 5901616 5902155 1.610000e-164 590.0
28 TraesCS6D01G015700 chr6A 83.077 585 69 17 1210 1774 5916509 5917083 5.980000e-139 505.0
29 TraesCS6D01G015700 chr6A 89.045 356 33 2 2016 2370 5917322 5917672 2.210000e-118 436.0
30 TraesCS6D01G015700 chr6A 87.126 334 43 0 2029 2362 5940439 5940772 3.780000e-101 379.0
31 TraesCS6D01G015700 chr6A 83.813 278 45 0 2269 2546 5940823 5941100 1.110000e-66 265.0
32 TraesCS6D01G015700 chr6A 95.062 162 8 0 1 162 5881657 5881818 6.650000e-64 255.0
33 TraesCS6D01G015700 chr6A 84.252 254 33 2 4409 4662 5920276 5920522 1.860000e-59 241.0
34 TraesCS6D01G015700 chr6A 91.720 157 10 2 785 941 5882485 5882638 1.130000e-51 215.0
35 TraesCS6D01G015700 chr6A 86.010 193 11 1 986 1162 5900366 5900558 5.290000e-45 193.0
36 TraesCS6D01G015700 chr6A 91.463 82 7 0 5097 5178 5906179 5906260 4.240000e-21 113.0
37 TraesCS6D01G015700 chr6B 85.609 2168 270 22 2043 4189 11793195 11795341 0.000000e+00 2237.0
38 TraesCS6D01G015700 chr6B 88.468 1188 136 1 2981 4168 11599607 11600793 0.000000e+00 1434.0
39 TraesCS6D01G015700 chr6B 87.675 1144 82 25 45 1168 11591588 11592692 0.000000e+00 1277.0
40 TraesCS6D01G015700 chr6B 87.110 737 76 2 1192 1912 11592836 11593569 0.000000e+00 817.0
41 TraesCS6D01G015700 chr6B 89.563 412 43 0 2528 2939 11599187 11599598 1.650000e-144 523.0
42 TraesCS6D01G015700 chr6B 90.155 386 33 3 2145 2530 11593572 11593952 1.000000e-136 497.0
43 TraesCS6D01G015700 chr6B 87.657 397 43 4 1192 1585 11792338 11792731 1.700000e-124 457.0
44 TraesCS6D01G015700 chr6B 85.308 422 56 6 4673 5091 11603788 11604206 1.030000e-116 431.0
45 TraesCS6D01G015700 chr6B 82.289 463 73 9 3958 4416 11795648 11796105 4.860000e-105 392.0
46 TraesCS6D01G015700 chr6B 89.734 263 24 3 4398 4660 11603544 11603803 2.990000e-87 333.0
47 TraesCS6D01G015700 chr1D 74.793 726 161 12 12 721 70334757 70334038 1.810000e-79 307.0
48 TraesCS6D01G015700 chr5D 74.861 720 158 13 12 714 73793775 73794488 6.510000e-79 305.0
49 TraesCS6D01G015700 chr5D 74.860 712 155 14 12 705 553903157 553903862 8.430000e-78 302.0
50 TraesCS6D01G015700 chr1B 73.901 705 164 10 12 700 207376146 207376846 1.110000e-66 265.0
51 TraesCS6D01G015700 chr2B 80.345 290 54 3 418 705 793654459 793654747 3.140000e-52 217.0
52 TraesCS6D01G015700 chr4A 78.788 297 58 4 412 705 604056581 604056875 1.470000e-45 195.0


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 TraesCS6D01G015700 chr6D 6369050 6374227 5177 False 9563.000000 9563 100.000000 1 5178 1 chr6D.!!$F1 5177
1 TraesCS6D01G015700 chr6D 6496275 6499343 3068 False 1577.500000 2351 85.628500 1192 4168 2 chr6D.!!$F6 2976
2 TraesCS6D01G015700 chr6D 6350257 6355039 4782 False 1283.250000 2580 88.052250 1 4389 4 chr6D.!!$F2 4388
3 TraesCS6D01G015700 chr6D 6425187 6429072 3885 False 1169.000000 3225 86.317000 1207 5091 4 chr6D.!!$F3 3884
4 TraesCS6D01G015700 chr6D 6441821 6443644 1823 False 664.333333 784 87.821667 1210 2898 3 chr6D.!!$F4 1688
5 TraesCS6D01G015700 chr6D 6465693 6467765 2072 False 600.666667 1317 85.883000 3059 4662 3 chr6D.!!$F5 1603
6 TraesCS6D01G015700 chr6A 6699821 6701376 1555 False 1247.000000 1247 81.206000 2548 4100 1 chr6A.!!$F1 1552
7 TraesCS6D01G015700 chr6A 5939554 5943522 3968 False 1213.000000 3404 86.458750 1207 5178 4 chr6A.!!$F5 3971
8 TraesCS6D01G015700 chr6A 5916509 5920522 4013 False 926.250000 2523 86.062750 1210 4662 4 chr6A.!!$F4 3452
9 TraesCS6D01G015700 chr6A 5900366 5906260 5894 False 775.166667 2180 87.248667 986 5178 6 chr6A.!!$F3 4192
10 TraesCS6D01G015700 chr6A 5881657 5882638 981 False 416.666667 780 92.548333 1 941 3 chr6A.!!$F2 940
11 TraesCS6D01G015700 chr6B 11792338 11796105 3767 False 1028.666667 2237 85.185000 1192 4416 3 chr6B.!!$F3 3224
12 TraesCS6D01G015700 chr6B 11591588 11593952 2364 False 863.666667 1277 88.313333 45 2530 3 chr6B.!!$F1 2485
13 TraesCS6D01G015700 chr6B 11599187 11604206 5019 False 680.250000 1434 88.268250 2528 5091 4 chr6B.!!$F2 2563
14 TraesCS6D01G015700 chr1D 70334038 70334757 719 True 307.000000 307 74.793000 12 721 1 chr1D.!!$R1 709
15 TraesCS6D01G015700 chr5D 73793775 73794488 713 False 305.000000 305 74.861000 12 714 1 chr5D.!!$F1 702
16 TraesCS6D01G015700 chr5D 553903157 553903862 705 False 302.000000 302 74.860000 12 705 1 chr5D.!!$F2 693
17 TraesCS6D01G015700 chr1B 207376146 207376846 700 False 265.000000 265 73.901000 12 700 1 chr1B.!!$F1 688

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
129 130 0.179089 CCAGCTTGGAGATGGTCTCG 60.179 60.0 4.13 0.0 46.23 4.04 F
855 968 0.389817 TGACCGGCGACTTCAGATTG 60.390 55.0 9.30 0.0 0.00 2.67 F
1124 1276 0.595053 CGACATCGATCTTGACCGGG 60.595 60.0 6.32 0.0 43.02 5.73 F
1948 2346 0.318120 CAACCACTTTGGCCATCCAC 59.682 55.0 6.09 0.0 42.67 4.02 F
2009 2407 0.613777 CTCGGCCTTTCTGGTACCTT 59.386 55.0 14.36 0.0 38.35 3.50 F
3679 4385 0.457851 CGCTCGACCTCTCAAGGAAT 59.542 55.0 0.00 0.0 46.67 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1866 2264 0.251916 CGAGGGATTGGTTGGCACTA 59.748 55.000 0.00 0.0 0.00 2.74 R
1872 2270 0.888736 TGTGTGCGAGGGATTGGTTG 60.889 55.000 0.00 0.0 0.00 3.77 R
2778 3484 1.210478 TCCCAAGCAGGCTGATCTTAC 59.790 52.381 20.86 0.0 35.39 2.34 R
3388 4094 0.469892 CAACCCCAGGCTTCTTTGGT 60.470 55.000 0.00 0.0 32.40 3.67 R
3864 4570 0.957395 CGGTGCATTGCTTCCTGAGT 60.957 55.000 10.49 0.0 0.00 3.41 R
4734 8522 1.588674 TTGTTGTTTGCGACCGAGAT 58.411 45.000 0.00 0.0 0.00 2.75 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
38 39 4.536765 ACATCCAAAGTTGACCTTCAAGT 58.463 39.130 0.00 0.00 41.46 3.16
129 130 0.179089 CCAGCTTGGAGATGGTCTCG 60.179 60.000 4.13 0.00 46.23 4.04
291 397 3.945346 AGCATACTCCGAGACGATAGAT 58.055 45.455 1.33 0.00 41.38 1.98
384 492 4.906747 ATGAGAGATGGATTAGCCCTTC 57.093 45.455 0.00 0.00 34.97 3.46
394 502 5.694995 TGGATTAGCCCTTCCTTATTCTTG 58.305 41.667 0.00 0.00 34.97 3.02
405 513 6.712547 CCTTCCTTATTCTTGTGAGTTCACTT 59.287 38.462 12.97 0.00 46.55 3.16
521 631 7.577303 AGTGTGTGGATATTAGTTCCATGATT 58.423 34.615 0.00 0.00 44.75 2.57
531 641 2.922283 AGTTCCATGATTGGGAAGGTCT 59.078 45.455 0.00 0.00 44.68 3.85
534 645 3.968265 TCCATGATTGGGAAGGTCTTTC 58.032 45.455 0.00 0.00 43.81 2.62
563 674 8.511321 AGCATTGTTATCGTTCTTGTAATCAAA 58.489 29.630 0.00 0.00 32.87 2.69
582 693 1.878522 CGGGTCATGTGCTAGCGAC 60.879 63.158 10.77 10.85 0.00 5.19
627 739 5.441718 TCCTTTAGTTGATTGGATGAGCT 57.558 39.130 0.00 0.00 0.00 4.09
644 756 1.279271 AGCTACATGGTTCTGTGGTCC 59.721 52.381 0.00 0.00 30.91 4.46
825 938 3.883489 CCACACATGCATCTCTCATCAAT 59.117 43.478 0.00 0.00 0.00 2.57
855 968 0.389817 TGACCGGCGACTTCAGATTG 60.390 55.000 9.30 0.00 0.00 2.67
869 982 2.093921 TCAGATTGTAAATCGCCGGTCA 60.094 45.455 1.90 0.00 0.00 4.02
941 1054 3.203710 TCCTGCCCAGTTACTAGCTACTA 59.796 47.826 7.83 0.00 0.00 1.82
942 1055 4.140994 TCCTGCCCAGTTACTAGCTACTAT 60.141 45.833 7.83 0.00 0.00 2.12
1066 1218 1.019278 CCTGTACGTGACCACCATGC 61.019 60.000 0.00 0.00 35.17 4.06
1100 1252 0.734889 CCCACGAATCAGTCCAATGC 59.265 55.000 0.00 0.00 0.00 3.56
1102 1254 2.019249 CCACGAATCAGTCCAATGCAT 58.981 47.619 0.00 0.00 0.00 3.96
1109 1261 1.001860 TCAGTCCAATGCATGACGACA 59.998 47.619 18.17 0.00 0.00 4.35
1124 1276 0.595053 CGACATCGATCTTGACCGGG 60.595 60.000 6.32 0.00 43.02 5.73
1162 1314 1.724582 GCGTCAGCCCAAACACTTGT 61.725 55.000 0.00 0.00 37.42 3.16
1187 1348 1.119684 TACCTCATCCATCCACACGG 58.880 55.000 0.00 0.00 0.00 4.94
1201 1478 3.857038 ACGGCCGACAACCACACT 61.857 61.111 35.90 0.68 0.00 3.55
1264 1541 2.825387 CTTATGGCAGCAGCGGCA 60.825 61.111 19.73 16.60 46.50 5.69
1280 1557 1.301677 GGCAACCTGGAGCTTCTTCG 61.302 60.000 0.00 0.00 0.00 3.79
1281 1558 1.916697 GCAACCTGGAGCTTCTTCGC 61.917 60.000 0.00 0.00 0.00 4.70
1306 1583 2.669569 GACGCAGGCAAGCTCCAA 60.670 61.111 0.00 0.00 0.00 3.53
1355 1632 1.331214 CTTGCTGGCCTTCAAGGAAA 58.669 50.000 22.08 0.00 37.67 3.13
1369 1649 5.739752 TCAAGGAAAGCATCAATGATACG 57.260 39.130 0.00 0.00 0.00 3.06
1370 1650 4.576053 TCAAGGAAAGCATCAATGATACGG 59.424 41.667 0.00 0.00 0.00 4.02
1371 1651 3.480470 AGGAAAGCATCAATGATACGGG 58.520 45.455 0.00 0.00 0.00 5.28
1372 1652 3.117888 AGGAAAGCATCAATGATACGGGT 60.118 43.478 0.00 0.00 0.00 5.28
1381 1664 1.405872 ATGATACGGGTGGCGAACTA 58.594 50.000 0.00 0.00 0.00 2.24
1410 1693 0.798776 CGACAAGAGCGCCAAGATTT 59.201 50.000 2.29 0.00 0.00 2.17
1453 1736 1.755405 GCGATAACGTAACCGGCCAC 61.755 60.000 0.00 0.00 41.98 5.01
1495 1778 4.062991 GCGGAAGATATTATTTGGTCGGT 58.937 43.478 0.00 0.00 0.00 4.69
1496 1779 4.084013 GCGGAAGATATTATTTGGTCGGTG 60.084 45.833 0.00 0.00 0.00 4.94
1510 1793 3.025262 GGTCGGTGAGATAAGTCCTTCT 58.975 50.000 0.00 0.00 0.00 2.85
1591 1890 1.743394 GATGGCCGTGTTCCTTAAAGG 59.257 52.381 0.00 0.00 36.46 3.11
1638 1937 4.028131 ACATGTCTTTCTCCGGTATGGTA 58.972 43.478 0.00 0.00 39.52 3.25
1645 1944 1.572415 TCTCCGGTATGGTACCTCCTT 59.428 52.381 14.36 0.00 46.81 3.36
1731 2129 3.516981 ATGGTCTCAACTGACATCTCG 57.483 47.619 0.00 0.00 38.61 4.04
1739 2137 4.556233 TCAACTGACATCTCGTGGTTAAG 58.444 43.478 0.00 0.00 0.00 1.85
1775 2173 5.355071 TGTTGGTGCATCTTGATATGAGTTC 59.645 40.000 0.00 0.00 0.00 3.01
1846 2244 3.012518 CCATCTTTGGAGTTGCTCGATT 58.987 45.455 0.00 0.00 46.92 3.34
1853 2251 2.813754 TGGAGTTGCTCGATTTTTCTGG 59.186 45.455 0.00 0.00 0.00 3.86
1859 2257 1.541588 GCTCGATTTTTCTGGGTGCTT 59.458 47.619 0.00 0.00 0.00 3.91
1866 2264 2.071778 TTTCTGGGTGCTTGCTTTCT 57.928 45.000 0.00 0.00 0.00 2.52
1872 2270 0.523519 GGTGCTTGCTTTCTAGTGCC 59.476 55.000 0.00 0.00 0.00 5.01
1891 2289 0.888736 CAACCAATCCCTCGCACACA 60.889 55.000 0.00 0.00 0.00 3.72
1912 2310 6.207417 ACACATAAACCTCACAAATCTTCAGG 59.793 38.462 0.00 0.00 0.00 3.86
1914 2312 6.656693 ACATAAACCTCACAAATCTTCAGGAG 59.343 38.462 0.00 0.00 0.00 3.69
1918 2316 4.077822 CCTCACAAATCTTCAGGAGCTTT 58.922 43.478 0.00 0.00 0.00 3.51
1919 2317 4.522022 CCTCACAAATCTTCAGGAGCTTTT 59.478 41.667 0.00 0.00 0.00 2.27
1948 2346 0.318120 CAACCACTTTGGCCATCCAC 59.682 55.000 6.09 0.00 42.67 4.02
1951 2349 1.341080 CCACTTTGGCCATCCACTTT 58.659 50.000 6.09 0.00 43.33 2.66
1971 2369 2.944129 TCCTCCAGTTGGTTTTGGAAG 58.056 47.619 0.00 0.00 42.61 3.46
2009 2407 0.613777 CTCGGCCTTTCTGGTACCTT 59.386 55.000 14.36 0.00 38.35 3.50
2014 2412 2.039879 GGCCTTTCTGGTACCTTTCTCA 59.960 50.000 14.36 0.00 38.35 3.27
2035 2510 6.327365 TCTCATTAGAATTGAGCTACATGGGA 59.673 38.462 0.00 0.00 0.00 4.37
2037 2512 7.520798 TCATTAGAATTGAGCTACATGGGAAT 58.479 34.615 0.00 0.00 0.00 3.01
2063 2538 2.744202 GCCACAATGACAGTAGACTTGG 59.256 50.000 0.00 0.00 0.00 3.61
2099 2574 5.607939 TTTGGAAGACCTATCGCTTGATA 57.392 39.130 0.00 0.00 37.04 2.15
2112 2587 2.102252 CGCTTGATAGAAGCCTCTCCTT 59.898 50.000 0.00 0.00 40.02 3.36
2256 2731 6.320418 ACCAACTTATCTTTGTTCGACCTTTT 59.680 34.615 0.00 0.00 0.00 2.27
2478 3178 7.337942 CCTTGACCTTTCTTACAATAGCATTCT 59.662 37.037 0.00 0.00 0.00 2.40
2518 3218 3.320541 TGTTAGGGAACTGCACCAAATTG 59.679 43.478 0.00 0.00 43.88 2.32
2546 3246 7.571025 TCACCTTACTCTTTCTAACAACCTTT 58.429 34.615 0.00 0.00 0.00 3.11
2627 3333 3.679389 AGCAACCATCTTACTGAACCTG 58.321 45.455 0.00 0.00 0.00 4.00
2636 3342 6.351033 CCATCTTACTGAACCTGTACTGCTAA 60.351 42.308 0.00 0.00 0.00 3.09
2733 3439 4.046286 TGGGGAATTGCACTAGTTTGAT 57.954 40.909 0.00 0.00 0.00 2.57
2734 3440 4.415596 TGGGGAATTGCACTAGTTTGATT 58.584 39.130 0.00 0.00 0.00 2.57
2743 3449 5.129634 TGCACTAGTTTGATTCACCTTTCA 58.870 37.500 0.00 0.00 0.00 2.69
2746 3452 6.426937 GCACTAGTTTGATTCACCTTTCACTA 59.573 38.462 0.00 0.00 0.00 2.74
2797 3503 1.065199 TGTAAGATCAGCCTGCTTGGG 60.065 52.381 0.00 0.00 36.00 4.12
2808 3514 2.242043 CCTGCTTGGGAATTTGACTGT 58.758 47.619 0.00 0.00 0.00 3.55
2844 3550 7.112122 AGCAACAATAATCTAGATGGTGTGAA 58.888 34.615 5.86 0.00 33.09 3.18
2915 3621 4.705110 TCACACAATTCTTTCTCAGGGA 57.295 40.909 0.00 0.00 0.00 4.20
2954 3660 5.511234 TGGAGCTTACGGATTAGTAGAAC 57.489 43.478 0.00 0.00 0.00 3.01
2958 3664 6.380095 AGCTTACGGATTAGTAGAACTGAG 57.620 41.667 0.00 0.00 0.00 3.35
2979 3685 8.383175 ACTGAGTTTATCCTCCAATTACTTCAA 58.617 33.333 0.00 0.00 0.00 2.69
3013 3719 7.792374 TCCTGAATCTATTTGTATGTTGAGC 57.208 36.000 0.00 0.00 0.00 4.26
3080 3786 3.452627 ACTTCCTCAGTGTTCTCACAAGT 59.547 43.478 1.36 0.00 46.01 3.16
3086 3792 5.451937 CCTCAGTGTTCTCACAAGTCTAACA 60.452 44.000 1.36 0.00 46.01 2.41
3091 3797 5.177696 GTGTTCTCACAAGTCTAACATGGTC 59.822 44.000 0.00 0.00 43.37 4.02
3114 3820 4.755266 TCCTCCTCTTAAGCCACAATAC 57.245 45.455 0.00 0.00 0.00 1.89
3127 3833 3.613910 GCCACAATACGTTTTCTGGCAAT 60.614 43.478 25.26 0.00 43.15 3.56
3253 3959 2.005451 CGCTTTCTGCAGCTAAGTCAT 58.995 47.619 21.75 0.00 43.06 3.06
3270 3976 7.550906 GCTAAGTCATAATTTCTTCTGTGGAGT 59.449 37.037 0.00 0.00 0.00 3.85
3292 3998 8.273635 GGAGTTATTCCGGTGACTATCACAAAA 61.274 40.741 10.90 2.65 41.75 2.44
3313 4019 7.448469 ACAAAACTTATACACCTTCATCAGCTT 59.552 33.333 0.00 0.00 0.00 3.74
3372 4078 6.215845 CCTGGTCTTTGTCAAATTTAACAGG 58.784 40.000 18.07 18.07 35.24 4.00
3388 4094 6.546428 TTAACAGGAATGACCCAAAAACAA 57.454 33.333 0.00 0.00 40.05 2.83
3397 4103 4.826556 TGACCCAAAAACAACCAAAGAAG 58.173 39.130 0.00 0.00 0.00 2.85
3424 4130 6.916909 TGGGGTTGACATGTTTATATGGTAT 58.083 36.000 0.00 0.00 32.32 2.73
3484 4190 2.289382 TGTGATGAAGCGCCAAGAACTA 60.289 45.455 2.29 0.00 0.00 2.24
3490 4196 3.744426 TGAAGCGCCAAGAACTAAAGTAC 59.256 43.478 2.29 0.00 0.00 2.73
3563 4269 3.299503 ACAGGTGAAATTCCATATGGGC 58.700 45.455 21.78 7.13 36.21 5.36
3577 4283 5.908831 TCCATATGGGCTTACCTCTCTTAAA 59.091 40.000 21.78 0.00 41.11 1.52
3642 4348 7.119387 GGAAAAATTCCTAGGAAGATTGGAGA 58.881 38.462 27.58 3.35 46.57 3.71
3679 4385 0.457851 CGCTCGACCTCTCAAGGAAT 59.542 55.000 0.00 0.00 46.67 3.01
3682 4388 3.428999 CGCTCGACCTCTCAAGGAATAAA 60.429 47.826 0.00 0.00 46.67 1.40
3864 4570 4.042809 TGGCACTCCTCTTGAAAGGAATTA 59.957 41.667 0.00 0.00 44.81 1.40
3873 4579 6.597280 CCTCTTGAAAGGAATTACTCAGGAAG 59.403 42.308 0.00 0.00 38.87 3.46
4089 5336 1.244816 GTTGTTACTTGGGGCAGGAC 58.755 55.000 0.00 0.00 0.00 3.85
4155 5402 6.263842 AGGTAATGCAAATCTGGTGATGTATG 59.736 38.462 0.00 0.00 32.44 2.39
4174 5964 4.955811 ATGTTCACCACTACTGAAGTCA 57.044 40.909 0.00 0.00 35.76 3.41
4192 5982 7.713750 TGAAGTCAGGAATAAATAGAGGTACG 58.286 38.462 0.00 0.00 0.00 3.67
4538 8317 7.707624 AGAGTGGCTGAAAATAAATGATTCA 57.292 32.000 0.00 0.00 0.00 2.57
4601 8381 4.867804 TGAAACCGATTCTTGCAATGGCA 61.868 43.478 0.00 0.00 42.57 4.92
4620 8400 6.418057 TGGCAATTACTCAAAAAGGAACAT 57.582 33.333 0.00 0.00 27.73 2.71
4649 8436 7.899178 TTTTCAAATCGTAGATGTAGCAAGA 57.101 32.000 0.00 0.00 45.12 3.02
4734 8522 5.640158 TTCTAAACCCCAAGAGACAAAGA 57.360 39.130 0.00 0.00 0.00 2.52
4800 8595 1.475034 CGGCACCAGCTACATACCATT 60.475 52.381 0.00 0.00 41.70 3.16
4801 8596 1.949525 GGCACCAGCTACATACCATTG 59.050 52.381 0.00 0.00 41.70 2.82
4861 8656 3.117888 AGGGCGGTCAAAACTCATATCAT 60.118 43.478 0.00 0.00 0.00 2.45
4872 8667 7.884877 TCAAAACTCATATCATTCACTCAAGGT 59.115 33.333 0.00 0.00 0.00 3.50
4892 8687 2.781681 AATGCACCTAACTACCGCTT 57.218 45.000 0.00 0.00 0.00 4.68
5113 10098 5.485620 GTCTAACAAAGAACCCGGTCTAAT 58.514 41.667 0.00 0.00 35.47 1.73
5116 10101 7.603784 GTCTAACAAAGAACCCGGTCTAATAAA 59.396 37.037 0.00 0.00 35.47 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 4.341235 CCAACCTCCGACTACAATGATCTA 59.659 45.833 0.00 0.00 0.00 1.98
259 352 4.466827 TCGGAGTATGCTACACCTTCATA 58.533 43.478 0.00 0.00 37.29 2.15
291 397 1.301716 GAGCCGCCAGAAACACTCA 60.302 57.895 0.00 0.00 0.00 3.41
405 513 0.614697 TCTGATTCCGCCTCCACTCA 60.615 55.000 0.00 0.00 0.00 3.41
488 596 5.643777 ACTAATATCCACACACTCTGCAAAC 59.356 40.000 0.00 0.00 0.00 2.93
521 631 4.202567 ACAATGCTTAGAAAGACCTTCCCA 60.203 41.667 0.00 0.00 34.21 4.37
531 641 8.094798 ACAAGAACGATAACAATGCTTAGAAA 57.905 30.769 0.00 0.00 0.00 2.52
534 645 9.638300 GATTACAAGAACGATAACAATGCTTAG 57.362 33.333 0.00 0.00 0.00 2.18
563 674 2.184322 CGCTAGCACATGACCCGT 59.816 61.111 16.45 0.00 0.00 5.28
627 739 1.344065 ACGGACCACAGAACCATGTA 58.656 50.000 0.00 0.00 0.00 2.29
794 907 1.155889 TGCATGTGTGGATGTCGTTC 58.844 50.000 0.00 0.00 0.00 3.95
855 968 0.730265 TGCAATGACCGGCGATTTAC 59.270 50.000 9.30 0.00 0.00 2.01
1017 1153 5.686841 CACAATTAAACATGTGGAGTGTGTG 59.313 40.000 19.95 16.12 42.46 3.82
1066 1218 2.438434 GGGGTGCTTCGTGGATGG 60.438 66.667 0.00 0.00 0.00 3.51
1100 1252 2.791560 GGTCAAGATCGATGTCGTCATG 59.208 50.000 0.54 0.00 40.80 3.07
1102 1254 1.202143 CGGTCAAGATCGATGTCGTCA 60.202 52.381 0.54 0.00 37.01 4.35
1109 1261 4.283467 TCATATTTCCCGGTCAAGATCGAT 59.717 41.667 3.98 0.00 37.01 3.59
1124 1276 2.535984 CGCGAGTCACCAGTCATATTTC 59.464 50.000 0.00 0.00 0.00 2.17
1162 1314 1.342574 TGGATGGATGAGGTACCACGA 60.343 52.381 15.94 0.00 39.06 4.35
1187 1348 1.693083 GCGATAGTGTGGTTGTCGGC 61.693 60.000 0.00 0.00 39.35 5.54
1201 1478 2.449031 GATCCATGGCGGTGGCGATA 62.449 60.000 6.96 0.00 41.24 2.92
1264 1541 1.003233 GGCGAAGAAGCTCCAGGTT 60.003 57.895 0.00 0.00 38.61 3.50
1306 1583 4.227134 CGCCCTATGCAGCTCGGT 62.227 66.667 0.00 0.00 41.33 4.69
1352 1629 3.003689 CCACCCGTATCATTGATGCTTTC 59.996 47.826 9.46 0.00 0.00 2.62
1355 1632 1.815408 GCCACCCGTATCATTGATGCT 60.815 52.381 9.46 0.00 0.00 3.79
1369 1649 2.582978 GACCCTAGTTCGCCACCC 59.417 66.667 0.00 0.00 0.00 4.61
1370 1650 2.183555 CGACCCTAGTTCGCCACC 59.816 66.667 0.00 0.00 0.00 4.61
1371 1651 1.445582 CACGACCCTAGTTCGCCAC 60.446 63.158 10.16 0.00 0.00 5.01
1372 1652 2.642254 CCACGACCCTAGTTCGCCA 61.642 63.158 10.16 0.00 0.00 5.69
1495 1778 6.773638 AGAAAGCAAAGAAGGACTTATCTCA 58.226 36.000 0.00 0.00 37.93 3.27
1496 1779 7.102993 AGAGAAAGCAAAGAAGGACTTATCTC 58.897 38.462 0.00 0.00 37.93 2.75
1591 1890 7.775053 AGGATAGATCAAGATACCTCAAGTC 57.225 40.000 0.00 0.00 0.00 3.01
1645 1944 2.615493 GCTTTGACAGGTTGCCTAGCTA 60.615 50.000 0.00 0.00 30.18 3.32
1697 2071 4.430007 TGAGACCATACTCGTATTGTTGC 58.570 43.478 0.00 0.00 39.49 4.17
1731 2129 1.823610 AGAGGTAGACGGCTTAACCAC 59.176 52.381 12.82 6.28 39.03 4.16
1739 2137 0.389948 CACCAACAGAGGTAGACGGC 60.390 60.000 0.00 0.00 40.77 5.68
1846 2244 2.387757 AGAAAGCAAGCACCCAGAAAA 58.612 42.857 0.00 0.00 0.00 2.29
1853 2251 0.523519 GGCACTAGAAAGCAAGCACC 59.476 55.000 0.00 0.00 0.00 5.01
1859 2257 2.356665 TTGGTTGGCACTAGAAAGCA 57.643 45.000 0.00 0.00 0.00 3.91
1866 2264 0.251916 CGAGGGATTGGTTGGCACTA 59.748 55.000 0.00 0.00 0.00 2.74
1872 2270 0.888736 TGTGTGCGAGGGATTGGTTG 60.889 55.000 0.00 0.00 0.00 3.77
1891 2289 5.649831 GCTCCTGAAGATTTGTGAGGTTTAT 59.350 40.000 0.00 0.00 0.00 1.40
1912 2310 4.452795 GTGGTTGTAGGAGAGAAAAAGCTC 59.547 45.833 0.00 0.00 35.11 4.09
1914 2312 4.390264 AGTGGTTGTAGGAGAGAAAAAGC 58.610 43.478 0.00 0.00 0.00 3.51
1918 2316 4.714632 CCAAAGTGGTTGTAGGAGAGAAA 58.285 43.478 0.00 0.00 35.23 2.52
1919 2317 3.496160 GCCAAAGTGGTTGTAGGAGAGAA 60.496 47.826 0.00 0.00 40.46 2.87
1948 2346 3.295973 TCCAAAACCAACTGGAGGAAAG 58.704 45.455 1.86 0.00 36.79 2.62
1951 2349 2.243736 ACTTCCAAAACCAACTGGAGGA 59.756 45.455 1.86 1.76 42.61 3.71
1971 2369 3.678548 CGAGGTACTTGAGGCTTGTTAAC 59.321 47.826 0.00 0.00 44.22 2.01
2009 2407 6.994496 CCCATGTAGCTCAATTCTAATGAGAA 59.006 38.462 7.67 0.00 45.74 2.87
2014 2412 7.520798 TGATTCCCATGTAGCTCAATTCTAAT 58.479 34.615 0.00 0.00 0.00 1.73
2035 2510 5.182001 GTCTACTGTCATTGTGGCTTTGATT 59.818 40.000 0.00 0.00 0.00 2.57
2037 2512 4.065088 GTCTACTGTCATTGTGGCTTTGA 58.935 43.478 0.00 0.00 0.00 2.69
2099 2574 2.443255 TGTTTCCAAAGGAGAGGCTTCT 59.557 45.455 0.00 0.00 36.01 2.85
2478 3178 4.938575 AACATTGGTGGTATAGGTCCAA 57.061 40.909 0.00 0.00 42.81 3.53
2518 3218 8.312564 AGGTTGTTAGAAAGAGTAAGGTGATAC 58.687 37.037 0.00 0.00 0.00 2.24
2546 3246 4.285003 CCATGGTGGTATATCTCCGGTAAA 59.715 45.833 2.57 0.00 31.35 2.01
2627 3333 4.093556 GCAACTCATTGTCCTTAGCAGTAC 59.906 45.833 0.00 0.00 38.17 2.73
2733 3439 7.554959 AGGTTCTTAGATAGTGAAAGGTGAA 57.445 36.000 0.00 0.00 0.00 3.18
2734 3440 7.455008 AGAAGGTTCTTAGATAGTGAAAGGTGA 59.545 37.037 0.00 0.00 32.55 4.02
2743 3449 5.659079 CCCAGTGAGAAGGTTCTTAGATAGT 59.341 44.000 0.00 0.00 37.73 2.12
2746 3452 3.198853 GCCCAGTGAGAAGGTTCTTAGAT 59.801 47.826 0.00 0.00 37.73 1.98
2778 3484 1.210478 TCCCAAGCAGGCTGATCTTAC 59.790 52.381 20.86 0.00 35.39 2.34
2797 3503 5.288952 GCTAAGGTCGAGTACAGTCAAATTC 59.711 44.000 0.00 0.00 0.00 2.17
2808 3514 7.108841 AGATTATTGTTGCTAAGGTCGAGTA 57.891 36.000 0.00 0.00 0.00 2.59
2844 3550 2.525105 AACCAGGTGTTCCTTTGTGT 57.475 45.000 0.00 0.00 43.07 3.72
2954 3660 8.792830 TTGAAGTAATTGGAGGATAAACTCAG 57.207 34.615 0.00 0.00 39.27 3.35
2958 3664 7.684428 GCCCATTGAAGTAATTGGAGGATAAAC 60.684 40.741 0.00 0.00 34.29 2.01
2979 3685 7.243824 ACAAATAGATTCAGGAATATGCCCAT 58.756 34.615 0.00 0.00 0.00 4.00
3013 3719 7.824289 TCTGATAAATCCAAGACAAGTAGGTTG 59.176 37.037 0.00 0.00 42.48 3.77
3080 3786 4.338795 AGAGGAGGAAGACCATGTTAGA 57.661 45.455 0.00 0.00 38.94 2.10
3086 3792 2.774809 GGCTTAAGAGGAGGAAGACCAT 59.225 50.000 6.67 0.00 38.94 3.55
3091 3797 3.703001 TTGTGGCTTAAGAGGAGGAAG 57.297 47.619 6.67 0.00 0.00 3.46
3114 3820 2.810439 TGGGAAATTGCCAGAAAACG 57.190 45.000 0.88 0.00 30.85 3.60
3127 3833 5.246981 AGTTCTTCAGTGATGATGGGAAA 57.753 39.130 9.35 0.00 0.00 3.13
3166 3872 8.868522 AGAAATTATTCACTGAAAGATCCACA 57.131 30.769 0.00 0.00 38.06 4.17
3253 3959 6.821665 CCGGAATAACTCCACAGAAGAAATTA 59.178 38.462 0.00 0.00 45.74 1.40
3270 3976 6.469410 AGTTTTGTGATAGTCACCGGAATAA 58.531 36.000 9.46 0.00 46.40 1.40
3292 3998 7.425224 ACTAAGCTGATGAAGGTGTATAAGT 57.575 36.000 0.00 0.00 36.51 2.24
3297 4003 6.106673 GCTAAACTAAGCTGATGAAGGTGTA 58.893 40.000 0.00 0.00 39.50 2.90
3372 4078 5.423886 TCTTTGGTTGTTTTTGGGTCATTC 58.576 37.500 0.00 0.00 0.00 2.67
3388 4094 0.469892 CAACCCCAGGCTTCTTTGGT 60.470 55.000 0.00 0.00 32.40 3.67
3397 4103 1.917872 TAAACATGTCAACCCCAGGC 58.082 50.000 0.00 0.00 0.00 4.85
3424 4130 2.810870 ATTTACCCACATGGCCGTTA 57.189 45.000 0.00 0.00 37.83 3.18
3484 4190 8.098912 ACATCCAAAATTCTAGTACCGTACTTT 58.901 33.333 16.28 2.32 40.14 2.66
3490 4196 5.183228 ACCACATCCAAAATTCTAGTACCG 58.817 41.667 0.00 0.00 0.00 4.02
3563 4269 6.994221 TCAACAGTCCTTTAAGAGAGGTAAG 58.006 40.000 0.00 0.00 35.71 2.34
3577 4283 5.070981 TGAGAAGTTCAGATTCAACAGTCCT 59.929 40.000 5.50 0.00 0.00 3.85
3642 4348 5.985530 TCGAGCGATTCAAGTGATTTCATAT 59.014 36.000 0.00 0.00 0.00 1.78
3679 4385 5.894393 TGTTGGGATTTCACCAGAAAGTTTA 59.106 36.000 0.00 0.00 46.13 2.01
3682 4388 3.909732 TGTTGGGATTTCACCAGAAAGT 58.090 40.909 0.00 0.00 46.13 2.66
3711 4417 7.494625 CCAAGGAGCTTAAATACGTCAAATCTA 59.505 37.037 0.00 0.00 0.00 1.98
3721 4427 5.938125 TGACAAGTCCAAGGAGCTTAAATAC 59.062 40.000 0.00 0.00 0.00 1.89
3864 4570 0.957395 CGGTGCATTGCTTCCTGAGT 60.957 55.000 10.49 0.00 0.00 3.41
3992 4698 7.523415 ACCCTCCAAACTTTCTTGAATAGTAA 58.477 34.615 0.00 0.00 0.00 2.24
4089 5336 4.705519 CTGCCGGCTTGCGGTTTG 62.706 66.667 29.70 2.49 32.81 2.93
4103 5350 3.363178 GTTGTCACACTTAAGTTGCTGC 58.637 45.455 5.07 0.00 0.00 5.25
4155 5402 3.321111 TCCTGACTTCAGTAGTGGTGAAC 59.679 47.826 5.53 0.00 42.27 3.18
4174 5964 5.601313 TGCTTCCGTACCTCTATTTATTCCT 59.399 40.000 0.00 0.00 0.00 3.36
4192 5982 2.817901 CATAAGCTGCCAAATGCTTCC 58.182 47.619 3.41 0.00 45.09 3.46
4635 8415 6.310711 GTGGTTACACTTCTTGCTACATCTAC 59.689 42.308 0.00 0.00 44.29 2.59
4734 8522 1.588674 TTGTTGTTTGCGACCGAGAT 58.411 45.000 0.00 0.00 0.00 2.75
4818 8613 7.908601 CGCCCTTATTTTAACTTGTACTGAATC 59.091 37.037 0.00 0.00 0.00 2.52
4872 8667 3.899052 AAGCGGTAGTTAGGTGCATTA 57.101 42.857 0.00 0.00 0.00 1.90
4892 8687 3.164977 TGGGTGTCCTCACGGCAA 61.165 61.111 0.00 0.00 44.68 4.52
4938 8737 7.560368 TGAAGAAGAAAGATACTGGGAATCTC 58.440 38.462 0.00 0.00 32.48 2.75
5073 8874 7.647907 TGTTAGACCAGTTCTTCGATTTTAC 57.352 36.000 0.00 0.00 35.55 2.01


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

AutoCloner maintained by Alex Coulton.