Multiple sequence alignment - TraesCS6A01G103100

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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 TraesCS6A01G103100 chr6A 100.000 3305 0 0 1 3305 72428433 72431737 0.000000e+00 6104.0
1 TraesCS6A01G103100 chr6A 78.756 1351 234 41 1020 2344 73063636 73064959 0.000000e+00 856.0
2 TraesCS6A01G103100 chr6A 77.213 1457 284 37 990 2421 71924709 71926142 0.000000e+00 808.0
3 TraesCS6A01G103100 chr6A 77.139 1461 289 37 989 2423 71948652 71950093 0.000000e+00 806.0
4 TraesCS6A01G103100 chr6A 100.000 29 0 0 743 771 461977177 461977149 2.000000e-03 54.7
5 TraesCS6A01G103100 chr6B 93.762 2036 106 1 935 2970 129268627 129270641 0.000000e+00 3037.0
6 TraesCS6A01G103100 chr6B 81.113 1419 236 26 990 2391 129447017 129448420 0.000000e+00 1107.0
7 TraesCS6A01G103100 chr6B 78.412 1348 247 36 1017 2344 129850434 129851757 0.000000e+00 837.0
8 TraesCS6A01G103100 chr6B 77.357 1453 285 33 990 2423 128016529 128017956 0.000000e+00 821.0
9 TraesCS6A01G103100 chr6B 76.912 1451 291 33 992 2423 129237149 129238574 0.000000e+00 784.0
10 TraesCS6A01G103100 chr6B 85.662 544 62 10 75 609 129263740 129264276 2.880000e-155 558.0
11 TraesCS6A01G103100 chr6B 80.032 621 107 11 1019 1626 129679513 129680129 8.420000e-121 444.0
12 TraesCS6A01G103100 chr6B 83.286 353 25 15 2969 3302 129270680 129271017 8.970000e-76 294.0
13 TraesCS6A01G103100 chr6B 82.129 263 45 2 2 263 189136213 189135952 1.190000e-54 224.0
14 TraesCS6A01G103100 chr6B 92.857 126 6 1 827 952 129265437 129265559 2.620000e-41 180.0
15 TraesCS6A01G103100 chr6B 100.000 28 0 0 743 770 576438760 576438733 6.000000e-03 52.8
16 TraesCS6A01G103100 chr6D 96.145 856 16 7 2467 3305 57216840 57217695 0.000000e+00 1382.0
17 TraesCS6A01G103100 chr6D 95.013 742 26 4 914 1648 57215820 57216557 0.000000e+00 1155.0
18 TraesCS6A01G103100 chr6D 80.493 1338 215 25 990 2315 57514184 57515487 0.000000e+00 983.0
19 TraesCS6A01G103100 chr6D 76.923 1456 289 36 990 2423 57171264 57172694 0.000000e+00 784.0
20 TraesCS6A01G103100 chr6D 77.459 1393 259 44 992 2360 57482402 57483763 0.000000e+00 782.0
21 TraesCS6A01G103100 chr6D 77.563 1346 230 45 1017 2322 57894085 57895398 0.000000e+00 747.0
22 TraesCS6A01G103100 chr6D 81.230 618 102 11 1019 1626 57782701 57783314 1.380000e-133 486.0
23 TraesCS6A01G103100 chr6D 94.737 57 3 0 827 883 57215764 57215820 4.540000e-14 89.8
24 TraesCS6A01G103100 chr1D 91.860 258 21 0 1 258 319628965 319629222 8.720000e-96 361.0
25 TraesCS6A01G103100 chr1D 82.576 264 41 5 2 263 265694813 265695073 9.230000e-56 228.0
26 TraesCS6A01G103100 chr7D 90.875 263 24 0 1 263 580703065 580702803 1.460000e-93 353.0
27 TraesCS6A01G103100 chr7D 84.906 106 13 1 262 364 5586543 5586648 1.620000e-18 104.0
28 TraesCS6A01G103100 chr7A 90.494 263 24 1 1 263 285369066 285368805 2.440000e-91 346.0
29 TraesCS6A01G103100 chr7A 89.147 258 27 1 1 258 565705155 565705411 1.480000e-83 320.0
30 TraesCS6A01G103100 chr7B 89.354 263 28 0 1 263 62823476 62823738 6.840000e-87 331.0
31 TraesCS6A01G103100 chr7B 82.955 264 41 4 2 263 328514882 328514621 5.510000e-58 235.0
32 TraesCS6A01G103100 chr7B 88.636 44 3 2 743 784 217457335 217457292 6.000000e-03 52.8
33 TraesCS6A01G103100 chr4D 83.019 159 22 4 262 416 107743392 107743235 4.450000e-29 139.0
34 TraesCS6A01G103100 chr4D 81.560 141 22 3 262 399 39614573 39614434 2.700000e-21 113.0
35 TraesCS6A01G103100 chr3D 78.431 153 22 10 417 564 11454043 11453897 4.540000e-14 89.8
36 TraesCS6A01G103100 chr3D 87.302 63 4 4 743 804 588310488 588310429 5.920000e-08 69.4
37 TraesCS6A01G103100 chr1A 77.070 157 25 7 419 567 182175273 182175120 2.730000e-11 80.5
38 TraesCS6A01G103100 chr2B 75.974 154 25 9 461 609 767473293 767473147 5.920000e-08 69.4
39 TraesCS6A01G103100 chr3B 85.246 61 5 4 453 510 813912742 813912801 3.560000e-05 60.2
40 TraesCS6A01G103100 chr5B 100.000 28 0 0 456 483 312597898 312597925 6.000000e-03 52.8
41 TraesCS6A01G103100 chr4B 100.000 28 0 0 743 770 72959642 72959669 6.000000e-03 52.8


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 TraesCS6A01G103100 chr6A 72428433 72431737 3304 False 6104.00 6104 100.000000 1 3305 1 chr6A.!!$F3 3304
1 TraesCS6A01G103100 chr6A 73063636 73064959 1323 False 856.00 856 78.756000 1020 2344 1 chr6A.!!$F4 1324
2 TraesCS6A01G103100 chr6A 71924709 71926142 1433 False 808.00 808 77.213000 990 2421 1 chr6A.!!$F1 1431
3 TraesCS6A01G103100 chr6A 71948652 71950093 1441 False 806.00 806 77.139000 989 2423 1 chr6A.!!$F2 1434
4 TraesCS6A01G103100 chr6B 129447017 129448420 1403 False 1107.00 1107 81.113000 990 2391 1 chr6B.!!$F3 1401
5 TraesCS6A01G103100 chr6B 129263740 129271017 7277 False 1017.25 3037 88.891750 75 3302 4 chr6B.!!$F6 3227
6 TraesCS6A01G103100 chr6B 129850434 129851757 1323 False 837.00 837 78.412000 1017 2344 1 chr6B.!!$F5 1327
7 TraesCS6A01G103100 chr6B 128016529 128017956 1427 False 821.00 821 77.357000 990 2423 1 chr6B.!!$F1 1433
8 TraesCS6A01G103100 chr6B 129237149 129238574 1425 False 784.00 784 76.912000 992 2423 1 chr6B.!!$F2 1431
9 TraesCS6A01G103100 chr6B 129679513 129680129 616 False 444.00 444 80.032000 1019 1626 1 chr6B.!!$F4 607
10 TraesCS6A01G103100 chr6D 57514184 57515487 1303 False 983.00 983 80.493000 990 2315 1 chr6D.!!$F3 1325
11 TraesCS6A01G103100 chr6D 57215764 57217695 1931 False 875.60 1382 95.298333 827 3305 3 chr6D.!!$F6 2478
12 TraesCS6A01G103100 chr6D 57171264 57172694 1430 False 784.00 784 76.923000 990 2423 1 chr6D.!!$F1 1433
13 TraesCS6A01G103100 chr6D 57482402 57483763 1361 False 782.00 782 77.459000 992 2360 1 chr6D.!!$F2 1368
14 TraesCS6A01G103100 chr6D 57894085 57895398 1313 False 747.00 747 77.563000 1017 2322 1 chr6D.!!$F5 1305
15 TraesCS6A01G103100 chr6D 57782701 57783314 613 False 486.00 486 81.230000 1019 1626 1 chr6D.!!$F4 607

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
267 268 0.170339 GTGCATGTCCGGTTTTAGGC 59.830 55.000 0.00 0.29 0.00 3.93 F
374 375 0.733909 CGTCGCTTCACAGCTGATGA 60.734 55.000 23.35 17.05 44.85 2.92 F
940 5014 1.134175 CCTGTTGTTGTTGTGTGACCC 59.866 52.381 0.00 0.00 0.00 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1425 5530 2.046892 ACTGACATGTGCTCGGGC 60.047 61.111 1.15 0.0 39.26 6.13 R
1575 5690 2.108976 CACCACTGGCGTGTGACT 59.891 61.111 11.24 0.0 40.12 3.41 R
2404 6552 0.032813 AATCATGGCCACCTTCCCTG 60.033 55.000 8.16 0.0 0.00 4.45 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
17 18 2.903357 TTCTCCTCCGCATGAGCC 59.097 61.111 0.00 0.00 39.98 4.70
18 19 1.989508 TTCTCCTCCGCATGAGCCA 60.990 57.895 0.00 0.00 39.98 4.75
19 20 1.552799 TTCTCCTCCGCATGAGCCAA 61.553 55.000 0.00 0.00 39.98 4.52
20 21 1.523258 CTCCTCCGCATGAGCCAAG 60.523 63.158 0.00 0.00 39.98 3.61
21 22 1.964608 CTCCTCCGCATGAGCCAAGA 61.965 60.000 0.00 0.00 39.98 3.02
22 23 1.523258 CCTCCGCATGAGCCAAGAG 60.523 63.158 0.00 0.00 39.98 2.85
23 24 1.519246 CTCCGCATGAGCCAAGAGA 59.481 57.895 0.00 0.00 37.52 3.10
24 25 0.530211 CTCCGCATGAGCCAAGAGAG 60.530 60.000 0.00 0.00 37.52 3.20
25 26 2.178890 CCGCATGAGCCAAGAGAGC 61.179 63.158 0.00 0.00 37.52 4.09
26 27 1.449070 CGCATGAGCCAAGAGAGCA 60.449 57.895 0.00 0.00 37.52 4.26
27 28 1.022982 CGCATGAGCCAAGAGAGCAA 61.023 55.000 0.00 0.00 37.52 3.91
28 29 1.390565 GCATGAGCCAAGAGAGCAAT 58.609 50.000 0.00 0.00 33.58 3.56
29 30 1.334243 GCATGAGCCAAGAGAGCAATC 59.666 52.381 0.00 0.00 33.58 2.67
30 31 2.640184 CATGAGCCAAGAGAGCAATCA 58.360 47.619 0.00 0.00 0.00 2.57
31 32 2.398252 TGAGCCAAGAGAGCAATCAG 57.602 50.000 0.00 0.00 0.00 2.90
32 33 1.065636 TGAGCCAAGAGAGCAATCAGG 60.066 52.381 0.00 0.00 0.00 3.86
33 34 0.394080 AGCCAAGAGAGCAATCAGGC 60.394 55.000 13.35 13.35 40.78 4.85
42 43 2.301577 AGCAATCAGGCTCTTCGTAC 57.698 50.000 0.00 0.00 41.05 3.67
43 44 1.550524 AGCAATCAGGCTCTTCGTACA 59.449 47.619 0.00 0.00 41.05 2.90
44 45 2.169352 AGCAATCAGGCTCTTCGTACAT 59.831 45.455 0.00 0.00 41.05 2.29
45 46 3.384789 AGCAATCAGGCTCTTCGTACATA 59.615 43.478 0.00 0.00 41.05 2.29
46 47 4.119862 GCAATCAGGCTCTTCGTACATAA 58.880 43.478 0.00 0.00 0.00 1.90
47 48 4.025647 GCAATCAGGCTCTTCGTACATAAC 60.026 45.833 0.00 0.00 0.00 1.89
48 49 5.109210 CAATCAGGCTCTTCGTACATAACA 58.891 41.667 0.00 0.00 0.00 2.41
49 50 4.794278 TCAGGCTCTTCGTACATAACAA 57.206 40.909 0.00 0.00 0.00 2.83
50 51 4.744570 TCAGGCTCTTCGTACATAACAAG 58.255 43.478 0.00 0.00 0.00 3.16
51 52 4.461431 TCAGGCTCTTCGTACATAACAAGA 59.539 41.667 0.00 0.00 0.00 3.02
52 53 5.047590 TCAGGCTCTTCGTACATAACAAGAA 60.048 40.000 0.00 0.00 30.21 2.52
53 54 5.812642 CAGGCTCTTCGTACATAACAAGAAT 59.187 40.000 0.00 0.00 30.21 2.40
54 55 6.978659 CAGGCTCTTCGTACATAACAAGAATA 59.021 38.462 0.00 0.00 30.21 1.75
55 56 7.491372 CAGGCTCTTCGTACATAACAAGAATAA 59.509 37.037 0.00 0.00 30.21 1.40
56 57 7.707035 AGGCTCTTCGTACATAACAAGAATAAG 59.293 37.037 0.00 0.00 30.21 1.73
57 58 7.491696 GGCTCTTCGTACATAACAAGAATAAGT 59.508 37.037 0.00 0.00 30.21 2.24
58 59 9.512435 GCTCTTCGTACATAACAAGAATAAGTA 57.488 33.333 0.00 0.00 30.21 2.24
61 62 9.245962 CTTCGTACATAACAAGAATAAGTAGGG 57.754 37.037 0.00 0.00 0.00 3.53
62 63 7.719483 TCGTACATAACAAGAATAAGTAGGGG 58.281 38.462 0.00 0.00 0.00 4.79
63 64 7.560991 TCGTACATAACAAGAATAAGTAGGGGA 59.439 37.037 0.00 0.00 0.00 4.81
64 65 8.199449 CGTACATAACAAGAATAAGTAGGGGAA 58.801 37.037 0.00 0.00 0.00 3.97
70 71 7.619512 ACAAGAATAAGTAGGGGAATAGAGG 57.380 40.000 0.00 0.00 0.00 3.69
71 72 6.559157 ACAAGAATAAGTAGGGGAATAGAGGG 59.441 42.308 0.00 0.00 0.00 4.30
72 73 6.310459 AGAATAAGTAGGGGAATAGAGGGT 57.690 41.667 0.00 0.00 0.00 4.34
73 74 6.324544 AGAATAAGTAGGGGAATAGAGGGTC 58.675 44.000 0.00 0.00 0.00 4.46
77 78 1.330155 AGGGGAATAGAGGGTCTCCA 58.670 55.000 0.00 0.00 36.80 3.86
81 82 2.635427 GGGAATAGAGGGTCTCCATGTC 59.365 54.545 0.00 0.00 34.83 3.06
105 106 4.035909 TCAAACCTCTCGTTGGCTTAAAAC 59.964 41.667 0.00 0.00 33.93 2.43
120 121 6.710744 TGGCTTAAAACTCTTAGTTTCCTCTG 59.289 38.462 5.57 0.00 46.78 3.35
130 131 6.100004 TCTTAGTTTCCTCTGTATTGAAGCG 58.900 40.000 0.00 0.00 0.00 4.68
146 147 2.180017 CGAACCCGGTACTCCACG 59.820 66.667 0.00 0.00 0.00 4.94
191 192 6.544928 AAGTTCACCCAGTTTTCTTGAAAT 57.455 33.333 0.00 0.00 29.58 2.17
194 195 3.895041 TCACCCAGTTTTCTTGAAATCCC 59.105 43.478 0.00 0.00 0.00 3.85
198 199 4.262164 CCCAGTTTTCTTGAAATCCCAGTG 60.262 45.833 0.00 0.00 0.00 3.66
239 240 3.311110 GGCCACTCCACTCGGTCA 61.311 66.667 0.00 0.00 34.01 4.02
242 243 0.753262 GCCACTCCACTCGGTCATAT 59.247 55.000 0.00 0.00 0.00 1.78
265 266 3.564511 CTTTGTGCATGTCCGGTTTTAG 58.435 45.455 0.00 0.00 0.00 1.85
267 268 0.170339 GTGCATGTCCGGTTTTAGGC 59.830 55.000 0.00 0.29 0.00 3.93
273 274 1.967494 TCCGGTTTTAGGCGCCAAC 60.967 57.895 31.54 23.53 0.00 3.77
356 357 4.135153 CCTCCTGGCTCGGTCACG 62.135 72.222 0.00 0.00 42.74 4.35
358 359 3.343788 CTCCTGGCTCGGTCACGTC 62.344 68.421 0.00 0.00 41.85 4.34
369 370 1.661821 GTCACGTCGCTTCACAGCT 60.662 57.895 0.00 0.00 44.85 4.24
371 372 1.661509 CACGTCGCTTCACAGCTGA 60.662 57.895 23.35 0.00 44.85 4.26
374 375 0.733909 CGTCGCTTCACAGCTGATGA 60.734 55.000 23.35 17.05 44.85 2.92
378 379 1.136141 CGCTTCACAGCTGATGAACAC 60.136 52.381 23.35 15.89 44.85 3.32
385 386 2.079158 CAGCTGATGAACACGGTTGAT 58.921 47.619 8.42 0.00 0.00 2.57
387 388 2.076100 GCTGATGAACACGGTTGATCA 58.924 47.619 14.51 14.51 38.74 2.92
388 389 2.679837 GCTGATGAACACGGTTGATCAT 59.320 45.455 15.25 8.40 45.33 2.45
472 479 9.434420 AGTTCACAAATTTGAAAAAGTTCATCA 57.566 25.926 24.64 0.00 43.29 3.07
493 500 8.415553 TCATCAGTTTTGAAAACAGTTCATCAT 58.584 29.630 21.34 1.14 36.78 2.45
593 600 9.434420 AAGTTCACAAATCTGTCAAAAATTTCA 57.566 25.926 0.00 0.00 31.64 2.69
732 739 4.575645 CCAAGTAAAACCGTAACTGAACCA 59.424 41.667 0.00 0.00 0.00 3.67
738 745 2.291365 ACCGTAACTGAACCACAAACC 58.709 47.619 0.00 0.00 0.00 3.27
739 746 2.290464 CCGTAACTGAACCACAAACCA 58.710 47.619 0.00 0.00 0.00 3.67
741 748 2.289547 CGTAACTGAACCACAAACCAGG 59.710 50.000 0.00 0.00 0.00 4.45
774 781 1.819288 GGAAGCTTCCCAAAACTAGGC 59.181 52.381 31.91 4.77 41.62 3.93
775 782 2.555448 GGAAGCTTCCCAAAACTAGGCT 60.555 50.000 31.91 0.00 41.62 4.58
777 784 3.244887 AGCTTCCCAAAACTAGGCTTT 57.755 42.857 0.00 0.00 0.00 3.51
778 785 3.157881 AGCTTCCCAAAACTAGGCTTTC 58.842 45.455 0.00 0.00 0.00 2.62
779 786 2.890945 GCTTCCCAAAACTAGGCTTTCA 59.109 45.455 0.00 0.00 0.00 2.69
780 787 3.305403 GCTTCCCAAAACTAGGCTTTCAC 60.305 47.826 0.00 0.00 0.00 3.18
781 788 2.500229 TCCCAAAACTAGGCTTTCACG 58.500 47.619 0.00 0.00 0.00 4.35
782 789 2.105134 TCCCAAAACTAGGCTTTCACGA 59.895 45.455 0.00 0.00 0.00 4.35
783 790 2.882137 CCCAAAACTAGGCTTTCACGAA 59.118 45.455 0.00 0.00 0.00 3.85
784 791 3.304458 CCCAAAACTAGGCTTTCACGAAC 60.304 47.826 0.00 0.00 0.00 3.95
785 792 3.541711 CAAAACTAGGCTTTCACGAACG 58.458 45.455 0.00 0.00 0.00 3.95
786 793 2.521105 AACTAGGCTTTCACGAACGT 57.479 45.000 0.00 0.00 0.00 3.99
787 794 1.779569 ACTAGGCTTTCACGAACGTG 58.220 50.000 19.22 19.22 46.64 4.49
805 812 6.086371 CGAACGTGAGAAAAGAAATAAAAGGC 59.914 38.462 0.00 0.00 0.00 4.35
806 813 5.769367 ACGTGAGAAAAGAAATAAAAGGCC 58.231 37.500 0.00 0.00 0.00 5.19
807 814 5.535030 ACGTGAGAAAAGAAATAAAAGGCCT 59.465 36.000 0.00 0.00 0.00 5.19
808 815 5.858581 CGTGAGAAAAGAAATAAAAGGCCTG 59.141 40.000 5.69 0.00 0.00 4.85
811 1773 4.840680 AGAAAAGAAATAAAAGGCCTGGCT 59.159 37.500 19.68 0.28 0.00 4.75
931 1923 1.208535 TCGTCACTCCCTGTTGTTGTT 59.791 47.619 0.00 0.00 0.00 2.83
932 1924 1.330521 CGTCACTCCCTGTTGTTGTTG 59.669 52.381 0.00 0.00 0.00 3.33
933 1925 2.365582 GTCACTCCCTGTTGTTGTTGT 58.634 47.619 0.00 0.00 0.00 3.32
940 5014 1.134175 CCTGTTGTTGTTGTGTGACCC 59.866 52.381 0.00 0.00 0.00 4.46
956 5030 2.535331 CCCCTCCAACGAAACCCCT 61.535 63.158 0.00 0.00 0.00 4.79
963 5037 2.079911 AACGAAACCCCTGTCCCCA 61.080 57.895 0.00 0.00 0.00 4.96
1015 5089 4.473520 CCATGGCTCCTTCGGCGT 62.474 66.667 6.85 0.00 0.00 5.68
1425 5530 3.818787 GTGCTGCTTCCGCCCATG 61.819 66.667 0.00 0.00 34.43 3.66
1575 5690 5.034852 TGGATGTGTTTGTCTTCTCTTCA 57.965 39.130 0.00 0.00 0.00 3.02
1587 5702 0.315251 TCTCTTCAGTCACACGCCAG 59.685 55.000 0.00 0.00 0.00 4.85
1616 5749 1.837789 CTGCATCTCCCAGCTGGAT 59.162 57.895 34.91 17.12 44.07 3.41
1660 5796 4.980903 GGCTGCGCGTGGTGTTTG 62.981 66.667 8.43 0.00 0.00 2.93
1661 5797 4.980903 GCTGCGCGTGGTGTTTGG 62.981 66.667 8.43 0.00 0.00 3.28
1733 5872 1.970917 GCGTCGCCATGGAAAGACAG 61.971 60.000 24.97 19.92 33.56 3.51
1920 6059 2.042569 TGTAGTGGGTAGAGAAGGAGCA 59.957 50.000 0.00 0.00 0.00 4.26
1962 6101 1.284785 GGGGATCACAGTCCAAATGGA 59.715 52.381 0.00 0.00 43.08 3.41
2436 6584 3.448301 GGCCATGATTTCATTTGTCTCCA 59.552 43.478 0.00 0.00 33.61 3.86
2488 6636 6.148150 GCAATTTCATTTCATTCCAGCAAAGA 59.852 34.615 0.00 0.00 0.00 2.52
2825 6973 5.280164 GGAGGATATACAAGATGGTGATGCA 60.280 44.000 0.00 0.00 0.00 3.96
2926 7074 1.818850 GTGTGCAGCATATTTCAGCG 58.181 50.000 0.00 0.00 35.48 5.18
3111 7321 2.322355 ACAATATGCTTCTGCTCGCT 57.678 45.000 0.00 0.00 40.48 4.93
3199 7429 4.986054 TTCAGTGTTTATGTGGGGTACT 57.014 40.909 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.552799 TTGGCTCATGCGGAGGAGAA 61.553 55.000 23.14 5.69 44.22 2.87
1 2 1.964608 CTTGGCTCATGCGGAGGAGA 61.965 60.000 23.14 0.00 44.22 3.71
3 4 1.964608 CTCTTGGCTCATGCGGAGGA 61.965 60.000 7.25 0.00 44.22 3.71
4 5 1.523258 CTCTTGGCTCATGCGGAGG 60.523 63.158 7.25 0.00 44.22 4.30
5 6 0.530211 CTCTCTTGGCTCATGCGGAG 60.530 60.000 1.05 1.05 46.93 4.63
6 7 1.519246 CTCTCTTGGCTCATGCGGA 59.481 57.895 0.00 0.00 40.82 5.54
7 8 2.178890 GCTCTCTTGGCTCATGCGG 61.179 63.158 0.00 0.00 40.82 5.69
8 9 1.022982 TTGCTCTCTTGGCTCATGCG 61.023 55.000 0.00 0.00 40.82 4.73
9 10 1.334243 GATTGCTCTCTTGGCTCATGC 59.666 52.381 0.00 0.00 38.76 4.06
10 11 2.614520 CTGATTGCTCTCTTGGCTCATG 59.385 50.000 0.00 0.00 0.00 3.07
11 12 2.421670 CCTGATTGCTCTCTTGGCTCAT 60.422 50.000 0.00 0.00 0.00 2.90
12 13 1.065636 CCTGATTGCTCTCTTGGCTCA 60.066 52.381 0.00 0.00 0.00 4.26
13 14 1.666054 CCTGATTGCTCTCTTGGCTC 58.334 55.000 0.00 0.00 0.00 4.70
14 15 0.394080 GCCTGATTGCTCTCTTGGCT 60.394 55.000 0.00 0.00 34.74 4.75
15 16 0.394080 AGCCTGATTGCTCTCTTGGC 60.394 55.000 12.09 12.09 36.75 4.52
16 17 3.877951 AGCCTGATTGCTCTCTTGG 57.122 52.632 0.00 0.00 36.75 3.61
23 24 1.550524 TGTACGAAGAGCCTGATTGCT 59.449 47.619 0.00 0.00 46.37 3.91
24 25 2.010145 TGTACGAAGAGCCTGATTGC 57.990 50.000 0.00 0.00 0.00 3.56
25 26 5.109210 TGTTATGTACGAAGAGCCTGATTG 58.891 41.667 0.00 0.00 0.00 2.67
26 27 5.339008 TGTTATGTACGAAGAGCCTGATT 57.661 39.130 0.00 0.00 0.00 2.57
27 28 5.127194 TCTTGTTATGTACGAAGAGCCTGAT 59.873 40.000 0.00 0.00 0.00 2.90
28 29 4.461431 TCTTGTTATGTACGAAGAGCCTGA 59.539 41.667 0.00 0.00 0.00 3.86
29 30 4.744570 TCTTGTTATGTACGAAGAGCCTG 58.255 43.478 0.00 0.00 0.00 4.85
30 31 5.401531 TTCTTGTTATGTACGAAGAGCCT 57.598 39.130 0.00 0.00 30.78 4.58
31 32 7.491696 ACTTATTCTTGTTATGTACGAAGAGCC 59.508 37.037 0.00 0.00 30.78 4.70
32 33 8.408743 ACTTATTCTTGTTATGTACGAAGAGC 57.591 34.615 0.00 0.00 30.78 4.09
35 36 9.245962 CCCTACTTATTCTTGTTATGTACGAAG 57.754 37.037 0.00 0.00 0.00 3.79
36 37 8.199449 CCCCTACTTATTCTTGTTATGTACGAA 58.801 37.037 0.00 0.00 0.00 3.85
37 38 7.560991 TCCCCTACTTATTCTTGTTATGTACGA 59.439 37.037 0.00 0.00 0.00 3.43
38 39 7.719483 TCCCCTACTTATTCTTGTTATGTACG 58.281 38.462 0.00 0.00 0.00 3.67
44 45 9.155785 CCTCTATTCCCCTACTTATTCTTGTTA 57.844 37.037 0.00 0.00 0.00 2.41
45 46 7.072581 CCCTCTATTCCCCTACTTATTCTTGTT 59.927 40.741 0.00 0.00 0.00 2.83
46 47 6.559157 CCCTCTATTCCCCTACTTATTCTTGT 59.441 42.308 0.00 0.00 0.00 3.16
47 48 6.559157 ACCCTCTATTCCCCTACTTATTCTTG 59.441 42.308 0.00 0.00 0.00 3.02
48 49 6.704792 ACCCTCTATTCCCCTACTTATTCTT 58.295 40.000 0.00 0.00 0.00 2.52
49 50 6.106494 AGACCCTCTATTCCCCTACTTATTCT 59.894 42.308 0.00 0.00 0.00 2.40
50 51 6.324544 AGACCCTCTATTCCCCTACTTATTC 58.675 44.000 0.00 0.00 0.00 1.75
51 52 6.310459 AGACCCTCTATTCCCCTACTTATT 57.690 41.667 0.00 0.00 0.00 1.40
52 53 5.222589 GGAGACCCTCTATTCCCCTACTTAT 60.223 48.000 0.00 0.00 0.00 1.73
53 54 4.107636 GGAGACCCTCTATTCCCCTACTTA 59.892 50.000 0.00 0.00 0.00 2.24
54 55 3.116668 GGAGACCCTCTATTCCCCTACTT 60.117 52.174 0.00 0.00 0.00 2.24
55 56 2.451659 GGAGACCCTCTATTCCCCTACT 59.548 54.545 0.00 0.00 0.00 2.57
56 57 2.179424 TGGAGACCCTCTATTCCCCTAC 59.821 54.545 0.00 0.00 0.00 3.18
57 58 2.521286 TGGAGACCCTCTATTCCCCTA 58.479 52.381 0.00 0.00 0.00 3.53
58 59 1.330155 TGGAGACCCTCTATTCCCCT 58.670 55.000 0.00 0.00 0.00 4.79
59 60 1.981495 CATGGAGACCCTCTATTCCCC 59.019 57.143 0.00 0.00 29.28 4.81
60 61 2.635427 GACATGGAGACCCTCTATTCCC 59.365 54.545 0.00 0.00 29.28 3.97
61 62 3.576550 GAGACATGGAGACCCTCTATTCC 59.423 52.174 0.00 0.00 29.28 3.01
62 63 4.219115 TGAGACATGGAGACCCTCTATTC 58.781 47.826 0.00 0.00 29.28 1.75
63 64 4.271807 TGAGACATGGAGACCCTCTATT 57.728 45.455 0.00 0.00 29.28 1.73
64 65 3.981516 TGAGACATGGAGACCCTCTAT 57.018 47.619 0.00 0.00 31.92 1.98
65 66 3.757947 TTGAGACATGGAGACCCTCTA 57.242 47.619 0.00 0.00 0.00 2.43
66 67 2.569404 GTTTGAGACATGGAGACCCTCT 59.431 50.000 0.00 0.00 0.00 3.69
67 68 2.355209 GGTTTGAGACATGGAGACCCTC 60.355 54.545 0.00 0.00 0.00 4.30
68 69 1.630878 GGTTTGAGACATGGAGACCCT 59.369 52.381 0.00 0.00 0.00 4.34
69 70 1.630878 AGGTTTGAGACATGGAGACCC 59.369 52.381 0.00 0.00 0.00 4.46
70 71 2.569404 AGAGGTTTGAGACATGGAGACC 59.431 50.000 0.00 0.00 0.00 3.85
71 72 3.674682 CGAGAGGTTTGAGACATGGAGAC 60.675 52.174 0.00 0.00 0.00 3.36
72 73 2.493675 CGAGAGGTTTGAGACATGGAGA 59.506 50.000 0.00 0.00 0.00 3.71
73 74 2.232452 ACGAGAGGTTTGAGACATGGAG 59.768 50.000 0.00 0.00 0.00 3.86
77 78 2.872038 GCCAACGAGAGGTTTGAGACAT 60.872 50.000 0.00 0.00 36.49 3.06
81 82 1.884235 AAGCCAACGAGAGGTTTGAG 58.116 50.000 0.00 0.00 36.49 3.02
105 106 6.254589 CGCTTCAATACAGAGGAAACTAAGAG 59.745 42.308 0.00 0.00 44.43 2.85
114 115 2.093658 GGGTTCGCTTCAATACAGAGGA 60.094 50.000 0.00 0.00 0.00 3.71
120 121 1.929169 GTACCGGGTTCGCTTCAATAC 59.071 52.381 4.31 0.00 34.56 1.89
130 131 0.179119 CATCGTGGAGTACCGGGTTC 60.179 60.000 4.31 0.00 39.42 3.62
146 147 8.383318 ACTTAGTTATGCAATGTGTATCCATC 57.617 34.615 0.00 0.00 0.00 3.51
166 167 6.693315 TTCAAGAAAACTGGGTGAACTTAG 57.307 37.500 0.00 0.00 0.00 2.18
191 192 4.104086 AGGAGATTATGTTGACACTGGGA 58.896 43.478 0.00 0.00 0.00 4.37
194 195 7.439157 TTTGAAGGAGATTATGTTGACACTG 57.561 36.000 0.00 0.00 0.00 3.66
231 232 2.009774 GCACAAAGCATATGACCGAGT 58.990 47.619 6.97 0.00 44.79 4.18
257 258 0.725117 CTAGTTGGCGCCTAAAACCG 59.275 55.000 29.70 13.40 0.00 4.44
258 259 1.092348 CCTAGTTGGCGCCTAAAACC 58.908 55.000 29.70 8.14 0.00 3.27
265 266 2.437895 GAACCCCTAGTTGGCGCC 60.438 66.667 22.73 22.73 39.40 6.53
267 268 1.078426 CCTGAACCCCTAGTTGGCG 60.078 63.158 0.00 0.00 39.40 5.69
273 274 4.176752 GGGCGCCTGAACCCCTAG 62.177 72.222 28.56 0.00 40.56 3.02
317 318 4.741781 CAGGGAGCGCGCGTTTTG 62.742 66.667 32.35 20.03 0.00 2.44
356 357 1.127582 GTTCATCAGCTGTGAAGCGAC 59.872 52.381 23.36 13.78 36.35 5.19
358 359 1.136141 GTGTTCATCAGCTGTGAAGCG 60.136 52.381 23.36 6.31 36.35 4.68
369 370 4.322567 TGAATGATCAACCGTGTTCATCA 58.677 39.130 0.00 5.97 41.36 3.07
567 574 9.434420 TGAAATTTTTGACAGATTTGTGAACTT 57.566 25.926 0.00 0.00 37.76 2.66
568 575 9.603921 ATGAAATTTTTGACAGATTTGTGAACT 57.396 25.926 0.00 0.00 37.76 3.01
695 702 8.139350 CGGTTTTACTTGGGTTTTTCTCTTTAT 58.861 33.333 0.00 0.00 0.00 1.40
696 703 7.122501 ACGGTTTTACTTGGGTTTTTCTCTTTA 59.877 33.333 0.00 0.00 0.00 1.85
697 704 6.071221 ACGGTTTTACTTGGGTTTTTCTCTTT 60.071 34.615 0.00 0.00 0.00 2.52
698 705 5.419788 ACGGTTTTACTTGGGTTTTTCTCTT 59.580 36.000 0.00 0.00 0.00 2.85
699 706 4.951715 ACGGTTTTACTTGGGTTTTTCTCT 59.048 37.500 0.00 0.00 0.00 3.10
703 710 6.152492 TCAGTTACGGTTTTACTTGGGTTTTT 59.848 34.615 0.00 0.00 0.00 1.94
704 711 5.651576 TCAGTTACGGTTTTACTTGGGTTTT 59.348 36.000 0.00 0.00 0.00 2.43
708 715 4.023792 GGTTCAGTTACGGTTTTACTTGGG 60.024 45.833 0.00 0.00 0.00 4.12
713 720 5.482686 TTGTGGTTCAGTTACGGTTTTAC 57.517 39.130 0.00 0.00 0.00 2.01
738 745 2.224042 GCTTCCCAAACCAGTTTTCCTG 60.224 50.000 0.00 0.00 41.15 3.86
739 746 2.039418 GCTTCCCAAACCAGTTTTCCT 58.961 47.619 0.00 0.00 0.00 3.36
741 748 3.492656 GGAAGCTTCCCAAACCAGTTTTC 60.493 47.826 31.91 4.13 41.62 2.29
764 771 3.001939 ACGTTCGTGAAAGCCTAGTTTTG 59.998 43.478 0.00 0.00 0.00 2.44
765 772 3.001939 CACGTTCGTGAAAGCCTAGTTTT 59.998 43.478 18.64 0.00 38.30 2.43
766 773 2.542595 CACGTTCGTGAAAGCCTAGTTT 59.457 45.455 18.64 0.00 38.30 2.66
767 774 2.132762 CACGTTCGTGAAAGCCTAGTT 58.867 47.619 18.64 0.00 38.30 2.24
768 775 1.338973 TCACGTTCGTGAAAGCCTAGT 59.661 47.619 22.64 0.00 41.49 2.57
769 776 1.986378 CTCACGTTCGTGAAAGCCTAG 59.014 52.381 24.31 10.65 43.42 3.02
771 778 0.387929 TCTCACGTTCGTGAAAGCCT 59.612 50.000 24.31 0.00 43.42 4.58
772 779 1.214367 TTCTCACGTTCGTGAAAGCC 58.786 50.000 24.31 0.00 43.42 4.35
774 781 4.772046 TCTTTTCTCACGTTCGTGAAAG 57.228 40.909 24.31 22.85 43.42 2.62
775 782 5.533533 TTTCTTTTCTCACGTTCGTGAAA 57.466 34.783 24.31 18.47 43.42 2.69
777 784 6.831727 TTATTTCTTTTCTCACGTTCGTGA 57.168 33.333 23.17 23.17 42.09 4.35
778 785 7.111593 CCTTTTATTTCTTTTCTCACGTTCGTG 59.888 37.037 17.57 17.57 37.47 4.35
779 786 7.130269 CCTTTTATTTCTTTTCTCACGTTCGT 58.870 34.615 0.00 0.00 0.00 3.85
780 787 6.086371 GCCTTTTATTTCTTTTCTCACGTTCG 59.914 38.462 0.00 0.00 0.00 3.95
781 788 6.362551 GGCCTTTTATTTCTTTTCTCACGTTC 59.637 38.462 0.00 0.00 0.00 3.95
782 789 6.040504 AGGCCTTTTATTTCTTTTCTCACGTT 59.959 34.615 0.00 0.00 0.00 3.99
783 790 5.535030 AGGCCTTTTATTTCTTTTCTCACGT 59.465 36.000 0.00 0.00 0.00 4.49
784 791 5.858581 CAGGCCTTTTATTTCTTTTCTCACG 59.141 40.000 0.00 0.00 0.00 4.35
785 792 6.159293 CCAGGCCTTTTATTTCTTTTCTCAC 58.841 40.000 0.00 0.00 0.00 3.51
786 793 5.279456 GCCAGGCCTTTTATTTCTTTTCTCA 60.279 40.000 0.00 0.00 0.00 3.27
787 794 5.047021 AGCCAGGCCTTTTATTTCTTTTCTC 60.047 40.000 8.22 0.00 0.00 2.87
900 1892 0.528470 GAGTGACGAGAGGGTTCCTG 59.472 60.000 0.00 0.00 31.76 3.86
931 1923 1.338890 TTCGTTGGAGGGGTCACACA 61.339 55.000 0.00 0.00 0.00 3.72
932 1924 0.179040 TTTCGTTGGAGGGGTCACAC 60.179 55.000 0.00 0.00 0.00 3.82
933 1925 0.179040 GTTTCGTTGGAGGGGTCACA 60.179 55.000 0.00 0.00 0.00 3.58
940 5014 0.605589 GACAGGGGTTTCGTTGGAGG 60.606 60.000 0.00 0.00 0.00 4.30
1008 5082 3.547249 GACGAGGTGTGACGCCGAA 62.547 63.158 9.85 0.00 39.30 4.30
1009 5083 4.034258 GACGAGGTGTGACGCCGA 62.034 66.667 9.85 0.00 39.30 5.54
1425 5530 2.046892 ACTGACATGTGCTCGGGC 60.047 61.111 1.15 0.00 39.26 6.13
1575 5690 2.108976 CACCACTGGCGTGTGACT 59.891 61.111 11.24 0.00 40.12 3.41
1616 5749 2.981350 GGTCCGCGCCCAAAGAAA 60.981 61.111 0.00 0.00 0.00 2.52
1733 5872 2.280797 TGTCCAGCACGAGCAACC 60.281 61.111 7.77 0.00 45.49 3.77
1832 5971 2.746362 CCATTGTCTCTGGCAGAAACTC 59.254 50.000 20.76 10.73 30.72 3.01
1962 6101 5.046529 GCTGTGTGATAGAGATGAAACGAT 58.953 41.667 0.00 0.00 0.00 3.73
2244 6383 8.883731 CCAAAGTACCAGTAAACATCTTCATAG 58.116 37.037 0.00 0.00 0.00 2.23
2404 6552 0.032813 AATCATGGCCACCTTCCCTG 60.033 55.000 8.16 0.00 0.00 4.45
2436 6584 1.985473 TGGCAGTTGCTGAACAAGAT 58.015 45.000 3.88 0.00 39.50 2.40
2488 6636 1.427368 TGTTCCCAAGGCCTACAATGT 59.573 47.619 5.16 0.00 0.00 2.71
2825 6973 8.625651 CGAGTACTATATCTAGCCAGCATATTT 58.374 37.037 0.00 0.00 0.00 1.40
2889 7037 5.068591 TGCACACGGACATATATAGTGAAGT 59.931 40.000 13.30 0.00 36.71 3.01
2907 7055 1.398041 TCGCTGAAATATGCTGCACAC 59.602 47.619 3.57 0.00 0.00 3.82
2926 7074 4.537135 TTCACCTCCTACAACATGTCTC 57.463 45.455 0.00 0.00 0.00 3.36
3009 7197 3.507162 TGTGTCATTCTCCCAACACAT 57.493 42.857 3.24 0.00 45.05 3.21
3111 7321 3.216800 GCATGGAAGCTGGATGAACATA 58.783 45.455 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.