Multiple sequence alignment - TraesCS1B01G112200

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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 TraesCS1B01G112200 chr1B 100.000 8319 0 0 1 8319 130357439 130349121 0.000000e+00 15363.0
1 TraesCS1B01G112200 chr1B 88.114 2280 247 16 1538 3805 130024222 130021955 0.000000e+00 2687.0
2 TraesCS1B01G112200 chr1B 86.624 2168 221 34 3798 5940 130021454 130019331 0.000000e+00 2333.0
3 TraesCS1B01G112200 chr1B 75.694 757 113 48 6018 6735 130019294 130018570 6.270000e-81 313.0
4 TraesCS1B01G112200 chr1B 75.957 470 75 21 5788 6249 130350050 130349611 3.040000e-49 207.0
5 TraesCS1B01G112200 chr1B 75.957 470 75 21 7390 7829 130351652 130351191 3.040000e-49 207.0
6 TraesCS1B01G112200 chr1D 93.504 8359 372 74 1 8286 79143487 79135227 0.000000e+00 12270.0
7 TraesCS1B01G112200 chr1D 78.082 292 47 9 5480 5769 79136395 79136119 1.440000e-37 169.0
8 TraesCS1B01G112200 chr1D 100.000 33 0 0 8287 8319 79135238 79135206 2.510000e-05 62.1
9 TraesCS1B01G112200 chr1A 90.787 5004 329 56 3067 8002 97954911 97949972 0.000000e+00 6565.0
10 TraesCS1B01G112200 chr1A 91.792 2461 152 28 634 3074 97957527 97955097 0.000000e+00 3380.0
11 TraesCS1B01G112200 chr1A 87.238 1669 203 9 2970 4631 97807002 97805337 0.000000e+00 1893.0
12 TraesCS1B01G112200 chr1A 87.769 1349 125 20 4625 5964 97803711 97802394 0.000000e+00 1541.0
13 TraesCS1B01G112200 chr1A 86.596 1231 160 3 1729 2955 97809180 97807951 0.000000e+00 1354.0
14 TraesCS1B01G112200 chr1A 89.841 502 31 5 4 504 97963865 97963383 1.970000e-175 627.0
15 TraesCS1B01G112200 chr1A 89.796 294 18 2 7993 8286 97942940 97942659 4.740000e-97 366.0
16 TraesCS1B01G112200 chr1A 92.982 114 8 0 268 381 97812026 97811913 5.160000e-37 167.0
17 TraesCS1B01G112200 chr1A 96.552 87 3 0 515 601 97957615 97957529 2.420000e-30 145.0
18 TraesCS1B01G112200 chr1A 100.000 33 0 0 8287 8319 97942670 97942638 2.510000e-05 62.1
19 TraesCS1B01G112200 chr4D 74.892 2314 514 54 1737 4007 1708232 1705943 0.000000e+00 992.0
20 TraesCS1B01G112200 chr2B 74.503 1510 348 32 1856 3348 693838672 693840161 9.170000e-174 621.0
21 TraesCS1B01G112200 chr2B 73.385 1409 323 42 2918 4294 693336549 693337937 2.100000e-130 477.0
22 TraesCS1B01G112200 chr2B 79.715 281 51 6 1027 1304 693837949 693838226 1.830000e-46 198.0
23 TraesCS1B01G112200 chr2B 82.938 211 33 3 2516 2724 667788588 667788797 3.960000e-43 187.0
24 TraesCS1B01G112200 chr2B 78.629 248 53 0 1028 1275 693321662 693321909 1.860000e-36 165.0
25 TraesCS1B01G112200 chr2B 75.660 341 75 6 1027 1365 693334159 693334493 6.680000e-36 163.0
26 TraesCS1B01G112200 chr2B 74.854 342 79 6 1028 1367 693448016 693448352 1.870000e-31 148.0
27 TraesCS1B01G112200 chrUn 82.335 334 51 3 1039 1365 316685535 316685867 4.920000e-72 283.0
28 TraesCS1B01G112200 chr6B 83.929 280 45 0 1028 1307 52180037 52179758 1.380000e-67 268.0
29 TraesCS1B01G112200 chr6B 78.571 210 42 3 5466 5673 51760179 51760387 1.460000e-27 135.0
30 TraesCS1B01G112200 chr6B 90.164 61 6 0 5603 5663 51950635 51950695 6.920000e-11 80.5
31 TraesCS1B01G112200 chr7D 80.687 233 44 1 2493 2724 633149148 633149380 6.630000e-41 180.0
32 TraesCS1B01G112200 chr2D 79.389 262 48 5 2509 2767 2094161 2094419 6.630000e-41 180.0
33 TraesCS1B01G112200 chr6A 81.383 188 34 1 5475 5661 100299799 100299986 1.450000e-32 152.0
34 TraesCS1B01G112200 chr6D 79.904 209 36 6 5456 5661 83171857 83172062 1.870000e-31 148.0
35 TraesCS1B01G112200 chr3D 76.000 275 58 8 1022 1292 613839628 613839898 1.460000e-27 135.0


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 TraesCS1B01G112200 chr1B 130349121 130357439 8318 True 15363.000000 15363 100.000000 1 8319 1 chr1B.!!$R1 8318
1 TraesCS1B01G112200 chr1B 130018570 130024222 5652 True 1777.666667 2687 83.477333 1538 6735 3 chr1B.!!$R2 5197
2 TraesCS1B01G112200 chr1B 130349611 130351652 2041 True 207.000000 207 75.957000 5788 7829 2 chr1B.!!$R3 2041
3 TraesCS1B01G112200 chr1D 79135206 79143487 8281 True 6166.050000 12270 96.752000 1 8319 2 chr1D.!!$R2 8318
4 TraesCS1B01G112200 chr1A 97949972 97957615 7643 True 3363.333333 6565 93.043667 515 8002 3 chr1A.!!$R4 7487
5 TraesCS1B01G112200 chr1A 97802394 97812026 9632 True 1238.750000 1893 88.646250 268 5964 4 chr1A.!!$R2 5696
6 TraesCS1B01G112200 chr4D 1705943 1708232 2289 True 992.000000 992 74.892000 1737 4007 1 chr4D.!!$R1 2270
7 TraesCS1B01G112200 chr2B 693837949 693840161 2212 False 409.500000 621 77.109000 1027 3348 2 chr2B.!!$F5 2321
8 TraesCS1B01G112200 chr2B 693334159 693337937 3778 False 320.000000 477 74.522500 1027 4294 2 chr2B.!!$F4 3267

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
534 1004 0.030773 GAGTAGACGATGCGATGCCA 59.969 55.000 0.00 0.0 0.00 4.92 F
790 2155 0.315886 CACGCGCCTACATATACCCA 59.684 55.000 5.73 0.0 0.00 4.51 F
877 2289 0.588980 CGATCATCGTCGTCTTCGCA 60.589 55.000 0.00 0.0 36.88 5.10 F
1488 2921 1.453524 CTATGTAGCATTCGCACTCGC 59.546 52.381 0.00 0.0 42.27 5.03 F
1588 3042 1.753930 CAGCACTGCCCACATTATCA 58.246 50.000 0.00 0.0 0.00 2.15 F
1878 3353 2.263545 ACCCCTAACCAAGACACTACC 58.736 52.381 0.00 0.0 0.00 3.18 F
1932 3407 3.454858 AGAGCCTGAGTTATTTGGGAGA 58.545 45.455 0.00 0.0 0.00 3.71 F
3466 6593 3.749981 GCATATGCGAGGTTGGGG 58.250 61.111 12.82 0.0 0.00 4.96 F
4092 7739 1.134280 ACTAGCCATCGAGCAAAGCAT 60.134 47.619 0.00 0.0 34.23 3.79 F
4866 10157 0.980423 GGCTCCAGAGTCTTTGTCCT 59.020 55.000 0.00 0.0 0.00 3.85 F
5741 11041 0.773644 ACACACTTTCCCAGCCTCAT 59.226 50.000 0.00 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1419 2849 0.107508 CGTCAGGATCACCATGGCTT 60.108 55.000 13.04 0.0 38.94 4.35 R
1611 3068 1.076533 CATCGTGAACGGACGGGAAG 61.077 60.000 2.59 0.0 39.88 3.46 R
1878 3353 2.035832 GGTGGTTTTGGGTCTGTTCATG 59.964 50.000 0.00 0.0 0.00 3.07 R
2904 4406 1.143684 ACCTTCACAGCCAAGTCATGT 59.856 47.619 0.00 0.0 0.00 3.21 R
3348 6475 1.742308 AGCTACCTCCCCAACTTTCA 58.258 50.000 0.00 0.0 0.00 2.69 R
3874 7509 2.113139 ACCAGCAACGAACCCCAG 59.887 61.111 0.00 0.0 0.00 4.45 R
4008 7655 4.457834 AAAGATGACCACCTCTAGAACG 57.542 45.455 0.00 0.0 0.00 3.95 R
4827 10118 0.249868 CTCCTCCGTGTTTGCTGTCA 60.250 55.000 0.00 0.0 0.00 3.58 R
5722 11022 0.773644 ATGAGGCTGGGAAAGTGTGT 59.226 50.000 0.00 0.0 0.00 3.72 R
5786 11086 6.253512 GGTGAAGCAAACAAAAAGACAACTAG 59.746 38.462 0.00 0.0 0.00 2.57 R
7860 13268 5.072329 ACAGTAGGAGATCCCATATTGTTGG 59.928 44.000 0.00 0.0 37.41 3.77 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
45 52 1.038681 TTCCCAGCCTCGCGTGTATA 61.039 55.000 5.77 0.00 0.00 1.47
60 67 2.351726 GTGTATAGCCTTTTCACGCTGG 59.648 50.000 0.00 0.00 36.53 4.85
61 68 2.027561 TGTATAGCCTTTTCACGCTGGT 60.028 45.455 0.00 0.00 36.53 4.00
64 71 1.166531 AGCCTTTTCACGCTGGTGTC 61.167 55.000 0.00 0.00 44.68 3.67
69 76 3.858868 TTCACGCTGGTGTCTCGGC 62.859 63.158 0.00 0.00 44.68 5.54
135 142 4.715130 CTCTCCCCCACCCACCGA 62.715 72.222 0.00 0.00 0.00 4.69
194 201 4.394712 CCCGCCTCGCTTTCCAGT 62.395 66.667 0.00 0.00 0.00 4.00
229 236 2.043248 TACCAGTCCTCCGCCTCC 60.043 66.667 0.00 0.00 0.00 4.30
248 255 2.280524 TTTCCAGTGCGTCGGTGG 60.281 61.111 0.00 0.00 0.00 4.61
259 266 3.691342 TCGGTGGCCTCGAAGTGG 61.691 66.667 17.03 0.00 45.21 4.00
315 322 4.792804 GGAGCACAGCTGGCCTCC 62.793 72.222 28.21 28.21 39.88 4.30
316 323 4.792804 GAGCACAGCTGGCCTCCC 62.793 72.222 19.93 5.00 39.88 4.30
351 358 2.304180 AGGATTGGTCTGTTCCTCTGTG 59.696 50.000 0.00 0.00 34.80 3.66
381 388 3.119849 GCAAATTACAATGGCGTCTGAGT 60.120 43.478 0.00 0.00 0.00 3.41
382 389 4.651994 CAAATTACAATGGCGTCTGAGTC 58.348 43.478 0.00 0.00 0.00 3.36
383 390 3.610040 ATTACAATGGCGTCTGAGTCA 57.390 42.857 0.00 0.00 0.00 3.41
384 391 2.654749 TACAATGGCGTCTGAGTCAG 57.345 50.000 14.36 14.36 0.00 3.51
385 392 0.969149 ACAATGGCGTCTGAGTCAGA 59.031 50.000 19.10 19.10 38.25 3.27
386 393 1.067283 ACAATGGCGTCTGAGTCAGAG 60.067 52.381 23.27 16.94 41.46 3.35
387 394 1.067283 CAATGGCGTCTGAGTCAGAGT 60.067 52.381 23.27 4.79 41.46 3.24
388 395 0.814457 ATGGCGTCTGAGTCAGAGTC 59.186 55.000 23.27 17.68 41.46 3.36
389 396 0.250945 TGGCGTCTGAGTCAGAGTCT 60.251 55.000 23.27 0.00 41.46 3.24
390 397 0.170116 GGCGTCTGAGTCAGAGTCTG 59.830 60.000 23.27 14.36 41.46 3.51
391 398 1.160989 GCGTCTGAGTCAGAGTCTGA 58.839 55.000 23.27 19.10 41.46 3.27
392 399 1.130373 GCGTCTGAGTCAGAGTCTGAG 59.870 57.143 23.27 11.57 41.46 3.35
448 903 1.021968 GACGTTGCCCAACTTCACTT 58.978 50.000 11.36 0.00 38.82 3.16
449 904 2.215196 GACGTTGCCCAACTTCACTTA 58.785 47.619 11.36 0.00 38.82 2.24
450 905 1.944709 ACGTTGCCCAACTTCACTTAC 59.055 47.619 9.23 0.00 39.08 2.34
451 906 1.944024 CGTTGCCCAACTTCACTTACA 59.056 47.619 9.23 0.00 39.08 2.41
452 907 2.032030 CGTTGCCCAACTTCACTTACAG 60.032 50.000 9.23 0.00 39.08 2.74
453 908 2.949644 GTTGCCCAACTTCACTTACAGT 59.050 45.455 3.99 0.00 38.25 3.55
454 909 3.290948 TGCCCAACTTCACTTACAGTT 57.709 42.857 0.00 0.00 33.29 3.16
455 910 4.425180 TGCCCAACTTCACTTACAGTTA 57.575 40.909 0.00 0.00 31.78 2.24
467 922 9.793245 CTTCACTTACAGTTACAGAATTAAACG 57.207 33.333 0.00 0.00 0.00 3.60
468 923 7.790000 TCACTTACAGTTACAGAATTAAACGC 58.210 34.615 0.00 0.00 0.00 4.84
498 954 4.445385 TCGTTAAAACAGCGAGGAGTTAAC 59.555 41.667 0.00 0.00 34.70 2.01
501 957 6.488817 GTTAAAACAGCGAGGAGTTAACAAA 58.511 36.000 8.61 0.00 33.62 2.83
503 959 2.767505 ACAGCGAGGAGTTAACAAAGG 58.232 47.619 8.61 0.00 0.00 3.11
504 960 1.464997 CAGCGAGGAGTTAACAAAGGC 59.535 52.381 8.61 4.63 0.00 4.35
506 962 2.084546 GCGAGGAGTTAACAAAGGCAT 58.915 47.619 8.61 0.00 0.00 4.40
534 1004 0.030773 GAGTAGACGATGCGATGCCA 59.969 55.000 0.00 0.00 0.00 4.92
715 1902 6.259550 AGAATCAAACGAAGGAAAGGAATG 57.740 37.500 0.00 0.00 0.00 2.67
761 1948 2.680352 GCCTCTCCTCCCACGACA 60.680 66.667 0.00 0.00 0.00 4.35
790 2155 0.315886 CACGCGCCTACATATACCCA 59.684 55.000 5.73 0.00 0.00 4.51
820 2185 1.173043 CCAGCTCCGGCAAAACAATA 58.827 50.000 0.00 0.00 41.70 1.90
877 2289 0.588980 CGATCATCGTCGTCTTCGCA 60.589 55.000 0.00 0.00 36.88 5.10
916 2330 6.260377 CGGATTCACATTCGTAAGTAGTACA 58.740 40.000 2.52 0.00 39.48 2.90
949 2368 4.112634 TCATGCTAGTCCCCAAACTTTT 57.887 40.909 0.00 0.00 0.00 2.27
957 2376 2.935849 GTCCCCAAACTTTTGCAACAAG 59.064 45.455 15.42 15.42 36.86 3.16
985 2404 4.012374 ACATCTGCATCTCGAAATGGTTT 58.988 39.130 0.04 0.00 0.00 3.27
1413 2843 2.280457 TCATGTTCGCGTGGTGCA 60.280 55.556 5.77 0.00 46.97 4.57
1488 2921 1.453524 CTATGTAGCATTCGCACTCGC 59.546 52.381 0.00 0.00 42.27 5.03
1588 3042 1.753930 CAGCACTGCCCACATTATCA 58.246 50.000 0.00 0.00 0.00 2.15
1611 3068 5.578727 CAGTAAGAACTTGACATGCTACTCC 59.421 44.000 0.00 0.00 31.97 3.85
1715 3184 2.613223 GGAAGTCCAAGGCAGTACAGAC 60.613 54.545 0.00 0.00 35.64 3.51
1737 3206 2.736670 ATCATGTAGGGCAAACTCCC 57.263 50.000 0.00 0.00 46.93 4.30
1878 3353 2.263545 ACCCCTAACCAAGACACTACC 58.736 52.381 0.00 0.00 0.00 3.18
1932 3407 3.454858 AGAGCCTGAGTTATTTGGGAGA 58.545 45.455 0.00 0.00 0.00 3.71
1938 3413 5.071115 GCCTGAGTTATTTGGGAGAGATAGT 59.929 44.000 0.00 0.00 0.00 2.12
2067 3542 9.639601 CTCACACAACACATATTTAGAGAACTA 57.360 33.333 0.00 0.00 0.00 2.24
2088 3563 6.217294 ACTAGAGAGTTCTTTCCAAGTTTCG 58.783 40.000 0.00 0.00 34.79 3.46
2131 3606 6.017934 TCTCGATTTTAATGCAGATAGGTTGC 60.018 38.462 0.00 0.00 41.86 4.17
2163 3638 7.918076 AGATTGTGAACAAGATCCCTAAAGTA 58.082 34.615 1.94 0.00 39.47 2.24
2177 3658 6.616577 TCCCTAAAGTAAATGGTGAAAAGGT 58.383 36.000 0.00 0.00 0.00 3.50
2214 3695 7.264947 ACCAAGAGTTAATTGAACAAAGGTTG 58.735 34.615 0.00 0.00 40.86 3.77
2498 3985 6.238374 CCTGAATTACGTGATGTTGGGAATAC 60.238 42.308 0.00 0.00 0.00 1.89
2666 4153 5.694995 TGCCCTAAAGCTTAGCTATGATTT 58.305 37.500 21.78 21.78 38.25 2.17
3209 6333 5.565439 GCACTATTTTTCTGTCTGGTGCATT 60.565 40.000 0.00 0.00 45.19 3.56
3210 6334 5.860182 CACTATTTTTCTGTCTGGTGCATTG 59.140 40.000 0.00 0.00 0.00 2.82
3324 6451 6.763610 GCTTACCTAGTGCATTGTTTAGATCT 59.236 38.462 0.00 0.00 0.00 2.75
3466 6593 3.749981 GCATATGCGAGGTTGGGG 58.250 61.111 12.82 0.00 0.00 4.96
3631 6758 7.148407 ACGAGGCAAATGAACTAAAACTGATAG 60.148 37.037 0.00 0.00 0.00 2.08
4008 7655 3.564225 ACGAACCTTGTCATTTGTTCTCC 59.436 43.478 0.00 0.00 35.97 3.71
4050 7697 7.481642 TCTTTATAGATTGTCCTGAACTCGTC 58.518 38.462 0.00 0.00 0.00 4.20
4092 7739 1.134280 ACTAGCCATCGAGCAAAGCAT 60.134 47.619 0.00 0.00 34.23 3.79
4248 7898 4.301072 TGAGCAGCTAGTTTACCCAAAT 57.699 40.909 0.00 0.00 0.00 2.32
4258 7908 6.478016 GCTAGTTTACCCAAATAACTACGGAG 59.522 42.308 0.00 0.00 34.26 4.63
4433 8083 2.424956 AGTTCCTCGTGATAACCGGTAC 59.575 50.000 8.00 0.01 0.00 3.34
4752 10043 1.988956 AGGAGGAGGTCTGCTGCTG 60.989 63.158 12.14 0.00 46.79 4.41
4814 10105 2.202756 GCTGCGGTTACTCTCCGG 60.203 66.667 0.00 0.00 46.90 5.14
4824 10115 1.263356 TACTCTCCGGTTCACTTGGG 58.737 55.000 0.00 0.00 0.00 4.12
4827 10118 1.279271 CTCTCCGGTTCACTTGGGAAT 59.721 52.381 0.00 0.00 0.00 3.01
4866 10157 0.980423 GGCTCCAGAGTCTTTGTCCT 59.020 55.000 0.00 0.00 0.00 3.85
5265 10556 2.588877 CTTACCGCGCCCATCTGG 60.589 66.667 0.00 0.00 37.09 3.86
5354 10645 2.124942 GCAAGAGGAGGCCCTTCG 60.125 66.667 0.00 0.00 44.53 3.79
5424 10715 4.834453 CGCCTCTCTGCAGGGCTG 62.834 72.222 24.35 16.28 43.29 4.85
5464 10755 3.045601 AGATATTACGCATCTGGTGGC 57.954 47.619 0.00 0.00 31.49 5.01
5523 10814 5.703130 ACCAAGTTCTCTGCAAGAATTAGAC 59.297 40.000 12.42 3.37 46.34 2.59
5722 11022 7.320443 GACATTTGATGGCTTGTACTCATTA 57.680 36.000 0.00 0.00 34.69 1.90
5735 11035 5.547465 TGTACTCATTACACACTTTCCCAG 58.453 41.667 0.00 0.00 35.64 4.45
5741 11041 0.773644 ACACACTTTCCCAGCCTCAT 59.226 50.000 0.00 0.00 0.00 2.90
7850 13258 0.692419 TCTCTCAAGGATGGCCTCCC 60.692 60.000 15.31 10.99 46.28 4.30
7860 13268 1.617947 ATGGCCTCCCGAGTTGTCTC 61.618 60.000 3.32 0.00 37.35 3.36
7907 13323 1.204231 GACGACCTCCTAAGTTCACCC 59.796 57.143 0.00 0.00 0.00 4.61
7964 13383 0.771127 AAAAGGCAGTCCAGCAGGTA 59.229 50.000 0.00 0.00 35.83 3.08
7965 13384 0.326264 AAAGGCAGTCCAGCAGGTAG 59.674 55.000 0.00 0.00 35.83 3.18
7968 13387 0.107945 GGCAGTCCAGCAGGTAGAAG 60.108 60.000 0.00 0.00 35.83 2.85
8133 13552 5.711506 TCTCTTTATGTTTGCATCACCACAT 59.288 36.000 0.00 0.00 36.58 3.21
8138 13557 9.800433 CTTTATGTTTGCATCACCACATTATTA 57.200 29.630 0.00 0.00 36.58 0.98
8139 13558 9.579768 TTTATGTTTGCATCACCACATTATTAC 57.420 29.630 0.00 0.00 36.58 1.89
8140 13559 6.581171 TGTTTGCATCACCACATTATTACA 57.419 33.333 0.00 0.00 0.00 2.41
8165 13584 4.908601 TTCATCTGACTAACCCACACAT 57.091 40.909 0.00 0.00 0.00 3.21
8177 13596 8.506168 ACTAACCCACACATGTTAATATTCTG 57.494 34.615 0.00 0.00 0.00 3.02
8227 13646 3.245052 ACATTCTTCTAGCCTTGCCTTGT 60.245 43.478 0.00 0.00 0.00 3.16
8228 13647 4.019321 ACATTCTTCTAGCCTTGCCTTGTA 60.019 41.667 0.00 0.00 0.00 2.41
8229 13648 3.895232 TCTTCTAGCCTTGCCTTGTAG 57.105 47.619 0.00 0.00 0.00 2.74
8230 13649 3.441101 TCTTCTAGCCTTGCCTTGTAGA 58.559 45.455 0.00 0.00 0.00 2.59
8231 13650 3.195825 TCTTCTAGCCTTGCCTTGTAGAC 59.804 47.826 0.00 0.00 0.00 2.59
8232 13651 1.831736 TCTAGCCTTGCCTTGTAGACC 59.168 52.381 0.00 0.00 0.00 3.85
8233 13652 0.909623 TAGCCTTGCCTTGTAGACCC 59.090 55.000 0.00 0.00 0.00 4.46
8234 13653 1.133809 AGCCTTGCCTTGTAGACCCA 61.134 55.000 0.00 0.00 0.00 4.51
8235 13654 0.251165 GCCTTGCCTTGTAGACCCAA 60.251 55.000 0.00 0.00 0.00 4.12
8248 13667 7.557719 CCTTGTAGACCCAATTATGTCTTTCAT 59.442 37.037 12.67 0.00 41.80 2.57
8265 13684 4.459390 TTCATGAAGTTGGCAATCCATG 57.541 40.909 22.27 22.27 43.05 3.66
8268 13687 1.273048 TGAAGTTGGCAATCCATGTGC 59.727 47.619 1.92 0.00 43.05 4.57
8274 13693 1.011333 GGCAATCCATGTGCAAATGC 58.989 50.000 11.71 0.67 44.07 3.56
8275 13694 1.011333 GCAATCCATGTGCAAATGCC 58.989 50.000 11.71 0.00 41.80 4.40
8276 13695 1.406341 GCAATCCATGTGCAAATGCCT 60.406 47.619 11.71 0.00 41.80 4.75
8277 13696 2.546778 CAATCCATGTGCAAATGCCTC 58.453 47.619 11.71 0.00 41.18 4.70
8278 13697 1.117150 ATCCATGTGCAAATGCCTCC 58.883 50.000 11.71 0.00 41.18 4.30
8279 13698 0.251698 TCCATGTGCAAATGCCTCCA 60.252 50.000 11.71 0.00 41.18 3.86
8280 13699 0.828022 CCATGTGCAAATGCCTCCAT 59.172 50.000 11.71 0.00 41.18 3.41
8281 13700 1.472552 CCATGTGCAAATGCCTCCATG 60.473 52.381 11.71 16.48 41.18 3.66
8282 13701 1.206132 CATGTGCAAATGCCTCCATGT 59.794 47.619 3.35 0.00 41.18 3.21
8283 13702 0.604073 TGTGCAAATGCCTCCATGTG 59.396 50.000 2.46 0.00 39.30 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.119137 GCGAGGCTGGGAAAAATGTATTT 60.119 43.478 0.00 0.00 0.00 1.40
21 22 1.137404 CGCGAGGCTGGGAAAAATG 59.863 57.895 0.00 0.00 0.00 2.32
24 25 2.102109 TACACGCGAGGCTGGGAAAA 62.102 55.000 15.93 0.00 0.00 2.29
45 52 1.152963 ACACCAGCGTGAAAAGGCT 60.153 52.632 0.00 0.00 43.14 4.58
114 121 1.616628 GTGGGTGGGGGAGAGTGAT 60.617 63.158 0.00 0.00 0.00 3.06
154 161 2.035442 GTGGCGAGCAGGGAAGTTC 61.035 63.158 0.00 0.00 0.00 3.01
177 184 4.394712 ACTGGAAAGCGAGGCGGG 62.395 66.667 0.00 0.00 0.00 6.13
229 236 2.030562 ACCGACGCACTGGAAAGG 59.969 61.111 0.00 0.00 0.00 3.11
248 255 1.374758 CCAGACACCACTTCGAGGC 60.375 63.158 0.00 0.00 0.00 4.70
256 263 0.250338 GAACACCTCCCAGACACCAC 60.250 60.000 0.00 0.00 0.00 4.16
259 266 0.319641 GTCGAACACCTCCCAGACAC 60.320 60.000 0.00 0.00 0.00 3.67
316 323 0.179000 AATCCTTACCTGCGAGGCTG 59.821 55.000 0.00 0.00 39.63 4.85
322 329 1.066143 ACAGACCAATCCTTACCTGCG 60.066 52.381 0.00 0.00 0.00 5.18
381 388 4.707448 GGATTACTCAACCTCAGACTCTGA 59.293 45.833 8.50 8.50 38.25 3.27
382 389 4.464244 TGGATTACTCAACCTCAGACTCTG 59.536 45.833 0.00 0.00 0.00 3.35
383 390 4.678256 TGGATTACTCAACCTCAGACTCT 58.322 43.478 0.00 0.00 0.00 3.24
384 391 5.407407 TTGGATTACTCAACCTCAGACTC 57.593 43.478 0.00 0.00 0.00 3.36
385 392 4.223923 CCTTGGATTACTCAACCTCAGACT 59.776 45.833 0.00 0.00 0.00 3.24
386 393 4.223032 TCCTTGGATTACTCAACCTCAGAC 59.777 45.833 0.00 0.00 0.00 3.51
387 394 4.223032 GTCCTTGGATTACTCAACCTCAGA 59.777 45.833 0.00 0.00 0.00 3.27
388 395 4.223923 AGTCCTTGGATTACTCAACCTCAG 59.776 45.833 0.00 0.00 0.00 3.35
389 396 4.020218 CAGTCCTTGGATTACTCAACCTCA 60.020 45.833 0.00 0.00 0.00 3.86
390 397 4.508662 CAGTCCTTGGATTACTCAACCTC 58.491 47.826 0.00 0.00 0.00 3.85
391 398 4.559862 CAGTCCTTGGATTACTCAACCT 57.440 45.455 0.00 0.00 0.00 3.50
392 399 6.390707 AGCCAGTCCTTGGATTACTCAACC 62.391 50.000 0.00 0.00 45.25 3.77
426 867 1.595929 GAAGTTGGGCAACGTCCGA 60.596 57.895 0.00 0.00 45.50 4.55
430 871 1.944709 GTAAGTGAAGTTGGGCAACGT 59.055 47.619 0.00 0.00 45.50 3.99
448 903 6.146510 CACCAGCGTTTAATTCTGTAACTGTA 59.853 38.462 0.00 0.00 0.00 2.74
449 904 5.049680 CACCAGCGTTTAATTCTGTAACTGT 60.050 40.000 0.00 0.00 0.00 3.55
450 905 5.382303 CACCAGCGTTTAATTCTGTAACTG 58.618 41.667 0.00 0.00 0.00 3.16
451 906 4.454504 CCACCAGCGTTTAATTCTGTAACT 59.545 41.667 0.00 0.00 0.00 2.24
452 907 4.214758 ACCACCAGCGTTTAATTCTGTAAC 59.785 41.667 0.00 0.00 0.00 2.50
453 908 4.391155 ACCACCAGCGTTTAATTCTGTAA 58.609 39.130 0.00 0.00 0.00 2.41
454 909 3.998341 GACCACCAGCGTTTAATTCTGTA 59.002 43.478 0.00 0.00 0.00 2.74
455 910 2.812011 GACCACCAGCGTTTAATTCTGT 59.188 45.455 0.00 0.00 0.00 3.41
467 922 1.334689 GCTGTTTTAACGACCACCAGC 60.335 52.381 0.00 0.00 37.31 4.85
468 923 1.070175 CGCTGTTTTAACGACCACCAG 60.070 52.381 0.00 0.00 0.00 4.00
498 954 6.199908 CGTCTACTCTCTTTCATATGCCTTTG 59.800 42.308 0.00 0.00 0.00 2.77
501 957 5.133941 TCGTCTACTCTCTTTCATATGCCT 58.866 41.667 0.00 0.00 0.00 4.75
503 959 5.344665 GCATCGTCTACTCTCTTTCATATGC 59.655 44.000 0.00 0.00 0.00 3.14
504 960 5.567154 CGCATCGTCTACTCTCTTTCATATG 59.433 44.000 0.00 0.00 0.00 1.78
506 962 4.814771 TCGCATCGTCTACTCTCTTTCATA 59.185 41.667 0.00 0.00 0.00 2.15
534 1004 3.517500 ACCAAACCCACACTTGTTTCATT 59.482 39.130 0.00 0.00 32.60 2.57
686 1873 6.036191 CCTTTCCTTCGTTTGATTCTACTAGC 59.964 42.308 0.00 0.00 0.00 3.42
687 1874 7.321153 TCCTTTCCTTCGTTTGATTCTACTAG 58.679 38.462 0.00 0.00 0.00 2.57
688 1875 7.235935 TCCTTTCCTTCGTTTGATTCTACTA 57.764 36.000 0.00 0.00 0.00 1.82
689 1876 6.110411 TCCTTTCCTTCGTTTGATTCTACT 57.890 37.500 0.00 0.00 0.00 2.57
715 1902 1.098050 CCATTAGCTGTTGGTGGAGC 58.902 55.000 0.00 0.00 35.28 4.70
820 2185 3.130693 CGACCGGAGTTCCTTTTCTCTAT 59.869 47.826 9.46 0.00 0.00 1.98
916 2330 6.998673 GGGGACTAGCATGAAAAAGTATGTAT 59.001 38.462 0.00 0.00 0.00 2.29
931 2350 1.960689 GCAAAAGTTTGGGGACTAGCA 59.039 47.619 5.95 0.00 38.57 3.49
949 2368 3.882288 TGCAGATGTTAGTTCTTGTTGCA 59.118 39.130 0.00 0.00 0.00 4.08
957 2376 6.417327 CATTTCGAGATGCAGATGTTAGTTC 58.583 40.000 2.64 0.00 0.00 3.01
985 2404 3.120385 CATCGCAACGCCAGCTGA 61.120 61.111 17.39 0.00 0.00 4.26
1413 2843 1.660560 GATCACCATGGCTTGCGCTT 61.661 55.000 13.04 0.00 36.09 4.68
1419 2849 0.107508 CGTCAGGATCACCATGGCTT 60.108 55.000 13.04 0.00 38.94 4.35
1488 2921 1.065273 GCTGATTTGATGCCTGCCG 59.935 57.895 0.00 0.00 0.00 5.69
1573 3027 5.045578 AGTTCTTACTGATAATGTGGGCAGT 60.046 40.000 0.00 0.00 43.40 4.40
1588 3042 5.482175 AGGAGTAGCATGTCAAGTTCTTACT 59.518 40.000 0.00 0.00 35.68 2.24
1611 3068 1.076533 CATCGTGAACGGACGGGAAG 61.077 60.000 2.59 0.00 39.88 3.46
1715 3184 3.131046 GGGAGTTTGCCCTACATGATTTG 59.869 47.826 0.00 0.00 45.12 2.32
1737 3206 5.396660 CCCCACCCTATCAAATTCCATTTTG 60.397 44.000 0.00 0.00 37.83 2.44
1878 3353 2.035832 GGTGGTTTTGGGTCTGTTCATG 59.964 50.000 0.00 0.00 0.00 3.07
1932 3407 6.591834 CCACGATGTTCTTTTTCAGACTATCT 59.408 38.462 0.00 0.00 0.00 1.98
1938 3413 5.304778 TCATCCACGATGTTCTTTTTCAGA 58.695 37.500 0.00 0.00 40.55 3.27
2088 3563 4.098044 TCGAGAGAGACACATATCCAAACC 59.902 45.833 0.00 0.00 34.84 3.27
2131 3606 6.314896 GGGATCTTGTTCACAATCTCTTGTAG 59.685 42.308 0.00 0.00 43.76 2.74
2163 3638 8.644374 TGCTAGTATTAACCTTTTCACCATTT 57.356 30.769 0.00 0.00 0.00 2.32
2214 3695 3.831715 AGCAACAACCGCTTAGATTTC 57.168 42.857 0.00 0.00 35.82 2.17
2305 3789 3.333680 ACCACATTACCCTTGTCTCCATT 59.666 43.478 0.00 0.00 0.00 3.16
2313 3797 6.650120 AGTGACTATAACCACATTACCCTTG 58.350 40.000 0.00 0.00 35.84 3.61
2411 3895 6.807789 ACTTCGAAGAAAGACATAGTATCCC 58.192 40.000 31.08 0.00 45.90 3.85
2666 4153 7.004086 ACATTGTTGTAGATGAAAAGGGAGAA 58.996 34.615 0.00 0.00 33.16 2.87
2869 4365 7.757526 TGAATAACATAACGAGGACCATTTTG 58.242 34.615 0.00 0.00 0.00 2.44
2904 4406 1.143684 ACCTTCACAGCCAAGTCATGT 59.856 47.619 0.00 0.00 0.00 3.21
2964 5895 4.046286 TGCAGGAATTTGTATGGACCTT 57.954 40.909 0.00 0.00 0.00 3.50
3209 6333 4.395854 GCAACACATCATCCACAGAATACA 59.604 41.667 0.00 0.00 0.00 2.29
3210 6334 4.637534 AGCAACACATCATCCACAGAATAC 59.362 41.667 0.00 0.00 0.00 1.89
3348 6475 1.742308 AGCTACCTCCCCAACTTTCA 58.258 50.000 0.00 0.00 0.00 2.69
3874 7509 2.113139 ACCAGCAACGAACCCCAG 59.887 61.111 0.00 0.00 0.00 4.45
4008 7655 4.457834 AAAGATGACCACCTCTAGAACG 57.542 45.455 0.00 0.00 0.00 3.95
4050 7697 2.029110 AGGGTGTGAAAATGGCAATTCG 60.029 45.455 10.57 0.00 0.00 3.34
4092 7739 6.962182 AGGAAACCAAGACATATTCTCATCA 58.038 36.000 0.00 0.00 31.02 3.07
4248 7898 2.756760 ACTCAATTCCGCTCCGTAGTTA 59.243 45.455 0.00 0.00 0.00 2.24
4258 7908 3.004315 TCAACTTCCAAACTCAATTCCGC 59.996 43.478 0.00 0.00 0.00 5.54
4667 9955 5.709631 TGCCTTTCTTGTGCATACTCAATTA 59.290 36.000 0.00 0.00 0.00 1.40
4814 10105 2.229792 TGCTGTCATTCCCAAGTGAAC 58.770 47.619 0.00 0.00 0.00 3.18
4824 10115 1.197721 CCTCCGTGTTTGCTGTCATTC 59.802 52.381 0.00 0.00 0.00 2.67
4827 10118 0.249868 CTCCTCCGTGTTTGCTGTCA 60.250 55.000 0.00 0.00 0.00 3.58
4866 10157 1.203237 AGGGAGCAGAGACTTTGGAGA 60.203 52.381 0.00 0.00 0.00 3.71
5265 10556 1.007842 AGGGAGGAAGAGAGGAGTTCC 59.992 57.143 0.00 0.00 42.38 3.62
5306 10597 1.578206 GCGCTCCACCTCTTTGTTCC 61.578 60.000 0.00 0.00 0.00 3.62
5354 10645 1.613630 TGGAGGGAACTGAGGAGGC 60.614 63.158 0.00 0.00 44.43 4.70
5413 10704 2.752358 CTTGGTCAGCCCTGCAGA 59.248 61.111 17.39 0.00 0.00 4.26
5464 10755 0.813184 AGCAATTGAATGGCTGGACG 59.187 50.000 6.20 0.00 36.34 4.79
5523 10814 0.900421 TGGCAGGACAGTCTCTGATG 59.100 55.000 18.30 5.10 35.18 3.07
5722 11022 0.773644 ATGAGGCTGGGAAAGTGTGT 59.226 50.000 0.00 0.00 0.00 3.72
5786 11086 6.253512 GGTGAAGCAAACAAAAAGACAACTAG 59.746 38.462 0.00 0.00 0.00 2.57
7860 13268 5.072329 ACAGTAGGAGATCCCATATTGTTGG 59.928 44.000 0.00 0.00 37.41 3.77
7864 13272 7.575909 CGTCTAACAGTAGGAGATCCCATATTG 60.576 44.444 0.00 0.00 37.41 1.90
7868 13276 4.141228 TCGTCTAACAGTAGGAGATCCCAT 60.141 45.833 0.00 0.00 37.41 4.00
7955 13374 0.984230 TGTTCCCTTCTACCTGCTGG 59.016 55.000 8.29 8.29 39.83 4.85
8025 13444 6.371825 GGAACCGATCAGAAGTTCTAACAAAT 59.628 38.462 4.74 0.00 39.82 2.32
8026 13445 5.699458 GGAACCGATCAGAAGTTCTAACAAA 59.301 40.000 4.74 0.00 39.82 2.83
8138 13557 6.016276 GTGTGGGTTAGTCAGATGAAAATTGT 60.016 38.462 0.00 0.00 0.00 2.71
8139 13558 6.016360 TGTGTGGGTTAGTCAGATGAAAATTG 60.016 38.462 0.00 0.00 0.00 2.32
8140 13559 6.068010 TGTGTGGGTTAGTCAGATGAAAATT 58.932 36.000 0.00 0.00 0.00 1.82
8165 13584 6.483307 GGCTCTGCACATACAGAATATTAACA 59.517 38.462 0.00 0.00 45.72 2.41
8177 13596 2.012673 CAAGAAGGGCTCTGCACATAC 58.987 52.381 0.00 0.00 32.33 2.39
8227 13646 8.328758 ACTTCATGAAAGACATAATTGGGTCTA 58.671 33.333 9.88 1.12 43.26 2.59
8228 13647 7.177878 ACTTCATGAAAGACATAATTGGGTCT 58.822 34.615 9.88 7.73 45.85 3.85
8229 13648 7.396540 ACTTCATGAAAGACATAATTGGGTC 57.603 36.000 9.88 3.80 38.44 4.46
8230 13649 7.309990 CCAACTTCATGAAAGACATAATTGGGT 60.310 37.037 9.88 0.00 38.44 4.51
8231 13650 7.037438 CCAACTTCATGAAAGACATAATTGGG 58.963 38.462 9.88 0.00 38.44 4.12
8232 13651 6.532657 GCCAACTTCATGAAAGACATAATTGG 59.467 38.462 9.88 12.66 38.44 3.16
8233 13652 7.092079 TGCCAACTTCATGAAAGACATAATTG 58.908 34.615 9.88 4.53 38.44 2.32
8234 13653 7.230849 TGCCAACTTCATGAAAGACATAATT 57.769 32.000 9.88 0.00 38.44 1.40
8235 13654 6.839124 TGCCAACTTCATGAAAGACATAAT 57.161 33.333 9.88 0.00 38.44 1.28
8265 13684 0.738412 GCACATGGAGGCATTTGCAC 60.738 55.000 4.74 0.00 44.36 4.57
8268 13687 0.108520 GGTGCACATGGAGGCATTTG 60.109 55.000 20.43 0.00 42.75 2.32
8274 13693 0.750546 CATGGAGGTGCACATGGAGG 60.751 60.000 20.43 0.00 40.50 4.30
8275 13694 0.034767 ACATGGAGGTGCACATGGAG 60.035 55.000 20.43 6.04 46.60 3.86
8276 13695 1.065491 GTACATGGAGGTGCACATGGA 60.065 52.381 20.43 7.55 46.60 3.41
8277 13696 1.339920 TGTACATGGAGGTGCACATGG 60.340 52.381 20.43 3.38 46.60 3.66
8279 13698 4.502105 TTATGTACATGGAGGTGCACAT 57.498 40.909 20.43 12.71 39.01 3.21
8280 13699 3.990959 TTATGTACATGGAGGTGCACA 57.009 42.857 20.43 0.00 36.22 4.57
8281 13700 4.094887 CAGTTTATGTACATGGAGGTGCAC 59.905 45.833 18.81 8.80 36.22 4.57
8282 13701 4.260985 CAGTTTATGTACATGGAGGTGCA 58.739 43.478 18.81 0.00 37.78 4.57
8283 13702 3.627577 CCAGTTTATGTACATGGAGGTGC 59.372 47.826 18.81 2.13 32.55 5.01
8284 13703 4.843728 ACCAGTTTATGTACATGGAGGTG 58.156 43.478 18.81 8.90 34.99 4.00
8285 13704 5.514500 AACCAGTTTATGTACATGGAGGT 57.486 39.130 18.81 14.65 34.99 3.85


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

AutoCloner maintained by Alex Coulton.