Multiple sequence alignment - TraesCS7D01G058500

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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 TraesCS7D01G058500 chr7D 100.000 5084 0 0 1 5084 31569522 31574605 0.000000e+00 9389.0
1 TraesCS7D01G058500 chr7D 82.440 3115 503 18 1975 5083 239683282 239680206 0.000000e+00 2682.0
2 TraesCS7D01G058500 chr7D 92.232 1017 37 12 365 1361 31473844 31474838 0.000000e+00 1402.0
3 TraesCS7D01G058500 chr7D 85.103 1121 94 32 365 1442 31458258 31459348 0.000000e+00 1077.0
4 TraesCS7D01G058500 chr7D 91.978 536 34 5 1345 1872 31474854 31475388 0.000000e+00 743.0
5 TraesCS7D01G058500 chr7D 77.863 1048 152 50 754 1753 31579536 31580551 1.230000e-160 577.0
6 TraesCS7D01G058500 chr7D 96.212 264 10 0 1 264 31473579 31473842 2.810000e-117 433.0
7 TraesCS7D01G058500 chr7D 93.357 286 18 1 1 285 31457977 31458262 6.090000e-114 422.0
8 TraesCS7D01G058500 chr7D 90.265 113 11 0 1 113 31489532 31489644 1.140000e-31 148.0
9 TraesCS7D01G058500 chr7D 90.909 110 9 1 9 117 31464112 31464221 4.100000e-31 147.0
10 TraesCS7D01G058500 chr7D 89.474 57 6 0 287 343 253157183 253157239 7.060000e-09 73.1
11 TraesCS7D01G058500 chr3D 90.549 3206 283 9 1882 5084 532163141 532166329 0.000000e+00 4224.0
12 TraesCS7D01G058500 chr2B 90.387 3204 290 8 1885 5084 137009865 137006676 0.000000e+00 4194.0
13 TraesCS7D01G058500 chr2B 80.499 3128 571 32 1970 5084 378052352 378055453 0.000000e+00 2361.0
14 TraesCS7D01G058500 chr2B 89.410 1643 170 3 1885 3525 137342331 137340691 0.000000e+00 2067.0
15 TraesCS7D01G058500 chr2B 86.885 61 7 1 281 341 748160296 748160355 3.290000e-07 67.6
16 TraesCS7D01G058500 chr2D 88.951 3204 340 11 1885 5084 154833191 154829998 0.000000e+00 3943.0
17 TraesCS7D01G058500 chr2D 84.567 2676 386 18 1885 4542 186666009 186663343 0.000000e+00 2628.0
18 TraesCS7D01G058500 chr4D 88.221 3209 361 13 1882 5084 394401981 394405178 0.000000e+00 3816.0
19 TraesCS7D01G058500 chr4D 93.393 2225 141 4 2862 5084 439885929 439883709 0.000000e+00 3290.0
20 TraesCS7D01G058500 chrUn 88.136 3203 365 11 1887 5084 70420600 70423792 0.000000e+00 3795.0
21 TraesCS7D01G058500 chrUn 88.060 268 14 6 793 1046 317737607 317737870 8.270000e-78 302.0
22 TraesCS7D01G058500 chr5D 88.120 3207 337 14 1885 5084 249905257 249902088 0.000000e+00 3771.0
23 TraesCS7D01G058500 chr1D 84.779 1787 258 11 1887 3666 233012941 233014720 0.000000e+00 1781.0
24 TraesCS7D01G058500 chr4A 84.605 760 57 27 653 1382 696118191 696117462 0.000000e+00 701.0
25 TraesCS7D01G058500 chr4A 91.365 498 28 3 844 1340 696082435 696081952 0.000000e+00 667.0
26 TraesCS7D01G058500 chr4A 91.304 483 33 5 368 848 696089648 696089173 0.000000e+00 651.0
27 TraesCS7D01G058500 chr4A 93.333 285 19 0 1 285 696089931 696089647 6.090000e-114 422.0
28 TraesCS7D01G058500 chr4A 88.328 317 17 11 1342 1651 696081785 696081482 3.740000e-96 363.0
29 TraesCS7D01G058500 chr4A 80.729 384 48 15 917 1284 696079313 696078940 5.010000e-70 276.0
30 TraesCS7D01G058500 chr4A 93.048 187 13 0 1686 1872 696081482 696081296 1.800000e-69 274.0
31 TraesCS7D01G058500 chr7A 88.497 539 34 11 531 1046 31921943 31922476 1.200000e-175 627.0
32 TraesCS7D01G058500 chr7A 88.312 539 35 11 531 1046 31950192 31950725 5.590000e-174 621.0
33 TraesCS7D01G058500 chr7A 85.106 423 26 18 1046 1442 31959859 31960270 1.030000e-106 398.0
34 TraesCS7D01G058500 chr7A 91.289 287 23 2 1 286 31949784 31950069 1.720000e-104 390.0
35 TraesCS7D01G058500 chr7A 90.941 287 24 2 1 286 31921535 31921820 7.980000e-103 385.0
36 TraesCS7D01G058500 chr7A 88.341 223 20 3 1653 1872 31997290 31997509 3.900000e-66 263.0
37 TraesCS7D01G058500 chr7A 90.526 190 15 3 1099 1286 32003520 32003332 1.090000e-61 248.0
38 TraesCS7D01G058500 chr7A 88.660 194 20 2 1391 1583 32003279 32003087 8.510000e-58 235.0
39 TraesCS7D01G058500 chr7A 84.892 139 16 3 365 502 31921816 31921950 8.880000e-28 135.0
40 TraesCS7D01G058500 chr7A 84.892 139 16 3 365 502 31950065 31950199 8.880000e-28 135.0
41 TraesCS7D01G058500 chr7A 86.667 120 16 0 1 120 31963277 31963396 3.190000e-27 134.0


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 TraesCS7D01G058500 chr7D 31569522 31574605 5083 False 9389.000000 9389 100.000000 1 5084 1 chr7D.!!$F3 5083
1 TraesCS7D01G058500 chr7D 239680206 239683282 3076 True 2682.000000 2682 82.440000 1975 5083 1 chr7D.!!$R1 3108
2 TraesCS7D01G058500 chr7D 31473579 31475388 1809 False 859.333333 1402 93.474000 1 1872 3 chr7D.!!$F7 1871
3 TraesCS7D01G058500 chr7D 31457977 31459348 1371 False 749.500000 1077 89.230000 1 1442 2 chr7D.!!$F6 1441
4 TraesCS7D01G058500 chr7D 31579536 31580551 1015 False 577.000000 577 77.863000 754 1753 1 chr7D.!!$F4 999
5 TraesCS7D01G058500 chr3D 532163141 532166329 3188 False 4224.000000 4224 90.549000 1882 5084 1 chr3D.!!$F1 3202
6 TraesCS7D01G058500 chr2B 137006676 137009865 3189 True 4194.000000 4194 90.387000 1885 5084 1 chr2B.!!$R1 3199
7 TraesCS7D01G058500 chr2B 378052352 378055453 3101 False 2361.000000 2361 80.499000 1970 5084 1 chr2B.!!$F1 3114
8 TraesCS7D01G058500 chr2B 137340691 137342331 1640 True 2067.000000 2067 89.410000 1885 3525 1 chr2B.!!$R2 1640
9 TraesCS7D01G058500 chr2D 154829998 154833191 3193 True 3943.000000 3943 88.951000 1885 5084 1 chr2D.!!$R1 3199
10 TraesCS7D01G058500 chr2D 186663343 186666009 2666 True 2628.000000 2628 84.567000 1885 4542 1 chr2D.!!$R2 2657
11 TraesCS7D01G058500 chr4D 394401981 394405178 3197 False 3816.000000 3816 88.221000 1882 5084 1 chr4D.!!$F1 3202
12 TraesCS7D01G058500 chr4D 439883709 439885929 2220 True 3290.000000 3290 93.393000 2862 5084 1 chr4D.!!$R1 2222
13 TraesCS7D01G058500 chrUn 70420600 70423792 3192 False 3795.000000 3795 88.136000 1887 5084 1 chrUn.!!$F1 3197
14 TraesCS7D01G058500 chr5D 249902088 249905257 3169 True 3771.000000 3771 88.120000 1885 5084 1 chr5D.!!$R1 3199
15 TraesCS7D01G058500 chr1D 233012941 233014720 1779 False 1781.000000 1781 84.779000 1887 3666 1 chr1D.!!$F1 1779
16 TraesCS7D01G058500 chr4A 696117462 696118191 729 True 701.000000 701 84.605000 653 1382 1 chr4A.!!$R1 729
17 TraesCS7D01G058500 chr4A 696089173 696089931 758 True 536.500000 651 92.318500 1 848 2 chr4A.!!$R3 847
18 TraesCS7D01G058500 chr4A 696078940 696082435 3495 True 395.000000 667 88.367500 844 1872 4 chr4A.!!$R2 1028
19 TraesCS7D01G058500 chr7A 31921535 31922476 941 False 382.333333 627 88.110000 1 1046 3 chr7A.!!$F2 1045
20 TraesCS7D01G058500 chr7A 31949784 31950725 941 False 382.000000 621 88.164333 1 1046 3 chr7A.!!$F3 1045
21 TraesCS7D01G058500 chr7A 31959859 31963396 3537 False 266.000000 398 85.886500 1 1442 2 chr7A.!!$F4 1441

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
328 330 0.399091 CCCCCAGCCTCTACATCTGA 60.399 60.0 0.00 0.0 0.00 3.27 F
719 731 0.740737 GCATGCGTTAGATTTGGCCT 59.259 50.0 0.00 0.0 0.00 5.19 F
1875 3491 0.037326 GAACATGTCGCAGAGGTGGA 60.037 55.0 0.00 0.0 36.95 4.02 F
2324 3947 0.469494 TCACTCAGCTGCTCCAAACA 59.531 50.0 9.47 0.0 0.00 2.83 F
3005 4679 0.535335 GGATGTGTGCCCGTCTTCTA 59.465 55.0 0.00 0.0 0.00 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1856 3472 0.037326 TCCACCTCTGCGACATGTTC 60.037 55.0 0.00 0.0 0.0 3.18 R
2384 4007 0.178961 AGACAAAAGGGAGGGTTGGC 60.179 55.0 0.00 0.0 0.0 4.52 R
2735 4358 0.036022 AACTGGTTGAGAGGCAGAGC 59.964 55.0 0.00 0.0 0.0 4.09 R
3276 4953 0.393132 GCTAGCAGGGTTCCCAAGAC 60.393 60.0 10.63 0.0 0.0 3.01 R
4577 8440 0.320374 AGGGAGTTCACGAATCGCAA 59.680 50.0 1.15 0.0 0.0 4.85 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
42 43 3.746492 GCTTATCGACCGATTAGCCAAAT 59.254 43.478 24.28 0.00 45.80 2.32
309 311 2.908688 TTTGGAAAAGGAGGCTTTGC 57.091 45.000 0.00 0.00 0.00 3.68
320 322 4.372999 GCTTTGCCCCCAGCCTCT 62.373 66.667 0.00 0.00 42.71 3.69
321 323 2.983879 GCTTTGCCCCCAGCCTCTA 61.984 63.158 0.00 0.00 42.71 2.43
322 324 1.077429 CTTTGCCCCCAGCCTCTAC 60.077 63.158 0.00 0.00 42.71 2.59
323 325 1.850289 TTTGCCCCCAGCCTCTACA 60.850 57.895 0.00 0.00 42.71 2.74
324 326 1.214305 TTTGCCCCCAGCCTCTACAT 61.214 55.000 0.00 0.00 42.71 2.29
325 327 1.635817 TTGCCCCCAGCCTCTACATC 61.636 60.000 0.00 0.00 42.71 3.06
326 328 1.768077 GCCCCCAGCCTCTACATCT 60.768 63.158 0.00 0.00 34.35 2.90
327 329 2.049627 GCCCCCAGCCTCTACATCTG 62.050 65.000 0.00 0.00 34.35 2.90
328 330 0.399091 CCCCCAGCCTCTACATCTGA 60.399 60.000 0.00 0.00 0.00 3.27
329 331 1.500474 CCCCAGCCTCTACATCTGAA 58.500 55.000 0.00 0.00 0.00 3.02
330 332 1.139853 CCCCAGCCTCTACATCTGAAC 59.860 57.143 0.00 0.00 0.00 3.18
331 333 1.202463 CCCAGCCTCTACATCTGAACG 60.202 57.143 0.00 0.00 0.00 3.95
332 334 1.751351 CCAGCCTCTACATCTGAACGA 59.249 52.381 0.00 0.00 0.00 3.85
333 335 2.363680 CCAGCCTCTACATCTGAACGAT 59.636 50.000 0.00 0.00 0.00 3.73
341 343 2.836479 CATCTGAACGATGCATGCAA 57.164 45.000 26.68 8.49 42.75 4.08
342 344 2.447250 CATCTGAACGATGCATGCAAC 58.553 47.619 26.68 21.63 42.75 4.17
343 345 1.521580 TCTGAACGATGCATGCAACA 58.478 45.000 26.68 17.29 0.00 3.33
344 346 1.878734 TCTGAACGATGCATGCAACAA 59.121 42.857 26.68 0.00 0.00 2.83
345 347 2.488937 TCTGAACGATGCATGCAACAAT 59.511 40.909 26.68 13.28 0.00 2.71
346 348 3.688673 TCTGAACGATGCATGCAACAATA 59.311 39.130 26.68 8.96 0.00 1.90
347 349 4.155644 TCTGAACGATGCATGCAACAATAA 59.844 37.500 26.68 8.78 0.00 1.40
348 350 4.802999 TGAACGATGCATGCAACAATAAA 58.197 34.783 26.68 5.29 0.00 1.40
349 351 5.225642 TGAACGATGCATGCAACAATAAAA 58.774 33.333 26.68 3.83 0.00 1.52
350 352 5.693555 TGAACGATGCATGCAACAATAAAAA 59.306 32.000 26.68 2.31 0.00 1.94
351 353 6.368243 TGAACGATGCATGCAACAATAAAAAT 59.632 30.769 26.68 3.17 0.00 1.82
352 354 6.335176 ACGATGCATGCAACAATAAAAATC 57.665 33.333 26.68 12.31 0.00 2.17
353 355 5.004630 ACGATGCATGCAACAATAAAAATCG 59.995 36.000 26.68 24.81 39.15 3.34
354 356 5.554883 CGATGCATGCAACAATAAAAATCGG 60.555 40.000 26.68 6.31 31.92 4.18
355 357 3.931468 TGCATGCAACAATAAAAATCGGG 59.069 39.130 20.30 0.00 0.00 5.14
356 358 3.242381 GCATGCAACAATAAAAATCGGGC 60.242 43.478 14.21 0.00 0.00 6.13
357 359 2.966050 TGCAACAATAAAAATCGGGCC 58.034 42.857 0.00 0.00 0.00 5.80
358 360 2.300152 TGCAACAATAAAAATCGGGCCA 59.700 40.909 4.39 0.00 0.00 5.36
359 361 3.055530 TGCAACAATAAAAATCGGGCCAT 60.056 39.130 4.39 0.00 0.00 4.40
360 362 3.938334 GCAACAATAAAAATCGGGCCATT 59.062 39.130 4.39 0.00 0.00 3.16
361 363 5.112686 GCAACAATAAAAATCGGGCCATTA 58.887 37.500 4.39 0.00 0.00 1.90
362 364 5.757808 GCAACAATAAAAATCGGGCCATTAT 59.242 36.000 4.39 0.00 0.00 1.28
363 365 6.926272 GCAACAATAAAAATCGGGCCATTATA 59.074 34.615 4.39 1.29 0.00 0.98
364 366 7.602265 GCAACAATAAAAATCGGGCCATTATAT 59.398 33.333 4.39 3.40 0.00 0.86
365 367 8.924691 CAACAATAAAAATCGGGCCATTATATG 58.075 33.333 4.39 4.67 0.00 1.78
380 382 5.163141 CCATTATATGGTTGGTAGGTGTCCA 60.163 44.000 0.00 0.00 45.54 4.02
393 395 1.804748 GGTGTCCAGGCGAAACTTAAG 59.195 52.381 0.00 0.00 0.00 1.85
409 411 3.896272 ACTTAAGTCTTCAACGAGGGTCT 59.104 43.478 1.12 0.00 0.00 3.85
410 412 5.075493 ACTTAAGTCTTCAACGAGGGTCTA 58.925 41.667 1.12 0.00 0.00 2.59
411 413 5.715753 ACTTAAGTCTTCAACGAGGGTCTAT 59.284 40.000 1.12 0.00 0.00 1.98
412 414 6.888632 ACTTAAGTCTTCAACGAGGGTCTATA 59.111 38.462 1.12 0.00 0.00 1.31
502 505 3.860930 ATGTCCGGGTTGTGGGCAC 62.861 63.158 0.00 0.00 45.34 5.01
522 525 1.001974 CGTTGATGGTGGAGGTTGAGA 59.998 52.381 0.00 0.00 0.00 3.27
557 560 6.454795 TGGCATTGTCCTTTCTTTTATGTTC 58.545 36.000 0.00 0.00 0.00 3.18
593 599 4.702131 AGTTGTCCCTTAATCAACATGCTC 59.298 41.667 9.35 0.00 42.33 4.26
632 638 4.006989 CGAATTTCCCATATAATCGGGCA 58.993 43.478 0.00 0.00 42.75 5.36
719 731 0.740737 GCATGCGTTAGATTTGGCCT 59.259 50.000 0.00 0.00 0.00 5.19
764 776 1.079127 CTGTACGGCCTGGGTTCAG 60.079 63.158 0.00 1.06 40.59 3.02
992 1026 2.444706 TCTCGGCCTCCCATCTGG 60.445 66.667 0.00 0.00 0.00 3.86
1347 1611 1.362406 GGCAGCAGCTAGAACGTTCC 61.362 60.000 24.22 9.68 41.70 3.62
1442 1808 5.769484 ATAAAGTGTACACGGATCGATCT 57.231 39.130 23.96 7.70 36.20 2.75
1445 1811 2.355132 AGTGTACACGGATCGATCTGTC 59.645 50.000 32.24 22.74 44.22 3.51
1449 1815 2.302260 ACACGGATCGATCTGTCAGAT 58.698 47.619 32.24 15.40 44.22 2.90
1487 1853 7.032580 ACAGAAATGTCATTTTCGTTTCACAA 58.967 30.769 12.04 0.00 40.88 3.33
1529 1895 7.027760 CGTAGTCAAACTTCAGAGCAAGTATA 58.972 38.462 0.00 0.00 35.45 1.47
1533 1899 8.097038 AGTCAAACTTCAGAGCAAGTATAATGA 58.903 33.333 0.00 0.00 35.45 2.57
1538 1904 9.899226 AACTTCAGAGCAAGTATAATGAAAAAC 57.101 29.630 0.00 0.00 35.45 2.43
1539 1905 8.230486 ACTTCAGAGCAAGTATAATGAAAAACG 58.770 33.333 0.00 0.00 34.70 3.60
1727 3333 9.667107 AAAAAGTGAAGTGATAATCTTCCGATA 57.333 29.630 0.00 0.00 40.10 2.92
1825 3441 3.504863 CATCATTCAAAGCAAGGGTTCG 58.495 45.455 0.00 0.00 0.00 3.95
1835 3451 1.197721 GCAAGGGTTCGTCTGTCATTG 59.802 52.381 0.00 0.00 0.00 2.82
1855 3471 0.613012 GAAGTGCCATTGGGGAAGCT 60.613 55.000 4.53 0.00 40.01 3.74
1856 3472 0.901580 AAGTGCCATTGGGGAAGCTG 60.902 55.000 4.53 0.00 40.01 4.24
1872 3488 0.671781 GCTGAACATGTCGCAGAGGT 60.672 55.000 24.74 0.00 36.95 3.85
1874 3490 0.320683 TGAACATGTCGCAGAGGTGG 60.321 55.000 0.00 0.00 36.95 4.61
1875 3491 0.037326 GAACATGTCGCAGAGGTGGA 60.037 55.000 0.00 0.00 36.95 4.02
1883 3499 4.504916 CAGAGGTGGAGCGCGAGG 62.505 72.222 12.10 0.00 0.00 4.63
2068 3687 3.123620 GCTGCTGCTTCGACTGGG 61.124 66.667 8.53 0.00 36.03 4.45
2149 3768 1.743252 GCAGCCTCCTCGTTCCTTG 60.743 63.158 0.00 0.00 0.00 3.61
2190 3809 1.079405 CTTCCCAGCGTTTCGGCTA 60.079 57.895 0.00 0.00 42.53 3.93
2210 3829 3.456365 GCTCCTCCTCTGCGCAGA 61.456 66.667 35.97 35.97 35.85 4.26
2324 3947 0.469494 TCACTCAGCTGCTCCAAACA 59.531 50.000 9.47 0.00 0.00 2.83
2384 4007 1.269413 GCCATTTCCAATCCAGATGCG 60.269 52.381 0.00 0.00 0.00 4.73
2412 4035 3.371917 CCTCCCTTTTGTCTGATATGCCA 60.372 47.826 0.00 0.00 0.00 4.92
2575 4198 0.681733 ATGCGGCTATCATCTCCGTT 59.318 50.000 0.00 0.00 44.58 4.44
2598 4221 1.783711 CGATCAAAAGATCTCTCCGCG 59.216 52.381 0.00 0.00 0.00 6.46
2838 4461 2.366916 GGGTGCTAGTAGATGATGTGCT 59.633 50.000 0.00 0.00 0.00 4.40
2994 4668 0.867746 CGTGGTTCTGTGGATGTGTG 59.132 55.000 0.00 0.00 0.00 3.82
3005 4679 0.535335 GGATGTGTGCCCGTCTTCTA 59.465 55.000 0.00 0.00 0.00 2.10
3046 4720 2.109126 GGTCGAAGGTGCTGATGCC 61.109 63.158 0.00 0.00 38.71 4.40
3082 4756 1.378514 GCCGCCTCCTTCCAATTCA 60.379 57.895 0.00 0.00 0.00 2.57
3091 4768 3.950395 CTCCTTCCAATTCAGTTGATCCC 59.050 47.826 0.00 0.00 40.37 3.85
3104 4781 4.934001 CAGTTGATCCCGATGATGATAAGG 59.066 45.833 0.00 0.00 32.41 2.69
3110 4787 2.234908 CCCGATGATGATAAGGAGGGAC 59.765 54.545 0.00 0.00 39.95 4.46
3187 4864 0.539051 CTGAGTGGGATGGTCTGGAC 59.461 60.000 0.00 0.00 0.00 4.02
3209 4886 4.265073 CCCTGAGGTGAAGGAACTATTTG 58.735 47.826 0.00 0.00 38.49 2.32
3276 4953 0.816825 CAGGTGATGGATGAAGCCCG 60.817 60.000 0.00 0.00 0.00 6.13
3344 5973 2.660064 AATCTTCCTGCTCGCCCGT 61.660 57.895 0.00 0.00 0.00 5.28
3401 6030 0.898789 GTCTCCTCCTCGGTCCAACA 60.899 60.000 0.00 0.00 0.00 3.33
3479 6142 0.693049 GGCTTCCTCTGGTTCCAAGA 59.307 55.000 0.00 0.00 0.00 3.02
3567 6926 3.630013 AGCCTCGCCTGTTGCTCA 61.630 61.111 0.00 0.00 38.05 4.26
3582 6941 1.078918 CTCATTCTCCGGTGCTGCA 60.079 57.895 0.00 0.00 0.00 4.41
3745 7115 3.424433 CGATTTGTCTCGTTTTACCTGCC 60.424 47.826 0.00 0.00 34.00 4.85
3772 7142 5.852827 TCGGATGATCATTTGCTACACATA 58.147 37.500 10.14 0.00 0.00 2.29
4194 7575 6.430308 GGAAACGTTTAAGGAATCCTTCTCTT 59.570 38.462 19.11 4.80 43.57 2.85
4195 7576 6.803154 AACGTTTAAGGAATCCTTCTCTTG 57.197 37.500 19.11 8.52 43.57 3.02
4370 7978 4.873827 GGTTCATCACCGACAGCTAAATAA 59.126 41.667 0.00 0.00 35.12 1.40
4375 7983 8.138365 TCATCACCGACAGCTAAATAATTTAC 57.862 34.615 0.00 0.00 0.00 2.01
4577 8440 8.313292 TGCCTTTATTGAGTTCATTAGCAATTT 58.687 29.630 0.00 0.00 33.45 1.82
4763 8750 1.290955 CTTTGGTGGTAGACGCGGA 59.709 57.895 12.47 0.00 0.00 5.54
4826 8813 1.280133 CTCATGGCTCCTTGTGGAAGA 59.720 52.381 0.00 0.00 42.66 2.87
4893 8880 4.323477 CGCCGGTCCTTTGTCCCA 62.323 66.667 1.90 0.00 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
208 209 6.368516 CCGCATATTGACTTTGAAAATGGTTT 59.631 34.615 0.00 0.00 0.00 3.27
288 290 3.540617 GCAAAGCCTCCTTTTCCAAAAA 58.459 40.909 0.00 0.00 39.20 1.94
289 291 2.158827 GGCAAAGCCTCCTTTTCCAAAA 60.159 45.455 0.00 0.00 46.69 2.44
290 292 1.416030 GGCAAAGCCTCCTTTTCCAAA 59.584 47.619 0.00 0.00 46.69 3.28
291 293 1.047801 GGCAAAGCCTCCTTTTCCAA 58.952 50.000 0.00 0.00 46.69 3.53
292 294 2.745379 GGCAAAGCCTCCTTTTCCA 58.255 52.632 0.00 0.00 46.69 3.53
293 295 1.544825 GGGGCAAAGCCTCCTTTTCC 61.545 60.000 8.08 0.00 44.86 3.13
294 296 1.975327 GGGGCAAAGCCTCCTTTTC 59.025 57.895 8.08 0.00 44.86 2.29
295 297 4.215370 GGGGCAAAGCCTCCTTTT 57.785 55.556 8.08 0.00 44.86 2.27
303 305 2.983879 TAGAGGCTGGGGGCAAAGC 61.984 63.158 0.00 0.00 44.01 3.51
304 306 1.077429 GTAGAGGCTGGGGGCAAAG 60.077 63.158 0.00 0.00 44.01 2.77
305 307 1.214305 ATGTAGAGGCTGGGGGCAAA 61.214 55.000 0.00 0.00 44.01 3.68
306 308 1.619363 ATGTAGAGGCTGGGGGCAA 60.619 57.895 0.00 0.00 44.01 4.52
307 309 2.042762 ATGTAGAGGCTGGGGGCA 59.957 61.111 0.00 0.00 44.01 5.36
308 310 1.768077 AGATGTAGAGGCTGGGGGC 60.768 63.158 0.00 0.00 40.90 5.80
309 311 0.399091 TCAGATGTAGAGGCTGGGGG 60.399 60.000 0.00 0.00 0.00 5.40
310 312 1.139853 GTTCAGATGTAGAGGCTGGGG 59.860 57.143 0.00 0.00 0.00 4.96
311 313 1.202463 CGTTCAGATGTAGAGGCTGGG 60.202 57.143 0.00 0.00 0.00 4.45
312 314 1.751351 TCGTTCAGATGTAGAGGCTGG 59.249 52.381 0.00 0.00 0.00 4.85
313 315 3.724508 ATCGTTCAGATGTAGAGGCTG 57.275 47.619 0.00 0.00 38.36 4.85
323 325 2.086094 TGTTGCATGCATCGTTCAGAT 58.914 42.857 23.37 0.00 41.01 2.90
324 326 1.521580 TGTTGCATGCATCGTTCAGA 58.478 45.000 23.37 0.00 0.00 3.27
325 327 2.334971 TTGTTGCATGCATCGTTCAG 57.665 45.000 23.37 0.00 0.00 3.02
326 328 4.431661 TTATTGTTGCATGCATCGTTCA 57.568 36.364 23.37 12.72 0.00 3.18
327 329 5.760193 TTTTATTGTTGCATGCATCGTTC 57.240 34.783 23.37 10.33 0.00 3.95
328 330 6.454054 CGATTTTTATTGTTGCATGCATCGTT 60.454 34.615 23.37 13.90 0.00 3.85
329 331 5.004630 CGATTTTTATTGTTGCATGCATCGT 59.995 36.000 23.37 15.24 0.00 3.73
330 332 5.417029 CGATTTTTATTGTTGCATGCATCG 58.583 37.500 23.37 18.80 0.00 3.84
331 333 5.276963 CCCGATTTTTATTGTTGCATGCATC 60.277 40.000 23.37 21.28 0.00 3.91
332 334 4.571580 CCCGATTTTTATTGTTGCATGCAT 59.428 37.500 23.37 9.20 0.00 3.96
333 335 3.931468 CCCGATTTTTATTGTTGCATGCA 59.069 39.130 18.46 18.46 0.00 3.96
334 336 3.242381 GCCCGATTTTTATTGTTGCATGC 60.242 43.478 11.82 11.82 0.00 4.06
335 337 3.309410 GGCCCGATTTTTATTGTTGCATG 59.691 43.478 0.00 0.00 0.00 4.06
336 338 3.055530 TGGCCCGATTTTTATTGTTGCAT 60.056 39.130 0.00 0.00 0.00 3.96
337 339 2.300152 TGGCCCGATTTTTATTGTTGCA 59.700 40.909 0.00 0.00 0.00 4.08
338 340 2.966050 TGGCCCGATTTTTATTGTTGC 58.034 42.857 0.00 0.00 0.00 4.17
339 341 8.924691 CATATAATGGCCCGATTTTTATTGTTG 58.075 33.333 0.00 0.00 0.00 3.33
340 342 8.093927 CCATATAATGGCCCGATTTTTATTGTT 58.906 33.333 0.00 0.00 44.70 2.83
341 343 7.610865 CCATATAATGGCCCGATTTTTATTGT 58.389 34.615 0.00 0.00 44.70 2.71
355 357 8.607808 TGGACACCTACCAACCATATAATGGC 62.608 46.154 5.84 0.00 42.27 4.40
356 358 5.163141 TGGACACCTACCAACCATATAATGG 60.163 44.000 4.36 4.36 43.25 3.16
357 359 5.935945 TGGACACCTACCAACCATATAATG 58.064 41.667 0.00 0.00 34.25 1.90
358 360 5.073144 CCTGGACACCTACCAACCATATAAT 59.927 44.000 0.00 0.00 36.95 1.28
359 361 4.410883 CCTGGACACCTACCAACCATATAA 59.589 45.833 0.00 0.00 36.95 0.98
360 362 3.971305 CCTGGACACCTACCAACCATATA 59.029 47.826 0.00 0.00 36.95 0.86
361 363 2.777692 CCTGGACACCTACCAACCATAT 59.222 50.000 0.00 0.00 36.95 1.78
362 364 2.193127 CCTGGACACCTACCAACCATA 58.807 52.381 0.00 0.00 36.95 2.74
363 365 0.991920 CCTGGACACCTACCAACCAT 59.008 55.000 0.00 0.00 36.95 3.55
364 366 1.774894 GCCTGGACACCTACCAACCA 61.775 60.000 0.00 0.00 36.95 3.67
365 367 1.002502 GCCTGGACACCTACCAACC 60.003 63.158 0.00 0.00 36.95 3.77
366 368 1.375523 CGCCTGGACACCTACCAAC 60.376 63.158 0.00 0.00 36.95 3.77
380 382 3.493503 CGTTGAAGACTTAAGTTTCGCCT 59.506 43.478 10.02 0.00 0.00 5.52
393 395 6.094061 GCATATATAGACCCTCGTTGAAGAC 58.906 44.000 0.00 0.00 0.00 3.01
409 411 2.816689 CCGAAATCGCCGGCATATATA 58.183 47.619 28.98 4.00 40.54 0.86
410 412 1.651987 CCGAAATCGCCGGCATATAT 58.348 50.000 28.98 11.07 40.54 0.86
411 413 3.131326 CCGAAATCGCCGGCATATA 57.869 52.632 28.98 8.91 40.54 0.86
412 414 3.966215 CCGAAATCGCCGGCATAT 58.034 55.556 28.98 16.71 40.54 1.78
502 505 1.001974 TCTCAACCTCCACCATCAACG 59.998 52.381 0.00 0.00 0.00 4.10
522 525 0.539438 ACAATGCCAACACCGGTCAT 60.539 50.000 2.59 1.00 0.00 3.06
593 599 4.675190 ATTCGATCAAAGAGCACAACAG 57.325 40.909 0.00 0.00 0.00 3.16
632 638 7.011016 CCGTTTAAGAGCAAGGAAAACAAAATT 59.989 33.333 0.00 0.00 31.85 1.82
719 731 8.707839 CATGCGTTCATACATGTATATTGTACA 58.292 33.333 17.86 12.17 39.05 2.90
764 776 3.313274 TGACGTTCTCTTGTTTTTCGC 57.687 42.857 0.00 0.00 0.00 4.70
790 802 6.384258 TTGAATTTTAGCTAACAGCACACA 57.616 33.333 5.45 0.00 45.56 3.72
992 1026 3.683365 ATGCTTTGGGTTTGGAATGAC 57.317 42.857 0.00 0.00 0.00 3.06
1340 1568 3.737266 CGTACAATACACAGTGGAACGTT 59.263 43.478 0.00 0.00 45.86 3.99
1347 1611 1.999735 CAGGGCGTACAATACACAGTG 59.000 52.381 0.00 0.00 0.00 3.66
1463 1829 7.448588 TTGTGAAACGAAAATGACATTTCTG 57.551 32.000 13.68 11.31 42.39 3.02
1727 3333 9.961265 GGTTTTTCAAAAAGCTAGTATGTTACT 57.039 29.630 16.01 0.00 42.68 2.24
1825 3441 1.896220 TGGCACTTCCAATGACAGAC 58.104 50.000 0.00 0.00 43.21 3.51
1835 3451 1.607801 GCTTCCCCAATGGCACTTCC 61.608 60.000 0.00 0.00 0.00 3.46
1844 3460 2.450476 GACATGTTCAGCTTCCCCAAT 58.550 47.619 0.00 0.00 0.00 3.16
1855 3471 0.320683 CCACCTCTGCGACATGTTCA 60.321 55.000 0.00 0.35 0.00 3.18
1856 3472 0.037326 TCCACCTCTGCGACATGTTC 60.037 55.000 0.00 0.00 0.00 3.18
2036 3652 0.685458 GCAGCAACCTCCCATGGATT 60.685 55.000 15.22 0.00 0.00 3.01
2068 3687 2.979649 GACGAGGAGGAACCACCC 59.020 66.667 3.81 0.00 42.04 4.61
2190 3809 3.859414 GCGCAGAGGAGGAGCCAT 61.859 66.667 0.30 0.00 40.02 4.40
2210 3829 2.426023 GCCACGGCGATCCCTAAT 59.574 61.111 16.62 0.00 0.00 1.73
2245 3864 1.383248 AAGGCAGGCGGAGGTAGAT 60.383 57.895 0.00 0.00 0.00 1.98
2324 3947 1.840635 GCATGTAAGGGAAGGAGAGGT 59.159 52.381 0.00 0.00 0.00 3.85
2384 4007 0.178961 AGACAAAAGGGAGGGTTGGC 60.179 55.000 0.00 0.00 0.00 4.52
2412 4035 2.909006 ACAGTCAGGTGTCCATCAGAAT 59.091 45.455 0.00 0.00 0.00 2.40
2598 4221 2.558359 CTCAAACCATCCAACAAGGTCC 59.442 50.000 0.00 0.00 39.02 4.46
2735 4358 0.036022 AACTGGTTGAGAGGCAGAGC 59.964 55.000 0.00 0.00 0.00 4.09
2838 4461 2.344500 CCGACCGCAAACCCACTA 59.656 61.111 0.00 0.00 0.00 2.74
2994 4668 0.323957 AACACCCTTAGAAGACGGGC 59.676 55.000 0.00 0.00 41.86 6.13
3005 4679 2.030562 CCGCAGTCGAACACCCTT 59.969 61.111 0.00 0.00 38.10 3.95
3067 4741 2.795329 TCAACTGAATTGGAAGGAGGC 58.205 47.619 0.00 0.00 38.98 4.70
3082 4756 4.840680 TCCTTATCATCATCGGGATCAACT 59.159 41.667 0.00 0.00 32.57 3.16
3091 4768 4.502016 CATGTCCCTCCTTATCATCATCG 58.498 47.826 0.00 0.00 0.00 3.84
3104 4781 1.070445 CAGCCGATCCATGTCCCTC 59.930 63.158 0.00 0.00 0.00 4.30
3110 4787 2.203252 CCCACCAGCCGATCCATG 60.203 66.667 0.00 0.00 0.00 3.66
3187 4864 4.019321 TCAAATAGTTCCTTCACCTCAGGG 60.019 45.833 0.00 0.00 38.88 4.45
3209 4886 0.608035 TCAACCGGGGCATTGTCTTC 60.608 55.000 6.32 0.00 0.00 2.87
3276 4953 0.393132 GCTAGCAGGGTTCCCAAGAC 60.393 60.000 10.63 0.00 0.00 3.01
3344 5973 2.569853 TCCCAGAAAATGAAGGCGACTA 59.430 45.455 0.00 0.00 42.68 2.59
3401 6030 6.198639 TCTTCTTCTTCTTAGATGTAGGCCT 58.801 40.000 11.78 11.78 0.00 5.19
3479 6142 3.179175 AGCCAGGCCCATCATGGATTT 62.179 52.381 8.22 0.00 43.50 2.17
3567 6926 1.078848 GACTGCAGCACCGGAGAAT 60.079 57.895 15.27 0.00 0.00 2.40
3772 7142 1.600485 GAAACACCAACGTCCGACAAT 59.400 47.619 0.00 0.00 0.00 2.71
4194 7575 3.325870 CAACCGCAGATAGTTCAGAACA 58.674 45.455 15.85 2.27 0.00 3.18
4195 7576 2.094417 GCAACCGCAGATAGTTCAGAAC 59.906 50.000 5.00 5.00 38.36 3.01
4271 7652 4.814771 CCCGTTTAGACCCAATCAGAATAC 59.185 45.833 0.00 0.00 0.00 1.89
4370 7978 5.431179 AACCACTAGACATTCCCGTAAAT 57.569 39.130 0.00 0.00 0.00 1.40
4375 7983 4.127171 CCATAAACCACTAGACATTCCCG 58.873 47.826 0.00 0.00 0.00 5.14
4451 8060 6.867662 ATAAAGGAATATTGCAAGACTCGG 57.132 37.500 9.81 0.00 0.00 4.63
4480 8089 4.379394 GCGCAAGAGATTAAAATCACCACA 60.379 41.667 0.30 0.00 43.02 4.17
4577 8440 0.320374 AGGGAGTTCACGAATCGCAA 59.680 50.000 1.15 0.00 0.00 4.85
4763 8750 7.334858 GGATGAAGTCAGAGAAGAATTAAGGT 58.665 38.462 0.00 0.00 0.00 3.50
4826 8813 3.545703 GTGGCCAGCATATCACTAAACT 58.454 45.455 5.11 0.00 0.00 2.66
4893 8880 2.093869 GCACTTGTGCCAATCATCCATT 60.094 45.455 14.17 0.00 0.00 3.16
4925 8912 1.002544 AGCCTCTTAAGAACTTGCGCT 59.997 47.619 9.73 4.22 0.00 5.92


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

AutoCloner maintained by Alex Coulton.