Multiple sequence alignment - TraesCS5D01G073400

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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 TraesCS5D01G073400 chr5D 100.000 3284 0 0 1 3284 72612275 72615558 0.000000e+00 6065.0
1 TraesCS5D01G073400 chr5D 87.443 1099 98 12 1205 2289 72589897 72590969 0.000000e+00 1229.0
2 TraesCS5D01G073400 chr5D 92.599 581 35 7 2712 3284 61485456 61484876 0.000000e+00 828.0
3 TraesCS5D01G073400 chr5D 90.909 187 16 1 366 552 72612282 72612467 1.960000e-62 250.0
4 TraesCS5D01G073400 chr5D 90.909 187 16 1 8 193 72612640 72612826 1.960000e-62 250.0
5 TraesCS5D01G073400 chr5B 91.170 1846 117 17 773 2588 79423977 79422148 0.000000e+00 2464.0
6 TraesCS5D01G073400 chr5B 87.245 1129 93 20 1219 2329 79562307 79561212 0.000000e+00 1240.0
7 TraesCS5D01G073400 chr5B 91.910 581 39 4 2712 3284 311547248 311547828 0.000000e+00 806.0
8 TraesCS5D01G073400 chr5B 91.608 429 21 11 353 773 79424468 79424047 2.200000e-161 579.0
9 TraesCS5D01G073400 chr5B 78.870 407 44 19 807 1193 79562798 79562414 1.520000e-58 237.0
10 TraesCS5D01G073400 chr5B 85.789 190 15 2 5 193 79424650 79424472 1.200000e-44 191.0
11 TraesCS5D01G073400 chr5B 90.845 142 5 7 2573 2706 79417199 79417058 2.010000e-42 183.0
12 TraesCS5D01G073400 chr5B 94.444 72 4 0 497 568 79426388 79426317 9.630000e-21 111.0
13 TraesCS5D01G073400 chr5B 77.604 192 34 7 1208 1399 79542429 79542247 1.250000e-19 108.0
14 TraesCS5D01G073400 chr5B 90.789 76 7 0 77 152 79465766 79465691 5.800000e-18 102.0
15 TraesCS5D01G073400 chr5B 98.182 55 1 0 138 192 79426388 79426334 2.700000e-16 97.1
16 TraesCS5D01G073400 chr5A 89.182 1784 146 19 773 2539 65354829 65356582 0.000000e+00 2182.0
17 TraesCS5D01G073400 chr5A 89.927 1102 93 5 1207 2295 65360196 65361292 0.000000e+00 1404.0
18 TraesCS5D01G073400 chr5A 89.156 1125 98 5 1218 2327 65011191 65012306 0.000000e+00 1380.0
19 TraesCS5D01G073400 chr5A 92.042 578 38 7 2712 3281 340811673 340812250 0.000000e+00 806.0
20 TraesCS5D01G073400 chr5A 85.315 572 58 7 2075 2633 67317611 67318169 4.760000e-158 568.0
21 TraesCS5D01G073400 chr5A 85.847 431 31 7 773 1200 65359663 65360066 6.510000e-117 431.0
22 TraesCS5D01G073400 chr5A 91.150 226 15 4 351 571 65354246 65354471 5.330000e-78 302.0
23 TraesCS5D01G073400 chr5A 94.737 190 9 1 1 189 65354051 65354240 8.910000e-76 294.0
24 TraesCS5D01G073400 chr5A 90.686 204 17 2 366 568 65354058 65354260 1.500000e-68 270.0
25 TraesCS5D01G073400 chr5A 86.222 225 18 8 549 773 65359382 65359593 7.090000e-57 231.0
26 TraesCS5D01G073400 chr5A 78.304 401 49 18 807 1193 65010710 65011086 1.190000e-54 224.0
27 TraesCS5D01G073400 chr5A 86.829 205 16 5 578 773 65354557 65354759 5.520000e-53 219.0
28 TraesCS5D01G073400 chr5A 91.892 74 4 2 2624 2696 67318308 67318380 5.800000e-18 102.0
29 TraesCS5D01G073400 chr2D 94.118 578 29 3 2712 3284 542198352 542197775 0.000000e+00 874.0
30 TraesCS5D01G073400 chr4A 92.042 578 38 6 2712 3281 598588955 598589532 0.000000e+00 806.0
31 TraesCS5D01G073400 chr4A 91.738 581 40 3 2712 3284 6819432 6818852 0.000000e+00 800.0
32 TraesCS5D01G073400 chr3D 92.042 578 36 4 2712 3281 581095638 581096213 0.000000e+00 804.0
33 TraesCS5D01G073400 chr3D 85.799 169 14 3 194 353 469389267 469389434 1.570000e-38 171.0
34 TraesCS5D01G073400 chr7A 91.869 578 39 2 2712 3281 437074373 437074950 0.000000e+00 800.0
35 TraesCS5D01G073400 chr7A 86.755 151 16 4 205 352 345878835 345878686 7.290000e-37 165.0
36 TraesCS5D01G073400 chr1B 91.869 578 39 7 2712 3281 666836640 666836063 0.000000e+00 800.0
37 TraesCS5D01G073400 chr1B 86.145 166 13 4 198 354 420865522 420865358 1.570000e-38 171.0
38 TraesCS5D01G073400 chr6B 86.550 171 11 5 193 352 207160606 207160437 9.360000e-41 178.0
39 TraesCS5D01G073400 chr6A 86.207 174 13 5 190 353 361884790 361884962 9.360000e-41 178.0
40 TraesCS5D01G073400 chr6A 86.145 166 13 5 196 352 22166173 22166337 1.570000e-38 171.0
41 TraesCS5D01G073400 chr3A 85.714 175 12 6 191 353 478426320 478426493 4.360000e-39 172.0
42 TraesCS5D01G073400 chr1D 86.061 165 12 4 199 353 485505245 485505408 2.030000e-37 167.0
43 TraesCS5D01G073400 chr3B 85.542 166 15 4 195 352 251025306 251025142 7.290000e-37 165.0


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 TraesCS5D01G073400 chr5D 72612275 72615558 3283 False 2188.333333 6065 93.939333 1 3284 3 chr5D.!!$F2 3283
1 TraesCS5D01G073400 chr5D 72589897 72590969 1072 False 1229.000000 1229 87.443000 1205 2289 1 chr5D.!!$F1 1084
2 TraesCS5D01G073400 chr5D 61484876 61485456 580 True 828.000000 828 92.599000 2712 3284 1 chr5D.!!$R1 572
3 TraesCS5D01G073400 chr5B 311547248 311547828 580 False 806.000000 806 91.910000 2712 3284 1 chr5B.!!$F1 572
4 TraesCS5D01G073400 chr5B 79561212 79562798 1586 True 738.500000 1240 83.057500 807 2329 2 chr5B.!!$R5 1522
5 TraesCS5D01G073400 chr5B 79422148 79426388 4240 True 688.420000 2464 92.238600 5 2588 5 chr5B.!!$R4 2583
6 TraesCS5D01G073400 chr5A 340811673 340812250 577 False 806.000000 806 92.042000 2712 3281 1 chr5A.!!$F1 569
7 TraesCS5D01G073400 chr5A 65010710 65012306 1596 False 802.000000 1380 83.730000 807 2327 2 chr5A.!!$F2 1520
8 TraesCS5D01G073400 chr5A 65354051 65361292 7241 False 666.625000 2182 89.322500 1 2539 8 chr5A.!!$F3 2538
9 TraesCS5D01G073400 chr5A 67317611 67318380 769 False 335.000000 568 88.603500 2075 2696 2 chr5A.!!$F4 621
10 TraesCS5D01G073400 chr2D 542197775 542198352 577 True 874.000000 874 94.118000 2712 3284 1 chr2D.!!$R1 572
11 TraesCS5D01G073400 chr4A 598588955 598589532 577 False 806.000000 806 92.042000 2712 3281 1 chr4A.!!$F1 569
12 TraesCS5D01G073400 chr4A 6818852 6819432 580 True 800.000000 800 91.738000 2712 3284 1 chr4A.!!$R1 572
13 TraesCS5D01G073400 chr3D 581095638 581096213 575 False 804.000000 804 92.042000 2712 3281 1 chr3D.!!$F2 569
14 TraesCS5D01G073400 chr7A 437074373 437074950 577 False 800.000000 800 91.869000 2712 3281 1 chr7A.!!$F1 569
15 TraesCS5D01G073400 chr1B 666836063 666836640 577 True 800.000000 800 91.869000 2712 3281 1 chr1B.!!$R2 569

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
423 2164 0.099436 GGCAAGTGGATGATGCGAAC 59.901 55.0 0.00 0.0 40.94 3.95 F
1122 3056 0.560688 AGCTCCTCCTAGAGAAGGGG 59.439 60.0 0.00 0.0 46.87 4.79 F
1869 3914 0.113776 ACCCGTCTCTAGTGTTGGGA 59.886 55.0 22.41 0.0 39.03 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1617 3656 0.317160 TCGCTCCAACATGTCTCGTT 59.683 50.0 0.00 0.0 0.00 3.85 R
2073 4118 0.460311 AGAACTTGGCGAGGATACGG 59.540 55.0 6.71 0.0 46.39 4.02 R
2955 8692 0.607217 TCTACACTCTTCACCGGCGA 60.607 55.0 9.30 0.0 0.00 5.54 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
96 1832 1.046204 TGCATGCAATCCACCAAACA 58.954 45.000 20.30 0.00 0.00 2.83
101 1837 4.381825 GCATGCAATCCACCAAACAGAATA 60.382 41.667 14.21 0.00 0.00 1.75
102 1838 5.682990 GCATGCAATCCACCAAACAGAATAT 60.683 40.000 14.21 0.00 0.00 1.28
257 1994 9.737427 AAGATTTCACTATGAACTACATACGAG 57.263 33.333 0.00 0.00 35.89 4.18
258 1995 7.863375 AGATTTCACTATGAACTACATACGAGC 59.137 37.037 0.00 0.00 35.89 5.03
259 1996 6.445357 TTCACTATGAACTACATACGAGCA 57.555 37.500 0.00 0.00 40.07 4.26
260 1997 6.445357 TCACTATGAACTACATACGAGCAA 57.555 37.500 0.00 0.00 40.07 3.91
261 1998 6.859017 TCACTATGAACTACATACGAGCAAA 58.141 36.000 0.00 0.00 40.07 3.68
262 1999 7.317390 TCACTATGAACTACATACGAGCAAAA 58.683 34.615 0.00 0.00 40.07 2.44
263 2000 7.979537 TCACTATGAACTACATACGAGCAAAAT 59.020 33.333 0.00 0.00 40.07 1.82
264 2001 8.058328 CACTATGAACTACATACGAGCAAAATG 58.942 37.037 0.00 0.00 40.07 2.32
265 2002 7.979537 ACTATGAACTACATACGAGCAAAATGA 59.020 33.333 0.00 0.00 40.07 2.57
266 2003 6.647212 TGAACTACATACGAGCAAAATGAG 57.353 37.500 0.00 0.00 0.00 2.90
267 2004 6.163476 TGAACTACATACGAGCAAAATGAGT 58.837 36.000 0.00 0.00 0.00 3.41
268 2005 6.090763 TGAACTACATACGAGCAAAATGAGTG 59.909 38.462 0.00 0.00 0.00 3.51
269 2006 5.720202 ACTACATACGAGCAAAATGAGTGA 58.280 37.500 0.00 0.00 0.00 3.41
270 2007 6.163476 ACTACATACGAGCAAAATGAGTGAA 58.837 36.000 0.00 0.00 0.00 3.18
271 2008 6.818644 ACTACATACGAGCAAAATGAGTGAAT 59.181 34.615 0.00 0.00 0.00 2.57
272 2009 6.111768 ACATACGAGCAAAATGAGTGAATC 57.888 37.500 0.00 0.00 0.00 2.52
273 2010 5.877012 ACATACGAGCAAAATGAGTGAATCT 59.123 36.000 0.00 0.00 0.00 2.40
274 2011 7.041721 ACATACGAGCAAAATGAGTGAATCTA 58.958 34.615 0.00 0.00 0.00 1.98
275 2012 5.786401 ACGAGCAAAATGAGTGAATCTAC 57.214 39.130 0.00 0.00 0.00 2.59
276 2013 5.237815 ACGAGCAAAATGAGTGAATCTACA 58.762 37.500 0.00 0.00 0.00 2.74
277 2014 5.877012 ACGAGCAAAATGAGTGAATCTACAT 59.123 36.000 0.00 0.00 0.00 2.29
278 2015 6.183360 ACGAGCAAAATGAGTGAATCTACATG 60.183 38.462 0.00 0.00 0.00 3.21
279 2016 5.888105 AGCAAAATGAGTGAATCTACATGC 58.112 37.500 0.00 0.00 0.00 4.06
280 2017 5.416639 AGCAAAATGAGTGAATCTACATGCA 59.583 36.000 0.00 0.00 31.79 3.96
281 2018 6.096423 AGCAAAATGAGTGAATCTACATGCAT 59.904 34.615 0.00 0.00 31.79 3.96
282 2019 6.417044 GCAAAATGAGTGAATCTACATGCATC 59.583 38.462 0.00 0.00 0.00 3.91
283 2020 7.681304 GCAAAATGAGTGAATCTACATGCATCT 60.681 37.037 0.00 0.00 0.00 2.90
284 2021 8.833493 CAAAATGAGTGAATCTACATGCATCTA 58.167 33.333 0.00 0.00 0.00 1.98
285 2022 9.570468 AAAATGAGTGAATCTACATGCATCTAT 57.430 29.630 0.00 0.00 0.00 1.98
300 2037 9.813446 ACATGCATCTATATACATCTGTATGTG 57.187 33.333 12.10 5.57 45.99 3.21
301 2038 9.257651 CATGCATCTATATACATCTGTATGTGG 57.742 37.037 12.10 8.21 45.99 4.17
302 2039 8.366359 TGCATCTATATACATCTGTATGTGGT 57.634 34.615 12.10 0.00 45.99 4.16
303 2040 8.470002 TGCATCTATATACATCTGTATGTGGTC 58.530 37.037 12.10 4.24 45.99 4.02
304 2041 7.923344 GCATCTATATACATCTGTATGTGGTCC 59.077 40.741 12.10 0.00 45.99 4.46
305 2042 8.971073 CATCTATATACATCTGTATGTGGTCCA 58.029 37.037 12.10 0.00 45.99 4.02
306 2043 9.720874 ATCTATATACATCTGTATGTGGTCCAT 57.279 33.333 12.10 0.47 45.99 3.41
309 2046 8.901472 ATATACATCTGTATGTGGTCCATAGT 57.099 34.615 12.10 0.00 45.99 2.12
310 2047 5.282055 ACATCTGTATGTGGTCCATAGTG 57.718 43.478 0.00 0.00 44.79 2.74
311 2048 4.962362 ACATCTGTATGTGGTCCATAGTGA 59.038 41.667 0.00 0.00 44.79 3.41
312 2049 5.425217 ACATCTGTATGTGGTCCATAGTGAA 59.575 40.000 0.00 0.00 44.79 3.18
313 2050 6.070251 ACATCTGTATGTGGTCCATAGTGAAA 60.070 38.462 0.00 0.00 44.79 2.69
314 2051 6.560003 TCTGTATGTGGTCCATAGTGAAAT 57.440 37.500 0.00 0.00 36.71 2.17
315 2052 6.582636 TCTGTATGTGGTCCATAGTGAAATC 58.417 40.000 0.00 0.00 36.71 2.17
316 2053 6.384015 TCTGTATGTGGTCCATAGTGAAATCT 59.616 38.462 0.00 0.00 36.71 2.40
317 2054 6.582636 TGTATGTGGTCCATAGTGAAATCTC 58.417 40.000 0.00 0.00 36.71 2.75
318 2055 5.965033 ATGTGGTCCATAGTGAAATCTCT 57.035 39.130 0.00 0.00 29.82 3.10
319 2056 7.563556 TGTATGTGGTCCATAGTGAAATCTCTA 59.436 37.037 0.00 0.00 36.71 2.43
320 2057 7.623999 ATGTGGTCCATAGTGAAATCTCTAT 57.376 36.000 0.00 0.37 34.17 1.98
321 2058 8.727100 ATGTGGTCCATAGTGAAATCTCTATA 57.273 34.615 0.00 0.00 33.04 1.31
322 2059 8.547481 TGTGGTCCATAGTGAAATCTCTATAA 57.453 34.615 0.00 0.00 33.04 0.98
323 2060 8.988060 TGTGGTCCATAGTGAAATCTCTATAAA 58.012 33.333 0.00 0.00 33.04 1.40
324 2061 9.482627 GTGGTCCATAGTGAAATCTCTATAAAG 57.517 37.037 0.00 0.00 33.04 1.85
325 2062 8.651389 TGGTCCATAGTGAAATCTCTATAAAGG 58.349 37.037 5.06 3.91 33.04 3.11
326 2063 7.604545 GGTCCATAGTGAAATCTCTATAAAGGC 59.395 40.741 5.06 0.90 33.04 4.35
327 2064 8.371699 GTCCATAGTGAAATCTCTATAAAGGCT 58.628 37.037 5.06 0.00 33.04 4.58
328 2065 8.938883 TCCATAGTGAAATCTCTATAAAGGCTT 58.061 33.333 0.00 0.00 33.04 4.35
346 2083 7.803279 AAGGCTTATTATTTAGGAACGAAGG 57.197 36.000 0.00 0.00 0.00 3.46
347 2084 6.296803 AGGCTTATTATTTAGGAACGAAGGG 58.703 40.000 0.00 0.00 0.00 3.95
348 2085 6.100714 AGGCTTATTATTTAGGAACGAAGGGA 59.899 38.462 0.00 0.00 0.00 4.20
349 2086 6.427242 GGCTTATTATTTAGGAACGAAGGGAG 59.573 42.308 0.00 0.00 0.00 4.30
364 2101 4.161754 CGAAGGGAGTAGGTTGGAACTTAT 59.838 45.833 0.00 0.00 0.00 1.73
423 2164 0.099436 GGCAAGTGGATGATGCGAAC 59.901 55.000 0.00 0.00 40.94 3.95
451 2192 2.512286 CGTGCATGCGATCCACCT 60.512 61.111 14.09 0.00 0.00 4.00
611 2439 3.494251 GCTTCCGTTCACATTGCATTTTT 59.506 39.130 0.00 0.00 0.00 1.94
655 2483 1.752498 TGACCGGTCAGCGTATTGTAT 59.248 47.619 33.23 0.00 34.14 2.29
656 2484 2.124903 GACCGGTCAGCGTATTGTATG 58.875 52.381 29.75 0.00 0.00 2.39
660 2488 3.245284 CCGGTCAGCGTATTGTATGAAAG 59.755 47.826 0.00 0.00 0.00 2.62
661 2489 3.863424 CGGTCAGCGTATTGTATGAAAGT 59.137 43.478 0.00 0.00 0.00 2.66
662 2490 4.259810 CGGTCAGCGTATTGTATGAAAGTG 60.260 45.833 0.00 0.00 0.00 3.16
663 2491 4.494199 GGTCAGCGTATTGTATGAAAGTGC 60.494 45.833 0.00 0.00 0.00 4.40
782 2687 3.550639 CGTGTGAAGGCAATTTGACACAT 60.551 43.478 4.79 0.00 39.70 3.21
796 2701 4.403015 TGACACATATTTGCAGTTGACG 57.597 40.909 0.00 0.00 0.00 4.35
806 2711 2.285083 TGCAGTTGACGCAAACTAAGT 58.715 42.857 3.25 0.00 38.34 2.24
815 2721 4.151689 TGACGCAAACTAAGTATGCAAGTC 59.848 41.667 0.00 0.00 40.04 3.01
884 2791 1.581447 GCCAAAAGGCGGTTCTCAG 59.419 57.895 0.00 0.00 0.00 3.35
885 2792 1.172812 GCCAAAAGGCGGTTCTCAGT 61.173 55.000 0.00 0.00 0.00 3.41
886 2793 1.318576 CCAAAAGGCGGTTCTCAGTT 58.681 50.000 0.00 0.00 0.00 3.16
887 2794 1.266989 CCAAAAGGCGGTTCTCAGTTC 59.733 52.381 0.00 0.00 0.00 3.01
888 2795 2.222027 CAAAAGGCGGTTCTCAGTTCT 58.778 47.619 0.00 0.00 0.00 3.01
889 2796 2.171341 AAAGGCGGTTCTCAGTTCTC 57.829 50.000 0.00 0.00 0.00 2.87
890 2797 1.048601 AAGGCGGTTCTCAGTTCTCA 58.951 50.000 0.00 0.00 0.00 3.27
1122 3056 0.560688 AGCTCCTCCTAGAGAAGGGG 59.439 60.000 0.00 0.00 46.87 4.79
1177 3117 1.999735 AGTACAATGCACCGTTCATCG 59.000 47.619 0.00 0.00 39.52 3.84
1200 3142 1.141657 TGCTAATCTCCATGCCTGGAC 59.858 52.381 6.63 0.00 46.95 4.02
1215 3159 3.012518 CCTGGACTGCATCTAACTTTGG 58.987 50.000 0.00 0.00 0.00 3.28
1350 3375 1.027357 CATTCCAAGGATGCGAAGGG 58.973 55.000 0.00 0.00 0.00 3.95
1353 3378 1.452108 CCAAGGATGCGAAGGGGTC 60.452 63.158 0.00 0.00 0.00 4.46
1413 3452 9.140874 GTACTTTACTTACCCACATAGGAGTAT 57.859 37.037 0.00 0.00 41.22 2.12
1427 3466 4.897025 AGGAGTATTACGCTACTGACAC 57.103 45.455 0.00 0.00 32.11 3.67
1437 3476 2.414957 CGCTACTGACACCGAATGTACA 60.415 50.000 0.00 0.00 43.56 2.90
1653 3692 0.734253 CGACCTCGAGTTCTGCAAGG 60.734 60.000 12.31 0.00 43.02 3.61
1689 3728 1.722011 AATTAACTCCCGCTCGTGTG 58.278 50.000 0.00 0.00 0.00 3.82
1690 3729 0.606604 ATTAACTCCCGCTCGTGTGT 59.393 50.000 0.00 0.00 0.00 3.72
1791 3836 3.429822 GGTACTGCTATGCAAAGACGGTA 60.430 47.826 0.00 0.00 38.41 4.02
1869 3914 0.113776 ACCCGTCTCTAGTGTTGGGA 59.886 55.000 22.41 0.00 39.03 4.37
2163 4208 3.175710 AAGGGGTGCCGGTTCAGT 61.176 61.111 1.90 0.00 0.00 3.41
2329 4374 2.045926 AAGTCAGATGCGTGCCCC 60.046 61.111 0.00 0.00 0.00 5.80
2363 4419 5.240403 GCATTGTATTCTCCATTTCCTCCTC 59.760 44.000 0.00 0.00 0.00 3.71
2375 4431 2.879103 TCCTCCTCATTTGTTCACCC 57.121 50.000 0.00 0.00 0.00 4.61
2456 4515 0.035725 TCTCAGACCGAGTAGCCGAA 60.036 55.000 0.00 0.00 42.88 4.30
2461 4520 2.163010 CAGACCGAGTAGCCGAAACTTA 59.837 50.000 0.00 0.00 0.00 2.24
2498 4559 0.317799 GCACACCATGTTCATTGGCA 59.682 50.000 0.00 0.00 37.81 4.92
2591 4717 1.687660 TGTGCACAATGTTCATTGGCT 59.312 42.857 19.28 6.64 35.93 4.75
2596 4722 3.674753 GCACAATGTTCATTGGCTACAAC 59.325 43.478 23.45 0.00 39.87 3.32
2599 4725 2.264005 TGTTCATTGGCTACAACGGT 57.736 45.000 0.00 0.00 39.87 4.83
2619 4745 3.869272 GCTGGCATCGCTTCACCG 61.869 66.667 0.00 0.00 0.00 4.94
2680 7303 1.586154 CTTGGATGCGCCGGTCTTTT 61.586 55.000 4.18 0.00 40.66 2.27
2955 8692 2.186826 GCACCAGAACAGCAACCGT 61.187 57.895 0.00 0.00 0.00 4.83
3025 8764 0.316204 ACCCGAACGACGAACAGATT 59.684 50.000 0.00 0.00 45.77 2.40
3038 8777 4.889832 GAACAGATTCGAGCAAATCCAT 57.110 40.909 3.66 0.00 36.49 3.41
3169 8910 1.585006 GTCGTCTCGCCTTCCTGAA 59.415 57.895 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 1775 2.358898 GCATCATCCACTTGCCGTAAAT 59.641 45.455 0.00 0.00 0.00 1.40
84 1820 9.093458 AGAGAAAAATATTCTGTTTGGTGGATT 57.907 29.630 0.00 0.00 0.00 3.01
96 1832 6.037098 CACGTCGAGGAGAGAAAAATATTCT 58.963 40.000 12.85 0.00 0.00 2.40
101 1837 3.936372 TCACGTCGAGGAGAGAAAAAT 57.064 42.857 12.85 0.00 0.00 1.82
102 1838 3.936372 ATCACGTCGAGGAGAGAAAAA 57.064 42.857 12.85 0.00 0.00 1.94
231 1968 9.737427 CTCGTATGTAGTTCATAGTGAAATCTT 57.263 33.333 0.00 0.00 38.22 2.40
232 1969 7.863375 GCTCGTATGTAGTTCATAGTGAAATCT 59.137 37.037 0.00 0.00 38.22 2.40
233 1970 7.648112 TGCTCGTATGTAGTTCATAGTGAAATC 59.352 37.037 0.00 0.00 38.22 2.17
234 1971 7.489160 TGCTCGTATGTAGTTCATAGTGAAAT 58.511 34.615 0.00 0.00 38.22 2.17
235 1972 6.859017 TGCTCGTATGTAGTTCATAGTGAAA 58.141 36.000 0.00 0.00 38.22 2.69
236 1973 6.445357 TGCTCGTATGTAGTTCATAGTGAA 57.555 37.500 0.00 0.00 39.36 3.18
237 1974 6.445357 TTGCTCGTATGTAGTTCATAGTGA 57.555 37.500 0.00 0.00 39.36 3.41
238 1975 7.520119 TTTTGCTCGTATGTAGTTCATAGTG 57.480 36.000 0.00 0.00 39.36 2.74
239 1976 7.979537 TCATTTTGCTCGTATGTAGTTCATAGT 59.020 33.333 0.00 0.00 39.36 2.12
240 1977 8.352752 TCATTTTGCTCGTATGTAGTTCATAG 57.647 34.615 0.00 0.00 39.36 2.23
241 1978 7.979537 ACTCATTTTGCTCGTATGTAGTTCATA 59.020 33.333 0.00 0.00 37.91 2.15
242 1979 6.818644 ACTCATTTTGCTCGTATGTAGTTCAT 59.181 34.615 0.00 0.00 40.25 2.57
243 1980 6.090763 CACTCATTTTGCTCGTATGTAGTTCA 59.909 38.462 0.00 0.00 0.00 3.18
244 1981 6.310467 TCACTCATTTTGCTCGTATGTAGTTC 59.690 38.462 0.00 0.00 0.00 3.01
245 1982 6.163476 TCACTCATTTTGCTCGTATGTAGTT 58.837 36.000 0.00 0.00 0.00 2.24
246 1983 5.720202 TCACTCATTTTGCTCGTATGTAGT 58.280 37.500 0.00 0.00 0.00 2.73
247 1984 6.647212 TTCACTCATTTTGCTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
248 1985 7.041721 AGATTCACTCATTTTGCTCGTATGTA 58.958 34.615 0.00 0.00 0.00 2.29
249 1986 5.877012 AGATTCACTCATTTTGCTCGTATGT 59.123 36.000 0.00 0.00 0.00 2.29
250 1987 6.355397 AGATTCACTCATTTTGCTCGTATG 57.645 37.500 0.00 0.00 0.00 2.39
251 1988 7.041721 TGTAGATTCACTCATTTTGCTCGTAT 58.958 34.615 0.00 0.00 0.00 3.06
252 1989 6.394809 TGTAGATTCACTCATTTTGCTCGTA 58.605 36.000 0.00 0.00 0.00 3.43
253 1990 5.237815 TGTAGATTCACTCATTTTGCTCGT 58.762 37.500 0.00 0.00 0.00 4.18
254 1991 5.784750 TGTAGATTCACTCATTTTGCTCG 57.215 39.130 0.00 0.00 0.00 5.03
255 1992 5.970023 GCATGTAGATTCACTCATTTTGCTC 59.030 40.000 0.00 0.00 0.00 4.26
256 1993 5.416639 TGCATGTAGATTCACTCATTTTGCT 59.583 36.000 0.00 0.00 0.00 3.91
257 1994 5.643664 TGCATGTAGATTCACTCATTTTGC 58.356 37.500 0.00 0.00 0.00 3.68
258 1995 7.704271 AGATGCATGTAGATTCACTCATTTTG 58.296 34.615 2.46 0.00 0.00 2.44
259 1996 7.876936 AGATGCATGTAGATTCACTCATTTT 57.123 32.000 2.46 0.00 0.00 1.82
274 2011 9.813446 CACATACAGATGTATATAGATGCATGT 57.187 33.333 2.46 1.37 44.82 3.21
275 2012 9.257651 CCACATACAGATGTATATAGATGCATG 57.742 37.037 2.46 0.00 44.82 4.06
276 2013 8.985922 ACCACATACAGATGTATATAGATGCAT 58.014 33.333 0.00 0.00 44.82 3.96
277 2014 8.366359 ACCACATACAGATGTATATAGATGCA 57.634 34.615 5.21 0.00 44.82 3.96
278 2015 7.923344 GGACCACATACAGATGTATATAGATGC 59.077 40.741 5.21 0.00 44.82 3.91
279 2016 8.971073 TGGACCACATACAGATGTATATAGATG 58.029 37.037 5.21 0.00 44.82 2.90
280 2017 9.720874 ATGGACCACATACAGATGTATATAGAT 57.279 33.333 0.00 0.00 44.82 1.98
283 2020 9.990868 ACTATGGACCACATACAGATGTATATA 57.009 33.333 0.00 0.00 44.82 0.86
284 2021 8.753133 CACTATGGACCACATACAGATGTATAT 58.247 37.037 0.00 0.00 44.82 0.86
285 2022 7.947890 TCACTATGGACCACATACAGATGTATA 59.052 37.037 0.00 0.00 44.82 1.47
286 2023 6.782494 TCACTATGGACCACATACAGATGTAT 59.218 38.462 0.00 0.00 44.82 2.29
287 2024 6.133356 TCACTATGGACCACATACAGATGTA 58.867 40.000 0.00 0.00 44.82 2.29
289 2026 5.535753 TCACTATGGACCACATACAGATG 57.464 43.478 0.00 0.00 41.03 2.90
290 2027 6.560003 TTTCACTATGGACCACATACAGAT 57.440 37.500 0.00 0.00 41.03 2.90
291 2028 6.384015 AGATTTCACTATGGACCACATACAGA 59.616 38.462 0.00 0.00 41.03 3.41
292 2029 6.586344 AGATTTCACTATGGACCACATACAG 58.414 40.000 0.00 0.00 41.03 2.74
293 2030 6.384015 AGAGATTTCACTATGGACCACATACA 59.616 38.462 0.00 0.00 41.03 2.29
294 2031 6.821388 AGAGATTTCACTATGGACCACATAC 58.179 40.000 0.00 0.00 41.03 2.39
295 2032 8.727100 ATAGAGATTTCACTATGGACCACATA 57.273 34.615 0.00 0.00 41.03 2.29
296 2033 5.965033 AGAGATTTCACTATGGACCACAT 57.035 39.130 0.00 0.00 43.68 3.21
297 2034 8.547481 TTATAGAGATTTCACTATGGACCACA 57.453 34.615 0.00 0.00 33.08 4.17
298 2035 9.482627 CTTTATAGAGATTTCACTATGGACCAC 57.517 37.037 0.00 0.00 33.08 4.16
299 2036 8.651389 CCTTTATAGAGATTTCACTATGGACCA 58.349 37.037 0.00 0.00 33.08 4.02
300 2037 7.604545 GCCTTTATAGAGATTTCACTATGGACC 59.395 40.741 7.52 0.00 33.08 4.46
301 2038 8.371699 AGCCTTTATAGAGATTTCACTATGGAC 58.628 37.037 7.52 0.31 33.08 4.02
302 2039 8.497910 AGCCTTTATAGAGATTTCACTATGGA 57.502 34.615 7.52 0.00 33.08 3.41
320 2057 9.333724 CCTTCGTTCCTAAATAATAAGCCTTTA 57.666 33.333 0.00 0.00 0.00 1.85
321 2058 7.284716 CCCTTCGTTCCTAAATAATAAGCCTTT 59.715 37.037 0.00 0.00 0.00 3.11
322 2059 6.771267 CCCTTCGTTCCTAAATAATAAGCCTT 59.229 38.462 0.00 0.00 0.00 4.35
323 2060 6.100714 TCCCTTCGTTCCTAAATAATAAGCCT 59.899 38.462 0.00 0.00 0.00 4.58
324 2061 6.293698 TCCCTTCGTTCCTAAATAATAAGCC 58.706 40.000 0.00 0.00 0.00 4.35
325 2062 6.990939 ACTCCCTTCGTTCCTAAATAATAAGC 59.009 38.462 0.00 0.00 0.00 3.09
326 2063 9.694137 CTACTCCCTTCGTTCCTAAATAATAAG 57.306 37.037 0.00 0.00 0.00 1.73
327 2064 8.645110 CCTACTCCCTTCGTTCCTAAATAATAA 58.355 37.037 0.00 0.00 0.00 1.40
328 2065 7.786464 ACCTACTCCCTTCGTTCCTAAATAATA 59.214 37.037 0.00 0.00 0.00 0.98
329 2066 6.614496 ACCTACTCCCTTCGTTCCTAAATAAT 59.386 38.462 0.00 0.00 0.00 1.28
330 2067 5.960202 ACCTACTCCCTTCGTTCCTAAATAA 59.040 40.000 0.00 0.00 0.00 1.40
331 2068 5.522641 ACCTACTCCCTTCGTTCCTAAATA 58.477 41.667 0.00 0.00 0.00 1.40
332 2069 4.359996 ACCTACTCCCTTCGTTCCTAAAT 58.640 43.478 0.00 0.00 0.00 1.40
333 2070 3.782992 ACCTACTCCCTTCGTTCCTAAA 58.217 45.455 0.00 0.00 0.00 1.85
334 2071 3.463048 ACCTACTCCCTTCGTTCCTAA 57.537 47.619 0.00 0.00 0.00 2.69
335 2072 3.094572 CAACCTACTCCCTTCGTTCCTA 58.905 50.000 0.00 0.00 0.00 2.94
336 2073 1.900486 CAACCTACTCCCTTCGTTCCT 59.100 52.381 0.00 0.00 0.00 3.36
337 2074 1.066358 CCAACCTACTCCCTTCGTTCC 60.066 57.143 0.00 0.00 0.00 3.62
338 2075 1.897802 TCCAACCTACTCCCTTCGTTC 59.102 52.381 0.00 0.00 0.00 3.95
339 2076 2.019807 TCCAACCTACTCCCTTCGTT 57.980 50.000 0.00 0.00 0.00 3.85
340 2077 1.622312 GTTCCAACCTACTCCCTTCGT 59.378 52.381 0.00 0.00 0.00 3.85
341 2078 1.900486 AGTTCCAACCTACTCCCTTCG 59.100 52.381 0.00 0.00 0.00 3.79
342 2079 5.695424 ATAAGTTCCAACCTACTCCCTTC 57.305 43.478 0.00 0.00 0.00 3.46
343 2080 6.464530 AAATAAGTTCCAACCTACTCCCTT 57.535 37.500 0.00 0.00 0.00 3.95
344 2081 6.464530 AAAATAAGTTCCAACCTACTCCCT 57.535 37.500 0.00 0.00 0.00 4.20
388 2129 2.851263 TGCCGTAAACAGGAGTGAAT 57.149 45.000 0.00 0.00 0.00 2.57
391 2132 1.531149 CACTTGCCGTAAACAGGAGTG 59.469 52.381 0.00 0.00 30.63 3.51
423 2164 3.425713 ATGCACGTTGCCTCTGCG 61.426 61.111 7.38 0.00 44.23 5.18
451 2192 5.184479 TCGAGGAGAGAAAAAGATTCCGTTA 59.816 40.000 0.00 0.00 33.16 3.18
571 2320 5.389830 CGGAAGCGCGTAGTACTATATTGTA 60.390 44.000 8.43 0.00 0.00 2.41
572 2321 4.612259 CGGAAGCGCGTAGTACTATATTGT 60.612 45.833 8.43 0.00 0.00 2.71
574 2323 3.499918 ACGGAAGCGCGTAGTACTATATT 59.500 43.478 8.43 0.00 0.00 1.28
575 2324 3.070018 ACGGAAGCGCGTAGTACTATAT 58.930 45.455 8.43 0.00 0.00 0.86
655 2483 3.916061 GCAAGTTCGTGCACTTTCA 57.084 47.368 16.19 0.00 44.29 2.69
720 2555 6.603237 TGATTCCATTTTCAGTATACAGCG 57.397 37.500 5.50 0.00 0.00 5.18
796 2701 3.682858 TCCGACTTGCATACTTAGTTTGC 59.317 43.478 18.39 18.39 40.05 3.68
801 2706 3.804325 CCACATCCGACTTGCATACTTAG 59.196 47.826 0.00 0.00 0.00 2.18
806 2711 0.541392 AGCCACATCCGACTTGCATA 59.459 50.000 0.00 0.00 0.00 3.14
815 2721 1.813753 CGGTTGGTAGCCACATCCG 60.814 63.158 7.65 7.65 36.68 4.18
848 2754 2.092267 TGGCCGGTATATATAGAGCCGA 60.092 50.000 17.50 8.02 44.57 5.54
884 2791 2.035961 TGAGCTGTGTACTGGTGAGAAC 59.964 50.000 0.00 0.00 0.00 3.01
885 2792 2.297315 CTGAGCTGTGTACTGGTGAGAA 59.703 50.000 0.00 0.00 30.74 2.87
886 2793 1.889170 CTGAGCTGTGTACTGGTGAGA 59.111 52.381 0.00 0.00 30.74 3.27
887 2794 1.615883 ACTGAGCTGTGTACTGGTGAG 59.384 52.381 0.00 6.15 34.08 3.51
888 2795 1.704641 ACTGAGCTGTGTACTGGTGA 58.295 50.000 0.00 0.00 0.00 4.02
889 2796 2.533266 AACTGAGCTGTGTACTGGTG 57.467 50.000 0.00 0.00 0.00 4.17
890 2797 2.485479 CCAAACTGAGCTGTGTACTGGT 60.485 50.000 0.00 0.00 0.00 4.00
972 2906 5.241506 TCAATCTGCAGAAATTTTCCGAACT 59.758 36.000 22.50 0.00 0.00 3.01
973 2907 5.460646 TCAATCTGCAGAAATTTTCCGAAC 58.539 37.500 22.50 0.00 0.00 3.95
974 2908 5.473162 TCTCAATCTGCAGAAATTTTCCGAA 59.527 36.000 22.50 0.00 0.00 4.30
1068 3002 4.652131 ATGAAACCACCGGCGCCA 62.652 61.111 28.98 2.90 0.00 5.69
1113 3047 2.036890 ACGGCGTACCCCTTCTCT 59.963 61.111 12.58 0.00 0.00 3.10
1177 3117 3.705043 CAGGCATGGAGATTAGCAAAC 57.295 47.619 0.00 0.00 0.00 2.93
1200 3142 3.814842 TCACACACCAAAGTTAGATGCAG 59.185 43.478 0.00 0.00 0.00 4.41
1215 3159 2.413112 CACGTCATCTGGAATCACACAC 59.587 50.000 0.00 0.00 0.00 3.82
1350 3375 1.166531 GGCATGCGGTATGGAAGACC 61.167 60.000 12.44 0.00 37.26 3.85
1353 3378 1.898574 GGGGCATGCGGTATGGAAG 60.899 63.158 12.44 0.00 37.26 3.46
1380 3405 2.159240 GGGTAAGTAAAGTACCGGGTCG 60.159 54.545 6.32 0.00 41.78 4.79
1413 3452 2.229543 ACATTCGGTGTCAGTAGCGTAA 59.770 45.455 0.00 0.00 41.82 3.18
1427 3466 1.337728 TGTCAGCCACTGTACATTCGG 60.338 52.381 0.00 0.00 32.61 4.30
1437 3476 2.664402 ATGAACCTTTGTCAGCCACT 57.336 45.000 0.00 0.00 0.00 4.00
1617 3656 0.317160 TCGCTCCAACATGTCTCGTT 59.683 50.000 0.00 0.00 0.00 3.85
1653 3692 7.203255 AGTTAATTAAGCTGACCTTTGTGTC 57.797 36.000 0.00 0.00 34.95 3.67
1689 3728 7.604164 AGCATGTATATGGTGCTTCTAACATAC 59.396 37.037 3.12 0.00 46.29 2.39
1690 3729 7.679783 AGCATGTATATGGTGCTTCTAACATA 58.320 34.615 3.12 0.00 46.29 2.29
1741 3786 5.987953 TCTGCATATGCTTACTTGTCAGATC 59.012 40.000 27.13 0.00 42.66 2.75
1869 3914 2.701780 CGCCGACTGTAGCAGAGGT 61.702 63.158 2.91 0.00 36.11 3.85
2010 4055 1.164041 GGCCATGCGCGTTAGGTATT 61.164 55.000 8.43 0.00 38.94 1.89
2017 4062 3.269347 GTATCGGCCATGCGCGTT 61.269 61.111 8.43 0.00 38.94 4.84
2073 4118 0.460311 AGAACTTGGCGAGGATACGG 59.540 55.000 6.71 0.00 46.39 4.02
2163 4208 1.188219 GCTCCATGATCCTCCGGCTA 61.188 60.000 0.00 0.00 0.00 3.93
2232 4277 1.377856 GCCCTTGTCCTGAAGGCTC 60.378 63.158 0.00 0.00 41.24 4.70
2270 4315 5.430886 CATGGAGTTGTCAGGACATATCAA 58.569 41.667 2.52 0.00 41.52 2.57
2316 4361 3.136123 CTTGGGGGCACGCATCTG 61.136 66.667 6.52 0.00 45.96 2.90
2363 4419 9.703892 TCACTTAAATTAATGGGTGAACAAATG 57.296 29.630 4.50 0.00 31.99 2.32
2456 4515 4.537135 TCTCGCCAAAGACTCATAAGTT 57.463 40.909 0.00 0.00 35.28 2.66
2461 4520 1.065926 TGCATCTCGCCAAAGACTCAT 60.066 47.619 0.00 0.00 41.33 2.90
2591 4717 1.737696 CGATGCCAGCTTACCGTTGTA 60.738 52.381 0.00 0.00 0.00 2.41
2596 4722 2.202932 AGCGATGCCAGCTTACCG 60.203 61.111 0.00 0.00 43.24 4.02
2783 7692 6.762661 GCTAGGTGGTTTACGGATGTAATTTA 59.237 38.462 0.00 0.00 40.14 1.40
2874 8611 7.157004 TGTCTACTACAACAAGGTTTGCCCT 62.157 44.000 0.00 0.00 39.57 5.19
2955 8692 0.607217 TCTACACTCTTCACCGGCGA 60.607 55.000 9.30 0.00 0.00 5.54
2961 8698 5.906113 TCCTTCTGATCTACACTCTTCAC 57.094 43.478 0.00 0.00 0.00 3.18
3025 8764 5.917462 TCTATCTTTGATGGATTTGCTCGA 58.083 37.500 0.00 0.00 0.00 4.04
3038 8777 1.613925 CTCCGGCGGATCTATCTTTGA 59.386 52.381 31.23 1.63 0.00 2.69
3169 8910 7.255001 CGAGTTTTGTTAGGTTTTGTGTCCTAT 60.255 37.037 0.00 0.00 36.39 2.57


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

AutoCloner maintained by Alex Coulton.