Multiple sequence alignment - TraesCS4A01G312800

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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 TraesCS4A01G312800 chr4A 100.000 5115 0 0 1 5115 603673525 603678639 0.000000e+00 9446.0
1 TraesCS4A01G312800 chr4A 100.000 4008 0 0 5337 9344 603678861 603682868 0.000000e+00 7402.0
2 TraesCS4A01G312800 chr4A 100.000 44 0 0 5580 5623 603679060 603679103 2.160000e-11 82.4
3 TraesCS4A01G312800 chr4A 100.000 44 0 0 5536 5579 603679104 603679147 2.160000e-11 82.4
4 TraesCS4A01G312800 chr5D 94.446 5221 126 40 1 5113 560494880 560500044 0.000000e+00 7884.0
5 TraesCS4A01G312800 chr5D 97.673 3782 67 10 5580 9344 560500540 560504317 0.000000e+00 6477.0
6 TraesCS4A01G312800 chr5D 84.816 2641 349 35 5640 8255 560534868 560532255 0.000000e+00 2608.0
7 TraesCS4A01G312800 chr5D 86.030 1539 176 20 1910 3443 555433595 555432091 0.000000e+00 1615.0
8 TraesCS4A01G312800 chr5D 88.684 1246 126 8 1910 3154 561950530 561951761 0.000000e+00 1506.0
9 TraesCS4A01G312800 chr5D 98.565 209 3 0 5371 5579 560500375 560500583 4.120000e-98 370.0
10 TraesCS4A01G312800 chr5D 84.274 248 39 0 1079 1326 560538944 560538697 9.370000e-60 243.0
11 TraesCS4A01G312800 chr5D 93.007 143 8 1 4651 4793 560484619 560484759 3.420000e-49 207.0
12 TraesCS4A01G312800 chr5D 80.978 184 30 4 1064 1246 560512569 560512748 3.520000e-29 141.0
13 TraesCS4A01G312800 chr5D 87.356 87 9 2 8799 8884 561667871 561667786 2.150000e-16 99.0
14 TraesCS4A01G312800 chr5D 97.619 42 1 0 753 794 560494971 560495012 1.300000e-08 73.1
15 TraesCS4A01G312800 chr5B 97.158 2850 75 3 5617 8461 711183965 711181117 0.000000e+00 4809.0
16 TraesCS4A01G312800 chr5B 95.972 2110 72 6 1888 3989 711187317 711185213 0.000000e+00 3413.0
17 TraesCS4A01G312800 chr5B 89.583 2592 265 5 5774 8363 711133838 711131250 0.000000e+00 3286.0
18 TraesCS4A01G312800 chr5B 89.045 2355 252 6 5753 8105 711240860 711238510 0.000000e+00 2915.0
19 TraesCS4A01G312800 chr5B 87.237 2476 314 2 5762 8236 695482687 695485161 0.000000e+00 2820.0
20 TraesCS4A01G312800 chr5B 87.008 2463 320 0 5762 8224 695787470 695789932 0.000000e+00 2776.0
21 TraesCS4A01G312800 chr5B 87.990 1532 153 20 1921 3443 711136910 711135401 0.000000e+00 1781.0
22 TraesCS4A01G312800 chr5B 94.401 1143 38 9 3975 5111 711185141 711184019 0.000000e+00 1733.0
23 TraesCS4A01G312800 chr5B 91.361 1308 49 25 488 1745 711188627 711187334 0.000000e+00 1731.0
24 TraesCS4A01G312800 chr5B 86.050 1534 178 21 1910 3440 695480934 695482434 0.000000e+00 1615.0
25 TraesCS4A01G312800 chr5B 89.196 1268 125 5 1909 3176 711941255 711942510 0.000000e+00 1572.0
26 TraesCS4A01G312800 chr5B 88.043 1313 140 9 1910 3221 695785687 695786983 0.000000e+00 1539.0
27 TraesCS4A01G312800 chr5B 94.521 803 34 7 8490 9286 711181119 711180321 0.000000e+00 1230.0
28 TraesCS4A01G312800 chr5B 94.545 330 17 1 8053 8382 711148353 711148025 8.370000e-140 508.0
29 TraesCS4A01G312800 chr5B 85.287 401 23 5 8784 9159 711130779 711130390 1.900000e-101 381.0
30 TraesCS4A01G312800 chr5B 86.752 234 28 1 1091 1324 710965272 710965042 3.350000e-64 257.0
31 TraesCS4A01G312800 chr5B 84.064 251 34 5 1094 1342 711244840 711244594 4.360000e-58 237.0
32 TraesCS4A01G312800 chr5B 88.272 162 17 2 5366 5527 711134248 711134089 9.580000e-45 193.0
33 TraesCS4A01G312800 chr5B 77.003 287 36 14 652 923 711138486 711138215 4.550000e-28 137.0
34 TraesCS4A01G312800 chr5B 82.895 152 23 2 740 890 711245515 711245366 5.890000e-27 134.0
35 TraesCS4A01G312800 chr5B 84.496 129 11 6 8623 8748 711130985 711130863 1.650000e-22 119.0
36 TraesCS4A01G312800 chr5B 80.833 120 16 7 8671 8786 643324461 643324345 4.650000e-13 87.9
37 TraesCS4A01G312800 chr5B 87.324 71 8 1 8309 8379 711247398 711247329 7.780000e-11 80.5
38 TraesCS4A01G312800 chr5B 91.071 56 3 1 412 467 711188786 711188733 3.620000e-09 75.0
39 TraesCS4A01G312800 chr5B 95.556 45 2 0 753 797 711189142 711189098 1.300000e-08 73.1
40 TraesCS4A01G312800 chr5B 80.899 89 17 0 8901 8989 710959134 710959046 4.680000e-08 71.3
41 TraesCS4A01G312800 chr5B 92.857 42 3 0 8696 8737 643324229 643324188 2.820000e-05 62.1
42 TraesCS4A01G312800 chr5B 100.000 28 0 0 466 493 711188719 711188692 1.700000e-02 52.8
43 TraesCS4A01G312800 chr7B 87.316 2586 324 4 5755 8338 1323006 1325589 0.000000e+00 2955.0
44 TraesCS4A01G312800 chr7B 87.264 1484 167 13 1966 3443 1313736 1315203 0.000000e+00 1674.0
45 TraesCS4A01G312800 chr7B 82.056 496 66 17 3541 4031 1315364 1315841 1.460000e-107 401.0
46 TraesCS4A01G312800 chr7B 79.143 350 41 18 8596 8928 1028388 1028054 7.350000e-51 213.0
47 TraesCS4A01G312800 chr7B 82.051 234 28 9 1091 1324 1093833 1093614 4.460000e-43 187.0
48 TraesCS4A01G312800 chr7B 85.047 107 10 5 8802 8904 826468 826364 4.620000e-18 104.0
49 TraesCS4A01G312800 chr7A 84.816 2878 377 44 5368 8226 688997821 688994985 0.000000e+00 2839.0
50 TraesCS4A01G312800 chr7A 87.407 1485 155 21 1957 3433 689000047 688998587 0.000000e+00 1677.0
51 TraesCS4A01G312800 chr7A 83.853 353 55 2 7987 8338 688995080 688994729 1.500000e-87 335.0


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 TraesCS4A01G312800 chr4A 603673525 603682868 9343 False 4253.200000 9446 100.000000 1 9344 4 chr4A.!!$F1 9343
1 TraesCS4A01G312800 chr5D 560494880 560500044 5164 False 7884.000000 7884 94.446000 1 5113 1 chr5D.!!$F2 5112
2 TraesCS4A01G312800 chr5D 560500375 560504317 3942 False 3423.500000 6477 98.119000 5371 9344 2 chr5D.!!$F6 3973
3 TraesCS4A01G312800 chr5D 555432091 555433595 1504 True 1615.000000 1615 86.030000 1910 3443 1 chr5D.!!$R1 1533
4 TraesCS4A01G312800 chr5D 561950530 561951761 1231 False 1506.000000 1506 88.684000 1910 3154 1 chr5D.!!$F5 1244
5 TraesCS4A01G312800 chr5D 560532255 560538944 6689 True 1425.500000 2608 84.545000 1079 8255 2 chr5D.!!$R3 7176
6 TraesCS4A01G312800 chr5B 695480934 695485161 4227 False 2217.500000 2820 86.643500 1910 8236 2 chr5B.!!$F2 6326
7 TraesCS4A01G312800 chr5B 695785687 695789932 4245 False 2157.500000 2776 87.525500 1910 8224 2 chr5B.!!$F3 6314
8 TraesCS4A01G312800 chr5B 711180321 711189142 8821 True 1639.612500 4809 95.005000 412 9286 8 chr5B.!!$R6 8874
9 TraesCS4A01G312800 chr5B 711941255 711942510 1255 False 1572.000000 1572 89.196000 1909 3176 1 chr5B.!!$F1 1267
10 TraesCS4A01G312800 chr5B 711130390 711138486 8096 True 982.833333 3286 85.438500 652 9159 6 chr5B.!!$R5 8507
11 TraesCS4A01G312800 chr5B 711238510 711247398 8888 True 841.625000 2915 85.832000 740 8379 4 chr5B.!!$R7 7639
12 TraesCS4A01G312800 chr7B 1323006 1325589 2583 False 2955.000000 2955 87.316000 5755 8338 1 chr7B.!!$F1 2583
13 TraesCS4A01G312800 chr7B 1313736 1315841 2105 False 1037.500000 1674 84.660000 1966 4031 2 chr7B.!!$F2 2065
14 TraesCS4A01G312800 chr7A 688994729 689000047 5318 True 1617.000000 2839 85.358667 1957 8338 3 chr7A.!!$R1 6381

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
224 252 0.312729 TGCTCACACAATGCAGCTTG 59.687 50.000 0.00 0.0 34.45 4.01 F
237 265 0.319405 CAGCTTGCCCCAAGAAAAGG 59.681 55.000 9.01 0.0 43.42 3.11 F
1682 3670 0.181350 AGGGATCCATTCTGCGTTCC 59.819 55.000 15.23 0.0 0.00 3.62 F
1897 3889 0.391661 TGCGTCCTTCTCAATCAGCC 60.392 55.000 0.00 0.0 0.00 4.85 F
2594 4598 2.207590 GGCAGCCGTGTTATAGTAACC 58.792 52.381 0.00 0.0 0.00 2.85 F
4262 6937 1.226974 CGCCACGACACAGGGATAG 60.227 63.158 0.00 0.0 0.00 2.08 F
5113 7827 0.441533 GAGCAGTGTGAATGTGAGCG 59.558 55.000 0.00 0.0 0.00 5.03 F
5594 10386 2.584835 AGCCTTCCTTGTATGCAACA 57.415 45.000 0.00 0.0 35.88 3.33 F
5595 10387 3.091633 AGCCTTCCTTGTATGCAACAT 57.908 42.857 0.00 0.0 38.10 2.71 F
7329 12170 1.279496 AATCAGTGCTGGACAGGCTA 58.721 50.000 1.24 0.0 0.00 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1466 3298 1.450312 CCGCTGTGGAGGGATTGAC 60.450 63.158 0.00 0.0 42.00 3.18 R
2158 4150 1.702182 TCCAGTTTTCATGCCAGCAA 58.298 45.000 0.00 0.0 0.00 3.91 R
2624 4628 0.814457 TTGCAAGAAAACCAGTGCGT 59.186 45.000 0.00 0.0 39.92 5.24 R
2882 4887 2.104170 TCCAAAACAACCTTGGTGTCC 58.896 47.619 1.76 0.0 43.33 4.02 R
4323 6998 0.319900 ACACTAGAACGCTGGCACTG 60.320 55.000 0.00 0.0 0.00 3.66 R
5936 10777 2.483876 CATGCCGGTAGTAATGAGGTG 58.516 52.381 1.90 0.0 0.00 4.00 R
6296 11137 1.198178 GTTTGCCGAGGCGACAAATAA 59.802 47.619 9.78 0.0 40.69 1.40 R
6856 11697 2.216898 GCATACTGACTCAGGCAATCC 58.783 52.381 10.86 0.0 35.51 3.01 R
7365 12206 2.550830 AATCCTTGCTGCTATACCCG 57.449 50.000 0.00 0.0 0.00 5.28 R
8861 13979 1.361668 AACAGCGATGTAAGCCTGCG 61.362 55.000 6.79 0.0 34.64 5.18 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
54 55 6.370994 GCACTTTATGTATCTCATCTCATGGG 59.629 42.308 0.00 0.00 37.91 4.00
58 59 3.580039 TGTATCTCATCTCATGGGCAGA 58.420 45.455 0.00 0.00 0.00 4.26
80 86 7.363431 CAGACACGCATAGATAGAATGTCTTA 58.637 38.462 1.36 0.00 41.87 2.10
91 97 4.828072 AGAATGTCTTAGGAGTTGGACC 57.172 45.455 0.00 0.00 0.00 4.46
150 178 8.961294 TCAATATTTTAATTTGAATGCCCTGG 57.039 30.769 0.00 0.00 0.00 4.45
153 181 1.494960 TAATTTGAATGCCCTGGCCC 58.505 50.000 5.57 0.00 41.09 5.80
166 194 1.202794 CCTGGCCCAAGCAAACAAAAT 60.203 47.619 0.00 0.00 42.56 1.82
198 226 4.543590 TCATTGTCTCTCTCTTCAACCC 57.456 45.455 0.00 0.00 0.00 4.11
199 227 3.903714 TCATTGTCTCTCTCTTCAACCCA 59.096 43.478 0.00 0.00 0.00 4.51
200 228 4.347876 TCATTGTCTCTCTCTTCAACCCAA 59.652 41.667 0.00 0.00 0.00 4.12
221 249 1.068125 TCAATGCTCACACAATGCAGC 60.068 47.619 0.00 0.00 40.18 5.25
224 252 0.312729 TGCTCACACAATGCAGCTTG 59.687 50.000 0.00 0.00 34.45 4.01
225 253 1.007336 GCTCACACAATGCAGCTTGC 61.007 55.000 0.00 1.70 45.29 4.01
226 254 0.388134 CTCACACAATGCAGCTTGCC 60.388 55.000 0.00 0.00 44.23 4.52
227 255 1.373748 CACACAATGCAGCTTGCCC 60.374 57.895 0.00 0.00 44.23 5.36
228 256 2.263540 CACAATGCAGCTTGCCCC 59.736 61.111 0.00 0.00 44.23 5.80
230 258 1.837947 ACAATGCAGCTTGCCCCAA 60.838 52.632 0.00 0.00 44.23 4.12
233 261 0.832983 AATGCAGCTTGCCCCAAGAA 60.833 50.000 9.01 0.00 44.23 2.52
234 262 0.832983 ATGCAGCTTGCCCCAAGAAA 60.833 50.000 9.01 0.00 44.23 2.52
236 264 0.320160 GCAGCTTGCCCCAAGAAAAG 60.320 55.000 9.01 0.00 43.42 2.27
237 265 0.319405 CAGCTTGCCCCAAGAAAAGG 59.681 55.000 9.01 0.00 43.42 3.11
241 269 2.528564 CTTGCCCCAAGAAAAGGATCA 58.471 47.619 0.00 0.00 43.42 2.92
242 270 2.692709 TGCCCCAAGAAAAGGATCAA 57.307 45.000 0.00 0.00 0.00 2.57
245 273 4.682563 TGCCCCAAGAAAAGGATCAATTA 58.317 39.130 0.00 0.00 0.00 1.40
256 284 5.936686 AAGGATCAATTATCATGTGCTCG 57.063 39.130 0.00 0.00 36.20 5.03
288 316 3.492102 AACTCTTGCCTCTGCTGTTAA 57.508 42.857 0.00 0.00 38.71 2.01
340 368 0.908656 ATCTGCAGCAGGAGGTGACT 60.909 55.000 22.62 0.00 45.95 3.41
355 383 4.470602 AGGTGACTTTTTAAAGGGTCTGG 58.529 43.478 17.41 0.00 40.31 3.86
356 384 3.572682 GGTGACTTTTTAAAGGGTCTGGG 59.427 47.826 17.41 0.00 40.31 4.45
357 385 4.466827 GTGACTTTTTAAAGGGTCTGGGA 58.533 43.478 17.41 2.34 40.31 4.37
359 387 4.891168 TGACTTTTTAAAGGGTCTGGGAAC 59.109 41.667 17.41 0.00 40.31 3.62
360 388 3.887110 ACTTTTTAAAGGGTCTGGGAACG 59.113 43.478 7.12 0.00 40.31 3.95
361 389 3.860968 TTTTAAAGGGTCTGGGAACGA 57.139 42.857 0.00 0.00 0.00 3.85
362 390 3.412237 TTTAAAGGGTCTGGGAACGAG 57.588 47.619 0.00 0.00 0.00 4.18
371 399 4.058817 GGTCTGGGAACGAGCATATTTAG 58.941 47.826 0.00 0.00 33.61 1.85
446 474 6.180472 TCTGAATATGTCCCCTTGAAACTTC 58.820 40.000 0.00 0.00 0.00 3.01
452 480 2.879026 GTCCCCTTGAAACTTCAGTCAC 59.121 50.000 0.00 0.00 38.61 3.67
453 481 2.507886 TCCCCTTGAAACTTCAGTCACA 59.492 45.455 0.00 0.00 38.61 3.58
454 482 3.138283 TCCCCTTGAAACTTCAGTCACAT 59.862 43.478 0.00 0.00 38.61 3.21
455 483 3.503748 CCCCTTGAAACTTCAGTCACATC 59.496 47.826 0.00 0.00 38.61 3.06
456 484 3.503748 CCCTTGAAACTTCAGTCACATCC 59.496 47.826 0.00 0.00 38.61 3.51
457 485 4.392940 CCTTGAAACTTCAGTCACATCCT 58.607 43.478 0.00 0.00 38.61 3.24
458 486 4.823989 CCTTGAAACTTCAGTCACATCCTT 59.176 41.667 0.00 0.00 38.61 3.36
459 487 5.049129 CCTTGAAACTTCAGTCACATCCTTC 60.049 44.000 0.00 0.00 38.61 3.46
460 488 5.034852 TGAAACTTCAGTCACATCCTTCA 57.965 39.130 0.00 0.00 32.50 3.02
461 489 5.436175 TGAAACTTCAGTCACATCCTTCAA 58.564 37.500 0.00 0.00 32.50 2.69
462 490 5.528690 TGAAACTTCAGTCACATCCTTCAAG 59.471 40.000 0.00 0.00 32.50 3.02
601 721 3.829948 CTTCATGTTCTGCATCACCAAC 58.170 45.455 0.00 0.00 35.19 3.77
625 745 3.907894 TGAAATAAAGTGGTTCGGCAC 57.092 42.857 0.00 0.00 0.00 5.01
707 845 4.475944 GCAAGTGGCAGTTAGTTTACATG 58.524 43.478 7.35 0.00 43.97 3.21
898 2053 3.251972 GCCTCCTTGTCTCTTGTTTTGAG 59.748 47.826 0.00 0.00 0.00 3.02
1414 3246 1.001020 TGTTAGGGCTGCACCATGG 60.001 57.895 11.19 11.19 42.05 3.66
1466 3298 0.994995 CTCAACGAACGGCTGAGATG 59.005 55.000 17.39 0.00 39.15 2.90
1682 3670 0.181350 AGGGATCCATTCTGCGTTCC 59.819 55.000 15.23 0.00 0.00 3.62
1775 3767 1.806623 CGAAGGGATTGGTTAGGAGCG 60.807 57.143 0.00 0.00 0.00 5.03
1819 3811 1.218316 GCTGCCCGTAAGTGTAGCT 59.782 57.895 0.00 0.00 0.00 3.32
1897 3889 0.391661 TGCGTCCTTCTCAATCAGCC 60.392 55.000 0.00 0.00 0.00 4.85
2158 4150 4.927557 TGCAGCCAACTGGAATGT 57.072 50.000 0.00 0.00 41.85 2.71
2198 4190 2.504519 GTGGGCAGGGGTATCGAC 59.495 66.667 0.00 0.00 0.00 4.20
2594 4598 2.207590 GGCAGCCGTGTTATAGTAACC 58.792 52.381 0.00 0.00 0.00 2.85
2624 4628 2.924926 CCTACGCGTAGTGCAACAATTA 59.075 45.455 36.49 7.40 46.97 1.40
3187 5192 6.814644 CACCATTTCTCTTGTACCGTTGTATA 59.185 38.462 0.00 0.00 0.00 1.47
3705 6271 2.695359 AGCAATAAGGCTTTCGAACGA 58.305 42.857 4.45 0.00 42.71 3.85
3807 6379 1.406887 CGGGAACAAACCTGGATCGAT 60.407 52.381 0.00 0.00 33.06 3.59
4037 6712 9.937577 GCGACAAACTCATAAAATTTAATTGAC 57.062 29.630 0.00 0.00 0.00 3.18
4142 6817 1.497722 GCAAGCTTTTCCTCGTCCG 59.502 57.895 0.00 0.00 0.00 4.79
4239 6914 2.104451 CTGGATGACAGGAGAGATTGGG 59.896 54.545 0.00 0.00 43.70 4.12
4262 6937 1.226974 CGCCACGACACAGGGATAG 60.227 63.158 0.00 0.00 0.00 2.08
4269 6944 2.032620 CGACACAGGGATAGGTAGCTT 58.967 52.381 0.00 0.00 0.00 3.74
4271 6946 3.253677 CGACACAGGGATAGGTAGCTTAG 59.746 52.174 0.00 0.00 0.00 2.18
4323 6998 3.827898 CAGAGGCGAGGTCGGGAC 61.828 72.222 0.89 0.00 40.23 4.46
4324 6999 4.361971 AGAGGCGAGGTCGGGACA 62.362 66.667 0.89 0.00 40.23 4.02
4336 7011 3.050275 GGGACAGTGCCAGCGTTC 61.050 66.667 6.15 0.00 0.00 3.95
4392 7067 1.073923 GACCATGGGGAATAGCCGAAT 59.926 52.381 18.09 0.00 37.63 3.34
4400 7075 3.432378 GGGAATAGCCGAATAGGAGAGA 58.568 50.000 0.00 0.00 45.00 3.10
4416 7091 0.905337 GAGATATAGGGCGGGCCAGT 60.905 60.000 23.67 12.79 37.98 4.00
4529 7238 1.002868 GCAGCTATGCGGGGATGAT 60.003 57.895 0.00 0.00 43.87 2.45
4534 7243 0.979665 CTATGCGGGGATGATGGACT 59.020 55.000 0.00 0.00 0.00 3.85
4583 7293 4.849813 TTTAGGTTTAGTCCCTTAGGGC 57.150 45.455 13.54 8.05 43.94 5.19
4805 7515 4.217550 CGGTGTCCACATATTTCAAGGTTT 59.782 41.667 0.00 0.00 0.00 3.27
5028 7738 1.136329 AGACCCCAAGCCATGAGTGT 61.136 55.000 0.00 0.00 0.00 3.55
5036 7746 1.876849 AGCCATGAGTGTCATCTCCT 58.123 50.000 0.00 0.00 34.28 3.69
5043 7753 4.527509 TGAGTGTCATCTCCTGAAGAAC 57.472 45.455 0.00 0.00 37.61 3.01
5052 7762 4.808414 TCTCCTGAAGAACATACCACAG 57.192 45.455 0.00 0.00 0.00 3.66
5113 7827 0.441533 GAGCAGTGTGAATGTGAGCG 59.558 55.000 0.00 0.00 0.00 5.03
5364 8078 3.606662 GGAGCGGCATAGGAGCGA 61.607 66.667 1.45 0.00 35.78 4.93
5570 10362 5.350504 ACATATGCTCTACTTGCTCTGTT 57.649 39.130 1.58 0.00 0.00 3.16
5571 10363 6.471233 ACATATGCTCTACTTGCTCTGTTA 57.529 37.500 1.58 0.00 0.00 2.41
5573 10365 6.097554 ACATATGCTCTACTTGCTCTGTTAGT 59.902 38.462 1.58 0.00 0.00 2.24
5575 10367 5.977489 TGCTCTACTTGCTCTGTTAGTTA 57.023 39.130 0.00 0.00 0.00 2.24
5576 10368 5.955488 TGCTCTACTTGCTCTGTTAGTTAG 58.045 41.667 0.00 0.00 0.00 2.34
5577 10369 4.801516 GCTCTACTTGCTCTGTTAGTTAGC 59.198 45.833 0.00 0.00 36.77 3.09
5578 10370 5.326200 TCTACTTGCTCTGTTAGTTAGCC 57.674 43.478 0.00 0.00 35.33 3.93
5580 10372 4.625607 ACTTGCTCTGTTAGTTAGCCTT 57.374 40.909 0.00 0.00 35.33 4.35
5581 10373 4.570930 ACTTGCTCTGTTAGTTAGCCTTC 58.429 43.478 0.00 0.00 35.33 3.46
5582 10374 3.611766 TGCTCTGTTAGTTAGCCTTCC 57.388 47.619 0.00 0.00 35.33 3.46
5583 10375 3.173965 TGCTCTGTTAGTTAGCCTTCCT 58.826 45.455 0.00 0.00 35.33 3.36
5584 10376 3.583086 TGCTCTGTTAGTTAGCCTTCCTT 59.417 43.478 0.00 0.00 35.33 3.36
5585 10377 3.935828 GCTCTGTTAGTTAGCCTTCCTTG 59.064 47.826 0.00 0.00 0.00 3.61
5586 10378 4.563786 GCTCTGTTAGTTAGCCTTCCTTGT 60.564 45.833 0.00 0.00 0.00 3.16
5587 10379 5.337330 GCTCTGTTAGTTAGCCTTCCTTGTA 60.337 44.000 0.00 0.00 0.00 2.41
5588 10380 6.630638 GCTCTGTTAGTTAGCCTTCCTTGTAT 60.631 42.308 0.00 0.00 0.00 2.29
5589 10381 6.640518 TCTGTTAGTTAGCCTTCCTTGTATG 58.359 40.000 0.00 0.00 0.00 2.39
5590 10382 5.183228 TGTTAGTTAGCCTTCCTTGTATGC 58.817 41.667 0.00 0.00 0.00 3.14
5591 10383 5.183228 GTTAGTTAGCCTTCCTTGTATGCA 58.817 41.667 0.00 0.00 0.00 3.96
5592 10384 4.301072 AGTTAGCCTTCCTTGTATGCAA 57.699 40.909 0.00 0.00 0.00 4.08
5593 10385 4.010349 AGTTAGCCTTCCTTGTATGCAAC 58.990 43.478 0.00 0.00 0.00 4.17
5594 10386 2.584835 AGCCTTCCTTGTATGCAACA 57.415 45.000 0.00 0.00 35.88 3.33
5595 10387 3.091633 AGCCTTCCTTGTATGCAACAT 57.908 42.857 0.00 0.00 38.10 2.71
5596 10388 4.235079 AGCCTTCCTTGTATGCAACATA 57.765 40.909 0.00 0.00 38.10 2.29
5597 10389 4.796606 AGCCTTCCTTGTATGCAACATAT 58.203 39.130 0.00 0.00 38.10 1.78
5598 10390 4.581824 AGCCTTCCTTGTATGCAACATATG 59.418 41.667 0.00 0.00 38.10 1.78
5612 10404 5.654317 CAACATATGCTCTACTTGCTCTG 57.346 43.478 1.58 0.00 0.00 3.35
5613 10405 5.114780 CAACATATGCTCTACTTGCTCTGT 58.885 41.667 1.58 0.00 0.00 3.41
6296 11137 4.098914 TGCTTGAAACCTTACCTGACAT 57.901 40.909 0.00 0.00 0.00 3.06
6341 11182 3.201930 TGCTATTTGGACCTATCTGGCAA 59.798 43.478 0.00 0.00 40.22 4.52
6856 11697 3.991367 ACAAGTTGTCCTAAACTCCGAG 58.009 45.455 1.64 0.00 39.48 4.63
6909 11750 3.119316 AGCTGAGGTGTCTCTATTTGTCG 60.119 47.826 0.00 0.00 40.58 4.35
7035 11876 1.620819 GGTGACATGACCAGTCTCACT 59.379 52.381 14.57 0.00 34.60 3.41
7329 12170 1.279496 AATCAGTGCTGGACAGGCTA 58.721 50.000 1.24 0.00 0.00 3.93
7365 12206 5.293560 ACTCTTGAACACTTTCAGCTACTC 58.706 41.667 0.00 0.00 42.79 2.59
7532 12373 9.921637 GTGTCTGAAAAACATTCCCAATATTAA 57.078 29.630 0.00 0.00 0.00 1.40
7762 12603 1.082756 GGTTTGAGCAACAGCGACG 60.083 57.895 0.00 0.00 37.07 5.12
7941 12783 1.651240 CTTTGCCAGAGGTCATGCGG 61.651 60.000 0.00 0.00 0.00 5.69
8020 12862 0.618458 GGTATGGTTGGGTCAGCTCA 59.382 55.000 0.00 0.00 0.00 4.26
8525 13515 4.774124 CATCTTCTCTGAGGCCATTGTTA 58.226 43.478 5.01 0.00 0.00 2.41
8677 13745 9.429359 GAAGCATATATACTGCAGTTGTTATCT 57.571 33.333 27.06 11.45 42.15 1.98
8855 13973 9.888878 CATCCACATGACTATTATTTGTCAATC 57.111 33.333 0.00 0.00 44.81 2.67
8861 13979 6.429624 TGACTATTATTTGTCAATCATGCGC 58.570 36.000 0.00 0.00 39.82 6.09
8917 14040 1.965643 TGCAAAAATGAGGCAGAGCTT 59.034 42.857 0.00 0.00 32.95 3.74
9135 14279 7.527084 AGATTACTAATTTCAACAGAGCGAC 57.473 36.000 0.00 0.00 0.00 5.19
9258 14408 2.556840 TACATCTTGGGCCTGCCTGC 62.557 60.000 4.53 0.00 36.10 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 6.545666 TGCCACTGGATATGTTAACTAAATGG 59.454 38.462 7.22 5.31 0.00 3.16
11 12 5.950544 AGTGCCACTGGATATGTTAACTA 57.049 39.130 7.22 0.00 0.00 2.24
54 55 4.302455 ACATTCTATCTATGCGTGTCTGC 58.698 43.478 0.00 0.00 0.00 4.26
58 59 6.490381 TCCTAAGACATTCTATCTATGCGTGT 59.510 38.462 0.00 0.00 0.00 4.49
80 86 2.704065 TCTTTTCTTCGGTCCAACTCCT 59.296 45.455 0.00 0.00 0.00 3.69
91 97 3.503748 AGTGGGCATCTTTCTTTTCTTCG 59.496 43.478 0.00 0.00 0.00 3.79
150 178 4.497842 CCTTTTGATTTTGTTTGCTTGGGC 60.498 41.667 0.00 0.00 39.26 5.36
153 181 6.622833 ATCCCTTTTGATTTTGTTTGCTTG 57.377 33.333 0.00 0.00 0.00 4.01
166 194 6.013032 AGAGAGAGACAATGAATCCCTTTTGA 60.013 38.462 0.00 0.00 0.00 2.69
198 226 3.580731 TGCATTGTGTGAGCATTGATTG 58.419 40.909 0.00 0.00 32.55 2.67
199 227 3.845178 CTGCATTGTGTGAGCATTGATT 58.155 40.909 0.00 0.00 37.68 2.57
200 228 2.416836 GCTGCATTGTGTGAGCATTGAT 60.417 45.455 0.00 0.00 37.68 2.57
221 249 2.528564 TGATCCTTTTCTTGGGGCAAG 58.471 47.619 0.00 0.00 42.25 4.01
224 252 5.363580 TGATAATTGATCCTTTTCTTGGGGC 59.636 40.000 0.00 0.00 33.07 5.80
225 253 7.070322 ACATGATAATTGATCCTTTTCTTGGGG 59.930 37.037 0.00 0.00 33.07 4.96
226 254 7.924412 CACATGATAATTGATCCTTTTCTTGGG 59.076 37.037 0.00 0.00 33.07 4.12
227 255 7.437267 GCACATGATAATTGATCCTTTTCTTGG 59.563 37.037 0.00 0.00 33.07 3.61
228 256 8.195436 AGCACATGATAATTGATCCTTTTCTTG 58.805 33.333 0.00 1.16 33.07 3.02
230 258 7.255035 CGAGCACATGATAATTGATCCTTTTCT 60.255 37.037 0.00 0.00 33.07 2.52
233 261 5.824624 ACGAGCACATGATAATTGATCCTTT 59.175 36.000 0.00 0.00 33.07 3.11
234 262 5.371526 ACGAGCACATGATAATTGATCCTT 58.628 37.500 0.00 0.00 33.07 3.36
236 264 5.679734 AACGAGCACATGATAATTGATCC 57.320 39.130 0.00 0.00 33.07 3.36
237 265 6.952743 AGAAACGAGCACATGATAATTGATC 58.047 36.000 0.00 0.00 34.84 2.92
241 269 7.144722 TGAAAGAAACGAGCACATGATAATT 57.855 32.000 0.00 0.00 0.00 1.40
242 270 6.741992 TGAAAGAAACGAGCACATGATAAT 57.258 33.333 0.00 0.00 0.00 1.28
245 273 6.741992 TTATGAAAGAAACGAGCACATGAT 57.258 33.333 0.00 0.00 0.00 2.45
256 284 7.080724 CAGAGGCAAGAGTTTATGAAAGAAAC 58.919 38.462 0.00 0.00 37.11 2.78
288 316 1.888512 AGCACGCAATTCCAACTGAAT 59.111 42.857 0.00 0.00 45.75 2.57
303 331 4.755388 CAGATGATGAATTTCGTAGCACG 58.245 43.478 2.79 2.79 44.19 5.34
340 368 4.139038 CTCGTTCCCAGACCCTTTAAAAA 58.861 43.478 0.00 0.00 0.00 1.94
355 383 3.139077 CCCCACTAAATATGCTCGTTCC 58.861 50.000 0.00 0.00 0.00 3.62
356 384 4.067972 TCCCCACTAAATATGCTCGTTC 57.932 45.455 0.00 0.00 0.00 3.95
357 385 4.102524 TGATCCCCACTAAATATGCTCGTT 59.897 41.667 0.00 0.00 0.00 3.85
359 387 4.271696 TGATCCCCACTAAATATGCTCG 57.728 45.455 0.00 0.00 0.00 5.03
360 388 5.376625 TGTTGATCCCCACTAAATATGCTC 58.623 41.667 0.00 0.00 0.00 4.26
361 389 5.387113 TGTTGATCCCCACTAAATATGCT 57.613 39.130 0.00 0.00 0.00 3.79
362 390 6.006449 AGATGTTGATCCCCACTAAATATGC 58.994 40.000 0.00 0.00 0.00 3.14
371 399 1.211457 AGAGCAGATGTTGATCCCCAC 59.789 52.381 0.00 0.00 43.25 4.61
446 474 2.775890 ACTGCTTGAAGGATGTGACTG 58.224 47.619 0.00 0.00 0.00 3.51
452 480 5.106555 ACGAACATTAACTGCTTGAAGGATG 60.107 40.000 0.00 0.00 0.00 3.51
453 481 5.003804 ACGAACATTAACTGCTTGAAGGAT 58.996 37.500 0.00 0.00 0.00 3.24
454 482 4.385825 ACGAACATTAACTGCTTGAAGGA 58.614 39.130 0.00 0.00 0.00 3.36
455 483 4.749245 ACGAACATTAACTGCTTGAAGG 57.251 40.909 0.00 0.00 0.00 3.46
456 484 5.747565 TGAACGAACATTAACTGCTTGAAG 58.252 37.500 0.00 0.00 0.00 3.02
457 485 5.743026 TGAACGAACATTAACTGCTTGAA 57.257 34.783 0.00 0.00 0.00 2.69
458 486 5.940192 ATGAACGAACATTAACTGCTTGA 57.060 34.783 0.00 0.00 0.00 3.02
459 487 6.955963 GTCTATGAACGAACATTAACTGCTTG 59.044 38.462 0.00 0.00 0.00 4.01
460 488 6.649141 TGTCTATGAACGAACATTAACTGCTT 59.351 34.615 0.00 0.00 0.00 3.91
461 489 6.163476 TGTCTATGAACGAACATTAACTGCT 58.837 36.000 0.00 0.00 0.00 4.24
462 490 6.310467 TCTGTCTATGAACGAACATTAACTGC 59.690 38.462 0.00 0.00 0.00 4.40
601 721 5.118510 GTGCCGAACCACTTTATTTCATTTG 59.881 40.000 0.00 0.00 33.02 2.32
625 745 6.183360 GGTGCTTATTGCTTAAAGTAGTGAGG 60.183 42.308 0.00 0.00 43.37 3.86
626 746 6.595716 AGGTGCTTATTGCTTAAAGTAGTGAG 59.404 38.462 0.00 0.00 43.37 3.51
627 747 6.472887 AGGTGCTTATTGCTTAAAGTAGTGA 58.527 36.000 0.00 0.00 43.37 3.41
628 748 6.371548 TGAGGTGCTTATTGCTTAAAGTAGTG 59.628 38.462 0.00 0.00 43.37 2.74
707 845 4.166011 GCCGGTGCGCATCTGAAC 62.166 66.667 20.15 1.37 0.00 3.18
806 1951 0.901124 ACCAAAGTTGCAACAAGCCA 59.099 45.000 30.11 0.00 44.83 4.75
1414 3246 3.485216 CGCTGTTGGTCGTTGGATAATTC 60.485 47.826 0.00 0.00 0.00 2.17
1466 3298 1.450312 CCGCTGTGGAGGGATTGAC 60.450 63.158 0.00 0.00 42.00 3.18
1775 3767 4.694037 ACAGGCAAATTAACTTACGGACTC 59.306 41.667 0.00 0.00 0.00 3.36
1825 3817 4.226427 TGGGCTATGGCATAATCAGATC 57.774 45.455 8.79 0.00 40.87 2.75
1897 3889 2.609427 TTCGGATTCTCATCTGCCTG 57.391 50.000 0.00 0.00 35.90 4.85
2158 4150 1.702182 TCCAGTTTTCATGCCAGCAA 58.298 45.000 0.00 0.00 0.00 3.91
2198 4190 3.814283 GCAGGCTGATTATCTTCTCCTTG 59.186 47.826 20.86 0.00 0.00 3.61
2624 4628 0.814457 TTGCAAGAAAACCAGTGCGT 59.186 45.000 0.00 0.00 39.92 5.24
2882 4887 2.104170 TCCAAAACAACCTTGGTGTCC 58.896 47.619 1.76 0.00 43.33 4.02
3462 5498 7.041508 CCAGGAATCGAAGGATAAGAAAGAATG 60.042 40.741 0.00 0.00 31.01 2.67
3687 6252 6.771188 AGATATCGTTCGAAAGCCTTATTG 57.229 37.500 6.19 0.00 0.00 1.90
3862 6446 2.108976 CGCTCACACACACCACCT 59.891 61.111 0.00 0.00 0.00 4.00
4037 6712 5.277345 CGGGTTTCTCACTGTTAGTTTGAAG 60.277 44.000 0.00 0.00 0.00 3.02
4229 6904 1.524849 GGCGCCTTCCCAATCTCTC 60.525 63.158 22.15 0.00 0.00 3.20
4234 6909 4.028490 TCGTGGCGCCTTCCCAAT 62.028 61.111 29.70 0.00 33.39 3.16
4239 6914 3.414700 CTGTGTCGTGGCGCCTTC 61.415 66.667 29.70 19.22 0.00 3.46
4262 6937 1.907255 ACAACACCTCCCTAAGCTACC 59.093 52.381 0.00 0.00 0.00 3.18
4269 6944 1.809133 TTGGTCACAACACCTCCCTA 58.191 50.000 0.00 0.00 37.34 3.53
4271 6946 1.202879 TCATTGGTCACAACACCTCCC 60.203 52.381 0.00 0.00 39.87 4.30
4323 6998 0.319900 ACACTAGAACGCTGGCACTG 60.320 55.000 0.00 0.00 0.00 3.66
4324 6999 0.319900 CACACTAGAACGCTGGCACT 60.320 55.000 0.00 0.00 0.00 4.40
4392 7067 1.063867 GCCCGCCCTATATCTCTCCTA 60.064 57.143 0.00 0.00 0.00 2.94
4400 7075 0.617820 CCTACTGGCCCGCCCTATAT 60.618 60.000 0.00 0.00 34.56 0.86
4416 7091 0.387929 CGTTTGCTAGCCCGATCCTA 59.612 55.000 13.29 0.00 0.00 2.94
4520 7229 0.687354 CCCTTAGTCCATCATCCCCG 59.313 60.000 0.00 0.00 0.00 5.73
4529 7238 0.398664 GCCTAGCCTCCCTTAGTCCA 60.399 60.000 0.00 0.00 0.00 4.02
4534 7243 0.759436 CCGAAGCCTAGCCTCCCTTA 60.759 60.000 0.00 0.00 0.00 2.69
4583 7293 1.001048 CATGTGTGACCACCTTTGCAG 60.001 52.381 0.00 0.00 41.09 4.41
4956 7666 0.527113 CATGGCGACCTTGCATTTCA 59.473 50.000 0.00 0.00 36.28 2.69
5028 7738 4.777366 TGTGGTATGTTCTTCAGGAGATGA 59.223 41.667 0.00 0.00 33.49 2.92
5036 7746 3.055385 GGGCTACTGTGGTATGTTCTTCA 60.055 47.826 0.00 0.00 0.00 3.02
5043 7753 2.821991 GCTAGGGCTACTGTGGTATG 57.178 55.000 0.00 0.00 35.22 2.39
5570 10362 5.183228 GTTGCATACAAGGAAGGCTAACTA 58.817 41.667 0.00 0.00 36.16 2.24
5571 10363 4.010349 GTTGCATACAAGGAAGGCTAACT 58.990 43.478 0.00 0.00 36.16 2.24
5573 10365 4.027674 TGTTGCATACAAGGAAGGCTAA 57.972 40.909 0.00 0.00 36.16 3.09
5575 10367 2.584835 TGTTGCATACAAGGAAGGCT 57.415 45.000 0.00 0.00 36.16 4.58
5576 10368 4.863491 CATATGTTGCATACAAGGAAGGC 58.137 43.478 5.94 0.00 40.89 4.35
5590 10382 5.114780 ACAGAGCAAGTAGAGCATATGTTG 58.885 41.667 4.29 1.06 0.00 3.33
5591 10383 5.350504 ACAGAGCAAGTAGAGCATATGTT 57.649 39.130 4.29 0.00 0.00 2.71
5592 10384 5.350504 AACAGAGCAAGTAGAGCATATGT 57.649 39.130 4.29 0.00 0.00 2.29
5593 10385 6.511416 ACTAACAGAGCAAGTAGAGCATATG 58.489 40.000 0.00 0.00 0.00 1.78
5594 10386 6.723298 ACTAACAGAGCAAGTAGAGCATAT 57.277 37.500 0.00 0.00 0.00 1.78
5595 10387 6.531503 AACTAACAGAGCAAGTAGAGCATA 57.468 37.500 0.00 0.00 0.00 3.14
5596 10388 5.413309 AACTAACAGAGCAAGTAGAGCAT 57.587 39.130 0.00 0.00 0.00 3.79
5597 10389 4.873746 AACTAACAGAGCAAGTAGAGCA 57.126 40.909 0.00 0.00 0.00 4.26
5598 10390 4.801516 GCTAACTAACAGAGCAAGTAGAGC 59.198 45.833 0.00 0.00 36.20 4.09
5599 10391 5.105716 TGGCTAACTAACAGAGCAAGTAGAG 60.106 44.000 0.00 0.00 37.98 2.43
5600 10392 4.770531 TGGCTAACTAACAGAGCAAGTAGA 59.229 41.667 0.00 0.00 37.98 2.59
5601 10393 5.073311 TGGCTAACTAACAGAGCAAGTAG 57.927 43.478 0.00 0.00 37.98 2.57
5602 10394 5.477607 TTGGCTAACTAACAGAGCAAGTA 57.522 39.130 0.00 0.00 37.98 2.24
5603 10395 4.351874 TTGGCTAACTAACAGAGCAAGT 57.648 40.909 0.00 0.00 37.98 3.16
5604 10396 4.757149 AGTTTGGCTAACTAACAGAGCAAG 59.243 41.667 12.62 0.00 45.22 4.01
5605 10397 4.714632 AGTTTGGCTAACTAACAGAGCAA 58.285 39.130 12.62 0.00 45.22 3.91
5606 10398 4.351874 AGTTTGGCTAACTAACAGAGCA 57.648 40.909 12.62 0.00 45.22 4.26
5607 10399 4.755123 TGAAGTTTGGCTAACTAACAGAGC 59.245 41.667 14.49 0.00 46.34 4.09
5608 10400 8.723942 ATATGAAGTTTGGCTAACTAACAGAG 57.276 34.615 14.49 0.00 46.34 3.35
5609 10401 9.515226 AAATATGAAGTTTGGCTAACTAACAGA 57.485 29.630 14.49 14.28 46.34 3.41
5936 10777 2.483876 CATGCCGGTAGTAATGAGGTG 58.516 52.381 1.90 0.00 0.00 4.00
6074 10915 3.653539 AGACACGTATGTACTTGCACA 57.346 42.857 0.00 0.00 39.95 4.57
6296 11137 1.198178 GTTTGCCGAGGCGACAAATAA 59.802 47.619 9.78 0.00 40.69 1.40
6465 11306 5.827797 ACAACAATCTGACATGTTTAGGTGT 59.172 36.000 0.00 7.47 37.66 4.16
6856 11697 2.216898 GCATACTGACTCAGGCAATCC 58.783 52.381 10.86 0.00 35.51 3.01
7035 11876 5.764686 AGTTGCAGTATCAATCACAAACTGA 59.235 36.000 5.03 0.00 39.93 3.41
7365 12206 2.550830 AATCCTTGCTGCTATACCCG 57.449 50.000 0.00 0.00 0.00 5.28
7532 12373 7.802117 TCCATAGAATTCCTTACCGATTTTCT 58.198 34.615 0.65 0.00 0.00 2.52
7762 12603 0.040067 CCTCGTTCTGGCAAAACTGC 60.040 55.000 1.76 0.00 0.00 4.40
7941 12783 2.036475 TCCAGTGAGAGAAGTGAAGCAC 59.964 50.000 0.00 0.00 34.10 4.40
8525 13515 1.789576 AAAATGGAGAGGTGGGCGGT 61.790 55.000 0.00 0.00 0.00 5.68
8621 13686 6.687081 TGAACTGTACCGAAAGAAACAAAT 57.313 33.333 0.00 0.00 0.00 2.32
8634 13699 2.427506 CTTCTGCCCTTGAACTGTACC 58.572 52.381 0.00 0.00 0.00 3.34
8855 13973 2.706523 GATGTAAGCCTGCGCGCATG 62.707 60.000 36.48 32.23 41.18 4.06
8861 13979 1.361668 AACAGCGATGTAAGCCTGCG 61.362 55.000 6.79 0.00 34.64 5.18
8917 14040 3.430453 CTTGGAATTGCCCACTTCCTTA 58.570 45.455 15.56 6.04 39.88 2.69
9258 14408 2.159282 ACTCGGTACCTAGTGATTTGCG 60.159 50.000 17.81 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.