Multiple sequence alignment - TraesCS7D01G297600

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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 TraesCS7D01G297600 chr7D 100.000 7254 0 0 1 7254 376348188 376355441 0.000000e+00 13396
1 TraesCS7D01G297600 chr7D 97.191 890 21 1 6369 7254 565667754 565666865 0.000000e+00 1502
2 TraesCS7D01G297600 chr7D 97.602 834 20 0 6421 7254 116361631 116360798 0.000000e+00 1430
3 TraesCS7D01G297600 chr7D 92.722 371 23 2 4576 4946 166366185 166366551 3.850000e-147 532
4 TraesCS7D01G297600 chr7B 96.197 5574 169 20 814 6359 371455405 371460963 0.000000e+00 9079
5 TraesCS7D01G297600 chr7B 84.405 840 75 23 1 813 371454537 371455347 0.000000e+00 774
6 TraesCS7D01G297600 chr7A 95.112 3335 97 16 814 4137 423555887 423559166 0.000000e+00 5195
7 TraesCS7D01G297600 chr7A 97.078 1061 27 1 4135 5195 423559467 423560523 0.000000e+00 1784
8 TraesCS7D01G297600 chr7A 94.232 1179 39 9 5183 6358 423562007 423563159 0.000000e+00 1773
9 TraesCS7D01G297600 chr7A 94.492 708 31 7 6356 7058 116010761 116011465 0.000000e+00 1085
10 TraesCS7D01G297600 chr7A 90.133 527 47 4 1 525 423553410 423553933 0.000000e+00 680
11 TraesCS7D01G297600 chr7A 91.283 413 27 3 4536 4943 40747250 40747658 8.220000e-154 555
12 TraesCS7D01G297600 chr7A 90.385 416 31 3 4536 4946 463422140 463421729 8.280000e-149 538
13 TraesCS7D01G297600 chr7A 89.956 229 17 3 585 813 423555615 423555837 2.560000e-74 291
14 TraesCS7D01G297600 chr7A 82.197 264 34 12 50 304 32698361 32698102 1.590000e-51 215
15 TraesCS7D01G297600 chr6D 97.856 886 19 0 6369 7254 133855453 133856338 0.000000e+00 1531
16 TraesCS7D01G297600 chr6D 94.695 886 21 8 6369 7254 137791490 137792349 0.000000e+00 1352
17 TraesCS7D01G297600 chr6D 92.683 410 26 2 4537 4946 393648871 393649276 8.110000e-164 588
18 TraesCS7D01G297600 chr1D 97.178 886 24 1 6369 7254 162712467 162713351 0.000000e+00 1496
19 TraesCS7D01G297600 chr1D 90.909 858 53 17 6369 7217 423059754 423060595 0.000000e+00 1129
20 TraesCS7D01G297600 chr4D 91.512 860 52 15 6365 7217 426647765 426646920 0.000000e+00 1164
21 TraesCS7D01G297600 chr4D 90.909 858 55 17 6369 7216 20120211 20119367 0.000000e+00 1131
22 TraesCS7D01G297600 chr4D 86.567 201 26 1 4044 4244 385736308 385736109 3.410000e-53 220
23 TraesCS7D01G297600 chr2D 95.994 699 24 4 6363 7058 498823191 498822494 0.000000e+00 1133
24 TraesCS7D01G297600 chr4A 92.736 647 31 4 4462 5107 733459384 733458753 0.000000e+00 920
25 TraesCS7D01G297600 chr4A 88.557 201 22 1 4044 4244 67171895 67171696 7.270000e-60 243
26 TraesCS7D01G297600 chr4A 82.677 254 33 10 46 291 608348615 608348865 1.590000e-51 215
27 TraesCS7D01G297600 chr1B 90.940 585 39 2 4523 5107 54982257 54981687 0.000000e+00 774
28 TraesCS7D01G297600 chr1B 90.144 416 32 3 4536 4946 34774708 34775119 3.850000e-147 532
29 TraesCS7D01G297600 chr1B 85.149 202 26 4 4048 4247 625912539 625912738 3.430000e-48 204
30 TraesCS7D01G297600 chr1B 90.756 119 6 4 4403 4519 47911487 47911602 3.500000e-33 154
31 TraesCS7D01G297600 chrUn 89.663 416 34 3 4536 4946 8430148 8430559 8.340000e-144 521
32 TraesCS7D01G297600 chrUn 91.053 190 15 2 7054 7242 231205633 231205445 9.340000e-64 255
33 TraesCS7D01G297600 chr1A 93.069 202 13 1 7054 7254 398108852 398108651 1.980000e-75 294
34 TraesCS7D01G297600 chr6A 93.684 190 11 1 7054 7242 199592830 199593019 4.280000e-72 283
35 TraesCS7D01G297600 chr5D 86.058 208 28 1 4037 4244 476701985 476702191 9.470000e-54 222
36 TraesCS7D01G297600 chr5D 82.510 263 34 12 50 304 112924506 112924764 3.410000e-53 220
37 TraesCS7D01G297600 chr2A 82.510 263 34 11 50 304 370218748 370219006 3.410000e-53 220
38 TraesCS7D01G297600 chr2A 85.279 197 28 1 4053 4249 763436133 763435938 1.230000e-47 202
39 TraesCS7D01G297600 chr2A 84.390 205 31 1 4040 4244 770193199 770192996 4.440000e-47 200
40 TraesCS7D01G297600 chr3B 86.432 199 24 3 4048 4245 419280030 419280226 1.590000e-51 215
41 TraesCS7D01G297600 chr4B 93.277 119 3 4 4403 4519 38585018 38585133 3.480000e-38 171
42 TraesCS7D01G297600 chr4B 93.277 119 3 4 4403 4519 150742348 150742233 3.480000e-38 171
43 TraesCS7D01G297600 chr3A 91.597 119 5 4 4403 4519 559796515 559796400 7.530000e-35 159


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 TraesCS7D01G297600 chr7D 376348188 376355441 7253 False 13396.0 13396 100.0000 1 7254 1 chr7D.!!$F2 7253
1 TraesCS7D01G297600 chr7D 565666865 565667754 889 True 1502.0 1502 97.1910 6369 7254 1 chr7D.!!$R2 885
2 TraesCS7D01G297600 chr7D 116360798 116361631 833 True 1430.0 1430 97.6020 6421 7254 1 chr7D.!!$R1 833
3 TraesCS7D01G297600 chr7B 371454537 371460963 6426 False 4926.5 9079 90.3010 1 6359 2 chr7B.!!$F1 6358
4 TraesCS7D01G297600 chr7A 423553410 423563159 9749 False 1944.6 5195 93.3022 1 6358 5 chr7A.!!$F3 6357
5 TraesCS7D01G297600 chr7A 116010761 116011465 704 False 1085.0 1085 94.4920 6356 7058 1 chr7A.!!$F2 702
6 TraesCS7D01G297600 chr6D 133855453 133856338 885 False 1531.0 1531 97.8560 6369 7254 1 chr6D.!!$F1 885
7 TraesCS7D01G297600 chr6D 137791490 137792349 859 False 1352.0 1352 94.6950 6369 7254 1 chr6D.!!$F2 885
8 TraesCS7D01G297600 chr1D 162712467 162713351 884 False 1496.0 1496 97.1780 6369 7254 1 chr1D.!!$F1 885
9 TraesCS7D01G297600 chr1D 423059754 423060595 841 False 1129.0 1129 90.9090 6369 7217 1 chr1D.!!$F2 848
10 TraesCS7D01G297600 chr4D 426646920 426647765 845 True 1164.0 1164 91.5120 6365 7217 1 chr4D.!!$R3 852
11 TraesCS7D01G297600 chr4D 20119367 20120211 844 True 1131.0 1131 90.9090 6369 7216 1 chr4D.!!$R1 847
12 TraesCS7D01G297600 chr2D 498822494 498823191 697 True 1133.0 1133 95.9940 6363 7058 1 chr2D.!!$R1 695
13 TraesCS7D01G297600 chr4A 733458753 733459384 631 True 920.0 920 92.7360 4462 5107 1 chr4A.!!$R2 645
14 TraesCS7D01G297600 chr1B 54981687 54982257 570 True 774.0 774 90.9400 4523 5107 1 chr1B.!!$R1 584

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
661 2307 0.107410 TTGCTGGACACGTTGGAACT 60.107 50.000 0.00 0.00 0.00 3.01 F
1340 3043 0.106719 CCCCGGCCTGTTATGATGTT 60.107 55.000 0.00 0.00 0.00 2.71 F
1499 3202 0.324943 TGCTCTTTGCTCCTGTACCC 59.675 55.000 0.00 0.00 43.37 3.69 F
1529 3233 0.986019 ATCTGGTTGGGGCGATGGTA 60.986 55.000 0.00 0.00 0.00 3.25 F
1553 3257 2.032924 TGATACACGATACTGCTGGTCG 59.967 50.000 15.48 15.48 40.91 4.79 F
2712 4418 2.110296 GCTGTCCAATTAGCCAGCC 58.890 57.895 0.00 0.00 43.45 4.85 F
3977 5690 1.638529 AGGAGAGGTTGTCAGTCCAG 58.361 55.000 0.00 0.00 0.00 3.86 F
4052 5765 0.108615 ATTGTGCTCGAAGGTCCTCG 60.109 55.000 0.00 0.00 40.25 4.63 F
4855 6871 1.053424 TGTCGCTTTCCCCAGTACTT 58.947 50.000 0.00 0.00 0.00 2.24 F
5836 9354 1.777272 ACTTCAGCCAAGAGGAGGTTT 59.223 47.619 0.03 0.00 36.89 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1539 3243 0.855349 GCAATCGACCAGCAGTATCG 59.145 55.000 0.00 0.0 37.20 2.92 R
2767 4473 1.495584 GAAGGAACGCAACGAGCACA 61.496 55.000 0.00 0.0 46.13 4.57 R
2989 4695 2.320339 GATCTGCTCGCTTTGCTGGC 62.320 60.000 0.00 0.0 0.00 4.85 R
2996 4702 2.496817 GACCCGATCTGCTCGCTT 59.503 61.111 0.00 0.0 46.25 4.68 R
3335 5044 5.163713 CCAGACAAGGCTATGAGTAAAAAGC 60.164 44.000 0.00 0.0 0.00 3.51 R
4029 5742 1.079127 ACCTTCGAGCACAATCCCG 60.079 57.895 0.00 0.0 0.00 5.14 R
5836 9354 0.866906 AACGAACGAGCGAACGAACA 60.867 50.000 16.11 0.0 37.03 3.18 R
6112 9639 7.973944 CCCTTTCTTGGAACGAAAATATTAAGG 59.026 37.037 0.00 0.0 30.73 2.69 R
6185 9714 0.449388 CAGATTTCAAGTCCGGCAGC 59.551 55.000 0.00 0.0 0.00 5.25 R
7102 10654 0.099791 AGTGGGTCGCGTTTTTGTTG 59.900 50.000 5.77 0.0 0.00 3.33 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
27 28 0.880278 TTCTGTCAAGCGACCAGTGC 60.880 55.000 0.00 0.00 41.85 4.40
40 41 1.363443 CAGTGCGGCCACAAAATGT 59.637 52.632 2.24 0.00 44.53 2.71
50 51 0.306228 CACAAAATGTGTCGACCGCA 59.694 50.000 14.12 12.57 43.08 5.69
55 56 2.087501 AATGTGTCGACCGCAATACA 57.912 45.000 14.12 9.87 37.07 2.29
71 72 5.332581 CGCAATACAAATCAGTATCGTCCTG 60.333 44.000 0.00 0.00 33.73 3.86
80 89 3.830178 TCAGTATCGTCCTGAACCTGAAA 59.170 43.478 0.00 0.00 36.07 2.69
85 94 2.135933 CGTCCTGAACCTGAAACTCAC 58.864 52.381 0.00 0.00 0.00 3.51
91 100 5.306937 TCCTGAACCTGAAACTCACAGATTA 59.693 40.000 0.00 0.00 37.54 1.75
128 137 1.531365 CCTTGGCAAAGCACTCCCA 60.531 57.895 0.00 0.00 31.51 4.37
165 174 5.878332 AAACATGCTCGATTTGTATGTCA 57.122 34.783 7.20 0.00 39.22 3.58
197 206 9.770097 TCTGAATTGACTAGGCATAAAATAGAG 57.230 33.333 0.00 0.00 0.00 2.43
410 434 3.118445 TGGTGGCTGAATTGATGTATCGA 60.118 43.478 0.00 0.00 0.00 3.59
451 475 9.922305 GAGAATTAAAGAAATGTGAATACGAGG 57.078 33.333 0.00 0.00 0.00 4.63
455 479 3.535561 AGAAATGTGAATACGAGGCTGG 58.464 45.455 0.00 0.00 0.00 4.85
457 481 3.350219 AATGTGAATACGAGGCTGGTT 57.650 42.857 7.67 0.00 0.00 3.67
501 525 8.801299 TCCTTTAAATGTAATTGTGATCTTGCA 58.199 29.630 0.00 0.00 36.10 4.08
504 528 9.979578 TTTAAATGTAATTGTGATCTTGCAAGT 57.020 25.926 25.19 13.20 36.10 3.16
525 549 7.306983 GCAAGTGATATAATTTGGAAATGCAGC 60.307 37.037 0.00 0.00 0.00 5.25
536 2166 2.257286 AAATGCAGCTGCGCTTACCG 62.257 55.000 32.11 0.00 45.83 4.02
540 2170 2.027073 CAGCTGCGCTTACCGTGAA 61.027 57.895 9.73 0.00 36.40 3.18
543 2173 0.300789 GCTGCGCTTACCGTGAATAC 59.699 55.000 9.73 0.00 39.71 1.89
610 2256 2.354821 GACCTGTTTTTCACGCACTTCT 59.645 45.455 0.00 0.00 0.00 2.85
652 2298 3.876274 TCTAGAGATGTTGCTGGACAC 57.124 47.619 0.00 0.00 31.30 3.67
661 2307 0.107410 TTGCTGGACACGTTGGAACT 60.107 50.000 0.00 0.00 0.00 3.01
746 2392 8.979574 GTTAAATAAGGTCTCCAAGTGATATCG 58.020 37.037 0.00 0.00 0.00 2.92
747 2393 5.730296 ATAAGGTCTCCAAGTGATATCGG 57.270 43.478 0.00 0.00 0.00 4.18
748 2394 3.314307 AGGTCTCCAAGTGATATCGGA 57.686 47.619 0.00 0.00 0.00 4.55
749 2395 3.643237 AGGTCTCCAAGTGATATCGGAA 58.357 45.455 0.00 0.00 0.00 4.30
836 2539 2.418368 AACAGCAATTGCCGGATCTA 57.582 45.000 26.45 0.00 43.38 1.98
911 2614 0.396435 AGGGCAAAGTCGTCACATCA 59.604 50.000 0.00 0.00 0.00 3.07
1205 2908 3.482783 GCTCGTCACCAAGCTCGC 61.483 66.667 0.00 0.00 35.60 5.03
1206 2909 2.259818 CTCGTCACCAAGCTCGCT 59.740 61.111 0.00 0.00 0.00 4.93
1340 3043 0.106719 CCCCGGCCTGTTATGATGTT 60.107 55.000 0.00 0.00 0.00 2.71
1475 3178 5.642063 TGTTCGATGATTTTGAGAGGTAACC 59.358 40.000 0.00 0.00 37.17 2.85
1498 3201 1.276421 TCTGCTCTTTGCTCCTGTACC 59.724 52.381 0.00 0.00 43.37 3.34
1499 3202 0.324943 TGCTCTTTGCTCCTGTACCC 59.675 55.000 0.00 0.00 43.37 3.69
1501 3204 1.280457 CTCTTTGCTCCTGTACCCCT 58.720 55.000 0.00 0.00 0.00 4.79
1502 3205 1.630878 CTCTTTGCTCCTGTACCCCTT 59.369 52.381 0.00 0.00 0.00 3.95
1529 3233 0.986019 ATCTGGTTGGGGCGATGGTA 60.986 55.000 0.00 0.00 0.00 3.25
1539 3243 2.480845 GGGCGATGGTAAGTGATACAC 58.519 52.381 0.00 0.00 36.14 2.90
1540 3244 2.124903 GGCGATGGTAAGTGATACACG 58.875 52.381 0.00 0.00 39.64 4.49
1553 3257 2.032924 TGATACACGATACTGCTGGTCG 59.967 50.000 15.48 15.48 40.91 4.79
1688 3392 2.618241 GCAGATGGTGAACACTGAACAA 59.382 45.455 4.62 0.00 33.08 2.83
2034 3738 5.864986 TCTTCTTTTGTTGTTCTCGTGTTC 58.135 37.500 0.00 0.00 0.00 3.18
2035 3739 4.253352 TCTTTTGTTGTTCTCGTGTTCG 57.747 40.909 0.00 0.00 38.55 3.95
2142 3847 4.572909 ACGTGAAGTATTTACCAAGACCC 58.427 43.478 0.00 0.00 29.65 4.46
2383 4088 8.466617 TTTGTTTACTTCTAATGGGCTAAACA 57.533 30.769 0.00 0.00 34.09 2.83
2712 4418 2.110296 GCTGTCCAATTAGCCAGCC 58.890 57.895 0.00 0.00 43.45 4.85
2723 4429 6.786959 TCCAATTAGCCAGCCCATATTTTAAT 59.213 34.615 0.00 0.00 0.00 1.40
2737 4443 8.299570 CCCATATTTTAATCAGTAGAATGTGGC 58.700 37.037 5.85 0.00 41.00 5.01
2767 4473 6.839124 TGTTGATGCCTTATTTGTGAAGAT 57.161 33.333 0.00 0.00 0.00 2.40
2910 4616 2.750637 AGCGTCGTCGGGAGATGT 60.751 61.111 3.90 0.00 45.94 3.06
2989 4695 3.937079 TGCACAGCATCTTCTGAAGTATG 59.063 43.478 16.43 17.27 37.51 2.39
2996 4702 3.701205 TCTTCTGAAGTATGCCAGCAA 57.299 42.857 16.43 0.00 0.00 3.91
3180 4889 9.681692 TTTGTCAACATTGATGAACTTATTGAG 57.318 29.630 0.00 0.00 39.73 3.02
3700 5409 5.121768 ACACATCTAACATTCGTTTACAGGC 59.878 40.000 0.00 0.00 36.52 4.85
3707 5416 2.505628 TTCGTTTACAGGCACGTACA 57.494 45.000 0.00 0.00 37.66 2.90
3801 5510 9.897744 CTCTTCTTTAATGTTACAATGCTTTGA 57.102 29.630 18.35 0.57 36.64 2.69
3817 5526 3.985925 GCTTTGATGCCTGAAACTTCTTG 59.014 43.478 0.00 0.00 0.00 3.02
3818 5527 4.500375 GCTTTGATGCCTGAAACTTCTTGT 60.500 41.667 0.00 0.00 0.00 3.16
3819 5528 4.836125 TTGATGCCTGAAACTTCTTGTC 57.164 40.909 0.00 0.00 0.00 3.18
3820 5529 3.819368 TGATGCCTGAAACTTCTTGTCA 58.181 40.909 0.00 0.00 0.00 3.58
3859 5572 9.555727 ACAGAACTGTCTTTAAATTACTTAGCA 57.444 29.630 1.32 0.00 40.24 3.49
3897 5610 3.685550 GCTGAAGAGGGCTAAATGGCTAA 60.686 47.826 0.00 0.00 41.48 3.09
3977 5690 1.638529 AGGAGAGGTTGTCAGTCCAG 58.361 55.000 0.00 0.00 0.00 3.86
4038 5751 2.093306 TGAGTAGTTGCGGGATTGTG 57.907 50.000 0.00 0.00 0.00 3.33
4052 5765 0.108615 ATTGTGCTCGAAGGTCCTCG 60.109 55.000 0.00 0.00 40.25 4.63
4077 5790 6.363577 AGTGCAATAAGTGTGTACATATGC 57.636 37.500 1.58 3.43 34.42 3.14
4093 5806 1.392589 ATGCGGCACCTCTAAAATGG 58.607 50.000 4.03 0.00 0.00 3.16
4271 6287 4.963276 TTTCATATCTTTGCGAGGGTTG 57.037 40.909 0.00 0.00 0.00 3.77
4304 6320 1.298014 GGGAGGCTCCACAAGACAG 59.702 63.158 33.27 0.00 38.64 3.51
4613 6629 4.530094 TTCATTACCTCGCGCTAAAATG 57.470 40.909 5.56 9.32 0.00 2.32
4614 6630 3.527533 TCATTACCTCGCGCTAAAATGT 58.472 40.909 5.56 0.00 0.00 2.71
4615 6631 4.684877 TCATTACCTCGCGCTAAAATGTA 58.315 39.130 5.56 0.00 0.00 2.29
4616 6632 5.110598 TCATTACCTCGCGCTAAAATGTAA 58.889 37.500 5.56 5.16 0.00 2.41
4855 6871 1.053424 TGTCGCTTTCCCCAGTACTT 58.947 50.000 0.00 0.00 0.00 2.24
4857 6873 2.633967 TGTCGCTTTCCCCAGTACTTTA 59.366 45.455 0.00 0.00 0.00 1.85
4859 6875 1.997606 CGCTTTCCCCAGTACTTTACG 59.002 52.381 0.00 0.00 0.00 3.18
5110 7126 2.489722 GACCATTTCCAGTCCTTTCTGC 59.510 50.000 0.00 0.00 34.47 4.26
5137 7156 2.902608 TGTGTTCTCTGTCCTGGGTAT 58.097 47.619 0.00 0.00 0.00 2.73
5245 8761 7.961283 TGCTATATCGTAACTAGCGTTAATGAG 59.039 37.037 0.00 0.00 40.57 2.90
5376 8892 4.078863 AGAGTAGGGTTATTCAGGAGCTCT 60.079 45.833 14.64 0.00 0.00 4.09
5462 8979 8.324306 AGTGGATTACATAATATGCTGTGCTAT 58.676 33.333 0.00 0.00 0.00 2.97
5465 8982 9.994432 GGATTACATAATATGCTGTGCTATTTC 57.006 33.333 0.00 0.00 0.00 2.17
5836 9354 1.777272 ACTTCAGCCAAGAGGAGGTTT 59.223 47.619 0.03 0.00 36.89 3.27
6112 9639 5.519722 TCAATTTGAAGCCGTTTCTTCTTC 58.480 37.500 0.00 0.00 42.15 2.87
6132 9661 9.774742 CTTCTTCCTTAATATTTTCGTTCCAAG 57.225 33.333 0.00 0.00 0.00 3.61
6163 9692 6.809196 GTGTTTTGTTTGTTCCTGTCAACATA 59.191 34.615 0.00 0.00 36.16 2.29
6185 9714 8.531146 ACATATTTACTTTTGTCCTTGGAATGG 58.469 33.333 0.00 0.00 0.00 3.16
6242 9771 3.530265 ATGAATGCATTTTGTGGCGAT 57.470 38.095 14.33 0.00 0.00 4.58
6259 9788 5.064707 GTGGCGATAGTTTCTTTTATGCTCA 59.935 40.000 0.00 0.00 39.35 4.26
6273 9802 0.817634 TGCTCAGGGTGGTTCAAACG 60.818 55.000 0.00 0.00 0.00 3.60
6297 9830 7.114811 ACGTCATCTTTTTATGAAAATGTGTGC 59.885 33.333 0.00 0.00 37.61 4.57
6360 9893 4.703575 TGTCACGAGTTAGCTATGTACCTT 59.296 41.667 0.00 0.00 0.00 3.50
6389 9927 2.817834 GTAATCTGCGCCGGTGCA 60.818 61.111 38.08 38.08 43.95 4.57
6439 9977 0.757935 AGCCGCCCGATTTACCTCTA 60.758 55.000 0.00 0.00 0.00 2.43
6464 10002 3.992260 AACCGTCAGATCTAATCCTCG 57.008 47.619 0.00 0.00 0.00 4.63
6486 10025 2.287788 CCAAGTCAAACGCAGCTCATTT 60.288 45.455 0.00 0.00 0.00 2.32
6908 10448 3.733988 GCGATTCACGAGGAGATACAACA 60.734 47.826 0.00 0.00 45.77 3.33
6996 10548 2.602257 AGGGCTGCTCAAAACAAAAC 57.398 45.000 0.74 0.00 0.00 2.43
7007 10559 8.539770 TGCTCAAAACAAAACAAGTTTCAATA 57.460 26.923 0.00 0.00 38.17 1.90
7049 10601 3.056607 CCATGGACGGAAAAAGCTTCAAT 60.057 43.478 5.56 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.805428 ATTTTGTGGCCGCACTGGTC 61.805 55.000 21.09 0.00 45.24 4.02
40 41 2.670905 CTGATTTGTATTGCGGTCGACA 59.329 45.455 18.91 0.00 0.00 4.35
41 42 2.671396 ACTGATTTGTATTGCGGTCGAC 59.329 45.455 7.13 7.13 0.00 4.20
50 51 6.761714 GGTTCAGGACGATACTGATTTGTATT 59.238 38.462 8.71 0.00 43.82 1.89
55 56 4.466370 TCAGGTTCAGGACGATACTGATTT 59.534 41.667 8.71 0.00 43.82 2.17
71 72 8.329203 AGAATTAATCTGTGAGTTTCAGGTTC 57.671 34.615 0.00 0.00 37.43 3.62
80 89 9.118300 GAATCCATGAAGAATTAATCTGTGAGT 57.882 33.333 0.00 0.00 38.79 3.41
85 94 7.866393 GGCTTGAATCCATGAAGAATTAATCTG 59.134 37.037 0.00 0.00 38.79 2.90
91 100 5.105064 CCAAGGCTTGAATCCATGAAGAATT 60.105 40.000 28.18 0.00 0.00 2.17
128 137 6.183360 CGAGCATGTTTATGGAACCTTGTAAT 60.183 38.462 0.00 0.00 37.45 1.89
215 226 5.233083 TGGGATGCTATTCACCTCAATAG 57.767 43.478 0.00 0.00 38.79 1.73
301 325 2.167693 CGGTAGGTGTAGCTCATTCCAA 59.832 50.000 0.00 0.00 0.00 3.53
359 383 1.134946 GGCCGCAGATAAAAATGTGCT 59.865 47.619 6.03 0.00 38.51 4.40
360 384 1.135141 TGGCCGCAGATAAAAATGTGC 60.135 47.619 0.00 0.00 37.46 4.57
365 389 4.887071 ACAATAGATGGCCGCAGATAAAAA 59.113 37.500 0.00 0.00 0.00 1.94
375 399 2.706636 CCACCACAATAGATGGCCG 58.293 57.895 0.00 0.00 41.31 6.13
428 452 8.184192 CAGCCTCGTATTCACATTTCTTTAATT 58.816 33.333 0.00 0.00 0.00 1.40
440 464 2.695359 TCAAACCAGCCTCGTATTCAC 58.305 47.619 0.00 0.00 0.00 3.18
455 479 8.538409 AAAGGAATACATTGCTGAATTCAAAC 57.462 30.769 9.88 5.44 38.51 2.93
475 499 8.801299 TGCAAGATCACAATTACATTTAAAGGA 58.199 29.630 6.90 0.00 0.00 3.36
490 514 8.407832 CCAAATTATATCACTTGCAAGATCACA 58.592 33.333 32.50 13.26 0.00 3.58
501 525 7.924412 CAGCTGCATTTCCAAATTATATCACTT 59.076 33.333 0.00 0.00 0.00 3.16
504 528 6.218019 GCAGCTGCATTTCCAAATTATATCA 58.782 36.000 33.36 0.00 41.59 2.15
525 549 1.635844 TGTATTCACGGTAAGCGCAG 58.364 50.000 11.47 0.00 0.00 5.18
536 2166 4.795278 GCTTGCTTTAGTGCATGTATTCAC 59.205 41.667 0.00 0.00 42.96 3.18
540 2170 4.264253 TCTGCTTGCTTTAGTGCATGTAT 58.736 39.130 0.00 0.00 42.96 2.29
543 2173 3.499048 CTTCTGCTTGCTTTAGTGCATG 58.501 45.455 0.00 0.00 42.96 4.06
589 2235 2.354821 AGAAGTGCGTGAAAAACAGGTC 59.645 45.455 0.00 0.00 36.83 3.85
732 2378 5.907207 TCTTTCTTCCGATATCACTTGGAG 58.093 41.667 3.12 0.00 30.19 3.86
746 2392 9.729023 CTCTTTTCTTCTTTCTTTCTTTCTTCC 57.271 33.333 0.00 0.00 0.00 3.46
747 2393 9.729023 CCTCTTTTCTTCTTTCTTTCTTTCTTC 57.271 33.333 0.00 0.00 0.00 2.87
748 2394 9.467796 TCCTCTTTTCTTCTTTCTTTCTTTCTT 57.532 29.630 0.00 0.00 0.00 2.52
749 2395 8.898761 GTCCTCTTTTCTTCTTTCTTTCTTTCT 58.101 33.333 0.00 0.00 0.00 2.52
791 2437 5.749596 TTTAATCCGTTGCATAGTCATGG 57.250 39.130 0.00 0.00 32.36 3.66
844 2547 2.192861 TGCGCCCCAAGTTTGAGTG 61.193 57.895 4.18 0.00 0.00 3.51
911 2614 6.694445 TTGGGGTTGGTTCATCAATTTATT 57.306 33.333 0.00 0.00 0.00 1.40
1205 2908 0.730840 CTAAAACCCGCGGGCTTAAG 59.269 55.000 43.58 29.79 39.32 1.85
1206 2909 1.307355 GCTAAAACCCGCGGGCTTAA 61.307 55.000 43.58 25.19 39.32 1.85
1285 2988 2.363925 AGAGACCCAGTACCGCCC 60.364 66.667 0.00 0.00 0.00 6.13
1340 3043 3.306088 GGATCAAGACTCAAGAACACCGA 60.306 47.826 0.00 0.00 0.00 4.69
1469 3172 1.079503 CAAAGAGCAGAGCGGTTACC 58.920 55.000 0.00 0.00 0.00 2.85
1498 3201 3.196254 CCCAACCAGATTCATTCAAAGGG 59.804 47.826 0.00 0.00 0.00 3.95
1499 3202 3.196254 CCCCAACCAGATTCATTCAAAGG 59.804 47.826 0.00 0.00 0.00 3.11
1501 3204 2.566724 GCCCCAACCAGATTCATTCAAA 59.433 45.455 0.00 0.00 0.00 2.69
1502 3205 2.178580 GCCCCAACCAGATTCATTCAA 58.821 47.619 0.00 0.00 0.00 2.69
1529 3233 3.447586 ACCAGCAGTATCGTGTATCACTT 59.552 43.478 0.00 0.00 31.34 3.16
1539 3243 0.855349 GCAATCGACCAGCAGTATCG 59.145 55.000 0.00 0.00 37.20 2.92
1540 3244 1.939974 TGCAATCGACCAGCAGTATC 58.060 50.000 4.36 0.00 33.75 2.24
1688 3392 3.261897 CACTAGTCATGTGACCCTTCCTT 59.738 47.826 9.41 0.00 45.85 3.36
1748 3452 3.966979 ACATTCACCATCTACCAATGCA 58.033 40.909 0.00 0.00 0.00 3.96
1924 3628 3.181454 GGACACTCTTCCAGGAACTTGAA 60.181 47.826 0.00 0.00 37.79 2.69
2034 3738 5.237779 ACTTTGGTACACAATTCAGTTACCG 59.762 40.000 0.00 0.00 39.29 4.02
2035 3739 6.628919 ACTTTGGTACACAATTCAGTTACC 57.371 37.500 0.00 0.00 39.29 2.85
2183 3888 6.861144 TGTCATCATTGAGAACACACAAAAA 58.139 32.000 0.00 0.00 30.85 1.94
2338 4043 7.733402 ACAAATCCTTGTTTCATGGAAATTG 57.267 32.000 19.40 19.40 43.45 2.32
2352 4057 7.035612 GCCCATTAGAAGTAAACAAATCCTTG 58.964 38.462 0.00 0.00 38.61 3.61
2712 4418 8.849168 TGCCACATTCTACTGATTAAAATATGG 58.151 33.333 0.00 0.00 0.00 2.74
2723 4429 3.769739 ACAACTGCCACATTCTACTGA 57.230 42.857 0.00 0.00 0.00 3.41
2737 4443 5.984926 ACAAATAAGGCATCAACAACAACTG 59.015 36.000 0.00 0.00 0.00 3.16
2767 4473 1.495584 GAAGGAACGCAACGAGCACA 61.496 55.000 0.00 0.00 46.13 4.57
2942 4648 2.431683 GCACCTGCCTCTTCACCA 59.568 61.111 0.00 0.00 34.31 4.17
2978 4684 2.489329 GCTTTGCTGGCATACTTCAGAA 59.511 45.455 0.00 0.00 33.11 3.02
2989 4695 2.320339 GATCTGCTCGCTTTGCTGGC 62.320 60.000 0.00 0.00 0.00 4.85
2996 4702 2.496817 GACCCGATCTGCTCGCTT 59.503 61.111 0.00 0.00 46.25 4.68
3180 4889 8.443953 AATATTGGAAGTGAAGCAGAAGATAC 57.556 34.615 0.00 0.00 0.00 2.24
3293 5002 9.119329 GATAATAAGTAACTACACATGCTCTCG 57.881 37.037 0.00 0.00 0.00 4.04
3335 5044 5.163713 CCAGACAAGGCTATGAGTAAAAAGC 60.164 44.000 0.00 0.00 0.00 3.51
3446 5155 6.925610 TCATGCACCTGAACATAGAAATAC 57.074 37.500 0.00 0.00 0.00 1.89
3707 5416 8.375234 TTGGGACCAAATTAAGCAAAGTGCAT 62.375 38.462 0.32 0.00 38.27 3.96
3801 5510 3.554934 TGTGACAAGAAGTTTCAGGCAT 58.445 40.909 0.00 0.00 0.00 4.40
3817 5526 4.097892 AGTTCTGTGGTTCCAAATTGTGAC 59.902 41.667 0.00 0.00 0.00 3.67
3818 5527 4.097741 CAGTTCTGTGGTTCCAAATTGTGA 59.902 41.667 0.00 0.00 0.00 3.58
3819 5528 4.142182 ACAGTTCTGTGGTTCCAAATTGTG 60.142 41.667 4.58 0.00 0.00 3.33
3820 5529 4.023291 ACAGTTCTGTGGTTCCAAATTGT 58.977 39.130 4.58 0.00 0.00 2.71
3859 5572 4.287067 TCTTCAGCTTTCTACAAGTCCCAT 59.713 41.667 0.00 0.00 0.00 4.00
3928 5641 3.128589 ACACCAAAGCGCAATAGGTATTG 59.871 43.478 11.47 5.50 44.44 1.90
3977 5690 9.694137 ACTTCACTTATAAGTTACAAGACAGAC 57.306 33.333 23.52 0.00 37.08 3.51
4025 5738 1.573829 TTCGAGCACAATCCCGCAAC 61.574 55.000 0.00 0.00 0.00 4.17
4029 5742 1.079127 ACCTTCGAGCACAATCCCG 60.079 57.895 0.00 0.00 0.00 5.14
4052 5765 6.907212 GCATATGTACACACTTATTGCACTTC 59.093 38.462 0.00 0.00 0.00 3.01
4077 5790 1.743394 GAACCCATTTTAGAGGTGCCG 59.257 52.381 0.00 0.00 33.05 5.69
4271 6287 4.355151 CCCATACAAAGGGGTGCC 57.645 61.111 0.00 0.00 42.12 5.01
4304 6320 3.336138 AACTAGTAAGGCCTGTTGAGC 57.664 47.619 5.69 0.00 0.00 4.26
4613 6629 7.710907 TCATTGGTCAGCATAACATCTACTTAC 59.289 37.037 0.00 0.00 0.00 2.34
4614 6630 7.710907 GTCATTGGTCAGCATAACATCTACTTA 59.289 37.037 0.00 0.00 0.00 2.24
4615 6631 6.540189 GTCATTGGTCAGCATAACATCTACTT 59.460 38.462 0.00 0.00 0.00 2.24
4616 6632 6.051717 GTCATTGGTCAGCATAACATCTACT 58.948 40.000 0.00 0.00 0.00 2.57
4690 6706 5.178797 TCTCCCTTCTTTAAAGCTTCATCG 58.821 41.667 10.51 0.00 0.00 3.84
4855 6871 4.571919 AGCACAAAACATAGCTACCGTAA 58.428 39.130 0.00 0.00 35.19 3.18
4857 6873 3.053831 AGCACAAAACATAGCTACCGT 57.946 42.857 0.00 0.00 35.19 4.83
4859 6875 7.326063 CACTTTTTAGCACAAAACATAGCTACC 59.674 37.037 0.00 0.00 39.11 3.18
4952 6968 3.725490 TCAAGAGATGATGCGAATCAGG 58.275 45.455 12.63 0.00 33.59 3.86
4953 6969 5.729974 TTTCAAGAGATGATGCGAATCAG 57.270 39.130 12.63 0.00 38.03 2.90
5110 7126 3.310774 CAGGACAGAGAACACAACAACAG 59.689 47.826 0.00 0.00 0.00 3.16
5137 7156 5.104735 AGGAAACAGTACAAAATGGGCAAAA 60.105 36.000 0.00 0.00 0.00 2.44
5245 8761 1.351350 ACCCTAGTTCCCTTGCAACTC 59.649 52.381 0.00 0.00 35.63 3.01
5376 8892 3.018856 CAGCATCTAATTGGGCAGACAA 58.981 45.455 0.00 0.00 34.41 3.18
5688 9206 9.291664 GCTATGATGTAGTCGATCCTAAAATAC 57.708 37.037 0.00 0.00 0.00 1.89
5691 9209 6.379386 CGCTATGATGTAGTCGATCCTAAAA 58.621 40.000 0.00 0.00 0.00 1.52
5712 9230 1.826024 CAGTATCTTCAGGGGCGCT 59.174 57.895 7.64 0.00 0.00 5.92
5795 9313 4.814234 AGTTGTACATCTTGTCAAGCGAAA 59.186 37.500 7.78 0.00 0.00 3.46
5836 9354 0.866906 AACGAACGAGCGAACGAACA 60.867 50.000 16.11 0.00 37.03 3.18
6112 9639 7.973944 CCCTTTCTTGGAACGAAAATATTAAGG 59.026 37.037 0.00 0.00 30.73 2.69
6132 9661 4.629634 CAGGAACAAACAAAACACCCTTTC 59.370 41.667 0.00 0.00 0.00 2.62
6163 9692 5.543790 AGCCATTCCAAGGACAAAAGTAAAT 59.456 36.000 0.00 0.00 0.00 1.40
6185 9714 0.449388 CAGATTTCAAGTCCGGCAGC 59.551 55.000 0.00 0.00 0.00 5.25
6242 9771 5.222048 ACCACCCTGAGCATAAAAGAAACTA 60.222 40.000 0.00 0.00 0.00 2.24
6259 9788 1.420138 AGATGACGTTTGAACCACCCT 59.580 47.619 0.00 0.00 0.00 4.34
6273 9802 7.325821 TCGCACACATTTTCATAAAAAGATGAC 59.674 33.333 0.00 0.00 37.76 3.06
6439 9977 7.628794 GCGAGGATTAGATCTGACGGTTAATAT 60.629 40.741 5.18 0.00 0.00 1.28
6464 10002 1.081840 GAGCTGCGTTTGACTTGGC 60.082 57.895 0.00 0.00 0.00 4.52
6486 10025 0.606604 GTACACCAGCGGAGGAAGAA 59.393 55.000 1.50 0.00 0.00 2.52
6684 10223 2.434185 GCGGAGTTGCGACCATCA 60.434 61.111 0.00 0.00 0.00 3.07
6828 10367 3.238597 CTTTTCCATCCAGGGGTTGAAA 58.761 45.455 0.00 0.00 38.24 2.69
7007 10559 6.816140 CCATGGTTGAAACTTTTGTGTAAACT 59.184 34.615 2.57 0.00 0.00 2.66
7021 10573 3.491792 GCTTTTTCCGTCCATGGTTGAAA 60.492 43.478 12.58 15.20 0.00 2.69
7102 10654 0.099791 AGTGGGTCGCGTTTTTGTTG 59.900 50.000 5.77 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.