Multiple sequence alignment - TraesCS7A01G487100

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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 TraesCS7A01G487100 chr7A 100.000 3206 0 0 1 3206 677824323 677827528 0.000000e+00 5921.0
1 TraesCS7A01G487100 chr7A 84.152 1527 216 16 941 2449 678146280 678144762 0.000000e+00 1456.0
2 TraesCS7A01G487100 chr7A 81.741 1298 204 21 1014 2289 677833050 677834336 0.000000e+00 1053.0
3 TraesCS7A01G487100 chr7A 76.231 1868 268 93 1014 2778 677723722 677721928 0.000000e+00 828.0
4 TraesCS7A01G487100 chr7A 88.031 259 23 8 2655 2909 677721589 677721335 1.870000e-77 300.0
5 TraesCS7A01G487100 chr7A 92.593 189 13 1 1 188 705601570 705601382 1.470000e-68 270.0
6 TraesCS7A01G487100 chr7A 81.481 108 20 0 2185 2292 677994098 677993991 4.410000e-14 89.8
7 TraesCS7A01G487100 chr7A 89.706 68 5 2 2539 2606 677999483 677999418 5.700000e-13 86.1
8 TraesCS7A01G487100 chr7B 88.810 1984 147 36 481 2448 657084138 657086062 0.000000e+00 2364.0
9 TraesCS7A01G487100 chr7B 82.986 1869 217 41 1014 2837 656529585 656527773 0.000000e+00 1596.0
10 TraesCS7A01G487100 chr7B 84.105 1447 203 14 1014 2449 657663279 657661849 0.000000e+00 1373.0
11 TraesCS7A01G487100 chr7B 81.608 1468 227 27 1014 2449 657313575 657315031 0.000000e+00 1175.0
12 TraesCS7A01G487100 chr7B 81.699 306 31 9 2925 3206 656527669 656527365 6.920000e-57 231.0
13 TraesCS7A01G487100 chr7B 79.273 275 37 12 511 776 657076478 657076741 1.180000e-39 174.0
14 TraesCS7A01G487100 chr7B 80.838 167 18 8 12 178 657083048 657083200 5.620000e-23 119.0
15 TraesCS7A01G487100 chr7B 81.333 150 22 4 1376 1522 657318354 657318500 2.020000e-22 117.0
16 TraesCS7A01G487100 chr7D 94.823 1526 60 6 938 2448 586700137 586701658 0.000000e+00 2362.0
17 TraesCS7A01G487100 chr7D 82.766 1880 200 55 603 2450 586502261 586500474 0.000000e+00 1563.0
18 TraesCS7A01G487100 chr7D 82.631 1376 208 20 1014 2369 586708185 586709549 0.000000e+00 1188.0
19 TraesCS7A01G487100 chr7D 76.669 1483 274 39 1014 2452 586832301 586830847 0.000000e+00 756.0
20 TraesCS7A01G487100 chr7D 77.312 1384 240 35 1014 2361 586754350 586755695 0.000000e+00 749.0
21 TraesCS7A01G487100 chr7D 88.033 610 41 19 1 608 586505864 586505285 0.000000e+00 693.0
22 TraesCS7A01G487100 chr7D 80.695 518 67 11 1014 1522 586745780 586746273 3.910000e-99 372.0
23 TraesCS7A01G487100 chr7D 82.609 299 35 4 2925 3206 586499776 586499478 6.870000e-62 248.0
24 TraesCS7A01G487100 chr7D 88.235 204 18 5 2704 2905 586500030 586499831 4.130000e-59 239.0
25 TraesCS7A01G487100 chr7D 90.141 71 3 3 2538 2606 586830884 586830816 4.410000e-14 89.8


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 TraesCS7A01G487100 chr7A 677824323 677827528 3205 False 5921.00 5921 100.00000 1 3206 1 chr7A.!!$F1 3205
1 TraesCS7A01G487100 chr7A 678144762 678146280 1518 True 1456.00 1456 84.15200 941 2449 1 chr7A.!!$R3 1508
2 TraesCS7A01G487100 chr7A 677833050 677834336 1286 False 1053.00 1053 81.74100 1014 2289 1 chr7A.!!$F2 1275
3 TraesCS7A01G487100 chr7A 677721335 677723722 2387 True 564.00 828 82.13100 1014 2909 2 chr7A.!!$R5 1895
4 TraesCS7A01G487100 chr7B 657661849 657663279 1430 True 1373.00 1373 84.10500 1014 2449 1 chr7B.!!$R1 1435
5 TraesCS7A01G487100 chr7B 657083048 657086062 3014 False 1241.50 2364 84.82400 12 2448 2 chr7B.!!$F2 2436
6 TraesCS7A01G487100 chr7B 656527365 656529585 2220 True 913.50 1596 82.34250 1014 3206 2 chr7B.!!$R2 2192
7 TraesCS7A01G487100 chr7B 657313575 657318500 4925 False 646.00 1175 81.47050 1014 2449 2 chr7B.!!$F3 1435
8 TraesCS7A01G487100 chr7D 586700137 586701658 1521 False 2362.00 2362 94.82300 938 2448 1 chr7D.!!$F1 1510
9 TraesCS7A01G487100 chr7D 586708185 586709549 1364 False 1188.00 1188 82.63100 1014 2369 1 chr7D.!!$F2 1355
10 TraesCS7A01G487100 chr7D 586754350 586755695 1345 False 749.00 749 77.31200 1014 2361 1 chr7D.!!$F4 1347
11 TraesCS7A01G487100 chr7D 586499478 586505864 6386 True 685.75 1563 85.41075 1 3206 4 chr7D.!!$R1 3205
12 TraesCS7A01G487100 chr7D 586830816 586832301 1485 True 422.90 756 83.40500 1014 2606 2 chr7D.!!$R2 1592

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
83 84 0.107508 GGCATCAGTTCAGCAGGCTA 60.108 55.0 0.0 0.0 0.0 3.93 F
905 4674 0.475048 GCCCCAACCCCTATAGCCTA 60.475 60.0 0.0 0.0 0.0 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1454 5264 1.203052 CCAGGTAAGCAATGCTGTTGG 59.797 52.381 9.14 10.55 39.62 3.77 R
2546 6573 0.743688 TGTTGCACATCAAAAGGCGT 59.256 45.000 0.00 0.00 36.26 5.68 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
25 26 0.464036 ATGATCCCTTCGCGTTGCTA 59.536 50.000 5.77 0.00 0.00 3.49
83 84 0.107508 GGCATCAGTTCAGCAGGCTA 60.108 55.000 0.00 0.00 0.00 3.93
114 115 2.410060 ACGCTGTCGACGTCAACA 59.590 55.556 17.16 13.23 40.28 3.33
117 118 1.275471 CGCTGTCGACGTCAACACAT 61.275 55.000 17.16 0.00 38.10 3.21
136 137 8.385858 CAACACATAAATATATGATCTCTGCCG 58.614 37.037 3.03 0.00 41.25 5.69
142 143 2.988010 TATGATCTCTGCCGCTTGTT 57.012 45.000 0.00 0.00 0.00 2.83
170 171 4.811908 TCAATGTGGATGCTGTGATTTTG 58.188 39.130 0.00 0.00 0.00 2.44
173 174 4.669206 TGTGGATGCTGTGATTTTGTTT 57.331 36.364 0.00 0.00 0.00 2.83
178 179 5.068855 TGGATGCTGTGATTTTGTTTCAGAA 59.931 36.000 0.00 0.00 0.00 3.02
180 181 4.681744 TGCTGTGATTTTGTTTCAGAACC 58.318 39.130 0.00 0.00 34.80 3.62
181 182 4.051237 GCTGTGATTTTGTTTCAGAACCC 58.949 43.478 0.00 0.00 34.80 4.11
182 183 4.202151 GCTGTGATTTTGTTTCAGAACCCT 60.202 41.667 0.00 0.00 34.80 4.34
183 184 5.261209 TGTGATTTTGTTTCAGAACCCTG 57.739 39.130 0.00 0.00 41.74 4.45
185 186 5.186797 TGTGATTTTGTTTCAGAACCCTGTT 59.813 36.000 0.00 0.00 41.16 3.16
188 189 6.593382 TGATTTTGTTTCAGAACCCTGTTTTG 59.407 34.615 0.00 0.00 41.16 2.44
189 190 5.476091 TTTGTTTCAGAACCCTGTTTTGT 57.524 34.783 0.00 0.00 41.16 2.83
191 192 5.570234 TGTTTCAGAACCCTGTTTTGTAC 57.430 39.130 0.00 0.00 41.16 2.90
192 193 5.258051 TGTTTCAGAACCCTGTTTTGTACT 58.742 37.500 0.00 0.00 41.16 2.73
193 194 5.355910 TGTTTCAGAACCCTGTTTTGTACTC 59.644 40.000 0.00 0.00 41.16 2.59
194 195 4.081322 TCAGAACCCTGTTTTGTACTCC 57.919 45.455 0.00 0.00 41.16 3.85
195 196 3.714798 TCAGAACCCTGTTTTGTACTCCT 59.285 43.478 0.00 0.00 41.16 3.69
196 197 3.815401 CAGAACCCTGTTTTGTACTCCTG 59.185 47.826 0.00 0.00 35.70 3.86
197 198 3.458487 AGAACCCTGTTTTGTACTCCTGT 59.542 43.478 0.00 0.00 0.00 4.00
198 199 3.208747 ACCCTGTTTTGTACTCCTGTG 57.791 47.619 0.00 0.00 0.00 3.66
199 200 2.775384 ACCCTGTTTTGTACTCCTGTGA 59.225 45.455 0.00 0.00 0.00 3.58
200 201 3.394606 ACCCTGTTTTGTACTCCTGTGAT 59.605 43.478 0.00 0.00 0.00 3.06
201 202 4.141251 ACCCTGTTTTGTACTCCTGTGATT 60.141 41.667 0.00 0.00 0.00 2.57
202 203 4.827284 CCCTGTTTTGTACTCCTGTGATTT 59.173 41.667 0.00 0.00 0.00 2.17
203 204 5.301805 CCCTGTTTTGTACTCCTGTGATTTT 59.698 40.000 0.00 0.00 0.00 1.82
204 205 6.208644 CCTGTTTTGTACTCCTGTGATTTTG 58.791 40.000 0.00 0.00 0.00 2.44
205 206 6.142818 TGTTTTGTACTCCTGTGATTTTGG 57.857 37.500 0.00 0.00 0.00 3.28
206 207 5.888724 TGTTTTGTACTCCTGTGATTTTGGA 59.111 36.000 0.00 0.00 0.00 3.53
280 347 5.890419 AGTCCAAAATCATGGGAAGATTCTC 59.110 40.000 0.00 0.00 41.05 2.87
282 349 6.153340 GTCCAAAATCATGGGAAGATTCTCAA 59.847 38.462 0.00 0.00 41.77 3.02
444 512 6.439375 TGGGAGCATGTACTTCTCTAACTAAA 59.561 38.462 0.00 0.00 0.00 1.85
487 1209 2.029828 GTCTCACGTCCAAGTGACTCAT 60.030 50.000 0.00 0.00 45.18 2.90
534 1256 9.752274 TTTATGAAAATCGCAATTTATTTGTGC 57.248 25.926 0.00 0.00 43.98 4.57
544 1266 7.812191 TCGCAATTTATTTGTGCTCTGTAAAAT 59.188 29.630 0.00 0.00 43.98 1.82
575 1297 8.291740 AAAATGAAACCAAGCATTTTTCTATGC 58.708 29.630 0.00 0.00 46.68 3.14
598 1320 5.502544 GCGACAATGGCTAGTTATTCACTTC 60.503 44.000 0.00 0.00 36.88 3.01
599 1321 5.580691 CGACAATGGCTAGTTATTCACTTCA 59.419 40.000 0.00 0.00 36.88 3.02
684 4436 4.640201 CCCACTATAAAATCCACACACAGG 59.360 45.833 0.00 0.00 0.00 4.00
694 4446 3.691575 TCCACACACAGGTTTCTTTTGA 58.308 40.909 0.00 0.00 0.00 2.69
748 4500 7.865385 TGAAATTTTCTGAAATAAACGGACCAG 59.135 33.333 10.33 0.00 34.44 4.00
752 4504 3.325425 TCTGAAATAAACGGACCAGGTGA 59.675 43.478 0.00 0.00 0.00 4.02
771 4523 7.194278 CAGGTGATCTTCATATCAAAGCAAAG 58.806 38.462 0.00 0.00 37.61 2.77
782 4535 8.084073 TCATATCAAAGCAAAGAAAACCTCAAG 58.916 33.333 0.00 0.00 0.00 3.02
885 4654 2.361357 CACTCCGTCGAGTCCCCT 60.361 66.667 0.00 0.00 46.90 4.79
893 4662 4.410400 CGAGTCCCCTGCCCCAAC 62.410 72.222 0.00 0.00 0.00 3.77
894 4663 4.048470 GAGTCCCCTGCCCCAACC 62.048 72.222 0.00 0.00 0.00 3.77
899 4668 2.699938 CCCTGCCCCAACCCCTAT 60.700 66.667 0.00 0.00 0.00 2.57
900 4669 1.386772 CCCTGCCCCAACCCCTATA 60.387 63.158 0.00 0.00 0.00 1.31
901 4670 1.427072 CCCTGCCCCAACCCCTATAG 61.427 65.000 0.00 0.00 0.00 1.31
902 4671 1.456287 CTGCCCCAACCCCTATAGC 59.544 63.158 0.00 0.00 0.00 2.97
903 4672 2.069165 CTGCCCCAACCCCTATAGCC 62.069 65.000 0.00 0.00 0.00 3.93
904 4673 1.774631 GCCCCAACCCCTATAGCCT 60.775 63.158 0.00 0.00 0.00 4.58
905 4674 0.475048 GCCCCAACCCCTATAGCCTA 60.475 60.000 0.00 0.00 0.00 3.93
906 4675 1.359168 CCCCAACCCCTATAGCCTAC 58.641 60.000 0.00 0.00 0.00 3.18
907 4676 1.359168 CCCAACCCCTATAGCCTACC 58.641 60.000 0.00 0.00 0.00 3.18
908 4677 1.359168 CCAACCCCTATAGCCTACCC 58.641 60.000 0.00 0.00 0.00 3.69
909 4678 1.415421 CCAACCCCTATAGCCTACCCA 60.415 57.143 0.00 0.00 0.00 4.51
910 4679 2.632537 CAACCCCTATAGCCTACCCAT 58.367 52.381 0.00 0.00 0.00 4.00
911 4680 2.986728 CAACCCCTATAGCCTACCCATT 59.013 50.000 0.00 0.00 0.00 3.16
912 4681 2.917205 ACCCCTATAGCCTACCCATTC 58.083 52.381 0.00 0.00 0.00 2.67
913 4682 2.197465 CCCCTATAGCCTACCCATTCC 58.803 57.143 0.00 0.00 0.00 3.01
914 4683 2.496523 CCCCTATAGCCTACCCATTCCA 60.497 54.545 0.00 0.00 0.00 3.53
915 4684 2.840651 CCCTATAGCCTACCCATTCCAG 59.159 54.545 0.00 0.00 0.00 3.86
916 4685 2.237392 CCTATAGCCTACCCATTCCAGC 59.763 54.545 0.00 0.00 0.00 4.85
917 4686 1.068121 ATAGCCTACCCATTCCAGCC 58.932 55.000 0.00 0.00 0.00 4.85
918 4687 1.407656 TAGCCTACCCATTCCAGCCG 61.408 60.000 0.00 0.00 0.00 5.52
919 4688 2.203209 CCTACCCATTCCAGCCGC 60.203 66.667 0.00 0.00 0.00 6.53
920 4689 2.203209 CTACCCATTCCAGCCGCC 60.203 66.667 0.00 0.00 0.00 6.13
921 4690 3.012119 TACCCATTCCAGCCGCCA 61.012 61.111 0.00 0.00 0.00 5.69
922 4691 3.338275 TACCCATTCCAGCCGCCAC 62.338 63.158 0.00 0.00 0.00 5.01
936 4705 3.966543 CCACCCCTTCCAAGCCGT 61.967 66.667 0.00 0.00 0.00 5.68
939 4708 4.016706 CCCCTTCCAAGCCGTCGT 62.017 66.667 0.00 0.00 0.00 4.34
1156 4945 3.522553 CCCGTGTACAGGAAGAAGATTC 58.477 50.000 16.93 0.00 0.00 2.52
1515 5325 3.885297 CCACTCAAGAGTTCCATGTGTTT 59.115 43.478 0.00 0.00 40.20 2.83
1541 5351 1.068125 TCTACACGAATGGTCACACCG 60.068 52.381 0.00 0.00 42.58 4.94
1554 5367 3.636231 CACCGGAACTGGGGCTCA 61.636 66.667 9.46 0.00 0.00 4.26
1914 5756 9.667107 CTTAGTGTTGAGATTTATAACTGGGAA 57.333 33.333 0.00 0.00 0.00 3.97
2234 6122 1.131883 CTGCTGATTGAAGAAAGGGCG 59.868 52.381 0.00 0.00 0.00 6.13
2343 6244 4.635765 CCAGCTTTCGTTTCCAGATTGATA 59.364 41.667 0.00 0.00 0.00 2.15
2379 6281 5.929415 TCATTTGTAGTATTTGTGTCGCTGA 59.071 36.000 0.00 0.00 0.00 4.26
2410 6312 4.118410 CTCATGGATGTGTTAGTCTGAGC 58.882 47.826 0.00 0.00 0.00 4.26
2459 6375 4.702131 GGGCAACAAGTATGAGACATTTCT 59.298 41.667 0.00 0.00 39.74 2.52
2491 6422 9.515226 AGCCAGAATTGTTTATGTTCTAGTTTA 57.485 29.630 0.00 0.00 31.40 2.01
2543 6570 4.859304 TGTACGAGACACTTGGTATGTT 57.141 40.909 0.00 0.00 31.20 2.71
2546 6573 5.706833 TGTACGAGACACTTGGTATGTTCTA 59.293 40.000 0.00 0.00 31.20 2.10
2547 6574 5.056894 ACGAGACACTTGGTATGTTCTAC 57.943 43.478 0.00 0.00 0.00 2.59
2583 6628 5.105187 TGCAACAAGTAGAGCTGTATGAGAT 60.105 40.000 0.00 0.00 0.00 2.75
2596 6647 5.220548 GCTGTATGAGATGCTTTAGTGTGTG 60.221 44.000 0.00 0.00 0.00 3.82
2597 6648 5.793817 TGTATGAGATGCTTTAGTGTGTGT 58.206 37.500 0.00 0.00 0.00 3.72
2599 6650 5.869753 ATGAGATGCTTTAGTGTGTGTTC 57.130 39.130 0.00 0.00 0.00 3.18
2601 6652 6.096673 TGAGATGCTTTAGTGTGTGTTCTA 57.903 37.500 0.00 0.00 0.00 2.10
2604 6655 7.661437 TGAGATGCTTTAGTGTGTGTTCTATTT 59.339 33.333 0.00 0.00 0.00 1.40
2676 7250 5.186996 TCTGGTGTTTGCAAGATTTTCTC 57.813 39.130 0.00 0.00 0.00 2.87
2723 7455 8.327941 TGATGCTATATTCATAGAAGTTTGCC 57.672 34.615 0.00 0.00 36.96 4.52
2742 7474 2.423185 GCCTATGTGTGCAGCATGTAAA 59.577 45.455 12.46 0.00 39.31 2.01
2792 7525 8.084073 TGAGAAAGGTCAATTTTGATGATTCAC 58.916 33.333 12.93 9.41 39.73 3.18
2805 7538 4.780815 GATGATTCACATCCCAGTTGGTA 58.219 43.478 0.00 0.00 46.78 3.25
2806 7539 4.649267 TGATTCACATCCCAGTTGGTAA 57.351 40.909 0.00 0.00 34.77 2.85
2813 7546 6.489603 TCACATCCCAGTTGGTAAATGTTAT 58.510 36.000 7.80 0.00 32.27 1.89
2814 7547 7.634718 TCACATCCCAGTTGGTAAATGTTATA 58.365 34.615 7.80 0.00 32.27 0.98
2815 7548 7.773224 TCACATCCCAGTTGGTAAATGTTATAG 59.227 37.037 7.80 0.86 32.27 1.31
2905 7643 7.372451 TGTAAGGATCCAAATTGAAAGTACG 57.628 36.000 15.82 0.00 0.00 3.67
2909 7647 4.157840 GGATCCAAATTGAAAGTACGGCTT 59.842 41.667 6.95 0.00 39.52 4.35
2910 7648 4.497473 TCCAAATTGAAAGTACGGCTTG 57.503 40.909 0.00 0.00 37.52 4.01
2911 7649 4.138290 TCCAAATTGAAAGTACGGCTTGA 58.862 39.130 0.00 0.00 37.52 3.02
2914 7652 6.431543 TCCAAATTGAAAGTACGGCTTGATTA 59.568 34.615 0.00 0.00 37.52 1.75
2916 7654 7.432252 CCAAATTGAAAGTACGGCTTGATTATC 59.568 37.037 0.00 0.00 37.52 1.75
2917 7655 7.865706 AATTGAAAGTACGGCTTGATTATCT 57.134 32.000 0.00 0.00 37.52 1.98
2923 7661 9.525409 GAAAGTACGGCTTGATTATCTACTTTA 57.475 33.333 12.06 0.00 37.52 1.85
2964 7802 2.532250 ATCCCTGATCCAAAACCACC 57.468 50.000 0.00 0.00 0.00 4.61
2965 7803 1.153539 TCCCTGATCCAAAACCACCA 58.846 50.000 0.00 0.00 0.00 4.17
2972 7810 5.105756 CCTGATCCAAAACCACCATAACTTC 60.106 44.000 0.00 0.00 0.00 3.01
2979 7817 6.350110 CCAAAACCACCATAACTTCATACTGG 60.350 42.308 0.00 0.00 0.00 4.00
2980 7818 3.886123 ACCACCATAACTTCATACTGGC 58.114 45.455 0.00 0.00 0.00 4.85
2997 7835 1.539157 GGCTTTTGTTGCTCTAGCCT 58.461 50.000 0.00 0.00 46.14 4.58
3002 7840 4.201861 GCTTTTGTTGCTCTAGCCTATGTC 60.202 45.833 0.00 0.00 41.18 3.06
3016 7863 3.864003 GCCTATGTCTTTTCGTACTCACC 59.136 47.826 0.00 0.00 0.00 4.02
3019 7866 1.345415 TGTCTTTTCGTACTCACCCCC 59.655 52.381 0.00 0.00 0.00 5.40
3034 7881 5.315109 ACTCACCCCCTTAGTTTTCCTATTT 59.685 40.000 0.00 0.00 0.00 1.40
3046 7893 4.591321 TTTCCTATTTCTGGCATCCTGT 57.409 40.909 0.00 0.00 0.00 4.00
3064 8609 7.633553 GCATCCTGTTATTTCCTGCCTTTATTT 60.634 37.037 0.00 0.00 0.00 1.40
3068 8613 9.533253 CCTGTTATTTCCTGCCTTTATTTATTG 57.467 33.333 0.00 0.00 0.00 1.90
3091 8639 4.813296 AGCTACACTTTTGTTTCTTCGG 57.187 40.909 0.00 0.00 37.15 4.30
3135 9984 4.104738 ACTTCCATTGAACCTCTTTCCTGA 59.895 41.667 0.00 0.00 32.58 3.86
3167 10028 4.997395 TCAGTATTCCAGCAAGTTCTGAAC 59.003 41.667 12.54 12.54 36.19 3.18
3183 10044 6.761714 AGTTCTGAACGTTGTACTGATTTTCT 59.238 34.615 5.00 0.00 36.23 2.52
3190 10051 4.024048 CGTTGTACTGATTTTCTGCCTTGT 60.024 41.667 0.00 0.00 0.00 3.16
3191 10052 5.452777 GTTGTACTGATTTTCTGCCTTGTC 58.547 41.667 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.816074 TTTTAGCAACGCGAAGGGAT 58.184 45.000 15.93 0.00 46.37 3.85
114 115 6.882656 AGCGGCAGAGATCATATATTTATGT 58.117 36.000 1.45 0.00 37.16 2.29
117 118 6.701340 ACAAGCGGCAGAGATCATATATTTA 58.299 36.000 1.45 0.00 0.00 1.40
132 133 1.532523 TTGATCATCAACAAGCGGCA 58.467 45.000 1.45 0.00 30.26 5.69
136 137 4.707030 TCCACATTGATCATCAACAAGC 57.293 40.909 0.98 0.00 39.45 4.01
142 143 3.630312 CACAGCATCCACATTGATCATCA 59.370 43.478 0.00 0.00 0.00 3.07
170 171 5.220989 GGAGTACAAAACAGGGTTCTGAAAC 60.221 44.000 0.00 0.00 43.49 2.78
173 174 3.714798 AGGAGTACAAAACAGGGTTCTGA 59.285 43.478 0.00 0.00 43.49 3.27
178 179 2.775384 TCACAGGAGTACAAAACAGGGT 59.225 45.455 0.00 0.00 0.00 4.34
180 181 6.208644 CAAAATCACAGGAGTACAAAACAGG 58.791 40.000 0.00 0.00 0.00 4.00
181 182 6.039270 TCCAAAATCACAGGAGTACAAAACAG 59.961 38.462 0.00 0.00 0.00 3.16
182 183 5.888724 TCCAAAATCACAGGAGTACAAAACA 59.111 36.000 0.00 0.00 0.00 2.83
183 184 6.385649 TCCAAAATCACAGGAGTACAAAAC 57.614 37.500 0.00 0.00 0.00 2.43
191 192 6.380274 TAGGTACTACTCCAAAATCACAGGAG 59.620 42.308 6.18 6.18 46.84 3.69
192 193 5.091552 AGGTACTACTCCAAAATCACAGGA 58.908 41.667 0.00 0.00 36.02 3.86
193 194 5.422214 AGGTACTACTCCAAAATCACAGG 57.578 43.478 0.00 0.00 36.02 4.00
194 195 6.043411 GCTAGGTACTACTCCAAAATCACAG 58.957 44.000 0.00 0.00 41.75 3.66
195 196 5.105064 GGCTAGGTACTACTCCAAAATCACA 60.105 44.000 0.00 0.00 41.75 3.58
196 197 5.128991 AGGCTAGGTACTACTCCAAAATCAC 59.871 44.000 0.00 0.00 41.75 3.06
197 198 5.278061 AGGCTAGGTACTACTCCAAAATCA 58.722 41.667 0.00 0.00 41.75 2.57
198 199 5.599242 AGAGGCTAGGTACTACTCCAAAATC 59.401 44.000 0.00 0.00 41.75 2.17
199 200 5.530243 AGAGGCTAGGTACTACTCCAAAAT 58.470 41.667 0.00 0.00 41.75 1.82
200 201 4.944177 AGAGGCTAGGTACTACTCCAAAA 58.056 43.478 0.00 0.00 41.75 2.44
201 202 4.534797 GAGAGGCTAGGTACTACTCCAAA 58.465 47.826 0.00 0.00 41.75 3.28
202 203 3.433314 CGAGAGGCTAGGTACTACTCCAA 60.433 52.174 0.00 0.00 41.75 3.53
203 204 2.104451 CGAGAGGCTAGGTACTACTCCA 59.896 54.545 0.00 0.00 41.75 3.86
204 205 2.104622 ACGAGAGGCTAGGTACTACTCC 59.895 54.545 0.00 0.00 41.75 3.85
205 206 3.473923 ACGAGAGGCTAGGTACTACTC 57.526 52.381 0.00 0.00 41.75 2.59
206 207 3.433456 GGAACGAGAGGCTAGGTACTACT 60.433 52.174 0.00 0.00 41.75 2.57
207 208 2.877786 GGAACGAGAGGCTAGGTACTAC 59.122 54.545 0.00 0.00 41.75 2.73
239 251 2.393646 GACTAGGCTTCCTCACAGGAT 58.606 52.381 0.00 0.00 45.34 3.24
460 538 4.208666 GTCACTTGGACGTGAGACTTTTAC 59.791 45.833 0.00 0.00 43.94 2.01
565 1287 4.941263 ACTAGCCATTGTCGCATAGAAAAA 59.059 37.500 0.00 0.00 28.30 1.94
575 1297 5.580691 TGAAGTGAATAACTAGCCATTGTCG 59.419 40.000 0.00 0.00 38.56 4.35
658 4409 5.013704 TGTGTGTGGATTTTATAGTGGGTCT 59.986 40.000 0.00 0.00 0.00 3.85
667 4418 6.976934 AAGAAACCTGTGTGTGGATTTTAT 57.023 33.333 0.00 0.00 0.00 1.40
697 4449 8.932791 CAAAGCTGAGCTGAAAATATGATTTTT 58.067 29.630 8.16 0.00 39.62 1.94
701 4453 7.400599 TTCAAAGCTGAGCTGAAAATATGAT 57.599 32.000 8.16 0.00 39.62 2.45
705 4457 8.891671 AAAATTTCAAAGCTGAGCTGAAAATA 57.108 26.923 20.76 4.40 39.62 1.40
741 4493 3.321968 TGATATGAAGATCACCTGGTCCG 59.678 47.826 0.00 0.00 30.75 4.79
748 4500 7.325660 TCTTTGCTTTGATATGAAGATCACC 57.674 36.000 0.00 0.00 35.56 4.02
752 4504 8.810041 AGGTTTTCTTTGCTTTGATATGAAGAT 58.190 29.630 0.71 0.00 0.00 2.40
771 4523 9.260002 TGCTTTGATTTATTTCTTGAGGTTTTC 57.740 29.630 0.00 0.00 0.00 2.29
820 4573 3.541632 GAAAAGGCCCACGATGAAGATA 58.458 45.455 0.00 0.00 0.00 1.98
821 4574 2.369394 GAAAAGGCCCACGATGAAGAT 58.631 47.619 0.00 0.00 0.00 2.40
822 4575 1.613255 GGAAAAGGCCCACGATGAAGA 60.613 52.381 0.00 0.00 0.00 2.87
885 4654 2.082414 GGCTATAGGGGTTGGGGCA 61.082 63.158 1.04 0.00 0.00 5.36
893 4662 2.197465 GGAATGGGTAGGCTATAGGGG 58.803 57.143 0.00 0.00 0.00 4.79
894 4663 2.840651 CTGGAATGGGTAGGCTATAGGG 59.159 54.545 0.00 0.00 0.00 3.53
895 4664 2.237392 GCTGGAATGGGTAGGCTATAGG 59.763 54.545 0.00 0.00 0.00 2.57
897 4666 2.266279 GGCTGGAATGGGTAGGCTATA 58.734 52.381 0.00 0.00 34.52 1.31
899 4668 1.407656 CGGCTGGAATGGGTAGGCTA 61.408 60.000 0.00 0.00 35.12 3.93
900 4669 2.746375 CGGCTGGAATGGGTAGGCT 61.746 63.158 0.00 0.00 35.12 4.58
901 4670 2.203209 CGGCTGGAATGGGTAGGC 60.203 66.667 0.00 0.00 0.00 3.93
902 4671 2.203209 GCGGCTGGAATGGGTAGG 60.203 66.667 0.00 0.00 0.00 3.18
903 4672 2.203209 GGCGGCTGGAATGGGTAG 60.203 66.667 0.00 0.00 0.00 3.18
904 4673 3.012119 TGGCGGCTGGAATGGGTA 61.012 61.111 11.43 0.00 0.00 3.69
905 4674 4.740822 GTGGCGGCTGGAATGGGT 62.741 66.667 11.43 0.00 0.00 4.51
919 4688 3.920093 GACGGCTTGGAAGGGGTGG 62.920 68.421 0.00 0.00 0.00 4.61
920 4689 2.359975 GACGGCTTGGAAGGGGTG 60.360 66.667 0.00 0.00 0.00 4.61
921 4690 4.016706 CGACGGCTTGGAAGGGGT 62.017 66.667 0.00 0.00 0.00 4.95
922 4691 3.952628 GACGACGGCTTGGAAGGGG 62.953 68.421 0.00 0.00 0.00 4.79
923 4692 2.434359 GACGACGGCTTGGAAGGG 60.434 66.667 0.00 0.00 0.00 3.95
924 4693 2.809601 CGACGACGGCTTGGAAGG 60.810 66.667 0.00 0.00 35.72 3.46
925 4694 3.479269 GCGACGACGGCTTGGAAG 61.479 66.667 9.67 0.00 40.15 3.46
1065 4850 1.429148 GAGATTTGTAGGGCACGCGG 61.429 60.000 12.47 0.00 0.00 6.46
1454 5264 1.203052 CCAGGTAAGCAATGCTGTTGG 59.797 52.381 9.14 10.55 39.62 3.77
1515 5325 4.202172 TGTGACCATTCGTGTAGAAACTCA 60.202 41.667 0.00 0.00 42.91 3.41
1541 5351 1.408969 TTTGTTTGAGCCCCAGTTCC 58.591 50.000 0.00 0.00 0.00 3.62
2234 6122 0.983378 AGAGTACCTCACCCATGGCC 60.983 60.000 6.09 0.00 32.06 5.36
2361 6262 5.779806 ACATTCAGCGACACAAATACTAC 57.220 39.130 0.00 0.00 0.00 2.73
2410 6312 6.159293 TCAAAAGACACAGAGCATACTACAG 58.841 40.000 0.00 0.00 0.00 2.74
2427 6331 5.076182 TCATACTTGTTGCCCATCAAAAGA 58.924 37.500 0.00 0.00 36.26 2.52
2459 6375 6.892658 ACATAAACAATTCTGGCTTACACA 57.107 33.333 0.00 0.00 0.00 3.72
2491 6422 2.947652 GGCTCAGATTGCATGTGTACAT 59.052 45.455 0.00 0.00 36.96 2.29
2542 6569 2.499197 TGCACATCAAAAGGCGTAGAA 58.501 42.857 0.00 0.00 0.00 2.10
2543 6570 2.177394 TGCACATCAAAAGGCGTAGA 57.823 45.000 0.00 0.00 0.00 2.59
2546 6573 0.743688 TGTTGCACATCAAAAGGCGT 59.256 45.000 0.00 0.00 36.26 5.68
2547 6574 1.788308 CTTGTTGCACATCAAAAGGCG 59.212 47.619 0.00 0.00 36.26 5.52
2575 6618 6.591834 AGAACACACACTAAAGCATCTCATAC 59.408 38.462 0.00 0.00 0.00 2.39
2618 6669 6.769512 TCTTGCTTAGACACTCAGGTAAAAT 58.230 36.000 0.00 0.00 0.00 1.82
2723 7455 4.392754 TCACTTTACATGCTGCACACATAG 59.607 41.667 3.57 2.92 0.00 2.23
2742 7474 4.469227 ACCTTCTGAGTTAGCATGATCACT 59.531 41.667 0.00 0.00 0.00 3.41
2755 7487 3.711704 TGACCTTTCTCAACCTTCTGAGT 59.288 43.478 0.86 0.00 42.93 3.41
2792 7525 9.793259 ATACTATAACATTTACCAACTGGGATG 57.207 33.333 0.00 4.44 41.15 3.51
2879 7614 7.962918 CGTACTTTCAATTTGGATCCTTACAAG 59.037 37.037 14.23 8.35 0.00 3.16
2923 7661 8.745590 GGGATATACCAACAGTGTTGTTAAATT 58.254 33.333 29.28 11.64 45.53 1.82
2935 7708 5.567037 TTGGATCAGGGATATACCAACAG 57.433 43.478 6.78 0.00 41.20 3.16
2964 7802 6.308766 GCAACAAAAGCCAGTATGAAGTTATG 59.691 38.462 0.00 0.00 39.69 1.90
2965 7803 6.209391 AGCAACAAAAGCCAGTATGAAGTTAT 59.791 34.615 0.00 0.00 39.69 1.89
2972 7810 4.437930 GCTAGAGCAACAAAAGCCAGTATG 60.438 45.833 0.00 0.00 41.59 2.39
2979 7817 3.691609 ACATAGGCTAGAGCAACAAAAGC 59.308 43.478 3.54 0.00 44.36 3.51
2980 7818 5.181748 AGACATAGGCTAGAGCAACAAAAG 58.818 41.667 3.54 0.00 44.36 2.27
2996 7834 4.430908 GGGGTGAGTACGAAAAGACATAG 58.569 47.826 0.00 0.00 0.00 2.23
2997 7835 3.196254 GGGGGTGAGTACGAAAAGACATA 59.804 47.826 0.00 0.00 0.00 2.29
3002 7840 2.853235 AAGGGGGTGAGTACGAAAAG 57.147 50.000 0.00 0.00 0.00 2.27
3016 7863 4.645136 GCCAGAAATAGGAAAACTAAGGGG 59.355 45.833 0.00 0.00 34.79 4.79
3019 7866 6.830838 AGGATGCCAGAAATAGGAAAACTAAG 59.169 38.462 0.00 0.00 34.79 2.18
3034 7881 3.889815 CAGGAAATAACAGGATGCCAGA 58.110 45.455 0.00 0.00 42.53 3.86
3064 8609 8.492748 CGAAGAAACAAAAGTGTAGCTACAATA 58.507 33.333 27.61 2.94 36.80 1.90
3068 8613 5.676953 CCGAAGAAACAAAAGTGTAGCTAC 58.323 41.667 17.30 17.30 36.80 3.58
3091 8639 0.543749 ACCTGCAGGAGATAACCAGC 59.456 55.000 39.19 0.00 41.71 4.85
3135 9984 5.946942 TGCTGGAATACTGAGAATCTCTT 57.053 39.130 11.92 1.24 34.92 2.85
3167 10028 4.024048 ACAAGGCAGAAAATCAGTACAACG 60.024 41.667 0.00 0.00 0.00 4.10
3183 10044 0.840617 TTAGTGTGTGGGACAAGGCA 59.159 50.000 0.00 0.00 44.16 4.75


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

AutoCloner maintained by Alex Coulton.