Multiple sequence alignment - TraesCS5B01G319300

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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 TraesCS5B01G319300 chr5B 100.000 5271 0 0 1 5271 503322638 503327908 0.000000e+00 9734.0
1 TraesCS5B01G319300 chr5B 92.779 457 7 2 1 431 680776494 680776950 5.760000e-179 638.0
2 TraesCS5B01G319300 chr5B 91.239 468 15 2 1 442 256586760 256586293 9.700000e-172 614.0
3 TraesCS5B01G319300 chr5B 97.546 163 4 0 269 431 503317018 503316856 4.020000e-71 279.0
4 TraesCS5B01G319300 chr5B 97.546 163 4 0 269 431 680770515 680770353 4.020000e-71 279.0
5 TraesCS5B01G319300 chr5D 94.664 4779 165 46 500 5247 416596195 416600914 0.000000e+00 7330.0
6 TraesCS5B01G319300 chr5A 93.539 4798 183 57 498 5271 529364592 529369286 0.000000e+00 7025.0
7 TraesCS5B01G319300 chr1D 87.680 763 58 17 1235 1976 59075671 59074924 0.000000e+00 856.0
8 TraesCS5B01G319300 chr6B 90.132 456 20 3 1 431 463362666 463363121 2.130000e-158 569.0
9 TraesCS5B01G319300 chr6B 95.851 241 8 2 207 447 95220374 95220136 6.400000e-104 388.0
10 TraesCS5B01G319300 chr6B 92.683 164 6 3 1 158 95220636 95220473 1.140000e-56 231.0
11 TraesCS5B01G319300 chr7B 89.189 444 38 6 1 434 15028305 15028748 3.590000e-151 545.0
12 TraesCS5B01G319300 chr7B 97.345 226 6 0 207 432 15022765 15022540 8.280000e-103 385.0
13 TraesCS5B01G319300 chr2B 97.696 217 5 0 207 423 41099029 41099245 1.790000e-99 374.0
14 TraesCS5B01G319300 chr3D 93.056 72 4 1 436 506 294599462 294599391 2.600000e-18 104.0
15 TraesCS5B01G319300 chr3D 94.118 68 4 0 436 503 456109645 456109712 2.600000e-18 104.0
16 TraesCS5B01G319300 chr3D 93.939 66 2 2 433 498 456108274 456108211 1.210000e-16 99.0
17 TraesCS5B01G319300 chr2D 94.030 67 4 0 436 502 3218709 3218643 9.340000e-18 102.0
18 TraesCS5B01G319300 chr4D 92.857 70 4 1 436 505 175784275 175784343 3.360000e-17 100.0
19 TraesCS5B01G319300 chr1B 93.846 65 4 0 436 500 641843630 641843566 1.210000e-16 99.0
20 TraesCS5B01G319300 chr7D 96.552 58 2 0 436 493 443327982 443328039 4.340000e-16 97.1
21 TraesCS5B01G319300 chr7D 89.231 65 7 0 1223 1287 117261119 117261183 1.220000e-11 82.4
22 TraesCS5B01G319300 chr6D 93.750 64 3 1 436 499 455571082 455571020 1.560000e-15 95.3
23 TraesCS5B01G319300 chr3B 89.610 77 5 2 433 507 41977853 41977778 1.560000e-15 95.3


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 TraesCS5B01G319300 chr5B 503322638 503327908 5270 False 9734.0 9734 100.000 1 5271 1 chr5B.!!$F1 5270
1 TraesCS5B01G319300 chr5D 416596195 416600914 4719 False 7330.0 7330 94.664 500 5247 1 chr5D.!!$F1 4747
2 TraesCS5B01G319300 chr5A 529364592 529369286 4694 False 7025.0 7025 93.539 498 5271 1 chr5A.!!$F1 4773
3 TraesCS5B01G319300 chr1D 59074924 59075671 747 True 856.0 856 87.680 1235 1976 1 chr1D.!!$R1 741
4 TraesCS5B01G319300 chr6B 95220136 95220636 500 True 309.5 388 94.267 1 447 2 chr6B.!!$R1 446

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
481 538 0.250510 TGCAGTACAACCGATGGCAA 60.251 50.0 0.00 0.0 0.00 4.52 F
1807 1902 0.319211 CAACTGGCACTGCAATGTGG 60.319 55.0 8.06 0.0 38.31 4.17 F
2365 2463 0.960861 TCGATGTGCTCTCGGTGTCT 60.961 55.0 7.45 0.0 36.78 3.41 F
3481 3584 0.038166 TGGCTTCATGGTCACCTTCC 59.962 55.0 0.00 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2308 2406 0.179111 CGTCGAAGGCAGCAAGGATA 60.179 55.000 0.0 0.0 0.00 2.59 R
2948 3051 0.965866 CGGTCTCTACTGCCACCTGA 60.966 60.000 0.0 0.0 0.00 3.86 R
4222 4327 0.547075 TTGTCCGAACCACCAAAGGA 59.453 50.000 0.0 0.0 0.00 3.36 R
4298 4404 1.000394 TGTTCTCATGACCGAAAGCGA 60.000 47.619 0.0 0.0 40.82 4.93 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
125 132 0.753262 GCTAGGGATTGAAGAGCGGA 59.247 55.000 0.00 0.00 0.00 5.54
155 178 2.277072 CGGGGAGAGAGAGGAGCA 59.723 66.667 0.00 0.00 0.00 4.26
159 197 0.755327 GGGAGAGAGAGGAGCAGGAC 60.755 65.000 0.00 0.00 0.00 3.85
161 199 1.493022 GGAGAGAGAGGAGCAGGACTA 59.507 57.143 0.00 0.00 0.00 2.59
169 207 2.103941 GAGGAGCAGGACTAGGGATTTG 59.896 54.545 0.00 0.00 0.00 2.32
187 225 1.682684 GACGGGGAGAGAGGAGCAA 60.683 63.158 0.00 0.00 0.00 3.91
189 227 2.907236 GGGGAGAGAGGAGCAAGC 59.093 66.667 0.00 0.00 0.00 4.01
192 230 1.521616 GGAGAGAGGAGCAAGCAGG 59.478 63.158 0.00 0.00 0.00 4.85
197 235 0.326427 AGAGGAGCAAGCAGGGAGAT 60.326 55.000 0.00 0.00 0.00 2.75
198 236 1.062581 AGAGGAGCAAGCAGGGAGATA 60.063 52.381 0.00 0.00 0.00 1.98
199 237 1.344114 GAGGAGCAAGCAGGGAGATAG 59.656 57.143 0.00 0.00 0.00 2.08
200 238 1.062581 AGGAGCAAGCAGGGAGATAGA 60.063 52.381 0.00 0.00 0.00 1.98
201 239 1.344114 GGAGCAAGCAGGGAGATAGAG 59.656 57.143 0.00 0.00 0.00 2.43
205 243 1.344114 CAAGCAGGGAGATAGAGGAGC 59.656 57.143 0.00 0.00 0.00 4.70
211 268 1.531840 GAGATAGAGGAGCGGGGCA 60.532 63.158 0.00 0.00 0.00 5.36
230 287 4.081862 GGGCAATTTTACACTTAACCCCTC 60.082 45.833 0.00 0.00 0.00 4.30
276 333 1.557443 GAGAACGTGGCGGTCAACAG 61.557 60.000 9.27 0.00 46.95 3.16
291 348 0.535102 AACAGGTGGTCAAAGGAGCG 60.535 55.000 0.00 0.00 44.47 5.03
301 358 0.741221 CAAAGGAGCGGCTACTCACC 60.741 60.000 16.56 5.82 38.50 4.02
387 444 7.487189 CGTATTTCTAAGTTCAGTGACCGTATT 59.513 37.037 0.00 0.00 0.00 1.89
432 489 6.465439 TGACCGTGAGTGTATTTATCTCAT 57.535 37.500 0.00 0.00 39.77 2.90
433 490 6.273071 TGACCGTGAGTGTATTTATCTCATG 58.727 40.000 0.00 0.00 41.83 3.07
459 516 6.715347 AAAAATTTAGTGGCAGAACTGAGT 57.285 33.333 5.97 0.00 0.00 3.41
460 517 7.817418 AAAAATTTAGTGGCAGAACTGAGTA 57.183 32.000 5.97 0.00 0.00 2.59
461 518 7.440523 AAAATTTAGTGGCAGAACTGAGTAG 57.559 36.000 5.97 0.00 0.00 2.57
462 519 5.746990 ATTTAGTGGCAGAACTGAGTAGT 57.253 39.130 5.97 0.00 39.32 2.73
463 520 4.521130 TTAGTGGCAGAACTGAGTAGTG 57.479 45.455 5.97 0.00 37.19 2.74
464 521 1.001406 AGTGGCAGAACTGAGTAGTGC 59.999 52.381 9.87 9.87 37.19 4.40
465 522 1.047801 TGGCAGAACTGAGTAGTGCA 58.952 50.000 17.61 4.89 37.19 4.57
466 523 1.001293 TGGCAGAACTGAGTAGTGCAG 59.999 52.381 17.61 0.00 37.19 4.41
468 525 2.231478 GGCAGAACTGAGTAGTGCAGTA 59.769 50.000 17.61 0.00 45.27 2.74
469 526 3.246619 GCAGAACTGAGTAGTGCAGTAC 58.753 50.000 21.85 21.85 45.27 2.73
470 527 3.305403 GCAGAACTGAGTAGTGCAGTACA 60.305 47.826 28.82 12.08 45.27 2.90
471 528 4.796290 GCAGAACTGAGTAGTGCAGTACAA 60.796 45.833 28.82 17.55 45.27 2.41
472 529 4.681942 CAGAACTGAGTAGTGCAGTACAAC 59.318 45.833 28.82 22.14 45.27 3.32
473 530 3.662247 ACTGAGTAGTGCAGTACAACC 57.338 47.619 28.82 18.73 44.27 3.77
474 531 2.030185 ACTGAGTAGTGCAGTACAACCG 60.030 50.000 28.82 20.38 44.27 4.44
475 532 2.228103 CTGAGTAGTGCAGTACAACCGA 59.772 50.000 28.82 10.15 0.00 4.69
476 533 2.823747 TGAGTAGTGCAGTACAACCGAT 59.176 45.455 28.82 10.92 0.00 4.18
477 534 3.179830 GAGTAGTGCAGTACAACCGATG 58.820 50.000 28.82 0.00 0.00 3.84
478 535 2.094182 AGTAGTGCAGTACAACCGATGG 60.094 50.000 28.82 0.00 0.00 3.51
479 536 0.673644 AGTGCAGTACAACCGATGGC 60.674 55.000 0.00 0.00 0.00 4.40
480 537 0.953471 GTGCAGTACAACCGATGGCA 60.953 55.000 0.00 0.00 0.00 4.92
481 538 0.250510 TGCAGTACAACCGATGGCAA 60.251 50.000 0.00 0.00 0.00 4.52
482 539 0.878416 GCAGTACAACCGATGGCAAA 59.122 50.000 0.00 0.00 0.00 3.68
483 540 1.268352 GCAGTACAACCGATGGCAAAA 59.732 47.619 0.00 0.00 0.00 2.44
484 541 2.920647 GCAGTACAACCGATGGCAAAAC 60.921 50.000 0.00 0.00 0.00 2.43
485 542 2.552315 CAGTACAACCGATGGCAAAACT 59.448 45.455 0.00 0.00 0.00 2.66
486 543 2.552315 AGTACAACCGATGGCAAAACTG 59.448 45.455 0.00 0.00 0.00 3.16
487 544 1.686355 ACAACCGATGGCAAAACTGA 58.314 45.000 0.00 0.00 0.00 3.41
488 545 2.238521 ACAACCGATGGCAAAACTGAT 58.761 42.857 0.00 0.00 0.00 2.90
489 546 3.417101 ACAACCGATGGCAAAACTGATA 58.583 40.909 0.00 0.00 0.00 2.15
490 547 3.823873 ACAACCGATGGCAAAACTGATAA 59.176 39.130 0.00 0.00 0.00 1.75
491 548 4.279671 ACAACCGATGGCAAAACTGATAAA 59.720 37.500 0.00 0.00 0.00 1.40
492 549 5.221342 ACAACCGATGGCAAAACTGATAAAA 60.221 36.000 0.00 0.00 0.00 1.52
493 550 5.461032 ACCGATGGCAAAACTGATAAAAA 57.539 34.783 0.00 0.00 0.00 1.94
494 551 6.036577 ACCGATGGCAAAACTGATAAAAAT 57.963 33.333 0.00 0.00 0.00 1.82
495 552 6.099341 ACCGATGGCAAAACTGATAAAAATC 58.901 36.000 0.00 0.00 0.00 2.17
496 553 5.519927 CCGATGGCAAAACTGATAAAAATCC 59.480 40.000 0.00 0.00 0.00 3.01
589 646 3.047877 GCAAACGGGTCGACAGGG 61.048 66.667 18.91 8.02 0.00 4.45
597 654 2.419739 GGTCGACAGGGGAGAGAGC 61.420 68.421 18.91 0.00 0.00 4.09
601 658 2.040278 ACAGGGGAGAGAGCAGGG 59.960 66.667 0.00 0.00 0.00 4.45
602 659 2.366167 CAGGGGAGAGAGCAGGGA 59.634 66.667 0.00 0.00 0.00 4.20
603 660 1.761667 CAGGGGAGAGAGCAGGGAG 60.762 68.421 0.00 0.00 0.00 4.30
714 771 7.067129 AGGAGGAAGAACAAAGAGTAAACAAAC 59.933 37.037 0.00 0.00 0.00 2.93
727 784 2.193306 AACAAACAGACAAGCAAGCG 57.807 45.000 0.00 0.00 0.00 4.68
728 785 0.381801 ACAAACAGACAAGCAAGCGG 59.618 50.000 0.00 0.00 0.00 5.52
729 786 0.662619 CAAACAGACAAGCAAGCGGA 59.337 50.000 0.00 0.00 0.00 5.54
730 787 1.267806 CAAACAGACAAGCAAGCGGAT 59.732 47.619 0.00 0.00 0.00 4.18
731 788 1.160137 AACAGACAAGCAAGCGGATC 58.840 50.000 0.00 0.00 0.00 3.36
732 789 0.674895 ACAGACAAGCAAGCGGATCC 60.675 55.000 0.00 0.00 0.00 3.36
734 791 0.674895 AGACAAGCAAGCGGATCCAC 60.675 55.000 13.41 0.99 0.00 4.02
735 792 0.955428 GACAAGCAAGCGGATCCACA 60.955 55.000 13.41 0.00 0.00 4.17
737 794 1.675641 AAGCAAGCGGATCCACACC 60.676 57.895 13.41 0.00 0.00 4.16
897 968 2.124487 CCTCTCTCTCGCCTCGGT 60.124 66.667 0.00 0.00 0.00 4.69
1126 1197 2.665165 TCAAGCTTCACCATGGTGTTT 58.335 42.857 37.49 25.36 45.55 2.83
1214 1285 2.026356 CACATTGTGTACATGGGGGAGA 60.026 50.000 8.69 0.00 0.00 3.71
1215 1286 2.239654 ACATTGTGTACATGGGGGAGAG 59.760 50.000 0.00 0.00 0.00 3.20
1228 1299 4.154347 GAGAGGCACCCGGAGCTG 62.154 72.222 16.69 4.36 0.00 4.24
1357 1447 1.208052 ACTCAAGAGCTGTGTGTGTGT 59.792 47.619 0.00 0.00 30.59 3.72
1358 1448 1.596260 CTCAAGAGCTGTGTGTGTGTG 59.404 52.381 0.00 0.00 0.00 3.82
1379 1469 1.602668 GCCTTGTGATTTCGCAGCAAA 60.603 47.619 0.00 0.00 37.69 3.68
1550 1640 4.344978 TGCTCCTTCTTCTCTGCTAACTA 58.655 43.478 0.00 0.00 0.00 2.24
1596 1688 1.644509 AAAAAGATTGGCCTGGGGTC 58.355 50.000 3.32 0.00 0.00 4.46
1699 1794 3.143338 GGAGCGGAATCCTCTCCC 58.857 66.667 24.24 9.08 40.29 4.30
1759 1854 3.504906 AGACACAGGTGAGATTGCATTTG 59.495 43.478 6.40 0.00 0.00 2.32
1807 1902 0.319211 CAACTGGCACTGCAATGTGG 60.319 55.000 8.06 0.00 38.31 4.17
1811 1906 2.177531 GCACTGCAATGTGGCGAG 59.822 61.111 8.06 0.00 38.31 5.03
1858 1954 1.908793 AGGGATATGGCCGGAGTCG 60.909 63.158 5.05 0.00 0.00 4.18
1870 1966 1.153349 GGAGTCGGCCAGCTTTAGG 60.153 63.158 2.24 0.00 0.00 2.69
1988 2086 4.047142 GCTCTTTCCTTTCAGTTTGCTTG 58.953 43.478 0.00 0.00 0.00 4.01
2137 2235 1.872234 CCACGAGTACATGTCGGCG 60.872 63.158 0.00 0.00 41.88 6.46
2143 2241 1.226888 GTACATGTCGGCGAGGGAC 60.227 63.158 11.20 6.27 34.99 4.46
2167 2265 4.722700 GGGCATGGGACGCACACT 62.723 66.667 0.00 0.00 31.27 3.55
2205 2303 2.992689 TCTAGTGCCCGACGCCAA 60.993 61.111 0.00 0.00 36.24 4.52
2290 2388 2.045926 GTGTGCTGGGCTACTGGG 60.046 66.667 0.00 0.00 0.00 4.45
2308 2406 1.771255 GGGGATTGTACCTCTGCAGAT 59.229 52.381 18.63 5.89 0.00 2.90
2326 2424 2.139118 GATATCCTTGCTGCCTTCGAC 58.861 52.381 0.00 0.00 0.00 4.20
2365 2463 0.960861 TCGATGTGCTCTCGGTGTCT 60.961 55.000 7.45 0.00 36.78 3.41
2413 2511 1.671979 ATGTTGATGATGTCCTGGCG 58.328 50.000 0.00 0.00 0.00 5.69
2491 2589 2.022195 TCCGGTCCTTATTCAGAGACG 58.978 52.381 0.00 0.00 0.00 4.18
2509 2607 2.460330 GGTGATCAACTCTGCACCG 58.540 57.895 2.64 0.00 41.08 4.94
2790 2889 5.528690 GCTGATGATACTGATGCAAGGTAAA 59.471 40.000 0.00 0.00 0.00 2.01
2791 2890 6.038603 GCTGATGATACTGATGCAAGGTAAAA 59.961 38.462 0.00 0.00 0.00 1.52
2821 2921 6.402550 CGTCATCCTTGTTCTGTCTTTATTGG 60.403 42.308 0.00 0.00 0.00 3.16
2824 2924 4.994852 TCCTTGTTCTGTCTTTATTGGTCG 59.005 41.667 0.00 0.00 0.00 4.79
2831 2931 8.842280 TGTTCTGTCTTTATTGGTCGTAAAAAT 58.158 29.630 0.00 0.00 0.00 1.82
2948 3051 2.049185 ACGAGGACAGCGAGCATCT 61.049 57.895 0.00 0.00 0.00 2.90
2999 3102 2.233922 CCGTGGTGTAGGAGTCATCTTT 59.766 50.000 0.00 0.00 0.00 2.52
3140 3243 9.692749 CAGTATTGTATATGATTCCGTAGTTGT 57.307 33.333 0.00 0.00 0.00 3.32
3145 3248 8.642908 TGTATATGATTCCGTAGTTGTGAAAG 57.357 34.615 0.00 0.00 0.00 2.62
3162 3265 9.132521 GTTGTGAAAGAACTGAATTTATGATGG 57.867 33.333 0.00 0.00 37.10 3.51
3372 3475 5.184864 CACCCAAGTTTGTCCTTAATGCATA 59.815 40.000 0.00 0.00 0.00 3.14
3481 3584 0.038166 TGGCTTCATGGTCACCTTCC 59.962 55.000 0.00 0.00 0.00 3.46
3687 3792 1.763545 CTCTCCCCCTAACTAACAGGC 59.236 57.143 0.00 0.00 0.00 4.85
3711 3816 2.158534 ACACCTTTGTAGCCAATGTCCA 60.159 45.455 0.00 0.00 32.60 4.02
3723 3828 3.741075 GCCAATGTCCATGACGAGTATGA 60.741 47.826 0.00 0.00 34.95 2.15
3826 3931 1.532078 TGCACACCCTGGTCTCGTA 60.532 57.895 0.00 0.00 0.00 3.43
3991 4096 0.401738 TTCCTGAACTGAGGGGCAAG 59.598 55.000 0.00 0.00 33.41 4.01
4021 4126 1.069513 TCGAGAACGGTCACCAATGTT 59.930 47.619 1.87 0.00 40.21 2.71
4031 4136 3.439540 CCAATGTTGGCCCGGTCG 61.440 66.667 0.00 0.00 42.21 4.79
4050 4155 1.972198 CGTCCAAGTACAGAGCCCA 59.028 57.895 0.00 0.00 0.00 5.36
4096 4201 3.239253 ACCGTGAACCCCTCGCTT 61.239 61.111 0.00 0.00 31.92 4.68
4139 4244 5.298276 GTCAACAGGTTAACATTCAAGGTGA 59.702 40.000 8.10 0.00 0.00 4.02
4213 4318 2.421739 GAGGACGGCACACACACT 59.578 61.111 0.00 0.00 0.00 3.55
4240 4345 0.547075 TTCCTTTGGTGGTTCGGACA 59.453 50.000 0.00 0.00 0.00 4.02
4261 4366 7.116948 CGGACAATGATCAATAGGTTCTATGTC 59.883 40.741 0.00 2.50 34.43 3.06
4282 4387 6.541969 TGTCAATGCATGAATAAGTAACACG 58.458 36.000 0.00 0.00 40.50 4.49
4283 4388 5.452302 GTCAATGCATGAATAAGTAACACGC 59.548 40.000 0.00 0.00 40.50 5.34
4298 4404 2.086869 ACACGCTGTAGTATGTACCGT 58.913 47.619 0.00 0.00 0.00 4.83
4299 4405 2.096496 ACACGCTGTAGTATGTACCGTC 59.904 50.000 0.00 0.00 0.00 4.79
4302 4408 1.332997 GCTGTAGTATGTACCGTCGCT 59.667 52.381 0.00 0.00 0.00 4.93
4303 4409 2.223433 GCTGTAGTATGTACCGTCGCTT 60.223 50.000 0.00 0.00 0.00 4.68
4321 4430 3.120199 CGCTTTCGGTCATGAGAACAAAT 60.120 43.478 0.00 0.00 0.00 2.32
4478 4587 5.417811 ACATGAATTGAAGTGTTGCACAAA 58.582 33.333 0.00 0.00 36.74 2.83
4479 4588 5.873712 ACATGAATTGAAGTGTTGCACAAAA 59.126 32.000 0.00 0.00 36.74 2.44
4530 4640 4.377839 TCTTTGGCGACACAAATTTGAA 57.622 36.364 24.64 3.75 42.67 2.69
4577 4687 2.624364 ACATGAATTGAACTGCTGCACA 59.376 40.909 0.00 0.00 0.00 4.57
4578 4688 3.068448 ACATGAATTGAACTGCTGCACAA 59.932 39.130 0.00 2.02 0.00 3.33
4694 4807 6.828273 ACAATGGATGTTTAGCTGTAATGCTA 59.172 34.615 0.00 0.00 40.06 3.49
4705 4818 4.999950 AGCTGTAATGCTATGAGTAATGCC 59.000 41.667 0.00 0.00 42.10 4.40
4706 4819 4.756642 GCTGTAATGCTATGAGTAATGCCA 59.243 41.667 0.00 0.00 0.00 4.92
4707 4820 5.334414 GCTGTAATGCTATGAGTAATGCCAC 60.334 44.000 0.00 0.00 0.00 5.01
5171 5296 0.966179 GTTTCCCGATTGGTTGGCTT 59.034 50.000 0.00 0.00 34.77 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 1.211457 CTTCAATCCCTAGCCAGCACT 59.789 52.381 0.00 0.00 0.00 4.40
105 112 0.250081 CCGCTCTTCAATCCCTAGCC 60.250 60.000 0.00 0.00 0.00 3.93
109 116 1.118838 CTCTCCGCTCTTCAATCCCT 58.881 55.000 0.00 0.00 0.00 4.20
125 132 1.994885 CTCCCCGCTCCTCTCTCTCT 61.995 65.000 0.00 0.00 0.00 3.10
155 178 1.497161 CCCGTCAAATCCCTAGTCCT 58.503 55.000 0.00 0.00 0.00 3.85
159 197 1.689273 CTCTCCCCGTCAAATCCCTAG 59.311 57.143 0.00 0.00 0.00 3.02
161 199 0.042731 TCTCTCCCCGTCAAATCCCT 59.957 55.000 0.00 0.00 0.00 4.20
169 207 1.671901 CTTGCTCCTCTCTCCCCGTC 61.672 65.000 0.00 0.00 0.00 4.79
187 225 0.539438 CGCTCCTCTATCTCCCTGCT 60.539 60.000 0.00 0.00 0.00 4.24
189 227 0.897863 CCCGCTCCTCTATCTCCCTG 60.898 65.000 0.00 0.00 0.00 4.45
192 230 2.279810 GCCCCGCTCCTCTATCTCC 61.280 68.421 0.00 0.00 0.00 3.71
197 235 0.623723 AAAATTGCCCCGCTCCTCTA 59.376 50.000 0.00 0.00 0.00 2.43
198 236 0.623723 TAAAATTGCCCCGCTCCTCT 59.376 50.000 0.00 0.00 0.00 3.69
199 237 0.738975 GTAAAATTGCCCCGCTCCTC 59.261 55.000 0.00 0.00 0.00 3.71
200 238 0.039035 TGTAAAATTGCCCCGCTCCT 59.961 50.000 0.00 0.00 0.00 3.69
201 239 0.172578 GTGTAAAATTGCCCCGCTCC 59.827 55.000 0.00 0.00 0.00 4.70
205 243 3.367600 GGGTTAAGTGTAAAATTGCCCCG 60.368 47.826 0.00 0.00 0.00 5.73
211 268 3.760151 GGCGAGGGGTTAAGTGTAAAATT 59.240 43.478 0.00 0.00 0.00 1.82
276 333 2.180159 TAGCCGCTCCTTTGACCACC 62.180 60.000 0.00 0.00 0.00 4.61
291 348 0.594284 GTCGTATGCGGTGAGTAGCC 60.594 60.000 2.62 0.00 38.89 3.93
301 358 0.713883 GTCACTGTTGGTCGTATGCG 59.286 55.000 0.00 0.00 39.92 4.73
352 409 5.574055 TGAACTTAGAAATACGGCTGTTACG 59.426 40.000 1.99 0.00 37.36 3.18
387 444 0.947180 GTAGTTGCGACGAAAGCCCA 60.947 55.000 0.00 0.00 0.00 5.36
441 498 4.799586 GCACTACTCAGTTCTGCCACTAAA 60.800 45.833 0.00 0.00 30.46 1.85
447 504 1.001406 ACTGCACTACTCAGTTCTGCC 59.999 52.381 4.37 0.00 41.61 4.85
448 505 2.447244 ACTGCACTACTCAGTTCTGC 57.553 50.000 0.27 0.27 41.61 4.26
449 506 4.505313 TGTACTGCACTACTCAGTTCTG 57.495 45.455 0.77 0.00 41.61 3.02
450 507 4.262079 GGTTGTACTGCACTACTCAGTTCT 60.262 45.833 0.77 0.00 41.61 3.01
451 508 3.988517 GGTTGTACTGCACTACTCAGTTC 59.011 47.826 0.77 0.00 41.61 3.01
452 509 3.552273 CGGTTGTACTGCACTACTCAGTT 60.552 47.826 0.77 0.00 41.61 3.16
453 510 2.030185 CGGTTGTACTGCACTACTCAGT 60.030 50.000 5.31 1.18 45.71 3.41
454 511 2.228103 TCGGTTGTACTGCACTACTCAG 59.772 50.000 5.31 0.00 33.89 3.35
455 512 2.232399 TCGGTTGTACTGCACTACTCA 58.768 47.619 5.31 0.00 33.89 3.41
456 513 3.179830 CATCGGTTGTACTGCACTACTC 58.820 50.000 5.31 0.03 33.89 2.59
457 514 2.094182 CCATCGGTTGTACTGCACTACT 60.094 50.000 5.31 0.00 33.89 2.57
458 515 2.268298 CCATCGGTTGTACTGCACTAC 58.732 52.381 0.00 0.00 32.78 2.73
459 516 1.404986 GCCATCGGTTGTACTGCACTA 60.405 52.381 0.00 0.00 0.00 2.74
460 517 0.673644 GCCATCGGTTGTACTGCACT 60.674 55.000 0.00 0.00 0.00 4.40
461 518 0.953471 TGCCATCGGTTGTACTGCAC 60.953 55.000 0.00 0.00 0.00 4.57
462 519 0.250510 TTGCCATCGGTTGTACTGCA 60.251 50.000 0.00 0.00 0.00 4.41
463 520 0.878416 TTTGCCATCGGTTGTACTGC 59.122 50.000 0.00 0.00 0.00 4.40
464 521 2.552315 AGTTTTGCCATCGGTTGTACTG 59.448 45.455 0.00 0.00 0.00 2.74
465 522 2.552315 CAGTTTTGCCATCGGTTGTACT 59.448 45.455 0.00 0.00 0.00 2.73
466 523 2.550606 TCAGTTTTGCCATCGGTTGTAC 59.449 45.455 0.00 0.00 0.00 2.90
467 524 2.852449 TCAGTTTTGCCATCGGTTGTA 58.148 42.857 0.00 0.00 0.00 2.41
468 525 1.686355 TCAGTTTTGCCATCGGTTGT 58.314 45.000 0.00 0.00 0.00 3.32
469 526 4.433186 TTATCAGTTTTGCCATCGGTTG 57.567 40.909 0.00 0.00 0.00 3.77
470 527 5.461032 TTTTATCAGTTTTGCCATCGGTT 57.539 34.783 0.00 0.00 0.00 4.44
471 528 5.461032 TTTTTATCAGTTTTGCCATCGGT 57.539 34.783 0.00 0.00 0.00 4.69
472 529 5.519927 GGATTTTTATCAGTTTTGCCATCGG 59.480 40.000 0.00 0.00 0.00 4.18
473 530 6.332630 AGGATTTTTATCAGTTTTGCCATCG 58.667 36.000 0.00 0.00 0.00 3.84
474 531 9.651913 TTAAGGATTTTTATCAGTTTTGCCATC 57.348 29.630 0.00 0.00 0.00 3.51
476 533 9.838339 TTTTAAGGATTTTTATCAGTTTTGCCA 57.162 25.926 0.00 0.00 0.00 4.92
589 646 2.441164 TCGCTCCCTGCTCTCTCC 60.441 66.667 0.00 0.00 40.11 3.71
714 771 0.674581 TGGATCCGCTTGCTTGTCTG 60.675 55.000 7.39 0.00 0.00 3.51
727 784 4.832608 GGTCGCCGGTGTGGATCC 62.833 72.222 16.01 4.20 42.00 3.36
897 968 1.348064 TTGAAAGGCGAGAGGAGGAA 58.652 50.000 0.00 0.00 0.00 3.36
1357 1447 1.865788 GCTGCGAAATCACAAGGCCA 61.866 55.000 5.01 0.00 0.00 5.36
1358 1448 1.153958 GCTGCGAAATCACAAGGCC 60.154 57.895 0.00 0.00 0.00 5.19
1537 1627 7.119846 GCAAAAGGAGAAATAGTTAGCAGAGAA 59.880 37.037 0.00 0.00 0.00 2.87
1550 1640 6.976934 TTTAACCAGAGCAAAAGGAGAAAT 57.023 33.333 0.00 0.00 0.00 2.17
1596 1688 4.973055 TTCCGAACCACCCGCACG 62.973 66.667 0.00 0.00 0.00 5.34
1751 1846 6.206438 TCTGCTATACAACTGAACAAATGCAA 59.794 34.615 0.00 0.00 0.00 4.08
1759 1854 6.818644 TCCTGATTTCTGCTATACAACTGAAC 59.181 38.462 0.00 0.00 0.00 3.18
1807 1902 2.774687 TCCCAAGAAAACCTTACTCGC 58.225 47.619 0.00 0.00 32.86 5.03
1811 1906 7.997773 AGTTAAGATCCCAAGAAAACCTTAC 57.002 36.000 0.00 0.00 32.86 2.34
1858 1954 1.449778 GTCGTCCCTAAAGCTGGCC 60.450 63.158 0.00 0.00 0.00 5.36
1973 2069 2.825861 ATGGCAAGCAAACTGAAAGG 57.174 45.000 0.00 0.00 39.30 3.11
1988 2086 3.665745 ACATTCTCACAACCAAATGGC 57.334 42.857 0.00 0.00 39.32 4.40
2290 2388 4.530161 AGGATATCTGCAGAGGTACAATCC 59.470 45.833 22.96 22.01 0.00 3.01
2308 2406 0.179111 CGTCGAAGGCAGCAAGGATA 60.179 55.000 0.00 0.00 0.00 2.59
2326 2424 3.254654 CCGTCGTGTATGGCAGCG 61.255 66.667 0.00 0.00 0.00 5.18
2365 2463 4.329545 GGTGGTGCTTGGCCGAGA 62.330 66.667 25.25 6.11 0.00 4.04
2491 2589 0.320771 ACGGTGCAGAGTTGATCACC 60.321 55.000 0.00 0.00 44.04 4.02
2509 2607 0.872388 CAGCAACGGTTAGAACCCAC 59.128 55.000 5.85 0.00 46.53 4.61
2790 2889 3.070018 CAGAACAAGGATGACGAAGCTT 58.930 45.455 0.00 0.00 0.00 3.74
2791 2890 2.037772 ACAGAACAAGGATGACGAAGCT 59.962 45.455 0.00 0.00 0.00 3.74
2821 2921 5.082251 AGGGGAGTGTAGATTTTTACGAC 57.918 43.478 0.00 0.00 0.00 4.34
2824 2924 6.571731 GCCAAAAGGGGAGTGTAGATTTTTAC 60.572 42.308 0.00 0.00 37.04 2.01
2831 2931 1.742308 AGCCAAAAGGGGAGTGTAGA 58.258 50.000 0.00 0.00 37.04 2.59
2948 3051 0.965866 CGGTCTCTACTGCCACCTGA 60.966 60.000 0.00 0.00 0.00 3.86
2999 3102 3.784701 TCTTTGGTTAAAAACTGCGCA 57.215 38.095 10.98 10.98 0.00 6.09
3162 3265 6.649141 TCAACATGGTTCAACAGACAGTATAC 59.351 38.462 0.00 0.00 0.00 1.47
3167 3270 4.129380 TCTCAACATGGTTCAACAGACAG 58.871 43.478 0.00 0.00 0.00 3.51
3178 3281 8.006298 TGTAGAAAAACAAATCTCAACATGGT 57.994 30.769 0.00 0.00 0.00 3.55
3400 3503 4.019860 AGTTAGATGGCAAGAGAAGAAGCA 60.020 41.667 0.00 0.00 0.00 3.91
3711 3816 5.010112 ACCATCTCGAATTCATACTCGTCAT 59.990 40.000 6.22 0.00 36.46 3.06
3723 3828 5.282055 TGCTTCAGATACCATCTCGAATT 57.718 39.130 0.00 0.00 37.58 2.17
3826 3931 5.798125 AATCAGATGGTCTCATGTCGTAT 57.202 39.130 0.00 0.00 32.98 3.06
3991 4096 2.081212 CGTTCTCGACACCGACAGC 61.081 63.158 0.00 0.00 40.30 4.40
4031 4136 1.448013 GGGCTCTGTACTTGGACGC 60.448 63.158 0.00 0.00 0.00 5.19
4050 4155 1.687612 CCTGGAGGTGCTTCCACAT 59.312 57.895 0.00 0.00 42.24 3.21
4096 4201 2.293677 GACTGTCGAGTTGAAGGTCAGA 59.706 50.000 3.37 0.00 33.33 3.27
4139 4244 2.242043 CTTCAGTTTGGCCTGGAATGT 58.758 47.619 3.32 0.00 33.14 2.71
4213 4318 1.780309 ACCACCAAAGGAATCCTCACA 59.220 47.619 0.56 0.00 30.89 3.58
4222 4327 0.547075 TTGTCCGAACCACCAAAGGA 59.453 50.000 0.00 0.00 0.00 3.36
4240 4345 8.790718 GCATTGACATAGAACCTATTGATCATT 58.209 33.333 0.00 0.00 0.00 2.57
4261 4366 5.453266 CAGCGTGTTACTTATTCATGCATTG 59.547 40.000 0.00 0.00 43.74 2.82
4282 4387 1.332997 AGCGACGGTACATACTACAGC 59.667 52.381 0.00 0.00 0.00 4.40
4283 4388 3.687572 AAGCGACGGTACATACTACAG 57.312 47.619 0.00 0.00 0.00 2.74
4298 4404 1.000394 TGTTCTCATGACCGAAAGCGA 60.000 47.619 0.00 0.00 40.82 4.93
4299 4405 1.428448 TGTTCTCATGACCGAAAGCG 58.572 50.000 0.00 0.00 37.24 4.68
4302 4408 5.473162 ACATCATTTGTTCTCATGACCGAAA 59.527 36.000 0.00 0.00 33.74 3.46
4303 4409 5.003160 ACATCATTTGTTCTCATGACCGAA 58.997 37.500 0.00 0.00 33.74 4.30
4321 4430 6.631016 AGAGATTAGCGAGTTTGTTACATCA 58.369 36.000 0.00 0.00 0.00 3.07
4478 4587 9.025041 CCTGGTTATCAATAGAAGTTCCTTTTT 57.975 33.333 0.00 0.00 0.00 1.94
4479 4588 8.390921 TCCTGGTTATCAATAGAAGTTCCTTTT 58.609 33.333 0.00 0.00 0.00 2.27
4530 4640 5.163513 GCACATACTTGCTGCTAAAATTGT 58.836 37.500 0.00 0.00 39.59 2.71
4577 4687 8.585018 CCTGGTTATGAATACAAGTTCCTTTTT 58.415 33.333 0.00 0.00 0.00 1.94
4578 4688 7.178451 CCCTGGTTATGAATACAAGTTCCTTTT 59.822 37.037 0.00 0.00 0.00 2.27
4694 4807 6.936900 GTGTAAGATATGGTGGCATTACTCAT 59.063 38.462 0.00 0.00 0.00 2.90
4705 4818 5.006153 TCTTGGTCGTGTAAGATATGGTG 57.994 43.478 0.00 0.00 0.00 4.17
4706 4819 5.670792 TTCTTGGTCGTGTAAGATATGGT 57.329 39.130 0.00 0.00 33.34 3.55
4707 4820 5.696724 GGATTCTTGGTCGTGTAAGATATGG 59.303 44.000 0.00 0.00 33.34 2.74
4863 4988 1.902508 CTCCAGGACTACAAGAAGGCA 59.097 52.381 0.00 0.00 0.00 4.75
4871 4996 1.025113 CGACGAGCTCCAGGACTACA 61.025 60.000 8.47 0.00 0.00 2.74
5171 5296 2.168496 CTCGTCCTCCCTACAAACTCA 58.832 52.381 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.