Multiple sequence alignment - TraesCS5B01G238600

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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 TraesCS5B01G238600 chr5B 100.000 3307 0 0 1 3307 419519919 419516613 0.000000e+00 6107
1 TraesCS5B01G238600 chr5D 86.704 1805 98 70 626 2331 354743016 354741255 0.000000e+00 1873
2 TraesCS5B01G238600 chr5D 84.714 1014 100 23 2327 3295 354741124 354740121 0.000000e+00 963
3 TraesCS5B01G238600 chr5D 89.683 252 23 2 1 251 354747030 354746781 5.330000e-83 318
4 TraesCS5B01G238600 chr5D 76.361 588 108 22 2502 3068 521721716 521721139 1.500000e-73 287
5 TraesCS5B01G238600 chr5D 92.118 203 13 3 308 509 354743406 354743206 1.940000e-72 283
6 TraesCS5B01G238600 chr5D 85.897 78 1 1 500 567 354743149 354743072 1.270000e-09 75
7 TraesCS5B01G238600 chr5A 88.389 1490 124 26 1856 3306 456744592 456743113 0.000000e+00 1748
8 TraesCS5B01G238600 chr5A 87.147 1027 58 28 815 1773 456745615 456744595 0.000000e+00 1098
9 TraesCS5B01G238600 chr2A 81.435 878 85 34 1185 2013 306424637 306423789 0.000000e+00 647
10 TraesCS5B01G238600 chr3B 80.866 878 91 38 1185 2013 34532335 34531486 1.300000e-173 619
11 TraesCS5B01G238600 chr3B 80.774 879 91 36 1185 2013 34478223 34477373 1.690000e-172 616
12 TraesCS5B01G238600 chr3B 80.774 879 91 37 1185 2013 468136712 468135862 1.690000e-172 616
13 TraesCS5B01G238600 chr3B 80.774 879 90 31 1185 2013 764673637 764672788 6.070000e-172 614
14 TraesCS5B01G238600 chr3B 81.911 586 49 23 1185 1723 35629538 35630113 3.030000e-120 442
15 TraesCS5B01G238600 chr3B 82.056 574 46 23 1185 1711 35562874 35563437 1.410000e-118 436
16 TraesCS5B01G238600 chr3B 74.845 644 121 29 2690 3304 774679369 774678738 1.520000e-63 254
17 TraesCS5B01G238600 chr3B 75.787 508 88 23 2809 3292 683110483 683109987 1.190000e-54 224
18 TraesCS5B01G238600 chr1B 80.499 882 90 34 1185 2013 566256774 566257626 4.720000e-168 601
19 TraesCS5B01G238600 chr2B 80.068 883 86 40 1185 2013 277273996 277274842 1.030000e-159 573
20 TraesCS5B01G238600 chr2B 77.202 386 77 9 2690 3070 715035117 715035496 7.190000e-52 215
21 TraesCS5B01G238600 chr2B 77.869 244 46 6 2691 2930 242943269 242943030 9.560000e-31 145
22 TraesCS5B01G238600 chr3D 79.381 582 90 17 2746 3304 305325022 305324448 1.860000e-102 383
23 TraesCS5B01G238600 chr3D 76.012 642 119 22 2690 3304 185057378 185058011 1.930000e-77 300
24 TraesCS5B01G238600 chr4B 77.449 643 104 28 2679 3306 416170845 416170229 2.440000e-91 346
25 TraesCS5B01G238600 chr7D 78.154 531 105 7 2777 3304 552926627 552927149 8.850000e-86 327
26 TraesCS5B01G238600 chr6D 78.894 398 72 10 2678 3070 451892259 451892649 3.270000e-65 259
27 TraesCS5B01G238600 chr7B 73.525 627 129 27 2706 3306 127625611 127626226 1.560000e-48 204
28 TraesCS5B01G238600 chr4A 87.333 150 9 3 1453 1602 632369779 632369918 2.640000e-36 163


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 TraesCS5B01G238600 chr5B 419516613 419519919 3306 True 6107.0 6107 100.0000 1 3307 1 chr5B.!!$R1 3306
1 TraesCS5B01G238600 chr5D 354740121 354747030 6909 True 702.4 1873 87.8232 1 3295 5 chr5D.!!$R2 3294
2 TraesCS5B01G238600 chr5D 521721139 521721716 577 True 287.0 287 76.3610 2502 3068 1 chr5D.!!$R1 566
3 TraesCS5B01G238600 chr5A 456743113 456745615 2502 True 1423.0 1748 87.7680 815 3306 2 chr5A.!!$R1 2491
4 TraesCS5B01G238600 chr2A 306423789 306424637 848 True 647.0 647 81.4350 1185 2013 1 chr2A.!!$R1 828
5 TraesCS5B01G238600 chr3B 34531486 34532335 849 True 619.0 619 80.8660 1185 2013 1 chr3B.!!$R2 828
6 TraesCS5B01G238600 chr3B 34477373 34478223 850 True 616.0 616 80.7740 1185 2013 1 chr3B.!!$R1 828
7 TraesCS5B01G238600 chr3B 468135862 468136712 850 True 616.0 616 80.7740 1185 2013 1 chr3B.!!$R3 828
8 TraesCS5B01G238600 chr3B 764672788 764673637 849 True 614.0 614 80.7740 1185 2013 1 chr3B.!!$R5 828
9 TraesCS5B01G238600 chr3B 35629538 35630113 575 False 442.0 442 81.9110 1185 1723 1 chr3B.!!$F2 538
10 TraesCS5B01G238600 chr3B 35562874 35563437 563 False 436.0 436 82.0560 1185 1711 1 chr3B.!!$F1 526
11 TraesCS5B01G238600 chr3B 774678738 774679369 631 True 254.0 254 74.8450 2690 3304 1 chr3B.!!$R6 614
12 TraesCS5B01G238600 chr1B 566256774 566257626 852 False 601.0 601 80.4990 1185 2013 1 chr1B.!!$F1 828
13 TraesCS5B01G238600 chr2B 277273996 277274842 846 False 573.0 573 80.0680 1185 2013 1 chr2B.!!$F1 828
14 TraesCS5B01G238600 chr3D 305324448 305325022 574 True 383.0 383 79.3810 2746 3304 1 chr3D.!!$R1 558
15 TraesCS5B01G238600 chr3D 185057378 185058011 633 False 300.0 300 76.0120 2690 3304 1 chr3D.!!$F1 614
16 TraesCS5B01G238600 chr4B 416170229 416170845 616 True 346.0 346 77.4490 2679 3306 1 chr4B.!!$R1 627
17 TraesCS5B01G238600 chr7D 552926627 552927149 522 False 327.0 327 78.1540 2777 3304 1 chr7D.!!$F1 527
18 TraesCS5B01G238600 chr7B 127625611 127626226 615 False 204.0 204 73.5250 2706 3306 1 chr7B.!!$F1 600

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
810 4229 0.393132 CCGGCTTCCTTTCCTTCTCC 60.393 60.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2739 6487 0.323629 TCCACCTCCCGAAACATGAC 59.676 55.0 0.0 0.0 0.0 3.06 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
33 34 1.841450 CCTTATCGAACCTGCGAGAC 58.159 55.000 0.00 0.00 44.26 3.36
60 61 1.263484 TCGACTCCGCTCGTATTCATC 59.737 52.381 0.00 0.00 35.10 2.92
61 62 1.002792 CGACTCCGCTCGTATTCATCA 60.003 52.381 0.00 0.00 0.00 3.07
76 78 3.303881 TCATCAGTGACGAAACCAGAG 57.696 47.619 0.00 0.00 0.00 3.35
83 85 2.548057 GTGACGAAACCAGAGCAATTGA 59.452 45.455 10.34 0.00 0.00 2.57
85 87 3.629855 TGACGAAACCAGAGCAATTGAAA 59.370 39.130 10.34 0.00 0.00 2.69
99 101 4.737352 GCAATTGAAACAGAAGGAGCAACA 60.737 41.667 10.34 0.00 0.00 3.33
117 119 8.286097 GGAGCAACATTAAGCTTATTGATAGAC 58.714 37.037 26.98 16.81 42.04 2.59
118 120 8.159344 AGCAACATTAAGCTTATTGATAGACC 57.841 34.615 26.98 12.99 38.01 3.85
120 122 8.405531 GCAACATTAAGCTTATTGATAGACCAA 58.594 33.333 26.98 4.20 0.00 3.67
137 139 9.378551 GATAGACCAATAACATCAAGTAACACA 57.621 33.333 0.00 0.00 0.00 3.72
138 140 9.905713 ATAGACCAATAACATCAAGTAACACAT 57.094 29.630 0.00 0.00 0.00 3.21
180 182 8.815565 TTGTATTTATTTGGTATTGCAGAGGA 57.184 30.769 0.00 0.00 0.00 3.71
211 213 8.691661 AATTTCTCTACGGGCACATTATTTAT 57.308 30.769 0.00 0.00 0.00 1.40
218 220 6.969993 ACGGGCACATTATTTATTTGGTAT 57.030 33.333 0.00 0.00 0.00 2.73
258 260 8.429493 ACTTTTGTAGATTAAACTATACGGGC 57.571 34.615 0.00 0.00 0.00 6.13
259 261 8.042515 ACTTTTGTAGATTAAACTATACGGGCA 58.957 33.333 0.00 0.00 0.00 5.36
260 262 7.775397 TTTGTAGATTAAACTATACGGGCAC 57.225 36.000 0.00 0.00 0.00 5.01
261 263 6.468333 TGTAGATTAAACTATACGGGCACA 57.532 37.500 0.00 0.00 0.00 4.57
262 264 6.275335 TGTAGATTAAACTATACGGGCACAC 58.725 40.000 0.00 0.00 0.00 3.82
298 3485 4.456662 TTTTAGGGGAAAAGGCACACTA 57.543 40.909 0.00 0.00 31.90 2.74
299 3486 4.668138 TTTAGGGGAAAAGGCACACTAT 57.332 40.909 0.00 0.00 0.00 2.12
300 3487 4.668138 TTAGGGGAAAAGGCACACTATT 57.332 40.909 0.00 0.00 0.00 1.73
301 3488 5.782677 TTAGGGGAAAAGGCACACTATTA 57.217 39.130 0.00 0.00 0.00 0.98
306 3626 5.163550 GGGGAAAAGGCACACTATTATTGAC 60.164 44.000 0.00 0.00 0.00 3.18
328 3648 5.925509 ACGGAGGCAGTATATTGTAATGTT 58.074 37.500 0.00 0.00 0.00 2.71
340 3660 9.174166 GTATATTGTAATGTTGTCCTGTCCTTT 57.826 33.333 0.00 0.00 0.00 3.11
359 3679 4.425520 CTTTGCACGGGTAAAAACAAAGA 58.574 39.130 1.73 0.00 44.11 2.52
400 3721 1.219393 GCTCCTGTGCACTAGGTCC 59.781 63.158 25.12 17.11 36.67 4.46
409 3730 1.890894 CACTAGGTCCGTCACAGGG 59.109 63.158 0.00 0.00 0.00 4.45
419 3740 4.988716 TCACAGGGACTCGGCGGT 62.989 66.667 7.21 3.45 34.60 5.68
464 3785 2.268920 CCCGTGCCACAGCTACAT 59.731 61.111 0.00 0.00 40.80 2.29
492 3813 3.187842 CGTGACGGTAGTAGCAGCATATA 59.812 47.826 0.00 0.00 0.00 0.86
494 3815 4.023450 GTGACGGTAGTAGCAGCATATACA 60.023 45.833 0.00 0.00 0.00 2.29
603 4011 4.388499 CCCCACCTCCACGGTTCG 62.388 72.222 0.00 0.00 46.37 3.95
604 4012 3.307906 CCCACCTCCACGGTTCGA 61.308 66.667 0.00 0.00 46.37 3.71
607 4015 3.677648 ACCTCCACGGTTCGACGG 61.678 66.667 0.00 0.00 46.37 4.79
608 4016 4.430765 CCTCCACGGTTCGACGGG 62.431 72.222 0.00 0.00 38.39 5.28
624 4032 2.512974 GGCCGTCCCACATTACCG 60.513 66.667 0.00 0.00 0.00 4.02
628 4036 3.560278 GTCCCACATTACCGCGCG 61.560 66.667 25.67 25.67 0.00 6.86
768 4187 4.091939 GTACGCCCCGCTCCCTTT 62.092 66.667 0.00 0.00 0.00 3.11
774 4193 3.798511 CCCGCTCCCTTTCCCCTC 61.799 72.222 0.00 0.00 0.00 4.30
775 4194 2.689034 CCGCTCCCTTTCCCCTCT 60.689 66.667 0.00 0.00 0.00 3.69
776 4195 2.736826 CCGCTCCCTTTCCCCTCTC 61.737 68.421 0.00 0.00 0.00 3.20
777 4196 2.904131 GCTCCCTTTCCCCTCTCG 59.096 66.667 0.00 0.00 0.00 4.04
785 4204 1.410882 CTTTCCCCTCTCGTCTCATCC 59.589 57.143 0.00 0.00 0.00 3.51
793 4212 0.595588 CTCGTCTCATCCCATCTCCG 59.404 60.000 0.00 0.00 0.00 4.63
801 4220 0.695803 ATCCCATCTCCGGCTTCCTT 60.696 55.000 0.00 0.00 0.00 3.36
808 4227 0.615850 CTCCGGCTTCCTTTCCTTCT 59.384 55.000 0.00 0.00 0.00 2.85
809 4228 0.613777 TCCGGCTTCCTTTCCTTCTC 59.386 55.000 0.00 0.00 0.00 2.87
810 4229 0.393132 CCGGCTTCCTTTCCTTCTCC 60.393 60.000 0.00 0.00 0.00 3.71
811 4230 0.615850 CGGCTTCCTTTCCTTCTCCT 59.384 55.000 0.00 0.00 0.00 3.69
812 4231 1.677217 CGGCTTCCTTTCCTTCTCCTG 60.677 57.143 0.00 0.00 0.00 3.86
813 4232 1.352687 GGCTTCCTTTCCTTCTCCTGT 59.647 52.381 0.00 0.00 0.00 4.00
822 4241 2.660572 TCCTTCTCCTGTGCTAGCTAG 58.339 52.381 16.84 16.84 0.00 3.42
855 4276 8.522542 AGCTGCTGTTAATTACTAGTAGTAGT 57.477 34.615 14.57 14.57 42.49 2.73
856 4277 9.624373 AGCTGCTGTTAATTACTAGTAGTAGTA 57.376 33.333 12.58 12.58 40.23 1.82
857 4278 9.662545 GCTGCTGTTAATTACTAGTAGTAGTAC 57.337 37.037 15.65 8.40 40.76 2.73
1090 4547 6.295249 ACAGGAGAGAAGGAAGAAAAGAAAG 58.705 40.000 0.00 0.00 0.00 2.62
1091 4548 6.100424 ACAGGAGAGAAGGAAGAAAAGAAAGA 59.900 38.462 0.00 0.00 0.00 2.52
1092 4549 6.995091 CAGGAGAGAAGGAAGAAAAGAAAGAA 59.005 38.462 0.00 0.00 0.00 2.52
1279 4762 0.601311 GCTGCGTGTGGAGTTCTCTT 60.601 55.000 0.00 0.00 35.69 2.85
1298 4781 3.606065 CTCACGCTTTGGCTGCTGC 62.606 63.158 7.10 7.10 36.09 5.25
1425 4909 1.005037 CTGCCAAGTGAGTACCGCA 60.005 57.895 0.00 0.00 0.00 5.69
1460 4960 2.474816 GCAACAGCTTCCTCCTATACG 58.525 52.381 0.00 0.00 0.00 3.06
1638 5165 4.568152 AAACGCTAGCATGTGTTTTTCT 57.432 36.364 16.45 0.00 44.92 2.52
1639 5166 3.542712 ACGCTAGCATGTGTTTTTCTG 57.457 42.857 16.45 0.00 0.00 3.02
1641 5168 3.315191 ACGCTAGCATGTGTTTTTCTGTT 59.685 39.130 16.45 0.00 0.00 3.16
1642 5169 3.665409 CGCTAGCATGTGTTTTTCTGTTG 59.335 43.478 16.45 0.00 0.00 3.33
1643 5170 3.426525 GCTAGCATGTGTTTTTCTGTTGC 59.573 43.478 10.63 0.00 0.00 4.17
1644 5171 3.806625 AGCATGTGTTTTTCTGTTGCT 57.193 38.095 0.00 0.00 34.34 3.91
1703 5247 7.414540 GGTGCTAGTGTATGAAGGAATTTGAAG 60.415 40.741 0.00 0.00 0.00 3.02
1718 5262 8.571336 AGGAATTTGAAGAAAATCACTACACAG 58.429 33.333 0.00 0.00 37.51 3.66
1723 5267 8.777865 TTGAAGAAAATCACTACACAGATAGG 57.222 34.615 0.00 0.00 0.00 2.57
1724 5268 7.331026 TGAAGAAAATCACTACACAGATAGGG 58.669 38.462 0.00 0.00 0.00 3.53
1725 5269 7.180229 TGAAGAAAATCACTACACAGATAGGGA 59.820 37.037 0.00 0.00 38.95 4.20
1731 5275 6.681729 TCACTACACAGATAGGGAGTTTTT 57.318 37.500 0.00 0.00 29.27 1.94
1732 5276 6.464222 TCACTACACAGATAGGGAGTTTTTG 58.536 40.000 0.00 0.00 29.27 2.44
1733 5277 6.269077 TCACTACACAGATAGGGAGTTTTTGA 59.731 38.462 0.00 0.00 29.27 2.69
1734 5278 6.591834 CACTACACAGATAGGGAGTTTTTGAG 59.408 42.308 0.00 0.00 0.00 3.02
1735 5279 4.327680 ACACAGATAGGGAGTTTTTGAGC 58.672 43.478 0.00 0.00 0.00 4.26
1736 5280 4.202461 ACACAGATAGGGAGTTTTTGAGCA 60.202 41.667 0.00 0.00 0.00 4.26
1738 5282 4.202461 ACAGATAGGGAGTTTTTGAGCACA 60.202 41.667 0.00 0.00 0.00 4.57
1779 5332 6.183360 TGGGGATCTTGGTCTTTTGTAAAAAC 60.183 38.462 0.00 0.00 0.00 2.43
1780 5333 6.220930 GGGATCTTGGTCTTTTGTAAAAACC 58.779 40.000 0.00 11.28 33.54 3.27
1781 5334 6.220930 GGATCTTGGTCTTTTGTAAAAACCC 58.779 40.000 13.67 7.72 32.74 4.11
1782 5335 6.183360 GGATCTTGGTCTTTTGTAAAAACCCA 60.183 38.462 13.67 9.47 32.74 4.51
1783 5336 5.968254 TCTTGGTCTTTTGTAAAAACCCAC 58.032 37.500 13.67 1.92 32.74 4.61
1784 5337 5.480772 TCTTGGTCTTTTGTAAAAACCCACA 59.519 36.000 13.67 0.00 32.74 4.17
1785 5338 5.074584 TGGTCTTTTGTAAAAACCCACAC 57.925 39.130 13.67 0.00 32.74 3.82
1786 5339 4.527038 TGGTCTTTTGTAAAAACCCACACA 59.473 37.500 13.67 0.00 32.74 3.72
1787 5340 4.865925 GGTCTTTTGTAAAAACCCACACAC 59.134 41.667 8.79 0.00 0.00 3.82
1788 5341 4.559643 GTCTTTTGTAAAAACCCACACACG 59.440 41.667 0.00 0.00 0.00 4.49
1789 5342 2.563471 TTGTAAAAACCCACACACGC 57.437 45.000 0.00 0.00 0.00 5.34
1793 5347 0.456995 AAAAACCCACACACGCAACG 60.457 50.000 0.00 0.00 0.00 4.10
1810 5364 2.284405 GGGGACGGACTGGGAGAA 60.284 66.667 0.00 0.00 0.00 2.87
1814 5368 0.902531 GGACGGACTGGGAGAATTCA 59.097 55.000 8.44 0.00 0.00 2.57
1815 5369 1.134670 GGACGGACTGGGAGAATTCAG 60.135 57.143 8.44 0.00 37.07 3.02
1817 5371 1.827969 ACGGACTGGGAGAATTCAGAG 59.172 52.381 8.44 0.23 35.20 3.35
1859 5414 9.656040 TGATTTCAACTCAATTATGGATTTTGG 57.344 29.630 0.00 0.00 0.00 3.28
1865 5420 8.392612 CAACTCAATTATGGATTTTGGCAAATC 58.607 33.333 14.29 12.57 45.42 2.17
1882 5437 5.689068 GGCAAATCAGCTCAAGCAATTATAC 59.311 40.000 4.59 0.00 45.16 1.47
1883 5438 6.267817 GCAAATCAGCTCAAGCAATTATACA 58.732 36.000 4.59 0.00 45.16 2.29
1884 5439 6.197842 GCAAATCAGCTCAAGCAATTATACAC 59.802 38.462 4.59 0.00 45.16 2.90
1885 5440 7.478322 CAAATCAGCTCAAGCAATTATACACT 58.522 34.615 4.59 0.00 45.16 3.55
1886 5441 8.615211 CAAATCAGCTCAAGCAATTATACACTA 58.385 33.333 4.59 0.00 45.16 2.74
1887 5442 7.721286 ATCAGCTCAAGCAATTATACACTAC 57.279 36.000 4.59 0.00 45.16 2.73
1888 5443 6.878317 TCAGCTCAAGCAATTATACACTACT 58.122 36.000 4.59 0.00 45.16 2.57
1890 5445 8.642432 TCAGCTCAAGCAATTATACACTACTAT 58.358 33.333 4.59 0.00 45.16 2.12
1891 5446 9.265901 CAGCTCAAGCAATTATACACTACTATT 57.734 33.333 4.59 0.00 45.16 1.73
1892 5447 9.838339 AGCTCAAGCAATTATACACTACTATTT 57.162 29.630 4.59 0.00 45.16 1.40
1922 5477 1.526686 TGAGGTTGGCAGTGCAGTG 60.527 57.895 18.61 17.56 0.00 3.66
1925 5480 2.492773 GGTTGGCAGTGCAGTGCTT 61.493 57.895 37.80 1.37 43.45 3.91
1931 5486 2.031516 CAGTGCAGTGCTTCTCCCG 61.032 63.158 17.60 0.21 0.00 5.14
1982 5537 6.537301 CGCTTTGGATTGAAGGTACAACTATA 59.463 38.462 0.00 0.00 32.50 1.31
2042 5597 3.138798 TCCGAGTGAGGCCGTAGC 61.139 66.667 0.00 0.00 38.76 3.58
2187 5754 3.721035 TCACGAGATGCCTAATCATGTG 58.279 45.455 0.00 0.00 40.94 3.21
2229 5799 0.038744 CCAGTGGATGCCCTGTTTCT 59.961 55.000 1.68 0.00 0.00 2.52
2325 5896 6.174451 TCTGTGTACATTGTCTCGTAGTAC 57.826 41.667 0.00 0.00 36.49 2.73
2356 6062 5.411831 TTGTTCTGACACTGCATATCTCT 57.588 39.130 0.00 0.00 34.98 3.10
2405 6119 6.922957 CAGCCTACTTTCAAAGCAAAAACATA 59.077 34.615 0.00 0.00 0.00 2.29
2410 6124 9.515020 CTACTTTCAAAGCAAAAACATACAGAA 57.485 29.630 0.00 0.00 0.00 3.02
2456 6174 2.126189 GTAGACGCACCCGGACAC 60.126 66.667 0.73 0.00 39.22 3.67
2479 6198 2.140792 AAGACAGTGTCCACGGCCT 61.141 57.895 19.71 0.00 36.20 5.19
2496 6215 2.092375 GGCCTCTTAAATGCCCTACTGT 60.092 50.000 0.00 0.00 39.30 3.55
2516 6235 2.194800 ACATCACACTGCTCGTATCG 57.805 50.000 0.00 0.00 0.00 2.92
2520 6239 3.503827 TCACACTGCTCGTATCGAAAT 57.496 42.857 0.00 0.00 34.74 2.17
2538 6257 4.738252 CGAAATCTCAAATCCATGCACATG 59.262 41.667 3.56 3.56 38.51 3.21
2642 6373 7.012989 AGTGTACAGTTCAAACATTAAACTCCC 59.987 37.037 0.00 0.00 31.04 4.30
2644 6375 7.558444 TGTACAGTTCAAACATTAAACTCCCTT 59.442 33.333 0.00 0.00 31.04 3.95
2650 6381 8.817100 GTTCAAACATTAAACTCCCTTTTTCTG 58.183 33.333 0.00 0.00 0.00 3.02
2661 6392 2.623416 CCCTTTTTCTGTTGTGGGTCTC 59.377 50.000 0.00 0.00 0.00 3.36
2739 6487 3.389687 AGTTCACAAATATGCTTCGCG 57.610 42.857 0.00 0.00 0.00 5.87
2800 6553 0.615331 ATCATGTGTTCGGACTGCCT 59.385 50.000 0.00 0.00 0.00 4.75
2804 6557 1.334160 TGTGTTCGGACTGCCTCTTA 58.666 50.000 0.00 0.00 0.00 2.10
2868 6621 0.603707 ATGTCGTCACCTGCCACAAG 60.604 55.000 0.00 0.00 0.00 3.16
2882 6636 2.099098 GCCACAAGGTATTTGATTCCCG 59.901 50.000 0.00 0.00 39.21 5.14
2922 6676 3.456380 ACAATACCCCAATGAGCTTGT 57.544 42.857 0.00 0.00 32.61 3.16
2979 6736 5.883673 AGGTACTTCTTGCACTGTTGTAAAA 59.116 36.000 0.00 0.00 27.25 1.52
3028 6788 3.301579 CGTATATGGTCTTCACAAACGCG 60.302 47.826 3.53 3.53 0.00 6.01
3085 6846 4.568072 TCCCATACATTGTAGTTGTGCT 57.432 40.909 2.53 0.00 0.00 4.40
3086 6847 4.260985 TCCCATACATTGTAGTTGTGCTG 58.739 43.478 2.53 0.00 0.00 4.41
3089 6850 1.877637 ACATTGTAGTTGTGCTGCGA 58.122 45.000 0.00 0.00 32.10 5.10
3090 6851 1.531149 ACATTGTAGTTGTGCTGCGAC 59.469 47.619 0.00 0.00 32.10 5.19
3092 6853 1.827315 TTGTAGTTGTGCTGCGACGC 61.827 55.000 14.19 14.19 36.60 5.19
3093 6854 2.028337 TAGTTGTGCTGCGACGCA 59.972 55.556 22.99 22.99 36.60 5.24
3094 6855 1.374125 TAGTTGTGCTGCGACGCAT 60.374 52.632 24.71 9.14 42.62 4.73
3104 6889 3.138625 CGACGCATCCCCCTACAT 58.861 61.111 0.00 0.00 0.00 2.29
3153 6939 0.516877 ACATTGATGTCGTTGTGCGG 59.483 50.000 0.00 0.00 41.72 5.69
3204 6990 4.474303 TCCATAAATCCCTTGATGCCAT 57.526 40.909 0.00 0.00 0.00 4.40
3261 7047 2.831685 TGGTACATCTCGTGCAAACT 57.168 45.000 0.00 0.00 30.59 2.66
3272 7059 1.570813 GTGCAAACTTTTGGGTCAGC 58.429 50.000 3.95 0.00 38.57 4.26
3306 7094 2.334971 TGCATGCAATCAACTGAACG 57.665 45.000 20.30 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.089201 TCAGTCTCGCAGGTTCGATAA 58.911 47.619 0.00 0.00 37.87 1.75
17 18 1.671328 CTCAGTCTCGCAGGTTCGATA 59.329 52.381 0.00 0.00 37.87 2.92
33 34 3.137459 AGCGGAGTCGAGGCTCAG 61.137 66.667 15.95 7.64 39.00 3.35
60 61 1.581934 TTGCTCTGGTTTCGTCACTG 58.418 50.000 0.00 0.00 0.00 3.66
61 62 2.549754 CAATTGCTCTGGTTTCGTCACT 59.450 45.455 0.00 0.00 0.00 3.41
76 78 3.648339 TGCTCCTTCTGTTTCAATTGC 57.352 42.857 0.00 0.00 0.00 3.56
83 85 4.829492 AGCTTAATGTTGCTCCTTCTGTTT 59.171 37.500 0.00 0.00 33.90 2.83
85 87 4.026356 AGCTTAATGTTGCTCCTTCTGT 57.974 40.909 0.00 0.00 33.90 3.41
117 119 9.988350 GTCTTATGTGTTACTTGATGTTATTGG 57.012 33.333 0.00 0.00 0.00 3.16
121 123 9.936759 TGATGTCTTATGTGTTACTTGATGTTA 57.063 29.630 0.00 0.00 0.00 2.41
122 124 8.846943 TGATGTCTTATGTGTTACTTGATGTT 57.153 30.769 0.00 0.00 0.00 2.71
178 180 5.236695 GTGCCCGTAGAGAAATTTATCTTCC 59.763 44.000 19.69 10.48 30.36 3.46
180 182 5.741011 TGTGCCCGTAGAGAAATTTATCTT 58.259 37.500 19.69 5.52 30.36 2.40
240 242 6.720112 AGTGTGCCCGTATAGTTTAATCTA 57.280 37.500 0.00 0.00 0.00 1.98
242 244 7.958053 AATAGTGTGCCCGTATAGTTTAATC 57.042 36.000 0.00 0.00 0.00 1.75
282 3469 4.953579 TCAATAATAGTGTGCCTTTTCCCC 59.046 41.667 0.00 0.00 0.00 4.81
283 3470 5.448632 CGTCAATAATAGTGTGCCTTTTCCC 60.449 44.000 0.00 0.00 0.00 3.97
284 3471 5.448632 CCGTCAATAATAGTGTGCCTTTTCC 60.449 44.000 0.00 0.00 0.00 3.13
286 3473 5.250200 TCCGTCAATAATAGTGTGCCTTTT 58.750 37.500 0.00 0.00 0.00 2.27
288 3475 4.442706 CTCCGTCAATAATAGTGTGCCTT 58.557 43.478 0.00 0.00 0.00 4.35
290 3477 3.131396 CCTCCGTCAATAATAGTGTGCC 58.869 50.000 0.00 0.00 0.00 5.01
291 3478 2.544267 GCCTCCGTCAATAATAGTGTGC 59.456 50.000 0.00 0.00 0.00 4.57
292 3479 3.792401 TGCCTCCGTCAATAATAGTGTG 58.208 45.455 0.00 0.00 0.00 3.82
294 3481 4.060038 ACTGCCTCCGTCAATAATAGTG 57.940 45.455 0.00 0.00 0.00 2.74
295 3482 7.719871 ATATACTGCCTCCGTCAATAATAGT 57.280 36.000 0.00 0.00 0.00 2.12
296 3483 8.035394 ACAATATACTGCCTCCGTCAATAATAG 58.965 37.037 0.00 0.00 0.00 1.73
298 3485 6.769512 ACAATATACTGCCTCCGTCAATAAT 58.230 36.000 0.00 0.00 0.00 1.28
299 3486 6.169557 ACAATATACTGCCTCCGTCAATAA 57.830 37.500 0.00 0.00 0.00 1.40
300 3487 5.801531 ACAATATACTGCCTCCGTCAATA 57.198 39.130 0.00 0.00 0.00 1.90
301 3488 4.689612 ACAATATACTGCCTCCGTCAAT 57.310 40.909 0.00 0.00 0.00 2.57
306 3626 5.758296 ACAACATTACAATATACTGCCTCCG 59.242 40.000 0.00 0.00 0.00 4.63
328 3648 1.227823 CCGTGCAAAGGACAGGACA 60.228 57.895 3.50 0.00 37.88 4.02
340 3660 3.886505 AGATCTTTGTTTTTACCCGTGCA 59.113 39.130 0.00 0.00 0.00 4.57
394 3715 4.428845 GTCCCTGTGACGGACCTA 57.571 61.111 0.00 0.00 43.48 3.08
419 3740 1.962306 GGCGGTTGCTACGGACAAA 60.962 57.895 9.88 0.00 42.25 2.83
464 3785 1.638388 CTACTACCGTCACGTGCCGA 61.638 60.000 21.94 0.00 0.00 5.54
476 3797 4.673061 CGAGCTGTATATGCTGCTACTACC 60.673 50.000 21.78 10.53 42.37 3.18
477 3798 4.407818 CGAGCTGTATATGCTGCTACTAC 58.592 47.826 21.78 10.83 42.37 2.73
571 3967 2.980233 GGGGGTAGATGCATGCGC 60.980 66.667 14.09 0.00 39.24 6.09
607 4015 2.512974 CGGTAATGTGGGACGGCC 60.513 66.667 0.00 0.00 0.00 6.13
608 4016 3.199891 GCGGTAATGTGGGACGGC 61.200 66.667 0.00 0.00 35.20 5.68
610 4018 3.560278 GCGCGGTAATGTGGGACG 61.560 66.667 8.83 0.00 0.00 4.79
611 4019 3.560278 CGCGCGGTAATGTGGGAC 61.560 66.667 24.84 0.00 34.56 4.46
768 4187 1.230497 GGGATGAGACGAGAGGGGA 59.770 63.158 0.00 0.00 0.00 4.81
773 4192 1.815795 CGGAGATGGGATGAGACGAGA 60.816 57.143 0.00 0.00 0.00 4.04
774 4193 0.595588 CGGAGATGGGATGAGACGAG 59.404 60.000 0.00 0.00 0.00 4.18
775 4194 0.823769 CCGGAGATGGGATGAGACGA 60.824 60.000 0.00 0.00 0.00 4.20
776 4195 1.662608 CCGGAGATGGGATGAGACG 59.337 63.158 0.00 0.00 0.00 4.18
777 4196 1.118356 AGCCGGAGATGGGATGAGAC 61.118 60.000 5.05 0.00 0.00 3.36
785 4204 0.464554 GGAAAGGAAGCCGGAGATGG 60.465 60.000 5.05 0.00 0.00 3.51
793 4212 1.352687 ACAGGAGAAGGAAAGGAAGCC 59.647 52.381 0.00 0.00 0.00 4.35
801 4220 1.944177 AGCTAGCACAGGAGAAGGAA 58.056 50.000 18.83 0.00 0.00 3.36
808 4227 2.025793 ACTCACTCTAGCTAGCACAGGA 60.026 50.000 18.83 8.00 0.00 3.86
809 4228 2.374184 ACTCACTCTAGCTAGCACAGG 58.626 52.381 18.83 9.75 0.00 4.00
810 4229 3.003275 GCTACTCACTCTAGCTAGCACAG 59.997 52.174 18.83 13.50 34.82 3.66
811 4230 2.946329 GCTACTCACTCTAGCTAGCACA 59.054 50.000 18.83 2.91 34.82 4.57
812 4231 3.003275 CAGCTACTCACTCTAGCTAGCAC 59.997 52.174 18.83 0.00 44.25 4.40
813 4232 3.210227 CAGCTACTCACTCTAGCTAGCA 58.790 50.000 18.83 4.45 44.25 3.49
822 4241 6.334202 AGTAATTAACAGCAGCTACTCACTC 58.666 40.000 0.00 0.00 0.00 3.51
865 4286 2.482333 CCGAGCCGAGAGATTCCGT 61.482 63.158 0.00 0.00 0.00 4.69
1279 4762 1.962822 CAGCAGCCAAAGCGTGAGA 60.963 57.895 0.00 0.00 46.67 3.27
1298 4781 3.716006 CCTGCGCACGACAACAGG 61.716 66.667 5.66 0.00 43.45 4.00
1299 4782 2.661537 TCCTGCGCACGACAACAG 60.662 61.111 5.66 0.00 0.00 3.16
1345 4828 4.458829 TCCATCTCCTCCGCCGGT 62.459 66.667 1.63 0.00 0.00 5.28
1425 4909 1.171308 GTTGCCTGACTCATGCATGT 58.829 50.000 25.43 8.12 35.22 3.21
1475 4975 4.020485 GCTACTCCCATATAAATCCACGGT 60.020 45.833 0.00 0.00 0.00 4.83
1623 5150 4.097741 ACAGCAACAGAAAAACACATGCTA 59.902 37.500 0.00 0.00 40.40 3.49
1632 5159 8.376889 AGAAAAAGAAAACAGCAACAGAAAAA 57.623 26.923 0.00 0.00 0.00 1.94
1638 5165 6.686630 TCAAGAGAAAAAGAAAACAGCAACA 58.313 32.000 0.00 0.00 0.00 3.33
1639 5166 7.581011 TTCAAGAGAAAAAGAAAACAGCAAC 57.419 32.000 0.00 0.00 0.00 4.17
1703 5247 6.879400 ACTCCCTATCTGTGTAGTGATTTTC 58.121 40.000 0.00 0.00 0.00 2.29
1718 5262 4.072131 TGTGTGCTCAAAAACTCCCTATC 58.928 43.478 0.00 0.00 0.00 2.08
1751 5303 4.492646 ACAAAAGACCAAGATCCCCATTT 58.507 39.130 0.00 0.00 0.00 2.32
1752 5304 4.132122 ACAAAAGACCAAGATCCCCATT 57.868 40.909 0.00 0.00 0.00 3.16
1753 5305 3.833559 ACAAAAGACCAAGATCCCCAT 57.166 42.857 0.00 0.00 0.00 4.00
1780 5333 4.920112 TCCCCGTTGCGTGTGTGG 62.920 66.667 0.00 0.00 0.00 4.17
1781 5334 3.645975 GTCCCCGTTGCGTGTGTG 61.646 66.667 0.00 0.00 0.00 3.82
1789 5342 4.388499 CCCAGTCCGTCCCCGTTG 62.388 72.222 0.00 0.00 0.00 4.10
1793 5347 1.272554 AATTCTCCCAGTCCGTCCCC 61.273 60.000 0.00 0.00 0.00 4.81
1796 5350 1.825474 TCTGAATTCTCCCAGTCCGTC 59.175 52.381 7.05 0.00 0.00 4.79
1810 5364 4.942761 TTTTTCCTTTGCTGCTCTGAAT 57.057 36.364 0.00 0.00 0.00 2.57
1835 5390 8.102047 TGCCAAAATCCATAATTGAGTTGAAAT 58.898 29.630 0.00 0.00 0.00 2.17
1838 5393 6.602410 TGCCAAAATCCATAATTGAGTTGA 57.398 33.333 0.00 0.00 0.00 3.18
1853 5408 3.244284 TGCTTGAGCTGATTTGCCAAAAT 60.244 39.130 4.44 0.00 42.66 1.82
1854 5409 2.102757 TGCTTGAGCTGATTTGCCAAAA 59.897 40.909 4.44 0.00 42.66 2.44
1859 5414 6.197842 GTGTATAATTGCTTGAGCTGATTTGC 59.802 38.462 4.44 0.00 42.66 3.68
1865 5420 8.824159 ATAGTAGTGTATAATTGCTTGAGCTG 57.176 34.615 4.44 0.00 42.66 4.24
1882 5437 8.507249 CCTCACTTTTTCTTGGAAATAGTAGTG 58.493 37.037 12.90 12.92 0.00 2.74
1883 5438 8.218488 ACCTCACTTTTTCTTGGAAATAGTAGT 58.782 33.333 12.90 9.61 0.00 2.73
1884 5439 8.622948 ACCTCACTTTTTCTTGGAAATAGTAG 57.377 34.615 12.90 11.07 0.00 2.57
1885 5440 8.846211 CAACCTCACTTTTTCTTGGAAATAGTA 58.154 33.333 12.90 5.14 0.00 1.82
1886 5441 7.201911 CCAACCTCACTTTTTCTTGGAAATAGT 60.202 37.037 9.22 9.22 31.49 2.12
1887 5442 7.147976 CCAACCTCACTTTTTCTTGGAAATAG 58.852 38.462 8.24 8.24 31.49 1.73
1888 5443 6.462347 GCCAACCTCACTTTTTCTTGGAAATA 60.462 38.462 0.00 0.00 31.49 1.40
1890 5445 4.382577 GCCAACCTCACTTTTTCTTGGAAA 60.383 41.667 0.00 0.00 31.49 3.13
1891 5446 3.132111 GCCAACCTCACTTTTTCTTGGAA 59.868 43.478 0.00 0.00 31.49 3.53
1892 5447 2.693074 GCCAACCTCACTTTTTCTTGGA 59.307 45.455 0.00 0.00 31.49 3.53
1893 5448 2.430332 TGCCAACCTCACTTTTTCTTGG 59.570 45.455 0.00 0.00 32.79 3.61
1894 5449 3.131046 ACTGCCAACCTCACTTTTTCTTG 59.869 43.478 0.00 0.00 0.00 3.02
1897 5452 2.799562 GCACTGCCAACCTCACTTTTTC 60.800 50.000 0.00 0.00 0.00 2.29
1922 5477 2.186532 AGAAAAGAACCGGGAGAAGC 57.813 50.000 6.32 0.00 0.00 3.86
1925 5480 2.629617 ACGTTAGAAAAGAACCGGGAGA 59.370 45.455 6.32 0.00 0.00 3.71
1931 5486 6.555812 AGATCCAAACGTTAGAAAAGAACC 57.444 37.500 0.00 0.00 0.00 3.62
2042 5597 1.230635 CGGCGGCATATCCTTCCTTG 61.231 60.000 10.53 0.00 0.00 3.61
2187 5754 4.712763 CGACTTTTACATGGTGAGCTTTC 58.287 43.478 0.00 0.00 0.00 2.62
2201 5768 1.448985 GCATCCACTGGCGACTTTTA 58.551 50.000 0.00 0.00 0.00 1.52
2202 5769 1.244019 GGCATCCACTGGCGACTTTT 61.244 55.000 0.00 0.00 41.02 2.27
2229 5799 3.703001 AAAAGCAAGCTAGCTACAGGA 57.297 42.857 19.70 0.00 45.89 3.86
2325 5896 5.753438 TGCAGTGTCAGAACAAAAGTACTAG 59.247 40.000 0.00 0.00 37.08 2.57
2356 6062 6.126911 TGGACTTACCATGCTATGATGTGTTA 60.127 38.462 0.00 0.00 44.64 2.41
2405 6119 0.898320 CGGATCTGTCCCAGTTCTGT 59.102 55.000 0.00 0.00 41.83 3.41
2410 6124 1.686110 GGGTCGGATCTGTCCCAGT 60.686 63.158 26.60 0.00 41.83 4.00
2419 6137 1.515736 GACGTTCACGGGTCGGATC 60.516 63.158 4.07 0.00 44.95 3.36
2456 6174 0.939577 CGTGGACACTGTCTTGGACG 60.940 60.000 9.08 8.59 34.95 4.79
2461 6180 2.100879 GAGGCCGTGGACACTGTCTT 62.101 60.000 9.08 0.00 30.66 3.01
2479 6198 6.070481 TGTGATGTACAGTAGGGCATTTAAGA 60.070 38.462 0.33 0.00 33.42 2.10
2496 6215 2.940410 TCGATACGAGCAGTGTGATGTA 59.060 45.455 0.00 0.00 0.00 2.29
2538 6257 6.726258 TTATGCGATTCATGTGTATGATCC 57.274 37.500 0.00 0.00 42.60 3.36
2610 6341 9.562583 TTAATGTTTGAACTGTACACTTGAAAC 57.437 29.630 17.20 17.20 0.00 2.78
2620 6351 8.528044 AAAGGGAGTTTAATGTTTGAACTGTA 57.472 30.769 2.59 0.00 34.02 2.74
2624 6355 8.817100 CAGAAAAAGGGAGTTTAATGTTTGAAC 58.183 33.333 0.00 0.00 0.00 3.18
2642 6373 3.287222 TGGAGACCCACAACAGAAAAAG 58.713 45.455 0.00 0.00 37.58 2.27
2644 6375 3.593442 ATGGAGACCCACAACAGAAAA 57.407 42.857 0.00 0.00 46.98 2.29
2650 6381 2.565841 GAGCATATGGAGACCCACAAC 58.434 52.381 4.56 0.00 46.98 3.32
2739 6487 0.323629 TCCACCTCCCGAAACATGAC 59.676 55.000 0.00 0.00 0.00 3.06
2800 6553 3.637229 GTCGAGGATGATGAGGGTTAAGA 59.363 47.826 0.00 0.00 0.00 2.10
2804 6557 1.866015 TGTCGAGGATGATGAGGGTT 58.134 50.000 0.00 0.00 0.00 4.11
2858 6611 3.131046 GGAATCAAATACCTTGTGGCAGG 59.869 47.826 0.00 0.00 40.23 4.85
2868 6621 4.549458 CAATGATGCGGGAATCAAATACC 58.451 43.478 0.00 0.00 39.90 2.73
2871 6624 3.102052 GCAATGATGCGGGAATCAAAT 57.898 42.857 0.00 0.00 43.83 2.32
2922 6676 2.700897 GGAGAGGGCATTTAGAGTGCTA 59.299 50.000 0.00 0.00 42.16 3.49
3085 6846 3.845259 GTAGGGGGATGCGTCGCA 61.845 66.667 24.05 24.05 44.86 5.10
3086 6847 1.812686 TATGTAGGGGGATGCGTCGC 61.813 60.000 11.10 11.10 36.63 5.19
3089 6850 1.133136 AGACTATGTAGGGGGATGCGT 60.133 52.381 0.00 0.00 0.00 5.24
3090 6851 1.546476 GAGACTATGTAGGGGGATGCG 59.454 57.143 0.00 0.00 0.00 4.73
3092 6853 2.558795 CACGAGACTATGTAGGGGGATG 59.441 54.545 0.00 0.00 0.00 3.51
3093 6854 2.445905 TCACGAGACTATGTAGGGGGAT 59.554 50.000 0.00 0.00 0.00 3.85
3094 6855 1.848388 TCACGAGACTATGTAGGGGGA 59.152 52.381 0.00 0.00 0.00 4.81
3098 6883 4.378563 CCGCTATTCACGAGACTATGTAGG 60.379 50.000 0.00 0.00 0.00 3.18
3104 6889 3.189618 TCTCCGCTATTCACGAGACTA 57.810 47.619 0.00 0.00 0.00 2.59
3153 6939 2.867647 GCTTTCTTTGGCATGGTTGGTC 60.868 50.000 0.00 0.00 0.00 4.02
3204 6990 5.030147 AGGTCACCATCATACTAGAACCAA 58.970 41.667 0.00 0.00 0.00 3.67
3261 7047 4.450053 CCAATGAAAAAGCTGACCCAAAA 58.550 39.130 0.00 0.00 0.00 2.44
3272 7059 3.753842 GCATGCATTGCCAATGAAAAAG 58.246 40.909 21.24 6.56 46.15 2.27


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

AutoCloner maintained by Alex Coulton.