Multiple sequence alignment - TraesCS2D01G294100

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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 TraesCS2D01G294100 chr2D 100.000 3186 0 0 1 3186 376357753 376354568 0.000000e+00 5884
1 TraesCS2D01G294100 chr2B 92.415 2663 109 46 565 3186 447826359 447823749 0.000000e+00 3712
2 TraesCS2D01G294100 chr2B 83.821 513 36 23 3 501 447826866 447826387 8.110000e-121 444
3 TraesCS2D01G294100 chr2A 92.590 1498 58 26 640 2114 509992935 509991468 0.000000e+00 2102
4 TraesCS2D01G294100 chr2A 92.567 1009 57 5 1107 2114 509581088 509580097 0.000000e+00 1432
5 TraesCS2D01G294100 chr2A 92.588 796 41 11 2098 2882 509580081 509579293 0.000000e+00 1127
6 TraesCS2D01G294100 chr2A 93.151 730 35 11 2102 2819 509991448 509990722 0.000000e+00 1057
7 TraesCS2D01G294100 chr2A 90.504 674 34 20 1 648 509996260 509995591 0.000000e+00 863
8 TraesCS2D01G294100 chr2A 82.293 785 67 36 270 1008 509727880 509727122 5.840000e-172 614
9 TraesCS2D01G294100 chr2A 96.040 303 11 1 2884 3186 509579167 509578866 2.860000e-135 492
10 TraesCS2D01G294100 chr3D 80.132 906 149 24 1071 1950 496768427 496767527 0.000000e+00 647
11 TraesCS2D01G294100 chr3D 83.009 565 86 6 1160 1720 546656024 546656582 1.320000e-138 503
12 TraesCS2D01G294100 chr3A 79.912 906 151 24 1071 1950 638016464 638015564 1.250000e-178 636
13 TraesCS2D01G294100 chr5B 79.418 928 140 38 1071 1950 661524920 661523996 2.720000e-170 608
14 TraesCS2D01G294100 chr5B 80.911 571 97 6 1392 1950 661612550 661613120 1.050000e-119 440
15 TraesCS2D01G294100 chr3B 79.318 909 151 27 1071 1950 656066803 656065903 1.260000e-168 603
16 TraesCS2D01G294100 chr5A 79.072 927 145 32 1071 1950 653475295 653474371 2.740000e-165 592
17 TraesCS2D01G294100 chr5A 76.907 931 163 31 1065 1945 653563419 653564347 6.180000e-132 481
18 TraesCS2D01G294100 chr5D 78.733 931 144 30 1071 1950 526411236 526410309 9.910000e-160 573
19 TraesCS2D01G294100 chr5D 81.050 438 69 7 1518 1942 526422497 526422933 1.420000e-88 337
20 TraesCS2D01G294100 chr1A 95.102 245 12 0 1724 1968 36265789 36266033 1.390000e-103 387
21 TraesCS2D01G294100 chr1A 91.837 98 6 2 1595 1690 36265694 36265791 5.540000e-28 135


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 TraesCS2D01G294100 chr2D 376354568 376357753 3185 True 5884.000000 5884 100.000000 1 3186 1 chr2D.!!$R1 3185
1 TraesCS2D01G294100 chr2B 447823749 447826866 3117 True 2078.000000 3712 88.118000 3 3186 2 chr2B.!!$R1 3183
2 TraesCS2D01G294100 chr2A 509990722 509996260 5538 True 1340.666667 2102 92.081667 1 2819 3 chr2A.!!$R3 2818
3 TraesCS2D01G294100 chr2A 509578866 509581088 2222 True 1017.000000 1432 93.731667 1107 3186 3 chr2A.!!$R2 2079
4 TraesCS2D01G294100 chr2A 509727122 509727880 758 True 614.000000 614 82.293000 270 1008 1 chr2A.!!$R1 738
5 TraesCS2D01G294100 chr3D 496767527 496768427 900 True 647.000000 647 80.132000 1071 1950 1 chr3D.!!$R1 879
6 TraesCS2D01G294100 chr3D 546656024 546656582 558 False 503.000000 503 83.009000 1160 1720 1 chr3D.!!$F1 560
7 TraesCS2D01G294100 chr3A 638015564 638016464 900 True 636.000000 636 79.912000 1071 1950 1 chr3A.!!$R1 879
8 TraesCS2D01G294100 chr5B 661523996 661524920 924 True 608.000000 608 79.418000 1071 1950 1 chr5B.!!$R1 879
9 TraesCS2D01G294100 chr5B 661612550 661613120 570 False 440.000000 440 80.911000 1392 1950 1 chr5B.!!$F1 558
10 TraesCS2D01G294100 chr3B 656065903 656066803 900 True 603.000000 603 79.318000 1071 1950 1 chr3B.!!$R1 879
11 TraesCS2D01G294100 chr5A 653474371 653475295 924 True 592.000000 592 79.072000 1071 1950 1 chr5A.!!$R1 879
12 TraesCS2D01G294100 chr5A 653563419 653564347 928 False 481.000000 481 76.907000 1065 1945 1 chr5A.!!$F1 880
13 TraesCS2D01G294100 chr5D 526410309 526411236 927 True 573.000000 573 78.733000 1071 1950 1 chr5D.!!$R1 879

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
678 3425 0.322456 TTGCAGGCATACAGACCACC 60.322 55.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2389 5315 1.006337 GCCAATGCTTTGCCGTTCA 60.006 52.632 6.81 0.0 33.53 3.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 5.527582 GTGGCTTAGACACGGAATCATAAAT 59.472 40.000 1.12 0.00 29.47 1.40
64 65 3.244976 CGCTCCCATTTTGACATGAAAC 58.755 45.455 0.00 0.00 0.00 2.78
337 365 0.396435 CAAGTCCCCAGCACACTGTA 59.604 55.000 0.00 0.00 42.81 2.74
403 437 2.634940 TCCGACGGCTACTAGTACCTAT 59.365 50.000 9.66 7.13 0.00 2.57
430 464 2.874780 GAGCACGCACGGTCGTAG 60.875 66.667 3.99 0.00 41.21 3.51
431 465 3.606065 GAGCACGCACGGTCGTAGT 62.606 63.158 3.99 0.00 41.21 2.73
432 466 2.176546 GCACGCACGGTCGTAGTA 59.823 61.111 3.99 0.00 41.21 1.82
437 471 1.186030 CGCACGGTCGTAGTAATGTC 58.814 55.000 0.00 0.00 0.00 3.06
449 498 6.978659 GTCGTAGTAATGTCCATGAGATGAAA 59.021 38.462 0.00 0.00 0.00 2.69
454 503 8.038862 AGTAATGTCCATGAGATGAAAGGTAT 57.961 34.615 0.00 0.00 0.00 2.73
557 614 1.746615 GGTCACCAGCGTGCATCAT 60.747 57.895 0.00 0.00 40.04 2.45
558 615 1.709147 GGTCACCAGCGTGCATCATC 61.709 60.000 0.00 0.00 40.04 2.92
586 643 0.894835 AAATGTTGGGCCGGCTAAAG 59.105 50.000 28.56 0.00 0.00 1.85
594 652 3.467226 CCGGCTAAAGAGGCCCGA 61.467 66.667 0.00 0.00 46.24 5.14
638 701 1.143183 GATTTGCCGGTCTCCGCTA 59.857 57.895 1.90 0.00 46.86 4.26
678 3425 0.322456 TTGCAGGCATACAGACCACC 60.322 55.000 0.00 0.00 0.00 4.61
764 3524 1.004745 GGGTGAAAGAGGAATGGCAGA 59.995 52.381 0.00 0.00 0.00 4.26
961 3728 4.251760 CGCATCCTCGCCATCTAC 57.748 61.111 0.00 0.00 0.00 2.59
962 3729 1.662608 CGCATCCTCGCCATCTACT 59.337 57.895 0.00 0.00 0.00 2.57
963 3730 0.881796 CGCATCCTCGCCATCTACTA 59.118 55.000 0.00 0.00 0.00 1.82
964 3731 1.135546 CGCATCCTCGCCATCTACTAG 60.136 57.143 0.00 0.00 0.00 2.57
965 3732 1.889829 GCATCCTCGCCATCTACTAGT 59.110 52.381 0.00 0.00 0.00 2.57
966 3733 3.082548 GCATCCTCGCCATCTACTAGTA 58.917 50.000 1.89 1.89 0.00 1.82
1044 3814 2.125350 CACTTCTCCAGGAGCCGC 60.125 66.667 12.26 0.00 0.00 6.53
1371 4182 1.303561 ACGTGTACTACAGGGGCGA 60.304 57.895 12.39 0.00 38.22 5.54
1849 4695 0.987294 TCAAGAGCAAGAAGGGGAGG 59.013 55.000 0.00 0.00 0.00 4.30
1850 4696 0.987294 CAAGAGCAAGAAGGGGAGGA 59.013 55.000 0.00 0.00 0.00 3.71
1851 4697 1.352352 CAAGAGCAAGAAGGGGAGGAA 59.648 52.381 0.00 0.00 0.00 3.36
1852 4698 1.284313 AGAGCAAGAAGGGGAGGAAG 58.716 55.000 0.00 0.00 0.00 3.46
1853 4699 0.254462 GAGCAAGAAGGGGAGGAAGG 59.746 60.000 0.00 0.00 0.00 3.46
1854 4700 0.178861 AGCAAGAAGGGGAGGAAGGA 60.179 55.000 0.00 0.00 0.00 3.36
1855 4701 0.254462 GCAAGAAGGGGAGGAAGGAG 59.746 60.000 0.00 0.00 0.00 3.69
1856 4702 1.958288 CAAGAAGGGGAGGAAGGAGA 58.042 55.000 0.00 0.00 0.00 3.71
1857 4703 1.836802 CAAGAAGGGGAGGAAGGAGAG 59.163 57.143 0.00 0.00 0.00 3.20
2319 5240 3.925630 ATTGGCAGCCACAGGACGG 62.926 63.158 15.89 0.00 30.78 4.79
2347 5268 3.133003 CGATCACAATCTACTGTTCCCCT 59.867 47.826 0.00 0.00 0.00 4.79
2483 5410 2.094906 TGTCGATGTCCACGAGGTTAAG 60.095 50.000 0.00 0.00 40.37 1.85
2515 5442 7.118971 GGAACATTATCTGATATGCTCTTGGAC 59.881 40.741 0.00 0.00 0.00 4.02
2522 5449 1.438651 TATGCTCTTGGACGTGTTGC 58.561 50.000 0.00 0.00 0.00 4.17
2572 5499 7.061441 ACAATATTACGCGTCGATTACATTAGG 59.939 37.037 18.63 3.05 0.00 2.69
2638 5565 0.095417 CGGCTTTTCTCTAACAGCGC 59.905 55.000 0.00 0.00 32.68 5.92
2656 5583 2.602217 GCGCCGCAATCTACCTTATTTG 60.602 50.000 3.15 0.00 0.00 2.32
2663 5590 7.962918 GCCGCAATCTACCTTATTTGTATTATG 59.037 37.037 0.00 0.00 0.00 1.90
2804 5732 5.288712 GTCGACATATATAACTCGCCCATTG 59.711 44.000 11.55 0.00 0.00 2.82
2847 5775 5.770417 CATTGCTCAGCTCTTCTTCTTTTT 58.230 37.500 0.00 0.00 0.00 1.94
2997 6049 3.247006 TCATCTCTTCCCGTGCTTTAC 57.753 47.619 0.00 0.00 0.00 2.01
3084 6136 1.202794 TGACAATGGTTGCTGAGCTCA 60.203 47.619 17.19 17.19 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 0.534412 ATGTTCAGTCAGCTCGGAGG 59.466 55.000 7.20 0.00 0.00 4.30
337 365 2.031870 GGGAAGGCTTTAATTCCGCAT 58.968 47.619 0.00 0.00 44.98 4.73
403 437 1.401018 CGTGCGTGCTCGGATGATATA 60.401 52.381 15.62 0.00 44.92 0.86
430 464 7.308229 GCATACCTTTCATCTCATGGACATTAC 60.308 40.741 0.00 0.00 0.00 1.89
431 465 6.712095 GCATACCTTTCATCTCATGGACATTA 59.288 38.462 0.00 0.00 0.00 1.90
432 466 5.533903 GCATACCTTTCATCTCATGGACATT 59.466 40.000 0.00 0.00 0.00 2.71
437 471 3.567164 GTGGCATACCTTTCATCTCATGG 59.433 47.826 0.00 0.00 36.63 3.66
454 503 4.069232 CTCTCGCTTCGGGTGGCA 62.069 66.667 0.00 0.00 0.00 4.92
460 509 2.876645 GACGTGCTCTCGCTTCGG 60.877 66.667 0.00 0.00 38.03 4.30
557 614 1.528292 CCCAACATTTTTCCCCGCGA 61.528 55.000 8.23 0.00 0.00 5.87
558 615 1.080161 CCCAACATTTTTCCCCGCG 60.080 57.895 0.00 0.00 0.00 6.46
560 617 1.295101 GGCCCAACATTTTTCCCCG 59.705 57.895 0.00 0.00 0.00 5.73
562 619 1.295101 CCGGCCCAACATTTTTCCC 59.705 57.895 0.00 0.00 0.00 3.97
563 620 1.375396 GCCGGCCCAACATTTTTCC 60.375 57.895 18.11 0.00 0.00 3.13
678 3425 1.493950 GCTCCGAGATCCATTGTGCG 61.494 60.000 0.00 0.00 0.00 5.34
740 3500 1.407437 CCATTCCTCTTTCACCCCTCG 60.407 57.143 0.00 0.00 0.00 4.63
741 3501 1.683319 GCCATTCCTCTTTCACCCCTC 60.683 57.143 0.00 0.00 0.00 4.30
742 3502 0.332972 GCCATTCCTCTTTCACCCCT 59.667 55.000 0.00 0.00 0.00 4.79
872 3639 2.207229 AGTACAGTGGCGTGGCAGA 61.207 57.895 0.00 0.00 0.00 4.26
958 3725 5.526846 GTGGCGGGCTATATAGTACTAGTAG 59.473 48.000 8.85 13.10 0.00 2.57
959 3726 5.431765 GTGGCGGGCTATATAGTACTAGTA 58.568 45.833 8.85 0.00 0.00 1.82
960 3727 4.268359 GTGGCGGGCTATATAGTACTAGT 58.732 47.826 8.85 0.00 0.00 2.57
961 3728 3.311871 CGTGGCGGGCTATATAGTACTAG 59.688 52.174 8.85 0.00 0.00 2.57
962 3729 3.273434 CGTGGCGGGCTATATAGTACTA 58.727 50.000 11.38 4.77 0.00 1.82
963 3730 2.089980 CGTGGCGGGCTATATAGTACT 58.910 52.381 11.38 0.00 0.00 2.73
964 3731 1.468736 GCGTGGCGGGCTATATAGTAC 60.469 57.143 11.38 5.05 0.00 2.73
965 3732 0.813184 GCGTGGCGGGCTATATAGTA 59.187 55.000 11.38 0.00 0.00 1.82
966 3733 1.183030 TGCGTGGCGGGCTATATAGT 61.183 55.000 11.38 0.00 0.00 2.12
1044 3814 1.206578 GCCACCATGTCGTTTCGTG 59.793 57.895 0.00 0.00 0.00 4.35
1630 4455 1.371558 GGTCTCGAAGTTGCACCCT 59.628 57.895 0.00 0.00 0.00 4.34
1699 4542 4.351938 CCGTCGGCGTTCTCCACA 62.352 66.667 9.28 0.00 36.15 4.17
1849 4695 3.191539 CGCGCCTTGCTCTCCTTC 61.192 66.667 0.00 0.00 43.27 3.46
1850 4696 3.240134 TTCGCGCCTTGCTCTCCTT 62.240 57.895 0.00 0.00 43.27 3.36
1851 4697 3.655810 CTTCGCGCCTTGCTCTCCT 62.656 63.158 0.00 0.00 43.27 3.69
1852 4698 3.191539 CTTCGCGCCTTGCTCTCC 61.192 66.667 0.00 0.00 43.27 3.71
1853 4699 2.125912 TCTTCGCGCCTTGCTCTC 60.126 61.111 0.00 0.00 43.27 3.20
1854 4700 2.125753 CTCTTCGCGCCTTGCTCT 60.126 61.111 0.00 0.00 43.27 4.09
1855 4701 2.125912 TCTCTTCGCGCCTTGCTC 60.126 61.111 0.00 0.00 43.27 4.26
1856 4702 2.125753 CTCTCTTCGCGCCTTGCT 60.126 61.111 0.00 0.00 43.27 3.91
1857 4703 3.191539 CCTCTCTTCGCGCCTTGC 61.192 66.667 0.00 0.00 41.47 4.01
2315 5236 4.030134 AGATTGTGATCGTACTTCCGTC 57.970 45.455 0.00 0.00 37.37 4.79
2319 5240 6.472808 GGAACAGTAGATTGTGATCGTACTTC 59.527 42.308 0.00 0.00 37.37 3.01
2331 5252 4.960469 TGTAGGTAGGGGAACAGTAGATTG 59.040 45.833 0.00 0.00 0.00 2.67
2376 5297 6.536731 TTTGCCGTTCATACGTACTTTAAA 57.463 33.333 0.00 0.00 46.20 1.52
2377 5298 5.389725 GCTTTGCCGTTCATACGTACTTTAA 60.390 40.000 0.00 0.00 46.20 1.52
2378 5299 4.091800 GCTTTGCCGTTCATACGTACTTTA 59.908 41.667 0.00 0.00 46.20 1.85
2379 5300 3.120442 GCTTTGCCGTTCATACGTACTTT 60.120 43.478 0.00 0.00 46.20 2.66
2381 5302 1.997606 GCTTTGCCGTTCATACGTACT 59.002 47.619 0.00 0.00 46.20 2.73
2382 5303 1.727880 TGCTTTGCCGTTCATACGTAC 59.272 47.619 0.00 0.00 46.20 3.67
2389 5315 1.006337 GCCAATGCTTTGCCGTTCA 60.006 52.632 6.81 0.00 33.53 3.18
2483 5410 6.939163 AGCATATCAGATAATGTTCCTGTTCC 59.061 38.462 0.00 0.00 0.00 3.62
2597 5524 6.360681 GCCGATGTGTAATTATGCTGAATTTC 59.639 38.462 2.38 0.00 31.51 2.17
2638 5565 8.999431 ACATAATACAAATAAGGTAGATTGCGG 58.001 33.333 0.00 0.00 0.00 5.69
2663 5590 4.676924 GTGCTGATGCTTGTAACTTCAAAC 59.323 41.667 0.00 0.00 40.48 2.93
2671 5598 2.032117 CGTGTTGTGCTGATGCTTGTAA 60.032 45.455 0.00 0.00 40.48 2.41
2804 5732 2.977405 CAAGCTTGCAACAGGTACTC 57.023 50.000 14.65 0.00 34.60 2.59
2847 5775 1.614996 TTGCCGCTCCATTTGAGAAA 58.385 45.000 0.00 0.00 44.42 2.52
2848 5776 1.614996 TTTGCCGCTCCATTTGAGAA 58.385 45.000 0.00 0.00 44.42 2.87
2849 5777 1.614996 TTTTGCCGCTCCATTTGAGA 58.385 45.000 0.00 0.00 44.42 3.27
2850 5778 2.437200 TTTTTGCCGCTCCATTTGAG 57.563 45.000 0.00 0.00 44.47 3.02
2882 5810 7.721286 AGTGCTGTTGCTAGTTCAATATATC 57.279 36.000 0.00 0.00 40.48 1.63
2920 5972 3.159472 TGAAGAACTAGCAGGAACCGTA 58.841 45.455 0.00 0.00 0.00 4.02
2997 6049 2.430610 CCTCCGAGGAAGAGGCCAG 61.431 68.421 9.01 0.00 44.30 4.85
3110 6162 2.741517 AGTTGTTTTGCTTGTTGTTGCC 59.258 40.909 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.