Multiple sequence alignment - TraesCS2D01G294200

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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 TraesCS2D01G294200 chr2D 100.000 2993 0 0 1 2993 376354757 376357749 0.000000e+00 5528
1 TraesCS2D01G294200 chr2B 92.037 2474 104 46 1 2433 447823938 447826359 0.000000e+00 3391
2 TraesCS2D01G294200 chr2B 83.757 511 36 23 2497 2993 447826387 447826864 9.850000e-120 440
3 TraesCS2D01G294200 chr2A 92.590 1498 58 26 884 2358 509991468 509992935 0.000000e+00 2102
4 TraesCS2D01G294200 chr2A 92.567 1009 57 5 884 1891 509580097 509581088 0.000000e+00 1432
5 TraesCS2D01G294200 chr2A 92.588 796 41 11 116 900 509579293 509580081 0.000000e+00 1127
6 TraesCS2D01G294200 chr2A 93.151 730 35 11 179 896 509990722 509991448 0.000000e+00 1057
7 TraesCS2D01G294200 chr2A 90.448 670 34 20 2350 2993 509995591 509996256 0.000000e+00 856
8 TraesCS2D01G294200 chr2A 82.293 785 67 36 1990 2728 509727122 509727880 5.480000e-172 614
9 TraesCS2D01G294200 chr2A 94.737 114 5 1 1 114 509579055 509579167 3.070000e-40 176
10 TraesCS2D01G294200 chr3D 80.132 906 149 24 1048 1927 496767527 496768427 0.000000e+00 647
11 TraesCS2D01G294200 chr3D 83.009 565 86 6 1278 1838 546656582 546656024 1.240000e-138 503
12 TraesCS2D01G294200 chr3A 79.912 906 151 24 1048 1927 638015564 638016464 1.170000e-178 636
13 TraesCS2D01G294200 chr5B 79.418 928 140 38 1048 1927 661523996 661524920 2.550000e-170 608
14 TraesCS2D01G294200 chr5B 80.911 571 97 6 1048 1606 661613120 661612550 9.850000e-120 440
15 TraesCS2D01G294200 chr3B 79.318 909 151 27 1048 1927 656065903 656066803 1.190000e-168 603
16 TraesCS2D01G294200 chr5A 79.072 927 145 32 1048 1927 653474371 653475295 2.570000e-165 592
17 TraesCS2D01G294200 chr5A 76.907 931 163 31 1053 1933 653564347 653563419 5.800000e-132 481
18 TraesCS2D01G294200 chr5D 78.733 931 144 30 1048 1927 526410309 526411236 9.310000e-160 573
19 TraesCS2D01G294200 chr5D 81.050 438 69 7 1056 1480 526422933 526422497 1.330000e-88 337
20 TraesCS2D01G294200 chr1A 95.102 245 12 0 1030 1274 36266033 36265789 1.300000e-103 387
21 TraesCS2D01G294200 chr1A 91.837 98 6 2 1308 1403 36265791 36265694 5.200000e-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 TraesCS2D01G294200 chr2D 376354757 376357749 2992 False 5528.000000 5528 100.000000 1 2993 1 chr2D.!!$F1 2992
1 TraesCS2D01G294200 chr2B 447823938 447826864 2926 False 1915.500000 3391 87.897000 1 2993 2 chr2B.!!$F1 2992
2 TraesCS2D01G294200 chr2A 509990722 509996256 5534 False 1338.333333 2102 92.063000 179 2993 3 chr2A.!!$F3 2814
3 TraesCS2D01G294200 chr2A 509579055 509581088 2033 False 911.666667 1432 93.297333 1 1891 3 chr2A.!!$F2 1890
4 TraesCS2D01G294200 chr2A 509727122 509727880 758 False 614.000000 614 82.293000 1990 2728 1 chr2A.!!$F1 738
5 TraesCS2D01G294200 chr3D 496767527 496768427 900 False 647.000000 647 80.132000 1048 1927 1 chr3D.!!$F1 879
6 TraesCS2D01G294200 chr3D 546656024 546656582 558 True 503.000000 503 83.009000 1278 1838 1 chr3D.!!$R1 560
7 TraesCS2D01G294200 chr3A 638015564 638016464 900 False 636.000000 636 79.912000 1048 1927 1 chr3A.!!$F1 879
8 TraesCS2D01G294200 chr5B 661523996 661524920 924 False 608.000000 608 79.418000 1048 1927 1 chr5B.!!$F1 879
9 TraesCS2D01G294200 chr5B 661612550 661613120 570 True 440.000000 440 80.911000 1048 1606 1 chr5B.!!$R1 558
10 TraesCS2D01G294200 chr3B 656065903 656066803 900 False 603.000000 603 79.318000 1048 1927 1 chr3B.!!$F1 879
11 TraesCS2D01G294200 chr5A 653474371 653475295 924 False 592.000000 592 79.072000 1048 1927 1 chr5A.!!$F1 879
12 TraesCS2D01G294200 chr5A 653563419 653564347 928 True 481.000000 481 76.907000 1053 1933 1 chr5A.!!$R1 880
13 TraesCS2D01G294200 chr5D 526410309 526411236 927 False 573.000000 573 78.733000 1048 1927 1 chr5D.!!$F1 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
607 734 1.006337 GCCAATGCTTTGCCGTTCA 60.006 52.632 6.81 0.0 33.53 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2318 2618 0.322456 TTGCAGGCATACAGACCACC 60.322 55.0 0.0 0.0 0.0 4.61 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
76 77 3.159472 TGAAGAACTAGCAGGAACCGTA 58.841 45.455 0.00 0.00 0.00 4.02
114 239 7.721286 AGTGCTGTTGCTAGTTCAATATATC 57.279 36.000 0.00 0.00 40.48 1.63
146 271 2.437200 TTTTTGCCGCTCCATTTGAG 57.563 45.000 0.00 0.00 44.47 3.02
147 272 1.614996 TTTTGCCGCTCCATTTGAGA 58.385 45.000 0.00 0.00 44.42 3.27
148 273 1.614996 TTTGCCGCTCCATTTGAGAA 58.385 45.000 0.00 0.00 44.42 2.87
149 274 1.614996 TTGCCGCTCCATTTGAGAAA 58.385 45.000 0.00 0.00 44.42 2.52
192 317 2.977405 CAAGCTTGCAACAGGTACTC 57.023 50.000 14.65 0.00 34.60 2.59
325 451 2.032117 CGTGTTGTGCTGATGCTTGTAA 60.032 45.455 0.00 0.00 40.48 2.41
333 459 4.676924 GTGCTGATGCTTGTAACTTCAAAC 59.323 41.667 0.00 0.00 40.48 2.93
358 484 8.999431 ACATAATACAAATAAGGTAGATTGCGG 58.001 33.333 0.00 0.00 0.00 5.69
399 525 6.360681 GCCGATGTGTAATTATGCTGAATTTC 59.639 38.462 2.38 0.00 31.51 2.17
513 639 6.939163 AGCATATCAGATAATGTTCCTGTTCC 59.061 38.462 0.00 0.00 0.00 3.62
607 734 1.006337 GCCAATGCTTTGCCGTTCA 60.006 52.632 6.81 0.00 33.53 3.18
614 741 1.727880 TGCTTTGCCGTTCATACGTAC 59.272 47.619 0.00 0.00 46.20 3.67
615 742 1.997606 GCTTTGCCGTTCATACGTACT 59.002 47.619 0.00 0.00 46.20 2.73
616 743 2.414138 GCTTTGCCGTTCATACGTACTT 59.586 45.455 0.00 0.00 46.20 2.24
617 744 3.120442 GCTTTGCCGTTCATACGTACTTT 60.120 43.478 0.00 0.00 46.20 2.66
618 745 4.091800 GCTTTGCCGTTCATACGTACTTTA 59.908 41.667 0.00 0.00 46.20 1.85
665 798 4.960469 TGTAGGTAGGGGAACAGTAGATTG 59.040 45.833 0.00 0.00 0.00 2.67
677 810 6.472808 GGAACAGTAGATTGTGATCGTACTTC 59.527 42.308 0.00 0.00 37.37 3.01
681 814 4.030134 AGATTGTGATCGTACTTCCGTC 57.970 45.455 0.00 0.00 37.37 4.79
1297 1511 4.351938 CCGTCGGCGTTCTCCACA 62.352 66.667 9.28 0.00 36.15 4.17
1366 1592 1.371558 GGTCTCGAAGTTGCACCCT 59.628 57.895 0.00 0.00 0.00 4.34
1952 2229 1.206578 GCCACCATGTCGTTTCGTG 59.793 57.895 0.00 0.00 0.00 4.35
2030 2310 1.183030 TGCGTGGCGGGCTATATAGT 61.183 55.000 11.38 0.00 0.00 2.12
2031 2311 0.813184 GCGTGGCGGGCTATATAGTA 59.187 55.000 11.38 0.00 0.00 1.82
2032 2312 1.468736 GCGTGGCGGGCTATATAGTAC 60.469 57.143 11.38 5.05 0.00 2.73
2033 2313 2.089980 CGTGGCGGGCTATATAGTACT 58.910 52.381 11.38 0.00 0.00 2.73
2034 2314 3.273434 CGTGGCGGGCTATATAGTACTA 58.727 50.000 11.38 4.77 0.00 1.82
2035 2315 3.311871 CGTGGCGGGCTATATAGTACTAG 59.688 52.174 8.85 0.00 0.00 2.57
2036 2316 4.268359 GTGGCGGGCTATATAGTACTAGT 58.732 47.826 8.85 0.00 0.00 2.57
2037 2317 5.431765 GTGGCGGGCTATATAGTACTAGTA 58.568 45.833 8.85 0.00 0.00 1.82
2038 2318 5.526846 GTGGCGGGCTATATAGTACTAGTAG 59.473 48.000 8.85 13.10 0.00 2.57
2124 2404 2.207229 AGTACAGTGGCGTGGCAGA 61.207 57.895 0.00 0.00 0.00 4.26
2254 2541 0.332972 GCCATTCCTCTTTCACCCCT 59.667 55.000 0.00 0.00 0.00 4.79
2255 2542 1.683319 GCCATTCCTCTTTCACCCCTC 60.683 57.143 0.00 0.00 0.00 4.30
2256 2543 1.407437 CCATTCCTCTTTCACCCCTCG 60.407 57.143 0.00 0.00 0.00 4.63
2318 2618 1.493950 GCTCCGAGATCCATTGTGCG 61.494 60.000 0.00 0.00 0.00 5.34
2433 5427 1.375396 GCCGGCCCAACATTTTTCC 60.375 57.895 18.11 0.00 0.00 3.13
2436 5430 1.295101 GGCCCAACATTTTTCCCCG 59.705 57.895 0.00 0.00 0.00 5.73
2439 5433 1.528292 CCCAACATTTTTCCCCGCGA 61.528 55.000 8.23 0.00 0.00 5.87
2536 5538 2.876645 GACGTGCTCTCGCTTCGG 60.877 66.667 0.00 0.00 38.03 4.30
2542 5544 4.069232 CTCTCGCTTCGGGTGGCA 62.069 66.667 0.00 0.00 0.00 4.92
2559 5576 3.567164 GTGGCATACCTTTCATCTCATGG 59.433 47.826 0.00 0.00 36.63 3.66
2564 5581 5.533903 GCATACCTTTCATCTCATGGACATT 59.466 40.000 0.00 0.00 0.00 2.71
2565 5582 6.712095 GCATACCTTTCATCTCATGGACATTA 59.288 38.462 0.00 0.00 0.00 1.90
2566 5583 7.308229 GCATACCTTTCATCTCATGGACATTAC 60.308 40.741 0.00 0.00 0.00 1.89
2590 5607 2.583319 CGTGCGTGCTCGGATGAT 60.583 61.111 15.62 0.00 44.92 2.45
2591 5608 1.299089 CGTGCGTGCTCGGATGATA 60.299 57.895 15.62 0.00 44.92 2.15
2592 5609 0.664466 CGTGCGTGCTCGGATGATAT 60.664 55.000 15.62 0.00 44.92 1.63
2659 5685 2.031870 GGGAAGGCTTTAATTCCGCAT 58.968 47.619 0.00 0.00 44.98 4.73
2932 5982 0.534412 ATGTTCAGTCAGCTCGGAGG 59.466 55.000 7.20 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
149 274 5.770417 CATTGCTCAGCTCTTCTTCTTTTT 58.230 37.500 0.00 0.00 0.00 1.94
192 317 5.288712 GTCGACATATATAACTCGCCCATTG 59.711 44.000 11.55 0.00 0.00 2.82
333 459 7.962918 GCCGCAATCTACCTTATTTGTATTATG 59.037 37.037 0.00 0.00 0.00 1.90
340 466 2.602217 GCGCCGCAATCTACCTTATTTG 60.602 50.000 3.15 0.00 0.00 2.32
358 484 0.095417 CGGCTTTTCTCTAACAGCGC 59.905 55.000 0.00 0.00 32.68 5.92
424 550 7.061441 ACAATATTACGCGTCGATTACATTAGG 59.939 37.037 18.63 3.05 0.00 2.69
474 600 1.438651 TATGCTCTTGGACGTGTTGC 58.561 50.000 0.00 0.00 0.00 4.17
481 607 7.118971 GGAACATTATCTGATATGCTCTTGGAC 59.881 40.741 0.00 0.00 0.00 4.02
513 639 2.094906 TGTCGATGTCCACGAGGTTAAG 60.095 50.000 0.00 0.00 40.37 1.85
649 781 3.133003 CGATCACAATCTACTGTTCCCCT 59.867 47.826 0.00 0.00 0.00 4.79
677 810 3.925630 ATTGGCAGCCACAGGACGG 62.926 63.158 15.89 0.00 30.78 4.79
1625 1862 1.303561 ACGTGTACTACAGGGGCGA 60.304 57.895 12.39 0.00 38.22 5.54
1952 2229 2.125350 CACTTCTCCAGGAGCCGC 60.125 66.667 12.26 0.00 0.00 6.53
2030 2310 3.082548 GCATCCTCGCCATCTACTAGTA 58.917 50.000 1.89 1.89 0.00 1.82
2031 2311 1.889829 GCATCCTCGCCATCTACTAGT 59.110 52.381 0.00 0.00 0.00 2.57
2032 2312 1.135546 CGCATCCTCGCCATCTACTAG 60.136 57.143 0.00 0.00 0.00 2.57
2033 2313 0.881796 CGCATCCTCGCCATCTACTA 59.118 55.000 0.00 0.00 0.00 1.82
2034 2314 1.662608 CGCATCCTCGCCATCTACT 59.337 57.895 0.00 0.00 0.00 2.57
2035 2315 4.251760 CGCATCCTCGCCATCTAC 57.748 61.111 0.00 0.00 0.00 2.59
2232 2519 1.004745 GGGTGAAAGAGGAATGGCAGA 59.995 52.381 0.00 0.00 0.00 4.26
2318 2618 0.322456 TTGCAGGCATACAGACCACC 60.322 55.000 0.00 0.00 0.00 4.61
2358 2680 1.143183 GATTTGCCGGTCTCCGCTA 59.857 57.895 1.90 0.00 46.86 4.26
2402 5395 3.467226 CCGGCTAAAGAGGCCCGA 61.467 66.667 0.00 0.00 46.24 5.14
2410 5404 0.894835 AAATGTTGGGCCGGCTAAAG 59.105 50.000 28.56 0.00 0.00 1.85
2439 5433 1.746615 GGTCACCAGCGTGCATCAT 60.747 57.895 0.00 0.00 40.04 2.45
2542 5544 8.038862 AGTAATGTCCATGAGATGAAAGGTAT 57.961 34.615 0.00 0.00 0.00 2.73
2547 5549 6.978659 GTCGTAGTAATGTCCATGAGATGAAA 59.021 38.462 0.00 0.00 0.00 2.69
2559 5576 1.186030 CGCACGGTCGTAGTAATGTC 58.814 55.000 0.00 0.00 0.00 3.06
2564 5581 2.176546 GCACGCACGGTCGTAGTA 59.823 61.111 3.99 0.00 41.21 1.82
2565 5582 3.606065 GAGCACGCACGGTCGTAGT 62.606 63.158 3.99 0.00 41.21 2.73
2566 5583 2.874780 GAGCACGCACGGTCGTAG 60.875 66.667 3.99 0.00 41.21 3.51
2589 5606 6.325028 TCCGACGGCTACTAGTACCTATATAT 59.675 42.308 9.66 0.00 0.00 0.86
2590 5607 5.656859 TCCGACGGCTACTAGTACCTATATA 59.343 44.000 9.66 0.00 0.00 0.86
2591 5608 4.467795 TCCGACGGCTACTAGTACCTATAT 59.532 45.833 9.66 0.00 0.00 0.86
2592 5609 3.832490 TCCGACGGCTACTAGTACCTATA 59.168 47.826 9.66 0.00 0.00 1.31
2659 5685 0.396435 CAAGTCCCCAGCACACTGTA 59.604 55.000 0.00 0.00 42.81 2.74
2932 5982 3.244976 CGCTCCCATTTTGACATGAAAC 58.755 45.455 0.00 0.00 0.00 2.78
2965 6015 5.527582 GTGGCTTAGACACGGAATCATAAAT 59.472 40.000 1.12 0.00 29.47 1.40


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

AutoCloner maintained by Alex Coulton.