Multiple sequence alignment - TraesCS2D01G140400

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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 TraesCS2D01G140400 chr2D 100.000 2405 0 0 1 2405 82835880 82833476 0.000000e+00 4442
1 TraesCS2D01G140400 chr2D 92.457 875 47 9 1 858 82873514 82872642 0.000000e+00 1232
2 TraesCS2D01G140400 chr2D 91.862 811 56 2 1 801 82655111 82654301 0.000000e+00 1123
3 TraesCS2D01G140400 chr2D 93.733 750 34 6 856 1604 82872607 82871870 0.000000e+00 1112
4 TraesCS2D01G140400 chr2D 87.963 756 67 12 858 1612 82654190 82653458 0.000000e+00 870
5 TraesCS2D01G140400 chr2D 84.906 636 80 10 855 1477 82891918 82891286 1.570000e-176 628
6 TraesCS2D01G140400 chr2D 81.314 776 130 11 22 787 82334688 82333918 1.220000e-172 616
7 TraesCS2D01G140400 chr2D 80.940 766 128 12 55 808 82892785 82892026 7.410000e-165 590
8 TraesCS2D01G140400 chr2D 86.200 500 69 0 971 1470 82645654 82645155 2.100000e-150 542
9 TraesCS2D01G140400 chr1D 98.739 793 10 0 1613 2405 439167288 439166496 0.000000e+00 1410
10 TraesCS2D01G140400 chr7D 98.361 793 13 0 1613 2405 199047681 199048473 0.000000e+00 1393
11 TraesCS2D01G140400 chr7D 97.610 795 13 1 1611 2405 599724184 599723396 0.000000e+00 1358
12 TraesCS2D01G140400 chr7D 97.674 86 2 0 2320 2405 519829564 519829649 5.360000e-32 148
13 TraesCS2D01G140400 chr6D 98.235 793 14 0 1613 2405 387403263 387402471 0.000000e+00 1387
14 TraesCS2D01G140400 chr6D 86.937 444 52 6 1611 2052 83157746 83157307 5.970000e-136 494
15 TraesCS2D01G140400 chr6D 100.000 78 0 0 2328 2405 404187789 404187712 6.930000e-31 145
16 TraesCS2D01G140400 chr3D 97.742 797 18 0 1609 2405 582737311 582738107 0.000000e+00 1373
17 TraesCS2D01G140400 chr2A 90.594 893 59 8 1 869 83586229 83585338 0.000000e+00 1160
18 TraesCS2D01G140400 chr2A 90.132 760 61 9 855 1612 83585317 83584570 0.000000e+00 976
19 TraesCS2D01G140400 chr2A 83.835 798 116 7 1 787 83421214 83420419 0.000000e+00 747
20 TraesCS2D01G140400 chr2A 82.434 797 129 10 1 787 83641018 83640223 0.000000e+00 686
21 TraesCS2D01G140400 chr2A 81.830 798 132 8 1 787 83428838 83428043 0.000000e+00 658
22 TraesCS2D01G140400 chr2A 81.032 775 131 13 22 785 83016363 83015594 9.510000e-169 603
23 TraesCS2D01G140400 chr2A 86.355 535 71 2 937 1470 83200628 83200095 1.240000e-162 582
24 TraesCS2D01G140400 chr2A 86.233 523 72 0 948 1470 83420206 83419684 3.470000e-158 568
25 TraesCS2D01G140400 chr2A 85.311 531 70 5 938 1460 83640026 83639496 2.100000e-150 542
26 TraesCS2D01G140400 chr2A 84.938 405 49 8 1 395 83468547 83468145 1.340000e-107 399
27 TraesCS2D01G140400 chr5D 97.218 647 14 3 1616 2261 497815683 497816326 0.000000e+00 1092
28 TraesCS2D01G140400 chr7B 91.069 795 62 7 1613 2405 592544529 592543742 0.000000e+00 1066
29 TraesCS2D01G140400 chr7B 91.337 531 28 5 1876 2405 684439383 684439896 0.000000e+00 710
30 TraesCS2D01G140400 chr5A 91.265 664 39 6 1744 2405 645288079 645287433 0.000000e+00 887
31 TraesCS2D01G140400 chr2B 85.139 794 108 3 1 787 134549420 134548630 0.000000e+00 804
32 TraesCS2D01G140400 chr2B 89.463 484 51 0 941 1424 134600941 134600458 1.580000e-171 612
33 TraesCS2D01G140400 chr2B 84.728 478 61 8 21 487 134568789 134568313 3.620000e-128 468


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 TraesCS2D01G140400 chr2D 82833476 82835880 2404 True 4442.0 4442 100.0000 1 2405 1 chr2D.!!$R3 2404
1 TraesCS2D01G140400 chr2D 82871870 82873514 1644 True 1172.0 1232 93.0950 1 1604 2 chr2D.!!$R5 1603
2 TraesCS2D01G140400 chr2D 82653458 82655111 1653 True 996.5 1123 89.9125 1 1612 2 chr2D.!!$R4 1611
3 TraesCS2D01G140400 chr2D 82333918 82334688 770 True 616.0 616 81.3140 22 787 1 chr2D.!!$R1 765
4 TraesCS2D01G140400 chr2D 82891286 82892785 1499 True 609.0 628 82.9230 55 1477 2 chr2D.!!$R6 1422
5 TraesCS2D01G140400 chr1D 439166496 439167288 792 True 1410.0 1410 98.7390 1613 2405 1 chr1D.!!$R1 792
6 TraesCS2D01G140400 chr7D 199047681 199048473 792 False 1393.0 1393 98.3610 1613 2405 1 chr7D.!!$F1 792
7 TraesCS2D01G140400 chr7D 599723396 599724184 788 True 1358.0 1358 97.6100 1611 2405 1 chr7D.!!$R1 794
8 TraesCS2D01G140400 chr6D 387402471 387403263 792 True 1387.0 1387 98.2350 1613 2405 1 chr6D.!!$R2 792
9 TraesCS2D01G140400 chr3D 582737311 582738107 796 False 1373.0 1373 97.7420 1609 2405 1 chr3D.!!$F1 796
10 TraesCS2D01G140400 chr2A 83584570 83586229 1659 True 1068.0 1160 90.3630 1 1612 2 chr2A.!!$R6 1611
11 TraesCS2D01G140400 chr2A 83428043 83428838 795 True 658.0 658 81.8300 1 787 1 chr2A.!!$R3 786
12 TraesCS2D01G140400 chr2A 83419684 83421214 1530 True 657.5 747 85.0340 1 1470 2 chr2A.!!$R5 1469
13 TraesCS2D01G140400 chr2A 83639496 83641018 1522 True 614.0 686 83.8725 1 1460 2 chr2A.!!$R7 1459
14 TraesCS2D01G140400 chr2A 83015594 83016363 769 True 603.0 603 81.0320 22 785 1 chr2A.!!$R1 763
15 TraesCS2D01G140400 chr2A 83200095 83200628 533 True 582.0 582 86.3550 937 1470 1 chr2A.!!$R2 533
16 TraesCS2D01G140400 chr5D 497815683 497816326 643 False 1092.0 1092 97.2180 1616 2261 1 chr5D.!!$F1 645
17 TraesCS2D01G140400 chr7B 592543742 592544529 787 True 1066.0 1066 91.0690 1613 2405 1 chr7B.!!$R1 792
18 TraesCS2D01G140400 chr7B 684439383 684439896 513 False 710.0 710 91.3370 1876 2405 1 chr7B.!!$F1 529
19 TraesCS2D01G140400 chr5A 645287433 645288079 646 True 887.0 887 91.2650 1744 2405 1 chr5A.!!$R1 661
20 TraesCS2D01G140400 chr2B 134548630 134549420 790 True 804.0 804 85.1390 1 787 1 chr2B.!!$R1 786

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
694 708 0.100146 GTGCATAGCTTCAAGCCTGC 59.9 55.0 22.0 22.0 45.28 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1529 1645 1.846439 TCATGGGATCTCCTTGGGTTC 59.154 52.381 12.91 0.0 40.13 3.62 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
24 25 7.404671 GGATGAACAAAATACCCACATACTT 57.595 36.000 0.00 0.00 0.00 2.24
73 75 1.272760 GGTCTGTTCCAGAGGAGGAGA 60.273 57.143 0.00 0.00 41.46 3.71
143 145 2.426842 AGGCTTGCTACCTTTGATCC 57.573 50.000 0.00 0.00 31.87 3.36
181 183 2.222727 AGCAGAGCAACAGGCCTCT 61.223 57.895 0.00 0.00 46.50 3.69
183 185 1.584380 GCAGAGCAACAGGCCTCTTG 61.584 60.000 15.87 15.87 46.50 3.02
214 216 5.119898 GTCATAGAGTTCACAAGCAACAGAG 59.880 44.000 0.00 0.00 0.00 3.35
215 217 2.843701 AGAGTTCACAAGCAACAGAGG 58.156 47.619 0.00 0.00 0.00 3.69
224 226 3.079578 CAAGCAACAGAGGTGACATGAT 58.920 45.455 0.00 0.00 0.00 2.45
279 290 3.672867 CGTTGAAGCTTCTGAGAAGACTC 59.327 47.826 25.34 18.67 42.88 3.36
320 331 3.120321 TGGTGTAACTTTGCGTCAGAT 57.880 42.857 0.00 0.00 36.74 2.90
527 541 2.037136 GCGCATCCTCAAGTGCAGT 61.037 57.895 0.30 0.00 41.32 4.40
677 691 1.134401 CCATAGTGGCAGGTACAGGTG 60.134 57.143 0.00 0.00 0.00 4.00
694 708 0.100146 GTGCATAGCTTCAAGCCTGC 59.900 55.000 22.00 22.00 45.28 4.85
722 736 4.994907 ATATGTGTGTGCATGCTCAATT 57.005 36.364 22.97 11.03 0.00 2.32
787 801 1.136147 GAGGTGAGCGCTGCAAATG 59.864 57.895 18.48 0.00 0.00 2.32
798 813 3.044986 CGCTGCAAATGTGGTTATATGC 58.955 45.455 0.00 0.00 0.00 3.14
824 869 9.142515 CGCGGATATTGTACCTTAATATTTACA 57.857 33.333 0.00 0.00 32.42 2.41
906 989 9.826574 ATACACCACACGACTAAATAAATACAT 57.173 29.630 0.00 0.00 0.00 2.29
907 990 7.970384 ACACCACACGACTAAATAAATACATG 58.030 34.615 0.00 0.00 0.00 3.21
908 991 7.065324 ACACCACACGACTAAATAAATACATGG 59.935 37.037 0.00 0.00 0.00 3.66
909 992 6.037830 ACCACACGACTAAATAAATACATGGC 59.962 38.462 0.00 0.00 0.00 4.40
910 993 6.037720 CCACACGACTAAATAAATACATGGCA 59.962 38.462 0.00 0.00 0.00 4.92
911 994 7.414651 CCACACGACTAAATAAATACATGGCAA 60.415 37.037 0.00 0.00 0.00 4.52
912 995 7.428183 CACACGACTAAATAAATACATGGCAAC 59.572 37.037 0.00 0.00 0.00 4.17
913 996 6.627276 CACGACTAAATAAATACATGGCAACG 59.373 38.462 0.00 0.00 42.51 4.10
914 997 6.314400 ACGACTAAATAAATACATGGCAACGT 59.686 34.615 0.00 0.00 42.51 3.99
946 1048 8.827177 TTCTACTTAACCATGTTACTGAAGTG 57.173 34.615 0.00 0.00 0.00 3.16
955 1057 7.394016 ACCATGTTACTGAAGTGTAATCATGA 58.606 34.615 19.15 0.00 39.99 3.07
1016 1121 4.356190 AGGAATAATGGATGCAGAAGGGAT 59.644 41.667 0.00 0.00 0.00 3.85
1273 1378 1.632409 ACTGGATGATGGAAGCACTGT 59.368 47.619 0.00 0.00 30.93 3.55
1298 1403 2.038557 AGGTGGAGCGTACAACTTCAAT 59.961 45.455 0.00 0.00 30.07 2.57
1299 1404 2.812011 GGTGGAGCGTACAACTTCAATT 59.188 45.455 0.00 0.00 0.00 2.32
1407 1512 3.462199 GATGGGCCGTGGGTAGCTC 62.462 68.421 1.02 0.00 0.00 4.09
1425 1539 3.244764 CTGAGGCATCAGCAGTGTT 57.755 52.632 16.38 0.00 46.19 3.32
1529 1645 8.633561 TCATCATAGTAGTGAGTTACTCATTGG 58.366 37.037 18.52 4.89 42.73 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 7.882791 TGTTTTGTAATCTTTCTCCAGCATCTA 59.117 33.333 0.00 0.00 0.00 1.98
73 75 1.482593 GAGATCCTGGTCGGTTGATGT 59.517 52.381 0.00 0.00 0.00 3.06
143 145 7.487484 TCTGCTGATTTCTATACAGTTCTCAG 58.513 38.462 0.00 0.00 34.60 3.35
181 183 5.924356 TGTGAACTCTATGACCTTTGACAA 58.076 37.500 0.00 0.00 0.00 3.18
183 185 5.106908 GCTTGTGAACTCTATGACCTTTGAC 60.107 44.000 0.00 0.00 0.00 3.18
214 216 7.438160 TGTCTCGTCAATATTTATCATGTCACC 59.562 37.037 0.00 0.00 0.00 4.02
215 217 8.269424 GTGTCTCGTCAATATTTATCATGTCAC 58.731 37.037 0.00 0.00 0.00 3.67
224 226 5.961272 TCAGCAGTGTCTCGTCAATATTTA 58.039 37.500 0.00 0.00 0.00 1.40
267 278 3.413327 AGTACTTGCGAGTCTTCTCAGA 58.587 45.455 10.71 0.00 40.44 3.27
279 290 4.621034 CCAAATTTGCCTTTAGTACTTGCG 59.379 41.667 12.92 0.00 0.00 4.85
320 331 6.881065 CCAAAGGAAGAGATGTTCTGTAATCA 59.119 38.462 0.00 0.00 35.91 2.57
527 541 7.272731 CGTTCATTCGTAGTAACTGATCTGAAA 59.727 37.037 6.60 0.00 0.00 2.69
677 691 0.381089 CAGCAGGCTTGAAGCTATGC 59.619 55.000 28.11 28.11 46.61 3.14
694 708 3.061563 GCATGCACACACATATTTTGCAG 59.938 43.478 14.21 0.00 45.80 4.41
722 736 2.048222 CCGAGTCGCCAAGCTCAA 60.048 61.111 7.12 0.00 0.00 3.02
765 779 2.104572 TTGCAGCGCTCACCTCTCTT 62.105 55.000 7.13 0.00 0.00 2.85
787 801 3.682858 ACAATATCCGCGCATATAACCAC 59.317 43.478 8.75 0.00 0.00 4.16
798 813 9.142515 TGTAAATATTAAGGTACAATATCCGCG 57.857 33.333 0.00 0.00 30.13 6.46
824 869 9.195411 CTACAGAAAATGTTGCAATAACATGTT 57.805 29.630 16.68 16.68 39.96 2.71
904 987 2.019249 AGAATCCATGACGTTGCCATG 58.981 47.619 8.38 8.38 40.66 3.66
905 988 2.425143 AGAATCCATGACGTTGCCAT 57.575 45.000 0.00 0.00 0.00 4.40
906 989 2.236146 AGTAGAATCCATGACGTTGCCA 59.764 45.455 0.00 0.00 0.00 4.92
907 990 2.906354 AGTAGAATCCATGACGTTGCC 58.094 47.619 0.00 0.00 0.00 4.52
908 991 5.220605 GGTTAAGTAGAATCCATGACGTTGC 60.221 44.000 0.00 0.00 0.00 4.17
909 992 5.872617 TGGTTAAGTAGAATCCATGACGTTG 59.127 40.000 0.00 0.00 0.00 4.10
910 993 6.045072 TGGTTAAGTAGAATCCATGACGTT 57.955 37.500 0.00 0.00 0.00 3.99
911 994 5.670792 TGGTTAAGTAGAATCCATGACGT 57.329 39.130 0.00 0.00 0.00 4.34
946 1048 6.758886 AGCTAAGCTGTGTAAGTCATGATTAC 59.241 38.462 15.45 15.45 37.57 1.89
955 1057 5.875359 GTGGAAATAGCTAAGCTGTGTAAGT 59.125 40.000 0.00 0.00 40.10 2.24
1016 1121 4.079253 GCCAACAAGAACCTCCAATTCTA 58.921 43.478 0.00 0.00 35.31 2.10
1273 1378 3.756933 AGTTGTACGCTCCACCTTTAA 57.243 42.857 0.00 0.00 0.00 1.52
1298 1403 6.293407 CGAGAAGAACCTGTAATTTTCAGCAA 60.293 38.462 0.00 0.00 0.00 3.91
1299 1404 5.179368 CGAGAAGAACCTGTAATTTTCAGCA 59.821 40.000 0.00 0.00 0.00 4.41
1407 1512 5.499315 AGGTAACACTGCTGATGCCTCAG 62.499 52.174 14.08 14.08 45.99 3.35
1425 1539 6.747414 ACCATCTAAATACATGCTCAGGTA 57.253 37.500 0.00 0.00 31.82 3.08
1529 1645 1.846439 TCATGGGATCTCCTTGGGTTC 59.154 52.381 12.91 0.00 40.13 3.62
1569 1685 5.004448 TGACTTGTCAACACAAACCAACTA 58.996 37.500 0.44 0.00 42.13 2.24
1728 1845 3.760151 GGTTTAATTTCTTAGCCACGGGT 59.240 43.478 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.