Multiple sequence alignment - TraesCS4D01G247300

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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 TraesCS4D01G247300 chr4D 100.000 2741 0 0 1 2741 416147395 416144655 0.000000e+00 5062.0
1 TraesCS4D01G247300 chr4D 88.080 1443 108 35 684 2089 416429791 416428376 0.000000e+00 1653.0
2 TraesCS4D01G247300 chr4D 89.587 1258 86 21 893 2122 416577811 416579051 0.000000e+00 1555.0
3 TraesCS4D01G247300 chr4D 98.923 836 9 0 1 836 416576967 416577802 0.000000e+00 1495.0
4 TraesCS4D01G247300 chr4D 94.762 630 33 0 1182 1811 416694201 416694830 0.000000e+00 981.0
5 TraesCS4D01G247300 chr4D 95.246 610 9 6 2141 2741 448377068 448377666 0.000000e+00 948.0
6 TraesCS4D01G247300 chr4D 88.102 706 52 14 955 1660 416422823 416422150 0.000000e+00 809.0
7 TraesCS4D01G247300 chr4D 89.037 602 44 11 709 1305 416693635 416694219 0.000000e+00 726.0
8 TraesCS4D01G247300 chr4D 88.704 602 46 11 709 1305 416642308 416642892 0.000000e+00 715.0
9 TraesCS4D01G247300 chr4D 90.456 241 19 2 684 924 416423059 416422823 5.700000e-82 315.0
10 TraesCS4D01G247300 chr4D 93.333 45 2 1 1923 1966 416694968 416694924 6.340000e-07 65.8
11 TraesCS4D01G247300 chr4B 89.759 2119 139 30 1 2064 513449872 513451967 0.000000e+00 2639.0
12 TraesCS4D01G247300 chr4B 91.298 1425 94 18 729 2148 512797963 512796564 0.000000e+00 1917.0
13 TraesCS4D01G247300 chr4B 97.619 42 0 1 546 586 513450376 513450417 1.360000e-08 71.3
14 TraesCS4D01G247300 chr4A 89.372 1496 128 15 642 2122 47456164 47454685 0.000000e+00 1853.0
15 TraesCS4D01G247300 chr4A 88.971 952 76 16 1182 2122 47709507 47710440 0.000000e+00 1149.0
16 TraesCS4D01G247300 chr4A 87.487 991 85 20 1182 2148 47736597 47737572 0.000000e+00 1107.0
17 TraesCS4D01G247300 chr4A 93.540 743 43 2 1184 1922 47650116 47650857 0.000000e+00 1101.0
18 TraesCS4D01G247300 chr4A 94.161 548 30 2 1 547 47708297 47708843 0.000000e+00 833.0
19 TraesCS4D01G247300 chr4A 91.388 569 33 7 38 595 47456723 47456160 0.000000e+00 765.0
20 TraesCS4D01G247300 chr4A 90.927 507 30 8 805 1305 47709029 47709525 0.000000e+00 667.0
21 TraesCS4D01G247300 chr4A 88.065 553 38 11 759 1305 47736064 47736594 4.980000e-177 630.0
22 TraesCS4D01G247300 chr4A 87.743 514 32 15 759 1263 47649746 47650237 3.060000e-159 571.0
23 TraesCS4D01G247300 chr4A 93.539 356 22 1 1 355 609017082 609017437 1.870000e-146 529.0
24 TraesCS4D01G247300 chr4A 93.750 224 11 1 546 766 47708803 47709026 1.570000e-87 333.0
25 TraesCS4D01G247300 chr5D 96.694 605 10 3 2147 2741 30726156 30725552 0.000000e+00 998.0
26 TraesCS4D01G247300 chr5D 91.763 607 24 11 2149 2741 139149658 139149064 0.000000e+00 821.0
27 TraesCS4D01G247300 chr5D 89.655 174 12 3 2572 2741 286395042 286394871 1.650000e-52 217.0
28 TraesCS4D01G247300 chr5D 92.029 138 7 1 2577 2710 481660793 481660656 1.000000e-44 191.0
29 TraesCS4D01G247300 chr2D 96.523 604 10 5 2148 2741 81477868 81478470 0.000000e+00 989.0
30 TraesCS4D01G247300 chr7D 93.137 612 23 8 2142 2741 566235703 566236307 0.000000e+00 880.0
31 TraesCS4D01G247300 chr5B 92.295 610 26 8 2147 2741 580696655 580697258 0.000000e+00 846.0
32 TraesCS4D01G247300 chr5B 85.738 610 26 24 2147 2741 429033384 429033947 3.040000e-164 588.0
33 TraesCS4D01G247300 chr3B 91.790 609 29 9 2148 2741 582468935 582469537 0.000000e+00 828.0
34 TraesCS4D01G247300 chr6A 91.823 587 39 2 1 587 26094885 26094308 0.000000e+00 809.0
35 TraesCS4D01G247300 chr6A 91.065 582 43 2 6 587 26028486 26027914 0.000000e+00 778.0
36 TraesCS4D01G247300 chr7A 90.971 587 43 3 1 587 646297878 646298454 0.000000e+00 782.0
37 TraesCS4D01G247300 chr7A 94.101 356 20 1 1 355 123685365 123685720 8.640000e-150 540.0
38 TraesCS4D01G247300 chr3A 89.200 250 17 3 338 587 244516570 244516809 1.230000e-78 303.0
39 TraesCS4D01G247300 chr3A 90.411 73 6 1 2148 2219 719800247 719800175 8.080000e-16 95.3
40 TraesCS4D01G247300 chr2A 89.831 236 15 2 352 587 491175922 491176148 7.420000e-76 294.0


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 TraesCS4D01G247300 chr4D 416144655 416147395 2740 True 5062.00 5062 100.00000 1 2741 1 chr4D.!!$R1 2740
1 TraesCS4D01G247300 chr4D 416428376 416429791 1415 True 1653.00 1653 88.08000 684 2089 1 chr4D.!!$R2 1405
2 TraesCS4D01G247300 chr4D 416576967 416579051 2084 False 1525.00 1555 94.25500 1 2122 2 chr4D.!!$F3 2121
3 TraesCS4D01G247300 chr4D 448377068 448377666 598 False 948.00 948 95.24600 2141 2741 1 chr4D.!!$F2 600
4 TraesCS4D01G247300 chr4D 416693635 416694830 1195 False 853.50 981 91.89950 709 1811 2 chr4D.!!$F4 1102
5 TraesCS4D01G247300 chr4D 416642308 416642892 584 False 715.00 715 88.70400 709 1305 1 chr4D.!!$F1 596
6 TraesCS4D01G247300 chr4D 416422150 416423059 909 True 562.00 809 89.27900 684 1660 2 chr4D.!!$R4 976
7 TraesCS4D01G247300 chr4B 512796564 512797963 1399 True 1917.00 1917 91.29800 729 2148 1 chr4B.!!$R1 1419
8 TraesCS4D01G247300 chr4B 513449872 513451967 2095 False 1355.15 2639 93.68900 1 2064 2 chr4B.!!$F1 2063
9 TraesCS4D01G247300 chr4A 47454685 47456723 2038 True 1309.00 1853 90.38000 38 2122 2 chr4A.!!$R1 2084
10 TraesCS4D01G247300 chr4A 47736064 47737572 1508 False 868.50 1107 87.77600 759 2148 2 chr4A.!!$F4 1389
11 TraesCS4D01G247300 chr4A 47649746 47650857 1111 False 836.00 1101 90.64150 759 1922 2 chr4A.!!$F2 1163
12 TraesCS4D01G247300 chr4A 47708297 47710440 2143 False 745.50 1149 91.95225 1 2122 4 chr4A.!!$F3 2121
13 TraesCS4D01G247300 chr5D 30725552 30726156 604 True 998.00 998 96.69400 2147 2741 1 chr5D.!!$R1 594
14 TraesCS4D01G247300 chr5D 139149064 139149658 594 True 821.00 821 91.76300 2149 2741 1 chr5D.!!$R2 592
15 TraesCS4D01G247300 chr2D 81477868 81478470 602 False 989.00 989 96.52300 2148 2741 1 chr2D.!!$F1 593
16 TraesCS4D01G247300 chr7D 566235703 566236307 604 False 880.00 880 93.13700 2142 2741 1 chr7D.!!$F1 599
17 TraesCS4D01G247300 chr5B 580696655 580697258 603 False 846.00 846 92.29500 2147 2741 1 chr5B.!!$F2 594
18 TraesCS4D01G247300 chr5B 429033384 429033947 563 False 588.00 588 85.73800 2147 2741 1 chr5B.!!$F1 594
19 TraesCS4D01G247300 chr3B 582468935 582469537 602 False 828.00 828 91.79000 2148 2741 1 chr3B.!!$F1 593
20 TraesCS4D01G247300 chr6A 26094308 26094885 577 True 809.00 809 91.82300 1 587 1 chr6A.!!$R2 586
21 TraesCS4D01G247300 chr6A 26027914 26028486 572 True 778.00 778 91.06500 6 587 1 chr6A.!!$R1 581
22 TraesCS4D01G247300 chr7A 646297878 646298454 576 False 782.00 782 90.97100 1 587 1 chr7A.!!$F2 586

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
842 869 1.154263 CGACTCTGGACGGACGAAC 60.154 63.158 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2410 2850 1.471501 CGTGAATCAAGATCGGCAGGA 60.472 52.381 0.0 0.0 0.0 3.86 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
103 104 6.005583 CAGTGCACAAATTTACTGTCATCT 57.994 37.500 21.04 0.0 36.63 2.90
217 219 1.633432 CATTACAGGTGGAGTTGGGGA 59.367 52.381 0.00 0.0 0.00 4.81
409 418 4.336713 TGTTGTCCGATGTTGAACAAATGA 59.663 37.500 0.62 0.0 33.75 2.57
657 676 9.696917 AAAGCGAAAAGAGAAATAACATCAAAT 57.303 25.926 0.00 0.0 0.00 2.32
841 868 3.260931 CGACTCTGGACGGACGAA 58.739 61.111 0.00 0.0 0.00 3.85
842 869 1.154263 CGACTCTGGACGGACGAAC 60.154 63.158 0.00 0.0 0.00 3.95
848 876 2.049802 GGACGGACGAACTCGCAA 60.050 61.111 0.00 0.0 44.43 4.85
850 878 2.049433 ACGGACGAACTCGCAAGG 60.049 61.111 0.00 0.0 44.43 3.61
1338 1726 1.513586 GTACACTTCGTCGAGCCCG 60.514 63.158 0.00 0.0 37.07 6.13
1437 1825 3.181489 ACGCTGCTACATCACCTTACTAC 60.181 47.826 0.00 0.0 0.00 2.73
1765 2157 7.497595 ACATCTCGTAAATTGTAATAGGAGCA 58.502 34.615 0.00 0.0 35.21 4.26
1766 2158 7.985184 ACATCTCGTAAATTGTAATAGGAGCAA 59.015 33.333 0.00 0.0 35.21 3.91
1794 2188 9.739276 ACAGATTGGATTCTCTTTGTGTAAATA 57.261 29.630 0.00 0.0 0.00 1.40
2092 2523 2.086054 ACTGAAGCTTGCCGTCTAAG 57.914 50.000 2.10 0.0 0.00 2.18
2231 2662 6.166984 TCCGATCTAAAGATGCAGAGATTT 57.833 37.500 0.00 0.0 34.37 2.17
2410 2850 7.164803 GTCTGCAGATTAATAGGGAAAGCTAT 58.835 38.462 21.47 0.0 0.00 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 104 9.607988 TCTGTTAGTCTGAATTTTGTTACTGAA 57.392 29.630 0.00 0.0 0.00 3.02
217 219 4.142359 CGGCTTCTACTGTGACTACTTCAT 60.142 45.833 0.00 0.0 36.32 2.57
657 676 4.789481 GCAGTTCAAACTTCTGCGATCAAA 60.789 41.667 0.00 0.0 43.49 2.69
741 768 3.492353 CACCCCGGAGCCCATGAT 61.492 66.667 0.73 0.0 0.00 2.45
839 866 3.056328 GGCCACCCTTGCGAGTTC 61.056 66.667 0.00 0.0 0.00 3.01
1061 1113 2.941583 GGCCCAGGAAGAAGGGGT 60.942 66.667 0.00 0.0 45.58 4.95
1087 1145 2.126812 GTCGCAGAACTCGTCGCT 60.127 61.111 0.00 0.0 39.69 4.93
1285 1673 1.003718 GGCTTGCCGGAGTGTAGTT 60.004 57.895 5.05 0.0 0.00 2.24
1338 1726 1.365699 TCATAAAAGCGAGCCGAACC 58.634 50.000 0.00 0.0 0.00 3.62
1590 1978 2.657237 GTGCTGGGCGTGTAGTCT 59.343 61.111 0.00 0.0 0.00 3.24
1677 2065 1.609501 AGTGCCGCTCCTCTGGTAA 60.610 57.895 0.00 0.0 0.00 2.85
1765 2157 7.352079 ACACAAAGAGAATCCAATCTGTTTT 57.648 32.000 0.00 0.0 39.94 2.43
1766 2158 6.966534 ACACAAAGAGAATCCAATCTGTTT 57.033 33.333 0.00 0.0 41.89 2.83
1794 2188 9.722056 GAATAAACAAAGTCATAGCAATTCGAT 57.278 29.630 0.00 0.0 0.00 3.59
1928 2347 5.185828 TCGATGAGAAACAAAGAGATCCAGA 59.814 40.000 0.00 0.0 0.00 3.86
2092 2523 6.208644 TGCTCTGTTTTCTTCAGCAAAATAC 58.791 36.000 0.00 0.0 33.48 1.89
2278 2710 4.806247 CAGGCCGACAAAACAAAACAATTA 59.194 37.500 0.00 0.0 0.00 1.40
2410 2850 1.471501 CGTGAATCAAGATCGGCAGGA 60.472 52.381 0.00 0.0 0.00 3.86


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

AutoCloner maintained by Alex Coulton.