Multiple sequence alignment - TraesCS1A01G188300

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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 TraesCS1A01G188300 chr1A 100.000 2324 0 0 1 2324 340070989 340073312 0.000000e+00 4292
1 TraesCS1A01G188300 chr1A 90.223 1074 72 20 580 1640 7956539 7957592 0.000000e+00 1371
2 TraesCS1A01G188300 chr3D 94.211 1710 80 8 1 1700 37627132 37628832 0.000000e+00 2591
3 TraesCS1A01G188300 chr3D 90.599 851 38 8 1 842 416551887 416552704 0.000000e+00 1090
4 TraesCS1A01G188300 chr3D 96.875 576 16 2 1 575 229427721 229427147 0.000000e+00 963
5 TraesCS1A01G188300 chr3D 93.939 627 33 5 1699 2321 37628711 37629336 0.000000e+00 942
6 TraesCS1A01G188300 chr3D 98.936 94 1 0 1607 1700 416553499 416553592 3.970000e-38 169
7 TraesCS1A01G188300 chr4B 93.277 1651 87 11 1 1640 343834206 343835843 0.000000e+00 2412
8 TraesCS1A01G188300 chr4B 89.078 1758 114 32 1 1697 368728971 368730711 0.000000e+00 2111
9 TraesCS1A01G188300 chr4B 92.857 1428 68 10 1 1423 505003571 505002173 0.000000e+00 2041
10 TraesCS1A01G188300 chr4B 92.687 629 40 5 1699 2324 6841915 6842540 0.000000e+00 902
11 TraesCS1A01G188300 chr4B 82.759 348 28 17 1382 1700 288453477 288453133 4.890000e-72 281
12 TraesCS1A01G188300 chr4B 80.795 302 32 15 1351 1640 667509512 667509799 1.810000e-51 213
13 TraesCS1A01G188300 chr5B 90.490 1735 111 23 1 1698 291681315 291679598 0.000000e+00 2241
14 TraesCS1A01G188300 chr5B 90.234 1669 86 35 1 1640 345115921 345117541 0.000000e+00 2108
15 TraesCS1A01G188300 chr5B 92.051 629 45 5 1699 2324 190333805 190334431 0.000000e+00 880
16 TraesCS1A01G188300 chr2B 90.299 1742 107 21 1 1700 32828782 32830503 0.000000e+00 2224
17 TraesCS1A01G188300 chr2B 84.808 757 67 31 957 1700 103757531 103756810 0.000000e+00 717
18 TraesCS1A01G188300 chr6B 90.473 1669 99 35 1 1640 70651219 70652856 0.000000e+00 2146
19 TraesCS1A01G188300 chr6B 90.490 1672 87 22 1 1640 238422248 238420617 0.000000e+00 2141
20 TraesCS1A01G188300 chr6B 82.133 347 32 14 1382 1700 244346930 244346586 1.060000e-68 270
21 TraesCS1A01G188300 chr6B 81.739 345 33 14 1382 1698 238420856 238420514 6.370000e-66 261
22 TraesCS1A01G188300 chr6B 96.000 125 5 0 1576 1700 425152219 425152343 1.090000e-48 204
23 TraesCS1A01G188300 chr7A 90.591 1456 71 34 1 1423 56073904 56075326 0.000000e+00 1869
24 TraesCS1A01G188300 chr4A 88.048 1163 85 37 580 1700 525153610 525152460 0.000000e+00 1328
25 TraesCS1A01G188300 chr4A 93.500 600 36 3 1727 2324 549635758 549636356 0.000000e+00 889
26 TraesCS1A01G188300 chr4A 96.008 526 19 2 1 524 404403586 404403061 0.000000e+00 854
27 TraesCS1A01G188300 chr7B 95.296 829 39 0 571 1399 551235474 551236302 0.000000e+00 1315
28 TraesCS1A01G188300 chr7B 93.656 599 34 3 1727 2324 713310793 713310198 0.000000e+00 893
29 TraesCS1A01G188300 chr7B 81.844 347 33 13 1382 1700 713311044 713310700 4.920000e-67 265
30 TraesCS1A01G188300 chr7B 86.100 259 17 8 1382 1640 713319863 713319624 6.370000e-66 261
31 TraesCS1A01G188300 chr6D 93.238 843 35 7 1 842 446364409 446363588 0.000000e+00 1221
32 TraesCS1A01G188300 chr7D 93.001 843 37 8 1 842 79226595 79227416 0.000000e+00 1210
33 TraesCS1A01G188300 chr5D 92.645 843 31 13 1 842 384512113 384511301 0.000000e+00 1184
34 TraesCS1A01G188300 chr2D 91.061 839 41 12 1 817 648995291 648996117 0.000000e+00 1103
35 TraesCS1A01G188300 chr3A 93.620 627 36 4 1699 2324 676004312 676004935 0.000000e+00 933
36 TraesCS1A01G188300 chr3A 94.010 601 29 6 1727 2324 733878187 733877591 0.000000e+00 904
37 TraesCS1A01G188300 chr3A 92.357 628 42 6 1699 2324 579909783 579909160 0.000000e+00 889
38 TraesCS1A01G188300 chr1B 92.147 624 43 5 1706 2324 6183091 6183713 0.000000e+00 876
39 TraesCS1A01G188300 chr3B 97.076 513 15 0 1 513 142227131 142227643 0.000000e+00 865
40 TraesCS1A01G188300 chr2A 94.065 556 24 2 596 1151 538628894 538628348 0.000000e+00 835
41 TraesCS1A01G188300 chrUn 94.118 136 8 0 1505 1640 478485245 478485380 8.420000e-50 207
42 TraesCS1A01G188300 chrUn 79.377 257 30 14 1465 1700 478485231 478485485 2.390000e-35 159


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 TraesCS1A01G188300 chr1A 340070989 340073312 2323 False 4292.0 4292 100.0000 1 2324 1 chr1A.!!$F2 2323
1 TraesCS1A01G188300 chr1A 7956539 7957592 1053 False 1371.0 1371 90.2230 580 1640 1 chr1A.!!$F1 1060
2 TraesCS1A01G188300 chr3D 37627132 37629336 2204 False 1766.5 2591 94.0750 1 2321 2 chr3D.!!$F1 2320
3 TraesCS1A01G188300 chr3D 229427147 229427721 574 True 963.0 963 96.8750 1 575 1 chr3D.!!$R1 574
4 TraesCS1A01G188300 chr3D 416551887 416553592 1705 False 629.5 1090 94.7675 1 1700 2 chr3D.!!$F2 1699
5 TraesCS1A01G188300 chr4B 343834206 343835843 1637 False 2412.0 2412 93.2770 1 1640 1 chr4B.!!$F2 1639
6 TraesCS1A01G188300 chr4B 368728971 368730711 1740 False 2111.0 2111 89.0780 1 1697 1 chr4B.!!$F3 1696
7 TraesCS1A01G188300 chr4B 505002173 505003571 1398 True 2041.0 2041 92.8570 1 1423 1 chr4B.!!$R2 1422
8 TraesCS1A01G188300 chr4B 6841915 6842540 625 False 902.0 902 92.6870 1699 2324 1 chr4B.!!$F1 625
9 TraesCS1A01G188300 chr5B 291679598 291681315 1717 True 2241.0 2241 90.4900 1 1698 1 chr5B.!!$R1 1697
10 TraesCS1A01G188300 chr5B 345115921 345117541 1620 False 2108.0 2108 90.2340 1 1640 1 chr5B.!!$F2 1639
11 TraesCS1A01G188300 chr5B 190333805 190334431 626 False 880.0 880 92.0510 1699 2324 1 chr5B.!!$F1 625
12 TraesCS1A01G188300 chr2B 32828782 32830503 1721 False 2224.0 2224 90.2990 1 1700 1 chr2B.!!$F1 1699
13 TraesCS1A01G188300 chr2B 103756810 103757531 721 True 717.0 717 84.8080 957 1700 1 chr2B.!!$R1 743
14 TraesCS1A01G188300 chr6B 70651219 70652856 1637 False 2146.0 2146 90.4730 1 1640 1 chr6B.!!$F1 1639
15 TraesCS1A01G188300 chr6B 238420514 238422248 1734 True 1201.0 2141 86.1145 1 1698 2 chr6B.!!$R2 1697
16 TraesCS1A01G188300 chr7A 56073904 56075326 1422 False 1869.0 1869 90.5910 1 1423 1 chr7A.!!$F1 1422
17 TraesCS1A01G188300 chr4A 525152460 525153610 1150 True 1328.0 1328 88.0480 580 1700 1 chr4A.!!$R2 1120
18 TraesCS1A01G188300 chr4A 549635758 549636356 598 False 889.0 889 93.5000 1727 2324 1 chr4A.!!$F1 597
19 TraesCS1A01G188300 chr4A 404403061 404403586 525 True 854.0 854 96.0080 1 524 1 chr4A.!!$R1 523
20 TraesCS1A01G188300 chr7B 551235474 551236302 828 False 1315.0 1315 95.2960 571 1399 1 chr7B.!!$F1 828
21 TraesCS1A01G188300 chr7B 713310198 713311044 846 True 579.0 893 87.7500 1382 2324 2 chr7B.!!$R2 942
22 TraesCS1A01G188300 chr6D 446363588 446364409 821 True 1221.0 1221 93.2380 1 842 1 chr6D.!!$R1 841
23 TraesCS1A01G188300 chr7D 79226595 79227416 821 False 1210.0 1210 93.0010 1 842 1 chr7D.!!$F1 841
24 TraesCS1A01G188300 chr5D 384511301 384512113 812 True 1184.0 1184 92.6450 1 842 1 chr5D.!!$R1 841
25 TraesCS1A01G188300 chr2D 648995291 648996117 826 False 1103.0 1103 91.0610 1 817 1 chr2D.!!$F1 816
26 TraesCS1A01G188300 chr3A 676004312 676004935 623 False 933.0 933 93.6200 1699 2324 1 chr3A.!!$F1 625
27 TraesCS1A01G188300 chr3A 733877591 733878187 596 True 904.0 904 94.0100 1727 2324 1 chr3A.!!$R2 597
28 TraesCS1A01G188300 chr3A 579909160 579909783 623 True 889.0 889 92.3570 1699 2324 1 chr3A.!!$R1 625
29 TraesCS1A01G188300 chr1B 6183091 6183713 622 False 876.0 876 92.1470 1706 2324 1 chr1B.!!$F1 618
30 TraesCS1A01G188300 chr3B 142227131 142227643 512 False 865.0 865 97.0760 1 513 1 chr3B.!!$F1 512
31 TraesCS1A01G188300 chr2A 538628348 538628894 546 True 835.0 835 94.0650 596 1151 1 chr2A.!!$R1 555

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
552 578 2.158475 ACCTCAGCCCTGTTTGATTCAA 60.158 45.455 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2169 2547 0.250234 CCACACCACGTCAGATCCAT 59.75 55.0 0.0 0.0 0.0 3.41 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
164 165 4.677673 TCTGCACATGATATGCTAGTGT 57.322 40.909 0.00 0.00 43.77 3.55
223 225 4.214119 CCTGTGTGTCGAACAAGATGAATT 59.786 41.667 0.00 0.00 41.57 2.17
253 255 5.455056 AGTCGTGTACAATCAGAGAACTT 57.545 39.130 0.00 0.00 0.00 2.66
346 348 6.968131 TCCTCGTTGAATAACATTTCTGAG 57.032 37.500 0.00 0.00 36.58 3.35
517 543 3.567164 AGTCACTCCATGCTTTGTTCAAG 59.433 43.478 0.00 0.00 35.29 3.02
552 578 2.158475 ACCTCAGCCCTGTTTGATTCAA 60.158 45.455 0.00 0.00 0.00 2.69
561 587 3.243975 CCTGTTTGATTCAAAGCCAGCTT 60.244 43.478 17.86 0.00 33.82 3.74
562 588 4.374399 CTGTTTGATTCAAAGCCAGCTTT 58.626 39.130 12.02 11.78 45.98 3.51
592 648 6.094719 TGTTGATGCTATTTGATGCTTTGAC 58.905 36.000 0.00 0.00 0.00 3.18
593 649 6.071784 TGTTGATGCTATTTGATGCTTTGACT 60.072 34.615 0.00 0.00 0.00 3.41
659 739 4.619973 TGTTCCATGCTTTGATGTTGTTC 58.380 39.130 0.00 0.00 0.00 3.18
761 854 3.340814 AGTTTGATGATCGGCTCACTT 57.659 42.857 0.00 0.00 36.48 3.16
786 879 6.505344 TGGGAAGCCATCTTATATAGAACCAT 59.495 38.462 0.00 0.00 36.22 3.55
1056 1213 3.002759 GTGAAGAGCCAAAGTCTGTTGTC 59.997 47.826 0.00 0.00 0.00 3.18
1107 1264 2.961062 AGTCAAGCAAAGCACATTCCTT 59.039 40.909 0.00 0.00 0.00 3.36
1128 1285 0.329596 GGAATGTTGGGCTCCAGTCT 59.670 55.000 0.00 0.00 33.81 3.24
1178 1335 1.202794 TGAAGTGGCTGCTCATGTTCA 60.203 47.619 0.00 7.08 0.00 3.18
1374 1532 3.263425 TCCTTGGAGCTAAGGTAGTTTGG 59.737 47.826 13.80 0.00 45.94 3.28
1377 1545 2.976882 TGGAGCTAAGGTAGTTTGGTGT 59.023 45.455 0.00 0.00 0.00 4.16
1489 1765 2.092429 TGTCTTTGGAGCTGTGAACCTT 60.092 45.455 0.00 0.00 0.00 3.50
1491 1767 2.172505 TCTTTGGAGCTGTGAACCTTGA 59.827 45.455 0.00 0.00 0.00 3.02
1507 1783 4.327680 ACCTTGAAGTAGTTTGATGGCTC 58.672 43.478 0.00 0.00 0.00 4.70
1578 1886 5.641209 AGCTGTGAAGTTATGTGATCTTGTC 59.359 40.000 0.00 0.00 0.00 3.18
1593 1901 6.857964 GTGATCTTGTCAACCTGTGTTTATTG 59.142 38.462 0.00 0.00 38.90 1.90
1754 2074 3.372422 TTGTGCACCTGGGCCTTGT 62.372 57.895 15.69 0.00 0.00 3.16
1763 2128 3.829601 CACCTGGGCCTTGTTGTTTATAA 59.170 43.478 4.53 0.00 0.00 0.98
1932 2301 8.932791 CAAATTCGAACTAGACTAAAAAGGCTA 58.067 33.333 0.00 0.00 0.00 3.93
1991 2363 2.899256 CAGAAAAAGGCTCCATTCCCAA 59.101 45.455 0.00 0.00 0.00 4.12
2032 2404 2.792947 GGCCAAGCCCATGCAGATG 61.793 63.158 0.00 0.00 44.06 2.90
2112 2490 1.223487 GCTGAAATGGACCGGGCTA 59.777 57.895 7.57 0.00 0.00 3.93
2139 2517 8.736751 TTCTATTTTACGACCTTTTCATTTGC 57.263 30.769 0.00 0.00 0.00 3.68
2156 2534 1.016627 TGCTCGTAATTCTGCCATGC 58.983 50.000 0.00 0.00 0.00 4.06
2169 2547 3.057548 CATGCCAGCTTGCCACGA 61.058 61.111 7.41 0.00 0.00 4.35
2313 2692 0.755327 ACGGCCAGCTTTTGACCTTT 60.755 50.000 2.24 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 0.606604 TCTGGCACCGGAGACTTAAC 59.393 55.000 9.46 0.00 0.00 2.01
223 225 6.277605 TCTGATTGTACACGACTTTTTCTCA 58.722 36.000 0.00 0.00 0.00 3.27
253 255 1.210722 TGTTGTGTAGTGCCTGGAACA 59.789 47.619 7.75 0.00 0.00 3.18
517 543 3.189495 GGCTGAGGTTTCTAGACAAAAGC 59.811 47.826 0.00 0.00 35.01 3.51
561 587 5.900865 TCAAATAGCATCAACAGCATCAA 57.099 34.783 0.00 0.00 0.00 2.57
562 588 5.735070 GCATCAAATAGCATCAACAGCATCA 60.735 40.000 0.00 0.00 0.00 3.07
563 589 4.680110 GCATCAAATAGCATCAACAGCATC 59.320 41.667 0.00 0.00 0.00 3.91
564 590 4.341235 AGCATCAAATAGCATCAACAGCAT 59.659 37.500 0.00 0.00 0.00 3.79
565 591 3.697542 AGCATCAAATAGCATCAACAGCA 59.302 39.130 0.00 0.00 0.00 4.41
566 592 4.303086 AGCATCAAATAGCATCAACAGC 57.697 40.909 0.00 0.00 0.00 4.40
567 593 6.252869 GTCAAAGCATCAAATAGCATCAACAG 59.747 38.462 0.00 0.00 0.00 3.16
568 594 6.071784 AGTCAAAGCATCAAATAGCATCAACA 60.072 34.615 0.00 0.00 0.00 3.33
569 595 6.327934 AGTCAAAGCATCAAATAGCATCAAC 58.672 36.000 0.00 0.00 0.00 3.18
592 648 4.154737 TCCGAATCAAACAGCATCAAAGAG 59.845 41.667 0.00 0.00 0.00 2.85
593 649 4.071423 TCCGAATCAAACAGCATCAAAGA 58.929 39.130 0.00 0.00 0.00 2.52
736 829 3.932710 TGAGCCGATCATCAAACTAACAC 59.067 43.478 0.00 0.00 31.12 3.32
809 905 9.713338 TGGAGACATGCAATTGGAACAATATGC 62.713 40.741 2.94 15.58 38.98 3.14
1107 1264 1.559682 GACTGGAGCCCAACATTCCTA 59.440 52.381 0.00 0.00 30.80 2.94
1128 1285 1.344065 TGCCGGAGTTGTTCCTAGAA 58.656 50.000 5.05 0.00 44.41 2.10
1354 1512 4.003648 CACCAAACTACCTTAGCTCCAAG 58.996 47.826 0.00 0.00 0.00 3.61
1374 1532 5.673337 TCAAAGACAAACTGCATAGACAC 57.327 39.130 0.00 0.00 0.00 3.67
1377 1545 5.376625 AGGTTCAAAGACAAACTGCATAGA 58.623 37.500 0.00 0.00 0.00 1.98
1489 1765 4.890158 TCAGAGCCATCAAACTACTTCA 57.110 40.909 0.00 0.00 0.00 3.02
1491 1767 4.042187 AGGTTCAGAGCCATCAAACTACTT 59.958 41.667 6.02 0.00 0.00 2.24
1507 1783 4.256920 CATCAAACTACTCCCAGGTTCAG 58.743 47.826 0.00 0.00 0.00 3.02
1578 1886 6.811170 ACTTCACAAACAATAAACACAGGTTG 59.189 34.615 0.00 0.00 37.30 3.77
1593 1901 4.630894 TGATCCACACAACTTCACAAAC 57.369 40.909 0.00 0.00 0.00 2.93
1661 1980 0.623723 TCGGCCTTTTTAGAGCCCAT 59.376 50.000 0.00 0.00 44.13 4.00
1763 2128 5.127031 AGCCCACGTTCTTATTTTGCATAAT 59.873 36.000 7.55 7.55 0.00 1.28
1781 2146 0.322187 TCGGCCTTTTTAGAGCCCAC 60.322 55.000 0.00 0.00 44.13 4.61
1876 2245 5.866633 TGGCCTTTTTATTTTCTGTTATGCG 59.133 36.000 3.32 0.00 0.00 4.73
1932 2301 3.011708 AGTCCACTATTCTTTTGGGCCAT 59.988 43.478 7.26 0.00 35.45 4.40
1964 2335 5.128335 GGAATGGAGCCTTTTTCTGATGAAT 59.872 40.000 0.00 0.00 31.56 2.57
2092 2470 2.354729 CCCGGTCCATTTCAGCCA 59.645 61.111 0.00 0.00 0.00 4.75
2139 2517 1.600957 CTGGCATGGCAGAATTACGAG 59.399 52.381 38.55 13.68 0.00 4.18
2156 2534 1.442526 GATCCATCGTGGCAAGCTGG 61.443 60.000 15.81 15.81 37.47 4.85
2169 2547 0.250234 CCACACCACGTCAGATCCAT 59.750 55.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.