Multiple sequence alignment - TraesCS3A01G270700

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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 TraesCS3A01G270700 chr3A 100.000 2588 0 0 1 2588 497760534 497757947 0.000000e+00 4780.0
1 TraesCS3A01G270700 chr3A 89.353 742 62 13 1848 2580 281233382 281232649 0.000000e+00 917.0
2 TraesCS3A01G270700 chr3A 90.521 211 19 1 1647 1856 497761185 497761395 7.050000e-71 278.0
3 TraesCS3A01G270700 chr6B 93.636 990 33 6 1 971 650650629 650651607 0.000000e+00 1452.0
4 TraesCS3A01G270700 chr6B 91.837 784 40 7 1083 1843 650651760 650652542 0.000000e+00 1072.0
5 TraesCS3A01G270700 chr6B 84.434 636 73 18 1927 2554 551835549 551836166 1.020000e-168 603.0
6 TraesCS3A01G270700 chr2A 93.434 990 35 6 1 971 469818420 469819398 0.000000e+00 1441.0
7 TraesCS3A01G270700 chr2A 91.363 741 54 5 1848 2580 656609655 656608917 0.000000e+00 1005.0
8 TraesCS3A01G270700 chr2A 90.343 787 40 7 1083 1846 469819551 469820324 0.000000e+00 1000.0
9 TraesCS3A01G270700 chr2A 90.133 750 57 12 1848 2588 685727104 685727845 0.000000e+00 959.0
10 TraesCS3A01G270700 chr1A 96.496 742 25 1 1847 2588 581470903 581470163 0.000000e+00 1225.0
11 TraesCS3A01G270700 chr1A 86.200 471 51 12 2096 2556 429380923 429380457 4.970000e-137 497.0
12 TraesCS3A01G270700 chr5A 95.816 717 29 1 1 716 55266799 55267515 0.000000e+00 1157.0
13 TraesCS3A01G270700 chr5A 92.005 788 39 7 1083 1846 55273260 55274047 0.000000e+00 1085.0
14 TraesCS3A01G270700 chr5A 91.049 648 41 4 971 1601 592035674 592036321 0.000000e+00 859.0
15 TraesCS3A01G270700 chr5A 93.562 466 17 2 519 971 592034664 592035129 0.000000e+00 682.0
16 TraesCS3A01G270700 chr5A 92.913 254 7 4 718 971 55272865 55273107 2.450000e-95 359.0
17 TraesCS3A01G270700 chr5A 82.692 312 42 6 519 818 592123043 592123354 1.530000e-67 267.0
18 TraesCS3A01G270700 chr6D 92.287 739 51 4 1847 2580 176994140 176994877 0.000000e+00 1044.0
19 TraesCS3A01G270700 chr6D 89.160 738 54 5 1848 2580 36957724 36958440 0.000000e+00 896.0
20 TraesCS3A01G270700 chr6D 90.278 216 18 3 1633 1846 454293539 454293753 1.960000e-71 279.0
21 TraesCS3A01G270700 chr6D 88.835 206 22 1 1642 1846 454277279 454277074 4.280000e-63 252.0
22 TraesCS3A01G270700 chr5D 93.056 648 28 4 971 1601 472522092 472522739 0.000000e+00 931.0
23 TraesCS3A01G270700 chr5D 89.684 475 27 10 519 971 472521031 472521505 1.030000e-163 586.0
24 TraesCS3A01G270700 chr5D 82.770 592 96 5 971 1556 472627885 472628476 8.210000e-145 523.0
25 TraesCS3A01G270700 chr5D 92.118 203 12 4 1646 1846 521255622 521255822 1.520000e-72 283.0
26 TraesCS3A01G270700 chr5D 82.692 312 42 5 519 818 472569164 472569475 1.530000e-67 267.0
27 TraesCS3A01G270700 chr4A 89.459 740 62 10 1848 2577 552586937 552587670 0.000000e+00 920.0
28 TraesCS3A01G270700 chr4A 91.083 471 42 0 7 477 549819915 549820385 2.810000e-179 638.0
29 TraesCS3A01G270700 chr4A 96.774 62 1 1 461 521 549820441 549820502 4.560000e-18 102.0
30 TraesCS3A01G270700 chr5B 91.199 659 41 4 971 1612 579521527 579522185 0.000000e+00 880.0
31 TraesCS3A01G270700 chr5B 90.557 413 21 4 519 913 579520762 579521174 4.900000e-147 531.0
32 TraesCS3A01G270700 chr5B 91.964 224 15 3 1631 1851 663517478 663517255 6.950000e-81 311.0
33 TraesCS3A01G270700 chr5B 82.692 312 42 5 519 818 579591567 579591878 1.530000e-67 267.0
34 TraesCS3A01G270700 chr5B 95.238 42 2 0 930 971 579521173 579521214 1.660000e-07 67.6
35 TraesCS3A01G270700 chr7B 89.692 650 55 9 1939 2580 530763200 530763845 0.000000e+00 819.0
36 TraesCS3A01G270700 chr4D 93.501 477 31 0 1 477 47895496 47895020 0.000000e+00 710.0
37 TraesCS3A01G270700 chr4D 96.774 62 1 1 461 521 47894964 47894903 4.560000e-18 102.0
38 TraesCS3A01G270700 chr2B 85.540 657 71 16 1905 2554 485385433 485384794 0.000000e+00 665.0
39 TraesCS3A01G270700 chr4B 91.126 462 38 2 16 477 70551620 70551162 7.860000e-175 623.0
40 TraesCS3A01G270700 chr4B 91.628 215 17 1 1633 1846 310958066 310957852 1.950000e-76 296.0
41 TraesCS3A01G270700 chr4B 96.774 62 1 1 461 521 70551106 70551045 4.560000e-18 102.0
42 TraesCS3A01G270700 chr6A 86.504 452 59 2 1861 2312 57210046 57210495 1.790000e-136 496.0
43 TraesCS3A01G270700 chr2D 86.070 402 46 8 2158 2553 290544880 290544483 8.560000e-115 424.0
44 TraesCS3A01G270700 chr2D 89.474 209 15 7 1642 1846 651701128 651700923 9.190000e-65 257.0
45 TraesCS3A01G270700 chr3D 90.995 211 12 6 1646 1851 32387663 32387455 7.050000e-71 278.0
46 TraesCS3A01G270700 chr3D 88.732 213 18 3 1635 1846 231173095 231173302 3.300000e-64 255.0


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 TraesCS3A01G270700 chr3A 497757947 497760534 2587 True 4780.000000 4780 100.000000 1 2588 1 chr3A.!!$R2 2587
1 TraesCS3A01G270700 chr3A 281232649 281233382 733 True 917.000000 917 89.353000 1848 2580 1 chr3A.!!$R1 732
2 TraesCS3A01G270700 chr6B 650650629 650652542 1913 False 1262.000000 1452 92.736500 1 1843 2 chr6B.!!$F2 1842
3 TraesCS3A01G270700 chr6B 551835549 551836166 617 False 603.000000 603 84.434000 1927 2554 1 chr6B.!!$F1 627
4 TraesCS3A01G270700 chr2A 469818420 469820324 1904 False 1220.500000 1441 91.888500 1 1846 2 chr2A.!!$F2 1845
5 TraesCS3A01G270700 chr2A 656608917 656609655 738 True 1005.000000 1005 91.363000 1848 2580 1 chr2A.!!$R1 732
6 TraesCS3A01G270700 chr2A 685727104 685727845 741 False 959.000000 959 90.133000 1848 2588 1 chr2A.!!$F1 740
7 TraesCS3A01G270700 chr1A 581470163 581470903 740 True 1225.000000 1225 96.496000 1847 2588 1 chr1A.!!$R2 741
8 TraesCS3A01G270700 chr5A 55266799 55267515 716 False 1157.000000 1157 95.816000 1 716 1 chr5A.!!$F1 715
9 TraesCS3A01G270700 chr5A 592034664 592036321 1657 False 770.500000 859 92.305500 519 1601 2 chr5A.!!$F4 1082
10 TraesCS3A01G270700 chr5A 55272865 55274047 1182 False 722.000000 1085 92.459000 718 1846 2 chr5A.!!$F3 1128
11 TraesCS3A01G270700 chr6D 176994140 176994877 737 False 1044.000000 1044 92.287000 1847 2580 1 chr6D.!!$F2 733
12 TraesCS3A01G270700 chr6D 36957724 36958440 716 False 896.000000 896 89.160000 1848 2580 1 chr6D.!!$F1 732
13 TraesCS3A01G270700 chr5D 472521031 472522739 1708 False 758.500000 931 91.370000 519 1601 2 chr5D.!!$F4 1082
14 TraesCS3A01G270700 chr5D 472627885 472628476 591 False 523.000000 523 82.770000 971 1556 1 chr5D.!!$F2 585
15 TraesCS3A01G270700 chr4A 552586937 552587670 733 False 920.000000 920 89.459000 1848 2577 1 chr4A.!!$F1 729
16 TraesCS3A01G270700 chr4A 549819915 549820502 587 False 370.000000 638 93.928500 7 521 2 chr4A.!!$F2 514
17 TraesCS3A01G270700 chr5B 579520762 579522185 1423 False 492.866667 880 92.331333 519 1612 3 chr5B.!!$F2 1093
18 TraesCS3A01G270700 chr7B 530763200 530763845 645 False 819.000000 819 89.692000 1939 2580 1 chr7B.!!$F1 641
19 TraesCS3A01G270700 chr4D 47894903 47895496 593 True 406.000000 710 95.137500 1 521 2 chr4D.!!$R1 520
20 TraesCS3A01G270700 chr2B 485384794 485385433 639 True 665.000000 665 85.540000 1905 2554 1 chr2B.!!$R1 649
21 TraesCS3A01G270700 chr4B 70551045 70551620 575 True 362.500000 623 93.950000 16 521 2 chr4B.!!$R2 505

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
378 379 0.106819 GGCTCTCCATCTGTGGCAAT 60.107 55.0 0.0 0.0 45.63 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1678 2430 0.165944 GTCAGCGCACGCAGTTTTAT 59.834 50.0 18.24 0.0 41.61 1.4 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
166 167 3.636231 CAAGGGACCCGGACTGCA 61.636 66.667 0.73 0.00 0.00 4.41
168 169 3.846405 AAGGGACCCGGACTGCAGA 62.846 63.158 23.35 0.00 0.00 4.26
194 195 0.250295 CCGGAGAGGTTGTTGAAGCA 60.250 55.000 0.00 0.00 34.51 3.91
237 238 1.371558 GAGACGTCCCAGCTTTGGT 59.628 57.895 13.01 0.00 0.00 3.67
249 250 1.821759 CTTTGGTGGCACCGTGTCA 60.822 57.895 30.14 10.98 42.58 3.58
279 280 1.141019 GCGGGAGATGTTCAGCGTA 59.859 57.895 0.00 0.00 0.00 4.42
372 373 1.118838 GCTACAGGCTCTCCATCTGT 58.881 55.000 0.00 0.00 43.26 3.41
378 379 0.106819 GGCTCTCCATCTGTGGCAAT 60.107 55.000 0.00 0.00 45.63 3.56
382 383 0.745486 CTCCATCTGTGGCAATGCGA 60.745 55.000 0.00 0.00 45.63 5.10
502 575 1.002888 TGTCGTAGAGGAAGACGGAGT 59.997 52.381 0.00 0.00 41.97 3.85
545 619 4.394712 CTGGAGGCGCGGGAGTTT 62.395 66.667 8.83 0.00 0.00 2.66
837 944 3.004419 GGTAAGTCACTTTTCCACTTGGC 59.996 47.826 0.00 0.00 32.56 4.52
1131 1870 3.746751 GCTACCTCCAGTGCATCATCAAT 60.747 47.826 0.00 0.00 0.00 2.57
1187 1926 4.148825 GCCGCACGAGTCCTCCAT 62.149 66.667 0.00 0.00 0.00 3.41
1212 1951 3.823330 AAGGTCGGCGGCTACGAG 61.823 66.667 12.73 0.00 44.60 4.18
1272 2011 3.000819 CACAGGGACCCGGCTGTA 61.001 66.667 11.05 0.00 0.00 2.74
1410 2149 2.845795 ACGGTCGGGGTGGTTCTT 60.846 61.111 0.00 0.00 0.00 2.52
1431 2170 2.516930 ACGCTGGTGCAGTGCTTT 60.517 55.556 17.60 0.00 44.75 3.51
1558 2309 3.317603 TGCGTGATGTTCTTCAGATCA 57.682 42.857 0.00 0.00 0.00 2.92
1614 2365 4.568380 CCAGTAGCATTGGCCCATATGTAT 60.568 45.833 0.00 0.00 42.56 2.29
1624 2375 7.626999 TTGGCCCATATGTATAGTAGTTTCT 57.373 36.000 0.00 0.00 0.00 2.52
1638 2390 6.150034 AGTAGTTTCTAGTAGAAGTGGGGA 57.850 41.667 12.28 0.00 35.37 4.81
1664 2416 2.162608 TGCGGGTTGATAATTGGAAACG 59.837 45.455 0.00 0.00 0.00 3.60
1676 2428 1.110518 TGGAAACGGCAGGGGTTTTC 61.111 55.000 0.00 0.00 37.70 2.29
1678 2430 1.546099 GGAAACGGCAGGGGTTTTCTA 60.546 52.381 0.00 0.00 37.70 2.10
1679 2431 2.443416 GAAACGGCAGGGGTTTTCTAT 58.557 47.619 0.00 0.00 37.70 1.98
1752 2515 5.397221 CCTGGGACTAAATCATCACATGAGT 60.397 44.000 0.00 0.00 43.53 3.41
1761 2524 6.822667 AATCATCACATGAGTTGCAAGTTA 57.177 33.333 8.48 4.49 43.53 2.24
1887 2651 1.898902 TAGAGTAGATCTGAGGCGCC 58.101 55.000 21.89 21.89 39.20 6.53
2203 2974 6.628844 GCAATCAGAGTTGCCCAATAGAAAAT 60.629 38.462 0.33 0.00 46.69 1.82
2399 3186 1.420138 ACGGATGGACTTCCTGTTTGT 59.580 47.619 0.00 0.00 36.82 2.83
2401 3188 3.263425 ACGGATGGACTTCCTGTTTGTAT 59.737 43.478 0.00 0.00 36.82 2.29
2414 3201 4.039124 CCTGTTTGTATTTTGGCCTCTTGT 59.961 41.667 3.32 0.00 0.00 3.16
2561 3356 7.934855 ACTTGAAGTTGATGCAGATTATTCT 57.065 32.000 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 2.502492 CGTCGGCATCCTCCTCCAT 61.502 63.158 0.00 0.00 0.00 3.41
106 107 1.536907 TCAACAACCCCGGGCTCTA 60.537 57.895 17.73 0.00 0.00 2.43
150 151 3.322466 CTGCAGTCCGGGTCCCTT 61.322 66.667 5.25 0.00 0.00 3.95
166 167 0.684805 AACCTCTCCGGCGAGATTCT 60.685 55.000 23.05 1.12 44.25 2.40
168 169 1.258445 ACAACCTCTCCGGCGAGATT 61.258 55.000 23.05 9.48 44.25 2.40
194 195 2.361357 CCGTCACCCTCGACCTCT 60.361 66.667 0.00 0.00 31.91 3.69
233 234 2.203139 CTGACACGGTGCCACCAA 60.203 61.111 15.45 0.00 38.47 3.67
234 235 3.157949 TCTGACACGGTGCCACCA 61.158 61.111 15.45 0.84 38.47 4.17
237 238 2.574018 CCTCTCTGACACGGTGCCA 61.574 63.158 8.30 1.83 0.00 4.92
312 313 3.770040 CTCACGGACGCCATCCCA 61.770 66.667 0.00 0.00 46.04 4.37
378 379 4.805231 CACATACCGGCCGTCGCA 62.805 66.667 26.12 6.00 37.59 5.10
538 612 1.534729 CACCACCTGCTTAAACTCCC 58.465 55.000 0.00 0.00 0.00 4.30
545 619 0.541063 TCTCGTCCACCACCTGCTTA 60.541 55.000 0.00 0.00 0.00 3.09
590 664 2.579657 CGGCAGGTAGTCCCACACA 61.580 63.158 0.00 0.00 34.66 3.72
709 783 4.271816 CGCCCTCGTCCATCCTCG 62.272 72.222 0.00 0.00 0.00 4.63
837 944 1.478510 ACTCGGGTATGTGAGAAGCAG 59.521 52.381 0.00 0.00 36.11 4.24
907 1014 8.579006 TGACTTAAACGAGTCCAAAATCTACTA 58.421 33.333 0.00 0.00 44.29 1.82
967 1094 1.006758 TGAGGTGGTCTCCGTTCCTAT 59.993 52.381 0.00 0.00 41.76 2.57
1041 1780 4.194720 GCGTCGATCTCGGCCTGT 62.195 66.667 0.00 0.00 41.58 4.00
1309 2048 3.717294 ATCGCCCTTGCCGTCCTT 61.717 61.111 0.00 0.00 0.00 3.36
1410 2149 4.624364 CACTGCACCAGCGTCCCA 62.624 66.667 0.00 0.00 46.23 4.37
1431 2170 4.242586 TCCACCCGGTCCCAGTCA 62.243 66.667 0.00 0.00 0.00 3.41
1558 2309 7.112122 TGTACATATGAGATGCCAAGAAGTTT 58.888 34.615 10.38 0.00 0.00 2.66
1614 2365 7.276088 TCCCCACTTCTACTAGAAACTACTA 57.724 40.000 0.00 0.00 33.19 1.82
1624 2375 3.031736 GCAGTCATCCCCACTTCTACTA 58.968 50.000 0.00 0.00 0.00 1.82
1638 2390 2.951642 CCAATTATCAACCCGCAGTCAT 59.048 45.455 0.00 0.00 0.00 3.06
1676 2428 1.658596 TCAGCGCACGCAGTTTTATAG 59.341 47.619 18.24 0.00 41.61 1.31
1678 2430 0.165944 GTCAGCGCACGCAGTTTTAT 59.834 50.000 18.24 0.00 41.61 1.40
1679 2431 1.567537 GTCAGCGCACGCAGTTTTA 59.432 52.632 18.24 0.00 41.61 1.52
1715 2478 1.304713 CCCAGGCCAATCACAGCTT 60.305 57.895 5.01 0.00 0.00 3.74
1728 2491 5.039920 TCATGTGATGATTTAGTCCCAGG 57.960 43.478 0.00 0.00 33.59 4.45
1752 2515 5.329399 ACCAAACCATATCCTAACTTGCAA 58.671 37.500 0.00 0.00 0.00 4.08
1761 2524 5.279456 GCAAAACTTGACCAAACCATATCCT 60.279 40.000 0.00 0.00 0.00 3.24
1805 2569 6.614087 AGGTACCCTAACTTGCATCTAATGTA 59.386 38.462 8.74 0.00 28.47 2.29
1809 2573 4.163458 CCAGGTACCCTAACTTGCATCTAA 59.837 45.833 8.74 0.00 29.64 2.10
1811 2575 2.505819 CCAGGTACCCTAACTTGCATCT 59.494 50.000 8.74 0.00 29.64 2.90
1813 2577 1.564348 CCCAGGTACCCTAACTTGCAT 59.436 52.381 8.74 0.00 29.64 3.96
2191 2962 6.709846 TGAAGCCAAAACAATTTTCTATTGGG 59.290 34.615 4.69 0.00 38.17 4.12
2203 2974 5.703592 AGTATATCACGTGAAGCCAAAACAA 59.296 36.000 24.13 0.00 0.00 2.83
2399 3186 4.301072 ACTGCTACAAGAGGCCAAAATA 57.699 40.909 5.01 0.00 0.00 1.40
2401 3188 2.656947 ACTGCTACAAGAGGCCAAAA 57.343 45.000 5.01 0.00 0.00 2.44
2414 3201 6.294508 GGAGCCAAATTTTGAAAGTACTGCTA 60.295 38.462 10.72 0.00 0.00 3.49
2468 3263 0.165944 GGTTTGAATCTGTGCGTCCG 59.834 55.000 0.00 0.00 0.00 4.79
2561 3356 9.573166 TTTTCTCAATGAAGAAGAACCTGATTA 57.427 29.630 0.00 0.00 36.66 1.75


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

AutoCloner maintained by Alex Coulton.