Multiple sequence alignment - TraesCS5B01G071800

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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 TraesCS5B01G071800 chr5B 100.000 2417 0 0 1 2417 83610994 83613410 0.000000e+00 4464
1 TraesCS5B01G071800 chr5D 94.143 1656 70 13 779 2415 75272394 75274041 0.000000e+00 2495
2 TraesCS5B01G071800 chr5A 92.617 1639 54 26 819 2417 70453950 70455561 0.000000e+00 2294
3 TraesCS5B01G071800 chr3B 88.366 808 65 10 1 784 595375503 595374701 0.000000e+00 944
4 TraesCS5B01G071800 chr6D 87.284 810 67 18 1 780 72401958 72402761 0.000000e+00 893
5 TraesCS5B01G071800 chr6D 87.179 819 63 18 1 780 200610179 200610994 0.000000e+00 893
6 TraesCS5B01G071800 chr4D 86.741 807 69 15 1 774 179923484 179924285 0.000000e+00 863
7 TraesCS5B01G071800 chr1B 85.530 774 99 9 12 780 218447287 218446522 0.000000e+00 797
8 TraesCS5B01G071800 chr1B 87.583 604 66 7 183 780 429705096 429704496 0.000000e+00 691
9 TraesCS5B01G071800 chr4B 91.002 589 45 8 198 785 60556192 60555611 0.000000e+00 787
10 TraesCS5B01G071800 chr7B 84.105 799 95 12 12 780 14729463 14728667 0.000000e+00 743
11 TraesCS5B01G071800 chr4A 84.029 814 84 28 1 780 432588562 432587761 0.000000e+00 741
12 TraesCS5B01G071800 chr2D 92.488 426 22 5 1 425 6307803 6307387 3.440000e-168 601
13 TraesCS5B01G071800 chr6B 96.250 80 3 0 1 80 103820956 103821035 5.420000e-27 132


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 TraesCS5B01G071800 chr5B 83610994 83613410 2416 False 4464 4464 100.000 1 2417 1 chr5B.!!$F1 2416
1 TraesCS5B01G071800 chr5D 75272394 75274041 1647 False 2495 2495 94.143 779 2415 1 chr5D.!!$F1 1636
2 TraesCS5B01G071800 chr5A 70453950 70455561 1611 False 2294 2294 92.617 819 2417 1 chr5A.!!$F1 1598
3 TraesCS5B01G071800 chr3B 595374701 595375503 802 True 944 944 88.366 1 784 1 chr3B.!!$R1 783
4 TraesCS5B01G071800 chr6D 72401958 72402761 803 False 893 893 87.284 1 780 1 chr6D.!!$F1 779
5 TraesCS5B01G071800 chr6D 200610179 200610994 815 False 893 893 87.179 1 780 1 chr6D.!!$F2 779
6 TraesCS5B01G071800 chr4D 179923484 179924285 801 False 863 863 86.741 1 774 1 chr4D.!!$F1 773
7 TraesCS5B01G071800 chr1B 218446522 218447287 765 True 797 797 85.530 12 780 1 chr1B.!!$R1 768
8 TraesCS5B01G071800 chr1B 429704496 429705096 600 True 691 691 87.583 183 780 1 chr1B.!!$R2 597
9 TraesCS5B01G071800 chr4B 60555611 60556192 581 True 787 787 91.002 198 785 1 chr4B.!!$R1 587
10 TraesCS5B01G071800 chr7B 14728667 14729463 796 True 743 743 84.105 12 780 1 chr7B.!!$R1 768
11 TraesCS5B01G071800 chr4A 432587761 432588562 801 True 741 741 84.029 1 780 1 chr4A.!!$R1 779

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
965 1017 0.251742 CCAATCACCACCACCACCAT 60.252 55.0 0.0 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1850 1925 1.355381 AGCCTCCAACATCAACCATCA 59.645 47.619 0.0 0.0 0.0 3.07 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
99 102 6.432472 TGATGGCAAGTAACAACATAACATGA 59.568 34.615 0.00 0.00 0.00 3.07
180 210 5.196695 CAAATTCCTCCTTTCTTCCCCTAG 58.803 45.833 0.00 0.00 0.00 3.02
248 278 2.618053 CCAACCCAGAAGCTTAGTACG 58.382 52.381 0.00 0.00 0.00 3.67
312 342 4.262851 GGCAAAGGGGAATACACACAAATT 60.263 41.667 0.00 0.00 0.00 1.82
477 526 2.184579 GTGTGGGAGGCGCTAGAC 59.815 66.667 7.64 0.00 0.00 2.59
480 529 1.227380 GTGGGAGGCGCTAGACATG 60.227 63.158 7.64 0.00 0.00 3.21
523 572 7.382110 CAACTAGAGAAGGAAGACAATGAAGA 58.618 38.462 0.00 0.00 0.00 2.87
573 622 3.637273 AGGTCGCACTGGGGTTCC 61.637 66.667 0.00 0.00 0.00 3.62
660 710 1.634757 GCGATTGTGCCACACATCGA 61.635 55.000 29.34 7.43 44.16 3.59
723 773 3.047877 GGGTTTGTCTCCGTGCCG 61.048 66.667 0.00 0.00 0.00 5.69
780 831 2.663606 CGTGTGTCAGTTATCGTCGTCA 60.664 50.000 0.00 0.00 0.00 4.35
805 856 1.949465 ATCAGCCGAACGGGATAAAC 58.051 50.000 15.01 0.00 38.47 2.01
816 867 5.232414 CGAACGGGATAAACATTTCTCTCTC 59.768 44.000 0.00 0.00 0.00 3.20
817 868 5.941555 ACGGGATAAACATTTCTCTCTCT 57.058 39.130 0.00 0.00 0.00 3.10
965 1017 0.251742 CCAATCACCACCACCACCAT 60.252 55.000 0.00 0.00 0.00 3.55
977 1041 3.402681 CACCATCGCCTCCACCCT 61.403 66.667 0.00 0.00 0.00 4.34
1132 1196 2.452937 CGGATCCCTTCCCCCTTCC 61.453 68.421 6.06 0.00 42.06 3.46
1181 1245 1.005394 CCGCACGGTAAGTCAACCT 60.005 57.895 0.00 0.00 37.39 3.50
1183 1247 1.342082 CGCACGGTAAGTCAACCTCG 61.342 60.000 0.00 0.00 37.39 4.63
1201 1265 2.419673 CTCGTGCACAATTAGGCATTCA 59.580 45.455 18.64 0.00 42.75 2.57
1244 1308 5.181009 TCTGATGTCCTCATGATGTTGTTC 58.819 41.667 0.00 0.00 34.06 3.18
1442 1508 8.734218 TCTAATCTAAGTTAGTGTCGTGATCT 57.266 34.615 9.71 0.00 34.16 2.75
1524 1590 3.866910 TCGACTTCTGCGTTAGTTTTTGT 59.133 39.130 0.00 0.00 0.00 2.83
1525 1591 3.960002 CGACTTCTGCGTTAGTTTTTGTG 59.040 43.478 0.00 0.00 0.00 3.33
1526 1592 4.260051 CGACTTCTGCGTTAGTTTTTGTGA 60.260 41.667 0.00 0.00 0.00 3.58
1541 1607 2.099141 TGTGATGAGTTGCCTAGCAC 57.901 50.000 0.00 0.00 38.71 4.40
1562 1628 5.414454 GCACTATGTTGAAGGTGGTCATTTA 59.586 40.000 0.00 0.00 0.00 1.40
1579 1647 6.102663 GTCATTTATCTGGGTCATAGATCCG 58.897 44.000 0.00 0.00 35.15 4.18
1606 1674 7.671398 ACTTGTTTTCTATCTGGAAATGGATGT 59.329 33.333 0.00 0.00 35.51 3.06
1607 1675 8.421249 TTGTTTTCTATCTGGAAATGGATGTT 57.579 30.769 0.00 0.00 35.51 2.71
1608 1676 7.829725 TGTTTTCTATCTGGAAATGGATGTTG 58.170 34.615 0.00 0.00 35.51 3.33
1649 1724 8.431910 AATTGGTTCTGTAACTCTAGTAGGAA 57.568 34.615 0.00 0.00 35.81 3.36
1691 1766 4.869297 TGAAACAGCATGAACAAAAACTGG 59.131 37.500 0.00 0.00 39.69 4.00
1705 1780 6.581712 ACAAAAACTGGTGCATTTTCTGTAT 58.418 32.000 0.00 0.00 0.00 2.29
1717 1792 7.596248 GTGCATTTTCTGTATAATGGGCTAATG 59.404 37.037 0.00 0.00 33.41 1.90
1810 1885 8.153550 TGTAAGTAATTGGCACCAAAATTGATT 58.846 29.630 6.14 0.00 39.55 2.57
1811 1886 8.998377 GTAAGTAATTGGCACCAAAATTGATTT 58.002 29.630 6.14 0.00 39.55 2.17
1850 1925 4.423275 TGGGATTTGATAGGAAATGGGGAT 59.577 41.667 0.00 0.00 0.00 3.85
2067 2158 7.802251 GTCTCAAATGTTCAAAATGTCTCTCTG 59.198 37.037 0.00 0.00 0.00 3.35
2076 2167 6.299141 TCAAAATGTCTCTCTGTTTTAGCCT 58.701 36.000 0.00 0.00 0.00 4.58
2391 2482 3.574826 GAGGTCTCATGGTATGGGTAGTC 59.425 52.174 0.00 0.00 31.00 2.59
2393 2484 3.904339 GGTCTCATGGTATGGGTAGTCAT 59.096 47.826 0.00 0.00 31.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 102 0.322456 TCTTTGCCGTTAGCTGCCAT 60.322 50.000 0.00 0.00 44.23 4.40
180 210 7.824779 AGAAGGATGTGTAGGATTCACTAAAAC 59.175 37.037 0.00 0.00 36.83 2.43
248 278 9.146586 AGATCTGCCATATTCTATCCTAGATTC 57.853 37.037 0.00 0.00 34.22 2.52
312 342 1.535028 GTCATGGCAAACACATCACGA 59.465 47.619 0.00 0.00 0.00 4.35
461 510 1.685765 ATGTCTAGCGCCTCCCACA 60.686 57.895 2.29 0.02 0.00 4.17
462 511 1.227380 CATGTCTAGCGCCTCCCAC 60.227 63.158 2.29 0.00 0.00 4.61
463 512 1.685765 ACATGTCTAGCGCCTCCCA 60.686 57.895 2.29 0.00 0.00 4.37
477 526 1.407618 CCATGGCAATCAGACCACATG 59.592 52.381 0.00 0.00 39.19 3.21
480 529 1.811860 GCCATGGCAATCAGACCAC 59.188 57.895 32.08 0.00 39.19 4.16
523 572 2.578940 CTCCTACCTCTCGATCCCCTAT 59.421 54.545 0.00 0.00 0.00 2.57
660 710 4.189580 AGCCACAGCCCACACGTT 62.190 61.111 0.00 0.00 41.25 3.99
785 836 2.285977 GTTTATCCCGTTCGGCTGATT 58.714 47.619 5.66 0.00 0.00 2.57
839 891 3.241067 ACTCGGCGCTTATTTCTGTTA 57.759 42.857 7.64 0.00 0.00 2.41
840 892 2.094762 ACTCGGCGCTTATTTCTGTT 57.905 45.000 7.64 0.00 0.00 3.16
965 1017 3.663815 GAGGAGAGGGTGGAGGCGA 62.664 68.421 0.00 0.00 0.00 5.54
977 1041 1.870941 TAGGGTTCAGGCGGAGGAGA 61.871 60.000 0.00 0.00 0.00 3.71
1181 1245 2.161410 GTGAATGCCTAATTGTGCACGA 59.839 45.455 9.77 9.77 40.88 4.35
1183 1247 3.057315 AGTGTGAATGCCTAATTGTGCAC 60.057 43.478 10.75 10.75 40.88 4.57
1201 1265 2.435586 GCCATCTCAGCGCAGTGT 60.436 61.111 11.47 0.00 0.00 3.55
1314 1380 2.900273 GTCATCCGCCCTAGCACA 59.100 61.111 0.00 0.00 39.83 4.57
1387 1453 1.459592 CTGACAAGTACGGCGGAAAAG 59.540 52.381 13.24 0.00 0.00 2.27
1465 1531 7.490657 AGTACACAATTCACCATCTACCTAA 57.509 36.000 0.00 0.00 0.00 2.69
1541 1607 7.012704 CCAGATAAATGACCACCTTCAACATAG 59.987 40.741 0.00 0.00 0.00 2.23
1562 1628 3.534357 AGTCGGATCTATGACCCAGAT 57.466 47.619 8.87 0.00 35.71 2.90
1579 1647 7.687941 TCCATTTCCAGATAGAAAACAAGTC 57.312 36.000 0.00 0.00 39.11 3.01
1606 1674 2.356665 TTAACTTGGGCTCACTGCAA 57.643 45.000 0.00 0.00 45.15 4.08
1607 1675 2.557924 CAATTAACTTGGGCTCACTGCA 59.442 45.455 0.00 0.00 45.15 4.41
1608 1676 3.221964 CAATTAACTTGGGCTCACTGC 57.778 47.619 0.00 0.00 41.94 4.40
1667 1742 5.005971 CCAGTTTTTGTTCATGCTGTTTCAG 59.994 40.000 0.00 0.00 34.12 3.02
1691 1766 5.520376 AGCCCATTATACAGAAAATGCAC 57.480 39.130 0.00 0.00 32.79 4.57
1705 1780 4.029520 ACCATTGCAACATTAGCCCATTA 58.970 39.130 0.00 0.00 0.00 1.90
1717 1792 3.121778 GCTTCGATTTTCACCATTGCAAC 59.878 43.478 0.00 0.00 0.00 4.17
1772 1847 9.344772 TGCCAATTACTTACAGAAGTAGAAAAA 57.655 29.630 0.00 0.00 46.39 1.94
1789 1864 9.824534 CTTAAAATCAATTTTGGTGCCAATTAC 57.175 29.630 10.27 0.00 40.00 1.89
1793 1868 6.595682 TCCTTAAAATCAATTTTGGTGCCAA 58.404 32.000 10.27 0.00 40.00 4.52
1796 1871 8.552083 AATCTCCTTAAAATCAATTTTGGTGC 57.448 30.769 10.27 0.00 40.00 5.01
1850 1925 1.355381 AGCCTCCAACATCAACCATCA 59.645 47.619 0.00 0.00 0.00 3.07
2067 2158 7.993758 ACTGGGAAGAGATAAATAGGCTAAAAC 59.006 37.037 0.00 0.00 0.00 2.43
2076 2167 6.151049 AGGGCTAACTGGGAAGAGATAAATA 58.849 40.000 0.00 0.00 0.00 1.40
2182 2273 7.878477 AGTTTCAATATTGAAGTGCACAATG 57.122 32.000 25.58 0.11 46.68 2.82
2216 2307 2.644798 AGCCCAACCATACATATCCTCC 59.355 50.000 0.00 0.00 0.00 4.30
2349 2440 7.001099 ACCTCATCAAGCTTTCATTCAAATT 57.999 32.000 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.