Multiple sequence alignment - TraesCS5B01G039200

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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 TraesCS5B01G039200 chr5B 100.000 4117 0 0 1 4117 44226890 44222774 0.000000e+00 7603.0
1 TraesCS5B01G039200 chr5B 96.810 2257 64 5 1166 3418 43925270 43927522 0.000000e+00 3762.0
2 TraesCS5B01G039200 chr5B 96.493 827 16 6 1 822 43888335 43889153 0.000000e+00 1354.0
3 TraesCS5B01G039200 chr5B 94.248 678 30 6 3441 4117 43927812 43928481 0.000000e+00 1027.0
4 TraesCS5B01G039200 chr5B 96.959 296 7 2 834 1128 43889138 43889432 2.860000e-136 496.0
5 TraesCS5B01G039200 chr5D 93.099 3811 158 39 1 3782 44493021 44496755 0.000000e+00 5483.0
6 TraesCS5B01G039200 chr5D 84.764 571 84 1 1193 1760 3765226 3765796 1.660000e-158 569.0
7 TraesCS5B01G039200 chr5D 80.105 759 135 14 2118 2868 3766508 3767258 6.010000e-153 551.0
8 TraesCS5B01G039200 chr5D 87.246 345 30 5 3778 4117 44496856 44497191 8.350000e-102 381.0
9 TraesCS5B01G039200 chr5D 83.750 80 7 3 3601 3679 549576654 549576580 2.050000e-08 71.3
10 TraesCS5B01G039200 chr5A 92.944 3302 157 35 855 4117 34908684 34911948 0.000000e+00 4737.0
11 TraesCS5B01G039200 chr5A 96.316 760 19 4 1 758 34907702 34908454 0.000000e+00 1240.0
12 TraesCS5B01G039200 chr5A 82.432 74 7 5 3602 3669 326662916 326662843 4.440000e-05 60.2
13 TraesCS5B01G039200 chr2B 84.364 857 109 19 1168 2002 41865833 41864980 0.000000e+00 817.0
14 TraesCS5B01G039200 chr2B 83.205 780 103 19 2127 2882 41864900 41864125 0.000000e+00 689.0
15 TraesCS5B01G039200 chr2B 86.531 542 64 6 2127 2662 41848003 41847465 4.580000e-164 588.0
16 TraesCS5B01G039200 chr2D 88.725 612 66 2 1157 1765 26560180 26559569 0.000000e+00 745.0
17 TraesCS5B01G039200 chr2D 83.075 774 107 18 2127 2882 26559208 26558441 0.000000e+00 682.0
18 TraesCS5B01G039200 chr2A 88.072 612 69 3 1156 1764 28809660 28809050 0.000000e+00 723.0
19 TraesCS5B01G039200 chr2A 82.202 781 105 22 2127 2882 28808722 28807951 3.470000e-180 641.0
20 TraesCS5B01G039200 chrUn 78.755 546 102 5 2131 2663 87283795 87283251 1.820000e-93 353.0
21 TraesCS5B01G039200 chr1A 83.544 79 7 3 3602 3679 164468716 164468789 7.380000e-08 69.4
22 TraesCS5B01G039200 chr1A 81.707 82 11 4 3593 3671 440441738 440441818 9.550000e-07 65.8
23 TraesCS5B01G039200 chr3B 82.353 85 8 2 3602 3679 482487885 482487801 2.660000e-07 67.6
24 TraesCS5B01G039200 chr1D 100.000 36 0 0 3594 3629 253526063 253526028 2.660000e-07 67.6


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 TraesCS5B01G039200 chr5B 44222774 44226890 4116 True 7603.0 7603 100.0000 1 4117 1 chr5B.!!$R1 4116
1 TraesCS5B01G039200 chr5B 43925270 43928481 3211 False 2394.5 3762 95.5290 1166 4117 2 chr5B.!!$F2 2951
2 TraesCS5B01G039200 chr5B 43888335 43889432 1097 False 925.0 1354 96.7260 1 1128 2 chr5B.!!$F1 1127
3 TraesCS5B01G039200 chr5D 44493021 44497191 4170 False 2932.0 5483 90.1725 1 4117 2 chr5D.!!$F2 4116
4 TraesCS5B01G039200 chr5D 3765226 3767258 2032 False 560.0 569 82.4345 1193 2868 2 chr5D.!!$F1 1675
5 TraesCS5B01G039200 chr5A 34907702 34911948 4246 False 2988.5 4737 94.6300 1 4117 2 chr5A.!!$F1 4116
6 TraesCS5B01G039200 chr2B 41864125 41865833 1708 True 753.0 817 83.7845 1168 2882 2 chr2B.!!$R2 1714
7 TraesCS5B01G039200 chr2B 41847465 41848003 538 True 588.0 588 86.5310 2127 2662 1 chr2B.!!$R1 535
8 TraesCS5B01G039200 chr2D 26558441 26560180 1739 True 713.5 745 85.9000 1157 2882 2 chr2D.!!$R1 1725
9 TraesCS5B01G039200 chr2A 28807951 28809660 1709 True 682.0 723 85.1370 1156 2882 2 chr2A.!!$R1 1726
10 TraesCS5B01G039200 chrUn 87283251 87283795 544 True 353.0 353 78.7550 2131 2663 1 chrUn.!!$R1 532

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
60 61 3.777106 TCATGTTCTTGGCTTCAGTCT 57.223 42.857 0.0 0.0 0.0 3.24 F
1186 1363 0.977627 ATGTCGATGGCAGTGGGAGA 60.978 55.000 0.0 0.0 0.0 3.71 F
2644 3343 2.351276 CCCCTCACCTTCAACCCG 59.649 66.667 0.0 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1501 1684 0.736053 GAACACGAACTTGTTGGCCA 59.264 50.0 0.00 0.00 39.88 5.36 R
2749 3489 0.907704 TGGTACGTCCCTGGCTTCAT 60.908 55.0 0.00 0.00 34.77 2.57 R
3478 4494 0.179468 TCTGTAGCCGGCCCATTTAC 59.821 55.0 26.15 19.04 0.00 2.01 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
60 61 3.777106 TCATGTTCTTGGCTTCAGTCT 57.223 42.857 0.00 0.00 0.00 3.24
71 72 6.772716 TCTTGGCTTCAGTCTTTTGTATTCTT 59.227 34.615 0.00 0.00 0.00 2.52
72 73 6.317789 TGGCTTCAGTCTTTTGTATTCTTG 57.682 37.500 0.00 0.00 0.00 3.02
73 74 6.061441 TGGCTTCAGTCTTTTGTATTCTTGA 58.939 36.000 0.00 0.00 0.00 3.02
74 75 6.716628 TGGCTTCAGTCTTTTGTATTCTTGAT 59.283 34.615 0.00 0.00 0.00 2.57
191 195 4.647964 AGCACGCATTATTGTTAAACTCG 58.352 39.130 0.00 0.00 0.00 4.18
843 1015 4.898829 TTTTTGCGCAGATATGCACTAT 57.101 36.364 11.31 0.00 41.57 2.12
845 1017 6.370433 TTTTTGCGCAGATATGCACTATAA 57.630 33.333 11.31 0.00 41.57 0.98
846 1018 6.558771 TTTTGCGCAGATATGCACTATAAT 57.441 33.333 11.31 0.00 41.57 1.28
847 1019 6.558771 TTTGCGCAGATATGCACTATAATT 57.441 33.333 11.31 0.00 41.57 1.40
848 1020 6.558771 TTGCGCAGATATGCACTATAATTT 57.441 33.333 11.31 0.00 41.57 1.82
849 1021 5.930405 TGCGCAGATATGCACTATAATTTG 58.070 37.500 13.57 0.00 35.90 2.32
850 1022 5.106594 TGCGCAGATATGCACTATAATTTGG 60.107 40.000 13.57 0.00 35.90 3.28
851 1023 5.122239 GCGCAGATATGCACTATAATTTGGA 59.878 40.000 13.57 0.00 34.41 3.53
852 1024 6.674037 GCGCAGATATGCACTATAATTTGGAG 60.674 42.308 13.57 0.00 34.41 3.86
877 1049 6.755206 GGGGGTAATTATGTTTTATTCAGCC 58.245 40.000 0.00 0.00 0.00 4.85
887 1059 6.182039 TGTTTTATTCAGCCGATCTTTCAG 57.818 37.500 0.00 0.00 0.00 3.02
1170 1347 4.290093 TCCAGGTACTAGCAGATCAATGT 58.710 43.478 0.00 0.00 36.02 2.71
1186 1363 0.977627 ATGTCGATGGCAGTGGGAGA 60.978 55.000 0.00 0.00 0.00 3.71
1501 1684 2.434884 CATTGCGTGCTCTCCGGT 60.435 61.111 0.00 0.00 0.00 5.28
1727 1910 3.716195 TGGGCAGACATGGGGACG 61.716 66.667 0.00 0.00 0.00 4.79
1832 2486 7.473735 TTCTCTTCTCTGTCAATAGTGATGT 57.526 36.000 0.00 0.00 35.80 3.06
2097 2777 6.084326 TGCTCCTTGTTTTTACAGAAATCC 57.916 37.500 0.00 0.00 0.00 3.01
2155 2840 2.733218 CGTCGGAAGCTGAACGCA 60.733 61.111 0.00 0.00 42.61 5.24
2602 3301 3.321648 TGGGTGAGGTCGCTGCAT 61.322 61.111 0.00 0.00 0.00 3.96
2644 3343 2.351276 CCCCTCACCTTCAACCCG 59.649 66.667 0.00 0.00 0.00 5.28
2683 3391 9.226345 GTAAGTTGTTGTTTTTCTCTCATTGAG 57.774 33.333 7.38 7.38 43.96 3.02
2749 3489 5.302568 AGAACTTGATGAATGCAGAAACCAA 59.697 36.000 0.00 0.00 0.00 3.67
2781 3521 1.298667 GTACCAGGCATTCGGTGGT 59.701 57.895 0.00 0.00 46.54 4.16
2960 3701 8.495361 TTTTATCTTGGCATTTGATTGATTGG 57.505 30.769 0.00 0.00 0.00 3.16
2961 3702 5.687166 ATCTTGGCATTTGATTGATTGGT 57.313 34.783 0.00 0.00 0.00 3.67
3261 4004 1.641123 GCAAGCAAACATGGGCATGC 61.641 55.000 9.90 9.90 45.58 4.06
3400 4144 0.767375 GCAATAGATGGGCCTGAGGA 59.233 55.000 0.65 0.00 0.00 3.71
3449 4465 2.424601 CCATATGTGGTCACAAGCCAAG 59.575 50.000 7.92 0.00 45.41 3.61
3464 4480 0.842635 CCAAGGATAGGCAAGCTCCT 59.157 55.000 0.00 0.00 41.19 3.69
3476 4492 2.564771 CAAGCTCCTGTGTGAAGTGAA 58.435 47.619 0.00 0.00 0.00 3.18
3478 4494 2.775890 AGCTCCTGTGTGAAGTGAATG 58.224 47.619 0.00 0.00 0.00 2.67
3672 4689 4.637276 TGCGACAATTAATATGGATCGGT 58.363 39.130 0.00 0.00 0.00 4.69
3760 4782 8.836413 TCATCCCATAGTAAAAAGAATTAAGCG 58.164 33.333 0.00 0.00 0.00 4.68
3870 4998 9.927668 ATGTTCATAGAGGGTTTAAAAATGTTG 57.072 29.630 0.00 0.00 0.00 3.33
3905 5033 6.168389 CAAAGAGGAAAGGGAAAATGGAATG 58.832 40.000 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 5.471797 TCAAGCCACGATCAAGAATACAAAA 59.528 36.000 0.00 0.00 0.00 2.44
71 72 2.204237 CGAATCATCAAGCCACGATCA 58.796 47.619 0.00 0.00 0.00 2.92
72 73 2.205074 ACGAATCATCAAGCCACGATC 58.795 47.619 0.00 0.00 0.00 3.69
73 74 2.315925 ACGAATCATCAAGCCACGAT 57.684 45.000 0.00 0.00 0.00 3.73
74 75 2.951457 TACGAATCATCAAGCCACGA 57.049 45.000 0.00 0.00 0.00 4.35
191 195 4.997395 TGAGGCGGCATAAGAGAAATAATC 59.003 41.667 13.08 0.00 0.00 1.75
270 277 5.355630 TGGTGTTCAAAATCTTCGAAACTGA 59.644 36.000 0.00 0.00 0.00 3.41
830 1002 6.600822 CCCCTCCAAATTATAGTGCATATCTG 59.399 42.308 0.00 0.00 0.00 2.90
832 1004 5.888161 CCCCCTCCAAATTATAGTGCATATC 59.112 44.000 0.00 0.00 0.00 1.63
833 1005 5.831103 CCCCCTCCAAATTATAGTGCATAT 58.169 41.667 0.00 0.00 0.00 1.78
834 1006 5.255397 CCCCCTCCAAATTATAGTGCATA 57.745 43.478 0.00 0.00 0.00 3.14
835 1007 4.118168 CCCCCTCCAAATTATAGTGCAT 57.882 45.455 0.00 0.00 0.00 3.96
836 1008 3.593442 CCCCCTCCAAATTATAGTGCA 57.407 47.619 0.00 0.00 0.00 4.57
1170 1347 1.617018 CCTTCTCCCACTGCCATCGA 61.617 60.000 0.00 0.00 0.00 3.59
1186 1363 3.133365 GCCCACTCACCCACACCTT 62.133 63.158 0.00 0.00 0.00 3.50
1501 1684 0.736053 GAACACGAACTTGTTGGCCA 59.264 50.000 0.00 0.00 39.88 5.36
1727 1910 1.519455 CTCGGTGGAGGCAACGATC 60.519 63.158 0.00 0.00 43.76 3.69
1782 2091 3.842923 ATGCTCGCCGAGGACTGG 61.843 66.667 16.95 0.00 31.84 4.00
1783 2092 2.584418 CATGCTCGCCGAGGACTG 60.584 66.667 16.95 9.59 31.84 3.51
1784 2093 4.521062 GCATGCTCGCCGAGGACT 62.521 66.667 16.95 0.46 31.84 3.85
1785 2094 4.819761 TGCATGCTCGCCGAGGAC 62.820 66.667 20.33 2.57 31.84 3.85
1787 2096 3.646976 CATGCATGCTCGCCGAGG 61.647 66.667 20.33 0.00 0.00 4.63
1832 2486 3.252215 CGTCACCTGTGCAATTTAAGGAA 59.748 43.478 7.43 0.00 33.78 3.36
2155 2840 1.220206 CAGCTCATGCCGGAAGACT 59.780 57.895 5.05 0.00 40.80 3.24
2602 3301 1.915489 TGGTAGTAGACTGGGTCGGTA 59.085 52.381 0.00 0.00 37.67 4.02
2644 3343 4.222124 ACAACTTACATCCCATCTGTCC 57.778 45.455 0.00 0.00 0.00 4.02
2749 3489 0.907704 TGGTACGTCCCTGGCTTCAT 60.908 55.000 0.00 0.00 34.77 2.57
2781 3521 1.338674 CCGGCGCAAATCCTATATCCA 60.339 52.381 10.83 0.00 0.00 3.41
3083 3825 1.549243 TACGGAAGGTCATGGCTGCA 61.549 55.000 0.50 0.00 0.00 4.41
3222 3964 5.247507 TGCAAAGATAATGTCATTTCCGG 57.752 39.130 2.79 0.00 0.00 5.14
3261 4004 6.146021 CCCTTGCAGTACAAATTTAAAAGCAG 59.854 38.462 0.00 0.00 37.96 4.24
3429 4173 2.424601 CCTTGGCTTGTGACCACATATG 59.575 50.000 0.00 0.00 41.52 1.78
3445 4461 0.842635 AGGAGCTTGCCTATCCTTGG 59.157 55.000 0.00 0.00 40.65 3.61
3449 4465 0.543749 ACACAGGAGCTTGCCTATCC 59.456 55.000 0.00 0.00 36.22 2.59
3464 4480 4.022416 GCCCATTTACATTCACTTCACACA 60.022 41.667 0.00 0.00 0.00 3.72
3476 4492 0.548989 TGTAGCCGGCCCATTTACAT 59.451 50.000 26.15 2.97 0.00 2.29
3478 4494 0.179468 TCTGTAGCCGGCCCATTTAC 59.821 55.000 26.15 19.04 0.00 2.01
3649 4666 5.245531 ACCGATCCATATTAATTGTCGCAT 58.754 37.500 0.00 0.00 0.00 4.73
3672 4689 5.128499 ACATGAACATTGTTTCCAACTCCAA 59.872 36.000 0.00 0.00 32.26 3.53
3751 4768 8.788813 CATGAATATTATTTCGGCGCTTAATTC 58.211 33.333 7.64 5.70 0.00 2.17


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

AutoCloner maintained by Alex Coulton.