Multiple sequence alignment - TraesCS5B01G016200

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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 TraesCS5B01G016200 chr5B 100.000 2687 0 0 1 2687 15192987 15190301 0.000000e+00 4963.0
1 TraesCS5B01G016200 chr5B 96.568 1049 23 3 1050 2098 15015055 15016090 0.000000e+00 1725.0
2 TraesCS5B01G016200 chr5B 86.855 1027 97 12 890 1882 15050491 15051513 0.000000e+00 1114.0
3 TraesCS5B01G016200 chr5B 94.833 600 23 2 2096 2687 15016350 15016949 0.000000e+00 929.0
4 TraesCS5B01G016200 chr5B 89.606 635 47 5 377 1010 15014432 15015048 0.000000e+00 789.0
5 TraesCS5B01G016200 chr5B 86.351 740 72 10 1167 1882 15094138 15094872 0.000000e+00 780.0
6 TraesCS5B01G016200 chr5B 85.815 712 65 18 1195 1882 15075230 15075929 0.000000e+00 723.0
7 TraesCS5B01G016200 chr5B 82.273 739 70 33 1168 1882 15128103 15128804 1.390000e-162 582.0
8 TraesCS5B01G016200 chr5B 81.395 688 113 11 1007 1688 15197073 15197751 5.060000e-152 547.0
9 TraesCS5B01G016200 chr5B 90.315 413 10 2 1 384 15013608 15014019 5.130000e-142 514.0
10 TraesCS5B01G016200 chr5B 83.333 156 21 4 635 788 442783451 442783299 3.610000e-29 139.0
11 TraesCS5B01G016200 chr5B 90.909 77 7 0 1966 2042 15051539 15051615 1.320000e-18 104.0
12 TraesCS5B01G016200 chr5B 89.706 68 7 0 1966 2033 15094898 15094965 1.330000e-13 87.9
13 TraesCS5B01G016200 chr5B 89.706 68 7 0 1966 2033 15128830 15128897 1.330000e-13 87.9
14 TraesCS5B01G016200 chr5A 90.472 1081 78 13 817 1890 14255355 14254293 0.000000e+00 1402.0
15 TraesCS5B01G016200 chr5A 84.276 566 77 6 303 864 14255911 14255354 2.350000e-150 542.0
16 TraesCS5B01G016200 chr5A 81.983 605 102 7 1088 1688 14416758 14417359 8.580000e-140 507.0
17 TraesCS5B01G016200 chr5A 94.444 144 8 0 1908 2051 14251589 14251446 3.480000e-54 222.0
18 TraesCS5B01G016200 chr5A 88.439 173 14 3 136 303 14256133 14255962 1.260000e-48 204.0
19 TraesCS5B01G016200 chr5A 85.714 105 15 0 2483 2587 555947009 555947113 7.860000e-21 111.0
20 TraesCS5B01G016200 chr5A 73.883 291 68 8 2301 2587 459375858 459375572 2.830000e-20 110.0
21 TraesCS5B01G016200 chr1B 80.992 605 101 9 2050 2642 72272787 72272185 4.050000e-128 468.0
22 TraesCS5B01G016200 chr1D 82.150 521 81 7 2132 2642 38920322 38919804 1.140000e-118 436.0
23 TraesCS5B01G016200 chr6B 75.225 444 87 17 2213 2642 199941454 199941888 3.530000e-44 189.0
24 TraesCS5B01G016200 chr7D 85.621 153 19 3 635 786 526525181 526525331 9.960000e-35 158.0
25 TraesCS5B01G016200 chr7D 86.765 68 7 1 2483 2550 63281167 63281232 1.030000e-09 75.0
26 TraesCS5B01G016200 chr2D 84.892 139 18 3 635 772 644149803 644149939 1.300000e-28 137.0
27 TraesCS5B01G016200 chr2B 82.390 159 24 2 632 788 331238598 331238754 4.670000e-28 135.0
28 TraesCS5B01G016200 chr5D 81.290 155 25 4 635 787 26715594 26715746 3.630000e-24 122.0
29 TraesCS5B01G016200 chr4D 80.723 166 24 7 635 797 416761846 416761686 3.630000e-24 122.0
30 TraesCS5B01G016200 chr4B 80.120 166 29 3 624 787 3940793 3940956 1.310000e-23 121.0
31 TraesCS5B01G016200 chrUn 86.765 68 7 1 2483 2550 91198383 91198318 1.030000e-09 75.0


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 TraesCS5B01G016200 chr5B 15190301 15192987 2686 True 4963.00 4963 100.00000 1 2687 1 chr5B.!!$R1 2686
1 TraesCS5B01G016200 chr5B 15013608 15016949 3341 False 989.25 1725 92.83050 1 2687 4 chr5B.!!$F3 2686
2 TraesCS5B01G016200 chr5B 15075230 15075929 699 False 723.00 723 85.81500 1195 1882 1 chr5B.!!$F1 687
3 TraesCS5B01G016200 chr5B 15050491 15051615 1124 False 609.00 1114 88.88200 890 2042 2 chr5B.!!$F4 1152
4 TraesCS5B01G016200 chr5B 15197073 15197751 678 False 547.00 547 81.39500 1007 1688 1 chr5B.!!$F2 681
5 TraesCS5B01G016200 chr5B 15094138 15094965 827 False 433.95 780 88.02850 1167 2033 2 chr5B.!!$F5 866
6 TraesCS5B01G016200 chr5B 15128103 15128897 794 False 334.95 582 85.98950 1168 2033 2 chr5B.!!$F6 865
7 TraesCS5B01G016200 chr5A 14251446 14256133 4687 True 592.50 1402 89.40775 136 2051 4 chr5A.!!$R2 1915
8 TraesCS5B01G016200 chr5A 14416758 14417359 601 False 507.00 507 81.98300 1088 1688 1 chr5A.!!$F1 600
9 TraesCS5B01G016200 chr1B 72272185 72272787 602 True 468.00 468 80.99200 2050 2642 1 chr1B.!!$R1 592
10 TraesCS5B01G016200 chr1D 38919804 38920322 518 True 436.00 436 82.15000 2132 2642 1 chr1D.!!$R1 510

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
629 1134 0.526662 CGGCCTTCTTGTCGTACTCT 59.473 55.0 0.0 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2416 5961 0.043485 TAGGGGCATACACACCTCCA 59.957 55.0 0.0 0.0 34.59 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
26 27 3.244770 GGACCAACTACACCTCCATCAAA 60.245 47.826 0.00 0.00 0.00 2.69
99 100 1.783711 GCGTCTCTTATCATGCTCACG 59.216 52.381 0.00 0.00 0.00 4.35
123 124 1.342275 TGGGGGATTTGCAATGAGAGG 60.342 52.381 0.00 0.00 0.00 3.69
362 443 1.917273 CTCGGCAATTTTCTGGCATG 58.083 50.000 0.00 0.00 41.82 4.06
552 1057 1.439353 AATCGCTGCATGGCTAACCG 61.439 55.000 0.00 0.00 39.70 4.44
560 1065 4.351192 CTGCATGGCTAACCGTTTTAATC 58.649 43.478 0.00 0.00 39.70 1.75
571 1076 2.476185 CCGTTTTAATCTTGAGCAGCCG 60.476 50.000 0.00 0.00 0.00 5.52
617 1122 1.597663 CGTTCAATATGTCCGGCCTTC 59.402 52.381 0.00 0.00 0.00 3.46
629 1134 0.526662 CGGCCTTCTTGTCGTACTCT 59.473 55.000 0.00 0.00 0.00 3.24
630 1135 1.741706 CGGCCTTCTTGTCGTACTCTA 59.258 52.381 0.00 0.00 0.00 2.43
632 1137 3.181489 CGGCCTTCTTGTCGTACTCTATT 60.181 47.826 0.00 0.00 0.00 1.73
633 1138 4.677250 CGGCCTTCTTGTCGTACTCTATTT 60.677 45.833 0.00 0.00 0.00 1.40
638 1143 6.310711 CCTTCTTGTCGTACTCTATTTGTTCC 59.689 42.308 0.00 0.00 0.00 3.62
642 1147 8.579006 TCTTGTCGTACTCTATTTGTTCCTAAA 58.421 33.333 0.00 0.00 0.00 1.85
643 1148 9.367444 CTTGTCGTACTCTATTTGTTCCTAAAT 57.633 33.333 0.00 0.00 34.78 1.40
684 1189 9.929180 ATACTTTATACTACGGACTACATACGA 57.071 33.333 0.00 0.00 0.00 3.43
765 1270 6.812879 ATACTAAAACCCCGAAAAGACTTG 57.187 37.500 0.00 0.00 0.00 3.16
772 1277 7.585579 AAACCCCGAAAAGACTTGTATTTAA 57.414 32.000 0.00 0.00 0.00 1.52
780 1285 9.224058 CGAAAAGACTTGTATTTAAAAACGGAA 57.776 29.630 0.00 0.00 0.00 4.30
983 1544 2.159226 GGTCCTCCATCGTTCACTACAG 60.159 54.545 0.00 0.00 0.00 2.74
1001 1562 2.760092 ACAGAGGCAACACAACAACAAT 59.240 40.909 0.00 0.00 41.41 2.71
1053 1614 2.354259 CTTGCTCTTCTCCTCGCAATT 58.646 47.619 0.00 0.00 41.02 2.32
1067 1628 3.055719 AATTGCTGCCACCGACGG 61.056 61.111 13.61 13.61 0.00 4.79
1709 2271 2.450160 GCGATTGGGCTTCAATTTACG 58.550 47.619 7.14 7.50 45.36 3.18
1725 2290 6.916387 TCAATTTACGTCGATGGATAAGTCTC 59.084 38.462 9.90 0.00 0.00 3.36
2002 5279 2.292828 AACAAGGCATTGGCTGTAGT 57.707 45.000 16.45 10.04 40.97 2.73
2186 5731 0.550914 AGCCAAACTGAGGGTTGACA 59.449 50.000 0.34 0.00 38.29 3.58
2221 5766 7.414984 GCAAGAGACCTAAATGAAGGATCTTTG 60.415 40.741 0.00 11.49 40.76 2.77
2223 5768 7.334858 AGAGACCTAAATGAAGGATCTTTGAC 58.665 38.462 0.00 0.00 39.15 3.18
2332 5877 3.800628 GGCATGTTGTGAAGCCTTC 57.199 52.632 0.00 0.00 43.70 3.46
2416 5961 6.281405 AGTACGAGACATTCAGAACAAAACT 58.719 36.000 0.00 0.00 0.00 2.66
2423 5968 4.339247 ACATTCAGAACAAAACTGGAGGTG 59.661 41.667 0.00 0.00 36.68 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 5.726793 ACCTATCTTTTGATGGAGGTGTAGT 59.273 40.000 0.00 0.00 42.99 2.73
26 27 1.906574 TCAAGGCGAACCACCTATCTT 59.093 47.619 0.00 0.00 36.14 2.40
74 75 3.866651 AGCATGATAAGAGACGCAAACT 58.133 40.909 0.00 0.00 0.00 2.66
99 100 2.101917 CTCATTGCAAATCCCCCATGAC 59.898 50.000 1.71 0.00 0.00 3.06
123 124 7.272731 GTGACCTTATTAAAAATCCTTGCGTTC 59.727 37.037 0.00 0.00 0.00 3.95
158 159 9.208022 CTCTAATCCTCGCAATTATTACATTCA 57.792 33.333 0.00 0.00 0.00 2.57
467 968 2.070783 TGACGCCGATAAGTTTGAACC 58.929 47.619 0.00 0.00 0.00 3.62
538 1043 3.840890 TTAAAACGGTTAGCCATGCAG 57.159 42.857 0.00 0.00 34.09 4.41
552 1057 3.492313 CACGGCTGCTCAAGATTAAAAC 58.508 45.455 0.00 0.00 0.00 2.43
560 1065 0.169672 CATTTCCACGGCTGCTCAAG 59.830 55.000 0.00 0.00 0.00 3.02
571 1076 3.682858 TCTCGATTTCCGTTCATTTCCAC 59.317 43.478 0.00 0.00 39.75 4.02
588 1093 4.617959 GGACATATTGAACGGATTCTCGA 58.382 43.478 0.00 0.00 35.69 4.04
617 1122 8.752766 TTTAGGAACAAATAGAGTACGACAAG 57.247 34.615 0.00 0.00 0.00 3.16
659 1164 9.758651 TTCGTATGTAGTCCGTAGTATAAAGTA 57.241 33.333 0.00 0.00 0.00 2.24
665 1170 8.662781 TTTACTTCGTATGTAGTCCGTAGTAT 57.337 34.615 0.00 0.00 35.44 2.12
666 1171 8.487313 TTTTACTTCGTATGTAGTCCGTAGTA 57.513 34.615 0.00 0.00 34.70 1.82
736 1241 9.435688 GTCTTTTCGGGGTTTTAGTATAAACTA 57.564 33.333 0.00 0.00 37.96 2.24
742 1247 6.301486 ACAAGTCTTTTCGGGGTTTTAGTAT 58.699 36.000 0.00 0.00 0.00 2.12
747 1252 6.474140 AAATACAAGTCTTTTCGGGGTTTT 57.526 33.333 0.00 0.00 0.00 2.43
751 1256 7.113825 CGTTTTTAAATACAAGTCTTTTCGGGG 59.886 37.037 9.09 0.00 0.00 5.73
765 1270 7.351414 ACGTACTCCTTCCGTTTTTAAATAC 57.649 36.000 0.00 0.00 0.00 1.89
772 1277 6.473455 CGATTAATACGTACTCCTTCCGTTTT 59.527 38.462 0.00 0.00 36.12 2.43
780 1285 4.139786 TCAGGCGATTAATACGTACTCCT 58.860 43.478 0.00 0.00 0.00 3.69
856 1361 5.298989 TGTGCCAAATTATATACCTCCGT 57.701 39.130 0.00 0.00 0.00 4.69
983 1544 2.472816 CCATTGTTGTTGTGTTGCCTC 58.527 47.619 0.00 0.00 0.00 4.70
1001 1562 1.451927 GAAGATGCCATGGTCGCCA 60.452 57.895 14.67 2.53 38.19 5.69
1053 1614 3.365291 GATACCGTCGGTGGCAGCA 62.365 63.158 27.20 5.92 36.19 4.41
1067 1628 4.219944 TGTTGAGTAGGTGGACAGTGATAC 59.780 45.833 0.00 0.00 0.00 2.24
1791 2376 6.972901 AGAAAGAAGTTGTCGAACAATTTTCC 59.027 34.615 15.58 5.95 40.59 3.13
2221 5766 2.028567 AGAGCTCCTACAAACAGCAGTC 60.029 50.000 10.93 0.00 35.46 3.51
2223 5768 2.028658 TCAGAGCTCCTACAAACAGCAG 60.029 50.000 10.93 0.00 35.46 4.24
2416 5961 0.043485 TAGGGGCATACACACCTCCA 59.957 55.000 0.00 0.00 34.59 3.86
2570 6115 7.114095 GGGAATATATCTGGCGGGTTTATAAA 58.886 38.462 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.