Multiple sequence alignment - TraesCS2B01G125100

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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 TraesCS2B01G125100 chr2B 100.000 2546 0 0 1 2546 93639690 93637145 0.000000e+00 4702.0
1 TraesCS2B01G125100 chr2B 86.120 1794 160 50 1 1772 93689769 93688043 0.000000e+00 1851.0
2 TraesCS2B01G125100 chr2B 85.380 1409 163 26 365 1756 93139383 93138001 0.000000e+00 1421.0
3 TraesCS2B01G125100 chr2B 94.366 781 34 7 1772 2546 792125521 792126297 0.000000e+00 1190.0
4 TraesCS2B01G125100 chr2B 90.973 853 57 13 934 1772 93446840 93445994 0.000000e+00 1131.0
5 TraesCS2B01G125100 chr2B 95.189 582 23 3 295 874 93447407 93446829 0.000000e+00 915.0
6 TraesCS2B01G125100 chr2B 79.588 1068 173 38 699 1749 93700771 93699732 0.000000e+00 723.0
7 TraesCS2B01G125100 chr2B 94.253 174 4 3 1 174 93453055 93452888 6.990000e-66 261.0
8 TraesCS2B01G125100 chr2B 88.189 127 9 4 178 300 93139522 93139398 2.040000e-31 147.0
9 TraesCS2B01G125100 chr2B 97.468 79 2 0 218 296 93452773 93452695 4.420000e-28 135.0
10 TraesCS2B01G125100 chr2B 83.607 122 16 3 178 295 93016467 93016588 7.450000e-21 111.0
11 TraesCS2B01G125100 chr2B 94.643 56 1 2 56 109 93139732 93139677 4.510000e-13 86.1
12 TraesCS2B01G125100 chr2B 100.000 35 0 0 178 212 93452833 93452799 5.880000e-07 65.8
13 TraesCS2B01G125100 chr2D 86.810 1812 153 50 1 1772 60016570 60014805 0.000000e+00 1943.0
14 TraesCS2B01G125100 chr2D 94.508 783 36 5 1766 2546 598653438 598652661 0.000000e+00 1201.0
15 TraesCS2B01G125100 chr2D 86.229 1082 120 20 690 1756 59731313 59730246 0.000000e+00 1146.0
16 TraesCS2B01G125100 chr2D 79.026 1068 174 38 699 1749 60022926 60021892 0.000000e+00 686.0
17 TraesCS2B01G125100 chr2D 86.916 107 12 1 178 282 59657739 59657845 4.450000e-23 119.0
18 TraesCS2B01G125100 chr2D 94.231 52 1 1 60 109 59731757 59731706 7.550000e-11 78.7
19 TraesCS2B01G125100 chr2A 83.619 1807 170 70 1 1772 59934234 59932519 0.000000e+00 1581.0
20 TraesCS2B01G125100 chr2A 83.324 1817 167 72 1 1772 59874212 59872487 0.000000e+00 1552.0
21 TraesCS2B01G125100 chr2A 84.539 1604 185 36 178 1756 59728658 59727093 0.000000e+00 1530.0
22 TraesCS2B01G125100 chr2A 81.532 444 43 22 178 609 59880935 59880519 1.890000e-86 329.0
23 TraesCS2B01G125100 chr2A 80.410 439 55 21 178 609 59943605 59943191 3.180000e-79 305.0
24 TraesCS2B01G125100 chr2A 85.714 217 28 3 699 912 59880438 59880222 2.550000e-55 226.0
25 TraesCS2B01G125100 chr6D 94.656 786 31 9 1768 2546 450350864 450350083 0.000000e+00 1208.0
26 TraesCS2B01G125100 chr7D 94.716 776 33 6 1772 2546 70149463 70148695 0.000000e+00 1199.0
27 TraesCS2B01G125100 chr6B 94.337 777 42 2 1770 2546 573275511 573274737 0.000000e+00 1190.0
28 TraesCS2B01G125100 chr5B 94.231 780 40 3 1769 2546 59690167 59690943 0.000000e+00 1186.0
29 TraesCS2B01G125100 chr5B 94.216 778 39 3 1769 2546 30872797 30872026 0.000000e+00 1182.0
30 TraesCS2B01G125100 chr3B 94.323 775 37 4 1772 2546 813154526 813153759 0.000000e+00 1181.0
31 TraesCS2B01G125100 chr3B 94.095 779 38 4 1768 2546 677780029 677780799 0.000000e+00 1177.0


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 TraesCS2B01G125100 chr2B 93637145 93639690 2545 True 4702.000000 4702 100.000 1 2546 1 chr2B.!!$R1 2545
1 TraesCS2B01G125100 chr2B 93688043 93689769 1726 True 1851.000000 1851 86.120 1 1772 1 chr2B.!!$R2 1771
2 TraesCS2B01G125100 chr2B 792125521 792126297 776 False 1190.000000 1190 94.366 1772 2546 1 chr2B.!!$F2 774
3 TraesCS2B01G125100 chr2B 93445994 93447407 1413 True 1023.000000 1131 93.081 295 1772 2 chr2B.!!$R5 1477
4 TraesCS2B01G125100 chr2B 93699732 93700771 1039 True 723.000000 723 79.588 699 1749 1 chr2B.!!$R3 1050
5 TraesCS2B01G125100 chr2B 93138001 93139732 1731 True 551.366667 1421 89.404 56 1756 3 chr2B.!!$R4 1700
6 TraesCS2B01G125100 chr2D 60014805 60016570 1765 True 1943.000000 1943 86.810 1 1772 1 chr2D.!!$R1 1771
7 TraesCS2B01G125100 chr2D 598652661 598653438 777 True 1201.000000 1201 94.508 1766 2546 1 chr2D.!!$R3 780
8 TraesCS2B01G125100 chr2D 60021892 60022926 1034 True 686.000000 686 79.026 699 1749 1 chr2D.!!$R2 1050
9 TraesCS2B01G125100 chr2D 59730246 59731757 1511 True 612.350000 1146 90.230 60 1756 2 chr2D.!!$R4 1696
10 TraesCS2B01G125100 chr2A 59932519 59934234 1715 True 1581.000000 1581 83.619 1 1772 1 chr2A.!!$R3 1771
11 TraesCS2B01G125100 chr2A 59872487 59874212 1725 True 1552.000000 1552 83.324 1 1772 1 chr2A.!!$R2 1771
12 TraesCS2B01G125100 chr2A 59727093 59728658 1565 True 1530.000000 1530 84.539 178 1756 1 chr2A.!!$R1 1578
13 TraesCS2B01G125100 chr2A 59880222 59880935 713 True 277.500000 329 83.623 178 912 2 chr2A.!!$R5 734
14 TraesCS2B01G125100 chr6D 450350083 450350864 781 True 1208.000000 1208 94.656 1768 2546 1 chr6D.!!$R1 778
15 TraesCS2B01G125100 chr7D 70148695 70149463 768 True 1199.000000 1199 94.716 1772 2546 1 chr7D.!!$R1 774
16 TraesCS2B01G125100 chr6B 573274737 573275511 774 True 1190.000000 1190 94.337 1770 2546 1 chr6B.!!$R1 776
17 TraesCS2B01G125100 chr5B 59690167 59690943 776 False 1186.000000 1186 94.231 1769 2546 1 chr5B.!!$F1 777
18 TraesCS2B01G125100 chr5B 30872026 30872797 771 True 1182.000000 1182 94.216 1769 2546 1 chr5B.!!$R1 777
19 TraesCS2B01G125100 chr3B 813153759 813154526 767 True 1181.000000 1181 94.323 1772 2546 1 chr3B.!!$R1 774
20 TraesCS2B01G125100 chr3B 677780029 677780799 770 False 1177.000000 1177 94.095 1768 2546 1 chr3B.!!$F1 778

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
47 48 0.033920 GGCCCTGTTGCAAGGAAAAG 59.966 55.000 5.98 0.0 40.02 2.27 F
1032 1253 1.011293 TCTGGGGAGAAGGGATTCCAT 59.989 52.381 4.80 0.0 35.09 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1061 1282 0.323629 TGTAAAGCTTGGGAGGTCCG 59.676 55.000 0.0 0.0 38.76 4.79 R
2033 2322 1.134175 GCGAGAAAGTGAGAGAGGGAG 59.866 57.143 0.0 0.0 0.00 4.30 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
22 23 3.409026 AAACGCCAAGAGAGATCACTT 57.591 42.857 0.00 0.00 0.00 3.16
43 44 1.832167 GTTGGCCCTGTTGCAAGGA 60.832 57.895 5.98 0.00 40.02 3.36
47 48 0.033920 GGCCCTGTTGCAAGGAAAAG 59.966 55.000 5.98 0.00 40.02 2.27
50 51 1.756538 CCCTGTTGCAAGGAAAAGTGT 59.243 47.619 5.98 0.00 40.02 3.55
116 186 2.675317 GCCTAGCCTTGGATATGTAGCG 60.675 54.545 0.00 0.00 0.00 4.26
118 188 1.717032 AGCCTTGGATATGTAGCGGA 58.283 50.000 0.00 0.00 0.00 5.54
120 190 1.608283 GCCTTGGATATGTAGCGGACC 60.608 57.143 0.00 0.00 0.00 4.46
161 232 3.725305 CGATCGAACGGCTAGCTATACAG 60.725 52.174 15.72 2.66 0.00 2.74
163 234 1.878088 CGAACGGCTAGCTATACAGGA 59.122 52.381 15.72 0.00 0.00 3.86
164 235 2.095668 CGAACGGCTAGCTATACAGGAG 60.096 54.545 15.72 0.00 0.00 3.69
166 237 3.784511 ACGGCTAGCTATACAGGAGTA 57.215 47.619 15.72 0.00 34.10 2.59
168 239 4.011023 ACGGCTAGCTATACAGGAGTATG 58.989 47.826 15.72 0.00 41.00 2.39
169 240 4.011023 CGGCTAGCTATACAGGAGTATGT 58.989 47.826 15.72 0.00 41.00 2.29
170 241 4.095185 CGGCTAGCTATACAGGAGTATGTC 59.905 50.000 15.72 0.00 41.00 3.06
456 602 4.175337 GGCCAGCTATCGCCCACA 62.175 66.667 0.00 0.00 39.39 4.17
533 679 4.077184 CGTAAGCAGCGACCCCCA 62.077 66.667 0.00 0.00 0.00 4.96
586 732 2.279582 CGACTGCTTCGTCCAAGTAT 57.720 50.000 0.63 0.00 43.24 2.12
603 749 4.137116 AGTATGTTGGTCACGTGCATAT 57.863 40.909 11.67 4.93 29.55 1.78
844 1050 2.805546 GTCTCCTGCGCCGACATA 59.194 61.111 4.18 0.00 0.00 2.29
920 1133 8.756486 TGATCATTTACATCATCAACTGGATT 57.244 30.769 0.00 0.00 32.57 3.01
930 1143 1.554617 TCAACTGGATTCTCGGCATCA 59.445 47.619 0.00 0.00 0.00 3.07
934 1147 1.938577 CTGGATTCTCGGCATCACTTG 59.061 52.381 0.00 0.00 0.00 3.16
1032 1253 1.011293 TCTGGGGAGAAGGGATTCCAT 59.989 52.381 4.80 0.00 35.09 3.41
1033 1254 2.252676 TCTGGGGAGAAGGGATTCCATA 59.747 50.000 4.80 0.00 35.09 2.74
1086 1307 4.104831 ACCTCCCAAGCTTTACATCTAGT 58.895 43.478 0.00 0.00 0.00 2.57
1137 1361 1.144057 GGGGCTCAACACGATCGAT 59.856 57.895 24.34 6.46 0.00 3.59
1400 1633 1.090625 TTCAACAACGACACCACCGG 61.091 55.000 0.00 0.00 0.00 5.28
1427 1660 2.809601 CCGGAACTTCGCGTCCAG 60.810 66.667 13.22 7.58 0.00 3.86
1488 1721 2.045438 ATGGGAAACATCGCGCCA 60.045 55.556 0.00 0.41 33.53 5.69
1625 1905 4.766891 CCAGTGGCCAATATAAATACCAGG 59.233 45.833 7.24 0.00 0.00 4.45
1652 1938 8.222433 TCTTGAAAACGTGTATTTTATGTACGG 58.778 33.333 0.00 0.00 38.92 4.02
1700 1986 9.880064 ATCTACACATATATATGTAACGATCGC 57.120 33.333 24.50 0.00 44.57 4.58
1828 2115 9.391006 AGAGAAAACATAACACACACTCTTAAA 57.609 29.630 0.00 0.00 0.00 1.52
1918 2206 1.346068 GCCGCTTATCCTCCTTCTCAT 59.654 52.381 0.00 0.00 0.00 2.90
1934 2222 2.764128 ATCCTCGCCGGTGATGGT 60.764 61.111 19.93 9.54 0.00 3.55
2032 2321 2.612251 CTCTCCCTCCCTCCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
2033 2322 3.036959 TCTCCCTCCCTCCCTCCC 61.037 72.222 0.00 0.00 0.00 4.30
2034 2323 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
2044 2347 1.230650 TCCCTCCCTCCCTCTCTCA 60.231 63.158 0.00 0.00 0.00 3.27
2047 2350 0.338120 CCTCCCTCCCTCTCTCACTT 59.662 60.000 0.00 0.00 0.00 3.16
2073 2376 2.032302 GCTTTCTCTCACTCTCGCGATA 59.968 50.000 10.36 0.10 0.00 2.92
2097 2400 5.701224 AGAAATCTGTTGTTTTCCCCTGTA 58.299 37.500 0.00 0.00 34.25 2.74
2170 2474 9.720769 CCTATATTGTTATAGTGGGGTGTTTAG 57.279 37.037 0.00 0.00 36.89 1.85
2210 2514 2.676342 CCGGTATGAAAGGAAAACGGAG 59.324 50.000 0.00 0.00 42.42 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.328279 GCAACAGGGCCAACTTAAGT 58.672 50.000 6.18 1.12 0.00 2.24
22 23 1.327303 CTTGCAACAGGGCCAACTTA 58.673 50.000 6.18 0.00 0.00 2.24
43 44 3.118920 GCCAAACCAACACCTACACTTTT 60.119 43.478 0.00 0.00 0.00 2.27
47 48 0.309612 CGCCAAACCAACACCTACAC 59.690 55.000 0.00 0.00 0.00 2.90
50 51 0.763652 TACCGCCAAACCAACACCTA 59.236 50.000 0.00 0.00 0.00 3.08
139 210 2.159037 TGTATAGCTAGCCGTTCGATCG 59.841 50.000 12.13 9.36 0.00 3.69
169 240 3.176924 GGATAGAGCATCCCTAGTGGA 57.823 52.381 2.84 2.84 46.85 4.02
209 326 1.763968 AGCTCACGTGCAGATACCTA 58.236 50.000 11.67 0.00 34.99 3.08
211 328 2.579207 TTAGCTCACGTGCAGATACC 57.421 50.000 11.67 0.00 34.99 2.73
586 732 4.055360 GCTATATATGCACGTGACCAACA 58.945 43.478 22.23 7.59 0.00 3.33
603 749 2.178325 TGCTACCACCTACCAGGCTATA 59.822 50.000 0.00 0.00 39.63 1.31
912 1125 1.556911 AGTGATGCCGAGAATCCAGTT 59.443 47.619 0.00 0.00 0.00 3.16
920 1133 0.037326 GGTGTCAAGTGATGCCGAGA 60.037 55.000 0.00 0.00 0.00 4.04
1032 1253 1.872237 GCCGCCTCGTTTGCATCTATA 60.872 52.381 0.00 0.00 0.00 1.31
1033 1254 1.160329 GCCGCCTCGTTTGCATCTAT 61.160 55.000 0.00 0.00 0.00 1.98
1061 1282 0.323629 TGTAAAGCTTGGGAGGTCCG 59.676 55.000 0.00 0.00 38.76 4.79
1086 1307 1.095600 CCGTCTCAAGATCTGACCGA 58.904 55.000 0.00 0.00 0.00 4.69
1400 1633 1.838568 GAAGTTCCGGACGGTGTTGC 61.839 60.000 1.83 0.00 36.47 4.17
1488 1721 2.750350 CCCTGCGTCCCTGTCTTT 59.250 61.111 0.00 0.00 0.00 2.52
1625 1905 9.033262 CGTACATAAAATACACGTTTTCAAGAC 57.967 33.333 0.00 0.00 33.62 3.01
1700 1986 4.524316 TTGCATGAGAAAGTGGGAATTG 57.476 40.909 0.00 0.00 0.00 2.32
1828 2115 1.216678 TCTTGGGTGATGGTTGTTGGT 59.783 47.619 0.00 0.00 0.00 3.67
1867 2154 8.602328 CAAATATGATGCCTCGCAAAAATAAAA 58.398 29.630 0.00 0.00 43.62 1.52
1918 2206 3.458163 GACCATCACCGGCGAGGA 61.458 66.667 9.30 5.56 45.00 3.71
1934 2222 2.701107 TGTTTTGTGTGAACACCGAGA 58.299 42.857 10.92 0.00 45.88 4.04
2032 2321 1.748493 CGAGAAAGTGAGAGAGGGAGG 59.252 57.143 0.00 0.00 0.00 4.30
2033 2322 1.134175 GCGAGAAAGTGAGAGAGGGAG 59.866 57.143 0.00 0.00 0.00 4.30
2034 2323 1.178276 GCGAGAAAGTGAGAGAGGGA 58.822 55.000 0.00 0.00 0.00 4.20
2044 2347 3.572255 AGAGTGAGAGAAAGCGAGAAAGT 59.428 43.478 0.00 0.00 0.00 2.66
2047 2350 2.160615 CGAGAGTGAGAGAAAGCGAGAA 59.839 50.000 0.00 0.00 0.00 2.87
2073 2376 4.962362 ACAGGGGAAAACAACAGATTTCTT 59.038 37.500 0.00 0.00 36.15 2.52
2097 2400 6.015180 ACACATGCATACCTCTGAAAAATGTT 60.015 34.615 0.00 0.00 0.00 2.71
2170 2474 3.810896 GGCGACCCGGATTGCAAC 61.811 66.667 11.17 0.00 0.00 4.17
2195 2499 2.803956 CGTAAGCTCCGTTTTCCTTTCA 59.196 45.455 0.00 0.00 0.00 2.69
2497 2802 7.854337 TCCATATCTTTTAAACCGTAACTCCT 58.146 34.615 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.