Multiple sequence alignment - TraesCS5B01G096400

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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 TraesCS5B01G096400 chr5B 100.000 2303 0 0 1 2303 127703830 127701528 0.000000e+00 4253.0
1 TraesCS5B01G096400 chr5B 97.608 627 15 0 1 627 527498707 527498081 0.000000e+00 1075.0
2 TraesCS5B01G096400 chr5B 97.008 635 19 0 1 635 467125485 467124851 0.000000e+00 1068.0
3 TraesCS5B01G096400 chr5B 96.984 630 19 0 1 630 315395259 315394630 0.000000e+00 1059.0
4 TraesCS5B01G096400 chr5B 96.688 634 21 0 1 634 580280589 580279956 0.000000e+00 1055.0
5 TraesCS5B01G096400 chr6B 89.010 1738 110 32 628 2303 270875061 270876779 0.000000e+00 2076.0
6 TraesCS5B01G096400 chr6B 97.927 627 13 0 1 627 644391092 644390466 0.000000e+00 1086.0
7 TraesCS5B01G096400 chr2A 93.741 1342 62 14 628 1959 689380662 689381991 0.000000e+00 1993.0
8 TraesCS5B01G096400 chr1B 87.729 1035 79 21 693 1706 473822518 473823525 0.000000e+00 1164.0
9 TraesCS5B01G096400 chr2B 97.031 640 18 1 1 640 433081128 433080490 0.000000e+00 1075.0
10 TraesCS5B01G096400 chr2B 84.953 638 52 18 695 1319 596912782 596912176 7.040000e-170 606.0
11 TraesCS5B01G096400 chr2B 92.350 366 25 2 1939 2303 596912179 596911816 3.390000e-143 518.0
12 TraesCS5B01G096400 chr7B 97.600 625 15 0 1 625 32327328 32327952 0.000000e+00 1072.0
13 TraesCS5B01G096400 chr7B 96.672 631 20 1 1 631 118975164 118975793 0.000000e+00 1048.0
14 TraesCS5B01G096400 chr4B 96.975 628 18 1 1 627 491803851 491804478 0.000000e+00 1053.0
15 TraesCS5B01G096400 chr1A 90.893 582 38 7 693 1260 452018787 452019367 0.000000e+00 767.0
16 TraesCS5B01G096400 chr1A 85.086 637 53 18 695 1319 244510330 244509724 1.510000e-171 612.0
17 TraesCS5B01G096400 chr1A 84.929 637 54 18 695 1319 97646466 97645860 7.040000e-170 606.0
18 TraesCS5B01G096400 chr1A 84.639 638 54 22 695 1319 587387568 587386962 1.520000e-166 595.0
19 TraesCS5B01G096400 chr1A 92.623 366 24 2 1939 2303 97645863 97645500 7.290000e-145 523.0
20 TraesCS5B01G096400 chr1A 92.623 366 24 2 1939 2303 587386965 587386602 7.290000e-145 523.0
21 TraesCS5B01G096400 chr1A 92.077 366 25 3 1939 2303 244509727 244509365 1.580000e-141 512.0
22 TraesCS5B01G096400 chr1A 88.267 375 34 6 1340 1706 452019376 452019748 7.550000e-120 440.0
23 TraesCS5B01G096400 chr1D 89.848 591 47 5 693 1270 351245792 351246382 0.000000e+00 747.0
24 TraesCS5B01G096400 chr1D 84.772 394 38 15 1324 1706 351246398 351246780 2.160000e-100 375.0
25 TraesCS5B01G096400 chr5A 86.318 592 45 15 695 1274 623555778 623555211 1.510000e-171 612.0
26 TraesCS5B01G096400 chr5A 84.615 637 56 20 695 1319 78265922 78265316 1.520000e-166 595.0
27 TraesCS5B01G096400 chr5A 84.615 637 56 20 695 1319 78324754 78324148 1.520000e-166 595.0
28 TraesCS5B01G096400 chr5A 92.896 366 23 2 1939 2303 623555193 623554830 1.570000e-146 529.0
29 TraesCS5B01G096400 chr5A 92.582 364 24 2 1941 2303 78265317 78264956 9.430000e-144 520.0
30 TraesCS5B01G096400 chr5A 92.582 364 24 2 1941 2303 78324149 78323788 9.430000e-144 520.0
31 TraesCS5B01G096400 chr5A 85.487 503 37 16 695 1185 426931704 426931226 2.060000e-135 492.0
32 TraesCS5B01G096400 chrUn 90.000 410 40 1 1785 2193 8502663 8503072 1.570000e-146 529.0
33 TraesCS5B01G096400 chr3D 95.918 49 2 0 1858 1906 211929759 211929807 1.900000e-11 80.5


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 TraesCS5B01G096400 chr5B 127701528 127703830 2302 True 4253.0 4253 100.0000 1 2303 1 chr5B.!!$R1 2302
1 TraesCS5B01G096400 chr5B 527498081 527498707 626 True 1075.0 1075 97.6080 1 627 1 chr5B.!!$R4 626
2 TraesCS5B01G096400 chr5B 467124851 467125485 634 True 1068.0 1068 97.0080 1 635 1 chr5B.!!$R3 634
3 TraesCS5B01G096400 chr5B 315394630 315395259 629 True 1059.0 1059 96.9840 1 630 1 chr5B.!!$R2 629
4 TraesCS5B01G096400 chr5B 580279956 580280589 633 True 1055.0 1055 96.6880 1 634 1 chr5B.!!$R5 633
5 TraesCS5B01G096400 chr6B 270875061 270876779 1718 False 2076.0 2076 89.0100 628 2303 1 chr6B.!!$F1 1675
6 TraesCS5B01G096400 chr6B 644390466 644391092 626 True 1086.0 1086 97.9270 1 627 1 chr6B.!!$R1 626
7 TraesCS5B01G096400 chr2A 689380662 689381991 1329 False 1993.0 1993 93.7410 628 1959 1 chr2A.!!$F1 1331
8 TraesCS5B01G096400 chr1B 473822518 473823525 1007 False 1164.0 1164 87.7290 693 1706 1 chr1B.!!$F1 1013
9 TraesCS5B01G096400 chr2B 433080490 433081128 638 True 1075.0 1075 97.0310 1 640 1 chr2B.!!$R1 639
10 TraesCS5B01G096400 chr2B 596911816 596912782 966 True 562.0 606 88.6515 695 2303 2 chr2B.!!$R2 1608
11 TraesCS5B01G096400 chr7B 32327328 32327952 624 False 1072.0 1072 97.6000 1 625 1 chr7B.!!$F1 624
12 TraesCS5B01G096400 chr7B 118975164 118975793 629 False 1048.0 1048 96.6720 1 631 1 chr7B.!!$F2 630
13 TraesCS5B01G096400 chr4B 491803851 491804478 627 False 1053.0 1053 96.9750 1 627 1 chr4B.!!$F1 626
14 TraesCS5B01G096400 chr1A 452018787 452019748 961 False 603.5 767 89.5800 693 1706 2 chr1A.!!$F1 1013
15 TraesCS5B01G096400 chr1A 97645500 97646466 966 True 564.5 606 88.7760 695 2303 2 chr1A.!!$R1 1608
16 TraesCS5B01G096400 chr1A 244509365 244510330 965 True 562.0 612 88.5815 695 2303 2 chr1A.!!$R2 1608
17 TraesCS5B01G096400 chr1A 587386602 587387568 966 True 559.0 595 88.6310 695 2303 2 chr1A.!!$R3 1608
18 TraesCS5B01G096400 chr1D 351245792 351246780 988 False 561.0 747 87.3100 693 1706 2 chr1D.!!$F1 1013
19 TraesCS5B01G096400 chr5A 623554830 623555778 948 True 570.5 612 89.6070 695 2303 2 chr5A.!!$R4 1608
20 TraesCS5B01G096400 chr5A 78264956 78265922 966 True 557.5 595 88.5985 695 2303 2 chr5A.!!$R2 1608
21 TraesCS5B01G096400 chr5A 78323788 78324754 966 True 557.5 595 88.5985 695 2303 2 chr5A.!!$R3 1608

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
728 741 1.149174 CGCATTGGGCCCTACAGAT 59.851 57.895 25.7 6.35 40.31 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1765 1862 0.253044 TGATTGGTACCTCAGCTGGC 59.747 55.0 15.13 0.0 0.0 4.85 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
264 265 6.784227 CGTTACAGAATCGTTACACTGAAAAC 59.216 38.462 0.00 0.00 34.88 2.43
268 269 6.129393 CAGAATCGTTACACTGAAAACACAG 58.871 40.000 0.00 0.00 42.78 3.66
368 369 4.158025 CGTTACACTGAGACAGGAACCTAT 59.842 45.833 0.00 0.00 35.51 2.57
681 687 2.265904 CCACGACCTGACTCCGTCA 61.266 63.158 0.00 0.00 40.50 4.35
728 741 1.149174 CGCATTGGGCCCTACAGAT 59.851 57.895 25.70 6.35 40.31 2.90
733 746 3.519510 GCATTGGGCCCTACAGATAGATA 59.480 47.826 25.70 0.00 36.11 1.98
835 860 2.202440 CTCGACGTCGTCCGCAAT 60.202 61.111 34.40 0.00 41.42 3.56
917 942 1.218047 CTCCGTTCCGCAGATTCCA 59.782 57.895 0.00 0.00 0.00 3.53
1199 1248 0.461548 CTCTACGGCATCTGCTTCCA 59.538 55.000 1.70 0.00 41.70 3.53
1336 1395 4.579454 ATGATCATTATGCTGGCAACAC 57.421 40.909 1.18 0.00 46.17 3.32
1338 1397 2.106477 TCATTATGCTGGCAACACGA 57.894 45.000 0.00 0.00 46.17 4.35
1371 1437 3.631686 CACTGGACAGTCAATTGTGGAAA 59.368 43.478 5.13 0.00 40.20 3.13
1375 1441 4.709397 TGGACAGTCAATTGTGGAAAAAGT 59.291 37.500 5.13 0.00 0.00 2.66
1448 1516 3.244078 ACTGCCTGTAGTGTCGAAAATGA 60.244 43.478 0.00 0.00 0.00 2.57
1458 1526 4.083643 AGTGTCGAAAATGATGTCAGCAAG 60.084 41.667 0.00 0.00 0.00 4.01
1659 1756 2.109774 GGGATGATGCCATGTTGGAAA 58.890 47.619 0.00 0.00 40.96 3.13
1743 1840 1.471119 TCCAATCTCGCCTACTTCGT 58.529 50.000 0.00 0.00 0.00 3.85
1745 1842 1.134367 CCAATCTCGCCTACTTCGTCA 59.866 52.381 0.00 0.00 0.00 4.35
1746 1843 2.416836 CCAATCTCGCCTACTTCGTCAA 60.417 50.000 0.00 0.00 0.00 3.18
1765 1862 0.872881 AAACACCGTCCACTCGAACG 60.873 55.000 0.41 0.41 38.58 3.95
1783 1880 0.811616 CGCCAGCTGAGGTACCAATC 60.812 60.000 17.39 4.25 0.00 2.67
1800 1897 9.301153 GGTACCAATCATCAATCATTGTTTTAC 57.699 33.333 7.15 0.00 0.00 2.01
1829 1926 4.514441 CCACATGAATCTCTTGCATAGTCC 59.486 45.833 0.00 0.00 0.00 3.85
2041 2139 5.587443 CAGATGGAGCAGTGATTTGTGATAA 59.413 40.000 0.00 0.00 0.00 1.75
2051 2149 7.329471 GCAGTGATTTGTGATAATCTAGCGATA 59.671 37.037 0.00 0.00 35.89 2.92
2061 2159 9.562583 GTGATAATCTAGCGATAAGTAGAAAGG 57.437 37.037 0.00 0.00 0.00 3.11
2122 2220 8.489489 ACAATCATGTACAGAGGATTAGTTCAT 58.511 33.333 15.62 0.00 38.24 2.57
2142 2240 7.669722 AGTTCATTTTAACTAGCAGGGATTCAA 59.330 33.333 0.00 0.00 37.93 2.69
2143 2241 7.630242 TCATTTTAACTAGCAGGGATTCAAG 57.370 36.000 0.00 0.00 0.00 3.02
2222 2320 5.058490 CAGATTTGGTGGCAAAACATTCTT 58.942 37.500 0.00 0.00 0.00 2.52
2282 2380 4.274147 TCTGGTTTTTGTAGCAGACCAAA 58.726 39.130 0.00 0.00 45.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
137 138 7.171337 TGAATTTAAGTTCATTTGCTTGCTTCC 59.829 33.333 9.15 0.00 33.41 3.46
219 220 2.519013 GAAGAATTGAGTTGCCCTGGT 58.481 47.619 0.00 0.00 0.00 4.00
264 265 2.521958 CTTGGCGGTAGGGTCCTGTG 62.522 65.000 0.00 0.00 0.00 3.66
268 269 4.484872 GCCTTGGCGGTAGGGTCC 62.485 72.222 0.00 0.00 33.19 4.46
535 536 3.572255 GTGATTTGACCCTTTTGCTACCA 59.428 43.478 0.00 0.00 0.00 3.25
569 571 5.339200 GGATTTCAGGATCTGACCCTTGTTA 60.339 44.000 0.00 0.00 40.46 2.41
728 741 1.342174 GTTGTCGGGGCGGAATATCTA 59.658 52.381 0.00 0.00 0.00 1.98
733 746 1.074248 AAAGTTGTCGGGGCGGAAT 59.926 52.632 0.00 0.00 0.00 3.01
835 860 2.989253 TCGCAGTTCTCGGCCTCA 60.989 61.111 0.00 0.00 0.00 3.86
917 942 1.728971 CAAAAGTCAGAATCGCTCGCT 59.271 47.619 0.00 0.00 0.00 4.93
939 964 1.002366 GCCTGACGACAAGCACATAG 58.998 55.000 3.57 0.00 34.05 2.23
940 965 0.608130 AGCCTGACGACAAGCACATA 59.392 50.000 10.93 0.00 36.08 2.29
987 1012 3.788145 CCCATGCCCGAACCGGTA 61.788 66.667 8.00 0.00 46.80 4.02
1199 1248 1.344953 TGTGGTCAGCTTGAGGGTGT 61.345 55.000 0.00 0.00 43.26 4.16
1336 1395 5.292765 ACTGTCCAGTGCTATAATTCATCG 58.707 41.667 0.00 0.00 40.75 3.84
1338 1397 6.239217 TGACTGTCCAGTGCTATAATTCAT 57.761 37.500 4.35 0.00 42.66 2.57
1375 1441 9.241919 ACCACAATATGACAATTGATAAACAGA 57.758 29.630 13.59 2.34 38.84 3.41
1448 1516 5.045578 ACCAGTTAGGATAACTTGCTGACAT 60.046 40.000 0.00 0.00 41.22 3.06
1458 1526 4.585879 TGGCTTCAACCAGTTAGGATAAC 58.414 43.478 0.00 0.00 41.22 1.89
1659 1756 7.750229 TCTCAGCAGATAAAACAAATTCAGT 57.250 32.000 0.00 0.00 0.00 3.41
1743 1840 0.460722 TCGAGTGGACGGTGTTTTGA 59.539 50.000 0.00 0.00 0.00 2.69
1745 1842 1.292992 GTTCGAGTGGACGGTGTTTT 58.707 50.000 0.00 0.00 0.00 2.43
1746 1843 0.872881 CGTTCGAGTGGACGGTGTTT 60.873 55.000 0.00 0.00 0.00 2.83
1765 1862 0.253044 TGATTGGTACCTCAGCTGGC 59.747 55.000 15.13 0.00 0.00 4.85
1783 1880 8.702438 GTGGAAACAGTAAAACAATGATTGATG 58.298 33.333 12.80 3.52 44.46 3.07
1800 1897 4.216902 TGCAAGAGATTCATGTGGAAACAG 59.783 41.667 0.00 0.00 44.46 3.16
1829 1926 0.813184 GCACAGGTGGTCATGATTGG 59.187 55.000 0.00 0.00 0.00 3.16
1947 2045 9.427821 ACAGTCAGTGTATTAATCCTCTATCTT 57.572 33.333 0.00 0.00 37.75 2.40
2041 2139 8.569641 CAGTTACCTTTCTACTTATCGCTAGAT 58.430 37.037 0.00 0.00 40.76 1.98
2061 2159 6.024049 GCAGAGCACATGATTTTACAGTTAC 58.976 40.000 0.00 0.00 0.00 2.50
2082 2180 4.023450 ACATGATTGTGACAAGAGTTGCAG 60.023 41.667 3.74 0.00 33.85 4.41
2122 2220 6.294508 GCAACTTGAATCCCTGCTAGTTAAAA 60.295 38.462 0.00 0.00 0.00 1.52
2142 2240 0.758734 TGTGCCACAGTAGAGCAACT 59.241 50.000 0.00 0.00 38.45 3.16
2143 2241 0.868406 GTGTGCCACAGTAGAGCAAC 59.132 55.000 0.00 0.00 38.45 4.17
2222 2320 0.906775 CCGGTTAACTGCTCCCCTAA 59.093 55.000 9.06 0.00 0.00 2.69
2282 2380 3.641434 AGAAGTACAATCTGCAGCCAT 57.359 42.857 9.47 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.