Multiple sequence alignment - TraesCS4B01G195800

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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 TraesCS4B01G195800 chr4B 100.000 1473 0 0 1 1473 422027794 422029266 0.000000e+00 2721.0
1 TraesCS4B01G195800 chr4B 91.514 1473 115 7 1 1473 144340459 144338997 0.000000e+00 2019.0
2 TraesCS4B01G195800 chr4B 100.000 648 0 0 1746 2393 422029539 422030186 0.000000e+00 1197.0
3 TraesCS4B01G195800 chr4B 95.385 65 2 1 2320 2384 422030052 422030115 4.210000e-18 102.0
4 TraesCS4B01G195800 chr4B 95.385 65 2 1 2259 2322 422030113 422030177 4.210000e-18 102.0
5 TraesCS4B01G195800 chr7D 92.068 1475 112 4 1 1473 7795916 7797387 0.000000e+00 2071.0
6 TraesCS4B01G195800 chr3B 91.185 1452 125 3 22 1473 125892123 125893571 0.000000e+00 1969.0
7 TraesCS4B01G195800 chr3B 87.571 177 12 8 2101 2267 781669441 781669617 1.880000e-46 196.0
8 TraesCS4B01G195800 chr5B 89.939 1471 140 7 6 1473 237158852 237157387 0.000000e+00 1890.0
9 TraesCS4B01G195800 chr7B 89.643 1458 148 3 3 1459 460570446 460571901 0.000000e+00 1853.0
10 TraesCS4B01G195800 chr6B 89.459 1461 148 6 12 1470 68900877 68902333 0.000000e+00 1840.0
11 TraesCS4B01G195800 chr6B 87.910 1464 171 6 12 1473 507581827 507580368 0.000000e+00 1718.0
12 TraesCS4B01G195800 chr1B 89.154 1466 152 5 3 1467 3693729 3695188 0.000000e+00 1820.0
13 TraesCS4B01G195800 chr7A 88.851 1471 158 6 5 1473 270771077 270772543 0.000000e+00 1803.0
14 TraesCS4B01G195800 chr4A 93.540 387 14 7 2017 2393 127280755 127281140 1.240000e-157 566.0
15 TraesCS4B01G195800 chr4A 91.584 404 23 6 1746 2140 127489580 127489179 4.500000e-152 547.0
16 TraesCS4B01G195800 chr4A 96.680 241 6 2 2154 2393 127487726 127487487 1.330000e-107 399.0
17 TraesCS4B01G195800 chr4A 84.015 269 16 7 1746 2012 127280411 127280654 1.430000e-57 233.0
18 TraesCS4B01G195800 chr4A 93.056 72 2 2 2315 2384 127280999 127281069 4.210000e-18 102.0
19 TraesCS4B01G195800 chr4A 95.385 65 2 1 2259 2322 127487560 127487496 4.210000e-18 102.0
20 TraesCS4B01G195800 chr4A 93.846 65 3 1 2320 2384 127487621 127487558 1.960000e-16 97.1
21 TraesCS4B01G195800 chr4D 94.509 346 18 1 1746 2090 340535613 340535958 1.260000e-147 532.0
22 TraesCS4B01G195800 chr4D 96.622 296 9 1 2098 2393 340548377 340548671 7.690000e-135 490.0
23 TraesCS4B01G195800 chr4D 94.444 72 1 2 2315 2384 340548530 340548600 9.050000e-20 108.0
24 TraesCS4B01G195800 chrUn 87.293 181 15 6 2101 2273 300192126 300191946 1.450000e-47 200.0
25 TraesCS4B01G195800 chrUn 87.293 181 15 6 2101 2273 321265564 321265384 1.450000e-47 200.0
26 TraesCS4B01G195800 chr3D 87.293 181 15 6 2101 2273 585618886 585618706 1.450000e-47 200.0
27 TraesCS4B01G195800 chr3D 87.293 181 15 6 2101 2273 585654406 585654226 1.450000e-47 200.0
28 TraesCS4B01G195800 chr3D 87.222 180 12 9 2102 2270 585467145 585467324 6.750000e-46 195.0


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 TraesCS4B01G195800 chr4B 422027794 422030186 2392 False 1030.500000 2721 97.692500 1 2393 4 chr4B.!!$F1 2392
1 TraesCS4B01G195800 chr4B 144338997 144340459 1462 True 2019.000000 2019 91.514000 1 1473 1 chr4B.!!$R1 1472
2 TraesCS4B01G195800 chr7D 7795916 7797387 1471 False 2071.000000 2071 92.068000 1 1473 1 chr7D.!!$F1 1472
3 TraesCS4B01G195800 chr3B 125892123 125893571 1448 False 1969.000000 1969 91.185000 22 1473 1 chr3B.!!$F1 1451
4 TraesCS4B01G195800 chr5B 237157387 237158852 1465 True 1890.000000 1890 89.939000 6 1473 1 chr5B.!!$R1 1467
5 TraesCS4B01G195800 chr7B 460570446 460571901 1455 False 1853.000000 1853 89.643000 3 1459 1 chr7B.!!$F1 1456
6 TraesCS4B01G195800 chr6B 68900877 68902333 1456 False 1840.000000 1840 89.459000 12 1470 1 chr6B.!!$F1 1458
7 TraesCS4B01G195800 chr6B 507580368 507581827 1459 True 1718.000000 1718 87.910000 12 1473 1 chr6B.!!$R1 1461
8 TraesCS4B01G195800 chr1B 3693729 3695188 1459 False 1820.000000 1820 89.154000 3 1467 1 chr1B.!!$F1 1464
9 TraesCS4B01G195800 chr7A 270771077 270772543 1466 False 1803.000000 1803 88.851000 5 1473 1 chr7A.!!$F1 1468
10 TraesCS4B01G195800 chr4A 127280411 127281140 729 False 300.333333 566 90.203667 1746 2393 3 chr4A.!!$F1 647
11 TraesCS4B01G195800 chr4A 127487487 127489580 2093 True 286.275000 547 94.373750 1746 2393 4 chr4A.!!$R1 647

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
891 896 0.620556 ACTCCTCCATTGTTGCGGAT 59.379 50.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 1917 1.065126 AGAGTGTAGCAGCCCATTTCC 60.065 52.381 0.0 0.0 0.0 3.13 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
276 279 5.867716 TCCTAAGTCAATCGTAGCAAAACTC 59.132 40.000 0.00 0.00 0.00 3.01
285 288 2.264813 GTAGCAAAACTCGACGCCATA 58.735 47.619 0.00 0.00 0.00 2.74
373 376 1.741145 ACGTTTGCAAACCGAAAGACT 59.259 42.857 31.14 10.58 35.51 3.24
552 555 7.394359 TCCTTCCTCTGGAAAATTATCAACAAG 59.606 37.037 0.53 0.00 41.54 3.16
603 606 3.281158 TGTGATCACATACAATGGCCTG 58.719 45.455 24.56 0.00 36.21 4.85
681 685 1.417890 CCCAACCTTCACTCACACTCT 59.582 52.381 0.00 0.00 0.00 3.24
727 732 3.727726 ACAGTTTGGCAAAATGGCTTAC 58.272 40.909 34.65 14.42 44.10 2.34
796 801 2.360553 TTGTGTGTTGTTGCTGTTGG 57.639 45.000 0.00 0.00 0.00 3.77
817 822 1.707427 AGGATTTTCAGCAGGTGGACT 59.293 47.619 0.00 0.00 0.00 3.85
888 893 1.656652 CCTACTCCTCCATTGTTGCG 58.343 55.000 0.00 0.00 0.00 4.85
891 896 0.620556 ACTCCTCCATTGTTGCGGAT 59.379 50.000 0.00 0.00 0.00 4.18
899 904 1.665169 CATTGTTGCGGATGATCACGA 59.335 47.619 9.68 0.00 0.00 4.35
923 928 3.248024 ACCCTCACCATGACTTTGTCTA 58.752 45.455 0.00 0.00 33.15 2.59
936 941 2.634639 TTGTCTAGGCCTCCAAGGTA 57.365 50.000 9.68 0.00 37.80 3.08
1023 1028 3.253230 GTTTCACAAGCATATTGCCCAC 58.747 45.455 0.00 0.00 46.52 4.61
1101 1106 0.386476 ACTGTTCCTACGCGACACAA 59.614 50.000 15.93 0.00 0.00 3.33
1224 1230 1.241165 TGACTGTTGCATGGAAGCTG 58.759 50.000 0.00 2.80 34.99 4.24
1274 1280 1.348064 AACGAGGATCACTCCCACAA 58.652 50.000 0.00 0.00 43.21 3.33
1275 1281 0.608640 ACGAGGATCACTCCCACAAC 59.391 55.000 0.00 0.00 43.21 3.32
1320 1326 4.411013 CAGATTTCTCCCTCTGGGTTTTT 58.589 43.478 2.25 0.00 44.74 1.94
1385 1391 4.878397 GCTTAATTTCCTCTCTGCTGCTAA 59.122 41.667 0.00 0.00 0.00 3.09
1399 1407 3.325230 CTGCTAATCACTAAAAGCGGC 57.675 47.619 0.00 0.00 37.80 6.53
1834 1846 7.748847 TCAAAGAGAATTAAACCTACGCATTC 58.251 34.615 0.00 0.00 0.00 2.67
1854 1866 1.847999 CGGCTTGCATAAAATTGCTCG 59.152 47.619 0.00 0.00 43.18 5.03
1857 1869 2.878580 CTTGCATAAAATTGCTCGGCA 58.121 42.857 0.00 0.00 43.18 5.69
1905 1917 3.884169 TCAAAAAGCAAACGATTCTCCG 58.116 40.909 0.00 0.00 0.00 4.63
1922 1934 1.376609 CCGGAAATGGGCTGCTACAC 61.377 60.000 0.00 0.00 0.00 2.90
1924 1936 1.383523 GGAAATGGGCTGCTACACTC 58.616 55.000 0.00 0.75 0.00 3.51
2098 2215 8.560374 AGAAAACGGTTCACAAAAATTCAAAAA 58.440 25.926 0.00 0.00 0.00 1.94
2239 3794 3.602390 AAACGAAGATGAAACACACCG 57.398 42.857 0.00 0.00 0.00 4.94
2252 3810 2.419667 ACACACCGCCTATTTACACAC 58.580 47.619 0.00 0.00 0.00 3.82
2285 3843 4.391405 TCATCGCTGACAGTCATATGTT 57.609 40.909 2.97 0.00 32.25 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.059942 GCTATGTTGTTTTGCGTGGC 58.940 50.000 0.00 0.00 0.00 5.01
276 279 4.944372 GCCCTCCGTATGGCGTCG 62.944 72.222 0.00 0.00 38.00 5.12
373 376 4.919774 TTTTAATGCCTAGACCACCAGA 57.080 40.909 0.00 0.00 0.00 3.86
552 555 1.881973 TCAATGAGCAGTGGCAAGTTC 59.118 47.619 0.00 0.00 44.61 3.01
621 625 2.159841 CGACTGTAACAGCCATTTGTCG 60.160 50.000 0.00 0.00 39.61 4.35
681 685 4.651778 CCACTAGAACCTTGTCATCCAAA 58.348 43.478 0.00 0.00 31.20 3.28
796 801 2.087646 GTCCACCTGCTGAAAATCCTC 58.912 52.381 0.00 0.00 0.00 3.71
834 839 2.352422 GGCAGCCCATGTGTGAGA 59.648 61.111 0.00 0.00 0.00 3.27
888 893 0.030908 GAGGGTCGTCGTGATCATCC 59.969 60.000 0.00 0.00 32.32 3.51
891 896 1.592400 GGTGAGGGTCGTCGTGATCA 61.592 60.000 0.00 0.00 0.00 2.92
899 904 1.056660 AAAGTCATGGTGAGGGTCGT 58.943 50.000 0.00 0.00 0.00 4.34
923 928 1.003051 ATCGGTACCTTGGAGGCCT 59.997 57.895 3.86 3.86 39.63 5.19
936 941 3.429547 CGAAGATCTTGACCTTGATCGGT 60.430 47.826 14.00 0.00 42.62 4.69
1023 1028 3.114616 CGTGGACAAGCAGCCGAG 61.115 66.667 0.00 0.00 0.00 4.63
1101 1106 0.771755 GACCCAAGGAGGACCAAACT 59.228 55.000 0.00 0.00 41.22 2.66
1204 1209 1.610038 CAGCTTCCATGCAACAGTCAA 59.390 47.619 0.00 0.00 34.99 3.18
1224 1230 0.733223 GAGCGTTTCTCGAGTCCCAC 60.733 60.000 13.13 4.35 42.86 4.61
1246 1252 5.221541 GGGAGTGATCCTCGTTTCTGAATAT 60.222 44.000 0.00 0.00 41.46 1.28
1320 1326 5.630661 TGTCTTCTTTGTTTTTGAACCGA 57.369 34.783 0.00 0.00 0.00 4.69
1385 1391 2.504367 ACAACAGCCGCTTTTAGTGAT 58.496 42.857 0.00 0.00 0.00 3.06
1399 1407 6.903883 ACAACAGTAGTTCAGTTACAACAG 57.096 37.500 0.00 0.00 35.28 3.16
1749 1760 3.806949 TCCTACTGGTTTGGCTCAAAT 57.193 42.857 4.07 0.00 35.74 2.32
1758 1769 5.333566 TGGGAAGAAATTCCTACTGGTTT 57.666 39.130 6.95 0.00 40.90 3.27
1823 1835 2.796483 TGCAAGCCGAATGCGTAGGT 62.796 55.000 0.00 0.00 46.76 3.08
1854 1866 3.515330 ATCAAGCAAGCTAAATGTGCC 57.485 42.857 3.72 0.00 39.13 5.01
1857 1869 3.441572 AGCGAATCAAGCAAGCTAAATGT 59.558 39.130 0.00 0.00 36.28 2.71
1905 1917 1.065126 AGAGTGTAGCAGCCCATTTCC 60.065 52.381 0.00 0.00 0.00 3.13
1922 1934 8.178313 GCTAAAAAGACTAGCAAAATACCAGAG 58.822 37.037 0.00 0.00 41.25 3.35
1924 1936 7.816640 TGCTAAAAAGACTAGCAAAATACCAG 58.183 34.615 2.15 0.00 46.69 4.00
1949 1962 3.886505 TGTACCTGAATTTTCCGCAAACT 59.113 39.130 0.00 0.00 0.00 2.66
2103 2220 4.993028 TGGTAAATAGGCTTGGTGAACTT 58.007 39.130 0.00 0.00 0.00 2.66
2104 2221 4.650972 TGGTAAATAGGCTTGGTGAACT 57.349 40.909 0.00 0.00 0.00 3.01
2239 3794 3.886123 AGTGATGGGTGTGTAAATAGGC 58.114 45.455 0.00 0.00 0.00 3.93
2252 3810 3.496130 GTCAGCGATGAATAAGTGATGGG 59.504 47.826 4.22 0.00 0.00 4.00
2285 3843 6.358974 TCTGGTTGAGTGATGAATAGTGAA 57.641 37.500 0.00 0.00 0.00 3.18
2348 3906 7.239763 TGTTCTGGTTGAGTGATGAATAGTA 57.760 36.000 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.