Multiple sequence alignment - TraesCS4B01G063500

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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 TraesCS4B01G063500 chr4B 100.000 2426 0 0 1 2426 55711390 55708965 0.000000e+00 4481.0
1 TraesCS4B01G063500 chr4B 86.819 789 103 1 1157 1944 550506150 550505362 0.000000e+00 880.0
2 TraesCS4B01G063500 chr4B 80.705 482 85 6 1199 1678 93618947 93618472 3.810000e-98 368.0
3 TraesCS4B01G063500 chr7B 93.766 1572 92 5 858 2426 498587114 498588682 0.000000e+00 2355.0
4 TraesCS4B01G063500 chr7B 84.691 405 52 5 348 744 621555147 621554745 1.750000e-106 396.0
5 TraesCS4B01G063500 chr3A 93.448 1572 96 6 858 2426 710609645 710611212 0.000000e+00 2326.0
6 TraesCS4B01G063500 chr5A 92.018 1541 120 3 886 2426 604240660 604239123 0.000000e+00 2161.0
7 TraesCS4B01G063500 chr5A 95.482 819 34 3 39 856 637709697 637708881 0.000000e+00 1304.0
8 TraesCS4B01G063500 chr5A 95.443 812 35 2 45 856 663342521 663341712 0.000000e+00 1293.0
9 TraesCS4B01G063500 chr4A 92.794 1249 90 0 1178 2426 131990321 131991569 0.000000e+00 1808.0
10 TraesCS4B01G063500 chr4A 85.319 831 76 18 45 856 702428972 702428169 0.000000e+00 817.0
11 TraesCS4B01G063500 chr4A 92.790 319 23 0 2057 2375 239585766 239585448 1.700000e-126 462.0
12 TraesCS4B01G063500 chr4A 89.286 84 8 1 773 856 76379739 76379657 1.190000e-18 104.0
13 TraesCS4B01G063500 chr1A 87.759 1544 183 5 888 2426 486756055 486757597 0.000000e+00 1799.0
14 TraesCS4B01G063500 chr1A 88.095 84 10 0 773 856 54006191 54006108 1.530000e-17 100.0
15 TraesCS4B01G063500 chr1A 88.095 84 9 1 773 856 109424088 109424006 5.520000e-17 99.0
16 TraesCS4B01G063500 chr6B 86.087 1495 206 2 878 2371 281621747 281623240 0.000000e+00 1607.0
17 TraesCS4B01G063500 chr7A 95.861 604 23 2 251 854 682173383 682173984 0.000000e+00 976.0
18 TraesCS4B01G063500 chr7A 90.224 624 60 1 1149 1772 672883282 672882660 0.000000e+00 813.0
19 TraesCS4B01G063500 chr7A 94.800 250 13 0 2175 2424 672882666 672882417 8.130000e-105 390.0
20 TraesCS4B01G063500 chr7A 90.503 179 16 1 881 1058 672883625 672883447 4.030000e-58 235.0
21 TraesCS4B01G063500 chr7A 95.455 110 5 0 45 154 682173278 682173387 2.480000e-40 176.0
22 TraesCS4B01G063500 chr7A 70.056 531 140 17 1757 2278 435830859 435831379 5.560000e-12 82.4
23 TraesCS4B01G063500 chr7A 70.588 391 99 14 1758 2140 78126814 78127196 1.200000e-08 71.3
24 TraesCS4B01G063500 chr5D 86.506 830 93 11 45 856 549426182 549425354 0.000000e+00 894.0
25 TraesCS4B01G063500 chr3B 86.923 650 69 11 218 856 255704127 255704771 0.000000e+00 715.0
26 TraesCS4B01G063500 chr2B 88.376 542 63 0 1885 2426 96219012 96219553 0.000000e+00 652.0


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 TraesCS4B01G063500 chr4B 55708965 55711390 2425 True 4481.000000 4481 100.000000 1 2426 1 chr4B.!!$R1 2425
1 TraesCS4B01G063500 chr4B 550505362 550506150 788 True 880.000000 880 86.819000 1157 1944 1 chr4B.!!$R3 787
2 TraesCS4B01G063500 chr7B 498587114 498588682 1568 False 2355.000000 2355 93.766000 858 2426 1 chr7B.!!$F1 1568
3 TraesCS4B01G063500 chr3A 710609645 710611212 1567 False 2326.000000 2326 93.448000 858 2426 1 chr3A.!!$F1 1568
4 TraesCS4B01G063500 chr5A 604239123 604240660 1537 True 2161.000000 2161 92.018000 886 2426 1 chr5A.!!$R1 1540
5 TraesCS4B01G063500 chr5A 637708881 637709697 816 True 1304.000000 1304 95.482000 39 856 1 chr5A.!!$R2 817
6 TraesCS4B01G063500 chr5A 663341712 663342521 809 True 1293.000000 1293 95.443000 45 856 1 chr5A.!!$R3 811
7 TraesCS4B01G063500 chr4A 131990321 131991569 1248 False 1808.000000 1808 92.794000 1178 2426 1 chr4A.!!$F1 1248
8 TraesCS4B01G063500 chr4A 702428169 702428972 803 True 817.000000 817 85.319000 45 856 1 chr4A.!!$R3 811
9 TraesCS4B01G063500 chr1A 486756055 486757597 1542 False 1799.000000 1799 87.759000 888 2426 1 chr1A.!!$F1 1538
10 TraesCS4B01G063500 chr6B 281621747 281623240 1493 False 1607.000000 1607 86.087000 878 2371 1 chr6B.!!$F1 1493
11 TraesCS4B01G063500 chr7A 682173278 682173984 706 False 576.000000 976 95.658000 45 854 2 chr7A.!!$F3 809
12 TraesCS4B01G063500 chr7A 672882417 672883625 1208 True 479.333333 813 91.842333 881 2424 3 chr7A.!!$R1 1543
13 TraesCS4B01G063500 chr5D 549425354 549426182 828 True 894.000000 894 86.506000 45 856 1 chr5D.!!$R1 811
14 TraesCS4B01G063500 chr3B 255704127 255704771 644 False 715.000000 715 86.923000 218 856 1 chr3B.!!$F1 638
15 TraesCS4B01G063500 chr2B 96219012 96219553 541 False 652.000000 652 88.376000 1885 2426 1 chr2B.!!$F1 541

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
867 1008 0.106708 GAGATTGCGGCACCCATCTA 59.893 55.0 13.95 0.0 0.0 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2155 2373 1.303236 CAATGGCCGACCTGAACCA 60.303 57.895 0.0 0.0 36.63 3.67 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
23 24 6.031549 CTTTACAAAACGCTTTCCCTTTTG 57.968 37.500 4.23 4.23 39.66 2.44
24 25 3.603158 ACAAAACGCTTTCCCTTTTGT 57.397 38.095 5.30 5.30 41.23 2.83
25 26 3.932822 ACAAAACGCTTTCCCTTTTGTT 58.067 36.364 5.30 0.00 42.65 2.83
26 27 5.074584 ACAAAACGCTTTCCCTTTTGTTA 57.925 34.783 5.30 0.00 42.65 2.41
27 28 4.865925 ACAAAACGCTTTCCCTTTTGTTAC 59.134 37.500 5.30 0.00 42.65 2.50
28 29 4.722361 AAACGCTTTCCCTTTTGTTACA 57.278 36.364 0.00 0.00 0.00 2.41
29 30 4.929819 AACGCTTTCCCTTTTGTTACAT 57.070 36.364 0.00 0.00 0.00 2.29
30 31 4.237349 ACGCTTTCCCTTTTGTTACATG 57.763 40.909 0.00 0.00 0.00 3.21
31 32 3.634910 ACGCTTTCCCTTTTGTTACATGT 59.365 39.130 2.69 2.69 0.00 3.21
32 33 4.098807 ACGCTTTCCCTTTTGTTACATGTT 59.901 37.500 2.30 0.00 0.00 2.71
33 34 5.047188 CGCTTTCCCTTTTGTTACATGTTT 58.953 37.500 2.30 0.00 0.00 2.83
34 35 5.522097 CGCTTTCCCTTTTGTTACATGTTTT 59.478 36.000 2.30 0.00 0.00 2.43
35 36 6.697892 CGCTTTCCCTTTTGTTACATGTTTTA 59.302 34.615 2.30 0.00 0.00 1.52
36 37 7.096230 CGCTTTCCCTTTTGTTACATGTTTTAG 60.096 37.037 2.30 0.00 0.00 1.85
37 38 7.709182 GCTTTCCCTTTTGTTACATGTTTTAGT 59.291 33.333 2.30 0.00 0.00 2.24
38 39 9.594478 CTTTCCCTTTTGTTACATGTTTTAGTT 57.406 29.630 2.30 0.00 0.00 2.24
48 49 8.822855 TGTTACATGTTTTAGTTATATGCTCGG 58.177 33.333 2.30 0.00 0.00 4.63
73 74 5.117584 TGCAAGCTTTCATTTGTTTGATGT 58.882 33.333 0.00 0.00 0.00 3.06
129 130 5.376854 ACATGGTGTGTAAGCTTTTGATC 57.623 39.130 3.20 0.00 39.91 2.92
139 140 6.979238 GTGTAAGCTTTTGATCGACCTATAGT 59.021 38.462 3.20 0.00 0.00 2.12
339 447 6.061441 TGTTGAAATCAAACTAGGAAGCAGA 58.939 36.000 0.00 0.00 37.63 4.26
430 544 0.382515 TTGTGCCCACTTAACGTTGC 59.617 50.000 11.99 4.98 0.00 4.17
447 561 2.680339 GTTGCCAGCTAGATCCTTTGTC 59.320 50.000 0.00 0.00 0.00 3.18
517 631 2.349590 TGCCGAGTGATGTTGAATCAG 58.650 47.619 0.00 0.00 0.00 2.90
562 677 3.565482 CCGATTGGTGATCCCATTGTAAG 59.435 47.826 4.04 0.00 44.74 2.34
667 789 4.500716 GGAAGGAGAGAGTACATAGCAAGC 60.501 50.000 0.00 0.00 0.00 4.01
669 791 2.287909 GGAGAGAGTACATAGCAAGCCG 60.288 54.545 0.00 0.00 0.00 5.52
843 984 1.961277 GCTGACAACGGTGAGGTGG 60.961 63.158 7.88 0.00 43.31 4.61
856 997 1.303309 GAGGTGGATTGGAGATTGCG 58.697 55.000 0.00 0.00 0.00 4.85
867 1008 0.106708 GAGATTGCGGCACCCATCTA 59.893 55.000 13.95 0.00 0.00 1.98
876 1017 1.359117 CACCCATCTACGCGACGAT 59.641 57.895 15.93 11.29 0.00 3.73
882 1023 3.323136 CTACGCGACGATGCAGCC 61.323 66.667 15.93 0.00 34.15 4.85
936 1077 4.660938 GCGGTCACCCCCTTTGCT 62.661 66.667 0.00 0.00 0.00 3.91
1084 1225 3.429372 TTCCGCAGCAACACCCCTT 62.429 57.895 0.00 0.00 0.00 3.95
1085 1226 2.912025 CCGCAGCAACACCCCTTT 60.912 61.111 0.00 0.00 0.00 3.11
1099 1240 3.688159 CTTTGCTGGTGGCTGCCC 61.688 66.667 17.53 7.43 42.39 5.36
1272 1487 1.835494 AGGAGAAGATGACGACCGAA 58.165 50.000 0.00 0.00 0.00 4.30
1341 1556 0.678395 ACATTGCGGTCATTGCCAAA 59.322 45.000 0.00 0.00 0.00 3.28
1502 1717 6.113411 GCTAGAGTTAGGTTTGCTTCCAATA 58.887 40.000 0.00 0.00 0.00 1.90
1566 1781 2.590092 GGCCTATTGGTGGTCGCT 59.410 61.111 0.00 0.00 35.27 4.93
1627 1842 4.952335 CCTGAGGCCATTTAGTGATTTTCT 59.048 41.667 5.01 0.00 0.00 2.52
1845 2063 1.744368 CTCGCTGACTGGCTGCATT 60.744 57.895 13.01 0.00 41.07 3.56
2103 2321 6.601613 TGATCAATGGCGACTTTAACCTAATT 59.398 34.615 0.00 0.00 0.00 1.40
2145 2363 3.642848 ACAACCTCAACCTTAACCGTAGA 59.357 43.478 0.00 0.00 0.00 2.59
2155 2373 4.779489 ACCTTAACCGTAGACTTATGGGTT 59.221 41.667 0.00 0.00 39.82 4.11
2255 2473 2.061848 TCAAGATCCCACCCTTGTCAA 58.938 47.619 0.00 0.00 40.32 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.031549 CAAAAGGGAAAGCGTTTTGTAAAG 57.968 37.500 0.59 0.00 36.72 1.85
4 5 3.603158 ACAAAAGGGAAAGCGTTTTGT 57.397 38.095 0.59 1.95 45.24 2.83
7 8 4.722361 TGTAACAAAAGGGAAAGCGTTT 57.278 36.364 0.00 0.00 0.00 3.60
8 9 4.098807 ACATGTAACAAAAGGGAAAGCGTT 59.901 37.500 0.00 0.00 0.00 4.84
9 10 3.634910 ACATGTAACAAAAGGGAAAGCGT 59.365 39.130 0.00 0.00 0.00 5.07
10 11 4.237349 ACATGTAACAAAAGGGAAAGCG 57.763 40.909 0.00 0.00 0.00 4.68
11 12 6.918892 AAAACATGTAACAAAAGGGAAAGC 57.081 33.333 0.00 0.00 0.00 3.51
12 13 9.594478 AACTAAAACATGTAACAAAAGGGAAAG 57.406 29.630 0.00 0.00 0.00 2.62
22 23 8.822855 CCGAGCATATAACTAAAACATGTAACA 58.177 33.333 0.00 0.00 0.00 2.41
23 24 7.797123 GCCGAGCATATAACTAAAACATGTAAC 59.203 37.037 0.00 0.00 0.00 2.50
24 25 7.713507 AGCCGAGCATATAACTAAAACATGTAA 59.286 33.333 0.00 0.00 0.00 2.41
25 26 7.170828 CAGCCGAGCATATAACTAAAACATGTA 59.829 37.037 0.00 0.00 0.00 2.29
26 27 6.017934 CAGCCGAGCATATAACTAAAACATGT 60.018 38.462 0.00 0.00 0.00 3.21
27 28 6.365839 CAGCCGAGCATATAACTAAAACATG 58.634 40.000 0.00 0.00 0.00 3.21
28 29 5.049405 GCAGCCGAGCATATAACTAAAACAT 60.049 40.000 0.00 0.00 0.00 2.71
29 30 4.272504 GCAGCCGAGCATATAACTAAAACA 59.727 41.667 0.00 0.00 0.00 2.83
30 31 4.272504 TGCAGCCGAGCATATAACTAAAAC 59.727 41.667 0.00 0.00 40.11 2.43
31 32 4.447290 TGCAGCCGAGCATATAACTAAAA 58.553 39.130 0.00 0.00 40.11 1.52
32 33 4.066646 TGCAGCCGAGCATATAACTAAA 57.933 40.909 0.00 0.00 40.11 1.85
33 34 3.744238 TGCAGCCGAGCATATAACTAA 57.256 42.857 0.00 0.00 40.11 2.24
34 35 3.653344 CTTGCAGCCGAGCATATAACTA 58.347 45.455 0.00 0.00 45.19 2.24
35 36 2.487934 CTTGCAGCCGAGCATATAACT 58.512 47.619 0.00 0.00 45.19 2.24
36 37 1.069636 GCTTGCAGCCGAGCATATAAC 60.070 52.381 11.86 0.00 45.99 1.89
37 38 1.229428 GCTTGCAGCCGAGCATATAA 58.771 50.000 11.86 0.00 45.99 0.98
38 39 2.918571 GCTTGCAGCCGAGCATATA 58.081 52.632 11.86 0.00 45.99 0.86
39 40 3.741860 GCTTGCAGCCGAGCATAT 58.258 55.556 11.86 0.00 45.99 1.78
43 44 1.930908 ATGAAAGCTTGCAGCCGAGC 61.931 55.000 13.80 9.32 46.90 5.03
48 49 3.556775 TCAAACAAATGAAAGCTTGCAGC 59.443 39.130 13.80 0.00 42.84 5.25
129 130 4.519730 AGGCAAGCTAACTACTATAGGTCG 59.480 45.833 4.43 0.00 31.12 4.79
139 140 8.100791 TCAAATAGAAAGAAGGCAAGCTAACTA 58.899 33.333 0.00 0.00 0.00 2.24
339 447 6.207417 CACAGGAAACAATAATCAACCTGACT 59.793 38.462 15.59 0.00 43.91 3.41
430 544 3.853355 ATGGACAAAGGATCTAGCTGG 57.147 47.619 0.00 0.00 0.00 4.85
481 595 0.175531 GGCAACATAATGGGTGTGGC 59.824 55.000 0.00 0.00 44.10 5.01
667 789 2.423446 GTCCTCTATGCCCTGCGG 59.577 66.667 0.00 0.00 0.00 5.69
669 791 2.280457 GCGTCCTCTATGCCCTGC 60.280 66.667 0.00 0.00 33.68 4.85
677 799 1.684450 TGTGACACTTTGCGTCCTCTA 59.316 47.619 7.20 0.00 32.15 2.43
715 837 0.868406 CTTGCTTGGGTCGACTGTTC 59.132 55.000 16.46 0.00 0.00 3.18
843 984 1.728490 GGGTGCCGCAATCTCCAATC 61.728 60.000 0.00 0.00 0.00 2.67
856 997 2.585247 GTCGCGTAGATGGGTGCC 60.585 66.667 5.77 0.00 0.00 5.01
923 1064 0.324275 GCCATTAGCAAAGGGGGTGA 60.324 55.000 0.00 0.00 42.97 4.02
924 1065 1.329913 GGCCATTAGCAAAGGGGGTG 61.330 60.000 0.00 0.00 46.50 4.61
936 1077 0.037590 AGCGGTTGAACTGGCCATTA 59.962 50.000 5.51 0.00 0.00 1.90
1000 1141 3.737172 GCAAACGCGGCTGGTCAT 61.737 61.111 12.47 0.00 0.00 3.06
1014 1155 1.297689 AGCGATCTCAAGCTGGCAA 59.702 52.632 0.00 0.00 42.82 4.52
1144 1288 2.046892 GTGGCGAGATGGTGCTGT 60.047 61.111 0.00 0.00 0.00 4.40
1145 1289 2.046988 TGTGGCGAGATGGTGCTG 60.047 61.111 0.00 0.00 0.00 4.41
1502 1717 3.519510 ACCACATTGGACTAGCACTACAT 59.480 43.478 0.00 0.00 40.96 2.29
1566 1781 1.902508 CTCTCTAGCAAGGGAACACCA 59.097 52.381 0.00 0.00 43.89 4.17
1627 1842 1.271379 ACTCGTGTTGCTCCGATAACA 59.729 47.619 0.00 0.00 34.66 2.41
1767 1985 3.026630 TCGATCTTCGTTTCTTGCAGT 57.973 42.857 0.00 0.00 41.35 4.40
2145 2363 2.290071 CGACCTGAACCAACCCATAAGT 60.290 50.000 0.00 0.00 0.00 2.24
2155 2373 1.303236 CAATGGCCGACCTGAACCA 60.303 57.895 0.00 0.00 36.63 3.67
2255 2473 4.202050 GGTTGCAGAAGAACTTGTCAATGT 60.202 41.667 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.