Multiple sequence alignment - TraesCS7D01G553600

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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 TraesCS7D01G553600 chr7D 100.000 3008 0 0 1 3008 636968414 636965407 0.000000e+00 5555.0
1 TraesCS7D01G553600 chr4A 95.726 3018 90 18 1 3008 236226264 236229252 0.000000e+00 4822.0
2 TraesCS7D01G553600 chr4A 91.571 522 39 4 434 951 561094309 561094829 0.000000e+00 715.0
3 TraesCS7D01G553600 chr4A 92.647 68 4 1 1620 1687 561094834 561094900 2.470000e-16 97.1
4 TraesCS7D01G553600 chr6A 94.895 2429 108 10 1 2427 443932324 443929910 0.000000e+00 3784.0
5 TraesCS7D01G553600 chr6A 93.048 561 26 8 2456 3008 443929913 443929358 0.000000e+00 808.0
6 TraesCS7D01G553600 chr3A 95.458 1277 49 7 357 1626 608075713 608076987 0.000000e+00 2028.0
7 TraesCS7D01G553600 chr3A 95.436 241 11 0 1807 2047 608076983 608077223 4.700000e-103 385.0
8 TraesCS7D01G553600 chr3A 92.683 246 17 1 1 246 608075476 608075720 1.330000e-93 353.0
9 TraesCS7D01G553600 chr3A 94.118 102 6 0 2189 2290 608077224 608077325 4.010000e-34 156.0
10 TraesCS7D01G553600 chr1B 90.990 899 53 10 61 956 206375673 206376546 0.000000e+00 1186.0
11 TraesCS7D01G553600 chr1B 91.247 457 28 6 2562 3008 206376668 206377122 1.980000e-171 612.0
12 TraesCS7D01G553600 chr1B 95.588 68 3 0 1620 1687 206376546 206376613 3.170000e-20 110.0
13 TraesCS7D01G553600 chr5B 87.356 957 62 10 1 956 166718401 166717503 0.000000e+00 1042.0
14 TraesCS7D01G553600 chr5B 86.938 957 66 16 1 956 166719048 166719946 0.000000e+00 1020.0
15 TraesCS7D01G553600 chr5B 86.450 952 69 15 1 951 161651469 161650577 0.000000e+00 989.0
16 TraesCS7D01G553600 chr5B 92.511 454 26 4 2562 3008 161650492 161650040 0.000000e+00 643.0
17 TraesCS7D01G553600 chr5B 92.511 454 26 4 2562 3008 166720026 166720478 0.000000e+00 643.0
18 TraesCS7D01G553600 chr5B 91.353 451 34 3 2562 3008 166717423 166716974 1.980000e-171 612.0
19 TraesCS7D01G553600 chr5B 97.059 68 2 0 1620 1687 161650572 161650505 6.810000e-22 115.0
20 TraesCS7D01G553600 chr5B 97.059 68 2 0 1620 1687 166717503 166717436 6.810000e-22 115.0
21 TraesCS7D01G553600 chr2D 88.106 681 44 9 956 1620 614849940 614850599 0.000000e+00 774.0
22 TraesCS7D01G553600 chr2D 92.000 525 39 3 434 956 68349984 68350507 0.000000e+00 734.0
23 TraesCS7D01G553600 chr2D 89.688 320 23 8 2562 2873 68350587 68350904 1.680000e-107 399.0
24 TraesCS7D01G553600 chr2D 92.647 68 5 0 1620 1687 68350507 68350574 6.860000e-17 99.0
25 TraesCS7D01G553600 chr2B 91.485 458 23 6 2565 3008 692734247 692733792 1.530000e-172 616.0
26 TraesCS7D01G553600 chr7A 92.840 405 21 4 1220 1621 68882301 68882700 5.590000e-162 580.0
27 TraesCS7D01G553600 chr7A 85.307 456 25 15 2562 3008 647721057 647720635 1.660000e-117 433.0
28 TraesCS7D01G553600 chr7B 91.811 403 22 5 1225 1621 6236255 6236652 4.380000e-153 551.0
29 TraesCS7D01G553600 chrUn 86.957 460 19 21 2562 3008 30885410 30885841 2.100000e-131 479.0
30 TraesCS7D01G553600 chr2A 85.934 455 31 16 2562 3008 424563911 424564340 3.530000e-124 455.0
31 TraesCS7D01G553600 chr2A 81.967 305 23 6 1686 1962 763967444 763967144 2.330000e-56 230.0
32 TraesCS7D01G553600 chr2A 80.216 278 27 12 2313 2563 763944647 763944371 1.840000e-42 183.0
33 TraesCS7D01G553600 chr2A 97.059 68 2 0 1620 1687 424563831 424563898 6.810000e-22 115.0
34 TraesCS7D01G553600 chr4D 93.289 149 10 0 1 149 285714676 285714528 1.400000e-53 220.0
35 TraesCS7D01G553600 chr4B 88.506 174 16 1 1 174 525748388 525748557 1.090000e-49 207.0
36 TraesCS7D01G553600 chr6D 95.522 67 3 0 1620 1686 211547822 211547756 1.140000e-19 108.0


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 TraesCS7D01G553600 chr7D 636965407 636968414 3007 True 5555.000000 5555 100.000000 1 3008 1 chr7D.!!$R1 3007
1 TraesCS7D01G553600 chr4A 236226264 236229252 2988 False 4822.000000 4822 95.726000 1 3008 1 chr4A.!!$F1 3007
2 TraesCS7D01G553600 chr4A 561094309 561094900 591 False 406.050000 715 92.109000 434 1687 2 chr4A.!!$F2 1253
3 TraesCS7D01G553600 chr6A 443929358 443932324 2966 True 2296.000000 3784 93.971500 1 3008 2 chr6A.!!$R1 3007
4 TraesCS7D01G553600 chr3A 608075476 608077325 1849 False 730.500000 2028 94.423750 1 2290 4 chr3A.!!$F1 2289
5 TraesCS7D01G553600 chr1B 206375673 206377122 1449 False 636.000000 1186 92.608333 61 3008 3 chr1B.!!$F1 2947
6 TraesCS7D01G553600 chr5B 166719048 166720478 1430 False 831.500000 1020 89.724500 1 3008 2 chr5B.!!$F1 3007
7 TraesCS7D01G553600 chr5B 166716974 166718401 1427 True 589.666667 1042 91.922667 1 3008 3 chr5B.!!$R2 3007
8 TraesCS7D01G553600 chr5B 161650040 161651469 1429 True 582.333333 989 92.006667 1 3008 3 chr5B.!!$R1 3007
9 TraesCS7D01G553600 chr2D 614849940 614850599 659 False 774.000000 774 88.106000 956 1620 1 chr2D.!!$F1 664
10 TraesCS7D01G553600 chr2D 68349984 68350904 920 False 410.666667 734 91.445000 434 2873 3 chr2D.!!$F2 2439
11 TraesCS7D01G553600 chr2A 424563831 424564340 509 False 285.000000 455 91.496500 1620 3008 2 chr2A.!!$F1 1388

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
951 1007 0.179032 TCCTGTTCACCAACGTGCAT 60.179 50.0 0.0 0.0 40.04 3.96 F
1592 1648 0.977395 AGCTCCTTACTTCGCTGGTT 59.023 50.0 0.0 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1986 2543 1.187087 AGCTTACTTCTGAGACCCGG 58.813 55.000 0.0 0.0 0.0 5.73 R
2423 2981 1.300620 CGTGAAGGCGTGAACTGGA 60.301 57.895 0.0 0.0 0.0 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
68 69 3.161450 GTGCCTCCCATCGCCCTA 61.161 66.667 0.00 0.00 0.00 3.53
179 180 2.357034 ACGGCACAACCAGCTACG 60.357 61.111 0.00 0.00 39.03 3.51
304 355 3.829048 TCCGACGAGGAGCATCTC 58.171 61.111 0.00 0.00 45.98 2.75
309 360 0.753479 GACGAGGAGCATCTCAGGGA 60.753 60.000 0.00 0.00 33.59 4.20
322 373 2.241430 TCTCAGGGACGAGGAACATCTA 59.759 50.000 0.00 0.00 33.59 1.98
851 907 1.227853 GTTGTTGACCTCGTGGCCT 60.228 57.895 3.32 0.00 36.63 5.19
890 946 3.349006 GTGTGTGGACTGCAGCGG 61.349 66.667 15.27 0.00 0.00 5.52
951 1007 0.179032 TCCTGTTCACCAACGTGCAT 60.179 50.000 0.00 0.00 40.04 3.96
1016 1072 4.790810 CATCGATGGATGTCTTGTCAAG 57.209 45.455 17.96 6.21 44.12 3.02
1067 1123 1.817099 GGAGCATCGCAACCTCTGG 60.817 63.158 0.00 0.00 34.37 3.86
1172 1228 8.827177 TTGAACCTGTTAGACATTACTTACAG 57.173 34.615 0.00 0.00 43.01 2.74
1282 1338 5.305585 TCTCGCTGGTTCTAACAATCTTTT 58.694 37.500 0.00 0.00 0.00 2.27
1359 1415 6.677781 ACTTTCTCAACGACAAGATGAAAA 57.322 33.333 0.00 0.00 31.05 2.29
1520 1576 3.031736 GAGTGGCTGGATAGTAGGTTCA 58.968 50.000 0.00 0.00 0.00 3.18
1592 1648 0.977395 AGCTCCTTACTTCGCTGGTT 59.023 50.000 0.00 0.00 0.00 3.67
1992 2549 3.942748 TGCACTTTTATTATGACCGGGTC 59.057 43.478 20.36 20.36 0.00 4.46
2082 2640 6.664384 AGGTTCAGAAGTAAGGAAGTACTAGG 59.336 42.308 0.00 0.00 33.05 3.02
2285 2843 2.272678 TCGTCTGTTGTTTCTTTCGCA 58.727 42.857 0.00 0.00 0.00 5.10
2424 2982 3.764237 TCCACTTGGGAGTTAACAGTC 57.236 47.619 8.61 0.00 42.15 3.51
2425 2983 2.370849 TCCACTTGGGAGTTAACAGTCC 59.629 50.000 8.61 6.86 42.15 3.85
2426 2984 2.105821 CCACTTGGGAGTTAACAGTCCA 59.894 50.000 14.08 11.78 43.84 4.02
2427 2985 3.403038 CACTTGGGAGTTAACAGTCCAG 58.597 50.000 14.08 7.61 43.84 3.86
2428 2986 3.046374 ACTTGGGAGTTAACAGTCCAGT 58.954 45.455 14.08 8.12 43.84 4.00
2429 2987 3.458487 ACTTGGGAGTTAACAGTCCAGTT 59.542 43.478 14.08 4.65 43.84 3.16
2430 2988 3.764237 TGGGAGTTAACAGTCCAGTTC 57.236 47.619 14.08 0.00 43.84 3.01
2431 2989 3.042682 TGGGAGTTAACAGTCCAGTTCA 58.957 45.455 14.08 2.52 43.84 3.18
2443 3001 1.594293 CAGTTCACGCCTTCACGGT 60.594 57.895 0.00 0.00 37.37 4.83
2713 3291 1.657822 TGTTGTGCGTGTGTGTGTAT 58.342 45.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
304 355 1.409427 GGTAGATGTTCCTCGTCCCTG 59.591 57.143 0.00 0.00 32.85 4.45
309 360 2.100989 GAGGTGGTAGATGTTCCTCGT 58.899 52.381 0.00 0.00 35.94 4.18
322 373 1.306226 GCACTAGGGAGGAGGTGGT 60.306 63.158 0.00 0.00 0.00 4.16
851 907 2.933906 GACAATAATCTCGGCCGTTTGA 59.066 45.455 27.15 21.17 0.00 2.69
890 946 0.245539 TGAAGGTCGGATTCGGTCAC 59.754 55.000 0.00 0.00 36.95 3.67
1016 1072 1.202359 AGCCGAAGAGAGCGAATCTTC 60.202 52.381 14.81 14.81 46.02 2.87
1067 1123 0.816373 GAAGGTAGGTCCGGTCTCAC 59.184 60.000 0.00 0.00 41.99 3.51
1172 1228 7.024171 GCAAGAGAAATAAACAAGTCTTAGGC 58.976 38.462 0.00 0.00 0.00 3.93
1282 1338 7.307278 GCTGCAACACAAAATCATCAATGTTAA 60.307 33.333 0.00 0.00 0.00 2.01
1359 1415 2.597510 GACGCCCTGCCAAGGTTT 60.598 61.111 0.00 0.00 42.74 3.27
1592 1648 9.868277 CAACCCAAGAATAAAAATACATAAGCA 57.132 29.630 0.00 0.00 0.00 3.91
1986 2543 1.187087 AGCTTACTTCTGAGACCCGG 58.813 55.000 0.00 0.00 0.00 5.73
1992 2549 8.352942 ACCAAATTGTTTTAGCTTACTTCTGAG 58.647 33.333 0.00 0.00 0.00 3.35
2410 2968 3.042682 TGAACTGGACTGTTAACTCCCA 58.957 45.455 7.22 9.97 0.00 4.37
2423 2981 1.300620 CGTGAAGGCGTGAACTGGA 60.301 57.895 0.00 0.00 0.00 3.86
2424 2982 2.317609 CCGTGAAGGCGTGAACTGG 61.318 63.158 0.00 0.00 0.00 4.00
2425 2983 1.594293 ACCGTGAAGGCGTGAACTG 60.594 57.895 0.00 0.00 46.52 3.16
2426 2984 1.594293 CACCGTGAAGGCGTGAACT 60.594 57.895 0.00 0.00 46.52 3.01
2427 2985 1.885850 ACACCGTGAAGGCGTGAAC 60.886 57.895 5.28 0.00 46.52 3.18
2428 2986 2.502093 ACACCGTGAAGGCGTGAA 59.498 55.556 5.28 0.00 46.52 3.18
2431 2989 3.750373 AAGCACACCGTGAAGGCGT 62.750 57.895 5.28 1.69 46.52 5.68
2443 3001 1.699083 TGGATTGGAGTCTGAAGCACA 59.301 47.619 0.00 0.00 0.00 4.57
2747 3325 8.783833 TTTTCTATGTTCTTTCTCTGATCTGG 57.216 34.615 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.