Multiple sequence alignment - TraesCS4D01G344900

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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 TraesCS4D01G344900 chr4D 100.000 3124 0 0 1 3124 499776854 499779977 0.000000e+00 5770
1 TraesCS4D01G344900 chr4D 91.477 1009 77 7 2120 3122 381098369 381097364 0.000000e+00 1378
2 TraesCS4D01G344900 chr4D 83.986 281 42 2 994 1274 499547326 499547049 1.850000e-67 267
3 TraesCS4D01G344900 chr6D 98.621 943 12 1 1 943 388633244 388632303 0.000000e+00 1668
4 TraesCS4D01G344900 chr6D 98.409 943 15 0 1 943 78512532 78513474 0.000000e+00 1659
5 TraesCS4D01G344900 chr6D 98.089 942 9 3 1 941 22154637 22155570 0.000000e+00 1631
6 TraesCS4D01G344900 chr6D 94.280 944 47 3 1 943 75868098 75867161 0.000000e+00 1437
7 TraesCS4D01G344900 chr6D 91.650 1006 75 7 2122 3122 139290594 139291595 0.000000e+00 1384
8 TraesCS4D01G344900 chr6D 91.434 1004 77 7 2124 3122 363868861 363867862 0.000000e+00 1369
9 TraesCS4D01G344900 chr7D 98.989 890 9 0 1 890 223108788 223109677 0.000000e+00 1594
10 TraesCS4D01G344900 chr7D 94.174 944 48 3 1 943 624775057 624775994 0.000000e+00 1432
11 TraesCS4D01G344900 chr2A 94.386 944 46 3 1 943 689755950 689756887 0.000000e+00 1443
12 TraesCS4D01G344900 chr5D 94.068 944 49 3 1 943 88170204 88169267 0.000000e+00 1426
13 TraesCS4D01G344900 chr5D 91.808 1001 71 7 2122 3119 431559409 431560401 0.000000e+00 1384
14 TraesCS4D01G344900 chr5D 85.906 298 36 6 994 1289 500646684 500646977 2.340000e-81 313
15 TraesCS4D01G344900 chr1D 93.962 944 50 3 1 943 11500560 11499623 0.000000e+00 1421
16 TraesCS4D01G344900 chr1D 90.457 1006 79 11 2122 3121 351507495 351508489 0.000000e+00 1310
17 TraesCS4D01G344900 chr2D 91.889 1011 71 6 2122 3122 127267995 127266986 0.000000e+00 1402
18 TraesCS4D01G344900 chr2D 90.448 1005 77 12 2127 3122 562893172 562894166 0.000000e+00 1306
19 TraesCS4D01G344900 chr5A 95.892 852 20 4 1276 2124 680742023 680742862 0.000000e+00 1365
20 TraesCS4D01G344900 chr5A 91.188 1010 77 10 2122 3122 311549050 311548044 0.000000e+00 1362
21 TraesCS4D01G344900 chr5A 90.149 1005 88 7 2122 3122 400669499 400670496 0.000000e+00 1297
22 TraesCS4D01G344900 chr5A 94.355 372 21 0 943 1314 680741622 680741993 3.500000e-159 571
23 TraesCS4D01G344900 chr5A 87.273 275 32 3 1009 1283 627014983 627015254 8.410000e-81 311
24 TraesCS4D01G344900 chr5A 84.321 287 41 3 995 1281 680512107 680511825 8.530000e-71 278
25 TraesCS4D01G344900 chr5A 75.676 592 105 25 1465 2026 680511581 680510999 3.090000e-65 259
26 TraesCS4D01G344900 chr5A 80.545 257 49 1 994 1249 680692382 680692126 2.460000e-46 196
27 TraesCS4D01G344900 chr4B 92.689 807 41 13 1323 2123 642958901 642959695 0.000000e+00 1147
28 TraesCS4D01G344900 chr4B 95.308 341 15 1 943 1283 642958568 642958907 9.860000e-150 540
29 TraesCS4D01G344900 chr4B 84.669 287 41 2 994 1280 642463198 642462915 1.830000e-72 283
30 TraesCS4D01G344900 chr4B 85.401 274 30 6 1009 1282 642537198 642536935 3.070000e-70 276
31 TraesCS4D01G344900 chr4B 80.163 368 60 8 1745 2105 642536153 642535792 2.390000e-66 263
32 TraesCS4D01G344900 chr4B 83.012 259 30 9 994 1249 642458726 642458479 4.060000e-54 222
33 TraesCS4D01G344900 chr5B 87.379 103 12 1 2005 2106 622063294 622063396 1.970000e-22 117


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 TraesCS4D01G344900 chr4D 499776854 499779977 3123 False 5770.0 5770 100.0000 1 3124 1 chr4D.!!$F1 3123
1 TraesCS4D01G344900 chr4D 381097364 381098369 1005 True 1378.0 1378 91.4770 2120 3122 1 chr4D.!!$R1 1002
2 TraesCS4D01G344900 chr6D 388632303 388633244 941 True 1668.0 1668 98.6210 1 943 1 chr6D.!!$R3 942
3 TraesCS4D01G344900 chr6D 78512532 78513474 942 False 1659.0 1659 98.4090 1 943 1 chr6D.!!$F2 942
4 TraesCS4D01G344900 chr6D 22154637 22155570 933 False 1631.0 1631 98.0890 1 941 1 chr6D.!!$F1 940
5 TraesCS4D01G344900 chr6D 75867161 75868098 937 True 1437.0 1437 94.2800 1 943 1 chr6D.!!$R1 942
6 TraesCS4D01G344900 chr6D 139290594 139291595 1001 False 1384.0 1384 91.6500 2122 3122 1 chr6D.!!$F3 1000
7 TraesCS4D01G344900 chr6D 363867862 363868861 999 True 1369.0 1369 91.4340 2124 3122 1 chr6D.!!$R2 998
8 TraesCS4D01G344900 chr7D 223108788 223109677 889 False 1594.0 1594 98.9890 1 890 1 chr7D.!!$F1 889
9 TraesCS4D01G344900 chr7D 624775057 624775994 937 False 1432.0 1432 94.1740 1 943 1 chr7D.!!$F2 942
10 TraesCS4D01G344900 chr2A 689755950 689756887 937 False 1443.0 1443 94.3860 1 943 1 chr2A.!!$F1 942
11 TraesCS4D01G344900 chr5D 88169267 88170204 937 True 1426.0 1426 94.0680 1 943 1 chr5D.!!$R1 942
12 TraesCS4D01G344900 chr5D 431559409 431560401 992 False 1384.0 1384 91.8080 2122 3119 1 chr5D.!!$F1 997
13 TraesCS4D01G344900 chr1D 11499623 11500560 937 True 1421.0 1421 93.9620 1 943 1 chr1D.!!$R1 942
14 TraesCS4D01G344900 chr1D 351507495 351508489 994 False 1310.0 1310 90.4570 2122 3121 1 chr1D.!!$F1 999
15 TraesCS4D01G344900 chr2D 127266986 127267995 1009 True 1402.0 1402 91.8890 2122 3122 1 chr2D.!!$R1 1000
16 TraesCS4D01G344900 chr2D 562893172 562894166 994 False 1306.0 1306 90.4480 2127 3122 1 chr2D.!!$F1 995
17 TraesCS4D01G344900 chr5A 311548044 311549050 1006 True 1362.0 1362 91.1880 2122 3122 1 chr5A.!!$R1 1000
18 TraesCS4D01G344900 chr5A 400669499 400670496 997 False 1297.0 1297 90.1490 2122 3122 1 chr5A.!!$F1 1000
19 TraesCS4D01G344900 chr5A 680741622 680742862 1240 False 968.0 1365 95.1235 943 2124 2 chr5A.!!$F3 1181
20 TraesCS4D01G344900 chr5A 680510999 680512107 1108 True 268.5 278 79.9985 995 2026 2 chr5A.!!$R3 1031
21 TraesCS4D01G344900 chr4B 642958568 642959695 1127 False 843.5 1147 93.9985 943 2123 2 chr4B.!!$F1 1180
22 TraesCS4D01G344900 chr4B 642535792 642537198 1406 True 269.5 276 82.7820 1009 2105 2 chr4B.!!$R3 1096

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
982 988 0.90891 TCGATTGGCAAAGGGCTAGA 59.091 50.0 3.01 0.0 44.01 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2214 2785 1.273455 CGAAAAACGGACGAGCGTCT 61.273 55.0 20.62 1.73 44.04 4.18 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
182 183 3.710722 CTCGGGGGCTGCTCAAGT 61.711 66.667 0.21 0.00 0.00 3.16
256 257 4.287781 TTCGAGGTTGCGGCGACA 62.288 61.111 21.24 5.31 33.33 4.35
547 549 2.581953 GCTCGCGCAAGAGGAGAG 60.582 66.667 8.75 4.91 40.53 3.20
964 970 5.629079 ACTTGCAGCTGTATTAAACCTTC 57.371 39.130 16.64 0.00 0.00 3.46
972 978 4.095782 GCTGTATTAAACCTTCGATTGGCA 59.904 41.667 5.06 0.00 0.00 4.92
982 988 0.908910 TCGATTGGCAAAGGGCTAGA 59.091 50.000 3.01 0.00 44.01 2.43
1023 1029 2.957006 GGGCATCATCAAGATCAAGCTT 59.043 45.455 0.00 0.00 33.72 3.74
1065 1071 1.811679 TGTGTTGTTCGCTGACGCA 60.812 52.632 0.00 0.00 39.84 5.24
1202 1208 1.537348 CGTCGACCACCTCAGAAACAA 60.537 52.381 10.58 0.00 0.00 2.83
1409 1594 3.123620 GCCAGGCTCTGCAAGTCG 61.124 66.667 3.29 0.00 33.62 4.18
1655 1873 2.649034 GTCGAAGTGAGCGTCCCA 59.351 61.111 0.00 0.00 0.00 4.37
1912 2481 4.410099 TCTGCAGGTTCAGAATGGAAAAT 58.590 39.130 15.13 0.00 39.89 1.82
1913 2482 5.569355 TCTGCAGGTTCAGAATGGAAAATA 58.431 37.500 15.13 0.00 39.89 1.40
1914 2483 6.009589 TCTGCAGGTTCAGAATGGAAAATAA 58.990 36.000 15.13 0.00 39.89 1.40
1915 2484 6.493115 TCTGCAGGTTCAGAATGGAAAATAAA 59.507 34.615 15.13 0.00 39.89 1.40
1916 2485 6.690530 TGCAGGTTCAGAATGGAAAATAAAG 58.309 36.000 0.00 0.00 36.16 1.85
1917 2486 6.101997 GCAGGTTCAGAATGGAAAATAAAGG 58.898 40.000 0.00 0.00 36.16 3.11
1918 2487 6.295292 GCAGGTTCAGAATGGAAAATAAAGGT 60.295 38.462 0.00 0.00 36.16 3.50
1998 2567 2.820059 TGAGTTTGTCGACATGCTCT 57.180 45.000 31.52 22.32 32.20 4.09
2107 2677 2.020720 AGAAGCGTCACTGATCTCGAT 58.979 47.619 1.61 0.00 0.00 3.59
2133 2703 2.944129 TGGGCACTTAAGAGCAACTTT 58.056 42.857 23.56 0.00 39.72 2.66
2190 2761 3.342627 CGGCGCGGACAAAAGTGA 61.343 61.111 9.72 0.00 0.00 3.41
2196 2767 1.444119 GCGGACAAAAGTGACAGCCA 61.444 55.000 0.00 0.00 35.35 4.75
2220 2791 2.030562 CCGACCCAAACAGACGCT 59.969 61.111 0.00 0.00 0.00 5.07
2277 2848 2.620242 CCAATTTTGAGCCGGATTTGG 58.380 47.619 5.05 5.49 0.00 3.28
2325 2898 3.121019 CGCCTACTCCTCTTCCCG 58.879 66.667 0.00 0.00 0.00 5.14
2328 2901 2.134933 CCTACTCCTCTTCCCGGGC 61.135 68.421 18.49 0.00 0.00 6.13
2361 2938 1.607467 GCAGCCACCACCATTTCCT 60.607 57.895 0.00 0.00 0.00 3.36
2369 2949 2.497273 CACCACCATTTCCTCCCATTTC 59.503 50.000 0.00 0.00 0.00 2.17
2386 2967 5.524535 CCATTTCCCCCAAAAATACTCCTA 58.475 41.667 0.00 0.00 0.00 2.94
2389 2970 3.822880 TCCCCCAAAAATACTCCTACCT 58.177 45.455 0.00 0.00 0.00 3.08
2421 3004 1.984026 CCCCCAACAAGCCATGGAC 60.984 63.158 18.40 7.03 39.12 4.02
2753 3358 4.681978 GTCCAAGCCACCGTCGCT 62.682 66.667 0.00 0.00 38.53 4.93
2847 3452 3.659089 ATCCCCGGCTTTCACGTCG 62.659 63.158 0.00 0.00 0.00 5.12
3122 3728 1.306642 CCGCTAGCTACGATCCCGAT 61.307 60.000 13.93 0.00 39.50 4.18
3123 3729 0.179187 CGCTAGCTACGATCCCGATG 60.179 60.000 13.93 0.00 39.50 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
182 183 4.631740 TCGCCACCTCCACCTCCA 62.632 66.667 0.00 0.00 0.00 3.86
547 549 2.393768 CCATGACGCCAGACAGCAC 61.394 63.158 0.00 0.00 0.00 4.40
588 590 3.636153 ATTGAGGCTTCTACCTTGTCC 57.364 47.619 0.00 0.00 41.32 4.02
925 931 6.144078 TGCAAGTTTTTAGAAAAGGAGGAC 57.856 37.500 0.00 0.00 0.00 3.85
964 970 1.750193 TTCTAGCCCTTTGCCAATCG 58.250 50.000 0.00 0.00 42.71 3.34
972 978 5.045578 TCAGCTTATCTGTTTCTAGCCCTTT 60.046 40.000 0.00 0.00 43.32 3.11
982 988 4.687219 GCCCATAGGTCAGCTTATCTGTTT 60.687 45.833 0.00 0.00 43.32 2.83
1369 1444 8.896744 TGGCAGTAGATCAAGAATAAGAATTTG 58.103 33.333 0.00 0.00 0.00 2.32
1409 1594 3.963428 AGGTCATTGGTACTGTCAGTC 57.037 47.619 9.26 1.42 0.00 3.51
1683 1902 6.481954 AATTGATTCCACTCTACAAACGAC 57.518 37.500 0.00 0.00 0.00 4.34
1912 2481 9.511272 GGTAAAAGACCTTTATCTTGACCTTTA 57.489 33.333 10.50 0.00 45.89 1.85
1913 2482 8.405418 GGTAAAAGACCTTTATCTTGACCTTT 57.595 34.615 10.50 0.00 45.89 3.11
1914 2483 7.997773 GGTAAAAGACCTTTATCTTGACCTT 57.002 36.000 10.50 0.00 45.89 3.50
1998 2567 5.659525 TGATAGGGTAAGTCAAGAATCCGAA 59.340 40.000 0.00 0.00 0.00 4.30
2107 2677 2.224744 TGCTCTTAAGTGCCCAACATCA 60.225 45.455 22.97 3.01 33.96 3.07
2154 2724 2.359354 CCCAAATGGACACGGCGA 60.359 61.111 16.62 0.00 37.39 5.54
2196 2767 3.956317 GTTTGGGTCGGCGCGTTT 61.956 61.111 8.43 0.00 0.00 3.60
2214 2785 1.273455 CGAAAAACGGACGAGCGTCT 61.273 55.000 20.62 1.73 44.04 4.18
2361 2938 4.358214 GAGTATTTTTGGGGGAAATGGGA 58.642 43.478 0.00 0.00 0.00 4.37
2369 2949 3.898482 CAGGTAGGAGTATTTTTGGGGG 58.102 50.000 0.00 0.00 0.00 5.40
2411 2994 3.329542 ATGGCGTCGTCCATGGCTT 62.330 57.895 16.96 0.00 44.72 4.35
2722 3327 4.008933 GGACGAGGCTGTGCTGGT 62.009 66.667 0.00 0.00 0.00 4.00
3060 3666 0.995024 AGGTTCTGCATGTAGCCCTT 59.005 50.000 13.57 0.00 44.83 3.95
3064 3670 3.191078 AGATGAGGTTCTGCATGTAGC 57.809 47.619 5.85 0.00 45.96 3.58


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

AutoCloner maintained by Alex Coulton.