Multiple sequence alignment - TraesCS4D01G229500

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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 TraesCS4D01G229500 chr4D 100.000 3211 0 0 1 3211 389453685 389450475 0 5930
1 TraesCS4D01G229500 chrUn 98.022 2325 46 0 1 2325 291535421 291537745 0 4039
2 TraesCS4D01G229500 chrUn 97.978 2325 46 1 1 2325 245706049 245708372 0 4032
3 TraesCS4D01G229500 chrUn 97.935 2325 48 0 1 2325 199874805 199877129 0 4028
4 TraesCS4D01G229500 chrUn 97.935 2325 48 0 1 2325 229310246 229307922 0 4028
5 TraesCS4D01G229500 chrUn 97.936 2326 47 1 1 2325 274341301 274338976 0 4028
6 TraesCS4D01G229500 chrUn 97.763 2325 52 0 1 2325 3845833 3843509 0 4006
7 TraesCS4D01G229500 chrUn 97.763 2325 52 0 1 2325 199904725 199907049 0 4006
8 TraesCS4D01G229500 chr1B 97.935 2325 46 1 1 2325 544593678 544596000 0 4026
9 TraesCS4D01G229500 chr5D 97.892 2325 49 0 1 2325 18998905 19001229 0 4023
10 TraesCS4D01G229500 chr6D 96.753 893 14 5 2334 3211 406409505 406408613 0 1474
11 TraesCS4D01G229500 chr3D 96.829 883 23 3 2334 3211 129178231 129179113 0 1471
12 TraesCS4D01G229500 chr1D 96.641 893 15 5 2334 3211 227545571 227546463 0 1469
13 TraesCS4D01G229500 chr1D 96.315 597 15 2 2334 2924 311116702 311116107 0 974
14 TraesCS4D01G229500 chr6A 95.986 872 29 6 2345 3211 160947318 160948188 0 1411
15 TraesCS4D01G229500 chr7B 95.449 879 35 4 2334 3211 329112826 329113700 0 1397
16 TraesCS4D01G229500 chr7A 95.136 884 36 5 2334 3211 392522152 392523034 0 1387
17 TraesCS4D01G229500 chr7A 89.932 884 66 9 2334 3211 297180194 297181060 0 1118
18 TraesCS4D01G229500 chr5A 94.767 879 44 2 2334 3211 343889838 343890715 0 1367
19 TraesCS4D01G229500 chr3A 94.337 883 45 3 2334 3211 519656798 519655916 0 1349
20 TraesCS4D01G229500 chr3A 93.446 885 51 5 2334 3211 122834130 122835014 0 1306


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 TraesCS4D01G229500 chr4D 389450475 389453685 3210 True 5930 5930 100.000 1 3211 1 chr4D.!!$R1 3210
1 TraesCS4D01G229500 chrUn 291535421 291537745 2324 False 4039 4039 98.022 1 2325 1 chrUn.!!$F4 2324
2 TraesCS4D01G229500 chrUn 245706049 245708372 2323 False 4032 4032 97.978 1 2325 1 chrUn.!!$F3 2324
3 TraesCS4D01G229500 chrUn 199874805 199877129 2324 False 4028 4028 97.935 1 2325 1 chrUn.!!$F1 2324
4 TraesCS4D01G229500 chrUn 229307922 229310246 2324 True 4028 4028 97.935 1 2325 1 chrUn.!!$R2 2324
5 TraesCS4D01G229500 chrUn 274338976 274341301 2325 True 4028 4028 97.936 1 2325 1 chrUn.!!$R3 2324
6 TraesCS4D01G229500 chrUn 3843509 3845833 2324 True 4006 4006 97.763 1 2325 1 chrUn.!!$R1 2324
7 TraesCS4D01G229500 chrUn 199904725 199907049 2324 False 4006 4006 97.763 1 2325 1 chrUn.!!$F2 2324
8 TraesCS4D01G229500 chr1B 544593678 544596000 2322 False 4026 4026 97.935 1 2325 1 chr1B.!!$F1 2324
9 TraesCS4D01G229500 chr5D 18998905 19001229 2324 False 4023 4023 97.892 1 2325 1 chr5D.!!$F1 2324
10 TraesCS4D01G229500 chr6D 406408613 406409505 892 True 1474 1474 96.753 2334 3211 1 chr6D.!!$R1 877
11 TraesCS4D01G229500 chr3D 129178231 129179113 882 False 1471 1471 96.829 2334 3211 1 chr3D.!!$F1 877
12 TraesCS4D01G229500 chr1D 227545571 227546463 892 False 1469 1469 96.641 2334 3211 1 chr1D.!!$F1 877
13 TraesCS4D01G229500 chr1D 311116107 311116702 595 True 974 974 96.315 2334 2924 1 chr1D.!!$R1 590
14 TraesCS4D01G229500 chr6A 160947318 160948188 870 False 1411 1411 95.986 2345 3211 1 chr6A.!!$F1 866
15 TraesCS4D01G229500 chr7B 329112826 329113700 874 False 1397 1397 95.449 2334 3211 1 chr7B.!!$F1 877
16 TraesCS4D01G229500 chr7A 392522152 392523034 882 False 1387 1387 95.136 2334 3211 1 chr7A.!!$F2 877
17 TraesCS4D01G229500 chr7A 297180194 297181060 866 False 1118 1118 89.932 2334 3211 1 chr7A.!!$F1 877
18 TraesCS4D01G229500 chr5A 343889838 343890715 877 False 1367 1367 94.767 2334 3211 1 chr5A.!!$F1 877
19 TraesCS4D01G229500 chr3A 519655916 519656798 882 True 1349 1349 94.337 2334 3211 1 chr3A.!!$R1 877
20 TraesCS4D01G229500 chr3A 122834130 122835014 884 False 1306 1306 93.446 2334 3211 1 chr3A.!!$F1 877

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
867 868 0.322456 CCTGGAAATGGTTCAGCCGA 60.322 55.0 0.0 0.0 41.21 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2325 2327 1.341531 CAGTACCTATTCCGCCTGAGG 59.658 57.143 0.0 0.0 35.05 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
74 75 4.365723 GGCGAAAGACTAATCGAACCATA 58.634 43.478 13.14 0.00 41.43 2.74
280 281 3.055167 GGGCCATTTTTGGTAAGCAGAAT 60.055 43.478 4.39 0.00 0.00 2.40
443 444 3.069586 CACCTATCGAATCAACTAGCCCA 59.930 47.826 0.00 0.00 0.00 5.36
521 522 1.457643 CCCGATGAGTAGGAGGGCA 60.458 63.158 0.00 0.00 35.09 5.36
724 725 4.545706 GATCACGCGCATCCCCCA 62.546 66.667 5.73 0.00 0.00 4.96
856 857 1.610379 GCCTGCCAACCCTGGAAAT 60.610 57.895 0.00 0.00 46.92 2.17
867 868 0.322456 CCTGGAAATGGTTCAGCCGA 60.322 55.000 0.00 0.00 41.21 5.54
943 944 2.120909 CGGCGGCCCATGAAAATCT 61.121 57.895 14.55 0.00 0.00 2.40
1008 1009 2.123589 TCAGGTCTCCAAGGTGAACAA 58.876 47.619 8.73 0.00 0.00 2.83
1053 1054 1.028905 CAAGGGAAGTCGGCAAAACA 58.971 50.000 0.00 0.00 0.00 2.83
1083 1084 2.171003 CTTCGGGAAAAGGATTGGCTT 58.829 47.619 0.00 0.00 0.00 4.35
1090 1091 3.771479 GGAAAAGGATTGGCTTTGAGGAT 59.229 43.478 0.00 0.00 0.00 3.24
1097 1098 0.114954 TGGCTTTGAGGATTGGGCTT 59.885 50.000 0.00 0.00 0.00 4.35
1202 1203 3.455469 GGACGGACCGGGAATCGT 61.455 66.667 20.00 9.98 38.62 3.73
1262 1263 0.971386 GAACTGGTACGGACAAGGGA 59.029 55.000 7.21 0.00 38.67 4.20
1348 1349 1.654954 CTGCCCAGTGCTCTGAATGC 61.655 60.000 17.19 15.36 43.76 3.56
1415 1416 6.380095 AACTATGACTCTCTTAAGGTAGCG 57.620 41.667 1.85 0.00 0.00 4.26
1478 1479 1.006758 ACGAGATTCCCACTGTCCCTA 59.993 52.381 0.00 0.00 0.00 3.53
1497 1498 5.903010 TCCCTATCTACTATCCAGCAAAACA 59.097 40.000 0.00 0.00 0.00 2.83
1501 1502 7.552687 CCTATCTACTATCCAGCAAAACAACAA 59.447 37.037 0.00 0.00 0.00 2.83
1605 1606 3.012502 TGAGAGGTGTAGGATAAGTGGGT 59.987 47.826 0.00 0.00 0.00 4.51
1871 1873 4.437930 GCTCGTTTGATTCTGATTTCCAGG 60.438 45.833 0.00 0.00 43.12 4.45
1905 1907 0.459585 TGAAAGCGTGGCCTATCGAC 60.460 55.000 16.80 9.58 0.00 4.20
1914 1916 2.433239 GTGGCCTATCGACCCTTTAGAA 59.567 50.000 3.32 0.00 0.00 2.10
1965 1967 7.236019 TCAGAAAAGTTACCACAGGGATAACTA 59.764 37.037 0.00 0.00 38.01 2.24
2041 2043 4.681781 CGGCTCTTCCTATCATTGTGAAGT 60.682 45.833 0.00 0.00 36.47 3.01
2166 2168 7.040892 TGTCGCGATAGTAATTCAACCTAGTAT 60.041 37.037 14.06 0.00 39.35 2.12
2290 2292 0.178767 ATCCAAGCTAGCATGCGACA 59.821 50.000 18.83 0.41 38.13 4.35
2325 2327 4.462280 CCCCGACCCACGTTAGGC 62.462 72.222 1.15 0.00 40.78 3.93
2326 2328 4.462280 CCCGACCCACGTTAGGCC 62.462 72.222 0.00 0.00 40.78 5.19
2327 2329 3.387947 CCGACCCACGTTAGGCCT 61.388 66.667 11.78 11.78 40.78 5.19
2328 2330 2.183555 CGACCCACGTTAGGCCTC 59.816 66.667 9.68 0.00 37.22 4.70
2329 2331 2.642254 CGACCCACGTTAGGCCTCA 61.642 63.158 9.68 0.00 37.22 3.86
2330 2332 1.218316 GACCCACGTTAGGCCTCAG 59.782 63.158 9.68 4.17 0.00 3.35
2331 2333 2.240162 GACCCACGTTAGGCCTCAGG 62.240 65.000 9.68 6.86 0.00 3.86
2598 2600 1.165270 GCCTTTACATTGCTCCGTGT 58.835 50.000 0.00 0.00 0.00 4.49
2619 2637 5.856455 GTGTGGTTCTTGTGTGCAATTATAC 59.144 40.000 0.00 0.00 33.65 1.47
2781 2799 7.323895 CAGAATATGTATCGTTTGTACTCGAGG 59.676 40.741 18.41 0.00 39.38 4.63
2794 2812 5.748402 TGTACTCGAGGTTAACTAGATGGA 58.252 41.667 18.41 0.00 30.12 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
240 241 0.609131 CCACTTGGAGCACCCGATTT 60.609 55.000 0.00 0.00 37.93 2.17
280 281 2.112198 GTTCATCCCGCATCGCCAA 61.112 57.895 0.00 0.00 0.00 4.52
426 427 4.487714 TTTCTGGGCTAGTTGATTCGAT 57.512 40.909 0.00 0.00 0.00 3.59
427 428 3.973206 TTTCTGGGCTAGTTGATTCGA 57.027 42.857 0.00 0.00 0.00 3.71
443 444 1.747355 CTTCAGCGCCATCCATTTTCT 59.253 47.619 2.29 0.00 0.00 2.52
724 725 5.421056 GGAAATCTTAACCCGATTCCCTTTT 59.579 40.000 0.00 0.00 31.12 2.27
773 774 3.087031 TCTCCGAACTTCCTAACGTCAT 58.913 45.455 0.00 0.00 0.00 3.06
774 775 2.227388 GTCTCCGAACTTCCTAACGTCA 59.773 50.000 0.00 0.00 0.00 4.35
810 811 5.505181 AGCAGAAAAGATAACTCTTCCCA 57.495 39.130 0.00 0.00 40.93 4.37
856 857 1.550130 CCCTACCTTCGGCTGAACCA 61.550 60.000 3.13 0.00 39.03 3.67
867 868 1.923909 GGCCACTGGACCCTACCTT 60.924 63.158 0.00 0.00 0.00 3.50
943 944 1.075482 AACGGTACTCGGTCCTCCA 59.925 57.895 8.31 0.00 44.45 3.86
1008 1009 0.482446 TTGTTCCATTGGCCAGAGGT 59.518 50.000 21.07 1.32 0.00 3.85
1083 1084 1.387737 CCCCAAGCCCAATCCTCAA 59.612 57.895 0.00 0.00 0.00 3.02
1125 1126 3.417275 CTCGAGCAATCCGCCGACT 62.417 63.158 0.00 0.00 44.04 4.18
1348 1349 5.234972 GCTTGGTTGAATTTCTTCACTTTGG 59.765 40.000 0.00 0.00 41.05 3.28
1415 1416 6.701841 TCACTAATTAGATGACGAGGCATTTC 59.298 38.462 19.38 0.00 0.00 2.17
1478 1479 6.151144 GGTTGTTGTTTTGCTGGATAGTAGAT 59.849 38.462 0.00 0.00 0.00 1.98
1497 1498 1.830847 GCCCGTTCCCTTGGTTGTT 60.831 57.895 0.00 0.00 0.00 2.83
1501 1502 2.115266 CAAGCCCGTTCCCTTGGT 59.885 61.111 0.00 0.00 35.86 3.67
1706 1708 2.364579 ATCGGCCCGGTAAGACCA 60.365 61.111 1.90 0.00 38.47 4.02
1871 1873 2.222442 GCTTTCACGGTTCGTATTCGTC 60.222 50.000 0.00 0.00 38.32 4.20
1905 1907 4.638304 TCAAACTCCGAAGTTCTAAAGGG 58.362 43.478 0.56 0.00 45.07 3.95
1914 1916 3.056465 CCTCTAGCTTCAAACTCCGAAGT 60.056 47.826 0.00 0.00 41.61 3.01
2166 2168 2.367241 TGTGAATCAACGGTTCCTCTCA 59.633 45.455 0.00 0.00 0.00 3.27
2325 2327 1.341531 CAGTACCTATTCCGCCTGAGG 59.658 57.143 0.00 0.00 35.05 3.86
2326 2328 2.307768 TCAGTACCTATTCCGCCTGAG 58.692 52.381 0.00 0.00 0.00 3.35
2327 2329 2.447408 TCAGTACCTATTCCGCCTGA 57.553 50.000 0.00 0.00 0.00 3.86
2328 2330 3.536956 TTTCAGTACCTATTCCGCCTG 57.463 47.619 0.00 0.00 0.00 4.85
2329 2331 4.259356 GTTTTTCAGTACCTATTCCGCCT 58.741 43.478 0.00 0.00 0.00 5.52
2330 2332 4.004982 TGTTTTTCAGTACCTATTCCGCC 58.995 43.478 0.00 0.00 0.00 6.13
2331 2333 4.094442 CCTGTTTTTCAGTACCTATTCCGC 59.906 45.833 0.00 0.00 42.19 5.54
2332 2334 5.484715 TCCTGTTTTTCAGTACCTATTCCG 58.515 41.667 0.00 0.00 42.19 4.30
2598 2600 5.182950 CAGGTATAATTGCACACAAGAACCA 59.817 40.000 0.00 0.00 39.69 3.67
2619 2637 2.118313 TGTCTTCCATGCATGTCAGG 57.882 50.000 24.58 10.13 0.00 3.86


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

AutoCloner maintained by Alex Coulton.