Multiple sequence alignment - TraesCS5A01G093000

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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 TraesCS5A01G093000 chr5A 100.000 2369 0 0 1 2369 129277454 129275086 0 4375
1 TraesCS5A01G093000 chr5D 93.264 2405 84 40 1 2369 119255112 119252750 0 3472
2 TraesCS5A01G093000 chr5B 93.822 1829 59 23 552 2369 131715844 131714059 0 2702
3 TraesCS5A01G093000 chr5B 93.525 556 28 4 1 552 131716725 131716174 0 821


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 TraesCS5A01G093000 chr5A 129275086 129277454 2368 True 4375.0 4375 100.0000 1 2369 1 chr5A.!!$R1 2368
1 TraesCS5A01G093000 chr5D 119252750 119255112 2362 True 3472.0 3472 93.2640 1 2369 1 chr5D.!!$R1 2368
2 TraesCS5A01G093000 chr5B 131714059 131716725 2666 True 1761.5 2702 93.6735 1 2369 2 chr5B.!!$R1 2368

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
981 1334 0.249911 ATTCATTCTCGCCCGCTACC 60.25 55.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2142 2515 0.520404 CAGCTCATGACCACTGCAAC 59.48 55.0 6.65 0.0 0.0 4.17 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
62 63 1.886886 TAGCACGTTGAGGGAAAACC 58.113 50.000 0.00 0.00 40.67 3.27
64 65 0.310854 GCACGTTGAGGGAAAACCAG 59.689 55.000 0.00 0.00 43.89 4.00
69 70 2.744202 CGTTGAGGGAAAACCAGAGATG 59.256 50.000 0.00 0.00 43.89 2.90
80 81 3.971245 ACCAGAGATGAACAGAAGACC 57.029 47.619 0.00 0.00 0.00 3.85
82 83 3.260380 ACCAGAGATGAACAGAAGACCAG 59.740 47.826 0.00 0.00 0.00 4.00
185 186 3.181454 GGAAAGAGGGTCAGTGACAAAGA 60.181 47.826 24.20 0.00 33.68 2.52
248 252 0.847035 GCGAGAGTTGCACGTATAGC 59.153 55.000 0.00 0.00 32.93 2.97
267 271 6.892658 ATAGCACAACTTTGTAAATCCACA 57.107 33.333 0.00 0.00 39.91 4.17
271 275 6.040842 AGCACAACTTTGTAAATCCACAGAAT 59.959 34.615 0.00 0.00 39.91 2.40
275 279 7.724061 ACAACTTTGTAAATCCACAGAATAGGT 59.276 33.333 0.00 0.00 40.16 3.08
296 300 0.526954 CAGATTTTGCAGCGATGGCC 60.527 55.000 1.46 0.00 41.24 5.36
300 304 0.390078 TTTTGCAGCGATGGCCATTG 60.390 50.000 26.56 26.56 41.24 2.82
362 366 2.844348 TCCCTCTCCTTTCCAATACACC 59.156 50.000 0.00 0.00 0.00 4.16
390 406 8.836413 TCTACCCTTAAAATTCGCTCAATAATG 58.164 33.333 0.00 0.00 0.00 1.90
391 407 6.805713 ACCCTTAAAATTCGCTCAATAATGG 58.194 36.000 0.00 0.00 0.00 3.16
392 408 6.605594 ACCCTTAAAATTCGCTCAATAATGGA 59.394 34.615 0.00 0.00 0.00 3.41
393 409 7.141363 CCCTTAAAATTCGCTCAATAATGGAG 58.859 38.462 0.00 0.00 35.47 3.86
394 410 7.201821 CCCTTAAAATTCGCTCAATAATGGAGT 60.202 37.037 0.00 0.00 34.83 3.85
463 480 3.357079 GCCAACAGACAGTGGCCG 61.357 66.667 3.21 0.00 38.01 6.13
467 484 0.813610 CAACAGACAGTGGCCGAACA 60.814 55.000 0.00 0.00 0.00 3.18
479 496 1.949257 CCGAACACCACAGGAAAGC 59.051 57.895 0.00 0.00 0.00 3.51
526 543 1.473965 CGATCCTCCATGTTCCCACAG 60.474 57.143 0.00 0.00 35.94 3.66
545 562 3.570550 ACAGCTCTCGTCCCATTATAGTC 59.429 47.826 0.00 0.00 0.00 2.59
546 563 3.570125 CAGCTCTCGTCCCATTATAGTCA 59.430 47.826 0.00 0.00 0.00 3.41
558 905 9.574516 GTCCCATTATAGTCAGGTTTTAATCAT 57.425 33.333 0.00 0.00 0.00 2.45
559 906 9.793259 TCCCATTATAGTCAGGTTTTAATCATC 57.207 33.333 0.00 0.00 0.00 2.92
564 911 3.941483 AGTCAGGTTTTAATCATCCAGCG 59.059 43.478 0.00 0.00 0.00 5.18
569 916 3.378427 GGTTTTAATCATCCAGCGAGCTT 59.622 43.478 0.00 0.00 0.00 3.74
584 937 0.461870 AGCTTTGCGCCGATCACATA 60.462 50.000 4.18 0.00 40.39 2.29
590 943 1.284715 CGCCGATCACATACCGCTA 59.715 57.895 0.00 0.00 0.00 4.26
649 1002 0.966875 TGCACATGGCCATTGTCTCC 60.967 55.000 17.92 8.83 43.89 3.71
651 1004 0.392863 CACATGGCCATTGTCTCCGA 60.393 55.000 17.92 0.00 0.00 4.55
653 1006 1.153369 ATGGCCATTGTCTCCGACG 60.153 57.895 14.09 0.00 34.95 5.12
765 1118 2.806237 CTACCGTTCTCCTCCGCC 59.194 66.667 0.00 0.00 0.00 6.13
766 1119 2.757099 TACCGTTCTCCTCCGCCC 60.757 66.667 0.00 0.00 0.00 6.13
856 1209 4.168291 CCGCTCCCCAGCCTCTTC 62.168 72.222 0.00 0.00 43.56 2.87
857 1210 4.168291 CGCTCCCCAGCCTCTTCC 62.168 72.222 0.00 0.00 43.56 3.46
884 1237 4.787280 CCTCTCGCCCACCTCCCT 62.787 72.222 0.00 0.00 0.00 4.20
885 1238 3.151022 CTCTCGCCCACCTCCCTC 61.151 72.222 0.00 0.00 0.00 4.30
886 1239 4.779733 TCTCGCCCACCTCCCTCC 62.780 72.222 0.00 0.00 0.00 4.30
887 1240 4.787280 CTCGCCCACCTCCCTCCT 62.787 72.222 0.00 0.00 0.00 3.69
888 1241 4.779733 TCGCCCACCTCCCTCCTC 62.780 72.222 0.00 0.00 0.00 3.71
897 1250 1.541672 CTCCCTCCTCTCCTCTCCC 59.458 68.421 0.00 0.00 0.00 4.30
970 1323 2.114670 CCCCACGCGCATTCATTCT 61.115 57.895 5.73 0.00 0.00 2.40
972 1325 1.011904 CCACGCGCATTCATTCTCG 60.012 57.895 5.73 0.00 0.00 4.04
975 1328 2.329339 GCGCATTCATTCTCGCCC 59.671 61.111 0.30 0.00 41.53 6.13
978 1331 2.182842 GCATTCATTCTCGCCCGCT 61.183 57.895 0.00 0.00 0.00 5.52
979 1332 0.880278 GCATTCATTCTCGCCCGCTA 60.880 55.000 0.00 0.00 0.00 4.26
981 1334 0.249911 ATTCATTCTCGCCCGCTACC 60.250 55.000 0.00 0.00 0.00 3.18
1403 1771 1.683319 CCCAGAGATCACGTCCTCTCA 60.683 57.143 20.40 0.00 40.31 3.27
1459 1827 1.681793 AGCGGTGCCACTAGTATACTG 59.318 52.381 15.90 8.03 0.00 2.74
1462 1830 2.543861 CGGTGCCACTAGTATACTGCTG 60.544 54.545 15.90 9.68 0.00 4.41
1610 1979 6.768029 TGTTATTCTTTGAAGTTTGCATGC 57.232 33.333 11.82 11.82 0.00 4.06
1729 2098 7.336176 GGTGTCGGGAGAAAAATAAATTCTACT 59.664 37.037 0.00 0.00 42.89 2.57
1730 2099 9.374838 GTGTCGGGAGAAAAATAAATTCTACTA 57.625 33.333 0.00 0.00 42.89 1.82
1731 2100 9.595823 TGTCGGGAGAAAAATAAATTCTACTAG 57.404 33.333 0.00 0.00 42.89 2.57
1781 2150 4.076394 GGATCTAGAGCGTAGAACCATCT 58.924 47.826 16.01 0.00 36.75 2.90
1853 2222 2.048601 CATGATGGAGGAGGAAGAGCT 58.951 52.381 0.00 0.00 0.00 4.09
1927 2300 2.157895 AGGGAGGTAGGTAGGTTGGTTT 60.158 50.000 0.00 0.00 0.00 3.27
1984 2357 1.287730 GCTCACTGCCTCACTTGTCG 61.288 60.000 0.00 0.00 35.15 4.35
2051 2424 9.613957 CTACAGTAGTACCATAAATCAATCGAG 57.386 37.037 0.00 0.00 0.00 4.04
2142 2515 7.148000 GGGAAAAGGGAGAAGATTGAGTAATTG 60.148 40.741 0.00 0.00 0.00 2.32
2165 2538 2.743538 GTGGTCATGAGCTGCGCA 60.744 61.111 24.30 10.98 0.00 6.09
2195 2568 4.644685 ACCATTCTCTTCTCTGAGCTACTC 59.355 45.833 0.00 0.00 34.29 2.59
2196 2569 4.644234 CCATTCTCTTCTCTGAGCTACTCA 59.356 45.833 0.00 0.00 38.25 3.41
2197 2570 5.450412 CCATTCTCTTCTCTGAGCTACTCAC 60.450 48.000 0.00 0.00 35.39 3.51
2198 2571 4.568072 TCTCTTCTCTGAGCTACTCACT 57.432 45.455 0.00 0.00 35.39 3.41
2199 2572 4.260985 TCTCTTCTCTGAGCTACTCACTG 58.739 47.826 0.00 0.00 35.39 3.66
2200 2573 4.009675 CTCTTCTCTGAGCTACTCACTGT 58.990 47.826 0.00 0.00 35.39 3.55
2252 2628 1.542987 GCCATTCTCTCAGGCTCATCC 60.543 57.143 0.00 0.00 44.92 3.51
2323 2702 9.018716 GTTTTTGGAATTGGTGCTTTAAAATTG 57.981 29.630 0.00 0.00 0.00 2.32
2336 2715 5.564455 GCTTTAAAATTGGCAAATGGGGTTG 60.564 40.000 3.01 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 4.797800 TCTGGTCTTCTGTTCATCTCTG 57.202 45.455 0.00 0.00 0.00 3.35
64 65 5.486526 ACATTCTGGTCTTCTGTTCATCTC 58.513 41.667 0.00 0.00 0.00 2.75
69 70 4.997395 TGCTTACATTCTGGTCTTCTGTTC 59.003 41.667 0.00 0.00 0.00 3.18
80 81 6.530181 TCAACATACTACGTGCTTACATTCTG 59.470 38.462 0.00 0.00 0.00 3.02
82 83 6.880822 TCAACATACTACGTGCTTACATTC 57.119 37.500 0.00 0.00 0.00 2.67
185 186 3.683847 GCAGTTATCCAGACATCCAAGCT 60.684 47.826 0.00 0.00 0.00 3.74
248 252 8.023128 CCTATTCTGTGGATTTACAAAGTTGTG 58.977 37.037 6.94 0.00 42.31 3.33
267 271 3.950395 GCTGCAAAATCTGGACCTATTCT 59.050 43.478 0.00 0.00 0.00 2.40
271 275 1.277842 TCGCTGCAAAATCTGGACCTA 59.722 47.619 0.00 0.00 0.00 3.08
275 279 1.097232 CCATCGCTGCAAAATCTGGA 58.903 50.000 0.00 0.00 0.00 3.86
362 366 4.178540 TGAGCGAATTTTAAGGGTAGACG 58.821 43.478 0.00 0.00 0.00 4.18
390 406 6.303839 TGGTGCCCTTTTATGATATTACTCC 58.696 40.000 0.00 0.00 0.00 3.85
391 407 7.665559 TGATGGTGCCCTTTTATGATATTACTC 59.334 37.037 0.00 0.00 0.00 2.59
392 408 7.526041 TGATGGTGCCCTTTTATGATATTACT 58.474 34.615 0.00 0.00 0.00 2.24
393 409 7.759489 TGATGGTGCCCTTTTATGATATTAC 57.241 36.000 0.00 0.00 0.00 1.89
394 410 8.393259 AGATGATGGTGCCCTTTTATGATATTA 58.607 33.333 0.00 0.00 0.00 0.98
463 480 0.467290 TGGGCTTTCCTGTGGTGTTC 60.467 55.000 0.00 0.00 36.20 3.18
467 484 2.084930 AGGTGGGCTTTCCTGTGGT 61.085 57.895 0.00 0.00 36.20 4.16
479 496 1.531365 TGGCAGCTTTTCAGGTGGG 60.531 57.895 3.76 0.00 46.93 4.61
526 543 3.057174 CCTGACTATAATGGGACGAGAGC 60.057 52.174 0.00 0.00 0.00 4.09
545 562 3.242870 GCTCGCTGGATGATTAAAACCTG 60.243 47.826 0.00 0.00 0.00 4.00
546 563 2.945668 GCTCGCTGGATGATTAAAACCT 59.054 45.455 0.00 0.00 0.00 3.50
569 916 1.880796 CGGTATGTGATCGGCGCAA 60.881 57.895 10.83 0.00 40.98 4.85
579 927 3.047796 GTGGTCGTAATAGCGGTATGTG 58.952 50.000 8.09 1.52 0.00 3.21
584 937 1.226773 GCGTGGTCGTAATAGCGGT 60.227 57.895 0.00 0.00 39.49 5.68
608 961 1.293924 CAGGCAATGGACGATGAGAC 58.706 55.000 0.00 0.00 0.00 3.36
649 1002 2.504244 GGAGGAAGCGTGTCGTCG 60.504 66.667 0.00 0.00 34.03 5.12
651 1004 2.637383 GGAGGAGGAAGCGTGTCGT 61.637 63.158 0.00 0.00 0.00 4.34
653 1006 1.513622 GAGGAGGAGGAAGCGTGTC 59.486 63.158 0.00 0.00 0.00 3.67
844 1197 1.793820 AAAGTGGGAAGAGGCTGGGG 61.794 60.000 0.00 0.00 0.00 4.96
853 1206 2.483889 GCGAGAGGGATAAAGTGGGAAG 60.484 54.545 0.00 0.00 0.00 3.46
854 1207 1.485066 GCGAGAGGGATAAAGTGGGAA 59.515 52.381 0.00 0.00 0.00 3.97
855 1208 1.120530 GCGAGAGGGATAAAGTGGGA 58.879 55.000 0.00 0.00 0.00 4.37
856 1209 0.106894 GGCGAGAGGGATAAAGTGGG 59.893 60.000 0.00 0.00 0.00 4.61
857 1210 0.106894 GGGCGAGAGGGATAAAGTGG 59.893 60.000 0.00 0.00 0.00 4.00
883 1236 1.541672 GGAGGGGAGAGGAGAGGAG 59.458 68.421 0.00 0.00 0.00 3.69
884 1237 2.015726 GGGAGGGGAGAGGAGAGGA 61.016 68.421 0.00 0.00 0.00 3.71
885 1238 2.612251 GGGAGGGGAGAGGAGAGG 59.388 72.222 0.00 0.00 0.00 3.69
886 1239 2.018086 AGGGGAGGGGAGAGGAGAG 61.018 68.421 0.00 0.00 0.00 3.20
887 1240 2.015726 GAGGGGAGGGGAGAGGAGA 61.016 68.421 0.00 0.00 0.00 3.71
888 1241 2.612251 GAGGGGAGGGGAGAGGAG 59.388 72.222 0.00 0.00 0.00 3.69
897 1250 1.755008 GTGACGAGAGGAGGGGAGG 60.755 68.421 0.00 0.00 0.00 4.30
1403 1771 5.239525 ACGAGAAGCAGCTTATTTTTGAACT 59.760 36.000 7.92 0.00 0.00 3.01
1610 1979 2.486716 AGAAGATGAAGGGAAGAGGGG 58.513 52.381 0.00 0.00 0.00 4.79
1729 2098 2.353406 GCCACAAGGAAAGCTCGTACTA 60.353 50.000 0.00 0.00 36.89 1.82
1730 2099 1.608283 GCCACAAGGAAAGCTCGTACT 60.608 52.381 0.00 0.00 36.89 2.73
1731 2100 0.796927 GCCACAAGGAAAGCTCGTAC 59.203 55.000 0.00 0.00 36.89 3.67
1781 2150 5.478407 TCATCTCTAGACACGAAAATTGCA 58.522 37.500 0.00 0.00 0.00 4.08
1853 2222 5.590259 GTGCAAGGAGGAAGAGCAAAATATA 59.410 40.000 0.00 0.00 36.91 0.86
1867 2236 1.503542 GCAACGATGTGCAAGGAGG 59.496 57.895 0.00 0.00 44.29 4.30
1911 2284 4.070009 CTCAACAAACCAACCTACCTACC 58.930 47.826 0.00 0.00 0.00 3.18
1912 2285 4.070009 CCTCAACAAACCAACCTACCTAC 58.930 47.826 0.00 0.00 0.00 3.18
1913 2286 3.497227 GCCTCAACAAACCAACCTACCTA 60.497 47.826 0.00 0.00 0.00 3.08
1984 2357 1.382692 GGCTTCAAGATGGCAGGAGC 61.383 60.000 0.00 0.00 41.10 4.70
2033 2406 5.607477 TCACCCTCGATTGATTTATGGTAC 58.393 41.667 0.00 0.00 0.00 3.34
2051 2424 7.562135 TCCACTAACTGAGTTAATTATCACCC 58.438 38.462 6.51 0.00 35.64 4.61
2142 2515 0.520404 CAGCTCATGACCACTGCAAC 59.480 55.000 6.65 0.00 0.00 4.17
2165 2538 6.150809 GCTCAGAGAAGAGAATGGTTCAATTT 59.849 38.462 0.00 0.00 37.87 1.82
2195 2568 3.032017 ACCTCGAGTCATTTCACAGTG 57.968 47.619 12.31 0.00 0.00 3.66
2196 2569 3.069586 TCAACCTCGAGTCATTTCACAGT 59.930 43.478 12.31 0.00 0.00 3.55
2197 2570 3.653344 TCAACCTCGAGTCATTTCACAG 58.347 45.455 12.31 0.00 0.00 3.66
2198 2571 3.653344 CTCAACCTCGAGTCATTTCACA 58.347 45.455 12.31 0.00 0.00 3.58
2199 2572 2.413453 GCTCAACCTCGAGTCATTTCAC 59.587 50.000 12.31 0.00 35.33 3.18
2200 2573 2.300152 AGCTCAACCTCGAGTCATTTCA 59.700 45.455 12.31 0.00 35.33 2.69
2250 2626 2.029020 CCTCGAGTCATTTCACAGTGGA 60.029 50.000 12.31 0.00 0.00 4.02
2252 2628 3.032017 ACCTCGAGTCATTTCACAGTG 57.968 47.619 12.31 0.00 0.00 3.66
2323 2702 0.761802 TTCAACCAACCCCATTTGCC 59.238 50.000 0.00 0.00 0.00 4.52
2336 2715 4.173256 CACGGCATTTATTCCTTTCAACC 58.827 43.478 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.