Multiple sequence alignment - TraesCS5A01G250800

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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 TraesCS5A01G250800 chr5A 100.000 2156 0 0 1 2156 466570576 466572731 0.000000e+00 3982
1 TraesCS5A01G250800 chr5A 86.059 373 50 2 280 651 415159442 415159813 1.200000e-107 399
2 TraesCS5A01G250800 chr5D 96.225 1139 33 3 774 1909 365081466 365082597 0.000000e+00 1857
3 TraesCS5A01G250800 chr5D 91.551 651 47 5 1 649 365079236 365079880 0.000000e+00 891
4 TraesCS5A01G250800 chr5D 96.429 252 8 1 1906 2156 365082630 365082881 4.280000e-112 414
5 TraesCS5A01G250800 chr5B 87.084 1231 66 41 703 1908 431060014 431061176 0.000000e+00 1306
6 TraesCS5A01G250800 chr5B 92.007 613 49 0 1 613 431057262 431057874 0.000000e+00 861
7 TraesCS5A01G250800 chr5B 91.589 107 8 1 1907 2012 431061210 431061316 1.720000e-31 147
8 TraesCS5A01G250800 chr2A 88.043 368 43 1 285 652 398458288 398458654 3.290000e-118 435
9 TraesCS5A01G250800 chr2A 88.043 368 43 1 285 652 398857285 398856919 3.290000e-118 435
10 TraesCS5A01G250800 chr2D 86.757 370 49 0 280 649 601705717 601706086 1.540000e-111 412
11 TraesCS5A01G250800 chr7B 86.981 361 45 2 281 640 99137673 99138032 2.580000e-109 405
12 TraesCS5A01G250800 chr3D 86.612 366 46 3 284 648 528071149 528070786 3.330000e-108 401
13 TraesCS5A01G250800 chr3D 75.969 258 57 5 17 271 549736167 549736422 6.250000e-26 128
14 TraesCS5A01G250800 chr6D 86.216 370 47 4 282 649 454014105 454014472 4.310000e-107 398
15 TraesCS5A01G250800 chr7D 82.131 291 42 10 1 286 36958949 36959234 7.690000e-60 241


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 TraesCS5A01G250800 chr5A 466570576 466572731 2155 False 3982.000000 3982 100.000000 1 2156 1 chr5A.!!$F2 2155
1 TraesCS5A01G250800 chr5D 365079236 365082881 3645 False 1054.000000 1857 94.735000 1 2156 3 chr5D.!!$F1 2155
2 TraesCS5A01G250800 chr5B 431057262 431061316 4054 False 771.333333 1306 90.226667 1 2012 3 chr5B.!!$F1 2011

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
661 837 0.313987 CAGCAACCGGTTTTCCCTTC 59.686 55.0 19.55 1.0 36.42 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1693 4856 1.072965 CAGCTTGGACTCCTTGGAGTT 59.927 52.381 21.61 7.48 35.23 3.01 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
48 49 1.145119 ACAGACCCCTCCCAAAGTTTC 59.855 52.381 0.00 0.00 0.00 2.78
49 50 0.778083 AGACCCCTCCCAAAGTTTCC 59.222 55.000 0.00 0.00 0.00 3.13
52 53 0.893727 CCCCTCCCAAAGTTTCCGTG 60.894 60.000 0.00 0.00 0.00 4.94
70 71 3.215244 CGTGCGAATTGTCAAGTTGTAC 58.785 45.455 10.43 10.43 0.00 2.90
101 102 5.699143 ACCATTTAGGCTCATCTTATTGCT 58.301 37.500 0.00 0.00 43.14 3.91
102 103 5.533903 ACCATTTAGGCTCATCTTATTGCTG 59.466 40.000 0.00 0.00 43.14 4.41
105 106 0.957362 GGCTCATCTTATTGCTGCCC 59.043 55.000 0.00 0.00 33.08 5.36
121 122 2.610374 CTGCCCAAATTTACATGCATGC 59.390 45.455 26.53 11.82 0.00 4.06
122 123 2.027469 TGCCCAAATTTACATGCATGCA 60.027 40.909 26.53 25.04 0.00 3.96
126 127 4.271533 CCCAAATTTACATGCATGCACATC 59.728 41.667 25.37 0.00 0.00 3.06
132 133 1.407618 ACATGCATGCACATCACCATC 59.592 47.619 25.37 0.00 0.00 3.51
134 135 1.842052 TGCATGCACATCACCATCTT 58.158 45.000 18.46 0.00 0.00 2.40
140 141 5.413523 GCATGCACATCACCATCTTATATCA 59.586 40.000 14.21 0.00 0.00 2.15
272 273 4.342092 ACTTTGCCTCAAACTTTGCATACT 59.658 37.500 0.00 0.00 33.08 2.12
277 278 6.991938 TGCCTCAAACTTTGCATACTTAATT 58.008 32.000 0.00 0.00 0.00 1.40
291 292 9.662947 TGCATACTTAATTATCATCATCCTCTG 57.337 33.333 0.00 0.00 0.00 3.35
317 318 5.937111 ACACTAAGCTCCCTAGTTTTGAAA 58.063 37.500 0.00 0.00 0.00 2.69
319 320 6.831868 ACACTAAGCTCCCTAGTTTTGAAAAA 59.168 34.615 0.00 0.00 0.00 1.94
378 379 5.416639 GTCACCTAATTTTGACCGGGTTAAT 59.583 40.000 6.32 1.76 36.85 1.40
409 410 6.906659 TCAAAGCTCTCACATTCAATTCTTC 58.093 36.000 0.00 0.00 0.00 2.87
444 446 8.204160 ACAATATGCTTCCTAATTTTTAAGGCC 58.796 33.333 0.00 0.00 32.55 5.19
449 451 5.419155 GCTTCCTAATTTTTAAGGCCTCACT 59.581 40.000 5.23 0.00 32.55 3.41
519 521 4.142160 GGGTCAACACTTTTTCAAGCTCTT 60.142 41.667 0.00 0.00 32.57 2.85
520 522 5.410924 GGTCAACACTTTTTCAAGCTCTTT 58.589 37.500 0.00 0.00 32.57 2.52
521 523 5.869344 GGTCAACACTTTTTCAAGCTCTTTT 59.131 36.000 0.00 0.00 32.57 2.27
652 828 0.322816 ATCAATCAGCAGCAACCGGT 60.323 50.000 0.00 0.00 0.00 5.28
655 831 1.039856 AATCAGCAGCAACCGGTTTT 58.960 45.000 19.55 6.14 0.00 2.43
656 832 0.598065 ATCAGCAGCAACCGGTTTTC 59.402 50.000 19.55 12.73 0.00 2.29
657 833 1.007387 CAGCAGCAACCGGTTTTCC 60.007 57.895 19.55 9.23 0.00 3.13
658 834 2.200337 AGCAGCAACCGGTTTTCCC 61.200 57.895 19.55 6.90 36.42 3.97
659 835 2.200337 GCAGCAACCGGTTTTCCCT 61.200 57.895 19.55 8.88 36.42 4.20
660 836 1.744320 GCAGCAACCGGTTTTCCCTT 61.744 55.000 19.55 0.00 36.42 3.95
661 837 0.313987 CAGCAACCGGTTTTCCCTTC 59.686 55.000 19.55 1.00 36.42 3.46
662 838 1.170290 AGCAACCGGTTTTCCCTTCG 61.170 55.000 19.55 4.73 36.42 3.79
663 839 1.953772 CAACCGGTTTTCCCTTCGG 59.046 57.895 19.55 0.00 46.95 4.30
664 840 0.535553 CAACCGGTTTTCCCTTCGGA 60.536 55.000 19.55 0.00 44.69 4.55
698 874 7.693951 CACTATCACATTTCCTGATTTCGAAAC 59.306 37.037 13.81 8.03 31.15 2.78
699 875 6.824305 ATCACATTTCCTGATTTCGAAACT 57.176 33.333 13.81 2.58 31.15 2.66
700 876 6.633500 TCACATTTCCTGATTTCGAAACTT 57.367 33.333 13.81 0.00 31.15 2.66
701 877 6.668323 TCACATTTCCTGATTTCGAAACTTC 58.332 36.000 13.81 8.64 31.15 3.01
776 3889 6.028146 TCACATTTTCTGATTTCCATGTGG 57.972 37.500 9.56 0.00 41.16 4.17
804 3946 0.320683 TCACGGTTCACAGATGGCAG 60.321 55.000 0.00 0.00 0.00 4.85
900 4045 0.468029 CTCCTCCTCCTCTGGCTCTC 60.468 65.000 0.00 0.00 0.00 3.20
901 4046 1.457455 CCTCCTCCTCTGGCTCTCC 60.457 68.421 0.00 0.00 0.00 3.71
1176 4326 4.463879 CGAGCTGCCTCCCACCAG 62.464 72.222 0.00 0.00 34.49 4.00
1218 4368 1.000506 TCCTAATCGTAAGCCCGATGC 59.999 52.381 4.54 0.00 46.23 3.91
1267 4422 2.672996 CCAAGGTTGTGCCCTCGG 60.673 66.667 0.00 0.00 38.26 4.63
1310 4465 0.026285 CGCGGTGGAATCGATTTGTC 59.974 55.000 12.81 6.16 0.00 3.18
1456 4619 2.666508 CGTTGTCGTACTTGGAATCCAG 59.333 50.000 0.86 0.00 33.81 3.86
1495 4658 2.576615 GATTCCCCTAGCATTGTGTCC 58.423 52.381 0.00 0.00 0.00 4.02
1531 4694 1.002624 GAGTCCGCACCATTTCCCA 60.003 57.895 0.00 0.00 0.00 4.37
1663 4826 0.970937 TAGCTCCCCTCGTTGTCCTG 60.971 60.000 0.00 0.00 0.00 3.86
1693 4856 6.070824 TGTTGTGATTGATAGCTTGGTAGAGA 60.071 38.462 0.00 0.00 0.00 3.10
1756 4922 2.283145 AGATTGTGCCTGCTGTTTCT 57.717 45.000 0.00 0.00 0.00 2.52
1983 5185 8.403236 ACTTTGGATAACTGTAACTTTCACAAC 58.597 33.333 0.00 0.00 0.00 3.32
1984 5186 7.867305 TTGGATAACTGTAACTTTCACAACA 57.133 32.000 0.00 0.00 0.00 3.33
2017 5220 3.387374 TCACAGCCAAAACCATGTGAATT 59.613 39.130 4.50 0.00 46.57 2.17
2028 5231 2.532235 CATGTGAATTGATTGTGCCCG 58.468 47.619 0.00 0.00 0.00 6.13
2056 5259 5.248640 TCACCCTCATCTGAATTCTGAAAC 58.751 41.667 17.62 0.00 0.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 1.002900 ACAACTTGACAATTCGCACGG 60.003 47.619 0.00 0.00 0.00 4.94
49 50 2.383298 ACAACTTGACAATTCGCACG 57.617 45.000 0.00 0.00 0.00 5.34
52 53 5.029650 TCATGTACAACTTGACAATTCGC 57.970 39.130 0.00 0.00 28.84 4.70
70 71 6.294473 AGATGAGCCTAAATGGTACTTCATG 58.706 40.000 0.00 0.00 38.35 3.07
101 102 2.027469 TGCATGCATGTAAATTTGGGCA 60.027 40.909 26.79 12.27 35.54 5.36
102 103 2.352342 GTGCATGCATGTAAATTTGGGC 59.648 45.455 25.64 9.74 0.00 5.36
105 106 5.220510 GGTGATGTGCATGCATGTAAATTTG 60.221 40.000 25.64 1.63 0.00 2.32
121 122 6.119240 AGGGTGATATAAGATGGTGATGTG 57.881 41.667 0.00 0.00 0.00 3.21
122 123 6.787458 TGTAGGGTGATATAAGATGGTGATGT 59.213 38.462 0.00 0.00 0.00 3.06
126 127 5.306937 TGGTGTAGGGTGATATAAGATGGTG 59.693 44.000 0.00 0.00 0.00 4.17
132 133 8.746052 TGATTTTTGGTGTAGGGTGATATAAG 57.254 34.615 0.00 0.00 0.00 1.73
134 135 6.770785 GCTGATTTTTGGTGTAGGGTGATATA 59.229 38.462 0.00 0.00 0.00 0.86
140 141 2.525368 GGCTGATTTTTGGTGTAGGGT 58.475 47.619 0.00 0.00 0.00 4.34
178 179 3.181526 GCTTTGTGATCTTGCTGTAGTCG 60.182 47.826 0.00 0.00 0.00 4.18
182 183 5.067674 ACAAAAGCTTTGTGATCTTGCTGTA 59.932 36.000 13.54 0.00 33.96 2.74
236 237 3.391296 GAGGCAAAGTGGATGGGTATAGA 59.609 47.826 0.00 0.00 0.00 1.98
240 241 1.367346 TGAGGCAAAGTGGATGGGTA 58.633 50.000 0.00 0.00 0.00 3.69
277 278 7.507277 AGCTTAGTGTTACAGAGGATGATGATA 59.493 37.037 0.00 0.00 0.00 2.15
291 292 6.461640 TCAAAACTAGGGAGCTTAGTGTTAC 58.538 40.000 0.15 0.00 29.57 2.50
317 318 4.482990 AGACCTCAATTGAATGTGGGTTT 58.517 39.130 15.30 8.82 38.09 3.27
319 320 3.562176 GGAGACCTCAATTGAATGTGGGT 60.562 47.826 14.36 14.36 38.09 4.51
378 379 7.984422 TGAATGTGAGAGCTTTGAGAAATTA 57.016 32.000 0.00 0.00 0.00 1.40
593 596 9.435688 GGCTCAATCAAAATAGTAAACCAAATT 57.564 29.630 0.00 0.00 0.00 1.82
614 790 5.193663 TGATTTGAAAAATCGTTGGCTCA 57.806 34.783 7.90 0.00 0.00 4.26
616 792 6.222389 TGATTGATTTGAAAAATCGTTGGCT 58.778 32.000 7.90 0.00 33.83 4.75
668 844 8.830580 CGAAATCAGGAAATGTGATAGTGTATT 58.169 33.333 0.00 0.00 33.34 1.89
671 847 6.406370 TCGAAATCAGGAAATGTGATAGTGT 58.594 36.000 0.00 0.00 33.34 3.55
673 849 7.607991 AGTTTCGAAATCAGGAAATGTGATAGT 59.392 33.333 14.69 0.00 33.34 2.12
674 850 7.978982 AGTTTCGAAATCAGGAAATGTGATAG 58.021 34.615 14.69 0.00 33.34 2.08
675 851 7.921786 AGTTTCGAAATCAGGAAATGTGATA 57.078 32.000 14.69 0.00 33.34 2.15
676 852 6.824305 AGTTTCGAAATCAGGAAATGTGAT 57.176 33.333 14.69 0.00 36.14 3.06
677 853 6.486657 AGAAGTTTCGAAATCAGGAAATGTGA 59.513 34.615 14.69 0.00 34.93 3.58
678 854 6.672147 AGAAGTTTCGAAATCAGGAAATGTG 58.328 36.000 14.69 0.00 34.93 3.21
679 855 6.884280 AGAAGTTTCGAAATCAGGAAATGT 57.116 33.333 14.69 0.00 34.93 2.71
748 3861 9.685276 ACATGGAAATCAGAAAATGTGATAGTA 57.315 29.630 0.00 0.00 33.34 1.82
749 3862 8.464404 CACATGGAAATCAGAAAATGTGATAGT 58.536 33.333 7.63 0.00 44.81 2.12
750 3863 7.919091 CCACATGGAAATCAGAAAATGTGATAG 59.081 37.037 13.60 0.00 44.81 2.08
776 3889 0.299597 GTGAACCGTGACACAACGAC 59.700 55.000 6.37 0.00 46.49 4.34
804 3946 4.803426 CACCTGGACGAGCGCTCC 62.803 72.222 30.66 19.07 0.00 4.70
972 4117 3.937372 TTCCCTTCCCCGACCCCTC 62.937 68.421 0.00 0.00 0.00 4.30
973 4118 3.945064 CTTCCCTTCCCCGACCCCT 62.945 68.421 0.00 0.00 0.00 4.79
974 4119 3.408853 CTTCCCTTCCCCGACCCC 61.409 72.222 0.00 0.00 0.00 4.95
975 4120 3.408853 CCTTCCCTTCCCCGACCC 61.409 72.222 0.00 0.00 0.00 4.46
1218 4368 6.389091 TGAAATGAACGGATGAAATTCTTGG 58.611 36.000 0.00 0.00 0.00 3.61
1267 4422 5.107298 GCTACATTCCAGTATTTCTCATCGC 60.107 44.000 0.00 0.00 0.00 4.58
1310 4465 6.206634 TCCAAAATTCACCACTAAAGTGCTAG 59.793 38.462 4.53 0.00 44.34 3.42
1456 4619 3.829886 TCGTGCTGAATGTCAATTTCC 57.170 42.857 0.00 0.00 0.00 3.13
1495 4658 5.573282 CGGACTCTGAAGTAATGTAACACAG 59.427 44.000 0.00 0.00 35.28 3.66
1531 4694 1.306654 TTAGGGCGACAGGGGTCAT 60.307 57.895 0.00 0.00 44.54 3.06
1663 4826 3.019564 AGCTATCAATCACAACAAGGCC 58.980 45.455 0.00 0.00 0.00 5.19
1693 4856 1.072965 CAGCTTGGACTCCTTGGAGTT 59.927 52.381 21.61 7.48 35.23 3.01
1756 4922 6.427853 CACACCAGATATTCTCAGAAACAACA 59.572 38.462 0.00 0.00 0.00 3.33
1900 5066 2.128035 AGTCGTTTCACTCAGCTTTCG 58.872 47.619 0.00 0.00 0.00 3.46
1983 5185 3.713858 TGGCTGTGAGTTGATGTTTTG 57.286 42.857 0.00 0.00 0.00 2.44
1984 5186 4.734398 TTTGGCTGTGAGTTGATGTTTT 57.266 36.364 0.00 0.00 0.00 2.43
2056 5259 8.807667 AAACTGCAAAAGAGATAATTGAGTTG 57.192 30.769 0.00 0.00 31.33 3.16
2088 5291 2.079925 CTGAACTAGCAAAGACAGGGC 58.920 52.381 0.00 0.00 33.21 5.19


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

AutoCloner maintained by Alex Coulton.