Multiple sequence alignment - TraesCS3A01G460200

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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 TraesCS3A01G460200 chr3A 100.000 3215 0 0 1 3215 696349245 696346031 0.000000e+00 5938
1 TraesCS3A01G460200 chr3A 93.472 2941 111 16 1 2899 629062751 629065652 0.000000e+00 4292
2 TraesCS3A01G460200 chr3A 94.091 220 10 2 2997 3215 629065759 629065976 6.650000e-87 331
3 TraesCS3A01G460200 chr3B 93.378 3262 134 20 4 3215 744542276 744539047 0.000000e+00 4752
4 TraesCS3A01G460200 chr3B 96.049 1721 47 8 772 2474 747099095 747100812 0.000000e+00 2782
5 TraesCS3A01G460200 chr3B 91.467 668 32 4 2474 3141 747102619 747103261 0.000000e+00 894
6 TraesCS3A01G460200 chr3B 92.071 618 40 6 117 728 747098480 747099094 0.000000e+00 861
7 TraesCS3A01G460200 chr3D 92.523 2889 131 29 51 2891 560281916 560279065 0.000000e+00 4060
8 TraesCS3A01G460200 chr3D 96.124 129 4 1 2961 3089 560279046 560278919 3.250000e-50 209
9 TraesCS3A01G460200 chr3D 94.203 69 4 0 3146 3214 560273839 560273771 4.390000e-19 106
10 TraesCS3A01G460200 chrUn 89.845 1812 143 20 593 2372 221377115 221378917 0.000000e+00 2289
11 TraesCS3A01G460200 chrUn 89.642 1815 147 20 593 2375 225550240 225552045 0.000000e+00 2272
12 TraesCS3A01G460200 chrUn 89.477 1815 150 20 593 2375 306578663 306576858 0.000000e+00 2255
13 TraesCS3A01G460200 chrUn 92.154 1300 93 8 1078 2375 285617361 285618653 0.000000e+00 1827
14 TraesCS3A01G460200 chrUn 89.283 1381 112 14 593 1943 228681984 228683358 0.000000e+00 1698
15 TraesCS3A01G460200 chrUn 91.614 942 71 7 1436 2375 387971966 387971031 0.000000e+00 1295
16 TraesCS3A01G460200 chrUn 80.611 1212 118 51 1 1147 318137034 318138193 0.000000e+00 828
17 TraesCS3A01G460200 chrUn 81.417 974 98 37 207 1147 322967832 322966909 0.000000e+00 719
18 TraesCS3A01G460200 chr7A 89.790 1812 144 20 593 2372 5794649 5796451 0.000000e+00 2283
19 TraesCS3A01G460200 chr7A 79.800 1198 135 50 1 1147 6162089 6163230 0.000000e+00 773
20 TraesCS3A01G460200 chr7A 81.223 932 95 35 1 887 5524051 5524947 0.000000e+00 678
21 TraesCS3A01G460200 chr4A 90.320 1126 77 15 666 1765 737716703 737715584 0.000000e+00 1447
22 TraesCS3A01G460200 chr4A 79.706 680 77 32 5 654 737717498 737716850 4.930000e-118 435
23 TraesCS3A01G460200 chr4A 89.958 239 20 1 2661 2899 738079319 738079553 4.030000e-79 305
24 TraesCS3A01G460200 chr4A 78.201 289 49 13 2902 3185 440191778 440192057 4.260000e-39 172
25 TraesCS3A01G460200 chr6D 81.566 1188 142 32 1529 2662 473059461 473060625 0.000000e+00 909
26 TraesCS3A01G460200 chr7B 81.163 860 111 31 1819 2649 705892355 705893192 0.000000e+00 643
27 TraesCS3A01G460200 chr6A 78.774 669 90 35 2234 2887 17945774 17945143 5.000000e-108 401
28 TraesCS3A01G460200 chr6B 75.595 840 150 39 1871 2689 30341300 30340495 6.550000e-97 364
29 TraesCS3A01G460200 chr1D 94.737 209 6 2 2798 3006 20478632 20478835 1.440000e-83 320


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 TraesCS3A01G460200 chr3A 696346031 696349245 3214 True 5938.000000 5938 100.000000 1 3215 1 chr3A.!!$R1 3214
1 TraesCS3A01G460200 chr3A 629062751 629065976 3225 False 2311.500000 4292 93.781500 1 3215 2 chr3A.!!$F1 3214
2 TraesCS3A01G460200 chr3B 744539047 744542276 3229 True 4752.000000 4752 93.378000 4 3215 1 chr3B.!!$R1 3211
3 TraesCS3A01G460200 chr3B 747098480 747103261 4781 False 1512.333333 2782 93.195667 117 3141 3 chr3B.!!$F1 3024
4 TraesCS3A01G460200 chr3D 560278919 560281916 2997 True 2134.500000 4060 94.323500 51 3089 2 chr3D.!!$R2 3038
5 TraesCS3A01G460200 chrUn 221377115 221378917 1802 False 2289.000000 2289 89.845000 593 2372 1 chrUn.!!$F1 1779
6 TraesCS3A01G460200 chrUn 225550240 225552045 1805 False 2272.000000 2272 89.642000 593 2375 1 chrUn.!!$F2 1782
7 TraesCS3A01G460200 chrUn 306576858 306578663 1805 True 2255.000000 2255 89.477000 593 2375 1 chrUn.!!$R1 1782
8 TraesCS3A01G460200 chrUn 285617361 285618653 1292 False 1827.000000 1827 92.154000 1078 2375 1 chrUn.!!$F4 1297
9 TraesCS3A01G460200 chrUn 228681984 228683358 1374 False 1698.000000 1698 89.283000 593 1943 1 chrUn.!!$F3 1350
10 TraesCS3A01G460200 chrUn 387971031 387971966 935 True 1295.000000 1295 91.614000 1436 2375 1 chrUn.!!$R3 939
11 TraesCS3A01G460200 chrUn 318137034 318138193 1159 False 828.000000 828 80.611000 1 1147 1 chrUn.!!$F5 1146
12 TraesCS3A01G460200 chrUn 322966909 322967832 923 True 719.000000 719 81.417000 207 1147 1 chrUn.!!$R2 940
13 TraesCS3A01G460200 chr7A 5794649 5796451 1802 False 2283.000000 2283 89.790000 593 2372 1 chr7A.!!$F2 1779
14 TraesCS3A01G460200 chr7A 6162089 6163230 1141 False 773.000000 773 79.800000 1 1147 1 chr7A.!!$F3 1146
15 TraesCS3A01G460200 chr7A 5524051 5524947 896 False 678.000000 678 81.223000 1 887 1 chr7A.!!$F1 886
16 TraesCS3A01G460200 chr4A 737715584 737717498 1914 True 941.000000 1447 85.013000 5 1765 2 chr4A.!!$R1 1760
17 TraesCS3A01G460200 chr6D 473059461 473060625 1164 False 909.000000 909 81.566000 1529 2662 1 chr6D.!!$F1 1133
18 TraesCS3A01G460200 chr7B 705892355 705893192 837 False 643.000000 643 81.163000 1819 2649 1 chr7B.!!$F1 830
19 TraesCS3A01G460200 chr6A 17945143 17945774 631 True 401.000000 401 78.774000 2234 2887 1 chr6A.!!$R1 653
20 TraesCS3A01G460200 chr6B 30340495 30341300 805 True 364.000000 364 75.595000 1871 2689 1 chr6B.!!$R1 818

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
803 1004 0.8364 AAGCTCTGTTTCCGGGGAGA 60.836 55.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2654 4829 1.301637 CACACCATGCCTGTCACGA 60.302 57.895 0.0 0.0 0.0 4.35 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
275 317 9.567848 AAAATGTTCAATGTGTATCGGTAAATC 57.432 29.630 0.00 0.00 0.00 2.17
398 442 8.757164 ATGTCATCGATTTTTAAAAACCTTCC 57.243 30.769 15.35 3.00 0.00 3.46
529 579 5.353123 AGCTCGATTTAAATTTCTGGCGTTA 59.647 36.000 1.43 0.00 0.00 3.18
803 1004 0.836400 AAGCTCTGTTTCCGGGGAGA 60.836 55.000 0.00 0.00 0.00 3.71
832 1038 1.499502 GAGCTTGCCGCAAACTCTC 59.500 57.895 23.41 17.17 42.61 3.20
903 1125 2.033448 CGGTGCAAGCCCAGGTTA 59.967 61.111 0.00 0.00 0.00 2.85
1064 1293 1.443194 GCTCTTGCGTAACGTCGGA 60.443 57.895 0.00 0.00 0.00 4.55
1114 1359 0.173708 CGTGGTCAAGGGCTACTCTC 59.826 60.000 0.00 0.00 0.00 3.20
1308 1553 2.291741 GGCCAAGTTCAGTTTCAGTCTG 59.708 50.000 0.00 0.00 0.00 3.51
1448 1693 2.622436 GCGATCAGCCAGTCTAAAGTT 58.378 47.619 0.00 0.00 40.81 2.66
1537 1788 3.691342 CCGGCACCGAGGTTCTCA 61.691 66.667 11.42 0.00 42.83 3.27
2215 2494 1.468520 CGTCAAACCAGCGGAAATGAT 59.531 47.619 1.50 0.00 0.00 2.45
2456 2784 3.125316 CAATGCACAAGTTTCCCAACAG 58.875 45.455 0.00 0.00 35.05 3.16
2654 4829 2.621526 GGTCACCAAGAATTTCGGTTGT 59.378 45.455 0.00 0.00 0.00 3.32
2731 4910 3.557898 GCTTGTTGTTCTCCTCAGATGGA 60.558 47.826 0.00 0.00 34.52 3.41
2761 4944 3.034721 TGACTTCCGTTGTGGTGTATC 57.965 47.619 0.00 0.00 39.52 2.24
2802 4985 3.861840 TGATTGCTGTCAGTTAGCTACC 58.138 45.455 0.93 0.00 41.66 3.18
2805 4988 1.067846 TGCTGTCAGTTAGCTACCGTG 60.068 52.381 0.93 0.00 41.66 4.94
2971 5238 5.296780 CCAACGAGCTATGTGATGGTTTTAT 59.703 40.000 0.00 0.00 30.86 1.40
3039 5306 6.038714 GGAAGTGGCAAAAATCTAGATACCAG 59.961 42.308 5.46 0.00 0.00 4.00
3061 5328 4.538738 GGTCTTCATACAGTCTAGACCCT 58.461 47.826 19.38 7.17 45.84 4.34
3084 5351 7.665974 CCCTGACACTTTCTAGTAAGGAAAATT 59.334 37.037 13.03 0.00 33.55 1.82
3164 5432 4.937620 GGTTATCAATGCAGTTCACAGAGA 59.062 41.667 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 117 5.163784 TGTTACAATCGTTTTTGAACGGTGA 60.164 36.000 17.01 3.10 45.45 4.02
172 185 9.773328 ACACATGACGAACATATTATTTCAAAG 57.227 29.630 0.00 0.00 37.46 2.77
398 442 1.933247 AACAAAACCATGGTTGCGTG 58.067 45.000 30.44 26.77 38.47 5.34
451 497 9.150348 CAAAGTAAATTTGTGTGAAGGAAAACT 57.850 29.630 0.00 0.00 42.84 2.66
522 572 1.025812 CACTGTTTTGGGTAACGCCA 58.974 50.000 0.00 0.00 39.65 5.69
529 579 1.476488 GCTCACAACACTGTTTTGGGT 59.524 47.619 8.62 0.00 31.64 4.51
770 959 3.965539 AGCTTTGCGGCGAGCTGAT 62.966 57.895 24.05 6.30 46.82 2.90
832 1038 3.058160 CTGCGCCACCCCAGAAAG 61.058 66.667 4.18 0.00 0.00 2.62
1114 1359 2.817258 TGGGCAACTCCTTTTTGATACG 59.183 45.455 0.00 0.00 34.39 3.06
1334 1579 0.239082 AGTCGCACGAATGTACGTCA 59.761 50.000 0.00 0.00 44.76 4.35
1537 1788 2.877097 TGTTGGTGTATGTCAGGCAT 57.123 45.000 0.00 0.00 41.42 4.40
1620 1871 1.827789 ACACCGGTGTGCAGCAAAT 60.828 52.632 38.46 11.33 46.86 2.32
1699 1968 7.038516 TGCTTCCATATCTGTGATCTGTATGAT 60.039 37.037 0.00 0.00 38.27 2.45
2215 2494 4.030216 TGAAGACCATGCATACCAGAGTA 58.970 43.478 0.00 0.00 0.00 2.59
2389 2714 4.593206 TCCTCACACCTGAATTTACAGACT 59.407 41.667 0.00 0.00 39.94 3.24
2654 4829 1.301637 CACACCATGCCTGTCACGA 60.302 57.895 0.00 0.00 0.00 4.35
2761 4944 4.196971 TCAATCATCATCTGTGCTTCCAG 58.803 43.478 0.00 0.00 0.00 3.86
2802 4985 6.311200 TCATCATCAACTCATTGTCTAACACG 59.689 38.462 0.00 0.00 37.11 4.49
2805 4988 9.897744 TTTTTCATCATCAACTCATTGTCTAAC 57.102 29.630 0.00 0.00 37.11 2.34
2833 5016 2.601367 ATGGCAAAGCAAGCGGGT 60.601 55.556 0.00 0.00 0.00 5.28
2971 5238 3.133691 GCGACATTCTAGATTGCATCCA 58.866 45.455 13.33 0.00 0.00 3.41
3061 5328 9.621629 TGAAATTTTCCTTACTAGAAAGTGTCA 57.378 29.630 6.68 0.00 35.82 3.58
3122 5390 8.081633 TGATAACCATCAATGAGAAAACAACAC 58.918 33.333 0.00 0.00 38.25 3.32


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

AutoCloner maintained by Alex Coulton.