Multiple sequence alignment - TraesCS1B01G119800

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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 TraesCS1B01G119800 chr1B 100.000 3085 0 0 1 3085 142092738 142095822 0.000000e+00 5698
1 TraesCS1B01G119800 chr1B 98.093 2098 35 5 1 2096 142036479 142038573 0.000000e+00 3648
2 TraesCS1B01G119800 chr1B 97.349 2037 47 6 1 2033 141843969 141846002 0.000000e+00 3456
3 TraesCS1B01G119800 chr1B 96.296 1215 36 6 51 1260 142025682 142026892 0.000000e+00 1986
4 TraesCS1B01G119800 chr1B 90.311 1383 85 16 735 2101 142134784 142133435 0.000000e+00 1766
5 TraesCS1B01G119800 chr1B 93.472 1103 71 1 932 2034 142086346 142087447 0.000000e+00 1637
6 TraesCS1B01G119800 chr1B 95.048 727 30 1 2365 3085 685091668 685090942 0.000000e+00 1138
7 TraesCS1B01G119800 chr1B 97.490 239 4 2 2101 2339 128813342 128813578 1.030000e-109 407
8 TraesCS1B01G119800 chr1D 93.298 2089 110 19 1 2077 87902649 87904719 0.000000e+00 3055
9 TraesCS1B01G119800 chr1D 91.831 1371 83 14 742 2101 88282852 88281500 0.000000e+00 1884
10 TraesCS1B01G119800 chr1D 92.308 728 41 10 1 721 88184090 88184809 0.000000e+00 1020
11 TraesCS1B01G119800 chr1D 91.141 745 47 11 742 1480 88244584 88243853 0.000000e+00 992
12 TraesCS1B01G119800 chr1D 94.661 487 21 2 1595 2077 88243854 88243369 0.000000e+00 750
13 TraesCS1B01G119800 chr1D 92.950 383 27 0 1695 2077 88215120 88215502 2.690000e-155 558
14 TraesCS1B01G119800 chr1D 83.293 413 37 19 1 409 87896500 87896884 4.890000e-93 351
15 TraesCS1B01G119800 chr1D 79.386 456 58 21 6 453 88283666 88283239 3.890000e-74 289
16 TraesCS1B01G119800 chr1D 96.450 169 5 1 1 168 87902434 87902602 8.430000e-71 278
17 TraesCS1B01G119800 chr1A 92.046 1295 74 15 736 2026 84796957 84795688 0.000000e+00 1794
18 TraesCS1B01G119800 chr1A 92.043 1219 68 12 813 2026 85006766 85005572 0.000000e+00 1687
19 TraesCS1B01G119800 chr1A 82.229 332 47 10 254 583 84620710 84621031 3.030000e-70 276
20 TraesCS1B01G119800 chr1A 80.874 366 53 15 254 616 84483469 84483820 3.920000e-69 272
21 TraesCS1B01G119800 chr1A 86.503 163 4 14 742 897 84621093 84621244 2.460000e-36 163
22 TraesCS1B01G119800 chr1A 93.506 77 1 2 742 814 84483852 84483928 9.040000e-21 111
23 TraesCS1B01G119800 chr1A 92.208 77 2 2 742 814 84055950 84056026 4.210000e-19 106
24 TraesCS1B01G119800 chr1A 90.361 83 4 2 736 814 84616123 84616205 4.210000e-19 106
25 TraesCS1B01G119800 chr4D 93.504 1170 63 4 929 2095 464798073 464796914 0.000000e+00 1727
26 TraesCS1B01G119800 chr4D 77.447 705 111 40 27 710 464798900 464798223 8.080000e-101 377
27 TraesCS1B01G119800 chr3B 94.334 1006 57 0 1065 2070 535705558 535704553 0.000000e+00 1543
28 TraesCS1B01G119800 chr3B 91.174 997 66 11 2096 3085 10752607 10751626 0.000000e+00 1334
29 TraesCS1B01G119800 chr3B 92.971 754 39 10 1 745 535709443 535708695 0.000000e+00 1086
30 TraesCS1B01G119800 chr3B 97.490 239 6 0 2101 2339 43059349 43059111 2.860000e-110 409
31 TraesCS1B01G119800 chr3B 97.490 239 4 2 2101 2339 65201424 65201660 1.030000e-109 407
32 TraesCS1B01G119800 chr5B 93.272 758 46 1 2333 3085 584257190 584257947 0.000000e+00 1112
33 TraesCS1B01G119800 chr5B 93.140 758 47 1 2333 3085 584262764 584263521 0.000000e+00 1107
34 TraesCS1B01G119800 chr5B 97.908 239 3 2 2101 2339 205156765 205156529 2.210000e-111 412
35 TraesCS1B01G119800 chr5B 86.000 150 17 2 2336 2484 599923617 599923471 1.150000e-34 158
36 TraesCS1B01G119800 chr4A 92.603 730 47 2 2362 3085 725556620 725555892 0.000000e+00 1042
37 TraesCS1B01G119800 chr7A 91.523 755 54 7 2339 3085 669193428 669192676 0.000000e+00 1031
38 TraesCS1B01G119800 chr7A 91.114 754 58 5 2339 3085 669149469 669148718 0.000000e+00 1013
39 TraesCS1B01G119800 chr7B 92.717 714 46 1 2378 3085 71304522 71303809 0.000000e+00 1026
40 TraesCS1B01G119800 chr7B 88.950 733 48 15 2101 2806 651444360 651445086 0.000000e+00 874
41 TraesCS1B01G119800 chr7B 88.989 445 31 12 2099 2534 69723239 69722804 4.530000e-148 534
42 TraesCS1B01G119800 chr5D 91.247 754 64 2 2333 3085 424060883 424061635 0.000000e+00 1026
43 TraesCS1B01G119800 chr2B 90.735 313 24 5 2101 2410 793644952 793644642 2.210000e-111 412
44 TraesCS1B01G119800 chr2B 99.115 226 2 0 2101 2326 757077208 757077433 1.030000e-109 407


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 TraesCS1B01G119800 chr1B 142092738 142095822 3084 False 5698.0 5698 100.0000 1 3085 1 chr1B.!!$F6 3084
1 TraesCS1B01G119800 chr1B 142036479 142038573 2094 False 3648.0 3648 98.0930 1 2096 1 chr1B.!!$F4 2095
2 TraesCS1B01G119800 chr1B 141843969 141846002 2033 False 3456.0 3456 97.3490 1 2033 1 chr1B.!!$F2 2032
3 TraesCS1B01G119800 chr1B 142025682 142026892 1210 False 1986.0 1986 96.2960 51 1260 1 chr1B.!!$F3 1209
4 TraesCS1B01G119800 chr1B 142133435 142134784 1349 True 1766.0 1766 90.3110 735 2101 1 chr1B.!!$R1 1366
5 TraesCS1B01G119800 chr1B 142086346 142087447 1101 False 1637.0 1637 93.4720 932 2034 1 chr1B.!!$F5 1102
6 TraesCS1B01G119800 chr1B 685090942 685091668 726 True 1138.0 1138 95.0480 2365 3085 1 chr1B.!!$R2 720
7 TraesCS1B01G119800 chr1D 87902434 87904719 2285 False 1666.5 3055 94.8740 1 2077 2 chr1D.!!$F4 2076
8 TraesCS1B01G119800 chr1D 88281500 88283666 2166 True 1086.5 1884 85.6085 6 2101 2 chr1D.!!$R2 2095
9 TraesCS1B01G119800 chr1D 88184090 88184809 719 False 1020.0 1020 92.3080 1 721 1 chr1D.!!$F2 720
10 TraesCS1B01G119800 chr1D 88243369 88244584 1215 True 871.0 992 92.9010 742 2077 2 chr1D.!!$R1 1335
11 TraesCS1B01G119800 chr1A 84795688 84796957 1269 True 1794.0 1794 92.0460 736 2026 1 chr1A.!!$R1 1290
12 TraesCS1B01G119800 chr1A 85005572 85006766 1194 True 1687.0 1687 92.0430 813 2026 1 chr1A.!!$R2 1213
13 TraesCS1B01G119800 chr1A 84620710 84621244 534 False 219.5 276 84.3660 254 897 2 chr1A.!!$F4 643
14 TraesCS1B01G119800 chr4D 464796914 464798900 1986 True 1052.0 1727 85.4755 27 2095 2 chr4D.!!$R1 2068
15 TraesCS1B01G119800 chr3B 10751626 10752607 981 True 1334.0 1334 91.1740 2096 3085 1 chr3B.!!$R1 989
16 TraesCS1B01G119800 chr3B 535704553 535709443 4890 True 1314.5 1543 93.6525 1 2070 2 chr3B.!!$R3 2069
17 TraesCS1B01G119800 chr5B 584257190 584257947 757 False 1112.0 1112 93.2720 2333 3085 1 chr5B.!!$F1 752
18 TraesCS1B01G119800 chr5B 584262764 584263521 757 False 1107.0 1107 93.1400 2333 3085 1 chr5B.!!$F2 752
19 TraesCS1B01G119800 chr4A 725555892 725556620 728 True 1042.0 1042 92.6030 2362 3085 1 chr4A.!!$R1 723
20 TraesCS1B01G119800 chr7A 669192676 669193428 752 True 1031.0 1031 91.5230 2339 3085 1 chr7A.!!$R2 746
21 TraesCS1B01G119800 chr7A 669148718 669149469 751 True 1013.0 1013 91.1140 2339 3085 1 chr7A.!!$R1 746
22 TraesCS1B01G119800 chr7B 71303809 71304522 713 True 1026.0 1026 92.7170 2378 3085 1 chr7B.!!$R2 707
23 TraesCS1B01G119800 chr7B 651444360 651445086 726 False 874.0 874 88.9500 2101 2806 1 chr7B.!!$F1 705
24 TraesCS1B01G119800 chr5D 424060883 424061635 752 False 1026.0 1026 91.2470 2333 3085 1 chr5D.!!$F1 752

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
363 592 8.907222 AAAAAGTGTTCATGCCTTTGAAATAT 57.093 26.923 0.0 0.0 37.36 1.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2123 5385 0.253327 AAACTGCTACTGGGCTAGGC 59.747 55.0 8.0 8.0 0.0 3.93 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
363 592 8.907222 AAAAAGTGTTCATGCCTTTGAAATAT 57.093 26.923 0.00 0.00 37.36 1.28
364 593 9.995003 AAAAAGTGTTCATGCCTTTGAAATATA 57.005 25.926 0.00 0.00 37.36 0.86
579 819 9.712305 TTGAAATTTTAAGGAGTGTTTCAACAA 57.288 25.926 6.91 0.00 41.21 2.83
1101 4352 3.197790 CGTCCATGGCGGCAAGAG 61.198 66.667 18.31 9.19 33.14 2.85
1231 4482 4.309950 GCCGTGAAGTGGGTCCGT 62.310 66.667 0.00 0.00 0.00 4.69
1321 4572 2.114625 TGTCGGGGTCACGAGTCT 59.885 61.111 0.00 0.00 44.42 3.24
1390 4641 0.965866 TCCTCGTCATGGAGCTCGTT 60.966 55.000 7.83 0.00 32.57 3.85
1621 4872 1.007721 AGAGTGCCCTATGAGGAGTGT 59.992 52.381 0.00 0.00 37.67 3.55
1678 4929 0.899720 TGGAAGGCAACCGGTACTAG 59.100 55.000 8.00 0.00 37.17 2.57
2111 5371 7.221450 TGTACTGTAGTAAGTGCTGGAATTTT 58.779 34.615 0.00 0.00 34.26 1.82
2115 5375 5.472137 TGTAGTAAGTGCTGGAATTTTGTCC 59.528 40.000 0.00 0.00 38.27 4.02
2117 5377 3.733443 AAGTGCTGGAATTTTGTCCAC 57.267 42.857 0.00 0.00 42.97 4.02
2120 5382 3.706086 AGTGCTGGAATTTTGTCCACTTT 59.294 39.130 0.00 0.00 42.97 2.66
2123 5385 3.803368 GCTGGAATTTTGTCCACTTTGGG 60.803 47.826 0.00 0.00 42.97 4.12
2124 5386 2.103941 TGGAATTTTGTCCACTTTGGGC 59.896 45.455 0.00 0.00 42.97 5.36
2125 5387 2.549992 GGAATTTTGTCCACTTTGGGCC 60.550 50.000 0.00 0.00 42.76 5.80
2126 5388 2.101640 ATTTTGTCCACTTTGGGCCT 57.898 45.000 4.53 0.00 42.76 5.19
2127 5389 2.757894 TTTTGTCCACTTTGGGCCTA 57.242 45.000 4.53 0.00 42.76 3.93
2128 5390 2.286365 TTTGTCCACTTTGGGCCTAG 57.714 50.000 4.53 4.77 42.76 3.02
2129 5391 0.251165 TTGTCCACTTTGGGCCTAGC 60.251 55.000 4.53 0.00 42.76 3.42
2130 5392 2.137177 TGTCCACTTTGGGCCTAGCC 62.137 60.000 4.53 0.00 42.76 3.93
2139 5401 2.825264 GGCCTAGCCCAGTAGCAG 59.175 66.667 0.00 0.00 44.06 4.24
2174 5436 3.771577 AATAAATCCTAGAGGCCCACG 57.228 47.619 0.00 0.00 34.44 4.94
2175 5437 0.756903 TAAATCCTAGAGGCCCACGC 59.243 55.000 0.00 0.00 34.44 5.34
2197 5459 0.680618 CCCATTTGTGCAAGGCAAGA 59.319 50.000 0.00 0.00 41.47 3.02
2199 5461 1.337447 CCATTTGTGCAAGGCAAGAGG 60.337 52.381 0.00 0.00 41.47 3.69
2201 5463 0.746063 TTTGTGCAAGGCAAGAGGTG 59.254 50.000 0.00 0.00 41.47 4.00
2202 5464 1.108727 TTGTGCAAGGCAAGAGGTGG 61.109 55.000 0.00 0.00 41.47 4.61
2203 5465 1.228245 GTGCAAGGCAAGAGGTGGA 60.228 57.895 0.00 0.00 41.47 4.02
2600 5886 4.591072 AGTTCTTGGCTCTAGTTTCTGTCT 59.409 41.667 0.00 0.00 0.00 3.41
2838 6131 8.434392 ACCTTATTATAGGCAATTTACCTCGAA 58.566 33.333 0.00 0.00 38.99 3.71
2927 6220 8.257822 GAGAGCAGTCTTATGGTTTCAAACCG 62.258 46.154 14.79 0.16 43.66 4.44
3013 6306 8.950210 CAAGCTTTTCAGAAAATGGATACTCTA 58.050 33.333 8.81 0.00 37.61 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
512 748 7.911727 GTGTGAACACTTCCTAAAAATTACGTT 59.088 33.333 6.33 0.00 43.25 3.99
514 750 7.411274 TGTGTGAACACTTCCTAAAAATTACG 58.589 34.615 14.28 0.00 46.55 3.18
1306 4557 2.715749 TAATAGACTCGTGACCCCGA 57.284 50.000 0.00 0.00 35.22 5.14
1321 4572 5.622233 CGCCACATCCAAGATCTCGATAATA 60.622 44.000 0.00 0.00 0.00 0.98
1419 4670 2.093537 CTCGGATACAGGCCTCCAGC 62.094 65.000 0.00 0.00 42.60 4.85
1601 4852 1.007721 ACACTCCTCATAGGGCACTCT 59.992 52.381 0.00 0.00 35.59 3.24
2111 5371 1.378762 GCTAGGCCCAAAGTGGACA 59.621 57.895 0.00 0.00 40.96 4.02
2123 5385 0.253327 AAACTGCTACTGGGCTAGGC 59.747 55.000 8.00 8.00 0.00 3.93
2124 5386 1.555075 TGAAACTGCTACTGGGCTAGG 59.445 52.381 2.02 0.00 0.00 3.02
2125 5387 2.497675 TCTGAAACTGCTACTGGGCTAG 59.502 50.000 0.00 0.00 0.00 3.42
2126 5388 2.536066 TCTGAAACTGCTACTGGGCTA 58.464 47.619 0.00 0.00 0.00 3.93
2127 5389 1.352083 TCTGAAACTGCTACTGGGCT 58.648 50.000 0.00 0.00 0.00 5.19
2128 5390 2.185004 TTCTGAAACTGCTACTGGGC 57.815 50.000 0.00 0.00 0.00 5.36
2129 5391 4.156739 GGAATTTCTGAAACTGCTACTGGG 59.843 45.833 4.73 0.00 0.00 4.45
2130 5392 5.006386 AGGAATTTCTGAAACTGCTACTGG 58.994 41.667 3.77 0.00 0.00 4.00
2131 5393 7.672983 TTAGGAATTTCTGAAACTGCTACTG 57.327 36.000 11.48 0.00 0.00 2.74
2136 5398 9.521503 GGATTTATTAGGAATTTCTGAAACTGC 57.478 33.333 4.73 0.00 0.00 4.40
2174 5436 1.375013 CCTTGCACAAATGGGCTGC 60.375 57.895 9.34 0.00 46.62 5.25
2175 5437 1.375013 GCCTTGCACAAATGGGCTG 60.375 57.895 9.34 2.06 46.62 4.85
2197 5459 4.661709 TGGGACTAAACTTTAGTTCCACCT 59.338 41.667 28.04 2.35 45.69 4.00
2201 5463 6.569801 GCAATGTGGGACTAAACTTTAGTTCC 60.570 42.308 24.49 24.49 42.37 3.62
2202 5464 6.206829 AGCAATGTGGGACTAAACTTTAGTTC 59.793 38.462 14.17 12.33 37.25 3.01
2203 5465 6.068670 AGCAATGTGGGACTAAACTTTAGTT 58.931 36.000 14.17 0.00 40.50 2.24
2250 5512 3.053826 GGGAAGGAGCCTCCCTTATAAA 58.946 50.000 7.26 0.00 45.97 1.40
2336 5598 2.490217 CTACTGTCCCGACCTGCG 59.510 66.667 0.00 0.00 40.47 5.18
2337 5599 2.893398 CCTACTGTCCCGACCTGC 59.107 66.667 0.00 0.00 0.00 4.85
2781 6074 9.768662 GGATTGTTGGAAATATGAGCAATTTAT 57.231 29.630 0.00 0.00 0.00 1.40
2834 6127 1.269448 GGAAGCAGCAAAACCATTCGA 59.731 47.619 0.00 0.00 0.00 3.71
2838 6131 2.232941 CTCATGGAAGCAGCAAAACCAT 59.767 45.455 0.00 1.00 41.25 3.55
2927 6220 0.721718 GTGGCGTCATAGCAACTCAC 59.278 55.000 0.00 0.00 38.03 3.51
3013 6306 4.260170 CACTCAAGAGAGCAGCCTTAAAT 58.740 43.478 3.73 0.00 46.09 1.40


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

AutoCloner maintained by Alex Coulton.