Multiple sequence alignment - TraesCS3B01G076100

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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 TraesCS3B01G076100 chr3B 100.000 2459 0 0 1 2459 46931306 46933764 0.000000e+00 4542.0
1 TraesCS3B01G076100 chr3B 95.241 1618 33 4 886 2459 46904121 46905738 0.000000e+00 2521.0
2 TraesCS3B01G076100 chr3B 98.217 729 13 0 1 729 46902027 46902755 0.000000e+00 1275.0
3 TraesCS3B01G076100 chr3B 87.084 782 81 3 886 1647 46033327 46032546 0.000000e+00 867.0
4 TraesCS3B01G076100 chr3B 100.000 155 0 0 733 887 46903767 46903921 1.110000e-73 287.0
5 TraesCS3B01G076100 chr3B 94.792 96 4 1 733 828 46793129 46793223 5.480000e-32 148.0
6 TraesCS3B01G076100 chr3B 92.405 79 5 1 451 529 169826635 169826558 7.190000e-21 111.0
7 TraesCS3B01G076100 chr3D 88.107 782 73 3 886 1647 27551169 27550388 0.000000e+00 911.0
8 TraesCS3B01G076100 chr3D 88.940 651 52 4 886 1516 27944103 27944753 0.000000e+00 785.0
9 TraesCS3B01G076100 chr3D 92.903 155 11 0 733 887 27943748 27943902 2.460000e-55 226.0
10 TraesCS3B01G076100 chr3A 87.484 767 87 6 888 1647 37651188 37650424 0.000000e+00 876.0
11 TraesCS3B01G076100 chr3A 88.226 654 57 3 886 1519 37827386 37826733 0.000000e+00 763.0
12 TraesCS3B01G076100 chr3A 94.839 155 8 0 733 887 37827741 37827587 2.440000e-60 243.0
13 TraesCS3B01G076100 chr3A 84.817 191 22 5 148 332 692035471 692035282 4.180000e-43 185.0
14 TraesCS3B01G076100 chr3A 100.000 31 0 0 574 604 300789625 300789655 9.500000e-05 58.4
15 TraesCS3B01G076100 chr3A 96.970 33 1 0 2094 2126 749822166 749822198 3.420000e-04 56.5
16 TraesCS3B01G076100 chrUn 84.520 646 80 15 889 1521 287642994 287642356 2.690000e-174 621.0
17 TraesCS3B01G076100 chrUn 80.155 388 52 11 2095 2459 19266516 19266131 1.450000e-67 267.0
18 TraesCS3B01G076100 chr4D 81.648 534 60 20 1959 2458 51507101 51506572 2.280000e-110 409.0
19 TraesCS3B01G076100 chr4D 83.819 309 23 15 44 332 183237305 183237606 4.030000e-68 268.0
20 TraesCS3B01G076100 chr4D 91.071 168 12 1 2295 2459 10675456 10675289 8.850000e-55 224.0
21 TraesCS3B01G076100 chr1D 84.986 353 22 19 1 334 10381476 10381136 1.820000e-86 329.0
22 TraesCS3B01G076100 chr1D 90.123 81 4 2 451 531 46104585 46104661 4.330000e-18 102.0
23 TraesCS3B01G076100 chr1D 81.679 131 11 9 115 233 90162788 90162917 2.010000e-16 97.1
24 TraesCS3B01G076100 chr1D 100.000 28 0 0 2095 2122 435034373 435034400 4.000000e-03 52.8
25 TraesCS3B01G076100 chr4B 83.380 361 28 16 2131 2459 642967235 642967595 3.070000e-79 305.0
26 TraesCS3B01G076100 chr2B 82.645 363 29 16 2131 2459 639545776 639545414 8.600000e-75 291.0
27 TraesCS3B01G076100 chr2B 94.231 156 6 1 2307 2459 719432378 719432223 4.090000e-58 235.0
28 TraesCS3B01G076100 chr2B 92.593 81 6 0 456 536 178771920 178772000 1.540000e-22 117.0
29 TraesCS3B01G076100 chr1A 85.563 284 19 11 1 279 12097339 12097073 6.700000e-71 278.0
30 TraesCS3B01G076100 chr1B 83.537 328 20 5 2163 2459 565500048 565499724 2.410000e-70 276.0
31 TraesCS3B01G076100 chr1B 88.095 84 6 3 451 531 605455619 605455537 2.010000e-16 97.1
32 TraesCS3B01G076100 chr5B 93.678 174 7 2 2290 2459 691228330 691228157 8.720000e-65 257.0
33 TraesCS3B01G076100 chr7D 82.958 311 24 12 44 332 564640209 564640512 1.130000e-63 254.0
34 TraesCS3B01G076100 chr7D 92.063 63 5 0 562 624 136257697 136257759 3.370000e-14 89.8
35 TraesCS3B01G076100 chr7D 100.000 32 0 0 575 606 134504820 134504789 2.640000e-05 60.2
36 TraesCS3B01G076100 chr7D 100.000 32 0 0 575 606 174179788 174179757 2.640000e-05 60.2
37 TraesCS3B01G076100 chr7D 96.875 32 1 0 2092 2123 505394194 505394225 1.000000e-03 54.7
38 TraesCS3B01G076100 chr5D 80.374 321 24 16 44 332 448285094 448285407 8.910000e-50 207.0
39 TraesCS3B01G076100 chr7B 91.358 81 7 0 456 536 244642026 244641946 7.190000e-21 111.0
40 TraesCS3B01G076100 chr7B 91.358 81 6 1 451 531 215236356 215236277 2.590000e-20 110.0
41 TraesCS3B01G076100 chr7B 100.000 32 0 0 575 606 215234878 215234847 2.640000e-05 60.2
42 TraesCS3B01G076100 chr5A 91.358 81 6 1 451 531 705521048 705521127 2.590000e-20 110.0
43 TraesCS3B01G076100 chr5A 86.047 86 12 0 148 233 689193560 689193475 2.600000e-15 93.5
44 TraesCS3B01G076100 chr5A 100.000 32 0 0 575 606 12876831 12876800 2.640000e-05 60.2
45 TraesCS3B01G076100 chr5A 100.000 29 0 0 2094 2122 565929329 565929357 1.000000e-03 54.7
46 TraesCS3B01G076100 chr5A 100.000 28 0 0 2095 2122 618232412 618232439 4.000000e-03 52.8
47 TraesCS3B01G076100 chr6B 93.617 47 3 0 485 531 255096449 255096495 1.220000e-08 71.3
48 TraesCS3B01G076100 chr6A 96.970 33 1 0 2095 2127 46728793 46728825 3.420000e-04 56.5
49 TraesCS3B01G076100 chr6D 100.000 29 0 0 2094 2122 16633137 16633165 1.000000e-03 54.7


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 TraesCS3B01G076100 chr3B 46931306 46933764 2458 False 4542.0 4542 100.000000 1 2459 1 chr3B.!!$F2 2458
1 TraesCS3B01G076100 chr3B 46902027 46905738 3711 False 1361.0 2521 97.819333 1 2459 3 chr3B.!!$F3 2458
2 TraesCS3B01G076100 chr3B 46032546 46033327 781 True 867.0 867 87.084000 886 1647 1 chr3B.!!$R1 761
3 TraesCS3B01G076100 chr3D 27550388 27551169 781 True 911.0 911 88.107000 886 1647 1 chr3D.!!$R1 761
4 TraesCS3B01G076100 chr3D 27943748 27944753 1005 False 505.5 785 90.921500 733 1516 2 chr3D.!!$F1 783
5 TraesCS3B01G076100 chr3A 37650424 37651188 764 True 876.0 876 87.484000 888 1647 1 chr3A.!!$R1 759
6 TraesCS3B01G076100 chr3A 37826733 37827741 1008 True 503.0 763 91.532500 733 1519 2 chr3A.!!$R3 786
7 TraesCS3B01G076100 chrUn 287642356 287642994 638 True 621.0 621 84.520000 889 1521 1 chrUn.!!$R2 632
8 TraesCS3B01G076100 chr4D 51506572 51507101 529 True 409.0 409 81.648000 1959 2458 1 chr4D.!!$R2 499

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
140 141 1.055849 AAGCCCAATTTTCCCCACAC 58.944 50.0 0.0 0.0 0.0 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2093 3339 1.215655 CGGCTTAGCTGTCGGCATAC 61.216 60.0 6.39 0.0 44.79 2.39 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
46 47 9.912634 TCTAAACTTTCAAGGCATTTCTATTTG 57.087 29.630 0.00 0.00 0.00 2.32
99 100 1.673665 CTGTGAGCCAACTGGAGCC 60.674 63.158 0.00 0.00 37.39 4.70
105 106 2.429930 CCAACTGGAGCCGGACAA 59.570 61.111 5.05 0.00 37.39 3.18
116 117 2.017049 AGCCGGACAAAGACAATATGC 58.983 47.619 5.05 0.00 0.00 3.14
140 141 1.055849 AAGCCCAATTTTCCCCACAC 58.944 50.000 0.00 0.00 0.00 3.82
196 197 5.804639 TCACACTGCAGACCTTGTTATTAT 58.195 37.500 23.35 0.00 0.00 1.28
282 283 2.052782 TGTGCAGAGCCGATCTACTA 57.947 50.000 0.00 0.00 36.10 1.82
405 406 3.243359 AGAACCAAATGAAGCCTTCCA 57.757 42.857 1.21 0.00 0.00 3.53
487 488 6.995686 TGAGCCTTTTAAACTACAACATCAGA 59.004 34.615 0.00 0.00 0.00 3.27
540 541 7.176165 TGCTCTGTTCATCATCTTCAGAATTTT 59.824 33.333 0.00 0.00 35.26 1.82
714 715 3.878778 CCTAATTGGTGACTGGAGAAGG 58.121 50.000 0.00 0.00 0.00 3.46
729 730 3.644265 GGAGAAGGGGAGGAGATTAACTC 59.356 52.174 0.00 0.00 44.24 3.01
1216 2446 1.369625 GGCGTCCGAGATGATGTTTT 58.630 50.000 0.00 0.00 0.00 2.43
1317 2547 2.241281 TCATCTTTCCCCGTGGTCTA 57.759 50.000 0.00 0.00 0.00 2.59
1380 2610 1.217511 CTCGGTGCTCAGCAGTCAT 59.782 57.895 0.00 0.00 40.08 3.06
1460 2691 1.148273 GCTGGTGGCCCGAATGATA 59.852 57.895 0.00 0.00 34.27 2.15
1506 2737 7.054124 TCCTGACAACAAGACTACTGATTTTT 58.946 34.615 0.00 0.00 0.00 1.94
1533 2764 9.482627 GATGGACTTCCTGATAAGTTATGTAAG 57.517 37.037 0.00 1.73 39.78 2.34
1670 2906 4.082625 CGTATATACCATGCACTACCGGAA 60.083 45.833 9.46 0.00 0.00 4.30
1753 2999 3.673594 GCTGCTGTCAGTGTAGATTACGT 60.674 47.826 0.93 0.00 42.29 3.57
1785 3031 5.479306 TCTTGTAAGACTGTTGGCATAGAC 58.521 41.667 6.31 0.87 0.00 2.59
1820 3066 2.439883 ACCTAGGACGACGGCCTC 60.440 66.667 29.43 0.00 36.96 4.70
1871 3117 1.268692 ACGTAGTTTTGCACGAGACGA 60.269 47.619 12.59 0.00 37.78 4.20
1874 3120 1.200839 GTTTTGCACGAGACGACCG 59.799 57.895 0.00 0.00 0.00 4.79
2038 3284 2.277084 GACAAAATCTATGCCGACGGT 58.723 47.619 16.73 0.00 0.00 4.83
2082 3328 0.537188 GTCGATCACTGGGTGTCCAT 59.463 55.000 0.00 0.00 43.11 3.41
2093 3339 3.660571 TGTCCATGGGTGCAGGGG 61.661 66.667 13.02 0.00 0.00 4.79
2213 3460 1.336125 GTAGCCATACCGACGCTAAGT 59.664 52.381 0.00 0.00 36.88 2.24
2224 3471 0.666913 ACGCTAAGTCGTCGGCATAT 59.333 50.000 0.00 0.00 38.44 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 4.527816 TGAAAGCACCAAATAGAAATGCCT 59.472 37.500 0.00 0.00 36.96 4.75
99 100 6.603237 TTATCTGCATATTGTCTTTGTCCG 57.397 37.500 0.00 0.00 0.00 4.79
105 106 5.052693 TGGGCTTATCTGCATATTGTCTT 57.947 39.130 0.00 0.00 34.04 3.01
116 117 3.132824 GTGGGGAAAATTGGGCTTATCTG 59.867 47.826 0.00 0.00 0.00 2.90
282 283 6.996282 TCATGCATTATCTTGTGATGTGATCT 59.004 34.615 0.00 0.00 34.32 2.75
405 406 2.158519 ACCCCTGTTTGATCGAACCTTT 60.159 45.455 20.83 1.03 0.00 3.11
415 416 2.554344 GCCAGTTGATACCCCTGTTTGA 60.554 50.000 0.00 0.00 0.00 2.69
729 730 2.224079 GTGCATTGTATATGGTGCTCGG 59.776 50.000 0.00 0.00 38.37 4.63
730 731 2.096762 CGTGCATTGTATATGGTGCTCG 60.097 50.000 12.66 12.66 44.34 5.03
731 732 2.349817 GCGTGCATTGTATATGGTGCTC 60.350 50.000 0.00 0.00 38.37 4.26
1216 2446 2.662596 CACGCTGCCACTAGGGAA 59.337 61.111 0.00 0.00 40.01 3.97
1240 2470 3.366052 ACCAGTGGTGTCAAAGAAAGT 57.634 42.857 15.86 0.00 32.98 2.66
1380 2610 3.911260 TGATTCCAACCACACTAGGGTTA 59.089 43.478 0.00 0.00 46.60 2.85
1452 2683 7.205992 TCCATCTCTCTGAACTTTATCATTCG 58.794 38.462 0.00 0.00 0.00 3.34
1460 2691 6.658391 CAGGAATTTCCATCTCTCTGAACTTT 59.342 38.462 17.57 0.00 39.61 2.66
1506 2737 7.437713 ACATAACTTATCAGGAAGTCCATCA 57.562 36.000 0.00 0.00 38.75 3.07
1753 2999 3.819337 ACAGTCTTACAAGAGTACGCTGA 59.181 43.478 0.00 0.00 36.59 4.26
1923 3169 4.681978 GGTCGTCGGCTTGCCTGT 62.682 66.667 10.12 0.00 0.00 4.00
2082 3328 3.738481 GGCATACCCCTGCACCCA 61.738 66.667 0.00 0.00 44.12 4.51
2093 3339 1.215655 CGGCTTAGCTGTCGGCATAC 61.216 60.000 6.39 0.00 44.79 2.39
2140 3386 0.179092 GCTATGCCGACGGGTAAGTT 60.179 55.000 17.22 0.00 34.97 2.66
2213 3460 3.186909 CAGAACAGAAATATGCCGACGA 58.813 45.455 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.