Multiple sequence alignment - TraesCS5B01G213000

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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 TraesCS5B01G213000 chr5B 100.000 3515 0 0 658 4172 383537009 383540523 0.000000e+00 6492
1 TraesCS5B01G213000 chr5B 100.000 391 0 0 1 391 383536352 383536742 0.000000e+00 723
2 TraesCS5B01G213000 chr5B 99.488 391 2 0 1 391 56907055 56906665 0.000000e+00 712
3 TraesCS5B01G213000 chr5B 75.535 1075 208 43 1255 2301 386639560 386638513 1.050000e-130 477
4 TraesCS5B01G213000 chr5B 94.492 236 11 2 658 892 514841404 514841170 3.070000e-96 363
5 TraesCS5B01G213000 chr5B 87.500 192 20 4 2304 2493 44657218 44657407 7.020000e-53 219
6 TraesCS5B01G213000 chr5D 98.202 3282 50 5 891 4170 330708154 330704880 0.000000e+00 5725
7 TraesCS5B01G213000 chr5D 83.636 220 32 4 2298 2515 488352312 488352529 1.970000e-48 204
8 TraesCS5B01G213000 chr5D 94.805 77 3 1 4085 4161 332506257 332506332 7.330000e-23 119
9 TraesCS5B01G213000 chr5A 99.488 391 2 0 1 391 346307029 346306639 0.000000e+00 712
10 TraesCS5B01G213000 chr5A 77.324 882 147 40 1442 2301 426268383 426267533 4.880000e-129 472
11 TraesCS5B01G213000 chr5A 80.577 520 77 12 2635 3152 426266416 426265919 3.040000e-101 379
12 TraesCS5B01G213000 chr5A 95.319 235 11 0 658 892 346306530 346306296 1.420000e-99 374
13 TraesCS5B01G213000 chr5A 86.700 203 25 2 2297 2499 569989743 569989543 1.510000e-54 224
14 TraesCS5B01G213000 chr5A 94.805 77 2 1 4086 4160 638032980 638032904 7.330000e-23 119
15 TraesCS5B01G213000 chr3B 99.488 391 2 0 1 391 546830649 546831039 0.000000e+00 712
16 TraesCS5B01G213000 chr3B 96.170 235 9 0 658 892 546831148 546831382 6.540000e-103 385
17 TraesCS5B01G213000 chr3B 94.894 235 12 0 658 892 681202676 681202910 6.590000e-98 368
18 TraesCS5B01G213000 chr2B 99.488 391 2 0 1 391 652849087 652849477 0.000000e+00 712
19 TraesCS5B01G213000 chr2B 92.771 83 3 2 4085 4165 514348604 514348523 2.640000e-22 117
20 TraesCS5B01G213000 chr2B 92.105 76 6 0 4085 4160 185025780 185025705 1.590000e-19 108
21 TraesCS5B01G213000 chr1A 99.488 391 2 0 1 391 63762968 63763358 0.000000e+00 712
22 TraesCS5B01G213000 chr1A 98.977 391 4 0 1 391 320479002 320479392 0.000000e+00 701
23 TraesCS5B01G213000 chr1A 98.844 173 0 2 3605 3775 464801221 464801049 1.460000e-79 307
24 TraesCS5B01G213000 chr1A 98.276 174 2 1 3601 3773 58842241 58842068 1.880000e-78 303
25 TraesCS5B01G213000 chr1A 85.784 204 23 5 2293 2495 581544089 581543891 1.180000e-50 211
26 TraesCS5B01G213000 chr4B 99.233 391 3 0 1 391 139743356 139742966 0.000000e+00 706
27 TraesCS5B01G213000 chr4B 95.319 235 11 0 658 892 139742857 139742623 1.420000e-99 374
28 TraesCS5B01G213000 chr4A 99.233 391 3 0 1 391 683251280 683251670 0.000000e+00 706
29 TraesCS5B01G213000 chr4A 86.275 204 25 2 2297 2497 83316631 83316834 7.020000e-53 219
30 TraesCS5B01G213000 chr1B 99.233 391 3 0 1 391 167929394 167929784 0.000000e+00 706
31 TraesCS5B01G213000 chr1B 93.750 80 3 2 4085 4163 634499561 634499483 7.330000e-23 119
32 TraesCS5B01G213000 chr3A 95.745 235 10 0 658 892 506481393 506481627 3.040000e-101 379
33 TraesCS5B01G213000 chr3A 95.217 230 11 0 661 890 199412288 199412059 8.520000e-97 364
34 TraesCS5B01G213000 chr2A 95.726 234 10 0 658 891 672537085 672536852 1.090000e-100 377
35 TraesCS5B01G213000 chr2A 86.341 205 22 6 2297 2499 584149442 584149642 7.020000e-53 219
36 TraesCS5B01G213000 chr2A 89.888 89 6 3 4078 4164 24112190 24112277 1.230000e-20 111
37 TraesCS5B01G213000 chr7B 94.894 235 12 0 658 892 504201789 504202023 6.590000e-98 368
38 TraesCS5B01G213000 chr7B 97.740 177 2 2 3603 3777 129222266 129222442 1.880000e-78 303
39 TraesCS5B01G213000 chr7B 94.764 191 5 5 3585 3771 678620576 678620765 4.080000e-75 292
40 TraesCS5B01G213000 chr7B 85.922 206 23 5 2296 2501 74193693 74193892 9.080000e-52 215
41 TraesCS5B01G213000 chr6B 98.830 171 1 1 3607 3776 26516717 26516887 1.880000e-78 303
42 TraesCS5B01G213000 chr6B 94.416 197 7 4 3578 3771 602841133 602840938 2.440000e-77 300
43 TraesCS5B01G213000 chr7A 95.699 186 4 3 3597 3780 348798027 348798210 3.150000e-76 296
44 TraesCS5B01G213000 chr7A 87.368 190 22 2 2312 2500 30808989 30808801 2.530000e-52 217
45 TraesCS5B01G213000 chrUn 93.878 196 8 4 3607 3800 10129539 10129732 4.080000e-75 292
46 TraesCS5B01G213000 chr2D 98.611 72 1 0 4086 4157 642198717 642198788 1.220000e-25 128
47 TraesCS5B01G213000 chr6D 95.890 73 3 0 4085 4157 12314739 12314811 7.330000e-23 119


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 TraesCS5B01G213000 chr5B 383536352 383540523 4171 False 3607.5 6492 100.0000 1 4172 2 chr5B.!!$F2 4171
1 TraesCS5B01G213000 chr5B 386638513 386639560 1047 True 477.0 477 75.5350 1255 2301 1 chr5B.!!$R2 1046
2 TraesCS5B01G213000 chr5D 330704880 330708154 3274 True 5725.0 5725 98.2020 891 4170 1 chr5D.!!$R1 3279
3 TraesCS5B01G213000 chr5A 346306296 346307029 733 True 543.0 712 97.4035 1 892 2 chr5A.!!$R3 891
4 TraesCS5B01G213000 chr5A 426265919 426268383 2464 True 425.5 472 78.9505 1442 3152 2 chr5A.!!$R4 1710
5 TraesCS5B01G213000 chr3B 546830649 546831382 733 False 548.5 712 97.8290 1 892 2 chr3B.!!$F2 891
6 TraesCS5B01G213000 chr4B 139742623 139743356 733 True 540.0 706 97.2760 1 892 2 chr4B.!!$R1 891

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
816 817 0.392998 CGCCCCAATCTTAGCACTGT 60.393 55.0 0.00 0.0 0.0 3.55 F
1391 1393 0.039708 GCCGCGTCCATAGGTAGTAC 60.040 60.0 4.92 0.0 0.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1805 1820 1.410882 GAGCACCACTACAGGGAGATC 59.589 57.143 0.0 0.0 0.0 2.75 R
3255 4130 1.967343 AACCCAACCCACCAACCCAT 61.967 55.000 0.0 0.0 0.0 4.00 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
129 130 2.171840 CGGGTCCTGAAGAGAGAAAGA 58.828 52.381 0.00 0.00 0.00 2.52
809 810 1.906105 AACGGCTCGCCCCAATCTTA 61.906 55.000 1.72 0.00 0.00 2.10
811 812 1.894282 GGCTCGCCCCAATCTTAGC 60.894 63.158 0.00 0.00 0.00 3.09
816 817 0.392998 CGCCCCAATCTTAGCACTGT 60.393 55.000 0.00 0.00 0.00 3.55
861 862 5.132648 TGGTATCAATCTACTTCCAATGCCT 59.867 40.000 0.00 0.00 0.00 4.75
862 863 6.064717 GGTATCAATCTACTTCCAATGCCTT 58.935 40.000 0.00 0.00 0.00 4.35
892 893 4.092968 GGTACTTCTGTGCAATTTACTCCG 59.907 45.833 0.00 0.00 0.00 4.63
893 894 4.002906 ACTTCTGTGCAATTTACTCCGA 57.997 40.909 0.00 0.00 0.00 4.55
894 895 3.746492 ACTTCTGTGCAATTTACTCCGAC 59.254 43.478 0.00 0.00 0.00 4.79
895 896 2.695359 TCTGTGCAATTTACTCCGACC 58.305 47.619 0.00 0.00 0.00 4.79
896 897 2.301870 TCTGTGCAATTTACTCCGACCT 59.698 45.455 0.00 0.00 0.00 3.85
942 943 2.197605 TGAGACGAGACGCACCCAA 61.198 57.895 0.00 0.00 0.00 4.12
975 976 1.493311 CTTTTGCTCGCGTCCAGTC 59.507 57.895 5.77 0.00 0.00 3.51
976 977 1.901650 CTTTTGCTCGCGTCCAGTCC 61.902 60.000 5.77 0.00 0.00 3.85
1166 1167 3.298619 TGCCCCGTGCTTACTAGTATTA 58.701 45.455 2.79 0.00 42.00 0.98
1206 1207 2.036604 GTCTCATAACCTAGCTCCCTGC 59.963 54.545 0.00 0.00 43.29 4.85
1253 1254 2.232298 GACTCGGAGTCCTGCCCAAG 62.232 65.000 24.41 0.00 39.28 3.61
1391 1393 0.039708 GCCGCGTCCATAGGTAGTAC 60.040 60.000 4.92 0.00 0.00 2.73
1587 1595 1.556911 TCTCATCAGGAAGCAGGGAAC 59.443 52.381 0.00 0.00 0.00 3.62
1805 1820 5.247507 TGTTTCCATTGATATTCAAGCCG 57.752 39.130 0.00 0.00 40.05 5.52
1893 1908 2.028203 CCATTGCCCGGAAATTTGAGTT 60.028 45.455 0.73 0.00 0.00 3.01
2073 2091 6.690530 TGCTTGCATTTATTGAAAGTAAGCT 58.309 32.000 15.96 0.00 42.35 3.74
2225 2256 5.584649 TGTTGGGATGAATTTCATAGACGAC 59.415 40.000 11.79 13.65 37.20 4.34
2261 2292 1.282875 GCCAGTTCAGGTTGTTCGC 59.717 57.895 0.00 0.00 0.00 4.70
2432 2463 6.016860 CAGGAATCTCGGCATAAAATCAATGA 60.017 38.462 0.00 0.00 0.00 2.57
2461 2492 8.480133 AGGACTTAGATGTACAATACTTAGGG 57.520 38.462 0.00 0.00 0.00 3.53
2807 3681 4.538490 TGGACATGGTACTTATCCAACCTT 59.462 41.667 0.00 0.00 36.51 3.50
3505 4380 8.285394 CACAGATGGATTTCATTTTAGGATACG 58.715 37.037 0.00 0.00 37.80 3.06
3516 4391 9.997482 TTCATTTTAGGATACGTTTTTGCTATC 57.003 29.630 0.00 0.00 46.39 2.08
3762 4638 0.543277 TGGGAGCTTCTATGCACTGG 59.457 55.000 0.00 0.00 34.99 4.00
3818 4694 5.453567 AAATGTAGGTTTCAAGCTGGTTC 57.546 39.130 1.40 0.00 37.33 3.62
3889 4765 3.708563 ATGTTGGCAATATTGTACCGC 57.291 42.857 16.61 8.01 0.00 5.68
3911 4787 4.816925 GCCTCTCCTGAAAATACCATACAC 59.183 45.833 0.00 0.00 0.00 2.90
4160 5036 1.732117 TTTTGGGACGGAGGGACTAA 58.268 50.000 0.00 0.00 41.55 2.24
4170 5046 4.091549 ACGGAGGGACTAATTGTGAGTTA 58.908 43.478 0.00 0.00 41.55 2.24
4171 5047 4.715297 ACGGAGGGACTAATTGTGAGTTAT 59.285 41.667 0.00 0.00 41.55 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
809 810 6.892658 TGGTAATTTTTACATGACAGTGCT 57.107 33.333 0.00 0.00 0.00 4.40
811 812 9.912634 AAGATTGGTAATTTTTACATGACAGTG 57.087 29.630 0.00 0.00 0.00 3.66
842 843 7.615365 ACAATTAAGGCATTGGAAGTAGATTGA 59.385 33.333 0.00 0.00 38.32 2.57
849 850 4.159557 ACCACAATTAAGGCATTGGAAGT 58.840 39.130 0.00 0.00 38.32 3.01
861 862 6.892658 ATTGCACAGAAGTACCACAATTAA 57.107 33.333 0.00 0.00 0.00 1.40
862 863 6.892658 AATTGCACAGAAGTACCACAATTA 57.107 33.333 0.00 0.00 35.22 1.40
992 993 1.040339 GGGAGAGCTCATCGTGGTCT 61.040 60.000 17.77 0.00 43.79 3.85
1033 1034 2.851588 GGGCATCTCCTCCCCCTC 60.852 72.222 0.00 0.00 36.50 4.30
1174 1175 7.041098 AGCTAGGTTATGAGACAAACAAAACAG 60.041 37.037 0.00 0.00 0.00 3.16
1175 1176 6.770785 AGCTAGGTTATGAGACAAACAAAACA 59.229 34.615 0.00 0.00 0.00 2.83
1176 1177 7.203255 AGCTAGGTTATGAGACAAACAAAAC 57.797 36.000 0.00 0.00 0.00 2.43
1177 1178 6.430000 GGAGCTAGGTTATGAGACAAACAAAA 59.570 38.462 0.00 0.00 0.00 2.44
1181 1182 4.162509 AGGGAGCTAGGTTATGAGACAAAC 59.837 45.833 0.00 0.00 0.00 2.93
1182 1183 4.162320 CAGGGAGCTAGGTTATGAGACAAA 59.838 45.833 0.00 0.00 0.00 2.83
1183 1184 3.706594 CAGGGAGCTAGGTTATGAGACAA 59.293 47.826 0.00 0.00 0.00 3.18
1206 1207 2.177531 CAGTACGTCCACGGGTCG 59.822 66.667 3.81 7.72 44.95 4.79
1391 1393 1.919918 TCGCAAAGCCAACAACAAAG 58.080 45.000 0.00 0.00 0.00 2.77
1587 1595 0.528924 TTCATGTACCTCGGTGTCGG 59.471 55.000 0.00 0.00 36.95 4.79
1805 1820 1.410882 GAGCACCACTACAGGGAGATC 59.589 57.143 0.00 0.00 0.00 2.75
1893 1908 3.796178 GCGTTTCATCTGCAAACTTTGAA 59.204 39.130 5.65 0.00 32.46 2.69
2225 2256 3.399330 TGGCAAGAAAGGAGTAGTTTCG 58.601 45.455 0.00 0.00 38.67 3.46
2261 2292 2.093306 TAAAGTGTGTCAGGCATCCG 57.907 50.000 0.00 0.00 0.00 4.18
2716 3590 2.557924 CAGCTTGGCTAATTCCAACACA 59.442 45.455 0.00 0.00 40.92 3.72
2807 3681 3.135167 AGAACCGTGGGTTTAAGACTTGA 59.865 43.478 0.97 0.00 46.95 3.02
3255 4130 1.967343 AACCCAACCCACCAACCCAT 61.967 55.000 0.00 0.00 0.00 4.00
3356 4231 6.943146 ACAAACAAACTTACCAAACCCAATTT 59.057 30.769 0.00 0.00 0.00 1.82
3448 4323 4.569966 GGAGTACTCATGAACATTGAGCAG 59.430 45.833 23.91 0.00 33.30 4.24
3633 4509 2.529744 GGCACAAGTGGGGAGGACT 61.530 63.158 2.00 0.00 0.00 3.85
3762 4638 4.141620 ACATCCTAACATCATGGACAGACC 60.142 45.833 0.00 0.00 39.54 3.85
3818 4694 1.825191 CGGGATCACCAGCAATGGG 60.825 63.158 0.00 0.00 40.22 4.00
3857 4733 3.331478 TGCCAACATTGCCTAATTTGG 57.669 42.857 1.04 1.04 37.43 3.28
3889 4765 5.050490 CGTGTATGGTATTTTCAGGAGAGG 58.950 45.833 0.00 0.00 0.00 3.69
3911 4787 3.187700 GGACAGTAGTGCCATTTACTCG 58.812 50.000 0.00 0.00 0.00 4.18
4128 5004 4.083484 CCGTCCCAAAATAAGTGACTCAAC 60.083 45.833 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.