Multiple sequence alignment - TraesCS3B01G033800

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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 TraesCS3B01G033800 chr3B 100.000 5615 0 0 687 6301 16137743 16132129 0.000000e+00 10370.0
1 TraesCS3B01G033800 chr3B 97.308 5350 104 21 687 6017 25166872 25172200 0.000000e+00 9046.0
2 TraesCS3B01G033800 chr3B 100.000 264 0 0 1 264 16138429 16138166 7.340000e-134 488.0
3 TraesCS3B01G033800 chr3B 98.106 264 5 0 1 264 25166481 25166744 1.600000e-125 460.0
4 TraesCS3B01G033800 chr3B 91.611 298 19 4 6005 6301 25172221 25172513 2.110000e-109 407.0
5 TraesCS3B01G033800 chr3B 95.238 42 1 1 3151 3192 25169377 25169417 1.470000e-06 65.8
6 TraesCS3B01G033800 chr3A 91.917 5085 327 43 688 5718 25871706 25876760 0.000000e+00 7036.0
7 TraesCS3B01G033800 chr3A 93.651 252 15 1 5783 6033 25877653 25877904 5.960000e-100 375.0
8 TraesCS3B01G033800 chr3A 93.388 121 5 3 6011 6129 25877914 25878033 6.490000e-40 176.0
9 TraesCS3B01G033800 chr3A 97.674 43 0 1 3151 3193 25874224 25874265 8.760000e-09 73.1
10 TraesCS3B01G033800 chr3D 91.647 5088 322 55 687 5718 11450200 11445160 0.000000e+00 6946.0
11 TraesCS3B01G033800 chr3D 93.728 287 15 2 6017 6301 11443910 11443625 1.620000e-115 427.0
12 TraesCS3B01G033800 chr3D 90.873 252 22 1 5783 6033 11444177 11443926 2.810000e-88 337.0
13 TraesCS3B01G033800 chr3D 90.217 184 14 1 1 180 11450694 11450511 2.940000e-58 237.0
14 TraesCS3B01G033800 chr3D 87.879 66 4 4 6123 6186 422957171 422957234 2.440000e-09 75.0
15 TraesCS3B01G033800 chr3D 97.619 42 0 1 3151 3192 11447685 11447645 3.150000e-08 71.3
16 TraesCS3B01G033800 chr3D 95.455 44 2 0 6148 6191 51439522 51439565 3.150000e-08 71.3
17 TraesCS3B01G033800 chr7B 92.833 293 18 2 6011 6301 165708108 165708399 7.550000e-114 422.0
18 TraesCS3B01G033800 chr7B 92.857 252 17 1 5783 6033 165707847 165708098 1.290000e-96 364.0
19 TraesCS3B01G033800 chr6D 87.097 93 12 0 6205 6297 19119916 19120008 8.640000e-19 106.0
20 TraesCS3B01G033800 chr5B 88.235 85 10 0 6208 6292 14286945 14286861 1.120000e-17 102.0
21 TraesCS3B01G033800 chr5B 83.654 104 17 0 6196 6299 429017725 429017828 1.450000e-16 99.0
22 TraesCS3B01G033800 chr6A 97.778 45 1 0 6148 6192 324253238 324253282 1.880000e-10 78.7
23 TraesCS3B01G033800 chrUn 95.745 47 1 1 6151 6197 29029246 29029291 2.440000e-09 75.0
24 TraesCS3B01G033800 chr2B 92.157 51 3 1 6151 6200 779319926 779319876 3.150000e-08 71.3
25 TraesCS3B01G033800 chr1D 92.000 50 4 0 6150 6199 462985105 462985154 3.150000e-08 71.3


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 TraesCS3B01G033800 chr3B 16132129 16138429 6300 True 5429.000 10370 100.00000 1 6301 2 chr3B.!!$R1 6300
1 TraesCS3B01G033800 chr3B 25166481 25172513 6032 False 2494.700 9046 95.56575 1 6301 4 chr3B.!!$F1 6300
2 TraesCS3B01G033800 chr3A 25871706 25878033 6327 False 1915.025 7036 94.15750 688 6129 4 chr3A.!!$F1 5441
3 TraesCS3B01G033800 chr3D 11443625 11450694 7069 True 1603.660 6946 92.81680 1 6301 5 chr3D.!!$R1 6300
4 TraesCS3B01G033800 chr7B 165707847 165708399 552 False 393.000 422 92.84500 5783 6301 2 chr7B.!!$F1 518

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
933 1014 1.305633 CCCACTCTCTGGCTCTCCA 60.306 63.158 0.00 0.0 39.01 3.86 F
1128 1209 2.288643 GATCCCCTCAGGCCTCCT 59.711 66.667 0.00 0.0 34.51 3.69 F
3060 3189 3.629087 AGCCGGTGTGTTCTAGTATAGT 58.371 45.455 1.90 0.0 40.38 2.12 F
4072 4212 2.267174 ATTCAATCATGAGCCCTCCG 57.733 50.000 0.09 0.0 36.78 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2708 2835 7.121907 GCCAGACTGAGAAATCTTAGGAAAAAT 59.878 37.037 3.32 0.0 34.28 1.82 R
3117 3246 7.816995 TGGTGGATATTTTAACAGCATTCAAAC 59.183 33.333 0.00 0.0 36.54 2.93 R
4084 4224 0.400213 AATCCAAGGAGGTGCGACAA 59.600 50.000 0.00 0.0 39.02 3.18 R
5367 5508 0.107897 ACACTCAAGTTGCACCACGA 60.108 50.000 0.00 0.0 0.00 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
933 1014 1.305633 CCCACTCTCTGGCTCTCCA 60.306 63.158 0.00 0.00 39.01 3.86
1128 1209 2.288643 GATCCCCTCAGGCCTCCT 59.711 66.667 0.00 0.00 34.51 3.69
1314 1396 6.780457 ATTACATCTTAGGCAGCAAACAAT 57.220 33.333 0.00 0.00 0.00 2.71
1315 1397 6.588719 TTACATCTTAGGCAGCAAACAATT 57.411 33.333 0.00 0.00 0.00 2.32
1410 1493 4.804261 GCACTCCTCTCATGGTACTTTGTT 60.804 45.833 0.00 0.00 0.00 2.83
2180 2302 8.134895 TCCAAAAGTGTTGATAGAATGTTGAAC 58.865 33.333 0.00 0.00 0.00 3.18
2571 2695 5.077564 TGTCTAGTTCAGCTCTAAGTTCCA 58.922 41.667 0.00 0.00 0.00 3.53
2572 2696 5.538813 TGTCTAGTTCAGCTCTAAGTTCCAA 59.461 40.000 0.00 0.00 0.00 3.53
2573 2697 6.211584 TGTCTAGTTCAGCTCTAAGTTCCAAT 59.788 38.462 0.00 0.00 0.00 3.16
2574 2698 7.396339 TGTCTAGTTCAGCTCTAAGTTCCAATA 59.604 37.037 0.00 0.00 0.00 1.90
2575 2699 8.417884 GTCTAGTTCAGCTCTAAGTTCCAATAT 58.582 37.037 0.00 0.00 0.00 1.28
3060 3189 3.629087 AGCCGGTGTGTTCTAGTATAGT 58.371 45.455 1.90 0.00 40.38 2.12
3312 3441 9.772973 TCAAGTTTGCTTTCTTATCTTGTACTA 57.227 29.630 0.00 0.00 34.43 1.82
3433 3562 3.252458 AGGAGTATGTTGCCAACGAAAAC 59.748 43.478 2.68 0.00 0.00 2.43
4025 4165 8.303876 GGATGAATATCTTTCTAGAGTCAGTCC 58.696 40.741 0.00 0.00 32.92 3.85
4072 4212 2.267174 ATTCAATCATGAGCCCTCCG 57.733 50.000 0.09 0.00 36.78 4.63
4084 4224 0.253327 GCCCTCCGGAGACTTCAATT 59.747 55.000 33.39 0.00 0.00 2.32
4388 4528 2.238521 TGGCAAGTGGAAACCTCATTC 58.761 47.619 0.00 0.00 0.00 2.67
4741 4881 2.366533 TGACCACATCCTCGAGTCTAC 58.633 52.381 12.31 0.00 0.00 2.59
5367 5508 0.744414 GTGTGGCGGCAGTGATATGT 60.744 55.000 13.91 0.00 0.00 2.29
5436 5579 9.463443 GATGTTTTATTTTATCGCCAAAGCTAT 57.537 29.630 0.00 0.00 36.60 2.97
5481 5624 5.652518 TGTGATAATTTGGTCATGTGCATG 58.347 37.500 5.86 5.86 40.09 4.06
5581 5724 2.972625 TGTCACTCCAATCGAATGGAC 58.027 47.619 18.43 9.86 44.52 4.02
5664 5809 5.662211 TCTTTTAAAAGTGTACGCTCACC 57.338 39.130 23.75 0.00 38.91 4.02
5738 5887 2.102925 CCCTTTGTTGAACCAAGTGCAT 59.897 45.455 8.14 0.00 0.00 3.96
5746 5895 4.465632 TGAACCAAGTGCATATCGTACT 57.534 40.909 0.00 0.00 43.17 2.73
5842 6911 3.439857 AAAGTGTACCCTGCATGTCAT 57.560 42.857 0.00 0.00 0.00 3.06
5888 6957 3.399330 TCCACCTGTCGACAATTTCTTC 58.601 45.455 20.49 0.00 0.00 2.87
5920 6990 9.840427 ATTGTTCTTGTTTATTCCATAACTTCG 57.160 29.630 0.00 0.00 0.00 3.79
5964 7034 3.489416 CGTGTGACAATACCATCATACCG 59.511 47.826 0.00 0.00 34.47 4.02
5969 7039 4.040339 TGACAATACCATCATACCGCTGAT 59.960 41.667 0.00 0.00 36.29 2.90
6078 7181 3.482436 CCAAGCCCAAAGTTGTACTGTA 58.518 45.455 0.00 0.00 0.00 2.74
6082 7185 5.767816 AGCCCAAAGTTGTACTGTAAAAG 57.232 39.130 0.00 0.00 0.00 2.27
6083 7186 5.442391 AGCCCAAAGTTGTACTGTAAAAGA 58.558 37.500 0.00 0.00 0.00 2.52
6186 7293 6.880484 TGCTCTTATATTTGTTTACGGAGGA 58.120 36.000 0.00 0.00 0.00 3.71
6192 7299 9.257651 CTTATATTTGTTTACGGAGGAAGTAGG 57.742 37.037 0.00 0.00 0.00 3.18
6214 7321 5.719085 AGGATATCATAAGGGAGTGTAGCAG 59.281 44.000 4.83 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
933 1014 9.319143 GCCTCAATTTTATCGCTAGATATATGT 57.681 33.333 0.00 0.00 38.95 2.29
1369 1451 5.458041 AGTGCGTTTAGTGAGGTAGTTAA 57.542 39.130 0.00 0.00 0.00 2.01
1410 1493 7.533426 CAAATTTGATTGGTTGTTTTGGTGAA 58.467 30.769 13.08 0.00 0.00 3.18
1430 1513 4.870123 TTGGTGATGTTGCTAGCAAATT 57.130 36.364 30.83 20.68 37.70 1.82
2660 2784 9.631257 TGAATGCCTCATATAGAATTCTGAAAA 57.369 29.630 18.47 0.00 33.00 2.29
2708 2835 7.121907 GCCAGACTGAGAAATCTTAGGAAAAAT 59.878 37.037 3.32 0.00 34.28 1.82
3117 3246 7.816995 TGGTGGATATTTTAACAGCATTCAAAC 59.183 33.333 0.00 0.00 36.54 2.93
3206 3335 8.810990 TTTTGTCTAAACTTTCAAGGGTTCTA 57.189 30.769 0.00 0.00 0.00 2.10
3828 3967 0.704664 AACCAACAATCTCCTCCCCC 59.295 55.000 0.00 0.00 0.00 5.40
3829 3968 2.576648 ACTAACCAACAATCTCCTCCCC 59.423 50.000 0.00 0.00 0.00 4.81
3830 3969 4.302559 AACTAACCAACAATCTCCTCCC 57.697 45.455 0.00 0.00 0.00 4.30
3831 3970 4.082733 GCAAACTAACCAACAATCTCCTCC 60.083 45.833 0.00 0.00 0.00 4.30
3832 3971 4.762251 AGCAAACTAACCAACAATCTCCTC 59.238 41.667 0.00 0.00 0.00 3.71
4004 4144 8.001875 TGCTAGGACTGACTCTAGAAAGATATT 58.998 37.037 0.00 0.00 36.08 1.28
4025 4165 3.545703 CCAAAGATAGGGTTGGTGCTAG 58.454 50.000 0.00 0.00 39.61 3.42
4072 4212 2.095718 GGTGCGACAAATTGAAGTCTCC 60.096 50.000 0.00 0.00 32.68 3.71
4084 4224 0.400213 AATCCAAGGAGGTGCGACAA 59.600 50.000 0.00 0.00 39.02 3.18
4337 4477 5.745769 GGAAAAAGAAGTCAAAAGACAGCAG 59.254 40.000 0.00 0.00 0.00 4.24
4542 4682 8.692710 TGAGAAAGATAATACCGATACACTTGT 58.307 33.333 0.00 0.00 0.00 3.16
4741 4881 3.368948 GGAGTTGGAGCAAGAGACCTTAG 60.369 52.174 0.00 0.00 0.00 2.18
5291 5431 2.736347 ACGCTAGTCACTTAGGGACAT 58.264 47.619 17.52 4.75 37.74 3.06
5343 5484 0.827368 TCACTGCCGCCACACATATA 59.173 50.000 0.00 0.00 0.00 0.86
5367 5508 0.107897 ACACTCAAGTTGCACCACGA 60.108 50.000 0.00 0.00 0.00 4.35
5481 5624 3.710326 AAAGCAAACCTTCTTCCGAAC 57.290 42.857 0.00 0.00 31.99 3.95
5496 5639 6.346477 ACGATCCTAGCTATGATAAAAGCA 57.654 37.500 11.05 0.00 41.32 3.91
5581 5724 3.792047 CCACGTGTGCTGCCGATG 61.792 66.667 15.65 0.00 0.00 3.84
5664 5809 9.322773 CTGACCATCAATAGCTAATGTATATGG 57.677 37.037 19.37 19.37 37.85 2.74
5746 5895 3.056607 GGAGGTAAGGCGTACAAGTACAA 60.057 47.826 12.54 0.00 35.87 2.41
5842 6911 9.162764 GAACTCTAATTCACTGCCTTTGTATTA 57.837 33.333 0.00 0.00 0.00 0.98
5993 7063 4.389382 TGCAAATCAATGTTACATTGCTGC 59.611 37.500 30.20 30.20 42.59 5.25
6186 7293 7.397761 GCTACACTCCCTTATGATATCCTACTT 59.602 40.741 0.00 0.00 0.00 2.24
6191 7298 5.717178 TCTGCTACACTCCCTTATGATATCC 59.283 44.000 0.00 0.00 0.00 2.59
6192 7299 6.435904 ACTCTGCTACACTCCCTTATGATATC 59.564 42.308 0.00 0.00 0.00 1.63
6214 7321 3.610242 CGATTGCTGAACTGTGTCTACTC 59.390 47.826 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.