Multiple sequence alignment - TraesCS5B01G236100

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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 TraesCS5B01G236100 chr5B 100.000 3271 0 0 1 3271 416852191 416848921 0.000000e+00 6041
1 TraesCS5B01G236100 chr5B 83.178 214 31 4 1046 1258 497757969 497757760 1.200000e-44 191
2 TraesCS5B01G236100 chr5D 93.575 3362 100 47 1 3271 352218160 352221496 0.000000e+00 4905
3 TraesCS5B01G236100 chr5D 82.805 221 35 2 1038 1258 413058989 413058772 9.260000e-46 195
4 TraesCS5B01G236100 chr5A 91.272 2303 93 38 599 2809 453877598 453875312 0.000000e+00 3040
5 TraesCS5B01G236100 chr5A 88.565 446 28 12 5 429 453878380 453877937 1.350000e-143 520
6 TraesCS5B01G236100 chr5A 82.222 225 37 2 1034 1258 525079281 525079060 1.200000e-44 191
7 TraesCS5B01G236100 chr4D 87.349 332 40 2 1474 1804 301763371 301763041 2.380000e-101 379
8 TraesCS5B01G236100 chr4D 87.640 89 10 1 984 1071 301763466 301763378 5.770000e-18 102
9 TraesCS5B01G236100 chr2B 86.634 202 24 2 1057 1258 146442449 146442251 1.530000e-53 220
10 TraesCS5B01G236100 chr2A 86.634 202 24 2 1057 1258 92318263 92318065 1.530000e-53 220
11 TraesCS5B01G236100 chr2D 87.179 195 22 2 1064 1258 94319393 94319202 5.500000e-53 219
12 TraesCS5B01G236100 chr2D 83.598 189 26 5 1071 1258 512043233 512043049 4.340000e-39 172


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 TraesCS5B01G236100 chr5B 416848921 416852191 3270 True 6041 6041 100.0000 1 3271 1 chr5B.!!$R1 3270
1 TraesCS5B01G236100 chr5D 352218160 352221496 3336 False 4905 4905 93.5750 1 3271 1 chr5D.!!$F1 3270
2 TraesCS5B01G236100 chr5A 453875312 453878380 3068 True 1780 3040 89.9185 5 2809 2 chr5A.!!$R2 2804

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
877 1147 0.105964 CCACCACCTCAAACTCGACA 59.894 55.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2471 2805 0.905357 AGTGCTGGGCGATTAGAGTT 59.095 50.0 0.0 0.0 0.0 3.01 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
24 25 1.229951 TCCAGGGGGAGCTTGTGAT 60.230 57.895 0.00 0.00 38.64 3.06
25 26 0.846427 TCCAGGGGGAGCTTGTGATT 60.846 55.000 0.00 0.00 38.64 2.57
69 73 3.678056 AGGACAGTCGCACAGAAAATA 57.322 42.857 0.00 0.00 0.00 1.40
81 85 6.017523 TCGCACAGAAAATATCAACTCAACAA 60.018 34.615 0.00 0.00 0.00 2.83
147 159 1.024579 GTGATGTGCACCGGTTAGGG 61.025 60.000 15.69 0.00 46.96 3.53
164 176 0.324645 GGGCACATGGGACTTGGAAT 60.325 55.000 0.00 0.00 0.00 3.01
198 214 0.181114 TCCATCCATCCAAAGGAGCG 59.819 55.000 0.00 0.00 38.83 5.03
220 236 2.203877 TGCCCCTTCGTACCCTGT 60.204 61.111 0.00 0.00 0.00 4.00
281 310 6.052360 TCATTTTTCTGCGGCATATACTGTA 58.948 36.000 1.75 0.00 0.00 2.74
429 458 1.591619 GGCGCGAAGAATACAAGGTAC 59.408 52.381 12.10 0.00 0.00 3.34
430 459 1.591619 GCGCGAAGAATACAAGGTACC 59.408 52.381 12.10 2.73 0.00 3.34
441 470 3.067684 ACAAGGTACCATTTTCCCGAG 57.932 47.619 15.94 0.00 0.00 4.63
446 475 1.065709 GTACCATTTTCCCGAGCCTGA 60.066 52.381 0.00 0.00 0.00 3.86
502 531 7.443879 TGTCTGTGTGACTAGCATTTGATTTTA 59.556 33.333 0.00 0.00 45.54 1.52
527 560 2.294233 GGAAAAAGGGTCGGGTGTAAAC 59.706 50.000 0.00 0.00 0.00 2.01
543 773 7.025365 GGGTGTAAACGAAATATTTTGGAGAC 58.975 38.462 17.84 12.38 0.00 3.36
588 818 2.052104 CGGAGGATGGTTTTGGGGC 61.052 63.158 0.00 0.00 0.00 5.80
660 914 2.039137 GGAACTCCCGACCCCTCT 59.961 66.667 0.00 0.00 0.00 3.69
665 919 2.944954 TCCCGACCCCTCTCTCCA 60.945 66.667 0.00 0.00 0.00 3.86
726 984 1.275002 ACATATTCCCTCCCACCACCT 60.275 52.381 0.00 0.00 0.00 4.00
731 989 2.203998 CCTCCCACCACCTCCACT 60.204 66.667 0.00 0.00 0.00 4.00
740 998 3.314331 ACCTCCACTGCCCACTCG 61.314 66.667 0.00 0.00 0.00 4.18
825 1088 3.787001 CCCACTCCCTTCCTCCGC 61.787 72.222 0.00 0.00 0.00 5.54
874 1144 1.202651 AGAACCACCACCTCAAACTCG 60.203 52.381 0.00 0.00 0.00 4.18
875 1145 0.834612 AACCACCACCTCAAACTCGA 59.165 50.000 0.00 0.00 0.00 4.04
876 1146 0.106149 ACCACCACCTCAAACTCGAC 59.894 55.000 0.00 0.00 0.00 4.20
877 1147 0.105964 CCACCACCTCAAACTCGACA 59.894 55.000 0.00 0.00 0.00 4.35
881 1151 0.951040 CACCTCAAACTCGACAGCCC 60.951 60.000 0.00 0.00 0.00 5.19
882 1152 1.738099 CCTCAAACTCGACAGCCCG 60.738 63.158 0.00 0.00 0.00 6.13
883 1153 1.289066 CTCAAACTCGACAGCCCGA 59.711 57.895 0.00 0.00 37.03 5.14
898 1169 1.271217 GCCCGAGTGAGTTAAAACCCT 60.271 52.381 0.00 0.00 0.00 4.34
971 1251 3.118408 TCCAACTGTTTCAGTGCAGTAGT 60.118 43.478 3.12 0.00 44.62 2.73
972 1252 3.002656 CCAACTGTTTCAGTGCAGTAGTG 59.997 47.826 3.12 0.00 44.62 2.74
973 1253 3.543680 ACTGTTTCAGTGCAGTAGTGT 57.456 42.857 0.00 0.00 43.63 3.55
1314 1612 2.411748 TGAGTTTGCTCTTTACGATGCG 59.588 45.455 0.00 0.00 42.13 4.73
1345 1650 2.669569 GCTGACGGTGTGTGGCAT 60.670 61.111 0.00 0.00 0.00 4.40
1349 1654 0.749818 TGACGGTGTGTGGCATTGTT 60.750 50.000 0.00 0.00 0.00 2.83
1835 2148 4.012895 GTGCAGAACCACGTGCGG 62.013 66.667 10.91 0.00 42.96 5.69
2184 2497 4.697756 CCCCTGCGACGAAGGCAA 62.698 66.667 17.25 0.00 40.39 4.52
2320 2641 1.202806 ACTCACCTAGCAAGCAAGCAA 60.203 47.619 3.19 0.00 36.85 3.91
2321 2642 1.467734 CTCACCTAGCAAGCAAGCAAG 59.532 52.381 3.19 0.00 36.85 4.01
2322 2643 0.109412 CACCTAGCAAGCAAGCAAGC 60.109 55.000 3.19 0.00 36.85 4.01
2323 2644 0.538057 ACCTAGCAAGCAAGCAAGCA 60.538 50.000 10.52 0.00 36.85 3.91
2389 2710 1.131126 TGTTCTAATCCGACCGACGTC 59.869 52.381 5.18 5.18 40.78 4.34
2393 2714 1.669779 CTAATCCGACCGACGTCTTCT 59.330 52.381 14.70 0.00 40.78 2.85
2427 2752 3.380320 AGACCAGTTGTTAGTTTGTTGCC 59.620 43.478 0.00 0.00 0.00 4.52
2471 2805 5.541101 TGCTTAGTTAGGGTTCTGTCTGTAA 59.459 40.000 0.00 0.00 0.00 2.41
2492 2826 0.749649 CTCTAATCGCCCAGCACTCT 59.250 55.000 0.00 0.00 0.00 3.24
2495 2829 0.901827 TAATCGCCCAGCACTCTGAA 59.098 50.000 0.00 0.00 42.95 3.02
2559 2917 4.814771 GTGTTTTTGTACAGTACTGCTCCT 59.185 41.667 22.90 5.86 0.00 3.69
2564 2922 5.995565 TTGTACAGTACTGCTCCTGTAAT 57.004 39.130 22.90 2.45 43.63 1.89
2579 2937 3.064545 CCTGTAATTAGCTGCTGAACTGC 59.935 47.826 13.43 0.44 43.18 4.40
2646 3004 2.254651 GCAGCAAGTCAGCAGCAC 59.745 61.111 0.00 0.00 45.12 4.40
2674 3036 7.808672 TCGATTTAAAATCGCTTTCTTTGGTA 58.191 30.769 0.00 0.00 40.95 3.25
2768 3136 0.107508 CTCGAGCCCATTGGTCACAT 60.108 55.000 0.00 0.00 41.69 3.21
2781 3161 3.093814 TGGTCACATACACAGGTCGTAT 58.906 45.455 0.00 0.00 0.00 3.06
2829 3209 3.529533 TGAGACGTAGGTAGAGTACTGC 58.470 50.000 0.00 0.00 0.00 4.40
2830 3210 3.055602 TGAGACGTAGGTAGAGTACTGCA 60.056 47.826 0.00 0.00 0.00 4.41
2831 3211 4.128643 GAGACGTAGGTAGAGTACTGCAT 58.871 47.826 0.00 0.00 0.00 3.96
2832 3212 3.878103 AGACGTAGGTAGAGTACTGCATG 59.122 47.826 0.00 0.00 0.00 4.06
3002 3386 2.686835 AGAGGACTGAGCTGGCCC 60.687 66.667 0.00 0.00 0.00 5.80
3034 3418 6.463755 GGAGAAGATCTTGGGAAGTCTAATCC 60.464 46.154 14.00 0.00 36.16 3.01
3090 3475 4.254709 TGGTTGCTGCTGCCTCGT 62.255 61.111 13.47 0.00 38.71 4.18
3105 3490 0.523966 CTCGTCTCAGCGAAACCTCT 59.476 55.000 0.00 0.00 40.57 3.69
3117 3506 0.827368 AAACCTCTCATCTCTCGGGC 59.173 55.000 0.00 0.00 0.00 6.13
3122 3511 1.826054 CTCATCTCTCGGGCGAGGT 60.826 63.158 0.00 0.00 42.20 3.85
3123 3512 1.791103 CTCATCTCTCGGGCGAGGTC 61.791 65.000 0.00 0.00 42.20 3.85
3125 3514 1.826054 ATCTCTCGGGCGAGGTCAG 60.826 63.158 0.00 0.00 42.20 3.51
3263 3670 1.139455 GGGTTCCCACGATATTCCGAA 59.861 52.381 2.59 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 85 6.206829 GCGGGGTTTCTCTATTTTGCTATTAT 59.793 38.462 0.00 0.00 0.00 1.28
147 159 2.684881 CACTATTCCAAGTCCCATGTGC 59.315 50.000 0.00 0.00 0.00 4.57
164 176 4.755437 TGGATGGATGGATCAGATCACTA 58.245 43.478 12.66 2.02 0.00 2.74
198 214 0.179065 GGGTACGAAGGGGCACATAC 60.179 60.000 0.00 0.00 0.00 2.39
220 236 1.241165 TCGCACGTGACCTCTTCTAA 58.759 50.000 22.23 0.00 0.00 2.10
309 338 3.009473 AGAGGAAAATAGAAGCAGTGCCA 59.991 43.478 12.58 0.00 0.00 4.92
321 350 4.017126 TGCAGAGAGACGAGAGGAAAATA 58.983 43.478 0.00 0.00 0.00 1.40
417 446 5.187687 TCGGGAAAATGGTACCTTGTATTC 58.812 41.667 14.36 11.84 0.00 1.75
418 447 5.182169 TCGGGAAAATGGTACCTTGTATT 57.818 39.130 14.36 1.06 0.00 1.89
429 458 1.544724 TTTCAGGCTCGGGAAAATGG 58.455 50.000 0.00 0.00 30.59 3.16
430 459 3.255642 TCTTTTTCAGGCTCGGGAAAATG 59.744 43.478 10.80 12.39 41.20 2.32
441 470 4.701956 TGGATCGATTTCTTTTTCAGGC 57.298 40.909 0.00 0.00 0.00 4.85
446 475 7.175641 AGTCTGATGTTGGATCGATTTCTTTTT 59.824 33.333 0.00 0.00 0.00 1.94
488 517 8.026607 CCTTTTTCCGTCTAAAATCAAATGCTA 58.973 33.333 0.00 0.00 0.00 3.49
502 531 1.373812 CCCGACCCTTTTTCCGTCT 59.626 57.895 0.00 0.00 0.00 4.18
527 560 5.448632 CCCTTTCGGTCTCCAAAATATTTCG 60.449 44.000 0.10 0.00 0.00 3.46
543 773 1.816835 GGCCTCTTTTAACCCTTTCGG 59.183 52.381 0.00 0.00 37.81 4.30
575 805 1.593265 CTGCAGCCCCAAAACCATC 59.407 57.895 0.00 0.00 0.00 3.51
580 810 2.918802 CTGCCTGCAGCCCCAAAA 60.919 61.111 8.66 0.00 42.71 2.44
654 908 2.152016 GTTTCGTTTTGGAGAGAGGGG 58.848 52.381 0.00 0.00 0.00 4.79
660 914 2.092861 TCTGGGTGTTTCGTTTTGGAGA 60.093 45.455 0.00 0.00 0.00 3.71
665 919 2.681344 GTCTGTCTGGGTGTTTCGTTTT 59.319 45.455 0.00 0.00 0.00 2.43
726 984 3.311110 GGACGAGTGGGCAGTGGA 61.311 66.667 0.00 0.00 0.00 4.02
825 1088 4.421365 CCAGGGTGGTGGTGAATG 57.579 61.111 0.00 0.00 31.35 2.67
857 1127 0.106149 GTCGAGTTTGAGGTGGTGGT 59.894 55.000 0.00 0.00 0.00 4.16
874 1144 2.450609 TTTAACTCACTCGGGCTGTC 57.549 50.000 0.00 0.00 0.00 3.51
875 1145 2.490991 GTTTTAACTCACTCGGGCTGT 58.509 47.619 0.00 0.00 0.00 4.40
876 1146 1.804748 GGTTTTAACTCACTCGGGCTG 59.195 52.381 0.00 0.00 0.00 4.85
877 1147 1.271217 GGGTTTTAACTCACTCGGGCT 60.271 52.381 0.00 0.00 0.00 5.19
881 1151 2.737252 GCTCAGGGTTTTAACTCACTCG 59.263 50.000 0.00 0.00 0.00 4.18
882 1152 3.075148 GGCTCAGGGTTTTAACTCACTC 58.925 50.000 0.00 0.00 0.00 3.51
883 1153 2.550208 CGGCTCAGGGTTTTAACTCACT 60.550 50.000 0.00 0.00 0.00 3.41
884 1154 1.804748 CGGCTCAGGGTTTTAACTCAC 59.195 52.381 0.00 0.00 0.00 3.51
898 1169 1.000486 ACTAGGGAAGCTCGGCTCA 60.000 57.895 0.00 0.00 38.25 4.26
1291 1588 4.436050 CGCATCGTAAAGAGCAAACTCAAT 60.436 41.667 0.00 0.00 46.09 2.57
1292 1589 3.120683 CGCATCGTAAAGAGCAAACTCAA 60.121 43.478 0.00 0.00 46.09 3.02
1295 1592 2.157668 CACGCATCGTAAAGAGCAAACT 59.842 45.455 0.00 0.00 38.32 2.66
1314 1612 3.807538 CAGCACCGCTCCATGCAC 61.808 66.667 0.00 0.00 44.59 4.57
1345 1650 0.392336 GAACCCCTGCATTGCAACAA 59.608 50.000 13.18 0.00 38.41 2.83
1349 1654 2.676121 CGGAACCCCTGCATTGCA 60.676 61.111 11.50 11.50 36.92 4.08
1502 1815 3.876589 GAACAGCGGGAAGTGCGGA 62.877 63.158 0.00 0.00 37.44 5.54
1532 1845 4.794439 TGGTGATGCGCGACCGAG 62.794 66.667 12.10 0.00 34.69 4.63
2006 2319 2.721167 CGCGGAGAGATGGTTGGGA 61.721 63.158 0.00 0.00 0.00 4.37
2174 2487 3.435186 GCCAGCCTTGCCTTCGTC 61.435 66.667 0.00 0.00 0.00 4.20
2183 2496 4.140599 CTCTCGAGCGCCAGCCTT 62.141 66.667 7.81 0.00 46.67 4.35
2320 2641 4.227134 CGCGGATGCTACCCTGCT 62.227 66.667 0.00 0.00 39.65 4.24
2321 2642 4.530857 ACGCGGATGCTACCCTGC 62.531 66.667 12.47 0.00 39.65 4.85
2322 2643 2.173669 CAACGCGGATGCTACCCTG 61.174 63.158 12.47 0.00 39.65 4.45
2323 2644 2.186903 CAACGCGGATGCTACCCT 59.813 61.111 12.47 0.00 39.65 4.34
2389 2710 6.347859 ACTGGTCTAAGTAGGAAACAGAAG 57.652 41.667 0.00 0.00 0.00 2.85
2393 2714 5.881923 ACAACTGGTCTAAGTAGGAAACA 57.118 39.130 0.00 0.00 0.00 2.83
2427 2752 1.630878 ACTTGCTAACTTCAGGAGGGG 59.369 52.381 0.00 0.00 0.00 4.79
2471 2805 0.905357 AGTGCTGGGCGATTAGAGTT 59.095 50.000 0.00 0.00 0.00 3.01
2492 2826 1.270274 GCACATGATGGCACTTGTTCA 59.730 47.619 0.00 0.00 0.00 3.18
2559 2917 2.672874 CGCAGTTCAGCAGCTAATTACA 59.327 45.455 0.00 0.00 0.00 2.41
2564 2922 2.034879 GCCGCAGTTCAGCAGCTAA 61.035 57.895 0.00 0.00 35.12 3.09
2646 3004 5.485662 AGAAAGCGATTTTAAATCGAGGG 57.514 39.130 34.70 13.39 43.59 4.30
2674 3036 4.030452 GAGCGCACGCAAAAGGCT 62.030 61.111 18.24 0.39 44.88 4.58
2768 3136 2.011947 CGGTGAGATACGACCTGTGTA 58.988 52.381 0.00 0.00 0.00 2.90
2781 3161 3.892122 GAGACTCGCTCGGTGAGA 58.108 61.111 17.67 2.78 42.10 3.27
2829 3209 5.277393 CGTACTGGTACTACTCTACAGCATG 60.277 48.000 8.89 0.00 36.57 4.06
2830 3210 4.815308 CGTACTGGTACTACTCTACAGCAT 59.185 45.833 8.89 0.00 34.04 3.79
2831 3211 4.081476 TCGTACTGGTACTACTCTACAGCA 60.081 45.833 8.89 0.00 34.04 4.41
2832 3212 4.437239 TCGTACTGGTACTACTCTACAGC 58.563 47.826 8.89 0.00 34.04 4.40
2900 3284 3.129462 TCTCTATCTTCACCTGTCAAGCG 59.871 47.826 0.00 0.00 0.00 4.68
3002 3386 1.202510 CCAAGATCTTCTCCAGGCTCG 60.203 57.143 4.57 0.00 0.00 5.03
3034 3418 1.226603 CTCTACGTTTCCGGCTCCG 60.227 63.158 0.00 0.48 38.78 4.63
3090 3475 2.425312 GAGATGAGAGGTTTCGCTGAGA 59.575 50.000 0.00 0.00 0.00 3.27
3105 3490 1.824329 GACCTCGCCCGAGAGATGA 60.824 63.158 18.41 0.00 44.53 2.92
3117 3506 3.077556 CCACCTCCCCTGACCTCG 61.078 72.222 0.00 0.00 0.00 4.63
3122 3511 3.083349 CGATGCCACCTCCCCTGA 61.083 66.667 0.00 0.00 0.00 3.86
3123 3512 4.181010 CCGATGCCACCTCCCCTG 62.181 72.222 0.00 0.00 0.00 4.45
3132 3521 1.377202 GAAACAGAGCCCGATGCCA 60.377 57.895 0.00 0.00 42.71 4.92


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

AutoCloner maintained by Alex Coulton.