Multiple sequence alignment - TraesCS5B01G487500

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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 TraesCS5B01G487500 chr5B 100.000 3386 0 0 1 3386 658461370 658457985 0.000000e+00 6253
1 TraesCS5B01G487500 chr5B 82.661 1834 247 39 1024 2846 658152710 658154483 0.000000e+00 1559
2 TraesCS5B01G487500 chr5B 83.051 1711 242 29 1025 2719 658172116 658173794 0.000000e+00 1509
3 TraesCS5B01G487500 chr5B 82.418 1729 234 36 1028 2723 658368740 658370431 0.000000e+00 1445
4 TraesCS5B01G487500 chr5B 85.156 768 100 8 1025 1784 658372351 658373112 0.000000e+00 774
5 TraesCS5B01G487500 chr5B 81.074 391 48 18 3012 3385 658145649 658146030 4.270000e-74 289
6 TraesCS5B01G487500 chr5B 86.517 178 14 6 2976 3144 658154484 658154660 1.600000e-43 187
7 TraesCS5B01G487500 chr5D 94.677 2799 83 19 611 3386 522156625 522153870 0.000000e+00 4283
8 TraesCS5B01G487500 chr5D 82.350 1711 252 33 1025 2719 521865744 521867420 0.000000e+00 1441
9 TraesCS5B01G487500 chr5D 84.256 1499 208 20 1024 2512 521836833 521838313 0.000000e+00 1435
10 TraesCS5B01G487500 chr5D 85.080 1374 192 9 1028 2392 521844070 521845439 0.000000e+00 1389
11 TraesCS5B01G487500 chr5D 94.071 624 34 1 1 621 522157273 522156650 0.000000e+00 944
12 TraesCS5B01G487500 chr5D 89.697 165 9 6 2987 3144 521839615 521839778 1.590000e-48 204
13 TraesCS5B01G487500 chr5D 91.667 108 6 3 3039 3144 446119176 446119070 2.720000e-31 147
14 TraesCS5B01G487500 chr5D 83.448 145 9 5 2551 2695 521839182 521839311 1.650000e-23 121
15 TraesCS5B01G487500 chr5A 94.432 1796 78 6 611 2398 650297401 650295620 0.000000e+00 2743
16 TraesCS5B01G487500 chr5A 84.944 1966 239 25 1024 2962 650141900 650143835 0.000000e+00 1938
17 TraesCS5B01G487500 chr5A 84.341 1456 212 9 1028 2477 650159858 650161303 0.000000e+00 1411
18 TraesCS5B01G487500 chr5A 91.615 322 24 3 3067 3386 650290099 650289779 3.100000e-120 442
19 TraesCS5B01G487500 chr5A 90.000 340 25 3 283 621 650297757 650297426 6.710000e-117 431
20 TraesCS5B01G487500 chr5A 96.313 217 7 1 1 217 650297970 650297755 4.160000e-94 355
21 TraesCS5B01G487500 chr5A 85.294 204 11 7 2956 3144 650143948 650144147 3.450000e-45 193
22 TraesCS5B01G487500 chr5A 84.737 190 21 4 2956 3139 650138005 650138192 2.080000e-42 183
23 TraesCS5B01G487500 chr7B 93.204 103 4 3 3048 3147 677754320 677754218 7.570000e-32 148


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 TraesCS5B01G487500 chr5B 658457985 658461370 3385 True 6253.000000 6253 100.000000 1 3386 1 chr5B.!!$R1 3385
1 TraesCS5B01G487500 chr5B 658172116 658173794 1678 False 1509.000000 1509 83.051000 1025 2719 1 chr5B.!!$F2 1694
2 TraesCS5B01G487500 chr5B 658368740 658373112 4372 False 1109.500000 1445 83.787000 1025 2723 2 chr5B.!!$F4 1698
3 TraesCS5B01G487500 chr5B 658152710 658154660 1950 False 873.000000 1559 84.589000 1024 3144 2 chr5B.!!$F3 2120
4 TraesCS5B01G487500 chr5D 522153870 522157273 3403 True 2613.500000 4283 94.374000 1 3386 2 chr5D.!!$R2 3385
5 TraesCS5B01G487500 chr5D 521865744 521867420 1676 False 1441.000000 1441 82.350000 1025 2719 1 chr5D.!!$F2 1694
6 TraesCS5B01G487500 chr5D 521844070 521845439 1369 False 1389.000000 1389 85.080000 1028 2392 1 chr5D.!!$F1 1364
7 TraesCS5B01G487500 chr5D 521836833 521839778 2945 False 586.666667 1435 85.800333 1024 3144 3 chr5D.!!$F3 2120
8 TraesCS5B01G487500 chr5A 650159858 650161303 1445 False 1411.000000 1411 84.341000 1028 2477 1 chr5A.!!$F1 1449
9 TraesCS5B01G487500 chr5A 650295620 650297970 2350 True 1176.333333 2743 93.581667 1 2398 3 chr5A.!!$R2 2397
10 TraesCS5B01G487500 chr5A 650138005 650144147 6142 False 771.333333 1938 84.991667 1024 3144 3 chr5A.!!$F2 2120

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
618 657 0.320683 GGCCATTTTGGTGTCTTGCC 60.321 55.000 0.0 0.0 40.46 4.52 F
859 901 1.073284 TGCAGTTTCCTTACAGGGTCC 59.927 52.381 0.0 0.0 35.59 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1434 4312 0.409092 TGTCTTGGGATGCAATGGGT 59.591 50.0 0.0 0.0 0.0 4.51 R
2817 6588 0.796927 GGGCTGAAGCTTGTAACGAC 59.203 55.0 2.1 0.0 41.7 4.34 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
270 271 2.688507 TCTGGACTTTCTTGACATCGC 58.311 47.619 0.00 0.00 0.00 4.58
279 280 0.379669 CTTGACATCGCCAGCAATCC 59.620 55.000 0.00 0.00 0.00 3.01
361 365 6.255887 CCTGTTGATCTTAACCGTCTGATTAC 59.744 42.308 0.00 0.00 0.00 1.89
385 389 2.468831 CGTGTTTGTTTGATGGTTGGG 58.531 47.619 0.00 0.00 0.00 4.12
525 529 8.190784 TCATCAGTCATATGTTATAGGCATACG 58.809 37.037 1.90 0.00 32.43 3.06
618 657 0.320683 GGCCATTTTGGTGTCTTGCC 60.321 55.000 0.00 0.00 40.46 4.52
634 673 7.700656 GGTGTCTTGCCATGTAATGTAATTTAC 59.299 37.037 0.00 0.00 44.81 2.01
742 781 2.931512 TGAATCGCGTGTCACATCTA 57.068 45.000 5.77 0.00 0.00 1.98
763 805 7.154435 TCTATTAGGCATATCGTGGTTCTAC 57.846 40.000 0.00 0.00 0.00 2.59
847 889 8.309163 TGATTTAAATTGGAATGTGCAGTTTC 57.691 30.769 1.43 0.00 31.01 2.78
853 895 3.826524 TGGAATGTGCAGTTTCCTTACA 58.173 40.909 22.00 5.55 41.65 2.41
858 900 2.152016 GTGCAGTTTCCTTACAGGGTC 58.848 52.381 0.00 0.00 35.59 4.46
859 901 1.073284 TGCAGTTTCCTTACAGGGTCC 59.927 52.381 0.00 0.00 35.59 4.46
860 902 1.073284 GCAGTTTCCTTACAGGGTCCA 59.927 52.381 0.00 0.00 35.59 4.02
861 903 2.488347 GCAGTTTCCTTACAGGGTCCAA 60.488 50.000 0.00 0.00 35.59 3.53
862 904 3.827722 CAGTTTCCTTACAGGGTCCAAA 58.172 45.455 0.00 0.00 35.59 3.28
863 905 4.407365 CAGTTTCCTTACAGGGTCCAAAT 58.593 43.478 0.00 0.00 35.59 2.32
865 907 5.414765 CAGTTTCCTTACAGGGTCCAAATAC 59.585 44.000 0.00 0.00 35.59 1.89
1010 1056 3.593328 AGGGAAAGACCAATGGAGATTCA 59.407 43.478 6.16 0.00 41.20 2.57
1308 4186 1.326951 ACAAAACCCGCTGTTTGGCT 61.327 50.000 2.47 0.00 46.39 4.75
1434 4312 4.700213 GGTGCAAGCCTCAACTTCTATAAA 59.300 41.667 0.00 0.00 0.00 1.40
1513 4400 2.284625 AGGCCACGAGGGATGTGA 60.285 61.111 5.01 0.00 39.73 3.58
1792 4682 1.396653 GGCAGCTGCTTATGATGGTT 58.603 50.000 35.82 0.00 41.70 3.67
1793 4683 1.336125 GGCAGCTGCTTATGATGGTTC 59.664 52.381 35.82 12.73 41.70 3.62
1898 4788 3.003763 GGAGCTCCCACCGGAAGT 61.004 66.667 23.19 0.00 37.86 3.01
1996 4886 2.030457 GTGTCACTCTGGAAACACAACG 59.970 50.000 0.00 0.00 41.24 4.10
2314 5207 1.063951 CTCGTTGTCGCTGGACGTAC 61.064 60.000 0.00 0.00 46.49 3.67
2477 5377 8.955061 AAGTGTTTTCTTTTGTATGATCATCG 57.045 30.769 12.53 0.00 0.00 3.84
2501 5401 8.129211 TCGTATCACAATAATGAGTAGTGACTG 58.871 37.037 0.00 0.00 41.43 3.51
2647 6414 7.455058 ACTATAAGTTGTGTTTGACCCATACA 58.545 34.615 0.00 0.00 0.00 2.29
2710 6480 4.030452 GTGCAAGTGACGCCAGGC 62.030 66.667 0.00 0.00 0.00 4.85
2798 6568 3.995705 CCTGTACCATGCCAAAACAAATG 59.004 43.478 0.00 0.00 0.00 2.32
2817 6588 1.740585 TGTTCAGGTTTCAACACGGTG 59.259 47.619 6.58 6.58 0.00 4.94
2884 6699 5.479306 GGTTAGTCAGAGAAGCATGTACAA 58.521 41.667 0.00 0.00 0.00 2.41
3002 6962 1.137282 GAAACGCCTTGTCCCCAAAAA 59.863 47.619 0.00 0.00 0.00 1.94
3007 6967 0.681175 CCTTGTCCCCAAAAAGGCAG 59.319 55.000 0.00 0.00 34.46 4.85
3121 9040 2.950309 GTGAGAGCCGAGTATCCTAACA 59.050 50.000 0.00 0.00 0.00 2.41
3147 9066 2.097142 AGACTACGACGGATTGTGCTAC 59.903 50.000 0.00 0.00 0.00 3.58
3148 9067 1.133790 ACTACGACGGATTGTGCTACC 59.866 52.381 0.00 0.00 0.00 3.18
3150 9069 0.319083 ACGACGGATTGTGCTACCAA 59.681 50.000 0.00 0.00 0.00 3.67
3153 9072 2.223021 CGACGGATTGTGCTACCAATTG 60.223 50.000 0.00 0.00 35.24 2.32
3220 9140 0.171455 ATTCAGTGTCGACTCGAGCC 59.829 55.000 17.92 0.00 36.23 4.70
3223 9143 1.302591 AGTGTCGACTCGAGCCAGA 60.303 57.895 17.92 6.67 36.23 3.86
3251 9171 5.493809 ACATGTGCTATACCCGTTACTTTT 58.506 37.500 0.00 0.00 0.00 2.27
3267 9187 6.074195 CGTTACTTTTAACTGACCGATTGACA 60.074 38.462 0.00 0.00 36.22 3.58
3270 9190 5.995282 ACTTTTAACTGACCGATTGACATGA 59.005 36.000 0.00 0.00 0.00 3.07
3294 9215 6.000840 AGGTGAGAGAAAAGAAGACCAATTC 58.999 40.000 0.00 0.00 0.00 2.17
3304 9225 4.641396 AGAAGACCAATTCACACGATCAA 58.359 39.130 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 6.605471 TTTGTCTCAAGCTAATACAGGAGA 57.395 37.500 0.00 0.00 0.00 3.71
361 365 1.332375 ACCATCAAACAAACACGGACG 59.668 47.619 0.00 0.00 0.00 4.79
385 389 2.902486 TCTCCTCCCATGCATATCACTC 59.098 50.000 0.00 0.00 0.00 3.51
424 428 1.310904 GCCCAAACAACCGTTGTCTA 58.689 50.000 17.11 0.00 44.59 2.59
502 506 6.436218 ACCGTATGCCTATAACATATGACTGA 59.564 38.462 10.38 0.00 38.67 3.41
525 529 4.111916 CAAACTGACAAACACATGGAACC 58.888 43.478 0.00 0.00 0.00 3.62
600 604 0.392336 TGGCAAGACACCAAAATGGC 59.608 50.000 0.00 0.00 42.67 4.40
605 609 3.894427 ACATTACATGGCAAGACACCAAA 59.106 39.130 0.00 0.00 41.49 3.28
618 657 8.458052 TGAACTGGCAGTAAATTACATTACATG 58.542 33.333 22.37 0.00 38.07 3.21
634 673 1.879380 TCAAACCGATTGAACTGGCAG 59.121 47.619 14.16 14.16 44.94 4.85
742 781 5.538813 TCTGTAGAACCACGATATGCCTAAT 59.461 40.000 0.00 0.00 0.00 1.73
763 805 6.662414 TCGACAAAGCTATGGTTATTTCTG 57.338 37.500 0.00 0.00 0.00 3.02
1308 4186 0.465460 ACTTCCGCACAAAGCTTGGA 60.465 50.000 8.15 2.74 42.61 3.53
1434 4312 0.409092 TGTCTTGGGATGCAATGGGT 59.591 50.000 0.00 0.00 0.00 4.51
1513 4400 5.356190 CAGTGAGAGGATTGCAAACACATAT 59.644 40.000 1.71 0.00 0.00 1.78
1701 4591 5.429762 AGATTCCATCCATGTTCCAGTCTTA 59.570 40.000 0.00 0.00 0.00 2.10
1898 4788 2.083774 CTGGATCCTTGTTGCGCTTTA 58.916 47.619 14.23 0.00 0.00 1.85
1953 4843 1.831580 GAAGGCCTTGCATGAAGAGT 58.168 50.000 26.25 0.00 32.82 3.24
1996 4886 1.227943 TGTCACTGCCAAGCTCACC 60.228 57.895 0.00 0.00 0.00 4.02
2314 5207 4.500375 CCTGTCTTGAGCCTTTTTCCTTTG 60.500 45.833 0.00 0.00 0.00 2.77
2447 5347 9.528018 GATCATACAAAAGAAAACACTTCCAAA 57.472 29.630 0.00 0.00 0.00 3.28
2477 5377 9.239002 GACAGTCACTACTCATTATTGTGATAC 57.761 37.037 0.00 0.00 39.39 2.24
2501 5401 6.694411 TCGTTAGACTGAAGTAACAAACTGAC 59.306 38.462 0.00 0.00 38.88 3.51
2645 6412 3.825014 AGCTCAGATGCAAAGACAAATGT 59.175 39.130 0.00 0.00 34.99 2.71
2647 6414 3.192844 CCAGCTCAGATGCAAAGACAAAT 59.807 43.478 0.00 0.00 34.99 2.32
2710 6480 3.629398 GGGAAATCTGACAACCATGCTAG 59.371 47.826 0.00 0.00 0.00 3.42
2798 6568 1.741145 ACACCGTGTTGAAACCTGAAC 59.259 47.619 0.00 0.00 0.00 3.18
2817 6588 0.796927 GGGCTGAAGCTTGTAACGAC 59.203 55.000 2.10 0.00 41.70 4.34
2884 6699 1.708341 AACAAAGCTGGCCTGTTGAT 58.292 45.000 16.68 5.28 32.19 2.57
3002 6962 6.156256 TCCTATGTATTGTGTTCTTACTGCCT 59.844 38.462 0.00 0.00 0.00 4.75
3007 6967 8.942338 TGATGTCCTATGTATTGTGTTCTTAC 57.058 34.615 0.00 0.00 0.00 2.34
3121 9040 3.128242 CACAATCCGTCGTAGTCTAGGTT 59.872 47.826 0.00 0.00 0.00 3.50
3167 9086 3.127895 CGCCAGAATGAAACGGGAATAAA 59.872 43.478 0.00 0.00 39.69 1.40
3170 9089 1.094785 CGCCAGAATGAAACGGGAAT 58.905 50.000 0.00 0.00 39.69 3.01
3171 9090 0.958382 CCGCCAGAATGAAACGGGAA 60.958 55.000 0.00 0.00 41.19 3.97
3173 9092 3.187058 CCGCCAGAATGAAACGGG 58.813 61.111 0.00 0.00 41.19 5.28
3176 9095 1.459450 TTAGCCCGCCAGAATGAAAC 58.541 50.000 0.00 0.00 39.69 2.78
3177 9096 2.023673 CATTAGCCCGCCAGAATGAAA 58.976 47.619 2.08 0.00 39.69 2.69
3220 9140 4.271049 CGGGTATAGCACATGTTCTTTCTG 59.729 45.833 2.60 0.00 0.00 3.02
3223 9143 4.216411 ACGGGTATAGCACATGTTCTTT 57.784 40.909 2.60 0.00 0.00 2.52
3251 9171 3.513912 ACCTCATGTCAATCGGTCAGTTA 59.486 43.478 0.00 0.00 0.00 2.24
3267 9187 4.594920 TGGTCTTCTTTTCTCTCACCTCAT 59.405 41.667 0.00 0.00 0.00 2.90
3270 9190 5.574970 ATTGGTCTTCTTTTCTCTCACCT 57.425 39.130 0.00 0.00 0.00 4.00
3294 9215 5.751680 ACATCTTGTTCTTTTGATCGTGTG 58.248 37.500 0.00 0.00 0.00 3.82
3304 9225 4.583871 CCCAGCTCTACATCTTGTTCTTT 58.416 43.478 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.