Multiple sequence alignment - TraesCS5D01G419400

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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 TraesCS5D01G419400 chr5D 100.000 3653 0 0 1 3653 480482364 480478712 0.000000e+00 6746
1 TraesCS5D01G419400 chr5D 90.473 1396 114 9 1412 2800 482298740 482300123 0.000000e+00 1823
2 TraesCS5D01G419400 chr5D 84.412 417 31 14 3193 3605 482300491 482300877 2.660000e-101 379
3 TraesCS5D01G419400 chr5D 84.000 225 16 7 2924 3148 482300192 482300396 8.000000e-47 198
4 TraesCS5D01G419400 chr5B 96.068 3230 109 7 1 3213 588684811 588681583 0.000000e+00 5245
5 TraesCS5D01G419400 chr5B 90.696 1322 113 5 1484 2800 591653549 591654865 0.000000e+00 1751
6 TraesCS5D01G419400 chr5B 82.155 297 34 7 3301 3597 591655427 591655704 1.700000e-58 237
7 TraesCS5D01G419400 chr5B 83.628 226 14 11 2924 3149 591654933 591655135 1.340000e-44 191
8 TraesCS5D01G419400 chr5B 88.235 102 5 4 3193 3294 591655239 591655333 8.290000e-22 115
9 TraesCS5D01G419400 chr5A 96.269 1742 54 1 1138 2868 599224093 599222352 0.000000e+00 2846
10 TraesCS5D01G419400 chr5A 90.942 1391 115 7 1412 2800 602003643 602005024 0.000000e+00 1860
11 TraesCS5D01G419400 chr5A 92.772 1093 46 18 72 1132 599225469 599224378 0.000000e+00 1550
12 TraesCS5D01G419400 chr5A 86.768 461 28 9 2841 3274 599222352 599221898 1.970000e-132 483
13 TraesCS5D01G419400 chr5A 86.441 177 14 3 2924 3096 602005092 602005262 6.230000e-43 185
14 TraesCS5D01G419400 chr5A 94.118 119 7 0 3535 3653 599221437 599221319 8.060000e-42 182
15 TraesCS5D01G419400 chr4B 79.103 1182 218 23 1497 2663 538999089 538997922 0.000000e+00 787
16 TraesCS5D01G419400 chr4D 78.644 1180 227 21 1497 2663 437028936 437027769 0.000000e+00 760
17 TraesCS5D01G419400 chr4A 78.160 1163 225 20 1497 2647 31414055 31415200 0.000000e+00 713


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 TraesCS5D01G419400 chr5D 480478712 480482364 3652 True 6746.00 6746 100.00000 1 3653 1 chr5D.!!$R1 3652
1 TraesCS5D01G419400 chr5D 482298740 482300877 2137 False 800.00 1823 86.29500 1412 3605 3 chr5D.!!$F1 2193
2 TraesCS5D01G419400 chr5B 588681583 588684811 3228 True 5245.00 5245 96.06800 1 3213 1 chr5B.!!$R1 3212
3 TraesCS5D01G419400 chr5B 591653549 591655704 2155 False 573.50 1751 86.17850 1484 3597 4 chr5B.!!$F1 2113
4 TraesCS5D01G419400 chr5A 599221319 599225469 4150 True 1265.25 2846 92.48175 72 3653 4 chr5A.!!$R1 3581
5 TraesCS5D01G419400 chr5A 602003643 602005262 1619 False 1022.50 1860 88.69150 1412 3096 2 chr5A.!!$F1 1684
6 TraesCS5D01G419400 chr4B 538997922 538999089 1167 True 787.00 787 79.10300 1497 2663 1 chr4B.!!$R1 1166
7 TraesCS5D01G419400 chr4D 437027769 437028936 1167 True 760.00 760 78.64400 1497 2663 1 chr4D.!!$R1 1166
8 TraesCS5D01G419400 chr4A 31414055 31415200 1145 False 713.00 713 78.16000 1497 2647 1 chr4A.!!$F1 1150

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
735 759 1.065551 GGCTTGACACTGTTTGGTCAC 59.934 52.381 0.00 0.00 43.22 3.67 F
1662 1976 0.466189 ATCCAATGCAACGCCTAGGG 60.466 55.000 11.72 3.13 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2076 2396 0.889638 CCTCATGGCTAGCAGCATGG 60.890 60.0 24.79 17.87 44.75 3.66 R
3131 3521 0.239347 GTGAGGACACATGCAACAGC 59.761 55.0 0.00 0.00 45.32 4.40 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
54 57 8.831715 TTCTTAAAAGAAATGCATTTCCTTCC 57.168 30.769 36.81 20.30 45.52 3.46
61 64 6.536447 AGAAATGCATTTCCTTCCAATTTGT 58.464 32.000 36.81 18.60 45.52 2.83
87 90 7.083858 TGAGTTTTTCATCGATTGAATTGTCC 58.916 34.615 0.00 0.00 43.73 4.02
164 173 8.433421 TGATTTTCTTTCTTTCTAGAACACGT 57.567 30.769 4.18 0.00 40.04 4.49
176 185 3.660501 AGAACACGTCTGCAACAGATA 57.339 42.857 0.00 0.00 42.73 1.98
249 258 5.510323 CGAATTACAACAAGGCGATTAAACC 59.490 40.000 0.00 0.00 0.00 3.27
478 502 4.559862 ACTATGGCCTTATATGTGAGCC 57.440 45.455 3.32 0.00 44.13 4.70
580 604 7.982761 TTCCTTTATCTAAAAACCTGCGTTA 57.017 32.000 0.00 0.00 0.00 3.18
581 605 7.368480 TCCTTTATCTAAAAACCTGCGTTAC 57.632 36.000 0.00 0.00 0.00 2.50
636 660 1.493022 TGGTAGCCAAACAAGGAGTGT 59.507 47.619 0.00 0.00 44.64 3.55
685 709 7.569043 GCTTCTTCTTAGTTCTTACCGTGAAAC 60.569 40.741 0.00 0.00 0.00 2.78
710 734 9.965824 ACGATTAGAAACATCAACTTCAAATTT 57.034 25.926 0.00 0.00 0.00 1.82
735 759 1.065551 GGCTTGACACTGTTTGGTCAC 59.934 52.381 0.00 0.00 43.22 3.67
879 903 6.808008 ATTGATGTGAGTTCAGGTGTTAAG 57.192 37.500 0.00 0.00 0.00 1.85
1053 1088 2.955614 GCTAAGGCTTCAGAACGTACA 58.044 47.619 1.30 0.00 35.22 2.90
1404 1718 3.939066 ACCGGATTTCCAGAGTAAACTG 58.061 45.455 9.46 0.00 37.61 3.16
1662 1976 0.466189 ATCCAATGCAACGCCTAGGG 60.466 55.000 11.72 3.13 0.00 3.53
1794 2114 1.039785 TCCTCTGTGAGATCTGCCCG 61.040 60.000 0.00 0.00 0.00 6.13
1818 2138 6.360329 GTTCTACAAGTTTGGTTACATGTCG 58.640 40.000 0.00 0.00 32.75 4.35
2055 2375 1.302033 CTCTGCTTCGTGTGGCCTT 60.302 57.895 3.32 0.00 0.00 4.35
2076 2396 3.149196 TCCCTTTGAGTTCAATGCTGTC 58.851 45.455 0.00 0.00 35.55 3.51
2117 2437 7.280876 TGAGGTTTATATTCAGCATCTTGACAC 59.719 37.037 0.00 0.00 0.00 3.67
2355 2675 7.386059 TGTTTGAGTCAATAGATGTTGCTCTA 58.614 34.615 6.36 0.00 35.35 2.43
2400 2720 1.643292 CACGGAGCAACACTGTGTG 59.357 57.895 15.11 9.76 39.09 3.82
2643 2963 0.874175 TGTTGGTCGTGTCTTCTGCG 60.874 55.000 0.00 0.00 0.00 5.18
2735 3062 4.224433 TCTTGAGTGATTCGTGTTACGTC 58.776 43.478 0.00 0.00 43.14 4.34
2771 3099 7.490657 TTTCTATAGCCTGACTTGTCCTTTA 57.509 36.000 0.00 0.00 0.00 1.85
2800 3128 4.679373 TCAGATGGAACCTGAGCTTATC 57.321 45.455 0.00 0.00 35.89 1.75
2815 3160 3.008049 AGCTTATCAGGTCGGTTCAGTTT 59.992 43.478 0.00 0.00 0.00 2.66
2861 3234 1.980765 TCACTGGAACCTGAGCTTGAT 59.019 47.619 4.82 0.00 0.00 2.57
2925 3301 0.468771 AAGGGCTTTGCTGCTTGTCT 60.469 50.000 0.00 0.00 0.00 3.41
3131 3521 2.874648 TATGCAGGCACAAGAGGCGG 62.875 60.000 0.00 0.00 39.37 6.13
3152 3542 1.802960 CTGTTGCATGTGTCCTCACTC 59.197 52.381 0.00 0.00 44.14 3.51
3157 3547 1.988063 CATGTGTCCTCACTCTCGTG 58.012 55.000 0.00 0.00 44.14 4.35
3167 3557 2.733552 CTCACTCTCGTGGATTTGTGTG 59.266 50.000 0.00 0.00 41.53 3.82
3190 3596 7.011016 TGTGATGATGACGTGATGGTTTATTAC 59.989 37.037 0.00 0.00 0.00 1.89
3294 3760 5.882557 AGGAAATATGTGATGAACCTGTGAC 59.117 40.000 0.00 0.00 0.00 3.67
3295 3761 5.220662 GGAAATATGTGATGAACCTGTGACG 60.221 44.000 0.00 0.00 0.00 4.35
3301 3767 4.082949 TGTGATGAACCTGTGACGTACTAG 60.083 45.833 0.00 0.00 0.00 2.57
3303 3769 5.122869 GTGATGAACCTGTGACGTACTAGTA 59.877 44.000 0.00 0.00 0.00 1.82
3305 3771 7.011763 GTGATGAACCTGTGACGTACTAGTATA 59.988 40.741 5.75 0.00 0.00 1.47
3306 3772 7.553760 TGATGAACCTGTGACGTACTAGTATAA 59.446 37.037 5.75 0.00 0.00 0.98
3307 3773 7.870509 TGAACCTGTGACGTACTAGTATAAT 57.129 36.000 5.75 0.00 0.00 1.28
3309 3775 6.069684 ACCTGTGACGTACTAGTATAATGC 57.930 41.667 5.75 0.00 0.00 3.56
3310 3776 5.009410 ACCTGTGACGTACTAGTATAATGCC 59.991 44.000 5.75 0.00 0.00 4.40
3311 3777 5.099484 TGTGACGTACTAGTATAATGCCG 57.901 43.478 5.75 6.35 0.00 5.69
3312 3778 3.910767 GTGACGTACTAGTATAATGCCGC 59.089 47.826 5.75 1.83 0.00 6.53
3365 4133 2.938451 TGTGCAATATGGAAAGCTCTCG 59.062 45.455 0.00 0.00 0.00 4.04
3396 4164 6.849085 TCTTCTCTGATACTTCTTCAAGCT 57.151 37.500 0.00 0.00 32.09 3.74
3402 4170 6.191315 TCTGATACTTCTTCAAGCTAGGAGT 58.809 40.000 1.55 1.55 35.62 3.85
3403 4171 6.096141 TCTGATACTTCTTCAAGCTAGGAGTG 59.904 42.308 6.23 0.00 33.51 3.51
3404 4172 5.717178 TGATACTTCTTCAAGCTAGGAGTGT 59.283 40.000 6.23 0.00 33.51 3.55
3405 4173 6.890268 TGATACTTCTTCAAGCTAGGAGTGTA 59.110 38.462 6.23 4.56 33.51 2.90
3406 4174 7.561722 TGATACTTCTTCAAGCTAGGAGTGTAT 59.438 37.037 6.23 8.04 33.51 2.29
3407 4175 6.613153 ACTTCTTCAAGCTAGGAGTGTATT 57.387 37.500 0.00 0.00 30.17 1.89
3449 4217 6.014584 GGGTCTTTGGAAGAATTACCAACAAT 60.015 38.462 9.70 0.00 44.34 2.71
3451 4219 7.090808 GTCTTTGGAAGAATTACCAACAATCC 58.909 38.462 9.70 0.00 44.34 3.01
3481 4249 5.587844 GCTTCTCATTTCTGGTATGTGTGAT 59.412 40.000 0.00 0.00 0.00 3.06
3515 4317 0.713883 CACCGCACGATTACAGTGAC 59.286 55.000 0.00 0.00 41.83 3.67
3529 4364 9.175060 CGATTACAGTGACTGATTATACAAGAG 57.825 37.037 20.97 0.00 35.18 2.85
3575 4414 7.170828 CAGTGTGTTACTAACTATGACAGCAAA 59.829 37.037 0.71 0.00 37.60 3.68
3576 4415 7.385205 AGTGTGTTACTAACTATGACAGCAAAG 59.615 37.037 0.71 0.00 38.04 2.77
3607 4446 4.462834 CGAGGAGCATATACCCATCTGTAA 59.537 45.833 0.00 0.00 0.00 2.41
3632 4471 6.782082 AAGATGGCCTAAATTTCTTCTTCC 57.218 37.500 3.32 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 36 8.354426 CAAATTGGAAGGAAATGCATTTCTTTT 58.646 29.630 35.70 31.21 43.33 2.27
35 37 7.503230 ACAAATTGGAAGGAAATGCATTTCTTT 59.497 29.630 35.89 35.89 45.11 2.52
38 40 6.806388 ACAAATTGGAAGGAAATGCATTTC 57.194 33.333 34.36 34.36 44.08 2.17
54 57 8.754096 TCAATCGATGAAAAACTCAACAAATTG 58.246 29.630 0.00 0.00 37.67 2.32
164 173 5.521906 CTACCTTAGCTATCTGTTGCAGA 57.478 43.478 0.00 1.06 44.99 4.26
439 455 2.116238 AGTTCCACCATGTATACGCCT 58.884 47.619 0.00 0.00 0.00 5.52
469 493 8.978874 AAATACATCAATAACAGGCTCACATA 57.021 30.769 0.00 0.00 0.00 2.29
580 604 3.003275 ACAATTGCGAATCAAACAGACGT 59.997 39.130 5.05 0.00 38.34 4.34
581 605 3.554524 ACAATTGCGAATCAAACAGACG 58.445 40.909 5.05 0.00 38.34 4.18
623 647 4.142403 TGCTTTCTTGACACTCCTTGTTTG 60.142 41.667 0.00 0.00 39.17 2.93
636 660 5.335897 GCAAGTTCACCATATGCTTTCTTGA 60.336 40.000 19.71 5.99 33.86 3.02
710 734 2.884012 CCAAACAGTGTCAAGCCACATA 59.116 45.455 0.00 0.00 37.82 2.29
879 903 4.161333 CGCATCCTGAGTCAATTTTGAAC 58.839 43.478 0.00 0.00 39.21 3.18
959 994 7.769044 TGATCCTGCCATCTTTAAAGTAAGTAC 59.231 37.037 14.74 2.71 0.00 2.73
1053 1088 9.961264 ATTTGTGAATCATCTGAGCATCTATAT 57.039 29.630 0.00 0.00 34.92 0.86
1404 1718 6.448207 AGAATTGCATTTTCTAGCTCCTTC 57.552 37.500 9.93 0.00 31.75 3.46
1662 1976 3.160679 AGGCCTTCCAACATATATGCC 57.839 47.619 12.79 5.55 37.91 4.40
1794 2114 6.360329 CGACATGTAACCAAACTTGTAGAAC 58.640 40.000 0.00 0.00 37.73 3.01
2055 2375 3.149196 GACAGCATTGAACTCAAAGGGA 58.851 45.455 0.00 0.00 39.55 4.20
2076 2396 0.889638 CCTCATGGCTAGCAGCATGG 60.890 60.000 24.79 17.87 44.75 3.66
2117 2437 1.133976 CAATAGCCTCCCCAGGTCTTG 60.134 57.143 0.00 0.00 42.74 3.02
2355 2675 1.417890 CGCCTCTTATCATCCCTTGGT 59.582 52.381 0.00 0.00 0.00 3.67
2391 2711 1.064003 TATCCCTTGCCACACAGTGT 58.936 50.000 0.00 0.00 0.00 3.55
2400 2720 6.575162 ATTAAATTGACGATATCCCTTGCC 57.425 37.500 0.00 0.00 0.00 4.52
2617 2937 1.222115 GACACGACCAACACTCTGCC 61.222 60.000 0.00 0.00 0.00 4.85
2643 2963 1.802960 CTCAAGACATGTCAGCACCAC 59.197 52.381 27.02 0.00 0.00 4.16
2735 3062 5.974158 CAGGCTATAGAAATATCGTGGATCG 59.026 44.000 3.21 0.00 41.41 3.69
2771 3099 3.075882 TCAGGTTCCATCTGAAATTGGGT 59.924 43.478 0.00 0.00 38.20 4.51
2800 3128 2.544267 GACAGAAAACTGAACCGACCTG 59.456 50.000 0.00 0.00 0.00 4.00
2815 3160 1.372683 GGCCAGTGAGCAGACAGAA 59.627 57.895 0.00 0.00 0.00 3.02
2861 3234 5.890985 TGAAACTGGAGAAAGGACAAATCAA 59.109 36.000 0.00 0.00 0.00 2.57
3131 3521 0.239347 GTGAGGACACATGCAACAGC 59.761 55.000 0.00 0.00 45.32 4.40
3152 3542 3.934579 TCATCATCACACAAATCCACGAG 59.065 43.478 0.00 0.00 0.00 4.18
3157 3547 3.684305 TCACGTCATCATCACACAAATCC 59.316 43.478 0.00 0.00 0.00 3.01
3167 3557 6.419710 TCGTAATAAACCATCACGTCATCATC 59.580 38.462 0.00 0.00 34.39 2.92
3190 3596 1.633852 GCAAGCAGCAGAAGAGGTCG 61.634 60.000 0.00 0.00 44.79 4.79
3191 3650 2.169842 GCAAGCAGCAGAAGAGGTC 58.830 57.895 0.00 0.00 44.79 3.85
3239 3698 6.315091 TCTCCTGAATCAGTACGCTATAAC 57.685 41.667 9.63 0.00 0.00 1.89
3294 3760 4.404324 CAGAGCGGCATTATACTAGTACG 58.596 47.826 4.31 4.41 0.00 3.67
3295 3761 4.458295 TCCAGAGCGGCATTATACTAGTAC 59.542 45.833 4.31 0.00 33.14 2.73
3301 3767 1.338200 CCCTCCAGAGCGGCATTATAC 60.338 57.143 1.45 0.00 33.14 1.47
3303 3769 0.764369 TCCCTCCAGAGCGGCATTAT 60.764 55.000 1.45 0.00 33.14 1.28
3305 3771 2.688666 TCCCTCCAGAGCGGCATT 60.689 61.111 1.45 0.00 33.14 3.56
3306 3772 2.961559 ATCTCCCTCCAGAGCGGCAT 62.962 60.000 1.45 0.00 33.66 4.40
3307 3773 3.686098 ATCTCCCTCCAGAGCGGCA 62.686 63.158 1.45 0.00 33.66 5.69
3309 3775 2.206536 GGATCTCCCTCCAGAGCGG 61.207 68.421 0.00 0.00 35.24 5.52
3310 3776 1.456518 TGGATCTCCCTCCAGAGCG 60.457 63.158 0.00 0.00 40.43 5.03
3311 3777 4.716025 TGGATCTCCCTCCAGAGC 57.284 61.111 0.00 0.00 40.43 4.09
3379 4147 6.127479 ACACTCCTAGCTTGAAGAAGTATCAG 60.127 42.308 0.00 0.00 0.00 2.90
3380 4148 5.717178 ACACTCCTAGCTTGAAGAAGTATCA 59.283 40.000 0.00 0.00 0.00 2.15
3384 4152 6.613153 AATACACTCCTAGCTTGAAGAAGT 57.387 37.500 0.00 0.00 0.00 3.01
3402 4170 9.974980 GACCCTTCTTTTTCAAATACAAATACA 57.025 29.630 0.00 0.00 0.00 2.29
3432 4200 5.163612 GCAGAGGATTGTTGGTAATTCTTCC 60.164 44.000 0.00 0.00 0.00 3.46
3449 4217 1.552337 AGAAATGAGAAGCGCAGAGGA 59.448 47.619 11.47 0.00 0.00 3.71
3451 4219 1.664659 CCAGAAATGAGAAGCGCAGAG 59.335 52.381 11.47 0.00 0.00 3.35
3481 4249 3.556775 GTGCGGTGTTCAGTTAAACTGTA 59.443 43.478 0.00 0.00 46.03 2.74
3493 4261 1.126113 CACTGTAATCGTGCGGTGTTC 59.874 52.381 0.00 0.00 40.70 3.18
3495 4263 0.315886 TCACTGTAATCGTGCGGTGT 59.684 50.000 4.10 0.00 44.57 4.16
3496 4264 0.713883 GTCACTGTAATCGTGCGGTG 59.286 55.000 0.00 0.00 45.35 4.94
3497 4265 0.601558 AGTCACTGTAATCGTGCGGT 59.398 50.000 0.00 0.00 32.54 5.68
3498 4266 0.992072 CAGTCACTGTAATCGTGCGG 59.008 55.000 0.00 0.00 32.54 5.69
3499 4267 1.977188 TCAGTCACTGTAATCGTGCG 58.023 50.000 4.28 0.00 32.61 5.34
3500 4268 6.695713 TGTATAATCAGTCACTGTAATCGTGC 59.304 38.462 4.28 0.00 32.61 5.34
3501 4269 8.628882 TTGTATAATCAGTCACTGTAATCGTG 57.371 34.615 4.28 0.00 32.61 4.35
3502 4270 8.683615 TCTTGTATAATCAGTCACTGTAATCGT 58.316 33.333 4.28 0.00 32.61 3.73
3601 4440 9.920946 AAGAAATTTAGGCCATCTTATTACAGA 57.079 29.630 5.01 0.00 0.00 3.41
3607 4446 8.285163 AGGAAGAAGAAATTTAGGCCATCTTAT 58.715 33.333 5.01 0.00 30.89 1.73
3616 4455 7.724490 AATGGGAAGGAAGAAGAAATTTAGG 57.276 36.000 0.00 0.00 0.00 2.69
3625 4464 5.379706 AGACCATAATGGGAAGGAAGAAG 57.620 43.478 0.00 0.00 43.37 2.85


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

AutoCloner maintained by Alex Coulton.