Multiple sequence alignment - TraesCS4D01G255900

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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 TraesCS4D01G255900 chr4D 100.000 3518 0 0 1 3518 424609705 424606188 0.000000e+00 6497
1 TraesCS4D01G255900 chr4D 77.479 2713 483 83 858 3505 424599348 424596699 0.000000e+00 1507
2 TraesCS4D01G255900 chr4A 93.379 3534 202 19 1 3516 39830013 39833532 0.000000e+00 5201
3 TraesCS4D01G255900 chr4A 83.784 370 58 1 2141 2510 40201186 40201553 2.010000e-92 350
4 TraesCS4D01G255900 chr4B 93.920 3240 170 16 1 3224 520524684 520521456 0.000000e+00 4867
5 TraesCS4D01G255900 chr4B 78.681 2350 397 59 1212 3505 520425783 520423482 0.000000e+00 1469
6 TraesCS4D01G255900 chr4B 92.749 331 17 4 3193 3516 520521457 520521127 4.110000e-129 472


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 TraesCS4D01G255900 chr4D 424606188 424609705 3517 True 6497.0 6497 100.0000 1 3518 1 chr4D.!!$R2 3517
1 TraesCS4D01G255900 chr4D 424596699 424599348 2649 True 1507.0 1507 77.4790 858 3505 1 chr4D.!!$R1 2647
2 TraesCS4D01G255900 chr4A 39830013 39833532 3519 False 5201.0 5201 93.3790 1 3516 1 chr4A.!!$F1 3515
3 TraesCS4D01G255900 chr4B 520521127 520524684 3557 True 2669.5 4867 93.3345 1 3516 2 chr4B.!!$R2 3515
4 TraesCS4D01G255900 chr4B 520423482 520425783 2301 True 1469.0 1469 78.6810 1212 3505 1 chr4B.!!$R1 2293

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
35 36 2.947652 CCTATGGCCTTCTGATGTGTTG 59.052 50.000 3.32 0.0 0.00 3.33 F
451 455 4.171754 GTCGCGTGGAAATTAAGAGTAGT 58.828 43.478 5.77 0.0 0.00 2.73 F
1326 1334 1.106351 TGTCAGCGGGTGCAATTTGT 61.106 50.000 1.51 0.0 46.23 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1203 1211 1.604755 TGTACGGCAAACTGCGAAATT 59.395 42.857 0.00 0.00 46.21 1.82 R
2314 2363 1.651770 TCCACTTCCCATAGGAGGAGT 59.348 52.381 0.00 0.00 45.19 3.85 R
2945 3001 0.168128 GTGGTCAGCGGTGCATTAAC 59.832 55.000 10.38 1.98 0.00 2.01 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
35 36 2.947652 CCTATGGCCTTCTGATGTGTTG 59.052 50.000 3.32 0.00 0.00 3.33
44 45 4.823989 CCTTCTGATGTGTTGAAACTTCCT 59.176 41.667 0.00 0.00 0.00 3.36
69 71 7.517614 ACACCATTTTTGTTTTGTTTTCCTT 57.482 28.000 0.00 0.00 0.00 3.36
70 72 7.366513 ACACCATTTTTGTTTTGTTTTCCTTG 58.633 30.769 0.00 0.00 0.00 3.61
80 82 6.992715 TGTTTTGTTTTCCTTGGACTTTTTCA 59.007 30.769 0.00 0.00 0.00 2.69
154 156 8.299570 GCATTGGGAACTGGATTAATATGTTAG 58.700 37.037 0.00 0.00 0.00 2.34
416 418 7.995663 AGGGGGTTGTATATCATTTATTGCTA 58.004 34.615 0.00 0.00 0.00 3.49
417 419 7.888546 AGGGGGTTGTATATCATTTATTGCTAC 59.111 37.037 0.00 0.00 0.00 3.58
451 455 4.171754 GTCGCGTGGAAATTAAGAGTAGT 58.828 43.478 5.77 0.00 0.00 2.73
477 481 7.794683 TCCCTCTATATAAAAGAACTCCCATGT 59.205 37.037 0.00 0.00 0.00 3.21
504 508 7.805083 ATATTGCTCTATATGTGTTCTCCCT 57.195 36.000 0.00 0.00 0.00 4.20
538 542 9.365906 AGATGTCTCATCTTCATCTAGTATTGT 57.634 33.333 6.45 0.00 43.98 2.71
694 698 9.631257 TCCATACATCAATGTACAATGAATCTT 57.369 29.630 17.20 5.23 45.11 2.40
724 728 6.276847 TGTTTATGTGTTTGGATGTGGAAAC 58.723 36.000 0.00 0.00 33.48 2.78
750 754 7.120285 CAGAAGATTCAACATACATGTGGAGTT 59.880 37.037 9.11 7.54 41.46 3.01
768 772 7.719193 TGTGGAGTTAATCAACAGAAGAATTCA 59.281 33.333 8.44 0.00 40.01 2.57
935 940 6.701841 TCGATGCTCATTAGTATGAAGGAAAC 59.298 38.462 0.00 0.00 40.17 2.78
1184 1192 7.681939 TTTGAAGTGTATGAATAACCTCCAC 57.318 36.000 0.00 0.00 0.00 4.02
1199 1207 5.319043 ACCTCCACCTTTAAATTGACTCA 57.681 39.130 0.00 0.00 0.00 3.41
1200 1208 5.892348 ACCTCCACCTTTAAATTGACTCAT 58.108 37.500 0.00 0.00 0.00 2.90
1201 1209 6.314917 ACCTCCACCTTTAAATTGACTCATT 58.685 36.000 0.00 0.00 0.00 2.57
1202 1210 6.782494 ACCTCCACCTTTAAATTGACTCATTT 59.218 34.615 0.00 0.00 0.00 2.32
1203 1211 7.947890 ACCTCCACCTTTAAATTGACTCATTTA 59.052 33.333 0.00 0.00 0.00 1.40
1229 1237 2.414029 CGCAGTTTGCCGTACATTTGAT 60.414 45.455 0.00 0.00 41.12 2.57
1233 1241 3.823873 AGTTTGCCGTACATTTGATGGAA 59.176 39.130 0.00 0.00 33.60 3.53
1326 1334 1.106351 TGTCAGCGGGTGCAATTTGT 61.106 50.000 1.51 0.00 46.23 2.83
1767 1781 3.214697 TGCGTAAATGCTTGACAATGG 57.785 42.857 0.00 0.00 35.36 3.16
1938 1963 6.417258 TGGAAGTGCAGAAAGATAATCATCA 58.583 36.000 0.00 0.00 33.21 3.07
2010 2035 2.224159 CCCCCATATCTCCCGGTGG 61.224 68.421 0.00 0.00 0.00 4.61
2081 2106 4.715527 ATTAGAGTGTCCAAGGTACGTC 57.284 45.455 0.00 0.00 0.00 4.34
2093 2118 4.023193 CCAAGGTACGTCTGCTCAATTTTT 60.023 41.667 0.00 0.00 0.00 1.94
2094 2119 4.749245 AGGTACGTCTGCTCAATTTTTG 57.251 40.909 0.00 0.00 0.00 2.44
2106 2131 6.454795 TGCTCAATTTTTGTTCATTAGGGAC 58.545 36.000 0.00 0.00 0.00 4.46
2303 2352 1.409427 AGGCCATGCTCGAAGTACTAC 59.591 52.381 5.01 0.00 0.00 2.73
2309 2358 5.522460 GCCATGCTCGAAGTACTACAAATAA 59.478 40.000 0.00 0.00 0.00 1.40
2312 2361 8.700644 CCATGCTCGAAGTACTACAAATAATAC 58.299 37.037 0.00 0.00 0.00 1.89
2314 2363 9.811995 ATGCTCGAAGTACTACAAATAATACAA 57.188 29.630 0.00 0.00 0.00 2.41
2533 2582 2.025226 TCTTAGTGAGGTGGATCCGAGT 60.025 50.000 7.39 0.00 41.99 4.18
2534 2583 1.763968 TAGTGAGGTGGATCCGAGTG 58.236 55.000 7.39 0.00 41.99 3.51
2570 2619 9.163899 TGCAATGCATGAATAAAACATTGTAAT 57.836 25.926 2.72 0.00 45.85 1.89
2721 2772 4.574421 CCATACTTGCATATTGTCGGAACA 59.426 41.667 0.00 0.00 0.00 3.18
2738 2789 7.011016 TGTCGGAACATAGTAAACATAGCATTG 59.989 37.037 0.00 0.00 0.00 2.82
2745 2796 7.992608 ACATAGTAAACATAGCATTGTGGATGA 59.007 33.333 0.00 0.00 38.03 2.92
3002 3058 0.768221 TCACCAAGGTTCTGGCTCCT 60.768 55.000 0.00 0.00 40.45 3.69
3031 3088 2.509336 CGCCTTACGTCCTGCCTG 60.509 66.667 0.00 0.00 36.87 4.85
3086 3148 7.940137 ACAACGGTGTAGATCTTATCTAGAGAT 59.060 37.037 2.99 0.00 42.20 2.75
3141 3203 4.141937 CCAATGATCTTTGACGGAGGTCTA 60.142 45.833 19.94 0.00 43.79 2.59
3212 3315 6.788598 ATGATATGATCGAGCAATCCTACT 57.211 37.500 7.76 0.00 0.00 2.57
3217 3320 5.791336 TGATCGAGCAATCCTACTGTTAT 57.209 39.130 0.00 0.00 0.00 1.89
3245 3350 8.928448 GGAATGATCTCCCATTATAGCTACATA 58.072 37.037 0.00 0.00 36.93 2.29
3251 3356 6.892456 TCTCCCATTATAGCTACATACCTGAG 59.108 42.308 0.00 0.00 0.00 3.35
3275 3380 1.217747 TGCACCCATCATTACCCCCA 61.218 55.000 0.00 0.00 0.00 4.96
3278 3383 2.131854 CACCCATCATTACCCCCACTA 58.868 52.381 0.00 0.00 0.00 2.74
3304 3409 2.476852 TACTTGGGCGCAATGAGGCA 62.477 55.000 17.30 0.00 35.71 4.75
3496 3605 7.041098 TCCAACTGTTCTCATTCTAAGCTTTTC 60.041 37.037 3.20 0.00 0.00 2.29
3516 3626 7.042051 GCTTTTCCCTATTTCCAAGAACAAAAC 60.042 37.037 0.00 0.00 0.00 2.43
3517 3627 5.699097 TCCCTATTTCCAAGAACAAAACG 57.301 39.130 0.00 0.00 0.00 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.053244 ACATCAGAAGGCCATAGGAGG 58.947 52.381 5.01 1.10 0.00 4.30
35 36 8.387354 CAAAACAAAAATGGTGTAGGAAGTTTC 58.613 33.333 0.00 0.00 0.00 2.78
44 45 8.507249 CAAGGAAAACAAAACAAAAATGGTGTA 58.493 29.630 0.00 0.00 0.00 2.90
69 71 6.806668 AGAAAAATCCCTTGAAAAAGTCCA 57.193 33.333 0.00 0.00 0.00 4.02
70 72 9.607988 TTTTAGAAAAATCCCTTGAAAAAGTCC 57.392 29.630 0.00 0.00 0.00 3.85
119 121 3.379372 CCAGTTCCCAATGCTAGTTCATG 59.621 47.826 0.00 0.00 0.00 3.07
231 233 9.589461 TTCCCTATCCAAAATTAAACAACTACA 57.411 29.630 0.00 0.00 0.00 2.74
360 362 7.428020 TCAAGAAACAAATGACCAAATCTCTG 58.572 34.615 0.00 0.00 0.00 3.35
377 379 2.876581 ACCCCCTCACAATCAAGAAAC 58.123 47.619 0.00 0.00 0.00 2.78
416 418 4.996434 GCGACCACAGCCTGCAGT 62.996 66.667 13.81 0.00 0.00 4.40
451 455 7.794683 ACATGGGAGTTCTTTTATATAGAGGGA 59.205 37.037 0.00 0.00 0.00 4.20
464 468 5.513233 AGCAATATTCACATGGGAGTTCTT 58.487 37.500 0.00 0.00 0.00 2.52
477 481 8.097038 GGGAGAACACATATAGAGCAATATTCA 58.903 37.037 0.00 0.00 0.00 2.57
679 683 7.765695 AACAACTGGAAGATTCATTGTACAT 57.234 32.000 0.00 0.00 37.43 2.29
694 698 5.596361 ACATCCAAACACATAAACAACTGGA 59.404 36.000 0.00 0.00 36.23 3.86
724 728 6.596888 ACTCCACATGTATGTTGAATCTTCTG 59.403 38.462 0.00 0.00 39.39 3.02
750 754 8.246180 GGAAAGCATGAATTCTTCTGTTGATTA 58.754 33.333 7.05 0.00 0.00 1.75
804 808 7.492344 GTGTGAAAACCAACTCATCTGAAAATT 59.508 33.333 0.00 0.00 0.00 1.82
810 814 3.303990 CGGTGTGAAAACCAACTCATCTG 60.304 47.826 0.00 0.00 40.53 2.90
821 825 4.231718 TCTTATTTGCCGGTGTGAAAAC 57.768 40.909 1.90 0.00 0.00 2.43
935 940 5.890985 TCCATATATTGTGAACTTGTTGGGG 59.109 40.000 0.00 0.00 0.00 4.96
1194 1202 5.060940 GGCAAACTGCGAAATTAAATGAGTC 59.939 40.000 0.00 0.00 46.21 3.36
1199 1207 3.908213 ACGGCAAACTGCGAAATTAAAT 58.092 36.364 0.00 0.00 46.21 1.40
1200 1208 3.357166 ACGGCAAACTGCGAAATTAAA 57.643 38.095 0.00 0.00 46.21 1.52
1201 1209 3.250280 TGTACGGCAAACTGCGAAATTAA 59.750 39.130 0.00 0.00 46.21 1.40
1202 1210 2.806818 TGTACGGCAAACTGCGAAATTA 59.193 40.909 0.00 0.00 46.21 1.40
1203 1211 1.604755 TGTACGGCAAACTGCGAAATT 59.395 42.857 0.00 0.00 46.21 1.82
1210 1218 3.190327 TCCATCAAATGTACGGCAAACTG 59.810 43.478 0.00 0.00 0.00 3.16
1245 1253 8.664669 TGTTAGCAGATATTCCATAGTATCCA 57.335 34.615 0.00 0.00 0.00 3.41
1326 1334 6.575244 ACATCACCTTCCCAGTTATGAATA 57.425 37.500 0.00 0.00 0.00 1.75
1491 1501 7.888021 TCATTAAATCGATATGGCCAAACCTAT 59.112 33.333 10.96 2.05 40.22 2.57
1878 1896 9.778741 TTTAGATGTCATCCCATATTGTCTAAC 57.221 33.333 9.29 0.00 0.00 2.34
1938 1963 2.508300 AGGTTGACACACCCTGTACTTT 59.492 45.455 0.00 0.00 37.58 2.66
2010 2035 2.028930 CCGGAGACAGGGCTTATGATAC 60.029 54.545 0.00 0.00 0.00 2.24
2081 2106 6.587608 GTCCCTAATGAACAAAAATTGAGCAG 59.412 38.462 0.00 0.00 0.00 4.24
2093 2118 2.301870 ACTTCTGCGTCCCTAATGAACA 59.698 45.455 0.00 0.00 0.00 3.18
2094 2119 2.673368 CACTTCTGCGTCCCTAATGAAC 59.327 50.000 0.00 0.00 0.00 3.18
2303 2352 7.745717 TCCCATAGGAGGAGTTGTATTATTTG 58.254 38.462 0.00 0.00 37.19 2.32
2309 2358 4.656112 CACTTCCCATAGGAGGAGTTGTAT 59.344 45.833 0.00 0.00 45.19 2.29
2312 2361 2.171448 CCACTTCCCATAGGAGGAGTTG 59.829 54.545 0.00 0.00 45.19 3.16
2314 2363 1.651770 TCCACTTCCCATAGGAGGAGT 59.348 52.381 0.00 0.00 45.19 3.85
2721 2772 8.213679 AGTCATCCACAATGCTATGTTTACTAT 58.786 33.333 0.00 0.00 35.17 2.12
2738 2789 7.584122 TGGAGTATTAGAACTAGTCATCCAC 57.416 40.000 0.00 0.00 0.00 4.02
2793 2847 9.959721 ATAGCCTTAGATACTTTTCAAGTGAAA 57.040 29.630 2.32 2.32 42.84 2.69
2931 2986 2.159338 GCATTAACCTCGAGACGGTACA 60.159 50.000 15.71 0.00 33.53 2.90
2935 2990 1.278238 GTGCATTAACCTCGAGACGG 58.722 55.000 15.71 0.00 0.00 4.79
2939 2994 0.460284 AGCGGTGCATTAACCTCGAG 60.460 55.000 5.13 5.13 38.14 4.04
2945 3001 0.168128 GTGGTCAGCGGTGCATTAAC 59.832 55.000 10.38 1.98 0.00 2.01
3002 3058 2.828877 CGTAAGGCGTTTATCCATCCA 58.171 47.619 0.00 0.00 35.54 3.41
3031 3088 7.715249 TCCTACCATTGATTAGTTAATGTCAGC 59.285 37.037 2.73 0.00 33.52 4.26
3086 3148 7.308450 AGGCATTTGACTCATAAGCTAGATA 57.692 36.000 0.00 0.00 0.00 1.98
3245 3350 1.279271 GATGGGTGCACTTACTCAGGT 59.721 52.381 17.98 0.00 33.91 4.00
3251 3356 2.949644 GGGTAATGATGGGTGCACTTAC 59.050 50.000 17.98 15.13 0.00 2.34
3275 3380 1.479730 GCGCCCAAGTAGGTACTTAGT 59.520 52.381 0.00 0.00 44.19 2.24
3278 3383 0.688487 TTGCGCCCAAGTAGGTACTT 59.312 50.000 4.18 0.00 46.76 2.24
3433 3542 4.470304 ACTCATCCCCTTAGAAGTACCAAC 59.530 45.833 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.