Multiple sequence alignment - TraesCS5B01G269800

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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 TraesCS5B01G269800 chr5B 100.000 3215 0 0 1 3215 455628868 455632082 0 5938
1 TraesCS5B01G269800 chr4D 97.138 3215 90 1 1 3213 123299970 123303184 0 5426
2 TraesCS5B01G269800 chr7B 97.046 3216 90 5 1 3213 644467524 644470737 0 5408
3 TraesCS5B01G269800 chr7D 96.829 3217 98 3 1 3213 203515556 203518772 0 5373
4 TraesCS5B01G269800 chr3A 96.608 3213 107 2 1 3213 633111334 633114544 0 5328
5 TraesCS5B01G269800 chr6B 96.301 3217 115 2 1 3213 306995910 306992694 0 5278
6 TraesCS5B01G269800 chr1B 96.241 3219 113 5 1 3213 638700586 638697370 0 5267
7 TraesCS5B01G269800 chr1B 96.049 3214 125 2 1 3213 672479241 672482453 0 5230
8 TraesCS5B01G269800 chr4B 96.081 3215 123 2 1 3213 209077438 209074225 0 5236
9 TraesCS5B01G269800 chr2A 96.049 3214 124 2 1 3213 332944217 332941006 0 5228


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 TraesCS5B01G269800 chr5B 455628868 455632082 3214 False 5938 5938 100.000 1 3215 1 chr5B.!!$F1 3214
1 TraesCS5B01G269800 chr4D 123299970 123303184 3214 False 5426 5426 97.138 1 3213 1 chr4D.!!$F1 3212
2 TraesCS5B01G269800 chr7B 644467524 644470737 3213 False 5408 5408 97.046 1 3213 1 chr7B.!!$F1 3212
3 TraesCS5B01G269800 chr7D 203515556 203518772 3216 False 5373 5373 96.829 1 3213 1 chr7D.!!$F1 3212
4 TraesCS5B01G269800 chr3A 633111334 633114544 3210 False 5328 5328 96.608 1 3213 1 chr3A.!!$F1 3212
5 TraesCS5B01G269800 chr6B 306992694 306995910 3216 True 5278 5278 96.301 1 3213 1 chr6B.!!$R1 3212
6 TraesCS5B01G269800 chr1B 638697370 638700586 3216 True 5267 5267 96.241 1 3213 1 chr1B.!!$R1 3212
7 TraesCS5B01G269800 chr1B 672479241 672482453 3212 False 5230 5230 96.049 1 3213 1 chr1B.!!$F1 3212
8 TraesCS5B01G269800 chr4B 209074225 209077438 3213 True 5236 5236 96.081 1 3213 1 chr4B.!!$R1 3212
9 TraesCS5B01G269800 chr2A 332941006 332944217 3211 True 5228 5228 96.049 1 3213 1 chr2A.!!$R1 3212

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
621 624 0.179051 GGAGGATCTGGCAGAAGCAG 60.179 60.000 22.84 0.0 37.72 4.24 F
1417 1433 1.202639 TCCATATAACTGCCTGCCACG 60.203 52.381 0.00 0.0 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1847 1864 0.036875 CCTGGGTCTTCTTCGGCTTT 59.963 55.0 0.0 0.0 0.0 3.51 R
2366 2385 1.255667 GGAGGGCCGACTACAAGACA 61.256 60.0 0.0 0.0 0.0 3.41 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
53 54 2.598787 CCCCGCCTCCACTTGGTTA 61.599 63.158 0.00 0.00 36.34 2.85
99 101 6.239396 GGACTACTTCCTTAAAGAGCCTTTT 58.761 40.000 5.65 0.00 41.95 2.27
280 283 4.141665 TGGTACCCGAATCCATTTACGATT 60.142 41.667 10.07 0.00 32.62 3.34
462 465 3.117046 GGAAGAGATCGACGATTCCAAC 58.883 50.000 18.63 4.59 37.67 3.77
482 485 4.353383 ACTTCTTTTACCCCACTCAGAC 57.647 45.455 0.00 0.00 0.00 3.51
531 534 1.984570 TGAGAAGGGCCCTGACTCG 60.985 63.158 34.30 0.00 35.03 4.18
589 592 5.453339 GGCAATATCTACCTACACAAGCTCA 60.453 44.000 0.00 0.00 0.00 4.26
621 624 0.179051 GGAGGATCTGGCAGAAGCAG 60.179 60.000 22.84 0.00 37.72 4.24
642 645 5.106515 GCAGGAAATTCCTCTTGTAGTGAAC 60.107 44.000 12.35 0.00 45.66 3.18
643 646 5.120830 CAGGAAATTCCTCTTGTAGTGAACG 59.879 44.000 12.35 0.00 45.66 3.95
706 709 8.299990 TGACCAAGAAAAGTATGGAAAAGAAA 57.700 30.769 0.00 0.00 37.66 2.52
906 922 1.271926 GCCTTCCTTAACAAGCCCTCA 60.272 52.381 0.00 0.00 0.00 3.86
948 964 1.412710 CTCATAGAAGCCGCTGGGTTA 59.587 52.381 11.12 0.00 43.92 2.85
1074 1090 3.190953 GCGAGGAGGCGATACTAGTTATT 59.809 47.826 0.00 0.00 0.00 1.40
1238 1254 5.452255 ACGTATCTCCCACTTCCTACAATA 58.548 41.667 0.00 0.00 0.00 1.90
1417 1433 1.202639 TCCATATAACTGCCTGCCACG 60.203 52.381 0.00 0.00 0.00 4.94
1427 1443 4.111016 CTGCCACGTACGCTCCGA 62.111 66.667 16.72 0.00 0.00 4.55
1482 1498 5.211973 AGTATCCCTATCAAAGAGCTGACA 58.788 41.667 0.00 0.00 0.00 3.58
1510 1526 1.310904 GAGCGGAAGAGGTCGTCTAT 58.689 55.000 0.00 0.00 32.65 1.98
1635 1651 2.158957 GGGGATCTCGTTGTTGCATAGA 60.159 50.000 0.00 0.00 0.00 1.98
1643 1659 2.282555 CGTTGTTGCATAGATCAGGTCG 59.717 50.000 0.00 0.00 0.00 4.79
1681 1697 1.581934 CGTTCAACAGGCAGTCTCAA 58.418 50.000 0.00 0.00 0.00 3.02
1682 1698 1.939934 CGTTCAACAGGCAGTCTCAAA 59.060 47.619 0.00 0.00 0.00 2.69
1688 1704 1.347707 ACAGGCAGTCTCAAAATCGGA 59.652 47.619 0.00 0.00 0.00 4.55
1737 1753 2.124507 CTCCCTTTGGTCGGAAGGCA 62.125 60.000 0.00 0.00 41.88 4.75
1823 1840 4.127171 GCGCCTATCAAAAAGATACTCCA 58.873 43.478 0.00 0.00 38.19 3.86
1847 1864 1.103803 CTTCGGGATCGAGGTCTCAA 58.896 55.000 0.00 0.00 46.75 3.02
1848 1865 1.476891 CTTCGGGATCGAGGTCTCAAA 59.523 52.381 0.00 0.00 46.75 2.69
1878 1895 1.906105 GACCCAGGCCAATCCACGTA 61.906 60.000 5.01 0.00 37.29 3.57
1889 1906 3.535561 CAATCCACGTAGCCTCTTTGAT 58.464 45.455 0.00 0.00 0.00 2.57
1920 1937 5.807520 CAGCGACAGAGACATAGTAAATTGT 59.192 40.000 0.00 0.00 0.00 2.71
1923 1940 6.531948 GCGACAGAGACATAGTAAATTGTTCT 59.468 38.462 0.00 0.00 0.00 3.01
2008 2025 5.407407 AACGATTGTCAACTACCAGATCT 57.593 39.130 0.00 0.00 0.00 2.75
2052 2069 1.340889 GCCCACAAGCACAAATCTTCA 59.659 47.619 0.00 0.00 0.00 3.02
2072 2089 5.339008 TCAGCGCGGAATATAATCCTAAT 57.661 39.130 8.08 0.00 37.34 1.73
2110 2127 9.606631 ACTCAAATATAGTCAATCAAGAAGGTC 57.393 33.333 0.00 0.00 0.00 3.85
2247 2264 7.915293 TTCTATTTGGATTTTAGCGAACAGA 57.085 32.000 0.00 0.00 0.00 3.41
2260 2277 3.935203 AGCGAACAGACATTTACATGAGG 59.065 43.478 0.00 0.00 34.11 3.86
2366 2385 4.827692 TCATGGCTTGTATTGTAGTCGTT 58.172 39.130 0.00 0.00 0.00 3.85
2448 2467 4.697828 TCATTCATTTTGCGGTAGCTTACA 59.302 37.500 0.00 0.00 45.42 2.41
2450 2469 3.403968 TCATTTTGCGGTAGCTTACACA 58.596 40.909 0.00 0.00 45.42 3.72
2468 2487 8.178313 GCTTACACATCAGAAAAATAGAACCTC 58.822 37.037 0.00 0.00 0.00 3.85
2554 2573 6.921857 GCTACCTTGAATCAATCAATGAATGG 59.078 38.462 0.00 0.00 46.62 3.16
2571 2590 0.466543 TGGATGATTCGTAACCCCCG 59.533 55.000 0.00 0.00 0.00 5.73
2623 2643 0.699231 GGGGGTCCAGATTCCAGGAT 60.699 60.000 0.00 0.00 36.11 3.24
2699 2719 2.063979 CCACCTATCAGGCCCGACA 61.064 63.158 0.00 0.00 39.63 4.35
2837 2857 8.095169 TCTGGTTTAGTATCAAGGTTCTTCTTC 58.905 37.037 0.00 0.00 0.00 2.87
2878 2898 2.176546 CGTGCAGCATTTCCACGG 59.823 61.111 0.00 0.00 46.03 4.94
2909 2929 4.870636 TGATCAATTAATGGGACTTGGCT 58.129 39.130 0.00 0.00 0.00 4.75
2980 3000 2.548057 TGTTTCAGTCACCTTTCGATGC 59.452 45.455 0.00 0.00 0.00 3.91
2998 3018 4.503123 CGATGCCTCCCTTAATGTATGTGA 60.503 45.833 0.00 0.00 0.00 3.58
3197 3217 2.434185 GTGAACCTGCGATCGCCA 60.434 61.111 35.12 22.87 41.09 5.69
3207 3227 0.666913 GCGATCGCCACCTCTAACTA 59.333 55.000 29.48 0.00 34.56 2.24
3213 3233 1.940613 CGCCACCTCTAACTAAATGCC 59.059 52.381 0.00 0.00 0.00 4.40
3214 3234 2.298610 GCCACCTCTAACTAAATGCCC 58.701 52.381 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 1.373812 GGCCCGACACTAACCAAGT 59.626 57.895 0.00 0.00 39.81 3.16
53 54 4.680537 ACTCTCGGGCCCGACACT 62.681 66.667 42.66 23.65 44.01 3.55
280 283 1.067846 CGATGTGTCTGGAAACTCGGA 60.068 52.381 5.49 0.00 0.00 4.55
338 341 2.290323 CCCCACTCTTCTTTGATCCGTT 60.290 50.000 0.00 0.00 0.00 4.44
368 371 4.582656 TGATGTCGAATTCCAAAAACCAGT 59.417 37.500 0.00 0.00 0.00 4.00
462 465 4.351874 TGTCTGAGTGGGGTAAAAGAAG 57.648 45.455 0.00 0.00 0.00 2.85
482 485 1.082366 CGTCCGGCGGAAAACTTTG 60.082 57.895 32.91 10.55 36.85 2.77
505 508 1.386057 GGCCCTTCTCACCCCCTAT 60.386 63.158 0.00 0.00 0.00 2.57
589 592 4.512574 CCAGATCCTCCCTATCTCCTGATT 60.513 50.000 0.00 0.00 31.22 2.57
621 624 4.995487 ACGTTCACTACAAGAGGAATTTCC 59.005 41.667 7.39 7.39 36.58 3.13
642 645 9.557338 CCTATTCTTAATAGAACCGATCTTACG 57.443 37.037 8.00 0.00 42.91 3.18
670 673 5.995282 ACTTTTCTTGGTCATCAATACGACA 59.005 36.000 0.00 0.00 34.45 4.35
832 847 2.846193 CGTTTTCTGGTCTTCCCTTCA 58.154 47.619 0.00 0.00 0.00 3.02
839 854 1.602377 CGAAAGGCGTTTTCTGGTCTT 59.398 47.619 5.76 0.00 42.47 3.01
876 892 2.891307 TAAGGAAGGCGGCTAGGGCT 62.891 60.000 13.71 0.00 45.86 5.19
948 964 3.449746 TTGAATTCATCCTTCGGGGTT 57.550 42.857 9.40 0.00 36.25 4.11
959 975 6.011122 AGCCTTCTCTACCATTGAATTCAT 57.989 37.500 9.40 0.00 0.00 2.57
960 976 5.441718 AGCCTTCTCTACCATTGAATTCA 57.558 39.130 3.38 3.38 0.00 2.57
1074 1090 0.260230 CCAGGCCTCTCTCTGACCTA 59.740 60.000 0.00 0.00 33.11 3.08
1222 1238 4.466370 CAGACTGTATTGTAGGAAGTGGGA 59.534 45.833 0.00 0.00 0.00 4.37
1417 1433 1.488527 GAATGGATGTCGGAGCGTAC 58.511 55.000 0.00 0.00 0.00 3.67
1427 1443 4.569865 GGTCCCTAAACTTGGAATGGATGT 60.570 45.833 0.00 0.00 31.03 3.06
1482 1498 0.543749 CTCTTCCGCTCATCCCCTTT 59.456 55.000 0.00 0.00 0.00 3.11
1510 1526 0.947180 GCTAGTTGAACCGCGTCCAA 60.947 55.000 4.92 2.97 0.00 3.53
1635 1651 1.599047 CACCTTGCTCCGACCTGAT 59.401 57.895 0.00 0.00 0.00 2.90
1643 1659 1.751927 CCTGATGGCACCTTGCTCC 60.752 63.158 0.00 0.00 44.28 4.70
1688 1704 4.963318 TTCTTCTTCAGGACACTCATGT 57.037 40.909 0.00 0.00 43.71 3.21
1737 1753 2.615288 CCCCTTCCTTCCCCTGCT 60.615 66.667 0.00 0.00 0.00 4.24
1823 1840 1.265454 ACCTCGATCCCGAAGCCTTT 61.265 55.000 0.00 0.00 45.04 3.11
1847 1864 0.036875 CCTGGGTCTTCTTCGGCTTT 59.963 55.000 0.00 0.00 0.00 3.51
1848 1865 1.679898 CCTGGGTCTTCTTCGGCTT 59.320 57.895 0.00 0.00 0.00 4.35
1878 1895 2.693069 CTGACGTTGATCAAAGAGGCT 58.307 47.619 25.27 5.25 0.00 4.58
1889 1906 0.040336 GTCTCTGTCGCTGACGTTGA 60.040 55.000 0.00 2.96 41.18 3.18
2008 2025 2.158871 GGGTGAATATAGCGGACCAACA 60.159 50.000 0.00 0.00 0.00 3.33
2052 2069 5.086104 ACATTAGGATTATATTCCGCGCT 57.914 39.130 5.56 0.00 40.94 5.92
2072 2089 7.181305 TGACTATATTTGAGTCTTTGGGGTACA 59.819 37.037 5.86 0.00 43.19 2.90
2110 2127 2.338500 GAACTCAGCAAGGGTCTTACG 58.662 52.381 0.00 0.00 0.00 3.18
2215 2232 9.065871 CGCTAAAATCCAAATAGAAAAAGACAG 57.934 33.333 0.00 0.00 0.00 3.51
2247 2264 8.041323 CCTACTCAACTAACCTCATGTAAATGT 58.959 37.037 0.00 0.00 0.00 2.71
2260 2277 3.336138 AGGCAAGCCTACTCAACTAAC 57.664 47.619 12.82 0.00 46.14 2.34
2366 2385 1.255667 GGAGGGCCGACTACAAGACA 61.256 60.000 0.00 0.00 0.00 3.41
2448 2467 6.109359 CGGAGAGGTTCTATTTTTCTGATGT 58.891 40.000 0.00 0.00 0.00 3.06
2450 2469 5.675538 CCGGAGAGGTTCTATTTTTCTGAT 58.324 41.667 0.00 0.00 34.51 2.90
2506 2525 3.264574 GCCATTGTGGGTAGAAGCA 57.735 52.632 0.00 0.00 38.19 3.91
2554 2573 1.578583 CACGGGGGTTACGAATCATC 58.421 55.000 0.00 0.00 34.93 2.92
2699 2719 4.379243 CAGCTCCGTGGACCGCTT 62.379 66.667 3.03 0.00 34.38 4.68
2837 2857 9.720769 ACGGACCCATATATATAGAAACAAAAG 57.279 33.333 0.00 0.00 0.00 2.27
2878 2898 9.436957 AGTCCCATTAATTGATCATAACGATAC 57.563 33.333 0.00 0.00 33.17 2.24
2909 2929 4.041567 TGATAGAGGCAAGAACACTTTCCA 59.958 41.667 0.00 0.00 31.24 3.53
2980 3000 4.408921 TCCTGTCACATACATTAAGGGAGG 59.591 45.833 0.00 0.00 37.50 4.30
2998 3018 3.181439 CCCCTTCAGAAGAAACTTCCTGT 60.181 47.826 12.14 0.00 32.35 4.00


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

AutoCloner maintained by Alex Coulton.