Multiple sequence alignment - TraesCS5B01G449900

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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 TraesCS5B01G449900 chr5B 100.000 3467 0 0 1 3467 622068028 622071494 0.000000e+00 6403
1 TraesCS5B01G449900 chr5D 97.177 3471 64 10 1 3467 500675660 500679100 0.000000e+00 5836
2 TraesCS5B01G449900 chr5D 79.343 213 42 2 2359 2570 555192293 555192504 7.750000e-32 148
3 TraesCS5B01G449900 chr2D 75.110 683 153 13 1962 2636 32365093 32365766 1.560000e-78 303


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 TraesCS5B01G449900 chr5B 622068028 622071494 3466 False 6403 6403 100.000 1 3467 1 chr5B.!!$F1 3466
1 TraesCS5B01G449900 chr5D 500675660 500679100 3440 False 5836 5836 97.177 1 3467 1 chr5D.!!$F1 3466
2 TraesCS5B01G449900 chr2D 32365093 32365766 673 False 303 303 75.110 1962 2636 1 chr2D.!!$F1 674

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
478 479 0.804364 GCATGAGTGCCATTCAACGA 59.196 50.0 0.0 0.0 45.76 3.85 F
1251 1252 0.172578 CGTCCAATGGTAGAGTGCGA 59.827 55.0 0.0 0.0 0.00 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1302 1303 0.110486 AGGCCATTCCGTCAACACTT 59.89 50.0 5.01 0.0 40.77 3.16 R
2579 2584 0.040058 TAAGAGGGGACGCTGTACCA 59.96 55.0 11.32 0.0 40.78 3.25 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
78 79 1.950828 CAGAGTGCTGCTATTGGAGG 58.049 55.000 0.00 0.00 34.95 4.30
79 80 1.483827 CAGAGTGCTGCTATTGGAGGA 59.516 52.381 0.00 0.00 34.95 3.71
80 81 1.761784 AGAGTGCTGCTATTGGAGGAG 59.238 52.381 0.00 0.00 46.16 3.69
250 251 3.181463 TGGTCACCAGTACCAGTAACAAC 60.181 47.826 0.00 0.00 42.10 3.32
283 284 1.077858 GGCCAAGGAAGAGGAGCAG 60.078 63.158 0.00 0.00 0.00 4.24
288 289 1.819288 CAAGGAAGAGGAGCAGTACGA 59.181 52.381 0.00 0.00 0.00 3.43
433 434 4.125703 CAAGTCATGCCAGTCCTATCTTC 58.874 47.826 0.00 0.00 0.00 2.87
442 443 2.237143 CAGTCCTATCTTCCCACAAGCA 59.763 50.000 0.00 0.00 0.00 3.91
443 444 3.118112 CAGTCCTATCTTCCCACAAGCAT 60.118 47.826 0.00 0.00 0.00 3.79
444 445 3.118112 AGTCCTATCTTCCCACAAGCATG 60.118 47.826 0.00 0.00 0.00 4.06
445 446 2.846206 TCCTATCTTCCCACAAGCATGT 59.154 45.455 0.00 0.00 41.61 3.21
446 447 3.266772 TCCTATCTTCCCACAAGCATGTT 59.733 43.478 0.00 0.00 37.82 2.71
461 462 6.127054 ACAAGCATGTTATCTTAGTCTAGGCA 60.127 38.462 0.00 0.00 35.91 4.75
478 479 0.804364 GCATGAGTGCCATTCAACGA 59.196 50.000 0.00 0.00 45.76 3.85
502 503 4.908736 AGTGACAACAGAAACGACATTTG 58.091 39.130 0.00 0.00 0.00 2.32
627 628 3.350377 CAACAATGCCCGGACGTT 58.650 55.556 0.73 0.00 0.00 3.99
825 826 3.667497 TGTGACCTGCTACTTCAGAAG 57.333 47.619 8.77 8.77 36.19 2.85
839 840 5.321983 CTTCAGAAGAAGTCGTTGACAAG 57.678 43.478 3.82 0.00 44.97 3.16
840 841 4.386867 TCAGAAGAAGTCGTTGACAAGT 57.613 40.909 0.00 0.00 34.60 3.16
841 842 4.360563 TCAGAAGAAGTCGTTGACAAGTC 58.639 43.478 0.00 0.00 34.60 3.01
867 868 2.945440 GCAGGCATATCCACAAACCTCA 60.945 50.000 0.00 0.00 37.29 3.86
885 886 1.493446 TCACCCTAGATGGCGAGTAGA 59.507 52.381 0.00 0.00 0.00 2.59
886 887 2.108425 TCACCCTAGATGGCGAGTAGAT 59.892 50.000 0.00 0.00 0.00 1.98
934 935 2.165437 TGAAGCCAAATTTATCCACCGC 59.835 45.455 0.00 0.00 0.00 5.68
1028 1029 3.375299 GGTGTGTCATTCCTTCTACATGC 59.625 47.826 0.00 0.00 0.00 4.06
1121 1122 2.815589 GCTTCACTGGGACAAACCTCAT 60.816 50.000 0.00 0.00 38.70 2.90
1199 1200 1.483415 GGTTAACCTCTACGGCCATGA 59.517 52.381 17.83 0.00 35.61 3.07
1245 1246 1.403647 CGCAAGTCGTCCAATGGTAGA 60.404 52.381 0.00 0.00 0.00 2.59
1251 1252 0.172578 CGTCCAATGGTAGAGTGCGA 59.827 55.000 0.00 0.00 0.00 5.10
1262 1263 0.459489 AGAGTGCGATCCTTCTCTGC 59.541 55.000 7.20 0.00 36.17 4.26
1295 1296 1.339291 CGGCATCAGCTCTGTCTATCA 59.661 52.381 0.00 0.00 41.70 2.15
1302 1303 8.398200 GCATCAGCTCTGTCTATCATGAGACA 62.398 46.154 14.93 14.93 44.51 3.41
1333 1334 2.580962 GAATGGCCTTCTTCATCTCCC 58.419 52.381 3.32 0.00 0.00 4.30
1479 1480 4.384940 TGAAGGACATCAACGACAATCAA 58.615 39.130 0.00 0.00 0.00 2.57
1605 1606 2.190398 TGCAGGTATGGGTGGACTAT 57.810 50.000 0.00 0.00 0.00 2.12
1826 1827 3.578456 GGTCATTGACACCGCCAG 58.422 61.111 18.09 0.00 33.68 4.85
1863 1864 5.998363 ACCTCAACTTGTTCTGAAGAATACC 59.002 40.000 0.08 0.00 36.33 2.73
1930 1931 1.098050 GGTGCTTGCTATGGGAACTG 58.902 55.000 0.00 0.00 0.00 3.16
1936 1937 0.179048 TGCTATGGGAACTGCCATCG 60.179 55.000 5.96 1.71 38.95 3.84
1966 1967 0.322816 ACGGAGGCGACTAAGGTACA 60.323 55.000 0.00 0.00 44.43 2.90
2026 2027 6.159988 CCACATCGGTTCTCCTATAAAGATC 58.840 44.000 0.00 0.00 0.00 2.75
2262 2263 3.433615 GTCGAAGAAACCATGAACTCCTG 59.566 47.826 0.00 0.00 39.69 3.86
2287 2288 5.995446 TGGTGTATGACTACATGCCAAATA 58.005 37.500 0.00 0.00 39.93 1.40
2504 2509 5.843452 CGACTTCGGTCTCGCAAGATTATAT 60.843 44.000 0.00 0.00 42.42 0.86
2579 2584 1.959042 CACCTGAGCTGACACAAACT 58.041 50.000 0.00 0.00 0.00 2.66
2584 2589 2.802816 CTGAGCTGACACAAACTGGTAC 59.197 50.000 0.00 0.00 0.00 3.34
2663 2669 1.672898 GCAAAGGCCCATCAAGCAA 59.327 52.632 0.00 0.00 0.00 3.91
2802 2808 6.483640 AGATGAGGTCTGTCTTGTGTTAAAAC 59.516 38.462 0.00 0.00 35.31 2.43
2813 2819 7.288389 TGTCTTGTGTTAAAACTAGGTCTCCTA 59.712 37.037 7.30 0.00 34.61 2.94
2853 2859 3.063704 CAAGGCCCAGCATGCGAA 61.064 61.111 13.01 0.00 31.97 4.70
2854 2860 2.283101 AAGGCCCAGCATGCGAAA 60.283 55.556 13.01 0.00 31.97 3.46
2965 2971 0.610232 GCAGGATCCATGCCATACCC 60.610 60.000 15.82 0.00 37.73 3.69
3049 3055 4.915806 GTCAGTGTGACATATGGTCTGGTC 60.916 50.000 7.80 0.00 46.22 4.02
3050 3056 7.076054 GTCAGTGTGACATATGGTCTGGTCT 62.076 48.000 7.80 0.00 46.22 3.85
3051 3057 8.991421 GTCAGTGTGACATATGGTCTGGTCTG 62.991 50.000 7.80 6.90 46.22 3.51
3054 3060 3.185246 GACATATGGTCTGGTCTGGTG 57.815 52.381 7.80 0.00 43.46 4.17
3055 3061 2.766263 GACATATGGTCTGGTCTGGTGA 59.234 50.000 7.80 0.00 43.46 4.02
3109 3115 2.421073 TGCATGTAAACTCTGCAGATGC 59.579 45.455 23.07 23.07 40.75 3.91
3135 3141 7.848051 CACTGCTTTGTTATATGAATCTCGAAC 59.152 37.037 0.00 0.00 0.00 3.95
3138 3144 5.900339 TTGTTATATGAATCTCGAACGGC 57.100 39.130 0.00 0.00 0.00 5.68
3374 3380 4.071961 AGGGACAAGAAAAACATTTGGC 57.928 40.909 0.00 0.00 0.00 4.52
3390 3396 7.393841 ACATTTGGCAATCCCATTAAAAATG 57.606 32.000 0.00 0.00 44.89 2.32
3409 3415 1.064758 TGCAAGCATCCGACCCTTTAT 60.065 47.619 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 3.125316 CCATTACGCTTCCACAAGTTCTC 59.875 47.826 0.00 0.00 31.45 2.87
79 80 3.074412 CCATTACGCTTCCACAAGTTCT 58.926 45.455 0.00 0.00 31.45 3.01
80 81 3.071479 TCCATTACGCTTCCACAAGTTC 58.929 45.455 0.00 0.00 31.45 3.01
132 133 1.282157 GGACCTAACCAATGGCTCTGT 59.718 52.381 0.00 0.00 0.00 3.41
182 183 0.246635 CCAATCTGGTTCTCGACGGT 59.753 55.000 0.00 0.00 31.35 4.83
208 209 3.196469 CCAGTTCATCTACTCTGGCTTCA 59.804 47.826 0.00 0.00 40.43 3.02
250 251 4.770010 TCCTTGGCCTTAACCAACAAATAG 59.230 41.667 3.32 0.00 44.80 1.73
283 284 2.496817 CTCTGCCCTGGCTCGTAC 59.503 66.667 9.97 0.00 42.51 3.67
428 429 5.121380 AGATAACATGCTTGTGGGAAGAT 57.879 39.130 5.94 0.00 35.83 2.40
433 434 5.431765 AGACTAAGATAACATGCTTGTGGG 58.568 41.667 5.94 0.00 35.83 4.61
442 443 7.665690 CACTCATGCCTAGACTAAGATAACAT 58.334 38.462 0.00 0.00 0.00 2.71
443 444 6.461648 GCACTCATGCCTAGACTAAGATAACA 60.462 42.308 0.00 0.00 46.97 2.41
444 445 5.923684 GCACTCATGCCTAGACTAAGATAAC 59.076 44.000 0.00 0.00 46.97 1.89
445 446 6.090483 GCACTCATGCCTAGACTAAGATAA 57.910 41.667 0.00 0.00 46.97 1.75
446 447 5.713792 GCACTCATGCCTAGACTAAGATA 57.286 43.478 0.00 0.00 46.97 1.98
461 462 3.873361 CACTATCGTTGAATGGCACTCAT 59.127 43.478 0.00 0.00 37.79 2.90
478 479 6.260050 ACAAATGTCGTTTCTGTTGTCACTAT 59.740 34.615 0.00 0.00 0.00 2.12
502 503 0.463654 TCATGTAGGCGCCCATCAAC 60.464 55.000 26.15 14.34 0.00 3.18
532 533 3.947910 ATTGGGTGCACAATTGAAGAG 57.052 42.857 20.43 0.13 37.81 2.85
673 674 7.072562 TCATAATACCAAGGGCCACATAATTT 58.927 34.615 6.18 0.00 0.00 1.82
713 714 2.222027 GGCATAAATCTTCTGGTCCCG 58.778 52.381 0.00 0.00 0.00 5.14
825 826 2.471743 CCGAAGACTTGTCAACGACTTC 59.528 50.000 16.18 12.55 33.15 3.01
831 832 0.868406 CCTGCCGAAGACTTGTCAAC 59.132 55.000 3.49 0.00 0.00 3.18
832 833 0.884704 GCCTGCCGAAGACTTGTCAA 60.885 55.000 3.49 0.00 0.00 3.18
833 834 1.301716 GCCTGCCGAAGACTTGTCA 60.302 57.895 3.49 0.00 0.00 3.58
834 835 0.674895 ATGCCTGCCGAAGACTTGTC 60.675 55.000 0.00 0.00 0.00 3.18
835 836 0.613260 TATGCCTGCCGAAGACTTGT 59.387 50.000 0.00 0.00 0.00 3.16
836 837 1.869767 GATATGCCTGCCGAAGACTTG 59.130 52.381 0.00 0.00 0.00 3.16
837 838 1.202698 GGATATGCCTGCCGAAGACTT 60.203 52.381 0.00 0.00 0.00 3.01
838 839 0.394565 GGATATGCCTGCCGAAGACT 59.605 55.000 0.00 0.00 0.00 3.24
839 840 0.106708 TGGATATGCCTGCCGAAGAC 59.893 55.000 0.00 0.00 37.63 3.01
840 841 0.106708 GTGGATATGCCTGCCGAAGA 59.893 55.000 0.00 0.00 37.63 2.87
841 842 0.179048 TGTGGATATGCCTGCCGAAG 60.179 55.000 0.00 0.00 37.63 3.79
867 868 2.982339 ATCTACTCGCCATCTAGGGT 57.018 50.000 0.00 0.00 38.09 4.34
885 886 2.104111 TGGCTAACTGGCAGCGTATTAT 59.896 45.455 15.89 0.00 46.76 1.28
886 887 1.483004 TGGCTAACTGGCAGCGTATTA 59.517 47.619 15.89 4.77 46.76 0.98
934 935 0.173708 GTGCTCGGTAGACCTCCAAG 59.826 60.000 0.00 0.00 0.00 3.61
1028 1029 1.488393 CCAAGCTAAGGAAGAGGAGGG 59.512 57.143 0.00 0.00 0.00 4.30
1138 1139 1.664965 GTCCGTCTGCTGTGACCAC 60.665 63.158 0.00 0.00 33.70 4.16
1149 1150 0.112606 TCACCTTGAGGAGTCCGTCT 59.887 55.000 2.76 0.00 38.94 4.18
1234 1235 1.412710 GGATCGCACTCTACCATTGGA 59.587 52.381 10.37 0.00 0.00 3.53
1245 1246 1.140589 CGCAGAGAAGGATCGCACT 59.859 57.895 0.00 0.00 0.00 4.40
1251 1252 1.546476 ACGAAAGACGCAGAGAAGGAT 59.454 47.619 0.00 0.00 46.94 3.24
1295 1296 3.469008 TTCCGTCAACACTTGTCTCAT 57.531 42.857 0.00 0.00 0.00 2.90
1302 1303 0.110486 AGGCCATTCCGTCAACACTT 59.890 50.000 5.01 0.00 40.77 3.16
1333 1334 2.489938 TTGGAGAAATGGTTCCTCGG 57.510 50.000 0.00 0.00 33.92 4.63
1605 1606 1.133181 TCTGTGTGGCCCCTTCATCA 61.133 55.000 0.00 0.00 0.00 3.07
1671 1672 2.351276 GTGGCCGAGACCAATGGT 59.649 61.111 3.74 3.74 42.70 3.55
1826 1827 3.084786 AGTTGAGGTAGCTTTGGCAATC 58.915 45.455 0.00 0.00 41.70 2.67
1863 1864 3.428725 CGATCTTCAAGACTCTGGACTGG 60.429 52.174 0.00 0.00 0.00 4.00
1930 1931 2.061773 CCGTATGATCAGAACGATGGC 58.938 52.381 26.37 0.00 38.89 4.40
1936 1937 1.337071 TCGCCTCCGTATGATCAGAAC 59.663 52.381 0.09 1.05 35.54 3.01
2016 2017 7.615582 TGTTGCAAGGAACAGATCTTTATAG 57.384 36.000 0.00 0.00 32.05 1.31
2181 2182 1.465689 CGGCCAATGCTTACAACTTCG 60.466 52.381 2.24 0.00 37.74 3.79
2262 2263 3.605634 TGGCATGTAGTCATACACCAAC 58.394 45.455 0.00 0.00 44.51 3.77
2504 2509 2.918345 CGGGTTCGTACCGTGGTCA 61.918 63.158 5.03 0.00 46.04 4.02
2579 2584 0.040058 TAAGAGGGGACGCTGTACCA 59.960 55.000 11.32 0.00 40.78 3.25
2584 2589 2.579878 TCTGTAAGAGGGGACGCTG 58.420 57.895 0.00 0.00 40.78 5.18
2802 2808 3.306641 GGATGCAAGCATAGGAGACCTAG 60.307 52.174 7.64 0.00 39.70 3.02
2813 2819 1.481871 CAGGGAAAGGATGCAAGCAT 58.518 50.000 7.35 7.35 39.69 3.79
2854 2860 1.958288 ATCAAGGTACTGGAGCACCT 58.042 50.000 0.71 0.00 44.46 4.00
3045 3051 2.024176 ATACACCAGTCACCAGACCA 57.976 50.000 0.00 0.00 46.15 4.02
3049 3055 3.541996 TGCATATACACCAGTCACCAG 57.458 47.619 0.00 0.00 0.00 4.00
3050 3056 3.990959 TTGCATATACACCAGTCACCA 57.009 42.857 0.00 0.00 0.00 4.17
3051 3057 4.450976 TCATTGCATATACACCAGTCACC 58.549 43.478 0.00 0.00 0.00 4.02
3052 3058 5.504665 GCTTCATTGCATATACACCAGTCAC 60.505 44.000 0.00 0.00 0.00 3.67
3053 3059 4.576053 GCTTCATTGCATATACACCAGTCA 59.424 41.667 0.00 0.00 0.00 3.41
3054 3060 4.818546 AGCTTCATTGCATATACACCAGTC 59.181 41.667 0.00 0.00 34.99 3.51
3055 3061 4.785301 AGCTTCATTGCATATACACCAGT 58.215 39.130 0.00 0.00 34.99 4.00
3109 3115 7.468922 TCGAGATTCATATAACAAAGCAGTG 57.531 36.000 0.00 0.00 0.00 3.66
3118 3124 3.364023 CCGCCGTTCGAGATTCATATAAC 59.636 47.826 0.00 0.00 41.67 1.89
3135 3141 3.181505 TGTTTCATATAACAAAGCCGCCG 60.182 43.478 0.00 0.00 35.22 6.46
3138 3144 5.299279 AGGGATGTTTCATATAACAAAGCCG 59.701 40.000 0.00 0.00 41.02 5.52
3348 3354 7.670364 CCAAATGTTTTTCTTGTCCCTTAGAT 58.330 34.615 0.00 0.00 0.00 1.98
3352 3358 4.080638 TGCCAAATGTTTTTCTTGTCCCTT 60.081 37.500 0.00 0.00 0.00 3.95
3374 3380 6.238538 GGATGCTTGCATTTTTAATGGGATTG 60.239 38.462 9.59 0.00 0.00 2.67
3390 3396 1.680338 ATAAAGGGTCGGATGCTTGC 58.320 50.000 0.00 0.00 0.00 4.01
3409 3415 6.378710 TGTGGTTTCACGATGTTATGAAAA 57.621 33.333 1.23 0.00 44.24 2.29


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

AutoCloner maintained by Alex Coulton.