Multiple sequence alignment - TraesCS7D01G315900

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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 TraesCS7D01G315900 chr7D 100.000 3790 0 0 1 3790 401839741 401835952 0.000000e+00 6999
1 TraesCS7D01G315900 chr7A 97.038 1958 40 13 1842 3790 459627405 459625457 0.000000e+00 3278
2 TraesCS7D01G315900 chr7A 93.145 1313 50 25 402 1703 459628949 459627666 0.000000e+00 1890
3 TraesCS7D01G315900 chr7A 95.000 380 13 4 1 378 459629433 459629058 3.260000e-165 592
4 TraesCS7D01G315900 chr7A 95.000 140 7 0 1691 1830 459627652 459627513 1.770000e-53 220
5 TraesCS7D01G315900 chr7B 94.171 1887 66 17 1 1854 411496709 411494834 0.000000e+00 2835
6 TraesCS7D01G315900 chr7B 96.718 1158 35 2 1947 3103 411494451 411493296 0.000000e+00 1925
7 TraesCS7D01G315900 chr7B 96.641 655 16 4 3140 3790 411493296 411492644 0.000000e+00 1083
8 TraesCS7D01G315900 chr1D 80.667 150 25 4 1001 1148 140519698 140519845 3.090000e-21 113
9 TraesCS7D01G315900 chr3D 80.986 142 25 2 1027 1167 100853602 100853742 1.110000e-20 111
10 TraesCS7D01G315900 chr3B 80.986 142 25 2 1027 1167 151444567 151444707 1.110000e-20 111
11 TraesCS7D01G315900 chr3A 80.986 142 25 2 1027 1167 555042244 555042104 1.110000e-20 111
12 TraesCS7D01G315900 chr1B 80.132 151 24 5 1001 1148 198153437 198153290 1.440000e-19 108
13 TraesCS7D01G315900 chr1A 80.132 151 24 5 1001 1148 150456400 150456253 1.440000e-19 108


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 TraesCS7D01G315900 chr7D 401835952 401839741 3789 True 6999.000000 6999 100.000000 1 3790 1 chr7D.!!$R1 3789
1 TraesCS7D01G315900 chr7A 459625457 459629433 3976 True 1495.000000 3278 95.045750 1 3790 4 chr7A.!!$R1 3789
2 TraesCS7D01G315900 chr7B 411492644 411496709 4065 True 1947.666667 2835 95.843333 1 3790 3 chr7B.!!$R1 3789

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
565 680 1.068472 ACGTCTCATCTTCGCGAACTT 60.068 47.619 19.38 5.1 0.0 2.66 F
1119 1241 1.138671 GCTCTCTGTCCTCTGCGAC 59.861 63.158 0.00 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1997 2540 3.954258 AGCAGGTTTCTAAGTTTGTGCTT 59.046 39.130 0.00 0.0 36.65 3.91 R
2861 3406 3.093717 AGTACCGGAGCAAATCATACG 57.906 47.619 9.46 0.0 0.00 3.06 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
99 100 6.379703 TGTCCAACAAAAGAGATGGAAAAGAA 59.620 34.615 0.00 0.00 41.38 2.52
240 241 1.666209 GCCACCTAATGTTGCGGCAT 61.666 55.000 2.28 0.00 39.38 4.40
322 329 8.627208 TCTGATCTCTTTACAATGCTTTTTCT 57.373 30.769 0.00 0.00 0.00 2.52
323 330 9.071276 TCTGATCTCTTTACAATGCTTTTTCTT 57.929 29.630 0.00 0.00 0.00 2.52
324 331 9.688592 CTGATCTCTTTACAATGCTTTTTCTTT 57.311 29.630 0.00 0.00 0.00 2.52
325 332 9.683069 TGATCTCTTTACAATGCTTTTTCTTTC 57.317 29.630 0.00 0.00 0.00 2.62
357 364 9.838339 CTATTTCCTTAGTCCATCATACTTGTT 57.162 33.333 0.00 0.00 0.00 2.83
367 374 5.939883 TCCATCATACTTGTTCCAACAGAAG 59.060 40.000 0.00 0.00 40.50 2.85
481 596 5.336150 TGACTTCAGAAAGCTCATCCTAG 57.664 43.478 0.00 0.00 35.81 3.02
501 616 1.814394 GCTGGCAGTCATGTCAATTGA 59.186 47.619 17.16 3.38 41.43 2.57
509 624 4.154737 CAGTCATGTCAATTGAACGGTCAT 59.845 41.667 10.35 6.20 32.48 3.06
513 628 4.944962 TGTCAATTGAACGGTCATGATC 57.055 40.909 10.35 0.00 32.48 2.92
514 629 3.370672 TGTCAATTGAACGGTCATGATCG 59.629 43.478 26.29 26.29 41.46 3.69
515 630 3.616821 GTCAATTGAACGGTCATGATCGA 59.383 43.478 33.74 12.71 38.51 3.59
516 631 4.271049 GTCAATTGAACGGTCATGATCGAT 59.729 41.667 33.74 23.35 38.51 3.59
517 632 4.270808 TCAATTGAACGGTCATGATCGATG 59.729 41.667 33.74 19.70 38.51 3.84
518 633 2.959507 TGAACGGTCATGATCGATGT 57.040 45.000 33.74 18.11 38.51 3.06
519 634 2.809446 TGAACGGTCATGATCGATGTC 58.191 47.619 33.74 24.55 38.51 3.06
546 661 1.579429 GTTCCATGAACCGCCACAC 59.421 57.895 0.00 0.00 36.65 3.82
565 680 1.068472 ACGTCTCATCTTCGCGAACTT 60.068 47.619 19.38 5.10 0.00 2.66
617 738 4.819630 AGTGTAAAGGGTGTACAACATGTG 59.180 41.667 14.02 0.00 33.40 3.21
755 876 9.429359 CTAGAGAGGCAAGTATTATTATTGTGG 57.571 37.037 0.00 0.00 0.00 4.17
955 1076 4.200874 TCTTCTTCGTCTCTCCATCTACC 58.799 47.826 0.00 0.00 0.00 3.18
985 1107 1.706866 TCATCCACCCATCCATCCATC 59.293 52.381 0.00 0.00 0.00 3.51
1107 1229 1.688884 GAAGGCCAGGGAGCTCTCT 60.689 63.158 11.38 11.38 0.00 3.10
1119 1241 1.138671 GCTCTCTGTCCTCTGCGAC 59.861 63.158 0.00 0.00 0.00 5.19
1149 1271 1.541889 GGCATCATCATCTTCTCCGCA 60.542 52.381 0.00 0.00 0.00 5.69
1267 1398 6.713903 AGCTCATTCATCTCTTTTTGTCTTGA 59.286 34.615 0.00 0.00 0.00 3.02
1269 1400 8.671921 GCTCATTCATCTCTTTTTGTCTTGATA 58.328 33.333 0.00 0.00 0.00 2.15
1334 1465 1.450312 GTGGAGAAGGCATGACCGG 60.450 63.158 0.00 0.00 46.52 5.28
1585 1716 4.613622 GCTTACTCATTTCGCTTTGCTTCA 60.614 41.667 0.00 0.00 0.00 3.02
1746 1903 2.673368 GACCTTCAACGCGATTTGAGAT 59.327 45.455 15.93 2.53 36.84 2.75
1799 1956 4.962155 AGGGCTAATCTAGTGTGTTATGC 58.038 43.478 0.00 0.00 0.00 3.14
1877 2130 2.287251 TTTTTGGGGTGGGGTGGG 59.713 61.111 0.00 0.00 0.00 4.61
1878 2131 3.412350 TTTTTGGGGTGGGGTGGGG 62.412 63.158 0.00 0.00 0.00 4.96
1971 2514 7.977789 TTGTTTACTTGCACAGAATCATCTA 57.022 32.000 0.00 0.00 33.50 1.98
1997 2540 4.941263 AGCAACACAAACTTGTCTGTAAGA 59.059 37.500 0.00 0.00 43.69 2.10
2134 2677 8.634444 TCTTCTAGCTATACTTTGATGAACTCC 58.366 37.037 0.00 0.00 0.00 3.85
2403 2946 4.456911 TGAAGAGCAAGGCAAGTCAATTAG 59.543 41.667 0.00 0.00 0.00 1.73
2867 3412 5.682943 AACAAAGCTTGCTTTACGTATGA 57.317 34.783 18.52 0.00 0.00 2.15
2875 3420 4.875544 TGCTTTACGTATGATTTGCTCC 57.124 40.909 0.00 0.00 0.00 4.70
2997 3544 2.235650 TCTTGAGGAGCTCTGATGTTGG 59.764 50.000 14.64 0.00 0.00 3.77
3137 3684 4.277423 TGCATGATATCAGCTTGGTTCATG 59.723 41.667 20.51 16.57 41.97 3.07
3149 3696 3.663995 TGGTTCATGAAGCAAATGTGG 57.336 42.857 32.21 0.00 44.63 4.17
3185 3732 6.867662 AACTGTTAGCATTATAGGCATGAC 57.132 37.500 0.00 0.00 0.00 3.06
3460 4009 2.439507 TCAAGTCAGGAAAGCTGGTTCT 59.560 45.455 0.00 0.00 0.00 3.01
3513 4063 2.225142 ACTTGCAGTAGGAGAGACCAGA 60.225 50.000 0.00 0.00 42.04 3.86
3713 4265 4.158209 CCATAGGTGCAAACATGAACATCA 59.842 41.667 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 4.380843 TTGGTGTCATGTCAATAACCCT 57.619 40.909 0.00 0.00 0.00 4.34
240 241 8.458573 TTTTAGAACAATTTGCTGACCTTCTA 57.541 30.769 0.00 0.00 0.00 2.10
278 281 8.034215 AGATCAGATAAGTGCTAGATGTAATGC 58.966 37.037 0.00 0.00 0.00 3.56
281 284 8.932434 AGAGATCAGATAAGTGCTAGATGTAA 57.068 34.615 0.00 0.00 0.00 2.41
322 329 7.808279 TGGACTAAGGAAATAGAGGAAGAAA 57.192 36.000 0.00 0.00 0.00 2.52
323 330 7.623677 TGATGGACTAAGGAAATAGAGGAAGAA 59.376 37.037 0.00 0.00 0.00 2.52
324 331 7.132805 TGATGGACTAAGGAAATAGAGGAAGA 58.867 38.462 0.00 0.00 0.00 2.87
325 332 7.366847 TGATGGACTAAGGAAATAGAGGAAG 57.633 40.000 0.00 0.00 0.00 3.46
451 544 2.287849 GCTTTCTGAAGTCAACCTTGGC 60.288 50.000 0.00 0.00 35.25 4.52
452 545 3.217626 AGCTTTCTGAAGTCAACCTTGG 58.782 45.455 0.00 0.00 35.25 3.61
453 546 3.879295 TGAGCTTTCTGAAGTCAACCTTG 59.121 43.478 0.00 0.00 35.25 3.61
481 596 1.814394 TCAATTGACATGACTGCCAGC 59.186 47.619 3.38 0.00 0.00 4.85
483 598 2.226200 CGTTCAATTGACATGACTGCCA 59.774 45.455 7.89 0.00 0.00 4.92
501 616 2.225068 GGACATCGATCATGACCGTT 57.775 50.000 9.81 0.00 37.54 4.44
513 628 0.870307 GGAACGGACATCGGACATCG 60.870 60.000 0.00 0.00 44.45 3.84
514 629 0.174845 TGGAACGGACATCGGACATC 59.825 55.000 0.00 0.00 44.45 3.06
515 630 0.830648 ATGGAACGGACATCGGACAT 59.169 50.000 0.00 0.00 44.45 3.06
516 631 0.108377 CATGGAACGGACATCGGACA 60.108 55.000 0.00 0.00 44.45 4.02
517 632 0.174845 TCATGGAACGGACATCGGAC 59.825 55.000 0.00 0.00 44.45 4.79
518 633 0.899019 TTCATGGAACGGACATCGGA 59.101 50.000 0.00 0.00 44.45 4.55
519 634 1.006832 GTTCATGGAACGGACATCGG 58.993 55.000 0.00 0.00 44.45 4.18
546 661 1.618861 AAGTTCGCGAAGATGAGACG 58.381 50.000 24.13 0.00 0.00 4.18
565 680 7.275183 CCTCATGACTGTGTTCCATTCTATTA 58.725 38.462 0.00 0.00 0.00 0.98
617 738 2.486504 CATGTGTGGCGATGCACC 59.513 61.111 0.00 0.00 34.94 5.01
955 1076 3.882102 TGGGTGGATGATTGATAAGGG 57.118 47.619 0.00 0.00 0.00 3.95
985 1107 1.743394 CGCCATGGATGATGATGATGG 59.257 52.381 18.40 0.00 37.27 3.51
1149 1271 1.080705 GTCGTAGAGCTTGCCGTGT 60.081 57.895 0.00 0.00 36.95 4.49
1267 1398 4.404640 CCATCCATGGTTCTGCTCAATAT 58.595 43.478 12.58 0.00 43.05 1.28
1269 1400 2.662866 CCATCCATGGTTCTGCTCAAT 58.337 47.619 12.58 0.00 43.05 2.57
1585 1716 6.849085 TGGGCATAAATAATGTGACTTGTT 57.151 33.333 0.00 0.00 37.93 2.83
1746 1903 5.962031 TCTACTTAAGACTCATTTAGCCCCA 59.038 40.000 10.09 0.00 0.00 4.96
1971 2514 4.881920 ACAGACAAGTTTGTGTTGCTTTT 58.118 34.783 1.62 0.00 42.43 2.27
1997 2540 3.954258 AGCAGGTTTCTAAGTTTGTGCTT 59.046 39.130 0.00 0.00 36.65 3.91
2124 2667 6.333416 CAAGATTAAGTCTCGGAGTTCATCA 58.667 40.000 4.69 0.00 35.67 3.07
2134 2677 6.182039 TCATTTTGCCAAGATTAAGTCTCG 57.818 37.500 0.00 0.00 35.67 4.04
2315 2858 4.099419 AGAAAGTTTTAGTGGTGCCCAAAG 59.901 41.667 0.00 0.00 34.18 2.77
2842 3387 7.640852 TCATACGTAAAGCAAGCTTTGTTAAA 58.359 30.769 25.64 6.58 44.84 1.52
2861 3406 3.093717 AGTACCGGAGCAAATCATACG 57.906 47.619 9.46 0.00 0.00 3.06
2867 3412 3.097614 ACAGAGTAGTACCGGAGCAAAT 58.902 45.455 9.46 0.00 0.00 2.32
3124 3671 3.374220 TTTGCTTCATGAACCAAGCTG 57.626 42.857 16.07 2.11 44.59 4.24
3137 3684 1.798283 TTGCATGCCACATTTGCTTC 58.202 45.000 16.68 0.00 37.28 3.86
3277 3824 6.270231 ACCCTGAGTTTAATTAGACTGTGTCT 59.730 38.462 13.04 5.53 45.54 3.41
3278 3825 6.465084 ACCCTGAGTTTAATTAGACTGTGTC 58.535 40.000 13.04 0.63 0.00 3.67
3460 4009 8.219868 TGATTCCAATTGCATAGGAGAATTCTA 58.780 33.333 8.25 0.00 32.11 2.10
3713 4265 3.840666 TGGGTTGCTCTCAGTTTCTCTAT 59.159 43.478 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.