Multiple sequence alignment - TraesCS7B01G119800

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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 TraesCS7B01G119800 chr7B 100.000 4028 0 0 1 4028 138884679 138880652 0.000000e+00 7439
1 TraesCS7B01G119800 chr7A 97.147 4031 90 13 1 4028 176436805 176432797 0.000000e+00 6783
2 TraesCS7B01G119800 chr7D 96.543 3066 81 12 1 3058 174448645 174445597 0.000000e+00 5051
3 TraesCS7B01G119800 chr7D 98.449 709 10 1 3090 3797 174445597 174444889 0.000000e+00 1247
4 TraesCS7B01G119800 chr7D 99.625 267 1 0 3762 4028 174444890 174444624 4.680000e-134 488


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 TraesCS7B01G119800 chr7B 138880652 138884679 4027 True 7439 7439 100.000000 1 4028 1 chr7B.!!$R1 4027
1 TraesCS7B01G119800 chr7A 176432797 176436805 4008 True 6783 6783 97.147000 1 4028 1 chr7A.!!$R1 4027
2 TraesCS7B01G119800 chr7D 174444624 174448645 4021 True 2262 5051 98.205667 1 4028 3 chr7D.!!$R1 4027

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
405 406 0.543749 TGGGGCTTTGGGTTTGTTTG 59.456 50.0 0.0 0.0 0.0 2.93 F
1677 1688 0.465097 AGCCAAATGATGAGGAGCCG 60.465 55.0 0.0 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2097 2108 0.108472 TCAGCTCAGTCTGATTGCCG 60.108 55.000 2.22 0.0 38.11 5.69 R
3063 3074 1.006922 GGAAGCCACAGCAAACAGC 60.007 57.895 0.00 0.0 43.56 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
111 112 2.279741 TGTCATCAACCGCTAGATTGC 58.720 47.619 0.00 0.00 0.00 3.56
152 153 1.593750 CCGCAGCAGCTGATCTACC 60.594 63.158 27.39 5.98 39.10 3.18
228 229 6.264841 GAAAGCTCCAAGATTTCTGTCATT 57.735 37.500 9.73 0.00 44.61 2.57
281 282 6.150140 ACTGCATCTGAATTTTTACTGACTCC 59.850 38.462 0.00 0.00 0.00 3.85
309 310 6.861572 CGAGATGAAATGTAATAGCCGTTAGA 59.138 38.462 0.00 0.00 0.00 2.10
314 315 9.944376 ATGAAATGTAATAGCCGTTAGATACAT 57.056 29.630 0.00 0.00 35.98 2.29
315 316 9.203421 TGAAATGTAATAGCCGTTAGATACATG 57.797 33.333 0.00 0.00 35.00 3.21
322 323 2.767505 CCGTTAGATACATGGGGAAGC 58.232 52.381 0.00 0.00 0.00 3.86
326 327 4.821805 CGTTAGATACATGGGGAAGCAAAT 59.178 41.667 0.00 0.00 0.00 2.32
327 328 5.049405 CGTTAGATACATGGGGAAGCAAATC 60.049 44.000 0.00 0.00 0.00 2.17
344 345 1.921243 ATCGCACGATTGTCGAATCA 58.079 45.000 6.34 0.00 43.74 2.57
351 352 3.061295 CACGATTGTCGAATCAAGAGGTG 59.939 47.826 6.34 0.00 43.74 4.00
390 391 1.895020 TTCCGGACTGAATCGTGGGG 61.895 60.000 1.83 0.00 0.00 4.96
405 406 0.543749 TGGGGCTTTGGGTTTGTTTG 59.456 50.000 0.00 0.00 0.00 2.93
591 592 6.954487 TCATATCTTCTGTACGAGGCTTAA 57.046 37.500 0.00 0.00 0.00 1.85
687 688 5.762825 AATGCTAACTCAAATCATGCGAT 57.237 34.783 0.00 0.00 0.00 4.58
699 700 3.724508 TCATGCGATGTGTTTTGGTTT 57.275 38.095 0.00 0.00 0.00 3.27
700 701 4.837896 TCATGCGATGTGTTTTGGTTTA 57.162 36.364 0.00 0.00 0.00 2.01
834 844 9.965824 ATTTCTCGTTTTGAATTTGATACTTGT 57.034 25.926 0.00 0.00 0.00 3.16
835 845 9.796120 TTTCTCGTTTTGAATTTGATACTTGTT 57.204 25.926 0.00 0.00 0.00 2.83
847 857 5.181690 TGATACTTGTTGCAGTTGTTTCC 57.818 39.130 0.00 0.00 0.00 3.13
848 858 4.642437 TGATACTTGTTGCAGTTGTTTCCA 59.358 37.500 0.00 0.00 0.00 3.53
949 960 2.450609 TTCGTAACAGCTTCCCACTC 57.549 50.000 0.00 0.00 0.00 3.51
1038 1049 1.634702 CTTTCTCGCACTCTAGCACC 58.365 55.000 0.00 0.00 0.00 5.01
1170 1181 3.305950 GCAGCTCTCTGATCGGTGATTAT 60.306 47.826 6.76 0.00 42.95 1.28
1320 1331 1.142688 AGGTGGCCCTCAATGTTCCT 61.143 55.000 0.00 0.00 35.62 3.36
1341 1352 2.432444 ACTGAGGAGAGTTCTCTGACG 58.568 52.381 7.09 0.00 42.48 4.35
1392 1403 2.356695 CAGCAGCATCCGAAATGATTCA 59.643 45.455 0.00 0.00 35.15 2.57
1677 1688 0.465097 AGCCAAATGATGAGGAGCCG 60.465 55.000 0.00 0.00 0.00 5.52
2088 2099 2.615747 GGTAAGAAAGGTGACAGGAGCC 60.616 54.545 0.00 0.00 0.00 4.70
2097 2108 1.936547 GTGACAGGAGCCGATCAATTC 59.063 52.381 0.00 0.00 0.00 2.17
2163 2174 2.769095 GCCAGAGTGTTTAGAGGATCCT 59.231 50.000 16.13 16.13 33.66 3.24
2295 2306 1.053835 TGCCTATGATCCGGGAAGCA 61.054 55.000 0.00 2.81 0.00 3.91
2304 2315 4.161295 CGGGAAGCATGCCTCCGA 62.161 66.667 28.66 0.00 42.94 4.55
2715 2726 5.440610 CCTGTCAATAAGTGGCTTCCTAAT 58.559 41.667 0.00 0.00 30.97 1.73
2825 2836 5.818136 TCTGTGAAAACCTCTGAAAACAG 57.182 39.130 0.00 0.00 36.08 3.16
2844 2855 2.054799 AGCCAAGTTGGTAACTGGAGA 58.945 47.619 22.85 0.00 41.91 3.71
2850 2861 0.320073 TTGGTAACTGGAGAACCGCG 60.320 55.000 0.00 0.00 39.42 6.46
2856 2867 0.108615 ACTGGAGAACCGCGAATGAG 60.109 55.000 8.23 0.00 39.42 2.90
3063 3074 1.534595 GAGAAGTCAGTTTGGCTGCTG 59.465 52.381 0.00 0.00 38.31 4.41
3213 3224 8.990163 TTTCCTGTACATAGTTTTCCTTCTTT 57.010 30.769 0.00 0.00 0.00 2.52
3325 3337 2.358582 TGATATGCATTCAAAGGTGCCG 59.641 45.455 3.54 0.00 40.56 5.69
3565 3577 2.171237 TGCTAGGTTATGCTGCTGTGAT 59.829 45.455 0.00 0.00 0.00 3.06
3732 3744 2.621070 TCCTGCCAAACTCTACCTTCT 58.379 47.619 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 3.372060 GCGTAAGGAAAGGCATTAATGC 58.628 45.455 28.68 28.68 46.07 3.56
111 112 1.550065 CGAGCTACACAATCGTCAGG 58.450 55.000 0.00 0.00 0.00 3.86
152 153 2.740055 AAGCTTCGCTCAGGCACG 60.740 61.111 0.00 0.00 38.25 5.34
239 240 2.544486 GCAGTTGTCAAAGCCTCAAAGG 60.544 50.000 0.85 0.00 38.80 3.11
240 241 2.099592 TGCAGTTGTCAAAGCCTCAAAG 59.900 45.455 8.34 0.00 0.00 2.77
241 242 2.098614 TGCAGTTGTCAAAGCCTCAAA 58.901 42.857 8.34 0.00 0.00 2.69
242 243 1.761449 TGCAGTTGTCAAAGCCTCAA 58.239 45.000 8.34 0.00 0.00 3.02
243 244 1.881973 GATGCAGTTGTCAAAGCCTCA 59.118 47.619 8.34 0.00 0.00 3.86
244 245 2.095364 CAGATGCAGTTGTCAAAGCCTC 60.095 50.000 8.34 8.09 0.00 4.70
245 246 1.884579 CAGATGCAGTTGTCAAAGCCT 59.115 47.619 8.34 0.08 0.00 4.58
246 247 1.881973 TCAGATGCAGTTGTCAAAGCC 59.118 47.619 8.34 0.00 0.00 4.35
247 248 3.631145 TTCAGATGCAGTTGTCAAAGC 57.369 42.857 0.00 4.70 0.00 3.51
281 282 4.088638 CGGCTATTACATTTCATCTCGACG 59.911 45.833 0.00 0.00 0.00 5.12
309 310 1.956477 GCGATTTGCTTCCCCATGTAT 59.044 47.619 0.00 0.00 41.73 2.29
314 315 2.331893 CGTGCGATTTGCTTCCCCA 61.332 57.895 0.00 0.00 46.63 4.96
315 316 1.376609 ATCGTGCGATTTGCTTCCCC 61.377 55.000 0.77 0.00 46.63 4.81
322 323 2.502280 TTCGACAATCGTGCGATTTG 57.498 45.000 15.97 13.57 42.30 2.32
326 327 1.653609 CTTGATTCGACAATCGTGCGA 59.346 47.619 0.00 0.00 41.41 5.10
327 328 1.653609 TCTTGATTCGACAATCGTGCG 59.346 47.619 0.00 0.00 41.41 5.34
344 345 2.943199 GCCAGCAGCTTAATCACCTCTT 60.943 50.000 0.00 0.00 38.99 2.85
351 352 2.189499 CCGGGCCAGCAGCTTAATC 61.189 63.158 4.39 0.00 43.05 1.75
390 391 1.013596 GTGGCAAACAAACCCAAAGC 58.986 50.000 0.00 0.00 0.00 3.51
405 406 5.904362 ATCTCTTAAACTTTCCATGTGGC 57.096 39.130 0.00 0.00 34.44 5.01
700 701 9.975218 AAACTCAACTACCCAGTTAATGAATAT 57.025 29.630 0.00 0.00 43.30 1.28
759 768 4.207891 ACCGATTCTTGCTCTGTAATGT 57.792 40.909 0.00 0.00 0.00 2.71
760 769 5.352284 ACTACCGATTCTTGCTCTGTAATG 58.648 41.667 0.00 0.00 0.00 1.90
822 832 6.701400 GGAAACAACTGCAACAAGTATCAAAT 59.299 34.615 0.00 0.00 0.00 2.32
823 833 6.039616 GGAAACAACTGCAACAAGTATCAAA 58.960 36.000 0.00 0.00 0.00 2.69
824 834 5.126222 TGGAAACAACTGCAACAAGTATCAA 59.874 36.000 0.00 0.00 37.44 2.57
826 836 5.181690 TGGAAACAACTGCAACAAGTATC 57.818 39.130 0.00 0.00 37.44 2.24
873 883 5.008619 TGCAAAAACAGAAAGAGCAATCA 57.991 34.783 0.00 0.00 0.00 2.57
874 884 4.446719 CCTGCAAAAACAGAAAGAGCAATC 59.553 41.667 0.00 0.00 40.25 2.67
1038 1049 1.394572 TCAAATTCTGCAGATGACGCG 59.605 47.619 19.04 3.53 0.00 6.01
1170 1181 3.119101 CCTCGCTTCTAGTTTTGCTAGGA 60.119 47.826 11.15 0.00 45.55 2.94
1239 1250 3.380004 CCAGTTGAACAGGCAGTACAAAA 59.620 43.478 0.00 0.00 0.00 2.44
1320 1331 3.601435 CGTCAGAGAACTCTCCTCAGTA 58.399 50.000 3.04 0.00 43.88 2.74
1341 1352 0.461548 TGAGGACATGATCACCGAGC 59.538 55.000 0.00 0.00 0.00 5.03
1392 1403 0.764369 TCTTGGTCAGGAGCAGTGGT 60.764 55.000 0.00 0.00 40.18 4.16
1677 1688 2.611225 TTGGATTGTTGGGTGCAAAC 57.389 45.000 0.00 0.00 0.00 2.93
2097 2108 0.108472 TCAGCTCAGTCTGATTGCCG 60.108 55.000 2.22 0.00 38.11 5.69
2105 2116 4.100808 GGTCAATAGGAATCAGCTCAGTCT 59.899 45.833 0.00 0.00 0.00 3.24
2295 2306 1.395826 GGACTAGCACTCGGAGGCAT 61.396 60.000 17.01 5.76 0.00 4.40
2304 2315 2.310779 TGGTTGAGAGGACTAGCACT 57.689 50.000 0.00 0.00 0.00 4.40
2715 2726 6.070251 TCAGTGAGGTTGATAGCTTGGAAATA 60.070 38.462 0.00 0.00 30.79 1.40
2825 2836 2.552743 GTTCTCCAGTTACCAACTTGGC 59.447 50.000 7.81 0.00 42.67 4.52
2844 2855 2.046892 AGCTGCTCATTCGCGGTT 60.047 55.556 6.13 0.00 38.54 4.44
2850 2861 1.471684 CTTGTTGGGAGCTGCTCATTC 59.528 52.381 28.95 18.13 31.08 2.67
2856 2867 4.410743 GCGCTTGTTGGGAGCTGC 62.411 66.667 0.00 0.00 37.99 5.25
3063 3074 1.006922 GGAAGCCACAGCAAACAGC 60.007 57.895 0.00 0.00 43.56 4.40
3565 3577 8.397906 GTTGCTGCATGAACTAGACAATAAATA 58.602 33.333 1.84 0.00 0.00 1.40
3732 3744 8.506921 TGGGTTGGAATAGATGTAAATAATCCA 58.493 33.333 0.00 0.00 34.10 3.41


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

AutoCloner maintained by Alex Coulton.