Multiple sequence alignment - TraesCS7B01G047700

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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 TraesCS7B01G047700 chr7B 100.000 3802 0 0 1 3802 47204747 47200946 0.000000e+00 7022
1 TraesCS7B01G047700 chr7B 97.129 3796 101 6 1 3793 698140159 698143949 0.000000e+00 6399
2 TraesCS7B01G047700 chr1B 97.287 3796 94 6 1 3793 683734143 683730354 0.000000e+00 6431
3 TraesCS7B01G047700 chrUn 96.945 3797 107 6 1 3793 40085858 40089649 0.000000e+00 6360
4 TraesCS7B01G047700 chr3B 96.918 3796 108 7 1 3793 92261855 92265644 0.000000e+00 6353
5 TraesCS7B01G047700 chr3B 96.891 3795 111 5 1 3793 92142923 92146712 0.000000e+00 6348
6 TraesCS7B01G047700 chr2A 96.918 3796 107 6 1 3793 563256641 563260429 0.000000e+00 6353
7 TraesCS7B01G047700 chr2A 96.732 3672 111 7 124 3791 735136912 735140578 0.000000e+00 6107
8 TraesCS7B01G047700 chr2A 97.068 2831 76 5 1 2829 605912878 605910053 0.000000e+00 4761
9 TraesCS7B01G047700 chr2A 98.701 77 1 0 3016 3092 94207834 94207910 1.840000e-28 137
10 TraesCS7B01G047700 chr5B 96.865 3796 108 7 1 3793 713082219 713078432 0.000000e+00 6340


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 TraesCS7B01G047700 chr7B 47200946 47204747 3801 True 7022 7022 100.000 1 3802 1 chr7B.!!$R1 3801
1 TraesCS7B01G047700 chr7B 698140159 698143949 3790 False 6399 6399 97.129 1 3793 1 chr7B.!!$F1 3792
2 TraesCS7B01G047700 chr1B 683730354 683734143 3789 True 6431 6431 97.287 1 3793 1 chr1B.!!$R1 3792
3 TraesCS7B01G047700 chrUn 40085858 40089649 3791 False 6360 6360 96.945 1 3793 1 chrUn.!!$F1 3792
4 TraesCS7B01G047700 chr3B 92261855 92265644 3789 False 6353 6353 96.918 1 3793 1 chr3B.!!$F2 3792
5 TraesCS7B01G047700 chr3B 92142923 92146712 3789 False 6348 6348 96.891 1 3793 1 chr3B.!!$F1 3792
6 TraesCS7B01G047700 chr2A 563256641 563260429 3788 False 6353 6353 96.918 1 3793 1 chr2A.!!$F2 3792
7 TraesCS7B01G047700 chr2A 735136912 735140578 3666 False 6107 6107 96.732 124 3791 1 chr2A.!!$F3 3667
8 TraesCS7B01G047700 chr2A 605910053 605912878 2825 True 4761 4761 97.068 1 2829 1 chr2A.!!$R1 2828
9 TraesCS7B01G047700 chr5B 713078432 713082219 3787 True 6340 6340 96.865 1 3793 1 chr5B.!!$R1 3792

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
548 549 1.798223 CTCGAGTTTTTGGTGCGATCA 59.202 47.619 3.62 0.0 0.00 2.92 F
1380 1383 2.079925 GAATCTTTCTGCGGTCTGCTT 58.920 47.619 5.01 0.0 46.63 3.91 F
1460 1463 0.037590 TGGGCGCTCCAAAGTAATGT 59.962 50.000 14.27 0.0 43.84 2.71 F
1603 1608 1.008538 CGAGTGGTGCTTGTTTGGC 60.009 57.895 0.00 0.0 0.00 4.52 F
2437 2443 1.130749 GTCAGACGACGACTACTGCAT 59.869 52.381 0.00 0.0 31.07 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1441 1444 0.037590 ACATTACTTTGGAGCGCCCA 59.962 50.000 12.86 12.86 44.93 5.36 R
2267 2273 0.322187 ACACAACATTAGGGGCGTCC 60.322 55.000 0.00 0.00 0.00 4.79 R
2510 2517 0.607489 AGCAACAAAGCGCTCATCCT 60.607 50.000 12.06 0.00 40.15 3.24 R
2549 2556 1.202475 CCAAAAACAAACCGACCCAGG 60.202 52.381 0.00 0.00 37.30 4.45 R
3270 3279 2.280552 AAACTACGCGAGCCTCCCA 61.281 57.895 15.93 0.00 0.00 4.37 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 7.561356 CCTATTATTCAAACCACAAAGGATCCT 59.439 37.037 9.02 9.02 41.22 3.24
171 172 4.079558 ACATCAATACTCCTTTCCATGGCT 60.080 41.667 6.96 0.00 0.00 4.75
262 263 2.461695 TCCATCTCACTCAGACCCTTC 58.538 52.381 0.00 0.00 32.26 3.46
338 339 3.706594 TCTTAGGAGCTGGTAATCACTGG 59.293 47.826 0.00 0.00 0.00 4.00
349 350 5.853936 TGGTAATCACTGGTATGCTCATAC 58.146 41.667 10.69 10.69 42.15 2.39
356 357 3.969976 ACTGGTATGCTCATACTGGTGAT 59.030 43.478 16.73 0.00 42.42 3.06
415 416 5.946942 ATGCCTCTAGAAAGATCAGACAA 57.053 39.130 0.00 0.00 0.00 3.18
439 440 8.656849 CAAAAGTAAGACGAGCTGTAATTGTAT 58.343 33.333 0.00 0.00 0.00 2.29
468 469 6.671614 TGTAAAGAACTCAAACGTGACAAT 57.328 33.333 0.00 0.00 0.00 2.71
495 496 8.565416 GGTATGATAATACGATATGATGACGGA 58.435 37.037 0.00 0.00 0.00 4.69
548 549 1.798223 CTCGAGTTTTTGGTGCGATCA 59.202 47.619 3.62 0.00 0.00 2.92
931 934 5.190330 ACATAGGTACCCTTTTTCGGTATGT 59.810 40.000 8.74 9.76 38.14 2.29
1014 1017 2.906389 AGAGCAGATGGTCCAACTACAA 59.094 45.455 8.34 0.00 43.11 2.41
1023 1026 7.444183 CAGATGGTCCAACTACAAAACTTCTTA 59.556 37.037 0.57 0.00 0.00 2.10
1090 1093 4.027132 CCGTACTATTGAAATGGTTCGTCG 60.027 45.833 14.19 7.79 38.38 5.12
1380 1383 2.079925 GAATCTTTCTGCGGTCTGCTT 58.920 47.619 5.01 0.00 46.63 3.91
1451 1454 4.783621 GCATGAGTGGGCGCTCCA 62.784 66.667 3.94 9.48 44.79 3.86
1460 1463 0.037590 TGGGCGCTCCAAAGTAATGT 59.962 50.000 14.27 0.00 43.84 2.71
1569 1572 1.140134 TTGGGCCTGTAGCTTTCCCT 61.140 55.000 4.53 0.00 43.05 4.20
1603 1608 1.008538 CGAGTGGTGCTTGTTTGGC 60.009 57.895 0.00 0.00 0.00 4.52
1649 1654 1.555075 TGAAGCTCTCGCCTTACCAAT 59.445 47.619 0.00 0.00 36.60 3.16
1819 1824 5.163195 GCCTCCTATTCTATTTGTTCAGGGA 60.163 44.000 0.00 0.00 0.00 4.20
1845 1850 2.480416 GGCGTGAACTCTGATTCGATCT 60.480 50.000 0.00 0.00 0.00 2.75
1906 1911 6.209774 TCCTTAACCTTGATAGGAAGATGGA 58.790 40.000 0.00 0.00 45.05 3.41
2231 2237 1.324383 GAACGGGCTTCCCAAAAAGA 58.676 50.000 2.47 0.00 45.83 2.52
2292 2298 1.626686 CCCTAATGTTGTGTTGGCCA 58.373 50.000 0.00 0.00 0.00 5.36
2355 2361 2.094649 GGCACAGCGTAACTAAGAGAGT 60.095 50.000 0.00 0.00 41.56 3.24
2437 2443 1.130749 GTCAGACGACGACTACTGCAT 59.869 52.381 0.00 0.00 31.07 3.96
2464 2470 7.661536 ATTAGATTCTATTAGCCGCCTATCA 57.338 36.000 0.00 0.00 0.00 2.15
2495 2502 4.837093 TGGGATGGAATAGAAAGAACGT 57.163 40.909 0.00 0.00 0.00 3.99
2699 2707 2.786495 CGGCCCGAGCTGTATGAGT 61.786 63.158 0.00 0.00 40.79 3.41
2730 2738 2.334946 CCACGTACGGTTCGGAGGA 61.335 63.158 21.06 0.00 32.35 3.71
2745 2753 4.791069 GGACGAGCCCCACCCCTA 62.791 72.222 0.00 0.00 0.00 3.53
2757 2765 2.243736 CCCACCCCTACAATAATGGTGT 59.756 50.000 6.27 0.00 43.92 4.16
2777 2785 5.484715 GTGTGGCTTAGGTCAACTAATACA 58.515 41.667 0.00 0.00 40.71 2.29
2811 2819 1.820519 TCACTCAATGATTGCCCTTGC 59.179 47.619 0.00 0.00 32.43 4.01
2845 2853 2.375014 ATGGGGAAGGAACGTTGTTT 57.625 45.000 5.00 0.00 0.00 2.83
3009 3017 6.753913 ACTTTCCTGCCTCATATGAGAATA 57.246 37.500 30.40 16.12 44.74 1.75
3127 3135 0.386858 CGAGAAACGAGGAGCACGAA 60.387 55.000 0.00 0.00 45.77 3.85
3270 3279 5.595952 GGATAGGATTTCTGTTGGCTTCATT 59.404 40.000 0.00 0.00 0.00 2.57
3328 3337 3.885297 AGGATAAGTTGCATTGGAATCGG 59.115 43.478 0.00 0.00 0.00 4.18
3338 3347 3.056891 GCATTGGAATCGGGAAAGTTTCA 60.057 43.478 17.16 0.00 0.00 2.69
3566 3575 5.940617 TCGATGGGAGAATGAAACCATTAT 58.059 37.500 0.00 0.00 43.40 1.28
3793 3802 3.771160 CAGCGGGGCGTCTTACCT 61.771 66.667 0.00 0.00 0.00 3.08
3794 3803 3.771160 AGCGGGGCGTCTTACCTG 61.771 66.667 0.00 0.00 36.18 4.00
3796 3805 4.077184 CGGGGCGTCTTACCTGCA 62.077 66.667 0.00 0.00 0.00 4.41
3797 3806 2.590092 GGGGCGTCTTACCTGCAT 59.410 61.111 0.00 0.00 0.00 3.96
3798 3807 1.523938 GGGGCGTCTTACCTGCATC 60.524 63.158 0.00 0.00 0.00 3.91
3799 3808 1.220749 GGGCGTCTTACCTGCATCA 59.779 57.895 0.00 0.00 0.00 3.07
3800 3809 0.392461 GGGCGTCTTACCTGCATCAA 60.392 55.000 0.00 0.00 0.00 2.57
3801 3810 1.668419 GGCGTCTTACCTGCATCAAT 58.332 50.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 112 4.864806 CGAGAAGATTGGACGATGAAAGAA 59.135 41.667 0.00 0.00 0.00 2.52
262 263 3.245284 CCGTTGTTATCCGCTACATTCAG 59.755 47.826 0.00 0.00 0.00 3.02
338 339 7.442364 ACAATAACATCACCAGTATGAGCATAC 59.558 37.037 11.68 11.68 42.96 2.39
349 350 4.771590 ACAGCAACAATAACATCACCAG 57.228 40.909 0.00 0.00 0.00 4.00
356 357 7.594758 GCTTCTTTGATTACAGCAACAATAACA 59.405 33.333 0.00 0.00 0.00 2.41
415 416 7.817962 ACATACAATTACAGCTCGTCTTACTTT 59.182 33.333 0.00 0.00 0.00 2.66
439 440 6.757478 TCACGTTTGAGTTCTTTACATGTACA 59.243 34.615 4.68 0.00 0.00 2.90
468 469 8.349983 CCGTCATCATATCGTATTATCATACCA 58.650 37.037 0.00 0.00 32.79 3.25
495 496 6.893554 TGGATTTCCTTCTTGATCAATGACAT 59.106 34.615 8.96 2.74 36.82 3.06
548 549 5.677319 TTCATAAGTCTCAATTCCCGAGT 57.323 39.130 0.00 0.00 0.00 4.18
730 733 8.873186 TCGAACCCTTCCTTTTATTAAGATTT 57.127 30.769 0.00 0.00 0.00 2.17
776 779 9.931210 CGTAGAAGTATTTTCACAAAGTTTTCT 57.069 29.630 0.00 0.00 0.00 2.52
822 825 6.943718 TGTTACTTTCCCTATGGTTTTCGAAT 59.056 34.615 0.00 0.00 0.00 3.34
931 934 6.252441 CGCTAAAAATGAAAGTGTTCACAACA 59.748 34.615 5.74 3.20 46.40 3.33
1023 1026 6.620678 CACGACCATGGAAGTAATGAAAAAT 58.379 36.000 21.47 0.00 0.00 1.82
1090 1093 2.093447 CACCAGTGGGAACATCTCTACC 60.093 54.545 15.21 0.00 46.14 3.18
1171 1174 9.813080 GCGTATGAATTTCCTTAAATGTAGATC 57.187 33.333 0.00 0.00 35.46 2.75
1216 1219 0.307760 GCTTTGACCAACACTCCACG 59.692 55.000 0.00 0.00 0.00 4.94
1293 1296 7.650104 TGAAGAACGGGAACAAAATGAAATAAC 59.350 33.333 0.00 0.00 0.00 1.89
1380 1383 8.882415 AGAGAGTACGAAAGAATTGTAAACAA 57.118 30.769 0.00 0.00 40.51 2.83
1436 1439 1.377725 CTTTGGAGCGCCCACTCAT 60.378 57.895 15.99 0.00 46.62 2.90
1441 1444 0.037590 ACATTACTTTGGAGCGCCCA 59.962 50.000 12.86 12.86 44.93 5.36
1451 1454 4.261447 GCCGAAGTGTTTGGACATTACTTT 60.261 41.667 0.00 0.00 38.23 2.66
1458 1461 0.759959 TAGGCCGAAGTGTTTGGACA 59.240 50.000 0.00 0.00 45.57 4.02
1460 1463 1.271163 CCTTAGGCCGAAGTGTTTGGA 60.271 52.381 22.28 0.00 36.18 3.53
1535 1538 1.546099 GCCCAAAACCTTCGACCCTTA 60.546 52.381 0.00 0.00 0.00 2.69
1617 1622 0.315251 GAGCTTCAAGCCCGCTTTTT 59.685 50.000 5.53 0.00 43.77 1.94
1618 1623 0.538287 AGAGCTTCAAGCCCGCTTTT 60.538 50.000 5.53 0.00 43.77 2.27
1819 1824 4.379243 CAGAGTTCACGCCGCCCT 62.379 66.667 0.00 0.00 0.00 5.19
1906 1911 8.977412 ACCCTTATGAACGAATTTTGGAATAAT 58.023 29.630 0.00 0.00 0.00 1.28
1923 1928 6.216662 TCATCCAAAGTTCCTTACCCTTATGA 59.783 38.462 0.00 0.00 0.00 2.15
2198 2203 2.110213 GTTCCCACCGTGCTCACA 59.890 61.111 0.69 0.00 0.00 3.58
2267 2273 0.322187 ACACAACATTAGGGGCGTCC 60.322 55.000 0.00 0.00 0.00 4.79
2268 2274 1.199097 CAACACAACATTAGGGGCGTC 59.801 52.381 0.00 0.00 0.00 5.19
2272 2278 0.894835 GGCCAACACAACATTAGGGG 59.105 55.000 0.00 0.00 0.00 4.79
2292 2298 1.001887 TTTTATCCGCCCGCAACCT 60.002 52.632 0.00 0.00 0.00 3.50
2332 2338 1.204941 CTCTTAGTTACGCTGTGCCCT 59.795 52.381 0.00 0.00 0.00 5.19
2355 2361 2.503765 TGTCTCGCCCTAAATGGAATGA 59.496 45.455 0.00 0.00 38.35 2.57
2464 2470 1.221635 TTCCATCCCATCCATTCCGT 58.778 50.000 0.00 0.00 0.00 4.69
2495 2502 1.271379 CATCCTTTGCTTGCTGCTTCA 59.729 47.619 0.00 0.00 43.37 3.02
2510 2517 0.607489 AGCAACAAAGCGCTCATCCT 60.607 50.000 12.06 0.00 40.15 3.24
2549 2556 1.202475 CCAAAAACAAACCGACCCAGG 60.202 52.381 0.00 0.00 37.30 4.45
2699 2707 1.267806 GTACGTGGGACGAGTTTCTGA 59.732 52.381 0.00 0.00 46.05 3.27
2730 2738 3.733445 TATTGTAGGGGTGGGGCTCGT 62.733 57.143 0.00 0.00 0.00 4.18
2745 2753 4.263727 TGACCTAAGCCACACCATTATTGT 60.264 41.667 0.00 0.00 0.00 2.71
2757 2765 9.391006 CTTATTTGTATTAGTTGACCTAAGCCA 57.609 33.333 0.00 0.00 38.99 4.75
2789 2797 3.306225 GCAAGGGCAATCATTGAGTGAAA 60.306 43.478 17.65 0.00 39.29 2.69
2799 2807 2.361104 GGGACGCAAGGGCAATCA 60.361 61.111 0.00 0.00 46.39 2.57
2845 2853 5.471797 TGTAAATGATCGAGACCTTGCAAAA 59.528 36.000 0.00 0.00 0.00 2.44
2851 2859 5.360591 GTCCATGTAAATGATCGAGACCTT 58.639 41.667 0.00 0.00 0.00 3.50
3027 3035 2.488204 TTCTTCATCCACCGATGCAA 57.512 45.000 0.00 0.00 44.83 4.08
3127 3135 7.517320 TGGATTTGTATGTATAGCCACTTCAT 58.483 34.615 0.00 0.00 0.00 2.57
3270 3279 2.280552 AAACTACGCGAGCCTCCCA 61.281 57.895 15.93 0.00 0.00 4.37
3566 3575 8.611257 TCCCATTCTTTCTTCTTTCCACTAATA 58.389 33.333 0.00 0.00 0.00 0.98
3776 3785 3.771160 AGGTAAGACGCCCCGCTG 61.771 66.667 0.00 0.00 0.00 5.18


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

AutoCloner maintained by Alex Coulton.