Multiple sequence alignment - TraesCS4B01G262200

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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 TraesCS4B01G262200 chr4B 100.000 3229 0 0 1 3229 531244549 531247777 0.000000e+00 5963.0
1 TraesCS4B01G262200 chr4B 95.722 748 32 0 2481 3228 609361513 609362260 0.000000e+00 1205.0
2 TraesCS4B01G262200 chr4B 81.310 931 136 26 1229 2152 465742029 465742928 0.000000e+00 721.0
3 TraesCS4B01G262200 chr4D 96.420 2486 79 7 1 2483 433219399 433221877 0.000000e+00 4089.0
4 TraesCS4B01G262200 chr4D 82.763 876 118 25 1229 2098 379154977 379155825 0.000000e+00 750.0
5 TraesCS4B01G262200 chr4D 91.441 222 16 2 2057 2277 433368616 433368835 5.240000e-78 302.0
6 TraesCS4B01G262200 chr4D 93.023 43 3 0 2359 2401 433368880 433368922 2.690000e-06 63.9
7 TraesCS4B01G262200 chr4A 91.462 1956 101 22 556 2483 34668793 34670710 0.000000e+00 2627.0
8 TraesCS4B01G262200 chr4A 93.143 525 33 3 1 524 34667688 34668210 0.000000e+00 767.0
9 TraesCS4B01G262200 chr4A 81.788 906 130 27 1229 2127 85893142 85892265 0.000000e+00 726.0
10 TraesCS4B01G262200 chr4A 92.952 227 15 1 5 231 34656612 34656837 2.400000e-86 329.0
11 TraesCS4B01G262200 chr4A 89.655 116 10 2 2057 2171 34745767 34745881 2.600000e-31 147.0
12 TraesCS4B01G262200 chr1B 95.612 752 31 2 2478 3228 635927629 635928379 0.000000e+00 1205.0
13 TraesCS4B01G262200 chr7B 95.576 746 32 1 2483 3228 624167227 624166483 0.000000e+00 1194.0
14 TraesCS4B01G262200 chr2B 94.940 751 34 1 2478 3228 744554768 744555514 0.000000e+00 1173.0
15 TraesCS4B01G262200 chr2B 95.040 746 33 1 2483 3228 615442544 615443285 0.000000e+00 1170.0
16 TraesCS4B01G262200 chr2B 95.034 745 32 1 2484 3228 154506223 154505484 0.000000e+00 1166.0
17 TraesCS4B01G262200 chr2B 94.533 750 35 2 2480 3228 483663328 483662584 0.000000e+00 1153.0
18 TraesCS4B01G262200 chr5B 95.047 747 32 2 2483 3228 471378615 471377873 0.000000e+00 1170.0
19 TraesCS4B01G262200 chr5A 94.800 750 35 1 2479 3228 109291657 109292402 0.000000e+00 1166.0
20 TraesCS4B01G262200 chr1D 100.000 31 0 0 2423 2453 73055788 73055818 1.250000e-04 58.4


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 TraesCS4B01G262200 chr4B 531244549 531247777 3228 False 5963 5963 100.0000 1 3229 1 chr4B.!!$F2 3228
1 TraesCS4B01G262200 chr4B 609361513 609362260 747 False 1205 1205 95.7220 2481 3228 1 chr4B.!!$F3 747
2 TraesCS4B01G262200 chr4B 465742029 465742928 899 False 721 721 81.3100 1229 2152 1 chr4B.!!$F1 923
3 TraesCS4B01G262200 chr4D 433219399 433221877 2478 False 4089 4089 96.4200 1 2483 1 chr4D.!!$F2 2482
4 TraesCS4B01G262200 chr4D 379154977 379155825 848 False 750 750 82.7630 1229 2098 1 chr4D.!!$F1 869
5 TraesCS4B01G262200 chr4A 34667688 34670710 3022 False 1697 2627 92.3025 1 2483 2 chr4A.!!$F3 2482
6 TraesCS4B01G262200 chr4A 85892265 85893142 877 True 726 726 81.7880 1229 2127 1 chr4A.!!$R1 898
7 TraesCS4B01G262200 chr1B 635927629 635928379 750 False 1205 1205 95.6120 2478 3228 1 chr1B.!!$F1 750
8 TraesCS4B01G262200 chr7B 624166483 624167227 744 True 1194 1194 95.5760 2483 3228 1 chr7B.!!$R1 745
9 TraesCS4B01G262200 chr2B 744554768 744555514 746 False 1173 1173 94.9400 2478 3228 1 chr2B.!!$F2 750
10 TraesCS4B01G262200 chr2B 615442544 615443285 741 False 1170 1170 95.0400 2483 3228 1 chr2B.!!$F1 745
11 TraesCS4B01G262200 chr2B 154505484 154506223 739 True 1166 1166 95.0340 2484 3228 1 chr2B.!!$R1 744
12 TraesCS4B01G262200 chr2B 483662584 483663328 744 True 1153 1153 94.5330 2480 3228 1 chr2B.!!$R2 748
13 TraesCS4B01G262200 chr5B 471377873 471378615 742 True 1170 1170 95.0470 2483 3228 1 chr5B.!!$R1 745
14 TraesCS4B01G262200 chr5A 109291657 109292402 745 False 1166 1166 94.8000 2479 3228 1 chr5A.!!$F1 749

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
836 1389 1.067250 GAGCCTCAGGTCATCTCGC 59.933 63.158 0.00 0.00 40.37 5.03 F
886 1439 1.279025 GGTACAAGGGGCCCATCAGA 61.279 60.000 27.72 1.29 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1945 2504 0.947244 CAAGACACGAAAAGCCAGCT 59.053 50.000 0.00 0.0 0.00 4.24 R
2647 3230 1.074775 GTTGACCATGGCAGTGGGA 59.925 57.895 13.04 0.0 43.77 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
98 99 3.648339 ATCGGCATACCATTTGCATTC 57.352 42.857 0.00 0.00 41.95 2.67
103 104 4.216042 CGGCATACCATTTGCATTCTATCA 59.784 41.667 0.00 0.00 41.95 2.15
135 136 5.290885 GCAATCCTTAAAAGTAAATTGCCCG 59.709 40.000 16.22 0.00 37.69 6.13
138 139 4.218852 TCCTTAAAAGTAAATTGCCCGGTG 59.781 41.667 0.00 0.00 0.00 4.94
144 145 1.790635 TAAATTGCCCGGTGGGTCCA 61.791 55.000 0.00 0.00 46.51 4.02
171 172 6.855836 TCCTTGCAGCAAATTAGTAGAAATG 58.144 36.000 9.65 0.00 0.00 2.32
181 182 6.422776 AATTAGTAGAAATGTGAAGGTGCG 57.577 37.500 0.00 0.00 0.00 5.34
239 240 3.354089 AAATCGGTGTGCTTTTGAGTG 57.646 42.857 0.00 0.00 0.00 3.51
380 382 9.774413 ACAAACTATAGCTACAGTTAAACAAGT 57.226 29.630 17.46 7.33 33.92 3.16
393 395 3.577805 AAACAAGTGCTCCCAACTACT 57.422 42.857 0.00 0.00 0.00 2.57
408 410 5.995282 CCCAACTACTAATGTCTCACAAACA 59.005 40.000 0.00 0.00 0.00 2.83
422 424 5.710099 TCTCACAAACAAAAGTCAGAAGGTT 59.290 36.000 0.00 0.00 0.00 3.50
426 428 6.813152 CACAAACAAAAGTCAGAAGGTTCATT 59.187 34.615 0.00 0.00 0.00 2.57
452 454 5.413499 CAGGACTAGCAAAATTTTGGATGG 58.587 41.667 27.60 14.17 38.57 3.51
482 484 4.036734 TCAAAAACTCAGCACTCATTCACC 59.963 41.667 0.00 0.00 0.00 4.02
547 550 3.032459 GGGGAAAAACTGTGGTAACCAA 58.968 45.455 0.00 0.00 34.18 3.67
613 1166 7.677982 GCAGTTTACGTTAACTTTTCAGAACCT 60.678 37.037 16.75 0.00 36.24 3.50
640 1193 2.126812 GTTCTCACGCGCTCTCGT 60.127 61.111 5.73 0.00 44.35 4.18
678 1231 1.623081 CGGTCACAATACGCAACGCT 61.623 55.000 0.00 0.00 0.00 5.07
717 1270 1.281867 TGTCCGGAAGCCATCAAGAAT 59.718 47.619 5.23 0.00 0.00 2.40
836 1389 1.067250 GAGCCTCAGGTCATCTCGC 59.933 63.158 0.00 0.00 40.37 5.03
886 1439 1.279025 GGTACAAGGGGCCCATCAGA 61.279 60.000 27.72 1.29 0.00 3.27
902 1455 4.043812 CCATCAGATAAACCATCCCCATCT 59.956 45.833 0.00 0.00 33.75 2.90
1031 1586 2.111043 ATTAGCCACCCCGATGCG 59.889 61.111 0.00 0.00 0.00 4.73
1052 1607 2.554032 GGAATGCACACTGTTGTTAGCT 59.446 45.455 0.00 0.00 31.66 3.32
1106 1661 2.802816 AGAAAGATAACATCATCGCCGC 59.197 45.455 0.00 0.00 0.00 6.53
1109 1664 2.771089 AGATAACATCATCGCCGCATT 58.229 42.857 0.00 0.00 0.00 3.56
2061 2620 1.447317 GGCTGGTGTTCCTGTGTGTG 61.447 60.000 0.00 0.00 35.49 3.82
2223 2790 5.009010 ACAATGACCACTTAAGTCAGCTTTG 59.991 40.000 4.77 13.10 46.76 2.77
2224 2791 4.150897 TGACCACTTAAGTCAGCTTTGT 57.849 40.909 4.77 0.00 39.29 2.83
2225 2792 3.876914 TGACCACTTAAGTCAGCTTTGTG 59.123 43.478 4.77 0.00 39.29 3.33
2226 2793 3.877508 GACCACTTAAGTCAGCTTTGTGT 59.122 43.478 4.77 0.00 36.82 3.72
2227 2794 3.627577 ACCACTTAAGTCAGCTTTGTGTG 59.372 43.478 4.77 0.00 36.82 3.82
2344 2926 5.630680 CCACATAACTTTGCTGATTGAACAC 59.369 40.000 0.00 0.00 0.00 3.32
2500 3082 4.646877 GGGAAACGTTCGGGGCCA 62.647 66.667 4.39 0.00 0.00 5.36
2542 3124 4.961511 GTCCAGTCCACACGCGCA 62.962 66.667 5.73 0.00 0.00 6.09
2625 3207 4.493618 TCCCTTTTCTCTTCTTCCTCTCA 58.506 43.478 0.00 0.00 0.00 3.27
2629 3211 2.208132 TCTCTTCTTCCTCTCACGCT 57.792 50.000 0.00 0.00 0.00 5.07
2647 3230 4.079253 ACGCTTCTCTCTCTTTCTCTCTT 58.921 43.478 0.00 0.00 0.00 2.85
2651 3234 4.666412 TCTCTCTCTTTCTCTCTTCCCA 57.334 45.455 0.00 0.00 0.00 4.37
2668 3251 1.968017 CACTGCCATGGTCAACGCT 60.968 57.895 14.67 0.00 0.00 5.07
2880 3463 1.021968 GCAACCGTTGACAGGAAAGT 58.978 50.000 15.63 0.00 0.00 2.66
2953 3536 1.403814 TCAGTGCTATCGAGGGAAGG 58.596 55.000 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 8.533569 TGGTATGCCGATTTCATATAGATAGA 57.466 34.615 0.00 0.00 37.67 1.98
135 136 1.603739 GCAAGGAACTGGACCCACC 60.604 63.158 0.00 0.00 40.86 4.61
138 139 1.973812 GCTGCAAGGAACTGGACCC 60.974 63.158 0.00 0.00 40.86 4.46
144 145 5.560724 TCTACTAATTTGCTGCAAGGAACT 58.439 37.500 15.39 2.62 46.77 3.01
171 172 0.313672 TGCCATTTTCGCACCTTCAC 59.686 50.000 0.00 0.00 0.00 3.18
181 182 9.294030 CATTTTTCATAGTCTAGTGCCATTTTC 57.706 33.333 0.00 0.00 0.00 2.29
258 260 5.556006 AGTAGGGCTTGTACAAAGTACAA 57.444 39.130 18.42 18.42 36.20 2.41
380 382 4.081642 GTGAGACATTAGTAGTTGGGAGCA 60.082 45.833 0.00 0.00 0.00 4.26
393 395 7.857734 TCTGACTTTTGTTTGTGAGACATTA 57.142 32.000 0.00 0.00 0.00 1.90
408 410 3.960102 TGGCAATGAACCTTCTGACTTTT 59.040 39.130 0.00 0.00 0.00 2.27
426 428 3.006752 CCAAAATTTTGCTAGTCCTGGCA 59.993 43.478 22.90 0.77 45.39 4.92
452 454 2.550180 GTGCTGAGTTTTTGAGGTCCTC 59.450 50.000 12.40 12.40 0.00 3.71
482 484 5.046529 CCATACTCTCTGATTTCACTTCCG 58.953 45.833 0.00 0.00 0.00 4.30
547 550 1.127567 TGGTAGCACCAGAAGCAGGT 61.128 55.000 4.16 0.00 44.79 4.00
640 1193 2.091102 GACAGGTCACGTTTCCCCGA 62.091 60.000 2.58 0.00 0.00 5.14
678 1231 2.167693 ACAGAGACACGTCAACTCCAAA 59.832 45.455 0.00 0.00 0.00 3.28
717 1270 9.612066 AATTCAGCTTAAAGGAAACAAAATCAA 57.388 25.926 0.00 0.00 0.00 2.57
755 1308 4.947645 ACTTGTTGGTGAATGAATTGTGG 58.052 39.130 0.00 0.00 0.00 4.17
886 1439 3.788142 AGTGTGAGATGGGGATGGTTTAT 59.212 43.478 0.00 0.00 0.00 1.40
902 1455 1.605232 CATGTTGCTTGCAGAGTGTGA 59.395 47.619 0.00 0.00 0.00 3.58
1031 1586 2.554032 AGCTAACAACAGTGTGCATTCC 59.446 45.455 0.00 0.00 38.27 3.01
1106 1661 7.148188 CCGGATCAACCAATCCTAATGATAATG 60.148 40.741 0.00 0.00 42.68 1.90
1109 1664 5.309543 ACCGGATCAACCAATCCTAATGATA 59.690 40.000 9.46 0.00 42.68 2.15
1692 2251 2.359107 ACGGCGTCGAGGTACAGA 60.359 61.111 20.03 0.00 40.11 3.41
1788 2347 1.599047 CACGACCAGAGGCTCCATT 59.401 57.895 11.71 0.00 0.00 3.16
1945 2504 0.947244 CAAGACACGAAAAGCCAGCT 59.053 50.000 0.00 0.00 0.00 4.24
1986 2545 2.354729 CCCTCGGCAATCACCCAA 59.645 61.111 0.00 0.00 0.00 4.12
2041 2600 1.152984 CACACAGGAACACCAGCCA 60.153 57.895 0.00 0.00 0.00 4.75
2061 2620 6.447162 CAAGAATCTGTAAACCTTCCCAAAC 58.553 40.000 0.00 0.00 0.00 2.93
2249 2829 5.971202 GCACACGAAATCCCAATTAACTATG 59.029 40.000 0.00 0.00 0.00 2.23
2352 2934 8.168626 CAGGAAGCTAAAACTTCAAAACAAAAC 58.831 33.333 6.61 0.00 46.48 2.43
2357 2939 7.222805 CCTTTCAGGAAGCTAAAACTTCAAAAC 59.777 37.037 6.61 0.00 46.48 2.43
2358 2940 7.123547 TCCTTTCAGGAAGCTAAAACTTCAAAA 59.876 33.333 6.61 3.62 46.48 2.44
2359 2941 6.605594 TCCTTTCAGGAAGCTAAAACTTCAAA 59.394 34.615 6.61 0.00 46.48 2.69
2360 2942 6.126409 TCCTTTCAGGAAGCTAAAACTTCAA 58.874 36.000 6.61 0.00 46.48 2.69
2413 2995 6.368779 TCTAGCCTACTTCTTGCCTTTTTA 57.631 37.500 0.00 0.00 0.00 1.52
2542 3124 2.261671 GTGAGTGGGTCGCATCGT 59.738 61.111 0.00 0.00 35.56 3.73
2625 3207 3.686016 AGAGAGAAAGAGAGAGAAGCGT 58.314 45.455 0.00 0.00 0.00 5.07
2629 3211 4.770010 GTGGGAAGAGAGAAAGAGAGAGAA 59.230 45.833 0.00 0.00 0.00 2.87
2647 3230 1.074775 GTTGACCATGGCAGTGGGA 59.925 57.895 13.04 0.00 43.77 4.37
2651 3234 1.228245 AAGCGTTGACCATGGCAGT 60.228 52.632 13.04 0.00 0.00 4.40
2851 3434 2.109739 AACGGTTGCAACACTCGCA 61.110 52.632 29.55 0.00 37.68 5.10
2880 3463 7.989741 TGAAGCATTTTTAATCTTGGGTTGAAA 59.010 29.630 0.00 0.00 0.00 2.69
3144 3729 3.556775 TGTAGCAAAAACACAGACGGTAC 59.443 43.478 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.