Multiple sequence alignment - TraesCS4B01G072600

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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 TraesCS4B01G072600 chr4B 100.000 2371 0 0 1 2371 68090117 68092487 0.000000e+00 4379.0
1 TraesCS4B01G072600 chr4B 84.288 681 58 25 1 672 68000592 68001232 9.310000e-174 619.0
2 TraesCS4B01G072600 chr4D 94.893 1547 60 7 834 2370 46592180 46593717 0.000000e+00 2401.0
3 TraesCS4B01G072600 chr4A 93.097 1492 71 6 881 2371 552413747 552412287 0.000000e+00 2156.0
4 TraesCS4B01G072600 chr1B 78.883 895 105 45 1 835 369229719 369228849 1.610000e-146 529.0
5 TraesCS4B01G072600 chr3B 81.286 700 70 31 9 691 810322514 810321859 5.850000e-141 510.0
6 TraesCS4B01G072600 chr3B 84.058 69 8 3 766 832 144190439 144190506 1.970000e-06 63.9
7 TraesCS4B01G072600 chr2D 81.000 700 84 32 80 759 464011774 464012444 5.850000e-141 510.0
8 TraesCS4B01G072600 chr2D 83.135 504 58 18 186 681 488224909 488225393 3.620000e-118 435.0
9 TraesCS4B01G072600 chr2D 90.722 97 9 0 9 105 464011672 464011768 1.910000e-26 130.0
10 TraesCS4B01G072600 chr6D 80.176 681 80 31 186 837 368212058 368211404 2.150000e-125 459.0
11 TraesCS4B01G072600 chr6D 75.514 584 93 33 1 546 75024876 75024305 8.470000e-60 241.0
12 TraesCS4B01G072600 chr5A 79.688 640 77 30 230 835 302711497 302712117 1.700000e-111 412.0
13 TraesCS4B01G072600 chr5A 80.864 486 55 18 267 734 472912277 472911812 4.850000e-92 348.0
14 TraesCS4B01G072600 chr5A 76.215 576 85 37 1 540 43392268 43391709 8.410000e-65 257.0
15 TraesCS4B01G072600 chr5A 74.221 578 97 41 1 540 415160793 415161356 6.690000e-46 195.0
16 TraesCS4B01G072600 chr5B 79.080 674 76 32 186 829 230885636 230886274 1.020000e-108 403.0
17 TraesCS4B01G072600 chr5B 75.338 592 78 37 302 832 396430344 396430928 3.070000e-54 222.0
18 TraesCS4B01G072600 chr2B 81.128 514 79 12 186 684 795920757 795920247 1.710000e-106 396.0
19 TraesCS4B01G072600 chr3D 78.253 584 86 23 291 835 501074367 501073786 1.050000e-88 337.0
20 TraesCS4B01G072600 chr3D 82.134 403 56 11 295 682 6515196 6514795 4.880000e-87 331.0
21 TraesCS4B01G072600 chr6A 76.224 572 91 32 1 546 416544116 416543564 6.500000e-66 261.0
22 TraesCS4B01G072600 chr7A 74.443 583 93 34 1 540 537514550 537515119 1.440000e-47 200.0
23 TraesCS4B01G072600 chr7A 75.406 431 59 20 443 835 530519627 530519206 5.240000e-37 165.0
24 TraesCS4B01G072600 chr7D 89.216 102 7 1 4 105 395971089 395970992 8.900000e-25 124.0
25 TraesCS4B01G072600 chr3A 88.571 105 8 1 1 105 617007231 617007131 8.900000e-25 124.0


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 TraesCS4B01G072600 chr4B 68090117 68092487 2370 False 4379 4379 100.000 1 2371 1 chr4B.!!$F2 2370
1 TraesCS4B01G072600 chr4B 68000592 68001232 640 False 619 619 84.288 1 672 1 chr4B.!!$F1 671
2 TraesCS4B01G072600 chr4D 46592180 46593717 1537 False 2401 2401 94.893 834 2370 1 chr4D.!!$F1 1536
3 TraesCS4B01G072600 chr4A 552412287 552413747 1460 True 2156 2156 93.097 881 2371 1 chr4A.!!$R1 1490
4 TraesCS4B01G072600 chr1B 369228849 369229719 870 True 529 529 78.883 1 835 1 chr1B.!!$R1 834
5 TraesCS4B01G072600 chr3B 810321859 810322514 655 True 510 510 81.286 9 691 1 chr3B.!!$R1 682
6 TraesCS4B01G072600 chr2D 464011672 464012444 772 False 320 510 85.861 9 759 2 chr2D.!!$F2 750
7 TraesCS4B01G072600 chr6D 368211404 368212058 654 True 459 459 80.176 186 837 1 chr6D.!!$R2 651
8 TraesCS4B01G072600 chr6D 75024305 75024876 571 True 241 241 75.514 1 546 1 chr6D.!!$R1 545
9 TraesCS4B01G072600 chr5A 302711497 302712117 620 False 412 412 79.688 230 835 1 chr5A.!!$F1 605
10 TraesCS4B01G072600 chr5A 43391709 43392268 559 True 257 257 76.215 1 540 1 chr5A.!!$R1 539
11 TraesCS4B01G072600 chr5B 230885636 230886274 638 False 403 403 79.080 186 829 1 chr5B.!!$F1 643
12 TraesCS4B01G072600 chr5B 396430344 396430928 584 False 222 222 75.338 302 832 1 chr5B.!!$F2 530
13 TraesCS4B01G072600 chr2B 795920247 795920757 510 True 396 396 81.128 186 684 1 chr2B.!!$R1 498
14 TraesCS4B01G072600 chr3D 501073786 501074367 581 True 337 337 78.253 291 835 1 chr3D.!!$R2 544
15 TraesCS4B01G072600 chr6A 416543564 416544116 552 True 261 261 76.224 1 546 1 chr6A.!!$R1 545

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
687 1025 0.039798 TTGCGTAGTCTCACGTGGTC 60.04 55.0 17.0 6.57 43.79 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1522 1894 1.615384 GCCATGATAGCAATCCTCCCC 60.615 57.143 0.0 0.0 0.0 4.81 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
27 28 1.964373 CCGTTAGCAAACCCAGCGT 60.964 57.895 0.00 0.00 37.01 5.07
112 175 0.094730 CCCGCTCGATCGTTTGTTTC 59.905 55.000 15.94 0.00 0.00 2.78
119 183 4.841306 GCTCGATCGTTTGTTTCTTCTTTC 59.159 41.667 15.94 0.00 0.00 2.62
120 184 5.338614 TCGATCGTTTGTTTCTTCTTTCC 57.661 39.130 15.94 0.00 0.00 3.13
140 206 2.497273 CCCTTCCCCAAAATTGCTACAG 59.503 50.000 0.00 0.00 0.00 2.74
177 243 9.729281 TTTCTCTTAGTATAAAAATCAACCGGT 57.271 29.630 0.00 0.00 0.00 5.28
178 244 9.729281 TTCTCTTAGTATAAAAATCAACCGGTT 57.271 29.630 15.86 15.86 0.00 4.44
179 245 9.729281 TCTCTTAGTATAAAAATCAACCGGTTT 57.271 29.630 19.55 4.38 0.00 3.27
182 248 9.563898 CTTAGTATAAAAATCAACCGGTTTTCC 57.436 33.333 19.55 1.40 0.00 3.13
183 249 6.927416 AGTATAAAAATCAACCGGTTTTCCC 58.073 36.000 19.55 1.05 36.42 3.97
184 250 6.722590 AGTATAAAAATCAACCGGTTTTCCCT 59.277 34.615 19.55 3.42 36.42 4.20
614 950 7.675161 AGGGAAAAAGGAAAGATGAAAGAAA 57.325 32.000 0.00 0.00 0.00 2.52
687 1025 0.039798 TTGCGTAGTCTCACGTGGTC 60.040 55.000 17.00 6.57 43.79 4.02
689 1027 1.904852 GCGTAGTCTCACGTGGTCGA 61.905 60.000 17.00 7.35 43.79 4.20
796 1158 2.354188 GCGCCCGTTTGTGGAAAC 60.354 61.111 0.00 0.00 38.51 2.78
801 1163 0.310854 CCCGTTTGTGGAAACAGCTC 59.689 55.000 0.00 0.00 44.46 4.09
869 1233 1.601419 CCTGACGCGAGGTTTCCCTA 61.601 60.000 15.93 0.00 42.86 3.53
875 1239 1.202336 CGCGAGGTTTCCCTACGTAAT 60.202 52.381 0.00 0.00 42.86 1.89
876 1240 2.736400 CGCGAGGTTTCCCTACGTAATT 60.736 50.000 0.00 0.00 42.86 1.40
877 1241 2.606272 GCGAGGTTTCCCTACGTAATTG 59.394 50.000 0.00 0.00 42.86 2.32
918 1287 1.606224 GCCCAGAACTGCACCATTTTG 60.606 52.381 0.00 0.00 0.00 2.44
1125 1494 4.147449 CGTCGCATCCCTGCCTCA 62.147 66.667 0.00 0.00 46.07 3.86
1194 1563 0.105964 CCCCGATACGCCAGAAATCA 59.894 55.000 0.00 0.00 0.00 2.57
1231 1600 6.042781 TGACTGTAACAAGTGGTCTTAATCCT 59.957 38.462 0.00 0.00 32.07 3.24
1267 1636 4.404098 GTTGATGGGGTCGCCGGT 62.404 66.667 1.90 0.00 0.00 5.28
1478 1848 7.126398 GGAACGTTCTAGATGTGAAATAATGC 58.874 38.462 26.32 0.84 0.00 3.56
1522 1894 6.141685 CGTGATGATTTGATATGTGTGCATTG 59.858 38.462 0.00 0.00 36.58 2.82
1670 2042 8.721133 ATGGAAGTATGTATATGTCCAGTGTA 57.279 34.615 10.42 0.00 38.49 2.90
1671 2043 8.721133 TGGAAGTATGTATATGTCCAGTGTAT 57.279 34.615 0.00 0.00 31.61 2.29
1803 2175 4.776837 TCAAGGGGTTAAAATGCATGATGT 59.223 37.500 0.00 0.00 0.00 3.06
1970 2342 8.064814 GCTTATTGCACATTAGTCTAGCTTAAC 58.935 37.037 0.00 0.00 42.31 2.01
2065 2438 8.831715 AACCTTGGTCATTATTTGCTTTAAAG 57.168 30.769 11.02 11.02 0.00 1.85
2086 2459 4.323417 AGTGCGAAATGGTATTTGTCTGA 58.677 39.130 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.559330 GGTTTGCTAACGGGCACG 59.441 61.111 6.92 6.92 42.27 5.34
27 28 4.967271 TGCAAGCGACGCAGCAGA 62.967 61.111 28.36 12.91 37.05 4.26
96 101 4.391140 AAGAAGAAACAAACGATCGAGC 57.609 40.909 24.34 0.00 0.00 5.03
112 175 4.803924 GCAATTTTGGGGAAGGGAAAGAAG 60.804 45.833 0.00 0.00 0.00 2.85
119 183 2.497273 CTGTAGCAATTTTGGGGAAGGG 59.503 50.000 0.00 0.00 0.00 3.95
120 184 3.165071 ACTGTAGCAATTTTGGGGAAGG 58.835 45.455 0.00 0.00 0.00 3.46
161 227 8.647256 TTAGGGAAAACCGGTTGATTTTTATA 57.353 30.769 23.08 4.24 46.96 0.98
163 229 6.973460 TTAGGGAAAACCGGTTGATTTTTA 57.027 33.333 23.08 7.08 46.96 1.52
164 230 5.873146 TTAGGGAAAACCGGTTGATTTTT 57.127 34.783 23.08 11.12 46.96 1.94
165 231 5.873146 TTTAGGGAAAACCGGTTGATTTT 57.127 34.783 23.08 11.56 46.96 1.82
166 232 5.873146 TTTTAGGGAAAACCGGTTGATTT 57.127 34.783 23.08 11.98 46.96 2.17
167 233 5.873146 TTTTTAGGGAAAACCGGTTGATT 57.127 34.783 23.08 12.83 46.96 2.57
674 1012 0.822532 AACCTCGACCACGTGAGACT 60.823 55.000 19.30 0.00 40.69 3.24
687 1025 1.476891 TCAAGGGAGAATCGAACCTCG 59.523 52.381 10.16 0.00 42.10 4.63
689 1027 2.234908 CACTCAAGGGAGAATCGAACCT 59.765 50.000 0.00 0.00 44.26 3.50
739 1087 1.472728 GCCGGTCCATCTCAACGTTAT 60.473 52.381 1.90 0.00 0.00 1.89
740 1088 0.108520 GCCGGTCCATCTCAACGTTA 60.109 55.000 1.90 0.00 0.00 3.18
754 1102 2.687566 CCCTCCTAACTGGCCGGT 60.688 66.667 12.85 12.85 35.26 5.28
796 1158 1.493950 CTTTGCGCCCGATAGAGCTG 61.494 60.000 4.18 0.00 39.76 4.24
801 1163 3.279875 GCCCTTTGCGCCCGATAG 61.280 66.667 4.18 0.00 0.00 2.08
847 1210 2.920912 AAACCTCGCGTCAGGGGA 60.921 61.111 17.27 0.00 37.96 4.81
869 1233 3.644738 CCCATCTACCCCTACAATTACGT 59.355 47.826 0.00 0.00 0.00 3.57
875 1239 0.045008 TGGCCCATCTACCCCTACAA 59.955 55.000 0.00 0.00 0.00 2.41
876 1240 0.399949 CTGGCCCATCTACCCCTACA 60.400 60.000 0.00 0.00 0.00 2.74
877 1241 0.105142 TCTGGCCCATCTACCCCTAC 60.105 60.000 0.00 0.00 0.00 3.18
918 1287 2.086869 GGCGAGGTTTAGGGTTTTACC 58.913 52.381 0.00 0.00 37.60 2.85
1194 1563 5.213891 TGTTACAGTCACATCACATCACT 57.786 39.130 0.00 0.00 0.00 3.41
1522 1894 1.615384 GCCATGATAGCAATCCTCCCC 60.615 57.143 0.00 0.00 0.00 4.81
1663 2035 9.988350 GACATACTCAAATACAAAATACACTGG 57.012 33.333 0.00 0.00 0.00 4.00
1695 2067 9.890629 ACTATAGTCATCAAGCAATTTCAACTA 57.109 29.630 0.00 0.00 0.00 2.24
1803 2175 8.801299 ACAATTCATACATTATGTGGACAAACA 58.199 29.630 8.26 0.00 37.45 2.83
1835 2207 2.755836 GTGTCGAAACAACACTGCAT 57.244 45.000 0.00 0.00 42.93 3.96
2057 2430 6.364976 ACAAATACCATTTCGCACTTTAAAGC 59.635 34.615 15.24 2.21 0.00 3.51
2065 2438 4.678509 TCAGACAAATACCATTTCGCAC 57.321 40.909 0.00 0.00 0.00 5.34
2086 2459 5.507315 GGGCAATAAGCTAACGCACATAATT 60.507 40.000 0.00 0.00 44.79 1.40


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

AutoCloner maintained by Alex Coulton.