Multiple sequence alignment - TraesCS4D01G302000

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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 TraesCS4D01G302000 chr4D 100.000 2679 0 0 507 3185 470122339 470119661 0.000000e+00 4948.0
1 TraesCS4D01G302000 chr4D 90.136 1328 110 10 864 2185 470138498 470137186 0.000000e+00 1707.0
2 TraesCS4D01G302000 chr4D 100.000 274 0 0 1 274 470122845 470122572 1.020000e-139 507.0
3 TraesCS4D01G302000 chr4D 83.226 155 17 5 649 800 470130624 470130476 1.990000e-27 134.0
4 TraesCS4D01G302000 chr4D 85.714 112 13 2 2673 2784 133626564 133626672 7.220000e-22 115.0
5 TraesCS4D01G302000 chr4A 95.517 1740 53 13 611 2340 677958906 677957182 0.000000e+00 2758.0
6 TraesCS4D01G302000 chr4A 90.090 1332 111 12 864 2189 677989004 677987688 0.000000e+00 1709.0
7 TraesCS4D01G302000 chr4A 89.430 1334 115 12 864 2186 677969653 677968335 0.000000e+00 1659.0
8 TraesCS4D01G302000 chr4A 94.688 866 23 12 2329 3185 677957086 677956235 0.000000e+00 1323.0
9 TraesCS4D01G302000 chr4A 89.565 230 12 4 1 229 677959630 677959412 6.730000e-72 281.0
10 TraesCS4D01G302000 chr4A 91.429 105 9 0 508 612 677959092 677958988 9.210000e-31 145.0
11 TraesCS4D01G302000 chr4A 84.821 112 14 2 2673 2784 427505753 427505645 3.360000e-20 110.0
12 TraesCS4D01G302000 chr4A 90.476 84 7 1 722 804 677989103 677989020 3.360000e-20 110.0
13 TraesCS4D01G302000 chr4B 92.911 1721 91 11 633 2339 591909728 591908025 0.000000e+00 2473.0
14 TraesCS4D01G302000 chr4B 91.794 1511 87 17 750 2249 591539901 591538417 0.000000e+00 2069.0
15 TraesCS4D01G302000 chr4B 90.841 1332 101 13 864 2189 592079737 592078421 0.000000e+00 1764.0
16 TraesCS4D01G302000 chr4B 90.430 1327 99 14 867 2189 592188170 592186868 0.000000e+00 1722.0
17 TraesCS4D01G302000 chr4B 90.924 1245 98 6 943 2185 591955113 591953882 0.000000e+00 1659.0
18 TraesCS4D01G302000 chr4B 91.768 413 16 6 2786 3185 591907630 591907223 2.770000e-155 558.0
19 TraesCS4D01G302000 chr4B 94.553 257 10 2 2932 3185 591537607 591537352 8.280000e-106 394.0
20 TraesCS4D01G302000 chr4B 89.427 227 23 1 526 752 591540448 591540223 5.200000e-73 285.0
21 TraesCS4D01G302000 chr4B 91.579 190 16 0 2458 2647 591907830 591908019 2.440000e-66 263.0
22 TraesCS4D01G302000 chr4B 83.624 287 30 9 1 273 591911375 591911092 1.470000e-63 254.0
23 TraesCS4D01G302000 chr4B 89.583 192 17 2 2458 2647 591537954 591538144 1.140000e-59 241.0
24 TraesCS4D01G302000 chr4B 94.872 117 6 0 2342 2458 591907673 591907789 1.950000e-42 183.0
25 TraesCS4D01G302000 chr4B 88.660 97 4 1 2362 2458 591537821 591537910 9.340000e-21 111.0
26 TraesCS4D01G302000 chr5D 85.965 114 8 6 2673 2786 276919833 276919728 7.220000e-22 115.0
27 TraesCS4D01G302000 chr5A 85.714 112 10 3 2674 2784 41454636 41454742 2.600000e-21 113.0
28 TraesCS4D01G302000 chr3D 88.889 90 8 2 2665 2752 89257968 89258057 3.360000e-20 110.0
29 TraesCS4D01G302000 chr3D 82.569 109 13 4 2665 2771 11430726 11430830 1.220000e-14 91.6
30 TraesCS4D01G302000 chr3D 87.500 80 6 1 2677 2752 89203141 89203220 4.380000e-14 89.8
31 TraesCS4D01G302000 chr5B 82.353 119 12 5 2665 2783 485878316 485878425 9.410000e-16 95.3


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 TraesCS4D01G302000 chr4D 470119661 470122845 3184 True 2727.50 4948 100.000000 1 3185 2 chr4D.!!$R3 3184
1 TraesCS4D01G302000 chr4D 470137186 470138498 1312 True 1707.00 1707 90.136000 864 2185 1 chr4D.!!$R2 1321
2 TraesCS4D01G302000 chr4A 677968335 677969653 1318 True 1659.00 1659 89.430000 864 2186 1 chr4A.!!$R2 1322
3 TraesCS4D01G302000 chr4A 677956235 677959630 3395 True 1126.75 2758 92.799750 1 3185 4 chr4A.!!$R3 3184
4 TraesCS4D01G302000 chr4A 677987688 677989103 1415 True 909.50 1709 90.283000 722 2189 2 chr4A.!!$R4 1467
5 TraesCS4D01G302000 chr4B 592078421 592079737 1316 True 1764.00 1764 90.841000 864 2189 1 chr4B.!!$R2 1325
6 TraesCS4D01G302000 chr4B 592186868 592188170 1302 True 1722.00 1722 90.430000 867 2189 1 chr4B.!!$R3 1322
7 TraesCS4D01G302000 chr4B 591953882 591955113 1231 True 1659.00 1659 90.924000 943 2185 1 chr4B.!!$R1 1242
8 TraesCS4D01G302000 chr4B 591907223 591911375 4152 True 1095.00 2473 89.434333 1 3185 3 chr4B.!!$R5 3184
9 TraesCS4D01G302000 chr4B 591537352 591540448 3096 True 916.00 2069 91.924667 526 3185 3 chr4B.!!$R4 2659

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
84 95 1.446272 GTCTCCCTCGTTGCTTCCG 60.446 63.158 0.0 0.0 0.00 4.3 F
1009 2643 1.302511 GGACACGTCATGGCAACCT 60.303 57.895 0.0 0.0 38.59 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1782 3416 0.254178 AGTCGCTCTTGATGGCCATT 59.746 50.0 21.84 3.11 0.0 3.16 R
2531 4457 0.108898 CCGCTGTCTCTCTGAACAGG 60.109 60.0 9.36 1.60 0.0 4.00 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
77 88 1.982938 CCCCTTCGTCTCCCTCGTT 60.983 63.158 0.00 0.00 0.00 3.85
84 95 1.446272 GTCTCCCTCGTTGCTTCCG 60.446 63.158 0.00 0.00 0.00 4.30
98 109 2.296692 CTTCCGCGCCATTTGTCTCG 62.297 60.000 0.00 0.00 0.00 4.04
101 112 2.802667 CGCGCCATTTGTCTCGGAG 61.803 63.158 0.00 0.00 0.00 4.63
175 186 6.291955 CGCGTCGCCTTCTTCTTTTATATTTA 60.292 38.462 12.44 0.00 0.00 1.40
211 222 8.049655 TCAATTCAATCACGAAAATGGACATA 57.950 30.769 0.00 0.00 0.00 2.29
237 248 4.201950 CCTTATCATCTGGCCGAAAACAAG 60.202 45.833 0.00 0.00 0.00 3.16
242 258 4.098654 TCATCTGGCCGAAAACAAGAAAAA 59.901 37.500 0.00 0.00 0.00 1.94
243 259 3.776340 TCTGGCCGAAAACAAGAAAAAC 58.224 40.909 0.00 0.00 0.00 2.43
245 261 1.855978 GGCCGAAAACAAGAAAAACGG 59.144 47.619 0.00 0.00 41.44 4.44
249 265 3.921630 CCGAAAACAAGAAAAACGGTGTT 59.078 39.130 0.00 0.00 34.69 3.32
250 266 4.201542 CCGAAAACAAGAAAAACGGTGTTG 60.202 41.667 0.00 0.00 33.95 3.33
260 276 8.690840 CAAGAAAAACGGTGTTGAATATTTCTC 58.309 33.333 6.72 0.00 35.48 2.87
273 289 1.839424 ATTTCTCCCCTTTGCCTTCG 58.161 50.000 0.00 0.00 0.00 3.79
600 981 3.876914 CCTAACTCTTGCGCCATTATCAA 59.123 43.478 4.18 0.00 0.00 2.57
696 1981 2.436646 AGCGCTCCGGGACAAATG 60.437 61.111 2.64 0.00 0.00 2.32
790 2400 5.280215 CCTCCTTCCTTTATGTTGACTGACT 60.280 44.000 0.00 0.00 0.00 3.41
1009 2643 1.302511 GGACACGTCATGGCAACCT 60.303 57.895 0.00 0.00 38.59 3.50
1203 2837 4.424566 TACTTCGTCCACGGCGGC 62.425 66.667 13.24 0.00 40.29 6.53
1239 2873 2.498248 GCGCTGCTCCAGATCTCA 59.502 61.111 0.00 0.00 32.44 3.27
1671 3305 1.375396 CGTTGAGGTCGCCATGGAA 60.375 57.895 18.40 0.00 0.00 3.53
1782 3416 1.446099 GATCGTGTGCTTGCTCGGA 60.446 57.895 0.00 0.00 0.00 4.55
2215 3849 1.191096 CAAGTTTTGTGTGCGACTGC 58.809 50.000 0.00 0.00 43.20 4.40
2249 4071 6.015434 TGTGGCTGATATACTGGTGTATAGTG 60.015 42.308 0.00 0.00 42.71 2.74
2287 4109 7.497579 TGCCTTTCATACATTGTGTACGATATT 59.502 33.333 0.00 0.00 35.42 1.28
2288 4110 7.798516 GCCTTTCATACATTGTGTACGATATTG 59.201 37.037 0.00 0.00 35.42 1.90
2297 4119 9.157104 ACATTGTGTACGATATTGTGTTTCATA 57.843 29.630 5.81 0.00 0.00 2.15
2370 4296 4.627284 TGGGTCGGTTTCTGAAATCTAA 57.373 40.909 11.31 0.00 0.00 2.10
2549 4475 0.884514 TCCTGTTCAGAGAGACAGCG 59.115 55.000 1.00 0.00 0.00 5.18
2635 4561 3.318839 TGGGCAAGAACTGAACATTTCTG 59.681 43.478 7.88 4.87 31.81 3.02
2750 4724 9.474920 TTTTGTGGTTGATTTCATTAATCTCAC 57.525 29.630 0.00 0.00 42.63 3.51
2830 4877 5.640147 AGAACAAACCCATTCCATCAACTA 58.360 37.500 0.00 0.00 0.00 2.24
2917 4978 1.598130 GCTGAAGACAACGCCTGGT 60.598 57.895 0.00 0.00 0.00 4.00
2923 4984 1.267121 AGACAACGCCTGGTGAGTAT 58.733 50.000 15.34 6.58 0.00 2.12
2924 4985 2.453521 AGACAACGCCTGGTGAGTATA 58.546 47.619 15.34 0.00 0.00 1.47
2925 4986 2.829720 AGACAACGCCTGGTGAGTATAA 59.170 45.455 15.34 0.00 0.00 0.98
2926 4987 3.259876 AGACAACGCCTGGTGAGTATAAA 59.740 43.478 15.34 0.00 0.00 1.40
2936 5001 5.523916 CCTGGTGAGTATAAATTTGACTCCG 59.476 44.000 22.50 13.24 39.10 4.63
2988 5054 3.886505 GTGGGGAATACAGACACAACAAA 59.113 43.478 0.00 0.00 32.58 2.83
3144 5212 3.135994 GCTGTTCTTTAACCCTTCGTGA 58.864 45.455 0.00 0.00 34.49 4.35
3147 5215 3.135994 GTTCTTTAACCCTTCGTGAGCA 58.864 45.455 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 95 2.464459 CCTCCGAGACAAATGGCGC 61.464 63.158 0.00 0.00 0.00 6.53
90 101 0.966920 GTGACCTCCTCCGAGACAAA 59.033 55.000 0.00 0.00 38.52 2.83
98 109 3.827898 CTCGCCGTGACCTCCTCC 61.828 72.222 0.00 0.00 0.00 4.30
149 160 0.599204 AAAAGAAGAAGGCGACGCGA 60.599 50.000 15.93 0.00 0.00 5.87
175 186 6.649973 TCGTGATTGAATTGAATTGCCAAAAT 59.350 30.769 0.00 0.00 0.00 1.82
211 222 2.088104 TCGGCCAGATGATAAGGAGT 57.912 50.000 2.24 0.00 0.00 3.85
237 248 6.584942 GGGAGAAATATTCAACACCGTTTTTC 59.415 38.462 0.00 0.00 0.00 2.29
242 258 3.265995 AGGGGAGAAATATTCAACACCGT 59.734 43.478 0.00 0.00 37.05 4.83
243 259 3.886123 AGGGGAGAAATATTCAACACCG 58.114 45.455 0.00 0.00 37.05 4.94
245 261 5.410924 GCAAAGGGGAGAAATATTCAACAC 58.589 41.667 0.00 0.00 0.00 3.32
249 265 4.608170 AGGCAAAGGGGAGAAATATTCA 57.392 40.909 0.00 0.00 0.00 2.57
250 266 4.036852 CGAAGGCAAAGGGGAGAAATATTC 59.963 45.833 0.00 0.00 0.00 1.75
531 583 0.969409 GGCATGAAGCTTTGAGGGCT 60.969 55.000 0.00 0.00 44.79 5.19
600 981 8.978564 TCGTGCATGTTTAATATTCATTTGTT 57.021 26.923 5.68 0.00 0.00 2.83
925 2545 1.064017 TGGACTGGCTCCTGTTTGTTT 60.064 47.619 0.00 0.00 40.26 2.83
1009 2643 2.611971 CCGAACTGGCACTAGCAGTTAA 60.612 50.000 12.47 0.00 44.61 2.01
1774 3408 0.323269 TTGATGGCCATTCCGAGCAA 60.323 50.000 21.84 15.14 37.80 3.91
1782 3416 0.254178 AGTCGCTCTTGATGGCCATT 59.746 50.000 21.84 3.11 0.00 3.16
1893 3527 0.256752 CCATGATGCCCAGGTTGAGA 59.743 55.000 0.00 0.00 0.00 3.27
2152 3786 1.079057 GCTCCAGGTCTCCGGTTTC 60.079 63.158 0.00 0.00 0.00 2.78
2210 3844 1.970917 GCCACACTACATGCGCAGTC 61.971 60.000 18.32 0.00 0.00 3.51
2215 3849 2.223537 TATCAGCCACACTACATGCG 57.776 50.000 0.00 0.00 0.00 4.73
2287 4109 6.816640 GTCTGTGCTACCTAATATGAAACACA 59.183 38.462 0.00 0.00 34.62 3.72
2288 4110 6.816640 TGTCTGTGCTACCTAATATGAAACAC 59.183 38.462 0.00 0.00 0.00 3.32
2297 4119 8.268850 CACTTAATTTGTCTGTGCTACCTAAT 57.731 34.615 0.00 0.00 0.00 1.73
2323 4145 9.930693 AAGGAAGTGAAAACTGAATAGTACTAG 57.069 33.333 8.85 0.00 35.69 2.57
2326 4148 7.094762 CCCAAGGAAGTGAAAACTGAATAGTAC 60.095 40.741 0.00 0.00 35.69 2.73
2370 4296 3.689347 TGAAGCAGCAATACTTGTCCAT 58.311 40.909 0.00 0.00 0.00 3.41
2531 4457 0.108898 CCGCTGTCTCTCTGAACAGG 60.109 60.000 9.36 1.60 0.00 4.00
2549 4475 1.802069 GTGGAACTCTTCTGCTGACC 58.198 55.000 0.00 0.00 0.00 4.02
2595 4521 5.853936 TGCCCATGAGTACAGTACAATATC 58.146 41.667 13.37 2.44 0.00 1.63
2635 4561 7.527457 GTGGAACTCACATTAGGTTACAATTC 58.473 38.462 0.00 0.00 45.39 2.17
2731 4705 7.396540 AGGTGGTGAGATTAATGAAATCAAC 57.603 36.000 0.00 0.00 45.58 3.18
2749 4723 7.913148 CTAGTATAGGGTCTCACATTAGGTGGT 60.913 44.444 0.00 0.00 40.65 4.16
2750 4724 6.434652 CTAGTATAGGGTCTCACATTAGGTGG 59.565 46.154 0.00 0.00 40.65 4.61
2917 4978 7.383687 ACTGAACGGAGTCAAATTTATACTCA 58.616 34.615 23.79 10.84 45.00 3.41
2923 4984 7.763356 TGAAAAACTGAACGGAGTCAAATTTA 58.237 30.769 0.00 0.00 45.00 1.40
2924 4985 6.626302 TGAAAAACTGAACGGAGTCAAATTT 58.374 32.000 0.00 0.00 45.00 1.82
2925 4986 6.202516 TGAAAAACTGAACGGAGTCAAATT 57.797 33.333 0.00 0.00 45.00 1.82
2926 4987 5.828299 TGAAAAACTGAACGGAGTCAAAT 57.172 34.783 0.00 0.00 45.00 2.32
2936 5001 3.365969 CCCGTGGCTATGAAAAACTGAAC 60.366 47.826 0.00 0.00 0.00 3.18
2988 5054 7.322664 CCTCTTTAACAATAACATGCACCAAT 58.677 34.615 0.00 0.00 0.00 3.16
3144 5212 5.186603 TCAGTAAATGACTCTGACAGATGCT 59.813 40.000 5.42 0.00 35.64 3.79
3147 5215 8.778358 GTTTTTCAGTAAATGACTCTGACAGAT 58.222 33.333 5.42 0.00 37.77 2.90


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

AutoCloner maintained by Alex Coulton.