Multiple sequence alignment - TraesCS2D01G247000

Loading Multiple Alignment...

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 TraesCS2D01G247000 chr2D 100.000 2243 0 0 1 2243 291443529 291441287 0 4143
1 TraesCS2D01G247000 chr2D 94.089 1252 62 8 992 2240 291774596 291775838 0 1892
2 TraesCS2D01G247000 chr2D 95.766 992 41 1 1 991 617757757 617756766 0 1598
3 TraesCS2D01G247000 chr2D 95.665 992 42 1 1 991 291451748 291450757 0 1592
4 TraesCS2D01G247000 chr5A 96.163 1251 44 4 992 2240 16545545 16546793 0 2041
5 TraesCS2D01G247000 chr7B 96.003 1251 46 4 992 2240 716785598 716786846 0 2030
6 TraesCS2D01G247000 chr7B 95.614 1254 51 4 992 2243 742947747 742946496 0 2008
7 TraesCS2D01G247000 chr7A 95.933 1254 47 4 992 2243 60167776 60166525 0 2030
8 TraesCS2D01G247000 chr7A 95.987 1246 46 4 992 2235 60085927 60087170 0 2021
9 TraesCS2D01G247000 chr1B 95.139 1255 56 5 992 2243 583560579 583559327 0 1975
10 TraesCS2D01G247000 chr1D 95.334 1243 52 5 992 2230 275779918 275781158 0 1969
11 TraesCS2D01G247000 chr1D 95.468 993 43 2 1 992 313003338 313004329 0 1583
12 TraesCS2D01G247000 chr6B 94.896 1254 60 4 992 2243 388227170 388225919 0 1958
13 TraesCS2D01G247000 chr5D 96.057 989 36 2 4 991 213721101 213720115 0 1607
14 TraesCS2D01G247000 chr5D 95.473 994 42 3 1 992 372124056 372125048 0 1583
15 TraesCS2D01G247000 chr7D 95.596 999 37 6 1 992 146337279 146336281 0 1594
16 TraesCS2D01G247000 chr7D 95.582 996 39 4 1 991 130391801 130390806 0 1591
17 TraesCS2D01G247000 chr6D 95.758 990 39 3 3 989 115613623 115614612 0 1592
18 TraesCS2D01G247000 chr4D 95.565 992 41 2 1 991 274143775 274142786 0 1585


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 TraesCS2D01G247000 chr2D 291441287 291443529 2242 True 4143 4143 100.000 1 2243 1 chr2D.!!$R1 2242
1 TraesCS2D01G247000 chr2D 291774596 291775838 1242 False 1892 1892 94.089 992 2240 1 chr2D.!!$F1 1248
2 TraesCS2D01G247000 chr2D 617756766 617757757 991 True 1598 1598 95.766 1 991 1 chr2D.!!$R3 990
3 TraesCS2D01G247000 chr2D 291450757 291451748 991 True 1592 1592 95.665 1 991 1 chr2D.!!$R2 990
4 TraesCS2D01G247000 chr5A 16545545 16546793 1248 False 2041 2041 96.163 992 2240 1 chr5A.!!$F1 1248
5 TraesCS2D01G247000 chr7B 716785598 716786846 1248 False 2030 2030 96.003 992 2240 1 chr7B.!!$F1 1248
6 TraesCS2D01G247000 chr7B 742946496 742947747 1251 True 2008 2008 95.614 992 2243 1 chr7B.!!$R1 1251
7 TraesCS2D01G247000 chr7A 60166525 60167776 1251 True 2030 2030 95.933 992 2243 1 chr7A.!!$R1 1251
8 TraesCS2D01G247000 chr7A 60085927 60087170 1243 False 2021 2021 95.987 992 2235 1 chr7A.!!$F1 1243
9 TraesCS2D01G247000 chr1B 583559327 583560579 1252 True 1975 1975 95.139 992 2243 1 chr1B.!!$R1 1251
10 TraesCS2D01G247000 chr1D 275779918 275781158 1240 False 1969 1969 95.334 992 2230 1 chr1D.!!$F1 1238
11 TraesCS2D01G247000 chr1D 313003338 313004329 991 False 1583 1583 95.468 1 992 1 chr1D.!!$F2 991
12 TraesCS2D01G247000 chr6B 388225919 388227170 1251 True 1958 1958 94.896 992 2243 1 chr6B.!!$R1 1251
13 TraesCS2D01G247000 chr5D 213720115 213721101 986 True 1607 1607 96.057 4 991 1 chr5D.!!$R1 987
14 TraesCS2D01G247000 chr5D 372124056 372125048 992 False 1583 1583 95.473 1 992 1 chr5D.!!$F1 991
15 TraesCS2D01G247000 chr7D 146336281 146337279 998 True 1594 1594 95.596 1 992 1 chr7D.!!$R2 991
16 TraesCS2D01G247000 chr7D 130390806 130391801 995 True 1591 1591 95.582 1 991 1 chr7D.!!$R1 990
17 TraesCS2D01G247000 chr6D 115613623 115614612 989 False 1592 1592 95.758 3 989 1 chr6D.!!$F1 986
18 TraesCS2D01G247000 chr4D 274142786 274143775 989 True 1585 1585 95.565 1 991 1 chr4D.!!$R1 990

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
74 75 0.319211 GTTGACGTGTCGATCCCACA 60.319 55.0 0.0 0.32 33.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 2437 0.61326 TCCCGGATGTATAGGCATGC 59.387 55.0 9.9 9.9 34.48 4.06 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
67 68 1.009335 CACCGAGTTGACGTGTCGA 60.009 57.895 0.00 0.00 35.70 4.20
74 75 0.319211 GTTGACGTGTCGATCCCACA 60.319 55.000 0.00 0.32 33.00 4.17
88 89 4.023707 CGATCCCACAGAAAATCCTAATGC 60.024 45.833 0.00 0.00 0.00 3.56
138 139 2.939103 GAGTTTCATGATTCGGTCCCAG 59.061 50.000 0.00 0.00 0.00 4.45
177 178 6.442952 TGTGTGTAATGGTTAGATTTTGTGC 58.557 36.000 0.00 0.00 0.00 4.57
197 198 3.306613 GCGGAGGCTATATATACCCCTT 58.693 50.000 8.08 0.00 35.83 3.95
382 385 5.392995 TCTTCTTTCCACCAAATCCAATCA 58.607 37.500 0.00 0.00 0.00 2.57
394 397 7.883833 CACCAAATCCAATCATATGAGAGAGAT 59.116 37.037 11.78 7.81 0.00 2.75
405 408 8.071177 TCATATGAGAGAGATTTGAGTGTTGA 57.929 34.615 0.00 0.00 0.00 3.18
452 455 5.366186 AGAGCTAGGAGTTCATCATCAACAT 59.634 40.000 0.00 0.00 0.00 2.71
468 471 6.601613 TCATCAACATACCATTTGTTACCTCC 59.398 38.462 0.00 0.00 35.61 4.30
550 553 3.699538 GGAGTTGAACCAAGGAGTTTGTT 59.300 43.478 0.00 0.00 34.87 2.83
564 567 4.336280 GAGTTTGTTAGGGCAAGGAGATT 58.664 43.478 0.00 0.00 0.00 2.40
637 640 1.477558 CCATGGTGGGATAGACAAGGC 60.478 57.143 2.57 0.00 32.67 4.35
647 650 3.369892 GGATAGACAAGGCTGCTTCTTCA 60.370 47.826 0.00 0.00 0.00 3.02
748 751 3.558033 TGTACGATAGCACCACCTATCA 58.442 45.455 9.17 0.00 42.36 2.15
823 826 4.103153 TCCTCCCTTTACCTTCATATGCAG 59.897 45.833 0.00 0.00 0.00 4.41
860 863 4.089208 CGCTGCTATACTCTTAGAATTGCG 59.911 45.833 0.00 0.00 0.00 4.85
946 949 8.755028 GGGAAAAGGCTAGATTTTTATTTGGTA 58.245 33.333 0.00 0.00 30.22 3.25
997 1000 3.079578 ACTTTCGATCCTACACGACTCA 58.920 45.455 0.00 0.00 38.24 3.41
1024 1027 9.905713 AGATGTTAGAAGGTGCTAAATCAATAA 57.094 29.630 0.00 0.00 32.58 1.40
1030 1033 4.599041 AGGTGCTAAATCAATAAGTGCCA 58.401 39.130 0.00 0.00 0.00 4.92
1101 1104 5.641209 CGTCCTCAGTTCTTTGATTCATTCT 59.359 40.000 0.00 0.00 0.00 2.40
1221 1340 5.091431 GCCTTTCTGATCTCATTCGTTTTG 58.909 41.667 0.00 0.00 0.00 2.44
1386 1847 2.354510 TGCTATGCAATTTCAGTACCGC 59.645 45.455 0.00 0.00 34.76 5.68
1405 1868 4.338118 ACCGCATCGATGTCCATTTATTTT 59.662 37.500 25.47 0.00 0.00 1.82
1478 1941 3.434309 ACTTTACTAACAGGTAGGGCGA 58.566 45.455 0.00 0.00 33.68 5.54
1479 1942 3.834231 ACTTTACTAACAGGTAGGGCGAA 59.166 43.478 0.00 0.00 33.68 4.70
1532 2004 8.967664 ACCCGCATGTTTAGATTATTTACTTA 57.032 30.769 0.00 0.00 0.00 2.24
1578 2050 5.301551 TGTCACCAACTTTGTTCAATGCTAT 59.698 36.000 0.00 0.00 0.00 2.97
1587 2059 5.811399 TTGTTCAATGCTATTCCCTAACG 57.189 39.130 0.00 0.00 0.00 3.18
1667 2139 1.167781 TTCGTTTTTCGCCACCTCCC 61.168 55.000 0.00 0.00 39.67 4.30
1676 2148 1.228154 GCCACCTCCCGTGTCTTTT 60.228 57.895 0.00 0.00 41.26 2.27
1768 2242 2.354510 CTGAACACCACGAAAGAAAGCA 59.645 45.455 0.00 0.00 0.00 3.91
1843 2317 1.880027 GGCATAGAAAAGGCATACGGG 59.120 52.381 0.00 0.00 0.00 5.28
1844 2318 2.572290 GCATAGAAAAGGCATACGGGT 58.428 47.619 0.00 0.00 0.00 5.28
1846 2320 3.380320 GCATAGAAAAGGCATACGGGTTT 59.620 43.478 0.00 0.00 0.00 3.27
1867 2341 7.331934 GGGTTTAAAGATTGATTGAAAAGAGGC 59.668 37.037 0.00 0.00 0.00 4.70
1909 2384 1.340211 GGAGAAGGAGACCTCTGTCGA 60.340 57.143 0.00 0.00 46.51 4.20
1923 2398 3.990092 TCTGTCGAAGCAAGCTAAAGAA 58.010 40.909 0.00 0.00 0.00 2.52
1924 2399 3.741344 TCTGTCGAAGCAAGCTAAAGAAC 59.259 43.478 0.00 0.00 0.00 3.01
1943 2418 3.722728 ACCCCACTTTATATCGTCGAC 57.277 47.619 5.18 5.18 0.00 4.20
1962 2437 1.546476 ACTTCAGGTAAGGCACTCGAG 59.454 52.381 11.84 11.84 38.49 4.04
1965 2440 0.176680 CAGGTAAGGCACTCGAGCAT 59.823 55.000 13.61 0.00 38.49 3.79
2030 2506 1.120184 TTGCTGCATTTCTTGGGCCA 61.120 50.000 0.00 0.00 0.00 5.36
2086 2562 2.176045 TGATCTACTTTCTGGTGCCGA 58.824 47.619 0.00 0.00 0.00 5.54
2099 2575 1.463674 GTGCCGATCCCTTCACAAAT 58.536 50.000 0.00 0.00 0.00 2.32
2216 2692 4.301072 TTCTTGGTTCGGAATCCAATCT 57.699 40.909 18.53 0.00 41.89 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 5.134725 AGCATTAGGATTTTCTGTGGGAT 57.865 39.130 0.00 0.00 0.00 3.85
74 75 8.125978 TCAAAATGTGAGCATTAGGATTTTCT 57.874 30.769 0.00 0.00 43.89 2.52
88 89 7.017645 CGGACTGATTTAGTTCAAAATGTGAG 58.982 38.462 0.00 0.00 40.53 3.51
138 139 3.959943 ACACACAATTTACCAAACTCGC 58.040 40.909 0.00 0.00 0.00 5.03
197 198 2.455674 CACGAATGAAGAGTGGGTGA 57.544 50.000 0.00 0.00 32.68 4.02
382 385 7.344093 TCCTCAACACTCAAATCTCTCTCATAT 59.656 37.037 0.00 0.00 0.00 1.78
394 397 6.611613 ATGATAGTCTCCTCAACACTCAAA 57.388 37.500 0.00 0.00 0.00 2.69
405 408 5.426689 TGTGCTTCAAATGATAGTCTCCT 57.573 39.130 0.00 0.00 0.00 3.69
433 436 6.806668 TGGTATGTTGATGATGAACTCCTA 57.193 37.500 0.00 0.00 0.00 2.94
452 455 4.431378 TCTCCAGGAGGTAACAAATGGTA 58.569 43.478 17.10 0.00 36.27 3.25
564 567 3.380637 GGTAGATCTTCACGAAGTAGGCA 59.619 47.826 0.00 0.00 41.61 4.75
637 640 2.363683 GAAGGGTCCATGAAGAAGCAG 58.636 52.381 0.00 0.00 0.00 4.24
823 826 3.349488 AGCAGCGGAAAGTAAAACAAC 57.651 42.857 0.00 0.00 0.00 3.32
860 863 3.815401 AGTCAAGCAATCAACCTACACAC 59.185 43.478 0.00 0.00 0.00 3.82
971 974 5.819379 AGTCGTGTAGGATCGAAAGTATGTA 59.181 40.000 0.00 0.00 37.81 2.29
997 1000 8.814038 ATTGATTTAGCACCTTCTAACATCTT 57.186 30.769 0.00 0.00 0.00 2.40
1024 1027 0.617413 ATTGTAGCAGCTCTGGCACT 59.383 50.000 0.00 0.00 41.70 4.40
1030 1033 3.376546 GCTAAAGCAATTGTAGCAGCTCT 59.623 43.478 17.28 0.00 40.02 4.09
1101 1104 0.747644 ATGATGGATTTCGCGCCACA 60.748 50.000 0.00 4.84 36.92 4.17
1221 1340 7.857389 TGATCTCATAACTTTTTATGCGATTGC 59.143 33.333 9.92 0.00 44.62 3.56
1386 1847 7.220683 GGACACAAAAATAAATGGACATCGATG 59.779 37.037 23.68 23.68 0.00 3.84
1405 1868 1.374125 CACGCGGATGAGGACACAA 60.374 57.895 12.47 0.00 0.00 3.33
1532 2004 2.361119 GCCGAAGAAAAAGTGAAAGGGT 59.639 45.455 0.00 0.00 0.00 4.34
1578 2050 3.815809 CCCTTATTCATGCGTTAGGGAA 58.184 45.455 13.08 0.00 44.13 3.97
1667 2139 5.399604 AAGACCTTAAACGAAAAGACACG 57.600 39.130 0.00 0.00 0.00 4.49
1676 2148 4.996122 TGCCGAATTAAAGACCTTAAACGA 59.004 37.500 0.00 0.00 36.42 3.85
1768 2242 8.075761 AGTCGGACCTTATTGAAAAGTAGTAT 57.924 34.615 4.14 0.00 0.00 2.12
1843 2317 8.816640 TGCCTCTTTTCAATCAATCTTTAAAC 57.183 30.769 0.00 0.00 0.00 2.01
1844 2318 8.090214 CCTGCCTCTTTTCAATCAATCTTTAAA 58.910 33.333 0.00 0.00 0.00 1.52
1846 2320 6.153340 CCCTGCCTCTTTTCAATCAATCTTTA 59.847 38.462 0.00 0.00 0.00 1.85
1867 2341 2.145397 TAGTAGCAGACCAGTCCCTG 57.855 55.000 0.00 0.00 0.00 4.45
1880 2354 2.960384 GGTCTCCTTCTCCCTTAGTAGC 59.040 54.545 0.00 0.00 0.00 3.58
1881 2355 4.167307 AGAGGTCTCCTTCTCCCTTAGTAG 59.833 50.000 0.00 0.00 31.76 2.57
1882 2356 4.079672 CAGAGGTCTCCTTCTCCCTTAGTA 60.080 50.000 0.00 0.00 31.76 1.82
1883 2357 2.930405 AGAGGTCTCCTTCTCCCTTAGT 59.070 50.000 0.00 0.00 31.76 2.24
1909 2384 2.158460 AGTGGGGTTCTTTAGCTTGCTT 60.158 45.455 0.00 0.00 0.00 3.91
1923 2398 3.294214 AGTCGACGATATAAAGTGGGGT 58.706 45.455 10.46 0.00 0.00 4.95
1924 2399 4.202080 TGAAGTCGACGATATAAAGTGGGG 60.202 45.833 10.46 0.00 0.00 4.96
1943 2418 1.737363 GCTCGAGTGCCTTACCTGAAG 60.737 57.143 15.13 0.00 34.63 3.02
1962 2437 0.613260 TCCCGGATGTATAGGCATGC 59.387 55.000 9.90 9.90 34.48 4.06
1965 2440 4.564821 GCTAAATTCCCGGATGTATAGGCA 60.565 45.833 0.73 0.00 0.00 4.75
2030 2506 2.231235 CGCCAAAATCAAGTAAAGCCCT 59.769 45.455 0.00 0.00 0.00 5.19
2086 2562 3.990245 AGGGGCTATATTTGTGAAGGGAT 59.010 43.478 0.00 0.00 0.00 3.85
2099 2575 5.846714 AGAATAAGAGCAAGAAGGGGCTATA 59.153 40.000 0.00 0.00 41.22 1.31
2192 2668 5.358160 AGATTGGATTCCGAACCAAGAAATC 59.642 40.000 15.71 10.71 46.95 2.17
2193 2669 5.264395 AGATTGGATTCCGAACCAAGAAAT 58.736 37.500 15.71 4.68 46.95 2.17
2216 2692 7.098074 ACGGGTAATTGTTTGTTTTCAACTA 57.902 32.000 0.00 0.00 39.73 2.24


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

AutoCloner maintained by Alex Coulton.