Multiple sequence alignment - TraesCS7A01G078600

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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 TraesCS7A01G078600 chr7A 100.000 2546 0 0 1 2546 43440223 43437678 0.000000e+00 4702.0
1 TraesCS7A01G078600 chr7A 97.785 1580 19 4 713 2276 43458187 43456608 0.000000e+00 2710.0
2 TraesCS7A01G078600 chr7A 91.015 946 30 6 1365 2276 43258423 43257499 0.000000e+00 1225.0
3 TraesCS7A01G078600 chr7A 88.017 918 78 19 683 1575 45603064 45602154 0.000000e+00 1057.0
4 TraesCS7A01G078600 chr7A 87.208 899 86 17 702 1575 45574345 45573451 0.000000e+00 996.0
5 TraesCS7A01G078600 chr7A 87.208 899 86 17 702 1575 45594035 45593141 0.000000e+00 996.0
6 TraesCS7A01G078600 chr7A 83.349 1045 109 31 1186 2197 44877557 44876545 0.000000e+00 905.0
7 TraesCS7A01G078600 chr7A 97.067 375 7 2 1 371 43460099 43459725 1.660000e-176 628.0
8 TraesCS7A01G078600 chr7A 93.668 379 24 0 245 623 45594429 45594051 3.680000e-158 568.0
9 TraesCS7A01G078600 chr7A 93.404 379 25 0 245 623 45574739 45574361 1.710000e-156 562.0
10 TraesCS7A01G078600 chr7A 93.158 380 26 0 244 623 45603440 45603061 2.210000e-155 558.0
11 TraesCS7A01G078600 chr7A 96.739 276 6 1 2274 2546 43455764 43455489 8.300000e-125 457.0
12 TraesCS7A01G078600 chr7A 97.619 252 5 1 369 620 43458471 43458221 5.030000e-117 431.0
13 TraesCS7A01G078600 chr7A 94.161 274 16 0 2273 2546 43256661 43256388 3.920000e-113 418.0
14 TraesCS7A01G078600 chr7A 85.979 378 31 11 758 1113 45186500 45186123 3.970000e-103 385.0
15 TraesCS7A01G078600 chr7A 92.251 271 20 1 2274 2544 44875603 44875334 1.430000e-102 383.0
16 TraesCS7A01G078600 chr7A 90.775 271 25 0 2274 2544 44934993 44934723 1.860000e-96 363.0
17 TraesCS7A01G078600 chr7A 95.946 148 5 1 1 147 45610342 45610195 3.270000e-59 239.0
18 TraesCS7A01G078600 chr7A 77.099 393 53 22 1907 2273 287246501 287246120 2.580000e-45 193.0
19 TraesCS7A01G078600 chr7A 98.750 80 1 0 621 700 43439564 43439485 2.640000e-30 143.0
20 TraesCS7A01G078600 chr7A 98.750 80 1 0 660 739 43439603 43439524 2.640000e-30 143.0
21 TraesCS7A01G078600 chr7A 82.286 175 15 11 1 167 45021831 45021665 1.230000e-28 137.0
22 TraesCS7A01G078600 chr7A 91.262 103 4 2 665 762 43458183 43458285 4.420000e-28 135.0
23 TraesCS7A01G078600 chr7A 81.818 176 14 12 1 167 45068648 45068482 5.720000e-27 132.0
24 TraesCS7A01G078600 chr7A 92.308 78 3 1 626 700 43458183 43458260 9.630000e-20 108.0
25 TraesCS7A01G078600 chr7A 100.000 41 0 0 660 700 15084464 15084504 2.720000e-10 76.8
26 TraesCS7A01G078600 chr7D 90.856 1553 78 28 756 2276 43430357 43428837 0.000000e+00 2023.0
27 TraesCS7A01G078600 chr7D 88.848 816 55 16 776 1574 43384815 43384019 0.000000e+00 970.0
28 TraesCS7A01G078600 chr7D 94.410 322 14 2 244 565 43430676 43430359 2.280000e-135 492.0
29 TraesCS7A01G078600 chr7D 95.255 274 13 0 2273 2546 43428000 43427727 3.890000e-118 435.0
30 TraesCS7A01G078600 chr7D 94.479 163 6 2 1 160 43430838 43430676 5.440000e-62 248.0
31 TraesCS7A01G078600 chr7D 87.379 103 9 3 561 661 614704937 614705037 5.760000e-22 115.0
32 TraesCS7A01G078600 chr7D 79.032 124 20 6 2424 2543 154918053 154918174 2.100000e-11 80.5
33 TraesCS7A01G078600 chr7D 79.464 112 16 6 2273 2378 6495967 6495857 3.510000e-09 73.1
34 TraesCS7A01G078600 chr4A 89.219 807 63 13 787 1575 651986141 651985341 0.000000e+00 987.0
35 TraesCS7A01G078600 chr4A 90.025 401 34 5 1180 1575 651637816 651637417 4.860000e-142 514.0
36 TraesCS7A01G078600 chr4A 86.860 449 26 14 756 1187 651638675 651638243 2.960000e-129 472.0
37 TraesCS7A01G078600 chr4A 85.981 107 11 2 558 661 729716576 729716681 7.450000e-21 111.0
38 TraesCS7A01G078600 chr4A 93.220 59 4 0 559 617 618085028 618085086 1.250000e-13 87.9
39 TraesCS7A01G078600 chr6A 89.286 196 12 4 565 758 200245822 200246010 1.180000e-58 237.0
40 TraesCS7A01G078600 chr6A 98.718 78 1 0 664 741 200245876 200245953 3.420000e-29 139.0
41 TraesCS7A01G078600 chr6A 96.250 80 3 0 621 700 200245911 200245990 5.720000e-27 132.0
42 TraesCS7A01G078600 chr3A 81.443 291 36 8 2274 2546 25891234 25891524 3.300000e-54 222.0
43 TraesCS7A01G078600 chr4B 77.427 412 54 25 1870 2254 554022648 554022249 2.570000e-50 209.0
44 TraesCS7A01G078600 chr4D 78.470 353 42 23 1930 2258 444270053 444269711 1.540000e-47 200.0
45 TraesCS7A01G078600 chr5B 77.612 335 51 18 1871 2192 377120572 377120249 5.600000e-42 182.0
46 TraesCS7A01G078600 chr5B 79.365 126 22 3 2424 2546 548988335 548988211 4.510000e-13 86.1
47 TraesCS7A01G078600 chr6D 83.696 184 24 6 2011 2192 45488927 45489106 4.360000e-38 169.0
48 TraesCS7A01G078600 chr6D 79.365 126 21 5 2424 2546 269274590 269274467 1.620000e-12 84.2
49 TraesCS7A01G078600 chr2B 94.845 97 5 0 663 759 715814711 715814807 4.390000e-33 152.0
50 TraesCS7A01G078600 chr2B 93.407 91 4 2 168 257 594258890 594258801 1.590000e-27 134.0
51 TraesCS7A01G078600 chr2D 82.065 184 26 7 2011 2192 552079101 552078923 1.580000e-32 150.0
52 TraesCS7A01G078600 chr2D 85.455 110 5 1 563 661 233429912 233429803 1.250000e-18 104.0
53 TraesCS7A01G078600 chr2D 79.545 132 21 6 2420 2546 186323503 186323633 3.490000e-14 89.8
54 TraesCS7A01G078600 chr1D 77.869 244 27 16 2049 2273 469061892 469062127 2.660000e-25 126.0
55 TraesCS7A01G078600 chr3D 93.902 82 4 1 168 249 574480405 574480485 3.440000e-24 122.0
56 TraesCS7A01G078600 chr2A 94.872 78 4 0 167 244 377762883 377762960 3.440000e-24 122.0
57 TraesCS7A01G078600 chr7B 93.443 61 4 0 555 615 329851506 329851566 9.700000e-15 91.6
58 TraesCS7A01G078600 chr5D 87.342 79 10 0 171 249 450376502 450376424 9.700000e-15 91.6
59 TraesCS7A01G078600 chr1B 81.513 119 8 2 559 663 637917125 637917243 4.510000e-13 86.1
60 TraesCS7A01G078600 chr1A 80.833 120 8 8 565 670 54354699 54354581 2.100000e-11 80.5


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 TraesCS7A01G078600 chr7A 43437678 43440223 2545 True 1662.666667 4702 99.166667 1 2546 3 chr7A.!!$R8 2545
1 TraesCS7A01G078600 chr7A 43455489 43460099 4610 True 1056.500000 2710 97.302500 1 2546 4 chr7A.!!$R9 2545
2 TraesCS7A01G078600 chr7A 43256388 43258423 2035 True 821.500000 1225 92.588000 1365 2546 2 chr7A.!!$R7 1181
3 TraesCS7A01G078600 chr7A 45602154 45603440 1286 True 807.500000 1057 90.587500 244 1575 2 chr7A.!!$R13 1331
4 TraesCS7A01G078600 chr7A 45593141 45594429 1288 True 782.000000 996 90.438000 245 1575 2 chr7A.!!$R12 1330
5 TraesCS7A01G078600 chr7A 45573451 45574739 1288 True 779.000000 996 90.306000 245 1575 2 chr7A.!!$R11 1330
6 TraesCS7A01G078600 chr7A 44875334 44877557 2223 True 644.000000 905 87.800000 1186 2544 2 chr7A.!!$R10 1358
7 TraesCS7A01G078600 chr7D 43384019 43384815 796 True 970.000000 970 88.848000 776 1574 1 chr7D.!!$R2 798
8 TraesCS7A01G078600 chr7D 43427727 43430838 3111 True 799.500000 2023 93.750000 1 2546 4 chr7D.!!$R3 2545
9 TraesCS7A01G078600 chr4A 651985341 651986141 800 True 987.000000 987 89.219000 787 1575 1 chr4A.!!$R1 788
10 TraesCS7A01G078600 chr4A 651637417 651638675 1258 True 493.000000 514 88.442500 756 1575 2 chr4A.!!$R2 819

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
229 235 0.532862 ACACTCCTTCCGCACACAAG 60.533 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1599 3380 3.262405 AGCCGTCCTTATGTTTACAAGGA 59.738 43.478 0.0 0.0 46.35 3.36 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
229 235 0.532862 ACACTCCTTCCGCACACAAG 60.533 55.000 0.00 0.00 0.00 3.16
263 269 8.445361 AAGGTAAGAATTGTAACTAGAAGGGA 57.555 34.615 0.00 0.00 0.00 4.20
293 299 3.750371 TCATGGAAGGTGAATGAACGTT 58.250 40.909 0.00 0.00 0.00 3.99
588 1851 4.042435 ACTCCTTCCGTCCCAAAATTCTTA 59.958 41.667 0.00 0.00 0.00 2.10
650 1913 7.367159 ACATCCGTATCTAGACGAATCTAAG 57.633 40.000 5.60 0.00 45.82 2.18
651 1914 7.160049 ACATCCGTATCTAGACGAATCTAAGA 58.840 38.462 5.60 0.00 45.82 2.10
652 1915 7.118101 ACATCCGTATCTAGACGAATCTAAGAC 59.882 40.741 5.60 0.00 45.82 3.01
653 1916 5.632764 TCCGTATCTAGACGAATCTAAGACG 59.367 44.000 5.60 0.00 45.82 4.18
654 1917 5.632764 CCGTATCTAGACGAATCTAAGACGA 59.367 44.000 5.60 0.00 45.82 4.20
655 1918 6.183360 CCGTATCTAGACGAATCTAAGACGAG 60.183 46.154 5.60 0.00 45.82 4.18
656 1919 6.581919 CGTATCTAGACGAATCTAAGACGAGA 59.418 42.308 0.00 0.00 45.82 4.04
657 1920 7.114670 CGTATCTAGACGAATCTAAGACGAGAA 59.885 40.741 0.00 0.00 45.82 2.87
658 1921 7.972832 ATCTAGACGAATCTAAGACGAGAAT 57.027 36.000 0.00 0.00 36.98 2.40
659 1922 7.789273 TCTAGACGAATCTAAGACGAGAATT 57.211 36.000 0.00 0.00 36.98 2.17
660 1923 8.211116 TCTAGACGAATCTAAGACGAGAATTT 57.789 34.615 0.00 0.00 36.98 1.82
661 1924 9.322773 TCTAGACGAATCTAAGACGAGAATTTA 57.677 33.333 0.00 0.00 36.98 1.40
662 1925 9.588774 CTAGACGAATCTAAGACGAGAATTTAG 57.411 37.037 0.00 0.00 36.98 1.85
663 1926 8.211116 AGACGAATCTAAGACGAGAATTTAGA 57.789 34.615 0.00 0.00 37.69 2.10
664 1927 8.842280 AGACGAATCTAAGACGAGAATTTAGAT 58.158 33.333 0.00 1.28 42.78 1.98
666 1929 9.881529 ACGAATCTAAGACGAGAATTTAGATAC 57.118 33.333 6.45 0.00 41.09 2.24
667 1930 9.880064 CGAATCTAAGACGAGAATTTAGATACA 57.120 33.333 6.45 0.00 41.09 2.29
671 1934 8.504815 TCTAAGACGAGAATTTAGATACATCCG 58.495 37.037 0.00 0.00 30.65 4.18
672 1935 6.636562 AGACGAGAATTTAGATACATCCGT 57.363 37.500 0.00 0.00 0.00 4.69
673 1936 7.741027 AGACGAGAATTTAGATACATCCGTA 57.259 36.000 0.00 0.00 0.00 4.02
674 1937 8.338072 AGACGAGAATTTAGATACATCCGTAT 57.662 34.615 0.00 0.00 41.16 3.06
689 1952 7.367159 ACATCCGTATCTAGACGAATCTAAG 57.633 40.000 5.60 0.00 45.82 2.18
690 1953 7.160049 ACATCCGTATCTAGACGAATCTAAGA 58.840 38.462 5.60 0.00 45.82 2.10
691 1954 7.118101 ACATCCGTATCTAGACGAATCTAAGAC 59.882 40.741 5.60 0.00 45.82 3.01
692 1955 6.519382 TCCGTATCTAGACGAATCTAAGACA 58.481 40.000 5.60 0.00 45.82 3.41
693 1956 6.988580 TCCGTATCTAGACGAATCTAAGACAA 59.011 38.462 5.60 0.00 45.82 3.18
694 1957 7.171167 TCCGTATCTAGACGAATCTAAGACAAG 59.829 40.741 5.60 0.00 45.82 3.16
695 1958 7.171167 CCGTATCTAGACGAATCTAAGACAAGA 59.829 40.741 5.60 0.00 45.82 3.02
696 1959 8.549548 CGTATCTAGACGAATCTAAGACAAGAA 58.450 37.037 0.00 0.00 45.82 2.52
1599 3380 0.819259 ACACTTGTGCTTCGGTGCAT 60.819 50.000 6.54 0.00 45.23 3.96
1928 3728 9.549923 GAAGTTTTTAAAAATTCGTGAACATCG 57.450 29.630 16.02 0.00 0.00 3.84
1977 3779 6.959639 AAACTGATGAGCCTTTTCTAAACA 57.040 33.333 0.00 0.00 0.00 2.83
2020 3841 8.845227 AGTTGGTGAACTTTGTTTTTCAAAATT 58.155 25.926 0.00 0.00 44.08 1.82
2142 3965 7.381948 CACGAACATCTTTTCAAATCCATGAAA 59.618 33.333 0.00 0.00 45.07 2.69
2236 4059 6.500041 TGAAGAAGTATTTTTGGTTGAACCG 58.500 36.000 10.16 0.00 42.58 4.44
2322 5052 3.455910 TCTGGCATGTAGTTGCTATCCTT 59.544 43.478 0.00 0.00 42.38 3.36
2338 5068 3.095912 TCCTTAGGGTCATCTTCGTCA 57.904 47.619 0.00 0.00 0.00 4.35
2452 5185 3.205056 TGGCCAGATAAGGTCATGGAAAT 59.795 43.478 0.00 0.00 38.62 2.17
2510 5244 1.006043 TCATAGATCGGGCCTCCTAGG 59.994 57.143 0.82 0.82 38.80 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
229 235 0.179081 ATTCTTACCTTCCTCGCGGC 60.179 55.000 6.13 0.00 0.00 6.53
263 269 3.181329 TCACCTTCCATGATACTGTGGT 58.819 45.455 0.00 0.00 36.84 4.16
293 299 1.955778 CCAACTGTTCAGGATGCAACA 59.044 47.619 0.00 0.00 35.75 3.33
570 1833 7.626390 TCTAAGATAAGAATTTTGGGACGGAA 58.374 34.615 0.00 0.00 0.00 4.30
631 1894 6.581919 TCTCGTCTTAGATTCGTCTAGATACG 59.418 42.308 0.00 0.00 44.19 3.06
632 1895 7.872163 TCTCGTCTTAGATTCGTCTAGATAC 57.128 40.000 0.00 0.00 0.00 2.24
635 1898 7.789273 AATTCTCGTCTTAGATTCGTCTAGA 57.211 36.000 0.00 0.00 0.00 2.43
636 1899 9.588774 CTAAATTCTCGTCTTAGATTCGTCTAG 57.411 37.037 0.00 0.00 0.00 2.43
638 1901 8.211116 TCTAAATTCTCGTCTTAGATTCGTCT 57.789 34.615 0.00 0.00 28.94 4.18
640 1903 9.881529 GTATCTAAATTCTCGTCTTAGATTCGT 57.118 33.333 8.42 0.00 40.87 3.85
641 1904 9.880064 TGTATCTAAATTCTCGTCTTAGATTCG 57.120 33.333 8.42 0.00 40.87 3.34
645 1908 8.504815 CGGATGTATCTAAATTCTCGTCTTAGA 58.495 37.037 0.00 0.00 36.40 2.10
646 1909 8.291032 ACGGATGTATCTAAATTCTCGTCTTAG 58.709 37.037 0.00 0.00 0.00 2.18
647 1910 8.162878 ACGGATGTATCTAAATTCTCGTCTTA 57.837 34.615 0.00 0.00 0.00 2.10
648 1911 7.040473 ACGGATGTATCTAAATTCTCGTCTT 57.960 36.000 0.00 0.00 0.00 3.01
649 1912 6.636562 ACGGATGTATCTAAATTCTCGTCT 57.363 37.500 0.00 0.00 0.00 4.18
663 1926 9.100554 CTTAGATTCGTCTAGATACGGATGTAT 57.899 37.037 2.64 0.00 41.14 2.29
664 1927 8.309656 TCTTAGATTCGTCTAGATACGGATGTA 58.690 37.037 2.64 1.02 41.14 2.29
665 1928 7.118101 GTCTTAGATTCGTCTAGATACGGATGT 59.882 40.741 2.64 1.92 41.14 3.06
666 1929 7.117956 TGTCTTAGATTCGTCTAGATACGGATG 59.882 40.741 2.64 0.00 41.14 3.51
667 1930 7.160049 TGTCTTAGATTCGTCTAGATACGGAT 58.840 38.462 0.00 0.00 43.73 4.18
668 1931 6.519382 TGTCTTAGATTCGTCTAGATACGGA 58.481 40.000 0.00 0.00 43.05 4.69
669 1932 6.782298 TGTCTTAGATTCGTCTAGATACGG 57.218 41.667 0.00 0.00 43.05 4.02
670 1933 8.074474 TCTTGTCTTAGATTCGTCTAGATACG 57.926 38.462 0.00 0.00 44.19 3.06
684 1947 9.967346 CGGATGTATCTAAATTCTTGTCTTAGA 57.033 33.333 0.00 0.00 36.40 2.10
685 1948 9.751542 ACGGATGTATCTAAATTCTTGTCTTAG 57.248 33.333 0.00 0.00 0.00 2.18
914 2202 1.575419 AATGCAAAGGATGGGCATGT 58.425 45.000 0.00 0.00 46.77 3.21
1599 3380 3.262405 AGCCGTCCTTATGTTTACAAGGA 59.738 43.478 0.00 0.00 46.35 3.36
1905 3705 9.678247 AAACGATGTTCACGAATTTTTAAAAAC 57.322 25.926 15.35 3.65 34.70 2.43
2142 3965 5.213891 AGCGGTTCATCTTTTTGGAAAAT 57.786 34.783 0.00 0.00 0.00 1.82
2236 4059 2.864931 CGCCTGATCGCTTCTTCGC 61.865 63.158 0.00 0.00 0.00 4.70
2322 5052 1.830279 ACGTGACGAAGATGACCCTA 58.170 50.000 13.70 0.00 0.00 3.53
2338 5068 2.031314 ACGACGACGATATGATCAACGT 59.969 45.455 20.01 20.01 42.66 3.99
2452 5185 4.352009 ACATCCTTGAATGCACCCAATTA 58.648 39.130 0.00 0.00 0.00 1.40
2510 5244 0.400594 ACAGAGGGTGTTTGGGTAGC 59.599 55.000 0.00 0.00 34.94 3.58


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

AutoCloner maintained by Alex Coulton.