Multiple sequence alignment - TraesCS7A01G068500

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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 TraesCS7A01G068500 chr7A 100.000 2975 0 0 1 2975 34709344 34706370 0.000000e+00 5494.0
1 TraesCS7A01G068500 chr7D 91.601 2155 128 34 17 2132 34304190 34302050 0.000000e+00 2928.0
2 TraesCS7A01G068500 chr7D 91.379 754 38 9 2181 2913 34302052 34301305 0.000000e+00 1007.0
3 TraesCS7A01G068500 chr7D 85.714 126 16 2 468 592 478795417 478795293 6.690000e-27 132.0
4 TraesCS7A01G068500 chr4A 90.675 2177 109 32 840 2975 691123851 691125974 0.000000e+00 2809.0
5 TraesCS7A01G068500 chr7B 84.000 175 22 4 429 599 161436274 161436102 2.370000e-36 163.0
6 TraesCS7A01G068500 chr7B 97.368 38 0 1 563 600 122668689 122668653 2.480000e-06 63.9
7 TraesCS7A01G068500 chr6B 82.486 177 25 4 429 602 276668777 276668950 1.850000e-32 150.0
8 TraesCS7A01G068500 chr5B 90.385 104 6 3 473 573 315893437 315893335 1.860000e-27 134.0
9 TraesCS7A01G068500 chr4D 89.524 105 11 0 468 572 12354797 12354693 1.860000e-27 134.0
10 TraesCS7A01G068500 chr4D 91.753 97 7 1 482 578 482704199 482704104 1.860000e-27 134.0
11 TraesCS7A01G068500 chr4D 83.784 74 11 1 300 372 468606618 468606545 5.320000e-08 69.4
12 TraesCS7A01G068500 chr5D 88.889 108 10 2 462 568 228447067 228446961 6.690000e-27 132.0
13 TraesCS7A01G068500 chr3B 91.579 95 8 0 473 567 40942856 40942762 6.690000e-27 132.0
14 TraesCS7A01G068500 chr4B 77.165 127 22 6 265 388 588207426 588207304 1.910000e-07 67.6
15 TraesCS7A01G068500 chr1B 82.895 76 7 4 577 649 643180829 643180901 2.480000e-06 63.9
16 TraesCS7A01G068500 chr3D 89.583 48 5 0 318 365 537797980 537797933 8.900000e-06 62.1
17 TraesCS7A01G068500 chr3A 91.304 46 2 2 328 372 673281616 673281572 8.900000e-06 62.1
18 TraesCS7A01G068500 chr2D 87.273 55 3 4 573 626 370129643 370129694 3.200000e-05 60.2
19 TraesCS7A01G068500 chr2A 88.000 50 3 3 573 621 501060483 501060530 4.140000e-04 56.5


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 TraesCS7A01G068500 chr7A 34706370 34709344 2974 True 5494.0 5494 100.000 1 2975 1 chr7A.!!$R1 2974
1 TraesCS7A01G068500 chr7D 34301305 34304190 2885 True 1967.5 2928 91.490 17 2913 2 chr7D.!!$R2 2896
2 TraesCS7A01G068500 chr4A 691123851 691125974 2123 False 2809.0 2809 90.675 840 2975 1 chr4A.!!$F1 2135

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
854 881 1.125633 ATATAAACGTGGCCCGGTCT 58.874 50.0 16.44 5.53 42.24 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2243 2315 0.249676 AGTCTGCTCTGCTCCACATG 59.75 55.0 0.0 0.0 0.0 3.21 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
127 130 9.969001 TTACTTAAAACTGCTAAATACATCCCT 57.031 29.630 0.00 0.00 0.00 4.20
130 133 9.125026 CTTAAAACTGCTAAATACATCCCTCAT 57.875 33.333 0.00 0.00 0.00 2.90
131 134 6.949352 AAACTGCTAAATACATCCCTCATG 57.051 37.500 0.00 0.00 38.64 3.07
155 158 9.965824 ATGTTTTAGAAAATGGTAAACTCACTG 57.034 29.630 0.00 0.00 31.71 3.66
194 197 9.894439 CGTGTAATTTTGGAAAAACTTTTGTAG 57.106 29.630 0.00 0.00 0.00 2.74
199 202 9.642327 AATTTTGGAAAAACTTTTGTAGTACGT 57.358 25.926 0.00 0.00 35.54 3.57
200 203 8.450385 TTTTGGAAAAACTTTTGTAGTACGTG 57.550 30.769 0.00 0.00 35.54 4.49
201 204 6.121613 TGGAAAAACTTTTGTAGTACGTGG 57.878 37.500 0.00 0.00 35.54 4.94
203 206 6.183360 TGGAAAAACTTTTGTAGTACGTGGAC 60.183 38.462 0.00 0.00 35.54 4.02
204 207 5.393902 AAAACTTTTGTAGTACGTGGACG 57.606 39.130 0.00 0.00 40.00 4.79
226 231 5.121768 ACGTGGTTGTGACATATAAGCTTTC 59.878 40.000 3.20 0.00 0.00 2.62
316 321 9.912634 TTTCCTACAATTCAAAAGATGTTCATC 57.087 29.630 4.80 4.80 0.00 2.92
358 363 8.366401 TCAAGCCTTTCAAAAATATGTTCATGA 58.634 29.630 0.00 0.00 0.00 3.07
429 435 9.030452 ACACATACCATACCAAAAATTATGTGT 57.970 29.630 15.37 15.37 46.92 3.72
482 491 6.560253 AAATTAACATGTGCTCTCTTCGTT 57.440 33.333 0.00 0.00 0.00 3.85
484 493 2.086054 ACATGTGCTCTCTTCGTTCC 57.914 50.000 0.00 0.00 0.00 3.62
549 558 8.088981 AGTTGTACTAAGGTTGAGACACTTATG 58.911 37.037 0.00 0.00 0.00 1.90
554 563 4.974645 AGGTTGAGACACTTATGTTGGA 57.025 40.909 0.00 0.00 39.95 3.53
565 574 3.326880 ACTTATGTTGGAACGGAGGAAGT 59.673 43.478 0.00 0.00 0.00 3.01
571 580 4.773674 TGTTGGAACGGAGGAAGTATCTAA 59.226 41.667 0.00 0.00 0.00 2.10
740 750 8.911247 AAACACATAGAAACAAACAAGAGAAC 57.089 30.769 0.00 0.00 0.00 3.01
748 758 5.830000 AACAAACAAGAGAACAACCCTAC 57.170 39.130 0.00 0.00 0.00 3.18
757 767 2.644798 AGAACAACCCTACATGGAAGCT 59.355 45.455 0.00 0.00 38.35 3.74
776 786 6.183360 GGAAGCTTCCAAAACCTTTCTAAACT 60.183 38.462 35.71 0.00 46.76 2.66
779 789 6.016192 AGCTTCCAAAACCTTTCTAAACTAGC 60.016 38.462 0.00 0.00 0.00 3.42
842 869 2.127383 GCGCCGCGGCATATAAAC 60.127 61.111 45.26 22.96 42.06 2.01
850 877 1.837538 CGGCATATAAACGTGGCCCG 61.838 60.000 11.48 11.48 41.58 6.13
854 881 1.125633 ATATAAACGTGGCCCGGTCT 58.874 50.000 16.44 5.53 42.24 3.85
880 907 4.696455 CAAAGAGTTGCAGGGAACAAATT 58.304 39.130 6.45 0.00 0.00 1.82
892 919 9.474313 TGCAGGGAACAAATTCTAATTAGTAAT 57.526 29.630 12.19 8.02 34.98 1.89
931 958 3.260632 CCACAAAAACCCTATCCCCAAAG 59.739 47.826 0.00 0.00 0.00 2.77
979 1006 2.859538 CTCGAAGAAGATTCAGCTGCTC 59.140 50.000 9.47 8.43 34.09 4.26
1984 2027 1.059264 GCTCGTCGTAGCAAATGTGTC 59.941 52.381 10.53 0.00 42.30 3.67
2076 2138 3.236816 GTGGTTCAAGCATGATTCGTTG 58.763 45.455 0.00 0.00 34.96 4.10
2095 2160 2.371923 TTGTCATCGTGCTGCGTCG 61.372 57.895 9.99 9.99 42.13 5.12
2133 2198 5.123820 CGCCATGAGTTTCTTCTTGGATAAA 59.876 40.000 10.94 0.00 42.19 1.40
2147 2212 4.541250 TGGATAAAGGAGGAATGCCATT 57.459 40.909 0.00 0.00 36.29 3.16
2148 2213 4.217510 TGGATAAAGGAGGAATGCCATTG 58.782 43.478 0.00 0.00 36.29 2.82
2167 2232 4.777384 CATGAATGGATCGGCGGA 57.223 55.556 7.21 0.00 0.00 5.54
2168 2233 2.536725 CATGAATGGATCGGCGGAG 58.463 57.895 7.21 0.00 0.00 4.63
2169 2234 0.250038 CATGAATGGATCGGCGGAGT 60.250 55.000 7.21 0.00 0.00 3.85
2170 2235 0.469917 ATGAATGGATCGGCGGAGTT 59.530 50.000 7.21 0.00 0.00 3.01
2171 2236 0.461870 TGAATGGATCGGCGGAGTTG 60.462 55.000 7.21 0.00 0.00 3.16
2172 2237 1.776034 GAATGGATCGGCGGAGTTGC 61.776 60.000 7.21 0.00 0.00 4.17
2173 2238 2.535485 AATGGATCGGCGGAGTTGCA 62.535 55.000 7.21 1.72 36.28 4.08
2174 2239 2.435938 GGATCGGCGGAGTTGCAA 60.436 61.111 7.21 0.00 36.28 4.08
2175 2240 2.464459 GGATCGGCGGAGTTGCAAG 61.464 63.158 7.21 0.00 36.28 4.01
2176 2241 3.100862 GATCGGCGGAGTTGCAAGC 62.101 63.158 7.21 0.00 36.28 4.01
2177 2242 3.612247 ATCGGCGGAGTTGCAAGCT 62.612 57.895 7.21 0.00 36.28 3.74
2178 2243 4.093952 CGGCGGAGTTGCAAGCTG 62.094 66.667 0.00 0.25 36.28 4.24
2179 2244 4.410743 GGCGGAGTTGCAAGCTGC 62.411 66.667 19.71 19.71 45.29 5.25
2224 2289 2.177950 CTGGTCTGAATGCCAGTGC 58.822 57.895 4.97 0.00 45.28 4.40
2235 2300 1.735920 GCCAGTGCACTCAGAGTCG 60.736 63.158 18.64 3.49 37.47 4.18
2243 2315 0.523966 CACTCAGAGTCGGTGAGGAC 59.476 60.000 12.58 0.00 44.96 3.85
2260 2332 0.248565 GACATGTGGAGCAGAGCAGA 59.751 55.000 1.15 0.00 0.00 4.26
2297 2373 3.813166 GAGAGCTCTGCTTATAGTCGAGT 59.187 47.826 23.91 0.00 39.88 4.18
2409 2487 4.242586 TGTCCTCCCCGTCCACCA 62.243 66.667 0.00 0.00 0.00 4.17
2411 2489 2.122324 TCCTCCCCGTCCACCAAA 60.122 61.111 0.00 0.00 0.00 3.28
2473 2551 2.179517 CTCACGGCCGTCTCTGTC 59.820 66.667 31.80 0.00 0.00 3.51
2913 3009 0.674895 CTCCACAAGCACCAGTAGGC 60.675 60.000 0.00 0.00 39.06 3.93
2917 3013 2.034879 CAAGCACCAGTAGGCACCG 61.035 63.158 0.00 0.00 39.06 4.94
2921 3017 2.034879 CACCAGTAGGCACCGCAAG 61.035 63.158 0.00 0.00 39.06 4.01
2927 3024 0.391130 GTAGGCACCGCAAGTCATGA 60.391 55.000 0.00 0.00 0.00 3.07
2930 3027 0.745845 GGCACCGCAAGTCATGATCT 60.746 55.000 0.00 0.00 0.00 2.75
2937 3034 3.495193 CGCAAGTCATGATCTTTGGTTG 58.505 45.455 15.12 2.05 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.618702 AATAAATGAAAACACATGCATTCCAA 57.381 26.923 0.00 0.00 31.16 3.53
1 2 8.618702 AAATAAATGAAAACACATGCATTCCA 57.381 26.923 0.00 0.00 31.16 3.53
124 127 8.585018 AGTTTACCATTTTCTAAAACATGAGGG 58.415 33.333 0.00 0.00 33.52 4.30
127 130 9.959749 GTGAGTTTACCATTTTCTAAAACATGA 57.040 29.630 0.00 0.00 33.52 3.07
130 133 7.918562 GCAGTGAGTTTACCATTTTCTAAAACA 59.081 33.333 0.00 0.00 33.52 2.83
131 134 7.918562 TGCAGTGAGTTTACCATTTTCTAAAAC 59.081 33.333 0.00 0.00 0.00 2.43
143 146 4.202212 ACCCAATTTTGCAGTGAGTTTACC 60.202 41.667 0.00 0.00 0.00 2.85
155 158 3.586100 ATTACACGGACCCAATTTTGC 57.414 42.857 0.00 0.00 0.00 3.68
197 200 0.878523 ATGTCACAACCACGTCCACG 60.879 55.000 0.00 0.00 46.33 4.94
198 201 2.157834 TATGTCACAACCACGTCCAC 57.842 50.000 0.00 0.00 0.00 4.02
199 202 4.500127 CTTATATGTCACAACCACGTCCA 58.500 43.478 0.00 0.00 0.00 4.02
200 203 3.308866 GCTTATATGTCACAACCACGTCC 59.691 47.826 0.00 0.00 0.00 4.79
201 204 4.181578 AGCTTATATGTCACAACCACGTC 58.818 43.478 0.00 0.00 0.00 4.34
203 206 5.447279 GGAAAGCTTATATGTCACAACCACG 60.447 44.000 0.00 0.00 0.00 4.94
204 207 5.414454 TGGAAAGCTTATATGTCACAACCAC 59.586 40.000 0.00 0.00 0.00 4.16
249 254 9.210426 CGTATAGTCATTGTTAAGAAATGTTGC 57.790 33.333 9.52 4.10 36.58 4.17
316 321 9.294030 GAAAGGCTTGAACATTCTATAAATGTG 57.706 33.333 0.00 0.00 40.43 3.21
462 468 3.994392 GGAACGAAGAGAGCACATGTTAA 59.006 43.478 0.00 0.00 0.00 2.01
463 469 3.006430 TGGAACGAAGAGAGCACATGTTA 59.994 43.478 0.00 0.00 0.00 2.41
471 480 5.179555 ACACTTATTTTGGAACGAAGAGAGC 59.820 40.000 0.00 0.00 0.00 4.09
475 484 8.553696 GTTAAGACACTTATTTTGGAACGAAGA 58.446 33.333 0.00 0.00 0.00 2.87
478 487 8.441312 AAGTTAAGACACTTATTTTGGAACGA 57.559 30.769 0.00 0.00 35.10 3.85
520 529 7.336396 AGTGTCTCAACCTTAGTACAACTTTT 58.664 34.615 0.00 0.00 0.00 2.27
524 533 7.871463 ACATAAGTGTCTCAACCTTAGTACAAC 59.129 37.037 0.00 0.00 31.41 3.32
526 535 7.534723 ACATAAGTGTCTCAACCTTAGTACA 57.465 36.000 0.00 0.00 31.41 2.90
539 548 3.306780 CCTCCGTTCCAACATAAGTGTCT 60.307 47.826 0.00 0.00 37.67 3.41
549 558 3.889520 AGATACTTCCTCCGTTCCAAC 57.110 47.619 0.00 0.00 0.00 3.77
554 563 7.166167 ACATGTTTTTAGATACTTCCTCCGTT 58.834 34.615 0.00 0.00 0.00 4.44
721 731 6.833933 AGGGTTGTTCTCTTGTTTGTTTCTAT 59.166 34.615 0.00 0.00 0.00 1.98
740 750 2.369394 GGAAGCTTCCATGTAGGGTTG 58.631 52.381 35.71 0.00 46.76 3.77
757 767 7.057894 TGAGCTAGTTTAGAAAGGTTTTGGAA 58.942 34.615 0.00 0.00 0.00 3.53
829 856 1.083015 GCCACGTTTATATGCCGCG 60.083 57.895 0.00 0.00 0.00 6.46
830 857 1.281656 GGCCACGTTTATATGCCGC 59.718 57.895 0.00 0.00 31.55 6.53
831 858 1.837538 CGGGCCACGTTTATATGCCG 61.838 60.000 4.39 0.00 43.09 5.69
832 859 1.512156 CCGGGCCACGTTTATATGCC 61.512 60.000 4.39 0.00 42.24 4.40
833 860 0.816421 ACCGGGCCACGTTTATATGC 60.816 55.000 6.32 0.00 42.24 3.14
834 861 1.202604 AGACCGGGCCACGTTTATATG 60.203 52.381 1.76 0.00 42.24 1.78
835 862 1.069668 GAGACCGGGCCACGTTTATAT 59.930 52.381 1.76 0.00 42.24 0.86
836 863 0.461135 GAGACCGGGCCACGTTTATA 59.539 55.000 1.76 0.00 42.24 0.98
838 865 2.658422 GAGACCGGGCCACGTTTA 59.342 61.111 1.76 0.00 42.24 2.01
858 885 3.799281 TTTGTTCCCTGCAACTCTTTG 57.201 42.857 0.00 0.00 35.62 2.77
861 888 3.837355 AGAATTTGTTCCCTGCAACTCT 58.163 40.909 0.00 0.00 0.00 3.24
862 889 5.705609 TTAGAATTTGTTCCCTGCAACTC 57.294 39.130 0.00 0.00 0.00 3.01
864 891 7.602753 ACTAATTAGAATTTGTTCCCTGCAAC 58.397 34.615 19.38 0.00 31.90 4.17
880 907 7.783596 AGACCCTCGGAGAAATTACTAATTAGA 59.216 37.037 19.38 0.00 34.09 2.10
892 919 2.291996 TGTGGATAGACCCTCGGAGAAA 60.292 50.000 6.58 0.00 38.00 2.52
894 921 0.924090 TGTGGATAGACCCTCGGAGA 59.076 55.000 6.58 0.00 38.00 3.71
898 925 3.007635 GGTTTTTGTGGATAGACCCTCG 58.992 50.000 0.00 0.00 38.00 4.63
931 958 4.416738 GGTGCTGGAGCTGGGGAC 62.417 72.222 0.00 0.00 42.66 4.46
1072 1100 2.493973 GAGCTGCGAGGACAGAGG 59.506 66.667 0.00 0.00 40.25 3.69
1404 1441 4.032452 TCCCGCAGCATGGCAAGA 62.032 61.111 0.00 0.00 35.86 3.02
1521 1558 4.593864 GCGGAGATGTCGGAGGCC 62.594 72.222 0.00 0.00 0.00 5.19
1524 1561 4.933064 GCGGCGGAGATGTCGGAG 62.933 72.222 9.78 0.00 0.00 4.63
1736 1779 1.140589 CTGATGACGAGCCGCTTCT 59.859 57.895 0.00 0.00 0.00 2.85
1984 2027 3.492102 ACAAATCCCGGTCTATGATGG 57.508 47.619 0.00 0.00 0.00 3.51
2133 2198 0.263765 ATGGCAATGGCATTCCTCCT 59.736 50.000 16.93 0.00 46.61 3.69
2160 2225 4.314440 AGCTTGCAACTCCGCCGA 62.314 61.111 0.00 0.00 0.00 5.54
2161 2226 4.093952 CAGCTTGCAACTCCGCCG 62.094 66.667 0.00 0.00 0.00 6.46
2162 2227 4.410743 GCAGCTTGCAACTCCGCC 62.411 66.667 0.00 0.00 44.26 6.13
2171 2236 1.069432 CGATGTCCATATGCAGCTTGC 60.069 52.381 0.00 1.70 45.29 4.01
2172 2237 2.479275 CTCGATGTCCATATGCAGCTTG 59.521 50.000 0.00 0.00 0.00 4.01
2173 2238 2.763933 CTCGATGTCCATATGCAGCTT 58.236 47.619 0.00 0.00 0.00 3.74
2174 2239 1.607509 GCTCGATGTCCATATGCAGCT 60.608 52.381 0.00 0.00 0.00 4.24
2175 2240 0.795085 GCTCGATGTCCATATGCAGC 59.205 55.000 0.00 0.00 0.00 5.25
2176 2241 2.159327 TGCTCGATGTCCATATGCAG 57.841 50.000 0.00 0.00 0.00 4.41
2177 2242 2.691927 GATGCTCGATGTCCATATGCA 58.308 47.619 0.00 0.00 0.00 3.96
2178 2243 1.657594 CGATGCTCGATGTCCATATGC 59.342 52.381 0.00 0.00 43.74 3.14
2179 2244 1.657594 GCGATGCTCGATGTCCATATG 59.342 52.381 9.32 0.00 43.74 1.78
2224 2289 0.523966 GTCCTCACCGACTCTGAGTG 59.476 60.000 16.28 4.24 34.42 3.51
2235 2300 0.392193 CTGCTCCACATGTCCTCACC 60.392 60.000 0.00 0.00 0.00 4.02
2243 2315 0.249676 AGTCTGCTCTGCTCCACATG 59.750 55.000 0.00 0.00 0.00 3.21
2260 2332 4.222588 AGAGCTCTCTGTTTTATCTGCAGT 59.777 41.667 11.45 3.75 38.75 4.40
2320 2398 4.728917 CTGCATTATCTTCAGCAGTAGC 57.271 45.455 0.00 0.00 46.92 3.58
2719 2803 2.047274 TTCTTGGCCTCCTTCGCG 60.047 61.111 3.32 0.00 0.00 5.87
2831 2927 1.335142 CCACTCGCGCCTTATCTCTAC 60.335 57.143 0.00 0.00 0.00 2.59
2913 3009 2.159476 CCAAAGATCATGACTTGCGGTG 60.159 50.000 0.00 0.00 0.00 4.94
2917 3013 4.771590 TCAACCAAAGATCATGACTTGC 57.228 40.909 0.00 0.00 0.00 4.01
2921 3017 4.699257 AGCTCTTCAACCAAAGATCATGAC 59.301 41.667 0.00 0.00 34.85 3.06
2927 3024 4.363991 ACAGAGCTCTTCAACCAAAGAT 57.636 40.909 15.27 0.00 34.85 2.40
2930 3027 3.884895 TCAACAGAGCTCTTCAACCAAA 58.115 40.909 15.27 0.00 0.00 3.28
2937 3034 6.529477 GCCATTTTTAATCAACAGAGCTCTTC 59.471 38.462 15.27 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.