Multiple sequence alignment - TraesCS7D01G528200

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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 TraesCS7D01G528200 chr7D 100.000 2333 0 0 1 2333 623358266 623360598 0.000000e+00 4309.0
1 TraesCS7D01G528200 chr7D 82.409 523 46 19 785 1278 622995222 622995727 4.640000e-112 414.0
2 TraesCS7D01G528200 chr7D 76.546 388 68 13 1005 1375 622993490 622993871 8.510000e-45 191.0
3 TraesCS7D01G528200 chr7D 86.000 100 11 1 1420 1516 336159859 336159760 1.140000e-18 104.0
4 TraesCS7D01G528200 chr7D 90.000 60 5 1 1691 1750 623011728 623011786 2.490000e-10 76.8
5 TraesCS7D01G528200 chr7A 92.743 1819 115 12 1 1815 718266179 718264374 0.000000e+00 2612.0
6 TraesCS7D01G528200 chr7A 84.611 1657 151 37 703 2333 718344180 718342602 0.000000e+00 1552.0
7 TraesCS7D01G528200 chr7A 83.910 752 92 16 696 1420 718427479 718426730 0.000000e+00 691.0
8 TraesCS7D01G528200 chr7A 87.143 490 30 9 1844 2333 718264383 718263927 2.050000e-145 525.0
9 TraesCS7D01G528200 chr7A 83.793 580 67 16 785 1357 718440912 718440353 2.050000e-145 525.0
10 TraesCS7D01G528200 chr7A 83.618 293 21 12 394 667 718344455 718344171 1.380000e-62 250.0
11 TraesCS7D01G528200 chr7A 76.578 491 81 26 926 1400 718518082 718517610 3.000000e-59 239.0
12 TraesCS7D01G528200 chr7A 78.466 339 62 7 1067 1400 719037301 719036969 6.530000e-51 211.0
13 TraesCS7D01G528200 chr7A 84.921 126 9 4 542 657 718427589 718427464 4.070000e-23 119.0
14 TraesCS7D01G528200 chr7A 86.000 100 11 1 1420 1516 379030523 379030424 1.140000e-18 104.0
15 TraesCS7D01G528200 chr7B 88.104 1656 143 24 703 2333 720829306 720827680 0.000000e+00 1917.0
16 TraesCS7D01G528200 chr7B 83.377 764 87 22 696 1420 720932905 720932143 0.000000e+00 671.0
17 TraesCS7D01G528200 chr7B 85.333 600 45 14 785 1357 720948744 720948161 4.320000e-162 580.0
18 TraesCS7D01G528200 chr7B 87.311 331 28 7 82 398 223332172 223331842 1.320000e-97 366.0
19 TraesCS7D01G528200 chr7B 75.951 815 127 39 1514 2310 720948125 720947362 2.850000e-94 355.0
20 TraesCS7D01G528200 chr7B 84.229 279 21 9 394 657 720829571 720829301 1.380000e-62 250.0
21 TraesCS7D01G528200 chr7B 81.655 278 26 10 394 657 720933157 720932891 8.450000e-50 207.0
22 TraesCS7D01G528200 chr7B 87.000 100 10 1 1420 1516 310413065 310413164 2.450000e-20 110.0
23 TraesCS7D01G528200 chr7B 83.019 106 15 2 1411 1513 504190092 504190197 2.470000e-15 93.5
24 TraesCS7D01G528200 chr7B 100.000 40 0 0 43 82 720873960 720873921 8.940000e-10 75.0
25 TraesCS7D01G528200 chr5B 88.073 327 26 8 82 395 385848807 385849133 2.190000e-100 375.0
26 TraesCS7D01G528200 chr5B 87.156 327 29 8 82 395 436416812 436417138 2.200000e-95 359.0
27 TraesCS7D01G528200 chr4B 87.195 328 28 9 82 395 424193079 424193406 6.130000e-96 361.0
28 TraesCS7D01G528200 chr4B 87.539 321 27 10 91 398 575703571 575703251 2.200000e-95 359.0
29 TraesCS7D01G528200 chr3B 87.578 322 26 8 91 398 576003511 576003190 6.130000e-96 361.0
30 TraesCS7D01G528200 chr1B 87.195 328 28 10 82 395 576989886 576990213 6.130000e-96 361.0
31 TraesCS7D01G528200 chr6B 87.539 321 26 7 91 398 627209275 627208956 2.200000e-95 359.0
32 TraesCS7D01G528200 chr2A 81.905 105 16 1 1412 1513 53078409 53078513 4.130000e-13 86.1
33 TraesCS7D01G528200 chr2D 81.111 90 14 1 1427 1513 589757260 589757349 4.160000e-08 69.4


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 TraesCS7D01G528200 chr7D 623358266 623360598 2332 False 4309.0 4309 100.0000 1 2333 1 chr7D.!!$F2 2332
1 TraesCS7D01G528200 chr7D 622993490 622995727 2237 False 302.5 414 79.4775 785 1375 2 chr7D.!!$F3 590
2 TraesCS7D01G528200 chr7A 718263927 718266179 2252 True 1568.5 2612 89.9430 1 2333 2 chr7A.!!$R5 2332
3 TraesCS7D01G528200 chr7A 718342602 718344455 1853 True 901.0 1552 84.1145 394 2333 2 chr7A.!!$R6 1939
4 TraesCS7D01G528200 chr7A 718440353 718440912 559 True 525.0 525 83.7930 785 1357 1 chr7A.!!$R2 572
5 TraesCS7D01G528200 chr7A 718426730 718427589 859 True 405.0 691 84.4155 542 1420 2 chr7A.!!$R7 878
6 TraesCS7D01G528200 chr7B 720827680 720829571 1891 True 1083.5 1917 86.1665 394 2333 2 chr7B.!!$R3 1939
7 TraesCS7D01G528200 chr7B 720947362 720948744 1382 True 467.5 580 80.6420 785 2310 2 chr7B.!!$R5 1525
8 TraesCS7D01G528200 chr7B 720932143 720933157 1014 True 439.0 671 82.5160 394 1420 2 chr7B.!!$R4 1026

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
783 812 0.818296 TGACCACAAACAAAACCGGG 59.182 50.0 6.32 0.0 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2225 3233 0.037734 AAGGGGTTGCGTAAAGGGAG 59.962 55.0 0.0 0.0 0.0 4.3 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
28 29 6.091441 TGGGACATTTTGTTTCTTCAAAAACG 59.909 34.615 8.30 6.11 45.87 3.60
36 37 9.575783 TTTTGTTTCTTCAAAAACGTAAGCTAT 57.424 25.926 0.00 0.00 42.02 2.97
37 38 9.575783 TTTGTTTCTTCAAAAACGTAAGCTATT 57.424 25.926 0.00 0.00 41.12 1.73
38 39 9.575783 TTGTTTCTTCAAAAACGTAAGCTATTT 57.424 25.926 0.00 0.00 41.12 1.40
39 40 9.575783 TGTTTCTTCAAAAACGTAAGCTATTTT 57.424 25.926 0.00 0.00 41.12 1.82
76 78 7.387119 AGAGTCCAATTTATTAACCGGTTTC 57.613 36.000 27.64 11.85 0.00 2.78
95 97 7.148457 CCGGTTTCACCTTACTATCTTCTTTTC 60.148 40.741 0.00 0.00 35.66 2.29
103 105 9.939802 ACCTTACTATCTTCTTTTCGTTTACAT 57.060 29.630 0.00 0.00 0.00 2.29
112 115 7.803189 TCTTCTTTTCGTTTACATGCTCAATTC 59.197 33.333 0.00 0.00 0.00 2.17
127 130 6.761312 TGCTCAATTCAAAAATCTCACCAAT 58.239 32.000 0.00 0.00 0.00 3.16
139 142 4.760530 TCTCACCAATCAAGGTAGATGG 57.239 45.455 0.00 0.00 40.77 3.51
145 148 4.194640 CCAATCAAGGTAGATGGTGAGTG 58.805 47.826 0.00 0.00 36.21 3.51
146 149 4.194640 CAATCAAGGTAGATGGTGAGTGG 58.805 47.826 0.00 0.00 33.61 4.00
148 151 2.567169 TCAAGGTAGATGGTGAGTGGTG 59.433 50.000 0.00 0.00 0.00 4.17
186 189 6.862944 TGTAAAAGCACTAAATTAATGCGC 57.137 33.333 0.00 0.00 44.25 6.09
193 196 6.616947 AGCACTAAATTAATGCGCTTGTAAA 58.383 32.000 9.73 0.00 44.25 2.01
194 197 7.087639 AGCACTAAATTAATGCGCTTGTAAAA 58.912 30.769 9.73 0.00 44.25 1.52
274 277 8.970691 TTGCTCAATTTTCTCTTAATACTTGC 57.029 30.769 0.00 0.00 0.00 4.01
301 304 8.027440 TGCAATGATTTAATGCACCTTAAAAC 57.973 30.769 8.82 7.35 44.52 2.43
304 307 8.658609 CAATGATTTAATGCACCTTAAAACCTG 58.341 33.333 8.82 4.46 35.02 4.00
324 327 5.305128 ACCTGAACATGTGATGGAAAACAAT 59.695 36.000 15.37 0.00 33.60 2.71
331 334 8.090250 ACATGTGATGGAAAACAATGAAATTG 57.910 30.769 0.00 0.00 46.91 2.32
388 391 8.664211 AGATAGCCTTATAAACCGAAAAAGAG 57.336 34.615 0.00 0.00 0.00 2.85
413 417 4.134563 AGTATATCACGATTTTGGTGCCC 58.865 43.478 0.00 0.00 35.39 5.36
436 440 4.911514 TGTTTTCAAAACTGTAGGCCTC 57.088 40.909 9.68 1.02 0.00 4.70
503 509 8.988060 TCATCCACATGTACTATCTTAGGAAAA 58.012 33.333 0.00 0.00 0.00 2.29
559 567 3.270027 CCCGTATGACATTGCAAGAGAA 58.730 45.455 4.94 0.00 0.00 2.87
602 622 4.217118 CAGAAAATATGGCCTCCTATGCAC 59.783 45.833 3.32 0.00 0.00 4.57
772 801 0.836606 TCTTGGCAGTCTGACCACAA 59.163 50.000 13.54 6.70 35.10 3.33
774 803 1.334869 CTTGGCAGTCTGACCACAAAC 59.665 52.381 13.54 0.00 35.10 2.93
776 805 1.340502 TGGCAGTCTGACCACAAACAA 60.341 47.619 2.39 0.00 0.00 2.83
779 808 3.179048 GCAGTCTGACCACAAACAAAAC 58.821 45.455 3.32 0.00 0.00 2.43
780 809 3.769536 CAGTCTGACCACAAACAAAACC 58.230 45.455 3.76 0.00 0.00 3.27
781 810 2.422127 AGTCTGACCACAAACAAAACCG 59.578 45.455 3.76 0.00 0.00 4.44
782 811 1.746220 TCTGACCACAAACAAAACCGG 59.254 47.619 0.00 0.00 0.00 5.28
783 812 0.818296 TGACCACAAACAAAACCGGG 59.182 50.000 6.32 0.00 0.00 5.73
788 817 2.137528 CAAACAAAACCGGGGCCCT 61.138 57.895 24.38 0.00 0.00 5.19
843 1792 4.874977 GCCAGAGCTACCGCGGAC 62.875 72.222 35.90 20.66 42.32 4.79
1268 2256 1.303888 CAGCAGAAGGTGGCATGGT 60.304 57.895 0.00 0.00 39.53 3.55
1281 2269 1.007038 CATGGTGCAAAAGCGCAGT 60.007 52.632 11.47 0.00 44.05 4.40
1338 2330 0.246635 CCCTCCGGCTATAATCGGTG 59.753 60.000 0.00 9.69 45.79 4.94
1375 2367 2.768527 CTCTGGAAGTATCCTTGCTCCA 59.231 50.000 0.00 0.00 46.70 3.86
1400 2392 3.244044 CCTCTCTATTTCTGGTGCTAGGC 60.244 52.174 0.00 0.00 0.00 3.93
1402 2394 3.386078 TCTCTATTTCTGGTGCTAGGCAG 59.614 47.826 0.00 0.00 40.08 4.85
1422 2414 4.745649 CAGGTGAGTGTTTAGCTACTACC 58.254 47.826 0.00 0.00 0.00 3.18
1433 2425 1.062352 AGCTACTACCCCCTCCGATTT 60.062 52.381 0.00 0.00 0.00 2.17
1440 2432 6.775234 ACTACCCCCTCCGATTTAAAATAT 57.225 37.500 0.00 0.00 0.00 1.28
1441 2433 7.157947 ACTACCCCCTCCGATTTAAAATATT 57.842 36.000 0.00 0.00 0.00 1.28
1737 2732 8.323567 TCAAGTTACGATATTTAAAGGACCCTT 58.676 33.333 0.00 0.00 37.98 3.95
1812 2808 8.196378 AGCCTCCGTAAGATAGATTTTTAGAT 57.804 34.615 0.00 0.00 43.02 1.98
1918 2916 3.385193 GCAATTTGCACCCAAACTAGT 57.615 42.857 16.35 0.00 43.20 2.57
1919 2917 3.059166 GCAATTTGCACCCAAACTAGTG 58.941 45.455 16.35 0.00 43.20 2.74
1920 2918 3.243704 GCAATTTGCACCCAAACTAGTGA 60.244 43.478 16.35 0.00 43.20 3.41
1921 2919 4.739137 GCAATTTGCACCCAAACTAGTGAA 60.739 41.667 16.35 0.00 43.20 3.18
1922 2920 4.584327 ATTTGCACCCAAACTAGTGAAC 57.416 40.909 0.00 0.00 43.20 3.18
1923 2921 3.290948 TTGCACCCAAACTAGTGAACT 57.709 42.857 0.00 0.00 36.01 3.01
1924 2922 3.290948 TGCACCCAAACTAGTGAACTT 57.709 42.857 0.00 0.00 36.01 2.66
1925 2923 3.211045 TGCACCCAAACTAGTGAACTTC 58.789 45.455 0.00 0.00 36.01 3.01
1928 2926 4.261197 GCACCCAAACTAGTGAACTTCTTG 60.261 45.833 0.00 0.00 36.01 3.02
1951 2949 0.392706 TTTGCTCCAGCTTCTCGTCA 59.607 50.000 0.00 0.00 42.66 4.35
1990 2988 7.651304 CAGAGGCAATAATTCTGTCAGTAGTAG 59.349 40.741 0.00 0.00 34.92 2.57
2002 3000 9.962783 TTCTGTCAGTAGTAGAAGTTAACTTTC 57.037 33.333 21.40 14.16 36.11 2.62
2067 3065 8.829373 AAATTAGCTGATTACTTCAAATCCCT 57.171 30.769 3.88 0.00 35.40 4.20
2068 3066 9.920946 AAATTAGCTGATTACTTCAAATCCCTA 57.079 29.630 3.88 0.00 35.40 3.53
2115 3121 5.681982 GCATATCGGCGTATAGATTACTCAC 59.318 44.000 6.85 0.00 0.00 3.51
2153 3159 1.608590 ACACGCCTTGAAATTGACCAG 59.391 47.619 0.00 0.00 0.00 4.00
2177 3183 1.634702 CTTAGCTCTGTTGCGAGGAC 58.365 55.000 0.00 0.00 38.13 3.85
2225 3233 1.250840 AAGATGGGCGACAAAAGGGC 61.251 55.000 0.00 0.00 0.00 5.19
2242 3250 2.044555 GCTCCCTTTACGCAACCCC 61.045 63.158 0.00 0.00 0.00 4.95
2311 3320 7.561251 TGATAATACTCGACATTTCCTTTCCA 58.439 34.615 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 78 9.199982 TGTAAACGAAAAGAAGATAGTAAGGTG 57.800 33.333 0.00 0.00 0.00 4.00
95 97 8.231304 AGATTTTTGAATTGAGCATGTAAACG 57.769 30.769 0.00 0.00 0.00 3.60
103 105 5.787953 TGGTGAGATTTTTGAATTGAGCA 57.212 34.783 0.00 0.00 0.00 4.26
112 115 7.452880 TCTACCTTGATTGGTGAGATTTTTG 57.547 36.000 0.00 0.00 41.05 2.44
127 130 2.567169 CACCACTCACCATCTACCTTGA 59.433 50.000 0.00 0.00 0.00 3.02
249 252 8.575589 TGCAAGTATTAAGAGAAAATTGAGCAA 58.424 29.630 0.00 0.00 0.00 3.91
274 277 7.773864 TTAAGGTGCATTAAATCATTGCATG 57.226 32.000 4.14 0.00 46.90 4.06
293 296 5.476599 TCCATCACATGTTCAGGTTTTAAGG 59.523 40.000 0.00 0.00 0.00 2.69
301 304 4.852134 TGTTTTCCATCACATGTTCAGG 57.148 40.909 0.00 0.00 0.00 3.86
304 307 7.712264 TTTCATTGTTTTCCATCACATGTTC 57.288 32.000 0.00 0.00 0.00 3.18
388 391 4.213482 GCACCAAAATCGTGATATACTCCC 59.787 45.833 0.00 0.00 32.77 4.30
413 417 5.200368 AGGCCTACAGTTTTGAAAACATG 57.800 39.130 21.34 17.32 0.00 3.21
436 440 3.708563 AATTGTCAAACAGGGTTCACG 57.291 42.857 0.00 0.00 0.00 4.35
503 509 7.178628 AGGTGTATGTGACTATGTGTACTTTCT 59.821 37.037 0.00 0.00 0.00 2.52
574 582 2.310538 GAGGCCATATTTTCTGTGGGG 58.689 52.381 5.01 0.00 36.66 4.96
684 712 1.396996 CACGGGCTATCGACCAAAAAG 59.603 52.381 0.00 0.00 38.74 2.27
694 722 2.690786 TGTTTACACACACGGGCTATC 58.309 47.619 0.00 0.00 0.00 2.08
772 801 2.523168 CAGGGCCCCGGTTTTGTT 60.523 61.111 21.43 0.00 0.00 2.83
774 803 4.614036 ACCAGGGCCCCGGTTTTG 62.614 66.667 25.31 11.93 29.08 2.44
843 1792 3.612479 GCTAATTGCCCTTGACACTGTTG 60.612 47.826 0.00 0.00 35.15 3.33
881 1830 2.063979 TGGAGGTAGCATGGACGGG 61.064 63.158 0.00 0.00 0.00 5.28
1272 2260 1.153745 CGAGCTCCTACTGCGCTTT 60.154 57.895 9.73 0.00 33.47 3.51
1400 2392 4.381718 GGGTAGTAGCTAAACACTCACCTG 60.382 50.000 0.00 0.00 0.00 4.00
1402 2394 3.118847 GGGGTAGTAGCTAAACACTCACC 60.119 52.174 9.06 6.94 0.00 4.02
1422 2414 6.038936 ACGACAAATATTTTAAATCGGAGGGG 59.961 38.462 18.02 0.92 32.56 4.79
1440 2432 7.614124 AACCTTAGTTCAAAACTACGACAAA 57.386 32.000 5.26 0.00 43.30 2.83
1441 2433 7.981225 ACTAACCTTAGTTCAAAACTACGACAA 59.019 33.333 5.26 0.00 43.30 3.18
1503 2498 2.563179 GCTTGAGACAAGTACTCCCTCA 59.437 50.000 14.19 14.19 33.95 3.86
1618 2613 6.538381 GTGAAATGGGAACTTTTTGTGTCAAT 59.462 34.615 0.00 0.00 37.77 2.57
1779 2774 7.308450 TCTATCTTACGGAGGCTAACTAGTA 57.692 40.000 0.00 0.00 0.00 1.82
1812 2808 8.595362 TTGAGAGATGTCTTAAAGGTCATAGA 57.405 34.615 0.00 0.00 30.97 1.98
1840 2836 3.537580 ACGCACTGAAGTTCTTAAACCA 58.462 40.909 4.17 0.00 35.92 3.67
1915 2913 3.117663 AGCAAACCCCAAGAAGTTCACTA 60.118 43.478 5.50 0.00 0.00 2.74
1916 2914 2.031870 GCAAACCCCAAGAAGTTCACT 58.968 47.619 5.50 0.00 0.00 3.41
1917 2915 2.031870 AGCAAACCCCAAGAAGTTCAC 58.968 47.619 5.50 0.00 0.00 3.18
1918 2916 2.306847 GAGCAAACCCCAAGAAGTTCA 58.693 47.619 5.50 0.00 0.00 3.18
1919 2917 1.613925 GGAGCAAACCCCAAGAAGTTC 59.386 52.381 0.00 0.00 0.00 3.01
1920 2918 1.063266 TGGAGCAAACCCCAAGAAGTT 60.063 47.619 0.00 0.00 0.00 2.66
1921 2919 0.555769 TGGAGCAAACCCCAAGAAGT 59.444 50.000 0.00 0.00 0.00 3.01
1922 2920 1.251251 CTGGAGCAAACCCCAAGAAG 58.749 55.000 0.00 0.00 31.11 2.85
1923 2921 0.827507 GCTGGAGCAAACCCCAAGAA 60.828 55.000 0.00 0.00 41.59 2.52
1924 2922 1.228552 GCTGGAGCAAACCCCAAGA 60.229 57.895 0.00 0.00 41.59 3.02
1925 2923 0.829182 AAGCTGGAGCAAACCCCAAG 60.829 55.000 0.65 0.00 45.16 3.61
1928 2926 0.962855 GAGAAGCTGGAGCAAACCCC 60.963 60.000 0.65 0.00 45.16 4.95
2002 3000 6.845302 TGTCTTTGTGCAGCTTTTATATCTG 58.155 36.000 0.00 0.00 0.00 2.90
2089 3087 6.095021 TGAGTAATCTATACGCCGATATGCTT 59.905 38.462 0.00 0.00 0.00 3.91
2153 3159 1.086634 CGCAACAGAGCTAAGGAGGC 61.087 60.000 0.00 0.00 0.00 4.70
2225 3233 0.037734 AAGGGGTTGCGTAAAGGGAG 59.962 55.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.