Multiple sequence alignment - TraesCS7D01G128000

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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 TraesCS7D01G128000 chr7D 100.000 1805 0 0 1 1805 80321372 80323176 0.000000e+00 3334.0
1 TraesCS7D01G128000 chr7D 97.010 1806 36 7 1 1788 80465965 80467770 0.000000e+00 3020.0
2 TraesCS7D01G128000 chr7D 88.370 963 65 20 642 1575 80389145 80390089 0.000000e+00 1114.0
3 TraesCS7D01G128000 chr7D 100.000 484 0 0 2033 2516 80323404 80323887 0.000000e+00 894.0
4 TraesCS7D01G128000 chr7D 86.255 793 69 17 966 1737 80459924 80460697 0.000000e+00 824.0
5 TraesCS7D01G128000 chr7D 87.255 408 32 7 2114 2513 80461100 80461495 4.940000e-122 448.0
6 TraesCS7D01G128000 chr7D 96.124 258 8 2 373 629 15027246 15026990 1.080000e-113 420.0
7 TraesCS7D01G128000 chr7D 96.429 252 7 2 373 623 242775554 242775804 5.010000e-112 414.0
8 TraesCS7D01G128000 chr7D 95.094 265 9 3 373 634 426172195 426171932 5.010000e-112 414.0
9 TraesCS7D01G128000 chr7D 94.361 266 12 3 371 634 574766123 574765859 3.010000e-109 405.0
10 TraesCS7D01G128000 chr7D 98.630 219 3 0 2058 2276 80468162 80468380 3.040000e-104 388.0
11 TraesCS7D01G128000 chr7D 89.671 213 10 3 633 839 80456991 80457197 6.900000e-66 261.0
12 TraesCS7D01G128000 chr7D 85.542 249 23 8 53 294 107199839 107200081 5.370000e-62 248.0
13 TraesCS7D01G128000 chr7D 84.615 221 20 5 2092 2308 80391135 80391345 9.120000e-50 207.0
14 TraesCS7D01G128000 chr7D 91.241 137 9 2 2382 2515 80416248 80416384 1.540000e-42 183.0
15 TraesCS7D01G128000 chr7D 97.030 101 3 0 2416 2516 80468381 80468481 1.200000e-38 171.0
16 TraesCS7D01G128000 chr7D 82.500 200 27 4 981 1178 85931879 85931686 4.300000e-38 169.0
17 TraesCS7D01G128000 chr7A 90.580 966 56 16 624 1575 83128754 83129698 0.000000e+00 1247.0
18 TraesCS7D01G128000 chr7A 87.703 431 34 6 2092 2515 83138273 83138691 3.760000e-133 484.0
19 TraesCS7D01G128000 chr7A 86.053 337 29 5 2092 2421 83223918 83224243 1.850000e-91 346.0
20 TraesCS7D01G128000 chr7A 85.306 245 22 7 56 294 379688283 379688047 8.990000e-60 241.0
21 TraesCS7D01G128000 chr7A 87.432 183 14 2 1402 1575 83216078 83216260 4.240000e-48 202.0
22 TraesCS7D01G128000 chr7A 90.741 108 7 3 2410 2515 83224258 83224364 9.380000e-30 141.0
23 TraesCS7D01G128000 chr7A 96.250 80 3 0 1330 1409 83215700 83215779 5.650000e-27 132.0
24 TraesCS7D01G128000 chr7A 88.525 61 6 1 1737 1797 83223463 83223522 3.470000e-09 73.1
25 TraesCS7D01G128000 chr7B 88.734 861 61 24 655 1497 27493543 27494385 0.000000e+00 1020.0
26 TraesCS7D01G128000 chr7B 88.012 342 27 4 2114 2443 27494783 27495122 2.350000e-105 392.0
27 TraesCS7D01G128000 chr7B 79.848 263 39 10 855 1110 35101479 35101224 1.990000e-41 180.0
28 TraesCS7D01G128000 chr7B 82.464 211 22 9 1526 1727 27494525 27494729 1.200000e-38 171.0
29 TraesCS7D01G128000 chr5D 96.484 256 6 3 368 622 87803617 87803364 1.080000e-113 420.0
30 TraesCS7D01G128000 chr5D 85.887 248 23 7 56 297 538171536 538171777 1.160000e-63 254.0
31 TraesCS7D01G128000 chr4D 94.834 271 9 4 370 636 48708921 48708652 3.870000e-113 418.0
32 TraesCS7D01G128000 chr4D 88.333 120 12 1 1617 1736 109275089 109274972 2.610000e-30 143.0
33 TraesCS7D01G128000 chr2D 95.113 266 10 3 373 637 315803520 315803257 1.390000e-112 416.0
34 TraesCS7D01G128000 chr2D 85.141 249 20 9 53 294 568859830 568860068 3.230000e-59 239.0
35 TraesCS7D01G128000 chr2D 88.525 122 12 1 1616 1737 607675860 607675741 2.020000e-31 147.0
36 TraesCS7D01G128000 chr2A 95.736 258 9 2 373 629 1882081 1882337 5.010000e-112 414.0
37 TraesCS7D01G128000 chr3D 94.424 269 11 3 373 638 416217590 416217323 6.480000e-111 411.0
38 TraesCS7D01G128000 chr3D 88.636 220 16 4 56 269 280046393 280046609 2.480000e-65 259.0
39 TraesCS7D01G128000 chr3D 86.345 249 21 6 56 298 501481013 501480772 2.480000e-65 259.0
40 TraesCS7D01G128000 chr4B 88.288 222 20 4 53 269 528259079 528259299 6.900000e-66 261.0
41 TraesCS7D01G128000 chr4B 86.992 123 14 1 1614 1736 167349962 167350082 1.210000e-28 137.0
42 TraesCS7D01G128000 chr6D 87.946 224 19 5 53 269 324114527 324114749 8.930000e-65 257.0
43 TraesCS7D01G128000 chr6D 88.000 125 13 1 1615 1739 410395466 410395588 2.020000e-31 147.0
44 TraesCS7D01G128000 chr6D 85.366 123 16 1 1617 1739 85797493 85797613 2.630000e-25 126.0
45 TraesCS7D01G128000 chr6D 85.484 124 13 2 1613 1736 87598714 87598596 9.450000e-25 124.0
46 TraesCS7D01G128000 chr6D 84.426 122 17 1 1616 1737 115788449 115788330 4.400000e-23 119.0
47 TraesCS7D01G128000 chr6D 83.471 121 18 1 1617 1737 384220927 384221045 7.360000e-21 111.0
48 TraesCS7D01G128000 chr6D 82.927 123 19 1 1614 1736 125239656 125239776 2.650000e-20 110.0
49 TraesCS7D01G128000 chr1D 76.042 384 72 17 1000 1372 419296600 419296226 5.530000e-42 182.0
50 TraesCS7D01G128000 chr1D 76.000 375 68 15 1000 1372 418756025 418755671 9.250000e-40 174.0
51 TraesCS7D01G128000 chr1D 87.611 113 12 1 1624 1736 120536245 120536355 2.030000e-26 130.0
52 TraesCS7D01G128000 chr1D 84.496 129 17 2 1613 1741 465887265 465887140 9.450000e-25 124.0
53 TraesCS7D01G128000 chr1D 82.090 134 18 5 1611 1741 448608373 448608243 2.650000e-20 110.0
54 TraesCS7D01G128000 chr5A 88.189 127 12 2 1610 1736 227926405 227926528 5.610000e-32 148.0
55 TraesCS7D01G128000 chr4A 87.805 123 13 1 1614 1736 467246482 467246602 2.610000e-30 143.0
56 TraesCS7D01G128000 chr4A 86.154 130 14 3 1613 1741 38657267 38657393 1.210000e-28 137.0
57 TraesCS7D01G128000 chr5B 86.992 123 14 1 1617 1739 661308808 661308688 1.210000e-28 137.0
58 TraesCS7D01G128000 chr5B 85.827 127 15 2 1615 1741 520571187 520571064 5.650000e-27 132.0
59 TraesCS7D01G128000 chr1B 84.559 136 18 2 1603 1737 325270498 325270365 5.650000e-27 132.0
60 TraesCS7D01G128000 chrUn 90.361 83 7 1 1615 1697 11850165 11850084 9.520000e-20 108.0
61 TraesCS7D01G128000 chrUn 90.361 83 7 1 1615 1697 351755190 351755271 9.520000e-20 108.0
62 TraesCS7D01G128000 chrUn 86.869 99 10 3 1601 1697 380526079 380526176 9.520000e-20 108.0
63 TraesCS7D01G128000 chrUn 86.364 66 8 1 1622 1687 15465960 15466024 1.250000e-08 71.3


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 TraesCS7D01G128000 chr7D 80321372 80323887 2515 False 2114.000000 3334 100.000000 1 2516 2 chr7D.!!$F4 2515
1 TraesCS7D01G128000 chr7D 80465965 80468481 2516 False 1193.000000 3020 97.556667 1 2516 3 chr7D.!!$F7 2515
2 TraesCS7D01G128000 chr7D 80389145 80391345 2200 False 660.500000 1114 86.492500 642 2308 2 chr7D.!!$F5 1666
3 TraesCS7D01G128000 chr7D 80456991 80461495 4504 False 511.000000 824 87.727000 633 2513 3 chr7D.!!$F6 1880
4 TraesCS7D01G128000 chr7A 83128754 83129698 944 False 1247.000000 1247 90.580000 624 1575 1 chr7A.!!$F1 951
5 TraesCS7D01G128000 chr7B 27493543 27495122 1579 False 527.666667 1020 86.403333 655 2443 3 chr7B.!!$F1 1788

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
892 1489 0.522705 AGCGTCGTACTATGTGCACG 60.523 55.0 13.13 0.0 36.81 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2413 6381 1.035139 ACTGTACGTTGGAGACCGTT 58.965 50.0 0.0 0.0 38.43 4.44 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
25 26 5.938322 ACTTGTATTGGCATGAAGTTTACG 58.062 37.500 0.00 0.00 0.00 3.18
27 28 4.580868 TGTATTGGCATGAAGTTTACGGA 58.419 39.130 0.00 0.00 0.00 4.69
28 29 5.004448 TGTATTGGCATGAAGTTTACGGAA 58.996 37.500 0.00 0.00 0.00 4.30
44 45 3.335579 ACGGAAATACCACTCTTTCTGC 58.664 45.455 4.26 0.00 40.04 4.26
70 71 8.675504 CATATAACTTATACTACCTCCGTCCTG 58.324 40.741 0.00 0.00 0.00 3.86
301 304 6.359804 ACATGACGGAGGTAGTATGTTACTA 58.640 40.000 0.00 0.00 40.14 1.82
371 374 4.914177 ACCCAAACGGAGGAAGTAATAA 57.086 40.909 0.00 0.00 34.64 1.40
505 509 7.807977 ATATGATGTGGAAGTACATTCAACC 57.192 36.000 0.00 0.00 40.68 3.77
649 655 9.862371 AGAGAGTACTACAATTTGTAAGATGTG 57.138 33.333 10.32 1.13 31.67 3.21
882 1463 2.533129 GTGCCTACAAATAGCGTCGTAC 59.467 50.000 0.00 0.00 0.00 3.67
883 1464 2.424601 TGCCTACAAATAGCGTCGTACT 59.575 45.455 0.00 0.00 0.00 2.73
884 1465 3.627123 TGCCTACAAATAGCGTCGTACTA 59.373 43.478 0.00 0.00 0.00 1.82
892 1489 0.522705 AGCGTCGTACTATGTGCACG 60.523 55.000 13.13 0.00 36.81 5.34
895 1492 1.189403 GTCGTACTATGTGCACGAGC 58.811 55.000 13.13 0.00 44.05 5.03
1319 3986 0.037326 TCCTGCAAGATGGACGTGAC 60.037 55.000 0.00 0.00 34.07 3.67
1431 4098 1.725557 GATACTGCGACCTCTGCCGA 61.726 60.000 0.00 0.00 0.00 5.54
1590 4374 0.670239 TGCATGCAGTGTGTACTCCG 60.670 55.000 18.46 0.00 34.07 4.63
1645 5117 2.159226 CCGTCCTGAATTACTTCTCGCT 60.159 50.000 0.00 0.00 32.29 4.93
1788 5620 1.001406 GTGTGTCACCCCTCTTCTCAG 59.999 57.143 0.00 0.00 0.00 3.35
1790 5622 1.216710 GTCACCCCTCTTCTCAGCG 59.783 63.158 0.00 0.00 0.00 5.18
1792 5624 2.604686 ACCCCTCTTCTCAGCGCA 60.605 61.111 11.47 0.00 0.00 6.09
1794 5626 2.659016 CCCTCTTCTCAGCGCACA 59.341 61.111 11.47 0.00 0.00 4.57
1795 5627 1.220206 CCCTCTTCTCAGCGCACAT 59.780 57.895 11.47 0.00 0.00 3.21
1796 5628 0.461548 CCCTCTTCTCAGCGCACATA 59.538 55.000 11.47 0.00 0.00 2.29
1797 5629 1.069823 CCCTCTTCTCAGCGCACATAT 59.930 52.381 11.47 0.00 0.00 1.78
1798 5630 2.133553 CCTCTTCTCAGCGCACATATG 58.866 52.381 11.47 0.00 0.00 1.78
2055 5887 0.408309 TCTCTCTCGGGTGGGAGAAA 59.592 55.000 0.00 0.00 42.20 2.52
2069 6023 0.606673 GAGAAAAGCAAGGCGGGAGT 60.607 55.000 0.00 0.00 0.00 3.85
2313 6272 9.695526 TGTTCAGTTTTCATTCATGATTTTAGG 57.304 29.630 0.00 0.00 36.56 2.69
2354 6313 5.716228 TCACCAAGCTGGACAATGATATTTT 59.284 36.000 8.91 0.00 40.96 1.82
2413 6381 4.079980 ACATACAAGCACCACTACAACA 57.920 40.909 0.00 0.00 0.00 3.33
2445 6413 5.495502 CAACGTACAGTTTGGTTGTACTTC 58.504 41.667 12.14 0.00 45.43 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 5.123186 TCCGTAAACTTCATGCCAATACAAG 59.877 40.000 0.00 0.00 0.00 3.16
25 26 8.560374 GTTATATGCAGAAAGAGTGGTATTTCC 58.440 37.037 0.00 0.00 34.91 3.13
27 28 9.686683 AAGTTATATGCAGAAAGAGTGGTATTT 57.313 29.630 0.00 0.00 0.00 1.40
44 45 8.675504 CAGGACGGAGGTAGTATAAGTTATATG 58.324 40.741 5.90 0.00 0.00 1.78
301 304 6.377146 AGCCAAAATTGACTATACATTTCCGT 59.623 34.615 0.00 0.00 0.00 4.69
304 307 9.638239 TTTGAGCCAAAATTGACTATACATTTC 57.362 29.630 0.00 0.00 29.89 2.17
346 349 2.854963 ACTTCCTCCGTTTGGGTTTAC 58.145 47.619 0.00 0.00 37.00 2.01
371 374 6.982724 CGGAGTAAATAAAAACGAGGGAGTAT 59.017 38.462 0.00 0.00 0.00 2.12
486 490 3.751175 CGTGGTTGAATGTACTTCCACAT 59.249 43.478 14.11 0.00 43.50 3.21
575 579 6.811665 AGTTTTTGGTCAAAGTCAAGCTTTAC 59.188 34.615 2.40 2.40 44.95 2.01
649 655 6.148480 AGCTGACTTCATTTATGACAAGTCAC 59.852 38.462 17.25 14.75 42.09 3.67
748 760 3.152341 CACCAAGTTGGAAGCTGAGATT 58.848 45.455 28.80 0.00 40.96 2.40
892 1489 3.311871 AGATGAAATGCGATGTCTTGCTC 59.688 43.478 0.00 0.00 32.50 4.26
895 1492 3.360533 GCAGATGAAATGCGATGTCTTG 58.639 45.455 0.00 0.00 33.31 3.02
1319 3986 2.694760 GCTTTCTTGCAGCCCTCGG 61.695 63.158 0.00 0.00 0.00 4.63
1608 5080 7.047460 TCAGGACGGAGGTAGTATTATTTTC 57.953 40.000 0.00 0.00 0.00 2.29
1720 5195 3.335183 CCTCTCATACTCCCTCCATCCTA 59.665 52.174 0.00 0.00 0.00 2.94
2044 5876 1.536073 GCCTTGCTTTTCTCCCACCC 61.536 60.000 0.00 0.00 0.00 4.61
2045 5877 1.866853 CGCCTTGCTTTTCTCCCACC 61.867 60.000 0.00 0.00 0.00 4.61
2046 5878 1.581447 CGCCTTGCTTTTCTCCCAC 59.419 57.895 0.00 0.00 0.00 4.61
2047 5879 1.603455 CCGCCTTGCTTTTCTCCCA 60.603 57.895 0.00 0.00 0.00 4.37
2049 5881 1.303317 TCCCGCCTTGCTTTTCTCC 60.303 57.895 0.00 0.00 0.00 3.71
2055 5887 4.351054 CCCACTCCCGCCTTGCTT 62.351 66.667 0.00 0.00 0.00 3.91
2069 6023 1.152030 ACCTCACTCCTGCTTCCCA 60.152 57.895 0.00 0.00 0.00 4.37
2293 6252 9.573133 AATCGACCTAAAATCATGAATGAAAAC 57.427 29.630 0.00 0.00 40.69 2.43
2301 6260 6.657117 TCACCAAAATCGACCTAAAATCATGA 59.343 34.615 0.00 0.00 0.00 3.07
2313 6272 3.537793 GTGAACCTCACCAAAATCGAC 57.462 47.619 0.00 0.00 41.37 4.20
2354 6313 7.385205 CGACTAAAGAACTTCTCCAGATCAAAA 59.615 37.037 0.00 0.00 0.00 2.44
2372 6338 2.672961 TCTGGACATGGCGACTAAAG 57.327 50.000 0.00 0.00 0.00 1.85
2413 6381 1.035139 ACTGTACGTTGGAGACCGTT 58.965 50.000 0.00 0.00 38.43 4.44
2473 6441 8.167605 TCAAACCGATTTGTAGAACCAAAATA 57.832 30.769 1.33 0.00 44.76 1.40


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

AutoCloner maintained by Alex Coulton.