Multiple sequence alignment - TraesCS7B01G319700

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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 TraesCS7B01G319700 chr7B 100.000 2720 0 0 1 2720 569887405 569890124 0.000000e+00 5024
1 TraesCS7B01G319700 chr7B 97.450 902 23 0 1819 2720 569916731 569917632 0.000000e+00 1539
2 TraesCS7B01G319700 chr7B 96.906 905 26 2 1817 2720 19043528 19042625 0.000000e+00 1515
3 TraesCS7B01G319700 chrUn 92.453 1272 77 5 561 1816 105335967 105334699 0.000000e+00 1799
4 TraesCS7B01G319700 chr3D 92.302 1273 76 5 564 1816 576579534 576578264 0.000000e+00 1788
5 TraesCS7B01G319700 chr3D 87.394 587 53 9 1 566 497382685 497382099 0.000000e+00 654
6 TraesCS7B01G319700 chr3D 86.411 574 65 10 4 566 569794185 569793614 1.380000e-172 616
7 TraesCS7B01G319700 chr4B 92.205 1270 76 5 564 1816 671183087 671184350 0.000000e+00 1775
8 TraesCS7B01G319700 chr4B 97.017 905 25 2 1817 2720 14882225 14881322 0.000000e+00 1520
9 TraesCS7B01G319700 chr4B 96.913 907 28 0 1814 2720 353874036 353874942 0.000000e+00 1520
10 TraesCS7B01G319700 chr4B 96.796 905 29 0 1816 2720 587905361 587906265 0.000000e+00 1511
11 TraesCS7B01G319700 chr6D 92.072 1274 77 5 564 1816 449138061 449136791 0.000000e+00 1772
12 TraesCS7B01G319700 chr6D 85.154 586 63 16 4 566 85963472 85962888 1.820000e-161 579
13 TraesCS7B01G319700 chr5B 85.272 1745 221 27 962 2689 65280415 65282140 0.000000e+00 1766
14 TraesCS7B01G319700 chr5B 96.799 906 27 1 1817 2720 439622906 439622001 0.000000e+00 1511
15 TraesCS7B01G319700 chr5B 84.983 586 67 15 1 566 202889667 202890251 2.350000e-160 575
16 TraesCS7B01G319700 chr2A 91.975 1271 80 13 564 1816 704738833 704737567 0.000000e+00 1762
17 TraesCS7B01G319700 chr1B 91.975 1271 78 4 569 1816 335763715 335764984 0.000000e+00 1760
18 TraesCS7B01G319700 chr1B 91.045 1273 83 7 564 1816 302009481 302008220 0.000000e+00 1690
19 TraesCS7B01G319700 chr2D 91.890 1270 84 4 564 1816 603142397 603143664 0.000000e+00 1757
20 TraesCS7B01G319700 chr2D 91.342 1282 89 7 554 1816 498273310 498274588 0.000000e+00 1733
21 TraesCS7B01G319700 chr2D 91.017 1269 79 6 564 1816 500667212 500665963 0.000000e+00 1679
22 TraesCS7B01G319700 chr2D 89.671 668 46 4 563 1208 50139066 50138400 0.000000e+00 830
23 TraesCS7B01G319700 chr2D 85.642 592 59 18 1 566 593127514 593128105 1.390000e-167 599
24 TraesCS7B01G319700 chr4D 91.523 1274 85 3 565 1816 481887026 481888298 0.000000e+00 1733
25 TraesCS7B01G319700 chr4D 91.413 1281 76 10 564 1816 486565782 486564508 0.000000e+00 1725
26 TraesCS7B01G319700 chr4D 85.473 592 56 11 1 566 467208030 467208617 8.390000e-165 590
27 TraesCS7B01G319700 chr2B 90.652 1273 84 6 560 1816 396181965 396180712 0.000000e+00 1659
28 TraesCS7B01G319700 chr2B 90.325 1261 109 5 565 1816 154225459 154224203 0.000000e+00 1640
29 TraesCS7B01G319700 chr6B 96.803 907 28 1 1815 2720 713085699 713084793 0.000000e+00 1513
30 TraesCS7B01G319700 chr6B 85.641 585 61 7 1 565 133171599 133171018 6.480000e-166 593
31 TraesCS7B01G319700 chr1D 91.786 1047 80 6 1676 2720 319502368 319503410 0.000000e+00 1452
32 TraesCS7B01G319700 chr1D 86.177 586 59 11 1 566 209758663 209758080 4.980000e-172 614
33 TraesCS7B01G319700 chr4A 86.441 590 55 7 1 566 675655243 675654655 8.270000e-175 623
34 TraesCS7B01G319700 chr3B 86.130 584 60 8 1 564 574268568 574267986 6.440000e-171 610


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 TraesCS7B01G319700 chr7B 569887405 569890124 2719 False 5024 5024 100.000 1 2720 1 chr7B.!!$F1 2719
1 TraesCS7B01G319700 chr7B 569916731 569917632 901 False 1539 1539 97.450 1819 2720 1 chr7B.!!$F2 901
2 TraesCS7B01G319700 chr7B 19042625 19043528 903 True 1515 1515 96.906 1817 2720 1 chr7B.!!$R1 903
3 TraesCS7B01G319700 chrUn 105334699 105335967 1268 True 1799 1799 92.453 561 1816 1 chrUn.!!$R1 1255
4 TraesCS7B01G319700 chr3D 576578264 576579534 1270 True 1788 1788 92.302 564 1816 1 chr3D.!!$R3 1252
5 TraesCS7B01G319700 chr3D 497382099 497382685 586 True 654 654 87.394 1 566 1 chr3D.!!$R1 565
6 TraesCS7B01G319700 chr3D 569793614 569794185 571 True 616 616 86.411 4 566 1 chr3D.!!$R2 562
7 TraesCS7B01G319700 chr4B 671183087 671184350 1263 False 1775 1775 92.205 564 1816 1 chr4B.!!$F3 1252
8 TraesCS7B01G319700 chr4B 14881322 14882225 903 True 1520 1520 97.017 1817 2720 1 chr4B.!!$R1 903
9 TraesCS7B01G319700 chr4B 353874036 353874942 906 False 1520 1520 96.913 1814 2720 1 chr4B.!!$F1 906
10 TraesCS7B01G319700 chr4B 587905361 587906265 904 False 1511 1511 96.796 1816 2720 1 chr4B.!!$F2 904
11 TraesCS7B01G319700 chr6D 449136791 449138061 1270 True 1772 1772 92.072 564 1816 1 chr6D.!!$R2 1252
12 TraesCS7B01G319700 chr6D 85962888 85963472 584 True 579 579 85.154 4 566 1 chr6D.!!$R1 562
13 TraesCS7B01G319700 chr5B 65280415 65282140 1725 False 1766 1766 85.272 962 2689 1 chr5B.!!$F1 1727
14 TraesCS7B01G319700 chr5B 439622001 439622906 905 True 1511 1511 96.799 1817 2720 1 chr5B.!!$R1 903
15 TraesCS7B01G319700 chr5B 202889667 202890251 584 False 575 575 84.983 1 566 1 chr5B.!!$F2 565
16 TraesCS7B01G319700 chr2A 704737567 704738833 1266 True 1762 1762 91.975 564 1816 1 chr2A.!!$R1 1252
17 TraesCS7B01G319700 chr1B 335763715 335764984 1269 False 1760 1760 91.975 569 1816 1 chr1B.!!$F1 1247
18 TraesCS7B01G319700 chr1B 302008220 302009481 1261 True 1690 1690 91.045 564 1816 1 chr1B.!!$R1 1252
19 TraesCS7B01G319700 chr2D 603142397 603143664 1267 False 1757 1757 91.890 564 1816 1 chr2D.!!$F3 1252
20 TraesCS7B01G319700 chr2D 498273310 498274588 1278 False 1733 1733 91.342 554 1816 1 chr2D.!!$F1 1262
21 TraesCS7B01G319700 chr2D 500665963 500667212 1249 True 1679 1679 91.017 564 1816 1 chr2D.!!$R2 1252
22 TraesCS7B01G319700 chr2D 50138400 50139066 666 True 830 830 89.671 563 1208 1 chr2D.!!$R1 645
23 TraesCS7B01G319700 chr2D 593127514 593128105 591 False 599 599 85.642 1 566 1 chr2D.!!$F2 565
24 TraesCS7B01G319700 chr4D 481887026 481888298 1272 False 1733 1733 91.523 565 1816 1 chr4D.!!$F2 1251
25 TraesCS7B01G319700 chr4D 486564508 486565782 1274 True 1725 1725 91.413 564 1816 1 chr4D.!!$R1 1252
26 TraesCS7B01G319700 chr4D 467208030 467208617 587 False 590 590 85.473 1 566 1 chr4D.!!$F1 565
27 TraesCS7B01G319700 chr2B 396180712 396181965 1253 True 1659 1659 90.652 560 1816 1 chr2B.!!$R2 1256
28 TraesCS7B01G319700 chr2B 154224203 154225459 1256 True 1640 1640 90.325 565 1816 1 chr2B.!!$R1 1251
29 TraesCS7B01G319700 chr6B 713084793 713085699 906 True 1513 1513 96.803 1815 2720 1 chr6B.!!$R2 905
30 TraesCS7B01G319700 chr6B 133171018 133171599 581 True 593 593 85.641 1 565 1 chr6B.!!$R1 564
31 TraesCS7B01G319700 chr1D 319502368 319503410 1042 False 1452 1452 91.786 1676 2720 1 chr1D.!!$F1 1044
32 TraesCS7B01G319700 chr1D 209758080 209758663 583 True 614 614 86.177 1 566 1 chr1D.!!$R1 565
33 TraesCS7B01G319700 chr4A 675654655 675655243 588 True 623 623 86.441 1 566 1 chr4A.!!$R1 565
34 TraesCS7B01G319700 chr3B 574267986 574268568 582 True 610 610 86.130 1 564 1 chr3B.!!$R1 563

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
718 771 0.108138 CCTCGGATCGGCAGTTTCTT 60.108 55.0 0.0 0.0 0.00 2.52 F
1437 1555 0.032678 ACACCAGTGTCGAAGAGCAG 59.967 55.0 0.0 0.0 40.24 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1605 1724 0.250793 TTGGGCTTCCGCGAATCTTA 59.749 50.0 8.23 0.0 36.88 2.10 R
2457 2588 1.115467 ACTTGCCCGAGATTCGATCT 58.885 50.0 0.00 0.0 43.74 2.75 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
40 41 1.667724 GTCTGATGGCGATCAAGTTGG 59.332 52.381 12.74 1.01 38.17 3.77
58 59 2.281208 CAAAGTGGAACGGCCCGA 60.281 61.111 11.71 0.00 45.86 5.14
136 172 2.746277 GGTGGCGCAGGAACGATT 60.746 61.111 10.83 0.00 34.06 3.34
156 192 2.813908 GATCACGGTCGTGGGTGC 60.814 66.667 21.05 6.81 45.43 5.01
250 288 1.007238 AGGAGGATCTAGAGGGGGCA 61.007 60.000 0.00 0.00 33.73 5.36
290 331 2.377628 GACTGGTGTTGAGGCCGTCA 62.378 60.000 0.00 0.00 32.62 4.35
331 372 1.810151 GACGCTAAAAACATGGAGCCA 59.190 47.619 0.00 0.00 0.00 4.75
354 399 4.475527 GGTGGTGCCGAAGAACTT 57.524 55.556 0.00 0.00 0.00 2.66
367 412 1.447314 GAACTTAGGCACCGACGGG 60.447 63.158 20.00 8.43 40.11 5.28
599 652 4.082523 CATCGAGCCCACCCACGT 62.083 66.667 0.00 0.00 0.00 4.49
657 710 2.757099 CCTGTTGGGCCTGCATCC 60.757 66.667 4.53 0.00 0.00 3.51
718 771 0.108138 CCTCGGATCGGCAGTTTCTT 60.108 55.000 0.00 0.00 0.00 2.52
793 851 2.203938 GGGGGATGGCGGGAGATA 60.204 66.667 0.00 0.00 0.00 1.98
819 894 0.679640 TGCCAAATTAGCCTCACCCG 60.680 55.000 0.00 0.00 0.00 5.28
903 978 3.008330 GCAGCTGTGATTTCAGATCTGT 58.992 45.455 21.92 3.10 37.61 3.41
918 1011 3.151710 TGTGCTATAGGCGGCGGT 61.152 61.111 9.78 0.00 45.43 5.68
971 1070 1.761174 GTGCTCCCCTTCCTGTTGA 59.239 57.895 0.00 0.00 0.00 3.18
1029 1130 0.605589 CTACGCCATCCTCATCTCCC 59.394 60.000 0.00 0.00 0.00 4.30
1119 1228 4.238761 TCGATTTCTCACTGAACGAACT 57.761 40.909 0.00 0.00 32.66 3.01
1126 1235 9.302345 GATTTCTCACTGAACGAACTATCAATA 57.698 33.333 0.00 0.00 33.88 1.90
1127 1236 8.462143 TTTCTCACTGAACGAACTATCAATAC 57.538 34.615 0.00 0.00 33.88 1.89
1242 1359 0.036952 CTGTTCGTCATGCTGGGAGT 60.037 55.000 0.00 0.00 0.00 3.85
1321 1439 6.813649 TCTGAACTACATCTACAACTGCAATC 59.186 38.462 0.00 0.00 0.00 2.67
1388 1506 1.048601 AGGCTTGTCGAGACCTTCAA 58.951 50.000 0.34 0.00 31.76 2.69
1437 1555 0.032678 ACACCAGTGTCGAAGAGCAG 59.967 55.000 0.00 0.00 40.24 4.24
1459 1578 1.203162 TGGCCATGTTCCTCCATGTTT 60.203 47.619 0.00 0.00 40.50 2.83
1481 1600 1.707989 TGGCCATAACCAGAGGTTCAA 59.292 47.619 0.00 0.00 43.05 2.69
1505 1624 3.498397 GTCATTCACAACACGTTCAGGAT 59.502 43.478 0.00 0.00 0.00 3.24
1597 1716 0.617413 CAAGAGACCATCTGGCCAGT 59.383 55.000 31.58 14.30 38.67 4.00
1602 1721 2.303549 GACCATCTGGCCAGTCTCCG 62.304 65.000 31.58 17.41 39.32 4.63
1605 1724 3.991924 ATCTGGCCAGTCTCCGCCT 62.992 63.158 31.58 5.48 45.90 5.52
1787 1909 1.625818 CACTGCCAGAGTTCCTAGGTT 59.374 52.381 9.08 0.00 29.75 3.50
1803 1925 4.039730 CCTAGGTTACAGTCTGCAGCATAT 59.960 45.833 9.47 0.00 0.00 1.78
2113 2242 4.330074 GCATAGCACAAGATCGTGTAGTTT 59.670 41.667 14.10 3.41 39.19 2.66
2183 2312 3.757493 GAGATCGTGTAACTCCCGGATAT 59.243 47.826 0.73 0.00 31.75 1.63
2286 2416 0.470341 TGTTGGGTTGACACGGATCA 59.530 50.000 0.00 0.00 0.00 2.92
2406 2537 2.547007 CGGGATCATGCATTACGGTACA 60.547 50.000 0.00 0.00 0.00 2.90
2413 2544 6.411630 TCATGCATTACGGTACAAGTAAAC 57.588 37.500 14.38 11.16 37.57 2.01
2531 2662 3.694566 GGGTTGCTTAAATCCTCGACATT 59.305 43.478 0.00 0.00 35.96 2.71
2540 2671 2.920724 TCCTCGACATTGTGGTTCAA 57.079 45.000 0.00 0.00 40.53 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.265739 GCCATCAGACTCACGCCA 59.734 61.111 0.00 0.00 0.00 5.69
40 41 4.038080 CGGGCCGTTCCACTTTGC 62.038 66.667 19.97 0.00 36.21 3.68
121 157 2.745884 CCAATCGTTCCTGCGCCA 60.746 61.111 4.18 0.00 0.00 5.69
373 418 4.658786 AACCTCCCACCTCGCCCT 62.659 66.667 0.00 0.00 0.00 5.19
425 472 1.082117 GCTTTGAGCGCCGTTAGCTA 61.082 55.000 2.29 0.00 46.13 3.32
438 485 0.516877 CATGACCGCTTTCGCTTTGA 59.483 50.000 0.00 0.00 0.00 2.69
440 487 0.889186 ACCATGACCGCTTTCGCTTT 60.889 50.000 0.00 0.00 0.00 3.51
506 553 0.252103 GTCCTCTACTCCACCCACCA 60.252 60.000 0.00 0.00 0.00 4.17
606 659 0.772124 AAACAGGCCTCTCCCTTCCA 60.772 55.000 0.00 0.00 31.24 3.53
718 771 4.383861 CACTCAGCCTGGCTCGCA 62.384 66.667 20.49 4.70 36.40 5.10
793 851 4.400567 GTGAGGCTAATTTGGCAGATTTCT 59.599 41.667 15.27 4.91 34.73 2.52
819 894 2.035442 GGGTGAGCGAGTGAAAGGC 61.035 63.158 0.00 0.00 0.00 4.35
903 978 3.923864 CCACCGCCGCCTATAGCA 61.924 66.667 0.00 0.00 44.04 3.49
918 1011 4.399395 CTGCTGCCTCTTCCGCCA 62.399 66.667 0.00 0.00 0.00 5.69
1127 1236 0.742505 TGCGTCCATAACCTAGTCGG 59.257 55.000 0.00 0.00 39.35 4.79
1242 1359 1.416401 GGACCATAGCGGATCAAAGGA 59.584 52.381 0.00 0.00 38.63 3.36
1321 1439 1.938657 ATCCACAGAGCCTCGACGTG 61.939 60.000 0.00 5.35 0.00 4.49
1437 1555 1.039233 CATGGAGGAACATGGCCACC 61.039 60.000 8.16 4.31 43.44 4.61
1459 1578 2.109128 TGAACCTCTGGTTATGGCCAAA 59.891 45.455 10.96 2.40 46.95 3.28
1481 1600 2.872245 CTGAACGTGTTGTGAATGACCT 59.128 45.455 0.00 0.00 0.00 3.85
1505 1624 5.970289 ACCTAGAGATGGTCTCCATTGATA 58.030 41.667 2.71 0.00 45.26 2.15
1597 1716 1.359117 CGCGAATCTTAGGCGGAGA 59.641 57.895 0.00 0.00 45.69 3.71
1602 1721 1.499688 GGCTTCCGCGAATCTTAGGC 61.500 60.000 8.23 3.79 36.88 3.93
1605 1724 0.250793 TTGGGCTTCCGCGAATCTTA 59.749 50.000 8.23 0.00 36.88 2.10
1637 1756 2.507484 TGTCAATGCTCACCTTGAAGG 58.493 47.619 10.24 10.24 42.49 3.46
1787 1909 2.899900 CCCCTATATGCTGCAGACTGTA 59.100 50.000 20.43 5.12 0.00 2.74
1803 1925 0.494551 TCCAACACTTCCTCCCCCTA 59.505 55.000 0.00 0.00 0.00 3.53
2113 2242 5.068987 ACATTGGAAAAGCTCTAGCAAAACA 59.931 36.000 4.54 0.00 45.16 2.83
2183 2312 3.290948 ACACCCAAAGCACTTCTACAA 57.709 42.857 0.00 0.00 0.00 2.41
2286 2416 2.289694 CGGAGTGACAAATCCCAGTCTT 60.290 50.000 3.03 0.00 35.81 3.01
2406 2537 4.510340 CGTTACCTGCAAGTCAGTTTACTT 59.490 41.667 0.00 0.00 41.25 2.24
2413 2544 2.724977 TCTCGTTACCTGCAAGTCAG 57.275 50.000 0.00 0.00 42.49 3.51
2422 2553 2.824341 ACCTCGTTCAATCTCGTTACCT 59.176 45.455 0.00 0.00 0.00 3.08
2457 2588 1.115467 ACTTGCCCGAGATTCGATCT 58.885 50.000 0.00 0.00 43.74 2.75
2531 2662 2.301583 TGATCTCATCGGTTGAACCACA 59.698 45.455 15.58 0.00 38.47 4.17
2627 2758 2.232941 GGTTCGGGAGACATGTAGACAA 59.767 50.000 0.00 0.00 39.59 3.18


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

AutoCloner maintained by Alex Coulton.