Multiple sequence alignment - TraesCS7D01G070200

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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 TraesCS7D01G070200 chr7D 100.000 2503 0 0 1 2503 41258589 41261091 0.000000e+00 4623.0
1 TraesCS7D01G070200 chr7D 96.823 1511 32 6 1 1507 41366844 41365346 0.000000e+00 2510.0
2 TraesCS7D01G070200 chr7D 89.526 802 60 7 480 1270 41274844 41275632 0.000000e+00 994.0
3 TraesCS7D01G070200 chr7D 89.228 622 52 11 887 1504 41325313 41325923 0.000000e+00 763.0
4 TraesCS7D01G070200 chr7D 87.473 455 48 6 2052 2499 41348818 41348366 1.330000e-142 516.0
5 TraesCS7D01G070200 chr7D 84.532 459 47 11 2045 2499 41401705 41402143 1.380000e-117 433.0
6 TraesCS7D01G070200 chr7D 85.934 391 36 9 455 838 41306750 41307128 1.390000e-107 399.0
7 TraesCS7D01G070200 chr7D 85.156 384 49 7 2 382 41274231 41274609 1.090000e-103 387.0
8 TraesCS7D01G070200 chr7D 84.416 385 56 4 2 382 41302604 41302988 2.350000e-100 375.0
9 TraesCS7D01G070200 chr7D 80.967 331 35 9 605 916 41273000 41273321 1.160000e-58 237.0
10 TraesCS7D01G070200 chr7D 87.200 125 11 2 462 581 41274712 41274836 1.210000e-28 137.0
11 TraesCS7D01G070200 chr7D 74.877 406 48 20 453 836 41344168 41343795 4.340000e-28 135.0
12 TraesCS7D01G070200 chr7A 87.282 1321 91 29 475 1757 40694881 40696162 0.000000e+00 1437.0
13 TraesCS7D01G070200 chr7A 92.683 451 29 3 2052 2499 40698008 40698457 0.000000e+00 647.0
14 TraesCS7D01G070200 chr7A 79.583 480 67 14 2 478 40693271 40693722 5.200000e-82 315.0
15 TraesCS7D01G070200 chr4A 91.071 784 53 7 1007 1781 648654189 648654964 0.000000e+00 1044.0
16 TraesCS7D01G070200 chr4A 85.221 1042 67 41 287 1303 648132815 648133794 0.000000e+00 990.0
17 TraesCS7D01G070200 chr4A 84.646 762 62 25 585 1303 648260572 648261321 0.000000e+00 708.0
18 TraesCS7D01G070200 chr4A 95.204 417 17 2 2016 2429 648142501 648142917 0.000000e+00 656.0
19 TraesCS7D01G070200 chr4A 88.278 418 40 4 1366 1781 648133883 648134293 2.240000e-135 492.0
20 TraesCS7D01G070200 chr4A 87.441 422 40 8 1366 1781 648261410 648261824 8.100000e-130 473.0
21 TraesCS7D01G070200 chr4A 88.824 340 38 0 962 1301 648337292 648337631 3.850000e-113 418.0
22 TraesCS7D01G070200 chr4A 89.354 263 22 2 2241 2503 648658424 648658680 2.400000e-85 326.0
23 TraesCS7D01G070200 chr4A 96.795 156 4 1 2052 2206 648658270 648658425 2.470000e-65 259.0
24 TraesCS7D01G070200 chr4A 86.592 179 19 2 1459 1637 648134564 648134737 2.540000e-45 193.0
25 TraesCS7D01G070200 chr4A 92.241 116 7 1 1897 2012 648263496 648263609 1.990000e-36 163.0
26 TraesCS7D01G070200 chr4A 90.179 112 10 1 450 560 648328159 648328270 7.220000e-31 145.0
27 TraesCS7D01G070200 chr4A 94.737 76 2 2 2387 2460 648142918 648142993 1.570000e-22 117.0
28 TraesCS7D01G070200 chr4A 87.879 99 12 0 450 548 648312213 648312311 1.570000e-22 117.0
29 TraesCS7D01G070200 chr4A 82.540 126 18 4 1381 1504 648671985 648672108 9.470000e-20 108.0
30 TraesCS7D01G070200 chr4A 84.545 110 13 2 590 699 648335570 648335675 3.400000e-19 106.0
31 TraesCS7D01G070200 chr4A 81.343 134 22 2 1371 1504 648582733 648582863 3.400000e-19 106.0
32 TraesCS7D01G070200 chr4A 95.349 43 2 0 1862 1904 648262390 648262432 4.470000e-08 69.4
33 TraesCS7D01G070200 chrUn 85.370 540 45 16 765 1283 48835683 48836209 1.700000e-146 529.0
34 TraesCS7D01G070200 chrUn 84.922 451 44 14 2052 2499 48812690 48813119 3.820000e-118 435.0
35 TraesCS7D01G070200 chrUn 82.418 91 14 2 1396 1485 48826707 48826796 7.420000e-11 78.7
36 TraesCS7D01G070200 chr5A 75.633 316 61 14 73 376 473037330 473037641 2.600000e-30 143.0
37 TraesCS7D01G070200 chr3B 100.000 29 0 0 2017 2045 675283770 675283742 1.000000e-03 54.7


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 TraesCS7D01G070200 chr7D 41258589 41261091 2502 False 4623.000000 4623 100.000000 1 2503 1 chr7D.!!$F1 2502
1 TraesCS7D01G070200 chr7D 41365346 41366844 1498 True 2510.000000 2510 96.823000 1 1507 1 chr7D.!!$R3 1506
2 TraesCS7D01G070200 chr7D 41325313 41325923 610 False 763.000000 763 89.228000 887 1504 1 chr7D.!!$F2 617
3 TraesCS7D01G070200 chr7D 41273000 41275632 2632 False 438.750000 994 85.712250 2 1270 4 chr7D.!!$F4 1268
4 TraesCS7D01G070200 chr7D 41302604 41307128 4524 False 387.000000 399 85.175000 2 838 2 chr7D.!!$F5 836
5 TraesCS7D01G070200 chr7A 40693271 40698457 5186 False 799.666667 1437 86.516000 2 2499 3 chr7A.!!$F1 2497
6 TraesCS7D01G070200 chr4A 648132815 648134737 1922 False 558.333333 990 86.697000 287 1781 3 chr4A.!!$F5 1494
7 TraesCS7D01G070200 chr4A 648654189 648658680 4491 False 543.000000 1044 92.406667 1007 2503 3 chr4A.!!$F9 1496
8 TraesCS7D01G070200 chr4A 648260572 648263609 3037 False 353.350000 708 89.919250 585 2012 4 chr4A.!!$F7 1427
9 TraesCS7D01G070200 chr4A 648335570 648337631 2061 False 262.000000 418 86.684500 590 1301 2 chr4A.!!$F8 711
10 TraesCS7D01G070200 chrUn 48835683 48836209 526 False 529.000000 529 85.370000 765 1283 1 chrUn.!!$F3 518


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
346 1584 1.670406 CTGTGCCTCTGTGCAGGAC 60.67 63.158 0.0 0.0 43.02 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2070 14483 0.106769 TGCTTCAAGTTGGCTGGACA 60.107 50.0 2.34 0.0 0.0 4.02 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
187 1419 3.733024 TTTAATACTTTGCACGAGCGG 57.267 42.857 0.00 0.00 46.23 5.52
218 1450 2.231964 TCACAACTTTAGTACCCGCGAT 59.768 45.455 8.23 0.00 0.00 4.58
346 1584 1.670406 CTGTGCCTCTGTGCAGGAC 60.670 63.158 0.00 0.00 43.02 3.85
1434 9206 1.374758 AACTTCTTCCTCTGCGCCG 60.375 57.895 4.18 0.00 0.00 6.46
1509 9281 6.064060 ACATGTCTTGATGTCTGAAGGAAAA 58.936 36.000 0.00 0.00 30.34 2.29
1510 9282 6.547141 ACATGTCTTGATGTCTGAAGGAAAAA 59.453 34.615 0.00 0.00 30.34 1.94
1649 9429 7.768582 TGTACGTAGTGTTAGCTTAGGTATACA 59.231 37.037 5.01 6.01 45.73 2.29
1665 9445 2.018542 TACATACAGTTCGGCCAAGC 57.981 50.000 2.24 0.00 0.00 4.01
1677 9457 1.260561 CGGCCAAGCAACGATACATAC 59.739 52.381 2.24 0.00 0.00 2.39
1781 9620 7.553504 TTATGTATGTACCTAGTGCCATGAT 57.446 36.000 0.00 0.00 0.00 2.45
1792 11664 3.674997 AGTGCCATGATGTTACGTTTCT 58.325 40.909 0.00 0.00 0.00 2.52
1793 11665 3.436704 AGTGCCATGATGTTACGTTTCTG 59.563 43.478 0.00 0.00 0.00 3.02
1794 11666 2.746904 TGCCATGATGTTACGTTTCTGG 59.253 45.455 0.00 0.00 0.00 3.86
1795 11667 3.006940 GCCATGATGTTACGTTTCTGGA 58.993 45.455 0.00 0.00 0.00 3.86
1796 11668 3.181510 GCCATGATGTTACGTTTCTGGAC 60.182 47.826 0.00 0.00 0.00 4.02
1797 11669 4.253685 CCATGATGTTACGTTTCTGGACT 58.746 43.478 0.00 0.00 0.00 3.85
1798 11670 5.416083 CCATGATGTTACGTTTCTGGACTA 58.584 41.667 0.00 0.00 0.00 2.59
1799 11671 5.872617 CCATGATGTTACGTTTCTGGACTAA 59.127 40.000 0.00 0.00 0.00 2.24
1800 11672 6.183360 CCATGATGTTACGTTTCTGGACTAAC 60.183 42.308 0.00 0.00 0.00 2.34
1801 11673 6.092955 TGATGTTACGTTTCTGGACTAACT 57.907 37.500 0.00 0.00 0.00 2.24
1802 11674 5.924254 TGATGTTACGTTTCTGGACTAACTG 59.076 40.000 0.00 0.00 0.00 3.16
1805 11677 6.518493 TGTTACGTTTCTGGACTAACTGAAT 58.482 36.000 0.00 0.00 0.00 2.57
1806 11678 6.422701 TGTTACGTTTCTGGACTAACTGAATG 59.577 38.462 0.00 0.00 0.00 2.67
1808 11680 3.745975 CGTTTCTGGACTAACTGAATGCA 59.254 43.478 0.00 0.00 0.00 3.96
1809 11681 4.393062 CGTTTCTGGACTAACTGAATGCAT 59.607 41.667 0.00 0.00 0.00 3.96
1810 11682 5.106555 CGTTTCTGGACTAACTGAATGCATT 60.107 40.000 12.83 12.83 0.00 3.56
1811 11683 6.317857 GTTTCTGGACTAACTGAATGCATTC 58.682 40.000 28.83 28.83 37.31 2.67
1813 11685 5.423015 TCTGGACTAACTGAATGCATTCTC 58.577 41.667 33.23 22.85 37.67 2.87
1814 11686 5.188555 TCTGGACTAACTGAATGCATTCTCT 59.811 40.000 33.23 21.70 37.67 3.10
1815 11687 5.181009 TGGACTAACTGAATGCATTCTCTG 58.819 41.667 33.23 25.25 37.67 3.35
1826 11698 2.671177 ATTCTCTGCACGCACGCAC 61.671 57.895 0.00 0.00 36.86 5.34
1834 11706 3.773630 ACGCACGCACGCACATAC 61.774 61.111 0.00 0.00 36.19 2.39
1835 11707 4.826605 CGCACGCACGCACATACG 62.827 66.667 0.00 0.00 39.50 3.06
1837 11709 3.772560 CACGCACGCACATACGCA 61.773 61.111 0.00 0.00 36.19 5.24
1839 11711 3.772560 CGCACGCACATACGCACA 61.773 61.111 0.00 0.00 36.19 4.57
1840 11712 2.202171 GCACGCACATACGCACAC 60.202 61.111 0.00 0.00 36.19 3.82
1842 11714 1.787215 CACGCACATACGCACACAT 59.213 52.632 0.00 0.00 36.19 3.21
1843 11715 0.518969 CACGCACATACGCACACATG 60.519 55.000 0.00 0.00 36.19 3.21
1858 11730 3.799963 CACACATGCACATGGATTATTGC 59.200 43.478 14.73 0.00 42.91 3.56
1867 11739 7.604549 TGCACATGGATTATTGCATAATAAGG 58.395 34.615 2.55 0.00 40.88 2.69
1954 13089 4.025647 CACCACGTCTTTCTCTCTTCAAAC 60.026 45.833 0.00 0.00 0.00 2.93
1979 13114 1.740380 CGGTGAGCCATGTCTAACTGG 60.740 57.143 0.00 0.00 35.53 4.00
1987 13122 3.659786 CCATGTCTAACTGGTGTCGAAA 58.340 45.455 0.00 0.00 0.00 3.46
2050 13769 1.824230 TGGCCTGCCACATAATGTTTC 59.176 47.619 6.80 0.00 41.89 2.78
2070 14483 6.015180 TGTTTCAGAATAGCCTTGCTTCATTT 60.015 34.615 0.00 0.00 40.44 2.32
2074 14487 4.400567 AGAATAGCCTTGCTTCATTTGTCC 59.599 41.667 0.00 0.00 40.44 4.02
2097 14510 5.232463 CAGCCAACTTGAAGCAAACATATT 58.768 37.500 0.00 0.00 0.00 1.28
2160 14574 7.181361 TCATGGATGTCTAATTTTTCCAGGAA 58.819 34.615 0.00 0.00 42.40 3.36
2225 14639 6.078456 ACAATCCAATTATCCTTGGTCTCA 57.922 37.500 3.00 0.00 44.99 3.27
2300 14714 7.397221 TCAGTAGACCAAATCAATTCAGATGT 58.603 34.615 0.00 0.00 0.00 3.06
2406 14822 3.223589 GCGAGGGAGAGAGGAGCC 61.224 72.222 0.00 0.00 0.00 4.70
2437 14853 4.621510 CGTTGATCATGACCTCTCAAGGAA 60.622 45.833 18.20 0.00 46.67 3.36
2468 14884 1.075050 CAATGGAGGGCTATGGCTCAT 59.925 52.381 2.87 0.00 42.42 2.90
2479 14895 4.451150 GGCTCATGTGCCGTCGGA 62.451 66.667 22.08 0.00 43.74 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 1326 3.074390 TGGATCTTCTTTGAAAGCCCTCA 59.926 43.478 0.00 0.00 0.00 3.86
179 1411 0.232303 GATTTTATCGGCCGCTCGTG 59.768 55.000 23.51 0.00 0.00 4.35
187 1419 7.184779 GGTACTAAAGTTGTGATTTTATCGGC 58.815 38.462 0.00 0.00 0.00 5.54
251 1487 9.289303 ACAATTTTATCAATTGCTCGTATCAAC 57.711 29.630 0.00 0.00 40.35 3.18
326 1562 1.670406 CCTGCACAGAGGCACAGTC 60.670 63.158 0.00 0.00 39.25 3.51
346 1584 5.018539 TCGTGATCCATAAAGTAGTTGGG 57.981 43.478 0.00 0.00 0.00 4.12
429 5190 0.733150 GCTTGTCCCAGTAATTCGCC 59.267 55.000 0.00 0.00 0.00 5.54
1360 9132 4.553323 GTCAAGAGCTGCATCAACAAATT 58.447 39.130 1.02 0.00 0.00 1.82
1361 9133 3.057033 GGTCAAGAGCTGCATCAACAAAT 60.057 43.478 1.02 0.00 0.00 2.32
1362 9134 2.294233 GGTCAAGAGCTGCATCAACAAA 59.706 45.455 1.02 0.00 0.00 2.83
1363 9135 1.881973 GGTCAAGAGCTGCATCAACAA 59.118 47.619 1.02 0.00 0.00 2.83
1468 9240 2.354109 TGTCAGTGATGAGCGAAGTC 57.646 50.000 0.00 0.00 0.00 3.01
1469 9241 2.028658 ACATGTCAGTGATGAGCGAAGT 60.029 45.455 0.00 0.00 0.00 3.01
1553 9332 9.292195 TCGAACATGAGTTATATATACTCCACA 57.708 33.333 0.00 4.13 41.02 4.17
1571 9350 4.455533 TCAACCAAAGAAGGATCGAACATG 59.544 41.667 0.00 0.00 0.00 3.21
1573 9352 4.079980 TCAACCAAAGAAGGATCGAACA 57.920 40.909 0.00 0.00 0.00 3.18
1649 9429 1.165270 GTTGCTTGGCCGAACTGTAT 58.835 50.000 0.00 0.00 0.00 2.29
1665 9445 6.305638 CGGACATGTATCTGTATGTATCGTTG 59.694 42.308 0.00 0.00 37.63 4.10
1677 9457 2.724977 ATACGCCGGACATGTATCTG 57.275 50.000 5.05 0.00 0.00 2.90
1707 9490 2.115348 CGTCGCCACGTACATATCTT 57.885 50.000 0.00 0.00 41.42 2.40
1748 9534 7.223971 CACTAGGTACATACATAAACGTTGCAT 59.776 37.037 0.00 0.00 0.00 3.96
1757 9596 6.987403 TCATGGCACTAGGTACATACATAA 57.013 37.500 0.00 0.00 0.00 1.90
1781 9620 5.518848 TCAGTTAGTCCAGAAACGTAACA 57.481 39.130 0.00 0.00 0.00 2.41
1792 11664 5.181009 CAGAGAATGCATTCAGTTAGTCCA 58.819 41.667 34.59 0.00 39.23 4.02
1793 11665 5.731599 CAGAGAATGCATTCAGTTAGTCC 57.268 43.478 34.59 15.86 39.23 3.85
1808 11680 2.357396 TGCGTGCGTGCAGAGAAT 60.357 55.556 0.00 0.00 40.62 2.40
1817 11689 3.773630 GTATGTGCGTGCGTGCGT 61.774 61.111 3.11 0.00 37.81 5.24
1818 11690 4.826605 CGTATGTGCGTGCGTGCG 62.827 66.667 0.00 0.00 37.81 5.34
1820 11692 3.772560 TGCGTATGTGCGTGCGTG 61.773 61.111 4.08 0.00 37.81 5.34
1821 11693 3.773630 GTGCGTATGTGCGTGCGT 61.774 61.111 4.08 0.00 37.81 5.24
1822 11694 3.772560 TGTGCGTATGTGCGTGCG 61.773 61.111 0.00 0.00 37.81 5.34
1823 11695 2.202171 GTGTGCGTATGTGCGTGC 60.202 61.111 0.00 0.00 37.81 5.34
1826 11698 1.580893 GCATGTGTGCGTATGTGCG 60.581 57.895 0.00 0.00 42.28 5.34
1827 11699 4.365287 GCATGTGTGCGTATGTGC 57.635 55.556 0.00 0.00 42.28 4.57
1836 11708 3.799963 GCAATAATCCATGTGCATGTGTG 59.200 43.478 10.76 0.00 37.11 3.82
1837 11709 3.447944 TGCAATAATCCATGTGCATGTGT 59.552 39.130 10.76 0.00 41.85 3.72
1842 11714 7.309928 CCCTTATTATGCAATAATCCATGTGCA 60.310 37.037 8.63 8.63 46.08 4.57
1843 11715 7.037438 CCCTTATTATGCAATAATCCATGTGC 58.963 38.462 0.00 0.00 46.08 4.57
1844 11716 7.037438 GCCCTTATTATGCAATAATCCATGTG 58.963 38.462 0.00 0.00 46.08 3.21
1845 11717 6.725369 TGCCCTTATTATGCAATAATCCATGT 59.275 34.615 0.00 0.00 46.08 3.21
1848 11720 5.185635 GCTGCCCTTATTATGCAATAATCCA 59.814 40.000 0.00 0.00 46.08 3.41
1849 11721 5.654497 GCTGCCCTTATTATGCAATAATCC 58.346 41.667 0.00 0.00 46.08 3.01
1850 11722 5.106157 ACGCTGCCCTTATTATGCAATAATC 60.106 40.000 0.00 0.00 46.08 1.75
1852 11724 4.141287 ACGCTGCCCTTATTATGCAATAA 58.859 39.130 0.00 0.00 44.01 1.40
1854 11726 2.554032 GACGCTGCCCTTATTATGCAAT 59.446 45.455 0.00 0.00 34.06 3.56
1858 11730 2.287915 GTGTGACGCTGCCCTTATTATG 59.712 50.000 0.00 0.00 0.00 1.90
1860 11732 1.737696 CGTGTGACGCTGCCCTTATTA 60.738 52.381 0.00 0.00 33.65 0.98
1861 11733 1.019278 CGTGTGACGCTGCCCTTATT 61.019 55.000 0.00 0.00 33.65 1.40
1973 13108 0.320073 CCGCCTTTCGACACCAGTTA 60.320 55.000 0.00 0.00 41.67 2.24
1979 13114 1.785951 GTAAGCCGCCTTTCGACAC 59.214 57.895 0.00 0.00 41.67 3.67
2000 13135 0.676782 CCTTTACGGCCCTCTGTTGG 60.677 60.000 0.00 0.00 33.08 3.77
2012 13147 0.368907 CATTCGTGGTCGCCTTTACG 59.631 55.000 0.00 0.00 37.85 3.18
2013 13148 0.725117 CCATTCGTGGTCGCCTTTAC 59.275 55.000 0.00 0.00 36.96 2.01
2015 13150 2.332654 GCCATTCGTGGTCGCCTTT 61.333 57.895 0.00 0.00 36.96 3.11
2045 13764 4.397420 TGAAGCAAGGCTATTCTGAAACA 58.603 39.130 0.00 0.00 38.25 2.83
2047 13766 6.015180 ACAAATGAAGCAAGGCTATTCTGAAA 60.015 34.615 0.00 0.00 38.25 2.69
2050 13769 5.320549 ACAAATGAAGCAAGGCTATTCTG 57.679 39.130 8.07 0.00 38.25 3.02
2070 14483 0.106769 TGCTTCAAGTTGGCTGGACA 60.107 50.000 2.34 0.00 0.00 4.02
2074 14487 2.582728 TGTTTGCTTCAAGTTGGCTG 57.417 45.000 2.34 0.00 0.00 4.85
2097 14510 6.827762 TGCAGACATTGTATATCCATTCACAA 59.172 34.615 0.00 0.00 35.53 3.33
2160 14574 5.574891 TGTGCTGAAGTTATTTGTGTTGT 57.425 34.783 0.00 0.00 0.00 3.32
2225 14639 5.774690 ACCCATATTTATCAATGTTGCCGAT 59.225 36.000 0.00 0.00 0.00 4.18
2300 14714 7.099266 TCTCCGTCAAACTATAATACCGAAA 57.901 36.000 0.00 0.00 0.00 3.46
2406 14822 1.061131 GTCATGATCAACGGTCTTGCG 59.939 52.381 0.00 0.00 0.00 4.85
2437 14853 2.687914 GCCCTCCATTGGCTTTGACTAT 60.688 50.000 0.00 0.00 45.70 2.12



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

AutoCloner maintained by Alex Coulton.