Multiple sequence alignment - TraesCS7A01G367800

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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 TraesCS7A01G367800 chr7A 100.000 2367 0 0 1 2367 540915967 540918333 0.000000e+00 4372.0
1 TraesCS7A01G367800 chr7A 98.182 110 1 1 1764 1872 651015714 651015823 8.630000e-45 191.0
2 TraesCS7A01G367800 chr7A 96.364 110 3 1 1764 1872 112624361 112624470 1.870000e-41 180.0
3 TraesCS7A01G367800 chr7A 95.745 47 2 0 1784 1830 651015810 651015856 2.520000e-10 76.8
4 TraesCS7A01G367800 chr7A 95.122 41 2 0 1790 1830 112624485 112624525 5.460000e-07 65.8
5 TraesCS7A01G367800 chr7A 97.143 35 1 0 2021 2055 540917939 540917973 2.540000e-05 60.2
6 TraesCS7A01G367800 chr7A 97.143 35 1 0 1973 2007 540917987 540918021 2.540000e-05 60.2
7 TraesCS7A01G367800 chr6D 92.680 1530 82 15 268 1771 219292935 219291410 0.000000e+00 2178.0
8 TraesCS7A01G367800 chr6D 100.000 40 0 0 2328 2367 467430043 467430004 9.070000e-10 75.0
9 TraesCS7A01G367800 chr6D 100.000 37 0 0 2126 2162 428950574 428950538 4.220000e-08 69.4
10 TraesCS7A01G367800 chr5D 91.762 1396 63 24 398 1767 489744754 489743385 0.000000e+00 1893.0
11 TraesCS7A01G367800 chr5D 96.121 232 9 0 742 973 472759333 472759102 1.720000e-101 379.0
12 TraesCS7A01G367800 chr2D 91.494 1399 73 20 398 1771 232180049 232178672 0.000000e+00 1882.0
13 TraesCS7A01G367800 chr2D 100.000 37 0 0 2126 2162 10039160 10039196 4.220000e-08 69.4
14 TraesCS7A01G367800 chr3D 91.435 1401 74 19 398 1771 497288826 497290207 0.000000e+00 1881.0
15 TraesCS7A01G367800 chr3D 91.304 828 44 5 970 1771 172531322 172530497 0.000000e+00 1105.0
16 TraesCS7A01G367800 chr3D 95.056 445 19 3 402 844 71520939 71520496 0.000000e+00 697.0
17 TraesCS7A01G367800 chr4D 91.149 1401 71 26 398 1771 200715358 200713984 0.000000e+00 1851.0
18 TraesCS7A01G367800 chr4D 100.000 37 0 0 2126 2162 356262628 356262664 4.220000e-08 69.4
19 TraesCS7A01G367800 chr7B 90.792 1401 79 23 398 1771 193200990 193202367 0.000000e+00 1827.0
20 TraesCS7A01G367800 chr7B 93.888 409 24 1 6 413 153178428 153178836 1.200000e-172 616.0
21 TraesCS7A01G367800 chr7B 91.262 412 34 2 1 411 549816572 549816162 5.710000e-156 560.0
22 TraesCS7A01G367800 chr7B 97.191 178 2 2 2157 2332 114569782 114569958 4.950000e-77 298.0
23 TraesCS7A01G367800 chr7B 96.629 178 3 2 2157 2332 157282199 157282375 2.300000e-75 292.0
24 TraesCS7A01G367800 chr7B 100.000 40 0 0 2328 2367 511938309 511938270 9.070000e-10 75.0
25 TraesCS7A01G367800 chr2A 90.486 1398 84 22 400 1771 460473263 460471889 0.000000e+00 1799.0
26 TraesCS7A01G367800 chr2A 90.207 1399 86 15 400 1771 299510506 299509132 0.000000e+00 1777.0
27 TraesCS7A01G367800 chr7D 90.326 982 72 7 806 1764 72785583 72786564 0.000000e+00 1266.0
28 TraesCS7A01G367800 chr7D 96.507 229 8 0 742 970 574406205 574406433 1.720000e-101 379.0
29 TraesCS7A01G367800 chr7D 100.000 37 0 0 2126 2162 38193663 38193699 4.220000e-08 69.4
30 TraesCS7A01G367800 chr7D 100.000 37 0 0 2126 2162 613221414 613221450 4.220000e-08 69.4
31 TraesCS7A01G367800 chr4B 89.596 990 76 13 807 1771 213965401 213966388 0.000000e+00 1232.0
32 TraesCS7A01G367800 chr4B 90.728 701 61 4 1 699 230399538 230400236 0.000000e+00 931.0
33 TraesCS7A01G367800 chr4B 90.728 701 61 4 1 699 230430441 230431139 0.000000e+00 931.0
34 TraesCS7A01G367800 chr4B 92.374 577 42 2 268 844 213964829 213965403 0.000000e+00 821.0
35 TraesCS7A01G367800 chr4B 92.029 414 32 1 1 413 9818211 9818624 4.390000e-162 580.0
36 TraesCS7A01G367800 chr4B 97.191 178 2 2 2157 2332 618095622 618095798 4.950000e-77 298.0
37 TraesCS7A01G367800 chr4B 96.629 178 3 2 2157 2332 569777855 569777679 2.300000e-75 292.0
38 TraesCS7A01G367800 chr3B 97.028 572 13 3 1764 2332 807980531 807979961 0.000000e+00 959.0
39 TraesCS7A01G367800 chr5B 90.076 655 35 4 1146 1771 288654651 288653998 0.000000e+00 822.0
40 TraesCS7A01G367800 chr5B 100.000 40 0 0 2328 2367 482933196 482933157 9.070000e-10 75.0
41 TraesCS7A01G367800 chr6B 96.259 401 14 1 75 475 16926281 16925882 0.000000e+00 656.0
42 TraesCS7A01G367800 chr6B 96.341 246 7 1 2124 2367 16925885 16925640 1.020000e-108 403.0
43 TraesCS7A01G367800 chr6B 100.000 40 0 0 2328 2367 673193069 673193030 9.070000e-10 75.0
44 TraesCS7A01G367800 chr1D 95.238 357 17 0 1771 2127 427938643 427938287 1.230000e-157 566.0
45 TraesCS7A01G367800 chr1D 94.828 232 12 0 742 973 475307023 475306792 1.730000e-96 363.0
46 TraesCS7A01G367800 chr1D 100.000 40 0 0 2328 2367 24597721 24597760 9.070000e-10 75.0
47 TraesCS7A01G367800 chr2B 90.580 414 23 2 1 413 361705206 361705604 3.460000e-148 534.0
48 TraesCS7A01G367800 chr2B 97.191 178 2 2 2157 2332 80318790 80318614 4.950000e-77 298.0
49 TraesCS7A01G367800 chr1B 97.191 178 2 2 2157 2332 683277540 683277364 4.950000e-77 298.0
50 TraesCS7A01G367800 chr1B 100.000 40 0 0 2328 2367 512224919 512224880 9.070000e-10 75.0
51 TraesCS7A01G367800 chr4A 96.629 178 3 2 2157 2332 697690534 697690358 2.300000e-75 292.0
52 TraesCS7A01G367800 chr4A 93.878 49 3 0 2319 2367 661952265 661952313 9.070000e-10 75.0
53 TraesCS7A01G367800 chr1A 87.611 226 12 1 1852 2077 584890315 584890524 5.050000e-62 248.0
54 TraesCS7A01G367800 chr1A 100.000 40 0 0 2328 2367 251741888 251741927 9.070000e-10 75.0
55 TraesCS7A01G367800 chr1A 100.000 37 0 0 2126 2162 21555269 21555305 4.220000e-08 69.4
56 TraesCS7A01G367800 chr1A 100.000 31 0 0 1973 2003 584890468 584890498 9.140000e-05 58.4
57 TraesCS7A01G367800 chr5A 92.857 126 8 1 3 127 415815651 415815526 5.200000e-42 182.0
58 TraesCS7A01G367800 chr5A 97.000 100 2 1 1764 1862 494220771 494220870 1.460000e-37 167.0
59 TraesCS7A01G367800 chr6A 100.000 37 0 0 2126 2162 37783750 37783786 4.220000e-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 TraesCS7A01G367800 chr7A 540915967 540918333 2366 False 1497.466667 4372 98.095333 1 2367 3 chr7A.!!$F2 2366
1 TraesCS7A01G367800 chr6D 219291410 219292935 1525 True 2178.000000 2178 92.680000 268 1771 1 chr6D.!!$R1 1503
2 TraesCS7A01G367800 chr5D 489743385 489744754 1369 True 1893.000000 1893 91.762000 398 1767 1 chr5D.!!$R2 1369
3 TraesCS7A01G367800 chr2D 232178672 232180049 1377 True 1882.000000 1882 91.494000 398 1771 1 chr2D.!!$R1 1373
4 TraesCS7A01G367800 chr3D 497288826 497290207 1381 False 1881.000000 1881 91.435000 398 1771 1 chr3D.!!$F1 1373
5 TraesCS7A01G367800 chr3D 172530497 172531322 825 True 1105.000000 1105 91.304000 970 1771 1 chr3D.!!$R2 801
6 TraesCS7A01G367800 chr4D 200713984 200715358 1374 True 1851.000000 1851 91.149000 398 1771 1 chr4D.!!$R1 1373
7 TraesCS7A01G367800 chr7B 193200990 193202367 1377 False 1827.000000 1827 90.792000 398 1771 1 chr7B.!!$F4 1373
8 TraesCS7A01G367800 chr2A 460471889 460473263 1374 True 1799.000000 1799 90.486000 400 1771 1 chr2A.!!$R2 1371
9 TraesCS7A01G367800 chr2A 299509132 299510506 1374 True 1777.000000 1777 90.207000 400 1771 1 chr2A.!!$R1 1371
10 TraesCS7A01G367800 chr7D 72785583 72786564 981 False 1266.000000 1266 90.326000 806 1764 1 chr7D.!!$F2 958
11 TraesCS7A01G367800 chr4B 213964829 213966388 1559 False 1026.500000 1232 90.985000 268 1771 2 chr4B.!!$F5 1503
12 TraesCS7A01G367800 chr4B 230399538 230400236 698 False 931.000000 931 90.728000 1 699 1 chr4B.!!$F2 698
13 TraesCS7A01G367800 chr4B 230430441 230431139 698 False 931.000000 931 90.728000 1 699 1 chr4B.!!$F3 698
14 TraesCS7A01G367800 chr3B 807979961 807980531 570 True 959.000000 959 97.028000 1764 2332 1 chr3B.!!$R1 568
15 TraesCS7A01G367800 chr5B 288653998 288654651 653 True 822.000000 822 90.076000 1146 1771 1 chr5B.!!$R1 625
16 TraesCS7A01G367800 chr6B 16925640 16926281 641 True 529.500000 656 96.300000 75 2367 2 chr6B.!!$R2 2292

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
52 54 0.611062 TCCGATCTGTTCCTGGTCGT 60.611 55.0 0.0 0.0 34.87 4.34 F
1164 1211 0.037605 ACAAGGTTAGGAGGCGTTCG 60.038 55.0 0.0 0.0 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1327 1379 1.056660 CCCGTACCTTGCCTATCCAT 58.943 55.000 0.00 0.0 0.0 3.41 R
1968 2043 6.596888 TGCCACACATTCAAAGAAATTTTCAA 59.403 30.769 11.53 0.0 0.0 2.69 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
30 31 8.718102 TTTCTTAGTTGTATGCAAGGATCTAC 57.282 34.615 0.00 0.00 34.94 2.59
40 41 4.667573 TGCAAGGATCTACTATCCGATCT 58.332 43.478 0.00 0.00 42.87 2.75
49 51 3.033659 ACTATCCGATCTGTTCCTGGT 57.966 47.619 0.00 0.00 0.00 4.00
50 52 2.959707 ACTATCCGATCTGTTCCTGGTC 59.040 50.000 0.00 0.00 0.00 4.02
52 54 0.611062 TCCGATCTGTTCCTGGTCGT 60.611 55.000 0.00 0.00 34.87 4.34
61 63 0.941542 TTCCTGGTCGTTGCTTTTCG 59.058 50.000 0.00 0.00 0.00 3.46
65 67 1.370051 GGTCGTTGCTTTTCGCCAC 60.370 57.895 0.00 0.00 38.05 5.01
78 80 3.391382 GCCACGGGAGCACCTAGT 61.391 66.667 0.00 0.00 36.97 2.57
114 116 1.660607 GATTTCTCGTCGCATCTGCAA 59.339 47.619 2.72 0.00 42.21 4.08
152 154 1.820519 TGCTGATGAAATGGCTTGTCC 59.179 47.619 0.00 0.00 0.00 4.02
206 208 5.874892 TTTTGGTTTTGCGAAGAAATACG 57.125 34.783 0.00 0.00 0.00 3.06
346 349 5.625568 AAACTGTACCTGTGTCCTAAACT 57.374 39.130 0.00 0.00 0.00 2.66
412 415 1.003696 GAGCTAGGTTTCAGTTGGCCT 59.996 52.381 3.32 0.00 35.28 5.19
556 559 3.490761 CGTATTTTGGGGGCATGATCAAC 60.491 47.826 0.00 0.00 0.00 3.18
716 724 4.533815 TCAATACCGATCTAGGTGACTGT 58.466 43.478 2.76 0.00 45.54 3.55
772 780 3.262420 GGTGTTAGTCGCAATGATCAGT 58.738 45.455 0.09 0.00 0.00 3.41
869 912 3.326747 GGTGCTCGATTTAGTCTGTTGT 58.673 45.455 0.00 0.00 0.00 3.32
875 918 5.446473 GCTCGATTTAGTCTGTTGTGAATGG 60.446 44.000 0.00 0.00 0.00 3.16
951 998 6.321181 ACTCGCTCAATCTCTCTCTATCTTTT 59.679 38.462 0.00 0.00 0.00 2.27
983 1030 2.066999 GGATTCGAGGGTGGAGCCT 61.067 63.158 0.00 0.00 37.43 4.58
1164 1211 0.037605 ACAAGGTTAGGAGGCGTTCG 60.038 55.000 0.00 0.00 0.00 3.95
1189 1236 3.370209 CCTGATTGATCTGTTCTGGAGCA 60.370 47.826 9.07 0.00 32.03 4.26
1443 1495 3.928992 AGCAAATGTGATCTGTCTGTACG 59.071 43.478 0.00 0.00 0.00 3.67
1547 1622 7.432869 ACTAAATTTGCTGTGCAGTATTGAAA 58.567 30.769 0.00 0.00 40.61 2.69
1657 1732 6.925718 TGAATGTTTTGTCGATTTTTATGGCA 59.074 30.769 0.00 0.00 0.00 4.92
1753 1828 5.689835 GAGGATCTATTTTTCTCCCTGCTT 58.310 41.667 0.00 0.00 0.00 3.91
1768 1843 3.998341 CCCTGCTTTGATTGGTTTCAATG 59.002 43.478 0.00 0.00 43.08 2.82
1769 1844 4.262549 CCCTGCTTTGATTGGTTTCAATGA 60.263 41.667 0.00 0.00 43.08 2.57
1789 1864 8.773645 TCAATGATTTGACACAGTAGTTAACAG 58.226 33.333 8.61 0.00 36.94 3.16
1794 1869 9.859692 GATTTGACACAGTAGTTAACAGTTAAC 57.140 33.333 23.58 23.58 44.49 2.01
1905 1980 4.486125 AACAGGAACATTGCCAAGTTTT 57.514 36.364 0.00 0.00 0.00 2.43
1968 2043 6.074648 TGAATTTTAGGGGTGTCAGATGTTT 58.925 36.000 0.00 0.00 0.00 2.83
1993 2068 6.111382 TGAAAATTTCTTTGAATGTGTGGCA 58.889 32.000 7.29 0.00 0.00 4.92
2026 2101 8.589629 GCATATTCTGAACATCACACAAATTTC 58.410 33.333 0.00 0.00 0.00 2.17
2230 2305 4.338964 CAGTCACTCTCAGATACTGCTGAT 59.661 45.833 0.00 0.00 43.43 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.030717 CGACCAGGAACAGATCGGATAG 60.031 54.545 0.00 0.00 22.37 2.08
40 41 1.673920 GAAAAGCAACGACCAGGAACA 59.326 47.619 0.00 0.00 0.00 3.18
61 63 2.955881 AACTAGGTGCTCCCGTGGC 61.956 63.158 0.00 0.00 38.74 5.01
65 67 0.608640 AGAACAACTAGGTGCTCCCG 59.391 55.000 7.97 0.00 38.74 5.14
78 80 5.178252 CGAGAAATCAAGAAGCAGAGAACAA 59.822 40.000 0.00 0.00 0.00 2.83
114 116 5.720202 TCAGCATAACGACTGATAACACTT 58.280 37.500 0.00 0.00 37.99 3.16
152 154 7.506938 AGGATAAACCAATCCACCATAAGATTG 59.493 37.037 5.72 5.88 46.81 2.67
206 208 7.284034 AGGTATCAAATTGTCAGAACATCATCC 59.716 37.037 0.00 0.00 34.73 3.51
575 578 5.951747 AGTAGAAGCAAATTTGGGCTATTCA 59.048 36.000 19.47 0.00 40.01 2.57
680 688 9.621629 AGATCGGTATTGATTAACATTAACCAA 57.378 29.630 0.00 0.00 31.15 3.67
716 724 5.162794 CGATTCCAGCAAATGTTGATTGAA 58.837 37.500 0.00 0.00 35.59 2.69
772 780 5.435686 AGGTACTGGTCATGCTATTGAAA 57.564 39.130 0.00 0.00 37.18 2.69
951 998 3.323758 AATCCAGCGGCGCCTACAA 62.324 57.895 30.40 10.49 0.00 2.41
1061 1108 1.407299 CCTGCGGACTTGATGATCCAA 60.407 52.381 0.00 0.00 34.35 3.53
1164 1211 2.295885 CAGAACAGATCAATCAGGCCC 58.704 52.381 0.00 0.00 0.00 5.80
1327 1379 1.056660 CCCGTACCTTGCCTATCCAT 58.943 55.000 0.00 0.00 0.00 3.41
1443 1495 5.346822 CACCGCATATATAAACCGAACTACC 59.653 44.000 0.00 0.00 0.00 3.18
1657 1732 1.269413 GCTCAGTTTGCAAGCACACAT 60.269 47.619 16.04 0.00 36.06 3.21
1666 1741 1.896220 CACCCTTAGCTCAGTTTGCA 58.104 50.000 0.00 0.00 0.00 4.08
1743 1818 2.978156 AACCAATCAAAGCAGGGAGA 57.022 45.000 0.00 0.00 0.00 3.71
1753 1828 7.712264 GTGTCAAATCATTGAAACCAATCAA 57.288 32.000 1.24 0.00 46.66 2.57
1768 1843 9.859692 GTTAACTGTTAACTACTGTGTCAAATC 57.140 33.333 27.65 4.12 41.69 2.17
1769 1844 9.386010 TGTTAACTGTTAACTACTGTGTCAAAT 57.614 29.630 31.82 0.00 44.46 2.32
1789 1864 5.296813 CAGGACTAAATGCACCTGTTAAC 57.703 43.478 9.98 0.00 43.16 2.01
1879 1954 4.588528 ACTTGGCAATGTTCCTGTTTACAT 59.411 37.500 0.00 0.00 36.58 2.29
1968 2043 6.596888 TGCCACACATTCAAAGAAATTTTCAA 59.403 30.769 11.53 0.00 0.00 2.69
1993 2068 7.011763 GTGTGATGTTCAGAATATGCAGTGTAT 59.988 37.037 0.00 0.00 0.00 2.29
2064 2139 8.755028 TGTTGGTTTAGAGTTAGATGCAGTATA 58.245 33.333 0.00 0.00 0.00 1.47
2082 2157 8.337532 GTCGTGTAACTAAATAACTGTTGGTTT 58.662 33.333 2.69 7.06 35.31 3.27
2230 2305 7.158697 TGAACTATACTAGCAACAGAAAGCAA 58.841 34.615 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.