Multiple sequence alignment - TraesCS7D01G074200

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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 TraesCS7D01G074200 chr7D 100.000 2682 0 0 1 2682 43431124 43428443 0.000000e+00 4953.0
1 TraesCS7D01G074200 chr7D 84.895 1622 140 48 4 1570 43385590 43384019 0.000000e+00 1541.0
2 TraesCS7D01G074200 chr7A 92.276 1955 93 31 768 2682 43458144 43456208 0.000000e+00 2721.0
3 TraesCS7D01G074200 chr7A 90.856 1553 78 28 768 2288 43439468 43437948 0.000000e+00 2023.0
4 TraesCS7D01G074200 chr7A 93.086 1345 45 14 1361 2682 43258423 43257104 0.000000e+00 1925.0
5 TraesCS7D01G074200 chr7A 82.095 1050 127 42 1183 2208 44877557 44876545 0.000000e+00 841.0
6 TraesCS7D01G074200 chr7A 95.730 445 17 2 1 443 45610628 45610184 0.000000e+00 715.0
7 TraesCS7D01G074200 chr7A 94.794 461 18 4 1 461 43460382 43459928 0.000000e+00 713.0
8 TraesCS7D01G074200 chr7A 89.594 567 42 10 1019 1571 45602717 45602154 0.000000e+00 704.0
9 TraesCS7D01G074200 chr7A 94.655 449 18 3 1 449 43440506 43440064 0.000000e+00 691.0
10 TraesCS7D01G074200 chr7A 88.556 568 48 9 1019 1571 45593706 45593141 0.000000e+00 673.0
11 TraesCS7D01G074200 chr7A 88.380 568 49 9 1019 1571 45574016 45573451 0.000000e+00 667.0
12 TraesCS7D01G074200 chr7A 83.333 702 70 24 153 843 45021965 45021300 2.950000e-169 604.0
13 TraesCS7D01G074200 chr7A 83.191 702 71 24 153 843 45068782 45068117 1.370000e-167 599.0
14 TraesCS7D01G074200 chr7A 87.625 501 39 19 1019 1502 45067559 45067065 6.480000e-156 560.0
15 TraesCS7D01G074200 chr7A 87.226 501 41 19 1019 1502 45020742 45020248 1.400000e-152 549.0
16 TraesCS7D01G074200 chr7A 80.559 715 101 23 1499 2208 45063102 45062421 1.420000e-142 516.0
17 TraesCS7D01G074200 chr7A 94.801 327 13 2 444 766 45574745 45574419 8.570000e-140 507.0
18 TraesCS7D01G074200 chr7A 94.801 327 13 2 444 766 45594435 45594109 8.570000e-140 507.0
19 TraesCS7D01G074200 chr7A 94.190 327 15 2 444 766 45603445 45603119 1.850000e-136 496.0
20 TraesCS7D01G074200 chr7A 94.410 322 14 2 449 766 43439980 43439659 2.400000e-135 492.0
21 TraesCS7D01G074200 chr7A 79.778 722 102 25 1499 2208 45016330 45015641 4.010000e-133 484.0
22 TraesCS7D01G074200 chr7A 88.822 331 26 6 702 1026 45186568 45186243 1.930000e-106 396.0
23 TraesCS7D01G074200 chr7A 94.595 259 9 2 768 1026 45593981 45593728 1.930000e-106 396.0
24 TraesCS7D01G074200 chr7A 94.595 259 9 1 768 1026 45602992 45602739 1.930000e-106 396.0
25 TraesCS7D01G074200 chr7A 94.208 259 10 1 768 1026 45574291 45574038 9.000000e-105 390.0
26 TraesCS7D01G074200 chr7A 76.695 811 112 46 1770 2522 541372434 541371643 1.950000e-101 379.0
27 TraesCS7D01G074200 chr7A 87.205 297 24 7 153 444 44885723 44885436 2.570000e-85 326.0
28 TraesCS7D01G074200 chr7A 95.288 191 7 2 577 766 43458465 43458276 4.340000e-78 302.0
29 TraesCS7D01G074200 chr7A 78.618 463 62 22 1905 2341 287246516 287246065 3.400000e-69 272.0
30 TraesCS7D01G074200 chr7A 84.677 248 20 7 789 1026 43260083 43259844 5.770000e-57 231.0
31 TraesCS7D01G074200 chr7A 94.531 128 7 0 449 576 43459852 43459725 5.860000e-47 198.0
32 TraesCS7D01G074200 chr7A 87.578 161 12 4 2526 2682 45015313 45015157 2.120000e-41 180.0
33 TraesCS7D01G074200 chr7A 87.578 161 12 4 2526 2682 45062093 45061937 2.120000e-41 180.0
34 TraesCS7D01G074200 chr7A 92.473 93 7 0 1019 1111 44884791 44884699 1.680000e-27 134.0
35 TraesCS7D01G074200 chr4A 86.887 816 56 27 795 1571 651986144 651985341 0.000000e+00 867.0
36 TraesCS7D01G074200 chr4A 81.809 951 86 37 281 1182 651639155 651638243 0.000000e+00 717.0
37 TraesCS7D01G074200 chr4A 88.557 402 39 6 1176 1571 651637817 651637417 5.190000e-132 481.0
38 TraesCS7D01G074200 chr4A 88.194 288 29 4 2240 2524 651984675 651984390 3.310000e-89 339.0
39 TraesCS7D01G074200 chr5B 82.247 445 72 6 2083 2524 661315299 661314859 7.010000e-101 377.0
40 TraesCS7D01G074200 chr2B 80.632 506 80 16 2028 2524 67272752 67273248 2.520000e-100 375.0
41 TraesCS7D01G074200 chr3A 81.473 448 68 12 2080 2524 37645714 37646149 1.180000e-93 353.0
42 TraesCS7D01G074200 chr1D 78.598 528 83 25 1857 2372 99688384 99688893 3.330000e-84 322.0
43 TraesCS7D01G074200 chr1D 79.263 434 59 19 2064 2478 469061894 469062315 9.460000e-70 274.0
44 TraesCS7D01G074200 chr4B 77.197 478 75 23 1881 2334 554022648 554022181 5.730000e-62 248.0
45 TraesCS7D01G074200 chr4B 78.431 153 29 3 1899 2050 366949150 366949001 2.200000e-16 97.1
46 TraesCS7D01G074200 chr2A 84.516 155 17 6 2374 2524 768531501 768531652 2.150000e-31 147.0


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 TraesCS7D01G074200 chr7D 43428443 43431124 2681 True 4953.000000 4953 100.000000 1 2682 1 chr7D.!!$R2 2681
1 TraesCS7D01G074200 chr7D 43384019 43385590 1571 True 1541.000000 1541 84.895000 4 1570 1 chr7D.!!$R1 1566
2 TraesCS7D01G074200 chr7A 43257104 43260083 2979 True 1078.000000 1925 88.881500 789 2682 2 chr7A.!!$R6 1893
3 TraesCS7D01G074200 chr7A 43437948 43440506 2558 True 1068.666667 2023 93.307000 1 2288 3 chr7A.!!$R7 2287
4 TraesCS7D01G074200 chr7A 43456208 43460382 4174 True 983.500000 2721 94.222250 1 2682 4 chr7A.!!$R8 2681
5 TraesCS7D01G074200 chr7A 44876545 44877557 1012 True 841.000000 841 82.095000 1183 2208 1 chr7A.!!$R1 1025
6 TraesCS7D01G074200 chr7A 45602154 45603445 1291 True 532.000000 704 92.793000 444 1571 3 chr7A.!!$R14 1127
7 TraesCS7D01G074200 chr7A 45593141 45594435 1294 True 525.333333 673 92.650667 444 1571 3 chr7A.!!$R13 1127
8 TraesCS7D01G074200 chr7A 45573451 45574745 1294 True 521.333333 667 92.463000 444 1571 3 chr7A.!!$R12 1127
9 TraesCS7D01G074200 chr7A 45061937 45068782 6845 True 463.750000 599 84.738250 153 2682 4 chr7A.!!$R11 2529
10 TraesCS7D01G074200 chr7A 45015157 45021965 6808 True 454.250000 604 84.478750 153 2682 4 chr7A.!!$R10 2529
11 TraesCS7D01G074200 chr7A 541371643 541372434 791 True 379.000000 379 76.695000 1770 2522 1 chr7A.!!$R5 752
12 TraesCS7D01G074200 chr7A 44884699 44885723 1024 True 230.000000 326 89.839000 153 1111 2 chr7A.!!$R9 958
13 TraesCS7D01G074200 chr4A 651984390 651986144 1754 True 603.000000 867 87.540500 795 2524 2 chr4A.!!$R2 1729
14 TraesCS7D01G074200 chr4A 651637417 651639155 1738 True 599.000000 717 85.183000 281 1571 2 chr4A.!!$R1 1290
15 TraesCS7D01G074200 chr1D 99688384 99688893 509 False 322.000000 322 78.598000 1857 2372 1 chr1D.!!$F1 515

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
520 620 0.8951 TGCATCCTGAACAGTTGGGC 60.895 55.0 0.0 0.82 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2334 10279 0.525668 CTAGTTAGTGGACGCAGCGG 60.526 60.0 21.15 0.7 0.0 5.52 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
38 39 9.951866 AAATAAGGGTGTAAAGGGATTATTGAT 57.048 29.630 0.00 0.00 0.00 2.57
83 84 2.203437 GGCAAACACCCCGGAAGT 60.203 61.111 0.73 0.00 0.00 3.01
329 330 6.547510 AGAGCATATGTTAAGGGATCAAAACC 59.452 38.462 4.29 0.00 0.00 3.27
520 620 0.895100 TGCATCCTGAACAGTTGGGC 60.895 55.000 0.00 0.82 0.00 5.36
552 710 7.254252 CCAACGTTTGAATGTTTTGATGCTTTA 60.254 33.333 0.00 0.00 36.05 1.85
814 2435 8.603242 AACTAATGTAGTACTCCAACAACAAG 57.397 34.615 0.00 1.10 38.26 3.16
815 2436 7.732996 ACTAATGTAGTACTCCAACAACAAGT 58.267 34.615 0.00 1.70 37.23 3.16
816 2437 8.863086 ACTAATGTAGTACTCCAACAACAAGTA 58.137 33.333 0.00 0.00 37.23 2.24
817 2438 7.958053 AATGTAGTACTCCAACAACAAGTAC 57.042 36.000 0.00 4.19 43.61 2.73
1091 4276 0.259647 TACTAGCCCTCGCCCTTGTA 59.740 55.000 0.00 0.00 34.57 2.41
1128 4313 2.882927 GCCCCATGCATGCATATATG 57.117 50.000 31.73 21.00 40.77 1.78
1175 4399 8.519799 AACTTTCAACTAAGAAATTGGAGTCA 57.480 30.769 0.00 0.00 36.94 3.41
1197 4857 6.530534 GTCAAATATATATACGCCTCGTGCTT 59.469 38.462 1.77 0.00 41.39 3.91
1234 4899 1.107945 TTCGATCCGTAGATGTGGCA 58.892 50.000 0.00 0.00 30.90 4.92
1236 4901 1.067060 TCGATCCGTAGATGTGGCAAG 59.933 52.381 0.00 0.00 30.90 4.01
1327 4992 1.246056 CCATCCCCGGCATATGCAAG 61.246 60.000 28.07 20.21 44.36 4.01
1356 5021 4.547859 CATGGAGTACTGCCAGGC 57.452 61.111 12.28 3.66 39.11 4.85
1480 5145 1.442526 ATACGCTGCTGCATGCTTCC 61.443 55.000 20.33 7.52 43.37 3.46
1606 9258 2.322081 CGGTGCACCCCTGTAAACG 61.322 63.158 29.95 11.03 0.00 3.60
1678 9386 9.529325 TGATGTGATTATATACCTTTATAGCGC 57.471 33.333 0.00 0.00 0.00 5.92
1747 9457 7.575332 TTCCTTTTCTTTTCTTGTTTGTTCG 57.425 32.000 0.00 0.00 0.00 3.95
1855 9568 7.509050 GCAATGTGCAAACTTTTCAATTTTT 57.491 28.000 0.00 0.00 44.26 1.94
2334 10279 2.325082 ATGAAAGGTGGCGTGCGAC 61.325 57.895 0.00 0.00 0.00 5.19
2358 10303 1.411493 GCGTCCACTAACTAGCGCAC 61.411 60.000 11.47 0.00 43.62 5.34
2537 10525 5.106277 GGATTACTTCCCGAACCTTTTCAAG 60.106 44.000 0.00 0.00 38.75 3.02
2578 10567 5.625311 GTGGAGCTTAATGTTCTTGTTTTCG 59.375 40.000 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 7.777910 CACATCAATAATCCCTTTACACCCTTA 59.222 37.037 0.00 0.00 0.00 2.69
53 54 0.819582 GTTTGCCATCACCCCATCAG 59.180 55.000 0.00 0.00 0.00 2.90
102 103 5.401033 TTTTTGGAATGCACATTTTCACG 57.599 34.783 0.00 0.00 0.00 4.35
343 344 0.901827 TGACACGCCACATATGACCT 59.098 50.000 10.38 0.00 0.00 3.85
708 2125 2.710096 GCCTTTATGTGGCCACTAGA 57.290 50.000 34.75 17.23 44.32 2.43
814 2435 5.334435 TCGAGTGCATATACGTACAGTAC 57.666 43.478 0.00 0.00 38.29 2.73
815 2436 7.656707 TTATCGAGTGCATATACGTACAGTA 57.343 36.000 0.00 0.00 40.03 2.74
816 2437 6.549912 TTATCGAGTGCATATACGTACAGT 57.450 37.500 0.00 0.00 0.00 3.55
817 2438 7.847166 TTTTATCGAGTGCATATACGTACAG 57.153 36.000 0.00 0.00 0.00 2.74
1091 4276 0.177604 GCATACCTGAGCAGAGCAGT 59.822 55.000 0.00 0.00 0.00 4.40
1127 4312 8.792633 AGTTTAAACTAATAAAGCATGAGTGCA 58.207 29.630 19.26 0.00 45.15 4.57
1128 4313 9.626045 AAGTTTAAACTAATAAAGCATGAGTGC 57.374 29.630 20.83 0.00 44.59 4.40
1149 4370 8.966868 TGACTCCAATTTCTTAGTTGAAAGTTT 58.033 29.630 0.00 0.00 39.01 2.66
1167 4391 7.094075 ACGAGGCGTATATATATTTGACTCCAA 60.094 37.037 17.61 0.00 38.73 3.53
1197 4857 2.096466 CGAACAGCGCACACAAGAAATA 60.096 45.455 11.47 0.00 0.00 1.40
1234 4899 2.430367 GCCGTCACCACCTTCCTT 59.570 61.111 0.00 0.00 0.00 3.36
1236 4901 2.798148 ATTCGCCGTCACCACCTTCC 62.798 60.000 0.00 0.00 0.00 3.46
1327 4992 0.607489 ACTCCATGCACTTGTCAGGC 60.607 55.000 0.00 0.00 0.00 4.85
1606 9258 2.098770 ACGTAATCTCAGCCGTCCTTAC 59.901 50.000 0.00 0.00 0.00 2.34
1672 9380 3.942115 GGAAGAAAGGAGAAAAGCGCTAT 59.058 43.478 12.05 1.76 0.00 2.97
1727 9435 7.650104 ACTGTTCGAACAAACAAGAAAAGAAAA 59.350 29.630 29.32 2.92 38.60 2.29
1728 9436 7.142680 ACTGTTCGAACAAACAAGAAAAGAAA 58.857 30.769 29.32 3.29 38.60 2.52
2272 10217 1.308783 ATCAGCTGTCGCTCGTGAGA 61.309 55.000 14.67 0.00 45.15 3.27
2334 10279 0.525668 CTAGTTAGTGGACGCAGCGG 60.526 60.000 21.15 0.70 0.00 5.52
2358 10303 1.520342 GCTCCTAGTCAGCGCTTGG 60.520 63.158 7.50 5.45 33.63 3.61
2436 10381 6.641161 AAAGGAAAGAAATTAATGGGCCAT 57.359 33.333 14.78 14.78 0.00 4.40
2537 10525 6.116126 AGCTCCACCTTAATCAATCTACAAC 58.884 40.000 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.