Multiple sequence alignment - TraesCS7D01G503000

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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 TraesCS7D01G503000 chr7D 100.000 2828 0 0 1 2828 608272620 608275447 0.000000e+00 5223
1 TraesCS7D01G503000 chr7D 92.824 2369 122 22 7 2350 610421769 610419424 0.000000e+00 3389
2 TraesCS7D01G503000 chr7D 89.239 2063 123 27 7 2045 608222314 608224301 0.000000e+00 2488
3 TraesCS7D01G503000 chr7D 94.199 362 16 3 2462 2823 514930675 514931031 5.330000e-152 547
4 TraesCS7D01G503000 chr7D 96.396 333 8 1 2500 2828 610416046 610415714 1.920000e-151 545
5 TraesCS7D01G503000 chr7D 99.107 112 1 0 2349 2460 610419391 610419280 4.780000e-48 202
6 TraesCS7D01G503000 chr7D 94.595 111 6 0 2351 2461 514920148 514920258 3.750000e-39 172
7 TraesCS7D01G503000 chr7D 92.079 101 7 1 108 208 514931869 514931968 1.060000e-29 141
8 TraesCS7D01G503000 chr7A 92.664 2290 113 17 1 2256 700300036 700302304 0.000000e+00 3247
9 TraesCS7D01G503000 chr7A 92.576 2290 115 17 1 2256 700337854 700340122 0.000000e+00 3236
10 TraesCS7D01G503000 chr7A 88.867 503 29 13 2351 2828 700340320 700340820 6.750000e-166 593
11 TraesCS7D01G503000 chr7A 88.668 503 30 13 2351 2828 700302502 700303002 3.140000e-164 588
12 TraesCS7D01G503000 chrUn 91.620 2315 146 18 64 2350 77521196 77523490 0.000000e+00 3157
13 TraesCS7D01G503000 chrUn 89.601 1529 121 13 7 1512 364810806 364809293 0.000000e+00 1908
14 TraesCS7D01G503000 chrUn 91.375 858 54 8 1501 2350 349917742 349916897 0.000000e+00 1157
15 TraesCS7D01G503000 chrUn 87.108 574 49 6 7 561 344773293 344772726 6.650000e-176 627
16 TraesCS7D01G503000 chrUn 96.185 367 14 0 2459 2825 77523665 77524031 4.030000e-168 601
17 TraesCS7D01G503000 chrUn 79.510 571 72 17 97 636 87678870 87678314 5.760000e-97 364
18 TraesCS7D01G503000 chrUn 95.495 111 5 0 2351 2461 77523525 77523635 8.050000e-41 178
19 TraesCS7D01G503000 chrUn 94.444 108 6 0 2351 2458 254017004 254017111 1.740000e-37 167
20 TraesCS7D01G503000 chrUn 94.444 108 6 0 2351 2458 254027893 254028000 1.740000e-37 167
21 TraesCS7D01G503000 chrUn 94.444 108 6 0 2351 2458 349916862 349916755 1.740000e-37 167
22 TraesCS7D01G503000 chr7B 92.353 2210 140 14 161 2350 698682699 698684899 0.000000e+00 3118
23 TraesCS7D01G503000 chr7B 90.520 2384 176 17 7 2350 696238578 696240951 0.000000e+00 3105
24 TraesCS7D01G503000 chr7B 92.667 1800 117 6 558 2344 693664476 693666273 0.000000e+00 2579
25 TraesCS7D01G503000 chr7B 89.646 1526 120 13 7 1509 693681699 693683209 0.000000e+00 1908
26 TraesCS7D01G503000 chr7B 93.864 766 45 2 1585 2350 694748766 694749529 0.000000e+00 1153
27 TraesCS7D01G503000 chr7B 89.379 499 30 7 2351 2827 694749564 694750061 8.660000e-170 606
28 TraesCS7D01G503000 chr7B 95.913 367 14 1 2459 2825 696241126 696241491 6.750000e-166 593
29 TraesCS7D01G503000 chr7B 94.851 369 19 0 2459 2827 698685073 698685441 6.790000e-161 577
30 TraesCS7D01G503000 chr7B 92.562 363 25 2 2467 2828 693699855 693700216 1.160000e-143 520
31 TraesCS7D01G503000 chr7B 91.026 390 24 5 1971 2350 693716221 693716609 1.500000e-142 516
32 TraesCS7D01G503000 chr7B 80.639 563 64 16 97 628 696249591 696250139 7.340000e-106 394
33 TraesCS7D01G503000 chr7B 91.713 181 10 1 7 182 693663853 693664033 2.180000e-61 246
34 TraesCS7D01G503000 chr7B 95.968 124 5 0 7 130 698682582 698682705 4.780000e-48 202
35 TraesCS7D01G503000 chr7B 94.595 111 6 0 2351 2461 693699699 693699809 3.750000e-39 172
36 TraesCS7D01G503000 chr7B 94.444 108 6 0 2351 2458 693685746 693685853 1.740000e-37 167
37 TraesCS7D01G503000 chr7B 95.238 105 5 0 2351 2455 693716644 693716748 1.740000e-37 167
38 TraesCS7D01G503000 chr7B 89.474 133 9 2 27 154 694747087 694747219 2.250000e-36 163
39 TraesCS7D01G503000 chr5B 85.003 1787 215 25 219 1973 5073009 5071244 0.000000e+00 1766
40 TraesCS7D01G503000 chr4A 86.606 545 49 12 1822 2350 662051488 662050952 5.250000e-162 580
41 TraesCS7D01G503000 chr4A 94.309 369 21 0 2459 2827 735216023 735215655 1.470000e-157 566
42 TraesCS7D01G503000 chr4A 89.899 297 25 1 1 292 662053040 662052744 7.400000e-101 377


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 TraesCS7D01G503000 chr7D 608272620 608275447 2827 False 5223.000000 5223 100.000000 1 2828 1 chr7D.!!$F3 2827
1 TraesCS7D01G503000 chr7D 608222314 608224301 1987 False 2488.000000 2488 89.239000 7 2045 1 chr7D.!!$F2 2038
2 TraesCS7D01G503000 chr7D 610415714 610421769 6055 True 1378.666667 3389 96.109000 7 2828 3 chr7D.!!$R1 2821
3 TraesCS7D01G503000 chr7D 514930675 514931968 1293 False 344.000000 547 93.139000 108 2823 2 chr7D.!!$F4 2715
4 TraesCS7D01G503000 chr7A 700300036 700303002 2966 False 1917.500000 3247 90.666000 1 2828 2 chr7A.!!$F1 2827
5 TraesCS7D01G503000 chr7A 700337854 700340820 2966 False 1914.500000 3236 90.721500 1 2828 2 chr7A.!!$F2 2827
6 TraesCS7D01G503000 chrUn 364809293 364810806 1513 True 1908.000000 1908 89.601000 7 1512 1 chrUn.!!$R3 1505
7 TraesCS7D01G503000 chrUn 77521196 77524031 2835 False 1312.000000 3157 94.433333 64 2825 3 chrUn.!!$F3 2761
8 TraesCS7D01G503000 chrUn 349916755 349917742 987 True 662.000000 1157 92.909500 1501 2458 2 chrUn.!!$R4 957
9 TraesCS7D01G503000 chrUn 344772726 344773293 567 True 627.000000 627 87.108000 7 561 1 chrUn.!!$R2 554
10 TraesCS7D01G503000 chrUn 87678314 87678870 556 True 364.000000 364 79.510000 97 636 1 chrUn.!!$R1 539
11 TraesCS7D01G503000 chr7B 696238578 696241491 2913 False 1849.000000 3105 93.216500 7 2825 2 chr7B.!!$F7 2818
12 TraesCS7D01G503000 chr7B 693663853 693666273 2420 False 1412.500000 2579 92.190000 7 2344 2 chr7B.!!$F2 2337
13 TraesCS7D01G503000 chr7B 698682582 698685441 2859 False 1299.000000 3118 94.390667 7 2827 3 chr7B.!!$F8 2820
14 TraesCS7D01G503000 chr7B 693681699 693685853 4154 False 1037.500000 1908 92.045000 7 2458 2 chr7B.!!$F3 2451
15 TraesCS7D01G503000 chr7B 694747087 694750061 2974 False 640.666667 1153 90.905667 27 2827 3 chr7B.!!$F6 2800
16 TraesCS7D01G503000 chr7B 696249591 696250139 548 False 394.000000 394 80.639000 97 628 1 chr7B.!!$F1 531
17 TraesCS7D01G503000 chr7B 693699699 693700216 517 False 346.000000 520 93.578500 2351 2828 2 chr7B.!!$F4 477
18 TraesCS7D01G503000 chr7B 693716221 693716748 527 False 341.500000 516 93.132000 1971 2455 2 chr7B.!!$F5 484
19 TraesCS7D01G503000 chr5B 5071244 5073009 1765 True 1766.000000 1766 85.003000 219 1973 1 chr5B.!!$R1 1754
20 TraesCS7D01G503000 chr4A 662050952 662053040 2088 True 478.500000 580 88.252500 1 2350 2 chr4A.!!$R2 2349

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
135 157 0.025770 CAACGACCACGACAACACAC 59.974 55.0 0.0 0.0 42.66 3.82 F
947 1348 0.033504 GAAGGAAGCTGTCACCGACA 59.966 55.0 0.0 0.0 40.50 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1462 1867 0.480252 ACCTTGAAGCCCTCAAAGCT 59.520 50.000 0.95 0.0 43.54 3.74 R
2237 4701 1.203052 AGAATGCAGAATTGGGTTGCG 59.797 47.619 0.00 0.0 40.62 4.85 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
86 87 2.032550 CCATGGACTGTTCGATCAATGC 59.967 50.000 5.56 0.00 0.00 3.56
87 88 2.768253 TGGACTGTTCGATCAATGCT 57.232 45.000 0.00 0.00 0.00 3.79
88 89 2.621338 TGGACTGTTCGATCAATGCTC 58.379 47.619 0.00 0.00 0.00 4.26
89 90 1.590238 GGACTGTTCGATCAATGCTCG 59.410 52.381 0.00 0.00 37.47 5.03
90 91 1.002366 ACTGTTCGATCAATGCTCGC 58.998 50.000 1.18 0.00 36.11 5.03
91 92 0.302890 CTGTTCGATCAATGCTCGCC 59.697 55.000 1.18 0.00 36.11 5.54
92 93 1.273887 GTTCGATCAATGCTCGCCG 59.726 57.895 1.18 0.00 36.11 6.46
93 94 1.882625 TTCGATCAATGCTCGCCGG 60.883 57.895 0.00 0.00 36.11 6.13
94 95 2.572095 TTCGATCAATGCTCGCCGGT 62.572 55.000 1.90 0.00 36.11 5.28
95 96 2.173669 CGATCAATGCTCGCCGGTT 61.174 57.895 1.90 0.00 0.00 4.44
111 133 1.194781 GGTTCTCCTCACCTGCTCCA 61.195 60.000 0.00 0.00 0.00 3.86
135 157 0.025770 CAACGACCACGACAACACAC 59.974 55.000 0.00 0.00 42.66 3.82
136 158 0.108520 AACGACCACGACAACACACT 60.109 50.000 0.00 0.00 42.66 3.55
139 166 1.801395 CGACCACGACAACACACTCTT 60.801 52.381 0.00 0.00 42.66 2.85
236 596 0.320374 CCAGGTCACTACGGCTTTCA 59.680 55.000 0.00 0.00 0.00 2.69
254 617 5.453587 GCTTTCAATCGACACAATATCAAGC 59.546 40.000 0.00 0.00 0.00 4.01
444 823 1.293458 ACCTCCAGATCACCATCTCCT 59.707 52.381 0.00 0.00 37.25 3.69
445 824 2.293452 ACCTCCAGATCACCATCTCCTT 60.293 50.000 0.00 0.00 37.25 3.36
446 825 2.368221 CCTCCAGATCACCATCTCCTTC 59.632 54.545 0.00 0.00 37.25 3.46
447 826 3.307506 CTCCAGATCACCATCTCCTTCT 58.692 50.000 0.00 0.00 37.25 2.85
448 827 3.303938 TCCAGATCACCATCTCCTTCTC 58.696 50.000 0.00 0.00 37.25 2.87
449 828 2.368221 CCAGATCACCATCTCCTTCTCC 59.632 54.545 0.00 0.00 37.25 3.71
759 1158 1.538512 TGTCGTTGACTCCTACCTTCG 59.461 52.381 0.00 0.00 33.15 3.79
769 1168 3.838903 ACTCCTACCTTCGTTTCATCCTT 59.161 43.478 0.00 0.00 0.00 3.36
884 1285 3.319198 GGAGCCACGTCCCCTTCA 61.319 66.667 0.00 0.00 0.00 3.02
942 1343 2.266554 CGATGAGAAGGAAGCTGTCAC 58.733 52.381 0.00 0.00 0.00 3.67
947 1348 0.033504 GAAGGAAGCTGTCACCGACA 59.966 55.000 0.00 0.00 40.50 4.35
1012 1414 2.363406 AAGGCATGGAAGCAGGGC 60.363 61.111 0.00 0.00 35.83 5.19
1050 1452 2.310233 CGACACTGGCAAGTCCACG 61.310 63.158 12.46 0.00 40.72 4.94
1058 1460 0.179111 GGCAAGTCCACGATGATCGA 60.179 55.000 22.88 0.00 43.97 3.59
1085 1487 0.522915 GCGAACTTCCTCGACTACGG 60.523 60.000 0.00 0.00 41.44 4.02
1217 1619 1.305201 GACTTCACAGGAAAACGCCA 58.695 50.000 0.00 0.00 31.35 5.69
1306 1711 0.321653 GAAGGACGATGCCACCAAGT 60.322 55.000 0.00 0.00 0.00 3.16
1400 1805 1.149101 ACCACCAACCACAAGGAGAT 58.851 50.000 0.00 0.00 38.69 2.75
1712 3975 1.229464 AGGCAGAGGAGGCTCAAGT 60.229 57.895 17.69 0.00 40.91 3.16
1849 4249 1.476891 GTGACATCACGCTAGGGAAGA 59.523 52.381 14.59 11.03 37.10 2.87
1890 4291 2.230508 TGTTCACTAGTGCTCCCTTACG 59.769 50.000 18.45 0.00 0.00 3.18
1923 4324 4.105486 GCAGTGTTTGGTGAGAGAAAAAC 58.895 43.478 0.00 0.00 33.98 2.43
1928 4329 6.071391 AGTGTTTGGTGAGAGAAAAACAATGT 60.071 34.615 1.73 0.00 42.37 2.71
1950 4351 8.723942 ATGTACCTCTCAACTGAAACAATATC 57.276 34.615 0.00 0.00 0.00 1.63
1979 4380 5.185828 TCTTCTCTCACTTGTAATGCTGCTA 59.814 40.000 0.00 0.00 0.00 3.49
1985 4391 6.703165 TCTCACTTGTAATGCTGCTACATATG 59.297 38.462 0.00 0.00 0.00 1.78
2232 4648 7.555087 TGGCCCTTTCATTCATTAATTAACTG 58.445 34.615 0.00 1.29 0.00 3.16
2485 5055 1.338337 CCTCCGACGTTATGATGAGCT 59.662 52.381 0.00 0.00 0.00 4.09
2559 8292 1.400846 CATGTGCAGAAGAGGCATGAC 59.599 52.381 0.00 0.00 44.11 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 2.182030 GTGAGGAGAACCGGCGAG 59.818 66.667 9.30 0.06 41.83 5.03
87 88 3.379445 GGTGAGGAGAACCGGCGA 61.379 66.667 9.30 0.00 41.83 5.54
88 89 3.382832 AGGTGAGGAGAACCGGCG 61.383 66.667 0.00 0.00 42.89 6.46
89 90 2.266055 CAGGTGAGGAGAACCGGC 59.734 66.667 0.00 0.00 42.89 6.13
90 91 2.232298 GAGCAGGTGAGGAGAACCGG 62.232 65.000 0.00 0.00 42.89 5.28
91 92 1.216710 GAGCAGGTGAGGAGAACCG 59.783 63.158 0.00 0.00 42.89 4.44
92 93 1.194781 TGGAGCAGGTGAGGAGAACC 61.195 60.000 0.00 0.00 38.03 3.62
93 94 0.248843 CTGGAGCAGGTGAGGAGAAC 59.751 60.000 0.00 0.00 0.00 3.01
94 95 1.548357 GCTGGAGCAGGTGAGGAGAA 61.548 60.000 0.00 0.00 41.59 2.87
95 96 1.986757 GCTGGAGCAGGTGAGGAGA 60.987 63.158 0.00 0.00 41.59 3.71
111 133 4.309950 GTCGTGGTCGTTGGGGCT 62.310 66.667 0.00 0.00 38.33 5.19
135 157 3.325293 TGCTGAGGTTGAAGCTAAGAG 57.675 47.619 12.82 3.46 40.21 2.85
136 158 3.769739 TTGCTGAGGTTGAAGCTAAGA 57.230 42.857 12.82 0.00 40.21 2.10
139 166 4.216257 GTGATTTTGCTGAGGTTGAAGCTA 59.784 41.667 0.00 0.00 40.21 3.32
236 596 3.792401 TCCGCTTGATATTGTGTCGATT 58.208 40.909 0.00 0.00 0.00 3.34
374 753 1.938585 CCCAAGTGGTGAGGTAGAGA 58.061 55.000 0.00 0.00 0.00 3.10
413 792 1.946984 TCTGGAGGTACGGGTTGAAT 58.053 50.000 0.00 0.00 0.00 2.57
444 823 2.812499 GGCGCCATACTCGGAGAA 59.188 61.111 24.80 0.00 34.09 2.87
445 824 3.592814 CGGCGCCATACTCGGAGA 61.593 66.667 28.98 0.00 0.00 3.71
446 825 3.544167 CTCGGCGCCATACTCGGAG 62.544 68.421 28.98 18.52 0.00 4.63
447 826 3.592814 CTCGGCGCCATACTCGGA 61.593 66.667 28.98 12.64 0.00 4.55
494 873 1.517361 CATCGCTGAGGTAGGCACA 59.483 57.895 0.00 0.00 0.00 4.57
884 1285 4.218686 AAAGGTGGCGGGGTGCTT 62.219 61.111 0.00 0.00 45.43 3.91
942 1343 1.635663 GAACGCCATGAGGTTGTCGG 61.636 60.000 6.14 0.00 37.19 4.79
947 1348 1.002134 CCTGGAACGCCATGAGGTT 60.002 57.895 0.00 0.00 44.91 3.50
1050 1452 3.248029 GCCATGGCGTCGATCATC 58.752 61.111 23.48 0.00 0.00 2.92
1217 1619 0.538287 GCTTGAGGCCTTGTCCTTGT 60.538 55.000 6.77 0.00 36.38 3.16
1274 1679 1.693627 GTCCTTCTCCGGCTCTATCA 58.306 55.000 0.00 0.00 0.00 2.15
1306 1711 2.361992 TAGGCCCGAGAGCGTCAA 60.362 61.111 0.00 0.00 35.23 3.18
1400 1805 2.891941 GATCAATGCCGGGTCCAGCA 62.892 60.000 2.18 8.17 44.45 4.41
1422 1827 2.933287 TTGTCCATCCTGCCCCGT 60.933 61.111 0.00 0.00 0.00 5.28
1462 1867 0.480252 ACCTTGAAGCCCTCAAAGCT 59.520 50.000 0.95 0.00 43.54 3.74
1712 3975 4.392940 CTCTTTCTCCTTGGCTTTCTTCA 58.607 43.478 0.00 0.00 0.00 3.02
1843 4243 4.461198 TCACTCTTTTTCCTTGTCTTCCC 58.539 43.478 0.00 0.00 0.00 3.97
1849 4249 4.273318 ACAAGCTCACTCTTTTTCCTTGT 58.727 39.130 0.00 0.00 37.27 3.16
1890 4291 5.121454 TCACCAAACACTGCATTTTTGTTTC 59.879 36.000 11.03 0.00 40.62 2.78
1923 4324 6.618287 TTGTTTCAGTTGAGAGGTACATTG 57.382 37.500 0.00 0.00 0.00 2.82
1928 4329 8.367660 AGAGATATTGTTTCAGTTGAGAGGTA 57.632 34.615 0.00 0.00 0.00 3.08
1950 4351 6.873076 AGCATTACAAGTGAGAGAAGAAAGAG 59.127 38.462 0.00 0.00 0.00 2.85
1979 4380 4.394610 TGTATTGTTGCACGCTTCATATGT 59.605 37.500 1.90 0.00 0.00 2.29
1985 4391 4.663889 GCATTTTGTATTGTTGCACGCTTC 60.664 41.667 0.00 0.00 33.58 3.86
2160 4576 3.709141 ACTCTAGGAGCAGGAGAAATTCC 59.291 47.826 0.00 0.00 38.61 3.01
2232 4648 2.163412 TGCAGAATTGGGTTGCGTAATC 59.837 45.455 0.00 0.00 40.62 1.75
2237 4701 1.203052 AGAATGCAGAATTGGGTTGCG 59.797 47.619 0.00 0.00 40.62 4.85
2309 4775 5.715429 TTTGTTTTGTAAACGACGCTCTA 57.285 34.783 0.00 0.00 0.00 2.43
2437 4967 4.162592 CCACAAGGTGAGCTTGCA 57.837 55.556 22.83 0.00 35.23 4.08
2485 5055 8.100164 TGCCGATCTATATATCCATCAAAACAA 58.900 33.333 0.00 0.00 0.00 2.83
2559 8292 7.656707 AGTTATGCTTAAATTTGGTGCAAAG 57.343 32.000 15.01 5.52 36.76 2.77
2597 8336 2.860735 GTTTCCTCAATCCGTCTCATCG 59.139 50.000 0.00 0.00 0.00 3.84


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

AutoCloner maintained by Alex Coulton.