Multiple sequence alignment - TraesCS5A01G556600

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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 TraesCS5A01G556600 chr5A 100.000 2576 0 0 1 2576 707848327 707850902 0.000000e+00 4758
1 TraesCS5A01G556600 chr5A 92.196 2063 61 23 22 2032 707983232 707985246 0.000000e+00 2826
2 TraesCS5A01G556600 chr5A 87.955 1345 101 25 572 1869 709530531 709531861 0.000000e+00 1530
3 TraesCS5A01G556600 chr5A 86.082 1164 86 36 647 1762 707578379 707579514 0.000000e+00 1182
4 TraesCS5A01G556600 chr4B 89.975 2434 86 54 1 2374 668513007 668515342 0.000000e+00 2998
5 TraesCS5A01G556600 chr4B 88.898 2450 124 58 1 2374 669558305 669560682 0.000000e+00 2881
6 TraesCS5A01G556600 chr4B 90.644 2095 80 36 1 2053 669471672 669473692 0.000000e+00 2676
7 TraesCS5A01G556600 chr4B 91.403 1896 80 29 1 1869 668972944 668974783 0.000000e+00 2521
8 TraesCS5A01G556600 chr4B 92.022 1805 68 26 1 1778 668587651 668589406 0.000000e+00 2466
9 TraesCS5A01G556600 chr4B 91.597 1785 86 24 1 1737 668649625 668651393 0.000000e+00 2407
10 TraesCS5A01G556600 chr4B 89.612 1906 108 36 1 1869 669342471 669340619 0.000000e+00 2340
11 TraesCS5A01G556600 chr4B 90.767 1343 91 18 540 1869 599588980 599587658 0.000000e+00 1762
12 TraesCS5A01G556600 chr4B 90.437 1328 81 13 566 1869 599464344 599463039 0.000000e+00 1707
13 TraesCS5A01G556600 chr4B 87.017 1371 72 32 552 1869 668402963 668404280 0.000000e+00 1448
14 TraesCS5A01G556600 chr4B 89.318 1011 50 18 877 1869 668216606 668217576 0.000000e+00 1216
15 TraesCS5A01G556600 chr4B 87.664 916 63 17 963 1869 669161606 669160732 0.000000e+00 1020
16 TraesCS5A01G556600 chr4B 89.239 539 19 14 1869 2374 669160673 669160141 2.800000e-179 638
17 TraesCS5A01G556600 chr4B 89.239 539 17 16 1869 2374 669340560 669340030 1.010000e-178 636
18 TraesCS5A01G556600 chr4B 86.957 552 22 18 1863 2374 668217629 668218170 2.220000e-160 575
19 TraesCS5A01G556600 chr4B 94.190 327 13 3 2052 2374 668596209 668596533 6.400000e-136 494
20 TraesCS5A01G556600 chr4B 93.846 325 13 6 2052 2374 668365587 668365906 1.390000e-132 483
21 TraesCS5A01G556600 chr4B 92.988 328 16 4 2052 2374 668447753 668448078 3.000000e-129 472
22 TraesCS5A01G556600 chr4B 91.950 323 17 4 2052 2374 669473720 669474033 6.540000e-121 444
23 TraesCS5A01G556600 chr4B 91.667 288 17 3 2091 2374 668451620 668451904 2.400000e-105 392
24 TraesCS5A01G556600 chr4B 96.040 202 8 0 2375 2576 668365835 668366036 1.910000e-86 329
25 TraesCS5A01G556600 chr4B 95.545 202 8 1 2375 2576 669473963 669474163 3.200000e-84 322
26 TraesCS5A01G556600 chr4B 95.050 202 9 1 2375 2576 668515272 668515472 1.490000e-82 316
27 TraesCS5A01G556600 chr4B 95.025 201 9 1 2376 2576 669560613 669560812 5.350000e-82 315
28 TraesCS5A01G556600 chr4B 94.241 191 6 1 1863 2053 668589690 668589875 1.170000e-73 287
29 TraesCS5A01G556600 chr4B 93.717 191 7 1 1863 2053 668365374 668365559 5.430000e-72 281
30 TraesCS5A01G556600 chr4B 88.182 220 8 6 2375 2576 669160212 669159993 1.980000e-61 246
31 TraesCS5A01G556600 chr4B 88.182 220 8 6 2375 2576 669340101 669339882 1.980000e-61 246
32 TraesCS5A01G556600 chr4B 88.426 216 7 6 2379 2576 668448011 668448226 7.120000e-61 244
33 TraesCS5A01G556600 chr4B 87.273 220 10 6 2375 2576 668596462 668596681 4.290000e-58 235
34 TraesCS5A01G556600 chr4B 87.273 220 9 7 2375 2576 668218100 668218318 1.540000e-57 233
35 TraesCS5A01G556600 chrUn 89.187 1378 86 19 547 1869 134396070 134394701 0.000000e+00 1661
36 TraesCS5A01G556600 chrUn 88.394 1370 80 21 547 1869 30530829 30529492 0.000000e+00 1576
37 TraesCS5A01G556600 chrUn 89.720 1177 74 17 537 1677 79803866 79805031 0.000000e+00 1459
38 TraesCS5A01G556600 chrUn 91.843 993 60 4 892 1870 29602423 29601438 0.000000e+00 1365
39 TraesCS5A01G556600 chrUn 96.644 745 13 4 1 734 346448735 346449478 0.000000e+00 1227
40 TraesCS5A01G556600 chrUn 96.644 745 13 4 1 734 348077197 348076454 0.000000e+00 1227
41 TraesCS5A01G556600 chrUn 89.588 874 68 11 892 1762 28897766 28898619 0.000000e+00 1088
42 TraesCS5A01G556600 chrUn 90.789 684 61 2 892 1574 29364873 29364191 0.000000e+00 913
43 TraesCS5A01G556600 chrUn 93.607 219 5 3 1658 1869 29364082 29363866 4.140000e-83 318
44 TraesCS5A01G556600 chr6D 86.608 1374 89 16 537 1869 1069944 1071263 0.000000e+00 1430


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 TraesCS5A01G556600 chr5A 707848327 707850902 2575 False 4758.000000 4758 100.000000 1 2576 1 chr5A.!!$F2 2575
1 TraesCS5A01G556600 chr5A 707983232 707985246 2014 False 2826.000000 2826 92.196000 22 2032 1 chr5A.!!$F3 2010
2 TraesCS5A01G556600 chr5A 709530531 709531861 1330 False 1530.000000 1530 87.955000 572 1869 1 chr5A.!!$F4 1297
3 TraesCS5A01G556600 chr5A 707578379 707579514 1135 False 1182.000000 1182 86.082000 647 1762 1 chr5A.!!$F1 1115
4 TraesCS5A01G556600 chr4B 668972944 668974783 1839 False 2521.000000 2521 91.403000 1 1869 1 chr4B.!!$F3 1868
5 TraesCS5A01G556600 chr4B 668649625 668651393 1768 False 2407.000000 2407 91.597000 1 1737 1 chr4B.!!$F2 1736
6 TraesCS5A01G556600 chr4B 599587658 599588980 1322 True 1762.000000 1762 90.767000 540 1869 1 chr4B.!!$R2 1329
7 TraesCS5A01G556600 chr4B 599463039 599464344 1305 True 1707.000000 1707 90.437000 566 1869 1 chr4B.!!$R1 1303
8 TraesCS5A01G556600 chr4B 668513007 668515472 2465 False 1657.000000 2998 92.512500 1 2576 2 chr4B.!!$F7 2575
9 TraesCS5A01G556600 chr4B 669558305 669560812 2507 False 1598.000000 2881 91.961500 1 2576 2 chr4B.!!$F11 2575
10 TraesCS5A01G556600 chr4B 668402963 668404280 1317 False 1448.000000 1448 87.017000 552 1869 1 chr4B.!!$F1 1317
11 TraesCS5A01G556600 chr4B 668587651 668589875 2224 False 1376.500000 2466 93.131500 1 2053 2 chr4B.!!$F8 2052
12 TraesCS5A01G556600 chr4B 669471672 669474163 2491 False 1147.333333 2676 92.713000 1 2576 3 chr4B.!!$F10 2575
13 TraesCS5A01G556600 chr4B 669339882 669342471 2589 True 1074.000000 2340 89.011000 1 2576 3 chr4B.!!$R4 2575
14 TraesCS5A01G556600 chr4B 668216606 668218318 1712 False 674.666667 1216 87.849333 877 2576 3 chr4B.!!$F4 1699
15 TraesCS5A01G556600 chr4B 669159993 669161606 1613 True 634.666667 1020 88.361667 963 2576 3 chr4B.!!$R3 1613
16 TraesCS5A01G556600 chr4B 668447753 668451904 4151 False 369.333333 472 91.027000 2052 2576 3 chr4B.!!$F6 524
17 TraesCS5A01G556600 chr4B 668365374 668366036 662 False 364.333333 483 94.534333 1863 2576 3 chr4B.!!$F5 713
18 TraesCS5A01G556600 chrUn 134394701 134396070 1369 True 1661.000000 1661 89.187000 547 1869 1 chrUn.!!$R3 1322
19 TraesCS5A01G556600 chrUn 30529492 30530829 1337 True 1576.000000 1576 88.394000 547 1869 1 chrUn.!!$R2 1322
20 TraesCS5A01G556600 chrUn 79803866 79805031 1165 False 1459.000000 1459 89.720000 537 1677 1 chrUn.!!$F2 1140
21 TraesCS5A01G556600 chrUn 29601438 29602423 985 True 1365.000000 1365 91.843000 892 1870 1 chrUn.!!$R1 978
22 TraesCS5A01G556600 chrUn 346448735 346449478 743 False 1227.000000 1227 96.644000 1 734 1 chrUn.!!$F3 733
23 TraesCS5A01G556600 chrUn 348076454 348077197 743 True 1227.000000 1227 96.644000 1 734 1 chrUn.!!$R4 733
24 TraesCS5A01G556600 chrUn 28897766 28898619 853 False 1088.000000 1088 89.588000 892 1762 1 chrUn.!!$F1 870
25 TraesCS5A01G556600 chrUn 29363866 29364873 1007 True 615.500000 913 92.198000 892 1869 2 chrUn.!!$R5 977
26 TraesCS5A01G556600 chr6D 1069944 1071263 1319 False 1430.000000 1430 86.608000 537 1869 1 chr6D.!!$F1 1332

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
112 117 3.959535 TTTTGTGGATGAAAGATGGGC 57.04 42.857 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1954 2418 0.032813 ATCCCTCCGTTCCGTTCCTA 60.033 55.0 0.0 0.0 0.0 2.94 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
112 117 3.959535 TTTTGTGGATGAAAGATGGGC 57.040 42.857 0.00 0.0 0.00 5.36
999 1116 0.320050 TTGGCCGCCAAAAGGAAATC 59.680 50.000 22.85 0.0 40.92 2.17
1007 1124 3.367703 CGCCAAAAGGAAATCATGCTCTT 60.368 43.478 0.00 0.0 0.00 2.85
1030 1147 0.032813 AATCCACTCCCATGCCCAAG 60.033 55.000 0.00 0.0 0.00 3.61
1167 1284 0.938637 CGCTGATCATGGAGTCGAGC 60.939 60.000 0.00 0.0 0.00 5.03
1227 1344 0.883833 CAGGCTTGTCGCTGGAAATT 59.116 50.000 0.00 0.0 39.13 1.82
1465 1594 6.371548 TGCTGTTCATGTACTCAAAGGTAATC 59.628 38.462 4.01 0.0 0.00 1.75
1469 1598 5.109210 TCATGTACTCAAAGGTAATCGCAG 58.891 41.667 0.00 0.0 0.00 5.18
1740 1975 5.706447 TCTCATTCTGTGCTAGTAGGGTAT 58.294 41.667 0.00 0.0 0.00 2.73
2195 2697 6.404954 CGTTCACCGGTTAATTTTTATCCCAT 60.405 38.462 2.97 0.0 0.00 4.00
2202 2704 7.363443 CCGGTTAATTTTTATCCCATCAACACT 60.363 37.037 0.00 0.0 0.00 3.55
2247 2755 2.824041 CCCGGGCCATCGAACAAG 60.824 66.667 8.08 0.0 0.00 3.16
2300 2809 2.088096 TCAAGGGGCCAAACCTCCA 61.088 57.895 4.39 0.0 41.62 3.86
2365 2874 5.874895 AAGACCTACGAAATTAAACCAGC 57.125 39.130 0.00 0.0 0.00 4.85
2366 2875 3.930848 AGACCTACGAAATTAAACCAGCG 59.069 43.478 0.00 0.0 0.00 5.18
2367 2876 3.928375 GACCTACGAAATTAAACCAGCGA 59.072 43.478 0.00 0.0 0.00 4.93
2368 2877 4.317488 ACCTACGAAATTAAACCAGCGAA 58.683 39.130 0.00 0.0 0.00 4.70
2369 2878 4.756135 ACCTACGAAATTAAACCAGCGAAA 59.244 37.500 0.00 0.0 0.00 3.46
2370 2879 5.239087 ACCTACGAAATTAAACCAGCGAAAA 59.761 36.000 0.00 0.0 0.00 2.29
2371 2880 6.144175 CCTACGAAATTAAACCAGCGAAAAA 58.856 36.000 0.00 0.0 0.00 1.94
2393 2902 6.902224 AAAAATCAAAACAAAGAGAACCGG 57.098 33.333 0.00 0.0 0.00 5.28
2394 2903 5.845391 AAATCAAAACAAAGAGAACCGGA 57.155 34.783 9.46 0.0 0.00 5.14
2395 2904 6.405278 AAATCAAAACAAAGAGAACCGGAT 57.595 33.333 9.46 0.0 0.00 4.18
2396 2905 4.829064 TCAAAACAAAGAGAACCGGATG 57.171 40.909 9.46 0.0 0.00 3.51
2397 2906 4.456535 TCAAAACAAAGAGAACCGGATGA 58.543 39.130 9.46 0.0 0.00 2.92
2398 2907 4.884744 TCAAAACAAAGAGAACCGGATGAA 59.115 37.500 9.46 0.0 0.00 2.57
2399 2908 5.358442 TCAAAACAAAGAGAACCGGATGAAA 59.642 36.000 9.46 0.0 0.00 2.69
2400 2909 5.845391 AAACAAAGAGAACCGGATGAAAA 57.155 34.783 9.46 0.0 0.00 2.29
2401 2910 5.845391 AACAAAGAGAACCGGATGAAAAA 57.155 34.783 9.46 0.0 0.00 1.94
2493 3002 0.685097 CCTCCTTCCTTCGAACCACA 59.315 55.000 0.00 0.0 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 0.040514 CAAAATCGCGACAGGCACAA 60.041 50.000 12.93 0.00 43.84 3.33
188 193 5.128663 CCTAATTCGAAATTTCCCCACCAAT 59.871 40.000 12.54 0.00 0.00 3.16
999 1116 3.129988 GGGAGTGGATTTTGAAGAGCATG 59.870 47.826 0.00 0.00 0.00 4.06
1007 1124 1.619432 GGGCATGGGAGTGGATTTTGA 60.619 52.381 0.00 0.00 0.00 2.69
1030 1147 2.360475 GGCCTGCAGGTCTTGGAC 60.360 66.667 32.81 14.74 36.72 4.02
1227 1344 2.417586 CACATCATGCTCGAGCTTTTGA 59.582 45.455 35.27 30.96 42.66 2.69
1469 1598 2.915738 CTCCTGAAGCAAGACAATGC 57.084 50.000 0.00 0.00 46.78 3.56
1497 1626 1.555075 GTGACCAGCTGGACCAGAATA 59.445 52.381 39.19 13.13 38.94 1.75
1498 1627 0.326264 GTGACCAGCTGGACCAGAAT 59.674 55.000 39.19 15.22 38.94 2.40
1940 2402 8.485591 CGTTCCGTTCCTAAATATATGTCTTTC 58.514 37.037 0.00 0.00 0.00 2.62
1951 2415 1.208776 CCCTCCGTTCCGTTCCTAAAT 59.791 52.381 0.00 0.00 0.00 1.40
1953 2417 0.251742 TCCCTCCGTTCCGTTCCTAA 60.252 55.000 0.00 0.00 0.00 2.69
1954 2418 0.032813 ATCCCTCCGTTCCGTTCCTA 60.033 55.000 0.00 0.00 0.00 2.94
1955 2419 1.305887 ATCCCTCCGTTCCGTTCCT 60.306 57.895 0.00 0.00 0.00 3.36
1956 2420 1.143401 GATCCCTCCGTTCCGTTCC 59.857 63.158 0.00 0.00 0.00 3.62
1957 2421 0.179108 CAGATCCCTCCGTTCCGTTC 60.179 60.000 0.00 0.00 0.00 3.95
1958 2422 0.903454 ACAGATCCCTCCGTTCCGTT 60.903 55.000 0.00 0.00 0.00 4.44
1959 2423 1.305046 ACAGATCCCTCCGTTCCGT 60.305 57.895 0.00 0.00 0.00 4.69
1960 2424 1.141881 CACAGATCCCTCCGTTCCG 59.858 63.158 0.00 0.00 0.00 4.30
2265 2774 2.154567 TGACTTCGTAGGGGCATAGT 57.845 50.000 0.00 0.00 0.00 2.12
2300 2809 2.561419 TCCGGTTCTCTCTGTTTCGATT 59.439 45.455 0.00 0.00 0.00 3.34
2340 2849 7.143340 GCTGGTTTAATTTCGTAGGTCTTTTT 58.857 34.615 0.00 0.00 0.00 1.94
2341 2850 6.567132 CGCTGGTTTAATTTCGTAGGTCTTTT 60.567 38.462 0.00 0.00 0.00 2.27
2342 2851 5.106830 CGCTGGTTTAATTTCGTAGGTCTTT 60.107 40.000 0.00 0.00 0.00 2.52
2343 2852 4.390909 CGCTGGTTTAATTTCGTAGGTCTT 59.609 41.667 0.00 0.00 0.00 3.01
2344 2853 3.930848 CGCTGGTTTAATTTCGTAGGTCT 59.069 43.478 0.00 0.00 0.00 3.85
2345 2854 3.928375 TCGCTGGTTTAATTTCGTAGGTC 59.072 43.478 0.00 0.00 0.00 3.85
2346 2855 3.929094 TCGCTGGTTTAATTTCGTAGGT 58.071 40.909 0.00 0.00 0.00 3.08
2347 2856 4.932268 TTCGCTGGTTTAATTTCGTAGG 57.068 40.909 0.00 0.00 0.00 3.18
2370 2879 6.635755 TCCGGTTCTCTTTGTTTTGATTTTT 58.364 32.000 0.00 0.00 0.00 1.94
2371 2880 6.215495 TCCGGTTCTCTTTGTTTTGATTTT 57.785 33.333 0.00 0.00 0.00 1.82
2372 2881 5.845391 TCCGGTTCTCTTTGTTTTGATTT 57.155 34.783 0.00 0.00 0.00 2.17
2373 2882 5.534654 TCATCCGGTTCTCTTTGTTTTGATT 59.465 36.000 0.00 0.00 0.00 2.57
2374 2883 5.070001 TCATCCGGTTCTCTTTGTTTTGAT 58.930 37.500 0.00 0.00 0.00 2.57
2375 2884 4.456535 TCATCCGGTTCTCTTTGTTTTGA 58.543 39.130 0.00 0.00 0.00 2.69
2376 2885 4.829064 TCATCCGGTTCTCTTTGTTTTG 57.171 40.909 0.00 0.00 0.00 2.44
2377 2886 5.845391 TTTCATCCGGTTCTCTTTGTTTT 57.155 34.783 0.00 0.00 0.00 2.43
2378 2887 5.845391 TTTTCATCCGGTTCTCTTTGTTT 57.155 34.783 0.00 0.00 0.00 2.83
2379 2888 5.845391 TTTTTCATCCGGTTCTCTTTGTT 57.155 34.783 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.