Multiple sequence alignment - TraesCS4D01G259700

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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 TraesCS4D01G259700 chr4D 100.000 4187 0 0 1 4187 428967066 428962880 0.000000e+00 7733
1 TraesCS4D01G259700 chr4D 98.207 725 12 1 3464 4187 428955598 428954874 0.000000e+00 1266
2 TraesCS4D01G259700 chr4D 91.736 726 57 3 3464 4187 39617306 39618030 0.000000e+00 1005
3 TraesCS4D01G259700 chr4B 95.879 3494 91 24 1 3463 527005580 527002109 0.000000e+00 5605
4 TraesCS4D01G259700 chr4B 82.450 302 17 15 1230 1505 365509285 365509576 9.050000e-57 231
5 TraesCS4D01G259700 chr4B 81.271 299 21 14 1230 1503 226623524 226623236 4.240000e-50 209
6 TraesCS4D01G259700 chr4A 97.119 1215 28 4 2256 3463 37307925 37309139 0.000000e+00 2043
7 TraesCS4D01G259700 chr4A 90.509 1296 53 24 255 1533 37305627 37306869 0.000000e+00 1648
8 TraesCS4D01G259700 chr4A 93.449 748 37 7 1534 2278 37307026 37307764 0.000000e+00 1099
9 TraesCS4D01G259700 chr4A 94.961 258 9 4 1 256 37305278 37305533 6.520000e-108 401
10 TraesCS4D01G259700 chr4A 82.042 284 16 13 1230 1488 667249700 667249973 4.240000e-50 209
11 TraesCS4D01G259700 chr4A 82.042 284 16 13 1230 1488 667271736 667272009 4.240000e-50 209
12 TraesCS4D01G259700 chr2D 97.376 724 18 1 3464 4187 474406691 474407413 0.000000e+00 1230
13 TraesCS4D01G259700 chr3A 90.634 726 62 5 3464 4187 120820160 120819439 0.000000e+00 959
14 TraesCS4D01G259700 chr5A 90.496 726 61 6 3464 4187 284243942 284243223 0.000000e+00 952
15 TraesCS4D01G259700 chr5A 90.247 728 59 8 3464 4187 284236219 284235500 0.000000e+00 941
16 TraesCS4D01G259700 chr5A 89.835 728 62 10 3464 4187 119409017 119409736 0.000000e+00 924
17 TraesCS4D01G259700 chr5A 82.943 299 16 14 1230 1503 639744882 639745170 1.950000e-58 237
18 TraesCS4D01G259700 chr1A 89.575 729 64 8 3464 4187 342821250 342820529 0.000000e+00 915
19 TraesCS4D01G259700 chr1A 89.394 726 68 6 3464 4187 342813982 342813264 0.000000e+00 905
20 TraesCS4D01G259700 chr6D 82.274 299 18 14 1230 1503 83695017 83694729 4.210000e-55 226
21 TraesCS4D01G259700 chr2B 82.155 297 18 13 1232 1503 47556162 47555876 5.450000e-54 222
22 TraesCS4D01G259700 chr2B 81.879 298 19 13 1230 1502 766616727 766616440 7.050000e-53 219
23 TraesCS4D01G259700 chr2B 80.268 299 24 16 1230 1503 81027380 81027668 4.270000e-45 193
24 TraesCS4D01G259700 chr6B 81.757 296 25 18 1230 1503 648563871 648563583 1.960000e-53 220
25 TraesCS4D01G259700 chr6B 81.605 299 20 11 1230 1503 697572910 697573198 9.120000e-52 215
26 TraesCS4D01G259700 chr6B 81.605 299 20 11 1230 1503 697596930 697597218 9.120000e-52 215
27 TraesCS4D01G259700 chr3B 81.940 299 19 11 1230 1503 755583252 755583540 1.960000e-53 220


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 TraesCS4D01G259700 chr4D 428962880 428967066 4186 True 7733.00 7733 100.0000 1 4187 1 chr4D.!!$R2 4186
1 TraesCS4D01G259700 chr4D 428954874 428955598 724 True 1266.00 1266 98.2070 3464 4187 1 chr4D.!!$R1 723
2 TraesCS4D01G259700 chr4D 39617306 39618030 724 False 1005.00 1005 91.7360 3464 4187 1 chr4D.!!$F1 723
3 TraesCS4D01G259700 chr4B 527002109 527005580 3471 True 5605.00 5605 95.8790 1 3463 1 chr4B.!!$R2 3462
4 TraesCS4D01G259700 chr4A 37305278 37309139 3861 False 1297.75 2043 94.0095 1 3463 4 chr4A.!!$F3 3462
5 TraesCS4D01G259700 chr2D 474406691 474407413 722 False 1230.00 1230 97.3760 3464 4187 1 chr2D.!!$F1 723
6 TraesCS4D01G259700 chr3A 120819439 120820160 721 True 959.00 959 90.6340 3464 4187 1 chr3A.!!$R1 723
7 TraesCS4D01G259700 chr5A 284243223 284243942 719 True 952.00 952 90.4960 3464 4187 1 chr5A.!!$R2 723
8 TraesCS4D01G259700 chr5A 284235500 284236219 719 True 941.00 941 90.2470 3464 4187 1 chr5A.!!$R1 723
9 TraesCS4D01G259700 chr5A 119409017 119409736 719 False 924.00 924 89.8350 3464 4187 1 chr5A.!!$F1 723
10 TraesCS4D01G259700 chr1A 342820529 342821250 721 True 915.00 915 89.5750 3464 4187 1 chr1A.!!$R2 723
11 TraesCS4D01G259700 chr1A 342813264 342813982 718 True 905.00 905 89.3940 3464 4187 1 chr1A.!!$R1 723

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
863 963 3.004419 TCAGCCCGTGATAGAATAGAACG 59.996 47.826 0.0 0.0 34.33 3.95 F
1285 1399 0.953960 ACGTTCGCCCCTTGCTTTAG 60.954 55.000 0.0 0.0 38.05 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1807 2106 0.675633 AGCGGCAAAGCAAGTTCATT 59.324 45.000 1.45 0.0 40.15 2.57 R
3277 3763 1.135139 CCTCTTGTCGACCATCATCGT 59.865 52.381 14.12 0.0 42.80 3.73 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
62 63 3.603532 TGCTCCTACATTCAGAAGCAAG 58.396 45.455 0.00 0.00 0.00 4.01
76 78 6.484288 TCAGAAGCAAGAAATAAGAATCCCA 58.516 36.000 0.00 0.00 0.00 4.37
82 84 6.071165 AGCAAGAAATAAGAATCCCAACCTTG 60.071 38.462 0.00 0.00 0.00 3.61
109 111 6.042093 CAGCTCTCCTACCAATAAGTTATCCA 59.958 42.308 0.00 0.00 0.00 3.41
116 118 9.053472 TCCTACCAATAAGTTATCCAAAGAAGA 57.947 33.333 0.00 0.00 0.00 2.87
119 121 8.934023 ACCAATAAGTTATCCAAAGAAGAACA 57.066 30.769 0.00 0.00 0.00 3.18
120 122 9.362151 ACCAATAAGTTATCCAAAGAAGAACAA 57.638 29.630 0.00 0.00 0.00 2.83
125 127 8.990163 AAGTTATCCAAAGAAGAACAACCTAA 57.010 30.769 0.00 0.00 0.00 2.69
216 218 7.120285 CGTGAGCCTAATATCCAATGAAATGAT 59.880 37.037 0.00 0.00 0.00 2.45
242 244 3.198635 CAGTGGCTGAAGAAGAGGGATTA 59.801 47.826 0.00 0.00 32.44 1.75
475 575 9.449719 GAATCCTAAATTACCAAGAGAACAGAA 57.550 33.333 0.00 0.00 0.00 3.02
863 963 3.004419 TCAGCCCGTGATAGAATAGAACG 59.996 47.826 0.00 0.00 34.33 3.95
1095 1209 2.782222 GGCGGCCATCGACTCTGTA 61.782 63.158 15.62 0.00 45.10 2.74
1285 1399 0.953960 ACGTTCGCCCCTTGCTTTAG 60.954 55.000 0.00 0.00 38.05 1.85
1339 1453 4.278419 GCTTTGGTTTCTTCTGCTCCTAAA 59.722 41.667 0.00 0.00 0.00 1.85
1359 1479 1.154016 CAGTGCTGCAGCTCATTGC 60.154 57.895 36.61 19.58 44.33 3.56
1493 1630 5.983720 CGGATTAGTCTGGGTTAACATAGTG 59.016 44.000 8.10 0.00 0.00 2.74
1508 1645 8.879759 GTTAACATAGTGAGTTAGCAATAGCAA 58.120 33.333 0.00 0.00 45.49 3.91
1514 1651 4.095483 GTGAGTTAGCAATAGCAACTGCAT 59.905 41.667 4.22 0.00 45.49 3.96
1515 1652 4.701651 TGAGTTAGCAATAGCAACTGCATT 59.298 37.500 4.22 0.00 45.49 3.56
1526 1663 4.275838 GCAACTGCATTTTTGCTTCAAA 57.724 36.364 16.58 0.00 43.96 2.69
1537 1830 8.375465 GCATTTTTGCTTCAAATGTACTGTATC 58.625 33.333 13.73 0.00 41.72 2.24
1542 1835 5.580691 TGCTTCAAATGTACTGTATCTTCGG 59.419 40.000 0.00 0.00 0.00 4.30
1547 1840 5.670792 AATGTACTGTATCTTCGGGTGAA 57.329 39.130 0.00 0.00 0.00 3.18
1578 1871 2.285083 GTTACCAGCGGATGCACATAA 58.715 47.619 0.00 0.00 46.23 1.90
1729 2024 3.005791 CCATTTTGGAGGTTTTCTCGCTT 59.994 43.478 0.00 0.00 40.96 4.68
1730 2025 3.708563 TTTTGGAGGTTTTCTCGCTTG 57.291 42.857 0.00 0.00 43.34 4.01
1731 2026 2.341846 TTGGAGGTTTTCTCGCTTGT 57.658 45.000 0.00 0.00 43.34 3.16
1732 2027 2.341846 TGGAGGTTTTCTCGCTTGTT 57.658 45.000 0.00 0.00 43.34 2.83
1765 2064 1.014352 CCACAACTTACTATGCCGCC 58.986 55.000 0.00 0.00 0.00 6.13
1782 2081 2.495669 CCGCCACCCAGTAAAAATCAAT 59.504 45.455 0.00 0.00 0.00 2.57
1803 2102 8.472007 TCAATTTTGTCAGTACCCAGTAAAAT 57.528 30.769 0.00 0.00 0.00 1.82
1804 2103 9.575868 TCAATTTTGTCAGTACCCAGTAAAATA 57.424 29.630 0.00 0.00 0.00 1.40
1824 2123 5.844301 ATAAAAATGAACTTGCTTTGCCG 57.156 34.783 0.00 0.00 0.00 5.69
1838 2137 3.066760 GCTTTGCCGCTAGGAAATAATGT 59.933 43.478 0.00 0.00 41.02 2.71
2138 2439 0.170561 GCAAGCCTGATGAGCAACTG 59.829 55.000 0.00 0.00 0.00 3.16
2736 3220 7.064253 GTGAGCTTATGGTCGTATGTTTTACTT 59.936 37.037 3.68 0.00 43.09 2.24
2998 3482 8.507249 AGTGCATACTTTAAATCACTCTTCAAC 58.493 33.333 0.00 0.00 31.66 3.18
3277 3763 9.820725 CTTCTATTTTGCCATTTATCCATTTGA 57.179 29.630 0.00 0.00 0.00 2.69
3420 3910 7.849804 ATGTTATATTCCAGGATTGATACGC 57.150 36.000 0.00 0.00 0.00 4.42
3421 3911 7.004555 TGTTATATTCCAGGATTGATACGCT 57.995 36.000 0.00 0.00 0.00 5.07
3423 3913 7.387673 TGTTATATTCCAGGATTGATACGCTTG 59.612 37.037 0.00 0.00 0.00 4.01
3424 3914 3.904800 TTCCAGGATTGATACGCTTGA 57.095 42.857 0.00 0.00 0.00 3.02
3425 3915 3.459232 TCCAGGATTGATACGCTTGAG 57.541 47.619 0.00 0.00 0.00 3.02
4047 4546 4.314440 ACACACGCCGTCCATGCT 62.314 61.111 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 6.625960 GCTGACAAGGTTGGGATTCTTATTTC 60.626 42.308 0.00 0.00 0.00 2.17
76 78 1.903183 GGTAGGAGAGCTGACAAGGTT 59.097 52.381 0.00 0.00 33.19 3.50
82 84 5.346181 AACTTATTGGTAGGAGAGCTGAC 57.654 43.478 0.00 0.00 0.00 3.51
109 111 6.826741 TGTAAGTGCTTAGGTTGTTCTTCTTT 59.173 34.615 0.00 0.00 0.00 2.52
116 118 6.952773 TTTGATGTAAGTGCTTAGGTTGTT 57.047 33.333 0.00 0.00 0.00 2.83
118 120 6.092122 TCGATTTGATGTAAGTGCTTAGGTTG 59.908 38.462 0.00 0.00 0.00 3.77
119 121 6.170506 TCGATTTGATGTAAGTGCTTAGGTT 58.829 36.000 0.00 0.00 0.00 3.50
120 122 5.730550 TCGATTTGATGTAAGTGCTTAGGT 58.269 37.500 0.00 0.00 0.00 3.08
125 127 4.327357 CGTCTTCGATTTGATGTAAGTGCT 59.673 41.667 0.00 0.00 39.71 4.40
216 218 3.198635 CCCTCTTCTTCAGCCACTGATTA 59.801 47.826 0.00 0.00 40.39 1.75
390 490 5.772393 TTCTTCCTTAGGGCATGAACTTA 57.228 39.130 0.00 0.00 0.00 2.24
475 575 3.350833 CTGGAAGATTTGCCTGCTTACT 58.649 45.455 0.00 0.00 34.07 2.24
527 627 2.803492 GCGTAATTGCCTACTCTCCCTG 60.803 54.545 0.00 0.00 0.00 4.45
917 1018 1.227823 CGGTTGTGCTCTGGGTTGA 60.228 57.895 0.00 0.00 0.00 3.18
1092 1206 1.327690 CGAAGCCCCCTACAGCTACA 61.328 60.000 0.00 0.00 38.74 2.74
1095 1209 3.083997 CCGAAGCCCCCTACAGCT 61.084 66.667 0.00 0.00 42.40 4.24
1320 1434 5.221925 ACTGATTTAGGAGCAGAAGAAACCA 60.222 40.000 0.00 0.00 33.94 3.67
1339 1453 1.095600 CAATGAGCTGCAGCACTGAT 58.904 50.000 38.24 20.56 45.16 2.90
1359 1479 5.009854 ACAAAACCAAAGACCATGTCAAG 57.990 39.130 0.00 0.00 34.60 3.02
1468 1605 3.899052 TGTTAACCCAGACTAATCCGG 57.101 47.619 2.48 0.00 0.00 5.14
1493 1630 4.889832 ATGCAGTTGCTATTGCTAACTC 57.110 40.909 15.75 8.89 42.66 3.01
1508 1645 6.201425 CAGTACATTTGAAGCAAAAATGCAGT 59.799 34.615 14.89 6.24 45.02 4.40
1514 1651 9.677567 GAAGATACAGTACATTTGAAGCAAAAA 57.322 29.630 0.00 0.00 36.90 1.94
1515 1652 8.015087 CGAAGATACAGTACATTTGAAGCAAAA 58.985 33.333 0.00 0.00 36.90 2.44
1526 1663 5.670792 TTTCACCCGAAGATACAGTACAT 57.329 39.130 0.00 0.00 31.28 2.29
1537 1830 7.170998 GGTAACACTGATATATTTCACCCGAAG 59.829 40.741 0.00 0.00 31.28 3.79
1542 1835 6.073765 CGCTGGTAACACTGATATATTTCACC 60.074 42.308 0.00 0.00 46.17 4.02
1547 1840 5.801531 TCCGCTGGTAACACTGATATATT 57.198 39.130 0.00 0.00 46.17 1.28
1605 1898 4.962995 TGGGTTTTCTCAATTTACCAACCA 59.037 37.500 0.00 0.00 34.96 3.67
1729 2024 6.344500 AGTTGTGGCATTTTATCAAACAACA 58.656 32.000 15.63 0.00 45.13 3.33
1730 2025 6.843069 AGTTGTGGCATTTTATCAAACAAC 57.157 33.333 7.50 7.50 43.79 3.32
1731 2026 8.200792 AGTAAGTTGTGGCATTTTATCAAACAA 58.799 29.630 0.00 0.00 0.00 2.83
1732 2027 7.721402 AGTAAGTTGTGGCATTTTATCAAACA 58.279 30.769 0.00 0.00 0.00 2.83
1765 2064 7.710475 ACTGACAAAATTGATTTTTACTGGGTG 59.290 33.333 0.00 0.00 37.86 4.61
1803 2102 3.492756 GCGGCAAAGCAAGTTCATTTTTA 59.507 39.130 0.00 0.00 37.05 1.52
1804 2103 2.287644 GCGGCAAAGCAAGTTCATTTTT 59.712 40.909 0.00 0.00 37.05 1.94
1805 2104 1.866601 GCGGCAAAGCAAGTTCATTTT 59.133 42.857 0.00 0.00 37.05 1.82
1806 2105 1.069049 AGCGGCAAAGCAAGTTCATTT 59.931 42.857 1.45 0.00 40.15 2.32
1807 2106 0.675633 AGCGGCAAAGCAAGTTCATT 59.324 45.000 1.45 0.00 40.15 2.57
1808 2107 1.470098 CTAGCGGCAAAGCAAGTTCAT 59.530 47.619 1.45 0.00 40.15 2.57
1809 2108 0.874390 CTAGCGGCAAAGCAAGTTCA 59.126 50.000 1.45 0.00 40.15 3.18
2069 2369 5.122239 TCTGAAAGGATCATGCAAGTAAACG 59.878 40.000 0.00 0.00 37.44 3.60
2138 2439 2.531522 ACATTGTGCCAGCTTTTTCC 57.468 45.000 0.00 0.00 0.00 3.13
2736 3220 7.445569 CTGAAATCAGGGTCGCAGTACGATA 62.446 48.000 2.38 0.00 45.69 2.92
2998 3482 1.314730 ACAAACCACCAAACTAGCCG 58.685 50.000 0.00 0.00 0.00 5.52
3151 3636 3.028850 CCAGCTGAAATGATCCACCATT 58.971 45.455 17.39 0.00 38.30 3.16
3223 3709 1.373246 CAATTGTGGGCTTGTGGCG 60.373 57.895 0.00 0.00 42.94 5.69
3277 3763 1.135139 CCTCTTGTCGACCATCATCGT 59.865 52.381 14.12 0.00 42.80 3.73
3415 3905 2.575694 CAGAGACTGCTCAAGCGTAT 57.424 50.000 0.00 0.00 43.81 3.06
3417 3907 4.983628 CAGAGACTGCTCAAGCGT 57.016 55.556 0.00 0.00 43.81 5.07


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

AutoCloner maintained by Alex Coulton.