Multiple sequence alignment - TraesCS7A01G064900

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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 TraesCS7A01G064900 chr7A 100.000 4368 0 0 1 4368 32411605 32415972 0.000000e+00 8067.0
1 TraesCS7A01G064900 chr7A 98.541 891 13 0 1 891 251808874 251809764 0.000000e+00 1574.0
2 TraesCS7A01G064900 chr7A 84.953 1482 178 32 1549 3006 47903757 47902297 0.000000e+00 1459.0
3 TraesCS7A01G064900 chr7D 96.901 2840 74 7 1538 4368 32250803 32253637 0.000000e+00 4745.0
4 TraesCS7A01G064900 chr7D 85.639 1323 164 15 1702 3006 45706525 45705211 0.000000e+00 1367.0
5 TraesCS7A01G064900 chr7D 92.758 649 31 12 885 1520 32250096 32250741 0.000000e+00 924.0
6 TraesCS7A01G064900 chr7D 79.732 745 91 31 3071 3767 45705180 45704448 6.570000e-133 484.0
7 TraesCS7A01G064900 chr7D 75.034 737 139 29 2069 2769 16709061 16709788 2.550000e-77 300.0
8 TraesCS7A01G064900 chr7D 94.643 56 3 0 3293 3348 32051723 32051778 2.160000e-13 87.9
9 TraesCS7A01G064900 chr4A 94.614 2692 103 12 1538 4220 694849171 694846513 0.000000e+00 4130.0
10 TraesCS7A01G064900 chr4A 98.765 891 10 1 1 891 671046472 671047361 0.000000e+00 1583.0
11 TraesCS7A01G064900 chr4A 98.427 890 13 1 1 889 695920477 695921366 0.000000e+00 1565.0
12 TraesCS7A01G064900 chr4A 98.101 895 15 2 1 894 676037502 676036609 0.000000e+00 1557.0
13 TraesCS7A01G064900 chr4A 89.560 182 13 3 1263 1438 694849546 694849365 4.400000e-55 226.0
14 TraesCS7A01G064900 chr4A 94.853 136 7 0 4233 4368 694846421 694846286 3.420000e-51 213.0
15 TraesCS7A01G064900 chr4A 89.937 159 16 0 1101 1259 694849775 694849617 5.730000e-49 206.0
16 TraesCS7A01G064900 chr4A 80.105 191 26 7 3160 3343 695101233 695101418 9.860000e-27 132.0
17 TraesCS7A01G064900 chr7B 98.544 893 13 0 1 893 606349751 606348859 0.000000e+00 1578.0
18 TraesCS7A01G064900 chr5A 98.650 889 12 0 1 889 51215479 51214591 0.000000e+00 1576.0
19 TraesCS7A01G064900 chr5A 98.650 889 12 0 1 889 586949602 586950490 0.000000e+00 1576.0
20 TraesCS7A01G064900 chr3B 98.224 901 14 2 1 900 154007755 154008654 0.000000e+00 1574.0
21 TraesCS7A01G064900 chr2A 98.538 889 13 0 1 889 40651625 40652513 0.000000e+00 1570.0
22 TraesCS7A01G064900 chr2A 74.650 1286 262 47 1702 2949 84153877 84152618 1.080000e-140 510.0
23 TraesCS7A01G064900 chrUn 84.865 1480 180 28 1551 3006 320961731 320963190 0.000000e+00 1452.0
24 TraesCS7A01G064900 chr2B 75.543 1288 252 47 1699 2951 136806564 136807823 3.790000e-160 575.0
25 TraesCS7A01G064900 chr2B 75.543 1288 252 47 1699 2951 136951614 136952873 3.790000e-160 575.0
26 TraesCS7A01G064900 chr2B 75.466 1288 253 47 1699 2951 137608694 137609953 1.760000e-158 569.0
27 TraesCS7A01G064900 chr2D 75.131 1331 273 41 1699 2998 85673869 85675172 4.900000e-159 571.0
28 TraesCS7A01G064900 chr2D 75.504 1290 249 49 1699 2951 85389456 85390715 1.760000e-158 569.0
29 TraesCS7A01G064900 chr2D 74.851 1340 262 54 1699 2998 84916882 84918186 4.970000e-149 538.0
30 TraesCS7A01G064900 chr2D 88.571 70 8 0 3614 3683 84918837 84918906 7.780000e-13 86.1


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 TraesCS7A01G064900 chr7A 32411605 32415972 4367 False 8067.00 8067 100.0000 1 4368 1 chr7A.!!$F1 4367
1 TraesCS7A01G064900 chr7A 251808874 251809764 890 False 1574.00 1574 98.5410 1 891 1 chr7A.!!$F2 890
2 TraesCS7A01G064900 chr7A 47902297 47903757 1460 True 1459.00 1459 84.9530 1549 3006 1 chr7A.!!$R1 1457
3 TraesCS7A01G064900 chr7D 32250096 32253637 3541 False 2834.50 4745 94.8295 885 4368 2 chr7D.!!$F3 3483
4 TraesCS7A01G064900 chr7D 45704448 45706525 2077 True 925.50 1367 82.6855 1702 3767 2 chr7D.!!$R1 2065
5 TraesCS7A01G064900 chr7D 16709061 16709788 727 False 300.00 300 75.0340 2069 2769 1 chr7D.!!$F1 700
6 TraesCS7A01G064900 chr4A 671046472 671047361 889 False 1583.00 1583 98.7650 1 891 1 chr4A.!!$F1 890
7 TraesCS7A01G064900 chr4A 695920477 695921366 889 False 1565.00 1565 98.4270 1 889 1 chr4A.!!$F3 888
8 TraesCS7A01G064900 chr4A 676036609 676037502 893 True 1557.00 1557 98.1010 1 894 1 chr4A.!!$R1 893
9 TraesCS7A01G064900 chr4A 694846286 694849775 3489 True 1193.75 4130 92.2410 1101 4368 4 chr4A.!!$R2 3267
10 TraesCS7A01G064900 chr7B 606348859 606349751 892 True 1578.00 1578 98.5440 1 893 1 chr7B.!!$R1 892
11 TraesCS7A01G064900 chr5A 51214591 51215479 888 True 1576.00 1576 98.6500 1 889 1 chr5A.!!$R1 888
12 TraesCS7A01G064900 chr5A 586949602 586950490 888 False 1576.00 1576 98.6500 1 889 1 chr5A.!!$F1 888
13 TraesCS7A01G064900 chr3B 154007755 154008654 899 False 1574.00 1574 98.2240 1 900 1 chr3B.!!$F1 899
14 TraesCS7A01G064900 chr2A 40651625 40652513 888 False 1570.00 1570 98.5380 1 889 1 chr2A.!!$F1 888
15 TraesCS7A01G064900 chr2A 84152618 84153877 1259 True 510.00 510 74.6500 1702 2949 1 chr2A.!!$R1 1247
16 TraesCS7A01G064900 chrUn 320961731 320963190 1459 False 1452.00 1452 84.8650 1551 3006 1 chrUn.!!$F1 1455
17 TraesCS7A01G064900 chr2B 136806564 136807823 1259 False 575.00 575 75.5430 1699 2951 1 chr2B.!!$F1 1252
18 TraesCS7A01G064900 chr2B 136951614 136952873 1259 False 575.00 575 75.5430 1699 2951 1 chr2B.!!$F2 1252
19 TraesCS7A01G064900 chr2B 137608694 137609953 1259 False 569.00 569 75.4660 1699 2951 1 chr2B.!!$F3 1252
20 TraesCS7A01G064900 chr2D 85673869 85675172 1303 False 571.00 571 75.1310 1699 2998 1 chr2D.!!$F2 1299
21 TraesCS7A01G064900 chr2D 85389456 85390715 1259 False 569.00 569 75.5040 1699 2951 1 chr2D.!!$F1 1252
22 TraesCS7A01G064900 chr2D 84916882 84918906 2024 False 312.05 538 81.7110 1699 3683 2 chr2D.!!$F3 1984

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
988 992 1.469767 CCGAATAAAAAGCCAGGCAGC 60.470 52.381 15.80 0.00 0.00 5.25 F
1013 1017 0.815095 CGTTCCAGCCAAATAACCCC 59.185 55.000 0.00 0.00 0.00 4.95 F
1053 1057 1.173913 CGATTCTTTTCCGCCCCTTT 58.826 50.000 0.00 0.00 0.00 3.11 F
1546 1729 1.808343 TGTGCTGAGCATGAACATGAC 59.192 47.619 11.58 10.86 41.91 3.06 F
2640 2869 1.067776 CGCCTCGACTTAACAGAACCT 60.068 52.381 0.00 0.00 0.00 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2106 2299 1.336887 TGGAGTGCTGAACTACGAAGC 60.337 52.381 0.0 0.0 43.57 3.86 R
2113 2306 1.765314 AGTCTGTTGGAGTGCTGAACT 59.235 47.619 0.0 0.0 43.85 3.01 R
2126 2319 3.461061 CGCATGTGATATGGAGTCTGTT 58.539 45.455 0.0 0.0 0.00 3.16 R
2956 3186 3.623510 GGCATGTCTAAGACTAGGCAAAC 59.376 47.826 0.0 0.0 42.91 2.93 R
3896 4398 0.541392 TACATCACCCTTGCAGCGAT 59.459 50.000 0.0 0.0 0.00 4.58 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
550 551 5.561499 CGTCGATTCAAAAGTCTTTCATGTG 59.439 40.000 0.00 0.00 0.00 3.21
627 629 6.538381 AGTTTGTGGTCCATGAAATTTGTTTC 59.462 34.615 0.00 0.00 0.00 2.78
909 912 8.361889 GCTAGTATTTAGAAAAGGAGGGAGTAG 58.638 40.741 0.00 0.00 0.00 2.57
916 919 3.562108 AAAGGAGGGAGTAGTGGAAGA 57.438 47.619 0.00 0.00 0.00 2.87
988 992 1.469767 CCGAATAAAAAGCCAGGCAGC 60.470 52.381 15.80 0.00 0.00 5.25
1010 1014 2.817844 AGGTTCGTTCCAGCCAAATAAC 59.182 45.455 2.12 0.00 0.00 1.89
1013 1017 0.815095 CGTTCCAGCCAAATAACCCC 59.185 55.000 0.00 0.00 0.00 4.95
1014 1018 0.815095 GTTCCAGCCAAATAACCCCG 59.185 55.000 0.00 0.00 0.00 5.73
1053 1057 1.173913 CGATTCTTTTCCGCCCCTTT 58.826 50.000 0.00 0.00 0.00 3.11
1242 1246 4.077822 CTCCTCTTCCTGATGCAAGTTTT 58.922 43.478 0.00 0.00 0.00 2.43
1247 1251 6.128063 CCTCTTCCTGATGCAAGTTTTTCTAG 60.128 42.308 0.00 0.00 0.00 2.43
1259 1263 3.951680 AGTTTTTCTAGTGGTTGTGGTGG 59.048 43.478 0.00 0.00 0.00 4.61
1260 1264 3.935818 TTTTCTAGTGGTTGTGGTGGA 57.064 42.857 0.00 0.00 0.00 4.02
1261 1265 4.447138 TTTTCTAGTGGTTGTGGTGGAT 57.553 40.909 0.00 0.00 0.00 3.41
1281 1352 8.686334 GGTGGATCATGAAATTGTGTAACTATT 58.314 33.333 0.00 0.00 43.92 1.73
1302 1377 8.545472 ACTATTTGCCTAGTGTTAATCTAACCA 58.455 33.333 0.00 0.00 37.88 3.67
1370 1445 4.223923 CCTAGGGATTGGGATAGCTAGTTG 59.776 50.000 0.00 0.00 0.00 3.16
1534 1717 2.551032 TGCTCTCAAATGTTGTGCTGAG 59.449 45.455 0.00 0.00 37.28 3.35
1545 1728 2.188062 TGTGCTGAGCATGAACATGA 57.812 45.000 11.58 0.00 41.91 3.07
1546 1729 1.808343 TGTGCTGAGCATGAACATGAC 59.192 47.619 11.58 10.86 41.91 3.06
1547 1730 1.808343 GTGCTGAGCATGAACATGACA 59.192 47.619 11.58 14.06 41.91 3.58
1548 1731 2.422479 GTGCTGAGCATGAACATGACAT 59.578 45.455 11.58 1.80 41.91 3.06
1549 1732 2.422127 TGCTGAGCATGAACATGACATG 59.578 45.455 22.87 22.87 45.19 3.21
1686 1870 6.267699 GCCCCTTAGCATTTCTAACCATTTAT 59.732 38.462 0.00 0.00 33.87 1.40
1778 1968 4.163839 AGAAGTTGCCATCATAGAGAAGCT 59.836 41.667 0.00 0.00 32.44 3.74
2021 2214 6.589135 ACACAGATCTTCATAATGCTCATCA 58.411 36.000 0.00 0.00 0.00 3.07
2106 2299 3.250744 TCCTGCGAAGACAAACTTATCG 58.749 45.455 0.00 0.00 39.13 2.92
2113 2306 4.556135 CGAAGACAAACTTATCGCTTCGTA 59.444 41.667 12.89 0.00 45.47 3.43
2126 2319 1.336887 GCTTCGTAGTTCAGCACTCCA 60.337 52.381 0.00 0.00 36.88 3.86
2640 2869 1.067776 CGCCTCGACTTAACAGAACCT 60.068 52.381 0.00 0.00 0.00 3.50
2692 2921 6.322456 GGAAAATTGGGCTCTCTTTATTAGCT 59.678 38.462 0.00 0.00 36.48 3.32
2956 3186 0.108615 ATCTTTGCTCGTCGTGGAGG 60.109 55.000 7.41 0.00 34.56 4.30
3288 3533 5.942872 ACTCTTTTGCTTTCATGGAATACG 58.057 37.500 0.00 0.00 0.00 3.06
3349 3613 7.383843 GCTCCTAAGATTGCATTCTTACTCTAC 59.616 40.741 21.48 10.48 37.20 2.59
3476 3942 7.312154 TCACACAACTTGCCAATGAATATTAC 58.688 34.615 0.00 0.00 0.00 1.89
3480 3946 6.440328 ACAACTTGCCAATGAATATTACCCTT 59.560 34.615 0.00 0.00 0.00 3.95
3709 4206 3.758554 ACGCCTAGAAGCATGACATTTTT 59.241 39.130 0.00 0.00 0.00 1.94
3785 4282 2.294233 ACACTCAACAGCGATGCAAAAT 59.706 40.909 0.00 0.00 0.00 1.82
3834 4335 3.674997 TGGACCTAGTTTGAACAGCATC 58.325 45.455 0.00 0.00 0.00 3.91
3896 4398 2.661537 CAGCCACTCACAACGCGA 60.662 61.111 15.93 0.00 0.00 5.87
4101 4603 3.011517 AGCACCGGGCCTCTGATT 61.012 61.111 6.32 0.00 46.50 2.57
4300 4881 2.310647 TGGTTTCCCCTTGTAGATTCCC 59.689 50.000 0.00 0.00 0.00 3.97
4311 4892 6.889722 CCCTTGTAGATTCCCTTGTTTGAATA 59.110 38.462 0.00 0.00 31.56 1.75
4357 4938 1.855295 TCTGCCAATCCATGCACATT 58.145 45.000 0.00 0.00 33.17 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
195 196 5.310720 ACTGCGGAAAATTTATGAGTTCC 57.689 39.130 0.00 0.0 36.89 3.62
550 551 6.904463 TTCCAAAAACTACCCAAATCCTAC 57.096 37.500 0.00 0.0 0.00 3.18
627 629 7.408290 CGCGCAAGAGATTGTTTAAAACTTTAG 60.408 37.037 8.75 0.0 40.82 1.85
872 875 6.001449 TCTAAATACTAGCAAACATGCCCT 57.999 37.500 0.00 0.0 34.90 5.19
898 901 1.717077 TGTCTTCCACTACTCCCTCCT 59.283 52.381 0.00 0.0 0.00 3.69
909 912 1.792006 CTTACCCGTGTGTCTTCCAC 58.208 55.000 0.00 0.0 44.78 4.02
916 919 2.747686 CCCAGCTTACCCGTGTGT 59.252 61.111 0.00 0.0 0.00 3.72
988 992 1.247567 ATTTGGCTGGAACGAACCTG 58.752 50.000 0.00 0.0 0.00 4.00
1010 1014 3.900892 CGGAGATGGTCGACGGGG 61.901 72.222 9.92 0.0 0.00 5.73
1134 1138 3.003173 TCTCCGGTGGCTCTTGGG 61.003 66.667 0.00 0.0 0.00 4.12
1242 1246 2.976185 TGATCCACCACAACCACTAGAA 59.024 45.455 0.00 0.0 0.00 2.10
1247 1251 2.198827 TCATGATCCACCACAACCAC 57.801 50.000 0.00 0.0 0.00 4.16
1259 1263 9.023967 GGCAAATAGTTACACAATTTCATGATC 57.976 33.333 0.00 0.0 0.00 2.92
1260 1264 8.752187 AGGCAAATAGTTACACAATTTCATGAT 58.248 29.630 0.00 0.0 0.00 2.45
1261 1265 8.121305 AGGCAAATAGTTACACAATTTCATGA 57.879 30.769 0.00 0.0 0.00 3.07
1281 1352 6.614694 TCTGGTTAGATTAACACTAGGCAA 57.385 37.500 0.00 0.0 40.39 4.52
1282 1353 6.614694 TTCTGGTTAGATTAACACTAGGCA 57.385 37.500 0.00 0.0 40.39 4.75
1302 1377 5.416271 AGCATCATGCCAAAATTCTTTCT 57.584 34.783 5.84 0.0 46.52 2.52
1545 1728 7.954666 AGGTATAGCAAAATAACCAACATGT 57.045 32.000 4.48 0.0 0.00 3.21
1778 1968 4.584325 AGCTGTGGCAAATTTTCTTAGACA 59.416 37.500 0.00 0.0 41.70 3.41
2021 2214 2.217510 ATCGTCGTCCCCTATATGCT 57.782 50.000 0.00 0.0 0.00 3.79
2046 2239 7.563724 TTTGGTGTTAGATAAAGGGTAGTCT 57.436 36.000 0.00 0.0 0.00 3.24
2106 2299 1.336887 TGGAGTGCTGAACTACGAAGC 60.337 52.381 0.00 0.0 43.57 3.86
2113 2306 1.765314 AGTCTGTTGGAGTGCTGAACT 59.235 47.619 0.00 0.0 43.85 3.01
2126 2319 3.461061 CGCATGTGATATGGAGTCTGTT 58.539 45.455 0.00 0.0 0.00 3.16
2640 2869 4.574674 ATCCAACTTCATCCACTTAGCA 57.425 40.909 0.00 0.0 0.00 3.49
2692 2921 6.636454 AAATGTAGAACTCCTGGTATCCAA 57.364 37.500 0.00 0.0 30.80 3.53
2956 3186 3.623510 GGCATGTCTAAGACTAGGCAAAC 59.376 47.826 0.00 0.0 42.91 2.93
3288 3533 5.989777 ACGAAACCATCCTATATACAACTGC 59.010 40.000 0.00 0.0 0.00 4.40
3476 3942 5.983720 CGACCAGAGTACAAATATACAAGGG 59.016 44.000 0.00 0.0 0.00 3.95
3480 3946 6.558009 GTGACGACCAGAGTACAAATATACA 58.442 40.000 0.00 0.0 0.00 2.29
3785 4282 5.134661 AGTGGAATGGTTCGTTTCCTTTTA 58.865 37.500 3.60 0.0 41.65 1.52
3896 4398 0.541392 TACATCACCCTTGCAGCGAT 59.459 50.000 0.00 0.0 0.00 4.58
3960 4462 1.000163 AGTGTACGCTCTGGTTGTGAG 60.000 52.381 2.24 0.0 34.87 3.51
4097 4599 4.104102 ACCTTGTAGTCACAAAGGGAATCA 59.896 41.667 8.38 0.0 43.92 2.57
4101 4603 2.775384 ACACCTTGTAGTCACAAAGGGA 59.225 45.455 8.38 0.0 43.92 4.20
4220 4722 7.862372 CACTTCAAACAACTATAACACATGCTT 59.138 33.333 0.00 0.0 0.00 3.91
4221 4723 7.362662 CACTTCAAACAACTATAACACATGCT 58.637 34.615 0.00 0.0 0.00 3.79
4300 4881 4.536065 TCGTTGCTGCTTATTCAAACAAG 58.464 39.130 0.00 0.0 0.00 3.16
4311 4892 0.731417 GATCATGCTCGTTGCTGCTT 59.269 50.000 0.00 0.0 43.37 3.91
4332 4913 1.273048 GCATGGATTGGCAGAAACACA 59.727 47.619 0.00 0.0 0.00 3.72


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

AutoCloner maintained by Alex Coulton.