Multiple sequence alignment - TraesCS5B01G473700

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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 TraesCS5B01G473700 chr5B 100.000 2207 0 0 1 2207 647657160 647654954 0.000000e+00 4076
1 TraesCS5B01G473700 chr5B 93.635 927 54 4 1283 2205 292128502 292127577 0.000000e+00 1380
2 TraesCS5B01G473700 chr5B 91.862 811 58 6 480 1285 647405290 647404483 0.000000e+00 1125
3 TraesCS5B01G473700 chr5B 91.822 807 56 7 484 1285 647464489 647463688 0.000000e+00 1116
4 TraesCS5B01G473700 chr5B 91.667 804 61 4 484 1286 647780940 647780142 0.000000e+00 1109
5 TraesCS5B01G473700 chr5B 91.407 803 63 4 484 1285 647698559 647697762 0.000000e+00 1096
6 TraesCS5B01G473700 chr5B 98.400 500 4 4 1 498 647619957 647620454 0.000000e+00 876
7 TraesCS5B01G473700 chr5B 92.969 512 13 4 1 489 649168054 649167543 0.000000e+00 725
8 TraesCS5B01G473700 chr5B 91.117 349 9 3 1 327 604701078 604700730 9.290000e-124 453
9 TraesCS5B01G473700 chr5B 99.401 167 1 0 319 485 604690237 604690071 9.900000e-79 303
10 TraesCS5B01G473700 chr4B 94.295 929 51 2 1279 2207 574606332 574605406 0.000000e+00 1421
11 TraesCS5B01G473700 chr4B 98.560 486 6 1 1 485 135721374 135721859 0.000000e+00 857
12 TraesCS5B01G473700 chr2B 93.998 933 48 7 1280 2207 718014321 718015250 0.000000e+00 1406
13 TraesCS5B01G473700 chr2B 93.878 931 56 1 1277 2207 715525793 715524864 0.000000e+00 1402
14 TraesCS5B01G473700 chr7B 93.878 931 54 2 1280 2207 444153549 444152619 0.000000e+00 1400
15 TraesCS5B01G473700 chr7B 97.183 426 9 2 69 491 728505539 728505114 0.000000e+00 717
16 TraesCS5B01G473700 chr7B 97.260 73 2 0 1 73 728505633 728505561 8.270000e-25 124
17 TraesCS5B01G473700 chr3B 93.750 928 54 4 1280 2207 551754925 551755848 0.000000e+00 1389
18 TraesCS5B01G473700 chr3B 93.670 932 54 3 1280 2207 659431658 659430728 0.000000e+00 1389
19 TraesCS5B01G473700 chr3B 93.555 931 57 2 1279 2207 561754337 561753408 0.000000e+00 1384
20 TraesCS5B01G473700 chr3B 89.498 219 22 1 276 494 592073126 592072909 2.160000e-70 276
21 TraesCS5B01G473700 chr1B 93.448 931 61 0 1277 2207 89882511 89881581 0.000000e+00 1382
22 TraesCS5B01G473700 chr5D 92.375 800 57 3 484 1282 514996178 514995382 0.000000e+00 1136
23 TraesCS5B01G473700 chr5D 91.500 800 64 3 484 1282 515025535 515024739 0.000000e+00 1098
24 TraesCS5B01G473700 chr5D 91.136 801 60 7 485 1282 514948332 514947540 0.000000e+00 1075
25 TraesCS5B01G473700 chr5D 90.875 800 64 5 484 1282 514974741 514973950 0.000000e+00 1064
26 TraesCS5B01G473700 chr5D 89.763 801 74 5 484 1282 514967014 514966220 0.000000e+00 1018
27 TraesCS5B01G473700 chr3A 91.153 373 26 6 127 494 654904712 654904342 1.180000e-137 499
28 TraesCS5B01G473700 chr3A 80.806 422 56 19 75 486 735192294 735192700 7.650000e-80 307
29 TraesCS5B01G473700 chr3D 83.803 142 21 2 353 493 24608322 24608182 1.370000e-27 134


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 TraesCS5B01G473700 chr5B 647654954 647657160 2206 True 4076.0 4076 100.0000 1 2207 1 chr5B.!!$R6 2206
1 TraesCS5B01G473700 chr5B 292127577 292128502 925 True 1380.0 1380 93.6350 1283 2205 1 chr5B.!!$R1 922
2 TraesCS5B01G473700 chr5B 647404483 647405290 807 True 1125.0 1125 91.8620 480 1285 1 chr5B.!!$R4 805
3 TraesCS5B01G473700 chr5B 647463688 647464489 801 True 1116.0 1116 91.8220 484 1285 1 chr5B.!!$R5 801
4 TraesCS5B01G473700 chr5B 647780142 647780940 798 True 1109.0 1109 91.6670 484 1286 1 chr5B.!!$R8 802
5 TraesCS5B01G473700 chr5B 647697762 647698559 797 True 1096.0 1096 91.4070 484 1285 1 chr5B.!!$R7 801
6 TraesCS5B01G473700 chr5B 649167543 649168054 511 True 725.0 725 92.9690 1 489 1 chr5B.!!$R9 488
7 TraesCS5B01G473700 chr4B 574605406 574606332 926 True 1421.0 1421 94.2950 1279 2207 1 chr4B.!!$R1 928
8 TraesCS5B01G473700 chr2B 718014321 718015250 929 False 1406.0 1406 93.9980 1280 2207 1 chr2B.!!$F1 927
9 TraesCS5B01G473700 chr2B 715524864 715525793 929 True 1402.0 1402 93.8780 1277 2207 1 chr2B.!!$R1 930
10 TraesCS5B01G473700 chr7B 444152619 444153549 930 True 1400.0 1400 93.8780 1280 2207 1 chr7B.!!$R1 927
11 TraesCS5B01G473700 chr7B 728505114 728505633 519 True 420.5 717 97.2215 1 491 2 chr7B.!!$R2 490
12 TraesCS5B01G473700 chr3B 551754925 551755848 923 False 1389.0 1389 93.7500 1280 2207 1 chr3B.!!$F1 927
13 TraesCS5B01G473700 chr3B 659430728 659431658 930 True 1389.0 1389 93.6700 1280 2207 1 chr3B.!!$R3 927
14 TraesCS5B01G473700 chr3B 561753408 561754337 929 True 1384.0 1384 93.5550 1279 2207 1 chr3B.!!$R1 928
15 TraesCS5B01G473700 chr1B 89881581 89882511 930 True 1382.0 1382 93.4480 1277 2207 1 chr1B.!!$R1 930
16 TraesCS5B01G473700 chr5D 514995382 514996178 796 True 1136.0 1136 92.3750 484 1282 1 chr5D.!!$R4 798
17 TraesCS5B01G473700 chr5D 515024739 515025535 796 True 1098.0 1098 91.5000 484 1282 1 chr5D.!!$R5 798
18 TraesCS5B01G473700 chr5D 514947540 514948332 792 True 1075.0 1075 91.1360 485 1282 1 chr5D.!!$R1 797
19 TraesCS5B01G473700 chr5D 514973950 514974741 791 True 1064.0 1064 90.8750 484 1282 1 chr5D.!!$R3 798
20 TraesCS5B01G473700 chr5D 514966220 514967014 794 True 1018.0 1018 89.7630 484 1282 1 chr5D.!!$R2 798

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
538 567 0.464554 GGCCTCCAATCGCTTTAGCT 60.465 55.0 0.0 0.0 39.32 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1669 1710 0.679002 ATCCTGCAGTGCAATCGCTT 60.679 50.0 20.22 0.0 38.41 4.68 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
97 124 4.968719 TGCAAGATGGGTAGAGGAAGATAA 59.031 41.667 0.00 0.00 0.00 1.75
125 152 6.665992 AGCCTTTAAGTATATGTCATCCGA 57.334 37.500 0.00 0.00 0.00 4.55
261 289 8.284945 TGACAAGCTAAGCATATCAGATTTTT 57.715 30.769 0.00 0.00 0.00 1.94
488 517 3.368116 GCGGGTCACACTACTAGTTTCAT 60.368 47.826 0.00 0.00 0.00 2.57
538 567 0.464554 GGCCTCCAATCGCTTTAGCT 60.465 55.000 0.00 0.00 39.32 3.32
722 752 7.833682 TGAAAGTAGGAAATAAATGCATCCTCA 59.166 33.333 7.56 0.00 41.33 3.86
913 943 2.288825 TGAGAAGGAGAACGAACGCAAT 60.289 45.455 0.00 0.00 0.00 3.56
926 956 2.768253 ACGCAATCCATCACTTGAGA 57.232 45.000 0.00 0.00 0.00 3.27
927 957 2.625737 ACGCAATCCATCACTTGAGAG 58.374 47.619 0.00 0.00 0.00 3.20
932 962 4.691175 CAATCCATCACTTGAGAGATCGT 58.309 43.478 0.00 0.00 0.00 3.73
944 974 5.914898 TGAGAGATCGTCCACTATTTCAA 57.085 39.130 0.00 0.00 0.00 2.69
945 975 6.471233 TGAGAGATCGTCCACTATTTCAAT 57.529 37.500 0.00 0.00 0.00 2.57
995 1034 3.878778 ACAAGAAGTCAAGAGCAACACT 58.121 40.909 0.00 0.00 0.00 3.55
1053 1092 1.288127 GCTGCTTCTGGCTGTTTGG 59.712 57.895 0.00 0.00 42.39 3.28
1077 1116 1.537889 AACCACCATCGTCCAGGGA 60.538 57.895 0.00 0.00 0.00 4.20
1182 1221 2.159366 CGTGCTCGGTGAGAACTCTAAT 60.159 50.000 0.00 0.00 36.13 1.73
1183 1222 3.673594 CGTGCTCGGTGAGAACTCTAATT 60.674 47.826 0.00 0.00 36.13 1.40
1189 1228 6.757010 GCTCGGTGAGAACTCTAATTATCAAA 59.243 38.462 0.00 0.00 31.93 2.69
1224 1263 9.803315 TGTTCTTGATGTATATACTGTGTTCTC 57.197 33.333 13.89 1.36 0.00 2.87
1258 1297 6.370442 TCTTATGTTAACTAATGCACGCAGTT 59.630 34.615 7.22 12.48 41.61 3.16
1320 1359 0.525761 CGTGACATTTTGGGCCGAAT 59.474 50.000 7.13 2.88 0.00 3.34
1416 1457 3.039011 GGTGGGCTCCTACTTCTATGAA 58.961 50.000 2.46 0.00 0.00 2.57
1530 1571 2.180276 GTGGTAGAAGCAAGGGAGAGA 58.820 52.381 0.00 0.00 0.00 3.10
1687 1728 1.302752 AAGCGATTGCACTGCAGGA 60.303 52.632 19.93 0.94 46.23 3.86
1716 1757 1.066143 ACTGAACCCGAGCGATTGATT 60.066 47.619 0.00 0.00 0.00 2.57
1781 1822 0.179111 TGCTAACTGAAGCCGATCGG 60.179 55.000 30.03 30.03 42.05 4.18
1807 1850 2.391724 GAACAGTGAGCGTTGGGGGA 62.392 60.000 0.00 0.00 0.00 4.81
1821 1868 3.377154 TGGGGGAGGGTGTATGAATAT 57.623 47.619 0.00 0.00 0.00 1.28
1856 1903 1.577736 CCTCTGGATGAACAGGACCT 58.422 55.000 0.00 0.00 38.98 3.85
1885 1932 3.391296 GTGGAGGGCTGGATGAATAGTAA 59.609 47.826 0.00 0.00 0.00 2.24
1888 1935 4.103311 GGAGGGCTGGATGAATAGTAAACT 59.897 45.833 0.00 0.00 0.00 2.66
1920 1967 1.378762 CGTGGAGGGGTGGTTGAAT 59.621 57.895 0.00 0.00 0.00 2.57
2005 2052 0.106419 GTGGAGGGGTGGTTGAACAA 60.106 55.000 0.00 0.00 0.00 2.83
2097 2144 2.128507 CCCGTGGAGGCTAGAGGAC 61.129 68.421 0.00 0.00 39.21 3.85
2167 2214 1.635817 CCACACCCCTCCCGATGAAT 61.636 60.000 0.00 0.00 0.00 2.57
2185 2232 3.581332 TGAATAGGACCCTTGTTTCGACT 59.419 43.478 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
538 567 6.899393 AATCTTGACTTTTCAACCATAGCA 57.101 33.333 0.00 0.0 36.79 3.49
658 688 6.567687 TTTCTTTTTCGTGGATGCATTAGA 57.432 33.333 0.00 0.0 0.00 2.10
722 752 9.650714 TCTGATCTTGGATTAATGGAAATGAAT 57.349 29.630 0.00 0.0 0.00 2.57
755 785 3.350219 TGCTACCAAATCCTCCAACTC 57.650 47.619 0.00 0.0 0.00 3.01
807 837 9.807649 GAATCTTGCCTTAAATGACACAAATAT 57.192 29.630 0.00 0.0 0.00 1.28
903 933 1.464608 CAAGTGATGGATTGCGTTCGT 59.535 47.619 0.00 0.0 0.00 3.85
913 943 2.690497 GGACGATCTCTCAAGTGATGGA 59.310 50.000 9.95 0.0 31.33 3.41
995 1034 1.444250 GTTCCCCGTGCCATCGATA 59.556 57.895 0.00 0.0 0.00 2.92
1053 1092 1.574428 GACGATGGTGGTTGCACAC 59.426 57.895 0.00 0.0 40.60 3.82
1077 1116 0.179029 CACCAACGGTCCACTCCTTT 60.179 55.000 0.00 0.0 31.02 3.11
1101 1140 1.830145 GCCGAAGCTCCATCCCTTA 59.170 57.895 0.00 0.0 35.50 2.69
1137 1176 2.401766 GGACTGGATGTGCTTGCCG 61.402 63.158 0.00 0.0 33.97 5.69
1167 1206 8.648557 TCATTTGATAATTAGAGTTCTCACCG 57.351 34.615 2.64 0.0 0.00 4.94
1183 1222 9.192642 ACATCAAGAACATCCAATCATTTGATA 57.807 29.630 0.00 0.0 33.62 2.15
1237 1276 5.371115 AAACTGCGTGCATTAGTTAACAT 57.629 34.783 8.61 0.0 33.82 2.71
1258 1297 5.011329 AGTGATACTCGGGTTGTACTTGAAA 59.989 40.000 0.00 0.0 0.00 2.69
1530 1571 2.037121 CTGGCAACTCCCCGAAATTTTT 59.963 45.455 0.00 0.0 37.61 1.94
1669 1710 0.679002 ATCCTGCAGTGCAATCGCTT 60.679 50.000 20.22 0.0 38.41 4.68
1716 1757 3.072330 TCAGGTTCAGTTAACAGCCATCA 59.928 43.478 8.61 0.0 40.08 3.07
1760 1801 1.202302 CGATCGGCTTCAGTTAGCAGA 60.202 52.381 7.38 0.0 46.59 4.26
1781 1822 1.512926 ACGCTCACTGTTCATCCAAC 58.487 50.000 0.00 0.0 35.28 3.77
1807 1850 3.391296 ACCGCTCAATATTCATACACCCT 59.609 43.478 0.00 0.0 0.00 4.34
1813 1860 2.224185 ACGCCACCGCTCAATATTCATA 60.224 45.455 0.00 0.0 38.22 2.15
1856 1903 3.625897 CAGCCCTCCACACCACGA 61.626 66.667 0.00 0.0 0.00 4.35
1885 1932 2.375345 CGGCCACCCCTCCATAGTT 61.375 63.158 2.24 0.0 0.00 2.24
1888 1935 3.087253 CACGGCCACCCCTCCATA 61.087 66.667 2.24 0.0 0.00 2.74
2005 2052 2.857744 GCGCTACTCCACCGGCTAT 61.858 63.158 0.00 0.0 0.00 2.97
2025 2072 1.133181 TGTTCATCCAGCCTCCACCA 61.133 55.000 0.00 0.0 0.00 4.17
2097 2144 1.135112 TGTTCATCTCCACCATCGACG 60.135 52.381 0.00 0.0 0.00 5.12
2167 2214 2.322658 ACAGTCGAAACAAGGGTCCTA 58.677 47.619 0.00 0.0 0.00 2.94
2185 2232 0.883833 GACGAAACGGACCTCCTACA 59.116 55.000 0.00 0.0 0.00 2.74


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

AutoCloner maintained by Alex Coulton.