Multiple sequence alignment - TraesCS1B01G013200

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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 TraesCS1B01G013200 chr1B 100.000 2514 0 0 1 2514 6326243 6328756 0.000000e+00 4643
1 TraesCS1B01G013200 chr1B 97.460 2520 57 3 1 2514 7928509 7925991 0.000000e+00 4292
2 TraesCS1B01G013200 chr1B 97.118 2221 55 5 1 2214 7130356 7128138 0.000000e+00 3738
3 TraesCS1B01G013200 chr1B 82.074 1138 169 20 143 1260 6340599 6341721 0.000000e+00 939
4 TraesCS1B01G013200 chr1B 81.930 1140 169 23 143 1260 6693307 6692183 0.000000e+00 929
5 TraesCS1B01G013200 chr1B 81.699 1142 167 26 143 1260 629702643 629703766 0.000000e+00 913
6 TraesCS1B01G013200 chr1D 86.201 2377 254 30 3 2332 3122848 3125197 0.000000e+00 2505
7 TraesCS1B01G013200 chr1D 79.301 2261 329 78 5 2205 3227784 3229965 0.000000e+00 1454
8 TraesCS1B01G013200 chr1D 93.736 910 45 8 1 901 3614355 3615261 0.000000e+00 1354
9 TraesCS1B01G013200 chr1D 88.383 835 75 6 964 1776 3615294 3616128 0.000000e+00 985
10 TraesCS1B01G013200 chr1D 84.937 239 30 6 1768 2003 3616158 3616393 1.160000e-58 237
11 TraesCS1B01G013200 chr1A 85.212 1393 164 20 357 1721 6499036 6497658 0.000000e+00 1393
12 TraesCS1B01G013200 chr1A 81.860 645 81 21 143 780 6439196 6438581 6.200000e-141 510
13 TraesCS1B01G013200 chr1A 86.207 319 37 5 27 338 6500315 6499997 3.100000e-89 339
14 TraesCS1B01G013200 chrUn 91.143 700 54 3 1 693 9820783 9820085 0.000000e+00 942
15 TraesCS1B01G013200 chrUn 91.654 659 47 5 978 1629 9819760 9819103 0.000000e+00 905
16 TraesCS1B01G013200 chrUn 89.308 318 25 3 634 942 9820074 9819757 8.430000e-105 390


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 TraesCS1B01G013200 chr1B 6326243 6328756 2513 False 4643.000000 4643 100.000000 1 2514 1 chr1B.!!$F1 2513
1 TraesCS1B01G013200 chr1B 7925991 7928509 2518 True 4292.000000 4292 97.460000 1 2514 1 chr1B.!!$R3 2513
2 TraesCS1B01G013200 chr1B 7128138 7130356 2218 True 3738.000000 3738 97.118000 1 2214 1 chr1B.!!$R2 2213
3 TraesCS1B01G013200 chr1B 6340599 6341721 1122 False 939.000000 939 82.074000 143 1260 1 chr1B.!!$F2 1117
4 TraesCS1B01G013200 chr1B 6692183 6693307 1124 True 929.000000 929 81.930000 143 1260 1 chr1B.!!$R1 1117
5 TraesCS1B01G013200 chr1B 629702643 629703766 1123 False 913.000000 913 81.699000 143 1260 1 chr1B.!!$F3 1117
6 TraesCS1B01G013200 chr1D 3122848 3125197 2349 False 2505.000000 2505 86.201000 3 2332 1 chr1D.!!$F1 2329
7 TraesCS1B01G013200 chr1D 3227784 3229965 2181 False 1454.000000 1454 79.301000 5 2205 1 chr1D.!!$F2 2200
8 TraesCS1B01G013200 chr1D 3614355 3616393 2038 False 858.666667 1354 89.018667 1 2003 3 chr1D.!!$F3 2002
9 TraesCS1B01G013200 chr1A 6497658 6500315 2657 True 866.000000 1393 85.709500 27 1721 2 chr1A.!!$R2 1694
10 TraesCS1B01G013200 chr1A 6438581 6439196 615 True 510.000000 510 81.860000 143 780 1 chr1A.!!$R1 637
11 TraesCS1B01G013200 chrUn 9819103 9820783 1680 True 745.666667 942 90.701667 1 1629 3 chrUn.!!$R1 1628

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
230 254 0.250727 GCTAAAGCTCCCCACACACA 60.251 55.0 0.0 0.0 38.21 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2013 3197 3.32952 GCCACTAATACCCACATATCCCA 59.67 47.826 0.0 0.0 0.0 4.37 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
67 75 7.913789 TCAATTAGGAGGTCTTAGCTGTTTTA 58.086 34.615 0.00 0.00 0.00 1.52
74 82 3.181496 GGTCTTAGCTGTTTTATGGCTGC 60.181 47.826 0.00 0.00 37.50 5.25
164 182 5.065218 CAGCTATAAATTGCGACCTTCACTT 59.935 40.000 0.00 0.00 33.76 3.16
195 218 4.277476 TCCTCACCAAACACATTGAAACT 58.723 39.130 0.00 0.00 41.85 2.66
230 254 0.250727 GCTAAAGCTCCCCACACACA 60.251 55.000 0.00 0.00 38.21 3.72
262 286 1.134189 GCCGCTACAAACCCTTCCTAT 60.134 52.381 0.00 0.00 0.00 2.57
435 1404 1.070914 TGCAAACGACTGGACCATACA 59.929 47.619 0.00 0.00 0.00 2.29
582 1553 6.121776 TCCCATCTTTTAGAGTTGTTAGCA 57.878 37.500 0.00 0.00 0.00 3.49
1369 2479 5.071250 TGTTACATCACTTACCTTGGTCAGT 59.929 40.000 1.13 1.13 0.00 3.41
1458 2568 4.093743 GGTAACAACATTGGGGGATTCTT 58.906 43.478 0.00 0.00 0.00 2.52
1460 2570 4.890158 AACAACATTGGGGGATTCTTTC 57.110 40.909 0.00 0.00 0.00 2.62
1609 2736 1.699634 CAGAAGGACAAGGGTCTTCCA 59.300 52.381 0.00 0.00 43.77 3.53
1975 3157 9.143631 GATTTTGGGTCTTGAAATATGACAAAG 57.856 33.333 0.00 0.00 35.69 2.77
2007 3190 2.749600 TGCATAAGTGGCCAAATCCAT 58.250 42.857 7.24 0.00 38.57 3.41
2013 3197 6.295462 GCATAAGTGGCCAAATCCATGATATT 60.295 38.462 7.24 0.00 38.57 1.28
2023 3207 7.632028 GCCAAATCCATGATATTGGGATATGTG 60.632 40.741 18.77 0.00 40.46 3.21
2351 3537 2.158696 ACAGTGAAAGAGCTTGAAGCCT 60.159 45.455 14.45 7.93 43.77 4.58
2385 3571 0.040067 CGGCTGGCAAAACAGAAGAC 60.040 55.000 1.08 0.00 40.97 3.01
2431 3617 6.934645 TCGAAGGCCCAAGAATAAATGTATAG 59.065 38.462 0.00 0.00 0.00 1.31
2494 3680 3.906846 CCTTGATGTAGCTCCTCCCTTAT 59.093 47.826 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 5.735766 ACAGCTAAGACCTCCTAATTGAAC 58.264 41.667 0.00 0.00 0.00 3.18
67 75 2.803030 ATGTTCTTCTCAGCAGCCAT 57.197 45.000 0.00 0.00 0.00 4.40
132 148 3.295973 GCAATTTATAGCTGGGGTTCCA 58.704 45.455 0.00 0.00 41.58 3.53
164 182 4.464244 TGTGTTTGGTGAGGAAATGAACAA 59.536 37.500 0.00 0.00 0.00 2.83
230 254 2.207229 TAGCGGCCATGGCTATCGT 61.207 57.895 34.70 20.74 41.80 3.73
435 1404 4.552365 CGGCAGCCGGACCATCAT 62.552 66.667 27.32 0.00 44.15 2.45
966 2042 4.597507 GGGATCTGGGTATAGGTGATCAAA 59.402 45.833 0.00 0.00 36.28 2.69
1369 2479 5.444744 AAGGCCCATATGTTGTAACACTA 57.555 39.130 0.00 0.00 42.51 2.74
1609 2736 5.752892 AATAGTACACGAGATCACGACAT 57.247 39.130 19.57 6.40 37.03 3.06
1955 3137 6.431234 AGTGTCTTTGTCATATTTCAAGACCC 59.569 38.462 9.34 0.58 0.00 4.46
1975 3157 4.731773 GCCACTTATGCATGCTAAAGTGTC 60.732 45.833 36.30 29.86 44.63 3.67
2007 3190 8.548025 CACTAATACCCACATATCCCAATATCA 58.452 37.037 0.00 0.00 0.00 2.15
2013 3197 3.329520 GCCACTAATACCCACATATCCCA 59.670 47.826 0.00 0.00 0.00 4.37
2023 3207 6.465439 AAGCTATTTTTGCCACTAATACCC 57.535 37.500 0.00 0.00 0.00 3.69
2385 3571 4.084171 CGAATACCAGCTCACATGCTATTG 60.084 45.833 0.00 0.00 41.98 1.90
2463 3649 1.410153 GCTACATCAAGGCCAAATGGG 59.590 52.381 5.01 4.49 40.85 4.00
2477 3663 3.928754 TCACATAAGGGAGGAGCTACAT 58.071 45.455 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.