Multiple sequence alignment - TraesCS1B01G007100

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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 TraesCS1B01G007100 chr1B 100.000 3408 0 0 1 3408 4096642 4100049 0.000000e+00 6294.0
1 TraesCS1B01G007100 chr1B 86.940 3170 359 29 16 3172 4823502 4820375 0.000000e+00 3509.0
2 TraesCS1B01G007100 chr1B 87.247 2721 321 14 2 2719 3965623 3968320 0.000000e+00 3079.0
3 TraesCS1B01G007100 chr1B 88.289 2502 277 13 2 2498 3952217 3954707 0.000000e+00 2983.0
4 TraesCS1B01G007100 chr1B 90.340 2267 195 16 1110 3366 4530466 4528214 0.000000e+00 2952.0
5 TraesCS1B01G007100 chr1B 86.336 2620 344 12 15 2629 4509758 4507148 0.000000e+00 2843.0
6 TraesCS1B01G007100 chr1B 88.798 1339 121 12 1618 2955 4842014 4840704 0.000000e+00 1615.0
7 TraesCS1B01G007100 chr1B 85.952 1502 174 12 1363 2864 3996855 3998319 0.000000e+00 1570.0
8 TraesCS1B01G007100 chr1B 88.682 1184 93 18 2084 3267 4862468 4861326 0.000000e+00 1406.0
9 TraesCS1B01G007100 chr1B 84.943 870 98 15 2000 2864 4153916 4154757 0.000000e+00 850.0
10 TraesCS1B01G007100 chr1B 90.984 610 50 3 2758 3366 3968320 3968925 0.000000e+00 817.0
11 TraesCS1B01G007100 chr1B 90.258 349 31 3 3061 3408 4498743 4498397 1.440000e-123 453.0
12 TraesCS1B01G007100 chr1B 83.594 384 56 5 2896 3273 4758583 4758201 1.500000e-93 353.0
13 TraesCS1B01G007100 chr1B 94.500 200 9 1 3209 3408 4820378 4820181 1.190000e-79 307.0
14 TraesCS1B01G007100 chr1B 89.500 200 20 1 3141 3339 4838437 4838238 5.650000e-63 252.0
15 TraesCS1B01G007100 chr1B 80.814 172 31 2 2896 3066 4564026 4563856 2.130000e-27 134.0
16 TraesCS1B01G007100 chr1B 96.429 56 2 0 3352 3407 3968938 3968993 3.620000e-15 93.5
17 TraesCS1B01G007100 chr1D 89.672 3263 314 15 89 3339 460326 463577 0.000000e+00 4137.0
18 TraesCS1B01G007100 chr1D 89.440 2500 254 7 2 2498 648628 651120 0.000000e+00 3145.0
19 TraesCS1B01G007100 chr1D 87.464 351 42 2 3058 3408 396707 397055 1.470000e-108 403.0
20 TraesCS1B01G007100 chr1A 96.302 2434 82 6 1 2431 3502802 3500374 0.000000e+00 3989.0
21 TraesCS1B01G007100 chr1A 85.844 2868 354 26 1 2864 27213194 27216013 0.000000e+00 3000.0
22 TraesCS1B01G007100 chr1A 88.423 2505 260 21 15 2508 3656138 3653653 0.000000e+00 2992.0
23 TraesCS1B01G007100 chr1A 81.675 382 65 2 2896 3273 2986440 2986820 2.550000e-81 313.0
24 TraesCS1B01G007100 chr1A 83.446 296 41 5 2896 3191 3487942 3487655 5.610000e-68 268.0
25 TraesCS1B01G007100 chr1A 92.593 81 6 0 3328 3408 3487661 3487581 2.150000e-22 117.0
26 TraesCS1B01G007100 chr3D 86.434 2860 338 29 15 2864 560057034 560054215 0.000000e+00 3086.0
27 TraesCS1B01G007100 chr7D 83.704 135 15 5 2634 2767 603770203 603770075 1.660000e-23 121.0


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 TraesCS1B01G007100 chr1B 4096642 4100049 3407 False 6294.000000 6294 100.000000 1 3408 1 chr1B.!!$F3 3407
1 TraesCS1B01G007100 chr1B 3952217 3954707 2490 False 2983.000000 2983 88.289000 2 2498 1 chr1B.!!$F1 2496
2 TraesCS1B01G007100 chr1B 4528214 4530466 2252 True 2952.000000 2952 90.340000 1110 3366 1 chr1B.!!$R3 2256
3 TraesCS1B01G007100 chr1B 4507148 4509758 2610 True 2843.000000 2843 86.336000 15 2629 1 chr1B.!!$R2 2614
4 TraesCS1B01G007100 chr1B 4820181 4823502 3321 True 1908.000000 3509 90.720000 16 3408 2 chr1B.!!$R7 3392
5 TraesCS1B01G007100 chr1B 3996855 3998319 1464 False 1570.000000 1570 85.952000 1363 2864 1 chr1B.!!$F2 1501
6 TraesCS1B01G007100 chr1B 4861326 4862468 1142 True 1406.000000 1406 88.682000 2084 3267 1 chr1B.!!$R6 1183
7 TraesCS1B01G007100 chr1B 3965623 3968993 3370 False 1329.833333 3079 91.553333 2 3407 3 chr1B.!!$F5 3405
8 TraesCS1B01G007100 chr1B 4838238 4842014 3776 True 933.500000 1615 89.149000 1618 3339 2 chr1B.!!$R8 1721
9 TraesCS1B01G007100 chr1B 4153916 4154757 841 False 850.000000 850 84.943000 2000 2864 1 chr1B.!!$F4 864
10 TraesCS1B01G007100 chr1D 460326 463577 3251 False 4137.000000 4137 89.672000 89 3339 1 chr1D.!!$F2 3250
11 TraesCS1B01G007100 chr1D 648628 651120 2492 False 3145.000000 3145 89.440000 2 2498 1 chr1D.!!$F3 2496
12 TraesCS1B01G007100 chr1A 3500374 3502802 2428 True 3989.000000 3989 96.302000 1 2431 1 chr1A.!!$R1 2430
13 TraesCS1B01G007100 chr1A 27213194 27216013 2819 False 3000.000000 3000 85.844000 1 2864 1 chr1A.!!$F2 2863
14 TraesCS1B01G007100 chr1A 3653653 3656138 2485 True 2992.000000 2992 88.423000 15 2508 1 chr1A.!!$R2 2493
15 TraesCS1B01G007100 chr3D 560054215 560057034 2819 True 3086.000000 3086 86.434000 15 2864 1 chr3D.!!$R1 2849

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
846 851 2.803030 TACCTGAGGAACTAGCGACT 57.197 50.0 4.99 0.0 41.55 4.18 F
1512 1518 0.839946 AGGCACAACTCCAAGACAGT 59.160 50.0 0.00 0.0 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2284 2294 0.538057 TTGGCCTTGCTTGTGGAGAG 60.538 55.0 3.32 0.0 0.0 3.20 R
2890 2931 1.425412 ACGCATCGACCACTTACAAC 58.575 50.0 0.00 0.0 0.0 3.32 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
339 340 4.082949 GGACCTTTACCCGCAAATATATGC 60.083 45.833 0.00 0.00 42.94 3.14
846 851 2.803030 TACCTGAGGAACTAGCGACT 57.197 50.000 4.99 0.00 41.55 4.18
1089 1095 0.944386 TGAGCCTTTCAACGCTTGAC 59.056 50.000 0.76 0.00 39.87 3.18
1225 1231 5.757850 ACTTTGTGATTCAACTCCAGTTC 57.242 39.130 0.00 0.00 35.83 3.01
1512 1518 0.839946 AGGCACAACTCCAAGACAGT 59.160 50.000 0.00 0.00 0.00 3.55
1682 1688 7.829378 AATTTCTTGTCTACGACTACATTCC 57.171 36.000 0.00 0.00 33.15 3.01
1780 1786 3.441222 TGTAAATGATGTGGCTCAAGCAG 59.559 43.478 4.13 0.00 44.36 4.24
1989 1995 8.749026 TGTACTAGTATAACCTTCCTTCTCAG 57.251 38.462 5.75 0.00 0.00 3.35
2058 2065 2.140065 TTCTGTGCAGAACTCTCGTG 57.860 50.000 10.26 0.00 42.06 4.35
2098 2105 6.364706 CGGAGAAATGTGATGTCTATAGCTTC 59.635 42.308 0.00 0.00 0.00 3.86
2251 2261 6.391227 ACAGAAGAGAATAGCTTAGCTCTC 57.609 41.667 11.09 11.84 40.44 3.20
2261 2271 3.641046 AGCTTAGCTCTCCTCATCAAGA 58.359 45.455 0.00 0.00 30.62 3.02
2284 2294 2.354103 GGCCTTTTCTTGCTTGGAATCC 60.354 50.000 0.00 0.00 0.00 3.01
2342 2353 1.480212 AACACTCATCCAGCGACCCA 61.480 55.000 0.00 0.00 0.00 4.51
2347 2358 1.450312 CATCCAGCGACCCACTTCC 60.450 63.158 0.00 0.00 0.00 3.46
2533 2571 7.531280 AAAAGTCTGTAATCATCTCATGTCG 57.469 36.000 0.00 0.00 0.00 4.35
2831 2872 2.118166 CGGTTTACGCAACGCAAAC 58.882 52.632 7.17 7.17 40.87 2.93
2872 2913 0.642156 TTCTCCCTCCCTATGCCTCA 59.358 55.000 0.00 0.00 0.00 3.86
2915 2956 2.380084 AGTGGTCGATGCGTAAACAT 57.620 45.000 0.00 0.00 0.00 2.71
2919 2960 3.067833 TGGTCGATGCGTAAACATGAAA 58.932 40.909 0.00 0.00 0.00 2.69
3019 4262 3.561725 GGCTGTATGGCAAGAGTATGAAC 59.438 47.826 0.00 0.00 41.37 3.18
3079 4791 0.820871 AGTCCTCGTCCTTCAGATGC 59.179 55.000 0.00 0.00 0.00 3.91
3273 5403 6.047870 ACTGCAATCATAGACATGAAGAGTC 58.952 40.000 0.00 0.00 44.27 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
339 340 5.723672 TTTGTTCTAGTCTACCACCTGAG 57.276 43.478 0.00 0.00 0.00 3.35
846 851 7.337938 TCTTCAAGGACAATAGTATGATGCAA 58.662 34.615 0.00 0.00 0.00 4.08
1126 1132 1.891150 AGCATTTTGGAGTTGCCTGAG 59.109 47.619 0.00 0.00 37.07 3.35
1225 1231 2.203280 TTTGTGGTGACCGGCTGG 60.203 61.111 11.02 11.02 42.84 4.85
1321 1327 5.646467 TTTGTCTTGTTACGACTAAGCAC 57.354 39.130 0.00 0.00 32.70 4.40
1682 1688 2.747855 GGTGGAGGCTTCCTTGCG 60.748 66.667 16.82 0.00 44.36 4.85
1780 1786 4.970003 GCATTCGTGGTGCAAATAAGATAC 59.030 41.667 0.00 0.00 42.08 2.24
2024 2031 5.702865 TGCACAGAATCAAAACATTAGAGC 58.297 37.500 0.00 0.00 0.00 4.09
2098 2105 1.291877 GCTCTAGCACAACCACACCG 61.292 60.000 0.00 0.00 41.59 4.94
2251 2261 3.629087 AGAAAAGGCCATCTTGATGAGG 58.371 45.455 5.01 0.00 35.55 3.86
2261 2271 2.014010 TCCAAGCAAGAAAAGGCCAT 57.986 45.000 5.01 0.00 0.00 4.40
2284 2294 0.538057 TTGGCCTTGCTTGTGGAGAG 60.538 55.000 3.32 0.00 0.00 3.20
2311 2321 3.370953 GGATGAGTGTTTGGTATGCCTCT 60.371 47.826 0.16 0.00 35.27 3.69
2347 2358 1.838073 AAGGCACGGGGTAGGAACTG 61.838 60.000 0.00 0.00 41.52 3.16
2831 2872 3.197333 AGAATCAGTGGACACTCAGGATG 59.803 47.826 1.21 0.00 40.20 3.51
2890 2931 1.425412 ACGCATCGACCACTTACAAC 58.575 50.000 0.00 0.00 0.00 3.32
3019 4262 3.574396 TGCTCCATCGTAAGGATAAGGAG 59.426 47.826 0.00 0.00 43.43 3.69
3273 5403 9.745018 AAAGATTATGGGATATGTTCATACCAG 57.255 33.333 7.75 0.00 42.36 4.00
3306 5437 4.351127 AGGTGAATCGGTACCTACTTTCT 58.649 43.478 10.90 0.00 45.20 2.52
3307 5438 4.732672 AGGTGAATCGGTACCTACTTTC 57.267 45.455 10.90 7.98 45.20 2.62


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

AutoCloner maintained by Alex Coulton.