Multiple sequence alignment - TraesCS1B01G160400

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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 TraesCS1B01G160400 chr1B 100.000 2348 0 0 1 2348 275468297 275470644 0.000000e+00 4337
1 TraesCS1B01G160400 chr1B 97.615 2348 46 2 1 2348 275371025 275373362 0.000000e+00 4017
2 TraesCS1B01G160400 chr1B 91.077 2107 172 11 69 2168 275675891 275677988 0.000000e+00 2835
3 TraesCS1B01G160400 chr1B 96.256 1469 47 5 883 2348 275602163 275603626 0.000000e+00 2401
4 TraesCS1B01G160400 chr1B 94.820 888 44 2 1 888 275588729 275589614 0.000000e+00 1384
5 TraesCS1B01G160400 chr1B 89.664 387 33 3 1783 2168 278630497 278630117 9.750000e-134 486
6 TraesCS1B01G160400 chr1A 93.578 1090 66 3 1079 2168 246090678 246089593 0.000000e+00 1622
7 TraesCS1B01G160400 chr1A 91.416 1130 66 22 1037 2166 245835348 245834250 0.000000e+00 1520
8 TraesCS1B01G160400 chr1A 93.651 945 59 1 69 1013 246125286 246124343 0.000000e+00 1411
9 TraesCS1B01G160400 chr1A 93.911 542 30 3 473 1013 245960344 245959805 0.000000e+00 815
10 TraesCS1B01G160400 chr3A 90.181 387 36 2 1784 2168 80004772 80004386 9.690000e-139 503
11 TraesCS1B01G160400 chr4B 89.637 386 38 2 1784 2168 54123076 54123460 7.540000e-135 490
12 TraesCS1B01G160400 chr4D 90.237 379 27 6 1792 2168 286415805 286415435 9.750000e-134 486
13 TraesCS1B01G160400 chr4D 97.238 181 5 0 2168 2348 130133895 130134075 8.150000e-80 307
14 TraesCS1B01G160400 chr4D 91.463 82 5 2 1 80 128001625 128001706 6.860000e-21 111
15 TraesCS1B01G160400 chr4D 92.405 79 3 3 1 76 491934123 491934201 2.470000e-20 110
16 TraesCS1B01G160400 chr7D 86.836 433 49 5 1357 1786 527766149 527766576 5.870000e-131 477
17 TraesCS1B01G160400 chr7D 97.727 176 4 0 2168 2343 327852835 327853010 1.050000e-78 303
18 TraesCS1B01G160400 chr7D 89.011 91 4 6 1 88 178508600 178508513 8.870000e-20 108
19 TraesCS1B01G160400 chr2B 86.183 427 58 1 1358 1783 195930232 195930658 5.910000e-126 460
20 TraesCS1B01G160400 chr2B 78.548 303 61 4 1047 1347 788496855 788497155 1.840000e-46 196
21 TraesCS1B01G160400 chr2B 97.222 72 1 1 1 71 594114612 594114541 1.140000e-23 121
22 TraesCS1B01G160400 chr3D 85.748 428 56 3 1357 1783 431537712 431537289 4.600000e-122 448
23 TraesCS1B01G160400 chr3D 87.712 236 26 3 1756 1991 503868287 503868055 2.970000e-69 272
24 TraesCS1B01G160400 chr3D 79.920 249 38 3 69 317 21817723 21817487 3.100000e-39 172
25 TraesCS1B01G160400 chr3D 94.667 75 2 2 1 74 305680479 305680406 5.300000e-22 115
26 TraesCS1B01G160400 chr3D 92.405 79 5 1 1 78 531379469 531379391 6.860000e-21 111
27 TraesCS1B01G160400 chr7B 85.514 428 56 4 1357 1783 564386732 564387154 2.140000e-120 442
28 TraesCS1B01G160400 chr7B 80.201 298 55 4 1047 1341 120467256 120467552 1.090000e-53 220
29 TraesCS1B01G160400 chr7A 81.618 408 70 2 1603 2005 465858527 465858934 1.340000e-87 333
30 TraesCS1B01G160400 chr5A 81.687 415 57 16 1763 2168 442779466 442779062 6.260000e-86 327
31 TraesCS1B01G160400 chr3B 97.253 182 5 0 2167 2348 312181893 312182074 2.270000e-80 309
32 TraesCS1B01G160400 chr3B 78.283 198 31 7 71 268 38052470 38052285 1.470000e-22 117
33 TraesCS1B01G160400 chr5D 96.703 182 6 0 2167 2348 56769498 56769317 1.050000e-78 303
34 TraesCS1B01G160400 chr6D 96.685 181 6 0 2168 2348 194038361 194038541 3.790000e-78 302
35 TraesCS1B01G160400 chr6D 93.878 196 10 2 2153 2348 286986306 286986499 6.350000e-76 294
36 TraesCS1B01G160400 chr6D 85.597 243 23 8 1755 1995 217431538 217431770 6.480000e-61 244
37 TraesCS1B01G160400 chr6D 97.183 71 1 1 1 70 383531773 383531843 4.100000e-23 119
38 TraesCS1B01G160400 chr6D 97.143 70 1 1 1 69 436005009 436004940 1.470000e-22 117
39 TraesCS1B01G160400 chr6D 95.833 72 2 1 1 71 289223953 289223882 5.300000e-22 115
40 TraesCS1B01G160400 chr6D 90.361 83 6 2 3 83 76140220 76140302 8.870000e-20 108
41 TraesCS1B01G160400 chr6D 88.889 90 7 3 1 87 467470610 467470699 8.870000e-20 108
42 TraesCS1B01G160400 chr2D 96.685 181 6 0 2168 2348 240964539 240964719 3.790000e-78 302
43 TraesCS1B01G160400 chr2D 97.183 71 1 1 1 70 195343371 195343301 4.100000e-23 119
44 TraesCS1B01G160400 chr1D 96.685 181 6 0 2168 2348 111749259 111749079 3.790000e-78 302
45 TraesCS1B01G160400 chr1D 95.833 72 2 1 1 71 64003186 64003115 5.300000e-22 115
46 TraesCS1B01G160400 chr1D 97.101 69 1 1 1 68 75823096 75823164 5.300000e-22 115
47 TraesCS1B01G160400 chr1D 97.101 69 1 1 1 68 110233192 110233260 5.300000e-22 115
48 TraesCS1B01G160400 chr1D 95.833 72 2 1 1 71 211967715 211967644 5.300000e-22 115
49 TraesCS1B01G160400 chr1D 97.101 69 1 1 1 68 237688226 237688158 5.300000e-22 115
50 TraesCS1B01G160400 chr1D 97.101 69 1 1 1 68 259058251 259058319 5.300000e-22 115
51 TraesCS1B01G160400 chr1D 93.590 78 3 2 1 77 287569917 287569841 5.300000e-22 115
52 TraesCS1B01G160400 chr1D 97.101 69 1 1 1 68 434122186 434122118 5.300000e-22 115
53 TraesCS1B01G160400 chrUn 80.195 308 57 4 1047 1351 474550410 474550716 6.530000e-56 228
54 TraesCS1B01G160400 chr6A 74.675 462 101 13 891 1347 454688137 454688587 8.560000e-45 191


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 TraesCS1B01G160400 chr1B 275468297 275470644 2347 False 4337 4337 100.000 1 2348 1 chr1B.!!$F2 2347
1 TraesCS1B01G160400 chr1B 275371025 275373362 2337 False 4017 4017 97.615 1 2348 1 chr1B.!!$F1 2347
2 TraesCS1B01G160400 chr1B 275675891 275677988 2097 False 2835 2835 91.077 69 2168 1 chr1B.!!$F5 2099
3 TraesCS1B01G160400 chr1B 275602163 275603626 1463 False 2401 2401 96.256 883 2348 1 chr1B.!!$F4 1465
4 TraesCS1B01G160400 chr1B 275588729 275589614 885 False 1384 1384 94.820 1 888 1 chr1B.!!$F3 887
5 TraesCS1B01G160400 chr1A 246089593 246090678 1085 True 1622 1622 93.578 1079 2168 1 chr1A.!!$R3 1089
6 TraesCS1B01G160400 chr1A 245834250 245835348 1098 True 1520 1520 91.416 1037 2166 1 chr1A.!!$R1 1129
7 TraesCS1B01G160400 chr1A 246124343 246125286 943 True 1411 1411 93.651 69 1013 1 chr1A.!!$R4 944
8 TraesCS1B01G160400 chr1A 245959805 245960344 539 True 815 815 93.911 473 1013 1 chr1A.!!$R2 540

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
500 501 0.109504 GTTCGCTCTGAGAAGCTCGT 60.11 55.0 9.28 0.0 40.23 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1676 1684 1.438651 TCGCACACACCTTAATCTGC 58.561 50.0 0.0 0.0 0.0 4.26 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
34 35 5.316987 TCCTAGATAGATCTTGCGTGATCA 58.683 41.667 17.28 0.00 43.76 2.92
41 42 5.480642 AGATCTTGCGTGATCATAGGAAT 57.519 39.130 17.28 0.00 43.76 3.01
85 86 3.469863 AACCGCACCATCACCACGT 62.470 57.895 0.00 0.00 0.00 4.49
380 381 7.523293 TGGATATGCGTTTGAATGGAAATAT 57.477 32.000 0.00 0.00 0.00 1.28
483 484 7.491696 GGTAAAGAACGACAGCTATATCTTGTT 59.508 37.037 0.00 0.00 0.00 2.83
488 489 3.666334 CGACAGCTATATCTTGTTCGCTC 59.334 47.826 0.00 0.00 0.00 5.03
500 501 0.109504 GTTCGCTCTGAGAAGCTCGT 60.110 55.000 9.28 0.00 40.23 4.18
536 537 1.367840 GCGGCCTAGTAGGTCATGG 59.632 63.158 20.67 5.76 40.96 3.66
1021 1022 0.231279 GTTGTGGAACTACGTGTGCG 59.769 55.000 0.00 0.00 40.50 5.34
1172 1180 3.312736 AGGTGTGAAAGGTTTCCATGT 57.687 42.857 0.05 0.00 36.36 3.21
1411 1419 3.981071 TCAGAGACCCATCGACAAAAT 57.019 42.857 0.00 0.00 0.00 1.82
1549 1557 5.233225 CGATACATGGCATACAGTTCATCT 58.767 41.667 0.00 0.00 0.00 2.90
1665 1673 5.843673 TTTGTGATTAGGAAACACAGCAA 57.156 34.783 0.00 0.00 43.62 3.91
1676 1684 3.457610 AACACAGCAAAATTGGTCAGG 57.542 42.857 0.00 0.00 36.65 3.86
2240 2257 2.290641 CCCCAAGAACAAGAAGAACACG 59.709 50.000 0.00 0.00 0.00 4.49
2241 2258 3.202906 CCCAAGAACAAGAAGAACACGA 58.797 45.455 0.00 0.00 0.00 4.35
2242 2259 3.625764 CCCAAGAACAAGAAGAACACGAA 59.374 43.478 0.00 0.00 0.00 3.85
2243 2260 4.260784 CCCAAGAACAAGAAGAACACGAAG 60.261 45.833 0.00 0.00 0.00 3.79
2244 2261 4.570772 CCAAGAACAAGAAGAACACGAAGA 59.429 41.667 0.00 0.00 0.00 2.87
2245 2262 5.064707 CCAAGAACAAGAAGAACACGAAGAA 59.935 40.000 0.00 0.00 0.00 2.52
2246 2263 5.720261 AGAACAAGAAGAACACGAAGAAC 57.280 39.130 0.00 0.00 0.00 3.01
2247 2264 5.175859 AGAACAAGAAGAACACGAAGAACA 58.824 37.500 0.00 0.00 0.00 3.18
2248 2265 4.859629 ACAAGAAGAACACGAAGAACAC 57.140 40.909 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
137 138 2.565391 ACGTCATGGTTAGATGTGGTCA 59.435 45.455 0.00 0.00 34.15 4.02
291 292 1.035032 CTTTTTCTTTCGTGCGCGTC 58.965 50.000 20.50 0.00 39.49 5.19
301 302 3.636764 ACACGATGGGAAGCTTTTTCTTT 59.363 39.130 0.00 0.00 0.00 2.52
488 489 2.088423 AGTACCTCACGAGCTTCTCAG 58.912 52.381 0.00 0.00 0.00 3.35
500 501 3.857052 CCGCAAATCTTACAGTACCTCA 58.143 45.455 0.00 0.00 0.00 3.86
536 537 0.606673 GAGCCCACACTCCTTGAACC 60.607 60.000 0.00 0.00 0.00 3.62
1172 1180 6.719829 TCCACTTCTTTCATCACTACTCACTA 59.280 38.462 0.00 0.00 0.00 2.74
1365 1373 2.202878 TCGCGTTAGCAGCATCCC 60.203 61.111 5.77 0.00 45.49 3.85
1665 1673 4.463891 CACCTTAATCTGCCTGACCAATTT 59.536 41.667 0.00 0.00 0.00 1.82
1676 1684 1.438651 TCGCACACACCTTAATCTGC 58.561 50.000 0.00 0.00 0.00 4.26
1726 1734 4.401022 TGTTGTCTTGGCTCATCAGAAAT 58.599 39.130 0.00 0.00 0.00 2.17
2123 2131 9.349713 TCTCCCTCGTATAAAATTGCAATAATT 57.650 29.630 13.39 13.24 0.00 1.40
2240 2257 4.881850 TGTTTTCCCTCTCTTGTGTTCTTC 59.118 41.667 0.00 0.00 0.00 2.87
2241 2258 4.640647 GTGTTTTCCCTCTCTTGTGTTCTT 59.359 41.667 0.00 0.00 0.00 2.52
2242 2259 4.080299 AGTGTTTTCCCTCTCTTGTGTTCT 60.080 41.667 0.00 0.00 0.00 3.01
2243 2260 4.200092 AGTGTTTTCCCTCTCTTGTGTTC 58.800 43.478 0.00 0.00 0.00 3.18
2244 2261 4.200092 GAGTGTTTTCCCTCTCTTGTGTT 58.800 43.478 0.00 0.00 0.00 3.32
2245 2262 3.199946 TGAGTGTTTTCCCTCTCTTGTGT 59.800 43.478 0.00 0.00 0.00 3.72
2246 2263 3.808728 TGAGTGTTTTCCCTCTCTTGTG 58.191 45.455 0.00 0.00 0.00 3.33
2247 2264 4.503714 TTGAGTGTTTTCCCTCTCTTGT 57.496 40.909 0.00 0.00 0.00 3.16
2248 2265 6.039717 TCAATTTGAGTGTTTTCCCTCTCTTG 59.960 38.462 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.