Multiple sequence alignment - TraesCS3B01G460100

Loading Multiple Alignment...

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 TraesCS3B01G460100 chr3B 100.000 2489 0 0 1 2489 703847025 703849513 0.000000e+00 4597
1 TraesCS3B01G460100 chr3B 82.429 700 83 18 1457 2125 650604231 650603541 2.150000e-160 575
2 TraesCS3B01G460100 chr3B 82.019 317 46 8 2126 2441 650603620 650603314 2.460000e-65 259
3 TraesCS3B01G460100 chr3B 86.387 191 23 2 518 708 17323452 17323265 3.240000e-49 206
4 TraesCS3B01G460100 chr3B 84.896 192 27 1 518 709 679709257 679709446 2.530000e-45 193
5 TraesCS3B01G460100 chr3B 84.967 153 15 5 1 145 680240089 680239937 5.550000e-32 148
6 TraesCS3B01G460100 chr3A 98.275 1971 31 2 519 2489 451665428 451663461 0.000000e+00 3448
7 TraesCS3B01G460100 chr3A 98.266 1961 33 1 529 2489 451657605 451659564 0.000000e+00 3432
8 TraesCS3B01G460100 chr3A 95.890 1971 52 3 519 2489 259837722 259839663 0.000000e+00 3164
9 TraesCS3B01G460100 chr3A 81.293 294 47 5 2136 2427 631283728 631283441 5.350000e-57 231
10 TraesCS3B01G460100 chr4A 90.986 1653 91 21 519 2125 703410863 703412503 0.000000e+00 2174
11 TraesCS3B01G460100 chr4A 92.603 365 23 2 2126 2489 703412425 703412786 2.840000e-144 521
12 TraesCS3B01G460100 chr5A 97.811 1142 22 2 519 1660 525733057 525734195 0.000000e+00 1967
13 TraesCS3B01G460100 chr5A 97.974 839 16 1 1651 2489 525734619 525735456 0.000000e+00 1454
14 TraesCS3B01G460100 chr5A 85.185 189 25 2 520 708 65999575 65999390 9.090000e-45 191
15 TraesCS3B01G460100 chr5A 97.590 83 2 0 2043 2125 525735093 525735175 2.580000e-30 143
16 TraesCS3B01G460100 chr5A 95.062 81 4 0 2126 2206 525735012 525735092 7.230000e-26 128
17 TraesCS3B01G460100 chr2A 86.546 498 37 5 942 1412 156666924 156667418 2.840000e-144 521
18 TraesCS3B01G460100 chr2A 84.974 386 54 2 138 520 24890594 24890978 3.000000e-104 388
19 TraesCS3B01G460100 chr2A 86.093 151 14 4 1 144 205198786 205198636 3.310000e-34 156
20 TraesCS3B01G460100 chr2D 86.583 477 37 6 945 1394 145363893 145363417 3.700000e-138 501
21 TraesCS3B01G460100 chr2B 85.744 477 41 10 945 1394 202921393 202920917 1.730000e-131 479
22 TraesCS3B01G460100 chr2B 82.298 322 30 16 1 298 153588882 153588564 1.140000e-63 254
23 TraesCS3B01G460100 chr2B 86.294 197 20 4 1933 2125 435339888 435340081 9.020000e-50 207
24 TraesCS3B01G460100 chr2B 88.806 134 10 4 1 129 438926322 438926189 2.560000e-35 159
25 TraesCS3B01G460100 chr5D 87.306 386 44 3 138 520 499237258 499236875 1.060000e-118 436
26 TraesCS3B01G460100 chr5D 87.681 138 8 5 1 129 499237463 499237326 4.290000e-33 152
27 TraesCS3B01G460100 chr7A 85.827 381 48 4 138 514 166723802 166724180 1.390000e-107 399
28 TraesCS3B01G460100 chr7A 87.075 147 12 5 1 140 166723599 166723745 2.560000e-35 159
29 TraesCS3B01G460100 chr7A 88.060 134 11 5 1 129 183487422 183487289 1.190000e-33 154
30 TraesCS3B01G460100 chr7A 87.681 138 8 6 1 129 463291194 463291057 4.290000e-33 152
31 TraesCS3B01G460100 chr6A 85.789 380 50 3 138 514 20280346 20279968 1.390000e-107 399
32 TraesCS3B01G460100 chr6A 84.677 372 49 6 148 514 583024621 583024989 5.060000e-97 364
33 TraesCS3B01G460100 chr6A 83.420 386 60 4 138 520 86441430 86441046 3.040000e-94 355
34 TraesCS3B01G460100 chr5B 85.789 380 50 2 138 514 577939296 577939674 1.390000e-107 399
35 TraesCS3B01G460100 chr5B 85.233 386 47 7 138 514 41955000 41954616 3.000000e-104 388
36 TraesCS3B01G460100 chr1B 85.789 380 49 3 138 514 60344245 60344622 4.990000e-107 398
37 TraesCS3B01G460100 chr1B 86.339 366 39 9 2126 2489 463545464 463545108 3.000000e-104 388
38 TraesCS3B01G460100 chr1B 87.037 216 21 5 1914 2125 463545597 463545385 1.150000e-58 237
39 TraesCS3B01G460100 chr3D 79.545 308 51 7 2126 2427 487395370 487395069 2.510000e-50 209
40 TraesCS3B01G460100 chr6B 86.294 197 20 4 1933 2125 208902052 208901859 9.020000e-50 207
41 TraesCS3B01G460100 chr6B 80.682 264 43 5 518 780 216416156 216416412 5.430000e-47 198
42 TraesCS3B01G460100 chr7D 84.577 201 22 6 1927 2125 627269142 627269335 9.090000e-45 191
43 TraesCS3B01G460100 chr7D 80.508 236 33 9 2126 2359 627269257 627269481 4.260000e-38 169
44 TraesCS3B01G460100 chr7D 84.868 152 14 8 1 145 626045056 626045205 7.170000e-31 145
45 TraesCS3B01G460100 chr1A 81.095 201 29 6 1927 2125 557329685 557329492 4.290000e-33 152
46 TraesCS3B01G460100 chr7B 81.452 124 20 3 663 786 63381522 63381642 5.670000e-17 99


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 TraesCS3B01G460100 chr3B 703847025 703849513 2488 False 4597.0 4597 100.00000 1 2489 1 chr3B.!!$F2 2488
1 TraesCS3B01G460100 chr3B 650603314 650604231 917 True 417.0 575 82.22400 1457 2441 2 chr3B.!!$R3 984
2 TraesCS3B01G460100 chr3A 451663461 451665428 1967 True 3448.0 3448 98.27500 519 2489 1 chr3A.!!$R1 1970
3 TraesCS3B01G460100 chr3A 451657605 451659564 1959 False 3432.0 3432 98.26600 529 2489 1 chr3A.!!$F2 1960
4 TraesCS3B01G460100 chr3A 259837722 259839663 1941 False 3164.0 3164 95.89000 519 2489 1 chr3A.!!$F1 1970
5 TraesCS3B01G460100 chr4A 703410863 703412786 1923 False 1347.5 2174 91.79450 519 2489 2 chr4A.!!$F1 1970
6 TraesCS3B01G460100 chr5A 525733057 525735456 2399 False 923.0 1967 97.10925 519 2489 4 chr5A.!!$F1 1970
7 TraesCS3B01G460100 chr5D 499236875 499237463 588 True 294.0 436 87.49350 1 520 2 chr5D.!!$R1 519
8 TraesCS3B01G460100 chr7A 166723599 166724180 581 False 279.0 399 86.45100 1 514 2 chr7A.!!$F1 513

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
312 381 1.630369 ACACAGCTGATCAGGCCTTAA 59.370 47.619 23.35 0.00 0.0 1.85 F
315 384 2.240667 ACAGCTGATCAGGCCTTAATGT 59.759 45.455 23.35 12.32 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1143 1236 1.138859 TGGAAGCCTATGATGTGGTCG 59.861 52.381 0.0 0.0 0.0 4.79 R
2154 2728 2.882927 ACTGCTCAACAACGACACTA 57.117 45.000 0.0 0.0 0.0 2.74 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
175 244 9.686683 GGAGTATTAATTAGCATATGGTTCCAT 57.313 33.333 13.49 9.37 0.00 3.41
185 254 4.036262 GCATATGGTTCCATGCGTAAGAAA 59.964 41.667 13.86 0.00 38.31 2.52
189 258 2.412325 GGTTCCATGCGTAAGAAACACG 60.412 50.000 1.91 0.00 42.24 4.49
190 259 2.442212 TCCATGCGTAAGAAACACGA 57.558 45.000 0.00 0.00 41.91 4.35
194 263 3.370978 CCATGCGTAAGAAACACGATCTT 59.629 43.478 0.00 0.00 41.91 2.40
211 280 9.268268 ACACGATCTTTAACTGAACTTAATTGA 57.732 29.630 0.00 0.00 0.00 2.57
276 345 8.301730 TGTAAAGATACTTTGGTTAGTTGTCG 57.698 34.615 6.95 0.00 32.98 4.35
305 374 3.488678 CGCTTATGTACACAGCTGATCAG 59.511 47.826 23.35 18.84 0.00 2.90
312 381 1.630369 ACACAGCTGATCAGGCCTTAA 59.370 47.619 23.35 0.00 0.00 1.85
314 383 2.617308 CACAGCTGATCAGGCCTTAATG 59.383 50.000 23.35 11.77 0.00 1.90
315 384 2.240667 ACAGCTGATCAGGCCTTAATGT 59.759 45.455 23.35 12.32 0.00 2.71
316 385 3.455910 ACAGCTGATCAGGCCTTAATGTA 59.544 43.478 23.35 0.00 0.00 2.29
317 386 4.103785 ACAGCTGATCAGGCCTTAATGTAT 59.896 41.667 23.35 0.00 0.00 2.29
318 387 5.068636 CAGCTGATCAGGCCTTAATGTATT 58.931 41.667 23.89 0.00 0.00 1.89
320 389 6.370994 CAGCTGATCAGGCCTTAATGTATTAG 59.629 42.308 23.89 0.00 0.00 1.73
381 453 8.174085 ACTAGTACTATTATGCCTTGATCCTCT 58.826 37.037 2.33 0.00 0.00 3.69
388 460 4.792513 ATGCCTTGATCCTCTCATTTCT 57.207 40.909 0.00 0.00 32.72 2.52
400 472 4.141959 CCTCTCATTTCTGTCTCTTCCTCC 60.142 50.000 0.00 0.00 0.00 4.30
437 509 3.094572 ACATGCTTCATTCCCTTTCCTG 58.905 45.455 0.00 0.00 0.00 3.86
439 511 3.243359 TGCTTCATTCCCTTTCCTGTT 57.757 42.857 0.00 0.00 0.00 3.16
523 595 3.225177 CCATCTGAATGGCCAATCTCT 57.775 47.619 21.32 3.67 45.88 3.10
524 596 4.362470 CCATCTGAATGGCCAATCTCTA 57.638 45.455 21.32 7.47 45.88 2.43
525 597 4.070716 CCATCTGAATGGCCAATCTCTAC 58.929 47.826 21.32 3.68 45.88 2.59
526 598 4.202440 CCATCTGAATGGCCAATCTCTACT 60.202 45.833 21.32 0.00 45.88 2.57
527 599 5.012458 CCATCTGAATGGCCAATCTCTACTA 59.988 44.000 21.32 0.00 45.88 1.82
1143 1236 4.292178 CTCCGCTCCCTCCATCGC 62.292 72.222 0.00 0.00 0.00 4.58
1235 1328 2.048222 CAACTCGGCGAGCCTTCA 60.048 61.111 34.76 0.00 32.04 3.02
1459 1563 2.035961 TCTCACACTTCTTGGTTCGGAG 59.964 50.000 0.00 0.00 0.00 4.63
2154 2728 1.611673 CCTGACAAATTGCTCCCTCGT 60.612 52.381 0.00 0.00 0.00 4.18
2165 2739 0.879765 CTCCCTCGTAGTGTCGTTGT 59.120 55.000 0.00 0.00 0.00 3.32
2288 2864 1.639722 ACAACCAATTTACCCCCTGC 58.360 50.000 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 6.589535 TGCATTGCATTGTGAAACAGAGGG 62.590 45.833 7.38 0.00 40.74 4.30
52 54 9.621629 TTTATTCTAGAAACTTGGTCAAAGACA 57.378 29.630 9.71 0.00 39.38 3.41
54 56 9.847224 AGTTTATTCTAGAAACTTGGTCAAAGA 57.153 29.630 9.71 0.00 43.03 2.52
145 214 8.686739 ACCATATGCTAATTAATACTCCCTCT 57.313 34.615 0.00 0.00 0.00 3.69
175 244 5.693104 AGTTAAAGATCGTGTTTCTTACGCA 59.307 36.000 0.00 0.00 41.08 5.24
178 247 8.762426 AGTTCAGTTAAAGATCGTGTTTCTTAC 58.238 33.333 0.00 0.00 33.17 2.34
185 254 9.268268 TCAATTAAGTTCAGTTAAAGATCGTGT 57.732 29.630 0.00 0.00 0.00 4.49
254 323 5.180680 GGCGACAACTAACCAAAGTATCTTT 59.819 40.000 0.00 0.00 0.00 2.52
261 330 0.515564 CCGGCGACAACTAACCAAAG 59.484 55.000 9.30 0.00 0.00 2.77
270 339 3.919973 TAAGCGACCCGGCGACAAC 62.920 63.158 9.30 0.00 38.18 3.32
273 342 2.340453 TACATAAGCGACCCGGCGAC 62.340 60.000 9.30 0.00 38.18 5.19
276 345 1.142314 TGTACATAAGCGACCCGGC 59.858 57.895 0.00 0.00 0.00 6.13
328 400 9.199982 GATTGATCACAGTTTTCATTTGAATGT 57.800 29.630 0.00 0.00 37.65 2.71
346 418 9.314133 AGGCATAATAGTACTAGTGATTGATCA 57.686 33.333 12.98 0.00 0.00 2.92
358 430 7.013220 TGAGAGGATCAAGGCATAATAGTACT 58.987 38.462 0.00 0.00 37.82 2.73
369 441 3.876320 GACAGAAATGAGAGGATCAAGGC 59.124 47.826 0.00 0.00 42.53 4.35
370 442 5.129155 AGAGACAGAAATGAGAGGATCAAGG 59.871 44.000 0.00 0.00 42.53 3.61
381 453 5.832221 TCTAGGAGGAAGAGACAGAAATGA 58.168 41.667 0.00 0.00 0.00 2.57
400 472 3.067461 AGCATGTTTCTAGCGACCTCTAG 59.933 47.826 0.00 0.00 37.87 2.43
407 479 3.623060 GGAATGAAGCATGTTTCTAGCGA 59.377 43.478 21.00 3.13 0.00 4.93
413 485 4.221482 AGGAAAGGGAATGAAGCATGTTTC 59.779 41.667 14.76 14.76 0.00 2.78
437 509 3.691049 TGCTTTGCACTGACTAACAAC 57.309 42.857 0.00 0.00 31.71 3.32
439 511 4.227512 CAATGCTTTGCACTGACTAACA 57.772 40.909 0.00 0.00 38.06 2.41
894 973 3.625897 TGGTGCTGCTGCTACGGT 61.626 61.111 17.00 0.00 40.48 4.83
926 1008 0.536006 GTTGCTGCTGTTCCTCCTGT 60.536 55.000 0.00 0.00 0.00 4.00
1143 1236 1.138859 TGGAAGCCTATGATGTGGTCG 59.861 52.381 0.00 0.00 0.00 4.79
2154 2728 2.882927 ACTGCTCAACAACGACACTA 57.117 45.000 0.00 0.00 0.00 2.74
2165 2739 6.109156 TGTACATCCTTTCTAACTGCTCAA 57.891 37.500 0.00 0.00 0.00 3.02
2231 2807 4.949856 AGGAAAAGACTTGCACTCTTTTGA 59.050 37.500 25.64 0.00 44.41 2.69
2234 2810 3.067320 GCAGGAAAAGACTTGCACTCTTT 59.933 43.478 11.30 11.30 41.41 2.52
2288 2864 7.710475 ACAAGAACATAAAATTGGGTTCACTTG 59.290 33.333 0.00 0.00 41.49 3.16


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

AutoCloner maintained by Alex Coulton.