Multiple sequence alignment - TraesCS5A01G319500

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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 TraesCS5A01G319500 chr5A 100.000 2480 0 0 1 2480 531398023 531395544 0.000000e+00 4580.0
1 TraesCS5A01G319500 chr5A 89.401 217 20 3 364 578 644353263 644353048 1.130000e-68 270.0
2 TraesCS5A01G319500 chr5A 96.471 85 3 0 2117 2201 531395823 531395907 9.250000e-30 141.0
3 TraesCS5A01G319500 chr5A 95.455 88 4 0 2114 2201 660790603 660790516 9.250000e-30 141.0
4 TraesCS5A01G319500 chr6A 96.657 2483 56 10 1 2480 604196224 604198682 0.000000e+00 4100.0
5 TraesCS5A01G319500 chr6A 91.163 215 17 2 363 576 25623555 25623342 8.680000e-75 291.0
6 TraesCS5A01G319500 chr6A 96.471 85 3 0 2117 2201 604198404 604198320 9.250000e-30 141.0
7 TraesCS5A01G319500 chr6B 88.753 818 64 13 977 1784 695834260 695835059 0.000000e+00 976.0
8 TraesCS5A01G319500 chr6B 86.182 550 70 6 1561 2108 649107899 649108444 7.640000e-165 590.0
9 TraesCS5A01G319500 chr6B 79.770 781 137 12 794 1563 649107009 649107779 4.660000e-152 547.0
10 TraesCS5A01G319500 chr6B 95.575 339 13 1 1781 2117 695840337 695840675 2.170000e-150 542.0
11 TraesCS5A01G319500 chr6B 97.849 279 6 0 2202 2480 695840677 695840955 1.330000e-132 483.0
12 TraesCS5A01G319500 chr6B 83.991 431 45 11 573 979 695821021 695821451 2.310000e-105 392.0
13 TraesCS5A01G319500 chr6B 88.433 268 31 0 2200 2467 649108452 649108719 8.550000e-85 324.0
14 TraesCS5A01G319500 chr6B 90.476 210 19 1 364 572 9364946 9365155 2.430000e-70 276.0
15 TraesCS5A01G319500 chr6B 95.455 88 4 0 2117 2204 187829333 187829246 9.250000e-30 141.0
16 TraesCS5A01G319500 chr6B 90.909 88 8 0 278 365 695820946 695821033 4.330000e-23 119.0
17 TraesCS5A01G319500 chr6D 94.737 342 11 2 1785 2119 457265074 457265415 2.180000e-145 525.0
18 TraesCS5A01G319500 chr6D 83.929 560 65 8 1561 2119 430706333 430706868 1.700000e-141 512.0
19 TraesCS5A01G319500 chr6D 97.509 281 7 0 2200 2480 457265413 457265693 4.800000e-132 481.0
20 TraesCS5A01G319500 chr6D 88.693 283 30 1 2200 2480 430706866 430707148 6.570000e-91 344.0
21 TraesCS5A01G319500 chr6D 91.441 222 13 1 573 794 457260266 457260481 1.440000e-77 300.0
22 TraesCS5A01G319500 chr6D 95.833 72 3 0 290 361 457260203 457260274 1.560000e-22 117.0
23 TraesCS5A01G319500 chr3A 90.821 207 18 1 364 569 290712318 290712524 2.430000e-70 276.0
24 TraesCS5A01G319500 chrUn 90.777 206 17 2 369 573 63263791 63263587 8.740000e-70 274.0
25 TraesCS5A01G319500 chrUn 95.402 87 4 0 2115 2201 100223737 100223823 3.330000e-29 139.0
26 TraesCS5A01G319500 chr4A 90.000 210 20 1 364 572 604639722 604639513 1.130000e-68 270.0
27 TraesCS5A01G319500 chr1A 90.000 210 20 1 364 572 402617218 402617427 1.130000e-68 270.0
28 TraesCS5A01G319500 chr1A 90.000 210 17 2 363 572 551528255 551528460 4.070000e-68 268.0
29 TraesCS5A01G319500 chr1B 96.591 88 3 0 2114 2201 328029465 328029552 1.990000e-31 147.0
30 TraesCS5A01G319500 chr2A 95.506 89 4 0 2113 2201 569281160 569281072 2.570000e-30 143.0
31 TraesCS5A01G319500 chr2A 96.471 85 3 0 2117 2201 709027584 709027668 9.250000e-30 141.0
32 TraesCS5A01G319500 chr3D 94.286 35 2 0 943 977 596080945 596080911 1.000000e-03 54.7


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 TraesCS5A01G319500 chr5A 531395544 531398023 2479 True 4580.0 4580 100.000 1 2480 1 chr5A.!!$R1 2479
1 TraesCS5A01G319500 chr6A 604196224 604198682 2458 False 4100.0 4100 96.657 1 2480 1 chr6A.!!$F1 2479
2 TraesCS5A01G319500 chr6B 695834260 695835059 799 False 976.0 976 88.753 977 1784 1 chr6B.!!$F2 807
3 TraesCS5A01G319500 chr6B 695840337 695840955 618 False 512.5 542 96.712 1781 2480 2 chr6B.!!$F5 699
4 TraesCS5A01G319500 chr6B 649107009 649108719 1710 False 487.0 590 84.795 794 2467 3 chr6B.!!$F3 1673
5 TraesCS5A01G319500 chr6B 695820946 695821451 505 False 255.5 392 87.450 278 979 2 chr6B.!!$F4 701
6 TraesCS5A01G319500 chr6D 457265074 457265693 619 False 503.0 525 96.123 1785 2480 2 chr6D.!!$F3 695
7 TraesCS5A01G319500 chr6D 430706333 430707148 815 False 428.0 512 86.311 1561 2480 2 chr6D.!!$F1 919


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
566 569 0.251474 AGAAGGAAGCATGCAAGCCA 60.251 50.0 21.98 0.0 34.23 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1860 2030 0.595588 CGCCCAGTGCACATTAACAA 59.404 50.0 21.04 0.0 41.33 2.83 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
86 88 2.045885 ACAGAATTCCCACCTCCTAGGA 59.954 50.000 11.98 11.98 37.67 2.94
118 120 1.841302 AAGAGTGCCGCCCTTCATGA 61.841 55.000 0.00 0.00 0.00 3.07
143 145 4.555709 TTCCAGGTTGCGTGCCGT 62.556 61.111 0.00 0.00 0.00 5.68
180 182 1.226802 CTCTGTGCCGTCCGATCTG 60.227 63.158 0.00 0.00 0.00 2.90
200 202 4.407694 TCGACGATGCGCAACCGA 62.408 61.111 32.21 25.15 36.29 4.69
257 259 4.812476 CGCGCTCGGGACCATCAA 62.812 66.667 5.56 0.00 0.00 2.57
262 264 1.447838 CTCGGGACCATCAACACGG 60.448 63.158 0.00 0.00 33.52 4.94
362 364 4.572571 TTTGCCTTGCGTCGGGGT 62.573 61.111 0.00 0.00 0.00 4.95
374 376 2.261671 CGGGGTGGACGAGACTTG 59.738 66.667 0.00 0.00 0.00 3.16
403 405 1.142965 CGTCGTGTGCCCATCCATA 59.857 57.895 0.00 0.00 0.00 2.74
435 437 4.298332 ACGTGGCTTGATTTGATTGAAAC 58.702 39.130 0.00 0.00 0.00 2.78
455 457 1.824852 CAAAATAAGGTCTGGCCCCAC 59.175 52.381 0.00 0.00 38.26 4.61
469 471 1.553651 GCCCCACCCCCTTAAAATCAA 60.554 52.381 0.00 0.00 0.00 2.57
471 473 2.466846 CCCACCCCCTTAAAATCAAGG 58.533 52.381 0.00 0.00 44.11 3.61
484 486 7.449704 CCTTAAAATCAAGGGGGAGATGATTAG 59.550 40.741 1.12 0.00 41.58 1.73
549 552 1.014044 GCACGGATGAAAGCACGAGA 61.014 55.000 0.00 0.00 0.00 4.04
550 553 1.428448 CACGGATGAAAGCACGAGAA 58.572 50.000 0.00 0.00 0.00 2.87
551 554 1.391485 CACGGATGAAAGCACGAGAAG 59.609 52.381 0.00 0.00 0.00 2.85
552 555 1.002366 CGGATGAAAGCACGAGAAGG 58.998 55.000 0.00 0.00 0.00 3.46
553 556 1.404181 CGGATGAAAGCACGAGAAGGA 60.404 52.381 0.00 0.00 0.00 3.36
554 557 2.699954 GGATGAAAGCACGAGAAGGAA 58.300 47.619 0.00 0.00 0.00 3.36
555 558 2.675348 GGATGAAAGCACGAGAAGGAAG 59.325 50.000 0.00 0.00 0.00 3.46
556 559 1.512926 TGAAAGCACGAGAAGGAAGC 58.487 50.000 0.00 0.00 0.00 3.86
557 560 1.202639 TGAAAGCACGAGAAGGAAGCA 60.203 47.619 0.00 0.00 0.00 3.91
558 561 2.079925 GAAAGCACGAGAAGGAAGCAT 58.920 47.619 0.00 0.00 0.00 3.79
559 562 1.446907 AAGCACGAGAAGGAAGCATG 58.553 50.000 0.00 0.00 0.00 4.06
560 563 1.023513 AGCACGAGAAGGAAGCATGC 61.024 55.000 10.51 10.51 0.00 4.06
561 564 1.300971 GCACGAGAAGGAAGCATGCA 61.301 55.000 21.98 0.00 0.00 3.96
566 569 0.251474 AGAAGGAAGCATGCAAGCCA 60.251 50.000 21.98 0.00 34.23 4.75
678 681 0.629058 ATTGGTCCCCATGTGGTACC 59.371 55.000 4.43 4.43 38.89 3.34
683 686 1.455587 CCCCATGTGGTACCCATGC 60.456 63.158 26.06 10.51 38.67 4.06
1056 1086 1.905354 GGCCAACAAGCTTGAGCCT 60.905 57.895 33.16 14.75 43.38 4.58
1237 1273 0.465278 GAAGAATGCAGAGGGCTCCC 60.465 60.000 0.00 0.00 45.15 4.30
1238 1274 1.210204 AAGAATGCAGAGGGCTCCCA 61.210 55.000 7.82 0.00 45.15 4.37
1239 1275 1.153005 GAATGCAGAGGGCTCCCAG 60.153 63.158 7.82 0.00 45.15 4.45
1240 1276 3.355957 AATGCAGAGGGCTCCCAGC 62.356 63.158 7.82 8.67 45.15 4.85
1435 1473 3.626930 TGTGGGTGCTTTCAGTTTACTT 58.373 40.909 0.00 0.00 0.00 2.24
1645 1807 6.872920 TGTTGTCTATTGGTTGCTTTTCTTT 58.127 32.000 0.00 0.00 0.00 2.52
1860 2030 7.826690 AGCAGAATTCACCGTAATTATTTTGT 58.173 30.769 8.44 0.00 0.00 2.83
2127 2300 0.831307 ATGGAAACTACTCCCTCCGC 59.169 55.000 0.00 0.00 34.22 5.54
2189 2362 7.148440 TGTCAAAAACGTTCTTATATTACGGGG 60.148 37.037 0.00 0.00 39.45 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 88 0.825010 CACTCTTGCCCACAAAGCCT 60.825 55.000 0.00 0.00 34.74 4.58
118 120 1.234615 CGCAACCTGGAAATGGACGT 61.235 55.000 0.00 0.00 0.00 4.34
143 145 2.059345 GAACCCCCGAAAGACCCACA 62.059 60.000 0.00 0.00 0.00 4.17
180 182 4.210304 GTTGCGCATCGTCGAGGC 62.210 66.667 21.24 21.24 35.92 4.70
362 364 2.159819 GAGCAGGCAAGTCTCGTCCA 62.160 60.000 0.00 0.00 0.00 4.02
363 365 1.446966 GAGCAGGCAAGTCTCGTCC 60.447 63.158 0.00 0.00 0.00 4.79
366 368 2.125350 GGGAGCAGGCAAGTCTCG 60.125 66.667 0.00 0.00 0.00 4.04
435 437 1.824852 GTGGGGCCAGACCTTATTTTG 59.175 52.381 4.39 0.00 39.10 2.44
447 449 1.456518 ATTTTAAGGGGGTGGGGCCA 61.457 55.000 4.39 0.00 39.65 5.36
458 460 5.129368 TCATCTCCCCCTTGATTTTAAGG 57.871 43.478 0.00 0.00 45.51 2.69
469 471 7.316841 TCTTTCTAATCTAATCATCTCCCCCT 58.683 38.462 0.00 0.00 0.00 4.79
471 473 9.853177 TTTTCTTTCTAATCTAATCATCTCCCC 57.147 33.333 0.00 0.00 0.00 4.81
502 504 6.993902 TCACTAAATCCTACGGTTGTCTTTTT 59.006 34.615 0.00 0.00 0.00 1.94
522 525 2.742053 GCTTTCATCCGTGCTTTCACTA 59.258 45.455 0.00 0.00 40.99 2.74
527 530 0.238289 CGTGCTTTCATCCGTGCTTT 59.762 50.000 0.00 0.00 0.00 3.51
528 531 0.602638 TCGTGCTTTCATCCGTGCTT 60.603 50.000 0.00 0.00 0.00 3.91
540 543 1.446907 CATGCTTCCTTCTCGTGCTT 58.553 50.000 0.00 0.00 0.00 3.91
549 552 0.251474 TCTGGCTTGCATGCTTCCTT 60.251 50.000 22.27 0.00 0.00 3.36
550 553 0.033405 ATCTGGCTTGCATGCTTCCT 60.033 50.000 22.27 4.81 0.00 3.36
551 554 0.384669 GATCTGGCTTGCATGCTTCC 59.615 55.000 22.27 16.53 0.00 3.46
552 555 0.384669 GGATCTGGCTTGCATGCTTC 59.615 55.000 22.27 14.04 0.00 3.86
553 556 0.033405 AGGATCTGGCTTGCATGCTT 60.033 50.000 22.27 6.98 0.00 3.91
554 557 0.752009 CAGGATCTGGCTTGCATGCT 60.752 55.000 22.27 4.22 0.00 3.79
555 558 1.734137 CAGGATCTGGCTTGCATGC 59.266 57.895 15.87 15.87 0.00 4.06
556 559 1.734137 GCAGGATCTGGCTTGCATG 59.266 57.895 0.00 0.00 40.23 4.06
557 560 1.822613 CGCAGGATCTGGCTTGCAT 60.823 57.895 0.00 0.00 40.49 3.96
558 561 2.437180 CGCAGGATCTGGCTTGCA 60.437 61.111 0.00 0.00 40.49 4.08
559 562 2.437359 ACGCAGGATCTGGCTTGC 60.437 61.111 7.39 0.00 37.50 4.01
560 563 2.169789 CGACGCAGGATCTGGCTTG 61.170 63.158 7.39 0.00 31.21 4.01
561 564 2.185350 CGACGCAGGATCTGGCTT 59.815 61.111 7.39 0.00 31.21 4.35
566 569 2.502492 CCATCCCGACGCAGGATCT 61.502 63.158 2.97 0.00 42.41 2.75
769 772 3.285407 GGACAACCACTACGTGACCGT 62.285 57.143 0.00 0.00 42.52 4.83
1056 1086 2.475466 CCCGTCGTAGCGCTCCTTA 61.475 63.158 16.34 0.00 0.00 2.69
1110 1140 0.250209 GATGCTCCATGATCGGTGCT 60.250 55.000 12.84 2.07 44.21 4.40
1237 1273 1.202627 GCTTAGAGACATGGGAGGCTG 60.203 57.143 0.00 0.00 0.00 4.85
1238 1274 1.127343 GCTTAGAGACATGGGAGGCT 58.873 55.000 0.00 0.00 0.00 4.58
1239 1275 0.249657 CGCTTAGAGACATGGGAGGC 60.250 60.000 0.00 0.00 0.00 4.70
1240 1276 0.249657 GCGCTTAGAGACATGGGAGG 60.250 60.000 0.00 0.00 0.00 4.30
1241 1277 0.749649 AGCGCTTAGAGACATGGGAG 59.250 55.000 2.64 0.00 0.00 4.30
1242 1278 0.747255 GAGCGCTTAGAGACATGGGA 59.253 55.000 13.26 0.00 0.00 4.37
1243 1279 0.596083 CGAGCGCTTAGAGACATGGG 60.596 60.000 13.26 0.00 0.00 4.00
1244 1280 0.382158 TCGAGCGCTTAGAGACATGG 59.618 55.000 13.26 0.00 0.00 3.66
1273 1311 5.784177 TCTTTTTCTCAACGAGAGCAGTAT 58.216 37.500 0.00 0.00 44.35 2.12
1357 1395 0.036164 CCCGTGACAATCCAGGAACA 59.964 55.000 0.00 0.00 0.00 3.18
1435 1473 4.082625 CCTTGTACGCGTGGGTATATATGA 60.083 45.833 24.59 0.00 0.00 2.15
1645 1807 3.181495 CGCAAAGACCAACTACACCAAAA 60.181 43.478 0.00 0.00 0.00 2.44
1710 1873 4.995920 GCTTAGCGATCACTCGTTTTATC 58.004 43.478 0.00 0.00 46.71 1.75
1806 1969 0.690762 GGAGAAGCCACCCACAACTA 59.309 55.000 0.00 0.00 36.34 2.24
1860 2030 0.595588 CGCCCAGTGCACATTAACAA 59.404 50.000 21.04 0.00 41.33 2.83
2127 2300 7.148440 TGTCAAAAACGTTCTTATATTACGGGG 60.148 37.037 0.00 0.00 39.45 5.73
2189 2362 2.578586 TACCCAGGTACTCCCTCCGC 62.579 65.000 0.00 0.00 43.86 5.54
2221 2394 5.297776 GCATGCTATTGTTACTCACCAATCT 59.702 40.000 11.37 0.00 33.54 2.40



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

AutoCloner maintained by Alex Coulton.