Multiple sequence alignment - TraesCS1D01G259000

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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 TraesCS1D01G259000 chr1D 100.000 4545 0 0 1 4545 351443348 351438804 0.000000e+00 8394
1 TraesCS1D01G259000 chr1B 94.279 4300 122 37 315 4545 474121307 474117063 0.000000e+00 6464
2 TraesCS1D01G259000 chr1B 90.966 321 9 5 1 321 474121638 474121338 9.100000e-112 414
3 TraesCS1D01G259000 chr1B 95.763 118 2 2 2296 2413 573578298 573578184 2.160000e-43 187
4 TraesCS1D01G259000 chr1A 93.295 4325 146 60 319 4545 452284443 452280165 0.000000e+00 6248
5 TraesCS1D01G259000 chr1A 91.154 260 14 2 17 267 452284789 452284530 1.210000e-90 344
6 TraesCS1D01G259000 chr3D 85.714 273 23 6 3275 3532 532938005 532938276 1.610000e-69 274
7 TraesCS1D01G259000 chr3A 85.892 241 23 7 2726 2956 668686670 668686909 3.510000e-61 246
8 TraesCS1D01G259000 chr3A 89.447 199 11 4 3343 3532 668688061 668688258 4.540000e-60 243


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 TraesCS1D01G259000 chr1D 351438804 351443348 4544 True 8394.0 8394 100.0000 1 4545 1 chr1D.!!$R1 4544
1 TraesCS1D01G259000 chr1B 474117063 474121638 4575 True 3439.0 6464 92.6225 1 4545 2 chr1B.!!$R2 4544
2 TraesCS1D01G259000 chr1A 452280165 452284789 4624 True 3296.0 6248 92.2245 17 4545 2 chr1A.!!$R1 4528
3 TraesCS1D01G259000 chr3A 668686670 668688258 1588 False 244.5 246 87.6695 2726 3532 2 chr3A.!!$F1 806

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
235 250 0.448197 GAGAGTGCATGTCGACTCGA 59.552 55.000 17.92 0.0 42.93 4.04 F
422 525 0.669318 CGCGGGTAGCTCTTGTTCAA 60.669 55.000 0.00 0.0 45.59 2.69 F
1356 1546 0.748729 AGGATGACGACTCCGACTCC 60.749 60.000 0.00 0.0 37.88 3.85 F
1515 1714 2.283809 GAGGAGCTGGAGGCCCTA 59.716 66.667 0.00 0.0 40.17 3.53 F
1539 1738 2.333688 ACGAGATCGATGAGGAGTCA 57.666 50.000 0.54 0.0 43.02 3.41 F
3207 3515 0.798776 AGAAATCAAGGCTTCGTGCG 59.201 50.000 0.00 0.0 44.05 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1539 1738 1.265454 GGACCTCCCCAACGATCTGT 61.265 60.000 0.00 0.0 0.00 3.41 R
2056 2259 1.552337 AGTGCAGATGGACTGGTACTG 59.448 52.381 6.17 0.0 45.18 2.74 R
2752 2957 0.250727 CCTCTTGTTTCCAAGGCGGA 60.251 55.000 2.88 0.0 46.65 5.54 R
3207 3515 0.251354 TGACTCCTGATGAAGGCTGC 59.749 55.000 0.00 0.0 46.92 5.25 R
3315 3627 2.813754 CGAACCATTTTCAGCTTCCTGA 59.186 45.455 0.00 0.0 46.03 3.86 R
4329 5445 0.677098 TAAATGGTGCGCGGGCTTTA 60.677 50.000 25.62 17.4 40.82 1.85 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
37 38 7.819415 TCATTTCAGTAATGGAGTAGTGAACAG 59.181 37.037 4.32 1.80 41.14 3.16
80 89 5.934781 AGGGATATTTGGTGAGATGAGAAC 58.065 41.667 0.00 0.00 0.00 3.01
169 184 9.774413 GTAGTTAATGCCAGTACCAAACTATAT 57.226 33.333 0.00 0.00 35.76 0.86
171 186 9.774413 AGTTAATGCCAGTACCAAACTATATAC 57.226 33.333 0.00 0.00 35.76 1.47
172 187 9.774413 GTTAATGCCAGTACCAAACTATATACT 57.226 33.333 0.00 0.00 35.76 2.12
235 250 0.448197 GAGAGTGCATGTCGACTCGA 59.552 55.000 17.92 0.00 42.93 4.04
322 396 2.033299 TGCACAAGGAAAAGAAGCGAAG 59.967 45.455 0.00 0.00 0.00 3.79
402 505 4.779733 AGGGAGGGGTCGTCGCAT 62.780 66.667 7.26 0.00 34.46 4.73
403 506 4.222847 GGGAGGGGTCGTCGCATC 62.223 72.222 2.99 2.99 36.76 3.91
404 507 4.570663 GGAGGGGTCGTCGCATCG 62.571 72.222 5.45 0.00 38.01 3.84
422 525 0.669318 CGCGGGTAGCTCTTGTTCAA 60.669 55.000 0.00 0.00 45.59 2.69
520 635 3.925090 GTCCCTATCCACCCGCCG 61.925 72.222 0.00 0.00 0.00 6.46
557 673 3.717294 CCCGACCCTTCCTGGTGG 61.717 72.222 0.00 0.00 39.24 4.61
795 928 3.805971 ACTCGGTTTTCTCGATTCGTTTT 59.194 39.130 5.89 0.00 36.01 2.43
796 929 4.084693 ACTCGGTTTTCTCGATTCGTTTTC 60.085 41.667 5.89 0.00 36.01 2.29
797 930 4.053295 TCGGTTTTCTCGATTCGTTTTCT 58.947 39.130 5.89 0.00 0.00 2.52
817 978 6.968004 TTCTGTTCGTCGATTTGATTTTTG 57.032 33.333 0.00 0.00 0.00 2.44
916 1088 2.796031 CCGCGGCGTAGTAATAATTTCA 59.204 45.455 22.00 0.00 0.00 2.69
970 1157 4.608948 AGTAGTGCTAGCTGTTTGTTCT 57.391 40.909 17.23 4.33 0.00 3.01
1356 1546 0.748729 AGGATGACGACTCCGACTCC 60.749 60.000 0.00 0.00 37.88 3.85
1515 1714 2.283809 GAGGAGCTGGAGGCCCTA 59.716 66.667 0.00 0.00 40.17 3.53
1539 1738 2.333688 ACGAGATCGATGAGGAGTCA 57.666 50.000 0.54 0.00 43.02 3.41
1602 1801 2.733227 GCACAAGCAAGACCATGTATGC 60.733 50.000 0.00 0.00 41.58 3.14
1785 1987 4.823989 GTCTCCACGCTTAAGGTACCTATA 59.176 45.833 16.67 7.26 0.00 1.31
1786 1988 5.476254 GTCTCCACGCTTAAGGTACCTATAT 59.524 44.000 16.67 1.66 0.00 0.86
1787 1989 6.656693 GTCTCCACGCTTAAGGTACCTATATA 59.343 42.308 16.67 0.49 0.00 0.86
1788 1990 7.338957 GTCTCCACGCTTAAGGTACCTATATAT 59.661 40.741 16.67 0.79 0.00 0.86
1824 2026 6.037172 GCATACGAGATATCTGGTTTTGTTGT 59.963 38.462 23.22 4.41 36.35 3.32
1942 2144 2.724377 CTCGCGCTGGCTCTCATA 59.276 61.111 5.56 0.00 36.88 2.15
1960 2162 6.341316 TCTCATACAGTAAGCTTCATGAACC 58.659 40.000 15.63 0.00 0.00 3.62
2041 2243 5.649831 AGGCAAATTACTTCTCTCATGTTCC 59.350 40.000 0.00 0.00 0.00 3.62
2056 2259 5.768317 TCATGTTCCGAAAAGATTTTGACC 58.232 37.500 0.00 0.00 0.00 4.02
2085 2288 3.126831 GTCCATCTGCACTGCTACATAC 58.873 50.000 1.98 0.00 0.00 2.39
2090 2293 2.825532 TCTGCACTGCTACATACTCACA 59.174 45.455 1.98 0.00 0.00 3.58
2106 2309 8.567948 ACATACTCACAATTTACCTTTGTTCAG 58.432 33.333 0.00 0.00 35.18 3.02
2131 2334 7.605309 AGCATCCCAAAGAAAAATGAGAAAATC 59.395 33.333 0.00 0.00 0.00 2.17
2274 2477 3.539604 CCTTGCAGGTAAAGGATCTGAG 58.460 50.000 0.00 0.00 46.08 3.35
2433 2636 4.945543 CCTTCTGTTGTGGATGATGATGAA 59.054 41.667 0.00 0.00 0.00 2.57
2556 2759 8.621532 TCTTGCTATCTGAATTGTTTTAGTGT 57.378 30.769 0.00 0.00 0.00 3.55
2557 2760 8.721478 TCTTGCTATCTGAATTGTTTTAGTGTC 58.279 33.333 0.00 0.00 0.00 3.67
2752 2957 5.237996 CAGACTTGAGACACAACAATGATGT 59.762 40.000 0.00 0.00 43.14 3.06
2753 2958 5.468072 AGACTTGAGACACAACAATGATGTC 59.532 40.000 0.00 1.48 39.40 3.06
3207 3515 0.798776 AGAAATCAAGGCTTCGTGCG 59.201 50.000 0.00 0.00 44.05 5.34
3315 3627 1.407979 CGTAGGCTCCAGGAACGTTAT 59.592 52.381 0.00 0.00 0.00 1.89
3340 4433 3.555518 GAAGCTGAAAATGGTTCGTGTC 58.444 45.455 0.00 0.00 33.30 3.67
3457 4565 3.181465 CGATACAAGTAATGGAGCTGGGT 60.181 47.826 0.00 0.00 0.00 4.51
3621 4730 3.181472 CCAAAAGGAAGCAGCTGAACTTT 60.181 43.478 20.43 17.02 0.00 2.66
3634 4743 1.341482 TGAACTTTGTTGCCAGGACCA 60.341 47.619 0.00 0.00 0.00 4.02
3756 4869 0.393402 ATGCATTCTCCGCTCTTGCA 60.393 50.000 0.00 0.00 46.22 4.08
3959 5072 0.768622 TTCCGTGGGACATTCTTGGT 59.231 50.000 0.00 0.00 44.52 3.67
4194 5309 6.967199 GGTTGCAAATTTCTAAGTTATCCTCG 59.033 38.462 0.00 0.00 0.00 4.63
4198 5313 6.354130 CAAATTTCTAAGTTATCCTCGGGGA 58.646 40.000 6.42 6.42 46.81 4.81
4219 5334 6.405842 GGGGAAAATTGCTTAGTTGTATGGAG 60.406 42.308 0.00 0.00 0.00 3.86
4233 5348 3.523157 TGTATGGAGAAGATGGGAGCAAA 59.477 43.478 0.00 0.00 0.00 3.68
4354 5470 1.588674 CCGCGCACCATTTATTCCTA 58.411 50.000 8.75 0.00 0.00 2.94
4483 5599 3.346631 CTTGTGAGCCGGCCATTGC 62.347 63.158 26.15 10.03 0.00 3.56
4509 5632 1.690633 TGGTCTGGCTCCAGGATCC 60.691 63.158 15.32 2.48 43.75 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 7.169158 TCCCTCCAAATCAATCAAACATAAC 57.831 36.000 0.00 0.00 0.00 1.89
80 89 4.268405 GTGCCAATTGATTGCCTAATTTCG 59.732 41.667 7.12 0.00 36.48 3.46
169 184 5.310451 CCCTGGTTTTGTTTAGCAGTAGTA 58.690 41.667 0.00 0.00 38.99 1.82
170 185 4.142038 CCCTGGTTTTGTTTAGCAGTAGT 58.858 43.478 0.00 0.00 38.99 2.73
171 186 3.506067 CCCCTGGTTTTGTTTAGCAGTAG 59.494 47.826 0.00 0.00 38.99 2.57
172 187 3.138653 TCCCCTGGTTTTGTTTAGCAGTA 59.861 43.478 0.00 0.00 38.99 2.74
173 188 2.091555 TCCCCTGGTTTTGTTTAGCAGT 60.092 45.455 0.00 0.00 38.99 4.40
240 255 4.324991 GGTTTGACCCCGCCGAGT 62.325 66.667 0.00 0.00 30.04 4.18
305 337 1.400242 CCGCTTCGCTTCTTTTCCTTG 60.400 52.381 0.00 0.00 0.00 3.61
387 490 4.570663 CGATGCGACGACCCCTCC 62.571 72.222 0.00 0.00 35.09 4.30
399 502 2.107141 AAGAGCTACCCGCGATGC 59.893 61.111 8.23 6.05 45.59 3.91
400 503 0.460284 AACAAGAGCTACCCGCGATG 60.460 55.000 8.23 0.00 45.59 3.84
401 504 0.179108 GAACAAGAGCTACCCGCGAT 60.179 55.000 8.23 0.00 45.59 4.58
402 505 1.214589 GAACAAGAGCTACCCGCGA 59.785 57.895 8.23 0.00 45.59 5.87
403 506 0.669318 TTGAACAAGAGCTACCCGCG 60.669 55.000 0.00 0.00 45.59 6.46
404 507 1.739067 ATTGAACAAGAGCTACCCGC 58.261 50.000 0.00 0.00 39.57 6.13
405 508 3.309954 GCTAATTGAACAAGAGCTACCCG 59.690 47.826 13.41 0.00 33.12 5.28
406 509 4.333926 CAGCTAATTGAACAAGAGCTACCC 59.666 45.833 19.20 0.00 39.86 3.69
407 510 4.201861 GCAGCTAATTGAACAAGAGCTACC 60.202 45.833 19.20 12.95 39.86 3.18
408 511 4.493220 CGCAGCTAATTGAACAAGAGCTAC 60.493 45.833 19.20 15.16 39.86 3.58
458 561 2.482333 CCGAGCCCACGAGGACTAG 61.482 68.421 0.00 0.00 38.24 2.57
573 689 2.503382 GGGGAGAAGGCGAGGCTAG 61.503 68.421 0.00 0.00 0.00 3.42
574 690 2.444140 GGGGAGAAGGCGAGGCTA 60.444 66.667 0.00 0.00 0.00 3.93
760 893 0.886563 ACCGAGTCGAGTTGGGTTAG 59.113 55.000 27.00 5.47 0.00 2.34
761 894 1.331214 AACCGAGTCGAGTTGGGTTA 58.669 50.000 27.00 0.00 39.10 2.85
795 928 5.448438 CCAAAAATCAAATCGACGAACAGA 58.552 37.500 0.00 0.00 0.00 3.41
796 929 4.616802 CCCAAAAATCAAATCGACGAACAG 59.383 41.667 0.00 0.00 0.00 3.16
797 930 4.541779 CCCAAAAATCAAATCGACGAACA 58.458 39.130 0.00 0.00 0.00 3.18
916 1088 1.968050 CTCCGCCGATTACCCCTTGT 61.968 60.000 0.00 0.00 0.00 3.16
1427 1617 2.363018 CGTCCTGCTCCTCCTCCA 60.363 66.667 0.00 0.00 0.00 3.86
1515 1714 2.099921 CTCCTCATCGATCTCGTTGGTT 59.900 50.000 0.00 0.00 38.98 3.67
1539 1738 1.265454 GGACCTCCCCAACGATCTGT 61.265 60.000 0.00 0.00 0.00 3.41
1602 1801 3.883830 AGAACTGCACAGATAGGAGTG 57.116 47.619 4.31 0.00 37.74 3.51
1618 1817 6.095377 CAGGTTTAGCAATGAATGGAAGAAC 58.905 40.000 0.00 0.00 0.00 3.01
1804 2006 9.277565 CAAATAACAACAAAACCAGATATCTCG 57.722 33.333 1.03 0.00 0.00 4.04
1824 2026 6.706295 CCCCAAAGATAAGCAAACCAAATAA 58.294 36.000 0.00 0.00 0.00 1.40
2041 2243 5.238650 ACTGGTACTGGTCAAAATCTTTTCG 59.761 40.000 0.00 0.00 0.00 3.46
2056 2259 1.552337 AGTGCAGATGGACTGGTACTG 59.448 52.381 6.17 0.00 45.18 2.74
2085 2288 5.830912 TGCTGAACAAAGGTAAATTGTGAG 58.169 37.500 0.00 0.00 39.98 3.51
2090 2293 4.837860 TGGGATGCTGAACAAAGGTAAATT 59.162 37.500 0.00 0.00 0.00 1.82
2106 2309 7.388500 TGATTTTCTCATTTTTCTTTGGGATGC 59.612 33.333 0.00 0.00 0.00 3.91
2131 2334 3.057969 TGGACTCATGCTAACAAGGTG 57.942 47.619 0.00 0.00 0.00 4.00
2556 2759 8.780846 TGGAAGTTAATTAGCTTATTGTTCGA 57.219 30.769 13.78 3.71 0.00 3.71
2752 2957 0.250727 CCTCTTGTTTCCAAGGCGGA 60.251 55.000 2.88 0.00 46.65 5.54
2753 2958 1.244019 CCCTCTTGTTTCCAAGGCGG 61.244 60.000 2.88 4.32 46.65 6.13
3207 3515 0.251354 TGACTCCTGATGAAGGCTGC 59.749 55.000 0.00 0.00 46.92 5.25
3315 3627 2.813754 CGAACCATTTTCAGCTTCCTGA 59.186 45.455 0.00 0.00 46.03 3.86
3340 4433 9.701355 AAAAGAAAATATTGCAACAAAAAGACG 57.299 25.926 0.00 0.00 0.00 4.18
3392 4500 3.380637 GCGGATGGAAGAGTACAGTTAGA 59.619 47.826 0.00 0.00 0.00 2.10
3457 4565 6.614694 TTACTCTTAGGCTTTGGTATGTCA 57.385 37.500 0.00 0.00 0.00 3.58
3756 4869 0.618968 AACTCTCCCGAGCTCCCAAT 60.619 55.000 8.47 0.00 41.09 3.16
3894 5007 5.511545 GGCTAGATGGAATGTACCGAGAATT 60.512 44.000 0.00 0.00 0.00 2.17
4194 5309 5.420739 TCCATACAACTAAGCAATTTTCCCC 59.579 40.000 0.00 0.00 0.00 4.81
4198 5313 8.635765 TCTTCTCCATACAACTAAGCAATTTT 57.364 30.769 0.00 0.00 0.00 1.82
4233 5348 4.927425 GCAATGCACATCTTCATCACTTTT 59.073 37.500 0.00 0.00 0.00 2.27
4329 5445 0.677098 TAAATGGTGCGCGGGCTTTA 60.677 50.000 25.62 17.40 40.82 1.85
4354 5470 7.231317 TGCAACAATGGATAAGAAGAAGAAAGT 59.769 33.333 0.00 0.00 0.00 2.66
4438 5554 3.467803 AGTCTTTGCTTGCTTCTACGTT 58.532 40.909 0.00 0.00 0.00 3.99
4439 5555 3.113260 AGTCTTTGCTTGCTTCTACGT 57.887 42.857 0.00 0.00 0.00 3.57
4440 5556 3.803555 CAAGTCTTTGCTTGCTTCTACG 58.196 45.455 0.00 0.00 39.26 3.51
4483 5599 1.612395 GGAGCCAGACCAGACTCCTG 61.612 65.000 0.00 0.00 44.41 3.86
4505 5628 2.037251 TGACCTAGCTATTTGCCGGATC 59.963 50.000 5.05 0.00 44.23 3.36


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

AutoCloner maintained by Alex Coulton.