Multiple sequence alignment - TraesCS3D01G414900

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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 TraesCS3D01G414900 chr3D 100.000 3614 0 0 1 3614 526975469 526971856 0.000000e+00 6674.0
1 TraesCS3D01G414900 chr3A 93.281 3676 111 49 1 3614 661474231 661470630 0.000000e+00 5295.0
2 TraesCS3D01G414900 chr3B 94.112 2038 68 16 1 2013 696329074 696327064 0.000000e+00 3051.0
3 TraesCS3D01G414900 chr3B 93.316 1526 66 24 2109 3614 696327007 696325498 0.000000e+00 2220.0
4 TraesCS3D01G414900 chr7D 90.525 591 48 4 1 588 496314719 496314134 0.000000e+00 774.0
5 TraesCS3D01G414900 chr7B 92.489 466 29 3 1526 1990 311927073 311927533 0.000000e+00 662.0
6 TraesCS3D01G414900 chr7B 92.489 466 27 3 1526 1990 312023748 312024206 0.000000e+00 660.0
7 TraesCS3D01G414900 chr7B 91.406 128 5 1 954 1075 312023623 312023750 1.730000e-38 171.0
8 TraesCS3D01G414900 chr7B 90.625 128 6 2 954 1075 311926948 311927075 8.030000e-37 165.0
9 TraesCS3D01G414900 chr7B 100.000 35 0 0 2007 2041 312025384 312025418 8.380000e-07 65.8


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 TraesCS3D01G414900 chr3D 526971856 526975469 3613 True 6674.000000 6674 100.000000 1 3614 1 chr3D.!!$R1 3613
1 TraesCS3D01G414900 chr3A 661470630 661474231 3601 True 5295.000000 5295 93.281000 1 3614 1 chr3A.!!$R1 3613
2 TraesCS3D01G414900 chr3B 696325498 696329074 3576 True 2635.500000 3051 93.714000 1 3614 2 chr3B.!!$R1 3613
3 TraesCS3D01G414900 chr7D 496314134 496314719 585 True 774.000000 774 90.525000 1 588 1 chr7D.!!$R1 587
4 TraesCS3D01G414900 chr7B 311926948 311927533 585 False 413.500000 662 91.557000 954 1990 2 chr7B.!!$F1 1036
5 TraesCS3D01G414900 chr7B 312023623 312025418 1795 False 298.933333 660 94.631667 954 2041 3 chr7B.!!$F2 1087

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
552 553 0.108186 CGCCATACCAGCTTCAGACA 60.108 55.0 0.0 0.0 0.00 3.41 F
599 602 0.890996 CACCAAGCTTCCACCCACTC 60.891 60.0 0.0 0.0 0.00 3.51 F
1658 1692 1.028905 CCAACAACATTGTGTCGGGT 58.971 50.0 0.0 0.0 41.31 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1711 1745 0.257328 TCATGTTGGGGTGTGTGTGT 59.743 50.000 0.00 0.0 0.0 3.72 R
1713 1747 1.144708 TGATCATGTTGGGGTGTGTGT 59.855 47.619 0.00 0.0 0.0 3.72 R
3517 4785 0.037975 TGACGGCGAACCTAAAGACC 60.038 55.000 16.62 0.0 0.0 3.85 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
130 131 1.227292 GGAATTCGTCGAGGAGCCC 60.227 63.158 7.98 7.23 0.00 5.19
543 544 4.609018 CGCCCCTCGCCATACCAG 62.609 72.222 0.00 0.00 0.00 4.00
545 546 3.164269 CCCCTCGCCATACCAGCT 61.164 66.667 0.00 0.00 0.00 4.24
546 547 2.746375 CCCCTCGCCATACCAGCTT 61.746 63.158 0.00 0.00 0.00 3.74
550 551 0.461548 CTCGCCATACCAGCTTCAGA 59.538 55.000 0.00 0.00 0.00 3.27
552 553 0.108186 CGCCATACCAGCTTCAGACA 60.108 55.000 0.00 0.00 0.00 3.41
553 554 1.675714 CGCCATACCAGCTTCAGACAA 60.676 52.381 0.00 0.00 0.00 3.18
594 597 1.227853 ACGACACCAAGCTTCCACC 60.228 57.895 0.00 0.00 0.00 4.61
599 602 0.890996 CACCAAGCTTCCACCCACTC 60.891 60.000 0.00 0.00 0.00 3.51
600 603 1.303643 CCAAGCTTCCACCCACTCC 60.304 63.158 0.00 0.00 0.00 3.85
601 604 1.303643 CAAGCTTCCACCCACTCCC 60.304 63.158 0.00 0.00 0.00 4.30
821 826 2.333701 AATAGTTAAGGCGGGCGGGG 62.334 60.000 0.00 0.00 0.00 5.73
1059 1078 1.454295 GGTCGAGGAGGAGGAGGAC 60.454 68.421 0.00 0.00 0.00 3.85
1185 1215 2.524306 TCGTTTCCTTCCATGCCATTT 58.476 42.857 0.00 0.00 0.00 2.32
1214 1244 5.166398 GGGAAACTTTCTTCAATGCTGATG 58.834 41.667 1.57 0.00 0.00 3.07
1232 1262 3.378112 TGATGCCGATGAAACTGAAATCC 59.622 43.478 0.00 0.00 0.00 3.01
1236 1266 1.737236 CGATGAAACTGAAATCCGGCA 59.263 47.619 0.00 0.00 0.00 5.69
1280 1313 5.064707 CGTCCATATGATCCTCGTTTGTTTT 59.935 40.000 3.65 0.00 0.00 2.43
1281 1314 6.487103 GTCCATATGATCCTCGTTTGTTTTC 58.513 40.000 3.65 0.00 0.00 2.29
1282 1315 6.316390 GTCCATATGATCCTCGTTTGTTTTCT 59.684 38.462 3.65 0.00 0.00 2.52
1283 1316 6.316140 TCCATATGATCCTCGTTTGTTTTCTG 59.684 38.462 3.65 0.00 0.00 3.02
1381 1414 1.207329 AGCTCGGAGGTTAACATCACC 59.793 52.381 20.75 5.35 34.06 4.02
1416 1450 2.897350 CGCCCGCTTCCTTGATCC 60.897 66.667 0.00 0.00 0.00 3.36
1658 1692 1.028905 CCAACAACATTGTGTCGGGT 58.971 50.000 0.00 0.00 41.31 5.28
1710 1744 2.288886 GGAGTAAGAGGTGACACCACAC 60.289 54.545 26.30 14.63 44.93 3.82
1711 1745 2.364324 GAGTAAGAGGTGACACCACACA 59.636 50.000 26.30 9.20 44.93 3.72
1712 1746 2.102588 AGTAAGAGGTGACACCACACAC 59.897 50.000 26.30 19.28 44.93 3.82
1713 1747 0.908910 AAGAGGTGACACCACACACA 59.091 50.000 26.30 0.00 44.93 3.72
1721 1755 0.958382 ACACCACACACACACACACC 60.958 55.000 0.00 0.00 0.00 4.16
1758 1793 7.659390 CACTCCTCCTAATGTCATTCTTTATCC 59.341 40.741 0.07 0.00 0.00 2.59
1911 1951 5.763204 TGAAATTTCCTGTGGTACTCTTCAC 59.237 40.000 15.48 0.00 34.71 3.18
1925 1965 6.643770 GGTACTCTTCACGAACATTTAAGACA 59.356 38.462 0.00 0.00 0.00 3.41
2067 3284 4.202151 GCTGAAATTGACACAATATCCCCC 60.202 45.833 0.00 0.00 0.00 5.40
2197 3415 7.602517 AGTGCTTATCTAACTGCAAAAGTAG 57.397 36.000 0.00 0.00 38.56 2.57
2514 3734 6.811253 TTAACCACTTCTGCAATTAACGAT 57.189 33.333 0.00 0.00 0.00 3.73
2783 4003 5.044558 CGAGCCTACTTAATTTCCACTCTC 58.955 45.833 0.00 0.00 0.00 3.20
2933 4155 3.616821 TCATGCTTTGTTCCGTCTTATCG 59.383 43.478 0.00 0.00 0.00 2.92
2982 4204 9.231297 AGTTAATTTCAGAGCTTAATTACTGCA 57.769 29.630 10.93 0.00 0.00 4.41
3010 4232 4.681835 TTTCTTCCGTCGTTGTGAAAAA 57.318 36.364 0.00 0.00 0.00 1.94
3105 4328 1.675310 TCTTTGGCTGCCATGTCGG 60.675 57.895 24.03 10.83 31.53 4.79
3133 4356 1.332904 CGTGCGTCTCAAGTTGTTTCC 60.333 52.381 2.11 0.00 0.00 3.13
3134 4357 1.940613 GTGCGTCTCAAGTTGTTTCCT 59.059 47.619 2.11 0.00 0.00 3.36
3142 4365 2.878406 TCAAGTTGTTTCCTGCACTAGC 59.122 45.455 2.11 0.00 42.57 3.42
3336 4584 1.153958 GGCTTAAAGCTTGCGCCTG 60.154 57.895 20.57 0.00 41.99 4.85
3385 4634 2.764314 CCCTGGCCGATTTCTTGCG 61.764 63.158 0.00 0.00 0.00 4.85
3409 4658 1.078848 AGTGATCCGGAAGTGCTGC 60.079 57.895 9.01 0.00 0.00 5.25
3478 4746 9.739786 GTTGTTTGTAACTGTTCTTCAAATTTG 57.260 29.630 12.15 12.15 32.16 2.32
3479 4747 9.698309 TTGTTTGTAACTGTTCTTCAAATTTGA 57.302 25.926 16.91 16.91 34.92 2.69
3480 4748 9.134734 TGTTTGTAACTGTTCTTCAAATTTGAC 57.865 29.630 20.35 10.22 36.83 3.18
3481 4749 9.353999 GTTTGTAACTGTTCTTCAAATTTGACT 57.646 29.630 20.35 1.46 36.83 3.41
3484 4752 9.997482 TGTAACTGTTCTTCAAATTTGACTAAC 57.003 29.630 24.75 24.75 36.83 2.34
3485 4753 9.155053 GTAACTGTTCTTCAAATTTGACTAACG 57.845 33.333 25.23 22.53 36.83 3.18
3486 4754 6.725246 ACTGTTCTTCAAATTTGACTAACGG 58.275 36.000 30.26 30.26 40.63 4.44
3487 4755 6.540914 ACTGTTCTTCAAATTTGACTAACGGA 59.459 34.615 34.22 20.92 38.97 4.69
3488 4756 7.066525 ACTGTTCTTCAAATTTGACTAACGGAA 59.933 33.333 34.22 22.72 38.97 4.30
3489 4757 7.936584 TGTTCTTCAAATTTGACTAACGGAAT 58.063 30.769 25.23 0.00 36.83 3.01
3490 4758 9.058174 TGTTCTTCAAATTTGACTAACGGAATA 57.942 29.630 25.23 16.45 36.83 1.75
3493 4761 9.226606 TCTTCAAATTTGACTAACGGAATATGT 57.773 29.630 20.35 0.00 36.83 2.29
3494 4762 9.277565 CTTCAAATTTGACTAACGGAATATGTG 57.722 33.333 20.35 0.00 36.83 3.21
3495 4763 8.330466 TCAAATTTGACTAACGGAATATGTGT 57.670 30.769 16.91 0.00 31.01 3.72
3496 4764 8.788806 TCAAATTTGACTAACGGAATATGTGTT 58.211 29.630 16.91 0.00 31.01 3.32
3501 4769 9.872721 TTTGACTAACGGAATATGTGTTATACA 57.127 29.630 0.00 0.00 44.87 2.29
3502 4770 9.524106 TTGACTAACGGAATATGTGTTATACAG 57.476 33.333 0.00 0.00 43.80 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
256 257 2.264480 CGTCCATTCCGCACCTCA 59.736 61.111 0.00 0.00 0.00 3.86
266 267 4.514577 CTCCTCGCCGCGTCCATT 62.515 66.667 13.39 0.00 0.00 3.16
542 543 1.543429 CGGGGAACTTTGTCTGAAGCT 60.543 52.381 0.00 0.00 0.00 3.74
543 544 0.875059 CGGGGAACTTTGTCTGAAGC 59.125 55.000 0.00 0.00 0.00 3.86
545 546 0.536460 GCCGGGGAACTTTGTCTGAA 60.536 55.000 2.18 0.00 0.00 3.02
546 547 1.072505 GCCGGGGAACTTTGTCTGA 59.927 57.895 2.18 0.00 0.00 3.27
550 551 2.203437 GTGGCCGGGGAACTTTGT 60.203 61.111 2.18 0.00 0.00 2.83
552 553 4.653888 CGGTGGCCGGGGAACTTT 62.654 66.667 2.18 0.00 44.15 2.66
578 581 1.150536 TGGGTGGAAGCTTGGTGTC 59.849 57.895 2.10 0.00 0.00 3.67
583 586 1.303643 GGGAGTGGGTGGAAGCTTG 60.304 63.158 2.10 0.00 0.00 4.01
585 588 2.936032 GGGGAGTGGGTGGAAGCT 60.936 66.667 0.00 0.00 0.00 3.74
586 589 4.048470 GGGGGAGTGGGTGGAAGC 62.048 72.222 0.00 0.00 0.00 3.86
821 826 4.615121 CGCTCTCTATCTTTTATGCTCGAC 59.385 45.833 0.00 0.00 0.00 4.20
1185 1215 6.721208 AGCATTGAAGAAAGTTTCCCAGAATA 59.279 34.615 12.05 0.00 0.00 1.75
1214 1244 1.064060 CCGGATTTCAGTTTCATCGGC 59.936 52.381 0.00 0.00 0.00 5.54
1232 1262 6.141211 CGAATCAATTCAACTAATCAATGCCG 59.859 38.462 3.81 0.00 36.61 5.69
1236 1266 8.279970 TGGACGAATCAATTCAACTAATCAAT 57.720 30.769 3.81 0.00 36.61 2.57
1280 1313 4.495422 CTGCATCGATCATCATCATCAGA 58.505 43.478 0.00 0.00 0.00 3.27
1281 1314 3.619038 CCTGCATCGATCATCATCATCAG 59.381 47.826 0.00 0.00 0.00 2.90
1282 1315 3.259876 TCCTGCATCGATCATCATCATCA 59.740 43.478 0.00 0.00 0.00 3.07
1283 1316 3.858247 TCCTGCATCGATCATCATCATC 58.142 45.455 0.00 0.00 0.00 2.92
1381 1414 4.029809 GGTGAGGGGAACGGTGGG 62.030 72.222 0.00 0.00 0.00 4.61
1403 1437 1.740025 GAAGTTGGGATCAAGGAAGCG 59.260 52.381 0.00 0.00 32.92 4.68
1416 1450 2.213499 GGCAGATGGATACGAAGTTGG 58.787 52.381 0.00 0.00 37.78 3.77
1658 1692 1.758280 ACGGTGTTGGTGTACTTGAGA 59.242 47.619 0.00 0.00 0.00 3.27
1710 1744 0.385029 CATGTTGGGGTGTGTGTGTG 59.615 55.000 0.00 0.00 0.00 3.82
1711 1745 0.257328 TCATGTTGGGGTGTGTGTGT 59.743 50.000 0.00 0.00 0.00 3.72
1712 1746 1.541147 GATCATGTTGGGGTGTGTGTG 59.459 52.381 0.00 0.00 0.00 3.82
1713 1747 1.144708 TGATCATGTTGGGGTGTGTGT 59.855 47.619 0.00 0.00 0.00 3.72
1721 1755 1.842562 AGGAGGAGTGATCATGTTGGG 59.157 52.381 0.00 0.00 0.00 4.12
1758 1793 6.256539 TCTGTACTAGTACGATCTAACAACCG 59.743 42.308 24.36 0.00 38.85 4.44
1825 1861 8.840867 CGATGTCACTTTAACAAATTTAAGAGC 58.159 33.333 5.62 0.00 30.60 4.09
1911 1951 9.663904 TCTTTTTCTTGATGTCTTAAATGTTCG 57.336 29.630 0.00 0.00 0.00 3.95
2067 3284 4.276678 TCAACTTTTCTCAAGTCATGCAGG 59.723 41.667 0.00 0.00 0.00 4.85
2068 3285 5.428496 TCAACTTTTCTCAAGTCATGCAG 57.572 39.130 0.00 0.00 0.00 4.41
2197 3415 7.601886 CCTATTCATGTACCAGATGATCTTGAC 59.398 40.741 0.01 0.00 29.96 3.18
2933 4155 6.151144 ACTGCCTAATGGACAGAAAATTACAC 59.849 38.462 11.39 0.00 39.28 2.90
2982 4204 5.929992 TCACAACGACGGAAGAAATTAAGAT 59.070 36.000 0.00 0.00 0.00 2.40
3142 4365 2.238847 TTACCCTACGGCAGCAGCAG 62.239 60.000 2.65 0.52 44.61 4.24
3336 4584 2.946762 GGCGCAAGTCAAGTCACC 59.053 61.111 10.83 0.00 45.31 4.02
3385 4634 1.407258 CACTTCCGGATCACTCTCCTC 59.593 57.143 4.15 0.00 32.77 3.71
3440 4689 1.935199 ACAAACAACACGAAGGTACCG 59.065 47.619 6.18 0.00 0.00 4.02
3482 4750 9.472361 GTCATACTGTATAACACATATTCCGTT 57.528 33.333 0.00 0.00 36.29 4.44
3483 4751 8.635328 TGTCATACTGTATAACACATATTCCGT 58.365 33.333 0.00 0.00 36.29 4.69
3484 4752 8.912658 GTGTCATACTGTATAACACATATTCCG 58.087 37.037 23.22 0.00 39.91 4.30
3485 4753 9.758651 TGTGTCATACTGTATAACACATATTCC 57.241 33.333 25.76 5.94 43.70 3.01
3497 4765 9.959721 AAAGACCTTATTTGTGTCATACTGTAT 57.040 29.630 0.00 0.00 0.00 2.29
3499 4767 9.436957 CTAAAGACCTTATTTGTGTCATACTGT 57.563 33.333 0.00 0.00 0.00 3.55
3500 4768 8.883731 CCTAAAGACCTTATTTGTGTCATACTG 58.116 37.037 0.00 0.00 0.00 2.74
3501 4769 8.603304 ACCTAAAGACCTTATTTGTGTCATACT 58.397 33.333 0.00 0.00 0.00 2.12
3502 4770 8.788325 ACCTAAAGACCTTATTTGTGTCATAC 57.212 34.615 0.00 0.00 0.00 2.39
3517 4785 0.037975 TGACGGCGAACCTAAAGACC 60.038 55.000 16.62 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.