Multiple sequence alignment - TraesCS1D01G103500

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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 TraesCS1D01G103500 chr1D 100.000 4127 0 0 1 4127 93106166 93102040 0.000000e+00 7622
1 TraesCS1D01G103500 chr1B 95.585 3715 115 26 416 4127 148416836 148413168 0.000000e+00 5906
2 TraesCS1D01G103500 chr1B 89.231 325 16 7 1 306 148420499 148420175 5.000000e-104 388
3 TraesCS1D01G103500 chr1B 91.071 56 3 2 329 383 148416903 148416849 1.590000e-09 75
4 TraesCS1D01G103500 chr1A 95.674 3514 107 16 617 4127 90163848 90160377 0.000000e+00 5605
5 TraesCS1D01G103500 chr1A 90.148 203 17 2 1 201 90173420 90173219 1.140000e-65 261
6 TraesCS1D01G103500 chr1A 90.909 165 13 2 212 375 90172796 90172633 1.930000e-53 220
7 TraesCS1D01G103500 chr1A 88.525 183 10 5 426 608 90170809 90170638 1.160000e-50 211
8 TraesCS1D01G103500 chr2B 90.215 2739 210 28 639 3349 214280766 214283474 0.000000e+00 3520
9 TraesCS1D01G103500 chr2B 89.703 2661 222 31 539 3169 214312467 214315105 0.000000e+00 3349
10 TraesCS1D01G103500 chr2D 89.458 2770 209 44 539 3252 156707004 156709746 0.000000e+00 3421
11 TraesCS1D01G103500 chr2D 92.265 2353 176 4 1010 3360 156592469 156594817 0.000000e+00 3332
12 TraesCS1D01G103500 chr2D 89.782 2574 210 30 620 3170 182576289 182573746 0.000000e+00 3247
13 TraesCS1D01G103500 chr2A 89.716 2606 201 37 609 3170 197566588 197564006 0.000000e+00 3265
14 TraesCS1D01G103500 chr2A 89.848 2571 217 28 628 3169 166627709 166630264 0.000000e+00 3262
15 TraesCS1D01G103500 chr2A 85.561 1025 115 23 721 1723 197344832 197343819 0.000000e+00 1042
16 TraesCS1D01G103500 chr2A 87.452 263 27 5 3100 3360 166256549 166256807 8.670000e-77 298


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 TraesCS1D01G103500 chr1D 93102040 93106166 4126 True 7622.000000 7622 100.000000 1 4127 1 chr1D.!!$R1 4126
1 TraesCS1D01G103500 chr1B 148413168 148420499 7331 True 2123.000000 5906 91.962333 1 4127 3 chr1B.!!$R1 4126
2 TraesCS1D01G103500 chr1A 90160377 90163848 3471 True 5605.000000 5605 95.674000 617 4127 1 chr1A.!!$R1 3510
3 TraesCS1D01G103500 chr1A 90170638 90173420 2782 True 230.666667 261 89.860667 1 608 3 chr1A.!!$R2 607
4 TraesCS1D01G103500 chr2B 214280766 214283474 2708 False 3520.000000 3520 90.215000 639 3349 1 chr2B.!!$F1 2710
5 TraesCS1D01G103500 chr2B 214312467 214315105 2638 False 3349.000000 3349 89.703000 539 3169 1 chr2B.!!$F2 2630
6 TraesCS1D01G103500 chr2D 156707004 156709746 2742 False 3421.000000 3421 89.458000 539 3252 1 chr2D.!!$F2 2713
7 TraesCS1D01G103500 chr2D 156592469 156594817 2348 False 3332.000000 3332 92.265000 1010 3360 1 chr2D.!!$F1 2350
8 TraesCS1D01G103500 chr2D 182573746 182576289 2543 True 3247.000000 3247 89.782000 620 3170 1 chr2D.!!$R1 2550
9 TraesCS1D01G103500 chr2A 197564006 197566588 2582 True 3265.000000 3265 89.716000 609 3170 1 chr2A.!!$R2 2561
10 TraesCS1D01G103500 chr2A 166627709 166630264 2555 False 3262.000000 3262 89.848000 628 3169 1 chr2A.!!$F2 2541
11 TraesCS1D01G103500 chr2A 197343819 197344832 1013 True 1042.000000 1042 85.561000 721 1723 1 chr2A.!!$R1 1002

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
870 6364 0.033405 CCCACCTCTCCTACCTCGAA 60.033 60.0 0.00 0.0 0.00 3.71 F
996 6538 0.034059 AAGACACAGCCTCGACCAAG 59.966 55.0 0.00 0.0 0.00 3.61 F
1869 7413 0.685458 AGGTGATGAATGGCAAGCCC 60.685 55.0 8.89 0.0 34.56 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2807 8351 0.822121 GGCAAACACCGAGGTTTCCT 60.822 55.0 0.00 0.0 38.86 3.36 R
3104 8648 1.743321 GCAGATAGGCAGAGGCTCGT 61.743 60.0 9.22 0.0 39.70 4.18 R
3750 9327 0.883833 GGGTCAGACTGTGCATTTGG 59.116 55.0 1.59 0.0 0.00 3.28 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
90 95 6.267699 TCATATCCGAAGACTACACCATCATT 59.732 38.462 0.00 0.00 0.00 2.57
163 170 3.014623 GGTAAAATTTCCCCCACTCTCG 58.985 50.000 0.00 0.00 0.00 4.04
173 180 0.962855 CCCACTCTCGTGCTCTCTCA 60.963 60.000 0.00 0.00 39.86 3.27
174 181 0.884514 CCACTCTCGTGCTCTCTCAA 59.115 55.000 0.00 0.00 39.86 3.02
195 202 4.640771 ACTCTCTTTGTATCTTTGGCCA 57.359 40.909 0.00 0.00 0.00 5.36
270 689 4.014847 TGAACAAGTTTTCTTCGCAGTG 57.985 40.909 0.00 0.00 38.17 3.66
275 694 3.340337 AGTTTTCTTCGCAGTGCTTTC 57.660 42.857 14.33 0.00 0.00 2.62
345 4014 2.106511 AGCCTTAGGAAAGTCTGCAACA 59.893 45.455 0.69 0.00 0.00 3.33
346 4015 2.884639 GCCTTAGGAAAGTCTGCAACAA 59.115 45.455 0.69 0.00 0.00 2.83
391 4060 9.688592 TTATTATTTAGAGAGGTAGCGCTTAAC 57.311 33.333 18.68 8.89 0.00 2.01
393 4062 4.897025 TTAGAGAGGTAGCGCTTAACTC 57.103 45.455 18.68 20.29 44.96 3.01
401 4070 3.001576 GCGCTTAACTCGCCAAAAG 57.998 52.632 0.00 0.00 46.18 2.27
402 4071 0.515564 GCGCTTAACTCGCCAAAAGA 59.484 50.000 0.00 0.00 46.18 2.52
403 4072 1.069500 GCGCTTAACTCGCCAAAAGAA 60.069 47.619 0.00 0.00 46.18 2.52
404 4073 2.839474 CGCTTAACTCGCCAAAAGAAG 58.161 47.619 0.00 0.00 0.00 2.85
411 4215 3.400255 ACTCGCCAAAAGAAGAGGTAAC 58.600 45.455 0.00 0.00 35.22 2.50
414 4218 2.546789 CGCCAAAAGAAGAGGTAACGTT 59.453 45.455 5.88 5.88 46.39 3.99
419 4223 6.635641 GCCAAAAGAAGAGGTAACGTTTAAAG 59.364 38.462 5.91 0.00 46.39 1.85
467 5909 1.985473 TGGACAAGTTTGCTGCTGAT 58.015 45.000 0.00 0.00 0.00 2.90
487 5929 1.250154 TGGCTGGTTTGTAGGCATGC 61.250 55.000 9.90 9.90 44.52 4.06
488 5930 1.137404 GCTGGTTTGTAGGCATGCG 59.863 57.895 12.44 0.00 0.00 4.73
489 5931 1.586154 GCTGGTTTGTAGGCATGCGT 61.586 55.000 18.09 18.09 0.00 5.24
509 5951 4.121669 GCTGCAGCTCGTCTCCGA 62.122 66.667 31.33 0.00 41.73 4.55
519 5961 2.704464 TCGTCTCCGAGTCTCCATAA 57.296 50.000 0.00 0.00 38.40 1.90
520 5962 2.562635 TCGTCTCCGAGTCTCCATAAG 58.437 52.381 0.00 0.00 38.40 1.73
521 5963 2.169978 TCGTCTCCGAGTCTCCATAAGA 59.830 50.000 0.00 0.00 38.40 2.10
593 6051 4.738345 AGCGTCGACTCGTGCGTC 62.738 66.667 14.70 10.10 35.42 5.19
642 6110 2.572191 TTAGTATCCCAAGTGTCGCG 57.428 50.000 0.00 0.00 0.00 5.87
701 6175 3.256960 ACGAGGCCACCAACCCAT 61.257 61.111 5.01 0.00 0.00 4.00
708 6182 1.305930 GCCACCAACCCATCTTCGTC 61.306 60.000 0.00 0.00 0.00 4.20
709 6183 1.019278 CCACCAACCCATCTTCGTCG 61.019 60.000 0.00 0.00 0.00 5.12
710 6184 0.320421 CACCAACCCATCTTCGTCGT 60.320 55.000 0.00 0.00 0.00 4.34
865 6359 0.764752 CATCCCCCACCTCTCCTACC 60.765 65.000 0.00 0.00 0.00 3.18
868 6362 1.455959 CCCCACCTCTCCTACCTCG 60.456 68.421 0.00 0.00 0.00 4.63
870 6364 0.033405 CCCACCTCTCCTACCTCGAA 60.033 60.000 0.00 0.00 0.00 3.71
996 6538 0.034059 AAGACACAGCCTCGACCAAG 59.966 55.000 0.00 0.00 0.00 3.61
997 6539 0.827925 AGACACAGCCTCGACCAAGA 60.828 55.000 0.00 0.00 0.00 3.02
1596 7139 4.827481 GCTTCCGGCGATCTTGTA 57.173 55.556 9.30 0.00 0.00 2.41
1794 7338 1.352156 GGCTCGCGTCGATTGTTCTT 61.352 55.000 5.77 0.00 34.61 2.52
1814 7358 2.818130 TTTGAAGCCAACATCCTTGC 57.182 45.000 0.00 0.00 30.88 4.01
1848 7392 0.745128 TTTTGTCGGCCGTGTTCTGT 60.745 50.000 27.15 0.00 0.00 3.41
1869 7413 0.685458 AGGTGATGAATGGCAAGCCC 60.685 55.000 8.89 0.00 34.56 5.19
1911 7455 2.028130 CACAAGTTAAAGCACCACCCA 58.972 47.619 0.00 0.00 0.00 4.51
2223 7767 1.237285 ACAACACGAGGCTTGCCATC 61.237 55.000 14.54 7.57 0.00 3.51
2807 8351 3.043713 CGAGGCTGAGCGCAACAA 61.044 61.111 11.47 0.00 41.67 2.83
3070 8614 1.144708 TGAACCAGGGAAAGCACATCA 59.855 47.619 0.00 0.00 0.00 3.07
3104 8648 1.118965 TGCCTGAAGGAGTGGAACGA 61.119 55.000 0.00 0.00 37.58 3.85
3143 8688 6.076653 TCTGCTAATCAGGAGATGAAGAGAT 58.923 40.000 0.00 0.00 43.61 2.75
3228 8801 1.532868 ACTTCTGAAGCGTTGATGCAC 59.467 47.619 17.00 0.00 37.31 4.57
3415 8992 7.946207 TGCAATATAAAGAGAAACAACACCAA 58.054 30.769 0.00 0.00 0.00 3.67
3647 9224 4.025040 TGATTGGTCTCAGCAAACATCT 57.975 40.909 0.00 0.00 39.20 2.90
3652 9229 0.322816 TCTCAGCAAACATCTGCCCC 60.323 55.000 0.00 0.00 43.73 5.80
3662 9239 3.979501 ACATCTGCCCCCAAATATCTT 57.020 42.857 0.00 0.00 0.00 2.40
3691 9268 5.413309 AGTATGGCTGCTATGGTTCTATC 57.587 43.478 8.91 0.00 0.00 2.08
3692 9269 5.090139 AGTATGGCTGCTATGGTTCTATCT 58.910 41.667 8.91 0.00 0.00 1.98
3750 9327 7.148672 CGATATACTCAAAGCATGAAGATGTCC 60.149 40.741 0.00 0.00 37.67 4.02
3753 9330 3.760151 CTCAAAGCATGAAGATGTCCCAA 59.240 43.478 0.00 0.00 37.67 4.12
4025 9603 2.829120 AGCACCTCCTTCTTGACTAGAC 59.171 50.000 0.00 0.00 30.90 2.59
4066 9644 5.482908 GCAGTAGGAAAAACAGAGATCAGA 58.517 41.667 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 57 4.082845 TCGGATATGACCTCCTTCATCTC 58.917 47.826 0.00 0.00 37.42 2.75
53 58 4.119556 TCGGATATGACCTCCTTCATCT 57.880 45.455 0.00 0.00 37.42 2.90
90 95 5.448654 CCAAGGAGGTTTATCCAATCATGA 58.551 41.667 0.00 0.00 42.26 3.07
142 149 3.014623 CGAGAGTGGGGGAAATTTTACC 58.985 50.000 1.31 1.31 0.00 2.85
163 170 3.988819 ACAAAGAGAGTTGAGAGAGCAC 58.011 45.455 0.00 0.00 32.59 4.40
173 180 4.985538 TGGCCAAAGATACAAAGAGAGTT 58.014 39.130 0.61 0.00 0.00 3.01
174 181 4.640771 TGGCCAAAGATACAAAGAGAGT 57.359 40.909 0.61 0.00 0.00 3.24
201 208 9.740239 GACGTTCACCTACATATTAGTAATCAA 57.260 33.333 0.00 0.00 0.00 2.57
202 209 8.355169 GGACGTTCACCTACATATTAGTAATCA 58.645 37.037 0.00 0.00 0.00 2.57
205 212 7.557358 TGAGGACGTTCACCTACATATTAGTAA 59.443 37.037 0.00 0.00 37.93 2.24
207 214 5.889853 TGAGGACGTTCACCTACATATTAGT 59.110 40.000 0.00 0.00 37.93 2.24
208 215 6.387041 TGAGGACGTTCACCTACATATTAG 57.613 41.667 0.00 0.00 37.93 1.73
209 216 6.971726 ATGAGGACGTTCACCTACATATTA 57.028 37.500 0.00 0.00 37.93 0.98
210 217 5.871396 ATGAGGACGTTCACCTACATATT 57.129 39.130 0.00 0.00 37.93 1.28
270 689 4.327680 AGAGACAGGTGTTAATGGAAAGC 58.672 43.478 0.00 0.00 0.00 3.51
275 694 7.612677 AGTACTTTAGAGACAGGTGTTAATGG 58.387 38.462 0.00 0.00 0.00 3.16
384 4053 2.478894 TCTTCTTTTGGCGAGTTAAGCG 59.521 45.455 0.00 0.00 35.00 4.68
385 4054 3.120165 CCTCTTCTTTTGGCGAGTTAAGC 60.120 47.826 0.00 0.00 0.00 3.09
386 4055 4.065789 ACCTCTTCTTTTGGCGAGTTAAG 58.934 43.478 0.00 0.00 0.00 1.85
389 4058 2.640316 ACCTCTTCTTTTGGCGAGTT 57.360 45.000 0.00 0.00 0.00 3.01
391 4060 2.412089 CGTTACCTCTTCTTTTGGCGAG 59.588 50.000 0.00 0.00 0.00 5.03
393 4062 2.140717 ACGTTACCTCTTCTTTTGGCG 58.859 47.619 0.00 0.00 0.00 5.69
394 4063 4.563337 AAACGTTACCTCTTCTTTTGGC 57.437 40.909 0.00 0.00 0.00 4.52
395 4064 7.700505 ACTTTAAACGTTACCTCTTCTTTTGG 58.299 34.615 0.00 0.00 0.00 3.28
438 5880 5.003804 AGCAAACTTGTCCATTATCGTCTT 58.996 37.500 0.00 0.00 0.00 3.01
439 5881 4.393062 CAGCAAACTTGTCCATTATCGTCT 59.607 41.667 0.00 0.00 0.00 4.18
467 5909 1.255882 CATGCCTACAAACCAGCCAA 58.744 50.000 0.00 0.00 0.00 4.52
511 5953 6.667848 TCAAGTCTGTTATGGTCTTATGGAGA 59.332 38.462 0.00 0.00 0.00 3.71
512 5954 6.878317 TCAAGTCTGTTATGGTCTTATGGAG 58.122 40.000 0.00 0.00 0.00 3.86
513 5955 6.867519 TCAAGTCTGTTATGGTCTTATGGA 57.132 37.500 0.00 0.00 0.00 3.41
514 5956 7.275183 TGATCAAGTCTGTTATGGTCTTATGG 58.725 38.462 0.00 0.00 0.00 2.74
515 5957 7.042187 GCTGATCAAGTCTGTTATGGTCTTATG 60.042 40.741 0.00 0.00 0.00 1.90
516 5958 6.989169 GCTGATCAAGTCTGTTATGGTCTTAT 59.011 38.462 0.00 0.00 0.00 1.73
517 5959 6.341316 GCTGATCAAGTCTGTTATGGTCTTA 58.659 40.000 0.00 0.00 0.00 2.10
518 5960 5.181748 GCTGATCAAGTCTGTTATGGTCTT 58.818 41.667 0.00 0.00 0.00 3.01
519 5961 4.383552 GGCTGATCAAGTCTGTTATGGTCT 60.384 45.833 0.00 0.00 0.00 3.85
520 5962 3.873952 GGCTGATCAAGTCTGTTATGGTC 59.126 47.826 0.00 0.00 0.00 4.02
521 5963 3.679917 CGGCTGATCAAGTCTGTTATGGT 60.680 47.826 0.00 0.00 0.00 3.55
593 6051 4.511246 ATGTGCCATGCGAGGGGG 62.511 66.667 0.00 0.00 0.00 5.40
615 6083 8.182881 GCGACACTTGGGATACTAATATACTAG 58.817 40.741 0.00 0.00 36.01 2.57
655 6125 4.437659 CGGACTAGGAAGAAGAAGACGAAG 60.438 50.000 0.00 0.00 0.00 3.79
656 6126 3.439476 CGGACTAGGAAGAAGAAGACGAA 59.561 47.826 0.00 0.00 0.00 3.85
658 6128 2.478200 GCGGACTAGGAAGAAGAAGACG 60.478 54.545 0.00 0.00 0.00 4.18
659 6129 2.492484 TGCGGACTAGGAAGAAGAAGAC 59.508 50.000 0.00 0.00 0.00 3.01
701 6175 3.998672 GGGTGGGCACGACGAAGA 61.999 66.667 0.00 0.00 38.18 2.87
754 6230 0.598065 GATTTGGTGTGGGCTGTGAC 59.402 55.000 0.00 0.00 0.00 3.67
755 6231 0.478072 AGATTTGGTGTGGGCTGTGA 59.522 50.000 0.00 0.00 0.00 3.58
756 6232 0.883833 GAGATTTGGTGTGGGCTGTG 59.116 55.000 0.00 0.00 0.00 3.66
996 6538 4.114997 CCGTTGGCCGCCATTGTC 62.115 66.667 14.30 3.81 31.53 3.18
1245 6788 1.181741 AGTCGCTGCTCTCCTTGACA 61.182 55.000 0.00 0.00 0.00 3.58
1560 7103 3.717294 GTGATGGTGCCCCGGAGT 61.717 66.667 0.73 0.00 0.00 3.85
1596 7139 2.491022 GGCGATGTAGGAGAGCGGT 61.491 63.158 0.00 0.00 0.00 5.68
1794 7338 2.699846 AGCAAGGATGTTGGCTTCAAAA 59.300 40.909 0.00 0.00 31.34 2.44
1814 7358 3.546815 CGACAAAACTTCAGCAAGGACAG 60.547 47.826 0.00 0.00 33.37 3.51
1848 7392 1.466856 GCTTGCCATTCATCACCTCA 58.533 50.000 0.00 0.00 0.00 3.86
1869 7413 1.211969 CAGGTGGTCGGTGTACTCG 59.788 63.158 0.00 0.00 0.00 4.18
1911 7455 3.532155 GCGGCCTCGATCTGTCCT 61.532 66.667 0.00 0.00 39.00 3.85
2806 8350 1.029681 GCAAACACCGAGGTTTCCTT 58.970 50.000 0.00 0.00 38.86 3.36
2807 8351 0.822121 GGCAAACACCGAGGTTTCCT 60.822 55.000 0.00 0.00 38.86 3.36
3104 8648 1.743321 GCAGATAGGCAGAGGCTCGT 61.743 60.000 9.22 0.00 39.70 4.18
3143 8688 1.825090 AATTCTGAAGCACGGCATCA 58.175 45.000 0.00 4.25 35.04 3.07
3228 8801 3.011760 GCTCCGGAAGAACGTTGCG 62.012 63.158 5.00 0.00 0.00 4.85
3415 8992 2.496899 ATTTGATGCCAGTCGGAACT 57.503 45.000 0.00 0.00 35.60 3.01
3628 9205 2.490903 GCAGATGTTTGCTGAGACCAAT 59.509 45.455 0.00 0.00 40.89 3.16
3647 9224 3.921104 TGCAATAAGATATTTGGGGGCA 58.079 40.909 0.00 0.00 0.00 5.36
3652 9229 7.811236 CAGCCATACTTGCAATAAGATATTTGG 59.189 37.037 0.00 0.00 0.00 3.28
3662 9239 4.074259 CCATAGCAGCCATACTTGCAATA 58.926 43.478 0.00 0.00 0.00 1.90
3691 9268 9.780186 CCTAAGGACCAAATTTCTACCTATAAG 57.220 37.037 0.00 5.92 0.00 1.73
3692 9269 9.287818 ACCTAAGGACCAAATTTCTACCTATAA 57.712 33.333 0.00 0.00 0.00 0.98
3750 9327 0.883833 GGGTCAGACTGTGCATTTGG 59.116 55.000 1.59 0.00 0.00 3.28
3753 9330 1.059098 TGAGGGTCAGACTGTGCATT 58.941 50.000 1.59 0.00 0.00 3.56
4025 9603 6.923508 CCTACTGCCTTTTGTTTTAAGGAAAG 59.076 38.462 5.85 4.93 44.01 2.62
4066 9644 2.546899 TGGCTGTATGACTGTAAGGGT 58.453 47.619 0.00 0.00 39.30 4.34


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

AutoCloner maintained by Alex Coulton.