Multiple sequence alignment - TraesCS3D01G340000

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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 TraesCS3D01G340000 chr3D 100.000 3151 0 0 1 3151 453628377 453631527 0.000000e+00 5819
1 TraesCS3D01G340000 chr3D 89.369 301 28 4 1 298 296836187 296836486 2.970000e-100 375
2 TraesCS3D01G340000 chr3A 95.129 2566 69 30 614 3151 595643721 595646258 0.000000e+00 3995
3 TraesCS3D01G340000 chr3B 93.882 2468 92 22 1 2447 596046625 596049054 0.000000e+00 3666
4 TraesCS3D01G340000 chr3B 93.635 707 38 6 2446 3151 596049347 596050047 0.000000e+00 1050
5 TraesCS3D01G340000 chr1D 89.967 299 29 1 1 298 380313566 380313864 4.930000e-103 385
6 TraesCS3D01G340000 chr1D 89.632 299 29 2 1 298 430235462 430235759 2.290000e-101 379
7 TraesCS3D01G340000 chr1D 89.333 300 29 3 1 298 153677711 153677413 1.070000e-99 374
8 TraesCS3D01G340000 chr1D 84.058 207 28 5 1717 1921 109477230 109477027 8.920000e-46 195
9 TraesCS3D01G340000 chr1D 87.162 148 19 0 1469 1616 109478071 109477924 5.400000e-38 169
10 TraesCS3D01G340000 chr1D 84.932 146 20 2 1473 1617 311750431 311750287 2.530000e-31 147
11 TraesCS3D01G340000 chr7D 89.667 300 29 2 1 298 424720604 424720903 6.380000e-102 381
12 TraesCS3D01G340000 chr4D 90.378 291 25 3 10 298 116166146 116165857 2.290000e-101 379
13 TraesCS3D01G340000 chr1A 89.439 303 27 3 1 298 475168692 475168994 8.250000e-101 377
14 TraesCS3D01G340000 chr1A 83.654 208 29 5 1717 1922 112943081 112942877 1.150000e-44 191
15 TraesCS3D01G340000 chr7B 89.369 301 27 5 1 298 299923463 299923165 1.070000e-99 374
16 TraesCS3D01G340000 chr1B 83.654 208 29 5 1717 1922 165076540 165076336 1.150000e-44 191
17 TraesCS3D01G340000 chr1B 87.838 148 18 0 1469 1616 165077397 165077250 1.160000e-39 174
18 TraesCS3D01G340000 chr1B 84.932 146 20 2 1473 1617 422346955 422346811 2.530000e-31 147


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 TraesCS3D01G340000 chr3D 453628377 453631527 3150 False 5819 5819 100.0000 1 3151 1 chr3D.!!$F2 3150
1 TraesCS3D01G340000 chr3A 595643721 595646258 2537 False 3995 3995 95.1290 614 3151 1 chr3A.!!$F1 2537
2 TraesCS3D01G340000 chr3B 596046625 596050047 3422 False 2358 3666 93.7585 1 3151 2 chr3B.!!$F1 3150

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
983 998 1.076727 TCTCTCCGTCTCCCAAGCA 59.923 57.895 0.0 0.0 0.00 3.91 F
1021 1040 1.075050 TGTCCACGGAGAGGTAAGAGT 59.925 52.381 0.0 0.0 39.94 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1871 1905 0.610174 TGTGCTTGAAGATCTCGGCT 59.390 50.000 0.0 0.0 0.0 5.52 R
2903 3246 2.525368 ACTTGATTTTGGCCCCAGTAC 58.475 47.619 0.0 0.0 0.0 2.73 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
65 66 4.473520 CGCCCTGGTGCCTAGTGG 62.474 72.222 0.00 0.00 0.00 4.00
95 97 2.352805 CCCTCCAGTGGGTCTTGC 59.647 66.667 9.92 0.00 42.25 4.01
111 113 7.381408 GTGGGTCTTGCTTCAAGTAATTTTTAC 59.619 37.037 6.47 0.00 41.66 2.01
149 151 5.545063 TCCCCAAAAAGTTTCTCCAATTC 57.455 39.130 0.00 0.00 0.00 2.17
150 152 4.346709 TCCCCAAAAAGTTTCTCCAATTCC 59.653 41.667 0.00 0.00 0.00 3.01
178 180 9.213799 AGAACTTTTATTTCTGCACAAAAACAA 57.786 25.926 0.00 0.00 31.88 2.83
192 194 5.872070 CACAAAAACAACACCATGGTAGTTT 59.128 36.000 25.03 25.03 32.34 2.66
216 218 6.236017 TGCTAAAAACATCGTTAGTTCAGG 57.764 37.500 0.00 0.00 31.24 3.86
220 222 8.284693 GCTAAAAACATCGTTAGTTCAGGTTAA 58.715 33.333 0.00 0.00 31.24 2.01
260 262 6.321181 TGCAAATTAGAGTCCAAAACAAGAGT 59.679 34.615 0.00 0.00 0.00 3.24
272 274 6.539464 TCCAAAACAAGAGTAAAAGCGTTAGA 59.461 34.615 0.00 0.00 0.00 2.10
282 284 9.194271 AGAGTAAAAGCGTTAGAAAAAGTAGAG 57.806 33.333 0.00 0.00 0.00 2.43
286 288 5.368256 AGCGTTAGAAAAAGTAGAGACGA 57.632 39.130 0.00 0.00 0.00 4.20
301 303 7.208777 AGTAGAGACGATGAAGACGTATTAGA 58.791 38.462 0.00 0.00 43.97 2.10
306 308 3.966844 CGATGAAGACGTATTAGACACGG 59.033 47.826 0.00 0.00 43.59 4.94
376 378 1.301009 GTCATCCGAATCGAGGGCC 60.301 63.158 3.36 0.00 0.00 5.80
427 429 2.439156 GGAAGCGGCAAGGCAGAT 60.439 61.111 1.45 0.00 34.64 2.90
428 430 2.768492 GGAAGCGGCAAGGCAGATG 61.768 63.158 1.45 0.00 34.64 2.90
433 435 2.123982 GGCAAGGCAGATGGGGAG 60.124 66.667 0.00 0.00 0.00 4.30
491 493 1.392534 GGAGAAGAGGAGGTGGGGA 59.607 63.158 0.00 0.00 0.00 4.81
555 558 2.042537 AGGAGAGCCATCTGCCGA 60.043 61.111 0.00 0.00 44.56 5.54
570 573 3.520317 TCTGCCGACTCCCCTTATTTTTA 59.480 43.478 0.00 0.00 0.00 1.52
606 609 6.628856 CGCATTTTATGTTAGAACCATCGAAG 59.371 38.462 0.00 0.00 0.00 3.79
609 612 9.916397 CATTTTATGTTAGAACCATCGAAGTAC 57.084 33.333 0.00 0.00 0.00 2.73
641 644 2.747446 CGAGGTAAAATGGTCAAGTGGG 59.253 50.000 0.00 0.00 0.00 4.61
642 645 3.558321 CGAGGTAAAATGGTCAAGTGGGA 60.558 47.826 0.00 0.00 0.00 4.37
644 647 4.600062 AGGTAAAATGGTCAAGTGGGATC 58.400 43.478 0.00 0.00 0.00 3.36
645 648 4.292306 AGGTAAAATGGTCAAGTGGGATCT 59.708 41.667 0.00 0.00 0.00 2.75
756 767 2.550978 CGGCCAACTAATCGAGTCAAT 58.449 47.619 2.24 0.00 37.44 2.57
952 964 2.275318 CCTCGCTCTCAATTGTTCCTC 58.725 52.381 5.13 0.00 0.00 3.71
957 969 3.668447 GCTCTCAATTGTTCCTCTGTCA 58.332 45.455 5.13 0.00 0.00 3.58
983 998 1.076727 TCTCTCCGTCTCCCAAGCA 59.923 57.895 0.00 0.00 0.00 3.91
1021 1040 1.075050 TGTCCACGGAGAGGTAAGAGT 59.925 52.381 0.00 0.00 39.94 3.24
1040 1059 2.108952 AGTCCCTCAAGAAACCATGCTT 59.891 45.455 0.00 0.00 0.00 3.91
1095 1114 3.541996 AAGGCTCCCTTTGTTTGTTTG 57.458 42.857 0.00 0.00 41.69 2.93
1233 1257 2.595386 CGGCCACAATTTTAGCACTTC 58.405 47.619 2.24 0.00 0.00 3.01
1297 1324 8.909423 TCCATCCAAAATAAACCCTAATCTTT 57.091 30.769 0.00 0.00 0.00 2.52
1298 1325 8.977412 TCCATCCAAAATAAACCCTAATCTTTC 58.023 33.333 0.00 0.00 0.00 2.62
1871 1905 4.074526 GAGCTGCAGGCCGTCAGA 62.075 66.667 25.16 0.00 43.05 3.27
1958 1998 2.126580 GACGACGTTAGTGCCGCT 60.127 61.111 0.13 0.00 0.00 5.52
2191 2231 3.619733 CGGTTCTGGTGATTGATGGAGAA 60.620 47.826 0.00 0.00 0.00 2.87
2307 2349 6.493166 TGTGGATATCTTGGGTGAGAAAAAT 58.507 36.000 2.05 0.00 0.00 1.82
2322 2364 7.182761 GTGAGAAAAATATTGTCCAGTGATCG 58.817 38.462 0.00 0.00 0.00 3.69
2323 2365 7.064609 GTGAGAAAAATATTGTCCAGTGATCGA 59.935 37.037 0.00 0.00 0.00 3.59
2452 2791 4.814771 ACACTTTAACTGACACTAGTTGCC 59.185 41.667 0.00 0.00 40.85 4.52
2462 2801 2.637872 ACACTAGTTGCCAGGCTTAGAA 59.362 45.455 14.15 0.00 0.00 2.10
2463 2802 3.264450 ACACTAGTTGCCAGGCTTAGAAT 59.736 43.478 14.15 0.00 0.00 2.40
2464 2803 4.263506 ACACTAGTTGCCAGGCTTAGAATT 60.264 41.667 14.15 0.00 0.00 2.17
2558 2897 5.733299 TGCAAGCGTGTATATATTTCAACG 58.267 37.500 0.59 0.00 0.00 4.10
2580 2919 4.616802 CGTGGTTATTTTTGCTAAGCAGTG 59.383 41.667 0.00 0.00 40.61 3.66
2811 3151 5.065218 CGAAAGTTTGGGGATCTCACATTAG 59.935 44.000 0.00 0.00 0.00 1.73
2847 3187 6.266786 GTCTTCATTTTCCCTCCAACCTTTTA 59.733 38.462 0.00 0.00 0.00 1.52
2903 3246 4.766404 AGCTGAAAAGGGTTTACAATCG 57.234 40.909 0.00 0.00 0.00 3.34
2924 3267 2.990740 ACTGGGGCCAAAATCAAGTA 57.009 45.000 4.39 0.00 0.00 2.24
2928 3271 4.597075 ACTGGGGCCAAAATCAAGTATTTT 59.403 37.500 4.39 0.00 46.48 1.82
2929 3272 5.073008 ACTGGGGCCAAAATCAAGTATTTTT 59.927 36.000 4.39 0.00 43.75 1.94
3113 3457 6.037610 TGTTTTGGCAATTCGTTATTTTTGCT 59.962 30.769 0.00 0.00 43.04 3.91
3118 3462 5.633182 GGCAATTCGTTATTTTTGCTCAAGA 59.367 36.000 6.46 0.00 43.04 3.02
3120 3464 7.148590 GGCAATTCGTTATTTTTGCTCAAGAAT 60.149 33.333 6.46 4.23 43.04 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 119 8.690203 AGAAACTTTTTGGGGAATTATTTTGG 57.310 30.769 0.00 0.00 0.00 3.28
129 131 4.038642 TCGGAATTGGAGAAACTTTTTGGG 59.961 41.667 0.00 0.00 0.00 4.12
130 132 5.009610 TCTCGGAATTGGAGAAACTTTTTGG 59.990 40.000 3.86 0.00 37.59 3.28
149 151 5.356882 TGTGCAGAAATAAAAGTTCTCGG 57.643 39.130 0.00 0.00 32.96 4.63
150 152 7.678194 TTTTGTGCAGAAATAAAAGTTCTCG 57.322 32.000 10.13 0.00 32.96 4.04
178 180 6.277605 GTTTTTAGCAAAACTACCATGGTGT 58.722 36.000 28.17 19.28 45.80 4.16
192 194 6.261381 ACCTGAACTAACGATGTTTTTAGCAA 59.739 34.615 0.00 0.00 0.00 3.91
203 205 9.226606 TGAATGAAATTAACCTGAACTAACGAT 57.773 29.630 0.00 0.00 36.07 3.73
236 238 6.739112 ACTCTTGTTTTGGACTCTAATTTGC 58.261 36.000 0.00 0.00 0.00 3.68
248 250 6.721321 TCTAACGCTTTTACTCTTGTTTTGG 58.279 36.000 0.00 0.00 0.00 3.28
254 256 9.582223 CTACTTTTTCTAACGCTTTTACTCTTG 57.418 33.333 0.00 0.00 0.00 3.02
260 262 7.862372 TCGTCTCTACTTTTTCTAACGCTTTTA 59.138 33.333 0.00 0.00 0.00 1.52
265 267 5.798934 TCATCGTCTCTACTTTTTCTAACGC 59.201 40.000 0.00 0.00 0.00 4.84
272 274 5.770417 ACGTCTTCATCGTCTCTACTTTTT 58.230 37.500 0.00 0.00 36.85 1.94
282 284 4.665292 CGTGTCTAATACGTCTTCATCGTC 59.335 45.833 0.00 0.00 41.72 4.20
286 288 3.490419 GGCCGTGTCTAATACGTCTTCAT 60.490 47.826 0.00 0.00 39.76 2.57
336 338 1.169661 CGAGTCGGAGGATGAGGAGG 61.170 65.000 4.10 0.00 0.00 4.30
359 361 2.507854 GGGCCCTCGATTCGGATGA 61.508 63.158 17.04 0.00 0.00 2.92
376 378 0.250295 TTCCTGTCAACCGCTTCTGG 60.250 55.000 0.00 0.00 0.00 3.86
417 419 2.123982 CCTCCCCATCTGCCTTGC 60.124 66.667 0.00 0.00 0.00 4.01
465 467 3.157949 CCTCTTCTCCCTCCCCGC 61.158 72.222 0.00 0.00 0.00 6.13
606 609 6.704512 TTTTACCTCGGTTACAATTCGTAC 57.295 37.500 0.00 0.00 0.00 3.67
609 612 5.122711 ACCATTTTACCTCGGTTACAATTCG 59.877 40.000 0.00 0.00 0.00 3.34
641 644 1.065564 ACAAGAAGCTGCCTGGAGATC 60.066 52.381 0.00 0.00 0.00 2.75
642 645 0.990374 ACAAGAAGCTGCCTGGAGAT 59.010 50.000 0.00 0.00 0.00 2.75
644 647 1.613836 AAACAAGAAGCTGCCTGGAG 58.386 50.000 0.00 0.00 0.00 3.86
645 648 1.956477 GAAAACAAGAAGCTGCCTGGA 59.044 47.619 0.00 0.00 0.00 3.86
756 767 1.747325 GCAAGCCAAGCCAAGGAACA 61.747 55.000 0.00 0.00 0.00 3.18
952 964 1.064803 CGGAGAGACGGAGAATGACAG 59.935 57.143 0.00 0.00 0.00 3.51
957 969 1.670791 GAGACGGAGAGACGGAGAAT 58.329 55.000 0.00 0.00 38.39 2.40
983 998 0.769873 CATAGAGGCATGCTCCCCTT 59.230 55.000 18.92 0.52 0.00 3.95
987 1002 0.761187 TGGACATAGAGGCATGCTCC 59.239 55.000 18.92 14.85 31.84 4.70
1021 1040 2.376518 AGAAGCATGGTTTCTTGAGGGA 59.623 45.455 12.13 0.00 30.98 4.20
1040 1059 5.700832 ACAAATCAAGTACAAGCATCGAAGA 59.299 36.000 0.00 0.00 45.75 2.87
1095 1114 6.240549 TCTTCTGACCAGAAAGGATAATCC 57.759 41.667 12.82 0.00 45.75 3.01
1156 1180 6.370718 TCTCTCGATAAACCTTTTAGGCAAAC 59.629 38.462 0.00 0.00 39.63 2.93
1297 1324 4.649705 TCCCTGGTGGAAGCCCGA 62.650 66.667 0.00 0.00 41.40 5.14
1298 1325 4.101448 CTCCCTGGTGGAAGCCCG 62.101 72.222 0.00 0.00 44.57 6.13
1381 1414 2.396955 CGGTGAGACGGCGACTACT 61.397 63.158 16.62 7.15 0.00 2.57
1871 1905 0.610174 TGTGCTTGAAGATCTCGGCT 59.390 50.000 0.00 0.00 0.00 5.52
2191 2231 5.583061 TGGCGAGTTAATTAATCGATTGTGT 59.417 36.000 20.87 7.60 38.72 3.72
2307 2349 6.717084 AGATACATCTCGATCACTGGACAATA 59.283 38.462 0.00 0.00 29.30 1.90
2322 2364 7.882271 AGAAATTTATGAGGGCAGATACATCTC 59.118 37.037 0.00 0.00 34.22 2.75
2323 2365 7.753630 AGAAATTTATGAGGGCAGATACATCT 58.246 34.615 0.00 0.00 37.72 2.90
2452 2791 8.964476 TCTATTTCCAACTAATTCTAAGCCTG 57.036 34.615 0.00 0.00 0.00 4.85
2539 2878 5.353938 ACCACGTTGAAATATATACACGCT 58.646 37.500 0.00 0.00 0.00 5.07
2558 2897 4.385748 GCACTGCTTAGCAAAAATAACCAC 59.614 41.667 8.68 0.00 38.41 4.16
2580 2919 3.471495 AGCACAACATAAAACTAGCGC 57.529 42.857 0.00 0.00 0.00 5.92
2811 3151 5.123979 GGGAAAATGAAGACACATACTCACC 59.876 44.000 0.00 0.00 0.00 4.02
2903 3246 2.525368 ACTTGATTTTGGCCCCAGTAC 58.475 47.619 0.00 0.00 0.00 2.73
2928 3271 7.389330 TGTCATTTCCGAGCTAATCAGTAAAAA 59.611 33.333 0.00 0.00 0.00 1.94
2929 3272 6.876789 TGTCATTTCCGAGCTAATCAGTAAAA 59.123 34.615 0.00 0.00 0.00 1.52
2932 3275 5.105513 TGTGTCATTTCCGAGCTAATCAGTA 60.106 40.000 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.