Multiple sequence alignment - TraesCS4D01G204000

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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 TraesCS4D01G204000 chr4D 100.000 3429 0 0 1 3429 351468425 351464997 0.000000e+00 6333
1 TraesCS4D01G204000 chr4A 93.770 1846 62 28 1620 3429 113853940 113855768 0.000000e+00 2723
2 TraesCS4D01G204000 chr4A 93.163 863 37 5 779 1619 113853031 113853893 0.000000e+00 1247
3 TraesCS4D01G204000 chr4A 93.553 760 39 3 1 759 113852168 113852918 0.000000e+00 1123
4 TraesCS4D01G204000 chr4A 88.539 349 23 7 414 751 120453618 120453276 1.150000e-109 407
5 TraesCS4D01G204000 chr4A 96.815 157 5 0 775 931 120413660 120413504 2.620000e-66 263
6 TraesCS4D01G204000 chr4B 91.469 926 47 14 2522 3429 434468535 434467624 0.000000e+00 1243
7 TraesCS4D01G204000 chr4B 92.865 869 36 11 1620 2476 434469385 434468531 0.000000e+00 1238
8 TraesCS4D01G204000 chr4B 92.882 857 24 6 779 1619 434470265 434469430 0.000000e+00 1210
9 TraesCS4D01G204000 chr4B 93.856 765 29 9 1 759 434471133 434470381 0.000000e+00 1136


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 TraesCS4D01G204000 chr4D 351464997 351468425 3428 True 6333.000000 6333 100.000000 1 3429 1 chr4D.!!$R1 3428
1 TraesCS4D01G204000 chr4A 113852168 113855768 3600 False 1697.666667 2723 93.495333 1 3429 3 chr4A.!!$F1 3428
2 TraesCS4D01G204000 chr4B 434467624 434471133 3509 True 1206.750000 1243 92.768000 1 3429 4 chr4B.!!$R1 3428

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
165 166 0.033011 ACGATGACCACCTAGAGGCT 60.033 55.0 0.00 0.0 39.32 4.58 F
1130 1249 0.319986 TGATTGCGCCGAACTGTACA 60.320 50.0 4.18 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2048 2238 0.103026 TGGCTGTCGATGAGATTCGG 59.897 55.0 0.00 0.0 39.56 4.30 R
2999 3216 0.462759 GAATGCGCAGAAGGGTAGCT 60.463 55.0 18.32 0.0 0.00 3.32 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
52 53 0.784778 GAAGTGCTCGGACAAGTTCG 59.215 55.000 0.00 0.00 0.00 3.95
83 84 5.500234 AGATAAGGTCTGCTTAATGTGCAA 58.500 37.500 0.00 0.00 40.13 4.08
138 139 2.442126 AGAGAAAGGAGGAACGGGTTTT 59.558 45.455 0.00 0.00 0.00 2.43
144 145 4.693525 GGAACGGGTTTTGCCGCG 62.694 66.667 0.00 0.00 38.44 6.46
165 166 0.033011 ACGATGACCACCTAGAGGCT 60.033 55.000 0.00 0.00 39.32 4.58
178 179 5.046950 CACCTAGAGGCTAAGAACTTCAAGT 60.047 44.000 0.00 0.00 39.32 3.16
227 228 0.905357 GTGAAGCCTGCTCCTAAGGA 59.095 55.000 0.00 0.00 36.91 3.36
276 277 7.262048 TGTTGTATAATGCTGTCAGTTATCGA 58.738 34.615 0.93 0.00 0.00 3.59
277 278 7.222031 TGTTGTATAATGCTGTCAGTTATCGAC 59.778 37.037 0.93 4.70 0.00 4.20
278 279 7.039313 TGTATAATGCTGTCAGTTATCGACT 57.961 36.000 0.93 0.00 39.89 4.18
279 280 7.489160 TGTATAATGCTGTCAGTTATCGACTT 58.511 34.615 0.93 0.00 36.10 3.01
280 281 8.626526 TGTATAATGCTGTCAGTTATCGACTTA 58.373 33.333 0.93 0.00 36.10 2.24
281 282 9.627395 GTATAATGCTGTCAGTTATCGACTTAT 57.373 33.333 0.93 0.00 36.10 1.73
282 283 8.749841 ATAATGCTGTCAGTTATCGACTTATC 57.250 34.615 0.93 0.00 36.10 1.75
397 399 3.419943 TCCAAGTGATAATGTGCTTGCA 58.580 40.909 0.00 0.00 37.56 4.08
421 423 3.371102 TTGCTCCGATGCAGTATCTAC 57.629 47.619 0.00 0.00 44.27 2.59
442 444 1.269448 GGATTTCTTTGGCGCTTGACA 59.731 47.619 7.64 0.00 0.00 3.58
449 451 0.592637 TTGGCGCTTGACATGTCTTG 59.407 50.000 25.55 18.18 0.00 3.02
458 460 3.988379 TGACATGTCTTGCCAGTTTTC 57.012 42.857 25.55 0.00 0.00 2.29
524 526 6.757010 TGTAAGAGCAGATATTCGTTTTCCTC 59.243 38.462 0.00 0.00 0.00 3.71
531 536 5.231568 CAGATATTCGTTTTCCTCGTACCAC 59.768 44.000 0.00 0.00 0.00 4.16
541 546 1.338674 CCTCGTACCACCATGCTTTGA 60.339 52.381 0.00 0.00 0.00 2.69
545 550 2.746904 CGTACCACCATGCTTTGATCAA 59.253 45.455 3.38 3.38 0.00 2.57
556 561 6.530534 CCATGCTTTGATCAAATTCAGAACTC 59.469 38.462 20.76 3.78 0.00 3.01
580 585 2.431454 GCCTCTTTGGAACTTCTGGAG 58.569 52.381 0.00 0.00 38.35 3.86
631 637 4.337836 GTCCCTAGTGGTAAGCAGTACTAC 59.662 50.000 0.00 6.10 42.88 2.73
735 741 9.237187 TCTACAGATTATGTCTCCATCTATGTC 57.763 37.037 0.00 0.00 42.70 3.06
754 760 2.865551 GTCGTTAAACCACAGGAAACGA 59.134 45.455 15.86 15.86 46.67 3.85
774 809 4.275936 ACGAAGAAAATCACCACAGGAAAG 59.724 41.667 0.00 0.00 0.00 2.62
775 810 4.515191 CGAAGAAAATCACCACAGGAAAGA 59.485 41.667 0.00 0.00 0.00 2.52
776 811 5.334414 CGAAGAAAATCACCACAGGAAAGAG 60.334 44.000 0.00 0.00 0.00 2.85
777 812 4.401925 AGAAAATCACCACAGGAAAGAGG 58.598 43.478 0.00 0.00 0.00 3.69
882 984 5.123820 TGAAAAGGATAATGGAAACGCTGAG 59.876 40.000 0.00 0.00 0.00 3.35
1035 1149 3.571401 AGAGCTTGATTTCCAAACAGGTG 59.429 43.478 0.00 0.00 39.02 4.00
1130 1249 0.319986 TGATTGCGCCGAACTGTACA 60.320 50.000 4.18 0.00 0.00 2.90
1139 1258 1.067846 CCGAACTGTACAGCTACTGCA 60.068 52.381 22.90 0.00 42.74 4.41
1160 1279 2.507944 CTGAATGGGGCTCCTCCG 59.492 66.667 3.07 0.00 34.94 4.63
1226 1345 5.140747 AGAGTAATTCTCGTCTGCTGTTT 57.859 39.130 0.00 0.00 46.86 2.83
1242 1361 8.289618 GTCTGCTGTTTATCTCAATGTGTTTTA 58.710 33.333 0.00 0.00 0.00 1.52
1262 1381 5.622346 TTAAAAGGTTGGCACAGGAAAAT 57.378 34.783 0.00 0.00 42.39 1.82
1285 1407 8.744568 AATTTGTTGATAGAATCTCTCTTCCC 57.255 34.615 0.00 0.00 35.41 3.97
1295 1417 4.946478 ATCTCTCTTCCCGACCTTATTG 57.054 45.455 0.00 0.00 0.00 1.90
1436 1558 1.174712 ATGGCAGCCGATATGCAACC 61.175 55.000 7.03 0.00 45.68 3.77
1544 1672 2.233186 AGTACCAAAGAACTACCGCTCC 59.767 50.000 0.00 0.00 0.00 4.70
1694 1883 5.336690 GCTTGGCTCTTGGATTTCACATAAA 60.337 40.000 0.00 0.00 0.00 1.40
1860 2049 3.130734 TGGATGAGGTAGGTAGCCTTT 57.869 47.619 0.00 0.00 36.29 3.11
1875 2064 1.133216 GCCTTTCGCCTGGATTTTCTC 59.867 52.381 0.00 0.00 0.00 2.87
2081 2273 3.744660 GACAGCCATAGAATTCCCGATT 58.255 45.455 0.65 0.00 0.00 3.34
2114 2306 4.992951 GCAAAGATTGGAAAAATGAGCAGT 59.007 37.500 0.00 0.00 0.00 4.40
2115 2307 5.467735 GCAAAGATTGGAAAAATGAGCAGTT 59.532 36.000 0.00 0.00 0.00 3.16
2116 2308 6.017687 GCAAAGATTGGAAAAATGAGCAGTTT 60.018 34.615 0.00 0.00 0.00 2.66
2117 2309 7.570161 CAAAGATTGGAAAAATGAGCAGTTTC 58.430 34.615 0.00 0.00 0.00 2.78
2494 2690 2.112297 GGGCGAAACCTGGTGTCA 59.888 61.111 16.99 0.00 39.10 3.58
2495 2691 2.258726 GGGCGAAACCTGGTGTCAC 61.259 63.158 16.99 7.15 39.10 3.67
2496 2692 2.604174 GGCGAAACCTGGTGTCACG 61.604 63.158 16.99 12.79 34.51 4.35
2586 2783 8.151141 TGTACGAATCTAGTAGAACCAGTATG 57.849 38.462 3.45 0.00 0.00 2.39
2692 2894 2.092538 TGTTCTTGTTTCCACGGGGTAA 60.093 45.455 2.12 0.00 34.93 2.85
2695 2897 2.089201 CTTGTTTCCACGGGGTAATCC 58.911 52.381 2.12 0.00 34.93 3.01
2716 2932 3.421741 CACACACGAACAAACGACAATT 58.578 40.909 0.00 0.00 37.03 2.32
2719 2935 4.201871 ACACACGAACAAACGACAATTCAT 60.202 37.500 0.00 0.00 37.03 2.57
2722 2938 5.006844 ACACGAACAAACGACAATTCATACA 59.993 36.000 0.00 0.00 37.03 2.29
2731 2947 4.024893 ACGACAATTCATACAATCATCGCC 60.025 41.667 0.00 0.00 0.00 5.54
2758 2974 5.657745 ACAGGCATATTCATGAAATCACCAA 59.342 36.000 13.09 0.00 33.67 3.67
2764 2980 9.321562 GCATATTCATGAAATCACCAAGAATTT 57.678 29.630 13.09 0.00 33.67 1.82
2816 3032 3.691118 CACACCTGAATCATCAAATCGGT 59.309 43.478 0.00 0.00 34.49 4.69
2999 3216 6.033341 CAGTCGAAAATTTTGTCAAGACCAA 58.967 36.000 8.47 0.00 0.00 3.67
3002 3219 5.043248 CGAAAATTTTGTCAAGACCAAGCT 58.957 37.500 8.47 0.00 0.00 3.74
3034 3251 0.676466 ATTCGGAACATCGCCAGCAA 60.676 50.000 0.00 0.00 0.00 3.91
3143 3361 7.448469 CCAACATTAATTACATTAGCCTAGCCT 59.552 37.037 0.00 0.00 0.00 4.58
3144 3362 9.502091 CAACATTAATTACATTAGCCTAGCCTA 57.498 33.333 0.00 0.00 0.00 3.93
3145 3363 9.726438 AACATTAATTACATTAGCCTAGCCTAG 57.274 33.333 0.00 0.00 0.00 3.02
3146 3364 7.824779 ACATTAATTACATTAGCCTAGCCTAGC 59.175 37.037 0.00 0.00 0.00 3.42
3147 3365 4.828072 ATTACATTAGCCTAGCCTAGCC 57.172 45.455 0.00 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.340088 TGCAGAAAACATGGCCACAT 58.660 45.000 8.16 0.00 37.99 3.21
83 84 1.134220 TCCTCTCTTTGCACGGTTTGT 60.134 47.619 0.00 0.00 0.00 2.83
144 145 0.103208 CCTCTAGGTGGTCATCGTGC 59.897 60.000 0.00 0.00 0.00 5.34
165 166 8.319146 CCACTCCCTAAATACTTGAAGTTCTTA 58.681 37.037 1.97 1.20 0.00 2.10
178 179 2.508300 GCCCAGAACCACTCCCTAAATA 59.492 50.000 0.00 0.00 0.00 1.40
227 228 9.243105 ACAACAGTTACATAATTGAAGGCTATT 57.757 29.630 1.58 0.00 0.00 1.73
276 277 3.898380 TCGTGCCACAACGATAAGT 57.102 47.368 0.00 0.00 46.99 2.24
282 283 5.428770 GTTACATATATTCGTGCCACAACG 58.571 41.667 0.00 0.00 44.92 4.10
283 284 5.526111 AGGTTACATATATTCGTGCCACAAC 59.474 40.000 0.00 0.00 0.00 3.32
397 399 2.472695 TACTGCATCGGAGCAAAACT 57.527 45.000 4.37 0.00 45.13 2.66
421 423 0.521291 TCAAGCGCCAAAGAAATCCG 59.479 50.000 2.29 0.00 0.00 4.18
442 444 5.536161 ACAACATAGAAAACTGGCAAGACAT 59.464 36.000 0.00 0.00 0.00 3.06
449 451 4.275936 AGTGTGACAACATAGAAAACTGGC 59.724 41.667 0.00 0.00 38.92 4.85
458 460 5.579904 CAGAATCTCCAGTGTGACAACATAG 59.420 44.000 0.00 0.00 38.92 2.23
524 526 2.355197 TGATCAAAGCATGGTGGTACG 58.645 47.619 0.00 0.00 0.00 3.67
531 536 6.395629 AGTTCTGAATTTGATCAAAGCATGG 58.604 36.000 24.17 14.03 33.32 3.66
541 546 2.369394 GCCCCGAGTTCTGAATTTGAT 58.631 47.619 1.99 0.00 0.00 2.57
545 550 0.253327 GAGGCCCCGAGTTCTGAATT 59.747 55.000 0.00 0.00 0.00 2.17
556 561 0.960861 GAAGTTCCAAAGAGGCCCCG 60.961 60.000 0.00 0.00 37.29 5.73
592 597 1.065709 GGGACTCTTTGGATTGCCGTA 60.066 52.381 0.00 0.00 36.79 4.02
595 600 2.239907 ACTAGGGACTCTTTGGATTGCC 59.760 50.000 0.00 0.00 41.75 4.52
631 637 5.647658 TGCAAAGGGATATGTTACAGACTTG 59.352 40.000 0.00 0.00 0.00 3.16
735 741 3.556775 TCTTCGTTTCCTGTGGTTTAACG 59.443 43.478 0.00 0.00 41.95 3.18
754 760 4.829492 CCTCTTTCCTGTGGTGATTTTCTT 59.171 41.667 0.00 0.00 0.00 2.52
774 809 5.712917 CCCTTCTGATGGATAGTACTACCTC 59.287 48.000 4.31 0.00 0.00 3.85
775 810 5.375956 TCCCTTCTGATGGATAGTACTACCT 59.624 44.000 4.31 0.00 0.00 3.08
776 811 5.642165 TCCCTTCTGATGGATAGTACTACC 58.358 45.833 4.31 9.33 0.00 3.18
777 812 7.451877 TCATTCCCTTCTGATGGATAGTACTAC 59.548 40.741 4.31 0.00 0.00 2.73
1035 1149 1.956477 ACAGGGTTCATTCAAGCACAC 59.044 47.619 0.00 0.00 33.79 3.82
1130 1249 1.681166 CCATTCAGCCTTGCAGTAGCT 60.681 52.381 1.71 1.71 42.74 3.32
1139 1258 1.931007 GAGGAGCCCCATTCAGCCTT 61.931 60.000 0.00 0.00 33.88 4.35
1160 1279 3.103911 CTCGCGTTCACCACCGAC 61.104 66.667 5.77 0.00 0.00 4.79
1226 1345 7.870445 GCCAACCTTTTAAAACACATTGAGATA 59.130 33.333 0.00 0.00 0.00 1.98
1242 1361 4.502105 AATTTTCCTGTGCCAACCTTTT 57.498 36.364 0.00 0.00 0.00 2.27
1262 1381 6.154534 TCGGGAAGAGAGATTCTATCAACAAA 59.845 38.462 10.72 0.00 34.14 2.83
1295 1417 5.412904 CCAATCTCCTTTTTGTGACCTCTAC 59.587 44.000 0.00 0.00 0.00 2.59
1464 1586 4.122776 CACACAATCCTACATGCTACTCC 58.877 47.826 0.00 0.00 0.00 3.85
1466 1588 4.681781 GCTCACACAATCCTACATGCTACT 60.682 45.833 0.00 0.00 0.00 2.57
1467 1589 3.557595 GCTCACACAATCCTACATGCTAC 59.442 47.826 0.00 0.00 0.00 3.58
1670 1845 1.888512 TGTGAAATCCAAGAGCCAAGC 59.111 47.619 0.00 0.00 0.00 4.01
1682 1865 6.368791 GGGGAACAAAAGCTTTATGTGAAATC 59.631 38.462 13.10 11.97 0.00 2.17
1683 1866 6.230472 GGGGAACAAAAGCTTTATGTGAAAT 58.770 36.000 13.10 4.48 0.00 2.17
1684 1867 5.454045 GGGGGAACAAAAGCTTTATGTGAAA 60.454 40.000 13.10 0.00 0.00 2.69
1694 1883 2.117423 CCCGGGGGAACAAAAGCT 59.883 61.111 14.71 0.00 37.50 3.74
1860 2049 0.895530 AGTCGAGAAAATCCAGGCGA 59.104 50.000 0.00 0.00 0.00 5.54
1875 2064 2.996621 GACAAGATCTGGTCCAAAGTCG 59.003 50.000 18.30 0.00 0.00 4.18
2048 2238 0.103026 TGGCTGTCGATGAGATTCGG 59.897 55.000 0.00 0.00 39.56 4.30
2099 2291 6.959639 AGTAAGAAACTGCTCATTTTTCCA 57.040 33.333 0.00 0.00 36.93 3.53
2114 2306 9.081997 CAATTTACAGCACAACAAAGTAAGAAA 57.918 29.630 0.00 0.00 0.00 2.52
2115 2307 7.704472 CCAATTTACAGCACAACAAAGTAAGAA 59.296 33.333 0.00 0.00 0.00 2.52
2116 2308 7.199766 CCAATTTACAGCACAACAAAGTAAGA 58.800 34.615 0.00 0.00 0.00 2.10
2117 2309 6.074356 GCCAATTTACAGCACAACAAAGTAAG 60.074 38.462 0.00 0.00 0.00 2.34
2520 2717 2.425539 TGAGCAATGCAGATTCGTTGA 58.574 42.857 8.35 0.00 35.53 3.18
2557 2754 5.651139 TGGTTCTACTAGATTCGTACAAGCT 59.349 40.000 0.00 0.00 0.00 3.74
2586 2783 8.986477 AGTAAATTTTGACCACTAATTCATGC 57.014 30.769 0.00 0.00 0.00 4.06
2633 2834 3.335183 CCTAGGATCATACTCCCTCTGGA 59.665 52.174 1.05 0.00 38.75 3.86
2692 2894 1.595794 GTCGTTTGTTCGTGTGTGGAT 59.404 47.619 0.00 0.00 0.00 3.41
2695 2897 2.512289 TTGTCGTTTGTTCGTGTGTG 57.488 45.000 0.00 0.00 0.00 3.82
2716 2932 3.627123 CCTGTTTGGCGATGATTGTATGA 59.373 43.478 0.00 0.00 0.00 2.15
2731 2947 6.477688 GGTGATTTCATGAATATGCCTGTTTG 59.522 38.462 9.40 0.00 34.21 2.93
2743 2959 8.869109 AGGTTAAATTCTTGGTGATTTCATGAA 58.131 29.630 3.38 3.38 34.39 2.57
2744 2960 8.421249 AGGTTAAATTCTTGGTGATTTCATGA 57.579 30.769 0.00 0.00 0.00 3.07
2774 2990 7.990886 AGGTGTGTGTAAAGAGAATTGTTCTTA 59.009 33.333 3.03 0.00 40.87 2.10
2775 2991 6.828785 AGGTGTGTGTAAAGAGAATTGTTCTT 59.171 34.615 0.00 0.00 40.87 2.52
2780 2996 6.618287 TTCAGGTGTGTGTAAAGAGAATTG 57.382 37.500 0.00 0.00 0.00 2.32
2782 2998 6.533730 TGATTCAGGTGTGTGTAAAGAGAAT 58.466 36.000 0.00 0.00 0.00 2.40
2785 3001 5.934043 TGATGATTCAGGTGTGTGTAAAGAG 59.066 40.000 0.00 0.00 0.00 2.85
2816 3032 6.072230 TCGATTCATTTCACCTTTGTAATGCA 60.072 34.615 0.00 0.00 39.28 3.96
2999 3216 0.462759 GAATGCGCAGAAGGGTAGCT 60.463 55.000 18.32 0.00 0.00 3.32
3002 3219 1.153449 CCGAATGCGCAGAAGGGTA 60.153 57.895 18.32 0.00 35.83 3.69
3168 3386 0.036199 TTGATGCAGCCCCATTTTGC 60.036 50.000 0.00 0.00 38.30 3.68


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

AutoCloner maintained by Alex Coulton.