Multiple sequence alignment - TraesCS2D01G374300

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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 TraesCS2D01G374300 chr2D 100.000 2827 0 0 1 2827 477629330 477626504 0.000000e+00 5221
1 TraesCS2D01G374300 chr2A 89.800 2843 128 68 1 2764 620214433 620211674 0.000000e+00 3494
2 TraesCS2D01G374300 chr2B 90.518 1487 72 24 1 1460 559555675 559554231 0.000000e+00 1901
3 TraesCS2D01G374300 chr2B 89.483 1103 49 20 1509 2572 559554028 559552954 0.000000e+00 1332
4 TraesCS2D01G374300 chr2B 93.488 215 8 5 2597 2811 559552444 559552236 5.880000e-82 315
5 TraesCS2D01G374300 chr5A 77.072 362 48 19 1287 1625 113807481 113807132 2.890000e-40 176
6 TraesCS2D01G374300 chr5B 78.859 298 33 14 1352 1631 119412057 119411772 1.040000e-39 174


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 TraesCS2D01G374300 chr2D 477626504 477629330 2826 True 5221.000000 5221 100.000 1 2827 1 chr2D.!!$R1 2826
1 TraesCS2D01G374300 chr2A 620211674 620214433 2759 True 3494.000000 3494 89.800 1 2764 1 chr2A.!!$R1 2763
2 TraesCS2D01G374300 chr2B 559552236 559555675 3439 True 1182.666667 1901 91.163 1 2811 3 chr2B.!!$R1 2810

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
491 500 0.455295 GAAGCGAGACAGACAGACGG 60.455 60.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1945 2199 0.109153 TGCATGAACACTCACAGGCT 59.891 50.0 0.0 0.0 42.86 4.58 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
77 82 2.568090 CCGGCTGTGTGCATTTCC 59.432 61.111 0.00 0.00 45.15 3.13
229 234 3.740044 AGTAAATTGTGGCGTGAATCG 57.260 42.857 0.00 0.00 43.12 3.34
273 278 1.065636 CCATCACTGTGGCAGAGACAT 60.066 52.381 19.57 6.47 34.31 3.06
274 279 2.617276 CCATCACTGTGGCAGAGACATT 60.617 50.000 19.57 0.00 34.31 2.71
278 283 1.625315 ACTGTGGCAGAGACATTGCTA 59.375 47.619 19.57 0.00 41.27 3.49
279 284 2.038952 ACTGTGGCAGAGACATTGCTAA 59.961 45.455 19.57 0.00 41.27 3.09
342 347 1.411246 ACGCCGCATAATCAAGGACTA 59.589 47.619 0.00 0.00 0.00 2.59
356 362 4.841813 TCAAGGACTACCACTTCCATTACA 59.158 41.667 0.00 0.00 38.94 2.41
362 368 6.405619 GGACTACCACTTCCATTACAGTACTC 60.406 46.154 0.00 0.00 35.97 2.59
452 461 0.883833 GCTACCTGCACAGCATTTGT 59.116 50.000 5.53 0.00 41.94 2.83
488 497 1.169577 GGAGAAGCGAGACAGACAGA 58.830 55.000 0.00 0.00 0.00 3.41
489 498 1.135517 GGAGAAGCGAGACAGACAGAC 60.136 57.143 0.00 0.00 0.00 3.51
490 499 0.519519 AGAAGCGAGACAGACAGACG 59.480 55.000 0.00 0.00 0.00 4.18
491 500 0.455295 GAAGCGAGACAGACAGACGG 60.455 60.000 0.00 0.00 0.00 4.79
663 678 2.731571 TATCCCTCGTGGTGCTGGC 61.732 63.158 2.33 0.00 34.77 4.85
918 936 4.500116 GGTGGCGACGCTCTCCTC 62.500 72.222 20.77 1.85 41.78 3.71
948 966 1.066858 CAGTCGCTCTCCAAAAGCCTA 60.067 52.381 0.00 0.00 36.36 3.93
994 1012 4.101430 ACGAGAAGAGTAGTCCTAGGTAGG 59.899 50.000 9.08 0.00 45.02 3.18
1135 1153 1.140161 TTCCGCGGTGAGTAATCGG 59.860 57.895 27.15 0.00 41.30 4.18
1169 1187 2.600867 CCGTTTCGATCTCTTCTGCTTC 59.399 50.000 0.00 0.00 0.00 3.86
1174 1194 4.116747 TCGATCTCTTCTGCTTCTTTCC 57.883 45.455 0.00 0.00 0.00 3.13
1176 1196 4.221703 TCGATCTCTTCTGCTTCTTTCCTT 59.778 41.667 0.00 0.00 0.00 3.36
1183 1203 0.472471 TGCTTCTTTCCTTCCGTGGT 59.528 50.000 0.00 0.00 0.00 4.16
1257 1280 3.013932 AGGGCCCTGGAGCTTCTG 61.014 66.667 28.05 0.00 0.00 3.02
1285 1308 1.067846 TGTGTGATCTTCCTCGAACCG 60.068 52.381 0.00 0.00 0.00 4.44
1332 1380 5.804979 GCATGTGTTTTACTGTGTGTTCTTT 59.195 36.000 0.00 0.00 0.00 2.52
1432 1480 7.685481 TCAAGAAGGTCAAGGTAATACATCAA 58.315 34.615 0.00 0.00 0.00 2.57
1433 1481 7.606456 TCAAGAAGGTCAAGGTAATACATCAAC 59.394 37.037 0.00 0.00 0.00 3.18
1434 1482 7.016153 AGAAGGTCAAGGTAATACATCAACA 57.984 36.000 0.00 0.00 0.00 3.33
1438 1486 5.938125 GGTCAAGGTAATACATCAACACACT 59.062 40.000 0.00 0.00 0.00 3.55
1450 1498 6.738114 ACATCAACACACTACATCCTTTTTG 58.262 36.000 0.00 0.00 0.00 2.44
1460 1508 4.326504 ACATCCTTTTTGTTCTTGCCAG 57.673 40.909 0.00 0.00 0.00 4.85
1537 1766 3.348647 TGACGATGGAAATGTGATGGT 57.651 42.857 0.00 0.00 0.00 3.55
1552 1781 2.283101 GGTTGCATGCAGGGGTCA 60.283 61.111 21.50 1.22 0.00 4.02
1591 1820 0.536724 CCGTGGTGATCATGTCCTCA 59.463 55.000 0.00 0.00 0.00 3.86
1636 1869 2.882761 CAGGTCAGTATTCCATGGCATG 59.117 50.000 20.56 20.56 0.00 4.06
1787 2022 4.020617 CTGAAGCCCGTCCAGCCA 62.021 66.667 0.00 0.00 0.00 4.75
1919 2173 1.524961 GGACATGGACGCATGGGTA 59.475 57.895 16.26 1.10 36.91 3.69
1935 2189 2.308690 GGGTAGCAGTAGAGTGGTAGG 58.691 57.143 0.00 0.00 31.19 3.18
1939 2193 2.672098 AGCAGTAGAGTGGTAGGATGG 58.328 52.381 0.00 0.00 0.00 3.51
1940 2194 1.069358 GCAGTAGAGTGGTAGGATGGC 59.931 57.143 0.00 0.00 0.00 4.40
1941 2195 2.672098 CAGTAGAGTGGTAGGATGGCT 58.328 52.381 0.00 0.00 0.00 4.75
1943 2197 2.023888 AGTAGAGTGGTAGGATGGCTGT 60.024 50.000 0.00 0.00 0.00 4.40
1944 2198 1.198713 AGAGTGGTAGGATGGCTGTG 58.801 55.000 0.00 0.00 0.00 3.66
1945 2199 1.195115 GAGTGGTAGGATGGCTGTGA 58.805 55.000 0.00 0.00 0.00 3.58
1946 2200 1.137872 GAGTGGTAGGATGGCTGTGAG 59.862 57.143 0.00 0.00 0.00 3.51
1947 2201 0.462759 GTGGTAGGATGGCTGTGAGC 60.463 60.000 0.00 0.00 41.46 4.26
1958 2212 0.533755 GCTGTGAGCCTGTGAGTGTT 60.534 55.000 0.00 0.00 34.48 3.32
1989 2243 1.405105 TGCAGTCTGTGTTTTGCTTCC 59.595 47.619 0.93 0.00 37.45 3.46
2015 2270 1.142688 AGGATGTGCCCTGTTTCCCT 61.143 55.000 0.00 0.00 37.37 4.20
2066 2334 2.747989 GTCAGTGTCTCGTGGATCAGTA 59.252 50.000 0.00 0.00 0.00 2.74
2100 2369 6.765915 AGGAAGTTTGCCTCAAGATATTTC 57.234 37.500 0.00 0.00 0.00 2.17
2161 2433 6.429692 TCTCGCTGAAAAATTTACTCCATCAA 59.570 34.615 0.00 0.00 0.00 2.57
2173 2445 1.197721 CTCCATCAAAGCGTTGGTCAC 59.802 52.381 12.54 0.00 36.10 3.67
2234 2507 3.602915 GTCGATCAAACTCGTACTGTCAC 59.397 47.826 0.00 0.00 39.62 3.67
2308 2581 3.438297 AAGGATGTCCGTAAGATCGTG 57.562 47.619 0.00 0.00 42.08 4.35
2309 2582 1.681793 AGGATGTCCGTAAGATCGTGG 59.318 52.381 0.00 0.00 42.08 4.94
2310 2583 1.407979 GGATGTCCGTAAGATCGTGGT 59.592 52.381 0.00 0.00 43.02 4.16
2316 2589 4.040376 GTCCGTAAGATCGTGGTACATTC 58.960 47.826 0.00 0.00 40.76 2.67
2320 2593 5.334337 CCGTAAGATCGTGGTACATTCGATA 60.334 44.000 15.26 2.79 45.29 2.92
2367 2640 6.471146 ACTCTGCTTCTGAGTTATTTGATGT 58.529 36.000 1.30 0.00 39.07 3.06
2477 2750 3.554324 GTGCATTTGATTGCCAGCATTAG 59.446 43.478 0.00 0.00 42.06 1.73
2582 2856 1.080093 CGTACCACTGTGACGGCAT 60.080 57.895 9.86 0.00 33.01 4.40
2583 2857 0.171679 CGTACCACTGTGACGGCATA 59.828 55.000 9.86 0.00 33.01 3.14
2594 2868 7.041440 CCACTGTGACGGCATATTATCATTTTA 60.041 37.037 9.86 0.00 0.00 1.52
2666 3423 4.565166 CGTGTCAGGATATTCAAAGCGTTA 59.435 41.667 0.00 0.00 0.00 3.18
2674 3431 8.276325 CAGGATATTCAAAGCGTTACATAGTTC 58.724 37.037 0.00 0.00 0.00 3.01
2676 3433 8.774586 GGATATTCAAAGCGTTACATAGTTCAT 58.225 33.333 0.00 0.00 0.00 2.57
2789 3546 3.938963 TGTCTCCGCCATTTGATAAAGTC 59.061 43.478 0.00 0.00 0.00 3.01
2811 3568 4.787280 AGGACTGGAGGAGGGCGG 62.787 72.222 0.00 0.00 0.00 6.13
2813 3570 4.779733 GACTGGAGGAGGGCGGGA 62.780 72.222 0.00 0.00 0.00 5.14
2814 3571 4.332543 ACTGGAGGAGGGCGGGAA 62.333 66.667 0.00 0.00 0.00 3.97
2815 3572 3.787001 CTGGAGGAGGGCGGGAAC 61.787 72.222 0.00 0.00 0.00 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 1.269174 CAATGTGTCCGGAAATGCACA 59.731 47.619 23.18 23.18 44.43 4.57
77 82 1.075542 ACGCATGTACAATGTGTCCG 58.924 50.000 14.67 6.21 38.22 4.79
229 234 4.089208 CGTATATGCGAGCATCAAAGAGTC 59.911 45.833 14.35 0.00 37.82 3.36
269 274 1.348594 GCGCGAGGTTAGCAATGTC 59.651 57.895 12.10 0.00 34.19 3.06
273 278 2.434185 CTGGCGCGAGGTTAGCAA 60.434 61.111 12.10 0.00 34.19 3.91
278 283 3.358076 GACTAGCTGGCGCGAGGTT 62.358 63.158 28.58 12.54 42.38 3.50
279 284 3.827898 GACTAGCTGGCGCGAGGT 61.828 66.667 26.79 26.79 42.38 3.85
342 347 4.321750 CGTGAGTACTGTAATGGAAGTGGT 60.322 45.833 0.00 0.00 0.00 4.16
384 393 0.436150 CGCGTGAGATGACAACAGTG 59.564 55.000 0.00 0.00 0.00 3.66
452 461 5.630069 GCTTCTCCATCATCCCTCTGTAAAA 60.630 44.000 0.00 0.00 0.00 1.52
488 497 3.650950 AGCATCCTTGGTGCCCGT 61.651 61.111 0.00 0.00 43.50 5.28
489 498 3.136123 CAGCATCCTTGGTGCCCG 61.136 66.667 0.00 0.00 43.71 6.13
638 653 1.272490 CACCACGAGGGATACGCATAT 59.728 52.381 3.29 0.00 41.15 1.78
644 659 1.144057 CCAGCACCACGAGGGATAC 59.856 63.158 3.29 0.00 41.15 2.24
948 966 3.913163 ACTGTGGAGAGAAAGGGAAAGAT 59.087 43.478 0.00 0.00 0.00 2.40
994 1012 2.468831 CTTGAAGCTCGCCATCTACTC 58.531 52.381 0.00 0.00 0.00 2.59
995 1013 1.137872 CCTTGAAGCTCGCCATCTACT 59.862 52.381 0.00 0.00 0.00 2.57
996 1014 1.576356 CCTTGAAGCTCGCCATCTAC 58.424 55.000 0.00 0.00 0.00 2.59
997 1015 0.465705 CCCTTGAAGCTCGCCATCTA 59.534 55.000 0.00 0.00 0.00 1.98
1107 1125 3.121030 CCGCGGAACTTGGAGCTG 61.121 66.667 24.07 0.00 0.00 4.24
1169 1187 2.685897 TCACAAAACCACGGAAGGAAAG 59.314 45.455 0.00 0.00 0.00 2.62
1174 1194 1.260561 CTCGTCACAAAACCACGGAAG 59.739 52.381 0.00 0.00 34.24 3.46
1176 1196 0.460722 TCTCGTCACAAAACCACGGA 59.539 50.000 0.00 0.00 34.24 4.69
1183 1203 1.260297 CGCACACATCTCGTCACAAAA 59.740 47.619 0.00 0.00 0.00 2.44
1257 1280 0.741221 GAAGATCACACACGGAGCCC 60.741 60.000 0.00 0.00 0.00 5.19
1266 1289 1.201647 TCGGTTCGAGGAAGATCACAC 59.798 52.381 0.00 0.00 0.00 3.82
1285 1308 5.456822 GCAAAGCACAAAGATATCCGAAATC 59.543 40.000 0.00 0.00 0.00 2.17
1297 1336 4.603231 AAAACACATGCAAAGCACAAAG 57.397 36.364 0.00 0.00 43.04 2.77
1432 1480 6.680378 GCAAGAACAAAAAGGATGTAGTGTGT 60.680 38.462 0.00 0.00 0.00 3.72
1433 1481 5.687285 GCAAGAACAAAAAGGATGTAGTGTG 59.313 40.000 0.00 0.00 0.00 3.82
1434 1482 5.221244 GGCAAGAACAAAAAGGATGTAGTGT 60.221 40.000 0.00 0.00 0.00 3.55
1438 1486 5.009610 GTCTGGCAAGAACAAAAAGGATGTA 59.990 40.000 0.00 0.00 33.05 2.29
1450 1498 2.479566 TCATGGAGTCTGGCAAGAAC 57.520 50.000 0.00 0.00 33.05 3.01
1501 1730 6.878923 TCCATCGTCATCTCAAACAAGTATTT 59.121 34.615 0.00 0.00 0.00 1.40
1537 1766 1.380246 GGATGACCCCTGCATGCAA 60.380 57.895 22.88 5.82 34.66 4.08
1552 1781 1.433121 GGATCTCCCTCAGCTTGGAT 58.567 55.000 4.18 0.00 0.00 3.41
1591 1820 1.629043 TCCTTGTAGGCACGTTCTCT 58.371 50.000 0.00 0.00 34.61 3.10
1640 1873 5.599656 ACAAAAGAATATAGCATGCATGGGT 59.400 36.000 27.34 15.75 0.00 4.51
1919 2173 2.672098 CCATCCTACCACTCTACTGCT 58.328 52.381 0.00 0.00 0.00 4.24
1939 2193 0.533755 AACACTCACAGGCTCACAGC 60.534 55.000 0.00 0.00 41.46 4.40
1940 2194 1.202568 TGAACACTCACAGGCTCACAG 60.203 52.381 0.00 0.00 0.00 3.66
1941 2195 0.829990 TGAACACTCACAGGCTCACA 59.170 50.000 0.00 0.00 0.00 3.58
1943 2197 1.879372 GCATGAACACTCACAGGCTCA 60.879 52.381 0.00 0.00 40.01 4.26
1944 2198 0.801251 GCATGAACACTCACAGGCTC 59.199 55.000 0.00 0.00 40.01 4.70
1945 2199 0.109153 TGCATGAACACTCACAGGCT 59.891 50.000 0.00 0.00 42.86 4.58
1946 2200 1.135489 CATGCATGAACACTCACAGGC 60.135 52.381 22.59 0.00 42.77 4.85
1947 2201 1.135489 GCATGCATGAACACTCACAGG 60.135 52.381 30.64 0.00 33.30 4.00
1948 2202 1.538075 TGCATGCATGAACACTCACAG 59.462 47.619 30.64 0.00 33.30 3.66
1949 2203 1.606903 TGCATGCATGAACACTCACA 58.393 45.000 30.64 12.71 33.30 3.58
1989 2243 1.091771 CAGGGCACATCCTACTTGCG 61.092 60.000 0.00 0.00 37.11 4.85
2015 2270 2.745821 ACGTCGACTGCTACATAACAGA 59.254 45.455 14.70 0.00 37.35 3.41
2066 2334 6.323739 TGAGGCAAACTTCCTTTTTACTGAAT 59.676 34.615 0.00 0.00 33.24 2.57
2100 2369 4.080582 TCAACATGTACCATAACAGAGGGG 60.081 45.833 0.00 0.00 31.20 4.79
2131 2400 6.963805 GGAGTAAATTTTTCAGCGAGATCAAG 59.036 38.462 0.00 0.00 0.00 3.02
2173 2445 0.593773 CCAAAGGGCACAAACGAACG 60.594 55.000 0.00 0.00 0.00 3.95
2174 2446 0.741915 TCCAAAGGGCACAAACGAAC 59.258 50.000 0.00 0.00 0.00 3.95
2308 2581 6.047231 ACCAAAAGTAGCTATCGAATGTACC 58.953 40.000 0.00 0.00 0.00 3.34
2309 2582 7.277098 TGAACCAAAAGTAGCTATCGAATGTAC 59.723 37.037 0.00 0.00 0.00 2.90
2310 2583 7.324935 TGAACCAAAAGTAGCTATCGAATGTA 58.675 34.615 0.00 0.00 0.00 2.29
2316 2589 5.122396 AGCTTTGAACCAAAAGTAGCTATCG 59.878 40.000 0.00 0.00 39.02 2.92
2320 2593 3.954258 ACAGCTTTGAACCAAAAGTAGCT 59.046 39.130 0.00 0.00 39.02 3.32
2477 2750 5.031578 CAGAGTACAGATCGAAGCAACTAC 58.968 45.833 0.00 0.00 0.00 2.73
2563 2836 3.110178 GCCGTCACAGTGGTACGC 61.110 66.667 12.51 6.23 40.45 4.42
2564 2837 0.171679 TATGCCGTCACAGTGGTACG 59.828 55.000 11.35 11.35 36.42 3.67
2635 3392 4.868171 TGAATATCCTGACACGCTTTGTAC 59.132 41.667 0.00 0.00 39.17 2.90
2676 3433 9.736414 CCTGGAGTAGCTAATACTGTATTAGTA 57.264 37.037 32.30 24.14 45.06 1.82
2677 3434 8.226112 ACCTGGAGTAGCTAATACTGTATTAGT 58.774 37.037 32.30 24.82 45.06 2.24
2678 3435 8.638629 ACCTGGAGTAGCTAATACTGTATTAG 57.361 38.462 30.13 30.13 45.06 1.73
2789 3546 1.053264 CCCTCCTCCAGTCCTCCATG 61.053 65.000 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.