Multiple sequence alignment - TraesCS3D01G217800

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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 TraesCS3D01G217800 chr3D 100.000 3262 0 0 1 3262 296038393 296041654 0.000000e+00 6024
1 TraesCS3D01G217800 chr3A 93.095 2578 68 26 730 3258 394025777 394028293 0.000000e+00 3674
2 TraesCS3D01G217800 chr3A 89.930 715 54 10 1 713 394025007 394025705 0.000000e+00 905
3 TraesCS3D01G217800 chr3B 92.058 1725 59 15 1573 3260 390453238 390454921 0.000000e+00 2355
4 TraesCS3D01G217800 chr3B 96.259 1203 34 7 393 1587 390452024 390453223 0.000000e+00 1962
5 TraesCS3D01G217800 chr3B 92.819 376 21 4 1 371 390451667 390452041 1.030000e-149 540


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 TraesCS3D01G217800 chr3D 296038393 296041654 3261 False 6024.0 6024 100.0000 1 3262 1 chr3D.!!$F1 3261
1 TraesCS3D01G217800 chr3A 394025007 394028293 3286 False 2289.5 3674 91.5125 1 3258 2 chr3A.!!$F1 3257
2 TraesCS3D01G217800 chr3B 390451667 390454921 3254 False 1619.0 2355 93.7120 1 3260 3 chr3B.!!$F1 3259

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
965 1058 2.427410 GCACCAAAAGACAGCGCG 60.427 61.111 0.00 0.00 0.00 6.86 F
1671 1828 0.250234 CAGGAGTTCCATGGAGCGAA 59.750 55.000 21.36 0.95 38.89 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1949 2106 0.175302 CCTGCAGTGGTTTGTTTGCA 59.825 50.000 13.81 0.0 43.62 4.08 R
2963 3152 1.349357 GTTGGCCAGGAAGAGAGAAGT 59.651 52.381 5.11 0.0 0.00 3.01 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
46 47 6.669591 TCAGTTGAGATGAGAAAGGAATCCTA 59.330 38.462 0.46 0.00 31.13 2.94
174 175 2.512515 GTGGTGCGAGATCCTGCC 60.513 66.667 4.50 0.00 0.00 4.85
214 216 5.412640 CATGTGAAAGAAAGCCATATTGCA 58.587 37.500 1.13 0.00 0.00 4.08
228 230 8.292444 AGCCATATTGCAAGACTTAATGTAAA 57.708 30.769 4.94 0.00 0.00 2.01
229 231 8.917088 AGCCATATTGCAAGACTTAATGTAAAT 58.083 29.630 4.94 0.00 0.00 1.40
371 404 9.440761 AGTAGAATGATACTCCCTTTGTATCTT 57.559 33.333 12.94 6.13 43.79 2.40
374 407 9.981460 AGAATGATACTCCCTTTGTATCTTTTT 57.019 29.630 12.94 7.27 43.79 1.94
519 552 7.404671 TGCCCTAATAAAAGAAGCCTAAAAG 57.595 36.000 0.00 0.00 0.00 2.27
531 564 8.697507 AAGAAGCCTAAAAGAAGATGAAAGAA 57.302 30.769 0.00 0.00 0.00 2.52
532 565 8.697507 AGAAGCCTAAAAGAAGATGAAAGAAA 57.302 30.769 0.00 0.00 0.00 2.52
691 725 3.825308 ACAGTGCAAATTTACGCATCAG 58.175 40.909 6.49 3.39 40.89 2.90
722 785 8.087750 TCAAATTACCAGTTAAATCCAAGCAAG 58.912 33.333 0.00 0.00 0.00 4.01
764 857 8.490355 CGAACAATAAGTACTTTTCTACGGTTT 58.510 33.333 14.49 0.00 0.00 3.27
832 925 6.876257 AGTAGAAGCAGCATATTTATAGTGGC 59.124 38.462 0.00 0.00 0.00 5.01
965 1058 2.427410 GCACCAAAAGACAGCGCG 60.427 61.111 0.00 0.00 0.00 6.86
1078 1174 1.819305 GCACAGGAAAGCAGGGAGAAA 60.819 52.381 0.00 0.00 0.00 2.52
1399 1500 4.153475 TGCCTAAACAGAAATACGCAGTTC 59.847 41.667 0.00 0.00 37.78 3.01
1443 1544 0.972134 TGCTAGGCTGGCTATGCTAG 59.028 55.000 23.69 11.91 40.15 3.42
1542 1697 9.309516 CTTGACCTAACTAATAAAGTCGCATTA 57.690 33.333 0.00 0.00 37.50 1.90
1543 1698 9.826574 TTGACCTAACTAATAAAGTCGCATTAT 57.173 29.630 0.00 0.00 37.50 1.28
1544 1699 9.472361 TGACCTAACTAATAAAGTCGCATTATC 57.528 33.333 0.00 0.00 37.50 1.75
1545 1700 8.828688 ACCTAACTAATAAAGTCGCATTATCC 57.171 34.615 0.00 0.00 37.50 2.59
1548 1703 7.964604 AACTAATAAAGTCGCATTATCCCTC 57.035 36.000 0.00 0.00 37.50 4.30
1549 1704 7.304497 ACTAATAAAGTCGCATTATCCCTCT 57.696 36.000 0.00 0.00 30.33 3.69
1550 1705 7.379750 ACTAATAAAGTCGCATTATCCCTCTC 58.620 38.462 0.00 0.00 30.33 3.20
1551 1706 5.808366 ATAAAGTCGCATTATCCCTCTCA 57.192 39.130 0.00 0.00 0.00 3.27
1552 1707 4.487714 AAAGTCGCATTATCCCTCTCAA 57.512 40.909 0.00 0.00 0.00 3.02
1553 1708 4.487714 AAGTCGCATTATCCCTCTCAAA 57.512 40.909 0.00 0.00 0.00 2.69
1554 1709 4.487714 AGTCGCATTATCCCTCTCAAAA 57.512 40.909 0.00 0.00 0.00 2.44
1555 1710 4.843728 AGTCGCATTATCCCTCTCAAAAA 58.156 39.130 0.00 0.00 0.00 1.94
1649 1806 3.407424 TGGTCCTTCTGTGAACATGAG 57.593 47.619 0.00 0.00 0.00 2.90
1671 1828 0.250234 CAGGAGTTCCATGGAGCGAA 59.750 55.000 21.36 0.95 38.89 4.70
1710 1867 2.125350 GTGGGCCTCGAGAAGCTG 60.125 66.667 15.71 0.00 0.00 4.24
1879 2036 8.653036 ACTGGAGTACTACATCTTAACTTCTT 57.347 34.615 8.62 0.00 0.00 2.52
1880 2037 9.750783 ACTGGAGTACTACATCTTAACTTCTTA 57.249 33.333 8.62 0.00 0.00 2.10
1942 2099 7.114754 ACATGTCAGATTCTGAATATGGTGTT 58.885 34.615 28.11 15.48 42.46 3.32
1943 2100 8.267183 ACATGTCAGATTCTGAATATGGTGTTA 58.733 33.333 28.11 2.88 42.46 2.41
1944 2101 8.554528 CATGTCAGATTCTGAATATGGTGTTAC 58.445 37.037 21.06 13.49 42.46 2.50
1945 2102 7.851228 TGTCAGATTCTGAATATGGTGTTACT 58.149 34.615 21.06 1.75 42.46 2.24
1946 2103 8.321353 TGTCAGATTCTGAATATGGTGTTACTT 58.679 33.333 21.06 0.00 42.46 2.24
1947 2104 8.607459 GTCAGATTCTGAATATGGTGTTACTTG 58.393 37.037 21.06 0.00 42.46 3.16
1948 2105 8.539544 TCAGATTCTGAATATGGTGTTACTTGA 58.460 33.333 21.06 0.00 37.57 3.02
1949 2106 9.334947 CAGATTCTGAATATGGTGTTACTTGAT 57.665 33.333 15.42 0.00 32.44 2.57
1950 2107 9.334947 AGATTCTGAATATGGTGTTACTTGATG 57.665 33.333 2.28 0.00 0.00 3.07
1951 2108 6.925610 TCTGAATATGGTGTTACTTGATGC 57.074 37.500 0.00 0.00 0.00 3.91
1952 2109 6.413892 TCTGAATATGGTGTTACTTGATGCA 58.586 36.000 0.00 0.00 0.00 3.96
1953 2110 6.883756 TCTGAATATGGTGTTACTTGATGCAA 59.116 34.615 0.00 0.00 0.00 4.08
1954 2111 7.392953 TCTGAATATGGTGTTACTTGATGCAAA 59.607 33.333 0.00 0.00 0.00 3.68
1955 2112 7.312154 TGAATATGGTGTTACTTGATGCAAAC 58.688 34.615 0.00 0.00 0.00 2.93
1956 2113 6.832520 ATATGGTGTTACTTGATGCAAACA 57.167 33.333 0.00 0.00 0.00 2.83
1957 2114 4.991153 TGGTGTTACTTGATGCAAACAA 57.009 36.364 1.13 5.42 33.92 2.83
1958 2115 5.330455 TGGTGTTACTTGATGCAAACAAA 57.670 34.783 10.12 0.00 33.92 2.83
1959 2116 5.105752 TGGTGTTACTTGATGCAAACAAAC 58.894 37.500 10.12 7.07 33.92 2.93
1960 2117 4.506288 GGTGTTACTTGATGCAAACAAACC 59.494 41.667 10.12 10.08 33.92 3.27
1961 2118 5.105752 GTGTTACTTGATGCAAACAAACCA 58.894 37.500 10.12 3.64 33.92 3.67
1962 2119 5.005299 GTGTTACTTGATGCAAACAAACCAC 59.995 40.000 10.12 9.83 33.92 4.16
1963 2120 5.105554 TGTTACTTGATGCAAACAAACCACT 60.106 36.000 10.12 0.00 0.00 4.00
2019 2176 2.954753 GAGCCGCTGACCAACAACG 61.955 63.158 0.00 0.00 37.75 4.10
2023 2180 2.970324 GCTGACCAACAACGGCGA 60.970 61.111 16.62 0.00 0.00 5.54
2026 2183 1.841663 CTGACCAACAACGGCGAAGG 61.842 60.000 16.62 10.04 0.00 3.46
2131 2291 0.179012 GGGGTTCCACTTTTGTCGGA 60.179 55.000 0.00 0.00 0.00 4.55
2356 2524 2.665000 GGCTGTGTCTGCTGCCTA 59.335 61.111 0.00 0.00 46.00 3.93
2393 2561 5.127519 CCAACCAATGCAAATGGAGATAAGA 59.872 40.000 24.23 0.00 40.56 2.10
2403 2571 6.767902 GCAAATGGAGATAAGACTATGGACAA 59.232 38.462 0.00 0.00 0.00 3.18
2404 2572 7.041508 GCAAATGGAGATAAGACTATGGACAAG 60.042 40.741 0.00 0.00 0.00 3.16
2507 2690 4.142469 CCGTCCATGTAAAAACCAGAATCC 60.142 45.833 0.00 0.00 0.00 3.01
2536 2719 1.383799 CATGCTCCTGTTCCCCCAA 59.616 57.895 0.00 0.00 0.00 4.12
2560 2743 0.528466 CGCATGCACTCGGATGTACT 60.528 55.000 19.57 0.00 42.60 2.73
2561 2744 1.212616 GCATGCACTCGGATGTACTC 58.787 55.000 14.21 0.00 42.60 2.59
2562 2745 1.858091 CATGCACTCGGATGTACTCC 58.142 55.000 0.00 0.00 41.07 3.85
2569 2752 2.681848 ACTCGGATGTACTCCTACAACG 59.318 50.000 8.96 0.00 42.47 4.10
2589 2772 5.326200 ACGAGTAGAATTTCGGTGAATCT 57.674 39.130 2.63 0.00 40.93 2.40
2661 2850 2.688446 TCAGATTCTTATCGTCGCCTGT 59.312 45.455 0.00 0.00 35.85 4.00
2711 2900 2.661675 CACTGGTTCTGTCGTACATTCG 59.338 50.000 0.00 0.00 0.00 3.34
2863 3052 0.586802 GGTTTGTCGCCTCTCAACAC 59.413 55.000 0.00 0.00 0.00 3.32
2963 3152 4.718961 AGGAAGCAAGAAAGCTAGAAACA 58.281 39.130 0.00 0.00 45.89 2.83
3030 3219 2.642171 TGAGGGGAGAAAAGCTAGGA 57.358 50.000 0.00 0.00 0.00 2.94
3074 3283 0.325296 AGTGGCTCAGGATTCCGGTA 60.325 55.000 0.00 0.00 0.00 4.02
3148 3357 2.002586 CGTCTGATTGGTGGCACTAAG 58.997 52.381 21.04 8.56 0.00 2.18
3200 3416 7.256494 ACAATTAATCACCATTCCAACCAAT 57.744 32.000 0.00 0.00 0.00 3.16
3236 3452 5.540337 TGTATAGGATGGAGAAAGGTAGCAG 59.460 44.000 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 6.845302 TCTCAACTGATGAATATTTGCACAC 58.155 36.000 0.00 0.00 37.67 3.82
133 134 4.333372 TCGACTGTGTTGGTTTTAGTTTCC 59.667 41.667 0.00 0.00 0.00 3.13
174 175 2.289195 ACATGCCTTCCAATGTTTGCAG 60.289 45.455 0.00 0.00 31.53 4.41
228 230 9.775854 CTCTATTCTCAACCATCTGTCATTTAT 57.224 33.333 0.00 0.00 0.00 1.40
229 231 8.762645 ACTCTATTCTCAACCATCTGTCATTTA 58.237 33.333 0.00 0.00 0.00 1.40
230 232 7.628234 ACTCTATTCTCAACCATCTGTCATTT 58.372 34.615 0.00 0.00 0.00 2.32
232 234 6.805016 ACTCTATTCTCAACCATCTGTCAT 57.195 37.500 0.00 0.00 0.00 3.06
233 235 6.611613 AACTCTATTCTCAACCATCTGTCA 57.388 37.500 0.00 0.00 0.00 3.58
235 237 7.175641 CCAAAAACTCTATTCTCAACCATCTGT 59.824 37.037 0.00 0.00 0.00 3.41
236 238 7.362401 CCCAAAAACTCTATTCTCAACCATCTG 60.362 40.741 0.00 0.00 0.00 2.90
237 239 6.660949 CCCAAAAACTCTATTCTCAACCATCT 59.339 38.462 0.00 0.00 0.00 2.90
251 256 6.994421 ACCAATTTGATACCCAAAAACTCT 57.006 33.333 0.00 0.00 46.64 3.24
294 299 7.329471 CGTTCACTTAAATCTTCTCATCTCACA 59.671 37.037 0.00 0.00 0.00 3.58
422 455 7.057894 TGCGGTATAAATTTGACCCTCTTAAT 58.942 34.615 15.01 0.00 0.00 1.40
473 506 5.621422 CAACACTCAATCCAACATACTTCG 58.379 41.667 0.00 0.00 0.00 3.79
490 523 4.462834 GGCTTCTTTTATTAGGGCAACACT 59.537 41.667 0.00 0.00 39.74 3.55
722 785 3.399330 TGTTCGAACCACCTTGATCTTC 58.601 45.455 24.78 0.00 0.00 2.87
832 925 2.039084 AGGGAGGAAACTTACACTGCAG 59.961 50.000 13.48 13.48 44.43 4.41
1060 1153 3.532641 AATTTCTCCCTGCTTTCCTGT 57.467 42.857 0.00 0.00 0.00 4.00
1078 1174 1.765314 ACCTCCTTCGCAGAGCATAAT 59.235 47.619 0.00 0.00 38.43 1.28
1116 1212 1.323271 CGAAGAGCCTCAGCCCACTA 61.323 60.000 0.00 0.00 41.25 2.74
1174 1270 4.598894 CCTCATGGAGGCGCCGAG 62.599 72.222 23.20 20.25 43.29 4.63
1443 1544 0.828022 TCCACCCCACGTATCATCAC 59.172 55.000 0.00 0.00 0.00 3.06
1608 1764 1.673665 CAGCTCAGGAGGCCACAAC 60.674 63.158 5.01 0.00 0.00 3.32
1649 1806 1.471676 CGCTCCATGGAACTCCTGTAC 60.472 57.143 17.00 0.00 36.82 2.90
1942 2099 4.736168 GCAGTGGTTTGTTTGCATCAAGTA 60.736 41.667 0.00 0.00 36.59 2.24
1943 2100 3.784338 CAGTGGTTTGTTTGCATCAAGT 58.216 40.909 0.00 0.00 0.00 3.16
1944 2101 2.540931 GCAGTGGTTTGTTTGCATCAAG 59.459 45.455 0.00 0.00 36.59 3.02
1945 2102 2.093816 TGCAGTGGTTTGTTTGCATCAA 60.094 40.909 0.00 0.00 41.23 2.57
1946 2103 1.479730 TGCAGTGGTTTGTTTGCATCA 59.520 42.857 0.00 0.00 41.23 3.07
1947 2104 2.129607 CTGCAGTGGTTTGTTTGCATC 58.870 47.619 5.25 0.00 44.61 3.91
1948 2105 1.202557 CCTGCAGTGGTTTGTTTGCAT 60.203 47.619 13.81 0.00 44.61 3.96
1949 2106 0.175302 CCTGCAGTGGTTTGTTTGCA 59.825 50.000 13.81 0.00 43.62 4.08
1950 2107 0.175531 ACCTGCAGTGGTTTGTTTGC 59.824 50.000 13.81 0.00 36.89 3.68
1951 2108 2.223711 GGTACCTGCAGTGGTTTGTTTG 60.224 50.000 13.81 0.00 41.22 2.93
1952 2109 2.028876 GGTACCTGCAGTGGTTTGTTT 58.971 47.619 13.81 0.00 41.22 2.83
1953 2110 1.687563 GGTACCTGCAGTGGTTTGTT 58.312 50.000 13.81 0.00 41.22 2.83
1954 2111 0.534203 CGGTACCTGCAGTGGTTTGT 60.534 55.000 13.81 4.58 41.22 2.83
1955 2112 0.250124 TCGGTACCTGCAGTGGTTTG 60.250 55.000 13.81 0.00 41.22 2.93
1956 2113 0.690762 ATCGGTACCTGCAGTGGTTT 59.309 50.000 13.81 0.00 41.22 3.27
1957 2114 0.249398 GATCGGTACCTGCAGTGGTT 59.751 55.000 13.81 0.00 41.22 3.67
1958 2115 0.614979 AGATCGGTACCTGCAGTGGT 60.615 55.000 13.81 8.01 43.66 4.16
1959 2116 0.179100 CAGATCGGTACCTGCAGTGG 60.179 60.000 13.81 0.88 0.00 4.00
1960 2117 3.352447 CAGATCGGTACCTGCAGTG 57.648 57.895 13.81 6.81 0.00 3.66
2026 2183 2.267324 GCAGAGAGGTGGAGGCAC 59.733 66.667 0.00 0.00 0.00 5.01
2281 2441 1.700985 GTCCTGGGTCTCCTCTCCT 59.299 63.158 0.00 0.00 0.00 3.69
2326 2488 5.288015 CAGACACAGCCTGATAAGTGATAG 58.712 45.833 0.00 0.00 35.97 2.08
2356 2524 1.352622 TGGTTGGACAGGTCAGGCTT 61.353 55.000 1.41 0.00 0.00 4.35
2393 2561 5.242795 ACTTTACAAGCCTTGTCCATAGT 57.757 39.130 14.46 10.10 44.12 2.12
2403 2571 1.566018 GCACGCGACTTTACAAGCCT 61.566 55.000 15.93 0.00 0.00 4.58
2404 2572 1.154469 GCACGCGACTTTACAAGCC 60.154 57.895 15.93 0.00 0.00 4.35
2423 2591 4.404715 ACGTATCCACAATTAGCACTACCT 59.595 41.667 0.00 0.00 0.00 3.08
2507 2690 2.409870 GGAGCATGCTTCGGTTGGG 61.410 63.158 23.61 0.00 0.00 4.12
2560 2743 4.460382 ACCGAAATTCTACTCGTTGTAGGA 59.540 41.667 14.70 9.21 46.45 2.94
2561 2744 4.561606 CACCGAAATTCTACTCGTTGTAGG 59.438 45.833 14.70 4.67 46.45 3.18
2569 2752 4.740695 CCGAGATTCACCGAAATTCTACTC 59.259 45.833 0.00 0.00 0.00 2.59
2589 2772 5.247337 TGGATTAATATGTATGGACAGCCGA 59.753 40.000 0.00 0.00 39.50 5.54
2863 3052 2.238646 TGGGCATCCAACTTGGTACTAG 59.761 50.000 7.72 0.00 40.73 2.57
2963 3152 1.349357 GTTGGCCAGGAAGAGAGAAGT 59.651 52.381 5.11 0.00 0.00 3.01
3030 3219 3.051940 TGGATAAGCACCAGATCTCCT 57.948 47.619 0.00 0.00 33.22 3.69
3074 3283 2.281070 CCGTCTGTTGCAGGTGCT 60.281 61.111 3.18 0.00 42.66 4.40
3148 3357 4.632153 TGGAGCAAAGAAGACACTCTAAC 58.368 43.478 0.00 0.00 0.00 2.34
3200 3416 4.038763 CCATCCTATACACGTCTGCCTTTA 59.961 45.833 0.00 0.00 0.00 1.85
3236 3452 3.671928 CAGCAGTGCAATACTTTTGCTTC 59.328 43.478 19.20 5.29 45.13 3.86


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

AutoCloner maintained by Alex Coulton.