Multiple sequence alignment - TraesCS4D01G112500

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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 TraesCS4D01G112500 chr4D 100.000 2796 0 0 1 2796 93385448 93388243 0.000000e+00 5164
1 TraesCS4D01G112500 chr4D 96.629 445 11 3 132 573 22227433 22226990 0.000000e+00 736
2 TraesCS4D01G112500 chr4B 92.523 2247 102 27 571 2796 131465305 131467506 0.000000e+00 3158
3 TraesCS4D01G112500 chr4A 90.394 1624 94 32 574 2173 488867173 488865588 0.000000e+00 2078
4 TraesCS4D01G112500 chr4A 84.368 435 54 13 2218 2646 488865596 488865170 5.570000e-112 414
5 TraesCS4D01G112500 chr2D 93.902 574 20 2 1 574 15191545 15192103 0.000000e+00 852
6 TraesCS4D01G112500 chr2D 95.161 124 6 0 1 124 88578411 88578534 2.200000e-46 196
7 TraesCS4D01G112500 chrUn 95.937 443 16 2 132 573 24148442 24148001 0.000000e+00 717
8 TraesCS4D01G112500 chr5A 92.584 445 30 3 132 573 502061942 502061498 1.090000e-178 636
9 TraesCS4D01G112500 chr5A 90.179 448 40 4 132 576 454765519 454765073 5.190000e-162 580
10 TraesCS4D01G112500 chr6A 91.892 444 34 2 132 573 593803538 593803981 1.100000e-173 619
11 TraesCS4D01G112500 chr6A 89.485 447 41 6 132 573 585417069 585417514 6.760000e-156 560
12 TraesCS4D01G112500 chr6B 91.724 435 28 3 141 574 543724509 543724082 5.150000e-167 597
13 TraesCS4D01G112500 chr2B 91.541 331 24 2 245 572 789539160 789539489 1.180000e-123 453
14 TraesCS4D01G112500 chr7A 95.161 124 6 0 1 124 735731314 735731191 2.200000e-46 196
15 TraesCS4D01G112500 chr5D 94.355 124 7 0 1 124 200804376 200804499 1.020000e-44 191
16 TraesCS4D01G112500 chr3B 94.355 124 7 0 1 124 480458109 480457986 1.020000e-44 191
17 TraesCS4D01G112500 chr5B 94.068 118 7 0 7 124 267833242 267833359 2.210000e-41 180
18 TraesCS4D01G112500 chr5B 92.683 123 9 0 2 124 102943384 102943262 7.960000e-41 178
19 TraesCS4D01G112500 chr3D 92.742 124 9 0 1 124 110263836 110263959 2.210000e-41 180


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 TraesCS4D01G112500 chr4D 93385448 93388243 2795 False 5164 5164 100.000 1 2796 1 chr4D.!!$F1 2795
1 TraesCS4D01G112500 chr4B 131465305 131467506 2201 False 3158 3158 92.523 571 2796 1 chr4B.!!$F1 2225
2 TraesCS4D01G112500 chr4A 488865170 488867173 2003 True 1246 2078 87.381 574 2646 2 chr4A.!!$R1 2072
3 TraesCS4D01G112500 chr2D 15191545 15192103 558 False 852 852 93.902 1 574 1 chr2D.!!$F1 573

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
422 423 0.462375 GGGCCGGTTTTGTCAGTTTT 59.538 50.0 1.9 0.0 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2072 2107 0.370273 CGTATCAAAGCCACGTCAGC 59.63 55.0 0.0 0.0 0.0 4.26 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
23 24 4.778415 CCTCGGAGCCACACGACG 62.778 72.222 0.00 0.00 35.04 5.12
58 59 2.363925 GTCCTGCTACCTCCCCGT 60.364 66.667 0.00 0.00 0.00 5.28
64 65 2.044650 CTACCTCCCCGTGTCCGA 60.045 66.667 0.00 0.00 35.63 4.55
97 98 4.951963 CCGCTCCTCGCCCGAATC 62.952 72.222 0.00 0.00 36.73 2.52
98 99 4.951963 CGCTCCTCGCCCGAATCC 62.952 72.222 0.00 0.00 34.21 3.01
99 100 4.951963 GCTCCTCGCCCGAATCCG 62.952 72.222 0.00 0.00 0.00 4.18
422 423 0.462375 GGGCCGGTTTTGTCAGTTTT 59.538 50.000 1.90 0.00 0.00 2.43
509 510 5.557891 TTTTCGGTAGTTTTCGGTCAAAA 57.442 34.783 0.00 0.00 0.00 2.44
514 515 6.200808 TCGGTAGTTTTCGGTCAAAATTTTC 58.799 36.000 0.00 0.00 36.35 2.29
527 528 7.276878 CGGTCAAAATTTTCAAAGTGGTAGTTT 59.723 33.333 0.00 0.00 0.00 2.66
536 537 3.655615 AAGTGGTAGTTTTGTGGGACA 57.344 42.857 0.00 0.00 0.00 4.02
537 538 3.655615 AGTGGTAGTTTTGTGGGACAA 57.344 42.857 0.00 0.00 44.16 3.18
549 550 5.066779 TTTGTGGGACAAAACCCCCTAAAA 61.067 41.667 0.00 0.00 44.23 1.52
644 645 2.095263 GCATGCTGGTTGATAACACGTT 60.095 45.455 11.37 0.00 0.00 3.99
701 702 0.530650 ATACCAGCGCATCACTTCCG 60.531 55.000 11.47 0.00 0.00 4.30
713 714 2.264480 CTTCCGTGCGATGGGTCA 59.736 61.111 0.00 0.00 0.00 4.02
724 725 4.758251 TGGGTCATGGCACTCGCG 62.758 66.667 0.00 0.00 39.92 5.87
762 763 7.812191 GCCACATTTATCACTAACAAAATCACA 59.188 33.333 0.00 0.00 0.00 3.58
826 827 1.804601 GTCGAACGTGGGAAAAGGAT 58.195 50.000 0.00 0.00 0.00 3.24
827 828 1.463444 GTCGAACGTGGGAAAAGGATG 59.537 52.381 0.00 0.00 0.00 3.51
828 829 0.802494 CGAACGTGGGAAAAGGATGG 59.198 55.000 0.00 0.00 0.00 3.51
830 831 0.481128 AACGTGGGAAAAGGATGGGT 59.519 50.000 0.00 0.00 0.00 4.51
831 832 1.364269 ACGTGGGAAAAGGATGGGTA 58.636 50.000 0.00 0.00 0.00 3.69
835 837 3.057104 CGTGGGAAAAGGATGGGTAAAAC 60.057 47.826 0.00 0.00 0.00 2.43
839 841 6.014012 TGGGAAAAGGATGGGTAAAACTAAG 58.986 40.000 0.00 0.00 0.00 2.18
884 892 2.363038 CCATTAATCCCCACTCGTCGTA 59.637 50.000 0.00 0.00 0.00 3.43
978 986 4.764336 TACAACCGCGTCGCCTCG 62.764 66.667 12.44 1.64 0.00 4.63
994 1002 1.002502 TCGCTCGGTCTCTCTCCAA 60.003 57.895 0.00 0.00 0.00 3.53
1005 1013 2.073213 CTCTCTCCAAGAGCAATGGCG 61.073 57.143 0.00 0.00 44.95 5.69
1017 1025 1.146930 AATGGCGATGACGATGGCT 59.853 52.632 0.00 0.00 42.66 4.75
1139 1147 3.611674 TTCGTGCGAGGTGAGGCA 61.612 61.111 0.00 0.00 36.70 4.75
1162 1170 4.719369 GCGACGACCACTCCGCTT 62.719 66.667 0.00 0.00 43.75 4.68
1548 1568 6.373216 CCAGGAACGGTAAGAATTGTTAATGA 59.627 38.462 0.00 0.00 0.00 2.57
1555 1575 6.127403 GGTAAGAATTGTTAATGATCGCGTC 58.873 40.000 5.77 3.66 0.00 5.19
1570 1590 2.251371 GTCGTGTGCTTTTCCGGC 59.749 61.111 0.00 0.00 0.00 6.13
1571 1591 3.342627 TCGTGTGCTTTTCCGGCG 61.343 61.111 0.00 0.00 0.00 6.46
1572 1592 3.342627 CGTGTGCTTTTCCGGCGA 61.343 61.111 9.30 0.00 0.00 5.54
1573 1593 2.677003 CGTGTGCTTTTCCGGCGAT 61.677 57.895 9.30 0.00 0.00 4.58
1943 1974 5.543714 TCGAGTGGAGTTGTATTGCTTTTA 58.456 37.500 0.00 0.00 0.00 1.52
1945 1978 6.092122 TCGAGTGGAGTTGTATTGCTTTTATG 59.908 38.462 0.00 0.00 0.00 1.90
2019 2054 8.673626 ATTGAATTTAAGCTGTTTGTCATACG 57.326 30.769 0.00 0.00 0.00 3.06
2020 2055 7.197071 TGAATTTAAGCTGTTTGTCATACGT 57.803 32.000 0.00 0.00 0.00 3.57
2021 2056 8.312896 TGAATTTAAGCTGTTTGTCATACGTA 57.687 30.769 0.00 0.00 0.00 3.57
2022 2057 8.225107 TGAATTTAAGCTGTTTGTCATACGTAC 58.775 33.333 0.00 0.00 0.00 3.67
2064 2099 0.645868 GACGAAAGCATACTCGGTGC 59.354 55.000 0.00 0.00 42.81 5.01
2116 2151 5.450818 TTGAAGGATATTGTTAGTGGGCT 57.549 39.130 0.00 0.00 0.00 5.19
2128 2163 4.403113 TGTTAGTGGGCTGACGTAATATCA 59.597 41.667 0.00 0.00 34.36 2.15
2145 2180 1.382522 TCAAATCCAAGAGCGCCATC 58.617 50.000 2.29 0.00 0.00 3.51
2164 2201 3.359695 TCTGGCCACAACCTAATAACC 57.640 47.619 0.00 0.00 0.00 2.85
2165 2202 2.916934 TCTGGCCACAACCTAATAACCT 59.083 45.455 0.00 0.00 0.00 3.50
2166 2203 3.332485 TCTGGCCACAACCTAATAACCTT 59.668 43.478 0.00 0.00 0.00 3.50
2167 2204 3.692690 TGGCCACAACCTAATAACCTTC 58.307 45.455 0.00 0.00 0.00 3.46
2168 2205 3.074687 TGGCCACAACCTAATAACCTTCA 59.925 43.478 0.00 0.00 0.00 3.02
2169 2206 4.083565 GGCCACAACCTAATAACCTTCAA 58.916 43.478 0.00 0.00 0.00 2.69
2170 2207 4.082408 GGCCACAACCTAATAACCTTCAAC 60.082 45.833 0.00 0.00 0.00 3.18
2171 2208 4.521256 GCCACAACCTAATAACCTTCAACA 59.479 41.667 0.00 0.00 0.00 3.33
2172 2209 5.185056 GCCACAACCTAATAACCTTCAACAT 59.815 40.000 0.00 0.00 0.00 2.71
2173 2210 6.295067 GCCACAACCTAATAACCTTCAACATT 60.295 38.462 0.00 0.00 0.00 2.71
2174 2211 7.666623 CCACAACCTAATAACCTTCAACATTT 58.333 34.615 0.00 0.00 0.00 2.32
2175 2212 7.598493 CCACAACCTAATAACCTTCAACATTTG 59.402 37.037 0.00 0.00 0.00 2.32
2176 2213 7.116233 CACAACCTAATAACCTTCAACATTTGC 59.884 37.037 0.00 0.00 0.00 3.68
2177 2214 7.015195 ACAACCTAATAACCTTCAACATTTGCT 59.985 33.333 0.00 0.00 0.00 3.91
2178 2215 7.158099 ACCTAATAACCTTCAACATTTGCTC 57.842 36.000 0.00 0.00 0.00 4.26
2179 2216 6.719370 ACCTAATAACCTTCAACATTTGCTCA 59.281 34.615 0.00 0.00 0.00 4.26
2180 2217 7.232534 ACCTAATAACCTTCAACATTTGCTCAA 59.767 33.333 0.00 0.00 0.00 3.02
2181 2218 8.087750 CCTAATAACCTTCAACATTTGCTCAAA 58.912 33.333 0.00 0.00 34.46 2.69
2182 2219 9.474920 CTAATAACCTTCAACATTTGCTCAAAA 57.525 29.630 0.00 0.00 33.56 2.44
2183 2220 8.729805 AATAACCTTCAACATTTGCTCAAAAA 57.270 26.923 0.00 0.00 33.56 1.94
2260 2297 5.244626 ACTCAAAATGGCATTTTAGCAGAGT 59.755 36.000 30.76 30.76 40.27 3.24
2295 2332 9.326413 GACCCCGATAATTATAATAACCATCAG 57.674 37.037 0.00 0.00 0.00 2.90
2330 2368 4.278170 TGGCTTAAAATGACACTTGACAGG 59.722 41.667 0.00 0.00 0.00 4.00
2430 2468 2.129555 GAGGGCCAGTTTGGAGCTCA 62.130 60.000 17.19 0.00 40.96 4.26
2485 2523 2.544721 TCAGCTTCTTCCTCCTCATGT 58.455 47.619 0.00 0.00 0.00 3.21
2529 2567 1.220749 GCTTCCCACGCACCATAGA 59.779 57.895 0.00 0.00 0.00 1.98
2541 2579 0.323178 ACCATAGACGACGGTCACCT 60.323 55.000 9.10 6.72 45.92 4.00
2598 2636 3.822192 CGGCTCGTCGGATGGTCA 61.822 66.667 0.00 0.00 0.00 4.02
2635 2673 1.947013 CTTGTGTGTGAGCAGCTGG 59.053 57.895 17.12 0.00 0.00 4.85
2637 2675 1.981951 TTGTGTGTGAGCAGCTGGGA 61.982 55.000 17.12 0.00 0.00 4.37
2640 2678 2.527624 TGTGAGCAGCTGGGAGGT 60.528 61.111 17.12 0.00 0.00 3.85
2662 2700 0.384353 GTGAGCGCCTTCGTGTTTTC 60.384 55.000 2.29 0.00 38.14 2.29
2735 2775 0.255890 TCCCTCTTAATGGCAGCCAC 59.744 55.000 19.10 0.00 35.80 5.01
2738 2778 0.737219 CTCTTAATGGCAGCCACAGC 59.263 55.000 19.10 0.00 35.80 4.40
2739 2779 0.038021 TCTTAATGGCAGCCACAGCA 59.962 50.000 19.10 0.00 43.56 4.41
2783 2823 1.565390 CCACTCTCTCCCATTGCCCA 61.565 60.000 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 4.681978 ACTGCAAGGACGACCGGC 62.682 66.667 14.44 14.44 39.30 6.13
38 39 1.306226 GGGGAGGTAGCAGGACACT 60.306 63.158 0.00 0.00 0.00 3.55
58 59 4.090588 GGGGCACGGATTCGGACA 62.091 66.667 0.00 0.00 41.39 4.02
449 450 9.772973 GTCCCTAAAAACTACCAATTTCATTTT 57.227 29.630 0.00 0.00 0.00 1.82
458 459 9.643735 TCTTAATTTGTCCCTAAAAACTACCAA 57.356 29.630 0.00 0.00 0.00 3.67
499 500 5.725362 ACCACTTTGAAAATTTTGACCGAA 58.275 33.333 8.47 0.00 0.00 4.30
500 501 5.331876 ACCACTTTGAAAATTTTGACCGA 57.668 34.783 8.47 0.00 0.00 4.69
509 510 6.155393 TCCCACAAAACTACCACTTTGAAAAT 59.845 34.615 1.80 0.00 36.30 1.82
514 515 3.697045 TGTCCCACAAAACTACCACTTTG 59.303 43.478 0.00 0.00 38.29 2.77
536 537 7.454553 AAAAACTACCATTTTAGGGGGTTTT 57.545 32.000 0.00 0.00 42.92 2.43
574 575 6.039616 GTCATGGTTGTAGTTTGCAAAAAGA 58.960 36.000 14.67 0.71 0.00 2.52
575 576 5.234116 GGTCATGGTTGTAGTTTGCAAAAAG 59.766 40.000 14.67 0.00 0.00 2.27
576 577 5.105146 AGGTCATGGTTGTAGTTTGCAAAAA 60.105 36.000 14.67 1.23 0.00 1.94
577 578 4.404073 AGGTCATGGTTGTAGTTTGCAAAA 59.596 37.500 14.67 0.00 0.00 2.44
644 645 6.993902 ACAAACTCGAAGTTTAGGGATGTAAA 59.006 34.615 11.08 0.00 45.84 2.01
678 679 0.250234 AGTGATGCGCTGGTATGTGT 59.750 50.000 9.73 0.00 0.00 3.72
701 702 2.438254 TGCCATGACCCATCGCAC 60.438 61.111 0.00 0.00 33.47 5.34
781 782 1.962547 CTTCGTGTGTGCGATTTTTCG 59.037 47.619 0.00 0.00 40.76 3.46
826 827 4.079901 TGTTCCCACACTTAGTTTTACCCA 60.080 41.667 0.00 0.00 0.00 4.51
827 828 4.463070 TGTTCCCACACTTAGTTTTACCC 58.537 43.478 0.00 0.00 0.00 3.69
884 892 1.589803 GGCATTTTATACCGCGGACT 58.410 50.000 35.90 20.63 0.00 3.85
978 986 2.875188 TCTTGGAGAGAGACCGAGC 58.125 57.895 0.00 0.00 38.44 5.03
994 1002 0.105593 ATCGTCATCGCCATTGCTCT 59.894 50.000 0.00 0.00 36.96 4.09
1005 1013 0.101399 AGTCGTCAGCCATCGTCATC 59.899 55.000 0.00 0.00 0.00 2.92
1017 1025 2.108514 CCCCGCGTAGTAGTCGTCA 61.109 63.158 4.92 0.00 0.00 4.35
1121 1129 3.112709 GCCTCACCTCGCACGAAC 61.113 66.667 0.00 0.00 0.00 3.95
1122 1130 3.611674 TGCCTCACCTCGCACGAA 61.612 61.111 0.00 0.00 0.00 3.85
1149 1157 2.030562 ACCAAAGCGGAGTGGTCG 59.969 61.111 0.00 0.00 45.18 4.79
1155 1163 2.804828 GGTCCTCCACCAAAGCGGAG 62.805 65.000 0.00 0.00 45.98 4.63
1156 1164 2.747686 GTCCTCCACCAAAGCGGA 59.252 61.111 0.00 0.00 38.63 5.54
1548 1568 1.491563 GAAAAGCACACGACGCGAT 59.508 52.632 15.93 0.00 0.00 4.58
1555 1575 2.563086 GATCGCCGGAAAAGCACACG 62.563 60.000 5.05 0.00 0.00 4.49
1582 1602 2.555199 GTTTGATCAGGCTGACGCTAT 58.445 47.619 21.37 2.69 36.09 2.97
1583 1603 1.735700 CGTTTGATCAGGCTGACGCTA 60.736 52.381 21.37 9.20 36.09 4.26
2019 2054 7.086376 TGTTTTCATACAGTTCTCCGTAGTAC 58.914 38.462 0.00 0.00 0.00 2.73
2020 2055 7.175467 TCTGTTTTCATACAGTTCTCCGTAGTA 59.825 37.037 0.00 0.00 44.62 1.82
2021 2056 6.015688 TCTGTTTTCATACAGTTCTCCGTAGT 60.016 38.462 0.00 0.00 44.62 2.73
2022 2057 6.308282 GTCTGTTTTCATACAGTTCTCCGTAG 59.692 42.308 0.00 0.00 44.62 3.51
2031 2066 4.814234 TGCTTTCGTCTGTTTTCATACAGT 59.186 37.500 0.00 0.00 44.62 3.55
2072 2107 0.370273 CGTATCAAAGCCACGTCAGC 59.630 55.000 0.00 0.00 0.00 4.26
2079 2114 4.584874 TCCTTCAATTCGTATCAAAGCCA 58.415 39.130 0.00 0.00 0.00 4.75
2116 2151 5.462068 CGCTCTTGGATTTGATATTACGTCA 59.538 40.000 0.00 0.00 0.00 4.35
2128 2163 1.386533 CAGATGGCGCTCTTGGATTT 58.613 50.000 7.64 0.00 0.00 2.17
2145 2180 3.366052 AGGTTATTAGGTTGTGGCCAG 57.634 47.619 5.11 0.00 0.00 4.85
2151 2188 7.015195 AGCAAATGTTGAAGGTTATTAGGTTGT 59.985 33.333 0.00 0.00 0.00 3.32
2235 2272 6.100404 TCTGCTAAAATGCCATTTTGAGTT 57.900 33.333 22.43 1.51 42.08 3.01
2295 2332 5.576384 TCATTTTAAGCCAAAATCGTCATGC 59.424 36.000 4.14 0.00 43.51 4.06
2330 2368 3.311322 CGATCGAGAGCTATATGAGGACC 59.689 52.174 10.26 0.00 0.00 4.46
2430 2468 2.801859 CAACGGTTGGGTTTGGAGT 58.198 52.632 13.03 0.00 0.00 3.85
2485 2523 1.441849 CTTCAAATTCCGCGCGCAA 60.442 52.632 32.61 19.02 0.00 4.85
2529 2567 1.255667 AATGGCTAGGTGACCGTCGT 61.256 55.000 0.00 0.00 0.00 4.34
2541 2579 1.808512 CGGGTGTCGCATTAATGGCTA 60.809 52.381 17.02 0.00 0.00 3.93
2598 2636 3.014304 AGCCTGAAGATGATGCATGTT 57.986 42.857 2.46 0.00 29.97 2.71
2635 2673 3.537206 AAGGCGCTCACACACCTCC 62.537 63.158 7.64 0.00 0.00 4.30
2637 2675 2.031163 GAAGGCGCTCACACACCT 59.969 61.111 7.64 0.00 0.00 4.00
2640 2678 2.661537 CACGAAGGCGCTCACACA 60.662 61.111 7.64 0.00 42.48 3.72
2755 2795 2.203640 AGAGAGTGGTGGCCGTGA 60.204 61.111 0.00 0.00 0.00 4.35
2759 2799 1.566298 AATGGGAGAGAGTGGTGGCC 61.566 60.000 0.00 0.00 0.00 5.36
2760 2800 0.393537 CAATGGGAGAGAGTGGTGGC 60.394 60.000 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.