Multiple sequence alignment - TraesCS4D01G098300

Loading Multiple Alignment...

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 TraesCS4D01G098300 chr4D 100.000 3080 0 0 1 3080 75053855 75050776 0.000000e+00 5688
1 TraesCS4D01G098300 chr4B 94.617 2991 116 21 104 3080 107459466 107456507 0.000000e+00 4590
2 TraesCS4D01G098300 chr4B 87.234 235 28 2 593 826 617392967 617392734 1.820000e-67 267
3 TraesCS4D01G098300 chr4A 92.461 3064 151 38 34 3080 512537010 512540010 0.000000e+00 4305
4 TraesCS4D01G098300 chr1D 87.649 251 28 2 593 841 302343349 302343100 3.890000e-74 289
5 TraesCS4D01G098300 chr5D 86.531 245 29 2 593 836 498176826 498177067 1.820000e-67 267
6 TraesCS4D01G098300 chr5D 87.234 235 29 1 593 826 536239768 536239534 1.820000e-67 267
7 TraesCS4D01G098300 chr6B 86.000 250 31 3 593 838 14232105 14231856 6.550000e-67 265
8 TraesCS4D01G098300 chr5B 86.235 247 31 3 593 837 464317341 464317586 6.550000e-67 265
9 TraesCS4D01G098300 chr7A 85.830 247 34 1 593 838 670247298 670247544 8.470000e-66 261


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 TraesCS4D01G098300 chr4D 75050776 75053855 3079 True 5688 5688 100.000 1 3080 1 chr4D.!!$R1 3079
1 TraesCS4D01G098300 chr4B 107456507 107459466 2959 True 4590 4590 94.617 104 3080 1 chr4B.!!$R1 2976
2 TraesCS4D01G098300 chr4A 512537010 512540010 3000 False 4305 4305 92.461 34 3080 1 chr4A.!!$F1 3046

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
315 327 0.755327 ACCTGGACAAACACCAAGGC 60.755 55.0 0.0 0.0 36.95 4.35 F
381 394 0.903454 CCCCTTCGGTAGGTGTGAGT 60.903 60.0 0.0 0.0 43.07 3.41 F
1945 1967 1.407936 ATCAGAGGATCACGTGGAGG 58.592 55.0 17.0 0.0 37.82 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1209 1231 2.436646 CACCTCATGGACACCGCC 60.437 66.667 0.0 0.0 37.04 6.13 R
2066 2088 3.118775 CCGATTCAGTTATGTGAGGACCA 60.119 47.826 0.0 0.0 0.00 4.02 R
2784 2810 2.434702 ACTCTACAAAGGCGGATTAGGG 59.565 50.000 0.0 0.0 0.00 3.53 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
19 20 2.736670 GGCAAGATATCCCCACAAGT 57.263 50.000 0.00 0.00 0.00 3.16
20 21 3.018423 GGCAAGATATCCCCACAAGTT 57.982 47.619 0.00 0.00 0.00 2.66
21 22 3.365472 GGCAAGATATCCCCACAAGTTT 58.635 45.455 0.00 0.00 0.00 2.66
22 23 3.769300 GGCAAGATATCCCCACAAGTTTT 59.231 43.478 0.00 0.00 0.00 2.43
23 24 4.222810 GGCAAGATATCCCCACAAGTTTTT 59.777 41.667 0.00 0.00 0.00 1.94
58 59 2.222027 GCGGAAAGATATCCCCACAAG 58.778 52.381 0.00 0.00 36.00 3.16
85 86 6.225981 GGAAGCATAATTCCAATCCAAACT 57.774 37.500 0.64 0.00 46.77 2.66
87 88 6.351286 GGAAGCATAATTCCAATCCAAACTGT 60.351 38.462 0.64 0.00 46.77 3.55
90 91 6.211184 AGCATAATTCCAATCCAAACTGTTGA 59.789 34.615 0.00 0.00 36.83 3.18
92 93 7.550196 GCATAATTCCAATCCAAACTGTTGAAT 59.450 33.333 0.00 0.00 36.83 2.57
99 100 9.844257 TCCAATCCAAACTGTTGAATTAATTTT 57.156 25.926 1.43 0.00 36.83 1.82
124 130 7.348815 TGTTTATTCATGATGAGTCCCAAGAT 58.651 34.615 0.00 0.00 0.00 2.40
132 138 4.590647 TGATGAGTCCCAAGATCAGTATCC 59.409 45.833 0.00 0.00 31.98 2.59
134 140 3.963374 TGAGTCCCAAGATCAGTATCCTG 59.037 47.826 0.00 0.00 40.25 3.86
164 170 3.142162 CGCCAAGCATGCATGGGA 61.142 61.111 35.67 0.00 35.54 4.37
172 178 2.749600 AGCATGCATGGGACCATTTTA 58.250 42.857 27.34 0.00 33.90 1.52
216 227 4.326255 CCTTGTCAGGGCATCACC 57.674 61.111 0.00 0.00 36.36 4.02
315 327 0.755327 ACCTGGACAAACACCAAGGC 60.755 55.000 0.00 0.00 36.95 4.35
380 393 1.614241 CCCCCTTCGGTAGGTGTGAG 61.614 65.000 0.00 0.00 43.07 3.51
381 394 0.903454 CCCCTTCGGTAGGTGTGAGT 60.903 60.000 0.00 0.00 43.07 3.41
382 395 1.617804 CCCCTTCGGTAGGTGTGAGTA 60.618 57.143 0.00 0.00 43.07 2.59
383 396 1.475682 CCCTTCGGTAGGTGTGAGTAC 59.524 57.143 0.00 0.00 43.07 2.73
386 404 3.626670 CCTTCGGTAGGTGTGAGTACTAG 59.373 52.174 0.00 0.00 39.39 2.57
437 455 5.411053 CAGACTTTGGATTTCAGACTTCTCC 59.589 44.000 0.00 0.00 0.00 3.71
493 511 4.685169 ATTGACTCAATTTGGTAGCACG 57.315 40.909 0.00 0.00 28.76 5.34
534 552 4.720649 TTGGTTGAAAAATGTCGTTCCA 57.279 36.364 0.00 0.00 0.00 3.53
537 555 4.082190 TGGTTGAAAAATGTCGTTCCAACA 60.082 37.500 0.00 0.00 0.00 3.33
559 577 2.093306 TGAGCGGTTCGATTCAACAT 57.907 45.000 0.00 0.00 0.00 2.71
568 586 4.381566 GGTTCGATTCAACATCAAAAACCG 59.618 41.667 0.00 0.00 0.00 4.44
660 678 1.827344 TCCCGACTCTCTACTACGACA 59.173 52.381 0.00 0.00 0.00 4.35
677 695 2.983592 AAGTTTTGCCCGGCTCCG 60.984 61.111 11.61 0.48 39.44 4.63
698 716 3.447025 GAGGAAGGGGCGATGACGG 62.447 68.421 0.00 0.00 40.15 4.79
725 743 2.084546 GCCTTCGGCTCACTTTAATGT 58.915 47.619 0.00 0.00 46.69 2.71
736 754 6.293244 GGCTCACTTTAATGTTTGTAGTCGTT 60.293 38.462 0.00 0.00 0.00 3.85
737 755 7.095523 GGCTCACTTTAATGTTTGTAGTCGTTA 60.096 37.037 0.00 0.00 0.00 3.18
801 819 7.517614 TTTGTATTCTTTGTACTGCCATGAA 57.482 32.000 0.00 0.00 0.00 2.57
870 892 7.175641 GTCCCAGATCAAATCAAAAGAAGAAGA 59.824 37.037 0.00 0.00 0.00 2.87
871 893 7.725397 TCCCAGATCAAATCAAAAGAAGAAGAA 59.275 33.333 0.00 0.00 0.00 2.52
872 894 8.027771 CCCAGATCAAATCAAAAGAAGAAGAAG 58.972 37.037 0.00 0.00 0.00 2.85
1039 1061 3.472652 TCTCTCTCGCTACATCTTCTCC 58.527 50.000 0.00 0.00 0.00 3.71
1647 1669 1.593787 CAGCATGGTCCTCGTCACT 59.406 57.895 0.00 0.00 0.00 3.41
1839 1861 1.421485 GCTGTCGGCAATCAACGAG 59.579 57.895 0.00 0.00 40.09 4.18
1842 1864 3.487202 TCGGCAATCAACGAGCGC 61.487 61.111 0.00 0.00 34.67 5.92
1945 1967 1.407936 ATCAGAGGATCACGTGGAGG 58.592 55.000 17.00 0.00 37.82 4.30
2064 2086 2.187239 TGCTGGGGATCTTCAGAGAT 57.813 50.000 16.26 0.00 45.27 2.75
2066 2088 3.866816 TGCTGGGGATCTTCAGAGATAT 58.133 45.455 16.26 0.00 42.66 1.63
2145 2167 6.477033 CCGTGTAAAAATTTGGTGATGTTTGA 59.523 34.615 0.00 0.00 0.00 2.69
2196 2220 6.073385 TGCTAATTCATCGATCAGCTGAAATC 60.073 38.462 22.50 13.90 38.32 2.17
2201 2225 5.767269 TCATCGATCAGCTGAAATCTCTAC 58.233 41.667 22.50 4.31 0.00 2.59
2203 2227 5.180367 TCGATCAGCTGAAATCTCTACAG 57.820 43.478 22.50 1.16 35.14 2.74
2204 2228 4.642437 TCGATCAGCTGAAATCTCTACAGT 59.358 41.667 22.50 0.00 34.60 3.55
2205 2229 5.823045 TCGATCAGCTGAAATCTCTACAGTA 59.177 40.000 22.50 0.00 34.60 2.74
2206 2230 6.488344 TCGATCAGCTGAAATCTCTACAGTAT 59.512 38.462 22.50 0.00 34.60 2.12
2207 2231 7.661847 TCGATCAGCTGAAATCTCTACAGTATA 59.338 37.037 22.50 0.00 34.60 1.47
2208 2232 8.458052 CGATCAGCTGAAATCTCTACAGTATAT 58.542 37.037 22.50 0.00 34.60 0.86
2209 2233 9.787532 GATCAGCTGAAATCTCTACAGTATATC 57.212 37.037 22.50 3.30 34.60 1.63
2210 2234 8.932434 TCAGCTGAAATCTCTACAGTATATCT 57.068 34.615 15.67 0.00 34.60 1.98
2318 2342 2.156051 GACAGTGTCCCGGGACTGAC 62.156 65.000 44.64 36.40 44.80 3.51
2434 2458 9.630098 CTCTTGAAGCAACATATTGTTTATTGT 57.370 29.630 0.00 0.00 38.77 2.71
2457 2482 3.242059 GCATTCAACACAAATAATGCGCC 60.242 43.478 4.18 0.00 43.17 6.53
2506 2531 6.038714 AGGTCAAGTTTGAGTGAAATGAGTTC 59.961 38.462 0.00 0.00 37.98 3.01
2525 2550 4.700213 AGTTCCCGGAATCAAACATAACAG 59.300 41.667 0.73 0.00 0.00 3.16
2657 2683 4.131649 TGGGTTACATGAGAATACACCG 57.868 45.455 0.00 0.00 0.00 4.94
2662 2688 5.694910 GGTTACATGAGAATACACCGTATGG 59.305 44.000 0.00 0.00 42.84 2.74
2782 2808 3.923017 ATGAAACCAAACAGCTAGCAC 57.077 42.857 18.83 0.00 0.00 4.40
2784 2810 2.878406 TGAAACCAAACAGCTAGCACTC 59.122 45.455 18.83 0.36 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.736670 ACTTGTGGGGATATCTTGCC 57.263 50.000 2.05 0.00 34.39 4.52
1 2 5.405935 AAAAACTTGTGGGGATATCTTGC 57.594 39.130 2.05 0.00 0.00 4.01
38 39 2.222027 CTTGTGGGGATATCTTTCCGC 58.778 52.381 2.05 9.24 46.19 5.54
39 40 3.560636 ACTTGTGGGGATATCTTTCCG 57.439 47.619 2.05 0.00 36.58 4.30
40 41 5.132144 TCCTAACTTGTGGGGATATCTTTCC 59.868 44.000 2.05 3.35 34.83 3.13
41 42 6.248569 TCCTAACTTGTGGGGATATCTTTC 57.751 41.667 2.05 0.00 0.00 2.62
42 43 6.652205 TTCCTAACTTGTGGGGATATCTTT 57.348 37.500 2.05 0.00 0.00 2.52
52 53 5.652014 TGGAATTATGCTTCCTAACTTGTGG 59.348 40.000 4.30 0.00 44.27 4.17
58 59 6.959639 TGGATTGGAATTATGCTTCCTAAC 57.040 37.500 4.30 0.00 44.27 2.34
97 98 7.669304 TCTTGGGACTCATCATGAATAAACAAA 59.331 33.333 0.00 0.00 0.00 2.83
99 100 6.720309 TCTTGGGACTCATCATGAATAAACA 58.280 36.000 0.00 0.00 0.00 2.83
132 138 0.597568 TGGCGCAATTCCTTCAACAG 59.402 50.000 10.83 0.00 0.00 3.16
134 140 1.701704 CTTGGCGCAATTCCTTCAAC 58.298 50.000 10.83 0.00 0.00 3.18
164 170 7.502226 TCACTCTTGTCACTGATTTAAAATGGT 59.498 33.333 0.00 0.00 0.00 3.55
172 178 6.821388 AGTAGTTCACTCTTGTCACTGATTT 58.179 36.000 0.00 0.00 28.33 2.17
315 327 1.228124 TCCAACCAACCAGGCTTCG 60.228 57.895 0.00 0.00 43.14 3.79
493 511 4.390909 CCAAATGAAGATTGCAAGAAAGGC 59.609 41.667 4.94 0.00 0.00 4.35
534 552 2.811431 TGAATCGAACCGCTCAAATGTT 59.189 40.909 0.00 0.00 0.00 2.71
537 555 2.811431 TGTTGAATCGAACCGCTCAAAT 59.189 40.909 0.00 0.00 33.10 2.32
543 561 2.892373 TTGATGTTGAATCGAACCGC 57.108 45.000 0.00 0.00 0.00 5.68
559 577 3.550436 GCGTAATTTGACCCGGTTTTTGA 60.550 43.478 0.00 0.00 0.00 2.69
568 586 3.058777 TCGTTCTTTGCGTAATTTGACCC 60.059 43.478 0.00 0.00 0.00 4.46
660 678 2.983592 CGGAGCCGGGCAAAACTT 60.984 61.111 23.09 0.00 35.56 2.66
677 695 2.190578 CATCGCCCCTTCCTCACC 59.809 66.667 0.00 0.00 0.00 4.02
678 696 1.153349 GTCATCGCCCCTTCCTCAC 60.153 63.158 0.00 0.00 0.00 3.51
725 743 9.935682 CGTAGATTACCTAATAACGACTACAAA 57.064 33.333 0.00 0.00 37.34 2.83
736 754 8.114102 ACATCCAGATCCGTAGATTACCTAATA 58.886 37.037 0.00 0.00 30.90 0.98
737 755 6.954684 ACATCCAGATCCGTAGATTACCTAAT 59.045 38.462 0.00 0.00 30.90 1.73
744 762 6.732896 AAACTACATCCAGATCCGTAGATT 57.267 37.500 10.51 4.44 35.86 2.40
745 763 6.732896 AAAACTACATCCAGATCCGTAGAT 57.267 37.500 10.51 0.00 35.86 1.98
780 798 7.320443 TCATTCATGGCAGTACAAAGAATAC 57.680 36.000 0.00 0.00 31.93 1.89
782 800 6.660521 TCTTCATTCATGGCAGTACAAAGAAT 59.339 34.615 0.00 0.00 32.75 2.40
786 804 5.945191 TCATCTTCATTCATGGCAGTACAAA 59.055 36.000 0.00 0.00 0.00 2.83
836 858 0.902531 TTGATCTGGGACCGGTTCTC 59.097 55.000 13.96 2.50 0.00 2.87
870 892 0.685097 TGCTTAACCTCTCCGCACTT 59.315 50.000 0.00 0.00 0.00 3.16
871 893 0.685097 TTGCTTAACCTCTCCGCACT 59.315 50.000 0.00 0.00 0.00 4.40
872 894 1.464997 CTTTGCTTAACCTCTCCGCAC 59.535 52.381 0.00 0.00 0.00 5.34
1065 1087 4.166888 AGGCATCGCATGGTCGCT 62.167 61.111 0.00 0.00 0.00 4.93
1209 1231 2.436646 CACCTCATGGACACCGCC 60.437 66.667 0.00 0.00 37.04 6.13
1787 1809 4.385405 GCAGCTGCTCTGGGACGT 62.385 66.667 31.33 0.00 43.06 4.34
2064 2086 5.221441 CCGATTCAGTTATGTGAGGACCATA 60.221 44.000 0.00 0.00 0.00 2.74
2066 2088 3.118775 CCGATTCAGTTATGTGAGGACCA 60.119 47.826 0.00 0.00 0.00 4.02
2348 2372 6.348213 GCTTGAAGCTATTTAACTCGTGGAAA 60.348 38.462 10.44 0.00 38.45 3.13
2408 2432 9.630098 ACAATAAACAATATGTTGCTTCAAGAG 57.370 29.630 1.57 0.00 40.14 2.85
2449 2473 7.066404 TGTCTGATATTTTTAAGTGGCGCATTA 59.934 33.333 10.83 1.87 0.00 1.90
2454 2479 8.687824 ATTTTGTCTGATATTTTTAAGTGGCG 57.312 30.769 0.00 0.00 0.00 5.69
2506 2531 4.881273 TGATCTGTTATGTTTGATTCCGGG 59.119 41.667 0.00 0.00 0.00 5.73
2525 2550 7.446001 ACTTTTGGAATCTTCAGACTTGATC 57.554 36.000 0.00 0.00 32.27 2.92
2639 2665 6.278363 ACCATACGGTGTATTCTCATGTAAC 58.722 40.000 0.00 0.00 46.79 2.50
2657 2683 1.831736 AGGCTCTGTGTACCACCATAC 59.168 52.381 0.00 0.00 32.73 2.39
2662 2688 1.376037 GCCAGGCTCTGTGTACCAC 60.376 63.158 3.29 0.00 34.56 4.16
2782 2808 2.698797 TCTACAAAGGCGGATTAGGGAG 59.301 50.000 0.00 0.00 0.00 4.30
2784 2810 2.434702 ACTCTACAAAGGCGGATTAGGG 59.565 50.000 0.00 0.00 0.00 3.53
2949 2975 3.517100 AGAAAGCAGAGATAGCACAAGGA 59.483 43.478 0.00 0.00 0.00 3.36
2950 2976 3.870419 GAGAAAGCAGAGATAGCACAAGG 59.130 47.826 0.00 0.00 0.00 3.61
2951 2977 4.757594 AGAGAAAGCAGAGATAGCACAAG 58.242 43.478 0.00 0.00 0.00 3.16
2952 2978 4.465660 AGAGAGAAAGCAGAGATAGCACAA 59.534 41.667 0.00 0.00 0.00 3.33
2953 2979 4.022603 AGAGAGAAAGCAGAGATAGCACA 58.977 43.478 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.