Multiple sequence alignment - TraesCS7A01G246600

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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 TraesCS7A01G246600 chr7A 100.000 3887 0 0 1 3887 226713261 226717147 0.000000e+00 7179
1 TraesCS7A01G246600 chr7B 96.871 3260 77 7 642 3887 186872472 186869224 0.000000e+00 5432
2 TraesCS7A01G246600 chr7B 90.204 490 41 4 107 596 186890782 186890300 1.970000e-177 632
3 TraesCS7A01G246600 chr7D 96.669 3212 70 14 701 3887 214328347 214331546 0.000000e+00 5304
4 TraesCS7A01G246600 chr7D 83.668 698 83 13 5 681 214327486 214328173 2.550000e-176 628


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 TraesCS7A01G246600 chr7A 226713261 226717147 3886 False 7179 7179 100.0000 1 3887 1 chr7A.!!$F1 3886
1 TraesCS7A01G246600 chr7B 186869224 186872472 3248 True 5432 5432 96.8710 642 3887 1 chr7B.!!$R1 3245
2 TraesCS7A01G246600 chr7D 214327486 214331546 4060 False 2966 5304 90.1685 5 3887 2 chr7D.!!$F1 3882

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
998 1180 0.037232 GCCGGAAGCAAGTGACTAGT 60.037 55.0 5.05 0.0 42.97 2.57 F
1231 1422 0.247736 GAACTCTGATGTCCAGCCGT 59.752 55.0 0.00 0.0 42.62 5.68 F
2289 2480 0.608130 TGTCTGCTGCGAGGTTATGT 59.392 50.0 0.00 0.0 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1899 2090 1.140816 GAGTTCGTCTCCAGTTGTGC 58.859 55.000 0.34 0.0 37.22 4.57 R
2424 2615 1.406069 GCCTTCACCATGTCGTCAGAT 60.406 52.381 0.00 0.0 0.00 2.90 R
3409 3602 5.006358 CACGCGTAATACTAAAATCAGCCTT 59.994 40.000 13.44 0.0 0.00 4.35 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
26 27 1.806623 CGTCGCTGGCCTTTTATAGCT 60.807 52.381 3.32 0.00 34.13 3.32
31 32 2.372172 GCTGGCCTTTTATAGCTAGGGA 59.628 50.000 3.32 0.00 37.99 4.20
32 33 3.807561 GCTGGCCTTTTATAGCTAGGGAC 60.808 52.174 3.32 0.00 37.99 4.46
36 37 2.609737 CCTTTTATAGCTAGGGACGGCG 60.610 54.545 4.80 4.80 37.09 6.46
61 62 2.200067 GCAGAACAGGAGATGATGTCG 58.800 52.381 0.00 0.00 0.00 4.35
62 63 2.159184 GCAGAACAGGAGATGATGTCGA 60.159 50.000 0.00 0.00 0.00 4.20
66 67 2.739943 ACAGGAGATGATGTCGAAGGA 58.260 47.619 0.00 0.00 0.00 3.36
89 90 2.596452 AGCATCGAACAAGTCACTACG 58.404 47.619 0.00 0.00 0.00 3.51
90 91 2.228103 AGCATCGAACAAGTCACTACGA 59.772 45.455 0.00 0.00 0.00 3.43
91 92 2.594654 GCATCGAACAAGTCACTACGAG 59.405 50.000 0.00 0.00 33.58 4.18
165 168 2.629656 CCCTCGCTGGTGGCTTTTG 61.630 63.158 0.00 0.00 39.13 2.44
170 173 1.008538 GCTGGTGGCTTTTGTGTCG 60.009 57.895 0.00 0.00 38.06 4.35
171 174 1.444119 GCTGGTGGCTTTTGTGTCGA 61.444 55.000 0.00 0.00 38.06 4.20
174 177 2.416547 CTGGTGGCTTTTGTGTCGATAG 59.583 50.000 0.00 0.00 0.00 2.08
198 201 2.248280 TGTACAGATGGCAACGTTGT 57.752 45.000 27.78 9.90 42.51 3.32
209 212 2.338500 GCAACGTTGTTTCAAACCCAA 58.662 42.857 27.78 0.00 0.00 4.12
222 225 6.428083 TTCAAACCCAACTATAGTGTGAGA 57.572 37.500 6.06 0.11 0.00 3.27
223 226 6.037786 TCAAACCCAACTATAGTGTGAGAG 57.962 41.667 6.06 3.17 0.00 3.20
228 231 5.546499 ACCCAACTATAGTGTGAGAGGAAAA 59.454 40.000 6.06 0.00 0.00 2.29
263 266 3.220940 TCATTCATGCCACAACAGTTGA 58.779 40.909 20.56 0.00 0.00 3.18
271 276 2.917933 CCACAACAGTTGAGTCTGGAA 58.082 47.619 20.56 0.00 39.48 3.53
289 294 3.118038 TGGAACACACTCCAAACTAAGCT 60.118 43.478 0.00 0.00 42.69 3.74
296 301 4.335594 ACACTCCAAACTAAGCTTTCACAC 59.664 41.667 3.20 0.00 0.00 3.82
309 314 6.029346 AGCTTTCACACCTTTCAAATATGG 57.971 37.500 0.00 0.00 0.00 2.74
324 329 0.962489 TATGGAGGCTAGAAGCTCGC 59.038 55.000 0.00 0.00 41.99 5.03
329 334 1.663135 GAGGCTAGAAGCTCGCTTTTG 59.337 52.381 5.53 1.20 41.99 2.44
330 335 1.276421 AGGCTAGAAGCTCGCTTTTGA 59.724 47.619 5.53 0.00 41.99 2.69
333 338 3.127721 GGCTAGAAGCTCGCTTTTGAAAT 59.872 43.478 5.53 0.00 41.99 2.17
334 339 4.094212 GCTAGAAGCTCGCTTTTGAAATG 58.906 43.478 5.53 0.00 38.45 2.32
337 342 5.382618 AGAAGCTCGCTTTTGAAATGAAT 57.617 34.783 5.53 0.00 36.26 2.57
343 348 6.587608 AGCTCGCTTTTGAAATGAATTTTAGG 59.412 34.615 0.00 0.00 0.00 2.69
430 435 8.615211 AGTTAGTACAACGATCGATAATGTACA 58.385 33.333 32.62 24.22 45.41 2.90
438 443 6.821482 ACGATCGATAATGTACAAATGCATC 58.179 36.000 24.34 0.00 29.77 3.91
441 446 7.359514 CGATCGATAATGTACAAATGCATCTGT 60.360 37.037 10.26 11.07 29.77 3.41
442 447 8.831715 ATCGATAATGTACAAATGCATCTGTA 57.168 30.769 8.83 8.83 29.77 2.74
451 456 6.699575 ACAAATGCATCTGTAATAGTTCCC 57.300 37.500 3.17 0.00 0.00 3.97
457 462 5.427157 TGCATCTGTAATAGTTCCCCTAACA 59.573 40.000 0.00 0.00 40.83 2.41
467 472 4.949121 AGTTCCCCTAACAGATGTACTCT 58.051 43.478 0.00 0.00 40.83 3.24
468 473 4.957327 AGTTCCCCTAACAGATGTACTCTC 59.043 45.833 0.00 0.00 40.83 3.20
469 474 3.912248 TCCCCTAACAGATGTACTCTCC 58.088 50.000 0.00 0.00 29.16 3.71
474 479 4.712337 CCTAACAGATGTACTCTCCCTGTT 59.288 45.833 16.56 16.56 46.13 3.16
493 498 4.850680 TGTTCGGGTTTATTAGGCATCTT 58.149 39.130 0.00 0.00 0.00 2.40
494 499 4.879545 TGTTCGGGTTTATTAGGCATCTTC 59.120 41.667 0.00 0.00 0.00 2.87
499 504 5.347907 CGGGTTTATTAGGCATCTTCGTATC 59.652 44.000 0.00 0.00 0.00 2.24
569 585 9.845214 ACTATATGACAGGTAGGAATCCTATTT 57.155 33.333 12.76 1.08 38.48 1.40
677 697 9.226606 AGTAGACGGTCAAAATTTGATCAAATA 57.773 29.630 29.16 14.30 40.87 1.40
698 873 9.057089 CAAATATTAGGAGATCCAGTAAACCAC 57.943 37.037 0.92 0.00 38.89 4.16
730 909 5.813157 GGAGTACTCTGTGAGCTAAATTTCC 59.187 44.000 21.88 0.00 32.04 3.13
957 1139 3.315191 TCCGAGCTTTCCTTCAGTTTTTG 59.685 43.478 0.00 0.00 0.00 2.44
998 1180 0.037232 GCCGGAAGCAAGTGACTAGT 60.037 55.000 5.05 0.00 42.97 2.57
1013 1195 0.390860 CTAGTCATGCTTAGGCGGCT 59.609 55.000 18.33 18.33 42.25 5.52
1094 1276 3.059325 GCGTATGCAAGAATCTGTGGATC 60.059 47.826 0.89 0.00 42.15 3.36
1131 1313 6.020121 TGACTAAAGATTCGCGTAAGTATTGC 60.020 38.462 5.77 0.00 41.68 3.56
1184 1375 5.915175 AGTTTTTAGAAGAGGAGTCGTTGT 58.085 37.500 0.00 0.00 0.00 3.32
1231 1422 0.247736 GAACTCTGATGTCCAGCCGT 59.752 55.000 0.00 0.00 42.62 5.68
1602 1793 5.894298 TGATATACCTGAAGGATGCTGTT 57.106 39.130 2.62 0.00 38.94 3.16
1642 1833 4.130118 CCAAGTACTCTGTGATTATGGCC 58.870 47.826 0.00 0.00 0.00 5.36
1701 1892 2.428171 CAATGAGGTGTTTGGCTATGGG 59.572 50.000 0.00 0.00 0.00 4.00
1899 2090 1.728971 GGTTTGTCAGATGAGAGCACG 59.271 52.381 0.00 0.00 0.00 5.34
1969 2160 2.033424 GGTTCCAACAACAAGACTCTGC 59.967 50.000 0.00 0.00 0.00 4.26
2142 2333 7.149973 TGAAATTTCCAAAGAATCTGCAGAAG 58.850 34.615 22.50 6.59 0.00 2.85
2289 2480 0.608130 TGTCTGCTGCGAGGTTATGT 59.392 50.000 0.00 0.00 0.00 2.29
2616 2807 7.281098 AGATCAGCTACATTCTGAATGACATT 58.719 34.615 31.11 14.93 43.01 2.71
2827 3018 6.037391 CAGGTTTGTGAAGCAATTTGTGAATT 59.963 34.615 0.00 0.00 36.89 2.17
2865 3056 3.006752 TGGATCAATGGCAAAGGTTGAAC 59.993 43.478 5.44 3.34 35.70 3.18
2868 3059 4.686191 TCAATGGCAAAGGTTGAACAAT 57.314 36.364 0.00 0.00 0.00 2.71
3084 3277 6.721318 TGACTGAAAAATTGCTAGGACCTAT 58.279 36.000 0.46 0.00 0.00 2.57
3213 3406 1.768684 ATGTGAGGTTGACCAGCGGT 61.769 55.000 2.56 0.00 39.44 5.68
3247 3440 3.010420 GCCAGTCAGTTTCCAGATTACC 58.990 50.000 0.00 0.00 0.00 2.85
3537 3730 7.253422 GCTGAATGTTTCTATGTATGCTTTGT 58.747 34.615 0.00 0.00 0.00 2.83
3538 3731 7.219535 GCTGAATGTTTCTATGTATGCTTTGTG 59.780 37.037 0.00 0.00 0.00 3.33
3539 3732 8.334263 TGAATGTTTCTATGTATGCTTTGTGA 57.666 30.769 0.00 0.00 0.00 3.58
3540 3733 8.959548 TGAATGTTTCTATGTATGCTTTGTGAT 58.040 29.630 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.462047 ATAAAAGGCCAGCGACGAGG 60.462 55.000 5.01 0.00 0.00 4.63
11 12 3.555168 CGTCCCTAGCTATAAAAGGCCAG 60.555 52.174 5.01 0.00 0.00 4.85
12 13 2.367567 CGTCCCTAGCTATAAAAGGCCA 59.632 50.000 5.01 0.00 0.00 5.36
15 16 2.609737 CGCCGTCCCTAGCTATAAAAGG 60.610 54.545 0.00 0.00 0.00 3.11
36 37 0.747283 CATCTCCTGTTCTGCAGCCC 60.747 60.000 9.47 1.80 43.71 5.19
44 45 3.131223 TCCTTCGACATCATCTCCTGTTC 59.869 47.826 0.00 0.00 0.00 3.18
48 49 2.739943 TGTCCTTCGACATCATCTCCT 58.260 47.619 0.00 0.00 44.20 3.69
61 62 2.808543 ACTTGTTCGATGCTTGTCCTTC 59.191 45.455 0.00 0.00 0.00 3.46
62 63 2.808543 GACTTGTTCGATGCTTGTCCTT 59.191 45.455 0.00 0.00 0.00 3.36
66 67 2.838736 AGTGACTTGTTCGATGCTTGT 58.161 42.857 0.00 0.00 0.00 3.16
68 69 2.987149 CGTAGTGACTTGTTCGATGCTT 59.013 45.455 0.00 0.00 0.00 3.91
69 70 2.228103 TCGTAGTGACTTGTTCGATGCT 59.772 45.455 0.00 0.00 0.00 3.79
75 76 3.852536 CGGATTCTCGTAGTGACTTGTTC 59.147 47.826 0.00 0.00 0.00 3.18
89 90 1.562017 GTTCGCTCCTTCGGATTCTC 58.438 55.000 0.00 0.00 0.00 2.87
90 91 0.179134 CGTTCGCTCCTTCGGATTCT 60.179 55.000 0.00 0.00 0.00 2.40
91 92 0.458025 ACGTTCGCTCCTTCGGATTC 60.458 55.000 0.00 0.00 0.00 2.52
106 107 2.415168 CACTCGCCATTAATGACACGTT 59.585 45.455 17.23 6.74 0.00 3.99
108 109 1.327460 CCACTCGCCATTAATGACACG 59.673 52.381 17.23 15.99 0.00 4.49
112 113 3.202906 GCTAACCACTCGCCATTAATGA 58.797 45.455 17.23 0.00 0.00 2.57
159 162 8.126871 TGTACATAATCTATCGACACAAAAGC 57.873 34.615 0.00 0.00 0.00 3.51
165 168 6.528423 GCCATCTGTACATAATCTATCGACAC 59.472 42.308 0.00 0.00 0.00 3.67
170 173 6.868864 ACGTTGCCATCTGTACATAATCTATC 59.131 38.462 0.00 0.00 0.00 2.08
171 174 6.759272 ACGTTGCCATCTGTACATAATCTAT 58.241 36.000 0.00 0.00 0.00 1.98
174 177 5.064707 ACAACGTTGCCATCTGTACATAATC 59.935 40.000 27.61 0.00 0.00 1.75
184 187 3.443976 GTTTGAAACAACGTTGCCATCT 58.556 40.909 27.61 5.29 0.00 2.90
185 188 2.538037 GGTTTGAAACAACGTTGCCATC 59.462 45.455 27.61 21.42 0.00 3.51
187 190 1.404315 GGGTTTGAAACAACGTTGCCA 60.404 47.619 27.61 19.18 0.00 4.92
189 192 1.997669 TGGGTTTGAAACAACGTTGC 58.002 45.000 27.61 12.48 0.00 4.17
198 201 6.833041 TCTCACACTATAGTTGGGTTTGAAA 58.167 36.000 1.56 0.00 0.00 2.69
239 242 4.247267 ACTGTTGTGGCATGAATGAAAG 57.753 40.909 0.00 0.00 0.00 2.62
245 248 2.618241 GACTCAACTGTTGTGGCATGAA 59.382 45.455 20.30 0.00 32.56 2.57
271 276 4.335594 GTGAAAGCTTAGTTTGGAGTGTGT 59.664 41.667 0.00 0.00 0.00 3.72
278 283 4.918810 AAGGTGTGAAAGCTTAGTTTGG 57.081 40.909 0.00 0.00 44.77 3.28
289 294 5.047377 GCCTCCATATTTGAAAGGTGTGAAA 60.047 40.000 6.48 0.00 31.65 2.69
296 301 5.240403 GCTTCTAGCCTCCATATTTGAAAGG 59.760 44.000 0.00 1.78 34.48 3.11
309 314 1.663135 CAAAAGCGAGCTTCTAGCCTC 59.337 52.381 11.01 0.00 43.77 4.70
351 356 9.474313 AAGGCATTTATAATAGTGAACAAAGGA 57.526 29.630 0.00 0.00 0.00 3.36
409 414 7.526186 GCATTTGTACATTATCGATCGTTGTAC 59.474 37.037 26.92 26.92 41.76 2.90
425 430 7.282224 GGGAACTATTACAGATGCATTTGTACA 59.718 37.037 25.16 17.59 30.03 2.90
426 431 7.255139 GGGGAACTATTACAGATGCATTTGTAC 60.255 40.741 25.16 14.60 30.03 2.90
430 435 6.018433 AGGGGAACTATTACAGATGCATTT 57.982 37.500 0.00 0.00 0.00 2.32
438 443 7.125792 ACATCTGTTAGGGGAACTATTACAG 57.874 40.000 0.00 0.00 39.93 2.74
441 446 8.287350 AGAGTACATCTGTTAGGGGAACTATTA 58.713 37.037 0.00 0.00 38.98 0.98
442 447 7.133483 AGAGTACATCTGTTAGGGGAACTATT 58.867 38.462 0.00 0.00 38.98 1.73
449 454 2.966516 GGGAGAGTACATCTGTTAGGGG 59.033 54.545 0.00 0.00 38.84 4.79
451 456 4.282496 ACAGGGAGAGTACATCTGTTAGG 58.718 47.826 0.00 0.00 38.84 2.69
457 462 2.379972 CCGAACAGGGAGAGTACATCT 58.620 52.381 0.00 0.00 42.61 2.90
469 474 2.993937 TGCCTAATAAACCCGAACAGG 58.006 47.619 0.00 0.00 40.63 4.00
474 479 3.133362 ACGAAGATGCCTAATAAACCCGA 59.867 43.478 0.00 0.00 0.00 5.14
478 483 6.929606 ACTGGATACGAAGATGCCTAATAAAC 59.070 38.462 0.00 0.00 42.51 2.01
650 670 6.721571 TGATCAAATTTTGACCGTCTACTC 57.278 37.500 13.80 6.16 43.48 2.59
677 697 4.960469 TCGTGGTTTACTGGATCTCCTAAT 59.040 41.667 0.00 0.00 36.82 1.73
680 700 2.496470 GTCGTGGTTTACTGGATCTCCT 59.504 50.000 0.00 0.00 36.82 3.69
730 909 3.270877 CCCTTTCTCGTATCCAAAGTGG 58.729 50.000 0.00 0.00 39.43 4.00
765 945 0.935196 AACGGTCAAACACTCGCTTC 59.065 50.000 0.00 0.00 0.00 3.86
957 1139 2.288518 GGTAGAGACATCGAGGGATTGC 60.289 54.545 0.69 0.00 0.00 3.56
998 1180 2.514592 GCAGCCGCCTAAGCATGA 60.515 61.111 0.00 0.00 39.83 3.07
1076 1258 2.423947 GGGGATCCACAGATTCTTGCAT 60.424 50.000 15.23 0.00 30.90 3.96
1094 1276 4.202245 TCTTTAGTCAGATTCAACGGGG 57.798 45.455 0.00 0.00 0.00 5.73
1131 1313 3.134458 GCGGAAACTGATAGGAGGATTG 58.866 50.000 0.00 0.00 0.00 2.67
1179 1370 0.591236 CGCCACAAGAACCAACAACG 60.591 55.000 0.00 0.00 0.00 4.10
1184 1375 0.179234 TCTCACGCCACAAGAACCAA 59.821 50.000 0.00 0.00 0.00 3.67
1274 1465 1.146263 GGCGAATCCGGGATCTTGT 59.854 57.895 10.56 0.00 36.06 3.16
1602 1793 5.324409 ACTTGGTAATTCTCCAGCAATTCA 58.676 37.500 3.16 0.00 36.28 2.57
1642 1833 1.308069 CCAATCTTGGTCCGTGGCAG 61.308 60.000 0.55 0.00 43.43 4.85
1695 1886 4.517285 AGAATAACACACTGTGCCCATAG 58.483 43.478 9.20 0.00 36.98 2.23
1701 1892 4.725556 TTTCGAGAATAACACACTGTGC 57.274 40.909 9.20 0.00 36.98 4.57
1899 2090 1.140816 GAGTTCGTCTCCAGTTGTGC 58.859 55.000 0.34 0.00 37.22 4.57
1969 2160 4.326826 TGTTCTTTGATCAGCCTTACCAG 58.673 43.478 0.00 0.00 0.00 4.00
2040 2231 2.925563 GCCAAATTTACACAGCATGCTC 59.074 45.455 19.68 0.00 42.53 4.26
2424 2615 1.406069 GCCTTCACCATGTCGTCAGAT 60.406 52.381 0.00 0.00 0.00 2.90
2616 2807 7.280876 GCAACAATAGATTCAAGAGTGTATCCA 59.719 37.037 0.00 0.00 33.25 3.41
2919 3110 9.846248 ATAAAGCTTGTGTGTCAGAATATTTTC 57.154 29.630 0.00 0.00 0.00 2.29
2929 3122 6.691754 TGAAGAAATAAAGCTTGTGTGTCA 57.308 33.333 0.00 0.00 0.00 3.58
2933 3126 5.766222 CAGCTGAAGAAATAAAGCTTGTGT 58.234 37.500 8.42 0.00 43.33 3.72
3071 3264 3.711704 CCTCTCCAAATAGGTCCTAGCAA 59.288 47.826 4.57 0.00 39.02 3.91
3084 3277 6.891306 TTCCAAGAGATATTCCTCTCCAAA 57.109 37.500 0.00 0.00 42.31 3.28
3181 3374 6.601613 GTCAACCTCACATGGGATGTTAATAA 59.398 38.462 16.93 2.82 42.70 1.40
3409 3602 5.006358 CACGCGTAATACTAAAATCAGCCTT 59.994 40.000 13.44 0.00 0.00 4.35
3541 3734 8.495949 CGACAAATCACAAAGTACTTATCAGTT 58.504 33.333 8.92 0.00 34.06 3.16
3542 3735 7.870954 TCGACAAATCACAAAGTACTTATCAGT 59.129 33.333 8.92 3.01 36.99 3.41
3543 3736 8.239681 TCGACAAATCACAAAGTACTTATCAG 57.760 34.615 8.92 2.37 0.00 2.90


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

AutoCloner maintained by Alex Coulton.