Multiple sequence alignment - TraesCS7D01G310200

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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 TraesCS7D01G310200 chr7D 100.000 4798 0 0 1 4798 393575016 393579813 0.000000e+00 8861
1 TraesCS7D01G310200 chr7D 85.303 347 32 11 4457 4798 116436612 116436944 1.650000e-89 340
2 TraesCS7D01G310200 chr7B 95.380 3355 120 19 58 3389 393313882 393317224 0.000000e+00 5304
3 TraesCS7D01G310200 chr7B 95.897 975 33 3 3386 4360 393317359 393318326 0.000000e+00 1572
4 TraesCS7D01G310200 chr7B 89.616 443 19 4 4358 4798 393318449 393318866 5.460000e-149 538
5 TraesCS7D01G310200 chr7B 86.804 341 26 8 4459 4798 75027462 75027784 3.530000e-96 363
6 TraesCS7D01G310200 chr7B 86.804 341 26 8 4459 4798 75034968 75035290 3.530000e-96 363
7 TraesCS7D01G310200 chr7A 94.779 3390 114 22 1 3377 446321397 446324736 0.000000e+00 5221
8 TraesCS7D01G310200 chr7A 94.452 1424 62 13 3386 4798 446324857 446326274 0.000000e+00 2176
9 TraesCS7D01G310200 chr7A 88.047 343 22 10 4457 4798 120466519 120466843 5.820000e-104 388
10 TraesCS7D01G310200 chr5A 84.906 265 40 0 3503 3767 707034119 707033855 7.920000e-68 268
11 TraesCS7D01G310200 chr5A 86.842 114 11 4 3964 4077 707032732 707032623 1.810000e-24 124
12 TraesCS7D01G310200 chr5D 76.961 204 45 2 3434 3635 546920918 546921121 1.090000e-21 115


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 TraesCS7D01G310200 chr7D 393575016 393579813 4797 False 8861.000000 8861 100.0000 1 4798 1 chr7D.!!$F2 4797
1 TraesCS7D01G310200 chr7B 393313882 393318866 4984 False 2471.333333 5304 93.6310 58 4798 3 chr7B.!!$F3 4740
2 TraesCS7D01G310200 chr7A 446321397 446326274 4877 False 3698.500000 5221 94.6155 1 4798 2 chr7A.!!$F2 4797

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
103 106 0.178301 GGAAGAGAATCCCGGTGTCC 59.822 60.000 0.00 0.0 33.66 4.02 F
632 698 0.252197 GAGGCCTCCACCACGTATTT 59.748 55.000 23.19 0.0 0.00 1.40 F
786 852 1.400629 GCGGTTCTTCTTTTTACGGGC 60.401 52.381 0.00 0.0 0.00 6.13 F
2097 2164 1.632589 AGGAGGTGATGTTTTTGGGC 58.367 50.000 0.00 0.0 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1188 1255 1.588674 CAACACCAGCGTTCCTGTTA 58.411 50.000 0.00 0.00 40.06 2.41 R
1692 1759 2.503824 TCCCTAGGATCCTCTGAGTCA 58.496 52.381 20.22 0.00 0.00 3.41 R
2712 2779 2.913617 ACCAAGTTAGGCTAAGCTTCCT 59.086 45.455 7.33 7.14 36.51 3.36 R
4028 4247 0.963355 GCCAGGACGGGTAATTTGCA 60.963 55.000 0.00 0.00 34.06 4.08 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
31 32 1.880675 AGCTCCACCGATCAGTATACG 59.119 52.381 0.00 0.00 0.00 3.06
103 106 0.178301 GGAAGAGAATCCCGGTGTCC 59.822 60.000 0.00 0.00 33.66 4.02
120 123 3.042682 TGTCCCGGCTTAATCCTCATAA 58.957 45.455 0.00 0.00 0.00 1.90
127 130 3.067833 GCTTAATCCTCATAAGGGCGAC 58.932 50.000 0.00 0.00 43.56 5.19
146 150 1.813753 CCTTGGACGTATGGTGGCG 60.814 63.158 0.00 0.00 0.00 5.69
246 250 0.601057 TCATGTCGTCTTCTTCGGCA 59.399 50.000 0.00 0.00 46.37 5.69
259 263 1.209504 CTTCGGCAATGAGGTTAGGGA 59.790 52.381 0.00 0.00 0.00 4.20
262 266 2.241176 TCGGCAATGAGGTTAGGGATTT 59.759 45.455 0.00 0.00 0.00 2.17
264 268 3.447229 CGGCAATGAGGTTAGGGATTTTT 59.553 43.478 0.00 0.00 0.00 1.94
307 330 6.549364 TGCCAGATCCGGTGAATTTTTATAAT 59.451 34.615 0.00 0.00 0.00 1.28
309 332 8.237267 GCCAGATCCGGTGAATTTTTATAATAG 58.763 37.037 0.00 0.00 0.00 1.73
310 333 9.502091 CCAGATCCGGTGAATTTTTATAATAGA 57.498 33.333 0.00 0.00 0.00 1.98
389 436 3.211045 GAAAACTGTGTTGAGCTGGGTA 58.789 45.455 0.00 0.00 0.00 3.69
476 524 4.442332 GGTCCAAAATGAAGGAAACGGTTT 60.442 41.667 5.68 5.68 35.29 3.27
612 678 4.699522 GACGCCTCCACCACCACC 62.700 72.222 0.00 0.00 0.00 4.61
632 698 0.252197 GAGGCCTCCACCACGTATTT 59.748 55.000 23.19 0.00 0.00 1.40
786 852 1.400629 GCGGTTCTTCTTTTTACGGGC 60.401 52.381 0.00 0.00 0.00 6.13
916 983 3.991773 TCTTTCGATGTTTCTTACGGTGG 59.008 43.478 0.00 0.00 0.00 4.61
1188 1255 1.958288 ATCCTGGGCAGAGTTACAGT 58.042 50.000 0.00 0.00 0.00 3.55
1551 1618 5.711976 GTCATTTGATTTGGAGGAGGAAGAA 59.288 40.000 0.00 0.00 0.00 2.52
1605 1672 5.674008 CAGATTGTCTTCGAACTGTTCTTG 58.326 41.667 17.60 8.11 0.00 3.02
1692 1759 3.641046 TCTCAGGCTGCTAGATCTCTTT 58.359 45.455 10.34 0.00 0.00 2.52
2097 2164 1.632589 AGGAGGTGATGTTTTTGGGC 58.367 50.000 0.00 0.00 0.00 5.36
2235 2302 2.041153 CAGAGTGCCAACCAAACCC 58.959 57.895 0.00 0.00 0.00 4.11
2398 2465 5.163774 GGTATATAGTGCGTACTAGTCCTGC 60.164 48.000 18.33 2.53 42.36 4.85
2481 2548 6.436847 TCATTAATTCCTTGCAAACAGGATCA 59.563 34.615 6.45 0.00 0.00 2.92
2725 2792 6.559157 ACCTATGTTATTAGGAAGCTTAGCCT 59.441 38.462 11.22 11.22 41.18 4.58
2821 2889 6.743575 AACAACTAACTCTGCCATATTGAC 57.256 37.500 0.00 0.00 0.00 3.18
2925 2994 3.802948 ACCTAGATGTGCTTAGTTCCG 57.197 47.619 0.00 0.00 0.00 4.30
2946 3015 3.198872 GCAGCTTTCTAGTGTACCCATC 58.801 50.000 0.00 0.00 0.00 3.51
2952 3021 5.105473 GCTTTCTAGTGTACCCATCTACACA 60.105 44.000 11.10 0.00 46.19 3.72
3011 3080 5.070580 AGTTACCTCTGTTTGCTACTTCACT 59.929 40.000 0.00 0.00 0.00 3.41
3014 3083 3.244215 CCTCTGTTTGCTACTTCACTGGA 60.244 47.826 0.00 0.00 0.00 3.86
3119 3188 2.087646 GAAGAAACTGCCCTGATCCAC 58.912 52.381 0.00 0.00 0.00 4.02
3142 3211 2.519771 TCCTGCATTGAGAATTGCCT 57.480 45.000 0.00 0.00 0.00 4.75
3163 3232 8.039603 TGCCTTTAAGTACATATCTGTGTTTG 57.960 34.615 0.00 0.00 36.79 2.93
3175 3244 9.167311 ACATATCTGTGTTTGTTCTATCCTTTC 57.833 33.333 0.00 0.00 33.22 2.62
3200 3269 5.982356 TCACTAAGTTAGCATTCTGAGCAT 58.018 37.500 9.92 0.00 0.00 3.79
3201 3270 5.814188 TCACTAAGTTAGCATTCTGAGCATG 59.186 40.000 9.92 0.00 0.00 4.06
3265 3336 9.023962 ACATTCATAAACAAGCTGATTTTCCTA 57.976 29.630 1.11 0.00 0.00 2.94
3413 3631 5.176958 CCCGTGCTACTTATTTAGTATGTGC 59.823 44.000 0.00 0.00 38.63 4.57
3542 3760 2.852449 ACTGCCCATAATCCTTCCTTCA 59.148 45.455 0.00 0.00 0.00 3.02
3638 3856 2.168728 GGACCATGACCCTGTACTCTTC 59.831 54.545 0.00 0.00 0.00 2.87
3650 3868 0.683504 TACTCTTCGAGGGGTGCCTC 60.684 60.000 10.84 0.00 33.35 4.70
3665 3883 3.416156 GTGCCTCAAGAAGTTTCAGGAT 58.584 45.455 1.99 0.00 0.00 3.24
3804 4022 4.547427 AGGGTTCTTCTACCTAACCTCCTA 59.453 45.833 0.00 0.00 41.95 2.94
4028 4247 1.400530 CGAGGGGCGAAGTAAGGGAT 61.401 60.000 0.00 0.00 44.57 3.85
4078 4297 2.637521 CATGTGCTGCAACAGGTCT 58.362 52.632 2.77 0.00 32.52 3.85
4145 4365 0.319813 GCTTGCCGGTGCTGATTTTT 60.320 50.000 1.90 0.00 38.71 1.94
4180 4400 6.403333 TGCGTTATGTATGAACAACTTCTC 57.597 37.500 0.00 0.00 39.58 2.87
4205 4425 8.928733 TCGTCTTTTGTCTTTGTAATATGTACC 58.071 33.333 0.00 0.00 0.00 3.34
4244 4464 5.860182 TGCTTCAGTAGACGTATACACAAAC 59.140 40.000 21.40 9.64 0.00 2.93
4275 4495 5.451937 GCAGGCAGAGGTTTTCTTTACTTTT 60.452 40.000 0.00 0.00 32.41 2.27
4473 4823 3.295093 TGCTGATGACCAAAGACCAAAA 58.705 40.909 0.00 0.00 0.00 2.44
4486 4836 6.991531 CCAAAGACCAAAAGGAATTCAATTCA 59.008 34.615 12.27 0.00 41.03 2.57
4522 4873 4.143094 GCTGAACGAAGATGTTGTAGGTTC 60.143 45.833 0.00 0.00 34.45 3.62
4651 5008 5.817816 GGTTCTTCAGACAAGAAGTTCAGAA 59.182 40.000 5.50 0.07 44.18 3.02
4667 5024 5.532779 AGTTCAGAAGTTTTCAGATCCAACC 59.467 40.000 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.915078 ATCGGTGGAGCTTGGAAGGG 61.915 60.000 0.00 0.00 0.00 3.95
7 8 0.904865 ACTGATCGGTGGAGCTTGGA 60.905 55.000 6.33 0.00 0.00 3.53
67 68 2.350895 CCCGCCACCAATCACTGA 59.649 61.111 0.00 0.00 0.00 3.41
101 104 2.637872 CCTTATGAGGATTAAGCCGGGA 59.362 50.000 2.18 0.00 46.74 5.14
103 106 2.876079 GCCCTTATGAGGATTAAGCCGG 60.876 54.545 4.80 0.00 46.74 6.13
127 130 1.451387 GCCACCATACGTCCAAGGG 60.451 63.158 0.00 0.00 0.00 3.95
137 141 1.209261 TGAAGATGAAGCGCCACCATA 59.791 47.619 2.29 0.00 0.00 2.74
146 150 3.190874 CCGACCTACTTGAAGATGAAGC 58.809 50.000 0.00 0.00 0.00 3.86
207 211 4.494484 TGAATCTACATCACAACTCCGTG 58.506 43.478 0.00 0.00 38.29 4.94
216 220 6.269315 AGAAGACGACATGAATCTACATCAC 58.731 40.000 0.00 0.00 0.00 3.06
220 224 5.332707 CGAAGAAGACGACATGAATCTACA 58.667 41.667 0.00 0.00 0.00 2.74
598 664 4.394712 CTCGGTGGTGGTGGAGGC 62.395 72.222 0.00 0.00 0.00 4.70
599 665 3.706373 CCTCGGTGGTGGTGGAGG 61.706 72.222 0.00 0.00 40.05 4.30
600 666 4.394712 GCCTCGGTGGTGGTGGAG 62.395 72.222 0.00 0.00 38.35 3.86
603 669 4.394712 GAGGCCTCGGTGGTGGTG 62.395 72.222 19.06 0.00 38.35 4.17
606 672 4.394712 GTGGAGGCCTCGGTGGTG 62.395 72.222 26.36 0.00 38.35 4.17
609 675 4.394712 GTGGTGGAGGCCTCGGTG 62.395 72.222 26.36 0.00 0.00 4.94
612 678 1.956629 AATACGTGGTGGAGGCCTCG 61.957 60.000 26.36 16.79 46.93 4.63
613 679 0.252197 AAATACGTGGTGGAGGCCTC 59.748 55.000 25.59 25.59 0.00 4.70
614 680 0.252197 GAAATACGTGGTGGAGGCCT 59.748 55.000 3.86 3.86 0.00 5.19
632 698 1.361204 TCCTGCAGAAATCTGTGGGA 58.639 50.000 17.39 16.62 45.45 4.37
852 918 5.348986 GCGAGAATGATAAGAGTACAACCA 58.651 41.667 0.00 0.00 0.00 3.67
916 983 7.541162 TCATTCATCAACCTGATCAAATCAAC 58.459 34.615 0.00 0.00 39.11 3.18
1188 1255 1.588674 CAACACCAGCGTTCCTGTTA 58.411 50.000 0.00 0.00 40.06 2.41
1551 1618 3.717294 GCCGGGTCCATGACAGGT 61.717 66.667 2.18 0.00 35.44 4.00
1605 1672 5.398603 TCTCTGGAGACTGAACAAATCTC 57.601 43.478 0.00 0.00 37.88 2.75
1692 1759 2.503824 TCCCTAGGATCCTCTGAGTCA 58.496 52.381 20.22 0.00 0.00 3.41
1968 2035 3.373130 CACAGTATGACAGTTGCTGATGG 59.627 47.826 2.91 0.00 39.69 3.51
2097 2164 5.044558 GCTTCCAATACTTCCTCTAACTCG 58.955 45.833 0.00 0.00 0.00 4.18
2329 2396 9.944376 AGTTCACTTGCATTAATAAGTTCTAGA 57.056 29.630 1.56 0.00 35.08 2.43
2481 2548 7.118245 GCCAAGTTAAAATCAGCAGCTTAAATT 59.882 33.333 0.00 0.00 0.00 1.82
2712 2779 2.913617 ACCAAGTTAGGCTAAGCTTCCT 59.086 45.455 7.33 7.14 36.51 3.36
2725 2792 7.016760 TGCATAGCAGGGTATATAACCAAGTTA 59.983 37.037 19.19 12.69 41.45 2.24
2925 2994 2.762535 TGGGTACACTAGAAAGCTGC 57.237 50.000 0.00 0.00 0.00 5.25
2992 3061 3.070018 CCAGTGAAGTAGCAAACAGAGG 58.930 50.000 0.00 0.00 0.00 3.69
3011 3080 3.388024 ACAGTTTTGACTGCTCTACTCCA 59.612 43.478 6.47 0.00 41.19 3.86
3014 3083 5.012148 ACCATACAGTTTTGACTGCTCTACT 59.988 40.000 6.47 0.00 41.19 2.57
3119 3188 3.930848 GGCAATTCTCAATGCAGGAAAAG 59.069 43.478 0.00 0.00 44.32 2.27
3163 3232 9.036671 GCTAACTTAGTGATGAAAGGATAGAAC 57.963 37.037 0.00 0.00 0.00 3.01
3175 3244 5.814188 TGCTCAGAATGCTAACTTAGTGATG 59.186 40.000 0.00 0.00 34.76 3.07
3265 3336 4.934356 AGGATGTATTGTGTTGGGAACAT 58.066 39.130 0.00 0.00 44.35 2.71
3355 3435 3.435327 ACACACACACACACACTAAACAG 59.565 43.478 0.00 0.00 0.00 3.16
3413 3631 8.530311 ACATAAGAGGAGTAGATGCATCATTAG 58.470 37.037 27.81 6.40 0.00 1.73
3458 3676 1.967319 TGTTCCACAGAAACAGAGCC 58.033 50.000 0.00 0.00 32.58 4.70
3542 3760 9.840427 CAATGACCTTTTGTATTTCGTTCTAAT 57.160 29.630 0.00 0.00 0.00 1.73
3650 3868 5.415077 AGCTTCATCATCCTGAAACTTCTTG 59.585 40.000 0.00 0.00 34.86 3.02
3665 3883 2.934553 CGCATCTTCTTGAGCTTCATCA 59.065 45.455 0.00 0.00 0.00 3.07
3783 4001 4.341806 GCTAGGAGGTTAGGTAGAAGAACC 59.658 50.000 0.00 0.00 42.54 3.62
3804 4022 1.809271 CGGCTCATATGCAAGTCAGCT 60.809 52.381 10.58 0.00 34.99 4.24
4028 4247 0.963355 GCCAGGACGGGTAATTTGCA 60.963 55.000 0.00 0.00 34.06 4.08
4145 4365 7.262048 TCATACATAACGCATTACAGTTCAGA 58.738 34.615 0.00 0.00 0.00 3.27
4180 4400 7.896274 CGGTACATATTACAAAGACAAAAGACG 59.104 37.037 0.00 0.00 0.00 4.18
4205 4425 3.958704 TGAAGCAAACAAATGTACACCG 58.041 40.909 0.00 0.00 0.00 4.94
4275 4495 7.394359 AGCCATTTACTAGAAGCTGATTTTTGA 59.606 33.333 0.00 0.00 0.00 2.69
4394 4743 8.550376 ACTGCACAAATTTTTACAACAATCATC 58.450 29.630 0.00 0.00 0.00 2.92
4473 4823 5.003096 AGGTGAACCTGAATTGAATTCCT 57.997 39.130 14.73 0.55 46.55 3.36
4522 4873 5.032327 TCATCTTCAACTCTCCATGATGG 57.968 43.478 4.74 4.74 39.43 3.51
4532 4883 7.060383 TCCTCCAATATCTCATCTTCAACTC 57.940 40.000 0.00 0.00 0.00 3.01
4651 5008 2.749621 GCGATGGTTGGATCTGAAAACT 59.250 45.455 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.