Multiple sequence alignment - TraesCS6D01G261600

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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 TraesCS6D01G261600 chr6D 100.000 3575 0 0 1 3575 369918648 369915074 0 6602
1 TraesCS6D01G261600 chr6D 97.122 2988 80 6 591 3575 283154172 283151188 0 5036
2 TraesCS6D01G261600 chrUn 98.180 3077 52 4 503 3575 186191555 186188479 0 5369
3 TraesCS6D01G261600 chr7B 97.919 3075 60 3 503 3573 743005923 743008997 0 5321
4 TraesCS6D01G261600 chr7D 97.888 3078 53 7 503 3575 579029599 579032669 0 5313
5 TraesCS6D01G261600 chr7A 97.463 3075 74 3 503 3575 120880310 120883382 0 5243
6 TraesCS6D01G261600 chr7A 95.413 436 15 3 503 937 211292179 211292610 0 689
7 TraesCS6D01G261600 chr4B 97.574 3050 68 5 530 3575 209271422 209268375 0 5217
8 TraesCS6D01G261600 chr1D 97.172 3076 65 10 503 3575 212467989 212464933 0 5179
9 TraesCS6D01G261600 chr1D 97.610 502 12 0 1 502 311324998 311324497 0 861
10 TraesCS6D01G261600 chr6A 96.230 3077 108 6 503 3575 79143538 79146610 0 5033
11 TraesCS6D01G261600 chr2B 94.378 3077 163 7 503 3575 343522118 343525188 0 4715
12 TraesCS6D01G261600 chr4D 97.809 502 10 1 1 502 41393459 41392959 0 865
13 TraesCS6D01G261600 chr4D 97.610 502 11 1 1 502 378878590 378878090 0 859
14 TraesCS6D01G261600 chr5D 97.610 502 11 1 1 502 385838474 385837974 0 859
15 TraesCS6D01G261600 chr5D 97.421 504 12 1 1 503 242862744 242862241 0 857
16 TraesCS6D01G261600 chr5D 96.693 514 14 3 1 513 303707182 303707693 0 852
17 TraesCS6D01G261600 chr5D 95.817 526 17 5 1 524 277149779 277149257 0 845
18 TraesCS6D01G261600 chr3D 97.610 502 10 2 1 502 396994561 396995060 0 859
19 TraesCS6D01G261600 chr3D 96.146 519 16 3 1 519 211653097 211653611 0 845


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 TraesCS6D01G261600 chr6D 369915074 369918648 3574 True 6602 6602 100.000 1 3575 1 chr6D.!!$R2 3574
1 TraesCS6D01G261600 chr6D 283151188 283154172 2984 True 5036 5036 97.122 591 3575 1 chr6D.!!$R1 2984
2 TraesCS6D01G261600 chrUn 186188479 186191555 3076 True 5369 5369 98.180 503 3575 1 chrUn.!!$R1 3072
3 TraesCS6D01G261600 chr7B 743005923 743008997 3074 False 5321 5321 97.919 503 3573 1 chr7B.!!$F1 3070
4 TraesCS6D01G261600 chr7D 579029599 579032669 3070 False 5313 5313 97.888 503 3575 1 chr7D.!!$F1 3072
5 TraesCS6D01G261600 chr7A 120880310 120883382 3072 False 5243 5243 97.463 503 3575 1 chr7A.!!$F1 3072
6 TraesCS6D01G261600 chr4B 209268375 209271422 3047 True 5217 5217 97.574 530 3575 1 chr4B.!!$R1 3045
7 TraesCS6D01G261600 chr1D 212464933 212467989 3056 True 5179 5179 97.172 503 3575 1 chr1D.!!$R1 3072
8 TraesCS6D01G261600 chr1D 311324497 311324998 501 True 861 861 97.610 1 502 1 chr1D.!!$R2 501
9 TraesCS6D01G261600 chr6A 79143538 79146610 3072 False 5033 5033 96.230 503 3575 1 chr6A.!!$F1 3072
10 TraesCS6D01G261600 chr2B 343522118 343525188 3070 False 4715 4715 94.378 503 3575 1 chr2B.!!$F1 3072
11 TraesCS6D01G261600 chr4D 41392959 41393459 500 True 865 865 97.809 1 502 1 chr4D.!!$R1 501
12 TraesCS6D01G261600 chr4D 378878090 378878590 500 True 859 859 97.610 1 502 1 chr4D.!!$R2 501
13 TraesCS6D01G261600 chr5D 385837974 385838474 500 True 859 859 97.610 1 502 1 chr5D.!!$R3 501
14 TraesCS6D01G261600 chr5D 242862241 242862744 503 True 857 857 97.421 1 503 1 chr5D.!!$R1 502
15 TraesCS6D01G261600 chr5D 303707182 303707693 511 False 852 852 96.693 1 513 1 chr5D.!!$F1 512
16 TraesCS6D01G261600 chr5D 277149257 277149779 522 True 845 845 95.817 1 524 1 chr5D.!!$R2 523
17 TraesCS6D01G261600 chr3D 211653097 211653611 514 False 845 845 96.146 1 519 1 chr3D.!!$F1 518

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
583 586 1.473434 GCCCTACTTGGTCGATGAAGG 60.473 57.143 10.21 2.84 0.00 3.46 F
1338 1350 0.108585 TGTGGCCACCAAGTCTCTTC 59.891 55.000 32.62 3.85 34.18 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1523 1535 2.171237 TGCATAGTCATTCCAGGTCCAG 59.829 50.0 0.00 0.0 0.00 3.86 R
2967 2985 1.000233 CATGCAACTGCTTGTCGCAC 61.000 55.0 8.92 0.0 45.47 5.34 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
59 60 3.581755 CTCGATCGGGTTCAGTTAACAA 58.418 45.455 16.41 0.00 40.08 2.83
260 261 3.084786 CTCTGAAATTTTCCTCGCCCTT 58.915 45.455 6.68 0.00 0.00 3.95
583 586 1.473434 GCCCTACTTGGTCGATGAAGG 60.473 57.143 10.21 2.84 0.00 3.46
1260 1272 5.366768 TGGATTTGGTAATTGGTTTGTTCCA 59.633 36.000 0.00 0.00 35.49 3.53
1289 1301 1.509463 GTGCACCTGACATGGCATG 59.491 57.895 25.31 25.31 38.68 4.06
1338 1350 0.108585 TGTGGCCACCAAGTCTCTTC 59.891 55.000 32.62 3.85 34.18 2.87
1354 1366 6.381250 AGTCTCTTCCTCCTATTAAGCTCAT 58.619 40.000 0.00 0.00 0.00 2.90
2197 2210 4.929479 TGCTGGATTTTACTATTGGGTGT 58.071 39.130 0.00 0.00 0.00 4.16
2346 2359 6.602406 GCATTCCAGATTATCCAGATGCTTAT 59.398 38.462 10.84 0.00 0.00 1.73
2359 2372 4.523173 CAGATGCTTATGCTGGATGGAATT 59.477 41.667 1.96 0.00 40.48 2.17
2435 2448 4.318475 CGTAGTTGTCGCAATCACTTCAAA 60.318 41.667 0.00 0.00 0.00 2.69
2743 2758 3.107601 CCTTCTTGGTGGAGATAGGTGA 58.892 50.000 0.00 0.00 0.00 4.02
2859 2876 5.048782 GGCAAGGCATATTCATATGTCGAAA 60.049 40.000 1.90 0.00 46.94 3.46
2937 2955 2.391926 TAGGGACCAAGGATGCGATA 57.608 50.000 0.00 0.00 0.00 2.92
2967 2985 0.681564 AGGTCGGAGTAGCAGGAGTG 60.682 60.000 0.00 0.00 0.00 3.51
3016 3034 4.330074 GTGGGTCTGTAACGAGATGAATTG 59.670 45.833 0.00 0.00 0.00 2.32
3106 3124 1.184322 TTACGGCGGTTGAGGGTACA 61.184 55.000 13.24 0.00 0.00 2.90
3110 3128 1.078426 GCGGTTGAGGGTACATGCT 60.078 57.895 0.00 0.00 0.00 3.79
3125 3143 3.794717 ACATGCTGTTCAGAGATGCTAG 58.205 45.455 3.84 0.00 0.00 3.42
3405 3423 2.200067 GACAGTCCTGCATCGAGATTG 58.800 52.381 0.00 0.00 0.00 2.67
3491 3510 9.468532 CTTACCAAAGAAAGAAAAAGGAATGAG 57.531 33.333 0.00 0.00 34.37 2.90
3540 3559 8.582891 AGAAATAGGATAAGGGTAAAGGTGAT 57.417 34.615 0.00 0.00 0.00 3.06
3559 3578 4.451096 GTGATGTTTTAGCTCTTCGTTCCA 59.549 41.667 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.081108 CCCGATCGAGCGATTCCTC 60.081 63.158 26.68 0.00 34.60 3.71
1223 1235 2.487086 CCAAATCCACCTATCATCGCCA 60.487 50.000 0.00 0.00 0.00 5.69
1260 1272 3.264193 TGTCAGGTGCACCTATCAGAATT 59.736 43.478 37.27 10.61 46.65 2.17
1322 1334 0.035915 GAGGAAGAGACTTGGTGGCC 60.036 60.000 0.00 0.00 0.00 5.36
1338 1350 6.926630 ACTAAGGATGAGCTTAATAGGAGG 57.073 41.667 0.00 0.00 0.00 4.30
1354 1366 1.831736 GCTGCCCACTTCTACTAAGGA 59.168 52.381 0.00 0.00 0.00 3.36
1419 1431 2.259917 TCAACTGCTCCTCCAGAATGA 58.740 47.619 0.00 0.00 39.69 2.57
1523 1535 2.171237 TGCATAGTCATTCCAGGTCCAG 59.829 50.000 0.00 0.00 0.00 3.86
2197 2210 6.540914 GGATATGTCCGACCAAAGATTTTACA 59.459 38.462 0.00 0.00 34.13 2.41
2262 2275 4.270834 GAAAGAAGGTCAGATTAACCCCC 58.729 47.826 0.00 0.00 37.52 5.40
2346 2359 2.421107 GCTCAGAGAATTCCATCCAGCA 60.421 50.000 0.00 0.00 0.00 4.41
2359 2372 3.845781 AGAACCAAAACTGCTCAGAGA 57.154 42.857 0.00 0.00 0.00 3.10
2435 2448 6.223120 GCACATTTTTGGTTCTTTCCACTAT 58.777 36.000 0.00 0.00 37.20 2.12
2617 2631 7.454380 TCAAATGAAGAACTTATTTCCCCACAT 59.546 33.333 0.00 0.00 34.32 3.21
2743 2758 2.258109 GACTTAGGTTGGACCAGGACT 58.742 52.381 0.00 0.00 41.95 3.85
2859 2876 3.274823 TGGAGACACTTCCCCCTTT 57.725 52.632 0.00 0.00 36.35 3.11
2920 2938 1.347707 TCATATCGCATCCTTGGTCCC 59.652 52.381 0.00 0.00 0.00 4.46
2937 2955 1.025812 CTCCGACCTACGCTTCTCAT 58.974 55.000 0.00 0.00 41.07 2.90
2967 2985 1.000233 CATGCAACTGCTTGTCGCAC 61.000 55.000 8.92 0.00 45.47 5.34
3016 3034 1.087501 GCGAGGATTCCAAGTGTTCC 58.912 55.000 5.29 0.00 0.00 3.62
3106 3124 2.169978 TGCTAGCATCTCTGAACAGCAT 59.830 45.455 14.93 0.00 32.94 3.79
3110 3128 3.095332 ACTCTGCTAGCATCTCTGAACA 58.905 45.455 19.72 0.00 0.00 3.18
3125 3143 3.611766 TGGCTAACTTTCCTACTCTGC 57.388 47.619 0.00 0.00 0.00 4.26
3491 3510 2.460757 TACTTGTAAACCAGACCGCC 57.539 50.000 0.00 0.00 0.00 6.13
3540 3559 4.056050 GAGTGGAACGAAGAGCTAAAACA 58.944 43.478 0.00 0.00 45.86 2.83


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

AutoCloner maintained by Alex Coulton.