Multiple sequence alignment - TraesCS1D01G210700

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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 TraesCS1D01G210700 chr1D 100.000 3430 0 0 1 3430 296768536 296771965 0.000000e+00 6335
1 TraesCS1D01G210700 chr1D 96.333 3436 117 7 1 3430 88013088 88009656 0.000000e+00 5638
2 TraesCS1D01G210700 chr5D 96.309 3441 111 14 1 3430 108670111 108666676 0.000000e+00 5637
3 TraesCS1D01G210700 chr7D 95.963 3443 123 14 1 3430 243734966 243731527 0.000000e+00 5574
4 TraesCS1D01G210700 chr3D 95.867 3436 129 10 1 3430 353281227 353284655 0.000000e+00 5546
5 TraesCS1D01G210700 chr2D 95.839 3437 133 8 1 3430 259247794 259244361 0.000000e+00 5546
6 TraesCS1D01G210700 chr4D 95.758 3442 129 14 1 3430 426270113 426266677 0.000000e+00 5531
7 TraesCS1D01G210700 chr1A 93.642 3240 183 19 206 3430 277154040 277150809 0.000000e+00 4820
8 TraesCS1D01G210700 chr1A 93.366 3241 190 20 206 3427 366070931 366074165 0.000000e+00 4771
9 TraesCS1D01G210700 chr2A 93.225 3247 192 22 206 3430 367432668 367429428 0.000000e+00 4752
10 TraesCS1D01G210700 chr7A 81.081 2664 336 87 23 2579 384857073 384854471 0.000000e+00 1973
11 TraesCS1D01G210700 chr7A 95.652 138 4 2 7 142 426102399 426102262 1.600000e-53 220
12 TraesCS1D01G210700 chr5A 82.831 664 58 22 23 640 499011079 499011732 8.370000e-151 544
13 TraesCS1D01G210700 chr5A 83.094 278 22 14 24 278 686267858 686267583 2.660000e-56 230
14 TraesCS1D01G210700 chr5A 95.035 141 5 2 4 142 368433205 368433065 1.600000e-53 220
15 TraesCS1D01G210700 chr3A 95.105 143 6 1 1 142 240525609 240525467 1.240000e-54 224
16 TraesCS1D01G210700 chr3A 94.444 144 6 2 1 142 521367782 521367925 1.600000e-53 220


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 TraesCS1D01G210700 chr1D 296768536 296771965 3429 False 6335 6335 100.000 1 3430 1 chr1D.!!$F1 3429
1 TraesCS1D01G210700 chr1D 88009656 88013088 3432 True 5638 5638 96.333 1 3430 1 chr1D.!!$R1 3429
2 TraesCS1D01G210700 chr5D 108666676 108670111 3435 True 5637 5637 96.309 1 3430 1 chr5D.!!$R1 3429
3 TraesCS1D01G210700 chr7D 243731527 243734966 3439 True 5574 5574 95.963 1 3430 1 chr7D.!!$R1 3429
4 TraesCS1D01G210700 chr3D 353281227 353284655 3428 False 5546 5546 95.867 1 3430 1 chr3D.!!$F1 3429
5 TraesCS1D01G210700 chr2D 259244361 259247794 3433 True 5546 5546 95.839 1 3430 1 chr2D.!!$R1 3429
6 TraesCS1D01G210700 chr4D 426266677 426270113 3436 True 5531 5531 95.758 1 3430 1 chr4D.!!$R1 3429
7 TraesCS1D01G210700 chr1A 277150809 277154040 3231 True 4820 4820 93.642 206 3430 1 chr1A.!!$R1 3224
8 TraesCS1D01G210700 chr1A 366070931 366074165 3234 False 4771 4771 93.366 206 3427 1 chr1A.!!$F1 3221
9 TraesCS1D01G210700 chr2A 367429428 367432668 3240 True 4752 4752 93.225 206 3430 1 chr2A.!!$R1 3224
10 TraesCS1D01G210700 chr7A 384854471 384857073 2602 True 1973 1973 81.081 23 2579 1 chr7A.!!$R1 2556
11 TraesCS1D01G210700 chr5A 499011079 499011732 653 False 544 544 82.831 23 640 1 chr5A.!!$F1 617

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
881 964 2.667318 CCGTCGACGCACTGCAAAT 61.667 57.895 31.73 0.0 38.18 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2457 2579 0.668535 GCACAAGCGGAAGGAAAACT 59.331 50.0 0.0 0.0 0.0 2.66 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
608 673 4.991687 GGGATAAGCAGCTGATAAGTACAC 59.008 45.833 20.43 0.00 0.00 2.90
720 788 2.959030 TGACAAGACTAGTCAGTGCAGT 59.041 45.455 24.44 12.42 40.80 4.40
728 796 6.915349 AGACTAGTCAGTGCAGTAGTAAAAG 58.085 40.000 24.44 0.00 33.40 2.27
752 832 5.472137 GCCATTTGACTTGGACAGTTACTTA 59.528 40.000 0.00 0.00 35.01 2.24
792 872 4.335647 CCCACTGAGCGGTTGCCT 62.336 66.667 0.00 0.00 44.31 4.75
837 919 3.319198 CCACTACACCCACGCCCT 61.319 66.667 0.00 0.00 0.00 5.19
881 964 2.667318 CCGTCGACGCACTGCAAAT 61.667 57.895 31.73 0.00 38.18 2.32
1060 1144 0.880278 GTCGGACAAGAGCAGCAACA 60.880 55.000 2.62 0.00 0.00 3.33
1170 1254 1.376424 CTGCACCAGCGAACCAGAT 60.376 57.895 0.00 0.00 46.23 2.90
1224 1308 2.180017 CTTGGTGGCATGCTTCGC 59.820 61.111 18.92 8.34 0.00 4.70
1309 1393 2.050351 AGTTGTGCGTCGACGAGG 60.050 61.111 39.74 13.47 43.02 4.63
1313 1397 1.229975 TTGTGCGTCGACGAGGTCTA 61.230 55.000 39.74 19.03 43.02 2.59
1569 1684 6.878923 TCTTGCGGAAGATTAATTTCTGAAGA 59.121 34.615 16.06 16.70 32.98 2.87
1590 1705 7.120726 TGAAGATGATCGACTAGTGTAGTTTCA 59.879 37.037 0.00 0.00 39.59 2.69
1603 1718 6.226787 AGTGTAGTTTCAGAACTTGATCCAG 58.773 40.000 0.00 0.00 43.48 3.86
1606 1721 7.819900 GTGTAGTTTCAGAACTTGATCCAGTAT 59.180 37.037 0.00 0.00 43.48 2.12
2414 2536 1.405121 GCGAAATTCTACGACCACCCT 60.405 52.381 0.00 0.00 0.00 4.34
2457 2579 5.602561 TGAAGATACATTAGAGCCTGCCTTA 59.397 40.000 0.00 0.00 0.00 2.69
2491 2613 3.922850 GCTTGTGCTTGCCTTTTATCTTC 59.077 43.478 0.00 0.00 36.03 2.87
2741 2864 4.034626 CACACAACGTTGTTCCATGTCTAA 59.965 41.667 30.49 0.00 39.91 2.10
2749 2872 6.183360 ACGTTGTTCCATGTCTAATTTCGATC 60.183 38.462 0.00 0.00 0.00 3.69
2810 2933 6.035866 CAGCACAATTTGAGTTGCTTAACAAA 59.964 34.615 9.54 0.00 40.82 2.83
2869 2992 9.671279 TTCATGTAGTGTTCTCATTCATATGTT 57.329 29.630 1.90 0.00 33.34 2.71
2926 3055 5.972107 AAAGTTAAGAAGCATCAGCACAT 57.028 34.783 0.00 0.00 45.49 3.21
2949 3078 1.725641 TATGTTGGTCGCTTGCAGAG 58.274 50.000 0.00 0.00 0.00 3.35
3004 3133 9.661187 CGGACAGTACATACTTACTACAATAAG 57.339 37.037 0.00 0.00 38.03 1.73
3238 3373 3.376540 GCTGCTAGATACTTGAACTCGG 58.623 50.000 0.00 0.00 0.00 4.63
3264 3399 4.712337 CCATAGGCGAATCCCTAGTAATCT 59.288 45.833 0.00 0.00 40.62 2.40
3297 3432 4.838152 CACCGATCAGGGCCCACG 62.838 72.222 27.56 22.17 46.96 4.94
3312 3451 1.257743 CCACGGGTCAAGAGAGAGAA 58.742 55.000 0.00 0.00 0.00 2.87
3410 3549 2.279408 GGAGCCCCCTCGACTAGT 59.721 66.667 0.00 0.00 39.06 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
287 326 1.078567 GGGACTGGCAGAAGCAGAG 60.079 63.158 23.66 0.00 44.61 3.35
608 673 2.158449 GCACTGATTCGTCTTGTCAAGG 59.842 50.000 12.66 0.00 0.00 3.61
720 788 6.065374 TGTCCAAGTCAAATGGCTTTTACTA 58.935 36.000 0.00 0.00 38.00 1.82
728 796 3.821033 AGTAACTGTCCAAGTCAAATGGC 59.179 43.478 0.00 0.00 38.56 4.40
752 832 4.047125 CGGGTGGTGGCCTGGAAT 62.047 66.667 3.32 0.00 0.00 3.01
792 872 1.896660 GCCGTTTGCAGTCCCTTGA 60.897 57.895 0.00 0.00 40.77 3.02
850 932 2.044352 GACGGGGATTTGTGGGGG 60.044 66.667 0.00 0.00 0.00 5.40
851 933 2.437716 CGACGGGGATTTGTGGGG 60.438 66.667 0.00 0.00 0.00 4.96
881 964 4.635473 AGAGATGGAAGAGAATGGGGTTA 58.365 43.478 0.00 0.00 0.00 2.85
1097 1181 2.646121 CCTCTGAGGGTTTTGGTGC 58.354 57.895 16.19 0.00 0.00 5.01
1170 1254 0.395311 AGATCACCTCGTCGGCCTTA 60.395 55.000 0.00 0.00 35.61 2.69
1224 1308 2.885644 CCAACGCCGACGATCCTG 60.886 66.667 0.00 0.00 43.93 3.86
1524 1639 7.973388 CGCAAGATTTTCCAAATAGTAATCCAA 59.027 33.333 0.00 0.00 43.02 3.53
1569 1684 7.121463 AGTTCTGAAACTACACTAGTCGATCAT 59.879 37.037 0.00 0.00 43.98 2.45
1714 1832 4.277423 ACACATAACCAGTGCTTTACCAAC 59.723 41.667 0.00 0.00 40.59 3.77
1777 1895 8.902540 AGTTTCAGTCAATGTTGTATGTTCTA 57.097 30.769 0.00 0.00 0.00 2.10
2016 2138 1.082496 GCTGCAGCAACTCGTTCAC 60.082 57.895 33.36 0.00 41.59 3.18
2114 2236 4.648762 TGAATGTTGATGAACTTGTTGGGT 59.351 37.500 0.00 0.00 32.79 4.51
2207 2329 3.010027 TCATGCCTTTGTAGAATGGGTGA 59.990 43.478 6.66 0.00 0.00 4.02
2457 2579 0.668535 GCACAAGCGGAAGGAAAACT 59.331 50.000 0.00 0.00 0.00 2.66
2515 2637 4.537751 TCATACTGGTTCAACCCAACAAA 58.462 39.130 3.42 0.00 37.50 2.83
2655 2777 6.809630 AGTTCCATTCAGAAGCTACTTTTC 57.190 37.500 0.00 0.00 0.00 2.29
2869 2992 7.979444 AGTACTTGTTAATTTTCTAGCAGCA 57.021 32.000 0.00 0.00 0.00 4.41
2926 3055 3.000041 CTGCAAGCGACCAACATAAGTA 59.000 45.455 0.00 0.00 0.00 2.24
2949 3078 9.557338 CAAGTGTACTAGTACTGTCATTCTTAC 57.443 37.037 28.56 16.45 37.00 2.34
3004 3133 4.979197 CGGACTGATGCTTCTATGTACTTC 59.021 45.833 0.88 0.00 0.00 3.01
3297 3432 1.135228 GCTCGTTCTCTCTCTTGACCC 60.135 57.143 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.