Multiple sequence alignment - TraesCS7B01G031700

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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 TraesCS7B01G031700 chr7B 100.000 6786 0 0 1 6786 32051445 32044660 0.000000e+00 12532.0
1 TraesCS7B01G031700 chr7B 85.900 461 53 3 4695 5143 32046295 32045835 1.320000e-131 481.0
2 TraesCS7B01G031700 chr7B 85.900 461 53 3 5151 5611 32046751 32046303 1.320000e-131 481.0
3 TraesCS7B01G031700 chr7B 100.000 30 0 0 6264 6293 387010323 387010294 1.000000e-03 56.5
4 TraesCS7B01G031700 chr2A 99.345 5805 22 5 1 5805 337663833 337669621 0.000000e+00 10495.0
5 TraesCS7B01G031700 chr2A 99.310 725 5 0 5633 6357 337669621 337670345 0.000000e+00 1312.0
6 TraesCS7B01G031700 chr2A 98.586 495 7 0 6292 6786 337670335 337670829 0.000000e+00 876.0
7 TraesCS7B01G031700 chr2A 86.026 458 52 3 5151 5608 337668511 337668956 1.320000e-131 481.0
8 TraesCS7B01G031700 chr2A 86.026 458 52 3 4695 5140 337668967 337669424 1.320000e-131 481.0
9 TraesCS7B01G031700 chr3D 97.472 5379 105 14 886 6242 442362877 442368246 0.000000e+00 9151.0
10 TraesCS7B01G031700 chr3D 93.007 858 38 12 1 852 442361893 442362734 0.000000e+00 1232.0
11 TraesCS7B01G031700 chr3D 86.026 458 52 3 5151 5608 442366686 442367131 1.320000e-131 481.0
12 TraesCS7B01G031700 chr3D 85.839 459 51 6 4695 5140 442367142 442367599 6.160000e-130 475.0
13 TraesCS7B01G031700 chr3D 85.000 180 15 6 6397 6570 442368322 442368495 9.050000e-39 172.0
14 TraesCS7B01G031700 chr3D 78.571 168 18 6 6572 6731 442369235 442369392 2.010000e-15 95.3
15 TraesCS7B01G031700 chr3D 100.000 30 0 0 6264 6293 83323044 83323015 1.000000e-03 56.5
16 TraesCS7B01G031700 chr3D 100.000 29 0 0 6265 6293 30986708 30986680 3.000000e-03 54.7
17 TraesCS7B01G031700 chr3D 91.892 37 3 0 6257 6293 419893752 419893788 1.200000e-02 52.8
18 TraesCS7B01G031700 chr3B 95.600 2318 90 5 850 3163 579885726 579888035 0.000000e+00 3705.0
19 TraesCS7B01G031700 chr3B 95.935 1353 47 4 4901 6253 579889880 579891224 0.000000e+00 2187.0
20 TraesCS7B01G031700 chr3B 97.126 1183 34 0 3692 4874 579888698 579889880 0.000000e+00 1997.0
21 TraesCS7B01G031700 chr3B 88.889 864 54 15 1 852 579884862 579885695 0.000000e+00 1026.0
22 TraesCS7B01G031700 chr3B 86.681 458 49 3 4695 5140 579890130 579890587 1.310000e-136 497.0
23 TraesCS7B01G031700 chr3B 85.106 282 18 3 6505 6786 579892379 579892636 4.030000e-67 267.0
24 TraesCS7B01G031700 chr3B 92.222 180 14 0 5151 5330 579889701 579889880 8.730000e-64 255.0
25 TraesCS7B01G031700 chr3A 88.838 878 46 18 1 852 583694898 583695749 0.000000e+00 1031.0
26 TraesCS7B01G031700 chr4D 85.000 100 10 2 6304 6398 451291043 451291142 5.600000e-16 97.1
27 TraesCS7B01G031700 chr4D 83.333 102 10 3 6304 6398 254662767 254662868 3.370000e-13 87.9
28 TraesCS7B01G031700 chr4D 94.286 35 1 1 6261 6295 348280233 348280200 1.200000e-02 52.8
29 TraesCS7B01G031700 chr2D 86.667 90 7 2 6304 6388 98725615 98725704 2.010000e-15 95.3
30 TraesCS7B01G031700 chr7A 100.000 29 0 0 6370 6398 402505379 402505351 3.000000e-03 54.7
31 TraesCS7B01G031700 chr6A 100.000 29 0 0 6265 6293 72919305 72919277 3.000000e-03 54.7
32 TraesCS7B01G031700 chr6A 96.970 33 0 1 6370 6402 514325694 514325663 3.000000e-03 54.7
33 TraesCS7B01G031700 chr1B 94.286 35 2 0 6259 6293 640602766 640602800 3.000000e-03 54.7
34 TraesCS7B01G031700 chr2B 94.118 34 2 0 6266 6299 639499763 639499730 1.200000e-02 52.8


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 TraesCS7B01G031700 chr7B 32044660 32051445 6785 True 12532.000000 12532 100.000000 1 6786 1 chr7B.!!$R1 6785
1 TraesCS7B01G031700 chr7B 32045835 32046751 916 True 481.000000 481 85.900000 4695 5611 2 chr7B.!!$R3 916
2 TraesCS7B01G031700 chr2A 337663833 337670829 6996 False 2729.000000 10495 93.858600 1 6786 5 chr2A.!!$F1 6785
3 TraesCS7B01G031700 chr3D 442361893 442369392 7499 False 1934.383333 9151 87.652500 1 6731 6 chr3D.!!$F2 6730
4 TraesCS7B01G031700 chr3B 579884862 579892636 7774 False 1419.142857 3705 91.651286 1 6786 7 chr3B.!!$F1 6785
5 TraesCS7B01G031700 chr3A 583694898 583695749 851 False 1031.000000 1031 88.838000 1 852 1 chr3A.!!$F1 851

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
488 521 2.423892 TCGTGCTATGACTCACCTTCTC 59.576 50.000 0.00 0.0 0.0 2.87 F
489 522 2.425312 CGTGCTATGACTCACCTTCTCT 59.575 50.000 0.00 0.0 0.0 3.10 F
1549 1702 3.539593 TTCCGTGGAGAGGCTGGGA 62.540 63.158 0.00 0.0 0.0 4.37 F
1648 1801 3.557595 CGCTAGCTTATTTGAAGGTCTGG 59.442 47.826 13.93 0.0 0.0 3.86 F
2454 2607 5.207110 ACCTTCCATATGATTCTGACGAG 57.793 43.478 3.65 0.0 0.0 4.18 F
3897 4196 3.354948 TGATTCCATGTCCTGTCCAAG 57.645 47.619 0.00 0.0 0.0 3.61 F
4468 4767 0.392060 CCCGTACTTACAACCCTGCC 60.392 60.000 0.00 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1475 1628 2.124122 GTTTGTCGCCATGTTCAAACC 58.876 47.619 15.10 4.8 41.76 3.27 R
1648 1801 2.686915 CCAAGGGTGCATTCTTCTCATC 59.313 50.000 0.00 0.0 0.00 2.92 R
2454 2607 3.521796 GAGCCAGGAATTGCCGCC 61.522 66.667 0.00 0.0 43.43 6.13 R
3630 3824 3.459710 TCCCATCCACCCGTTAATTTT 57.540 42.857 0.00 0.0 0.00 1.82 R
4406 4705 2.526888 TCCAGTCTCACCGGTTCTAT 57.473 50.000 2.97 0.0 0.00 1.98 R
5627 5926 0.613012 ATGTTGCTTTCAGGCTCCCC 60.613 55.000 0.00 0.0 0.00 4.81 R
6352 6949 4.636206 AGTCTTTAGATTTCAATGCGGACC 59.364 41.667 0.00 0.0 0.00 4.46 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
478 511 4.403453 GTTTCCATTGTTCGTGCTATGAC 58.597 43.478 5.43 0.00 0.00 3.06
486 519 2.924290 GTTCGTGCTATGACTCACCTTC 59.076 50.000 0.00 0.00 0.00 3.46
487 520 2.447443 TCGTGCTATGACTCACCTTCT 58.553 47.619 0.00 0.00 0.00 2.85
488 521 2.423892 TCGTGCTATGACTCACCTTCTC 59.576 50.000 0.00 0.00 0.00 2.87
489 522 2.425312 CGTGCTATGACTCACCTTCTCT 59.575 50.000 0.00 0.00 0.00 3.10
490 523 3.628032 CGTGCTATGACTCACCTTCTCTA 59.372 47.826 0.00 0.00 0.00 2.43
491 524 4.260990 CGTGCTATGACTCACCTTCTCTAG 60.261 50.000 0.00 0.00 0.00 2.43
492 525 4.884744 GTGCTATGACTCACCTTCTCTAGA 59.115 45.833 0.00 0.00 0.00 2.43
734 772 6.014012 AGCTAGTTCTCCTATGGATCTAACC 58.986 44.000 0.00 0.00 0.00 2.85
1475 1628 7.549839 AGAAGAGTTGATGAAGAAGATGAGAG 58.450 38.462 0.00 0.00 0.00 3.20
1549 1702 3.539593 TTCCGTGGAGAGGCTGGGA 62.540 63.158 0.00 0.00 0.00 4.37
1648 1801 3.557595 CGCTAGCTTATTTGAAGGTCTGG 59.442 47.826 13.93 0.00 0.00 3.86
2454 2607 5.207110 ACCTTCCATATGATTCTGACGAG 57.793 43.478 3.65 0.00 0.00 4.18
3630 3824 7.504926 AGTCCACTAATAAAATAGGTCCACA 57.495 36.000 0.00 0.00 0.00 4.17
3897 4196 3.354948 TGATTCCATGTCCTGTCCAAG 57.645 47.619 0.00 0.00 0.00 3.61
3935 4234 3.769300 ACAAAACCTTATTCATGGGCCTC 59.231 43.478 4.53 0.00 0.00 4.70
3936 4235 3.756082 AAACCTTATTCATGGGCCTCA 57.244 42.857 4.53 0.00 0.00 3.86
4406 4705 2.678934 CGGTGGGAGACTTCCGGA 60.679 66.667 0.00 0.00 45.04 5.14
4468 4767 0.392060 CCCGTACTTACAACCCTGCC 60.392 60.000 0.00 0.00 0.00 4.85
5627 5926 0.313043 GCATTTGGCCGGAGATGATG 59.687 55.000 5.05 3.11 36.11 3.07
6275 6817 5.918608 TGCCTGTCAGATTTATACTCCTTC 58.081 41.667 0.00 0.00 0.00 3.46
6352 6949 9.616634 AAGTACGTTTATATACATCCGTATGTG 57.383 33.333 3.56 0.00 45.99 3.21
6359 6956 1.142965 CATCCGTATGTGGTCCGCA 59.857 57.895 7.77 7.77 0.00 5.69
6579 8896 0.865769 AAGATTTGTGCCACGTCGAC 59.134 50.000 5.18 5.18 0.00 4.20
6602 8919 0.175760 GGGTCGCTGATCTGTGCTAA 59.824 55.000 8.19 0.00 0.00 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
280 293 4.521062 CGAGGAAGCTCTGGCGGG 62.521 72.222 0.00 0.00 44.37 6.13
281 294 4.521062 CCGAGGAAGCTCTGGCGG 62.521 72.222 4.07 4.07 44.37 6.13
282 295 3.423162 CTCCGAGGAAGCTCTGGCG 62.423 68.421 0.00 0.00 44.37 5.69
283 296 2.498726 CTCCGAGGAAGCTCTGGC 59.501 66.667 0.00 0.00 39.06 4.85
478 511 5.047847 CGACTAGAGTCTAGAGAAGGTGAG 58.952 50.000 29.87 5.99 42.66 3.51
486 519 3.564053 AACCCCGACTAGAGTCTAGAG 57.436 52.381 29.87 21.81 42.66 2.43
487 520 4.685575 GCTAAACCCCGACTAGAGTCTAGA 60.686 50.000 29.87 6.70 42.66 2.43
488 521 3.565063 GCTAAACCCCGACTAGAGTCTAG 59.435 52.174 23.12 23.12 42.66 2.43
489 522 3.201708 AGCTAAACCCCGACTAGAGTCTA 59.798 47.826 8.01 0.00 42.66 2.59
490 523 2.025131 AGCTAAACCCCGACTAGAGTCT 60.025 50.000 8.01 0.00 42.66 3.24
491 524 2.377073 AGCTAAACCCCGACTAGAGTC 58.623 52.381 0.00 0.00 41.47 3.36
492 525 2.528673 AGCTAAACCCCGACTAGAGT 57.471 50.000 0.00 0.00 0.00 3.24
734 772 5.412640 TGCAATTGAGCCAAATACAAGATG 58.587 37.500 10.34 0.00 0.00 2.90
762 800 2.371841 TCAGTAGACCAACTGCACCAAT 59.628 45.455 0.00 0.00 45.34 3.16
1475 1628 2.124122 GTTTGTCGCCATGTTCAAACC 58.876 47.619 15.10 4.80 41.76 3.27
1549 1702 6.192773 GGTTAAAGTTTAAGCCCTCCCTAAT 58.807 40.000 21.63 0.00 0.00 1.73
1648 1801 2.686915 CCAAGGGTGCATTCTTCTCATC 59.313 50.000 0.00 0.00 0.00 2.92
2454 2607 3.521796 GAGCCAGGAATTGCCGCC 61.522 66.667 0.00 0.00 43.43 6.13
3630 3824 3.459710 TCCCATCCACCCGTTAATTTT 57.540 42.857 0.00 0.00 0.00 1.82
3897 4196 6.172630 AGGTTTTGTAATGGGATTTCATTGC 58.827 36.000 0.00 0.00 39.23 3.56
3935 4234 5.947228 TCAAAATCAGTTAGCAAGTCCTG 57.053 39.130 0.00 0.00 0.00 3.86
3936 4235 6.959639 TTTCAAAATCAGTTAGCAAGTCCT 57.040 33.333 0.00 0.00 0.00 3.85
4406 4705 2.526888 TCCAGTCTCACCGGTTCTAT 57.473 50.000 2.97 0.00 0.00 1.98
4468 4767 1.728971 GAGTCTTCTGCAACACCATCG 59.271 52.381 0.00 0.00 0.00 3.84
5627 5926 0.613012 ATGTTGCTTTCAGGCTCCCC 60.613 55.000 0.00 0.00 0.00 4.81
6275 6817 9.852091 GGACTACATACTTATATTTAGGAACGG 57.148 37.037 0.00 0.00 28.87 4.44
6352 6949 4.636206 AGTCTTTAGATTTCAATGCGGACC 59.364 41.667 0.00 0.00 0.00 4.46
6579 8896 0.738762 CACAGATCAGCGACCCACAG 60.739 60.000 0.00 0.00 0.00 3.66
6602 8919 9.448294 GATATACAGAAACGAGTTTACGAATCT 57.552 33.333 0.76 0.00 37.03 2.40


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

AutoCloner maintained by Alex Coulton.