Multiple sequence alignment - TraesCS7A01G100100

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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 TraesCS7A01G100100 chr7A 100.000 2509 0 0 1 2509 61541759 61539251 0 4634
1 TraesCS7A01G100100 chr7A 96.307 2491 89 3 21 2509 678409466 678406977 0 4087
2 TraesCS7A01G100100 chr3A 97.189 2490 68 2 21 2509 178144710 178142222 0 4209
3 TraesCS7A01G100100 chr3A 96.473 2495 82 6 21 2509 597895987 597893493 0 4115
4 TraesCS7A01G100100 chr3A 96.348 2492 86 5 21 2508 679680157 679682647 0 4093
5 TraesCS7A01G100100 chr3A 96.158 2499 86 7 21 2509 446308463 446310961 0 4074
6 TraesCS7A01G100100 chr5A 96.709 2492 79 2 21 2509 538783203 538780712 0 4145
7 TraesCS7A01G100100 chr5A 96.304 2489 84 8 28 2509 610715590 610718077 0 4080
8 TraesCS7A01G100100 chr2A 96.552 2494 76 7 21 2509 651452705 651455193 0 4120
9 TraesCS7A01G100100 chr2A 96.310 2493 84 8 21 2509 643207805 643210293 0 4087


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 TraesCS7A01G100100 chr7A 61539251 61541759 2508 True 4634 4634 100.000 1 2509 1 chr7A.!!$R1 2508
1 TraesCS7A01G100100 chr7A 678406977 678409466 2489 True 4087 4087 96.307 21 2509 1 chr7A.!!$R2 2488
2 TraesCS7A01G100100 chr3A 178142222 178144710 2488 True 4209 4209 97.189 21 2509 1 chr3A.!!$R1 2488
3 TraesCS7A01G100100 chr3A 597893493 597895987 2494 True 4115 4115 96.473 21 2509 1 chr3A.!!$R2 2488
4 TraesCS7A01G100100 chr3A 679680157 679682647 2490 False 4093 4093 96.348 21 2508 1 chr3A.!!$F2 2487
5 TraesCS7A01G100100 chr3A 446308463 446310961 2498 False 4074 4074 96.158 21 2509 1 chr3A.!!$F1 2488
6 TraesCS7A01G100100 chr5A 538780712 538783203 2491 True 4145 4145 96.709 21 2509 1 chr5A.!!$R1 2488
7 TraesCS7A01G100100 chr5A 610715590 610718077 2487 False 4080 4080 96.304 28 2509 1 chr5A.!!$F1 2481
8 TraesCS7A01G100100 chr2A 651452705 651455193 2488 False 4120 4120 96.552 21 2509 1 chr2A.!!$F2 2488
9 TraesCS7A01G100100 chr2A 643207805 643210293 2488 False 4087 4087 96.310 21 2509 1 chr2A.!!$F1 2488

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
796 808 0.462937 AACAACTGCCGTGCACACTA 60.463 50.0 18.64 0.42 33.79 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1843 1860 0.108329 ACCGGTGCTAGAAACGATGG 60.108 55.0 10.62 0.0 0.0 3.51 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
130 131 0.838987 GGTAGTTCACCCACCTCCCA 60.839 60.000 0.00 0.00 42.07 4.37
169 170 3.685550 CGAATTCAGGGCCACTAAGGAAT 60.686 47.826 6.18 2.58 41.22 3.01
444 454 2.489329 CCAAAGTCATTCAATGCGGAGT 59.511 45.455 0.00 0.00 0.00 3.85
452 462 0.599060 TCAATGCGGAGTGACGTACA 59.401 50.000 1.96 0.00 35.98 2.90
501 511 2.959707 TGAGGCCAAACGGTAAAATGTT 59.040 40.909 5.01 0.00 0.00 2.71
581 591 5.611919 CCGACAAGATAATCATGCATTACG 58.388 41.667 0.00 0.00 29.24 3.18
670 680 2.549754 CGGTGAATTCAAGCTCACACTT 59.450 45.455 10.35 0.00 43.11 3.16
781 793 4.370049 CAGATGTTTTCATGTGGCAACAA 58.630 39.130 0.00 0.00 45.44 2.83
796 808 0.462937 AACAACTGCCGTGCACACTA 60.463 50.000 18.64 0.42 33.79 2.74
850 862 9.243105 ACTATGTGGCAACTTGATAGTAAAATT 57.757 29.630 1.73 0.00 33.79 1.82
929 942 5.622770 AACCAAACATTCTACGTGATTCC 57.377 39.130 0.00 0.00 0.00 3.01
1150 1165 0.464452 AGACCTTACTACGCATGCCC 59.536 55.000 13.15 0.00 0.00 5.36
1231 1246 2.103094 CAGATCAGGCATTTCCCGACTA 59.897 50.000 0.00 0.00 34.51 2.59
1270 1285 4.152759 CGAAGCAAGGGAACACGTAATTTA 59.847 41.667 0.00 0.00 0.00 1.40
1325 1340 3.642141 ACCCCTCTTTTGTTGTCACATT 58.358 40.909 0.00 0.00 31.06 2.71
1357 1372 6.821031 AGTCTATCTTTGTTACGTCTGTCT 57.179 37.500 0.00 0.00 0.00 3.41
1507 1522 5.188163 TCCGGAAAATCTACACATGGAACTA 59.812 40.000 0.00 0.00 0.00 2.24
1512 1527 7.148239 GGAAAATCTACACATGGAACTAGTTGG 60.148 40.741 14.14 2.37 0.00 3.77
1709 1725 3.934579 TGTGTGCTATGTTATGACTGCAG 59.065 43.478 13.48 13.48 31.76 4.41
1740 1757 2.483188 GCCTACTATGTAGTGGTGGTGC 60.483 54.545 3.00 0.00 37.10 5.01
1763 1780 6.991485 CGTGAGCAACATTTGAATAGTTTT 57.009 33.333 0.00 0.00 0.00 2.43
1796 1813 7.966246 ATGTGTGTACGTGAACCTATTTTAA 57.034 32.000 0.00 0.00 0.00 1.52
1956 1973 6.413526 TGAAAGTCATCGTCGTTTTTCATTTG 59.586 34.615 0.00 0.00 31.72 2.32
2117 2136 0.669619 TGTGTCTCTAAACCGCGTCA 59.330 50.000 4.92 0.00 0.00 4.35
2199 2218 4.428294 ACAGCTAACATGGCAGATACAT 57.572 40.909 0.00 0.00 0.00 2.29
2243 2262 7.003482 TCCAGCATAATTAACATGGCAGATAA 58.997 34.615 0.00 0.00 0.00 1.75
2260 2279 6.821665 GGCAGATAAAGTACAACTAACATGGA 59.178 38.462 0.00 0.00 0.00 3.41
2461 2481 4.804868 AACATGGCAACTGCATTTATCA 57.195 36.364 3.76 0.00 44.36 2.15
2462 2482 5.347620 AACATGGCAACTGCATTTATCAT 57.652 34.783 3.76 0.00 44.36 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.805807 GCCACTACACCACAACACTACAT 60.806 47.826 0.00 0.00 0.00 2.29
1 2 2.484065 GCCACTACACCACAACACTACA 60.484 50.000 0.00 0.00 0.00 2.74
2 3 2.140717 GCCACTACACCACAACACTAC 58.859 52.381 0.00 0.00 0.00 2.73
3 4 1.763545 TGCCACTACACCACAACACTA 59.236 47.619 0.00 0.00 0.00 2.74
4 5 0.544223 TGCCACTACACCACAACACT 59.456 50.000 0.00 0.00 0.00 3.55
5 6 1.333619 CTTGCCACTACACCACAACAC 59.666 52.381 0.00 0.00 0.00 3.32
6 7 1.674359 CTTGCCACTACACCACAACA 58.326 50.000 0.00 0.00 0.00 3.33
7 8 0.951558 CCTTGCCACTACACCACAAC 59.048 55.000 0.00 0.00 0.00 3.32
8 9 0.179004 CCCTTGCCACTACACCACAA 60.179 55.000 0.00 0.00 0.00 3.33
9 10 1.454104 CCCTTGCCACTACACCACA 59.546 57.895 0.00 0.00 0.00 4.17
10 11 1.971695 GCCCTTGCCACTACACCAC 60.972 63.158 0.00 0.00 0.00 4.16
11 12 2.000825 TTGCCCTTGCCACTACACCA 62.001 55.000 0.00 0.00 36.33 4.17
12 13 0.611896 ATTGCCCTTGCCACTACACC 60.612 55.000 0.00 0.00 36.33 4.16
13 14 0.811281 GATTGCCCTTGCCACTACAC 59.189 55.000 0.00 0.00 36.33 2.90
14 15 0.403655 TGATTGCCCTTGCCACTACA 59.596 50.000 0.00 0.00 36.33 2.74
15 16 1.474077 CTTGATTGCCCTTGCCACTAC 59.526 52.381 0.00 0.00 36.33 2.73
16 17 1.075374 ACTTGATTGCCCTTGCCACTA 59.925 47.619 0.00 0.00 36.33 2.74
17 18 0.178953 ACTTGATTGCCCTTGCCACT 60.179 50.000 0.00 0.00 36.33 4.00
18 19 0.681175 AACTTGATTGCCCTTGCCAC 59.319 50.000 0.00 0.00 36.33 5.01
19 20 0.968405 GAACTTGATTGCCCTTGCCA 59.032 50.000 0.00 0.00 36.33 4.92
130 131 2.404995 CGGGCTCGTAGTCTTCCGT 61.405 63.158 0.00 0.00 33.63 4.69
169 170 3.072211 CGATATCGTACAGCTGGGTCTA 58.928 50.000 19.93 3.30 34.11 2.59
444 454 0.963856 ACCCAGCTCGATGTACGTCA 60.964 55.000 15.24 2.08 43.13 4.35
452 462 0.179062 GCAAGATCACCCAGCTCGAT 60.179 55.000 0.00 0.00 0.00 3.59
501 511 1.393196 CGCATGCAACTACATTCGTCA 59.607 47.619 19.57 0.00 33.00 4.35
554 564 2.874701 GCATGATTATCTTGTCGGCACT 59.125 45.455 0.00 0.00 0.00 4.40
581 591 2.166254 CCCATATTTTGCAGGTCACACC 59.834 50.000 0.00 0.00 38.99 4.16
670 680 7.844779 AGGGAAGGAGTACTCACATATTTCTTA 59.155 37.037 23.91 0.00 0.00 2.10
781 793 0.179056 AAGTTAGTGTGCACGGCAGT 60.179 50.000 13.13 0.00 40.08 4.40
796 808 4.039124 ACGGGATGCAAAAATCAAGAAGTT 59.961 37.500 0.00 0.00 0.00 2.66
850 862 3.565902 TGTATGAACAAAATGTGCCGTGA 59.434 39.130 0.00 0.00 30.91 4.35
1150 1165 9.403110 CTCTTTGAGGTTGTTAATGAAGAATTG 57.597 33.333 0.00 0.00 0.00 2.32
1231 1246 0.037697 TTCGCAGTCGCCACATACTT 60.038 50.000 0.00 0.00 35.26 2.24
1270 1285 2.905415 TGGCACATGAAGGAAGGAAT 57.095 45.000 0.00 0.00 0.00 3.01
1325 1340 9.268268 ACGTAACAAAGATAGACTTCAATTCAA 57.732 29.630 0.00 0.00 37.93 2.69
1365 1380 4.646572 GAGGAAAAGAGTCAGGTGAACAT 58.353 43.478 0.00 0.00 0.00 2.71
1396 1411 2.617274 GCGTGAAAGCCACAGTCCC 61.617 63.158 0.00 0.00 45.98 4.46
1507 1522 4.278170 TGTTGAAATCTTCATTCGCCAACT 59.722 37.500 0.00 0.00 39.84 3.16
1512 1527 3.299020 CGCTTGTTGAAATCTTCATTCGC 59.701 43.478 0.00 0.00 39.84 4.70
1709 1725 2.273912 ATAGTAGGCTACGCGGGGC 61.274 63.158 18.41 15.46 0.00 5.80
1740 1757 6.991485 AAAACTATTCAAATGTTGCTCACG 57.009 33.333 0.00 0.00 0.00 4.35
1763 1780 8.252417 AGGTTCACGTACACACATATATTACAA 58.748 33.333 0.00 0.00 0.00 2.41
1779 1796 6.865726 TGTAACGCTTAAAATAGGTTCACGTA 59.134 34.615 0.00 0.00 0.00 3.57
1796 1813 5.880054 AAAAACATATCTGCTGTAACGCT 57.120 34.783 0.00 0.00 0.00 5.07
1843 1860 0.108329 ACCGGTGCTAGAAACGATGG 60.108 55.000 10.62 0.00 0.00 3.51
1956 1973 3.459232 AAAGAAGAAGCAAAACAGCCC 57.541 42.857 0.00 0.00 34.23 5.19
2243 2262 7.016153 TGGATCTTCCATGTTAGTTGTACTT 57.984 36.000 0.00 0.00 42.67 2.24
2260 2279 6.245408 TGCCATTTTAGTTGTACTGGATCTT 58.755 36.000 0.00 0.00 0.00 2.40
2461 2481 8.654094 AGAAGTGGAAGGAAAATTCATTGAAAT 58.346 29.630 2.68 0.00 30.50 2.17
2462 2482 7.927629 CAGAAGTGGAAGGAAAATTCATTGAAA 59.072 33.333 2.68 0.00 30.50 2.69


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

AutoCloner maintained by Alex Coulton.