Multiple sequence alignment - TraesCS7B01G051000

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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 TraesCS7B01G051000 chr7B 100.000 2447 0 0 1 2447 52952787 52950341 0 4519
1 TraesCS7B01G051000 chr7B 97.447 1606 41 0 842 2447 742965082 742966687 0 2739
2 TraesCS7B01G051000 chr6B 95.917 2449 86 6 1 2447 625538245 625535809 0 3956
3 TraesCS7B01G051000 chr1B 95.755 2450 98 6 1 2447 286076166 286078612 0 3943
4 TraesCS7B01G051000 chr1B 97.192 926 21 4 1 921 619179140 619178215 0 1561
5 TraesCS7B01G051000 chr6D 98.258 1607 27 1 842 2447 430466784 430465178 0 2811
6 TraesCS7B01G051000 chr3D 98.257 1606 28 0 842 2447 202625480 202623875 0 2811
7 TraesCS7B01G051000 chr5A 97.581 1612 39 0 836 2447 162145422 162143811 0 2761
8 TraesCS7B01G051000 chr5A 96.976 926 23 4 1 921 420172533 420173458 0 1550
9 TraesCS7B01G051000 chr3B 97.198 1606 45 0 842 2447 201583761 201582156 0 2717
10 TraesCS7B01G051000 chr1D 97.198 1606 45 0 842 2447 350977670 350979275 0 2717
11 TraesCS7B01G051000 chr4D 97.136 1606 45 1 842 2447 97361819 97363423 0 2710
12 TraesCS7B01G051000 chr5B 97.408 926 19 4 1 921 130584980 130584055 0 1572
13 TraesCS7B01G051000 chr3A 97.300 926 20 4 1 921 122210591 122209666 0 1567
14 TraesCS7B01G051000 chr3A 97.084 926 21 5 1 921 247671828 247672752 0 1555
15 TraesCS7B01G051000 chr2B 97.084 926 22 4 1 921 234506699 234505774 0 1555
16 TraesCS7B01G051000 chrUn 96.976 926 23 4 1 921 222870893 222871818 0 1550
17 TraesCS7B01G051000 chr7A 96.976 926 23 4 1 921 60196409 60195484 0 1550


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 TraesCS7B01G051000 chr7B 52950341 52952787 2446 True 4519 4519 100.000 1 2447 1 chr7B.!!$R1 2446
1 TraesCS7B01G051000 chr7B 742965082 742966687 1605 False 2739 2739 97.447 842 2447 1 chr7B.!!$F1 1605
2 TraesCS7B01G051000 chr6B 625535809 625538245 2436 True 3956 3956 95.917 1 2447 1 chr6B.!!$R1 2446
3 TraesCS7B01G051000 chr1B 286076166 286078612 2446 False 3943 3943 95.755 1 2447 1 chr1B.!!$F1 2446
4 TraesCS7B01G051000 chr1B 619178215 619179140 925 True 1561 1561 97.192 1 921 1 chr1B.!!$R1 920
5 TraesCS7B01G051000 chr6D 430465178 430466784 1606 True 2811 2811 98.258 842 2447 1 chr6D.!!$R1 1605
6 TraesCS7B01G051000 chr3D 202623875 202625480 1605 True 2811 2811 98.257 842 2447 1 chr3D.!!$R1 1605
7 TraesCS7B01G051000 chr5A 162143811 162145422 1611 True 2761 2761 97.581 836 2447 1 chr5A.!!$R1 1611
8 TraesCS7B01G051000 chr5A 420172533 420173458 925 False 1550 1550 96.976 1 921 1 chr5A.!!$F1 920
9 TraesCS7B01G051000 chr3B 201582156 201583761 1605 True 2717 2717 97.198 842 2447 1 chr3B.!!$R1 1605
10 TraesCS7B01G051000 chr1D 350977670 350979275 1605 False 2717 2717 97.198 842 2447 1 chr1D.!!$F1 1605
11 TraesCS7B01G051000 chr4D 97361819 97363423 1604 False 2710 2710 97.136 842 2447 1 chr4D.!!$F1 1605
12 TraesCS7B01G051000 chr5B 130584055 130584980 925 True 1572 1572 97.408 1 921 1 chr5B.!!$R1 920
13 TraesCS7B01G051000 chr3A 122209666 122210591 925 True 1567 1567 97.300 1 921 1 chr3A.!!$R1 920
14 TraesCS7B01G051000 chr3A 247671828 247672752 924 False 1555 1555 97.084 1 921 1 chr3A.!!$F1 920
15 TraesCS7B01G051000 chr2B 234505774 234506699 925 True 1555 1555 97.084 1 921 1 chr2B.!!$R1 920
16 TraesCS7B01G051000 chrUn 222870893 222871818 925 False 1550 1550 96.976 1 921 1 chrUn.!!$F1 920
17 TraesCS7B01G051000 chr7A 60195484 60196409 925 True 1550 1550 96.976 1 921 1 chr7A.!!$R1 920

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
680 682 0.892755 GGATGTGCCCGGTATCGATA 59.107 55.0 0.0 0.0 39.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2194 2201 0.175531 TGCTTGAATGATCGCTCCGA 59.824 50.0 0.0 0.0 41.13 4.55 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
102 103 5.509670 GGATTGCCTAGTTGCTTTTGAGTTT 60.510 40.000 0.00 0.00 0.00 2.66
240 241 2.456733 AGGGATAGATAGGGCTGGAGTT 59.543 50.000 0.00 0.00 0.00 3.01
294 296 8.229253 AGCATAATTGATTTTCTCACTGCATA 57.771 30.769 0.00 0.00 32.17 3.14
328 330 9.654919 AGTAACCGGTTAATAATACTAAGGGTA 57.345 33.333 28.11 0.00 34.62 3.69
388 390 7.392494 TCTCGGCCTTGATATATACTAACAG 57.608 40.000 0.00 0.00 0.00 3.16
455 457 1.343782 TGGAGACAGATGGAGGAGCAT 60.344 52.381 0.00 0.00 35.01 3.79
537 539 2.045926 GTGCCGGCCTGTGAGAAT 60.046 61.111 26.77 0.00 0.00 2.40
680 682 0.892755 GGATGTGCCCGGTATCGATA 59.107 55.000 0.00 0.00 39.00 2.92
702 704 3.126722 GAAACATCGGCTCGACGCG 62.127 63.158 3.53 3.53 39.18 6.01
775 778 1.523711 CGGCCAGCGGTATCATTGT 60.524 57.895 2.24 0.00 0.00 2.71
793 796 2.977718 TTGCTCCCCGCCTAATGCA 61.978 57.895 0.00 0.00 41.33 3.96
935 941 1.749063 AGATGGACAGTAACGATCGCA 59.251 47.619 16.60 2.33 0.00 5.10
957 963 6.037062 CGCATAATATCAATTTATCGGCCTCA 59.963 38.462 0.00 0.00 0.00 3.86
1076 1082 5.056480 TCGCATGATCGATGGTAAAAGAAT 58.944 37.500 0.54 0.00 33.02 2.40
1124 1130 0.108804 TTTCACCGCCTAGCTCGAAG 60.109 55.000 0.00 0.00 0.00 3.79
1156 1162 8.178964 GCGATGTAATAAAACTTATGGTTGACA 58.821 33.333 0.00 0.00 38.29 3.58
1285 1291 0.911769 TCGTTGGATCCTTGGAGCAT 59.088 50.000 14.23 0.00 0.00 3.79
1339 1345 7.928307 AGCTTAGAGAAATGTTCATTTGCTA 57.072 32.000 14.29 12.08 0.00 3.49
1668 1674 1.143073 ACTCTTGTTCCAACCTCACCC 59.857 52.381 0.00 0.00 0.00 4.61
1767 1773 1.241165 TCGTTTGACTCGTGGAGCTA 58.759 50.000 0.00 0.00 32.04 3.32
1941 1948 1.202521 GGTGTTGTGCTTTTTCCCCTG 60.203 52.381 0.00 0.00 0.00 4.45
2153 2160 2.369532 TCCTAACTAACGGTTGGCAAGT 59.630 45.455 0.00 0.00 38.75 3.16
2194 2201 0.616111 AAGATCAGACGGCCCAGAGT 60.616 55.000 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 6.959639 AAGCTTGGAAACTAGTTCAAATCA 57.040 33.333 8.95 0.90 38.06 2.57
240 241 5.550290 TCACATTTCATTCTAGCACTGACA 58.450 37.500 0.00 0.00 0.00 3.58
282 284 8.509690 GGTTACTATACGTATATGCAGTGAGAA 58.490 37.037 15.42 1.65 0.00 2.87
455 457 3.006430 TCACGCCACAATCTCTCACTTTA 59.994 43.478 0.00 0.00 0.00 1.85
537 539 2.158330 CGCAACGCTATGACGAGCA 61.158 57.895 0.00 0.00 42.99 4.26
680 682 1.393539 CGTCGAGCCGATGTTTCATTT 59.606 47.619 8.19 0.00 38.42 2.32
702 704 6.687105 CGATGTTTTCGTTCTATTGAAATCCC 59.313 38.462 0.00 0.00 43.01 3.85
793 796 5.358725 TCACATAAGCATTGCACAATGATCT 59.641 36.000 23.92 11.46 45.49 2.75
862 865 2.796557 AGGAGACTGATCTTGACGTCA 58.203 47.619 15.76 15.76 41.13 4.35
935 941 9.857656 ATGATGAGGCCGATAAATTGATATTAT 57.142 29.630 0.00 0.00 0.00 1.28
957 963 0.107703 TGGAAGCCGCTTTCGATGAT 60.108 50.000 7.16 0.00 38.10 2.45
1050 1056 5.527214 TCTTTTACCATCGATCATGCGAAAT 59.473 36.000 0.00 0.00 44.22 2.17
1076 1082 8.766000 TTTATAAACAATAGCACGAACTCTCA 57.234 30.769 0.00 0.00 0.00 3.27
1124 1130 9.169468 CCATAAGTTTTATTACATCGCATTCAC 57.831 33.333 0.00 0.00 0.00 3.18
1156 1162 9.326413 GCATATTGGCTTTATATTATCTACGGT 57.674 33.333 0.00 0.00 0.00 4.83
1285 1291 6.380995 TGTAGCTTATACGTCGTTTGAAAGA 58.619 36.000 1.78 0.00 0.00 2.52
1339 1345 6.591935 TCTTTCGGTAAGCATCCAATATCTT 58.408 36.000 0.00 0.00 33.66 2.40
1345 1351 2.355716 CCCTCTTTCGGTAAGCATCCAA 60.356 50.000 0.00 0.00 33.66 3.53
1668 1674 3.555956 CCTTTCGTATTCATTCGACCTGG 59.444 47.826 0.00 0.00 35.82 4.45
1694 1700 8.761497 CATTCATGGCTTATTGATTTGATTGAC 58.239 33.333 0.00 0.00 0.00 3.18
1767 1773 7.560796 TCCCTCTCTTTGAAGTAGATTTCTT 57.439 36.000 0.00 0.00 0.00 2.52
1941 1948 1.411612 ACTAGTACCAATAGGCGGCAC 59.588 52.381 13.08 0.00 39.06 5.01
2001 2008 7.770897 AGATTTGAGTATTGAGCGAAAGGTTAT 59.229 33.333 0.00 0.00 45.11 1.89
2153 2160 1.988107 GGGATGCAGAATAGGGGATCA 59.012 52.381 0.00 0.00 34.00 2.92
2194 2201 0.175531 TGCTTGAATGATCGCTCCGA 59.824 50.000 0.00 0.00 41.13 4.55


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

AutoCloner maintained by Alex Coulton.