Multiple sequence alignment - TraesCS7B01G346400

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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 TraesCS7B01G346400 chr7B 100.000 2549 0 0 1 2549 602141869 602144417 0.000000e+00 4708
1 TraesCS7B01G346400 chr7B 95.329 1991 86 7 562 2549 720989197 720987211 0.000000e+00 3155
2 TraesCS7B01G346400 chr7B 95.118 1987 86 9 569 2549 677862790 677860809 0.000000e+00 3121
3 TraesCS7B01G346400 chr4A 96.016 1983 72 6 569 2549 705529252 705527275 0.000000e+00 3217
4 TraesCS7B01G346400 chr2B 95.867 1984 74 7 568 2549 458657422 458659399 0.000000e+00 3203
5 TraesCS7B01G346400 chr2B 95.221 1988 86 8 568 2549 492636664 492638648 0.000000e+00 3136
6 TraesCS7B01G346400 chr1B 95.720 1986 79 5 568 2549 581717562 581715579 0.000000e+00 3192
7 TraesCS7B01G346400 chr1B 95.310 1983 84 7 569 2549 520844119 520842144 0.000000e+00 3138
8 TraesCS7B01G346400 chr1B 95.782 569 21 3 1 568 392608303 392607737 0.000000e+00 915
9 TraesCS7B01G346400 chr1B 95.088 570 26 2 1 568 673337046 673336477 0.000000e+00 896
10 TraesCS7B01G346400 chr3B 95.411 1983 89 2 568 2549 108092313 108090332 0.000000e+00 3157
11 TraesCS7B01G346400 chr5B 95.262 1984 87 5 569 2549 497276165 497278144 0.000000e+00 3136
12 TraesCS7B01G346400 chr1D 95.034 584 12 7 1 568 382055850 382056432 0.000000e+00 902
13 TraesCS7B01G346400 chr1D 97.835 508 10 1 1 508 458520649 458521155 0.000000e+00 876
14 TraesCS7B01G346400 chr1D 97.638 508 11 1 1 508 268331945 268331439 0.000000e+00 870
15 TraesCS7B01G346400 chr3D 98.031 508 9 1 1 508 614161104 614160598 0.000000e+00 881
16 TraesCS7B01G346400 chr6D 97.642 509 11 1 1 508 434291646 434292154 0.000000e+00 872
17 TraesCS7B01G346400 chr4B 93.241 577 29 6 1 568 453720333 453720908 0.000000e+00 841
18 TraesCS7B01G346400 chr4B 92.894 577 31 6 1 568 596263220 596263795 0.000000e+00 830
19 TraesCS7B01G346400 chr4D 93.151 73 3 2 497 568 127482103 127482032 3.470000e-19 106
20 TraesCS7B01G346400 chr4D 93.151 73 3 2 497 568 130996496 130996567 3.470000e-19 106
21 TraesCS7B01G346400 chr4D 93.151 73 3 2 497 568 139250609 139250680 3.470000e-19 106
22 TraesCS7B01G346400 chr4D 93.151 73 3 2 497 568 146229814 146229885 3.470000e-19 106
23 TraesCS7B01G346400 chr4D 93.151 73 3 2 497 568 174069372 174069443 3.470000e-19 106


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 TraesCS7B01G346400 chr7B 602141869 602144417 2548 False 4708 4708 100.000 1 2549 1 chr7B.!!$F1 2548
1 TraesCS7B01G346400 chr7B 720987211 720989197 1986 True 3155 3155 95.329 562 2549 1 chr7B.!!$R2 1987
2 TraesCS7B01G346400 chr7B 677860809 677862790 1981 True 3121 3121 95.118 569 2549 1 chr7B.!!$R1 1980
3 TraesCS7B01G346400 chr4A 705527275 705529252 1977 True 3217 3217 96.016 569 2549 1 chr4A.!!$R1 1980
4 TraesCS7B01G346400 chr2B 458657422 458659399 1977 False 3203 3203 95.867 568 2549 1 chr2B.!!$F1 1981
5 TraesCS7B01G346400 chr2B 492636664 492638648 1984 False 3136 3136 95.221 568 2549 1 chr2B.!!$F2 1981
6 TraesCS7B01G346400 chr1B 581715579 581717562 1983 True 3192 3192 95.720 568 2549 1 chr1B.!!$R3 1981
7 TraesCS7B01G346400 chr1B 520842144 520844119 1975 True 3138 3138 95.310 569 2549 1 chr1B.!!$R2 1980
8 TraesCS7B01G346400 chr1B 392607737 392608303 566 True 915 915 95.782 1 568 1 chr1B.!!$R1 567
9 TraesCS7B01G346400 chr1B 673336477 673337046 569 True 896 896 95.088 1 568 1 chr1B.!!$R4 567
10 TraesCS7B01G346400 chr3B 108090332 108092313 1981 True 3157 3157 95.411 568 2549 1 chr3B.!!$R1 1981
11 TraesCS7B01G346400 chr5B 497276165 497278144 1979 False 3136 3136 95.262 569 2549 1 chr5B.!!$F1 1980
12 TraesCS7B01G346400 chr1D 382055850 382056432 582 False 902 902 95.034 1 568 1 chr1D.!!$F1 567
13 TraesCS7B01G346400 chr1D 458520649 458521155 506 False 876 876 97.835 1 508 1 chr1D.!!$F2 507
14 TraesCS7B01G346400 chr1D 268331439 268331945 506 True 870 870 97.638 1 508 1 chr1D.!!$R1 507
15 TraesCS7B01G346400 chr3D 614160598 614161104 506 True 881 881 98.031 1 508 1 chr3D.!!$R1 507
16 TraesCS7B01G346400 chr6D 434291646 434292154 508 False 872 872 97.642 1 508 1 chr6D.!!$F1 507
17 TraesCS7B01G346400 chr4B 453720333 453720908 575 False 841 841 93.241 1 568 1 chr4B.!!$F1 567
18 TraesCS7B01G346400 chr4B 596263220 596263795 575 False 830 830 92.894 1 568 1 chr4B.!!$F2 567

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
790 815 2.045926 GTGGCTTGCGAGACCCAT 60.046 61.111 3.72 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2392 2431 1.405821 CTAACCAAAACCACGTGGCAA 59.594 47.619 34.26 9.7 38.58 4.52 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
205 206 4.142513 TGCATGCTTTAACATTACGATGCA 60.143 37.500 20.33 0.00 41.87 3.96
242 244 7.787725 AGTAGAAAAACAACACTAGTCAAGG 57.212 36.000 0.00 0.00 0.00 3.61
519 544 3.947612 AGATTAGTACCTCCGTCCTGA 57.052 47.619 0.00 0.00 0.00 3.86
755 780 3.921257 GCAGAGGCAGCCAATTTTT 57.079 47.368 15.80 0.00 40.72 1.94
790 815 2.045926 GTGGCTTGCGAGACCCAT 60.046 61.111 3.72 0.00 0.00 4.00
982 1011 2.283529 ACGGTGGCGTTGAGATCCT 61.284 57.895 0.00 0.00 0.00 3.24
1071 1100 0.976641 TGGAGATGCCTGTCTTCGTT 59.023 50.000 0.00 0.00 37.63 3.85
1084 1113 4.595538 TCGTTTGTCCGCGGTGCT 62.596 61.111 27.15 0.00 0.00 4.40
1171 1200 2.771943 AGCGAGAATGGGGTAAGAATCA 59.228 45.455 0.00 0.00 0.00 2.57
1290 1319 4.440880 CTCTGGCCAAGACTCTGATAAAG 58.559 47.826 7.01 0.00 0.00 1.85
1296 1325 5.104900 GGCCAAGACTCTGATAAAGGAACTA 60.105 44.000 0.00 0.00 38.49 2.24
1488 1517 7.390162 CCAATACCCATTTGCAAATACTTTTGT 59.610 33.333 23.69 15.48 43.43 2.83
1857 1890 4.755629 CCAAAATGTCATGGAAAATGTGCA 59.244 37.500 0.00 0.00 39.12 4.57
1931 1965 8.506168 TTAAGGGCATTACATTGAGTAGAAAG 57.494 34.615 0.00 0.00 33.43 2.62
2050 2085 1.480954 CACTGGTAACCGCTAGGACAT 59.519 52.381 0.00 0.00 41.02 3.06
2113 2148 6.992123 ACATAGTGAGACTGTGAAATTTGTCA 59.008 34.615 7.40 0.00 39.34 3.58
2321 2360 3.525059 CGTGAATGTTTGCACACGT 57.475 47.368 14.91 4.56 46.75 4.49
2417 2456 3.199677 CACGTGGTTTTGGTTAGAGTGA 58.800 45.455 7.95 0.00 0.00 3.41
2494 2533 9.793252 AATTTGCATGTTAGTTCATGACTTATC 57.207 29.630 10.28 0.00 45.41 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
242 244 5.633996 TTTGCATTGAATCGTTTCACAAC 57.366 34.783 8.41 2.31 41.50 3.32
563 588 8.673456 AGGCAAAAGGATAATTAACCCTTAAA 57.327 30.769 17.67 0.00 39.21 1.52
783 808 0.616111 AACGGCTCTCTGATGGGTCT 60.616 55.000 0.00 0.00 0.00 3.85
790 815 1.406898 CTATGCTCAACGGCTCTCTGA 59.593 52.381 0.00 0.00 0.00 3.27
1045 1074 3.695606 AGGCATCTCCACACGCGT 61.696 61.111 5.58 5.58 37.29 6.01
1084 1113 1.211212 CCTCTGATCAATGCTCACCCA 59.789 52.381 0.00 0.00 0.00 4.51
1088 1117 3.265221 AGAAACCCTCTGATCAATGCTCA 59.735 43.478 0.00 0.00 31.12 4.26
1093 1122 4.042062 TGTGTGAGAAACCCTCTGATCAAT 59.958 41.667 0.00 0.00 42.44 2.57
1100 1129 0.393077 CGGTGTGTGAGAAACCCTCT 59.607 55.000 0.00 0.00 42.44 3.69
1171 1200 1.338011 CGAAAATGGTGCAATTGCCCT 60.338 47.619 26.94 11.63 41.18 5.19
1290 1319 5.423015 TCATCATGCTCTTCTTGTAGTTCC 58.577 41.667 0.00 0.00 0.00 3.62
1296 1325 4.597004 ACCATTCATCATGCTCTTCTTGT 58.403 39.130 0.00 0.00 0.00 3.16
1488 1517 4.513692 GCGATTACCATACCTACAAATGCA 59.486 41.667 0.00 0.00 0.00 3.96
1668 1699 7.946776 TGAATTCCTCATTTCTTCTCCTTTTCT 59.053 33.333 2.27 0.00 0.00 2.52
1669 1700 8.115490 TGAATTCCTCATTTCTTCTCCTTTTC 57.885 34.615 2.27 0.00 0.00 2.29
1734 1767 9.528489 AATTCTAACCTTAATTGTTTGGCTCTA 57.472 29.630 0.00 0.00 0.00 2.43
1857 1890 5.395768 GGTGTAAACATCTACCAGAGCTGAT 60.396 44.000 0.00 0.00 33.42 2.90
2050 2085 3.245229 ACCCATGTCAAACTCTTGCCATA 60.245 43.478 0.00 0.00 29.52 2.74
2294 2333 2.226437 GCAAACATTCACGGTCTCACAT 59.774 45.455 0.00 0.00 0.00 3.21
2321 2360 3.963129 ACAAAGGAAAACCACTCTCACA 58.037 40.909 0.00 0.00 0.00 3.58
2381 2420 2.608998 CCACGTGGCAATGCAAACATAA 60.609 45.455 24.02 0.00 34.62 1.90
2392 2431 1.405821 CTAACCAAAACCACGTGGCAA 59.594 47.619 34.26 9.70 38.58 4.52


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

AutoCloner maintained by Alex Coulton.