Multiple sequence alignment - TraesCS7B01G422300

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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 TraesCS7B01G422300 chr7B 100.000 2590 0 0 1 2590 691926897 691929486 0.000000e+00 4783.0
1 TraesCS7B01G422300 chr7B 96.203 2607 73 5 1 2590 691965027 691967624 0.000000e+00 4242.0
2 TraesCS7B01G422300 chr7B 95.847 2071 69 2 445 2498 691998994 692001064 0.000000e+00 3332.0
3 TraesCS7B01G422300 chr7B 92.424 594 12 6 1 576 691998128 691998706 0.000000e+00 817.0
4 TraesCS7B01G422300 chr7B 100.000 291 0 0 2817 3107 691929713 691930003 3.530000e-149 538.0
5 TraesCS7B01G422300 chr7B 95.189 291 9 2 234 524 691998935 691999220 3.650000e-124 455.0
6 TraesCS7B01G422300 chr7B 95.357 280 12 1 2829 3107 692001369 692001648 7.910000e-121 444.0
7 TraesCS7B01G422300 chr7B 96.887 257 8 0 2851 3107 691967949 691968205 6.160000e-117 431.0
8 TraesCS7B01G422300 chr7B 90.833 240 18 2 293 532 691965393 691965628 5.000000e-83 318.0
9 TraesCS7B01G422300 chr7B 87.162 296 18 3 367 646 691998411 691998702 5.000000e-83 318.0
10 TraesCS7B01G422300 chr7B 86.275 306 21 5 367 655 691965319 691965620 2.330000e-81 313.0
11 TraesCS7B01G422300 chr7B 91.150 226 16 1 293 518 691998485 691998706 1.400000e-78 303.0
12 TraesCS7B01G422300 chr7B 90.517 232 17 2 293 524 691965467 691965693 5.040000e-78 302.0
13 TraesCS7B01G422300 chr7B 85.965 228 15 2 445 655 691998411 691998638 8.670000e-56 228.0
14 TraesCS7B01G422300 chr7B 90.361 166 12 2 367 532 691998994 691999155 6.750000e-52 215.0
15 TraesCS7B01G422300 chr7B 84.211 228 19 2 445 655 691965319 691965546 4.060000e-49 206.0
16 TraesCS7B01G422300 chr7B 94.074 135 8 0 293 427 691999068 691999202 4.060000e-49 206.0
17 TraesCS7B01G422300 chr7B 83.621 232 17 4 445 655 691927189 691927420 6.800000e-47 198.0
18 TraesCS7B01G422300 chr7B 76.142 197 44 3 1910 2104 691275730 691275535 1.970000e-17 100.0
19 TraesCS7B01G422300 chr7A 91.935 1240 100 0 969 2208 699126933 699128172 0.000000e+00 1736.0
20 TraesCS7B01G422300 chr7A 87.683 820 76 9 171 972 699097072 699097884 0.000000e+00 931.0
21 TraesCS7B01G422300 chr7A 86.632 389 37 7 2202 2588 699142584 699142959 1.720000e-112 416.0
22 TraesCS7B01G422300 chr7A 86.632 389 37 7 2202 2588 699162468 699162093 1.720000e-112 416.0
23 TraesCS7B01G422300 chr7A 89.003 291 30 2 2817 3107 699142983 699143271 2.950000e-95 359.0
24 TraesCS7B01G422300 chr7A 89.003 291 30 2 2817 3107 699162069 699161781 2.950000e-95 359.0
25 TraesCS7B01G422300 chr7A 88.235 238 24 2 295 532 699097268 699097501 6.560000e-72 281.0
26 TraesCS7B01G422300 chr7A 84.141 227 20 4 445 655 699097193 699097419 4.060000e-49 206.0
27 TraesCS7B01G422300 chr7A 91.935 62 5 0 63 124 699096867 699096928 1.530000e-13 87.9
28 TraesCS7B01G422300 chrUn 86.632 389 37 7 2202 2588 342627550 342627175 1.720000e-112 416.0
29 TraesCS7B01G422300 chrUn 89.003 291 30 2 2817 3107 342627151 342626863 2.950000e-95 359.0
30 TraesCS7B01G422300 chr3D 81.609 174 30 2 2415 2588 110402552 110402381 3.230000e-30 143.0
31 TraesCS7B01G422300 chr6B 83.505 97 15 1 2861 2957 19495047 19494952 4.270000e-14 89.8
32 TraesCS7B01G422300 chr6A 86.842 76 9 1 2853 2928 12212121 12212195 1.990000e-12 84.2


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 TraesCS7B01G422300 chr7B 691926897 691930003 3106 False 1839.666667 4783 94.540333 1 3107 3 chr7B.!!$F1 3106
1 TraesCS7B01G422300 chr7B 691965027 691968205 3178 False 968.666667 4242 90.821000 1 3107 6 chr7B.!!$F2 3106
2 TraesCS7B01G422300 chr7B 691998128 692001648 3520 False 702.000000 3332 91.947667 1 3107 9 chr7B.!!$F3 3106
3 TraesCS7B01G422300 chr7A 699126933 699128172 1239 False 1736.000000 1736 91.935000 969 2208 1 chr7A.!!$F1 1239
4 TraesCS7B01G422300 chr7A 699142584 699143271 687 False 387.500000 416 87.817500 2202 3107 2 chr7A.!!$F3 905
5 TraesCS7B01G422300 chr7A 699161781 699162468 687 True 387.500000 416 87.817500 2202 3107 2 chr7A.!!$R1 905
6 TraesCS7B01G422300 chr7A 699096867 699097884 1017 False 376.475000 931 87.998500 63 972 4 chr7A.!!$F2 909
7 TraesCS7B01G422300 chrUn 342626863 342627550 687 True 387.500000 416 87.817500 2202 3107 2 chrUn.!!$R1 905

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
980 1533 1.822990 CTTCACTGCTCCCGGTTAGTA 59.177 52.381 0.00 0.00 0.0 1.82 F
1185 1738 0.108041 GCATCCGTTTCTACCCCGAA 60.108 55.000 0.00 0.00 0.0 4.30 F
1384 1937 0.396435 TGACAAACTCGAGGCATGGT 59.604 50.000 18.41 6.12 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1787 2340 0.18135 CCCACTAGCATTGAGGTCCC 59.819 60.000 0.00 0.0 0.00 4.46 R
2079 2632 0.46729 TTCGAGCCTTGGTTGCCTTT 60.467 50.000 0.00 0.0 0.00 3.11 R
3021 3638 1.00456 CACACACGGTGGAGCTGAT 60.005 57.895 13.48 0.0 44.04 2.90 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
202 300 2.614481 GGACTGGCGAGTACCAATTGAA 60.614 50.000 7.12 0.00 39.86 2.69
427 525 4.400251 TCGGTGAGATATAAACGTTGGAGT 59.600 41.667 0.00 0.00 0.00 3.85
428 526 4.738740 CGGTGAGATATAAACGTTGGAGTC 59.261 45.833 0.00 0.00 0.00 3.36
429 527 5.657474 GGTGAGATATAAACGTTGGAGTCA 58.343 41.667 0.00 0.00 0.00 3.41
430 528 6.103997 GGTGAGATATAAACGTTGGAGTCAA 58.896 40.000 0.00 0.00 0.00 3.18
461 559 3.792124 GCCAAGAATATAGCCGTTGTTGC 60.792 47.826 0.00 0.00 29.98 4.17
484 582 5.221067 GCATAGAGACGTTGGAGATTAGTCA 60.221 44.000 0.00 0.00 34.56 3.41
639 1188 5.231568 CGGTGAGATATAAACGTTGGAGAAC 59.768 44.000 0.00 0.00 0.00 3.01
767 1319 2.893489 GTGGGGATTTAATGGCTCCATC 59.107 50.000 1.31 0.00 35.31 3.51
980 1533 1.822990 CTTCACTGCTCCCGGTTAGTA 59.177 52.381 0.00 0.00 0.00 1.82
993 1546 3.370978 CCGGTTAGTATTTGCACTCACAG 59.629 47.826 0.00 0.00 0.00 3.66
1023 1576 3.484806 ACGCCCCAGAACACACCA 61.485 61.111 0.00 0.00 0.00 4.17
1033 1586 2.358582 CAGAACACACCAATGCTGACAA 59.641 45.455 0.00 0.00 0.00 3.18
1143 1696 1.003118 TGCATCCAGTCCGCTAACTTT 59.997 47.619 0.00 0.00 0.00 2.66
1173 1726 2.797837 CCATGAATGGTGCATCCGT 58.202 52.632 0.00 0.00 43.05 4.69
1185 1738 0.108041 GCATCCGTTTCTACCCCGAA 60.108 55.000 0.00 0.00 0.00 4.30
1213 1766 6.092955 ACAACGAGGATAACAAAGACTACA 57.907 37.500 0.00 0.00 0.00 2.74
1272 1825 3.904339 AGGTGAGGGCGATATACAATCTT 59.096 43.478 0.00 0.00 0.00 2.40
1384 1937 0.396435 TGACAAACTCGAGGCATGGT 59.604 50.000 18.41 6.12 0.00 3.55
1436 1989 5.699915 AGATCGAAGGCTCATCATACATTTG 59.300 40.000 0.00 0.00 0.00 2.32
1458 2011 2.033407 GGACAACTCAATCATCATCGCG 60.033 50.000 0.00 0.00 0.00 5.87
1780 2333 0.806868 CTACACCGACTCGTTGCCTA 59.193 55.000 0.00 0.00 0.00 3.93
1879 2432 4.022068 TGAAAAGGATGAAGTCAATGTGCC 60.022 41.667 0.00 0.00 0.00 5.01
1939 2492 2.422597 CGACAACATTAGTTCTGGCCA 58.577 47.619 4.71 4.71 35.28 5.36
1959 2512 3.490249 CCATCCAGTACAATTGCAGCATG 60.490 47.826 5.05 0.00 40.87 4.06
1994 2547 7.975616 TGCTTGCATTAAATTTATCAACTCCTC 59.024 33.333 0.00 0.00 0.00 3.71
2079 2632 3.576078 ATCTTTGCCGATATGTGGGAA 57.424 42.857 0.00 0.00 34.77 3.97
2446 2999 7.823745 ACACCACAATTTCTAGAACAATTCT 57.176 32.000 4.18 0.00 43.72 2.40
2561 3114 0.751643 AGCTTTGACTTGCACGGGTT 60.752 50.000 0.00 0.00 0.00 4.11
3021 3638 1.879737 TTGGTTCGCCGCTGCTACTA 61.880 55.000 0.00 0.00 41.18 1.82
3034 3651 1.033574 GCTACTATCAGCTCCACCGT 58.966 55.000 0.00 0.00 38.57 4.83
3088 3705 1.689575 GGGCCTCTCTACTGATGGTCA 60.690 57.143 0.84 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
202 300 5.675684 AATGTATTCCGGCTTTGGATTTT 57.324 34.783 0.00 0.00 38.00 1.82
301 399 9.512588 AATCTTCAACATCTCTATTCAACAACT 57.487 29.630 0.00 0.00 0.00 3.16
427 525 7.445402 GGCTATATTCTTGGCAGTCTATTTTGA 59.555 37.037 0.00 0.00 0.00 2.69
428 526 7.571983 CGGCTATATTCTTGGCAGTCTATTTTG 60.572 40.741 0.00 0.00 0.00 2.44
429 527 6.428159 CGGCTATATTCTTGGCAGTCTATTTT 59.572 38.462 0.00 0.00 0.00 1.82
430 528 5.934625 CGGCTATATTCTTGGCAGTCTATTT 59.065 40.000 0.00 0.00 0.00 1.40
437 535 3.206150 ACAACGGCTATATTCTTGGCAG 58.794 45.455 0.00 0.00 0.00 4.85
461 559 6.038825 ACTGACTAATCTCCAACGTCTCTATG 59.961 42.308 0.00 0.00 0.00 2.23
484 582 9.132923 TCTATTCTCCAACGTTTATATCTCACT 57.867 33.333 0.00 0.00 0.00 3.41
639 1188 6.537660 TCAAATGTTCATATCTCAGCACTCTG 59.462 38.462 0.00 0.00 41.67 3.35
767 1319 4.342378 ACATCTATATATAGTGGCAGCGGG 59.658 45.833 17.44 3.48 0.00 6.13
980 1533 3.144657 TGATGGTCTGTGAGTGCAAAT 57.855 42.857 0.00 0.00 0.00 2.32
1033 1586 1.004560 CTGGGACGCACACTGATGT 60.005 57.895 0.00 0.00 40.80 3.06
1143 1696 0.034574 ATTCATGGCCGCCAACAGTA 60.035 50.000 18.00 3.97 36.95 2.74
1185 1738 4.222145 TCTTTGTTATCCTCGTTGTAGCCT 59.778 41.667 0.00 0.00 0.00 4.58
1213 1766 4.090761 TGAGCTGGAGAAAAACTGACAT 57.909 40.909 0.00 0.00 0.00 3.06
1272 1825 5.192176 TGTATTGCTTGATTGACCAGCATA 58.808 37.500 0.00 0.00 35.33 3.14
1384 1937 4.891627 TCTTCTTGAATGCGACAAAACA 57.108 36.364 0.00 0.00 0.00 2.83
1436 1989 2.289002 GCGATGATGATTGAGTTGTCCC 59.711 50.000 0.00 0.00 0.00 4.46
1453 2006 6.860023 GTGATAATAGTAAGGTTACACGCGAT 59.140 38.462 15.93 2.23 36.12 4.58
1644 2197 4.388499 AAGACCGGCGACCGCAAT 62.388 61.111 9.30 0.40 46.86 3.56
1787 2340 0.181350 CCCACTAGCATTGAGGTCCC 59.819 60.000 0.00 0.00 0.00 4.46
1801 2354 2.674177 CGAGCATTTCTTCGTACCCACT 60.674 50.000 0.00 0.00 0.00 4.00
1879 2432 3.217626 ACCTCTGGCAAAGTTTTCTCTG 58.782 45.455 0.00 0.00 0.00 3.35
1939 2492 2.100252 GCATGCTGCAATTGTACTGGAT 59.900 45.455 11.37 0.00 44.26 3.41
1959 2512 6.657836 AATTTAATGCAAGCATCTTTGAGC 57.342 33.333 8.14 0.00 35.31 4.26
1994 2547 1.404181 CCACACCATCCACAGTACTCG 60.404 57.143 0.00 0.00 0.00 4.18
2079 2632 0.467290 TTCGAGCCTTGGTTGCCTTT 60.467 50.000 0.00 0.00 0.00 3.11
2213 2766 7.375834 TCTAATTGGATACTGTTGGTATAGCG 58.624 38.462 0.00 0.00 40.82 4.26
2437 2990 4.572909 ACGTTACACCCCTAGAATTGTTC 58.427 43.478 0.00 0.00 0.00 3.18
2446 2999 2.528564 AGCACTTACGTTACACCCCTA 58.471 47.619 0.00 0.00 0.00 3.53
2561 3114 5.878332 CACATGATAGTGGTAAACTTGCA 57.122 39.130 0.00 0.00 40.56 4.08
3021 3638 1.004560 CACACACGGTGGAGCTGAT 60.005 57.895 13.48 0.00 44.04 2.90


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

AutoCloner maintained by Alex Coulton.