Multiple sequence alignment - TraesCS6B01G126700

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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 TraesCS6B01G126700 chr6B 100.000 3609 0 0 1 3609 122188688 122185080 0.000000e+00 6665.0
1 TraesCS6B01G126700 chr6B 96.000 3625 129 9 1 3609 121962150 121958526 0.000000e+00 5877.0
2 TraesCS6B01G126700 chr6B 85.670 321 37 8 1 319 121437333 121437020 2.690000e-86 329.0
3 TraesCS6B01G126700 chr6D 93.256 3633 199 21 1 3609 49180721 49184331 0.000000e+00 5310.0
4 TraesCS6B01G126700 chr6D 88.825 1736 156 17 1910 3609 50604941 50606674 0.000000e+00 2097.0
5 TraesCS6B01G126700 chr6D 80.481 2121 305 54 1399 3441 430846269 430844180 0.000000e+00 1522.0
6 TraesCS6B01G126700 chr6D 85.099 1369 165 21 2059 3391 50179795 50181160 0.000000e+00 1362.0
7 TraesCS6B01G126700 chr6D 87.541 923 113 2 1 923 50602773 50603693 0.000000e+00 1066.0
8 TraesCS6B01G126700 chr6D 85.312 320 42 4 1 319 50114519 50114834 3.470000e-85 326.0
9 TraesCS6B01G126700 chr7A 84.466 3193 371 58 472 3609 591022665 591025787 0.000000e+00 3033.0
10 TraesCS6B01G126700 chr7A 82.689 543 78 16 1 537 551545409 551544877 5.460000e-128 468.0
11 TraesCS6B01G126700 chrUn 88.659 1737 157 22 1910 3609 277361152 277362885 0.000000e+00 2080.0
12 TraesCS6B01G126700 chrUn 84.076 1055 141 13 786 1814 373934200 373933147 0.000000e+00 992.0
13 TraesCS6B01G126700 chrUn 88.520 784 87 2 1 784 71748840 71749620 0.000000e+00 946.0
14 TraesCS6B01G126700 chrUn 90.558 699 54 5 1910 2596 373933137 373932439 0.000000e+00 915.0
15 TraesCS6B01G126700 chr6A 88.543 1737 159 22 1910 3609 64679792 64678059 0.000000e+00 2069.0
16 TraesCS6B01G126700 chr6A 86.289 1838 224 15 1 1814 64681635 64679802 0.000000e+00 1973.0
17 TraesCS6B01G126700 chr6A 84.688 1378 167 22 2062 3401 64908453 64907082 0.000000e+00 1336.0
18 TraesCS6B01G126700 chr7B 80.934 2056 281 62 1445 3440 517933887 517931883 0.000000e+00 1522.0
19 TraesCS6B01G126700 chr7B 80.107 2056 290 58 1445 3440 509737169 509735173 0.000000e+00 1421.0
20 TraesCS6B01G126700 chr7B 80.131 609 103 16 1 604 517936163 517935568 4.280000e-119 438.0
21 TraesCS6B01G126700 chr7D 80.641 1715 241 54 1782 3440 489302131 489300452 0.000000e+00 1243.0
22 TraesCS6B01G126700 chr7D 80.488 492 69 16 2965 3433 484070769 484070282 5.730000e-93 351.0
23 TraesCS6B01G126700 chr7D 73.844 627 131 24 754 1355 489311907 489311289 6.070000e-53 219.0
24 TraesCS6B01G126700 chr2D 81.366 703 87 27 1742 2415 89468724 89469411 1.910000e-147 532.0
25 TraesCS6B01G126700 chr2B 81.513 119 21 1 3452 3569 142297550 142297668 2.970000e-16 97.1


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 TraesCS6B01G126700 chr6B 122185080 122188688 3608 True 6665.0 6665 100.0000 1 3609 1 chr6B.!!$R3 3608
1 TraesCS6B01G126700 chr6B 121958526 121962150 3624 True 5877.0 5877 96.0000 1 3609 1 chr6B.!!$R2 3608
2 TraesCS6B01G126700 chr6D 49180721 49184331 3610 False 5310.0 5310 93.2560 1 3609 1 chr6D.!!$F1 3608
3 TraesCS6B01G126700 chr6D 50602773 50606674 3901 False 1581.5 2097 88.1830 1 3609 2 chr6D.!!$F4 3608
4 TraesCS6B01G126700 chr6D 430844180 430846269 2089 True 1522.0 1522 80.4810 1399 3441 1 chr6D.!!$R1 2042
5 TraesCS6B01G126700 chr6D 50179795 50181160 1365 False 1362.0 1362 85.0990 2059 3391 1 chr6D.!!$F3 1332
6 TraesCS6B01G126700 chr7A 591022665 591025787 3122 False 3033.0 3033 84.4660 472 3609 1 chr7A.!!$F1 3137
7 TraesCS6B01G126700 chr7A 551544877 551545409 532 True 468.0 468 82.6890 1 537 1 chr7A.!!$R1 536
8 TraesCS6B01G126700 chrUn 277361152 277362885 1733 False 2080.0 2080 88.6590 1910 3609 1 chrUn.!!$F2 1699
9 TraesCS6B01G126700 chrUn 373932439 373934200 1761 True 953.5 992 87.3170 786 2596 2 chrUn.!!$R1 1810
10 TraesCS6B01G126700 chrUn 71748840 71749620 780 False 946.0 946 88.5200 1 784 1 chrUn.!!$F1 783
11 TraesCS6B01G126700 chr6A 64678059 64681635 3576 True 2021.0 2069 87.4160 1 3609 2 chr6A.!!$R2 3608
12 TraesCS6B01G126700 chr6A 64907082 64908453 1371 True 1336.0 1336 84.6880 2062 3401 1 chr6A.!!$R1 1339
13 TraesCS6B01G126700 chr7B 509735173 509737169 1996 True 1421.0 1421 80.1070 1445 3440 1 chr7B.!!$R1 1995
14 TraesCS6B01G126700 chr7B 517931883 517936163 4280 True 980.0 1522 80.5325 1 3440 2 chr7B.!!$R2 3439
15 TraesCS6B01G126700 chr7D 489300452 489302131 1679 True 1243.0 1243 80.6410 1782 3440 1 chr7D.!!$R2 1658
16 TraesCS6B01G126700 chr7D 489311289 489311907 618 True 219.0 219 73.8440 754 1355 1 chr7D.!!$R3 601
17 TraesCS6B01G126700 chr2D 89468724 89469411 687 False 532.0 532 81.3660 1742 2415 1 chr2D.!!$F1 673

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
957 1663 0.74299 TTACCAATTCAGGCGAGGCG 60.743 55.0 0.0 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2665 3956 0.694771 TCCAAGTCAGAGCAGCCAAT 59.305 50.0 0.0 0.0 0.0 3.16 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
59 60 3.352554 TTGCACACAAAGTACATGCTG 57.647 42.857 0.00 0.00 37.20 4.41
70 71 6.996282 ACAAAGTACATGCTGGTAACTAAACT 59.004 34.615 0.00 0.00 37.61 2.66
100 101 8.405531 CAACTTTCCTTTTCACTGAGAACAATA 58.594 33.333 0.00 0.00 35.56 1.90
547 1247 5.413213 TGGTTAAACGTTCGATTGGATGAAT 59.587 36.000 0.00 0.00 0.00 2.57
673 1373 6.151985 TGCCTACAAAGAAAGAAAGTGAAACA 59.848 34.615 0.00 0.00 41.43 2.83
728 1430 3.610911 CAGGAATACCACTTCTCCCAAC 58.389 50.000 0.00 0.00 38.94 3.77
729 1431 3.264450 CAGGAATACCACTTCTCCCAACT 59.736 47.826 0.00 0.00 38.94 3.16
863 1566 2.687370 CGTCTTCACATGTCCATCACA 58.313 47.619 0.00 0.00 40.18 3.58
948 1651 9.094578 TGAAAATTCTACCCAATTACCAATTCA 57.905 29.630 0.00 0.00 0.00 2.57
957 1663 0.742990 TTACCAATTCAGGCGAGGCG 60.743 55.000 0.00 0.00 0.00 5.52
1046 2071 1.270839 CGTCAAGGTTCCCACAGTGAT 60.271 52.381 0.62 0.00 0.00 3.06
1234 2280 2.101415 CGCACTATGGTGGATGAGAAGA 59.899 50.000 11.53 0.00 43.18 2.87
1262 2308 1.025812 GACGAGGTCGGTGAGATCAT 58.974 55.000 4.13 0.00 44.95 2.45
1283 2329 2.258013 CCTTTGCCGCCGTCAAGAA 61.258 57.895 0.00 0.00 0.00 2.52
1454 2663 5.258051 TGTGTAGGTTTTCTTGTTGGAAGT 58.742 37.500 0.00 0.00 0.00 3.01
1590 2811 2.287608 GGTAGGCTGTTTTTGACACTGC 60.288 50.000 0.00 0.00 38.13 4.40
1667 2889 8.671384 TTATAATTTTCTACACCTTCGATGGG 57.329 34.615 20.44 12.14 0.00 4.00
1700 2922 5.419155 AGCTTAGAATTTAGTCAAAAGGGGC 59.581 40.000 0.00 0.00 0.00 5.80
1714 2936 1.205460 AGGGGCAGTAAATCCGTGGT 61.205 55.000 0.00 0.00 0.00 4.16
1797 3020 2.105134 TGGTTGTAGGTGTGTGTAAGGG 59.895 50.000 0.00 0.00 0.00 3.95
2186 3458 7.156876 TCTTAAAATGACTTAAGCACCATGG 57.843 36.000 11.19 11.19 38.33 3.66
2373 3657 3.488047 GCTTATGATGTTGAAGCACGCAT 60.488 43.478 1.13 0.00 44.05 4.73
2409 3693 2.963101 AGGCCAAGGTTAACTTTCCAAC 59.037 45.455 5.01 0.00 37.29 3.77
2469 3753 2.471255 CTCCTAAAGCACCCAAGCG 58.529 57.895 0.00 0.00 40.15 4.68
2624 3909 2.364970 CAATGAACTTTGTTGCCCCTGA 59.635 45.455 0.00 0.00 0.00 3.86
2625 3910 2.151502 TGAACTTTGTTGCCCCTGAA 57.848 45.000 0.00 0.00 0.00 3.02
2626 3911 2.461695 TGAACTTTGTTGCCCCTGAAA 58.538 42.857 0.00 0.00 0.00 2.69
2633 3924 4.329462 TTGTTGCCCCTGAAAATGTTAC 57.671 40.909 0.00 0.00 0.00 2.50
2665 3956 1.059584 TGACCAGGGAAGCAACTCCA 61.060 55.000 0.00 0.00 37.20 3.86
3008 4303 0.179062 GGAGCTTCGATGACATGCCT 60.179 55.000 1.89 0.00 0.00 4.75
3177 4477 5.398012 GGAGATTAGGAAGCACCCTATTGTT 60.398 44.000 5.15 0.00 38.50 2.83
3239 4553 2.226912 CGAGTCTCTTTTCTGGTCGACT 59.773 50.000 16.46 0.00 34.71 4.18
3535 4863 1.607148 GAGTGTGTGTTAGGCCAAACC 59.393 52.381 5.01 0.00 39.61 3.27
3569 4897 2.849294 ACCTCTTCACTTCAAGCTCC 57.151 50.000 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 7.741027 AGGAAAGTTGCTTAGTTTAGTTACC 57.259 36.000 0.00 0.00 29.47 2.85
70 71 6.119536 TCTCAGTGAAAAGGAAAGTTGCTTA 58.880 36.000 0.00 0.00 37.91 3.09
422 764 3.689161 TCAATATTGTACTGCACACCTGC 59.311 43.478 14.97 0.00 44.52 4.85
458 800 9.719355 TTTTGTGAATCACTCATAGCTAGTTAA 57.281 29.630 14.97 0.00 36.14 2.01
479 821 8.810652 ATTACGTGTAATGCAAAGATTTTTGT 57.189 26.923 10.14 0.00 44.41 2.83
547 1247 2.841266 TCGTCTGGGTTTATTGGATGGA 59.159 45.455 0.00 0.00 0.00 3.41
673 1373 5.967884 TGGGGAATGAATGGATGAATGTAT 58.032 37.500 0.00 0.00 0.00 2.29
728 1430 0.314935 AAATCTTGCGTGTTGGGCAG 59.685 50.000 0.00 0.00 42.12 4.85
729 1431 0.313672 GAAATCTTGCGTGTTGGGCA 59.686 50.000 0.00 0.00 38.93 5.36
863 1566 2.955461 GCGAGGCCAGTCCCCTATATAT 60.955 54.545 5.01 0.00 34.51 0.86
1046 2071 0.250684 TGCCTTTGTCATCTTCCGCA 60.251 50.000 0.00 0.00 0.00 5.69
1254 2300 2.013563 GCGGCAAAGGACATGATCTCA 61.014 52.381 0.00 0.00 0.00 3.27
1262 2308 3.758973 TTGACGGCGGCAAAGGACA 62.759 57.895 28.31 0.73 0.00 4.02
1283 2329 1.651770 TGATACCTTGGGAGAGGGAGT 59.348 52.381 0.00 0.00 41.31 3.85
1454 2663 4.263156 GGAGTAACACCACCCAAACATAGA 60.263 45.833 0.00 0.00 0.00 1.98
1590 2811 3.146104 TGCTTCTCTGAAAGAAAGGGG 57.854 47.619 4.49 0.00 46.34 4.79
1667 2889 9.561069 TTGACTAAATTCTAAGCTTATGGATCC 57.439 33.333 6.64 4.20 0.00 3.36
1683 2905 6.987403 TTTACTGCCCCTTTTGACTAAATT 57.013 33.333 0.00 0.00 0.00 1.82
1700 2922 2.285977 GCCCTTACCACGGATTTACTG 58.714 52.381 0.00 0.00 0.00 2.74
1714 2936 4.262851 GCAAAAGGAGAAATTTGGCCCTTA 60.263 41.667 0.00 0.00 36.31 2.69
2119 3379 3.938963 GACCAACACTCACAAACTTCTCA 59.061 43.478 0.00 0.00 0.00 3.27
2186 3458 2.162408 GACCATCAAAACCTGCAGTAGC 59.838 50.000 13.81 0.00 42.57 3.58
2373 3657 2.550487 GCCTTGTTGCCACGTATCA 58.450 52.632 0.00 0.00 0.00 2.15
2469 3753 1.251251 AGGTTCATGTGCCAAGCTTC 58.749 50.000 0.00 0.00 0.00 3.86
2474 3758 2.229792 GACAGAAGGTTCATGTGCCAA 58.770 47.619 10.09 0.00 0.00 4.52
2624 3909 7.280205 GGTCAGAGTATGGATTCGTAACATTTT 59.720 37.037 0.00 0.00 0.00 1.82
2625 3910 6.761714 GGTCAGAGTATGGATTCGTAACATTT 59.238 38.462 0.00 0.00 0.00 2.32
2626 3911 6.127168 TGGTCAGAGTATGGATTCGTAACATT 60.127 38.462 0.00 0.00 0.00 2.71
2633 3924 2.036475 CCCTGGTCAGAGTATGGATTCG 59.964 54.545 0.00 0.00 0.00 3.34
2665 3956 0.694771 TCCAAGTCAGAGCAGCCAAT 59.305 50.000 0.00 0.00 0.00 3.16
2934 4228 6.036470 GCACATTAAAATTCAGAAGGCTACC 58.964 40.000 0.00 0.00 0.00 3.18
3008 4303 5.067153 CCCTCATAAAAATTCGCCACACATA 59.933 40.000 0.00 0.00 0.00 2.29
3177 4477 2.743636 GCATATGCTAGCCGAAGGTA 57.256 50.000 20.64 0.00 44.80 3.08
3212 4526 2.497675 CCAGAAAAGAGACTCGGGATGA 59.502 50.000 0.00 0.00 0.00 2.92
3239 4553 6.321435 CACATAGACAGTTGAGTAGGGACATA 59.679 42.308 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.