Multiple sequence alignment - TraesCS6B01G073500

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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 TraesCS6B01G073500 chr6B 100.000 2730 0 0 1 2730 49877288 49880017 0.000000e+00 5042.0
1 TraesCS6B01G073500 chr6B 97.008 1103 24 5 820 1915 49663818 49664918 0.000000e+00 1845.0
2 TraesCS6B01G073500 chr6B 91.471 809 46 13 1942 2730 49664917 49665722 0.000000e+00 1090.0
3 TraesCS6B01G073500 chr6B 83.920 653 90 8 1242 1890 49762931 49763572 6.460000e-171 610.0
4 TraesCS6B01G073500 chr6B 86.466 133 13 4 2369 2497 517413643 517413774 1.020000e-29 141.0
5 TraesCS6B01G073500 chr6D 93.968 1923 90 17 822 2730 27201519 27203429 0.000000e+00 2885.0
6 TraesCS6B01G073500 chr6D 80.532 827 116 28 1242 2051 27118908 27119706 6.510000e-166 593.0
7 TraesCS6B01G073500 chr3A 94.750 819 20 4 1 818 58842792 58843588 0.000000e+00 1253.0
8 TraesCS6B01G073500 chr3A 76.561 785 109 42 85 827 617012085 617011334 7.190000e-96 361.0
9 TraesCS6B01G073500 chr1B 95.067 669 14 6 16 669 7506370 7507034 0.000000e+00 1035.0
10 TraesCS6B01G073500 chr1B 88.732 426 40 3 4 429 184211428 184211845 5.210000e-142 514.0
11 TraesCS6B01G073500 chr1B 94.512 164 9 0 654 817 7507053 7507216 1.250000e-63 254.0
12 TraesCS6B01G073500 chr1B 89.773 88 5 2 2188 2275 605451241 605451158 2.870000e-20 110.0
13 TraesCS6B01G073500 chr2D 90.926 540 36 9 18 556 600031147 600030620 0.000000e+00 713.0
14 TraesCS6B01G073500 chr2D 87.681 138 16 1 2369 2505 522609134 522609271 2.810000e-35 159.0
15 TraesCS6B01G073500 chr2D 84.706 85 8 3 2214 2297 10985517 10985437 2.250000e-11 80.5
16 TraesCS6B01G073500 chr2D 95.745 47 2 0 2172 2218 188588154 188588108 2.920000e-10 76.8
17 TraesCS6B01G073500 chr6A 82.331 815 122 12 1244 2051 28430197 28430996 0.000000e+00 688.0
18 TraesCS6B01G073500 chr6A 77.129 411 83 10 1241 1646 28349983 28350387 7.600000e-56 228.0
19 TraesCS6B01G073500 chr7A 90.966 476 33 6 82 556 701885487 701885021 1.380000e-177 632.0
20 TraesCS6B01G073500 chr3D 76.562 768 112 42 85 818 22124005 22124738 2.580000e-95 359.0
21 TraesCS6B01G073500 chr3D 89.051 137 15 0 2369 2505 593206611 593206475 1.300000e-38 171.0
22 TraesCS6B01G073500 chr3D 95.745 47 2 0 2174 2220 505937306 505937352 2.920000e-10 76.8
23 TraesCS6B01G073500 chr7D 81.818 374 47 15 85 452 175915222 175915580 7.390000e-76 294.0
24 TraesCS6B01G073500 chr7D 86.709 158 19 2 2369 2525 189169563 189169407 1.000000e-39 174.0
25 TraesCS6B01G073500 chr7D 87.129 101 10 3 2171 2269 390929900 390929801 7.990000e-21 111.0
26 TraesCS6B01G073500 chr5B 93.590 156 6 3 49 204 356195075 356195226 2.110000e-56 230.0
27 TraesCS6B01G073500 chr5B 87.681 138 17 0 2371 2508 102083319 102083456 7.820000e-36 161.0
28 TraesCS6B01G073500 chr3B 91.667 156 10 3 49 204 752392545 752392393 2.130000e-51 213.0
29 TraesCS6B01G073500 chr4B 94.853 136 6 1 49 184 417131103 417131237 7.660000e-51 211.0
30 TraesCS6B01G073500 chr4B 85.816 141 20 0 2365 2505 497859396 497859536 1.690000e-32 150.0
31 TraesCS6B01G073500 chr4B 87.255 102 6 4 2174 2275 640009051 640009145 2.870000e-20 110.0
32 TraesCS6B01G073500 chr4B 86.316 95 12 1 719 812 638485764 638485670 4.810000e-18 102.0
33 TraesCS6B01G073500 chr4B 89.333 75 4 3 2213 2286 586248460 586248531 1.040000e-14 91.6
34 TraesCS6B01G073500 chr4B 81.481 108 12 5 2168 2275 111787950 111788049 6.270000e-12 82.4
35 TraesCS6B01G073500 chr4B 92.593 54 3 1 2174 2226 42939388 42939335 2.920000e-10 76.8
36 TraesCS6B01G073500 chr7B 84.892 139 21 0 2369 2507 333743049 333742911 1.020000e-29 141.0
37 TraesCS6B01G073500 chr7B 86.486 74 6 3 2214 2286 639796210 639796280 8.100000e-11 78.7


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 TraesCS6B01G073500 chr6B 49877288 49880017 2729 False 5042.0 5042 100.0000 1 2730 1 chr6B.!!$F2 2729
1 TraesCS6B01G073500 chr6B 49663818 49665722 1904 False 1467.5 1845 94.2395 820 2730 2 chr6B.!!$F4 1910
2 TraesCS6B01G073500 chr6B 49762931 49763572 641 False 610.0 610 83.9200 1242 1890 1 chr6B.!!$F1 648
3 TraesCS6B01G073500 chr6D 27201519 27203429 1910 False 2885.0 2885 93.9680 822 2730 1 chr6D.!!$F2 1908
4 TraesCS6B01G073500 chr6D 27118908 27119706 798 False 593.0 593 80.5320 1242 2051 1 chr6D.!!$F1 809
5 TraesCS6B01G073500 chr3A 58842792 58843588 796 False 1253.0 1253 94.7500 1 818 1 chr3A.!!$F1 817
6 TraesCS6B01G073500 chr3A 617011334 617012085 751 True 361.0 361 76.5610 85 827 1 chr3A.!!$R1 742
7 TraesCS6B01G073500 chr1B 7506370 7507216 846 False 644.5 1035 94.7895 16 817 2 chr1B.!!$F2 801
8 TraesCS6B01G073500 chr2D 600030620 600031147 527 True 713.0 713 90.9260 18 556 1 chr2D.!!$R3 538
9 TraesCS6B01G073500 chr6A 28430197 28430996 799 False 688.0 688 82.3310 1244 2051 1 chr6A.!!$F2 807
10 TraesCS6B01G073500 chr3D 22124005 22124738 733 False 359.0 359 76.5620 85 818 1 chr3D.!!$F1 733

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
772 868 0.1023 TCATCGCCACGTCATTCGAT 59.898 50.0 5.34 5.34 41.66 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2104 2232 0.034337 TATAAGGACGGGCCAATCGC 59.966 55.0 4.39 0.0 40.02 4.58 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
61 62 4.036734 ACGGATATCAGCGCAAATGAAATT 59.963 37.500 11.47 0.00 38.98 1.82
425 439 5.201713 TCTTTATCCTCAAGTCTATGGCG 57.798 43.478 0.00 0.00 0.00 5.69
467 481 4.553330 ATCTTTTTCCAGAGAGCCGTTA 57.447 40.909 0.00 0.00 0.00 3.18
567 581 1.880027 GCACGGGAGAAGTTTGAATGT 59.120 47.619 0.00 0.00 0.00 2.71
723 818 1.616628 GGGGGAGAAAGGAGCCTGA 60.617 63.158 0.00 0.00 0.00 3.86
772 868 0.102300 TCATCGCCACGTCATTCGAT 59.898 50.000 5.34 5.34 41.66 3.59
808 904 4.600692 TTCTCAGTCGAATGAGTTCCAA 57.399 40.909 34.16 22.12 45.70 3.53
818 914 0.902984 TGAGTTCCAAGCGCTCCCTA 60.903 55.000 12.06 0.00 0.00 3.53
819 915 0.466124 GAGTTCCAAGCGCTCCCTAT 59.534 55.000 12.06 0.00 0.00 2.57
820 916 1.687123 GAGTTCCAAGCGCTCCCTATA 59.313 52.381 12.06 0.00 0.00 1.31
828 924 7.907841 TCCAAGCGCTCCCTATAATATATAA 57.092 36.000 12.06 0.00 0.00 0.98
829 925 7.952671 TCCAAGCGCTCCCTATAATATATAAG 58.047 38.462 12.06 0.00 0.00 1.73
1006 1108 0.955428 TCTGCCGATTTGGTGCTGAC 60.955 55.000 0.00 0.00 41.21 3.51
1357 1459 4.394300 CAGTTCTCCAATTACTCCTGCAAG 59.606 45.833 0.00 0.00 0.00 4.01
1378 1480 1.472878 TGCTACCGAGAGTGCTACTTG 59.527 52.381 0.00 0.00 0.00 3.16
1635 1750 1.134461 TGTGCTTGCACTGCCATTTTT 60.134 42.857 23.53 0.00 0.00 1.94
1636 1751 1.262151 GTGCTTGCACTGCCATTTTTG 59.738 47.619 17.36 0.00 0.00 2.44
1637 1752 0.236449 GCTTGCACTGCCATTTTTGC 59.764 50.000 0.00 0.00 35.45 3.68
1638 1753 1.584175 CTTGCACTGCCATTTTTGCA 58.416 45.000 0.00 0.00 43.11 4.08
1639 1754 2.147958 CTTGCACTGCCATTTTTGCAT 58.852 42.857 0.00 0.00 44.16 3.96
1640 1755 3.327626 CTTGCACTGCCATTTTTGCATA 58.672 40.909 0.00 0.00 44.16 3.14
1641 1756 3.613494 TGCACTGCCATTTTTGCATAT 57.387 38.095 0.00 0.00 40.01 1.78
1965 2093 6.011122 AGGAATAAGTAACGTAGGAGAGGA 57.989 41.667 0.00 0.00 0.00 3.71
2007 2135 8.579682 AAGAATTCAAACATCAGCAAACTAAC 57.420 30.769 8.44 0.00 0.00 2.34
2019 2147 1.606668 CAAACTAACCGAAGCCTTGCA 59.393 47.619 0.00 0.00 0.00 4.08
2104 2232 2.542766 ATAAGCCGCAATTTGACGTG 57.457 45.000 0.00 0.33 0.00 4.49
2105 2233 0.109964 TAAGCCGCAATTTGACGTGC 60.110 50.000 0.00 8.88 37.40 5.34
2202 2332 7.788026 TCCTTCCGTAAAGAAATATAAGAGCA 58.212 34.615 0.00 0.00 37.12 4.26
2264 2394 5.467705 ACTTTAGTGATCTAAACGACGCTT 58.532 37.500 0.00 0.00 40.05 4.68
2317 2465 1.803334 TTGTACTAGCCTTGCGGTTG 58.197 50.000 0.00 0.00 0.00 3.77
2319 2467 1.071071 TGTACTAGCCTTGCGGTTGTT 59.929 47.619 0.00 0.00 0.00 2.83
2320 2468 1.730612 GTACTAGCCTTGCGGTTGTTC 59.269 52.381 0.00 0.00 0.00 3.18
2325 2473 1.244019 GCCTTGCGGTTGTTCATCCT 61.244 55.000 0.00 0.00 0.00 3.24
2328 2476 2.161609 CCTTGCGGTTGTTCATCCTAAC 59.838 50.000 0.00 0.00 0.00 2.34
2344 2492 3.573967 TCCTAACGACCCGAGTTTAGTTT 59.426 43.478 0.00 0.00 33.42 2.66
2420 2568 6.062258 TGATTTAGAAAATTCCGAGGACCT 57.938 37.500 0.00 0.00 0.00 3.85
2424 2572 1.472878 GAAAATTCCGAGGACCTTGCC 59.527 52.381 2.75 0.00 0.00 4.52
2457 2605 5.925509 ACTCATACTAAAATGGCCGTATGT 58.074 37.500 19.43 10.25 39.87 2.29
2461 2609 7.672240 TCATACTAAAATGGCCGTATGTATCA 58.328 34.615 19.43 3.65 39.87 2.15
2551 2699 1.251527 ACAGGGAGGCGACTACACTG 61.252 60.000 15.28 15.28 46.31 3.66
2553 2701 1.982938 GGGAGGCGACTACACTGGT 60.983 63.158 0.98 0.00 46.31 4.00
2675 2823 4.489771 GGTGGCGGAGGTCCCATG 62.490 72.222 0.00 0.00 32.95 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
585 614 2.169561 GGCCTTTTTGGGTTGTCAAGAA 59.830 45.455 0.00 0.00 36.00 2.52
586 615 1.760029 GGCCTTTTTGGGTTGTCAAGA 59.240 47.619 0.00 0.00 36.00 3.02
587 616 1.202639 GGGCCTTTTTGGGTTGTCAAG 60.203 52.381 0.84 0.00 36.00 3.02
589 618 0.325671 TGGGCCTTTTTGGGTTGTCA 60.326 50.000 4.53 0.00 36.00 3.58
723 818 1.910580 ATTTGTCCCAGCCCGATCGT 61.911 55.000 15.09 0.00 0.00 3.73
772 868 7.158697 TCGACTGAGAAATAAAATGGTCTCAA 58.841 34.615 4.01 0.00 44.33 3.02
1357 1459 1.096416 AGTAGCACTCTCGGTAGCAC 58.904 55.000 0.00 0.00 0.00 4.40
1378 1480 2.970974 GAAGGCGTGCTTGCACTCC 61.971 63.158 22.66 22.66 36.28 3.85
1644 1761 1.961277 GCTACAATATGCGGCGCCT 60.961 57.895 30.82 22.88 0.00 5.52
1645 1762 2.556287 GCTACAATATGCGGCGCC 59.444 61.111 30.82 19.07 0.00 6.53
1653 1770 1.965935 TGCACGCATGGCTACAATAT 58.034 45.000 0.00 0.00 0.00 1.28
1840 1958 7.174253 GGGATTTACCAAATGCATCGATAACTA 59.826 37.037 0.00 0.00 40.53 2.24
1895 2020 3.262660 TGATCTTGCAATCTGGTCAGAGT 59.737 43.478 0.00 0.91 41.33 3.24
2007 2135 0.392193 AGACTCATGCAAGGCTTCGG 60.392 55.000 0.00 0.00 26.49 4.30
2019 2147 9.768662 AATTATTTTGCTTTTGTTCAGACTCAT 57.231 25.926 0.00 0.00 0.00 2.90
2104 2232 0.034337 TATAAGGACGGGCCAATCGC 59.966 55.000 4.39 0.00 40.02 4.58
2105 2233 1.069513 TGTATAAGGACGGGCCAATCG 59.930 52.381 4.39 0.56 40.02 3.34
2317 2465 1.475682 ACTCGGGTCGTTAGGATGAAC 59.524 52.381 0.00 0.00 0.00 3.18
2319 2467 1.843368 AACTCGGGTCGTTAGGATGA 58.157 50.000 0.00 0.00 0.00 2.92
2320 2468 2.667473 AAACTCGGGTCGTTAGGATG 57.333 50.000 0.00 0.00 0.00 3.51
2325 2473 4.853924 AGAAACTAAACTCGGGTCGTTA 57.146 40.909 0.00 0.00 0.00 3.18
2328 2476 4.691860 TCTAGAAACTAAACTCGGGTCG 57.308 45.455 0.00 0.00 0.00 4.79
2344 2492 9.434275 TTCTCCCTGTACATTATCAATTCTAGA 57.566 33.333 0.00 0.00 0.00 2.43
2360 2508 3.184382 TCATGAGTGGTTCTCCCTGTA 57.816 47.619 0.00 0.00 42.12 2.74
2398 2546 6.678164 GCAAGGTCCTCGGAATTTTCTAAATC 60.678 42.308 0.00 0.00 0.00 2.17
2412 2560 1.757118 TGAAGATAGGCAAGGTCCTCG 59.243 52.381 0.00 0.00 37.66 4.63
2457 2605 2.168521 GCCTCTGCACCAACTAGTGATA 59.831 50.000 0.00 0.00 40.34 2.15
2461 2609 0.322975 CAGCCTCTGCACCAACTAGT 59.677 55.000 0.00 0.00 41.13 2.57


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

AutoCloner maintained by Alex Coulton.