Multiple sequence alignment - TraesCS3A01G343500

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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 TraesCS3A01G343500 chr3A 100.000 3922 0 0 1 3922 592214609 592218530 0.000000e+00 7243.0
1 TraesCS3A01G343500 chr3A 99.437 2130 10 1 1793 3922 592170172 592172299 0.000000e+00 3866.0
2 TraesCS3A01G343500 chr3A 98.425 1778 26 2 1 1778 592143521 592145296 0.000000e+00 3127.0
3 TraesCS3A01G343500 chr3D 93.488 2150 108 15 1793 3922 449284057 449286194 0.000000e+00 3166.0
4 TraesCS3A01G343500 chr3D 92.065 983 43 5 796 1748 449282187 449283164 0.000000e+00 1351.0
5 TraesCS3A01G343500 chr3D 93.333 90 5 1 560 648 590751759 590751848 8.840000e-27 132.0
6 TraesCS3A01G343500 chr3B 92.040 1784 106 19 1793 3562 590453699 590455460 0.000000e+00 2475.0
7 TraesCS3A01G343500 chr3B 92.435 1031 44 18 747 1748 590451783 590452808 0.000000e+00 1441.0
8 TraesCS3A01G343500 chr3B 83.516 546 85 5 1 544 590451233 590451775 4.520000e-139 505.0
9 TraesCS3A01G343500 chr3B 100.000 29 0 0 649 677 68449325 68449353 2.000000e-03 54.7
10 TraesCS3A01G343500 chr5B 81.466 464 84 2 81 543 467374243 467374705 2.860000e-101 379.0
11 TraesCS3A01G343500 chr5B 86.640 247 27 5 3442 3682 591822752 591822506 6.460000e-68 268.0
12 TraesCS3A01G343500 chr7A 83.632 391 64 0 153 543 732001955 732002345 6.190000e-98 368.0
13 TraesCS3A01G343500 chr7A 81.174 409 59 15 131 533 261219945 261220341 2.940000e-81 313.0
14 TraesCS3A01G343500 chr1B 80.349 458 81 9 78 533 642075982 642076432 4.850000e-89 339.0
15 TraesCS3A01G343500 chr1B 77.516 467 89 14 80 543 137451871 137451418 2.320000e-67 267.0
16 TraesCS3A01G343500 chr1B 86.777 242 25 6 3447 3682 624023483 624023243 3.010000e-66 263.0
17 TraesCS3A01G343500 chr1B 86.364 242 27 5 3447 3682 619395845 619396086 3.890000e-65 259.0
18 TraesCS3A01G343500 chr5A 79.694 458 89 4 81 538 550533467 550533014 1.050000e-85 327.0
19 TraesCS3A01G343500 chr5A 100.000 28 0 0 650 677 545863401 545863428 7.000000e-03 52.8
20 TraesCS3A01G343500 chr7D 87.815 238 26 3 3447 3682 567477187 567476951 3.860000e-70 276.0
21 TraesCS3A01G343500 chr7D 91.176 102 6 2 550 648 25510804 25510703 6.840000e-28 135.0
22 TraesCS3A01G343500 chr6B 87.124 233 26 3 3447 3675 55433120 55432888 1.080000e-65 261.0
23 TraesCS3A01G343500 chr2D 86.134 238 31 2 3446 3682 619831589 619831353 5.030000e-64 255.0
24 TraesCS3A01G343500 chr2D 84.647 241 29 7 3446 3682 351970680 351970916 2.360000e-57 233.0
25 TraesCS3A01G343500 chr2D 100.000 28 0 0 650 677 22836870 22836897 7.000000e-03 52.8
26 TraesCS3A01G343500 chr2B 77.885 416 89 1 128 543 55609365 55609777 5.030000e-64 255.0
27 TraesCS3A01G343500 chr2B 93.258 89 6 0 560 648 354729424 354729336 8.840000e-27 132.0
28 TraesCS3A01G343500 chr2B 100.000 28 0 0 650 677 391758636 391758609 7.000000e-03 52.8
29 TraesCS3A01G343500 chr4B 94.382 89 5 0 560 648 517983242 517983330 1.900000e-28 137.0
30 TraesCS3A01G343500 chr2A 93.333 90 5 1 560 648 729555240 729555151 8.840000e-27 132.0
31 TraesCS3A01G343500 chr2A 86.555 119 8 5 560 677 655281306 655281195 1.480000e-24 124.0
32 TraesCS3A01G343500 chr1D 93.258 89 6 0 560 648 318585629 318585717 8.840000e-27 132.0
33 TraesCS3A01G343500 chr4A 85.246 122 14 4 560 677 554638906 554638785 5.320000e-24 122.0
34 TraesCS3A01G343500 chr6A 100.000 28 0 0 649 676 66429134 66429107 7.000000e-03 52.8
35 TraesCS3A01G343500 chr6A 100.000 28 0 0 650 677 505355530 505355557 7.000000e-03 52.8


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 TraesCS3A01G343500 chr3A 592214609 592218530 3921 False 7243.000000 7243 100.000000 1 3922 1 chr3A.!!$F3 3921
1 TraesCS3A01G343500 chr3A 592170172 592172299 2127 False 3866.000000 3866 99.437000 1793 3922 1 chr3A.!!$F2 2129
2 TraesCS3A01G343500 chr3A 592143521 592145296 1775 False 3127.000000 3127 98.425000 1 1778 1 chr3A.!!$F1 1777
3 TraesCS3A01G343500 chr3D 449282187 449286194 4007 False 2258.500000 3166 92.776500 796 3922 2 chr3D.!!$F2 3126
4 TraesCS3A01G343500 chr3B 590451233 590455460 4227 False 1473.666667 2475 89.330333 1 3562 3 chr3B.!!$F2 3561

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
684 687 0.179215 GAAAGCGCATCGTGGACTTG 60.179 55.000 11.47 0.0 0.0 3.16 F
716 719 0.747255 CTCGGATACCACTGTCCCTG 59.253 60.000 0.00 0.0 0.0 4.45 F
1184 1190 1.226717 GGGCGTCTCTGTCGATGTC 60.227 63.158 0.00 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1750 1784 0.243907 CGTGGTCACTCACTCCGATT 59.756 55.0 0.00 0.0 35.63 3.34 R
1751 1785 1.595993 CCGTGGTCACTCACTCCGAT 61.596 60.0 0.00 0.0 35.63 4.18 R
3153 4055 4.260579 CGAGCTAGTCACAGACTATGAGTG 60.261 50.0 7.28 0.0 43.08 3.51 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
180 183 3.180984 GAAGCGTGTCTTCGTCAGT 57.819 52.632 0.00 0.00 41.48 3.41
413 416 3.797353 GGGGCGATGAAGGAGGCA 61.797 66.667 0.00 0.00 0.00 4.75
426 429 2.048127 AGGCACGCCTTCGACTTC 60.048 61.111 4.27 0.00 45.70 3.01
436 439 0.390472 CTTCGACTTCCTCCAGTGCC 60.390 60.000 0.00 0.00 0.00 5.01
451 454 0.248134 GTGCCTGTAGTCGTCGCTAG 60.248 60.000 0.00 0.00 0.00 3.42
610 613 0.249322 ATACGCGCATACACTCACCC 60.249 55.000 5.73 0.00 0.00 4.61
657 660 1.534175 CCACTATGAGCGAACGTCTCC 60.534 57.143 12.85 0.00 0.00 3.71
676 679 1.464687 CCTTTCACTGAAAGCGCATCG 60.465 52.381 21.67 6.82 45.19 3.84
684 687 0.179215 GAAAGCGCATCGTGGACTTG 60.179 55.000 11.47 0.00 0.00 3.16
716 719 0.747255 CTCGGATACCACTGTCCCTG 59.253 60.000 0.00 0.00 0.00 4.45
725 728 4.062490 ACCACTGTCCCTGTAACTATCT 57.938 45.455 0.00 0.00 0.00 1.98
868 874 3.288308 CTGACGGCAGAGGAGCGTT 62.288 63.158 14.96 0.00 45.17 4.84
1184 1190 1.226717 GGGCGTCTCTGTCGATGTC 60.227 63.158 0.00 0.00 0.00 3.06
1778 1812 1.535687 AGTGACCACGGGTAGCCTT 60.536 57.895 9.73 0.00 35.25 4.35
1779 1813 0.251922 AGTGACCACGGGTAGCCTTA 60.252 55.000 9.73 0.00 35.25 2.69
1780 1814 0.828677 GTGACCACGGGTAGCCTTAT 59.171 55.000 9.73 0.00 35.25 1.73
1781 1815 1.208776 GTGACCACGGGTAGCCTTATT 59.791 52.381 9.73 0.00 35.25 1.40
1782 1816 1.910671 TGACCACGGGTAGCCTTATTT 59.089 47.619 9.73 0.00 35.25 1.40
1783 1817 2.306512 TGACCACGGGTAGCCTTATTTT 59.693 45.455 9.73 0.00 35.25 1.82
1784 1818 2.941064 GACCACGGGTAGCCTTATTTTC 59.059 50.000 9.73 0.00 35.25 2.29
1786 1820 3.244981 ACCACGGGTAGCCTTATTTTCAA 60.245 43.478 9.73 0.00 32.11 2.69
1787 1821 3.951680 CCACGGGTAGCCTTATTTTCAAT 59.048 43.478 9.73 0.00 0.00 2.57
1788 1822 5.127491 CCACGGGTAGCCTTATTTTCAATA 58.873 41.667 9.73 0.00 0.00 1.90
1789 1823 5.008316 CCACGGGTAGCCTTATTTTCAATAC 59.992 44.000 9.73 0.00 0.00 1.89
1790 1824 5.587043 CACGGGTAGCCTTATTTTCAATACA 59.413 40.000 9.73 0.00 0.00 2.29
1795 2687 9.515226 GGGTAGCCTTATTTTCAATACATATGA 57.485 33.333 10.38 0.00 0.00 2.15
2952 3853 3.136123 CAGCCAATCAGCCACGGG 61.136 66.667 0.00 0.00 0.00 5.28
3153 4055 4.454717 CGCACGGCTTAAACGGCC 62.455 66.667 0.00 0.00 45.57 6.13
3850 4771 8.761497 CGTAAGGTTTCGTAAATCATCACATAT 58.239 33.333 0.00 0.00 0.00 1.78
3891 4812 6.995511 TTAGAAAGGTTATAGCGCACAAAT 57.004 33.333 11.47 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
180 183 1.008881 CGATCGAATCCCGCGAGAA 60.009 57.895 10.26 0.00 41.49 2.87
413 416 1.878656 CTGGAGGAAGTCGAAGGCGT 61.879 60.000 0.00 0.00 36.95 5.68
451 454 1.393539 CAATCATGTTCGTGGACCGTC 59.606 52.381 0.00 0.00 37.94 4.79
676 679 0.537371 CCACCAGGGTTCAAGTCCAC 60.537 60.000 0.00 0.00 0.00 4.02
700 703 3.105283 AGTTACAGGGACAGTGGTATCC 58.895 50.000 0.00 0.00 0.00 2.59
868 874 4.951715 TGGTGGAGCTAGTTTTATAGACGA 59.048 41.667 0.00 0.00 0.00 4.20
1147 1153 2.149578 CCTGAACACCTGAGAAAGCTG 58.850 52.381 0.00 0.00 0.00 4.24
1184 1190 3.294493 CACTGTTGCCGGGGTTGG 61.294 66.667 2.18 0.00 0.00 3.77
1750 1784 0.243907 CGTGGTCACTCACTCCGATT 59.756 55.000 0.00 0.00 35.63 3.34
1751 1785 1.595993 CCGTGGTCACTCACTCCGAT 61.596 60.000 0.00 0.00 35.63 4.18
1782 1816 8.349245 CGGGTAAGCAAATTCATATGTATTGAA 58.651 33.333 8.18 0.00 37.49 2.69
1783 1817 7.040755 CCGGGTAAGCAAATTCATATGTATTGA 60.041 37.037 8.18 0.00 0.00 2.57
1784 1818 7.040755 TCCGGGTAAGCAAATTCATATGTATTG 60.041 37.037 8.18 9.90 0.00 1.90
1786 1820 6.539173 TCCGGGTAAGCAAATTCATATGTAT 58.461 36.000 0.00 0.00 0.00 2.29
1787 1821 5.931294 TCCGGGTAAGCAAATTCATATGTA 58.069 37.500 0.00 0.00 0.00 2.29
1788 1822 4.787551 TCCGGGTAAGCAAATTCATATGT 58.212 39.130 0.00 0.00 0.00 2.29
1789 1823 5.766150 TTCCGGGTAAGCAAATTCATATG 57.234 39.130 0.00 0.00 0.00 1.78
1790 1824 7.724061 ACTTATTCCGGGTAAGCAAATTCATAT 59.276 33.333 20.55 2.53 33.47 1.78
1795 2687 9.010029 CATATACTTATTCCGGGTAAGCAAATT 57.990 33.333 20.55 8.97 33.47 1.82
3153 4055 4.260579 CGAGCTAGTCACAGACTATGAGTG 60.261 50.000 7.28 0.00 43.08 3.51
3866 4787 6.995511 TTGTGCGCTATAACCTTTCTAAAT 57.004 33.333 9.73 0.00 0.00 1.40
3891 4812 2.022764 TAGACCGAACGACGATGGTA 57.977 50.000 0.00 0.00 45.77 3.25


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

AutoCloner maintained by Alex Coulton.