Multiple sequence alignment - TraesCS4D01G259300

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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 TraesCS4D01G259300 chr4D 100.000 3968 0 0 1 3968 428726812 428730779 0.000000e+00 7328
1 TraesCS4D01G259300 chr4B 91.276 3416 194 50 1 3356 526727179 526723808 0.000000e+00 4562
2 TraesCS4D01G259300 chr4B 85.209 311 37 6 3597 3901 339154741 339155048 1.070000e-80 311
3 TraesCS4D01G259300 chr4A 94.211 2021 78 18 1 2004 37776667 37774669 0.000000e+00 3048
4 TraesCS4D01G259300 chr4A 97.553 1594 28 5 1990 3574 37774518 37772927 0.000000e+00 2717
5 TraesCS4D01G259300 chr4A 94.074 270 10 3 3566 3829 37771660 37771391 4.770000e-109 405
6 TraesCS4D01G259300 chr4A 94.483 145 7 1 3825 3968 37771089 37770945 5.160000e-54 222
7 TraesCS4D01G259300 chr6D 86.218 312 34 6 3596 3901 281921924 281921616 2.960000e-86 329
8 TraesCS4D01G259300 chr6B 84.543 317 35 10 3597 3905 364745316 364745626 6.440000e-78 302


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 TraesCS4D01G259300 chr4D 428726812 428730779 3967 False 7328 7328 100.00000 1 3968 1 chr4D.!!$F1 3967
1 TraesCS4D01G259300 chr4B 526723808 526727179 3371 True 4562 4562 91.27600 1 3356 1 chr4B.!!$R1 3355
2 TraesCS4D01G259300 chr4A 37770945 37776667 5722 True 1598 3048 95.08025 1 3968 4 chr4A.!!$R1 3967

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
868 872 0.670854 GTCAGGGAAACTCGGAGTGC 60.671 60.000 12.12 7.05 0.00 4.40 F
1795 1823 0.178981 AAGTGATTGCAGTGCCCACT 60.179 50.000 21.65 21.65 43.61 4.00 F
1835 1863 2.489329 GCTTGTGATGCATGGTTAGTGT 59.511 45.455 2.46 0.00 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2286 2487 0.654683 GGACATCAGCAACGCAGATC 59.345 55.000 0.00 0.0 32.63 2.75 R
2879 3110 2.100749 TGTATCCGTGTCAGCGATTCAT 59.899 45.455 0.00 0.0 0.00 2.57 R
3766 5289 2.165030 CCATGGCCATTCTCAACACTTC 59.835 50.000 17.92 0.0 0.00 3.01 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
86 87 6.035843 CAGGGTATTGCACATTCATGTAAAC 58.964 40.000 0.00 0.00 39.39 2.01
97 98 7.677276 GCACATTCATGTAAACTCTACCATCAC 60.677 40.741 0.00 0.00 39.39 3.06
270 271 8.494347 GTCTGTTATGCTAAAGCTCTGAATATG 58.506 37.037 3.26 0.00 42.66 1.78
868 872 0.670854 GTCAGGGAAACTCGGAGTGC 60.671 60.000 12.12 7.05 0.00 4.40
879 884 3.334054 GGAGTGCCTTCCCCTGCT 61.334 66.667 0.00 0.00 0.00 4.24
905 920 2.598686 GGATACGTTTGACTCCTCCC 57.401 55.000 0.00 0.00 0.00 4.30
906 921 2.108970 GGATACGTTTGACTCCTCCCT 58.891 52.381 0.00 0.00 0.00 4.20
907 922 2.500504 GGATACGTTTGACTCCTCCCTT 59.499 50.000 0.00 0.00 0.00 3.95
908 923 3.055312 GGATACGTTTGACTCCTCCCTTT 60.055 47.826 0.00 0.00 0.00 3.11
909 924 2.256117 ACGTTTGACTCCTCCCTTTG 57.744 50.000 0.00 0.00 0.00 2.77
910 925 1.489230 ACGTTTGACTCCTCCCTTTGT 59.511 47.619 0.00 0.00 0.00 2.83
912 927 2.548480 CGTTTGACTCCTCCCTTTGTTC 59.452 50.000 0.00 0.00 0.00 3.18
913 928 3.744530 CGTTTGACTCCTCCCTTTGTTCT 60.745 47.826 0.00 0.00 0.00 3.01
914 929 4.502604 CGTTTGACTCCTCCCTTTGTTCTA 60.503 45.833 0.00 0.00 0.00 2.10
916 931 5.640158 TTGACTCCTCCCTTTGTTCTAAA 57.360 39.130 0.00 0.00 0.00 1.85
917 932 5.843019 TGACTCCTCCCTTTGTTCTAAAT 57.157 39.130 0.00 0.00 0.00 1.40
1102 1120 2.031258 ATCTCTCTTCGTCTCTGCGA 57.969 50.000 0.00 0.00 39.28 5.10
1108 1126 2.614520 CTCTTCGTCTCTGCGATTCCTA 59.385 50.000 0.00 0.00 40.76 2.94
1174 1192 1.884067 GCTAGGCAGCTTGTTGTTCCT 60.884 52.381 0.00 0.00 44.93 3.36
1185 1203 5.001232 GCTTGTTGTTCCTATGGTACTGAA 58.999 41.667 0.00 0.00 0.00 3.02
1189 1207 6.774673 TGTTGTTCCTATGGTACTGAATTCA 58.225 36.000 8.12 8.12 0.00 2.57
1367 1392 8.773033 ATCCCTTTTATTTAGCACATGAGAAT 57.227 30.769 0.00 0.00 0.00 2.40
1368 1393 8.593945 TCCCTTTTATTTAGCACATGAGAATT 57.406 30.769 0.00 0.00 0.00 2.17
1369 1394 9.693739 TCCCTTTTATTTAGCACATGAGAATTA 57.306 29.630 0.00 0.00 0.00 1.40
1370 1395 9.956720 CCCTTTTATTTAGCACATGAGAATTAG 57.043 33.333 0.00 0.00 0.00 1.73
1492 1518 4.260170 TGCTCTTTTTGTTTGGCATTTGT 58.740 34.783 0.00 0.00 0.00 2.83
1511 1537 3.133691 TGTCTGCTGCTTACTGAAGTTG 58.866 45.455 0.00 0.00 34.90 3.16
1795 1823 0.178981 AAGTGATTGCAGTGCCCACT 60.179 50.000 21.65 21.65 43.61 4.00
1835 1863 2.489329 GCTTGTGATGCATGGTTAGTGT 59.511 45.455 2.46 0.00 0.00 3.55
1896 1927 3.595709 TGCCTTCTTTTAAACGTCGTG 57.404 42.857 0.00 0.00 0.00 4.35
2203 2404 3.889815 TGGGTTCATCCATGATTCACTC 58.110 45.455 0.00 0.00 36.56 3.51
2428 2629 8.665685 GGGATACTACACTACATTTCAGTTTTG 58.334 37.037 0.00 0.00 0.00 2.44
2879 3110 9.431887 GTCTTAAGTACAGTATCCAAATTGACA 57.568 33.333 1.63 0.00 0.00 3.58
3047 3281 7.862372 TGATGTTCTTTGTGATTTTACTCTTGC 59.138 33.333 0.00 0.00 0.00 4.01
3060 3294 5.694231 TTACTCTTGCGTCACTGTAACTA 57.306 39.130 0.00 0.00 0.00 2.24
3082 3316 9.476202 AACTATTTGGTTGAAGCATTAGTTTTC 57.524 29.630 19.05 0.00 34.30 2.29
3121 3356 1.346395 ACGACAATGCCCTTACAGACA 59.654 47.619 0.00 0.00 0.00 3.41
3415 3658 0.179000 CTTGGCATCTAGGGCGTTCT 59.821 55.000 0.00 0.00 35.84 3.01
3513 3756 8.514330 ACAATAGTTGACTACTTTTCCAACAA 57.486 30.769 0.00 0.00 40.77 2.83
3522 3765 8.361139 TGACTACTTTTCCAACAAAAGTTTGAA 58.639 29.630 15.61 0.00 45.20 2.69
3558 3801 0.321653 ACAGATCGACCAAAGCCCAC 60.322 55.000 0.00 0.00 0.00 4.61
3653 5171 7.214381 TCGTCCTGGTCTTATGGTTTTATATG 58.786 38.462 0.00 0.00 0.00 1.78
3712 5230 6.096282 TGAGTATGCTAGCACTACAATACACA 59.904 38.462 22.07 17.88 0.00 3.72
3717 5235 5.408299 TGCTAGCACTACAATACACAGTTTG 59.592 40.000 14.93 0.00 0.00 2.93
3739 5257 7.670009 TTGTTGCAGGAAATAAAATTGATGG 57.330 32.000 0.00 0.00 0.00 3.51
3761 5284 8.691661 ATGGTTACATCATATCACCTTAAACC 57.308 34.615 0.00 0.00 34.58 3.27
3766 5289 7.496529 ACATCATATCACCTTAAACCGATTG 57.503 36.000 0.00 0.00 0.00 2.67
3782 5305 3.426695 CCGATTGAAGTGTTGAGAATGGC 60.427 47.826 0.00 0.00 0.00 4.40
3785 5308 3.159213 TGAAGTGTTGAGAATGGCCAT 57.841 42.857 14.09 14.09 0.00 4.40
3829 5353 4.385825 AGAATGCTTTCCAACAACTACGA 58.614 39.130 8.62 0.00 31.84 3.43
3830 5354 4.213482 AGAATGCTTTCCAACAACTACGAC 59.787 41.667 8.62 0.00 31.84 4.34
3831 5355 1.862201 TGCTTTCCAACAACTACGACG 59.138 47.619 0.00 0.00 0.00 5.12
3832 5356 1.862827 GCTTTCCAACAACTACGACGT 59.137 47.619 5.52 5.52 0.00 4.34
3833 5357 2.097056 GCTTTCCAACAACTACGACGTC 60.097 50.000 2.43 5.18 0.00 4.34
3834 5358 2.867287 TTCCAACAACTACGACGTCA 57.133 45.000 17.16 0.00 0.00 4.35
3835 5359 2.410785 TCCAACAACTACGACGTCAG 57.589 50.000 17.16 8.90 0.00 3.51
3855 5686 7.174946 ACGTCAGATGACATTTTACCAATCTTT 59.825 33.333 13.09 0.00 44.99 2.52
3884 5715 6.931840 GGGCCAAAATTGTAGTTTGTGAATAA 59.068 34.615 4.39 0.00 34.75 1.40
3943 5774 5.046910 ACTGGTCAATTTTACATTCAGCG 57.953 39.130 0.00 0.00 0.00 5.18
3962 5793 4.269123 CAGCGCCGTATGTACAATCTTTAA 59.731 41.667 2.29 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 7.596749 AGTTTAAATGTTCGTGATGGTAGAG 57.403 36.000 0.00 0.00 0.00 2.43
97 98 6.176975 TGCAGGTCATAGTTTAAATGTTCG 57.823 37.500 0.00 0.00 0.00 3.95
207 208 8.507249 GTTGACATTTTAAAGTGTGAGCTAGAT 58.493 33.333 19.70 0.00 0.00 1.98
840 844 3.190738 TTTCCCTGACAGGTGGGCG 62.191 63.158 20.24 4.60 43.04 6.13
857 861 2.593956 GGGGAAGGCACTCCGAGTT 61.594 63.158 0.00 0.00 38.49 3.01
868 872 1.153289 CGACATGAGCAGGGGAAGG 60.153 63.158 0.00 0.00 0.00 3.46
879 884 3.428452 GGAGTCAAACGTATCCGACATGA 60.428 47.826 0.00 0.00 37.88 3.07
905 920 9.399403 GAACCTGAGCTTTTATTTAGAACAAAG 57.601 33.333 0.00 0.00 0.00 2.77
906 921 9.131791 AGAACCTGAGCTTTTATTTAGAACAAA 57.868 29.630 0.00 0.00 0.00 2.83
907 922 8.691661 AGAACCTGAGCTTTTATTTAGAACAA 57.308 30.769 0.00 0.00 0.00 2.83
908 923 7.390718 GGAGAACCTGAGCTTTTATTTAGAACA 59.609 37.037 0.00 0.00 0.00 3.18
909 924 7.608376 AGGAGAACCTGAGCTTTTATTTAGAAC 59.392 37.037 0.00 0.00 45.92 3.01
910 925 7.690256 AGGAGAACCTGAGCTTTTATTTAGAA 58.310 34.615 0.00 0.00 45.92 2.10
1064 1081 1.035932 TACGTACCTCTGAGCCAGCC 61.036 60.000 0.00 0.00 0.00 4.85
1102 1120 1.143073 GGGGAGCAAACGGATAGGAAT 59.857 52.381 0.00 0.00 0.00 3.01
1108 1126 1.222567 ATTAGGGGGAGCAAACGGAT 58.777 50.000 0.00 0.00 0.00 4.18
1325 1350 8.655935 AAAAGGGATTTCAGTGAATAACAGAT 57.344 30.769 6.36 0.00 0.00 2.90
1369 1394 9.726438 AACAGCTTAATCAAACTAACAGATACT 57.274 29.630 0.00 0.00 0.00 2.12
1380 1405 8.000780 AGGATTCCATAACAGCTTAATCAAAC 57.999 34.615 5.29 0.00 0.00 2.93
1388 1413 6.302269 CCTTATGAGGATTCCATAACAGCTT 58.698 40.000 5.29 0.00 46.74 3.74
1474 1500 4.590226 GCAGACAAATGCCAAACAAAAAG 58.410 39.130 0.00 0.00 40.43 2.27
1492 1518 2.146342 GCAACTTCAGTAAGCAGCAGA 58.854 47.619 0.00 0.00 36.40 4.26
1535 1563 8.751335 CACAACACCTCAATAAAATAAACACAC 58.249 33.333 0.00 0.00 0.00 3.82
1542 1570 9.308000 AGGATTTCACAACACCTCAATAAAATA 57.692 29.630 0.00 0.00 0.00 1.40
1556 1584 3.081804 ACCCGAATGAGGATTTCACAAC 58.918 45.455 0.00 0.00 38.99 3.32
1786 1814 4.262463 CCGTATATTGTATCAGTGGGCACT 60.262 45.833 0.00 0.00 43.61 4.40
1795 1823 6.037720 CACAAGCAAACCCGTATATTGTATCA 59.962 38.462 0.00 0.00 0.00 2.15
1835 1863 8.564574 TCTTAGCGCAAAGAGAAATTAAGAAAA 58.435 29.630 11.47 0.00 31.85 2.29
1937 1968 6.095440 GGATTTTCTGTGCTATACAACCACAT 59.905 38.462 0.00 0.00 39.20 3.21
2203 2404 6.075918 CAGAACTGTCATGACGAGAATTTTG 58.924 40.000 23.48 13.95 0.00 2.44
2286 2487 0.654683 GGACATCAGCAACGCAGATC 59.345 55.000 0.00 0.00 32.63 2.75
2428 2629 5.339990 TGCAGTTTAACAAAGAAGCTTGAC 58.660 37.500 2.10 0.00 0.00 3.18
2879 3110 2.100749 TGTATCCGTGTCAGCGATTCAT 59.899 45.455 0.00 0.00 0.00 2.57
2983 3215 8.576442 ACAACCTAATTAAACAGGAAATGAGTG 58.424 33.333 11.62 2.77 35.76 3.51
3047 3281 6.533819 TTCAACCAAATAGTTACAGTGACG 57.466 37.500 0.00 0.00 0.00 4.35
3060 3294 7.657354 GGAAGAAAACTAATGCTTCAACCAAAT 59.343 33.333 0.00 0.00 38.72 2.32
3081 3315 6.103997 GTCGTGGATATTGTTACAAGGAAGA 58.896 40.000 3.63 0.00 0.00 2.87
3082 3316 5.872617 TGTCGTGGATATTGTTACAAGGAAG 59.127 40.000 3.63 0.00 0.00 3.46
3121 3356 6.054860 ACTGAAGGTTACAGTAGATTGCAT 57.945 37.500 0.00 0.00 45.10 3.96
3174 3409 2.936498 GCATACGAGTGCCACTGTAATT 59.064 45.455 0.00 0.00 39.18 1.40
3369 3612 3.364549 ACCAATCAACATACCACCATGG 58.635 45.455 11.19 11.19 45.02 3.66
3370 3613 5.450412 GCTAACCAATCAACATACCACCATG 60.450 44.000 0.00 0.00 0.00 3.66
3372 3615 4.013728 GCTAACCAATCAACATACCACCA 58.986 43.478 0.00 0.00 0.00 4.17
3373 3616 4.013728 TGCTAACCAATCAACATACCACC 58.986 43.478 0.00 0.00 0.00 4.61
3380 3623 2.295909 GCCAAGTGCTAACCAATCAACA 59.704 45.455 0.00 0.00 36.87 3.33
3522 3765 7.810282 GTCGATCTGTACACATAGCTTCATATT 59.190 37.037 0.00 0.00 0.00 1.28
3528 3771 3.699538 TGGTCGATCTGTACACATAGCTT 59.300 43.478 0.00 0.00 0.00 3.74
3558 3801 9.250624 GAAATCACTAGTAAATACTACAGGCAG 57.749 37.037 0.00 0.00 37.73 4.85
3678 5196 6.065374 AGTGCTAGCATACTCACTATACACT 58.935 40.000 22.51 4.74 37.94 3.55
3712 5230 8.776470 CATCAATTTTATTTCCTGCAACAAACT 58.224 29.630 0.00 0.00 0.00 2.66
3717 5235 7.671495 AACCATCAATTTTATTTCCTGCAAC 57.329 32.000 0.00 0.00 0.00 4.17
3739 5257 8.603242 ATCGGTTTAAGGTGATATGATGTAAC 57.397 34.615 0.00 0.00 0.00 2.50
3747 5265 7.110155 ACACTTCAATCGGTTTAAGGTGATAT 58.890 34.615 7.24 0.00 0.00 1.63
3761 5284 3.426695 GGCCATTCTCAACACTTCAATCG 60.427 47.826 0.00 0.00 0.00 3.34
3766 5289 2.165030 CCATGGCCATTCTCAACACTTC 59.835 50.000 17.92 0.00 0.00 3.01
3831 5355 7.274250 GCAAAGATTGGTAAAATGTCATCTGAC 59.726 37.037 3.34 3.34 44.97 3.51
3832 5356 7.177216 AGCAAAGATTGGTAAAATGTCATCTGA 59.823 33.333 0.00 0.00 40.04 3.27
3833 5357 7.274904 CAGCAAAGATTGGTAAAATGTCATCTG 59.725 37.037 0.00 0.00 39.79 2.90
3834 5358 7.318141 CAGCAAAGATTGGTAAAATGTCATCT 58.682 34.615 0.00 0.00 39.79 2.90
3835 5359 6.532657 CCAGCAAAGATTGGTAAAATGTCATC 59.467 38.462 0.00 0.00 39.79 2.92
3855 5686 2.008242 ACTACAATTTTGGCCCAGCA 57.992 45.000 0.00 0.00 0.00 4.41
3943 5774 4.758561 CGCTTAAAGATTGTACATACGGC 58.241 43.478 0.00 0.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.