Multiple sequence alignment - TraesCS5D01G415100

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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 TraesCS5D01G415100 chr5D 100.000 3131 0 0 1 3131 477327597 477330727 0.000000e+00 5782.0
1 TraesCS5D01G415100 chr5D 92.308 39 2 1 150 187 114976482 114976444 2.000000e-03 54.7
2 TraesCS5D01G415100 chr5B 94.324 2484 105 12 670 3131 585000049 585002518 0.000000e+00 3773.0
3 TraesCS5D01G415100 chr5B 90.681 279 20 4 11 288 584998843 584999116 1.770000e-97 366.0
4 TraesCS5D01G415100 chr5B 96.933 163 4 1 421 583 584999850 585000011 3.980000e-69 272.0
5 TraesCS5D01G415100 chr5B 93.902 82 5 0 277 358 584999502 584999583 1.180000e-24 124.0
6 TraesCS5D01G415100 chr5A 92.742 2535 121 23 488 2992 596559645 596562146 0.000000e+00 3603.0
7 TraesCS5D01G415100 chr5A 87.405 524 35 14 1 498 596559104 596559622 9.740000e-160 573.0
8 TraesCS5D01G415100 chr5A 88.660 97 11 0 3035 3131 596562145 596562241 5.490000e-23 119.0
9 TraesCS5D01G415100 chr1D 91.489 47 1 3 150 193 307409267 307409221 9.380000e-06 62.1
10 TraesCS5D01G415100 chr7D 91.111 45 1 3 156 198 623392355 623392312 1.210000e-04 58.4
11 TraesCS5D01G415100 chr7B 94.595 37 0 1 158 194 720810192 720810226 4.360000e-04 56.5
12 TraesCS5D01G415100 chr1A 96.970 33 1 0 155 187 49268492 49268460 4.360000e-04 56.5


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 TraesCS5D01G415100 chr5D 477327597 477330727 3130 False 5782.000000 5782 100.000000 1 3131 1 chr5D.!!$F1 3130
1 TraesCS5D01G415100 chr5B 584998843 585002518 3675 False 1133.750000 3773 93.960000 11 3131 4 chr5B.!!$F1 3120
2 TraesCS5D01G415100 chr5A 596559104 596562241 3137 False 1431.666667 3603 89.602333 1 3131 3 chr5A.!!$F1 3130

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
970 1640 1.074775 TCCCCCATCCGAACCCTAG 60.075 63.158 0.00 0.0 0.0 3.02 F
1500 2170 0.387929 TAATGGCCTTCTACTCCGCG 59.612 55.000 3.32 0.0 0.0 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 2482 0.731417 CACTGCCACTGCTATTGCTC 59.269 55.0 0.0 0.0 40.48 4.26 R
2942 3628 1.843368 ACCATGAAGCCATGTCCAAG 58.157 50.0 0.0 0.0 46.68 3.61 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
243 255 4.357142 CATAATTGCATGTGGTGAGAAGC 58.643 43.478 0.00 0.00 0.00 3.86
245 257 1.689984 TTGCATGTGGTGAGAAGCAA 58.310 45.000 0.00 0.00 39.38 3.91
351 758 3.140519 ACTCTATGGAACGGAGGGAGTAT 59.859 47.826 0.00 0.00 31.93 2.12
354 769 5.900437 TCTATGGAACGGAGGGAGTATAAT 58.100 41.667 0.00 0.00 0.00 1.28
363 778 7.860649 ACGGAGGGAGTATAATTTATTGGTA 57.139 36.000 0.00 0.00 0.00 3.25
400 815 2.651455 GGGGAAAACAGTAGTATGGGC 58.349 52.381 0.00 0.00 0.00 5.36
405 820 5.193679 GGAAAACAGTAGTATGGGCTTGAT 58.806 41.667 0.00 0.00 0.00 2.57
539 1190 4.999950 CCTGCATGTAGAGACAGAGTTTTT 59.000 41.667 12.93 0.00 39.50 1.94
583 1239 2.100631 CAATCGGCCCGGCGATATC 61.101 63.158 23.99 0.00 0.00 1.63
614 1276 5.643379 TTTTTGCGAGAAGGCATTATCTT 57.357 34.783 4.07 0.00 43.52 2.40
616 1278 4.621068 TTGCGAGAAGGCATTATCTTTG 57.379 40.909 4.07 0.00 43.52 2.77
619 1281 3.378427 GCGAGAAGGCATTATCTTTGGTT 59.622 43.478 4.07 0.00 0.00 3.67
620 1282 4.731773 GCGAGAAGGCATTATCTTTGGTTG 60.732 45.833 4.07 0.00 0.00 3.77
621 1283 4.676546 GAGAAGGCATTATCTTTGGTTGC 58.323 43.478 0.00 0.00 0.00 4.17
622 1284 3.129287 AGAAGGCATTATCTTTGGTTGCG 59.871 43.478 0.00 0.00 34.17 4.85
623 1285 1.750778 AGGCATTATCTTTGGTTGCGG 59.249 47.619 0.00 0.00 34.17 5.69
624 1286 1.748493 GGCATTATCTTTGGTTGCGGA 59.252 47.619 0.00 0.00 34.17 5.54
626 1288 3.179048 GCATTATCTTTGGTTGCGGAAC 58.821 45.455 11.85 11.85 0.00 3.62
627 1289 3.366883 GCATTATCTTTGGTTGCGGAACA 60.367 43.478 21.74 5.04 33.27 3.18
628 1290 4.804108 CATTATCTTTGGTTGCGGAACAA 58.196 39.130 21.74 7.60 33.27 2.83
629 1291 4.920640 TTATCTTTGGTTGCGGAACAAA 57.079 36.364 21.74 14.14 40.82 2.83
640 1302 1.187715 CGGAACAAAAACTGCACGTG 58.812 50.000 12.28 12.28 0.00 4.49
646 1308 3.498082 ACAAAAACTGCACGTGTCTTTC 58.502 40.909 18.38 0.00 0.00 2.62
699 1361 2.361610 ACGAAGCCCAGGCCATTG 60.362 61.111 5.01 0.00 43.17 2.82
912 1582 1.779061 AACCCATCACGGCAGTCCTT 61.779 55.000 0.00 0.00 0.00 3.36
918 1588 4.681978 ACGGCAGTCCTTCACGCC 62.682 66.667 0.00 0.00 39.76 5.68
969 1639 1.383525 GTCCCCCATCCGAACCCTA 60.384 63.158 0.00 0.00 0.00 3.53
970 1640 1.074775 TCCCCCATCCGAACCCTAG 60.075 63.158 0.00 0.00 0.00 3.02
971 1641 2.819284 CCCCCATCCGAACCCTAGC 61.819 68.421 0.00 0.00 0.00 3.42
1500 2170 0.387929 TAATGGCCTTCTACTCCGCG 59.612 55.000 3.32 0.00 0.00 6.46
1812 2482 2.287788 GGATAACAATGGCGATGGCAAG 60.288 50.000 1.01 0.00 42.43 4.01
1819 2489 0.107263 TGGCGATGGCAAGAGCAATA 60.107 50.000 12.81 0.00 44.61 1.90
1821 2491 0.040603 GCGATGGCAAGAGCAATAGC 60.041 55.000 0.00 0.00 43.91 2.97
1829 2499 1.400846 CAAGAGCAATAGCAGTGGCAG 59.599 52.381 0.00 0.00 45.49 4.85
1834 2504 1.746615 AATAGCAGTGGCAGTGGCG 60.747 57.895 22.98 0.00 44.61 5.69
1920 2590 6.183360 ACAGGAATTTTGTGCTTGATGTTACA 60.183 34.615 0.00 0.00 0.00 2.41
1941 2611 1.630878 GGGAGGGTGACATTTGAGACT 59.369 52.381 0.00 0.00 0.00 3.24
2083 2753 1.202521 TCGCCACGATCTGCATAACAT 60.203 47.619 0.00 0.00 0.00 2.71
2131 2801 2.280628 GATTCCTGGTTACCGCTTGAG 58.719 52.381 0.00 0.00 0.00 3.02
2159 2829 1.152333 AACAGGGTGGGGGCTTTTC 60.152 57.895 0.00 0.00 0.00 2.29
2195 2865 6.149129 TGCACATTGTTTATGTACAAACCA 57.851 33.333 0.00 0.00 45.71 3.67
2260 2932 0.965866 GCTGAAAGGGGGTACTTGGC 60.966 60.000 0.00 0.00 0.00 4.52
2377 3049 5.221303 CGGCATTATTTGGAATGGAGATGTT 60.221 40.000 0.00 0.00 37.31 2.71
2421 3093 7.500720 TGTATCACTGGCATCTTTATCATTG 57.499 36.000 0.00 0.00 0.00 2.82
2458 3130 9.746711 GATATCATCAATATCGAAAGTTTTCCG 57.253 33.333 0.00 0.00 37.55 4.30
2460 3132 5.878116 TCATCAATATCGAAAGTTTTCCGGT 59.122 36.000 0.00 0.00 33.68 5.28
2608 3288 6.347696 TGAATGCTTTGTTTGGATTCAAAGT 58.652 32.000 15.60 0.99 44.86 2.66
2745 3431 7.639113 TGAATGGGATCTTACAAACATTACC 57.361 36.000 0.00 0.00 0.00 2.85
2752 3438 6.766467 GGATCTTACAAACATTACCCTAGTGG 59.234 42.308 0.00 0.00 41.37 4.00
2801 3487 1.777272 CCCCTCCTCCCCAAAGATAAG 59.223 57.143 0.00 0.00 0.00 1.73
2856 3542 7.464178 CGTCTTAGTTTACATGATACAGTTGCC 60.464 40.741 0.00 0.00 0.00 4.52
2857 3543 7.333423 GTCTTAGTTTACATGATACAGTTGCCA 59.667 37.037 0.00 0.00 0.00 4.92
2864 3550 3.641437 TGATACAGTTGCCAAAACAGC 57.359 42.857 0.00 0.00 0.00 4.40
2890 3576 8.684386 TTTTGACATACTGGTGTTAGATTTGA 57.316 30.769 0.00 0.00 31.16 2.69
2891 3577 7.667043 TTGACATACTGGTGTTAGATTTGAC 57.333 36.000 0.00 0.00 31.16 3.18
2926 3612 7.994425 TTGCATATTGTTTCTCTAACTTCCA 57.006 32.000 0.00 0.00 37.64 3.53
2942 3628 9.063615 TCTAACTTCCATTTTAAACTGTTCCTC 57.936 33.333 5.01 0.00 0.00 3.71
2992 3678 5.625150 AGAAAAGAAACTGCAGTATCCACT 58.375 37.500 22.01 11.93 34.42 4.00
3119 3805 5.978814 ACTCTGACACTTTGTGAAGTTAGT 58.021 37.500 4.61 0.92 43.48 2.24
3121 3807 5.116180 TCTGACACTTTGTGAAGTTAGTGG 58.884 41.667 4.61 0.00 43.48 4.00
3126 3812 6.357367 ACACTTTGTGAAGTTAGTGGAAGAT 58.643 36.000 4.61 0.00 43.48 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 7.741027 ATTATCATGCTCCAGTCACATTTAG 57.259 36.000 0.00 0.00 0.00 1.85
243 255 9.449719 ACTAAATAGGTGATCCTTGTTAACTTG 57.550 33.333 7.22 0.00 42.12 3.16
310 717 9.831737 CATAGAGTTTAGTTCAAATTTGGACTG 57.168 33.333 33.40 16.01 46.27 3.51
383 798 5.648092 ACATCAAGCCCATACTACTGTTTTC 59.352 40.000 0.00 0.00 0.00 2.29
400 815 4.860907 GGCATTCAGCTTTGTAACATCAAG 59.139 41.667 0.00 0.00 44.79 3.02
405 820 5.252547 TCTATGGCATTCAGCTTTGTAACA 58.747 37.500 4.78 0.00 44.79 2.41
539 1190 8.567285 CCTCTATGGCTTCTCTTAAAAGAAAA 57.433 34.615 0.00 0.00 34.95 2.29
607 1269 5.461032 TTTGTTCCGCAACCAAAGATAAT 57.539 34.783 0.00 0.00 36.72 1.28
612 1274 3.061965 CAGTTTTTGTTCCGCAACCAAAG 59.938 43.478 0.00 0.00 36.72 2.77
614 1276 2.611518 CAGTTTTTGTTCCGCAACCAA 58.388 42.857 0.00 0.00 36.72 3.67
616 1278 0.927537 GCAGTTTTTGTTCCGCAACC 59.072 50.000 0.00 0.00 36.72 3.77
619 1281 0.524392 CGTGCAGTTTTTGTTCCGCA 60.524 50.000 0.00 0.00 0.00 5.69
620 1282 0.524604 ACGTGCAGTTTTTGTTCCGC 60.525 50.000 0.00 0.00 0.00 5.54
621 1283 1.187715 CACGTGCAGTTTTTGTTCCG 58.812 50.000 0.82 0.00 0.00 4.30
622 1284 2.159435 AGACACGTGCAGTTTTTGTTCC 60.159 45.455 17.22 0.00 0.00 3.62
623 1285 3.131240 AGACACGTGCAGTTTTTGTTC 57.869 42.857 17.22 1.04 0.00 3.18
624 1286 3.569250 AAGACACGTGCAGTTTTTGTT 57.431 38.095 17.22 0.00 0.00 2.83
626 1288 3.758300 AGAAAGACACGTGCAGTTTTTG 58.242 40.909 17.22 0.00 0.00 2.44
627 1289 3.485216 CGAGAAAGACACGTGCAGTTTTT 60.485 43.478 17.22 7.96 0.00 1.94
628 1290 2.030457 CGAGAAAGACACGTGCAGTTTT 59.970 45.455 17.22 10.87 0.00 2.43
629 1291 1.593006 CGAGAAAGACACGTGCAGTTT 59.407 47.619 17.22 12.57 0.00 2.66
640 1302 2.467566 TACTTTGGGCCGAGAAAGAC 57.532 50.000 21.23 0.00 34.02 3.01
646 1308 2.158813 ACCATACATACTTTGGGCCGAG 60.159 50.000 0.00 1.53 34.72 4.63
699 1361 1.593265 CTGTGGATTTTGGGGCTGC 59.407 57.895 0.00 0.00 0.00 5.25
854 1524 0.944311 CGCCGATAAAGACGATGGGG 60.944 60.000 0.00 0.00 0.00 4.96
912 1582 4.794439 CGGATGAGCGTGGCGTGA 62.794 66.667 0.00 0.00 0.00 4.35
951 1621 1.383525 TAGGGTTCGGATGGGGGAC 60.384 63.158 0.00 0.00 0.00 4.46
969 1639 4.335647 CTGGTCAACGGGGCTGCT 62.336 66.667 0.00 0.00 0.00 4.24
1728 2398 1.455849 CAAAGTCTCCACTGCCCCA 59.544 57.895 0.00 0.00 31.06 4.96
1804 2474 2.033049 CACTGCTATTGCTCTTGCCATC 59.967 50.000 0.00 0.00 40.48 3.51
1812 2482 0.731417 CACTGCCACTGCTATTGCTC 59.269 55.000 0.00 0.00 40.48 4.26
1821 2491 2.816958 CTAGCGCCACTGCCACTG 60.817 66.667 2.29 0.00 34.65 3.66
1847 2517 2.606519 TCTCCACCCACCCTTCCG 60.607 66.667 0.00 0.00 0.00 4.30
1920 2590 1.630878 GTCTCAAATGTCACCCTCCCT 59.369 52.381 0.00 0.00 0.00 4.20
1941 2611 5.066375 CACAAACTCAAGAAATGACCTCACA 59.934 40.000 0.00 0.00 33.47 3.58
1992 2662 1.004918 CACGGTGTCCCCACTCTTC 60.005 63.158 0.00 0.00 41.53 2.87
2028 2698 1.607148 TCACTCATATACCTCACGGCG 59.393 52.381 4.80 4.80 0.00 6.46
2083 2753 1.109609 TTCAACACATGCAGGCACAA 58.890 45.000 0.00 0.00 0.00 3.33
2131 2801 1.582968 CACCCTGTTGACTGCATGC 59.417 57.895 11.82 11.82 0.00 4.06
2159 2829 6.630676 AACAATGTGCAAATAATACAAGCG 57.369 33.333 0.00 0.00 0.00 4.68
2260 2932 4.660789 AAGCCATAATAAAGCCTTGCAG 57.339 40.909 0.00 0.00 0.00 4.41
2275 2947 2.901291 ACAACCCCAAACATAAGCCAT 58.099 42.857 0.00 0.00 0.00 4.40
2456 3128 5.219633 CAAGACAATTAGGAAACAAACCGG 58.780 41.667 0.00 0.00 0.00 5.28
2458 3130 8.487313 AAAACAAGACAATTAGGAAACAAACC 57.513 30.769 0.00 0.00 0.00 3.27
2545 3220 7.604927 TGAGGACGTTAAGCTATGTTTTACATT 59.395 33.333 0.00 0.00 39.88 2.71
2550 3225 7.174253 TGAAATGAGGACGTTAAGCTATGTTTT 59.826 33.333 0.00 0.00 0.00 2.43
2631 3312 4.579454 TTTCGTCCCGAATCTACATAGG 57.421 45.455 0.00 0.00 45.28 2.57
2645 3326 5.701290 CAGGATGGATAATAGGTTTTCGTCC 59.299 44.000 0.00 0.00 0.00 4.79
2648 3329 6.055588 ACACAGGATGGATAATAGGTTTTCG 58.944 40.000 0.00 0.00 43.62 3.46
2651 3332 7.691993 AGTACACAGGATGGATAATAGGTTT 57.308 36.000 0.00 0.00 43.62 3.27
2697 3383 7.874528 TCAATATGTGATACCTACTGCTTCATG 59.125 37.037 0.00 0.00 0.00 3.07
2745 3431 4.360563 GACAATACATCGACACCACTAGG 58.639 47.826 0.00 0.00 42.21 3.02
2785 3471 7.136885 TGTTAGTATCTTATCTTTGGGGAGGA 58.863 38.462 0.00 0.00 0.00 3.71
2786 3472 7.290248 TCTGTTAGTATCTTATCTTTGGGGAGG 59.710 40.741 0.00 0.00 0.00 4.30
2787 3473 8.251383 TCTGTTAGTATCTTATCTTTGGGGAG 57.749 38.462 0.00 0.00 0.00 4.30
2788 3474 8.798975 ATCTGTTAGTATCTTATCTTTGGGGA 57.201 34.615 0.00 0.00 0.00 4.81
2815 3501 4.773149 ACTAAGACGGAGGAACTGAAATCT 59.227 41.667 0.00 0.00 41.55 2.40
2857 3543 5.127031 ACACCAGTATGTCAAAAGCTGTTTT 59.873 36.000 0.00 0.00 36.22 2.43
2864 3550 8.783093 TCAAATCTAACACCAGTATGTCAAAAG 58.217 33.333 0.00 0.00 30.55 2.27
2890 3576 8.090214 AGAAACAATATGCAATTAACAAGCAGT 58.910 29.630 0.00 0.00 42.14 4.40
2891 3577 8.470040 AGAAACAATATGCAATTAACAAGCAG 57.530 30.769 0.00 0.00 42.14 4.24
2942 3628 1.843368 ACCATGAAGCCATGTCCAAG 58.157 50.000 0.00 0.00 46.68 3.61
2992 3678 2.142292 GAAGGCCCCTCCAAAGCTCA 62.142 60.000 0.00 0.00 37.29 4.26
3093 3779 8.038944 ACTAACTTCACAAAGTGTCAGAGTTAA 58.961 33.333 13.30 0.00 45.07 2.01


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

AutoCloner maintained by Alex Coulton.