Multiple sequence alignment - TraesCS5D01G338800

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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 TraesCS5D01G338800 chr5D 100.000 2822 0 0 1 2822 428373767 428376588 0.000000e+00 5212.0
1 TraesCS5D01G338800 chr5D 81.687 415 55 15 979 1379 428307032 428307439 2.710000e-85 326.0
2 TraesCS5D01G338800 chr5D 76.012 667 119 28 1 640 200903128 200903780 9.820000e-80 307.0
3 TraesCS5D01G338800 chr5D 85.926 135 11 6 2295 2424 428308363 428308494 1.360000e-28 137.0
4 TraesCS5D01G338800 chr5A 93.521 1991 66 15 873 2822 543916168 543918136 0.000000e+00 2904.0
5 TraesCS5D01G338800 chr5A 92.903 775 46 2 1 766 543915191 543915965 0.000000e+00 1118.0
6 TraesCS5D01G338800 chr5A 82.913 357 45 11 1035 1379 543714066 543714418 9.820000e-80 307.0
7 TraesCS5D01G338800 chr5A 84.444 135 13 7 2295 2424 543715330 543715461 2.950000e-25 126.0
8 TraesCS5D01G338800 chr5A 78.906 128 22 5 2290 2414 541941098 541941223 6.480000e-12 82.4
9 TraesCS5D01G338800 chr5B 90.530 1605 93 11 1140 2711 517557148 517558726 0.000000e+00 2067.0
10 TraesCS5D01G338800 chr5B 82.126 414 52 16 979 1379 517503416 517503820 4.500000e-88 335.0
11 TraesCS5D01G338800 chr5B 81.221 213 32 6 647 854 517546732 517546941 6.250000e-37 165.0
12 TraesCS5D01G338800 chr7D 82.055 652 88 16 1 640 595787951 595787317 1.930000e-146 529.0
13 TraesCS5D01G338800 chr1D 87.405 262 32 1 208 468 189426162 189426423 1.640000e-77 300.0
14 TraesCS5D01G338800 chr1A 78.208 491 90 10 138 612 104197300 104196811 5.910000e-77 298.0
15 TraesCS5D01G338800 chr2D 77.326 516 85 20 138 630 636009560 636009054 2.770000e-70 276.0
16 TraesCS5D01G338800 chr6D 77.108 498 90 20 138 617 372046354 372045863 1.670000e-67 267.0
17 TraesCS5D01G338800 chr6D 79.540 391 58 17 1 378 312551918 312551537 2.790000e-65 259.0
18 TraesCS5D01G338800 chr6A 79.070 387 60 17 1 375 449154487 449154110 2.170000e-61 246.0
19 TraesCS5D01G338800 chr3A 76.667 420 77 17 66 472 498747127 498746716 2.200000e-51 213.0
20 TraesCS5D01G338800 chr7A 79.412 136 26 2 496 630 77354312 77354446 8.320000e-16 95.3


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 TraesCS5D01G338800 chr5D 428373767 428376588 2821 False 5212.0 5212 100.0000 1 2822 1 chr5D.!!$F2 2821
1 TraesCS5D01G338800 chr5D 200903128 200903780 652 False 307.0 307 76.0120 1 640 1 chr5D.!!$F1 639
2 TraesCS5D01G338800 chr5D 428307032 428308494 1462 False 231.5 326 83.8065 979 2424 2 chr5D.!!$F3 1445
3 TraesCS5D01G338800 chr5A 543915191 543918136 2945 False 2011.0 2904 93.2120 1 2822 2 chr5A.!!$F3 2821
4 TraesCS5D01G338800 chr5A 543714066 543715461 1395 False 216.5 307 83.6785 1035 2424 2 chr5A.!!$F2 1389
5 TraesCS5D01G338800 chr5B 517557148 517558726 1578 False 2067.0 2067 90.5300 1140 2711 1 chr5B.!!$F3 1571
6 TraesCS5D01G338800 chr7D 595787317 595787951 634 True 529.0 529 82.0550 1 640 1 chr7D.!!$R1 639
7 TraesCS5D01G338800 chr2D 636009054 636009560 506 True 276.0 276 77.3260 138 630 1 chr2D.!!$R1 492

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
835 907 0.109873 ACGAGCGTGAAACTAGACCG 60.11 55.0 0.0 0.0 31.75 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2652 2937 0.542232 ACCAAGCTAGACGGTGGAGT 60.542 55.0 6.87 0.0 0.0 3.85 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
140 143 6.672218 TGAATTAATAGAGAGTGGACTTGGGA 59.328 38.462 0.00 0.00 0.00 4.37
167 170 8.598916 CATAGGTTCACTAGAGGTATCTCTCTA 58.401 40.741 9.32 3.37 46.79 2.43
196 201 0.863957 CAAACGGCGTGGTGACAAAC 60.864 55.000 15.70 0.00 46.06 2.93
480 504 7.174253 ACAACAATACAATATGTGTTTCGTCCT 59.826 33.333 0.00 0.00 41.98 3.85
510 548 1.079127 CACCGCGAGATTGAACCCT 60.079 57.895 8.23 0.00 0.00 4.34
530 568 2.501723 CTGTACTATGCACCACTCCCTT 59.498 50.000 0.00 0.00 0.00 3.95
565 603 3.623906 TCAATCTTGGCCAGAGAAGAG 57.376 47.619 17.79 7.50 33.87 2.85
567 605 3.779183 TCAATCTTGGCCAGAGAAGAGAT 59.221 43.478 17.79 13.86 33.87 2.75
588 626 8.099537 AGAGATATTGATCGGAAAGCATACATT 58.900 33.333 0.00 0.00 37.15 2.71
660 698 8.777578 TGAATAGTTAGCCTGGAATAGTTAGA 57.222 34.615 0.00 0.00 0.00 2.10
695 733 2.441750 ACTAAGGGCTTTGTGGAACTGA 59.558 45.455 0.00 0.00 38.04 3.41
697 735 2.683211 AGGGCTTTGTGGAACTGATT 57.317 45.000 0.00 0.00 38.04 2.57
717 755 7.657761 ACTGATTTTCTAGTTACTGGTGTGAAG 59.342 37.037 0.00 0.00 0.00 3.02
722 760 3.679824 AGTTACTGGTGTGAAGCTACC 57.320 47.619 0.00 0.00 37.48 3.18
723 761 2.029290 AGTTACTGGTGTGAAGCTACCG 60.029 50.000 0.00 0.00 39.87 4.02
731 769 1.204704 TGTGAAGCTACCGGTGATGAG 59.795 52.381 19.93 7.68 0.00 2.90
792 864 2.095372 GTGATTGTGTTTACCTAGCCGC 59.905 50.000 0.00 0.00 0.00 6.53
793 865 1.669265 GATTGTGTTTACCTAGCCGCC 59.331 52.381 0.00 0.00 0.00 6.13
810 882 0.724549 GCCGTGTGAATATGCAACGA 59.275 50.000 15.69 0.00 0.00 3.85
828 900 2.154389 ACGATAACAACGAGCGTGAAAC 59.846 45.455 0.00 0.00 33.52 2.78
835 907 0.109873 ACGAGCGTGAAACTAGACCG 60.110 55.000 0.00 0.00 31.75 4.79
850 922 8.891671 AAACTAGACCGAAAACAAGTTACATA 57.108 30.769 0.00 0.00 0.00 2.29
876 995 1.673993 AACGCGATGTGCCAATGGA 60.674 52.632 15.93 0.00 42.08 3.41
877 996 1.922135 AACGCGATGTGCCAATGGAC 61.922 55.000 15.93 0.00 42.08 4.02
878 997 2.404789 GCGATGTGCCAATGGACG 59.595 61.111 2.05 1.25 37.76 4.79
882 1001 0.881118 GATGTGCCAATGGACGTGTT 59.119 50.000 2.05 0.00 0.00 3.32
883 1002 0.597568 ATGTGCCAATGGACGTGTTG 59.402 50.000 2.05 0.00 0.00 3.33
884 1003 1.285641 GTGCCAATGGACGTGTTGG 59.714 57.895 2.05 15.89 46.03 3.77
885 1004 1.149401 TGCCAATGGACGTGTTGGA 59.851 52.632 21.65 8.95 46.15 3.53
909 1043 3.656045 CGGTTGGACGGGTTGTGC 61.656 66.667 0.00 0.00 39.78 4.57
911 1045 2.589442 GTTGGACGGGTTGTGCGA 60.589 61.111 0.00 0.00 42.78 5.10
917 1051 1.429148 GACGGGTTGTGCGATGGATC 61.429 60.000 0.00 0.00 0.00 3.36
927 1061 0.742990 GCGATGGATCAACCGGACAA 60.743 55.000 9.46 0.00 42.61 3.18
929 1063 1.006832 GATGGATCAACCGGACAACG 58.993 55.000 9.46 0.00 42.61 4.10
972 1111 4.318263 CGGAATACGGCTTAACGGTAATTG 60.318 45.833 0.00 0.00 37.58 2.32
976 1115 1.465387 CGGCTTAACGGTAATTGCACA 59.535 47.619 6.76 0.00 0.00 4.57
996 1135 1.087202 TGTCGGGCCAAATCGATTCG 61.087 55.000 11.83 10.31 37.73 3.34
1048 1188 9.383519 CTACCTGCTAGAGAAATAATTGAAACA 57.616 33.333 0.00 0.00 0.00 2.83
1098 1238 9.237187 AGAGAAATAAAATCCAAGTCTCTTTCC 57.763 33.333 0.00 0.00 37.65 3.13
1252 1400 3.119096 GAGGCAGAACCGGCGAAC 61.119 66.667 9.30 0.00 46.52 3.95
1501 1658 1.427819 CGCCGTAATTCTTGGTGGC 59.572 57.895 0.00 0.00 39.10 5.01
1511 1668 4.182433 TTGGTGGCTGCGTGGACA 62.182 61.111 0.00 0.00 0.00 4.02
1532 1689 0.397957 GGAGGAAGAGGAGGAGGACC 60.398 65.000 0.00 0.00 0.00 4.46
1689 1857 4.518249 GGAGAGGGACCTTCTTGTAATTG 58.482 47.826 7.68 0.00 0.00 2.32
1705 1873 5.754782 TGTAATTGACATGATTGCTAGGGT 58.245 37.500 0.00 0.00 31.20 4.34
1736 1904 4.548451 TGTTCGAGTCTGTAGTCCTCTA 57.452 45.455 0.00 0.00 0.00 2.43
1843 2017 2.224378 CGGAGCTGAATACATCCATGGT 60.224 50.000 12.58 0.00 0.00 3.55
1847 2021 2.934887 CTGAATACATCCATGGTGGCA 58.065 47.619 12.58 2.93 37.47 4.92
1886 2060 7.045126 TGAATTGGTTAATTTGGTTCGTCTT 57.955 32.000 0.00 0.00 36.66 3.01
2181 2403 0.243636 CCAGCGGAAATGTTGGTTCC 59.756 55.000 0.00 0.00 41.08 3.62
2182 2404 0.243636 CAGCGGAAATGTTGGTTCCC 59.756 55.000 0.00 0.00 41.39 3.97
2288 2539 3.773630 CGGCGTGTGCGTTCGATT 61.774 61.111 0.00 0.00 44.10 3.34
2483 2759 3.426787 TTCCTTTCGGATTAAGCCACA 57.573 42.857 10.94 0.00 39.58 4.17
2568 2850 4.142600 GGTTGTTGCAATGATCAGGTCTAC 60.143 45.833 0.59 0.60 0.00 2.59
2645 2930 1.515020 TGCAAGCCAGCAACGTTTT 59.485 47.368 0.00 0.00 42.46 2.43
2652 2937 2.685897 AGCCAGCAACGTTTTCTTGTAA 59.314 40.909 0.00 0.00 0.00 2.41
2653 2938 2.787129 GCCAGCAACGTTTTCTTGTAAC 59.213 45.455 0.00 0.00 0.00 2.50
2654 2939 3.488553 GCCAGCAACGTTTTCTTGTAACT 60.489 43.478 0.00 0.00 0.00 2.24
2657 2942 3.942748 AGCAACGTTTTCTTGTAACTCCA 59.057 39.130 0.00 0.00 0.00 3.86
2658 2943 4.033019 GCAACGTTTTCTTGTAACTCCAC 58.967 43.478 0.00 0.00 0.00 4.02
2746 3036 3.040795 CGAGCTATGCATGCATGTTTTC 58.959 45.455 37.43 26.45 37.82 2.29
2747 3037 3.040795 GAGCTATGCATGCATGTTTTCG 58.959 45.455 37.43 20.50 37.82 3.46
2760 3050 3.469863 TTTTCGGCGCCACCTGACT 62.470 57.895 28.98 0.00 35.61 3.41
2786 3076 7.133513 GTGTAAAGATACATACAGAGAGGTCG 58.866 42.308 0.00 0.00 43.60 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 130 2.304761 TGAACCTATGTCCCAAGTCCAC 59.695 50.000 0.00 0.00 0.00 4.02
167 170 1.732259 CACGCCGTTTGCTATCTTTCT 59.268 47.619 0.00 0.00 38.05 2.52
180 183 0.877213 GTAGTTTGTCACCACGCCGT 60.877 55.000 0.00 0.00 0.00 5.68
196 201 3.536956 TCTATTCTTGCCCAACCGTAG 57.463 47.619 0.00 0.00 0.00 3.51
200 205 5.921962 AAGATTTCTATTCTTGCCCAACC 57.078 39.130 0.00 0.00 32.30 3.77
429 452 5.006746 CACTAAGGATAAAGCGACATGGTTC 59.993 44.000 0.00 0.00 37.29 3.62
473 497 4.499188 CGGTGCTCTGATAATAAGGACGAA 60.499 45.833 0.00 0.00 32.73 3.85
475 499 3.309388 CGGTGCTCTGATAATAAGGACG 58.691 50.000 0.00 0.00 32.73 4.79
480 504 2.621526 TCTCGCGGTGCTCTGATAATAA 59.378 45.455 6.13 0.00 0.00 1.40
485 509 0.529337 CAATCTCGCGGTGCTCTGAT 60.529 55.000 6.13 0.00 0.00 2.90
487 511 0.737367 TTCAATCTCGCGGTGCTCTG 60.737 55.000 6.13 0.00 0.00 3.35
510 548 2.247699 AGGGAGTGGTGCATAGTACA 57.752 50.000 0.00 0.00 0.00 2.90
530 568 9.651913 GGCCAAGATTGATAATTAGTTTTTCAA 57.348 29.630 0.00 1.92 38.88 2.69
646 684 9.265901 CTGTATGTCAAATCTAACTATTCCAGG 57.734 37.037 0.00 0.00 0.00 4.45
660 698 4.475016 AGCCCTTAGTCCTGTATGTCAAAT 59.525 41.667 0.00 0.00 0.00 2.32
695 733 6.534634 AGCTTCACACCAGTAACTAGAAAAT 58.465 36.000 0.00 0.00 0.00 1.82
697 735 5.546621 AGCTTCACACCAGTAACTAGAAA 57.453 39.130 0.00 0.00 0.00 2.52
717 755 1.448985 TTTTGCTCATCACCGGTAGC 58.551 50.000 18.33 18.33 35.51 3.58
722 760 5.327091 CACTCTAAATTTTGCTCATCACCG 58.673 41.667 0.00 0.00 0.00 4.94
723 761 5.098211 GCACTCTAAATTTTGCTCATCACC 58.902 41.667 0.00 0.00 32.00 4.02
731 769 6.529463 ACAATGTTGCACTCTAAATTTTGC 57.471 33.333 5.76 5.76 35.45 3.68
766 804 5.935789 GGCTAGGTAAACACAATCACTACAA 59.064 40.000 0.00 0.00 0.00 2.41
781 853 1.534336 TTCACACGGCGGCTAGGTAA 61.534 55.000 13.24 0.00 0.00 2.85
792 864 4.033472 TGTTATCGTTGCATATTCACACGG 59.967 41.667 5.13 0.00 0.00 4.94
793 865 5.137524 TGTTATCGTTGCATATTCACACG 57.862 39.130 0.00 0.00 0.00 4.49
810 882 4.620184 GTCTAGTTTCACGCTCGTTGTTAT 59.380 41.667 0.00 0.00 0.00 1.89
828 900 9.028185 GGTATATGTAACTTGTTTTCGGTCTAG 57.972 37.037 0.00 0.00 0.00 2.43
835 907 9.537848 CGTTGAAGGTATATGTAACTTGTTTTC 57.462 33.333 4.28 0.00 37.96 2.29
850 922 1.006832 GCACATCGCGTTGAAGGTAT 58.993 50.000 23.12 0.00 0.00 2.73
876 995 0.108041 ACCGAGTTTGTCCAACACGT 60.108 50.000 6.03 0.00 45.07 4.49
877 996 1.011333 AACCGAGTTTGTCCAACACG 58.989 50.000 0.53 0.53 45.82 4.49
878 997 1.064952 CCAACCGAGTTTGTCCAACAC 59.935 52.381 0.00 0.00 37.93 3.32
882 1001 0.531090 CGTCCAACCGAGTTTGTCCA 60.531 55.000 0.00 0.00 0.00 4.02
883 1002 1.226030 CCGTCCAACCGAGTTTGTCC 61.226 60.000 0.00 0.00 0.00 4.02
884 1003 1.226030 CCCGTCCAACCGAGTTTGTC 61.226 60.000 0.00 0.00 0.00 3.18
885 1004 1.227734 CCCGTCCAACCGAGTTTGT 60.228 57.895 0.00 0.00 0.00 2.83
909 1043 1.006832 GTTGTCCGGTTGATCCATCG 58.993 55.000 0.00 0.00 35.57 3.84
911 1045 3.153024 CGTTGTCCGGTTGATCCAT 57.847 52.632 0.00 0.00 35.57 3.41
927 1061 0.306533 GTGAAACGCATGACAACCGT 59.693 50.000 0.00 0.00 36.68 4.83
956 1095 1.465387 TGTGCAATTACCGTTAAGCCG 59.535 47.619 0.00 0.00 0.00 5.52
972 1111 1.139520 GATTTGGCCCGACATGTGC 59.860 57.895 1.15 0.00 0.00 4.57
976 1115 1.308998 GAATCGATTTGGCCCGACAT 58.691 50.000 12.81 0.00 37.64 3.06
996 1135 8.814235 GCTTTGCATAAATATCATTATGGCATC 58.186 33.333 1.65 0.00 41.49 3.91
1098 1238 3.384467 TGTCCTTTTCCTCTTGCTTTTGG 59.616 43.478 0.00 0.00 0.00 3.28
1252 1400 3.200887 CTCCGGCTCGATCTTCCCG 62.201 68.421 0.00 7.55 40.39 5.14
1272 1420 1.605451 TCGGCCCTCTTCGTCTTGA 60.605 57.895 0.00 0.00 0.00 3.02
1501 1658 2.513026 CTTCCTCCCTGTCCACGCAG 62.513 65.000 0.00 0.00 36.31 5.18
1511 1668 0.556380 TCCTCCTCCTCTTCCTCCCT 60.556 60.000 0.00 0.00 0.00 4.20
1689 1857 3.134458 GCTACACCCTAGCAATCATGTC 58.866 50.000 0.00 0.00 40.14 3.06
1736 1904 2.756283 CTCCGGGCGAGAGGAAGT 60.756 66.667 0.00 0.00 41.63 3.01
1843 2017 4.290711 TCAGTTCAGAATTCAGATGCCA 57.709 40.909 8.44 0.00 0.00 4.92
1847 2021 7.771927 AACCAATTCAGTTCAGAATTCAGAT 57.228 32.000 8.44 0.00 44.16 2.90
1886 2060 0.608130 CCAGCTAGCACCACAGTACA 59.392 55.000 18.83 0.00 0.00 2.90
2014 2219 2.476534 AAATTGCTTGGACGCAGGCG 62.477 55.000 12.71 12.71 41.55 5.52
2097 2312 3.239483 CGAATCAAACAAACACAACACCG 59.761 43.478 0.00 0.00 0.00 4.94
2181 2403 3.139077 GACCAAAGTTCTACCACACAGG 58.861 50.000 0.00 0.00 45.67 4.00
2182 2404 3.139077 GGACCAAAGTTCTACCACACAG 58.861 50.000 0.00 0.00 0.00 3.66
2239 2470 3.963687 CTGCGATGAGTGGCCAGCA 62.964 63.158 5.11 10.77 0.00 4.41
2288 2539 3.307691 CCAAACCAGTATGAAGAGGCAGA 60.308 47.826 0.00 0.00 39.69 4.26
2399 2666 2.027192 TGGAGGCGCTTCTAGAACATTT 60.027 45.455 19.65 0.00 0.00 2.32
2483 2759 8.143193 CAGTAGTCTCAGATGATAAGCTTGATT 58.857 37.037 9.86 0.00 0.00 2.57
2568 2850 5.419542 TCTACTTGGAGAATCACATTTCCG 58.580 41.667 0.00 0.00 36.25 4.30
2641 2926 4.124970 AGACGGTGGAGTTACAAGAAAAC 58.875 43.478 0.00 0.00 0.00 2.43
2645 2930 2.490903 GCTAGACGGTGGAGTTACAAGA 59.509 50.000 0.00 0.00 0.00 3.02
2652 2937 0.542232 ACCAAGCTAGACGGTGGAGT 60.542 55.000 6.87 0.00 0.00 3.85
2653 2938 0.608640 AACCAAGCTAGACGGTGGAG 59.391 55.000 6.87 0.00 31.94 3.86
2654 2939 1.927487 TAACCAAGCTAGACGGTGGA 58.073 50.000 6.87 0.00 31.94 4.02
2657 2942 4.698780 GGAAAATTAACCAAGCTAGACGGT 59.301 41.667 0.00 0.00 33.32 4.83
2658 2943 4.941873 AGGAAAATTAACCAAGCTAGACGG 59.058 41.667 0.00 0.00 0.00 4.79
2747 3037 2.725203 TTACACAGTCAGGTGGCGCC 62.725 60.000 22.73 22.73 43.08 6.53
2760 3050 7.201705 CGACCTCTCTGTATGTATCTTTACACA 60.202 40.741 0.00 0.00 41.02 3.72
2786 3076 4.380867 CCTGTTAATTTCACACAGCCCATC 60.381 45.833 0.00 0.00 37.24 3.51


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

AutoCloner maintained by Alex Coulton.