Multiple sequence alignment - TraesCS5D01G211800

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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 TraesCS5D01G211800 chr5D 100.000 4352 0 0 1 4352 320876320 320871969 0.000000e+00 8037.0
1 TraesCS5D01G211800 chr5A 93.325 3775 152 40 1 3706 413426977 413430720 0.000000e+00 5483.0
2 TraesCS5D01G211800 chr5A 90.043 462 24 9 3897 4352 413431073 413431518 2.920000e-161 579.0
3 TraesCS5D01G211800 chr5A 90.863 197 18 0 3702 3898 413430808 413431004 9.280000e-67 265.0
4 TraesCS5D01G211800 chr5B 93.518 3147 120 33 785 3887 372083320 372080214 0.000000e+00 4604.0
5 TraesCS5D01G211800 chr5B 89.740 692 32 16 104 788 372084053 372083394 0.000000e+00 848.0
6 TraesCS5D01G211800 chr5B 88.889 459 45 6 3897 4350 372080135 372079678 1.060000e-155 560.0
7 TraesCS5D01G211800 chr5B 92.857 70 2 1 1 67 372084125 372084056 9.960000e-17 99.0
8 TraesCS5D01G211800 chr7A 80.630 413 67 9 2408 2812 471551458 471551865 1.520000e-79 307.0
9 TraesCS5D01G211800 chr7D 81.233 373 55 9 2408 2771 410522548 410522182 1.980000e-73 287.0
10 TraesCS5D01G211800 chr7B 84.291 261 39 2 1697 1955 425158274 425158534 2.010000e-63 254.0
11 TraesCS5D01G211800 chr7B 79.088 373 60 11 2408 2771 425158910 425159273 1.560000e-59 241.0
12 TraesCS5D01G211800 chr7B 82.857 105 18 0 2633 2737 61627835 61627731 1.290000e-15 95.3
13 TraesCS5D01G211800 chr7B 81.905 105 19 0 2633 2737 61746182 61746078 5.990000e-14 89.8
14 TraesCS5D01G211800 chrUn 89.583 96 6 2 1 92 382168867 382168962 7.650000e-23 119.0
15 TraesCS5D01G211800 chr2A 82.353 102 12 4 2633 2731 100627751 100627653 2.790000e-12 84.2
16 TraesCS5D01G211800 chr2D 81.731 104 13 4 2631 2731 100432471 100432571 1.000000e-11 82.4


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 TraesCS5D01G211800 chr5D 320871969 320876320 4351 True 8037.00 8037 100.000000 1 4352 1 chr5D.!!$R1 4351
1 TraesCS5D01G211800 chr5A 413426977 413431518 4541 False 2109.00 5483 91.410333 1 4352 3 chr5A.!!$F1 4351
2 TraesCS5D01G211800 chr5B 372079678 372084125 4447 True 1527.75 4604 91.251000 1 4350 4 chr5B.!!$R1 4349
3 TraesCS5D01G211800 chr7B 425158274 425159273 999 False 247.50 254 81.689500 1697 2771 2 chr7B.!!$F1 1074

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
656 680 0.255890 ATTAAGGCGCCCACTCATGT 59.744 50.0 26.15 0.0 0.00 3.21 F
1671 1821 0.234884 GTTCGTTTTCCTGACCGCAG 59.765 55.0 0.00 0.0 41.93 5.18 F
1675 1825 0.238553 GTTTTCCTGACCGCAGCTTC 59.761 55.0 0.00 0.0 40.91 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2049 2208 0.242017 GATGTGGCTGCAAGTGAACC 59.758 55.0 0.50 0.00 35.30 3.62 R
3060 3275 0.894184 AGATGGACTCGTCGTGGTGT 60.894 55.0 0.00 0.00 34.23 4.16 R
3653 3880 1.410737 CGTTACACGCGGATGTGAGG 61.411 60.0 12.47 5.49 42.55 3.86 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
38 39 4.741239 TCCTGGGGCTGGACCTCC 62.741 72.222 0.00 0.00 38.71 4.30
79 83 7.286316 AGCCTTATAATTAGCAGAACAGCATTT 59.714 33.333 5.42 0.00 36.85 2.32
129 133 5.335113 CGAGTGCTCATTTTGGAATTTCTCA 60.335 40.000 0.00 0.00 0.00 3.27
183 193 2.604046 AGCTATGCGTACAAAGGGAG 57.396 50.000 0.00 0.00 0.00 4.30
248 260 1.207089 TCTAGTTCCTTGGCGTCCATG 59.793 52.381 0.00 2.71 31.53 3.66
253 265 2.046023 CTTGGCGTCCATGGAGCA 60.046 61.111 26.93 15.96 31.53 4.26
284 296 2.004733 TCAGCGATTGCAGATGTTCTG 58.995 47.619 7.90 0.08 46.90 3.02
285 297 1.736126 CAGCGATTGCAGATGTTCTGT 59.264 47.619 7.90 0.00 45.94 3.41
286 298 2.931969 CAGCGATTGCAGATGTTCTGTA 59.068 45.455 7.90 0.00 45.94 2.74
287 299 3.558829 CAGCGATTGCAGATGTTCTGTAT 59.441 43.478 7.90 1.29 45.94 2.29
288 300 4.746611 CAGCGATTGCAGATGTTCTGTATA 59.253 41.667 7.90 0.00 45.94 1.47
289 301 5.407691 CAGCGATTGCAGATGTTCTGTATAT 59.592 40.000 7.90 0.00 45.94 0.86
290 302 6.587608 CAGCGATTGCAGATGTTCTGTATATA 59.412 38.462 7.90 0.00 45.94 0.86
291 303 7.277319 CAGCGATTGCAGATGTTCTGTATATAT 59.723 37.037 7.90 0.00 45.94 0.86
292 304 7.277319 AGCGATTGCAGATGTTCTGTATATATG 59.723 37.037 7.90 0.00 45.94 1.78
293 305 7.063898 GCGATTGCAGATGTTCTGTATATATGT 59.936 37.037 0.00 0.00 45.94 2.29
294 306 9.573133 CGATTGCAGATGTTCTGTATATATGTA 57.427 33.333 6.40 0.00 45.94 2.29
296 308 8.742554 TTGCAGATGTTCTGTATATATGTACG 57.257 34.615 6.40 1.40 45.94 3.67
297 309 7.882179 TGCAGATGTTCTGTATATATGTACGT 58.118 34.615 6.40 0.00 45.94 3.57
298 310 7.807907 TGCAGATGTTCTGTATATATGTACGTG 59.192 37.037 0.00 1.74 45.94 4.49
299 311 7.808381 GCAGATGTTCTGTATATATGTACGTGT 59.192 37.037 0.00 0.00 45.94 4.49
300 312 9.118236 CAGATGTTCTGTATATATGTACGTGTG 57.882 37.037 0.00 0.00 39.58 3.82
301 313 8.847196 AGATGTTCTGTATATATGTACGTGTGT 58.153 33.333 0.00 0.00 0.00 3.72
347 366 4.753516 TGTGTATTGGGACTCCTGTATG 57.246 45.455 0.00 0.00 0.00 2.39
348 367 4.101114 TGTGTATTGGGACTCCTGTATGT 58.899 43.478 0.00 0.00 0.00 2.29
469 493 3.142174 AGCAGCTAATTAAGAATCGCCC 58.858 45.455 0.00 0.00 0.00 6.13
547 571 6.415206 ACACTACTACTTTTTGCTAGTGGA 57.585 37.500 8.33 0.00 39.00 4.02
604 628 0.531200 AAGAGTAAACCCTCTCGGCG 59.469 55.000 0.00 0.00 40.93 6.46
652 676 2.102588 TCTCTAATTAAGGCGCCCACTC 59.897 50.000 26.15 0.00 0.00 3.51
656 680 0.255890 ATTAAGGCGCCCACTCATGT 59.744 50.000 26.15 0.00 0.00 3.21
870 989 2.453521 ACTACGTGCCAGTAATCTCCA 58.546 47.619 0.00 0.00 0.00 3.86
897 1016 7.283580 GCTCTATCGGTATATATATAGCCCAGG 59.716 44.444 20.89 10.69 34.15 4.45
1056 1188 1.598130 GGTTGTCTCGGTGCTGCTT 60.598 57.895 0.00 0.00 0.00 3.91
1612 1753 1.000955 CCTGACAAGCTCAAGGTACGT 59.999 52.381 0.00 0.00 0.00 3.57
1613 1754 2.329379 CTGACAAGCTCAAGGTACGTC 58.671 52.381 0.00 5.28 0.00 4.34
1614 1755 1.335597 TGACAAGCTCAAGGTACGTCG 60.336 52.381 0.00 0.00 33.45 5.12
1615 1756 0.666577 ACAAGCTCAAGGTACGTCGC 60.667 55.000 0.00 0.00 0.00 5.19
1616 1757 1.080025 AAGCTCAAGGTACGTCGCC 60.080 57.895 0.00 0.00 0.00 5.54
1660 1810 1.538075 CATTGCCTACCGGTTCGTTTT 59.462 47.619 15.04 0.00 0.00 2.43
1670 1820 1.161563 GGTTCGTTTTCCTGACCGCA 61.162 55.000 0.00 0.00 0.00 5.69
1671 1821 0.234884 GTTCGTTTTCCTGACCGCAG 59.765 55.000 0.00 0.00 41.93 5.18
1673 1823 1.961277 CGTTTTCCTGACCGCAGCT 60.961 57.895 0.00 0.00 40.91 4.24
1675 1825 0.238553 GTTTTCCTGACCGCAGCTTC 59.761 55.000 0.00 0.00 40.91 3.86
1676 1826 1.227999 TTTTCCTGACCGCAGCTTCG 61.228 55.000 0.00 0.00 40.91 3.79
1685 1835 3.918220 GCAGCTTCGGATCGCACG 61.918 66.667 0.00 0.00 0.00 5.34
1686 1836 2.507102 CAGCTTCGGATCGCACGT 60.507 61.111 0.00 0.00 0.00 4.49
1687 1837 1.226575 CAGCTTCGGATCGCACGTA 60.227 57.895 0.00 0.00 0.00 3.57
1688 1838 1.226603 AGCTTCGGATCGCACGTAC 60.227 57.895 0.00 0.00 0.00 3.67
1689 1839 2.565394 GCTTCGGATCGCACGTACG 61.565 63.158 15.01 15.01 0.00 3.67
1690 1840 1.226211 CTTCGGATCGCACGTACGT 60.226 57.895 16.72 16.72 0.00 3.57
1881 2031 1.817099 GCGCATCTTCCACCTCCTG 60.817 63.158 0.30 0.00 0.00 3.86
1961 2120 1.087501 TGAGTCACGATCACCTCTCG 58.912 55.000 0.00 0.00 41.77 4.04
2049 2208 2.644992 GCCCTTGTCGCCACTTTG 59.355 61.111 0.00 0.00 0.00 2.77
2579 2792 1.135139 CGCCGAGATGGAGAAGAAGAA 59.865 52.381 0.00 0.00 40.56 2.52
2706 2919 0.970427 TCACCTGGACGCTCATGCTA 60.970 55.000 0.00 0.00 36.97 3.49
2916 3131 2.111932 TTTCTTGTGTGCGCGCGAAT 62.112 50.000 37.18 0.00 0.00 3.34
3060 3275 0.107831 GGATACCCGTGCTGGCAATA 59.892 55.000 0.00 0.00 35.87 1.90
3455 3670 2.373335 ACCTGTCTGACTGACTGACT 57.627 50.000 15.25 3.43 45.54 3.41
3459 3674 1.133482 TGTCTGACTGACTGACTGGGA 60.133 52.381 9.51 0.00 45.54 4.37
3478 3693 4.643387 GGCCGGCCTGTCAGTTGT 62.643 66.667 38.76 0.00 0.00 3.32
3533 3751 4.833390 GTGGAGTTCCTGCACTAGTTATT 58.167 43.478 8.42 0.00 46.69 1.40
3653 3880 7.865385 TGCACCTTCTAAAACAACAAATGATAC 59.135 33.333 0.00 0.00 0.00 2.24
3660 3887 9.295825 TCTAAAACAACAAATGATACCTCACAT 57.704 29.630 0.00 0.00 33.22 3.21
3664 3891 3.206150 ACAAATGATACCTCACATCCGC 58.794 45.455 0.00 0.00 33.22 5.54
3706 4025 3.501349 ACCGTAGAGACCATGCAGATAT 58.499 45.455 0.00 0.00 0.00 1.63
3708 4027 3.761218 CCGTAGAGACCATGCAGATATCT 59.239 47.826 0.00 0.00 0.00 1.98
3756 4083 3.916544 CCTCCGCCGATGCAGCTA 61.917 66.667 0.00 0.00 37.32 3.32
3807 4141 2.700371 TCCAATACATCACTCCTCGCAT 59.300 45.455 0.00 0.00 0.00 4.73
3838 4172 1.626654 CGCTAGTGTTGTCGCTTGGG 61.627 60.000 0.00 0.00 35.84 4.12
3887 4221 2.943690 CTCGGTAATGACTCCTTCTCGA 59.056 50.000 0.00 0.00 0.00 4.04
3888 4222 3.552875 TCGGTAATGACTCCTTCTCGAT 58.447 45.455 0.00 0.00 0.00 3.59
3894 4228 1.833630 TGACTCCTTCTCGATGGCATT 59.166 47.619 0.00 0.00 0.00 3.56
3909 4313 1.255882 GCATTGTGACCATGGGTGAA 58.744 50.000 18.09 3.41 35.25 3.18
4024 4430 0.179084 AAATCGATGACGCGGTCCAT 60.179 50.000 12.47 10.96 39.58 3.41
4029 4435 1.601914 CGATGACGCGGTCCATAATGA 60.602 52.381 12.47 0.00 0.00 2.57
4030 4436 1.792949 GATGACGCGGTCCATAATGAC 59.207 52.381 12.47 0.00 34.42 3.06
4037 4443 1.299541 GGTCCATAATGACGGTGCAG 58.700 55.000 0.00 0.00 36.07 4.41
4069 4475 1.027357 GGTGGACATGATGGCATCAC 58.973 55.000 30.96 18.82 43.01 3.06
4121 4527 6.455647 CGGGTTAATAGCTCATTCTACATCA 58.544 40.000 0.00 0.00 0.00 3.07
4131 4537 3.197766 TCATTCTACATCAAGACGGGCTT 59.802 43.478 0.00 0.00 37.29 4.35
4190 4602 2.224185 ACAACAGTGTCCGCAATGAGTA 60.224 45.455 0.00 0.00 42.66 2.59
4197 4609 3.188460 GTGTCCGCAATGAGTATGTGTTT 59.812 43.478 0.00 0.00 0.00 2.83
4252 4665 2.297698 TGGAGTAAGAAGGGTCGACA 57.702 50.000 18.91 0.00 0.00 4.35
4283 4696 7.450074 ACATGATACTCTTGTTGAAGGTGTTA 58.550 34.615 0.00 0.00 31.72 2.41
4289 4702 4.776349 TCTTGTTGAAGGTGTTAGCTCAA 58.224 39.130 0.00 0.00 0.00 3.02
4316 4729 2.674357 CGTTTTAGGGGTGATAACCACG 59.326 50.000 0.36 0.00 46.62 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 2.410469 GCTTAGGCAGCGGCATTG 59.590 61.111 11.88 1.44 43.71 2.82
129 133 7.340743 ACAGAAGAGACAGCAATATAGTACACT 59.659 37.037 0.00 0.00 0.00 3.55
176 186 8.895737 CAATTTATTATGCAAAATGCTCCCTTT 58.104 29.630 3.78 0.00 45.31 3.11
248 260 0.320247 CTGACTGACAGGTGTGCTCC 60.320 60.000 7.51 0.00 42.39 4.70
253 265 0.681733 AATCGCTGACTGACAGGTGT 59.318 50.000 7.51 0.00 45.82 4.16
323 342 6.385759 ACATACAGGAGTCCCAATACACATAA 59.614 38.462 5.25 0.00 33.88 1.90
325 344 4.721776 ACATACAGGAGTCCCAATACACAT 59.278 41.667 5.25 0.00 33.88 3.21
329 348 4.755266 ACACATACAGGAGTCCCAATAC 57.245 45.455 5.25 0.00 33.88 1.89
342 361 6.151817 TGCCAAAAGTTGCATATACACATACA 59.848 34.615 0.00 0.00 31.31 2.29
604 628 1.609208 ACGGGATTGGATTGCTATGC 58.391 50.000 0.00 0.00 0.00 3.14
652 676 1.464608 CTTTGGTGCGGTCACTACATG 59.535 52.381 0.00 0.00 42.72 3.21
656 680 0.320374 CTCCTTTGGTGCGGTCACTA 59.680 55.000 3.32 0.00 42.72 2.74
798 903 2.981859 TCCTAAGATCGGTTGCCTTC 57.018 50.000 0.00 0.00 0.00 3.46
844 951 5.598769 AGATTACTGGCACGTAGTAATTCC 58.401 41.667 18.57 10.26 46.09 3.01
845 952 5.690857 GGAGATTACTGGCACGTAGTAATTC 59.309 44.000 18.57 16.50 46.09 2.17
846 953 5.128171 TGGAGATTACTGGCACGTAGTAATT 59.872 40.000 18.57 11.32 46.09 1.40
870 989 7.929959 TGGGCTATATATATACCGATAGAGCT 58.070 38.462 13.36 0.00 40.88 4.09
897 1016 3.443925 GGCTTTCCCTGCGCTTCC 61.444 66.667 9.73 0.00 0.00 3.46
935 1054 2.159226 CGAGAATTGGAGGCGTTACTCT 60.159 50.000 0.00 0.00 37.63 3.24
1040 1172 0.601046 CAGAAGCAGCACCGAGACAA 60.601 55.000 0.00 0.00 0.00 3.18
1056 1188 2.063979 CACCCATACCGCCCTCAGA 61.064 63.158 0.00 0.00 0.00 3.27
1615 1756 3.103911 GTGTTCGACGAGGTGCGG 61.104 66.667 0.00 0.00 46.49 5.69
1621 1762 1.626654 GCCACCATGTGTTCGACGAG 61.627 60.000 0.00 0.00 0.00 4.18
1622 1763 1.666553 GCCACCATGTGTTCGACGA 60.667 57.895 0.00 0.00 0.00 4.20
1660 1810 4.069232 CCGAAGCTGCGGTCAGGA 62.069 66.667 26.15 0.00 46.07 3.86
1670 1820 1.226603 GTACGTGCGATCCGAAGCT 60.227 57.895 0.00 0.00 0.00 3.74
1671 1821 2.565394 CGTACGTGCGATCCGAAGC 61.565 63.158 21.98 0.00 0.00 3.86
1673 1823 1.512522 CACGTACGTGCGATCCGAA 60.513 57.895 32.93 0.00 39.39 4.30
2049 2208 0.242017 GATGTGGCTGCAAGTGAACC 59.758 55.000 0.50 0.00 35.30 3.62
2357 2564 1.449423 CCATGATCGGCCGAACACA 60.449 57.895 36.29 30.64 29.96 3.72
2579 2792 3.710722 CGCCTGCACCCTTCTCCT 61.711 66.667 0.00 0.00 0.00 3.69
2781 2994 3.254024 TTTGGAGAGCTGGTCGGCC 62.254 63.158 0.00 0.00 0.00 6.13
2838 3053 3.259064 TGACATAAGACCTTGCTTACGC 58.741 45.455 0.00 0.00 33.53 4.42
2848 3063 5.276868 CCGAACGATCAAATGACATAAGACC 60.277 44.000 0.00 0.00 0.00 3.85
2857 3072 2.672961 AGAGCCGAACGATCAAATGA 57.327 45.000 0.00 0.00 0.00 2.57
3009 3224 4.899239 CGCGGCAGGTGGAGATCC 62.899 72.222 0.00 0.00 0.00 3.36
3060 3275 0.894184 AGATGGACTCGTCGTGGTGT 60.894 55.000 0.00 0.00 34.23 4.16
3459 3674 3.570212 AACTGACAGGCCGGCCTT 61.570 61.111 45.58 33.65 45.70 4.35
3478 3693 2.057830 CAGCATATACCAGCCGGGA 58.942 57.895 2.18 0.00 41.15 5.14
3533 3751 7.422878 TGTCGTTTGCATACATTGTAAGTAA 57.577 32.000 8.06 0.00 31.22 2.24
3555 3775 9.651913 GGATTACCATAACAAAAATTGTCATGT 57.348 29.630 5.81 1.20 37.55 3.21
3631 3858 8.792633 TGAGGTATCATTTGTTGTTTTAGAAGG 58.207 33.333 0.00 0.00 0.00 3.46
3653 3880 1.410737 CGTTACACGCGGATGTGAGG 61.411 60.000 12.47 5.49 42.55 3.86
3679 3906 1.043673 ATGGTCTCTACGGTCTGCCC 61.044 60.000 0.00 0.00 0.00 5.36
3706 4025 4.518970 GGATTGAGTTGTGGCAGTTTAAGA 59.481 41.667 0.00 0.00 0.00 2.10
3708 4027 4.469657 AGGATTGAGTTGTGGCAGTTTAA 58.530 39.130 0.00 0.00 0.00 1.52
3756 4083 4.021192 CCAAGGTGAGGCAACACATAAATT 60.021 41.667 14.60 1.89 40.09 1.82
3887 4221 0.041535 ACCCATGGTCACAATGCCAT 59.958 50.000 11.73 0.00 45.55 4.40
3888 4222 0.899253 CACCCATGGTCACAATGCCA 60.899 55.000 11.73 0.00 39.33 4.92
3894 4228 0.536233 CGGTTTCACCCATGGTCACA 60.536 55.000 11.73 0.00 33.75 3.58
3921 4325 1.605058 ATGAACTCGTCCCGACCAGG 61.605 60.000 0.00 0.00 40.63 4.45
4024 4430 2.097444 GCATGCTGCACCGTCATTA 58.903 52.632 11.37 0.00 44.26 1.90
4069 4475 0.868406 AAAGGAGAGCGACAAAAGCG 59.132 50.000 0.00 0.00 40.04 4.68
4121 4527 0.674895 GAGCATCACAAGCCCGTCTT 60.675 55.000 0.00 0.00 32.08 3.01
4131 4537 1.337167 CGTGAAGGTCTGAGCATCACA 60.337 52.381 31.52 14.97 42.56 3.58
4180 4592 3.919804 CCCAAAAACACATACTCATTGCG 59.080 43.478 0.00 0.00 0.00 4.85
4181 4593 4.244862 CCCCAAAAACACATACTCATTGC 58.755 43.478 0.00 0.00 0.00 3.56
4190 4602 3.264450 TGTTTTCACCCCCAAAAACACAT 59.736 39.130 8.80 0.00 45.48 3.21
4283 4696 3.568430 CCCCTAAAACGAAACTTTGAGCT 59.432 43.478 0.00 0.00 0.00 4.09
4289 4702 5.474532 GGTTATCACCCCTAAAACGAAACTT 59.525 40.000 0.00 0.00 37.03 2.66


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

AutoCloner maintained by Alex Coulton.