Multiple sequence alignment - TraesCS5B01G226800

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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 TraesCS5B01G226800 chr5B 100.000 4060 0 0 1 4060 403708858 403704799 0.000000e+00 7498.0
1 TraesCS5B01G226800 chr5B 76.737 662 121 25 1998 2635 522861124 522860472 5.030000e-89 339.0
2 TraesCS5B01G226800 chr5B 76.205 664 129 21 1994 2635 522408981 522409637 1.410000e-84 324.0
3 TraesCS5B01G226800 chr5B 91.975 162 11 1 128 289 665744619 665744460 4.080000e-55 226.0
4 TraesCS5B01G226800 chr5B 81.421 183 28 6 1019 1198 522408463 522408642 1.180000e-30 145.0
5 TraesCS5B01G226800 chr5B 80.874 183 29 6 1019 1198 522861648 522861469 5.470000e-29 139.0
6 TraesCS5B01G226800 chr5D 98.048 3483 55 6 582 4060 347444250 347447723 0.000000e+00 6043.0
7 TraesCS5B01G226800 chr5D 96.758 586 16 2 1 583 347443596 347444181 0.000000e+00 974.0
8 TraesCS5B01G226800 chr5D 76.923 663 124 25 1995 2635 431781542 431782197 2.320000e-92 350.0
9 TraesCS5B01G226800 chr5D 76.992 665 120 25 1995 2635 513308674 513309329 2.320000e-92 350.0
10 TraesCS5B01G226800 chr5D 77.996 559 96 23 1998 2538 433684217 433683668 3.910000e-85 326.0
11 TraesCS5B01G226800 chr5D 91.875 160 11 2 128 286 175300057 175299899 5.280000e-54 222.0
12 TraesCS5B01G226800 chr5D 91.358 162 12 1 128 289 528717428 528717269 1.900000e-53 220.0
13 TraesCS5B01G226800 chr5D 81.765 170 27 4 1019 1186 431781023 431781190 5.470000e-29 139.0
14 TraesCS5B01G226800 chr5D 80.874 183 29 6 1019 1198 433684738 433684559 5.470000e-29 139.0
15 TraesCS5B01G226800 chr5A 97.677 3487 63 7 582 4060 444532819 444529343 0.000000e+00 5975.0
16 TraesCS5B01G226800 chr5A 95.820 311 12 1 1 311 444533424 444533115 6.060000e-138 501.0
17 TraesCS5B01G226800 chr5A 96.567 233 7 1 352 583 444533120 444532888 6.370000e-103 385.0
18 TraesCS5B01G226800 chr5A 75.898 668 128 24 1998 2641 546770166 546769508 1.100000e-80 311.0
19 TraesCS5B01G226800 chr5A 91.358 162 12 1 128 289 656872435 656872276 1.900000e-53 220.0
20 TraesCS5B01G226800 chr5A 80.874 183 29 6 1019 1198 546770686 546770507 5.470000e-29 139.0
21 TraesCS5B01G226800 chr5A 100.000 30 0 0 1806 1835 526395784 526395813 5.670000e-04 56.5
22 TraesCS5B01G226800 chr3A 88.889 639 53 12 3433 4060 431819373 431818742 0.000000e+00 771.0
23 TraesCS5B01G226800 chr3A 93.064 173 12 0 3264 3436 431819683 431819511 1.870000e-63 254.0
24 TraesCS5B01G226800 chr3D 89.842 571 39 11 3502 4060 302933678 302934241 0.000000e+00 715.0
25 TraesCS5B01G226800 chr3D 90.377 239 17 4 3264 3500 302933276 302933510 3.940000e-80 309.0
26 TraesCS5B01G226800 chr3D 96.970 33 0 1 1806 1837 838149 838181 2.000000e-03 54.7
27 TraesCS5B01G226800 chr2D 83.587 329 48 6 1994 2319 25348151 25348476 1.830000e-78 303.0
28 TraesCS5B01G226800 chr2D 92.453 159 11 1 127 284 79056320 79056162 4.080000e-55 226.0
29 TraesCS5B01G226800 chr2D 85.211 142 21 0 1044 1185 25339037 25339178 3.270000e-31 147.0
30 TraesCS5B01G226800 chr7A 91.975 162 12 1 124 285 421785161 421785001 4.080000e-55 226.0
31 TraesCS5B01G226800 chr7B 91.824 159 13 0 127 285 369872872 369872714 5.280000e-54 222.0
32 TraesCS5B01G226800 chr7B 100.000 29 0 0 1805 1833 164500712 164500740 2.000000e-03 54.7
33 TraesCS5B01G226800 chr2B 85.211 142 21 0 1044 1185 41132734 41132875 3.270000e-31 147.0
34 TraesCS5B01G226800 chr1A 100.000 32 0 0 1803 1834 49259280 49259311 4.380000e-05 60.2
35 TraesCS5B01G226800 chr3B 100.000 30 0 0 1806 1835 134272189 134272218 5.670000e-04 56.5
36 TraesCS5B01G226800 chrUn 87.755 49 2 3 1805 1849 348428590 348428542 2.000000e-03 54.7
37 TraesCS5B01G226800 chr2A 87.500 48 3 3 1788 1832 444756502 444756549 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 TraesCS5B01G226800 chr5B 403704799 403708858 4059 True 7498.0 7498 100.0000 1 4060 1 chr5B.!!$R1 4059
1 TraesCS5B01G226800 chr5B 522860472 522861648 1176 True 239.0 339 78.8055 1019 2635 2 chr5B.!!$R3 1616
2 TraesCS5B01G226800 chr5B 522408463 522409637 1174 False 234.5 324 78.8130 1019 2635 2 chr5B.!!$F1 1616
3 TraesCS5B01G226800 chr5D 347443596 347447723 4127 False 3508.5 6043 97.4030 1 4060 2 chr5D.!!$F2 4059
4 TraesCS5B01G226800 chr5D 513308674 513309329 655 False 350.0 350 76.9920 1995 2635 1 chr5D.!!$F1 640
5 TraesCS5B01G226800 chr5D 431781023 431782197 1174 False 244.5 350 79.3440 1019 2635 2 chr5D.!!$F3 1616
6 TraesCS5B01G226800 chr5D 433683668 433684738 1070 True 232.5 326 79.4350 1019 2538 2 chr5D.!!$R3 1519
7 TraesCS5B01G226800 chr5A 444529343 444533424 4081 True 2287.0 5975 96.6880 1 4060 3 chr5A.!!$R2 4059
8 TraesCS5B01G226800 chr5A 546769508 546770686 1178 True 225.0 311 78.3860 1019 2641 2 chr5A.!!$R3 1622
9 TraesCS5B01G226800 chr3A 431818742 431819683 941 True 512.5 771 90.9765 3264 4060 2 chr3A.!!$R1 796
10 TraesCS5B01G226800 chr3D 302933276 302934241 965 False 512.0 715 90.1095 3264 4060 2 chr3D.!!$F2 796

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
458 461 0.662619 TGTTGCCAAGCTTGTCTTCG 59.337 50.0 24.35 10.22 31.27 3.79 F
1446 1525 0.674581 TCACCATCTTGCTTCTGCGG 60.675 55.0 0.00 0.00 43.34 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1975 2309 3.312736 TCTTTTTCCCCAGAACTTGCT 57.687 42.857 0.00 0.0 0.00 3.91 R
3336 3687 2.636893 ACTGAGTCAGGATCTTTGCTGT 59.363 45.455 23.79 0.0 41.68 4.40 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
314 317 7.390718 ACTGTTCAAACCATACCTGATTTCTAC 59.609 37.037 0.00 0.00 0.00 2.59
458 461 0.662619 TGTTGCCAAGCTTGTCTTCG 59.337 50.000 24.35 10.22 31.27 3.79
609 683 7.775053 ATAGGAGCCTAGAAATCTAACAGAG 57.225 40.000 2.33 0.00 31.45 3.35
664 738 4.985538 ACTAGTTTCCTACCTCATGTCG 57.014 45.455 0.00 0.00 0.00 4.35
681 755 5.348451 TCATGTCGTCAAGTTACACATGATG 59.652 40.000 0.00 4.85 45.28 3.07
688 762 2.009774 AGTTACACATGATGCCTTCGC 58.990 47.619 0.00 0.00 0.00 4.70
794 871 9.632807 CCATATTAGATAACTGTCAGTAAGAGC 57.367 37.037 5.77 0.00 0.00 4.09
851 928 6.932947 ACAAGGGATATAAATAGTAGACCGC 58.067 40.000 0.00 0.00 0.00 5.68
914 993 3.665190 GTGAGTTTGTCTTCACCTAGGG 58.335 50.000 14.81 2.03 0.00 3.53
969 1048 7.509318 TCCATATAGGTAATACAAGAGCAGTGT 59.491 37.037 0.00 0.00 39.02 3.55
1028 1107 6.611613 TGAGAGAAGTGATATGGACAAGTT 57.388 37.500 0.00 0.00 0.00 2.66
1037 1116 4.345257 TGATATGGACAAGTTAGAGGAGGC 59.655 45.833 0.00 0.00 0.00 4.70
1198 1277 3.451178 CCCAAGTAAGCTGCTACCTTCTA 59.549 47.826 0.90 0.00 0.00 2.10
1439 1518 1.059098 TCCACACTCACCATCTTGCT 58.941 50.000 0.00 0.00 0.00 3.91
1440 1519 1.421268 TCCACACTCACCATCTTGCTT 59.579 47.619 0.00 0.00 0.00 3.91
1441 1520 1.808945 CCACACTCACCATCTTGCTTC 59.191 52.381 0.00 0.00 0.00 3.86
1442 1521 2.551721 CCACACTCACCATCTTGCTTCT 60.552 50.000 0.00 0.00 0.00 2.85
1443 1522 2.483106 CACACTCACCATCTTGCTTCTG 59.517 50.000 0.00 0.00 0.00 3.02
1444 1523 1.467734 CACTCACCATCTTGCTTCTGC 59.532 52.381 0.00 0.00 40.20 4.26
1445 1524 0.725686 CTCACCATCTTGCTTCTGCG 59.274 55.000 0.00 0.00 43.34 5.18
1446 1525 0.674581 TCACCATCTTGCTTCTGCGG 60.675 55.000 0.00 0.00 43.34 5.69
1920 2000 7.837202 AACATTACTTCATTGCATTGGATTG 57.163 32.000 8.64 0.00 0.00 2.67
1975 2309 7.396339 TCATTACCTTGCTCTCACTTAGAACTA 59.604 37.037 0.00 0.00 32.46 2.24
2149 2483 2.708325 AGGCCTGAAGAAGTCTCTTGTT 59.292 45.455 3.11 0.00 42.19 2.83
2799 3148 1.435408 GAATGAAGCCTCGCCAGAGC 61.435 60.000 0.00 0.00 43.05 4.09
3188 3539 7.399191 TCAGTGTATACTTTGTGAATCCTACCT 59.601 37.037 4.17 0.00 34.07 3.08
3346 3697 7.849804 ATGACGAATTAAGTACAGCAAAGAT 57.150 32.000 0.00 0.00 0.00 2.40
3388 3741 4.702612 TCGGTGCAAATTTAGAAAGGCATA 59.297 37.500 2.43 0.00 33.43 3.14
3431 3784 6.600822 AGGAACAAATGTCACTAATCAGATGG 59.399 38.462 0.00 0.00 0.00 3.51
3564 4225 1.474478 CTGGCGCTCTTCTCAGAACTA 59.526 52.381 7.64 0.00 0.00 2.24
3567 4228 1.474879 GCGCTCTTCTCAGAACTACCT 59.525 52.381 0.00 0.00 0.00 3.08
3794 4465 8.926710 GGGTCATAATTATCTTCACGTATCTTG 58.073 37.037 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
745 822 6.184789 GGTACAGGAATTTATCAACCCAGAA 58.815 40.000 0.00 0.0 0.00 3.02
794 871 1.730064 GCTTGTGCAAAGATGGCAATG 59.270 47.619 11.34 0.0 43.91 2.82
795 872 2.088950 GCTTGTGCAAAGATGGCAAT 57.911 45.000 11.34 0.0 43.91 3.56
851 928 3.871006 TGCAAGGACTTATCAACTATGCG 59.129 43.478 0.00 0.0 34.16 4.73
914 993 5.121298 GTGTATGGTTTTAGGGTCGAAGTTC 59.879 44.000 0.00 0.0 0.00 3.01
1037 1116 2.325082 CGGAAACCCGGCAGAAGTG 61.325 63.158 0.00 0.0 43.22 3.16
1839 1919 4.398319 TGGTTTTCTGATGAGAAGGTTCC 58.602 43.478 0.00 0.0 39.44 3.62
1878 1958 9.905713 AGTAATGTTTGCAGATATTTAAGGAGA 57.094 29.630 4.55 0.0 0.00 3.71
1975 2309 3.312736 TCTTTTTCCCCAGAACTTGCT 57.687 42.857 0.00 0.0 0.00 3.91
2149 2483 6.909550 TTTGCTGCTCTCCCTTTATAAAAA 57.090 33.333 0.00 0.0 0.00 1.94
2799 3148 4.703897 TGTTCAGGGTGTTCAAACTCTAG 58.296 43.478 0.00 0.0 0.00 2.43
3188 3539 9.650714 TCTATTAGCCTATCTTTTGTACAGGTA 57.349 33.333 0.00 0.0 0.00 3.08
3336 3687 2.636893 ACTGAGTCAGGATCTTTGCTGT 59.363 45.455 23.79 0.0 41.68 4.40
3346 3697 3.056821 CCGACAATACAACTGAGTCAGGA 60.057 47.826 23.79 6.9 35.51 3.86
3388 3741 3.192944 TCCTGATCATGGGGAAGACTTT 58.807 45.455 0.00 0.0 0.00 2.66
3431 3784 5.993441 TGGTAGTTGTTCTAAACCTGTTAGC 59.007 40.000 0.00 0.0 0.00 3.09
3564 4225 8.618702 GATGAAATAATGACATCATCTCAGGT 57.381 34.615 8.20 0.0 42.99 4.00
3641 4302 9.209175 GGATTGAGTATGGTGTATAGTGAAATC 57.791 37.037 0.00 0.0 31.30 2.17
3650 4313 3.976654 AGCCTGGATTGAGTATGGTGTAT 59.023 43.478 0.00 0.0 0.00 2.29
3794 4465 7.181143 TGTACTTGGACGATTTGTAGAAAAC 57.819 36.000 0.00 0.0 0.00 2.43


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

AutoCloner maintained by Alex Coulton.