Multiple sequence alignment - TraesCS5B01G407800

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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 TraesCS5B01G407800 chr5B 100.000 2228 0 0 1 2228 583473254 583475481 0.000000e+00 4115
1 TraesCS5B01G407800 chr5D 90.944 1844 80 37 1 1778 476011721 476013543 0.000000e+00 2399
2 TraesCS5B01G407800 chr5D 90.968 465 29 5 1774 2228 476013593 476014054 4.070000e-172 614
3 TraesCS5B01G407800 chr5A 90.805 1403 59 29 216 1563 595408663 595410050 0.000000e+00 1812
4 TraesCS5B01G407800 chr5A 88.921 686 56 7 1559 2228 595413204 595413885 0.000000e+00 828


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 TraesCS5B01G407800 chr5B 583473254 583475481 2227 False 4115.0 4115 100.000 1 2228 1 chr5B.!!$F1 2227
1 TraesCS5B01G407800 chr5D 476011721 476014054 2333 False 1506.5 2399 90.956 1 2228 2 chr5D.!!$F1 2227
2 TraesCS5B01G407800 chr5A 595408663 595413885 5222 False 1320.0 1812 89.863 216 2228 2 chr5A.!!$F1 2012

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
860 913 0.034059 CTTCCTTCACACCTGCGAGT 59.966 55.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1991 5324 0.321564 TGTTTGGAGAGGCGGTGATG 60.322 55.0 0.0 0.0 0.0 3.07 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
29 30 7.867752 AGTAGTAGCGAAATATCTCTCTTCAC 58.132 38.462 0.00 0.00 0.00 3.18
69 88 1.216122 TACGTTTTTGGAACGGACGG 58.784 50.000 14.68 0.00 46.86 4.79
79 98 1.145803 GAACGGACGGGAAACTCAAG 58.854 55.000 0.00 0.00 0.00 3.02
101 120 9.671279 TCAAGCTTGACATAAAGAAATATCTCA 57.329 29.630 25.16 0.00 30.57 3.27
102 121 9.713740 CAAGCTTGACATAAAGAAATATCTCAC 57.286 33.333 22.31 0.00 33.77 3.51
141 160 6.560253 TGCTTCAATTCTTACCAGAAACTC 57.440 37.500 0.00 0.00 42.53 3.01
160 179 6.656632 AACTCAGACATGAAGTACAGAAGA 57.343 37.500 0.00 0.00 34.23 2.87
195 215 1.597937 GCCAGTGCAACGTTTTCTCTG 60.598 52.381 16.42 16.42 45.86 3.35
197 217 2.354510 CCAGTGCAACGTTTTCTCTGAA 59.645 45.455 21.43 0.00 45.86 3.02
285 305 1.871039 CACCTCACAAAACGTTCCGAT 59.129 47.619 0.00 0.00 0.00 4.18
487 522 2.032681 GGGCAGTCAGTGGTCACC 59.967 66.667 0.00 0.00 0.00 4.02
488 523 2.357517 GGCAGTCAGTGGTCACCG 60.358 66.667 0.00 0.00 0.00 4.94
860 913 0.034059 CTTCCTTCACACCTGCGAGT 59.966 55.000 0.00 0.00 0.00 4.18
878 931 3.640592 GAGTTGTATAAGTAGAGCCGGC 58.359 50.000 21.89 21.89 0.00 6.13
879 932 3.028850 AGTTGTATAAGTAGAGCCGGCA 58.971 45.455 31.54 4.59 0.00 5.69
882 935 3.028850 TGTATAAGTAGAGCCGGCAACT 58.971 45.455 31.54 27.52 0.00 3.16
928 990 4.000331 TCCAAGCAGTGAAAGAGAAGAG 58.000 45.455 0.00 0.00 0.00 2.85
960 1023 3.480470 CTCAACAGCCTTCTTTTCCAGA 58.520 45.455 0.00 0.00 0.00 3.86
1308 1405 4.785453 CGGGCACAAGGGAGGAGC 62.785 72.222 0.00 0.00 0.00 4.70
1310 1407 3.650950 GGCACAAGGGAGGAGCCA 61.651 66.667 0.00 0.00 44.59 4.75
1311 1408 2.679716 GCACAAGGGAGGAGCCAT 59.320 61.111 0.00 0.00 38.95 4.40
1312 1409 1.635817 GGCACAAGGGAGGAGCCATA 61.636 60.000 0.00 0.00 44.59 2.74
1313 1410 0.464554 GCACAAGGGAGGAGCCATAC 60.465 60.000 0.00 0.00 38.95 2.39
1315 1412 0.044855 ACAAGGGAGGAGCCATACCT 59.955 55.000 0.00 0.00 40.80 3.08
1317 1414 1.216990 AAGGGAGGAGCCATACCTTG 58.783 55.000 2.95 0.00 39.89 3.61
1318 1415 0.343372 AGGGAGGAGCCATACCTTGA 59.657 55.000 0.00 0.00 37.93 3.02
1321 1418 1.771255 GGAGGAGCCATACCTTGATGT 59.229 52.381 0.00 0.00 37.93 3.06
1322 1419 2.486191 GGAGGAGCCATACCTTGATGTG 60.486 54.545 0.00 0.00 37.93 3.21
1323 1420 1.133976 AGGAGCCATACCTTGATGTGC 60.134 52.381 0.00 0.00 33.55 4.57
1392 1506 3.886505 AGTAGTAGTAGTGCTCATGCCTC 59.113 47.826 0.00 0.00 38.71 4.70
1429 1546 7.203255 AGATAAATAAATAAAGCGCCCAGTC 57.797 36.000 2.29 0.00 0.00 3.51
1462 1579 9.760926 ACTGTATCATATCATGTACTCCTATGT 57.239 33.333 0.00 0.00 0.00 2.29
1603 4878 4.946157 TCTGCTCAATCTTCTTCCATTTCC 59.054 41.667 0.00 0.00 0.00 3.13
1615 4895 9.421399 TCTTCTTCCATTTCCTTTTAGAAAAGT 57.579 29.630 12.51 0.00 42.92 2.66
1617 4897 7.433680 TCTTCCATTTCCTTTTAGAAAAGTGC 58.566 34.615 12.51 0.00 42.92 4.40
1653 4933 1.682323 TGCAGCATTTTGTCAAGAGCA 59.318 42.857 0.00 0.00 0.00 4.26
1673 4953 3.694072 GCAGTTTATTGACACCTGGCATA 59.306 43.478 0.00 0.00 30.06 3.14
1674 4954 4.157656 GCAGTTTATTGACACCTGGCATAA 59.842 41.667 0.00 0.00 30.06 1.90
1675 4955 5.163519 GCAGTTTATTGACACCTGGCATAAT 60.164 40.000 0.00 0.00 30.06 1.28
1676 4956 6.039270 GCAGTTTATTGACACCTGGCATAATA 59.961 38.462 0.00 0.00 30.06 0.98
1683 4963 5.704354 TGACACCTGGCATAATAATCCAAT 58.296 37.500 0.00 0.00 0.00 3.16
1861 5194 8.966155 TGATCTATAGGATTGTGTATTACCCA 57.034 34.615 0.00 0.00 34.33 4.51
1899 5232 4.332683 ACCTGGACTTACATCCTACTGA 57.667 45.455 0.00 0.00 39.75 3.41
1936 5269 4.129380 TGAAAGATATGGGATGCACGAAG 58.871 43.478 0.00 0.00 0.00 3.79
1976 5309 1.409064 GAGGACATCCATACTGCGACA 59.591 52.381 0.00 0.00 38.89 4.35
1991 5324 1.401539 GCGACAACCTTCATCTTTGGC 60.402 52.381 0.00 0.00 0.00 4.52
1999 5332 0.810648 TTCATCTTTGGCATCACCGC 59.189 50.000 0.00 0.00 43.94 5.68
2012 5345 0.250295 TCACCGCCTCTCCAAACAAG 60.250 55.000 0.00 0.00 0.00 3.16
2037 5370 4.925054 CGATAAGGTGGTTGTTTTCTCGTA 59.075 41.667 0.00 0.00 0.00 3.43
2148 5490 1.877443 GCGGAAGTGCCACTCTTAAAA 59.123 47.619 0.00 0.00 35.94 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 88 6.560253 TCTTTATGTCAAGCTTGAGTTTCC 57.440 37.500 29.13 17.08 37.98 3.13
79 98 9.928236 GAAGTGAGATATTTCTTTATGTCAAGC 57.072 33.333 0.00 0.00 34.70 4.01
101 120 4.937620 TGAAGCAAAATATCTCAGCGAAGT 59.062 37.500 0.00 0.00 0.00 3.01
102 121 5.475273 TGAAGCAAAATATCTCAGCGAAG 57.525 39.130 0.00 0.00 0.00 3.79
106 125 9.230932 GTAAGAATTGAAGCAAAATATCTCAGC 57.769 33.333 0.00 0.00 0.00 4.26
141 160 5.173664 TGCATCTTCTGTACTTCATGTCTG 58.826 41.667 0.00 0.00 0.00 3.51
160 179 1.339055 ACTGGCTAACACACGATGCAT 60.339 47.619 0.00 0.00 0.00 3.96
197 217 0.398318 GGGCAGGTGAAGTTCAGACT 59.602 55.000 5.62 4.99 37.87 3.24
229 249 4.138487 ACGTTGAGGTTCAGAGAAAACT 57.862 40.909 0.00 0.00 0.00 2.66
302 322 0.029300 CAAGGTTTATGCCGCCGATG 59.971 55.000 0.00 0.00 0.00 3.84
306 326 1.312371 TGAGCAAGGTTTATGCCGCC 61.312 55.000 0.00 0.00 44.91 6.13
382 416 2.594013 TGCTCGCATGGTTGTGCA 60.594 55.556 0.00 0.00 45.30 4.57
832 882 1.541588 GTGTGAAGGAAGGCACCAATC 59.458 52.381 3.78 2.63 34.19 2.67
835 885 4.898607 GTGTGAAGGAAGGCACCA 57.101 55.556 3.78 0.00 34.19 4.17
860 913 3.449737 AGTTGCCGGCTCTACTTATACAA 59.550 43.478 29.70 5.56 0.00 2.41
878 931 4.515567 GGGTGTTCCTTTAACTCTGAGTTG 59.484 45.833 28.46 14.58 39.11 3.16
879 932 4.165372 TGGGTGTTCCTTTAACTCTGAGTT 59.835 41.667 24.80 24.80 38.99 3.01
882 935 3.714798 AGTGGGTGTTCCTTTAACTCTGA 59.285 43.478 0.00 0.00 38.99 3.27
960 1023 1.068472 GCTACGTACACAGCACACTCT 60.068 52.381 10.10 0.00 37.73 3.24
1308 1405 0.107214 ACCCGCACATCAAGGTATGG 60.107 55.000 0.00 0.00 0.00 2.74
1310 1407 1.408266 GGAACCCGCACATCAAGGTAT 60.408 52.381 0.00 0.00 30.63 2.73
1311 1408 0.035820 GGAACCCGCACATCAAGGTA 60.036 55.000 0.00 0.00 30.63 3.08
1312 1409 1.303317 GGAACCCGCACATCAAGGT 60.303 57.895 0.00 0.00 0.00 3.50
1313 1410 1.002134 AGGAACCCGCACATCAAGG 60.002 57.895 0.00 0.00 0.00 3.61
1315 1412 0.400213 AAGAGGAACCCGCACATCAA 59.600 50.000 0.00 0.00 0.00 2.57
1317 1414 0.321653 ACAAGAGGAACCCGCACATC 60.322 55.000 0.00 0.00 0.00 3.06
1318 1415 0.981183 TACAAGAGGAACCCGCACAT 59.019 50.000 0.00 0.00 0.00 3.21
1321 1418 0.981183 ATGTACAAGAGGAACCCGCA 59.019 50.000 0.00 0.00 0.00 5.69
1322 1419 2.973694 TATGTACAAGAGGAACCCGC 57.026 50.000 0.00 0.00 0.00 6.13
1323 1420 3.118738 AGCTTATGTACAAGAGGAACCCG 60.119 47.826 0.00 0.00 0.00 5.28
1370 1476 3.886505 GAGGCATGAGCACTACTACTACT 59.113 47.826 0.00 0.00 44.61 2.57
1417 1534 0.605319 TTGATTCGACTGGGCGCTTT 60.605 50.000 7.64 0.00 0.00 3.51
1419 1536 1.741770 GTTGATTCGACTGGGCGCT 60.742 57.895 7.64 0.00 0.00 5.92
1423 1540 4.123497 TGATACAGTTGATTCGACTGGG 57.877 45.455 29.23 12.63 46.83 4.45
1429 1546 9.631452 AGTACATGATATGATACAGTTGATTCG 57.369 33.333 0.00 0.00 0.00 3.34
1461 1578 8.421784 TCCATTCAAAGGATACAGTCATACTAC 58.578 37.037 0.00 0.00 41.41 2.73
1462 1579 8.547481 TCCATTCAAAGGATACAGTCATACTA 57.453 34.615 0.00 0.00 41.41 1.82
1463 1580 7.437713 TCCATTCAAAGGATACAGTCATACT 57.562 36.000 0.00 0.00 41.41 2.12
1614 4894 2.349532 GCAAGAACTGTAAACTCCGCAC 60.350 50.000 0.00 0.00 0.00 5.34
1615 4895 1.871039 GCAAGAACTGTAAACTCCGCA 59.129 47.619 0.00 0.00 0.00 5.69
1617 4897 2.096218 GCTGCAAGAACTGTAAACTCCG 60.096 50.000 0.00 0.00 34.07 4.63
1653 4933 8.766994 ATTATTATGCCAGGTGTCAATAAACT 57.233 30.769 0.00 0.00 0.00 2.66
1665 4945 8.585471 AACATAGATTGGATTATTATGCCAGG 57.415 34.615 0.00 0.00 32.47 4.45
1673 4953 8.966868 ACAACGGAAAACATAGATTGGATTATT 58.033 29.630 0.00 0.00 0.00 1.40
1674 4954 8.519799 ACAACGGAAAACATAGATTGGATTAT 57.480 30.769 0.00 0.00 0.00 1.28
1675 4955 7.931578 ACAACGGAAAACATAGATTGGATTA 57.068 32.000 0.00 0.00 0.00 1.75
1676 4956 6.834168 ACAACGGAAAACATAGATTGGATT 57.166 33.333 0.00 0.00 0.00 3.01
1683 4963 6.987992 AGTAGTTCAACAACGGAAAACATAGA 59.012 34.615 0.00 0.00 37.61 1.98
1773 5053 4.788679 TCCTCGTGGTATCTTCTATGTCA 58.211 43.478 2.99 0.00 34.23 3.58
1811 5144 2.699554 TGGGGGTGGGGATGATGG 60.700 66.667 0.00 0.00 0.00 3.51
1857 5190 0.608640 GAGTGTTCGACTCCATGGGT 59.391 55.000 13.02 8.85 44.95 4.51
1880 5213 6.540189 CCATTTTCAGTAGGATGTAAGTCCAG 59.460 42.308 0.00 0.00 40.90 3.86
1922 5255 3.204827 GCGCTTCGTGCATCCCAT 61.205 61.111 0.00 0.00 43.06 4.00
1936 5269 2.396157 CCCCTAAAAGTCGTGGCGC 61.396 63.158 0.00 0.00 0.00 6.53
1942 5275 0.459759 GTCCTCGCCCCTAAAAGTCG 60.460 60.000 0.00 0.00 0.00 4.18
1976 5309 2.827921 GGTGATGCCAAAGATGAAGGTT 59.172 45.455 0.00 0.00 37.17 3.50
1991 5324 0.321564 TGTTTGGAGAGGCGGTGATG 60.322 55.000 0.00 0.00 0.00 3.07
1999 5332 4.184629 CCTTATCGTCTTGTTTGGAGAGG 58.815 47.826 0.00 0.00 0.00 3.69
2012 5345 4.143179 CGAGAAAACAACCACCTTATCGTC 60.143 45.833 0.00 0.00 0.00 4.20
2037 5370 3.003378 GCACGAAGAAAGGTAAAGTTGCT 59.997 43.478 0.00 0.00 0.00 3.91
2103 5436 3.336468 ACACAACCAAGTTAACACGTCA 58.664 40.909 8.61 0.00 0.00 4.35
2106 5439 4.784079 GCACTACACAACCAAGTTAACACG 60.784 45.833 8.61 0.00 0.00 4.49
2148 5490 4.145807 TGTGTTTGGTATTCGGTGGATTT 58.854 39.130 0.00 0.00 0.00 2.17
2151 5493 2.879646 GTTGTGTTTGGTATTCGGTGGA 59.120 45.455 0.00 0.00 0.00 4.02
2152 5494 2.030628 GGTTGTGTTTGGTATTCGGTGG 60.031 50.000 0.00 0.00 0.00 4.61
2154 5496 2.933573 TGGTTGTGTTTGGTATTCGGT 58.066 42.857 0.00 0.00 0.00 4.69
2155 5497 3.992260 TTGGTTGTGTTTGGTATTCGG 57.008 42.857 0.00 0.00 0.00 4.30
2157 5499 5.980715 ACGATTTTGGTTGTGTTTGGTATTC 59.019 36.000 0.00 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.