Multiple sequence alignment - TraesCS5B01G249800

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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 TraesCS5B01G249800 chr5B 100.000 2846 0 0 1 2846 432322296 432325141 0.000000e+00 5256.0
1 TraesCS5B01G249800 chr5B 94.118 51 3 0 1601 1651 432323788 432323838 8.450000e-11 78.7
2 TraesCS5B01G249800 chr5B 94.118 51 3 0 1493 1543 432323896 432323946 8.450000e-11 78.7
3 TraesCS5B01G249800 chr5D 93.241 2589 91 33 323 2846 365991771 365994340 0.000000e+00 3735.0
4 TraesCS5B01G249800 chr5D 93.361 241 15 1 1 240 365991512 365991752 3.490000e-94 355.0
5 TraesCS5B01G249800 chr5D 83.333 168 20 3 1460 1620 365992963 365993129 6.350000e-32 148.0
6 TraesCS5B01G249800 chr5D 91.228 57 4 1 1601 1656 365992945 365993001 3.040000e-10 76.8
7 TraesCS5B01G249800 chr5D 97.500 40 0 1 2398 2437 365993839 365993877 1.830000e-07 67.6
8 TraesCS5B01G249800 chr5A 86.477 2995 179 107 3 2846 467584639 467587558 0.000000e+00 3079.0
9 TraesCS5B01G249800 chr5A 92.857 56 4 0 1493 1548 467586304 467586359 6.530000e-12 82.4
10 TraesCS5B01G249800 chr6D 88.742 151 17 0 1139 1289 358326157 358326007 4.840000e-43 185.0
11 TraesCS5B01G249800 chr6D 88.000 150 18 0 1139 1288 378379440 378379291 8.100000e-41 178.0
12 TraesCS5B01G249800 chr6A 88.742 151 17 0 1139 1289 500083776 500083626 4.840000e-43 185.0
13 TraesCS5B01G249800 chr6A 88.000 150 18 0 1139 1288 520355710 520355561 8.100000e-41 178.0
14 TraesCS5B01G249800 chr6B 88.079 151 18 0 1139 1289 539727701 539727551 2.250000e-41 180.0
15 TraesCS5B01G249800 chr3D 87.097 155 18 2 1135 1288 61703553 61703400 1.050000e-39 174.0
16 TraesCS5B01G249800 chr2D 87.417 151 19 0 1139 1289 32763270 32763420 1.050000e-39 174.0
17 TraesCS5B01G249800 chr2B 100.000 28 0 0 1291 1318 693005282 693005309 5.000000e-03 52.8
18 TraesCS5B01G249800 chr1D 100.000 28 0 0 1290 1317 40202574 40202601 5.000000e-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 TraesCS5B01G249800 chr5B 432322296 432325141 2845 False 1804.466667 5256 96.078667 1 2846 3 chr5B.!!$F1 2845
1 TraesCS5B01G249800 chr5D 365991512 365994340 2828 False 876.480000 3735 91.732600 1 2846 5 chr5D.!!$F1 2845
2 TraesCS5B01G249800 chr5A 467584639 467587558 2919 False 1580.700000 3079 89.667000 3 2846 2 chr5A.!!$F1 2843

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
671 753 1.445582 CGGCTGGTTCGTGGTACTC 60.446 63.158 0.0 0.0 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2308 2479 0.459489 GCACGCTCTCCTCTCTTCAT 59.541 55.0 0.0 0.0 0.0 2.57 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
87 88 2.788640 GCAATGGCGGCATCATGGT 61.789 57.895 25.97 6.05 0.00 3.55
94 95 2.404789 GGCATCATGGTGCGAACG 59.595 61.111 24.11 0.00 45.97 3.95
261 263 2.752358 CAGAGGCCAGAGCAACCA 59.248 61.111 5.01 0.00 42.56 3.67
393 423 2.046507 GGGTGCCACTGCTGAGAG 60.047 66.667 0.00 0.00 38.71 3.20
482 528 1.582968 GTTCCTGTACGTGCCGAGA 59.417 57.895 0.00 0.00 0.00 4.04
626 702 1.642037 CGCGTCGTCTCAAGGGAGTA 61.642 60.000 0.00 0.00 42.05 2.59
671 753 1.445582 CGGCTGGTTCGTGGTACTC 60.446 63.158 0.00 0.00 0.00 2.59
776 861 1.961277 CACACCGCTCCAACAGTCC 60.961 63.158 0.00 0.00 0.00 3.85
809 906 3.361158 CACCGTCAAATGCCGCCA 61.361 61.111 0.00 0.00 0.00 5.69
1302 1412 1.599606 GCAAGAGCTCCTCCTCGTCA 61.600 60.000 10.93 0.00 36.95 4.35
1466 1585 0.946221 GAGGACGTCACAACAGCTGG 60.946 60.000 19.93 3.21 0.00 4.85
1471 1590 0.735978 CGTCACAACAGCTGGCGATA 60.736 55.000 19.93 0.00 0.00 2.92
1564 1683 2.676342 GACAGGTGTTTCACTTTCACGT 59.324 45.455 0.06 0.00 34.40 4.49
1981 2111 9.353999 GTAGTATTTGGAAATTTTCATGTCACC 57.646 33.333 11.09 0.00 0.00 4.02
2018 2148 3.678072 TCGATCTAAGAAGCCGTTTGTTG 59.322 43.478 0.00 0.00 0.00 3.33
2143 2277 3.243002 GCGATTAGCGAACTACCACTACT 60.243 47.826 0.00 0.00 44.57 2.57
2274 2431 2.830651 ACCTGTAGCTAGCCAGTACT 57.169 50.000 12.13 0.00 0.00 2.73
2280 2437 2.054232 AGCTAGCCAGTACTTCGCTA 57.946 50.000 12.13 16.80 34.03 4.26
2288 2445 3.252701 GCCAGTACTTCGCTACTAGCATA 59.747 47.826 8.78 0.00 42.58 3.14
2294 2451 4.145807 ACTTCGCTACTAGCATACCTGAT 58.854 43.478 8.78 0.00 42.58 2.90
2308 2479 0.107993 CCTGATGCTTCTTGCTCCGA 60.108 55.000 0.88 0.00 43.37 4.55
2369 2568 0.393944 AGCACAGGCATGTCCAGATG 60.394 55.000 0.00 0.00 44.61 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.078143 GGTGCCCAGTGACTGATCC 60.078 63.158 15.33 6.84 32.44 3.36
8 9 0.036732 TTGGTGCCCAGTGACTGATC 59.963 55.000 15.33 5.65 33.81 2.92
94 95 1.154205 CGATGGTGCCACGAATCTCC 61.154 60.000 7.34 0.00 0.00 3.71
245 247 3.076092 CTGGTTGCTCTGGCCTCT 58.924 61.111 3.32 0.00 37.74 3.69
671 753 0.040958 GTACGGGCATACGACGTAGG 60.041 60.000 14.94 14.94 42.82 3.18
809 906 1.165270 GGAGCAGCATTTTACGGTGT 58.835 50.000 0.00 0.00 34.37 4.16
1302 1412 2.783275 CTGGACGACGACGACGAT 59.217 61.111 25.15 10.17 42.66 3.73
1420 1536 3.745803 GGCCTCCTTCGTCGTCGT 61.746 66.667 0.00 0.00 38.33 4.34
1545 1664 2.031683 GGACGTGAAAGTGAAACACCTG 59.968 50.000 0.00 0.00 41.43 4.00
1546 1665 2.285977 GGACGTGAAAGTGAAACACCT 58.714 47.619 0.00 0.00 41.43 4.00
1873 1992 3.927548 TGCCGTGCTCAGCTCACA 61.928 61.111 0.00 0.00 34.27 3.58
2018 2148 3.669354 CCTTCCGATCAGGCACTAC 57.331 57.895 0.00 0.00 40.77 2.73
2274 2431 4.505313 CATCAGGTATGCTAGTAGCGAA 57.495 45.455 17.16 4.96 46.26 4.70
2308 2479 0.459489 GCACGCTCTCCTCTCTTCAT 59.541 55.000 0.00 0.00 0.00 2.57
2369 2568 5.511088 CACTGTACGTGAAGTTATGAACC 57.489 43.478 10.97 0.00 46.81 3.62
2392 2591 1.376466 CCTGTGCTGTACTGCCCTT 59.624 57.895 20.46 0.00 0.00 3.95
2828 3046 4.789075 ACCACGGCCGAATCGACG 62.789 66.667 35.90 15.56 34.51 5.12


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

AutoCloner maintained by Alex Coulton.