Multiple sequence alignment - TraesCS1B01G337000

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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 TraesCS1B01G337000 chr1B 100.000 2444 0 0 1 2444 564123446 564121003 0.000000e+00 4514
1 TraesCS1B01G337000 chr1B 79.479 307 50 11 790 1087 509053323 509053021 3.190000e-49 206
2 TraesCS1B01G337000 chr2B 97.001 1667 50 0 778 2444 68371882 68373548 0.000000e+00 2802
3 TraesCS1B01G337000 chr2B 90.085 1654 145 12 790 2441 12252140 12253776 0.000000e+00 2128
4 TraesCS1B01G337000 chr2B 88.985 1625 155 20 826 2444 709427959 709429565 0.000000e+00 1988
5 TraesCS1B01G337000 chr5B 96.041 1667 63 1 778 2444 546131055 546129392 0.000000e+00 2710
6 TraesCS1B01G337000 chr6B 95.743 1668 69 2 778 2444 18756505 18754839 0.000000e+00 2686
7 TraesCS1B01G337000 chr4A 92.164 1659 124 5 790 2444 713935714 713937370 0.000000e+00 2338
8 TraesCS1B01G337000 chr2A 88.875 1636 165 13 819 2444 572592594 572594222 0.000000e+00 1997
9 TraesCS1B01G337000 chr2A 91.142 1445 124 2 1000 2444 70695822 70697262 0.000000e+00 1956
10 TraesCS1B01G337000 chr2A 90.634 1452 130 2 993 2444 753053795 753055240 0.000000e+00 1923
11 TraesCS1B01G337000 chr7A 88.364 1650 171 11 790 2434 707761366 707762999 0.000000e+00 1964
12 TraesCS1B01G337000 chr7A 88.051 1657 179 9 790 2442 710542576 710540935 0.000000e+00 1945
13 TraesCS1B01G337000 chr5D 93.487 783 40 10 1 777 74768738 74769515 0.000000e+00 1153
14 TraesCS1B01G337000 chr5D 93.453 779 43 8 1 777 42358878 42358106 0.000000e+00 1149
15 TraesCS1B01G337000 chr2D 93.376 785 39 10 1 777 536502233 536503012 0.000000e+00 1149
16 TraesCS1B01G337000 chr2D 93.121 785 42 7 1 777 124071840 124071060 0.000000e+00 1140
17 TraesCS1B01G337000 chrUn 93.248 785 41 8 1 777 131998365 131999145 0.000000e+00 1146
18 TraesCS1B01G337000 chr7D 93.240 784 44 8 1 777 526137374 526138155 0.000000e+00 1146
19 TraesCS1B01G337000 chr4D 93.240 784 43 6 1 777 362822834 362822054 0.000000e+00 1146
20 TraesCS1B01G337000 chr4D 93.205 780 46 7 1 777 364240658 364239883 0.000000e+00 1140
21 TraesCS1B01G337000 chr4D 93.121 785 42 7 1 777 481096386 481095606 0.000000e+00 1140
22 TraesCS1B01G337000 chr1D 83.735 166 20 4 778 938 394843333 394843170 1.510000e-32 150


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 TraesCS1B01G337000 chr1B 564121003 564123446 2443 True 4514 4514 100.000 1 2444 1 chr1B.!!$R2 2443
1 TraesCS1B01G337000 chr2B 68371882 68373548 1666 False 2802 2802 97.001 778 2444 1 chr2B.!!$F2 1666
2 TraesCS1B01G337000 chr2B 12252140 12253776 1636 False 2128 2128 90.085 790 2441 1 chr2B.!!$F1 1651
3 TraesCS1B01G337000 chr2B 709427959 709429565 1606 False 1988 1988 88.985 826 2444 1 chr2B.!!$F3 1618
4 TraesCS1B01G337000 chr5B 546129392 546131055 1663 True 2710 2710 96.041 778 2444 1 chr5B.!!$R1 1666
5 TraesCS1B01G337000 chr6B 18754839 18756505 1666 True 2686 2686 95.743 778 2444 1 chr6B.!!$R1 1666
6 TraesCS1B01G337000 chr4A 713935714 713937370 1656 False 2338 2338 92.164 790 2444 1 chr4A.!!$F1 1654
7 TraesCS1B01G337000 chr2A 572592594 572594222 1628 False 1997 1997 88.875 819 2444 1 chr2A.!!$F2 1625
8 TraesCS1B01G337000 chr2A 70695822 70697262 1440 False 1956 1956 91.142 1000 2444 1 chr2A.!!$F1 1444
9 TraesCS1B01G337000 chr2A 753053795 753055240 1445 False 1923 1923 90.634 993 2444 1 chr2A.!!$F3 1451
10 TraesCS1B01G337000 chr7A 707761366 707762999 1633 False 1964 1964 88.364 790 2434 1 chr7A.!!$F1 1644
11 TraesCS1B01G337000 chr7A 710540935 710542576 1641 True 1945 1945 88.051 790 2442 1 chr7A.!!$R1 1652
12 TraesCS1B01G337000 chr5D 74768738 74769515 777 False 1153 1153 93.487 1 777 1 chr5D.!!$F1 776
13 TraesCS1B01G337000 chr5D 42358106 42358878 772 True 1149 1149 93.453 1 777 1 chr5D.!!$R1 776
14 TraesCS1B01G337000 chr2D 536502233 536503012 779 False 1149 1149 93.376 1 777 1 chr2D.!!$F1 776
15 TraesCS1B01G337000 chr2D 124071060 124071840 780 True 1140 1140 93.121 1 777 1 chr2D.!!$R1 776
16 TraesCS1B01G337000 chrUn 131998365 131999145 780 False 1146 1146 93.248 1 777 1 chrUn.!!$F1 776
17 TraesCS1B01G337000 chr7D 526137374 526138155 781 False 1146 1146 93.240 1 777 1 chr7D.!!$F1 776
18 TraesCS1B01G337000 chr4D 362822054 362822834 780 True 1146 1146 93.240 1 777 1 chr4D.!!$R1 776
19 TraesCS1B01G337000 chr4D 364239883 364240658 775 True 1140 1140 93.205 1 777 1 chr4D.!!$R2 776
20 TraesCS1B01G337000 chr4D 481095606 481096386 780 True 1140 1140 93.121 1 777 1 chr4D.!!$R3 776

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
609 631 0.034477 AAACTTTCCCGATGGCCGAT 60.034 50.0 0.0 0.0 41.76 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2091 2144 0.171455 GACGCTCCAGGTCACTAGTG 59.829 60.0 17.17 17.17 34.56 2.74 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
42 43 1.611977 AGAACGTCGTTGATGGAGTCA 59.388 47.619 16.75 0.0 34.25 3.41
48 49 3.181500 CGTCGTTGATGGAGTCATACTCA 60.181 47.826 9.15 0.0 46.79 3.41
85 86 0.753262 AATGATCCTAGCGCCGAACT 59.247 50.000 2.29 0.0 0.00 3.01
110 111 1.070786 ACCTCCGCGTTCAACACAT 59.929 52.632 4.92 0.0 0.00 3.21
216 217 2.044946 GTGGAAGCAGCGGGGATT 60.045 61.111 0.00 0.0 0.00 3.01
260 261 1.592400 CGCGAGGGAGAGGTGTTACA 61.592 60.000 0.00 0.0 0.00 2.41
502 524 0.476771 TGGTTCCCTTCCCACTTCAC 59.523 55.000 0.00 0.0 0.00 3.18
578 600 0.903942 GGTGGTCCCGGTACAATACA 59.096 55.000 0.00 0.0 0.00 2.29
579 601 1.278699 GGTGGTCCCGGTACAATACAA 59.721 52.381 0.00 0.0 0.00 2.41
588 610 2.624636 GGTACAATACAAGTGACCCCG 58.375 52.381 0.00 0.0 0.00 5.73
609 631 0.034477 AAACTTTCCCGATGGCCGAT 60.034 50.000 0.00 0.0 41.76 4.18
641 663 9.440761 ACTTCCTATATACAAATCTTCACCTCT 57.559 33.333 0.00 0.0 0.00 3.69
681 703 1.886542 CGTGATGTCCGGGATCTCATA 59.113 52.381 0.00 0.0 0.00 2.15
702 724 1.487142 TGGGACTCCGAACAACTTTCA 59.513 47.619 0.00 0.0 35.24 2.69
703 725 2.092861 TGGGACTCCGAACAACTTTCAA 60.093 45.455 0.00 0.0 35.24 2.69
710 732 4.773013 TCCGAACAACTTTCAAGTTACCT 58.227 39.130 4.61 0.0 46.89 3.08
765 787 4.566987 GAACCTTAAGTGTGTAGACCCTG 58.433 47.826 0.97 0.0 0.00 4.45
824 846 9.865321 GTAACATAACTCTGTATTGTTGGTCTA 57.135 33.333 0.00 0.0 0.00 2.59
1026 1076 3.706373 GGTTCCTCCTCCGCAGCA 61.706 66.667 0.00 0.0 0.00 4.41
1065 1115 2.605607 CCCTGTGGTGATGCCTCCA 61.606 63.158 0.00 0.0 38.35 3.86
1370 1420 2.496070 TGATTAGCTGTAAGTCCGCTGT 59.504 45.455 0.00 0.0 37.22 4.40
1497 1547 1.548719 AGCGAGTACATGCACAAGGTA 59.451 47.619 11.30 0.0 0.00 3.08
1704 1754 1.820906 GCAGCAGGCCGATGATGAA 60.821 57.895 13.95 0.0 38.89 2.57
1725 1775 3.000819 TGGACCTCGTCGGCCAAT 61.001 61.111 2.24 0.0 36.45 3.16
1971 2021 0.527817 GTCACGAAGCCGATACCTGG 60.528 60.000 0.00 0.0 39.50 4.45
2091 2144 2.125106 GGCACCACGGATCACCTC 60.125 66.667 0.00 0.0 0.00 3.85
2160 2213 0.706433 ATCAGGTTCAGGTGGCCAAT 59.294 50.000 7.24 0.0 0.00 3.16
2219 2272 3.323979 ACTTTAGCCGGTTCTTCTCTTCA 59.676 43.478 1.90 0.0 0.00 3.02
2268 2321 9.606631 CCTAATATTAGCCAACATCTTCTATCC 57.393 37.037 15.86 0.0 0.00 2.59
2426 2479 1.153765 CTTCGCATGAGTCCGAGCA 60.154 57.895 0.00 0.0 34.68 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 4.261197 CGATGAGTATGACTCCATCAACGA 60.261 45.833 4.24 0.00 44.44 3.85
29 30 3.977579 CGATGAGTATGACTCCATCAACG 59.022 47.826 4.24 0.00 44.44 4.10
66 67 0.753262 AGTTCGGCGCTAGGATCATT 59.247 50.000 7.64 0.00 0.00 2.57
110 111 0.538057 ACGTCTCTCCCAACCGTACA 60.538 55.000 0.00 0.00 0.00 2.90
195 196 4.335647 CCCGCTGCTTCCACCACT 62.336 66.667 0.00 0.00 0.00 4.00
243 244 0.818296 CCTGTAACACCTCTCCCTCG 59.182 60.000 0.00 0.00 0.00 4.63
268 269 1.304464 CCCCTGGTGCCTTCCTTTC 60.304 63.158 0.00 0.00 0.00 2.62
270 271 3.984732 GCCCCTGGTGCCTTCCTT 61.985 66.667 0.00 0.00 0.00 3.36
578 600 1.478105 GGAAAGTTTCCGGGGTCACTT 60.478 52.381 18.70 1.97 40.59 3.16
579 601 0.109913 GGAAAGTTTCCGGGGTCACT 59.890 55.000 18.70 0.00 40.59 3.41
641 663 0.546747 AGGAGTTCCGGAATGGTCCA 60.547 55.000 30.22 5.90 45.26 4.02
681 703 2.105821 TGAAAGTTGTTCGGAGTCCCAT 59.894 45.455 2.80 0.00 0.00 4.00
710 732 9.463902 GCTAGGGTTGTAGAGATATTAGTATGA 57.536 37.037 0.00 0.00 0.00 2.15
765 787 3.131478 CCAACATCCCGAACCCGC 61.131 66.667 0.00 0.00 0.00 6.13
824 846 7.612244 AGCCTCCGCATATCTCGTATATATATT 59.388 37.037 0.00 0.00 37.52 1.28
990 1040 1.088340 CAGAAGCCATCACGCAGAGG 61.088 60.000 0.00 0.00 0.00 3.69
991 1041 1.088340 CCAGAAGCCATCACGCAGAG 61.088 60.000 0.00 0.00 0.00 3.35
1026 1076 0.464036 CAATGATGGCCAGCTGCATT 59.536 50.000 23.69 18.95 43.89 3.56
1211 1261 2.117206 GGGTGATGGTTGTGGGCA 59.883 61.111 0.00 0.00 0.00 5.36
1704 1754 3.063084 GCCGACGAGGTCCACTCT 61.063 66.667 0.00 0.00 44.33 3.24
1971 2021 5.349824 AGTCTGAATCAAAACGCTTCTTC 57.650 39.130 0.00 0.00 0.00 2.87
2091 2144 0.171455 GACGCTCCAGGTCACTAGTG 59.829 60.000 17.17 17.17 34.56 2.74
2160 2213 3.334691 CGAAATAGACAAACCTGAGCCA 58.665 45.455 0.00 0.00 0.00 4.75
2219 2272 6.713450 AGGAACGTGTAAAATATTGTTCAGGT 59.287 34.615 13.15 9.51 37.91 4.00
2426 2479 4.115279 CGCTGGATGACGCTTGAT 57.885 55.556 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.