Multiple sequence alignment - TraesCS7B01G398600

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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 TraesCS7B01G398600 chr7B 100.000 2264 0 0 1 2264 664951467 664949204 0 4181
1 TraesCS7B01G398600 chr7B 97.792 1585 32 3 1 1583 666615844 666617427 0 2730
2 TraesCS7B01G398600 chr7B 97.539 1585 33 5 1 1583 535437148 535435568 0 2706
3 TraesCS7B01G398600 chr7B 97.926 675 12 2 1592 2264 666618484 666619158 0 1168
4 TraesCS7B01G398600 chr5B 97.541 1586 32 6 1 1583 123786976 123788557 0 2706
5 TraesCS7B01G398600 chr5B 97.415 1586 38 3 1 1583 353930733 353929148 0 2699
6 TraesCS7B01G398600 chr5B 97.037 1586 41 4 1 1583 18184114 18185696 0 2663
7 TraesCS7B01G398600 chr5B 98.233 679 10 2 1588 2264 353928322 353927644 0 1186
8 TraesCS7B01G398600 chr5B 97.644 679 14 2 1588 2264 18186525 18187203 0 1164
9 TraesCS7B01G398600 chr5B 96.465 679 20 4 1588 2264 123789463 123790139 0 1118
10 TraesCS7B01G398600 chr5B 96.058 685 24 3 1582 2264 514053205 514053888 0 1112
11 TraesCS7B01G398600 chr3B 97.350 1585 39 3 1 1583 734227363 734225780 0 2691
12 TraesCS7B01G398600 chr3B 91.488 1586 120 10 1 1583 21644989 21646562 0 2167
13 TraesCS7B01G398600 chr3B 97.938 679 12 2 1588 2264 734224671 734223993 0 1175
14 TraesCS7B01G398600 chr3D 95.400 1587 65 7 1 1583 581472631 581474213 0 2519
15 TraesCS7B01G398600 chr6B 91.384 1590 120 10 1 1583 715471834 715470255 0 2161
16 TraesCS7B01G398600 chr6B 94.551 679 32 5 1588 2264 77325790 77325115 0 1044
17 TraesCS7B01G398600 chr4B 96.471 680 18 4 1588 2264 522406316 522406992 0 1118
18 TraesCS7B01G398600 chr4A 95.729 679 25 4 1588 2264 692374617 692373941 0 1090


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 TraesCS7B01G398600 chr7B 664949204 664951467 2263 True 4181.0 4181 100.0000 1 2264 1 chr7B.!!$R2 2263
1 TraesCS7B01G398600 chr7B 535435568 535437148 1580 True 2706.0 2706 97.5390 1 1583 1 chr7B.!!$R1 1582
2 TraesCS7B01G398600 chr7B 666615844 666619158 3314 False 1949.0 2730 97.8590 1 2264 2 chr7B.!!$F1 2263
3 TraesCS7B01G398600 chr5B 353927644 353930733 3089 True 1942.5 2699 97.8240 1 2264 2 chr5B.!!$R1 2263
4 TraesCS7B01G398600 chr5B 18184114 18187203 3089 False 1913.5 2663 97.3405 1 2264 2 chr5B.!!$F2 2263
5 TraesCS7B01G398600 chr5B 123786976 123790139 3163 False 1912.0 2706 97.0030 1 2264 2 chr5B.!!$F3 2263
6 TraesCS7B01G398600 chr5B 514053205 514053888 683 False 1112.0 1112 96.0580 1582 2264 1 chr5B.!!$F1 682
7 TraesCS7B01G398600 chr3B 21644989 21646562 1573 False 2167.0 2167 91.4880 1 1583 1 chr3B.!!$F1 1582
8 TraesCS7B01G398600 chr3B 734223993 734227363 3370 True 1933.0 2691 97.6440 1 2264 2 chr3B.!!$R1 2263
9 TraesCS7B01G398600 chr3D 581472631 581474213 1582 False 2519.0 2519 95.4000 1 1583 1 chr3D.!!$F1 1582
10 TraesCS7B01G398600 chr6B 715470255 715471834 1579 True 2161.0 2161 91.3840 1 1583 1 chr6B.!!$R2 1582
11 TraesCS7B01G398600 chr6B 77325115 77325790 675 True 1044.0 1044 94.5510 1588 2264 1 chr6B.!!$R1 676
12 TraesCS7B01G398600 chr4B 522406316 522406992 676 False 1118.0 1118 96.4710 1588 2264 1 chr4B.!!$F1 676
13 TraesCS7B01G398600 chr4A 692373941 692374617 676 True 1090.0 1090 95.7290 1588 2264 1 chr4A.!!$R1 676

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
709 720 1.418637 GTGGTTGTAGAGGTGGTTCCA 59.581 52.381 0.0 0.0 39.02 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1982 3238 0.518636 TCTTTTGCTGTCAGCGATGC 59.481 50.0 19.68 0.0 46.26 3.91 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
230 233 3.181442 TGCGAGAGGCCTAGTAAGTATCT 60.181 47.826 4.42 0.00 42.61 1.98
256 259 3.264947 CCATGCTCTCATCTTTTGACGA 58.735 45.455 0.00 0.00 0.00 4.20
496 503 3.958798 GGACAACCTAGCTGGATACACTA 59.041 47.826 0.00 0.00 46.17 2.74
683 694 2.043248 TGGTCGTAGAGGAGGGGC 60.043 66.667 0.00 0.00 36.95 5.80
694 705 3.647771 GAGGGGCTTCCGGTGGTT 61.648 66.667 0.00 0.00 41.52 3.67
709 720 1.418637 GTGGTTGTAGAGGTGGTTCCA 59.581 52.381 0.00 0.00 39.02 3.53
751 762 1.834263 GAGGTGCTAGGAGTGGACAAT 59.166 52.381 0.00 0.00 0.00 2.71
1011 1026 2.074576 CTCATAGGCATGGCTTCATCG 58.925 52.381 28.30 11.35 32.61 3.84
1220 1235 3.054508 TGTCCCAACTATGCACATGATCA 60.055 43.478 0.00 0.00 0.00 2.92
1221 1236 4.139786 GTCCCAACTATGCACATGATCAT 58.860 43.478 1.18 1.18 0.00 2.45
1258 1273 1.618837 CCTATGACATCCCACCGGTAG 59.381 57.143 6.87 0.00 0.00 3.18
1481 1497 2.903404 GGAACGTCCTGAGAGGGAT 58.097 57.895 0.00 0.00 37.73 3.85
1581 1597 2.125952 CGAGGACTCGCATGCACA 60.126 61.111 19.57 1.88 46.50 4.57
1583 1599 1.086067 CGAGGACTCGCATGCACAAT 61.086 55.000 19.57 0.00 46.50 2.71
1586 1602 0.804364 GGACTCGCATGCACAATGAA 59.196 50.000 19.57 0.00 38.72 2.57
1874 3129 1.582610 GCGGCGGATGAAAAGAACCA 61.583 55.000 9.78 0.00 0.00 3.67
1935 3190 0.248784 GCGATGCAAGGAATGAAGCC 60.249 55.000 0.00 0.00 0.00 4.35
1937 3192 1.382522 GATGCAAGGAATGAAGCCGA 58.617 50.000 0.00 0.00 0.00 5.54
1992 3248 2.735663 CTCAGATAATGGCATCGCTGAC 59.264 50.000 17.52 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
152 155 3.118592 TGCACGACCACCATATGACATAA 60.119 43.478 3.65 0.00 0.00 1.90
230 233 2.519771 AAGATGAGAGCATGGCCAAA 57.480 45.000 10.96 0.00 34.11 3.28
683 694 0.974383 ACCTCTACAACCACCGGAAG 59.026 55.000 9.46 0.00 0.00 3.46
694 705 0.685097 GCACTGGAACCACCTCTACA 59.315 55.000 0.00 0.00 39.86 2.74
709 720 0.758685 CTAGGGCCTCTAGCAGCACT 60.759 60.000 10.74 12.48 46.68 4.40
751 762 0.901114 TTAGCGCCACCTCTACCACA 60.901 55.000 2.29 0.00 0.00 4.17
793 804 1.215647 CACCTCTACGAGCACCACC 59.784 63.158 0.00 0.00 0.00 4.61
1011 1026 4.754667 GGCCTCGTCGTGGAACCC 62.755 72.222 17.27 5.23 0.00 4.11
1177 1192 7.039714 GGGACACACAAAATATCTTCTTCCTTT 60.040 37.037 0.00 0.00 0.00 3.11
1258 1273 6.885922 TGGAGAATAGCCTACTTTTCTAACC 58.114 40.000 0.00 0.01 42.21 2.85
1471 1487 2.247358 GCTCCTTCCTATCCCTCTCAG 58.753 57.143 0.00 0.00 0.00 3.35
1481 1497 0.824759 GCTTCTTCCGCTCCTTCCTA 59.175 55.000 0.00 0.00 0.00 2.94
1569 1585 2.871133 CAATTCATTGTGCATGCGAGT 58.129 42.857 14.09 0.00 33.22 4.18
1874 3129 8.608844 AGTCATCTTTTCTTTAATGAGTTCGT 57.391 30.769 0.00 0.00 29.61 3.85
1935 3190 1.153939 CCGTGCAGAGTTCCTCTCG 60.154 63.158 0.00 0.00 46.86 4.04
1937 3192 1.629043 TAACCGTGCAGAGTTCCTCT 58.371 50.000 4.61 0.00 42.11 3.69
1982 3238 0.518636 TCTTTTGCTGTCAGCGATGC 59.481 50.000 19.68 0.00 46.26 3.91


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

AutoCloner maintained by Alex Coulton.