Multiple sequence alignment - TraesCS1B01G230700

Loading Multiple Alignment...

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 TraesCS1B01G230700 chr1B 100.000 2759 0 0 1 2759 414555933 414558691 0.000000e+00 5096
1 TraesCS1B01G230700 chr1B 97.740 1814 41 0 1 1814 494555810 494553997 0.000000e+00 3123
2 TraesCS1B01G230700 chr1B 89.348 1962 178 23 3 1934 497826964 497828924 0.000000e+00 2436
3 TraesCS1B01G230700 chr1B 97.573 824 17 1 1939 2759 633387452 633388275 0.000000e+00 1408
4 TraesCS1B01G230700 chr1B 87.934 663 63 10 1290 1937 46156545 46155885 0.000000e+00 765
5 TraesCS1B01G230700 chr1B 88.525 122 7 7 1817 1937 494553949 494553834 1.030000e-29 141
6 TraesCS1B01G230700 chr6B 96.817 1948 53 9 1 1941 132659296 132657351 0.000000e+00 3245
7 TraesCS1B01G230700 chr5A 96.801 1938 52 8 1 1937 651582348 651580420 0.000000e+00 3227
8 TraesCS1B01G230700 chr5A 93.341 1802 120 0 1 1802 697888605 697890406 0.000000e+00 2663
9 TraesCS1B01G230700 chr5A 89.993 1529 139 10 416 1934 476064524 476063000 0.000000e+00 1964
10 TraesCS1B01G230700 chr4B 96.292 1942 63 9 1 1934 502275561 502277501 0.000000e+00 3179
11 TraesCS1B01G230700 chr4A 97.960 1814 37 0 1 1814 718009351 718007538 0.000000e+00 3145
12 TraesCS1B01G230700 chr2B 97.548 1835 45 0 1 1835 138738664 138736830 0.000000e+00 3140
13 TraesCS1B01G230700 chr3D 95.717 1938 75 7 1 1934 134639019 134640952 0.000000e+00 3112
14 TraesCS1B01G230700 chr3D 97.573 824 17 1 1939 2759 28565403 28564580 0.000000e+00 1408
15 TraesCS1B01G230700 chr2D 94.070 1956 99 8 1 1941 573648889 573650842 0.000000e+00 2953
16 TraesCS1B01G230700 chr2D 97.573 824 17 1 1939 2759 537845101 537844278 0.000000e+00 1408
17 TraesCS1B01G230700 chr5D 90.825 1951 171 7 1 1948 354745344 354743399 0.000000e+00 2604
18 TraesCS1B01G230700 chr4D 97.694 824 16 1 1939 2759 121775006 121774183 0.000000e+00 1413
19 TraesCS1B01G230700 chr4D 97.451 824 18 1 1939 2759 415823784 415822961 0.000000e+00 1402
20 TraesCS1B01G230700 chr7B 97.573 824 17 1 1939 2759 660281626 660280803 0.000000e+00 1408
21 TraesCS1B01G230700 chr6D 97.573 824 17 1 1939 2759 46967534 46966711 0.000000e+00 1408
22 TraesCS1B01G230700 chr6D 97.451 824 18 1 1939 2759 128151929 128151106 0.000000e+00 1402
23 TraesCS1B01G230700 chr7D 97.455 825 17 2 1939 2759 626778066 626777242 0.000000e+00 1404


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 TraesCS1B01G230700 chr1B 414555933 414558691 2758 False 5096 5096 100.0000 1 2759 1 chr1B.!!$F1 2758
1 TraesCS1B01G230700 chr1B 497826964 497828924 1960 False 2436 2436 89.3480 3 1934 1 chr1B.!!$F2 1931
2 TraesCS1B01G230700 chr1B 494553834 494555810 1976 True 1632 3123 93.1325 1 1937 2 chr1B.!!$R2 1936
3 TraesCS1B01G230700 chr1B 633387452 633388275 823 False 1408 1408 97.5730 1939 2759 1 chr1B.!!$F3 820
4 TraesCS1B01G230700 chr1B 46155885 46156545 660 True 765 765 87.9340 1290 1937 1 chr1B.!!$R1 647
5 TraesCS1B01G230700 chr6B 132657351 132659296 1945 True 3245 3245 96.8170 1 1941 1 chr6B.!!$R1 1940
6 TraesCS1B01G230700 chr5A 651580420 651582348 1928 True 3227 3227 96.8010 1 1937 1 chr5A.!!$R2 1936
7 TraesCS1B01G230700 chr5A 697888605 697890406 1801 False 2663 2663 93.3410 1 1802 1 chr5A.!!$F1 1801
8 TraesCS1B01G230700 chr5A 476063000 476064524 1524 True 1964 1964 89.9930 416 1934 1 chr5A.!!$R1 1518
9 TraesCS1B01G230700 chr4B 502275561 502277501 1940 False 3179 3179 96.2920 1 1934 1 chr4B.!!$F1 1933
10 TraesCS1B01G230700 chr4A 718007538 718009351 1813 True 3145 3145 97.9600 1 1814 1 chr4A.!!$R1 1813
11 TraesCS1B01G230700 chr2B 138736830 138738664 1834 True 3140 3140 97.5480 1 1835 1 chr2B.!!$R1 1834
12 TraesCS1B01G230700 chr3D 134639019 134640952 1933 False 3112 3112 95.7170 1 1934 1 chr3D.!!$F1 1933
13 TraesCS1B01G230700 chr3D 28564580 28565403 823 True 1408 1408 97.5730 1939 2759 1 chr3D.!!$R1 820
14 TraesCS1B01G230700 chr2D 573648889 573650842 1953 False 2953 2953 94.0700 1 1941 1 chr2D.!!$F1 1940
15 TraesCS1B01G230700 chr2D 537844278 537845101 823 True 1408 1408 97.5730 1939 2759 1 chr2D.!!$R1 820
16 TraesCS1B01G230700 chr5D 354743399 354745344 1945 True 2604 2604 90.8250 1 1948 1 chr5D.!!$R1 1947
17 TraesCS1B01G230700 chr4D 121774183 121775006 823 True 1413 1413 97.6940 1939 2759 1 chr4D.!!$R1 820
18 TraesCS1B01G230700 chr4D 415822961 415823784 823 True 1402 1402 97.4510 1939 2759 1 chr4D.!!$R2 820
19 TraesCS1B01G230700 chr7B 660280803 660281626 823 True 1408 1408 97.5730 1939 2759 1 chr7B.!!$R1 820
20 TraesCS1B01G230700 chr6D 46966711 46967534 823 True 1408 1408 97.5730 1939 2759 1 chr6D.!!$R1 820
21 TraesCS1B01G230700 chr6D 128151106 128151929 823 True 1402 1402 97.4510 1939 2759 1 chr6D.!!$R2 820
22 TraesCS1B01G230700 chr7D 626777242 626778066 824 True 1404 1404 97.4550 1939 2759 1 chr7D.!!$R1 820

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
61 62 3.191669 GGTAAACGCAACTTGGCTTTTT 58.808 40.909 0.0 0.0 36.71 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1937 2038 1.838715 AGATGGTGATCTGCTGCTTCT 59.161 47.619 0.0 0.0 37.56 2.85 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
61 62 3.191669 GGTAAACGCAACTTGGCTTTTT 58.808 40.909 0.00 0.00 36.71 1.94
71 72 4.649088 ACTTGGCTTTTTGTGGAAGTAC 57.351 40.909 0.00 0.00 0.00 2.73
118 119 9.971922 ATAATGGTAATTTCTTAGCTTGCATTC 57.028 29.630 0.00 0.00 36.51 2.67
539 540 9.338622 CGGTTCTAATATGAAAGGAAAATACCT 57.661 33.333 0.00 0.00 42.69 3.08
652 653 7.707624 ATGGAAAAATCATGTGAGAAAGCTA 57.292 32.000 0.00 0.00 0.00 3.32
886 887 9.965902 ACACTGATCCTAAAGATAAAAGTGATT 57.034 29.630 14.58 0.00 40.33 2.57
936 937 6.810182 GTCGCTTTGAGTTTCTAGTTGGTATA 59.190 38.462 0.00 0.00 0.00 1.47
1267 1270 4.129380 TGATATGGCGATCACTTCTTTGG 58.871 43.478 0.00 0.00 30.75 3.28
1337 1340 1.273759 TTGAGCTCAGGCACTCTCAT 58.726 50.000 17.43 0.00 36.84 2.90
1420 1424 7.397221 TCTTAATGGTTCATCTGATGTTGAGT 58.603 34.615 16.66 3.05 0.00 3.41
1499 1509 6.493116 CAATGTCTGCTATGGAGATTTTCAC 58.507 40.000 0.00 0.00 0.00 3.18
1541 1551 8.231007 TGATTGTTACCCCAATATATCCATTGT 58.769 33.333 0.00 0.00 35.24 2.71
1567 1577 5.270893 TCGCATCTTATTTACTGTGCCTA 57.729 39.130 0.00 0.00 0.00 3.93
1934 2035 1.218047 CGAAATCTCAGGACCGGCA 59.782 57.895 0.00 0.00 0.00 5.69
1937 2038 1.480954 GAAATCTCAGGACCGGCACTA 59.519 52.381 0.00 0.00 0.00 2.74
2257 2358 4.057432 CACAAATCTTTCCCAAATGCGTT 58.943 39.130 0.00 0.00 0.00 4.84
2425 2526 2.267174 AGATGGAAAGATGGCGATGG 57.733 50.000 0.00 0.00 0.00 3.51
2520 2621 5.227569 TGCTGAAACAAGAGAGGATGTAA 57.772 39.130 0.00 0.00 0.00 2.41
2746 2851 4.032960 ACAACATGCCTCCAAATGTCTA 57.967 40.909 0.00 0.00 35.99 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 1.342074 AGCTGCTCAGTACTTCCACA 58.658 50.000 0.00 0.00 0.00 4.17
71 72 3.603532 TCATCCTTGTAAAGCTGCTCAG 58.396 45.455 1.00 0.00 44.44 3.35
118 119 7.658261 ACCATATCAAATTCTGCAATCATCTG 58.342 34.615 0.00 0.00 0.00 2.90
495 496 5.602978 AGAACCGTTATCATATCCTTGACCT 59.397 40.000 0.00 0.00 0.00 3.85
539 540 6.744822 TCAAGTAACCTAGATTGTACCCCTA 58.255 40.000 0.00 0.00 0.00 3.53
697 698 4.729868 ACATTCCACCTTTTTGTAGAGCT 58.270 39.130 0.00 0.00 0.00 4.09
886 887 7.718753 ACCAAGTGCATCAAATAAATTTTTGGA 59.281 29.630 13.89 5.25 37.23 3.53
936 937 8.800332 GCAAATAGAACATCATCCCAGATAATT 58.200 33.333 0.00 0.00 0.00 1.40
1145 1147 4.021016 ACTGTTTCTTCCTCTTAGCACGAT 60.021 41.667 0.00 0.00 0.00 3.73
1285 1288 9.706691 TCCGAATATATCTTTAAAGACCATGAC 57.293 33.333 19.94 9.79 37.98 3.06
1499 1509 3.434641 ACAATCAACTTCTCTGACATGCG 59.565 43.478 0.00 0.00 0.00 4.73
1541 1551 5.926542 GGCACAGTAAATAAGATGCGATAGA 59.073 40.000 0.00 0.00 39.76 1.98
1567 1577 4.891727 GGCCGATGCGACCGTCAT 62.892 66.667 0.00 0.00 38.85 3.06
1934 2035 2.182827 TGGTGATCTGCTGCTTCTAGT 58.817 47.619 0.00 0.00 0.00 2.57
1937 2038 1.838715 AGATGGTGATCTGCTGCTTCT 59.161 47.619 0.00 0.00 37.56 2.85
2016 2117 5.503846 GCATTGTTTCAATGTTGGTCAAACC 60.504 40.000 19.11 0.00 38.06 3.27
2131 2232 8.306313 TGAGAATACTGACAGCTTATTTCCTA 57.694 34.615 1.25 0.00 0.00 2.94
2520 2621 2.092212 CCTGGTTCCTAGAATGCCACAT 60.092 50.000 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.