Multiple sequence alignment - TraesCS4D01G112000

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 TraesCS4D01G112000 chr4D 100.000 2366 0 0 1 2366 93070903 93068538 0.000000e+00 4370.0
1 TraesCS4D01G112000 chr4D 77.966 413 59 22 960 1365 450331681 450332068 1.830000e-56 230.0
2 TraesCS4D01G112000 chr4A 93.515 1619 53 23 788 2366 489434033 489435639 0.000000e+00 2361.0
3 TraesCS4D01G112000 chr4A 94.335 759 22 13 1 748 489433048 489433796 0.000000e+00 1144.0
4 TraesCS4D01G112000 chr4A 77.404 416 62 18 960 1368 16247786 16247396 3.960000e-53 219.0
5 TraesCS4D01G112000 chr4A 89.286 56 2 2 747 802 489433957 489434008 1.520000e-07 67.6
6 TraesCS4D01G112000 chr4B 94.882 1446 37 17 944 2366 130625260 130623829 0.000000e+00 2226.0
7 TraesCS4D01G112000 chr4B 90.368 924 27 27 1 909 130626136 130625260 0.000000e+00 1157.0
8 TraesCS4D01G112000 chr4B 78.019 414 57 23 960 1365 563628017 563628404 1.830000e-56 230.0
9 TraesCS4D01G112000 chr2D 95.455 110 5 0 1139 1248 81515039 81515148 2.420000e-40 176.0
10 TraesCS4D01G112000 chr6B 97.030 101 3 0 1148 1248 507373571 507373471 1.120000e-38 171.0
11 TraesCS4D01G112000 chr6B 95.876 97 4 0 1151 1247 615607436 615607532 8.750000e-35 158.0
12 TraesCS4D01G112000 chr5B 93.578 109 7 0 1139 1247 625119396 625119504 1.880000e-36 163.0
13 TraesCS4D01G112000 chr5B 91.743 109 9 0 1139 1247 628698945 628699053 4.070000e-33 152.0
14 TraesCS4D01G112000 chr7A 95.000 100 5 0 1148 1247 487478632 487478533 8.750000e-35 158.0
15 TraesCS4D01G112000 chr7A 83.158 95 16 0 958 1052 8916271 8916177 1.160000e-13 87.9
16 TraesCS4D01G112000 chr1D 86.726 113 8 4 182 292 269726379 269726486 4.130000e-23 119.0
17 TraesCS4D01G112000 chr1A 86.726 113 8 4 182 292 333135563 333135670 4.130000e-23 119.0
18 TraesCS4D01G112000 chr1B 84.956 113 10 4 182 292 342973154 342973261 8.940000e-20 108.0
19 TraesCS4D01G112000 chr7D 98.333 60 1 0 233 292 477932212 477932153 3.220000e-19 106.0
20 TraesCS4D01G112000 chr7D 85.263 95 14 0 958 1052 8479898 8479804 5.380000e-17 99.0
21 TraesCS4D01G112000 chr3B 96.721 61 2 0 232 292 624317534 624317594 4.160000e-18 102.0
22 TraesCS4D01G112000 chr3A 96.721 61 2 0 232 292 612524213 612524273 4.160000e-18 102.0
23 TraesCS4D01G112000 chr2A 96.721 61 2 0 232 292 138533284 138533224 4.160000e-18 102.0


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 TraesCS4D01G112000 chr4D 93068538 93070903 2365 True 4370.000000 4370 100.000000 1 2366 1 chr4D.!!$R1 2365
1 TraesCS4D01G112000 chr4A 489433048 489435639 2591 False 1190.866667 2361 92.378667 1 2366 3 chr4A.!!$F1 2365
2 TraesCS4D01G112000 chr4B 130623829 130626136 2307 True 1691.500000 2226 92.625000 1 2366 2 chr4B.!!$R1 2365

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
344 347 0.179029 ACCAAGCCGCAGTAACAGTT 60.179 50.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1376 1610 1.064017 TGGGATCTAATGTGGTTGGGC 60.064 52.381 0.0 0.0 0.0 5.36 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
335 338 2.331893 CGGATCAAACCAAGCCGCA 61.332 57.895 0.00 0.00 35.17 5.69
344 347 0.179029 ACCAAGCCGCAGTAACAGTT 60.179 50.000 0.00 0.00 0.00 3.16
396 400 3.379688 GGATCAAACTGAAGAAGGATGGC 59.620 47.826 0.00 0.00 0.00 4.40
407 412 5.416952 TGAAGAAGGATGGCTGAGATTTTTC 59.583 40.000 0.00 0.00 0.00 2.29
567 572 1.818363 TTTTGGGCGTGCACGTACA 60.818 52.632 36.80 31.01 42.22 2.90
599 604 3.952508 TGGAGGTGCCATGCGTGT 61.953 61.111 4.96 0.00 43.33 4.49
671 682 4.513318 CGTGCTATGTCTATGTCTCTCTCA 59.487 45.833 0.00 0.00 0.00 3.27
672 683 5.181056 CGTGCTATGTCTATGTCTCTCTCAT 59.819 44.000 0.00 0.00 0.00 2.90
673 684 6.380995 GTGCTATGTCTATGTCTCTCTCATG 58.619 44.000 0.00 0.00 0.00 3.07
674 685 5.048154 TGCTATGTCTATGTCTCTCTCATGC 60.048 44.000 0.00 0.00 0.00 4.06
675 686 5.048154 GCTATGTCTATGTCTCTCTCATGCA 60.048 44.000 0.00 0.00 0.00 3.96
867 1089 7.645340 CCTTATAATCCGAAACAATTCAAGCAG 59.355 37.037 0.00 0.00 35.15 4.24
915 1145 3.985019 TGGCGGTAAAGTTATCCAAGA 57.015 42.857 0.00 0.00 0.00 3.02
921 1151 5.005107 GCGGTAAAGTTATCCAAGAACGTAG 59.995 44.000 0.00 0.00 31.85 3.51
923 1153 7.250569 CGGTAAAGTTATCCAAGAACGTAGTA 58.749 38.462 0.00 0.00 45.00 1.82
924 1154 7.218963 CGGTAAAGTTATCCAAGAACGTAGTAC 59.781 40.741 0.00 0.00 45.00 2.73
1064 1298 1.000646 TGCTCTGCATCATGCCCAA 60.001 52.632 7.30 0.00 44.23 4.12
1116 1350 3.896133 TCGATGTACCGGAGCCGC 61.896 66.667 9.46 0.00 38.24 6.53
1119 1353 3.420214 GATGTACCGGAGCCGCGAA 62.420 63.158 9.46 0.00 38.24 4.70
1375 1609 1.893544 CTCCACCTGATCATGCCATC 58.106 55.000 0.00 0.00 0.00 3.51
1376 1610 0.107268 TCCACCTGATCATGCCATCG 59.893 55.000 0.00 0.00 0.00 3.84
1381 1619 0.820482 CTGATCATGCCATCGCCCAA 60.820 55.000 0.00 0.00 0.00 4.12
1399 1637 3.309121 CCCAACCACATTAGATCCCAGTT 60.309 47.826 0.00 0.00 0.00 3.16
2037 2313 9.516314 TGTCACTTTTATAATCTCTATCACACG 57.484 33.333 0.00 0.00 0.00 4.49
2083 2359 7.820648 ACTACCAGAGCTGATTTGTAAATTTG 58.179 34.615 0.00 0.00 0.00 2.32
2134 2410 6.884280 AACTGTAGCTGTAATTCTGCTTTT 57.116 33.333 0.00 2.97 46.51 2.27
2165 2445 8.758829 AGACAATACTGGTCAGTGTTTATATCA 58.241 33.333 13.32 0.00 40.13 2.15
2274 2554 2.014010 TCCAGCAAATCAAAGGCCTT 57.986 45.000 13.78 13.78 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
396 400 3.600388 AGCCAGGTACGAAAAATCTCAG 58.400 45.455 0.00 0.00 0.00 3.35
407 412 1.949847 CTCACCAGGAGCCAGGTACG 61.950 65.000 3.05 0.00 36.69 3.67
567 572 1.268896 CCTCCATTCGTACGTGCGTAT 60.269 52.381 24.94 18.45 32.82 3.06
671 682 2.565647 TGCGGTACTTGCATTGCAT 58.434 47.368 12.95 0.58 38.76 3.96
672 683 4.071459 TGCGGTACTTGCATTGCA 57.929 50.000 7.38 7.38 37.44 4.08
719 740 6.488769 AATCATGCATTTCTCTCTCTCTCT 57.511 37.500 0.00 0.00 0.00 3.10
720 741 8.836268 ATTAATCATGCATTTCTCTCTCTCTC 57.164 34.615 0.00 0.00 0.00 3.20
765 948 1.405463 CAGGTGAACTCCATCGATCGA 59.595 52.381 21.86 21.86 0.00 3.59
766 949 1.135139 ACAGGTGAACTCCATCGATCG 59.865 52.381 9.36 9.36 0.00 3.69
767 950 2.969628 ACAGGTGAACTCCATCGATC 57.030 50.000 0.00 0.00 0.00 3.69
911 1141 6.158175 ACGTACTACTGTACTACGTTCTTG 57.842 41.667 19.84 2.19 44.97 3.02
915 1145 6.468319 CGTACTACGTACTACTGTACTACGTT 59.532 42.308 26.08 17.09 44.97 3.99
921 1151 5.172411 GCTCTCGTACTACGTACTACTGTAC 59.828 48.000 8.42 10.48 43.14 2.90
922 1152 5.163652 TGCTCTCGTACTACGTACTACTGTA 60.164 44.000 8.42 0.43 43.14 2.74
923 1153 4.109050 GCTCTCGTACTACGTACTACTGT 58.891 47.826 8.42 1.27 43.14 3.55
924 1154 4.108336 TGCTCTCGTACTACGTACTACTG 58.892 47.826 8.42 5.08 43.14 2.74
940 1170 0.801251 GTGCTTCACACCATGCTCTC 59.199 55.000 0.00 0.00 44.02 3.20
1375 1609 1.308998 GGATCTAATGTGGTTGGGCG 58.691 55.000 0.00 0.00 0.00 6.13
1376 1610 1.064017 TGGGATCTAATGTGGTTGGGC 60.064 52.381 0.00 0.00 0.00 5.36
1381 1619 4.104086 TCTGAACTGGGATCTAATGTGGT 58.896 43.478 0.00 0.00 0.00 4.16
1786 2042 4.023193 ACCTTTAACTTTGTTGCCTGATCG 60.023 41.667 0.00 0.00 0.00 3.69
1863 2123 7.928307 TTGAGATAGGAAAAAGAACTCATGG 57.072 36.000 0.00 0.00 33.90 3.66
2134 2410 8.514330 AAACACTGACCAGTATTGTCTTTTAA 57.486 30.769 1.95 0.00 40.20 1.52
2274 2554 1.145571 AGTTGTTGGGGTAGCCAAGA 58.854 50.000 14.06 1.25 0.00 3.02


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

AutoCloner maintained by Alex Coulton.