Multiple sequence alignment - TraesCS4A01G011300

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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 TraesCS4A01G011300 chr4A 100.000 2429 0 0 1 2429 6459812 6462240 0.000000e+00 4486.0
1 TraesCS4A01G011300 chr4A 97.455 2043 38 8 1 2042 6434623 6436652 0.000000e+00 3472.0
2 TraesCS4A01G011300 chr4A 85.677 1159 136 15 569 1714 6491942 6493083 0.000000e+00 1194.0
3 TraesCS4A01G011300 chr4A 97.661 684 14 2 1747 2429 6436636 6437318 0.000000e+00 1173.0
4 TraesCS4A01G011300 chr4A 85.489 317 38 7 1714 2027 6463932 6463621 8.380000e-85 324.0
5 TraesCS4A01G011300 chr4A 94.286 210 12 0 1 210 560268212 560268003 3.010000e-84 322.0
6 TraesCS4A01G011300 chr4D 94.044 1511 54 19 208 1713 462497487 462498966 0.000000e+00 2259.0
7 TraesCS4A01G011300 chr4D 86.967 1197 103 29 569 1736 462548743 462549915 0.000000e+00 1297.0
8 TraesCS4A01G011300 chr4D 87.715 871 71 21 570 1429 462502232 462503077 0.000000e+00 983.0
9 TraesCS4A01G011300 chr4B 92.247 1522 97 9 208 1713 578532951 578531435 0.000000e+00 2137.0
10 TraesCS4A01G011300 chr4B 85.629 1169 121 25 569 1714 578350436 578349292 0.000000e+00 1184.0
11 TraesCS4A01G011300 chr4B 85.282 1189 124 27 569 1731 578408225 578407062 0.000000e+00 1179.0
12 TraesCS4A01G011300 chr4B 85.042 1190 126 28 569 1731 578480484 578479320 0.000000e+00 1164.0
13 TraesCS4A01G011300 chr4B 84.861 1189 122 31 569 1731 578432618 578431462 0.000000e+00 1146.0
14 TraesCS4A01G011300 chrUn 85.282 1189 124 27 569 1731 363045197 363044034 0.000000e+00 1179.0
15 TraesCS4A01G011300 chrUn 87.838 222 27 0 2202 2423 91512443 91512222 6.660000e-66 261.0
16 TraesCS4A01G011300 chr5B 93.781 402 22 3 1713 2112 37733902 37733502 3.460000e-168 601.0
17 TraesCS4A01G011300 chr5B 89.869 306 29 2 2126 2429 37733397 37733092 2.260000e-105 392.0
18 TraesCS4A01G011300 chr5B 83.750 320 41 9 1713 2027 37732436 37732749 2.360000e-75 292.0
19 TraesCS4A01G011300 chr5B 86.029 136 17 1 2126 2259 332362703 332362568 7.000000e-31 145.0
20 TraesCS4A01G011300 chr6A 95.714 210 9 0 1 210 124259976 124259767 2.990000e-89 339.0
21 TraesCS4A01G011300 chr6A 96.135 207 8 0 1 207 429915750 429915956 2.990000e-89 339.0
22 TraesCS4A01G011300 chr6A 94.762 210 11 0 1 210 206457221 206457430 6.480000e-86 327.0
23 TraesCS4A01G011300 chr6A 94.286 210 12 0 1 210 404200995 404200786 3.010000e-84 322.0
24 TraesCS4A01G011300 chr2A 95.714 210 9 0 1 210 438828433 438828224 2.990000e-89 339.0
25 TraesCS4A01G011300 chr2A 91.975 162 11 2 2126 2285 535236201 535236040 2.430000e-55 226.0
26 TraesCS4A01G011300 chr2A 97.849 93 2 0 2020 2112 535236398 535236306 6.950000e-36 161.0
27 TraesCS4A01G011300 chr7A 95.238 210 10 0 1 210 245767399 245767190 1.390000e-87 333.0
28 TraesCS4A01G011300 chr3A 94.286 210 12 0 1 210 215741583 215741374 3.010000e-84 322.0
29 TraesCS4A01G011300 chr3B 85.542 249 33 3 1715 1961 191258884 191259131 8.620000e-65 257.0
30 TraesCS4A01G011300 chr3B 84.483 116 13 3 569 684 759107313 759107203 2.550000e-20 110.0
31 TraesCS4A01G011300 chr1A 84.733 262 34 5 1713 1969 124344929 124344669 8.620000e-65 257.0
32 TraesCS4A01G011300 chr1D 83.858 254 37 4 1714 1965 313666954 313666703 3.120000e-59 239.0
33 TraesCS4A01G011300 chr6D 83.004 253 41 2 1714 1965 429079585 429079334 6.760000e-56 228.0
34 TraesCS4A01G011300 chr7B 86.765 136 16 2 2126 2259 39542495 39542360 1.500000e-32 150.0
35 TraesCS4A01G011300 chr7B 97.015 67 2 0 2044 2110 39542668 39542602 1.970000e-21 113.0
36 TraesCS4A01G011300 chr7B 97.015 67 2 0 2044 2110 711498753 711498687 1.970000e-21 113.0
37 TraesCS4A01G011300 chr7B 81.148 122 16 4 569 689 575370991 575370876 9.250000e-15 91.6
38 TraesCS4A01G011300 chr5D 86.466 133 16 2 2126 2256 370110249 370110381 7.000000e-31 145.0
39 TraesCS4A01G011300 chr5D 84.615 117 13 3 569 685 6385495 6385384 7.100000e-21 111.0
40 TraesCS4A01G011300 chr2B 94.118 51 3 0 2055 2105 751842990 751842940 7.200000e-11 78.7


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 TraesCS4A01G011300 chr4A 6459812 6462240 2428 False 4486.0 4486 100.0000 1 2429 1 chr4A.!!$F1 2428
1 TraesCS4A01G011300 chr4A 6434623 6437318 2695 False 2322.5 3472 97.5580 1 2429 2 chr4A.!!$F3 2428
2 TraesCS4A01G011300 chr4A 6491942 6493083 1141 False 1194.0 1194 85.6770 569 1714 1 chr4A.!!$F2 1145
3 TraesCS4A01G011300 chr4D 462497487 462503077 5590 False 1621.0 2259 90.8795 208 1713 2 chr4D.!!$F2 1505
4 TraesCS4A01G011300 chr4D 462548743 462549915 1172 False 1297.0 1297 86.9670 569 1736 1 chr4D.!!$F1 1167
5 TraesCS4A01G011300 chr4B 578531435 578532951 1516 True 2137.0 2137 92.2470 208 1713 1 chr4B.!!$R5 1505
6 TraesCS4A01G011300 chr4B 578349292 578350436 1144 True 1184.0 1184 85.6290 569 1714 1 chr4B.!!$R1 1145
7 TraesCS4A01G011300 chr4B 578407062 578408225 1163 True 1179.0 1179 85.2820 569 1731 1 chr4B.!!$R2 1162
8 TraesCS4A01G011300 chr4B 578479320 578480484 1164 True 1164.0 1164 85.0420 569 1731 1 chr4B.!!$R4 1162
9 TraesCS4A01G011300 chr4B 578431462 578432618 1156 True 1146.0 1146 84.8610 569 1731 1 chr4B.!!$R3 1162
10 TraesCS4A01G011300 chrUn 363044034 363045197 1163 True 1179.0 1179 85.2820 569 1731 1 chrUn.!!$R2 1162
11 TraesCS4A01G011300 chr5B 37733092 37733902 810 True 496.5 601 91.8250 1713 2429 2 chr5B.!!$R2 716

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
62 63 1.982938 GAGTCTGTGGTACCGCCCT 60.983 63.158 22.54 14.92 36.04 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1894 2364 1.369839 TTGACTTTGCCGCACGTCAA 61.37 50.0 23.52 23.52 42.23 3.18 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
62 63 1.982938 GAGTCTGTGGTACCGCCCT 60.983 63.158 22.54 14.92 36.04 5.19
352 366 2.178580 GGTTGCATGGAAGGAAATGGA 58.821 47.619 0.00 0.00 0.00 3.41
924 957 6.312918 GGACAACATATATAATACACGGCCAG 59.687 42.308 2.24 0.00 0.00 4.85
925 958 6.170506 ACAACATATATAATACACGGCCAGG 58.829 40.000 2.24 0.00 0.00 4.45
926 959 5.353394 ACATATATAATACACGGCCAGGG 57.647 43.478 2.24 0.00 0.00 4.45
927 960 2.781681 ATATAATACACGGCCAGGGC 57.218 50.000 2.24 1.81 41.06 5.19
1032 1078 2.741228 GCATCTGCTCCTCATCGTCTTT 60.741 50.000 0.00 0.00 38.21 2.52
1432 1483 2.439156 CCAGGTGCAGCTAAGGGC 60.439 66.667 19.71 0.00 42.19 5.19
1894 2364 0.475828 AAGGGCCCACTAGTCAAGGT 60.476 55.000 27.56 0.00 0.00 3.50
2103 3226 4.873129 CCCCGGTGCATCGAGTCG 62.873 72.222 23.56 6.09 0.00 4.18
2251 4923 1.524002 CACCATCATCACCGAGGCT 59.476 57.895 0.00 0.00 0.00 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.146640 GCTTGCGCGTTAAAAGGG 57.853 55.556 8.43 0.00 0.00 3.95
249 250 3.004734 CCTGCAGTTGTCGATTCCTTTTT 59.995 43.478 13.81 0.00 0.00 1.94
352 366 1.370810 CAACCGCCCAAATGCCTTT 59.629 52.632 0.00 0.00 0.00 3.11
925 958 4.687215 TGCGTGCAGACTGAGGCC 62.687 66.667 6.65 0.00 0.00 5.19
926 959 3.418068 GTGCGTGCAGACTGAGGC 61.418 66.667 6.65 9.26 0.00 4.70
927 960 1.287730 GAAGTGCGTGCAGACTGAGG 61.288 60.000 6.65 0.00 0.00 3.86
928 961 1.287730 GGAAGTGCGTGCAGACTGAG 61.288 60.000 6.65 0.00 0.00 3.35
929 962 1.300931 GGAAGTGCGTGCAGACTGA 60.301 57.895 6.65 0.00 0.00 3.41
930 963 2.320587 GGGAAGTGCGTGCAGACTG 61.321 63.158 0.00 0.00 0.00 3.51
931 964 2.031163 GGGAAGTGCGTGCAGACT 59.969 61.111 0.00 0.00 0.00 3.24
932 965 3.050275 GGGGAAGTGCGTGCAGAC 61.050 66.667 0.00 0.00 0.00 3.51
933 966 2.410322 AATGGGGAAGTGCGTGCAGA 62.410 55.000 0.00 0.00 0.00 4.26
934 967 1.926511 GAATGGGGAAGTGCGTGCAG 61.927 60.000 0.00 0.00 0.00 4.41
935 968 1.971167 GAATGGGGAAGTGCGTGCA 60.971 57.895 0.00 0.00 0.00 4.57
1032 1078 1.535444 TTGGAGGACGGAAGCCAGA 60.535 57.895 0.00 0.00 0.00 3.86
1432 1483 3.688185 CGATGCATCCCTAATCAATCAGG 59.312 47.826 20.87 0.00 0.00 3.86
1544 1597 2.867109 AGGTCTTGGAACCATGACTG 57.133 50.000 26.97 6.12 45.00 3.51
1894 2364 1.369839 TTGACTTTGCCGCACGTCAA 61.370 50.000 23.52 23.52 42.23 3.18
2103 3226 1.715585 CAACGTGATGTGGATCCGC 59.284 57.895 18.84 18.84 0.00 5.54


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

AutoCloner maintained by Alex Coulton.