Multiple sequence alignment - TraesCS6D01G109200

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 TraesCS6D01G109200 chr6D 100.000 3598 0 0 1 3598 74263367 74259770 0.000000e+00 6645.0
1 TraesCS6D01G109200 chr6D 97.862 3602 48 14 1 3598 74281472 74285048 0.000000e+00 6198.0
2 TraesCS6D01G109200 chr6D 98.122 1065 15 4 1 1062 73846146 73847208 0.000000e+00 1851.0
3 TraesCS6D01G109200 chr6D 94.184 705 36 4 2131 2832 73633537 73634239 0.000000e+00 1070.0
4 TraesCS6D01G109200 chr6D 91.818 660 53 1 1982 2640 73787202 73787861 0.000000e+00 918.0
5 TraesCS6D01G109200 chr6D 88.450 329 17 2 2844 3172 73643455 73643762 9.430000e-101 377.0
6 TraesCS6D01G109200 chr6D 91.154 260 20 2 1497 1756 73786789 73787045 2.060000e-92 350.0
7 TraesCS6D01G109200 chr6D 89.883 257 12 10 1414 1670 74284379 74284621 5.800000e-83 318.0
8 TraesCS6D01G109200 chr6D 89.494 257 14 9 1414 1670 74260439 74260196 2.700000e-81 313.0
9 TraesCS6D01G109200 chr6D 89.494 257 14 9 2929 3172 74261954 74261698 2.700000e-81 313.0
10 TraesCS6D01G109200 chr6D 89.243 251 14 10 2929 3166 74282872 74283122 5.840000e-78 302.0
11 TraesCS6D01G109200 chr6D 100.000 28 0 0 1143 1170 20234069 20234042 6.000000e-03 52.8
12 TraesCS6D01G109200 chr6A 95.697 1859 60 7 1745 3598 90780866 90782709 0.000000e+00 2972.0
13 TraesCS6D01G109200 chr6A 91.450 1462 68 18 1406 2832 90218216 90219655 0.000000e+00 1954.0
14 TraesCS6D01G109200 chr6A 90.794 554 41 9 604 1147 90217664 90218217 0.000000e+00 732.0
15 TraesCS6D01G109200 chr6A 87.521 585 62 6 1 577 90194947 90195528 0.000000e+00 665.0
16 TraesCS6D01G109200 chr6A 91.461 445 38 0 2196 2640 90750804 90751248 2.370000e-171 612.0
17 TraesCS6D01G109200 chr6A 89.518 353 23 4 2833 3172 90218131 90218482 5.520000e-118 435.0
18 TraesCS6D01G109200 chr6A 87.273 330 19 8 2844 3172 90329167 90329474 4.420000e-94 355.0
19 TraesCS6D01G109200 chr6A 91.903 247 19 1 1510 1756 90749891 90750136 9.560000e-91 344.0
20 TraesCS6D01G109200 chr6A 88.123 261 16 11 1410 1670 90782037 90782282 2.720000e-76 296.0
21 TraesCS6D01G109200 chr6A 91.935 186 14 1 1982 2166 90750293 90750478 3.560000e-65 259.0
22 TraesCS6D01G109200 chr6B 96.619 1183 34 4 1859 3038 148332008 148333187 0.000000e+00 1958.0
23 TraesCS6D01G109200 chr6B 95.225 733 35 0 1859 2591 148083951 148084683 0.000000e+00 1160.0
24 TraesCS6D01G109200 chr6B 94.824 483 22 3 1406 1886 148331587 148332068 0.000000e+00 750.0
25 TraesCS6D01G109200 chr6B 90.239 543 46 5 614 1149 148080395 148080937 0.000000e+00 702.0
26 TraesCS6D01G109200 chr6B 89.065 567 38 11 593 1149 148331038 148331590 0.000000e+00 682.0
27 TraesCS6D01G109200 chr6B 88.536 567 26 16 3032 3596 148335837 148336366 0.000000e+00 651.0
28 TraesCS6D01G109200 chr6B 91.977 349 24 4 1536 1881 148083659 148084006 1.500000e-133 486.0
29 TraesCS6D01G109200 chr6B 88.506 348 21 12 2840 3172 148331508 148331851 1.560000e-108 403.0
30 TraesCS6D01G109200 chr6B 83.271 269 42 3 1146 1413 2614244 2614510 9.980000e-61 244.0
31 TraesCS6D01G109200 chr6B 96.875 32 1 0 1139 1170 498585360 498585329 2.000000e-03 54.7
32 TraesCS6D01G109200 chr7A 80.769 598 90 17 2 582 418616845 418617434 9.170000e-121 444.0
33 TraesCS6D01G109200 chr7A 86.747 83 7 4 3207 3289 25849520 25849442 4.950000e-14 89.8
34 TraesCS6D01G109200 chr7B 85.608 403 49 5 3199 3598 667194069 667193673 7.190000e-112 414.0
35 TraesCS6D01G109200 chr1D 84.511 368 49 7 3201 3563 248925419 248925055 1.230000e-94 357.0
36 TraesCS6D01G109200 chr2A 81.278 454 56 21 2 440 398707365 398706926 1.240000e-89 340.0
37 TraesCS6D01G109200 chr2A 81.543 363 49 9 1 352 207351007 207350652 2.110000e-72 283.0
38 TraesCS6D01G109200 chr2A 95.745 47 2 0 2595 2641 186441009 186440963 3.850000e-10 76.8
39 TraesCS6D01G109200 chr5A 81.890 381 51 13 2 372 516816886 516816514 4.510000e-79 305.0
40 TraesCS6D01G109200 chr5A 81.215 362 48 11 3 352 20235058 20235411 1.270000e-69 274.0
41 TraesCS6D01G109200 chr5D 80.585 376 55 11 2 366 424109277 424109645 1.270000e-69 274.0
42 TraesCS6D01G109200 chr5B 83.582 268 43 1 1143 1410 247282958 247283224 2.140000e-62 250.0
43 TraesCS6D01G109200 chr5B 81.679 262 46 2 1146 1407 595286082 595286341 2.180000e-52 217.0
44 TraesCS6D01G109200 chr1B 83.395 271 43 2 1142 1412 266927241 266927509 2.140000e-62 250.0
45 TraesCS6D01G109200 chr2B 81.164 292 41 10 1127 1407 712836662 712836950 4.680000e-54 222.0
46 TraesCS6D01G109200 chr2B 92.188 64 3 2 3209 3272 190988989 190989050 4.950000e-14 89.8
47 TraesCS6D01G109200 chr3B 74.539 271 56 12 1146 1410 29495713 29495450 4.910000e-19 106.0
48 TraesCS6D01G109200 chr4B 90.000 70 4 3 3203 3272 597062254 597062320 1.780000e-13 87.9
49 TraesCS6D01G109200 chr4A 93.220 59 2 2 3202 3260 729709486 729709542 6.400000e-13 86.1
50 TraesCS6D01G109200 chr3D 94.118 34 2 0 1137 1170 327381708 327381741 6.000000e-03 52.8


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 TraesCS6D01G109200 chr6D 74259770 74263367 3597 True 2423.666667 6645 92.996000 1 3598 3 chr6D.!!$R2 3597
1 TraesCS6D01G109200 chr6D 74281472 74285048 3576 False 2272.666667 6198 92.329333 1 3598 3 chr6D.!!$F5 3597
2 TraesCS6D01G109200 chr6D 73846146 73847208 1062 False 1851.000000 1851 98.122000 1 1062 1 chr6D.!!$F3 1061
3 TraesCS6D01G109200 chr6D 73633537 73634239 702 False 1070.000000 1070 94.184000 2131 2832 1 chr6D.!!$F1 701
4 TraesCS6D01G109200 chr6D 73786789 73787861 1072 False 634.000000 918 91.486000 1497 2640 2 chr6D.!!$F4 1143
5 TraesCS6D01G109200 chr6A 90780866 90782709 1843 False 1634.000000 2972 91.910000 1410 3598 2 chr6A.!!$F5 2188
6 TraesCS6D01G109200 chr6A 90217664 90219655 1991 False 1040.333333 1954 90.587333 604 3172 3 chr6A.!!$F3 2568
7 TraesCS6D01G109200 chr6A 90194947 90195528 581 False 665.000000 665 87.521000 1 577 1 chr6A.!!$F1 576
8 TraesCS6D01G109200 chr6A 90749891 90751248 1357 False 405.000000 612 91.766333 1510 2640 3 chr6A.!!$F4 1130
9 TraesCS6D01G109200 chr6B 148331038 148336366 5328 False 888.800000 1958 91.510000 593 3596 5 chr6B.!!$F3 3003
10 TraesCS6D01G109200 chr6B 148080395 148084683 4288 False 782.666667 1160 92.480333 614 2591 3 chr6B.!!$F2 1977
11 TraesCS6D01G109200 chr7A 418616845 418617434 589 False 444.000000 444 80.769000 2 582 1 chr7A.!!$F1 580

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
316 326 0.107361 TGGCCTAGTGATCTCGACGA 60.107 55.000 3.32 0.0 0.0 4.20 F
542 565 1.036707 TCGGTTTGAAAAAGCTGGGG 58.963 50.000 0.00 0.0 0.0 4.96 F
744 770 3.469863 TTCTTTGGTCGGCAGCGGT 62.470 57.895 0.00 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1585 4225 1.202452 ACATTCAGCGCGATCATCAGA 60.202 47.619 12.10 0.0 0.0 3.27 R
2476 5428 1.705186 TGGTCTTGGGCTTAGCTCTTT 59.295 47.619 5.43 0.0 0.0 2.52 R
3278 8914 1.027357 CCCATCCCATTGCTCTTTCG 58.973 55.000 0.00 0.0 0.0 3.46 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
122 125 2.030185 GCGTCTACCAGTGAAGTTCTGA 60.030 50.000 4.17 0.0 35.20 3.27
266 269 2.109799 ATGCGAGGGAAGGCATCG 59.890 61.111 0.00 0.0 46.31 3.84
274 277 0.468226 GGGAAGGCATCGTCACCATA 59.532 55.000 0.00 0.0 0.00 2.74
314 324 1.103803 TGTGGCCTAGTGATCTCGAC 58.896 55.000 3.32 0.0 0.00 4.20
316 326 0.107361 TGGCCTAGTGATCTCGACGA 60.107 55.000 3.32 0.0 0.00 4.20
542 565 1.036707 TCGGTTTGAAAAAGCTGGGG 58.963 50.000 0.00 0.0 0.00 4.96
744 770 3.469863 TTCTTTGGTCGGCAGCGGT 62.470 57.895 0.00 0.0 0.00 5.68
1164 1203 4.080299 GTCTTACTCCCTCCATTCCACAAT 60.080 45.833 0.00 0.0 0.00 2.71
1313 1353 7.572523 AATAATGTGCATATGATATTCCGGG 57.427 36.000 6.97 0.0 0.00 5.73
2767 5742 6.453092 CATCTAATCCATTTTCATGAAGGGC 58.547 40.000 8.41 0.0 30.78 5.19
3008 5985 4.160252 AGACAGAGGTTTGCACAACATTTT 59.840 37.500 11.93 0.0 0.00 1.82
3040 6017 2.067766 CTTCTCTTGAGCTCACAGCAC 58.932 52.381 18.03 0.0 45.56 4.40
3294 8930 2.496899 ACACGAAAGAGCAATGGGAT 57.503 45.000 0.00 0.0 0.00 3.85
3488 9124 1.507141 AAGCGTGGAAGGTTGCTTCG 61.507 55.000 0.00 0.0 43.77 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 145 3.681593 GGCACCACCACAAGTTTCTATA 58.318 45.455 0.00 0.00 38.86 1.31
143 146 2.514803 GGCACCACCACAAGTTTCTAT 58.485 47.619 0.00 0.00 38.86 1.98
191 194 2.282674 CTTCCTTGCCCAGCAGCA 60.283 61.111 0.00 0.00 40.61 4.41
266 269 3.741344 CCGGAGAAAATCGATATGGTGAC 59.259 47.826 0.00 0.00 0.00 3.67
274 277 0.460311 ACTCGCCGGAGAAAATCGAT 59.540 50.000 9.83 0.00 43.27 3.59
314 324 1.840741 CGTTATCAGCACGTCTCTTCG 59.159 52.381 0.00 0.00 32.80 3.79
1187 1226 6.153067 TCAAAGTTGACAACGTTTGACATTT 58.847 32.000 25.51 13.30 35.56 2.32
1188 1227 5.704888 TCAAAGTTGACAACGTTTGACATT 58.295 33.333 25.51 9.36 35.56 2.71
1190 1229 4.750952 TCAAAGTTGACAACGTTTGACA 57.249 36.364 25.51 14.80 35.56 3.58
1381 1421 9.530633 GTACTCCCTTAATTCTGTAATGTAGTG 57.469 37.037 0.00 0.00 0.00 2.74
1382 1422 9.490083 AGTACTCCCTTAATTCTGTAATGTAGT 57.510 33.333 0.00 0.00 0.00 2.73
1585 4225 1.202452 ACATTCAGCGCGATCATCAGA 60.202 47.619 12.10 0.00 0.00 3.27
1759 4405 4.300803 TGTGTAGCTTGACGTCGTTAATT 58.699 39.130 11.62 0.00 0.00 1.40
2476 5428 1.705186 TGGTCTTGGGCTTAGCTCTTT 59.295 47.619 5.43 0.00 0.00 2.52
3278 8914 1.027357 CCCATCCCATTGCTCTTTCG 58.973 55.000 0.00 0.00 0.00 3.46
3294 8930 2.668632 GACCCACTTCATCGCCCA 59.331 61.111 0.00 0.00 0.00 5.36
3488 9124 2.476619 CGCAATGGATGTATCTTCGACC 59.523 50.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.