Multiple sequence alignment - TraesCS6B01G203500

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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 TraesCS6B01G203500 chr6B 100.000 2213 0 0 1 2213 249497931 249495719 0.000000e+00 4087.0
1 TraesCS6B01G203500 chr6B 88.036 1003 92 13 416 1392 433047851 433046851 0.000000e+00 1162.0
2 TraesCS6B01G203500 chr6B 94.640 541 25 4 1460 1998 187091673 187091135 0.000000e+00 835.0
3 TraesCS6B01G203500 chr6B 96.078 204 6 2 1 204 269687091 269686890 4.550000e-87 331.0
4 TraesCS6B01G203500 chr2B 93.238 1124 74 2 328 1451 34080797 34079676 0.000000e+00 1653.0
5 TraesCS6B01G203500 chr2B 95.410 719 31 2 1460 2177 651649171 651648454 0.000000e+00 1144.0
6 TraesCS6B01G203500 chr2B 86.938 934 84 16 533 1451 98131996 98132906 0.000000e+00 1014.0
7 TraesCS6B01G203500 chr2B 88.000 325 13 6 1 325 34081125 34080827 5.810000e-96 361.0
8 TraesCS6B01G203500 chr2B 87.712 236 27 2 237 471 219261842 219262076 7.780000e-70 274.0
9 TraesCS6B01G203500 chr6D 88.035 1262 96 14 216 1451 390608825 390610057 0.000000e+00 1443.0
10 TraesCS6B01G203500 chr6D 86.651 1251 137 8 216 1451 76006872 76008107 0.000000e+00 1358.0
11 TraesCS6B01G203500 chr6D 88.714 824 64 10 465 1272 28030260 28029450 0.000000e+00 979.0
12 TraesCS6B01G203500 chr6D 87.704 675 47 12 581 1240 435987790 435987137 0.000000e+00 754.0
13 TraesCS6B01G203500 chr6D 86.611 478 42 7 416 893 432969164 432968709 1.960000e-140 508.0
14 TraesCS6B01G203500 chr6D 95.455 44 2 0 161 204 390608795 390608838 1.100000e-08 71.3
15 TraesCS6B01G203500 chr5D 89.689 931 74 10 533 1451 294588695 294589615 0.000000e+00 1168.0
16 TraesCS6B01G203500 chr5D 85.363 936 93 14 471 1379 220775557 220774639 0.000000e+00 929.0
17 TraesCS6B01G203500 chr5D 87.850 535 55 8 533 1067 420607990 420608514 8.680000e-174 619.0
18 TraesCS6B01G203500 chr4D 88.206 992 91 13 429 1394 443715360 443714369 0.000000e+00 1160.0
19 TraesCS6B01G203500 chr4D 85.341 996 114 17 429 1395 451883014 451882022 0.000000e+00 1002.0
20 TraesCS6B01G203500 chr4D 86.920 841 61 18 581 1394 416824454 416823636 0.000000e+00 898.0
21 TraesCS6B01G203500 chr4D 86.223 842 64 21 581 1394 36607044 36606227 0.000000e+00 865.0
22 TraesCS6B01G203500 chr3D 87.933 1011 88 14 416 1394 206164615 206165623 0.000000e+00 1160.0
23 TraesCS6B01G203500 chr3D 87.637 1003 95 14 419 1394 549726222 549725222 0.000000e+00 1138.0
24 TraesCS6B01G203500 chr3D 93.485 307 18 1 294 600 603162553 603162857 2.590000e-124 455.0
25 TraesCS6B01G203500 chr3D 95.098 204 5 2 1 204 603162329 603162527 1.280000e-82 316.0
26 TraesCS6B01G203500 chr3D 86.873 259 29 4 216 471 290307005 290306749 3.600000e-73 285.0
27 TraesCS6B01G203500 chr3D 90.256 195 19 0 236 430 206164406 206164600 2.820000e-64 255.0
28 TraesCS6B01G203500 chr3D 85.965 171 23 1 218 388 455015864 455015695 4.850000e-42 182.0
29 TraesCS6B01G203500 chr1B 94.195 758 39 5 1460 2213 24022889 24022133 0.000000e+00 1151.0
30 TraesCS6B01G203500 chr1B 93.779 643 27 3 1469 2098 315576701 315576059 0.000000e+00 953.0
31 TraesCS6B01G203500 chr1B 91.564 652 37 7 1460 2098 56125351 56125997 0.000000e+00 883.0
32 TraesCS6B01G203500 chr1B 94.257 505 24 5 1460 1962 328501824 328501323 0.000000e+00 767.0
33 TraesCS6B01G203500 chr1B 89.888 178 18 0 2036 2213 328501312 328501135 1.710000e-56 230.0
34 TraesCS6B01G203500 chr1B 100.000 37 0 0 167 203 470881778 470881742 3.940000e-08 69.4
35 TraesCS6B01G203500 chr4B 87.737 1003 95 11 416 1392 301726935 301725935 0.000000e+00 1146.0
36 TraesCS6B01G203500 chr4B 87.537 1003 97 12 416 1392 301700388 301699388 0.000000e+00 1134.0
37 TraesCS6B01G203500 chr4B 87.438 1003 98 13 416 1392 301754204 301753204 0.000000e+00 1129.0
38 TraesCS6B01G203500 chr4B 87.338 1003 99 13 416 1392 301810745 301809745 0.000000e+00 1123.0
39 TraesCS6B01G203500 chr4B 88.329 814 73 11 429 1227 420221140 420220334 0.000000e+00 957.0
40 TraesCS6B01G203500 chr4B 94.690 565 27 3 1460 2022 524138863 524138300 0.000000e+00 874.0
41 TraesCS6B01G203500 chr4B 95.349 43 2 0 161 203 649830174 649830216 3.940000e-08 69.4
42 TraesCS6B01G203500 chr7D 87.960 1005 72 17 416 1394 118446333 118447314 0.000000e+00 1140.0
43 TraesCS6B01G203500 chr7D 86.359 931 85 11 471 1374 59671582 59670667 0.000000e+00 977.0
44 TraesCS6B01G203500 chr5A 87.861 1005 73 17 416 1394 567112593 567111612 0.000000e+00 1134.0
45 TraesCS6B01G203500 chr4A 93.395 757 44 5 1460 2213 711869045 711869798 0.000000e+00 1116.0
46 TraesCS6B01G203500 chr7A 89.347 873 69 13 416 1272 200655344 200656208 0.000000e+00 1075.0
47 TraesCS6B01G203500 chr7A 88.147 869 69 6 303 1157 3809513 3808665 0.000000e+00 1003.0
48 TraesCS6B01G203500 chr7A 86.266 932 94 12 533 1451 191846758 191847668 0.000000e+00 981.0
49 TraesCS6B01G203500 chr7A 89.666 329 22 1 1135 1451 77667963 77668291 2.050000e-110 409.0
50 TraesCS6B01G203500 chr7A 89.057 265 16 5 1199 1451 3808665 3808402 1.280000e-82 316.0
51 TraesCS6B01G203500 chr5B 91.622 752 55 8 1460 2208 447879549 447880295 0.000000e+00 1033.0
52 TraesCS6B01G203500 chr5B 88.146 329 27 8 1135 1451 491820423 491820751 4.460000e-102 381.0
53 TraesCS6B01G203500 chr5B 88.274 307 23 9 1157 1451 460273266 460272961 2.700000e-94 355.0
54 TraesCS6B01G203500 chr5B 89.888 178 18 0 2036 2213 447880435 447880612 1.710000e-56 230.0
55 TraesCS6B01G203500 chr3B 91.711 748 56 6 1463 2207 685950066 685949322 0.000000e+00 1033.0
56 TraesCS6B01G203500 chr3B 87.259 259 29 3 216 471 570066067 570066324 2.150000e-75 292.0
57 TraesCS6B01G203500 chr1A 91.600 750 54 8 1467 2213 590528614 590527871 0.000000e+00 1027.0
58 TraesCS6B01G203500 chr6A 84.639 996 121 16 429 1395 602833764 602834756 0.000000e+00 963.0
59 TraesCS6B01G203500 chr6A 84.221 995 125 17 430 1395 74542655 74543646 0.000000e+00 939.0
60 TraesCS6B01G203500 chr6A 90.863 197 18 0 2017 2213 35118304 35118108 4.690000e-67 265.0
61 TraesCS6B01G203500 chr2D 83.968 998 123 22 429 1395 344568133 344569124 0.000000e+00 922.0
62 TraesCS6B01G203500 chr2D 86.550 171 22 1 218 388 356535094 356534925 1.040000e-43 187.0
63 TraesCS6B01G203500 chrUn 100.000 37 0 0 167 203 369753895 369753859 3.940000e-08 69.4
64 TraesCS6B01G203500 chr7B 95.349 43 2 0 161 203 653185749 653185791 3.940000e-08 69.4
65 TraesCS6B01G203500 chr7B 93.478 46 3 0 158 203 653245928 653245973 3.940000e-08 69.4


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 TraesCS6B01G203500 chr6B 249495719 249497931 2212 True 4087.00 4087 100.0000 1 2213 1 chr6B.!!$R2 2212
1 TraesCS6B01G203500 chr6B 433046851 433047851 1000 True 1162.00 1162 88.0360 416 1392 1 chr6B.!!$R4 976
2 TraesCS6B01G203500 chr6B 187091135 187091673 538 True 835.00 835 94.6400 1460 1998 1 chr6B.!!$R1 538
3 TraesCS6B01G203500 chr2B 651648454 651649171 717 True 1144.00 1144 95.4100 1460 2177 1 chr2B.!!$R1 717
4 TraesCS6B01G203500 chr2B 98131996 98132906 910 False 1014.00 1014 86.9380 533 1451 1 chr2B.!!$F1 918
5 TraesCS6B01G203500 chr2B 34079676 34081125 1449 True 1007.00 1653 90.6190 1 1451 2 chr2B.!!$R2 1450
6 TraesCS6B01G203500 chr6D 76006872 76008107 1235 False 1358.00 1358 86.6510 216 1451 1 chr6D.!!$F1 1235
7 TraesCS6B01G203500 chr6D 28029450 28030260 810 True 979.00 979 88.7140 465 1272 1 chr6D.!!$R1 807
8 TraesCS6B01G203500 chr6D 390608795 390610057 1262 False 757.15 1443 91.7450 161 1451 2 chr6D.!!$F2 1290
9 TraesCS6B01G203500 chr6D 435987137 435987790 653 True 754.00 754 87.7040 581 1240 1 chr6D.!!$R3 659
10 TraesCS6B01G203500 chr5D 294588695 294589615 920 False 1168.00 1168 89.6890 533 1451 1 chr5D.!!$F1 918
11 TraesCS6B01G203500 chr5D 220774639 220775557 918 True 929.00 929 85.3630 471 1379 1 chr5D.!!$R1 908
12 TraesCS6B01G203500 chr5D 420607990 420608514 524 False 619.00 619 87.8500 533 1067 1 chr5D.!!$F2 534
13 TraesCS6B01G203500 chr4D 443714369 443715360 991 True 1160.00 1160 88.2060 429 1394 1 chr4D.!!$R3 965
14 TraesCS6B01G203500 chr4D 451882022 451883014 992 True 1002.00 1002 85.3410 429 1395 1 chr4D.!!$R4 966
15 TraesCS6B01G203500 chr4D 416823636 416824454 818 True 898.00 898 86.9200 581 1394 1 chr4D.!!$R2 813
16 TraesCS6B01G203500 chr4D 36606227 36607044 817 True 865.00 865 86.2230 581 1394 1 chr4D.!!$R1 813
17 TraesCS6B01G203500 chr3D 549725222 549726222 1000 True 1138.00 1138 87.6370 419 1394 1 chr3D.!!$R3 975
18 TraesCS6B01G203500 chr3D 206164406 206165623 1217 False 707.50 1160 89.0945 236 1394 2 chr3D.!!$F1 1158
19 TraesCS6B01G203500 chr3D 603162329 603162857 528 False 385.50 455 94.2915 1 600 2 chr3D.!!$F2 599
20 TraesCS6B01G203500 chr1B 24022133 24022889 756 True 1151.00 1151 94.1950 1460 2213 1 chr1B.!!$R1 753
21 TraesCS6B01G203500 chr1B 315576059 315576701 642 True 953.00 953 93.7790 1469 2098 1 chr1B.!!$R2 629
22 TraesCS6B01G203500 chr1B 56125351 56125997 646 False 883.00 883 91.5640 1460 2098 1 chr1B.!!$F1 638
23 TraesCS6B01G203500 chr1B 328501135 328501824 689 True 498.50 767 92.0725 1460 2213 2 chr1B.!!$R4 753
24 TraesCS6B01G203500 chr4B 301725935 301726935 1000 True 1146.00 1146 87.7370 416 1392 1 chr4B.!!$R2 976
25 TraesCS6B01G203500 chr4B 301699388 301700388 1000 True 1134.00 1134 87.5370 416 1392 1 chr4B.!!$R1 976
26 TraesCS6B01G203500 chr4B 301753204 301754204 1000 True 1129.00 1129 87.4380 416 1392 1 chr4B.!!$R3 976
27 TraesCS6B01G203500 chr4B 301809745 301810745 1000 True 1123.00 1123 87.3380 416 1392 1 chr4B.!!$R4 976
28 TraesCS6B01G203500 chr4B 420220334 420221140 806 True 957.00 957 88.3290 429 1227 1 chr4B.!!$R5 798
29 TraesCS6B01G203500 chr4B 524138300 524138863 563 True 874.00 874 94.6900 1460 2022 1 chr4B.!!$R6 562
30 TraesCS6B01G203500 chr7D 118446333 118447314 981 False 1140.00 1140 87.9600 416 1394 1 chr7D.!!$F1 978
31 TraesCS6B01G203500 chr7D 59670667 59671582 915 True 977.00 977 86.3590 471 1374 1 chr7D.!!$R1 903
32 TraesCS6B01G203500 chr5A 567111612 567112593 981 True 1134.00 1134 87.8610 416 1394 1 chr5A.!!$R1 978
33 TraesCS6B01G203500 chr4A 711869045 711869798 753 False 1116.00 1116 93.3950 1460 2213 1 chr4A.!!$F1 753
34 TraesCS6B01G203500 chr7A 200655344 200656208 864 False 1075.00 1075 89.3470 416 1272 1 chr7A.!!$F3 856
35 TraesCS6B01G203500 chr7A 191846758 191847668 910 False 981.00 981 86.2660 533 1451 1 chr7A.!!$F2 918
36 TraesCS6B01G203500 chr7A 3808402 3809513 1111 True 659.50 1003 88.6020 303 1451 2 chr7A.!!$R1 1148
37 TraesCS6B01G203500 chr5B 447879549 447880612 1063 False 631.50 1033 90.7550 1460 2213 2 chr5B.!!$F2 753
38 TraesCS6B01G203500 chr3B 685949322 685950066 744 True 1033.00 1033 91.7110 1463 2207 1 chr3B.!!$R1 744
39 TraesCS6B01G203500 chr1A 590527871 590528614 743 True 1027.00 1027 91.6000 1467 2213 1 chr1A.!!$R1 746
40 TraesCS6B01G203500 chr6A 602833764 602834756 992 False 963.00 963 84.6390 429 1395 1 chr6A.!!$F2 966
41 TraesCS6B01G203500 chr6A 74542655 74543646 991 False 939.00 939 84.2210 430 1395 1 chr6A.!!$F1 965
42 TraesCS6B01G203500 chr2D 344568133 344569124 991 False 922.00 922 83.9680 429 1395 1 chr2D.!!$F1 966

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
623 688 1.379527 CCTGGAAAGTACATTCGCCC 58.62 55.0 4.86 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1465 1580 4.835284 AACTGTTTGTGGTCCCAAAAAT 57.165 36.364 5.01 0.0 35.82 1.82 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
28 29 5.538433 CAGATAAGGTTTGGTTTGGGAAAGA 59.462 40.000 0.00 0.0 0.00 2.52
35 36 3.963476 TGGTTTGGGAAAGAAGGAGAA 57.037 42.857 0.00 0.0 0.00 2.87
71 72 2.170187 CTGGGAAAGGATGAGGTGAGAG 59.830 54.545 0.00 0.0 0.00 3.20
107 108 5.475909 GGAGTTAGTCGATGTATATGGGTCA 59.524 44.000 0.00 0.0 0.00 4.02
263 264 2.550208 GGGTCCAGTAGGTGTTCTGTTG 60.550 54.545 0.00 0.0 35.89 3.33
338 366 8.356657 GCTTACTACTTCTCACTGATCATACAT 58.643 37.037 0.00 0.0 0.00 2.29
349 377 9.872721 CTCACTGATCATACATGATAAATAGCT 57.127 33.333 0.00 0.0 46.84 3.32
469 529 6.094186 GTCCTCTATTTGATGTTCCAAACTCC 59.906 42.308 0.00 0.0 38.65 3.85
620 685 5.175859 TCTAAAGCCTGGAAAGTACATTCG 58.824 41.667 0.00 0.0 0.00 3.34
623 688 1.379527 CCTGGAAAGTACATTCGCCC 58.620 55.000 4.86 0.0 0.00 6.13
628 693 2.433436 GAAAGTACATTCGCCCTGGTT 58.567 47.619 0.00 0.0 0.00 3.67
690 767 8.587627 CAACAACTGCTAAACGATATAACTTG 57.412 34.615 0.00 0.0 0.00 3.16
776 858 1.537202 GGGCAACACAGTTAAGCTCTG 59.463 52.381 0.00 0.0 38.68 3.35
780 862 3.851105 GCAACACAGTTAAGCTCTGCAAG 60.851 47.826 0.97 0.0 36.50 4.01
813 895 6.986250 TCATAGACTATGAAAGATCATGCGT 58.014 36.000 20.55 0.0 45.82 5.24
994 1095 4.395625 CTTTTCTACGGGTTCCCTTTTCT 58.604 43.478 6.31 0.0 0.00 2.52
997 1098 3.178865 TCTACGGGTTCCCTTTTCTCAT 58.821 45.455 6.31 0.0 0.00 2.90
1012 1113 6.769822 CCTTTTCTCATACATGGATGCTAACT 59.230 38.462 13.54 0.0 0.00 2.24
1295 1398 8.066612 ACTTATGTGTTTATCATCCTTTTGGG 57.933 34.615 0.00 0.0 40.87 4.12
1330 1445 2.352651 CCTAAGACCATCATGTGCGTTG 59.647 50.000 0.00 0.0 0.00 4.10
1451 1566 1.976474 ATTGGCGCAACGGGTCATT 60.976 52.632 10.83 0.0 28.70 2.57
1452 1567 1.531739 ATTGGCGCAACGGGTCATTT 61.532 50.000 10.83 0.0 28.70 2.32
1453 1568 2.126502 GGCGCAACGGGTCATTTG 60.127 61.111 10.83 0.0 0.00 2.32
1454 1569 2.126502 GCGCAACGGGTCATTTGG 60.127 61.111 0.30 0.0 0.00 3.28
1455 1570 2.566010 CGCAACGGGTCATTTGGG 59.434 61.111 0.00 0.0 0.00 4.12
1456 1571 2.265182 CGCAACGGGTCATTTGGGT 61.265 57.895 0.00 0.0 32.50 4.51
1457 1572 0.956410 CGCAACGGGTCATTTGGGTA 60.956 55.000 0.00 0.0 32.50 3.69
1458 1573 1.249407 GCAACGGGTCATTTGGGTAA 58.751 50.000 0.00 0.0 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 2.092699 CCTCATCCTTTCCCAGTTCTCC 60.093 54.545 0.00 0.00 0.00 3.71
71 72 3.291101 TAACTCCCACGCACGCTCC 62.291 63.158 0.00 0.00 0.00 4.70
107 108 1.533711 GCCCAGCCCACATACATCT 59.466 57.895 0.00 0.00 0.00 2.90
234 235 2.840651 CACCTACTGGACCCTGAAAGAT 59.159 50.000 0.00 0.00 34.14 2.40
263 264 3.484407 ACCAGAGCATCAATGAATAGCC 58.516 45.455 0.00 0.00 37.82 3.93
623 688 7.451877 TGAGAAGAGTAATATAGCCCTAACCAG 59.548 40.741 0.00 0.00 0.00 4.00
628 693 7.454694 TGCAATGAGAAGAGTAATATAGCCCTA 59.545 37.037 0.00 0.00 0.00 3.53
776 858 8.315391 TCATAGTCTATGAACATTATGCTTGC 57.685 34.615 18.41 0.00 41.89 4.01
813 895 0.177141 GATTAGGCGTGGTGGTGCTA 59.823 55.000 0.00 0.00 0.00 3.49
855 937 0.094216 CGTCTGCTGCAAATGTCTCG 59.906 55.000 3.02 0.00 0.00 4.04
994 1095 4.164030 ACCACAGTTAGCATCCATGTATGA 59.836 41.667 1.88 0.00 0.00 2.15
997 1098 3.517500 TCACCACAGTTAGCATCCATGTA 59.482 43.478 0.00 0.00 0.00 2.29
1274 1376 6.256053 AGACCCAAAAGGATGATAAACACAT 58.744 36.000 0.00 0.00 39.89 3.21
1295 1398 6.742559 TGGTCTTAGGGGATTACATAAGAC 57.257 41.667 17.47 17.47 46.95 3.01
1330 1445 3.065371 ACACAACAGTCTAAGCAGCAAAC 59.935 43.478 0.00 0.00 0.00 2.93
1407 1522 4.390048 GGCCGAGTGTAAGCCAAA 57.610 55.556 0.00 0.00 46.34 3.28
1451 1566 6.292150 GTCCCAAAAATTGTTCATTACCCAA 58.708 36.000 0.00 0.00 0.00 4.12
1452 1567 5.221742 GGTCCCAAAAATTGTTCATTACCCA 60.222 40.000 0.00 0.00 0.00 4.51
1453 1568 5.221742 TGGTCCCAAAAATTGTTCATTACCC 60.222 40.000 0.00 0.00 0.00 3.69
1454 1569 5.699001 GTGGTCCCAAAAATTGTTCATTACC 59.301 40.000 0.00 0.00 0.00 2.85
1455 1570 6.284459 TGTGGTCCCAAAAATTGTTCATTAC 58.716 36.000 0.00 0.00 0.00 1.89
1456 1571 6.485830 TGTGGTCCCAAAAATTGTTCATTA 57.514 33.333 0.00 0.00 0.00 1.90
1457 1572 5.365021 TGTGGTCCCAAAAATTGTTCATT 57.635 34.783 0.00 0.00 0.00 2.57
1458 1573 5.365021 TTGTGGTCCCAAAAATTGTTCAT 57.635 34.783 0.00 0.00 0.00 2.57
1465 1580 4.835284 AACTGTTTGTGGTCCCAAAAAT 57.165 36.364 5.01 0.00 35.82 1.82
1983 2124 6.811170 ACGCCATGTTCCTAAAAATATGTTTG 59.189 34.615 0.78 0.00 0.00 2.93
1984 2125 6.930731 ACGCCATGTTCCTAAAAATATGTTT 58.069 32.000 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.