Multiple sequence alignment - TraesCS2D01G022000

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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 TraesCS2D01G022000 chr2D 100.000 4073 0 0 1 4073 10095940 10100012 0.000000e+00 7522.0
1 TraesCS2D01G022000 chr2D 93.127 2488 159 8 814 3294 10025070 10022588 0.000000e+00 3637.0
2 TraesCS2D01G022000 chr2D 82.321 2206 341 30 829 3025 19462072 19464237 0.000000e+00 1868.0
3 TraesCS2D01G022000 chr2D 77.116 3072 520 84 85 3032 19579298 19582310 0.000000e+00 1609.0
4 TraesCS2D01G022000 chr2D 79.072 1983 350 48 815 2778 36435568 36433632 0.000000e+00 1303.0
5 TraesCS2D01G022000 chr2D 88.557 769 32 16 1 717 10167063 10166299 0.000000e+00 881.0
6 TraesCS2D01G022000 chr2D 87.359 443 53 2 3333 3774 91488563 91489003 4.700000e-139 505.0
7 TraesCS2D01G022000 chr2A 94.552 2937 105 17 445 3327 10197766 10200701 0.000000e+00 4486.0
8 TraesCS2D01G022000 chr2A 82.636 2102 341 17 935 3025 20502583 20504671 0.000000e+00 1838.0
9 TraesCS2D01G022000 chr2A 76.298 2447 469 77 638 3029 40342648 40340258 0.000000e+00 1203.0
10 TraesCS2D01G022000 chr2A 87.847 757 46 14 1 717 9681707 9682457 0.000000e+00 846.0
11 TraesCS2D01G022000 chr2A 87.847 757 46 14 1 717 10413219 10412469 0.000000e+00 846.0
12 TraesCS2D01G022000 chr2A 81.959 776 120 13 752 1510 10373566 10374338 1.230000e-179 640.0
13 TraesCS2D01G022000 chr2A 89.520 458 36 5 262 717 9369247 9369694 1.640000e-158 569.0
14 TraesCS2D01G022000 chr2A 90.406 271 10 6 1 261 9368916 9369180 3.900000e-90 342.0
15 TraesCS2D01G022000 chr2A 81.115 323 36 12 391 695 9320556 9320871 6.810000e-58 235.0
16 TraesCS2D01G022000 chr2A 79.134 254 48 5 2526 2778 9778958 9779207 1.950000e-38 171.0
17 TraesCS2D01G022000 chr2A 80.579 242 28 10 3 234 10197184 10197416 7.000000e-38 169.0
18 TraesCS2D01G022000 chr2A 83.505 97 10 5 516 608 10235949 10235855 7.250000e-13 86.1
19 TraesCS2D01G022000 chr2B 91.850 2957 200 25 407 3327 13495485 13492534 0.000000e+00 4087.0
20 TraesCS2D01G022000 chr2B 86.425 1790 202 23 1554 3327 13735738 13737502 0.000000e+00 1921.0
21 TraesCS2D01G022000 chr2B 77.421 2737 492 79 391 3045 31424699 31422007 0.000000e+00 1515.0
22 TraesCS2D01G022000 chr2B 79.574 1126 195 25 1538 2661 13480857 13479765 0.000000e+00 773.0
23 TraesCS2D01G022000 chr2B 80.515 816 137 14 715 1512 13734825 13735636 1.250000e-169 606.0
24 TraesCS2D01G022000 chr2B 80.148 811 134 18 715 1511 13481714 13480917 7.590000e-162 580.0
25 TraesCS2D01G022000 chr2B 87.313 268 17 10 1 259 31425113 31424854 1.430000e-74 291.0
26 TraesCS2D01G022000 chr7D 93.591 749 37 6 3333 4073 584679338 584680083 0.000000e+00 1107.0
27 TraesCS2D01G022000 chr7D 93.351 752 40 6 3331 4073 79360860 79361610 0.000000e+00 1103.0
28 TraesCS2D01G022000 chr7D 91.655 743 30 15 3333 4073 43660191 43659479 0.000000e+00 1000.0
29 TraesCS2D01G022000 chr7D 90.823 741 17 3 3333 4073 43681550 43680861 0.000000e+00 944.0
30 TraesCS2D01G022000 chr3D 93.609 751 33 9 3332 4073 598572452 598571708 0.000000e+00 1107.0
31 TraesCS2D01G022000 chr3D 93.094 753 40 8 3331 4073 575467287 575468037 0.000000e+00 1092.0
32 TraesCS2D01G022000 chr3D 93.085 752 40 8 3332 4073 582262252 582261503 0.000000e+00 1090.0
33 TraesCS2D01G022000 chr3D 93.484 706 36 6 3372 4068 30590525 30591229 0.000000e+00 1040.0
34 TraesCS2D01G022000 chr3D 86.559 372 35 5 3332 3690 30249035 30249404 2.950000e-106 396.0
35 TraesCS2D01G022000 chr5D 92.725 756 41 7 3330 4073 59394324 59395077 0.000000e+00 1079.0
36 TraesCS2D01G022000 chr1D 95.404 544 22 1 3328 3868 6711721 6711178 0.000000e+00 863.0
37 TraesCS2D01G022000 chr1D 98.392 311 5 0 3332 3642 289551035 289551345 7.700000e-152 547.0
38 TraesCS2D01G022000 chr1D 87.081 418 40 4 3332 3736 30294588 30295004 1.030000e-125 460.0
39 TraesCS2D01G022000 chr6A 83.223 757 81 32 3332 4073 29091369 29092094 0.000000e+00 652.0
40 TraesCS2D01G022000 chr6A 79.121 182 30 7 1132 1310 603691365 603691189 7.150000e-23 119.0
41 TraesCS2D01G022000 chr6D 82.225 737 82 24 3332 4068 31969072 31969759 1.260000e-164 590.0
42 TraesCS2D01G022000 chr5B 77.239 268 46 13 1132 1393 456461045 456461303 4.240000e-30 143.0
43 TraesCS2D01G022000 chrUn 76.329 207 39 8 1132 1334 76986490 76986690 7.200000e-18 102.0
44 TraesCS2D01G022000 chrUn 76.329 207 39 8 1132 1334 341414585 341414785 7.200000e-18 102.0
45 TraesCS2D01G022000 chrUn 75.845 207 40 8 1132 1334 440995623 440995823 3.350000e-16 97.1
46 TraesCS2D01G022000 chrUn 83.505 97 16 0 1238 1334 105377256 105377160 1.560000e-14 91.6


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 TraesCS2D01G022000 chr2D 10095940 10100012 4072 False 7522.0 7522 100.0000 1 4073 1 chr2D.!!$F1 4072
1 TraesCS2D01G022000 chr2D 10022588 10025070 2482 True 3637.0 3637 93.1270 814 3294 1 chr2D.!!$R1 2480
2 TraesCS2D01G022000 chr2D 19462072 19464237 2165 False 1868.0 1868 82.3210 829 3025 1 chr2D.!!$F2 2196
3 TraesCS2D01G022000 chr2D 19579298 19582310 3012 False 1609.0 1609 77.1160 85 3032 1 chr2D.!!$F3 2947
4 TraesCS2D01G022000 chr2D 36433632 36435568 1936 True 1303.0 1303 79.0720 815 2778 1 chr2D.!!$R3 1963
5 TraesCS2D01G022000 chr2D 10166299 10167063 764 True 881.0 881 88.5570 1 717 1 chr2D.!!$R2 716
6 TraesCS2D01G022000 chr2A 10197184 10200701 3517 False 2327.5 4486 87.5655 3 3327 2 chr2A.!!$F7 3324
7 TraesCS2D01G022000 chr2A 20502583 20504671 2088 False 1838.0 1838 82.6360 935 3025 1 chr2A.!!$F5 2090
8 TraesCS2D01G022000 chr2A 40340258 40342648 2390 True 1203.0 1203 76.2980 638 3029 1 chr2A.!!$R3 2391
9 TraesCS2D01G022000 chr2A 9681707 9682457 750 False 846.0 846 87.8470 1 717 1 chr2A.!!$F2 716
10 TraesCS2D01G022000 chr2A 10412469 10413219 750 True 846.0 846 87.8470 1 717 1 chr2A.!!$R2 716
11 TraesCS2D01G022000 chr2A 10373566 10374338 772 False 640.0 640 81.9590 752 1510 1 chr2A.!!$F4 758
12 TraesCS2D01G022000 chr2A 9368916 9369694 778 False 455.5 569 89.9630 1 717 2 chr2A.!!$F6 716
13 TraesCS2D01G022000 chr2B 13492534 13495485 2951 True 4087.0 4087 91.8500 407 3327 1 chr2B.!!$R1 2920
14 TraesCS2D01G022000 chr2B 13734825 13737502 2677 False 1263.5 1921 83.4700 715 3327 2 chr2B.!!$F1 2612
15 TraesCS2D01G022000 chr2B 31422007 31425113 3106 True 903.0 1515 82.3670 1 3045 2 chr2B.!!$R3 3044
16 TraesCS2D01G022000 chr2B 13479765 13481714 1949 True 676.5 773 79.8610 715 2661 2 chr2B.!!$R2 1946
17 TraesCS2D01G022000 chr7D 584679338 584680083 745 False 1107.0 1107 93.5910 3333 4073 1 chr7D.!!$F2 740
18 TraesCS2D01G022000 chr7D 79360860 79361610 750 False 1103.0 1103 93.3510 3331 4073 1 chr7D.!!$F1 742
19 TraesCS2D01G022000 chr7D 43659479 43660191 712 True 1000.0 1000 91.6550 3333 4073 1 chr7D.!!$R1 740
20 TraesCS2D01G022000 chr7D 43680861 43681550 689 True 944.0 944 90.8230 3333 4073 1 chr7D.!!$R2 740
21 TraesCS2D01G022000 chr3D 598571708 598572452 744 True 1107.0 1107 93.6090 3332 4073 1 chr3D.!!$R2 741
22 TraesCS2D01G022000 chr3D 575467287 575468037 750 False 1092.0 1092 93.0940 3331 4073 1 chr3D.!!$F3 742
23 TraesCS2D01G022000 chr3D 582261503 582262252 749 True 1090.0 1090 93.0850 3332 4073 1 chr3D.!!$R1 741
24 TraesCS2D01G022000 chr3D 30590525 30591229 704 False 1040.0 1040 93.4840 3372 4068 1 chr3D.!!$F2 696
25 TraesCS2D01G022000 chr5D 59394324 59395077 753 False 1079.0 1079 92.7250 3330 4073 1 chr5D.!!$F1 743
26 TraesCS2D01G022000 chr1D 6711178 6711721 543 True 863.0 863 95.4040 3328 3868 1 chr1D.!!$R1 540
27 TraesCS2D01G022000 chr6A 29091369 29092094 725 False 652.0 652 83.2230 3332 4073 1 chr6A.!!$F1 741
28 TraesCS2D01G022000 chr6D 31969072 31969759 687 False 590.0 590 82.2250 3332 4068 1 chr6D.!!$F1 736

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
389 528 1.002430 CCTGTTAGTTGCTCCTGCTCA 59.998 52.381 0.00 0.00 40.48 4.26 F
750 1022 1.832167 TTGGCACTCCTTGTTGGCC 60.832 57.895 0.00 0.00 44.82 5.36 F
1310 1646 1.315690 TACGCCCTCGAGGATAACAG 58.684 55.000 33.39 15.67 38.24 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1269 1605 2.224159 AGTGATGTTGTCCGGGCCT 61.224 57.895 2.12 0.0 0.00 5.19 R
1659 2070 2.284625 TCAGTCGGGCCATCTGGT 60.285 61.111 19.92 0.0 37.57 4.00 R
3267 3716 1.202533 CGAACTAAGATGCCGATGGGT 60.203 52.381 0.00 0.0 34.97 4.51 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
51 55 7.171630 TCCCTTGCTTTAGTTTGTTTTGTAA 57.828 32.000 0.00 0.00 0.00 2.41
52 56 7.787028 TCCCTTGCTTTAGTTTGTTTTGTAAT 58.213 30.769 0.00 0.00 0.00 1.89
280 382 9.464714 CTGTCTAACGAGCATACATTTTAGTAT 57.535 33.333 0.00 0.00 35.14 2.12
389 528 1.002430 CCTGTTAGTTGCTCCTGCTCA 59.998 52.381 0.00 0.00 40.48 4.26
476 718 2.484417 CCATCACATGCTCTGGGAGTAC 60.484 54.545 0.00 0.00 41.69 2.73
615 861 9.534565 TCGTCTTTTCCTTTCTAATATGATGAG 57.465 33.333 0.00 0.00 0.00 2.90
629 892 2.849942 TGATGAGTTGGTGAGTTGGTG 58.150 47.619 0.00 0.00 0.00 4.17
750 1022 1.832167 TTGGCACTCCTTGTTGGCC 60.832 57.895 0.00 0.00 44.82 5.36
763 1042 3.364442 TGGCCGCACCATGAAAAG 58.636 55.556 0.00 0.00 46.36 2.27
805 1089 6.008331 TGACTTGACAGTGTACTACCACTAT 58.992 40.000 0.00 0.00 43.70 2.12
876 1194 5.568685 TTCTTCAGAGTTGAGAGGTATCG 57.431 43.478 0.00 0.00 34.15 2.92
941 1266 6.500684 AGTCTGTGCATTACCATGTTTAAG 57.499 37.500 0.00 0.00 32.28 1.85
1269 1605 2.659016 CTTCTGCTGCACCTCGGA 59.341 61.111 0.00 0.00 0.00 4.55
1310 1646 1.315690 TACGCCCTCGAGGATAACAG 58.684 55.000 33.39 15.67 38.24 3.16
1632 2043 1.775039 TTCATATCTGCAAGCGCGGC 61.775 55.000 18.37 18.37 44.81 6.53
1659 2070 1.275291 GATTCAGTGGTCGAGGTGGAA 59.725 52.381 0.00 0.00 0.00 3.53
1895 2309 3.932822 TGAGCGGCAAAGATAGTTACAA 58.067 40.909 1.45 0.00 0.00 2.41
2885 3314 7.400915 TGTTATAATACTTGACAGTGGGGTAGT 59.599 37.037 0.00 0.00 34.06 2.73
2982 3411 0.622665 ATGCCCAGAAGCTTAGCACT 59.377 50.000 7.07 2.36 36.06 4.40
3124 3573 3.376234 CAGGACCATGCATAGTTTCACTG 59.624 47.826 0.00 2.65 0.00 3.66
3192 3641 5.189659 ACGTATCTTGTAAGCATCTCTCC 57.810 43.478 0.00 0.00 0.00 3.71
3252 3701 5.692115 TGTGGCTTCTTATGGAGAATACA 57.308 39.130 0.00 0.00 43.23 2.29
3267 3716 5.048083 GGAGAATACATTGGAGCACAAAACA 60.048 40.000 0.00 0.00 43.46 2.83
3286 3736 2.213499 CACCCATCGGCATCTTAGTTC 58.787 52.381 0.00 0.00 0.00 3.01
3327 3777 7.798516 GTGAACAAATTGTACTGTGTATCTGTG 59.201 37.037 0.00 0.00 0.00 3.66
3328 3778 7.497579 TGAACAAATTGTACTGTGTATCTGTGT 59.502 33.333 0.00 0.00 0.00 3.72
3354 3804 6.095021 AGTCACTACCAGAAAAACTTGGTTTC 59.905 38.462 1.03 0.00 34.43 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
476 718 6.157904 TGCATTCAATCAACCAACAATACTG 58.842 36.000 0.00 0.00 0.00 2.74
610 856 2.549754 CACACCAACTCACCAACTCATC 59.450 50.000 0.00 0.00 0.00 2.92
612 858 1.280710 ACACACCAACTCACCAACTCA 59.719 47.619 0.00 0.00 0.00 3.41
613 859 2.038387 ACACACCAACTCACCAACTC 57.962 50.000 0.00 0.00 0.00 3.01
615 861 1.134175 CCAACACACCAACTCACCAAC 59.866 52.381 0.00 0.00 0.00 3.77
619 882 1.001378 GCATCCAACACACCAACTCAC 60.001 52.381 0.00 0.00 0.00 3.51
647 910 2.163010 GGAATCACATGTGAAGGTGCAG 59.837 50.000 31.00 0.00 43.58 4.41
648 911 2.161855 GGAATCACATGTGAAGGTGCA 58.838 47.619 31.00 8.13 43.58 4.57
750 1022 2.807967 TGAGTCTTCTTTTCATGGTGCG 59.192 45.455 0.00 0.00 0.00 5.34
763 1042 6.646653 TCAAGTCAACATACATGTGAGTCTTC 59.353 38.462 9.11 1.61 41.61 2.87
876 1194 1.063174 GAGATCACGAAATGGCAGTGC 59.937 52.381 6.55 6.55 35.97 4.40
941 1266 7.435068 ACACAGATAAAATCAGTAACCACAC 57.565 36.000 0.00 0.00 0.00 3.82
1269 1605 2.224159 AGTGATGTTGTCCGGGCCT 61.224 57.895 2.12 0.00 0.00 5.19
1632 2043 4.115516 CCTCGACCACTGAATCAACTATG 58.884 47.826 0.00 0.00 0.00 2.23
1659 2070 2.284625 TCAGTCGGGCCATCTGGT 60.285 61.111 19.92 0.00 37.57 4.00
2885 3314 1.762957 GCAGCAGACCCACCTTATCTA 59.237 52.381 0.00 0.00 0.00 1.98
2982 3411 4.357947 GTCACGAGCTCACCGCCA 62.358 66.667 15.40 0.00 40.39 5.69
3171 3620 4.038042 TGGGAGAGATGCTTACAAGATACG 59.962 45.833 0.00 0.00 0.00 3.06
3192 3641 4.730949 AAGTTGGATGCTGAATTGATGG 57.269 40.909 0.00 0.00 0.00 3.51
3252 3701 1.786937 TGGGTGTTTTGTGCTCCAAT 58.213 45.000 0.00 0.00 31.81 3.16
3267 3716 1.202533 CGAACTAAGATGCCGATGGGT 60.203 52.381 0.00 0.00 34.97 4.51
3286 3736 2.743664 TGTTCACTGAATCATTGCTCCG 59.256 45.455 0.00 0.00 0.00 4.63
3327 3777 6.053650 ACCAAGTTTTTCTGGTAGTGACTAC 58.946 40.000 14.19 14.19 36.33 2.73
3328 3778 6.243216 ACCAAGTTTTTCTGGTAGTGACTA 57.757 37.500 0.00 0.00 32.13 2.59
3354 3804 1.507141 GCATAGATTTGGCCGTCGGG 61.507 60.000 14.38 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.