Multiple sequence alignment - TraesCS5B01G355400

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 TraesCS5B01G355400 chr5B 100.000 3320 0 0 1 3320 534918734 534915415 0.000000e+00 6131.0
1 TraesCS5B01G355400 chr5B 87.646 1546 182 7 944 2485 534862386 534860846 0.000000e+00 1788.0
2 TraesCS5B01G355400 chr5D 95.721 2664 102 7 655 3318 439793625 439790974 0.000000e+00 4277.0
3 TraesCS5B01G355400 chr5D 87.101 690 46 15 9 659 439794343 439793658 0.000000e+00 741.0
4 TraesCS5B01G355400 chrUn 97.656 2346 52 1 973 3318 80087870 80090212 0.000000e+00 4024.0
5 TraesCS5B01G355400 chrUn 96.583 1317 45 0 2002 3318 376485072 376486388 0.000000e+00 2183.0
6 TraesCS5B01G355400 chrUn 98.582 1128 16 0 1493 2620 436077349 436078476 0.000000e+00 1995.0
7 TraesCS5B01G355400 chrUn 87.321 1680 202 9 944 2618 80135707 80137380 0.000000e+00 1912.0
8 TraesCS5B01G355400 chrUn 97.611 837 19 1 655 1491 325202284 325203119 0.000000e+00 1434.0
9 TraesCS5B01G355400 chrUn 87.755 686 46 16 9 659 325201569 325202251 0.000000e+00 767.0
10 TraesCS5B01G355400 chrUn 82.609 690 110 8 2637 3320 223958630 223957945 4.740000e-168 601.0
11 TraesCS5B01G355400 chrUn 82.344 691 110 10 2637 3320 80137468 80138153 1.030000e-164 590.0
12 TraesCS5B01G355400 chrUn 78.107 169 32 3 257 421 96029526 96029693 5.860000e-18 102.0
13 TraesCS5B01G355400 chrUn 79.861 144 24 4 268 406 347177055 347177198 2.110000e-17 100.0
14 TraesCS5B01G355400 chrUn 79.861 144 24 4 268 406 460318789 460318932 2.110000e-17 100.0
15 TraesCS5B01G355400 chr1B 84.238 2671 379 25 655 3303 24163489 24160839 0.000000e+00 2562.0
16 TraesCS5B01G355400 chr1B 83.713 2634 368 32 697 3304 22843890 22841292 0.000000e+00 2431.0
17 TraesCS5B01G355400 chr1B 85.844 2211 290 10 697 2899 24152561 24150366 0.000000e+00 2327.0
18 TraesCS5B01G355400 chr1B 84.132 2401 322 29 728 3090 22887159 22884780 0.000000e+00 2268.0
19 TraesCS5B01G355400 chr1B 83.461 393 62 2 2931 3320 24145306 24144914 2.430000e-96 363.0
20 TraesCS5B01G355400 chr6A 83.529 1791 255 24 994 2766 570740852 570742620 0.000000e+00 1637.0
21 TraesCS5B01G355400 chr4A 84.784 1597 231 7 758 2348 743448289 743446699 0.000000e+00 1592.0
22 TraesCS5B01G355400 chr4A 91.379 58 3 2 536 593 743448556 743448501 9.870000e-11 78.7
23 TraesCS5B01G355400 chr7A 83.282 975 157 3 2352 3320 654345 653371 0.000000e+00 893.0
24 TraesCS5B01G355400 chr6D 82.482 685 104 10 2627 3303 425067939 425067263 1.330000e-163 586.0
25 TraesCS5B01G355400 chr1D 78.313 166 30 3 256 418 125087066 125086904 5.860000e-18 102.0
26 TraesCS5B01G355400 chr6B 79.861 144 24 4 268 406 689060918 689061061 2.110000e-17 100.0
27 TraesCS5B01G355400 chr7B 85.915 71 8 2 340 410 77428650 77428718 1.280000e-09 75.0
28 TraesCS5B01G355400 chr2A 75.974 154 29 5 1477 1629 16525421 16525275 4.590000e-09 73.1
29 TraesCS5B01G355400 chr2B 82.278 79 9 5 335 412 798377683 798377757 2.770000e-06 63.9


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 TraesCS5B01G355400 chr5B 534915415 534918734 3319 True 6131.00 6131 100.0000 1 3320 1 chr5B.!!$R2 3319
1 TraesCS5B01G355400 chr5B 534860846 534862386 1540 True 1788.00 1788 87.6460 944 2485 1 chr5B.!!$R1 1541
2 TraesCS5B01G355400 chr5D 439790974 439794343 3369 True 2509.00 4277 91.4110 9 3318 2 chr5D.!!$R1 3309
3 TraesCS5B01G355400 chrUn 80087870 80090212 2342 False 4024.00 4024 97.6560 973 3318 1 chrUn.!!$F1 2345
4 TraesCS5B01G355400 chrUn 376485072 376486388 1316 False 2183.00 2183 96.5830 2002 3318 1 chrUn.!!$F4 1316
5 TraesCS5B01G355400 chrUn 436077349 436078476 1127 False 1995.00 1995 98.5820 1493 2620 1 chrUn.!!$F5 1127
6 TraesCS5B01G355400 chrUn 80135707 80138153 2446 False 1251.00 1912 84.8325 944 3320 2 chrUn.!!$F7 2376
7 TraesCS5B01G355400 chrUn 325201569 325203119 1550 False 1100.50 1434 92.6830 9 1491 2 chrUn.!!$F8 1482
8 TraesCS5B01G355400 chrUn 223957945 223958630 685 True 601.00 601 82.6090 2637 3320 1 chrUn.!!$R1 683
9 TraesCS5B01G355400 chr1B 24160839 24163489 2650 True 2562.00 2562 84.2380 655 3303 1 chr1B.!!$R5 2648
10 TraesCS5B01G355400 chr1B 22841292 22843890 2598 True 2431.00 2431 83.7130 697 3304 1 chr1B.!!$R1 2607
11 TraesCS5B01G355400 chr1B 24150366 24152561 2195 True 2327.00 2327 85.8440 697 2899 1 chr1B.!!$R4 2202
12 TraesCS5B01G355400 chr1B 22884780 22887159 2379 True 2268.00 2268 84.1320 728 3090 1 chr1B.!!$R2 2362
13 TraesCS5B01G355400 chr6A 570740852 570742620 1768 False 1637.00 1637 83.5290 994 2766 1 chr6A.!!$F1 1772
14 TraesCS5B01G355400 chr4A 743446699 743448556 1857 True 835.35 1592 88.0815 536 2348 2 chr4A.!!$R1 1812
15 TraesCS5B01G355400 chr7A 653371 654345 974 True 893.00 893 83.2820 2352 3320 1 chr7A.!!$R1 968
16 TraesCS5B01G355400 chr6D 425067263 425067939 676 True 586.00 586 82.4820 2627 3303 1 chr6D.!!$R1 676

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
133 135 0.324943 ATGCACCTTGGACGCTAAGT 59.675 50.000 0.00 0.0 0.0 2.24 F
858 958 1.394917 GCATGTCGCGAATTCTTCAGT 59.605 47.619 12.06 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1378 1491 3.888930 TCCTTCATTTCTTTTTCACGGCT 59.111 39.130 0.0 0.0 0.00 5.52 R
2814 3032 3.914426 TTCTCTAAACTGAGGGCATCC 57.086 47.619 0.0 0.0 34.98 3.51 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
22 23 1.203025 ACGGAGGGAGTAATAGCCGAT 60.203 52.381 0.00 0.00 41.11 4.18
32 33 5.527582 GGAGTAATAGCCGATTTGTCATTGT 59.472 40.000 0.00 0.00 0.00 2.71
71 72 9.813826 ATTTCAAATACCAGGCTATAGCTTTAT 57.186 29.630 23.53 9.58 41.70 1.40
78 79 7.850935 ACCAGGCTATAGCTTTATTGTAGTA 57.149 36.000 23.53 0.00 41.70 1.82
82 83 8.244802 CAGGCTATAGCTTTATTGTAGTATCGT 58.755 37.037 23.53 0.00 41.70 3.73
115 117 5.010933 TGATAGCCTACTCGCTAAAGCTAT 58.989 41.667 2.17 2.17 44.25 2.97
120 122 1.941325 ACTCGCTAAAGCTATGCACC 58.059 50.000 0.00 0.00 39.32 5.01
127 129 1.453155 AAAGCTATGCACCTTGGACG 58.547 50.000 0.00 0.00 0.00 4.79
133 135 0.324943 ATGCACCTTGGACGCTAAGT 59.675 50.000 0.00 0.00 0.00 2.24
145 147 6.621316 TGGACGCTAAGTTGAAAAATACAA 57.379 33.333 0.00 0.00 0.00 2.41
207 209 4.932789 TTAGCACCGCTAAGCCAG 57.067 55.556 4.36 0.00 44.75 4.85
223 225 2.121385 AGTGCAGCCAGAGAGGGA 59.879 61.111 0.00 0.00 38.09 4.20
254 263 2.361610 CACAAGGCCGCCCATCTT 60.362 61.111 5.55 0.00 0.00 2.40
352 361 5.782893 TTGGTGTTCTTTTAATGTCTGGG 57.217 39.130 0.00 0.00 0.00 4.45
353 362 5.055265 TGGTGTTCTTTTAATGTCTGGGA 57.945 39.130 0.00 0.00 0.00 4.37
360 369 5.076182 TCTTTTAATGTCTGGGAATGTGCA 58.924 37.500 0.00 0.00 0.00 4.57
361 370 5.716228 TCTTTTAATGTCTGGGAATGTGCAT 59.284 36.000 0.00 0.00 0.00 3.96
365 374 2.300433 TGTCTGGGAATGTGCATATGC 58.700 47.619 21.09 21.09 42.50 3.14
480 498 4.479619 CTTTTCACAACTTCTGGCATAGC 58.520 43.478 0.00 0.00 0.00 2.97
499 517 4.385358 AGCCCCGCTATTTAAAACATTG 57.615 40.909 0.00 0.00 36.99 2.82
501 519 4.109766 GCCCCGCTATTTAAAACATTGTC 58.890 43.478 0.00 0.00 0.00 3.18
504 522 6.394809 CCCCGCTATTTAAAACATTGTCTTT 58.605 36.000 0.00 0.00 0.00 2.52
506 524 7.148656 CCCCGCTATTTAAAACATTGTCTTTTG 60.149 37.037 0.00 0.00 0.00 2.44
508 526 6.942224 CGCTATTTAAAACATTGTCTTTTGCG 59.058 34.615 0.00 0.00 0.00 4.85
527 545 3.873952 TGCGCATATAGTTTACATGCACA 59.126 39.130 5.66 0.09 44.19 4.57
622 661 2.158449 CGTGCCTTTCTTCAGTCATGAC 59.842 50.000 18.47 18.47 34.35 3.06
644 702 1.837439 TCACTCACTGACCAACCACTT 59.163 47.619 0.00 0.00 0.00 3.16
711 811 6.650120 GGAGTCTGTCCATTCTAAATGGTTA 58.350 40.000 16.22 7.66 46.10 2.85
716 816 8.044908 GTCTGTCCATTCTAAATGGTTACCTTA 58.955 37.037 16.22 0.00 40.06 2.69
736 836 6.941436 ACCTTATTCCGATATCGTACTCTTCT 59.059 38.462 22.81 2.65 37.74 2.85
858 958 1.394917 GCATGTCGCGAATTCTTCAGT 59.605 47.619 12.06 0.00 0.00 3.41
914 1014 2.033407 CACAGAACACTTCAGAGTTGCG 60.033 50.000 0.00 0.00 32.54 4.85
1858 1984 3.987745 AGATCTCCTGAGGTTGCTAAGA 58.012 45.455 0.00 0.00 0.00 2.10
2394 2544 2.936498 GCATGATACGGCACAACTAGTT 59.064 45.455 1.12 1.12 0.00 2.24
2780 2998 4.020928 TCTCAAAGTTATAGACCGTGGCAA 60.021 41.667 0.00 0.00 0.00 4.52
2813 3031 3.312736 AAGTTTTCCTCCAGGCTTCAA 57.687 42.857 0.00 0.00 34.44 2.69
2814 3032 2.868899 AGTTTTCCTCCAGGCTTCAAG 58.131 47.619 0.00 0.00 34.44 3.02
2909 3136 1.686355 ACATGGTCCTTTTTGCGTCA 58.314 45.000 0.00 0.00 0.00 4.35
2912 3139 0.958091 TGGTCCTTTTTGCGTCATGG 59.042 50.000 0.00 0.00 0.00 3.66
2913 3140 0.388520 GGTCCTTTTTGCGTCATGGC 60.389 55.000 0.00 0.00 0.00 4.40
2937 3164 3.696051 CGGTGAAGATGGTGGAAAATCAT 59.304 43.478 0.00 0.00 0.00 2.45
3084 3314 5.874810 GTGTGAAGTGAAGAGCATACCATTA 59.125 40.000 0.00 0.00 0.00 1.90
3291 3524 1.694150 CTTGACCTCACTTCCCTCACA 59.306 52.381 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.597072 CGGCTATTACTCCCTCCGTC 59.403 60.000 0.00 0.00 32.93 4.79
2 3 0.184451 TCGGCTATTACTCCCTCCGT 59.816 55.000 0.00 0.00 38.18 4.69
3 4 1.546961 ATCGGCTATTACTCCCTCCG 58.453 55.000 0.00 0.00 38.34 4.63
4 5 3.071167 ACAAATCGGCTATTACTCCCTCC 59.929 47.826 0.00 0.00 0.00 4.30
5 6 4.202223 TGACAAATCGGCTATTACTCCCTC 60.202 45.833 0.00 0.00 0.00 4.30
6 7 3.709653 TGACAAATCGGCTATTACTCCCT 59.290 43.478 0.00 0.00 0.00 4.20
7 8 4.067972 TGACAAATCGGCTATTACTCCC 57.932 45.455 0.00 0.00 0.00 4.30
41 42 7.779798 AGCTATAGCCTGGTATTTGAAATTTCA 59.220 33.333 21.17 16.91 43.38 2.69
56 57 8.244802 ACGATACTACAATAAAGCTATAGCCTG 58.755 37.037 21.17 12.66 43.38 4.85
92 94 3.223435 AGCTTTAGCGAGTAGGCTATCA 58.777 45.455 0.00 0.00 44.43 2.15
115 117 0.107831 AACTTAGCGTCCAAGGTGCA 59.892 50.000 8.36 0.00 0.00 4.57
120 122 6.664515 TGTATTTTTCAACTTAGCGTCCAAG 58.335 36.000 0.00 0.00 0.00 3.61
169 171 8.030692 TGCTAAATGAGTCTAAACTAAACGCTA 58.969 33.333 0.00 0.00 35.28 4.26
178 180 3.933332 AGCGGTGCTAAATGAGTCTAAAC 59.067 43.478 0.00 0.00 36.99 2.01
182 184 3.887621 TTAGCGGTGCTAAATGAGTCT 57.112 42.857 8.70 0.00 46.30 3.24
207 209 2.267324 GTCCCTCTCTGGCTGCAC 59.733 66.667 0.50 0.00 0.00 4.57
242 251 0.178990 AATAAGGAAGATGGGCGGCC 60.179 55.000 23.42 23.42 0.00 6.13
246 255 4.445557 AGGAAGAATAAGGAAGATGGGC 57.554 45.455 0.00 0.00 0.00 5.36
300 309 9.143631 GACATATTAATTCAACAAGCAAGCTTT 57.856 29.630 4.24 0.00 33.42 3.51
331 340 5.055265 TCCCAGACATTAAAAGAACACCA 57.945 39.130 0.00 0.00 0.00 4.17
338 347 5.389859 TGCACATTCCCAGACATTAAAAG 57.610 39.130 0.00 0.00 0.00 2.27
352 361 7.025365 CACATATACTTGGCATATGCACATTC 58.975 38.462 28.07 11.58 44.36 2.67
353 362 6.716173 TCACATATACTTGGCATATGCACATT 59.284 34.615 28.07 15.03 44.36 2.71
422 433 7.094377 TGCTAAACACCATTTTTCTAGGTCATC 60.094 37.037 0.00 0.00 32.15 2.92
428 439 6.842163 ACGATGCTAAACACCATTTTTCTAG 58.158 36.000 0.00 0.00 0.00 2.43
480 498 5.576447 AGACAATGTTTTAAATAGCGGGG 57.424 39.130 0.00 0.00 0.00 5.73
495 513 7.696035 TGTAAACTATATGCGCAAAAGACAATG 59.304 33.333 17.11 0.43 0.00 2.82
499 517 6.140737 GCATGTAAACTATATGCGCAAAAGAC 59.859 38.462 17.11 7.22 42.08 3.01
501 519 6.424557 GCATGTAAACTATATGCGCAAAAG 57.575 37.500 17.11 14.83 42.08 2.27
644 702 8.635765 ACCTTCTATATTTGCTCAAACTTCAA 57.364 30.769 0.00 0.00 32.51 2.69
711 811 6.941436 AGAAGAGTACGATATCGGAATAAGGT 59.059 38.462 27.58 7.85 44.95 3.50
716 816 7.982761 AGTTAGAAGAGTACGATATCGGAAT 57.017 36.000 27.58 20.24 44.95 3.01
858 958 4.188462 CCGTTATAACTGATGCAGTCCAA 58.812 43.478 13.56 0.00 44.62 3.53
903 1003 3.005791 TGTCTTCATCTCGCAACTCTGAA 59.994 43.478 0.00 0.00 0.00 3.02
914 1014 2.672381 GCAGCTGTCTTGTCTTCATCTC 59.328 50.000 16.64 0.00 0.00 2.75
1378 1491 3.888930 TCCTTCATTTCTTTTTCACGGCT 59.111 39.130 0.00 0.00 0.00 5.52
1858 1984 9.911788 CTCATAATTATTCATAGGGCCAACTAT 57.088 33.333 6.18 0.00 34.06 2.12
2780 2998 7.563906 TGGAGGAAAACTTTCAATCAAACAAT 58.436 30.769 4.67 0.00 38.92 2.71
2814 3032 3.914426 TTCTCTAAACTGAGGGCATCC 57.086 47.619 0.00 0.00 34.98 3.51
2850 3068 5.940470 AGAGTGGTCCTTGTTATAAGCAAAG 59.060 40.000 0.00 0.00 0.00 2.77
2891 3109 2.598589 CATGACGCAAAAAGGACCATG 58.401 47.619 0.00 0.00 0.00 3.66
2909 3136 0.677731 CACCATCTTCACCGTGCCAT 60.678 55.000 0.00 0.00 0.00 4.40
2912 3139 0.605319 TTCCACCATCTTCACCGTGC 60.605 55.000 0.00 0.00 0.00 5.34
2913 3140 1.890876 TTTCCACCATCTTCACCGTG 58.109 50.000 0.00 0.00 0.00 4.94
2937 3164 6.884472 TTCCAGTGAGGTAATCTTTCCATA 57.116 37.500 0.00 0.00 39.02 2.74
3084 3314 4.000988 GTGACACATCTAACGGGACAAAT 58.999 43.478 0.00 0.00 0.00 2.32
3116 3349 9.692749 GACGATTAATGTTATCTGAAGGTGATA 57.307 33.333 0.00 0.00 0.00 2.15
3172 3405 3.575805 TCAAGCCTTCCCAACTGATTTT 58.424 40.909 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.