Multiple sequence alignment - TraesCS1A01G135500

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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 TraesCS1A01G135500 chr1A 100.000 3294 0 0 1 3294 208727336 208724043 0.000000e+00 6083
1 TraesCS1A01G135500 chr1A 96.331 3325 89 7 1 3294 14198373 14195051 0.000000e+00 5433
2 TraesCS1A01G135500 chr3A 91.082 1211 101 6 664 1873 724555064 724556268 0.000000e+00 1631
3 TraesCS1A01G135500 chr3A 92.953 596 42 0 1 596 724554470 724555065 0.000000e+00 869
4 TraesCS1A01G135500 chr4A 83.498 1212 172 20 9 1205 78286013 78284815 0.000000e+00 1105
5 TraesCS1A01G135500 chr3B 90.959 365 33 0 3 367 705355589 705355225 2.950000e-135 492
6 TraesCS1A01G135500 chr3B 89.437 284 30 0 84 367 93907304 93907587 3.130000e-95 359
7 TraesCS1A01G135500 chr2B 89.610 154 16 0 2080 2233 794585195 794585042 2.590000e-46 196
8 TraesCS1A01G135500 chrUn 77.419 186 34 8 977 1158 478654057 478653876 1.620000e-18 104
9 TraesCS1A01G135500 chr6B 79.487 156 24 8 977 1128 558747717 558747868 1.620000e-18 104
10 TraesCS1A01G135500 chr6B 79.487 156 24 8 977 1128 558830302 558830453 1.620000e-18 104
11 TraesCS1A01G135500 chr4B 73.404 282 69 6 375 652 22985762 22985483 2.090000e-17 100


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 TraesCS1A01G135500 chr1A 208724043 208727336 3293 True 6083 6083 100.0000 1 3294 1 chr1A.!!$R2 3293
1 TraesCS1A01G135500 chr1A 14195051 14198373 3322 True 5433 5433 96.3310 1 3294 1 chr1A.!!$R1 3293
2 TraesCS1A01G135500 chr3A 724554470 724556268 1798 False 1250 1631 92.0175 1 1873 2 chr3A.!!$F1 1872
3 TraesCS1A01G135500 chr4A 78284815 78286013 1198 True 1105 1105 83.4980 9 1205 1 chr4A.!!$R1 1196

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
297 298 0.252479 AGCAGAGACCAAGCAGATGG 59.748 55.0 2.02 2.02 46.38 3.51 F
352 353 0.972134 TGAAGCAGAGTGACCCTGAG 59.028 55.0 0.00 0.00 33.65 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1147 1194 0.034380 TCTTCCCGGTCTCTGTCGAT 60.034 55.0 0.0 0.0 0.0 3.59 R
2293 2350 0.112412 ATTTGTGTCCTTCGCCCCTT 59.888 50.0 0.0 0.0 0.0 3.95 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
124 125 2.221299 CCACTTCCCTTCCCACCGA 61.221 63.158 0.00 0.00 0.00 4.69
190 191 6.094603 GTCAGAATAATGTCAACCTCAGCAAT 59.905 38.462 0.00 0.00 0.00 3.56
297 298 0.252479 AGCAGAGACCAAGCAGATGG 59.748 55.000 2.02 2.02 46.38 3.51
352 353 0.972134 TGAAGCAGAGTGACCCTGAG 59.028 55.000 0.00 0.00 33.65 3.35
378 399 7.205737 TCACTTATACAGTTCGTGTAGACAA 57.794 36.000 0.00 0.00 45.06 3.18
398 419 8.588290 AGACAATGAGAGTAGAGTTAGAACAT 57.412 34.615 0.00 0.00 0.00 2.71
494 515 7.987458 CCTACAGGACAAATCTATACAACATGT 59.013 37.037 0.00 0.00 37.39 3.21
720 767 7.666804 TGGTTGGATCTGATATTGACCAATATG 59.333 37.037 17.17 6.80 42.32 1.78
1024 1071 2.288518 TGGGCGAAACCTTATTTTGCAC 60.289 45.455 12.43 9.79 41.43 4.57
1032 1079 4.929819 ACCTTATTTTGCACGGAAGTTT 57.070 36.364 0.00 0.00 46.40 2.66
1160 1207 1.656095 GCTTCAAATCGACAGAGACCG 59.344 52.381 0.00 0.00 0.00 4.79
1188 1235 5.648960 AGAAGGTTTCCAAGAAAAACGTACA 59.351 36.000 0.00 0.00 37.46 2.90
1376 1423 5.399301 CACGAGGACAATGTTTGAAATGTTC 59.601 40.000 0.00 0.00 0.00 3.18
1377 1424 5.299279 ACGAGGACAATGTTTGAAATGTTCT 59.701 36.000 0.00 0.00 34.34 3.01
1528 1585 5.456921 ACTGATGATGGGGAAAAGTACAT 57.543 39.130 0.00 0.00 0.00 2.29
1778 1835 6.479001 CCTACCTGACCATCTTAAACATTACG 59.521 42.308 0.00 0.00 0.00 3.18
1838 1895 2.553602 CACTCTGCTTTGTACAATGCCA 59.446 45.455 31.87 21.82 39.75 4.92
1852 1909 0.178981 ATGCCACACTTGAGCTGGTT 60.179 50.000 0.00 0.00 0.00 3.67
1978 2035 2.159254 TGTGTTGGACAAAGCTTCAAGC 60.159 45.455 0.00 0.00 42.84 4.01
2148 2205 3.718815 ACGAAGGTGAAAGTTCAGAGTC 58.281 45.455 0.00 0.00 37.98 3.36
2197 2254 1.831106 AGTCACCATGAGTTATCCGCA 59.169 47.619 0.00 0.00 0.00 5.69
2293 2350 5.668471 AGATCGAGATTCTGCAAGATTTGA 58.332 37.500 0.00 0.00 46.36 2.69
2324 2381 3.052036 GGACACAAATGCACAACATGTC 58.948 45.455 0.00 10.10 39.60 3.06
2342 2399 2.240414 TGTCCAATGAGAGGTGATGCAT 59.760 45.455 0.00 0.00 0.00 3.96
2404 2461 1.609635 TAGCAGGGCATCGACGGAAA 61.610 55.000 0.00 0.00 0.00 3.13
2406 2463 1.582610 GCAGGGCATCGACGGAAAAA 61.583 55.000 0.00 0.00 0.00 1.94
2423 2480 0.037975 AAATTGCGGCAAGAAGGCAG 60.038 50.000 21.11 0.00 44.47 4.85
2524 2581 5.260900 CAACATGTATCTGCGATGAAACAG 58.739 41.667 0.00 0.00 35.15 3.16
2706 2763 8.780846 TTTTATTAATGAGTTCCTCAACGCTA 57.219 30.769 0.00 0.00 44.04 4.26
2707 2764 8.420374 TTTATTAATGAGTTCCTCAACGCTAG 57.580 34.615 0.00 0.00 44.04 3.42
2709 2766 0.895530 TGAGTTCCTCAACGCTAGGG 59.104 55.000 5.05 5.05 37.57 3.53
2860 2917 4.706608 TACCGCCGCCATGTTGCA 62.707 61.111 0.00 0.00 0.00 4.08
2940 2997 7.448161 ACATGTTCATTCTTTTGTCATGTAGGA 59.552 33.333 0.00 0.00 39.18 2.94
2953 3010 7.135591 TGTCATGTAGGATGAAATGGACATA 57.864 36.000 0.00 0.00 0.00 2.29
2984 3041 1.528129 GAGGCCAACTTGAAGGAGTG 58.472 55.000 5.01 0.00 0.00 3.51
3017 3074 4.741676 GCCTGCAATTAATACAATCAGTGC 59.258 41.667 0.00 0.00 0.00 4.40
3028 3085 3.091545 ACAATCAGTGCCGGATTCAAAT 58.908 40.909 5.05 0.00 32.86 2.32
3051 3108 3.487576 AAAAACGACAGCAGGACCA 57.512 47.368 0.00 0.00 0.00 4.02
3055 3112 2.031012 CGACAGCAGGACCAAGCA 59.969 61.111 11.02 0.00 0.00 3.91
3126 3183 5.695851 GCACATAGCCTATACTTGCAAAT 57.304 39.130 0.00 0.00 37.23 2.32
3140 3197 4.516698 ACTTGCAAATGTGAGTTAGACCTG 59.483 41.667 0.00 0.00 0.00 4.00
3285 3342 7.865385 TCAAATTGTTGCTATTTTACTCCACAC 59.135 33.333 0.00 0.00 34.50 3.82
3286 3343 5.351233 TTGTTGCTATTTTACTCCACACG 57.649 39.130 0.00 0.00 0.00 4.49
3288 3345 5.057819 TGTTGCTATTTTACTCCACACGAA 58.942 37.500 0.00 0.00 0.00 3.85
3289 3346 5.049954 TGTTGCTATTTTACTCCACACGAAC 60.050 40.000 0.00 0.00 0.00 3.95
3290 3347 4.890088 TGCTATTTTACTCCACACGAACT 58.110 39.130 0.00 0.00 0.00 3.01
3291 3348 6.028146 TGCTATTTTACTCCACACGAACTA 57.972 37.500 0.00 0.00 0.00 2.24
3292 3349 6.097356 TGCTATTTTACTCCACACGAACTAG 58.903 40.000 0.00 0.00 0.00 2.57
3293 3350 6.098017 GCTATTTTACTCCACACGAACTAGT 58.902 40.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.752472 CAGTTCTCAGCAATCTAATCATCGT 59.248 40.000 0.00 0.00 0.00 3.73
124 125 6.591834 GCTCTCTTGTGTATTTGTCTATGTGT 59.408 38.462 0.00 0.00 0.00 3.72
190 191 8.588290 AAAATGTCCCTATTATGCTGTAAACA 57.412 30.769 0.00 0.00 0.00 2.83
352 353 7.080099 TGTCTACACGAACTGTATAAGTGAAC 58.920 38.462 10.34 7.06 39.81 3.18
398 419 4.626287 GCTCTTCCCAGTTGTCCATATCAA 60.626 45.833 0.00 0.00 0.00 2.57
494 515 3.009695 ACCCCAACAAATAGTCCGAATGA 59.990 43.478 0.00 0.00 0.00 2.57
720 767 5.295787 TGCTTGGTCCGTGAATATTACATTC 59.704 40.000 0.00 0.00 0.00 2.67
735 782 1.318158 CCATGGCTCTTGCTTGGTCC 61.318 60.000 0.00 0.00 37.53 4.46
1024 1071 1.068333 CATCCTGGCACAAAACTTCCG 60.068 52.381 0.00 0.00 38.70 4.30
1032 1079 3.861341 GCTAGTCATCCTGGCACAA 57.139 52.632 0.00 0.00 46.29 3.33
1147 1194 0.034380 TCTTCCCGGTCTCTGTCGAT 60.034 55.000 0.00 0.00 0.00 3.59
1160 1207 5.357257 GTTTTTCTTGGAAACCTTCTTCCC 58.643 41.667 0.09 0.00 43.78 3.97
1188 1235 7.562135 TGAGTACTGAAACTTTTACCAGTCTT 58.438 34.615 0.00 0.00 40.07 3.01
1376 1423 5.106791 GCCAGCTGCATACATATAAGAACAG 60.107 44.000 8.66 0.00 40.77 3.16
1377 1424 4.756642 GCCAGCTGCATACATATAAGAACA 59.243 41.667 8.66 0.00 40.77 3.18
1528 1585 2.036604 TCGAATAGTCCGCATTGGCATA 59.963 45.455 0.00 0.00 41.24 3.14
1568 1625 5.527214 CGAAGATACCTTGATTATGTGGCAA 59.473 40.000 0.00 0.00 31.62 4.52
1627 1684 6.370166 GTCAATCTACCTTAGCAATCATAGGC 59.630 42.308 0.00 0.00 0.00 3.93
1778 1835 5.359194 TCAATAGGACCCATGTCTTTCTC 57.641 43.478 0.00 0.00 41.47 2.87
1838 1895 3.495100 CCAAGTCTAACCAGCTCAAGTGT 60.495 47.826 0.00 0.00 0.00 3.55
1852 1909 3.120321 ACATTTGTGTCGCCAAGTCTA 57.880 42.857 0.00 0.00 0.00 2.59
1978 2035 2.987413 TTGCATTTGACCTAGCAACG 57.013 45.000 0.00 0.00 41.55 4.10
2033 2090 3.587797 AAATTCTTGTGCATCAGCTGG 57.412 42.857 15.13 0.00 42.74 4.85
2148 2205 5.812127 TCAGGTGAGAATACATCGTTCATTG 59.188 40.000 0.00 0.00 0.00 2.82
2230 2287 0.952984 GCGCCTTCTCTCTTGCTGTT 60.953 55.000 0.00 0.00 0.00 3.16
2293 2350 0.112412 ATTTGTGTCCTTCGCCCCTT 59.888 50.000 0.00 0.00 0.00 3.95
2324 2381 1.871676 CGATGCATCACCTCTCATTGG 59.128 52.381 25.70 1.65 0.00 3.16
2404 2461 0.037975 CTGCCTTCTTGCCGCAATTT 60.038 50.000 6.19 0.00 30.85 1.82
2406 2463 1.604593 ACTGCCTTCTTGCCGCAAT 60.605 52.632 6.19 0.00 30.85 3.56
2423 2480 5.851177 CCATAACAATCTTGTCGTTGAACAC 59.149 40.000 0.00 0.00 41.31 3.32
2702 2759 6.551601 AGGTGGATAATAATATCTCCCTAGCG 59.448 42.308 6.89 0.00 37.09 4.26
2706 2763 7.517604 ACACAAGGTGGATAATAATATCTCCCT 59.482 37.037 1.07 1.54 38.81 4.20
2707 2764 7.690256 ACACAAGGTGGATAATAATATCTCCC 58.310 38.462 1.07 0.00 38.39 4.30
2940 2997 4.586001 GCCCATCAGTTATGTCCATTTCAT 59.414 41.667 0.00 0.00 33.34 2.57
3038 3095 2.031012 TGCTTGGTCCTGCTGTCG 59.969 61.111 8.49 0.00 0.00 4.35
3042 3099 2.281070 CACGTGCTTGGTCCTGCT 60.281 61.111 0.82 0.00 0.00 4.24
3051 3108 0.944311 AAAGACGATCGCACGTGCTT 60.944 50.000 35.27 23.78 46.52 3.91


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

AutoCloner maintained by Alex Coulton.