Multiple sequence alignment - TraesCS2D01G530700

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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 TraesCS2D01G530700 chr2D 100.000 4143 0 0 1 4143 617074840 617070698 0.000000e+00 7651.0
1 TraesCS2D01G530700 chr2A 95.837 4156 127 19 1 4143 747145727 747141605 0.000000e+00 6674.0
2 TraesCS2D01G530700 chr2A 88.439 839 79 11 1 827 746978707 746977875 0.000000e+00 996.0
3 TraesCS2D01G530700 chr2A 85.817 557 69 3 942 1491 746977660 746977107 2.150000e-162 582.0
4 TraesCS2D01G530700 chr2A 91.111 135 8 4 44 176 746980190 746980322 3.290000e-41 180.0
5 TraesCS2D01G530700 chr2A 100.000 30 0 0 3288 3317 746974798 746974769 5.790000e-04 56.5
6 TraesCS2D01G530700 chr2B 92.864 3363 181 26 3 3325 752831855 752828512 0.000000e+00 4826.0
7 TraesCS2D01G530700 chr3B 84.718 2251 296 34 965 3193 671747470 671745246 0.000000e+00 2207.0
8 TraesCS2D01G530700 chr3B 81.897 232 38 3 1104 1333 13965227 13965456 4.230000e-45 193.0
9 TraesCS2D01G530700 chr3B 76.154 260 44 9 2834 3076 28337273 28337531 2.020000e-23 121.0
10 TraesCS2D01G530700 chr5A 82.163 2293 331 47 960 3217 584507059 584509308 0.000000e+00 1897.0
11 TraesCS2D01G530700 chr5A 80.488 820 106 22 1 775 584490944 584491754 2.780000e-161 579.0
12 TraesCS2D01G530700 chr5B 87.624 1212 147 2 2009 3217 570935943 570937154 0.000000e+00 1404.0
13 TraesCS2D01G530700 chr5B 87.500 1152 132 7 2009 3158 571174101 571175242 0.000000e+00 1319.0
14 TraesCS2D01G530700 chr5B 81.078 835 111 24 1 796 570933639 570934465 1.260000e-174 623.0
15 TraesCS2D01G530700 chr5B 75.361 1039 190 37 960 1967 570934758 570935761 1.370000e-119 440.0
16 TraesCS2D01G530700 chr5B 81.282 577 76 18 291 837 571122031 571122605 4.920000e-119 438.0
17 TraesCS2D01G530700 chr5D 88.225 1155 132 2 2009 3159 464078504 464079658 0.000000e+00 1376.0
18 TraesCS2D01G530700 chr5D 82.023 1107 185 8 2048 3141 544697176 544696071 0.000000e+00 929.0
19 TraesCS2D01G530700 chr5D 81.818 770 93 27 113 837 464076394 464077161 1.650000e-168 603.0
20 TraesCS2D01G530700 chr5D 76.600 1000 182 27 990 1965 464077349 464078320 1.720000e-138 503.0
21 TraesCS2D01G530700 chr1A 82.204 1107 183 8 2048 3141 569451281 569452386 0.000000e+00 941.0


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 TraesCS2D01G530700 chr2D 617070698 617074840 4142 True 7651.000000 7651 100.000000 1 4143 1 chr2D.!!$R1 4142
1 TraesCS2D01G530700 chr2A 747141605 747145727 4122 True 6674.000000 6674 95.837000 1 4143 1 chr2A.!!$R1 4142
2 TraesCS2D01G530700 chr2A 746974769 746978707 3938 True 544.833333 996 91.418667 1 3317 3 chr2A.!!$R2 3316
3 TraesCS2D01G530700 chr2B 752828512 752831855 3343 True 4826.000000 4826 92.864000 3 3325 1 chr2B.!!$R1 3322
4 TraesCS2D01G530700 chr3B 671745246 671747470 2224 True 2207.000000 2207 84.718000 965 3193 1 chr3B.!!$R1 2228
5 TraesCS2D01G530700 chr5A 584507059 584509308 2249 False 1897.000000 1897 82.163000 960 3217 1 chr5A.!!$F2 2257
6 TraesCS2D01G530700 chr5A 584490944 584491754 810 False 579.000000 579 80.488000 1 775 1 chr5A.!!$F1 774
7 TraesCS2D01G530700 chr5B 571174101 571175242 1141 False 1319.000000 1319 87.500000 2009 3158 1 chr5B.!!$F2 1149
8 TraesCS2D01G530700 chr5B 570933639 570937154 3515 False 822.333333 1404 81.354333 1 3217 3 chr5B.!!$F3 3216
9 TraesCS2D01G530700 chr5B 571122031 571122605 574 False 438.000000 438 81.282000 291 837 1 chr5B.!!$F1 546
10 TraesCS2D01G530700 chr5D 544696071 544697176 1105 True 929.000000 929 82.023000 2048 3141 1 chr5D.!!$R1 1093
11 TraesCS2D01G530700 chr5D 464076394 464079658 3264 False 827.333333 1376 82.214333 113 3159 3 chr5D.!!$F1 3046
12 TraesCS2D01G530700 chr1A 569451281 569452386 1105 False 941.000000 941 82.204000 2048 3141 1 chr1A.!!$F1 1093

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
38 39 0.179000 CTGAGTAATCCCGCTTGGCT 59.821 55.0 0.00 0.00 0.00 4.75 F
157 158 0.249826 TCTGAATCACTGTGCACGCA 60.250 50.0 13.13 0.00 0.00 5.24 F
1017 1312 0.680921 CGATGCCTCCATGGTGGTTT 60.681 55.0 29.03 18.82 39.03 3.27 F
1206 1513 0.898320 AGCTGACTTGCACCGATAGT 59.102 50.0 0.00 0.00 34.99 2.12 F
2332 3324 0.947244 GTAAATCCAGCTGCGATGGG 59.053 55.0 8.66 0.00 38.44 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1017 1312 0.320683 CGACCATGAAGTGCACCAGA 60.321 55.000 14.63 0.0 0.00 3.86 R
2038 2676 6.071672 ACCTGCATAGTACTGCACATATAGAG 60.072 42.308 5.39 0.0 46.76 2.43 R
2332 3324 2.869192 GACCTCGCTGATGAAATCTTCC 59.131 50.000 0.00 0.0 45.81 3.46 R
2507 3499 3.733443 GCCCAAGGCGATTTCATTAAT 57.267 42.857 0.00 0.0 39.62 1.40 R
3694 4781 2.103771 AGCTCACTGATCCATTATGCGT 59.896 45.455 0.00 0.0 0.00 5.24 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
38 39 0.179000 CTGAGTAATCCCGCTTGGCT 59.821 55.000 0.00 0.00 0.00 4.75
111 112 2.072487 AGTGGTGGCCAGTGTCAGT 61.072 57.895 5.11 2.49 35.61 3.41
147 148 7.651304 ACTTGTCGATATGAGATTCTGAATCAC 59.349 37.037 27.06 22.23 40.42 3.06
157 158 0.249826 TCTGAATCACTGTGCACGCA 60.250 50.000 13.13 0.00 0.00 5.24
307 330 4.248058 CGCAGGATGATGATGTATTGCTA 58.752 43.478 0.00 0.00 39.69 3.49
408 437 1.078214 CATCCCAAGCTGCCGAAGA 60.078 57.895 0.00 0.00 0.00 2.87
627 675 4.760204 ACCTCCTGTATGTTGTTTTGTAGC 59.240 41.667 0.00 0.00 0.00 3.58
981 1268 4.500375 GCAACAAAGCCAGAACAAGAGATT 60.500 41.667 0.00 0.00 0.00 2.40
1017 1312 0.680921 CGATGCCTCCATGGTGGTTT 60.681 55.000 29.03 18.82 39.03 3.27
1206 1513 0.898320 AGCTGACTTGCACCGATAGT 59.102 50.000 0.00 0.00 34.99 2.12
1723 2174 8.215132 GCTTTGTGTGAGTTTATATCTATACGC 58.785 37.037 0.00 0.00 0.00 4.42
1978 2456 4.155310 TGCTGGTACGTCGATACATATG 57.845 45.455 0.00 0.00 0.00 1.78
1986 2464 3.752222 ACGTCGATACATATGGAGGACTC 59.248 47.826 15.97 0.00 32.84 3.36
2038 2676 4.291540 TGGCGATCTCATGTAAAATTGC 57.708 40.909 0.00 0.00 0.00 3.56
2332 3324 0.947244 GTAAATCCAGCTGCGATGGG 59.053 55.000 8.66 0.00 38.44 4.00
2483 3475 3.380637 GGACAAGTACATCTTCTCGGCTA 59.619 47.826 0.00 0.00 33.63 3.93
2507 3499 1.978580 GGAGTTTCTCCTGGGACAAGA 59.021 52.381 8.38 0.00 46.41 3.02
3320 4403 3.913799 TCATTTGACCTCCAACCTTAGGA 59.086 43.478 4.77 0.00 36.66 2.94
3331 4414 4.625607 CAACCTTAGGAGGATGGTATCC 57.374 50.000 4.77 0.00 46.74 2.59
3341 4424 3.297134 GGATGGTATCCTTTGCCAGAA 57.703 47.619 0.61 0.00 43.96 3.02
3342 4425 3.631250 GGATGGTATCCTTTGCCAGAAA 58.369 45.455 0.61 0.00 43.96 2.52
3343 4426 4.023291 GGATGGTATCCTTTGCCAGAAAA 58.977 43.478 0.61 0.00 43.96 2.29
3344 4427 4.098501 GGATGGTATCCTTTGCCAGAAAAG 59.901 45.833 0.61 0.00 43.96 2.27
3345 4428 4.112634 TGGTATCCTTTGCCAGAAAAGT 57.887 40.909 0.00 0.00 34.82 2.66
3361 4444 7.522073 GCCAGAAAAGTTGTGAGATGTTATGAA 60.522 37.037 0.00 0.00 0.00 2.57
3362 4445 8.352201 CCAGAAAAGTTGTGAGATGTTATGAAA 58.648 33.333 0.00 0.00 0.00 2.69
3363 4446 9.734620 CAGAAAAGTTGTGAGATGTTATGAAAA 57.265 29.630 0.00 0.00 0.00 2.29
3464 4548 4.448210 GCCTGATGATGCCAAATGAAAAT 58.552 39.130 0.00 0.00 0.00 1.82
3488 4574 3.893326 TCTGATGATGTCGACCACATT 57.107 42.857 20.02 8.83 46.53 2.71
3694 4781 0.660488 ACACGAGCGACATTTGCAAA 59.340 45.000 15.44 15.44 33.85 3.68
3860 4947 3.127425 AGAGGAGTGCAACCTGTTTAC 57.873 47.619 16.86 4.13 37.80 2.01
3862 4949 3.073062 AGAGGAGTGCAACCTGTTTACAT 59.927 43.478 16.86 0.00 37.80 2.29
3876 4963 5.514136 CCTGTTTACATACCTCCTGTTTGGA 60.514 44.000 0.00 0.00 43.86 3.53
3900 4987 6.914259 AGCTTAAATGTTGCTCCTAAAACTC 58.086 36.000 0.00 0.00 30.41 3.01
3904 4991 9.399403 CTTAAATGTTGCTCCTAAAACTCTTTC 57.601 33.333 0.00 0.00 0.00 2.62
3927 5014 5.471797 TCGAATGTTGAATGTTGCTCCTAAA 59.528 36.000 0.00 0.00 0.00 1.85
4035 5122 5.591877 AGTTTGTGTTTTCTGCTCTCAAGAT 59.408 36.000 0.00 0.00 0.00 2.40
4085 5172 6.827727 AGTGTGTTGTCTCTAGTTATTTGGT 58.172 36.000 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 0.250901 GGCTGCTCAAGGGAGTTCAA 60.251 55.000 0.00 0.00 43.37 2.69
111 112 0.677288 ATCGACAAGTTCACCACCGA 59.323 50.000 0.00 0.00 0.00 4.69
147 148 1.630244 GCTTACCTCTGCGTGCACAG 61.630 60.000 18.64 7.88 39.12 3.66
157 158 0.617820 ACATCACCCCGCTTACCTCT 60.618 55.000 0.00 0.00 0.00 3.69
307 330 0.909610 TCCCACTCCGGCTTGATTCT 60.910 55.000 0.00 0.00 0.00 2.40
428 457 2.360475 GGTCTGCCTTGTCAGCCC 60.360 66.667 0.00 0.00 34.19 5.19
490 519 4.299978 GCTTACCTTCATCCATCTCGTAC 58.700 47.826 0.00 0.00 0.00 3.67
627 675 1.995484 CTACAACGATGCAGTCACCTG 59.005 52.381 0.00 0.00 41.91 4.00
1017 1312 0.320683 CGACCATGAAGTGCACCAGA 60.321 55.000 14.63 0.00 0.00 3.86
1206 1513 7.066163 CCTGTGTTGATCTGAATTGTAGCATTA 59.934 37.037 0.00 0.00 0.00 1.90
1723 2174 8.081633 TGTATGTATTTTCCAAAACAGAAGCAG 58.918 33.333 0.00 0.00 0.00 4.24
1978 2456 6.658188 AGCTTGTATATGTAAGAGTCCTCC 57.342 41.667 5.31 0.00 0.00 4.30
2038 2676 6.071672 ACCTGCATAGTACTGCACATATAGAG 60.072 42.308 5.39 0.00 46.76 2.43
2332 3324 2.869192 GACCTCGCTGATGAAATCTTCC 59.131 50.000 0.00 0.00 45.81 3.46
2507 3499 3.733443 GCCCAAGGCGATTTCATTAAT 57.267 42.857 0.00 0.00 39.62 1.40
2815 3815 4.109675 CCCGGGTCGGCATTCCTT 62.110 66.667 14.18 0.00 46.86 3.36
3322 4405 4.706962 ACTTTTCTGGCAAAGGATACCATC 59.293 41.667 2.76 0.00 37.98 3.51
3323 4406 4.677182 ACTTTTCTGGCAAAGGATACCAT 58.323 39.130 2.76 0.00 37.98 3.55
3324 4407 4.112634 ACTTTTCTGGCAAAGGATACCA 57.887 40.909 2.76 0.00 37.98 3.25
3325 4408 4.280929 ACAACTTTTCTGGCAAAGGATACC 59.719 41.667 2.76 0.00 37.98 2.73
3326 4409 5.009610 TCACAACTTTTCTGGCAAAGGATAC 59.990 40.000 2.76 0.00 37.98 2.24
3327 4410 5.136828 TCACAACTTTTCTGGCAAAGGATA 58.863 37.500 2.76 0.00 37.98 2.59
3328 4411 3.960102 TCACAACTTTTCTGGCAAAGGAT 59.040 39.130 2.76 0.00 37.98 3.24
3329 4412 3.360867 TCACAACTTTTCTGGCAAAGGA 58.639 40.909 2.76 0.00 37.98 3.36
3330 4413 3.381272 TCTCACAACTTTTCTGGCAAAGG 59.619 43.478 2.76 0.00 37.98 3.11
3331 4414 4.637483 TCTCACAACTTTTCTGGCAAAG 57.363 40.909 0.00 0.00 39.35 2.77
3332 4415 4.402155 ACATCTCACAACTTTTCTGGCAAA 59.598 37.500 0.00 0.00 0.00 3.68
3333 4416 3.953612 ACATCTCACAACTTTTCTGGCAA 59.046 39.130 0.00 0.00 0.00 4.52
3334 4417 3.554934 ACATCTCACAACTTTTCTGGCA 58.445 40.909 0.00 0.00 0.00 4.92
3335 4418 4.574599 AACATCTCACAACTTTTCTGGC 57.425 40.909 0.00 0.00 0.00 4.85
3336 4419 7.439157 TCATAACATCTCACAACTTTTCTGG 57.561 36.000 0.00 0.00 0.00 3.86
3337 4420 9.734620 TTTTCATAACATCTCACAACTTTTCTG 57.265 29.630 0.00 0.00 0.00 3.02
3442 4526 3.530265 TTTCATTTGGCATCATCAGGC 57.470 42.857 0.00 0.00 0.00 4.85
3445 4529 9.320352 CAGATTTATTTTCATTTGGCATCATCA 57.680 29.630 0.00 0.00 0.00 3.07
3451 4535 9.320352 CATCATCAGATTTATTTTCATTTGGCA 57.680 29.630 0.00 0.00 30.20 4.92
3464 4548 5.337578 TGTGGTCGACATCATCAGATTTA 57.662 39.130 18.91 0.00 30.20 1.40
3488 4574 8.750515 TTCATAATGTGCCATGAAGAAAGATA 57.249 30.769 0.00 0.00 36.49 1.98
3516 4602 5.278463 CCCATGGAGAGTGTAAGTTGTTTTG 60.278 44.000 15.22 0.00 0.00 2.44
3694 4781 2.103771 AGCTCACTGATCCATTATGCGT 59.896 45.455 0.00 0.00 0.00 5.24
3876 4963 6.717084 AGAGTTTTAGGAGCAACATTTAAGCT 59.283 34.615 0.00 0.00 42.17 3.74
3900 4987 4.618489 GGAGCAACATTCAACATTCGAAAG 59.382 41.667 0.00 0.00 0.00 2.62
3904 4991 3.837213 AGGAGCAACATTCAACATTCG 57.163 42.857 0.00 0.00 0.00 3.34
3927 5014 2.249139 AGCCAGAGAAAGGTACGAGTT 58.751 47.619 0.00 0.00 0.00 3.01
4035 5122 9.993454 TCAAACATCAAATGGTTTATCATTTCA 57.007 25.926 0.00 0.00 43.16 2.69


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

AutoCloner maintained by Alex Coulton.