Multiple sequence alignment - TraesCS5B01G105500

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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 TraesCS5B01G105500 chr5B 100.000 3857 0 0 1 3857 141576005 141572149 0.000000e+00 7123
1 TraesCS5B01G105500 chr5B 98.259 632 10 1 311 941 125796090 125796721 0.000000e+00 1105
2 TraesCS5B01G105500 chr5B 98.446 193 3 0 1 193 125795671 125795863 1.330000e-89 340
3 TraesCS5B01G105500 chr5A 97.467 2921 54 6 939 3857 144708478 144705576 0.000000e+00 4966
4 TraesCS5B01G105500 chr5A 98.406 941 13 2 1 940 368097820 368096881 0.000000e+00 1653
5 TraesCS5B01G105500 chr5D 97.269 2929 58 8 937 3857 129478772 129475858 0.000000e+00 4946
6 TraesCS5B01G105500 chr1A 98.093 944 14 3 1 942 96444860 96445801 0.000000e+00 1640
7 TraesCS5B01G105500 chr1A 97.662 941 14 4 1 940 401681005 401680072 0.000000e+00 1609
8 TraesCS5B01G105500 chr1A 81.102 381 65 7 1463 1839 52237608 52237231 8.100000e-77 298
9 TraesCS5B01G105500 chr4A 96.089 946 28 3 1 939 63749498 63748555 0.000000e+00 1533
10 TraesCS5B01G105500 chr4A 97.971 690 11 2 252 940 492347809 492348496 0.000000e+00 1194
11 TraesCS5B01G105500 chr4A 86.123 699 78 10 252 943 519197409 519198095 0.000000e+00 736
12 TraesCS5B01G105500 chr4A 97.183 142 4 0 1 142 492347609 492347750 1.380000e-59 241
13 TraesCS5B01G105500 chr3B 97.234 687 12 3 262 941 426996405 426995719 0.000000e+00 1157
14 TraesCS5B01G105500 chr3B 98.446 193 3 0 1 193 426997250 426997058 1.330000e-89 340
15 TraesCS5B01G105500 chr2B 98.280 407 5 1 536 940 214003368 214003774 0.000000e+00 712
16 TraesCS5B01G105500 chr2B 97.494 399 5 2 1 395 214002571 214002968 0.000000e+00 676
17 TraesCS5B01G105500 chr4B 87.252 353 40 3 252 604 580379905 580380252 7.760000e-107 398
18 TraesCS5B01G105500 chr1B 81.117 376 65 6 1467 1839 83640134 83639762 2.910000e-76 296
19 TraesCS5B01G105500 chr1D 80.840 381 66 7 1463 1839 52576433 52576056 3.770000e-75 292


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 TraesCS5B01G105500 chr5B 141572149 141576005 3856 True 7123.0 7123 100.0000 1 3857 1 chr5B.!!$R1 3856
1 TraesCS5B01G105500 chr5B 125795671 125796721 1050 False 722.5 1105 98.3525 1 941 2 chr5B.!!$F1 940
2 TraesCS5B01G105500 chr5A 144705576 144708478 2902 True 4966.0 4966 97.4670 939 3857 1 chr5A.!!$R1 2918
3 TraesCS5B01G105500 chr5A 368096881 368097820 939 True 1653.0 1653 98.4060 1 940 1 chr5A.!!$R2 939
4 TraesCS5B01G105500 chr5D 129475858 129478772 2914 True 4946.0 4946 97.2690 937 3857 1 chr5D.!!$R1 2920
5 TraesCS5B01G105500 chr1A 96444860 96445801 941 False 1640.0 1640 98.0930 1 942 1 chr1A.!!$F1 941
6 TraesCS5B01G105500 chr1A 401680072 401681005 933 True 1609.0 1609 97.6620 1 940 1 chr1A.!!$R2 939
7 TraesCS5B01G105500 chr4A 63748555 63749498 943 True 1533.0 1533 96.0890 1 939 1 chr4A.!!$R1 938
8 TraesCS5B01G105500 chr4A 519197409 519198095 686 False 736.0 736 86.1230 252 943 1 chr4A.!!$F1 691
9 TraesCS5B01G105500 chr4A 492347609 492348496 887 False 717.5 1194 97.5770 1 940 2 chr4A.!!$F2 939
10 TraesCS5B01G105500 chr3B 426995719 426997250 1531 True 748.5 1157 97.8400 1 941 2 chr3B.!!$R1 940
11 TraesCS5B01G105500 chr2B 214002571 214003774 1203 False 694.0 712 97.8870 1 940 2 chr2B.!!$F1 939

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
829 1684 0.107703 CGGCTGGGCTGTTAAGATGA 60.108 55.0 0.0 0.0 0.00 2.92 F
966 1821 0.611896 CCCCGCTTTCCACCATTTCT 60.612 55.0 0.0 0.0 0.00 2.52 F
2752 3607 0.321564 CAGTGCCATCTTGGGTCGAA 60.322 55.0 0.0 0.0 38.19 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2556 3411 0.170561 ACCGGAGATCAAACGACGAG 59.829 55.0 9.46 0.00 0.00 4.18 R
2774 3629 1.030488 GTCCTCCTCACCGTCGATGA 61.030 60.0 6.11 0.00 0.00 2.92 R
3745 4606 2.916089 CTCATCGATAGCGCATCAGAAG 59.084 50.0 11.47 9.53 37.46 2.85 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
90 91 4.643387 GTCGTTGCCTGGCAGGGT 62.643 66.667 33.43 0.0 40.61 4.34
151 152 1.494721 TGAGCTTCCCCTTGTTCTTGT 59.505 47.619 0.00 0.0 0.00 3.16
829 1684 0.107703 CGGCTGGGCTGTTAAGATGA 60.108 55.000 0.00 0.0 0.00 2.92
837 1692 5.007034 TGGGCTGTTAAGATGAATTTTCGA 58.993 37.500 0.00 0.0 0.00 3.71
966 1821 0.611896 CCCCGCTTTCCACCATTTCT 60.612 55.000 0.00 0.0 0.00 2.52
1350 2205 4.083862 GTTTCCCGCCTCCTCGCT 62.084 66.667 0.00 0.0 0.00 4.93
2181 3036 1.197721 CTTGTGCCGTCAAATCTGGAC 59.802 52.381 0.00 0.0 0.00 4.02
2343 3198 1.915266 CACCCCAGAGCCTGTCTCA 60.915 63.158 2.18 0.0 44.35 3.27
2433 3288 1.220477 GAGCTCAAGAGACCTGGGC 59.780 63.158 9.40 0.0 0.00 5.36
2559 3414 2.202492 CGTCTCAAGCGGTCCTCG 60.202 66.667 0.00 0.0 42.76 4.63
2752 3607 0.321564 CAGTGCCATCTTGGGTCGAA 60.322 55.000 0.00 0.0 38.19 3.71
2817 3672 1.375908 CACTGGTGTCATCGGTGGG 60.376 63.158 16.22 0.0 37.73 4.61
2857 3712 5.009110 CAGCTCGATGAGATGGTAGTTTAGA 59.991 44.000 4.22 0.0 41.66 2.10
2892 3747 5.012458 ACACAGATGAATCAAGAGAGGTGAA 59.988 40.000 0.00 0.0 0.00 3.18
2894 3749 6.598457 CACAGATGAATCAAGAGAGGTGAAAT 59.402 38.462 0.00 0.0 0.00 2.17
3024 3879 4.597507 TGGTGTAGAAGGTGAGGAGATTTT 59.402 41.667 0.00 0.0 0.00 1.82
3027 3882 6.819146 GGTGTAGAAGGTGAGGAGATTTTTAG 59.181 42.308 0.00 0.0 0.00 1.85
3084 3939 3.067320 GGAAATGGAGCCTAATCAACTGC 59.933 47.826 0.00 0.0 0.00 4.40
3091 3946 4.158394 GGAGCCTAATCAACTGCATCAAAA 59.842 41.667 0.00 0.0 0.00 2.44
3267 4122 2.693074 GGTTGTGTTGTGAACCAAGGAT 59.307 45.455 0.00 0.0 41.24 3.24
3289 4145 6.613679 GGATTAGGAGGGGAGAAGGATATTAG 59.386 46.154 0.00 0.0 0.00 1.73
3290 4146 6.562845 TTAGGAGGGGAGAAGGATATTAGT 57.437 41.667 0.00 0.0 0.00 2.24
3291 4147 7.674327 TTAGGAGGGGAGAAGGATATTAGTA 57.326 40.000 0.00 0.0 0.00 1.82
3292 4148 6.761424 AGGAGGGGAGAAGGATATTAGTAT 57.239 41.667 0.00 0.0 0.00 2.12
3293 4149 7.134857 AGGAGGGGAGAAGGATATTAGTATT 57.865 40.000 0.00 0.0 0.00 1.89
3294 4150 8.258641 AGGAGGGGAGAAGGATATTAGTATTA 57.741 38.462 0.00 0.0 0.00 0.98
3347 4203 9.236691 CTCATGGTTGTTGTAATAACATATTGC 57.763 33.333 6.58 0.0 34.97 3.56
3485 4341 6.647212 TGAACTGTCTAAATGCAGATTACG 57.353 37.500 0.00 0.0 36.62 3.18
3618 4479 0.613572 GGGCGGGGAAAAAGAATCCA 60.614 55.000 0.00 0.0 38.80 3.41
3745 4606 2.022129 CGACCACTGCGAGGTTCAC 61.022 63.158 0.00 0.0 40.09 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
258 259 5.086727 GTCCTTTTTAAATCTAGCGTGTGC 58.913 41.667 0.00 0.00 43.24 4.57
677 1521 3.202373 GCCCTAAAAACTACTCCCTCCAT 59.798 47.826 0.00 0.00 0.00 3.41
678 1522 2.574824 GCCCTAAAAACTACTCCCTCCA 59.425 50.000 0.00 0.00 0.00 3.86
829 1684 2.876079 GCCTCACTCCTGGTCGAAAATT 60.876 50.000 0.00 0.00 0.00 1.82
837 1692 1.920835 GAAGGGCCTCACTCCTGGT 60.921 63.158 6.46 0.00 32.95 4.00
966 1821 1.135489 CGATCGGAGAAGGTGTTCGAA 60.135 52.381 7.38 0.00 43.58 3.71
1419 2274 0.472471 TCTTGAGGGGCAACGAGTTT 59.528 50.000 0.00 0.00 37.60 2.66
1643 2498 0.736325 CACGCAGCTGTAGTGGTACC 60.736 60.000 26.29 4.43 32.68 3.34
2181 3036 1.801913 CTCCGCCGAGAACAGTTCG 60.802 63.158 7.68 0.00 38.52 3.95
2514 3369 4.243008 TCGTTGTCAGCGCCCCAA 62.243 61.111 2.29 1.11 0.00 4.12
2520 3375 2.016704 AAGCTCGTCGTTGTCAGCG 61.017 57.895 2.22 2.22 36.95 5.18
2523 3378 1.954146 GCCAAGCTCGTCGTTGTCA 60.954 57.895 0.00 0.00 0.00 3.58
2556 3411 0.170561 ACCGGAGATCAAACGACGAG 59.829 55.000 9.46 0.00 0.00 4.18
2559 3414 1.630148 CAGACCGGAGATCAAACGAC 58.370 55.000 9.46 0.00 0.00 4.34
2752 3607 2.029073 CTCACGGTGGTTCGCTGT 59.971 61.111 8.50 0.00 33.37 4.40
2774 3629 1.030488 GTCCTCCTCACCGTCGATGA 61.030 60.000 6.11 0.00 0.00 2.92
2775 3630 1.433879 GTCCTCCTCACCGTCGATG 59.566 63.158 0.00 0.00 0.00 3.84
2776 3631 2.113433 CGTCCTCCTCACCGTCGAT 61.113 63.158 0.00 0.00 0.00 3.59
2857 3712 5.126869 TGATTCATCTGTGTGTTTGGTTGTT 59.873 36.000 0.00 0.00 0.00 2.83
3024 3879 1.094785 GGCCAAGCTCGAAATGCTAA 58.905 50.000 0.00 0.00 40.22 3.09
3027 3882 1.153958 GTGGCCAAGCTCGAAATGC 60.154 57.895 7.24 0.00 0.00 3.56
3084 3939 3.465122 GCAAAGCTGGCAATTTTGATG 57.535 42.857 20.95 3.39 34.55 3.07
3139 3994 1.420430 TCAACGAGAAAGGGGACACT 58.580 50.000 0.00 0.00 0.00 3.55
3143 3998 5.693769 ATAAAGATCAACGAGAAAGGGGA 57.306 39.130 0.00 0.00 0.00 4.81
3207 4062 8.585881 GGCAACAGATAAGATAGTACCATAAGA 58.414 37.037 0.00 0.00 0.00 2.10
3208 4063 7.819900 GGGCAACAGATAAGATAGTACCATAAG 59.180 40.741 0.00 0.00 39.74 1.73
3209 4064 7.256547 GGGGCAACAGATAAGATAGTACCATAA 60.257 40.741 0.00 0.00 39.74 1.90
3210 4065 6.212791 GGGGCAACAGATAAGATAGTACCATA 59.787 42.308 0.00 0.00 39.74 2.74
3211 4066 5.013183 GGGGCAACAGATAAGATAGTACCAT 59.987 44.000 0.00 0.00 39.74 3.55
3267 4122 6.562845 ACTAATATCCTTCTCCCCTCCTAA 57.437 41.667 0.00 0.00 0.00 2.69
3289 4145 8.190122 TCATGGAGCAACAATTTGATGTAATAC 58.810 33.333 2.79 0.00 34.24 1.89
3290 4146 8.190122 GTCATGGAGCAACAATTTGATGTAATA 58.810 33.333 2.79 0.00 34.24 0.98
3291 4147 7.037438 GTCATGGAGCAACAATTTGATGTAAT 58.963 34.615 2.79 0.00 34.24 1.89
3292 4148 6.209192 AGTCATGGAGCAACAATTTGATGTAA 59.791 34.615 2.79 0.00 34.24 2.41
3293 4149 5.711506 AGTCATGGAGCAACAATTTGATGTA 59.288 36.000 2.79 0.00 34.24 2.29
3294 4150 4.525487 AGTCATGGAGCAACAATTTGATGT 59.475 37.500 2.79 0.00 34.24 3.06
3347 4203 6.427853 TGGTTCATGAATCTCAAGTACAACAG 59.572 38.462 19.21 0.00 0.00 3.16
3485 4341 6.603237 TGTAATGCTGTGTGATGCTATAAC 57.397 37.500 0.00 0.00 0.00 1.89
3592 4453 3.572222 TTTCCCCGCCCGGAAAGT 61.572 61.111 0.73 0.00 45.05 2.66
3618 4479 3.661648 AATGCCCCTGCCGACCTT 61.662 61.111 0.00 0.00 36.33 3.50
3745 4606 2.916089 CTCATCGATAGCGCATCAGAAG 59.084 50.000 11.47 9.53 37.46 2.85


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

AutoCloner maintained by Alex Coulton.