Multiple sequence alignment - TraesCS5B01G450500

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 TraesCS5B01G450500 chr5B 100.000 3933 0 0 1 3933 622396488 622400420 0 7263
1 TraesCS5B01G450500 chr5B 90.881 987 83 7 2949 3933 388558407 388557426 0 1317
2 TraesCS5B01G450500 chr5D 96.660 2964 79 10 1 2954 500866204 500869157 0 4907
3 TraesCS5B01G450500 chr5A 97.072 1810 48 4 1148 2954 624735469 624733662 0 3044
4 TraesCS5B01G450500 chr5A 93.402 1167 62 9 1 1162 624736646 624735490 0 1714
5 TraesCS5B01G450500 chr4B 92.675 983 67 5 2949 3930 173161363 173162341 0 1411
6 TraesCS5B01G450500 chr4D 92.510 988 64 7 2949 3933 111463831 111462851 0 1406
7 TraesCS5B01G450500 chr4D 92.347 980 67 8 2949 3926 98114713 98115686 0 1387
8 TraesCS5B01G450500 chr1B 91.988 986 75 4 2949 3933 288628336 288627354 0 1380
9 TraesCS5B01G450500 chr7D 91.988 986 71 8 2949 3933 204483445 204484423 0 1376
10 TraesCS5B01G450500 chr6B 91.810 989 68 10 2949 3932 394638819 394639799 0 1365
11 TraesCS5B01G450500 chr7B 91.224 980 77 9 2949 3924 526103111 526104085 0 1325
12 TraesCS5B01G450500 chr1D 90.616 991 79 12 2949 3930 406987411 406986426 0 1303


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 TraesCS5B01G450500 chr5B 622396488 622400420 3932 False 7263 7263 100.000 1 3933 1 chr5B.!!$F1 3932
1 TraesCS5B01G450500 chr5B 388557426 388558407 981 True 1317 1317 90.881 2949 3933 1 chr5B.!!$R1 984
2 TraesCS5B01G450500 chr5D 500866204 500869157 2953 False 4907 4907 96.660 1 2954 1 chr5D.!!$F1 2953
3 TraesCS5B01G450500 chr5A 624733662 624736646 2984 True 2379 3044 95.237 1 2954 2 chr5A.!!$R1 2953
4 TraesCS5B01G450500 chr4B 173161363 173162341 978 False 1411 1411 92.675 2949 3930 1 chr4B.!!$F1 981
5 TraesCS5B01G450500 chr4D 111462851 111463831 980 True 1406 1406 92.510 2949 3933 1 chr4D.!!$R1 984
6 TraesCS5B01G450500 chr4D 98114713 98115686 973 False 1387 1387 92.347 2949 3926 1 chr4D.!!$F1 977
7 TraesCS5B01G450500 chr1B 288627354 288628336 982 True 1380 1380 91.988 2949 3933 1 chr1B.!!$R1 984
8 TraesCS5B01G450500 chr7D 204483445 204484423 978 False 1376 1376 91.988 2949 3933 1 chr7D.!!$F1 984
9 TraesCS5B01G450500 chr6B 394638819 394639799 980 False 1365 1365 91.810 2949 3932 1 chr6B.!!$F1 983
10 TraesCS5B01G450500 chr7B 526103111 526104085 974 False 1325 1325 91.224 2949 3924 1 chr7B.!!$F1 975
11 TraesCS5B01G450500 chr1D 406986426 406987411 985 True 1303 1303 90.616 2949 3930 1 chr1D.!!$R1 981

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
947 961 1.303898 TCCCTGATAAATGGCCACCA 58.696 50.0 8.16 0.0 38.19 4.17 F
2225 2279 0.108992 TCACGAGTTGGACGGTATGC 60.109 55.0 0.00 0.0 34.93 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2251 2307 2.254546 TTGTGTGCTACAGTTGAGGG 57.745 50.0 0.00 0.00 41.10 4.30 R
3414 3473 0.251121 CTGTGGGTTATGGCCACACA 60.251 55.0 21.08 21.08 39.17 3.72 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
36 37 8.893563 AATATTGAAAAACTAATGGGGACTCA 57.106 30.769 0.00 0.00 0.00 3.41
48 49 8.696374 ACTAATGGGGACTCATATATATTCGTG 58.304 37.037 0.00 0.00 0.00 4.35
184 185 2.364002 TGACAAAGCTTTGGCCTTTACC 59.636 45.455 36.11 17.15 45.65 2.85
202 203 7.817478 GCCTTTACCAAATAGTTTGCTTAATGT 59.183 33.333 0.00 0.00 39.31 2.71
238 242 9.685276 TTCTTCATTTACACATTGTCCATATCT 57.315 29.630 0.00 0.00 0.00 1.98
384 388 5.228945 ACTCATCCCTTGTAAATATCCGG 57.771 43.478 0.00 0.00 0.00 5.14
395 399 6.182507 TGTAAATATCCGGTCTTGGCTAAT 57.817 37.500 0.00 0.00 0.00 1.73
477 488 4.576053 TGCACCTTGTCATATGTATTCAGC 59.424 41.667 1.90 1.79 0.00 4.26
565 576 5.456548 TGTGAAGATTTGTGATGCACATT 57.543 34.783 0.62 0.00 44.16 2.71
616 627 3.328505 TGCAGATATACATGCATGGACG 58.671 45.455 29.41 10.18 46.97 4.79
693 704 8.877779 ACGTTCTTTCATATCTTCTGAAATGAG 58.122 33.333 4.11 0.00 40.69 2.90
739 750 7.162761 TCGTCCTTTTCATTTACATTAGACCA 58.837 34.615 0.00 0.00 0.00 4.02
771 782 5.414454 CCTTTGTTGTTATTTGATCTCCGGA 59.586 40.000 2.93 2.93 0.00 5.14
785 796 7.904558 TGATCTCCGGATAATATAGCAAGAT 57.095 36.000 3.57 0.00 31.46 2.40
897 911 9.614792 AAAGATGTGAAGATATAAGTTGTACCC 57.385 33.333 0.00 0.00 0.00 3.69
917 931 4.764823 ACCCACTTTATTTGCGAGATTTGA 59.235 37.500 0.00 0.00 0.00 2.69
947 961 1.303898 TCCCTGATAAATGGCCACCA 58.696 50.000 8.16 0.00 38.19 4.17
1043 1057 9.347240 AGGATTACATATTCTTGCCATATATGC 57.653 33.333 7.24 3.97 36.27 3.14
1051 1065 5.422666 TCTTGCCATATATGCTGTTTTCG 57.577 39.130 7.24 0.00 0.00 3.46
1103 1117 4.799255 GCATCCAACCAACCAAAAGGTAAG 60.799 45.833 0.00 0.00 37.07 2.34
1162 1211 2.191128 CCAAGGGGTGATATAGCAGC 57.809 55.000 11.65 11.65 35.63 5.25
1285 1335 3.628008 TCTCATAGCGAAGGTGTAGGAA 58.372 45.455 0.00 0.00 40.22 3.36
1304 1354 6.893020 AGGAATTTGGAGTATAGGAGTTGT 57.107 37.500 0.00 0.00 0.00 3.32
1587 1637 9.988815 ACCTTTAAAATGTATATTTTGTGCACA 57.011 25.926 17.42 17.42 44.12 4.57
1777 1831 3.924686 GCACATGCTTCTCCATCAAAAAG 59.075 43.478 0.00 0.00 38.21 2.27
1893 1947 2.221055 CCTTCTACAGTTTGCGACACAC 59.779 50.000 0.00 0.00 0.00 3.82
2150 2204 8.786898 GCCATTTATAATGCTCTTAATGACTCA 58.213 33.333 0.00 0.00 0.00 3.41
2225 2279 0.108992 TCACGAGTTGGACGGTATGC 60.109 55.000 0.00 0.00 34.93 3.14
2251 2307 5.470098 TCTGCCTTTTCACTCAAACTATGTC 59.530 40.000 0.00 0.00 0.00 3.06
2705 2761 4.321601 CGACCCAAATTTCAATTGGTAGCA 60.322 41.667 5.42 0.00 44.77 3.49
2761 2817 1.668826 TGGGTAGTGGATTCTTGCCT 58.331 50.000 0.00 0.00 0.00 4.75
2786 2842 7.628769 TCTGATAAAGCTGCATTAATCACAA 57.371 32.000 1.02 0.00 0.00 3.33
2966 3022 7.841222 AGATTTTACTCATAAATTCCTTGCCCT 59.159 33.333 0.00 0.00 33.78 5.19
2999 3055 5.106876 TGGTTTAATACTTGGAGCCCTAC 57.893 43.478 0.00 0.00 0.00 3.18
3071 3127 2.562738 CACCTTTCCTTTCCATTGGTCC 59.437 50.000 1.86 0.00 0.00 4.46
3088 3144 8.840321 CCATTGGTCCGATTATCATAATAATCC 58.160 37.037 3.42 0.00 45.90 3.01
3117 3173 6.042638 TCCTTTCCATTGTTTTGTTTCACA 57.957 33.333 0.00 0.00 0.00 3.58
3148 3204 4.734398 ATCTAACTTGTCTGAGCAGAGG 57.266 45.455 0.00 0.00 38.27 3.69
3163 3219 3.471680 GCAGAGGTAAATCCCTGCTTAG 58.528 50.000 15.01 0.00 46.81 2.18
3186 3242 0.756903 AGCACCTCGGTGTACAACTT 59.243 50.000 16.77 0.00 46.90 2.66
3187 3243 1.140252 AGCACCTCGGTGTACAACTTT 59.860 47.619 16.77 0.00 46.90 2.66
3227 3283 7.100409 TGTTACTATTGTTGATGACATTCCGA 58.900 34.615 0.00 0.00 38.26 4.55
3269 3325 0.913205 TTGCCTATTGGTCCGCCTTA 59.087 50.000 0.00 0.00 35.27 2.69
3327 3384 1.335496 CCTTGGTACCAACGTTGTTGG 59.665 52.381 23.69 23.42 44.91 3.77
3329 3386 1.280444 GGTACCAACGTTGTTGGCG 59.720 57.895 25.63 13.02 43.23 5.69
3350 3407 3.553096 CGACATAACTGACAGGCTATCCC 60.553 52.174 7.51 0.00 0.00 3.85
3363 3421 1.133668 GCTATCCCCTGACATGCCTTT 60.134 52.381 0.00 0.00 0.00 3.11
3366 3424 1.380380 CCCCTGACATGCCTTTCCC 60.380 63.158 0.00 0.00 0.00 3.97
3391 3449 0.036732 ACCGTGCAAGATGTCACCAT 59.963 50.000 0.00 0.00 0.00 3.55
3401 3460 4.762289 AGATGTCACCATTCTTCCTACC 57.238 45.455 0.00 0.00 0.00 3.18
3408 3467 5.350640 GTCACCATTCTTCCTACCTTTAACG 59.649 44.000 0.00 0.00 0.00 3.18
3414 3473 4.901868 TCTTCCTACCTTTAACGCACATT 58.098 39.130 0.00 0.00 0.00 2.71
3418 3477 3.500680 CCTACCTTTAACGCACATTGTGT 59.499 43.478 17.64 1.40 43.87 3.72
3463 3522 1.446272 CGAAACCCGACTCTCCTGC 60.446 63.158 0.00 0.00 41.76 4.85
3573 3632 6.822442 TCAGACGCAATACTTATTCCCATTA 58.178 36.000 0.00 0.00 0.00 1.90
3578 3637 7.959175 ACGCAATACTTATTCCCATTACTCTA 58.041 34.615 0.00 0.00 0.00 2.43
3584 3643 7.766736 ACTTATTCCCATTACTCTAAACCCT 57.233 36.000 0.00 0.00 0.00 4.34
3590 3649 6.243148 TCCCATTACTCTAAACCCTTTTCAC 58.757 40.000 0.00 0.00 0.00 3.18
3674 3738 3.579709 TGCTCTCGATGACTTTCTTGAC 58.420 45.455 0.00 0.00 0.00 3.18
3766 3833 0.889306 CGTCCTTCCCGAGTCTTTCT 59.111 55.000 0.00 0.00 0.00 2.52
3827 3896 6.428083 TGTAGTGGAGGAGATTTGTAACAA 57.572 37.500 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 6.310467 TCTCAAATCTTCACTAATACGTGCAC 59.690 38.462 6.82 6.82 34.92 4.57
458 469 4.060900 AGCGCTGAATACATATGACAAGG 58.939 43.478 10.39 0.00 0.00 3.61
477 488 7.371126 TCAATATCTCACTGTATCTCTAGCG 57.629 40.000 0.00 0.00 0.00 4.26
565 576 2.649531 ACGTTCTGGTTCCATGGAAA 57.350 45.000 28.64 13.55 35.75 3.13
616 627 6.129194 CGCTGCCTTAGTACAATTTTGAAAAC 60.129 38.462 0.00 0.00 0.00 2.43
693 704 0.898320 TCTGGTCTTCTGCTAGCCAC 59.102 55.000 13.29 0.90 0.00 5.01
739 750 7.639113 TCAAATAACAACAAAGGACAAGTCT 57.361 32.000 0.00 0.00 0.00 3.24
872 886 8.768397 TGGGTACAACTTATATCTTCACATCTT 58.232 33.333 0.00 0.00 0.00 2.40
897 911 7.591057 TGAGTTTCAAATCTCGCAAATAAAGTG 59.409 33.333 0.00 0.00 33.88 3.16
917 931 6.183347 CCATTTATCAGGGAAGAGTGAGTTT 58.817 40.000 0.00 0.00 0.00 2.66
1043 1057 2.842208 TTGGTGAGCAACGAAAACAG 57.158 45.000 0.00 0.00 0.00 3.16
1051 1065 2.165030 CTCCATGGATTTGGTGAGCAAC 59.835 50.000 16.63 0.00 38.01 4.17
1103 1117 4.602995 TCAAATTTGTAGGAACAACACGC 58.397 39.130 17.47 0.00 45.18 5.34
1199 1249 8.950007 TTTCACCTTCTTTTGGTAAGGAATAT 57.050 30.769 8.06 0.00 44.27 1.28
1202 1252 7.669089 ATTTTCACCTTCTTTTGGTAAGGAA 57.331 32.000 8.06 0.00 44.27 3.36
1206 1256 9.635404 TTCTCTATTTTCACCTTCTTTTGGTAA 57.365 29.630 0.00 0.00 35.80 2.85
1285 1335 5.340027 CCCCAACAACTCCTATACTCCAAAT 60.340 44.000 0.00 0.00 0.00 2.32
1304 1354 4.310022 AATCCAGTTCGAATAACCCCAA 57.690 40.909 0.00 0.00 0.00 4.12
1598 1648 7.232127 AGCTTAAATAGTTATAGCGGGTGACTA 59.768 37.037 9.71 0.00 36.96 2.59
1751 1805 4.094830 TGATGGAGAAGCATGTGCATAT 57.905 40.909 7.83 0.00 45.16 1.78
1777 1831 6.128282 ACTCACATAAACGATGTCATTGGAAC 60.128 38.462 5.04 0.00 46.33 3.62
2070 2124 8.218338 AGATGGCTACAATCTGTAAAAATCAG 57.782 34.615 0.00 0.00 31.67 2.90
2150 2204 3.498661 GGTCAACCTGGGAAGAAACTGAT 60.499 47.826 0.00 0.00 0.00 2.90
2225 2279 4.907879 AGTTTGAGTGAAAAGGCAGAAG 57.092 40.909 0.00 0.00 0.00 2.85
2251 2307 2.254546 TTGTGTGCTACAGTTGAGGG 57.745 50.000 0.00 0.00 41.10 4.30
2620 2676 2.855014 ACCGGTGTTGGGGCCTTA 60.855 61.111 6.12 0.00 0.00 2.69
2761 2817 7.628769 TGTGATTAATGCAGCTTTATCAGAA 57.371 32.000 2.76 0.00 0.00 3.02
2786 2842 6.552350 CCATCTTCCCCAATGAGTGAAATATT 59.448 38.462 0.00 0.00 0.00 1.28
2999 3055 0.815734 CAAGGAAAGGCAGAGCATGG 59.184 55.000 0.00 0.00 0.00 3.66
3041 3097 5.954757 TGGAAAGGAAAGGTGTTTATACCA 58.045 37.500 0.00 0.00 43.37 3.25
3088 3144 6.940831 ACAAAACAATGGAAAGGAAAATGG 57.059 33.333 0.00 0.00 0.00 3.16
3117 3173 8.940952 GCTCAGACAAGTTAGATTACAAGAAAT 58.059 33.333 0.00 0.00 0.00 2.17
3227 3283 1.771565 TCTCGTCCATCGGTGGTTAT 58.228 50.000 15.92 0.00 46.16 1.89
3327 3384 2.579207 TAGCCTGTCAGTTATGTCGC 57.421 50.000 0.00 0.00 0.00 5.19
3329 3386 3.244249 GGGGATAGCCTGTCAGTTATGTC 60.244 52.174 0.00 0.00 0.00 3.06
3350 3407 0.329261 TGAGGGAAAGGCATGTCAGG 59.671 55.000 0.00 0.00 0.00 3.86
3363 3421 1.191489 TCTTGCACGGTCATGAGGGA 61.191 55.000 0.00 0.00 0.00 4.20
3366 3424 1.662629 GACATCTTGCACGGTCATGAG 59.337 52.381 0.00 0.00 0.00 2.90
3391 3449 4.339872 TGTGCGTTAAAGGTAGGAAGAA 57.660 40.909 0.00 0.00 0.00 2.52
3401 3460 2.050691 GCCACACAATGTGCGTTAAAG 58.949 47.619 14.01 0.00 46.51 1.85
3408 3467 1.404047 GGTTATGGCCACACAATGTGC 60.404 52.381 8.16 0.00 46.51 4.57
3414 3473 0.251121 CTGTGGGTTATGGCCACACA 60.251 55.000 21.08 21.08 39.17 3.72
3418 3477 1.145945 TGAAACTGTGGGTTATGGCCA 59.854 47.619 8.56 8.56 37.12 5.36
3420 3479 2.235016 TGTGAAACTGTGGGTTATGGC 58.765 47.619 0.00 0.00 37.12 4.40
3452 3511 1.821061 AAGGGTGTGCAGGAGAGTCG 61.821 60.000 0.00 0.00 0.00 4.18
3463 3522 6.894339 AATAACCTTAGAAACAAGGGTGTG 57.106 37.500 2.67 0.00 45.47 3.82
3573 3632 2.109480 GGGGGTGAAAAGGGTTTAGAGT 59.891 50.000 0.00 0.00 0.00 3.24
3578 3637 1.009060 ACAAGGGGGTGAAAAGGGTTT 59.991 47.619 0.00 0.00 0.00 3.27
3584 3643 2.393646 CCTGAAACAAGGGGGTGAAAA 58.606 47.619 0.00 0.00 33.28 2.29
3590 3649 0.758685 TGTTGCCTGAAACAAGGGGG 60.759 55.000 0.00 0.00 37.12 5.40
3674 3738 3.119173 AGAGGCATCTCTCGAGTTGAAAG 60.119 47.826 13.13 1.69 46.79 2.62
3766 3833 5.360144 CGAGATTTAAGAGGTGGAGTAAGGA 59.640 44.000 0.00 0.00 0.00 3.36
3827 3896 0.615331 CTGTAGCATGACACTGGGGT 59.385 55.000 0.00 0.00 0.00 4.95


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

AutoCloner maintained by Alex Coulton.