Multiple sequence alignment - TraesCS1A01G245900

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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 TraesCS1A01G245900 chr1A 100.000 3040 0 0 1 3040 435200541 435197502 0.000000e+00 5614
1 TraesCS1A01G245900 chr1A 93.280 625 30 4 2415 3038 366077892 366077279 0.000000e+00 911
2 TraesCS1A01G245900 chr7D 95.257 3057 116 11 1 3038 387298847 387295801 0.000000e+00 4815
3 TraesCS1A01G245900 chr6D 94.735 3058 132 11 1 3038 249270157 249267109 0.000000e+00 4728
4 TraesCS1A01G245900 chr1D 94.799 3057 117 23 1 3038 95402440 95405473 0.000000e+00 4726
5 TraesCS1A01G245900 chr1D 95.545 2200 90 5 1 2200 285945065 285942874 0.000000e+00 3513
6 TraesCS1A01G245900 chr1D 95.059 2206 95 9 1 2200 88002822 88005019 0.000000e+00 3458
7 TraesCS1A01G245900 chr1D 92.200 859 43 15 2200 3038 285942771 285941917 0.000000e+00 1194
8 TraesCS1A01G245900 chr1D 92.200 859 42 16 2200 3038 78747198 78748051 0.000000e+00 1192
9 TraesCS1A01G245900 chr3D 94.497 3071 124 20 1 3038 353290907 353287849 0.000000e+00 4693
10 TraesCS1A01G245900 chr3D 95.229 2201 95 8 1 2200 254413509 254415700 0.000000e+00 3474
11 TraesCS1A01G245900 chr2A 94.181 3059 137 16 1 3038 433273456 433270418 0.000000e+00 4625
12 TraesCS1A01G245900 chr2A 91.289 3088 189 49 9 3038 367421150 367424215 0.000000e+00 4139
13 TraesCS1A01G245900 chr2A 91.463 82 7 0 2957 3038 264101767 264101848 2.480000e-21 113
14 TraesCS1A01G245900 chr3A 93.942 3054 144 26 1 3035 204302822 204305853 0.000000e+00 4577
15 TraesCS1A01G245900 chr3A 91.618 859 38 19 2200 3038 665593266 665592422 0.000000e+00 1157
16 TraesCS1A01G245900 chr3A 90.255 862 49 19 2200 3038 610672661 610671812 0.000000e+00 1094
17 TraesCS1A01G245900 chr3A 91.850 454 34 2 2200 2650 698778940 698778487 5.530000e-177 630
18 TraesCS1A01G245900 chr4A 93.856 3060 149 18 1 3040 247015306 247018346 0.000000e+00 4573
19 TraesCS1A01G245900 chr4D 92.791 860 38 14 2200 3038 426262553 426263409 0.000000e+00 1223
20 TraesCS1A01G245900 chr5D 91.915 470 19 3 2200 2650 108662074 108662543 9.190000e-180 640


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 TraesCS1A01G245900 chr1A 435197502 435200541 3039 True 5614.0 5614 100.0000 1 3040 1 chr1A.!!$R2 3039
1 TraesCS1A01G245900 chr1A 366077279 366077892 613 True 911.0 911 93.2800 2415 3038 1 chr1A.!!$R1 623
2 TraesCS1A01G245900 chr7D 387295801 387298847 3046 True 4815.0 4815 95.2570 1 3038 1 chr7D.!!$R1 3037
3 TraesCS1A01G245900 chr6D 249267109 249270157 3048 True 4728.0 4728 94.7350 1 3038 1 chr6D.!!$R1 3037
4 TraesCS1A01G245900 chr1D 95402440 95405473 3033 False 4726.0 4726 94.7990 1 3038 1 chr1D.!!$F3 3037
5 TraesCS1A01G245900 chr1D 88002822 88005019 2197 False 3458.0 3458 95.0590 1 2200 1 chr1D.!!$F2 2199
6 TraesCS1A01G245900 chr1D 285941917 285945065 3148 True 2353.5 3513 93.8725 1 3038 2 chr1D.!!$R1 3037
7 TraesCS1A01G245900 chr1D 78747198 78748051 853 False 1192.0 1192 92.2000 2200 3038 1 chr1D.!!$F1 838
8 TraesCS1A01G245900 chr3D 353287849 353290907 3058 True 4693.0 4693 94.4970 1 3038 1 chr3D.!!$R1 3037
9 TraesCS1A01G245900 chr3D 254413509 254415700 2191 False 3474.0 3474 95.2290 1 2200 1 chr3D.!!$F1 2199
10 TraesCS1A01G245900 chr2A 433270418 433273456 3038 True 4625.0 4625 94.1810 1 3038 1 chr2A.!!$R1 3037
11 TraesCS1A01G245900 chr2A 367421150 367424215 3065 False 4139.0 4139 91.2890 9 3038 1 chr2A.!!$F2 3029
12 TraesCS1A01G245900 chr3A 204302822 204305853 3031 False 4577.0 4577 93.9420 1 3035 1 chr3A.!!$F1 3034
13 TraesCS1A01G245900 chr3A 665592422 665593266 844 True 1157.0 1157 91.6180 2200 3038 1 chr3A.!!$R2 838
14 TraesCS1A01G245900 chr3A 610671812 610672661 849 True 1094.0 1094 90.2550 2200 3038 1 chr3A.!!$R1 838
15 TraesCS1A01G245900 chr4A 247015306 247018346 3040 False 4573.0 4573 93.8560 1 3040 1 chr4A.!!$F1 3039
16 TraesCS1A01G245900 chr4D 426262553 426263409 856 False 1223.0 1223 92.7910 2200 3038 1 chr4D.!!$F1 838

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
404 411 0.191064 TGGGAAGAGTCACCAGGAGT 59.809 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2241 2368 1.065551 ACTTTTCCAGCAACAACTCGC 59.934 47.619 0.0 0.0 0.0 5.03 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
45 47 8.372521 CGTAATGCATGACCTTTTGTAATTTTC 58.627 33.333 8.70 0.00 0.00 2.29
74 76 6.998673 AGCTTGTACTTCTTTGATTGGTACTT 59.001 34.615 0.00 0.00 35.29 2.24
179 186 3.521126 AGCATGACTACAGGATCTTTGGT 59.479 43.478 0.00 0.00 0.00 3.67
197 204 0.533032 GTAGCCAGTTCTCGGAGCTT 59.467 55.000 0.00 0.00 35.03 3.74
226 233 5.753921 GCGTAACTATTGATCTTAGCCAGTT 59.246 40.000 0.00 0.00 0.00 3.16
336 343 4.412199 CCTCTACACCCAAGAATCCCATTA 59.588 45.833 0.00 0.00 0.00 1.90
404 411 0.191064 TGGGAAGAGTCACCAGGAGT 59.809 55.000 0.00 0.00 0.00 3.85
584 591 3.471306 ACCCTCATAGATTCCCTCACCTA 59.529 47.826 0.00 0.00 0.00 3.08
637 644 1.937278 AGCGATGAAGCATGTGAGAG 58.063 50.000 0.00 0.00 40.15 3.20
638 645 1.479730 AGCGATGAAGCATGTGAGAGA 59.520 47.619 0.00 0.00 40.15 3.10
645 652 5.411831 TGAAGCATGTGAGAGAAGTATGT 57.588 39.130 0.00 0.00 0.00 2.29
769 777 4.758674 TGCTATGAATGCCTTATCTTGCTC 59.241 41.667 0.00 0.00 0.00 4.26
773 781 1.527457 ATGCCTTATCTTGCTCCCCT 58.473 50.000 0.00 0.00 0.00 4.79
797 809 3.242936 GCTTTTTGTTCTTGTCCGTGCTA 60.243 43.478 0.00 0.00 0.00 3.49
942 954 9.790344 CTTATTGATGATTGGAAGTAAGATCCT 57.210 33.333 0.00 0.00 37.85 3.24
965 977 7.335673 TCCTGATAGAAATGTTGATTTTGCGTA 59.664 33.333 0.00 0.00 31.58 4.42
1018 1030 9.809395 ATTTCATCATGGTAATCAATCAGATCT 57.191 29.630 0.00 0.00 35.39 2.75
1078 1092 8.669394 ACGAGTTTTAATAATACTTTGCTTGC 57.331 30.769 0.00 0.00 0.00 4.01
1092 1106 1.074405 TGCTTGCTGATCCTTTCCACT 59.926 47.619 0.00 0.00 0.00 4.00
1206 1220 4.674662 CGAGAGATTTCAAGAGCTATGTCG 59.325 45.833 0.00 0.00 0.00 4.35
1212 1226 6.756074 AGATTTCAAGAGCTATGTCGAAGAAG 59.244 38.462 0.00 0.00 39.69 2.85
1285 1300 8.777865 TTGGTTTTATTTGTTTGTTGTCATGA 57.222 26.923 0.00 0.00 0.00 3.07
1458 1475 7.416890 CGACATCCTTGACTCTTTACCTTATCT 60.417 40.741 0.00 0.00 0.00 1.98
1465 1482 9.883142 CTTGACTCTTTACCTTATCTGAAGAAT 57.117 33.333 0.00 0.00 0.00 2.40
1501 1518 8.375506 TCAAAGAACACCTATCATAAAGACTGT 58.624 33.333 0.00 0.00 0.00 3.55
1507 1524 7.324178 ACACCTATCATAAAGACTGTGAGAAC 58.676 38.462 0.00 0.00 0.00 3.01
1551 1568 9.675464 TTATCTGTACTGGATTAATTTTTCCGT 57.325 29.630 7.10 5.85 34.58 4.69
1564 1581 8.989653 TTAATTTTTCCGTGTCTTTGTTTCTT 57.010 26.923 0.00 0.00 0.00 2.52
1590 1609 3.141398 TCTGAGACCTGAAAATGTGTGC 58.859 45.455 0.00 0.00 0.00 4.57
1649 1669 5.812127 CCAAGTAATGAAGGCTTTTTATGGC 59.188 40.000 0.00 0.00 0.00 4.40
1839 1860 4.532834 TGTGGGTTCTAGTTGAGCTTTTT 58.467 39.130 0.00 0.00 0.00 1.94
1847 1868 8.403236 GGTTCTAGTTGAGCTTTTTCACTTTTA 58.597 33.333 0.00 0.00 0.00 1.52
2080 2104 8.800370 TTTGCATAGTGAAATGGATAGTTGTA 57.200 30.769 0.00 0.00 0.00 2.41
2241 2368 4.670896 ACACCTTTTCCCAAGTTCATTG 57.329 40.909 0.00 0.00 38.74 2.82
2271 2399 7.994425 TGTTGCTGGAAAAGTGAGATTTATA 57.006 32.000 0.00 0.00 0.00 0.98
2286 2416 9.941664 GTGAGATTTATATGGTTTTCATCTGTG 57.058 33.333 0.00 0.00 37.30 3.66
2609 2776 6.866770 TCTTGGATTGTAGTAGTTGAACTTCG 59.133 38.462 1.97 0.00 0.00 3.79
2662 2832 5.601313 AGCTACATTTAAATAGGTCTCCGGA 59.399 40.000 2.93 2.93 0.00 5.14
2697 2872 3.685139 TTCTAGGCTGTGGTTCTTCTG 57.315 47.619 0.00 0.00 0.00 3.02
2714 2889 6.072112 TCTTCTGAAGGCAATGTTTTGTAC 57.928 37.500 16.83 0.00 35.17 2.90
2754 2929 7.085116 CCTTACAGACTAAGTTGTACTGACAG 58.915 42.308 0.00 0.00 36.76 3.51
2789 2964 8.480643 ACTATTACTGTTATTCTTGAGTGTGC 57.519 34.615 0.00 0.00 0.00 4.57
2817 2992 7.815840 TGTTTTATGGAATGTGAACTGAAGA 57.184 32.000 0.00 0.00 0.00 2.87
2948 3126 5.592282 TCTTTGATTTTCCTGTTGCAGTACA 59.408 36.000 0.00 0.00 0.00 2.90
2959 3137 6.993308 TCCTGTTGCAGTACACAGTAAATTTA 59.007 34.615 13.72 0.00 0.00 1.40
3000 3187 5.922739 TGCTGTTAGTAGTGAATGTTGTG 57.077 39.130 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.955428 TACGTACAGGGTTCGACGCT 60.955 55.000 2.48 0.00 42.51 5.07
6 7 1.922545 GCATTACGTACAGGGTTCGAC 59.077 52.381 0.00 0.00 31.23 4.20
45 47 5.152097 CAATCAAAGAAGTACAAGCTGCAG 58.848 41.667 10.11 10.11 0.00 4.41
98 100 1.200020 GAAAAGACCGCATCAAGGGTG 59.800 52.381 0.00 0.00 36.46 4.61
179 186 0.532573 CAAGCTCCGAGAACTGGCTA 59.467 55.000 0.00 0.00 32.64 3.93
197 204 3.710326 AGATCAATAGTTACGCGCTCA 57.290 42.857 5.73 0.00 0.00 4.26
226 233 5.930135 ACCTTGTCTTTTCTAGAGAAAGCA 58.070 37.500 16.34 14.83 43.90 3.91
229 236 6.099845 ACCAGACCTTGTCTTTTCTAGAGAAA 59.900 38.462 0.46 0.46 41.37 2.52
336 343 7.219322 TCATCATCGTTGTCTATCAATTCCAT 58.781 34.615 0.00 0.00 38.38 3.41
584 591 0.179045 ACAACTTGCGAGCCTTGTCT 60.179 50.000 0.00 0.00 0.00 3.41
637 644 6.854496 AGAGATACTCACTCGACATACTTC 57.146 41.667 0.00 0.00 39.12 3.01
638 645 6.854496 GAGAGATACTCACTCGACATACTT 57.146 41.667 0.00 0.00 44.36 2.24
664 671 4.381411 AGAGGAAAAGAAGAGGAAACGTG 58.619 43.478 0.00 0.00 0.00 4.49
769 777 3.457234 GACAAGAACAAAAAGCAAGGGG 58.543 45.455 0.00 0.00 0.00 4.79
773 781 3.506810 CACGGACAAGAACAAAAAGCAA 58.493 40.909 0.00 0.00 0.00 3.91
797 809 7.285566 AGGTATCATTGAGAATGTATTGCTGT 58.714 34.615 0.00 0.00 39.87 4.40
942 954 7.914871 CCATACGCAAAATCAACATTTCTATCA 59.085 33.333 0.00 0.00 30.37 2.15
965 977 3.011708 ACTCAGCAATACCCTTTTCCCAT 59.988 43.478 0.00 0.00 0.00 4.00
1018 1030 6.092748 GCAGTCTTGTTTGAGAGAAACAAAA 58.907 36.000 12.40 0.00 45.85 2.44
1078 1092 7.108847 AGAAATAGACAAGTGGAAAGGATCAG 58.891 38.462 0.00 0.00 0.00 2.90
1092 1106 6.976934 AAAGCCCAGAAAAGAAATAGACAA 57.023 33.333 0.00 0.00 0.00 3.18
1206 1220 3.993736 GTGAGCAAGTCTTCCTCTTCTTC 59.006 47.826 5.14 0.00 0.00 2.87
1212 1226 1.437625 GCAGTGAGCAAGTCTTCCTC 58.562 55.000 0.00 0.00 44.79 3.71
1458 1475 5.793817 TCTTTGAAGGACGATGATTCTTCA 58.206 37.500 0.00 0.00 42.34 3.02
1465 1482 3.071023 AGGTGTTCTTTGAAGGACGATGA 59.929 43.478 0.00 0.00 37.34 2.92
1501 1518 7.984422 ATAAATGTCACTCACAATGTTCTCA 57.016 32.000 0.00 0.00 38.97 3.27
1551 1568 7.148239 GGTCTCAGAAAAGAAGAAACAAAGACA 60.148 37.037 0.00 0.00 32.04 3.41
1564 1581 6.038603 CACACATTTTCAGGTCTCAGAAAAGA 59.961 38.462 0.00 0.00 44.18 2.52
1649 1669 1.520174 CTCGCATTGTACTGAGCATCG 59.480 52.381 0.00 0.00 38.61 3.84
1839 1860 7.651304 CACAATAAGCCAAACACATAAAAGTGA 59.349 33.333 0.57 0.00 42.05 3.41
1847 1868 7.466746 AGAATACACAATAAGCCAAACACAT 57.533 32.000 0.00 0.00 0.00 3.21
1918 1942 3.635373 CCAATCAACAATATGAGGCTGCT 59.365 43.478 0.00 0.00 31.76 4.24
1996 2020 2.376518 TGAAACTCCTTGGGAAGCTCAT 59.623 45.455 0.00 0.00 0.00 2.90
2241 2368 1.065551 ACTTTTCCAGCAACAACTCGC 59.934 47.619 0.00 0.00 0.00 5.03
2271 2399 2.299867 GGTTGGCACAGATGAAAACCAT 59.700 45.455 0.00 0.00 42.39 3.55
2344 2476 9.884636 ACATTACAATTCAGTACTAACATAGCA 57.115 29.630 0.00 0.00 0.00 3.49
2378 2510 8.410673 TGACACCAAATATTAAAAGCCTTACA 57.589 30.769 0.00 0.00 0.00 2.41
2479 2634 9.840427 AACTTGGTCGTAAATAATTTCAATCAG 57.160 29.630 0.00 0.00 0.00 2.90
2589 2745 9.831737 TTACTACGAAGTTCAACTACTACAATC 57.168 33.333 3.32 0.00 37.78 2.67
2669 2844 4.929146 ACCACAGCCTAGAAAAATAGGT 57.071 40.909 0.00 0.00 43.74 3.08
2670 2845 5.501156 AGAACCACAGCCTAGAAAAATAGG 58.499 41.667 0.00 0.00 44.54 2.57
2674 2849 4.821805 CAGAAGAACCACAGCCTAGAAAAA 59.178 41.667 0.00 0.00 0.00 1.94
2697 2872 5.041951 TGATCGTACAAAACATTGCCTTC 57.958 39.130 0.00 0.00 0.00 3.46
2714 2889 5.915758 GTCTGTAAGGCAAGTACTATGATCG 59.084 44.000 0.00 0.00 39.41 3.69
2789 2964 7.377398 TCAGTTCACATTCCATAAAACATTGG 58.623 34.615 0.00 0.00 0.00 3.16
2930 3108 4.207165 ACTGTGTACTGCAACAGGAAAAT 58.793 39.130 18.07 0.00 35.51 1.82
3000 3187 5.681337 AAAAGACTAAGTTTCAGCTGAGC 57.319 39.130 17.43 13.77 0.00 4.26


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

AutoCloner maintained by Alex Coulton.