Multiple sequence alignment - TraesCS2B01G419100

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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 TraesCS2B01G419100 chr2B 100.000 3441 0 0 1 3441 600710312 600706872 0.000000e+00 6355.0
1 TraesCS2B01G419100 chr2D 93.229 3249 126 34 259 3441 511529623 511526403 0.000000e+00 4695.0
2 TraesCS2B01G419100 chr2D 94.805 231 10 2 5 235 511530081 511529853 3.270000e-95 359.0
3 TraesCS2B01G419100 chr2A 88.269 3299 207 79 238 3436 654876626 654873408 0.000000e+00 3783.0
4 TraesCS2B01G419100 chr2A 93.991 233 12 2 4 236 654876908 654876678 5.460000e-93 351.0
5 TraesCS2B01G419100 chr1A 87.508 1529 107 45 1470 2948 12181845 12183339 0.000000e+00 1688.0
6 TraesCS2B01G419100 chr4A 91.238 913 51 13 1470 2368 453299790 453300687 0.000000e+00 1216.0
7 TraesCS2B01G419100 chr4A 83.497 612 47 29 2365 2948 453307117 453307702 3.940000e-144 521.0
8 TraesCS2B01G419100 chr4B 84.800 125 19 0 2018 2142 646974747 646974623 3.610000e-25 126.0
9 TraesCS2B01G419100 chr5D 81.600 125 16 6 1222 1341 412602064 412601942 2.830000e-16 97.1


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 TraesCS2B01G419100 chr2B 600706872 600710312 3440 True 6355 6355 100.000 1 3441 1 chr2B.!!$R1 3440
1 TraesCS2B01G419100 chr2D 511526403 511530081 3678 True 2527 4695 94.017 5 3441 2 chr2D.!!$R1 3436
2 TraesCS2B01G419100 chr2A 654873408 654876908 3500 True 2067 3783 91.130 4 3436 2 chr2A.!!$R1 3432
3 TraesCS2B01G419100 chr1A 12181845 12183339 1494 False 1688 1688 87.508 1470 2948 1 chr1A.!!$F1 1478
4 TraesCS2B01G419100 chr4A 453299790 453300687 897 False 1216 1216 91.238 1470 2368 1 chr4A.!!$F1 898
5 TraesCS2B01G419100 chr4A 453307117 453307702 585 False 521 521 83.497 2365 2948 1 chr4A.!!$F2 583

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
878 1115 0.312729 GGGTTAAAGCCACCACAACG 59.687 55.0 0.0 0.0 35.80 4.10 F
1761 2037 0.033306 GGTCTACCTCTTCTCGGGGT 60.033 60.0 0.0 0.0 37.16 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1966 2259 0.249398 GCTGTAGATGGACGGTGGTT 59.751 55.000 0.0 0.0 0.00 3.67 R
2562 2880 1.134220 ACGCCTCTTGGACAACAAAGA 60.134 47.619 0.0 0.0 38.91 2.52 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
59 60 4.433615 TCGGATTCGATCTCTCCAAAAAG 58.566 43.478 0.00 0.00 40.88 2.27
60 61 4.159693 TCGGATTCGATCTCTCCAAAAAGA 59.840 41.667 0.00 0.00 40.88 2.52
197 198 7.172532 CCTTGTAATAGCAGTGTTGAACTAACA 59.827 37.037 0.00 0.00 46.62 2.41
206 207 0.993532 TTGAACTAACATACGCGGCG 59.006 50.000 22.36 22.36 0.00 6.46
210 211 1.587876 CTAACATACGCGGCGCTCA 60.588 57.895 30.54 17.51 0.00 4.26
228 229 1.734477 ATATCGCACTCGCCATCGC 60.734 57.895 0.00 0.00 35.26 4.58
236 237 1.665679 CACTCGCCATCGCAAATACTT 59.334 47.619 0.00 0.00 35.26 2.24
240 363 2.605818 TCGCCATCGCAAATACTTGTAC 59.394 45.455 0.00 0.00 34.79 2.90
248 371 5.992729 TCGCAAATACTTGTACCTTTCAAC 58.007 37.500 0.00 0.00 34.79 3.18
250 373 5.048991 CGCAAATACTTGTACCTTTCAACCT 60.049 40.000 0.00 0.00 34.79 3.50
265 472 5.640218 TTCAACCTTAACGACGTAAACAG 57.360 39.130 0.00 0.00 0.00 3.16
304 511 8.796475 AGCAAGAAAGACTAAAATTAAGCATGA 58.204 29.630 0.00 0.00 0.00 3.07
319 526 2.554032 AGCATGACCAGAAACTTTTCGG 59.446 45.455 0.00 9.59 41.92 4.30
521 742 2.747822 GCATCAGTGTCGCCAGCAG 61.748 63.158 0.00 0.00 0.00 4.24
543 764 2.029918 GCTTCCAGTTGGTTGGTTGATC 60.030 50.000 0.00 0.00 39.35 2.92
592 813 5.910723 CGCGTGTAAAAGTATTTCACCTTTT 59.089 36.000 0.00 0.00 37.28 2.27
593 814 6.415573 CGCGTGTAAAAGTATTTCACCTTTTT 59.584 34.615 0.00 0.00 37.28 1.94
698 925 2.880890 ACTTCTAATTGCGCCATCATCC 59.119 45.455 4.18 0.00 0.00 3.51
728 955 0.405585 AACCCACAGACCCTCCAATG 59.594 55.000 0.00 0.00 0.00 2.82
729 956 0.475632 ACCCACAGACCCTCCAATGA 60.476 55.000 0.00 0.00 0.00 2.57
730 957 0.698238 CCCACAGACCCTCCAATGAA 59.302 55.000 0.00 0.00 0.00 2.57
735 962 3.944015 CACAGACCCTCCAATGAATCTTC 59.056 47.826 0.00 0.00 0.00 2.87
766 993 1.148498 CCCGCCAACTCCTAATCCC 59.852 63.158 0.00 0.00 0.00 3.85
768 995 1.345715 CCGCCAACTCCTAATCCCCT 61.346 60.000 0.00 0.00 0.00 4.79
844 1081 8.073355 ACTAGATAAAACAAGAAACACGTCTG 57.927 34.615 0.00 0.00 0.00 3.51
878 1115 0.312729 GGGTTAAAGCCACCACAACG 59.687 55.000 0.00 0.00 35.80 4.10
910 1147 1.417890 CAAACACCAGGTCTCCAGTCT 59.582 52.381 0.00 0.00 0.00 3.24
929 1174 0.318441 TTCGTCTCCTCAACCAGCAG 59.682 55.000 0.00 0.00 0.00 4.24
957 1202 1.754621 TTTGCACCGAACAGGCCAA 60.755 52.632 5.01 0.00 46.52 4.52
1359 1621 2.954989 AGCGCACAGATATCTTCTCTCA 59.045 45.455 11.47 0.00 29.93 3.27
1368 1630 0.399091 ATCTTCTCTCATCCCCGCCA 60.399 55.000 0.00 0.00 0.00 5.69
1385 1647 3.059325 CCGCCATCTCAAATCTTTCGATC 60.059 47.826 0.00 0.00 0.00 3.69
1398 1664 5.344743 TCTTTCGATCCTCTTGCTTGTAT 57.655 39.130 0.00 0.00 0.00 2.29
1456 1726 4.525949 GGGAAGTACGGCGGGCTC 62.526 72.222 13.24 1.66 0.00 4.70
1482 1756 4.263572 CAAGGTGGTGCACGGGGA 62.264 66.667 11.45 0.00 34.83 4.81
1609 1883 1.153449 CGGATTCTGTAAGCGCCCA 60.153 57.895 2.29 0.00 0.00 5.36
1676 1950 2.277884 GTGCGCACGCTGTTTTGT 60.278 55.556 26.77 0.00 42.51 2.83
1761 2037 0.033306 GGTCTACCTCTTCTCGGGGT 60.033 60.000 0.00 0.00 37.16 4.95
1929 2213 2.162608 CGTCTCTGCTACTACTGCTTGT 59.837 50.000 0.00 0.00 0.00 3.16
1932 2216 4.991687 GTCTCTGCTACTACTGCTTGTTTT 59.008 41.667 0.00 0.00 0.00 2.43
1941 2225 4.887071 ACTACTGCTTGTTTTGGTTCATGA 59.113 37.500 0.00 0.00 0.00 3.07
1977 2270 0.474614 TGGAATGAAACCACCGTCCA 59.525 50.000 0.00 0.00 32.03 4.02
1981 2274 3.370103 GGAATGAAACCACCGTCCATCTA 60.370 47.826 0.00 0.00 0.00 1.98
2029 2322 2.203070 ATCGCCGCCATCAACCTC 60.203 61.111 0.00 0.00 0.00 3.85
2320 2622 5.804639 TCTGAAGCCATGTTTGTATGTACT 58.195 37.500 0.00 0.00 0.00 2.73
2321 2623 5.643348 TCTGAAGCCATGTTTGTATGTACTG 59.357 40.000 0.00 0.00 0.00 2.74
2322 2624 5.312895 TGAAGCCATGTTTGTATGTACTGT 58.687 37.500 0.00 0.00 0.00 3.55
2323 2625 6.468543 TGAAGCCATGTTTGTATGTACTGTA 58.531 36.000 0.00 0.00 0.00 2.74
2324 2626 6.370442 TGAAGCCATGTTTGTATGTACTGTAC 59.630 38.462 10.98 10.98 0.00 2.90
2541 2859 5.928153 ACTTTTGCGCTGTATAGAAACTTC 58.072 37.500 9.73 0.00 0.00 3.01
2686 3004 4.768448 TCTTTGGTTCTACATAGTCGGTCA 59.232 41.667 0.00 0.00 0.00 4.02
2731 3050 1.372623 GGCGAAGAACGAACGTCCT 60.373 57.895 0.00 0.00 45.77 3.85
2745 3071 1.219522 CGTCCTTTTTCCGTCGCTGT 61.220 55.000 0.00 0.00 0.00 4.40
2761 3087 2.799978 CGCTGTATGAATTGGTGCGATA 59.200 45.455 0.00 0.00 43.81 2.92
2780 3111 2.611225 AAGTATGCACTAGCCTGCTC 57.389 50.000 6.85 0.00 41.13 4.26
2781 3112 1.786937 AGTATGCACTAGCCTGCTCT 58.213 50.000 6.85 1.25 41.13 4.09
2782 3113 2.950781 AGTATGCACTAGCCTGCTCTA 58.049 47.619 6.85 0.00 41.13 2.43
2783 3114 2.625790 AGTATGCACTAGCCTGCTCTAC 59.374 50.000 6.85 8.11 41.13 2.59
2784 3115 1.786937 ATGCACTAGCCTGCTCTACT 58.213 50.000 6.85 0.00 41.13 2.57
2785 3116 2.437085 TGCACTAGCCTGCTCTACTA 57.563 50.000 6.85 0.00 41.13 1.82
2857 3203 6.975197 TGAGTCATCTTTCAACGCTAATAGAG 59.025 38.462 0.00 0.00 0.00 2.43
2934 3283 5.534654 CCATACACTTTTCACAAGGGAGAAA 59.465 40.000 0.00 0.00 32.79 2.52
3002 3353 1.672145 GGAAGGGCTACAGAACACGTC 60.672 57.143 0.00 0.00 0.00 4.34
3015 3366 4.150627 CAGAACACGTCGAAAGAATCACAT 59.849 41.667 0.00 0.00 45.01 3.21
3090 3447 3.405170 AAAGCTATTTCCGCATCAACG 57.595 42.857 0.00 0.00 0.00 4.10
3130 3487 1.505538 TCCAACCCATCCCCAAAAGAA 59.494 47.619 0.00 0.00 0.00 2.52
3152 3509 8.530804 AGAATCAAAATCAGGGGAATCTAAAG 57.469 34.615 0.00 0.00 0.00 1.85
3206 3563 8.819643 GGATACAACTAAACTATCCTGATGTC 57.180 38.462 0.00 0.00 35.10 3.06
3308 3665 1.100510 TAGTCCACCGAATCGACTGG 58.899 55.000 3.36 8.59 37.43 4.00
3395 3752 1.837439 AGTATGCGGTCCATCTCCAAA 59.163 47.619 0.00 0.00 35.34 3.28
3433 3790 5.444122 GTCACATCTGCAACAAGTAGAAAC 58.556 41.667 0.00 0.00 42.43 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 4.822896 AGTTGCGTGGTTAAGGTTCAATAA 59.177 37.500 0.00 0.00 0.00 1.40
197 198 1.514228 CGATATGAGCGCCGCGTAT 60.514 57.895 15.34 8.12 0.00 3.06
206 207 0.668706 ATGGCGAGTGCGATATGAGC 60.669 55.000 0.00 0.00 44.10 4.26
210 211 1.734477 GCGATGGCGAGTGCGATAT 60.734 57.895 0.00 0.00 39.87 1.63
228 229 9.673454 GTTAAGGTTGAAAGGTACAAGTATTTG 57.327 33.333 0.00 0.00 40.24 2.32
236 237 4.050553 CGTCGTTAAGGTTGAAAGGTACA 58.949 43.478 0.00 0.00 0.00 2.90
240 363 5.006552 TGTTTACGTCGTTAAGGTTGAAAGG 59.993 40.000 1.78 0.00 0.00 3.11
248 371 2.159881 GCTGCTGTTTACGTCGTTAAGG 60.160 50.000 1.78 0.00 0.00 2.69
250 373 1.452773 CGCTGCTGTTTACGTCGTTAA 59.547 47.619 1.78 0.00 0.00 2.01
265 472 1.091771 TCTTGCTAGGATTGCGCTGC 61.092 55.000 9.73 0.00 0.00 5.25
304 511 1.139455 TCGTCCCGAAAAGTTTCTGGT 59.861 47.619 12.30 0.00 40.91 4.00
320 527 4.876107 TCTCAGCCTATTTTGGAAATCGTC 59.124 41.667 0.00 0.00 0.00 4.20
322 529 4.035675 GGTCTCAGCCTATTTTGGAAATCG 59.964 45.833 0.00 0.00 0.00 3.34
336 543 2.970974 GCGCTTGTTGGTCTCAGCC 61.971 63.158 0.00 0.00 0.00 4.85
463 676 3.973305 TGTCCAGATGCATGGTAGGATAA 59.027 43.478 2.46 0.00 41.43 1.75
503 724 2.743538 TGCTGGCGACACTGATGC 60.744 61.111 0.00 0.00 35.60 3.91
521 742 0.389025 CAACCAACCAACTGGAAGCC 59.611 55.000 1.86 0.00 38.96 4.35
543 764 5.993106 GATCAACGGATCCTTTCTTTAGG 57.007 43.478 10.75 0.00 43.44 2.69
558 779 1.015085 TTTACACGCGGGGATCAACG 61.015 55.000 15.46 4.15 0.00 4.10
560 781 1.270947 ACTTTTACACGCGGGGATCAA 60.271 47.619 15.46 0.00 0.00 2.57
567 788 3.434299 AGGTGAAATACTTTTACACGCGG 59.566 43.478 12.47 1.27 31.42 6.46
568 789 4.657075 AGGTGAAATACTTTTACACGCG 57.343 40.909 3.53 3.53 31.42 6.01
698 925 1.142870 TCTGTGGGTTCAAGGAGTTGG 59.857 52.381 0.00 0.00 34.09 3.77
728 955 6.294010 GGCGGGAAGTTTTATATGGAAGATTC 60.294 42.308 0.00 0.00 0.00 2.52
729 956 5.535030 GGCGGGAAGTTTTATATGGAAGATT 59.465 40.000 0.00 0.00 0.00 2.40
730 957 5.070685 GGCGGGAAGTTTTATATGGAAGAT 58.929 41.667 0.00 0.00 0.00 2.40
735 962 3.951680 AGTTGGCGGGAAGTTTTATATGG 59.048 43.478 0.00 0.00 0.00 2.74
766 993 2.440409 CAATCTGGTTGTTGGAGGAGG 58.560 52.381 0.00 0.00 33.01 4.30
768 995 1.144708 TGCAATCTGGTTGTTGGAGGA 59.855 47.619 2.18 0.00 40.07 3.71
878 1115 1.754226 TGGTGTTTGTTTGGAGCCTTC 59.246 47.619 0.00 0.00 0.00 3.46
910 1147 0.318441 CTGCTGGTTGAGGAGACGAA 59.682 55.000 0.00 0.00 42.77 3.85
983 1233 1.345741 ACATGGCCTCGATCGATGAAT 59.654 47.619 22.40 12.46 0.00 2.57
1068 1324 2.440796 CCCGCGTAGTACCTCCCA 60.441 66.667 4.92 0.00 0.00 4.37
1109 1371 2.025727 CGTAGTAGAAGGGCGCCG 59.974 66.667 22.54 0.00 0.00 6.46
1269 1531 2.264794 GAGAAGCGGCGGAGGAAA 59.735 61.111 9.78 0.00 0.00 3.13
1359 1621 1.143813 AGATTTGAGATGGCGGGGAT 58.856 50.000 0.00 0.00 0.00 3.85
1385 1647 2.289002 GCCGATGAATACAAGCAAGAGG 59.711 50.000 0.00 0.00 0.00 3.69
1398 1664 0.467804 TGATCCAATCCGCCGATGAA 59.532 50.000 0.00 0.00 0.00 2.57
1456 1726 1.373748 CACCACCTTGTACCGGTCG 60.374 63.158 12.40 0.00 30.82 4.79
1609 1883 2.282040 AGAGTCGTCGGTCGGGTT 60.282 61.111 0.00 0.00 40.32 4.11
1676 1950 5.177696 CCGGTCAAAACAAGACAAAACAAAA 59.822 36.000 0.00 0.00 37.74 2.44
1711 1987 4.736631 CTGCACGACGCGACGAGA 62.737 66.667 34.99 17.32 46.97 4.04
1769 2045 4.731612 AGCACCGAGAGCACGCTG 62.732 66.667 0.00 0.00 0.00 5.18
1826 2102 2.756283 CCGAGGAGGCCGAAGAGT 60.756 66.667 0.00 0.00 0.00 3.24
1904 2184 2.907634 CAGTAGTAGCAGAGACGAGGA 58.092 52.381 0.00 0.00 0.00 3.71
1941 2225 2.803956 TCCATGTCAGTAGGAGTTCGT 58.196 47.619 0.00 0.00 0.00 3.85
1947 2231 4.288366 TGGTTTCATTCCATGTCAGTAGGA 59.712 41.667 0.00 0.00 0.00 2.94
1951 2235 3.157087 GGTGGTTTCATTCCATGTCAGT 58.843 45.455 0.00 0.00 37.30 3.41
1966 2259 0.249398 GCTGTAGATGGACGGTGGTT 59.751 55.000 0.00 0.00 0.00 3.67
1971 2264 1.299468 GCGAGCTGTAGATGGACGG 60.299 63.158 0.00 0.00 0.00 4.79
1972 2265 1.655654 CGCGAGCTGTAGATGGACG 60.656 63.158 0.00 0.00 0.00 4.79
1973 2266 1.299468 CCGCGAGCTGTAGATGGAC 60.299 63.158 8.23 0.00 0.00 4.02
1977 2270 2.502492 ATGGCCGCGAGCTGTAGAT 61.502 57.895 8.23 0.00 43.05 1.98
2320 2622 0.876777 CAACGGCGAACCTGTGTACA 60.877 55.000 16.62 0.00 0.00 2.90
2321 2623 1.562575 CCAACGGCGAACCTGTGTAC 61.563 60.000 16.62 0.00 0.00 2.90
2322 2624 1.301087 CCAACGGCGAACCTGTGTA 60.301 57.895 16.62 0.00 0.00 2.90
2323 2625 2.391724 ATCCAACGGCGAACCTGTGT 62.392 55.000 16.62 0.00 0.00 3.72
2324 2626 1.234615 AATCCAACGGCGAACCTGTG 61.235 55.000 16.62 1.14 0.00 3.66
2559 2877 3.181491 CGCCTCTTGGACAACAAAGAAAA 60.181 43.478 0.00 0.00 38.91 2.29
2562 2880 1.134220 ACGCCTCTTGGACAACAAAGA 60.134 47.619 0.00 0.00 38.91 2.52
2686 3004 8.629158 TGTTTTAGTCTCTAACATTGCAAATGT 58.371 29.630 1.71 5.96 0.00 2.71
2731 3050 4.378978 CCAATTCATACAGCGACGGAAAAA 60.379 41.667 0.00 0.00 0.00 1.94
2745 3071 5.994668 TGCATACTTATCGCACCAATTCATA 59.005 36.000 0.00 0.00 0.00 2.15
2761 3087 2.114616 AGAGCAGGCTAGTGCATACTT 58.885 47.619 7.95 0.00 46.60 2.24
2780 3111 4.749099 GCCATTTCATGACTCTGCTAGTAG 59.251 45.833 0.63 0.63 39.07 2.57
2781 3112 4.162131 TGCCATTTCATGACTCTGCTAGTA 59.838 41.667 0.00 0.00 39.07 1.82
2782 3113 3.054875 TGCCATTTCATGACTCTGCTAGT 60.055 43.478 0.00 0.00 42.80 2.57
2783 3114 3.538591 TGCCATTTCATGACTCTGCTAG 58.461 45.455 0.00 0.00 0.00 3.42
2784 3115 3.632643 TGCCATTTCATGACTCTGCTA 57.367 42.857 0.00 0.00 0.00 3.49
2785 3116 2.502142 TGCCATTTCATGACTCTGCT 57.498 45.000 0.00 0.00 0.00 4.24
2857 3203 6.781138 TGTTCGATCTTGCAATATAAACCAC 58.219 36.000 0.00 0.00 0.00 4.16
3002 3353 3.996363 TGAGGTGTGATGTGATTCTTTCG 59.004 43.478 0.00 0.00 0.00 3.46
3015 3366 6.550108 AGAAAGAGTTAGTTACTGAGGTGTGA 59.450 38.462 0.00 0.00 37.17 3.58
3090 3447 4.284490 TGGAGGGATTAGCACTGATATCAC 59.716 45.833 0.00 0.00 0.00 3.06
3130 3487 6.138967 CCCTTTAGATTCCCCTGATTTTGAT 58.861 40.000 0.00 0.00 0.00 2.57
3206 3563 6.128849 CGAAAACATTTTGGAAGCTACCATTG 60.129 38.462 0.00 0.00 39.82 2.82
3395 3752 5.182570 CAGATGTGACCTGTTTGATGTCATT 59.817 40.000 0.00 0.00 40.75 2.57


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

AutoCloner maintained by Alex Coulton.