Multiple sequence alignment - TraesCS2B01G503800

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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 TraesCS2B01G503800 chr2B 100.000 2920 0 0 1 2920 698002575 698005494 0.000000e+00 5393
1 TraesCS2B01G503800 chr2B 91.284 1503 101 14 944 2425 709999556 709998063 0.000000e+00 2023
2 TraesCS2B01G503800 chr2B 93.542 542 28 4 391 927 141155416 141155955 0.000000e+00 800
3 TraesCS2B01G503800 chr2B 90.027 371 37 0 20 390 709999920 709999550 5.660000e-132 481
4 TraesCS2B01G503800 chr2B 84.478 393 56 5 1 390 709848557 709848167 1.640000e-102 383
5 TraesCS2B01G503800 chr2B 84.512 297 29 5 2624 2920 709997876 709997597 7.970000e-71 278
6 TraesCS2B01G503800 chr2A 97.523 1978 37 4 943 2920 717556759 717554794 0.000000e+00 3371
7 TraesCS2B01G503800 chr2A 98.205 390 7 0 1 390 717557141 717556752 0.000000e+00 682
8 TraesCS2B01G503800 chr2A 94.972 358 18 0 389 746 44026005 44025648 1.960000e-156 562
9 TraesCS2B01G503800 chr2A 82.099 324 54 3 69 390 673344731 673345052 1.030000e-69 274
10 TraesCS2B01G503800 chr2D 92.253 1536 93 7 943 2465 587370364 587368842 0.000000e+00 2154
11 TraesCS2B01G503800 chr2D 91.644 371 31 0 20 390 587370727 587370357 5.580000e-142 514
12 TraesCS2B01G503800 chr2D 82.653 392 64 4 1 390 587306102 587305713 7.750000e-91 344
13 TraesCS2B01G503800 chr2D 94.624 186 6 2 2283 2465 587595005 587594821 4.760000e-73 285
14 TraesCS2B01G503800 chr2D 94.086 186 7 2 2283 2465 644591202 644591018 2.220000e-71 279
15 TraesCS2B01G503800 chr2D 89.831 59 4 1 2864 2920 587368583 587368525 1.120000e-09 75
16 TraesCS2B01G503800 chr7B 98.221 562 7 3 390 949 728934641 728935201 0.000000e+00 979
17 TraesCS2B01G503800 chr3A 93.896 557 27 4 391 942 77482911 77482357 0.000000e+00 833
18 TraesCS2B01G503800 chr3A 80.122 327 63 2 60 385 114433546 114433871 2.910000e-60 243
19 TraesCS2B01G503800 chr5A 93.250 563 31 5 385 942 606545637 606546197 0.000000e+00 822
20 TraesCS2B01G503800 chr1B 92.532 549 39 2 391 938 67502281 67502828 0.000000e+00 785
21 TraesCS2B01G503800 chr6B 91.621 549 44 2 394 942 291257055 291256509 0.000000e+00 758
22 TraesCS2B01G503800 chr6B 95.103 388 17 2 556 942 257598642 257599028 6.920000e-171 610
23 TraesCS2B01G503800 chrUn 92.067 416 29 2 390 801 117082499 117082084 1.510000e-162 582
24 TraesCS2B01G503800 chr4A 84.492 561 48 14 388 942 515418105 515418632 4.310000e-143 518
25 TraesCS2B01G503800 chr7D 95.122 205 9 1 743 946 268833763 268833967 3.630000e-84 322
26 TraesCS2B01G503800 chr4D 81.366 322 59 1 60 381 41920328 41920648 8.030000e-66 261
27 TraesCS2B01G503800 chr3D 82.500 280 49 0 102 381 516666939 516666660 2.250000e-61 246


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 TraesCS2B01G503800 chr2B 698002575 698005494 2919 False 5393.000000 5393 100.000000 1 2920 1 chr2B.!!$F2 2919
1 TraesCS2B01G503800 chr2B 709997597 709999920 2323 True 927.333333 2023 88.607667 20 2920 3 chr2B.!!$R2 2900
2 TraesCS2B01G503800 chr2B 141155416 141155955 539 False 800.000000 800 93.542000 391 927 1 chr2B.!!$F1 536
3 TraesCS2B01G503800 chr2A 717554794 717557141 2347 True 2026.500000 3371 97.864000 1 2920 2 chr2A.!!$R2 2919
4 TraesCS2B01G503800 chr2D 587368525 587370727 2202 True 914.333333 2154 91.242667 20 2920 3 chr2D.!!$R4 2900
5 TraesCS2B01G503800 chr7B 728934641 728935201 560 False 979.000000 979 98.221000 390 949 1 chr7B.!!$F1 559
6 TraesCS2B01G503800 chr3A 77482357 77482911 554 True 833.000000 833 93.896000 391 942 1 chr3A.!!$R1 551
7 TraesCS2B01G503800 chr5A 606545637 606546197 560 False 822.000000 822 93.250000 385 942 1 chr5A.!!$F1 557
8 TraesCS2B01G503800 chr1B 67502281 67502828 547 False 785.000000 785 92.532000 391 938 1 chr1B.!!$F1 547
9 TraesCS2B01G503800 chr6B 291256509 291257055 546 True 758.000000 758 91.621000 394 942 1 chr6B.!!$R1 548
10 TraesCS2B01G503800 chr4A 515418105 515418632 527 False 518.000000 518 84.492000 388 942 1 chr4A.!!$F1 554

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
88 89 0.821517 ACTATGTCCGATTCCGTGCA 59.178 50.0 0.0 0.0 0.0 4.57 F
383 384 1.019278 CCCCTTCACCGACGACAATG 61.019 60.0 0.0 0.0 0.0 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1646 1680 0.036732 AGGACTCGGTACACCACGTA 59.963 55.0 0.00 0.00 35.14 3.57 R
2293 2348 4.506288 AGGTTTTTACGCAGTTCAAATTGC 59.494 37.5 0.54 0.54 37.78 3.56 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
56 57 4.096003 GCTGGCGGGTCTTGGCTA 62.096 66.667 0.00 0.00 0.00 3.93
88 89 0.821517 ACTATGTCCGATTCCGTGCA 59.178 50.000 0.00 0.00 0.00 4.57
381 382 2.135581 ACCCCTTCACCGACGACAA 61.136 57.895 0.00 0.00 0.00 3.18
382 383 1.295423 CCCCTTCACCGACGACAAT 59.705 57.895 0.00 0.00 0.00 2.71
383 384 1.019278 CCCCTTCACCGACGACAATG 61.019 60.000 0.00 0.00 0.00 2.82
615 616 4.100498 TCACAAACTCCTCGTTTTACTCCT 59.900 41.667 0.00 0.00 43.06 3.69
630 631 3.292492 ACTCCTTGTCCCGTTCTTTTT 57.708 42.857 0.00 0.00 0.00 1.94
823 856 4.157656 GGAATTGAATGGATCACGTTTCCA 59.842 41.667 17.06 17.06 46.86 3.53
1064 1098 2.172372 CAGTGAGCGCAGATGGAGC 61.172 63.158 11.47 0.00 43.37 4.70
1107 1141 2.027003 TTAAATTGGGACGGGTAGCG 57.973 50.000 0.00 0.00 0.00 4.26
1111 1145 1.833787 ATTGGGACGGGTAGCGTGTT 61.834 55.000 0.00 0.00 0.00 3.32
1646 1680 1.078214 CAGCGGATGGGTGTGTCAT 60.078 57.895 0.00 0.00 39.31 3.06
1759 1793 9.262472 CTTTGTTGTTACTTAATTCGAGCATAC 57.738 33.333 0.00 0.00 0.00 2.39
2132 2184 8.828688 TTTGTGATATGAATTGTGCAATCAAA 57.171 26.923 0.00 0.37 0.00 2.69
2230 2285 7.415229 TGACTGCGTTGTAGTACTGAATATAG 58.585 38.462 5.39 0.00 0.00 1.31
2293 2348 3.016736 AGCCTATGGTTGAAATGGAACG 58.983 45.455 0.00 0.00 0.00 3.95
2561 2678 7.506114 TGTGTTCTTAAAATCCACACTAGAGT 58.494 34.615 0.00 0.00 38.84 3.24
2578 2695 2.235898 AGAGTGTCCTTCTTGATGCTCC 59.764 50.000 0.00 0.00 0.00 4.70
2580 2697 1.280421 GTGTCCTTCTTGATGCTCCCT 59.720 52.381 0.00 0.00 0.00 4.20
2598 2715 2.704065 CCCTCCGTCCCATAATGTAAGT 59.296 50.000 0.00 0.00 0.00 2.24
2599 2716 3.494398 CCCTCCGTCCCATAATGTAAGTG 60.494 52.174 0.00 0.00 0.00 3.16
2600 2717 3.134081 CCTCCGTCCCATAATGTAAGTGT 59.866 47.826 0.00 0.00 0.00 3.55
2601 2718 4.342951 CCTCCGTCCCATAATGTAAGTGTA 59.657 45.833 0.00 0.00 0.00 2.90
2602 2719 5.163385 CCTCCGTCCCATAATGTAAGTGTAA 60.163 44.000 0.00 0.00 0.00 2.41
2603 2720 5.909477 TCCGTCCCATAATGTAAGTGTAAG 58.091 41.667 0.00 0.00 0.00 2.34
2604 2721 5.657745 TCCGTCCCATAATGTAAGTGTAAGA 59.342 40.000 0.00 0.00 0.00 2.10
2605 2722 5.751990 CCGTCCCATAATGTAAGTGTAAGAC 59.248 44.000 0.00 0.00 0.00 3.01
2606 2723 5.457799 CGTCCCATAATGTAAGTGTAAGACG 59.542 44.000 0.00 0.00 36.66 4.18
2607 2724 6.335777 GTCCCATAATGTAAGTGTAAGACGT 58.664 40.000 0.00 0.00 0.00 4.34
2608 2725 6.815142 GTCCCATAATGTAAGTGTAAGACGTT 59.185 38.462 0.00 0.00 0.00 3.99
2662 2779 1.336440 CTACCTCTCCGAGCATCACAG 59.664 57.143 0.00 0.00 33.17 3.66
2719 2836 6.511767 GCAATTAGCATGTATGTGGTACTGTC 60.512 42.308 0.00 0.00 44.79 3.51
2840 2957 4.953940 AGGTGTGCATTGGTTTTTGTAT 57.046 36.364 0.00 0.00 0.00 2.29
2841 2958 5.289083 AGGTGTGCATTGGTTTTTGTATT 57.711 34.783 0.00 0.00 0.00 1.89
2842 2959 6.412362 AGGTGTGCATTGGTTTTTGTATTA 57.588 33.333 0.00 0.00 0.00 0.98
2843 2960 6.821388 AGGTGTGCATTGGTTTTTGTATTAA 58.179 32.000 0.00 0.00 0.00 1.40
2890 3007 2.227865 GCGGTATGGTGTGTCAATGTTT 59.772 45.455 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.354259 GATCAGGCTGACCAAGTCTTG 58.646 52.381 21.37 5.53 37.71 3.02
40 41 2.125106 GTAGCCAAGACCCGCCAG 60.125 66.667 0.00 0.00 0.00 4.85
56 57 3.615110 CGGACATAGTCAAGCAAGTCAGT 60.615 47.826 0.00 0.00 33.68 3.41
271 272 1.581447 GTTGCTGAAAAGCGGGAGG 59.419 57.895 0.00 0.00 37.69 4.30
381 382 1.048601 CGGCTACTATGGGTCCACAT 58.951 55.000 0.00 0.00 34.90 3.21
382 383 1.046472 CCGGCTACTATGGGTCCACA 61.046 60.000 0.00 0.00 0.00 4.17
383 384 0.757935 TCCGGCTACTATGGGTCCAC 60.758 60.000 0.00 0.00 0.00 4.02
466 467 0.538584 AACCTTACCGAATCGACCCC 59.461 55.000 3.36 0.00 0.00 4.95
615 616 2.946990 GGAGTGAAAAAGAACGGGACAA 59.053 45.455 0.00 0.00 0.00 3.18
630 631 3.958798 CGAGGAGTTATTTAGGGGAGTGA 59.041 47.826 0.00 0.00 0.00 3.41
724 755 0.035317 GGCTGCATCGTGGATCCATA 59.965 55.000 19.62 10.10 0.00 2.74
1111 1145 2.905996 GCTGGTCCATGGTGGTGGA 61.906 63.158 12.58 0.00 45.78 4.02
1150 1184 2.287788 GCCTCCAACCATTTGATATGCG 60.288 50.000 0.00 0.00 34.24 4.73
1551 1585 3.850122 TGGAGATGTACAACAGAGTCG 57.150 47.619 0.00 0.00 0.00 4.18
1646 1680 0.036732 AGGACTCGGTACACCACGTA 59.963 55.000 0.00 0.00 35.14 3.57
1759 1793 6.615264 AATCAGCTCAACAAGTAGCATATG 57.385 37.500 0.00 0.00 41.32 1.78
2230 2285 6.263617 TCCTATTGTAAATATTTTGCCCCGAC 59.736 38.462 5.91 0.00 0.00 4.79
2293 2348 4.506288 AGGTTTTTACGCAGTTCAAATTGC 59.494 37.500 0.54 0.54 37.78 3.56
2561 2678 1.556911 GAGGGAGCATCAAGAAGGACA 59.443 52.381 0.00 0.00 36.25 4.02
2578 2695 3.134081 ACACTTACATTATGGGACGGAGG 59.866 47.826 0.00 0.00 0.00 4.30
2580 2697 5.657745 TCTTACACTTACATTATGGGACGGA 59.342 40.000 0.00 0.00 0.00 4.69
2617 2734 9.549078 AGCTTAAAAGATAGTAAATGCCTACTC 57.451 33.333 0.00 0.00 34.03 2.59
2719 2836 7.500227 AGTGATCATGTTACAATGGTTATCAGG 59.500 37.037 0.00 0.00 0.00 3.86
2840 2957 3.639094 CACAAGTGACCCCCAACAATTAA 59.361 43.478 0.00 0.00 0.00 1.40
2841 2958 3.226777 CACAAGTGACCCCCAACAATTA 58.773 45.455 0.00 0.00 0.00 1.40
2842 2959 2.038659 CACAAGTGACCCCCAACAATT 58.961 47.619 0.00 0.00 0.00 2.32
2843 2960 1.063266 ACACAAGTGACCCCCAACAAT 60.063 47.619 7.28 0.00 0.00 2.71
2890 3007 9.337396 TGCATTTTCTCTTCTCTAACAAAACTA 57.663 29.630 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.