Multiple sequence alignment - TraesCS4D01G129400

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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 TraesCS4D01G129400 chr4D 100.000 3045 0 0 288 3332 115054598 115057642 0.000000e+00 5624.0
1 TraesCS4D01G129400 chr4D 100.000 65 0 0 1 65 115054311 115054375 1.620000e-23 121.0
2 TraesCS4D01G129400 chr4A 93.922 2912 128 19 446 3332 462212514 462209627 0.000000e+00 4351.0
3 TraesCS4D01G129400 chr4A 98.361 61 0 1 1 61 462212722 462212663 4.550000e-19 106.0
4 TraesCS4D01G129400 chr4B 95.612 2575 84 12 775 3331 175543984 175546547 0.000000e+00 4102.0
5 TraesCS4D01G129400 chr4B 77.953 254 50 6 327 578 37555812 37555563 1.600000e-33 154.0
6 TraesCS4D01G129400 chr4B 93.333 60 2 2 659 716 175543544 175543603 1.650000e-13 87.9
7 TraesCS4D01G129400 chr4B 94.545 55 1 2 8 61 175543498 175543551 2.130000e-12 84.2
8 TraesCS4D01G129400 chr2D 80.533 375 60 12 290 658 481611073 481610706 3.270000e-70 276.0
9 TraesCS4D01G129400 chr2D 79.921 254 43 5 327 577 591946456 591946704 2.640000e-41 180.0
10 TraesCS4D01G129400 chr3D 79.444 360 61 12 324 674 6302370 6302725 3.320000e-60 243.0
11 TraesCS4D01G129400 chr3D 78.333 360 66 9 307 658 545256734 545256379 4.330000e-54 222.0
12 TraesCS4D01G129400 chr3D 77.083 336 64 10 327 659 293807916 293807591 7.340000e-42 182.0
13 TraesCS4D01G129400 chr1D 78.529 340 59 12 327 655 33857323 33857659 9.370000e-51 211.0
14 TraesCS4D01G129400 chr2B 81.707 246 37 7 426 665 621066036 621066279 7.290000e-47 198.0
15 TraesCS4D01G129400 chr2B 83.654 104 13 4 514 614 624888855 624888753 9.840000e-16 95.3
16 TraesCS4D01G129400 chr5A 77.259 343 60 11 327 659 447316537 447316203 5.680000e-43 185.0
17 TraesCS4D01G129400 chr7B 75.000 344 66 12 327 658 589393385 589393050 1.250000e-29 141.0


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 TraesCS4D01G129400 chr4D 115054311 115057642 3331 False 2872.5 5624 100.000000 1 3332 2 chr4D.!!$F1 3331
1 TraesCS4D01G129400 chr4A 462209627 462212722 3095 True 2228.5 4351 96.141500 1 3332 2 chr4A.!!$R1 3331
2 TraesCS4D01G129400 chr4B 175543498 175546547 3049 False 1424.7 4102 94.496667 8 3331 3 chr4B.!!$F1 3323

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
751 759 2.170397 TCGTGATGTGTATGCTCCCAAT 59.830 45.455 0.0 0.0 0.00 3.16 F
1035 1046 1.665599 CCACCCGTCCACGTACAAC 60.666 63.158 0.0 0.0 37.74 3.32 F
2022 2033 1.122632 TTCGTTGGGTCTGGCCACTA 61.123 55.000 0.0 0.0 39.65 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1629 1640 0.391661 TGCTTCCACTTGGAGCGATC 60.392 55.000 12.27 0.0 46.36 3.69 R
2226 2240 0.748729 AGCTAGAAGACGACCCCTCG 60.749 60.000 0.00 0.0 46.06 4.63 R
3043 3073 6.127111 TGCATACCACAAAAATGATATGGCTT 60.127 34.615 0.00 0.0 33.46 4.35 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
325 326 6.561737 TTTTAAAAATGCCGGGGAAAATTC 57.438 33.333 2.18 0.00 0.00 2.17
357 360 4.961730 TGGGATTTTGGGATATCAAACTGG 59.038 41.667 4.83 0.00 36.49 4.00
370 373 7.038799 GGATATCAAACTGGATGCCCAATAAAT 60.039 37.037 4.83 0.00 42.98 1.40
374 377 3.308401 ACTGGATGCCCAATAAATTCCC 58.692 45.455 0.00 0.00 42.98 3.97
376 379 2.316108 GGATGCCCAATAAATTCCCGT 58.684 47.619 0.00 0.00 0.00 5.28
379 382 3.367646 TGCCCAATAAATTCCCGTGTA 57.632 42.857 0.00 0.00 0.00 2.90
385 388 6.693466 CCCAATAAATTCCCGTGTAAAGTTT 58.307 36.000 0.00 0.00 0.00 2.66
389 392 9.124807 CAATAAATTCCCGTGTAAAGTTTCTTC 57.875 33.333 0.00 0.00 0.00 2.87
418 421 8.814038 AAAATAGCAGGAAATGTATTCTCAGT 57.186 30.769 0.00 0.00 0.00 3.41
484 487 5.279708 GGATGGATCATAGGTTGGACTGTAG 60.280 48.000 0.00 0.00 0.00 2.74
508 511 4.471904 TCTTCGCCACAGATACATTTCT 57.528 40.909 0.00 0.00 0.00 2.52
704 710 9.709495 ATTGTTTCAACAGTATTATTTGTGCAT 57.291 25.926 0.00 0.00 40.50 3.96
705 711 8.518151 TGTTTCAACAGTATTATTTGTGCATG 57.482 30.769 0.00 0.00 34.30 4.06
707 713 7.459795 TTCAACAGTATTATTTGTGCATGGA 57.540 32.000 0.00 0.00 0.00 3.41
751 759 2.170397 TCGTGATGTGTATGCTCCCAAT 59.830 45.455 0.00 0.00 0.00 3.16
755 763 3.455543 TGATGTGTATGCTCCCAATCTCA 59.544 43.478 0.00 0.00 0.00 3.27
770 778 4.637534 CCAATCTCAGTGGTTATCAACTGG 59.362 45.833 8.22 0.95 0.00 4.00
795 803 2.755655 CTGGTGAGAGATAACGTGGACT 59.244 50.000 0.00 0.00 0.00 3.85
1034 1045 2.132996 ACCACCCGTCCACGTACAA 61.133 57.895 0.00 0.00 37.74 2.41
1035 1046 1.665599 CCACCCGTCCACGTACAAC 60.666 63.158 0.00 0.00 37.74 3.32
1036 1047 1.665599 CACCCGTCCACGTACAACC 60.666 63.158 0.00 0.00 37.74 3.77
1158 1169 3.068881 CTGGTTGCCTTCCTCGGA 58.931 61.111 0.00 0.00 0.00 4.55
1183 1194 3.209812 TCATCTCCGCGGTCCTCG 61.210 66.667 27.15 11.37 42.76 4.63
1629 1640 5.122239 TCACATTCAGATTAAAACAGAGGCG 59.878 40.000 0.00 0.00 0.00 5.52
1633 1644 4.112634 TCAGATTAAAACAGAGGCGATCG 58.887 43.478 11.69 11.69 0.00 3.69
1635 1646 2.380084 TTAAAACAGAGGCGATCGCT 57.620 45.000 36.25 23.50 41.60 4.93
1805 1816 1.229082 AGTACTGGGAAGGCCACGA 60.229 57.895 5.01 0.00 35.15 4.35
1814 1825 3.515316 AAGGCCACGACCGTCACAG 62.515 63.158 5.01 0.00 33.69 3.66
1965 1976 1.141858 TGGACAATGTGTGTGTGGCTA 59.858 47.619 0.00 0.00 41.96 3.93
2022 2033 1.122632 TTCGTTGGGTCTGGCCACTA 61.123 55.000 0.00 0.00 39.65 2.74
2036 2047 1.707632 CCACTAGCGCTATCTGCATC 58.292 55.000 19.19 0.00 43.06 3.91
2297 2312 1.690219 GACGATCATGGGGAGCCACT 61.690 60.000 0.00 0.00 0.00 4.00
2311 2326 1.136147 CCACTTGCTGCTCGATTGC 59.864 57.895 0.00 0.00 0.00 3.56
2322 2337 2.202878 CGATTGCCCGTGTCCGAT 60.203 61.111 0.00 0.00 35.63 4.18
2385 2400 2.217750 TGACCGTTGATCACAGTTTGG 58.782 47.619 0.00 0.00 0.00 3.28
2422 2437 2.975489 GGAGATCTGAAGGGCTTCCATA 59.025 50.000 0.00 0.00 38.77 2.74
2603 2620 5.069648 TCACAGATGTTGGATAGATGAGGAC 59.930 44.000 0.00 0.00 0.00 3.85
2628 2645 5.458041 AGTAGTAGCTTGTTACCGTTTCA 57.542 39.130 0.00 0.00 0.00 2.69
2629 2646 5.467705 AGTAGTAGCTTGTTACCGTTTCAG 58.532 41.667 0.00 0.00 0.00 3.02
2650 2667 3.093057 GAGACTTTCAGGTCAGCCTCTA 58.907 50.000 0.00 0.00 44.97 2.43
2718 2735 2.749621 CACTTGCTTTCCTGTGATACCC 59.250 50.000 0.00 0.00 32.72 3.69
2729 2746 3.275143 CTGTGATACCCATTTTACCGCA 58.725 45.455 0.00 0.00 0.00 5.69
2940 2969 8.552083 TTCATTCGATTTATGGGATCATGTAG 57.448 34.615 0.00 0.00 34.96 2.74
2960 2989 9.848172 CATGTAGCTTTGTTTGATGTTAAAAAC 57.152 29.630 0.00 0.00 36.92 2.43
2968 2997 8.696410 TTGTTTGATGTTAAAAACTGTCCTTC 57.304 30.769 3.01 0.00 37.22 3.46
3043 3073 2.886523 CAGGGACAATTTCAGAACAGCA 59.113 45.455 0.00 0.00 0.00 4.41
3168 3199 3.062639 CCCATCGTCATCATTTATAGCGC 59.937 47.826 0.00 0.00 0.00 5.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
304 305 5.228945 TGAATTTTCCCCGGCATTTTTAA 57.771 34.783 0.00 0.00 0.00 1.52
305 306 4.891992 TGAATTTTCCCCGGCATTTTTA 57.108 36.364 0.00 0.00 0.00 1.52
345 348 6.899393 TTATTGGGCATCCAGTTTGATATC 57.101 37.500 0.00 0.00 45.04 1.63
357 360 2.693074 ACACGGGAATTTATTGGGCATC 59.307 45.455 0.00 0.00 0.00 3.91
370 373 6.512342 TTTTGAAGAAACTTTACACGGGAA 57.488 33.333 0.00 0.00 0.00 3.97
484 487 4.946784 AATGTATCTGTGGCGAAGAAAC 57.053 40.909 0.00 0.00 0.00 2.78
724 732 2.159184 AGCATACACATCACGACTGGAG 60.159 50.000 0.00 0.00 0.00 3.86
728 736 1.137086 GGGAGCATACACATCACGACT 59.863 52.381 0.00 0.00 0.00 4.18
731 739 2.022764 TTGGGAGCATACACATCACG 57.977 50.000 0.00 0.00 0.00 4.35
751 759 3.901222 TCACCAGTTGATAACCACTGAGA 59.099 43.478 5.86 1.74 32.38 3.27
755 763 3.244561 CCAGTCACCAGTTGATAACCACT 60.245 47.826 0.00 0.00 36.32 4.00
770 778 3.502920 CACGTTATCTCTCACCAGTCAC 58.497 50.000 0.00 0.00 0.00 3.67
795 803 1.435515 GCCAACCGCTTTTGTCACA 59.564 52.632 0.00 0.00 0.00 3.58
1034 1045 1.384783 TAGTGGTGGTGGTGGTGGT 60.385 57.895 0.00 0.00 0.00 4.16
1035 1046 1.072505 GTAGTGGTGGTGGTGGTGG 59.927 63.158 0.00 0.00 0.00 4.61
1036 1047 1.072505 GGTAGTGGTGGTGGTGGTG 59.927 63.158 0.00 0.00 0.00 4.17
1290 1301 4.699522 AGGGCCGCGAAGGTGAAC 62.700 66.667 8.23 0.00 43.70 3.18
1629 1640 0.391661 TGCTTCCACTTGGAGCGATC 60.392 55.000 12.27 0.00 46.36 3.69
1633 1644 1.228245 TGGTGCTTCCACTTGGAGC 60.228 57.895 10.90 10.90 46.36 4.70
1656 1667 1.302949 GTATGGCTGGGTGGCTGAA 59.697 57.895 0.00 0.00 42.34 3.02
1681 1692 2.711922 CCGGAGCGCTCTTGTACCT 61.712 63.158 34.46 0.00 0.00 3.08
1805 1816 2.561956 CGTGTCCTCCTGTGACGGT 61.562 63.158 0.00 0.00 35.46 4.83
1814 1825 1.142748 CTGATGAGCCGTGTCCTCC 59.857 63.158 0.00 0.00 0.00 4.30
1965 1976 6.614906 AGAGAATGACATAGACCCAGAAAGAT 59.385 38.462 0.00 0.00 0.00 2.40
2036 2047 1.189524 TAACCCCCTGTGACTGTCCG 61.190 60.000 5.17 0.00 0.00 4.79
2225 2239 1.726533 GCTAGAAGACGACCCCTCGG 61.727 65.000 0.00 0.00 44.80 4.63
2226 2240 0.748729 AGCTAGAAGACGACCCCTCG 60.749 60.000 0.00 0.00 46.06 4.63
2297 2312 3.126879 CGGGCAATCGAGCAGCAA 61.127 61.111 8.48 0.00 35.83 3.91
2311 2326 2.268298 CTAACAAGAATCGGACACGGG 58.732 52.381 0.00 0.00 41.39 5.28
2322 2337 4.765273 TGCACTGACTGAACTAACAAGAA 58.235 39.130 0.00 0.00 0.00 2.52
2422 2437 2.733026 GCGTTATTATATGCCGTTCCGT 59.267 45.455 0.00 0.00 0.00 4.69
2467 2482 7.279536 CCTGCAGCTTATCGATTAATACATGAT 59.720 37.037 8.66 0.00 0.00 2.45
2468 2483 6.591448 CCTGCAGCTTATCGATTAATACATGA 59.409 38.462 8.66 0.00 0.00 3.07
2469 2484 6.183360 CCCTGCAGCTTATCGATTAATACATG 60.183 42.308 8.66 0.00 0.00 3.21
2603 2620 2.421424 ACGGTAACAAGCTACTACTCCG 59.579 50.000 12.30 12.30 40.94 4.63
2620 2637 2.434702 ACCTGAAAGTCTCTGAAACGGT 59.565 45.455 0.00 0.00 0.00 4.83
2650 2667 7.161773 AGTGTGCAAAGACATATAATTGCTT 57.838 32.000 10.25 0.00 46.27 3.91
2718 2735 7.344910 ACACAATACAATTTGCGGTAAAATG 57.655 32.000 5.26 5.26 35.69 2.32
2923 2952 7.902920 AACAAAGCTACATGATCCCATAAAT 57.097 32.000 0.00 0.00 0.00 1.40
2940 2969 7.277760 AGGACAGTTTTTAACATCAAACAAAGC 59.722 33.333 3.93 0.00 35.66 3.51
2960 2989 8.269424 CGAATGATTAAAATACTCGAAGGACAG 58.731 37.037 0.00 0.00 0.00 3.51
2968 2997 8.601243 AAGTTTGCGAATGATTAAAATACTCG 57.399 30.769 0.00 0.00 0.00 4.18
3043 3073 6.127111 TGCATACCACAAAAATGATATGGCTT 60.127 34.615 0.00 0.00 33.46 4.35


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

AutoCloner maintained by Alex Coulton.