Multiple sequence alignment - TraesCS6B01G199800

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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 TraesCS6B01G199800 chr6B 100.000 2615 0 0 1 2615 239728190 239730804 0.000000e+00 4830
1 TraesCS6B01G199800 chr6D 95.038 2096 44 16 552 2615 139915809 139917876 0.000000e+00 3240
2 TraesCS6B01G199800 chr6D 90.855 339 17 2 3 327 409333423 409333085 2.390000e-120 442
3 TraesCS6B01G199800 chr6A 94.682 2106 44 14 562 2615 183187655 183189744 0.000000e+00 3206
4 TraesCS6B01G199800 chr3D 91.993 562 30 3 3 550 143157968 143157408 0.000000e+00 774
5 TraesCS6B01G199800 chr3D 90.962 520 32 3 3 508 80415847 80416365 0.000000e+00 686
6 TraesCS6B01G199800 chr1D 91.993 562 30 3 3 550 466100838 466100278 0.000000e+00 774
7 TraesCS6B01G199800 chr1D 88.068 176 19 2 1075 1249 410072045 410071871 9.490000e-50 207
8 TraesCS6B01G199800 chr4A 91.815 562 31 3 3 550 675794976 675794416 0.000000e+00 769
9 TraesCS6B01G199800 chr2D 91.637 562 32 3 3 550 575333293 575333853 0.000000e+00 763
10 TraesCS6B01G199800 chr2D 90.395 177 15 2 1071 1246 538055273 538055098 5.630000e-57 231
11 TraesCS6B01G199800 chr2D 82.857 140 24 0 1068 1207 367089160 367089299 2.730000e-25 126
12 TraesCS6B01G199800 chr5D 91.103 562 35 3 3 550 35660793 35661353 0.000000e+00 747
13 TraesCS6B01G199800 chr5B 90.925 562 32 4 3 550 325799311 325799867 0.000000e+00 737
14 TraesCS6B01G199800 chr4B 91.977 511 25 9 3 498 652397270 652396761 0.000000e+00 702
15 TraesCS6B01G199800 chr4D 88.809 554 48 7 3 543 43609225 43608673 0.000000e+00 667
16 TraesCS6B01G199800 chr7D 91.495 388 19 2 3 376 579995909 579995522 2.980000e-144 521
17 TraesCS6B01G199800 chr2A 91.525 177 13 2 1071 1246 680357725 680357550 2.600000e-60 243
18 TraesCS6B01G199800 chr2B 90.960 177 14 2 1071 1246 640765313 640765138 1.210000e-58 237
19 TraesCS6B01G199800 chr1B 85.185 216 29 3 1035 1249 552474296 552474083 4.380000e-53 219
20 TraesCS6B01G199800 chr1A 88.068 176 19 2 1075 1249 505925841 505925667 9.490000e-50 207


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 TraesCS6B01G199800 chr6B 239728190 239730804 2614 False 4830 4830 100.000 1 2615 1 chr6B.!!$F1 2614
1 TraesCS6B01G199800 chr6D 139915809 139917876 2067 False 3240 3240 95.038 552 2615 1 chr6D.!!$F1 2063
2 TraesCS6B01G199800 chr6A 183187655 183189744 2089 False 3206 3206 94.682 562 2615 1 chr6A.!!$F1 2053
3 TraesCS6B01G199800 chr3D 143157408 143157968 560 True 774 774 91.993 3 550 1 chr3D.!!$R1 547
4 TraesCS6B01G199800 chr3D 80415847 80416365 518 False 686 686 90.962 3 508 1 chr3D.!!$F1 505
5 TraesCS6B01G199800 chr1D 466100278 466100838 560 True 774 774 91.993 3 550 1 chr1D.!!$R2 547
6 TraesCS6B01G199800 chr4A 675794416 675794976 560 True 769 769 91.815 3 550 1 chr4A.!!$R1 547
7 TraesCS6B01G199800 chr2D 575333293 575333853 560 False 763 763 91.637 3 550 1 chr2D.!!$F2 547
8 TraesCS6B01G199800 chr5D 35660793 35661353 560 False 747 747 91.103 3 550 1 chr5D.!!$F1 547
9 TraesCS6B01G199800 chr5B 325799311 325799867 556 False 737 737 90.925 3 550 1 chr5B.!!$F1 547
10 TraesCS6B01G199800 chr4B 652396761 652397270 509 True 702 702 91.977 3 498 1 chr4B.!!$R1 495
11 TraesCS6B01G199800 chr4D 43608673 43609225 552 True 667 667 88.809 3 543 1 chr4D.!!$R1 540

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
883 914 0.178935 CCATCCTCCTCCTCCTCCTC 60.179 65.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1751 1824 1.603172 CCGATTCGTAGATCAGGCCAC 60.603 57.143 5.01 0.0 35.04 5.01 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
107 109 0.687354 ATATAGCTTGGGCCGACCTG 59.313 55.000 0.00 0.00 41.11 4.00
246 248 6.489361 GGTACTTTTGGATAGTAGGAGATCGA 59.511 42.308 0.00 0.00 0.00 3.59
266 282 3.287222 GACCATCTCTCTCTACTGTGCT 58.713 50.000 0.00 0.00 0.00 4.40
376 392 2.038033 CAGTCCGAACTACAAAGGGGAA 59.962 50.000 0.00 0.00 33.25 3.97
420 436 3.064271 GTCTGTTCGCTAAAACACCACAA 59.936 43.478 0.00 0.00 35.39 3.33
451 467 1.882623 CTCCAAGCAAAGTCCTCCAAC 59.117 52.381 0.00 0.00 0.00 3.77
492 508 2.898705 TGGCACACACAATTTCCAAAC 58.101 42.857 0.00 0.00 0.00 2.93
540 560 2.484264 AGGCTTGTAATGAGTTTGTCGC 59.516 45.455 0.00 0.00 0.00 5.19
550 570 1.264288 GAGTTTGTCGCCCTCAACTTG 59.736 52.381 0.00 0.00 0.00 3.16
558 578 3.560068 GTCGCCCTCAACTTGTATATTGG 59.440 47.826 0.00 0.00 0.00 3.16
883 914 0.178935 CCATCCTCCTCCTCCTCCTC 60.179 65.000 0.00 0.00 0.00 3.71
884 915 0.178935 CATCCTCCTCCTCCTCCTCC 60.179 65.000 0.00 0.00 0.00 4.30
885 916 0.330431 ATCCTCCTCCTCCTCCTCCT 60.330 60.000 0.00 0.00 0.00 3.69
886 917 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
887 918 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
888 919 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
935 979 2.582436 GATTCCCGTTCCGAGCCA 59.418 61.111 0.00 0.00 0.00 4.75
1293 1354 1.455959 CAGCTACTCGCCCTACCCT 60.456 63.158 0.00 0.00 40.39 4.34
1720 1793 2.353839 CCACGCTGTTGTTGCTGC 60.354 61.111 0.00 0.00 0.00 5.25
1725 1798 1.371389 GCTGTTGTTGCTGCTGCTC 60.371 57.895 17.00 10.19 40.48 4.26
1964 2038 7.043458 GCTCATTTGTTTCGAATTGAGAACAAA 60.043 33.333 19.97 19.97 43.42 2.83
2111 2185 5.162980 ACCTGAATACCCCCATTATTCTTCC 60.163 44.000 0.00 0.00 37.02 3.46
2357 2431 6.206243 ACACCTTCAGCTATGATTAATGCATC 59.794 38.462 0.00 0.00 34.73 3.91
2358 2432 5.709164 ACCTTCAGCTATGATTAATGCATCC 59.291 40.000 0.00 0.00 34.73 3.51
2427 2501 5.532032 TCATGAGCTGAAATCAACAGACAAA 59.468 36.000 0.00 0.00 37.54 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 109 2.362397 TGAGAACATCTATGAGTCGGCC 59.638 50.000 0.00 0.00 0.00 6.13
246 248 3.023119 CAGCACAGTAGAGAGAGATGGT 58.977 50.000 0.00 0.00 0.00 3.55
266 282 5.426689 ACAGGAGCTAGTGAATGAAATCA 57.573 39.130 1.81 0.00 0.00 2.57
353 369 2.612221 CCCCTTTGTAGTTCGGACTGTC 60.612 54.545 6.62 0.00 36.60 3.51
376 392 6.006275 ACATATGATTACAAGCTCCCAGTT 57.994 37.500 10.38 0.00 0.00 3.16
420 436 3.439857 TTGCTTGGAGCTATTCCTTGT 57.560 42.857 1.29 0.00 46.92 3.16
451 467 6.149640 TGCCATCAAAAATCAAAATCCATGTG 59.850 34.615 0.00 0.00 0.00 3.21
480 496 1.267533 GGCGTACCGTTTGGAAATTGT 59.732 47.619 0.00 0.00 39.21 2.71
492 508 1.028330 TAGTCCAGTCTGGCGTACCG 61.028 60.000 14.64 0.00 37.47 4.02
540 560 6.601613 TGCTTAACCAATATACAAGTTGAGGG 59.398 38.462 10.54 4.08 0.00 4.30
550 570 9.869757 ATTTGTTTCCTTGCTTAACCAATATAC 57.130 29.630 0.00 0.00 0.00 1.47
558 578 8.419076 TTTGAAGATTTGTTTCCTTGCTTAAC 57.581 30.769 0.00 0.00 0.00 2.01
757 785 4.974721 CACCACCACCACCAGCCC 62.975 72.222 0.00 0.00 0.00 5.19
758 786 4.974721 CCACCACCACCACCAGCC 62.975 72.222 0.00 0.00 0.00 4.85
759 787 4.204028 ACCACCACCACCACCAGC 62.204 66.667 0.00 0.00 0.00 4.85
760 788 2.203337 CACCACCACCACCACCAG 60.203 66.667 0.00 0.00 0.00 4.00
761 789 3.814906 CCACCACCACCACCACCA 61.815 66.667 0.00 0.00 0.00 4.17
762 790 3.816090 ACCACCACCACCACCACC 61.816 66.667 0.00 0.00 0.00 4.61
763 791 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
764 792 3.814906 CCACCACCACCACCACCA 61.815 66.667 0.00 0.00 0.00 4.17
765 793 4.596585 CCCACCACCACCACCACC 62.597 72.222 0.00 0.00 0.00 4.61
766 794 3.491598 CTCCCACCACCACCACCAC 62.492 68.421 0.00 0.00 0.00 4.16
1520 1590 4.452733 GGTCGAACGGGAGCAGGG 62.453 72.222 0.00 0.00 34.64 4.45
1720 1793 4.676546 TCATCAGATCACGTAAAGAGCAG 58.323 43.478 0.00 0.00 0.00 4.24
1751 1824 1.603172 CCGATTCGTAGATCAGGCCAC 60.603 57.143 5.01 0.00 35.04 5.01
1905 1978 6.768861 AGTAACAGTAACACATGTGGCTAAAA 59.231 34.615 28.64 9.67 34.19 1.52
2427 2501 5.999600 TCTTGTGTCATCATGATCAGTTGTT 59.000 36.000 4.86 0.00 0.00 2.83
2563 2639 8.541133 TCGTTATCATACATCAAACAGAAACA 57.459 30.769 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.