Multiple sequence alignment - TraesCS6B01G174600

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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 TraesCS6B01G174600 chr6B 100.000 3062 0 0 1 3062 189130810 189133871 0.000000e+00 5655.0
1 TraesCS6B01G174600 chr6B 92.492 1545 99 6 856 2384 80770519 80768976 0.000000e+00 2194.0
2 TraesCS6B01G174600 chr6B 90.205 684 54 5 2380 3062 80765377 80764706 0.000000e+00 880.0
3 TraesCS6B01G174600 chr1D 94.671 2233 98 10 837 3062 265699440 265697222 0.000000e+00 3445.0
4 TraesCS6B01G174600 chr6D 94.597 2221 98 7 856 3062 455670553 455668341 0.000000e+00 3417.0
5 TraesCS6B01G174600 chr6D 88.207 619 36 12 1 608 104062577 104063169 0.000000e+00 704.0
6 TraesCS6B01G174600 chr6D 93.717 191 12 0 648 838 104063242 104063432 1.390000e-73 287.0
7 TraesCS6B01G174600 chr2A 92.873 2231 119 21 837 3062 741092725 741090530 0.000000e+00 3203.0
8 TraesCS6B01G174600 chr5B 96.209 1609 53 7 837 2442 685323786 685325389 0.000000e+00 2627.0
9 TraesCS6B01G174600 chr5B 91.483 317 12 3 2423 2739 685338476 685338777 3.650000e-114 422.0
10 TraesCS6B01G174600 chr5B 94.972 179 9 0 2884 3062 685351430 685351608 6.460000e-72 281.0
11 TraesCS6B01G174600 chr5B 95.098 102 5 0 2786 2887 685339085 685339186 8.790000e-36 161.0
12 TraesCS6B01G174600 chr2B 96.382 1161 40 2 839 1998 731073559 731072400 0.000000e+00 1910.0
13 TraesCS6B01G174600 chr2B 94.819 1023 47 3 2041 3062 731063287 731062270 0.000000e+00 1591.0
14 TraesCS6B01G174600 chr2B 89.991 1079 83 8 1987 3062 503087656 503088712 0.000000e+00 1371.0
15 TraesCS6B01G174600 chr2B 77.457 173 27 6 635 798 498446982 498446813 3.250000e-15 93.5
16 TraesCS6B01G174600 chr1A 88.879 1088 101 9 1737 2819 175186184 175185112 0.000000e+00 1321.0
17 TraesCS6B01G174600 chr3A 79.125 1485 269 27 1253 2712 435809944 435811412 0.000000e+00 987.0
18 TraesCS6B01G174600 chr6A 93.134 568 21 2 1 550 125485478 125486045 0.000000e+00 817.0
19 TraesCS6B01G174600 chr6A 92.771 166 12 0 673 838 125486160 125486325 1.100000e-59 241.0
20 TraesCS6B01G174600 chr3B 74.207 725 176 11 1618 2336 485405614 485404895 2.990000e-75 292.0
21 TraesCS6B01G174600 chr7D 81.061 132 15 9 677 800 168488695 168488824 2.510000e-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 TraesCS6B01G174600 chr6B 189130810 189133871 3061 False 5655.0 5655 100.0000 1 3062 1 chr6B.!!$F1 3061
1 TraesCS6B01G174600 chr6B 80764706 80770519 5813 True 1537.0 2194 91.3485 856 3062 2 chr6B.!!$R1 2206
2 TraesCS6B01G174600 chr1D 265697222 265699440 2218 True 3445.0 3445 94.6710 837 3062 1 chr1D.!!$R1 2225
3 TraesCS6B01G174600 chr6D 455668341 455670553 2212 True 3417.0 3417 94.5970 856 3062 1 chr6D.!!$R1 2206
4 TraesCS6B01G174600 chr6D 104062577 104063432 855 False 495.5 704 90.9620 1 838 2 chr6D.!!$F1 837
5 TraesCS6B01G174600 chr2A 741090530 741092725 2195 True 3203.0 3203 92.8730 837 3062 1 chr2A.!!$R1 2225
6 TraesCS6B01G174600 chr5B 685323786 685325389 1603 False 2627.0 2627 96.2090 837 2442 1 chr5B.!!$F1 1605
7 TraesCS6B01G174600 chr5B 685338476 685339186 710 False 291.5 422 93.2905 2423 2887 2 chr5B.!!$F3 464
8 TraesCS6B01G174600 chr2B 731072400 731073559 1159 True 1910.0 1910 96.3820 839 1998 1 chr2B.!!$R3 1159
9 TraesCS6B01G174600 chr2B 731062270 731063287 1017 True 1591.0 1591 94.8190 2041 3062 1 chr2B.!!$R2 1021
10 TraesCS6B01G174600 chr2B 503087656 503088712 1056 False 1371.0 1371 89.9910 1987 3062 1 chr2B.!!$F1 1075
11 TraesCS6B01G174600 chr1A 175185112 175186184 1072 True 1321.0 1321 88.8790 1737 2819 1 chr1A.!!$R1 1082
12 TraesCS6B01G174600 chr3A 435809944 435811412 1468 False 987.0 987 79.1250 1253 2712 1 chr3A.!!$F1 1459
13 TraesCS6B01G174600 chr6A 125485478 125486325 847 False 529.0 817 92.9525 1 838 2 chr6A.!!$F1 837
14 TraesCS6B01G174600 chr3B 485404895 485405614 719 True 292.0 292 74.2070 1618 2336 1 chr3B.!!$R1 718

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
235 236 0.459489 GCACAGAGTTGGTTGCCAAA 59.541 50.0 1.79 0.0 45.73 3.28 F
635 707 0.912486 ATAACTGAGGGTGGCAGACC 59.088 55.0 0.00 0.0 45.28 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1082 1156 0.877071 CTGATTGTCGCTGTTGCCTT 59.123 50.000 0.00 0.0 35.36 4.35 R
2231 2334 3.326006 ACATATGTCCTATCAGCCCACAG 59.674 47.826 1.41 0.0 0.00 3.66 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
235 236 0.459489 GCACAGAGTTGGTTGCCAAA 59.541 50.000 1.79 0.00 45.73 3.28
245 246 1.082104 GTTGCCAAAGACGGAAGCG 60.082 57.895 0.00 0.00 0.00 4.68
320 324 8.879759 CGTTAGGTTCAATGTTTATGTAGTGAT 58.120 33.333 0.00 0.00 0.00 3.06
333 337 4.471904 TGTAGTGATAGCCTTTCACCAG 57.528 45.455 11.09 0.00 43.62 4.00
346 350 3.940209 TTCACCAGGAAATGCATGAAC 57.060 42.857 0.00 0.00 31.26 3.18
372 376 1.133253 CGGCACATCAGCTTGTTCG 59.867 57.895 0.00 0.00 34.17 3.95
396 402 1.810755 GTTCTGGTTTCGTGGAATCCC 59.189 52.381 0.00 0.00 32.23 3.85
428 434 1.782201 TTGCATGGCTCAGGTCCAGT 61.782 55.000 0.00 0.00 36.98 4.00
524 547 2.842208 TTTGAGCCTTGTTTGTGTCG 57.158 45.000 0.00 0.00 0.00 4.35
527 550 2.051345 GCCTTGTTTGTGTCGGCG 60.051 61.111 0.00 0.00 0.00 6.46
556 579 4.344865 GTCCTCCTTTGGCCCGCA 62.345 66.667 0.00 0.00 0.00 5.69
557 580 3.338250 TCCTCCTTTGGCCCGCAT 61.338 61.111 0.00 0.00 0.00 4.73
628 700 6.753279 CACATTGCAATAAATAACTGAGGGTG 59.247 38.462 12.53 7.39 0.00 4.61
632 704 4.202050 GCAATAAATAACTGAGGGTGGCAG 60.202 45.833 0.00 0.00 39.26 4.85
633 705 5.192927 CAATAAATAACTGAGGGTGGCAGA 58.807 41.667 0.00 0.00 36.86 4.26
634 706 2.789409 AATAACTGAGGGTGGCAGAC 57.211 50.000 0.00 0.00 36.86 3.51
635 707 0.912486 ATAACTGAGGGTGGCAGACC 59.088 55.000 0.00 0.00 45.28 3.85
644 716 3.153024 GTGGCAGACCGCAATAAGA 57.847 52.632 0.00 0.00 46.41 2.10
645 717 1.448985 GTGGCAGACCGCAATAAGAA 58.551 50.000 0.00 0.00 46.41 2.52
646 718 1.810151 GTGGCAGACCGCAATAAGAAA 59.190 47.619 0.00 0.00 46.41 2.52
647 719 2.227865 GTGGCAGACCGCAATAAGAAAA 59.772 45.455 0.00 0.00 46.41 2.29
648 720 2.887783 TGGCAGACCGCAATAAGAAAAA 59.112 40.909 0.00 0.00 45.17 1.94
669 741 2.270986 GGCACCTTCTGGTTGCCTG 61.271 63.158 15.99 0.00 46.05 4.85
674 746 0.962356 CCTTCTGGTTGCCTGCGATT 60.962 55.000 0.00 0.00 0.00 3.34
694 766 4.766404 TTGCGCTTCAGATATCGATCTA 57.234 40.909 9.73 0.00 40.68 1.98
705 777 4.941263 AGATATCGATCTACACTGGAGCTC 59.059 45.833 4.71 4.71 40.85 4.09
794 866 8.559536 CGTTAATCAGCATACCATTACTCAATT 58.440 33.333 0.00 0.00 0.00 2.32
802 874 3.697166 ACCATTACTCAATTCCACCCAC 58.303 45.455 0.00 0.00 0.00 4.61
826 898 1.473434 GCATGGCTCCTAGCTAACGTT 60.473 52.381 5.88 5.88 41.99 3.99
1082 1156 2.358247 GAGAGTGGCGGCCGAAAA 60.358 61.111 33.48 10.54 0.00 2.29
1569 1671 4.329545 TCCGGAAGTGTGCCTGCC 62.330 66.667 0.00 0.00 35.14 4.85
1586 1688 4.749166 GCCTGCCATTATGGAGAAGAATCT 60.749 45.833 16.46 0.00 40.96 2.40
1627 1729 2.610859 AGGGCGTGGGGAAGACAT 60.611 61.111 0.00 0.00 0.00 3.06
2040 2142 0.972983 AGGATGTGGGTCGGTCTCTG 60.973 60.000 0.00 0.00 0.00 3.35
2214 2317 7.867403 AGTTTGATGTTCGCTATGAAAAATTGT 59.133 29.630 0.00 0.00 38.60 2.71
2231 2334 7.510428 AAAATTGTCATCGTATTGTGAATGC 57.490 32.000 0.00 0.00 0.00 3.56
2241 2344 0.178995 TTGTGAATGCTGTGGGCTGA 60.179 50.000 0.00 0.00 42.39 4.26
2585 6301 4.135153 GCTCGGAGCGGCTTCAGA 62.135 66.667 15.09 5.93 0.00 3.27
2591 6307 4.400961 AGCGGCTTCAGACCAGGC 62.401 66.667 0.00 0.00 0.00 4.85
2768 6486 4.393778 GTCAGGAGGACCGGGGGA 62.394 72.222 6.32 0.00 40.83 4.81
2855 6853 1.453745 CACCCCACTGCTGTTGTGT 60.454 57.895 0.00 0.00 33.92 3.72
2954 6953 1.608717 CCAGCCGAGAGTTACTGGCT 61.609 60.000 8.66 8.66 46.19 4.75
2967 6966 1.311403 CTGGCTAGGAGGGTCAGGA 59.689 63.158 0.00 0.00 33.32 3.86
2987 6989 1.285962 AGGTCATGCAGCTGGGTAATT 59.714 47.619 17.12 0.00 0.00 1.40
3028 7030 3.317571 AGCGTGCTGGAGGCTCTT 61.318 61.111 15.23 0.00 42.21 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
235 236 1.373497 CAACTCTGCGCTTCCGTCT 60.373 57.895 9.73 0.00 36.67 4.18
245 246 0.961019 TCATTGGCAACCAACTCTGC 59.039 50.000 0.00 0.00 46.95 4.26
333 337 3.426695 CGTCTTCTGGTTCATGCATTTCC 60.427 47.826 0.00 0.14 0.00 3.13
346 350 1.364626 GCTGATGTGCCGTCTTCTGG 61.365 60.000 0.00 0.00 0.00 3.86
372 376 1.305201 TCCACGAAACCAGAACAAGC 58.695 50.000 0.00 0.00 0.00 4.01
396 402 2.673043 GCCATGCAAGACACAATTCTGG 60.673 50.000 0.00 0.00 0.00 3.86
428 434 2.874664 CGGACCCAAACAGACCCGA 61.875 63.158 0.00 0.00 39.31 5.14
500 523 5.083533 ACACAAACAAGGCTCAAATTTGA 57.916 34.783 19.45 19.45 34.93 2.69
556 579 2.064581 GTAGGCGTCCCCTCCACAT 61.065 63.158 0.00 0.00 44.96 3.21
557 580 2.682494 GTAGGCGTCCCCTCCACA 60.682 66.667 0.00 0.00 44.96 4.17
572 595 1.344087 GGAGAGATGGGAACTGGGGTA 60.344 57.143 0.00 0.00 0.00 3.69
579 602 2.447443 GTTTTGGGGAGAGATGGGAAC 58.553 52.381 0.00 0.00 0.00 3.62
628 700 3.569250 TTTTTCTTATTGCGGTCTGCC 57.431 42.857 0.00 0.00 45.60 4.85
674 746 3.502211 TGTAGATCGATATCTGAAGCGCA 59.498 43.478 11.47 0.00 42.60 6.09
715 787 3.055080 TATCACGTCCGCGGTGTCC 62.055 63.158 27.15 10.76 43.45 4.02
718 790 1.444724 TTGTATCACGTCCGCGGTG 60.445 57.895 27.15 21.14 43.45 4.94
802 874 4.632974 GCTAGGAGCCATGCCCCG 62.633 72.222 0.00 0.00 34.48 5.73
826 898 0.961358 CCGCCGGGTTTGATTTGGTA 60.961 55.000 2.18 0.00 0.00 3.25
897 969 2.683475 CTGGGCCCCCGAAGAAAT 59.317 61.111 22.27 0.00 39.42 2.17
1082 1156 0.877071 CTGATTGTCGCTGTTGCCTT 59.123 50.000 0.00 0.00 35.36 4.35
1569 1671 6.297582 AGCAGGAAGATTCTTCTCCATAATG 58.702 40.000 22.34 12.36 0.00 1.90
1586 1688 4.722535 AGGAGGCCGGAGCAGGAA 62.723 66.667 5.05 0.00 42.56 3.36
1955 2057 3.835134 TGGATCCAAGGTCCACCC 58.165 61.111 13.46 0.00 40.72 4.61
2185 2288 5.940192 TTCATAGCGAACATCAAACTGTT 57.060 34.783 0.00 0.00 41.92 3.16
2186 2289 5.940192 TTTCATAGCGAACATCAAACTGT 57.060 34.783 0.00 0.00 31.73 3.55
2214 2317 3.622612 CCACAGCATTCACAATACGATGA 59.377 43.478 0.00 0.00 0.00 2.92
2231 2334 3.326006 ACATATGTCCTATCAGCCCACAG 59.674 47.826 1.41 0.00 0.00 3.66
2241 2344 7.126421 ACAAAACCTCTCTGACATATGTCCTAT 59.874 37.037 28.64 8.31 44.15 2.57
2387 6103 3.636231 CTTCGGTGGCCCTGGACA 61.636 66.667 0.00 0.00 0.00 4.02
2954 6953 1.062886 CATGACCTCCTGACCCTCCTA 60.063 57.143 0.00 0.00 0.00 2.94
2967 6966 0.921896 ATTACCCAGCTGCATGACCT 59.078 50.000 8.66 0.00 0.00 3.85
2987 6989 5.596361 TGGGTTTAAAGAGCAAATGTTCAGA 59.404 36.000 0.12 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.