Multiple sequence alignment - TraesCS3B01G136700

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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 TraesCS3B01G136700 chr3B 100.000 2549 0 0 1 2549 119650952 119653500 0 4708
1 TraesCS3B01G136700 chr3B 94.859 1984 94 8 568 2549 108092313 108090336 0 3092
2 TraesCS3B01G136700 chr3B 94.861 1985 89 8 568 2549 46395681 46393707 0 3088
3 TraesCS3B01G136700 chr3B 93.961 563 32 2 6 568 216756939 216756379 0 850
4 TraesCS3B01G136700 chr3B 93.194 573 34 4 1 568 768404786 768404214 0 837
5 TraesCS3B01G136700 chr1B 95.217 1986 85 9 568 2549 581717562 581715583 0 3133
6 TraesCS3B01G136700 chr1B 94.965 1986 90 7 565 2549 671392206 671394182 0 3105
7 TraesCS3B01G136700 chr1B 94.902 1981 92 5 569 2549 561526130 561528101 0 3090
8 TraesCS3B01G136700 chr1B 94.415 573 26 4 1 568 662778002 662778573 0 876
9 TraesCS3B01G136700 chr7B 94.965 1986 89 8 567 2549 720989192 720987215 0 3103
10 TraesCS3B01G136700 chr2B 94.957 1983 91 8 568 2549 692955896 692957870 0 3099
11 TraesCS3B01G136700 chr2B 94.955 1982 84 11 569 2548 667899785 667897818 0 3092
12 TraesCS3B01G136700 chr2B 93.838 568 30 3 6 568 495450462 495451029 0 850
13 TraesCS3B01G136700 chr4A 94.907 1983 90 9 569 2549 705529252 705527279 0 3092
14 TraesCS3B01G136700 chr6B 93.695 571 33 2 1 568 187178338 187178908 0 852
15 TraesCS3B01G136700 chr6B 92.469 571 38 3 1 568 631788271 631787703 0 811
16 TraesCS3B01G136700 chr5B 92.483 572 39 2 1 568 592235450 592236021 0 815
17 TraesCS3B01G136700 chr2A 92.670 573 31 8 6 568 523705598 523705027 0 815
18 TraesCS3B01G136700 chr1A 92.509 574 31 8 6 568 346164021 346163449 0 811


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 TraesCS3B01G136700 chr3B 119650952 119653500 2548 False 4708 4708 100.000 1 2549 1 chr3B.!!$F1 2548
1 TraesCS3B01G136700 chr3B 108090336 108092313 1977 True 3092 3092 94.859 568 2549 1 chr3B.!!$R2 1981
2 TraesCS3B01G136700 chr3B 46393707 46395681 1974 True 3088 3088 94.861 568 2549 1 chr3B.!!$R1 1981
3 TraesCS3B01G136700 chr3B 216756379 216756939 560 True 850 850 93.961 6 568 1 chr3B.!!$R3 562
4 TraesCS3B01G136700 chr3B 768404214 768404786 572 True 837 837 93.194 1 568 1 chr3B.!!$R4 567
5 TraesCS3B01G136700 chr1B 581715583 581717562 1979 True 3133 3133 95.217 568 2549 1 chr1B.!!$R1 1981
6 TraesCS3B01G136700 chr1B 671392206 671394182 1976 False 3105 3105 94.965 565 2549 1 chr1B.!!$F3 1984
7 TraesCS3B01G136700 chr1B 561526130 561528101 1971 False 3090 3090 94.902 569 2549 1 chr1B.!!$F1 1980
8 TraesCS3B01G136700 chr1B 662778002 662778573 571 False 876 876 94.415 1 568 1 chr1B.!!$F2 567
9 TraesCS3B01G136700 chr7B 720987215 720989192 1977 True 3103 3103 94.965 567 2549 1 chr7B.!!$R1 1982
10 TraesCS3B01G136700 chr2B 692955896 692957870 1974 False 3099 3099 94.957 568 2549 1 chr2B.!!$F2 1981
11 TraesCS3B01G136700 chr2B 667897818 667899785 1967 True 3092 3092 94.955 569 2548 1 chr2B.!!$R1 1979
12 TraesCS3B01G136700 chr2B 495450462 495451029 567 False 850 850 93.838 6 568 1 chr2B.!!$F1 562
13 TraesCS3B01G136700 chr4A 705527279 705529252 1973 True 3092 3092 94.907 569 2549 1 chr4A.!!$R1 1980
14 TraesCS3B01G136700 chr6B 187178338 187178908 570 False 852 852 93.695 1 568 1 chr6B.!!$F1 567
15 TraesCS3B01G136700 chr6B 631787703 631788271 568 True 811 811 92.469 1 568 1 chr6B.!!$R1 567
16 TraesCS3B01G136700 chr5B 592235450 592236021 571 False 815 815 92.483 1 568 1 chr5B.!!$F1 567
17 TraesCS3B01G136700 chr2A 523705027 523705598 571 True 815 815 92.670 6 568 1 chr2A.!!$R1 562
18 TraesCS3B01G136700 chr1A 346163449 346164021 572 True 811 811 92.509 6 568 1 chr1A.!!$R1 562

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
694 715 0.179067 TGAACTTTGGCGTCTCCGTT 60.179 50.0 0.0 0.0 37.8 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2022 2051 1.064685 GGTTACCAGCACAGCCCTAAT 60.065 52.381 0.0 0.0 0.0 1.73 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
73 74 4.488879 GGTCCAATGAAAATCTTCTGTGC 58.511 43.478 0.00 0.00 32.33 4.57
153 154 2.337583 TCAAGAGACGCTTCAATTCCG 58.662 47.619 0.00 0.00 33.60 4.30
253 254 1.135575 GCCTCTTCCACGAGCAAAATG 60.136 52.381 0.00 0.00 0.00 2.32
552 573 4.522405 TGTTGTCATTTGATGAACGGGATT 59.478 37.500 0.00 0.00 41.69 3.01
553 574 4.700268 TGTCATTTGATGAACGGGATTG 57.300 40.909 0.00 0.00 41.69 2.67
580 601 9.155975 CATCATTAGGAGAAGGGTTAATTATCG 57.844 37.037 0.00 0.00 0.00 2.92
605 626 2.116238 GCCCTTAGTGGTGTCCATCTA 58.884 52.381 0.00 0.00 35.28 1.98
635 656 1.883638 GCCCTCAGATGCAAAGTGTGA 60.884 52.381 0.00 0.00 0.00 3.58
694 715 0.179067 TGAACTTTGGCGTCTCCGTT 60.179 50.000 0.00 0.00 37.80 4.44
773 794 0.319986 TATTCAGACCGTTGCACGCA 60.320 50.000 0.00 0.00 40.91 5.24
895 918 1.069204 GTGCTGACCACTGTGAGAGAA 59.931 52.381 9.86 0.00 41.35 2.87
1070 1093 0.532573 GTGGAGATGCCTGTCTTCGA 59.467 55.000 0.00 0.00 37.63 3.71
1102 1125 4.681978 GGGCGAGCGTTGAGTGGT 62.682 66.667 0.00 0.00 0.00 4.16
1238 1261 1.061131 GATCTGTTCCGTGTTCATGCG 59.939 52.381 0.00 0.00 0.00 4.73
1316 1339 1.133790 GCAAGAAGAGCATGGCGAATT 59.866 47.619 0.00 0.00 0.00 2.17
1380 1403 1.689575 CCCGAAGAAGAGATGGAGGGA 60.690 57.143 0.00 0.00 39.95 4.20
1388 1411 1.198713 GAGATGGAGGGAGAAGCACA 58.801 55.000 0.00 0.00 0.00 4.57
1413 1436 2.893489 TGACAGAGAGCTAGCTGTTGAA 59.107 45.455 24.99 10.12 44.77 2.69
1716 1744 9.820725 TTCAGAAACTTTTGATCAATGAAATGT 57.179 25.926 9.40 0.00 0.00 2.71
1761 1789 8.831715 AGCCAAACAATTAAGGTTAGAAATTG 57.168 30.769 5.67 5.67 43.18 2.32
1862 1890 3.229293 TGTCATGGAAAATGTGCCTCAA 58.771 40.909 0.00 0.00 0.00 3.02
1888 1916 6.250711 TCTGGTAGATGTTTACACCTAGTGA 58.749 40.000 0.96 0.00 36.96 3.41
2022 2051 2.897846 CGCGTGGGTTTGTGGTGA 60.898 61.111 0.00 0.00 0.00 4.02
2032 2061 2.514803 GTTTGTGGTGATTAGGGCTGT 58.485 47.619 0.00 0.00 0.00 4.40
2043 2072 1.559065 TAGGGCTGTGCTGGTAACCC 61.559 60.000 0.00 0.00 37.63 4.11
2044 2073 2.757077 GGCTGTGCTGGTAACCCT 59.243 61.111 0.00 0.00 0.00 4.34
2372 2406 2.972021 ACTGAAATTTTGGAGGGTTGGG 59.028 45.455 0.00 0.00 0.00 4.12
2444 2479 5.365619 CACTTGGTTTAGTGTTAGAGTGGT 58.634 41.667 0.00 0.00 40.48 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 6.923012 AGATCAGATATGAACTCCTTCATCG 58.077 40.000 0.00 0.00 42.54 3.84
49 50 4.523943 CACAGAAGATTTTCATTGGACCCA 59.476 41.667 0.00 0.00 35.70 4.51
73 74 1.826720 AGGCAATTGCACCAGTATTGG 59.173 47.619 30.32 2.07 43.43 3.16
153 154 2.600731 CTCTGACACTTGATGACGGAC 58.399 52.381 0.00 0.00 34.04 4.79
253 254 0.807496 GGAGCTTTGGTGCTGATCAC 59.193 55.000 0.00 0.00 44.17 3.06
473 485 7.387119 TGATTAACGAGCTAGTCAAGTAGAA 57.613 36.000 0.00 0.00 0.00 2.10
552 573 5.708736 TTAACCCTTCTCCTAATGATGCA 57.291 39.130 0.00 0.00 0.00 3.96
553 574 8.870075 ATAATTAACCCTTCTCCTAATGATGC 57.130 34.615 0.00 0.00 0.00 3.91
580 601 1.611977 GGACACCACTAAGGGCAAAAC 59.388 52.381 0.00 0.00 43.89 2.43
605 626 2.787994 CATCTGAGGGCAAAACTGAGT 58.212 47.619 0.00 0.00 0.00 3.41
630 651 1.620822 AGGGGCAAAACTGATCACAC 58.379 50.000 0.00 0.00 0.00 3.82
635 656 1.992557 TGGACTAGGGGCAAAACTGAT 59.007 47.619 0.00 0.00 0.00 2.90
746 767 4.520874 TGCAACGGTCTGAATAAAATTGGA 59.479 37.500 0.00 0.00 0.00 3.53
773 794 4.431131 CTGGGTCCCGCAAGCCAT 62.431 66.667 2.65 0.00 45.28 4.40
886 909 0.238553 CGTGCTCTCGTTCTCTCACA 59.761 55.000 0.00 0.00 0.00 3.58
888 911 0.517755 GTCGTGCTCTCGTTCTCTCA 59.482 55.000 0.00 0.00 0.00 3.27
914 937 1.142748 CCTCCACAGCTAGCTTCCG 59.857 63.158 16.46 6.77 0.00 4.30
996 1019 1.599542 GAGCTTGCGGAATACATGGAC 59.400 52.381 0.00 0.00 0.00 4.02
1098 1121 1.308998 CTGTGTGAGAAACCCACCAC 58.691 55.000 0.00 0.00 33.80 4.16
1102 1125 0.249868 CTCGCTGTGTGAGAAACCCA 60.250 55.000 2.30 0.00 42.10 4.51
1117 1140 1.359459 GGACGATTGTGGTTCCTCGC 61.359 60.000 0.00 0.00 34.60 5.03
1238 1261 3.305608 CCAAAGAAAGAAGCATGTCACCC 60.306 47.826 0.00 0.00 0.00 4.61
1362 1385 2.660572 TCTCCCTCCATCTCTTCTTCG 58.339 52.381 0.00 0.00 0.00 3.79
1380 1403 2.034878 TCTCTGTCAGTGTGTGCTTCT 58.965 47.619 0.00 0.00 0.00 2.85
1388 1411 1.818060 CAGCTAGCTCTCTGTCAGTGT 59.182 52.381 16.15 0.00 0.00 3.55
1413 1436 6.441088 ACCTTCTTCTTCAACATCCTAAGT 57.559 37.500 0.00 0.00 0.00 2.24
1716 1744 7.078249 TGGCTCTGGAATAATTCATTAGCTA 57.922 36.000 0.00 0.00 32.75 3.32
1817 1845 9.271828 ACATTTTGGTCTTTGATTTAAATCACC 57.728 29.630 26.69 23.33 44.54 4.02
1862 1890 6.153000 CACTAGGTGTAAACATCTACCAGAGT 59.847 42.308 0.00 0.00 38.47 3.24
1983 2012 2.203182 TGGGTTCGAGTCCCCAGT 59.797 61.111 20.23 0.00 46.06 4.00
2004 2033 2.951475 ATCACCACAAACCCACGCGT 62.951 55.000 5.58 5.58 0.00 6.01
2022 2051 1.064685 GGTTACCAGCACAGCCCTAAT 60.065 52.381 0.00 0.00 0.00 1.73
2032 2061 1.906574 CTGTCCTAAGGGTTACCAGCA 59.093 52.381 2.98 0.00 40.13 4.41
2043 2072 3.902881 ACTCTTGCCATCTGTCCTAAG 57.097 47.619 0.00 0.00 0.00 2.18
2044 2073 4.041567 TCAAACTCTTGCCATCTGTCCTAA 59.958 41.667 0.00 0.00 32.14 2.69
2167 2200 4.675029 ACGCGGTCTTGGGTTCGG 62.675 66.667 12.47 0.00 0.00 4.30
2372 2406 4.439776 GTGCAAACATACGTTTTCAACCTC 59.560 41.667 0.00 0.00 42.82 3.85
2444 2479 8.866970 ATTCCGTTTAAATCCTAAACCAAGTA 57.133 30.769 0.00 0.00 34.81 2.24


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

AutoCloner maintained by Alex Coulton.