Multiple sequence alignment - TraesCS6D01G404800

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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 TraesCS6D01G404800 chr6D 100.000 4052 0 0 1 4052 472360115 472356064 0.000000e+00 7483.0
1 TraesCS6D01G404800 chr6D 80.600 433 76 8 1189 1617 344207866 344208294 1.090000e-85 327.0
2 TraesCS6D01G404800 chr6B 90.667 3343 172 65 779 4052 717077279 717074008 0.000000e+00 4316.0
3 TraesCS6D01G404800 chr6B 90.688 741 37 17 7 717 717078023 717077285 0.000000e+00 957.0
4 TraesCS6D01G404800 chr6B 88.822 501 46 7 3558 4052 717060256 717059760 1.250000e-169 606.0
5 TraesCS6D01G404800 chr6B 80.139 433 78 8 1189 1617 519720394 519720822 2.350000e-82 316.0
6 TraesCS6D01G404800 chr6B 88.372 86 10 0 3207 3292 717060186 717060101 1.990000e-18 104.0
7 TraesCS6D01G404800 chr6B 88.372 86 10 0 3207 3292 717074434 717074349 1.990000e-18 104.0
8 TraesCS6D01G404800 chr6A 93.248 1792 71 23 2292 4052 617657965 617659737 0.000000e+00 2593.0
9 TraesCS6D01G404800 chr6A 98.225 1465 24 1 587 2049 617656483 617657947 0.000000e+00 2560.0
10 TraesCS6D01G404800 chr6A 93.511 601 23 6 1 585 617655736 617656336 0.000000e+00 880.0
11 TraesCS6D01G404800 chr6A 80.831 433 75 8 1189 1617 484608438 484608866 2.330000e-87 333.0
12 TraesCS6D01G404800 chr6A 82.927 82 13 1 323 403 3014684 3014603 5.620000e-09 73.1
13 TraesCS6D01G404800 chr2D 84.543 427 62 4 1214 1638 564095485 564095061 1.740000e-113 420.0
14 TraesCS6D01G404800 chr2D 80.342 117 18 2 287 402 628273475 628273587 2.600000e-12 84.2
15 TraesCS6D01G404800 chr2A 84.543 427 62 4 1214 1638 704776740 704776316 1.740000e-113 420.0
16 TraesCS6D01G404800 chr2B 84.309 427 63 4 1214 1638 675356171 675355747 8.100000e-112 414.0
17 TraesCS6D01G404800 chr2B 80.087 231 38 8 323 550 200904535 200904760 9.010000e-37 165.0
18 TraesCS6D01G404800 chr1B 79.337 392 67 14 1233 1617 671202668 671202284 3.110000e-66 263.0
19 TraesCS6D01G404800 chr1A 80.464 302 51 6 1703 2000 500342868 500342571 1.470000e-54 224.0
20 TraesCS6D01G404800 chr1A 90.722 97 7 2 1 95 542141812 542141716 1.180000e-25 128.0
21 TraesCS6D01G404800 chr4A 78.808 302 58 6 1703 2001 466926509 466926807 8.880000e-47 198.0
22 TraesCS6D01G404800 chr4A 90.722 97 7 2 1 95 433081081 433081177 1.180000e-25 128.0
23 TraesCS6D01G404800 chr4D 78.146 302 60 6 1703 2001 109911468 109911170 1.920000e-43 187.0
24 TraesCS6D01G404800 chr5B 77.926 299 60 5 1704 1999 259538749 259539044 8.950000e-42 182.0
25 TraesCS6D01G404800 chr5A 78.000 300 58 6 1704 1999 310874436 310874141 8.950000e-42 182.0
26 TraesCS6D01G404800 chr5A 81.383 188 27 5 1703 1886 505612649 505612466 3.260000e-31 147.0
27 TraesCS6D01G404800 chr3D 78.333 240 43 8 324 560 548494951 548494718 3.260000e-31 147.0
28 TraesCS6D01G404800 chr5D 80.851 188 28 5 1703 1886 400280928 400280745 1.520000e-29 141.0
29 TraesCS6D01G404800 chr3B 91.000 100 7 2 2 99 582366129 582366030 2.540000e-27 134.0
30 TraesCS6D01G404800 chr3B 90.099 101 8 2 1 100 826319553 826319652 3.290000e-26 130.0
31 TraesCS6D01G404800 chr7A 91.000 100 6 3 1 98 421857 421955 9.140000e-27 132.0
32 TraesCS6D01G404800 chr7A 90.816 98 8 1 1 97 424628843 424628940 3.290000e-26 130.0
33 TraesCS6D01G404800 chr7A 81.250 96 13 2 294 388 716248552 716248643 5.620000e-09 73.1
34 TraesCS6D01G404800 chr4B 89.000 100 10 1 2 100 633220886 633220985 5.500000e-24 122.0
35 TraesCS6D01G404800 chrUn 85.000 80 11 1 323 402 12528224 12528302 3.360000e-11 80.5


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 TraesCS6D01G404800 chr6D 472356064 472360115 4051 True 7483.000000 7483 100.000000 1 4052 1 chr6D.!!$R1 4051
1 TraesCS6D01G404800 chr6B 717074008 717078023 4015 True 1792.333333 4316 89.909000 7 4052 3 chr6B.!!$R2 4045
2 TraesCS6D01G404800 chr6A 617655736 617659737 4001 False 2011.000000 2593 94.994667 1 4052 3 chr6A.!!$F2 4051

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
827 1000 0.179018 CGGGCTCAAATTAGGAGGGG 60.179 60.0 8.61 0.0 32.96 4.79 F
855 1030 0.328258 CCCCGAAACAATGGAGAGGT 59.672 55.0 0.00 0.0 0.00 3.85 F
2406 2648 0.035881 CCAGGCTCAAGCAGTTCTCA 59.964 55.0 4.13 0.0 44.36 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2406 2648 0.400213 TCTTCAACCGGTTCATGGCT 59.600 50.0 19.24 0.00 0.00 4.75 R
2835 3077 6.327279 TGAAGAGAAAATCGAGTACTCACA 57.673 37.5 22.37 8.73 0.00 3.58 R
4020 4301 0.031616 CCTCCTAGGAGAGGCTGGTT 60.032 60.0 36.08 0.00 46.76 3.67 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
79 80 9.088987 ACAAAATACAATGAGGACCAATAAACT 57.911 29.630 0.00 0.00 0.00 2.66
109 110 5.770663 GGAGATAGTATTAGACTCCACAGCA 59.229 44.000 9.67 0.00 44.31 4.41
168 169 0.544223 GAGCCTCCCCTTCTTCCTTC 59.456 60.000 0.00 0.00 0.00 3.46
305 306 4.405116 ACTACTACTACTCTCTCCGGTG 57.595 50.000 0.00 0.00 0.00 4.94
577 601 1.120530 ACTACTGTATGAAGCCCGGG 58.879 55.000 19.09 19.09 0.00 5.73
614 783 1.444553 CACGACGTTGAGGAGAGGC 60.445 63.158 10.51 0.00 0.00 4.70
827 1000 0.179018 CGGGCTCAAATTAGGAGGGG 60.179 60.000 8.61 0.00 32.96 4.79
855 1030 0.328258 CCCCGAAACAATGGAGAGGT 59.672 55.000 0.00 0.00 0.00 3.85
1758 1976 3.036429 GCCCGGCCAGATCTTCACT 62.036 63.158 2.24 0.00 0.00 3.41
1854 2072 2.335369 GCCGGCGTCATCGTCTAT 59.665 61.111 12.58 0.00 39.73 1.98
2060 2282 4.549458 ACCAAAGATTCACTTTCAATGCG 58.451 39.130 0.00 0.00 45.66 4.73
2066 2288 6.116680 AGATTCACTTTCAATGCGAGATTC 57.883 37.500 0.00 0.00 0.00 2.52
2071 2293 4.796830 CACTTTCAATGCGAGATTCCAATG 59.203 41.667 0.00 0.00 0.00 2.82
2075 2297 5.840243 TCAATGCGAGATTCCAATGAAAT 57.160 34.783 0.00 0.00 33.32 2.17
2076 2298 6.211587 TCAATGCGAGATTCCAATGAAATT 57.788 33.333 0.00 0.00 36.63 1.82
2077 2299 6.267817 TCAATGCGAGATTCCAATGAAATTC 58.732 36.000 0.00 0.00 31.22 2.17
2079 2301 4.985413 TGCGAGATTCCAATGAAATTCAC 58.015 39.130 0.00 0.00 31.22 3.18
2081 2303 5.032863 GCGAGATTCCAATGAAATTCACTG 58.967 41.667 0.00 0.00 31.22 3.66
2083 2305 6.623549 GCGAGATTCCAATGAAATTCACTGAA 60.624 38.462 5.96 6.14 31.22 3.02
2087 2309 8.809066 AGATTCCAATGAAATTCACTGAATGAA 58.191 29.630 16.16 8.41 40.96 2.57
2140 2371 7.575365 CCTTTTGGTCAAAATATTTCAGCAAC 58.425 34.615 17.79 6.89 39.29 4.17
2151 2385 8.732746 AAATATTTCAGCAACTTCGGTAGTAT 57.267 30.769 0.00 0.00 35.54 2.12
2167 2401 6.071560 TCGGTAGTATGCAGGAATTCGAATAT 60.072 38.462 11.83 2.56 0.00 1.28
2220 2454 2.514458 AGATGAATGTTTCGGCCCTT 57.486 45.000 0.00 0.00 0.00 3.95
2221 2455 2.807676 AGATGAATGTTTCGGCCCTTT 58.192 42.857 0.00 0.00 0.00 3.11
2239 2477 2.996249 TTGGCCAAAATGCAACTTGA 57.004 40.000 17.98 0.00 0.00 3.02
2240 2478 2.996249 TGGCCAAAATGCAACTTGAA 57.004 40.000 0.61 0.00 0.00 2.69
2243 2481 4.965814 TGGCCAAAATGCAACTTGAAATA 58.034 34.783 0.61 0.00 0.00 1.40
2406 2648 0.035881 CCAGGCTCAAGCAGTTCTCA 59.964 55.000 4.13 0.00 44.36 3.27
2835 3077 1.265454 GGGAGGTCGACCAGGACAAT 61.265 60.000 35.00 13.86 38.70 2.71
2846 3100 2.231478 ACCAGGACAATGTGAGTACTCG 59.769 50.000 17.85 5.83 0.00 4.18
2847 3101 2.492088 CCAGGACAATGTGAGTACTCGA 59.508 50.000 17.85 7.58 0.00 4.04
2848 3102 3.131223 CCAGGACAATGTGAGTACTCGAT 59.869 47.826 17.85 9.58 0.00 3.59
2849 3103 4.382040 CCAGGACAATGTGAGTACTCGATT 60.382 45.833 17.85 14.63 0.00 3.34
2850 3104 5.171476 CAGGACAATGTGAGTACTCGATTT 58.829 41.667 17.85 8.08 0.00 2.17
2851 3105 5.639506 CAGGACAATGTGAGTACTCGATTTT 59.360 40.000 17.85 11.15 0.00 1.82
2852 3106 5.869888 AGGACAATGTGAGTACTCGATTTTC 59.130 40.000 17.85 17.61 0.00 2.29
2853 3107 5.869888 GGACAATGTGAGTACTCGATTTTCT 59.130 40.000 21.35 9.33 0.00 2.52
2854 3108 6.035112 GGACAATGTGAGTACTCGATTTTCTC 59.965 42.308 21.35 14.34 0.00 2.87
2855 3109 6.692486 ACAATGTGAGTACTCGATTTTCTCT 58.308 36.000 17.85 0.00 0.00 3.10
2856 3110 7.155328 ACAATGTGAGTACTCGATTTTCTCTT 58.845 34.615 17.85 0.00 0.00 2.85
2857 3111 7.329717 ACAATGTGAGTACTCGATTTTCTCTTC 59.670 37.037 17.85 0.00 0.00 2.87
2979 3233 1.143813 AGAAGGGGATCATCGGCAAT 58.856 50.000 0.00 0.00 0.00 3.56
3091 3345 2.433145 CCGGCCATCCATCGATCG 60.433 66.667 9.36 9.36 0.00 3.69
3092 3346 2.650778 CGGCCATCCATCGATCGA 59.349 61.111 21.86 21.86 0.00 3.59
3093 3347 1.216444 CGGCCATCCATCGATCGAT 59.784 57.895 24.60 24.60 34.81 3.59
3094 3348 0.803768 CGGCCATCCATCGATCGATC 60.804 60.000 27.20 15.68 31.62 3.69
3177 3435 6.563422 AGAAGAGAACGATGATGAAGAAGAG 58.437 40.000 0.00 0.00 0.00 2.85
3678 3950 5.562506 TGACGAGTGAGTAGTTCTATTGG 57.437 43.478 0.00 0.00 0.00 3.16
3681 3953 5.008331 ACGAGTGAGTAGTTCTATTGGTCA 58.992 41.667 0.00 0.00 0.00 4.02
3691 3963 4.935808 AGTTCTATTGGTCAATCGTTGGTC 59.064 41.667 0.00 0.00 32.50 4.02
3773 4045 2.715046 TCGATTTTCAAGCAGAGGCAT 58.285 42.857 0.00 0.00 44.61 4.40
3780 4052 1.561076 TCAAGCAGAGGCATGTATGGT 59.439 47.619 0.00 0.00 44.61 3.55
3798 4070 1.720852 GGTTCGTTCAAACATGCATGC 59.279 47.619 26.53 11.82 0.00 4.06
3801 4073 2.932498 TCGTTCAAACATGCATGCTTC 58.068 42.857 26.53 8.13 0.00 3.86
3900 4181 1.080995 GCGCACTGAGAAGCCACTAG 61.081 60.000 0.30 0.00 0.00 2.57
3904 4185 2.175202 CACTGAGAAGCCACTAGTCCT 58.825 52.381 0.00 0.00 0.00 3.85
3906 4187 3.957497 CACTGAGAAGCCACTAGTCCTAT 59.043 47.826 0.00 0.00 0.00 2.57
4020 4301 0.752658 CTATCTGCATCGTGTCCCCA 59.247 55.000 0.00 0.00 0.00 4.96
4022 4303 0.392998 ATCTGCATCGTGTCCCCAAC 60.393 55.000 0.00 0.00 0.00 3.77
4024 4305 2.033448 GCATCGTGTCCCCAACCA 59.967 61.111 0.00 0.00 0.00 3.67
4025 4306 2.040544 GCATCGTGTCCCCAACCAG 61.041 63.158 0.00 0.00 0.00 4.00
4026 4307 2.040544 CATCGTGTCCCCAACCAGC 61.041 63.158 0.00 0.00 0.00 4.85
4028 4309 3.953775 CGTGTCCCCAACCAGCCT 61.954 66.667 0.00 0.00 0.00 4.58
4029 4310 2.034221 GTGTCCCCAACCAGCCTC 59.966 66.667 0.00 0.00 0.00 4.70
4033 4318 2.612115 CCCCAACCAGCCTCTCCT 60.612 66.667 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.910637 AACAAAATGTTCATGCATGTCAC 57.089 34.783 25.43 21.75 35.27 3.67
79 80 5.514484 GGAGTCTAATACTATCTCCGTCCCA 60.514 48.000 0.00 0.00 39.07 4.37
109 110 4.278975 AGAGAAAGATTGGAAGTCGCTT 57.721 40.909 0.00 0.00 0.00 4.68
168 169 3.619038 GGTAACAAGAGAGAATTGGCTCG 59.381 47.826 0.00 0.00 39.87 5.03
827 1000 2.081425 TTGTTTCGGGGTGTGCATGC 62.081 55.000 11.82 11.82 0.00 4.06
855 1030 1.376942 GGACGACGACCTCTCCTCA 60.377 63.158 9.18 0.00 0.00 3.86
989 1186 2.046411 TGCCCATGCATCGTCGTT 60.046 55.556 0.00 0.00 44.23 3.85
1341 1538 3.654143 TCCTCCACGTCCTCCGGA 61.654 66.667 2.93 2.93 42.24 5.14
1500 1697 1.951631 GGAGAAGTATCCGCGCTGC 60.952 63.158 5.56 0.00 0.00 5.25
1854 2072 2.758327 ACGCCGGACAGCAGGATA 60.758 61.111 5.05 0.00 0.00 2.59
2060 2282 8.464404 TCATTCAGTGAATTTCATTGGAATCTC 58.536 33.333 15.85 0.00 35.19 2.75
2076 2298 5.064707 GCGCCTACTAAAATTCATTCAGTGA 59.935 40.000 0.00 0.00 34.25 3.41
2077 2299 5.065218 AGCGCCTACTAAAATTCATTCAGTG 59.935 40.000 2.29 0.00 0.00 3.66
2079 2301 5.741388 AGCGCCTACTAAAATTCATTCAG 57.259 39.130 2.29 0.00 0.00 3.02
2115 2346 7.442062 AGTTGCTGAAATATTTTGACCAAAAGG 59.558 33.333 12.61 0.00 42.72 3.11
2122 2353 6.149633 ACCGAAGTTGCTGAAATATTTTGAC 58.850 36.000 1.43 0.00 0.00 3.18
2126 2357 8.612619 CATACTACCGAAGTTGCTGAAATATTT 58.387 33.333 0.00 0.00 39.80 1.40
2140 2371 3.736252 CGAATTCCTGCATACTACCGAAG 59.264 47.826 0.00 0.00 0.00 3.79
2151 2385 8.824159 TTTTGAAAAATATTCGAATTCCTGCA 57.176 26.923 17.19 5.67 0.00 4.41
2203 2437 1.550072 CCAAAGGGCCGAAACATTCAT 59.450 47.619 0.00 0.00 0.00 2.57
2220 2454 2.996249 TCAAGTTGCATTTTGGCCAA 57.004 40.000 16.05 16.05 0.00 4.52
2221 2455 2.996249 TTCAAGTTGCATTTTGGCCA 57.004 40.000 0.00 0.00 0.00 5.36
2226 2464 8.611654 ATTTCAGCTATTTCAAGTTGCATTTT 57.388 26.923 0.00 0.00 0.00 1.82
2262 2500 4.513198 TTCAACAAATCCGGAAATCACC 57.487 40.909 9.01 0.00 0.00 4.02
2302 2540 2.289444 ACAACACCTGGTCGGTTATCAG 60.289 50.000 0.00 0.00 46.37 2.90
2406 2648 0.400213 TCTTCAACCGGTTCATGGCT 59.600 50.000 19.24 0.00 0.00 4.75
2835 3077 6.327279 TGAAGAGAAAATCGAGTACTCACA 57.673 37.500 22.37 8.73 0.00 3.58
2979 3233 1.609239 CCTCATGGTAAGCCTGCCA 59.391 57.895 0.00 0.00 42.09 4.92
3091 3345 0.583438 CACAACCATGGCGATCGATC 59.417 55.000 21.57 15.68 0.00 3.69
3092 3346 1.439353 GCACAACCATGGCGATCGAT 61.439 55.000 21.57 0.00 0.00 3.59
3093 3347 2.106074 GCACAACCATGGCGATCGA 61.106 57.895 21.57 0.00 0.00 3.59
3094 3348 2.404789 GCACAACCATGGCGATCG 59.595 61.111 13.04 11.69 0.00 3.69
3678 3950 5.416947 AGTACATTAGGACCAACGATTGAC 58.583 41.667 0.00 0.00 0.00 3.18
3681 3953 6.786967 AGTAGTACATTAGGACCAACGATT 57.213 37.500 2.52 0.00 0.00 3.34
3720 3992 6.884836 GGTACATTCAATTACTTTCTCCCACT 59.115 38.462 0.00 0.00 0.00 4.00
3737 4009 7.919690 TGAAAATCGATTGATCAGGTACATTC 58.080 34.615 12.25 7.52 32.24 2.67
3773 4045 3.565902 TGCATGTTTGAACGAACCATACA 59.434 39.130 0.00 0.00 31.92 2.29
3780 4052 3.004629 AGAAGCATGCATGTTTGAACGAA 59.995 39.130 30.21 0.00 31.18 3.85
3798 4070 6.739331 AGGGGTAATAGACTTGATGAGAAG 57.261 41.667 0.00 0.00 0.00 2.85
3843 4115 8.428063 TGTGTTTAACAATGGGAGAATTTTGAT 58.572 29.630 0.00 0.00 35.24 2.57
3968 4249 3.670377 GGGCGCGCAAGAAAGGTT 61.670 61.111 34.42 0.00 43.02 3.50
3969 4250 4.947147 TGGGCGCGCAAGAAAGGT 62.947 61.111 34.42 0.00 43.02 3.50
3970 4251 3.443045 ATGGGCGCGCAAGAAAGG 61.443 61.111 34.42 0.00 43.02 3.11
3990 4271 2.146061 GCAGATAGCAGGAGGGGCT 61.146 63.158 0.00 0.00 44.79 5.19
4003 4284 0.392998 GTTGGGGACACGATGCAGAT 60.393 55.000 0.00 0.00 42.67 2.90
4013 4294 2.121963 AGAGGCTGGTTGGGGACA 60.122 61.111 0.00 0.00 39.83 4.02
4020 4301 0.031616 CCTCCTAGGAGAGGCTGGTT 60.032 60.000 36.08 0.00 46.76 3.67
4022 4303 4.617200 CCTCCTAGGAGAGGCTGG 57.383 66.667 36.08 18.16 46.76 4.85
4028 4309 3.192799 CGCAAGTCCTCCTAGGAGA 57.807 57.895 36.08 20.79 46.90 3.71


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

AutoCloner maintained by Alex Coulton.