Multiple sequence alignment - TraesCS3B01G384200

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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 TraesCS3B01G384200 chr3B 100.000 2264 0 0 1 2264 604266042 604263779 0.000000e+00 4181.0
1 TraesCS3B01G384200 chr3B 92.784 97 7 0 2168 2264 420918900 420918804 8.430000e-30 141.0
2 TraesCS3B01G384200 chr3B 80.342 117 12 4 2149 2264 558276176 558276070 6.700000e-11 78.7
3 TraesCS3B01G384200 chr2B 97.020 2215 58 5 1 2213 549352846 549355054 0.000000e+00 3718.0
4 TraesCS3B01G384200 chr2B 96.721 2074 59 7 1 2072 454449226 454451292 0.000000e+00 3445.0
5 TraesCS3B01G384200 chr2B 96.577 2074 62 7 1 2072 454473359 454475425 0.000000e+00 3428.0
6 TraesCS3B01G384200 chr5B 95.984 2266 73 8 1 2264 506965544 506967793 0.000000e+00 3664.0
7 TraesCS3B01G384200 chr5B 92.655 354 22 1 1911 2264 584814785 584814436 7.220000e-140 507.0
8 TraesCS3B01G384200 chr5B 90.722 97 7 2 2168 2264 701831218 701831124 6.560000e-26 128.0
9 TraesCS3B01G384200 chr4B 96.521 2156 59 12 1 2154 551060038 551062179 0.000000e+00 3552.0
10 TraesCS3B01G384200 chr4B 96.721 61 2 0 2204 2264 588826067 588826127 3.980000e-18 102.0
11 TraesCS3B01G384200 chr6B 96.148 2155 75 6 1 2153 181111563 181109415 0.000000e+00 3513.0
12 TraesCS3B01G384200 chr6B 96.769 1981 59 2 201 2181 599876301 599878276 0.000000e+00 3299.0
13 TraesCS3B01G384200 chr6B 95.798 476 15 2 1789 2264 679253384 679253854 0.000000e+00 763.0
14 TraesCS3B01G384200 chr1B 97.081 2021 55 2 1 2021 571422403 571420387 0.000000e+00 3402.0
15 TraesCS3B01G384200 chr7D 91.704 2206 163 16 1 2196 528561188 528563383 0.000000e+00 3042.0
16 TraesCS3B01G384200 chrUn 89.691 97 9 1 2168 2264 480941029 480941124 3.050000e-24 122.0
17 TraesCS3B01G384200 chrUn 83.761 117 8 4 2149 2264 86409123 86409229 1.430000e-17 100.0


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 TraesCS3B01G384200 chr3B 604263779 604266042 2263 True 4181 4181 100.000 1 2264 1 chr3B.!!$R3 2263
1 TraesCS3B01G384200 chr2B 549352846 549355054 2208 False 3718 3718 97.020 1 2213 1 chr2B.!!$F3 2212
2 TraesCS3B01G384200 chr2B 454449226 454451292 2066 False 3445 3445 96.721 1 2072 1 chr2B.!!$F1 2071
3 TraesCS3B01G384200 chr2B 454473359 454475425 2066 False 3428 3428 96.577 1 2072 1 chr2B.!!$F2 2071
4 TraesCS3B01G384200 chr5B 506965544 506967793 2249 False 3664 3664 95.984 1 2264 1 chr5B.!!$F1 2263
5 TraesCS3B01G384200 chr4B 551060038 551062179 2141 False 3552 3552 96.521 1 2154 1 chr4B.!!$F1 2153
6 TraesCS3B01G384200 chr6B 181109415 181111563 2148 True 3513 3513 96.148 1 2153 1 chr6B.!!$R1 2152
7 TraesCS3B01G384200 chr6B 599876301 599878276 1975 False 3299 3299 96.769 201 2181 1 chr6B.!!$F1 1980
8 TraesCS3B01G384200 chr1B 571420387 571422403 2016 True 3402 3402 97.081 1 2021 1 chr1B.!!$R1 2020
9 TraesCS3B01G384200 chr7D 528561188 528563383 2195 False 3042 3042 91.704 1 2196 1 chr7D.!!$F1 2195

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
244 245 1.067974 GCCTTAAAAACCGTTGGTGCT 59.932 47.619 0.0 0.0 35.34 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2122 2243 0.108329 CTACCGCCAACGATCTTGGT 60.108 55.0 19.0 5.35 43.93 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
172 173 5.857268 TGATCTATCAAATCAATGAGCCGA 58.143 37.500 0.00 0.00 33.08 5.54
244 245 1.067974 GCCTTAAAAACCGTTGGTGCT 59.932 47.619 0.00 0.00 35.34 4.40
447 448 2.897271 ATGTTGGGCCAGACATTGTA 57.103 45.000 21.19 0.00 32.85 2.41
492 493 5.398467 GCCTATGAGGGGAAGAAGAAGAAAT 60.398 44.000 0.00 0.00 35.37 2.17
651 652 3.426963 GCAAGAAACGAAGAACCAACACA 60.427 43.478 0.00 0.00 0.00 3.72
692 693 1.153269 GGAGCAGTAGCCTTGGAGC 60.153 63.158 0.00 0.00 43.56 4.70
864 865 2.044492 TGATAGGGGAAGGCCTATCGAT 59.956 50.000 5.16 2.16 44.45 3.59
1118 1120 2.705658 AGGATGTGAAGATTCCGCCATA 59.294 45.455 0.00 0.00 34.61 2.74
1216 1218 3.834813 TGTTTGCCCCAATTATGCTTACA 59.165 39.130 0.00 0.00 0.00 2.41
1333 1335 1.264749 TATGCAGTCACCGCCTCCTT 61.265 55.000 0.00 0.00 0.00 3.36
1465 1467 0.809385 CTTGGAGGAAGAGCGTCGTA 59.191 55.000 0.00 0.00 32.82 3.43
1629 1631 0.674534 GGCCCCGTATGACTCAGTAG 59.325 60.000 0.00 0.00 0.00 2.57
1637 1639 3.628032 CGTATGACTCAGTAGAGCCTTCA 59.372 47.826 0.00 0.00 46.09 3.02
1714 1716 9.953565 TGAACTATGTAGTACTAAGGCAAAAAT 57.046 29.630 3.61 0.00 34.99 1.82
1773 1775 7.119553 GCCATTTGTATTGAATTTGGTGTGAAT 59.880 33.333 0.00 0.00 0.00 2.57
1871 1874 3.198068 GTTGTGCTGTGAAGAGAAGTGA 58.802 45.455 0.00 0.00 0.00 3.41
1979 2100 4.875713 GCATGGCGGTAGGGGGTG 62.876 72.222 0.00 0.00 0.00 4.61
1980 2101 4.189580 CATGGCGGTAGGGGGTGG 62.190 72.222 0.00 0.00 0.00 4.61
2122 2243 2.589798 ACGGTTCTGTGACGAAGAAA 57.410 45.000 0.00 0.00 35.50 2.52
2129 2250 4.336889 TCTGTGACGAAGAAACCAAGAT 57.663 40.909 0.00 0.00 0.00 2.40
2145 2270 0.683504 AGATCGTTGGCGGTAGGACT 60.684 55.000 0.00 0.00 38.89 3.85
2186 2311 3.702048 GCGGTAGGGTGCTGGACA 61.702 66.667 0.77 0.00 0.00 4.02
2260 2385 3.118223 TGCCCCATATGTGTCGAATGTTA 60.118 43.478 1.24 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
172 173 1.450211 CGTCCCTTGTTGTCCCACT 59.550 57.895 0.00 0.00 0.00 4.00
447 448 1.524002 CATGAGTGCGGGATCTGGT 59.476 57.895 0.00 0.00 0.00 4.00
492 493 3.384789 CCATGTCACTCCGGAATCTCTTA 59.615 47.826 5.23 0.00 0.00 2.10
651 652 1.540363 CCACGTGTTTGACTAGTGCCT 60.540 52.381 15.65 0.00 0.00 4.75
864 865 1.452110 CATCCGGATTGAGCAACACA 58.548 50.000 16.19 0.00 0.00 3.72
922 924 4.229096 GGGCAAATATATCAACACATGCG 58.771 43.478 0.00 0.00 33.53 4.73
982 984 4.716287 AGCCATGCCCTACAACAAATAAAT 59.284 37.500 0.00 0.00 0.00 1.40
1118 1120 2.596346 TGCAAACATCTCCACACCAAT 58.404 42.857 0.00 0.00 0.00 3.16
1216 1218 1.463444 GTTAGTTGGAAGCGCACGATT 59.537 47.619 11.47 0.00 0.00 3.34
1333 1335 4.551702 TCCAGCTGAAGTACTTGCATAA 57.448 40.909 17.39 0.00 0.00 1.90
1714 1716 2.479837 GACAAGTTGACGACACATGGA 58.520 47.619 10.54 0.00 0.00 3.41
1773 1775 6.510536 TCATTCACAACACATTGCAAACATA 58.489 32.000 1.71 0.00 39.66 2.29
1871 1874 6.804677 CAGAGCACTCTGTTCTGTTATATCT 58.195 40.000 17.73 0.00 46.36 1.98
1978 2099 3.494254 ACAGAACCGTTGCCCCCA 61.494 61.111 0.00 0.00 0.00 4.96
1979 2100 2.983592 CACAGAACCGTTGCCCCC 60.984 66.667 0.00 0.00 0.00 5.40
1980 2101 2.112297 TCACAGAACCGTTGCCCC 59.888 61.111 0.00 0.00 0.00 5.80
1981 2102 2.604174 CGTCACAGAACCGTTGCCC 61.604 63.158 0.00 0.00 0.00 5.36
2104 2225 1.525619 GGTTTCTTCGTCACAGAACCG 59.474 52.381 0.00 0.00 29.70 4.44
2122 2243 0.108329 CTACCGCCAACGATCTTGGT 60.108 55.000 19.00 5.35 43.93 3.67
2129 2250 2.642254 CCAGTCCTACCGCCAACGA 61.642 63.158 0.00 0.00 43.93 3.85
2132 2253 2.288025 GGTCCAGTCCTACCGCCAA 61.288 63.158 0.00 0.00 0.00 4.52
2145 2270 3.000819 CTGTGGCGGTAGGGTCCA 61.001 66.667 0.00 0.00 0.00 4.02
2186 2311 3.009115 ACAGGCCATGGCGGTAGT 61.009 61.111 29.90 21.00 43.06 2.73
2213 2338 1.629297 GGGAGAGGAGGGACCAGAT 59.371 63.158 0.00 0.00 42.04 2.90


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

AutoCloner maintained by Alex Coulton.