Multiple sequence alignment - TraesCS7B01G147100

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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 TraesCS7B01G147100 chr7B 100.000 3170 0 0 1 3170 192803502 192800333 0.000000e+00 5854.0
1 TraesCS7B01G147100 chr7B 90.897 2296 189 7 876 3170 552706186 552703910 0.000000e+00 3064.0
2 TraesCS7B01G147100 chr7B 90.810 2296 189 8 876 3170 552753174 552750900 0.000000e+00 3051.0
3 TraesCS7B01G147100 chr7B 86.667 150 17 3 399 547 189689063 189688916 2.530000e-36 163.0
4 TraesCS7B01G147100 chr5B 91.573 2302 190 3 872 3170 348580251 348577951 0.000000e+00 3173.0
5 TraesCS7B01G147100 chr5A 91.541 1785 142 6 1386 3170 71136085 71137860 0.000000e+00 2451.0
6 TraesCS7B01G147100 chr5A 83.333 228 34 4 389 614 576591091 576590866 1.150000e-49 207.0
7 TraesCS7B01G147100 chr6B 85.683 2284 315 9 892 3170 87507254 87504978 0.000000e+00 2396.0
8 TraesCS7B01G147100 chr6B 94.650 1327 70 1 876 2202 151413897 151412572 0.000000e+00 2056.0
9 TraesCS7B01G147100 chr6B 95.052 970 48 0 2201 3170 151390000 151389031 0.000000e+00 1526.0
10 TraesCS7B01G147100 chr6B 76.565 2236 468 45 877 3084 478890193 478887986 0.000000e+00 1175.0
11 TraesCS7B01G147100 chr4A 88.068 1299 145 4 877 2173 676919844 676918554 0.000000e+00 1531.0
12 TraesCS7B01G147100 chr4A 87.992 966 115 1 2205 3170 676918258 676917294 0.000000e+00 1140.0
13 TraesCS7B01G147100 chr3B 94.306 966 54 1 2205 3170 766175612 766174648 0.000000e+00 1478.0
14 TraesCS7B01G147100 chr3B 94.602 352 19 0 1826 2177 766176280 766175929 2.150000e-151 545.0
15 TraesCS7B01G147100 chr2B 92.060 932 73 1 1273 2203 534688099 534689030 0.000000e+00 1310.0
16 TraesCS7B01G147100 chr2B 77.140 1986 418 32 886 2856 751298110 751296146 0.000000e+00 1120.0
17 TraesCS7B01G147100 chr2B 84.492 187 21 7 399 579 248151854 248152038 9.040000e-41 178.0
18 TraesCS7B01G147100 chr7A 93.257 697 39 8 1 695 221675222 221675912 0.000000e+00 1020.0
19 TraesCS7B01G147100 chr7A 92.771 166 12 0 697 862 221675954 221676119 1.140000e-59 241.0
20 TraesCS7B01G147100 chr7D 95.089 448 18 4 1 447 208543794 208544238 0.000000e+00 702.0
21 TraesCS7B01G147100 chr7D 92.841 433 30 1 2739 3170 615914337 615913905 7.460000e-176 627.0
22 TraesCS7B01G147100 chr7D 96.139 259 8 2 440 697 208544456 208544713 3.780000e-114 422.0
23 TraesCS7B01G147100 chr7D 94.904 157 8 0 697 853 208544753 208544909 2.440000e-61 246.0
24 TraesCS7B01G147100 chr6A 81.046 612 88 19 45 645 80648896 80648302 2.230000e-126 462.0
25 TraesCS7B01G147100 chr6D 81.198 601 81 28 64 650 62882671 62882089 3.730000e-124 455.0
26 TraesCS7B01G147100 chr1A 83.209 268 34 9 32 295 577864129 577864389 5.290000e-58 235.0
27 TraesCS7B01G147100 chr1B 82.778 180 23 5 430 605 222990860 222991035 1.520000e-33 154.0
28 TraesCS7B01G147100 chr1D 77.005 187 32 10 397 577 201531451 201531270 2.600000e-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 TraesCS7B01G147100 chr7B 192800333 192803502 3169 True 5854.000000 5854 100.000000 1 3170 1 chr7B.!!$R2 3169
1 TraesCS7B01G147100 chr7B 552703910 552706186 2276 True 3064.000000 3064 90.897000 876 3170 1 chr7B.!!$R3 2294
2 TraesCS7B01G147100 chr7B 552750900 552753174 2274 True 3051.000000 3051 90.810000 876 3170 1 chr7B.!!$R4 2294
3 TraesCS7B01G147100 chr5B 348577951 348580251 2300 True 3173.000000 3173 91.573000 872 3170 1 chr5B.!!$R1 2298
4 TraesCS7B01G147100 chr5A 71136085 71137860 1775 False 2451.000000 2451 91.541000 1386 3170 1 chr5A.!!$F1 1784
5 TraesCS7B01G147100 chr6B 87504978 87507254 2276 True 2396.000000 2396 85.683000 892 3170 1 chr6B.!!$R1 2278
6 TraesCS7B01G147100 chr6B 151412572 151413897 1325 True 2056.000000 2056 94.650000 876 2202 1 chr6B.!!$R3 1326
7 TraesCS7B01G147100 chr6B 151389031 151390000 969 True 1526.000000 1526 95.052000 2201 3170 1 chr6B.!!$R2 969
8 TraesCS7B01G147100 chr6B 478887986 478890193 2207 True 1175.000000 1175 76.565000 877 3084 1 chr6B.!!$R4 2207
9 TraesCS7B01G147100 chr4A 676917294 676919844 2550 True 1335.500000 1531 88.030000 877 3170 2 chr4A.!!$R1 2293
10 TraesCS7B01G147100 chr3B 766174648 766176280 1632 True 1011.500000 1478 94.454000 1826 3170 2 chr3B.!!$R1 1344
11 TraesCS7B01G147100 chr2B 534688099 534689030 931 False 1310.000000 1310 92.060000 1273 2203 1 chr2B.!!$F2 930
12 TraesCS7B01G147100 chr2B 751296146 751298110 1964 True 1120.000000 1120 77.140000 886 2856 1 chr2B.!!$R1 1970
13 TraesCS7B01G147100 chr7A 221675222 221676119 897 False 630.500000 1020 93.014000 1 862 2 chr7A.!!$F1 861
14 TraesCS7B01G147100 chr7D 208543794 208544909 1115 False 456.666667 702 95.377333 1 853 3 chr7D.!!$F1 852
15 TraesCS7B01G147100 chr6A 80648302 80648896 594 True 462.000000 462 81.046000 45 645 1 chr6A.!!$R1 600
16 TraesCS7B01G147100 chr6D 62882089 62882671 582 True 455.000000 455 81.198000 64 650 1 chr6D.!!$R1 586

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
825 1107 1.066143 GTCAGGTCATTGGGATCACGT 60.066 52.381 0.0 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2615 3205 0.684535 TTCTGAACGCATGGTCCTCA 59.315 50.0 0.0 0.0 0.0 3.86 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
87 88 9.952030 AACTTTGAAAGAACAAAAATCCCTAAA 57.048 25.926 12.53 0.00 38.90 1.85
95 96 6.714810 AGAACAAAAATCCCTAAATTTTGCCC 59.285 34.615 9.42 3.38 44.08 5.36
119 120 4.103153 TGTGCCCATTACAAATCCCAAAAA 59.897 37.500 0.00 0.00 0.00 1.94
622 863 7.605410 TTTTATTCTGTAGACCGTGGAATTC 57.395 36.000 0.00 0.00 0.00 2.17
767 1049 6.821160 ACCAATTAACTGGAACTTTTGTTTGG 59.179 34.615 10.51 1.67 43.66 3.28
782 1064 7.933033 ACTTTTGTTTGGCATGATGATTAAAGT 59.067 29.630 0.00 0.95 0.00 2.66
811 1093 3.624777 CCCATCAAATAGCTTGTCAGGT 58.375 45.455 0.00 0.00 36.34 4.00
822 1104 2.618816 GCTTGTCAGGTCATTGGGATCA 60.619 50.000 0.00 0.00 0.00 2.92
825 1107 1.066143 GTCAGGTCATTGGGATCACGT 60.066 52.381 0.00 0.00 0.00 4.49
862 1144 9.095065 GTTCTAGCGAACTAAATCATTCCTTAA 57.905 33.333 0.00 0.00 44.80 1.85
863 1145 9.832445 TTCTAGCGAACTAAATCATTCCTTAAT 57.168 29.630 0.00 0.00 0.00 1.40
910 1193 1.278413 GCCTAGGGTTTTCTTCCTCGT 59.722 52.381 11.72 0.00 34.75 4.18
913 1196 1.430992 AGGGTTTTCTTCCTCGTGGA 58.569 50.000 1.10 1.10 41.36 4.02
1110 1394 6.602406 AGCTAGATCTAAACGACAAGGAGTTA 59.398 38.462 3.57 0.00 0.00 2.24
1135 1419 5.641789 TGATGTGGAGATTGATGAGGAAT 57.358 39.130 0.00 0.00 0.00 3.01
1165 1449 0.535102 CAAGGAAAGCGTGAGGTGGT 60.535 55.000 0.00 0.00 43.76 4.16
1209 1493 0.765510 ACAAAACCTTCTCTCCGGCT 59.234 50.000 0.00 0.00 0.00 5.52
1258 1544 1.472728 GGAATCCGACGCAACCAGTAT 60.473 52.381 0.00 0.00 0.00 2.12
1353 1639 2.440599 GGGCCCTGGCTCTTTCAA 59.559 61.111 17.04 0.00 38.85 2.69
1384 1670 4.238514 GGTCCTTATGTGCTCGTATGATC 58.761 47.826 3.23 0.00 0.00 2.92
1470 1758 2.498885 ACCGGATCCCTACTGTAAACAC 59.501 50.000 9.46 0.00 0.00 3.32
1690 1979 7.148086 GCAAATTCTGTGGTCTAATTGGACATA 60.148 37.037 21.72 8.81 37.91 2.29
1783 2072 2.053865 CCTAACCACCCGCGTCCTA 61.054 63.158 4.92 0.00 0.00 2.94
1838 2127 0.250901 ACGAAGAACAATGGCAGCCT 60.251 50.000 14.15 0.00 0.00 4.58
1966 2256 8.776061 AGAAGCTAGGAAGAGACTTAATATGT 57.224 34.615 0.00 0.00 0.00 2.29
2143 2433 0.827925 TGAGATATCGGCGGCTTCCT 60.828 55.000 7.21 0.00 0.00 3.36
2160 2450 2.599281 TGTGAGGAAGACCGCCGA 60.599 61.111 0.00 0.00 41.83 5.54
2173 2463 2.612212 GACCGCCGAACACAATGAATAT 59.388 45.455 0.00 0.00 0.00 1.28
2308 2898 7.736893 AGTATCAGTTAAAGTGGAGAAGTTGT 58.263 34.615 0.00 0.00 0.00 3.32
2348 2938 3.576078 AGGATTTCATGGCGTGGATAA 57.424 42.857 6.90 0.00 0.00 1.75
2502 3092 0.339162 TCTATGGTGAACCCCGGGTA 59.661 55.000 21.85 0.79 33.12 3.69
2615 3205 0.255033 TGGCAGCATGAGCATCTCTT 59.745 50.000 11.88 0.00 45.49 2.85
2656 3246 0.392461 TCAGATGGTGGCGTTTAGGC 60.392 55.000 0.00 0.00 46.95 3.93
2677 3267 3.386237 GCCTGGAGGTCTGCGAGT 61.386 66.667 0.00 0.00 37.57 4.18
2866 3458 2.368548 CCCGTGGTGATTATGATGGAGA 59.631 50.000 0.00 0.00 0.00 3.71
2880 3472 1.361204 TGGAGAGGATGCAAGACCAA 58.639 50.000 9.88 0.00 0.00 3.67
2950 3542 1.874129 AACCCTACCGGATGTGATCA 58.126 50.000 9.46 0.00 34.64 2.92
3124 3716 2.981400 ACAAAATTTAGGTGCGGACG 57.019 45.000 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 8.551205 GGATTTTTGTTCTTTCAAAGTTGGATC 58.449 33.333 0.00 0.00 38.32 3.36
95 96 2.455557 TGGGATTTGTAATGGGCACAG 58.544 47.619 0.00 0.00 0.00 3.66
344 351 9.790344 AAATTGACATGGTCCAAATAATGAAAA 57.210 25.926 0.00 0.00 0.00 2.29
383 391 6.212388 TGGTGTAATTAGTGAATTTGCCCATT 59.788 34.615 0.00 0.00 36.62 3.16
395 403 9.832445 AATAGAACTACCATGGTGTAATTAGTG 57.168 33.333 28.17 8.10 0.00 2.74
508 744 3.517296 TGCCATGGTCTACCTGAAAAA 57.483 42.857 14.67 0.00 36.82 1.94
622 863 7.251704 TCAAAGAAGTTGCTAGACAAAGAAG 57.748 36.000 0.00 0.00 40.82 2.85
767 1049 4.457257 GCCTCCCTACTTTAATCATCATGC 59.543 45.833 0.00 0.00 0.00 4.06
782 1064 1.705186 GCTATTTGATGGGCCTCCCTA 59.295 52.381 4.53 0.00 45.70 3.53
811 1093 0.695924 ACCCAACGTGATCCCAATGA 59.304 50.000 0.00 0.00 0.00 2.57
822 1104 2.567985 CTAGAACAAACCACCCAACGT 58.432 47.619 0.00 0.00 0.00 3.99
825 1107 1.141254 TCGCTAGAACAAACCACCCAA 59.859 47.619 0.00 0.00 0.00 4.12
862 1144 6.338937 AGCGAAGAGGAACGTTTTCTAATAT 58.661 36.000 14.28 2.27 31.71 1.28
863 1145 5.717119 AGCGAAGAGGAACGTTTTCTAATA 58.283 37.500 14.28 0.00 31.71 0.98
864 1146 4.566987 AGCGAAGAGGAACGTTTTCTAAT 58.433 39.130 14.28 3.14 31.71 1.73
865 1147 3.985925 GAGCGAAGAGGAACGTTTTCTAA 59.014 43.478 14.28 0.00 31.71 2.10
866 1148 3.005050 TGAGCGAAGAGGAACGTTTTCTA 59.995 43.478 14.28 0.00 31.71 2.10
867 1149 2.223971 TGAGCGAAGAGGAACGTTTTCT 60.224 45.455 0.46 6.34 31.71 2.52
868 1150 2.096860 GTGAGCGAAGAGGAACGTTTTC 60.097 50.000 0.46 3.85 0.00 2.29
869 1151 1.865340 GTGAGCGAAGAGGAACGTTTT 59.135 47.619 0.46 0.00 0.00 2.43
870 1152 1.499049 GTGAGCGAAGAGGAACGTTT 58.501 50.000 0.46 0.00 0.00 3.60
1110 1394 6.009908 TCCTCATCAATCTCCACATCATTT 57.990 37.500 0.00 0.00 0.00 2.32
1135 1419 1.476833 GCTTTCCTTGATGCCGGGATA 60.477 52.381 9.09 0.00 0.00 2.59
1258 1544 1.182385 GGGCCAACCGAATGAAACCA 61.182 55.000 4.39 0.00 36.48 3.67
1267 1553 0.923358 AATCTATTGGGGCCAACCGA 59.077 50.000 4.39 0.00 41.60 4.69
1352 1638 2.491693 CACATAAGGACCGCCATGTTTT 59.508 45.455 6.06 0.00 30.65 2.43
1353 1639 2.091541 CACATAAGGACCGCCATGTTT 58.908 47.619 6.06 0.00 30.65 2.83
1384 1670 3.119990 ACATCATCCGCTTTGGTAAAACG 60.120 43.478 0.00 0.00 39.52 3.60
1470 1758 1.670590 GAGCCTCTCCATGATCCCG 59.329 63.158 0.00 0.00 0.00 5.14
1709 1998 6.016860 CAGTTTCTTCTGATCATGAACACCAA 60.017 38.462 0.00 0.00 37.61 3.67
1838 2127 1.053424 AGGAACCAACGGAGCACTTA 58.947 50.000 0.00 0.00 0.00 2.24
1966 2256 5.245977 TCAGAACATCATCACCAGAGTTGTA 59.754 40.000 0.00 0.00 0.00 2.41
2143 2433 2.204461 TTCGGCGGTCTTCCTCACA 61.204 57.895 7.21 0.00 0.00 3.58
2160 2450 7.943079 TCCAGAACATGATATTCATTGTGTT 57.057 32.000 0.00 0.00 34.28 3.32
2173 2463 1.271543 CCCAGCAGTTCCAGAACATGA 60.272 52.381 12.76 0.00 43.47 3.07
2308 2898 1.699730 TTCAGACCGAGTCTCCAACA 58.300 50.000 3.87 0.00 41.37 3.33
2348 2938 2.200081 AGCCACCACTTCTACCATCAT 58.800 47.619 0.00 0.00 0.00 2.45
2502 3092 4.342951 TCCCACATACGGTATCGATTTTCT 59.657 41.667 1.71 0.00 40.11 2.52
2615 3205 0.684535 TTCTGAACGCATGGTCCTCA 59.315 50.000 0.00 0.00 0.00 3.86
2656 3246 2.046507 GCAGACCTCCAGGCAGTG 60.047 66.667 0.00 0.00 39.32 3.66
2677 3267 0.693049 GAGAAGCCAAGGTCCTCCAA 59.307 55.000 0.00 0.00 35.89 3.53
2866 3458 0.957395 CGCTGTTGGTCTTGCATCCT 60.957 55.000 0.00 0.00 0.00 3.24
3124 3716 0.608035 TTGGACCGGATTTCAGCACC 60.608 55.000 9.46 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.