Multiple sequence alignment - TraesCS1A01G398700

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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 TraesCS1A01G398700 chr1A 100.000 2477 0 0 1 2477 563721766 563724242 0.000000e+00 4575
1 TraesCS1A01G398700 chr4A 92.507 2042 128 14 456 2477 718636584 718638620 0.000000e+00 2900
2 TraesCS1A01G398700 chr2B 88.374 2030 201 21 456 2463 651668661 651666645 0.000000e+00 2409
3 TraesCS1A01G398700 chr2B 90.661 439 38 3 8 445 651669575 651669139 4.590000e-162 580
4 TraesCS1A01G398700 chr3B 87.769 2044 199 22 456 2463 26458406 26460434 0.000000e+00 2342
5 TraesCS1A01G398700 chr3B 86.997 1838 193 24 456 2259 750387441 750385616 0.000000e+00 2028
6 TraesCS1A01G398700 chr3B 85.664 1430 171 20 558 1966 728847983 728849399 0.000000e+00 1474
7 TraesCS1A01G398700 chr3B 90.828 447 36 5 1 445 26457484 26457927 5.900000e-166 593
8 TraesCS1A01G398700 chr1B 87.769 1995 204 26 492 2463 178500056 178498079 0.000000e+00 2296
9 TraesCS1A01G398700 chr4B 88.661 1905 183 18 579 2463 524158400 524156509 0.000000e+00 2290
10 TraesCS1A01G398700 chr4B 89.910 446 42 3 1 445 524159722 524159279 2.760000e-159 571
11 TraesCS1A01G398700 chr7B 87.613 1994 207 27 492 2463 74784505 74782530 0.000000e+00 2278
12 TraesCS1A01G398700 chr7B 87.852 1029 102 16 348 1359 88124339 88125361 0.000000e+00 1186
13 TraesCS1A01G398700 chr7B 91.599 857 66 6 1406 2259 88125357 88126210 0.000000e+00 1179
14 TraesCS1A01G398700 chr7B 88.991 436 45 3 11 445 74785439 74785006 1.010000e-148 536
15 TraesCS1A01G398700 chr7B 93.631 157 10 0 2321 2477 88126210 88126366 4.120000e-58 235
16 TraesCS1A01G398700 chr6B 87.161 1994 215 27 492 2463 113014199 113016173 0.000000e+00 2226
17 TraesCS1A01G398700 chr6B 88.117 446 50 3 1 445 113013256 113013699 6.070000e-146 527
18 TraesCS1A01G398700 chr3A 92.296 1350 78 11 456 1788 562968726 562967386 0.000000e+00 1893
19 TraesCS1A01G398700 chr3A 94.382 445 22 3 2 445 562969647 562969205 0.000000e+00 680
20 TraesCS1A01G398700 chr6D 89.672 1433 125 12 555 1966 413785637 413787067 0.000000e+00 1805
21 TraesCS1A01G398700 chr5D 89.191 1434 132 13 555 1966 327276743 327278175 0.000000e+00 1768
22 TraesCS1A01G398700 chr5D 87.116 1366 152 14 552 1894 231583185 231584549 0.000000e+00 1526
23 TraesCS1A01G398700 chr5D 88.547 358 37 3 89 445 327275456 327275810 4.890000e-117 431
24 TraesCS1A01G398700 chr5B 89.192 1027 85 18 348 1355 50316452 50315433 0.000000e+00 1258
25 TraesCS1A01G398700 chr5B 92.765 857 53 7 1406 2259 50315433 50314583 0.000000e+00 1230
26 TraesCS1A01G398700 chr7A 89.828 639 62 3 1829 2465 299550277 299550914 0.000000e+00 817
27 TraesCS1A01G398700 chr7A 93.197 441 27 3 1 440 8443523 8443961 0.000000e+00 645
28 TraesCS1A01G398700 chr6A 95.067 446 20 2 1 445 30113701 30113257 0.000000e+00 701
29 TraesCS1A01G398700 chr6A 89.961 259 21 2 2211 2465 30113065 30112808 1.840000e-86 329


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 TraesCS1A01G398700 chr1A 563721766 563724242 2476 False 4575.000000 4575 100.000000 1 2477 1 chr1A.!!$F1 2476
1 TraesCS1A01G398700 chr4A 718636584 718638620 2036 False 2900.000000 2900 92.507000 456 2477 1 chr4A.!!$F1 2021
2 TraesCS1A01G398700 chr2B 651666645 651669575 2930 True 1494.500000 2409 89.517500 8 2463 2 chr2B.!!$R1 2455
3 TraesCS1A01G398700 chr3B 750385616 750387441 1825 True 2028.000000 2028 86.997000 456 2259 1 chr3B.!!$R1 1803
4 TraesCS1A01G398700 chr3B 728847983 728849399 1416 False 1474.000000 1474 85.664000 558 1966 1 chr3B.!!$F1 1408
5 TraesCS1A01G398700 chr3B 26457484 26460434 2950 False 1467.500000 2342 89.298500 1 2463 2 chr3B.!!$F2 2462
6 TraesCS1A01G398700 chr1B 178498079 178500056 1977 True 2296.000000 2296 87.769000 492 2463 1 chr1B.!!$R1 1971
7 TraesCS1A01G398700 chr4B 524156509 524159722 3213 True 1430.500000 2290 89.285500 1 2463 2 chr4B.!!$R1 2462
8 TraesCS1A01G398700 chr7B 74782530 74785439 2909 True 1407.000000 2278 88.302000 11 2463 2 chr7B.!!$R1 2452
9 TraesCS1A01G398700 chr7B 88124339 88126366 2027 False 866.666667 1186 91.027333 348 2477 3 chr7B.!!$F1 2129
10 TraesCS1A01G398700 chr6B 113013256 113016173 2917 False 1376.500000 2226 87.639000 1 2463 2 chr6B.!!$F1 2462
11 TraesCS1A01G398700 chr3A 562967386 562969647 2261 True 1286.500000 1893 93.339000 2 1788 2 chr3A.!!$R1 1786
12 TraesCS1A01G398700 chr6D 413785637 413787067 1430 False 1805.000000 1805 89.672000 555 1966 1 chr6D.!!$F1 1411
13 TraesCS1A01G398700 chr5D 231583185 231584549 1364 False 1526.000000 1526 87.116000 552 1894 1 chr5D.!!$F1 1342
14 TraesCS1A01G398700 chr5D 327275456 327278175 2719 False 1099.500000 1768 88.869000 89 1966 2 chr5D.!!$F2 1877
15 TraesCS1A01G398700 chr5B 50314583 50316452 1869 True 1244.000000 1258 90.978500 348 2259 2 chr5B.!!$R1 1911
16 TraesCS1A01G398700 chr7A 299550277 299550914 637 False 817.000000 817 89.828000 1829 2465 1 chr7A.!!$F2 636
17 TraesCS1A01G398700 chr6A 30112808 30113701 893 True 515.000000 701 92.514000 1 2465 2 chr6A.!!$R1 2464

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
55 56 1.169577 TCGTGTGTTGTTGTGCCTTT 58.830 45.0 0.00 0.0 0.00 3.11 F
1289 2462 0.752658 TGGGATATCCAGCGTGACAG 59.247 55.0 23.27 0.0 41.46 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1440 2613 0.036732 CAGCTGGTGGTGGCTTCTTA 59.963 55.000 5.57 0.0 37.97 2.10 R
2274 3483 3.054655 ACACGGTCCAATAGCTACCAAAT 60.055 43.478 0.00 0.0 32.55 2.32 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
55 56 1.169577 TCGTGTGTTGTTGTGCCTTT 58.830 45.000 0.00 0.00 0.00 3.11
85 86 3.525199 AGCAAGGATTCCACTAAGATGGT 59.475 43.478 5.29 0.00 40.95 3.55
87 88 4.706962 GCAAGGATTCCACTAAGATGGTTT 59.293 41.667 5.29 0.00 40.95 3.27
132 134 1.529244 GTTGCACCCAGCCAAGACT 60.529 57.895 0.00 0.00 44.83 3.24
146 148 2.415090 CCAAGACTATTTGCTGTGCTGC 60.415 50.000 0.00 0.00 0.00 5.25
147 149 2.189594 AGACTATTTGCTGTGCTGCA 57.810 45.000 0.00 0.00 41.65 4.41
148 150 2.719739 AGACTATTTGCTGTGCTGCAT 58.280 42.857 5.27 0.00 42.96 3.96
184 186 6.609237 ATGTTCATCGAAATGTGTATCCTG 57.391 37.500 0.00 0.00 34.32 3.86
215 217 6.994421 TGCCATGTAATACTAGGATTCTCA 57.006 37.500 2.60 5.76 0.00 3.27
237 239 8.267183 TCTCATTTTACCTTATGATGAGAGCAA 58.733 33.333 9.56 0.00 44.50 3.91
276 278 5.384063 TTGGTTACATCCGTACGAACTAA 57.616 39.130 18.76 13.49 0.00 2.24
281 283 4.445452 ACATCCGTACGAACTAACATGT 57.555 40.909 18.76 9.52 0.00 3.21
317 320 9.593134 CTCTTAGCTAATTTTCTAGAGCAAGAA 57.407 33.333 6.64 0.00 37.40 2.52
782 1937 3.243569 CCGGTGTTTACAAAATGGCAAGA 60.244 43.478 0.00 0.00 0.00 3.02
958 2115 4.563374 CCCTTTAATCAGCCAAACCCAAAG 60.563 45.833 0.00 0.00 0.00 2.77
1036 2208 6.558771 ACAACATCGATGATGAAGAACAAA 57.441 33.333 34.01 0.00 42.09 2.83
1098 2270 5.047566 TGGAACAAGATGAGGAAGAACAA 57.952 39.130 0.00 0.00 31.92 2.83
1127 2300 2.567862 TGGGAATGTTGGTGAGGGATA 58.432 47.619 0.00 0.00 0.00 2.59
1269 2442 1.064463 CATGCACATGTCCCCTTAGGT 60.064 52.381 0.00 0.00 36.75 3.08
1289 2462 0.752658 TGGGATATCCAGCGTGACAG 59.247 55.000 23.27 0.00 41.46 3.51
1440 2613 5.049612 CGAGAAGCATATTCAAGCATGTGAT 60.050 40.000 0.00 0.00 0.00 3.06
1557 2744 7.686938 CGTTCGGACTTGAACAATAATAAAGTC 59.313 37.037 7.33 5.50 46.77 3.01
1873 3070 2.239654 TCTTTGATCTCCTCCGCCAATT 59.760 45.455 0.00 0.00 0.00 2.32
1904 3103 4.858850 TCCTACTAATCCGTGTTACAGGA 58.141 43.478 6.62 6.34 41.30 3.86
2128 3329 4.816984 GCAGCAGCCAGGCCTCAT 62.817 66.667 8.22 0.00 33.58 2.90
2146 3347 4.462508 TCATGCGTTGAGAGAGAAAGAT 57.537 40.909 0.00 0.00 0.00 2.40
2274 3483 8.035165 ACGCACAAATAGACAACATTATAACA 57.965 30.769 0.00 0.00 0.00 2.41
2301 3510 4.339247 GGTAGCTATTGGACCGTGTACTTA 59.661 45.833 0.00 0.00 0.00 2.24
2405 3630 8.858003 AGAATACACAATATTCTCACGTAGTG 57.142 34.615 3.80 0.00 42.99 2.74
2443 3669 5.225642 TGACATAGATGATGATCGTGAAGC 58.774 41.667 7.39 0.00 39.06 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 2.335011 GTCCCGCAAAGGCACAAC 59.665 61.111 0.00 0.00 41.24 3.32
47 48 2.594303 CTGTCCCGCAAAGGCACA 60.594 61.111 0.00 0.00 41.24 4.57
55 56 1.377202 GAATCCTTGCTGTCCCGCA 60.377 57.895 0.00 0.00 38.31 5.69
85 86 0.923358 ACCACCCTCAGACCAACAAA 59.077 50.000 0.00 0.00 0.00 2.83
87 88 1.754380 CGACCACCCTCAGACCAACA 61.754 60.000 0.00 0.00 0.00 3.33
170 172 6.203723 GGCATCTAGAACAGGATACACATTTC 59.796 42.308 0.00 0.00 41.41 2.17
184 186 8.123639 TCCTAGTATTACATGGCATCTAGAAC 57.876 38.462 16.15 5.72 0.00 3.01
215 217 6.830324 TGCTTGCTCTCATCATAAGGTAAAAT 59.170 34.615 0.00 0.00 0.00 1.82
225 227 4.959560 ATCTAGTGCTTGCTCTCATCAT 57.040 40.909 0.23 0.00 0.00 2.45
237 239 9.686683 ATGTAACCAAAAGAATAATCTAGTGCT 57.313 29.630 0.00 0.00 33.77 4.40
276 278 4.223923 AGCTAAGAGCCTTACTTGACATGT 59.776 41.667 0.00 0.00 43.77 3.21
281 283 8.322091 AGAAAATTAGCTAAGAGCCTTACTTGA 58.678 33.333 12.54 0.00 43.77 3.02
499 1031 4.156373 ACGAGGTTTGTTTCTTCCGAAAAA 59.844 37.500 0.00 0.00 40.57 1.94
503 1035 2.607631 ACGAGGTTTGTTTCTTCCGA 57.392 45.000 0.00 0.00 0.00 4.55
504 1036 3.991773 TCATACGAGGTTTGTTTCTTCCG 59.008 43.478 0.00 0.00 0.00 4.30
813 1969 1.358877 TGTGATTCGGCGTGATCAAG 58.641 50.000 22.79 4.06 0.00 3.02
958 2115 0.464452 AGGGTGTTAGAGCGGTATGC 59.536 55.000 0.00 0.00 46.98 3.14
1036 2208 2.553247 GGTGCAGCTCCCTAGTTTCTTT 60.553 50.000 9.07 0.00 0.00 2.52
1098 2270 1.683011 CCAACATTCCCATCTCGGCTT 60.683 52.381 0.00 0.00 0.00 4.35
1127 2300 4.207891 AGTTTCTTACATCTCGGTGCAT 57.792 40.909 0.00 0.00 0.00 3.96
1269 2442 1.138859 CTGTCACGCTGGATATCCCAA 59.861 52.381 19.34 0.10 46.07 4.12
1289 2462 2.203480 TTGCTGCACTTGACCCCC 60.203 61.111 0.00 0.00 0.00 5.40
1440 2613 0.036732 CAGCTGGTGGTGGCTTCTTA 59.963 55.000 5.57 0.00 37.97 2.10
1557 2744 7.491372 AGCATGCATAAATGAACTGAAAATGAG 59.509 33.333 21.98 0.00 0.00 2.90
1873 3070 4.753610 CACGGATTAGTAGGATCGTAGTGA 59.246 45.833 12.10 5.29 31.69 3.41
1904 3103 2.305927 ACAATGGAGGGAAGTCAACGAT 59.694 45.455 0.00 0.00 0.00 3.73
2128 3329 5.358160 TCATCTATCTTTCTCTCTCAACGCA 59.642 40.000 0.00 0.00 0.00 5.24
2274 3483 3.054655 ACACGGTCCAATAGCTACCAAAT 60.055 43.478 0.00 0.00 32.55 2.32
2287 3496 9.273016 GTAATAGTAGTATAAGTACACGGTCCA 57.727 37.037 0.00 0.00 33.09 4.02
2301 3510 6.222389 AGAGCACGTCTCGTAATAGTAGTAT 58.778 40.000 8.66 0.00 46.44 2.12
2398 3623 9.332502 TGTCAAATAATATAATTGCCACTACGT 57.667 29.630 0.00 0.00 0.00 3.57
2423 3649 7.009357 CACATAGCTTCACGATCATCATCTATG 59.991 40.741 0.00 12.44 37.76 2.23
2439 3665 8.954950 ATATATCATGCCTAACACATAGCTTC 57.045 34.615 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.