Multiple sequence alignment - TraesCS6B01G154200

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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 TraesCS6B01G154200 chr6B 100.000 3458 0 0 1 3458 157780809 157777352 0.000000e+00 6386.0
1 TraesCS6B01G154200 chr6B 93.953 1356 71 6 784 2128 157911283 157912638 0.000000e+00 2039.0
2 TraesCS6B01G154200 chr6B 89.701 1340 104 10 2109 3425 157930704 157932032 0.000000e+00 1679.0
3 TraesCS6B01G154200 chr6B 78.771 1969 388 20 1034 2985 156418364 156416409 0.000000e+00 1293.0
4 TraesCS6B01G154200 chr6B 74.244 2446 556 52 901 3298 157900242 157902661 0.000000e+00 959.0
5 TraesCS6B01G154200 chr6B 91.030 602 36 13 197 788 157910643 157911236 0.000000e+00 797.0
6 TraesCS6B01G154200 chr6B 75.568 1629 348 38 1043 2653 157790317 157788721 0.000000e+00 758.0
7 TraesCS6B01G154200 chr6B 97.778 45 1 0 3414 3458 157932048 157932092 1.030000e-10 78.7
8 TraesCS6B01G154200 chr6D 94.727 2693 116 11 784 3458 82964830 82962146 0.000000e+00 4163.0
9 TraesCS6B01G154200 chr6D 79.091 1937 377 19 1034 2954 81750104 81748180 0.000000e+00 1308.0
10 TraesCS6B01G154200 chr6D 84.197 1177 171 7 1038 2211 81920692 81919528 0.000000e+00 1129.0
11 TraesCS6B01G154200 chr6D 92.791 541 14 6 1 517 82970395 82969856 0.000000e+00 760.0
12 TraesCS6B01G154200 chr6D 74.503 1510 342 30 1628 3121 46902106 46903588 1.760000e-172 616.0
13 TraesCS6B01G154200 chr6D 91.986 287 15 8 511 793 82965151 82964869 2.500000e-106 396.0
14 TraesCS6B01G154200 chr6D 91.667 48 2 2 465 511 467193755 467193709 8.010000e-07 65.8
15 TraesCS6B01G154200 chr6A 93.316 2693 154 11 784 3458 99787116 99784432 0.000000e+00 3952.0
16 TraesCS6B01G154200 chr6A 78.619 1969 391 20 1034 2985 98242378 98240423 0.000000e+00 1277.0
17 TraesCS6B01G154200 chr6A 76.637 2123 451 33 1026 3121 99795635 99793531 0.000000e+00 1131.0
18 TraesCS6B01G154200 chr6A 75.554 2258 479 58 904 3117 99931622 99929394 0.000000e+00 1044.0
19 TraesCS6B01G154200 chr6A 74.811 2116 489 36 1025 3117 100363390 100361296 0.000000e+00 915.0
20 TraesCS6B01G154200 chr6A 93.494 538 16 10 272 793 99787690 99787156 0.000000e+00 782.0
21 TraesCS6B01G154200 chr6A 95.257 253 11 1 2 254 99790336 99790085 1.930000e-107 399.0
22 TraesCS6B01G154200 chr5D 87.785 2677 264 32 784 3432 372060510 372057869 0.000000e+00 3073.0
23 TraesCS6B01G154200 chr5D 76.721 2251 463 35 904 3120 372064173 372061950 0.000000e+00 1197.0
24 TraesCS6B01G154200 chr5D 84.643 280 31 9 509 784 372060831 372060560 5.690000e-68 268.0
25 TraesCS6B01G154200 chr1B 92.593 54 1 2 462 513 410794015 410793963 1.330000e-09 75.0
26 TraesCS6B01G154200 chr1A 92.593 54 1 2 462 513 380947125 380947073 1.330000e-09 75.0
27 TraesCS6B01G154200 chr4D 97.500 40 1 0 472 511 394960655 394960694 6.190000e-08 69.4
28 TraesCS6B01G154200 chr2B 93.478 46 3 0 474 519 720478111 720478066 6.190000e-08 69.4
29 TraesCS6B01G154200 chr1D 97.500 40 1 0 472 511 238320678 238320717 6.190000e-08 69.4


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 TraesCS6B01G154200 chr6B 157777352 157780809 3457 True 6386.000000 6386 100.000000 1 3458 1 chr6B.!!$R2 3457
1 TraesCS6B01G154200 chr6B 157910643 157912638 1995 False 1418.000000 2039 92.491500 197 2128 2 chr6B.!!$F2 1931
2 TraesCS6B01G154200 chr6B 156416409 156418364 1955 True 1293.000000 1293 78.771000 1034 2985 1 chr6B.!!$R1 1951
3 TraesCS6B01G154200 chr6B 157900242 157902661 2419 False 959.000000 959 74.244000 901 3298 1 chr6B.!!$F1 2397
4 TraesCS6B01G154200 chr6B 157930704 157932092 1388 False 878.850000 1679 93.739500 2109 3458 2 chr6B.!!$F3 1349
5 TraesCS6B01G154200 chr6B 157788721 157790317 1596 True 758.000000 758 75.568000 1043 2653 1 chr6B.!!$R3 1610
6 TraesCS6B01G154200 chr6D 82962146 82965151 3005 True 2279.500000 4163 93.356500 511 3458 2 chr6D.!!$R5 2947
7 TraesCS6B01G154200 chr6D 81748180 81750104 1924 True 1308.000000 1308 79.091000 1034 2954 1 chr6D.!!$R1 1920
8 TraesCS6B01G154200 chr6D 81919528 81920692 1164 True 1129.000000 1129 84.197000 1038 2211 1 chr6D.!!$R2 1173
9 TraesCS6B01G154200 chr6D 82969856 82970395 539 True 760.000000 760 92.791000 1 517 1 chr6D.!!$R3 516
10 TraesCS6B01G154200 chr6D 46902106 46903588 1482 False 616.000000 616 74.503000 1628 3121 1 chr6D.!!$F1 1493
11 TraesCS6B01G154200 chr6A 99784432 99795635 11203 True 1566.000000 3952 89.676000 2 3458 4 chr6A.!!$R4 3456
12 TraesCS6B01G154200 chr6A 98240423 98242378 1955 True 1277.000000 1277 78.619000 1034 2985 1 chr6A.!!$R1 1951
13 TraesCS6B01G154200 chr6A 99929394 99931622 2228 True 1044.000000 1044 75.554000 904 3117 1 chr6A.!!$R2 2213
14 TraesCS6B01G154200 chr6A 100361296 100363390 2094 True 915.000000 915 74.811000 1025 3117 1 chr6A.!!$R3 2092
15 TraesCS6B01G154200 chr5D 372057869 372064173 6304 True 1512.666667 3073 83.049667 509 3432 3 chr5D.!!$R1 2923

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
290 299 0.252881 AGTGGAGCCAGGAGAATGGA 60.253 55.0 0.00 0.0 43.57 3.41 F
1055 9081 0.255318 CTGCTGATCTCCTTGGCCTT 59.745 55.0 3.32 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1101 9128 0.962489 ACGACAGACCACTGAGGAAG 59.038 55.0 0.00 0.0 46.03 3.46 R
2816 10860 0.675633 GGTTGTTCAATGCAGCTGGT 59.324 50.0 17.12 0.0 0.00 4.00 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
75 76 5.703592 ACTGAACTAATTAACAATCCGTGCA 59.296 36.000 0.00 0.00 0.00 4.57
136 137 5.278610 CCACACAAGCATCAAAAGATCAGAA 60.279 40.000 0.00 0.00 0.00 3.02
230 239 4.272504 CAGTTTACTTTGAACTGCTTCCGA 59.727 41.667 4.31 0.00 45.02 4.55
268 277 5.126869 CCACCAAATCCACAATAATAGTGCA 59.873 40.000 0.00 0.00 35.69 4.57
270 279 5.714333 ACCAAATCCACAATAATAGTGCACA 59.286 36.000 21.04 5.47 35.69 4.57
290 299 0.252881 AGTGGAGCCAGGAGAATGGA 60.253 55.000 0.00 0.00 43.57 3.41
321 330 3.753272 AGCAGCAAACGTAAACATCAGAT 59.247 39.130 0.00 0.00 0.00 2.90
463 483 6.449635 TTCACAATAATGCTTCCCATGTAC 57.550 37.500 0.00 0.00 33.49 2.90
472 492 5.791336 TGCTTCCCATGTACTACTATCAG 57.209 43.478 0.00 0.00 0.00 2.90
473 493 5.208890 TGCTTCCCATGTACTACTATCAGT 58.791 41.667 0.00 0.00 0.00 3.41
474 494 5.069119 TGCTTCCCATGTACTACTATCAGTG 59.931 44.000 0.00 0.00 0.00 3.66
476 496 6.710597 TTCCCATGTACTACTATCAGTGTC 57.289 41.667 0.00 0.00 0.00 3.67
477 497 5.762279 TCCCATGTACTACTATCAGTGTCA 58.238 41.667 0.00 0.00 0.00 3.58
501 526 7.669304 TCAGAAATGATCTTACATTTTGGGACA 59.331 33.333 0.00 0.00 46.18 4.02
699 8648 4.628963 ATTTAGTGAAGGTGGTAACGGT 57.371 40.909 0.00 0.00 42.51 4.83
744 8698 7.504922 TTGCGATATGCTGTTAAAATTCAAC 57.495 32.000 0.00 0.00 46.63 3.18
747 8701 7.758980 TGCGATATGCTGTTAAAATTCAACAAT 59.241 29.630 6.93 2.77 46.63 2.71
779 8733 7.870509 TCAAGGATGACCAGAAAAGATAATG 57.129 36.000 0.00 0.00 38.94 1.90
842 8845 2.368548 TGAACTAAGAAGCTGCTGGTGA 59.631 45.455 1.35 0.00 0.00 4.02
852 8855 2.427320 GCTGGTGAGCAGGTGTCA 59.573 61.111 14.04 0.00 45.46 3.58
868 8871 2.031157 GTGTCAGATTTTGTTGACCCCG 60.031 50.000 2.56 0.00 42.30 5.73
969 8983 2.608090 GCTTCCACGCTAGTTTCCATAC 59.392 50.000 0.00 0.00 0.00 2.39
972 8986 1.924524 CCACGCTAGTTTCCATACACG 59.075 52.381 0.00 0.00 0.00 4.49
977 8991 2.218759 GCTAGTTTCCATACACGATGCG 59.781 50.000 0.00 0.00 33.79 4.73
1001 9015 4.199310 CCACTCCATTTTCCATACACGAT 58.801 43.478 0.00 0.00 0.00 3.73
1055 9081 0.255318 CTGCTGATCTCCTTGGCCTT 59.745 55.000 3.32 0.00 0.00 4.35
1274 9302 1.299648 CATCCCTCGGCAACCTTGA 59.700 57.895 0.00 0.00 0.00 3.02
1536 9564 2.165030 GCTCAATGCCAGCAATAACAGT 59.835 45.455 0.00 0.00 36.82 3.55
2435 10472 4.526262 TGAAAATCAACCACCGGATCAATT 59.474 37.500 9.46 0.00 0.00 2.32
2561 10598 3.257127 AGTCAGAGAAGACTACAACCAGC 59.743 47.826 0.00 0.00 46.52 4.85
2567 10604 5.955355 AGAGAAGACTACAACCAGCTTAGAT 59.045 40.000 0.00 0.00 0.00 1.98
2655 10692 1.203928 CGAAGTGCTGGATCTAAGCG 58.796 55.000 13.79 0.00 43.88 4.68
2777 10821 1.337703 TGCAATCTCACAAACCTGCAC 59.662 47.619 0.00 0.00 35.02 4.57
2904 10948 2.171840 CTATCCCATACGGAGGTCAGG 58.828 57.143 0.00 0.00 46.60 3.86
2907 10951 0.909623 CCCATACGGAGGTCAGGTTT 59.090 55.000 0.00 0.00 0.00 3.27
3127 11177 2.167398 TTGCGCTAGGACTGTCCACC 62.167 60.000 27.48 14.04 39.61 4.61
3133 11183 1.827969 CTAGGACTGTCCACCTTCCAG 59.172 57.143 27.48 9.33 39.61 3.86
3269 11340 2.415168 TGAAGCGTGATTCCATTTCGTC 59.585 45.455 0.00 0.00 0.00 4.20
3373 11447 7.421530 TCCGTGTATTTTCTTCTTCTTTCAG 57.578 36.000 0.00 0.00 0.00 3.02
3374 11448 6.426937 TCCGTGTATTTTCTTCTTCTTTCAGG 59.573 38.462 0.00 0.00 0.00 3.86
3375 11449 6.426937 CCGTGTATTTTCTTCTTCTTTCAGGA 59.573 38.462 0.00 0.00 0.00 3.86
3376 11450 7.041372 CCGTGTATTTTCTTCTTCTTTCAGGAA 60.041 37.037 0.00 0.00 0.00 3.36
3377 11451 8.342634 CGTGTATTTTCTTCTTCTTTCAGGAAA 58.657 33.333 0.00 0.00 0.00 3.13
3412 11486 8.283291 ACGAATTCTGTACTGAAACTTCAATTC 58.717 33.333 17.70 13.43 36.64 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 8.970691 AAGTTAAGAATCACATTTCCATTTCG 57.029 30.769 0.00 0.00 0.00 3.46
136 137 8.353423 AGTAGCAAAATCATTGATTACTTGGT 57.647 30.769 22.33 22.33 35.80 3.67
230 239 0.478072 TGGTGGTTGCCATCTGAACT 59.522 50.000 0.00 0.00 35.30 3.01
268 277 1.004044 CATTCTCCTGGCTCCACTTGT 59.996 52.381 0.00 0.00 0.00 3.16
270 279 0.622665 CCATTCTCCTGGCTCCACTT 59.377 55.000 0.00 0.00 0.00 3.16
472 492 7.756722 CCCAAAATGTAAGATCATTTCTGACAC 59.243 37.037 0.00 0.00 46.63 3.67
474 494 7.970614 GTCCCAAAATGTAAGATCATTTCTGAC 59.029 37.037 0.00 8.20 44.10 3.51
476 496 7.829725 TGTCCCAAAATGTAAGATCATTTCTG 58.170 34.615 0.00 6.36 44.10 3.02
477 497 7.890127 TCTGTCCCAAAATGTAAGATCATTTCT 59.110 33.333 0.00 0.00 44.10 2.52
501 526 4.528076 TGAGCAAGATAGTACTCCCTCT 57.472 45.455 0.00 0.00 0.00 3.69
603 8552 5.880054 AACAGGAAAATACGTGAATCCAG 57.120 39.130 0.00 0.36 32.47 3.86
699 8648 6.183360 CGCAATTAAACTTGAGCAGACATCTA 60.183 38.462 0.00 0.00 0.00 1.98
744 8698 4.644103 GTCATCCTTGACCCAATCATTG 57.356 45.455 0.00 0.00 45.45 2.82
777 8731 1.631405 TTGGCTGCCTGCTAAAACAT 58.369 45.000 21.03 0.00 39.21 2.71
778 8732 1.631405 ATTGGCTGCCTGCTAAAACA 58.369 45.000 21.03 0.00 45.05 2.83
779 8733 2.480244 GCTATTGGCTGCCTGCTAAAAC 60.480 50.000 21.03 0.00 45.05 2.43
815 8818 2.096019 GCAGCTTCTTAGTTCACACTGC 60.096 50.000 0.00 0.00 42.00 4.40
842 8845 3.316308 GTCAACAAAATCTGACACCTGCT 59.684 43.478 0.00 0.00 41.35 4.24
845 8848 3.222603 GGGTCAACAAAATCTGACACCT 58.777 45.455 4.74 0.00 43.11 4.00
852 8855 4.407365 AGAAATCGGGGTCAACAAAATCT 58.593 39.130 0.00 0.00 0.00 2.40
868 8871 6.889177 AGAGAATGAGGGGAAAGAAAGAAATC 59.111 38.462 0.00 0.00 0.00 2.17
969 8983 4.758251 TGGAGTGGCCGCATCGTG 62.758 66.667 20.59 0.00 40.66 4.35
972 8986 0.101219 GAAAATGGAGTGGCCGCATC 59.899 55.000 20.59 12.72 40.66 3.91
977 8991 2.427095 GTGTATGGAAAATGGAGTGGCC 59.573 50.000 0.00 0.00 37.10 5.36
1001 9015 6.147864 AGAAAGTTAATTTTCTGCTGCACA 57.852 33.333 21.23 0.00 43.75 4.57
1055 9081 0.257328 TGTGCAAGAACTGGTGGGAA 59.743 50.000 0.00 0.00 0.00 3.97
1101 9128 0.962489 ACGACAGACCACTGAGGAAG 59.038 55.000 0.00 0.00 46.03 3.46
1536 9564 1.074084 TCCGGTATTTGCCCAGTGAAA 59.926 47.619 0.00 0.00 0.00 2.69
1703 9732 5.936956 AGTAAGGAAGCATCAAAGAGTTCAG 59.063 40.000 0.00 0.00 0.00 3.02
2561 10598 2.573369 TCGAAGACCCTCGGATCTAAG 58.427 52.381 0.00 0.00 39.35 2.18
2567 10604 1.457346 GTAGTTCGAAGACCCTCGGA 58.543 55.000 0.00 0.00 39.35 4.55
2655 10692 7.775561 AGGGATCTCACCAGTTAATTTATTGTC 59.224 37.037 0.00 0.00 0.00 3.18
2777 10821 3.190744 TGTTGCTAGAGAAGTCCAGTACG 59.809 47.826 0.00 0.00 0.00 3.67
2816 10860 0.675633 GGTTGTTCAATGCAGCTGGT 59.324 50.000 17.12 0.00 0.00 4.00
2904 10948 7.158099 AGCTAGAATTTGGGAATGTGTAAAC 57.842 36.000 0.00 0.00 0.00 2.01
2907 10951 5.584649 CGAAGCTAGAATTTGGGAATGTGTA 59.415 40.000 0.00 0.00 0.00 2.90
3246 11317 3.120199 ACGAAATGGAATCACGCTTCAAG 60.120 43.478 0.00 0.00 0.00 3.02
3247 11318 2.811431 ACGAAATGGAATCACGCTTCAA 59.189 40.909 0.00 0.00 0.00 2.69
3373 11447 5.588240 ACAGAATTCGTTTTCCACTTTTCC 58.412 37.500 0.00 0.00 0.00 3.13
3374 11448 7.376072 CAGTACAGAATTCGTTTTCCACTTTTC 59.624 37.037 7.96 0.00 0.00 2.29
3375 11449 7.066525 TCAGTACAGAATTCGTTTTCCACTTTT 59.933 33.333 7.96 0.00 0.00 2.27
3376 11450 6.540914 TCAGTACAGAATTCGTTTTCCACTTT 59.459 34.615 7.96 0.00 0.00 2.66
3377 11451 6.053005 TCAGTACAGAATTCGTTTTCCACTT 58.947 36.000 7.96 0.00 0.00 3.16
3378 11452 5.607477 TCAGTACAGAATTCGTTTTCCACT 58.393 37.500 7.96 3.66 0.00 4.00
3379 11453 5.917541 TCAGTACAGAATTCGTTTTCCAC 57.082 39.130 7.96 1.82 0.00 4.02
3380 11454 6.540914 AGTTTCAGTACAGAATTCGTTTTCCA 59.459 34.615 1.13 0.00 0.00 3.53
3412 11486 4.534168 CATGAAGCAAAGTGAACTGTGAG 58.466 43.478 4.76 0.00 32.93 3.51


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

AutoCloner maintained by Alex Coulton.