Multiple sequence alignment - TraesCS3B01G242400

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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 TraesCS3B01G242400 chr3B 100.000 3034 0 0 1 3034 382316950 382319983 0.000000e+00 5603.0
1 TraesCS3B01G242400 chr3D 98.222 1406 13 3 1634 3034 290015632 290017030 0.000000e+00 2447.0
2 TraesCS3B01G242400 chr3D 98.385 991 12 2 649 1636 290014561 290015550 0.000000e+00 1738.0
3 TraesCS3B01G242400 chr3D 89.596 644 42 10 83 707 290012900 290013537 0.000000e+00 795.0
4 TraesCS3B01G242400 chr3D 85.920 348 32 2 225 555 31098953 31099300 3.720000e-94 355.0
5 TraesCS3B01G242400 chr3D 93.902 82 4 1 2 83 326701490 326701410 4.110000e-24 122.0
6 TraesCS3B01G242400 chr3D 100.000 40 0 0 700 739 290014517 290014556 1.170000e-09 75.0
7 TraesCS3B01G242400 chr3A 95.745 1457 46 5 1587 3034 381293299 381294748 0.000000e+00 2333.0
8 TraesCS3B01G242400 chr3A 98.013 755 15 0 799 1553 381292543 381293297 0.000000e+00 1312.0
9 TraesCS3B01G242400 chr3A 95.385 260 12 0 557 816 381292266 381292525 6.050000e-112 414.0
10 TraesCS3B01G242400 chr3A 86.577 149 13 6 83 224 381292133 381292281 1.130000e-34 158.0
11 TraesCS3B01G242400 chr3A 97.590 83 2 0 1 83 534189461 534189379 3.150000e-30 143.0
12 TraesCS3B01G242400 chr3A 94.048 84 4 1 1 84 213239443 213239361 3.180000e-25 126.0
13 TraesCS3B01G242400 chr3A 92.771 83 6 0 1 83 584094329 584094411 1.480000e-23 121.0
14 TraesCS3B01G242400 chr1D 86.969 353 28 3 225 559 334455369 334455721 6.140000e-102 381.0
15 TraesCS3B01G242400 chr1D 93.023 43 3 0 1549 1591 473785734 473785776 2.530000e-06 63.9
16 TraesCS3B01G242400 chr4B 86.932 352 28 3 225 559 168151591 168151941 2.210000e-101 379.0
17 TraesCS3B01G242400 chr4A 86.313 358 31 3 225 564 640912351 640912708 1.030000e-99 374.0
18 TraesCS3B01G242400 chr4A 85.933 327 27 4 251 558 32409911 32409585 6.270000e-87 331.0
19 TraesCS3B01G242400 chr4A 85.417 336 30 6 251 567 677125110 677125445 6.270000e-87 331.0
20 TraesCS3B01G242400 chr6A 85.795 352 33 4 225 559 49742703 49742352 1.030000e-94 357.0
21 TraesCS3B01G242400 chr2A 84.986 353 36 7 225 560 519349602 519349954 2.900000e-90 342.0
22 TraesCS3B01G242400 chr2A 97.727 44 1 0 1549 1592 31984558 31984601 3.240000e-10 76.8
23 TraesCS3B01G242400 chr7A 84.943 352 35 4 225 558 643253025 643253376 1.040000e-89 340.0
24 TraesCS3B01G242400 chr7A 84.375 352 36 5 225 558 635371383 635371033 8.110000e-86 327.0
25 TraesCS3B01G242400 chr7A 88.525 61 5 2 1538 1597 732036874 732036815 4.200000e-09 73.1
26 TraesCS3B01G242400 chr5A 84.286 350 38 3 225 557 404011843 404012192 2.920000e-85 326.0
27 TraesCS3B01G242400 chr5A 95.122 41 2 0 1549 1589 656937068 656937028 7.020000e-07 65.8
28 TraesCS3B01G242400 chr1B 85.366 328 30 3 251 560 363451112 363450785 1.050000e-84 324.0
29 TraesCS3B01G242400 chr1B 93.976 83 5 0 1 83 558549621 558549703 3.180000e-25 126.0
30 TraesCS3B01G242400 chr5D 81.654 387 35 7 206 558 435968279 435967895 3.830000e-74 289.0
31 TraesCS3B01G242400 chr5D 85.388 219 15 7 362 563 53873810 53874028 8.520000e-51 211.0
32 TraesCS3B01G242400 chr5D 97.674 43 1 0 1548 1590 173753662 173753620 1.170000e-09 75.0
33 TraesCS3B01G242400 chr6B 97.590 83 2 0 1 83 100869138 100869056 3.150000e-30 143.0
34 TraesCS3B01G242400 chr6B 91.489 47 2 1 1549 1593 678748021 678748067 2.530000e-06 63.9
35 TraesCS3B01G242400 chr5B 96.471 85 3 0 1 85 98504271 98504187 1.130000e-29 141.0
36 TraesCS3B01G242400 chr7D 93.902 82 3 2 2 83 88371717 88371638 4.110000e-24 122.0
37 TraesCS3B01G242400 chr4D 91.463 82 6 1 2 83 17255523 17255603 8.890000e-21 111.0
38 TraesCS3B01G242400 chr6D 94.340 53 2 1 1538 1590 469221232 469221283 2.510000e-11 80.5
39 TraesCS3B01G242400 chr1A 95.556 45 2 0 1549 1593 513890300 513890256 4.200000e-09 73.1


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 TraesCS3B01G242400 chr3B 382316950 382319983 3033 False 5603.00 5603 100.00000 1 3034 1 chr3B.!!$F1 3033
1 TraesCS3B01G242400 chr3D 290012900 290017030 4130 False 1263.75 2447 96.55075 83 3034 4 chr3D.!!$F2 2951
2 TraesCS3B01G242400 chr3A 381292133 381294748 2615 False 1054.25 2333 93.93000 83 3034 4 chr3A.!!$F2 2951

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
307 315 0.036388 GCTCATCCTCACGGTTTGGA 60.036 55.000 1.96 1.96 0.0 3.53 F
807 1914 1.154413 CGCATCACCAACGTCTTGC 60.154 57.895 0.00 0.00 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1179 2321 3.077556 CTCGGAGGGGTGGACAGG 61.078 72.222 0.0 0.0 0.0 4.00 R
2779 4017 2.427753 CGCCTCCCTATCCCAAGC 59.572 66.667 0.0 0.0 0.0 4.01 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
54 55 8.472007 TTCCTCTCTCTTCTATAAAGCTAAGG 57.528 38.462 0.00 0.00 0.00 2.69
55 56 7.588169 TCCTCTCTCTTCTATAAAGCTAAGGT 58.412 38.462 0.00 0.00 0.00 3.50
56 57 8.725256 TCCTCTCTCTTCTATAAAGCTAAGGTA 58.275 37.037 0.00 0.00 0.00 3.08
57 58 8.789762 CCTCTCTCTTCTATAAAGCTAAGGTAC 58.210 40.741 0.00 0.00 0.00 3.34
58 59 8.380743 TCTCTCTTCTATAAAGCTAAGGTACG 57.619 38.462 0.00 0.00 0.00 3.67
59 60 6.968250 TCTCTTCTATAAAGCTAAGGTACGC 58.032 40.000 0.00 0.00 0.00 4.42
60 61 6.016443 TCTCTTCTATAAAGCTAAGGTACGCC 60.016 42.308 0.00 0.00 0.00 5.68
75 76 3.782042 GCCTTTGGCGTACTCTCG 58.218 61.111 0.00 0.00 39.62 4.04
76 77 1.810030 GCCTTTGGCGTACTCTCGG 60.810 63.158 0.00 0.00 39.62 4.63
77 78 1.888018 CCTTTGGCGTACTCTCGGA 59.112 57.895 0.00 0.00 0.00 4.55
78 79 0.245539 CCTTTGGCGTACTCTCGGAA 59.754 55.000 0.00 0.00 0.00 4.30
79 80 1.337447 CCTTTGGCGTACTCTCGGAAA 60.337 52.381 0.00 0.00 0.00 3.13
80 81 2.409975 CTTTGGCGTACTCTCGGAAAA 58.590 47.619 0.00 0.00 0.00 2.29
81 82 2.529780 TTGGCGTACTCTCGGAAAAA 57.470 45.000 0.00 0.00 0.00 1.94
113 114 2.611292 GCATCTCAATGTAGTGGCTCAC 59.389 50.000 0.00 0.00 35.18 3.51
126 127 2.939103 GTGGCTCACATGTTAGCTAAGG 59.061 50.000 26.60 2.34 38.80 2.69
150 151 9.569122 AGGCTTGTAAGAATCTTAGTGTTTTTA 57.431 29.630 2.48 0.00 0.00 1.52
167 173 9.705290 AGTGTTTTTATGTTTTTGTTCTGTTCT 57.295 25.926 0.00 0.00 0.00 3.01
243 251 1.486310 TCAAGAAGAGTGGCGCCATAT 59.514 47.619 35.23 24.91 0.00 1.78
244 252 1.600957 CAAGAAGAGTGGCGCCATATG 59.399 52.381 35.23 18.68 0.00 1.78
255 263 1.228124 GCCATATGTAAGGCGCCCA 60.228 57.895 26.15 15.43 41.70 5.36
274 282 3.220110 CCACAGCTGCTTAATGGATGAT 58.780 45.455 15.27 0.00 31.69 2.45
281 289 1.541588 GCTTAATGGATGATTCCCGGC 59.458 52.381 0.00 0.00 41.83 6.13
282 290 2.815589 GCTTAATGGATGATTCCCGGCT 60.816 50.000 0.00 0.00 41.83 5.52
284 292 1.143813 AATGGATGATTCCCGGCTCT 58.856 50.000 0.00 0.00 41.83 4.09
294 302 2.279784 CCGGCTCTTCGGCTCATC 60.280 66.667 0.00 0.00 43.71 2.92
297 305 1.068921 GGCTCTTCGGCTCATCCTC 59.931 63.158 0.00 0.00 34.85 3.71
307 315 0.036388 GCTCATCCTCACGGTTTGGA 60.036 55.000 1.96 1.96 0.00 3.53
310 318 1.905894 TCATCCTCACGGTTTGGATCA 59.094 47.619 8.26 0.00 38.41 2.92
339 347 1.467342 GTTTTGGCGTGGTCCACTATC 59.533 52.381 19.82 9.35 35.50 2.08
355 363 4.700213 CCACTATCTTTTGTCGGGATGTTT 59.300 41.667 0.00 0.00 0.00 2.83
359 367 3.546724 TCTTTTGTCGGGATGTTTGTGA 58.453 40.909 0.00 0.00 0.00 3.58
393 401 2.289382 TGTGGTGTACAAGCATGACGAT 60.289 45.455 0.00 0.00 38.84 3.73
435 459 2.560861 CGGGTTGCACGTGATTGG 59.439 61.111 22.23 0.00 0.00 3.16
465 489 9.131791 GTAACCCAATTATGGTCTGATTGTATT 57.868 33.333 0.00 0.00 46.01 1.89
478 502 7.277098 GGTCTGATTGTATTAGTTTTAGCACGA 59.723 37.037 0.00 0.00 0.00 4.35
494 518 5.713822 AGCACGATTTTCCGTAGATTAAC 57.286 39.130 0.00 0.00 41.29 2.01
495 519 5.172934 AGCACGATTTTCCGTAGATTAACA 58.827 37.500 0.00 0.00 41.29 2.41
505 529 4.163458 TCCGTAGATTAACAGGGCAATTCT 59.837 41.667 0.00 0.00 0.00 2.40
506 530 4.881850 CCGTAGATTAACAGGGCAATTCTT 59.118 41.667 0.00 0.00 0.00 2.52
507 531 5.357032 CCGTAGATTAACAGGGCAATTCTTT 59.643 40.000 0.00 0.00 0.00 2.52
517 541 7.544804 ACAGGGCAATTCTTTTCTTCTTAAT 57.455 32.000 0.00 0.00 0.00 1.40
535 559 9.956720 CTTCTTAATTAATCGATGAGGCAATTT 57.043 29.630 0.00 0.00 0.00 1.82
807 1914 1.154413 CGCATCACCAACGTCTTGC 60.154 57.895 0.00 0.00 0.00 4.01
919 2061 1.990614 GCGTTCCCTCCTTCCCTCT 60.991 63.158 0.00 0.00 0.00 3.69
982 2124 2.693069 AGAGACAATCAAGAACGCCAG 58.307 47.619 0.00 0.00 0.00 4.85
1179 2321 4.785453 CCTCCCAAGACGCCAGCC 62.785 72.222 0.00 0.00 0.00 4.85
1338 2483 1.204113 AGAGGAAGGTGGCCAAGGAG 61.204 60.000 7.24 0.00 0.00 3.69
1699 2930 6.509418 TGTAATTAGTTCTTGGGCATGTTC 57.491 37.500 0.00 0.00 0.00 3.18
1745 2976 5.212532 TGGTGAAGTTGCTGCAAATTATT 57.787 34.783 25.45 13.98 31.79 1.40
2064 3295 2.264005 TGGCGGTGTTGTTCTGTATT 57.736 45.000 0.00 0.00 0.00 1.89
2065 3296 2.577700 TGGCGGTGTTGTTCTGTATTT 58.422 42.857 0.00 0.00 0.00 1.40
2066 3297 2.550606 TGGCGGTGTTGTTCTGTATTTC 59.449 45.455 0.00 0.00 0.00 2.17
2067 3298 2.812011 GGCGGTGTTGTTCTGTATTTCT 59.188 45.455 0.00 0.00 0.00 2.52
2068 3299 3.998341 GGCGGTGTTGTTCTGTATTTCTA 59.002 43.478 0.00 0.00 0.00 2.10
2069 3300 4.634443 GGCGGTGTTGTTCTGTATTTCTAT 59.366 41.667 0.00 0.00 0.00 1.98
2779 4017 4.619160 GCAAGGTTAGGGATCTTTTTGCAG 60.619 45.833 0.00 0.00 39.41 4.41
2863 4101 8.366401 TGAATAGCAAAAATGACCTCAAATTCA 58.634 29.630 0.00 0.00 0.00 2.57
2931 4170 3.550678 GTCCGAAGAGGTTAACAATAGCG 59.449 47.826 8.10 5.32 41.99 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 8.919145 CCTTAGCTTTATAGAAGAGAGAGGAAA 58.081 37.037 0.00 0.0 0.00 3.13
29 30 8.062536 ACCTTAGCTTTATAGAAGAGAGAGGAA 58.937 37.037 0.00 0.0 0.00 3.36
30 31 7.588169 ACCTTAGCTTTATAGAAGAGAGAGGA 58.412 38.462 0.00 0.0 0.00 3.71
31 32 7.833285 ACCTTAGCTTTATAGAAGAGAGAGG 57.167 40.000 0.00 0.0 0.00 3.69
32 33 8.500773 CGTACCTTAGCTTTATAGAAGAGAGAG 58.499 40.741 0.00 0.0 0.00 3.20
33 34 7.041235 GCGTACCTTAGCTTTATAGAAGAGAGA 60.041 40.741 0.00 0.0 0.00 3.10
34 35 7.079475 GCGTACCTTAGCTTTATAGAAGAGAG 58.921 42.308 0.00 0.0 0.00 3.20
35 36 6.016443 GGCGTACCTTAGCTTTATAGAAGAGA 60.016 42.308 0.00 0.0 0.00 3.10
36 37 6.151004 GGCGTACCTTAGCTTTATAGAAGAG 58.849 44.000 0.00 0.0 0.00 2.85
37 38 6.081872 GGCGTACCTTAGCTTTATAGAAGA 57.918 41.667 0.00 0.0 0.00 2.87
58 59 1.810030 CCGAGAGTACGCCAAAGGC 60.810 63.158 0.00 0.0 46.75 4.35
59 60 0.245539 TTCCGAGAGTACGCCAAAGG 59.754 55.000 0.00 0.0 0.00 3.11
60 61 2.074547 TTTCCGAGAGTACGCCAAAG 57.925 50.000 0.00 0.0 0.00 2.77
61 62 2.529780 TTTTCCGAGAGTACGCCAAA 57.470 45.000 0.00 0.0 0.00 3.28
62 63 2.529780 TTTTTCCGAGAGTACGCCAA 57.470 45.000 0.00 0.0 0.00 4.52
78 79 7.322664 ACATTGAGATGCCGATAAACATTTTT 58.677 30.769 0.00 0.0 36.72 1.94
79 80 6.866480 ACATTGAGATGCCGATAAACATTTT 58.134 32.000 0.00 0.0 36.72 1.82
80 81 6.455360 ACATTGAGATGCCGATAAACATTT 57.545 33.333 0.00 0.0 36.72 2.32
81 82 6.767902 ACTACATTGAGATGCCGATAAACATT 59.232 34.615 0.00 0.0 36.72 2.71
87 88 3.554960 GCCACTACATTGAGATGCCGATA 60.555 47.826 0.00 0.0 36.72 2.92
88 89 2.808202 GCCACTACATTGAGATGCCGAT 60.808 50.000 0.00 0.0 36.72 4.18
150 151 6.877236 ACAATCCAGAACAGAACAAAAACAT 58.123 32.000 0.00 0.0 0.00 2.71
255 263 3.887716 GGAATCATCCATTAAGCAGCTGT 59.112 43.478 16.64 0.0 45.79 4.40
281 289 0.248825 CGTGAGGATGAGCCGAAGAG 60.249 60.000 0.00 0.0 43.43 2.85
282 290 1.809869 CGTGAGGATGAGCCGAAGA 59.190 57.895 0.00 0.0 43.43 2.87
297 305 3.427909 CCACAATGATGATCCAAACCGTG 60.428 47.826 0.00 0.0 0.00 4.94
307 315 2.562298 ACGCCAAAACCACAATGATGAT 59.438 40.909 0.00 0.0 0.00 2.45
310 318 1.000731 CCACGCCAAAACCACAATGAT 59.999 47.619 0.00 0.0 0.00 2.45
339 347 3.628017 GTCACAAACATCCCGACAAAAG 58.372 45.455 0.00 0.0 0.00 2.27
355 363 2.099921 CCACAATTTTGAACCCGTCACA 59.900 45.455 0.00 0.0 35.39 3.58
359 367 2.104170 ACACCACAATTTTGAACCCGT 58.896 42.857 0.00 0.0 0.00 5.28
393 401 5.010213 GCAAACCCTCCTAACACACAATAAA 59.990 40.000 0.00 0.0 0.00 1.40
450 474 8.893727 GTGCTAAAACTAATACAATCAGACCAT 58.106 33.333 0.00 0.0 0.00 3.55
465 489 6.389091 TCTACGGAAAATCGTGCTAAAACTA 58.611 36.000 0.00 0.0 43.70 2.24
466 490 5.232463 TCTACGGAAAATCGTGCTAAAACT 58.768 37.500 0.00 0.0 43.70 2.66
478 502 4.850680 TGCCCTGTTAATCTACGGAAAAT 58.149 39.130 0.00 0.0 0.00 1.82
494 518 9.927668 TTAATTAAGAAGAAAAGAATTGCCCTG 57.072 29.630 0.00 0.0 0.00 4.45
505 529 9.173021 TGCCTCATCGATTAATTAAGAAGAAAA 57.827 29.630 3.94 0.0 0.00 2.29
506 530 8.731275 TGCCTCATCGATTAATTAAGAAGAAA 57.269 30.769 3.94 0.0 0.00 2.52
507 531 8.731275 TTGCCTCATCGATTAATTAAGAAGAA 57.269 30.769 3.94 0.0 0.00 2.52
585 610 5.518847 CACTTTTCTGAACGTGAGACTTACA 59.481 40.000 11.53 0.0 37.23 2.41
919 2061 0.323542 GACGGAGGGGAAGAGAGTGA 60.324 60.000 0.00 0.0 0.00 3.41
982 2124 0.319405 ATTGCTTGGTTTGAGCTGCC 59.681 50.000 0.00 0.0 40.75 4.85
1179 2321 3.077556 CTCGGAGGGGTGGACAGG 61.078 72.222 0.00 0.0 0.00 4.00
1338 2483 7.532682 CTTCTTCTTGAAGTATTCCTGTAGC 57.467 40.000 9.80 0.0 46.93 3.58
1745 2976 6.636454 AGTACATGAGGGGAAAAGAACATA 57.364 37.500 0.00 0.0 0.00 2.29
1865 3096 5.911752 TGCAGGAACAAGCAATCTTAAAAA 58.088 33.333 0.00 0.0 38.58 1.94
1866 3097 5.528043 TGCAGGAACAAGCAATCTTAAAA 57.472 34.783 0.00 0.0 38.58 1.52
2117 3353 8.668510 AAACTCAAGGATATAATAGTGTGCAG 57.331 34.615 0.00 0.0 0.00 4.41
2169 3405 6.332630 AGCTGGAAATTGGATTTTACATTCG 58.667 36.000 0.00 0.0 31.47 3.34
2779 4017 2.427753 CGCCTCCCTATCCCAAGC 59.572 66.667 0.00 0.0 0.00 4.01
2863 4101 9.582648 AGGTACATGGTGTTTTTAACTTATCTT 57.417 29.630 0.00 0.0 0.00 2.40


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

AutoCloner maintained by Alex Coulton.