Multiple sequence alignment - TraesCS2B01G463800

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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 TraesCS2B01G463800 chr2B 100.000 4330 0 0 1 4330 657789633 657793962 0.000000e+00 7997.0
1 TraesCS2B01G463800 chr2A 96.254 3631 102 18 1 3628 692753538 692757137 0.000000e+00 5921.0
2 TraesCS2B01G463800 chr2A 91.618 346 20 3 3624 3963 692757183 692757525 1.820000e-128 470.0
3 TraesCS2B01G463800 chr2A 90.213 235 12 3 4107 4330 692757534 692757768 3.270000e-76 296.0
4 TraesCS2B01G463800 chr2A 77.612 134 27 1 1795 1928 692707663 692707793 1.290000e-10 78.7
5 TraesCS2B01G463800 chr2A 90.000 50 3 2 3627 3675 297253203 297253251 3.610000e-06 63.9
6 TraesCS2B01G463800 chr2D 95.933 3639 111 16 1 3628 552139880 552143492 0.000000e+00 5866.0
7 TraesCS2B01G463800 chr2D 91.040 692 33 10 3664 4330 552143495 552144182 0.000000e+00 907.0
8 TraesCS2B01G463800 chr2D 80.872 711 129 5 2662 3370 551932707 551933412 1.760000e-153 553.0
9 TraesCS2B01G463800 chr6A 95.745 47 1 1 3617 3662 426639338 426639384 1.670000e-09 75.0
10 TraesCS2B01G463800 chr7B 97.619 42 1 0 3622 3663 482484996 482485037 6.010000e-09 73.1
11 TraesCS2B01G463800 chr5A 92.157 51 3 1 3627 3677 332288520 332288471 2.160000e-08 71.3
12 TraesCS2B01G463800 chr7D 92.000 50 3 1 3624 3673 571471668 571471716 7.770000e-08 69.4
13 TraesCS2B01G463800 chr6B 93.617 47 2 1 3617 3662 458576552 458576506 7.770000e-08 69.4
14 TraesCS2B01G463800 chr3D 87.719 57 5 1 3608 3662 7428376 7428432 1.010000e-06 65.8
15 TraesCS2B01G463800 chr4B 88.679 53 5 1 3610 3662 235384228 235384177 3.610000e-06 63.9


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 TraesCS2B01G463800 chr2B 657789633 657793962 4329 False 7997.0 7997 100.0000 1 4330 1 chr2B.!!$F1 4329
1 TraesCS2B01G463800 chr2A 692753538 692757768 4230 False 2229.0 5921 92.6950 1 4330 3 chr2A.!!$F3 4329
2 TraesCS2B01G463800 chr2D 552139880 552144182 4302 False 3386.5 5866 93.4865 1 4330 2 chr2D.!!$F2 4329
3 TraesCS2B01G463800 chr2D 551932707 551933412 705 False 553.0 553 80.8720 2662 3370 1 chr2D.!!$F1 708

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
856 858 5.716228 AGATCAGTCCATATCTAAGAGGCTG 59.284 44.0 0.00 0.0 30.65 4.85 F
1653 1656 0.459489 TGCCGCAAAATTATGGGCTC 59.541 50.0 10.04 0.0 44.07 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2120 2131 0.819259 TGGTGTTGCCACTTCTGAGC 60.819 55.000 0.00 0.0 43.61 4.26 R
3411 3424 3.228453 ACTTTCCTCACGGACAGAACTA 58.772 45.455 1.83 0.0 39.07 2.24 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
151 152 8.417780 TCATTTTTGTGTGACAACCAAATTAG 57.582 30.769 2.77 0.00 37.90 1.73
486 487 5.863397 TGCTACTAAACATTTTGCTGATTGC 59.137 36.000 0.00 0.00 43.25 3.56
852 854 7.177216 AGCTCAAGATCAGTCCATATCTAAGAG 59.823 40.741 0.00 0.00 37.46 2.85
856 858 5.716228 AGATCAGTCCATATCTAAGAGGCTG 59.284 44.000 0.00 0.00 30.65 4.85
1253 1256 2.281761 GGATATGCCGCCAGTGGG 60.282 66.667 12.15 0.59 37.18 4.61
1299 1302 3.896888 TCTGCACCATTCAAGACCAAATT 59.103 39.130 0.00 0.00 0.00 1.82
1572 1575 7.344612 AGTGGATTAATGTACACTAGTGATCCA 59.655 37.037 29.30 26.85 41.95 3.41
1653 1656 0.459489 TGCCGCAAAATTATGGGCTC 59.541 50.000 10.04 0.00 44.07 4.70
1725 1728 7.010771 TCGGAGGAGATCTTTTTCAGGATATA 58.989 38.462 0.00 0.00 0.00 0.86
1767 1770 0.710588 TACTGGAGGGCAGAAGAGGA 59.289 55.000 0.00 0.00 0.00 3.71
1785 1788 2.173996 AGGAAAGGGTGAGTTCGGAAAA 59.826 45.455 0.00 0.00 0.00 2.29
1833 1836 2.380249 TGAGAGAGAGAGGAGGGAACAA 59.620 50.000 0.00 0.00 0.00 2.83
1836 1839 2.758423 GAGAGAGAGGAGGGAACAACTC 59.242 54.545 0.00 0.00 36.11 3.01
1854 1857 7.582435 ACAACTCAATGTGAAGTATAAGACG 57.418 36.000 0.00 0.00 30.82 4.18
1875 1878 3.127030 CGTTAAGAATGCTCTTCCCCAAC 59.873 47.826 0.00 0.00 41.19 3.77
1920 1923 7.092137 TCATCATTTTGCACATTTAGGAGAG 57.908 36.000 0.00 0.00 0.00 3.20
2054 2058 1.001378 CAGGCCACTTTCCAGTTTTCG 60.001 52.381 5.01 0.00 0.00 3.46
2065 2069 5.640189 TTCCAGTTTTCGTTGGTTTTGTA 57.360 34.783 0.00 0.00 35.89 2.41
2068 2072 6.631962 TCCAGTTTTCGTTGGTTTTGTAAAT 58.368 32.000 0.00 0.00 35.89 1.40
2107 2118 8.208718 TGAATAACTTCACCCATTTATTCTCG 57.791 34.615 11.98 0.00 39.83 4.04
2120 2131 6.455113 CCATTTATTCTCGGTGTGTTAAGACG 60.455 42.308 0.00 0.00 0.00 4.18
2164 2175 6.561519 AGTACTATGCAGTCCAATAAACCT 57.438 37.500 0.00 0.00 36.14 3.50
2171 2182 3.366374 GCAGTCCAATAAACCTGTGCTTC 60.366 47.826 0.00 0.00 0.00 3.86
2191 2202 8.603181 GTGCTTCATAAAACATCAACAAAAACT 58.397 29.630 0.00 0.00 0.00 2.66
2296 2307 2.225467 AGTTCTTCAAGCTCTGTTGCC 58.775 47.619 0.00 0.00 0.00 4.52
2360 2371 5.530519 TTGACATGAAATAGTTGCTCGTC 57.469 39.130 0.00 0.00 0.00 4.20
2389 2400 5.873732 GCTCTTTGCAGATACTTTTAGTGG 58.126 41.667 0.00 0.00 42.31 4.00
2397 2408 7.735917 TGCAGATACTTTTAGTGGCATACTAT 58.264 34.615 0.00 0.00 41.36 2.12
2421 2432 3.744660 ACCCCATTTATCTTGATCGAGC 58.255 45.455 4.94 0.00 0.00 5.03
2438 2449 4.002982 TCGAGCGTGTTAGTACCTTCTAA 58.997 43.478 0.00 0.00 0.00 2.10
2608 2619 8.352201 CACTTCCTGATTTACTCAATGAAAACA 58.648 33.333 0.00 0.00 32.14 2.83
3085 3096 6.752285 TTCCATCTTGAGATCATCCATGTA 57.248 37.500 0.00 0.00 31.21 2.29
3190 3203 3.809905 GAACTCCTTTCCCGATATTGCT 58.190 45.455 0.00 0.00 0.00 3.91
3210 3223 7.920160 TTGCTGATTGTCATTGACAGTAATA 57.080 32.000 18.27 5.20 43.69 0.98
3370 3383 8.376270 AGTAACTATTTGAAGAAGTGCCTAGTT 58.624 33.333 0.00 0.00 33.90 2.24
3386 3399 4.630676 GCCTAGTTTACTACTCTCCCTGGA 60.631 50.000 0.00 0.00 38.33 3.86
3402 3415 4.159879 TCCCTGGAGAGAGTCGTAATTTTC 59.840 45.833 0.00 0.00 0.00 2.29
3411 3424 8.664211 AGAGAGTCGTAATTTTCTTTTCTGTT 57.336 30.769 0.00 0.00 0.00 3.16
3414 3427 9.543783 AGAGTCGTAATTTTCTTTTCTGTTAGT 57.456 29.630 0.00 0.00 0.00 2.24
3481 3495 3.454447 TGCCTTTACCATTAGCTAGCTCA 59.546 43.478 23.26 11.58 0.00 4.26
3487 3501 7.500559 CCTTTACCATTAGCTAGCTCAGAAAAT 59.499 37.037 23.26 12.25 0.00 1.82
3488 3502 8.438676 TTTACCATTAGCTAGCTCAGAAAATC 57.561 34.615 23.26 0.00 0.00 2.17
3516 3531 2.436417 TCTGGCATGCCTTAACTGTTC 58.564 47.619 35.53 7.29 36.94 3.18
3575 3590 4.973168 TGACTCTTTGCCTCAGTATTTGT 58.027 39.130 0.00 0.00 0.00 2.83
3591 3606 9.076781 TCAGTATTTGTTTCCATCATCTTTTCA 57.923 29.630 0.00 0.00 0.00 2.69
3634 3699 9.237846 GTTGGCTTCAAAATATAGTAAATCAGC 57.762 33.333 0.00 0.00 31.46 4.26
3728 3794 5.238650 TCTTTTACAGAAAGTGGCTTAGTGC 59.761 40.000 0.00 0.00 41.94 4.40
3743 3809 1.730547 GTGCGTTGCATTCACTGGC 60.731 57.895 0.00 0.00 41.91 4.85
3768 3834 7.920151 GCATCAGTATCACATCTCATAGGATAC 59.080 40.741 0.00 0.00 40.19 2.24
3809 3875 4.583871 ACTTCGCAGAGATCCAAAATCTT 58.416 39.130 0.00 0.00 38.43 2.40
3936 4015 8.311650 TGTCTTAGCTACAAGATGAGAAAAAC 57.688 34.615 2.33 0.00 36.93 2.43
3940 4019 6.707599 AGCTACAAGATGAGAAAAACGTAC 57.292 37.500 0.00 0.00 0.00 3.67
3941 4020 6.220930 AGCTACAAGATGAGAAAAACGTACA 58.779 36.000 0.00 0.00 0.00 2.90
3948 4027 6.161381 AGATGAGAAAAACGTACAACGGTAT 58.839 36.000 4.32 0.00 42.91 2.73
3963 4042 6.235664 ACAACGGTATGGTCTTACATTCTTT 58.764 36.000 0.00 0.00 32.39 2.52
3986 4065 2.092968 GTCCCATGCCATCACAGAGTTA 60.093 50.000 0.00 0.00 0.00 2.24
3989 4068 1.945394 CATGCCATCACAGAGTTAGGC 59.055 52.381 0.00 0.00 42.32 3.93
4006 4085 2.625906 CCACGAGCAACACACACG 59.374 61.111 0.00 0.00 0.00 4.49
4081 4161 1.069204 GATCAGCATCCTTACCTCGCA 59.931 52.381 0.00 0.00 0.00 5.10
4186 4266 3.737172 CCCCGCAACGGCAAAGAG 61.737 66.667 0.00 0.00 46.86 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
151 152 2.109425 AGCGGTAAGTCATGAAACCC 57.891 50.000 14.42 9.22 0.00 4.11
460 461 6.573664 ATCAGCAAAATGTTTAGTAGCACA 57.426 33.333 0.00 0.00 0.00 4.57
486 487 3.195610 TCAACTACCACATGCTCAGTAGG 59.804 47.826 13.43 0.00 37.18 3.18
787 789 7.687941 AATTACTTGCAGTGCACTTACTAAT 57.312 32.000 19.58 10.71 38.71 1.73
852 854 4.875544 TCGAATAACAAATACAGCAGCC 57.124 40.909 0.00 0.00 0.00 4.85
856 858 7.920738 AGAGGAAATCGAATAACAAATACAGC 58.079 34.615 0.00 0.00 0.00 4.40
1194 1197 1.065199 TGATGCTGGAGGTGGTTGATC 60.065 52.381 0.00 0.00 0.00 2.92
1253 1256 0.824759 AGTATCCCAGGTCGCAGTTC 59.175 55.000 0.00 0.00 0.00 3.01
1299 1302 4.099419 TCTTCGCTAAGCTGATGGTTGATA 59.901 41.667 0.00 0.00 35.36 2.15
1572 1575 1.633432 TGGTACCCTAACTGCAATGCT 59.367 47.619 10.07 0.00 0.00 3.79
1653 1656 2.573462 TCTTTCATCCTCACTGGGGAAG 59.427 50.000 0.39 0.00 36.37 3.46
1725 1728 5.503927 ACAGTATCAAATTGCCTGTCATCT 58.496 37.500 6.86 0.00 30.94 2.90
1767 1770 2.173996 TCCTTTTCCGAACTCACCCTTT 59.826 45.455 0.00 0.00 0.00 3.11
1785 1788 5.601662 GCAAAGTTAGCTTTTCCTTTTCCT 58.398 37.500 1.27 0.00 42.54 3.36
1833 1836 9.355215 CTTAACGTCTTATACTTCACATTGAGT 57.645 33.333 0.00 0.00 0.00 3.41
1854 1857 3.444034 GGTTGGGGAAGAGCATTCTTAAC 59.556 47.826 2.22 5.27 43.63 2.01
1875 1878 3.223674 ACAAGACAAACCTTGGTAGGG 57.776 47.619 8.29 0.00 46.58 3.53
2094 2098 5.878116 TCTTAACACACCGAGAATAAATGGG 59.122 40.000 0.00 0.00 0.00 4.00
2107 2118 2.433868 TCTGAGCGTCTTAACACACC 57.566 50.000 0.00 0.00 0.00 4.16
2120 2131 0.819259 TGGTGTTGCCACTTCTGAGC 60.819 55.000 0.00 0.00 43.61 4.26
2164 2175 8.386606 GTTTTTGTTGATGTTTTATGAAGCACA 58.613 29.630 0.00 0.00 0.00 4.57
2171 2182 9.782028 CGAATGAGTTTTTGTTGATGTTTTATG 57.218 29.630 0.00 0.00 0.00 1.90
2191 2202 3.814842 ACAGATGACAGTTTTGCGAATGA 59.185 39.130 0.00 0.00 0.00 2.57
2341 2352 3.367932 CACGACGAGCAACTATTTCATGT 59.632 43.478 0.00 0.00 0.00 3.21
2342 2353 3.782250 GCACGACGAGCAACTATTTCATG 60.782 47.826 12.54 0.00 0.00 3.07
2383 2394 6.773583 ATGGGGTAAATAGTATGCCACTAA 57.226 37.500 0.00 0.00 43.00 2.24
2389 2400 9.515226 TCAAGATAAATGGGGTAAATAGTATGC 57.485 33.333 0.00 0.00 0.00 3.14
2397 2408 5.763204 GCTCGATCAAGATAAATGGGGTAAA 59.237 40.000 0.00 0.00 0.00 2.01
2577 2588 7.502226 TCATTGAGTAAATCAGGAAGTGTTGTT 59.498 33.333 0.00 0.00 39.68 2.83
2691 2702 8.807118 TGTCATTCTAGAGAACAGTTCTGTAAT 58.193 33.333 21.00 10.96 40.87 1.89
3085 3096 4.478317 TGATCACCAATAATCCCTCCAACT 59.522 41.667 0.00 0.00 0.00 3.16
3190 3203 9.631257 ATGGAATATTACTGTCAATGACAATCA 57.369 29.630 17.41 0.00 42.26 2.57
3210 3223 5.245301 CCTGCATTATTGTGGATGATGGAAT 59.755 40.000 0.00 0.00 32.93 3.01
3363 3376 3.637694 CCAGGGAGAGTAGTAAACTAGGC 59.362 52.174 0.00 0.00 39.07 3.93
3386 3399 8.664211 AACAGAAAAGAAAATTACGACTCTCT 57.336 30.769 0.00 0.00 0.00 3.10
3402 3415 5.047847 TCACGGACAGAACTAACAGAAAAG 58.952 41.667 0.00 0.00 0.00 2.27
3411 3424 3.228453 ACTTTCCTCACGGACAGAACTA 58.772 45.455 1.83 0.00 39.07 2.24
3414 3427 4.884668 ATAACTTTCCTCACGGACAGAA 57.115 40.909 1.83 0.00 39.07 3.02
3443 3457 6.603599 GGTAAAGGCAAAGTTCTCTCCAATAT 59.396 38.462 0.00 0.00 0.00 1.28
3444 3458 5.944007 GGTAAAGGCAAAGTTCTCTCCAATA 59.056 40.000 0.00 0.00 0.00 1.90
3445 3459 4.767409 GGTAAAGGCAAAGTTCTCTCCAAT 59.233 41.667 0.00 0.00 0.00 3.16
3461 3475 5.537300 TCTGAGCTAGCTAATGGTAAAGG 57.463 43.478 19.38 0.00 0.00 3.11
3575 3590 9.027202 TGAAATGAGATGAAAAGATGATGGAAA 57.973 29.630 0.00 0.00 0.00 3.13
3591 3606 5.021458 AGCCAACTCCAAATGAAATGAGAT 58.979 37.500 0.00 0.00 0.00 2.75
3634 3699 4.870426 CCCTCCGATCCATATTAATTGTCG 59.130 45.833 0.00 0.00 0.00 4.35
3728 3794 0.522626 TGATGCCAGTGAATGCAACG 59.477 50.000 0.00 0.00 41.50 4.10
3743 3809 9.187996 AGTATCCTATGAGATGTGATACTGATG 57.812 37.037 9.08 0.00 43.80 3.07
3768 3834 7.065894 GCGAAGTTTTCATATGCATGTAGTAG 58.934 38.462 10.16 0.00 33.57 2.57
3769 3835 6.536941 TGCGAAGTTTTCATATGCATGTAGTA 59.463 34.615 10.16 0.00 33.57 1.82
3770 3836 5.353956 TGCGAAGTTTTCATATGCATGTAGT 59.646 36.000 10.16 0.00 33.57 2.73
3809 3875 3.068024 CCCAGCTTGTAAAAGTTCTGCAA 59.932 43.478 0.00 0.00 0.00 4.08
3874 3945 1.656587 TGGGCGGCATATTCCTCTAT 58.343 50.000 12.47 0.00 0.00 1.98
3889 3960 4.535526 ATGGTTTTGACAACTATTGGGC 57.464 40.909 0.00 0.00 34.12 5.36
3936 4015 4.095410 TGTAAGACCATACCGTTGTACG 57.905 45.455 0.00 0.00 42.11 3.67
3940 4019 6.737254 AAAGAATGTAAGACCATACCGTTG 57.263 37.500 0.00 0.00 0.00 4.10
3941 4020 7.618137 ACTAAAGAATGTAAGACCATACCGTT 58.382 34.615 0.00 0.00 0.00 4.44
3948 4027 6.414732 CATGGGACTAAAGAATGTAAGACCA 58.585 40.000 0.00 0.00 0.00 4.02
3963 4042 1.764723 CTCTGTGATGGCATGGGACTA 59.235 52.381 3.81 0.00 0.00 2.59
3986 4065 2.591715 GTGTGTTGCTCGTGGCCT 60.592 61.111 3.32 0.00 40.92 5.19
3989 4068 2.625906 CGTGTGTGTTGCTCGTGG 59.374 61.111 0.00 0.00 0.00 4.94
4006 4085 3.757184 TGTCATACATTCGCATTGTTGC 58.243 40.909 0.00 0.00 45.78 4.17
4047 4127 4.268797 TGCTGATCTATTGCCATCTCTC 57.731 45.455 0.00 0.00 0.00 3.20
4081 4161 4.740822 GGACGCAGGGGCATTGGT 62.741 66.667 0.00 0.00 41.24 3.67
4185 4265 1.582968 CTGCAATTCGCTTGTGGCT 59.417 52.632 0.00 0.00 43.06 4.75
4186 4266 2.090524 GCTGCAATTCGCTTGTGGC 61.091 57.895 0.00 0.00 43.06 5.01


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

AutoCloner maintained by Alex Coulton.