Multiple sequence alignment - TraesCS6B01G357600

Loading Multiple Alignment...

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 TraesCS6B01G357600 chr6B 100.000 4229 0 0 1 4229 625782018 625777790 0.000000e+00 7810.0
1 TraesCS6B01G357600 chr6A 94.627 4262 173 28 1 4229 560035458 560031220 0.000000e+00 6551.0
2 TraesCS6B01G357600 chr6D 94.731 3910 144 26 1 3892 415030367 415026502 0.000000e+00 6023.0
3 TraesCS6B01G357600 chr7D 87.255 102 13 0 2603 2704 55252731 55252832 2.670000e-22 117.0
4 TraesCS6B01G357600 chr7D 87.255 102 13 0 2603 2704 55269813 55269914 2.670000e-22 117.0
5 TraesCS6B01G357600 chr1A 84.553 123 13 4 3739 3857 458568036 458567916 2.670000e-22 117.0
6 TraesCS6B01G357600 chr1A 85.057 87 13 0 3740 3826 369087183 369087269 5.820000e-14 89.8
7 TraesCS6B01G357600 chr5A 82.353 136 18 5 3709 3844 689927489 689927360 3.460000e-21 113.0
8 TraesCS6B01G357600 chr7A 86.275 102 14 0 2603 2704 59204447 59204548 1.240000e-20 111.0
9 TraesCS6B01G357600 chr3D 90.411 73 5 2 2633 2704 154180335 154180264 1.250000e-15 95.3
10 TraesCS6B01G357600 chr3B 83.654 104 13 4 2603 2704 226789214 226789315 1.250000e-15 95.3
11 TraesCS6B01G357600 chr2B 83.178 107 12 4 3719 3823 27921903 27921801 4.500000e-15 93.5
12 TraesCS6B01G357600 chr1D 85.393 89 13 0 3738 3826 296363128 296363216 4.500000e-15 93.5
13 TraesCS6B01G357600 chr1B 85.556 90 11 2 3738 3826 397817813 397817901 4.500000e-15 93.5
14 TraesCS6B01G357600 chr4A 83.871 93 14 1 3738 3829 580297851 580297759 2.090000e-13 87.9
15 TraesCS6B01G357600 chr3A 88.889 72 6 2 2633 2703 172964411 172964341 2.090000e-13 87.9


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 TraesCS6B01G357600 chr6B 625777790 625782018 4228 True 7810 7810 100.000 1 4229 1 chr6B.!!$R1 4228
1 TraesCS6B01G357600 chr6A 560031220 560035458 4238 True 6551 6551 94.627 1 4229 1 chr6A.!!$R1 4228
2 TraesCS6B01G357600 chr6D 415026502 415030367 3865 True 6023 6023 94.731 1 3892 1 chr6D.!!$R1 3891

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
582 589 1.944032 CTCCACGCATCACATGATCA 58.056 50.0 0.0 0.0 31.21 2.92 F
2192 2219 0.671251 GAGAGCAGTAGGATGTCCCG 59.329 60.0 0.0 0.0 40.87 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2379 2407 0.250124 ACCCGTCGTTCATCTGCAAA 60.25 50.000 0.0 0.0 0.0 3.68 R
3742 3781 1.400142 CCGTTCGATTTGCCATGCTAA 59.60 47.619 0.0 0.0 0.0 3.09 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
470 477 4.928263 TGTGTCATATTTTGGTGATGGGA 58.072 39.130 0.00 0.00 0.00 4.37
582 589 1.944032 CTCCACGCATCACATGATCA 58.056 50.000 0.00 0.00 31.21 2.92
655 662 2.203195 TGCACTGCACACACCCTC 60.203 61.111 0.00 0.00 31.71 4.30
690 698 7.445402 CCCTTCACCATTAATTCATCGATTAGT 59.555 37.037 0.00 0.00 0.00 2.24
835 843 6.485830 TGTGATAACAGGATTAAGAGAGGG 57.514 41.667 0.00 0.00 0.00 4.30
1313 1321 2.945398 GATGAGGAGAGCGACGGTGC 62.945 65.000 3.31 0.00 0.00 5.01
1314 1322 3.749064 GAGGAGAGCGACGGTGCA 61.749 66.667 3.31 0.00 37.31 4.57
1332 1340 1.075425 CAGGAACTCGCGCAGAAGAG 61.075 60.000 8.75 8.47 34.60 2.85
1447 1463 3.735746 GTGGTGCAACAAGTAGCAAATTC 59.264 43.478 5.70 0.00 41.93 2.17
1627 1643 2.109126 GGCCGCTTACCAGAAGCAG 61.109 63.158 9.73 0.00 43.15 4.24
1734 1760 7.492994 GCTAATTAAGCTTCAACACTAGCTAGT 59.507 37.037 20.95 20.95 46.53 2.57
1758 1784 7.284716 AGTTAAGCTAGGCCATTAACCAATTAC 59.715 37.037 20.32 4.55 39.24 1.89
1763 1790 7.017651 AGCTAGGCCATTAACCAATTACTCTAT 59.982 37.037 5.01 0.00 0.00 1.98
1824 1851 3.554524 CATGGCGCCGTTAATTATTCTG 58.445 45.455 21.21 0.00 0.00 3.02
1854 1881 4.207165 ACACACCATAATTACCATCTGGC 58.793 43.478 2.54 0.00 39.32 4.85
1855 1882 3.569701 CACACCATAATTACCATCTGGCC 59.430 47.826 0.00 0.00 39.32 5.36
1856 1883 2.813754 CACCATAATTACCATCTGGCCG 59.186 50.000 0.00 0.00 39.32 6.13
1903 1930 4.813697 TCGAGTGTGATTTGATTTGTGTGA 59.186 37.500 0.00 0.00 0.00 3.58
2031 2058 2.737376 GTGGGAAGCGACGACACC 60.737 66.667 0.00 0.00 0.00 4.16
2192 2219 0.671251 GAGAGCAGTAGGATGTCCCG 59.329 60.000 0.00 0.00 40.87 5.14
2199 2226 3.993865 TAGGATGTCCCGGCCTGCA 62.994 63.158 7.75 0.00 40.87 4.41
2202 2229 3.405093 GATGTCCCGGCCTGCATCA 62.405 63.158 15.86 4.53 38.02 3.07
2366 2394 6.864165 CACTCTTCTTGGAGTACTAACAAGTC 59.136 42.308 26.47 4.15 43.75 3.01
2379 2407 4.997395 ACTAACAAGTCACAATTCGATGCT 59.003 37.500 0.00 0.00 0.00 3.79
2522 2552 2.978278 TGAGACCAAATTTGCCCCATTT 59.022 40.909 12.92 0.00 0.00 2.32
2523 2553 3.393941 TGAGACCAAATTTGCCCCATTTT 59.606 39.130 12.92 0.00 0.00 1.82
2567 2597 2.094659 GCCTGATCGTCACGTGTGG 61.095 63.158 16.51 8.81 0.00 4.17
2582 2612 2.173669 GTGGACCGTGCATGGATCG 61.174 63.158 31.74 9.51 0.00 3.69
2847 2877 2.294791 CTCTAGCTCCCAATACCACTCG 59.705 54.545 0.00 0.00 0.00 4.18
2958 2988 0.458543 CAGCGACGCACCTCAAGTAT 60.459 55.000 23.70 0.00 0.00 2.12
3215 3249 1.075536 GGGGGTGGTTGAATCACTTCT 59.924 52.381 8.65 0.00 35.61 2.85
3333 3367 0.611896 GGAGGGGAACACACATTGGG 60.612 60.000 0.00 0.00 0.00 4.12
3435 3469 9.128107 GGTAAATTACAACATTGATTCACTGTG 57.872 33.333 10.06 0.17 28.09 3.66
3446 3480 8.963725 ACATTGATTCACTGTGTCATCATTATT 58.036 29.630 19.16 8.98 0.00 1.40
3489 3523 6.153851 GCAAAATACTACCAAGGTGGGTAATT 59.846 38.462 7.54 5.05 43.37 1.40
3491 3525 8.590204 CAAAATACTACCAAGGTGGGTAATTTT 58.410 33.333 7.54 11.70 43.37 1.82
3506 3544 7.011016 GTGGGTAATTTTGGTTGCTATATTTGC 59.989 37.037 0.00 0.00 0.00 3.68
3590 3629 9.515226 AGAAAAATAAAGGTGCAACACTATCTA 57.485 29.630 3.64 0.00 39.98 1.98
3601 3640 7.553044 GGTGCAACACTATCTAGGAAAGTTTAT 59.447 37.037 0.00 0.00 39.98 1.40
3727 3766 7.382218 ACTTTTTGGATTTTGCTACAAATCGAG 59.618 33.333 0.00 0.00 36.53 4.04
3737 3776 4.042398 GCTACAAATCGAGCGTCTGATTA 58.958 43.478 0.00 0.00 33.85 1.75
3741 3780 6.422776 ACAAATCGAGCGTCTGATTATTTT 57.577 33.333 0.00 0.00 33.85 1.82
3742 3781 6.842163 ACAAATCGAGCGTCTGATTATTTTT 58.158 32.000 0.00 0.00 33.85 1.94
3771 3810 4.043073 GGCAAATCGAACGGTTTTTACAA 58.957 39.130 2.65 0.00 0.00 2.41
3817 3856 4.497300 GCAATTTCCTTTAGCAAGCATGA 58.503 39.130 0.00 0.00 0.00 3.07
3923 3962 6.144078 ACCTTTGACCACTAACAATGTTTC 57.856 37.500 3.17 0.00 0.00 2.78
3933 3972 9.405587 ACCACTAACAATGTTTCAAATATTTCG 57.594 29.630 3.17 0.00 0.00 3.46
3939 3978 9.912634 AACAATGTTTCAAATATTTCGACTGAT 57.087 25.926 0.00 0.00 0.00 2.90
4022 4073 7.050970 AGAAGTTTTGGTCAAAGGTAAATCC 57.949 36.000 0.00 0.00 0.00 3.01
4037 4088 6.415573 AGGTAAATCCTGTCAGTATCCAAAC 58.584 40.000 0.00 0.00 46.19 2.93
4057 4108 9.573166 TCCAAACCTAATATTTGTGATATGGAG 57.427 33.333 0.00 0.00 35.65 3.86
4059 4110 8.796475 CAAACCTAATATTTGTGATATGGAGGG 58.204 37.037 0.00 0.00 33.27 4.30
4060 4111 7.888514 ACCTAATATTTGTGATATGGAGGGA 57.111 36.000 0.00 0.00 0.00 4.20
4061 4112 7.922382 ACCTAATATTTGTGATATGGAGGGAG 58.078 38.462 0.00 0.00 0.00 4.30
4062 4113 7.517604 ACCTAATATTTGTGATATGGAGGGAGT 59.482 37.037 0.00 0.00 0.00 3.85
4069 4120 4.593206 TGTGATATGGAGGGAGTAACATCC 59.407 45.833 0.00 0.00 38.76 3.51
4075 4126 2.188817 GAGGGAGTAACATCCTGTGGT 58.811 52.381 0.00 0.00 39.50 4.16
4133 4184 3.891977 GCTCAAATCCCCTAATCCCTTTC 59.108 47.826 0.00 0.00 0.00 2.62
4134 4185 4.474394 CTCAAATCCCCTAATCCCTTTCC 58.526 47.826 0.00 0.00 0.00 3.13
4187 4241 3.788227 AGAATGGACTAAAGTGTGGCA 57.212 42.857 0.00 0.00 0.00 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 132 1.100463 TTGAGTTGCTTGAGCGGCAA 61.100 50.000 1.45 5.60 45.70 4.52
287 291 1.306997 CCCCTGGTGGCTTAGAGGA 60.307 63.158 0.00 0.00 0.00 3.71
288 292 0.326238 TACCCCTGGTGGCTTAGAGG 60.326 60.000 0.00 0.00 36.19 3.69
289 293 0.831307 GTACCCCTGGTGGCTTAGAG 59.169 60.000 0.00 0.00 36.19 2.43
291 295 2.170012 TAGTACCCCTGGTGGCTTAG 57.830 55.000 0.00 0.00 36.19 2.18
292 296 2.645951 TTAGTACCCCTGGTGGCTTA 57.354 50.000 0.00 0.00 36.19 3.09
294 298 1.981259 ATTTAGTACCCCTGGTGGCT 58.019 50.000 0.00 0.00 36.19 4.75
295 299 2.820728 AATTTAGTACCCCTGGTGGC 57.179 50.000 0.00 0.00 36.19 5.01
365 371 3.381136 GCAGGCCGGCCATTCAAA 61.381 61.111 45.13 0.00 38.92 2.69
413 420 5.178797 AGACTCGGTTTCCTTTCATACATG 58.821 41.667 0.00 0.00 0.00 3.21
470 477 4.385310 GCTACCATCACCCACCTTAATCTT 60.385 45.833 0.00 0.00 0.00 2.40
582 589 1.153756 CAAGGTCAAGTTGGGGCCT 59.846 57.895 0.84 5.94 0.00 5.19
655 662 8.317679 TGAATTAATGGTGAAGGGTTAATTTGG 58.682 33.333 0.00 0.00 37.06 3.28
690 698 5.231702 ACGGGTCTTAATTACAGGTCAAA 57.768 39.130 0.00 0.00 0.00 2.69
1105 1113 2.290514 TGATTTGTCCCTCCTTCTGCAG 60.291 50.000 7.63 7.63 0.00 4.41
1286 1294 0.665835 GCTCTCCTCATCGTCGATGT 59.334 55.000 29.22 0.00 40.55 3.06
1313 1321 1.075425 CTCTTCTGCGCGAGTTCCTG 61.075 60.000 12.10 0.00 0.00 3.86
1314 1322 1.214062 CTCTTCTGCGCGAGTTCCT 59.786 57.895 12.10 0.00 0.00 3.36
1332 1340 0.811616 CCGCCTCTACCATGTGCTTC 60.812 60.000 0.00 0.00 0.00 3.86
1498 1514 0.671472 CCTGCATCGTGCTCAACTGA 60.671 55.000 10.54 0.00 45.31 3.41
1627 1643 4.925861 GGCTCCTGATCTGCCGGC 62.926 72.222 22.73 22.73 37.11 6.13
1734 1760 7.351166 AGTAATTGGTTAATGGCCTAGCTTAA 58.649 34.615 3.32 0.33 0.00 1.85
1750 1776 7.220030 CCTAGAACATGCATAGAGTAATTGGT 58.780 38.462 0.00 0.00 0.00 3.67
1758 1784 3.377346 ACGCCTAGAACATGCATAGAG 57.623 47.619 0.00 0.00 0.00 2.43
1763 1790 4.796290 GCTTATCTACGCCTAGAACATGCA 60.796 45.833 0.00 0.00 32.49 3.96
1787 1814 3.451556 ATGCACGAGATGAGCCCCG 62.452 63.158 0.00 0.00 32.62 5.73
1824 1851 1.448985 ATTATGGTGTGTCACGTGGC 58.551 50.000 14.58 14.58 34.83 5.01
1854 1881 2.963498 TCGCACGTATCTAGAATCGG 57.037 50.000 19.01 11.66 0.00 4.18
1855 1882 3.084988 CGATCGCACGTATCTAGAATCG 58.915 50.000 0.26 15.15 0.00 3.34
1856 1883 4.323537 TCGATCGCACGTATCTAGAATC 57.676 45.455 11.09 0.00 34.70 2.52
1903 1930 1.194781 ACCTCGGTCTCCTGTGCAAT 61.195 55.000 0.00 0.00 0.00 3.56
1969 1996 2.510238 CTTGCTCTTCGCCTCCGG 60.510 66.667 0.00 0.00 38.05 5.14
2031 2058 4.796231 CCCTCCTTGCCGTCGTCG 62.796 72.222 0.00 0.00 0.00 5.12
2042 2069 1.311747 GACAGCCCTAGACCCTCCT 59.688 63.158 0.00 0.00 0.00 3.69
2172 2199 1.044611 GGGACATCCTACTGCTCTCC 58.955 60.000 0.00 0.00 35.95 3.71
2181 2208 3.161450 GCAGGCCGGGACATCCTA 61.161 66.667 0.92 0.00 35.95 2.94
2366 2394 3.206034 TCTGCAAAGCATCGAATTGTG 57.794 42.857 0.00 0.00 38.13 3.33
2379 2407 0.250124 ACCCGTCGTTCATCTGCAAA 60.250 50.000 0.00 0.00 0.00 3.68
2487 2515 2.210013 TCTCACCTGCTTCCGCACT 61.210 57.895 0.00 0.00 42.25 4.40
2567 2597 0.928229 GTTACGATCCATGCACGGTC 59.072 55.000 0.00 0.00 0.00 4.79
2582 2612 4.320494 CCTGCACCATCTCAAAACAGTTAC 60.320 45.833 0.00 0.00 0.00 2.50
2785 2815 3.902086 GTAGGAGGAGGACGCGGC 61.902 72.222 12.47 7.53 0.00 6.53
2787 2817 2.124236 AGGTAGGAGGAGGACGCG 60.124 66.667 3.53 3.53 0.00 6.01
2847 2877 4.587189 ATTAGCGGCGAGGCGGAC 62.587 66.667 20.06 4.98 38.18 4.79
2895 2925 1.003355 CCCGAACATGCTGAGGTGT 60.003 57.895 0.00 0.00 0.00 4.16
2990 3020 2.156774 CCCCCTCCTAGCCCAATCC 61.157 68.421 0.00 0.00 0.00 3.01
2992 3022 2.778717 GCCCCCTCCTAGCCCAAT 60.779 66.667 0.00 0.00 0.00 3.16
2993 3023 3.901005 TTGCCCCCTCCTAGCCCAA 62.901 63.158 0.00 0.00 0.00 4.12
3060 3090 2.568090 CCGGCATTGTCAGGCAAC 59.432 61.111 0.00 0.00 40.28 4.17
3091 3121 2.154462 CGCAGAGAACTGATTTGGGTT 58.846 47.619 0.00 0.00 46.03 4.11
3215 3249 5.162870 ACTCACATATCCTACTCATGGGGTA 60.163 44.000 0.00 0.00 0.00 3.69
3435 3469 8.598075 GCTTTGATTGGTTGAAATAATGATGAC 58.402 33.333 0.00 0.00 0.00 3.06
3446 3480 3.815856 TGCAAGCTTTGATTGGTTGAA 57.184 38.095 0.00 0.00 43.17 2.69
3506 3544 3.744426 ACGAAGGACTTGGATTTACGTTG 59.256 43.478 0.00 0.00 0.00 4.10
3563 3601 9.515226 AGATAGTGTTGCACCTTTATTTTTCTA 57.485 29.630 0.00 0.00 34.49 2.10
3665 3704 5.629020 CAGGTCCAAAACGACATGTTATTTG 59.371 40.000 17.91 17.91 40.84 2.32
3741 3780 2.159448 CCGTTCGATTTGCCATGCTAAA 60.159 45.455 0.00 0.00 0.00 1.85
3742 3781 1.400142 CCGTTCGATTTGCCATGCTAA 59.600 47.619 0.00 0.00 0.00 3.09
3771 3810 6.620678 CCATCCTCGTGAAAACATAATTTGT 58.379 36.000 0.00 0.00 41.53 2.83
3783 3822 2.091541 GGAAATTGCCATCCTCGTGAA 58.908 47.619 0.00 0.00 32.75 3.18
3817 3856 4.338879 AGCTGAACATAGCAAGGATTTGT 58.661 39.130 0.00 0.00 46.07 2.83
3992 4031 9.856162 TTACCTTTGACCAAAACTTCTACTATT 57.144 29.630 0.00 0.00 0.00 1.73
3993 4032 9.856162 TTTACCTTTGACCAAAACTTCTACTAT 57.144 29.630 0.00 0.00 0.00 2.12
3995 4034 8.762481 ATTTACCTTTGACCAAAACTTCTACT 57.238 30.769 0.00 0.00 0.00 2.57
3996 4035 8.080417 GGATTTACCTTTGACCAAAACTTCTAC 58.920 37.037 0.00 0.00 35.41 2.59
3997 4036 8.173542 GGATTTACCTTTGACCAAAACTTCTA 57.826 34.615 0.00 0.00 35.41 2.10
3998 4037 7.050970 GGATTTACCTTTGACCAAAACTTCT 57.949 36.000 0.00 0.00 35.41 2.85
4022 4073 9.396022 ACAAATATTAGGTTTGGATACTGACAG 57.604 33.333 0.00 0.00 40.08 3.51
4024 4075 9.391006 TCACAAATATTAGGTTTGGATACTGAC 57.609 33.333 3.97 0.00 40.08 3.51
4037 4088 7.922382 ACTCCCTCCATATCACAAATATTAGG 58.078 38.462 0.00 0.00 0.00 2.69
4091 4142 4.286707 AGCAACCCAAGACCTAAAGTTTT 58.713 39.130 0.00 0.00 0.00 2.43
4092 4143 3.889538 GAGCAACCCAAGACCTAAAGTTT 59.110 43.478 0.00 0.00 0.00 2.66
4174 4227 2.894763 TACACGTGCCACACTTTAGT 57.105 45.000 17.22 0.00 31.34 2.24
4175 4228 3.122948 GTGATACACGTGCCACACTTTAG 59.877 47.826 22.96 0.00 31.34 1.85


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

AutoCloner maintained by Alex Coulton.