Multiple sequence alignment - TraesCS1D01G221000

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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 TraesCS1D01G221000 chr1D 100.000 5142 0 0 1 5142 308581309 308586450 0.000000e+00 9496.0
1 TraesCS1D01G221000 chr1D 77.187 583 112 17 86 659 130294779 130295349 2.310000e-83 320.0
2 TraesCS1D01G221000 chr1A 94.559 5054 191 39 132 5142 388155914 388160926 0.000000e+00 7733.0
3 TraesCS1D01G221000 chr1B 94.228 5111 202 39 63 5142 418668339 418673387 0.000000e+00 7718.0
4 TraesCS1D01G221000 chr1B 78.910 422 76 12 5 423 217169480 217169891 1.820000e-69 274.0
5 TraesCS1D01G221000 chr2A 81.660 518 89 3 1 515 711878190 711878704 4.760000e-115 425.0
6 TraesCS1D01G221000 chr2A 75.441 680 132 17 4 661 18830057 18830723 1.080000e-76 298.0
7 TraesCS1D01G221000 chr2A 78.233 464 83 12 22 482 3866536 3866984 1.090000e-71 281.0
8 TraesCS1D01G221000 chr2D 77.434 678 108 34 20 662 117395664 117394997 3.780000e-96 363.0
9 TraesCS1D01G221000 chr6B 76.097 661 138 17 22 673 187167724 187168373 1.380000e-85 327.0
10 TraesCS1D01G221000 chr6A 75.193 649 136 21 22 659 122789225 122789859 3.030000e-72 283.0
11 TraesCS1D01G221000 chr2B 84.615 78 7 4 1887 1961 581997618 581997543 7.140000e-09 73.1
12 TraesCS1D01G221000 chr2B 89.655 58 3 3 1905 1961 191749495 191749440 2.570000e-08 71.3
13 TraesCS1D01G221000 chr6D 83.333 78 8 4 1887 1961 437590104 437590029 3.320000e-07 67.6


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 TraesCS1D01G221000 chr1D 308581309 308586450 5141 False 9496 9496 100.000 1 5142 1 chr1D.!!$F2 5141
1 TraesCS1D01G221000 chr1D 130294779 130295349 570 False 320 320 77.187 86 659 1 chr1D.!!$F1 573
2 TraesCS1D01G221000 chr1A 388155914 388160926 5012 False 7733 7733 94.559 132 5142 1 chr1A.!!$F1 5010
3 TraesCS1D01G221000 chr1B 418668339 418673387 5048 False 7718 7718 94.228 63 5142 1 chr1B.!!$F2 5079
4 TraesCS1D01G221000 chr2A 711878190 711878704 514 False 425 425 81.660 1 515 1 chr2A.!!$F3 514
5 TraesCS1D01G221000 chr2A 18830057 18830723 666 False 298 298 75.441 4 661 1 chr2A.!!$F2 657
6 TraesCS1D01G221000 chr2D 117394997 117395664 667 True 363 363 77.434 20 662 1 chr2D.!!$R1 642
7 TraesCS1D01G221000 chr6B 187167724 187168373 649 False 327 327 76.097 22 673 1 chr6B.!!$F1 651
8 TraesCS1D01G221000 chr6A 122789225 122789859 634 False 283 283 75.193 22 659 1 chr6A.!!$F1 637

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
979 1072 0.119155 TCCACAGTCAATCCCCTCCT 59.881 55.000 0.00 0.0 0.00 3.69 F
1064 1158 1.075600 CCACCTCTCCTCTCCCCTC 60.076 68.421 0.00 0.0 0.00 4.30 F
1811 1906 1.136110 TGTCAAGAGCGGCGATCATAA 59.864 47.619 27.88 8.6 0.00 1.90 F
2005 2100 1.174712 GGCTTTGCTCTGTGCTTCCA 61.175 55.000 3.20 0.0 43.37 3.53 F
3842 3946 0.960364 GACAATCGGCTTTCCAGGCA 60.960 55.000 0.00 0.0 46.30 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1786 1881 1.741401 CGCCGCTCTTGACAATCCA 60.741 57.895 0.00 0.00 0.00 3.41 R
2863 2960 2.203379 TGCACACAGCCATGCAGT 60.203 55.556 0.00 0.00 46.63 4.40 R
3118 3215 1.281867 CCTACCTCATCAGGCACCAAA 59.718 52.381 0.00 0.00 45.05 3.28 R
3875 3980 1.019673 AGTGCAGTTTGTGTGCTGAG 58.980 50.000 0.00 0.00 41.78 3.35 R
4664 4772 1.065782 CCGTCTCTCAGAGTCAGAGGA 60.066 57.143 12.17 6.25 38.39 3.71 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
18 19 2.180204 ACTATGAATGGCACGGCGC 61.180 57.895 6.90 0.00 41.28 6.53
38 39 4.554036 GATGCCGGGGACTGCCTC 62.554 72.222 2.18 0.00 40.23 4.70
67 68 0.533491 TTGGCGGCGTAGAAGTACAT 59.467 50.000 9.37 0.00 0.00 2.29
81 82 5.186198 AGAAGTACATGGCCTTGTAATGTC 58.814 41.667 27.82 23.53 36.08 3.06
84 85 3.719268 ACATGGCCTTGTAATGTCTCA 57.281 42.857 22.02 0.00 28.38 3.27
107 108 0.826256 ATGGCGGCATCTGCATGATT 60.826 50.000 20.18 0.00 44.36 2.57
149 158 4.410400 CCCCGACCTCCACCTTGC 62.410 72.222 0.00 0.00 0.00 4.01
153 162 3.637273 GACCTCCACCTTGCCCGT 61.637 66.667 0.00 0.00 0.00 5.28
181 217 4.742201 CCCACCGCCTCGTCTGTG 62.742 72.222 0.00 0.00 0.00 3.66
261 300 2.123988 TTTGACGCGGCGATTTTGCT 62.124 50.000 30.94 3.83 34.52 3.91
321 361 0.760945 ATCCTCCACCATCTCCGTCC 60.761 60.000 0.00 0.00 0.00 4.79
325 365 3.075005 CACCATCTCCGTCCCCGT 61.075 66.667 0.00 0.00 0.00 5.28
341 381 1.677966 CGTCAGGTTCTCCTCCGGA 60.678 63.158 2.93 2.93 43.07 5.14
468 515 1.915141 AGTGCAGGCAGCTACAAAAT 58.085 45.000 2.86 0.00 45.94 1.82
511 562 2.284625 ATGAGTCGGGGGTGCTGA 60.285 61.111 0.00 0.00 0.00 4.26
522 574 1.448013 GGTGCTGAAGTCCTACGCC 60.448 63.158 0.00 0.00 0.00 5.68
609 674 1.144057 GCTTCACGGATCGATGGGT 59.856 57.895 0.54 0.00 0.00 4.51
610 675 0.876342 GCTTCACGGATCGATGGGTC 60.876 60.000 0.54 0.00 0.00 4.46
611 676 0.459899 CTTCACGGATCGATGGGTCA 59.540 55.000 0.54 0.00 0.00 4.02
612 677 1.069204 CTTCACGGATCGATGGGTCAT 59.931 52.381 0.54 0.00 0.00 3.06
626 693 2.026729 TGGGTCATCGTTGAATGGCTTA 60.027 45.455 0.00 0.00 32.48 3.09
671 738 2.496942 GGATACCGAGGACGTTGGA 58.503 57.895 8.47 0.00 37.88 3.53
673 740 1.386533 GATACCGAGGACGTTGGAGA 58.613 55.000 8.47 0.00 37.88 3.71
790 879 2.781595 GAAAGGAGGCGACCGCAAGA 62.782 60.000 16.47 0.00 44.11 3.02
932 1025 2.127297 CCTCCCTTCCCTTCCCCA 59.873 66.667 0.00 0.00 0.00 4.96
979 1072 0.119155 TCCACAGTCAATCCCCTCCT 59.881 55.000 0.00 0.00 0.00 3.69
993 1086 1.522900 CCTCCTCTCCTCTCCTCTCT 58.477 60.000 0.00 0.00 0.00 3.10
1060 1154 2.063378 CAGCCCACCTCTCCTCTCC 61.063 68.421 0.00 0.00 0.00 3.71
1061 1155 2.766229 GCCCACCTCTCCTCTCCC 60.766 72.222 0.00 0.00 0.00 4.30
1062 1156 2.041405 CCCACCTCTCCTCTCCCC 60.041 72.222 0.00 0.00 0.00 4.81
1063 1157 2.641746 CCCACCTCTCCTCTCCCCT 61.642 68.421 0.00 0.00 0.00 4.79
1064 1158 1.075600 CCACCTCTCCTCTCCCCTC 60.076 68.421 0.00 0.00 0.00 4.30
1673 1768 4.726825 TCTTGAGCTAATAATCAACCCCCT 59.273 41.667 0.00 0.00 32.25 4.79
1786 1881 3.709653 TGGATTCGTTTAGCAGGGACTAT 59.290 43.478 0.00 0.00 36.02 2.12
1792 1887 3.809832 CGTTTAGCAGGGACTATGGATTG 59.190 47.826 0.00 0.00 36.02 2.67
1811 1906 1.136110 TGTCAAGAGCGGCGATCATAA 59.864 47.619 27.88 8.60 0.00 1.90
2005 2100 1.174712 GGCTTTGCTCTGTGCTTCCA 61.175 55.000 3.20 0.00 43.37 3.53
2305 2401 5.056480 TGACCAGTGATTAGTGTCTTTGTG 58.944 41.667 0.00 0.00 0.00 3.33
2581 2677 2.387757 ACTTGACATTTGTTGCACCCT 58.612 42.857 0.00 0.00 0.00 4.34
2583 2679 2.363306 TGACATTTGTTGCACCCTCT 57.637 45.000 0.00 0.00 0.00 3.69
2680 2776 7.849804 ATTTACCAGTTATGTTCACTAGCTG 57.150 36.000 0.00 0.00 0.00 4.24
2956 3053 3.193691 GGACTGAAGAAGAACATCGGAGA 59.806 47.826 0.00 0.00 45.75 3.71
3155 3252 6.382859 TGAGGTAGGTTGCTACATCTTATGAA 59.617 38.462 0.00 0.00 40.16 2.57
3193 3290 4.941263 GTGTGGCATAACTTGACCTGATTA 59.059 41.667 0.00 0.00 29.16 1.75
3539 3643 3.668447 TGTCATTGCAGAGAGTTCTTCC 58.332 45.455 0.00 0.00 0.00 3.46
3779 3883 1.543429 GGGGATCCCAAGCAAGATACG 60.543 57.143 32.07 0.00 44.65 3.06
3842 3946 0.960364 GACAATCGGCTTTCCAGGCA 60.960 55.000 0.00 0.00 46.30 4.75
4182 4289 6.988580 TCTGCTCATTCTGTTCTATACAATGG 59.011 38.462 0.00 0.00 36.02 3.16
4210 4317 4.252073 ACTGAATGATGAAGCACTGTCTC 58.748 43.478 0.00 0.00 0.00 3.36
4274 4381 8.539117 TCCAGTCACTCATTCAAGATCTTATA 57.461 34.615 7.86 0.00 0.00 0.98
4623 4731 1.535462 CAAGGGCCTGTCACTTTTACG 59.465 52.381 6.92 0.00 0.00 3.18
4664 4772 4.160642 TGCATAATCAGACAATCCAGCT 57.839 40.909 0.00 0.00 0.00 4.24
4666 4774 3.501445 GCATAATCAGACAATCCAGCTCC 59.499 47.826 0.00 0.00 0.00 4.70
4667 4775 4.746089 GCATAATCAGACAATCCAGCTCCT 60.746 45.833 0.00 0.00 0.00 3.69
4668 4776 3.557228 AATCAGACAATCCAGCTCCTC 57.443 47.619 0.00 0.00 0.00 3.71
4669 4777 2.244486 TCAGACAATCCAGCTCCTCT 57.756 50.000 0.00 0.00 0.00 3.69
4670 4778 1.829849 TCAGACAATCCAGCTCCTCTG 59.170 52.381 0.00 0.00 42.49 3.35
4671 4779 1.829849 CAGACAATCCAGCTCCTCTGA 59.170 52.381 0.00 0.00 45.72 3.27
4692 4800 2.294791 ACTCTGAGAGACGGTTCACTTG 59.705 50.000 17.71 0.00 33.32 3.16
4695 4803 3.252701 TCTGAGAGACGGTTCACTTGTAC 59.747 47.826 0.00 0.00 0.00 2.90
4699 4807 5.123502 TGAGAGACGGTTCACTTGTACTATC 59.876 44.000 0.00 0.00 0.00 2.08
4861 4972 9.301153 GCTAATTAAAATCCTGTACCATGTTTG 57.699 33.333 0.00 0.00 0.00 2.93
4912 5024 1.840737 TCAGAAGTCGCTAGGAGCTT 58.159 50.000 0.00 0.00 39.60 3.74
4920 5032 1.227118 GCTAGGAGCTTGGCGAGTC 60.227 63.158 3.19 0.07 38.45 3.36
4928 5040 1.079503 GCTTGGCGAGTCGATTTTCT 58.920 50.000 18.61 0.00 0.00 2.52
4948 5068 5.053978 TCTTTTCTTGCCTCTCCTTTTCT 57.946 39.130 0.00 0.00 0.00 2.52
4964 5084 6.712276 TCCTTTTCTTCCTCTTCCTTATCAC 58.288 40.000 0.00 0.00 0.00 3.06
5001 5121 1.821136 CTTCTTCCAGAACCAATGCCC 59.179 52.381 0.00 0.00 29.89 5.36
5044 5164 3.077359 CTCCATCGGAAGCTTCTTTGTT 58.923 45.455 25.05 8.63 0.00 2.83
5100 5220 0.583438 CATATCCACGCGGCAAAGAG 59.417 55.000 12.47 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 1.340017 GGCTGAGACATTACAAGGCCA 60.340 52.381 5.01 0.00 38.35 5.36
96 97 2.422519 GGACCTCACCAATCATGCAGAT 60.423 50.000 0.00 0.00 39.09 2.90
181 217 0.459237 CGATGGAGAGTGTGCTGGTC 60.459 60.000 0.00 0.00 0.00 4.02
261 300 2.288825 GGAAGATCAACTCGGTGACACA 60.289 50.000 8.08 0.00 0.00 3.72
341 381 4.552365 CGCCGCTGACCCATGGAT 62.552 66.667 15.22 0.00 0.00 3.41
484 531 1.550524 CCCCGACTCATCAGAAACTGA 59.449 52.381 3.95 3.95 44.99 3.41
485 532 1.406069 CCCCCGACTCATCAGAAACTG 60.406 57.143 0.00 0.00 0.00 3.16
522 574 2.126580 GGAGTCCGGACACGAACG 60.127 66.667 35.00 0.00 44.60 3.95
541 593 5.773176 AGTCGAAACAAATTGGGGACTTTAT 59.227 36.000 0.00 0.00 29.61 1.40
577 642 3.440173 CCGTGAAGCAGTTTGAACCATAT 59.560 43.478 0.00 0.00 0.00 1.78
594 659 0.673985 GATGACCCATCGATCCGTGA 59.326 55.000 0.00 0.00 31.01 4.35
609 674 2.093921 TCCGTAAGCCATTCAACGATGA 60.094 45.455 0.00 0.00 37.53 2.92
610 675 2.276201 TCCGTAAGCCATTCAACGATG 58.724 47.619 0.00 0.00 37.53 3.84
611 676 2.093658 ACTCCGTAAGCCATTCAACGAT 60.094 45.455 0.00 0.00 37.53 3.73
612 677 1.274167 ACTCCGTAAGCCATTCAACGA 59.726 47.619 0.00 0.00 37.53 3.85
626 693 2.989824 CACCTGTCCGGACTCCGT 60.990 66.667 33.39 22.76 46.80 4.69
662 729 1.450312 CCAGGCATCTCCAACGTCC 60.450 63.158 0.00 0.00 37.29 4.79
663 730 0.321653 AACCAGGCATCTCCAACGTC 60.322 55.000 0.00 0.00 37.29 4.34
664 731 0.606401 CAACCAGGCATCTCCAACGT 60.606 55.000 0.00 0.00 37.29 3.99
665 732 0.606401 ACAACCAGGCATCTCCAACG 60.606 55.000 0.00 0.00 37.29 4.10
668 735 2.790433 GTTTACAACCAGGCATCTCCA 58.210 47.619 0.00 0.00 37.29 3.86
691 780 5.692204 GCTAGCTAATTAATGCTTCTCGTCA 59.308 40.000 7.70 0.00 40.35 4.35
790 879 5.394224 TTTTCTTTCTTTGGACACGGTTT 57.606 34.783 0.00 0.00 0.00 3.27
932 1025 4.324991 GTTTCGGTGGTCGGGGCT 62.325 66.667 0.00 0.00 39.77 5.19
946 1039 2.091885 ACTGTGGAGTGGTGATTGGTTT 60.092 45.455 0.00 0.00 0.00 3.27
979 1072 1.518367 GGAGGAGAGAGGAGAGGAGA 58.482 60.000 0.00 0.00 0.00 3.71
993 1086 2.043852 GCAGAGGAGACGGGAGGA 60.044 66.667 0.00 0.00 0.00 3.71
1601 1696 4.527816 TGGAAAATACCATTGCAGCTTCTT 59.472 37.500 0.00 0.00 34.77 2.52
1750 1845 3.181471 ACGAATCCATACCTGAGCTTCTG 60.181 47.826 0.00 0.00 0.00 3.02
1786 1881 1.741401 CGCCGCTCTTGACAATCCA 60.741 57.895 0.00 0.00 0.00 3.41
1792 1887 1.789464 CTTATGATCGCCGCTCTTGAC 59.211 52.381 0.00 0.00 0.00 3.18
1863 1958 5.463392 CACACGTAGCATGATTAAGCACTAT 59.537 40.000 0.00 0.00 0.00 2.12
1867 1962 2.351418 GCACACGTAGCATGATTAAGCA 59.649 45.455 0.00 0.00 0.00 3.91
1963 2058 8.656806 AGCCAAATTTATGATGAATCATCCAAT 58.343 29.630 19.38 12.15 43.72 3.16
2005 2100 2.873133 GTGGCTCTATACACGCTTCT 57.127 50.000 0.00 0.00 0.00 2.85
2316 2412 3.621682 AAACCCCAACCTTGATAACCA 57.378 42.857 0.00 0.00 0.00 3.67
2532 2628 6.219772 TCCTATCCCTGGACAAGCTATATAGA 59.780 42.308 14.16 0.00 0.00 1.98
2680 2776 3.017442 GGGGGAACATGAAACTAGAAGC 58.983 50.000 0.00 0.00 0.00 3.86
2794 2890 6.509418 ACTTACAAACAGAAGCACAAGAAA 57.491 33.333 0.00 0.00 0.00 2.52
2863 2960 2.203379 TGCACACAGCCATGCAGT 60.203 55.556 0.00 0.00 46.63 4.40
3118 3215 1.281867 CCTACCTCATCAGGCACCAAA 59.718 52.381 0.00 0.00 45.05 3.28
3155 3252 4.854173 TGCCACACAGGTGTAATAATCAT 58.146 39.130 4.52 0.00 42.83 2.45
3193 3290 1.875488 AATCCCCTTGCGGTACTACT 58.125 50.000 0.00 0.00 0.00 2.57
3285 3389 3.888323 TGTCCATGCAACACTACACAATT 59.112 39.130 0.00 0.00 0.00 2.32
3316 3420 6.348498 TCCTAATGAAATGCGAGATGAGAAA 58.652 36.000 0.00 0.00 0.00 2.52
3358 3462 8.008513 ACCGTTCAGTTCTGAGTTATATACAT 57.991 34.615 2.77 0.00 0.00 2.29
3539 3643 3.434873 CTCAGGCATGATAGCAGAAGCG 61.435 54.545 0.00 0.00 39.49 4.68
3875 3980 1.019673 AGTGCAGTTTGTGTGCTGAG 58.980 50.000 0.00 0.00 41.78 3.35
4261 4368 9.167311 GGCTTCTTTCAACTATAAGATCTTGAA 57.833 33.333 18.47 9.50 32.16 2.69
4274 4381 5.990120 ATTTAGCATGGCTTCTTTCAACT 57.010 34.783 0.00 0.00 40.44 3.16
4569 4677 2.330254 CACTCGTGCACAACCCAAT 58.670 52.632 18.64 0.00 0.00 3.16
4608 4716 4.377124 GCTAAAGACGTAAAAGTGACAGGC 60.377 45.833 0.00 0.00 0.00 4.85
4623 4731 5.702865 TGCATCATGACTTTTGCTAAAGAC 58.297 37.500 24.36 18.94 42.78 3.01
4664 4772 1.065782 CCGTCTCTCAGAGTCAGAGGA 60.066 57.143 12.17 6.25 38.39 3.71
4666 4774 2.107950 ACCGTCTCTCAGAGTCAGAG 57.892 55.000 6.21 6.21 39.11 3.35
4667 4775 2.224548 TGAACCGTCTCTCAGAGTCAGA 60.225 50.000 0.36 0.00 0.00 3.27
4668 4776 2.095466 GTGAACCGTCTCTCAGAGTCAG 60.095 54.545 0.36 0.00 0.00 3.51
4669 4777 1.880675 GTGAACCGTCTCTCAGAGTCA 59.119 52.381 0.36 0.00 0.00 3.41
4670 4778 2.156098 AGTGAACCGTCTCTCAGAGTC 58.844 52.381 0.36 0.00 0.00 3.36
4671 4779 2.279935 AGTGAACCGTCTCTCAGAGT 57.720 50.000 0.36 0.00 0.00 3.24
4854 4965 2.880268 TCAGACTGCAAGGACAAACATG 59.120 45.455 0.00 0.00 39.30 3.21
4861 4972 2.479566 TTCCATCAGACTGCAAGGAC 57.520 50.000 9.11 0.00 39.30 3.85
4912 5024 3.399330 AGAAAAGAAAATCGACTCGCCA 58.601 40.909 0.00 0.00 0.00 5.69
4920 5032 4.457257 AGGAGAGGCAAGAAAAGAAAATCG 59.543 41.667 0.00 0.00 0.00 3.34
4928 5040 4.584743 GGAAGAAAAGGAGAGGCAAGAAAA 59.415 41.667 0.00 0.00 0.00 2.29
4948 5068 4.699994 AGGAAGGTGATAAGGAAGAGGAA 58.300 43.478 0.00 0.00 0.00 3.36
4964 5084 2.310052 AGAAGATTGTTGGGGAGGAAGG 59.690 50.000 0.00 0.00 0.00 3.46
5001 5121 1.692042 ATGGAGCAGGTCTGGAGGG 60.692 63.158 0.00 0.00 0.00 4.30
5044 5164 2.501723 GGTCTATCTGTTCCTGCCAGAA 59.498 50.000 0.00 0.00 41.93 3.02
5083 5203 1.153449 CCTCTTTGCCGCGTGGATA 60.153 57.895 21.76 3.31 37.49 2.59


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

AutoCloner maintained by Alex Coulton.