Multiple sequence alignment - TraesCS7B01G329300

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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 TraesCS7B01G329300 chr7B 100.000 2698 0 0 644 3341 584304825 584307522 0.000000e+00 4983
1 TraesCS7B01G329300 chr7B 100.000 404 0 0 1 404 584304182 584304585 0.000000e+00 747
2 TraesCS7B01G329300 chr7D 96.347 2710 74 3 644 3341 540845696 540848392 0.000000e+00 4433
3 TraesCS7B01G329300 chr7A 96.233 2708 91 3 644 3341 623448662 623451368 0.000000e+00 4425
4 TraesCS7B01G329300 chr7A 87.500 296 31 5 113 404 623448282 623448575 1.490000e-88 337


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 TraesCS7B01G329300 chr7B 584304182 584307522 3340 False 2865 4983 100.0000 1 3341 2 chr7B.!!$F1 3340
1 TraesCS7B01G329300 chr7D 540845696 540848392 2696 False 4433 4433 96.3470 644 3341 1 chr7D.!!$F1 2697
2 TraesCS7B01G329300 chr7A 623448282 623451368 3086 False 2381 4425 91.8665 113 3341 2 chr7A.!!$F1 3228

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
112 113 0.026803 CTGAATAGTTTGCCTCGCGC 59.973 55.0 0.0 0.0 38.31 6.86 F
141 142 0.535553 TTTTACACCAGCCACCGTCC 60.536 55.0 0.0 0.0 0.00 4.79 F
788 792 0.970937 TTCTCCCGCCTCCTACACAG 60.971 60.0 0.0 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1099 1103 0.888736 CACGCCACCATGTCCTTCAA 60.889 55.0 0.00 0.0 0.00 2.69 R
1749 1753 0.982852 TCCCATGGATCCGACAAGCT 60.983 55.0 15.22 0.0 0.00 3.74 R
2674 2678 0.598065 GTGGGCAGTGTTTCACCATC 59.402 55.0 0.00 0.0 34.49 3.51 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 3.650409 CATACAGACAGCCCGAGAC 57.350 57.895 0.00 0.00 0.00 3.36
19 20 1.107114 CATACAGACAGCCCGAGACT 58.893 55.000 0.00 0.00 0.00 3.24
20 21 1.107114 ATACAGACAGCCCGAGACTG 58.893 55.000 0.00 0.00 41.08 3.51
21 22 0.037734 TACAGACAGCCCGAGACTGA 59.962 55.000 0.00 0.00 38.55 3.41
22 23 1.247419 ACAGACAGCCCGAGACTGAG 61.247 60.000 0.00 0.00 38.55 3.35
23 24 1.680651 AGACAGCCCGAGACTGAGG 60.681 63.158 6.34 0.00 38.55 3.86
24 25 1.679305 GACAGCCCGAGACTGAGGA 60.679 63.158 6.34 0.00 38.55 3.71
25 26 1.662438 GACAGCCCGAGACTGAGGAG 61.662 65.000 6.34 0.00 38.55 3.69
26 27 2.043450 AGCCCGAGACTGAGGAGG 60.043 66.667 0.00 0.00 0.00 4.30
27 28 3.844090 GCCCGAGACTGAGGAGGC 61.844 72.222 0.00 0.00 0.00 4.70
28 29 3.151022 CCCGAGACTGAGGAGGCC 61.151 72.222 0.00 0.00 0.00 5.19
29 30 3.151022 CCGAGACTGAGGAGGCCC 61.151 72.222 0.00 0.00 0.00 5.80
30 31 2.363018 CGAGACTGAGGAGGCCCA 60.363 66.667 0.00 0.00 33.88 5.36
31 32 2.422231 CGAGACTGAGGAGGCCCAG 61.422 68.421 0.00 1.32 36.53 4.45
32 33 1.000993 GAGACTGAGGAGGCCCAGA 59.999 63.158 13.03 0.00 34.65 3.86
33 34 1.001503 AGACTGAGGAGGCCCAGAG 59.998 63.158 13.03 0.00 34.65 3.35
34 35 2.686835 ACTGAGGAGGCCCAGAGC 60.687 66.667 13.03 0.00 42.60 4.09
54 55 2.474712 CGTCGCTCGGGAAAAAGC 59.525 61.111 0.00 0.00 35.71 3.51
58 59 3.361977 GCTCGGGAAAAAGCGGCA 61.362 61.111 1.45 0.00 0.00 5.69
59 60 2.870372 CTCGGGAAAAAGCGGCAG 59.130 61.111 1.45 0.00 0.00 4.85
60 61 3.328288 CTCGGGAAAAAGCGGCAGC 62.328 63.158 0.00 0.00 45.58 5.25
88 89 4.154347 GCCCTGCCCGAGACTGAG 62.154 72.222 0.00 0.00 0.00 3.35
89 90 3.465403 CCCTGCCCGAGACTGAGG 61.465 72.222 0.00 0.00 0.00 3.86
93 94 4.500116 GCCCGAGACTGAGGCGTC 62.500 72.222 0.00 0.00 36.84 5.19
94 95 2.752238 CCCGAGACTGAGGCGTCT 60.752 66.667 8.06 0.00 46.39 4.18
95 96 2.487428 CCGAGACTGAGGCGTCTG 59.513 66.667 11.23 11.23 43.91 3.51
96 97 2.041115 CCGAGACTGAGGCGTCTGA 61.041 63.158 18.57 0.00 43.91 3.27
97 98 1.587043 CCGAGACTGAGGCGTCTGAA 61.587 60.000 18.57 0.00 43.91 3.02
98 99 0.453793 CGAGACTGAGGCGTCTGAAT 59.546 55.000 18.57 7.35 43.91 2.57
99 100 1.671328 CGAGACTGAGGCGTCTGAATA 59.329 52.381 18.57 0.00 43.91 1.75
100 101 2.286713 CGAGACTGAGGCGTCTGAATAG 60.287 54.545 18.57 4.90 43.91 1.73
101 102 2.685897 GAGACTGAGGCGTCTGAATAGT 59.314 50.000 18.57 8.02 43.91 2.12
102 103 3.093057 AGACTGAGGCGTCTGAATAGTT 58.907 45.455 18.57 0.00 42.39 2.24
103 104 3.511934 AGACTGAGGCGTCTGAATAGTTT 59.488 43.478 18.57 1.31 42.39 2.66
104 105 3.589988 ACTGAGGCGTCTGAATAGTTTG 58.410 45.455 18.57 0.00 0.00 2.93
105 106 2.346803 TGAGGCGTCTGAATAGTTTGC 58.653 47.619 8.06 0.00 0.00 3.68
106 107 1.666189 GAGGCGTCTGAATAGTTTGCC 59.334 52.381 0.00 0.00 37.05 4.52
107 108 1.279271 AGGCGTCTGAATAGTTTGCCT 59.721 47.619 0.00 0.00 39.90 4.75
108 109 1.666189 GGCGTCTGAATAGTTTGCCTC 59.334 52.381 0.00 0.00 35.32 4.70
109 110 1.324736 GCGTCTGAATAGTTTGCCTCG 59.675 52.381 0.00 0.00 0.00 4.63
110 111 1.324736 CGTCTGAATAGTTTGCCTCGC 59.675 52.381 0.00 0.00 0.00 5.03
111 112 1.324736 GTCTGAATAGTTTGCCTCGCG 59.675 52.381 0.00 0.00 0.00 5.87
112 113 0.026803 CTGAATAGTTTGCCTCGCGC 59.973 55.000 0.00 0.00 38.31 6.86
113 114 1.352056 GAATAGTTTGCCTCGCGCC 59.648 57.895 0.00 0.00 36.24 6.53
114 115 2.361427 GAATAGTTTGCCTCGCGCCG 62.361 60.000 0.00 0.00 36.24 6.46
141 142 0.535553 TTTTACACCAGCCACCGTCC 60.536 55.000 0.00 0.00 0.00 4.79
142 143 2.718747 TTTACACCAGCCACCGTCCG 62.719 60.000 0.00 0.00 0.00 4.79
248 252 3.376078 CATGGTGCACCTGGCCAC 61.376 66.667 34.75 8.75 43.89 5.01
249 253 3.583380 ATGGTGCACCTGGCCACT 61.583 61.111 34.75 9.35 43.89 4.00
783 787 1.230497 CCTCTTCTCCCGCCTCCTA 59.770 63.158 0.00 0.00 0.00 2.94
788 792 0.970937 TTCTCCCGCCTCCTACACAG 60.971 60.000 0.00 0.00 0.00 3.66
1413 1417 2.092753 TGGGATGCAGGAGAAGAATGTC 60.093 50.000 0.00 0.00 0.00 3.06
1419 1423 3.182967 GCAGGAGAAGAATGTCTACACG 58.817 50.000 0.00 0.00 29.94 4.49
1422 1426 5.333513 CAGGAGAAGAATGTCTACACGTAC 58.666 45.833 0.00 0.00 29.94 3.67
1440 1444 3.436704 CGTACAGCTCAATGATTGTTGGT 59.563 43.478 4.93 2.86 0.00 3.67
1499 1503 4.015872 TGTTCAAGGACATGGTTAGGAC 57.984 45.455 0.00 0.00 0.00 3.85
1548 1552 5.691896 ACCTTTATAGGGTTATTGACAGCC 58.308 41.667 4.12 0.00 46.58 4.85
1571 1575 1.380246 GCCATGCAGGGATGGTCAA 60.380 57.895 24.18 0.00 44.37 3.18
1680 1684 2.000701 TCGGGCTGGATTGGTGGAT 61.001 57.895 0.00 0.00 0.00 3.41
1695 1699 2.968574 GGTGGATGAAGCTCTGGATCTA 59.031 50.000 0.00 0.00 0.00 1.98
1740 1744 3.480133 GGCGGTGTATGGGGAGCT 61.480 66.667 0.00 0.00 0.00 4.09
1749 1753 0.326522 TATGGGGAGCTCTGCTTGGA 60.327 55.000 14.64 0.00 39.88 3.53
1888 1892 2.093764 GGACAGTGGGATGAAGTCTCAG 60.094 54.545 0.00 0.00 38.21 3.35
1889 1893 2.564947 GACAGTGGGATGAAGTCTCAGT 59.435 50.000 0.00 0.00 41.83 3.41
1983 1987 1.522668 TGGTCCATCAGTTCTTTGCG 58.477 50.000 0.00 0.00 0.00 4.85
2130 2134 4.089361 AGAAAGAAAGGCTGTTAATGGGG 58.911 43.478 0.00 0.00 0.00 4.96
2241 2245 2.865551 GGATTGCCATTTGTTTATGCGG 59.134 45.455 0.00 0.00 0.00 5.69
2469 2473 6.486657 TGGCACTCAATATTAAATAGCAGGAC 59.513 38.462 0.00 0.00 0.00 3.85
2548 2552 4.035091 TGCTACGATTTGTTACATGATGCC 59.965 41.667 0.00 0.00 0.00 4.40
2565 2569 0.179056 GCCGACCTAAGCTGGCAATA 60.179 55.000 5.66 0.00 46.76 1.90
2569 2573 3.632145 CCGACCTAAGCTGGCAATATTTT 59.368 43.478 0.00 0.00 0.00 1.82
2654 2658 6.785191 ACTTTAACTTACATTGGATGATGCG 58.215 36.000 0.00 0.00 0.00 4.73
2674 2678 3.061161 GCGGATAAACAAAGCAAATGCAG 59.939 43.478 8.28 0.00 45.16 4.41
2679 2683 3.756933 AACAAAGCAAATGCAGATGGT 57.243 38.095 8.28 0.00 45.16 3.55
2707 2720 0.746923 GCCCACGGTGTAGAATTCCC 60.747 60.000 7.45 0.00 0.00 3.97
2709 2722 2.112998 CCCACGGTGTAGAATTCCCTA 58.887 52.381 7.45 0.00 0.00 3.53
2890 2904 1.055849 TCCTTGTGCTTGACAGCCTA 58.944 50.000 0.00 0.00 46.74 3.93
3208 3225 2.561569 ACACTCCAACTTTCACCTTCG 58.438 47.619 0.00 0.00 0.00 3.79
3262 3279 4.938832 TGGTTTCTTGAAGTTTCTTCGTCA 59.061 37.500 5.28 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.107114 CAGTCTCGGGCTGTCTGTAT 58.893 55.000 0.00 0.00 0.00 2.29
2 3 0.037734 TCAGTCTCGGGCTGTCTGTA 59.962 55.000 6.62 2.34 35.60 2.74
3 4 1.228583 TCAGTCTCGGGCTGTCTGT 60.229 57.895 6.62 0.00 35.60 3.41
4 5 1.510383 CTCAGTCTCGGGCTGTCTG 59.490 63.158 6.62 1.72 35.60 3.51
5 6 1.680651 CCTCAGTCTCGGGCTGTCT 60.681 63.158 6.62 0.00 35.60 3.41
7 8 1.680651 CTCCTCAGTCTCGGGCTGT 60.681 63.158 6.62 0.00 35.60 4.40
8 9 2.422231 CCTCCTCAGTCTCGGGCTG 61.422 68.421 0.83 0.83 35.43 4.85
9 10 2.043450 CCTCCTCAGTCTCGGGCT 60.043 66.667 0.00 0.00 0.00 5.19
10 11 3.844090 GCCTCCTCAGTCTCGGGC 61.844 72.222 0.00 0.00 0.00 6.13
12 13 3.151022 GGGCCTCCTCAGTCTCGG 61.151 72.222 0.84 0.00 0.00 4.63
13 14 2.363018 TGGGCCTCCTCAGTCTCG 60.363 66.667 4.53 0.00 0.00 4.04
14 15 1.000993 TCTGGGCCTCCTCAGTCTC 59.999 63.158 4.53 0.00 33.13 3.36
15 16 1.001503 CTCTGGGCCTCCTCAGTCT 59.998 63.158 4.53 0.00 33.13 3.24
16 17 2.730524 GCTCTGGGCCTCCTCAGTC 61.731 68.421 4.53 0.00 34.27 3.51
17 18 2.686835 GCTCTGGGCCTCCTCAGT 60.687 66.667 4.53 0.00 34.27 3.41
37 38 2.474712 GCTTTTTCCCGAGCGACG 59.525 61.111 0.00 0.00 42.18 5.12
41 42 3.328288 CTGCCGCTTTTTCCCGAGC 62.328 63.158 0.00 0.00 35.58 5.03
42 43 2.870372 CTGCCGCTTTTTCCCGAG 59.130 61.111 0.00 0.00 0.00 4.63
43 44 3.361977 GCTGCCGCTTTTTCCCGA 61.362 61.111 0.00 0.00 0.00 5.14
44 45 4.759096 CGCTGCCGCTTTTTCCCG 62.759 66.667 0.00 0.00 0.00 5.14
71 72 4.154347 CTCAGTCTCGGGCAGGGC 62.154 72.222 0.00 0.00 0.00 5.19
72 73 3.465403 CCTCAGTCTCGGGCAGGG 61.465 72.222 0.00 0.00 0.00 4.45
73 74 4.154347 GCCTCAGTCTCGGGCAGG 62.154 72.222 7.51 0.00 44.69 4.85
74 75 4.504916 CGCCTCAGTCTCGGGCAG 62.505 72.222 11.70 3.09 45.50 4.85
76 77 4.500116 GACGCCTCAGTCTCGGGC 62.500 72.222 3.20 3.20 42.18 6.13
82 83 3.512033 AACTATTCAGACGCCTCAGTC 57.488 47.619 0.00 0.00 41.23 3.51
83 84 3.589988 CAAACTATTCAGACGCCTCAGT 58.410 45.455 0.00 0.00 0.00 3.41
84 85 2.349886 GCAAACTATTCAGACGCCTCAG 59.650 50.000 0.00 0.00 0.00 3.35
85 86 2.346803 GCAAACTATTCAGACGCCTCA 58.653 47.619 0.00 0.00 0.00 3.86
86 87 1.666189 GGCAAACTATTCAGACGCCTC 59.334 52.381 0.00 0.00 33.73 4.70
87 88 1.279271 AGGCAAACTATTCAGACGCCT 59.721 47.619 0.00 0.00 38.51 5.52
88 89 1.666189 GAGGCAAACTATTCAGACGCC 59.334 52.381 0.00 0.00 35.48 5.68
89 90 1.324736 CGAGGCAAACTATTCAGACGC 59.675 52.381 0.00 0.00 0.00 5.19
90 91 1.324736 GCGAGGCAAACTATTCAGACG 59.675 52.381 0.00 0.00 0.00 4.18
91 92 1.324736 CGCGAGGCAAACTATTCAGAC 59.675 52.381 0.00 0.00 0.00 3.51
92 93 1.640428 CGCGAGGCAAACTATTCAGA 58.360 50.000 0.00 0.00 0.00 3.27
93 94 0.026803 GCGCGAGGCAAACTATTCAG 59.973 55.000 12.10 0.00 42.87 3.02
94 95 2.086510 GCGCGAGGCAAACTATTCA 58.913 52.632 12.10 0.00 42.87 2.57
95 96 4.976619 GCGCGAGGCAAACTATTC 57.023 55.556 12.10 0.00 42.87 1.75
121 122 1.310904 GACGGTGGCTGGTGTAAAAA 58.689 50.000 0.00 0.00 0.00 1.94
122 123 0.535553 GGACGGTGGCTGGTGTAAAA 60.536 55.000 0.00 0.00 0.00 1.52
123 124 1.071814 GGACGGTGGCTGGTGTAAA 59.928 57.895 0.00 0.00 0.00 2.01
124 125 2.745037 GGACGGTGGCTGGTGTAA 59.255 61.111 0.00 0.00 0.00 2.41
125 126 3.687102 CGGACGGTGGCTGGTGTA 61.687 66.667 0.00 0.00 0.00 2.90
177 180 3.041940 GTGTTCTGGGCGACGGTG 61.042 66.667 0.00 0.00 0.00 4.94
178 181 4.309950 GGTGTTCTGGGCGACGGT 62.310 66.667 0.00 0.00 0.00 4.83
223 227 3.762247 GTGCACCATGCCGGCATT 61.762 61.111 38.86 23.68 44.23 3.56
1099 1103 0.888736 CACGCCACCATGTCCTTCAA 60.889 55.000 0.00 0.00 0.00 2.69
1413 1417 4.864806 ACAATCATTGAGCTGTACGTGTAG 59.135 41.667 3.79 0.00 0.00 2.74
1419 1423 4.697352 AGACCAACAATCATTGAGCTGTAC 59.303 41.667 3.79 0.00 0.00 2.90
1422 1426 3.181513 CGAGACCAACAATCATTGAGCTG 60.182 47.826 3.79 0.00 0.00 4.24
1440 1444 1.456518 CCTCCCATGAGAGGCGAGA 60.457 63.158 10.72 0.00 46.76 4.04
1571 1575 2.359900 CAAAGTAGAAGCGCCCATCTT 58.640 47.619 2.29 0.00 0.00 2.40
1680 1684 3.295093 CCTCACTAGATCCAGAGCTTCA 58.705 50.000 0.00 0.00 0.00 3.02
1731 1735 1.617536 TCCAAGCAGAGCTCCCCAT 60.618 57.895 10.93 0.00 38.25 4.00
1740 1744 1.004560 CCGACAAGCTCCAAGCAGA 60.005 57.895 1.29 0.00 45.56 4.26
1749 1753 0.982852 TCCCATGGATCCGACAAGCT 60.983 55.000 15.22 0.00 0.00 3.74
1870 1874 2.354503 CCACTGAGACTTCATCCCACTG 60.355 54.545 0.00 0.00 31.68 3.66
1888 1892 4.142881 GCTTCTCATTAGTTTCCGAACCAC 60.143 45.833 0.00 0.00 36.39 4.16
1889 1893 4.000988 GCTTCTCATTAGTTTCCGAACCA 58.999 43.478 0.00 0.00 36.39 3.67
1983 1987 3.019564 CCTTGGATGAGAATTGTCACCC 58.980 50.000 9.14 9.14 0.00 4.61
2047 2051 1.268386 CGCATAACCAGCATGCTTCAG 60.268 52.381 19.98 12.54 45.32 3.02
2066 2070 3.535561 ACAATAGAAGTCAGGATTGGCG 58.464 45.455 0.00 0.00 34.30 5.69
2130 2134 2.032204 CAGAGCAAGTTTCTCACTGTGC 60.032 50.000 5.31 0.00 38.66 4.57
2214 2218 1.477553 ACAAATGGCAATCCTCGCAT 58.522 45.000 0.00 0.00 0.00 4.73
2469 2473 3.065233 TGTTGCACACTGAAGTTAGCTTG 59.935 43.478 0.00 0.00 34.61 4.01
2497 2501 1.196354 CAAGCCAAAACTGCTCTCGAG 59.804 52.381 5.93 5.93 38.34 4.04
2548 2552 4.498009 CCAAAATATTGCCAGCTTAGGTCG 60.498 45.833 0.00 0.00 35.10 4.79
2579 2583 5.941555 TTTGTAATCAAACACCCTGGTTT 57.058 34.783 0.00 0.00 41.44 3.27
2584 2588 4.587262 GGACCTTTTGTAATCAAACACCCT 59.413 41.667 0.00 0.00 42.28 4.34
2596 2600 7.038729 TGCAAAATGAATATGGGACCTTTTGTA 60.039 33.333 10.99 5.89 35.57 2.41
2654 2658 5.292589 CCATCTGCATTTGCTTTGTTTATCC 59.707 40.000 3.94 0.00 42.66 2.59
2674 2678 0.598065 GTGGGCAGTGTTTCACCATC 59.402 55.000 0.00 0.00 34.49 3.51
2679 2683 1.821759 CACCGTGGGCAGTGTTTCA 60.822 57.895 0.00 0.00 0.00 2.69
2707 2720 6.763355 AGTTATGTCCACCAATGCTCTATAG 58.237 40.000 0.00 0.00 0.00 1.31
2709 2722 5.636903 AGTTATGTCCACCAATGCTCTAT 57.363 39.130 0.00 0.00 0.00 1.98
2890 2904 3.895232 TGCGGAATTCTAGAGCTTCTT 57.105 42.857 5.23 0.00 0.00 2.52
2996 3013 3.826729 AGAAGCAAATGTTAACACCTCCC 59.173 43.478 11.22 0.00 0.00 4.30
3000 3017 4.972286 GCAAGAAGCAAATGTTAACACC 57.028 40.909 11.22 0.00 44.79 4.16
3101 3118 0.318441 CACTGGCTCTTCTCCGACAA 59.682 55.000 0.00 0.00 0.00 3.18
3208 3225 5.241662 AGACCAGAAAGCAGTAAATCAGTC 58.758 41.667 0.00 0.00 0.00 3.51
3262 3279 4.520492 CCAGTGTCATGCTTAAACCTCTTT 59.480 41.667 0.00 0.00 0.00 2.52
3298 3315 2.056577 GTACCCGAACAGTCGTTTCTG 58.943 52.381 0.00 0.00 46.21 3.02


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

AutoCloner maintained by Alex Coulton.