Multiple sequence alignment - TraesCS3B01G226200

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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 TraesCS3B01G226200 chr3B 100.000 2625 0 0 1 2625 313807135 313809759 0.000000e+00 4848.0
1 TraesCS3B01G226200 chr3D 95.302 1639 49 7 180 1802 252334087 252335713 0.000000e+00 2575.0
2 TraesCS3B01G226200 chr3D 91.304 828 69 3 1800 2625 281006376 281007202 0.000000e+00 1127.0
3 TraesCS3B01G226200 chr3D 90.493 831 74 4 1799 2625 480355916 480356745 0.000000e+00 1092.0
4 TraesCS3B01G226200 chr3A 94.354 1541 54 21 292 1802 332220749 332219212 0.000000e+00 2333.0
5 TraesCS3B01G226200 chr3A 96.850 127 4 0 180 306 332227577 332227451 2.050000e-51 213.0
6 TraesCS3B01G226200 chr3A 88.679 159 13 3 1 159 332227711 332227558 3.450000e-44 189.0
7 TraesCS3B01G226200 chr2D 91.283 826 70 2 1802 2625 387480937 387480112 0.000000e+00 1125.0
8 TraesCS3B01G226200 chr2D 90.953 829 67 4 1802 2625 353544574 353543749 0.000000e+00 1109.0
9 TraesCS3B01G226200 chr5B 91.041 826 70 4 1801 2625 369162822 369163644 0.000000e+00 1112.0
10 TraesCS3B01G226200 chr5B 90.459 828 73 5 1800 2625 22029983 22030806 0.000000e+00 1086.0
11 TraesCS3B01G226200 chr5B 96.491 57 2 0 892 948 322858705 322858761 7.730000e-16 95.3
12 TraesCS3B01G226200 chr5B 86.275 51 7 0 903 953 123761094 123761044 3.650000e-04 56.5
13 TraesCS3B01G226200 chr5D 90.229 829 74 5 1800 2623 400366374 400367200 0.000000e+00 1075.0
14 TraesCS3B01G226200 chr5D 96.491 57 2 0 892 948 285247432 285247488 7.730000e-16 95.3
15 TraesCS3B01G226200 chr5D 88.235 51 6 0 903 953 113391895 113391845 7.840000e-06 62.1
16 TraesCS3B01G226200 chr2B 90.194 826 76 4 1800 2621 104933388 104932564 0.000000e+00 1072.0
17 TraesCS3B01G226200 chr4D 89.808 834 79 4 1795 2625 115402216 115401386 0.000000e+00 1064.0
18 TraesCS3B01G226200 chr6D 98.182 55 1 0 898 952 52724695 52724641 2.150000e-16 97.1
19 TraesCS3B01G226200 chr6B 98.182 55 1 0 898 952 119849607 119849553 2.150000e-16 97.1
20 TraesCS3B01G226200 chr6A 98.182 55 1 0 898 952 63610635 63610581 2.150000e-16 97.1
21 TraesCS3B01G226200 chr5A 96.491 57 2 0 892 948 377119601 377119657 7.730000e-16 95.3


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 TraesCS3B01G226200 chr3B 313807135 313809759 2624 False 4848 4848 100.000 1 2625 1 chr3B.!!$F1 2624
1 TraesCS3B01G226200 chr3D 252334087 252335713 1626 False 2575 2575 95.302 180 1802 1 chr3D.!!$F1 1622
2 TraesCS3B01G226200 chr3D 281006376 281007202 826 False 1127 1127 91.304 1800 2625 1 chr3D.!!$F2 825
3 TraesCS3B01G226200 chr3D 480355916 480356745 829 False 1092 1092 90.493 1799 2625 1 chr3D.!!$F3 826
4 TraesCS3B01G226200 chr3A 332219212 332220749 1537 True 2333 2333 94.354 292 1802 1 chr3A.!!$R1 1510
5 TraesCS3B01G226200 chr2D 387480112 387480937 825 True 1125 1125 91.283 1802 2625 1 chr2D.!!$R2 823
6 TraesCS3B01G226200 chr2D 353543749 353544574 825 True 1109 1109 90.953 1802 2625 1 chr2D.!!$R1 823
7 TraesCS3B01G226200 chr5B 369162822 369163644 822 False 1112 1112 91.041 1801 2625 1 chr5B.!!$F3 824
8 TraesCS3B01G226200 chr5B 22029983 22030806 823 False 1086 1086 90.459 1800 2625 1 chr5B.!!$F1 825
9 TraesCS3B01G226200 chr5D 400366374 400367200 826 False 1075 1075 90.229 1800 2623 1 chr5D.!!$F2 823
10 TraesCS3B01G226200 chr2B 104932564 104933388 824 True 1072 1072 90.194 1800 2621 1 chr2B.!!$R1 821
11 TraesCS3B01G226200 chr4D 115401386 115402216 830 True 1064 1064 89.808 1795 2625 1 chr4D.!!$R1 830

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
128 129 0.03392 CTCTTTGGTTGGCTTTGGGC 59.966 55.0 0.0 0.0 40.90 5.36 F
134 135 0.03392 GGTTGGCTTTGGGCTTTCAG 59.966 55.0 0.0 0.0 41.46 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1531 1554 0.441533 GCATCGACAACACAGAGCTG 59.558 55.0 0.00 0.00 0.0 4.24 R
2074 2121 0.939106 GCCAAAACAAGCGCGTGAAT 60.939 50.0 29.85 14.79 0.0 2.57 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
17 18 4.660938 AAGCCCTGTTGGTCGGCC 62.661 66.667 0.00 0.00 44.13 6.13
26 27 2.506962 TGGTCGGCCAAAACTCGT 59.493 55.556 6.10 0.00 42.83 4.18
27 28 1.153127 TGGTCGGCCAAAACTCGTT 60.153 52.632 6.10 0.00 42.83 3.85
28 29 1.161563 TGGTCGGCCAAAACTCGTTC 61.162 55.000 6.10 0.00 42.83 3.95
29 30 1.203313 GTCGGCCAAAACTCGTTCG 59.797 57.895 2.24 0.00 0.00 3.95
30 31 1.957186 TCGGCCAAAACTCGTTCGG 60.957 57.895 2.24 0.00 0.00 4.30
31 32 2.951458 GGCCAAAACTCGTTCGGG 59.049 61.111 0.00 0.00 0.00 5.14
32 33 1.598685 GGCCAAAACTCGTTCGGGA 60.599 57.895 0.00 0.00 0.00 5.14
33 34 1.167781 GGCCAAAACTCGTTCGGGAA 61.168 55.000 0.00 0.00 0.00 3.97
34 35 0.040692 GCCAAAACTCGTTCGGGAAC 60.041 55.000 0.00 1.45 37.92 3.62
35 36 1.589803 CCAAAACTCGTTCGGGAACT 58.410 50.000 9.62 0.00 39.08 3.01
36 37 1.263217 CCAAAACTCGTTCGGGAACTG 59.737 52.381 9.62 5.27 39.08 3.16
37 38 0.942252 AAAACTCGTTCGGGAACTGC 59.058 50.000 9.62 0.00 39.08 4.40
38 39 0.883370 AAACTCGTTCGGGAACTGCC 60.883 55.000 9.62 0.00 39.08 4.85
39 40 2.035237 AACTCGTTCGGGAACTGCCA 62.035 55.000 9.62 0.00 39.08 4.92
40 41 1.738099 CTCGTTCGGGAACTGCCAG 60.738 63.158 9.62 0.00 39.08 4.85
41 42 2.154798 CTCGTTCGGGAACTGCCAGA 62.155 60.000 0.00 0.00 39.22 3.86
42 43 2.027625 CGTTCGGGAACTGCCAGAC 61.028 63.158 0.00 0.00 40.76 3.51
43 44 1.671379 GTTCGGGAACTGCCAGACC 60.671 63.158 0.00 1.16 40.76 3.85
44 45 2.144078 TTCGGGAACTGCCAGACCA 61.144 57.895 0.00 0.00 40.76 4.02
45 46 2.358737 CGGGAACTGCCAGACCAC 60.359 66.667 0.00 0.00 38.95 4.16
46 47 2.836154 GGGAACTGCCAGACCACA 59.164 61.111 0.00 0.00 38.95 4.17
47 48 1.600916 GGGAACTGCCAGACCACAC 60.601 63.158 0.00 0.00 38.95 3.82
48 49 1.148273 GGAACTGCCAGACCACACA 59.852 57.895 0.00 0.00 36.34 3.72
49 50 0.886490 GGAACTGCCAGACCACACAG 60.886 60.000 0.00 0.00 36.34 3.66
50 51 0.179045 GAACTGCCAGACCACACAGT 60.179 55.000 0.00 0.00 44.96 3.55
51 52 0.179045 AACTGCCAGACCACACAGTC 60.179 55.000 0.00 0.00 42.34 3.51
52 53 1.302033 CTGCCAGACCACACAGTCC 60.302 63.158 0.00 0.00 37.49 3.85
53 54 2.032681 GCCAGACCACACAGTCCC 59.967 66.667 0.00 0.00 37.49 4.46
54 55 2.343758 CCAGACCACACAGTCCCG 59.656 66.667 0.00 0.00 37.49 5.14
55 56 2.507854 CCAGACCACACAGTCCCGT 61.508 63.158 0.00 0.00 37.49 5.28
56 57 1.006102 CAGACCACACAGTCCCGTC 60.006 63.158 0.00 0.00 37.49 4.79
57 58 1.152525 AGACCACACAGTCCCGTCT 60.153 57.895 0.00 0.00 37.49 4.18
58 59 1.006102 GACCACACAGTCCCGTCTG 60.006 63.158 0.00 0.00 40.80 3.51
59 60 2.343758 CCACACAGTCCCGTCTGG 59.656 66.667 0.00 0.00 39.48 3.86
69 70 2.424302 CCGTCTGGGTGTTTCGGT 59.576 61.111 0.00 0.00 36.99 4.69
70 71 1.959226 CCGTCTGGGTGTTTCGGTG 60.959 63.158 0.00 0.00 36.99 4.94
71 72 1.227438 CGTCTGGGTGTTTCGGTGT 60.227 57.895 0.00 0.00 0.00 4.16
72 73 1.219522 CGTCTGGGTGTTTCGGTGTC 61.220 60.000 0.00 0.00 0.00 3.67
73 74 1.068417 TCTGGGTGTTTCGGTGTCG 59.932 57.895 0.00 0.00 37.82 4.35
74 75 1.959226 CTGGGTGTTTCGGTGTCGG 60.959 63.158 0.00 0.00 36.95 4.79
75 76 2.109593 GGGTGTTTCGGTGTCGGT 59.890 61.111 0.00 0.00 36.95 4.69
76 77 1.367102 GGGTGTTTCGGTGTCGGTA 59.633 57.895 0.00 0.00 36.95 4.02
77 78 0.037046 GGGTGTTTCGGTGTCGGTAT 60.037 55.000 0.00 0.00 36.95 2.73
78 79 1.073177 GGTGTTTCGGTGTCGGTATG 58.927 55.000 0.00 0.00 36.95 2.39
79 80 1.337074 GGTGTTTCGGTGTCGGTATGA 60.337 52.381 0.00 0.00 36.95 2.15
94 95 3.520290 GTATGACACCATCGAGTTGGA 57.480 47.619 12.02 0.00 39.25 3.53
95 96 2.680312 ATGACACCATCGAGTTGGAG 57.320 50.000 12.02 6.51 39.25 3.86
96 97 1.627864 TGACACCATCGAGTTGGAGA 58.372 50.000 12.02 0.00 39.25 3.71
97 98 2.179427 TGACACCATCGAGTTGGAGAT 58.821 47.619 12.02 0.00 39.25 2.75
98 99 2.094026 TGACACCATCGAGTTGGAGATG 60.094 50.000 12.02 2.74 42.71 2.90
99 100 1.293924 CACCATCGAGTTGGAGATGC 58.706 55.000 12.02 0.00 41.98 3.91
100 101 1.134580 CACCATCGAGTTGGAGATGCT 60.135 52.381 12.02 0.00 41.98 3.79
101 102 1.137872 ACCATCGAGTTGGAGATGCTC 59.862 52.381 12.02 0.00 41.98 4.26
102 103 1.411977 CCATCGAGTTGGAGATGCTCT 59.588 52.381 0.00 0.00 41.98 4.09
103 104 2.625314 CCATCGAGTTGGAGATGCTCTA 59.375 50.000 0.00 0.00 41.98 2.43
104 105 3.068732 CCATCGAGTTGGAGATGCTCTAA 59.931 47.826 0.00 0.00 41.98 2.10
105 106 4.262377 CCATCGAGTTGGAGATGCTCTAAT 60.262 45.833 0.00 0.00 41.98 1.73
106 107 5.295950 CATCGAGTTGGAGATGCTCTAATT 58.704 41.667 0.00 0.00 37.94 1.40
107 108 5.344743 TCGAGTTGGAGATGCTCTAATTT 57.655 39.130 0.00 0.00 33.81 1.82
108 109 6.465439 TCGAGTTGGAGATGCTCTAATTTA 57.535 37.500 0.00 0.00 33.81 1.40
109 110 6.273825 TCGAGTTGGAGATGCTCTAATTTAC 58.726 40.000 0.00 0.00 33.81 2.01
110 111 6.096987 TCGAGTTGGAGATGCTCTAATTTACT 59.903 38.462 0.00 0.00 33.81 2.24
111 112 6.419413 CGAGTTGGAGATGCTCTAATTTACTC 59.581 42.308 0.00 0.00 33.81 2.59
112 113 7.430760 AGTTGGAGATGCTCTAATTTACTCT 57.569 36.000 0.00 0.00 33.81 3.24
113 114 7.856415 AGTTGGAGATGCTCTAATTTACTCTT 58.144 34.615 0.00 0.00 33.81 2.85
114 115 8.325046 AGTTGGAGATGCTCTAATTTACTCTTT 58.675 33.333 0.00 0.00 33.81 2.52
115 116 8.394121 GTTGGAGATGCTCTAATTTACTCTTTG 58.606 37.037 0.00 0.00 33.81 2.77
116 117 7.050377 TGGAGATGCTCTAATTTACTCTTTGG 58.950 38.462 0.00 0.00 0.00 3.28
117 118 7.051000 GGAGATGCTCTAATTTACTCTTTGGT 58.949 38.462 0.00 0.00 0.00 3.67
118 119 7.554476 GGAGATGCTCTAATTTACTCTTTGGTT 59.446 37.037 0.00 0.00 0.00 3.67
119 120 8.273780 AGATGCTCTAATTTACTCTTTGGTTG 57.726 34.615 0.00 0.00 0.00 3.77
120 121 6.817765 TGCTCTAATTTACTCTTTGGTTGG 57.182 37.500 0.00 0.00 0.00 3.77
121 122 5.183140 TGCTCTAATTTACTCTTTGGTTGGC 59.817 40.000 0.00 0.00 0.00 4.52
122 123 5.416013 GCTCTAATTTACTCTTTGGTTGGCT 59.584 40.000 0.00 0.00 0.00 4.75
123 124 6.071896 GCTCTAATTTACTCTTTGGTTGGCTT 60.072 38.462 0.00 0.00 0.00 4.35
124 125 7.523873 GCTCTAATTTACTCTTTGGTTGGCTTT 60.524 37.037 0.00 0.00 0.00 3.51
125 126 7.657336 TCTAATTTACTCTTTGGTTGGCTTTG 58.343 34.615 0.00 0.00 0.00 2.77
126 127 4.664150 TTTACTCTTTGGTTGGCTTTGG 57.336 40.909 0.00 0.00 0.00 3.28
127 128 1.413118 ACTCTTTGGTTGGCTTTGGG 58.587 50.000 0.00 0.00 0.00 4.12
128 129 0.033920 CTCTTTGGTTGGCTTTGGGC 59.966 55.000 0.00 0.00 40.90 5.36
129 130 0.398381 TCTTTGGTTGGCTTTGGGCT 60.398 50.000 0.00 0.00 41.46 5.19
130 131 0.469494 CTTTGGTTGGCTTTGGGCTT 59.531 50.000 0.00 0.00 41.46 4.35
131 132 0.915364 TTTGGTTGGCTTTGGGCTTT 59.085 45.000 0.00 0.00 41.46 3.51
132 133 0.467804 TTGGTTGGCTTTGGGCTTTC 59.532 50.000 0.00 0.00 41.46 2.62
133 134 0.689080 TGGTTGGCTTTGGGCTTTCA 60.689 50.000 0.00 0.00 41.46 2.69
134 135 0.033920 GGTTGGCTTTGGGCTTTCAG 59.966 55.000 0.00 0.00 41.46 3.02
135 136 0.601046 GTTGGCTTTGGGCTTTCAGC 60.601 55.000 0.00 0.00 41.46 4.26
136 137 1.047596 TTGGCTTTGGGCTTTCAGCA 61.048 50.000 0.00 0.00 44.75 4.41
137 138 1.291272 GGCTTTGGGCTTTCAGCAG 59.709 57.895 0.00 0.00 44.75 4.24
138 139 1.373873 GCTTTGGGCTTTCAGCAGC 60.374 57.895 0.00 0.00 44.75 5.25
155 156 2.663196 CCGAAGGCTCCTCCGTTT 59.337 61.111 0.00 0.00 46.14 3.60
156 157 1.003718 CCGAAGGCTCCTCCGTTTT 60.004 57.895 0.00 0.00 46.14 2.43
157 158 0.605589 CCGAAGGCTCCTCCGTTTTT 60.606 55.000 0.00 0.00 46.14 1.94
203 204 0.606673 GCTCCTCCGTTCTTTGCCTT 60.607 55.000 0.00 0.00 0.00 4.35
206 207 0.881796 CCTCCGTTCTTTGCCTTTCC 59.118 55.000 0.00 0.00 0.00 3.13
253 254 3.825160 TTCTCACCACCAGCGCACC 62.825 63.158 11.47 0.00 0.00 5.01
323 324 3.746492 CACTTAACTCCTAAGCAAACGCT 59.254 43.478 0.00 0.00 40.78 5.07
382 383 2.225624 CCCCAATTCCCTTTTCCCTCTT 60.226 50.000 0.00 0.00 0.00 2.85
389 396 5.403558 TTCCCTTTTCCCTCTTTCTCTTT 57.596 39.130 0.00 0.00 0.00 2.52
541 548 1.423921 ACCACCTTTAGTTCCCTGTGG 59.576 52.381 5.01 5.01 46.70 4.17
606 613 8.587608 TCTACCATCTAGCTTAGTACTACTCTC 58.412 40.741 0.91 0.00 0.00 3.20
649 656 1.598130 GCTGTTCAGGGCGACACTT 60.598 57.895 0.00 0.00 0.00 3.16
686 693 0.178961 AGAAACCCCCTTGTTCAGGC 60.179 55.000 0.00 0.00 42.29 4.85
691 698 2.742372 CCCTTGTTCAGGCCGTCG 60.742 66.667 0.00 0.00 42.29 5.12
712 719 2.704572 CTCTGCCGAAATTTCCTGTCT 58.295 47.619 12.54 0.00 0.00 3.41
894 901 5.008019 CGCTGCTTTTATGATAACATCCACT 59.992 40.000 0.00 0.00 37.87 4.00
1067 1075 2.239907 GTGTAAGGAAATGGCCTCTCCT 59.760 50.000 13.34 13.34 41.51 3.69
1080 1088 2.989824 CTCCTGGTCCCGTCACGT 60.990 66.667 0.00 0.00 0.00 4.49
1085 1093 4.748679 GGTCCCGTCACGTCGTCG 62.749 72.222 0.00 0.00 43.34 5.12
1145 1168 2.756283 ACCGAGGAGAGGAAGCGG 60.756 66.667 0.00 0.00 46.83 5.52
1169 1192 1.738099 CAAGGAGTCGAACCGGCTG 60.738 63.158 0.00 0.00 43.67 4.85
1385 1408 1.604185 GCCGAGCTGATCCAGTACATC 60.604 57.143 0.00 0.00 33.43 3.06
1520 1543 0.443088 GCTAGCAGATCGCATCATGC 59.557 55.000 10.63 0.00 46.13 4.06
1531 1554 1.430632 CATCATGCTGGTTCCGTGC 59.569 57.895 0.00 1.00 0.00 5.34
1546 1572 1.566563 GTGCAGCTCTGTGTTGTCG 59.433 57.895 0.00 0.00 0.00 4.35
1554 1580 0.313987 TCTGTGTTGTCGATGCGTCT 59.686 50.000 4.05 0.00 0.00 4.18
1555 1581 1.538075 TCTGTGTTGTCGATGCGTCTA 59.462 47.619 4.05 0.00 0.00 2.59
1556 1582 1.914051 CTGTGTTGTCGATGCGTCTAG 59.086 52.381 4.05 0.00 0.00 2.43
1557 1583 1.268625 TGTGTTGTCGATGCGTCTAGT 59.731 47.619 4.05 0.00 0.00 2.57
1558 1584 2.485038 TGTGTTGTCGATGCGTCTAGTA 59.515 45.455 4.05 0.00 0.00 1.82
1559 1585 3.099362 GTGTTGTCGATGCGTCTAGTAG 58.901 50.000 4.05 0.00 0.00 2.57
1587 1622 2.825532 GTGCTTATGCTTTTCCTCCCAA 59.174 45.455 1.96 0.00 40.48 4.12
1599 1634 2.736347 TCCTCCCAAGTAGAGTAGTGC 58.264 52.381 0.00 0.00 0.00 4.40
1636 1672 3.368427 GGGCAAGGAAATTAAAGAGTGGC 60.368 47.826 0.00 0.00 0.00 5.01
1642 1678 5.254115 AGGAAATTAAAGAGTGGCTGTACC 58.746 41.667 0.00 0.00 39.84 3.34
1646 1682 4.699925 TTAAAGAGTGGCTGTACCTGTT 57.300 40.909 0.00 0.00 40.22 3.16
1677 1713 4.397103 ACTTTATAGTGTGACATCGACGGA 59.603 41.667 0.00 0.00 31.99 4.69
1678 1714 4.547406 TTATAGTGTGACATCGACGGAG 57.453 45.455 0.00 0.00 0.00 4.63
1784 1820 2.363680 ACATCGCCTATCACTCTCCAAG 59.636 50.000 0.00 0.00 0.00 3.61
1823 1859 3.239253 AACTCCAACGGGCCGACT 61.239 61.111 35.78 16.74 0.00 4.18
1942 1980 0.679640 GCCGACCCATTTCATGACCA 60.680 55.000 0.00 0.00 0.00 4.02
1945 1983 1.821216 GACCCATTTCATGACCACGT 58.179 50.000 0.00 0.00 0.00 4.49
1949 1989 0.516877 CATTTCATGACCACGTGCGT 59.483 50.000 10.91 9.84 33.49 5.24
2074 2121 1.544825 CCTCCAGAGTGCGGGAAAGA 61.545 60.000 0.00 0.00 37.94 2.52
2144 2192 1.752436 CGCTCCCTCCATACTCAGTCT 60.752 57.143 0.00 0.00 0.00 3.24
2167 2215 3.083349 CCACTCATCTCGCCCCCA 61.083 66.667 0.00 0.00 0.00 4.96
2206 2254 2.511373 GCGCCACCATGTCGATGA 60.511 61.111 0.00 0.00 0.00 2.92
2309 2357 2.503061 CCTCATCCTCGGCACCTG 59.497 66.667 0.00 0.00 0.00 4.00
2596 2647 1.398799 AAGGAGGAAGGAGAGGGAGA 58.601 55.000 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.572941 GAACGAGTTTTGGCCGACC 59.427 57.895 0.00 0.00 0.00 4.79
11 12 1.203313 CGAACGAGTTTTGGCCGAC 59.797 57.895 0.00 0.00 0.00 4.79
12 13 1.957186 CCGAACGAGTTTTGGCCGA 60.957 57.895 0.00 0.00 31.46 5.54
13 14 2.554272 CCGAACGAGTTTTGGCCG 59.446 61.111 0.00 0.00 31.46 6.13
14 15 1.167781 TTCCCGAACGAGTTTTGGCC 61.168 55.000 0.00 0.00 37.43 5.36
15 16 0.040692 GTTCCCGAACGAGTTTTGGC 60.041 55.000 0.00 0.00 37.43 4.52
16 17 1.263217 CAGTTCCCGAACGAGTTTTGG 59.737 52.381 2.06 0.00 45.50 3.28
17 18 1.333791 GCAGTTCCCGAACGAGTTTTG 60.334 52.381 2.06 0.00 45.50 2.44
18 19 0.942252 GCAGTTCCCGAACGAGTTTT 59.058 50.000 2.06 0.00 45.50 2.43
19 20 0.883370 GGCAGTTCCCGAACGAGTTT 60.883 55.000 2.06 0.00 45.50 2.66
20 21 1.301479 GGCAGTTCCCGAACGAGTT 60.301 57.895 2.06 0.00 45.50 3.01
21 22 2.342648 GGCAGTTCCCGAACGAGT 59.657 61.111 2.06 0.00 45.50 4.18
22 23 1.738099 CTGGCAGTTCCCGAACGAG 60.738 63.158 6.28 1.20 45.50 4.18
23 24 2.204461 TCTGGCAGTTCCCGAACGA 61.204 57.895 15.27 0.00 45.50 3.85
24 25 2.027625 GTCTGGCAGTTCCCGAACG 61.028 63.158 15.27 0.00 45.50 3.95
25 26 1.671379 GGTCTGGCAGTTCCCGAAC 60.671 63.158 15.27 2.92 41.45 3.95
26 27 2.144078 TGGTCTGGCAGTTCCCGAA 61.144 57.895 15.27 0.74 29.46 4.30
27 28 2.525629 TGGTCTGGCAGTTCCCGA 60.526 61.111 15.27 1.42 0.00 5.14
28 29 2.358737 GTGGTCTGGCAGTTCCCG 60.359 66.667 15.27 0.00 0.00 5.14
29 30 1.600916 GTGTGGTCTGGCAGTTCCC 60.601 63.158 15.27 13.20 0.00 3.97
30 31 0.886490 CTGTGTGGTCTGGCAGTTCC 60.886 60.000 15.27 17.57 0.00 3.62
31 32 0.179045 ACTGTGTGGTCTGGCAGTTC 60.179 55.000 15.27 8.98 38.86 3.01
32 33 0.179045 GACTGTGTGGTCTGGCAGTT 60.179 55.000 15.27 0.00 41.59 3.16
33 34 1.447643 GACTGTGTGGTCTGGCAGT 59.552 57.895 15.27 0.00 43.85 4.40
34 35 1.302033 GGACTGTGTGGTCTGGCAG 60.302 63.158 8.58 8.58 36.55 4.85
35 36 2.818169 GGGACTGTGTGGTCTGGCA 61.818 63.158 0.00 0.00 36.55 4.92
36 37 2.032681 GGGACTGTGTGGTCTGGC 59.967 66.667 0.00 0.00 36.55 4.85
37 38 2.343758 CGGGACTGTGTGGTCTGG 59.656 66.667 0.00 0.00 36.55 3.86
38 39 1.006102 GACGGGACTGTGTGGTCTG 60.006 63.158 0.00 0.00 36.55 3.51
39 40 1.152525 AGACGGGACTGTGTGGTCT 60.153 57.895 0.00 0.00 36.55 3.85
40 41 1.006102 CAGACGGGACTGTGTGGTC 60.006 63.158 0.77 0.00 33.73 4.02
41 42 2.507854 CCAGACGGGACTGTGTGGT 61.508 63.158 16.90 0.00 45.59 4.16
42 43 2.343758 CCAGACGGGACTGTGTGG 59.656 66.667 12.37 12.37 45.46 4.17
53 54 1.219522 GACACCGAAACACCCAGACG 61.220 60.000 0.00 0.00 0.00 4.18
54 55 1.219522 CGACACCGAAACACCCAGAC 61.220 60.000 0.00 0.00 38.22 3.51
55 56 1.068417 CGACACCGAAACACCCAGA 59.932 57.895 0.00 0.00 38.22 3.86
56 57 1.959226 CCGACACCGAAACACCCAG 60.959 63.158 0.00 0.00 38.22 4.45
57 58 1.398174 TACCGACACCGAAACACCCA 61.398 55.000 0.00 0.00 38.22 4.51
58 59 0.037046 ATACCGACACCGAAACACCC 60.037 55.000 0.00 0.00 38.22 4.61
59 60 1.073177 CATACCGACACCGAAACACC 58.927 55.000 0.00 0.00 38.22 4.16
60 61 1.723003 GTCATACCGACACCGAAACAC 59.277 52.381 0.00 0.00 44.69 3.32
61 62 2.068837 GTCATACCGACACCGAAACA 57.931 50.000 0.00 0.00 44.69 2.83
74 75 3.130516 TCTCCAACTCGATGGTGTCATAC 59.869 47.826 5.00 0.00 41.46 2.39
75 76 3.361786 TCTCCAACTCGATGGTGTCATA 58.638 45.455 5.00 0.00 41.46 2.15
76 77 2.179427 TCTCCAACTCGATGGTGTCAT 58.821 47.619 5.00 0.00 41.46 3.06
77 78 1.627864 TCTCCAACTCGATGGTGTCA 58.372 50.000 5.00 0.00 41.46 3.58
78 79 2.544685 CATCTCCAACTCGATGGTGTC 58.455 52.381 5.00 0.00 41.46 3.67
79 80 1.406069 GCATCTCCAACTCGATGGTGT 60.406 52.381 5.00 0.00 41.46 4.16
80 81 1.134580 AGCATCTCCAACTCGATGGTG 60.135 52.381 5.00 3.15 44.09 4.17
81 82 1.198713 AGCATCTCCAACTCGATGGT 58.801 50.000 5.00 0.00 41.86 3.55
82 83 1.863267 GAGCATCTCCAACTCGATGG 58.137 55.000 0.00 0.00 42.12 3.51
95 96 7.475840 CCAACCAAAGAGTAAATTAGAGCATC 58.524 38.462 0.00 0.00 0.00 3.91
96 97 6.127619 GCCAACCAAAGAGTAAATTAGAGCAT 60.128 38.462 0.00 0.00 0.00 3.79
97 98 5.183140 GCCAACCAAAGAGTAAATTAGAGCA 59.817 40.000 0.00 0.00 0.00 4.26
98 99 5.416013 AGCCAACCAAAGAGTAAATTAGAGC 59.584 40.000 0.00 0.00 0.00 4.09
99 100 7.454260 AAGCCAACCAAAGAGTAAATTAGAG 57.546 36.000 0.00 0.00 0.00 2.43
100 101 7.255801 CCAAAGCCAACCAAAGAGTAAATTAGA 60.256 37.037 0.00 0.00 0.00 2.10
101 102 6.868339 CCAAAGCCAACCAAAGAGTAAATTAG 59.132 38.462 0.00 0.00 0.00 1.73
102 103 6.239458 CCCAAAGCCAACCAAAGAGTAAATTA 60.239 38.462 0.00 0.00 0.00 1.40
103 104 5.454613 CCCAAAGCCAACCAAAGAGTAAATT 60.455 40.000 0.00 0.00 0.00 1.82
104 105 4.040339 CCCAAAGCCAACCAAAGAGTAAAT 59.960 41.667 0.00 0.00 0.00 1.40
105 106 3.386402 CCCAAAGCCAACCAAAGAGTAAA 59.614 43.478 0.00 0.00 0.00 2.01
106 107 2.962421 CCCAAAGCCAACCAAAGAGTAA 59.038 45.455 0.00 0.00 0.00 2.24
107 108 2.593026 CCCAAAGCCAACCAAAGAGTA 58.407 47.619 0.00 0.00 0.00 2.59
108 109 1.413118 CCCAAAGCCAACCAAAGAGT 58.587 50.000 0.00 0.00 0.00 3.24
109 110 0.033920 GCCCAAAGCCAACCAAAGAG 59.966 55.000 0.00 0.00 34.35 2.85
110 111 0.398381 AGCCCAAAGCCAACCAAAGA 60.398 50.000 0.00 0.00 45.47 2.52
111 112 0.469494 AAGCCCAAAGCCAACCAAAG 59.531 50.000 0.00 0.00 45.47 2.77
112 113 0.915364 AAAGCCCAAAGCCAACCAAA 59.085 45.000 0.00 0.00 45.47 3.28
113 114 0.467804 GAAAGCCCAAAGCCAACCAA 59.532 50.000 0.00 0.00 45.47 3.67
114 115 0.689080 TGAAAGCCCAAAGCCAACCA 60.689 50.000 0.00 0.00 45.47 3.67
115 116 0.033920 CTGAAAGCCCAAAGCCAACC 59.966 55.000 0.00 0.00 45.47 3.77
116 117 3.593834 CTGAAAGCCCAAAGCCAAC 57.406 52.632 0.00 0.00 45.47 3.77
128 129 2.873288 GCCTTCGGCTGCTGAAAG 59.127 61.111 22.95 18.48 46.69 2.62
164 165 2.808567 GCCATCCCCGCAAAAAGAAAAA 60.809 45.455 0.00 0.00 0.00 1.94
165 166 1.270571 GCCATCCCCGCAAAAAGAAAA 60.271 47.619 0.00 0.00 0.00 2.29
166 167 0.320050 GCCATCCCCGCAAAAAGAAA 59.680 50.000 0.00 0.00 0.00 2.52
167 168 0.541764 AGCCATCCCCGCAAAAAGAA 60.542 50.000 0.00 0.00 0.00 2.52
168 169 0.965363 GAGCCATCCCCGCAAAAAGA 60.965 55.000 0.00 0.00 0.00 2.52
169 170 1.512694 GAGCCATCCCCGCAAAAAG 59.487 57.895 0.00 0.00 0.00 2.27
170 171 1.981853 GGAGCCATCCCCGCAAAAA 60.982 57.895 0.00 0.00 40.03 1.94
171 172 2.362375 GGAGCCATCCCCGCAAAA 60.362 61.111 0.00 0.00 40.03 2.44
180 181 1.373570 CAAAGAACGGAGGAGCCATC 58.626 55.000 0.00 0.00 35.94 3.51
181 182 0.678048 GCAAAGAACGGAGGAGCCAT 60.678 55.000 0.00 0.00 35.94 4.40
182 183 1.302511 GCAAAGAACGGAGGAGCCA 60.303 57.895 0.00 0.00 35.94 4.75
203 204 0.178891 AAGCAGAGGGAGACAGGGAA 60.179 55.000 0.00 0.00 0.00 3.97
206 207 1.818642 CAAAAGCAGAGGGAGACAGG 58.181 55.000 0.00 0.00 0.00 4.00
323 324 0.564171 TTTATAGGCGGGGAGGAGGA 59.436 55.000 0.00 0.00 0.00 3.71
382 383 3.275848 TCCAGAGAGGGGAAAAGAGAA 57.724 47.619 0.00 0.00 38.24 2.87
389 396 0.793617 AGTCCTTCCAGAGAGGGGAA 59.206 55.000 0.00 0.00 39.73 3.97
541 548 3.817647 ACTTTCACACAGAATCTCCAAGC 59.182 43.478 0.00 0.00 35.83 4.01
606 613 1.438651 TTCGTCGCAAGGATTCCAAG 58.561 50.000 5.29 0.00 38.47 3.61
649 656 5.451798 GGTTTCTGACTGGAAATTTCAGCAA 60.452 40.000 19.49 3.11 37.31 3.91
686 693 1.635663 AAATTTCGGCAGAGCGACGG 61.636 55.000 0.00 0.00 0.00 4.79
691 698 1.131315 GACAGGAAATTTCGGCAGAGC 59.869 52.381 11.95 0.00 0.00 4.09
894 901 0.112606 AGAAGGACTGGACGAGGACA 59.887 55.000 0.00 0.00 0.00 4.02
1067 1075 3.663176 GACGACGTGACGGGACCA 61.663 66.667 10.66 0.00 37.61 4.02
1080 1088 2.427905 CGAGCCGTTCAACGACGA 60.428 61.111 12.68 0.00 46.05 4.20
1085 1093 3.119096 GCCTCCGAGCCGTTCAAC 61.119 66.667 0.00 0.00 0.00 3.18
1086 1094 4.735132 CGCCTCCGAGCCGTTCAA 62.735 66.667 0.00 0.00 36.29 2.69
1130 1153 1.435515 CTTCCGCTTCCTCTCCTCG 59.564 63.158 0.00 0.00 0.00 4.63
1145 1168 1.627550 GGTTCGACTCCTTGCGCTTC 61.628 60.000 9.73 0.00 0.00 3.86
1196 1219 4.687215 TCGTCCACCTGCAGCAGC 62.687 66.667 17.81 1.71 42.57 5.25
1491 1514 2.486203 CGATCTGCTAGCAGTAGTAGGG 59.514 54.545 36.99 19.67 43.96 3.53
1520 1543 2.031516 CAGAGCTGCACGGAACCAG 61.032 63.158 1.02 0.00 0.00 4.00
1531 1554 0.441533 GCATCGACAACACAGAGCTG 59.558 55.000 0.00 0.00 0.00 4.24
1546 1572 5.179742 AGCACATACTACTACTAGACGCATC 59.820 44.000 0.00 0.00 0.00 3.91
1554 1580 9.745880 GAAAAGCATAAGCACATACTACTACTA 57.254 33.333 0.00 0.00 45.49 1.82
1555 1581 7.711339 GGAAAAGCATAAGCACATACTACTACT 59.289 37.037 0.00 0.00 45.49 2.57
1556 1582 7.711339 AGGAAAAGCATAAGCACATACTACTAC 59.289 37.037 0.00 0.00 45.49 2.73
1557 1583 7.792032 AGGAAAAGCATAAGCACATACTACTA 58.208 34.615 0.00 0.00 45.49 1.82
1558 1584 6.653989 AGGAAAAGCATAAGCACATACTACT 58.346 36.000 0.00 0.00 45.49 2.57
1559 1585 6.017852 GGAGGAAAAGCATAAGCACATACTAC 60.018 42.308 0.00 0.00 45.49 2.73
1587 1622 3.961408 CCACCCAATAGCACTACTCTACT 59.039 47.826 0.00 0.00 0.00 2.57
1599 1634 2.603008 CCCCTGCCCACCCAATAG 59.397 66.667 0.00 0.00 0.00 1.73
1636 1672 3.644884 AGTCAGTCGAAACAGGTACAG 57.355 47.619 0.00 0.00 0.00 2.74
1642 1678 6.861572 TCACACTATAAAGTCAGTCGAAACAG 59.138 38.462 0.00 0.00 31.97 3.16
1646 1682 6.321848 TGTCACACTATAAAGTCAGTCGAA 57.678 37.500 0.00 0.00 31.97 3.71
1677 1713 2.325583 AACCACACACATTGTCGTCT 57.674 45.000 0.00 0.00 35.67 4.18
1678 1714 4.742438 ATAAACCACACACATTGTCGTC 57.258 40.909 0.00 0.00 35.67 4.20
1784 1820 7.106890 AGTTGCTCTTATTACTCTTTTCTCCC 58.893 38.462 0.00 0.00 0.00 4.30
1883 1919 4.903045 ACCCAAATCTAAAAGAGGACGA 57.097 40.909 0.00 0.00 0.00 4.20
1942 1980 1.396996 GGCATGATCTAAAACGCACGT 59.603 47.619 0.00 0.00 0.00 4.49
1945 1983 1.401552 GCTGGCATGATCTAAAACGCA 59.598 47.619 0.00 0.00 0.00 5.24
2074 2121 0.939106 GCCAAAACAAGCGCGTGAAT 60.939 50.000 29.85 14.79 0.00 2.57
2144 2192 4.147449 CGAGATGAGTGGGCGGCA 62.147 66.667 12.47 0.00 0.00 5.69
2167 2215 3.827898 GCGGCGAGGCTAGTGAGT 61.828 66.667 12.98 0.00 0.00 3.41
2217 2265 0.096454 CTCCGCGAAAATCCGAAACC 59.904 55.000 8.23 0.00 0.00 3.27
2371 2419 2.999331 GGGAAAATTCATCTCCCGACA 58.001 47.619 0.00 0.00 39.59 4.35
2411 2462 4.212913 GAGGCGCGAGATCCTGCA 62.213 66.667 12.10 0.00 31.71 4.41
2496 2547 1.191489 TGGCTTCCACGTCCATCTCA 61.191 55.000 0.00 0.00 0.00 3.27
2596 2647 2.282958 TTGCTCCGTCCTCCTCGT 60.283 61.111 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.