Multiple sequence alignment - TraesCS3B01G503000

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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 TraesCS3B01G503000 chr3B 100.000 3227 0 0 1 3227 747098325 747101551 0.000000e+00 5960
1 TraesCS3B01G503000 chr3B 97.042 1724 34 3 771 2488 744541498 744539786 0.000000e+00 2885
2 TraesCS3B01G503000 chr3B 86.656 637 50 14 156 771 744542163 744541541 0.000000e+00 673
3 TraesCS3B01G503000 chr3A 96.628 1720 53 3 772 2488 629063523 629065240 0.000000e+00 2850
4 TraesCS3B01G503000 chr3A 96.049 1721 47 8 771 2488 696348474 696346772 0.000000e+00 2782
5 TraesCS3B01G503000 chr3A 93.548 744 42 4 2488 3227 704647656 704648397 0.000000e+00 1103
6 TraesCS3B01G503000 chr3A 92.829 753 47 5 2479 3227 459080733 459079984 0.000000e+00 1085
7 TraesCS3B01G503000 chr3A 92.071 618 40 6 156 770 696349129 696348518 0.000000e+00 861
8 TraesCS3B01G503000 chr3A 86.427 641 47 8 156 771 629062867 629063492 0.000000e+00 665
9 TraesCS3B01G503000 chr3D 95.894 1729 47 9 772 2488 560281207 560279491 0.000000e+00 2778
10 TraesCS3B01G503000 chr3D 88.474 616 53 9 162 771 560281841 560281238 0.000000e+00 728
11 TraesCS3B01G503000 chr7A 91.422 1632 114 20 771 2386 5794830 5796451 0.000000e+00 2215
12 TraesCS3B01G503000 chr7A 93.674 743 41 4 2488 3227 615547908 615547169 0.000000e+00 1107
13 TraesCS3B01G503000 chr7A 81.705 645 73 24 157 771 5524178 5524807 2.240000e-136 496
14 TraesCS3B01G503000 chr7A 83.490 533 61 17 247 769 6162307 6162822 3.770000e-129 472
15 TraesCS3B01G503000 chrUn 91.299 1632 116 20 771 2386 221377296 221378917 0.000000e+00 2204
16 TraesCS3B01G503000 chrUn 91.193 1635 118 20 771 2389 225550421 225552045 0.000000e+00 2198
17 TraesCS3B01G503000 chrUn 91.131 1635 119 20 771 2389 306578482 306576858 0.000000e+00 2193
18 TraesCS3B01G503000 chrUn 92.934 1302 81 10 1090 2389 285617361 285618653 0.000000e+00 1884
19 TraesCS3B01G503000 chrUn 91.326 1199 85 13 771 1955 228682165 228683358 0.000000e+00 1620
20 TraesCS3B01G503000 chrUn 81.677 644 68 28 157 769 318137161 318137785 1.040000e-134 490
21 TraesCS3B01G503000 chrUn 83.490 533 61 17 247 769 322967832 322967317 3.770000e-129 472
22 TraesCS3B01G503000 chrUn 81.282 390 48 11 776 1159 318137823 318138193 3.150000e-75 292
23 TraesCS3B01G503000 chrUn 85.106 141 15 5 635 771 221377115 221377253 4.340000e-29 139
24 TraesCS3B01G503000 chr2A 93.085 752 47 3 2479 3227 398875523 398876272 0.000000e+00 1096
25 TraesCS3B01G503000 chr2A 93.298 746 42 4 2488 3227 48841086 48841829 0.000000e+00 1094
26 TraesCS3B01G503000 chr4A 92.867 757 45 6 2478 3227 118952455 118951701 0.000000e+00 1090
27 TraesCS3B01G503000 chr1A 93.271 743 45 3 2488 3227 353632332 353633072 0.000000e+00 1090
28 TraesCS3B01G503000 chr6B 93.020 745 46 4 2488 3227 557939845 557939102 0.000000e+00 1083
29 TraesCS3B01G503000 chr6B 93.011 744 46 4 2488 3227 232747232 232746491 0.000000e+00 1081


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 TraesCS3B01G503000 chr3B 747098325 747101551 3226 False 5960.0 5960 100.0000 1 3227 1 chr3B.!!$F1 3226
1 TraesCS3B01G503000 chr3B 744539786 744542163 2377 True 1779.0 2885 91.8490 156 2488 2 chr3B.!!$R1 2332
2 TraesCS3B01G503000 chr3A 696346772 696349129 2357 True 1821.5 2782 94.0600 156 2488 2 chr3A.!!$R2 2332
3 TraesCS3B01G503000 chr3A 629062867 629065240 2373 False 1757.5 2850 91.5275 156 2488 2 chr3A.!!$F2 2332
4 TraesCS3B01G503000 chr3A 704647656 704648397 741 False 1103.0 1103 93.5480 2488 3227 1 chr3A.!!$F1 739
5 TraesCS3B01G503000 chr3A 459079984 459080733 749 True 1085.0 1085 92.8290 2479 3227 1 chr3A.!!$R1 748
6 TraesCS3B01G503000 chr3D 560279491 560281841 2350 True 1753.0 2778 92.1840 162 2488 2 chr3D.!!$R1 2326
7 TraesCS3B01G503000 chr7A 5794830 5796451 1621 False 2215.0 2215 91.4220 771 2386 1 chr7A.!!$F2 1615
8 TraesCS3B01G503000 chr7A 615547169 615547908 739 True 1107.0 1107 93.6740 2488 3227 1 chr7A.!!$R1 739
9 TraesCS3B01G503000 chr7A 5524178 5524807 629 False 496.0 496 81.7050 157 771 1 chr7A.!!$F1 614
10 TraesCS3B01G503000 chr7A 6162307 6162822 515 False 472.0 472 83.4900 247 769 1 chr7A.!!$F3 522
11 TraesCS3B01G503000 chrUn 225550421 225552045 1624 False 2198.0 2198 91.1930 771 2389 1 chrUn.!!$F1 1618
12 TraesCS3B01G503000 chrUn 306576858 306578482 1624 True 2193.0 2193 91.1310 771 2389 1 chrUn.!!$R1 1618
13 TraesCS3B01G503000 chrUn 285617361 285618653 1292 False 1884.0 1884 92.9340 1090 2389 1 chrUn.!!$F3 1299
14 TraesCS3B01G503000 chrUn 228682165 228683358 1193 False 1620.0 1620 91.3260 771 1955 1 chrUn.!!$F2 1184
15 TraesCS3B01G503000 chrUn 221377115 221378917 1802 False 1171.5 2204 88.2025 635 2386 2 chrUn.!!$F4 1751
16 TraesCS3B01G503000 chrUn 322967317 322967832 515 True 472.0 472 83.4900 247 769 1 chrUn.!!$R2 522
17 TraesCS3B01G503000 chrUn 318137161 318138193 1032 False 391.0 490 81.4795 157 1159 2 chrUn.!!$F5 1002
18 TraesCS3B01G503000 chr2A 398875523 398876272 749 False 1096.0 1096 93.0850 2479 3227 1 chr2A.!!$F2 748
19 TraesCS3B01G503000 chr2A 48841086 48841829 743 False 1094.0 1094 93.2980 2488 3227 1 chr2A.!!$F1 739
20 TraesCS3B01G503000 chr4A 118951701 118952455 754 True 1090.0 1090 92.8670 2478 3227 1 chr4A.!!$R1 749
21 TraesCS3B01G503000 chr1A 353632332 353633072 740 False 1090.0 1090 93.2710 2488 3227 1 chr1A.!!$F1 739
22 TraesCS3B01G503000 chr6B 557939102 557939845 743 True 1083.0 1083 93.0200 2488 3227 1 chr6B.!!$R2 739
23 TraesCS3B01G503000 chr6B 232746491 232747232 741 True 1081.0 1081 93.0110 2488 3227 1 chr6B.!!$R1 739

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
110 111 0.035458 CTCAGACTTCGGCCTGGTTT 59.965 55.0 0.0 0.0 0.0 3.27 F
615 675 0.035820 TAACGCCCAGTAAAGCCCAG 60.036 55.0 0.0 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2102 2287 0.535553 ACGCGAGGGAGATAGGACTC 60.536 60.000 15.93 0.0 36.31 3.36 R
2605 2792 3.381590 GGCTAGGGTAAGAAAAATGGCAG 59.618 47.826 0.00 0.0 0.00 4.85 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
21 22 4.046938 TCTCACACGAGATATGGCTTTC 57.953 45.455 0.00 0.00 43.55 2.62
22 23 3.701542 TCTCACACGAGATATGGCTTTCT 59.298 43.478 0.00 0.00 43.55 2.52
23 24 4.046938 TCACACGAGATATGGCTTTCTC 57.953 45.455 0.00 0.00 35.97 2.87
24 25 3.701542 TCACACGAGATATGGCTTTCTCT 59.298 43.478 0.00 0.00 36.94 3.10
25 26 4.160439 TCACACGAGATATGGCTTTCTCTT 59.840 41.667 0.00 0.00 36.94 2.85
26 27 4.269603 CACACGAGATATGGCTTTCTCTTG 59.730 45.833 12.99 12.99 41.49 3.02
27 28 4.081420 ACACGAGATATGGCTTTCTCTTGT 60.081 41.667 13.88 13.88 42.94 3.16
28 29 4.872691 CACGAGATATGGCTTTCTCTTGTT 59.127 41.667 0.00 0.00 36.94 2.83
29 30 5.352569 CACGAGATATGGCTTTCTCTTGTTT 59.647 40.000 0.00 0.00 36.94 2.83
30 31 5.940470 ACGAGATATGGCTTTCTCTTGTTTT 59.060 36.000 0.00 0.00 36.94 2.43
31 32 6.431234 ACGAGATATGGCTTTCTCTTGTTTTT 59.569 34.615 0.00 0.00 36.94 1.94
32 33 6.963805 CGAGATATGGCTTTCTCTTGTTTTTC 59.036 38.462 9.22 0.00 36.94 2.29
33 34 7.361201 CGAGATATGGCTTTCTCTTGTTTTTCA 60.361 37.037 9.22 0.00 36.94 2.69
34 35 8.358582 AGATATGGCTTTCTCTTGTTTTTCAT 57.641 30.769 0.00 0.00 0.00 2.57
35 36 8.810041 AGATATGGCTTTCTCTTGTTTTTCATT 58.190 29.630 0.00 0.00 0.00 2.57
36 37 8.992835 ATATGGCTTTCTCTTGTTTTTCATTC 57.007 30.769 0.00 0.00 0.00 2.67
37 38 6.219417 TGGCTTTCTCTTGTTTTTCATTCA 57.781 33.333 0.00 0.00 0.00 2.57
38 39 6.819284 TGGCTTTCTCTTGTTTTTCATTCAT 58.181 32.000 0.00 0.00 0.00 2.57
39 40 7.274447 TGGCTTTCTCTTGTTTTTCATTCATT 58.726 30.769 0.00 0.00 0.00 2.57
40 41 7.769970 TGGCTTTCTCTTGTTTTTCATTCATTT 59.230 29.630 0.00 0.00 0.00 2.32
41 42 8.066000 GGCTTTCTCTTGTTTTTCATTCATTTG 58.934 33.333 0.00 0.00 0.00 2.32
42 43 7.585210 GCTTTCTCTTGTTTTTCATTCATTTGC 59.415 33.333 0.00 0.00 0.00 3.68
43 44 8.489990 TTTCTCTTGTTTTTCATTCATTTGCA 57.510 26.923 0.00 0.00 0.00 4.08
44 45 8.665643 TTCTCTTGTTTTTCATTCATTTGCAT 57.334 26.923 0.00 0.00 0.00 3.96
45 46 8.665643 TCTCTTGTTTTTCATTCATTTGCATT 57.334 26.923 0.00 0.00 0.00 3.56
46 47 9.761504 TCTCTTGTTTTTCATTCATTTGCATTA 57.238 25.926 0.00 0.00 0.00 1.90
51 52 9.880064 TGTTTTTCATTCATTTGCATTATGTTG 57.120 25.926 8.63 8.17 0.00 3.33
52 53 9.881529 GTTTTTCATTCATTTGCATTATGTTGT 57.118 25.926 8.63 0.00 0.00 3.32
55 56 9.880064 TTTCATTCATTTGCATTATGTTGTTTG 57.120 25.926 8.63 3.14 0.00 2.93
56 57 8.030744 TCATTCATTTGCATTATGTTGTTTGG 57.969 30.769 8.63 0.00 0.00 3.28
57 58 6.798315 TTCATTTGCATTATGTTGTTTGGG 57.202 33.333 8.63 0.00 0.00 4.12
58 59 4.694509 TCATTTGCATTATGTTGTTTGGGC 59.305 37.500 8.63 0.00 0.00 5.36
59 60 4.348863 TTTGCATTATGTTGTTTGGGCT 57.651 36.364 0.00 0.00 0.00 5.19
60 61 3.316071 TGCATTATGTTGTTTGGGCTG 57.684 42.857 0.00 0.00 0.00 4.85
61 62 2.001872 GCATTATGTTGTTTGGGCTGC 58.998 47.619 0.00 0.00 0.00 5.25
62 63 2.620242 CATTATGTTGTTTGGGCTGCC 58.380 47.619 11.05 11.05 0.00 4.85
63 64 0.972883 TTATGTTGTTTGGGCTGCCC 59.027 50.000 30.97 30.97 45.71 5.36
64 65 0.114168 TATGTTGTTTGGGCTGCCCT 59.886 50.000 35.80 17.32 45.70 5.19
65 66 1.474332 ATGTTGTTTGGGCTGCCCTG 61.474 55.000 35.80 0.00 45.70 4.45
66 67 2.523902 TTGTTTGGGCTGCCCTGG 60.524 61.111 35.80 0.00 45.70 4.45
78 79 4.305956 CCCTGGCCTGCCCTTTGT 62.306 66.667 3.32 0.00 34.56 2.83
79 80 2.763215 CCTGGCCTGCCCTTTGTA 59.237 61.111 3.32 0.00 34.56 2.41
80 81 1.076549 CCTGGCCTGCCCTTTGTAA 59.923 57.895 3.32 0.00 34.56 2.41
81 82 0.324645 CCTGGCCTGCCCTTTGTAAT 60.325 55.000 3.32 0.00 34.56 1.89
82 83 1.560505 CTGGCCTGCCCTTTGTAATT 58.439 50.000 3.32 0.00 34.56 1.40
83 84 1.205417 CTGGCCTGCCCTTTGTAATTG 59.795 52.381 3.32 0.00 34.56 2.32
84 85 1.203112 TGGCCTGCCCTTTGTAATTGA 60.203 47.619 3.32 0.00 34.56 2.57
85 86 1.899142 GGCCTGCCCTTTGTAATTGAA 59.101 47.619 0.00 0.00 0.00 2.69
86 87 2.353704 GGCCTGCCCTTTGTAATTGAAC 60.354 50.000 0.00 0.00 0.00 3.18
87 88 2.562738 GCCTGCCCTTTGTAATTGAACT 59.437 45.455 0.00 0.00 0.00 3.01
88 89 3.761752 GCCTGCCCTTTGTAATTGAACTA 59.238 43.478 0.00 0.00 0.00 2.24
89 90 4.402474 GCCTGCCCTTTGTAATTGAACTAT 59.598 41.667 0.00 0.00 0.00 2.12
90 91 5.592688 GCCTGCCCTTTGTAATTGAACTATA 59.407 40.000 0.00 0.00 0.00 1.31
91 92 6.459710 GCCTGCCCTTTGTAATTGAACTATAC 60.460 42.308 0.00 0.00 0.00 1.47
92 93 6.828785 CCTGCCCTTTGTAATTGAACTATACT 59.171 38.462 0.00 0.00 0.00 2.12
93 94 7.012421 CCTGCCCTTTGTAATTGAACTATACTC 59.988 40.741 0.00 0.00 0.00 2.59
94 95 7.398829 TGCCCTTTGTAATTGAACTATACTCA 58.601 34.615 0.00 0.00 0.00 3.41
95 96 7.552687 TGCCCTTTGTAATTGAACTATACTCAG 59.447 37.037 0.00 0.00 0.00 3.35
96 97 7.769044 GCCCTTTGTAATTGAACTATACTCAGA 59.231 37.037 0.00 0.00 0.00 3.27
97 98 9.099454 CCCTTTGTAATTGAACTATACTCAGAC 57.901 37.037 0.00 0.00 0.00 3.51
98 99 9.877178 CCTTTGTAATTGAACTATACTCAGACT 57.123 33.333 0.00 0.00 0.00 3.24
101 102 9.569167 TTGTAATTGAACTATACTCAGACTTCG 57.431 33.333 0.00 0.00 0.00 3.79
102 103 8.188799 TGTAATTGAACTATACTCAGACTTCGG 58.811 37.037 0.00 0.00 0.00 4.30
103 104 4.634184 TGAACTATACTCAGACTTCGGC 57.366 45.455 0.00 0.00 0.00 5.54
104 105 3.380637 TGAACTATACTCAGACTTCGGCC 59.619 47.826 0.00 0.00 0.00 6.13
105 106 3.300239 ACTATACTCAGACTTCGGCCT 57.700 47.619 0.00 0.00 0.00 5.19
106 107 2.952978 ACTATACTCAGACTTCGGCCTG 59.047 50.000 0.00 0.00 0.00 4.85
107 108 1.115467 ATACTCAGACTTCGGCCTGG 58.885 55.000 0.00 0.00 0.00 4.45
108 109 0.251653 TACTCAGACTTCGGCCTGGT 60.252 55.000 0.00 0.00 0.00 4.00
109 110 1.122019 ACTCAGACTTCGGCCTGGTT 61.122 55.000 0.00 0.00 0.00 3.67
110 111 0.035458 CTCAGACTTCGGCCTGGTTT 59.965 55.000 0.00 0.00 0.00 3.27
111 112 0.250295 TCAGACTTCGGCCTGGTTTG 60.250 55.000 0.00 2.58 0.00 2.93
112 113 1.073199 AGACTTCGGCCTGGTTTGG 59.927 57.895 0.00 0.00 0.00 3.28
113 114 1.072505 GACTTCGGCCTGGTTTGGA 59.927 57.895 0.00 0.00 0.00 3.53
114 115 0.536460 GACTTCGGCCTGGTTTGGAA 60.536 55.000 0.00 0.00 0.00 3.53
115 116 0.112412 ACTTCGGCCTGGTTTGGAAT 59.888 50.000 0.00 0.00 0.00 3.01
116 117 1.353022 ACTTCGGCCTGGTTTGGAATA 59.647 47.619 0.00 0.00 0.00 1.75
117 118 1.743394 CTTCGGCCTGGTTTGGAATAC 59.257 52.381 0.00 0.00 0.00 1.89
118 119 0.693622 TCGGCCTGGTTTGGAATACA 59.306 50.000 0.00 0.00 0.00 2.29
119 120 1.283613 TCGGCCTGGTTTGGAATACAT 59.716 47.619 0.00 0.00 0.00 2.29
120 121 2.506231 TCGGCCTGGTTTGGAATACATA 59.494 45.455 0.00 0.00 0.00 2.29
121 122 3.054287 TCGGCCTGGTTTGGAATACATAA 60.054 43.478 0.00 0.00 0.00 1.90
122 123 3.315191 CGGCCTGGTTTGGAATACATAAG 59.685 47.826 0.00 0.00 0.00 1.73
123 124 3.636764 GGCCTGGTTTGGAATACATAAGG 59.363 47.826 0.00 0.00 0.00 2.69
124 125 4.278310 GCCTGGTTTGGAATACATAAGGT 58.722 43.478 0.00 0.00 0.00 3.50
125 126 5.442391 GCCTGGTTTGGAATACATAAGGTA 58.558 41.667 0.00 0.00 36.16 3.08
126 127 5.531287 GCCTGGTTTGGAATACATAAGGTAG 59.469 44.000 0.00 0.00 34.92 3.18
127 128 6.634039 GCCTGGTTTGGAATACATAAGGTAGA 60.634 42.308 0.00 0.00 34.92 2.59
128 129 6.766467 CCTGGTTTGGAATACATAAGGTAGAC 59.234 42.308 0.00 0.00 34.92 2.59
129 130 7.365652 CCTGGTTTGGAATACATAAGGTAGACT 60.366 40.741 0.00 0.00 34.92 3.24
130 131 7.335627 TGGTTTGGAATACATAAGGTAGACTG 58.664 38.462 0.00 0.00 34.92 3.51
131 132 7.037873 TGGTTTGGAATACATAAGGTAGACTGT 60.038 37.037 0.00 0.00 34.92 3.55
132 133 7.280205 GGTTTGGAATACATAAGGTAGACTGTG 59.720 40.741 0.00 0.00 34.92 3.66
133 134 6.479972 TGGAATACATAAGGTAGACTGTGG 57.520 41.667 0.00 0.00 34.92 4.17
134 135 5.163343 TGGAATACATAAGGTAGACTGTGGC 60.163 44.000 0.00 0.00 34.92 5.01
135 136 4.957684 ATACATAAGGTAGACTGTGGCC 57.042 45.455 0.00 0.00 34.92 5.36
136 137 2.834113 ACATAAGGTAGACTGTGGCCT 58.166 47.619 3.32 0.00 0.00 5.19
137 138 3.990369 ACATAAGGTAGACTGTGGCCTA 58.010 45.455 3.32 0.00 0.00 3.93
138 139 3.705072 ACATAAGGTAGACTGTGGCCTAC 59.295 47.826 3.32 0.69 35.67 3.18
143 144 3.697619 GTAGACTGTGGCCTACCTTTT 57.302 47.619 3.32 0.00 36.63 2.27
144 145 4.017177 GTAGACTGTGGCCTACCTTTTT 57.983 45.455 3.32 0.00 36.63 1.94
145 146 5.156608 GTAGACTGTGGCCTACCTTTTTA 57.843 43.478 3.32 0.00 36.63 1.52
146 147 4.929146 AGACTGTGGCCTACCTTTTTAT 57.071 40.909 3.32 0.00 36.63 1.40
147 148 4.844884 AGACTGTGGCCTACCTTTTTATC 58.155 43.478 3.32 0.00 36.63 1.75
148 149 3.945921 GACTGTGGCCTACCTTTTTATCC 59.054 47.826 3.32 0.00 36.63 2.59
149 150 3.332485 ACTGTGGCCTACCTTTTTATCCA 59.668 43.478 3.32 0.00 36.63 3.41
150 151 4.202631 ACTGTGGCCTACCTTTTTATCCAA 60.203 41.667 3.32 0.00 36.63 3.53
151 152 4.742012 TGTGGCCTACCTTTTTATCCAAA 58.258 39.130 3.32 0.00 36.63 3.28
152 153 5.148502 TGTGGCCTACCTTTTTATCCAAAA 58.851 37.500 3.32 0.00 36.63 2.44
153 154 5.602978 TGTGGCCTACCTTTTTATCCAAAAA 59.397 36.000 3.32 0.00 40.47 1.94
486 543 9.638239 TTAAATTCCTCAGCACAAATTCATAAC 57.362 29.630 0.00 0.00 0.00 1.89
490 547 7.288810 TCCTCAGCACAAATTCATAACTTTT 57.711 32.000 0.00 0.00 0.00 2.27
615 675 0.035820 TAACGCCCAGTAAAGCCCAG 60.036 55.000 0.00 0.00 0.00 4.45
708 770 1.599542 GAATTCTCCATCTTTCCGCGG 59.400 52.381 22.12 22.12 0.00 6.46
777 913 4.357947 GCCGACCACGTCAGCTCA 62.358 66.667 0.00 0.00 33.67 4.26
834 975 0.661483 GCTTGCCGCAAACTCTGTTC 60.661 55.000 7.33 0.00 38.92 3.18
841 988 1.527433 GCAAACTCTGTTCCTGGGGC 61.527 60.000 0.00 0.00 0.00 5.80
893 1052 3.329889 TGAGGCCTCCGGTGCAAT 61.330 61.111 29.95 7.91 0.00 3.56
976 1138 1.002430 TGGTGGCTGAGTTGACAGATC 59.998 52.381 0.00 0.00 39.94 2.75
2039 2224 4.148825 GAGCTCGGTGGCGTCCAT 62.149 66.667 0.00 0.00 35.28 3.41
2102 2287 1.202031 GGCGTGCTTGAAGTTTATCCG 60.202 52.381 0.00 0.00 0.00 4.18
2222 2407 2.175184 CTTGCGTCAAACCAGCGGAG 62.175 60.000 1.50 0.00 0.00 4.63
2269 2454 4.198530 TCAAGTGACACTCTTTTGCATCA 58.801 39.130 8.93 0.00 0.00 3.07
2611 2798 2.441532 GGCTCACCATGCTGCCAT 60.442 61.111 0.00 0.00 44.34 4.40
2616 2803 2.613691 CTCACCATGCTGCCATTTTTC 58.386 47.619 0.00 0.00 0.00 2.29
2683 2870 0.176219 TCGACGCGGTAAATCCCAAT 59.824 50.000 12.47 0.00 0.00 3.16
2714 2901 2.740440 CGGTGCATGCCACACGTA 60.740 61.111 16.68 0.00 46.50 3.57
2744 2931 3.951775 TGCGCAAGGGAACATTTAAAT 57.048 38.095 8.16 0.00 38.28 1.40
2785 2972 0.320697 AGCACGAACTACTCCCAACC 59.679 55.000 0.00 0.00 0.00 3.77
2805 2992 6.318900 CCAACCCCAAGACATATAAAGACTTC 59.681 42.308 0.00 0.00 0.00 3.01
2866 3053 6.486248 TGAATCAGTGAACAGTTTTTCGAAG 58.514 36.000 0.00 0.00 0.00 3.79
3111 3309 9.354673 AGATTCCCGAATATGTTTTGAATACAT 57.645 29.630 6.51 6.51 39.44 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.047822 GAGAAAGCCATATCTCGTGTGAG 58.952 47.826 0.00 0.00 43.99 3.51
3 4 4.052159 AGAGAAAGCCATATCTCGTGTG 57.948 45.455 0.00 0.00 45.34 3.82
4 5 4.437239 CAAGAGAAAGCCATATCTCGTGT 58.563 43.478 9.55 0.00 45.34 4.49
7 8 6.428385 AAAACAAGAGAAAGCCATATCTCG 57.572 37.500 0.00 0.00 45.34 4.04
8 9 7.820648 TGAAAAACAAGAGAAAGCCATATCTC 58.179 34.615 0.00 0.00 41.92 2.75
9 10 7.765695 TGAAAAACAAGAGAAAGCCATATCT 57.234 32.000 0.00 0.00 0.00 1.98
10 11 8.992835 AATGAAAAACAAGAGAAAGCCATATC 57.007 30.769 0.00 0.00 0.00 1.63
11 12 8.587608 TGAATGAAAAACAAGAGAAAGCCATAT 58.412 29.630 0.00 0.00 0.00 1.78
12 13 7.950512 TGAATGAAAAACAAGAGAAAGCCATA 58.049 30.769 0.00 0.00 0.00 2.74
13 14 6.819284 TGAATGAAAAACAAGAGAAAGCCAT 58.181 32.000 0.00 0.00 0.00 4.40
14 15 6.219417 TGAATGAAAAACAAGAGAAAGCCA 57.781 33.333 0.00 0.00 0.00 4.75
15 16 7.719778 AATGAATGAAAAACAAGAGAAAGCC 57.280 32.000 0.00 0.00 0.00 4.35
16 17 7.585210 GCAAATGAATGAAAAACAAGAGAAAGC 59.415 33.333 0.00 0.00 0.00 3.51
17 18 8.605746 TGCAAATGAATGAAAAACAAGAGAAAG 58.394 29.630 0.00 0.00 0.00 2.62
18 19 8.489990 TGCAAATGAATGAAAAACAAGAGAAA 57.510 26.923 0.00 0.00 0.00 2.52
19 20 8.665643 ATGCAAATGAATGAAAAACAAGAGAA 57.334 26.923 0.00 0.00 0.00 2.87
20 21 8.665643 AATGCAAATGAATGAAAAACAAGAGA 57.334 26.923 0.00 0.00 0.00 3.10
25 26 9.880064 CAACATAATGCAAATGAATGAAAAACA 57.120 25.926 16.80 0.00 0.00 2.83
26 27 9.881529 ACAACATAATGCAAATGAATGAAAAAC 57.118 25.926 16.80 0.00 0.00 2.43
29 30 9.880064 CAAACAACATAATGCAAATGAATGAAA 57.120 25.926 16.80 0.00 0.00 2.69
30 31 8.504815 CCAAACAACATAATGCAAATGAATGAA 58.495 29.630 16.80 0.00 0.00 2.57
31 32 7.119407 CCCAAACAACATAATGCAAATGAATGA 59.881 33.333 16.80 0.00 0.00 2.57
32 33 7.244898 CCCAAACAACATAATGCAAATGAATG 58.755 34.615 16.80 15.70 0.00 2.67
33 34 6.127952 GCCCAAACAACATAATGCAAATGAAT 60.128 34.615 16.80 5.03 0.00 2.57
34 35 5.180868 GCCCAAACAACATAATGCAAATGAA 59.819 36.000 16.80 0.00 0.00 2.57
35 36 4.694509 GCCCAAACAACATAATGCAAATGA 59.305 37.500 16.80 0.00 0.00 2.57
36 37 4.696402 AGCCCAAACAACATAATGCAAATG 59.304 37.500 10.08 10.08 0.00 2.32
37 38 4.696402 CAGCCCAAACAACATAATGCAAAT 59.304 37.500 0.00 0.00 0.00 2.32
38 39 4.063689 CAGCCCAAACAACATAATGCAAA 58.936 39.130 0.00 0.00 0.00 3.68
39 40 3.661944 CAGCCCAAACAACATAATGCAA 58.338 40.909 0.00 0.00 0.00 4.08
40 41 2.612471 GCAGCCCAAACAACATAATGCA 60.612 45.455 0.00 0.00 0.00 3.96
41 42 2.001872 GCAGCCCAAACAACATAATGC 58.998 47.619 0.00 0.00 0.00 3.56
42 43 2.620242 GGCAGCCCAAACAACATAATG 58.380 47.619 0.00 0.00 0.00 1.90
43 44 1.554617 GGGCAGCCCAAACAACATAAT 59.445 47.619 27.33 0.00 44.65 1.28
44 45 0.972883 GGGCAGCCCAAACAACATAA 59.027 50.000 27.33 0.00 44.65 1.90
45 46 2.664825 GGGCAGCCCAAACAACATA 58.335 52.632 27.33 0.00 44.65 2.29
46 47 3.470433 GGGCAGCCCAAACAACAT 58.530 55.556 27.33 0.00 44.65 2.71
61 62 2.439553 TTACAAAGGGCAGGCCAGGG 62.440 60.000 16.94 6.03 37.98 4.45
62 63 0.324645 ATTACAAAGGGCAGGCCAGG 60.325 55.000 16.94 6.41 37.98 4.45
63 64 1.205417 CAATTACAAAGGGCAGGCCAG 59.795 52.381 16.94 7.18 37.98 4.85
64 65 1.203112 TCAATTACAAAGGGCAGGCCA 60.203 47.619 16.94 0.00 37.98 5.36
65 66 1.555967 TCAATTACAAAGGGCAGGCC 58.444 50.000 4.33 4.33 0.00 5.19
66 67 2.562738 AGTTCAATTACAAAGGGCAGGC 59.437 45.455 0.00 0.00 0.00 4.85
67 68 6.828785 AGTATAGTTCAATTACAAAGGGCAGG 59.171 38.462 0.00 0.00 0.00 4.85
68 69 7.552687 TGAGTATAGTTCAATTACAAAGGGCAG 59.447 37.037 0.00 0.00 0.00 4.85
69 70 7.398829 TGAGTATAGTTCAATTACAAAGGGCA 58.601 34.615 0.00 0.00 0.00 5.36
70 71 7.769044 TCTGAGTATAGTTCAATTACAAAGGGC 59.231 37.037 0.00 0.00 0.00 5.19
71 72 9.099454 GTCTGAGTATAGTTCAATTACAAAGGG 57.901 37.037 0.00 0.00 0.00 3.95
72 73 9.877178 AGTCTGAGTATAGTTCAATTACAAAGG 57.123 33.333 0.00 0.00 0.00 3.11
75 76 9.569167 CGAAGTCTGAGTATAGTTCAATTACAA 57.431 33.333 0.00 0.00 0.00 2.41
76 77 8.188799 CCGAAGTCTGAGTATAGTTCAATTACA 58.811 37.037 0.00 0.00 0.00 2.41
77 78 7.167801 GCCGAAGTCTGAGTATAGTTCAATTAC 59.832 40.741 0.00 0.00 0.00 1.89
78 79 7.201145 GCCGAAGTCTGAGTATAGTTCAATTA 58.799 38.462 0.00 0.00 0.00 1.40
79 80 6.043411 GCCGAAGTCTGAGTATAGTTCAATT 58.957 40.000 0.00 0.00 0.00 2.32
80 81 5.452077 GGCCGAAGTCTGAGTATAGTTCAAT 60.452 44.000 0.00 0.00 0.00 2.57
81 82 4.142227 GGCCGAAGTCTGAGTATAGTTCAA 60.142 45.833 0.00 0.00 0.00 2.69
82 83 3.380637 GGCCGAAGTCTGAGTATAGTTCA 59.619 47.826 0.00 0.00 0.00 3.18
83 84 3.633065 AGGCCGAAGTCTGAGTATAGTTC 59.367 47.826 0.00 0.00 0.00 3.01
84 85 3.381908 CAGGCCGAAGTCTGAGTATAGTT 59.618 47.826 0.00 0.00 33.11 2.24
85 86 2.952978 CAGGCCGAAGTCTGAGTATAGT 59.047 50.000 0.00 0.00 33.11 2.12
86 87 2.294791 CCAGGCCGAAGTCTGAGTATAG 59.705 54.545 0.00 0.00 33.11 1.31
87 88 2.307768 CCAGGCCGAAGTCTGAGTATA 58.692 52.381 0.00 0.00 33.11 1.47
88 89 1.115467 CCAGGCCGAAGTCTGAGTAT 58.885 55.000 0.00 0.00 33.11 2.12
89 90 0.251653 ACCAGGCCGAAGTCTGAGTA 60.252 55.000 0.00 0.00 33.11 2.59
90 91 1.122019 AACCAGGCCGAAGTCTGAGT 61.122 55.000 0.00 0.00 33.11 3.41
91 92 0.035458 AAACCAGGCCGAAGTCTGAG 59.965 55.000 0.00 0.00 33.11 3.35
92 93 0.250295 CAAACCAGGCCGAAGTCTGA 60.250 55.000 0.00 0.00 33.11 3.27
93 94 1.237285 CCAAACCAGGCCGAAGTCTG 61.237 60.000 0.00 0.00 0.00 3.51
94 95 1.073199 CCAAACCAGGCCGAAGTCT 59.927 57.895 0.00 0.00 0.00 3.24
95 96 0.536460 TTCCAAACCAGGCCGAAGTC 60.536 55.000 0.00 0.00 0.00 3.01
96 97 0.112412 ATTCCAAACCAGGCCGAAGT 59.888 50.000 0.00 0.00 0.00 3.01
97 98 1.743394 GTATTCCAAACCAGGCCGAAG 59.257 52.381 0.00 0.00 0.00 3.79
98 99 1.074084 TGTATTCCAAACCAGGCCGAA 59.926 47.619 0.00 0.00 0.00 4.30
99 100 0.693622 TGTATTCCAAACCAGGCCGA 59.306 50.000 0.00 0.00 0.00 5.54
100 101 1.762708 ATGTATTCCAAACCAGGCCG 58.237 50.000 0.00 0.00 0.00 6.13
101 102 3.636764 CCTTATGTATTCCAAACCAGGCC 59.363 47.826 0.00 0.00 0.00 5.19
102 103 4.278310 ACCTTATGTATTCCAAACCAGGC 58.722 43.478 0.00 0.00 0.00 4.85
103 104 6.766467 GTCTACCTTATGTATTCCAAACCAGG 59.234 42.308 0.00 0.00 0.00 4.45
104 105 7.495934 CAGTCTACCTTATGTATTCCAAACCAG 59.504 40.741 0.00 0.00 0.00 4.00
105 106 7.037873 ACAGTCTACCTTATGTATTCCAAACCA 60.038 37.037 0.00 0.00 0.00 3.67
106 107 7.280205 CACAGTCTACCTTATGTATTCCAAACC 59.720 40.741 0.00 0.00 0.00 3.27
107 108 7.280205 CCACAGTCTACCTTATGTATTCCAAAC 59.720 40.741 0.00 0.00 0.00 2.93
108 109 7.335627 CCACAGTCTACCTTATGTATTCCAAA 58.664 38.462 0.00 0.00 0.00 3.28
109 110 6.631766 GCCACAGTCTACCTTATGTATTCCAA 60.632 42.308 0.00 0.00 0.00 3.53
110 111 5.163343 GCCACAGTCTACCTTATGTATTCCA 60.163 44.000 0.00 0.00 0.00 3.53
111 112 5.298347 GCCACAGTCTACCTTATGTATTCC 58.702 45.833 0.00 0.00 0.00 3.01
112 113 5.070580 AGGCCACAGTCTACCTTATGTATTC 59.929 44.000 5.01 0.00 0.00 1.75
113 114 4.969359 AGGCCACAGTCTACCTTATGTATT 59.031 41.667 5.01 0.00 0.00 1.89
114 115 4.557705 AGGCCACAGTCTACCTTATGTAT 58.442 43.478 5.01 0.00 0.00 2.29
115 116 3.990369 AGGCCACAGTCTACCTTATGTA 58.010 45.455 5.01 0.00 0.00 2.29
116 117 2.834113 AGGCCACAGTCTACCTTATGT 58.166 47.619 5.01 0.00 0.00 2.29
117 118 4.323553 GTAGGCCACAGTCTACCTTATG 57.676 50.000 5.01 0.00 44.06 1.90
124 125 5.104652 GGATAAAAAGGTAGGCCACAGTCTA 60.105 44.000 5.01 0.00 37.19 2.59
125 126 4.324331 GGATAAAAAGGTAGGCCACAGTCT 60.324 45.833 5.01 0.00 37.19 3.24
126 127 3.945921 GGATAAAAAGGTAGGCCACAGTC 59.054 47.826 5.01 0.00 37.19 3.51
127 128 3.332485 TGGATAAAAAGGTAGGCCACAGT 59.668 43.478 5.01 0.00 37.19 3.55
128 129 3.963129 TGGATAAAAAGGTAGGCCACAG 58.037 45.455 5.01 0.00 37.19 3.66
129 130 4.390129 TTGGATAAAAAGGTAGGCCACA 57.610 40.909 5.01 0.00 37.19 4.17
130 131 5.731957 TTTTGGATAAAAAGGTAGGCCAC 57.268 39.130 5.01 0.31 32.72 5.01
400 456 7.627585 AATCGATGACATTTTGACAAGTTTG 57.372 32.000 0.00 0.00 0.00 2.93
428 484 4.338682 ACCATGGTTGCGTACAAGTTTTTA 59.661 37.500 13.00 0.00 36.16 1.52
433 489 1.975660 AACCATGGTTGCGTACAAGT 58.024 45.000 29.32 0.25 36.16 3.16
437 493 2.785713 ACAAAACCATGGTTGCGTAC 57.214 45.000 30.44 0.00 38.47 3.67
544 602 5.504665 CGCCTGAAATTTAAATCGAGCTGAT 60.505 40.000 0.10 0.00 39.67 2.90
615 675 8.801913 GTTCAATATTGACCTACTACACGTTAC 58.198 37.037 17.76 4.74 36.83 2.50
688 750 1.599542 CCGCGGAAAGATGGAGAATTC 59.400 52.381 24.07 0.00 0.00 2.17
691 753 2.282827 TCCGCGGAAAGATGGAGAA 58.717 52.632 28.99 0.00 0.00 2.87
777 913 1.507141 CGGAAACAGAGCTTTGCGGT 61.507 55.000 3.74 0.00 40.21 5.68
893 1052 2.451493 TGGGGAGCAAACCTGGGA 60.451 61.111 0.00 0.00 0.00 4.37
976 1138 2.738521 CCTGCGACCACACCGAAG 60.739 66.667 0.00 0.00 32.61 3.79
2102 2287 0.535553 ACGCGAGGGAGATAGGACTC 60.536 60.000 15.93 0.00 36.31 3.36
2222 2407 3.801698 ACATGCATACCAGAGTGTCATC 58.198 45.455 0.00 0.00 0.00 2.92
2302 2489 5.990408 ACGAGACAATTAAAAGCAGAACAG 58.010 37.500 0.00 0.00 0.00 3.16
2359 2546 5.787494 AGAGACTATATGCCCATATGTTGGT 59.213 40.000 10.29 5.02 44.83 3.67
2397 2584 4.396166 CACCTGAATTTACAGACCATCCAC 59.604 45.833 0.00 0.00 39.94 4.02
2605 2792 3.381590 GGCTAGGGTAAGAAAAATGGCAG 59.618 47.826 0.00 0.00 0.00 4.85
2611 2798 4.829872 TCATCGGCTAGGGTAAGAAAAA 57.170 40.909 0.00 0.00 0.00 1.94
2616 2803 2.751166 CCATCATCGGCTAGGGTAAG 57.249 55.000 0.00 0.00 0.00 2.34
2683 2870 1.305219 GCACCGGCAAACTCATAGCA 61.305 55.000 0.00 0.00 40.72 3.49
2714 2901 2.653726 TCCCTTGCGCAACATAATGAT 58.346 42.857 21.02 0.00 0.00 2.45
2767 2954 0.672711 GGGTTGGGAGTAGTTCGTGC 60.673 60.000 0.00 0.00 0.00 5.34
2785 2972 5.057149 CCGGAAGTCTTTATATGTCTTGGG 58.943 45.833 0.00 0.00 0.00 4.12
2805 2992 6.821665 TGTCTAGGATTTGATTAGTTTTCCGG 59.178 38.462 0.00 0.00 0.00 5.14
2947 3144 5.915758 TGTTAATGAATTCGAAACCGGTTTG 59.084 36.000 36.17 25.58 32.11 2.93
2948 3145 6.074544 TGTTAATGAATTCGAAACCGGTTT 57.925 33.333 32.08 32.08 35.14 3.27
3002 3199 9.914131 GCTCCATAATTTAAAAGAAAGTTCAGT 57.086 29.630 0.00 0.00 0.00 3.41
3003 3200 9.912634 TGCTCCATAATTTAAAAGAAAGTTCAG 57.087 29.630 0.00 0.00 0.00 3.02
3188 3387 2.990514 GTGGTTTTGCAAAACTGTTCGT 59.009 40.909 39.36 0.00 45.70 3.85


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

AutoCloner maintained by Alex Coulton.