Multiple sequence alignment - TraesCS3D01G334800

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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 TraesCS3D01G334800 chr3D 100.000 3951 0 0 1 3951 446853249 446857199 0.000000e+00 7297
1 TraesCS3D01G334800 chr3D 87.231 603 54 12 1418 2014 446910626 446911211 0.000000e+00 665
2 TraesCS3D01G334800 chr3D 91.295 448 35 2 2550 2993 446912631 446913078 3.380000e-170 608
3 TraesCS3D01G334800 chr3D 88.542 480 41 9 2056 2522 446911199 446911677 1.590000e-158 569
4 TraesCS3D01G334800 chr3D 95.252 337 16 0 970 1306 446910081 446910417 5.810000e-148 534
5 TraesCS3D01G334800 chr3B 95.093 2323 65 20 813 3109 586340795 586343094 0.000000e+00 3613
6 TraesCS3D01G334800 chr3B 96.569 787 24 3 3167 3951 689421037 689421822 0.000000e+00 1301
7 TraesCS3D01G334800 chr3B 86.648 1071 99 24 970 2013 586421935 586422988 0.000000e+00 1146
8 TraesCS3D01G334800 chr3B 89.107 560 49 5 185 733 586339950 586340508 0.000000e+00 686
9 TraesCS3D01G334800 chr3B 94.048 420 25 0 2550 2969 586426563 586426982 4.310000e-179 638
10 TraesCS3D01G334800 chr3B 87.002 477 51 9 2056 2522 586422977 586423452 9.720000e-146 527
11 TraesCS3D01G334800 chr3B 81.910 199 31 5 422 620 586214429 586214622 3.160000e-36 163
12 TraesCS3D01G334800 chr3A 93.825 2332 84 34 821 3109 588657530 588659844 0.000000e+00 3454
13 TraesCS3D01G334800 chr3A 86.866 769 61 17 935 1684 588724451 588725198 0.000000e+00 824
14 TraesCS3D01G334800 chr3A 94.048 420 25 0 2550 2969 588728006 588728425 4.310000e-179 638
15 TraesCS3D01G334800 chr3A 89.362 423 37 7 2056 2471 588725576 588725997 3.500000e-145 525
16 TraesCS3D01G334800 chr3A 91.857 307 25 0 1708 2014 588725282 588725588 2.820000e-116 429
17 TraesCS3D01G334800 chr3A 83.871 434 29 11 286 715 588655772 588656168 3.730000e-100 375
18 TraesCS3D01G334800 chr3A 92.562 121 9 0 164 284 588644691 588644811 1.460000e-39 174
19 TraesCS3D01G334800 chr7D 97.633 845 16 4 3109 3951 49861959 49862801 0.000000e+00 1447
20 TraesCS3D01G334800 chr7D 90.632 854 65 8 3102 3951 517993129 517992287 0.000000e+00 1120
21 TraesCS3D01G334800 chr7D 88.538 855 71 16 3109 3951 630679455 630680294 0.000000e+00 1011
22 TraesCS3D01G334800 chr1A 81.658 1423 173 54 1399 2763 337985548 337986940 0.000000e+00 1101
23 TraesCS3D01G334800 chr1A 86.604 321 32 6 995 1305 337981718 337982037 1.050000e-90 344
24 TraesCS3D01G334800 chr1A 88.304 171 15 1 2760 2930 337987267 337987432 2.410000e-47 200
25 TraesCS3D01G334800 chr1D 90.284 844 66 10 3109 3951 482101960 482102788 0.000000e+00 1090
26 TraesCS3D01G334800 chr1D 81.614 1425 162 61 1399 2763 261881253 261879869 0.000000e+00 1088
27 TraesCS3D01G334800 chr1D 90.000 180 18 0 2760 2939 261879713 261879534 2.370000e-57 233
28 TraesCS3D01G334800 chr5D 90.094 848 70 9 3105 3951 57216429 57217263 0.000000e+00 1088
29 TraesCS3D01G334800 chr5D 90.035 853 56 9 3100 3951 510166335 510167159 0.000000e+00 1077
30 TraesCS3D01G334800 chr5D 89.333 300 32 0 3652 3951 510167589 510167888 1.040000e-100 377
31 TraesCS3D01G334800 chr1B 82.640 1106 118 41 1420 2481 349839433 349840508 0.000000e+00 911
32 TraesCS3D01G334800 chr1B 88.235 323 23 7 995 1305 349838132 349838451 4.820000e-99 372
33 TraesCS3D01G334800 chr1B 88.889 216 24 0 2548 2763 349840596 349840811 2.340000e-67 267
34 TraesCS3D01G334800 chr1B 92.398 171 13 0 2760 2930 349840966 349841136 1.100000e-60 244
35 TraesCS3D01G334800 chr7B 95.568 519 21 2 3109 3626 639810791 639810274 0.000000e+00 830
36 TraesCS3D01G334800 chr7B 96.024 327 12 1 3625 3951 639810170 639809845 7.520000e-147 531
37 TraesCS3D01G334800 chr6A 92.252 413 28 4 3106 3516 22430026 22430436 2.050000e-162 582
38 TraesCS3D01G334800 chr6A 89.908 436 34 4 3516 3951 22430744 22431169 1.600000e-153 553
39 TraesCS3D01G334800 chr5B 90.635 299 24 4 3652 3949 617040287 617040582 1.030000e-105 394


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 TraesCS3D01G334800 chr3D 446853249 446857199 3950 False 7297.000000 7297 100.000000 1 3951 1 chr3D.!!$F1 3950
1 TraesCS3D01G334800 chr3D 446910081 446913078 2997 False 594.000000 665 90.580000 970 2993 4 chr3D.!!$F2 2023
2 TraesCS3D01G334800 chr3B 586339950 586343094 3144 False 2149.500000 3613 92.100000 185 3109 2 chr3B.!!$F3 2924
3 TraesCS3D01G334800 chr3B 689421037 689421822 785 False 1301.000000 1301 96.569000 3167 3951 1 chr3B.!!$F2 784
4 TraesCS3D01G334800 chr3B 586421935 586426982 5047 False 770.333333 1146 89.232667 970 2969 3 chr3B.!!$F4 1999
5 TraesCS3D01G334800 chr3A 588655772 588659844 4072 False 1914.500000 3454 88.848000 286 3109 2 chr3A.!!$F2 2823
6 TraesCS3D01G334800 chr3A 588724451 588728425 3974 False 604.000000 824 90.533250 935 2969 4 chr3A.!!$F3 2034
7 TraesCS3D01G334800 chr7D 49861959 49862801 842 False 1447.000000 1447 97.633000 3109 3951 1 chr7D.!!$F1 842
8 TraesCS3D01G334800 chr7D 517992287 517993129 842 True 1120.000000 1120 90.632000 3102 3951 1 chr7D.!!$R1 849
9 TraesCS3D01G334800 chr7D 630679455 630680294 839 False 1011.000000 1011 88.538000 3109 3951 1 chr7D.!!$F2 842
10 TraesCS3D01G334800 chr1A 337981718 337987432 5714 False 548.333333 1101 85.522000 995 2930 3 chr1A.!!$F1 1935
11 TraesCS3D01G334800 chr1D 482101960 482102788 828 False 1090.000000 1090 90.284000 3109 3951 1 chr1D.!!$F1 842
12 TraesCS3D01G334800 chr1D 261879534 261881253 1719 True 660.500000 1088 85.807000 1399 2939 2 chr1D.!!$R1 1540
13 TraesCS3D01G334800 chr5D 57216429 57217263 834 False 1088.000000 1088 90.094000 3105 3951 1 chr5D.!!$F1 846
14 TraesCS3D01G334800 chr5D 510166335 510167888 1553 False 727.000000 1077 89.684000 3100 3951 2 chr5D.!!$F2 851
15 TraesCS3D01G334800 chr1B 349838132 349841136 3004 False 448.500000 911 88.040500 995 2930 4 chr1B.!!$F1 1935
16 TraesCS3D01G334800 chr7B 639809845 639810791 946 True 680.500000 830 95.796000 3109 3951 2 chr7B.!!$R1 842
17 TraesCS3D01G334800 chr6A 22430026 22431169 1143 False 567.500000 582 91.080000 3106 3951 2 chr6A.!!$F1 845

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
758 810 1.269448 ACATTTTGCTAAGGTGGCACG 59.731 47.619 12.17 0.0 39.55 5.34 F
773 1886 2.290916 TGGCACGCAATTAAACGAGAAA 59.709 40.909 0.00 0.0 0.00 2.52 F
2608 11718 2.978010 CCCAACGGCTTCAGCGTT 60.978 61.111 0.00 0.0 43.26 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2608 11718 0.544357 ACACGATGTCTCCCTTCCCA 60.544 55.000 0.00 0.0 0.00 4.37 R
2728 11839 1.128188 ACTTGAAAGGGCTCTCCGGT 61.128 55.000 0.00 0.0 41.52 5.28 R
3668 13580 4.101274 CCATGGATCAAATACCAATGCCAA 59.899 41.667 5.56 0.0 39.69 4.52 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
37 38 7.420184 AAAATCGAAAAACATCCATGGAAAC 57.580 32.000 20.67 4.53 0.00 2.78
58 59 5.734855 ACATATATGTTTTCCACACGAGC 57.265 39.130 12.75 0.00 38.61 5.03
59 60 5.182487 ACATATATGTTTTCCACACGAGCA 58.818 37.500 12.75 0.00 38.61 4.26
60 61 5.822519 ACATATATGTTTTCCACACGAGCAT 59.177 36.000 12.75 0.00 38.61 3.79
61 62 2.995466 ATGTTTTCCACACGAGCATG 57.005 45.000 0.00 0.00 38.61 4.06
62 63 1.674359 TGTTTTCCACACGAGCATGT 58.326 45.000 0.00 0.00 0.00 3.21
71 72 2.560504 ACACGAGCATGTGAAAACTCA 58.439 42.857 14.37 0.00 42.55 3.41
72 73 3.141398 ACACGAGCATGTGAAAACTCAT 58.859 40.909 14.37 0.00 42.55 2.90
73 74 3.565482 ACACGAGCATGTGAAAACTCATT 59.435 39.130 14.37 0.00 42.55 2.57
74 75 4.036734 ACACGAGCATGTGAAAACTCATTT 59.963 37.500 14.37 0.00 42.55 2.32
75 76 4.380678 CACGAGCATGTGAAAACTCATTTG 59.619 41.667 2.42 0.00 42.55 2.32
76 77 4.275689 ACGAGCATGTGAAAACTCATTTGA 59.724 37.500 0.00 0.00 0.00 2.69
77 78 5.048504 ACGAGCATGTGAAAACTCATTTGAT 60.049 36.000 0.00 0.00 0.00 2.57
78 79 5.860182 CGAGCATGTGAAAACTCATTTGATT 59.140 36.000 0.00 0.00 0.00 2.57
79 80 6.364165 CGAGCATGTGAAAACTCATTTGATTT 59.636 34.615 0.00 0.00 0.00 2.17
80 81 7.095940 CGAGCATGTGAAAACTCATTTGATTTT 60.096 33.333 0.00 0.00 0.00 1.82
81 82 9.195411 GAGCATGTGAAAACTCATTTGATTTTA 57.805 29.630 0.00 0.00 0.00 1.52
82 83 8.981647 AGCATGTGAAAACTCATTTGATTTTAC 58.018 29.630 0.00 0.00 0.00 2.01
83 84 7.946237 GCATGTGAAAACTCATTTGATTTTACG 59.054 33.333 0.00 0.00 0.00 3.18
84 85 8.967218 CATGTGAAAACTCATTTGATTTTACGT 58.033 29.630 0.00 0.00 0.00 3.57
90 91 8.447787 AAACTCATTTGATTTTACGTATGTGC 57.552 30.769 0.00 0.00 0.00 4.57
91 92 6.551736 ACTCATTTGATTTTACGTATGTGCC 58.448 36.000 0.00 0.00 0.00 5.01
92 93 6.374333 ACTCATTTGATTTTACGTATGTGCCT 59.626 34.615 0.00 0.00 0.00 4.75
93 94 7.551262 ACTCATTTGATTTTACGTATGTGCCTA 59.449 33.333 0.00 0.00 0.00 3.93
94 95 7.690228 TCATTTGATTTTACGTATGTGCCTAC 58.310 34.615 0.00 0.00 0.00 3.18
95 96 7.334671 TCATTTGATTTTACGTATGTGCCTACA 59.665 33.333 0.00 0.00 41.89 2.74
96 97 7.436430 TTTGATTTTACGTATGTGCCTACAA 57.564 32.000 0.00 0.00 40.84 2.41
97 98 6.656314 TGATTTTACGTATGTGCCTACAAG 57.344 37.500 0.00 0.00 40.84 3.16
98 99 6.399743 TGATTTTACGTATGTGCCTACAAGA 58.600 36.000 0.00 0.00 40.84 3.02
99 100 6.874664 TGATTTTACGTATGTGCCTACAAGAA 59.125 34.615 0.00 0.00 40.84 2.52
100 101 7.388224 TGATTTTACGTATGTGCCTACAAGAAA 59.612 33.333 0.00 0.00 40.84 2.52
101 102 7.493743 TTTTACGTATGTGCCTACAAGAAAA 57.506 32.000 0.00 0.00 40.84 2.29
102 103 7.675962 TTTACGTATGTGCCTACAAGAAAAT 57.324 32.000 0.00 0.00 40.84 1.82
103 104 8.774890 TTTACGTATGTGCCTACAAGAAAATA 57.225 30.769 0.00 0.00 40.84 1.40
104 105 8.774890 TTACGTATGTGCCTACAAGAAAATAA 57.225 30.769 0.00 0.00 40.84 1.40
105 106 7.675962 ACGTATGTGCCTACAAGAAAATAAA 57.324 32.000 0.00 0.00 40.84 1.40
106 107 8.101654 ACGTATGTGCCTACAAGAAAATAAAA 57.898 30.769 0.00 0.00 40.84 1.52
107 108 8.736244 ACGTATGTGCCTACAAGAAAATAAAAT 58.264 29.630 0.00 0.00 40.84 1.82
108 109 9.567848 CGTATGTGCCTACAAGAAAATAAAATT 57.432 29.630 0.00 0.00 40.84 1.82
111 112 9.643693 ATGTGCCTACAAGAAAATAAAATTCTG 57.356 29.630 0.00 0.00 40.84 3.02
112 113 8.087750 TGTGCCTACAAGAAAATAAAATTCTGG 58.912 33.333 0.00 0.00 37.22 3.86
113 114 7.063426 GTGCCTACAAGAAAATAAAATTCTGGC 59.937 37.037 7.87 7.87 40.22 4.85
114 115 6.535150 GCCTACAAGAAAATAAAATTCTGGCC 59.465 38.462 0.00 0.00 36.77 5.36
115 116 7.041721 CCTACAAGAAAATAAAATTCTGGCCC 58.958 38.462 0.00 0.00 37.22 5.80
116 117 6.432403 ACAAGAAAATAAAATTCTGGCCCA 57.568 33.333 0.00 0.00 37.22 5.36
117 118 6.836242 ACAAGAAAATAAAATTCTGGCCCAA 58.164 32.000 0.00 0.00 37.22 4.12
118 119 6.710295 ACAAGAAAATAAAATTCTGGCCCAAC 59.290 34.615 0.00 0.00 37.22 3.77
119 120 6.432403 AGAAAATAAAATTCTGGCCCAACA 57.568 33.333 0.00 0.00 35.85 3.33
120 121 6.836242 AGAAAATAAAATTCTGGCCCAACAA 58.164 32.000 0.00 0.00 35.85 2.83
121 122 6.710295 AGAAAATAAAATTCTGGCCCAACAAC 59.290 34.615 0.00 0.00 35.85 3.32
122 123 5.559148 AATAAAATTCTGGCCCAACAACA 57.441 34.783 0.00 0.00 0.00 3.33
123 124 2.908688 AAATTCTGGCCCAACAACAC 57.091 45.000 0.00 0.00 0.00 3.32
124 125 1.786937 AATTCTGGCCCAACAACACA 58.213 45.000 0.00 0.00 0.00 3.72
125 126 1.786937 ATTCTGGCCCAACAACACAA 58.213 45.000 0.00 0.00 0.00 3.33
126 127 1.561643 TTCTGGCCCAACAACACAAA 58.438 45.000 0.00 0.00 0.00 2.83
127 128 1.561643 TCTGGCCCAACAACACAAAA 58.438 45.000 0.00 0.00 0.00 2.44
128 129 1.902508 TCTGGCCCAACAACACAAAAA 59.097 42.857 0.00 0.00 0.00 1.94
129 130 2.093764 TCTGGCCCAACAACACAAAAAG 60.094 45.455 0.00 0.00 0.00 2.27
130 131 1.902508 TGGCCCAACAACACAAAAAGA 59.097 42.857 0.00 0.00 0.00 2.52
131 132 2.503356 TGGCCCAACAACACAAAAAGAT 59.497 40.909 0.00 0.00 0.00 2.40
132 133 3.130633 GGCCCAACAACACAAAAAGATC 58.869 45.455 0.00 0.00 0.00 2.75
133 134 2.794350 GCCCAACAACACAAAAAGATCG 59.206 45.455 0.00 0.00 0.00 3.69
134 135 2.794350 CCCAACAACACAAAAAGATCGC 59.206 45.455 0.00 0.00 0.00 4.58
135 136 2.794350 CCAACAACACAAAAAGATCGCC 59.206 45.455 0.00 0.00 0.00 5.54
136 137 2.793278 ACAACACAAAAAGATCGCCC 57.207 45.000 0.00 0.00 0.00 6.13
137 138 2.028130 ACAACACAAAAAGATCGCCCA 58.972 42.857 0.00 0.00 0.00 5.36
138 139 2.627699 ACAACACAAAAAGATCGCCCAT 59.372 40.909 0.00 0.00 0.00 4.00
139 140 3.244976 CAACACAAAAAGATCGCCCATC 58.755 45.455 0.00 0.00 0.00 3.51
140 141 2.795329 ACACAAAAAGATCGCCCATCT 58.205 42.857 0.00 0.00 44.56 2.90
151 152 6.365970 AGATCGCCCATCTTAGAAATATGT 57.634 37.500 0.00 0.00 38.95 2.29
152 153 6.773638 AGATCGCCCATCTTAGAAATATGTT 58.226 36.000 0.00 0.00 38.95 2.71
153 154 7.227156 AGATCGCCCATCTTAGAAATATGTTT 58.773 34.615 0.00 0.00 38.95 2.83
154 155 7.721399 AGATCGCCCATCTTAGAAATATGTTTT 59.279 33.333 0.00 0.00 38.95 2.43
155 156 7.639113 TCGCCCATCTTAGAAATATGTTTTT 57.361 32.000 0.00 0.00 0.00 1.94
156 157 7.703328 TCGCCCATCTTAGAAATATGTTTTTC 58.297 34.615 0.00 0.00 36.13 2.29
157 158 6.918022 CGCCCATCTTAGAAATATGTTTTTCC 59.082 38.462 0.00 0.00 36.47 3.13
158 159 7.210174 GCCCATCTTAGAAATATGTTTTTCCC 58.790 38.462 0.00 0.00 36.47 3.97
159 160 7.069950 GCCCATCTTAGAAATATGTTTTTCCCT 59.930 37.037 0.00 0.00 36.47 4.20
160 161 9.640952 CCCATCTTAGAAATATGTTTTTCCCTA 57.359 33.333 0.00 0.00 36.47 3.53
242 243 6.165577 TGTATGACACAATCCATATCCGATG 58.834 40.000 0.00 0.00 32.95 3.84
245 246 5.436175 TGACACAATCCATATCCGATGTTT 58.564 37.500 0.00 0.00 0.00 2.83
253 254 5.863965 TCCATATCCGATGTTTGATGCTTA 58.136 37.500 0.00 0.00 0.00 3.09
273 274 6.127196 TGCTTACCACCAAATTTTCTTGAACT 60.127 34.615 0.00 0.00 0.00 3.01
312 321 2.602257 TTATGTCGGTGGATGCAGAG 57.398 50.000 0.00 0.00 0.00 3.35
333 342 6.742718 CAGAGGTACAAATGAAAAATACGCAG 59.257 38.462 0.00 0.00 0.00 5.18
336 345 3.584834 ACAAATGAAAAATACGCAGCCC 58.415 40.909 0.00 0.00 0.00 5.19
343 352 3.785189 AATACGCAGCCCGCTACCG 62.785 63.158 7.21 7.21 41.76 4.02
409 418 3.492337 TCGGTATTCAAAACCTTGGCTT 58.508 40.909 0.00 0.00 34.66 4.35
413 422 5.606505 GGTATTCAAAACCTTGGCTTCAAA 58.393 37.500 0.00 0.00 33.97 2.69
449 458 2.736144 TAACAGTGTAGGTCTTGCCG 57.264 50.000 0.00 0.00 43.70 5.69
477 487 4.820897 TCATCGTTGAGTCAGCATAGTTT 58.179 39.130 7.79 0.00 0.00 2.66
479 489 4.521130 TCGTTGAGTCAGCATAGTTTCT 57.479 40.909 7.79 0.00 0.00 2.52
494 505 9.539825 AGCATAGTTTCTCATAGACTACATTTG 57.460 33.333 0.00 0.00 0.00 2.32
564 577 9.866798 GCACTAGTACCAACTTAACTAATTAGT 57.133 33.333 12.50 12.50 37.15 2.24
683 697 2.092103 AGTTGACTTGGCCCAGTTAACA 60.092 45.455 32.87 16.97 42.81 2.41
740 754 8.502047 TGAGTATCATAGGTAGTAGTAGGACA 57.498 38.462 0.00 0.00 42.56 4.02
741 755 9.113797 TGAGTATCATAGGTAGTAGTAGGACAT 57.886 37.037 0.00 0.00 42.56 3.06
751 803 6.985059 GGTAGTAGTAGGACATTTTGCTAAGG 59.015 42.308 0.00 0.00 28.34 2.69
758 810 1.269448 ACATTTTGCTAAGGTGGCACG 59.731 47.619 12.17 0.00 39.55 5.34
767 819 2.432206 AAGGTGGCACGCAATTAAAC 57.568 45.000 12.17 0.00 43.02 2.01
773 1886 2.290916 TGGCACGCAATTAAACGAGAAA 59.709 40.909 0.00 0.00 0.00 2.52
775 1888 3.731717 GGCACGCAATTAAACGAGAAAAA 59.268 39.130 0.00 0.00 0.00 1.94
776 1889 4.143618 GGCACGCAATTAAACGAGAAAAAG 60.144 41.667 0.00 0.00 0.00 2.27
777 1890 4.673311 GCACGCAATTAAACGAGAAAAAGA 59.327 37.500 0.00 0.00 0.00 2.52
780 1893 6.300902 CACGCAATTAAACGAGAAAAAGAGAG 59.699 38.462 0.00 0.00 0.00 3.20
781 1894 5.790495 CGCAATTAAACGAGAAAAAGAGAGG 59.210 40.000 0.00 0.00 0.00 3.69
783 1896 7.530863 GCAATTAAACGAGAAAAAGAGAGGAT 58.469 34.615 0.00 0.00 0.00 3.24
785 1898 8.721478 CAATTAAACGAGAAAAAGAGAGGATGA 58.279 33.333 0.00 0.00 0.00 2.92
786 1899 7.891183 TTAAACGAGAAAAAGAGAGGATGAG 57.109 36.000 0.00 0.00 0.00 2.90
788 1901 6.591750 AACGAGAAAAAGAGAGGATGAGTA 57.408 37.500 0.00 0.00 0.00 2.59
789 1902 6.783708 ACGAGAAAAAGAGAGGATGAGTAT 57.216 37.500 0.00 0.00 0.00 2.12
790 1903 6.801575 ACGAGAAAAAGAGAGGATGAGTATC 58.198 40.000 0.00 0.00 0.00 2.24
855 2156 5.872617 AGTTTGTGCGTCTTAAGTATGCATA 59.127 36.000 18.47 15.03 37.93 3.14
870 2171 7.430992 AGTATGCATAGTGCTGATGTATTTG 57.569 36.000 13.36 0.00 45.31 2.32
921 2227 6.607198 ACATAGCAGGCACCAAATAGTTAAAT 59.393 34.615 0.00 0.00 0.00 1.40
1032 2350 3.073735 CCAGAGTGCTCTCCGGCT 61.074 66.667 12.06 0.00 41.26 5.52
1412 6171 6.901887 GCTGACATATATTCTGAACAAACACG 59.098 38.462 0.00 0.00 0.00 4.49
1671 6433 3.053455 GCTCTGATTAATTCCGAGACCG 58.947 50.000 11.49 0.00 37.77 4.79
2058 6916 4.036734 CCTGCATCAACTTGTTGTAACACT 59.963 41.667 12.44 0.00 38.92 3.55
2059 6917 5.238432 CCTGCATCAACTTGTTGTAACACTA 59.762 40.000 12.44 0.00 38.92 2.74
2060 6918 6.055231 TGCATCAACTTGTTGTAACACTAC 57.945 37.500 12.44 0.00 38.92 2.73
2061 6919 5.820423 TGCATCAACTTGTTGTAACACTACT 59.180 36.000 12.44 0.00 38.92 2.57
2062 6920 6.987404 TGCATCAACTTGTTGTAACACTACTA 59.013 34.615 12.44 0.00 38.92 1.82
2063 6921 7.042321 TGCATCAACTTGTTGTAACACTACTAC 60.042 37.037 12.44 0.00 38.92 2.73
2064 6922 7.042321 GCATCAACTTGTTGTAACACTACTACA 60.042 37.037 12.44 0.00 40.51 2.74
2101 6959 5.067283 GGCTTGAAACTAAAGTTGAGGTTCA 59.933 40.000 15.70 15.70 46.41 3.18
2478 7359 5.012458 GTGAGTCCATCCATCTAATCCATCA 59.988 44.000 0.00 0.00 0.00 3.07
2542 9600 7.095565 GCAGATCTGAGTGATGATATCTGTTTG 60.096 40.741 27.04 0.00 41.40 2.93
2608 11718 2.978010 CCCAACGGCTTCAGCGTT 60.978 61.111 0.00 0.00 43.26 4.84
2728 11839 4.189188 GAGCGCGGCGAGTTCCTA 62.189 66.667 28.54 0.00 0.00 2.94
2749 11860 1.545651 CCGGAGAGCCCTTTCAAGTTT 60.546 52.381 0.00 0.00 0.00 2.66
3810 13731 6.914259 TGCACACGGTTTGAATATAAATTGA 58.086 32.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 7.497249 TGTTTCCATGGATGTTTTTCGATTTTT 59.503 29.630 17.06 0.00 0.00 1.94
13 14 6.989169 TGTTTCCATGGATGTTTTTCGATTTT 59.011 30.769 17.06 0.00 0.00 1.82
14 15 6.520272 TGTTTCCATGGATGTTTTTCGATTT 58.480 32.000 17.06 0.00 0.00 2.17
15 16 6.095432 TGTTTCCATGGATGTTTTTCGATT 57.905 33.333 17.06 0.00 0.00 3.34
16 17 5.720371 TGTTTCCATGGATGTTTTTCGAT 57.280 34.783 17.06 0.00 0.00 3.59
17 18 5.720371 ATGTTTCCATGGATGTTTTTCGA 57.280 34.783 17.06 0.00 0.00 3.71
18 19 9.184062 CATATATGTTTCCATGGATGTTTTTCG 57.816 33.333 17.06 0.00 32.29 3.46
36 37 5.182487 TGCTCGTGTGGAAAACATATATGT 58.818 37.500 12.75 12.75 41.97 2.29
37 38 5.733226 TGCTCGTGTGGAAAACATATATG 57.267 39.130 11.29 11.29 41.97 1.78
38 39 5.822519 ACATGCTCGTGTGGAAAACATATAT 59.177 36.000 0.00 0.00 41.97 0.86
39 40 5.064579 CACATGCTCGTGTGGAAAACATATA 59.935 40.000 13.01 0.00 44.41 0.86
40 41 4.009675 ACATGCTCGTGTGGAAAACATAT 58.990 39.130 0.00 0.00 41.97 1.78
41 42 3.188254 CACATGCTCGTGTGGAAAACATA 59.812 43.478 13.01 0.00 44.41 2.29
42 43 2.030893 CACATGCTCGTGTGGAAAACAT 60.031 45.455 13.01 0.00 44.41 2.71
43 44 1.333308 CACATGCTCGTGTGGAAAACA 59.667 47.619 13.01 0.00 44.41 2.83
44 45 2.036556 CACATGCTCGTGTGGAAAAC 57.963 50.000 13.01 0.00 44.41 2.43
45 46 2.685388 TTTCACATGCTCGTGTGGAAAA 59.315 40.909 18.77 11.73 42.94 2.29
46 47 2.293170 TTTCACATGCTCGTGTGGAAA 58.707 42.857 18.77 14.80 42.94 3.13
51 52 2.560504 TGAGTTTTCACATGCTCGTGT 58.439 42.857 0.00 0.00 38.12 4.49
52 53 3.818961 ATGAGTTTTCACATGCTCGTG 57.181 42.857 0.00 0.17 35.83 4.35
53 54 4.275689 TCAAATGAGTTTTCACATGCTCGT 59.724 37.500 0.00 0.00 35.83 4.18
54 55 4.786507 TCAAATGAGTTTTCACATGCTCG 58.213 39.130 0.00 0.00 35.83 5.03
55 56 7.647907 AAATCAAATGAGTTTTCACATGCTC 57.352 32.000 0.00 0.00 35.83 4.26
56 57 8.981647 GTAAAATCAAATGAGTTTTCACATGCT 58.018 29.630 13.22 0.00 41.69 3.79
57 58 7.946237 CGTAAAATCAAATGAGTTTTCACATGC 59.054 33.333 13.22 0.00 41.69 4.06
58 59 8.967218 ACGTAAAATCAAATGAGTTTTCACATG 58.033 29.630 13.22 4.83 41.69 3.21
64 65 8.911662 GCACATACGTAAAATCAAATGAGTTTT 58.088 29.630 13.22 10.07 41.69 2.43
65 66 7.540745 GGCACATACGTAAAATCAAATGAGTTT 59.459 33.333 12.68 12.68 43.54 2.66
66 67 7.027161 GGCACATACGTAAAATCAAATGAGTT 58.973 34.615 0.00 0.00 33.37 3.01
67 68 6.374333 AGGCACATACGTAAAATCAAATGAGT 59.626 34.615 0.00 0.00 0.00 3.41
68 69 6.785191 AGGCACATACGTAAAATCAAATGAG 58.215 36.000 0.00 0.00 0.00 2.90
69 70 6.751514 AGGCACATACGTAAAATCAAATGA 57.248 33.333 0.00 0.00 0.00 2.57
70 71 7.468441 TGTAGGCACATACGTAAAATCAAATG 58.532 34.615 0.00 0.00 0.00 2.32
71 72 7.618502 TGTAGGCACATACGTAAAATCAAAT 57.381 32.000 0.00 0.00 0.00 2.32
72 73 7.388224 TCTTGTAGGCACATACGTAAAATCAAA 59.612 33.333 0.00 0.00 33.76 2.69
73 74 6.874664 TCTTGTAGGCACATACGTAAAATCAA 59.125 34.615 0.00 0.00 33.76 2.57
74 75 6.399743 TCTTGTAGGCACATACGTAAAATCA 58.600 36.000 0.00 0.00 33.76 2.57
75 76 6.897259 TCTTGTAGGCACATACGTAAAATC 57.103 37.500 0.00 0.00 33.76 2.17
76 77 7.675962 TTTCTTGTAGGCACATACGTAAAAT 57.324 32.000 0.00 0.00 33.76 1.82
77 78 7.493743 TTTTCTTGTAGGCACATACGTAAAA 57.506 32.000 0.00 0.00 33.76 1.52
78 79 7.675962 ATTTTCTTGTAGGCACATACGTAAA 57.324 32.000 0.00 0.00 33.76 2.01
79 80 8.774890 TTATTTTCTTGTAGGCACATACGTAA 57.225 30.769 0.00 0.00 33.76 3.18
80 81 8.774890 TTTATTTTCTTGTAGGCACATACGTA 57.225 30.769 0.00 0.00 33.76 3.57
81 82 7.675962 TTTATTTTCTTGTAGGCACATACGT 57.324 32.000 0.00 0.00 33.76 3.57
82 83 9.567848 AATTTTATTTTCTTGTAGGCACATACG 57.432 29.630 0.00 0.00 33.76 3.06
85 86 9.643693 CAGAATTTTATTTTCTTGTAGGCACAT 57.356 29.630 0.00 0.00 33.76 3.21
86 87 8.087750 CCAGAATTTTATTTTCTTGTAGGCACA 58.912 33.333 0.00 0.00 31.11 4.57
87 88 7.063426 GCCAGAATTTTATTTTCTTGTAGGCAC 59.937 37.037 0.00 0.00 37.96 5.01
88 89 7.096551 GCCAGAATTTTATTTTCTTGTAGGCA 58.903 34.615 0.00 0.00 37.96 4.75
89 90 6.535150 GGCCAGAATTTTATTTTCTTGTAGGC 59.465 38.462 0.00 0.00 37.61 3.93
90 91 7.041721 GGGCCAGAATTTTATTTTCTTGTAGG 58.958 38.462 4.39 0.00 31.11 3.18
91 92 7.610865 TGGGCCAGAATTTTATTTTCTTGTAG 58.389 34.615 0.00 0.00 31.11 2.74
92 93 7.546250 TGGGCCAGAATTTTATTTTCTTGTA 57.454 32.000 0.00 0.00 31.11 2.41
93 94 6.432403 TGGGCCAGAATTTTATTTTCTTGT 57.568 33.333 0.00 0.00 31.11 3.16
94 95 6.709846 TGTTGGGCCAGAATTTTATTTTCTTG 59.290 34.615 6.23 0.00 31.11 3.02
95 96 6.836242 TGTTGGGCCAGAATTTTATTTTCTT 58.164 32.000 6.23 0.00 31.11 2.52
96 97 6.432403 TGTTGGGCCAGAATTTTATTTTCT 57.568 33.333 6.23 0.00 33.75 2.52
97 98 6.484977 TGTTGTTGGGCCAGAATTTTATTTTC 59.515 34.615 6.23 0.00 0.00 2.29
98 99 6.262049 GTGTTGTTGGGCCAGAATTTTATTTT 59.738 34.615 6.23 0.00 0.00 1.82
99 100 5.762711 GTGTTGTTGGGCCAGAATTTTATTT 59.237 36.000 6.23 0.00 0.00 1.40
100 101 5.163258 TGTGTTGTTGGGCCAGAATTTTATT 60.163 36.000 6.23 0.00 0.00 1.40
101 102 4.346418 TGTGTTGTTGGGCCAGAATTTTAT 59.654 37.500 6.23 0.00 0.00 1.40
102 103 3.706594 TGTGTTGTTGGGCCAGAATTTTA 59.293 39.130 6.23 0.00 0.00 1.52
103 104 2.503356 TGTGTTGTTGGGCCAGAATTTT 59.497 40.909 6.23 0.00 0.00 1.82
104 105 2.114616 TGTGTTGTTGGGCCAGAATTT 58.885 42.857 6.23 0.00 0.00 1.82
105 106 1.786937 TGTGTTGTTGGGCCAGAATT 58.213 45.000 6.23 0.00 0.00 2.17
106 107 1.786937 TTGTGTTGTTGGGCCAGAAT 58.213 45.000 6.23 0.00 0.00 2.40
107 108 1.561643 TTTGTGTTGTTGGGCCAGAA 58.438 45.000 6.23 0.41 0.00 3.02
108 109 1.561643 TTTTGTGTTGTTGGGCCAGA 58.438 45.000 6.23 0.00 0.00 3.86
109 110 2.093764 TCTTTTTGTGTTGTTGGGCCAG 60.094 45.455 6.23 0.00 0.00 4.85
110 111 1.902508 TCTTTTTGTGTTGTTGGGCCA 59.097 42.857 0.00 0.00 0.00 5.36
111 112 2.682155 TCTTTTTGTGTTGTTGGGCC 57.318 45.000 0.00 0.00 0.00 5.80
112 113 2.794350 CGATCTTTTTGTGTTGTTGGGC 59.206 45.455 0.00 0.00 0.00 5.36
113 114 2.794350 GCGATCTTTTTGTGTTGTTGGG 59.206 45.455 0.00 0.00 0.00 4.12
114 115 2.794350 GGCGATCTTTTTGTGTTGTTGG 59.206 45.455 0.00 0.00 0.00 3.77
115 116 2.794350 GGGCGATCTTTTTGTGTTGTTG 59.206 45.455 0.00 0.00 0.00 3.33
116 117 2.428890 TGGGCGATCTTTTTGTGTTGTT 59.571 40.909 0.00 0.00 0.00 2.83
117 118 2.028130 TGGGCGATCTTTTTGTGTTGT 58.972 42.857 0.00 0.00 0.00 3.32
118 119 2.791383 TGGGCGATCTTTTTGTGTTG 57.209 45.000 0.00 0.00 0.00 3.33
119 120 3.157087 AGATGGGCGATCTTTTTGTGTT 58.843 40.909 6.15 0.00 38.35 3.32
120 121 2.795329 AGATGGGCGATCTTTTTGTGT 58.205 42.857 6.15 0.00 38.35 3.72
128 129 6.365970 ACATATTTCTAAGATGGGCGATCT 57.634 37.500 6.15 6.15 43.91 2.75
129 130 7.440523 AAACATATTTCTAAGATGGGCGATC 57.559 36.000 0.65 0.65 0.00 3.69
130 131 7.823745 AAAACATATTTCTAAGATGGGCGAT 57.176 32.000 0.00 0.00 0.00 4.58
131 132 7.201785 GGAAAAACATATTTCTAAGATGGGCGA 60.202 37.037 0.00 0.00 38.92 5.54
132 133 6.918022 GGAAAAACATATTTCTAAGATGGGCG 59.082 38.462 0.00 0.00 38.92 6.13
133 134 7.069950 AGGGAAAAACATATTTCTAAGATGGGC 59.930 37.037 0.00 0.00 38.92 5.36
134 135 8.539117 AGGGAAAAACATATTTCTAAGATGGG 57.461 34.615 0.00 0.00 38.92 4.00
219 220 6.166279 ACATCGGATATGGATTGTGTCATAC 58.834 40.000 0.00 0.00 0.00 2.39
228 229 5.319453 AGCATCAAACATCGGATATGGATT 58.681 37.500 0.00 0.00 0.00 3.01
239 240 4.782019 TTGGTGGTAAGCATCAAACATC 57.218 40.909 0.00 0.00 32.86 3.06
242 243 6.705825 AGAAAATTTGGTGGTAAGCATCAAAC 59.294 34.615 0.00 0.00 32.86 2.93
245 246 6.041409 TCAAGAAAATTTGGTGGTAAGCATCA 59.959 34.615 0.00 0.00 32.86 3.07
253 254 6.326323 ACCATAGTTCAAGAAAATTTGGTGGT 59.674 34.615 9.20 0.00 42.94 4.16
300 309 2.489938 TTTGTACCTCTGCATCCACC 57.510 50.000 0.00 0.00 0.00 4.61
312 321 4.561213 GGCTGCGTATTTTTCATTTGTACC 59.439 41.667 0.00 0.00 0.00 3.34
336 345 4.728102 TCGGTTGCCACGGTAGCG 62.728 66.667 13.69 13.69 0.00 4.26
343 352 4.522971 GAGATCCTCGGTTGCCAC 57.477 61.111 0.00 0.00 0.00 5.01
380 389 3.192633 GGTTTTGAATACCGAATGCACCT 59.807 43.478 0.00 0.00 0.00 4.00
382 391 4.434713 AGGTTTTGAATACCGAATGCAC 57.565 40.909 0.00 0.00 40.69 4.57
383 392 4.321601 CCAAGGTTTTGAATACCGAATGCA 60.322 41.667 0.00 0.00 40.69 3.96
384 393 4.173256 CCAAGGTTTTGAATACCGAATGC 58.827 43.478 0.00 0.00 40.69 3.56
429 438 2.677037 GCGGCAAGACCTACACTGTTAT 60.677 50.000 0.00 0.00 35.61 1.89
436 445 0.036164 AATGTGCGGCAAGACCTACA 59.964 50.000 3.23 0.00 37.51 2.74
449 458 2.475187 GCTGACTCAACGATGAATGTGC 60.475 50.000 0.00 0.00 34.49 4.57
477 487 7.625828 TCTTCGTCAAATGTAGTCTATGAGA 57.374 36.000 0.00 0.00 0.00 3.27
479 489 9.483916 TTTTTCTTCGTCAAATGTAGTCTATGA 57.516 29.630 0.00 0.00 0.00 2.15
633 646 6.696148 CGTCCATTCAGAAGTTGTATAGTACC 59.304 42.308 0.00 0.00 0.00 3.34
683 697 5.056553 TGGCCTTACTAGGTTTTGACTTT 57.943 39.130 3.32 0.00 44.00 2.66
705 719 9.422681 ACTACCTATGATACTCACATTGTTACT 57.577 33.333 0.00 0.00 0.00 2.24
733 747 3.128764 GCCACCTTAGCAAAATGTCCTAC 59.871 47.826 0.00 0.00 0.00 3.18
736 750 1.892474 TGCCACCTTAGCAAAATGTCC 59.108 47.619 0.00 0.00 37.28 4.02
738 752 1.269448 CGTGCCACCTTAGCAAAATGT 59.731 47.619 0.00 0.00 43.02 2.71
740 754 0.243636 GCGTGCCACCTTAGCAAAAT 59.756 50.000 0.00 0.00 43.02 1.82
741 755 1.103987 TGCGTGCCACCTTAGCAAAA 61.104 50.000 0.00 0.00 43.02 2.44
751 803 1.195900 TCTCGTTTAATTGCGTGCCAC 59.804 47.619 0.00 0.00 0.00 5.01
758 810 6.899114 TCCTCTCTTTTTCTCGTTTAATTGC 58.101 36.000 0.00 0.00 0.00 3.56
767 819 6.800543 TGATACTCATCCTCTCTTTTTCTCG 58.199 40.000 0.00 0.00 0.00 4.04
855 2156 9.938280 TTAGTTAGTAACAAATACATCAGCACT 57.062 29.630 15.28 0.00 36.94 4.40
870 2171 7.333423 TGTTCCATGTCAGCATTAGTTAGTAAC 59.667 37.037 4.78 4.78 31.99 2.50
898 2203 6.265422 GGATTTAACTATTTGGTGCCTGCTAT 59.735 38.462 0.00 0.00 0.00 2.97
899 2204 5.592688 GGATTTAACTATTTGGTGCCTGCTA 59.407 40.000 0.00 0.00 0.00 3.49
1412 6171 2.934553 AGTTAGACGCGCCCTTTTAATC 59.065 45.455 5.73 0.00 0.00 1.75
1671 6433 2.701107 GGCAAAGTTAGGTCAGAGGAC 58.299 52.381 0.00 0.00 43.55 3.85
1825 6677 4.331166 TCGCTGGCGTCGTCGAAA 62.331 61.111 14.55 0.00 40.74 3.46
2060 6918 8.818057 GTTTCAAGCCTAACATACTACATGTAG 58.182 37.037 27.66 27.66 39.04 2.74
2061 6919 8.537016 AGTTTCAAGCCTAACATACTACATGTA 58.463 33.333 5.25 5.25 35.37 2.29
2062 6920 7.394816 AGTTTCAAGCCTAACATACTACATGT 58.605 34.615 2.69 2.69 0.00 3.21
2063 6921 7.849804 AGTTTCAAGCCTAACATACTACATG 57.150 36.000 0.00 0.00 0.00 3.21
2064 6922 9.953565 TTTAGTTTCAAGCCTAACATACTACAT 57.046 29.630 0.00 0.00 0.00 2.29
2069 6927 8.780249 TCAACTTTAGTTTCAAGCCTAACATAC 58.220 33.333 0.00 0.00 35.83 2.39
2101 6959 3.935203 CTGTCAAGTATCAACGCCAAGAT 59.065 43.478 0.00 0.00 0.00 2.40
2333 7214 2.994995 ATGGACGACGTGGCCTCA 60.995 61.111 4.58 1.77 0.00 3.86
2478 7359 2.227194 GACTCCCAACAATTCGTGGTT 58.773 47.619 3.75 0.00 0.00 3.67
2542 9600 2.823747 GTTATCCTGAAACACCCCCAAC 59.176 50.000 0.00 0.00 0.00 3.77
2608 11718 0.544357 ACACGATGTCTCCCTTCCCA 60.544 55.000 0.00 0.00 0.00 4.37
2695 11806 2.964911 CTCGTCGAGCCATCTTTCC 58.035 57.895 9.74 0.00 0.00 3.13
2728 11839 1.128188 ACTTGAAAGGGCTCTCCGGT 61.128 55.000 0.00 0.00 41.52 5.28
3668 13580 4.101274 CCATGGATCAAATACCAATGCCAA 59.899 41.667 5.56 0.00 39.69 4.52


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

AutoCloner maintained by Alex Coulton.