Multiple sequence alignment - TraesCS3A01G413000

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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 TraesCS3A01G413000 chr3A 100.000 3283 0 0 1 3283 656253164 656256446 0.000000e+00 6063.0
1 TraesCS3A01G413000 chr3A 95.355 2002 52 27 425 2403 656423238 656425221 0.000000e+00 3144.0
2 TraesCS3A01G413000 chr3A 99.694 1634 5 0 1650 3283 656339249 656340882 0.000000e+00 2990.0
3 TraesCS3A01G413000 chr3A 90.440 1318 90 18 1136 2426 656134859 656136167 0.000000e+00 1703.0
4 TraesCS3A01G413000 chr3A 96.239 585 18 2 2424 3007 656348804 656349385 0.000000e+00 955.0
5 TraesCS3A01G413000 chr3A 96.233 584 18 3 2424 3007 656264458 656265037 0.000000e+00 953.0
6 TraesCS3A01G413000 chr3A 94.863 584 26 2 2424 3007 656260926 656261505 0.000000e+00 909.0
7 TraesCS3A01G413000 chr3A 94.863 584 26 2 2424 3007 656345117 656345696 0.000000e+00 909.0
8 TraesCS3A01G413000 chr3A 96.830 347 11 0 425 771 656338905 656339251 6.110000e-162 580.0
9 TraesCS3A01G413000 chr3A 90.942 276 20 4 3008 3283 17303022 17303292 1.860000e-97 366.0
10 TraesCS3A01G413000 chr3A 90.580 276 25 1 3008 3283 650735743 650736017 6.690000e-97 364.0
11 TraesCS3A01G413000 chr3A 88.679 265 23 5 2424 2686 656176350 656176609 1.900000e-82 316.0
12 TraesCS3A01G413000 chr3A 75.328 685 152 13 1495 2177 596357498 596358167 2.460000e-81 313.0
13 TraesCS3A01G413000 chr3A 93.467 199 8 2 2228 2426 656264227 656264420 1.150000e-74 291.0
14 TraesCS3A01G413000 chr3A 87.854 247 26 3 2765 3007 656176896 656177142 1.490000e-73 287.0
15 TraesCS3A01G413000 chr3A 93.401 197 8 2 2230 2426 656260696 656260887 1.490000e-73 287.0
16 TraesCS3A01G413000 chr3A 92.965 199 9 2 2228 2426 656348573 656348766 5.360000e-73 285.0
17 TraesCS3A01G413000 chr3A 92.386 197 10 2 2230 2426 656344887 656345078 3.230000e-70 276.0
18 TraesCS3A01G413000 chr3A 87.023 131 15 2 74 202 458873380 458873510 2.640000e-31 147.0
19 TraesCS3A01G413000 chr3A 80.000 160 8 10 791 930 656134429 656134584 2.700000e-16 97.1
20 TraesCS3A01G413000 chr3A 83.333 96 16 0 106 201 274870098 274870003 4.510000e-14 89.8
21 TraesCS3A01G413000 chr3B 92.742 1364 63 24 1080 2418 686524454 686525806 0.000000e+00 1938.0
22 TraesCS3A01G413000 chr3B 91.411 1304 85 14 1136 2426 686492194 686493483 0.000000e+00 1762.0
23 TraesCS3A01G413000 chr3B 87.921 712 40 20 402 1082 686523715 686524411 0.000000e+00 797.0
24 TraesCS3A01G413000 chr3B 90.385 312 24 5 2424 2734 686493522 686493828 3.940000e-109 405.0
25 TraesCS3A01G413000 chr3B 91.209 273 20 4 3008 3279 314281076 314281345 5.180000e-98 368.0
26 TraesCS3A01G413000 chr3B 89.964 279 24 4 3008 3283 790310564 790310287 1.120000e-94 357.0
27 TraesCS3A01G413000 chr3B 73.262 1021 201 52 1195 2179 596852747 596853731 1.140000e-79 307.0
28 TraesCS3A01G413000 chr3B 73.232 594 119 31 1200 1773 39581672 39581099 2.600000e-41 180.0
29 TraesCS3A01G413000 chr3B 75.915 328 39 23 633 930 686491597 686491914 7.390000e-27 132.0
30 TraesCS3A01G413000 chr3B 93.846 65 3 1 207 271 686523560 686523623 2.700000e-16 97.1
31 TraesCS3A01G413000 chr3B 77.236 123 24 4 93 212 599697808 599697929 5.880000e-08 69.4
32 TraesCS3A01G413000 chr3D 92.375 1377 58 28 1080 2418 520862717 520864084 0.000000e+00 1917.0
33 TraesCS3A01G413000 chr3D 85.217 1752 135 68 780 2425 520823825 520825558 0.000000e+00 1687.0
34 TraesCS3A01G413000 chr3D 92.756 704 23 11 383 1082 520861995 520862674 0.000000e+00 992.0
35 TraesCS3A01G413000 chr3D 91.026 312 24 3 2424 2734 520825597 520825905 5.070000e-113 418.0
36 TraesCS3A01G413000 chr3D 73.653 1002 215 36 1195 2179 454219320 454220289 3.140000e-90 342.0
37 TraesCS3A01G413000 chr3D 87.854 247 25 4 2765 3006 520826174 520826420 5.360000e-73 285.0
38 TraesCS3A01G413000 chr3D 95.690 116 5 0 207 322 520861894 520862009 1.560000e-43 187.0
39 TraesCS3A01G413000 chr3D 93.103 58 4 0 152 209 584729663 584729720 5.840000e-13 86.1
40 TraesCS3A01G413000 chrUn 96.890 418 13 0 2480 2897 476916015 476915598 0.000000e+00 701.0
41 TraesCS3A01G413000 chrUn 96.830 347 11 0 425 771 478590686 478591032 6.110000e-162 580.0
42 TraesCS3A01G413000 chr6B 93.600 250 15 1 3007 3256 340874766 340875014 4.000000e-99 372.0
43 TraesCS3A01G413000 chr6B 90.580 276 23 3 3008 3283 341374970 341375242 2.410000e-96 363.0
44 TraesCS3A01G413000 chr6B 91.418 268 16 5 3008 3275 362478911 362478651 8.660000e-96 361.0
45 TraesCS3A01G413000 chr6B 84.615 130 17 3 86 213 23177353 23177481 3.440000e-25 126.0
46 TraesCS3A01G413000 chr4A 91.045 268 24 0 3008 3275 607906397 607906130 2.410000e-96 363.0
47 TraesCS3A01G413000 chr4A 77.778 225 19 21 12 208 719834196 719833975 3.460000e-20 110.0
48 TraesCS3A01G413000 chr5D 74.667 600 114 29 1564 2154 75997831 75997261 7.080000e-57 231.0
49 TraesCS3A01G413000 chr5A 73.013 604 121 32 1563 2154 71453630 71453057 1.210000e-39 174.0
50 TraesCS3A01G413000 chr6D 72.379 601 126 34 1570 2153 114848129 114847552 1.580000e-33 154.0
51 TraesCS3A01G413000 chr7A 88.525 122 12 2 86 206 574591095 574591215 2.640000e-31 147.0
52 TraesCS3A01G413000 chr7A 84.956 113 10 5 94 206 714176774 714176879 1.250000e-19 108.0
53 TraesCS3A01G413000 chr2D 87.379 103 12 1 98 200 430402783 430402884 2.070000e-22 117.0
54 TraesCS3A01G413000 chr5B 93.333 60 3 1 2669 2728 673287151 673287093 1.620000e-13 87.9
55 TraesCS3A01G413000 chr7D 93.103 58 4 0 152 209 16130636 16130579 5.840000e-13 86.1


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 TraesCS3A01G413000 chr3A 656253164 656256446 3282 False 6063.000000 6063 100.000000 1 3283 1 chr3A.!!$F5 3282
1 TraesCS3A01G413000 chr3A 656423238 656425221 1983 False 3144.000000 3144 95.355000 425 2403 1 chr3A.!!$F6 1978
2 TraesCS3A01G413000 chr3A 656338905 656340882 1977 False 1785.000000 2990 98.262000 425 3283 2 chr3A.!!$F10 2858
3 TraesCS3A01G413000 chr3A 656134429 656136167 1738 False 900.050000 1703 85.220000 791 2426 2 chr3A.!!$F7 1635
4 TraesCS3A01G413000 chr3A 656260696 656265037 4341 False 610.000000 953 94.491000 2228 3007 4 chr3A.!!$F9 779
5 TraesCS3A01G413000 chr3A 656344887 656349385 4498 False 606.250000 955 94.113250 2228 3007 4 chr3A.!!$F11 779
6 TraesCS3A01G413000 chr3A 596357498 596358167 669 False 313.000000 313 75.328000 1495 2177 1 chr3A.!!$F3 682
7 TraesCS3A01G413000 chr3A 656176350 656177142 792 False 301.500000 316 88.266500 2424 3007 2 chr3A.!!$F8 583
8 TraesCS3A01G413000 chr3B 686523560 686525806 2246 False 944.033333 1938 91.503000 207 2418 3 chr3B.!!$F5 2211
9 TraesCS3A01G413000 chr3B 686491597 686493828 2231 False 766.333333 1762 85.903667 633 2734 3 chr3B.!!$F4 2101
10 TraesCS3A01G413000 chr3B 596852747 596853731 984 False 307.000000 307 73.262000 1195 2179 1 chr3B.!!$F2 984
11 TraesCS3A01G413000 chr3D 520861894 520864084 2190 False 1032.000000 1917 93.607000 207 2418 3 chr3D.!!$F4 2211
12 TraesCS3A01G413000 chr3D 520823825 520826420 2595 False 796.666667 1687 88.032333 780 3006 3 chr3D.!!$F3 2226
13 TraesCS3A01G413000 chr3D 454219320 454220289 969 False 342.000000 342 73.653000 1195 2179 1 chr3D.!!$F1 984
14 TraesCS3A01G413000 chr5D 75997261 75997831 570 True 231.000000 231 74.667000 1564 2154 1 chr5D.!!$R1 590

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
370 429 0.101399 GACCTCTGCATCACGACGAT 59.899 55.0 0.0 0.0 33.27 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3073 4881 2.362736 CTAGTGGCGTGGTACTAGTGA 58.637 52.381 5.39 0.0 40.78 3.41 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
19 20 2.165319 GGTACGTGAGCTGGTTTCTT 57.835 50.000 0.00 0.00 0.00 2.52
20 21 3.308438 GGTACGTGAGCTGGTTTCTTA 57.692 47.619 0.00 0.00 0.00 2.10
22 23 4.251268 GGTACGTGAGCTGGTTTCTTAAT 58.749 43.478 0.00 0.00 0.00 1.40
23 24 4.329256 GGTACGTGAGCTGGTTTCTTAATC 59.671 45.833 0.00 0.00 0.00 1.75
24 25 4.273148 ACGTGAGCTGGTTTCTTAATCT 57.727 40.909 0.00 0.00 0.00 2.40
25 26 3.997021 ACGTGAGCTGGTTTCTTAATCTG 59.003 43.478 0.00 0.00 0.00 2.90
26 27 3.372206 CGTGAGCTGGTTTCTTAATCTGG 59.628 47.826 0.00 0.00 0.00 3.86
29 30 5.065731 GTGAGCTGGTTTCTTAATCTGGATG 59.934 44.000 0.00 0.00 0.00 3.51
30 31 5.184892 AGCTGGTTTCTTAATCTGGATGT 57.815 39.130 0.00 0.00 0.00 3.06
31 32 5.574188 AGCTGGTTTCTTAATCTGGATGTT 58.426 37.500 0.00 0.00 0.00 2.71
32 33 5.416952 AGCTGGTTTCTTAATCTGGATGTTG 59.583 40.000 0.00 0.00 0.00 3.33
33 34 5.183904 GCTGGTTTCTTAATCTGGATGTTGT 59.816 40.000 0.00 0.00 0.00 3.32
34 35 6.374333 GCTGGTTTCTTAATCTGGATGTTGTA 59.626 38.462 0.00 0.00 0.00 2.41
37 38 9.308000 TGGTTTCTTAATCTGGATGTTGTATTT 57.692 29.630 0.00 0.00 0.00 1.40
38 39 9.788960 GGTTTCTTAATCTGGATGTTGTATTTC 57.211 33.333 0.00 0.00 0.00 2.17
41 42 8.737168 TCTTAATCTGGATGTTGTATTTCAGG 57.263 34.615 0.00 0.00 0.00 3.86
42 43 7.775093 TCTTAATCTGGATGTTGTATTTCAGGG 59.225 37.037 0.00 0.00 0.00 4.45
45 46 2.922955 TGGATGTTGTATTTCAGGGGGA 59.077 45.455 0.00 0.00 0.00 4.81
46 47 3.335183 TGGATGTTGTATTTCAGGGGGAA 59.665 43.478 0.00 0.00 0.00 3.97
74 75 9.806203 AAAATCATGGACATTGTAACATGTATG 57.194 29.630 22.81 1.28 41.01 2.39
76 77 9.625747 AATCATGGACATTGTAACATGTATGTA 57.374 29.630 22.81 11.41 40.80 2.29
79 80 8.551205 CATGGACATTGTAACATGTATGTACTC 58.449 37.037 18.29 9.90 40.80 2.59
80 81 7.847096 TGGACATTGTAACATGTATGTACTCT 58.153 34.615 18.29 0.00 40.80 3.24
81 82 8.318412 TGGACATTGTAACATGTATGTACTCTT 58.682 33.333 18.29 0.00 40.80 2.85
82 83 8.604035 GGACATTGTAACATGTATGTACTCTTG 58.396 37.037 12.59 7.70 40.80 3.02
83 84 8.492673 ACATTGTAACATGTATGTACTCTTGG 57.507 34.615 9.70 0.00 40.80 3.61
84 85 7.552687 ACATTGTAACATGTATGTACTCTTGGG 59.447 37.037 9.70 0.00 40.80 4.12
86 87 7.432148 TGTAACATGTATGTACTCTTGGGAT 57.568 36.000 0.00 0.00 40.80 3.85
87 88 7.857456 TGTAACATGTATGTACTCTTGGGATT 58.143 34.615 0.00 0.00 40.80 3.01
89 90 7.865706 AACATGTATGTACTCTTGGGATTTC 57.134 36.000 0.00 0.00 40.80 2.17
91 92 6.158695 ACATGTATGTACTCTTGGGATTTCCT 59.841 38.462 0.00 0.00 39.68 3.36
93 94 7.931015 TGTATGTACTCTTGGGATTTCCTAT 57.069 36.000 0.00 0.00 36.20 2.57
94 95 7.963532 TGTATGTACTCTTGGGATTTCCTATC 58.036 38.462 0.00 0.00 36.20 2.08
95 96 5.531122 TGTACTCTTGGGATTTCCTATCG 57.469 43.478 0.00 0.00 36.20 2.92
98 99 5.437191 ACTCTTGGGATTTCCTATCGTTT 57.563 39.130 0.00 0.00 36.20 3.60
99 100 5.816682 ACTCTTGGGATTTCCTATCGTTTT 58.183 37.500 0.00 0.00 36.20 2.43
100 101 5.880887 ACTCTTGGGATTTCCTATCGTTTTC 59.119 40.000 0.00 0.00 36.20 2.29
101 102 5.811190 TCTTGGGATTTCCTATCGTTTTCA 58.189 37.500 0.00 0.00 36.20 2.69
102 103 6.242396 TCTTGGGATTTCCTATCGTTTTCAA 58.758 36.000 0.00 0.00 36.20 2.69
104 105 6.693315 TGGGATTTCCTATCGTTTTCAATC 57.307 37.500 0.00 0.00 36.20 2.67
105 106 5.592688 TGGGATTTCCTATCGTTTTCAATCC 59.407 40.000 0.00 0.00 38.22 3.01
106 107 5.828328 GGGATTTCCTATCGTTTTCAATCCT 59.172 40.000 7.72 0.00 38.74 3.24
107 108 6.996282 GGGATTTCCTATCGTTTTCAATCCTA 59.004 38.462 7.72 0.00 38.74 2.94
108 109 7.173390 GGGATTTCCTATCGTTTTCAATCCTAG 59.827 40.741 7.72 0.00 38.74 3.02
109 110 7.931948 GGATTTCCTATCGTTTTCAATCCTAGA 59.068 37.037 0.00 0.00 36.69 2.43
110 111 8.664211 ATTTCCTATCGTTTTCAATCCTAGAC 57.336 34.615 0.00 0.00 0.00 2.59
112 113 4.444720 CCTATCGTTTTCAATCCTAGACGC 59.555 45.833 0.00 0.00 0.00 5.19
113 114 3.306917 TCGTTTTCAATCCTAGACGCA 57.693 42.857 0.00 0.00 0.00 5.24
114 115 3.857052 TCGTTTTCAATCCTAGACGCAT 58.143 40.909 0.00 0.00 0.00 4.73
115 116 5.001237 TCGTTTTCAATCCTAGACGCATA 57.999 39.130 0.00 0.00 0.00 3.14
116 117 5.412640 TCGTTTTCAATCCTAGACGCATAA 58.587 37.500 0.00 0.00 0.00 1.90
117 118 6.046593 TCGTTTTCAATCCTAGACGCATAAT 58.953 36.000 0.00 0.00 0.00 1.28
118 119 6.537301 TCGTTTTCAATCCTAGACGCATAATT 59.463 34.615 0.00 0.00 0.00 1.40
119 120 7.707464 TCGTTTTCAATCCTAGACGCATAATTA 59.293 33.333 0.00 0.00 0.00 1.40
120 121 7.792508 CGTTTTCAATCCTAGACGCATAATTAC 59.207 37.037 0.00 0.00 0.00 1.89
121 122 7.402811 TTTCAATCCTAGACGCATAATTACG 57.597 36.000 0.00 0.00 0.00 3.18
122 123 6.321848 TCAATCCTAGACGCATAATTACGA 57.678 37.500 2.82 0.00 0.00 3.43
123 124 6.920817 TCAATCCTAGACGCATAATTACGAT 58.079 36.000 2.82 0.00 0.00 3.73
124 125 7.027760 TCAATCCTAGACGCATAATTACGATC 58.972 38.462 2.82 0.00 0.00 3.69
125 126 6.761099 ATCCTAGACGCATAATTACGATCT 57.239 37.500 2.82 4.85 0.00 2.75
126 127 7.860918 ATCCTAGACGCATAATTACGATCTA 57.139 36.000 2.82 5.54 0.00 1.98
128 129 8.277490 TCCTAGACGCATAATTACGATCTAAT 57.723 34.615 2.82 0.00 0.00 1.73
129 130 8.182227 TCCTAGACGCATAATTACGATCTAATG 58.818 37.037 2.82 0.00 0.00 1.90
130 131 7.432545 CCTAGACGCATAATTACGATCTAATGG 59.567 40.741 2.82 2.78 0.00 3.16
131 132 6.688578 AGACGCATAATTACGATCTAATGGT 58.311 36.000 2.82 0.00 0.00 3.55
132 133 6.807230 AGACGCATAATTACGATCTAATGGTC 59.193 38.462 2.82 0.00 0.00 4.02
133 134 6.452242 ACGCATAATTACGATCTAATGGTCA 58.548 36.000 2.82 0.00 0.00 4.02
136 137 8.443160 CGCATAATTACGATCTAATGGTCATTT 58.557 33.333 1.28 0.00 32.50 2.32
142 143 9.832445 ATTACGATCTAATGGTCATTTTACAGT 57.168 29.630 1.28 1.63 32.50 3.55
153 154 7.891561 TGGTCATTTTACAGTAATTTTGGAGG 58.108 34.615 0.00 0.00 0.00 4.30
155 156 8.749354 GGTCATTTTACAGTAATTTTGGAGGAT 58.251 33.333 0.00 0.00 0.00 3.24
161 162 8.851541 TTACAGTAATTTTGGAGGATTAACGT 57.148 30.769 0.00 0.00 0.00 3.99
163 164 8.488651 ACAGTAATTTTGGAGGATTAACGTAG 57.511 34.615 0.00 0.00 0.00 3.51
164 165 8.316214 ACAGTAATTTTGGAGGATTAACGTAGA 58.684 33.333 0.00 0.00 0.00 2.59
166 167 7.985752 AGTAATTTTGGAGGATTAACGTAGAGG 59.014 37.037 0.00 0.00 0.00 3.69
167 168 3.814005 TTGGAGGATTAACGTAGAGGC 57.186 47.619 0.00 0.00 0.00 4.70
168 169 3.028094 TGGAGGATTAACGTAGAGGCT 57.972 47.619 0.00 0.00 0.00 4.58
170 171 2.030981 GGAGGATTAACGTAGAGGCTCG 60.031 54.545 9.22 0.00 0.00 5.03
171 172 2.617774 GAGGATTAACGTAGAGGCTCGT 59.382 50.000 9.22 0.70 42.12 4.18
172 173 3.812053 GAGGATTAACGTAGAGGCTCGTA 59.188 47.826 9.22 0.00 39.39 3.43
173 174 4.396522 AGGATTAACGTAGAGGCTCGTAT 58.603 43.478 9.22 0.00 39.39 3.06
174 175 4.215827 AGGATTAACGTAGAGGCTCGTATG 59.784 45.833 9.22 9.71 39.39 2.39
175 176 3.976793 TTAACGTAGAGGCTCGTATGG 57.023 47.619 9.22 0.89 39.39 2.74
176 177 1.760192 AACGTAGAGGCTCGTATGGT 58.240 50.000 9.22 3.62 39.39 3.55
177 178 1.022735 ACGTAGAGGCTCGTATGGTG 58.977 55.000 9.22 0.00 38.52 4.17
178 179 0.317938 CGTAGAGGCTCGTATGGTGC 60.318 60.000 9.22 0.00 0.00 5.01
180 181 1.409427 GTAGAGGCTCGTATGGTGCTT 59.591 52.381 9.22 0.00 35.51 3.91
183 184 1.681793 GAGGCTCGTATGGTGCTTCTA 59.318 52.381 0.00 0.00 37.99 2.10
184 185 2.100916 GAGGCTCGTATGGTGCTTCTAA 59.899 50.000 0.00 0.00 37.99 2.10
186 187 3.134804 AGGCTCGTATGGTGCTTCTAATT 59.865 43.478 0.00 0.00 35.51 1.40
188 189 4.686554 GGCTCGTATGGTGCTTCTAATTAG 59.313 45.833 6.11 6.11 35.51 1.73
189 190 5.290386 GCTCGTATGGTGCTTCTAATTAGT 58.710 41.667 12.19 0.00 32.48 2.24
190 191 6.444633 GCTCGTATGGTGCTTCTAATTAGTA 58.555 40.000 12.19 2.01 32.48 1.82
191 192 6.921857 GCTCGTATGGTGCTTCTAATTAGTAA 59.078 38.462 12.19 5.09 32.48 2.24
192 193 7.437267 GCTCGTATGGTGCTTCTAATTAGTAAA 59.563 37.037 12.19 0.00 32.48 2.01
193 194 9.477484 CTCGTATGGTGCTTCTAATTAGTAAAT 57.523 33.333 12.19 1.89 0.00 1.40
265 266 9.860898 AACACTCCAAAATAAGATAAAATCTGC 57.139 29.630 0.00 0.00 40.13 4.26
288 347 7.264221 TGCTAAAACCATAAAATGTAGCATGG 58.736 34.615 0.00 0.00 43.02 3.66
316 375 2.095604 TGGACGATGGATCCATGGTA 57.904 50.000 34.27 21.49 43.56 3.25
317 376 2.619931 TGGACGATGGATCCATGGTAT 58.380 47.619 34.27 18.63 43.56 2.73
359 418 2.109425 AATTTACCCGTGACCTCTGC 57.891 50.000 0.00 0.00 0.00 4.26
361 420 0.981183 TTTACCCGTGACCTCTGCAT 59.019 50.000 0.00 0.00 0.00 3.96
362 421 0.535335 TTACCCGTGACCTCTGCATC 59.465 55.000 0.00 0.00 0.00 3.91
364 423 1.448540 CCCGTGACCTCTGCATCAC 60.449 63.158 7.91 7.91 41.54 3.06
368 427 1.073216 GTGACCTCTGCATCACGACG 61.073 60.000 2.60 0.00 36.20 5.12
369 428 1.241315 TGACCTCTGCATCACGACGA 61.241 55.000 0.00 0.00 0.00 4.20
370 429 0.101399 GACCTCTGCATCACGACGAT 59.899 55.000 0.00 0.00 33.27 3.73
378 437 0.367887 CATCACGACGATGCACACAG 59.632 55.000 0.00 0.00 44.95 3.66
379 438 1.354337 ATCACGACGATGCACACAGC 61.354 55.000 0.00 0.00 45.96 4.40
380 439 2.738521 ACGACGATGCACACAGCC 60.739 61.111 0.00 0.00 44.83 4.85
381 440 2.738139 CGACGATGCACACAGCCA 60.738 61.111 0.00 0.00 44.83 4.75
382 441 2.316867 CGACGATGCACACAGCCAA 61.317 57.895 0.00 0.00 44.83 4.52
383 442 1.638388 CGACGATGCACACAGCCAAT 61.638 55.000 0.00 0.00 44.83 3.16
384 443 0.179181 GACGATGCACACAGCCAATG 60.179 55.000 0.00 0.00 44.83 2.82
385 444 1.515519 CGATGCACACAGCCAATGC 60.516 57.895 0.00 0.00 44.83 3.56
387 446 2.729455 TGCACACAGCCAATGCAC 59.271 55.556 0.00 0.00 44.17 4.57
388 447 2.429571 GCACACAGCCAATGCACG 60.430 61.111 0.00 0.00 41.13 5.34
391 450 1.072332 ACACAGCCAATGCACGGTA 59.928 52.632 5.91 0.00 41.13 4.02
392 451 1.234615 ACACAGCCAATGCACGGTAC 61.235 55.000 5.91 0.00 41.13 3.34
393 452 1.072332 ACAGCCAATGCACGGTACA 59.928 52.632 5.91 0.00 41.13 2.90
394 453 0.322456 ACAGCCAATGCACGGTACAT 60.322 50.000 5.91 0.00 41.13 2.29
395 454 0.378257 CAGCCAATGCACGGTACATC 59.622 55.000 5.91 0.00 41.13 3.06
397 456 0.378257 GCCAATGCACGGTACATCTG 59.622 55.000 5.91 0.00 37.47 2.90
398 457 1.737838 CCAATGCACGGTACATCTGT 58.262 50.000 0.00 0.00 35.83 3.41
399 458 1.398041 CCAATGCACGGTACATCTGTG 59.602 52.381 0.00 2.86 40.57 3.66
400 459 1.086696 AATGCACGGTACATCTGTGC 58.913 50.000 20.40 20.40 40.57 4.57
432 515 7.573968 AATGCCAATTCTCCTAATTACAGTC 57.426 36.000 0.00 0.00 0.00 3.51
439 522 6.777213 TTCTCCTAATTACAGTCTGTCTCC 57.223 41.667 9.26 0.00 0.00 3.71
455 538 3.417101 GTCTCCTGACACTTGAGAGAGA 58.583 50.000 0.00 0.00 42.48 3.10
478 564 0.739813 GTGAAGGCGAGCAATACCGT 60.740 55.000 0.00 0.00 0.00 4.83
3232 5040 2.840974 GCACCACATAGAAGTGCGT 58.159 52.632 0.00 0.00 46.43 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.997021 CAGATTAAGAAACCAGCTCACGT 59.003 43.478 0.00 0.00 0.00 4.49
5 6 4.579869 TCCAGATTAAGAAACCAGCTCAC 58.420 43.478 0.00 0.00 0.00 3.51
6 7 4.908601 TCCAGATTAAGAAACCAGCTCA 57.091 40.909 0.00 0.00 0.00 4.26
7 8 5.189180 ACATCCAGATTAAGAAACCAGCTC 58.811 41.667 0.00 0.00 0.00 4.09
8 9 5.184892 ACATCCAGATTAAGAAACCAGCT 57.815 39.130 0.00 0.00 0.00 4.24
9 10 5.183904 ACAACATCCAGATTAAGAAACCAGC 59.816 40.000 0.00 0.00 0.00 4.85
10 11 6.824305 ACAACATCCAGATTAAGAAACCAG 57.176 37.500 0.00 0.00 0.00 4.00
11 12 8.877864 AATACAACATCCAGATTAAGAAACCA 57.122 30.769 0.00 0.00 0.00 3.67
12 13 9.788960 GAAATACAACATCCAGATTAAGAAACC 57.211 33.333 0.00 0.00 0.00 3.27
15 16 9.177608 CCTGAAATACAACATCCAGATTAAGAA 57.822 33.333 0.00 0.00 0.00 2.52
17 18 7.013655 CCCCTGAAATACAACATCCAGATTAAG 59.986 40.741 0.00 0.00 0.00 1.85
19 20 6.364701 CCCCTGAAATACAACATCCAGATTA 58.635 40.000 0.00 0.00 0.00 1.75
20 21 5.203528 CCCCTGAAATACAACATCCAGATT 58.796 41.667 0.00 0.00 0.00 2.40
22 23 3.053693 CCCCCTGAAATACAACATCCAGA 60.054 47.826 0.00 0.00 0.00 3.86
23 24 3.053693 TCCCCCTGAAATACAACATCCAG 60.054 47.826 0.00 0.00 0.00 3.86
24 25 2.922955 TCCCCCTGAAATACAACATCCA 59.077 45.455 0.00 0.00 0.00 3.41
25 26 3.662759 TCCCCCTGAAATACAACATCC 57.337 47.619 0.00 0.00 0.00 3.51
26 27 5.993748 TTTTCCCCCTGAAATACAACATC 57.006 39.130 0.00 0.00 42.38 3.06
53 54 8.437360 AGTACATACATGTTACAATGTCCATG 57.563 34.615 13.85 18.48 41.09 3.66
55 56 7.847096 AGAGTACATACATGTTACAATGTCCA 58.153 34.615 13.85 0.00 41.09 4.02
56 57 8.604035 CAAGAGTACATACATGTTACAATGTCC 58.396 37.037 13.85 4.90 41.09 4.02
57 58 8.604035 CCAAGAGTACATACATGTTACAATGTC 58.396 37.037 13.85 7.62 41.09 3.06
59 60 7.768582 TCCCAAGAGTACATACATGTTACAATG 59.231 37.037 2.30 4.02 41.97 2.82
61 62 7.247456 TCCCAAGAGTACATACATGTTACAA 57.753 36.000 2.30 0.00 41.97 2.41
62 63 6.860790 TCCCAAGAGTACATACATGTTACA 57.139 37.500 2.30 0.00 41.97 2.41
63 64 8.732746 AAATCCCAAGAGTACATACATGTTAC 57.267 34.615 2.30 0.17 41.97 2.50
64 65 7.990886 GGAAATCCCAAGAGTACATACATGTTA 59.009 37.037 2.30 0.00 37.26 2.41
66 67 6.158695 AGGAAATCCCAAGAGTACATACATGT 59.841 38.462 2.69 2.69 40.16 3.21
67 68 6.595682 AGGAAATCCCAAGAGTACATACATG 58.404 40.000 0.00 0.00 37.41 3.21
68 69 6.831664 AGGAAATCCCAAGAGTACATACAT 57.168 37.500 0.00 0.00 37.41 2.29
69 70 7.255836 CGATAGGAAATCCCAAGAGTACATACA 60.256 40.741 0.00 0.00 37.41 2.29
70 71 7.091443 CGATAGGAAATCCCAAGAGTACATAC 58.909 42.308 0.00 0.00 37.41 2.39
71 72 6.781014 ACGATAGGAAATCCCAAGAGTACATA 59.219 38.462 0.00 0.00 43.77 2.29
72 73 5.602978 ACGATAGGAAATCCCAAGAGTACAT 59.397 40.000 0.00 0.00 43.77 2.29
73 74 4.960469 ACGATAGGAAATCCCAAGAGTACA 59.040 41.667 0.00 0.00 43.77 2.90
74 75 5.532664 ACGATAGGAAATCCCAAGAGTAC 57.467 43.478 0.00 0.00 43.77 2.73
76 77 5.437191 AAACGATAGGAAATCCCAAGAGT 57.563 39.130 0.00 0.00 43.77 3.24
79 80 6.509418 TTGAAAACGATAGGAAATCCCAAG 57.491 37.500 0.00 0.00 43.77 3.61
80 81 6.096282 GGATTGAAAACGATAGGAAATCCCAA 59.904 38.462 0.00 0.00 36.94 4.12
81 82 5.592688 GGATTGAAAACGATAGGAAATCCCA 59.407 40.000 0.00 0.00 36.94 4.37
82 83 5.828328 AGGATTGAAAACGATAGGAAATCCC 59.172 40.000 7.68 0.00 41.56 3.85
83 84 6.944234 AGGATTGAAAACGATAGGAAATCC 57.056 37.500 0.00 0.00 41.14 3.01
84 85 8.766151 GTCTAGGATTGAAAACGATAGGAAATC 58.234 37.037 0.00 0.00 43.77 2.17
86 87 6.755141 CGTCTAGGATTGAAAACGATAGGAAA 59.245 38.462 0.00 0.00 43.77 3.13
87 88 6.270815 CGTCTAGGATTGAAAACGATAGGAA 58.729 40.000 0.00 0.00 43.77 3.36
89 90 4.444720 GCGTCTAGGATTGAAAACGATAGG 59.555 45.833 0.00 0.00 43.77 2.57
91 92 5.001237 TGCGTCTAGGATTGAAAACGATA 57.999 39.130 0.00 0.00 32.17 2.92
93 94 3.306917 TGCGTCTAGGATTGAAAACGA 57.693 42.857 0.00 0.00 32.17 3.85
94 95 5.712217 TTATGCGTCTAGGATTGAAAACG 57.288 39.130 0.00 0.00 31.61 3.60
95 96 7.792508 CGTAATTATGCGTCTAGGATTGAAAAC 59.207 37.037 0.00 0.00 31.61 2.43
98 99 6.741109 TCGTAATTATGCGTCTAGGATTGAA 58.259 36.000 0.00 0.00 35.99 2.69
99 100 6.321848 TCGTAATTATGCGTCTAGGATTGA 57.678 37.500 0.00 0.00 35.99 2.57
100 101 7.030165 AGATCGTAATTATGCGTCTAGGATTG 58.970 38.462 9.40 0.00 35.99 2.67
101 102 7.159322 AGATCGTAATTATGCGTCTAGGATT 57.841 36.000 9.40 0.00 35.99 3.01
102 103 6.761099 AGATCGTAATTATGCGTCTAGGAT 57.239 37.500 9.40 0.00 35.99 3.24
104 105 7.432545 CCATTAGATCGTAATTATGCGTCTAGG 59.567 40.741 14.17 11.40 35.99 3.02
105 106 7.968956 ACCATTAGATCGTAATTATGCGTCTAG 59.031 37.037 14.17 9.29 35.99 2.43
106 107 7.823665 ACCATTAGATCGTAATTATGCGTCTA 58.176 34.615 12.12 12.12 35.99 2.59
107 108 6.688578 ACCATTAGATCGTAATTATGCGTCT 58.311 36.000 13.49 13.49 35.99 4.18
108 109 6.584942 TGACCATTAGATCGTAATTATGCGTC 59.415 38.462 0.00 1.63 35.99 5.19
109 110 6.452242 TGACCATTAGATCGTAATTATGCGT 58.548 36.000 0.00 0.00 35.99 5.24
110 111 6.944557 TGACCATTAGATCGTAATTATGCG 57.055 37.500 0.00 0.00 35.85 4.73
116 117 9.832445 ACTGTAAAATGACCATTAGATCGTAAT 57.168 29.630 0.00 0.00 0.00 1.89
119 120 9.832445 ATTACTGTAAAATGACCATTAGATCGT 57.168 29.630 4.11 0.00 0.00 3.73
126 127 9.927668 CTCCAAAATTACTGTAAAATGACCATT 57.072 29.630 4.11 0.00 0.00 3.16
128 129 7.726291 TCCTCCAAAATTACTGTAAAATGACCA 59.274 33.333 4.11 0.00 0.00 4.02
129 130 8.117813 TCCTCCAAAATTACTGTAAAATGACC 57.882 34.615 4.11 0.00 0.00 4.02
136 137 8.851541 ACGTTAATCCTCCAAAATTACTGTAA 57.148 30.769 2.26 2.26 0.00 2.41
138 139 8.316214 TCTACGTTAATCCTCCAAAATTACTGT 58.684 33.333 0.00 0.00 0.00 3.55
139 140 8.712285 TCTACGTTAATCCTCCAAAATTACTG 57.288 34.615 0.00 0.00 0.00 2.74
140 141 7.985752 CCTCTACGTTAATCCTCCAAAATTACT 59.014 37.037 0.00 0.00 0.00 2.24
142 143 6.764560 GCCTCTACGTTAATCCTCCAAAATTA 59.235 38.462 0.00 0.00 0.00 1.40
143 144 5.589050 GCCTCTACGTTAATCCTCCAAAATT 59.411 40.000 0.00 0.00 0.00 1.82
144 145 5.104485 AGCCTCTACGTTAATCCTCCAAAAT 60.104 40.000 0.00 0.00 0.00 1.82
146 147 3.773119 AGCCTCTACGTTAATCCTCCAAA 59.227 43.478 0.00 0.00 0.00 3.28
148 149 2.957006 GAGCCTCTACGTTAATCCTCCA 59.043 50.000 0.00 0.00 0.00 3.86
149 150 2.030981 CGAGCCTCTACGTTAATCCTCC 60.031 54.545 0.00 0.00 0.00 4.30
150 151 2.617774 ACGAGCCTCTACGTTAATCCTC 59.382 50.000 0.00 0.00 39.75 3.71
153 154 4.023365 ACCATACGAGCCTCTACGTTAATC 60.023 45.833 0.00 0.00 42.61 1.75
155 156 3.065786 CACCATACGAGCCTCTACGTTAA 59.934 47.826 0.00 0.00 42.61 2.01
157 158 1.404391 CACCATACGAGCCTCTACGTT 59.596 52.381 0.00 0.00 42.61 3.99
158 159 1.022735 CACCATACGAGCCTCTACGT 58.977 55.000 0.00 0.00 44.72 3.57
159 160 0.317938 GCACCATACGAGCCTCTACG 60.318 60.000 0.00 0.00 0.00 3.51
160 161 1.033574 AGCACCATACGAGCCTCTAC 58.966 55.000 0.00 0.00 0.00 2.59
161 162 1.681793 GAAGCACCATACGAGCCTCTA 59.318 52.381 0.00 0.00 0.00 2.43
163 164 0.461961 AGAAGCACCATACGAGCCTC 59.538 55.000 0.00 0.00 0.00 4.70
164 165 1.776662 TAGAAGCACCATACGAGCCT 58.223 50.000 0.00 0.00 0.00 4.58
166 167 5.290386 ACTAATTAGAAGCACCATACGAGC 58.710 41.667 19.38 0.00 0.00 5.03
167 168 8.867112 TTTACTAATTAGAAGCACCATACGAG 57.133 34.615 19.38 0.00 0.00 4.18
203 204 8.856103 TCCCTTTTTCATTTTTCGAAGTATCTT 58.144 29.630 0.00 0.00 0.00 2.40
205 206 9.471084 TTTCCCTTTTTCATTTTTCGAAGTATC 57.529 29.630 0.00 0.00 0.00 2.24
262 263 7.436080 CCATGCTACATTTTATGGTTTTAGCAG 59.564 37.037 12.31 7.21 41.40 4.24
265 266 7.920682 GGTCCATGCTACATTTTATGGTTTTAG 59.079 37.037 0.00 0.00 40.68 1.85
279 338 1.271325 CCACTGTTGGTCCATGCTACA 60.271 52.381 0.00 0.00 38.23 2.74
288 347 0.320374 TCCATCGTCCACTGTTGGTC 59.680 55.000 0.00 0.00 44.35 4.02
337 396 3.254903 GCAGAGGTCACGGGTAAATTTTT 59.745 43.478 0.00 0.00 0.00 1.94
338 397 2.817844 GCAGAGGTCACGGGTAAATTTT 59.182 45.455 0.00 0.00 0.00 1.82
339 398 2.224670 TGCAGAGGTCACGGGTAAATTT 60.225 45.455 0.00 0.00 0.00 1.82
340 399 1.349688 TGCAGAGGTCACGGGTAAATT 59.650 47.619 0.00 0.00 0.00 1.82
342 401 0.981183 ATGCAGAGGTCACGGGTAAA 59.019 50.000 0.00 0.00 0.00 2.01
343 402 0.535335 GATGCAGAGGTCACGGGTAA 59.465 55.000 0.00 0.00 0.00 2.85
344 403 0.613572 TGATGCAGAGGTCACGGGTA 60.614 55.000 0.00 0.00 0.00 3.69
346 405 1.448540 GTGATGCAGAGGTCACGGG 60.449 63.158 2.60 0.00 35.85 5.28
347 406 4.192000 GTGATGCAGAGGTCACGG 57.808 61.111 2.60 0.00 35.85 4.94
349 408 1.073216 CGTCGTGATGCAGAGGTCAC 61.073 60.000 7.91 7.91 40.94 3.67
352 411 2.193532 ATCGTCGTGATGCAGAGGT 58.806 52.632 0.00 0.00 35.45 3.85
361 420 2.021584 GCTGTGTGCATCGTCGTGA 61.022 57.895 0.00 0.00 42.31 4.35
362 421 2.471607 GCTGTGTGCATCGTCGTG 59.528 61.111 0.00 0.00 42.31 4.35
364 423 1.638388 ATTGGCTGTGTGCATCGTCG 61.638 55.000 0.00 0.00 45.15 5.12
365 424 0.179181 CATTGGCTGTGTGCATCGTC 60.179 55.000 0.00 0.00 45.15 4.20
366 425 1.878070 CATTGGCTGTGTGCATCGT 59.122 52.632 0.00 0.00 45.15 3.73
368 427 1.587568 TGCATTGGCTGTGTGCATC 59.412 52.632 0.00 0.00 43.30 3.91
369 428 3.780357 TGCATTGGCTGTGTGCAT 58.220 50.000 0.00 0.00 43.30 3.96
370 429 2.729455 GTGCATTGGCTGTGTGCA 59.271 55.556 0.00 0.00 45.69 4.57
371 430 2.429571 CGTGCATTGGCTGTGTGC 60.430 61.111 0.00 0.00 41.91 4.57
374 433 1.233950 TGTACCGTGCATTGGCTGTG 61.234 55.000 7.79 0.00 41.91 3.66
375 434 0.322456 ATGTACCGTGCATTGGCTGT 60.322 50.000 7.79 0.00 41.91 4.40
376 435 0.378257 GATGTACCGTGCATTGGCTG 59.622 55.000 3.44 0.00 41.91 4.85
378 437 0.378257 CAGATGTACCGTGCATTGGC 59.622 55.000 3.44 0.00 41.68 4.52
379 438 1.398041 CACAGATGTACCGTGCATTGG 59.602 52.381 3.44 6.41 0.00 3.16
380 439 2.811902 CACAGATGTACCGTGCATTG 57.188 50.000 3.44 6.83 0.00 2.82
385 444 1.009078 CCATGCACAGATGTACCGTG 58.991 55.000 0.00 0.00 0.00 4.94
386 445 0.613260 ACCATGCACAGATGTACCGT 59.387 50.000 0.00 0.00 0.00 4.83
387 446 2.595124 TACCATGCACAGATGTACCG 57.405 50.000 0.00 0.00 0.00 4.02
388 447 5.581605 CATTTTACCATGCACAGATGTACC 58.418 41.667 0.00 0.00 0.00 3.34
400 459 5.603170 AGGAGAATTGGCATTTTACCATG 57.397 39.130 15.40 0.00 36.96 3.66
439 522 4.946772 TCACCTATCTCTCTCAAGTGTCAG 59.053 45.833 0.00 0.00 0.00 3.51
455 538 2.224305 GGTATTGCTCGCCTTCACCTAT 60.224 50.000 0.00 0.00 0.00 2.57
3073 4881 2.362736 CTAGTGGCGTGGTACTAGTGA 58.637 52.381 5.39 0.00 40.78 3.41


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

AutoCloner maintained by Alex Coulton.