Multiple sequence alignment - TraesCS1A01G404600

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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 TraesCS1A01G404600 chr1A 100.000 4270 0 0 1 4270 568029471 568025202 0.000000e+00 7886.0
1 TraesCS1A01G404600 chr1A 89.679 436 15 12 393 826 568041132 568040725 3.540000e-146 529.0
2 TraesCS1A01G404600 chr1A 100.000 249 0 0 4912 5160 568024560 568024312 1.310000e-125 460.0
3 TraesCS1A01G404600 chr1A 77.064 327 43 20 1175 1477 568077207 568076889 5.350000e-35 159.0
4 TraesCS1A01G404600 chr1D 94.965 3138 112 19 1163 4270 473710908 473707787 0.000000e+00 4878.0
5 TraesCS1A01G404600 chr1D 95.287 785 22 3 393 1165 473711734 473710953 0.000000e+00 1230.0
6 TraesCS1A01G404600 chr1D 83.056 1080 147 21 3192 4258 473641770 473640714 0.000000e+00 948.0
7 TraesCS1A01G404600 chr1D 82.179 1083 142 26 3189 4249 473700472 473699419 0.000000e+00 883.0
8 TraesCS1A01G404600 chr1D 82.000 750 106 15 1912 2652 473659202 473658473 1.230000e-170 610.0
9 TraesCS1A01G404600 chr1D 95.000 200 10 0 196 395 207230513 207230712 1.080000e-81 315.0
10 TraesCS1A01G404600 chr1D 80.804 448 45 26 1347 1765 473659848 473659413 3.880000e-81 313.0
11 TraesCS1A01G404600 chr1D 94.500 200 11 0 196 395 15107337 15107536 5.020000e-80 309.0
12 TraesCS1A01G404600 chr1D 94.500 200 11 0 196 395 15109070 15109269 5.020000e-80 309.0
13 TraesCS1A01G404600 chr1D 87.600 250 26 4 4912 5160 473707744 473707499 8.460000e-73 285.0
14 TraesCS1A01G404600 chr1D 89.316 234 14 2 2367 2600 473701148 473700926 3.040000e-72 283.0
15 TraesCS1A01G404600 chr1D 87.705 122 11 2 827 948 473676194 473676077 6.970000e-29 139.0
16 TraesCS1A01G404600 chr1D 89.706 68 5 2 1846 1913 56744928 56744863 9.210000e-13 86.1
17 TraesCS1A01G404600 chr1B 93.087 2141 119 15 2143 4270 658709823 658707699 0.000000e+00 3107.0
18 TraesCS1A01G404600 chr1B 92.276 725 53 3 1897 2621 658700163 658699442 0.000000e+00 1026.0
19 TraesCS1A01G404600 chr1B 79.518 1079 181 22 3218 4266 658713103 658712035 0.000000e+00 732.0
20 TraesCS1A01G404600 chr1B 92.130 432 26 3 1376 1804 658700697 658700271 2.060000e-168 603.0
21 TraesCS1A01G404600 chr1B 93.173 249 15 1 4912 5160 658707648 658707402 1.060000e-96 364.0
22 TraesCS1A01G404600 chr1B 91.667 192 12 2 1908 2096 658710741 658710551 3.960000e-66 263.0
23 TraesCS1A01G404600 chr1B 94.643 112 2 2 1748 1859 658710841 658710734 2.470000e-38 171.0
24 TraesCS1A01G404600 chr1B 90.756 119 11 0 1185 1303 658701032 658700914 5.350000e-35 159.0
25 TraesCS1A01G404600 chr1B 95.455 88 4 0 1387 1474 658715074 658714987 1.940000e-29 141.0
26 TraesCS1A01G404600 chr1B 91.304 69 3 1 1791 1859 658700212 658700147 1.980000e-14 91.6
27 TraesCS1A01G404600 chr1B 91.803 61 3 2 1853 1913 648621100 648621042 3.310000e-12 84.2
28 TraesCS1A01G404600 chr1B 96.875 32 1 0 2554 2585 658738341 658738310 3.000000e-03 54.7
29 TraesCS1A01G404600 chr6A 87.342 395 41 8 1 392 117425305 117424917 1.320000e-120 444.0
30 TraesCS1A01G404600 chr6D 74.941 846 172 30 3324 4159 13977742 13978557 8.220000e-93 351.0
31 TraesCS1A01G404600 chr3A 96.209 211 6 2 1 209 373339305 373339515 1.380000e-90 344.0
32 TraesCS1A01G404600 chr3A 94.924 197 7 3 1 196 373344304 373344498 6.490000e-79 305.0
33 TraesCS1A01G404600 chr7A 91.270 252 16 3 1 251 640659998 640659752 6.400000e-89 339.0
34 TraesCS1A01G404600 chr7A 95.431 197 7 2 1 196 640646049 640645854 3.880000e-81 313.0
35 TraesCS1A01G404600 chr5A 94.949 198 10 0 196 393 5755488 5755291 1.400000e-80 311.0
36 TraesCS1A01G404600 chr5A 92.063 63 2 3 1848 1910 535672463 535672522 9.210000e-13 86.1
37 TraesCS1A01G404600 chr2B 94.527 201 11 0 196 396 798140883 798140683 1.400000e-80 311.0
38 TraesCS1A01G404600 chr2B 90.566 212 16 4 1 209 33925437 33925227 1.420000e-70 278.0
39 TraesCS1A01G404600 chr2B 90.566 212 16 4 1 209 33930407 33930197 1.420000e-70 278.0
40 TraesCS1A01G404600 chr2B 91.803 61 3 1 1853 1913 64607502 64607444 3.310000e-12 84.2
41 TraesCS1A01G404600 chr2B 91.803 61 3 2 1853 1913 64620899 64620841 3.310000e-12 84.2
42 TraesCS1A01G404600 chr2B 91.803 61 3 1 1853 1913 64664555 64664497 3.310000e-12 84.2
43 TraesCS1A01G404600 chr2B 91.803 61 3 2 1853 1913 64703572 64703514 3.310000e-12 84.2
44 TraesCS1A01G404600 chrUn 94.500 200 11 0 196 395 9873148 9872949 5.020000e-80 309.0
45 TraesCS1A01G404600 chr6B 93.720 207 11 2 188 393 305729060 305729265 5.020000e-80 309.0
46 TraesCS1A01G404600 chr6B 73.815 844 185 25 3324 4159 25555404 25554589 8.400000e-78 302.0
47 TraesCS1A01G404600 chr6B 82.682 358 35 19 42 395 655773562 655773228 5.050000e-75 292.0
48 TraesCS1A01G404600 chr6B 91.133 203 15 3 1 201 716271043 716270842 6.580000e-69 272.0
49 TraesCS1A01G404600 chr5B 89.100 211 19 4 2 209 37458575 37458366 5.130000e-65 259.0
50 TraesCS1A01G404600 chr5B 93.333 60 2 2 1854 1913 673993303 673993246 2.560000e-13 87.9


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 TraesCS1A01G404600 chr1A 568024312 568029471 5159 True 4173.000000 7886 100.000000 1 5160 2 chr1A.!!$R3 5159
1 TraesCS1A01G404600 chr1D 473707499 473711734 4235 True 2131.000000 4878 92.617333 393 5160 3 chr1D.!!$R6 4767
2 TraesCS1A01G404600 chr1D 473640714 473641770 1056 True 948.000000 948 83.056000 3192 4258 1 chr1D.!!$R2 1066
3 TraesCS1A01G404600 chr1D 473699419 473701148 1729 True 583.000000 883 85.747500 2367 4249 2 chr1D.!!$R5 1882
4 TraesCS1A01G404600 chr1D 473658473 473659848 1375 True 461.500000 610 81.402000 1347 2652 2 chr1D.!!$R4 1305
5 TraesCS1A01G404600 chr1D 15107337 15109269 1932 False 309.000000 309 94.500000 196 395 2 chr1D.!!$F2 199
6 TraesCS1A01G404600 chr1B 658707402 658715074 7672 True 796.333333 3107 91.257167 1387 5160 6 chr1B.!!$R4 3773
7 TraesCS1A01G404600 chr1B 658699442 658701032 1590 True 469.900000 1026 91.616500 1185 2621 4 chr1B.!!$R3 1436
8 TraesCS1A01G404600 chr6D 13977742 13978557 815 False 351.000000 351 74.941000 3324 4159 1 chr6D.!!$F1 835
9 TraesCS1A01G404600 chr6B 25554589 25555404 815 True 302.000000 302 73.815000 3324 4159 1 chr6B.!!$R1 835

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
274 275 0.249447 TGATTCTGCGGCCTACATCG 60.249 55.0 0.00 0.00 0.00 3.84 F
1112 1125 0.030908 GGAGGATCTCGCAAGGTACG 59.969 60.0 0.00 0.00 38.47 3.67 F
1477 1691 0.251354 AGACTTGCAGGTCATCGCAT 59.749 50.0 28.25 6.05 38.10 4.73 F
3372 8271 0.898320 TCTTAGCAGCAGTGGGAGAC 59.102 55.0 0.00 0.00 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2139 6663 1.241165 CTGCAGTGGAAGCACAATGA 58.759 50.000 5.25 0.00 38.62 2.57 R
2990 7859 0.321298 ACCTTGTGTCCATGGCGTAC 60.321 55.000 6.96 6.39 39.04 3.67 R
3384 8283 0.324943 CCATGGACGTCCCTGACTTT 59.675 55.000 33.55 9.04 34.09 2.66 R
4236 10030 1.552337 GAGAGAGAGCCCACATGTCAA 59.448 52.381 0.00 0.00 0.00 3.18 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
23 24 5.952347 AGGATAGATAGTTGGTTCGGTTT 57.048 39.130 0.00 0.00 0.00 3.27
25 26 6.814043 AGGATAGATAGTTGGTTCGGTTTAC 58.186 40.000 0.00 0.00 0.00 2.01
26 27 6.381994 AGGATAGATAGTTGGTTCGGTTTACA 59.618 38.462 0.00 0.00 0.00 2.41
27 28 7.070821 AGGATAGATAGTTGGTTCGGTTTACAT 59.929 37.037 0.00 0.00 0.00 2.29
28 29 7.170998 GGATAGATAGTTGGTTCGGTTTACATG 59.829 40.741 0.00 0.00 0.00 3.21
29 30 5.801380 AGATAGTTGGTTCGGTTTACATGT 58.199 37.500 2.69 2.69 0.00 3.21
30 31 6.938507 AGATAGTTGGTTCGGTTTACATGTA 58.061 36.000 0.08 0.08 0.00 2.29
31 32 7.388437 AGATAGTTGGTTCGGTTTACATGTAA 58.612 34.615 14.35 14.35 0.00 2.41
32 33 8.044908 AGATAGTTGGTTCGGTTTACATGTAAT 58.955 33.333 18.69 2.55 0.00 1.89
33 34 6.887626 AGTTGGTTCGGTTTACATGTAATT 57.112 33.333 18.69 0.00 0.00 1.40
34 35 6.905578 AGTTGGTTCGGTTTACATGTAATTC 58.094 36.000 18.69 14.07 0.00 2.17
35 36 6.713450 AGTTGGTTCGGTTTACATGTAATTCT 59.287 34.615 18.69 3.81 0.00 2.40
36 37 7.879160 AGTTGGTTCGGTTTACATGTAATTCTA 59.121 33.333 18.69 1.36 0.00 2.10
37 38 8.671028 GTTGGTTCGGTTTACATGTAATTCTAT 58.329 33.333 18.69 0.00 0.00 1.98
38 39 8.428186 TGGTTCGGTTTACATGTAATTCTATC 57.572 34.615 18.69 3.86 0.00 2.08
39 40 8.262227 TGGTTCGGTTTACATGTAATTCTATCT 58.738 33.333 18.69 0.00 0.00 1.98
40 41 8.762426 GGTTCGGTTTACATGTAATTCTATCTC 58.238 37.037 18.69 6.44 0.00 2.75
41 42 9.530633 GTTCGGTTTACATGTAATTCTATCTCT 57.469 33.333 18.69 0.00 0.00 3.10
62 63 9.930158 ATCTCTTTATCTCCTGTAACTACTTCT 57.070 33.333 0.00 0.00 0.00 2.85
70 71 8.740123 TCTCCTGTAACTACTTCTATCTCTTG 57.260 38.462 0.00 0.00 0.00 3.02
71 72 8.330247 TCTCCTGTAACTACTTCTATCTCTTGT 58.670 37.037 0.00 0.00 0.00 3.16
72 73 8.880991 TCCTGTAACTACTTCTATCTCTTGTT 57.119 34.615 0.00 0.00 0.00 2.83
73 74 8.958506 TCCTGTAACTACTTCTATCTCTTGTTC 58.041 37.037 0.00 0.00 0.00 3.18
74 75 8.962679 CCTGTAACTACTTCTATCTCTTGTTCT 58.037 37.037 0.00 0.00 0.00 3.01
75 76 9.997482 CTGTAACTACTTCTATCTCTTGTTCTC 57.003 37.037 0.00 0.00 0.00 2.87
76 77 8.958506 TGTAACTACTTCTATCTCTTGTTCTCC 58.041 37.037 0.00 0.00 0.00 3.71
77 78 8.958506 GTAACTACTTCTATCTCTTGTTCTCCA 58.041 37.037 0.00 0.00 0.00 3.86
78 79 8.423906 AACTACTTCTATCTCTTGTTCTCCAA 57.576 34.615 0.00 0.00 0.00 3.53
88 89 4.813296 CTTGTTCTCCAAGTTGTACACC 57.187 45.455 0.00 0.00 44.64 4.16
89 90 4.451900 CTTGTTCTCCAAGTTGTACACCT 58.548 43.478 0.00 0.00 44.64 4.00
90 91 4.067972 TGTTCTCCAAGTTGTACACCTC 57.932 45.455 0.00 0.00 0.00 3.85
91 92 3.709653 TGTTCTCCAAGTTGTACACCTCT 59.290 43.478 0.00 0.00 0.00 3.69
92 93 4.163458 TGTTCTCCAAGTTGTACACCTCTT 59.837 41.667 0.00 0.00 0.00 2.85
93 94 4.336889 TCTCCAAGTTGTACACCTCTTG 57.663 45.455 19.28 19.28 37.57 3.02
94 95 3.709653 TCTCCAAGTTGTACACCTCTTGT 59.290 43.478 22.01 0.00 42.84 3.16
95 96 4.897076 TCTCCAAGTTGTACACCTCTTGTA 59.103 41.667 22.01 12.86 39.91 2.41
96 97 5.364446 TCTCCAAGTTGTACACCTCTTGTAA 59.636 40.000 22.01 14.23 42.56 2.41
97 98 5.991861 TCCAAGTTGTACACCTCTTGTAAA 58.008 37.500 22.01 11.78 42.56 2.01
98 99 6.416415 TCCAAGTTGTACACCTCTTGTAAAA 58.584 36.000 22.01 10.24 42.56 1.52
99 100 7.057894 TCCAAGTTGTACACCTCTTGTAAAAT 58.942 34.615 22.01 0.00 42.56 1.82
100 101 7.227910 TCCAAGTTGTACACCTCTTGTAAAATC 59.772 37.037 22.01 0.00 42.56 2.17
101 102 7.228706 CCAAGTTGTACACCTCTTGTAAAATCT 59.771 37.037 22.01 0.00 42.56 2.40
102 103 7.964604 AGTTGTACACCTCTTGTAAAATCTC 57.035 36.000 0.00 0.00 42.56 2.75
103 104 6.935208 AGTTGTACACCTCTTGTAAAATCTCC 59.065 38.462 0.00 0.00 42.56 3.71
104 105 6.428083 TGTACACCTCTTGTAAAATCTCCA 57.572 37.500 0.00 0.00 42.56 3.86
105 106 6.833041 TGTACACCTCTTGTAAAATCTCCAA 58.167 36.000 0.00 0.00 42.56 3.53
106 107 6.708949 TGTACACCTCTTGTAAAATCTCCAAC 59.291 38.462 0.00 0.00 42.56 3.77
107 108 4.755123 ACACCTCTTGTAAAATCTCCAACG 59.245 41.667 0.00 0.00 36.32 4.10
108 109 4.994852 CACCTCTTGTAAAATCTCCAACGA 59.005 41.667 0.00 0.00 0.00 3.85
109 110 5.643777 CACCTCTTGTAAAATCTCCAACGAT 59.356 40.000 0.00 0.00 0.00 3.73
110 111 5.643777 ACCTCTTGTAAAATCTCCAACGATG 59.356 40.000 0.00 0.00 0.00 3.84
111 112 5.643777 CCTCTTGTAAAATCTCCAACGATGT 59.356 40.000 0.00 0.00 0.00 3.06
112 113 6.816640 CCTCTTGTAAAATCTCCAACGATGTA 59.183 38.462 0.00 0.00 0.00 2.29
113 114 7.495934 CCTCTTGTAAAATCTCCAACGATGTAT 59.504 37.037 0.00 0.00 0.00 2.29
114 115 8.196802 TCTTGTAAAATCTCCAACGATGTATG 57.803 34.615 0.00 0.00 0.00 2.39
115 116 6.358118 TGTAAAATCTCCAACGATGTATGC 57.642 37.500 0.00 0.00 0.00 3.14
116 117 5.877564 TGTAAAATCTCCAACGATGTATGCA 59.122 36.000 0.00 0.00 0.00 3.96
117 118 4.882671 AAATCTCCAACGATGTATGCAC 57.117 40.909 0.00 0.00 0.00 4.57
118 119 3.827008 ATCTCCAACGATGTATGCACT 57.173 42.857 0.00 0.00 0.00 4.40
119 120 3.610040 TCTCCAACGATGTATGCACTT 57.390 42.857 0.00 0.00 0.00 3.16
120 121 3.521560 TCTCCAACGATGTATGCACTTC 58.478 45.455 0.00 0.00 0.00 3.01
121 122 2.609459 CTCCAACGATGTATGCACTTCC 59.391 50.000 0.00 0.00 0.00 3.46
122 123 2.027653 TCCAACGATGTATGCACTTCCA 60.028 45.455 0.00 0.00 0.00 3.53
123 124 2.352651 CCAACGATGTATGCACTTCCAG 59.647 50.000 0.00 0.00 0.00 3.86
124 125 2.315925 ACGATGTATGCACTTCCAGG 57.684 50.000 0.00 0.00 0.00 4.45
125 126 1.134401 ACGATGTATGCACTTCCAGGG 60.134 52.381 0.00 0.00 0.00 4.45
126 127 1.138859 CGATGTATGCACTTCCAGGGA 59.861 52.381 0.00 0.00 0.00 4.20
127 128 2.804572 CGATGTATGCACTTCCAGGGAG 60.805 54.545 0.00 0.00 0.00 4.30
128 129 0.911769 TGTATGCACTTCCAGGGAGG 59.088 55.000 0.00 0.00 39.47 4.30
129 130 0.912486 GTATGCACTTCCAGGGAGGT 59.088 55.000 0.00 0.00 39.02 3.85
132 133 2.046892 CACTTCCAGGGAGGTGCG 60.047 66.667 16.30 0.00 43.34 5.34
133 134 4.021925 ACTTCCAGGGAGGTGCGC 62.022 66.667 0.00 0.00 39.02 6.09
134 135 4.785453 CTTCCAGGGAGGTGCGCC 62.785 72.222 8.71 8.71 39.02 6.53
141 142 3.480133 GGAGGTGCGCCCCTGTAT 61.480 66.667 18.84 0.00 34.03 2.29
142 143 2.138179 GGAGGTGCGCCCCTGTATA 61.138 63.158 18.84 0.00 34.03 1.47
143 144 1.481056 GGAGGTGCGCCCCTGTATAT 61.481 60.000 18.84 0.00 34.03 0.86
144 145 1.263356 GAGGTGCGCCCCTGTATATA 58.737 55.000 18.84 0.00 34.03 0.86
145 146 1.621814 GAGGTGCGCCCCTGTATATAA 59.378 52.381 18.84 0.00 34.03 0.98
146 147 1.346722 AGGTGCGCCCCTGTATATAAC 59.653 52.381 11.85 0.00 32.11 1.89
147 148 1.071071 GGTGCGCCCCTGTATATAACA 59.929 52.381 4.45 0.00 36.42 2.41
148 149 2.140717 GTGCGCCCCTGTATATAACAC 58.859 52.381 4.18 0.00 33.45 3.32
149 150 1.269883 TGCGCCCCTGTATATAACACG 60.270 52.381 4.18 0.00 33.45 4.49
150 151 1.269936 GCGCCCCTGTATATAACACGT 60.270 52.381 0.00 0.00 33.45 4.49
151 152 2.030007 GCGCCCCTGTATATAACACGTA 60.030 50.000 0.00 0.00 33.45 3.57
152 153 3.829948 CGCCCCTGTATATAACACGTAG 58.170 50.000 0.00 0.00 33.45 3.51
153 154 3.582780 GCCCCTGTATATAACACGTAGC 58.417 50.000 0.00 0.00 33.45 3.58
154 155 3.006110 GCCCCTGTATATAACACGTAGCA 59.994 47.826 0.00 0.00 33.45 3.49
155 156 4.553323 CCCCTGTATATAACACGTAGCAC 58.447 47.826 0.00 0.00 33.45 4.40
165 166 2.577112 CGTAGCACGTCGCCTCAG 60.577 66.667 6.39 0.00 44.04 3.35
166 167 2.202623 GTAGCACGTCGCCTCAGG 60.203 66.667 6.39 0.00 44.04 3.86
167 168 2.675423 TAGCACGTCGCCTCAGGT 60.675 61.111 0.00 0.00 44.04 4.00
168 169 2.697761 TAGCACGTCGCCTCAGGTC 61.698 63.158 0.00 0.00 44.04 3.85
170 171 3.733960 CACGTCGCCTCAGGTCGA 61.734 66.667 6.17 6.17 0.00 4.20
171 172 3.432588 ACGTCGCCTCAGGTCGAG 61.433 66.667 10.09 7.61 41.89 4.04
182 183 4.035278 CTCAGGTCGAGGTAAGACATTC 57.965 50.000 0.00 0.00 40.20 2.67
183 184 2.758979 TCAGGTCGAGGTAAGACATTCC 59.241 50.000 0.00 0.00 40.20 3.01
184 185 1.749634 AGGTCGAGGTAAGACATTCCG 59.250 52.381 0.00 0.00 40.20 4.30
185 186 1.557651 GTCGAGGTAAGACATTCCGC 58.442 55.000 0.00 0.00 38.42 5.54
186 187 0.458669 TCGAGGTAAGACATTCCGCC 59.541 55.000 0.00 0.00 0.00 6.13
187 188 0.460311 CGAGGTAAGACATTCCGCCT 59.540 55.000 0.00 0.00 0.00 5.52
188 189 1.802880 CGAGGTAAGACATTCCGCCTG 60.803 57.143 0.00 0.00 0.00 4.85
189 190 1.207329 GAGGTAAGACATTCCGCCTGT 59.793 52.381 0.00 0.00 0.00 4.00
190 191 1.207329 AGGTAAGACATTCCGCCTGTC 59.793 52.381 2.98 2.98 42.68 3.51
191 192 1.278238 GTAAGACATTCCGCCTGTCG 58.722 55.000 0.00 0.00 46.05 4.35
192 193 0.459585 TAAGACATTCCGCCTGTCGC 60.460 55.000 0.00 0.00 46.05 5.19
193 194 2.434185 GACATTCCGCCTGTCGCA 60.434 61.111 0.00 0.00 37.30 5.10
194 195 2.740714 GACATTCCGCCTGTCGCAC 61.741 63.158 0.00 0.00 37.30 5.34
211 212 2.016604 GCACATGGTATCCGAGCCAAA 61.017 52.381 0.00 0.00 38.38 3.28
218 219 2.433239 GGTATCCGAGCCAAAAGGTCTA 59.567 50.000 0.00 0.00 41.03 2.59
224 225 3.557264 CCGAGCCAAAAGGTCTAGAGTTT 60.557 47.826 0.00 0.00 41.03 2.66
273 274 2.175878 ATGATTCTGCGGCCTACATC 57.824 50.000 0.00 0.00 0.00 3.06
274 275 0.249447 TGATTCTGCGGCCTACATCG 60.249 55.000 0.00 0.00 0.00 3.84
350 351 2.081161 GCCCACCTCCCTCCATCAT 61.081 63.158 0.00 0.00 0.00 2.45
354 355 1.565759 CCACCTCCCTCCATCATTTCA 59.434 52.381 0.00 0.00 0.00 2.69
373 374 4.437682 TCAGACTTTTGGATGAGTTGGT 57.562 40.909 0.00 0.00 0.00 3.67
387 388 3.896888 TGAGTTGGTTGGAGCATGAATTT 59.103 39.130 0.00 0.00 0.00 1.82
453 454 6.825213 CAGTTGATAGAGGATTCATGTTTCCA 59.175 38.462 15.81 0.43 34.27 3.53
487 488 9.719355 AATATGTTTGTATAATACTCCGCATCA 57.281 29.630 0.00 0.00 0.00 3.07
607 608 5.372343 TCAGCTATGTGTAATGGACCATT 57.628 39.130 23.00 23.00 37.80 3.16
631 632 8.529424 TTGAAGCAAAGAGATGGATTATTCAT 57.471 30.769 0.00 0.00 0.00 2.57
640 641 4.600547 AGATGGATTATTCATGGGAGAGCA 59.399 41.667 0.00 0.00 0.00 4.26
807 808 2.985847 GGGTGCACCAGTTCTGCC 60.986 66.667 35.78 13.32 39.85 4.85
857 861 6.043243 TGTCCATTATTCCTCCTCTATGGAAC 59.957 42.308 0.00 0.00 45.63 3.62
865 869 0.250467 CCTCTATGGAACGGCCCATG 60.250 60.000 17.71 9.86 45.89 3.66
1026 1039 0.167470 TCTACACGCGTTCTTCCTCG 59.833 55.000 10.22 0.00 0.00 4.63
1078 1091 1.592939 TGCTCGTGCACGCTGTTAA 60.593 52.632 33.63 14.98 45.31 2.01
1111 1124 1.338655 GAGGAGGATCTCGCAAGGTAC 59.661 57.143 0.00 0.00 38.47 3.34
1112 1125 0.030908 GGAGGATCTCGCAAGGTACG 59.969 60.000 0.00 0.00 38.47 3.67
1113 1126 0.739561 GAGGATCTCGCAAGGTACGT 59.260 55.000 0.00 0.00 38.47 3.57
1114 1127 1.945394 GAGGATCTCGCAAGGTACGTA 59.055 52.381 0.00 0.00 38.47 3.57
1115 1128 2.357009 GAGGATCTCGCAAGGTACGTAA 59.643 50.000 0.00 0.00 38.47 3.18
1150 1163 7.948357 TCGGTACTATATGCATGTTTAGAGTT 58.052 34.615 10.16 0.00 0.00 3.01
1178 1238 9.836864 ATGCACATACGACCATGAATAATATAT 57.163 29.630 0.00 0.00 0.00 0.86
1344 1430 2.078849 ACGGCCTTTGCTTAATTTGC 57.921 45.000 0.00 0.00 37.74 3.68
1477 1691 0.251354 AGACTTGCAGGTCATCGCAT 59.749 50.000 28.25 6.05 38.10 4.73
1530 1762 5.934781 ACCTGGTTTGATCTAAGATCCATC 58.065 41.667 0.00 0.00 0.00 3.51
1561 1794 4.795970 AATAAGTAGCTAACGTGCATGC 57.204 40.909 11.82 11.82 34.99 4.06
1724 2093 3.846360 CAACTTCGGAGAGGACGTAATT 58.154 45.455 0.00 0.00 38.43 1.40
1808 5972 2.394632 TGGCCGTCCACTCACTAATAT 58.605 47.619 0.00 0.00 37.47 1.28
1813 5977 5.242393 GGCCGTCCACTCACTAATATTAGTA 59.758 44.000 24.29 13.58 41.82 1.82
1814 5978 6.380190 GCCGTCCACTCACTAATATTAGTAG 58.620 44.000 24.29 21.51 41.82 2.57
1862 6026 7.122501 GGCCACTAACTAATATACTACTCCCTC 59.877 44.444 0.00 0.00 0.00 4.30
1882 6046 5.007724 CCCTCTCCGTTGCTAAATATTTGTC 59.992 44.000 11.05 3.17 0.00 3.18
2528 7389 2.879907 GTTCCCGACGGTGATCGA 59.120 61.111 13.94 0.00 45.13 3.59
2605 7466 3.658757 TCAACTCATCATCACACACGA 57.341 42.857 0.00 0.00 0.00 4.35
2636 7497 4.598406 TCACAAAGCTTATATGTGCACG 57.402 40.909 20.25 0.00 43.15 5.34
2637 7498 3.100817 CACAAAGCTTATATGTGCACGC 58.899 45.455 14.94 8.23 38.14 5.34
2678 7539 4.551215 AACTCCCTATCTCTGACCTGAT 57.449 45.455 0.00 0.00 0.00 2.90
2910 7779 1.225637 GCGCAATACACAACGGACG 60.226 57.895 0.30 0.00 0.00 4.79
2990 7859 1.916506 TCTCCAGGAGGATATGCGAG 58.083 55.000 17.10 0.00 44.70 5.03
3035 7904 5.345202 CGTCCACACAAGTAATTCTACAGTC 59.655 44.000 0.00 0.00 0.00 3.51
3108 7983 3.957260 ACGTGAGTGCATGCAGTC 58.043 55.556 37.64 37.64 46.97 3.51
3372 8271 0.898320 TCTTAGCAGCAGTGGGAGAC 59.102 55.000 0.00 0.00 0.00 3.36
3384 8283 2.440409 GTGGGAGACTCCTACGTAACA 58.560 52.381 20.85 6.28 38.26 2.41
3528 8463 5.301551 ACAACATGCAAGTAGAACATCCAAA 59.698 36.000 0.00 0.00 0.00 3.28
3572 8511 5.049612 GCACTTGTGGTCTTTACCTAAGTTC 60.050 44.000 12.14 6.93 44.38 3.01
3769 8708 7.533900 CACGATTACAACAAATTCTTTCGATGT 59.466 33.333 0.00 0.00 0.00 3.06
3976 9187 2.716424 AGTCAAGATGGAGGTTTTCCCA 59.284 45.455 0.00 0.00 46.19 4.37
3988 9199 4.546674 AGGTTTTCCCAGATGTTCTTGTT 58.453 39.130 0.00 0.00 41.86 2.83
4123 9894 1.079405 GATTCCAGTTGCGACCCGA 60.079 57.895 0.00 0.00 0.00 5.14
4236 10030 4.910304 ACTGATTAGGAAGCCATATCACCT 59.090 41.667 0.00 0.00 35.11 4.00
4971 10765 9.196552 GCTTTTGCTAATTTTCAGTTGTCTTAT 57.803 29.630 0.00 0.00 43.35 1.73
5010 10804 1.279271 AGGTCGCCTAGCAAGTTTGAT 59.721 47.619 0.00 0.00 28.47 2.57
5039 10833 2.228822 GCAAAACCTGTCACGATGGAAT 59.771 45.455 0.00 0.00 0.00 3.01
5046 10840 3.133003 CCTGTCACGATGGAATCCTAACT 59.867 47.826 0.00 0.00 41.39 2.24
5063 10857 7.979444 TCCTAACTGTAAATCTGGTTCAAAG 57.021 36.000 0.00 0.00 0.00 2.77
5084 10878 8.524487 TCAAAGTAGAGTTTTGGTGCTTAAAAA 58.476 29.630 0.00 0.00 36.44 1.94
5120 10916 9.845305 GCGACACAAAATATTATACTAAGTGTC 57.155 33.333 0.00 0.00 45.77 3.67
5156 10952 1.203052 CCATTGTGATCCTTGTGGTGC 59.797 52.381 0.00 0.00 34.23 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.560991 TGTAAACCGAACCAACTATCTATCCTA 59.439 37.037 0.00 0.00 0.00 2.94
1 2 5.952347 AAACCGAACCAACTATCTATCCT 57.048 39.130 0.00 0.00 0.00 3.24
2 3 6.576185 TGTAAACCGAACCAACTATCTATCC 58.424 40.000 0.00 0.00 0.00 2.59
3 4 7.709613 ACATGTAAACCGAACCAACTATCTATC 59.290 37.037 0.00 0.00 0.00 2.08
4 5 7.562135 ACATGTAAACCGAACCAACTATCTAT 58.438 34.615 0.00 0.00 0.00 1.98
5 6 6.938507 ACATGTAAACCGAACCAACTATCTA 58.061 36.000 0.00 0.00 0.00 1.98
6 7 5.801380 ACATGTAAACCGAACCAACTATCT 58.199 37.500 0.00 0.00 0.00 1.98
7 8 7.599630 TTACATGTAAACCGAACCAACTATC 57.400 36.000 15.92 0.00 0.00 2.08
8 9 8.570068 AATTACATGTAAACCGAACCAACTAT 57.430 30.769 21.57 0.00 0.00 2.12
9 10 7.879160 AGAATTACATGTAAACCGAACCAACTA 59.121 33.333 21.57 0.00 0.00 2.24
10 11 6.713450 AGAATTACATGTAAACCGAACCAACT 59.287 34.615 21.57 0.00 0.00 3.16
11 12 6.905578 AGAATTACATGTAAACCGAACCAAC 58.094 36.000 21.57 5.06 0.00 3.77
12 13 8.795842 ATAGAATTACATGTAAACCGAACCAA 57.204 30.769 21.57 0.00 0.00 3.67
13 14 8.262227 AGATAGAATTACATGTAAACCGAACCA 58.738 33.333 21.57 0.00 0.00 3.67
14 15 8.658499 AGATAGAATTACATGTAAACCGAACC 57.342 34.615 21.57 9.07 0.00 3.62
15 16 9.530633 AGAGATAGAATTACATGTAAACCGAAC 57.469 33.333 21.57 12.12 0.00 3.95
36 37 9.930158 AGAAGTAGTTACAGGAGATAAAGAGAT 57.070 33.333 0.00 0.00 0.00 2.75
44 45 9.349713 CAAGAGATAGAAGTAGTTACAGGAGAT 57.650 37.037 0.00 0.00 0.00 2.75
45 46 8.330247 ACAAGAGATAGAAGTAGTTACAGGAGA 58.670 37.037 0.00 0.00 0.00 3.71
46 47 8.514330 ACAAGAGATAGAAGTAGTTACAGGAG 57.486 38.462 0.00 0.00 0.00 3.69
47 48 8.880991 AACAAGAGATAGAAGTAGTTACAGGA 57.119 34.615 0.00 0.00 0.00 3.86
48 49 8.962679 AGAACAAGAGATAGAAGTAGTTACAGG 58.037 37.037 0.00 0.00 0.00 4.00
49 50 9.997482 GAGAACAAGAGATAGAAGTAGTTACAG 57.003 37.037 0.00 0.00 0.00 2.74
50 51 8.958506 GGAGAACAAGAGATAGAAGTAGTTACA 58.041 37.037 0.00 0.00 0.00 2.41
51 52 8.958506 TGGAGAACAAGAGATAGAAGTAGTTAC 58.041 37.037 0.00 0.00 0.00 2.50
52 53 9.529823 TTGGAGAACAAGAGATAGAAGTAGTTA 57.470 33.333 0.00 0.00 33.18 2.24
53 54 8.423906 TTGGAGAACAAGAGATAGAAGTAGTT 57.576 34.615 0.00 0.00 33.18 2.24
68 69 4.163458 AGAGGTGTACAACTTGGAGAACAA 59.837 41.667 16.11 0.00 37.55 2.83
69 70 3.709653 AGAGGTGTACAACTTGGAGAACA 59.290 43.478 16.11 0.00 0.00 3.18
70 71 4.338379 AGAGGTGTACAACTTGGAGAAC 57.662 45.455 16.11 0.00 0.00 3.01
71 72 4.163458 ACAAGAGGTGTACAACTTGGAGAA 59.837 41.667 26.88 0.00 42.39 2.87
72 73 3.709653 ACAAGAGGTGTACAACTTGGAGA 59.290 43.478 26.88 0.00 42.39 3.71
73 74 4.073293 ACAAGAGGTGTACAACTTGGAG 57.927 45.455 26.88 16.99 42.39 3.86
74 75 5.617528 TTACAAGAGGTGTACAACTTGGA 57.382 39.130 26.88 21.62 42.56 3.53
75 76 6.687081 TTTTACAAGAGGTGTACAACTTGG 57.313 37.500 26.88 18.30 42.56 3.61
76 77 8.154649 AGATTTTACAAGAGGTGTACAACTTG 57.845 34.615 16.11 21.52 42.56 3.16
77 78 7.444487 GGAGATTTTACAAGAGGTGTACAACTT 59.556 37.037 16.11 9.81 42.56 2.66
78 79 6.935208 GGAGATTTTACAAGAGGTGTACAACT 59.065 38.462 14.75 14.75 42.56 3.16
79 80 6.708949 TGGAGATTTTACAAGAGGTGTACAAC 59.291 38.462 1.50 1.50 42.56 3.32
80 81 6.833041 TGGAGATTTTACAAGAGGTGTACAA 58.167 36.000 0.00 0.00 42.56 2.41
81 82 6.428083 TGGAGATTTTACAAGAGGTGTACA 57.572 37.500 0.00 0.00 42.56 2.90
82 83 6.128634 CGTTGGAGATTTTACAAGAGGTGTAC 60.129 42.308 0.00 0.00 42.56 2.90
83 84 5.929992 CGTTGGAGATTTTACAAGAGGTGTA 59.070 40.000 0.00 0.00 41.98 2.90
84 85 4.755123 CGTTGGAGATTTTACAAGAGGTGT 59.245 41.667 0.00 0.00 44.82 4.16
85 86 4.994852 TCGTTGGAGATTTTACAAGAGGTG 59.005 41.667 0.00 0.00 0.00 4.00
86 87 5.223449 TCGTTGGAGATTTTACAAGAGGT 57.777 39.130 0.00 0.00 0.00 3.85
87 88 5.643777 ACATCGTTGGAGATTTTACAAGAGG 59.356 40.000 0.00 0.00 0.00 3.69
88 89 6.727824 ACATCGTTGGAGATTTTACAAGAG 57.272 37.500 0.00 0.00 0.00 2.85
89 90 7.201609 GCATACATCGTTGGAGATTTTACAAGA 60.202 37.037 0.00 0.00 0.00 3.02
90 91 6.907212 GCATACATCGTTGGAGATTTTACAAG 59.093 38.462 0.00 0.00 0.00 3.16
91 92 6.372937 TGCATACATCGTTGGAGATTTTACAA 59.627 34.615 0.00 0.00 0.00 2.41
92 93 5.877564 TGCATACATCGTTGGAGATTTTACA 59.122 36.000 0.00 0.00 0.00 2.41
93 94 6.037172 AGTGCATACATCGTTGGAGATTTTAC 59.963 38.462 0.00 0.00 0.00 2.01
94 95 6.112734 AGTGCATACATCGTTGGAGATTTTA 58.887 36.000 0.00 0.00 0.00 1.52
95 96 4.943705 AGTGCATACATCGTTGGAGATTTT 59.056 37.500 0.00 0.00 0.00 1.82
96 97 4.517285 AGTGCATACATCGTTGGAGATTT 58.483 39.130 0.00 0.00 0.00 2.17
97 98 4.142609 AGTGCATACATCGTTGGAGATT 57.857 40.909 0.00 0.00 0.00 2.40
98 99 3.827008 AGTGCATACATCGTTGGAGAT 57.173 42.857 0.00 0.00 0.00 2.75
99 100 3.521560 GAAGTGCATACATCGTTGGAGA 58.478 45.455 0.00 0.00 0.00 3.71
100 101 2.609459 GGAAGTGCATACATCGTTGGAG 59.391 50.000 0.00 0.00 0.00 3.86
101 102 2.027653 TGGAAGTGCATACATCGTTGGA 60.028 45.455 0.00 0.00 0.00 3.53
102 103 2.352651 CTGGAAGTGCATACATCGTTGG 59.647 50.000 0.00 0.00 0.00 3.77
103 104 2.352651 CCTGGAAGTGCATACATCGTTG 59.647 50.000 0.00 0.00 0.00 4.10
104 105 2.632377 CCTGGAAGTGCATACATCGTT 58.368 47.619 0.00 0.00 0.00 3.85
105 106 1.134401 CCCTGGAAGTGCATACATCGT 60.134 52.381 0.00 0.00 0.00 3.73
106 107 1.138859 TCCCTGGAAGTGCATACATCG 59.861 52.381 0.00 0.00 0.00 3.84
107 108 2.486191 CCTCCCTGGAAGTGCATACATC 60.486 54.545 0.00 0.00 38.35 3.06
108 109 1.492176 CCTCCCTGGAAGTGCATACAT 59.508 52.381 0.00 0.00 38.35 2.29
109 110 0.911769 CCTCCCTGGAAGTGCATACA 59.088 55.000 0.00 0.00 38.35 2.29
110 111 0.912486 ACCTCCCTGGAAGTGCATAC 59.088 55.000 0.00 0.00 39.71 2.39
111 112 0.911769 CACCTCCCTGGAAGTGCATA 59.088 55.000 2.13 0.00 39.71 3.14
112 113 1.687612 CACCTCCCTGGAAGTGCAT 59.312 57.895 2.13 0.00 39.71 3.96
113 114 3.160585 CACCTCCCTGGAAGTGCA 58.839 61.111 2.13 0.00 39.71 4.57
115 116 2.046892 CGCACCTCCCTGGAAGTG 60.047 66.667 10.05 10.05 39.02 3.16
116 117 4.021925 GCGCACCTCCCTGGAAGT 62.022 66.667 0.30 0.00 39.71 3.01
117 118 4.785453 GGCGCACCTCCCTGGAAG 62.785 72.222 10.83 0.00 39.71 3.46
124 125 1.481056 ATATACAGGGGCGCACCTCC 61.481 60.000 33.10 14.46 39.34 4.30
125 126 1.263356 TATATACAGGGGCGCACCTC 58.737 55.000 33.10 1.79 39.34 3.85
126 127 1.346722 GTTATATACAGGGGCGCACCT 59.653 52.381 29.92 29.92 43.08 4.00
127 128 1.071071 TGTTATATACAGGGGCGCACC 59.929 52.381 24.88 24.88 39.11 5.01
128 129 2.140717 GTGTTATATACAGGGGCGCAC 58.859 52.381 10.83 4.83 37.45 5.34
129 130 1.269883 CGTGTTATATACAGGGGCGCA 60.270 52.381 10.83 0.00 38.63 6.09
130 131 1.269936 ACGTGTTATATACAGGGGCGC 60.270 52.381 0.00 0.00 44.83 6.53
131 132 2.806608 ACGTGTTATATACAGGGGCG 57.193 50.000 0.00 0.00 44.83 6.13
132 133 3.006110 TGCTACGTGTTATATACAGGGGC 59.994 47.826 0.00 0.00 44.83 5.80
133 134 4.553323 GTGCTACGTGTTATATACAGGGG 58.447 47.826 0.00 0.00 44.83 4.79
134 135 4.224433 CGTGCTACGTGTTATATACAGGG 58.776 47.826 0.00 0.00 44.83 4.45
149 150 2.202623 CCTGAGGCGACGTGCTAC 60.203 66.667 0.00 0.00 45.43 3.58
150 151 2.675423 ACCTGAGGCGACGTGCTA 60.675 61.111 0.00 0.00 45.43 3.49
151 152 4.057428 GACCTGAGGCGACGTGCT 62.057 66.667 0.00 0.00 45.43 4.40
153 154 3.669036 CTCGACCTGAGGCGACGTG 62.669 68.421 12.70 7.28 41.29 4.49
154 155 3.432588 CTCGACCTGAGGCGACGT 61.433 66.667 12.70 0.00 41.29 4.34
161 162 3.181485 GGAATGTCTTACCTCGACCTGAG 60.181 52.174 0.00 0.00 44.83 3.35
162 163 2.758979 GGAATGTCTTACCTCGACCTGA 59.241 50.000 0.00 0.00 0.00 3.86
163 164 2.479730 CGGAATGTCTTACCTCGACCTG 60.480 54.545 0.00 0.00 0.00 4.00
164 165 1.749634 CGGAATGTCTTACCTCGACCT 59.250 52.381 0.00 0.00 0.00 3.85
165 166 1.801765 GCGGAATGTCTTACCTCGACC 60.802 57.143 0.00 0.00 0.00 4.79
166 167 1.557651 GCGGAATGTCTTACCTCGAC 58.442 55.000 0.00 0.00 0.00 4.20
167 168 0.458669 GGCGGAATGTCTTACCTCGA 59.541 55.000 0.00 0.00 0.00 4.04
168 169 0.460311 AGGCGGAATGTCTTACCTCG 59.540 55.000 0.00 0.00 0.00 4.63
169 170 1.207329 ACAGGCGGAATGTCTTACCTC 59.793 52.381 0.00 0.00 0.00 3.85
170 171 1.207329 GACAGGCGGAATGTCTTACCT 59.793 52.381 0.00 0.00 43.03 3.08
171 172 1.653151 GACAGGCGGAATGTCTTACC 58.347 55.000 0.00 0.00 43.03 2.85
172 173 1.278238 CGACAGGCGGAATGTCTTAC 58.722 55.000 10.14 0.00 43.95 2.34
173 174 0.459585 GCGACAGGCGGAATGTCTTA 60.460 55.000 0.00 0.00 43.95 2.10
174 175 1.741770 GCGACAGGCGGAATGTCTT 60.742 57.895 0.00 0.00 43.95 3.01
175 176 2.125512 GCGACAGGCGGAATGTCT 60.126 61.111 0.00 0.00 43.95 3.41
184 185 1.160329 GGATACCATGTGCGACAGGC 61.160 60.000 0.00 0.00 43.96 4.85
185 186 0.875908 CGGATACCATGTGCGACAGG 60.876 60.000 0.00 0.00 31.71 4.00
186 187 0.102300 TCGGATACCATGTGCGACAG 59.898 55.000 0.00 0.00 34.50 3.51
187 188 0.102300 CTCGGATACCATGTGCGACA 59.898 55.000 0.00 0.00 34.50 4.35
188 189 1.215655 GCTCGGATACCATGTGCGAC 61.216 60.000 0.00 0.00 34.50 5.19
189 190 1.067416 GCTCGGATACCATGTGCGA 59.933 57.895 0.00 0.00 37.09 5.10
190 191 1.956170 GGCTCGGATACCATGTGCG 60.956 63.158 0.00 0.00 0.00 5.34
191 192 0.463654 TTGGCTCGGATACCATGTGC 60.464 55.000 1.20 0.00 35.42 4.57
192 193 2.036958 TTTGGCTCGGATACCATGTG 57.963 50.000 1.20 0.00 35.42 3.21
193 194 2.643551 CTTTTGGCTCGGATACCATGT 58.356 47.619 1.20 0.00 35.42 3.21
194 195 1.949525 CCTTTTGGCTCGGATACCATG 59.050 52.381 1.20 0.00 35.42 3.66
199 200 3.637229 CTCTAGACCTTTTGGCTCGGATA 59.363 47.826 0.00 0.00 45.59 2.59
218 219 2.550208 CGTTGGCAGGGTCTTAAACTCT 60.550 50.000 0.00 0.00 40.28 3.24
224 225 3.152865 TGCGTTGGCAGGGTCTTA 58.847 55.556 0.00 0.00 46.21 2.10
253 254 2.352715 CGATGTAGGCCGCAGAATCATA 60.353 50.000 8.88 0.00 0.00 2.15
273 274 3.940723 GTCCTTAGACGTGGGATCG 57.059 57.895 0.00 0.00 32.18 3.69
350 351 5.200483 ACCAACTCATCCAAAAGTCTGAAA 58.800 37.500 0.00 0.00 0.00 2.69
354 355 3.891366 CCAACCAACTCATCCAAAAGTCT 59.109 43.478 0.00 0.00 0.00 3.24
399 400 6.789262 AGCAACATAACTTTAGTGATGCATC 58.211 36.000 20.14 20.14 42.06 3.91
405 406 9.502091 ACTGAATTAGCAACATAACTTTAGTGA 57.498 29.630 0.00 0.00 0.00 3.41
437 438 9.657419 ATTTAACAATTGGAAACATGAATCCTC 57.343 29.630 10.83 1.00 42.32 3.71
550 551 7.116376 CCAATATTCACTGCATACTTACTACCG 59.884 40.741 0.00 0.00 0.00 4.02
607 608 7.013942 CCATGAATAATCCATCTCTTTGCTTCA 59.986 37.037 0.00 0.00 0.00 3.02
631 632 4.087892 GGCTCGCTTGCTCTCCCA 62.088 66.667 0.00 0.00 0.00 4.37
807 808 1.016627 CCATGTATCCAGTGCAACCG 58.983 55.000 0.00 0.00 37.80 4.44
865 869 0.827507 ACTGGTGCACCCAACCATTC 60.828 55.000 32.62 5.17 44.65 2.67
1045 1058 2.197643 GAGCAAAGCAGCAGGAGCAC 62.198 60.000 0.00 0.00 45.49 4.40
1071 1084 0.447801 CGTGTGCCCTGATTAACAGC 59.552 55.000 0.00 0.00 44.52 4.40
1078 1091 2.284625 TCCTCCGTGTGCCCTGAT 60.285 61.111 0.00 0.00 0.00 2.90
1111 1124 9.222916 CATATAGTACCGATCAAGCTTATTACG 57.777 37.037 0.00 3.15 0.00 3.18
1112 1125 9.021863 GCATATAGTACCGATCAAGCTTATTAC 57.978 37.037 0.00 0.00 0.00 1.89
1113 1126 8.745590 TGCATATAGTACCGATCAAGCTTATTA 58.254 33.333 0.00 0.00 0.00 0.98
1114 1127 7.611770 TGCATATAGTACCGATCAAGCTTATT 58.388 34.615 0.00 0.00 0.00 1.40
1115 1128 7.170393 TGCATATAGTACCGATCAAGCTTAT 57.830 36.000 0.00 0.00 0.00 1.73
1150 1163 2.977772 TCATGGTCGTATGTGCATGA 57.022 45.000 0.00 0.00 0.00 3.07
1344 1430 5.469479 ACAAAGTTTCAAAAGTCAGTGGTG 58.531 37.500 0.00 0.00 0.00 4.17
1477 1691 7.986085 AGCTAGAAATCAAAGCAAAACTCTA 57.014 32.000 0.00 0.00 38.75 2.43
1530 1762 9.395707 CACGTTAGCTACTTATTATAGGACTTG 57.604 37.037 0.00 0.00 0.00 3.16
1561 1794 1.886861 AAACTCTGCACGCGCGTAAG 61.887 55.000 37.24 32.34 42.97 2.34
1808 5972 8.736244 GCTTTCAATCCATTAACCAACTACTAA 58.264 33.333 0.00 0.00 0.00 2.24
1813 5977 4.082245 CGGCTTTCAATCCATTAACCAACT 60.082 41.667 0.00 0.00 0.00 3.16
1814 5978 4.173256 CGGCTTTCAATCCATTAACCAAC 58.827 43.478 0.00 0.00 0.00 3.77
1862 6026 7.752695 AGAAAGACAAATATTTAGCAACGGAG 58.247 34.615 0.00 0.00 0.00 4.63
1896 6060 5.627499 ACCGATTACGTAGTCACTTGTTA 57.373 39.130 17.02 0.00 43.93 2.41
1902 6066 5.581605 TCCATTAACCGATTACGTAGTCAC 58.418 41.667 17.02 0.68 43.93 3.67
1909 6073 3.186409 CCTGCATCCATTAACCGATTACG 59.814 47.826 0.00 0.00 39.43 3.18
2139 6663 1.241165 CTGCAGTGGAAGCACAATGA 58.759 50.000 5.25 0.00 38.62 2.57
2166 7021 4.814294 CCGTCCACGCCTACAGCC 62.814 72.222 0.00 0.00 38.78 4.85
2527 7388 1.000938 CTGCTGCTTGTTTCCCAACTC 60.001 52.381 0.00 0.00 33.58 3.01
2528 7389 1.035139 CTGCTGCTTGTTTCCCAACT 58.965 50.000 0.00 0.00 33.58 3.16
2605 7466 7.607991 ACATATAAGCTTTGTGAAACTGCTAGT 59.392 33.333 3.20 0.00 37.53 2.57
2636 7497 3.847037 TTTTCGTTTGTACTCACGAGC 57.153 42.857 16.28 0.00 45.63 5.03
2666 7527 2.093288 GCATGGTTGATCAGGTCAGAGA 60.093 50.000 0.00 0.00 38.29 3.10
2948 7817 2.554806 AGATGTCGACGATAACGCAA 57.445 45.000 11.62 0.00 43.96 4.85
2990 7859 0.321298 ACCTTGTGTCCATGGCGTAC 60.321 55.000 6.96 6.39 39.04 3.67
3003 7872 1.483415 ACTTGTGTGGACGTACCTTGT 59.517 47.619 0.00 0.00 39.86 3.16
3035 7904 4.570772 CCACATCAGTAGGTTTAATCCGTG 59.429 45.833 0.00 0.00 0.00 4.94
3167 8061 6.623329 AGAAGATCAGATTCAGGGATAGACT 58.377 40.000 0.00 0.00 0.00 3.24
3170 8064 8.838365 CAAAAAGAAGATCAGATTCAGGGATAG 58.162 37.037 0.00 0.00 0.00 2.08
3175 8069 6.263516 TGCAAAAAGAAGATCAGATTCAGG 57.736 37.500 0.00 0.00 0.00 3.86
3210 8109 1.336795 GGTTCGATTTTTGCTGTGGGG 60.337 52.381 0.00 0.00 0.00 4.96
3372 8271 3.508793 TCCCTGACTTTGTTACGTAGGAG 59.491 47.826 0.00 0.00 0.00 3.69
3384 8283 0.324943 CCATGGACGTCCCTGACTTT 59.675 55.000 33.55 9.04 34.09 2.66
3528 8463 7.072263 AGTGCATGAACTAGCTAGGATTTAT 57.928 36.000 24.35 10.07 0.00 1.40
3572 8511 1.868498 CCATGCAAGCAAAACCAACAG 59.132 47.619 0.00 0.00 0.00 3.16
3769 8708 2.429930 CCCTCCTTGACGTTGGCA 59.570 61.111 0.00 0.00 0.00 4.92
3809 8748 1.195115 TCTGGCATAGAGGTGGTGTC 58.805 55.000 0.00 0.00 0.00 3.67
3976 9187 4.614535 GCAGCATCGAAAACAAGAACATCT 60.615 41.667 0.00 0.00 0.00 2.90
4123 9894 7.502226 TCCGCATAGAAATCCTGAATTGTAATT 59.498 33.333 0.00 0.00 0.00 1.40
4176 9969 9.161629 TCTCGATTTTATTTTAAGCATGAGACA 57.838 29.630 0.00 0.00 0.00 3.41
4236 10030 1.552337 GAGAGAGAGCCCACATGTCAA 59.448 52.381 0.00 0.00 0.00 3.18
4989 10783 1.897133 TCAAACTTGCTAGGCGACCTA 59.103 47.619 0.00 5.64 34.61 3.08
5010 10804 5.543714 TCGTGACAGGTTTTGCTCTAATTA 58.456 37.500 0.00 0.00 0.00 1.40
5039 10833 7.514721 ACTTTGAACCAGATTTACAGTTAGGA 58.485 34.615 0.00 0.00 0.00 2.94
5046 10840 8.974060 AAACTCTACTTTGAACCAGATTTACA 57.026 30.769 0.00 0.00 0.00 2.41
5063 10857 7.207383 ACCATTTTTAAGCACCAAAACTCTAC 58.793 34.615 0.00 0.00 0.00 2.59
5084 10878 3.724508 TTTTGTGTCGCATTGAACCAT 57.275 38.095 0.00 0.00 0.00 3.55
5120 10916 6.739112 TCACAATGGTCGTTCTGAGATATAG 58.261 40.000 0.00 0.00 0.00 1.31
5121 10917 6.709018 TCACAATGGTCGTTCTGAGATATA 57.291 37.500 0.00 0.00 0.00 0.86
5122 10918 5.598416 TCACAATGGTCGTTCTGAGATAT 57.402 39.130 0.00 0.00 0.00 1.63
5123 10919 5.451937 GGATCACAATGGTCGTTCTGAGATA 60.452 44.000 0.00 0.00 0.00 1.98
5124 10920 3.961480 TCACAATGGTCGTTCTGAGAT 57.039 42.857 0.00 0.00 0.00 2.75
5131 10927 2.813754 CACAAGGATCACAATGGTCGTT 59.186 45.455 0.00 0.00 36.17 3.85


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

AutoCloner maintained by Alex Coulton.