Multiple sequence alignment - TraesCS1A01G378500

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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 TraesCS1A01G378500 chr1A 100.000 2761 0 0 1 2761 551215002 551212242 0.000000e+00 5099
1 TraesCS1A01G378500 chr1B 89.798 1637 87 36 484 2087 630522344 630520755 0.000000e+00 2025
2 TraesCS1A01G378500 chr1B 93.884 327 13 3 2229 2552 630520718 630520396 1.150000e-133 486
3 TraesCS1A01G378500 chr1B 90.426 282 14 4 207 483 630522717 630522444 2.610000e-95 359
4 TraesCS1A01G378500 chr1B 93.443 183 12 0 2544 2726 630520211 630520029 3.500000e-69 272
5 TraesCS1A01G378500 chr1D 89.864 1618 60 44 484 2069 458786039 458784494 0.000000e+00 1984
6 TraesCS1A01G378500 chr1D 93.613 501 24 5 2229 2726 458784445 458783950 0.000000e+00 741
7 TraesCS1A01G378500 chr1D 89.644 309 14 6 181 483 458786436 458786140 7.220000e-101 377
8 TraesCS1A01G378500 chr4A 92.821 195 13 1 1 194 731427580 731427386 5.820000e-72 281
9 TraesCS1A01G378500 chr7A 92.228 193 15 0 1 193 29535928 29536120 9.740000e-70 274
10 TraesCS1A01G378500 chr7A 92.973 185 13 0 1 185 549715396 549715212 1.260000e-68 270
11 TraesCS1A01G378500 chr7A 95.714 140 5 1 2083 2221 41866904 41866765 9.950000e-55 224
12 TraesCS1A01G378500 chr6A 92.670 191 13 1 1 191 65071194 65071383 9.740000e-70 274
13 TraesCS1A01G378500 chr6A 92.973 185 13 0 1 185 410575578 410575762 1.260000e-68 270
14 TraesCS1A01G378500 chr6B 93.048 187 12 1 1 186 547713774 547713960 3.500000e-69 272
15 TraesCS1A01G378500 chr6B 97.059 136 4 0 2086 2221 34685453 34685588 2.140000e-56 230
16 TraesCS1A01G378500 chr3A 91.795 195 14 2 1 193 451653400 451653206 1.260000e-68 270
17 TraesCS1A01G378500 chr2A 92.973 185 13 0 4 188 15845564 15845380 1.260000e-68 270
18 TraesCS1A01G378500 chr2A 92.973 185 13 0 1 185 18596871 18596687 1.260000e-68 270
19 TraesCS1A01G378500 chr2A 95.745 141 5 1 2081 2221 434579955 434580094 2.770000e-55 226
20 TraesCS1A01G378500 chr2A 95.105 143 5 2 2080 2221 7915775 7915634 9.950000e-55 224
21 TraesCS1A01G378500 chr3B 95.238 147 5 2 2076 2221 798949914 798950059 5.950000e-57 231
22 TraesCS1A01G378500 chr3B 96.350 137 5 0 2085 2221 8462722 8462858 2.770000e-55 226
23 TraesCS1A01G378500 chr2B 97.059 136 4 0 2086 2221 110817813 110817948 2.140000e-56 230
24 TraesCS1A01G378500 chr2B 97.744 133 3 0 2089 2221 757357515 757357647 2.140000e-56 230
25 TraesCS1A01G378500 chr7D 91.720 157 7 5 2066 2221 577365794 577365643 2.150000e-51 213


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 TraesCS1A01G378500 chr1A 551212242 551215002 2760 True 5099.0 5099 100.000000 1 2761 1 chr1A.!!$R1 2760
1 TraesCS1A01G378500 chr1B 630520029 630522717 2688 True 785.5 2025 91.887750 207 2726 4 chr1B.!!$R1 2519
2 TraesCS1A01G378500 chr1D 458783950 458786436 2486 True 1034.0 1984 91.040333 181 2726 3 chr1D.!!$R1 2545

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
842 971 0.045623 ACCCCATCATCCACACCCTA 59.954 55.0 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2111 2271 0.159554 CGCGTGTATATGAGCGCTTG 59.84 55.0 13.26 0.0 46.56 4.01 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
55 56 9.540538 TTTTATTTTCCTATGAAATGTGGAGGA 57.459 29.630 0.00 0.00 40.08 3.71
56 57 9.713684 TTTATTTTCCTATGAAATGTGGAGGAT 57.286 29.630 0.00 0.00 40.08 3.24
58 59 8.930846 ATTTTCCTATGAAATGTGGAGGATAG 57.069 34.615 0.00 0.00 40.08 2.08
59 60 6.439636 TTCCTATGAAATGTGGAGGATAGG 57.560 41.667 0.00 0.00 36.22 2.57
60 61 5.726560 TCCTATGAAATGTGGAGGATAGGA 58.273 41.667 0.00 0.00 39.29 2.94
61 62 6.150332 TCCTATGAAATGTGGAGGATAGGAA 58.850 40.000 0.00 0.00 38.86 3.36
62 63 6.043243 TCCTATGAAATGTGGAGGATAGGAAC 59.957 42.308 0.00 0.00 38.86 3.62
63 64 4.503714 TGAAATGTGGAGGATAGGAACC 57.496 45.455 0.00 0.00 0.00 3.62
64 65 3.849574 TGAAATGTGGAGGATAGGAACCA 59.150 43.478 0.00 0.00 0.00 3.67
65 66 4.290985 TGAAATGTGGAGGATAGGAACCAA 59.709 41.667 0.00 0.00 34.11 3.67
66 67 5.044179 TGAAATGTGGAGGATAGGAACCAAT 60.044 40.000 0.00 0.00 34.11 3.16
67 68 5.472301 AATGTGGAGGATAGGAACCAATT 57.528 39.130 0.00 0.00 34.11 2.32
68 69 4.503714 TGTGGAGGATAGGAACCAATTC 57.496 45.455 0.00 0.00 34.11 2.17
69 70 4.111577 TGTGGAGGATAGGAACCAATTCT 58.888 43.478 0.00 0.00 34.98 2.40
70 71 5.285401 TGTGGAGGATAGGAACCAATTCTA 58.715 41.667 0.00 0.00 34.98 2.10
71 72 5.911178 TGTGGAGGATAGGAACCAATTCTAT 59.089 40.000 0.00 0.00 34.98 1.98
72 73 6.183361 TGTGGAGGATAGGAACCAATTCTATG 60.183 42.308 0.00 0.00 34.98 2.23
73 74 5.911178 TGGAGGATAGGAACCAATTCTATGT 59.089 40.000 0.00 0.00 34.98 2.29
74 75 7.016268 GTGGAGGATAGGAACCAATTCTATGTA 59.984 40.741 0.00 0.00 34.98 2.29
75 76 7.235606 TGGAGGATAGGAACCAATTCTATGTAG 59.764 40.741 0.00 0.00 34.98 2.74
76 77 7.455008 GGAGGATAGGAACCAATTCTATGTAGA 59.545 40.741 0.00 0.00 34.98 2.59
77 78 8.798975 AGGATAGGAACCAATTCTATGTAGAA 57.201 34.615 5.05 5.05 45.43 2.10
78 79 9.225682 AGGATAGGAACCAATTCTATGTAGAAA 57.774 33.333 6.57 0.00 44.63 2.52
83 84 9.225682 AGGAACCAATTCTATGTAGAAATAGGA 57.774 33.333 17.75 0.00 44.63 2.94
84 85 9.847224 GGAACCAATTCTATGTAGAAATAGGAA 57.153 33.333 17.75 0.00 44.63 3.36
107 108 5.659440 TCCATTCCTATGAACCAAAAAGC 57.341 39.130 0.00 0.00 33.37 3.51
108 109 5.332743 TCCATTCCTATGAACCAAAAAGCT 58.667 37.500 0.00 0.00 33.37 3.74
109 110 5.418840 TCCATTCCTATGAACCAAAAAGCTC 59.581 40.000 0.00 0.00 33.37 4.09
110 111 5.420104 CCATTCCTATGAACCAAAAAGCTCT 59.580 40.000 0.00 0.00 33.37 4.09
111 112 6.603201 CCATTCCTATGAACCAAAAAGCTCTA 59.397 38.462 0.00 0.00 33.37 2.43
112 113 7.122650 CCATTCCTATGAACCAAAAAGCTCTAA 59.877 37.037 0.00 0.00 33.37 2.10
113 114 8.522830 CATTCCTATGAACCAAAAAGCTCTAAA 58.477 33.333 0.00 0.00 33.37 1.85
114 115 7.687941 TCCTATGAACCAAAAAGCTCTAAAG 57.312 36.000 0.00 0.00 0.00 1.85
115 116 6.659242 TCCTATGAACCAAAAAGCTCTAAAGG 59.341 38.462 0.00 0.00 0.00 3.11
116 117 6.659242 CCTATGAACCAAAAAGCTCTAAAGGA 59.341 38.462 0.00 0.00 0.00 3.36
117 118 6.976934 ATGAACCAAAAAGCTCTAAAGGAA 57.023 33.333 0.00 0.00 0.00 3.36
118 119 6.783708 TGAACCAAAAAGCTCTAAAGGAAA 57.216 33.333 0.00 0.00 0.00 3.13
119 120 7.176589 TGAACCAAAAAGCTCTAAAGGAAAA 57.823 32.000 0.00 0.00 0.00 2.29
120 121 7.616313 TGAACCAAAAAGCTCTAAAGGAAAAA 58.384 30.769 0.00 0.00 0.00 1.94
206 207 1.070471 GTTAAATGGCAAGCACGGCG 61.070 55.000 4.80 4.80 0.00 6.46
207 208 2.810903 TTAAATGGCAAGCACGGCGC 62.811 55.000 6.90 0.00 42.91 6.53
280 286 4.220382 TGAATATTGACAAGCCAAACCCAG 59.780 41.667 0.00 0.00 0.00 4.45
312 323 4.858935 ACGACATCCAACAAAAAGACATG 58.141 39.130 0.00 0.00 0.00 3.21
330 341 5.306419 AGACATGCAATATCTTGAGCTCCTA 59.694 40.000 12.15 0.00 34.04 2.94
353 364 4.264460 ACTCACTCATTCTTCAGTCCAC 57.736 45.455 0.00 0.00 0.00 4.02
355 366 2.890945 TCACTCATTCTTCAGTCCACGA 59.109 45.455 0.00 0.00 0.00 4.35
356 367 2.989840 CACTCATTCTTCAGTCCACGAC 59.010 50.000 0.00 0.00 0.00 4.34
357 368 2.894126 ACTCATTCTTCAGTCCACGACT 59.106 45.455 0.00 0.00 44.44 4.18
421 432 1.795286 CGCTTTCTCACTGGAAGACAC 59.205 52.381 0.00 0.00 37.43 3.67
422 433 2.803133 CGCTTTCTCACTGGAAGACACA 60.803 50.000 0.00 0.00 37.43 3.72
427 438 3.797039 TCTCACTGGAAGACACAACAAG 58.203 45.455 0.00 0.00 37.43 3.16
447 459 9.778993 CAACAAGTAATCTGAATGATTTACCTG 57.221 33.333 0.00 0.00 42.28 4.00
465 477 8.729805 TTTACCTGAACAAATGCTTTTGAAAT 57.270 26.923 26.53 14.48 44.11 2.17
504 619 1.148157 CGCTGACGCCCTTAGATGTG 61.148 60.000 0.00 0.00 0.00 3.21
527 644 5.931146 TGCAAAGACAACAAAAAGAATGTGT 59.069 32.000 0.00 0.00 0.00 3.72
564 682 2.430546 TACAAAAACCCATGCAAGCG 57.569 45.000 0.00 0.00 0.00 4.68
588 706 5.124936 GCCGGATTTAGGAAATACAGTTTGT 59.875 40.000 5.05 0.00 30.79 2.83
591 709 7.551617 CCGGATTTAGGAAATACAGTTTGTAGT 59.448 37.037 0.00 0.00 36.14 2.73
632 751 2.851195 TCTGAAGCCAGAAAAGGTGTC 58.149 47.619 0.00 0.00 45.74 3.67
713 833 1.589630 GGGGCGACACCATTTTTCC 59.410 57.895 0.00 0.00 42.05 3.13
736 860 0.958876 GAACATTCCGACCCACCCAC 60.959 60.000 0.00 0.00 0.00 4.61
737 861 1.710996 AACATTCCGACCCACCCACA 61.711 55.000 0.00 0.00 0.00 4.17
738 862 1.674322 CATTCCGACCCACCCACAC 60.674 63.158 0.00 0.00 0.00 3.82
739 863 2.902457 ATTCCGACCCACCCACACC 61.902 63.158 0.00 0.00 0.00 4.16
799 927 4.794439 TCGCAGATCACCACCGCG 62.794 66.667 0.00 0.00 46.92 6.46
842 971 0.045623 ACCCCATCATCCACACCCTA 59.954 55.000 0.00 0.00 0.00 3.53
880 1009 2.122954 GGAGACACCCACCTCCCT 59.877 66.667 0.00 0.00 42.35 4.20
881 1010 1.990614 GGAGACACCCACCTCCCTC 60.991 68.421 0.00 0.00 42.35 4.30
882 1011 1.990614 GAGACACCCACCTCCCTCC 60.991 68.421 0.00 0.00 0.00 4.30
883 1012 3.009714 GACACCCACCTCCCTCCC 61.010 72.222 0.00 0.00 0.00 4.30
1031 1165 1.305219 ACCACCGCAAACATCCATCG 61.305 55.000 0.00 0.00 0.00 3.84
1034 1168 2.749865 CCGCAAACATCCATCGCGT 61.750 57.895 5.77 0.00 44.23 6.01
1035 1169 1.134487 CGCAAACATCCATCGCGTT 59.866 52.632 5.77 0.00 40.99 4.84
1038 1172 0.098728 CAAACATCCATCGCGTTCCC 59.901 55.000 5.77 0.00 0.00 3.97
1039 1173 1.366111 AAACATCCATCGCGTTCCCG 61.366 55.000 5.77 0.00 37.07 5.14
1040 1174 2.967076 CATCCATCGCGTTCCCGG 60.967 66.667 5.77 0.00 33.68 5.73
1041 1175 4.910585 ATCCATCGCGTTCCCGGC 62.911 66.667 5.77 0.00 33.68 6.13
1048 1189 4.699522 GCGTTCCCGGCCACTTCT 62.700 66.667 2.24 0.00 33.68 2.85
1097 1254 0.398696 TTGTTTTAGCTCGGCCTCCA 59.601 50.000 0.00 0.00 0.00 3.86
1099 1256 1.300481 GTTTTAGCTCGGCCTCCATC 58.700 55.000 0.00 0.00 0.00 3.51
1100 1257 0.180406 TTTTAGCTCGGCCTCCATCC 59.820 55.000 0.00 0.00 0.00 3.51
1129 1286 0.819259 TCCTTGCGCAACAGCTTCTT 60.819 50.000 21.02 0.00 38.13 2.52
1132 1289 0.308684 TTGCGCAACAGCTTCTTCTG 59.691 50.000 21.02 0.00 39.86 3.02
1133 1290 1.208614 GCGCAACAGCTTCTTCTGG 59.791 57.895 0.30 0.00 38.36 3.86
1134 1291 1.510480 GCGCAACAGCTTCTTCTGGT 61.510 55.000 0.30 0.00 38.36 4.00
1138 1295 1.605710 CAACAGCTTCTTCTGGTGTGG 59.394 52.381 0.95 0.00 44.54 4.17
1139 1296 0.839946 ACAGCTTCTTCTGGTGTGGT 59.160 50.000 0.00 0.00 43.32 4.16
1140 1297 1.233019 CAGCTTCTTCTGGTGTGGTG 58.767 55.000 0.00 0.00 0.00 4.17
1141 1298 0.839946 AGCTTCTTCTGGTGTGGTGT 59.160 50.000 0.00 0.00 0.00 4.16
1142 1299 0.947244 GCTTCTTCTGGTGTGGTGTG 59.053 55.000 0.00 0.00 0.00 3.82
1143 1300 0.947244 CTTCTTCTGGTGTGGTGTGC 59.053 55.000 0.00 0.00 0.00 4.57
1144 1301 0.813610 TTCTTCTGGTGTGGTGTGCG 60.814 55.000 0.00 0.00 0.00 5.34
1145 1302 1.227527 CTTCTGGTGTGGTGTGCGA 60.228 57.895 0.00 0.00 0.00 5.10
1146 1303 1.224069 CTTCTGGTGTGGTGTGCGAG 61.224 60.000 0.00 0.00 0.00 5.03
1147 1304 3.349006 CTGGTGTGGTGTGCGAGC 61.349 66.667 0.00 0.00 0.00 5.03
1170 1327 1.003233 GCGGTTCTTGGAGGAGCTT 60.003 57.895 0.00 0.00 0.00 3.74
1172 1329 0.610687 CGGTTCTTGGAGGAGCTTCT 59.389 55.000 0.00 0.00 0.00 2.85
1211 1369 0.618458 GCATGGGGAACTACCTGTCA 59.382 55.000 0.00 0.00 38.98 3.58
1436 1594 2.046285 CGCCACCTTCCCCATGAAC 61.046 63.158 0.00 0.00 0.00 3.18
1529 1687 2.047179 GCCAAGGTGTCCTCCGTC 60.047 66.667 0.00 0.00 30.89 4.79
1763 1921 4.503910 TGTGCAGACGCTGAAATATACTT 58.496 39.130 10.46 0.00 39.64 2.24
1877 2035 5.707298 ACCAAGGAATTGATTGTACAGTCTG 59.293 40.000 17.99 7.12 0.00 3.51
1886 2044 5.056480 TGATTGTACAGTCTGACTTTGTGG 58.944 41.667 17.99 0.00 0.00 4.17
1950 2108 3.244181 GCCATTTGTTTGTTCATCCCTGT 60.244 43.478 0.00 0.00 0.00 4.00
1983 2142 7.721286 AAACATGTTAAAATTCGAAATGGCA 57.279 28.000 12.39 0.00 0.00 4.92
2114 2274 6.603237 TTTGAACATCAGTACAGACACAAG 57.397 37.500 0.00 0.00 0.00 3.16
2115 2275 4.058124 TGAACATCAGTACAGACACAAGC 58.942 43.478 0.00 0.00 0.00 4.01
2116 2276 2.677199 ACATCAGTACAGACACAAGCG 58.323 47.619 0.00 0.00 0.00 4.68
2117 2277 1.391485 CATCAGTACAGACACAAGCGC 59.609 52.381 0.00 0.00 0.00 5.92
2118 2278 0.673985 TCAGTACAGACACAAGCGCT 59.326 50.000 2.64 2.64 0.00 5.92
2119 2279 1.063806 CAGTACAGACACAAGCGCTC 58.936 55.000 12.06 0.00 0.00 5.03
2120 2280 0.673985 AGTACAGACACAAGCGCTCA 59.326 50.000 12.06 0.00 0.00 4.26
2121 2281 1.273606 AGTACAGACACAAGCGCTCAT 59.726 47.619 12.06 0.00 0.00 2.90
2122 2282 2.492088 AGTACAGACACAAGCGCTCATA 59.508 45.455 12.06 0.00 0.00 2.15
2123 2283 2.680312 ACAGACACAAGCGCTCATAT 57.320 45.000 12.06 0.00 0.00 1.78
2124 2284 3.801114 ACAGACACAAGCGCTCATATA 57.199 42.857 12.06 0.00 0.00 0.86
2125 2285 3.448686 ACAGACACAAGCGCTCATATAC 58.551 45.455 12.06 1.00 0.00 1.47
2126 2286 3.119137 ACAGACACAAGCGCTCATATACA 60.119 43.478 12.06 0.00 0.00 2.29
2127 2287 3.243877 CAGACACAAGCGCTCATATACAC 59.756 47.826 12.06 0.00 0.00 2.90
2128 2288 2.193447 ACACAAGCGCTCATATACACG 58.807 47.619 12.06 0.00 0.00 4.49
2132 2292 3.916439 CGCTCATATACACGCGCA 58.084 55.556 5.73 0.00 39.11 6.09
2133 2293 2.434688 CGCTCATATACACGCGCAT 58.565 52.632 5.73 0.00 39.11 4.73
2134 2294 1.613270 CGCTCATATACACGCGCATA 58.387 50.000 5.73 1.53 39.11 3.14
2135 2295 1.317611 CGCTCATATACACGCGCATAC 59.682 52.381 5.73 0.00 39.11 2.39
2136 2296 2.324860 GCTCATATACACGCGCATACA 58.675 47.619 5.73 0.00 0.00 2.29
2137 2297 2.090658 GCTCATATACACGCGCATACAC 59.909 50.000 5.73 0.00 0.00 2.90
2138 2298 3.565516 CTCATATACACGCGCATACACT 58.434 45.455 5.73 0.00 0.00 3.55
2139 2299 3.561503 TCATATACACGCGCATACACTC 58.438 45.455 5.73 0.00 0.00 3.51
2140 2300 3.003897 TCATATACACGCGCATACACTCA 59.996 43.478 5.73 0.00 0.00 3.41
2141 2301 2.509052 ATACACGCGCATACACTCAT 57.491 45.000 5.73 0.00 0.00 2.90
2142 2302 1.835121 TACACGCGCATACACTCATC 58.165 50.000 5.73 0.00 0.00 2.92
2143 2303 0.806102 ACACGCGCATACACTCATCC 60.806 55.000 5.73 0.00 0.00 3.51
2144 2304 1.227263 ACGCGCATACACTCATCCC 60.227 57.895 5.73 0.00 0.00 3.85
2145 2305 1.068083 CGCGCATACACTCATCCCT 59.932 57.895 8.75 0.00 0.00 4.20
2146 2306 0.313987 CGCGCATACACTCATCCCTA 59.686 55.000 8.75 0.00 0.00 3.53
2147 2307 1.067565 CGCGCATACACTCATCCCTAT 60.068 52.381 8.75 0.00 0.00 2.57
2148 2308 2.341257 GCGCATACACTCATCCCTATG 58.659 52.381 0.30 0.00 0.00 2.23
2149 2309 2.029020 GCGCATACACTCATCCCTATGA 60.029 50.000 0.30 0.00 39.87 2.15
2150 2310 3.554960 GCGCATACACTCATCCCTATGAA 60.555 47.826 0.30 0.00 41.57 2.57
2151 2311 3.990469 CGCATACACTCATCCCTATGAAC 59.010 47.826 0.00 0.00 41.57 3.18
2152 2312 3.990469 GCATACACTCATCCCTATGAACG 59.010 47.826 0.00 0.00 41.57 3.95
2153 2313 2.604046 ACACTCATCCCTATGAACGC 57.396 50.000 0.00 0.00 41.57 4.84
2154 2314 1.831106 ACACTCATCCCTATGAACGCA 59.169 47.619 0.00 0.00 41.57 5.24
2155 2315 2.205074 CACTCATCCCTATGAACGCAC 58.795 52.381 0.00 0.00 41.57 5.34
2156 2316 1.831106 ACTCATCCCTATGAACGCACA 59.169 47.619 0.00 0.00 41.57 4.57
2157 2317 2.205074 CTCATCCCTATGAACGCACAC 58.795 52.381 0.00 0.00 41.57 3.82
2158 2318 1.552792 TCATCCCTATGAACGCACACA 59.447 47.619 0.00 0.00 39.20 3.72
2159 2319 1.665679 CATCCCTATGAACGCACACAC 59.334 52.381 0.00 0.00 34.84 3.82
2160 2320 0.389296 TCCCTATGAACGCACACACG 60.389 55.000 0.00 0.00 39.50 4.49
2161 2321 1.419922 CCTATGAACGCACACACGC 59.580 57.895 0.00 0.00 36.19 5.34
2162 2322 1.288419 CCTATGAACGCACACACGCA 61.288 55.000 0.00 0.00 36.19 5.24
2163 2323 0.179250 CTATGAACGCACACACGCAC 60.179 55.000 0.00 0.00 36.19 5.34
2164 2324 0.876342 TATGAACGCACACACGCACA 60.876 50.000 0.00 0.00 36.19 4.57
2165 2325 2.350760 GAACGCACACACGCACAC 60.351 61.111 0.00 0.00 36.19 3.82
2166 2326 3.783588 GAACGCACACACGCACACC 62.784 63.158 0.00 0.00 36.19 4.16
2169 2329 2.280524 GCACACACGCACACCCTA 60.281 61.111 0.00 0.00 0.00 3.53
2170 2330 2.604174 GCACACACGCACACCCTAC 61.604 63.158 0.00 0.00 0.00 3.18
2171 2331 1.959226 CACACACGCACACCCTACC 60.959 63.158 0.00 0.00 0.00 3.18
2172 2332 2.358247 CACACGCACACCCTACCC 60.358 66.667 0.00 0.00 0.00 3.69
2173 2333 3.633116 ACACGCACACCCTACCCC 61.633 66.667 0.00 0.00 0.00 4.95
2174 2334 3.319198 CACGCACACCCTACCCCT 61.319 66.667 0.00 0.00 0.00 4.79
2175 2335 1.985662 CACGCACACCCTACCCCTA 60.986 63.158 0.00 0.00 0.00 3.53
2176 2336 1.002533 ACGCACACCCTACCCCTAT 59.997 57.895 0.00 0.00 0.00 2.57
2177 2337 1.335132 ACGCACACCCTACCCCTATG 61.335 60.000 0.00 0.00 0.00 2.23
2178 2338 1.046472 CGCACACCCTACCCCTATGA 61.046 60.000 0.00 0.00 0.00 2.15
2179 2339 0.759346 GCACACCCTACCCCTATGAG 59.241 60.000 0.00 0.00 0.00 2.90
2180 2340 0.759346 CACACCCTACCCCTATGAGC 59.241 60.000 0.00 0.00 0.00 4.26
2181 2341 0.341961 ACACCCTACCCCTATGAGCA 59.658 55.000 0.00 0.00 0.00 4.26
2182 2342 1.061346 ACACCCTACCCCTATGAGCAT 60.061 52.381 0.00 0.00 0.00 3.79
2183 2343 1.625818 CACCCTACCCCTATGAGCATC 59.374 57.143 0.00 0.00 0.00 3.91
2184 2344 1.509961 ACCCTACCCCTATGAGCATCT 59.490 52.381 0.00 0.00 34.92 2.90
2185 2345 2.183679 CCCTACCCCTATGAGCATCTC 58.816 57.143 0.00 0.00 34.92 2.75
2186 2346 2.183679 CCTACCCCTATGAGCATCTCC 58.816 57.143 0.00 0.00 34.92 3.71
2187 2347 2.493500 CCTACCCCTATGAGCATCTCCA 60.494 54.545 0.00 0.00 34.92 3.86
2188 2348 2.196742 ACCCCTATGAGCATCTCCAA 57.803 50.000 0.00 0.00 34.92 3.53
2189 2349 2.492025 ACCCCTATGAGCATCTCCAAA 58.508 47.619 0.00 0.00 34.92 3.28
2190 2350 2.852449 ACCCCTATGAGCATCTCCAAAA 59.148 45.455 0.00 0.00 34.92 2.44
2191 2351 3.269381 ACCCCTATGAGCATCTCCAAAAA 59.731 43.478 0.00 0.00 34.92 1.94
2208 2368 2.418368 AAAACTGAGCCGGCATATCA 57.582 45.000 31.54 22.44 0.00 2.15
2209 2369 2.645838 AAACTGAGCCGGCATATCAT 57.354 45.000 31.54 6.18 0.00 2.45
2210 2370 2.175878 AACTGAGCCGGCATATCATC 57.824 50.000 31.54 16.99 0.00 2.92
2211 2371 1.346062 ACTGAGCCGGCATATCATCT 58.654 50.000 31.54 4.27 0.00 2.90
2212 2372 1.696336 ACTGAGCCGGCATATCATCTT 59.304 47.619 31.54 3.33 0.00 2.40
2213 2373 2.074576 CTGAGCCGGCATATCATCTTG 58.925 52.381 31.54 7.95 0.00 3.02
2214 2374 1.693606 TGAGCCGGCATATCATCTTGA 59.306 47.619 31.54 0.00 0.00 3.02
2215 2375 2.289257 TGAGCCGGCATATCATCTTGAG 60.289 50.000 31.54 0.00 0.00 3.02
2216 2376 1.973515 AGCCGGCATATCATCTTGAGA 59.026 47.619 31.54 0.00 0.00 3.27
2217 2377 2.570752 AGCCGGCATATCATCTTGAGAT 59.429 45.455 31.54 0.00 34.56 2.75
2218 2378 3.008813 AGCCGGCATATCATCTTGAGATT 59.991 43.478 31.54 0.00 31.21 2.40
2219 2379 3.755378 GCCGGCATATCATCTTGAGATTT 59.245 43.478 24.80 0.00 31.21 2.17
2220 2380 4.937620 GCCGGCATATCATCTTGAGATTTA 59.062 41.667 24.80 0.00 31.21 1.40
2221 2381 5.412594 GCCGGCATATCATCTTGAGATTTAA 59.587 40.000 24.80 0.00 31.21 1.52
2222 2382 6.094603 GCCGGCATATCATCTTGAGATTTAAT 59.905 38.462 24.80 0.00 31.21 1.40
2223 2383 7.362401 GCCGGCATATCATCTTGAGATTTAATT 60.362 37.037 24.80 0.00 31.21 1.40
2224 2384 9.166173 CCGGCATATCATCTTGAGATTTAATTA 57.834 33.333 0.00 0.00 31.21 1.40
2331 2492 6.412653 ACGTTTTAGAATGTTTTGTACGCAAG 59.587 34.615 0.00 0.00 35.82 4.01
2503 2667 6.183360 GGCGATCCAAAGAAATGTTTGAGATA 60.183 38.462 4.74 0.00 39.40 1.98
2520 2684 7.885009 TTGAGATATTGATTTGAAGATGGCA 57.115 32.000 0.00 0.00 0.00 4.92
2521 2685 7.506328 TGAGATATTGATTTGAAGATGGCAG 57.494 36.000 0.00 0.00 0.00 4.85
2609 2966 3.958147 TCTGCCACGTAGGATAATTCTCA 59.042 43.478 8.04 0.00 41.22 3.27
2620 2977 3.003689 GGATAATTCTCAATGTGCACGGG 59.996 47.826 13.13 4.03 0.00 5.28
2710 3067 6.425114 ACATTGACCTATTTAATGCTAGCTCG 59.575 38.462 17.23 0.00 35.71 5.03
2726 3083 3.760537 AGCTCGTCGTTTAGAATCAGTC 58.239 45.455 0.00 0.00 0.00 3.51
2727 3084 2.853003 GCTCGTCGTTTAGAATCAGTCC 59.147 50.000 0.00 0.00 0.00 3.85
2728 3085 3.436496 CTCGTCGTTTAGAATCAGTCCC 58.564 50.000 0.00 0.00 0.00 4.46
2729 3086 2.159476 TCGTCGTTTAGAATCAGTCCCG 60.159 50.000 0.00 0.00 0.00 5.14
2730 3087 1.925185 GTCGTTTAGAATCAGTCCCGC 59.075 52.381 0.00 0.00 0.00 6.13
2731 3088 1.546923 TCGTTTAGAATCAGTCCCGCA 59.453 47.619 0.00 0.00 0.00 5.69
2732 3089 2.167693 TCGTTTAGAATCAGTCCCGCAT 59.832 45.455 0.00 0.00 0.00 4.73
2733 3090 2.936498 CGTTTAGAATCAGTCCCGCATT 59.064 45.455 0.00 0.00 0.00 3.56
2734 3091 3.242413 CGTTTAGAATCAGTCCCGCATTG 60.242 47.826 0.00 0.00 0.00 2.82
2735 3092 2.620251 TAGAATCAGTCCCGCATTGG 57.380 50.000 0.00 0.00 37.55 3.16
2736 3093 0.911769 AGAATCAGTCCCGCATTGGA 59.088 50.000 0.00 0.00 42.00 3.53
2737 3094 1.281867 AGAATCAGTCCCGCATTGGAA 59.718 47.619 0.00 0.00 42.00 3.53
2738 3095 2.091541 GAATCAGTCCCGCATTGGAAA 58.908 47.619 0.00 0.00 42.00 3.13
2739 3096 1.755179 ATCAGTCCCGCATTGGAAAG 58.245 50.000 0.00 0.00 42.00 2.62
2740 3097 0.400213 TCAGTCCCGCATTGGAAAGT 59.600 50.000 0.00 0.00 42.00 2.66
2741 3098 0.523072 CAGTCCCGCATTGGAAAGTG 59.477 55.000 0.00 0.00 42.00 3.16
2742 3099 0.110486 AGTCCCGCATTGGAAAGTGT 59.890 50.000 0.00 0.00 42.00 3.55
2743 3100 0.521735 GTCCCGCATTGGAAAGTGTC 59.478 55.000 0.00 0.00 42.00 3.67
2744 3101 0.953471 TCCCGCATTGGAAAGTGTCG 60.953 55.000 0.00 0.00 42.00 4.35
2745 3102 1.234615 CCCGCATTGGAAAGTGTCGT 61.235 55.000 0.00 0.00 42.00 4.34
2746 3103 1.434555 CCGCATTGGAAAGTGTCGTA 58.565 50.000 0.00 0.00 42.00 3.43
2747 3104 2.006888 CCGCATTGGAAAGTGTCGTAT 58.993 47.619 0.00 0.00 42.00 3.06
2748 3105 3.191669 CCGCATTGGAAAGTGTCGTATA 58.808 45.455 0.00 0.00 42.00 1.47
2749 3106 3.000925 CCGCATTGGAAAGTGTCGTATAC 59.999 47.826 0.00 0.00 42.00 1.47
2750 3107 3.863424 CGCATTGGAAAGTGTCGTATACT 59.137 43.478 0.56 0.00 0.00 2.12
2751 3108 5.038683 CGCATTGGAAAGTGTCGTATACTA 58.961 41.667 0.56 0.00 0.00 1.82
2752 3109 5.173312 CGCATTGGAAAGTGTCGTATACTAG 59.827 44.000 0.56 0.00 0.00 2.57
2753 3110 5.050972 GCATTGGAAAGTGTCGTATACTAGC 60.051 44.000 0.56 0.00 0.00 3.42
2754 3111 5.909621 TTGGAAAGTGTCGTATACTAGCT 57.090 39.130 0.56 0.00 0.00 3.32
2755 3112 7.423199 CATTGGAAAGTGTCGTATACTAGCTA 58.577 38.462 0.56 0.00 0.00 3.32
2756 3113 7.395190 TTGGAAAGTGTCGTATACTAGCTAA 57.605 36.000 0.56 0.00 0.00 3.09
2757 3114 7.578310 TGGAAAGTGTCGTATACTAGCTAAT 57.422 36.000 0.56 0.00 0.00 1.73
2758 3115 8.681486 TGGAAAGTGTCGTATACTAGCTAATA 57.319 34.615 0.56 0.00 0.00 0.98
2759 3116 9.293404 TGGAAAGTGTCGTATACTAGCTAATAT 57.707 33.333 0.00 0.00 0.00 1.28
2760 3117 9.771915 GGAAAGTGTCGTATACTAGCTAATATC 57.228 37.037 0.00 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.694093 AGTCTAGACTCAATGGAAAAATTCCT 58.306 34.615 20.00 0.00 43.58 3.36
1 2 7.929941 AGTCTAGACTCAATGGAAAAATTCC 57.070 36.000 20.00 2.12 43.52 3.01
29 30 9.540538 TCCTCCACATTTCATAGGAAAATAAAA 57.459 29.630 6.65 0.00 45.52 1.52
30 31 9.713684 ATCCTCCACATTTCATAGGAAAATAAA 57.286 29.630 6.65 0.00 45.52 1.40
33 34 7.946776 CCTATCCTCCACATTTCATAGGAAAAT 59.053 37.037 6.65 0.00 45.52 1.82
34 35 7.128728 TCCTATCCTCCACATTTCATAGGAAAA 59.871 37.037 6.65 0.00 45.52 2.29
35 36 6.619437 TCCTATCCTCCACATTTCATAGGAAA 59.381 38.462 4.85 4.85 46.36 3.13
36 37 6.150332 TCCTATCCTCCACATTTCATAGGAA 58.850 40.000 3.47 0.00 39.17 3.36
37 38 5.726560 TCCTATCCTCCACATTTCATAGGA 58.273 41.667 2.01 2.01 39.61 2.94
38 39 6.234177 GTTCCTATCCTCCACATTTCATAGG 58.766 44.000 0.00 0.00 35.93 2.57
39 40 6.183361 TGGTTCCTATCCTCCACATTTCATAG 60.183 42.308 0.00 0.00 0.00 2.23
40 41 5.669904 TGGTTCCTATCCTCCACATTTCATA 59.330 40.000 0.00 0.00 0.00 2.15
41 42 4.478317 TGGTTCCTATCCTCCACATTTCAT 59.522 41.667 0.00 0.00 0.00 2.57
42 43 3.849574 TGGTTCCTATCCTCCACATTTCA 59.150 43.478 0.00 0.00 0.00 2.69
43 44 4.503714 TGGTTCCTATCCTCCACATTTC 57.496 45.455 0.00 0.00 0.00 2.17
44 45 4.946160 TTGGTTCCTATCCTCCACATTT 57.054 40.909 0.00 0.00 0.00 2.32
45 46 5.194537 AGAATTGGTTCCTATCCTCCACATT 59.805 40.000 0.00 0.00 34.81 2.71
46 47 4.728860 AGAATTGGTTCCTATCCTCCACAT 59.271 41.667 0.00 0.00 34.81 3.21
47 48 4.111577 AGAATTGGTTCCTATCCTCCACA 58.888 43.478 0.00 0.00 34.81 4.17
48 49 4.779993 AGAATTGGTTCCTATCCTCCAC 57.220 45.455 0.00 0.00 34.81 4.02
49 50 5.911178 ACATAGAATTGGTTCCTATCCTCCA 59.089 40.000 0.00 0.00 34.81 3.86
50 51 6.441088 ACATAGAATTGGTTCCTATCCTCC 57.559 41.667 0.00 0.00 34.81 4.30
51 52 8.423906 TCTACATAGAATTGGTTCCTATCCTC 57.576 38.462 0.00 0.00 34.81 3.71
52 53 8.798975 TTCTACATAGAATTGGTTCCTATCCT 57.201 34.615 0.00 0.00 37.40 3.24
57 58 9.225682 TCCTATTTCTACATAGAATTGGTTCCT 57.774 33.333 2.25 0.00 41.52 3.36
58 59 9.847224 TTCCTATTTCTACATAGAATTGGTTCC 57.153 33.333 2.25 0.00 41.52 3.62
82 83 6.758416 GCTTTTTGGTTCATAGGAATGGATTC 59.242 38.462 0.00 0.00 35.05 2.52
83 84 6.441604 AGCTTTTTGGTTCATAGGAATGGATT 59.558 34.615 0.00 0.00 35.05 3.01
84 85 5.960202 AGCTTTTTGGTTCATAGGAATGGAT 59.040 36.000 0.00 0.00 35.05 3.41
85 86 5.332743 AGCTTTTTGGTTCATAGGAATGGA 58.667 37.500 0.00 0.00 35.05 3.41
86 87 5.420104 AGAGCTTTTTGGTTCATAGGAATGG 59.580 40.000 0.00 0.00 35.05 3.16
87 88 6.521151 AGAGCTTTTTGGTTCATAGGAATG 57.479 37.500 0.00 0.00 35.05 2.67
88 89 8.650143 TTTAGAGCTTTTTGGTTCATAGGAAT 57.350 30.769 0.00 0.00 35.05 3.01
89 90 7.176690 CCTTTAGAGCTTTTTGGTTCATAGGAA 59.823 37.037 0.00 0.00 0.00 3.36
90 91 6.659242 CCTTTAGAGCTTTTTGGTTCATAGGA 59.341 38.462 0.00 0.00 0.00 2.94
91 92 6.659242 TCCTTTAGAGCTTTTTGGTTCATAGG 59.341 38.462 0.00 0.00 0.00 2.57
92 93 7.687941 TCCTTTAGAGCTTTTTGGTTCATAG 57.312 36.000 0.00 0.00 0.00 2.23
93 94 8.472007 TTTCCTTTAGAGCTTTTTGGTTCATA 57.528 30.769 0.00 0.00 0.00 2.15
94 95 6.976934 TTCCTTTAGAGCTTTTTGGTTCAT 57.023 33.333 0.00 0.00 0.00 2.57
95 96 6.783708 TTTCCTTTAGAGCTTTTTGGTTCA 57.216 33.333 0.00 0.00 0.00 3.18
154 155 9.462606 GGTCTCCTTTTATTTAGAGGAATTTCA 57.537 33.333 0.00 0.00 39.00 2.69
155 156 9.688091 AGGTCTCCTTTTATTTAGAGGAATTTC 57.312 33.333 0.00 0.00 39.00 2.17
161 162 9.343539 CCATTTAGGTCTCCTTTTATTTAGAGG 57.656 37.037 0.00 0.00 34.61 3.69
179 180 4.869861 GTGCTTGCCATTTAACCATTTAGG 59.130 41.667 0.00 0.00 45.67 2.69
222 223 0.879400 TTTCCGCACGCCTTAAACGA 60.879 50.000 4.70 0.00 0.00 3.85
280 286 1.243902 TGGATGTCGTTTTCTTGGGC 58.756 50.000 0.00 0.00 0.00 5.36
312 323 6.811170 GTGAGTATAGGAGCTCAAGATATTGC 59.189 42.308 17.19 5.24 42.51 3.56
330 341 5.393569 CGTGGACTGAAGAATGAGTGAGTAT 60.394 44.000 0.00 0.00 0.00 2.12
353 364 8.488764 CCTTGTTTTCTTCTTCTTTAGTAGTCG 58.511 37.037 0.00 0.00 0.00 4.18
355 366 7.773690 TGCCTTGTTTTCTTCTTCTTTAGTAGT 59.226 33.333 0.00 0.00 0.00 2.73
356 367 8.154649 TGCCTTGTTTTCTTCTTCTTTAGTAG 57.845 34.615 0.00 0.00 0.00 2.57
357 368 8.514330 TTGCCTTGTTTTCTTCTTCTTTAGTA 57.486 30.769 0.00 0.00 0.00 1.82
421 432 9.778993 CAGGTAAATCATTCAGATTACTTGTTG 57.221 33.333 0.00 0.00 46.09 3.33
422 433 9.739276 TCAGGTAAATCATTCAGATTACTTGTT 57.261 29.630 0.00 0.00 46.09 2.83
447 459 6.038050 TGGGTTGATTTCAAAAGCATTTGTTC 59.962 34.615 13.61 9.95 45.02 3.18
465 477 2.422235 CGGCATTATTAGGGTGGGTTGA 60.422 50.000 0.00 0.00 0.00 3.18
504 619 6.407475 ACACATTCTTTTTGTTGTCTTTGC 57.593 33.333 0.00 0.00 0.00 3.68
548 666 1.301637 GGCGCTTGCATGGGTTTTT 60.302 52.632 7.64 0.00 41.71 1.94
564 682 5.124936 ACAAACTGTATTTCCTAAATCCGGC 59.875 40.000 0.00 0.00 32.38 6.13
588 706 2.054799 AGACCCAACAGCCAAGAACTA 58.945 47.619 0.00 0.00 0.00 2.24
591 709 0.843309 TCAGACCCAACAGCCAAGAA 59.157 50.000 0.00 0.00 0.00 2.52
632 751 2.345641 CGTCTATTTCAGGCTGTCAACG 59.654 50.000 15.27 12.54 0.00 4.10
643 763 2.188469 GGGCGCCCGTCTATTTCA 59.812 61.111 33.60 0.00 0.00 2.69
713 833 1.006832 GTGGGTCGGAATGTTCGATG 58.993 55.000 0.00 0.00 38.93 3.84
740 864 4.486503 GAGCTCCCCTGCTGGCTG 62.487 72.222 0.87 0.00 44.17 4.85
880 1009 2.347490 GAAGGCAAGTCAGCGGGA 59.653 61.111 0.00 0.00 34.64 5.14
881 1010 3.121030 CGAAGGCAAGTCAGCGGG 61.121 66.667 0.00 0.00 34.64 6.13
882 1011 3.793144 GCGAAGGCAAGTCAGCGG 61.793 66.667 0.00 0.00 39.62 5.52
1006 1140 0.827368 ATGTTTGCGGTGGTTGGTTT 59.173 45.000 0.00 0.00 0.00 3.27
1034 1168 0.035739 GTTGTAGAAGTGGCCGGGAA 59.964 55.000 2.18 0.00 0.00 3.97
1035 1169 1.675219 GTTGTAGAAGTGGCCGGGA 59.325 57.895 2.18 0.00 0.00 5.14
1038 1172 1.298859 GCAGGTTGTAGAAGTGGCCG 61.299 60.000 0.00 0.00 0.00 6.13
1039 1173 0.036875 AGCAGGTTGTAGAAGTGGCC 59.963 55.000 0.00 0.00 0.00 5.36
1040 1174 1.897560 AAGCAGGTTGTAGAAGTGGC 58.102 50.000 0.00 0.00 0.00 5.01
1041 1175 2.030805 GCAAAGCAGGTTGTAGAAGTGG 60.031 50.000 0.00 0.00 0.00 4.00
1048 1189 1.234821 CGGAAGCAAAGCAGGTTGTA 58.765 50.000 0.00 0.00 0.00 2.41
1082 1239 1.696097 GGGATGGAGGCCGAGCTAAA 61.696 60.000 0.00 0.00 0.00 1.85
1097 1254 3.017581 AAGGAGCCAAGCGGGGAT 61.018 61.111 0.42 0.00 37.04 3.85
1129 1286 2.421314 CTCGCACACCACACCAGA 59.579 61.111 0.00 0.00 0.00 3.86
1149 1306 4.735132 TCCTCCAAGAACCGCGCG 62.735 66.667 25.67 25.67 0.00 6.86
1150 1307 2.815647 CTCCTCCAAGAACCGCGC 60.816 66.667 0.00 0.00 0.00 6.86
1151 1308 2.788191 AAGCTCCTCCAAGAACCGCG 62.788 60.000 0.00 0.00 0.00 6.46
1152 1309 1.003233 AAGCTCCTCCAAGAACCGC 60.003 57.895 0.00 0.00 0.00 5.68
1211 1369 3.058160 GTCTTGGCCAGCGTGCAT 61.058 61.111 5.11 0.00 0.00 3.96
1561 1719 4.100084 TGATGGCCGGCTCTGGTG 62.100 66.667 28.56 0.00 0.00 4.17
1562 1720 4.101448 GTGATGGCCGGCTCTGGT 62.101 66.667 28.56 7.88 0.00 4.00
1565 1723 3.011517 AAGGTGATGGCCGGCTCT 61.012 61.111 28.56 14.25 0.00 4.09
1763 1921 7.390027 AGAAGAAGAAAAATGAGCTGCTAGTA 58.610 34.615 0.15 0.00 0.00 1.82
1877 2035 6.033966 ACGTTTTGAATTCTTCCACAAAGTC 58.966 36.000 7.05 0.00 36.31 3.01
1909 2067 1.883638 GCAAAGCTGACCTGATCCACA 60.884 52.381 0.00 0.00 0.00 4.17
1910 2068 0.807496 GCAAAGCTGACCTGATCCAC 59.193 55.000 0.00 0.00 0.00 4.02
2016 2175 7.337436 ACAATGATATTGGCCCAAAATTCAAAG 59.663 33.333 0.00 4.19 0.00 2.77
2089 2249 6.993786 TGTGTCTGTACTGATGTTCAAAAA 57.006 33.333 5.69 0.00 0.00 1.94
2091 2251 5.007626 GCTTGTGTCTGTACTGATGTTCAAA 59.992 40.000 5.69 0.00 0.00 2.69
2094 2254 3.121944 CGCTTGTGTCTGTACTGATGTTC 59.878 47.826 5.69 0.00 0.00 3.18
2095 2255 3.059884 CGCTTGTGTCTGTACTGATGTT 58.940 45.455 5.69 0.00 0.00 2.71
2096 2256 2.677199 CGCTTGTGTCTGTACTGATGT 58.323 47.619 5.69 0.00 0.00 3.06
2098 2258 1.273606 AGCGCTTGTGTCTGTACTGAT 59.726 47.619 2.64 0.00 0.00 2.90
2100 2260 1.063806 GAGCGCTTGTGTCTGTACTG 58.936 55.000 13.26 0.00 0.00 2.74
2101 2261 0.673985 TGAGCGCTTGTGTCTGTACT 59.326 50.000 13.26 0.00 0.00 2.73
2102 2262 1.714794 ATGAGCGCTTGTGTCTGTAC 58.285 50.000 13.26 0.00 0.00 2.90
2105 2265 3.243877 GTGTATATGAGCGCTTGTGTCTG 59.756 47.826 13.26 0.00 0.00 3.51
2106 2266 3.448686 GTGTATATGAGCGCTTGTGTCT 58.551 45.455 13.26 0.00 0.00 3.41
2107 2267 2.216488 CGTGTATATGAGCGCTTGTGTC 59.784 50.000 13.26 0.00 0.00 3.67
2109 2269 1.071239 GCGTGTATATGAGCGCTTGTG 60.071 52.381 13.26 0.00 45.48 3.33
2111 2271 0.159554 CGCGTGTATATGAGCGCTTG 59.840 55.000 13.26 0.00 46.56 4.01
2116 2276 2.090658 GTGTATGCGCGTGTATATGAGC 59.909 50.000 13.61 0.41 38.85 4.26
2117 2277 3.565516 AGTGTATGCGCGTGTATATGAG 58.434 45.455 13.61 0.00 0.00 2.90
2118 2278 3.003897 TGAGTGTATGCGCGTGTATATGA 59.996 43.478 13.61 0.00 0.00 2.15
2119 2279 3.305110 TGAGTGTATGCGCGTGTATATG 58.695 45.455 13.61 0.00 0.00 1.78
2120 2280 3.636282 TGAGTGTATGCGCGTGTATAT 57.364 42.857 13.61 0.00 0.00 0.86
2121 2281 3.561503 GATGAGTGTATGCGCGTGTATA 58.438 45.455 13.61 2.40 0.00 1.47
2122 2282 2.394708 GATGAGTGTATGCGCGTGTAT 58.605 47.619 13.61 4.63 0.00 2.29
2123 2283 1.535226 GGATGAGTGTATGCGCGTGTA 60.535 52.381 13.61 0.00 0.00 2.90
2124 2284 0.806102 GGATGAGTGTATGCGCGTGT 60.806 55.000 13.61 0.00 0.00 4.49
2125 2285 1.490693 GGGATGAGTGTATGCGCGTG 61.491 60.000 13.61 0.00 0.00 5.34
2126 2286 1.227263 GGGATGAGTGTATGCGCGT 60.227 57.895 8.43 7.55 0.00 6.01
2127 2287 0.313987 TAGGGATGAGTGTATGCGCG 59.686 55.000 0.00 0.00 0.00 6.86
2128 2288 2.029020 TCATAGGGATGAGTGTATGCGC 60.029 50.000 0.00 0.00 37.15 6.09
2129 2289 3.942130 TCATAGGGATGAGTGTATGCG 57.058 47.619 0.00 0.00 37.15 4.73
2130 2290 3.990469 CGTTCATAGGGATGAGTGTATGC 59.010 47.826 0.00 0.00 43.03 3.14
2131 2291 3.990469 GCGTTCATAGGGATGAGTGTATG 59.010 47.826 0.00 0.00 43.03 2.39
2132 2292 3.641436 TGCGTTCATAGGGATGAGTGTAT 59.359 43.478 0.00 0.00 43.03 2.29
2133 2293 3.028130 TGCGTTCATAGGGATGAGTGTA 58.972 45.455 0.00 0.00 43.03 2.90
2134 2294 1.831106 TGCGTTCATAGGGATGAGTGT 59.169 47.619 0.00 0.00 43.03 3.55
2135 2295 2.205074 GTGCGTTCATAGGGATGAGTG 58.795 52.381 0.00 0.00 43.03 3.51
2136 2296 1.831106 TGTGCGTTCATAGGGATGAGT 59.169 47.619 0.00 0.00 43.03 3.41
2137 2297 2.205074 GTGTGCGTTCATAGGGATGAG 58.795 52.381 0.00 0.00 43.03 2.90
2138 2298 1.552792 TGTGTGCGTTCATAGGGATGA 59.447 47.619 0.00 0.00 40.45 2.92
2139 2299 1.665679 GTGTGTGCGTTCATAGGGATG 59.334 52.381 0.00 0.00 0.00 3.51
2140 2300 1.739035 CGTGTGTGCGTTCATAGGGAT 60.739 52.381 0.00 0.00 0.00 3.85
2141 2301 0.389296 CGTGTGTGCGTTCATAGGGA 60.389 55.000 0.00 0.00 0.00 4.20
2142 2302 1.966493 GCGTGTGTGCGTTCATAGGG 61.966 60.000 0.00 0.00 0.00 3.53
2143 2303 1.288419 TGCGTGTGTGCGTTCATAGG 61.288 55.000 0.00 0.00 37.81 2.57
2144 2304 0.179250 GTGCGTGTGTGCGTTCATAG 60.179 55.000 0.00 0.00 37.81 2.23
2145 2305 0.876342 TGTGCGTGTGTGCGTTCATA 60.876 50.000 0.00 0.00 37.81 2.15
2146 2306 2.176926 TGTGCGTGTGTGCGTTCAT 61.177 52.632 0.00 0.00 37.81 2.57
2147 2307 2.815647 TGTGCGTGTGTGCGTTCA 60.816 55.556 0.00 0.00 37.81 3.18
2148 2308 2.350760 GTGTGCGTGTGTGCGTTC 60.351 61.111 0.00 0.00 37.81 3.95
2149 2309 3.871574 GGTGTGCGTGTGTGCGTT 61.872 61.111 0.00 0.00 37.81 4.84
2152 2312 2.280524 TAGGGTGTGCGTGTGTGC 60.281 61.111 0.00 0.00 0.00 4.57
2153 2313 1.959226 GGTAGGGTGTGCGTGTGTG 60.959 63.158 0.00 0.00 0.00 3.82
2154 2314 2.424302 GGTAGGGTGTGCGTGTGT 59.576 61.111 0.00 0.00 0.00 3.72
2155 2315 2.358247 GGGTAGGGTGTGCGTGTG 60.358 66.667 0.00 0.00 0.00 3.82
2156 2316 2.735151 TAGGGGTAGGGTGTGCGTGT 62.735 60.000 0.00 0.00 0.00 4.49
2157 2317 1.335132 ATAGGGGTAGGGTGTGCGTG 61.335 60.000 0.00 0.00 0.00 5.34
2158 2318 1.002533 ATAGGGGTAGGGTGTGCGT 59.997 57.895 0.00 0.00 0.00 5.24
2159 2319 1.046472 TCATAGGGGTAGGGTGTGCG 61.046 60.000 0.00 0.00 0.00 5.34
2160 2320 0.759346 CTCATAGGGGTAGGGTGTGC 59.241 60.000 0.00 0.00 0.00 4.57
2161 2321 0.759346 GCTCATAGGGGTAGGGTGTG 59.241 60.000 0.00 0.00 0.00 3.82
2162 2322 0.341961 TGCTCATAGGGGTAGGGTGT 59.658 55.000 0.00 0.00 0.00 4.16
2163 2323 1.625818 GATGCTCATAGGGGTAGGGTG 59.374 57.143 0.00 0.00 0.00 4.61
2164 2324 1.509961 AGATGCTCATAGGGGTAGGGT 59.490 52.381 0.00 0.00 0.00 4.34
2165 2325 2.183679 GAGATGCTCATAGGGGTAGGG 58.816 57.143 0.00 0.00 0.00 3.53
2166 2326 2.183679 GGAGATGCTCATAGGGGTAGG 58.816 57.143 0.00 0.00 31.08 3.18
2167 2327 2.894731 TGGAGATGCTCATAGGGGTAG 58.105 52.381 0.00 0.00 31.08 3.18
2168 2328 3.344535 TTGGAGATGCTCATAGGGGTA 57.655 47.619 0.00 0.00 31.08 3.69
2169 2329 2.196742 TTGGAGATGCTCATAGGGGT 57.803 50.000 0.00 0.00 31.08 4.95
2170 2330 3.582998 TTTTGGAGATGCTCATAGGGG 57.417 47.619 0.00 0.00 31.08 4.79
2188 2348 2.722094 TGATATGCCGGCTCAGTTTTT 58.278 42.857 29.70 3.35 0.00 1.94
2189 2349 2.418368 TGATATGCCGGCTCAGTTTT 57.582 45.000 29.70 5.10 0.00 2.43
2190 2350 2.105477 AGATGATATGCCGGCTCAGTTT 59.895 45.455 29.70 8.26 0.00 2.66
2191 2351 1.696336 AGATGATATGCCGGCTCAGTT 59.304 47.619 29.70 9.04 0.00 3.16
2192 2352 1.346062 AGATGATATGCCGGCTCAGT 58.654 50.000 29.70 13.44 0.00 3.41
2193 2353 2.074576 CAAGATGATATGCCGGCTCAG 58.925 52.381 29.70 7.35 0.00 3.35
2194 2354 1.693606 TCAAGATGATATGCCGGCTCA 59.306 47.619 29.70 23.34 0.00 4.26
2195 2355 2.028658 TCTCAAGATGATATGCCGGCTC 60.029 50.000 29.70 17.89 0.00 4.70
2196 2356 1.973515 TCTCAAGATGATATGCCGGCT 59.026 47.619 29.70 15.76 0.00 5.52
2197 2357 2.462456 TCTCAAGATGATATGCCGGC 57.538 50.000 22.73 22.73 0.00 6.13
2198 2358 7.621428 ATTAAATCTCAAGATGATATGCCGG 57.379 36.000 0.00 0.00 34.49 6.13
2274 2434 7.543520 GCCAAAATTTCCTATCTTTGACTTCTG 59.456 37.037 0.00 0.00 31.77 3.02
2331 2492 8.865420 TTGTCTAGTGATATGACCTAGTATCC 57.135 38.462 0.00 0.00 32.01 2.59
2378 2539 6.888105 ACAAAAGGTTGAAACATGGAGATTT 58.112 32.000 0.00 0.00 38.20 2.17
2454 2618 1.539496 GCAGTTCCTTGTACGGTGTCA 60.539 52.381 0.00 0.00 0.00 3.58
2457 2621 0.250124 TGGCAGTTCCTTGTACGGTG 60.250 55.000 0.00 0.00 35.26 4.94
2503 2667 7.893124 AATACTCTGCCATCTTCAAATCAAT 57.107 32.000 0.00 0.00 0.00 2.57
2570 2927 6.404623 CGTGGCAGAAATAAAAATCATCTCCA 60.405 38.462 0.00 0.00 0.00 3.86
2571 2928 5.973565 CGTGGCAGAAATAAAAATCATCTCC 59.026 40.000 0.00 0.00 0.00 3.71
2609 2966 1.272212 GTTTGATTCCCCGTGCACATT 59.728 47.619 18.64 0.00 0.00 2.71
2657 3014 3.004419 GGCAACAAGGTTGACTCCTTAAC 59.996 47.826 12.90 0.00 44.87 2.01
2710 3067 1.925185 GCGGGACTGATTCTAAACGAC 59.075 52.381 0.00 0.00 0.00 4.34
2726 3083 1.234615 ACGACACTTTCCAATGCGGG 61.235 55.000 0.00 0.00 34.36 6.13
2727 3084 1.434555 TACGACACTTTCCAATGCGG 58.565 50.000 0.00 0.00 0.00 5.69
2728 3085 3.863424 AGTATACGACACTTTCCAATGCG 59.137 43.478 0.00 0.00 0.00 4.73
2729 3086 5.050972 GCTAGTATACGACACTTTCCAATGC 60.051 44.000 0.00 0.00 0.00 3.56
2730 3087 6.273825 AGCTAGTATACGACACTTTCCAATG 58.726 40.000 0.00 0.00 0.00 2.82
2731 3088 6.466885 AGCTAGTATACGACACTTTCCAAT 57.533 37.500 0.00 0.00 0.00 3.16
2732 3089 5.909621 AGCTAGTATACGACACTTTCCAA 57.090 39.130 0.00 0.00 0.00 3.53
2733 3090 7.578310 ATTAGCTAGTATACGACACTTTCCA 57.422 36.000 0.00 0.00 0.00 3.53
2734 3091 9.771915 GATATTAGCTAGTATACGACACTTTCC 57.228 37.037 8.61 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.