Multiple sequence alignment - TraesCS2B01G578000

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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 TraesCS2B01G578000 chr2B 100.000 2942 0 0 1 2942 766180835 766177894 0.000000e+00 5433
1 TraesCS2B01G578000 chr2B 77.317 917 162 26 999 1889 714502193 714503089 1.570000e-137 499
2 TraesCS2B01G578000 chr2B 75.741 911 175 29 999 1889 714519302 714518418 1.630000e-112 416
3 TraesCS2B01G578000 chr2B 94.595 111 4 1 2832 2942 794617150 794617258 1.400000e-38 171
4 TraesCS2B01G578000 chr2B 87.255 102 10 3 755 855 766178380 766178479 2.400000e-21 113
5 TraesCS2B01G578000 chr2B 87.255 102 10 3 2357 2456 766179981 766180081 2.400000e-21 113
6 TraesCS2B01G578000 chr2A 92.963 2032 99 20 129 2120 755681091 755679064 0.000000e+00 2920
7 TraesCS2B01G578000 chr2A 85.569 492 51 12 2251 2726 755677730 755677243 5.660000e-137 497
8 TraesCS2B01G578000 chr2A 77.099 917 158 33 999 1889 724380629 724381519 1.590000e-132 483
9 TraesCS2B01G578000 chr2A 79.436 603 107 12 1291 1889 724425239 724424650 7.590000e-111 411
10 TraesCS2B01G578000 chr2A 82.596 339 32 17 4 326 755678211 755677884 1.040000e-69 274
11 TraesCS2B01G578000 chr2A 97.842 139 3 0 1 139 755687520 755687382 1.050000e-59 241
12 TraesCS2B01G578000 chr2A 84.659 176 23 3 504 675 755677787 755677612 3.900000e-39 172
13 TraesCS2B01G578000 chr2A 87.037 108 10 4 2352 2456 755680361 755680467 5.150000e-23 119
14 TraesCS2B01G578000 chr2A 85.047 107 8 2 755 857 755677515 755677617 5.190000e-18 102
15 TraesCS2B01G578000 chr2D 94.658 1797 90 3 326 2116 624265331 624263535 0.000000e+00 2782
16 TraesCS2B01G578000 chr2D 87.994 658 44 18 1 655 624284055 624283430 0.000000e+00 745
17 TraesCS2B01G578000 chr2D 77.571 914 162 23 999 1889 590081077 590081970 2.020000e-141 512
18 TraesCS2B01G578000 chr2D 76.304 920 166 34 999 1889 590074987 590075883 7.480000e-121 444
19 TraesCS2B01G578000 chr2D 93.772 289 17 1 889 1177 624265618 624265331 1.620000e-117 433
20 TraesCS2B01G578000 chr2D 78.300 659 116 18 1291 1937 590091625 590090982 1.640000e-107 399
21 TraesCS2B01G578000 chr2D 80.594 505 59 26 2251 2735 624262302 624261817 1.300000e-93 353
22 TraesCS2B01G578000 chr2D 83.962 318 47 3 354 667 624262509 624262192 4.770000e-78 302
23 TraesCS2B01G578000 chr2D 92.593 135 4 2 755 887 624283163 624283033 3.870000e-44 189
24 TraesCS2B01G578000 chr2D 82.500 200 22 6 2357 2548 624283067 624283261 2.350000e-36 163
25 TraesCS2B01G578000 chr2D 84.762 105 8 6 2357 2456 624264800 624264901 6.710000e-17 99
26 TraesCS2B01G578000 chr4A 84.496 129 17 3 2793 2919 660880543 660880416 1.110000e-24 124


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 TraesCS2B01G578000 chr2B 766177894 766180835 2941 True 5433.00 5433 100.00000 1 2942 1 chr2B.!!$R2 2941
1 TraesCS2B01G578000 chr2B 714502193 714503089 896 False 499.00 499 77.31700 999 1889 1 chr2B.!!$F1 890
2 TraesCS2B01G578000 chr2B 714518418 714519302 884 True 416.00 416 75.74100 999 1889 1 chr2B.!!$R1 890
3 TraesCS2B01G578000 chr2A 755677243 755681091 3848 True 965.75 2920 86.44675 4 2726 4 chr2A.!!$R3 2722
4 TraesCS2B01G578000 chr2A 724380629 724381519 890 False 483.00 483 77.09900 999 1889 1 chr2A.!!$F1 890
5 TraesCS2B01G578000 chr2A 724424650 724425239 589 True 411.00 411 79.43600 1291 1889 1 chr2A.!!$R1 598
6 TraesCS2B01G578000 chr2D 624261817 624265618 3801 True 967.50 2782 88.24650 326 2735 4 chr2D.!!$R2 2409
7 TraesCS2B01G578000 chr2D 590081077 590081970 893 False 512.00 512 77.57100 999 1889 1 chr2D.!!$F2 890
8 TraesCS2B01G578000 chr2D 624283033 624284055 1022 True 467.00 745 90.29350 1 887 2 chr2D.!!$R3 886
9 TraesCS2B01G578000 chr2D 590074987 590075883 896 False 444.00 444 76.30400 999 1889 1 chr2D.!!$F1 890
10 TraesCS2B01G578000 chr2D 590090982 590091625 643 True 399.00 399 78.30000 1291 1937 1 chr2D.!!$R1 646

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
60 61 3.527253 TCAATGGGGGAGCTCTATTTTCA 59.473 43.478 14.64 4.63 0.00 2.69 F
1158 2205 1.219124 GTTCATCCAGCCTCTCGCA 59.781 57.895 0.00 0.00 41.38 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1518 2592 0.687354 GGCCCTGAACAGAGAGAACA 59.313 55.0 3.19 0.0 0.0 3.18 R
2839 5341 0.179062 GATCTGCGGGCTGAAGTGAT 60.179 55.0 0.06 0.0 0.0 3.06 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
59 60 4.170468 TCAATGGGGGAGCTCTATTTTC 57.830 45.455 14.64 0.00 0.00 2.29
60 61 3.527253 TCAATGGGGGAGCTCTATTTTCA 59.473 43.478 14.64 4.63 0.00 2.69
61 62 4.017591 TCAATGGGGGAGCTCTATTTTCAA 60.018 41.667 14.64 0.00 0.00 2.69
182 184 8.856153 TTCTCTTGCCAACTATTTGTATTGTA 57.144 30.769 0.00 0.00 0.00 2.41
183 185 9.461312 TTCTCTTGCCAACTATTTGTATTGTAT 57.539 29.630 0.00 0.00 0.00 2.29
184 186 9.461312 TCTCTTGCCAACTATTTGTATTGTATT 57.539 29.630 0.00 0.00 0.00 1.89
247 251 8.630054 TGTTGTGACACCTTATTAAGCTATTT 57.370 30.769 2.45 0.00 0.00 1.40
295 299 7.445900 ACTTTGTATTACACGTGTGATATCG 57.554 36.000 28.96 20.44 30.78 2.92
302 307 4.258935 ACACGTGTGATATCGCATTTTC 57.741 40.909 22.71 8.19 38.74 2.29
311 316 7.748683 GTGTGATATCGCATTTTCTTAACACAA 59.251 33.333 21.21 0.00 38.74 3.33
326 331 4.486125 AACACAACCTTTGGCAAATTCT 57.514 36.364 13.89 0.00 34.12 2.40
557 562 9.396022 TCTTTTTCATAGAATAGCAAAGGTAGG 57.604 33.333 0.00 0.00 0.00 3.18
558 563 9.178758 CTTTTTCATAGAATAGCAAAGGTAGGT 57.821 33.333 0.00 0.00 0.00 3.08
693 776 8.117813 ACGGTGTTATTAAAGGATGAAATGTT 57.882 30.769 0.00 0.00 0.00 2.71
839 1012 4.285863 TGGTGGACTGATTTTTCCAAGTT 58.714 39.130 0.00 0.00 43.67 2.66
892 1072 6.655425 GGTTTCTAATTTCTCCACTAACTGCT 59.345 38.462 0.00 0.00 0.00 4.24
936 1121 5.221864 CCCCTCAACTATATAAACCTCCACC 60.222 48.000 0.00 0.00 0.00 4.61
953 1138 3.572682 TCCACCGCATTATCTAGTCGATT 59.427 43.478 0.00 0.00 33.48 3.34
963 1151 7.386299 GCATTATCTAGTCGATTCACAATCCTT 59.614 37.037 0.00 0.00 34.35 3.36
972 1160 4.142600 CGATTCACAATCCTTTCTTCCCAC 60.143 45.833 0.00 0.00 34.35 4.61
994 1182 4.096984 ACACCTTGAAGAAGCTTCAACAAG 59.903 41.667 33.70 33.70 39.67 3.16
1158 2205 1.219124 GTTCATCCAGCCTCTCGCA 59.781 57.895 0.00 0.00 41.38 5.10
1215 2262 1.296715 GAACACCGGCATCTCCTGT 59.703 57.895 0.00 0.00 31.96 4.00
1218 2265 4.457496 ACCGGCATCTCCTGTGCG 62.457 66.667 0.00 0.00 43.40 5.34
1530 2604 0.398318 GCTGGGGTGTTCTCTCTGTT 59.602 55.000 0.00 0.00 0.00 3.16
1541 2615 2.125350 CTCTGTTCAGGGCCTCGC 60.125 66.667 0.95 0.00 0.00 5.03
1813 2890 0.099436 GCTCGCTGGGTATGCTTTTG 59.901 55.000 0.00 0.00 0.00 2.44
1820 2897 1.268352 TGGGTATGCTTTTGTGTTCGC 59.732 47.619 0.00 0.00 0.00 4.70
1844 2921 0.106335 CTGCAGCTGGTCTATCTGGG 59.894 60.000 17.12 0.00 0.00 4.45
1943 3026 2.482664 CCGGTGAAGGAGATGTCTGATG 60.483 54.545 0.00 0.00 0.00 3.07
1944 3027 2.428530 CGGTGAAGGAGATGTCTGATGA 59.571 50.000 0.00 0.00 0.00 2.92
1945 3028 3.069300 CGGTGAAGGAGATGTCTGATGAT 59.931 47.826 0.00 0.00 0.00 2.45
1948 3031 4.744137 GTGAAGGAGATGTCTGATGATTCG 59.256 45.833 0.00 0.00 0.00 3.34
1949 3032 4.403752 TGAAGGAGATGTCTGATGATTCGT 59.596 41.667 0.00 0.00 0.00 3.85
2009 3092 6.490040 GGAGGCTTTATCCTGCAATAATGTAA 59.510 38.462 0.00 0.00 43.22 2.41
2042 3128 6.430308 TCTGTAAGATTATACGTAGCCAGAGG 59.570 42.308 0.08 0.00 38.67 3.69
2045 3131 3.827302 AGATTATACGTAGCCAGAGGGTG 59.173 47.826 0.08 0.00 34.28 4.61
2088 3189 4.396790 GCTTGTGGATAAAACCGTATTCCA 59.603 41.667 0.00 0.00 0.00 3.53
2120 3221 1.413812 ACTAGATGATGATGCGCCACA 59.586 47.619 4.18 5.36 0.00 4.17
2121 3222 2.158914 ACTAGATGATGATGCGCCACAA 60.159 45.455 4.18 0.00 0.00 3.33
2123 3224 1.134310 AGATGATGATGCGCCACAAGA 60.134 47.619 4.18 0.00 0.00 3.02
2125 3226 2.618442 TGATGATGCGCCACAAGATA 57.382 45.000 4.18 0.00 0.00 1.98
2127 3228 3.277715 TGATGATGCGCCACAAGATAAA 58.722 40.909 4.18 0.00 0.00 1.40
2128 3229 3.693578 TGATGATGCGCCACAAGATAAAA 59.306 39.130 4.18 0.00 0.00 1.52
2130 3231 2.163412 TGATGCGCCACAAGATAAAACC 59.837 45.455 4.18 0.00 0.00 3.27
2132 3233 0.519961 GCGCCACAAGATAAAACCGT 59.480 50.000 0.00 0.00 0.00 4.83
2133 3234 1.733360 GCGCCACAAGATAAAACCGTA 59.267 47.619 0.00 0.00 0.00 4.02
2134 3235 2.353579 GCGCCACAAGATAAAACCGTAT 59.646 45.455 0.00 0.00 0.00 3.06
2135 3236 3.181504 GCGCCACAAGATAAAACCGTATT 60.182 43.478 0.00 0.00 0.00 1.89
2136 3237 4.584394 CGCCACAAGATAAAACCGTATTC 58.416 43.478 0.00 0.00 0.00 1.75
2138 3239 4.396790 GCCACAAGATAAAACCGTATTCCA 59.603 41.667 0.00 0.00 0.00 3.53
2139 3240 5.106078 GCCACAAGATAAAACCGTATTCCAA 60.106 40.000 0.00 0.00 0.00 3.53
2141 3242 6.972328 CCACAAGATAAAACCGTATTCCAATG 59.028 38.462 0.00 0.00 0.00 2.82
2142 3243 7.362574 CCACAAGATAAAACCGTATTCCAATGT 60.363 37.037 0.00 0.00 0.00 2.71
2143 3244 8.670135 CACAAGATAAAACCGTATTCCAATGTA 58.330 33.333 0.00 0.00 0.00 2.29
2193 4674 8.270744 AGCAAAGATTATATCCAATAGCTAGGG 58.729 37.037 7.72 7.72 0.00 3.53
2194 4675 8.267894 GCAAAGATTATATCCAATAGCTAGGGA 58.732 37.037 16.75 16.75 34.70 4.20
2205 4686 9.755122 ATCCAATAGCTAGGGAATTTATTTACC 57.245 33.333 17.96 0.00 33.73 2.85
2206 4687 8.955794 TCCAATAGCTAGGGAATTTATTTACCT 58.044 33.333 13.13 0.00 33.74 3.08
2207 4688 9.588096 CCAATAGCTAGGGAATTTATTTACCTT 57.412 33.333 8.24 0.00 32.24 3.50
2216 4697 9.555411 AGGGAATTTATTTACCTTGTATTGGTT 57.445 29.630 0.00 0.00 38.88 3.67
2221 4702 7.721409 TTATTTACCTTGTATTGGTTTCCCC 57.279 36.000 0.00 0.00 38.88 4.81
2222 4703 4.743705 TTACCTTGTATTGGTTTCCCCA 57.256 40.909 0.00 0.00 43.27 4.96
2223 4704 3.845109 ACCTTGTATTGGTTTCCCCAT 57.155 42.857 0.00 0.00 44.74 4.00
2224 4705 3.440127 ACCTTGTATTGGTTTCCCCATG 58.560 45.455 0.00 0.00 44.74 3.66
2225 4706 2.168313 CCTTGTATTGGTTTCCCCATGC 59.832 50.000 0.00 0.00 44.74 4.06
2226 4707 1.859302 TGTATTGGTTTCCCCATGCC 58.141 50.000 0.00 0.00 44.74 4.40
2227 4708 1.360852 TGTATTGGTTTCCCCATGCCT 59.639 47.619 0.00 0.00 44.74 4.75
2228 4709 2.583101 TGTATTGGTTTCCCCATGCCTA 59.417 45.455 0.00 0.00 44.74 3.93
2229 4710 2.159179 ATTGGTTTCCCCATGCCTAC 57.841 50.000 0.00 0.00 44.74 3.18
2230 4711 0.780637 TTGGTTTCCCCATGCCTACA 59.219 50.000 0.00 0.00 44.74 2.74
2231 4712 0.780637 TGGTTTCCCCATGCCTACAA 59.219 50.000 0.00 0.00 38.72 2.41
2232 4713 1.272425 TGGTTTCCCCATGCCTACAAG 60.272 52.381 0.00 0.00 38.72 3.16
2233 4714 1.005450 GGTTTCCCCATGCCTACAAGA 59.995 52.381 0.00 0.00 0.00 3.02
2234 4715 2.358195 GGTTTCCCCATGCCTACAAGAT 60.358 50.000 0.00 0.00 0.00 2.40
2235 4716 3.365472 GTTTCCCCATGCCTACAAGATT 58.635 45.455 0.00 0.00 0.00 2.40
2236 4717 4.532834 GTTTCCCCATGCCTACAAGATTA 58.467 43.478 0.00 0.00 0.00 1.75
2237 4718 5.140454 GTTTCCCCATGCCTACAAGATTAT 58.860 41.667 0.00 0.00 0.00 1.28
2238 4719 6.303839 GTTTCCCCATGCCTACAAGATTATA 58.696 40.000 0.00 0.00 0.00 0.98
2239 4720 6.718593 TTCCCCATGCCTACAAGATTATAT 57.281 37.500 0.00 0.00 0.00 0.86
2240 4721 6.313519 TCCCCATGCCTACAAGATTATATC 57.686 41.667 0.00 0.00 0.00 1.63
2241 4722 5.191722 TCCCCATGCCTACAAGATTATATCC 59.808 44.000 0.00 0.00 0.00 2.59
2242 4723 5.044919 CCCCATGCCTACAAGATTATATCCA 60.045 44.000 0.00 0.00 0.00 3.41
2243 4724 6.484288 CCCATGCCTACAAGATTATATCCAA 58.516 40.000 0.00 0.00 0.00 3.53
2244 4725 7.121382 CCCATGCCTACAAGATTATATCCAAT 58.879 38.462 0.00 0.00 0.00 3.16
2245 4726 8.274322 CCCATGCCTACAAGATTATATCCAATA 58.726 37.037 0.00 0.00 0.00 1.90
2246 4727 9.334947 CCATGCCTACAAGATTATATCCAATAG 57.665 37.037 0.00 0.00 0.00 1.73
2247 4728 8.834465 CATGCCTACAAGATTATATCCAATAGC 58.166 37.037 0.00 0.00 0.00 2.97
2248 4729 8.150827 TGCCTACAAGATTATATCCAATAGCT 57.849 34.615 0.00 0.00 0.00 3.32
2249 4730 9.267071 TGCCTACAAGATTATATCCAATAGCTA 57.733 33.333 0.00 0.00 0.00 3.32
2261 4742 2.300433 CAATAGCTAGGGCAATGCACA 58.700 47.619 11.17 0.00 41.70 4.57
2323 4804 8.153550 GTCCATGACTAAGGAAGTGATCATTAT 58.846 37.037 0.00 0.00 39.07 1.28
2350 4840 5.622346 AGAAGGGTTGAAGATAGTGATCC 57.378 43.478 0.00 0.00 31.81 3.36
2355 4850 8.798975 AAGGGTTGAAGATAGTGATCCTTATA 57.201 34.615 0.00 0.00 31.81 0.98
2422 4917 8.083828 ACTATTGTAACATGAAGGAGAGTCAT 57.916 34.615 0.00 0.00 36.11 3.06
2437 4933 5.153950 AGAGTCATGAAAGTAAGGGTGTC 57.846 43.478 0.00 0.00 0.00 3.67
2474 4970 3.978718 TTGACATGTCAATGCGTCAAA 57.021 38.095 32.36 11.63 43.40 2.69
2475 4971 4.502171 TTGACATGTCAATGCGTCAAAT 57.498 36.364 32.36 0.00 43.40 2.32
2535 5033 4.752063 ACTTTAAATTTCTTGGCCCTCCT 58.248 39.130 0.00 0.00 0.00 3.69
2552 5050 5.105513 GCCCTCCTATCTAATCTAACTCTGC 60.106 48.000 0.00 0.00 0.00 4.26
2578 5076 8.657074 TCGACCAGAGTTACATATTAATTTGG 57.343 34.615 10.17 0.00 0.00 3.28
2618 5116 9.518906 TTGTGAATAATTTCGGATTCATGAATG 57.481 29.630 25.37 12.10 42.43 2.67
2646 5144 8.798748 TTTGCAAATTTATGAGCAATTTTTGG 57.201 26.923 8.05 0.00 45.23 3.28
2648 5146 8.162878 TGCAAATTTATGAGCAATTTTTGGAA 57.837 26.923 0.00 0.00 32.57 3.53
2650 5148 9.281075 GCAAATTTATGAGCAATTTTTGGAATC 57.719 29.630 0.00 0.00 32.57 2.52
2655 5153 9.504708 TTTATGAGCAATTTTTGGAATCACAAT 57.495 25.926 0.00 0.00 0.00 2.71
2661 5159 8.508875 AGCAATTTTTGGAATCACAATCAATTC 58.491 29.630 0.00 0.00 28.70 2.17
2676 5174 7.999878 CACAATCAATTCTTCAATTTGTGAACG 59.000 33.333 6.99 0.00 41.47 3.95
2757 5259 8.984891 TTATTGTTTTGCTGTAGATCCATTTG 57.015 30.769 0.00 0.00 0.00 2.32
2758 5260 6.403866 TTGTTTTGCTGTAGATCCATTTGT 57.596 33.333 0.00 0.00 0.00 2.83
2759 5261 6.012658 TGTTTTGCTGTAGATCCATTTGTC 57.987 37.500 0.00 0.00 0.00 3.18
2760 5262 4.944962 TTTGCTGTAGATCCATTTGTCG 57.055 40.909 0.00 0.00 0.00 4.35
2761 5263 3.610040 TGCTGTAGATCCATTTGTCGT 57.390 42.857 0.00 0.00 0.00 4.34
2762 5264 3.521560 TGCTGTAGATCCATTTGTCGTC 58.478 45.455 0.00 0.00 0.00 4.20
2763 5265 3.056179 TGCTGTAGATCCATTTGTCGTCA 60.056 43.478 0.00 0.00 0.00 4.35
2764 5266 4.122776 GCTGTAGATCCATTTGTCGTCAT 58.877 43.478 0.00 0.00 0.00 3.06
2765 5267 5.163457 TGCTGTAGATCCATTTGTCGTCATA 60.163 40.000 0.00 0.00 0.00 2.15
2766 5268 5.175856 GCTGTAGATCCATTTGTCGTCATAC 59.824 44.000 0.00 0.00 0.00 2.39
2767 5269 6.215495 TGTAGATCCATTTGTCGTCATACA 57.785 37.500 0.00 0.00 0.00 2.29
2768 5270 6.816136 TGTAGATCCATTTGTCGTCATACAT 58.184 36.000 0.00 0.00 0.00 2.29
2769 5271 7.272244 TGTAGATCCATTTGTCGTCATACATT 58.728 34.615 0.00 0.00 0.00 2.71
2770 5272 7.768582 TGTAGATCCATTTGTCGTCATACATTT 59.231 33.333 0.00 0.00 0.00 2.32
2771 5273 7.019774 AGATCCATTTGTCGTCATACATTTG 57.980 36.000 0.00 0.00 0.00 2.32
2772 5274 6.599244 AGATCCATTTGTCGTCATACATTTGT 59.401 34.615 0.00 0.00 0.00 2.83
2773 5275 7.768582 AGATCCATTTGTCGTCATACATTTGTA 59.231 33.333 0.00 0.00 34.67 2.41
2774 5276 7.674471 TCCATTTGTCGTCATACATTTGTAA 57.326 32.000 0.00 0.00 33.76 2.41
2775 5277 8.275015 TCCATTTGTCGTCATACATTTGTAAT 57.725 30.769 0.00 0.00 33.76 1.89
2776 5278 8.735315 TCCATTTGTCGTCATACATTTGTAATT 58.265 29.630 0.00 0.00 33.76 1.40
2777 5279 9.352784 CCATTTGTCGTCATACATTTGTAATTT 57.647 29.630 0.00 0.00 33.76 1.82
2799 5301 8.874745 ATTTTAGAAACGACAAATGTATGACG 57.125 30.769 0.00 0.00 42.63 4.35
2800 5302 7.640616 TTTAGAAACGACAAATGTATGACGA 57.359 32.000 6.21 0.00 40.11 4.20
2801 5303 5.511088 AGAAACGACAAATGTATGACGAC 57.489 39.130 6.21 0.00 40.11 4.34
2802 5304 5.227908 AGAAACGACAAATGTATGACGACT 58.772 37.500 6.21 1.10 40.11 4.18
2803 5305 5.345202 AGAAACGACAAATGTATGACGACTC 59.655 40.000 6.21 2.84 40.11 3.36
2804 5306 3.168963 ACGACAAATGTATGACGACTCG 58.831 45.455 6.21 0.00 40.11 4.18
2805 5307 3.120095 ACGACAAATGTATGACGACTCGA 60.120 43.478 5.20 0.00 40.11 4.04
2806 5308 3.849708 CGACAAATGTATGACGACTCGAA 59.150 43.478 5.20 0.00 40.11 3.71
2807 5309 4.258899 CGACAAATGTATGACGACTCGAAC 60.259 45.833 5.20 0.00 40.11 3.95
2808 5310 4.806330 ACAAATGTATGACGACTCGAACT 58.194 39.130 5.20 0.00 0.00 3.01
2809 5311 4.857588 ACAAATGTATGACGACTCGAACTC 59.142 41.667 5.20 0.00 0.00 3.01
2810 5312 4.696899 AATGTATGACGACTCGAACTCA 57.303 40.909 5.20 0.00 0.00 3.41
2811 5313 3.741805 TGTATGACGACTCGAACTCAG 57.258 47.619 5.20 0.00 0.00 3.35
2812 5314 2.418976 TGTATGACGACTCGAACTCAGG 59.581 50.000 5.20 0.00 0.00 3.86
2813 5315 1.535833 ATGACGACTCGAACTCAGGT 58.464 50.000 5.20 0.00 0.00 4.00
2814 5316 2.174363 TGACGACTCGAACTCAGGTA 57.826 50.000 5.20 0.00 0.00 3.08
2815 5317 2.708051 TGACGACTCGAACTCAGGTAT 58.292 47.619 5.20 0.00 0.00 2.73
2816 5318 3.865446 TGACGACTCGAACTCAGGTATA 58.135 45.455 5.20 0.00 0.00 1.47
2817 5319 4.449131 TGACGACTCGAACTCAGGTATAT 58.551 43.478 5.20 0.00 0.00 0.86
2818 5320 4.510711 TGACGACTCGAACTCAGGTATATC 59.489 45.833 5.20 0.00 0.00 1.63
2819 5321 4.706035 ACGACTCGAACTCAGGTATATCT 58.294 43.478 5.20 0.00 0.00 1.98
2820 5322 5.124645 ACGACTCGAACTCAGGTATATCTT 58.875 41.667 5.20 0.00 0.00 2.40
2821 5323 5.589452 ACGACTCGAACTCAGGTATATCTTT 59.411 40.000 5.20 0.00 0.00 2.52
2822 5324 5.910166 CGACTCGAACTCAGGTATATCTTTG 59.090 44.000 0.00 0.00 0.00 2.77
2823 5325 6.238402 CGACTCGAACTCAGGTATATCTTTGA 60.238 42.308 0.00 0.00 0.00 2.69
2824 5326 7.406031 ACTCGAACTCAGGTATATCTTTGAA 57.594 36.000 0.00 0.00 0.00 2.69
2825 5327 7.837863 ACTCGAACTCAGGTATATCTTTGAAA 58.162 34.615 0.00 0.00 0.00 2.69
2826 5328 7.976734 ACTCGAACTCAGGTATATCTTTGAAAG 59.023 37.037 0.00 0.00 0.00 2.62
2827 5329 8.063200 TCGAACTCAGGTATATCTTTGAAAGA 57.937 34.615 10.39 10.39 42.69 2.52
2840 5342 7.951347 ATCTTTGAAAGATGGTTCAGCTAAT 57.049 32.000 18.83 0.00 46.16 1.73
2841 5343 7.383102 TCTTTGAAAGATGGTTCAGCTAATC 57.617 36.000 3.02 0.00 38.69 1.75
2842 5344 6.942005 TCTTTGAAAGATGGTTCAGCTAATCA 59.058 34.615 3.02 0.00 38.69 2.57
2843 5345 6.500684 TTGAAAGATGGTTCAGCTAATCAC 57.499 37.500 0.00 0.00 38.69 3.06
2844 5346 5.809001 TGAAAGATGGTTCAGCTAATCACT 58.191 37.500 0.00 0.00 32.56 3.41
2845 5347 6.240894 TGAAAGATGGTTCAGCTAATCACTT 58.759 36.000 0.00 0.00 32.56 3.16
2846 5348 6.372659 TGAAAGATGGTTCAGCTAATCACTTC 59.627 38.462 0.00 0.00 32.56 3.01
2847 5349 5.426689 AGATGGTTCAGCTAATCACTTCA 57.573 39.130 0.00 0.00 28.71 3.02
2848 5350 5.426504 AGATGGTTCAGCTAATCACTTCAG 58.573 41.667 0.00 0.00 28.71 3.02
2849 5351 3.338249 TGGTTCAGCTAATCACTTCAGC 58.662 45.455 0.00 0.00 35.49 4.26
2850 5352 2.680339 GGTTCAGCTAATCACTTCAGCC 59.320 50.000 0.00 0.00 35.88 4.85
2851 5353 2.680339 GTTCAGCTAATCACTTCAGCCC 59.320 50.000 0.00 0.00 35.88 5.19
2852 5354 1.134699 TCAGCTAATCACTTCAGCCCG 60.135 52.381 0.00 0.00 35.88 6.13
2853 5355 0.462759 AGCTAATCACTTCAGCCCGC 60.463 55.000 0.00 0.00 35.88 6.13
2854 5356 0.744414 GCTAATCACTTCAGCCCGCA 60.744 55.000 0.00 0.00 0.00 5.69
2855 5357 1.293924 CTAATCACTTCAGCCCGCAG 58.706 55.000 0.00 0.00 0.00 5.18
2856 5358 0.901827 TAATCACTTCAGCCCGCAGA 59.098 50.000 0.00 0.00 0.00 4.26
2857 5359 0.254178 AATCACTTCAGCCCGCAGAT 59.746 50.000 0.00 0.00 0.00 2.90
2858 5360 0.179062 ATCACTTCAGCCCGCAGATC 60.179 55.000 0.00 0.00 0.00 2.75
2859 5361 2.169789 CACTTCAGCCCGCAGATCG 61.170 63.158 0.00 0.00 38.08 3.69
2860 5362 3.267860 CTTCAGCCCGCAGATCGC 61.268 66.667 0.23 0.23 36.73 4.58
2861 5363 3.729965 CTTCAGCCCGCAGATCGCT 62.730 63.158 7.71 0.00 39.08 4.93
2863 5365 4.827087 CAGCCCGCAGATCGCTGT 62.827 66.667 10.39 0.00 43.98 4.40
2872 5374 3.375911 GCAGATCGCTGTGACTAAAAC 57.624 47.619 0.00 0.00 44.17 2.43
2873 5375 2.222596 GCAGATCGCTGTGACTAAAACG 60.223 50.000 0.00 0.00 44.17 3.60
2874 5376 3.242518 CAGATCGCTGTGACTAAAACGA 58.757 45.455 0.00 0.00 37.37 3.85
2875 5377 3.673338 CAGATCGCTGTGACTAAAACGAA 59.327 43.478 0.00 0.00 37.37 3.85
2876 5378 3.673809 AGATCGCTGTGACTAAAACGAAC 59.326 43.478 0.00 0.00 32.79 3.95
2877 5379 2.811855 TCGCTGTGACTAAAACGAACA 58.188 42.857 0.00 0.00 0.00 3.18
2878 5380 2.536803 TCGCTGTGACTAAAACGAACAC 59.463 45.455 0.00 0.00 0.00 3.32
2879 5381 2.655577 CGCTGTGACTAAAACGAACACG 60.656 50.000 0.00 0.00 34.72 4.49
2880 5382 2.536803 GCTGTGACTAAAACGAACACGA 59.463 45.455 0.00 0.00 34.72 4.35
2881 5383 3.000523 GCTGTGACTAAAACGAACACGAA 59.999 43.478 0.00 0.00 34.72 3.85
2882 5384 4.502558 CTGTGACTAAAACGAACACGAAC 58.497 43.478 0.00 0.00 34.72 3.95
2883 5385 3.925299 TGTGACTAAAACGAACACGAACA 59.075 39.130 0.00 0.00 34.72 3.18
2884 5386 4.201608 TGTGACTAAAACGAACACGAACAC 60.202 41.667 0.00 0.00 34.72 3.32
2885 5387 4.032104 GTGACTAAAACGAACACGAACACT 59.968 41.667 0.00 0.00 0.00 3.55
2886 5388 4.626604 TGACTAAAACGAACACGAACACTT 59.373 37.500 0.00 0.00 0.00 3.16
2887 5389 5.804473 TGACTAAAACGAACACGAACACTTA 59.196 36.000 0.00 0.00 0.00 2.24
2888 5390 6.309980 TGACTAAAACGAACACGAACACTTAA 59.690 34.615 0.00 0.00 0.00 1.85
2889 5391 7.059448 ACTAAAACGAACACGAACACTTAAA 57.941 32.000 0.00 0.00 0.00 1.52
2890 5392 7.175410 ACTAAAACGAACACGAACACTTAAAG 58.825 34.615 0.00 0.00 0.00 1.85
2891 5393 5.783100 AAACGAACACGAACACTTAAAGA 57.217 34.783 0.00 0.00 0.00 2.52
2892 5394 5.783100 AACGAACACGAACACTTAAAGAA 57.217 34.783 0.00 0.00 0.00 2.52
2893 5395 5.134978 ACGAACACGAACACTTAAAGAAC 57.865 39.130 0.00 0.00 0.00 3.01
2894 5396 4.866486 ACGAACACGAACACTTAAAGAACT 59.134 37.500 0.00 0.00 0.00 3.01
2895 5397 6.035843 ACGAACACGAACACTTAAAGAACTA 58.964 36.000 0.00 0.00 0.00 2.24
2896 5398 6.698766 ACGAACACGAACACTTAAAGAACTAT 59.301 34.615 0.00 0.00 0.00 2.12
2897 5399 7.223387 ACGAACACGAACACTTAAAGAACTATT 59.777 33.333 0.00 0.00 0.00 1.73
2898 5400 7.526186 CGAACACGAACACTTAAAGAACTATTG 59.474 37.037 0.00 0.00 0.00 1.90
2899 5401 8.428186 AACACGAACACTTAAAGAACTATTGA 57.572 30.769 0.00 0.00 0.00 2.57
2900 5402 8.428186 ACACGAACACTTAAAGAACTATTGAA 57.572 30.769 0.00 0.00 0.00 2.69
2901 5403 8.548721 ACACGAACACTTAAAGAACTATTGAAG 58.451 33.333 0.00 0.00 0.00 3.02
2902 5404 7.530861 CACGAACACTTAAAGAACTATTGAAGC 59.469 37.037 0.00 0.00 0.00 3.86
2903 5405 7.015877 CGAACACTTAAAGAACTATTGAAGCC 58.984 38.462 0.00 0.00 0.00 4.35
2904 5406 6.481954 ACACTTAAAGAACTATTGAAGCCG 57.518 37.500 0.00 0.00 0.00 5.52
2905 5407 5.106673 ACACTTAAAGAACTATTGAAGCCGC 60.107 40.000 0.00 0.00 0.00 6.53
2906 5408 4.092968 ACTTAAAGAACTATTGAAGCCGCG 59.907 41.667 0.00 0.00 0.00 6.46
2907 5409 2.094762 AAGAACTATTGAAGCCGCGT 57.905 45.000 4.92 0.00 0.00 6.01
2908 5410 2.094762 AGAACTATTGAAGCCGCGTT 57.905 45.000 4.92 0.00 0.00 4.84
2909 5411 3.241067 AGAACTATTGAAGCCGCGTTA 57.759 42.857 4.92 0.00 0.00 3.18
2910 5412 3.793559 AGAACTATTGAAGCCGCGTTAT 58.206 40.909 4.92 0.00 0.00 1.89
2911 5413 4.189231 AGAACTATTGAAGCCGCGTTATT 58.811 39.130 4.92 0.00 0.00 1.40
2912 5414 4.634443 AGAACTATTGAAGCCGCGTTATTT 59.366 37.500 4.92 0.00 0.00 1.40
2913 5415 5.813672 AGAACTATTGAAGCCGCGTTATTTA 59.186 36.000 4.92 0.00 0.00 1.40
2914 5416 6.482308 AGAACTATTGAAGCCGCGTTATTTAT 59.518 34.615 4.92 0.00 0.00 1.40
2915 5417 6.613755 ACTATTGAAGCCGCGTTATTTATT 57.386 33.333 4.92 0.00 0.00 1.40
2916 5418 7.718272 ACTATTGAAGCCGCGTTATTTATTA 57.282 32.000 4.92 0.00 0.00 0.98
2917 5419 7.570161 ACTATTGAAGCCGCGTTATTTATTAC 58.430 34.615 4.92 0.00 0.00 1.89
2918 5420 4.440851 TGAAGCCGCGTTATTTATTACG 57.559 40.909 4.92 0.00 40.55 3.18
2931 5433 8.466026 CGTTATTTATTACGCAATAAACCTTGC 58.534 33.333 14.28 0.00 45.05 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 1.004745 GAGCTCCCCCATTGAAAGTCA 59.995 52.381 0.87 0.00 0.00 3.41
59 60 7.221452 GCCATGAAAGCATCAACTATACTTTTG 59.779 37.037 0.00 0.00 42.54 2.44
60 61 7.093814 TGCCATGAAAGCATCAACTATACTTTT 60.094 33.333 0.00 0.00 42.54 2.27
61 62 6.377996 TGCCATGAAAGCATCAACTATACTTT 59.622 34.615 0.00 0.00 42.54 2.66
142 144 7.946207 TGGCAAGAGAAGTAGTCTTATATGAG 58.054 38.462 0.00 0.00 36.41 2.90
272 276 6.020201 TGCGATATCACACGTGTAATACAAAG 60.020 38.462 22.90 10.06 0.00 2.77
295 299 5.277297 GCCAAAGGTTGTGTTAAGAAAATGC 60.277 40.000 0.00 0.00 0.00 3.56
302 307 6.048509 AGAATTTGCCAAAGGTTGTGTTAAG 58.951 36.000 0.00 0.00 0.00 1.85
363 368 3.065371 GTGGAGATAAGAATTTGCCACGG 59.935 47.826 0.00 0.00 35.53 4.94
557 562 4.759096 GCGACGTGCATTGCCCAC 62.759 66.667 6.12 0.00 45.45 4.61
593 598 8.347771 CCTTAGTCATGAACCATGTATGATTTG 58.652 37.037 0.00 0.00 41.98 2.32
738 821 7.281100 GGGATTTGATTAGTCCAACAACTCTAG 59.719 40.741 0.00 0.00 33.62 2.43
818 991 4.937201 AACTTGGAAAAATCAGTCCACC 57.063 40.909 0.00 0.00 43.67 4.61
839 1012 3.066900 CACGTTGTTGTACCCAATGGAAA 59.933 43.478 0.00 0.00 33.96 3.13
892 1072 2.916502 AAACCGCTGACGTGTGCTCA 62.917 55.000 0.00 0.00 37.70 4.26
936 1121 6.183360 GGATTGTGAATCGACTAGATAATGCG 60.183 42.308 0.00 0.00 38.98 4.73
953 1138 3.486383 GTGTGGGAAGAAAGGATTGTGA 58.514 45.455 0.00 0.00 0.00 3.58
972 1160 4.096984 ACTTGTTGAAGCTTCTTCAAGGTG 59.903 41.667 36.44 25.95 39.53 4.00
1158 2205 2.660064 GGACCTGGCCATGTCGTCT 61.660 63.158 28.15 1.60 32.19 4.18
1218 2265 4.742201 TCGAGCTTGGCGCACTCC 62.742 66.667 10.83 0.00 42.61 3.85
1514 2588 1.002544 CCTGAACAGAGAGAACACCCC 59.997 57.143 3.19 0.00 0.00 4.95
1518 2592 0.687354 GGCCCTGAACAGAGAGAACA 59.313 55.000 3.19 0.00 0.00 3.18
1541 2615 1.671901 GAGGAGCGTGAGGAGGAAGG 61.672 65.000 0.00 0.00 0.00 3.46
1672 2749 1.385206 GGCCCTCCTTCCTCCTCAT 60.385 63.158 0.00 0.00 0.00 2.90
1844 2921 3.248446 TAGAACACCGTGGCTGCCC 62.248 63.158 17.53 6.66 0.00 5.36
1943 3026 0.992802 GAGCGACCACTTGACGAATC 59.007 55.000 0.00 0.00 0.00 2.52
1944 3027 0.732880 CGAGCGACCACTTGACGAAT 60.733 55.000 0.00 0.00 0.00 3.34
1945 3028 1.371267 CGAGCGACCACTTGACGAA 60.371 57.895 0.00 0.00 0.00 3.85
1948 3031 1.071567 GTAGCGAGCGACCACTTGAC 61.072 60.000 0.00 0.00 0.00 3.18
1949 3032 1.211969 GTAGCGAGCGACCACTTGA 59.788 57.895 0.00 0.00 0.00 3.02
2042 3128 4.580580 CCAAAGCCAAGAGAATATACCACC 59.419 45.833 0.00 0.00 0.00 4.61
2045 3131 4.464947 AGCCAAAGCCAAGAGAATATACC 58.535 43.478 0.00 0.00 41.25 2.73
2127 3228 9.106070 GAGTCTTTATTACATTGGAATACGGTT 57.894 33.333 0.56 0.00 0.00 4.44
2128 3229 8.483758 AGAGTCTTTATTACATTGGAATACGGT 58.516 33.333 0.56 0.00 0.00 4.83
2148 3249 9.950496 TCTTTGCTATTCTATGAAAAAGAGTCT 57.050 29.630 0.00 0.00 30.82 3.24
2179 4660 9.755122 GGTAAATAAATTCCCTAGCTATTGGAT 57.245 33.333 11.75 2.34 0.00 3.41
2180 4661 8.955794 AGGTAAATAAATTCCCTAGCTATTGGA 58.044 33.333 7.83 7.83 0.00 3.53
2181 4662 9.588096 AAGGTAAATAAATTCCCTAGCTATTGG 57.412 33.333 0.00 0.00 0.00 3.16
2190 4671 9.555411 AACCAATACAAGGTAAATAAATTCCCT 57.445 29.630 0.00 0.00 38.76 4.20
2214 4695 2.507407 TCTTGTAGGCATGGGGAAAC 57.493 50.000 0.00 0.00 0.00 2.78
2215 4696 3.756082 AATCTTGTAGGCATGGGGAAA 57.244 42.857 0.00 0.00 0.00 3.13
2216 4697 6.297010 GGATATAATCTTGTAGGCATGGGGAA 60.297 42.308 0.00 0.00 0.00 3.97
2217 4698 5.191722 GGATATAATCTTGTAGGCATGGGGA 59.808 44.000 0.00 0.00 0.00 4.81
2218 4699 5.044919 TGGATATAATCTTGTAGGCATGGGG 60.045 44.000 0.00 0.00 0.00 4.96
2219 4700 6.065976 TGGATATAATCTTGTAGGCATGGG 57.934 41.667 0.00 0.00 0.00 4.00
2220 4701 9.334947 CTATTGGATATAATCTTGTAGGCATGG 57.665 37.037 0.00 0.00 0.00 3.66
2221 4702 8.834465 GCTATTGGATATAATCTTGTAGGCATG 58.166 37.037 0.00 0.00 0.00 4.06
2222 4703 8.776119 AGCTATTGGATATAATCTTGTAGGCAT 58.224 33.333 0.00 0.00 0.00 4.40
2223 4704 8.150827 AGCTATTGGATATAATCTTGTAGGCA 57.849 34.615 0.00 0.00 0.00 4.75
2224 4705 9.757227 CTAGCTATTGGATATAATCTTGTAGGC 57.243 37.037 0.00 0.00 0.00 3.93
2227 4708 8.705594 GCCCTAGCTATTGGATATAATCTTGTA 58.294 37.037 12.46 0.00 35.50 2.41
2228 4709 7.182749 TGCCCTAGCTATTGGATATAATCTTGT 59.817 37.037 12.46 0.00 40.80 3.16
2229 4710 7.568349 TGCCCTAGCTATTGGATATAATCTTG 58.432 38.462 12.46 0.00 40.80 3.02
2230 4711 7.755666 TGCCCTAGCTATTGGATATAATCTT 57.244 36.000 12.46 0.00 40.80 2.40
2231 4712 7.755666 TTGCCCTAGCTATTGGATATAATCT 57.244 36.000 12.46 0.00 40.80 2.40
2232 4713 7.040823 GCATTGCCCTAGCTATTGGATATAATC 60.041 40.741 12.46 0.00 40.80 1.75
2233 4714 6.774656 GCATTGCCCTAGCTATTGGATATAAT 59.225 38.462 12.46 5.32 40.80 1.28
2234 4715 6.122277 GCATTGCCCTAGCTATTGGATATAA 58.878 40.000 12.46 3.63 40.80 0.98
2235 4716 5.191522 TGCATTGCCCTAGCTATTGGATATA 59.808 40.000 12.46 0.00 40.80 0.86
2236 4717 4.018141 TGCATTGCCCTAGCTATTGGATAT 60.018 41.667 12.46 3.33 40.80 1.63
2237 4718 3.330405 TGCATTGCCCTAGCTATTGGATA 59.670 43.478 12.46 1.40 40.80 2.59
2238 4719 2.108776 TGCATTGCCCTAGCTATTGGAT 59.891 45.455 12.46 0.00 40.80 3.41
2239 4720 1.494296 TGCATTGCCCTAGCTATTGGA 59.506 47.619 12.46 0.00 40.80 3.53
2240 4721 1.610522 GTGCATTGCCCTAGCTATTGG 59.389 52.381 6.12 0.00 40.80 3.16
2241 4722 2.300433 TGTGCATTGCCCTAGCTATTG 58.700 47.619 6.12 0.00 40.80 1.90
2242 4723 2.734755 TGTGCATTGCCCTAGCTATT 57.265 45.000 6.12 0.00 40.80 1.73
2243 4724 2.787994 GATGTGCATTGCCCTAGCTAT 58.212 47.619 6.12 0.00 40.80 2.97
2244 4725 1.541015 CGATGTGCATTGCCCTAGCTA 60.541 52.381 6.12 0.00 40.80 3.32
2245 4726 0.816825 CGATGTGCATTGCCCTAGCT 60.817 55.000 6.12 0.00 40.80 3.32
2246 4727 1.650912 CGATGTGCATTGCCCTAGC 59.349 57.895 6.12 0.00 40.48 3.42
2247 4728 1.650912 GCGATGTGCATTGCCCTAG 59.349 57.895 12.20 0.00 45.45 3.02
2248 4729 3.826221 GCGATGTGCATTGCCCTA 58.174 55.556 12.20 0.00 45.45 3.53
2261 4742 5.940192 TTTACATTGTTTGTCTCTGCGAT 57.060 34.783 0.00 0.00 39.87 4.58
2323 4804 9.449719 GATCACTATCTTCAACCCTTCTTTTTA 57.550 33.333 0.00 0.00 0.00 1.52
2350 4840 8.840321 CAAGTCTTCCATTGGGTACAATATAAG 58.160 37.037 2.09 0.00 45.24 1.73
2416 4911 3.927142 CGACACCCTTACTTTCATGACTC 59.073 47.826 0.00 0.00 0.00 3.36
2417 4912 3.323979 ACGACACCCTTACTTTCATGACT 59.676 43.478 0.00 0.00 0.00 3.41
2418 4913 3.660865 ACGACACCCTTACTTTCATGAC 58.339 45.455 0.00 0.00 0.00 3.06
2419 4914 5.232463 GTTACGACACCCTTACTTTCATGA 58.768 41.667 0.00 0.00 0.00 3.07
2420 4915 4.090930 CGTTACGACACCCTTACTTTCATG 59.909 45.833 0.00 0.00 0.00 3.07
2422 4917 3.068024 ACGTTACGACACCCTTACTTTCA 59.932 43.478 13.03 0.00 0.00 2.69
2423 4918 3.426525 CACGTTACGACACCCTTACTTTC 59.573 47.826 13.03 0.00 0.00 2.62
2437 4933 3.433957 TGTCAATCAAATCCCACGTTACG 59.566 43.478 2.19 2.19 0.00 3.18
2514 5012 6.836007 AGATAGGAGGGCCAAGAAATTTAAAG 59.164 38.462 6.18 0.00 36.29 1.85
2518 5016 4.888626 AGATAGGAGGGCCAAGAAATTT 57.111 40.909 6.18 0.00 36.29 1.82
2535 5033 6.296803 TGGTCGAGCAGAGTTAGATTAGATA 58.703 40.000 14.39 0.00 0.00 1.98
2552 5050 8.765219 CCAAATTAATATGTAACTCTGGTCGAG 58.235 37.037 0.00 0.00 45.56 4.04
2611 5109 9.057365 GCTCATAAATTTGCAAAAACATTCATG 57.943 29.630 17.19 7.90 0.00 3.07
2617 5115 9.798994 AAAATTGCTCATAAATTTGCAAAAACA 57.201 22.222 17.19 4.20 46.31 2.83
2636 5134 8.508875 AGAATTGATTGTGATTCCAAAAATTGC 58.491 29.630 11.86 0.00 33.72 3.56
2645 5143 9.211485 ACAAATTGAAGAATTGATTGTGATTCC 57.789 29.630 0.00 0.00 33.72 3.01
2648 5146 9.767228 TTCACAAATTGAAGAATTGATTGTGAT 57.233 25.926 16.28 0.00 41.75 3.06
2650 5148 7.999878 CGTTCACAAATTGAAGAATTGATTGTG 59.000 33.333 0.00 8.91 45.23 3.33
2651 5149 7.706179 ACGTTCACAAATTGAAGAATTGATTGT 59.294 29.630 0.00 0.00 45.23 2.71
2655 5153 8.472683 AAAACGTTCACAAATTGAAGAATTGA 57.527 26.923 0.00 0.00 45.23 2.57
2735 5237 6.403866 ACAAATGGATCTACAGCAAAACAA 57.596 33.333 0.00 0.00 0.00 2.83
2736 5238 5.334802 CGACAAATGGATCTACAGCAAAACA 60.335 40.000 0.00 0.00 0.00 2.83
2737 5239 5.088739 CGACAAATGGATCTACAGCAAAAC 58.911 41.667 0.00 0.00 0.00 2.43
2738 5240 4.759693 ACGACAAATGGATCTACAGCAAAA 59.240 37.500 0.00 0.00 0.00 2.44
2739 5241 4.323417 ACGACAAATGGATCTACAGCAAA 58.677 39.130 0.00 0.00 0.00 3.68
2740 5242 3.932710 GACGACAAATGGATCTACAGCAA 59.067 43.478 0.00 0.00 0.00 3.91
2741 5243 3.056179 TGACGACAAATGGATCTACAGCA 60.056 43.478 0.00 0.00 0.00 4.41
2742 5244 3.521560 TGACGACAAATGGATCTACAGC 58.478 45.455 0.00 0.00 0.00 4.40
2743 5245 6.273071 TGTATGACGACAAATGGATCTACAG 58.727 40.000 0.00 0.00 0.00 2.74
2744 5246 6.215495 TGTATGACGACAAATGGATCTACA 57.785 37.500 0.00 0.00 0.00 2.74
2745 5247 7.715265 AATGTATGACGACAAATGGATCTAC 57.285 36.000 0.00 0.00 31.83 2.59
2746 5248 7.768582 ACAAATGTATGACGACAAATGGATCTA 59.231 33.333 0.00 0.00 31.83 1.98
2747 5249 6.599244 ACAAATGTATGACGACAAATGGATCT 59.401 34.615 0.00 0.00 31.83 2.75
2748 5250 6.785191 ACAAATGTATGACGACAAATGGATC 58.215 36.000 0.00 0.00 31.83 3.36
2749 5251 6.757897 ACAAATGTATGACGACAAATGGAT 57.242 33.333 0.00 0.00 31.83 3.41
2750 5252 7.674471 TTACAAATGTATGACGACAAATGGA 57.326 32.000 0.00 0.00 31.83 3.41
2751 5253 8.909708 AATTACAAATGTATGACGACAAATGG 57.090 30.769 0.00 0.00 31.83 3.16
2773 5275 9.325150 CGTCATACATTTGTCGTTTCTAAAATT 57.675 29.630 0.00 0.00 0.00 1.82
2774 5276 8.714179 TCGTCATACATTTGTCGTTTCTAAAAT 58.286 29.630 0.00 0.00 31.55 1.82
2775 5277 8.005466 GTCGTCATACATTTGTCGTTTCTAAAA 58.995 33.333 0.00 0.00 31.55 1.52
2776 5278 7.383029 AGTCGTCATACATTTGTCGTTTCTAAA 59.617 33.333 0.00 0.00 31.55 1.85
2777 5279 6.864685 AGTCGTCATACATTTGTCGTTTCTAA 59.135 34.615 0.00 0.00 31.55 2.10
2778 5280 6.384224 AGTCGTCATACATTTGTCGTTTCTA 58.616 36.000 0.00 0.00 31.55 2.10
2779 5281 5.227908 AGTCGTCATACATTTGTCGTTTCT 58.772 37.500 0.00 0.00 31.55 2.52
2780 5282 5.511088 AGTCGTCATACATTTGTCGTTTC 57.489 39.130 0.00 0.00 31.55 2.78
2781 5283 4.089493 CGAGTCGTCATACATTTGTCGTTT 59.911 41.667 3.82 0.00 31.55 3.60
2782 5284 3.606777 CGAGTCGTCATACATTTGTCGTT 59.393 43.478 3.82 0.00 31.55 3.85
2783 5285 3.120095 TCGAGTCGTCATACATTTGTCGT 60.120 43.478 13.12 0.00 31.55 4.34
2784 5286 3.422655 TCGAGTCGTCATACATTTGTCG 58.577 45.455 13.12 0.00 0.00 4.35
2785 5287 4.857588 AGTTCGAGTCGTCATACATTTGTC 59.142 41.667 13.12 0.00 0.00 3.18
2786 5288 4.806330 AGTTCGAGTCGTCATACATTTGT 58.194 39.130 13.12 0.00 0.00 2.83
2787 5289 4.857037 TGAGTTCGAGTCGTCATACATTTG 59.143 41.667 13.12 0.00 0.00 2.32
2788 5290 5.055642 TGAGTTCGAGTCGTCATACATTT 57.944 39.130 13.12 0.00 0.00 2.32
2789 5291 4.438880 CCTGAGTTCGAGTCGTCATACATT 60.439 45.833 13.12 0.00 0.00 2.71
2790 5292 3.065510 CCTGAGTTCGAGTCGTCATACAT 59.934 47.826 13.12 0.00 0.00 2.29
2791 5293 2.418976 CCTGAGTTCGAGTCGTCATACA 59.581 50.000 13.12 7.13 0.00 2.29
2792 5294 2.419324 ACCTGAGTTCGAGTCGTCATAC 59.581 50.000 13.12 7.03 0.00 2.39
2793 5295 2.708051 ACCTGAGTTCGAGTCGTCATA 58.292 47.619 13.12 0.00 0.00 2.15
2794 5296 1.535833 ACCTGAGTTCGAGTCGTCAT 58.464 50.000 13.12 0.00 0.00 3.06
2795 5297 2.174363 TACCTGAGTTCGAGTCGTCA 57.826 50.000 13.12 8.24 0.00 4.35
2796 5298 4.751098 AGATATACCTGAGTTCGAGTCGTC 59.249 45.833 13.12 3.44 0.00 4.20
2797 5299 4.706035 AGATATACCTGAGTTCGAGTCGT 58.294 43.478 13.12 0.00 0.00 4.34
2798 5300 5.676532 AAGATATACCTGAGTTCGAGTCG 57.323 43.478 6.09 6.09 0.00 4.18
2799 5301 7.028926 TCAAAGATATACCTGAGTTCGAGTC 57.971 40.000 0.00 0.00 0.00 3.36
2800 5302 7.406031 TTCAAAGATATACCTGAGTTCGAGT 57.594 36.000 0.00 0.00 0.00 4.18
2801 5303 8.191446 TCTTTCAAAGATATACCTGAGTTCGAG 58.809 37.037 0.00 0.00 31.20 4.04
2802 5304 8.063200 TCTTTCAAAGATATACCTGAGTTCGA 57.937 34.615 0.00 0.00 31.20 3.71
2803 5305 8.759641 CATCTTTCAAAGATATACCTGAGTTCG 58.240 37.037 12.46 0.00 46.20 3.95
2804 5306 9.050601 CCATCTTTCAAAGATATACCTGAGTTC 57.949 37.037 12.46 0.00 46.20 3.01
2805 5307 8.552296 ACCATCTTTCAAAGATATACCTGAGTT 58.448 33.333 12.46 0.00 46.20 3.01
2806 5308 8.095452 ACCATCTTTCAAAGATATACCTGAGT 57.905 34.615 12.46 0.00 46.20 3.41
2807 5309 8.970859 AACCATCTTTCAAAGATATACCTGAG 57.029 34.615 12.46 0.00 46.20 3.35
2808 5310 8.548025 TGAACCATCTTTCAAAGATATACCTGA 58.452 33.333 12.46 0.00 46.20 3.86
2809 5311 8.737168 TGAACCATCTTTCAAAGATATACCTG 57.263 34.615 12.46 0.96 46.20 4.00
2810 5312 7.500559 GCTGAACCATCTTTCAAAGATATACCT 59.499 37.037 12.46 0.00 46.20 3.08
2811 5313 7.500559 AGCTGAACCATCTTTCAAAGATATACC 59.499 37.037 12.46 4.05 46.20 2.73
2812 5314 8.443953 AGCTGAACCATCTTTCAAAGATATAC 57.556 34.615 12.46 5.77 46.20 1.47
2814 5316 9.638176 ATTAGCTGAACCATCTTTCAAAGATAT 57.362 29.630 12.46 1.50 46.20 1.63
2815 5317 9.113838 GATTAGCTGAACCATCTTTCAAAGATA 57.886 33.333 12.46 0.00 46.20 1.98
2817 5319 6.942005 TGATTAGCTGAACCATCTTTCAAAGA 59.058 34.615 1.30 1.30 42.69 2.52
2818 5320 7.025963 GTGATTAGCTGAACCATCTTTCAAAG 58.974 38.462 0.00 0.00 35.07 2.77
2819 5321 6.716628 AGTGATTAGCTGAACCATCTTTCAAA 59.283 34.615 0.00 0.00 35.07 2.69
2820 5322 6.240894 AGTGATTAGCTGAACCATCTTTCAA 58.759 36.000 0.00 0.00 35.07 2.69
2821 5323 5.809001 AGTGATTAGCTGAACCATCTTTCA 58.191 37.500 0.00 0.00 34.30 2.69
2822 5324 6.372659 TGAAGTGATTAGCTGAACCATCTTTC 59.627 38.462 0.00 0.00 0.00 2.62
2823 5325 6.240894 TGAAGTGATTAGCTGAACCATCTTT 58.759 36.000 0.00 0.00 0.00 2.52
2824 5326 5.809001 TGAAGTGATTAGCTGAACCATCTT 58.191 37.500 0.00 0.00 0.00 2.40
2825 5327 5.426504 CTGAAGTGATTAGCTGAACCATCT 58.573 41.667 0.00 0.00 0.00 2.90
2826 5328 4.034975 GCTGAAGTGATTAGCTGAACCATC 59.965 45.833 0.00 0.00 34.70 3.51
2827 5329 3.944015 GCTGAAGTGATTAGCTGAACCAT 59.056 43.478 0.00 0.00 34.70 3.55
2828 5330 3.338249 GCTGAAGTGATTAGCTGAACCA 58.662 45.455 0.00 0.00 34.70 3.67
2829 5331 2.680339 GGCTGAAGTGATTAGCTGAACC 59.320 50.000 0.00 0.00 37.58 3.62
2830 5332 2.680339 GGGCTGAAGTGATTAGCTGAAC 59.320 50.000 0.00 0.00 37.58 3.18
2831 5333 2.677902 CGGGCTGAAGTGATTAGCTGAA 60.678 50.000 0.00 0.00 37.58 3.02
2832 5334 1.134699 CGGGCTGAAGTGATTAGCTGA 60.135 52.381 0.00 0.00 37.58 4.26
2833 5335 1.293924 CGGGCTGAAGTGATTAGCTG 58.706 55.000 0.00 0.00 37.58 4.24
2834 5336 0.462759 GCGGGCTGAAGTGATTAGCT 60.463 55.000 0.00 0.00 37.58 3.32
2835 5337 0.744414 TGCGGGCTGAAGTGATTAGC 60.744 55.000 0.00 0.00 36.74 3.09
2836 5338 1.134699 TCTGCGGGCTGAAGTGATTAG 60.135 52.381 0.06 0.00 0.00 1.73
2837 5339 0.901827 TCTGCGGGCTGAAGTGATTA 59.098 50.000 0.06 0.00 0.00 1.75
2838 5340 0.254178 ATCTGCGGGCTGAAGTGATT 59.746 50.000 0.06 0.00 0.00 2.57
2839 5341 0.179062 GATCTGCGGGCTGAAGTGAT 60.179 55.000 0.06 0.00 0.00 3.06
2840 5342 1.219124 GATCTGCGGGCTGAAGTGA 59.781 57.895 0.06 0.00 0.00 3.41
2841 5343 2.169789 CGATCTGCGGGCTGAAGTG 61.170 63.158 0.06 0.00 36.03 3.16
2842 5344 2.185350 CGATCTGCGGGCTGAAGT 59.815 61.111 0.06 0.00 36.03 3.01
2843 5345 3.267860 GCGATCTGCGGGCTGAAG 61.268 66.667 0.00 0.00 41.29 3.02
2852 5354 2.222596 CGTTTTAGTCACAGCGATCTGC 60.223 50.000 1.92 1.92 44.10 4.26
2853 5355 3.242518 TCGTTTTAGTCACAGCGATCTG 58.757 45.455 0.00 0.00 45.71 2.90
2854 5356 3.570926 TCGTTTTAGTCACAGCGATCT 57.429 42.857 0.00 0.00 0.00 2.75
2855 5357 3.427528 TGTTCGTTTTAGTCACAGCGATC 59.572 43.478 0.00 0.00 0.00 3.69
2856 5358 3.183775 GTGTTCGTTTTAGTCACAGCGAT 59.816 43.478 0.00 0.00 0.00 4.58
2857 5359 2.536803 GTGTTCGTTTTAGTCACAGCGA 59.463 45.455 0.00 0.00 0.00 4.93
2858 5360 2.655577 CGTGTTCGTTTTAGTCACAGCG 60.656 50.000 0.00 0.00 0.00 5.18
2859 5361 2.536803 TCGTGTTCGTTTTAGTCACAGC 59.463 45.455 0.00 0.00 38.33 4.40
2860 5362 4.031991 TGTTCGTGTTCGTTTTAGTCACAG 59.968 41.667 0.00 0.00 38.33 3.66
2861 5363 3.925299 TGTTCGTGTTCGTTTTAGTCACA 59.075 39.130 0.00 0.00 38.33 3.58
2862 5364 4.032104 AGTGTTCGTGTTCGTTTTAGTCAC 59.968 41.667 0.00 0.00 38.33 3.67
2863 5365 4.175516 AGTGTTCGTGTTCGTTTTAGTCA 58.824 39.130 0.00 0.00 38.33 3.41
2864 5366 4.766969 AGTGTTCGTGTTCGTTTTAGTC 57.233 40.909 0.00 0.00 38.33 2.59
2865 5367 6.645700 TTAAGTGTTCGTGTTCGTTTTAGT 57.354 33.333 0.00 0.00 38.33 2.24
2866 5368 7.393327 TCTTTAAGTGTTCGTGTTCGTTTTAG 58.607 34.615 0.00 0.00 38.33 1.85
2867 5369 7.288317 TCTTTAAGTGTTCGTGTTCGTTTTA 57.712 32.000 0.00 0.00 38.33 1.52
2868 5370 6.168164 TCTTTAAGTGTTCGTGTTCGTTTT 57.832 33.333 0.00 0.00 38.33 2.43
2869 5371 5.783100 TCTTTAAGTGTTCGTGTTCGTTT 57.217 34.783 0.00 0.00 38.33 3.60
2870 5372 5.349543 AGTTCTTTAAGTGTTCGTGTTCGTT 59.650 36.000 0.00 0.00 38.33 3.85
2871 5373 4.866486 AGTTCTTTAAGTGTTCGTGTTCGT 59.134 37.500 0.00 0.00 38.33 3.85
2872 5374 5.385396 AGTTCTTTAAGTGTTCGTGTTCG 57.615 39.130 0.00 0.00 38.55 3.95
2873 5375 8.545420 TCAATAGTTCTTTAAGTGTTCGTGTTC 58.455 33.333 0.00 0.00 0.00 3.18
2874 5376 8.428186 TCAATAGTTCTTTAAGTGTTCGTGTT 57.572 30.769 0.00 0.00 0.00 3.32
2875 5377 8.428186 TTCAATAGTTCTTTAAGTGTTCGTGT 57.572 30.769 0.00 0.00 0.00 4.49
2876 5378 7.530861 GCTTCAATAGTTCTTTAAGTGTTCGTG 59.469 37.037 0.00 0.00 0.00 4.35
2877 5379 7.307811 GGCTTCAATAGTTCTTTAAGTGTTCGT 60.308 37.037 0.00 0.00 0.00 3.85
2878 5380 7.015877 GGCTTCAATAGTTCTTTAAGTGTTCG 58.984 38.462 0.00 0.00 0.00 3.95
2879 5381 7.015877 CGGCTTCAATAGTTCTTTAAGTGTTC 58.984 38.462 0.00 0.00 0.00 3.18
2880 5382 6.567891 GCGGCTTCAATAGTTCTTTAAGTGTT 60.568 38.462 0.00 0.00 0.00 3.32
2881 5383 5.106673 GCGGCTTCAATAGTTCTTTAAGTGT 60.107 40.000 0.00 0.00 0.00 3.55
2882 5384 5.324697 GCGGCTTCAATAGTTCTTTAAGTG 58.675 41.667 0.00 0.00 0.00 3.16
2883 5385 4.092968 CGCGGCTTCAATAGTTCTTTAAGT 59.907 41.667 0.00 0.00 0.00 2.24
2884 5386 4.092968 ACGCGGCTTCAATAGTTCTTTAAG 59.907 41.667 12.47 0.00 0.00 1.85
2885 5387 3.998341 ACGCGGCTTCAATAGTTCTTTAA 59.002 39.130 12.47 0.00 0.00 1.52
2886 5388 3.592059 ACGCGGCTTCAATAGTTCTTTA 58.408 40.909 12.47 0.00 0.00 1.85
2887 5389 2.423577 ACGCGGCTTCAATAGTTCTTT 58.576 42.857 12.47 0.00 0.00 2.52
2888 5390 2.094762 ACGCGGCTTCAATAGTTCTT 57.905 45.000 12.47 0.00 0.00 2.52
2889 5391 2.094762 AACGCGGCTTCAATAGTTCT 57.905 45.000 12.47 0.00 0.00 3.01
2890 5392 4.531659 AATAACGCGGCTTCAATAGTTC 57.468 40.909 12.47 0.00 0.00 3.01
2891 5393 4.957759 AAATAACGCGGCTTCAATAGTT 57.042 36.364 12.47 0.00 0.00 2.24
2892 5394 6.613755 AATAAATAACGCGGCTTCAATAGT 57.386 33.333 12.47 0.00 0.00 2.12
2893 5395 6.730619 CGTAATAAATAACGCGGCTTCAATAG 59.269 38.462 12.47 0.00 31.66 1.73
2894 5396 6.583160 CGTAATAAATAACGCGGCTTCAATA 58.417 36.000 12.47 0.00 31.66 1.90
2895 5397 5.437263 CGTAATAAATAACGCGGCTTCAAT 58.563 37.500 12.47 0.00 31.66 2.57
2896 5398 4.824301 CGTAATAAATAACGCGGCTTCAA 58.176 39.130 12.47 0.00 31.66 2.69
2897 5399 4.440851 CGTAATAAATAACGCGGCTTCA 57.559 40.909 12.47 0.00 31.66 3.02
2905 5407 8.466026 GCAAGGTTTATTGCGTAATAAATAACG 58.534 33.333 26.87 18.81 45.45 3.18


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

AutoCloner maintained by Alex Coulton.