Multiple sequence alignment - TraesCS6B01G295900

Loading Multiple Alignment...

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 TraesCS6B01G295900 chr6B 100.000 4231 0 0 1 4231 531738080 531733850 0.000000e+00 7814.0
1 TraesCS6B01G295900 chr6B 82.635 167 20 6 4065 4229 56002772 56002931 5.700000e-29 139.0
2 TraesCS6B01G295900 chr6A 95.198 3561 101 17 1 3515 495448412 495444876 0.000000e+00 5565.0
3 TraesCS6B01G295900 chr6A 91.525 413 25 4 3508 3913 495443603 495443194 1.030000e-155 560.0
4 TraesCS6B01G295900 chr6D 95.460 3480 102 20 1 3438 348088198 348091663 0.000000e+00 5500.0
5 TraesCS6B01G295900 chr6D 91.787 414 21 7 3506 3913 348091666 348092072 7.940000e-157 564.0
6 TraesCS6B01G295900 chr4A 81.749 263 25 13 3983 4231 465797947 465797694 9.280000e-47 198.0
7 TraesCS6B01G295900 chr4D 81.028 253 26 13 3980 4218 111135513 111135757 9.340000e-42 182.0
8 TraesCS6B01G295900 chr4B 79.554 269 27 7 3983 4229 299560101 299560363 2.620000e-37 167.0
9 TraesCS6B01G295900 chr4B 78.182 275 31 11 3979 4231 404562514 404562781 9.480000e-32 148.0
10 TraesCS6B01G295900 chr3A 80.269 223 23 3 4024 4231 551761468 551761252 9.480000e-32 148.0
11 TraesCS6B01G295900 chr3A 82.857 105 12 2 4115 4219 144532069 144532167 5.830000e-14 89.8
12 TraesCS6B01G295900 chr2B 85.039 127 11 3 4105 4231 250761418 250761536 5.740000e-24 122.0
13 TraesCS6B01G295900 chr3B 80.870 115 14 4 4105 4219 188228672 188228778 2.710000e-12 84.2


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 TraesCS6B01G295900 chr6B 531733850 531738080 4230 True 7814.0 7814 100.0000 1 4231 1 chr6B.!!$R1 4230
1 TraesCS6B01G295900 chr6A 495443194 495448412 5218 True 3062.5 5565 93.3615 1 3913 2 chr6A.!!$R1 3912
2 TraesCS6B01G295900 chr6D 348088198 348092072 3874 False 3032.0 5500 93.6235 1 3913 2 chr6D.!!$F1 3912

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
55 56 2.886523 CTGTTGTTTCCATGCCTTCAGA 59.113 45.455 0.00 0.00 0.00 3.27 F
280 283 4.280929 AGTGCTACTGTCAAGACACACATA 59.719 41.667 18.05 3.07 37.18 2.29 F
1542 1545 2.098770 GGGAAGAGCAATTCATGACAGC 59.901 50.000 0.00 0.00 0.00 4.40 F
2006 2016 0.527113 CAGATGTGGCGCCATTTCAA 59.473 50.000 35.23 16.43 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1542 1545 0.250038 AATCACCGAGCATCATCCCG 60.250 55.000 0.00 0.0 33.17 5.14 R
1707 1710 1.342076 TGCCTCCCGTCTATCTCTTGT 60.342 52.381 0.00 0.0 0.00 3.16 R
3188 3230 0.320247 GGTGCTCCATCTCCATAGCG 60.320 60.000 0.00 0.0 37.80 4.26 R
3965 5305 0.106335 TAAAGGAAACACCGGCGTCA 59.894 50.000 6.01 0.0 44.74 4.35 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 2.886523 CTGTTGTTTCCATGCCTTCAGA 59.113 45.455 0.00 0.00 0.00 3.27
91 92 6.437928 CAGTTACATTTTGCTTGCTAGTTCA 58.562 36.000 0.00 0.00 0.00 3.18
92 93 6.580041 CAGTTACATTTTGCTTGCTAGTTCAG 59.420 38.462 0.00 0.00 0.00 3.02
118 119 6.068971 ACCATAGTCTTCTCTAGTCCCTACAA 60.069 42.308 0.00 0.00 0.00 2.41
186 188 6.148480 AGCTACTAGTTTCTGAGCAACATTTG 59.852 38.462 15.22 0.00 35.55 2.32
280 283 4.280929 AGTGCTACTGTCAAGACACACATA 59.719 41.667 18.05 3.07 37.18 2.29
281 284 5.047021 AGTGCTACTGTCAAGACACACATAT 60.047 40.000 18.05 2.19 37.18 1.78
475 478 7.255139 GGTCACTACCCATGATTTTGTATTAGC 60.255 40.741 0.00 0.00 40.21 3.09
843 846 7.288560 AGATCCAAGCTATTTCAGTTGATCAT 58.711 34.615 0.00 0.00 0.00 2.45
986 989 9.567776 TTGTTGTTTTAGATATTGAGTGAAGGA 57.432 29.630 0.00 0.00 0.00 3.36
1542 1545 2.098770 GGGAAGAGCAATTCATGACAGC 59.901 50.000 0.00 0.00 0.00 4.40
1707 1710 5.841237 AGTAGGAGCTGCAGGAAATATTCTA 59.159 40.000 17.12 0.00 0.00 2.10
1885 1888 5.467399 CCTACGAAGGTTTGTTCAACACATA 59.533 40.000 0.00 0.00 38.19 2.29
1893 1896 9.520515 AAGGTTTGTTCAACACATATTCTCTAT 57.479 29.630 0.00 0.00 37.07 1.98
1968 1978 7.812191 GGCAACTAATCACATGTACAAAATTCA 59.188 33.333 0.00 0.00 0.00 2.57
1969 1979 9.357652 GCAACTAATCACATGTACAAAATTCAT 57.642 29.630 0.00 0.00 0.00 2.57
2006 2016 0.527113 CAGATGTGGCGCCATTTCAA 59.473 50.000 35.23 16.43 0.00 2.69
2018 2028 4.624015 CGCCATTTCAATATGAAGCCAAT 58.376 39.130 0.00 0.00 37.70 3.16
2052 2062 8.594550 TCTAAGAGTATAAAAAGAACCACTGCT 58.405 33.333 0.00 0.00 0.00 4.24
2078 2088 4.338118 TGGCACTTAGAAGGTCAAAACAAG 59.662 41.667 0.00 0.00 0.00 3.16
2079 2089 4.338400 GGCACTTAGAAGGTCAAAACAAGT 59.662 41.667 0.00 0.00 0.00 3.16
2081 2091 5.738370 CACTTAGAAGGTCAAAACAAGTCG 58.262 41.667 0.00 0.00 0.00 4.18
2090 2100 4.796830 GGTCAAAACAAGTCGGAACTTTTC 59.203 41.667 0.00 0.00 43.28 2.29
2091 2101 5.395642 GTCAAAACAAGTCGGAACTTTTCA 58.604 37.500 0.00 0.00 43.28 2.69
2092 2102 6.033966 GTCAAAACAAGTCGGAACTTTTCAT 58.966 36.000 0.00 0.00 43.28 2.57
2096 2106 8.865001 CAAAACAAGTCGGAACTTTTCATTAAA 58.135 29.630 0.00 0.00 43.28 1.52
2097 2107 8.989653 AAACAAGTCGGAACTTTTCATTAAAA 57.010 26.923 0.00 0.00 43.28 1.52
2098 2108 8.989653 AACAAGTCGGAACTTTTCATTAAAAA 57.010 26.923 0.00 0.00 43.28 1.94
2141 2151 5.232838 CAGCAAGCTTTTACAAAGTTTCCTG 59.767 40.000 0.00 3.32 0.00 3.86
2256 2273 7.162761 TCTCGGTGGATTTAGTTGACAAATTA 58.837 34.615 0.00 0.00 0.00 1.40
2299 2316 9.226606 AGTATCCAAAGACAACAAATTCGAATA 57.773 29.630 11.83 0.00 0.00 1.75
2452 2494 4.574421 TGATTTGACATACCCAGCATTACG 59.426 41.667 0.00 0.00 0.00 3.18
2502 2544 7.097623 AGAGGTATCTTCAGGCTATCTAAGA 57.902 40.000 0.00 0.00 28.57 2.10
3031 3073 5.574082 TGTTCAACACAAAGGTAACAATCG 58.426 37.500 0.00 0.00 31.99 3.34
3034 3076 4.273969 TCAACACAAAGGTAACAATCGGAC 59.726 41.667 0.00 0.00 41.41 4.79
3054 3096 5.559035 CGGACTTCTTTACTCAAAGCAACAG 60.559 44.000 0.00 0.00 40.89 3.16
3429 3474 4.098501 ACACTCGCTGTAATGATCTGATGA 59.901 41.667 0.00 0.00 0.00 2.92
3470 3515 2.632996 GGCACTATCACCCACTGCTATA 59.367 50.000 0.00 0.00 0.00 1.31
3484 3533 5.104900 CCACTGCTATATCCATTACTACCCC 60.105 48.000 0.00 0.00 0.00 4.95
3497 3546 6.490040 CCATTACTACCCCCTTTGATTGTATG 59.510 42.308 0.00 0.00 0.00 2.39
3594 4925 3.135530 AGATGGGACTGGTGCTTTAGATC 59.864 47.826 0.00 0.00 0.00 2.75
3612 4943 0.474854 TCCTTACCACCTTGAGCCCA 60.475 55.000 0.00 0.00 0.00 5.36
3613 4944 0.625849 CCTTACCACCTTGAGCCCAT 59.374 55.000 0.00 0.00 0.00 4.00
3614 4945 1.408822 CCTTACCACCTTGAGCCCATC 60.409 57.143 0.00 0.00 0.00 3.51
3680 5015 1.594021 CACCCGCTGCACGCATATA 60.594 57.895 0.00 0.00 41.76 0.86
3736 5071 8.735692 TCTGATTGTGAGTAATGCAATTGATA 57.264 30.769 10.34 0.00 36.99 2.15
3767 5102 5.603813 GGGGTGGTATTAGTATTACCAGTCA 59.396 44.000 19.64 0.99 43.69 3.41
3891 5231 1.134461 CAGGATCTGCCAGGACTTCAG 60.134 57.143 0.00 0.00 40.02 3.02
3901 5241 2.634940 CCAGGACTTCAGTCTTCAGGAA 59.365 50.000 6.91 0.00 44.20 3.36
3904 5244 4.039730 CAGGACTTCAGTCTTCAGGAAAGA 59.960 45.833 6.91 0.00 44.20 2.52
3913 5253 3.187432 GTCTTCAGGAAAGAAAGAAGGCG 59.813 47.826 0.00 0.00 45.50 5.52
3914 5254 3.071023 TCTTCAGGAAAGAAAGAAGGCGA 59.929 43.478 0.00 0.00 41.10 5.54
3915 5255 3.703001 TCAGGAAAGAAAGAAGGCGAT 57.297 42.857 0.00 0.00 0.00 4.58
3916 5256 3.338249 TCAGGAAAGAAAGAAGGCGATG 58.662 45.455 0.00 0.00 0.00 3.84
3917 5257 2.087646 AGGAAAGAAAGAAGGCGATGC 58.912 47.619 0.00 0.00 0.00 3.91
3928 5268 3.857854 GCGATGCCACTGACTGCG 61.858 66.667 0.00 0.00 0.00 5.18
3929 5269 3.190849 CGATGCCACTGACTGCGG 61.191 66.667 0.00 0.00 0.00 5.69
3930 5270 2.046892 GATGCCACTGACTGCGGT 60.047 61.111 0.00 0.00 0.00 5.68
3952 5292 3.460144 GGCGGACGAAAAGAGTCG 58.540 61.111 0.00 0.00 46.54 4.18
3959 5299 1.407329 CGAAAAGAGTCGTCGTGCG 59.593 57.895 5.95 0.00 43.01 5.34
3960 5300 1.128015 GAAAAGAGTCGTCGTGCGC 59.872 57.895 0.00 0.00 41.07 6.09
3961 5301 2.515901 GAAAAGAGTCGTCGTGCGCG 62.516 60.000 14.79 14.79 41.07 6.86
3962 5302 3.818982 AAAGAGTCGTCGTGCGCGT 62.819 57.895 20.50 0.00 41.07 6.01
3963 5303 4.738345 AGAGTCGTCGTGCGCGTC 62.738 66.667 20.50 13.51 41.07 5.19
3964 5304 4.738345 GAGTCGTCGTGCGCGTCT 62.738 66.667 20.50 13.34 41.07 4.18
3965 5305 4.323843 AGTCGTCGTGCGCGTCTT 62.324 61.111 20.50 0.00 41.07 3.01
3966 5306 4.104633 GTCGTCGTGCGCGTCTTG 62.105 66.667 20.50 8.10 41.07 3.02
3967 5307 4.316571 TCGTCGTGCGCGTCTTGA 62.317 61.111 20.50 10.32 41.07 3.02
3968 5308 4.104633 CGTCGTGCGCGTCTTGAC 62.105 66.667 20.50 8.97 39.49 3.18
3969 5309 4.104633 GTCGTGCGCGTCTTGACG 62.105 66.667 20.50 17.53 39.49 4.35
3977 5317 2.660552 CGTCTTGACGCCGGTGTT 60.661 61.111 23.85 5.89 0.00 3.32
3978 5318 2.241880 CGTCTTGACGCCGGTGTTT 61.242 57.895 23.85 0.00 0.00 2.83
3979 5319 1.568025 GTCTTGACGCCGGTGTTTC 59.432 57.895 23.85 11.19 0.00 2.78
3980 5320 1.595929 TCTTGACGCCGGTGTTTCC 60.596 57.895 23.85 10.39 0.00 3.13
3981 5321 1.597027 CTTGACGCCGGTGTTTCCT 60.597 57.895 23.85 0.00 0.00 3.36
3982 5322 1.153127 TTGACGCCGGTGTTTCCTT 60.153 52.632 23.85 0.00 0.00 3.36
3983 5323 0.748729 TTGACGCCGGTGTTTCCTTT 60.749 50.000 23.85 0.00 0.00 3.11
3984 5324 0.106335 TGACGCCGGTGTTTCCTTTA 59.894 50.000 23.85 0.40 0.00 1.85
3985 5325 1.270947 TGACGCCGGTGTTTCCTTTAT 60.271 47.619 23.85 0.00 0.00 1.40
3986 5326 2.028294 TGACGCCGGTGTTTCCTTTATA 60.028 45.455 23.85 0.00 0.00 0.98
3987 5327 3.200483 GACGCCGGTGTTTCCTTTATAT 58.800 45.455 23.85 0.00 0.00 0.86
3988 5328 3.200483 ACGCCGGTGTTTCCTTTATATC 58.800 45.455 16.69 0.00 0.00 1.63
3989 5329 2.220133 CGCCGGTGTTTCCTTTATATCG 59.780 50.000 6.91 0.00 0.00 2.92
3990 5330 2.032290 GCCGGTGTTTCCTTTATATCGC 60.032 50.000 1.90 0.00 0.00 4.58
3991 5331 2.220133 CCGGTGTTTCCTTTATATCGCG 59.780 50.000 0.00 0.00 0.00 5.87
3992 5332 2.220133 CGGTGTTTCCTTTATATCGCGG 59.780 50.000 6.13 0.00 0.00 6.46
3993 5333 3.460103 GGTGTTTCCTTTATATCGCGGA 58.540 45.455 6.13 0.00 0.00 5.54
3994 5334 3.246936 GGTGTTTCCTTTATATCGCGGAC 59.753 47.826 6.13 0.00 0.00 4.79
3995 5335 3.246936 GTGTTTCCTTTATATCGCGGACC 59.753 47.826 6.13 0.00 0.00 4.46
3996 5336 2.427232 TTCCTTTATATCGCGGACCG 57.573 50.000 10.29 10.29 38.61 4.79
3997 5337 1.321474 TCCTTTATATCGCGGACCGT 58.679 50.000 16.73 0.00 38.35 4.83
3998 5338 2.503331 TCCTTTATATCGCGGACCGTA 58.497 47.619 16.73 4.51 38.35 4.02
3999 5339 2.884012 TCCTTTATATCGCGGACCGTAA 59.116 45.455 16.73 4.13 38.35 3.18
4000 5340 3.317711 TCCTTTATATCGCGGACCGTAAA 59.682 43.478 16.73 10.63 38.35 2.01
4001 5341 3.426525 CCTTTATATCGCGGACCGTAAAC 59.573 47.826 16.73 0.00 38.35 2.01
4002 5342 3.988379 TTATATCGCGGACCGTAAACT 57.012 42.857 16.73 0.75 38.35 2.66
4003 5343 5.431420 TTTATATCGCGGACCGTAAACTA 57.569 39.130 16.73 1.30 38.35 2.24
4004 5344 3.988379 ATATCGCGGACCGTAAACTAA 57.012 42.857 16.73 0.00 38.35 2.24
4005 5345 2.199291 ATCGCGGACCGTAAACTAAG 57.801 50.000 16.73 0.00 38.35 2.18
4006 5346 0.881118 TCGCGGACCGTAAACTAAGT 59.119 50.000 16.73 0.00 38.35 2.24
4007 5347 1.269448 TCGCGGACCGTAAACTAAGTT 59.731 47.619 16.73 0.00 38.35 2.66
4008 5348 2.061028 CGCGGACCGTAAACTAAGTTT 58.939 47.619 16.73 0.00 39.24 2.66
4009 5349 3.057876 TCGCGGACCGTAAACTAAGTTTA 60.058 43.478 16.73 0.00 34.55 2.01
4021 5361 5.902051 AACTAAGTTTACAGTTCGCAGAC 57.098 39.130 0.00 0.00 34.32 3.51
4022 5362 4.940463 ACTAAGTTTACAGTTCGCAGACA 58.060 39.130 0.00 0.00 34.32 3.41
4023 5363 4.982916 ACTAAGTTTACAGTTCGCAGACAG 59.017 41.667 0.00 0.00 34.32 3.51
4024 5364 3.728076 AGTTTACAGTTCGCAGACAGA 57.272 42.857 0.00 0.00 34.32 3.41
4025 5365 4.258702 AGTTTACAGTTCGCAGACAGAT 57.741 40.909 0.00 0.00 34.32 2.90
4026 5366 5.386958 AGTTTACAGTTCGCAGACAGATA 57.613 39.130 0.00 0.00 34.32 1.98
4027 5367 5.162075 AGTTTACAGTTCGCAGACAGATAC 58.838 41.667 0.00 0.00 34.32 2.24
4028 5368 2.264109 ACAGTTCGCAGACAGATACG 57.736 50.000 0.00 0.00 34.32 3.06
4029 5369 1.135373 ACAGTTCGCAGACAGATACGG 60.135 52.381 0.00 0.00 34.32 4.02
4030 5370 0.456221 AGTTCGCAGACAGATACGGG 59.544 55.000 0.00 0.00 34.32 5.28
4031 5371 1.141019 TTCGCAGACAGATACGGGC 59.859 57.895 0.00 0.00 34.32 6.13
4032 5372 2.279517 CGCAGACAGATACGGGCC 60.280 66.667 0.00 0.00 0.00 5.80
4033 5373 2.279517 GCAGACAGATACGGGCCG 60.280 66.667 27.06 27.06 0.00 6.13
4034 5374 2.782222 GCAGACAGATACGGGCCGA 61.782 63.158 35.78 17.07 0.00 5.54
4035 5375 1.813859 CAGACAGATACGGGCCGAA 59.186 57.895 35.78 0.00 0.00 4.30
4036 5376 0.174845 CAGACAGATACGGGCCGAAA 59.825 55.000 35.78 20.72 0.00 3.46
4037 5377 0.899720 AGACAGATACGGGCCGAAAA 59.100 50.000 35.78 17.91 0.00 2.29
4038 5378 1.004595 GACAGATACGGGCCGAAAAC 58.995 55.000 35.78 18.30 0.00 2.43
4039 5379 0.322322 ACAGATACGGGCCGAAAACA 59.678 50.000 35.78 12.08 0.00 2.83
4040 5380 1.006832 CAGATACGGGCCGAAAACAG 58.993 55.000 35.78 13.58 0.00 3.16
4041 5381 0.743345 AGATACGGGCCGAAAACAGC 60.743 55.000 35.78 14.12 0.00 4.40
4042 5382 2.032185 GATACGGGCCGAAAACAGCG 62.032 60.000 35.78 2.05 0.00 5.18
4048 5388 3.339731 CCGAAAACAGCGGCAGAA 58.660 55.556 1.45 0.00 42.55 3.02
4049 5389 1.082104 CCGAAAACAGCGGCAGAAC 60.082 57.895 1.45 0.00 42.55 3.01
4050 5390 1.646540 CGAAAACAGCGGCAGAACA 59.353 52.632 1.45 0.00 0.00 3.18
4051 5391 0.384725 CGAAAACAGCGGCAGAACAG 60.385 55.000 1.45 0.00 0.00 3.16
4052 5392 0.944386 GAAAACAGCGGCAGAACAGA 59.056 50.000 1.45 0.00 0.00 3.41
4053 5393 1.333619 GAAAACAGCGGCAGAACAGAA 59.666 47.619 1.45 0.00 0.00 3.02
4054 5394 1.388547 AAACAGCGGCAGAACAGAAA 58.611 45.000 1.45 0.00 0.00 2.52
4055 5395 1.609208 AACAGCGGCAGAACAGAAAT 58.391 45.000 1.45 0.00 0.00 2.17
4056 5396 0.877071 ACAGCGGCAGAACAGAAATG 59.123 50.000 1.45 0.00 0.00 2.32
4057 5397 0.877071 CAGCGGCAGAACAGAAATGT 59.123 50.000 1.45 0.00 0.00 2.71
4058 5398 2.076100 CAGCGGCAGAACAGAAATGTA 58.924 47.619 1.45 0.00 0.00 2.29
4059 5399 2.483877 CAGCGGCAGAACAGAAATGTAA 59.516 45.455 1.45 0.00 0.00 2.41
4060 5400 3.058293 CAGCGGCAGAACAGAAATGTAAA 60.058 43.478 1.45 0.00 0.00 2.01
4061 5401 3.568007 AGCGGCAGAACAGAAATGTAAAA 59.432 39.130 1.45 0.00 0.00 1.52
4062 5402 4.218417 AGCGGCAGAACAGAAATGTAAAAT 59.782 37.500 1.45 0.00 0.00 1.82
4063 5403 4.324402 GCGGCAGAACAGAAATGTAAAATG 59.676 41.667 0.00 0.00 0.00 2.32
4064 5404 5.698832 CGGCAGAACAGAAATGTAAAATGA 58.301 37.500 0.00 0.00 0.00 2.57
4065 5405 6.148948 CGGCAGAACAGAAATGTAAAATGAA 58.851 36.000 0.00 0.00 0.00 2.57
4066 5406 6.088085 CGGCAGAACAGAAATGTAAAATGAAC 59.912 38.462 0.00 0.00 0.00 3.18
4067 5407 6.366061 GGCAGAACAGAAATGTAAAATGAACC 59.634 38.462 0.00 0.00 0.00 3.62
4068 5408 7.147976 GCAGAACAGAAATGTAAAATGAACCT 58.852 34.615 0.00 0.00 0.00 3.50
4069 5409 7.115378 GCAGAACAGAAATGTAAAATGAACCTG 59.885 37.037 0.00 0.00 0.00 4.00
4070 5410 8.137437 CAGAACAGAAATGTAAAATGAACCTGT 58.863 33.333 0.00 0.00 34.28 4.00
4071 5411 9.349713 AGAACAGAAATGTAAAATGAACCTGTA 57.650 29.630 0.00 0.00 32.76 2.74
4072 5412 9.959749 GAACAGAAATGTAAAATGAACCTGTAA 57.040 29.630 0.00 0.00 32.76 2.41
4079 5419 8.980143 ATGTAAAATGAACCTGTAAATTTCGG 57.020 30.769 0.00 0.00 0.00 4.30
4080 5420 8.167605 TGTAAAATGAACCTGTAAATTTCGGA 57.832 30.769 0.00 0.00 0.00 4.55
4081 5421 8.630917 TGTAAAATGAACCTGTAAATTTCGGAA 58.369 29.630 0.00 0.00 0.00 4.30
4082 5422 9.124807 GTAAAATGAACCTGTAAATTTCGGAAG 57.875 33.333 0.00 0.00 0.00 3.46
4083 5423 4.759516 TGAACCTGTAAATTTCGGAAGC 57.240 40.909 0.00 0.00 0.00 3.86
4084 5424 3.187637 TGAACCTGTAAATTTCGGAAGCG 59.812 43.478 0.00 0.00 0.00 4.68
4085 5425 2.081462 ACCTGTAAATTTCGGAAGCGG 58.919 47.619 0.00 0.00 0.00 5.52
4086 5426 2.289819 ACCTGTAAATTTCGGAAGCGGA 60.290 45.455 0.00 0.00 0.00 5.54
4087 5427 2.745281 CCTGTAAATTTCGGAAGCGGAA 59.255 45.455 0.00 0.00 0.00 4.30
4088 5428 3.425758 CCTGTAAATTTCGGAAGCGGAAC 60.426 47.826 0.00 0.00 0.00 3.62
4089 5429 3.404899 TGTAAATTTCGGAAGCGGAACT 58.595 40.909 0.00 0.00 0.00 3.01
4090 5430 3.816523 TGTAAATTTCGGAAGCGGAACTT 59.183 39.130 0.00 0.00 42.98 2.66
4097 5437 3.144285 AAGCGGAACTTCACGGGA 58.856 55.556 0.00 0.00 30.77 5.14
4098 5438 1.004918 AAGCGGAACTTCACGGGAG 60.005 57.895 0.00 0.00 30.77 4.30
4099 5439 1.469335 AAGCGGAACTTCACGGGAGA 61.469 55.000 0.00 0.00 30.77 3.71
4100 5440 1.218316 GCGGAACTTCACGGGAGAT 59.782 57.895 0.00 0.00 0.00 2.75
4101 5441 0.458669 GCGGAACTTCACGGGAGATA 59.541 55.000 0.00 0.00 0.00 1.98
4102 5442 1.068741 GCGGAACTTCACGGGAGATAT 59.931 52.381 0.00 0.00 0.00 1.63
4103 5443 2.862921 GCGGAACTTCACGGGAGATATC 60.863 54.545 0.00 0.00 0.00 1.63
4104 5444 2.604855 CGGAACTTCACGGGAGATATCG 60.605 54.545 0.00 0.00 0.00 2.92
4105 5445 2.621998 GGAACTTCACGGGAGATATCGA 59.378 50.000 0.00 0.00 0.00 3.59
4106 5446 3.067742 GGAACTTCACGGGAGATATCGAA 59.932 47.826 0.00 0.00 0.00 3.71
4107 5447 3.712091 ACTTCACGGGAGATATCGAAC 57.288 47.619 0.00 0.00 0.00 3.95
4108 5448 3.288964 ACTTCACGGGAGATATCGAACT 58.711 45.455 0.00 0.00 0.00 3.01
4109 5449 4.458397 ACTTCACGGGAGATATCGAACTA 58.542 43.478 0.00 0.00 0.00 2.24
4110 5450 4.275443 ACTTCACGGGAGATATCGAACTAC 59.725 45.833 0.00 0.00 0.00 2.73
4111 5451 4.082665 TCACGGGAGATATCGAACTACT 57.917 45.455 0.00 0.00 0.00 2.57
4112 5452 4.458397 TCACGGGAGATATCGAACTACTT 58.542 43.478 0.00 0.00 0.00 2.24
4113 5453 4.514441 TCACGGGAGATATCGAACTACTTC 59.486 45.833 0.00 0.00 0.00 3.01
4114 5454 4.275196 CACGGGAGATATCGAACTACTTCA 59.725 45.833 0.00 0.00 0.00 3.02
4115 5455 4.515944 ACGGGAGATATCGAACTACTTCAG 59.484 45.833 0.00 0.00 0.00 3.02
4116 5456 4.515944 CGGGAGATATCGAACTACTTCAGT 59.484 45.833 0.00 0.00 40.05 3.41
4117 5457 5.561145 CGGGAGATATCGAACTACTTCAGTG 60.561 48.000 0.00 0.00 37.63 3.66
4118 5458 5.299782 GGGAGATATCGAACTACTTCAGTGT 59.700 44.000 0.00 0.00 37.63 3.55
4119 5459 6.183360 GGGAGATATCGAACTACTTCAGTGTT 60.183 42.308 0.00 0.00 37.63 3.32
4120 5460 6.913673 GGAGATATCGAACTACTTCAGTGTTC 59.086 42.308 0.00 10.09 37.63 3.18
4121 5461 7.392494 AGATATCGAACTACTTCAGTGTTCA 57.608 36.000 16.03 8.50 37.63 3.18
4122 5462 8.001881 AGATATCGAACTACTTCAGTGTTCAT 57.998 34.615 16.03 12.40 37.63 2.57
4123 5463 9.121658 AGATATCGAACTACTTCAGTGTTCATA 57.878 33.333 16.03 13.41 37.63 2.15
4124 5464 9.388346 GATATCGAACTACTTCAGTGTTCATAG 57.612 37.037 16.03 6.37 37.63 2.23
4125 5465 6.570672 TCGAACTACTTCAGTGTTCATAGT 57.429 37.500 16.03 0.00 37.63 2.12
4126 5466 7.677454 TCGAACTACTTCAGTGTTCATAGTA 57.323 36.000 16.03 0.00 37.63 1.82
4127 5467 7.524912 TCGAACTACTTCAGTGTTCATAGTAC 58.475 38.462 16.03 0.00 37.63 2.73
4128 5468 7.389884 TCGAACTACTTCAGTGTTCATAGTACT 59.610 37.037 0.00 0.00 37.63 2.73
4129 5469 8.021973 CGAACTACTTCAGTGTTCATAGTACTT 58.978 37.037 0.00 0.00 37.63 2.24
4130 5470 9.130312 GAACTACTTCAGTGTTCATAGTACTTG 57.870 37.037 0.00 0.00 37.63 3.16
4131 5471 8.405418 ACTACTTCAGTGTTCATAGTACTTGA 57.595 34.615 0.00 2.08 35.62 3.02
4132 5472 9.026121 ACTACTTCAGTGTTCATAGTACTTGAT 57.974 33.333 0.00 0.00 35.62 2.57
4133 5473 9.509855 CTACTTCAGTGTTCATAGTACTTGATC 57.490 37.037 0.00 5.16 0.00 2.92
4134 5474 7.896811 ACTTCAGTGTTCATAGTACTTGATCA 58.103 34.615 0.00 7.56 0.00 2.92
4135 5475 8.535335 ACTTCAGTGTTCATAGTACTTGATCAT 58.465 33.333 0.00 0.00 0.00 2.45
4136 5476 8.932945 TTCAGTGTTCATAGTACTTGATCATC 57.067 34.615 0.00 5.91 0.00 2.92
4137 5477 8.066612 TCAGTGTTCATAGTACTTGATCATCA 57.933 34.615 0.00 0.00 0.00 3.07
4138 5478 8.699130 TCAGTGTTCATAGTACTTGATCATCAT 58.301 33.333 0.00 0.05 0.00 2.45
4139 5479 9.971922 CAGTGTTCATAGTACTTGATCATCATA 57.028 33.333 0.00 0.00 0.00 2.15
4140 5480 9.973450 AGTGTTCATAGTACTTGATCATCATAC 57.027 33.333 0.00 0.00 0.00 2.39
4141 5481 9.750125 GTGTTCATAGTACTTGATCATCATACA 57.250 33.333 0.00 2.28 0.00 2.29
4176 5516 9.547753 ACATAGGAGTAGCATATTTGTACAAAG 57.452 33.333 24.22 13.22 33.32 2.77
4177 5517 9.547753 CATAGGAGTAGCATATTTGTACAAAGT 57.452 33.333 24.22 13.78 33.32 2.66
4180 5520 8.978472 AGGAGTAGCATATTTGTACAAAGTAGA 58.022 33.333 24.22 11.27 33.32 2.59
4181 5521 9.765795 GGAGTAGCATATTTGTACAAAGTAGAT 57.234 33.333 24.22 16.74 33.32 1.98
4186 5526 9.890629 AGCATATTTGTACAAAGTAGATCAGAA 57.109 29.630 24.22 0.00 33.32 3.02
4190 5530 7.891183 TTTGTACAAAGTAGATCAGAAGAGC 57.109 36.000 17.01 0.00 0.00 4.09
4191 5531 5.641709 TGTACAAAGTAGATCAGAAGAGCG 58.358 41.667 0.00 0.00 34.73 5.03
4192 5532 4.116747 ACAAAGTAGATCAGAAGAGCGG 57.883 45.455 0.00 0.00 34.73 5.52
4193 5533 2.863137 CAAAGTAGATCAGAAGAGCGGC 59.137 50.000 0.00 0.00 34.73 6.53
4194 5534 0.665835 AGTAGATCAGAAGAGCGGCG 59.334 55.000 0.51 0.51 34.73 6.46
4195 5535 0.318275 GTAGATCAGAAGAGCGGCGG 60.318 60.000 9.78 0.00 34.73 6.13
4196 5536 2.076622 TAGATCAGAAGAGCGGCGGC 62.077 60.000 9.78 8.43 34.73 6.53
4197 5537 4.537433 ATCAGAAGAGCGGCGGCC 62.537 66.667 13.24 9.54 41.24 6.13
4210 5550 4.146075 CGGCCGCCGTAAACCCTA 62.146 66.667 24.08 0.00 42.73 3.53
4211 5551 2.512286 GGCCGCCGTAAACCCTAC 60.512 66.667 0.00 0.00 0.00 3.18
4212 5552 2.580815 GCCGCCGTAAACCCTACT 59.419 61.111 0.00 0.00 0.00 2.57
4213 5553 1.812507 GCCGCCGTAAACCCTACTG 60.813 63.158 0.00 0.00 0.00 2.74
4214 5554 1.593265 CCGCCGTAAACCCTACTGT 59.407 57.895 0.00 0.00 0.00 3.55
4215 5555 0.459063 CCGCCGTAAACCCTACTGTC 60.459 60.000 0.00 0.00 0.00 3.51
4216 5556 0.244450 CGCCGTAAACCCTACTGTCA 59.756 55.000 0.00 0.00 0.00 3.58
4217 5557 1.337074 CGCCGTAAACCCTACTGTCAA 60.337 52.381 0.00 0.00 0.00 3.18
4218 5558 2.769893 GCCGTAAACCCTACTGTCAAA 58.230 47.619 0.00 0.00 0.00 2.69
4219 5559 3.140623 GCCGTAAACCCTACTGTCAAAA 58.859 45.455 0.00 0.00 0.00 2.44
4220 5560 3.754850 GCCGTAAACCCTACTGTCAAAAT 59.245 43.478 0.00 0.00 0.00 1.82
4221 5561 4.216902 GCCGTAAACCCTACTGTCAAAATT 59.783 41.667 0.00 0.00 0.00 1.82
4222 5562 5.278610 GCCGTAAACCCTACTGTCAAAATTT 60.279 40.000 0.00 0.00 0.00 1.82
4223 5563 6.146898 CCGTAAACCCTACTGTCAAAATTTG 58.853 40.000 0.00 0.00 0.00 2.32
4224 5564 6.146898 CGTAAACCCTACTGTCAAAATTTGG 58.853 40.000 5.83 0.00 0.00 3.28
4225 5565 4.600692 AACCCTACTGTCAAAATTTGGC 57.399 40.909 2.97 2.97 35.37 4.52
4226 5566 3.844640 ACCCTACTGTCAAAATTTGGCT 58.155 40.909 11.79 0.00 35.94 4.75
4227 5567 3.826729 ACCCTACTGTCAAAATTTGGCTC 59.173 43.478 11.79 1.52 35.94 4.70
4228 5568 3.826157 CCCTACTGTCAAAATTTGGCTCA 59.174 43.478 11.79 5.65 35.94 4.26
4229 5569 4.321230 CCCTACTGTCAAAATTTGGCTCAC 60.321 45.833 11.79 0.46 35.94 3.51
4230 5570 3.733443 ACTGTCAAAATTTGGCTCACC 57.267 42.857 11.79 0.00 35.94 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 2.949177 TGTAACTGGCATGTGAAGGT 57.051 45.000 0.00 0.00 0.00 3.50
92 93 5.056553 AGGGACTAGAGAAGACTATGGTC 57.943 47.826 0.00 0.00 42.36 4.02
118 119 4.106341 AGTTGGGGTGCTATGCCTATAATT 59.894 41.667 0.00 0.00 0.00 1.40
124 125 0.916358 AGAGTTGGGGTGCTATGCCT 60.916 55.000 0.00 0.00 0.00 4.75
186 188 5.232463 TCTTTTTGCCAGATCAAATGAAGC 58.768 37.500 0.00 0.00 36.04 3.86
336 339 4.949856 AGTTCTCTGAACAAAAGGCAGAAA 59.050 37.500 12.16 0.00 38.12 2.52
383 386 9.734620 CAAGAAATCATAAGTTGTTGAAAGTGA 57.265 29.630 0.00 0.00 36.23 3.41
399 402 6.889301 TTCTCAGAAAGTGCAAGAAATCAT 57.111 33.333 0.00 0.00 0.00 2.45
475 478 5.990668 ACCTTACCAGTTAATAAGCAGAGG 58.009 41.667 0.00 0.00 0.00 3.69
843 846 7.228507 ACAAATGACACAGTAGCATGTTAGAAA 59.771 33.333 0.00 0.00 0.00 2.52
986 989 2.027837 GCAATCATTTTGGCCTCTGGTT 60.028 45.455 3.32 0.00 0.00 3.67
1122 1125 4.849810 TCTTCTATGAAAAAGGAGGGACCA 59.150 41.667 0.00 0.00 42.04 4.02
1448 1451 6.227522 TCACCAAAGATATGTTCTGTCGAAA 58.772 36.000 0.00 0.00 33.93 3.46
1542 1545 0.250038 AATCACCGAGCATCATCCCG 60.250 55.000 0.00 0.00 33.17 5.14
1707 1710 1.342076 TGCCTCCCGTCTATCTCTTGT 60.342 52.381 0.00 0.00 0.00 3.16
1910 1913 8.807118 AGTGATTTATCTGTAACTGTGAGAAGA 58.193 33.333 0.00 0.00 0.00 2.87
1911 1914 8.994429 AGTGATTTATCTGTAACTGTGAGAAG 57.006 34.615 0.00 0.00 0.00 2.85
2050 2060 2.233922 TGACCTTCTAAGTGCCAGTAGC 59.766 50.000 0.00 0.00 44.14 3.58
2052 2062 4.967084 TTTGACCTTCTAAGTGCCAGTA 57.033 40.909 0.00 0.00 0.00 2.74
2060 2070 5.054477 TCCGACTTGTTTTGACCTTCTAAG 58.946 41.667 0.00 0.00 0.00 2.18
2097 2107 8.674263 TTGCTGGTGATGAAAACATAATTTTT 57.326 26.923 0.00 0.00 0.00 1.94
2098 2108 7.095102 GCTTGCTGGTGATGAAAACATAATTTT 60.095 33.333 0.00 0.00 0.00 1.82
2099 2109 6.369615 GCTTGCTGGTGATGAAAACATAATTT 59.630 34.615 0.00 0.00 0.00 1.82
2100 2110 5.870978 GCTTGCTGGTGATGAAAACATAATT 59.129 36.000 0.00 0.00 0.00 1.40
2101 2111 5.186409 AGCTTGCTGGTGATGAAAACATAAT 59.814 36.000 0.00 0.00 0.00 1.28
2141 2151 3.629142 ATTAGGTGGACTGTTGTAGCC 57.371 47.619 0.00 0.00 0.00 3.93
2256 2273 6.545567 TGGATACTAATGATCCATGCACATT 58.454 36.000 0.13 12.33 46.40 2.71
2265 2282 8.506168 TTGTTGTCTTTGGATACTAATGATCC 57.494 34.615 0.00 0.00 42.90 3.36
2299 2316 9.515226 TTTATGCTTCATAAACTAAGGAGTTGT 57.485 29.630 7.65 0.00 45.50 3.32
2441 2483 2.912771 TGGTGATAACGTAATGCTGGG 58.087 47.619 0.00 0.00 0.00 4.45
2452 2494 4.117685 GGATCAGTACGGTTGGTGATAAC 58.882 47.826 0.00 0.00 29.66 1.89
2502 2544 8.805175 TGTCATGATTCCATTTGTCTTATTTGT 58.195 29.630 0.00 0.00 0.00 2.83
2563 2605 5.984725 ACCCGTAATATCACATTCACAAGA 58.015 37.500 0.00 0.00 0.00 3.02
2566 2608 9.263538 GTAATAACCCGTAATATCACATTCACA 57.736 33.333 0.00 0.00 0.00 3.58
2610 2652 1.267261 CCAACTATAGAGGCTCGGTCG 59.733 57.143 9.22 2.24 0.00 4.79
3031 3073 5.527582 TCTGTTGCTTTGAGTAAAGAAGTCC 59.472 40.000 4.10 0.00 44.87 3.85
3034 3076 7.848716 CAATCTGTTGCTTTGAGTAAAGAAG 57.151 36.000 4.10 0.00 44.87 2.85
3054 3096 2.193248 CGGGGAAGAGGGGCAATC 59.807 66.667 0.00 0.00 0.00 2.67
3059 3101 0.540454 GTAGAAACGGGGAAGAGGGG 59.460 60.000 0.00 0.00 0.00 4.79
3152 3194 0.391661 CCAACGCACTGGCATAGACT 60.392 55.000 0.00 0.00 41.24 3.24
3188 3230 0.320247 GGTGCTCCATCTCCATAGCG 60.320 60.000 0.00 0.00 37.80 4.26
3279 3321 9.467258 GTAACGGTAGATGCTAACATAAATACA 57.533 33.333 0.00 0.00 36.35 2.29
3280 3322 8.919661 GGTAACGGTAGATGCTAACATAAATAC 58.080 37.037 0.00 0.00 36.35 1.89
3281 3323 8.640651 TGGTAACGGTAGATGCTAACATAAATA 58.359 33.333 0.00 0.00 36.23 1.40
3282 3324 7.502696 TGGTAACGGTAGATGCTAACATAAAT 58.497 34.615 0.00 0.00 36.23 1.40
3283 3325 6.876155 TGGTAACGGTAGATGCTAACATAAA 58.124 36.000 0.00 0.00 36.23 1.40
3301 3343 6.453092 TCTAGTAAGCTCACACTTTGGTAAC 58.547 40.000 0.00 0.00 0.00 2.50
3395 3437 2.658707 GCGAGTGTGCAAGACGGTC 61.659 63.158 0.00 0.00 33.85 4.79
3398 3440 0.663269 TACAGCGAGTGTGCAAGACG 60.663 55.000 0.00 0.00 40.69 4.18
3429 3474 6.154021 AGTGCCAGAAAATGCTAAATCAGAAT 59.846 34.615 0.00 0.00 0.00 2.40
3470 3515 5.195756 ACAATCAAAGGGGGTAGTAATGGAT 59.804 40.000 0.00 0.00 0.00 3.41
3484 3533 5.902613 TCTTTCTGCCATACAATCAAAGG 57.097 39.130 0.00 0.00 0.00 3.11
3497 3546 8.011673 GCAAGTTAATTTTGAATTCTTTCTGCC 58.988 33.333 7.05 0.00 32.78 4.85
3525 4856 2.387757 AGTGTTGCAACCCAAGACATT 58.612 42.857 26.14 0.65 46.88 2.71
3560 4891 1.570979 GTCCCATCTCCCCTTTTGGAT 59.429 52.381 0.00 0.00 44.07 3.41
3594 4925 0.625849 ATGGGCTCAAGGTGGTAAGG 59.374 55.000 0.00 0.00 0.00 2.69
3612 4943 1.531423 GCCCGCATTCAGATGATGAT 58.469 50.000 0.00 0.00 37.89 2.45
3613 4944 0.535780 GGCCCGCATTCAGATGATGA 60.536 55.000 0.00 0.00 35.16 2.92
3614 4945 0.820482 TGGCCCGCATTCAGATGATG 60.820 55.000 0.00 0.00 35.16 3.07
3676 5011 5.393569 CGTTTCATCCAGATCTCGCCTATAT 60.394 44.000 0.00 0.00 0.00 0.86
3680 5015 1.202463 CGTTTCATCCAGATCTCGCCT 60.202 52.381 0.00 0.00 0.00 5.52
3736 5071 3.231699 ACTAATACCACCCCCTCCTTT 57.768 47.619 0.00 0.00 0.00 3.11
3767 5102 0.465097 CAGGCAGCCCGAATCAATCT 60.465 55.000 8.22 0.00 35.76 2.40
3792 5127 1.069765 CCGCCGATCTTGCTGGTAT 59.930 57.895 0.00 0.00 0.00 2.73
3817 5152 2.863988 CCAGTTTCCCCCACCCCT 60.864 66.667 0.00 0.00 0.00 4.79
3826 5161 4.660938 ACTGCCGCCCCAGTTTCC 62.661 66.667 0.00 0.00 43.19 3.13
3891 5231 3.187432 CGCCTTCTTTCTTTCCTGAAGAC 59.813 47.826 0.00 0.00 43.90 3.01
3932 5272 3.488090 CTCTTTTCGTCCGCCGGC 61.488 66.667 19.07 19.07 37.11 6.13
3933 5273 2.048503 ACTCTTTTCGTCCGCCGG 60.049 61.111 0.00 0.00 37.11 6.13
3934 5274 2.434134 CGACTCTTTTCGTCCGCCG 61.434 63.158 0.00 0.00 34.16 6.46
3935 5275 3.460144 CGACTCTTTTCGTCCGCC 58.540 61.111 0.00 0.00 34.16 6.13
3951 5291 4.104633 GTCAAGACGCGCACGACG 62.105 66.667 5.73 0.00 43.93 5.12
3961 5301 1.568025 GAAACACCGGCGTCAAGAC 59.432 57.895 6.01 0.00 0.00 3.01
3962 5302 1.595929 GGAAACACCGGCGTCAAGA 60.596 57.895 6.01 0.00 0.00 3.02
3963 5303 1.164041 AAGGAAACACCGGCGTCAAG 61.164 55.000 6.01 0.00 44.74 3.02
3964 5304 0.748729 AAAGGAAACACCGGCGTCAA 60.749 50.000 6.01 0.00 44.74 3.18
3965 5305 0.106335 TAAAGGAAACACCGGCGTCA 59.894 50.000 6.01 0.00 44.74 4.35
3966 5306 1.445871 ATAAAGGAAACACCGGCGTC 58.554 50.000 6.01 0.00 44.74 5.19
3967 5307 2.766345 TATAAAGGAAACACCGGCGT 57.234 45.000 6.01 0.00 44.74 5.68
3968 5308 2.220133 CGATATAAAGGAAACACCGGCG 59.780 50.000 0.00 0.00 44.74 6.46
3969 5309 2.032290 GCGATATAAAGGAAACACCGGC 60.032 50.000 0.00 0.00 44.74 6.13
3970 5310 2.220133 CGCGATATAAAGGAAACACCGG 59.780 50.000 0.00 0.00 44.74 5.28
3971 5311 2.220133 CCGCGATATAAAGGAAACACCG 59.780 50.000 8.23 0.00 44.74 4.94
3972 5312 3.246936 GTCCGCGATATAAAGGAAACACC 59.753 47.826 8.23 0.00 34.17 4.16
3973 5313 3.246936 GGTCCGCGATATAAAGGAAACAC 59.753 47.826 8.23 0.00 34.17 3.32
3974 5314 3.460103 GGTCCGCGATATAAAGGAAACA 58.540 45.455 8.23 0.00 34.17 2.83
3975 5315 2.473984 CGGTCCGCGATATAAAGGAAAC 59.526 50.000 8.23 0.00 34.17 2.78
3976 5316 2.101249 ACGGTCCGCGATATAAAGGAAA 59.899 45.455 12.28 0.00 34.17 3.13
3977 5317 1.682854 ACGGTCCGCGATATAAAGGAA 59.317 47.619 12.28 0.00 34.17 3.36
3978 5318 1.321474 ACGGTCCGCGATATAAAGGA 58.679 50.000 12.28 0.00 0.00 3.36
3979 5319 2.995466 TACGGTCCGCGATATAAAGG 57.005 50.000 12.28 0.00 0.00 3.11
3980 5320 4.293415 AGTTTACGGTCCGCGATATAAAG 58.707 43.478 12.28 0.00 0.00 1.85
3981 5321 4.305989 AGTTTACGGTCCGCGATATAAA 57.694 40.909 12.28 5.57 0.00 1.40
3982 5322 3.988379 AGTTTACGGTCCGCGATATAA 57.012 42.857 12.28 0.00 0.00 0.98
3983 5323 4.515191 ACTTAGTTTACGGTCCGCGATATA 59.485 41.667 12.28 0.00 0.00 0.86
3984 5324 3.316308 ACTTAGTTTACGGTCCGCGATAT 59.684 43.478 12.28 0.00 0.00 1.63
3985 5325 2.682856 ACTTAGTTTACGGTCCGCGATA 59.317 45.455 12.28 0.00 0.00 2.92
3986 5326 1.474077 ACTTAGTTTACGGTCCGCGAT 59.526 47.619 12.28 0.00 0.00 4.58
3987 5327 0.881118 ACTTAGTTTACGGTCCGCGA 59.119 50.000 12.28 0.00 0.00 5.87
3988 5328 1.701704 AACTTAGTTTACGGTCCGCG 58.298 50.000 12.28 0.00 0.00 6.46
3989 5329 4.568229 GTAAACTTAGTTTACGGTCCGC 57.432 45.455 25.73 7.66 44.97 5.54
3997 5337 6.979817 TGTCTGCGAACTGTAAACTTAGTTTA 59.020 34.615 12.92 12.92 37.27 2.01
3998 5338 5.813672 TGTCTGCGAACTGTAAACTTAGTTT 59.186 36.000 14.99 14.99 37.27 2.66
3999 5339 5.353938 TGTCTGCGAACTGTAAACTTAGTT 58.646 37.500 0.00 0.00 39.67 2.24
4000 5340 4.940463 TGTCTGCGAACTGTAAACTTAGT 58.060 39.130 0.00 0.00 0.00 2.24
4001 5341 5.220381 TCTGTCTGCGAACTGTAAACTTAG 58.780 41.667 0.00 0.00 0.00 2.18
4002 5342 5.190992 TCTGTCTGCGAACTGTAAACTTA 57.809 39.130 0.00 0.00 0.00 2.24
4003 5343 4.054780 TCTGTCTGCGAACTGTAAACTT 57.945 40.909 0.00 0.00 0.00 2.66
4004 5344 3.728076 TCTGTCTGCGAACTGTAAACT 57.272 42.857 0.00 0.00 0.00 2.66
4005 5345 4.030306 CGTATCTGTCTGCGAACTGTAAAC 59.970 45.833 0.00 0.00 0.00 2.01
4006 5346 4.163552 CGTATCTGTCTGCGAACTGTAAA 58.836 43.478 0.00 0.00 0.00 2.01
4007 5347 3.427098 CCGTATCTGTCTGCGAACTGTAA 60.427 47.826 0.00 0.00 0.00 2.41
4008 5348 2.096980 CCGTATCTGTCTGCGAACTGTA 59.903 50.000 0.00 0.00 0.00 2.74
4009 5349 1.135373 CCGTATCTGTCTGCGAACTGT 60.135 52.381 0.00 0.00 0.00 3.55
4010 5350 1.550065 CCGTATCTGTCTGCGAACTG 58.450 55.000 0.00 0.00 0.00 3.16
4011 5351 0.456221 CCCGTATCTGTCTGCGAACT 59.544 55.000 0.00 0.00 0.00 3.01
4012 5352 1.146358 GCCCGTATCTGTCTGCGAAC 61.146 60.000 0.00 0.00 0.00 3.95
4013 5353 1.141019 GCCCGTATCTGTCTGCGAA 59.859 57.895 0.00 0.00 0.00 4.70
4014 5354 2.782222 GGCCCGTATCTGTCTGCGA 61.782 63.158 0.00 0.00 0.00 5.10
4015 5355 2.279517 GGCCCGTATCTGTCTGCG 60.280 66.667 0.00 0.00 0.00 5.18
4016 5356 2.279517 CGGCCCGTATCTGTCTGC 60.280 66.667 0.00 0.00 0.00 4.26
4017 5357 0.174845 TTTCGGCCCGTATCTGTCTG 59.825 55.000 1.63 0.00 0.00 3.51
4018 5358 0.899720 TTTTCGGCCCGTATCTGTCT 59.100 50.000 1.63 0.00 0.00 3.41
4019 5359 1.004595 GTTTTCGGCCCGTATCTGTC 58.995 55.000 1.63 0.00 0.00 3.51
4020 5360 0.322322 TGTTTTCGGCCCGTATCTGT 59.678 50.000 1.63 0.00 0.00 3.41
4021 5361 1.006832 CTGTTTTCGGCCCGTATCTG 58.993 55.000 1.63 0.00 0.00 2.90
4022 5362 0.743345 GCTGTTTTCGGCCCGTATCT 60.743 55.000 1.63 0.00 45.68 1.98
4023 5363 1.719709 GCTGTTTTCGGCCCGTATC 59.280 57.895 1.63 0.00 45.68 2.24
4024 5364 3.899395 GCTGTTTTCGGCCCGTAT 58.101 55.556 1.63 0.00 45.68 3.06
4032 5372 0.384725 CTGTTCTGCCGCTGTTTTCG 60.385 55.000 0.00 0.00 0.00 3.46
4033 5373 0.944386 TCTGTTCTGCCGCTGTTTTC 59.056 50.000 0.00 0.00 0.00 2.29
4034 5374 1.388547 TTCTGTTCTGCCGCTGTTTT 58.611 45.000 0.00 0.00 0.00 2.43
4035 5375 1.388547 TTTCTGTTCTGCCGCTGTTT 58.611 45.000 0.00 0.00 0.00 2.83
4036 5376 1.267806 CATTTCTGTTCTGCCGCTGTT 59.732 47.619 0.00 0.00 0.00 3.16
4037 5377 0.877071 CATTTCTGTTCTGCCGCTGT 59.123 50.000 0.00 0.00 0.00 4.40
4038 5378 0.877071 ACATTTCTGTTCTGCCGCTG 59.123 50.000 0.00 0.00 28.70 5.18
4039 5379 2.472695 TACATTTCTGTTCTGCCGCT 57.527 45.000 0.00 0.00 36.79 5.52
4040 5380 3.552604 TTTACATTTCTGTTCTGCCGC 57.447 42.857 0.00 0.00 36.79 6.53
4041 5381 5.698832 TCATTTTACATTTCTGTTCTGCCG 58.301 37.500 0.00 0.00 36.79 5.69
4042 5382 6.366061 GGTTCATTTTACATTTCTGTTCTGCC 59.634 38.462 0.00 0.00 36.79 4.85
4043 5383 7.115378 CAGGTTCATTTTACATTTCTGTTCTGC 59.885 37.037 0.00 0.00 36.79 4.26
4044 5384 8.137437 ACAGGTTCATTTTACATTTCTGTTCTG 58.863 33.333 0.00 0.00 36.79 3.02
4045 5385 8.237811 ACAGGTTCATTTTACATTTCTGTTCT 57.762 30.769 0.00 0.00 36.79 3.01
4046 5386 9.959749 TTACAGGTTCATTTTACATTTCTGTTC 57.040 29.630 0.00 0.00 36.79 3.18
4053 5393 9.418045 CCGAAATTTACAGGTTCATTTTACATT 57.582 29.630 0.00 0.00 0.00 2.71
4054 5394 8.798402 TCCGAAATTTACAGGTTCATTTTACAT 58.202 29.630 0.00 0.00 0.00 2.29
4055 5395 8.167605 TCCGAAATTTACAGGTTCATTTTACA 57.832 30.769 0.00 0.00 0.00 2.41
4056 5396 9.124807 CTTCCGAAATTTACAGGTTCATTTTAC 57.875 33.333 0.00 0.00 0.00 2.01
4057 5397 7.810759 GCTTCCGAAATTTACAGGTTCATTTTA 59.189 33.333 0.00 0.00 0.00 1.52
4058 5398 6.645003 GCTTCCGAAATTTACAGGTTCATTTT 59.355 34.615 0.00 0.00 0.00 1.82
4059 5399 6.156519 GCTTCCGAAATTTACAGGTTCATTT 58.843 36.000 0.00 0.00 0.00 2.32
4060 5400 5.619086 CGCTTCCGAAATTTACAGGTTCATT 60.619 40.000 0.00 0.00 36.29 2.57
4061 5401 4.142687 CGCTTCCGAAATTTACAGGTTCAT 60.143 41.667 0.00 0.00 36.29 2.57
4062 5402 3.187637 CGCTTCCGAAATTTACAGGTTCA 59.812 43.478 0.00 0.00 36.29 3.18
4063 5403 3.425758 CCGCTTCCGAAATTTACAGGTTC 60.426 47.826 0.00 0.00 36.29 3.62
4064 5404 2.486592 CCGCTTCCGAAATTTACAGGTT 59.513 45.455 0.00 0.00 36.29 3.50
4065 5405 2.081462 CCGCTTCCGAAATTTACAGGT 58.919 47.619 0.00 0.00 36.29 4.00
4066 5406 2.352388 TCCGCTTCCGAAATTTACAGG 58.648 47.619 0.00 0.00 36.29 4.00
4067 5407 3.435671 AGTTCCGCTTCCGAAATTTACAG 59.564 43.478 0.00 0.00 36.29 2.74
4068 5408 3.404899 AGTTCCGCTTCCGAAATTTACA 58.595 40.909 0.00 0.00 36.29 2.41
4069 5409 4.400845 GAAGTTCCGCTTCCGAAATTTAC 58.599 43.478 0.00 0.00 45.95 2.01
4070 5410 4.673534 GAAGTTCCGCTTCCGAAATTTA 57.326 40.909 0.00 0.00 45.95 1.40
4071 5411 3.554259 GAAGTTCCGCTTCCGAAATTT 57.446 42.857 0.00 0.00 45.95 1.82
4080 5420 1.004918 CTCCCGTGAAGTTCCGCTT 60.005 57.895 0.00 0.00 40.76 4.68
4081 5421 1.258445 ATCTCCCGTGAAGTTCCGCT 61.258 55.000 0.00 0.00 0.00 5.52
4082 5422 0.458669 TATCTCCCGTGAAGTTCCGC 59.541 55.000 0.00 0.00 0.00 5.54
4083 5423 2.604855 CGATATCTCCCGTGAAGTTCCG 60.605 54.545 0.00 3.74 0.00 4.30
4084 5424 2.621998 TCGATATCTCCCGTGAAGTTCC 59.378 50.000 0.00 0.00 0.00 3.62
4085 5425 3.984508 TCGATATCTCCCGTGAAGTTC 57.015 47.619 0.34 0.00 0.00 3.01
4086 5426 3.700038 AGTTCGATATCTCCCGTGAAGTT 59.300 43.478 0.34 0.00 0.00 2.66
4087 5427 3.288964 AGTTCGATATCTCCCGTGAAGT 58.711 45.455 0.34 0.00 0.00 3.01
4088 5428 3.992260 AGTTCGATATCTCCCGTGAAG 57.008 47.619 0.34 0.00 0.00 3.02
4089 5429 4.458397 AGTAGTTCGATATCTCCCGTGAA 58.542 43.478 0.34 0.00 0.00 3.18
4090 5430 4.082665 AGTAGTTCGATATCTCCCGTGA 57.917 45.455 0.34 0.00 0.00 4.35
4091 5431 4.275196 TGAAGTAGTTCGATATCTCCCGTG 59.725 45.833 5.84 0.00 35.17 4.94
4092 5432 4.458397 TGAAGTAGTTCGATATCTCCCGT 58.542 43.478 5.84 0.00 35.17 5.28
4093 5433 4.515944 ACTGAAGTAGTTCGATATCTCCCG 59.484 45.833 5.84 0.00 35.67 5.14
4094 5434 5.299782 ACACTGAAGTAGTTCGATATCTCCC 59.700 44.000 5.84 0.00 37.60 4.30
4095 5435 6.380095 ACACTGAAGTAGTTCGATATCTCC 57.620 41.667 5.84 0.00 37.60 3.71
4096 5436 7.473366 TGAACACTGAAGTAGTTCGATATCTC 58.527 38.462 5.84 0.00 43.36 2.75
4097 5437 7.392494 TGAACACTGAAGTAGTTCGATATCT 57.608 36.000 5.84 0.00 43.36 1.98
4098 5438 9.388346 CTATGAACACTGAAGTAGTTCGATATC 57.612 37.037 5.84 0.00 43.36 1.63
4099 5439 8.904834 ACTATGAACACTGAAGTAGTTCGATAT 58.095 33.333 5.84 9.48 43.36 1.63
4100 5440 8.277490 ACTATGAACACTGAAGTAGTTCGATA 57.723 34.615 5.84 13.03 43.36 2.92
4101 5441 7.159322 ACTATGAACACTGAAGTAGTTCGAT 57.841 36.000 5.84 12.77 43.36 3.59
4102 5442 6.570672 ACTATGAACACTGAAGTAGTTCGA 57.429 37.500 5.84 0.00 43.36 3.71
4103 5443 7.528307 AGTACTATGAACACTGAAGTAGTTCG 58.472 38.462 5.84 3.71 43.36 3.95
4104 5444 9.130312 CAAGTACTATGAACACTGAAGTAGTTC 57.870 37.037 3.15 3.15 41.42 3.01
4105 5445 8.857098 TCAAGTACTATGAACACTGAAGTAGTT 58.143 33.333 0.00 0.00 37.60 2.24
4106 5446 8.405418 TCAAGTACTATGAACACTGAAGTAGT 57.595 34.615 0.00 0.00 41.36 2.73
4107 5447 9.509855 GATCAAGTACTATGAACACTGAAGTAG 57.490 37.037 0.00 0.00 0.00 2.57
4108 5448 9.020731 TGATCAAGTACTATGAACACTGAAGTA 57.979 33.333 0.00 0.00 0.00 2.24
4109 5449 7.896811 TGATCAAGTACTATGAACACTGAAGT 58.103 34.615 0.00 0.00 0.00 3.01
4110 5450 8.939201 ATGATCAAGTACTATGAACACTGAAG 57.061 34.615 15.13 0.00 33.26 3.02
4111 5451 8.531146 TGATGATCAAGTACTATGAACACTGAA 58.469 33.333 15.13 4.80 33.26 3.02
4112 5452 8.066612 TGATGATCAAGTACTATGAACACTGA 57.933 34.615 15.13 6.24 33.26 3.41
4113 5453 8.883954 ATGATGATCAAGTACTATGAACACTG 57.116 34.615 15.13 1.67 33.26 3.66
4114 5454 9.973450 GTATGATGATCAAGTACTATGAACACT 57.027 33.333 15.13 8.61 33.26 3.55
4115 5455 9.750125 TGTATGATGATCAAGTACTATGAACAC 57.250 33.333 15.13 11.54 33.26 3.32
4150 5490 9.547753 CTTTGTACAAATATGCTACTCCTATGT 57.452 33.333 20.83 0.00 0.00 2.29
4151 5491 9.547753 ACTTTGTACAAATATGCTACTCCTATG 57.452 33.333 20.83 6.53 0.00 2.23
4154 5494 8.978472 TCTACTTTGTACAAATATGCTACTCCT 58.022 33.333 20.83 0.00 0.00 3.69
4155 5495 9.765795 ATCTACTTTGTACAAATATGCTACTCC 57.234 33.333 20.83 0.00 0.00 3.85
4160 5500 9.890629 TTCTGATCTACTTTGTACAAATATGCT 57.109 29.630 20.83 6.97 0.00 3.79
4164 5504 9.587772 GCTCTTCTGATCTACTTTGTACAAATA 57.412 33.333 20.83 13.70 0.00 1.40
4165 5505 7.276658 CGCTCTTCTGATCTACTTTGTACAAAT 59.723 37.037 20.83 13.33 0.00 2.32
4166 5506 6.586463 CGCTCTTCTGATCTACTTTGTACAAA 59.414 38.462 19.53 19.53 0.00 2.83
4167 5507 6.093404 CGCTCTTCTGATCTACTTTGTACAA 58.907 40.000 3.59 3.59 0.00 2.41
4168 5508 5.393135 CCGCTCTTCTGATCTACTTTGTACA 60.393 44.000 0.00 0.00 0.00 2.90
4169 5509 5.038033 CCGCTCTTCTGATCTACTTTGTAC 58.962 45.833 0.00 0.00 0.00 2.90
4170 5510 4.440250 GCCGCTCTTCTGATCTACTTTGTA 60.440 45.833 0.00 0.00 0.00 2.41
4171 5511 3.677424 GCCGCTCTTCTGATCTACTTTGT 60.677 47.826 0.00 0.00 0.00 2.83
4172 5512 2.863137 GCCGCTCTTCTGATCTACTTTG 59.137 50.000 0.00 0.00 0.00 2.77
4173 5513 2.480416 CGCCGCTCTTCTGATCTACTTT 60.480 50.000 0.00 0.00 0.00 2.66
4174 5514 1.066303 CGCCGCTCTTCTGATCTACTT 59.934 52.381 0.00 0.00 0.00 2.24
4175 5515 0.665835 CGCCGCTCTTCTGATCTACT 59.334 55.000 0.00 0.00 0.00 2.57
4176 5516 0.318275 CCGCCGCTCTTCTGATCTAC 60.318 60.000 0.00 0.00 0.00 2.59
4177 5517 2.033793 CCGCCGCTCTTCTGATCTA 58.966 57.895 0.00 0.00 0.00 1.98
4178 5518 2.811101 CCGCCGCTCTTCTGATCT 59.189 61.111 0.00 0.00 0.00 2.75
4179 5519 2.964389 GCCGCCGCTCTTCTGATC 60.964 66.667 0.00 0.00 0.00 2.92
4180 5520 4.537433 GGCCGCCGCTCTTCTGAT 62.537 66.667 0.00 0.00 34.44 2.90
4194 5534 2.512286 GTAGGGTTTACGGCGGCC 60.512 66.667 13.24 9.54 0.00 6.13
4195 5535 1.812507 CAGTAGGGTTTACGGCGGC 60.813 63.158 13.24 0.00 0.00 6.53
4196 5536 0.459063 GACAGTAGGGTTTACGGCGG 60.459 60.000 13.24 0.00 0.00 6.13
4197 5537 0.244450 TGACAGTAGGGTTTACGGCG 59.756 55.000 4.80 4.80 0.00 6.46
4198 5538 2.460757 TTGACAGTAGGGTTTACGGC 57.539 50.000 0.00 0.00 0.00 5.68
4199 5539 5.952526 AATTTTGACAGTAGGGTTTACGG 57.047 39.130 0.00 0.00 0.00 4.02
4200 5540 6.146898 CCAAATTTTGACAGTAGGGTTTACG 58.853 40.000 10.72 0.00 0.00 3.18
4201 5541 5.924254 GCCAAATTTTGACAGTAGGGTTTAC 59.076 40.000 10.72 0.00 0.00 2.01
4202 5542 5.836358 AGCCAAATTTTGACAGTAGGGTTTA 59.164 36.000 10.72 0.00 0.00 2.01
4203 5543 4.653801 AGCCAAATTTTGACAGTAGGGTTT 59.346 37.500 10.72 0.00 0.00 3.27
4204 5544 4.223144 AGCCAAATTTTGACAGTAGGGTT 58.777 39.130 10.72 0.00 0.00 4.11
4205 5545 3.826729 GAGCCAAATTTTGACAGTAGGGT 59.173 43.478 10.72 0.00 0.00 4.34
4206 5546 3.826157 TGAGCCAAATTTTGACAGTAGGG 59.174 43.478 10.72 0.00 0.00 3.53
4207 5547 4.321230 GGTGAGCCAAATTTTGACAGTAGG 60.321 45.833 10.72 0.00 34.09 3.18
4208 5548 4.798574 GGTGAGCCAAATTTTGACAGTAG 58.201 43.478 10.72 0.00 34.09 2.57
4209 5549 4.846779 GGTGAGCCAAATTTTGACAGTA 57.153 40.909 10.72 0.00 34.09 2.74
4210 5550 3.733443 GGTGAGCCAAATTTTGACAGT 57.267 42.857 10.72 0.00 34.09 3.55


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

AutoCloner maintained by Alex Coulton.