Multiple sequence alignment - TraesCS4A01G387700

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 TraesCS4A01G387700 chr4A 100.000 4690 0 0 1 4690 665500063 665504752 0.000000e+00 8661.0
1 TraesCS4A01G387700 chr4A 100.000 244 0 0 4942 5185 665505004 665505247 7.920000e-123 451.0
2 TraesCS4A01G387700 chr7A 91.683 4485 243 64 251 4690 53958576 53954177 0.000000e+00 6096.0
3 TraesCS4A01G387700 chr7A 84.685 222 7 10 1 214 53959103 53958901 4.100000e-46 196.0
4 TraesCS4A01G387700 chr7D 92.023 3786 172 52 550 4303 51525108 51521421 0.000000e+00 5199.0
5 TraesCS4A01G387700 chr7D 92.602 392 18 6 4300 4690 51521394 51521013 2.110000e-153 553.0
6 TraesCS4A01G387700 chr7D 83.032 554 42 33 1 529 51525689 51525163 6.120000e-124 455.0
7 TraesCS4A01G387700 chr7D 74.713 261 40 15 4942 5185 51520997 51520746 5.530000e-15 93.5


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 TraesCS4A01G387700 chr4A 665500063 665505247 5184 False 4556.000 8661 100.0000 1 5185 2 chr4A.!!$F1 5184
1 TraesCS4A01G387700 chr7A 53954177 53959103 4926 True 3146.000 6096 88.1840 1 4690 2 chr7A.!!$R1 4689
2 TraesCS4A01G387700 chr7D 51520746 51525689 4943 True 1575.125 5199 85.5925 1 5185 4 chr7D.!!$R1 5184

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
748 1100 0.108774 GCTCCCTATCCTTTTCCCCG 59.891 60.0 0.00 0.0 0.00 5.73 F
2262 2637 0.179094 TTCGCTCAACGTTGTGGTCT 60.179 50.0 26.47 0.0 44.19 3.85 F
2517 2896 0.323302 TGCGTTAGATTGTGGCTCCA 59.677 50.0 0.00 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2745 3127 1.066929 GGGCCAGCACCACTTAATTTG 60.067 52.381 4.39 0.0 0.00 2.32 R
3914 4301 0.322456 TTGAAATCGGGGCACTCTGG 60.322 55.000 0.00 0.0 0.00 3.86 R
4515 4933 0.897401 GCTGCAGCCTTCCTTTCCTT 60.897 55.000 28.76 0.0 34.31 3.36 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
119 134 3.382832 CAACCTCGCCTCTCCCGT 61.383 66.667 0.00 0.00 0.00 5.28
244 273 3.462678 GCGGTGAGTCCCTCTCCC 61.463 72.222 6.74 0.21 39.99 4.30
245 274 2.360980 CGGTGAGTCCCTCTCCCT 59.639 66.667 6.74 0.00 39.99 4.20
247 276 1.382009 GGTGAGTCCCTCTCCCTCC 60.382 68.421 1.72 0.00 42.12 4.30
249 278 2.284151 GAGTCCCTCTCCCTCCCC 59.716 72.222 0.00 0.00 37.22 4.81
386 699 2.037208 CCCTTGCGGTGGGGATTT 59.963 61.111 0.00 0.00 45.18 2.17
429 743 4.351938 GTTTGGCCCGTTTCGCCC 62.352 66.667 0.00 0.00 46.48 6.13
472 786 2.746277 GGCAGCGTTGGATTCGGT 60.746 61.111 0.16 0.00 39.57 4.69
484 799 2.597117 GATTCGGTGGCAATGCGGTG 62.597 60.000 0.00 0.00 0.00 4.94
530 849 4.176752 GGACGGATGGACAGGGCC 62.177 72.222 0.00 0.00 0.00 5.80
576 928 2.614013 TCCAAGGAGAAGGGGGCC 60.614 66.667 0.00 0.00 0.00 5.80
599 951 8.647226 GGCCATTTATTTTGCGATTATTATGTC 58.353 33.333 0.00 0.00 0.00 3.06
613 965 7.692291 CGATTATTATGTCATGGTAAATTCGGC 59.308 37.037 0.00 0.00 0.00 5.54
662 1014 2.356382 TGTTTGGATGTCAACAACGACC 59.644 45.455 0.00 0.00 34.67 4.79
700 1052 1.602605 GGTCGTTGGAGGTTTGGGG 60.603 63.158 0.00 0.00 0.00 4.96
748 1100 0.108774 GCTCCCTATCCTTTTCCCCG 59.891 60.000 0.00 0.00 0.00 5.73
769 1121 0.982852 ATGAGGAACAGCGGGATCCA 60.983 55.000 15.23 0.00 35.62 3.41
812 1166 8.655651 TTTACATGGAATCTTTTTGTTGTTCC 57.344 30.769 0.00 0.00 38.99 3.62
815 1169 6.762661 ACATGGAATCTTTTTGTTGTTCCTTG 59.237 34.615 13.49 13.49 43.83 3.61
840 1194 4.033932 TCGTGAATGTTGTTGTTCTGTCAG 59.966 41.667 0.00 0.00 0.00 3.51
935 1289 3.305608 CCTGTTGCTCATCCTTTTGTTCC 60.306 47.826 0.00 0.00 0.00 3.62
936 1290 3.565307 TGTTGCTCATCCTTTTGTTCCT 58.435 40.909 0.00 0.00 0.00 3.36
937 1291 3.960102 TGTTGCTCATCCTTTTGTTCCTT 59.040 39.130 0.00 0.00 0.00 3.36
938 1292 4.037923 TGTTGCTCATCCTTTTGTTCCTTC 59.962 41.667 0.00 0.00 0.00 3.46
939 1293 4.104383 TGCTCATCCTTTTGTTCCTTCT 57.896 40.909 0.00 0.00 0.00 2.85
940 1294 4.074970 TGCTCATCCTTTTGTTCCTTCTC 58.925 43.478 0.00 0.00 0.00 2.87
941 1295 3.441922 GCTCATCCTTTTGTTCCTTCTCC 59.558 47.826 0.00 0.00 0.00 3.71
948 1302 5.132816 TCCTTTTGTTCCTTCTCCTTCTTCT 59.867 40.000 0.00 0.00 0.00 2.85
972 1326 1.628846 AGGTTGGAGCGTAATCTTGGT 59.371 47.619 0.00 0.00 0.00 3.67
1093 1447 3.743521 TCCAAGAACATGTCTGGTGAAG 58.256 45.455 16.86 0.00 36.40 3.02
1194 1548 2.296190 CCAAGCACTTCCCAAGGTTAAC 59.704 50.000 0.00 0.00 0.00 2.01
1410 1764 5.048083 TGACACATTTGGCTTTGGTAGAATC 60.048 40.000 0.00 0.00 0.00 2.52
1580 1950 5.298527 CACTATTGATGCCATCAGTTCACAT 59.701 40.000 8.06 0.60 40.94 3.21
1590 1960 5.243981 CCATCAGTTCACATCAGTCTTCTT 58.756 41.667 0.00 0.00 0.00 2.52
1595 1965 7.272244 TCAGTTCACATCAGTCTTCTTAAACA 58.728 34.615 0.00 0.00 0.00 2.83
1601 1971 9.119418 TCACATCAGTCTTCTTAAACAAATTCA 57.881 29.630 0.00 0.00 0.00 2.57
1754 2124 6.018433 AGCATTATCCCTCATGGTACTTTT 57.982 37.500 0.00 0.00 34.77 2.27
1784 2154 8.723311 CAAGCCATAATTGTTGATGTCATTTTT 58.277 29.630 0.00 0.00 0.00 1.94
1802 2172 3.356529 TTTCTGGCAAATCCTCTCTCC 57.643 47.619 0.00 0.00 35.26 3.71
1819 2189 6.295802 CCTCTCTCCTTTTCTCACTTTCAGAT 60.296 42.308 0.00 0.00 0.00 2.90
1822 2192 7.995488 TCTCTCCTTTTCTCACTTTCAGATTTT 59.005 33.333 0.00 0.00 0.00 1.82
1840 2210 8.671921 TCAGATTTTCAGTCAAATTCATAGCTC 58.328 33.333 0.00 0.00 29.93 4.09
1844 2214 6.408858 TTCAGTCAAATTCATAGCTCGAAC 57.591 37.500 0.00 0.00 0.00 3.95
1847 2217 6.752351 TCAGTCAAATTCATAGCTCGAACTAC 59.248 38.462 0.00 0.00 0.00 2.73
1931 2301 4.590226 CTTTTTGGCACACATTTTGAAGC 58.410 39.130 0.00 0.00 39.29 3.86
1937 2307 3.253230 GCACACATTTTGAAGCCATACC 58.747 45.455 0.00 0.00 0.00 2.73
1944 2314 7.613801 ACACATTTTGAAGCCATACCTGTATAA 59.386 33.333 0.00 0.00 0.00 0.98
1948 2318 4.314961 TGAAGCCATACCTGTATAATGCG 58.685 43.478 0.00 0.00 0.00 4.73
2050 2422 7.144722 TCATAACATTCTACAAACTGCCTTG 57.855 36.000 0.00 0.00 0.00 3.61
2061 2433 1.299541 ACTGCCTTGTGAGTTTGTCG 58.700 50.000 0.00 0.00 0.00 4.35
2130 2505 3.975168 ACTAAGTTGGCCTTACGTCAT 57.025 42.857 3.32 0.00 34.46 3.06
2203 2578 3.012518 GCACCACTCAAACATGCTCTAT 58.987 45.455 0.00 0.00 33.44 1.98
2245 2620 6.560253 AACAACACATCATGTCCTAGTTTC 57.440 37.500 0.00 0.00 42.31 2.78
2253 2628 2.060326 TGTCCTAGTTTCGCTCAACG 57.940 50.000 0.00 0.00 45.62 4.10
2260 2635 0.375803 GTTTCGCTCAACGTTGTGGT 59.624 50.000 26.47 0.00 44.19 4.16
2261 2636 0.653636 TTTCGCTCAACGTTGTGGTC 59.346 50.000 26.47 12.05 44.19 4.02
2262 2637 0.179094 TTCGCTCAACGTTGTGGTCT 60.179 50.000 26.47 0.00 44.19 3.85
2296 2671 4.919168 CACATTGATTGCTAAACACAGTGG 59.081 41.667 5.31 0.00 0.00 4.00
2309 2684 2.747446 ACACAGTGGCGATTTATGGAAC 59.253 45.455 5.31 0.00 0.00 3.62
2323 2698 5.554822 TTATGGAACGGCAATACAAGTTC 57.445 39.130 0.00 0.00 41.40 3.01
2325 2700 3.417101 TGGAACGGCAATACAAGTTCAT 58.583 40.909 9.01 0.00 43.24 2.57
2385 2760 1.241990 ATGTCAGCAGTGCAGGCTTG 61.242 55.000 19.20 6.41 40.23 4.01
2403 2781 4.096532 GGCTTGGTTCCTGCTAGAATTAAC 59.903 45.833 0.00 0.00 0.00 2.01
2414 2793 7.820386 TCCTGCTAGAATTAACGATTGTTTACA 59.180 33.333 3.03 0.00 39.54 2.41
2426 2805 6.970484 ACGATTGTTTACAAATCAGAAGCTT 58.030 32.000 0.00 0.00 39.55 3.74
2464 2843 4.540099 TCATCCTACATGAAAAACTCCCCT 59.460 41.667 0.00 0.00 0.00 4.79
2465 2844 5.015178 TCATCCTACATGAAAAACTCCCCTT 59.985 40.000 0.00 0.00 0.00 3.95
2500 2879 5.409520 TGATTCTGTTGTTCTACACAGATGC 59.590 40.000 2.96 0.30 36.71 3.91
2511 2890 5.102313 TCTACACAGATGCGTTAGATTGTG 58.898 41.667 1.27 1.27 41.12 3.33
2515 2894 2.286294 CAGATGCGTTAGATTGTGGCTC 59.714 50.000 0.00 0.00 0.00 4.70
2517 2896 0.323302 TGCGTTAGATTGTGGCTCCA 59.677 50.000 0.00 0.00 0.00 3.86
2564 2944 5.555017 TCTTTAGCAATCAGAAGTTCTGCT 58.445 37.500 25.31 21.37 43.95 4.24
2565 2945 5.641209 TCTTTAGCAATCAGAAGTTCTGCTC 59.359 40.000 25.31 14.28 43.95 4.26
2566 2946 3.413846 AGCAATCAGAAGTTCTGCTCA 57.586 42.857 25.31 11.13 43.95 4.26
2567 2947 3.072944 AGCAATCAGAAGTTCTGCTCAC 58.927 45.455 25.31 15.35 43.95 3.51
2568 2948 2.810274 GCAATCAGAAGTTCTGCTCACA 59.190 45.455 25.31 10.43 43.95 3.58
2569 2949 3.120269 GCAATCAGAAGTTCTGCTCACAG 60.120 47.826 25.31 13.37 43.95 3.66
2622 3002 6.659242 ACCTTAAATCGATTGTTCCACTTGAT 59.341 34.615 12.25 0.00 0.00 2.57
2633 3013 5.432645 TGTTCCACTTGATTGTAACAGACA 58.567 37.500 0.00 0.00 35.78 3.41
2683 3064 5.869888 ACGATCATCTTTTCTTGTGTCTACC 59.130 40.000 0.00 0.00 0.00 3.18
2685 3066 6.254589 CGATCATCTTTTCTTGTGTCTACCTC 59.745 42.308 0.00 0.00 0.00 3.85
2745 3127 4.743644 ACGTATTAAATGCTCGAAGCTACC 59.256 41.667 8.07 0.00 42.97 3.18
2849 3231 8.469200 CCTTTATTGCTGGATTAAATGACTTGA 58.531 33.333 0.00 0.00 0.00 3.02
2852 3234 7.649533 ATTGCTGGATTAAATGACTTGATCA 57.350 32.000 0.00 0.00 43.13 2.92
2881 3263 2.203669 TGCTGTGGGCTGCCAAAT 60.204 55.556 22.05 0.00 42.39 2.32
2948 3333 4.801330 TTGGTCTGTGTACCTGATACTG 57.199 45.455 0.00 0.00 40.44 2.74
3046 3431 7.165427 GAAAAGCAATTTCAGTTTGGTAGTG 57.835 36.000 9.39 0.00 45.58 2.74
3073 3458 7.152645 TCTAGTTGTTCTGTAGCTTTACTTGG 58.847 38.462 0.00 0.00 0.00 3.61
3081 3466 7.900782 TCTGTAGCTTTACTTGGTGATTTAC 57.099 36.000 0.00 0.00 0.00 2.01
3246 3631 6.321181 ACAATCTTGAAAGCTACAAGGTTTGA 59.679 34.615 29.10 17.15 44.89 2.69
3269 3654 6.203145 TGAATTCCATGTGTTTGCATTTTGAG 59.797 34.615 2.27 0.00 0.00 3.02
3326 3711 3.030291 TGTGCTTCCCATTTGACACTTT 58.970 40.909 0.00 0.00 0.00 2.66
3407 3792 6.989169 CAGATGAAGTTAGAGGTGAAATAGGG 59.011 42.308 0.00 0.00 0.00 3.53
3428 3813 1.134226 CGCACTTTAACGACCGTTCT 58.866 50.000 11.27 0.00 39.31 3.01
3570 3955 3.297134 ACCATCACTCAGTTTGGTGTT 57.703 42.857 8.19 0.00 40.87 3.32
3580 3967 4.269183 TCAGTTTGGTGTTTGTGTCATCT 58.731 39.130 0.00 0.00 0.00 2.90
3704 4091 7.014326 GGGTGGATCCTTGAGGTAATTTATTTC 59.986 40.741 14.23 0.00 36.34 2.17
3708 4095 6.668133 TCCTTGAGGTAATTTATTTCCCCT 57.332 37.500 0.00 0.00 36.34 4.79
3709 4096 7.774694 TCCTTGAGGTAATTTATTTCCCCTA 57.225 36.000 0.00 0.00 36.34 3.53
3727 4114 5.307196 TCCCCTATATTCTCTAGTGTTTGGC 59.693 44.000 0.00 0.00 0.00 4.52
3732 4119 7.227512 CCTATATTCTCTAGTGTTTGGCCAAAG 59.772 40.741 31.09 18.82 0.00 2.77
3788 4175 3.357919 TGGTACCACCAGACGTCG 58.642 61.111 11.60 5.16 44.79 5.12
3789 4176 1.529010 TGGTACCACCAGACGTCGT 60.529 57.895 11.60 0.00 44.79 4.34
3830 4217 1.808945 GAGCATCAGGTCTGGTGTTTG 59.191 52.381 12.20 0.00 43.37 2.93
3870 4257 5.757988 TGTTCTCATTCCCAATCATCATCA 58.242 37.500 0.00 0.00 0.00 3.07
3871 4258 6.370453 TGTTCTCATTCCCAATCATCATCAT 58.630 36.000 0.00 0.00 0.00 2.45
3872 4259 7.519927 TGTTCTCATTCCCAATCATCATCATA 58.480 34.615 0.00 0.00 0.00 2.15
3873 4260 7.664318 TGTTCTCATTCCCAATCATCATCATAG 59.336 37.037 0.00 0.00 0.00 2.23
3914 4301 7.881775 TCCTGAGCTTTATTTATTCCCTTTC 57.118 36.000 0.00 0.00 0.00 2.62
3923 4310 3.366052 TTATTCCCTTTCCAGAGTGCC 57.634 47.619 0.00 0.00 0.00 5.01
4028 4415 1.890510 ACTGACCAACGTTTCGGGC 60.891 57.895 12.29 8.43 0.00 6.13
4074 4461 1.750399 GCCATCCAGTGCGACCATT 60.750 57.895 0.00 0.00 0.00 3.16
4115 4502 1.446907 CTGATGTGGTCAAGGCTCAC 58.553 55.000 0.00 0.00 36.14 3.51
4157 4544 1.803289 GCATGGCGAAGGAAACCTC 59.197 57.895 0.00 0.00 30.89 3.85
4181 4568 3.744719 TTCCCGGTCGAGAGTGCG 61.745 66.667 0.00 0.00 0.00 5.34
4219 4606 0.817013 AATACGGCAAGCATGGGTTG 59.183 50.000 3.93 3.93 42.93 3.77
4225 4612 1.824230 GGCAAGCATGGGTTGTTATGA 59.176 47.619 9.54 0.00 42.18 2.15
4286 4673 4.082845 TGAAGGAATTATTTTGTGCCGGA 58.917 39.130 5.05 0.00 0.00 5.14
4321 4739 2.283298 CACACATTCTGATTCGGGGAG 58.717 52.381 0.00 0.00 0.00 4.30
4372 4790 4.463050 ACTGTTTTGGGAGGAAATGGTA 57.537 40.909 0.00 0.00 0.00 3.25
4420 4838 1.344763 GAGCTTCACTGGTGGTACTGT 59.655 52.381 0.70 0.00 0.00 3.55
4431 4849 5.308759 ACTGGTGGTACTGTAGTAATTTGGT 59.691 40.000 0.00 0.00 31.52 3.67
4438 4856 4.855340 ACTGTAGTAATTTGGTGGATGGG 58.145 43.478 0.00 0.00 0.00 4.00
4447 4865 0.848648 TGGTGGATGGGGAATGGTGA 60.849 55.000 0.00 0.00 0.00 4.02
4456 4874 3.088532 TGGGGAATGGTGAAATTTCGAG 58.911 45.455 13.34 0.00 0.00 4.04
4464 4882 4.513442 TGGTGAAATTTCGAGTATGGGAG 58.487 43.478 13.34 0.00 0.00 4.30
4470 4888 2.160721 TTCGAGTATGGGAGAAGGCT 57.839 50.000 0.00 0.00 0.00 4.58
4494 4912 1.806542 GCTTGTGTGTGGTGATAGTGG 59.193 52.381 0.00 0.00 0.00 4.00
4514 4932 2.229784 GGTTTGAGCTGATTGGTGAAGG 59.770 50.000 0.00 0.00 0.00 3.46
4515 4933 3.149196 GTTTGAGCTGATTGGTGAAGGA 58.851 45.455 0.00 0.00 0.00 3.36
4516 4934 3.507162 TTGAGCTGATTGGTGAAGGAA 57.493 42.857 0.00 0.00 0.00 3.36
4517 4935 3.063510 TGAGCTGATTGGTGAAGGAAG 57.936 47.619 0.00 0.00 0.00 3.46
4518 4936 2.290514 TGAGCTGATTGGTGAAGGAAGG 60.291 50.000 0.00 0.00 0.00 3.46
4519 4937 1.988107 AGCTGATTGGTGAAGGAAGGA 59.012 47.619 0.00 0.00 0.00 3.36
4527 4945 2.108250 TGGTGAAGGAAGGAAAGGAAGG 59.892 50.000 0.00 0.00 0.00 3.46
4528 4946 2.163509 GTGAAGGAAGGAAAGGAAGGC 58.836 52.381 0.00 0.00 0.00 4.35
4634 5053 1.055849 TAGCCCAGATGTGTGTGTGT 58.944 50.000 0.00 0.00 0.00 3.72
4635 5054 0.535780 AGCCCAGATGTGTGTGTGTG 60.536 55.000 0.00 0.00 0.00 3.82
4636 5055 0.819259 GCCCAGATGTGTGTGTGTGT 60.819 55.000 0.00 0.00 0.00 3.72
4638 5057 0.946528 CCAGATGTGTGTGTGTGTGG 59.053 55.000 0.00 0.00 0.00 4.17
4639 5058 1.474855 CCAGATGTGTGTGTGTGTGGA 60.475 52.381 0.00 0.00 0.00 4.02
4640 5059 1.869132 CAGATGTGTGTGTGTGTGGAG 59.131 52.381 0.00 0.00 0.00 3.86
4641 5060 1.202687 AGATGTGTGTGTGTGTGGAGG 60.203 52.381 0.00 0.00 0.00 4.30
4642 5061 0.819259 ATGTGTGTGTGTGTGGAGGC 60.819 55.000 0.00 0.00 0.00 4.70
4643 5062 2.203001 TGTGTGTGTGTGGAGGCG 60.203 61.111 0.00 0.00 0.00 5.52
4644 5063 2.972505 GTGTGTGTGTGGAGGCGG 60.973 66.667 0.00 0.00 0.00 6.13
4994 5413 0.321122 CAGCTCTCCTGCGTTTCCTT 60.321 55.000 0.00 0.00 38.13 3.36
4995 5414 0.321122 AGCTCTCCTGCGTTTCCTTG 60.321 55.000 0.00 0.00 38.13 3.61
4996 5415 1.301677 GCTCTCCTGCGTTTCCTTGG 61.302 60.000 0.00 0.00 0.00 3.61
4997 5416 0.035458 CTCTCCTGCGTTTCCTTGGT 59.965 55.000 0.00 0.00 0.00 3.67
4998 5417 0.472471 TCTCCTGCGTTTCCTTGGTT 59.528 50.000 0.00 0.00 0.00 3.67
4999 5418 0.593128 CTCCTGCGTTTCCTTGGTTG 59.407 55.000 0.00 0.00 0.00 3.77
5000 5419 0.821711 TCCTGCGTTTCCTTGGTTGG 60.822 55.000 0.00 0.00 0.00 3.77
5001 5420 0.821711 CCTGCGTTTCCTTGGTTGGA 60.822 55.000 0.00 0.00 0.00 3.53
5002 5421 1.028905 CTGCGTTTCCTTGGTTGGAA 58.971 50.000 0.00 0.00 43.63 3.53
5015 5434 0.725117 GTTGGAAACCTATGCGTCCG 59.275 55.000 0.00 0.00 42.21 4.79
5016 5435 0.322322 TTGGAAACCTATGCGTCCGT 59.678 50.000 0.00 0.00 32.45 4.69
5017 5436 0.322322 TGGAAACCTATGCGTCCGTT 59.678 50.000 0.00 0.00 32.45 4.44
5018 5437 0.725117 GGAAACCTATGCGTCCGTTG 59.275 55.000 0.00 0.00 0.00 4.10
5019 5438 0.096454 GAAACCTATGCGTCCGTTGC 59.904 55.000 0.00 0.00 0.00 4.17
5020 5439 1.303091 AAACCTATGCGTCCGTTGCC 61.303 55.000 0.00 0.00 0.00 4.52
5021 5440 3.261951 CCTATGCGTCCGTTGCCG 61.262 66.667 0.00 0.00 0.00 5.69
5028 5447 2.742372 GTCCGTTGCCGCTGTCAT 60.742 61.111 0.00 0.00 0.00 3.06
5029 5448 2.741985 TCCGTTGCCGCTGTCATG 60.742 61.111 0.00 0.00 0.00 3.07
5030 5449 3.049674 CCGTTGCCGCTGTCATGT 61.050 61.111 0.00 0.00 0.00 3.21
5031 5450 2.174107 CGTTGCCGCTGTCATGTG 59.826 61.111 0.00 0.00 0.00 3.21
5032 5451 2.126734 GTTGCCGCTGTCATGTGC 60.127 61.111 0.00 0.00 0.00 4.57
5033 5452 2.281692 TTGCCGCTGTCATGTGCT 60.282 55.556 0.00 0.00 0.00 4.40
5034 5453 1.003959 TTGCCGCTGTCATGTGCTA 60.004 52.632 0.00 0.00 0.00 3.49
5035 5454 1.020861 TTGCCGCTGTCATGTGCTAG 61.021 55.000 0.00 0.00 0.00 3.42
5036 5455 2.817423 GCCGCTGTCATGTGCTAGC 61.817 63.158 8.10 8.10 0.00 3.42
5037 5456 2.176273 CCGCTGTCATGTGCTAGCC 61.176 63.158 13.29 4.15 32.70 3.93
5051 5470 2.031097 GCTAGCCCCCATGCTTGAAAT 61.031 52.381 2.29 0.00 42.75 2.17
5052 5471 1.684983 CTAGCCCCCATGCTTGAAATG 59.315 52.381 0.22 0.00 42.75 2.32
5053 5472 0.041535 AGCCCCCATGCTTGAAATGA 59.958 50.000 0.22 0.00 38.85 2.57
5054 5473 1.125633 GCCCCCATGCTTGAAATGAT 58.874 50.000 0.22 0.00 0.00 2.45
5057 5476 3.036091 CCCCCATGCTTGAAATGATTCT 58.964 45.455 0.22 0.00 36.48 2.40
5058 5477 4.217510 CCCCCATGCTTGAAATGATTCTA 58.782 43.478 0.22 0.00 36.48 2.10
5059 5478 4.038402 CCCCCATGCTTGAAATGATTCTAC 59.962 45.833 0.22 0.00 36.48 2.59
5060 5479 4.891756 CCCCATGCTTGAAATGATTCTACT 59.108 41.667 0.22 0.00 36.48 2.57
5063 5482 6.543465 CCCATGCTTGAAATGATTCTACTGTA 59.457 38.462 0.22 0.00 36.48 2.74
5064 5483 7.230108 CCCATGCTTGAAATGATTCTACTGTAT 59.770 37.037 0.22 0.00 36.48 2.29
5065 5484 8.074370 CCATGCTTGAAATGATTCTACTGTATG 58.926 37.037 0.22 0.00 36.48 2.39
5066 5485 7.019774 TGCTTGAAATGATTCTACTGTATGC 57.980 36.000 0.00 0.00 36.48 3.14
5068 5487 7.130917 GCTTGAAATGATTCTACTGTATGCTG 58.869 38.462 0.00 0.00 36.48 4.41
5071 5490 5.998454 AATGATTCTACTGTATGCTGTGC 57.002 39.130 3.59 0.00 0.00 4.57
5073 5492 2.691409 TTCTACTGTATGCTGTGCCC 57.309 50.000 3.59 0.00 0.00 5.36
5074 5493 1.866015 TCTACTGTATGCTGTGCCCT 58.134 50.000 3.59 0.00 0.00 5.19
5075 5494 1.757118 TCTACTGTATGCTGTGCCCTC 59.243 52.381 3.59 0.00 0.00 4.30
5076 5495 0.459899 TACTGTATGCTGTGCCCTCG 59.540 55.000 3.59 0.00 0.00 4.63
5077 5496 1.219124 CTGTATGCTGTGCCCTCGT 59.781 57.895 0.00 0.00 0.00 4.18
5078 5497 0.391661 CTGTATGCTGTGCCCTCGTT 60.392 55.000 0.00 0.00 0.00 3.85
5079 5498 0.899019 TGTATGCTGTGCCCTCGTTA 59.101 50.000 0.00 0.00 0.00 3.18
5082 5545 0.391661 ATGCTGTGCCCTCGTTACTG 60.392 55.000 0.00 0.00 0.00 2.74
5086 5549 1.805945 GTGCCCTCGTTACTGCTCG 60.806 63.158 0.00 0.00 0.00 5.03
5091 5554 1.433879 CTCGTTACTGCTCGGAGGG 59.566 63.158 7.20 0.00 0.00 4.30
5142 5612 0.474660 AGGCTCTCTCTTGTGGGGTT 60.475 55.000 0.00 0.00 0.00 4.11
5144 5614 1.528129 GCTCTCTCTTGTGGGGTTTG 58.472 55.000 0.00 0.00 0.00 2.93
5145 5615 1.202818 GCTCTCTCTTGTGGGGTTTGT 60.203 52.381 0.00 0.00 0.00 2.83
5149 5619 3.023832 CTCTCTTGTGGGGTTTGTGTTT 58.976 45.455 0.00 0.00 0.00 2.83
5150 5620 3.436243 TCTCTTGTGGGGTTTGTGTTTT 58.564 40.909 0.00 0.00 0.00 2.43
5151 5621 3.194542 TCTCTTGTGGGGTTTGTGTTTTG 59.805 43.478 0.00 0.00 0.00 2.44
5152 5622 3.165875 TCTTGTGGGGTTTGTGTTTTGA 58.834 40.909 0.00 0.00 0.00 2.69
5153 5623 3.194542 TCTTGTGGGGTTTGTGTTTTGAG 59.805 43.478 0.00 0.00 0.00 3.02
5155 5625 2.900546 TGTGGGGTTTGTGTTTTGAGTT 59.099 40.909 0.00 0.00 0.00 3.01
5156 5626 3.258228 GTGGGGTTTGTGTTTTGAGTTG 58.742 45.455 0.00 0.00 0.00 3.16
5157 5627 2.900546 TGGGGTTTGTGTTTTGAGTTGT 59.099 40.909 0.00 0.00 0.00 3.32
5158 5628 3.056465 TGGGGTTTGTGTTTTGAGTTGTC 60.056 43.478 0.00 0.00 0.00 3.18
5159 5629 3.194755 GGGGTTTGTGTTTTGAGTTGTCT 59.805 43.478 0.00 0.00 0.00 3.41
5165 5636 6.811253 TTGTGTTTTGAGTTGTCTAAGTGT 57.189 33.333 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 109 4.265056 GGCGAGGTTGGTGGTGGT 62.265 66.667 0.00 0.00 0.00 4.16
95 110 3.901797 GAGGCGAGGTTGGTGGTGG 62.902 68.421 0.00 0.00 0.00 4.61
96 111 2.358737 GAGGCGAGGTTGGTGGTG 60.359 66.667 0.00 0.00 0.00 4.17
97 112 2.526873 AGAGGCGAGGTTGGTGGT 60.527 61.111 0.00 0.00 0.00 4.16
239 257 3.036959 GGAGGAGGGGGAGGGAGA 61.037 72.222 0.00 0.00 0.00 3.71
307 610 0.890683 AAAATGCAGAGCCCGGAAAG 59.109 50.000 0.73 0.00 0.00 2.62
472 786 2.025767 AAAACAGCACCGCATTGCCA 62.026 50.000 2.41 0.00 44.14 4.92
484 799 6.242829 CACACAAAACAAATCTGAAAACAGC 58.757 36.000 0.00 0.00 0.00 4.40
554 906 2.510238 CCTTCTCCTTGGAGCGCG 60.510 66.667 11.61 0.00 0.00 6.86
599 951 2.923020 GTTTGCAGCCGAATTTACCATG 59.077 45.455 0.00 0.00 0.00 3.66
613 965 1.247419 TATTGGGGCCGTGTTTGCAG 61.247 55.000 0.00 0.00 0.00 4.41
679 1031 0.889186 CCAAACCTCCAACGACCAGG 60.889 60.000 0.00 0.00 0.00 4.45
700 1052 3.799281 TGCCCCATTCGAATCAATTTC 57.201 42.857 7.92 0.00 0.00 2.17
748 1100 1.587547 GATCCCGCTGTTCCTCATTC 58.412 55.000 0.00 0.00 0.00 2.67
769 1121 7.230108 CCATGTAAAATTGAGATATGAGCCACT 59.770 37.037 0.00 0.00 0.00 4.00
804 1158 3.692101 ACATTCACGAACAAGGAACAACA 59.308 39.130 0.00 0.00 0.00 3.33
805 1159 4.287238 ACATTCACGAACAAGGAACAAC 57.713 40.909 0.00 0.00 0.00 3.32
806 1160 4.156922 ACAACATTCACGAACAAGGAACAA 59.843 37.500 0.00 0.00 0.00 2.83
807 1161 3.692101 ACAACATTCACGAACAAGGAACA 59.308 39.130 0.00 0.00 0.00 3.18
808 1162 4.287238 ACAACATTCACGAACAAGGAAC 57.713 40.909 0.00 0.00 0.00 3.62
809 1163 4.156922 ACAACAACATTCACGAACAAGGAA 59.843 37.500 0.00 0.00 0.00 3.36
810 1164 3.692101 ACAACAACATTCACGAACAAGGA 59.308 39.130 0.00 0.00 0.00 3.36
811 1165 4.027572 ACAACAACATTCACGAACAAGG 57.972 40.909 0.00 0.00 0.00 3.61
812 1166 5.227805 CAGAACAACAACATTCACGAACAAG 59.772 40.000 0.00 0.00 0.00 3.16
815 1169 4.658071 ACAGAACAACAACATTCACGAAC 58.342 39.130 0.00 0.00 0.00 3.95
840 1194 7.766738 AGAAGAGAAGGGAGACGAAATAAAATC 59.233 37.037 0.00 0.00 0.00 2.17
903 1257 4.498682 GGATGAGCAACAGGATTTATGCAC 60.499 45.833 0.00 0.00 41.18 4.57
906 1260 6.461110 AAAGGATGAGCAACAGGATTTATG 57.539 37.500 0.00 0.00 0.00 1.90
935 1289 4.759183 CCAACCTGAAAGAAGAAGGAGAAG 59.241 45.833 0.00 0.00 34.07 2.85
936 1290 4.412199 TCCAACCTGAAAGAAGAAGGAGAA 59.588 41.667 0.00 0.00 34.07 2.87
937 1291 3.973973 TCCAACCTGAAAGAAGAAGGAGA 59.026 43.478 0.00 0.00 34.07 3.71
938 1292 4.322567 CTCCAACCTGAAAGAAGAAGGAG 58.677 47.826 0.00 0.00 34.07 3.69
939 1293 3.496870 GCTCCAACCTGAAAGAAGAAGGA 60.497 47.826 0.00 0.00 34.07 3.36
940 1294 2.816672 GCTCCAACCTGAAAGAAGAAGG 59.183 50.000 0.00 0.00 34.07 3.46
941 1295 2.481952 CGCTCCAACCTGAAAGAAGAAG 59.518 50.000 0.00 0.00 34.07 2.85
948 1302 3.695830 AGATTACGCTCCAACCTGAAA 57.304 42.857 0.00 0.00 0.00 2.69
972 1326 2.353406 GCCGTACTACAGCTTCAGGAAA 60.353 50.000 0.00 0.00 0.00 3.13
1044 1398 4.394712 AACGCAGCCGGGGAAGAG 62.395 66.667 2.18 0.00 39.22 2.85
1093 1447 3.612004 CGGACACTCAAAGTCTCAGGTAC 60.612 52.174 0.00 0.00 36.29 3.34
1590 1960 8.511604 TTCCTGCCAAAATTTGAATTTGTTTA 57.488 26.923 7.37 0.00 38.53 2.01
1595 1965 6.459985 GCTGTTTCCTGCCAAAATTTGAATTT 60.460 34.615 7.37 0.00 40.15 1.82
1601 1971 3.389002 AGAGCTGTTTCCTGCCAAAATTT 59.611 39.130 0.00 0.00 36.27 1.82
1675 2045 4.817517 TCAAGTTCCGTTTACTCATCTCC 58.182 43.478 0.00 0.00 0.00 3.71
1754 2124 4.463539 ACATCAACAATTATGGCTTGCAGA 59.536 37.500 0.00 0.00 0.00 4.26
1784 2154 2.260639 AGGAGAGAGGATTTGCCAGA 57.739 50.000 0.00 0.00 40.02 3.86
1802 2172 8.400947 TGACTGAAAATCTGAAAGTGAGAAAAG 58.599 33.333 0.00 0.00 33.76 2.27
1819 2189 7.173218 AGTTCGAGCTATGAATTTGACTGAAAA 59.827 33.333 0.00 0.00 0.00 2.29
1822 2192 5.724328 AGTTCGAGCTATGAATTTGACTGA 58.276 37.500 0.00 0.00 0.00 3.41
1840 2210 5.536554 AAAGAATGCACATGAGTAGTTCG 57.463 39.130 0.00 0.00 0.00 3.95
1844 2214 7.228108 ACATCCATAAAGAATGCACATGAGTAG 59.772 37.037 0.00 0.00 33.92 2.57
1847 2217 6.206498 CACATCCATAAAGAATGCACATGAG 58.794 40.000 0.00 0.00 33.92 2.90
1909 2279 4.496175 GGCTTCAAAATGTGTGCCAAAAAG 60.496 41.667 0.00 0.00 42.96 2.27
1917 2287 4.022068 ACAGGTATGGCTTCAAAATGTGTG 60.022 41.667 0.00 0.00 0.00 3.82
1931 2301 8.547967 AAATAAGACGCATTATACAGGTATGG 57.452 34.615 2.25 0.00 0.00 2.74
2036 2406 4.900635 AAACTCACAAGGCAGTTTGTAG 57.099 40.909 0.00 1.84 40.56 2.74
2043 2415 1.581934 TCGACAAACTCACAAGGCAG 58.418 50.000 0.00 0.00 0.00 4.85
2050 2422 5.637810 TGGAAGTTCATATCGACAAACTCAC 59.362 40.000 5.01 0.00 30.99 3.51
2061 2433 6.757897 TGACAACCAATGGAAGTTCATATC 57.242 37.500 6.16 0.00 0.00 1.63
2100 2472 9.106070 CGTAAGGCCAACTTAGTTATAAGAAAT 57.894 33.333 5.01 0.00 42.12 2.17
2260 2635 8.579850 AGCAATCAATGTGGTAAATAAGAAGA 57.420 30.769 0.00 0.00 0.00 2.87
2278 2653 1.535028 CGCCACTGTGTTTAGCAATCA 59.465 47.619 7.08 0.00 0.00 2.57
2289 2664 2.223021 CGTTCCATAAATCGCCACTGTG 60.223 50.000 0.00 0.00 0.00 3.66
2296 2671 2.774439 ATTGCCGTTCCATAAATCGC 57.226 45.000 0.00 0.00 0.00 4.58
2309 2684 5.991328 ATAGTCATGAACTTGTATTGCCG 57.009 39.130 0.00 0.00 39.55 5.69
2323 2698 6.885918 TCCCATGGCATACATAAATAGTCATG 59.114 38.462 6.09 0.00 37.84 3.07
2325 2700 6.446909 TCCCATGGCATACATAAATAGTCA 57.553 37.500 6.09 0.00 37.84 3.41
2356 2731 6.028146 TGCACTGCTGACATTATTTTTCAT 57.972 33.333 1.98 0.00 0.00 2.57
2357 2732 5.450592 TGCACTGCTGACATTATTTTTCA 57.549 34.783 1.98 0.00 0.00 2.69
2385 2760 5.585047 ACAATCGTTAATTCTAGCAGGAACC 59.415 40.000 0.00 0.00 0.00 3.62
2403 2781 9.003112 CATAAGCTTCTGATTTGTAAACAATCG 57.997 33.333 0.00 0.00 35.55 3.34
2414 2793 6.176183 AGCAGTACACATAAGCTTCTGATTT 58.824 36.000 17.84 4.75 29.98 2.17
2426 2805 7.833285 TGTAGGATGATAAGCAGTACACATA 57.167 36.000 0.00 0.00 0.00 2.29
2464 2843 9.342308 AGAACAACAGAATCAGAAACATAGAAA 57.658 29.630 0.00 0.00 0.00 2.52
2465 2844 8.908786 AGAACAACAGAATCAGAAACATAGAA 57.091 30.769 0.00 0.00 0.00 2.10
2511 2890 4.790765 AAATTCTAGCAAAAGTGGAGCC 57.209 40.909 0.00 0.00 0.00 4.70
2515 2894 7.542025 AGCATTCTAAATTCTAGCAAAAGTGG 58.458 34.615 0.00 0.00 0.00 4.00
2564 2944 5.289595 GTGAAACATACTCTGTGACTGTGA 58.710 41.667 0.00 0.00 38.39 3.58
2565 2945 4.148871 CGTGAAACATACTCTGTGACTGTG 59.851 45.833 0.00 0.00 38.39 3.66
2566 2946 4.202121 ACGTGAAACATACTCTGTGACTGT 60.202 41.667 0.00 0.00 38.39 3.55
2567 2947 4.148871 CACGTGAAACATACTCTGTGACTG 59.851 45.833 10.90 0.00 38.39 3.51
2568 2948 4.202121 ACACGTGAAACATACTCTGTGACT 60.202 41.667 25.01 0.00 38.39 3.41
2569 2949 4.049186 ACACGTGAAACATACTCTGTGAC 58.951 43.478 25.01 0.00 38.39 3.67
2683 3064 6.463995 ACTAGATTCTTCTACCTTGCAGAG 57.536 41.667 0.00 0.00 33.17 3.35
2685 3066 7.099764 TCAAACTAGATTCTTCTACCTTGCAG 58.900 38.462 0.00 0.00 33.17 4.41
2697 3078 9.606631 GTGGTCTTATCAATCAAACTAGATTCT 57.393 33.333 0.00 0.00 36.13 2.40
2745 3127 1.066929 GGGCCAGCACCACTTAATTTG 60.067 52.381 4.39 0.00 0.00 2.32
2881 3263 6.053632 TGCCAATCTAGATCAGTTTCTTCA 57.946 37.500 5.51 0.00 0.00 3.02
2929 3314 2.496070 TGCAGTATCAGGTACACAGACC 59.504 50.000 0.00 0.00 40.08 3.85
2948 3333 3.243501 TGCTGACATCAAAGGAAAACTGC 60.244 43.478 0.00 0.00 0.00 4.40
3041 3426 6.679843 AGCTACAGAACAACTAGAACACTAC 58.320 40.000 0.00 0.00 0.00 2.73
3046 3431 8.488764 CAAGTAAAGCTACAGAACAACTAGAAC 58.511 37.037 0.00 0.00 0.00 3.01
3073 3458 5.863935 GGTCATTTTTCAGCCTGTAAATCAC 59.136 40.000 0.00 0.17 0.00 3.06
3081 3466 8.682936 ATTATACTAGGTCATTTTTCAGCCTG 57.317 34.615 0.00 0.00 0.00 4.85
3246 3631 6.056884 ACTCAAAATGCAAACACATGGAATT 58.943 32.000 0.00 0.00 0.00 2.17
3326 3711 3.701542 TCATAACCCAAACACTGCAAACA 59.298 39.130 0.00 0.00 0.00 2.83
3407 3792 1.834458 AACGGTCGTTAAAGTGCGGC 61.834 55.000 6.99 0.00 36.46 6.53
3428 3813 0.543277 CCTGCTCCTCTGTTATGGCA 59.457 55.000 0.00 0.00 0.00 4.92
3544 3929 7.001674 ACACCAAACTGAGTGATGGTAATTAA 58.998 34.615 19.18 0.00 44.12 1.40
3545 3930 6.539173 ACACCAAACTGAGTGATGGTAATTA 58.461 36.000 19.18 0.00 44.12 1.40
3546 3931 5.385198 ACACCAAACTGAGTGATGGTAATT 58.615 37.500 19.18 7.60 44.12 1.40
3592 3979 6.011628 AGGATGAAGGAGTTCCCATAAGAAAA 60.012 38.462 0.00 0.00 37.41 2.29
3704 4091 5.513267 GGCCAAACACTAGAGAATATAGGGG 60.513 48.000 0.00 0.00 0.00 4.79
3708 4095 7.552687 CACTTTGGCCAAACACTAGAGAATATA 59.447 37.037 27.13 0.72 0.00 0.86
3709 4096 6.375455 CACTTTGGCCAAACACTAGAGAATAT 59.625 38.462 27.13 0.00 0.00 1.28
3727 4114 4.097892 AGAAAAGTAGCCACAACACTTTGG 59.902 41.667 0.13 0.00 40.63 3.28
3732 4119 3.000082 GCAGAAAAGTAGCCACAACAC 58.000 47.619 0.00 0.00 0.00 3.32
3757 4144 2.289631 TGGTACCAGCAGAGTTCATGTG 60.290 50.000 11.60 0.00 0.00 3.21
3787 4174 6.958255 TCCACAATAATAGATGCATGAAACG 58.042 36.000 2.46 0.00 0.00 3.60
3788 4175 6.860023 GCTCCACAATAATAGATGCATGAAAC 59.140 38.462 2.46 0.00 0.00 2.78
3789 4176 6.546772 TGCTCCACAATAATAGATGCATGAAA 59.453 34.615 2.46 0.00 0.00 2.69
3870 4257 8.540507 TCAGGAATCTTAAGCAGTCTTACTAT 57.459 34.615 0.00 0.00 34.71 2.12
3871 4258 7.416890 GCTCAGGAATCTTAAGCAGTCTTACTA 60.417 40.741 0.00 0.00 34.71 1.82
3872 4259 6.629291 GCTCAGGAATCTTAAGCAGTCTTACT 60.629 42.308 0.00 0.00 34.71 2.24
3873 4260 5.522097 GCTCAGGAATCTTAAGCAGTCTTAC 59.478 44.000 0.00 0.00 34.71 2.34
3914 4301 0.322456 TTGAAATCGGGGCACTCTGG 60.322 55.000 0.00 0.00 0.00 3.86
3923 4310 4.157656 TGCTTTTCCAGTATTGAAATCGGG 59.842 41.667 0.00 0.00 32.19 5.14
4013 4400 1.571215 ATTCGCCCGAAACGTTGGTC 61.571 55.000 0.00 0.00 37.69 4.02
4028 4415 2.711311 CTGCCATCCACGCATTCG 59.289 61.111 0.00 0.00 42.43 3.34
4115 4502 1.300080 CTTTGGCCGCCAAGTTGTG 60.300 57.895 23.64 10.05 44.84 3.33
4181 4568 5.445641 CGTATTTAACATTTGACGCGGTTAC 59.554 40.000 12.47 0.00 0.00 2.50
4189 4576 5.157781 TGCTTGCCGTATTTAACATTTGAC 58.842 37.500 0.00 0.00 0.00 3.18
4219 4606 9.178427 GCAAGATTAGAATTTGCATCTCATAAC 57.822 33.333 12.93 0.00 44.88 1.89
4225 4612 4.037208 CCGGCAAGATTAGAATTTGCATCT 59.963 41.667 16.65 0.00 46.74 2.90
4286 4673 1.073763 TGTGTGTGGCTTGGCTTATCT 59.926 47.619 0.00 0.00 0.00 1.98
4321 4739 1.371635 GCCACCATGTTCGTTGCAC 60.372 57.895 0.00 0.00 0.00 4.57
4372 4790 2.242043 CACCCAAGGCTGTCAAATTCT 58.758 47.619 0.00 0.00 0.00 2.40
4420 4838 5.454062 CATTCCCCATCCACCAAATTACTA 58.546 41.667 0.00 0.00 0.00 1.82
4431 4849 3.488355 AATTTCACCATTCCCCATCCA 57.512 42.857 0.00 0.00 0.00 3.41
4438 4856 5.221048 CCCATACTCGAAATTTCACCATTCC 60.221 44.000 17.99 0.00 0.00 3.01
4447 4865 4.080299 AGCCTTCTCCCATACTCGAAATTT 60.080 41.667 0.00 0.00 0.00 1.82
4456 4874 1.839894 CCCCAGCCTTCTCCCATAC 59.160 63.158 0.00 0.00 0.00 2.39
4464 4882 2.116125 ACACAAGCCCCAGCCTTC 59.884 61.111 0.00 0.00 41.25 3.46
4470 4888 2.005606 ATCACCACACACAAGCCCCA 62.006 55.000 0.00 0.00 0.00 4.96
4494 4912 3.149196 TCCTTCACCAATCAGCTCAAAC 58.851 45.455 0.00 0.00 0.00 2.93
4514 4932 1.172175 CTGCAGCCTTCCTTTCCTTC 58.828 55.000 0.00 0.00 0.00 3.46
4515 4933 0.897401 GCTGCAGCCTTCCTTTCCTT 60.897 55.000 28.76 0.00 34.31 3.36
4516 4934 1.303970 GCTGCAGCCTTCCTTTCCT 60.304 57.895 28.76 0.00 34.31 3.36
4517 4935 2.694760 CGCTGCAGCCTTCCTTTCC 61.695 63.158 32.07 1.67 37.91 3.13
4518 4936 2.694760 CCGCTGCAGCCTTCCTTTC 61.695 63.158 32.07 2.46 37.91 2.62
4519 4937 2.674380 CCGCTGCAGCCTTCCTTT 60.674 61.111 32.07 0.00 37.91 3.11
4634 5053 1.048601 GATAGGATTCCGCCTCCACA 58.951 55.000 0.00 0.00 39.50 4.17
4635 5054 0.321996 GGATAGGATTCCGCCTCCAC 59.678 60.000 13.31 0.00 39.50 4.02
4636 5055 0.836400 GGGATAGGATTCCGCCTCCA 60.836 60.000 17.57 0.00 39.50 3.86
4638 5057 1.002544 CAAGGGATAGGATTCCGCCTC 59.997 57.143 10.70 3.81 39.50 4.70
4639 5058 1.059913 CAAGGGATAGGATTCCGCCT 58.940 55.000 10.70 0.00 42.15 5.52
4640 5059 0.765510 ACAAGGGATAGGATTCCGCC 59.234 55.000 0.00 0.60 36.58 6.13
4641 5060 3.181458 TGTTACAAGGGATAGGATTCCGC 60.181 47.826 0.00 0.00 36.58 5.54
4642 5061 4.632153 CTGTTACAAGGGATAGGATTCCG 58.368 47.826 0.00 0.00 36.58 4.30
4643 5062 4.390264 GCTGTTACAAGGGATAGGATTCC 58.610 47.826 0.00 0.00 34.83 3.01
4644 5063 4.103311 AGGCTGTTACAAGGGATAGGATTC 59.897 45.833 0.00 0.00 0.00 2.52
4941 5360 3.924114 TTCAACCAACAAGACAGGAGA 57.076 42.857 0.00 0.00 0.00 3.71
4942 5361 3.187227 CGATTCAACCAACAAGACAGGAG 59.813 47.826 0.00 0.00 0.00 3.69
4943 5362 3.138304 CGATTCAACCAACAAGACAGGA 58.862 45.455 0.00 0.00 0.00 3.86
4944 5363 3.138304 TCGATTCAACCAACAAGACAGG 58.862 45.455 0.00 0.00 0.00 4.00
4945 5364 4.811555 TTCGATTCAACCAACAAGACAG 57.188 40.909 0.00 0.00 0.00 3.51
4996 5415 0.725117 CGGACGCATAGGTTTCCAAC 59.275 55.000 0.00 0.00 0.00 3.77
4997 5416 0.322322 ACGGACGCATAGGTTTCCAA 59.678 50.000 0.00 0.00 0.00 3.53
4998 5417 0.322322 AACGGACGCATAGGTTTCCA 59.678 50.000 0.00 0.00 0.00 3.53
4999 5418 0.725117 CAACGGACGCATAGGTTTCC 59.275 55.000 0.00 0.00 0.00 3.13
5000 5419 0.096454 GCAACGGACGCATAGGTTTC 59.904 55.000 0.00 0.00 0.00 2.78
5001 5420 1.303091 GGCAACGGACGCATAGGTTT 61.303 55.000 0.00 0.00 0.00 3.27
5002 5421 1.743995 GGCAACGGACGCATAGGTT 60.744 57.895 0.00 0.00 0.00 3.50
5003 5422 2.125269 GGCAACGGACGCATAGGT 60.125 61.111 0.00 0.00 0.00 3.08
5015 5434 1.298157 TAGCACATGACAGCGGCAAC 61.298 55.000 0.00 0.00 35.48 4.17
5016 5435 1.003959 TAGCACATGACAGCGGCAA 60.004 52.632 0.00 0.00 35.48 4.52
5017 5436 1.448365 CTAGCACATGACAGCGGCA 60.448 57.895 0.00 0.00 35.48 5.69
5018 5437 2.817423 GCTAGCACATGACAGCGGC 61.817 63.158 10.63 7.17 35.48 6.53
5019 5438 2.176273 GGCTAGCACATGACAGCGG 61.176 63.158 18.24 1.10 34.80 5.52
5020 5439 2.176273 GGGCTAGCACATGACAGCG 61.176 63.158 18.24 0.00 34.80 5.18
5021 5440 1.821332 GGGGCTAGCACATGACAGC 60.821 63.158 20.77 0.00 0.00 4.40
5022 5441 1.153086 GGGGGCTAGCACATGACAG 60.153 63.158 20.77 0.00 0.00 3.51
5023 5442 1.281199 ATGGGGGCTAGCACATGACA 61.281 55.000 20.77 12.11 0.00 3.58
5024 5443 0.820891 CATGGGGGCTAGCACATGAC 60.821 60.000 28.13 14.28 42.39 3.06
5025 5444 1.533219 CATGGGGGCTAGCACATGA 59.467 57.895 28.13 11.26 42.39 3.07
5026 5445 2.198287 GCATGGGGGCTAGCACATG 61.198 63.158 27.91 27.91 42.61 3.21
5027 5446 1.941403 AAGCATGGGGGCTAGCACAT 61.941 55.000 20.77 15.36 45.07 3.21
5028 5447 2.615465 AAGCATGGGGGCTAGCACA 61.615 57.895 20.77 13.65 45.07 4.57
5029 5448 2.123428 CAAGCATGGGGGCTAGCAC 61.123 63.158 18.24 14.02 45.07 4.40
5030 5449 1.862049 TTCAAGCATGGGGGCTAGCA 61.862 55.000 18.24 0.00 45.07 3.49
5031 5450 0.684153 TTTCAAGCATGGGGGCTAGC 60.684 55.000 6.04 6.04 45.07 3.42
5032 5451 1.684983 CATTTCAAGCATGGGGGCTAG 59.315 52.381 0.00 0.00 45.07 3.42
5033 5452 1.287442 TCATTTCAAGCATGGGGGCTA 59.713 47.619 0.00 0.00 45.07 3.93
5035 5454 1.125633 ATCATTTCAAGCATGGGGGC 58.874 50.000 0.00 0.00 0.00 5.80
5036 5455 3.036091 AGAATCATTTCAAGCATGGGGG 58.964 45.455 0.00 0.00 34.08 5.40
5037 5456 4.891756 AGTAGAATCATTTCAAGCATGGGG 59.108 41.667 0.00 0.00 34.08 4.96
5051 5470 3.432186 GGGCACAGCATACAGTAGAATCA 60.432 47.826 0.00 0.00 0.00 2.57
5052 5471 3.134458 GGGCACAGCATACAGTAGAATC 58.866 50.000 0.00 0.00 0.00 2.52
5053 5472 2.774234 AGGGCACAGCATACAGTAGAAT 59.226 45.455 0.00 0.00 0.00 2.40
5054 5473 2.168521 GAGGGCACAGCATACAGTAGAA 59.831 50.000 0.00 0.00 0.00 2.10
5057 5476 0.459899 CGAGGGCACAGCATACAGTA 59.540 55.000 0.00 0.00 0.00 2.74
5058 5477 1.219124 CGAGGGCACAGCATACAGT 59.781 57.895 0.00 0.00 0.00 3.55
5059 5478 0.391661 AACGAGGGCACAGCATACAG 60.392 55.000 0.00 0.00 0.00 2.74
5060 5479 0.899019 TAACGAGGGCACAGCATACA 59.101 50.000 0.00 0.00 0.00 2.29
5063 5482 0.391661 CAGTAACGAGGGCACAGCAT 60.392 55.000 0.00 0.00 0.00 3.79
5064 5483 1.005037 CAGTAACGAGGGCACAGCA 60.005 57.895 0.00 0.00 0.00 4.41
5065 5484 2.391389 GCAGTAACGAGGGCACAGC 61.391 63.158 0.00 0.00 0.00 4.40
5066 5485 0.737715 GAGCAGTAACGAGGGCACAG 60.738 60.000 0.00 0.00 0.00 3.66
5068 5487 1.805945 CGAGCAGTAACGAGGGCAC 60.806 63.158 0.00 0.00 0.00 5.01
5071 5490 1.433879 CTCCGAGCAGTAACGAGGG 59.566 63.158 0.00 0.00 0.00 4.30
5073 5492 1.433879 CCCTCCGAGCAGTAACGAG 59.566 63.158 0.00 0.00 0.00 4.18
5074 5493 2.050350 CCCCTCCGAGCAGTAACGA 61.050 63.158 0.00 0.00 0.00 3.85
5075 5494 2.050350 TCCCCTCCGAGCAGTAACG 61.050 63.158 0.00 0.00 0.00 3.18
5076 5495 1.516423 GTCCCCTCCGAGCAGTAAC 59.484 63.158 0.00 0.00 0.00 2.50
5077 5496 2.050350 CGTCCCCTCCGAGCAGTAA 61.050 63.158 0.00 0.00 0.00 2.24
5078 5497 2.439701 CGTCCCCTCCGAGCAGTA 60.440 66.667 0.00 0.00 0.00 2.74
5086 5549 2.138453 AAAAAGAGCCCGTCCCCTCC 62.138 60.000 0.00 0.00 0.00 4.30
5108 5578 0.709992 AGCCTGTCTTCTCTCCCTCT 59.290 55.000 0.00 0.00 0.00 3.69
5115 5585 2.825532 ACAAGAGAGAGCCTGTCTTCTC 59.174 50.000 10.38 1.72 41.20 2.87
5123 5593 0.474660 AACCCCACAAGAGAGAGCCT 60.475 55.000 0.00 0.00 0.00 4.58
5130 5600 3.194542 TCAAAACACAAACCCCACAAGAG 59.805 43.478 0.00 0.00 0.00 2.85
5142 5612 6.607689 CACACTTAGACAACTCAAAACACAA 58.392 36.000 0.00 0.00 0.00 3.33
5144 5614 5.028375 GCACACTTAGACAACTCAAAACAC 58.972 41.667 0.00 0.00 0.00 3.32
5145 5615 4.697828 TGCACACTTAGACAACTCAAAACA 59.302 37.500 0.00 0.00 0.00 2.83
5149 5619 2.872245 GCTGCACACTTAGACAACTCAA 59.128 45.455 0.00 0.00 0.00 3.02
5150 5620 2.103094 AGCTGCACACTTAGACAACTCA 59.897 45.455 1.02 0.00 0.00 3.41
5151 5621 2.478134 CAGCTGCACACTTAGACAACTC 59.522 50.000 0.00 0.00 0.00 3.01
5152 5622 2.487934 CAGCTGCACACTTAGACAACT 58.512 47.619 0.00 0.00 0.00 3.16
5153 5623 1.532868 CCAGCTGCACACTTAGACAAC 59.467 52.381 8.66 0.00 0.00 3.32
5155 5625 0.603707 GCCAGCTGCACACTTAGACA 60.604 55.000 8.66 0.00 40.77 3.41
5156 5626 1.630244 CGCCAGCTGCACACTTAGAC 61.630 60.000 8.66 0.00 41.33 2.59
5157 5627 1.374631 CGCCAGCTGCACACTTAGA 60.375 57.895 8.66 0.00 41.33 2.10
5158 5628 3.031964 GCGCCAGCTGCACACTTAG 62.032 63.158 8.66 0.00 41.33 2.18
5159 5629 3.049674 GCGCCAGCTGCACACTTA 61.050 61.111 8.66 0.00 41.33 2.24


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

AutoCloner maintained by Alex Coulton.