Multiple sequence alignment - TraesCS1D01G291100

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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 TraesCS1D01G291100 chr1D 100.000 3765 0 0 1 3765 389430319 389426555 0.000000e+00 6953.0
1 TraesCS1D01G291100 chr1D 90.872 1457 89 19 652 2070 389796688 389798138 0.000000e+00 1914.0
2 TraesCS1D01G291100 chr1D 94.428 1041 46 8 2146 3181 389798272 389799305 0.000000e+00 1591.0
3 TraesCS1D01G291100 chr1D 99.112 563 5 0 3203 3765 421868907 421869469 0.000000e+00 1013.0
4 TraesCS1D01G291100 chr1D 80.706 850 136 13 841 1688 390686560 390685737 1.480000e-178 636.0
5 TraesCS1D01G291100 chr1D 78.846 988 160 29 712 1685 390665756 390666708 4.130000e-174 621.0
6 TraesCS1D01G291100 chr1D 77.220 518 35 34 264 735 389953334 389952854 3.780000e-55 226.0
7 TraesCS1D01G291100 chr1D 81.494 308 23 20 242 545 389794189 389794466 4.890000e-54 222.0
8 TraesCS1D01G291100 chr1D 87.234 188 13 1 726 902 389952824 389952637 1.770000e-48 204.0
9 TraesCS1D01G291100 chr1D 87.255 102 3 1 570 661 389796565 389796666 1.430000e-19 108.0
10 TraesCS1D01G291100 chr1A 89.177 3012 188 63 251 3172 488186530 488189493 0.000000e+00 3629.0
11 TraesCS1D01G291100 chr1A 79.931 867 138 20 825 1685 488229397 488228561 4.160000e-169 604.0
12 TraesCS1D01G291100 chr1A 88.415 164 15 4 478 637 10733426 10733263 1.070000e-45 195.0
13 TraesCS1D01G291100 chr1B 90.578 987 48 22 2244 3203 522755936 522756904 0.000000e+00 1266.0
14 TraesCS1D01G291100 chr1B 88.703 956 64 18 1294 2217 522755001 522755944 0.000000e+00 1127.0
15 TraesCS1D01G291100 chr1B 91.252 583 35 4 712 1283 522753929 522754506 0.000000e+00 780.0
16 TraesCS1D01G291100 chr1B 78.991 971 159 25 728 1685 523150618 523149680 4.130000e-174 621.0
17 TraesCS1D01G291100 chr1B 78.888 971 160 25 728 1685 523008796 523009734 1.920000e-172 616.0
18 TraesCS1D01G291100 chr1B 97.403 77 2 0 659 735 522753832 522753908 8.490000e-27 132.0
19 TraesCS1D01G291100 chr1B 83.721 129 11 2 543 661 522753675 522753803 3.070000e-21 113.0
20 TraesCS1D01G291100 chr5D 98.934 563 6 0 3203 3765 29140559 29141121 0.000000e+00 1007.0
21 TraesCS1D01G291100 chr5D 98.401 563 9 0 3203 3765 408619733 408619171 0.000000e+00 990.0
22 TraesCS1D01G291100 chr5D 98.182 55 1 0 1 55 204869290 204869344 3.100000e-16 97.1
23 TraesCS1D01G291100 chr2D 98.757 563 7 0 3203 3765 22832516 22833078 0.000000e+00 1002.0
24 TraesCS1D01G291100 chr2D 98.401 563 9 0 3203 3765 122956578 122957140 0.000000e+00 990.0
25 TraesCS1D01G291100 chr2D 88.333 60 4 2 2825 2884 559209302 559209246 6.750000e-08 69.4
26 TraesCS1D01G291100 chrUn 98.401 563 9 0 3203 3765 413858880 413859442 0.000000e+00 990.0
27 TraesCS1D01G291100 chr7D 98.401 563 9 0 3203 3765 47001533 47000971 0.000000e+00 990.0
28 TraesCS1D01G291100 chr7D 93.750 64 0 2 2825 2884 506141362 506141299 4.000000e-15 93.5
29 TraesCS1D01G291100 chr7D 97.561 41 1 0 2821 2861 634214348 634214308 1.880000e-08 71.3
30 TraesCS1D01G291100 chr6D 98.401 563 9 0 3203 3765 68638748 68638186 0.000000e+00 990.0
31 TraesCS1D01G291100 chr4D 98.401 563 9 0 3203 3765 402966107 402966669 0.000000e+00 990.0
32 TraesCS1D01G291100 chr4D 95.652 46 1 1 2817 2861 358476944 358476899 5.220000e-09 73.1
33 TraesCS1D01G291100 chr7A 90.240 625 55 1 1178 1796 299027716 299028340 0.000000e+00 811.0
34 TraesCS1D01G291100 chr7A 85.714 154 20 2 5 157 518951128 518951280 1.080000e-35 161.0
35 TraesCS1D01G291100 chr7A 84.615 78 5 5 2817 2887 573676688 573676765 1.880000e-08 71.3
36 TraesCS1D01G291100 chr2A 90.854 164 11 3 478 637 777200012 777200175 2.280000e-52 217.0
37 TraesCS1D01G291100 chr2A 89.571 163 13 1 478 636 39910333 39910495 1.770000e-48 204.0
38 TraesCS1D01G291100 chr2A 90.000 60 3 1 2825 2884 699796402 699796346 1.450000e-09 75.0
39 TraesCS1D01G291100 chr2A 100.000 39 0 0 2823 2861 176676453 176676415 5.220000e-09 73.1
40 TraesCS1D01G291100 chr3A 90.798 163 11 4 478 636 603858855 603858693 8.190000e-52 215.0
41 TraesCS1D01G291100 chr3A 86.111 72 4 3 2818 2884 568019710 568019780 5.220000e-09 73.1
42 TraesCS1D01G291100 chr6B 89.103 156 17 0 5 160 75278923 75278768 1.070000e-45 195.0
43 TraesCS1D01G291100 chr6A 87.755 147 16 2 3 148 420407472 420407327 1.800000e-38 171.0
44 TraesCS1D01G291100 chr5B 89.474 57 5 1 2825 2880 691153428 691153484 1.880000e-08 71.3
45 TraesCS1D01G291100 chr2B 84.615 65 5 4 2824 2887 742820325 742820265 4.060000e-05 60.2


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 TraesCS1D01G291100 chr1D 389426555 389430319 3764 True 6953.00 6953 100.00000 1 3765 1 chr1D.!!$R1 3764
1 TraesCS1D01G291100 chr1D 421868907 421869469 562 False 1013.00 1013 99.11200 3203 3765 1 chr1D.!!$F2 562
2 TraesCS1D01G291100 chr1D 389794189 389799305 5116 False 958.75 1914 88.51225 242 3181 4 chr1D.!!$F3 2939
3 TraesCS1D01G291100 chr1D 390685737 390686560 823 True 636.00 636 80.70600 841 1688 1 chr1D.!!$R2 847
4 TraesCS1D01G291100 chr1D 390665756 390666708 952 False 621.00 621 78.84600 712 1685 1 chr1D.!!$F1 973
5 TraesCS1D01G291100 chr1D 389952637 389953334 697 True 215.00 226 82.22700 264 902 2 chr1D.!!$R3 638
6 TraesCS1D01G291100 chr1A 488186530 488189493 2963 False 3629.00 3629 89.17700 251 3172 1 chr1A.!!$F1 2921
7 TraesCS1D01G291100 chr1A 488228561 488229397 836 True 604.00 604 79.93100 825 1685 1 chr1A.!!$R2 860
8 TraesCS1D01G291100 chr1B 522753675 522756904 3229 False 683.60 1266 90.33140 543 3203 5 chr1B.!!$F2 2660
9 TraesCS1D01G291100 chr1B 523149680 523150618 938 True 621.00 621 78.99100 728 1685 1 chr1B.!!$R1 957
10 TraesCS1D01G291100 chr1B 523008796 523009734 938 False 616.00 616 78.88800 728 1685 1 chr1B.!!$F1 957
11 TraesCS1D01G291100 chr5D 29140559 29141121 562 False 1007.00 1007 98.93400 3203 3765 1 chr5D.!!$F1 562
12 TraesCS1D01G291100 chr5D 408619171 408619733 562 True 990.00 990 98.40100 3203 3765 1 chr5D.!!$R1 562
13 TraesCS1D01G291100 chr2D 22832516 22833078 562 False 1002.00 1002 98.75700 3203 3765 1 chr2D.!!$F1 562
14 TraesCS1D01G291100 chr2D 122956578 122957140 562 False 990.00 990 98.40100 3203 3765 1 chr2D.!!$F2 562
15 TraesCS1D01G291100 chrUn 413858880 413859442 562 False 990.00 990 98.40100 3203 3765 1 chrUn.!!$F1 562
16 TraesCS1D01G291100 chr7D 47000971 47001533 562 True 990.00 990 98.40100 3203 3765 1 chr7D.!!$R1 562
17 TraesCS1D01G291100 chr6D 68638186 68638748 562 True 990.00 990 98.40100 3203 3765 1 chr6D.!!$R1 562
18 TraesCS1D01G291100 chr4D 402966107 402966669 562 False 990.00 990 98.40100 3203 3765 1 chr4D.!!$F1 562
19 TraesCS1D01G291100 chr7A 299027716 299028340 624 False 811.00 811 90.24000 1178 1796 1 chr7A.!!$F1 618

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
200 201 0.037697 CAGTCGTGGGGTGATTTCGA 60.038 55.0 0.00 0.00 0.0 3.71 F
223 224 0.109735 CAACGTCGCTACTCTGCAGA 60.110 55.0 17.19 17.19 0.0 4.26 F
225 226 0.169230 ACGTCGCTACTCTGCAGAAG 59.831 55.0 18.85 14.27 0.0 2.85 F
2096 4871 0.599558 CATGGCCCTTGTGAGTTGTG 59.400 55.0 0.00 0.00 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1341 4037 0.109412 CCTTGGACACCTCGACGTAC 60.109 60.000 0.00 0.0 0.0 3.67 R
2070 4801 1.304381 ACAAGGGCCATGCGACATT 60.304 52.632 9.01 0.0 0.0 2.71 R
2162 4959 2.872245 CAGGTACCACAACTCAACACAG 59.128 50.000 15.94 0.0 0.0 3.66 R
3143 5968 0.370273 CGGAAGCGAGATTTGAACCG 59.630 55.000 0.00 0.0 0.0 4.44 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
33 34 8.807948 TCTTCATCCCAAACTTTAGAATTAGG 57.192 34.615 0.00 0.00 0.00 2.69
34 35 8.390921 TCTTCATCCCAAACTTTAGAATTAGGT 58.609 33.333 0.00 0.00 0.00 3.08
35 36 8.950007 TTCATCCCAAACTTTAGAATTAGGTT 57.050 30.769 0.00 0.00 0.00 3.50
36 37 8.950007 TCATCCCAAACTTTAGAATTAGGTTT 57.050 30.769 0.00 0.00 0.00 3.27
37 38 9.020731 TCATCCCAAACTTTAGAATTAGGTTTC 57.979 33.333 0.00 0.00 0.00 2.78
38 39 7.770366 TCCCAAACTTTAGAATTAGGTTTCC 57.230 36.000 0.00 0.00 0.00 3.13
39 40 7.299134 TCCCAAACTTTAGAATTAGGTTTCCA 58.701 34.615 0.00 0.00 0.00 3.53
40 41 7.785506 TCCCAAACTTTAGAATTAGGTTTCCAA 59.214 33.333 0.00 0.00 0.00 3.53
41 42 8.425703 CCCAAACTTTAGAATTAGGTTTCCAAA 58.574 33.333 0.00 0.00 0.00 3.28
42 43 9.476202 CCAAACTTTAGAATTAGGTTTCCAAAG 57.524 33.333 4.35 4.35 39.05 2.77
46 47 9.807921 ACTTTAGAATTAGGTTTCCAAAGATCA 57.192 29.630 10.58 0.00 36.83 2.92
48 49 9.807921 TTTAGAATTAGGTTTCCAAAGATCACT 57.192 29.630 0.00 0.00 0.00 3.41
51 52 9.981460 AGAATTAGGTTTCCAAAGATCACTAAT 57.019 29.630 0.00 0.00 0.00 1.73
56 57 8.000780 AGGTTTCCAAAGATCACTAATAATGC 57.999 34.615 0.00 0.00 0.00 3.56
57 58 7.836183 AGGTTTCCAAAGATCACTAATAATGCT 59.164 33.333 0.00 0.00 0.00 3.79
58 59 9.120538 GGTTTCCAAAGATCACTAATAATGCTA 57.879 33.333 0.00 0.00 0.00 3.49
60 61 8.908786 TTCCAAAGATCACTAATAATGCTAGG 57.091 34.615 0.00 0.00 0.00 3.02
61 62 8.262601 TCCAAAGATCACTAATAATGCTAGGA 57.737 34.615 0.00 0.00 0.00 2.94
62 63 8.150945 TCCAAAGATCACTAATAATGCTAGGAC 58.849 37.037 0.00 0.00 0.00 3.85
63 64 7.933577 CCAAAGATCACTAATAATGCTAGGACA 59.066 37.037 0.00 0.00 0.00 4.02
64 65 9.330063 CAAAGATCACTAATAATGCTAGGACAA 57.670 33.333 0.00 0.00 0.00 3.18
65 66 9.553064 AAAGATCACTAATAATGCTAGGACAAG 57.447 33.333 0.00 0.00 0.00 3.16
66 67 7.675062 AGATCACTAATAATGCTAGGACAAGG 58.325 38.462 0.00 0.00 0.00 3.61
67 68 5.611374 TCACTAATAATGCTAGGACAAGGC 58.389 41.667 0.00 0.00 0.00 4.35
68 69 4.757149 CACTAATAATGCTAGGACAAGGCC 59.243 45.833 0.00 0.00 0.00 5.19
69 70 2.959465 ATAATGCTAGGACAAGGCCC 57.041 50.000 0.00 0.00 0.00 5.80
70 71 1.590591 TAATGCTAGGACAAGGCCCA 58.409 50.000 0.00 0.00 0.00 5.36
71 72 0.929244 AATGCTAGGACAAGGCCCAT 59.071 50.000 0.00 0.00 0.00 4.00
72 73 0.929244 ATGCTAGGACAAGGCCCATT 59.071 50.000 0.00 0.00 0.00 3.16
73 74 0.255890 TGCTAGGACAAGGCCCATTC 59.744 55.000 0.00 0.00 0.00 2.67
74 75 0.255890 GCTAGGACAAGGCCCATTCA 59.744 55.000 0.00 0.00 0.00 2.57
75 76 1.340991 GCTAGGACAAGGCCCATTCAA 60.341 52.381 0.00 0.00 0.00 2.69
76 77 2.648059 CTAGGACAAGGCCCATTCAAG 58.352 52.381 0.00 0.00 0.00 3.02
77 78 0.779997 AGGACAAGGCCCATTCAAGT 59.220 50.000 0.00 0.00 0.00 3.16
78 79 1.147817 AGGACAAGGCCCATTCAAGTT 59.852 47.619 0.00 0.00 0.00 2.66
79 80 1.273327 GGACAAGGCCCATTCAAGTTG 59.727 52.381 0.00 0.00 0.00 3.16
80 81 1.273327 GACAAGGCCCATTCAAGTTGG 59.727 52.381 0.00 0.00 0.00 3.77
90 91 4.813027 CCATTCAAGTTGGGTTTGAGATG 58.187 43.478 2.34 0.00 36.07 2.90
91 92 4.523943 CCATTCAAGTTGGGTTTGAGATGA 59.476 41.667 2.34 0.00 36.07 2.92
92 93 5.186409 CCATTCAAGTTGGGTTTGAGATGAT 59.814 40.000 2.34 0.00 36.07 2.45
93 94 5.964958 TTCAAGTTGGGTTTGAGATGATC 57.035 39.130 2.34 0.00 36.07 2.92
94 95 4.984295 TCAAGTTGGGTTTGAGATGATCA 58.016 39.130 0.00 0.00 35.62 2.92
95 96 5.573219 TCAAGTTGGGTTTGAGATGATCAT 58.427 37.500 8.25 8.25 37.89 2.45
96 97 6.720309 TCAAGTTGGGTTTGAGATGATCATA 58.280 36.000 8.54 0.00 37.89 2.15
97 98 7.174413 TCAAGTTGGGTTTGAGATGATCATAA 58.826 34.615 8.54 0.00 37.89 1.90
98 99 7.669304 TCAAGTTGGGTTTGAGATGATCATAAA 59.331 33.333 8.54 3.03 37.89 1.40
99 100 8.472413 CAAGTTGGGTTTGAGATGATCATAAAT 58.528 33.333 8.54 0.00 37.89 1.40
100 101 8.599624 AGTTGGGTTTGAGATGATCATAAATT 57.400 30.769 8.54 0.00 37.89 1.82
101 102 9.039165 AGTTGGGTTTGAGATGATCATAAATTT 57.961 29.630 8.54 0.00 37.89 1.82
102 103 9.657419 GTTGGGTTTGAGATGATCATAAATTTT 57.343 29.630 8.54 0.00 37.89 1.82
103 104 9.656040 TTGGGTTTGAGATGATCATAAATTTTG 57.344 29.630 8.54 0.00 37.89 2.44
104 105 8.814931 TGGGTTTGAGATGATCATAAATTTTGT 58.185 29.630 8.54 0.00 37.89 2.83
105 106 9.305925 GGGTTTGAGATGATCATAAATTTTGTC 57.694 33.333 8.54 0.00 37.89 3.18
106 107 9.305925 GGTTTGAGATGATCATAAATTTTGTCC 57.694 33.333 8.54 0.00 37.89 4.02
107 108 9.305925 GTTTGAGATGATCATAAATTTTGTCCC 57.694 33.333 8.54 0.00 37.89 4.46
108 109 8.592529 TTGAGATGATCATAAATTTTGTCCCA 57.407 30.769 8.54 0.00 37.89 4.37
109 110 8.592529 TGAGATGATCATAAATTTTGTCCCAA 57.407 30.769 8.54 0.00 31.12 4.12
110 111 9.204337 TGAGATGATCATAAATTTTGTCCCAAT 57.796 29.630 8.54 0.00 31.12 3.16
111 112 9.688592 GAGATGATCATAAATTTTGTCCCAATC 57.311 33.333 8.54 0.00 0.00 2.67
112 113 9.430399 AGATGATCATAAATTTTGTCCCAATCT 57.570 29.630 8.54 0.00 0.00 2.40
115 116 9.656040 TGATCATAAATTTTGTCCCAATCTTTG 57.344 29.630 0.00 0.00 0.00 2.77
116 117 7.903995 TCATAAATTTTGTCCCAATCTTTGC 57.096 32.000 0.00 0.00 0.00 3.68
117 118 7.448420 TCATAAATTTTGTCCCAATCTTTGCA 58.552 30.769 0.00 0.00 0.00 4.08
118 119 7.387397 TCATAAATTTTGTCCCAATCTTTGCAC 59.613 33.333 0.00 0.00 0.00 4.57
119 120 3.467374 TTTTGTCCCAATCTTTGCACC 57.533 42.857 0.00 0.00 0.00 5.01
120 121 2.079170 TTGTCCCAATCTTTGCACCA 57.921 45.000 0.00 0.00 0.00 4.17
121 122 2.079170 TGTCCCAATCTTTGCACCAA 57.921 45.000 0.00 0.00 0.00 3.67
122 123 1.962807 TGTCCCAATCTTTGCACCAAG 59.037 47.619 0.00 0.00 0.00 3.61
123 124 1.273327 GTCCCAATCTTTGCACCAAGG 59.727 52.381 0.00 0.00 0.00 3.61
124 125 1.146774 TCCCAATCTTTGCACCAAGGA 59.853 47.619 0.00 0.00 34.19 3.36
125 126 2.181975 CCCAATCTTTGCACCAAGGAT 58.818 47.619 0.00 0.00 40.91 3.24
126 127 2.568509 CCCAATCTTTGCACCAAGGATT 59.431 45.455 8.83 8.83 46.14 3.01
129 130 4.961438 AATCTTTGCACCAAGGATTGTT 57.039 36.364 12.57 0.00 44.46 2.83
130 131 4.525912 ATCTTTGCACCAAGGATTGTTC 57.474 40.909 0.00 0.00 46.99 3.18
131 132 2.627699 TCTTTGCACCAAGGATTGTTCC 59.372 45.455 0.00 0.00 46.99 3.62
132 133 2.079170 TTGCACCAAGGATTGTTCCA 57.921 45.000 0.00 0.00 46.99 3.53
133 134 2.079170 TGCACCAAGGATTGTTCCAA 57.921 45.000 0.00 0.00 46.99 3.53
134 135 2.392662 TGCACCAAGGATTGTTCCAAA 58.607 42.857 0.00 0.00 46.99 3.28
135 136 2.971330 TGCACCAAGGATTGTTCCAAAT 59.029 40.909 0.00 0.00 46.99 2.32
136 137 3.244146 TGCACCAAGGATTGTTCCAAATG 60.244 43.478 0.00 0.00 46.99 2.32
137 138 3.865684 GCACCAAGGATTGTTCCAAATGG 60.866 47.826 0.00 8.90 46.99 3.16
138 139 3.577848 CACCAAGGATTGTTCCAAATGGA 59.422 43.478 14.57 0.00 46.99 3.41
139 140 3.834231 ACCAAGGATTGTTCCAAATGGAG 59.166 43.478 14.57 0.00 46.99 3.86
140 141 3.196254 CCAAGGATTGTTCCAAATGGAGG 59.804 47.826 1.86 0.00 46.99 4.30
141 142 4.088634 CAAGGATTGTTCCAAATGGAGGA 58.911 43.478 1.86 0.00 45.30 3.71
142 143 3.973425 AGGATTGTTCCAAATGGAGGAG 58.027 45.455 1.86 0.00 46.36 3.69
143 144 3.334881 AGGATTGTTCCAAATGGAGGAGT 59.665 43.478 1.86 0.00 46.36 3.85
144 145 4.089361 GGATTGTTCCAAATGGAGGAGTT 58.911 43.478 1.86 0.00 46.36 3.01
145 146 5.015178 AGGATTGTTCCAAATGGAGGAGTTA 59.985 40.000 1.86 0.00 46.36 2.24
146 147 5.125578 GGATTGTTCCAAATGGAGGAGTTAC 59.874 44.000 1.86 0.00 46.36 2.50
147 148 4.028993 TGTTCCAAATGGAGGAGTTACC 57.971 45.455 1.86 0.00 46.36 2.85
148 149 9.871500 GGATTGTTCCAAATGGAGGAGTTACCT 62.872 44.444 1.86 0.00 46.36 3.08
165 166 9.096160 GGAGTTACCTTTAGTAATTTGCTACTC 57.904 37.037 0.00 0.00 42.81 2.59
166 167 9.872721 GAGTTACCTTTAGTAATTTGCTACTCT 57.127 33.333 0.00 0.00 42.81 3.24
167 168 9.654663 AGTTACCTTTAGTAATTTGCTACTCTG 57.345 33.333 0.00 0.00 42.81 3.35
168 169 9.433153 GTTACCTTTAGTAATTTGCTACTCTGT 57.567 33.333 0.00 0.00 42.81 3.41
170 171 8.919777 ACCTTTAGTAATTTGCTACTCTGTTT 57.080 30.769 0.00 0.00 34.03 2.83
171 172 9.350951 ACCTTTAGTAATTTGCTACTCTGTTTT 57.649 29.630 0.00 0.00 34.03 2.43
190 191 4.889807 TGGTTTTCCAGTCGTGGG 57.110 55.556 0.00 0.00 46.22 4.61
191 192 1.149627 TGGTTTTCCAGTCGTGGGG 59.850 57.895 0.00 0.00 46.22 4.96
192 193 1.149854 GGTTTTCCAGTCGTGGGGT 59.850 57.895 0.00 0.00 45.11 4.95
193 194 1.170290 GGTTTTCCAGTCGTGGGGTG 61.170 60.000 0.00 0.00 45.11 4.61
194 195 0.179040 GTTTTCCAGTCGTGGGGTGA 60.179 55.000 0.00 0.00 45.11 4.02
195 196 0.768622 TTTTCCAGTCGTGGGGTGAT 59.231 50.000 0.00 0.00 45.11 3.06
196 197 0.768622 TTTCCAGTCGTGGGGTGATT 59.231 50.000 0.00 0.00 45.11 2.57
197 198 0.768622 TTCCAGTCGTGGGGTGATTT 59.231 50.000 0.00 0.00 45.11 2.17
198 199 0.323629 TCCAGTCGTGGGGTGATTTC 59.676 55.000 0.00 0.00 45.11 2.17
199 200 1.019278 CCAGTCGTGGGGTGATTTCG 61.019 60.000 0.00 0.00 40.67 3.46
200 201 0.037697 CAGTCGTGGGGTGATTTCGA 60.038 55.000 0.00 0.00 0.00 3.71
201 202 0.682852 AGTCGTGGGGTGATTTCGAA 59.317 50.000 0.00 0.00 32.56 3.71
202 203 0.794473 GTCGTGGGGTGATTTCGAAC 59.206 55.000 0.00 0.00 32.56 3.95
203 204 0.393448 TCGTGGGGTGATTTCGAACA 59.607 50.000 0.00 0.00 0.00 3.18
204 205 0.515564 CGTGGGGTGATTTCGAACAC 59.484 55.000 9.74 9.74 36.44 3.32
205 206 1.600023 GTGGGGTGATTTCGAACACA 58.400 50.000 17.57 9.60 38.57 3.72
206 207 1.950909 GTGGGGTGATTTCGAACACAA 59.049 47.619 17.57 3.60 38.57 3.33
207 208 1.950909 TGGGGTGATTTCGAACACAAC 59.049 47.619 17.57 13.60 38.57 3.32
208 209 1.069500 GGGGTGATTTCGAACACAACG 60.069 52.381 17.57 0.00 38.57 4.10
209 210 1.600485 GGGTGATTTCGAACACAACGT 59.400 47.619 17.57 0.00 38.57 3.99
210 211 2.349155 GGGTGATTTCGAACACAACGTC 60.349 50.000 17.57 3.40 38.57 4.34
211 212 2.546665 GTGATTTCGAACACAACGTCG 58.453 47.619 12.58 0.00 37.05 5.12
212 213 1.071107 TGATTTCGAACACAACGTCGC 60.071 47.619 0.00 0.00 0.00 5.19
213 214 1.191647 GATTTCGAACACAACGTCGCT 59.808 47.619 0.00 0.00 0.00 4.93
214 215 1.837648 TTTCGAACACAACGTCGCTA 58.162 45.000 0.00 0.00 0.00 4.26
215 216 1.122849 TTCGAACACAACGTCGCTAC 58.877 50.000 0.00 0.00 0.00 3.58
216 217 0.308684 TCGAACACAACGTCGCTACT 59.691 50.000 0.00 0.00 0.00 2.57
217 218 0.701303 CGAACACAACGTCGCTACTC 59.299 55.000 0.00 0.00 0.00 2.59
218 219 1.662309 CGAACACAACGTCGCTACTCT 60.662 52.381 0.00 0.00 0.00 3.24
219 220 1.714460 GAACACAACGTCGCTACTCTG 59.286 52.381 0.00 0.00 0.00 3.35
220 221 0.663568 ACACAACGTCGCTACTCTGC 60.664 55.000 0.00 0.00 0.00 4.26
221 222 0.663269 CACAACGTCGCTACTCTGCA 60.663 55.000 0.00 0.00 0.00 4.41
222 223 0.387367 ACAACGTCGCTACTCTGCAG 60.387 55.000 7.63 7.63 0.00 4.41
223 224 0.109735 CAACGTCGCTACTCTGCAGA 60.110 55.000 17.19 17.19 0.00 4.26
224 225 0.596577 AACGTCGCTACTCTGCAGAA 59.403 50.000 18.85 2.48 0.00 3.02
225 226 0.169230 ACGTCGCTACTCTGCAGAAG 59.831 55.000 18.85 14.27 0.00 2.85
226 227 1.136872 CGTCGCTACTCTGCAGAAGC 61.137 60.000 24.53 24.53 42.57 3.86
236 237 2.359602 GCAGAAGCAGAGCAGGCA 60.360 61.111 0.00 0.00 41.58 4.75
237 238 2.400158 GCAGAAGCAGAGCAGGCAG 61.400 63.158 0.00 0.00 41.58 4.85
238 239 1.745864 CAGAAGCAGAGCAGGCAGG 60.746 63.158 0.00 0.00 0.00 4.85
239 240 2.222727 AGAAGCAGAGCAGGCAGGT 61.223 57.895 0.00 0.00 0.00 4.00
240 241 2.033757 AAGCAGAGCAGGCAGGTG 59.966 61.111 0.00 0.00 0.00 4.00
255 256 1.221840 GGTGGCGTGAGTGATGGAT 59.778 57.895 0.00 0.00 0.00 3.41
274 275 3.795638 GGTCACGGAGCGAATTCC 58.204 61.111 0.00 0.00 0.00 3.01
304 305 2.224042 GCTGGGTCAAAACTCAAAAGGG 60.224 50.000 0.00 0.00 34.79 3.95
309 310 4.207955 GGTCAAAACTCAAAAGGGAGAGT 58.792 43.478 0.00 0.00 46.45 3.24
378 388 4.363990 ACAGCAGTCCTCGCGTGG 62.364 66.667 20.92 20.92 0.00 4.94
386 398 4.003788 CCTCGCGTGGACCCAACT 62.004 66.667 22.35 0.00 0.00 3.16
406 418 2.608368 CAACCCACCTCCCCCGTA 60.608 66.667 0.00 0.00 0.00 4.02
413 425 4.157120 CCTCCCCCGTACCGCAAG 62.157 72.222 0.00 0.00 0.00 4.01
414 426 3.387947 CTCCCCCGTACCGCAAGT 61.388 66.667 0.00 0.00 0.00 3.16
417 431 4.807039 CCCCGTACCGCAAGTCCG 62.807 72.222 0.00 0.00 0.00 4.79
563 2660 4.849310 GCATACCGGGCGCCTTCA 62.849 66.667 28.56 9.81 0.00 3.02
959 3168 3.077556 CCTCCTCACCCAGTCCCG 61.078 72.222 0.00 0.00 0.00 5.14
1016 3228 1.134367 CGAGATGTTTACTGCCGGAGA 59.866 52.381 5.05 0.00 0.00 3.71
1295 3991 4.221422 CATGGCGTCGACGGGGAT 62.221 66.667 36.13 0.00 40.23 3.85
1340 4036 1.989508 TCAGCGAGGGGAAGATGCA 60.990 57.895 0.00 0.00 0.00 3.96
1341 4037 1.523258 CAGCGAGGGGAAGATGCAG 60.523 63.158 0.00 0.00 0.00 4.41
1588 4284 9.399797 TCGATGTGGTTACTAAGAAGATAACTA 57.600 33.333 0.00 0.00 0.00 2.24
1711 4407 2.486982 CACATTTGCTTGAGTCCTGGAG 59.513 50.000 0.00 0.00 0.00 3.86
1715 4411 1.376553 GCTTGAGTCCTGGAGGTGC 60.377 63.158 0.00 0.00 36.34 5.01
1832 4540 4.383552 GGCTTATGCAGGGTCCTCTATATG 60.384 50.000 2.72 0.00 41.91 1.78
1844 4552 6.159988 GGTCCTCTATATGTACACAGATTGC 58.840 44.000 0.00 0.00 0.00 3.56
1893 4603 7.286313 GGAAATTGAGATGAATTAGAGGGAGT 58.714 38.462 0.00 0.00 0.00 3.85
1894 4604 7.228308 GGAAATTGAGATGAATTAGAGGGAGTG 59.772 40.741 0.00 0.00 0.00 3.51
1895 4605 6.821616 ATTGAGATGAATTAGAGGGAGTGT 57.178 37.500 0.00 0.00 0.00 3.55
1909 4630 2.618709 GGGAGTGTTGTTTGGAGTCTTG 59.381 50.000 0.00 0.00 0.00 3.02
1942 4663 6.243216 TCCACCAGTACTAGAAACAAAAGT 57.757 37.500 0.00 0.00 0.00 2.66
1945 4666 6.987992 CCACCAGTACTAGAAACAAAAGTACA 59.012 38.462 12.79 0.00 45.17 2.90
1947 4668 7.924412 CACCAGTACTAGAAACAAAAGTACAGA 59.076 37.037 12.79 0.00 45.17 3.41
1948 4669 8.648693 ACCAGTACTAGAAACAAAAGTACAGAT 58.351 33.333 12.79 0.00 45.17 2.90
1954 4675 8.035984 ACTAGAAACAAAAGTACAGATAGGAGC 58.964 37.037 0.00 0.00 0.00 4.70
1955 4676 7.010339 AGAAACAAAAGTACAGATAGGAGCT 57.990 36.000 0.00 0.00 0.00 4.09
1956 4677 7.454225 AGAAACAAAAGTACAGATAGGAGCTT 58.546 34.615 0.00 0.00 0.00 3.74
1977 4708 5.335504 GCTTTGGATGGAATATAGCTCAAGC 60.336 44.000 0.00 0.00 42.49 4.01
1978 4709 4.980339 TGGATGGAATATAGCTCAAGCA 57.020 40.909 4.59 0.00 45.16 3.91
1985 4716 4.261783 GGAATATAGCTCAAGCAAAAGGCC 60.262 45.833 4.59 0.00 46.50 5.19
1996 4727 1.132453 GCAAAAGGCCGAGTATGTTCC 59.868 52.381 0.00 0.00 36.11 3.62
2070 4801 3.891977 CACCTCTTATCCTAGTAGCAGCA 59.108 47.826 0.00 0.00 0.00 4.41
2091 4866 2.046023 TCGCATGGCCCTTGTGAG 60.046 61.111 13.42 3.95 0.00 3.51
2092 4867 2.360350 CGCATGGCCCTTGTGAGT 60.360 61.111 10.07 0.00 0.00 3.41
2093 4868 1.973281 CGCATGGCCCTTGTGAGTT 60.973 57.895 10.07 0.00 0.00 3.01
2094 4869 1.588082 GCATGGCCCTTGTGAGTTG 59.412 57.895 0.00 0.00 0.00 3.16
2095 4870 1.181098 GCATGGCCCTTGTGAGTTGT 61.181 55.000 0.00 0.00 0.00 3.32
2096 4871 0.599558 CATGGCCCTTGTGAGTTGTG 59.400 55.000 0.00 0.00 0.00 3.33
2162 4959 7.619050 TGGAGAAAATATCAGCCTATCATCTC 58.381 38.462 0.00 0.00 0.00 2.75
2219 5016 6.982724 TGCTCAGTACTGAAATCATGTCTATG 59.017 38.462 25.14 10.62 39.39 2.23
2222 5020 8.707938 TCAGTACTGAAATCATGTCTATGTTG 57.292 34.615 23.24 0.00 36.53 3.33
2275 5076 1.081892 CTTCCTCTCATGCACAACCG 58.918 55.000 0.00 0.00 0.00 4.44
2300 5101 2.817258 CGTGTCTCCCCAAAAATTGCTA 59.183 45.455 0.00 0.00 0.00 3.49
2346 5147 0.178068 GCGCACCTTCCCTCTCAATA 59.822 55.000 0.30 0.00 0.00 1.90
2363 5164 4.517285 TCAATACTGTTCCATGGAGCTTC 58.483 43.478 26.58 13.87 0.00 3.86
2389 5190 8.938801 TGTGCCACCTTATATTATCATTTCAT 57.061 30.769 0.00 0.00 0.00 2.57
2416 5225 8.428852 TGTTGCTTCTATATTTCTATACCAGCA 58.571 33.333 0.00 0.00 32.66 4.41
2488 5298 3.887621 TTGTGTATCAGGGCAGACTAC 57.112 47.619 0.00 0.00 0.00 2.73
2489 5299 3.101643 TGTGTATCAGGGCAGACTACT 57.898 47.619 0.00 0.00 0.00 2.57
2490 5300 4.245251 TGTGTATCAGGGCAGACTACTA 57.755 45.455 0.00 0.00 0.00 1.82
2502 5312 4.404715 GGCAGACTACTAGGGAACATGTTA 59.595 45.833 11.95 0.00 0.00 2.41
2503 5313 5.349809 GCAGACTACTAGGGAACATGTTAC 58.650 45.833 12.76 12.76 0.00 2.50
2504 5314 5.105473 GCAGACTACTAGGGAACATGTTACA 60.105 44.000 22.22 1.81 0.00 2.41
2524 5335 9.823647 TGTTACATGTTTATTTGTTTGATTGGT 57.176 25.926 2.30 0.00 0.00 3.67
2632 5446 9.658799 ATTTACGCTATGCAGAGAAATGTATAT 57.341 29.630 13.69 6.57 29.11 0.86
2752 5566 6.016777 GGGAGAATTTGCATGTCGAAATAGAT 60.017 38.462 0.00 0.00 0.00 1.98
2753 5567 7.420800 GGAGAATTTGCATGTCGAAATAGATT 58.579 34.615 0.00 0.00 0.00 2.40
2793 5607 6.231211 CACCGGCTAATCTTTCTTATGGTAT 58.769 40.000 0.00 0.00 0.00 2.73
3076 5899 2.894763 ATTTGCTGCTTGTTCTTGCA 57.105 40.000 0.00 0.00 37.63 4.08
3143 5968 5.408880 ACCTTTTGGCTCTACTACTCTTC 57.591 43.478 0.00 0.00 45.59 2.87
3262 6090 2.436646 CCGCTTTCATGCCGGACT 60.437 61.111 5.05 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 9.413734 CCTAATTCTAAAGTTTGGGATGAAGAT 57.586 33.333 0.00 0.00 0.00 2.40
8 9 8.390921 ACCTAATTCTAAAGTTTGGGATGAAGA 58.609 33.333 0.00 0.00 0.00 2.87
9 10 8.581253 ACCTAATTCTAAAGTTTGGGATGAAG 57.419 34.615 0.00 0.00 0.00 3.02
10 11 8.950007 AACCTAATTCTAAAGTTTGGGATGAA 57.050 30.769 0.00 0.00 0.00 2.57
11 12 8.950007 AAACCTAATTCTAAAGTTTGGGATGA 57.050 30.769 0.00 0.00 29.89 2.92
12 13 8.251026 GGAAACCTAATTCTAAAGTTTGGGATG 58.749 37.037 0.00 0.00 31.14 3.51
13 14 7.953493 TGGAAACCTAATTCTAAAGTTTGGGAT 59.047 33.333 0.00 0.00 31.14 3.85
14 15 7.299134 TGGAAACCTAATTCTAAAGTTTGGGA 58.701 34.615 0.00 0.00 31.14 4.37
15 16 7.533289 TGGAAACCTAATTCTAAAGTTTGGG 57.467 36.000 0.00 0.00 31.14 4.12
16 17 9.476202 CTTTGGAAACCTAATTCTAAAGTTTGG 57.524 33.333 14.14 0.00 45.38 3.28
22 23 9.807921 AGTGATCTTTGGAAACCTAATTCTAAA 57.192 29.630 0.00 0.00 37.41 1.85
25 26 9.981460 ATTAGTGATCTTTGGAAACCTAATTCT 57.019 29.630 0.00 0.00 0.00 2.40
30 31 9.120538 GCATTATTAGTGATCTTTGGAAACCTA 57.879 33.333 0.00 0.00 0.00 3.08
31 32 7.836183 AGCATTATTAGTGATCTTTGGAAACCT 59.164 33.333 0.00 0.00 0.00 3.50
32 33 8.000780 AGCATTATTAGTGATCTTTGGAAACC 57.999 34.615 0.00 0.00 0.00 3.27
34 35 9.342308 CCTAGCATTATTAGTGATCTTTGGAAA 57.658 33.333 0.00 0.00 0.00 3.13
35 36 8.713971 TCCTAGCATTATTAGTGATCTTTGGAA 58.286 33.333 0.00 0.00 0.00 3.53
36 37 8.150945 GTCCTAGCATTATTAGTGATCTTTGGA 58.849 37.037 0.00 0.00 0.00 3.53
37 38 7.933577 TGTCCTAGCATTATTAGTGATCTTTGG 59.066 37.037 0.00 0.00 0.00 3.28
38 39 8.893219 TGTCCTAGCATTATTAGTGATCTTTG 57.107 34.615 0.00 0.00 0.00 2.77
39 40 9.553064 CTTGTCCTAGCATTATTAGTGATCTTT 57.447 33.333 0.00 0.00 0.00 2.52
40 41 8.153550 CCTTGTCCTAGCATTATTAGTGATCTT 58.846 37.037 0.00 0.00 0.00 2.40
41 42 7.675062 CCTTGTCCTAGCATTATTAGTGATCT 58.325 38.462 0.00 0.00 0.00 2.75
42 43 6.370166 GCCTTGTCCTAGCATTATTAGTGATC 59.630 42.308 0.00 0.00 0.00 2.92
43 44 6.234177 GCCTTGTCCTAGCATTATTAGTGAT 58.766 40.000 0.00 0.00 0.00 3.06
44 45 5.454755 GGCCTTGTCCTAGCATTATTAGTGA 60.455 44.000 0.00 0.00 0.00 3.41
45 46 4.757149 GGCCTTGTCCTAGCATTATTAGTG 59.243 45.833 0.00 0.00 0.00 2.74
46 47 4.202472 GGGCCTTGTCCTAGCATTATTAGT 60.202 45.833 0.84 0.00 0.00 2.24
47 48 4.202461 TGGGCCTTGTCCTAGCATTATTAG 60.202 45.833 4.53 0.00 0.00 1.73
48 49 3.719479 TGGGCCTTGTCCTAGCATTATTA 59.281 43.478 4.53 0.00 0.00 0.98
49 50 2.513738 TGGGCCTTGTCCTAGCATTATT 59.486 45.455 4.53 0.00 0.00 1.40
50 51 2.135189 TGGGCCTTGTCCTAGCATTAT 58.865 47.619 4.53 0.00 0.00 1.28
51 52 1.590591 TGGGCCTTGTCCTAGCATTA 58.409 50.000 4.53 0.00 0.00 1.90
52 53 0.929244 ATGGGCCTTGTCCTAGCATT 59.071 50.000 4.53 0.00 0.00 3.56
53 54 0.929244 AATGGGCCTTGTCCTAGCAT 59.071 50.000 4.53 0.00 0.00 3.79
54 55 0.255890 GAATGGGCCTTGTCCTAGCA 59.744 55.000 4.53 0.00 0.00 3.49
55 56 0.255890 TGAATGGGCCTTGTCCTAGC 59.744 55.000 4.53 0.00 0.00 3.42
56 57 2.025887 ACTTGAATGGGCCTTGTCCTAG 60.026 50.000 4.53 2.78 0.00 3.02
57 58 1.992557 ACTTGAATGGGCCTTGTCCTA 59.007 47.619 4.53 0.00 0.00 2.94
58 59 0.779997 ACTTGAATGGGCCTTGTCCT 59.220 50.000 4.53 0.00 0.00 3.85
59 60 1.273327 CAACTTGAATGGGCCTTGTCC 59.727 52.381 4.53 0.00 0.00 4.02
60 61 1.273327 CCAACTTGAATGGGCCTTGTC 59.727 52.381 4.53 0.00 34.15 3.18
61 62 1.341080 CCAACTTGAATGGGCCTTGT 58.659 50.000 4.53 0.00 34.15 3.16
68 69 4.523943 TCATCTCAAACCCAACTTGAATGG 59.476 41.667 0.00 0.00 37.71 3.16
69 70 5.710513 TCATCTCAAACCCAACTTGAATG 57.289 39.130 0.00 0.00 32.57 2.67
70 71 6.012113 TGATCATCTCAAACCCAACTTGAAT 58.988 36.000 0.00 0.00 32.57 2.57
71 72 5.384336 TGATCATCTCAAACCCAACTTGAA 58.616 37.500 0.00 0.00 32.57 2.69
72 73 4.984295 TGATCATCTCAAACCCAACTTGA 58.016 39.130 0.00 0.00 0.00 3.02
73 74 5.909621 ATGATCATCTCAAACCCAACTTG 57.090 39.130 1.18 0.00 37.44 3.16
74 75 8.599624 ATTTATGATCATCTCAAACCCAACTT 57.400 30.769 12.53 0.00 37.44 2.66
75 76 8.599624 AATTTATGATCATCTCAAACCCAACT 57.400 30.769 12.53 0.00 37.44 3.16
76 77 9.657419 AAAATTTATGATCATCTCAAACCCAAC 57.343 29.630 12.53 0.00 37.44 3.77
77 78 9.656040 CAAAATTTATGATCATCTCAAACCCAA 57.344 29.630 12.53 0.00 37.44 4.12
78 79 8.814931 ACAAAATTTATGATCATCTCAAACCCA 58.185 29.630 12.53 0.00 37.44 4.51
79 80 9.305925 GACAAAATTTATGATCATCTCAAACCC 57.694 33.333 12.53 0.00 37.44 4.11
80 81 9.305925 GGACAAAATTTATGATCATCTCAAACC 57.694 33.333 12.53 0.80 37.44 3.27
81 82 9.305925 GGGACAAAATTTATGATCATCTCAAAC 57.694 33.333 12.53 0.00 37.44 2.93
82 83 9.033711 TGGGACAAAATTTATGATCATCTCAAA 57.966 29.630 12.53 8.01 33.53 2.69
83 84 8.592529 TGGGACAAAATTTATGATCATCTCAA 57.407 30.769 12.53 4.46 33.53 3.02
102 103 1.962807 CTTGGTGCAAAGATTGGGACA 59.037 47.619 0.00 0.00 0.00 4.02
103 104 1.273327 CCTTGGTGCAAAGATTGGGAC 59.727 52.381 0.00 0.00 0.00 4.46
104 105 1.146774 TCCTTGGTGCAAAGATTGGGA 59.853 47.619 0.00 0.00 0.00 4.37
105 106 1.631405 TCCTTGGTGCAAAGATTGGG 58.369 50.000 0.00 0.00 0.00 4.12
106 107 3.592059 CAATCCTTGGTGCAAAGATTGG 58.408 45.455 1.31 2.74 43.17 3.16
107 108 8.631068 TGGAACAATCCTTGGTGCAAAGATTG 62.631 42.308 17.17 17.17 46.02 2.67
108 109 4.262592 GGAACAATCCTTGGTGCAAAGATT 60.263 41.667 0.00 0.00 42.93 2.40
109 110 3.259123 GGAACAATCCTTGGTGCAAAGAT 59.741 43.478 0.00 0.00 42.93 2.40
110 111 2.627699 GGAACAATCCTTGGTGCAAAGA 59.372 45.455 0.00 0.00 42.93 2.52
111 112 2.364970 TGGAACAATCCTTGGTGCAAAG 59.635 45.455 0.00 0.00 46.02 2.77
112 113 2.392662 TGGAACAATCCTTGGTGCAAA 58.607 42.857 0.00 0.00 46.02 3.68
113 114 2.079170 TGGAACAATCCTTGGTGCAA 57.921 45.000 0.00 0.00 46.02 4.08
114 115 3.837893 TGGAACAATCCTTGGTGCA 57.162 47.368 0.00 0.00 46.85 4.57
126 127 4.028993 GGTAACTCCTCCATTTGGAACA 57.971 45.455 0.18 0.00 44.91 3.18
138 139 8.823794 AGTAGCAAATTACTAAAGGTAACTCCT 58.176 33.333 0.00 0.00 42.35 3.69
139 140 9.096160 GAGTAGCAAATTACTAAAGGTAACTCC 57.904 37.037 0.00 0.00 42.35 3.85
140 141 9.872721 AGAGTAGCAAATTACTAAAGGTAACTC 57.127 33.333 0.00 0.00 42.35 3.01
141 142 9.654663 CAGAGTAGCAAATTACTAAAGGTAACT 57.345 33.333 0.00 0.00 42.35 2.24
142 143 9.433153 ACAGAGTAGCAAATTACTAAAGGTAAC 57.567 33.333 0.00 0.00 42.35 2.50
145 146 8.919777 AAACAGAGTAGCAAATTACTAAAGGT 57.080 30.769 0.00 0.00 34.13 3.50
169 170 2.166664 CCCACGACTGGAAAACCAAAAA 59.833 45.455 0.00 0.00 40.55 1.94
170 171 1.751924 CCCACGACTGGAAAACCAAAA 59.248 47.619 0.00 0.00 40.55 2.44
171 172 1.394618 CCCACGACTGGAAAACCAAA 58.605 50.000 0.00 0.00 40.55 3.28
172 173 0.466555 CCCCACGACTGGAAAACCAA 60.467 55.000 0.00 0.00 40.55 3.67
173 174 1.149627 CCCCACGACTGGAAAACCA 59.850 57.895 0.00 0.00 40.55 3.67
174 175 1.149854 ACCCCACGACTGGAAAACC 59.850 57.895 0.00 0.00 40.55 3.27
175 176 0.179040 TCACCCCACGACTGGAAAAC 60.179 55.000 0.00 0.00 40.55 2.43
176 177 0.768622 ATCACCCCACGACTGGAAAA 59.231 50.000 0.00 0.00 40.55 2.29
177 178 0.768622 AATCACCCCACGACTGGAAA 59.231 50.000 0.00 0.00 40.55 3.13
178 179 0.768622 AAATCACCCCACGACTGGAA 59.231 50.000 0.00 0.00 40.55 3.53
179 180 0.323629 GAAATCACCCCACGACTGGA 59.676 55.000 0.00 0.00 40.55 3.86
180 181 1.019278 CGAAATCACCCCACGACTGG 61.019 60.000 0.00 0.00 37.29 4.00
181 182 0.037697 TCGAAATCACCCCACGACTG 60.038 55.000 0.00 0.00 0.00 3.51
182 183 0.682852 TTCGAAATCACCCCACGACT 59.317 50.000 0.00 0.00 32.89 4.18
183 184 0.794473 GTTCGAAATCACCCCACGAC 59.206 55.000 0.00 0.00 32.89 4.34
184 185 0.393448 TGTTCGAAATCACCCCACGA 59.607 50.000 0.00 0.00 0.00 4.35
185 186 0.515564 GTGTTCGAAATCACCCCACG 59.484 55.000 0.00 0.00 0.00 4.94
186 187 1.600023 TGTGTTCGAAATCACCCCAC 58.400 50.000 14.28 10.21 34.14 4.61
187 188 1.950909 GTTGTGTTCGAAATCACCCCA 59.049 47.619 14.28 0.00 34.14 4.96
188 189 1.069500 CGTTGTGTTCGAAATCACCCC 60.069 52.381 14.28 5.90 34.14 4.95
189 190 1.600485 ACGTTGTGTTCGAAATCACCC 59.400 47.619 14.28 6.18 34.14 4.61
190 191 2.658224 CGACGTTGTGTTCGAAATCACC 60.658 50.000 14.28 3.19 34.14 4.02
191 192 2.546665 CGACGTTGTGTTCGAAATCAC 58.453 47.619 10.99 10.99 35.43 3.06
192 193 1.071107 GCGACGTTGTGTTCGAAATCA 60.071 47.619 0.00 0.00 0.00 2.57
193 194 1.191647 AGCGACGTTGTGTTCGAAATC 59.808 47.619 0.00 0.00 0.00 2.17
194 195 1.214367 AGCGACGTTGTGTTCGAAAT 58.786 45.000 0.00 0.00 0.00 2.17
195 196 1.518102 GTAGCGACGTTGTGTTCGAAA 59.482 47.619 0.00 0.00 0.00 3.46
196 197 1.122849 GTAGCGACGTTGTGTTCGAA 58.877 50.000 4.37 0.00 0.00 3.71
197 198 0.308684 AGTAGCGACGTTGTGTTCGA 59.691 50.000 4.37 0.00 0.00 3.71
198 199 0.701303 GAGTAGCGACGTTGTGTTCG 59.299 55.000 4.37 0.00 0.00 3.95
199 200 1.714460 CAGAGTAGCGACGTTGTGTTC 59.286 52.381 4.37 0.00 0.00 3.18
200 201 1.767289 CAGAGTAGCGACGTTGTGTT 58.233 50.000 4.37 0.00 0.00 3.32
201 202 0.663568 GCAGAGTAGCGACGTTGTGT 60.664 55.000 4.37 0.00 0.00 3.72
202 203 0.663269 TGCAGAGTAGCGACGTTGTG 60.663 55.000 4.37 0.00 37.31 3.33
203 204 0.387367 CTGCAGAGTAGCGACGTTGT 60.387 55.000 8.42 0.00 37.31 3.32
204 205 0.109735 TCTGCAGAGTAGCGACGTTG 60.110 55.000 13.74 0.00 37.31 4.10
205 206 0.596577 TTCTGCAGAGTAGCGACGTT 59.403 50.000 17.43 0.00 37.31 3.99
206 207 0.169230 CTTCTGCAGAGTAGCGACGT 59.831 55.000 17.43 0.00 37.31 4.34
207 208 1.136872 GCTTCTGCAGAGTAGCGACG 61.137 60.000 21.36 4.82 33.49 5.12
208 209 0.109086 TGCTTCTGCAGAGTAGCGAC 60.109 55.000 27.13 9.36 43.69 5.19
209 210 2.267045 TGCTTCTGCAGAGTAGCGA 58.733 52.632 27.13 17.35 43.69 4.93
210 211 4.898002 TGCTTCTGCAGAGTAGCG 57.102 55.556 27.13 12.98 43.69 4.26
219 220 2.359602 TGCCTGCTCTGCTTCTGC 60.360 61.111 0.00 0.00 40.20 4.26
220 221 1.745864 CCTGCCTGCTCTGCTTCTG 60.746 63.158 0.00 0.00 0.00 3.02
221 222 2.222727 ACCTGCCTGCTCTGCTTCT 61.223 57.895 0.00 0.00 0.00 2.85
222 223 2.039405 CACCTGCCTGCTCTGCTTC 61.039 63.158 0.00 0.00 0.00 3.86
223 224 2.033757 CACCTGCCTGCTCTGCTT 59.966 61.111 0.00 0.00 0.00 3.91
224 225 4.031129 CCACCTGCCTGCTCTGCT 62.031 66.667 0.00 0.00 0.00 4.24
231 232 4.320456 ACTCACGCCACCTGCCTG 62.320 66.667 0.00 0.00 36.24 4.85
232 233 4.320456 CACTCACGCCACCTGCCT 62.320 66.667 0.00 0.00 36.24 4.75
233 234 3.612247 ATCACTCACGCCACCTGCC 62.612 63.158 0.00 0.00 36.24 4.85
234 235 2.046892 ATCACTCACGCCACCTGC 60.047 61.111 0.00 0.00 0.00 4.85
235 236 1.742880 CCATCACTCACGCCACCTG 60.743 63.158 0.00 0.00 0.00 4.00
236 237 1.267574 ATCCATCACTCACGCCACCT 61.268 55.000 0.00 0.00 0.00 4.00
237 238 0.811616 GATCCATCACTCACGCCACC 60.812 60.000 0.00 0.00 0.00 4.61
238 239 1.148157 CGATCCATCACTCACGCCAC 61.148 60.000 0.00 0.00 0.00 5.01
239 240 1.141665 CGATCCATCACTCACGCCA 59.858 57.895 0.00 0.00 0.00 5.69
240 241 1.592669 CCGATCCATCACTCACGCC 60.593 63.158 0.00 0.00 0.00 5.68
247 248 0.249073 CTCCGTGACCGATCCATCAC 60.249 60.000 12.12 12.12 41.54 3.06
248 249 2.016393 GCTCCGTGACCGATCCATCA 62.016 60.000 0.00 0.00 35.63 3.07
255 256 1.153901 GAATTCGCTCCGTGACCGA 60.154 57.895 0.00 0.00 35.63 4.69
274 275 1.679139 TTTGACCCAGCTGTCTGTTG 58.321 50.000 13.81 0.00 38.66 3.33
286 287 3.562182 TCTCCCTTTTGAGTTTTGACCC 58.438 45.455 0.00 0.00 33.93 4.46
304 305 1.821216 TTTCGGCATTTCCCACTCTC 58.179 50.000 0.00 0.00 0.00 3.20
378 388 1.228459 GTGGGTTGGGAGTTGGGTC 60.228 63.158 0.00 0.00 0.00 4.46
405 417 2.735478 CGTTGCGGACTTGCGGTA 60.735 61.111 0.00 0.00 37.81 4.02
446 460 1.185618 GGGTTTTTGGAGTGGGAGCC 61.186 60.000 0.00 0.00 0.00 4.70
511 525 4.418328 CGGGTGGGGCGATTTGGA 62.418 66.667 0.00 0.00 0.00 3.53
683 2830 4.342086 AGGTGGGCGGGGAAGGTA 62.342 66.667 0.00 0.00 0.00 3.08
805 3011 4.834453 CCAGGAGAGGCTGCGCAG 62.834 72.222 32.83 32.83 0.00 5.18
1291 3503 1.531602 GGTGGCTGCCCAATATCCC 60.532 63.158 17.53 0.84 44.33 3.85
1295 3991 4.813235 GCCGGTGGCTGCCCAATA 62.813 66.667 17.53 0.00 46.69 1.90
1317 4013 4.332543 TTCCCCTCGCTGACCCCT 62.333 66.667 0.00 0.00 0.00 4.79
1340 4036 0.879765 CTTGGACACCTCGACGTACT 59.120 55.000 0.00 0.00 0.00 2.73
1341 4037 0.109412 CCTTGGACACCTCGACGTAC 60.109 60.000 0.00 0.00 0.00 3.67
1588 4284 5.993748 GCTATAGCTAGACCAGAAATCCT 57.006 43.478 17.75 0.00 38.21 3.24
1711 4407 3.166489 AGTATACTCGCTTTCAGCACC 57.834 47.619 0.00 0.00 42.58 5.01
1715 4411 6.799441 CAGCTGTATAGTATACTCGCTTTCAG 59.201 42.308 23.39 11.13 0.00 3.02
1737 4442 3.128764 GTCCAATGGGCTAAACTAACAGC 59.871 47.826 0.00 0.00 37.05 4.40
1748 4453 2.307496 TGAAATGTGTCCAATGGGCT 57.693 45.000 5.15 0.00 0.00 5.19
1787 4492 1.474077 CCAAGGCTCCAAGCACATAAC 59.526 52.381 0.86 0.00 44.75 1.89
1832 4540 5.258622 CAAATTCTAGCGCAATCTGTGTAC 58.741 41.667 11.47 0.00 0.00 2.90
1844 4552 3.119495 CCCAGTTTTCCCAAATTCTAGCG 60.119 47.826 0.00 0.00 0.00 4.26
1878 4588 5.711976 CCAAACAACACTCCCTCTAATTCAT 59.288 40.000 0.00 0.00 0.00 2.57
1885 4595 2.104963 GACTCCAAACAACACTCCCTCT 59.895 50.000 0.00 0.00 0.00 3.69
1893 4603 4.279671 ACAACAACAAGACTCCAAACAACA 59.720 37.500 0.00 0.00 0.00 3.33
1894 4604 4.621034 CACAACAACAAGACTCCAAACAAC 59.379 41.667 0.00 0.00 0.00 3.32
1895 4605 4.520874 TCACAACAACAAGACTCCAAACAA 59.479 37.500 0.00 0.00 0.00 2.83
1942 4663 4.556697 TCCATCCAAAGCTCCTATCTGTA 58.443 43.478 0.00 0.00 0.00 2.74
1945 4666 6.966637 ATATTCCATCCAAAGCTCCTATCT 57.033 37.500 0.00 0.00 0.00 1.98
1947 4668 6.446434 AGCTATATTCCATCCAAAGCTCCTAT 59.554 38.462 0.00 0.00 33.78 2.57
1948 4669 5.787494 AGCTATATTCCATCCAAAGCTCCTA 59.213 40.000 0.00 0.00 33.78 2.94
1949 4670 4.600983 AGCTATATTCCATCCAAAGCTCCT 59.399 41.667 0.00 0.00 33.78 3.69
1950 4671 4.916183 AGCTATATTCCATCCAAAGCTCC 58.084 43.478 0.00 0.00 33.78 4.70
1954 4675 5.766670 TGCTTGAGCTATATTCCATCCAAAG 59.233 40.000 4.44 0.00 42.66 2.77
1955 4676 5.693961 TGCTTGAGCTATATTCCATCCAAA 58.306 37.500 4.44 0.00 42.66 3.28
1956 4677 5.308976 TGCTTGAGCTATATTCCATCCAA 57.691 39.130 4.44 0.00 42.66 3.53
1977 4708 2.420022 CTGGAACATACTCGGCCTTTTG 59.580 50.000 0.00 0.00 38.20 2.44
1978 4709 2.039879 ACTGGAACATACTCGGCCTTTT 59.960 45.455 0.00 0.00 38.20 2.27
1985 4716 4.174411 TGAACAGACTGGAACATACTCG 57.826 45.455 7.51 0.00 38.20 4.18
1996 4727 4.689812 CAGAACCAGAAGATGAACAGACTG 59.310 45.833 0.00 0.00 0.00 3.51
2070 4801 1.304381 ACAAGGGCCATGCGACATT 60.304 52.632 9.01 0.00 0.00 2.71
2136 4912 8.160434 AGATGATAGGCTGATATTTTCTCCAT 57.840 34.615 0.00 0.00 0.00 3.41
2137 4913 7.457218 AGAGATGATAGGCTGATATTTTCTCCA 59.543 37.037 0.00 0.00 30.91 3.86
2162 4959 2.872245 CAGGTACCACAACTCAACACAG 59.128 50.000 15.94 0.00 0.00 3.66
2244 5042 5.614308 CATGAGAGGAAGGCACATACATAA 58.386 41.667 0.00 0.00 0.00 1.90
2256 5057 1.081892 CGGTTGTGCATGAGAGGAAG 58.918 55.000 0.00 0.00 0.00 3.46
2300 5101 2.037620 GATGCCATCGAGCTCCCAGT 62.038 60.000 8.47 0.00 0.00 4.00
2363 5164 8.394971 TGAAATGATAATATAAGGTGGCACAG 57.605 34.615 20.82 0.00 41.80 3.66
2389 5190 9.273016 GCTGGTATAGAAATATAGAAGCAACAA 57.727 33.333 0.00 0.00 0.00 2.83
2416 5225 6.323739 AGAAACAGGGATACAAACAACAATGT 59.676 34.615 0.00 0.00 39.52 2.71
2488 5298 9.787532 CAAATAAACATGTAACATGTTCCCTAG 57.212 33.333 15.85 5.46 40.94 3.02
2489 5299 9.303116 ACAAATAAACATGTAACATGTTCCCTA 57.697 29.630 15.85 11.06 40.94 3.53
2490 5300 8.189119 ACAAATAAACATGTAACATGTTCCCT 57.811 30.769 15.85 0.00 40.94 4.20
2632 5446 8.347035 GCAAGAACTTAAACAACTATAACACCA 58.653 33.333 0.00 0.00 0.00 4.17
2752 5566 3.443037 CGGTGCACTTCATTTCAACAAA 58.557 40.909 17.98 0.00 0.00 2.83
2753 5567 2.223688 CCGGTGCACTTCATTTCAACAA 60.224 45.455 17.98 0.00 0.00 2.83
2793 5607 7.246171 ACAAGGAGAGCTAGTTATGAGAAAA 57.754 36.000 0.00 0.00 0.00 2.29
3058 5881 2.094078 AGTTGCAAGAACAAGCAGCAAA 60.094 40.909 0.00 0.00 45.46 3.68
3076 5899 5.594317 GGGCAATCCATATACTTCAACAGTT 59.406 40.000 0.00 0.00 34.44 3.16
3143 5968 0.370273 CGGAAGCGAGATTTGAACCG 59.630 55.000 0.00 0.00 0.00 4.44
3262 6090 0.482446 ACCCCTTCAAGGATGTTGCA 59.518 50.000 4.43 0.00 37.67 4.08


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

AutoCloner maintained by Alex Coulton.