Multiple sequence alignment - TraesCS5D01G569500

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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 TraesCS5D01G569500 chr5D 100.000 3602 0 0 1 3602 565832564 565828963 0.000000e+00 6652
1 TraesCS5D01G569500 chr5D 82.533 1895 304 20 658 2538 565713987 565712106 0.000000e+00 1640
2 TraesCS5D01G569500 chr5D 82.042 1342 216 17 1173 2497 565736020 565734687 0.000000e+00 1120
3 TraesCS5D01G569500 chr5D 84.578 1031 153 3 1475 2502 565719869 565718842 0.000000e+00 1018
4 TraesCS5D01G569500 chr5D 81.629 1007 176 8 1506 2508 565729344 565728343 0.000000e+00 826
5 TraesCS5D01G569500 chr5D 80.465 860 138 21 658 1500 565732060 565731214 6.560000e-177 630
6 TraesCS5D01G569500 chr5D 99.390 164 1 0 113 276 432167259 432167422 7.560000e-77 298
7 TraesCS5D01G569500 chr5D 97.143 175 5 0 102 276 466142528 466142354 2.720000e-76 296
8 TraesCS5D01G569500 chr5D 96.610 177 3 3 101 276 504064020 504063846 1.270000e-74 291
9 TraesCS5D01G569500 chr5D 94.000 150 9 0 636 785 565841274 565841125 1.010000e-55 228
10 TraesCS5D01G569500 chr5D 95.000 120 5 1 362 481 565895473 565895355 1.710000e-43 187
11 TraesCS5D01G569500 chr5B 94.832 2206 101 6 340 2538 707190523 707192722 0.000000e+00 3430
12 TraesCS5D01G569500 chr5B 95.966 1066 42 1 2538 3602 195739762 195740827 0.000000e+00 1729
13 TraesCS5D01G569500 chr5B 83.002 1859 294 16 658 2510 707407891 707409733 0.000000e+00 1663
14 TraesCS5D01G569500 chr5B 82.365 1894 308 19 659 2538 707420161 707422042 0.000000e+00 1624
15 TraesCS5D01G569500 chr5B 79.923 1295 252 8 638 1927 707414197 707415488 0.000000e+00 944
16 TraesCS5D01G569500 chr5B 87.080 565 73 0 1938 2502 707415555 707416119 1.090000e-179 640
17 TraesCS5D01G569500 chr5A 96.811 1066 31 2 2538 3601 299619563 299620627 0.000000e+00 1777
18 TraesCS5D01G569500 chr5A 95.888 1070 39 4 2538 3602 522364981 522363912 0.000000e+00 1727
19 TraesCS5D01G569500 chr5A 93.913 115 6 1 4 118 259489199 259489086 4.780000e-39 172
20 TraesCS5D01G569500 chr1D 96.805 1064 34 0 2539 3602 111513217 111512154 0.000000e+00 1777
21 TraesCS5D01G569500 chr2D 96.623 1066 35 1 2538 3602 605181981 605183046 0.000000e+00 1768
22 TraesCS5D01G569500 chr2D 98.837 172 1 1 112 282 527495190 527495019 4.520000e-79 305
23 TraesCS5D01G569500 chr2D 97.143 175 5 0 102 276 12376947 12377121 2.720000e-76 296
24 TraesCS5D01G569500 chr2D 94.915 118 5 1 1 118 221404044 221404160 2.210000e-42 183
25 TraesCS5D01G569500 chr2D 94.068 118 5 2 1 118 508975991 508976106 1.030000e-40 178
26 TraesCS5D01G569500 chr2A 96.338 1065 36 3 2539 3602 117355337 117354275 0.000000e+00 1748
27 TraesCS5D01G569500 chr6B 96.157 1067 40 1 2537 3602 44069597 44070663 0.000000e+00 1742
28 TraesCS5D01G569500 chr6D 95.876 1067 42 2 2537 3602 368116737 368117802 0.000000e+00 1725
29 TraesCS5D01G569500 chr6D 74.959 1226 275 26 1240 2446 24335147 24333935 5.290000e-148 534
30 TraesCS5D01G569500 chr6D 97.175 177 4 1 104 280 27399063 27398888 7.560000e-77 298
31 TraesCS5D01G569500 chr6D 96.522 115 3 1 4 118 411871397 411871284 4.750000e-44 189
32 TraesCS5D01G569500 chr6D 92.373 118 7 1 1 118 109270744 109270859 2.220000e-37 167
33 TraesCS5D01G569500 chr1A 95.794 1070 42 3 2535 3602 464122564 464123632 0.000000e+00 1724
34 TraesCS5D01G569500 chr1A 88.983 118 11 2 1 117 430607671 430607787 1.040000e-30 145
35 TraesCS5D01G569500 chr4A 82.928 1851 294 18 658 2496 607279991 607278151 0.000000e+00 1648
36 TraesCS5D01G569500 chr4A 74.456 1699 386 35 807 2487 632733528 632735196 0.000000e+00 689
37 TraesCS5D01G569500 chrUn 73.123 1239 285 41 1238 2451 18014174 18015389 2.010000e-107 399
38 TraesCS5D01G569500 chr7D 97.207 179 4 1 99 276 14654699 14654521 5.840000e-78 302
39 TraesCS5D01G569500 chr7D 94.068 118 6 1 1 118 425263371 425263487 1.030000e-40 178
40 TraesCS5D01G569500 chr4D 98.214 168 3 0 112 279 10770691 10770524 9.780000e-76 294
41 TraesCS5D01G569500 chr4D 96.591 176 5 1 101 276 509819051 509818877 1.270000e-74 291
42 TraesCS5D01G569500 chr4D 93.043 115 6 1 4 118 362510685 362510573 2.220000e-37 167
43 TraesCS5D01G569500 chr1B 89.831 118 11 1 1 118 553972067 553972183 2.240000e-32 150


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 TraesCS5D01G569500 chr5D 565828963 565832564 3601 True 6652.000000 6652 100.000000 1 3602 1 chr5D.!!$R5 3601
1 TraesCS5D01G569500 chr5D 565712106 565713987 1881 True 1640.000000 1640 82.533000 658 2538 1 chr5D.!!$R3 1880
2 TraesCS5D01G569500 chr5D 565718842 565719869 1027 True 1018.000000 1018 84.578000 1475 2502 1 chr5D.!!$R4 1027
3 TraesCS5D01G569500 chr5D 565728343 565736020 7677 True 858.666667 1120 81.378667 658 2508 3 chr5D.!!$R8 1850
4 TraesCS5D01G569500 chr5B 707190523 707192722 2199 False 3430.000000 3430 94.832000 340 2538 1 chr5B.!!$F2 2198
5 TraesCS5D01G569500 chr5B 195739762 195740827 1065 False 1729.000000 1729 95.966000 2538 3602 1 chr5B.!!$F1 1064
6 TraesCS5D01G569500 chr5B 707407891 707409733 1842 False 1663.000000 1663 83.002000 658 2510 1 chr5B.!!$F3 1852
7 TraesCS5D01G569500 chr5B 707420161 707422042 1881 False 1624.000000 1624 82.365000 659 2538 1 chr5B.!!$F4 1879
8 TraesCS5D01G569500 chr5B 707414197 707416119 1922 False 792.000000 944 83.501500 638 2502 2 chr5B.!!$F5 1864
9 TraesCS5D01G569500 chr5A 299619563 299620627 1064 False 1777.000000 1777 96.811000 2538 3601 1 chr5A.!!$F1 1063
10 TraesCS5D01G569500 chr5A 522363912 522364981 1069 True 1727.000000 1727 95.888000 2538 3602 1 chr5A.!!$R2 1064
11 TraesCS5D01G569500 chr1D 111512154 111513217 1063 True 1777.000000 1777 96.805000 2539 3602 1 chr1D.!!$R1 1063
12 TraesCS5D01G569500 chr2D 605181981 605183046 1065 False 1768.000000 1768 96.623000 2538 3602 1 chr2D.!!$F4 1064
13 TraesCS5D01G569500 chr2A 117354275 117355337 1062 True 1748.000000 1748 96.338000 2539 3602 1 chr2A.!!$R1 1063
14 TraesCS5D01G569500 chr6B 44069597 44070663 1066 False 1742.000000 1742 96.157000 2537 3602 1 chr6B.!!$F1 1065
15 TraesCS5D01G569500 chr6D 368116737 368117802 1065 False 1725.000000 1725 95.876000 2537 3602 1 chr6D.!!$F2 1065
16 TraesCS5D01G569500 chr6D 24333935 24335147 1212 True 534.000000 534 74.959000 1240 2446 1 chr6D.!!$R1 1206
17 TraesCS5D01G569500 chr1A 464122564 464123632 1068 False 1724.000000 1724 95.794000 2535 3602 1 chr1A.!!$F2 1067
18 TraesCS5D01G569500 chr4A 607278151 607279991 1840 True 1648.000000 1648 82.928000 658 2496 1 chr4A.!!$R1 1838
19 TraesCS5D01G569500 chr4A 632733528 632735196 1668 False 689.000000 689 74.456000 807 2487 1 chr4A.!!$F1 1680
20 TraesCS5D01G569500 chrUn 18014174 18015389 1215 False 399.000000 399 73.123000 1238 2451 1 chrUn.!!$F1 1213

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
81 82 0.033011 TAGCCGGCTCCTCTTCTCTT 60.033 55.0 36.73 6.99 0.00 2.85 F
341 342 0.036164 TGGATGTCCCACTCGTTTGG 59.964 55.0 0.00 0.00 40.82 3.28 F
1504 6697 0.387565 CTGGTTTTGGGGTTTGACCG 59.612 55.0 0.00 0.00 39.83 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1877 7076 1.070758 GGTCCAGTTCAGTCAGCTTCA 59.929 52.381 0.00 0.0 0.00 3.02 R
1934 7133 4.774200 AGCTTTCAAGGCCTGATAAATGTT 59.226 37.500 5.69 0.0 32.78 2.71 R
3367 8632 0.609131 CCTGACACAAGGCCGGAATT 60.609 55.000 5.05 0.0 0.00 2.17 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
17 18 2.951813 TGACCCACCTCCCACTCT 59.048 61.111 0.00 0.00 0.00 3.24
18 19 1.229209 TGACCCACCTCCCACTCTC 60.229 63.158 0.00 0.00 0.00 3.20
19 20 1.229209 GACCCACCTCCCACTCTCA 60.229 63.158 0.00 0.00 0.00 3.27
20 21 1.536662 ACCCACCTCCCACTCTCAC 60.537 63.158 0.00 0.00 0.00 3.51
23 24 1.622449 CCCACCTCCCACTCTCACATA 60.622 57.143 0.00 0.00 0.00 2.29
24 25 1.759445 CCACCTCCCACTCTCACATAG 59.241 57.143 0.00 0.00 0.00 2.23
25 26 2.461695 CACCTCCCACTCTCACATAGT 58.538 52.381 0.00 0.00 0.00 2.12
26 27 2.167281 CACCTCCCACTCTCACATAGTG 59.833 54.545 0.00 0.00 43.26 2.74
29 30 1.198713 CCCACTCTCACATAGTGCCT 58.801 55.000 0.00 0.00 42.47 4.75
31 32 2.363680 CCCACTCTCACATAGTGCCTAG 59.636 54.545 0.00 0.00 42.47 3.02
32 33 2.363680 CCACTCTCACATAGTGCCTAGG 59.636 54.545 3.67 3.67 42.47 3.02
33 34 3.291584 CACTCTCACATAGTGCCTAGGA 58.708 50.000 14.75 0.00 38.08 2.94
34 35 3.317711 CACTCTCACATAGTGCCTAGGAG 59.682 52.174 14.75 0.00 38.08 3.69
51 52 4.380628 GCACGTGCTGCAGCTGAC 62.381 66.667 36.61 26.48 46.29 3.51
52 53 2.664185 CACGTGCTGCAGCTGACT 60.664 61.111 36.61 15.57 42.66 3.41
54 55 2.048409 CGTGCTGCAGCTGACTCT 60.048 61.111 36.61 0.00 42.66 3.24
56 57 0.389037 CGTGCTGCAGCTGACTCTTA 60.389 55.000 36.61 13.65 42.66 2.10
57 58 1.738365 CGTGCTGCAGCTGACTCTTAT 60.738 52.381 36.61 0.00 42.66 1.73
58 59 2.354259 GTGCTGCAGCTGACTCTTATT 58.646 47.619 36.61 0.00 42.66 1.40
59 60 2.351111 GTGCTGCAGCTGACTCTTATTC 59.649 50.000 36.61 6.22 42.66 1.75
61 62 2.608546 GCTGCAGCTGACTCTTATTCTG 59.391 50.000 31.33 1.28 38.21 3.02
62 63 3.859443 CTGCAGCTGACTCTTATTCTGT 58.141 45.455 20.43 0.00 0.00 3.41
63 64 4.679106 GCTGCAGCTGACTCTTATTCTGTA 60.679 45.833 31.33 0.00 38.21 2.74
64 65 5.003692 TGCAGCTGACTCTTATTCTGTAG 57.996 43.478 20.43 0.00 0.00 2.74
65 66 3.801594 GCAGCTGACTCTTATTCTGTAGC 59.198 47.826 20.43 0.00 0.00 3.58
66 67 4.367450 CAGCTGACTCTTATTCTGTAGCC 58.633 47.826 8.42 0.00 0.00 3.93
67 68 3.067461 AGCTGACTCTTATTCTGTAGCCG 59.933 47.826 0.00 0.00 0.00 5.52
68 69 3.797184 GCTGACTCTTATTCTGTAGCCGG 60.797 52.174 0.00 0.00 0.00 6.13
70 71 2.362717 GACTCTTATTCTGTAGCCGGCT 59.637 50.000 34.85 34.85 0.00 5.52
71 72 2.362717 ACTCTTATTCTGTAGCCGGCTC 59.637 50.000 36.73 24.38 0.00 4.70
72 73 1.687123 TCTTATTCTGTAGCCGGCTCC 59.313 52.381 36.73 24.70 0.00 4.70
74 75 1.329256 TATTCTGTAGCCGGCTCCTC 58.671 55.000 36.73 24.11 0.00 3.71
75 76 0.397816 ATTCTGTAGCCGGCTCCTCT 60.398 55.000 36.73 12.19 0.00 3.69
76 77 0.614979 TTCTGTAGCCGGCTCCTCTT 60.615 55.000 36.73 11.27 0.00 2.85
77 78 1.038130 TCTGTAGCCGGCTCCTCTTC 61.038 60.000 36.73 17.21 0.00 2.87
78 79 1.000486 TGTAGCCGGCTCCTCTTCT 60.000 57.895 36.73 9.44 0.00 2.85
81 82 0.033011 TAGCCGGCTCCTCTTCTCTT 60.033 55.000 36.73 6.99 0.00 2.85
83 84 1.819905 CCGGCTCCTCTTCTCTTCC 59.180 63.158 0.00 0.00 0.00 3.46
85 86 0.686112 CGGCTCCTCTTCTCTTCCCT 60.686 60.000 0.00 0.00 0.00 4.20
86 87 1.119684 GGCTCCTCTTCTCTTCCCTC 58.880 60.000 0.00 0.00 0.00 4.30
87 88 1.119684 GCTCCTCTTCTCTTCCCTCC 58.880 60.000 0.00 0.00 0.00 4.30
88 89 1.621072 GCTCCTCTTCTCTTCCCTCCA 60.621 57.143 0.00 0.00 0.00 3.86
89 90 2.107366 CTCCTCTTCTCTTCCCTCCAC 58.893 57.143 0.00 0.00 0.00 4.02
90 91 0.820871 CCTCTTCTCTTCCCTCCACG 59.179 60.000 0.00 0.00 0.00 4.94
91 92 1.551452 CTCTTCTCTTCCCTCCACGT 58.449 55.000 0.00 0.00 0.00 4.49
92 93 1.474879 CTCTTCTCTTCCCTCCACGTC 59.525 57.143 0.00 0.00 0.00 4.34
93 94 1.203013 TCTTCTCTTCCCTCCACGTCA 60.203 52.381 0.00 0.00 0.00 4.35
94 95 1.203523 CTTCTCTTCCCTCCACGTCAG 59.796 57.143 0.00 0.00 0.00 3.51
95 96 1.216710 CTCTTCCCTCCACGTCAGC 59.783 63.158 0.00 0.00 0.00 4.26
96 97 1.533033 TCTTCCCTCCACGTCAGCA 60.533 57.895 0.00 0.00 0.00 4.41
98 99 1.533033 TTCCCTCCACGTCAGCAGA 60.533 57.895 0.00 0.00 0.00 4.26
99 100 1.118965 TTCCCTCCACGTCAGCAGAA 61.119 55.000 0.00 0.00 0.00 3.02
100 101 1.118965 TCCCTCCACGTCAGCAGAAA 61.119 55.000 0.00 0.00 0.00 2.52
101 102 0.250295 CCCTCCACGTCAGCAGAAAA 60.250 55.000 0.00 0.00 0.00 2.29
102 103 1.593196 CCTCCACGTCAGCAGAAAAA 58.407 50.000 0.00 0.00 0.00 1.94
126 127 8.687292 AAATTATATTTTACTCCCTCCGTTCC 57.313 34.615 0.00 0.00 0.00 3.62
127 128 7.628501 ATTATATTTTACTCCCTCCGTTCCT 57.371 36.000 0.00 0.00 0.00 3.36
128 129 8.731591 ATTATATTTTACTCCCTCCGTTCCTA 57.268 34.615 0.00 0.00 0.00 2.94
130 131 5.767277 ATTTTACTCCCTCCGTTCCTAAA 57.233 39.130 0.00 0.00 0.00 1.85
131 132 5.767277 TTTTACTCCCTCCGTTCCTAAAT 57.233 39.130 0.00 0.00 0.00 1.40
132 133 6.872585 TTTTACTCCCTCCGTTCCTAAATA 57.127 37.500 0.00 0.00 0.00 1.40
133 134 5.859205 TTACTCCCTCCGTTCCTAAATAC 57.141 43.478 0.00 0.00 0.00 1.89
134 135 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
135 136 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
136 137 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
138 139 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
139 140 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
140 141 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
141 142 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
142 143 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
143 144 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
145 146 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
146 147 7.491696 CCGTTCCTAAATACTTGTCTTTCTAGG 59.508 40.741 0.00 0.00 0.00 3.02
147 148 7.010275 CGTTCCTAAATACTTGTCTTTCTAGGC 59.990 40.741 0.00 0.00 0.00 3.93
148 149 7.490657 TCCTAAATACTTGTCTTTCTAGGCA 57.509 36.000 0.00 0.00 33.22 4.75
149 150 8.090788 TCCTAAATACTTGTCTTTCTAGGCAT 57.909 34.615 0.00 0.00 35.56 4.40
150 151 8.548877 TCCTAAATACTTGTCTTTCTAGGCATT 58.451 33.333 0.00 0.00 35.56 3.56
153 154 8.635765 AAATACTTGTCTTTCTAGGCATTTCA 57.364 30.769 0.00 0.00 35.56 2.69
157 158 7.373493 ACTTGTCTTTCTAGGCATTTCAAATG 58.627 34.615 5.68 5.68 35.56 2.32
158 159 7.231317 ACTTGTCTTTCTAGGCATTTCAAATGA 59.769 33.333 14.65 0.00 35.56 2.57
161 162 9.241919 TGTCTTTCTAGGCATTTCAAATGATTA 57.758 29.630 14.65 4.37 29.10 1.75
166 167 8.750515 TCTAGGCATTTCAAATGATTATCACA 57.249 30.769 14.65 0.00 0.00 3.58
167 168 9.358406 TCTAGGCATTTCAAATGATTATCACAT 57.642 29.630 14.65 0.00 0.00 3.21
170 171 8.077991 AGGCATTTCAAATGATTATCACATACG 58.922 33.333 14.65 0.00 0.00 3.06
171 172 7.326789 GGCATTTCAAATGATTATCACATACGG 59.673 37.037 14.65 0.00 0.00 4.02
172 173 8.075574 GCATTTCAAATGATTATCACATACGGA 58.924 33.333 14.65 0.00 0.00 4.69
176 177 9.771534 TTCAAATGATTATCACATACGGATGTA 57.228 29.630 14.23 0.00 44.82 2.29
218 219 8.467402 AGTGTAGATTCACTCATTTTACTTCG 57.533 34.615 0.00 0.00 44.07 3.79
219 220 8.088981 AGTGTAGATTCACTCATTTTACTTCGT 58.911 33.333 0.00 0.00 44.07 3.85
220 221 9.350357 GTGTAGATTCACTCATTTTACTTCGTA 57.650 33.333 0.00 0.00 35.68 3.43
227 228 8.906636 TCACTCATTTTACTTCGTATGTAGTC 57.093 34.615 0.00 0.00 0.00 2.59
228 229 8.517056 TCACTCATTTTACTTCGTATGTAGTCA 58.483 33.333 0.00 0.00 0.00 3.41
229 230 8.584600 CACTCATTTTACTTCGTATGTAGTCAC 58.415 37.037 0.00 0.00 0.00 3.67
230 231 8.521176 ACTCATTTTACTTCGTATGTAGTCACT 58.479 33.333 0.00 0.00 0.00 3.41
231 232 9.355215 CTCATTTTACTTCGTATGTAGTCACTT 57.645 33.333 0.00 0.00 0.00 3.16
232 233 9.135843 TCATTTTACTTCGTATGTAGTCACTTG 57.864 33.333 0.00 0.00 0.00 3.16
233 234 8.922676 CATTTTACTTCGTATGTAGTCACTTGT 58.077 33.333 0.00 0.00 0.00 3.16
234 235 8.876275 TTTTACTTCGTATGTAGTCACTTGTT 57.124 30.769 0.00 0.00 0.00 2.83
235 236 7.862741 TTACTTCGTATGTAGTCACTTGTTG 57.137 36.000 0.00 0.00 0.00 3.33
236 237 6.080648 ACTTCGTATGTAGTCACTTGTTGA 57.919 37.500 0.00 0.00 0.00 3.18
237 238 6.509656 ACTTCGTATGTAGTCACTTGTTGAA 58.490 36.000 0.00 0.00 35.39 2.69
238 239 6.982141 ACTTCGTATGTAGTCACTTGTTGAAA 59.018 34.615 0.00 0.00 35.39 2.69
239 240 7.656137 ACTTCGTATGTAGTCACTTGTTGAAAT 59.344 33.333 0.00 0.00 35.39 2.17
241 242 6.015504 CGTATGTAGTCACTTGTTGAAATGC 58.984 40.000 0.00 0.00 35.39 3.56
243 244 4.460263 TGTAGTCACTTGTTGAAATGCCT 58.540 39.130 0.00 0.00 35.39 4.75
245 246 5.700832 TGTAGTCACTTGTTGAAATGCCTAG 59.299 40.000 0.00 0.00 35.39 3.02
246 247 4.973168 AGTCACTTGTTGAAATGCCTAGA 58.027 39.130 0.00 0.00 35.39 2.43
247 248 5.376625 AGTCACTTGTTGAAATGCCTAGAA 58.623 37.500 0.00 0.00 35.39 2.10
248 249 5.827797 AGTCACTTGTTGAAATGCCTAGAAA 59.172 36.000 0.00 0.00 35.39 2.52
249 250 6.016777 AGTCACTTGTTGAAATGCCTAGAAAG 60.017 38.462 0.00 0.00 35.39 2.62
250 251 6.017109 GTCACTTGTTGAAATGCCTAGAAAGA 60.017 38.462 0.00 0.00 35.39 2.52
252 253 5.827797 ACTTGTTGAAATGCCTAGAAAGACA 59.172 36.000 0.00 0.00 0.00 3.41
253 254 6.321181 ACTTGTTGAAATGCCTAGAAAGACAA 59.679 34.615 0.00 0.00 0.00 3.18
254 255 6.317789 TGTTGAAATGCCTAGAAAGACAAG 57.682 37.500 0.00 0.00 0.00 3.16
255 256 5.827797 TGTTGAAATGCCTAGAAAGACAAGT 59.172 36.000 0.00 0.00 0.00 3.16
257 258 7.665559 TGTTGAAATGCCTAGAAAGACAAGTAT 59.334 33.333 0.00 0.00 0.00 2.12
258 259 8.515414 GTTGAAATGCCTAGAAAGACAAGTATT 58.485 33.333 0.00 0.00 0.00 1.89
260 261 9.733556 TGAAATGCCTAGAAAGACAAGTATTTA 57.266 29.630 0.00 0.00 0.00 1.40
264 265 7.913789 TGCCTAGAAAGACAAGTATTTAGGAA 58.086 34.615 11.40 1.02 26.70 3.36
265 266 7.822822 TGCCTAGAAAGACAAGTATTTAGGAAC 59.177 37.037 11.40 0.00 26.70 3.62
266 267 7.010275 GCCTAGAAAGACAAGTATTTAGGAACG 59.990 40.741 11.40 0.00 26.70 3.95
267 268 7.491696 CCTAGAAAGACAAGTATTTAGGAACGG 59.508 40.741 4.01 0.00 26.70 4.44
268 269 7.001099 AGAAAGACAAGTATTTAGGAACGGA 57.999 36.000 0.00 0.00 0.00 4.69
269 270 7.097834 AGAAAGACAAGTATTTAGGAACGGAG 58.902 38.462 0.00 0.00 0.00 4.63
270 271 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
271 272 4.161754 AGACAAGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
272 273 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
273 274 4.161754 ACAAGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
274 275 3.991683 AGTATTTAGGAACGGAGGGAGT 58.008 45.455 0.00 0.00 0.00 3.85
276 277 5.522641 AGTATTTAGGAACGGAGGGAGTAA 58.477 41.667 0.00 0.00 0.00 2.24
277 278 6.141790 AGTATTTAGGAACGGAGGGAGTAAT 58.858 40.000 0.00 0.00 0.00 1.89
278 279 5.970501 ATTTAGGAACGGAGGGAGTAATT 57.029 39.130 0.00 0.00 0.00 1.40
281 282 4.652679 AGGAACGGAGGGAGTAATTTTT 57.347 40.909 0.00 0.00 0.00 1.94
283 284 6.323210 AGGAACGGAGGGAGTAATTTTTAT 57.677 37.500 0.00 0.00 0.00 1.40
284 285 7.441903 AGGAACGGAGGGAGTAATTTTTATA 57.558 36.000 0.00 0.00 0.00 0.98
285 286 7.506971 AGGAACGGAGGGAGTAATTTTTATAG 58.493 38.462 0.00 0.00 0.00 1.31
286 287 6.204301 GGAACGGAGGGAGTAATTTTTATAGC 59.796 42.308 0.00 0.00 0.00 2.97
287 288 5.618236 ACGGAGGGAGTAATTTTTATAGCC 58.382 41.667 0.00 0.00 0.00 3.93
288 289 5.368816 ACGGAGGGAGTAATTTTTATAGCCT 59.631 40.000 0.00 0.00 0.00 4.58
289 290 5.701290 CGGAGGGAGTAATTTTTATAGCCTG 59.299 44.000 0.00 0.00 0.00 4.85
290 291 5.473846 GGAGGGAGTAATTTTTATAGCCTGC 59.526 44.000 0.00 0.00 0.00 4.85
291 292 6.267492 AGGGAGTAATTTTTATAGCCTGCT 57.733 37.500 0.00 0.00 0.00 4.24
292 293 6.673583 AGGGAGTAATTTTTATAGCCTGCTT 58.326 36.000 0.00 0.00 0.00 3.91
293 294 6.547510 AGGGAGTAATTTTTATAGCCTGCTTG 59.452 38.462 0.00 0.00 0.00 4.01
294 295 6.321435 GGGAGTAATTTTTATAGCCTGCTTGT 59.679 38.462 0.00 0.00 0.00 3.16
295 296 7.501225 GGGAGTAATTTTTATAGCCTGCTTGTA 59.499 37.037 0.00 0.00 0.00 2.41
321 322 7.976135 AAGCTTATTATACTTGCTCTCATGG 57.024 36.000 0.00 0.00 33.10 3.66
322 323 7.072263 AGCTTATTATACTTGCTCTCATGGT 57.928 36.000 0.00 0.00 0.00 3.55
323 324 6.933521 AGCTTATTATACTTGCTCTCATGGTG 59.066 38.462 0.00 0.00 0.00 4.17
325 326 5.894298 ATTATACTTGCTCTCATGGTGGA 57.106 39.130 0.00 0.00 0.00 4.02
327 328 2.414994 ACTTGCTCTCATGGTGGATG 57.585 50.000 0.00 0.00 0.00 3.51
330 331 0.543277 TGCTCTCATGGTGGATGTCC 59.457 55.000 0.00 0.00 33.29 4.02
331 332 0.179034 GCTCTCATGGTGGATGTCCC 60.179 60.000 0.00 0.00 33.29 4.46
332 333 1.206878 CTCTCATGGTGGATGTCCCA 58.793 55.000 0.00 0.00 44.25 4.37
340 341 3.623848 TGGATGTCCCACTCGTTTG 57.376 52.632 0.00 0.00 40.82 2.93
341 342 0.036164 TGGATGTCCCACTCGTTTGG 59.964 55.000 0.00 0.00 40.82 3.28
350 351 2.614057 CCCACTCGTTTGGATATGCTTC 59.386 50.000 6.63 0.00 39.24 3.86
351 352 2.614057 CCACTCGTTTGGATATGCTTCC 59.386 50.000 0.00 0.00 39.24 3.46
360 361 3.609853 TGGATATGCTTCCAGACAACAC 58.390 45.455 0.00 0.00 40.90 3.32
380 381 4.404394 ACACGGTCTTGGAAAAGGAAAAAT 59.596 37.500 0.00 0.00 0.00 1.82
401 402 3.662759 AAGAGGAAACTTGGTGGACAA 57.337 42.857 0.00 0.00 44.43 3.18
423 424 2.218603 GACCGAGACAGGCTTTTTGAA 58.781 47.619 0.00 0.00 33.69 2.69
424 425 2.814336 GACCGAGACAGGCTTTTTGAAT 59.186 45.455 0.00 0.00 33.69 2.57
444 445 3.702048 CCGCCGGTCTCCTTTCCA 61.702 66.667 1.90 0.00 0.00 3.53
473 474 5.504853 AGAGATTTTCATTTCCTCTCCACC 58.495 41.667 0.00 0.00 34.26 4.61
492 493 4.573607 CCACCTGTAATCACATCATGACAG 59.426 45.833 0.00 0.00 41.24 3.51
540 541 9.162764 CTTGTTCAATAATATATCCTAACCCCG 57.837 37.037 0.00 0.00 0.00 5.73
606 607 5.337554 AGAAAACGGAACACTTACTTTTGC 58.662 37.500 0.00 0.00 0.00 3.68
609 610 6.380095 AAACGGAACACTTACTTTTGCATA 57.620 33.333 0.00 0.00 0.00 3.14
615 616 6.391227 AACACTTACTTTTGCATAGCTTGT 57.609 33.333 0.00 0.00 0.00 3.16
621 622 7.876068 ACTTACTTTTGCATAGCTTGTACTACA 59.124 33.333 0.00 0.00 0.00 2.74
697 4002 1.210204 AGAGCCCCAATGGAGAAGCA 61.210 55.000 0.00 0.00 35.39 3.91
702 4007 2.224967 GCCCCAATGGAGAAGCATCTAT 60.225 50.000 0.00 0.00 35.54 1.98
801 4123 3.797039 TCATCCTAGCCATTCAAACGAG 58.203 45.455 0.00 0.00 0.00 4.18
854 4176 0.582005 GCGCTTGTCGACTTCAAAGT 59.418 50.000 17.92 0.00 43.16 2.66
1139 4461 4.249661 GGTTCTCTCCACAAGTTGAGATC 58.750 47.826 10.54 0.91 37.03 2.75
1147 4469 3.368843 CCACAAGTTGAGATCCATCGACT 60.369 47.826 10.54 0.03 44.30 4.18
1209 4531 2.543238 CGGTAATCTCTCCAACCTACGC 60.543 54.545 0.00 0.00 0.00 4.42
1211 4533 2.969628 AATCTCTCCAACCTACGCTG 57.030 50.000 0.00 0.00 0.00 5.18
1393 4721 4.737765 GTCTTAGCGACTGCAATCTTAGAG 59.262 45.833 0.00 0.00 46.23 2.43
1463 4791 7.514721 ACACTTGACCTTTCCTACAATTTCTA 58.485 34.615 0.00 0.00 0.00 2.10
1504 6697 0.387565 CTGGTTTTGGGGTTTGACCG 59.612 55.000 0.00 0.00 39.83 4.79
1728 6921 1.234615 TGCGCTTGCCTAGTTGTTCC 61.235 55.000 9.73 0.00 38.03 3.62
1746 6939 4.062991 GTTCCTGGAATAAGTTGACACGT 58.937 43.478 13.07 0.00 0.00 4.49
1747 6940 3.659786 TCCTGGAATAAGTTGACACGTG 58.340 45.455 15.48 15.48 0.00 4.49
1751 6944 2.806244 GGAATAAGTTGACACGTGTGCT 59.194 45.455 28.82 17.68 0.00 4.40
1753 6946 4.261031 GGAATAAGTTGACACGTGTGCTTT 60.261 41.667 28.82 16.31 0.00 3.51
1756 6949 4.893424 AAGTTGACACGTGTGCTTTTAT 57.107 36.364 28.82 0.00 0.00 1.40
1813 7012 4.800023 ACTAAAACCCTTAAGCAACCTGT 58.200 39.130 0.00 0.00 0.00 4.00
1877 7076 3.390639 CCACTTTGGATAGGAGAGCTCAT 59.609 47.826 17.77 0.00 40.96 2.90
1934 7133 5.509498 CCTGGAGGGTTTCATAAATGAAGA 58.491 41.667 5.60 0.00 46.34 2.87
2019 7274 0.320946 TGAATTCGACGTGGGTTCCC 60.321 55.000 0.00 0.12 0.00 3.97
2129 7384 7.819415 AGACAATCTTGATATCTCAAACACGAA 59.181 33.333 3.98 0.00 40.78 3.85
2346 7604 9.989869 GATCTTAGTAGAAACAATTTAGTTGGC 57.010 33.333 0.00 0.00 36.68 4.52
2713 7978 3.692101 CAGTAGAGCCCTATAGACCGATG 59.308 52.174 0.00 0.00 0.00 3.84
2856 8121 2.824936 TCCTCCGGTCGTTGTAACATAA 59.175 45.455 0.00 0.00 0.00 1.90
2896 8161 3.056250 TGCGTACACCGGAAAATAACCTA 60.056 43.478 9.46 0.00 36.94 3.08
2977 8242 3.290948 AATTAAGGCATACGCTCCCAA 57.709 42.857 0.00 0.00 38.60 4.12
3065 8330 3.360867 TGTGGGCGGATACAAATTTGAT 58.639 40.909 24.64 12.99 0.00 2.57
3130 8395 3.069443 TGGAAAAGGAGGTGTTTGATTGC 59.931 43.478 0.00 0.00 0.00 3.56
3197 8462 1.057847 CGTCGTGCGAGATTGTCTTTC 59.942 52.381 0.00 0.00 44.77 2.62
3295 8560 7.549147 TCTTGTTATTACTCACTGGTACCTT 57.451 36.000 14.36 0.00 0.00 3.50
3309 8574 3.580895 TGGTACCTTAGAATGTGTGAGCA 59.419 43.478 14.36 0.00 0.00 4.26
3328 8593 5.998363 TGAGCACACGATACATAGAGTCTAT 59.002 40.000 6.86 6.86 0.00 1.98
3343 8608 5.833340 AGAGTCTATAGTGAAAGACCCTGT 58.167 41.667 0.00 0.00 42.56 4.00
3367 8632 3.202829 AGTAAGGTTCCAGCGAAACAA 57.797 42.857 0.00 0.00 38.24 2.83
3370 8635 4.583073 AGTAAGGTTCCAGCGAAACAAATT 59.417 37.500 0.00 0.00 38.24 1.82
3404 8669 3.446161 TCAGGTTAATCGAATCCAGTCGT 59.554 43.478 0.00 0.00 41.80 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.911525 ATGTGAGAGTGGGAGGTGGG 60.912 60.000 0.00 0.00 0.00 4.61
4 5 1.759445 CTATGTGAGAGTGGGAGGTGG 59.241 57.143 0.00 0.00 0.00 4.61
6 7 2.461695 CACTATGTGAGAGTGGGAGGT 58.538 52.381 0.00 0.00 40.58 3.85
9 10 1.195115 GGCACTATGTGAGAGTGGGA 58.805 55.000 5.05 0.00 43.78 4.37
10 11 1.198713 AGGCACTATGTGAGAGTGGG 58.801 55.000 5.05 0.00 43.78 4.61
12 13 3.291584 TCCTAGGCACTATGTGAGAGTG 58.708 50.000 2.96 0.00 45.90 3.51
13 14 3.561143 CTCCTAGGCACTATGTGAGAGT 58.439 50.000 2.96 0.00 41.70 3.24
17 18 2.159179 TGCTCCTAGGCACTATGTGA 57.841 50.000 2.96 0.00 41.70 3.58
37 38 0.389037 TAAGAGTCAGCTGCAGCACG 60.389 55.000 38.24 28.24 45.16 5.34
38 39 2.021355 ATAAGAGTCAGCTGCAGCAC 57.979 50.000 38.24 28.18 45.16 4.40
39 40 2.235650 AGAATAAGAGTCAGCTGCAGCA 59.764 45.455 38.24 18.36 45.16 4.41
40 41 2.608546 CAGAATAAGAGTCAGCTGCAGC 59.391 50.000 31.53 31.53 42.49 5.25
41 42 3.859443 ACAGAATAAGAGTCAGCTGCAG 58.141 45.455 10.11 10.11 0.00 4.41
43 44 3.801594 GCTACAGAATAAGAGTCAGCTGC 59.198 47.826 9.47 4.26 0.00 5.25
44 45 4.367450 GGCTACAGAATAAGAGTCAGCTG 58.633 47.826 7.63 7.63 0.00 4.24
46 47 3.376540 CGGCTACAGAATAAGAGTCAGC 58.623 50.000 0.00 0.00 0.00 4.26
49 50 2.362717 AGCCGGCTACAGAATAAGAGTC 59.637 50.000 31.86 0.00 0.00 3.36
51 52 2.288518 GGAGCCGGCTACAGAATAAGAG 60.289 54.545 34.40 0.00 0.00 2.85
52 53 1.687123 GGAGCCGGCTACAGAATAAGA 59.313 52.381 34.40 0.00 0.00 2.10
54 55 1.687123 GAGGAGCCGGCTACAGAATAA 59.313 52.381 39.38 0.00 0.00 1.40
56 57 0.397816 AGAGGAGCCGGCTACAGAAT 60.398 55.000 39.38 20.40 0.00 2.40
57 58 0.614979 AAGAGGAGCCGGCTACAGAA 60.615 55.000 39.38 0.00 0.00 3.02
58 59 1.000486 AAGAGGAGCCGGCTACAGA 60.000 57.895 39.38 0.00 0.00 3.41
59 60 1.040339 AGAAGAGGAGCCGGCTACAG 61.040 60.000 39.38 0.00 0.00 2.74
61 62 0.753848 AGAGAAGAGGAGCCGGCTAC 60.754 60.000 32.56 32.56 0.00 3.58
62 63 0.033011 AAGAGAAGAGGAGCCGGCTA 60.033 55.000 32.97 0.00 0.00 3.93
63 64 1.305718 AAGAGAAGAGGAGCCGGCT 60.306 57.895 33.48 33.48 0.00 5.52
64 65 1.142965 GAAGAGAAGAGGAGCCGGC 59.857 63.158 21.89 21.89 0.00 6.13
65 66 1.681486 GGGAAGAGAAGAGGAGCCGG 61.681 65.000 0.00 0.00 0.00 6.13
66 67 0.686112 AGGGAAGAGAAGAGGAGCCG 60.686 60.000 0.00 0.00 0.00 5.52
67 68 1.119684 GAGGGAAGAGAAGAGGAGCC 58.880 60.000 0.00 0.00 0.00 4.70
68 69 1.119684 GGAGGGAAGAGAAGAGGAGC 58.880 60.000 0.00 0.00 0.00 4.70
70 71 1.617263 CGTGGAGGGAAGAGAAGAGGA 60.617 57.143 0.00 0.00 0.00 3.71
71 72 0.820871 CGTGGAGGGAAGAGAAGAGG 59.179 60.000 0.00 0.00 0.00 3.69
72 73 1.474879 GACGTGGAGGGAAGAGAAGAG 59.525 57.143 0.00 0.00 0.00 2.85
74 75 1.203523 CTGACGTGGAGGGAAGAGAAG 59.796 57.143 0.00 0.00 0.00 2.85
75 76 1.257743 CTGACGTGGAGGGAAGAGAA 58.742 55.000 0.00 0.00 0.00 2.87
76 77 1.251527 GCTGACGTGGAGGGAAGAGA 61.252 60.000 0.00 0.00 0.00 3.10
77 78 1.216710 GCTGACGTGGAGGGAAGAG 59.783 63.158 0.00 0.00 0.00 2.85
78 79 1.533033 TGCTGACGTGGAGGGAAGA 60.533 57.895 0.00 0.00 0.00 2.87
81 82 1.118965 TTTCTGCTGACGTGGAGGGA 61.119 55.000 0.00 0.00 0.00 4.20
83 84 1.593196 TTTTTCTGCTGACGTGGAGG 58.407 50.000 0.00 0.00 0.00 4.30
100 101 9.128404 GGAACGGAGGGAGTAAAATATAATTTT 57.872 33.333 3.38 3.38 0.00 1.82
101 102 8.500238 AGGAACGGAGGGAGTAAAATATAATTT 58.500 33.333 0.00 0.00 0.00 1.82
102 103 8.042286 AGGAACGGAGGGAGTAAAATATAATT 57.958 34.615 0.00 0.00 0.00 1.40
104 105 8.551682 TTAGGAACGGAGGGAGTAAAATATAA 57.448 34.615 0.00 0.00 0.00 0.98
105 106 8.551682 TTTAGGAACGGAGGGAGTAAAATATA 57.448 34.615 0.00 0.00 0.00 0.86
106 107 7.441903 TTTAGGAACGGAGGGAGTAAAATAT 57.558 36.000 0.00 0.00 0.00 1.28
108 109 5.767277 TTTAGGAACGGAGGGAGTAAAAT 57.233 39.130 0.00 0.00 0.00 1.82
109 110 5.767277 ATTTAGGAACGGAGGGAGTAAAA 57.233 39.130 0.00 0.00 0.00 1.52
111 112 5.522641 AGTATTTAGGAACGGAGGGAGTAA 58.477 41.667 0.00 0.00 0.00 2.24
113 114 3.991683 AGTATTTAGGAACGGAGGGAGT 58.008 45.455 0.00 0.00 0.00 3.85
115 116 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
117 118 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
118 119 7.097834 AGAAAGACAAGTATTTAGGAACGGAG 58.902 38.462 0.00 0.00 0.00 4.63
119 120 7.001099 AGAAAGACAAGTATTTAGGAACGGA 57.999 36.000 0.00 0.00 0.00 4.69
120 121 7.491696 CCTAGAAAGACAAGTATTTAGGAACGG 59.508 40.741 4.01 0.00 26.70 4.44
121 122 7.010275 GCCTAGAAAGACAAGTATTTAGGAACG 59.990 40.741 11.40 0.00 26.70 3.95
122 123 7.822822 TGCCTAGAAAGACAAGTATTTAGGAAC 59.177 37.037 11.40 0.00 26.70 3.62
123 124 7.913789 TGCCTAGAAAGACAAGTATTTAGGAA 58.086 34.615 11.40 1.02 26.70 3.36
124 125 7.490657 TGCCTAGAAAGACAAGTATTTAGGA 57.509 36.000 11.40 0.00 26.70 2.94
127 128 9.733556 TGAAATGCCTAGAAAGACAAGTATTTA 57.266 29.630 0.00 0.00 0.00 1.40
128 129 8.635765 TGAAATGCCTAGAAAGACAAGTATTT 57.364 30.769 0.00 0.00 0.00 1.40
130 131 8.635765 TTTGAAATGCCTAGAAAGACAAGTAT 57.364 30.769 0.00 0.00 0.00 2.12
131 132 8.514594 CATTTGAAATGCCTAGAAAGACAAGTA 58.485 33.333 4.82 0.00 0.00 2.24
132 133 6.959639 TTTGAAATGCCTAGAAAGACAAGT 57.040 33.333 0.00 0.00 0.00 3.16
133 134 7.596494 TCATTTGAAATGCCTAGAAAGACAAG 58.404 34.615 12.86 0.00 0.00 3.16
134 135 7.523293 TCATTTGAAATGCCTAGAAAGACAA 57.477 32.000 12.86 0.00 0.00 3.18
135 136 7.707624 ATCATTTGAAATGCCTAGAAAGACA 57.292 32.000 12.86 0.00 0.00 3.41
140 141 9.187996 TGTGATAATCATTTGAAATGCCTAGAA 57.812 29.630 12.86 0.00 0.00 2.10
141 142 8.750515 TGTGATAATCATTTGAAATGCCTAGA 57.249 30.769 12.86 0.00 0.00 2.43
145 146 7.326789 CCGTATGTGATAATCATTTGAAATGCC 59.673 37.037 12.86 1.28 0.00 4.40
146 147 8.075574 TCCGTATGTGATAATCATTTGAAATGC 58.924 33.333 12.86 0.00 0.00 3.56
149 150 9.119418 ACATCCGTATGTGATAATCATTTGAAA 57.881 29.630 0.00 0.00 44.79 2.69
150 151 8.675705 ACATCCGTATGTGATAATCATTTGAA 57.324 30.769 0.00 0.00 44.79 2.69
152 153 9.977762 CATACATCCGTATGTGATAATCATTTG 57.022 33.333 3.56 0.00 46.70 2.32
194 195 8.240883 ACGAAGTAAAATGAGTGAATCTACAC 57.759 34.615 0.00 0.00 41.94 2.90
212 213 7.650890 TTCAACAAGTGACTACATACGAAGTA 58.349 34.615 0.00 0.00 41.66 2.24
213 214 6.509656 TTCAACAAGTGACTACATACGAAGT 58.490 36.000 0.00 0.00 39.84 3.01
215 216 7.570507 GCATTTCAACAAGTGACTACATACGAA 60.571 37.037 0.00 0.00 35.39 3.85
216 217 6.128661 GCATTTCAACAAGTGACTACATACGA 60.129 38.462 0.00 0.00 35.39 3.43
217 218 6.015504 GCATTTCAACAAGTGACTACATACG 58.984 40.000 0.00 0.00 35.39 3.06
218 219 6.149474 AGGCATTTCAACAAGTGACTACATAC 59.851 38.462 0.00 0.00 35.84 2.39
219 220 6.237901 AGGCATTTCAACAAGTGACTACATA 58.762 36.000 0.00 0.00 35.84 2.29
220 221 5.072741 AGGCATTTCAACAAGTGACTACAT 58.927 37.500 0.00 0.00 35.84 2.29
221 222 4.460263 AGGCATTTCAACAAGTGACTACA 58.540 39.130 0.00 0.00 35.84 2.74
222 223 5.932303 TCTAGGCATTTCAACAAGTGACTAC 59.068 40.000 0.00 0.00 38.51 2.73
224 225 4.973168 TCTAGGCATTTCAACAAGTGACT 58.027 39.130 0.00 0.00 40.60 3.41
225 226 5.689383 TTCTAGGCATTTCAACAAGTGAC 57.311 39.130 0.00 0.00 35.39 3.67
227 228 6.145535 GTCTTTCTAGGCATTTCAACAAGTG 58.854 40.000 0.00 0.00 0.00 3.16
228 229 5.827797 TGTCTTTCTAGGCATTTCAACAAGT 59.172 36.000 0.00 0.00 29.10 3.16
229 230 6.317789 TGTCTTTCTAGGCATTTCAACAAG 57.682 37.500 0.00 0.00 29.10 3.16
230 231 6.321181 ACTTGTCTTTCTAGGCATTTCAACAA 59.679 34.615 0.00 0.00 35.56 2.83
231 232 5.827797 ACTTGTCTTTCTAGGCATTTCAACA 59.172 36.000 0.00 0.00 35.56 3.33
232 233 6.319141 ACTTGTCTTTCTAGGCATTTCAAC 57.681 37.500 0.00 0.00 35.56 3.18
233 234 8.635765 AATACTTGTCTTTCTAGGCATTTCAA 57.364 30.769 0.00 0.00 35.56 2.69
234 235 8.635765 AAATACTTGTCTTTCTAGGCATTTCA 57.364 30.769 0.00 0.00 35.56 2.69
236 237 9.178758 CCTAAATACTTGTCTTTCTAGGCATTT 57.821 33.333 0.00 0.00 35.56 2.32
237 238 8.548877 TCCTAAATACTTGTCTTTCTAGGCATT 58.451 33.333 0.00 0.00 35.56 3.56
238 239 8.090788 TCCTAAATACTTGTCTTTCTAGGCAT 57.909 34.615 0.00 0.00 35.56 4.40
239 240 7.490657 TCCTAAATACTTGTCTTTCTAGGCA 57.509 36.000 0.00 0.00 33.22 4.75
241 242 7.491696 CCGTTCCTAAATACTTGTCTTTCTAGG 59.508 40.741 0.00 0.00 0.00 3.02
243 244 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
245 246 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
246 247 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
247 248 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
248 249 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
249 250 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
250 251 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
252 253 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
253 254 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
254 255 5.859205 TTACTCCCTCCGTTCCTAAATAC 57.141 43.478 0.00 0.00 0.00 1.89
255 256 7.441903 AAATTACTCCCTCCGTTCCTAAATA 57.558 36.000 0.00 0.00 0.00 1.40
257 258 5.767277 AAATTACTCCCTCCGTTCCTAAA 57.233 39.130 0.00 0.00 0.00 1.85
258 259 5.767277 AAAATTACTCCCTCCGTTCCTAA 57.233 39.130 0.00 0.00 0.00 2.69
260 261 4.652679 AAAAATTACTCCCTCCGTTCCT 57.347 40.909 0.00 0.00 0.00 3.36
261 262 6.204301 GCTATAAAAATTACTCCCTCCGTTCC 59.796 42.308 0.00 0.00 0.00 3.62
264 265 5.368816 AGGCTATAAAAATTACTCCCTCCGT 59.631 40.000 0.00 0.00 0.00 4.69
265 266 5.701290 CAGGCTATAAAAATTACTCCCTCCG 59.299 44.000 0.00 0.00 0.00 4.63
266 267 5.473846 GCAGGCTATAAAAATTACTCCCTCC 59.526 44.000 0.00 0.00 0.00 4.30
267 268 6.299922 AGCAGGCTATAAAAATTACTCCCTC 58.700 40.000 0.00 0.00 0.00 4.30
268 269 6.267492 AGCAGGCTATAAAAATTACTCCCT 57.733 37.500 0.00 0.00 0.00 4.20
269 270 6.321435 ACAAGCAGGCTATAAAAATTACTCCC 59.679 38.462 0.00 0.00 0.00 4.30
270 271 7.334844 ACAAGCAGGCTATAAAAATTACTCC 57.665 36.000 0.00 0.00 0.00 3.85
295 296 9.664332 CCATGAGAGCAAGTATAATAAGCTTAT 57.336 33.333 13.37 13.37 35.36 1.73
298 299 6.933521 CACCATGAGAGCAAGTATAATAAGCT 59.066 38.462 0.00 0.35 38.43 3.74
299 300 6.148480 CCACCATGAGAGCAAGTATAATAAGC 59.852 42.308 0.00 0.00 0.00 3.09
300 301 7.445121 TCCACCATGAGAGCAAGTATAATAAG 58.555 38.462 0.00 0.00 0.00 1.73
301 302 7.373617 TCCACCATGAGAGCAAGTATAATAA 57.626 36.000 0.00 0.00 0.00 1.40
302 303 6.994421 TCCACCATGAGAGCAAGTATAATA 57.006 37.500 0.00 0.00 0.00 0.98
305 306 4.655649 ACATCCACCATGAGAGCAAGTATA 59.344 41.667 0.00 0.00 36.21 1.47
306 307 3.457380 ACATCCACCATGAGAGCAAGTAT 59.543 43.478 0.00 0.00 36.21 2.12
307 308 2.840038 ACATCCACCATGAGAGCAAGTA 59.160 45.455 0.00 0.00 36.21 2.24
308 309 1.632409 ACATCCACCATGAGAGCAAGT 59.368 47.619 0.00 0.00 36.21 3.16
309 310 2.286872 GACATCCACCATGAGAGCAAG 58.713 52.381 0.00 0.00 36.21 4.01
311 312 0.543277 GGACATCCACCATGAGAGCA 59.457 55.000 0.00 0.00 36.21 4.26
312 313 0.179034 GGGACATCCACCATGAGAGC 60.179 60.000 0.00 0.00 37.91 4.09
314 315 3.415509 TGGGACATCCACCATGAGA 57.584 52.632 0.00 0.00 41.46 3.27
322 323 0.036164 CCAAACGAGTGGGACATCCA 59.964 55.000 0.00 0.00 44.52 3.41
323 324 0.323629 TCCAAACGAGTGGGACATCC 59.676 55.000 8.87 0.00 44.52 3.51
325 326 3.808728 CATATCCAAACGAGTGGGACAT 58.191 45.455 8.87 0.00 44.52 3.06
327 328 1.940613 GCATATCCAAACGAGTGGGAC 59.059 52.381 8.87 0.00 39.34 4.46
330 331 2.614057 GGAAGCATATCCAAACGAGTGG 59.386 50.000 0.00 0.00 39.42 4.00
331 332 3.270027 TGGAAGCATATCCAAACGAGTG 58.730 45.455 3.66 0.00 46.36 3.51
332 333 3.627395 TGGAAGCATATCCAAACGAGT 57.373 42.857 3.66 0.00 46.36 4.18
340 341 2.609459 CGTGTTGTCTGGAAGCATATCC 59.391 50.000 0.00 0.00 40.10 2.59
341 342 2.609459 CCGTGTTGTCTGGAAGCATATC 59.391 50.000 0.00 0.00 0.00 1.63
350 351 0.105964 TCCAAGACCGTGTTGTCTGG 59.894 55.000 7.56 0.00 44.68 3.86
351 352 1.948104 TTCCAAGACCGTGTTGTCTG 58.052 50.000 7.56 0.00 44.68 3.51
360 361 6.977213 TCTTATTTTTCCTTTTCCAAGACCG 58.023 36.000 0.00 0.00 30.57 4.79
380 381 4.714632 CTTGTCCACCAAGTTTCCTCTTA 58.285 43.478 0.00 0.00 44.64 2.10
401 402 0.765510 AAAAAGCCTGTCTCGGTCCT 59.234 50.000 0.00 0.00 0.00 3.85
406 407 2.669391 GCCATTCAAAAAGCCTGTCTCG 60.669 50.000 0.00 0.00 0.00 4.04
442 443 6.058183 AGGAAATGAAAATCTCTACCGATGG 58.942 40.000 0.00 0.00 0.00 3.51
444 445 7.130681 AGAGGAAATGAAAATCTCTACCGAT 57.869 36.000 0.00 0.00 33.58 4.18
473 474 4.193865 TGCCTGTCATGATGTGATTACAG 58.806 43.478 0.00 0.00 40.79 2.74
516 517 7.238096 ACCGGGGTTAGGATATATTATTGAACA 59.762 37.037 6.32 0.00 0.00 3.18
532 533 2.089201 GTCCATTTTCACCGGGGTTAG 58.911 52.381 2.12 0.00 0.00 2.34
533 534 1.272037 GGTCCATTTTCACCGGGGTTA 60.272 52.381 2.12 0.00 0.00 2.85
536 537 4.012138 GGTCCATTTTCACCGGGG 57.988 61.111 6.32 0.00 0.00 5.73
540 541 3.934457 AATGTTCGGTCCATTTTCACC 57.066 42.857 0.00 0.00 0.00 4.02
577 578 3.007473 AGTGTTCCGTTTTCTCCCAAA 57.993 42.857 0.00 0.00 0.00 3.28
589 590 4.154195 AGCTATGCAAAAGTAAGTGTTCCG 59.846 41.667 0.00 0.00 0.00 4.30
590 591 5.629079 AGCTATGCAAAAGTAAGTGTTCC 57.371 39.130 0.00 0.00 0.00 3.62
609 610 9.809096 GCATGATATATGTATGTAGTACAAGCT 57.191 33.333 7.16 0.00 45.87 3.74
615 616 8.150296 GCCATGGCATGATATATGTATGTAGTA 58.850 37.037 32.08 0.00 41.49 1.82
621 622 5.039920 ACGCCATGGCATGATATATGTAT 57.960 39.130 34.93 0.00 42.06 2.29
673 3978 1.004745 TCTCCATTGGGGCTCTTTCAC 59.995 52.381 2.09 0.00 36.21 3.18
697 4002 7.682787 ACTAAGTGGATGTTGGAGAATAGAT 57.317 36.000 0.00 0.00 0.00 1.98
702 4007 6.681729 AGTTACTAAGTGGATGTTGGAGAA 57.318 37.500 0.00 0.00 0.00 2.87
766 4071 5.412640 GCTAGGATGATGATGATGACTCTG 58.587 45.833 0.00 0.00 0.00 3.35
801 4123 1.933853 GCAATACATCTGGTGACCGTC 59.066 52.381 0.00 0.00 0.00 4.79
854 4176 0.975556 TGCAGGGTCCGAGATGCTTA 60.976 55.000 8.05 0.00 39.42 3.09
1139 4461 5.605534 AGGTTGATCTTGATAAGTCGATGG 58.394 41.667 0.00 0.00 0.00 3.51
1147 4469 4.081142 TCCGCTGAAGGTTGATCTTGATAA 60.081 41.667 0.00 0.00 0.00 1.75
1209 4531 1.135721 GCCCAGCCAAGATTTAAGCAG 59.864 52.381 0.00 0.00 0.00 4.24
1211 4533 1.135721 CTGCCCAGCCAAGATTTAAGC 59.864 52.381 0.00 0.00 0.00 3.09
1393 4721 7.493971 TGAAATCTGAAGTGAATAAGAGCTAGC 59.506 37.037 6.62 6.62 0.00 3.42
1463 4791 5.705441 CAGTTGGGTGTGATACTTGTATTGT 59.295 40.000 0.00 0.00 0.00 2.71
1504 6697 7.201902 CCATGAGATATCTAGATACTTGAGGCC 60.202 44.444 14.71 0.00 0.00 5.19
1728 6921 3.363970 GCACACGTGTCAACTTATTCCAG 60.364 47.826 20.49 3.71 0.00 3.86
1746 6939 7.437862 GTCAAATTGTTGGAAGATAAAAGCACA 59.562 33.333 0.00 0.00 35.29 4.57
1747 6940 7.437862 TGTCAAATTGTTGGAAGATAAAAGCAC 59.562 33.333 0.00 0.00 35.29 4.40
1751 6944 8.243961 TCCTGTCAAATTGTTGGAAGATAAAA 57.756 30.769 0.00 0.00 35.29 1.52
1753 6946 7.831691 TTCCTGTCAAATTGTTGGAAGATAA 57.168 32.000 10.85 0.00 35.29 1.75
1813 7012 5.104444 TGTTATTACCAAGAATAAGGCCGGA 60.104 40.000 5.05 0.00 33.10 5.14
1877 7076 1.070758 GGTCCAGTTCAGTCAGCTTCA 59.929 52.381 0.00 0.00 0.00 3.02
1934 7133 4.774200 AGCTTTCAAGGCCTGATAAATGTT 59.226 37.500 5.69 0.00 32.78 2.71
2346 7604 2.571653 TCCAAAGTCTGATGGTAGTGGG 59.428 50.000 5.16 0.00 37.94 4.61
2567 7826 5.606505 TGTATCCGCTTGATGCTACATTTA 58.393 37.500 3.59 0.00 37.04 1.40
2713 7978 2.417924 CCTCCATCGACATAGGCATAGC 60.418 54.545 0.00 0.00 0.00 2.97
2856 8121 2.095213 CGCAATTGCTACGTATGTGGTT 59.905 45.455 26.86 0.00 39.32 3.67
2977 8242 7.933215 AATAGGTTCAAAACGCTAATAAGGT 57.067 32.000 0.00 0.00 0.00 3.50
3065 8330 3.609853 GTGGTCAGTCATCCAAATAGCA 58.390 45.455 0.00 0.00 35.38 3.49
3134 8399 7.697691 AGAAGTGTTGTTTTTGTACTCATGAG 58.302 34.615 21.37 21.37 0.00 2.90
3309 8574 9.557061 TTTCACTATAGACTCTATGTATCGTGT 57.443 33.333 6.78 0.00 33.96 4.49
3328 8593 6.014840 CCTTACTACAACAGGGTCTTTCACTA 60.015 42.308 0.00 0.00 0.00 2.74
3343 8608 4.060205 GTTTCGCTGGAACCTTACTACAA 58.940 43.478 0.00 0.00 0.00 2.41
3367 8632 0.609131 CCTGACACAAGGCCGGAATT 60.609 55.000 5.05 0.00 0.00 2.17
3370 8635 1.122632 TAACCTGACACAAGGCCGGA 61.123 55.000 5.05 0.00 41.46 5.14
3404 8669 7.878547 TGTGTCATGGCATAATCTTTTATCA 57.121 32.000 1.89 0.00 0.00 2.15
3506 8771 2.565367 ACAACGTTGTTCGCGATAAC 57.435 45.000 27.70 17.31 44.19 1.89
3520 8785 6.706270 AGAACAATATCCAGGCTTATACAACG 59.294 38.462 0.00 0.00 0.00 4.10


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

AutoCloner maintained by Alex Coulton.