Multiple sequence alignment - TraesCS2D01G513300

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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 TraesCS2D01G513300 chr2D 100.000 2984 0 0 857 3840 605181323 605178340 0.000000e+00 5511.0
1 TraesCS2D01G513300 chr2D 100.000 473 0 0 1 473 605182179 605181707 0.000000e+00 874.0
2 TraesCS2D01G513300 chr2D 92.000 450 32 4 2880 3327 16707426 16707873 2.520000e-176 628.0
3 TraesCS2D01G513300 chr2D 97.030 202 6 0 1 202 111989533 111989734 1.320000e-89 340.0
4 TraesCS2D01G513300 chr2D 85.887 248 33 2 207 452 203783129 203782882 2.940000e-66 263.0
5 TraesCS2D01G513300 chr2D 90.323 155 14 1 3687 3840 16708571 16708725 6.500000e-48 202.0
6 TraesCS2D01G513300 chr2D 92.562 121 8 1 981 1100 605328162 605328042 5.100000e-39 172.0
7 TraesCS2D01G513300 chr2D 78.906 256 34 13 1425 1672 605077717 605077960 5.140000e-34 156.0
8 TraesCS2D01G513300 chr2A 98.196 1164 14 2 1664 2827 736365949 736364793 0.000000e+00 2026.0
9 TraesCS2D01G513300 chr2A 96.822 818 19 3 857 1668 736372033 736371217 0.000000e+00 1360.0
10 TraesCS2D01G513300 chr2A 94.258 209 12 0 262 470 736372266 736372058 1.720000e-83 320.0
11 TraesCS2D01G513300 chr2A 94.258 209 12 0 262 470 736376281 736376073 1.720000e-83 320.0
12 TraesCS2D01G513300 chr2A 94.258 209 12 0 262 470 736379134 736378926 1.720000e-83 320.0
13 TraesCS2D01G513300 chr2A 87.226 274 33 2 202 473 448539168 448539441 1.040000e-80 311.0
14 TraesCS2D01G513300 chr2A 94.301 193 10 1 857 1049 736378901 736378710 1.040000e-75 294.0
15 TraesCS2D01G513300 chr2A 95.062 162 7 1 857 1018 736376048 736375888 1.770000e-63 254.0
16 TraesCS2D01G513300 chr2A 92.562 121 8 1 981 1100 736463213 736463093 5.100000e-39 172.0
17 TraesCS2D01G513300 chr2A 79.297 256 33 13 1425 1672 736233119 736232876 1.100000e-35 161.0
18 TraesCS2D01G513300 chr2A 95.745 47 2 0 202 248 736372310 736372264 4.110000e-10 76.8
19 TraesCS2D01G513300 chr2A 95.745 47 2 0 202 248 736376325 736376279 4.110000e-10 76.8
20 TraesCS2D01G513300 chr2A 95.745 47 2 0 202 248 736379178 736379132 4.110000e-10 76.8
21 TraesCS2D01G513300 chr1D 89.234 836 37 6 2877 3685 206064562 206063753 0.000000e+00 996.0
22 TraesCS2D01G513300 chr1D 97.561 205 3 2 1 204 221884201 221883998 2.200000e-92 350.0
23 TraesCS2D01G513300 chr1D 98.485 198 2 1 1 198 111513021 111513217 7.900000e-92 348.0
24 TraesCS2D01G513300 chr1D 96.947 131 4 0 3710 3840 206063554 206063424 1.800000e-53 220.0
25 TraesCS2D01G513300 chr1D 92.308 39 2 1 2663 2700 198753844 198753806 2.000000e-03 54.7
26 TraesCS2D01G513300 chr3B 89.216 612 55 8 2881 3482 762328980 762329590 0.000000e+00 754.0
27 TraesCS2D01G513300 chr3B 83.598 378 40 11 3480 3840 762330119 762330491 6.150000e-88 335.0
28 TraesCS2D01G513300 chr7A 91.328 369 13 3 3479 3833 717248250 717248613 1.600000e-133 486.0
29 TraesCS2D01G513300 chr4D 98.507 201 3 0 1 201 495093975 495094175 4.720000e-94 355.0
30 TraesCS2D01G513300 chr4D 96.552 203 6 1 1 202 342540843 342541045 6.150000e-88 335.0
31 TraesCS2D01G513300 chr5D 98.000 200 3 1 1 200 439300148 439300346 2.840000e-91 346.0
32 TraesCS2D01G513300 chr5D 77.447 235 47 5 215 445 136493385 136493153 6.690000e-28 135.0
33 TraesCS2D01G513300 chr5D 87.500 56 7 0 2879 2934 556447670 556447615 8.900000e-07 65.8
34 TraesCS2D01G513300 chr6D 97.990 199 3 1 1 199 368116935 368116738 1.020000e-90 344.0
35 TraesCS2D01G513300 chr5A 96.569 204 3 2 1 200 522364779 522364982 6.150000e-88 335.0
36 TraesCS2D01G513300 chr5A 87.162 148 18 1 202 348 479680945 479680798 2.370000e-37 167.0
37 TraesCS2D01G513300 chr1A 97.000 200 5 1 1 199 11790556 11790755 6.150000e-88 335.0
38 TraesCS2D01G513300 chr3A 88.172 279 32 1 3204 3482 715496631 715496908 7.950000e-87 331.0
39 TraesCS2D01G513300 chr3A 94.828 58 3 0 3781 3838 715541766 715541823 1.470000e-14 91.6
40 TraesCS2D01G513300 chr3A 97.727 44 1 0 2880 2923 640744816 640744773 4.110000e-10 76.8
41 TraesCS2D01G513300 chr7D 88.235 119 8 3 859 977 453127868 453127980 1.860000e-28 137.0
42 TraesCS2D01G513300 chr6B 77.083 240 50 5 2881 3117 662192646 662192883 2.410000e-27 134.0
43 TraesCS2D01G513300 chr6B 76.571 175 30 11 2880 3050 521445012 521445179 6.840000e-13 86.1
44 TraesCS2D01G513300 chr1B 86.087 115 9 5 3726 3840 26860940 26860833 2.420000e-22 117.0
45 TraesCS2D01G513300 chr1B 85.047 107 10 4 3726 3832 26861041 26860941 1.890000e-18 104.0
46 TraesCS2D01G513300 chr1B 81.633 98 16 2 2881 2977 32953361 32953265 3.180000e-11 80.5
47 TraesCS2D01G513300 chr1B 85.246 61 7 2 2641 2700 278631397 278631338 1.150000e-05 62.1
48 TraesCS2D01G513300 chr4B 75.983 229 51 4 2881 3107 20682498 20682724 8.720000e-22 115.0
49 TraesCS2D01G513300 chr3D 77.714 175 34 5 2967 3139 40185791 40185620 6.790000e-18 102.0
50 TraesCS2D01G513300 chrUn 93.617 47 3 0 2881 2927 303803301 303803255 1.910000e-08 71.3


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 TraesCS2D01G513300 chr2D 605178340 605182179 3839 True 3192.500000 5511 100.000000 1 3840 2 chr2D.!!$R3 3839
1 TraesCS2D01G513300 chr2D 16707426 16708725 1299 False 415.000000 628 91.161500 2880 3840 2 chr2D.!!$F3 960
2 TraesCS2D01G513300 chr2A 736364793 736365949 1156 True 2026.000000 2026 98.196000 1664 2827 1 chr2A.!!$R2 1163
3 TraesCS2D01G513300 chr2A 736371217 736379178 7961 True 344.266667 1360 95.132667 202 1668 9 chr2A.!!$R4 1466
4 TraesCS2D01G513300 chr1D 206063424 206064562 1138 True 608.000000 996 93.090500 2877 3840 2 chr1D.!!$R3 963
5 TraesCS2D01G513300 chr3B 762328980 762330491 1511 False 544.500000 754 86.407000 2881 3840 2 chr3B.!!$F1 959

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
52 53 0.107654 GGGCTCTACTGTTGCCGATT 60.108 55.0 11.18 0.00 46.97 3.34 F
472 7124 0.108963 TCCCTAGCTACCTCGAGAGC 59.891 60.0 15.71 16.04 39.08 4.09 F
1111 7763 0.598065 GACGCATGAAGGTTTTGGCT 59.402 50.0 0.00 0.00 0.00 4.75 F
2596 9254 0.462225 CTGTGGAGAGCAGCATCCTG 60.462 60.0 15.67 4.97 42.13 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1018 7670 0.320771 CGTGCAGGTCACTTTAGGCT 60.321 55.000 0.00 0.0 43.46 4.58 R
2160 8818 1.666700 CTCGGTCGTCTCTTTCTCGAT 59.333 52.381 0.00 0.0 36.08 3.59 R
2837 9495 0.438830 CGAGGCACGTTGCTAGTTTC 59.561 55.000 9.31 1.7 44.28 2.78 R
3434 10145 0.036765 AGCCTGTATTTTCGCACGGA 60.037 50.000 0.00 0.0 0.00 4.69 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
20 21 3.516981 CCTCCATCGACATAGGCATAG 57.483 52.381 0.00 0.00 0.00 2.23
22 23 3.367806 CCTCCATCGACATAGGCATAGTG 60.368 52.174 0.00 0.00 0.00 2.74
24 25 3.641436 TCCATCGACATAGGCATAGTGTT 59.359 43.478 0.00 0.00 0.00 3.32
26 27 3.452755 TCGACATAGGCATAGTGTTGG 57.547 47.619 7.75 0.70 0.00 3.77
27 28 2.764010 TCGACATAGGCATAGTGTTGGT 59.236 45.455 7.75 0.00 0.00 3.67
32 33 6.072119 CGACATAGGCATAGTGTTGGTCTATA 60.072 42.308 0.00 0.00 0.00 1.31
34 35 6.211584 ACATAGGCATAGTGTTGGTCTATAGG 59.788 42.308 0.00 0.00 0.00 2.57
35 36 3.904339 AGGCATAGTGTTGGTCTATAGGG 59.096 47.826 0.00 0.00 0.00 3.53
37 38 3.325135 GCATAGTGTTGGTCTATAGGGCT 59.675 47.826 0.00 0.00 0.00 5.19
38 39 4.561734 GCATAGTGTTGGTCTATAGGGCTC 60.562 50.000 0.00 0.00 0.00 4.70
40 41 4.537945 AGTGTTGGTCTATAGGGCTCTA 57.462 45.455 0.00 0.00 0.00 2.43
41 42 4.216708 AGTGTTGGTCTATAGGGCTCTAC 58.783 47.826 0.00 0.00 0.00 2.59
42 43 4.079096 AGTGTTGGTCTATAGGGCTCTACT 60.079 45.833 0.00 0.00 0.00 2.57
43 44 4.038162 GTGTTGGTCTATAGGGCTCTACTG 59.962 50.000 0.00 0.00 0.00 2.74
44 45 4.216708 GTTGGTCTATAGGGCTCTACTGT 58.783 47.826 0.00 0.00 0.00 3.55
45 46 4.537945 TGGTCTATAGGGCTCTACTGTT 57.462 45.455 0.00 0.00 0.00 3.16
48 49 3.006003 GTCTATAGGGCTCTACTGTTGCC 59.994 52.174 0.00 9.63 45.42 4.52
49 50 0.753262 ATAGGGCTCTACTGTTGCCG 59.247 55.000 0.00 0.00 46.97 5.69
50 51 0.323999 TAGGGCTCTACTGTTGCCGA 60.324 55.000 11.18 2.40 46.97 5.54
51 52 0.978146 AGGGCTCTACTGTTGCCGAT 60.978 55.000 11.18 2.91 46.97 4.18
52 53 0.107654 GGGCTCTACTGTTGCCGATT 60.108 55.000 11.18 0.00 46.97 3.34
54 55 1.398390 GGCTCTACTGTTGCCGATTTG 59.602 52.381 4.02 0.00 37.11 2.32
55 56 2.076863 GCTCTACTGTTGCCGATTTGT 58.923 47.619 0.00 0.00 0.00 2.83
56 57 2.094417 GCTCTACTGTTGCCGATTTGTC 59.906 50.000 0.00 0.00 0.00 3.18
95 96 6.588719 TTTTTGTCAGACCTTCATATTGGG 57.411 37.500 0.00 0.00 0.00 4.12
96 97 3.281727 TGTCAGACCTTCATATTGGGC 57.718 47.619 0.00 0.00 0.00 5.36
97 98 2.092429 TGTCAGACCTTCATATTGGGCC 60.092 50.000 0.00 0.00 29.76 5.80
98 99 1.140852 TCAGACCTTCATATTGGGCCG 59.859 52.381 0.00 0.00 29.76 6.13
99 100 1.134098 CAGACCTTCATATTGGGCCGT 60.134 52.381 0.00 0.00 29.76 5.68
103 104 0.381801 CTTCATATTGGGCCGTGTGC 59.618 55.000 0.00 0.00 40.16 4.57
104 105 0.322906 TTCATATTGGGCCGTGTGCA 60.323 50.000 0.00 0.00 43.89 4.57
106 107 0.311790 CATATTGGGCCGTGTGCATC 59.688 55.000 0.00 0.00 43.89 3.91
107 108 0.823356 ATATTGGGCCGTGTGCATCC 60.823 55.000 0.00 0.00 43.89 3.51
108 109 1.920734 TATTGGGCCGTGTGCATCCT 61.921 55.000 0.00 0.00 43.89 3.24
109 110 1.920734 ATTGGGCCGTGTGCATCCTA 61.921 55.000 0.00 0.00 43.89 2.94
110 111 2.130821 TTGGGCCGTGTGCATCCTAA 62.131 55.000 0.00 0.00 43.89 2.69
111 112 1.152963 GGGCCGTGTGCATCCTAAT 60.153 57.895 0.00 0.00 43.89 1.73
114 115 2.504367 GGCCGTGTGCATCCTAATTAT 58.496 47.619 0.00 0.00 43.89 1.28
115 116 2.226437 GGCCGTGTGCATCCTAATTATG 59.774 50.000 0.00 0.00 43.89 1.90
124 125 2.839486 TCCTAATTATGCAGAGGCCG 57.161 50.000 0.00 0.00 40.13 6.13
125 126 1.347707 TCCTAATTATGCAGAGGCCGG 59.652 52.381 0.00 0.00 40.13 6.13
126 127 1.611673 CCTAATTATGCAGAGGCCGGG 60.612 57.143 2.18 0.00 40.13 5.73
127 128 1.072331 CTAATTATGCAGAGGCCGGGT 59.928 52.381 2.18 0.00 40.13 5.28
128 129 0.466189 AATTATGCAGAGGCCGGGTG 60.466 55.000 2.18 0.00 40.13 4.61
129 130 1.635817 ATTATGCAGAGGCCGGGTGT 61.636 55.000 2.18 0.00 40.13 4.16
130 131 1.847798 TTATGCAGAGGCCGGGTGTT 61.848 55.000 2.18 0.00 40.13 3.32
131 132 0.978667 TATGCAGAGGCCGGGTGTTA 60.979 55.000 2.18 0.00 40.13 2.41
132 133 2.436115 GCAGAGGCCGGGTGTTAC 60.436 66.667 2.18 0.00 0.00 2.50
133 134 2.955881 GCAGAGGCCGGGTGTTACT 61.956 63.158 2.18 0.00 0.00 2.24
134 135 1.218316 CAGAGGCCGGGTGTTACTC 59.782 63.158 2.18 0.00 0.00 2.59
135 136 1.229082 AGAGGCCGGGTGTTACTCA 60.229 57.895 2.18 0.00 0.00 3.41
136 137 0.617820 AGAGGCCGGGTGTTACTCAT 60.618 55.000 2.18 0.00 0.00 2.90
137 138 1.117150 GAGGCCGGGTGTTACTCATA 58.883 55.000 2.18 0.00 0.00 2.15
138 139 1.483415 GAGGCCGGGTGTTACTCATAA 59.517 52.381 2.18 0.00 0.00 1.90
140 141 2.158813 AGGCCGGGTGTTACTCATAATG 60.159 50.000 2.18 0.00 0.00 1.90
141 142 1.602377 GCCGGGTGTTACTCATAATGC 59.398 52.381 2.18 0.00 0.00 3.56
142 143 2.745152 GCCGGGTGTTACTCATAATGCT 60.745 50.000 2.18 0.00 0.00 3.79
143 144 3.541632 CCGGGTGTTACTCATAATGCTT 58.458 45.455 0.00 0.00 0.00 3.91
144 145 3.945285 CCGGGTGTTACTCATAATGCTTT 59.055 43.478 0.00 0.00 0.00 3.51
145 146 4.201910 CCGGGTGTTACTCATAATGCTTTG 60.202 45.833 0.00 0.00 0.00 2.77
146 147 4.394920 CGGGTGTTACTCATAATGCTTTGT 59.605 41.667 0.00 0.00 0.00 2.83
148 149 6.260050 CGGGTGTTACTCATAATGCTTTGTAT 59.740 38.462 0.00 0.00 0.00 2.29
149 150 7.518370 CGGGTGTTACTCATAATGCTTTGTATC 60.518 40.741 0.00 0.00 0.00 2.24
150 151 7.255139 GGGTGTTACTCATAATGCTTTGTATCC 60.255 40.741 0.00 0.00 0.00 2.59
151 152 7.345192 GTGTTACTCATAATGCTTTGTATCCG 58.655 38.462 0.00 0.00 0.00 4.18
152 153 6.018262 TGTTACTCATAATGCTTTGTATCCGC 60.018 38.462 0.00 0.00 0.00 5.54
153 154 4.708177 ACTCATAATGCTTTGTATCCGCT 58.292 39.130 0.00 0.00 0.00 5.52
154 155 5.126067 ACTCATAATGCTTTGTATCCGCTT 58.874 37.500 0.00 0.00 0.00 4.68
155 156 5.008019 ACTCATAATGCTTTGTATCCGCTTG 59.992 40.000 0.00 0.00 0.00 4.01
156 157 5.122519 TCATAATGCTTTGTATCCGCTTGA 58.877 37.500 0.00 0.00 0.00 3.02
157 158 5.764686 TCATAATGCTTTGTATCCGCTTGAT 59.235 36.000 0.00 0.00 37.49 2.57
158 159 3.976793 ATGCTTTGTATCCGCTTGATG 57.023 42.857 0.00 0.00 34.76 3.07
159 160 1.401552 TGCTTTGTATCCGCTTGATGC 59.598 47.619 0.00 0.00 36.68 3.91
160 161 1.672881 GCTTTGTATCCGCTTGATGCT 59.327 47.619 3.59 0.00 37.04 3.79
162 163 3.303395 GCTTTGTATCCGCTTGATGCTAC 60.303 47.826 3.59 0.00 37.04 3.58
163 164 3.535280 TTGTATCCGCTTGATGCTACA 57.465 42.857 3.59 0.00 37.04 2.74
165 166 4.071961 TGTATCCGCTTGATGCTACATT 57.928 40.909 3.59 0.00 37.04 2.71
166 167 4.450976 TGTATCCGCTTGATGCTACATTT 58.549 39.130 3.59 0.00 37.04 2.32
167 168 3.976793 ATCCGCTTGATGCTACATTTG 57.023 42.857 0.00 0.00 40.11 2.32
168 169 2.984562 TCCGCTTGATGCTACATTTGA 58.015 42.857 0.00 0.00 40.11 2.69
169 170 2.938451 TCCGCTTGATGCTACATTTGAG 59.062 45.455 0.00 0.00 40.11 3.02
170 171 2.938451 CCGCTTGATGCTACATTTGAGA 59.062 45.455 0.00 0.00 40.11 3.27
171 172 3.562973 CCGCTTGATGCTACATTTGAGAT 59.437 43.478 0.00 0.00 40.11 2.75
174 175 6.072838 CCGCTTGATGCTACATTTGAGATAAT 60.073 38.462 0.00 0.00 40.11 1.28
175 176 7.118245 CCGCTTGATGCTACATTTGAGATAATA 59.882 37.037 0.00 0.00 40.11 0.98
176 177 8.498358 CGCTTGATGCTACATTTGAGATAATAA 58.502 33.333 0.00 0.00 40.11 1.40
183 184 8.289618 TGCTACATTTGAGATAATAAAATCGCC 58.710 33.333 0.00 0.00 0.00 5.54
184 185 7.750903 GCTACATTTGAGATAATAAAATCGCCC 59.249 37.037 0.00 0.00 0.00 6.13
185 186 7.823745 ACATTTGAGATAATAAAATCGCCCT 57.176 32.000 0.00 0.00 0.00 5.19
186 187 8.237811 ACATTTGAGATAATAAAATCGCCCTT 57.762 30.769 0.00 0.00 0.00 3.95
191 192 8.251750 TGAGATAATAAAATCGCCCTTTATCG 57.748 34.615 0.00 0.00 33.43 2.92
192 193 7.333423 TGAGATAATAAAATCGCCCTTTATCGG 59.667 37.037 0.00 0.00 33.43 4.18
193 194 7.391620 AGATAATAAAATCGCCCTTTATCGGA 58.608 34.615 0.00 0.00 33.43 4.55
195 196 6.702716 AATAAAATCGCCCTTTATCGGAAA 57.297 33.333 0.00 0.00 30.41 3.13
196 197 6.702716 ATAAAATCGCCCTTTATCGGAAAA 57.297 33.333 0.00 0.00 0.00 2.29
197 198 5.394224 AAAATCGCCCTTTATCGGAAAAA 57.606 34.783 0.00 0.00 0.00 1.94
248 2901 0.469331 CTATGGCCCGGTCACTAGGA 60.469 60.000 0.00 0.00 0.00 2.94
249 2902 0.757935 TATGGCCCGGTCACTAGGAC 60.758 60.000 0.00 0.00 46.20 3.85
259 2912 3.870633 GTCACTAGGACCACGAGAAAT 57.129 47.619 0.00 0.00 40.83 2.17
260 2913 4.978083 GTCACTAGGACCACGAGAAATA 57.022 45.455 0.00 0.00 40.83 1.40
304 6956 3.134623 ACATCAAACATCCGGCTGATCTA 59.865 43.478 13.24 0.00 0.00 1.98
310 6962 7.097192 TCAAACATCCGGCTGATCTATTATAC 58.903 38.462 13.24 0.00 0.00 1.47
329 6981 8.986477 ATTATACAAATTGGTGTCTTTCTTGC 57.014 30.769 0.00 0.00 32.75 4.01
342 6994 2.979676 CTTGCAGCCGTGGAAGCA 60.980 61.111 2.14 2.14 44.12 3.91
392 7044 4.120244 AGGAGCTCGCCTCAAAGA 57.880 55.556 7.83 0.00 42.62 2.52
403 7055 1.067354 GCCTCAAAGATGTGGGCAAAG 60.067 52.381 0.00 0.00 42.03 2.77
438 7090 1.873270 CGATCGACACAGGGACACCA 61.873 60.000 10.26 0.00 40.13 4.17
442 7094 2.445085 ACACAGGGACACCACCGA 60.445 61.111 0.00 0.00 40.13 4.69
466 7118 1.881324 GACGTCATCCCTAGCTACCTC 59.119 57.143 11.55 0.00 0.00 3.85
470 7122 2.055579 TCATCCCTAGCTACCTCGAGA 58.944 52.381 15.71 0.00 0.00 4.04
472 7124 0.108963 TCCCTAGCTACCTCGAGAGC 59.891 60.000 15.71 16.04 39.08 4.09
901 7553 5.067413 TCTCTCTGTCTTTATTTCGGCGTAT 59.933 40.000 6.85 4.59 0.00 3.06
917 7569 4.219033 GGCGTATTCTGTCAAACTTGTTG 58.781 43.478 0.00 0.00 0.00 3.33
923 7575 7.058354 CGTATTCTGTCAAACTTGTTGAATTCG 59.942 37.037 0.04 0.00 33.18 3.34
1033 7685 0.798776 CGCAAGCCTAAAGTGACCTG 59.201 55.000 0.00 0.00 0.00 4.00
1111 7763 0.598065 GACGCATGAAGGTTTTGGCT 59.402 50.000 0.00 0.00 0.00 4.75
1234 7887 3.931907 TGATGGGTAGGACAGGATTTG 57.068 47.619 0.00 0.00 0.00 2.32
1293 7946 1.876664 GTTTTTCTCCGCCCTCTGC 59.123 57.895 0.00 0.00 0.00 4.26
1375 8028 5.939883 CACTGGTCTTTTCCTCATTACATCA 59.060 40.000 0.00 0.00 0.00 3.07
1377 8030 7.121759 CACTGGTCTTTTCCTCATTACATCAAT 59.878 37.037 0.00 0.00 0.00 2.57
1680 8338 5.319931 GGTGCGCTACGTACTAATATCTAC 58.680 45.833 9.73 0.00 41.78 2.59
1681 8339 5.121454 GGTGCGCTACGTACTAATATCTACT 59.879 44.000 9.73 0.00 41.78 2.57
1682 8340 6.311445 GGTGCGCTACGTACTAATATCTACTA 59.689 42.308 9.73 0.00 41.78 1.82
1737 8395 6.528826 CATGCGTTAGTCAATCTATATGTGC 58.471 40.000 0.00 0.00 0.00 4.57
1949 8607 4.978580 CGTATTCGAGAGCATGATCAAAGA 59.021 41.667 14.38 6.35 39.71 2.52
2117 8775 9.195411 GTTTCCGTATTGATCAAACCGTATATA 57.805 33.333 21.37 3.90 0.00 0.86
2160 8818 0.809636 CATGTAGGCGACCGATTGCA 60.810 55.000 0.00 0.00 36.89 4.08
2184 8842 2.678836 GAGAAAGAGACGACCGAGATCA 59.321 50.000 0.00 0.00 0.00 2.92
2252 8910 1.736681 GTGAACAATCTGCAGCCTCTC 59.263 52.381 9.47 2.38 0.00 3.20
2596 9254 0.462225 CTGTGGAGAGCAGCATCCTG 60.462 60.000 15.67 4.97 42.13 3.86
2619 9277 7.228906 CCTGACACGGACTATCTTTTCTATCTA 59.771 40.741 0.00 0.00 0.00 1.98
2704 9362 2.476854 GCCGTTATGAAGCAGCTTGAAG 60.477 50.000 13.91 0.00 0.00 3.02
2705 9363 3.002791 CCGTTATGAAGCAGCTTGAAGA 58.997 45.455 13.91 0.00 0.00 2.87
2706 9364 3.436704 CCGTTATGAAGCAGCTTGAAGAA 59.563 43.478 13.91 1.18 0.00 2.52
2707 9365 4.398247 CGTTATGAAGCAGCTTGAAGAAC 58.602 43.478 13.91 12.76 0.00 3.01
2746 9404 3.072622 AGGGGTTGTCTAGAAGTTTGGTC 59.927 47.826 0.00 0.00 0.00 4.02
2810 9468 2.159282 GCTCTGGCCAAAATGATGTCAG 60.159 50.000 7.01 0.00 0.00 3.51
2811 9469 1.820519 TCTGGCCAAAATGATGTCAGC 59.179 47.619 7.01 0.00 0.00 4.26
2827 9485 6.982724 TGATGTCAGCTGAGTAGTAATTCATG 59.017 38.462 18.89 0.00 0.00 3.07
2828 9486 6.286240 TGTCAGCTGAGTAGTAATTCATGT 57.714 37.500 18.89 0.00 0.00 3.21
2829 9487 6.101997 TGTCAGCTGAGTAGTAATTCATGTG 58.898 40.000 18.89 0.00 0.00 3.21
2830 9488 6.102663 GTCAGCTGAGTAGTAATTCATGTGT 58.897 40.000 18.89 0.00 0.00 3.72
2831 9489 6.591834 GTCAGCTGAGTAGTAATTCATGTGTT 59.408 38.462 18.89 0.00 0.00 3.32
2832 9490 7.118390 GTCAGCTGAGTAGTAATTCATGTGTTT 59.882 37.037 18.89 0.00 0.00 2.83
2833 9491 7.118245 TCAGCTGAGTAGTAATTCATGTGTTTG 59.882 37.037 13.74 0.00 0.00 2.93
2834 9492 7.118245 CAGCTGAGTAGTAATTCATGTGTTTGA 59.882 37.037 8.42 0.00 0.00 2.69
2835 9493 7.661437 AGCTGAGTAGTAATTCATGTGTTTGAA 59.339 33.333 0.00 0.00 39.77 2.69
2836 9494 8.454106 GCTGAGTAGTAATTCATGTGTTTGAAT 58.546 33.333 0.00 0.00 45.85 2.57
2837 9495 9.764870 CTGAGTAGTAATTCATGTGTTTGAATG 57.235 33.333 0.80 0.00 43.73 2.67
2838 9496 9.500785 TGAGTAGTAATTCATGTGTTTGAATGA 57.499 29.630 0.80 0.00 43.73 2.57
2845 9503 8.524870 AATTCATGTGTTTGAATGAAACTAGC 57.475 30.769 2.52 0.00 43.73 3.42
2846 9504 6.631971 TCATGTGTTTGAATGAAACTAGCA 57.368 33.333 0.00 0.00 43.90 3.49
2847 9505 7.036996 TCATGTGTTTGAATGAAACTAGCAA 57.963 32.000 0.00 0.00 43.90 3.91
2848 9506 6.917477 TCATGTGTTTGAATGAAACTAGCAAC 59.083 34.615 0.00 0.00 43.90 4.17
2849 9507 5.270083 TGTGTTTGAATGAAACTAGCAACG 58.730 37.500 0.00 0.00 43.90 4.10
2850 9508 5.163703 TGTGTTTGAATGAAACTAGCAACGT 60.164 36.000 0.00 0.00 43.90 3.99
2851 9509 5.171337 GTGTTTGAATGAAACTAGCAACGTG 59.829 40.000 0.00 0.00 43.90 4.49
2852 9510 3.536158 TGAATGAAACTAGCAACGTGC 57.464 42.857 0.00 0.00 45.46 5.34
2853 9511 2.225491 TGAATGAAACTAGCAACGTGCC 59.775 45.455 6.39 0.00 46.52 5.01
2854 9512 2.185004 ATGAAACTAGCAACGTGCCT 57.815 45.000 6.39 0.48 46.52 4.75
2855 9513 1.508632 TGAAACTAGCAACGTGCCTC 58.491 50.000 6.39 0.00 46.52 4.70
2856 9514 0.438830 GAAACTAGCAACGTGCCTCG 59.561 55.000 6.39 0.00 46.52 4.63
2857 9515 0.949105 AAACTAGCAACGTGCCTCGG 60.949 55.000 6.39 0.00 46.52 4.63
2858 9516 3.188786 CTAGCAACGTGCCTCGGC 61.189 66.667 0.00 0.00 46.52 5.54
2859 9517 3.932580 CTAGCAACGTGCCTCGGCA 62.933 63.158 6.52 6.52 46.52 5.69
2868 9526 3.430862 GCCTCGGCATTTGTCGCA 61.431 61.111 2.41 0.00 43.77 5.10
2869 9527 2.480555 CCTCGGCATTTGTCGCAC 59.519 61.111 0.00 0.00 43.77 5.34
2870 9528 2.480555 CTCGGCATTTGTCGCACC 59.519 61.111 0.00 0.00 43.77 5.01
2871 9529 2.031919 TCGGCATTTGTCGCACCT 59.968 55.556 0.00 0.00 43.77 4.00
2872 9530 0.739462 CTCGGCATTTGTCGCACCTA 60.739 55.000 0.00 0.00 43.77 3.08
2873 9531 0.739462 TCGGCATTTGTCGCACCTAG 60.739 55.000 0.00 0.00 43.77 3.02
2874 9532 0.739462 CGGCATTTGTCGCACCTAGA 60.739 55.000 0.00 0.00 35.94 2.43
2875 9533 1.668419 GGCATTTGTCGCACCTAGAT 58.332 50.000 0.00 0.00 0.00 1.98
2936 9594 7.340122 CCATCGATATGGTGTCTCTATACAT 57.660 40.000 0.00 0.00 46.68 2.29
3071 9737 3.130869 GCATCCTGCATGTGGATAAACAA 59.869 43.478 17.78 0.00 44.26 2.83
3143 9810 0.724785 GGCGCGTTCTACAAAGCAAC 60.725 55.000 8.43 0.00 36.86 4.17
3175 9842 6.018751 GCGATGATGCTGTTACAATAAGAAGA 60.019 38.462 0.00 0.00 0.00 2.87
3245 9912 2.286595 CGGTCAGTACATGCATGCATTC 60.287 50.000 30.32 21.44 33.90 2.67
3347 10058 9.614792 ACTTCTTTGTAGACTACATTTCTTGTT 57.385 29.630 15.93 0.00 39.87 2.83
3366 10077 3.266772 TGTTTAGGAAGCTGGACATCCAT 59.733 43.478 0.00 0.00 46.46 3.41
3379 10090 4.070716 GGACATCCATGATCATCCTCAAC 58.929 47.826 4.86 0.00 35.64 3.18
3426 10137 1.640210 AACACGCGACACTGCAACAA 61.640 50.000 15.93 0.00 34.15 2.83
3460 10171 2.789893 GCGAAAATACAGGCTCTCGTAG 59.210 50.000 0.00 0.00 0.00 3.51
3492 10735 6.148811 GCACACCTTAGATAACTTACTTGCAA 59.851 38.462 0.00 0.00 0.00 4.08
3494 10737 7.602644 CACACCTTAGATAACTTACTTGCAAGA 59.397 37.037 32.50 13.49 0.00 3.02
3507 10750 2.988010 TGCAAGAAGATAGGTCGCAT 57.012 45.000 0.00 0.00 0.00 4.73
3516 10759 7.664082 AGAAGATAGGTCGCATGAAATATTG 57.336 36.000 0.00 0.00 0.00 1.90
3521 10764 9.725019 AGATAGGTCGCATGAAATATTGAATTA 57.275 29.630 0.00 0.00 0.00 1.40
3700 10959 0.588252 GAAACACATGCACGCAGTCT 59.412 50.000 0.00 0.00 41.61 3.24
3708 10968 0.249826 TGCACGCAGTCTCATCAACA 60.250 50.000 0.00 0.00 41.61 3.33
3749 11168 1.616374 TGCACTCACAGATCACGGTAA 59.384 47.619 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.828520 ACTATGCCTATGTCGATGGAGG 59.171 50.000 5.35 5.35 0.00 4.30
1 2 3.256879 ACACTATGCCTATGTCGATGGAG 59.743 47.826 0.00 0.00 0.00 3.86
2 3 3.230976 ACACTATGCCTATGTCGATGGA 58.769 45.455 0.00 0.00 0.00 3.41
4 5 3.742882 CCAACACTATGCCTATGTCGATG 59.257 47.826 0.00 0.00 0.00 3.84
5 6 3.388024 ACCAACACTATGCCTATGTCGAT 59.612 43.478 0.00 0.00 0.00 3.59
6 7 2.764010 ACCAACACTATGCCTATGTCGA 59.236 45.455 0.00 0.00 0.00 4.20
7 8 3.123804 GACCAACACTATGCCTATGTCG 58.876 50.000 0.00 0.00 0.00 4.35
9 10 6.211584 CCTATAGACCAACACTATGCCTATGT 59.788 42.308 0.00 0.00 33.43 2.29
11 12 5.721960 CCCTATAGACCAACACTATGCCTAT 59.278 44.000 0.00 0.00 33.43 2.57
13 14 3.904339 CCCTATAGACCAACACTATGCCT 59.096 47.826 0.00 0.00 33.43 4.75
15 16 3.325135 AGCCCTATAGACCAACACTATGC 59.675 47.826 0.00 0.00 33.43 3.14
16 17 4.835615 AGAGCCCTATAGACCAACACTATG 59.164 45.833 0.00 0.00 33.43 2.23
18 19 4.537945 AGAGCCCTATAGACCAACACTA 57.462 45.455 0.00 0.00 0.00 2.74
19 20 3.406512 AGAGCCCTATAGACCAACACT 57.593 47.619 0.00 0.00 0.00 3.55
20 21 4.038162 CAGTAGAGCCCTATAGACCAACAC 59.962 50.000 0.00 0.00 0.00 3.32
22 23 4.216708 ACAGTAGAGCCCTATAGACCAAC 58.783 47.826 0.00 0.00 0.00 3.77
24 25 4.215908 CAACAGTAGAGCCCTATAGACCA 58.784 47.826 0.00 0.00 0.00 4.02
26 27 3.006003 GGCAACAGTAGAGCCCTATAGAC 59.994 52.174 0.00 0.00 42.58 2.59
27 28 3.231818 GGCAACAGTAGAGCCCTATAGA 58.768 50.000 0.00 0.00 42.58 1.98
32 33 0.978146 ATCGGCAACAGTAGAGCCCT 60.978 55.000 6.12 0.00 45.56 5.19
34 35 1.398390 CAAATCGGCAACAGTAGAGCC 59.602 52.381 0.00 0.00 44.89 4.70
35 36 2.076863 ACAAATCGGCAACAGTAGAGC 58.923 47.619 0.00 0.00 0.00 4.09
37 38 2.333926 CGACAAATCGGCAACAGTAGA 58.666 47.619 0.00 0.00 44.99 2.59
38 39 2.787723 CGACAAATCGGCAACAGTAG 57.212 50.000 0.00 0.00 44.99 2.57
72 73 5.047377 GCCCAATATGAAGGTCTGACAAAAA 60.047 40.000 10.38 0.00 0.00 1.94
73 74 4.462483 GCCCAATATGAAGGTCTGACAAAA 59.538 41.667 10.38 0.00 0.00 2.44
74 75 4.016444 GCCCAATATGAAGGTCTGACAAA 58.984 43.478 10.38 0.00 0.00 2.83
76 77 2.092429 GGCCCAATATGAAGGTCTGACA 60.092 50.000 10.38 0.00 0.00 3.58
77 78 2.576615 GGCCCAATATGAAGGTCTGAC 58.423 52.381 0.00 0.00 0.00 3.51
78 79 1.140852 CGGCCCAATATGAAGGTCTGA 59.859 52.381 0.00 0.00 0.00 3.27
79 80 1.134098 ACGGCCCAATATGAAGGTCTG 60.134 52.381 0.00 0.00 0.00 3.51
80 81 1.134098 CACGGCCCAATATGAAGGTCT 60.134 52.381 0.00 0.00 0.00 3.85
81 82 1.308998 CACGGCCCAATATGAAGGTC 58.691 55.000 0.00 0.00 0.00 3.85
82 83 0.623723 ACACGGCCCAATATGAAGGT 59.376 50.000 0.00 0.00 0.00 3.50
83 84 1.024271 CACACGGCCCAATATGAAGG 58.976 55.000 0.00 0.00 0.00 3.46
84 85 0.381801 GCACACGGCCCAATATGAAG 59.618 55.000 0.00 0.00 36.11 3.02
85 86 0.322906 TGCACACGGCCCAATATGAA 60.323 50.000 0.00 0.00 43.89 2.57
87 88 0.311790 GATGCACACGGCCCAATATG 59.688 55.000 0.00 0.00 43.89 1.78
88 89 0.823356 GGATGCACACGGCCCAATAT 60.823 55.000 0.00 0.00 43.89 1.28
92 93 1.920734 ATTAGGATGCACACGGCCCA 61.921 55.000 0.00 0.00 43.89 5.36
93 94 0.751643 AATTAGGATGCACACGGCCC 60.752 55.000 0.00 0.00 43.89 5.80
94 95 1.961793 TAATTAGGATGCACACGGCC 58.038 50.000 0.00 0.00 43.89 6.13
95 96 3.542712 CATAATTAGGATGCACACGGC 57.457 47.619 0.00 0.00 45.13 5.68
103 104 3.005554 CGGCCTCTGCATAATTAGGATG 58.994 50.000 0.00 0.00 40.13 3.51
104 105 2.026822 CCGGCCTCTGCATAATTAGGAT 60.027 50.000 0.00 0.00 40.13 3.24
106 107 1.611673 CCCGGCCTCTGCATAATTAGG 60.612 57.143 0.00 0.00 40.13 2.69
107 108 1.072331 ACCCGGCCTCTGCATAATTAG 59.928 52.381 0.00 0.00 40.13 1.73
108 109 1.136828 ACCCGGCCTCTGCATAATTA 58.863 50.000 0.00 0.00 40.13 1.40
109 110 0.466189 CACCCGGCCTCTGCATAATT 60.466 55.000 0.00 0.00 40.13 1.40
110 111 1.149174 CACCCGGCCTCTGCATAAT 59.851 57.895 0.00 0.00 40.13 1.28
111 112 1.847798 AACACCCGGCCTCTGCATAA 61.848 55.000 0.00 0.00 40.13 1.90
114 115 2.925706 TAACACCCGGCCTCTGCA 60.926 61.111 0.00 0.00 40.13 4.41
115 116 2.436115 GTAACACCCGGCCTCTGC 60.436 66.667 0.00 0.00 0.00 4.26
117 118 0.617820 ATGAGTAACACCCGGCCTCT 60.618 55.000 0.00 0.00 0.00 3.69
118 119 1.117150 TATGAGTAACACCCGGCCTC 58.883 55.000 0.00 0.00 0.00 4.70
119 120 1.575419 TTATGAGTAACACCCGGCCT 58.425 50.000 0.00 0.00 0.00 5.19
121 122 1.602377 GCATTATGAGTAACACCCGGC 59.398 52.381 0.00 0.00 0.00 6.13
122 123 3.194005 AGCATTATGAGTAACACCCGG 57.806 47.619 0.00 0.00 0.00 5.73
123 124 4.394920 ACAAAGCATTATGAGTAACACCCG 59.605 41.667 0.00 0.00 0.00 5.28
124 125 5.897377 ACAAAGCATTATGAGTAACACCC 57.103 39.130 0.00 0.00 0.00 4.61
125 126 7.518370 CGGATACAAAGCATTATGAGTAACACC 60.518 40.741 0.00 0.00 0.00 4.16
126 127 7.345192 CGGATACAAAGCATTATGAGTAACAC 58.655 38.462 0.00 0.00 0.00 3.32
127 128 6.018262 GCGGATACAAAGCATTATGAGTAACA 60.018 38.462 0.00 0.00 0.00 2.41
128 129 6.202954 AGCGGATACAAAGCATTATGAGTAAC 59.797 38.462 0.00 0.00 0.00 2.50
129 130 6.288294 AGCGGATACAAAGCATTATGAGTAA 58.712 36.000 0.00 0.00 0.00 2.24
130 131 5.853936 AGCGGATACAAAGCATTATGAGTA 58.146 37.500 0.00 0.00 0.00 2.59
131 132 4.708177 AGCGGATACAAAGCATTATGAGT 58.292 39.130 0.00 0.00 0.00 3.41
132 133 5.237127 TCAAGCGGATACAAAGCATTATGAG 59.763 40.000 0.00 0.00 0.00 2.90
133 134 5.122519 TCAAGCGGATACAAAGCATTATGA 58.877 37.500 0.00 0.00 0.00 2.15
134 135 5.422666 TCAAGCGGATACAAAGCATTATG 57.577 39.130 0.00 0.00 0.00 1.90
135 136 5.563475 GCATCAAGCGGATACAAAGCATTAT 60.563 40.000 0.00 0.00 33.95 1.28
136 137 4.261155 GCATCAAGCGGATACAAAGCATTA 60.261 41.667 0.00 0.00 33.95 1.90
137 138 3.489738 GCATCAAGCGGATACAAAGCATT 60.490 43.478 0.00 0.00 33.95 3.56
138 139 2.033801 GCATCAAGCGGATACAAAGCAT 59.966 45.455 0.00 0.00 33.95 3.79
140 141 2.111041 GCATCAAGCGGATACAAAGC 57.889 50.000 0.00 0.00 33.95 3.51
156 157 9.831737 GCGATTTTATTATCTCAAATGTAGCAT 57.168 29.630 0.00 0.00 0.00 3.79
157 158 8.289618 GGCGATTTTATTATCTCAAATGTAGCA 58.710 33.333 0.00 0.00 0.00 3.49
158 159 7.750903 GGGCGATTTTATTATCTCAAATGTAGC 59.249 37.037 0.00 0.00 0.00 3.58
159 160 9.003658 AGGGCGATTTTATTATCTCAAATGTAG 57.996 33.333 0.00 0.00 0.00 2.74
160 161 8.918202 AGGGCGATTTTATTATCTCAAATGTA 57.082 30.769 0.00 0.00 0.00 2.29
165 166 8.717821 CGATAAAGGGCGATTTTATTATCTCAA 58.282 33.333 0.00 0.00 32.42 3.02
166 167 7.333423 CCGATAAAGGGCGATTTTATTATCTCA 59.667 37.037 0.00 0.00 32.42 3.27
167 168 7.548075 TCCGATAAAGGGCGATTTTATTATCTC 59.452 37.037 0.00 0.00 32.42 2.75
168 169 7.391620 TCCGATAAAGGGCGATTTTATTATCT 58.608 34.615 0.00 0.00 32.42 1.98
169 170 7.605410 TCCGATAAAGGGCGATTTTATTATC 57.395 36.000 0.00 0.00 32.42 1.75
170 171 7.989416 TTCCGATAAAGGGCGATTTTATTAT 57.011 32.000 0.00 0.00 32.42 1.28
171 172 7.804843 TTTCCGATAAAGGGCGATTTTATTA 57.195 32.000 0.00 0.00 32.42 0.98
174 175 6.512342 TTTTTCCGATAAAGGGCGATTTTA 57.488 33.333 0.00 0.00 0.00 1.52
175 176 5.394224 TTTTTCCGATAAAGGGCGATTTT 57.606 34.783 0.00 0.00 0.00 1.82
197 198 1.203100 AGCCTGGCCATCAGTCTTTTT 60.203 47.619 16.57 0.00 41.83 1.94
198 199 0.407139 AGCCTGGCCATCAGTCTTTT 59.593 50.000 16.57 0.00 41.83 2.27
199 200 1.211457 CTAGCCTGGCCATCAGTCTTT 59.789 52.381 16.57 0.00 41.83 2.52
200 201 0.835941 CTAGCCTGGCCATCAGTCTT 59.164 55.000 16.57 0.00 41.83 3.01
201 202 1.053264 CCTAGCCTGGCCATCAGTCT 61.053 60.000 16.57 1.55 41.83 3.24
202 203 1.050988 TCCTAGCCTGGCCATCAGTC 61.051 60.000 16.57 0.00 41.83 3.51
203 204 0.401105 ATCCTAGCCTGGCCATCAGT 60.401 55.000 16.57 0.00 41.83 3.41
204 205 0.769873 AATCCTAGCCTGGCCATCAG 59.230 55.000 16.57 7.60 43.00 2.90
213 2866 2.107204 CCATAGCACCAAATCCTAGCCT 59.893 50.000 0.00 0.00 0.00 4.58
248 2901 3.950397 TCAATGCCTTATTTCTCGTGGT 58.050 40.909 0.00 0.00 0.00 4.16
249 2902 5.991606 TCTATCAATGCCTTATTTCTCGTGG 59.008 40.000 0.00 0.00 0.00 4.94
250 2903 6.146837 CCTCTATCAATGCCTTATTTCTCGTG 59.853 42.308 0.00 0.00 0.00 4.35
251 2904 6.226787 CCTCTATCAATGCCTTATTTCTCGT 58.773 40.000 0.00 0.00 0.00 4.18
252 2905 5.641209 CCCTCTATCAATGCCTTATTTCTCG 59.359 44.000 0.00 0.00 0.00 4.04
253 2906 6.652900 GTCCCTCTATCAATGCCTTATTTCTC 59.347 42.308 0.00 0.00 0.00 2.87
254 2907 6.101734 TGTCCCTCTATCAATGCCTTATTTCT 59.898 38.462 0.00 0.00 0.00 2.52
255 2908 6.299141 TGTCCCTCTATCAATGCCTTATTTC 58.701 40.000 0.00 0.00 0.00 2.17
256 2909 6.266131 TGTCCCTCTATCAATGCCTTATTT 57.734 37.500 0.00 0.00 0.00 1.40
258 2911 5.912149 TTGTCCCTCTATCAATGCCTTAT 57.088 39.130 0.00 0.00 0.00 1.73
259 2912 5.912149 ATTGTCCCTCTATCAATGCCTTA 57.088 39.130 0.00 0.00 31.77 2.69
260 2913 4.803329 ATTGTCCCTCTATCAATGCCTT 57.197 40.909 0.00 0.00 31.77 4.35
304 6956 8.584157 TGCAAGAAAGACACCAATTTGTATAAT 58.416 29.630 0.00 0.00 0.00 1.28
310 6962 3.492011 GCTGCAAGAAAGACACCAATTTG 59.508 43.478 0.00 0.00 34.07 2.32
329 6981 1.639298 GCTAGTTGCTTCCACGGCTG 61.639 60.000 0.00 0.00 38.95 4.85
342 6994 1.066358 GGTCTTACCGCCTTGCTAGTT 60.066 52.381 0.00 0.00 0.00 2.24
354 7006 2.884207 CGCGCCTTCGGTCTTACC 60.884 66.667 0.00 0.00 35.95 2.85
392 7044 2.783135 CTCAGTACACTTTGCCCACAT 58.217 47.619 0.00 0.00 0.00 3.21
403 7055 0.179161 ATCGACGCAGCTCAGTACAC 60.179 55.000 0.00 0.00 0.00 2.90
442 7094 1.781786 AGCTAGGGATGACGTCATGT 58.218 50.000 34.48 20.24 36.57 3.21
867 7519 9.814899 AAATAAAGACAGAGAGAGATACATGTG 57.185 33.333 9.11 0.00 0.00 3.21
872 7524 6.639279 GCCGAAATAAAGACAGAGAGAGATAC 59.361 42.308 0.00 0.00 0.00 2.24
901 7553 6.189677 ACGAATTCAACAAGTTTGACAGAA 57.810 33.333 6.22 0.90 0.00 3.02
917 7569 2.693267 ACTGAGGCCCTTACGAATTC 57.307 50.000 0.00 0.00 0.00 2.17
985 7637 2.101185 CGTGATCGCTGACTCGCT 59.899 61.111 4.48 0.00 0.00 4.93
1018 7670 0.320771 CGTGCAGGTCACTTTAGGCT 60.321 55.000 0.00 0.00 43.46 4.58
1033 7685 0.528684 GTAGGCAGATCACTCCGTGC 60.529 60.000 0.00 0.00 32.98 5.34
1078 7730 2.203771 GCGTCCCGATCTCCTCCAT 61.204 63.158 0.00 0.00 0.00 3.41
1234 7887 3.392882 CAAATGGGTGTTGCTTTCCTTC 58.607 45.455 0.00 0.00 0.00 3.46
1375 8028 6.605849 CAAAACAGATGACAACGATCAGATT 58.394 36.000 0.00 0.00 30.46 2.40
1377 8030 4.083855 GCAAAACAGATGACAACGATCAGA 60.084 41.667 0.00 0.00 30.46 3.27
1524 8182 2.554032 CGACATCTCAAAGTTGCCCTTT 59.446 45.455 0.00 0.00 44.30 3.11
1630 8288 5.123820 TGAAATCGGATTGAACCATGAAGTC 59.876 40.000 3.59 0.00 0.00 3.01
1680 8338 4.151335 GGTAGTGCATGCGATCAAGATTAG 59.849 45.833 14.09 0.00 0.00 1.73
1681 8339 4.058124 GGTAGTGCATGCGATCAAGATTA 58.942 43.478 14.09 0.00 0.00 1.75
1682 8340 2.874701 GGTAGTGCATGCGATCAAGATT 59.125 45.455 14.09 0.00 0.00 2.40
1737 8395 9.950680 ACAAAGTGAATGTTCATACTAAAAGTG 57.049 29.630 0.00 0.00 39.73 3.16
1949 8607 2.691526 TGGTTATGCGAGATAGTTCCGT 59.308 45.455 0.00 0.00 0.00 4.69
2117 8775 6.770785 TGAAAACTTGGTAAGCTACAGACAAT 59.229 34.615 0.00 0.00 0.00 2.71
2160 8818 1.666700 CTCGGTCGTCTCTTTCTCGAT 59.333 52.381 0.00 0.00 36.08 3.59
2184 8842 2.514592 CCGCTGGGTGATCGCAAT 60.515 61.111 8.82 0.00 36.14 3.56
2252 8910 3.494378 CAGAATGGAGTGCAGCCG 58.506 61.111 0.00 0.00 0.00 5.52
2322 8980 4.560136 TCAGCTTTTTATTGTGCACGAA 57.440 36.364 11.67 7.51 0.00 3.85
2354 9012 5.319043 TGAAGATACCTTTGTTCCTTGGT 57.681 39.130 0.00 0.00 36.66 3.67
2355 9013 7.112779 ACTATGAAGATACCTTTGTTCCTTGG 58.887 38.462 0.00 0.00 31.62 3.61
2596 9254 7.539366 GCATAGATAGAAAAGATAGTCCGTGTC 59.461 40.741 0.00 0.00 0.00 3.67
2619 9277 0.681175 GTTTGCTTGGGTCCTTGCAT 59.319 50.000 7.89 0.00 35.27 3.96
2704 9362 4.944317 CCCTAAGAACTCTTTGATGGGTTC 59.056 45.833 0.00 0.00 37.40 3.62
2705 9363 4.263949 CCCCTAAGAACTCTTTGATGGGTT 60.264 45.833 0.00 0.00 37.40 4.11
2706 9364 3.267031 CCCCTAAGAACTCTTTGATGGGT 59.733 47.826 0.00 0.00 37.40 4.51
2707 9365 3.267031 ACCCCTAAGAACTCTTTGATGGG 59.733 47.826 11.14 11.14 36.77 4.00
2746 9404 6.128553 TGCTTCATCACTTCTTTACGCTAAAG 60.129 38.462 9.75 9.75 44.99 1.85
2810 9468 7.364522 TCAAACACATGAATTACTACTCAGC 57.635 36.000 0.00 0.00 0.00 4.26
2811 9469 9.764870 CATTCAAACACATGAATTACTACTCAG 57.235 33.333 0.00 0.00 45.39 3.35
2827 9485 5.171337 CACGTTGCTAGTTTCATTCAAACAC 59.829 40.000 0.00 0.00 46.20 3.32
2828 9486 5.270083 CACGTTGCTAGTTTCATTCAAACA 58.730 37.500 0.00 0.00 46.20 2.83
2829 9487 4.146443 GCACGTTGCTAGTTTCATTCAAAC 59.854 41.667 0.00 0.00 41.58 2.93
2830 9488 4.286910 GCACGTTGCTAGTTTCATTCAAA 58.713 39.130 0.00 0.00 40.96 2.69
2831 9489 3.304391 GGCACGTTGCTAGTTTCATTCAA 60.304 43.478 9.31 0.00 44.28 2.69
2832 9490 2.225491 GGCACGTTGCTAGTTTCATTCA 59.775 45.455 9.31 0.00 44.28 2.57
2833 9491 2.484264 AGGCACGTTGCTAGTTTCATTC 59.516 45.455 9.31 0.00 44.28 2.67
2834 9492 2.484264 GAGGCACGTTGCTAGTTTCATT 59.516 45.455 9.31 0.00 44.28 2.57
2835 9493 2.076863 GAGGCACGTTGCTAGTTTCAT 58.923 47.619 9.31 0.00 44.28 2.57
2836 9494 1.508632 GAGGCACGTTGCTAGTTTCA 58.491 50.000 9.31 0.00 44.28 2.69
2837 9495 0.438830 CGAGGCACGTTGCTAGTTTC 59.561 55.000 9.31 1.70 44.28 2.78
2838 9496 0.949105 CCGAGGCACGTTGCTAGTTT 60.949 55.000 3.22 0.00 44.28 2.66
2839 9497 1.374252 CCGAGGCACGTTGCTAGTT 60.374 57.895 3.22 0.00 44.28 2.24
2840 9498 2.261671 CCGAGGCACGTTGCTAGT 59.738 61.111 3.22 0.00 44.28 2.57
2841 9499 3.188786 GCCGAGGCACGTTGCTAG 61.189 66.667 9.58 0.00 44.28 3.42
2851 9509 3.430862 TGCGACAAATGCCGAGGC 61.431 61.111 7.26 7.26 42.35 4.70
2852 9510 2.480555 GTGCGACAAATGCCGAGG 59.519 61.111 0.00 0.00 0.00 4.63
2853 9511 0.739462 TAGGTGCGACAAATGCCGAG 60.739 55.000 0.00 0.00 0.00 4.63
2854 9512 0.739462 CTAGGTGCGACAAATGCCGA 60.739 55.000 0.00 0.00 0.00 5.54
2855 9513 0.739462 TCTAGGTGCGACAAATGCCG 60.739 55.000 0.00 0.00 0.00 5.69
2856 9514 1.668419 ATCTAGGTGCGACAAATGCC 58.332 50.000 0.00 0.00 0.00 4.40
2857 9515 2.792542 GCAATCTAGGTGCGACAAATGC 60.793 50.000 3.94 0.00 31.20 3.56
2858 9516 2.679837 AGCAATCTAGGTGCGACAAATG 59.320 45.455 12.00 0.00 46.86 2.32
2859 9517 2.991250 AGCAATCTAGGTGCGACAAAT 58.009 42.857 12.00 0.00 46.86 2.32
2860 9518 2.472695 AGCAATCTAGGTGCGACAAA 57.527 45.000 12.00 0.00 46.86 2.83
2861 9519 2.496070 AGTAGCAATCTAGGTGCGACAA 59.504 45.455 23.83 8.15 46.35 3.18
2862 9520 2.100197 AGTAGCAATCTAGGTGCGACA 58.900 47.619 23.83 9.68 46.35 4.35
2863 9521 2.873133 AGTAGCAATCTAGGTGCGAC 57.127 50.000 18.29 18.29 46.86 5.19
2864 9522 2.293677 GCTAGTAGCAATCTAGGTGCGA 59.706 50.000 17.47 6.01 46.86 5.10
2865 9523 2.667137 GCTAGTAGCAATCTAGGTGCG 58.333 52.381 17.47 1.82 46.86 5.34
3071 9737 9.685276 TCAAAGATGTATCAACATGTATTTCCT 57.315 29.630 0.00 0.00 46.49 3.36
3145 9812 2.794350 TGTAACAGCATCATCGCATACG 59.206 45.455 0.00 0.00 42.01 3.06
3175 9842 3.072915 TGAAAGTATGATCATCCGGGCAT 59.927 43.478 12.53 0.76 0.00 4.40
3245 9912 1.766494 TTTGATGGGCCAGCATGTAG 58.234 50.000 27.05 0.00 27.29 2.74
3379 10090 1.074951 GGTGGTCCCAAGTTCCTGG 59.925 63.158 0.00 0.00 36.10 4.45
3390 10101 1.202557 TGTTACTTCACGTGGTGGTCC 60.203 52.381 17.00 7.25 33.87 4.46
3401 10112 1.483316 CAGTGTCGCGTGTTACTTCA 58.517 50.000 5.77 0.00 0.00 3.02
3426 10137 2.853731 TTTTCGCACGGACAATTGTT 57.146 40.000 13.36 0.00 0.00 2.83
3434 10145 0.036765 AGCCTGTATTTTCGCACGGA 60.037 50.000 0.00 0.00 0.00 4.69
3460 10171 5.589192 AGTTATCTAAGGTGTGCGTGTATC 58.411 41.667 0.00 0.00 0.00 2.24
3492 10735 7.445121 TCAATATTTCATGCGACCTATCTTCT 58.555 34.615 0.00 0.00 0.00 2.85
3494 10737 8.627208 ATTCAATATTTCATGCGACCTATCTT 57.373 30.769 0.00 0.00 0.00 2.40
3516 10759 7.970061 TGCATGTGTCTGCTTTCTTTATAATTC 59.030 33.333 0.00 0.00 42.75 2.17
3521 10764 4.378770 CGTGCATGTGTCTGCTTTCTTTAT 60.379 41.667 0.00 0.00 42.75 1.40
3620 10865 0.394488 TTGGTGGGTGCTTTGTCGAA 60.394 50.000 0.00 0.00 0.00 3.71
3650 10895 8.623903 GGATTGCATCATACTATTTCTTGTGAA 58.376 33.333 0.00 0.00 0.00 3.18
3667 10912 2.557924 TGTGTTTCCAGTGGATTGCATC 59.442 45.455 14.00 7.86 0.00 3.91
3700 10959 3.056588 TGCAGCTGTGTATGTTGATGA 57.943 42.857 16.64 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.