Multiple sequence alignment - TraesCS3D01G117800

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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 TraesCS3D01G117800 chr3D 100.000 3494 0 0 1 3494 71500473 71496980 0.000000e+00 6453.0
1 TraesCS3D01G117800 chr3D 90.566 159 15 0 794 952 346060172 346060330 9.830000e-51 211.0
2 TraesCS3D01G117800 chr3B 91.436 1518 81 24 1517 3015 117556121 117554634 0.000000e+00 2037.0
3 TraesCS3D01G117800 chr3B 93.171 1318 46 22 225 1519 117557462 117556166 0.000000e+00 1895.0
4 TraesCS3D01G117800 chr3B 91.284 218 15 4 1 215 117563457 117563241 9.480000e-76 294.0
5 TraesCS3D01G117800 chr3B 90.566 159 15 0 794 952 445202332 445202490 9.830000e-51 211.0
6 TraesCS3D01G117800 chr3B 88.971 136 9 6 3359 3494 117554528 117554399 2.790000e-36 163.0
7 TraesCS3D01G117800 chr3A 94.870 1267 45 11 1517 2768 83727427 83726166 0.000000e+00 1962.0
8 TraesCS3D01G117800 chr3A 93.360 1265 46 16 273 1519 83728716 83727472 0.000000e+00 1836.0
9 TraesCS3D01G117800 chr3A 89.506 162 17 0 794 955 457664602 457664441 4.570000e-49 206.0
10 TraesCS3D01G117800 chr3A 84.492 187 17 9 3314 3494 83725979 83725799 1.290000e-39 174.0
11 TraesCS3D01G117800 chr3A 84.472 161 12 6 2831 2988 83726142 83725992 2.810000e-31 147.0
12 TraesCS3D01G117800 chr3A 89.320 103 7 4 3000 3100 661433395 661433295 3.660000e-25 126.0
13 TraesCS3D01G117800 chr5A 94.444 90 5 0 3405 3494 691735420 691735509 4.700000e-29 139.0
14 TraesCS3D01G117800 chr2B 95.402 87 3 1 3409 3494 65318004 65317918 1.690000e-28 137.0
15 TraesCS3D01G117800 chr2B 88.119 101 9 3 3003 3102 674741184 674741282 2.200000e-22 117.0
16 TraesCS3D01G117800 chr1D 93.478 92 6 0 3403 3494 478271230 478271321 1.690000e-28 137.0
17 TraesCS3D01G117800 chr6A 93.617 94 1 4 3402 3494 22187288 22187377 6.080000e-28 135.0
18 TraesCS3D01G117800 chr4B 93.478 92 5 1 3404 3494 656304556 656304647 6.080000e-28 135.0
19 TraesCS3D01G117800 chr4B 89.000 100 9 2 3002 3100 564881237 564881335 4.740000e-24 122.0
20 TraesCS3D01G117800 chr4B 88.350 103 8 4 3000 3100 544209998 544209898 1.700000e-23 121.0
21 TraesCS3D01G117800 chr2D 98.684 76 1 0 3419 3494 486252336 486252261 6.080000e-28 135.0
22 TraesCS3D01G117800 chr1A 94.318 88 5 0 3407 3494 256826491 256826578 6.080000e-28 135.0
23 TraesCS3D01G117800 chr1A 89.796 98 9 1 3004 3100 79757142 79757239 1.320000e-24 124.0
24 TraesCS3D01G117800 chr6B 90.909 99 6 3 3004 3100 658580279 658580182 2.830000e-26 130.0
25 TraesCS3D01G117800 chr6B 89.320 103 9 2 2999 3100 107822439 107822338 1.020000e-25 128.0
26 TraesCS3D01G117800 chr6B 90.722 97 7 2 3005 3100 282993075 282992980 1.020000e-25 128.0
27 TraesCS3D01G117800 chr1B 89.796 98 9 1 3004 3100 592500656 592500753 1.320000e-24 124.0
28 TraesCS3D01G117800 chr7D 89.474 57 5 1 91 147 424221813 424221868 1.740000e-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 TraesCS3D01G117800 chr3D 71496980 71500473 3493 True 6453.00 6453 100.000000 1 3494 1 chr3D.!!$R1 3493
1 TraesCS3D01G117800 chr3B 117554399 117557462 3063 True 1365.00 2037 91.192667 225 3494 3 chr3B.!!$R2 3269
2 TraesCS3D01G117800 chr3A 83725799 83728716 2917 True 1029.75 1962 89.298500 273 3494 4 chr3A.!!$R3 3221

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
43 44 0.415429 AGGAGAGAGAAAGGCTGGGA 59.585 55.000 0.0 0.0 0.00 4.37 F
44 45 0.539518 GGAGAGAGAAAGGCTGGGAC 59.460 60.000 0.0 0.0 0.00 4.46 F
144 145 0.883833 CTTACCAAGCTGGCCACTTG 59.116 55.000 27.6 27.6 42.67 3.16 F
1029 1049 1.001764 CCTTCTGATGTGGCTGGCA 60.002 57.895 0.0 0.0 0.00 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1208 1228 0.390866 AGCTTCTGGTCGCACATCTG 60.391 55.0 0.0 0.0 0.0 2.90 R
1212 1232 0.679505 AGTTAGCTTCTGGTCGCACA 59.320 50.0 0.0 0.0 0.0 4.57 R
1213 1233 1.071605 CAGTTAGCTTCTGGTCGCAC 58.928 55.0 0.0 0.0 0.0 5.34 R
2801 2906 0.030638 CCACCGTCCACTGCAAAAAG 59.969 55.0 0.0 0.0 0.0 2.27 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
24 25 6.479972 TGTAGTGACTCTTGAAAGGAAAGA 57.520 37.500 0.00 0.00 32.80 2.52
31 32 5.736951 CTCTTGAAAGGAAAGAGGAGAGA 57.263 43.478 5.46 0.00 44.57 3.10
32 33 5.723295 CTCTTGAAAGGAAAGAGGAGAGAG 58.277 45.833 5.46 0.00 44.57 3.20
33 34 5.398236 TCTTGAAAGGAAAGAGGAGAGAGA 58.602 41.667 0.00 0.00 0.00 3.10
34 35 5.841237 TCTTGAAAGGAAAGAGGAGAGAGAA 59.159 40.000 0.00 0.00 0.00 2.87
35 36 6.327626 TCTTGAAAGGAAAGAGGAGAGAGAAA 59.672 38.462 0.00 0.00 0.00 2.52
36 37 6.107901 TGAAAGGAAAGAGGAGAGAGAAAG 57.892 41.667 0.00 0.00 0.00 2.62
37 38 5.012561 TGAAAGGAAAGAGGAGAGAGAAAGG 59.987 44.000 0.00 0.00 0.00 3.11
38 39 2.837591 AGGAAAGAGGAGAGAGAAAGGC 59.162 50.000 0.00 0.00 0.00 4.35
39 40 2.837591 GGAAAGAGGAGAGAGAAAGGCT 59.162 50.000 0.00 0.00 0.00 4.58
40 41 3.369366 GGAAAGAGGAGAGAGAAAGGCTG 60.369 52.174 0.00 0.00 0.00 4.85
41 42 1.864669 AGAGGAGAGAGAAAGGCTGG 58.135 55.000 0.00 0.00 0.00 4.85
42 43 0.829990 GAGGAGAGAGAAAGGCTGGG 59.170 60.000 0.00 0.00 0.00 4.45
43 44 0.415429 AGGAGAGAGAAAGGCTGGGA 59.585 55.000 0.00 0.00 0.00 4.37
44 45 0.539518 GGAGAGAGAAAGGCTGGGAC 59.460 60.000 0.00 0.00 0.00 4.46
45 46 1.270907 GAGAGAGAAAGGCTGGGACA 58.729 55.000 0.00 0.00 0.00 4.02
46 47 1.836802 GAGAGAGAAAGGCTGGGACAT 59.163 52.381 0.00 0.00 38.20 3.06
47 48 3.034635 GAGAGAGAAAGGCTGGGACATA 58.965 50.000 0.00 0.00 38.20 2.29
48 49 3.452627 GAGAGAGAAAGGCTGGGACATAA 59.547 47.826 0.00 0.00 38.20 1.90
49 50 3.846588 AGAGAGAAAGGCTGGGACATAAA 59.153 43.478 0.00 0.00 38.20 1.40
50 51 4.476479 AGAGAGAAAGGCTGGGACATAAAT 59.524 41.667 0.00 0.00 38.20 1.40
51 52 4.530875 AGAGAAAGGCTGGGACATAAATG 58.469 43.478 0.00 0.00 38.20 2.32
52 53 4.228210 AGAGAAAGGCTGGGACATAAATGA 59.772 41.667 0.00 0.00 38.20 2.57
53 54 4.934356 AGAAAGGCTGGGACATAAATGAA 58.066 39.130 0.00 0.00 38.20 2.57
54 55 5.522641 AGAAAGGCTGGGACATAAATGAAT 58.477 37.500 0.00 0.00 38.20 2.57
55 56 6.672593 AGAAAGGCTGGGACATAAATGAATA 58.327 36.000 0.00 0.00 38.20 1.75
56 57 7.300658 AGAAAGGCTGGGACATAAATGAATAT 58.699 34.615 0.00 0.00 38.20 1.28
57 58 8.448008 AGAAAGGCTGGGACATAAATGAATATA 58.552 33.333 0.00 0.00 38.20 0.86
58 59 8.641498 AAAGGCTGGGACATAAATGAATATAG 57.359 34.615 0.00 0.00 38.20 1.31
59 60 7.335127 AGGCTGGGACATAAATGAATATAGT 57.665 36.000 0.00 0.00 38.20 2.12
60 61 7.759607 AGGCTGGGACATAAATGAATATAGTT 58.240 34.615 0.00 0.00 38.20 2.24
61 62 8.890472 AGGCTGGGACATAAATGAATATAGTTA 58.110 33.333 0.00 0.00 38.20 2.24
62 63 9.515226 GGCTGGGACATAAATGAATATAGTTAA 57.485 33.333 0.00 0.00 38.20 2.01
143 144 3.346426 CTTACCAAGCTGGCCACTT 57.654 52.632 0.00 8.14 42.67 3.16
144 145 0.883833 CTTACCAAGCTGGCCACTTG 59.116 55.000 27.60 27.60 42.67 3.16
147 148 4.819783 CAAGCTGGCCACTTGGTA 57.180 55.556 27.19 0.00 40.68 3.25
148 149 3.034924 CAAGCTGGCCACTTGGTAA 57.965 52.632 27.19 0.00 40.68 2.85
149 150 1.327303 CAAGCTGGCCACTTGGTAAA 58.673 50.000 27.19 0.00 40.68 2.01
150 151 1.895131 CAAGCTGGCCACTTGGTAAAT 59.105 47.619 27.19 4.60 40.68 1.40
151 152 1.549203 AGCTGGCCACTTGGTAAATG 58.451 50.000 0.00 0.00 37.57 2.32
152 153 1.075374 AGCTGGCCACTTGGTAAATGA 59.925 47.619 0.00 0.00 37.57 2.57
153 154 1.892474 GCTGGCCACTTGGTAAATGAA 59.108 47.619 0.00 0.00 37.57 2.57
154 155 2.497273 GCTGGCCACTTGGTAAATGAAT 59.503 45.455 0.00 0.00 37.57 2.57
155 156 3.699038 GCTGGCCACTTGGTAAATGAATA 59.301 43.478 0.00 0.00 37.57 1.75
156 157 4.342092 GCTGGCCACTTGGTAAATGAATAT 59.658 41.667 0.00 0.00 37.57 1.28
157 158 5.534654 GCTGGCCACTTGGTAAATGAATATA 59.465 40.000 0.00 0.00 37.57 0.86
158 159 6.294176 GCTGGCCACTTGGTAAATGAATATAG 60.294 42.308 0.00 0.00 37.57 1.31
159 160 6.668645 TGGCCACTTGGTAAATGAATATAGT 58.331 36.000 0.00 0.00 37.57 2.12
160 161 7.122715 TGGCCACTTGGTAAATGAATATAGTT 58.877 34.615 0.00 0.00 37.57 2.24
161 162 8.275758 TGGCCACTTGGTAAATGAATATAGTTA 58.724 33.333 0.00 0.00 37.57 2.24
162 163 9.297037 GGCCACTTGGTAAATGAATATAGTTAT 57.703 33.333 0.00 0.00 37.57 1.89
181 182 9.930693 ATAGTTATCTTAGTTACCATTAGCTGC 57.069 33.333 0.00 0.00 0.00 5.25
182 183 7.792032 AGTTATCTTAGTTACCATTAGCTGCA 58.208 34.615 1.02 0.00 0.00 4.41
183 184 7.928706 AGTTATCTTAGTTACCATTAGCTGCAG 59.071 37.037 10.11 10.11 0.00 4.41
184 185 4.442706 TCTTAGTTACCATTAGCTGCAGC 58.557 43.478 31.53 31.53 42.49 5.25
185 186 2.787473 AGTTACCATTAGCTGCAGCA 57.213 45.000 38.24 21.24 45.16 4.41
186 187 3.071874 AGTTACCATTAGCTGCAGCAA 57.928 42.857 38.24 28.44 45.16 3.91
187 188 3.624777 AGTTACCATTAGCTGCAGCAAT 58.375 40.909 38.24 29.22 45.16 3.56
188 189 4.780815 AGTTACCATTAGCTGCAGCAATA 58.219 39.130 38.24 23.37 45.16 1.90
189 190 4.818546 AGTTACCATTAGCTGCAGCAATAG 59.181 41.667 38.24 27.00 45.16 1.73
190 191 3.565764 ACCATTAGCTGCAGCAATAGA 57.434 42.857 38.24 19.66 45.16 1.98
191 192 3.889815 ACCATTAGCTGCAGCAATAGAA 58.110 40.909 38.24 23.11 45.16 2.10
192 193 4.272489 ACCATTAGCTGCAGCAATAGAAA 58.728 39.130 38.24 21.57 45.16 2.52
193 194 4.706476 ACCATTAGCTGCAGCAATAGAAAA 59.294 37.500 38.24 19.97 45.16 2.29
194 195 5.361857 ACCATTAGCTGCAGCAATAGAAAAT 59.638 36.000 38.24 21.11 45.16 1.82
195 196 5.690409 CCATTAGCTGCAGCAATAGAAAATG 59.310 40.000 38.24 28.16 45.16 2.32
196 197 5.902613 TTAGCTGCAGCAATAGAAAATGT 57.097 34.783 38.24 16.87 45.16 2.71
197 198 4.796038 AGCTGCAGCAATAGAAAATGTT 57.204 36.364 38.24 11.97 45.16 2.71
198 199 5.902613 AGCTGCAGCAATAGAAAATGTTA 57.097 34.783 38.24 0.00 45.16 2.41
199 200 5.644644 AGCTGCAGCAATAGAAAATGTTAC 58.355 37.500 38.24 4.68 45.16 2.50
200 201 5.183713 AGCTGCAGCAATAGAAAATGTTACA 59.816 36.000 38.24 0.00 45.16 2.41
201 202 5.863397 GCTGCAGCAATAGAAAATGTTACAA 59.137 36.000 33.36 0.00 41.59 2.41
202 203 6.183360 GCTGCAGCAATAGAAAATGTTACAAC 60.183 38.462 33.36 0.00 41.59 3.32
203 204 6.155827 TGCAGCAATAGAAAATGTTACAACC 58.844 36.000 0.00 0.00 0.00 3.77
204 205 6.015519 TGCAGCAATAGAAAATGTTACAACCT 60.016 34.615 0.00 0.00 0.00 3.50
205 206 6.308766 GCAGCAATAGAAAATGTTACAACCTG 59.691 38.462 0.00 0.00 0.00 4.00
206 207 6.308766 CAGCAATAGAAAATGTTACAACCTGC 59.691 38.462 0.00 0.00 0.00 4.85
207 208 6.015519 AGCAATAGAAAATGTTACAACCTGCA 60.016 34.615 0.00 0.00 0.00 4.41
208 209 6.089417 GCAATAGAAAATGTTACAACCTGCAC 59.911 38.462 0.00 0.00 0.00 4.57
209 210 7.370383 CAATAGAAAATGTTACAACCTGCACT 58.630 34.615 0.00 0.00 0.00 4.40
210 211 8.511321 CAATAGAAAATGTTACAACCTGCACTA 58.489 33.333 0.00 0.00 0.00 2.74
211 212 8.807948 ATAGAAAATGTTACAACCTGCACTAT 57.192 30.769 0.00 0.00 0.00 2.12
212 213 9.899661 ATAGAAAATGTTACAACCTGCACTATA 57.100 29.630 0.00 0.00 0.00 1.31
213 214 8.630054 AGAAAATGTTACAACCTGCACTATAA 57.370 30.769 0.00 0.00 0.00 0.98
214 215 9.073475 AGAAAATGTTACAACCTGCACTATAAA 57.927 29.630 0.00 0.00 0.00 1.40
215 216 9.685828 GAAAATGTTACAACCTGCACTATAAAA 57.314 29.630 0.00 0.00 0.00 1.52
246 247 3.945346 ACCAACGTGGATGCACTTTATA 58.055 40.909 15.82 0.00 40.96 0.98
248 249 4.947388 ACCAACGTGGATGCACTTTATATT 59.053 37.500 15.82 0.00 40.96 1.28
249 250 5.417580 ACCAACGTGGATGCACTTTATATTT 59.582 36.000 15.82 0.00 40.96 1.40
250 251 6.600032 ACCAACGTGGATGCACTTTATATTTA 59.400 34.615 15.82 0.00 40.96 1.40
251 252 7.284489 ACCAACGTGGATGCACTTTATATTTAT 59.716 33.333 15.82 0.00 40.96 1.40
252 253 8.779303 CCAACGTGGATGCACTTTATATTTATA 58.221 33.333 15.82 0.00 40.96 0.98
285 286 4.656041 CTCAAAATGAAACTCGCATCTCC 58.344 43.478 0.00 0.00 0.00 3.71
298 299 4.779733 TCTCCCTCCCTCCCACGC 62.780 72.222 0.00 0.00 0.00 5.34
307 308 4.082523 CTCCCACGCGTCCACCAT 62.083 66.667 9.86 0.00 0.00 3.55
348 349 1.448985 GTGGCTCCTCGTGCAATTAA 58.551 50.000 0.00 0.00 0.00 1.40
350 351 2.423538 GTGGCTCCTCGTGCAATTAATT 59.576 45.455 0.00 0.00 0.00 1.40
352 353 4.095782 GTGGCTCCTCGTGCAATTAATTAA 59.904 41.667 0.00 0.00 0.00 1.40
353 354 4.095782 TGGCTCCTCGTGCAATTAATTAAC 59.904 41.667 0.00 2.11 0.00 2.01
392 393 2.960170 CCAGCTGCCACTGCTTTC 59.040 61.111 8.66 0.00 36.55 2.62
443 446 4.569180 ATCCCGCGGCCATTCCAG 62.569 66.667 22.85 2.99 34.01 3.86
492 495 1.380380 CCCTCCCCATCAAACAGCC 60.380 63.158 0.00 0.00 0.00 4.85
512 515 1.372499 TCGCGAACTCAACGGGAAG 60.372 57.895 6.20 0.00 46.18 3.46
952 965 1.559682 AGTTCATCAACGCCAGGGTAT 59.440 47.619 0.00 0.00 37.61 2.73
956 969 2.102420 TCATCAACGCCAGGGTATGTAG 59.898 50.000 0.00 0.00 0.00 2.74
957 970 1.563924 TCAACGCCAGGGTATGTAGT 58.436 50.000 0.00 0.00 0.00 2.73
958 971 1.206132 TCAACGCCAGGGTATGTAGTG 59.794 52.381 0.00 0.00 0.00 2.74
959 972 1.066430 CAACGCCAGGGTATGTAGTGT 60.066 52.381 0.00 0.00 0.00 3.55
960 973 2.148446 ACGCCAGGGTATGTAGTGTA 57.852 50.000 0.00 0.00 0.00 2.90
972 985 2.136728 TGTAGTGTACGCAACGCAATT 58.863 42.857 9.48 0.00 41.29 2.32
973 993 2.156117 TGTAGTGTACGCAACGCAATTC 59.844 45.455 9.48 0.00 41.29 2.17
1029 1049 1.001764 CCTTCTGATGTGGCTGGCA 60.002 57.895 0.00 0.00 0.00 4.92
1149 1169 1.279496 CTGGACCCAAGGACATCTCA 58.721 55.000 0.00 0.00 0.00 3.27
1182 1202 2.619074 GCTGAGGTAGGCTTGGTGAATT 60.619 50.000 0.00 0.00 0.00 2.17
1205 1225 3.126000 GCGATTCCTTCTTATGCTATGGC 59.874 47.826 0.00 0.00 39.26 4.40
1206 1226 3.369147 CGATTCCTTCTTATGCTATGGCG 59.631 47.826 0.00 0.00 42.25 5.69
1208 1228 1.160137 CCTTCTTATGCTATGGCGGC 58.840 55.000 0.00 0.00 42.25 6.53
1209 1229 1.543208 CCTTCTTATGCTATGGCGGCA 60.543 52.381 16.34 16.34 44.05 5.69
1210 1230 1.802960 CTTCTTATGCTATGGCGGCAG 59.197 52.381 19.29 5.75 43.15 4.85
1211 1231 1.047801 TCTTATGCTATGGCGGCAGA 58.952 50.000 19.29 12.84 43.15 4.26
1212 1232 1.625315 TCTTATGCTATGGCGGCAGAT 59.375 47.619 19.29 3.67 43.15 2.90
1213 1233 1.736126 CTTATGCTATGGCGGCAGATG 59.264 52.381 19.29 10.87 43.15 2.90
1256 1285 1.949525 GGCATTGTATGAATCAGGCGT 59.050 47.619 0.00 0.00 0.00 5.68
1448 1477 5.046950 AGAGACCAGACAAGTGACCTTAATC 60.047 44.000 0.00 0.00 0.00 1.75
1464 1493 8.028938 TGACCTTAATCGTAAGTAGTTGTTACC 58.971 37.037 0.00 0.00 35.82 2.85
1596 1672 8.903820 CCTTATTTAAGCATAAACTAGCACCTT 58.096 33.333 0.00 0.00 33.98 3.50
1618 1694 5.818136 TGTTGCATATTTAGAAGAGCACC 57.182 39.130 0.00 0.00 0.00 5.01
1624 1700 8.696043 TGCATATTTAGAAGAGCACCAAATAT 57.304 30.769 0.00 0.00 33.96 1.28
1654 1731 2.684001 TTATTGATGGTCGCCTCGTT 57.316 45.000 0.00 0.00 0.00 3.85
1655 1732 2.684001 TATTGATGGTCGCCTCGTTT 57.316 45.000 0.00 0.00 0.00 3.60
1680 1759 4.503741 TTTTGTGCTGCTTAGTGATTCC 57.496 40.909 0.00 0.00 0.00 3.01
1701 1780 3.004734 CCAGGAACATTGACAGTTTGGTC 59.995 47.826 0.00 0.00 38.29 4.02
1745 1824 5.574443 GCTGATTGCACTTTTGTTAATCTCC 59.426 40.000 0.00 0.00 42.31 3.71
1978 2057 4.650972 TTACTTGTTTGATACCCCTGCT 57.349 40.909 0.00 0.00 0.00 4.24
2106 2185 7.818997 ATGTGATGAATACTTCAGAATGCAT 57.181 32.000 0.00 0.00 43.98 3.96
2130 2209 6.827641 TGATTGCACGCTAAAACTACTTTAG 58.172 36.000 0.00 0.80 46.44 1.85
2186 2265 5.013547 TCCTTTGTTTGTCAGGAGAAAACA 58.986 37.500 6.26 6.26 40.90 2.83
2294 2373 1.272490 TCTCGGTAAGCTCCACAACAG 59.728 52.381 0.00 0.00 0.00 3.16
2351 2430 3.801698 TCAATCTATCAAGGCTGACTGC 58.198 45.455 0.00 0.00 41.94 4.40
2497 2578 0.883833 CAACCCAACCAGCTGATCAC 59.116 55.000 17.39 0.00 0.00 3.06
2509 2590 2.891936 GATCACGCGCATGGCTCA 60.892 61.111 5.73 0.00 40.44 4.26
2523 2606 6.038356 CGCATGGCTCATTCTTTTTCTTATT 58.962 36.000 0.00 0.00 0.00 1.40
2524 2607 7.195646 CGCATGGCTCATTCTTTTTCTTATTA 58.804 34.615 0.00 0.00 0.00 0.98
2525 2608 7.864379 CGCATGGCTCATTCTTTTTCTTATTAT 59.136 33.333 0.00 0.00 0.00 1.28
2529 2612 9.407380 TGGCTCATTCTTTTTCTTATTATAGCA 57.593 29.630 0.00 0.00 0.00 3.49
2530 2613 9.670719 GGCTCATTCTTTTTCTTATTATAGCAC 57.329 33.333 0.00 0.00 0.00 4.40
2555 2639 1.807000 CGCCTCTCGAGTAGCTCTGTA 60.807 57.143 21.30 0.00 41.67 2.74
2594 2680 3.896888 TCTTGTTCATCAGCCAATTTGGT 59.103 39.130 16.62 1.39 40.46 3.67
2709 2798 3.000041 TCACCTGTTACATCGTTCATGC 59.000 45.455 0.00 0.00 35.65 4.06
2737 2832 3.265221 AGAATCTCTTGGGTTGCTCATGA 59.735 43.478 0.00 0.00 0.00 3.07
2748 2843 4.641989 GGGTTGCTCATGAAGATATTGTGT 59.358 41.667 0.00 0.00 0.00 3.72
2769 2866 2.582052 TGTGAACCCTGAAACCATGAC 58.418 47.619 0.00 0.00 0.00 3.06
2846 2951 3.064987 GCTGCTGCATCTGCCCTTG 62.065 63.158 11.11 0.00 41.18 3.61
2880 2985 1.730547 GTGTTTGCCGTGCTGCATC 60.731 57.895 5.27 0.00 41.70 3.91
2883 2988 2.334946 TTTGCCGTGCTGCATCCTC 61.335 57.895 5.27 0.00 41.70 3.71
2890 2995 0.103755 GTGCTGCATCCTCTCATCGA 59.896 55.000 5.27 0.00 0.00 3.59
2896 3001 1.342496 GCATCCTCTCATCGATGGTGA 59.658 52.381 24.61 20.06 37.05 4.02
2899 3004 2.027385 TCCTCTCATCGATGGTGAGTG 58.973 52.381 29.43 24.03 42.82 3.51
2902 3007 2.627221 CTCTCATCGATGGTGAGTGGAT 59.373 50.000 26.55 0.00 42.82 3.41
2922 3027 2.112928 TGCTGCAGGCGGAAAAGA 59.887 55.556 17.12 0.00 45.43 2.52
2944 3051 2.437359 ATGCCTCTTCACCGCTGC 60.437 61.111 0.00 0.00 0.00 5.25
2952 3059 3.842925 TTCACCGCTGCCCTGTTCC 62.843 63.158 0.00 0.00 0.00 3.62
3004 3111 2.176273 GCCGTGATCGCTGCAAGAT 61.176 57.895 16.62 4.23 34.07 2.40
3005 3112 0.875908 GCCGTGATCGCTGCAAGATA 60.876 55.000 16.62 0.00 34.07 1.98
3006 3113 0.855349 CCGTGATCGCTGCAAGATAC 59.145 55.000 4.48 3.93 34.07 2.24
3007 3114 1.536922 CCGTGATCGCTGCAAGATACT 60.537 52.381 4.48 0.00 34.07 2.12
3008 3115 1.783711 CGTGATCGCTGCAAGATACTC 59.216 52.381 4.48 0.00 34.07 2.59
3009 3116 2.131183 GTGATCGCTGCAAGATACTCC 58.869 52.381 0.00 0.00 34.07 3.85
3010 3117 2.034878 TGATCGCTGCAAGATACTCCT 58.965 47.619 0.00 0.00 34.07 3.69
3011 3118 2.035193 TGATCGCTGCAAGATACTCCTC 59.965 50.000 0.00 0.00 34.07 3.71
3012 3119 0.747255 TCGCTGCAAGATACTCCTCC 59.253 55.000 0.00 0.00 34.07 4.30
3013 3120 0.596083 CGCTGCAAGATACTCCTCCG 60.596 60.000 0.00 0.00 34.07 4.63
3014 3121 0.461961 GCTGCAAGATACTCCTCCGT 59.538 55.000 0.00 0.00 34.07 4.69
3015 3122 1.134670 GCTGCAAGATACTCCTCCGTT 60.135 52.381 0.00 0.00 34.07 4.44
3016 3123 2.815478 CTGCAAGATACTCCTCCGTTC 58.185 52.381 0.00 0.00 34.07 3.95
3017 3124 2.166459 CTGCAAGATACTCCTCCGTTCA 59.834 50.000 0.00 0.00 34.07 3.18
3018 3125 2.166459 TGCAAGATACTCCTCCGTTCAG 59.834 50.000 0.00 0.00 0.00 3.02
3019 3126 2.427453 GCAAGATACTCCTCCGTTCAGA 59.573 50.000 0.00 0.00 0.00 3.27
3020 3127 3.119101 GCAAGATACTCCTCCGTTCAGAA 60.119 47.826 0.00 0.00 0.00 3.02
3021 3128 4.620803 GCAAGATACTCCTCCGTTCAGAAA 60.621 45.833 0.00 0.00 0.00 2.52
3022 3129 5.665459 CAAGATACTCCTCCGTTCAGAAAT 58.335 41.667 0.00 0.00 0.00 2.17
3023 3130 6.683110 GCAAGATACTCCTCCGTTCAGAAATA 60.683 42.308 0.00 0.00 0.00 1.40
3024 3131 7.437748 CAAGATACTCCTCCGTTCAGAAATAT 58.562 38.462 0.00 0.00 0.00 1.28
3025 3132 7.604657 AGATACTCCTCCGTTCAGAAATATT 57.395 36.000 0.00 0.00 0.00 1.28
3026 3133 8.024145 AGATACTCCTCCGTTCAGAAATATTT 57.976 34.615 0.00 0.00 0.00 1.40
3027 3134 7.928706 AGATACTCCTCCGTTCAGAAATATTTG 59.071 37.037 5.17 0.00 0.00 2.32
3028 3135 5.805728 ACTCCTCCGTTCAGAAATATTTGT 58.194 37.500 5.17 0.00 0.00 2.83
3029 3136 5.875359 ACTCCTCCGTTCAGAAATATTTGTC 59.125 40.000 5.17 0.00 0.00 3.18
3030 3137 5.800296 TCCTCCGTTCAGAAATATTTGTCA 58.200 37.500 5.17 0.00 0.00 3.58
3031 3138 6.414732 TCCTCCGTTCAGAAATATTTGTCAT 58.585 36.000 5.17 0.00 0.00 3.06
3032 3139 6.538742 TCCTCCGTTCAGAAATATTTGTCATC 59.461 38.462 5.17 0.00 0.00 2.92
3033 3140 6.316140 CCTCCGTTCAGAAATATTTGTCATCA 59.684 38.462 5.17 0.00 0.00 3.07
3034 3141 7.148255 CCTCCGTTCAGAAATATTTGTCATCAA 60.148 37.037 5.17 0.00 0.00 2.57
3035 3142 8.105097 TCCGTTCAGAAATATTTGTCATCAAA 57.895 30.769 5.17 0.00 45.71 2.69
3036 3143 8.572185 TCCGTTCAGAAATATTTGTCATCAAAA 58.428 29.630 5.17 0.00 44.97 2.44
3037 3144 9.357652 CCGTTCAGAAATATTTGTCATCAAAAT 57.642 29.630 5.17 0.00 44.97 1.82
3062 3169 9.698309 ATGGATAAAAGAAGATGTATCTACACG 57.302 33.333 0.00 0.00 39.30 4.49
3063 3170 7.652105 TGGATAAAAGAAGATGTATCTACACGC 59.348 37.037 0.00 0.00 39.30 5.34
3064 3171 7.652105 GGATAAAAGAAGATGTATCTACACGCA 59.348 37.037 0.00 0.00 39.30 5.24
3065 3172 9.197694 GATAAAAGAAGATGTATCTACACGCAT 57.802 33.333 0.00 0.00 39.30 4.73
3066 3173 7.849804 AAAAGAAGATGTATCTACACGCATT 57.150 32.000 0.00 0.00 39.30 3.56
3067 3174 7.849804 AAAGAAGATGTATCTACACGCATTT 57.150 32.000 0.00 0.00 39.30 2.32
3068 3175 7.849804 AAGAAGATGTATCTACACGCATTTT 57.150 32.000 0.00 0.00 39.30 1.82
3069 3176 8.942338 AAGAAGATGTATCTACACGCATTTTA 57.058 30.769 0.00 0.00 39.30 1.52
3070 3177 8.581057 AGAAGATGTATCTACACGCATTTTAG 57.419 34.615 0.00 0.00 39.30 1.85
3071 3178 8.198109 AGAAGATGTATCTACACGCATTTTAGT 58.802 33.333 0.00 0.00 39.30 2.24
3072 3179 8.718102 AAGATGTATCTACACGCATTTTAGTT 57.282 30.769 0.00 0.00 39.30 2.24
3073 3180 8.718102 AGATGTATCTACACGCATTTTAGTTT 57.282 30.769 0.00 0.00 39.30 2.66
3074 3181 9.162764 AGATGTATCTACACGCATTTTAGTTTT 57.837 29.630 0.00 0.00 39.30 2.43
3077 3184 9.642327 TGTATCTACACGCATTTTAGTTTTAGA 57.358 29.630 0.00 0.00 0.00 2.10
3227 3334 0.966370 GGGAGTACTGCTCAGTCGGT 60.966 60.000 14.52 0.00 45.88 4.69
3247 3354 2.032981 CTTCACCGTTGGCTTTGCT 58.967 52.632 0.00 0.00 0.00 3.91
3284 3391 2.699954 AGAACGCAGTACATGGAAAGG 58.300 47.619 0.00 0.00 45.00 3.11
3287 3394 1.623811 ACGCAGTACATGGAAAGGAGT 59.376 47.619 0.00 0.00 41.94 3.85
3288 3395 2.038557 ACGCAGTACATGGAAAGGAGTT 59.961 45.455 0.00 0.00 41.94 3.01
3289 3396 3.074412 CGCAGTACATGGAAAGGAGTTT 58.926 45.455 0.00 0.00 0.00 2.66
3290 3397 4.250464 CGCAGTACATGGAAAGGAGTTTA 58.750 43.478 0.00 0.00 0.00 2.01
3292 3399 6.046593 CGCAGTACATGGAAAGGAGTTTATA 58.953 40.000 0.00 0.00 0.00 0.98
3293 3400 6.018994 CGCAGTACATGGAAAGGAGTTTATAC 60.019 42.308 0.00 0.00 0.00 1.47
3294 3401 6.821665 GCAGTACATGGAAAGGAGTTTATACA 59.178 38.462 0.00 0.00 0.00 2.29
3295 3402 7.011482 GCAGTACATGGAAAGGAGTTTATACAG 59.989 40.741 0.00 0.00 0.00 2.74
3296 3403 8.041323 CAGTACATGGAAAGGAGTTTATACAGT 58.959 37.037 0.00 0.00 0.00 3.55
3325 3434 6.794534 ACTTCTTTTCCTCCCATGTTAAGAT 58.205 36.000 0.00 0.00 0.00 2.40
3334 3443 3.266772 TCCCATGTTAAGATGGAAGCTGT 59.733 43.478 28.58 0.00 45.24 4.40
3337 3446 4.701651 CCATGTTAAGATGGAAGCTGTTGA 59.298 41.667 23.99 0.00 45.24 3.18
3355 3464 1.845809 GAAGCACGTTGTGGCCTCAG 61.846 60.000 7.68 0.00 33.64 3.35
3356 3465 4.030452 GCACGTTGTGGCCTCAGC 62.030 66.667 11.26 11.26 33.64 4.26
3357 3466 2.591429 CACGTTGTGGCCTCAGCA 60.591 61.111 19.72 4.37 42.56 4.41
3380 3492 3.000724 GCTAGAAATGCTCAAGTGCGTAG 59.999 47.826 0.00 0.00 35.36 3.51
3383 3495 3.681897 AGAAATGCTCAAGTGCGTAGAAG 59.318 43.478 0.00 0.00 35.36 2.85
3384 3496 3.319137 AATGCTCAAGTGCGTAGAAGA 57.681 42.857 0.00 0.00 35.36 2.87
3387 3500 1.989165 GCTCAAGTGCGTAGAAGACAG 59.011 52.381 0.00 0.00 0.00 3.51
3388 3501 1.989165 CTCAAGTGCGTAGAAGACAGC 59.011 52.381 0.00 0.00 0.00 4.40
3393 3506 1.993370 GTGCGTAGAAGACAGCGATTT 59.007 47.619 0.00 0.00 32.43 2.17
3395 3508 3.611113 GTGCGTAGAAGACAGCGATTTAA 59.389 43.478 0.00 0.00 32.43 1.52
3396 3509 3.611113 TGCGTAGAAGACAGCGATTTAAC 59.389 43.478 0.00 0.00 32.43 2.01
3397 3510 3.301007 GCGTAGAAGACAGCGATTTAACG 60.301 47.826 0.00 0.00 0.00 3.18
3398 3511 4.093514 CGTAGAAGACAGCGATTTAACGA 58.906 43.478 0.00 0.00 35.09 3.85
3407 3520 5.560148 ACAGCGATTTAACGAGCATAAAAG 58.440 37.500 0.00 0.00 35.09 2.27
3408 3521 5.350365 ACAGCGATTTAACGAGCATAAAAGA 59.650 36.000 0.00 0.00 35.09 2.52
3409 3522 6.128391 ACAGCGATTTAACGAGCATAAAAGAA 60.128 34.615 0.00 0.00 35.09 2.52
3410 3523 6.740905 CAGCGATTTAACGAGCATAAAAGAAA 59.259 34.615 0.00 0.00 35.09 2.52
3411 3524 6.961554 AGCGATTTAACGAGCATAAAAGAAAG 59.038 34.615 0.00 0.00 35.09 2.62
3412 3525 6.741358 GCGATTTAACGAGCATAAAAGAAAGT 59.259 34.615 0.00 0.00 35.09 2.66
3413 3526 7.901377 GCGATTTAACGAGCATAAAAGAAAGTA 59.099 33.333 0.00 0.00 35.09 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.884832 TCTTTCCTTTCAAGAGTCACTACAA 58.115 36.000 0.00 0.00 0.00 2.41
1 2 6.463049 CCTCTTTCCTTTCAAGAGTCACTACA 60.463 42.308 8.49 0.00 44.05 2.74
2 3 5.929415 CCTCTTTCCTTTCAAGAGTCACTAC 59.071 44.000 8.49 0.00 44.05 2.73
3 4 5.839063 TCCTCTTTCCTTTCAAGAGTCACTA 59.161 40.000 8.49 0.00 44.05 2.74
4 5 4.656112 TCCTCTTTCCTTTCAAGAGTCACT 59.344 41.667 8.49 0.00 44.05 3.41
5 6 4.962155 TCCTCTTTCCTTTCAAGAGTCAC 58.038 43.478 8.49 0.00 44.05 3.67
6 7 4.901849 TCTCCTCTTTCCTTTCAAGAGTCA 59.098 41.667 8.49 0.00 44.05 3.41
7 8 5.245075 TCTCTCCTCTTTCCTTTCAAGAGTC 59.755 44.000 8.49 0.00 44.05 3.36
8 9 5.151454 TCTCTCCTCTTTCCTTTCAAGAGT 58.849 41.667 8.49 0.00 44.05 3.24
9 10 5.480073 TCTCTCTCCTCTTTCCTTTCAAGAG 59.520 44.000 3.14 3.14 44.81 2.85
10 11 5.398236 TCTCTCTCCTCTTTCCTTTCAAGA 58.602 41.667 0.00 0.00 0.00 3.02
11 12 5.736951 TCTCTCTCCTCTTTCCTTTCAAG 57.263 43.478 0.00 0.00 0.00 3.02
12 13 6.465035 CCTTTCTCTCTCCTCTTTCCTTTCAA 60.465 42.308 0.00 0.00 0.00 2.69
13 14 5.012561 CCTTTCTCTCTCCTCTTTCCTTTCA 59.987 44.000 0.00 0.00 0.00 2.69
14 15 5.487433 CCTTTCTCTCTCCTCTTTCCTTTC 58.513 45.833 0.00 0.00 0.00 2.62
15 16 4.263287 GCCTTTCTCTCTCCTCTTTCCTTT 60.263 45.833 0.00 0.00 0.00 3.11
16 17 3.263170 GCCTTTCTCTCTCCTCTTTCCTT 59.737 47.826 0.00 0.00 0.00 3.36
17 18 2.837591 GCCTTTCTCTCTCCTCTTTCCT 59.162 50.000 0.00 0.00 0.00 3.36
18 19 2.837591 AGCCTTTCTCTCTCCTCTTTCC 59.162 50.000 0.00 0.00 0.00 3.13
19 20 3.369366 CCAGCCTTTCTCTCTCCTCTTTC 60.369 52.174 0.00 0.00 0.00 2.62
20 21 2.571202 CCAGCCTTTCTCTCTCCTCTTT 59.429 50.000 0.00 0.00 0.00 2.52
21 22 2.187100 CCAGCCTTTCTCTCTCCTCTT 58.813 52.381 0.00 0.00 0.00 2.85
22 23 1.622173 CCCAGCCTTTCTCTCTCCTCT 60.622 57.143 0.00 0.00 0.00 3.69
23 24 0.829990 CCCAGCCTTTCTCTCTCCTC 59.170 60.000 0.00 0.00 0.00 3.71
24 25 0.415429 TCCCAGCCTTTCTCTCTCCT 59.585 55.000 0.00 0.00 0.00 3.69
25 26 0.539518 GTCCCAGCCTTTCTCTCTCC 59.460 60.000 0.00 0.00 0.00 3.71
26 27 1.270907 TGTCCCAGCCTTTCTCTCTC 58.729 55.000 0.00 0.00 0.00 3.20
27 28 1.963985 ATGTCCCAGCCTTTCTCTCT 58.036 50.000 0.00 0.00 0.00 3.10
28 29 3.914426 TTATGTCCCAGCCTTTCTCTC 57.086 47.619 0.00 0.00 0.00 3.20
29 30 4.228210 TCATTTATGTCCCAGCCTTTCTCT 59.772 41.667 0.00 0.00 0.00 3.10
30 31 4.526970 TCATTTATGTCCCAGCCTTTCTC 58.473 43.478 0.00 0.00 0.00 2.87
31 32 4.591321 TCATTTATGTCCCAGCCTTTCT 57.409 40.909 0.00 0.00 0.00 2.52
32 33 5.859205 ATTCATTTATGTCCCAGCCTTTC 57.141 39.130 0.00 0.00 0.00 2.62
33 34 8.227507 ACTATATTCATTTATGTCCCAGCCTTT 58.772 33.333 0.00 0.00 0.00 3.11
34 35 7.759607 ACTATATTCATTTATGTCCCAGCCTT 58.240 34.615 0.00 0.00 0.00 4.35
35 36 7.335127 ACTATATTCATTTATGTCCCAGCCT 57.665 36.000 0.00 0.00 0.00 4.58
36 37 9.515226 TTAACTATATTCATTTATGTCCCAGCC 57.485 33.333 0.00 0.00 0.00 4.85
125 126 0.883833 CAAGTGGCCAGCTTGGTAAG 59.116 55.000 27.19 11.57 40.46 2.34
126 127 3.034924 CAAGTGGCCAGCTTGGTAA 57.965 52.632 27.19 0.00 40.46 2.85
127 128 4.819783 CAAGTGGCCAGCTTGGTA 57.180 55.556 27.19 0.00 40.46 3.25
130 131 1.327303 TTTACCAAGTGGCCAGCTTG 58.673 50.000 27.60 27.60 42.00 4.01
131 132 1.895131 CATTTACCAAGTGGCCAGCTT 59.105 47.619 5.11 10.42 39.32 3.74
132 133 1.075374 TCATTTACCAAGTGGCCAGCT 59.925 47.619 5.11 3.37 39.32 4.24
133 134 1.544724 TCATTTACCAAGTGGCCAGC 58.455 50.000 5.11 0.39 39.32 4.85
134 135 6.772716 ACTATATTCATTTACCAAGTGGCCAG 59.227 38.462 5.11 0.00 39.32 4.85
135 136 6.668645 ACTATATTCATTTACCAAGTGGCCA 58.331 36.000 0.00 0.00 39.32 5.36
136 137 7.582667 AACTATATTCATTTACCAAGTGGCC 57.417 36.000 0.00 0.00 39.32 5.36
155 156 9.930693 GCAGCTAATGGTAACTAAGATAACTAT 57.069 33.333 0.00 0.00 37.61 2.12
156 157 8.920174 TGCAGCTAATGGTAACTAAGATAACTA 58.080 33.333 0.00 0.00 37.61 2.24
157 158 7.792032 TGCAGCTAATGGTAACTAAGATAACT 58.208 34.615 0.00 0.00 37.61 2.24
158 159 7.307455 GCTGCAGCTAATGGTAACTAAGATAAC 60.307 40.741 31.33 0.00 38.21 1.89
159 160 6.706270 GCTGCAGCTAATGGTAACTAAGATAA 59.294 38.462 31.33 0.00 38.21 1.75
160 161 6.183360 TGCTGCAGCTAATGGTAACTAAGATA 60.183 38.462 36.61 9.39 42.66 1.98
161 162 5.059833 GCTGCAGCTAATGGTAACTAAGAT 58.940 41.667 31.33 0.00 38.21 2.40
162 163 4.081142 TGCTGCAGCTAATGGTAACTAAGA 60.081 41.667 36.61 10.16 42.66 2.10
163 164 4.191544 TGCTGCAGCTAATGGTAACTAAG 58.808 43.478 36.61 0.00 42.66 2.18
164 165 4.214986 TGCTGCAGCTAATGGTAACTAA 57.785 40.909 36.61 11.32 42.66 2.24
165 166 3.904800 TGCTGCAGCTAATGGTAACTA 57.095 42.857 36.61 11.53 42.66 2.24
166 167 2.787473 TGCTGCAGCTAATGGTAACT 57.213 45.000 36.61 0.00 42.66 2.24
167 168 4.816385 TCTATTGCTGCAGCTAATGGTAAC 59.184 41.667 36.61 6.97 42.66 2.50
168 169 5.034852 TCTATTGCTGCAGCTAATGGTAA 57.965 39.130 36.61 22.13 42.66 2.85
169 170 4.687901 TCTATTGCTGCAGCTAATGGTA 57.312 40.909 36.61 18.47 42.66 3.25
170 171 3.565764 TCTATTGCTGCAGCTAATGGT 57.434 42.857 36.61 18.34 42.66 3.55
171 172 4.906065 TTTCTATTGCTGCAGCTAATGG 57.094 40.909 36.61 30.37 42.66 3.16
172 173 6.270815 ACATTTTCTATTGCTGCAGCTAATG 58.729 36.000 36.61 27.59 42.66 1.90
173 174 6.461110 ACATTTTCTATTGCTGCAGCTAAT 57.539 33.333 36.61 31.22 42.66 1.73
174 175 5.902613 ACATTTTCTATTGCTGCAGCTAA 57.097 34.783 36.61 27.79 42.66 3.09
175 176 5.902613 AACATTTTCTATTGCTGCAGCTA 57.097 34.783 36.61 30.87 42.66 3.32
176 177 4.796038 AACATTTTCTATTGCTGCAGCT 57.204 36.364 36.61 21.93 42.66 4.24
177 178 5.401550 TGTAACATTTTCTATTGCTGCAGC 58.598 37.500 31.89 31.89 42.50 5.25
178 179 6.308766 GGTTGTAACATTTTCTATTGCTGCAG 59.691 38.462 10.11 10.11 0.00 4.41
179 180 6.015519 AGGTTGTAACATTTTCTATTGCTGCA 60.016 34.615 0.00 0.00 0.00 4.41
180 181 6.308766 CAGGTTGTAACATTTTCTATTGCTGC 59.691 38.462 0.00 0.00 0.00 5.25
181 182 6.308766 GCAGGTTGTAACATTTTCTATTGCTG 59.691 38.462 0.00 0.00 0.00 4.41
182 183 6.015519 TGCAGGTTGTAACATTTTCTATTGCT 60.016 34.615 0.00 0.00 0.00 3.91
183 184 6.089417 GTGCAGGTTGTAACATTTTCTATTGC 59.911 38.462 0.00 0.00 0.00 3.56
184 185 7.370383 AGTGCAGGTTGTAACATTTTCTATTG 58.630 34.615 0.00 0.00 0.00 1.90
185 186 7.524717 AGTGCAGGTTGTAACATTTTCTATT 57.475 32.000 0.00 0.00 0.00 1.73
186 187 8.807948 ATAGTGCAGGTTGTAACATTTTCTAT 57.192 30.769 0.00 0.00 0.00 1.98
187 188 9.727859 TTATAGTGCAGGTTGTAACATTTTCTA 57.272 29.630 0.00 0.00 0.00 2.10
188 189 8.630054 TTATAGTGCAGGTTGTAACATTTTCT 57.370 30.769 0.00 0.00 0.00 2.52
189 190 9.685828 TTTTATAGTGCAGGTTGTAACATTTTC 57.314 29.630 0.00 0.00 0.00 2.29
213 214 5.326200 TCCACGTTGGTTGTAACATTTTT 57.674 34.783 0.00 0.00 39.03 1.94
214 215 4.985538 TCCACGTTGGTTGTAACATTTT 57.014 36.364 0.00 0.00 39.03 1.82
215 216 4.794655 GCATCCACGTTGGTTGTAACATTT 60.795 41.667 13.21 0.00 38.99 2.32
216 217 3.305064 GCATCCACGTTGGTTGTAACATT 60.305 43.478 13.21 0.00 38.99 2.71
217 218 2.227865 GCATCCACGTTGGTTGTAACAT 59.772 45.455 13.21 0.00 38.99 2.71
218 219 1.604755 GCATCCACGTTGGTTGTAACA 59.395 47.619 13.21 0.00 38.99 2.41
219 220 1.604755 TGCATCCACGTTGGTTGTAAC 59.395 47.619 13.21 0.00 38.99 2.50
220 221 1.604755 GTGCATCCACGTTGGTTGTAA 59.395 47.619 13.21 4.14 38.99 2.41
221 222 1.202710 AGTGCATCCACGTTGGTTGTA 60.203 47.619 13.21 8.47 46.62 2.41
222 223 0.465460 AGTGCATCCACGTTGGTTGT 60.465 50.000 13.21 0.00 46.62 3.32
223 224 0.667993 AAGTGCATCCACGTTGGTTG 59.332 50.000 0.00 9.44 46.62 3.77
262 263 4.088823 AGATGCGAGTTTCATTTTGAGC 57.911 40.909 0.00 0.00 0.00 4.26
269 270 1.139853 GGAGGGAGATGCGAGTTTCAT 59.860 52.381 0.00 0.00 0.00 2.57
298 299 2.811747 TTGCGCGTATGGTGGACG 60.812 61.111 8.43 0.00 43.19 4.79
348 349 4.107820 AGAAGCTTCCAGGGAGAGTTAAT 58.892 43.478 22.81 0.00 0.00 1.40
350 351 3.100671 GAGAAGCTTCCAGGGAGAGTTA 58.899 50.000 22.81 0.00 0.00 2.24
352 353 1.567357 GAGAAGCTTCCAGGGAGAGT 58.433 55.000 22.81 0.40 0.00 3.24
353 354 0.829990 GGAGAAGCTTCCAGGGAGAG 59.170 60.000 22.81 0.00 37.20 3.20
392 393 2.572333 ATCGGGATTGTTGCTGGGGG 62.572 60.000 0.00 0.00 0.00 5.40
459 462 4.074408 GGGGATTGGGGTGGTGGG 62.074 72.222 0.00 0.00 0.00 4.61
492 495 2.758770 TTCCCGTTGAGTTCGCGAGG 62.759 60.000 9.59 4.96 0.00 4.63
952 965 1.785768 ATTGCGTTGCGTACACTACA 58.214 45.000 0.00 0.00 0.00 2.74
956 969 0.515564 AGGAATTGCGTTGCGTACAC 59.484 50.000 0.00 0.00 32.72 2.90
957 970 1.231221 AAGGAATTGCGTTGCGTACA 58.769 45.000 0.00 0.00 32.72 2.90
958 971 1.976045 CAAAGGAATTGCGTTGCGTAC 59.024 47.619 12.14 0.00 32.72 3.67
959 972 2.323939 CAAAGGAATTGCGTTGCGTA 57.676 45.000 12.14 0.00 32.72 4.42
960 973 3.177883 CAAAGGAATTGCGTTGCGT 57.822 47.368 12.14 0.00 32.72 5.24
972 985 1.609208 GAGCAAGGAACAGCAAAGGA 58.391 50.000 0.00 0.00 34.11 3.36
973 993 0.600057 GGAGCAAGGAACAGCAAAGG 59.400 55.000 0.00 0.00 34.11 3.11
1149 1169 1.988956 CCTCAGCCTCTGCCAGAGT 60.989 63.158 19.89 0.00 40.72 3.24
1182 1202 4.318332 CCATAGCATAAGAAGGAATCGCA 58.682 43.478 0.00 0.00 0.00 5.10
1205 1225 3.190849 CTGGTCGCACATCTGCCG 61.191 66.667 0.00 0.00 40.73 5.69
1206 1226 1.364626 CTTCTGGTCGCACATCTGCC 61.365 60.000 0.00 0.00 40.73 4.85
1208 1228 0.390866 AGCTTCTGGTCGCACATCTG 60.391 55.000 0.00 0.00 0.00 2.90
1209 1229 1.186200 TAGCTTCTGGTCGCACATCT 58.814 50.000 0.00 0.00 0.00 2.90
1210 1230 1.661112 GTTAGCTTCTGGTCGCACATC 59.339 52.381 0.00 0.00 0.00 3.06
1211 1231 1.276421 AGTTAGCTTCTGGTCGCACAT 59.724 47.619 0.00 0.00 0.00 3.21
1212 1232 0.679505 AGTTAGCTTCTGGTCGCACA 59.320 50.000 0.00 0.00 0.00 4.57
1213 1233 1.071605 CAGTTAGCTTCTGGTCGCAC 58.928 55.000 0.00 0.00 0.00 5.34
1406 1435 9.133627 CTGGTCTCTTCGTATATCATAATGTTG 57.866 37.037 0.00 0.00 0.00 3.33
1448 1477 4.083324 TCAGGTCGGTAACAACTACTTACG 60.083 45.833 0.00 0.00 0.00 3.18
1464 1493 5.018539 TCCATATAAACAAGGTCAGGTCG 57.981 43.478 0.00 0.00 0.00 4.79
1596 1672 5.252547 TGGTGCTCTTCTAAATATGCAACA 58.747 37.500 0.00 0.00 44.32 3.33
1624 1700 9.349713 AGGCGACCATCAATAATAGAATTTTTA 57.650 29.630 0.00 0.00 0.00 1.52
1627 1704 6.147821 CGAGGCGACCATCAATAATAGAATTT 59.852 38.462 0.00 0.00 0.00 1.82
1628 1705 5.639506 CGAGGCGACCATCAATAATAGAATT 59.360 40.000 0.00 0.00 0.00 2.17
1629 1706 5.171476 CGAGGCGACCATCAATAATAGAAT 58.829 41.667 0.00 0.00 0.00 2.40
1630 1707 4.038763 ACGAGGCGACCATCAATAATAGAA 59.961 41.667 0.00 0.00 0.00 2.10
1633 1710 4.330944 AACGAGGCGACCATCAATAATA 57.669 40.909 0.00 0.00 0.00 0.98
1680 1759 3.885297 AGACCAAACTGTCAATGTTCCTG 59.115 43.478 0.00 0.00 37.73 3.86
1701 1780 5.412594 TCAGCTACAGAAAATAAACAGGCAG 59.587 40.000 0.00 0.00 0.00 4.85
1970 2049 2.039879 ACGTCTGAAATTAAGCAGGGGT 59.960 45.455 0.00 0.00 33.05 4.95
1978 2057 5.106712 GCTGTTCATCCACGTCTGAAATTAA 60.107 40.000 6.36 0.00 33.45 1.40
2106 2185 5.682943 AAAGTAGTTTTAGCGTGCAATCA 57.317 34.783 0.00 0.00 0.00 2.57
2186 2265 4.082408 TGTTTCGACTTCTACATCGGATGT 60.082 41.667 25.36 25.36 46.92 3.06
2294 2373 8.213518 TGAGTAGATACATTTCAATTGCCTTC 57.786 34.615 0.00 0.00 0.00 3.46
2351 2430 5.813157 GGAGATAGAGGAAGAACCGAAAAAG 59.187 44.000 0.00 0.00 44.74 2.27
2497 2578 0.179156 AAAAGAATGAGCCATGCGCG 60.179 50.000 0.00 0.00 44.76 6.86
2523 2606 1.257743 GAGAGGCGATGGGTGCTATA 58.742 55.000 0.00 0.00 0.00 1.31
2524 2607 1.810606 CGAGAGGCGATGGGTGCTAT 61.811 60.000 0.00 0.00 44.57 2.97
2525 2608 2.490148 CGAGAGGCGATGGGTGCTA 61.490 63.158 0.00 0.00 44.57 3.49
2527 2610 3.838271 TCGAGAGGCGATGGGTGC 61.838 66.667 0.00 0.00 45.59 5.01
2594 2680 5.484715 ACTACTAGCCTAAACGATTTGCAA 58.515 37.500 0.00 0.00 0.00 4.08
2727 2816 6.525628 CACAACACAATATCTTCATGAGCAAC 59.474 38.462 0.00 0.00 0.00 4.17
2737 2832 5.630121 TCAGGGTTCACAACACAATATCTT 58.370 37.500 0.00 0.00 37.23 2.40
2748 2843 2.955660 GTCATGGTTTCAGGGTTCACAA 59.044 45.455 0.00 0.00 0.00 3.33
2796 2901 1.269051 CGTCCACTGCAAAAAGAACCC 60.269 52.381 0.00 0.00 0.00 4.11
2801 2906 0.030638 CCACCGTCCACTGCAAAAAG 59.969 55.000 0.00 0.00 0.00 2.27
2802 2907 2.010582 GCCACCGTCCACTGCAAAAA 62.011 55.000 0.00 0.00 0.00 1.94
2846 2951 0.459585 ACACATACGCATCCGGTGAC 60.460 55.000 0.00 0.00 39.22 3.67
2880 2985 1.068281 CCACTCACCATCGATGAGAGG 59.932 57.143 32.38 24.56 45.46 3.69
2890 2995 0.393944 CAGCAGCATCCACTCACCAT 60.394 55.000 0.00 0.00 0.00 3.55
2921 3026 1.363744 CGGTGAAGAGGCATCAACTC 58.636 55.000 0.00 0.00 32.22 3.01
2922 3027 0.674895 GCGGTGAAGAGGCATCAACT 60.675 55.000 0.00 0.00 32.22 3.16
2944 3051 2.816672 GCAGAGAGAAAAAGGAACAGGG 59.183 50.000 0.00 0.00 0.00 4.45
2952 3059 2.478134 CACGTCAGGCAGAGAGAAAAAG 59.522 50.000 0.00 0.00 0.00 2.27
3004 3111 6.942976 ACAAATATTTCTGAACGGAGGAGTA 58.057 36.000 0.00 0.00 0.00 2.59
3005 3112 5.805728 ACAAATATTTCTGAACGGAGGAGT 58.194 37.500 0.00 0.00 0.00 3.85
3006 3113 5.874810 TGACAAATATTTCTGAACGGAGGAG 59.125 40.000 0.00 0.00 0.00 3.69
3007 3114 5.800296 TGACAAATATTTCTGAACGGAGGA 58.200 37.500 0.00 0.00 0.00 3.71
3008 3115 6.316140 TGATGACAAATATTTCTGAACGGAGG 59.684 38.462 0.00 0.00 0.00 4.30
3009 3116 7.307493 TGATGACAAATATTTCTGAACGGAG 57.693 36.000 0.00 0.00 0.00 4.63
3010 3117 7.680442 TTGATGACAAATATTTCTGAACGGA 57.320 32.000 0.00 0.00 32.73 4.69
3011 3118 8.741101 TTTTGATGACAAATATTTCTGAACGG 57.259 30.769 0.00 0.00 43.99 4.44
3036 3143 9.698309 CGTGTAGATACATCTTCTTTTATCCAT 57.302 33.333 0.00 0.00 38.63 3.41
3037 3144 7.652105 GCGTGTAGATACATCTTCTTTTATCCA 59.348 37.037 0.00 0.00 38.63 3.41
3038 3145 7.652105 TGCGTGTAGATACATCTTCTTTTATCC 59.348 37.037 0.00 0.00 38.63 2.59
3039 3146 8.575565 TGCGTGTAGATACATCTTCTTTTATC 57.424 34.615 0.00 0.00 38.63 1.75
3040 3147 9.547753 AATGCGTGTAGATACATCTTCTTTTAT 57.452 29.630 0.00 0.00 38.63 1.40
3041 3148 8.942338 AATGCGTGTAGATACATCTTCTTTTA 57.058 30.769 0.00 0.00 38.63 1.52
3042 3149 7.849804 AATGCGTGTAGATACATCTTCTTTT 57.150 32.000 0.00 0.00 38.63 2.27
3043 3150 7.849804 AAATGCGTGTAGATACATCTTCTTT 57.150 32.000 0.00 0.00 38.63 2.52
3044 3151 7.849804 AAAATGCGTGTAGATACATCTTCTT 57.150 32.000 0.00 0.00 38.63 2.52
3045 3152 8.198109 ACTAAAATGCGTGTAGATACATCTTCT 58.802 33.333 0.00 0.00 38.63 2.85
3046 3153 8.354011 ACTAAAATGCGTGTAGATACATCTTC 57.646 34.615 0.00 0.00 38.63 2.87
3047 3154 8.718102 AACTAAAATGCGTGTAGATACATCTT 57.282 30.769 0.00 0.00 38.63 2.40
3048 3155 8.718102 AAACTAAAATGCGTGTAGATACATCT 57.282 30.769 4.34 0.00 38.63 2.90
3051 3158 9.642327 TCTAAAACTAAAATGCGTGTAGATACA 57.358 29.630 4.34 0.00 0.00 2.29
3196 3303 2.038033 CAGTACTCCCTCCGTCCAAAAA 59.962 50.000 0.00 0.00 0.00 1.94
3197 3304 1.621814 CAGTACTCCCTCCGTCCAAAA 59.378 52.381 0.00 0.00 0.00 2.44
3198 3305 1.263356 CAGTACTCCCTCCGTCCAAA 58.737 55.000 0.00 0.00 0.00 3.28
3199 3306 1.255667 GCAGTACTCCCTCCGTCCAA 61.256 60.000 0.00 0.00 0.00 3.53
3200 3307 1.681327 GCAGTACTCCCTCCGTCCA 60.681 63.158 0.00 0.00 0.00 4.02
3201 3308 1.380112 AGCAGTACTCCCTCCGTCC 60.380 63.158 0.00 0.00 0.00 4.79
3202 3309 0.680280 TGAGCAGTACTCCCTCCGTC 60.680 60.000 14.42 0.00 45.61 4.79
3203 3310 0.681564 CTGAGCAGTACTCCCTCCGT 60.682 60.000 14.42 0.00 45.61 4.69
3204 3311 0.681564 ACTGAGCAGTACTCCCTCCG 60.682 60.000 14.42 11.59 45.61 4.63
3205 3312 1.107945 GACTGAGCAGTACTCCCTCC 58.892 60.000 14.42 0.54 45.61 4.30
3206 3313 0.736053 CGACTGAGCAGTACTCCCTC 59.264 60.000 2.65 11.45 45.61 4.30
3207 3314 0.681564 CCGACTGAGCAGTACTCCCT 60.682 60.000 2.65 0.00 45.61 4.20
3208 3315 0.966370 ACCGACTGAGCAGTACTCCC 60.966 60.000 2.65 0.00 45.61 4.30
3209 3316 0.171455 CACCGACTGAGCAGTACTCC 59.829 60.000 2.65 0.00 45.61 3.85
3210 3317 0.456995 GCACCGACTGAGCAGTACTC 60.457 60.000 2.65 0.00 46.45 2.59
3211 3318 0.896019 AGCACCGACTGAGCAGTACT 60.896 55.000 2.65 0.00 42.66 2.73
3212 3319 0.038159 AAGCACCGACTGAGCAGTAC 60.038 55.000 2.65 0.00 42.66 2.73
3227 3334 1.732917 CAAAGCCAACGGTGAAGCA 59.267 52.632 0.00 0.00 0.00 3.91
3247 3354 2.835895 TACTGGATAGCCGGCGCA 60.836 61.111 23.20 14.18 44.98 6.09
3256 3363 4.037565 CCATGTACTGCGTTCTACTGGATA 59.962 45.833 0.00 0.00 0.00 2.59
3260 3367 3.503827 TCCATGTACTGCGTTCTACTG 57.496 47.619 0.00 0.00 0.00 2.74
3289 3396 8.975295 GGGAGGAAAAGAAGTTACTACTGTATA 58.025 37.037 0.00 0.00 34.01 1.47
3290 3397 7.456902 TGGGAGGAAAAGAAGTTACTACTGTAT 59.543 37.037 0.00 0.00 34.01 2.29
3292 3399 5.605488 TGGGAGGAAAAGAAGTTACTACTGT 59.395 40.000 0.00 0.00 34.01 3.55
3293 3400 6.110411 TGGGAGGAAAAGAAGTTACTACTG 57.890 41.667 0.00 0.00 34.01 2.74
3294 3401 6.272558 ACATGGGAGGAAAAGAAGTTACTACT 59.727 38.462 0.00 0.00 35.68 2.57
3295 3402 6.473758 ACATGGGAGGAAAAGAAGTTACTAC 58.526 40.000 0.00 0.00 0.00 2.73
3296 3403 6.697641 ACATGGGAGGAAAAGAAGTTACTA 57.302 37.500 0.00 0.00 0.00 1.82
3334 3443 1.444119 GAGGCCACAACGTGCTTCAA 61.444 55.000 5.01 0.00 31.34 2.69
3337 3446 1.893808 CTGAGGCCACAACGTGCTT 60.894 57.895 5.01 0.00 31.34 3.91
3342 3451 2.786539 TAGCTGCTGAGGCCACAACG 62.787 60.000 13.43 0.00 37.74 4.10
3344 3453 1.194121 TCTAGCTGCTGAGGCCACAA 61.194 55.000 13.43 0.00 37.74 3.33
3355 3464 2.477525 GCACTTGAGCATTTCTAGCTGC 60.478 50.000 0.00 0.00 43.58 5.25
3356 3465 2.222976 CGCACTTGAGCATTTCTAGCTG 60.223 50.000 0.00 0.00 43.58 4.24
3357 3466 2.005451 CGCACTTGAGCATTTCTAGCT 58.995 47.619 0.00 0.00 46.82 3.32
3371 3483 0.596577 TCGCTGTCTTCTACGCACTT 59.403 50.000 0.00 0.00 0.00 3.16
3380 3492 2.666508 TGCTCGTTAAATCGCTGTCTTC 59.333 45.455 0.00 0.00 0.00 2.87
3383 3495 4.772046 TTATGCTCGTTAAATCGCTGTC 57.228 40.909 0.00 0.00 0.00 3.51
3384 3496 5.350365 TCTTTTATGCTCGTTAAATCGCTGT 59.650 36.000 0.00 0.00 0.00 4.40
3387 3500 6.741358 ACTTTCTTTTATGCTCGTTAAATCGC 59.259 34.615 0.00 0.00 0.00 4.58
3388 3501 9.749490 TTACTTTCTTTTATGCTCGTTAAATCG 57.251 29.630 0.00 0.00 0.00 3.34
3407 3520 7.407337 CGGCTGGTGTATTTTCTATTACTTTC 58.593 38.462 0.00 0.00 0.00 2.62
3408 3521 6.317893 CCGGCTGGTGTATTTTCTATTACTTT 59.682 38.462 2.29 0.00 0.00 2.66
3409 3522 5.820947 CCGGCTGGTGTATTTTCTATTACTT 59.179 40.000 2.29 0.00 0.00 2.24
3410 3523 5.365619 CCGGCTGGTGTATTTTCTATTACT 58.634 41.667 2.29 0.00 0.00 2.24
3411 3524 4.514066 CCCGGCTGGTGTATTTTCTATTAC 59.486 45.833 11.58 0.00 0.00 1.89
3412 3525 4.409574 TCCCGGCTGGTGTATTTTCTATTA 59.590 41.667 11.58 0.00 34.77 0.98
3413 3526 3.201266 TCCCGGCTGGTGTATTTTCTATT 59.799 43.478 11.58 0.00 34.77 1.73
3415 3528 2.189676 TCCCGGCTGGTGTATTTTCTA 58.810 47.619 11.58 0.00 34.77 2.10
3417 3530 1.828979 TTCCCGGCTGGTGTATTTTC 58.171 50.000 11.58 0.00 34.77 2.29
3423 3536 2.589157 TTCGATTCCCGGCTGGTGT 61.589 57.895 11.58 0.00 39.14 4.16


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

AutoCloner maintained by Alex Coulton.