Multiple sequence alignment - TraesCS3D01G390900

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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 TraesCS3D01G390900 chr3D 100.000 3593 0 0 1 3593 506000350 505996758 0.000000e+00 6636.0
1 TraesCS3D01G390900 chr3D 81.918 730 66 35 945 1668 505982560 505981891 1.130000e-154 556.0
2 TraesCS3D01G390900 chr3D 90.296 371 25 3 1092 1457 505779679 505779315 3.250000e-130 475.0
3 TraesCS3D01G390900 chr3D 85.895 475 29 20 965 1439 505795477 505795041 4.200000e-129 472.0
4 TraesCS3D01G390900 chr3D 93.706 286 15 3 2312 2595 505974220 505973936 3.320000e-115 425.0
5 TraesCS3D01G390900 chr3D 76.941 837 135 37 2476 3258 505794982 505794150 1.190000e-114 424.0
6 TraesCS3D01G390900 chr3D 95.397 239 11 0 1 239 588018740 588018978 7.280000e-102 381.0
7 TraesCS3D01G390900 chr3D 89.573 211 16 1 3389 3593 505973298 505973088 2.750000e-66 263.0
8 TraesCS3D01G390900 chr3D 85.000 180 7 2 2169 2328 505981898 505981719 7.980000e-37 165.0
9 TraesCS3D01G390900 chr3D 95.098 102 4 1 1664 1765 450575188 450575288 3.710000e-35 159.0
10 TraesCS3D01G390900 chr3D 88.800 125 5 4 2597 2720 505973897 505973781 1.040000e-30 145.0
11 TraesCS3D01G390900 chr3D 96.341 82 3 0 3307 3388 505973411 505973330 6.260000e-28 135.0
12 TraesCS3D01G390900 chr3D 82.031 128 16 7 937 1058 505779812 505779686 6.350000e-18 102.0
13 TraesCS3D01G390900 chr3D 85.870 92 8 3 2233 2320 505778133 505778043 3.820000e-15 93.5
14 TraesCS3D01G390900 chr3A 89.814 805 43 25 891 1669 644667768 644666977 0.000000e+00 996.0
15 TraesCS3D01G390900 chr3A 88.150 692 61 13 2597 3275 644666487 644665804 0.000000e+00 804.0
16 TraesCS3D01G390900 chr3A 89.640 444 25 10 2172 2594 644666982 644666539 2.440000e-151 545.0
17 TraesCS3D01G390900 chr3A 86.860 449 27 17 1001 1449 644623538 644623122 1.170000e-129 473.0
18 TraesCS3D01G390900 chr3A 89.415 359 33 3 1092 1449 644610836 644610482 7.080000e-122 448.0
19 TraesCS3D01G390900 chr3A 87.455 279 18 10 318 581 644668532 644668256 4.510000e-79 305.0
20 TraesCS3D01G390900 chr3A 84.058 207 26 3 3388 3588 644665591 644665386 3.660000e-45 193.0
21 TraesCS3D01G390900 chr3A 88.235 119 13 1 2476 2593 644623071 644622953 1.340000e-29 141.0
22 TraesCS3D01G390900 chr3A 83.516 91 10 3 2232 2318 644609258 644609169 2.970000e-11 80.5
23 TraesCS3D01G390900 chr3B 90.691 666 46 9 891 1545 667709592 667708932 0.000000e+00 872.0
24 TraesCS3D01G390900 chr3B 85.540 574 31 17 359 895 667710295 667709737 1.460000e-153 553.0
25 TraesCS3D01G390900 chr3B 88.591 447 26 6 2597 3028 667707605 667707169 1.480000e-143 520.0
26 TraesCS3D01G390900 chr3B 86.463 458 47 9 1089 1535 667644889 667644436 4.170000e-134 488.0
27 TraesCS3D01G390900 chr3B 86.481 466 22 25 976 1440 667681412 667680987 1.170000e-129 473.0
28 TraesCS3D01G390900 chr3B 85.405 370 21 5 2232 2595 667707991 667707649 1.590000e-93 353.0
29 TraesCS3D01G390900 chr3B 92.946 241 15 1 3046 3284 667707066 667706826 2.050000e-92 350.0
30 TraesCS3D01G390900 chr3B 90.517 116 10 1 2481 2595 667680887 667680772 6.210000e-33 152.0
31 TraesCS3D01G390900 chr3B 91.667 72 6 0 987 1058 667644964 667644893 2.280000e-17 100.0
32 TraesCS3D01G390900 chr3B 91.803 61 5 0 3328 3388 545194394 545194334 6.390000e-13 86.1
33 TraesCS3D01G390900 chr3B 84.091 88 9 3 2235 2318 667643600 667643514 2.970000e-11 80.5
34 TraesCS3D01G390900 chr4D 95.833 408 17 0 1761 2168 442184112 442183705 0.000000e+00 660.0
35 TraesCS3D01G390900 chr4D 96.875 96 3 0 1670 1765 69396040 69396135 1.030000e-35 161.0
36 TraesCS3D01G390900 chr4D 93.396 106 6 1 1660 1765 507857160 507857056 4.800000e-34 156.0
37 TraesCS3D01G390900 chr1D 95.588 408 18 0 1761 2168 250741238 250740831 0.000000e+00 654.0
38 TraesCS3D01G390900 chr1D 93.200 250 11 4 1 244 474020975 474021224 2.640000e-96 363.0
39 TraesCS3D01G390900 chr1D 93.249 237 10 2 1 237 300633109 300632879 9.550000e-91 344.0
40 TraesCS3D01G390900 chr1D 83.333 162 15 8 1289 1449 286389469 286389619 4.840000e-29 139.0
41 TraesCS3D01G390900 chr1D 83.333 90 12 2 2232 2318 328845091 328845002 2.970000e-11 80.5
42 TraesCS3D01G390900 chr7D 95.567 406 18 0 1763 2168 549746021 549745616 0.000000e+00 651.0
43 TraesCS3D01G390900 chr7D 94.245 417 22 2 1761 2177 136707998 136707584 1.410000e-178 636.0
44 TraesCS3D01G390900 chr7D 94.340 106 4 2 1661 1765 136708155 136708051 1.030000e-35 161.0
45 TraesCS3D01G390900 chr5B 95.366 410 18 1 1761 2170 318172948 318173356 0.000000e+00 651.0
46 TraesCS3D01G390900 chr1B 95.098 408 20 0 1761 2168 305284723 305284316 0.000000e+00 643.0
47 TraesCS3D01G390900 chrUn 95.098 408 19 1 1761 2168 115109917 115110323 3.020000e-180 641.0
48 TraesCS3D01G390900 chr6B 94.076 422 21 3 1761 2178 175219809 175219388 3.910000e-179 638.0
49 TraesCS3D01G390900 chr2D 94.245 417 21 2 1763 2177 102277776 102277361 5.060000e-178 634.0
50 TraesCS3D01G390900 chr7A 95.600 250 10 1 1 250 732859994 732859746 2.010000e-107 399.0
51 TraesCS3D01G390900 chr7A 93.227 251 14 2 1 250 732858549 732858797 2.040000e-97 366.0
52 TraesCS3D01G390900 chr4A 93.385 257 16 1 1 256 600684270 600684526 2.620000e-101 379.0
53 TraesCS3D01G390900 chr4A 92.339 248 17 2 2 248 709789588 709789834 5.710000e-93 351.0
54 TraesCS3D01G390900 chr5A 94.000 250 8 2 1 250 705956872 705956630 4.380000e-99 372.0
55 TraesCS3D01G390900 chr2A 95.946 222 7 2 1 221 770979130 770978910 3.410000e-95 359.0
56 TraesCS3D01G390900 chr4B 96.939 98 3 0 1670 1767 12866771 12866868 7.980000e-37 165.0
57 TraesCS3D01G390900 chr4B 87.719 57 7 0 3332 3388 12240755 12240699 2.320000e-07 67.6
58 TraesCS3D01G390900 chr5D 96.875 96 3 0 1670 1765 265671376 265671281 1.030000e-35 161.0
59 TraesCS3D01G390900 chr5D 96.875 96 3 0 1670 1765 342525685 342525780 1.030000e-35 161.0
60 TraesCS3D01G390900 chr5D 93.519 108 6 1 1658 1765 291356217 291356111 3.710000e-35 159.0
61 TraesCS3D01G390900 chr7B 89.167 120 9 3 1649 1765 607328182 607328300 2.890000e-31 147.0
62 TraesCS3D01G390900 chr6D 83.750 80 9 2 2232 2307 429742761 429742682 4.980000e-09 73.1


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 TraesCS3D01G390900 chr3D 505996758 506000350 3592 True 6636.000000 6636 100.000000 1 3593 1 chr3D.!!$R1 3592
1 TraesCS3D01G390900 chr3D 505794150 505795477 1327 True 448.000000 472 81.418000 965 3258 2 chr3D.!!$R3 2293
2 TraesCS3D01G390900 chr3D 505981719 505982560 841 True 360.500000 556 83.459000 945 2328 2 chr3D.!!$R5 1383
3 TraesCS3D01G390900 chr3D 505973088 505974220 1132 True 242.000000 425 92.105000 2312 3593 4 chr3D.!!$R4 1281
4 TraesCS3D01G390900 chr3D 505778043 505779812 1769 True 223.500000 475 86.065667 937 2320 3 chr3D.!!$R2 1383
5 TraesCS3D01G390900 chr3A 644665386 644668532 3146 True 568.600000 996 87.823400 318 3588 5 chr3A.!!$R3 3270
6 TraesCS3D01G390900 chr3A 644622953 644623538 585 True 307.000000 473 87.547500 1001 2593 2 chr3A.!!$R2 1592
7 TraesCS3D01G390900 chr3A 644609169 644610836 1667 True 264.250000 448 86.465500 1092 2318 2 chr3A.!!$R1 1226
8 TraesCS3D01G390900 chr3B 667706826 667710295 3469 True 529.600000 872 88.634600 359 3284 5 chr3B.!!$R4 2925
9 TraesCS3D01G390900 chr3B 667680772 667681412 640 True 312.500000 473 88.499000 976 2595 2 chr3B.!!$R3 1619
10 TraesCS3D01G390900 chr3B 667643514 667644964 1450 True 222.833333 488 87.407000 987 2318 3 chr3B.!!$R2 1331
11 TraesCS3D01G390900 chr7D 136707584 136708155 571 True 398.500000 636 94.292500 1661 2177 2 chr7D.!!$R2 516

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
351 352 0.248949 GTTACTGAGGCCGTCGGATC 60.249 60.0 17.49 12.63 35.24 3.36 F
1014 1266 0.179100 AGAACATGGCGACCATCTCG 60.179 55.0 8.21 1.87 43.15 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1933 2777 0.032130 TAGGCGCTGCACTGTATAGC 59.968 55.0 7.64 5.63 0.00 2.97 R
2595 4772 1.027357 GCCCATCTTAGCACACATGG 58.973 55.0 0.00 0.00 36.32 3.66 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 2.501610 GGCCGAGACACCAGATCC 59.498 66.667 0.00 0.00 0.00 3.36
18 19 2.359169 GGCCGAGACACCAGATCCA 61.359 63.158 0.00 0.00 0.00 3.41
19 20 1.153549 GCCGAGACACCAGATCCAC 60.154 63.158 0.00 0.00 0.00 4.02
20 21 1.517832 CCGAGACACCAGATCCACC 59.482 63.158 0.00 0.00 0.00 4.61
21 22 1.139734 CGAGACACCAGATCCACCG 59.860 63.158 0.00 0.00 0.00 4.94
22 23 1.153549 GAGACACCAGATCCACCGC 60.154 63.158 0.00 0.00 0.00 5.68
23 24 2.125106 GACACCAGATCCACCGCC 60.125 66.667 0.00 0.00 0.00 6.13
24 25 3.682292 GACACCAGATCCACCGCCC 62.682 68.421 0.00 0.00 0.00 6.13
25 26 4.838152 CACCAGATCCACCGCCCG 62.838 72.222 0.00 0.00 0.00 6.13
57 58 4.440127 GGCCGTGCCTTGCCAATG 62.440 66.667 7.58 0.00 46.69 2.82
58 59 4.440127 GCCGTGCCTTGCCAATGG 62.440 66.667 0.00 0.00 0.00 3.16
59 60 2.676121 CCGTGCCTTGCCAATGGA 60.676 61.111 2.05 0.00 0.00 3.41
60 61 2.703798 CCGTGCCTTGCCAATGGAG 61.704 63.158 2.05 0.00 0.00 3.86
61 62 2.575461 GTGCCTTGCCAATGGAGC 59.425 61.111 2.05 0.00 0.00 4.70
62 63 2.681064 TGCCTTGCCAATGGAGCC 60.681 61.111 2.05 0.00 0.00 4.70
63 64 3.830192 GCCTTGCCAATGGAGCCG 61.830 66.667 2.05 0.00 0.00 5.52
64 65 3.830192 CCTTGCCAATGGAGCCGC 61.830 66.667 2.05 0.00 0.00 6.53
65 66 3.830192 CTTGCCAATGGAGCCGCC 61.830 66.667 2.05 0.00 37.10 6.13
78 79 4.598894 CCGCCGCTCCAGATCCAG 62.599 72.222 0.00 0.00 0.00 3.86
79 80 4.598894 CGCCGCTCCAGATCCAGG 62.599 72.222 0.00 0.00 0.00 4.45
80 81 4.247380 GCCGCTCCAGATCCAGGG 62.247 72.222 2.24 0.00 0.00 4.45
81 82 2.765807 CCGCTCCAGATCCAGGGT 60.766 66.667 2.24 0.00 0.00 4.34
82 83 2.370445 CCGCTCCAGATCCAGGGTT 61.370 63.158 2.24 0.00 0.00 4.11
83 84 1.144936 CGCTCCAGATCCAGGGTTC 59.855 63.158 2.24 0.00 0.00 3.62
84 85 1.529309 GCTCCAGATCCAGGGTTCC 59.471 63.158 2.24 0.00 0.00 3.62
85 86 1.988982 GCTCCAGATCCAGGGTTCCC 61.989 65.000 0.00 0.00 0.00 3.97
86 87 1.307866 TCCAGATCCAGGGTTCCCC 60.308 63.158 4.02 0.00 45.90 4.81
95 96 2.438434 GGGTTCCCCACGCAGATG 60.438 66.667 0.00 0.00 44.65 2.90
96 97 3.134127 GGTTCCCCACGCAGATGC 61.134 66.667 0.00 0.00 37.78 3.91
97 98 2.359850 GTTCCCCACGCAGATGCA 60.360 61.111 5.55 0.00 42.21 3.96
98 99 2.046023 TTCCCCACGCAGATGCAG 60.046 61.111 5.55 0.69 42.21 4.41
99 100 3.626996 TTCCCCACGCAGATGCAGG 62.627 63.158 5.55 6.01 42.21 4.85
103 104 3.057548 CACGCAGATGCAGGGCAA 61.058 61.111 5.55 0.00 43.62 4.52
104 105 3.058160 ACGCAGATGCAGGGCAAC 61.058 61.111 5.55 0.00 43.62 4.17
180 181 4.840005 GGCGGCGAGGAAGGGAAG 62.840 72.222 12.98 0.00 0.00 3.46
181 182 4.840005 GCGGCGAGGAAGGGAAGG 62.840 72.222 12.98 0.00 0.00 3.46
182 183 4.162690 CGGCGAGGAAGGGAAGGG 62.163 72.222 0.00 0.00 0.00 3.95
183 184 3.798511 GGCGAGGAAGGGAAGGGG 61.799 72.222 0.00 0.00 0.00 4.79
184 185 3.798511 GCGAGGAAGGGAAGGGGG 61.799 72.222 0.00 0.00 0.00 5.40
199 200 4.364686 GGGGGAAGGGGGTGAGGA 62.365 72.222 0.00 0.00 0.00 3.71
200 201 2.692741 GGGGAAGGGGGTGAGGAG 60.693 72.222 0.00 0.00 0.00 3.69
201 202 2.692741 GGGAAGGGGGTGAGGAGG 60.693 72.222 0.00 0.00 0.00 4.30
202 203 2.454941 GGAAGGGGGTGAGGAGGA 59.545 66.667 0.00 0.00 0.00 3.71
203 204 1.690985 GGAAGGGGGTGAGGAGGAG 60.691 68.421 0.00 0.00 0.00 3.69
204 205 1.690985 GAAGGGGGTGAGGAGGAGG 60.691 68.421 0.00 0.00 0.00 4.30
205 206 3.274550 AAGGGGGTGAGGAGGAGGG 62.275 68.421 0.00 0.00 0.00 4.30
206 207 4.825679 GGGGGTGAGGAGGAGGGG 62.826 77.778 0.00 0.00 0.00 4.79
212 213 4.541648 GAGGAGGAGGGGCGGCTA 62.542 72.222 9.56 0.00 0.00 3.93
213 214 4.548513 AGGAGGAGGGGCGGCTAG 62.549 72.222 9.56 0.00 0.00 3.42
218 219 4.176752 GAGGGGCGGCTAGGGTTG 62.177 72.222 9.56 0.00 0.00 3.77
222 223 4.176752 GGCGGCTAGGGTTGGGAG 62.177 72.222 0.00 0.00 0.00 4.30
223 224 4.176752 GCGGCTAGGGTTGGGAGG 62.177 72.222 0.00 0.00 0.00 4.30
224 225 2.365105 CGGCTAGGGTTGGGAGGA 60.365 66.667 0.00 0.00 0.00 3.71
225 226 2.435693 CGGCTAGGGTTGGGAGGAG 61.436 68.421 0.00 0.00 0.00 3.69
226 227 2.073101 GGCTAGGGTTGGGAGGAGG 61.073 68.421 0.00 0.00 0.00 4.30
227 228 1.003051 GCTAGGGTTGGGAGGAGGA 59.997 63.158 0.00 0.00 0.00 3.71
228 229 1.051556 GCTAGGGTTGGGAGGAGGAG 61.052 65.000 0.00 0.00 0.00 3.69
229 230 1.003051 TAGGGTTGGGAGGAGGAGC 59.997 63.158 0.00 0.00 0.00 4.70
230 231 2.873557 TAGGGTTGGGAGGAGGAGCG 62.874 65.000 0.00 0.00 0.00 5.03
231 232 3.787001 GGTTGGGAGGAGGAGCGG 61.787 72.222 0.00 0.00 0.00 5.52
232 233 4.475135 GTTGGGAGGAGGAGCGGC 62.475 72.222 0.00 0.00 0.00 6.53
233 234 4.722535 TTGGGAGGAGGAGCGGCT 62.723 66.667 0.00 0.00 0.00 5.52
248 249 4.741239 GCTGGGGTGGGAGGAGGA 62.741 72.222 0.00 0.00 0.00 3.71
249 250 2.366167 CTGGGGTGGGAGGAGGAG 60.366 72.222 0.00 0.00 0.00 3.69
250 251 4.741239 TGGGGTGGGAGGAGGAGC 62.741 72.222 0.00 0.00 0.00 4.70
252 253 4.741239 GGGTGGGAGGAGGAGCCA 62.741 72.222 0.00 0.00 40.02 4.75
253 254 2.610859 GGTGGGAGGAGGAGCCAA 60.611 66.667 0.00 0.00 40.02 4.52
254 255 2.003548 GGTGGGAGGAGGAGCCAAT 61.004 63.158 0.00 0.00 40.02 3.16
255 256 1.575447 GGTGGGAGGAGGAGCCAATT 61.575 60.000 0.00 0.00 40.02 2.32
256 257 0.332972 GTGGGAGGAGGAGCCAATTT 59.667 55.000 0.00 0.00 40.02 1.82
257 258 1.564348 GTGGGAGGAGGAGCCAATTTA 59.436 52.381 0.00 0.00 40.02 1.40
258 259 2.025321 GTGGGAGGAGGAGCCAATTTAA 60.025 50.000 0.00 0.00 40.02 1.52
259 260 2.652348 TGGGAGGAGGAGCCAATTTAAA 59.348 45.455 0.00 0.00 40.02 1.52
260 261 3.272020 TGGGAGGAGGAGCCAATTTAAAT 59.728 43.478 0.00 0.00 40.02 1.40
261 262 4.480537 TGGGAGGAGGAGCCAATTTAAATA 59.519 41.667 0.01 0.00 40.02 1.40
262 263 5.043732 TGGGAGGAGGAGCCAATTTAAATAA 60.044 40.000 0.01 0.00 40.02 1.40
263 264 5.897250 GGGAGGAGGAGCCAATTTAAATAAA 59.103 40.000 0.01 0.00 40.02 1.40
264 265 6.040955 GGGAGGAGGAGCCAATTTAAATAAAG 59.959 42.308 0.01 0.00 40.02 1.85
265 266 6.461648 GGAGGAGGAGCCAATTTAAATAAAGC 60.462 42.308 0.01 5.15 40.02 3.51
266 267 6.197903 AGGAGGAGCCAATTTAAATAAAGCT 58.802 36.000 15.53 15.53 40.02 3.74
267 268 6.669591 AGGAGGAGCCAATTTAAATAAAGCTT 59.330 34.615 16.29 0.00 40.02 3.74
268 269 6.758416 GGAGGAGCCAATTTAAATAAAGCTTG 59.242 38.462 16.29 5.75 36.34 4.01
269 270 6.108687 AGGAGCCAATTTAAATAAAGCTTGC 58.891 36.000 16.29 0.00 28.40 4.01
270 271 6.070596 AGGAGCCAATTTAAATAAAGCTTGCT 60.071 34.615 16.29 0.00 28.40 3.91
271 272 6.595326 GGAGCCAATTTAAATAAAGCTTGCTT 59.405 34.615 16.29 1.55 28.40 3.91
272 273 7.368480 AGCCAATTTAAATAAAGCTTGCTTG 57.632 32.000 8.73 0.51 0.00 4.01
273 274 6.936335 AGCCAATTTAAATAAAGCTTGCTTGT 59.064 30.769 8.73 2.61 0.00 3.16
274 275 7.445096 AGCCAATTTAAATAAAGCTTGCTTGTT 59.555 29.630 8.73 4.78 0.00 2.83
275 276 8.716909 GCCAATTTAAATAAAGCTTGCTTGTTA 58.283 29.630 8.73 5.67 0.00 2.41
280 281 9.601971 TTTAAATAAAGCTTGCTTGTTAGTACG 57.398 29.630 8.73 0.00 0.00 3.67
281 282 6.796705 AATAAAGCTTGCTTGTTAGTACGT 57.203 33.333 8.73 0.00 0.00 3.57
282 283 4.727235 AAAGCTTGCTTGTTAGTACGTC 57.273 40.909 8.73 0.00 0.00 4.34
283 284 3.662247 AGCTTGCTTGTTAGTACGTCT 57.338 42.857 0.00 0.00 0.00 4.18
284 285 3.991367 AGCTTGCTTGTTAGTACGTCTT 58.009 40.909 0.00 0.00 0.00 3.01
285 286 5.130292 AGCTTGCTTGTTAGTACGTCTTA 57.870 39.130 0.00 0.00 0.00 2.10
286 287 5.535333 AGCTTGCTTGTTAGTACGTCTTAA 58.465 37.500 0.00 0.00 0.00 1.85
287 288 6.164176 AGCTTGCTTGTTAGTACGTCTTAAT 58.836 36.000 0.00 0.00 0.00 1.40
288 289 7.318141 AGCTTGCTTGTTAGTACGTCTTAATA 58.682 34.615 0.00 0.00 0.00 0.98
289 290 7.980099 AGCTTGCTTGTTAGTACGTCTTAATAT 59.020 33.333 0.00 0.00 0.00 1.28
290 291 8.601476 GCTTGCTTGTTAGTACGTCTTAATATT 58.399 33.333 0.00 0.00 0.00 1.28
297 298 9.816354 TGTTAGTACGTCTTAATATTTTACCCC 57.184 33.333 0.00 0.00 0.00 4.95
298 299 8.968242 GTTAGTACGTCTTAATATTTTACCCCG 58.032 37.037 0.00 0.00 0.00 5.73
299 300 6.515832 AGTACGTCTTAATATTTTACCCCGG 58.484 40.000 0.00 0.00 0.00 5.73
300 301 5.357742 ACGTCTTAATATTTTACCCCGGT 57.642 39.130 0.00 0.00 0.00 5.28
301 302 6.478512 ACGTCTTAATATTTTACCCCGGTA 57.521 37.500 0.00 0.00 0.00 4.02
302 303 6.280643 ACGTCTTAATATTTTACCCCGGTAC 58.719 40.000 0.00 0.00 0.00 3.34
303 304 6.098266 ACGTCTTAATATTTTACCCCGGTACT 59.902 38.462 0.00 0.00 0.00 2.73
304 305 6.642540 CGTCTTAATATTTTACCCCGGTACTC 59.357 42.308 0.00 0.00 0.00 2.59
305 306 6.931281 GTCTTAATATTTTACCCCGGTACTCC 59.069 42.308 0.00 0.00 0.00 3.85
331 332 5.433526 TGTCTAAACTGCTAGTGGTGTTTT 58.566 37.500 0.00 0.00 34.88 2.43
348 349 0.320073 TTTGTTACTGAGGCCGTCGG 60.320 55.000 6.99 6.99 37.60 4.79
351 352 0.248949 GTTACTGAGGCCGTCGGATC 60.249 60.000 17.49 12.63 35.24 3.36
480 485 1.439365 GCTGCAGAAACTTGTCGCG 60.439 57.895 20.43 0.00 0.00 5.87
481 486 1.439365 CTGCAGAAACTTGTCGCGC 60.439 57.895 8.42 0.00 0.00 6.86
482 487 1.835483 CTGCAGAAACTTGTCGCGCT 61.835 55.000 8.42 0.00 0.00 5.92
483 488 1.439365 GCAGAAACTTGTCGCGCTG 60.439 57.895 5.56 0.81 0.00 5.18
574 593 4.755437 AGGGTTCTAGTGGTGGTTACTTA 58.245 43.478 0.00 0.00 0.00 2.24
595 614 2.342650 GGAGTGGCCACGTACCGTA 61.343 63.158 29.68 0.00 38.32 4.02
611 630 1.370900 GTACGCACGAGAACACGGT 60.371 57.895 0.00 0.00 37.61 4.83
759 824 5.407407 AGAGTGACATTTACTCCGTCATT 57.593 39.130 0.00 0.00 44.35 2.57
807 875 5.185249 ACACTGAAGTAGTACGATGGAACAT 59.815 40.000 0.00 0.00 40.11 2.71
819 900 2.443958 TGGAACATGGTGTTGGTTGA 57.556 45.000 0.00 0.00 41.28 3.18
846 927 0.730265 TTTATTAAGCACGCGCCCAG 59.270 50.000 5.73 0.00 39.83 4.45
856 937 4.803908 GCGCCCAGCTAAGCCCTT 62.804 66.667 0.00 0.00 44.04 3.95
876 957 1.147557 GCGCATGGCATGGCTAAAAC 61.148 55.000 27.48 9.03 42.87 2.43
920 1155 3.997021 CCTGCCTCTATAAATAAGCCACG 59.003 47.826 0.00 0.00 0.00 4.94
954 1190 3.811083 TCTAAAACCGACCAAGAAGCAA 58.189 40.909 0.00 0.00 0.00 3.91
955 1191 4.200874 TCTAAAACCGACCAAGAAGCAAA 58.799 39.130 0.00 0.00 0.00 3.68
983 1235 3.181510 ACAAACTCACAAACGTCTCAAGC 60.182 43.478 0.00 0.00 0.00 4.01
1006 1258 0.976641 AGACAAGGAGAACATGGCGA 59.023 50.000 0.00 0.00 0.00 5.54
1014 1266 0.179100 AGAACATGGCGACCATCTCG 60.179 55.000 8.21 1.87 43.15 4.04
1148 1403 2.125912 GTGCGTCATGCTCGAGGT 60.126 61.111 15.58 0.00 46.63 3.85
1179 1434 4.016706 GGTAGTGGCAGTGGCGGT 62.017 66.667 12.58 3.99 42.47 5.68
1235 1493 2.588989 CCTGGAGGAGCTCAAGGC 59.411 66.667 17.19 0.00 43.79 4.35
1285 1543 2.527875 ATGAGATCCCGGGCCTCC 60.528 66.667 28.56 16.96 0.00 4.30
1412 1670 3.866582 GCCCATCCCGGACTGGAG 61.867 72.222 20.32 12.73 42.00 3.86
1507 1776 3.174375 GCGAAGATGGCAATGTTTTCTC 58.826 45.455 0.00 0.00 0.00 2.87
1509 1778 4.409570 CGAAGATGGCAATGTTTTCTCTG 58.590 43.478 0.00 0.00 0.00 3.35
1510 1779 3.863142 AGATGGCAATGTTTTCTCTGC 57.137 42.857 0.00 0.00 0.00 4.26
1512 1781 4.592942 AGATGGCAATGTTTTCTCTGCTA 58.407 39.130 0.00 0.00 35.13 3.49
1516 1785 6.100404 TGGCAATGTTTTCTCTGCTATTTT 57.900 33.333 0.00 0.00 35.13 1.82
1517 1786 5.927689 TGGCAATGTTTTCTCTGCTATTTTG 59.072 36.000 0.00 0.00 35.13 2.44
1519 1788 5.163923 GCAATGTTTTCTCTGCTATTTTGGC 60.164 40.000 0.00 0.00 0.00 4.52
1563 2011 8.223100 GCTTTCATGTTTTGCCTTTTATTGTAG 58.777 33.333 0.00 0.00 0.00 2.74
1581 2029 5.330648 TGTAGGGATCAGATCATCAGAGA 57.669 43.478 12.66 0.00 0.00 3.10
1720 2507 6.381801 ACGAAATCAAATCACAGAATGAACC 58.618 36.000 0.00 0.00 41.93 3.62
1730 2517 0.673644 AGAATGAACCGCCCGTGAAG 60.674 55.000 0.00 0.00 0.00 3.02
1797 2641 1.396996 CACCCGTGTGATCCGAAAATC 59.603 52.381 0.00 0.00 45.76 2.17
1822 2666 2.974148 CAGTGTGCAGCGCCTGAA 60.974 61.111 15.59 0.00 32.44 3.02
1863 2707 3.566322 ACAGTGTATCGCCTAGCTTCTAG 59.434 47.826 0.00 0.00 0.00 2.43
1885 2729 1.069906 CGTTGCACTAGTGGTTGCTTC 60.070 52.381 23.95 6.25 0.00 3.86
1933 2777 3.764810 CTGAGAGCTAGGCGCCACG 62.765 68.421 31.54 19.97 40.39 4.94
1992 2836 6.033831 CACAATGACTTAGCAATTTTTAGGCG 59.966 38.462 0.00 0.00 0.00 5.52
2058 2933 1.393539 GCGTTGCATAGTGTAGTGTGG 59.606 52.381 0.00 0.00 0.00 4.17
2060 2935 1.393539 GTTGCATAGTGTAGTGTGGCG 59.606 52.381 0.00 0.00 0.00 5.69
2093 2968 3.541632 GGAGTCACACAAAAAGGTCAGA 58.458 45.455 0.00 0.00 0.00 3.27
2127 3068 1.795768 TCACGGACAGTTCATTCTGC 58.204 50.000 0.00 0.00 38.84 4.26
2141 3082 6.583806 AGTTCATTCTGCGATTTGATTTTGTC 59.416 34.615 0.00 0.00 0.00 3.18
2149 3090 4.795962 GCGATTTGATTTTGTCCACAGGTT 60.796 41.667 0.00 0.00 0.00 3.50
2150 3091 5.563867 GCGATTTGATTTTGTCCACAGGTTA 60.564 40.000 0.00 0.00 0.00 2.85
2173 3114 3.749665 TTTGTCAAATTTGCCTGAGGG 57.250 42.857 13.54 0.00 0.00 4.30
2174 3115 2.673775 TGTCAAATTTGCCTGAGGGA 57.326 45.000 13.54 0.00 33.58 4.20
2175 3116 2.517959 TGTCAAATTTGCCTGAGGGAG 58.482 47.619 13.54 0.00 33.58 4.30
2450 4598 9.250624 GCTATTCATTTACGATGATACCCTATC 57.749 37.037 0.00 0.00 35.74 2.08
2499 4675 2.502947 TGCTCATGGCTGATCAGTTACT 59.497 45.455 23.38 4.21 42.39 2.24
2546 4723 1.074752 GAAGTGAAAGCTCGGCTCAG 58.925 55.000 0.00 0.00 38.25 3.35
2636 4862 0.475906 AACTGAAGGTGGCTGAAGCT 59.524 50.000 1.74 0.00 41.70 3.74
2637 4863 0.250640 ACTGAAGGTGGCTGAAGCTG 60.251 55.000 1.74 0.00 41.70 4.24
2638 4864 0.035881 CTGAAGGTGGCTGAAGCTGA 59.964 55.000 1.74 0.00 41.70 4.26
2639 4865 0.473755 TGAAGGTGGCTGAAGCTGAA 59.526 50.000 1.74 0.00 41.70 3.02
2640 4866 1.163554 GAAGGTGGCTGAAGCTGAAG 58.836 55.000 1.74 0.00 41.70 3.02
2641 4867 0.892814 AAGGTGGCTGAAGCTGAAGC 60.893 55.000 11.57 11.57 41.70 3.86
2667 4894 5.320549 AGAATTTGCTTACATGGCTCAAG 57.679 39.130 0.00 0.00 0.00 3.02
2668 4895 5.012239 AGAATTTGCTTACATGGCTCAAGA 58.988 37.500 0.00 0.00 0.00 3.02
2669 4896 5.655532 AGAATTTGCTTACATGGCTCAAGAT 59.344 36.000 0.00 0.00 0.00 2.40
2670 4897 6.830324 AGAATTTGCTTACATGGCTCAAGATA 59.170 34.615 0.00 0.00 0.00 1.98
2671 4898 7.504911 AGAATTTGCTTACATGGCTCAAGATAT 59.495 33.333 0.00 0.00 0.00 1.63
2672 4899 6.381481 TTTGCTTACATGGCTCAAGATATG 57.619 37.500 0.00 0.00 0.00 1.78
2673 4900 5.039920 TGCTTACATGGCTCAAGATATGT 57.960 39.130 0.00 0.00 37.51 2.29
2675 4902 6.591001 TGCTTACATGGCTCAAGATATGTTA 58.409 36.000 0.00 0.00 35.55 2.41
2694 4924 6.025749 TGTTATATACCGAGGAGATGCTTG 57.974 41.667 0.00 0.00 0.00 4.01
2726 4956 6.100004 CGCTATCGGGATAACATAACAGATT 58.900 40.000 0.00 0.00 0.00 2.40
2823 5053 4.201628 CGTCGTCTGAGCTTTAATGAAAGG 60.202 45.833 4.66 0.00 42.12 3.11
2836 5072 4.715527 AATGAAAGGATCAGAAGCTTGC 57.284 40.909 2.10 0.00 42.53 4.01
2914 5170 5.918608 TCTTCCTTGTAATGATCACTAGGC 58.081 41.667 0.00 0.00 38.37 3.93
2922 5178 0.901827 TGATCACTAGGCGCTCCAAA 59.098 50.000 7.64 0.00 33.74 3.28
2924 5180 2.698274 TGATCACTAGGCGCTCCAAATA 59.302 45.455 7.64 0.00 33.74 1.40
2965 5221 3.505680 TGAGCTTTGCAAATATGTCGGTT 59.494 39.130 13.23 0.00 0.00 4.44
3148 5504 3.691049 GCTTAACAGCAAGTTGTGTCA 57.309 42.857 4.48 0.00 46.49 3.58
3149 5505 4.027572 GCTTAACAGCAAGTTGTGTCAA 57.972 40.909 4.48 0.15 46.49 3.18
3245 5610 8.195436 GGTGACATAACTAACTGAGCACTATTA 58.805 37.037 0.00 0.00 0.00 0.98
3261 5626 7.328737 AGCACTATTAACCGAAATAAGACAGT 58.671 34.615 0.00 0.00 0.00 3.55
3275 5640 2.625639 AGACAGTGGATCCCTTCAACT 58.374 47.619 9.90 2.14 39.36 3.16
3280 5645 4.163078 ACAGTGGATCCCTTCAACTCATAG 59.837 45.833 9.90 0.00 36.40 2.23
3336 6054 6.316390 GGACGTTCATGAAATAAGTTCCAGAT 59.684 38.462 10.35 0.00 35.12 2.90
3402 6157 5.827797 ACTCAAGATTTCTGCAACCAAACTA 59.172 36.000 0.00 0.00 0.00 2.24
3418 6173 8.621286 CAACCAAACTAGTTGAATAAACTCTGT 58.379 33.333 9.34 0.00 46.60 3.41
3500 6261 1.374125 CACACACGGATCGAAGCCA 60.374 57.895 8.23 0.00 0.00 4.75
3513 6274 2.475371 GAAGCCAGAGCCCTGCAGAA 62.475 60.000 17.39 0.00 41.25 3.02
3562 6323 7.703328 ACGATCTGTTAAAAACACAATCACTT 58.297 30.769 0.00 0.00 36.25 3.16
3570 6331 2.995466 ACACAATCACTTCGGCAATG 57.005 45.000 0.00 0.00 0.00 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.359169 TGGATCTGGTGTCTCGGCC 61.359 63.158 0.00 0.00 0.00 6.13
41 42 4.440127 CCATTGGCAAGGCACGGC 62.440 66.667 6.33 0.00 0.00 5.68
42 43 2.676121 TCCATTGGCAAGGCACGG 60.676 61.111 6.33 0.28 0.00 4.94
43 44 2.879907 CTCCATTGGCAAGGCACG 59.120 61.111 6.33 0.00 0.00 5.34
44 45 2.575461 GCTCCATTGGCAAGGCAC 59.425 61.111 6.33 0.00 0.00 5.01
45 46 2.681064 GGCTCCATTGGCAAGGCA 60.681 61.111 6.33 0.00 35.78 4.75
46 47 3.830192 CGGCTCCATTGGCAAGGC 61.830 66.667 6.33 3.22 0.00 4.35
47 48 3.830192 GCGGCTCCATTGGCAAGG 61.830 66.667 5.96 5.28 0.00 3.61
48 49 3.830192 GGCGGCTCCATTGGCAAG 61.830 66.667 5.96 0.00 34.01 4.01
61 62 4.598894 CTGGATCTGGAGCGGCGG 62.599 72.222 9.78 0.00 0.00 6.13
62 63 4.598894 CCTGGATCTGGAGCGGCG 62.599 72.222 0.51 0.51 0.00 6.46
63 64 4.247380 CCCTGGATCTGGAGCGGC 62.247 72.222 0.00 0.00 0.00 6.53
64 65 2.317149 GAACCCTGGATCTGGAGCGG 62.317 65.000 0.00 1.68 0.00 5.52
65 66 1.144936 GAACCCTGGATCTGGAGCG 59.855 63.158 0.00 0.00 0.00 5.03
66 67 1.529309 GGAACCCTGGATCTGGAGC 59.471 63.158 0.00 0.00 0.00 4.70
80 81 2.359850 TGCATCTGCGTGGGGAAC 60.360 61.111 0.00 0.00 45.83 3.62
81 82 2.046023 CTGCATCTGCGTGGGGAA 60.046 61.111 0.00 0.00 45.83 3.97
82 83 4.100084 CCTGCATCTGCGTGGGGA 62.100 66.667 6.24 0.00 45.83 4.81
86 87 3.057548 TTGCCCTGCATCTGCGTG 61.058 61.111 0.00 0.00 45.83 5.34
87 88 3.058160 GTTGCCCTGCATCTGCGT 61.058 61.111 0.00 0.00 45.83 5.24
88 89 3.818787 GGTTGCCCTGCATCTGCG 61.819 66.667 0.00 0.00 45.83 5.18
89 90 3.818787 CGGTTGCCCTGCATCTGC 61.819 66.667 0.00 0.00 38.76 4.26
90 91 2.046023 TCGGTTGCCCTGCATCTG 60.046 61.111 0.00 0.55 38.76 2.90
91 92 2.270205 CTCGGTTGCCCTGCATCT 59.730 61.111 0.00 0.00 38.76 2.90
92 93 2.825836 CCTCGGTTGCCCTGCATC 60.826 66.667 0.00 0.00 38.76 3.91
163 164 4.840005 CTTCCCTTCCTCGCCGCC 62.840 72.222 0.00 0.00 0.00 6.13
164 165 4.840005 CCTTCCCTTCCTCGCCGC 62.840 72.222 0.00 0.00 0.00 6.53
165 166 4.162690 CCCTTCCCTTCCTCGCCG 62.163 72.222 0.00 0.00 0.00 6.46
166 167 3.798511 CCCCTTCCCTTCCTCGCC 61.799 72.222 0.00 0.00 0.00 5.54
167 168 3.798511 CCCCCTTCCCTTCCTCGC 61.799 72.222 0.00 0.00 0.00 5.03
182 183 4.364686 TCCTCACCCCCTTCCCCC 62.365 72.222 0.00 0.00 0.00 5.40
183 184 2.692741 CTCCTCACCCCCTTCCCC 60.693 72.222 0.00 0.00 0.00 4.81
184 185 2.692741 CCTCCTCACCCCCTTCCC 60.693 72.222 0.00 0.00 0.00 3.97
185 186 1.690985 CTCCTCCTCACCCCCTTCC 60.691 68.421 0.00 0.00 0.00 3.46
186 187 1.690985 CCTCCTCCTCACCCCCTTC 60.691 68.421 0.00 0.00 0.00 3.46
187 188 2.456840 CCTCCTCCTCACCCCCTT 59.543 66.667 0.00 0.00 0.00 3.95
188 189 3.700350 CCCTCCTCCTCACCCCCT 61.700 72.222 0.00 0.00 0.00 4.79
189 190 4.825679 CCCCTCCTCCTCACCCCC 62.826 77.778 0.00 0.00 0.00 5.40
195 196 4.541648 TAGCCGCCCCTCCTCCTC 62.542 72.222 0.00 0.00 0.00 3.71
196 197 4.548513 CTAGCCGCCCCTCCTCCT 62.549 72.222 0.00 0.00 0.00 3.69
201 202 4.176752 CAACCCTAGCCGCCCCTC 62.177 72.222 0.00 0.00 0.00 4.30
205 206 4.176752 CTCCCAACCCTAGCCGCC 62.177 72.222 0.00 0.00 0.00 6.13
206 207 4.176752 CCTCCCAACCCTAGCCGC 62.177 72.222 0.00 0.00 0.00 6.53
207 208 2.365105 TCCTCCCAACCCTAGCCG 60.365 66.667 0.00 0.00 0.00 5.52
208 209 2.073101 CCTCCTCCCAACCCTAGCC 61.073 68.421 0.00 0.00 0.00 3.93
209 210 1.003051 TCCTCCTCCCAACCCTAGC 59.997 63.158 0.00 0.00 0.00 3.42
210 211 1.051556 GCTCCTCCTCCCAACCCTAG 61.052 65.000 0.00 0.00 0.00 3.02
211 212 1.003051 GCTCCTCCTCCCAACCCTA 59.997 63.158 0.00 0.00 0.00 3.53
212 213 2.285743 GCTCCTCCTCCCAACCCT 60.286 66.667 0.00 0.00 0.00 4.34
213 214 3.787001 CGCTCCTCCTCCCAACCC 61.787 72.222 0.00 0.00 0.00 4.11
214 215 3.787001 CCGCTCCTCCTCCCAACC 61.787 72.222 0.00 0.00 0.00 3.77
215 216 4.475135 GCCGCTCCTCCTCCCAAC 62.475 72.222 0.00 0.00 0.00 3.77
216 217 4.722535 AGCCGCTCCTCCTCCCAA 62.723 66.667 0.00 0.00 0.00 4.12
231 232 4.741239 TCCTCCTCCCACCCCAGC 62.741 72.222 0.00 0.00 0.00 4.85
232 233 2.366167 CTCCTCCTCCCACCCCAG 60.366 72.222 0.00 0.00 0.00 4.45
233 234 4.741239 GCTCCTCCTCCCACCCCA 62.741 72.222 0.00 0.00 0.00 4.96
235 236 4.741239 TGGCTCCTCCTCCCACCC 62.741 72.222 0.00 0.00 35.26 4.61
236 237 1.575447 AATTGGCTCCTCCTCCCACC 61.575 60.000 0.00 0.00 35.26 4.61
237 238 0.332972 AAATTGGCTCCTCCTCCCAC 59.667 55.000 0.00 0.00 35.26 4.61
238 239 1.979809 TAAATTGGCTCCTCCTCCCA 58.020 50.000 0.00 0.00 35.26 4.37
239 240 3.382083 TTTAAATTGGCTCCTCCTCCC 57.618 47.619 0.00 0.00 35.26 4.30
240 241 6.461648 GCTTTATTTAAATTGGCTCCTCCTCC 60.462 42.308 5.91 0.00 35.26 4.30
241 242 6.322456 AGCTTTATTTAAATTGGCTCCTCCTC 59.678 38.462 5.91 0.00 35.26 3.71
242 243 6.197903 AGCTTTATTTAAATTGGCTCCTCCT 58.802 36.000 5.91 0.00 35.26 3.69
243 244 6.471233 AGCTTTATTTAAATTGGCTCCTCC 57.529 37.500 5.91 0.00 0.00 4.30
244 245 6.256539 GCAAGCTTTATTTAAATTGGCTCCTC 59.743 38.462 5.91 4.01 0.00 3.71
245 246 6.070596 AGCAAGCTTTATTTAAATTGGCTCCT 60.071 34.615 5.91 10.09 0.00 3.69
246 247 6.108687 AGCAAGCTTTATTTAAATTGGCTCC 58.891 36.000 5.91 8.42 0.00 4.70
247 248 7.118245 ACAAGCAAGCTTTATTTAAATTGGCTC 59.882 33.333 5.91 3.92 33.42 4.70
248 249 6.936335 ACAAGCAAGCTTTATTTAAATTGGCT 59.064 30.769 5.91 10.46 33.42 4.75
249 250 7.132694 ACAAGCAAGCTTTATTTAAATTGGC 57.867 32.000 5.91 8.48 33.42 4.52
254 255 9.601971 CGTACTAACAAGCAAGCTTTATTTAAA 57.398 29.630 4.24 0.00 33.42 1.52
255 256 8.776470 ACGTACTAACAAGCAAGCTTTATTTAA 58.224 29.630 4.24 0.00 33.42 1.52
256 257 8.314143 ACGTACTAACAAGCAAGCTTTATTTA 57.686 30.769 4.24 2.97 33.42 1.40
257 258 7.172703 AGACGTACTAACAAGCAAGCTTTATTT 59.827 33.333 4.24 1.95 33.42 1.40
258 259 6.649557 AGACGTACTAACAAGCAAGCTTTATT 59.350 34.615 4.24 5.55 33.42 1.40
259 260 6.164176 AGACGTACTAACAAGCAAGCTTTAT 58.836 36.000 4.24 0.00 33.42 1.40
260 261 5.535333 AGACGTACTAACAAGCAAGCTTTA 58.465 37.500 4.24 0.00 33.42 1.85
261 262 4.377897 AGACGTACTAACAAGCAAGCTTT 58.622 39.130 4.24 0.00 33.42 3.51
262 263 3.991367 AGACGTACTAACAAGCAAGCTT 58.009 40.909 0.59 0.59 36.60 3.74
263 264 3.662247 AGACGTACTAACAAGCAAGCT 57.338 42.857 0.00 0.00 0.00 3.74
264 265 5.834239 TTAAGACGTACTAACAAGCAAGC 57.166 39.130 0.00 0.00 0.00 4.01
271 272 9.816354 GGGGTAAAATATTAAGACGTACTAACA 57.184 33.333 0.00 0.00 0.00 2.41
272 273 8.968242 CGGGGTAAAATATTAAGACGTACTAAC 58.032 37.037 0.00 0.00 0.00 2.34
273 274 8.141268 CCGGGGTAAAATATTAAGACGTACTAA 58.859 37.037 0.00 0.00 0.00 2.24
274 275 7.286775 ACCGGGGTAAAATATTAAGACGTACTA 59.713 37.037 6.32 0.00 0.00 1.82
275 276 6.098266 ACCGGGGTAAAATATTAAGACGTACT 59.902 38.462 6.32 0.00 0.00 2.73
276 277 6.280643 ACCGGGGTAAAATATTAAGACGTAC 58.719 40.000 6.32 0.00 0.00 3.67
277 278 6.478512 ACCGGGGTAAAATATTAAGACGTA 57.521 37.500 6.32 0.00 0.00 3.57
278 279 5.357742 ACCGGGGTAAAATATTAAGACGT 57.642 39.130 6.32 0.00 0.00 4.34
279 280 6.515832 AGTACCGGGGTAAAATATTAAGACG 58.484 40.000 6.32 0.00 31.86 4.18
280 281 6.931281 GGAGTACCGGGGTAAAATATTAAGAC 59.069 42.308 6.32 0.00 31.86 3.01
281 282 7.066307 GGAGTACCGGGGTAAAATATTAAGA 57.934 40.000 6.32 0.00 31.86 2.10
298 299 3.130693 AGCAGTTTAGACATCGGAGTACC 59.869 47.826 0.00 0.00 0.00 3.34
299 300 4.373348 AGCAGTTTAGACATCGGAGTAC 57.627 45.455 0.00 0.00 0.00 2.73
300 301 5.066117 CACTAGCAGTTTAGACATCGGAGTA 59.934 44.000 0.00 0.00 0.00 2.59
301 302 4.017808 ACTAGCAGTTTAGACATCGGAGT 58.982 43.478 0.00 0.00 0.00 3.85
302 303 4.355437 CACTAGCAGTTTAGACATCGGAG 58.645 47.826 0.00 0.00 0.00 4.63
303 304 3.130516 CCACTAGCAGTTTAGACATCGGA 59.869 47.826 0.00 0.00 0.00 4.55
304 305 3.119101 ACCACTAGCAGTTTAGACATCGG 60.119 47.826 0.00 0.00 0.00 4.18
305 306 3.859961 CACCACTAGCAGTTTAGACATCG 59.140 47.826 0.00 0.00 0.00 3.84
306 307 4.822026 ACACCACTAGCAGTTTAGACATC 58.178 43.478 0.00 0.00 0.00 3.06
307 308 4.891992 ACACCACTAGCAGTTTAGACAT 57.108 40.909 0.00 0.00 0.00 3.06
308 309 4.682778 AACACCACTAGCAGTTTAGACA 57.317 40.909 0.00 0.00 0.00 3.41
309 310 5.296035 ACAAAACACCACTAGCAGTTTAGAC 59.704 40.000 0.00 0.00 33.45 2.59
310 311 5.433526 ACAAAACACCACTAGCAGTTTAGA 58.566 37.500 0.00 0.00 33.45 2.10
311 312 5.751243 ACAAAACACCACTAGCAGTTTAG 57.249 39.130 0.00 0.00 33.45 1.85
312 313 6.824704 AGTAACAAAACACCACTAGCAGTTTA 59.175 34.615 0.00 0.00 33.45 2.01
313 314 5.650703 AGTAACAAAACACCACTAGCAGTTT 59.349 36.000 0.00 0.00 35.87 2.66
314 315 5.065988 CAGTAACAAAACACCACTAGCAGTT 59.934 40.000 0.00 0.00 0.00 3.16
315 316 4.574828 CAGTAACAAAACACCACTAGCAGT 59.425 41.667 0.00 0.00 0.00 4.40
316 317 4.814234 TCAGTAACAAAACACCACTAGCAG 59.186 41.667 0.00 0.00 0.00 4.24
331 332 0.968901 ATCCGACGGCCTCAGTAACA 60.969 55.000 9.66 0.00 0.00 2.41
430 431 5.221165 GCTCTTTTACTTTTACTTGCACCCA 60.221 40.000 0.00 0.00 0.00 4.51
480 485 1.451028 GTGATCACTCCCAGCCAGC 60.451 63.158 18.83 0.00 0.00 4.85
481 486 1.153489 CGTGATCACTCCCAGCCAG 60.153 63.158 22.95 0.89 0.00 4.85
482 487 0.977627 ATCGTGATCACTCCCAGCCA 60.978 55.000 22.95 0.00 0.00 4.75
483 488 0.531532 CATCGTGATCACTCCCAGCC 60.532 60.000 22.95 0.00 0.00 4.85
491 496 1.662629 CCTCAGCAACATCGTGATCAC 59.337 52.381 16.21 16.21 0.00 3.06
492 497 1.405933 CCCTCAGCAACATCGTGATCA 60.406 52.381 0.00 0.00 0.00 2.92
527 546 4.120589 AGAAAACACAACTCGAACTCCTC 58.879 43.478 0.00 0.00 0.00 3.71
536 555 6.694877 AGAACCCTAAAGAAAACACAACTC 57.305 37.500 0.00 0.00 0.00 3.01
574 593 2.341176 GTACGTGGCCACTCCGTT 59.659 61.111 32.28 14.05 37.80 4.44
595 614 2.354305 GACCGTGTTCTCGTGCGT 60.354 61.111 0.00 0.00 0.00 5.24
599 618 3.048602 CAGGGACCGTGTTCTCGT 58.951 61.111 6.00 0.00 0.00 4.18
607 626 3.731728 ATGCATGGCAGGGACCGT 61.732 61.111 0.00 0.00 43.65 4.83
725 790 1.986757 TCACTCTCCTCCTGCTGCC 60.987 63.158 0.00 0.00 0.00 4.85
726 791 1.217779 GTCACTCTCCTCCTGCTGC 59.782 63.158 0.00 0.00 0.00 5.25
729 794 2.777832 AAATGTCACTCTCCTCCTGC 57.222 50.000 0.00 0.00 0.00 4.85
733 798 3.444388 ACGGAGTAAATGTCACTCTCCTC 59.556 47.826 0.00 0.00 41.94 3.71
819 900 4.155449 CGCGTGCTTAATAAACAATGTGT 58.845 39.130 0.00 0.00 0.00 3.72
822 903 2.529894 GGCGCGTGCTTAATAAACAATG 59.470 45.455 21.89 0.00 42.25 2.82
826 907 0.448593 TGGGCGCGTGCTTAATAAAC 59.551 50.000 21.89 0.54 42.25 2.01
846 927 2.410469 CATGCGCAAGGGCTTAGC 59.590 61.111 17.11 0.00 38.10 3.09
954 1190 3.190535 ACGTTTGTGAGTTTGTCTGCTTT 59.809 39.130 0.00 0.00 0.00 3.51
955 1191 2.747446 ACGTTTGTGAGTTTGTCTGCTT 59.253 40.909 0.00 0.00 0.00 3.91
983 1235 2.160417 GCCATGTTCTCCTTGTCTTTCG 59.840 50.000 0.00 0.00 0.00 3.46
1006 1258 0.629596 TAGGAGGTGGACGAGATGGT 59.370 55.000 0.00 0.00 0.00 3.55
1014 1266 2.380941 GAGGAGAAGTAGGAGGTGGAC 58.619 57.143 0.00 0.00 0.00 4.02
1148 1403 0.034380 ACTACCAGAGGCAGCGTCTA 60.034 55.000 17.16 1.74 0.00 2.59
1412 1670 1.759459 CTTACCAGGGCCGGAGATCC 61.759 65.000 19.10 0.00 0.00 3.36
1507 1776 0.447801 AGTTCGCGCCAAAATAGCAG 59.552 50.000 0.00 0.00 0.00 4.24
1509 1778 0.727398 AGAGTTCGCGCCAAAATAGC 59.273 50.000 0.00 0.00 0.00 2.97
1510 1779 2.029728 CAGAGAGTTCGCGCCAAAATAG 59.970 50.000 0.00 0.00 0.00 1.73
1512 1781 0.798776 CAGAGAGTTCGCGCCAAAAT 59.201 50.000 0.00 0.00 0.00 1.82
1516 1785 0.315886 TAAACAGAGAGTTCGCGCCA 59.684 50.000 0.00 0.00 40.26 5.69
1517 1786 1.324736 CATAAACAGAGAGTTCGCGCC 59.675 52.381 0.00 0.00 40.26 6.53
1519 1788 2.263077 AGCATAAACAGAGAGTTCGCG 58.737 47.619 0.00 0.00 40.26 5.87
1563 2011 4.588106 TCAACTCTCTGATGATCTGATCCC 59.412 45.833 14.71 7.54 0.00 3.85
1581 2029 8.744568 AAAGAAACAGAGAGAGAAAATCAACT 57.255 30.769 0.00 0.00 0.00 3.16
1720 2507 2.762360 TGAAATAGCTTCACGGGCG 58.238 52.632 0.00 0.00 39.20 6.13
1730 2517 1.348594 GTCAGCCGCGTGAAATAGC 59.651 57.895 4.92 0.00 0.00 2.97
1775 2619 2.384653 TTTCGGATCACACGGGTGCA 62.385 55.000 14.50 2.22 44.87 4.57
1863 2707 1.574428 CAACCACTAGTGCAACGCC 59.426 57.895 17.86 0.00 45.86 5.68
1885 2729 5.451908 CACTAGTGGTTGCACTACAAAATG 58.548 41.667 15.49 0.00 40.82 2.32
1933 2777 0.032130 TAGGCGCTGCACTGTATAGC 59.968 55.000 7.64 5.63 0.00 2.97
1964 2808 6.774354 AAAAATTGCTAAGTCATTGTGCAG 57.226 33.333 0.00 0.00 33.13 4.41
1992 2836 4.643387 AGCGTTGCACCCCAGACC 62.643 66.667 0.00 0.00 0.00 3.85
2060 2935 2.126031 GACTCCCGACACGAAGGC 60.126 66.667 0.00 0.00 0.00 4.35
2074 2949 2.936498 CGTCTGACCTTTTTGTGTGACT 59.064 45.455 1.55 0.00 0.00 3.41
2127 3068 4.503741 ACCTGTGGACAAAATCAAATCG 57.496 40.909 0.00 0.00 0.00 3.34
2141 3082 7.131565 GCAAATTTGACAAATTTAACCTGTGG 58.868 34.615 29.34 18.99 46.34 4.17
2149 3090 6.042552 TCCCTCAGGCAAATTTGACAAATTTA 59.957 34.615 29.34 17.47 46.34 1.40
2173 3114 1.902508 TGTGACTTGAGTGGGGATCTC 59.097 52.381 0.00 0.00 0.00 2.75
2174 3115 2.030027 TGTGACTTGAGTGGGGATCT 57.970 50.000 0.00 0.00 0.00 2.75
2175 3116 2.420687 GGATGTGACTTGAGTGGGGATC 60.421 54.545 0.00 0.00 0.00 3.36
2285 4426 6.935208 GGGTAATTATGTGTTGGAGATAGGAC 59.065 42.308 0.00 0.00 0.00 3.85
2290 4431 5.994416 AGGGGTAATTATGTGTTGGAGAT 57.006 39.130 0.00 0.00 0.00 2.75
2369 4513 8.893727 ACTGCTGGTTTTGTATGAAGATATAAC 58.106 33.333 0.00 0.00 0.00 1.89
2407 4555 5.474532 TGAATAGCAAATCAAACACAGCTCT 59.525 36.000 0.00 0.00 33.83 4.09
2499 4675 1.350684 TCATCACCTGCAAAGCCAGTA 59.649 47.619 0.00 0.00 0.00 2.74
2508 4685 1.522092 GTCGGGATCATCACCTGCA 59.478 57.895 0.00 0.00 34.13 4.41
2546 4723 1.453155 CACTGTCTGTGCCCAATACC 58.547 55.000 0.00 0.00 40.06 2.73
2595 4772 1.027357 GCCCATCTTAGCACACATGG 58.973 55.000 0.00 0.00 36.32 3.66
2636 4862 6.384224 CATGTAAGCAAATTCTTCAGCTTCA 58.616 36.000 1.40 2.05 45.28 3.02
2637 4863 5.803967 CCATGTAAGCAAATTCTTCAGCTTC 59.196 40.000 1.40 0.00 45.28 3.86
2639 4865 4.381292 GCCATGTAAGCAAATTCTTCAGCT 60.381 41.667 0.00 0.00 39.37 4.24
2640 4866 3.861689 GCCATGTAAGCAAATTCTTCAGC 59.138 43.478 0.00 0.00 0.00 4.26
2641 4867 5.106038 TGAGCCATGTAAGCAAATTCTTCAG 60.106 40.000 0.00 0.00 0.00 3.02
2650 4877 5.439721 ACATATCTTGAGCCATGTAAGCAA 58.560 37.500 0.00 0.00 30.04 3.91
2667 4894 8.172352 AGCATCTCCTCGGTATATAACATATC 57.828 38.462 0.00 0.00 0.00 1.63
2668 4895 8.417106 CAAGCATCTCCTCGGTATATAACATAT 58.583 37.037 0.00 0.00 0.00 1.78
2669 4896 7.147897 CCAAGCATCTCCTCGGTATATAACATA 60.148 40.741 0.00 0.00 0.00 2.29
2670 4897 6.351371 CCAAGCATCTCCTCGGTATATAACAT 60.351 42.308 0.00 0.00 0.00 2.71
2671 4898 5.047306 CCAAGCATCTCCTCGGTATATAACA 60.047 44.000 0.00 0.00 0.00 2.41
2672 4899 5.411781 CCAAGCATCTCCTCGGTATATAAC 58.588 45.833 0.00 0.00 0.00 1.89
2673 4900 4.466370 CCCAAGCATCTCCTCGGTATATAA 59.534 45.833 0.00 0.00 0.00 0.98
2675 4902 2.834549 CCCAAGCATCTCCTCGGTATAT 59.165 50.000 0.00 0.00 0.00 0.86
2726 4956 2.357637 CTGAAGTTTTCGGAAAGCACCA 59.642 45.455 17.68 13.23 38.34 4.17
2800 5030 4.201628 CCTTTCATTAAAGCTCAGACGACG 60.202 45.833 0.00 0.00 40.73 5.12
2823 5053 2.012673 ACGAATGGCAAGCTTCTGATC 58.987 47.619 0.00 0.00 0.00 2.92
2836 5072 5.005394 CGTTTAGAACACCTATGACGAATGG 59.995 44.000 0.00 0.00 38.47 3.16
2914 5170 3.544048 CGCAGTACAACATATTTGGAGCG 60.544 47.826 0.00 0.00 0.00 5.03
2922 5178 2.985896 ACTTGGCGCAGTACAACATAT 58.014 42.857 10.83 0.00 0.00 1.78
2924 5180 1.266718 CAACTTGGCGCAGTACAACAT 59.733 47.619 10.83 0.00 0.00 2.71
2965 5221 3.370840 AAGCCATACTTGAGCCAATCA 57.629 42.857 0.00 0.00 37.17 2.57
3013 5279 8.798859 ATACATTGTCTACTCTTTCAAAGCAT 57.201 30.769 0.00 0.00 0.00 3.79
3221 5586 9.582431 GTTAATAGTGCTCAGTTAGTTATGTCA 57.418 33.333 0.00 0.00 0.00 3.58
3245 5610 4.514401 GGATCCACTGTCTTATTTCGGTT 58.486 43.478 6.95 0.00 0.00 4.44
3261 5626 6.043243 GGTAATCTATGAGTTGAAGGGATCCA 59.957 42.308 15.23 0.00 0.00 3.41
3275 5640 1.618837 GAGCCGCCAGGTAATCTATGA 59.381 52.381 0.00 0.00 40.50 2.15
3280 5645 2.280186 CCGAGCCGCCAGGTAATC 60.280 66.667 0.00 0.00 40.50 1.75
3303 5745 7.987458 ACTTATTTCATGAACGTCCTATGATGT 59.013 33.333 7.89 0.00 42.59 3.06
3418 6173 2.745884 CGGCTGGAATCGGTTGCA 60.746 61.111 1.62 1.62 34.32 4.08
3437 6192 1.825090 CTTATGGCCTCTGTGTGCAA 58.175 50.000 3.32 0.00 0.00 4.08
3486 6247 1.880340 GCTCTGGCTTCGATCCGTG 60.880 63.158 0.00 0.00 35.22 4.94
3500 6261 0.251077 CAGGTTTTCTGCAGGGCTCT 60.251 55.000 15.13 2.89 36.60 4.09
3513 6274 4.388577 ACTCCTAATTCCTTGCAGGTTT 57.611 40.909 0.00 0.00 36.53 3.27
3524 6285 9.798994 TTTTAACAGATCGTCTACTCCTAATTC 57.201 33.333 0.00 0.00 0.00 2.17
3533 6294 8.492748 TGATTGTGTTTTTAACAGATCGTCTAC 58.507 33.333 0.00 0.00 43.10 2.59
3570 6331 4.295051 ACACGACATAACAAAAACATGGC 58.705 39.130 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.