Multiple sequence alignment - TraesCS2A01G084500

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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 TraesCS2A01G084500 chr2A 100.000 2730 0 0 1 2730 38811159 38813888 0.000000e+00 5042.0
1 TraesCS2A01G084500 chr2A 90.628 1227 63 16 486 1700 38754556 38755742 0.000000e+00 1581.0
2 TraesCS2A01G084500 chr2A 94.754 896 46 1 1836 2730 751946496 751945601 0.000000e+00 1393.0
3 TraesCS2A01G084500 chr2A 94.488 635 34 1 2097 2730 691537537 691538171 0.000000e+00 977.0
4 TraesCS2A01G084500 chr2A 82.721 926 94 32 816 1691 38908438 38909347 0.000000e+00 763.0
5 TraesCS2A01G084500 chr2A 83.819 686 79 11 888 1560 38878849 38879515 8.300000e-175 623.0
6 TraesCS2A01G084500 chr2A 92.233 206 10 4 221 421 605033408 605033612 1.240000e-73 287.0
7 TraesCS2A01G084500 chr2A 92.195 205 10 4 222 421 413332950 413333153 4.450000e-73 285.0
8 TraesCS2A01G084500 chr2A 92.174 115 4 1 594 703 38908247 38908361 1.010000e-34 158.0
9 TraesCS2A01G084500 chr2A 97.403 77 2 0 409 485 756106458 756106382 6.130000e-27 132.0
10 TraesCS2A01G084500 chr2A 96.104 77 3 0 409 485 193545695 193545619 2.850000e-25 126.0
11 TraesCS2A01G084500 chr2A 96.104 77 3 0 409 485 605033742 605033818 2.850000e-25 126.0
12 TraesCS2A01G084500 chr2A 96.053 76 3 0 409 484 251826823 251826898 1.030000e-24 124.0
13 TraesCS2A01G084500 chr2D 88.263 1261 84 34 486 1700 35531336 35532578 0.000000e+00 1450.0
14 TraesCS2A01G084500 chr2D 87.536 698 58 19 994 1675 35639069 35639753 0.000000e+00 780.0
15 TraesCS2A01G084500 chr2D 95.533 291 13 0 996 1286 35564373 35564663 1.480000e-127 466.0
16 TraesCS2A01G084500 chr2D 87.562 402 35 7 486 885 42092137 42091749 4.150000e-123 451.0
17 TraesCS2A01G084500 chr2D 84.878 410 40 11 1376 1781 35564738 35565129 7.090000e-106 394.0
18 TraesCS2A01G084500 chr2D 82.367 431 58 13 1293 1706 42075347 42074918 2.580000e-95 359.0
19 TraesCS2A01G084500 chr2D 95.872 218 8 1 1044 1260 42076260 42076043 4.330000e-93 351.0
20 TraesCS2A01G084500 chr2D 89.189 222 22 2 1 221 35531124 35531344 2.680000e-70 276.0
21 TraesCS2A01G084500 chr2D 83.030 165 18 6 513 677 35677342 35677496 1.020000e-29 141.0
22 TraesCS2A01G084500 chr2D 88.182 110 9 2 594 703 35638646 35638751 7.930000e-26 128.0
23 TraesCS2A01G084500 chr6A 94.754 896 41 2 1836 2730 573401753 573400863 0.000000e+00 1389.0
24 TraesCS2A01G084500 chr6A 93.714 859 52 2 1836 2693 124263162 124264019 0.000000e+00 1286.0
25 TraesCS2A01G084500 chr6A 92.195 205 11 4 220 421 384029731 384029933 4.450000e-73 285.0
26 TraesCS2A01G084500 chr4A 92.189 909 43 4 1836 2730 583725849 583724955 0.000000e+00 1260.0
27 TraesCS2A01G084500 chr1A 91.527 897 69 4 1836 2730 543057628 543056737 0.000000e+00 1229.0
28 TraesCS2A01G084500 chr1A 94.872 78 4 0 409 486 51979984 51980061 3.690000e-24 122.0
29 TraesCS2A01G084500 chr3B 90.279 895 86 1 1836 2729 578287628 578286734 0.000000e+00 1170.0
30 TraesCS2A01G084500 chr5B 90.842 819 70 3 1899 2716 705898720 705899534 0.000000e+00 1092.0
31 TraesCS2A01G084500 chr1D 91.983 711 54 3 1956 2664 447228189 447227480 0.000000e+00 994.0
32 TraesCS2A01G084500 chr1D 94.262 122 7 0 1837 1958 447241311 447241190 1.290000e-43 187.0
33 TraesCS2A01G084500 chr2B 84.736 891 101 22 805 1665 58825999 58826884 0.000000e+00 859.0
34 TraesCS2A01G084500 chr2B 82.545 951 115 31 790 1700 58689219 58690158 0.000000e+00 789.0
35 TraesCS2A01G084500 chr2B 86.815 584 50 15 997 1560 58791520 58792096 6.420000e-176 627.0
36 TraesCS2A01G084500 chr2B 90.546 476 39 3 811 1286 58773222 58773691 2.310000e-175 625.0
37 TraesCS2A01G084500 chr2B 89.916 238 11 3 1556 1781 58792175 58792411 7.390000e-76 294.0
38 TraesCS2A01G084500 chr2B 92.195 205 10 4 222 421 798805070 798804867 4.450000e-73 285.0
39 TraesCS2A01G084500 chr2B 88.745 231 18 4 486 713 58772921 58773146 2.680000e-70 276.0
40 TraesCS2A01G084500 chr2B 87.013 231 18 4 486 713 58688974 58689195 1.620000e-62 250.0
41 TraesCS2A01G084500 chr2B 82.990 194 14 3 33 221 58688803 58688982 1.010000e-34 158.0
42 TraesCS2A01G084500 chr5D 90.741 594 49 2 2137 2729 505911011 505910423 0.000000e+00 787.0
43 TraesCS2A01G084500 chr5D 93.916 263 16 0 1845 2107 505915702 505915440 5.480000e-107 398.0
44 TraesCS2A01G084500 chr7A 93.171 205 8 4 222 421 34516640 34516437 2.060000e-76 296.0
45 TraesCS2A01G084500 chr7A 92.308 208 10 5 219 421 34967439 34967645 9.560000e-75 291.0
46 TraesCS2A01G084500 chr7A 91.707 205 11 4 222 421 636888006 636887803 2.070000e-71 279.0
47 TraesCS2A01G084500 chr7A 97.368 76 2 0 410 485 73939152 73939227 2.210000e-26 130.0
48 TraesCS2A01G084500 chr7A 96.154 78 3 0 409 486 34516309 34516232 7.930000e-26 128.0
49 TraesCS2A01G084500 chr7A 96.104 77 3 0 409 485 647184753 647184829 2.850000e-25 126.0
50 TraesCS2A01G084500 chr3D 92.683 205 9 4 222 421 582214251 582214048 9.560000e-75 291.0
51 TraesCS2A01G084500 chr3D 91.209 91 6 2 409 497 582213918 582213828 3.690000e-24 122.0
52 TraesCS2A01G084500 chr5A 91.787 207 10 4 221 421 450158095 450158300 5.760000e-72 281.0
53 TraesCS2A01G084500 chr7D 100.000 36 0 0 151 186 214990250 214990285 1.750000e-07 67.6


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 TraesCS2A01G084500 chr2A 38811159 38813888 2729 False 5042.0 5042 100.000000 1 2730 1 chr2A.!!$F2 2729
1 TraesCS2A01G084500 chr2A 38754556 38755742 1186 False 1581.0 1581 90.628000 486 1700 1 chr2A.!!$F1 1214
2 TraesCS2A01G084500 chr2A 751945601 751946496 895 True 1393.0 1393 94.754000 1836 2730 1 chr2A.!!$R2 894
3 TraesCS2A01G084500 chr2A 691537537 691538171 634 False 977.0 977 94.488000 2097 2730 1 chr2A.!!$F6 633
4 TraesCS2A01G084500 chr2A 38878849 38879515 666 False 623.0 623 83.819000 888 1560 1 chr2A.!!$F3 672
5 TraesCS2A01G084500 chr2A 38908247 38909347 1100 False 460.5 763 87.447500 594 1691 2 chr2A.!!$F7 1097
6 TraesCS2A01G084500 chr2D 35531124 35532578 1454 False 863.0 1450 88.726000 1 1700 2 chr2D.!!$F2 1699
7 TraesCS2A01G084500 chr2D 35638646 35639753 1107 False 454.0 780 87.859000 594 1675 2 chr2D.!!$F4 1081
8 TraesCS2A01G084500 chr2D 35564373 35565129 756 False 430.0 466 90.205500 996 1781 2 chr2D.!!$F3 785
9 TraesCS2A01G084500 chr2D 42074918 42076260 1342 True 355.0 359 89.119500 1044 1706 2 chr2D.!!$R2 662
10 TraesCS2A01G084500 chr6A 573400863 573401753 890 True 1389.0 1389 94.754000 1836 2730 1 chr6A.!!$R1 894
11 TraesCS2A01G084500 chr6A 124263162 124264019 857 False 1286.0 1286 93.714000 1836 2693 1 chr6A.!!$F1 857
12 TraesCS2A01G084500 chr4A 583724955 583725849 894 True 1260.0 1260 92.189000 1836 2730 1 chr4A.!!$R1 894
13 TraesCS2A01G084500 chr1A 543056737 543057628 891 True 1229.0 1229 91.527000 1836 2730 1 chr1A.!!$R1 894
14 TraesCS2A01G084500 chr3B 578286734 578287628 894 True 1170.0 1170 90.279000 1836 2729 1 chr3B.!!$R1 893
15 TraesCS2A01G084500 chr5B 705898720 705899534 814 False 1092.0 1092 90.842000 1899 2716 1 chr5B.!!$F1 817
16 TraesCS2A01G084500 chr1D 447227480 447228189 709 True 994.0 994 91.983000 1956 2664 1 chr1D.!!$R1 708
17 TraesCS2A01G084500 chr2B 58825999 58826884 885 False 859.0 859 84.736000 805 1665 1 chr2B.!!$F1 860
18 TraesCS2A01G084500 chr2B 58791520 58792411 891 False 460.5 627 88.365500 997 1781 2 chr2B.!!$F4 784
19 TraesCS2A01G084500 chr2B 58772921 58773691 770 False 450.5 625 89.645500 486 1286 2 chr2B.!!$F3 800
20 TraesCS2A01G084500 chr2B 58688803 58690158 1355 False 399.0 789 84.182667 33 1700 3 chr2B.!!$F2 1667
21 TraesCS2A01G084500 chr5D 505910423 505911011 588 True 787.0 787 90.741000 2137 2729 1 chr5D.!!$R1 592

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
454 460 0.034896 TCAAGTCAAACTCGGGCTCC 59.965 55.0 0.0 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2021 3008 0.53578 TTCCCAGAGTTGCACTGCAG 60.536 55.0 13.48 13.48 40.61 4.41 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
28 29 7.596494 TGTGGATGTTGATTTTTCATCTTCTC 58.404 34.615 0.00 0.00 38.28 2.87
29 30 7.031975 GTGGATGTTGATTTTTCATCTTCTCC 58.968 38.462 0.00 0.00 38.28 3.71
31 32 6.094048 GGATGTTGATTTTTCATCTTCTCCGA 59.906 38.462 0.00 0.00 38.28 4.55
55 56 7.219917 CGATGAACTTGCTCAAACTTTACAAAA 59.780 33.333 0.00 0.00 0.00 2.44
58 59 8.868916 TGAACTTGCTCAAACTTTACAAAATTC 58.131 29.630 0.00 0.00 0.00 2.17
65 66 6.553524 TCAAACTTTACAAAATTCGAACCGT 58.446 32.000 0.00 0.00 0.00 4.83
75 76 4.625972 AATTCGAACCGTGACAAAACTT 57.374 36.364 0.00 0.00 0.00 2.66
78 79 4.977741 TCGAACCGTGACAAAACTTATC 57.022 40.909 0.00 0.00 0.00 1.75
84 85 4.518970 ACCGTGACAAAACTTATCTGCAAT 59.481 37.500 0.00 0.00 0.00 3.56
86 87 6.205853 ACCGTGACAAAACTTATCTGCAATAA 59.794 34.615 0.00 0.00 0.00 1.40
135 136 6.889301 ACTTCGTCCGATCCATATTAACTA 57.111 37.500 0.00 0.00 0.00 2.24
186 187 4.762289 ATTAATATGGATCGGAGGGAGC 57.238 45.455 0.00 0.00 0.00 4.70
215 221 6.639632 TTTTTGCAGATTCTTAGAGCAGTT 57.360 33.333 0.00 0.00 36.47 3.16
216 222 5.618056 TTTGCAGATTCTTAGAGCAGTTG 57.382 39.130 0.00 0.00 36.47 3.16
217 223 4.541973 TGCAGATTCTTAGAGCAGTTGA 57.458 40.909 0.00 0.00 0.00 3.18
218 224 4.898320 TGCAGATTCTTAGAGCAGTTGAA 58.102 39.130 0.00 0.00 0.00 2.69
219 225 5.494724 TGCAGATTCTTAGAGCAGTTGAAT 58.505 37.500 0.00 0.00 0.00 2.57
220 226 5.583854 TGCAGATTCTTAGAGCAGTTGAATC 59.416 40.000 0.00 0.00 41.67 2.52
221 227 5.276773 GCAGATTCTTAGAGCAGTTGAATCG 60.277 44.000 0.00 0.00 44.28 3.34
222 228 6.038985 CAGATTCTTAGAGCAGTTGAATCGA 58.961 40.000 0.00 0.00 44.28 3.59
223 229 6.198778 CAGATTCTTAGAGCAGTTGAATCGAG 59.801 42.308 0.00 0.00 44.28 4.04
224 230 5.392767 TTCTTAGAGCAGTTGAATCGAGT 57.607 39.130 0.00 0.00 0.00 4.18
225 231 6.510879 TTCTTAGAGCAGTTGAATCGAGTA 57.489 37.500 0.00 0.00 0.00 2.59
226 232 6.125327 TCTTAGAGCAGTTGAATCGAGTAG 57.875 41.667 0.00 0.00 0.00 2.57
227 233 3.791973 AGAGCAGTTGAATCGAGTAGG 57.208 47.619 0.00 0.00 0.00 3.18
228 234 2.428890 AGAGCAGTTGAATCGAGTAGGG 59.571 50.000 0.00 0.00 0.00 3.53
229 235 1.134670 AGCAGTTGAATCGAGTAGGGC 60.135 52.381 0.00 0.00 0.00 5.19
230 236 1.560923 CAGTTGAATCGAGTAGGGCG 58.439 55.000 0.00 0.00 0.00 6.13
231 237 1.135083 CAGTTGAATCGAGTAGGGCGT 60.135 52.381 0.00 0.00 0.00 5.68
232 238 1.549170 AGTTGAATCGAGTAGGGCGTT 59.451 47.619 0.00 0.00 0.00 4.84
233 239 2.028385 AGTTGAATCGAGTAGGGCGTTT 60.028 45.455 0.00 0.00 0.00 3.60
234 240 2.740447 GTTGAATCGAGTAGGGCGTTTT 59.260 45.455 0.00 0.00 0.00 2.43
235 241 3.872511 TGAATCGAGTAGGGCGTTTTA 57.127 42.857 0.00 0.00 0.00 1.52
236 242 4.395959 TGAATCGAGTAGGGCGTTTTAT 57.604 40.909 0.00 0.00 0.00 1.40
237 243 5.518848 TGAATCGAGTAGGGCGTTTTATA 57.481 39.130 0.00 0.00 0.00 0.98
238 244 5.526115 TGAATCGAGTAGGGCGTTTTATAG 58.474 41.667 0.00 0.00 0.00 1.31
239 245 3.360249 TCGAGTAGGGCGTTTTATAGC 57.640 47.619 0.00 0.00 0.00 2.97
240 246 2.954318 TCGAGTAGGGCGTTTTATAGCT 59.046 45.455 0.00 0.00 0.00 3.32
241 247 3.004106 TCGAGTAGGGCGTTTTATAGCTC 59.996 47.826 0.00 0.00 0.00 4.09
242 248 3.306818 GAGTAGGGCGTTTTATAGCTCG 58.693 50.000 0.00 0.00 39.21 5.03
243 249 2.035576 AGTAGGGCGTTTTATAGCTCGG 59.964 50.000 0.00 0.00 39.21 4.63
244 250 0.532196 AGGGCGTTTTATAGCTCGGC 60.532 55.000 8.09 8.09 45.47 5.54
245 251 1.939597 GGCGTTTTATAGCTCGGCC 59.060 57.895 5.61 0.00 41.64 6.13
246 252 0.532196 GGCGTTTTATAGCTCGGCCT 60.532 55.000 0.00 0.00 41.64 5.19
247 253 0.859882 GCGTTTTATAGCTCGGCCTC 59.140 55.000 0.00 0.00 0.00 4.70
248 254 1.499049 CGTTTTATAGCTCGGCCTCC 58.501 55.000 0.00 0.00 0.00 4.30
249 255 1.202486 CGTTTTATAGCTCGGCCTCCA 60.202 52.381 0.00 0.00 0.00 3.86
250 256 2.548067 CGTTTTATAGCTCGGCCTCCAT 60.548 50.000 0.00 0.00 0.00 3.41
251 257 2.808543 GTTTTATAGCTCGGCCTCCATG 59.191 50.000 0.00 0.00 0.00 3.66
252 258 0.976641 TTATAGCTCGGCCTCCATGG 59.023 55.000 4.97 4.97 39.35 3.66
253 259 0.114364 TATAGCTCGGCCTCCATGGA 59.886 55.000 15.27 15.27 38.35 3.41
254 260 1.190833 ATAGCTCGGCCTCCATGGAG 61.191 60.000 31.69 31.69 41.63 3.86
263 269 3.502164 CTCCATGGAGGCCGAATTT 57.498 52.632 31.14 0.00 38.51 1.82
264 270 1.767759 CTCCATGGAGGCCGAATTTT 58.232 50.000 31.14 0.00 38.51 1.82
265 271 2.102578 CTCCATGGAGGCCGAATTTTT 58.897 47.619 31.14 0.00 38.51 1.94
291 297 8.819152 TGAAAAATTCAAAATTCGCACTTTTC 57.181 26.923 0.00 0.00 36.59 2.29
292 298 8.446273 TGAAAAATTCAAAATTCGCACTTTTCA 58.554 25.926 0.00 0.00 37.71 2.69
293 299 8.825064 AAAAATTCAAAATTCGCACTTTTCAG 57.175 26.923 0.00 0.00 0.00 3.02
294 300 7.538303 AAATTCAAAATTCGCACTTTTCAGT 57.462 28.000 0.00 0.00 0.00 3.41
295 301 7.538303 AATTCAAAATTCGCACTTTTCAGTT 57.462 28.000 0.00 0.00 0.00 3.16
296 302 6.959671 TTCAAAATTCGCACTTTTCAGTTT 57.040 29.167 0.00 0.00 0.00 2.66
297 303 8.641499 ATTCAAAATTCGCACTTTTCAGTTTA 57.359 26.923 0.00 0.00 0.00 2.01
298 304 8.467402 TTCAAAATTCGCACTTTTCAGTTTAA 57.533 26.923 0.00 0.00 0.00 1.52
299 305 8.467402 TCAAAATTCGCACTTTTCAGTTTAAA 57.533 26.923 0.00 0.00 0.00 1.52
300 306 8.926710 TCAAAATTCGCACTTTTCAGTTTAAAA 58.073 25.926 0.00 0.00 0.00 1.52
301 307 9.535270 CAAAATTCGCACTTTTCAGTTTAAAAA 57.465 25.926 0.00 0.00 0.00 1.94
329 335 9.683069 AACTGAAAAATCATACAAGTAAGCAAG 57.317 29.630 0.00 0.00 0.00 4.01
330 336 8.299570 ACTGAAAAATCATACAAGTAAGCAAGG 58.700 33.333 0.00 0.00 0.00 3.61
331 337 8.402798 TGAAAAATCATACAAGTAAGCAAGGA 57.597 30.769 0.00 0.00 0.00 3.36
332 338 9.023962 TGAAAAATCATACAAGTAAGCAAGGAT 57.976 29.630 0.00 0.00 0.00 3.24
333 339 9.294030 GAAAAATCATACAAGTAAGCAAGGATG 57.706 33.333 0.00 0.00 0.00 3.51
334 340 7.944729 AAATCATACAAGTAAGCAAGGATGT 57.055 32.000 0.00 0.00 0.00 3.06
335 341 7.944729 AATCATACAAGTAAGCAAGGATGTT 57.055 32.000 0.00 0.00 0.00 2.71
336 342 9.461312 AAATCATACAAGTAAGCAAGGATGTTA 57.539 29.630 0.00 0.00 0.00 2.41
337 343 9.632638 AATCATACAAGTAAGCAAGGATGTTAT 57.367 29.630 0.00 0.00 0.00 1.89
338 344 8.437360 TCATACAAGTAAGCAAGGATGTTATG 57.563 34.615 0.00 0.00 0.00 1.90
339 345 8.046708 TCATACAAGTAAGCAAGGATGTTATGT 58.953 33.333 0.00 0.00 0.00 2.29
340 346 9.325198 CATACAAGTAAGCAAGGATGTTATGTA 57.675 33.333 0.00 0.00 0.00 2.29
342 348 8.213518 ACAAGTAAGCAAGGATGTTATGTATG 57.786 34.615 0.00 0.00 0.00 2.39
343 349 7.829211 ACAAGTAAGCAAGGATGTTATGTATGT 59.171 33.333 0.00 0.00 0.00 2.29
344 350 9.325198 CAAGTAAGCAAGGATGTTATGTATGTA 57.675 33.333 0.00 0.00 0.00 2.29
346 352 9.494271 AGTAAGCAAGGATGTTATGTATGTATG 57.506 33.333 0.00 0.00 0.00 2.39
347 353 9.273016 GTAAGCAAGGATGTTATGTATGTATGT 57.727 33.333 0.00 0.00 0.00 2.29
349 355 9.845740 AAGCAAGGATGTTATGTATGTATGTAA 57.154 29.630 0.00 0.00 0.00 2.41
350 356 9.845740 AGCAAGGATGTTATGTATGTATGTAAA 57.154 29.630 0.00 0.00 0.00 2.01
370 376 8.893563 TGTAAAATTTGAGGATGAAATACCCT 57.106 30.769 0.00 0.00 28.06 4.34
371 377 9.983024 TGTAAAATTTGAGGATGAAATACCCTA 57.017 29.630 0.00 0.00 28.06 3.53
377 383 6.959639 TGAGGATGAAATACCCTAAAATGC 57.040 37.500 0.00 0.00 0.00 3.56
378 384 5.530915 TGAGGATGAAATACCCTAAAATGCG 59.469 40.000 0.00 0.00 0.00 4.73
379 385 5.690865 AGGATGAAATACCCTAAAATGCGA 58.309 37.500 0.00 0.00 0.00 5.10
380 386 6.306987 AGGATGAAATACCCTAAAATGCGAT 58.693 36.000 0.00 0.00 0.00 4.58
381 387 6.431234 AGGATGAAATACCCTAAAATGCGATC 59.569 38.462 0.00 0.00 0.00 3.69
382 388 6.431234 GGATGAAATACCCTAAAATGCGATCT 59.569 38.462 0.00 0.00 0.00 2.75
383 389 6.618287 TGAAATACCCTAAAATGCGATCTG 57.382 37.500 0.00 0.00 0.00 2.90
384 390 5.008613 TGAAATACCCTAAAATGCGATCTGC 59.991 40.000 3.07 3.07 46.70 4.26
413 419 8.652810 AAAAAGACAAATTCATGGACTTTGAG 57.347 30.769 16.97 0.00 36.28 3.02
414 420 7.587037 AAAGACAAATTCATGGACTTTGAGA 57.413 32.000 16.97 0.00 36.28 3.27
415 421 6.566197 AGACAAATTCATGGACTTTGAGAC 57.434 37.500 16.97 10.45 36.28 3.36
416 422 6.064060 AGACAAATTCATGGACTTTGAGACA 58.936 36.000 16.97 0.00 36.28 3.41
417 423 6.718454 AGACAAATTCATGGACTTTGAGACAT 59.282 34.615 16.97 0.00 36.28 3.06
418 424 6.684686 ACAAATTCATGGACTTTGAGACATG 58.315 36.000 16.97 0.00 41.44 3.21
419 425 6.491062 ACAAATTCATGGACTTTGAGACATGA 59.509 34.615 16.97 12.45 45.53 3.07
424 430 7.528996 TCATGGACTTTGAGACATGAAAATT 57.471 32.000 0.00 0.00 44.60 1.82
425 431 7.954835 TCATGGACTTTGAGACATGAAAATTT 58.045 30.769 0.00 0.00 44.60 1.82
426 432 7.868922 TCATGGACTTTGAGACATGAAAATTTG 59.131 33.333 0.00 0.00 44.60 2.32
427 433 7.345422 TGGACTTTGAGACATGAAAATTTGA 57.655 32.000 0.00 0.00 0.00 2.69
428 434 7.780064 TGGACTTTGAGACATGAAAATTTGAA 58.220 30.769 0.00 0.00 0.00 2.69
429 435 8.423349 TGGACTTTGAGACATGAAAATTTGAAT 58.577 29.630 0.00 0.00 0.00 2.57
430 436 9.264719 GGACTTTGAGACATGAAAATTTGAATT 57.735 29.630 0.00 0.00 0.00 2.17
451 457 1.808411 TGATCAAGTCAAACTCGGGC 58.192 50.000 0.00 0.00 32.78 6.13
452 458 1.347707 TGATCAAGTCAAACTCGGGCT 59.652 47.619 0.00 0.00 32.78 5.19
453 459 2.003301 GATCAAGTCAAACTCGGGCTC 58.997 52.381 0.00 0.00 0.00 4.70
454 460 0.034896 TCAAGTCAAACTCGGGCTCC 59.965 55.000 0.00 0.00 0.00 4.70
455 461 0.250295 CAAGTCAAACTCGGGCTCCA 60.250 55.000 0.00 0.00 0.00 3.86
456 462 0.693049 AAGTCAAACTCGGGCTCCAT 59.307 50.000 0.00 0.00 0.00 3.41
457 463 0.036010 AGTCAAACTCGGGCTCCATG 60.036 55.000 0.00 0.00 0.00 3.66
458 464 1.026718 GTCAAACTCGGGCTCCATGG 61.027 60.000 4.97 4.97 0.00 3.66
459 465 1.198094 TCAAACTCGGGCTCCATGGA 61.198 55.000 15.27 15.27 0.00 3.41
460 466 0.745845 CAAACTCGGGCTCCATGGAG 60.746 60.000 33.73 33.73 44.56 3.86
478 484 3.989104 GCCCGAGCTATAAAGAGCA 57.011 52.632 0.00 0.00 45.43 4.26
479 485 2.464157 GCCCGAGCTATAAAGAGCAT 57.536 50.000 0.00 0.00 45.43 3.79
480 486 2.772287 GCCCGAGCTATAAAGAGCATT 58.228 47.619 0.00 0.00 45.43 3.56
481 487 3.142174 GCCCGAGCTATAAAGAGCATTT 58.858 45.455 0.00 0.00 45.43 2.32
482 488 3.565902 GCCCGAGCTATAAAGAGCATTTT 59.434 43.478 0.00 0.00 45.43 1.82
483 489 4.319839 GCCCGAGCTATAAAGAGCATTTTC 60.320 45.833 0.00 0.00 45.43 2.29
484 490 4.084328 CCCGAGCTATAAAGAGCATTTTCG 60.084 45.833 0.00 0.00 45.43 3.46
515 521 5.428253 TCCCTCTGCATAGATTAAACACAC 58.572 41.667 0.00 0.00 31.21 3.82
885 935 5.347635 GTCCGGAAGTTGATTTAAAATTGGC 59.652 40.000 5.23 0.00 0.00 4.52
902 966 2.656069 GCTCCTCGCTAACCCCACA 61.656 63.158 0.00 0.00 35.14 4.17
918 982 1.000646 ACACCTCTCCCTCTCGTCC 60.001 63.158 0.00 0.00 0.00 4.79
976 1052 3.036819 TCATCAGAATCCAGAGTCCAGG 58.963 50.000 0.00 0.00 0.00 4.45
1014 1142 1.076549 GGACATGGGGAACTGCCAA 59.923 57.895 0.00 0.00 38.95 4.52
1149 1278 2.573869 CTCGTCGTCCTGCACCAT 59.426 61.111 0.00 0.00 0.00 3.55
1287 2075 1.672356 CTCCCAAGGTTCGTGCCTG 60.672 63.158 1.62 0.00 39.17 4.85
1290 2078 1.308069 CCCAAGGTTCGTGCCTGATG 61.308 60.000 1.62 0.00 39.17 3.07
1324 2148 4.160439 GGTTCTTGGATTGGATTCTTTCCC 59.840 45.833 0.00 0.00 44.77 3.97
1334 2160 3.397618 TGGATTCTTTCCCCTTCTTGTCA 59.602 43.478 0.00 0.00 44.77 3.58
1675 2630 1.517257 GTCATCGTGGAGCGGACAG 60.517 63.158 0.00 0.00 41.72 3.51
1788 2762 8.445275 TGTATACATACATTAGGCAAACTTGG 57.555 34.615 0.08 0.00 38.28 3.61
1789 2763 8.050325 TGTATACATACATTAGGCAAACTTGGT 58.950 33.333 0.08 0.00 38.28 3.67
1790 2764 9.550406 GTATACATACATTAGGCAAACTTGGTA 57.450 33.333 0.00 0.00 33.52 3.25
1791 2765 6.753107 ACATACATTAGGCAAACTTGGTAC 57.247 37.500 0.00 0.00 0.00 3.34
1792 2766 6.242396 ACATACATTAGGCAAACTTGGTACA 58.758 36.000 0.00 0.00 0.00 2.90
1793 2767 6.889722 ACATACATTAGGCAAACTTGGTACAT 59.110 34.615 0.00 0.00 39.30 2.29
1794 2768 7.396055 ACATACATTAGGCAAACTTGGTACATT 59.604 33.333 0.00 0.00 39.30 2.71
1795 2769 6.664428 ACATTAGGCAAACTTGGTACATTT 57.336 33.333 0.00 0.00 39.30 2.32
1796 2770 7.061566 ACATTAGGCAAACTTGGTACATTTT 57.938 32.000 0.00 0.00 39.30 1.82
1797 2771 8.184304 ACATTAGGCAAACTTGGTACATTTTA 57.816 30.769 0.00 0.00 39.30 1.52
1798 2772 8.643324 ACATTAGGCAAACTTGGTACATTTTAA 58.357 29.630 0.00 0.00 39.30 1.52
1799 2773 9.139174 CATTAGGCAAACTTGGTACATTTTAAG 57.861 33.333 0.00 0.00 39.30 1.85
1800 2774 6.724893 AGGCAAACTTGGTACATTTTAAGT 57.275 33.333 0.00 0.00 39.30 2.24
1801 2775 7.119709 AGGCAAACTTGGTACATTTTAAGTT 57.880 32.000 0.00 0.00 43.11 2.66
1802 2776 8.240267 AGGCAAACTTGGTACATTTTAAGTTA 57.760 30.769 0.00 0.00 41.13 2.24
1803 2777 8.697292 AGGCAAACTTGGTACATTTTAAGTTAA 58.303 29.630 0.00 0.00 41.13 2.01
1804 2778 8.974408 GGCAAACTTGGTACATTTTAAGTTAAG 58.026 33.333 0.00 0.00 41.13 1.85
1805 2779 9.524106 GCAAACTTGGTACATTTTAAGTTAAGT 57.476 29.630 0.00 0.00 41.13 2.24
1809 2783 8.565416 ACTTGGTACATTTTAAGTTAAGTCTGC 58.435 33.333 0.00 0.00 39.30 4.26
1810 2784 8.453238 TTGGTACATTTTAAGTTAAGTCTGCA 57.547 30.769 0.00 0.00 39.30 4.41
1811 2785 8.630054 TGGTACATTTTAAGTTAAGTCTGCAT 57.370 30.769 0.00 0.00 0.00 3.96
1812 2786 9.727859 TGGTACATTTTAAGTTAAGTCTGCATA 57.272 29.630 0.00 0.00 0.00 3.14
1821 2795 6.867662 AGTTAAGTCTGCATATAACATGGC 57.132 37.500 0.00 0.00 32.10 4.40
1822 2796 6.595682 AGTTAAGTCTGCATATAACATGGCT 58.404 36.000 0.00 0.00 32.10 4.75
1823 2797 7.056635 AGTTAAGTCTGCATATAACATGGCTT 58.943 34.615 0.00 3.15 32.10 4.35
1824 2798 7.557719 AGTTAAGTCTGCATATAACATGGCTTT 59.442 33.333 0.00 0.00 32.10 3.51
1825 2799 6.780457 AAGTCTGCATATAACATGGCTTTT 57.220 33.333 0.00 0.00 0.00 2.27
1826 2800 6.140303 AGTCTGCATATAACATGGCTTTTG 57.860 37.500 0.00 0.00 0.00 2.44
1827 2801 5.887598 AGTCTGCATATAACATGGCTTTTGA 59.112 36.000 0.00 0.00 0.00 2.69
1828 2802 6.039047 AGTCTGCATATAACATGGCTTTTGAG 59.961 38.462 0.00 0.00 0.00 3.02
1829 2803 5.300034 TCTGCATATAACATGGCTTTTGAGG 59.700 40.000 0.00 0.00 0.00 3.86
1830 2804 5.199723 TGCATATAACATGGCTTTTGAGGA 58.800 37.500 0.00 0.00 0.00 3.71
1831 2805 5.300034 TGCATATAACATGGCTTTTGAGGAG 59.700 40.000 0.00 0.00 0.00 3.69
1832 2806 5.300286 GCATATAACATGGCTTTTGAGGAGT 59.700 40.000 0.00 0.00 0.00 3.85
1833 2807 6.514048 GCATATAACATGGCTTTTGAGGAGTC 60.514 42.308 0.00 0.00 0.00 3.36
1834 2808 2.957402 ACATGGCTTTTGAGGAGTCA 57.043 45.000 0.00 0.00 32.61 3.41
1842 2816 3.470709 CTTTTGAGGAGTCACTTGCTGA 58.529 45.455 0.00 0.00 30.10 4.26
1962 2936 5.180680 GCGTGGATTAGAGGTAACAAGTTTT 59.819 40.000 0.00 0.00 41.41 2.43
1971 2945 3.628942 AGGTAACAAGTTTTTGTCCGGTC 59.371 43.478 0.00 0.00 46.54 4.79
2021 3008 2.436646 CCTGTGTCGATGCCCACC 60.437 66.667 1.89 0.00 0.00 4.61
2191 3178 2.618241 TGTTGGCATAATCGGAATGAGC 59.382 45.455 0.00 0.00 0.00 4.26
2267 3254 4.929808 CAGCTACCTTGAGTCGTTAATTGT 59.070 41.667 0.00 0.00 0.00 2.71
2295 3282 7.707624 AGCTCAAAATTCTAATTGTGATCCA 57.292 32.000 8.40 0.00 40.75 3.41
2309 3296 5.304686 TGTGATCCAGTGAAAGGTAAAGT 57.695 39.130 0.00 0.00 0.00 2.66
2420 3408 2.158957 GGGTGAAGCTCAATACGGATGA 60.159 50.000 0.00 0.00 0.00 2.92
2505 3493 7.118723 ACATTATTTACTCATCTTGCAGGGAA 58.881 34.615 0.00 0.00 0.00 3.97
2566 3554 1.881973 CATGCATGGAGGGTTTATCCG 59.118 52.381 19.40 0.00 39.91 4.18
2726 3716 8.556517 TTCGAACGACTAGTATTGTTCATATG 57.443 34.615 23.76 13.78 40.47 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.031975 GGAGAAGATGAAAAATCAACATCCAC 58.968 38.462 0.00 0.00 40.55 4.02
21 22 3.196469 TGAGCAAGTTCATCGGAGAAGAT 59.804 43.478 0.00 0.00 43.58 2.40
28 29 3.904136 AAGTTTGAGCAAGTTCATCGG 57.096 42.857 0.00 0.00 0.00 4.18
29 30 5.747565 TGTAAAGTTTGAGCAAGTTCATCG 58.252 37.500 0.00 0.00 0.00 3.84
31 32 8.947055 ATTTTGTAAAGTTTGAGCAAGTTCAT 57.053 26.923 0.00 0.00 0.00 2.57
55 56 5.699458 AGATAAGTTTTGTCACGGTTCGAAT 59.301 36.000 0.00 0.00 0.00 3.34
58 59 4.698276 CAGATAAGTTTTGTCACGGTTCG 58.302 43.478 0.00 0.00 0.00 3.95
115 116 4.154737 CGGTAGTTAATATGGATCGGACGA 59.845 45.833 0.00 0.00 0.00 4.20
135 136 6.926272 GCTGATTTAGAGACTAAATCATCGGT 59.074 38.462 29.88 8.40 46.47 4.69
160 161 6.711277 TCCCTCCGATCCATATTAATTCTTG 58.289 40.000 0.00 0.00 0.00 3.02
161 162 6.577239 GCTCCCTCCGATCCATATTAATTCTT 60.577 42.308 0.00 0.00 0.00 2.52
163 164 5.119694 GCTCCCTCCGATCCATATTAATTC 58.880 45.833 0.00 0.00 0.00 2.17
200 206 6.039616 ACTCGATTCAACTGCTCTAAGAATC 58.960 40.000 0.00 0.00 40.51 2.52
212 218 1.183549 ACGCCCTACTCGATTCAACT 58.816 50.000 0.00 0.00 0.00 3.16
213 219 2.005971 AACGCCCTACTCGATTCAAC 57.994 50.000 0.00 0.00 0.00 3.18
214 220 2.754946 AAACGCCCTACTCGATTCAA 57.245 45.000 0.00 0.00 0.00 2.69
215 221 2.754946 AAAACGCCCTACTCGATTCA 57.245 45.000 0.00 0.00 0.00 2.57
216 222 4.385146 GCTATAAAACGCCCTACTCGATTC 59.615 45.833 0.00 0.00 0.00 2.52
217 223 4.038883 AGCTATAAAACGCCCTACTCGATT 59.961 41.667 0.00 0.00 0.00 3.34
218 224 3.573110 AGCTATAAAACGCCCTACTCGAT 59.427 43.478 0.00 0.00 0.00 3.59
219 225 2.954318 AGCTATAAAACGCCCTACTCGA 59.046 45.455 0.00 0.00 0.00 4.04
220 226 3.306818 GAGCTATAAAACGCCCTACTCG 58.693 50.000 0.00 0.00 0.00 4.18
221 227 3.306818 CGAGCTATAAAACGCCCTACTC 58.693 50.000 0.00 0.00 0.00 2.59
222 228 2.035576 CCGAGCTATAAAACGCCCTACT 59.964 50.000 0.00 0.00 0.00 2.57
223 229 2.401351 CCGAGCTATAAAACGCCCTAC 58.599 52.381 0.00 0.00 0.00 3.18
224 230 1.269936 GCCGAGCTATAAAACGCCCTA 60.270 52.381 0.00 0.00 0.00 3.53
225 231 0.532196 GCCGAGCTATAAAACGCCCT 60.532 55.000 0.00 0.00 0.00 5.19
226 232 1.504647 GGCCGAGCTATAAAACGCCC 61.505 60.000 0.00 0.00 0.00 6.13
227 233 0.532196 AGGCCGAGCTATAAAACGCC 60.532 55.000 0.00 0.00 0.00 5.68
228 234 0.859882 GAGGCCGAGCTATAAAACGC 59.140 55.000 0.00 0.00 0.00 4.84
229 235 1.202486 TGGAGGCCGAGCTATAAAACG 60.202 52.381 0.00 0.00 0.00 3.60
230 236 2.614829 TGGAGGCCGAGCTATAAAAC 57.385 50.000 0.00 0.00 0.00 2.43
231 237 2.224523 CCATGGAGGCCGAGCTATAAAA 60.225 50.000 5.56 0.00 0.00 1.52
232 238 1.347707 CCATGGAGGCCGAGCTATAAA 59.652 52.381 5.56 0.00 0.00 1.40
233 239 0.976641 CCATGGAGGCCGAGCTATAA 59.023 55.000 5.56 0.00 0.00 0.98
234 240 0.114364 TCCATGGAGGCCGAGCTATA 59.886 55.000 11.44 0.00 37.29 1.31
235 241 1.152247 TCCATGGAGGCCGAGCTAT 60.152 57.895 11.44 0.00 37.29 2.97
236 242 1.834378 CTCCATGGAGGCCGAGCTA 60.834 63.158 31.14 0.00 38.51 3.32
237 243 3.160047 CTCCATGGAGGCCGAGCT 61.160 66.667 31.14 0.00 38.51 4.09
245 251 1.767759 AAAATTCGGCCTCCATGGAG 58.232 50.000 31.69 31.69 41.63 3.86
246 252 2.230130 AAAAATTCGGCCTCCATGGA 57.770 45.000 15.27 15.27 38.35 3.41
266 272 8.446273 TGAAAAGTGCGAATTTTGAATTTTTCA 58.554 25.926 17.79 17.79 38.76 2.69
267 273 8.819152 TGAAAAGTGCGAATTTTGAATTTTTC 57.181 26.923 14.33 14.33 34.38 2.29
268 274 8.450180 ACTGAAAAGTGCGAATTTTGAATTTTT 58.550 25.926 0.00 0.00 30.22 1.94
269 275 7.973601 ACTGAAAAGTGCGAATTTTGAATTTT 58.026 26.923 0.00 0.00 30.22 1.82
270 276 7.538303 ACTGAAAAGTGCGAATTTTGAATTT 57.462 28.000 0.00 0.00 30.22 1.82
271 277 7.538303 AACTGAAAAGTGCGAATTTTGAATT 57.462 28.000 0.00 0.00 30.22 2.17
272 278 7.538303 AAACTGAAAAGTGCGAATTTTGAAT 57.462 28.000 0.00 0.00 30.22 2.57
273 279 6.959671 AAACTGAAAAGTGCGAATTTTGAA 57.040 29.167 0.00 0.00 30.22 2.69
274 280 8.467402 TTTAAACTGAAAAGTGCGAATTTTGA 57.533 26.923 0.00 0.00 30.22 2.69
275 281 9.535270 TTTTTAAACTGAAAAGTGCGAATTTTG 57.465 25.926 0.00 0.00 30.22 2.44
303 309 9.683069 CTTGCTTACTTGTATGATTTTTCAGTT 57.317 29.630 0.00 0.00 0.00 3.16
304 310 8.299570 CCTTGCTTACTTGTATGATTTTTCAGT 58.700 33.333 0.00 0.00 0.00 3.41
305 311 8.514594 TCCTTGCTTACTTGTATGATTTTTCAG 58.485 33.333 0.00 0.00 0.00 3.02
306 312 8.402798 TCCTTGCTTACTTGTATGATTTTTCA 57.597 30.769 0.00 0.00 0.00 2.69
307 313 9.294030 CATCCTTGCTTACTTGTATGATTTTTC 57.706 33.333 0.00 0.00 0.00 2.29
308 314 8.806146 ACATCCTTGCTTACTTGTATGATTTTT 58.194 29.630 0.00 0.00 0.00 1.94
309 315 8.353423 ACATCCTTGCTTACTTGTATGATTTT 57.647 30.769 0.00 0.00 0.00 1.82
310 316 7.944729 ACATCCTTGCTTACTTGTATGATTT 57.055 32.000 0.00 0.00 0.00 2.17
311 317 7.944729 AACATCCTTGCTTACTTGTATGATT 57.055 32.000 0.00 0.00 0.00 2.57
312 318 9.060347 CATAACATCCTTGCTTACTTGTATGAT 57.940 33.333 0.00 0.00 0.00 2.45
313 319 8.046708 ACATAACATCCTTGCTTACTTGTATGA 58.953 33.333 0.00 0.00 0.00 2.15
314 320 8.213518 ACATAACATCCTTGCTTACTTGTATG 57.786 34.615 0.00 0.00 0.00 2.39
316 322 9.325198 CATACATAACATCCTTGCTTACTTGTA 57.675 33.333 0.00 0.00 0.00 2.41
317 323 7.829211 ACATACATAACATCCTTGCTTACTTGT 59.171 33.333 0.00 0.00 0.00 3.16
318 324 8.213518 ACATACATAACATCCTTGCTTACTTG 57.786 34.615 0.00 0.00 0.00 3.16
320 326 9.494271 CATACATACATAACATCCTTGCTTACT 57.506 33.333 0.00 0.00 0.00 2.24
321 327 9.273016 ACATACATACATAACATCCTTGCTTAC 57.727 33.333 0.00 0.00 0.00 2.34
323 329 9.845740 TTACATACATACATAACATCCTTGCTT 57.154 29.630 0.00 0.00 0.00 3.91
324 330 9.845740 TTTACATACATACATAACATCCTTGCT 57.154 29.630 0.00 0.00 0.00 3.91
344 350 9.492730 AGGGTATTTCATCCTCAAATTTTACAT 57.507 29.630 0.00 0.00 0.00 2.29
345 351 8.893563 AGGGTATTTCATCCTCAAATTTTACA 57.106 30.769 0.00 0.00 0.00 2.41
351 357 8.424133 GCATTTTAGGGTATTTCATCCTCAAAT 58.576 33.333 0.00 0.00 35.86 2.32
352 358 7.416213 CGCATTTTAGGGTATTTCATCCTCAAA 60.416 37.037 0.00 0.00 31.11 2.69
353 359 6.039270 CGCATTTTAGGGTATTTCATCCTCAA 59.961 38.462 0.00 0.00 32.46 3.02
354 360 5.530915 CGCATTTTAGGGTATTTCATCCTCA 59.469 40.000 0.00 0.00 32.46 3.86
355 361 5.763204 TCGCATTTTAGGGTATTTCATCCTC 59.237 40.000 0.00 0.00 32.46 3.71
356 362 5.690865 TCGCATTTTAGGGTATTTCATCCT 58.309 37.500 0.00 0.00 34.85 3.24
357 363 6.431234 AGATCGCATTTTAGGGTATTTCATCC 59.569 38.462 0.00 0.00 0.00 3.51
358 364 7.301054 CAGATCGCATTTTAGGGTATTTCATC 58.699 38.462 0.00 0.00 0.00 2.92
359 365 6.294176 GCAGATCGCATTTTAGGGTATTTCAT 60.294 38.462 4.93 0.00 41.79 2.57
360 366 5.008613 GCAGATCGCATTTTAGGGTATTTCA 59.991 40.000 4.93 0.00 41.79 2.69
361 367 5.452777 GCAGATCGCATTTTAGGGTATTTC 58.547 41.667 4.93 0.00 41.79 2.17
362 368 4.024048 CGCAGATCGCATTTTAGGGTATTT 60.024 41.667 9.58 0.00 42.60 1.40
363 369 3.498397 CGCAGATCGCATTTTAGGGTATT 59.502 43.478 9.58 0.00 42.60 1.89
364 370 3.067106 CGCAGATCGCATTTTAGGGTAT 58.933 45.455 9.58 0.00 42.60 2.73
365 371 2.479837 CGCAGATCGCATTTTAGGGTA 58.520 47.619 9.58 0.00 42.60 3.69
366 372 1.299541 CGCAGATCGCATTTTAGGGT 58.700 50.000 9.58 0.00 42.60 4.34
388 394 8.477256 TCTCAAAGTCCATGAATTTGTCTTTTT 58.523 29.630 14.32 0.00 44.49 1.94
389 395 7.922811 GTCTCAAAGTCCATGAATTTGTCTTTT 59.077 33.333 14.32 0.00 44.49 2.27
390 396 7.068593 TGTCTCAAAGTCCATGAATTTGTCTTT 59.931 33.333 14.32 3.09 44.49 2.52
391 397 6.547141 TGTCTCAAAGTCCATGAATTTGTCTT 59.453 34.615 14.32 0.00 44.49 3.01
392 398 6.064060 TGTCTCAAAGTCCATGAATTTGTCT 58.936 36.000 14.32 0.00 44.49 3.41
393 399 6.317789 TGTCTCAAAGTCCATGAATTTGTC 57.682 37.500 14.32 8.68 44.49 3.18
394 400 6.491062 TCATGTCTCAAAGTCCATGAATTTGT 59.509 34.615 14.32 0.00 44.49 2.83
395 401 6.916440 TCATGTCTCAAAGTCCATGAATTTG 58.084 36.000 9.93 9.93 45.19 2.32
396 402 7.528996 TTCATGTCTCAAAGTCCATGAATTT 57.471 32.000 9.21 0.00 44.82 1.82
399 405 6.957920 TTTTCATGTCTCAAAGTCCATGAA 57.042 33.333 9.21 9.21 46.78 2.57
400 406 7.528996 AATTTTCATGTCTCAAAGTCCATGA 57.471 32.000 0.00 0.00 41.27 3.07
401 407 7.868922 TCAAATTTTCATGTCTCAAAGTCCATG 59.131 33.333 0.00 0.00 36.80 3.66
402 408 7.954835 TCAAATTTTCATGTCTCAAAGTCCAT 58.045 30.769 0.00 0.00 0.00 3.41
403 409 7.345422 TCAAATTTTCATGTCTCAAAGTCCA 57.655 32.000 0.00 0.00 0.00 4.02
404 410 8.822652 ATTCAAATTTTCATGTCTCAAAGTCC 57.177 30.769 0.00 0.00 0.00 3.85
431 437 2.151202 GCCCGAGTTTGACTTGATCAA 58.849 47.619 8.12 8.12 45.92 2.57
432 438 1.347707 AGCCCGAGTTTGACTTGATCA 59.652 47.619 0.00 0.00 31.05 2.92
433 439 2.003301 GAGCCCGAGTTTGACTTGATC 58.997 52.381 0.00 0.00 31.05 2.92
434 440 1.339151 GGAGCCCGAGTTTGACTTGAT 60.339 52.381 0.00 0.00 31.05 2.57
435 441 0.034896 GGAGCCCGAGTTTGACTTGA 59.965 55.000 0.00 0.00 31.05 3.02
436 442 0.250295 TGGAGCCCGAGTTTGACTTG 60.250 55.000 0.00 0.00 0.00 3.16
437 443 0.693049 ATGGAGCCCGAGTTTGACTT 59.307 50.000 0.00 0.00 0.00 3.01
438 444 0.036010 CATGGAGCCCGAGTTTGACT 60.036 55.000 0.00 0.00 0.00 3.41
439 445 1.026718 CCATGGAGCCCGAGTTTGAC 61.027 60.000 5.56 0.00 0.00 3.18
440 446 1.198094 TCCATGGAGCCCGAGTTTGA 61.198 55.000 11.44 0.00 0.00 2.69
441 447 0.745845 CTCCATGGAGCCCGAGTTTG 60.746 60.000 28.45 2.18 35.31 2.93
442 448 1.604378 CTCCATGGAGCCCGAGTTT 59.396 57.895 28.45 0.00 35.31 2.66
443 449 3.313874 CTCCATGGAGCCCGAGTT 58.686 61.111 28.45 0.00 35.31 3.01
460 466 2.464157 ATGCTCTTTATAGCTCGGGC 57.536 50.000 0.00 0.00 43.19 6.13
461 467 4.084328 CGAAAATGCTCTTTATAGCTCGGG 60.084 45.833 0.00 0.00 43.19 5.14
462 468 4.745125 TCGAAAATGCTCTTTATAGCTCGG 59.255 41.667 0.00 0.00 43.19 4.63
463 469 5.460419 ACTCGAAAATGCTCTTTATAGCTCG 59.540 40.000 0.00 0.00 43.19 5.03
464 470 6.836577 ACTCGAAAATGCTCTTTATAGCTC 57.163 37.500 0.00 0.00 43.19 4.09
465 471 6.818644 TCAACTCGAAAATGCTCTTTATAGCT 59.181 34.615 0.00 0.00 43.19 3.32
466 472 7.005062 TCAACTCGAAAATGCTCTTTATAGC 57.995 36.000 0.00 0.00 43.08 2.97
467 473 9.643652 GATTCAACTCGAAAATGCTCTTTATAG 57.356 33.333 0.00 0.00 37.12 1.31
468 474 8.612619 GGATTCAACTCGAAAATGCTCTTTATA 58.387 33.333 0.00 0.00 37.12 0.98
469 475 7.415653 GGGATTCAACTCGAAAATGCTCTTTAT 60.416 37.037 0.00 0.00 37.12 1.40
470 476 6.128007 GGGATTCAACTCGAAAATGCTCTTTA 60.128 38.462 0.00 0.00 37.12 1.85
471 477 5.335976 GGGATTCAACTCGAAAATGCTCTTT 60.336 40.000 0.00 0.00 37.12 2.52
472 478 4.156739 GGGATTCAACTCGAAAATGCTCTT 59.843 41.667 0.00 0.00 37.12 2.85
473 479 3.691609 GGGATTCAACTCGAAAATGCTCT 59.308 43.478 0.00 0.00 37.12 4.09
474 480 3.691609 AGGGATTCAACTCGAAAATGCTC 59.308 43.478 0.00 0.00 37.12 4.26
475 481 3.690460 AGGGATTCAACTCGAAAATGCT 58.310 40.909 0.00 0.00 37.12 3.79
476 482 3.691609 AGAGGGATTCAACTCGAAAATGC 59.308 43.478 0.00 0.00 37.12 3.56
477 483 4.437930 GCAGAGGGATTCAACTCGAAAATG 60.438 45.833 0.00 0.00 37.12 2.32
478 484 3.691609 GCAGAGGGATTCAACTCGAAAAT 59.308 43.478 0.00 0.00 37.12 1.82
479 485 3.074412 GCAGAGGGATTCAACTCGAAAA 58.926 45.455 0.00 0.00 37.12 2.29
480 486 2.038426 TGCAGAGGGATTCAACTCGAAA 59.962 45.455 0.00 0.00 37.12 3.46
481 487 1.623311 TGCAGAGGGATTCAACTCGAA 59.377 47.619 0.00 0.00 38.72 3.71
482 488 1.266178 TGCAGAGGGATTCAACTCGA 58.734 50.000 0.00 0.00 38.72 4.04
483 489 2.322355 ATGCAGAGGGATTCAACTCG 57.678 50.000 0.00 0.00 38.72 4.18
484 490 4.679373 TCTATGCAGAGGGATTCAACTC 57.321 45.455 8.78 0.72 0.00 3.01
515 521 4.065423 ACGCGTTTCATAAACATGTCTG 57.935 40.909 5.58 0.00 41.44 3.51
885 935 1.218316 GTGTGGGGTTAGCGAGGAG 59.782 63.158 0.00 0.00 0.00 3.69
902 966 2.684735 GGGACGAGAGGGAGAGGT 59.315 66.667 0.00 0.00 0.00 3.85
918 982 1.074248 GGTTATATGGGGGTGCCGG 59.926 63.158 0.00 0.00 0.00 6.13
986 1062 2.434185 CCATGTCCGTCGGTGTGG 60.434 66.667 11.88 13.58 0.00 4.17
1675 2630 2.099921 ACATGTATCCTCGCAGTCTGTC 59.900 50.000 0.00 0.00 0.00 3.51
1783 2757 8.565416 GCAGACTTAACTTAAAATGTACCAAGT 58.435 33.333 0.00 0.00 32.73 3.16
1784 2758 8.564574 TGCAGACTTAACTTAAAATGTACCAAG 58.435 33.333 0.00 0.00 0.00 3.61
1785 2759 8.453238 TGCAGACTTAACTTAAAATGTACCAA 57.547 30.769 0.00 0.00 0.00 3.67
1786 2760 8.630054 ATGCAGACTTAACTTAAAATGTACCA 57.370 30.769 0.00 0.00 0.00 3.25
1795 2769 8.836413 GCCATGTTATATGCAGACTTAACTTAA 58.164 33.333 6.44 0.00 0.00 1.85
1796 2770 8.210946 AGCCATGTTATATGCAGACTTAACTTA 58.789 33.333 6.44 0.00 0.00 2.24
1797 2771 7.056635 AGCCATGTTATATGCAGACTTAACTT 58.943 34.615 6.44 0.00 0.00 2.66
1798 2772 6.595682 AGCCATGTTATATGCAGACTTAACT 58.404 36.000 6.44 0.00 0.00 2.24
1799 2773 6.867662 AGCCATGTTATATGCAGACTTAAC 57.132 37.500 0.00 0.00 0.00 2.01
1800 2774 7.880160 AAAGCCATGTTATATGCAGACTTAA 57.120 32.000 0.00 0.00 0.00 1.85
1801 2775 7.555914 TCAAAAGCCATGTTATATGCAGACTTA 59.444 33.333 0.00 0.00 0.00 2.24
1802 2776 6.377996 TCAAAAGCCATGTTATATGCAGACTT 59.622 34.615 0.00 0.00 0.00 3.01
1803 2777 5.887598 TCAAAAGCCATGTTATATGCAGACT 59.112 36.000 0.00 0.00 0.00 3.24
1804 2778 6.135290 TCAAAAGCCATGTTATATGCAGAC 57.865 37.500 0.00 0.00 0.00 3.51
1805 2779 5.300034 CCTCAAAAGCCATGTTATATGCAGA 59.700 40.000 0.00 0.00 0.00 4.26
1806 2780 5.300034 TCCTCAAAAGCCATGTTATATGCAG 59.700 40.000 0.00 0.00 0.00 4.41
1807 2781 5.199723 TCCTCAAAAGCCATGTTATATGCA 58.800 37.500 0.00 0.00 0.00 3.96
1808 2782 5.300286 ACTCCTCAAAAGCCATGTTATATGC 59.700 40.000 0.00 0.00 0.00 3.14
1809 2783 6.543465 TGACTCCTCAAAAGCCATGTTATATG 59.457 38.462 0.00 0.00 0.00 1.78
1810 2784 6.543831 GTGACTCCTCAAAAGCCATGTTATAT 59.456 38.462 0.00 0.00 0.00 0.86
1811 2785 5.880332 GTGACTCCTCAAAAGCCATGTTATA 59.120 40.000 0.00 0.00 0.00 0.98
1812 2786 4.702131 GTGACTCCTCAAAAGCCATGTTAT 59.298 41.667 0.00 0.00 0.00 1.89
1813 2787 4.072131 GTGACTCCTCAAAAGCCATGTTA 58.928 43.478 0.00 0.00 0.00 2.41
1814 2788 2.887152 GTGACTCCTCAAAAGCCATGTT 59.113 45.455 0.00 0.00 0.00 2.71
1815 2789 2.107204 AGTGACTCCTCAAAAGCCATGT 59.893 45.455 0.00 0.00 0.00 3.21
1816 2790 2.787994 AGTGACTCCTCAAAAGCCATG 58.212 47.619 0.00 0.00 0.00 3.66
1817 2791 3.152341 CAAGTGACTCCTCAAAAGCCAT 58.848 45.455 0.00 0.00 0.00 4.40
1818 2792 2.575532 CAAGTGACTCCTCAAAAGCCA 58.424 47.619 0.00 0.00 0.00 4.75
1819 2793 1.268079 GCAAGTGACTCCTCAAAAGCC 59.732 52.381 0.00 0.00 0.00 4.35
1820 2794 2.031333 CAGCAAGTGACTCCTCAAAAGC 60.031 50.000 0.00 0.00 0.00 3.51
1821 2795 3.470709 TCAGCAAGTGACTCCTCAAAAG 58.529 45.455 0.00 0.00 0.00 2.27
1822 2796 3.558931 TCAGCAAGTGACTCCTCAAAA 57.441 42.857 0.00 0.00 0.00 2.44
1823 2797 3.558931 TTCAGCAAGTGACTCCTCAAA 57.441 42.857 0.00 0.00 33.71 2.69
1824 2798 3.470709 CTTTCAGCAAGTGACTCCTCAA 58.529 45.455 0.00 0.00 33.71 3.02
1825 2799 2.808202 GCTTTCAGCAAGTGACTCCTCA 60.808 50.000 0.00 0.00 41.89 3.86
1826 2800 1.803555 GCTTTCAGCAAGTGACTCCTC 59.196 52.381 0.00 0.00 41.89 3.71
1827 2801 1.419387 AGCTTTCAGCAAGTGACTCCT 59.581 47.619 0.00 0.00 45.56 3.69
1828 2802 1.889545 AGCTTTCAGCAAGTGACTCC 58.110 50.000 0.00 0.00 45.56 3.85
1829 2803 6.238320 CCATATTAGCTTTCAGCAAGTGACTC 60.238 42.308 0.00 0.00 45.56 3.36
1830 2804 5.587844 CCATATTAGCTTTCAGCAAGTGACT 59.412 40.000 0.00 0.00 45.56 3.41
1831 2805 5.586243 TCCATATTAGCTTTCAGCAAGTGAC 59.414 40.000 0.00 0.00 45.56 3.67
1832 2806 5.744171 TCCATATTAGCTTTCAGCAAGTGA 58.256 37.500 0.00 0.00 45.56 3.41
1833 2807 5.819379 TCTCCATATTAGCTTTCAGCAAGTG 59.181 40.000 0.00 0.00 45.56 3.16
1834 2808 5.994250 TCTCCATATTAGCTTTCAGCAAGT 58.006 37.500 0.00 0.00 45.56 3.16
1842 2816 7.065443 GGTACGTTTGTTCTCCATATTAGCTTT 59.935 37.037 0.00 0.00 0.00 3.51
1962 2936 0.813610 CAGTTGCACAGACCGGACAA 60.814 55.000 9.46 0.00 0.00 3.18
1971 2945 0.873054 CTTCAGGCTCAGTTGCACAG 59.127 55.000 0.00 0.00 34.04 3.66
2021 3008 0.535780 TTCCCAGAGTTGCACTGCAG 60.536 55.000 13.48 13.48 40.61 4.41
2166 3153 5.132502 TCATTCCGATTATGCCAACATCTT 58.867 37.500 0.00 0.00 37.74 2.40
2191 3178 7.425606 GGTGCTGGAATTTTATTATGTACCAG 58.574 38.462 0.00 0.00 44.15 4.00
2295 3282 7.259088 AGATATCACCACTTTACCTTTCACT 57.741 36.000 5.32 0.00 0.00 3.41
2309 3296 5.306937 ACCGTTGGATCATAAGATATCACCA 59.693 40.000 5.32 0.00 33.72 4.17
2373 3361 0.695347 CTGGAGGAGGAAGCCACTTT 59.305 55.000 0.00 0.00 0.00 2.66
2420 3408 4.386088 CCCTTCCATCATCAGTCCAGAAAT 60.386 45.833 0.00 0.00 0.00 2.17
2566 3554 1.392510 GTTCCGTCCGTGAATAGCAAC 59.607 52.381 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.