Multiple sequence alignment - TraesCS3B01G086500

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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 TraesCS3B01G086500 chr3B 100.000 4445 0 0 1 4445 54783828 54788272 0.000000e+00 8209.0
1 TraesCS3B01G086500 chr3B 91.089 2222 184 8 2229 4445 54795612 54797824 0.000000e+00 2994.0
2 TraesCS3B01G086500 chr3B 86.942 1769 202 14 459 2210 54793762 54795518 0.000000e+00 1960.0
3 TraesCS3B01G086500 chr3B 87.273 275 21 6 1 269 54793489 54793755 7.230000e-78 302.0
4 TraesCS3B01G086500 chr3B 94.245 139 8 0 261 399 40625388 40625526 3.480000e-51 213.0
5 TraesCS3B01G086500 chr3D 90.045 2220 191 14 2229 4443 32300899 32303093 0.000000e+00 2848.0
6 TraesCS3B01G086500 chr3D 83.838 1751 254 23 482 2220 32278387 32280120 0.000000e+00 1639.0
7 TraesCS3B01G086500 chr3D 84.771 1635 223 19 597 2210 32299191 32300820 0.000000e+00 1616.0
8 TraesCS3B01G086500 chr3D 89.151 1272 127 6 2251 3521 32280226 32281487 0.000000e+00 1574.0
9 TraesCS3B01G086500 chr3D 80.610 918 122 32 3535 4439 32281465 32282339 0.000000e+00 658.0
10 TraesCS3B01G086500 chr3A 89.691 2231 162 29 2229 4445 44711141 44713317 0.000000e+00 2784.0
11 TraesCS3B01G086500 chr3A 86.833 1762 211 11 459 2210 44638970 44640720 0.000000e+00 1949.0
12 TraesCS3B01G086500 chr3A 89.104 1294 136 3 2229 3521 44640814 44642103 0.000000e+00 1604.0
13 TraesCS3B01G086500 chr3A 83.095 1745 260 22 488 2220 44709339 44711060 0.000000e+00 1555.0
14 TraesCS3B01G086500 chr3A 80.894 738 100 22 3535 4254 44642081 44642795 1.090000e-150 544.0
15 TraesCS3B01G086500 chr3A 87.319 276 21 6 1 269 44638695 44638963 2.010000e-78 303.0
16 TraesCS3B01G086500 chr3A 95.588 136 6 0 257 392 598561962 598561827 7.490000e-53 219.0
17 TraesCS3B01G086500 chr5B 85.770 1286 161 11 939 2210 515184046 515185323 0.000000e+00 1341.0
18 TraesCS3B01G086500 chr5B 80.417 1583 244 38 657 2215 113683988 113682448 0.000000e+00 1146.0
19 TraesCS3B01G086500 chr5B 84.525 1105 150 17 2399 3499 113676713 113675626 0.000000e+00 1074.0
20 TraesCS3B01G086500 chr5B 91.275 149 11 2 268 415 191505810 191505663 7.540000e-48 202.0
21 TraesCS3B01G086500 chr5B 97.059 34 0 1 758 790 515183906 515183939 6.210000e-04 56.5
22 TraesCS3B01G086500 chr4D 81.376 1643 265 26 589 2215 1994950 1996567 0.000000e+00 1301.0
23 TraesCS3B01G086500 chr4D 83.568 1205 162 20 2270 3472 1996688 1997858 0.000000e+00 1096.0
24 TraesCS3B01G086500 chr5A 84.137 1286 182 8 939 2210 540051930 540053207 0.000000e+00 1225.0
25 TraesCS3B01G086500 chr5D 84.109 1246 178 11 975 2210 425838914 425840149 0.000000e+00 1186.0
26 TraesCS3B01G086500 chr5D 84.887 1105 148 16 2399 3499 104256102 104255013 0.000000e+00 1098.0
27 TraesCS3B01G086500 chr4B 83.292 1197 168 20 2400 3589 2336122 2334951 0.000000e+00 1074.0
28 TraesCS3B01G086500 chr6B 95.000 140 5 2 264 401 191198003 191198142 7.490000e-53 219.0
29 TraesCS3B01G086500 chr2B 95.620 137 5 1 265 400 800544907 800545043 7.490000e-53 219.0
30 TraesCS3B01G086500 chr2B 90.566 159 10 5 268 423 281876487 281876643 5.830000e-49 206.0
31 TraesCS3B01G086500 chr1B 97.619 126 3 0 267 392 102627726 102627851 2.690000e-52 217.0
32 TraesCS3B01G086500 chr7B 97.600 125 3 0 268 392 141907362 141907238 9.680000e-52 215.0
33 TraesCS3B01G086500 chr2D 91.720 157 10 3 248 401 348846399 348846555 9.680000e-52 215.0


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 TraesCS3B01G086500 chr3B 54783828 54788272 4444 False 8209.000000 8209 100.000000 1 4445 1 chr3B.!!$F2 4444
1 TraesCS3B01G086500 chr3B 54793489 54797824 4335 False 1752.000000 2994 88.434667 1 4445 3 chr3B.!!$F3 4444
2 TraesCS3B01G086500 chr3D 32299191 32303093 3902 False 2232.000000 2848 87.408000 597 4443 2 chr3D.!!$F2 3846
3 TraesCS3B01G086500 chr3D 32278387 32282339 3952 False 1290.333333 1639 84.533000 482 4439 3 chr3D.!!$F1 3957
4 TraesCS3B01G086500 chr3A 44709339 44713317 3978 False 2169.500000 2784 86.393000 488 4445 2 chr3A.!!$F2 3957
5 TraesCS3B01G086500 chr3A 44638695 44642795 4100 False 1100.000000 1949 86.037500 1 4254 4 chr3A.!!$F1 4253
6 TraesCS3B01G086500 chr5B 113682448 113683988 1540 True 1146.000000 1146 80.417000 657 2215 1 chr5B.!!$R2 1558
7 TraesCS3B01G086500 chr5B 113675626 113676713 1087 True 1074.000000 1074 84.525000 2399 3499 1 chr5B.!!$R1 1100
8 TraesCS3B01G086500 chr5B 515183906 515185323 1417 False 698.750000 1341 91.414500 758 2210 2 chr5B.!!$F1 1452
9 TraesCS3B01G086500 chr4D 1994950 1997858 2908 False 1198.500000 1301 82.472000 589 3472 2 chr4D.!!$F1 2883
10 TraesCS3B01G086500 chr5A 540051930 540053207 1277 False 1225.000000 1225 84.137000 939 2210 1 chr5A.!!$F1 1271
11 TraesCS3B01G086500 chr5D 425838914 425840149 1235 False 1186.000000 1186 84.109000 975 2210 1 chr5D.!!$F1 1235
12 TraesCS3B01G086500 chr5D 104255013 104256102 1089 True 1098.000000 1098 84.887000 2399 3499 1 chr5D.!!$R1 1100
13 TraesCS3B01G086500 chr4B 2334951 2336122 1171 True 1074.000000 1074 83.292000 2400 3589 1 chr4B.!!$R1 1189

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
284 292 0.038744 ACTACTCCCTCCGTCCGAAA 59.961 55.000 0.00 0.0 0.0 3.46 F
2135 2199 0.034756 CAGGTGGACGTGTGGATTGA 59.965 55.000 0.00 0.0 0.0 2.57 F
2319 2464 0.037046 TGAGCACGCATGTCATCTGT 60.037 50.000 0.00 0.0 0.0 3.41 F
2322 2467 0.933097 GCACGCATGTCATCTGTAGG 59.067 55.000 0.00 0.0 0.0 3.18 F
2415 2560 1.600663 CCTACATGTGATCTCGTCCGC 60.601 57.143 9.11 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2246 2391 0.034670 AGTTCCAATGAGGGCTGCTC 60.035 55.000 0.00 0.00 38.24 4.26 R
2967 3112 1.893786 CTGCAGCCGGAAGTACTCT 59.106 57.895 5.05 0.00 0.00 3.24 R
3319 3464 1.949799 AGAGATGAAGCACCCTCTGT 58.050 50.000 0.00 0.00 34.96 3.41 R
3394 3542 2.042686 AATATGGCTTTCTGCGCTGA 57.957 45.000 13.46 13.46 44.05 4.26 R
4267 4453 3.194861 AGCGCGAACTGCATATTTTAGA 58.805 40.909 12.10 0.00 46.97 2.10 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 3.417101 ACTGTGTGTTTTGGAGTGACAA 58.583 40.909 0.00 0.00 0.00 3.18
30 31 5.288472 GTGTGTTTTGGAGTGACAACAATTC 59.712 40.000 0.00 0.00 31.10 2.17
100 104 6.026947 TCTTGAACCTAGCAAGAAGAGTAC 57.973 41.667 8.36 0.00 46.19 2.73
101 105 4.803098 TGAACCTAGCAAGAAGAGTACC 57.197 45.455 0.00 0.00 0.00 3.34
102 106 4.417437 TGAACCTAGCAAGAAGAGTACCT 58.583 43.478 0.00 0.00 0.00 3.08
118 124 5.183522 AGAGTACCTCTTCTTAGTGGAAACG 59.816 44.000 0.00 0.00 37.60 3.60
155 161 5.006649 GCAAGTTGTCCACCAATTTCTTTTC 59.993 40.000 4.48 0.00 35.02 2.29
157 163 5.906073 AGTTGTCCACCAATTTCTTTTCTG 58.094 37.500 0.00 0.00 35.02 3.02
158 164 4.935352 TGTCCACCAATTTCTTTTCTGG 57.065 40.909 0.00 0.00 34.95 3.86
159 165 4.541705 TGTCCACCAATTTCTTTTCTGGA 58.458 39.130 0.00 0.00 32.97 3.86
160 166 4.959210 TGTCCACCAATTTCTTTTCTGGAA 59.041 37.500 0.00 0.00 32.97 3.53
161 167 5.602145 TGTCCACCAATTTCTTTTCTGGAAT 59.398 36.000 0.00 0.00 32.97 3.01
162 168 6.159293 GTCCACCAATTTCTTTTCTGGAATC 58.841 40.000 0.00 0.00 32.97 2.52
163 169 6.015095 GTCCACCAATTTCTTTTCTGGAATCT 60.015 38.462 0.00 0.00 32.97 2.40
164 170 6.015180 TCCACCAATTTCTTTTCTGGAATCTG 60.015 38.462 0.00 0.00 32.97 2.90
228 235 0.108585 ACGGACTGTTGCTCCATGTT 59.891 50.000 0.00 0.00 0.00 2.71
273 281 9.439500 TTTTGTACACAAATGTATACTACTCCC 57.561 33.333 8.27 0.00 44.30 4.30
275 283 8.004087 TGTACACAAATGTATACTACTCCCTC 57.996 38.462 4.17 0.00 43.21 4.30
276 284 6.481434 ACACAAATGTATACTACTCCCTCC 57.519 41.667 4.17 0.00 37.26 4.30
277 285 5.068723 ACACAAATGTATACTACTCCCTCCG 59.931 44.000 4.17 0.00 37.26 4.63
278 286 5.068723 CACAAATGTATACTACTCCCTCCGT 59.931 44.000 4.17 0.00 0.00 4.69
279 287 5.301298 ACAAATGTATACTACTCCCTCCGTC 59.699 44.000 4.17 0.00 0.00 4.79
280 288 3.498774 TGTATACTACTCCCTCCGTCC 57.501 52.381 4.17 0.00 0.00 4.79
281 289 2.224378 TGTATACTACTCCCTCCGTCCG 60.224 54.545 4.17 0.00 0.00 4.79
282 290 1.135094 ATACTACTCCCTCCGTCCGA 58.865 55.000 0.00 0.00 0.00 4.55
283 291 0.911769 TACTACTCCCTCCGTCCGAA 59.088 55.000 0.00 0.00 0.00 4.30
284 292 0.038744 ACTACTCCCTCCGTCCGAAA 59.961 55.000 0.00 0.00 0.00 3.46
285 293 1.180029 CTACTCCCTCCGTCCGAAAA 58.820 55.000 0.00 0.00 0.00 2.29
286 294 1.755380 CTACTCCCTCCGTCCGAAAAT 59.245 52.381 0.00 0.00 0.00 1.82
287 295 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
288 296 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
289 297 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
290 298 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
291 299 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
292 300 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
293 301 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
294 302 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
295 303 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
296 304 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
297 305 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
298 306 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
299 307 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
300 308 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
301 309 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
302 310 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
303 311 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
304 312 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
305 313 7.273381 CCGAAAATACTTGTCATCAAAATGGAC 59.727 37.037 0.00 0.00 33.42 4.02
306 314 7.807433 CGAAAATACTTGTCATCAAAATGGACA 59.193 33.333 0.00 0.00 33.42 4.02
307 315 9.474920 GAAAATACTTGTCATCAAAATGGACAA 57.525 29.630 0.00 0.00 34.59 3.18
308 316 9.829507 AAAATACTTGTCATCAAAATGGACAAA 57.170 25.926 7.70 0.00 34.98 2.83
309 317 9.829507 AAATACTTGTCATCAAAATGGACAAAA 57.170 25.926 7.70 0.84 34.98 2.44
310 318 9.480053 AATACTTGTCATCAAAATGGACAAAAG 57.520 29.630 7.70 0.73 34.98 2.27
311 319 6.282930 ACTTGTCATCAAAATGGACAAAAGG 58.717 36.000 7.70 0.41 34.98 3.11
312 320 5.212532 TGTCATCAAAATGGACAAAAGGG 57.787 39.130 0.00 0.00 33.42 3.95
313 321 4.040217 TGTCATCAAAATGGACAAAAGGGG 59.960 41.667 0.00 0.00 33.42 4.79
314 322 4.283212 GTCATCAAAATGGACAAAAGGGGA 59.717 41.667 0.00 0.00 33.42 4.81
315 323 5.046376 GTCATCAAAATGGACAAAAGGGGAT 60.046 40.000 0.00 0.00 33.42 3.85
316 324 4.888326 TCAAAATGGACAAAAGGGGATG 57.112 40.909 0.00 0.00 0.00 3.51
317 325 4.230455 TCAAAATGGACAAAAGGGGATGT 58.770 39.130 0.00 0.00 0.00 3.06
318 326 5.398236 TCAAAATGGACAAAAGGGGATGTA 58.602 37.500 0.00 0.00 0.00 2.29
319 327 6.022315 TCAAAATGGACAAAAGGGGATGTAT 58.978 36.000 0.00 0.00 0.00 2.29
320 328 6.154363 TCAAAATGGACAAAAGGGGATGTATC 59.846 38.462 0.00 0.00 0.00 2.24
321 329 5.472301 AATGGACAAAAGGGGATGTATCT 57.528 39.130 0.00 0.00 0.00 1.98
322 330 6.590656 AATGGACAAAAGGGGATGTATCTA 57.409 37.500 0.00 0.00 0.00 1.98
323 331 5.630415 TGGACAAAAGGGGATGTATCTAG 57.370 43.478 0.00 0.00 0.00 2.43
324 332 5.285401 TGGACAAAAGGGGATGTATCTAGA 58.715 41.667 0.00 0.00 0.00 2.43
325 333 5.729229 TGGACAAAAGGGGATGTATCTAGAA 59.271 40.000 0.00 0.00 0.00 2.10
326 334 6.056236 GGACAAAAGGGGATGTATCTAGAAC 58.944 44.000 0.00 0.00 0.00 3.01
327 335 6.126739 GGACAAAAGGGGATGTATCTAGAACT 60.127 42.308 0.00 0.00 0.00 3.01
328 336 7.070821 GGACAAAAGGGGATGTATCTAGAACTA 59.929 40.741 0.00 0.00 0.00 2.24
329 337 8.388656 ACAAAAGGGGATGTATCTAGAACTAA 57.611 34.615 0.00 0.00 0.00 2.24
330 338 8.832735 ACAAAAGGGGATGTATCTAGAACTAAA 58.167 33.333 0.00 0.00 0.00 1.85
331 339 9.681062 CAAAAGGGGATGTATCTAGAACTAAAA 57.319 33.333 0.00 0.00 0.00 1.52
335 343 9.670442 AGGGGATGTATCTAGAACTAAAATACA 57.330 33.333 0.00 13.81 37.26 2.29
351 359 9.845214 ACTAAAATACATCTAGATACATCCCCT 57.155 33.333 4.54 0.00 0.00 4.79
359 367 9.170890 ACATCTAGATACATCCCCTTTTATTCA 57.829 33.333 4.54 0.00 0.00 2.57
360 368 9.442047 CATCTAGATACATCCCCTTTTATTCAC 57.558 37.037 4.54 0.00 0.00 3.18
361 369 8.798975 TCTAGATACATCCCCTTTTATTCACT 57.201 34.615 0.00 0.00 0.00 3.41
362 370 9.225682 TCTAGATACATCCCCTTTTATTCACTT 57.774 33.333 0.00 0.00 0.00 3.16
363 371 9.853177 CTAGATACATCCCCTTTTATTCACTTT 57.147 33.333 0.00 0.00 0.00 2.66
364 372 8.525290 AGATACATCCCCTTTTATTCACTTTG 57.475 34.615 0.00 0.00 0.00 2.77
365 373 8.336235 AGATACATCCCCTTTTATTCACTTTGA 58.664 33.333 0.00 0.00 0.00 2.69
366 374 9.136323 GATACATCCCCTTTTATTCACTTTGAT 57.864 33.333 0.00 0.00 0.00 2.57
367 375 7.174107 ACATCCCCTTTTATTCACTTTGATG 57.826 36.000 0.00 0.00 33.80 3.07
368 376 6.953520 ACATCCCCTTTTATTCACTTTGATGA 59.046 34.615 0.00 0.00 32.39 2.92
369 377 6.834168 TCCCCTTTTATTCACTTTGATGAC 57.166 37.500 0.00 0.00 0.00 3.06
370 378 6.310941 TCCCCTTTTATTCACTTTGATGACA 58.689 36.000 0.00 0.00 0.00 3.58
371 379 6.780031 TCCCCTTTTATTCACTTTGATGACAA 59.220 34.615 0.00 0.00 0.00 3.18
372 380 7.039784 TCCCCTTTTATTCACTTTGATGACAAG 60.040 37.037 0.00 0.00 37.32 3.16
373 381 7.255942 CCCCTTTTATTCACTTTGATGACAAGT 60.256 37.037 0.00 0.00 37.32 3.16
374 382 8.792633 CCCTTTTATTCACTTTGATGACAAGTA 58.207 33.333 0.00 0.00 37.32 2.24
379 387 6.817765 TTCACTTTGATGACAAGTATTCCC 57.182 37.500 0.00 0.00 37.32 3.97
380 388 4.935205 TCACTTTGATGACAAGTATTCCCG 59.065 41.667 0.00 0.00 37.32 5.14
381 389 4.094887 CACTTTGATGACAAGTATTCCCGG 59.905 45.833 0.00 0.00 37.32 5.73
382 390 4.019681 ACTTTGATGACAAGTATTCCCGGA 60.020 41.667 0.73 0.00 37.32 5.14
383 391 3.536956 TGATGACAAGTATTCCCGGAC 57.463 47.619 0.73 0.00 0.00 4.79
384 392 2.159156 TGATGACAAGTATTCCCGGACG 60.159 50.000 0.73 0.00 0.00 4.79
385 393 0.533491 TGACAAGTATTCCCGGACGG 59.467 55.000 0.73 3.25 0.00 4.79
386 394 0.819582 GACAAGTATTCCCGGACGGA 59.180 55.000 13.13 0.00 39.68 4.69
387 395 0.822164 ACAAGTATTCCCGGACGGAG 59.178 55.000 13.13 2.58 43.39 4.63
388 396 0.104304 CAAGTATTCCCGGACGGAGG 59.896 60.000 13.13 0.00 43.39 4.30
395 403 3.630289 CCGGACGGAGGGAGAAAT 58.370 61.111 4.40 0.00 37.50 2.17
396 404 2.816746 CCGGACGGAGGGAGAAATA 58.183 57.895 4.40 0.00 37.50 1.40
397 405 1.339097 CCGGACGGAGGGAGAAATAT 58.661 55.000 4.40 0.00 37.50 1.28
398 406 1.692519 CCGGACGGAGGGAGAAATATT 59.307 52.381 4.40 0.00 37.50 1.28
399 407 2.895404 CCGGACGGAGGGAGAAATATTA 59.105 50.000 4.40 0.00 37.50 0.98
400 408 3.305881 CCGGACGGAGGGAGAAATATTAC 60.306 52.174 4.40 0.00 37.50 1.89
401 409 3.611057 CGGACGGAGGGAGAAATATTACG 60.611 52.174 0.00 0.00 0.00 3.18
402 410 3.571401 GGACGGAGGGAGAAATATTACGA 59.429 47.826 0.00 0.00 0.00 3.43
403 411 4.220163 GGACGGAGGGAGAAATATTACGAT 59.780 45.833 0.00 0.00 0.00 3.73
404 412 5.135508 ACGGAGGGAGAAATATTACGATG 57.864 43.478 0.00 0.00 0.00 3.84
405 413 4.587684 ACGGAGGGAGAAATATTACGATGT 59.412 41.667 0.00 0.00 0.00 3.06
406 414 5.070047 ACGGAGGGAGAAATATTACGATGTT 59.930 40.000 0.00 0.00 0.00 2.71
407 415 5.989777 CGGAGGGAGAAATATTACGATGTTT 59.010 40.000 0.00 0.00 30.38 2.83
408 416 6.482308 CGGAGGGAGAAATATTACGATGTTTT 59.518 38.462 0.00 0.00 28.21 2.43
409 417 7.654520 CGGAGGGAGAAATATTACGATGTTTTA 59.345 37.037 0.00 0.00 28.21 1.52
410 418 8.989980 GGAGGGAGAAATATTACGATGTTTTAG 58.010 37.037 0.00 0.00 28.21 1.85
411 419 9.760077 GAGGGAGAAATATTACGATGTTTTAGA 57.240 33.333 0.00 0.00 28.21 2.10
447 455 8.705048 AGTCGTCTAAAAGATCTTATGTTTCC 57.295 34.615 8.75 0.00 0.00 3.13
448 456 8.532819 AGTCGTCTAAAAGATCTTATGTTTCCT 58.467 33.333 8.75 0.00 0.00 3.36
449 457 9.152595 GTCGTCTAAAAGATCTTATGTTTCCTT 57.847 33.333 8.75 0.00 0.00 3.36
457 465 7.130681 AGATCTTATGTTTCCTTACAGAGGG 57.869 40.000 0.00 0.00 46.31 4.30
465 473 5.179533 GTTTCCTTACAGAGGGACTTGATC 58.820 45.833 0.00 0.00 46.31 2.92
472 480 4.424842 ACAGAGGGACTTGATCTCTTTCT 58.575 43.478 0.00 0.00 38.77 2.52
480 488 7.039223 AGGGACTTGATCTCTTTCTTAAACGTA 60.039 37.037 0.00 0.00 32.33 3.57
499 509 6.452494 ACGTAGTTTGTACATGCTAGATCT 57.548 37.500 0.00 0.00 37.78 2.75
504 514 6.940739 AGTTTGTACATGCTAGATCTTCACT 58.059 36.000 0.00 0.00 0.00 3.41
550 562 8.587952 ACTTTTGTTTAGCTAAATTTTCGCAT 57.412 26.923 21.28 2.30 0.00 4.73
553 565 7.575332 TTGTTTAGCTAAATTTTCGCATTCC 57.425 32.000 21.28 5.33 0.00 3.01
620 639 5.048434 GCAGCCTTTGTCTATTTCTGTCTTT 60.048 40.000 0.00 0.00 0.00 2.52
643 662 3.065648 TGGTACAGTTTTCAACTTTCGGC 59.934 43.478 0.00 0.00 40.46 5.54
660 679 2.093216 GCGATGCCAGGAACTTCAG 58.907 57.895 0.00 0.00 34.60 3.02
701 720 8.726988 TGCAATTATTAGTTGTGTTCTCTTACC 58.273 33.333 1.54 0.00 0.00 2.85
835 855 4.353777 TCTAGGTGTGCCTTCTTCACTAT 58.646 43.478 0.00 0.00 44.18 2.12
853 873 7.142306 TCACTATACAATAGCACGATCCTAC 57.858 40.000 0.00 0.00 0.00 3.18
906 929 6.073602 GCCTCAAATTCCAAGAAAATCACAAC 60.074 38.462 0.00 0.00 0.00 3.32
921 944 6.893958 AATCACAACGTTCTTGCTCTATAG 57.106 37.500 0.00 0.00 0.00 1.31
922 945 5.386958 TCACAACGTTCTTGCTCTATAGT 57.613 39.130 0.00 0.00 0.00 2.12
923 946 5.399858 TCACAACGTTCTTGCTCTATAGTC 58.600 41.667 0.00 0.00 0.00 2.59
924 947 5.183331 TCACAACGTTCTTGCTCTATAGTCT 59.817 40.000 0.00 0.00 0.00 3.24
925 948 6.373495 TCACAACGTTCTTGCTCTATAGTCTA 59.627 38.462 0.00 0.00 0.00 2.59
926 949 7.067129 TCACAACGTTCTTGCTCTATAGTCTAT 59.933 37.037 0.00 0.00 0.00 1.98
927 950 8.343366 CACAACGTTCTTGCTCTATAGTCTATA 58.657 37.037 0.00 0.00 0.00 1.31
952 986 4.002797 CCCCCTGTAGCAAGTTGC 57.997 61.111 20.44 20.44 45.46 4.17
1056 1099 3.508012 TCCTCACACTGTTAGCTCTCTTC 59.492 47.826 0.00 0.00 0.00 2.87
1182 1225 4.892002 GACACCGGGTCCAAGTTT 57.108 55.556 6.32 0.00 40.83 2.66
1353 1396 7.821652 TCTACTTCTATCCGATTGCTTATGAG 58.178 38.462 0.00 0.00 0.00 2.90
1427 1470 6.076981 ACTCTTAAATGGTTTCAGTGCTTG 57.923 37.500 0.00 0.00 0.00 4.01
1490 1533 6.438763 GTGAATTCTCGGTGAATGTTTCTTT 58.561 36.000 7.05 0.00 43.99 2.52
1525 1571 1.304713 ACCTTTGCCCCATCAGCAG 60.305 57.895 0.00 0.00 42.17 4.24
1595 1641 6.406370 CCACTCCTGACATCTTTACAACATA 58.594 40.000 0.00 0.00 0.00 2.29
1615 1667 1.960417 TGACACAAGATTTGTCGGCA 58.040 45.000 0.00 0.00 45.44 5.69
1616 1668 2.503331 TGACACAAGATTTGTCGGCAT 58.497 42.857 0.00 0.00 45.44 4.40
1617 1669 3.669536 TGACACAAGATTTGTCGGCATA 58.330 40.909 0.00 0.00 45.44 3.14
1618 1670 3.684305 TGACACAAGATTTGTCGGCATAG 59.316 43.478 0.00 0.00 45.44 2.23
1619 1671 3.009723 ACACAAGATTTGTCGGCATAGG 58.990 45.455 0.00 0.00 43.23 2.57
1624 1676 1.742831 GATTTGTCGGCATAGGCACAA 59.257 47.619 0.15 1.00 43.71 3.33
1686 1738 2.035626 CGGCTCAATGTTGGGGGT 59.964 61.111 0.00 0.00 0.00 4.95
1703 1755 1.313091 GGTGAAGCCATTTCCCCGAC 61.313 60.000 0.00 0.00 34.77 4.79
1737 1792 2.186602 TTTACCGCTCATGGGCCGAA 62.187 55.000 13.12 0.11 0.00 4.30
1760 1824 6.529084 AGATTCCCCATACATATTTGGTGA 57.471 37.500 0.00 0.00 0.00 4.02
1768 1832 5.163205 CCATACATATTTGGTGACTCTGGGA 60.163 44.000 0.00 0.00 0.00 4.37
1770 1834 7.256655 CCATACATATTTGGTGACTCTGGGATA 60.257 40.741 0.00 0.00 0.00 2.59
1771 1835 6.770286 ACATATTTGGTGACTCTGGGATAT 57.230 37.500 0.00 0.00 0.00 1.63
1787 1851 8.143673 TCTGGGATATCATTCTCCAAAGATAG 57.856 38.462 4.83 0.00 32.90 2.08
1870 1934 2.849096 TACAGCTCGGTCGATGGGGT 62.849 60.000 0.00 0.00 0.00 4.95
1883 1947 1.259840 ATGGGGTCAAATGCACAGGC 61.260 55.000 0.00 0.00 41.68 4.85
1904 1968 4.525100 GGCCAACCTGAATTACAACCTTAA 59.475 41.667 0.00 0.00 0.00 1.85
1935 1999 1.714899 CGGTTGATGCGGGGTTCATC 61.715 60.000 0.00 0.00 40.42 2.92
1971 2035 7.824779 AGGTTCCATTTCTGTGAGATTAAGTAC 59.175 37.037 0.00 0.00 0.00 2.73
2017 2081 4.265556 GGTCGTTCTTCATCTACATCAACG 59.734 45.833 0.00 0.00 37.17 4.10
2099 2163 9.809096 AACAACATACAGAGACTATGTTATCAG 57.191 33.333 8.24 0.00 41.05 2.90
2100 2164 7.923344 ACAACATACAGAGACTATGTTATCAGC 59.077 37.037 8.24 0.00 41.05 4.26
2135 2199 0.034756 CAGGTGGACGTGTGGATTGA 59.965 55.000 0.00 0.00 0.00 2.57
2142 2206 2.480419 GGACGTGTGGATTGAACTTCAG 59.520 50.000 0.00 0.00 0.00 3.02
2160 2224 5.703130 ACTTCAGCCTGATCTTTCAAGTAAC 59.297 40.000 0.00 0.00 0.00 2.50
2216 2280 2.168728 AGATCTTCAAGCTACCGGGTTC 59.831 50.000 4.31 0.00 32.86 3.62
2237 2382 4.658063 TCCGGTACAAATGAATCCAAAGT 58.342 39.130 0.00 0.00 0.00 2.66
2246 2391 3.557577 TGAATCCAAAGTTGACATGCG 57.442 42.857 0.00 0.00 0.00 4.73
2267 2412 1.849039 AGCAGCCCTCATTGGAACTAT 59.151 47.619 0.00 0.00 38.35 2.12
2268 2413 2.158696 AGCAGCCCTCATTGGAACTATC 60.159 50.000 0.00 0.00 38.35 2.08
2296 2441 5.526846 GGTTTTTCTTTGATGTTGATTGCCA 59.473 36.000 0.00 0.00 0.00 4.92
2301 2446 6.788684 TCTTTGATGTTGATTGCCATTTTG 57.211 33.333 0.00 0.00 0.00 2.44
2308 2453 0.994263 GATTGCCATTTTGAGCACGC 59.006 50.000 0.00 0.00 39.10 5.34
2309 2454 0.317799 ATTGCCATTTTGAGCACGCA 59.682 45.000 0.00 0.00 39.10 5.24
2313 2458 1.621107 CCATTTTGAGCACGCATGTC 58.379 50.000 0.00 0.00 0.00 3.06
2319 2464 0.037046 TGAGCACGCATGTCATCTGT 60.037 50.000 0.00 0.00 0.00 3.41
2322 2467 0.933097 GCACGCATGTCATCTGTAGG 59.067 55.000 0.00 0.00 0.00 3.18
2335 2480 2.811410 TCTGTAGGCGGAAGAAGGTAA 58.189 47.619 0.00 0.00 0.00 2.85
2336 2481 3.167485 TCTGTAGGCGGAAGAAGGTAAA 58.833 45.455 0.00 0.00 0.00 2.01
2378 2523 3.014623 ACTACGGACATCTGAATCGTCA 58.985 45.455 0.00 0.00 35.60 4.35
2387 2532 3.726291 TCTGAATCGTCACACTGAACA 57.274 42.857 0.00 0.00 0.00 3.18
2388 2533 4.053469 TCTGAATCGTCACACTGAACAA 57.947 40.909 0.00 0.00 0.00 2.83
2395 2540 3.063452 TCGTCACACTGAACAAAGAAAGC 59.937 43.478 0.00 0.00 0.00 3.51
2415 2560 1.600663 CCTACATGTGATCTCGTCCGC 60.601 57.143 9.11 0.00 0.00 5.54
3108 3253 1.893808 CTTGCGTGACTGGGCACTT 60.894 57.895 5.00 0.00 39.20 3.16
3373 3521 1.811965 TGCATTCAGACAAACCATCCG 59.188 47.619 0.00 0.00 0.00 4.18
3394 3542 2.484264 GCCAACTCAACAATTAGCGTCT 59.516 45.455 0.00 0.00 0.00 4.18
3399 3547 1.992667 TCAACAATTAGCGTCTCAGCG 59.007 47.619 0.00 0.00 43.00 5.18
3446 3594 1.002033 GCATGCAGAAGGCCGATAAAG 60.002 52.381 14.21 0.00 43.89 1.85
3668 3842 6.836577 TTTGTTATTTTGCTACAAGGTTGC 57.163 33.333 0.00 0.00 33.74 4.17
3693 3867 3.199508 AGTGCCTCAGTTATCTTGATGCT 59.800 43.478 4.61 0.00 0.00 3.79
3724 3898 5.939764 AACTACAGCCATATCTGACTGAA 57.060 39.130 1.38 0.00 37.51 3.02
3745 3919 5.369699 TGAACTATCAAGGATAAAGGAGGGG 59.630 44.000 0.00 0.00 30.99 4.79
3752 3926 3.930035 AGGATAAAGGAGGGGTCTACAG 58.070 50.000 0.00 0.00 0.00 2.74
3757 3931 4.628661 AAAGGAGGGGTCTACAGTAGAT 57.371 45.455 13.59 0.00 37.13 1.98
3806 3980 4.180057 CCTTCTCCGAGTCAATGAAGAAG 58.820 47.826 12.37 12.37 37.03 2.85
3811 3985 4.498241 TCCGAGTCAATGAAGAAGTCATG 58.502 43.478 0.00 0.00 46.80 3.07
3982 4156 0.256752 AGCCTCATTGGTGCTATGCA 59.743 50.000 0.00 0.00 38.35 3.96
4127 4303 6.136071 CCTACACTCAAACTTTTCACATTCG 58.864 40.000 0.00 0.00 0.00 3.34
4128 4304 4.351192 ACACTCAAACTTTTCACATTCGC 58.649 39.130 0.00 0.00 0.00 4.70
4131 4307 3.872354 TCAAACTTTTCACATTCGCTCG 58.128 40.909 0.00 0.00 0.00 5.03
4136 4312 2.941891 TTTCACATTCGCTCGAACAC 57.058 45.000 6.88 0.00 36.91 3.32
4158 4334 7.560368 ACACTTTGTTCACCCATTCATTTTAA 58.440 30.769 0.00 0.00 0.00 1.52
4193 4369 8.070171 GCAACTTACGCATATTCTGTAATCATT 58.930 33.333 0.00 0.00 0.00 2.57
4209 4385 5.228635 GTAATCATTGATTTTGCACTCGCAG 59.771 40.000 16.62 0.00 40.19 5.18
4230 4407 8.726068 TCGCAGATTCATGTGTTTTCTTTATTA 58.274 29.630 0.00 0.00 32.46 0.98
4283 4469 7.912250 CACACCTGAATCTAAAATATGCAGTTC 59.088 37.037 0.00 0.00 29.11 3.01
4286 4472 5.737353 TGAATCTAAAATATGCAGTTCGCG 58.263 37.500 0.00 0.00 46.97 5.87
4351 4539 3.137728 ACCAGCACCCTTTTTACTGTACT 59.862 43.478 0.00 0.00 0.00 2.73
4352 4540 4.142038 CCAGCACCCTTTTTACTGTACTT 58.858 43.478 0.00 0.00 0.00 2.24
4353 4541 5.163174 ACCAGCACCCTTTTTACTGTACTTA 60.163 40.000 0.00 0.00 0.00 2.24
4407 4595 5.707764 GGAGCTTCTATTTGGTCAAGAGTTT 59.292 40.000 0.00 0.00 32.93 2.66
4418 4606 7.654022 TTGGTCAAGAGTTTGTTATTCCTTT 57.346 32.000 0.00 0.00 35.73 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 4.918810 AAACCTGAATTGTTGTCACTCC 57.081 40.909 0.00 0.00 0.00 3.85
24 25 7.839680 ACAATCTAAGGAAAACCTGAATTGT 57.160 32.000 13.38 13.38 0.00 2.71
30 31 8.716646 AAACAAAACAATCTAAGGAAAACCTG 57.283 30.769 0.00 0.00 0.00 4.00
78 82 5.046950 AGGTACTCTTCTTGCTAGGTTCAAG 60.047 44.000 0.00 3.01 41.57 3.02
80 84 4.417437 AGGTACTCTTCTTGCTAGGTTCA 58.583 43.478 0.00 0.00 0.00 3.18
100 104 4.252971 TGACGTTTCCACTAAGAAGAGG 57.747 45.455 0.00 0.00 34.96 3.69
101 105 6.598753 TTTTGACGTTTCCACTAAGAAGAG 57.401 37.500 0.00 0.00 0.00 2.85
102 106 8.665643 TTATTTTGACGTTTCCACTAAGAAGA 57.334 30.769 0.00 0.00 0.00 2.87
105 109 8.347035 CCTTTTATTTTGACGTTTCCACTAAGA 58.653 33.333 0.00 0.00 0.00 2.10
106 110 7.114388 GCCTTTTATTTTGACGTTTCCACTAAG 59.886 37.037 0.00 0.00 0.00 2.18
111 117 5.263968 TGCCTTTTATTTTGACGTTTCCA 57.736 34.783 0.00 0.00 0.00 3.53
118 124 6.019075 GTGGACAACTTGCCTTTTATTTTGAC 60.019 38.462 4.52 0.00 0.00 3.18
155 161 4.160642 TGATTCCACATCCAGATTCCAG 57.839 45.455 0.00 0.00 0.00 3.86
157 163 4.722220 TGATGATTCCACATCCAGATTCC 58.278 43.478 0.00 0.00 43.96 3.01
158 164 6.489022 TGAATGATGATTCCACATCCAGATTC 59.511 38.462 2.25 0.00 43.96 2.52
159 165 6.370453 TGAATGATGATTCCACATCCAGATT 58.630 36.000 2.25 0.00 43.96 2.40
160 166 5.948842 TGAATGATGATTCCACATCCAGAT 58.051 37.500 2.25 0.00 43.96 2.90
161 167 5.374071 CTGAATGATGATTCCACATCCAGA 58.626 41.667 2.25 0.00 43.96 3.86
162 168 4.519350 CCTGAATGATGATTCCACATCCAG 59.481 45.833 2.25 0.00 43.96 3.86
163 169 4.166531 TCCTGAATGATGATTCCACATCCA 59.833 41.667 2.25 0.00 43.96 3.41
164 170 4.518211 GTCCTGAATGATGATTCCACATCC 59.482 45.833 2.25 0.00 43.96 3.51
210 216 1.238439 AAACATGGAGCAACAGTCCG 58.762 50.000 0.00 0.00 36.82 4.79
251 258 7.432059 GGAGGGAGTAGTATACATTTGTGTAC 58.568 42.308 5.50 8.95 46.26 2.90
252 259 6.263842 CGGAGGGAGTAGTATACATTTGTGTA 59.736 42.308 5.50 0.00 46.26 2.90
269 277 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
271 279 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
272 280 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
273 281 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
275 283 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
276 284 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
277 285 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
278 286 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
279 287 7.273381 GTCCATTTTGATGACAAGTATTTTCGG 59.727 37.037 0.00 0.00 37.32 4.30
280 288 7.807433 TGTCCATTTTGATGACAAGTATTTTCG 59.193 33.333 0.00 0.00 37.32 3.46
281 289 9.474920 TTGTCCATTTTGATGACAAGTATTTTC 57.525 29.630 0.00 0.00 37.32 2.29
282 290 9.829507 TTTGTCCATTTTGATGACAAGTATTTT 57.170 25.926 0.00 0.00 37.13 1.82
283 291 9.829507 TTTTGTCCATTTTGATGACAAGTATTT 57.170 25.926 0.00 0.00 37.13 1.40
284 292 9.480053 CTTTTGTCCATTTTGATGACAAGTATT 57.520 29.630 0.00 0.00 37.13 1.89
285 293 8.090214 CCTTTTGTCCATTTTGATGACAAGTAT 58.910 33.333 0.00 0.00 37.13 2.12
286 294 7.432869 CCTTTTGTCCATTTTGATGACAAGTA 58.567 34.615 0.00 0.00 37.13 2.24
287 295 6.282930 CCTTTTGTCCATTTTGATGACAAGT 58.717 36.000 0.00 0.00 37.13 3.16
288 296 5.697633 CCCTTTTGTCCATTTTGATGACAAG 59.302 40.000 0.00 0.00 37.13 3.16
289 297 5.454471 CCCCTTTTGTCCATTTTGATGACAA 60.454 40.000 0.00 0.00 34.47 3.18
290 298 4.040217 CCCCTTTTGTCCATTTTGATGACA 59.960 41.667 0.00 0.00 0.00 3.58
291 299 4.283212 TCCCCTTTTGTCCATTTTGATGAC 59.717 41.667 0.00 0.00 0.00 3.06
292 300 4.487804 TCCCCTTTTGTCCATTTTGATGA 58.512 39.130 0.00 0.00 0.00 2.92
293 301 4.888326 TCCCCTTTTGTCCATTTTGATG 57.112 40.909 0.00 0.00 0.00 3.07
294 302 4.845796 ACATCCCCTTTTGTCCATTTTGAT 59.154 37.500 0.00 0.00 0.00 2.57
295 303 4.230455 ACATCCCCTTTTGTCCATTTTGA 58.770 39.130 0.00 0.00 0.00 2.69
296 304 4.622260 ACATCCCCTTTTGTCCATTTTG 57.378 40.909 0.00 0.00 0.00 2.44
297 305 6.263754 AGATACATCCCCTTTTGTCCATTTT 58.736 36.000 0.00 0.00 0.00 1.82
298 306 5.842339 AGATACATCCCCTTTTGTCCATTT 58.158 37.500 0.00 0.00 0.00 2.32
299 307 5.472301 AGATACATCCCCTTTTGTCCATT 57.528 39.130 0.00 0.00 0.00 3.16
300 308 5.911178 TCTAGATACATCCCCTTTTGTCCAT 59.089 40.000 0.00 0.00 0.00 3.41
301 309 5.285401 TCTAGATACATCCCCTTTTGTCCA 58.715 41.667 0.00 0.00 0.00 4.02
302 310 5.888982 TCTAGATACATCCCCTTTTGTCC 57.111 43.478 0.00 0.00 0.00 4.02
303 311 6.890293 AGTTCTAGATACATCCCCTTTTGTC 58.110 40.000 0.00 0.00 0.00 3.18
304 312 6.893020 AGTTCTAGATACATCCCCTTTTGT 57.107 37.500 0.00 0.00 0.00 2.83
305 313 9.681062 TTTTAGTTCTAGATACATCCCCTTTTG 57.319 33.333 0.00 0.00 0.00 2.44
309 317 9.670442 TGTATTTTAGTTCTAGATACATCCCCT 57.330 33.333 0.00 0.00 30.60 4.79
325 333 9.845214 AGGGGATGTATCTAGATGTATTTTAGT 57.155 33.333 15.79 0.00 0.00 2.24
333 341 9.170890 TGAATAAAAGGGGATGTATCTAGATGT 57.829 33.333 15.79 1.25 0.00 3.06
334 342 9.442047 GTGAATAAAAGGGGATGTATCTAGATG 57.558 37.037 15.79 0.00 0.00 2.90
335 343 9.398921 AGTGAATAAAAGGGGATGTATCTAGAT 57.601 33.333 10.73 10.73 0.00 1.98
336 344 8.798975 AGTGAATAAAAGGGGATGTATCTAGA 57.201 34.615 0.00 0.00 0.00 2.43
337 345 9.853177 AAAGTGAATAAAAGGGGATGTATCTAG 57.147 33.333 0.00 0.00 0.00 2.43
338 346 9.627123 CAAAGTGAATAAAAGGGGATGTATCTA 57.373 33.333 0.00 0.00 0.00 1.98
339 347 8.336235 TCAAAGTGAATAAAAGGGGATGTATCT 58.664 33.333 0.00 0.00 0.00 1.98
340 348 8.519799 TCAAAGTGAATAAAAGGGGATGTATC 57.480 34.615 0.00 0.00 0.00 2.24
341 349 8.917088 CATCAAAGTGAATAAAAGGGGATGTAT 58.083 33.333 0.00 0.00 0.00 2.29
342 350 8.112822 TCATCAAAGTGAATAAAAGGGGATGTA 58.887 33.333 0.00 0.00 32.47 2.29
343 351 6.953520 TCATCAAAGTGAATAAAAGGGGATGT 59.046 34.615 0.00 0.00 32.47 3.06
344 352 7.093814 TGTCATCAAAGTGAATAAAAGGGGATG 60.094 37.037 0.00 0.00 0.00 3.51
345 353 6.953520 TGTCATCAAAGTGAATAAAAGGGGAT 59.046 34.615 0.00 0.00 0.00 3.85
346 354 6.310941 TGTCATCAAAGTGAATAAAAGGGGA 58.689 36.000 0.00 0.00 0.00 4.81
347 355 6.588719 TGTCATCAAAGTGAATAAAAGGGG 57.411 37.500 0.00 0.00 0.00 4.79
348 356 7.661040 ACTTGTCATCAAAGTGAATAAAAGGG 58.339 34.615 0.00 0.00 32.87 3.95
353 361 8.956426 GGGAATACTTGTCATCAAAGTGAATAA 58.044 33.333 0.00 0.00 32.87 1.40
354 362 7.279981 CGGGAATACTTGTCATCAAAGTGAATA 59.720 37.037 0.00 0.00 32.87 1.75
355 363 6.094048 CGGGAATACTTGTCATCAAAGTGAAT 59.906 38.462 0.00 0.00 32.87 2.57
356 364 5.411361 CGGGAATACTTGTCATCAAAGTGAA 59.589 40.000 0.00 0.00 32.87 3.18
357 365 4.935205 CGGGAATACTTGTCATCAAAGTGA 59.065 41.667 0.00 0.00 32.87 3.41
358 366 4.094887 CCGGGAATACTTGTCATCAAAGTG 59.905 45.833 0.00 0.00 32.87 3.16
359 367 4.019681 TCCGGGAATACTTGTCATCAAAGT 60.020 41.667 0.00 0.00 32.87 2.66
360 368 4.332819 GTCCGGGAATACTTGTCATCAAAG 59.667 45.833 0.00 0.00 32.87 2.77
361 369 4.258543 GTCCGGGAATACTTGTCATCAAA 58.741 43.478 0.00 0.00 32.87 2.69
362 370 3.677700 CGTCCGGGAATACTTGTCATCAA 60.678 47.826 0.00 0.00 0.00 2.57
363 371 2.159156 CGTCCGGGAATACTTGTCATCA 60.159 50.000 0.00 0.00 0.00 3.07
364 372 2.470821 CGTCCGGGAATACTTGTCATC 58.529 52.381 0.00 0.00 0.00 2.92
365 373 1.138266 CCGTCCGGGAATACTTGTCAT 59.862 52.381 0.00 0.00 38.47 3.06
366 374 0.533491 CCGTCCGGGAATACTTGTCA 59.467 55.000 0.00 0.00 38.47 3.58
367 375 0.819582 TCCGTCCGGGAATACTTGTC 59.180 55.000 0.00 0.00 43.62 3.18
368 376 0.822164 CTCCGTCCGGGAATACTTGT 59.178 55.000 0.00 0.00 46.61 3.16
369 377 0.104304 CCTCCGTCCGGGAATACTTG 59.896 60.000 0.00 0.00 46.61 3.16
370 378 1.047034 CCCTCCGTCCGGGAATACTT 61.047 60.000 0.00 0.00 46.61 2.24
371 379 1.457079 CCCTCCGTCCGGGAATACT 60.457 63.158 0.00 0.00 46.61 2.12
372 380 3.135814 CCCTCCGTCCGGGAATAC 58.864 66.667 0.00 0.00 46.61 1.89
377 385 0.757935 TATTTCTCCCTCCGTCCGGG 60.758 60.000 0.00 0.00 43.38 5.73
378 386 1.339097 ATATTTCTCCCTCCGTCCGG 58.661 55.000 0.00 0.00 0.00 5.14
379 387 3.611057 CGTAATATTTCTCCCTCCGTCCG 60.611 52.174 0.00 0.00 0.00 4.79
380 388 3.571401 TCGTAATATTTCTCCCTCCGTCC 59.429 47.826 0.00 0.00 0.00 4.79
381 389 4.843220 TCGTAATATTTCTCCCTCCGTC 57.157 45.455 0.00 0.00 0.00 4.79
382 390 4.587684 ACATCGTAATATTTCTCCCTCCGT 59.412 41.667 0.00 0.00 0.00 4.69
383 391 5.135508 ACATCGTAATATTTCTCCCTCCG 57.864 43.478 0.00 0.00 0.00 4.63
384 392 7.803279 AAAACATCGTAATATTTCTCCCTCC 57.197 36.000 0.00 0.00 0.00 4.30
385 393 9.760077 TCTAAAACATCGTAATATTTCTCCCTC 57.240 33.333 0.00 0.00 0.00 4.30
421 429 9.798994 GGAAACATAAGATCTTTTAGACGACTA 57.201 33.333 14.36 0.00 0.00 2.59
422 430 8.532819 AGGAAACATAAGATCTTTTAGACGACT 58.467 33.333 14.36 1.51 0.00 4.18
423 431 8.705048 AGGAAACATAAGATCTTTTAGACGAC 57.295 34.615 14.36 0.00 0.00 4.34
446 454 4.285863 AGAGATCAAGTCCCTCTGTAAGG 58.714 47.826 0.00 0.00 45.77 2.69
447 455 5.930837 AAGAGATCAAGTCCCTCTGTAAG 57.069 43.478 0.00 0.00 37.35 2.34
448 456 6.019748 AGAAAGAGATCAAGTCCCTCTGTAA 58.980 40.000 0.00 0.00 37.35 2.41
449 457 5.584913 AGAAAGAGATCAAGTCCCTCTGTA 58.415 41.667 0.00 0.00 37.35 2.74
450 458 4.424842 AGAAAGAGATCAAGTCCCTCTGT 58.575 43.478 0.00 0.00 37.35 3.41
451 459 5.419239 AAGAAAGAGATCAAGTCCCTCTG 57.581 43.478 0.00 0.00 37.35 3.35
452 460 7.390823 GTTTAAGAAAGAGATCAAGTCCCTCT 58.609 38.462 0.00 0.00 38.79 3.69
453 461 6.311690 CGTTTAAGAAAGAGATCAAGTCCCTC 59.688 42.308 0.00 0.00 0.00 4.30
454 462 6.166982 CGTTTAAGAAAGAGATCAAGTCCCT 58.833 40.000 0.00 0.00 0.00 4.20
455 463 5.932883 ACGTTTAAGAAAGAGATCAAGTCCC 59.067 40.000 0.00 0.00 0.00 4.46
456 464 7.813627 ACTACGTTTAAGAAAGAGATCAAGTCC 59.186 37.037 0.00 0.00 0.00 3.85
457 465 8.745464 ACTACGTTTAAGAAAGAGATCAAGTC 57.255 34.615 0.00 0.00 0.00 3.01
465 473 9.793245 CATGTACAAACTACGTTTAAGAAAGAG 57.207 33.333 0.00 0.00 33.70 2.85
472 480 8.991243 ATCTAGCATGTACAAACTACGTTTAA 57.009 30.769 0.00 0.00 33.70 1.52
480 488 6.940739 AGTGAAGATCTAGCATGTACAAACT 58.059 36.000 0.00 2.68 0.00 2.66
529 539 7.375053 AGGAATGCGAAAATTTAGCTAAACAA 58.625 30.769 20.85 0.00 0.00 2.83
643 662 1.813513 AACTGAAGTTCCTGGCATCG 58.186 50.000 0.00 0.00 31.64 3.84
701 720 1.334960 GCAGAACATCCACGTGTTTGG 60.335 52.381 15.65 0.00 42.08 3.28
835 855 5.292671 GATCGTAGGATCGTGCTATTGTA 57.707 43.478 9.51 0.00 39.72 2.41
853 873 2.627945 TGTCGGGAAAATTGAGGATCG 58.372 47.619 0.00 0.00 38.61 3.69
906 929 8.561212 AGTTGTATAGACTATAGAGCAAGAACG 58.439 37.037 6.78 0.00 0.00 3.95
952 986 2.781681 AATTGGGGACTCCGTTACAG 57.218 50.000 0.00 0.00 38.76 2.74
958 992 5.473504 CAGGATAAAATAATTGGGGACTCCG 59.526 44.000 0.00 0.00 38.76 4.63
1011 1054 4.546829 TGTGAGGGTAACTGGTAATGTC 57.453 45.455 0.00 0.00 0.00 3.06
1014 1057 4.788617 AGGAATGTGAGGGTAACTGGTAAT 59.211 41.667 0.00 0.00 0.00 1.89
1077 1120 1.610102 CCAGAGGCTGTGGAGTTCTTG 60.610 57.143 25.63 0.00 37.23 3.02
1080 1123 1.376553 GCCAGAGGCTGTGGAGTTC 60.377 63.158 32.84 12.30 46.69 3.01
1182 1225 1.985159 ACTCCTTCCAGTAATGGTGCA 59.015 47.619 9.41 0.00 0.00 4.57
1218 1261 2.170817 GGGGAGTGAAGGGTCTTGATAC 59.829 54.545 0.00 0.00 0.00 2.24
1253 1296 2.029728 GTGAAGATGCGTGCAGTCATAC 59.970 50.000 0.00 0.00 0.00 2.39
1353 1396 2.866762 GGCATCGGAGACAACATAGTTC 59.133 50.000 0.00 0.00 42.51 3.01
1427 1470 2.669569 TCGCCTGAGCAGTTTGCC 60.670 61.111 0.00 0.00 46.52 4.52
1490 1533 1.553690 GGTGAGGTCCAAGCTGCCTA 61.554 60.000 0.00 0.00 31.89 3.93
1525 1571 7.486647 ACAAATGCATAAGAACCATTCTGATC 58.513 34.615 0.00 0.00 40.59 2.92
1595 1641 2.503331 TGCCGACAAATCTTGTGTCAT 58.497 42.857 5.50 0.00 45.52 3.06
1615 1667 4.785346 ATGAGAATGGAGTTGTGCCTAT 57.215 40.909 0.00 0.00 0.00 2.57
1616 1668 4.517285 GAATGAGAATGGAGTTGTGCCTA 58.483 43.478 0.00 0.00 0.00 3.93
1617 1669 3.350833 GAATGAGAATGGAGTTGTGCCT 58.649 45.455 0.00 0.00 0.00 4.75
1618 1670 2.096496 CGAATGAGAATGGAGTTGTGCC 59.904 50.000 0.00 0.00 0.00 5.01
1619 1671 2.476854 GCGAATGAGAATGGAGTTGTGC 60.477 50.000 0.00 0.00 0.00 4.57
1624 1676 0.811616 GCGGCGAATGAGAATGGAGT 60.812 55.000 12.98 0.00 0.00 3.85
1652 1704 2.029623 GCCGGTACATAGTCTGGAAGA 58.970 52.381 1.90 0.00 43.69 2.87
1686 1738 0.111446 TTGTCGGGGAAATGGCTTCA 59.889 50.000 0.00 0.00 35.55 3.02
1703 1755 3.487563 GGTAAAAGCCCGAGTCATTTG 57.512 47.619 0.00 0.00 0.00 2.32
1737 1792 6.529084 TCACCAAATATGTATGGGGAATCT 57.471 37.500 5.21 0.00 45.94 2.40
1760 1824 5.907662 TCTTTGGAGAATGATATCCCAGAGT 59.092 40.000 12.31 0.00 36.01 3.24
1870 1934 0.469705 AGGTTGGCCTGTGCATTTGA 60.470 50.000 3.32 0.00 45.05 2.69
1883 1947 7.039363 TCCATTTAAGGTTGTAATTCAGGTTGG 60.039 37.037 0.00 0.00 0.00 3.77
1904 1968 3.181491 CGCATCAACCGGTAAAATCCATT 60.181 43.478 8.00 0.00 0.00 3.16
1971 2035 5.652452 CCTCTGGTTTATCTTGGTAAAAGGG 59.348 44.000 0.00 0.00 0.00 3.95
2046 2110 0.685131 TTCCTCCGCTCCAACCGATA 60.685 55.000 0.00 0.00 0.00 2.92
2051 2115 1.521681 CCGATTCCTCCGCTCCAAC 60.522 63.158 0.00 0.00 0.00 3.77
2099 2163 2.290323 ACCTGACCAGAACCAATAGTGC 60.290 50.000 0.00 0.00 0.00 4.40
2100 2164 3.338249 CACCTGACCAGAACCAATAGTG 58.662 50.000 0.00 0.00 0.00 2.74
2125 2189 2.227388 CAGGCTGAAGTTCAATCCACAC 59.773 50.000 9.42 3.08 0.00 3.82
2135 2199 4.723309 ACTTGAAAGATCAGGCTGAAGTT 58.277 39.130 22.84 14.62 36.17 2.66
2142 2206 3.686016 TGGGTTACTTGAAAGATCAGGC 58.314 45.455 0.00 0.00 36.17 4.85
2216 2280 5.048364 TCAACTTTGGATTCATTTGTACCGG 60.048 40.000 0.00 0.00 0.00 5.28
2221 2366 5.697633 GCATGTCAACTTTGGATTCATTTGT 59.302 36.000 0.00 0.00 0.00 2.83
2225 2370 3.758023 TCGCATGTCAACTTTGGATTCAT 59.242 39.130 0.00 0.00 0.00 2.57
2226 2371 3.145286 TCGCATGTCAACTTTGGATTCA 58.855 40.909 0.00 0.00 0.00 2.57
2227 2372 3.751621 CTCGCATGTCAACTTTGGATTC 58.248 45.455 0.00 0.00 0.00 2.52
2237 2382 2.747460 GGGCTGCTCGCATGTCAA 60.747 61.111 0.00 0.00 41.67 3.18
2246 2391 0.034670 AGTTCCAATGAGGGCTGCTC 60.035 55.000 0.00 0.00 38.24 4.26
2254 2399 3.543680 ACCACCGATAGTTCCAATGAG 57.456 47.619 0.00 0.00 0.00 2.90
2258 2403 4.721132 AGAAAAACCACCGATAGTTCCAA 58.279 39.130 0.00 0.00 0.00 3.53
2267 2412 4.399618 TCAACATCAAAGAAAAACCACCGA 59.600 37.500 0.00 0.00 0.00 4.69
2268 2413 4.677584 TCAACATCAAAGAAAAACCACCG 58.322 39.130 0.00 0.00 0.00 4.94
2296 2441 2.751259 AGATGACATGCGTGCTCAAAAT 59.249 40.909 5.64 0.00 0.00 1.82
2301 2446 1.857217 CTACAGATGACATGCGTGCTC 59.143 52.381 5.64 3.80 0.00 4.26
2308 2453 2.101415 TCTTCCGCCTACAGATGACATG 59.899 50.000 0.00 0.00 0.00 3.21
2309 2454 2.388735 TCTTCCGCCTACAGATGACAT 58.611 47.619 0.00 0.00 0.00 3.06
2313 2458 1.482593 ACCTTCTTCCGCCTACAGATG 59.517 52.381 0.00 0.00 0.00 2.90
2319 2464 4.091549 TCTTCTTTACCTTCTTCCGCCTA 58.908 43.478 0.00 0.00 0.00 3.93
2322 2467 3.927854 ACTCTTCTTTACCTTCTTCCGC 58.072 45.455 0.00 0.00 0.00 5.54
2336 2481 2.365617 TCGGTCTTGCAAGAACTCTTCT 59.634 45.455 35.02 0.00 40.62 2.85
2378 2523 4.523083 TGTAGGCTTTCTTTGTTCAGTGT 58.477 39.130 0.00 0.00 0.00 3.55
2387 2532 4.872691 CGAGATCACATGTAGGCTTTCTTT 59.127 41.667 0.00 0.00 0.00 2.52
2388 2533 4.081420 ACGAGATCACATGTAGGCTTTCTT 60.081 41.667 0.00 0.00 0.00 2.52
2395 2540 1.600663 GCGGACGAGATCACATGTAGG 60.601 57.143 0.00 0.00 0.00 3.18
2415 2560 7.386848 ACTTGAATTTCTGCAAATGAGAAATGG 59.613 33.333 10.57 5.87 45.35 3.16
2703 2848 4.672587 TCTGGTGTTGTATAGATGCTCC 57.327 45.455 0.00 0.00 0.00 4.70
2967 3112 1.893786 CTGCAGCCGGAAGTACTCT 59.106 57.895 5.05 0.00 0.00 3.24
3108 3253 3.297134 ACACCTCTCTTTTGGCAAGAA 57.703 42.857 0.00 0.00 0.00 2.52
3319 3464 1.949799 AGAGATGAAGCACCCTCTGT 58.050 50.000 0.00 0.00 34.96 3.41
3373 3521 2.484264 AGACGCTAATTGTTGAGTTGGC 59.516 45.455 0.00 0.00 0.00 4.52
3394 3542 2.042686 AATATGGCTTTCTGCGCTGA 57.957 45.000 13.46 13.46 44.05 4.26
3399 3547 7.115947 GCAATATCTGAAAATATGGCTTTCTGC 59.884 37.037 1.25 0.00 36.17 4.26
3403 3551 5.922544 GCGCAATATCTGAAAATATGGCTTT 59.077 36.000 0.30 0.00 36.70 3.51
3724 3898 4.908481 GACCCCTCCTTTATCCTTGATAGT 59.092 45.833 0.00 0.00 0.00 2.12
3757 3931 9.485206 GAGAGTGCTTAAAATTCGGGTAATATA 57.515 33.333 0.00 0.00 0.00 0.86
3811 3985 7.339466 ACCCCAATTAGATTGATTACACTGTTC 59.661 37.037 2.37 0.00 42.83 3.18
3982 4156 4.340666 CACTAGCTCCATATATCTGGCGAT 59.659 45.833 2.21 0.00 36.16 4.58
4020 4194 7.797038 AAAAACGTATGTCTACCTTTCACTT 57.203 32.000 0.00 0.00 0.00 3.16
4077 4251 9.213799 GTGGGCATTGAATTAAACAATTCTTAA 57.786 29.630 10.49 0.32 39.33 1.85
4158 4334 8.840321 AGAATATGCGTAAGTTGCAAGATTATT 58.160 29.630 0.00 0.00 46.87 1.40
4174 4350 9.454585 CAAAATCAATGATTACAGAATATGCGT 57.545 29.630 9.09 0.00 31.46 5.24
4267 4453 3.194861 AGCGCGAACTGCATATTTTAGA 58.805 40.909 12.10 0.00 46.97 2.10
4283 4469 3.708220 GAGGACTCCAGGAAGCGCG 62.708 68.421 0.00 0.00 0.00 6.86
4379 4567 6.248433 TCTTGACCAAATAGAAGCTCCAAAT 58.752 36.000 0.00 0.00 0.00 2.32
4407 4595 7.452880 CAAGATCTTGGACAAAGGAATAACA 57.547 36.000 25.14 0.00 36.46 2.41


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

AutoCloner maintained by Alex Coulton.