Multiple sequence alignment - TraesCS1D01G379000

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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 TraesCS1D01G379000 chr1D 100.000 5508 0 0 1 5508 455086098 455080591 0.000000e+00 10172
1 TraesCS1D01G379000 chr1B 91.592 4472 271 51 578 4985 625572310 625567880 0.000000e+00 6078
2 TraesCS1D01G379000 chr1B 90.193 3477 217 46 1358 4798 625508626 625505238 0.000000e+00 4418
3 TraesCS1D01G379000 chr1B 86.174 311 28 10 5076 5383 625567585 625567287 6.880000e-84 322
4 TraesCS1D01G379000 chr1B 84.685 222 20 7 371 590 625572540 625572331 5.590000e-50 209
5 TraesCS1D01G379000 chr1B 92.437 119 7 1 5390 5508 625543942 625543826 9.490000e-38 169
6 TraesCS1D01G379000 chr1A 91.958 4290 238 51 578 4793 548945337 548941081 0.000000e+00 5912
7 TraesCS1D01G379000 chr1A 83.915 516 43 15 4791 5276 548934293 548933788 1.810000e-124 457
8 TraesCS1D01G379000 chr1A 93.532 201 8 3 5313 5508 548932025 548931825 1.500000e-75 294
9 TraesCS1D01G379000 chr4B 84.896 384 22 18 567 916 236135830 236136211 6.790000e-94 355
10 TraesCS1D01G379000 chr4B 84.703 353 25 12 592 916 294099505 294099856 5.320000e-85 326
11 TraesCS1D01G379000 chr4B 82.700 237 29 8 1223 1449 237985489 237985255 3.360000e-47 200
12 TraesCS1D01G379000 chr4B 77.903 267 30 14 32 292 236135017 236135260 7.440000e-29 139
13 TraesCS1D01G379000 chr4B 77.068 266 34 13 32 292 294098669 294098912 1.610000e-25 128
14 TraesCS1D01G379000 chr7B 84.615 377 24 16 573 916 596287352 596286977 1.470000e-90 344
15 TraesCS1D01G379000 chr2B 83.408 223 23 9 1233 1443 190181056 190180836 1.570000e-45 195
16 TraesCS1D01G379000 chr7A 82.018 228 28 9 1233 1449 643653687 643653462 1.220000e-41 182
17 TraesCS1D01G379000 chr3A 80.156 257 21 11 40 292 358269958 358269728 1.230000e-36 165
18 TraesCS1D01G379000 chr3A 79.608 255 25 9 40 292 630363997 630363768 2.050000e-34 158


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 TraesCS1D01G379000 chr1D 455080591 455086098 5507 True 10172.0 10172 100.000000 1 5508 1 chr1D.!!$R1 5507
1 TraesCS1D01G379000 chr1B 625505238 625508626 3388 True 4418.0 4418 90.193000 1358 4798 1 chr1B.!!$R1 3440
2 TraesCS1D01G379000 chr1B 625567287 625572540 5253 True 2203.0 6078 87.483667 371 5383 3 chr1B.!!$R3 5012
3 TraesCS1D01G379000 chr1A 548941081 548945337 4256 True 5912.0 5912 91.958000 578 4793 1 chr1A.!!$R1 4215
4 TraesCS1D01G379000 chr1A 548931825 548934293 2468 True 375.5 457 88.723500 4791 5508 2 chr1A.!!$R2 717
5 TraesCS1D01G379000 chr4B 236135017 236136211 1194 False 247.0 355 81.399500 32 916 2 chr4B.!!$F1 884
6 TraesCS1D01G379000 chr4B 294098669 294099856 1187 False 227.0 326 80.885500 32 916 2 chr4B.!!$F2 884

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
158 162 0.032952 TTTAGCGCGTCTCTGTTGGT 59.967 50.000 8.43 0.00 0.00 3.67 F
159 163 0.032952 TTAGCGCGTCTCTGTTGGTT 59.967 50.000 8.43 0.00 0.00 3.67 F
1117 1460 0.179240 GAACGTGCTCATCTTGCGTG 60.179 55.000 0.00 0.00 35.88 5.34 F
1143 1486 1.302511 ATCCCGTTCACTGTGCACC 60.303 57.895 15.69 0.00 0.00 5.01 F
1607 1957 2.961526 TCTGGAAGGTAAGCGTGATC 57.038 50.000 0.00 0.00 0.00 2.92 F
3150 3525 0.597568 TGCAGGAAAGGTGCATTTCG 59.402 50.000 6.68 0.00 45.96 3.46 F
4104 4508 0.179134 GTCTCTGACGGCGCTAATGT 60.179 55.000 6.90 0.34 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1143 1486 0.316442 GTTCATCATCATGGCGCACG 60.316 55.000 10.83 0.00 0.00 5.34 R
1484 1834 1.000052 TCGTGTCAACCTGCGTCAATA 60.000 47.619 0.00 0.00 0.00 1.90 R
2458 2830 0.036010 TAGCTGGCCTGACAAGAAGC 60.036 55.000 14.77 6.57 0.00 3.86 R
2741 3114 2.673368 GGATGTGTTAGGAAACGAGCAG 59.327 50.000 0.00 0.00 38.53 4.24 R
3473 3851 0.548926 TCCCAGTGGGACCTGCATAA 60.549 55.000 28.04 0.86 46.17 1.90 R
4471 4880 0.599991 CGCCGCCATTATCTACAGCA 60.600 55.000 0.00 0.00 0.00 4.41 R
5412 7836 0.514691 GCAGTTCCAAGAGCTCAACG 59.485 55.000 17.77 8.83 0.00 4.10 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
30 31 2.502080 CGACGTCGCTGTCCACTC 60.502 66.667 26.59 0.00 35.40 3.51
31 32 2.126424 GACGTCGCTGTCCACTCC 60.126 66.667 0.00 0.00 32.61 3.85
32 33 3.948086 GACGTCGCTGTCCACTCCG 62.948 68.421 0.00 0.00 32.61 4.63
98 102 0.325110 TGCCTTCTCCTCCTCCTCTG 60.325 60.000 0.00 0.00 0.00 3.35
101 105 1.380515 TTCTCCTCCTCCTCTGCCG 60.381 63.158 0.00 0.00 0.00 5.69
121 125 3.470888 CGGCCTCGGTTCCTCCAT 61.471 66.667 0.00 0.00 35.57 3.41
122 126 2.998949 GGCCTCGGTTCCTCCATT 59.001 61.111 0.00 0.00 35.57 3.16
123 127 1.452108 GGCCTCGGTTCCTCCATTG 60.452 63.158 0.00 0.00 35.57 2.82
133 137 2.409870 CCTCCATTGGTTGCGCCTC 61.410 63.158 4.18 0.00 38.35 4.70
136 140 2.361610 CATTGGTTGCGCCTCCCT 60.362 61.111 4.18 0.00 38.35 4.20
148 152 1.218316 CCTCCCTCTTTTAGCGCGT 59.782 57.895 8.43 0.00 0.00 6.01
158 162 0.032952 TTTAGCGCGTCTCTGTTGGT 59.967 50.000 8.43 0.00 0.00 3.67
159 163 0.032952 TTAGCGCGTCTCTGTTGGTT 59.967 50.000 8.43 0.00 0.00 3.67
160 164 0.883153 TAGCGCGTCTCTGTTGGTTA 59.117 50.000 8.43 0.00 0.00 2.85
161 165 0.246635 AGCGCGTCTCTGTTGGTTAT 59.753 50.000 8.43 0.00 0.00 1.89
162 166 1.076332 GCGCGTCTCTGTTGGTTATT 58.924 50.000 8.43 0.00 0.00 1.40
163 167 1.201921 GCGCGTCTCTGTTGGTTATTG 60.202 52.381 8.43 0.00 0.00 1.90
164 168 2.066262 CGCGTCTCTGTTGGTTATTGT 58.934 47.619 0.00 0.00 0.00 2.71
170 174 4.691216 GTCTCTGTTGGTTATTGTCCTCAC 59.309 45.833 0.00 0.00 0.00 3.51
172 176 2.147958 TGTTGGTTATTGTCCTCACGC 58.852 47.619 0.00 0.00 0.00 5.34
179 183 4.246458 GTTATTGTCCTCACGCTTCTCTT 58.754 43.478 0.00 0.00 0.00 2.85
180 184 2.440539 TTGTCCTCACGCTTCTCTTC 57.559 50.000 0.00 0.00 0.00 2.87
184 188 2.230266 GTCCTCACGCTTCTCTTCTCTT 59.770 50.000 0.00 0.00 0.00 2.85
185 189 2.490115 TCCTCACGCTTCTCTTCTCTTC 59.510 50.000 0.00 0.00 0.00 2.87
186 190 2.491693 CCTCACGCTTCTCTTCTCTTCT 59.508 50.000 0.00 0.00 0.00 2.85
187 191 3.427503 CCTCACGCTTCTCTTCTCTTCTC 60.428 52.174 0.00 0.00 0.00 2.87
189 193 2.491693 CACGCTTCTCTTCTCTTCTCCT 59.508 50.000 0.00 0.00 0.00 3.69
190 194 3.692101 CACGCTTCTCTTCTCTTCTCCTA 59.308 47.826 0.00 0.00 0.00 2.94
191 195 3.692593 ACGCTTCTCTTCTCTTCTCCTAC 59.307 47.826 0.00 0.00 0.00 3.18
192 196 3.242608 CGCTTCTCTTCTCTTCTCCTACG 60.243 52.174 0.00 0.00 0.00 3.51
193 197 3.942748 GCTTCTCTTCTCTTCTCCTACGA 59.057 47.826 0.00 0.00 0.00 3.43
194 198 4.578928 GCTTCTCTTCTCTTCTCCTACGAT 59.421 45.833 0.00 0.00 0.00 3.73
195 199 5.067283 GCTTCTCTTCTCTTCTCCTACGATT 59.933 44.000 0.00 0.00 0.00 3.34
196 200 6.443934 TTCTCTTCTCTTCTCCTACGATTG 57.556 41.667 0.00 0.00 0.00 2.67
252 259 3.541713 GGGGAGAGGCAGCTACCG 61.542 72.222 0.00 0.00 40.01 4.02
253 260 2.442272 GGGAGAGGCAGCTACCGA 60.442 66.667 0.00 0.00 33.69 4.69
255 262 2.787567 GGAGAGGCAGCTACCGACC 61.788 68.421 0.00 0.00 33.69 4.79
297 304 4.452733 GGTTCCCGCTCCCGTCAG 62.453 72.222 0.00 0.00 0.00 3.51
298 305 4.452733 GTTCCCGCTCCCGTCAGG 62.453 72.222 0.00 0.00 37.24 3.86
299 306 4.689549 TTCCCGCTCCCGTCAGGA 62.690 66.667 0.00 0.00 44.91 3.86
300 307 4.689549 TCCCGCTCCCGTCAGGAA 62.690 66.667 0.00 0.00 46.94 3.36
301 308 4.452733 CCCGCTCCCGTCAGGAAC 62.453 72.222 0.00 0.00 46.94 3.62
311 318 4.302509 TCAGGAACGCCGCCGAAA 62.303 61.111 0.00 0.00 39.96 3.46
312 319 3.350612 CAGGAACGCCGCCGAAAA 61.351 61.111 0.00 0.00 39.96 2.29
313 320 3.351416 AGGAACGCCGCCGAAAAC 61.351 61.111 0.00 0.00 39.96 2.43
314 321 3.652000 GGAACGCCGCCGAAAACA 61.652 61.111 0.00 0.00 38.29 2.83
315 322 2.559330 GAACGCCGCCGAAAACAT 59.441 55.556 0.00 0.00 38.29 2.71
317 324 1.334288 GAACGCCGCCGAAAACATTG 61.334 55.000 0.00 0.00 38.29 2.82
318 325 2.503809 CGCCGCCGAAAACATTGG 60.504 61.111 0.00 0.00 36.29 3.16
322 329 0.450184 CCGCCGAAAACATTGGGTAG 59.550 55.000 0.00 0.00 32.49 3.18
324 331 1.541379 GCCGAAAACATTGGGTAGGT 58.459 50.000 0.00 0.00 32.49 3.08
326 333 1.201414 CCGAAAACATTGGGTAGGTGC 59.799 52.381 0.00 0.00 0.00 5.01
327 334 1.201414 CGAAAACATTGGGTAGGTGCC 59.799 52.381 0.00 0.00 0.00 5.01
328 335 2.243810 GAAAACATTGGGTAGGTGCCA 58.756 47.619 0.00 0.00 0.00 4.92
329 336 1.627864 AAACATTGGGTAGGTGCCAC 58.372 50.000 0.00 0.00 0.00 5.01
331 338 0.480690 ACATTGGGTAGGTGCCACAA 59.519 50.000 0.00 0.00 0.00 3.33
332 339 1.133325 ACATTGGGTAGGTGCCACAAA 60.133 47.619 0.00 0.00 0.00 2.83
333 340 2.178580 CATTGGGTAGGTGCCACAAAT 58.821 47.619 0.00 0.00 0.00 2.32
334 341 1.917872 TTGGGTAGGTGCCACAAATC 58.082 50.000 0.00 0.00 0.00 2.17
336 343 0.683179 GGGTAGGTGCCACAAATCCC 60.683 60.000 0.00 0.00 0.00 3.85
337 344 0.331616 GGTAGGTGCCACAAATCCCT 59.668 55.000 0.00 0.00 0.00 4.20
338 345 1.272480 GGTAGGTGCCACAAATCCCTT 60.272 52.381 0.00 0.00 0.00 3.95
339 346 2.525368 GTAGGTGCCACAAATCCCTTT 58.475 47.619 0.00 0.00 0.00 3.11
340 347 2.101640 AGGTGCCACAAATCCCTTTT 57.898 45.000 0.00 0.00 0.00 2.27
341 348 1.970640 AGGTGCCACAAATCCCTTTTC 59.029 47.619 0.00 0.00 0.00 2.29
342 349 1.970640 GGTGCCACAAATCCCTTTTCT 59.029 47.619 0.00 0.00 0.00 2.52
343 350 2.368548 GGTGCCACAAATCCCTTTTCTT 59.631 45.455 0.00 0.00 0.00 2.52
346 367 3.321682 TGCCACAAATCCCTTTTCTTCTG 59.678 43.478 0.00 0.00 0.00 3.02
354 375 1.537202 CCCTTTTCTTCTGCTGTTCCG 59.463 52.381 0.00 0.00 0.00 4.30
355 376 1.068954 CCTTTTCTTCTGCTGTTCCGC 60.069 52.381 0.00 0.00 0.00 5.54
358 379 3.121030 CTTCTGCTGTTCCGCCCG 61.121 66.667 0.00 0.00 0.00 6.13
421 442 2.644676 GATTTCTAACTGCTCCCACCC 58.355 52.381 0.00 0.00 0.00 4.61
500 583 4.876107 TCTCGCTTTTAATTCCCTGATGAC 59.124 41.667 0.00 0.00 0.00 3.06
501 584 4.843728 TCGCTTTTAATTCCCTGATGACT 58.156 39.130 0.00 0.00 0.00 3.41
502 585 4.876107 TCGCTTTTAATTCCCTGATGACTC 59.124 41.667 0.00 0.00 0.00 3.36
503 586 4.635765 CGCTTTTAATTCCCTGATGACTCA 59.364 41.667 0.00 0.00 0.00 3.41
504 587 5.297776 CGCTTTTAATTCCCTGATGACTCAT 59.702 40.000 0.00 0.00 0.00 2.90
505 588 6.501781 GCTTTTAATTCCCTGATGACTCATG 58.498 40.000 0.00 0.00 0.00 3.07
508 591 8.827832 TTTTAATTCCCTGATGACTCATGATT 57.172 30.769 0.00 0.00 0.00 2.57
516 599 7.052873 CCCTGATGACTCATGATTATTATCCC 58.947 42.308 0.00 0.00 0.00 3.85
523 606 6.533730 ACTCATGATTATTATCCCTCGCAAA 58.466 36.000 0.00 0.00 0.00 3.68
553 826 9.632638 ATTACCAATAATTCATCTTGCTGTAGT 57.367 29.630 0.00 0.00 0.00 2.73
570 843 8.942338 TGCTGTAGTATTAATTTCCTACTGTG 57.058 34.615 17.65 11.31 34.06 3.66
675 989 0.320771 AGGCCATTGACACGACACTC 60.321 55.000 5.01 0.00 0.00 3.51
773 1088 1.833787 TACTGGCCACCCTTTCCGTC 61.834 60.000 0.00 0.00 0.00 4.79
869 1211 2.821969 ACATGGAGTTTGCATCTTCCAC 59.178 45.455 13.76 0.00 0.00 4.02
947 1289 5.801350 TGTTCTGCTATGATTGTTACAGC 57.199 39.130 0.00 0.00 0.00 4.40
996 1339 2.693591 TGGCCTAGAAAGTACATCGAGG 59.306 50.000 17.81 17.81 41.18 4.63
1083 1426 1.499949 GCGCGCACCAATAAACAGA 59.500 52.632 29.10 0.00 0.00 3.41
1103 1446 2.031163 GACCAGGCAGCAGAACGT 59.969 61.111 0.00 0.00 0.00 3.99
1117 1460 0.179240 GAACGTGCTCATCTTGCGTG 60.179 55.000 0.00 0.00 35.88 5.34
1143 1486 1.302511 ATCCCGTTCACTGTGCACC 60.303 57.895 15.69 0.00 0.00 5.01
1406 1756 4.521146 AGATGGTGATAGCTTTCAGGTTG 58.479 43.478 7.15 0.00 0.00 3.77
1444 1794 9.361315 CTGATCAATGTTTTTCTTGCATGATTA 57.639 29.630 2.75 0.00 0.00 1.75
1484 1834 6.522054 TGACGATTCTTCTGAACTTTTACCT 58.478 36.000 0.00 0.00 34.71 3.08
1603 1953 3.260884 TGAGAAATCTGGAAGGTAAGCGT 59.739 43.478 0.00 0.00 0.00 5.07
1607 1957 2.961526 TCTGGAAGGTAAGCGTGATC 57.038 50.000 0.00 0.00 0.00 2.92
1864 2221 9.624697 CTTATTTTGTGCTGCTTTAAGATAACA 57.375 29.630 0.00 0.00 0.00 2.41
1892 2251 5.986741 TCACGAACTTGAAAGTGCATTAGTA 59.013 36.000 2.18 0.00 39.66 1.82
2247 2617 8.795842 TTACTGTCTAAGTTCAAACTTCCAAA 57.204 30.769 11.22 0.00 45.65 3.28
2261 2631 4.461198 ACTTCCAAACTGTTAGGAACCAG 58.539 43.478 0.00 0.00 36.55 4.00
2276 2646 3.941483 GGAACCAGTGGTGATCATTGTAG 59.059 47.826 17.56 0.00 35.34 2.74
2410 2782 6.677913 ACAACTTGGTACTTGCACATATTTC 58.322 36.000 0.00 0.00 0.00 2.17
2416 2788 4.338400 GGTACTTGCACATATTTCCCCTTC 59.662 45.833 0.00 0.00 0.00 3.46
2458 2830 3.384668 CATTGCTATCCTGACGGTACTG 58.615 50.000 0.00 0.00 0.00 2.74
2492 2864 3.763897 GCCAGCTAATTGGAGGAAAAAGA 59.236 43.478 5.15 0.00 40.87 2.52
2533 2905 5.469373 TCATGTTGAATGTTCATAGTCGC 57.531 39.130 0.00 0.00 37.00 5.19
2600 2973 8.616942 TCTTCAGTCTAGATCTCTTCATAAACG 58.383 37.037 0.00 0.00 0.00 3.60
2751 3125 8.021396 AGTTGTATTAATTTTCCTGCTCGTTTC 58.979 33.333 0.00 0.00 0.00 2.78
2765 3139 3.782046 CTCGTTTCCTAACACATCCGAT 58.218 45.455 0.00 0.00 33.75 4.18
2892 3267 6.463995 TTCTTATGCACTGAAACAACCTTT 57.536 33.333 0.00 0.00 0.00 3.11
2893 3268 7.575414 TTCTTATGCACTGAAACAACCTTTA 57.425 32.000 0.00 0.00 0.00 1.85
2896 3271 9.461312 TCTTATGCACTGAAACAACCTTTATAT 57.539 29.630 0.00 0.00 0.00 0.86
2913 3288 9.975218 ACCTTTATATTCACACAAGAATACCTT 57.025 29.630 0.00 0.00 41.72 3.50
2951 3326 5.859521 TTGATTTGCATGGTTATTTGTGC 57.140 34.783 0.00 0.00 38.05 4.57
2956 3331 2.492881 TGCATGGTTATTTGTGCTCAGG 59.507 45.455 0.00 0.00 38.37 3.86
2985 3360 1.404391 TCGACTTCTAATCGTGCTCCC 59.596 52.381 0.00 0.00 40.50 4.30
3030 3405 2.664698 GCAGCGAAACCTTTTCTTACCG 60.665 50.000 0.00 0.00 0.00 4.02
3052 3427 5.181245 CCGTTCATTGACACCTTGAAAGTAT 59.819 40.000 0.00 0.00 31.66 2.12
3094 3469 3.377346 TCTCTGCTGTCTGAAGTTCAC 57.623 47.619 0.08 0.00 0.00 3.18
3150 3525 0.597568 TGCAGGAAAGGTGCATTTCG 59.402 50.000 6.68 0.00 45.96 3.46
3192 3567 1.342174 GACTACCGTCAACTGGGTTCA 59.658 52.381 0.00 0.00 39.98 3.18
3207 3582 3.329520 TGGGTTCAGTATGTTGCCTACTT 59.670 43.478 0.00 0.00 37.40 2.24
3209 3584 4.395231 GGGTTCAGTATGTTGCCTACTTTC 59.605 45.833 0.00 0.00 37.40 2.62
3211 3586 3.857052 TCAGTATGTTGCCTACTTTCGG 58.143 45.455 0.00 0.00 37.40 4.30
3219 3594 4.933400 TGTTGCCTACTTTCGGAAGTTATC 59.067 41.667 15.75 4.67 43.48 1.75
3220 3595 4.811969 TGCCTACTTTCGGAAGTTATCA 57.188 40.909 15.75 7.29 43.48 2.15
3221 3596 4.755411 TGCCTACTTTCGGAAGTTATCAG 58.245 43.478 15.75 5.74 43.48 2.90
3223 3598 4.567159 GCCTACTTTCGGAAGTTATCAGTG 59.433 45.833 15.75 1.89 43.48 3.66
3257 3633 6.550854 TCAGTTTTCCCTTTCATGACATCTTT 59.449 34.615 0.00 0.00 0.00 2.52
3300 3676 9.243105 TGGAGAAGGTTTCTATTTTATTGGAAG 57.757 33.333 0.00 0.00 40.87 3.46
3473 3851 5.765182 CACTCTGTAATTCTTGAACCTTGGT 59.235 40.000 0.00 0.00 0.00 3.67
3599 3977 5.701290 AGTATAGTTGTTCAGTGCAGTTTCC 59.299 40.000 0.00 0.00 0.00 3.13
3607 3985 3.202906 TCAGTGCAGTTTCCACAGTTAC 58.797 45.455 0.00 0.00 35.69 2.50
3616 3994 4.992951 AGTTTCCACAGTTACGGATTACAC 59.007 41.667 0.00 0.00 0.00 2.90
3623 4001 4.391830 ACAGTTACGGATTACACAATGCTG 59.608 41.667 0.00 0.00 30.72 4.41
3730 4132 5.059161 GGATATCATAACAGAACAGCAGCA 58.941 41.667 4.83 0.00 0.00 4.41
3762 4164 6.252967 TGTCACATTGGTTGATGTATGTTC 57.747 37.500 0.00 0.00 38.15 3.18
3804 4206 9.340695 TGTCATCTTTTATGTTTTAATCTTGCG 57.659 29.630 0.00 0.00 0.00 4.85
3820 4223 3.249080 TCTTGCGTTAGCCTTGTGTTTAC 59.751 43.478 0.00 0.00 44.33 2.01
3821 4224 2.841215 TGCGTTAGCCTTGTGTTTACT 58.159 42.857 0.00 0.00 44.33 2.24
3822 4225 2.546368 TGCGTTAGCCTTGTGTTTACTG 59.454 45.455 0.00 0.00 44.33 2.74
3823 4226 2.546789 GCGTTAGCCTTGTGTTTACTGT 59.453 45.455 0.00 0.00 37.42 3.55
3824 4227 3.002965 GCGTTAGCCTTGTGTTTACTGTT 59.997 43.478 0.00 0.00 37.42 3.16
3825 4228 4.496840 GCGTTAGCCTTGTGTTTACTGTTT 60.497 41.667 0.00 0.00 37.42 2.83
3826 4229 5.277442 GCGTTAGCCTTGTGTTTACTGTTTA 60.277 40.000 0.00 0.00 37.42 2.01
3834 4237 6.072673 CCTTGTGTTTACTGTTTAGACATCCC 60.073 42.308 0.00 0.00 34.72 3.85
3838 4241 5.308497 TGTTTACTGTTTAGACATCCCTCCA 59.692 40.000 0.00 0.00 34.72 3.86
3854 4257 5.509498 TCCCTCCATTCTAATTTGGAACTG 58.491 41.667 0.00 0.00 41.36 3.16
3876 4279 3.433740 GGACACCTTGAAGACCTGAAACT 60.434 47.826 0.00 0.00 0.00 2.66
3887 4291 2.743636 CCTGAAACTTACAGGCTCGA 57.256 50.000 0.00 0.00 46.30 4.04
3888 4292 3.252974 CCTGAAACTTACAGGCTCGAT 57.747 47.619 0.00 0.00 46.30 3.59
3893 4297 7.227603 CCTGAAACTTACAGGCTCGATAGATG 61.228 46.154 0.00 0.00 46.30 2.90
3918 4322 6.434018 ACACTTTCCTTAGTAGTAGTAGCG 57.566 41.667 0.00 0.00 0.00 4.26
3919 4323 5.163673 ACACTTTCCTTAGTAGTAGTAGCGC 60.164 44.000 0.00 0.00 0.00 5.92
3920 4324 4.946157 ACTTTCCTTAGTAGTAGTAGCGCA 59.054 41.667 11.47 0.00 0.00 6.09
3921 4325 4.889832 TTCCTTAGTAGTAGTAGCGCAC 57.110 45.455 11.47 5.97 0.00 5.34
3922 4326 4.148128 TCCTTAGTAGTAGTAGCGCACT 57.852 45.455 11.47 13.82 41.62 4.40
3925 4329 4.516359 CTTAGTAGTAGTAGCGCACTTCG 58.484 47.826 11.47 0.00 38.80 3.79
3927 4331 2.746362 AGTAGTAGTAGCGCACTTCGTT 59.254 45.455 11.47 0.00 38.80 3.85
3928 4332 3.935203 AGTAGTAGTAGCGCACTTCGTTA 59.065 43.478 11.47 0.00 38.80 3.18
3929 4333 4.574013 AGTAGTAGTAGCGCACTTCGTTAT 59.426 41.667 11.47 0.00 38.80 1.89
3932 4336 5.166398 AGTAGTAGCGCACTTCGTTATTTT 58.834 37.500 11.47 0.00 38.80 1.82
3953 4357 8.763049 ATTTTGCATTTTTAAAGAGCCTAGTC 57.237 30.769 0.00 0.00 0.00 2.59
3954 4358 5.897377 TGCATTTTTAAAGAGCCTAGTCC 57.103 39.130 6.26 0.00 0.00 3.85
3955 4359 5.321102 TGCATTTTTAAAGAGCCTAGTCCA 58.679 37.500 6.26 0.00 0.00 4.02
3956 4360 5.415701 TGCATTTTTAAAGAGCCTAGTCCAG 59.584 40.000 6.26 0.00 0.00 3.86
3957 4361 5.648092 GCATTTTTAAAGAGCCTAGTCCAGA 59.352 40.000 0.00 0.00 0.00 3.86
3958 4362 6.319911 GCATTTTTAAAGAGCCTAGTCCAGAT 59.680 38.462 0.00 0.00 0.00 2.90
3973 4377 2.768527 TCCAGATTCCTGAAGCTAGTGG 59.231 50.000 0.00 0.00 43.02 4.00
3975 4379 3.706594 CCAGATTCCTGAAGCTAGTGGTA 59.293 47.826 0.00 0.00 43.02 3.25
3976 4380 4.442192 CCAGATTCCTGAAGCTAGTGGTAC 60.442 50.000 0.00 0.00 43.02 3.34
3983 4387 4.767928 CCTGAAGCTAGTGGTACCCTATAG 59.232 50.000 10.07 9.81 0.00 1.31
4104 4508 0.179134 GTCTCTGACGGCGCTAATGT 60.179 55.000 6.90 0.34 0.00 2.71
4120 4524 7.193595 GCGCTAATGTTTTTCAGGTTATGTAT 58.806 34.615 0.00 0.00 0.00 2.29
4180 4584 5.621104 CGAGCCAATAGAGCTATTCGAGAAT 60.621 44.000 3.67 3.67 41.75 2.40
4233 4637 0.382158 CCTAGATCTTCACGCTCGCA 59.618 55.000 0.00 0.00 0.00 5.10
4234 4638 1.599171 CCTAGATCTTCACGCTCGCAG 60.599 57.143 0.00 0.00 0.00 5.18
4258 4662 0.318275 GTGACGATCCCGATCTCTGC 60.318 60.000 3.35 0.00 39.50 4.26
4364 4772 5.914085 ATTCTGAACTTCAGTTTCGTCTG 57.086 39.130 16.75 0.00 44.58 3.51
4379 4787 1.676006 CGTCTGAAACCTGTTTTGCCT 59.324 47.619 0.00 0.00 32.11 4.75
4380 4788 2.541588 CGTCTGAAACCTGTTTTGCCTG 60.542 50.000 0.00 0.00 32.11 4.85
4471 4880 2.772224 TGGCAACATCCCCTGCAT 59.228 55.556 0.00 0.00 46.17 3.96
4529 4938 1.214589 GCAGGGCTTCATGTGCAAG 59.785 57.895 13.49 2.67 35.91 4.01
4572 4990 1.729586 TCTATTATCCCGCCTGGCTT 58.270 50.000 17.92 1.39 0.00 4.35
4631 5049 4.560035 GTGATGCATGTAATTTCAGTGTGC 59.440 41.667 2.46 3.07 0.00 4.57
4639 5061 2.953466 ATTTCAGTGTGCCATGATGC 57.047 45.000 0.00 0.00 0.00 3.91
4711 5133 3.890756 TGTGTCATGTCTTGCTGGAATTT 59.109 39.130 0.00 0.00 0.00 1.82
4752 5174 8.868522 ATGAAACTGGAAATCTTCAGATAACA 57.131 30.769 0.00 0.00 33.73 2.41
4769 5191 6.189677 GATAACAAACGATGTGATCCCAAA 57.810 37.500 10.54 0.00 42.20 3.28
4826 5248 7.373778 TGAGTTGAGATGAATCATGAAACTG 57.626 36.000 15.28 0.00 0.00 3.16
4842 5265 4.141711 TGAAACTGGTAGCAGACTCTTGTT 60.142 41.667 27.87 8.19 0.00 2.83
4913 5336 8.906867 TCCTTGAGATTCATTGGAAATGATTAC 58.093 33.333 3.65 0.25 36.43 1.89
4939 5362 7.201478 CGAGGCAGAGAGTTACAAAGAAATTAG 60.201 40.741 0.00 0.00 0.00 1.73
4947 5370 9.077885 AGAGTTACAAAGAAATTAGCAATGGAA 57.922 29.630 0.00 0.00 0.00 3.53
5000 5442 3.781079 TTGCACAGCACCAAATATAGC 57.219 42.857 0.00 0.00 38.71 2.97
5001 5443 2.720915 TGCACAGCACCAAATATAGCA 58.279 42.857 0.00 0.00 31.71 3.49
5002 5444 2.684374 TGCACAGCACCAAATATAGCAG 59.316 45.455 0.00 0.00 31.71 4.24
5003 5445 2.542411 GCACAGCACCAAATATAGCAGC 60.542 50.000 0.00 0.00 0.00 5.25
5004 5446 2.033801 CACAGCACCAAATATAGCAGCC 59.966 50.000 0.00 0.00 0.00 4.85
5013 5455 4.398358 CCAAATATAGCAGCCCATGATGAG 59.602 45.833 0.00 0.00 0.00 2.90
5037 5479 0.189574 TCCATTGCAAACTTGGGGGA 59.810 50.000 15.81 6.58 0.00 4.81
5045 5487 0.860457 AAACTTGGGGGAAAGAGCCT 59.140 50.000 0.00 0.00 0.00 4.58
5054 5497 2.355209 GGGGAAAGAGCCTAAGTGTCAG 60.355 54.545 0.00 0.00 0.00 3.51
5057 5500 4.382147 GGGAAAGAGCCTAAGTGTCAGTAG 60.382 50.000 0.00 0.00 0.00 2.57
5072 5515 4.180057 GTCAGTAGGACTTCATCAAGCAG 58.820 47.826 0.00 0.00 43.46 4.24
5150 5841 4.731313 AAAGTCCCAGAACAAAGGAGAT 57.269 40.909 0.00 0.00 0.00 2.75
5172 5863 6.774656 AGATCAGTTTCTTCAGTGTTGGAATT 59.225 34.615 0.00 0.00 0.00 2.17
5173 5864 6.773976 TCAGTTTCTTCAGTGTTGGAATTT 57.226 33.333 0.00 0.00 0.00 1.82
5174 5865 6.563422 TCAGTTTCTTCAGTGTTGGAATTTG 58.437 36.000 0.00 0.00 0.00 2.32
5176 5867 7.068593 TCAGTTTCTTCAGTGTTGGAATTTGAT 59.931 33.333 0.00 0.00 0.00 2.57
5177 5868 7.168637 CAGTTTCTTCAGTGTTGGAATTTGATG 59.831 37.037 0.00 0.00 0.00 3.07
5178 5869 5.710513 TCTTCAGTGTTGGAATTTGATGG 57.289 39.130 0.00 0.00 0.00 3.51
5179 5870 5.384336 TCTTCAGTGTTGGAATTTGATGGA 58.616 37.500 0.00 0.00 0.00 3.41
5180 5871 5.474532 TCTTCAGTGTTGGAATTTGATGGAG 59.525 40.000 0.00 0.00 0.00 3.86
5181 5872 4.984295 TCAGTGTTGGAATTTGATGGAGA 58.016 39.130 0.00 0.00 0.00 3.71
5182 5873 5.005740 TCAGTGTTGGAATTTGATGGAGAG 58.994 41.667 0.00 0.00 0.00 3.20
5185 5876 4.022068 GTGTTGGAATTTGATGGAGAGCAA 60.022 41.667 0.00 0.00 0.00 3.91
5187 5878 5.070180 TGTTGGAATTTGATGGAGAGCAAAA 59.930 36.000 0.00 0.00 40.69 2.44
5188 5879 5.804944 TGGAATTTGATGGAGAGCAAAAA 57.195 34.783 0.00 0.00 40.69 1.94
5243 5935 2.129555 TTGGAGCAGGTTCCTGGAGC 62.130 60.000 18.81 1.35 38.12 4.70
5252 5944 1.549170 GGTTCCTGGAGCTAACTCGAA 59.451 52.381 10.49 0.00 44.48 3.71
5268 5960 1.020861 CGAACATACAGCAGCAGCCA 61.021 55.000 0.00 0.00 43.56 4.75
5282 7672 3.185797 CAGCAGCCAAAAGAAGATTTTGC 59.814 43.478 7.41 4.26 37.89 3.68
5287 7677 6.392354 CAGCCAAAAGAAGATTTTGCATCTA 58.608 36.000 7.41 0.00 37.89 1.98
5301 7691 3.608796 TGCATCTAAGCATTGTAGCACA 58.391 40.909 0.00 0.00 40.11 4.57
5303 7693 4.641541 TGCATCTAAGCATTGTAGCACATT 59.358 37.500 0.00 0.00 40.11 2.71
5309 7699 4.870123 AGCATTGTAGCACATTTCCAAA 57.130 36.364 0.00 0.00 36.85 3.28
5383 7804 6.099269 TCCAGGGATAGTACCAAATGTCTAAC 59.901 42.308 0.00 0.00 0.00 2.34
5385 7806 4.748600 GGGATAGTACCAAATGTCTAACGC 59.251 45.833 0.00 0.00 0.00 4.84
5412 7836 2.690786 TGGAATTTGATGCAAAGCAGC 58.309 42.857 0.00 0.00 45.81 5.25
5443 7868 1.251251 GGAACTGCTGAATGGCTTGT 58.749 50.000 0.00 0.00 0.00 3.16
5459 7884 2.005451 CTTGTGTAGACAGAGGCATGC 58.995 52.381 9.90 9.90 32.26 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.502080 GAGTGGACAGCGACGTCG 60.502 66.667 32.57 32.57 43.27 5.12
14 15 2.126424 GGAGTGGACAGCGACGTC 60.126 66.667 5.18 5.18 35.03 4.34
15 16 4.039357 CGGAGTGGACAGCGACGT 62.039 66.667 0.00 0.00 0.00 4.34
38 39 3.645268 AATCAGGCGGCAGGAACCC 62.645 63.158 13.08 0.00 0.00 4.11
42 43 4.161295 CGGAATCAGGCGGCAGGA 62.161 66.667 13.08 8.98 0.00 3.86
54 55 0.815615 GAATCGAAGCCTGGCGGAAT 60.816 55.000 13.96 5.39 0.00 3.01
62 63 0.179108 GCAGTACCGAATCGAAGCCT 60.179 55.000 3.36 0.00 0.00 4.58
64 65 0.179108 AGGCAGTACCGAATCGAAGC 60.179 55.000 3.36 0.21 46.52 3.86
106 110 1.452108 CCAATGGAGGAACCGAGGC 60.452 63.158 0.00 0.00 42.61 4.70
107 111 0.328258 AACCAATGGAGGAACCGAGG 59.672 55.000 6.16 0.00 42.61 4.63
114 118 2.361104 GGCGCAACCAATGGAGGA 60.361 61.111 10.83 0.00 38.86 3.71
115 119 2.361610 AGGCGCAACCAATGGAGG 60.362 61.111 10.83 0.00 43.14 4.30
116 120 2.409870 GGAGGCGCAACCAATGGAG 61.410 63.158 10.83 0.00 43.14 3.86
117 121 2.361104 GGAGGCGCAACCAATGGA 60.361 61.111 10.83 0.00 43.14 3.41
118 122 3.451894 GGGAGGCGCAACCAATGG 61.452 66.667 20.43 0.00 43.14 3.16
119 123 2.361610 AGGGAGGCGCAACCAATG 60.362 61.111 20.43 0.00 43.14 2.82
120 124 2.044946 GAGGGAGGCGCAACCAAT 60.045 61.111 20.43 10.55 43.14 3.16
121 125 2.351924 AAAGAGGGAGGCGCAACCAA 62.352 55.000 20.43 0.00 43.14 3.67
122 126 2.351924 AAAAGAGGGAGGCGCAACCA 62.352 55.000 20.43 0.00 43.14 3.67
123 127 0.322187 TAAAAGAGGGAGGCGCAACC 60.322 55.000 10.83 11.94 39.61 3.77
133 137 0.173708 AGAGACGCGCTAAAAGAGGG 59.826 55.000 5.73 0.00 41.08 4.30
136 140 2.058798 CAACAGAGACGCGCTAAAAGA 58.941 47.619 5.73 0.00 0.00 2.52
148 152 4.560716 CGTGAGGACAATAACCAACAGAGA 60.561 45.833 0.00 0.00 0.00 3.10
158 162 4.220821 AGAAGAGAAGCGTGAGGACAATAA 59.779 41.667 0.00 0.00 0.00 1.40
159 163 3.764434 AGAAGAGAAGCGTGAGGACAATA 59.236 43.478 0.00 0.00 0.00 1.90
160 164 2.564947 AGAAGAGAAGCGTGAGGACAAT 59.435 45.455 0.00 0.00 0.00 2.71
161 165 1.964223 AGAAGAGAAGCGTGAGGACAA 59.036 47.619 0.00 0.00 0.00 3.18
162 166 1.542030 GAGAAGAGAAGCGTGAGGACA 59.458 52.381 0.00 0.00 0.00 4.02
163 167 1.816224 AGAGAAGAGAAGCGTGAGGAC 59.184 52.381 0.00 0.00 0.00 3.85
164 168 2.208132 AGAGAAGAGAAGCGTGAGGA 57.792 50.000 0.00 0.00 0.00 3.71
170 174 3.242608 CGTAGGAGAAGAGAAGAGAAGCG 60.243 52.174 0.00 0.00 0.00 4.68
172 176 6.459573 CCAATCGTAGGAGAAGAGAAGAGAAG 60.460 46.154 0.00 0.00 0.00 2.85
179 183 4.342378 CCAATCCAATCGTAGGAGAAGAGA 59.658 45.833 0.00 0.00 38.83 3.10
180 184 4.342378 TCCAATCCAATCGTAGGAGAAGAG 59.658 45.833 0.00 0.00 38.83 2.85
184 188 4.743651 GCAATCCAATCCAATCGTAGGAGA 60.744 45.833 0.00 0.00 38.83 3.71
185 189 3.499918 GCAATCCAATCCAATCGTAGGAG 59.500 47.826 0.00 0.00 38.83 3.69
186 190 3.476552 GCAATCCAATCCAATCGTAGGA 58.523 45.455 0.00 0.00 39.97 2.94
187 191 2.554032 GGCAATCCAATCCAATCGTAGG 59.446 50.000 0.00 0.00 0.00 3.18
189 193 3.289407 TGGCAATCCAATCCAATCGTA 57.711 42.857 0.00 0.00 39.99 3.43
190 194 2.142356 TGGCAATCCAATCCAATCGT 57.858 45.000 0.00 0.00 39.99 3.73
240 247 2.496817 CTGGTCGGTAGCTGCCTC 59.503 66.667 19.36 11.30 0.00 4.70
295 302 3.350612 TTTTCGGCGGCGTTCCTG 61.351 61.111 31.06 1.53 0.00 3.86
296 303 3.351416 GTTTTCGGCGGCGTTCCT 61.351 61.111 31.06 0.00 0.00 3.36
297 304 2.466520 AATGTTTTCGGCGGCGTTCC 62.467 55.000 31.06 17.06 0.00 3.62
298 305 1.081708 AATGTTTTCGGCGGCGTTC 60.082 52.632 31.06 18.52 0.00 3.95
299 306 1.371145 CAATGTTTTCGGCGGCGTT 60.371 52.632 31.06 14.08 0.00 4.84
300 307 2.254051 CAATGTTTTCGGCGGCGT 59.746 55.556 31.06 7.80 0.00 5.68
301 308 2.503809 CCAATGTTTTCGGCGGCG 60.504 61.111 27.15 27.15 0.00 6.46
302 309 1.587933 TACCCAATGTTTTCGGCGGC 61.588 55.000 7.21 0.00 0.00 6.53
306 313 1.201414 GCACCTACCCAATGTTTTCGG 59.799 52.381 0.00 0.00 0.00 4.30
307 314 1.201414 GGCACCTACCCAATGTTTTCG 59.799 52.381 0.00 0.00 0.00 3.46
308 315 2.029380 GTGGCACCTACCCAATGTTTTC 60.029 50.000 6.29 0.00 33.39 2.29
309 316 1.967779 GTGGCACCTACCCAATGTTTT 59.032 47.619 6.29 0.00 33.39 2.43
311 318 0.480690 TGTGGCACCTACCCAATGTT 59.519 50.000 16.26 0.00 33.39 2.71
312 319 0.480690 TTGTGGCACCTACCCAATGT 59.519 50.000 16.26 0.00 33.39 2.71
313 320 1.626686 TTTGTGGCACCTACCCAATG 58.373 50.000 16.26 0.00 33.39 2.82
314 321 2.456577 GATTTGTGGCACCTACCCAAT 58.543 47.619 16.26 3.81 33.39 3.16
315 322 1.549037 GGATTTGTGGCACCTACCCAA 60.549 52.381 16.26 0.00 33.39 4.12
317 324 0.683179 GGGATTTGTGGCACCTACCC 60.683 60.000 16.26 17.49 0.00 3.69
318 325 0.331616 AGGGATTTGTGGCACCTACC 59.668 55.000 16.26 10.02 0.00 3.18
322 329 1.970640 AGAAAAGGGATTTGTGGCACC 59.029 47.619 16.26 0.00 0.00 5.01
324 331 3.321682 CAGAAGAAAAGGGATTTGTGGCA 59.678 43.478 0.00 0.00 0.00 4.92
326 333 3.575687 AGCAGAAGAAAAGGGATTTGTGG 59.424 43.478 0.00 0.00 0.00 4.17
327 334 4.038402 ACAGCAGAAGAAAAGGGATTTGTG 59.962 41.667 0.00 0.00 0.00 3.33
328 335 4.218312 ACAGCAGAAGAAAAGGGATTTGT 58.782 39.130 0.00 0.00 0.00 2.83
329 336 4.861102 ACAGCAGAAGAAAAGGGATTTG 57.139 40.909 0.00 0.00 0.00 2.32
331 338 3.829026 GGAACAGCAGAAGAAAAGGGATT 59.171 43.478 0.00 0.00 0.00 3.01
332 339 3.425659 GGAACAGCAGAAGAAAAGGGAT 58.574 45.455 0.00 0.00 0.00 3.85
333 340 2.810400 CGGAACAGCAGAAGAAAAGGGA 60.810 50.000 0.00 0.00 0.00 4.20
334 341 1.537202 CGGAACAGCAGAAGAAAAGGG 59.463 52.381 0.00 0.00 0.00 3.95
336 343 1.068954 GGCGGAACAGCAGAAGAAAAG 60.069 52.381 0.00 0.00 39.27 2.27
337 344 0.951558 GGCGGAACAGCAGAAGAAAA 59.048 50.000 0.00 0.00 39.27 2.29
338 345 0.889186 GGGCGGAACAGCAGAAGAAA 60.889 55.000 0.00 0.00 39.27 2.52
339 346 1.302511 GGGCGGAACAGCAGAAGAA 60.303 57.895 0.00 0.00 39.27 2.52
340 347 2.347490 GGGCGGAACAGCAGAAGA 59.653 61.111 0.00 0.00 39.27 2.87
341 348 3.121030 CGGGCGGAACAGCAGAAG 61.121 66.667 0.00 0.00 39.27 2.85
362 383 2.204448 ATTTGGGGAGGGGAGCCA 60.204 61.111 0.00 0.00 0.00 4.75
363 384 2.168272 AACATTTGGGGAGGGGAGCC 62.168 60.000 0.00 0.00 0.00 4.70
365 386 3.288099 CAACATTTGGGGAGGGGAG 57.712 57.895 0.00 0.00 0.00 4.30
405 426 0.116342 TGAGGGTGGGAGCAGTTAGA 59.884 55.000 0.00 0.00 0.00 2.10
406 427 1.134280 CATGAGGGTGGGAGCAGTTAG 60.134 57.143 0.00 0.00 0.00 2.34
411 432 1.997311 CTCCATGAGGGTGGGAGCA 60.997 63.158 0.00 0.00 41.53 4.26
421 442 3.037549 AGGGTAGAAGAAGCTCCATGAG 58.962 50.000 0.00 0.00 0.00 2.90
469 552 9.388506 CAGGGAATTAAAAGCGAGATATATCAT 57.611 33.333 15.08 0.33 0.00 2.45
470 553 8.593679 TCAGGGAATTAAAAGCGAGATATATCA 58.406 33.333 15.08 0.00 0.00 2.15
471 554 9.606631 ATCAGGGAATTAAAAGCGAGATATATC 57.393 33.333 4.42 4.42 0.00 1.63
473 556 8.593679 TCATCAGGGAATTAAAAGCGAGATATA 58.406 33.333 0.00 0.00 0.00 0.86
483 566 8.827832 AATCATGAGTCATCAGGGAATTAAAA 57.172 30.769 1.56 0.00 39.29 1.52
490 573 7.092712 GGGATAATAATCATGAGTCATCAGGGA 60.093 40.741 1.56 0.00 39.29 4.20
500 583 7.439157 TTTTGCGAGGGATAATAATCATGAG 57.561 36.000 0.09 0.00 33.41 2.90
501 584 7.815840 TTTTTGCGAGGGATAATAATCATGA 57.184 32.000 0.00 0.00 33.41 3.07
570 843 4.201822 GGGAAACTCGCATCAATCAACTAC 60.202 45.833 0.00 0.00 0.00 2.73
576 850 2.098117 CCAAGGGAAACTCGCATCAATC 59.902 50.000 0.00 0.00 0.00 2.67
773 1088 1.369625 AAGGCTACCGCGAAAATGAG 58.630 50.000 8.23 0.00 36.88 2.90
869 1211 2.849096 ATCAGTGCTGGGCCATGTGG 62.849 60.000 6.72 0.00 38.53 4.17
947 1289 1.396996 CAACGGGCGAAGTTATGGAAG 59.603 52.381 0.00 0.00 0.00 3.46
996 1339 1.867698 GCTACCGCTGCTCTCATCTTC 60.868 57.143 0.00 0.00 0.00 2.87
1083 1426 1.072159 GTTCTGCTGCCTGGTCAGT 59.928 57.895 16.03 0.00 36.49 3.41
1103 1446 0.955428 GGAACCACGCAAGATGAGCA 60.955 55.000 0.00 0.00 43.62 4.26
1117 1460 2.046700 TGAACGGGATGCGGAACC 60.047 61.111 0.00 0.00 0.00 3.62
1143 1486 0.316442 GTTCATCATCATGGCGCACG 60.316 55.000 10.83 0.00 0.00 5.34
1153 1496 5.041287 CACAAATCTGCCATGTTCATCATC 58.959 41.667 0.00 0.00 34.09 2.92
1266 1609 5.570589 CCAGCAGAAAATAAGAAAGCTTTCG 59.429 40.000 28.67 14.95 41.92 3.46
1271 1614 4.676459 GCCTCCAGCAGAAAATAAGAAAGC 60.676 45.833 0.00 0.00 42.97 3.51
1342 1692 7.521748 GCAATTCTCTTCTCATATTCCACCATG 60.522 40.741 0.00 0.00 0.00 3.66
1406 1756 5.649782 ACATTGATCAGGTCCAATTCAAC 57.350 39.130 0.00 0.00 31.25 3.18
1444 1794 4.395959 TCGTCAGTAAAACACTCAAGGT 57.604 40.909 0.00 0.00 34.26 3.50
1484 1834 1.000052 TCGTGTCAACCTGCGTCAATA 60.000 47.619 0.00 0.00 0.00 1.90
1603 1953 5.065235 TGTGAATTCACTGCTTTCAGATCA 58.935 37.500 32.57 10.59 46.55 2.92
1607 1957 6.492007 ACTATGTGAATTCACTGCTTTCAG 57.508 37.500 32.57 21.07 46.55 3.02
1672 2029 2.815589 GCCACCTTCTCCTGTCAAACAT 60.816 50.000 0.00 0.00 0.00 2.71
1864 2221 4.992688 TGCACTTTCAAGTTCGTGATTTT 58.007 34.783 0.00 0.00 37.08 1.82
1892 2251 7.795047 TGAATATATCTGGTGACATGTTCAGT 58.205 34.615 18.03 11.52 41.51 3.41
1979 2338 8.492673 ACGAATGTGAACTGTTATATGAACAT 57.507 30.769 0.00 0.00 0.00 2.71
2276 2646 9.705290 ACCATTGGTTCTGTTGATTAATAAAAC 57.295 29.630 1.37 6.56 27.29 2.43
2292 2662 3.882888 TCAGAACTTGACACCATTGGTTC 59.117 43.478 5.34 8.15 31.02 3.62
2353 2725 8.466798 GTTAATACCACATAGCAAAAGAACCAT 58.533 33.333 0.00 0.00 0.00 3.55
2410 2782 7.587037 TTATTGAAGAAATGCATAGAAGGGG 57.413 36.000 0.00 0.00 0.00 4.79
2458 2830 0.036010 TAGCTGGCCTGACAAGAAGC 60.036 55.000 14.77 6.57 0.00 3.86
2492 2864 7.206981 ACATGAAATCGTGAAAGTGAATTCT 57.793 32.000 9.51 0.00 36.72 2.40
2693 3066 8.358148 AGTAAGGATACACATACCATAAACTCG 58.642 37.037 0.00 0.00 41.41 4.18
2735 3108 4.215613 GTGTTAGGAAACGAGCAGGAAAAT 59.784 41.667 0.00 0.00 38.53 1.82
2736 3109 3.562557 GTGTTAGGAAACGAGCAGGAAAA 59.437 43.478 0.00 0.00 38.53 2.29
2741 3114 2.673368 GGATGTGTTAGGAAACGAGCAG 59.327 50.000 0.00 0.00 38.53 4.24
2751 3125 8.139350 TGTAAAGTATGTATCGGATGTGTTAGG 58.861 37.037 0.00 0.00 0.00 2.69
2765 3139 9.647797 CAACATCAGTTACCTGTAAAGTATGTA 57.352 33.333 10.37 0.00 39.82 2.29
2913 3288 9.990360 ATGCAAATCAATCAATGCTAAATATCA 57.010 25.926 0.00 0.00 39.49 2.15
2915 3290 9.214957 CCATGCAAATCAATCAATGCTAAATAT 57.785 29.630 0.00 0.00 39.49 1.28
2921 3296 4.481368 ACCATGCAAATCAATCAATGCT 57.519 36.364 0.00 0.00 39.49 3.79
2931 3306 5.170021 TGAGCACAAATAACCATGCAAATC 58.830 37.500 0.00 0.00 40.63 2.17
2932 3307 5.149973 TGAGCACAAATAACCATGCAAAT 57.850 34.783 0.00 0.00 40.63 2.32
2951 3326 5.379732 AGAAGTCGAAACTAGAACCTGAG 57.620 43.478 0.00 0.00 33.48 3.35
2956 3331 6.237253 GCACGATTAGAAGTCGAAACTAGAAC 60.237 42.308 0.00 0.00 41.40 3.01
2985 3360 2.922758 GCCACCTTCGTATAGCTGATCG 60.923 54.545 0.00 0.00 0.00 3.69
3030 3405 6.857964 CACATACTTTCAAGGTGTCAATGAAC 59.142 38.462 0.00 0.00 33.13 3.18
3052 3427 8.519526 AGAGAAACTGACAAATAAAACAACACA 58.480 29.630 0.00 0.00 0.00 3.72
3094 3469 8.709386 AAATTAACATGAGTACACTAGCAGAG 57.291 34.615 0.00 0.00 0.00 3.35
3106 3481 9.044150 CAACAATCCACAAAAATTAACATGAGT 57.956 29.630 0.00 0.00 0.00 3.41
3192 3567 4.020485 ACTTCCGAAAGTAGGCAACATACT 60.020 41.667 0.00 0.00 43.98 2.12
3232 3608 5.634118 AGATGTCATGAAAGGGAAAACTGA 58.366 37.500 0.00 0.00 0.00 3.41
3257 3633 4.226384 TCTCCAGCCTGCTCATAAGATTA 58.774 43.478 0.00 0.00 0.00 1.75
3300 3676 4.921470 TTAAGAACTGTACTGCATTCGC 57.079 40.909 0.00 0.00 39.24 4.70
3473 3851 0.548926 TCCCAGTGGGACCTGCATAA 60.549 55.000 28.04 0.86 46.17 1.90
3599 3977 4.391830 AGCATTGTGTAATCCGTAACTGTG 59.608 41.667 0.00 0.00 0.00 3.66
3607 3985 2.283298 AGAGCAGCATTGTGTAATCCG 58.717 47.619 0.00 0.00 0.00 4.18
3616 3994 3.628032 AGATCACATCAAGAGCAGCATTG 59.372 43.478 0.00 0.00 0.00 2.82
3623 4001 5.290643 GTGTCAGTTAGATCACATCAAGAGC 59.709 44.000 0.00 0.00 32.25 4.09
3730 4132 5.007034 TCAACCAATGTGACAAACCGATAT 58.993 37.500 0.00 0.00 0.00 1.63
3762 4164 6.232581 AGATGACAGACTAAGGAAAGATGG 57.767 41.667 0.00 0.00 0.00 3.51
3804 4206 7.011669 TGTCTAAACAGTAAACACAAGGCTAAC 59.988 37.037 0.00 0.00 0.00 2.34
3820 4223 5.365021 AGAATGGAGGGATGTCTAAACAG 57.635 43.478 0.00 0.00 39.20 3.16
3821 4224 6.884472 TTAGAATGGAGGGATGTCTAAACA 57.116 37.500 0.00 0.00 40.38 2.83
3822 4225 8.624776 CAAATTAGAATGGAGGGATGTCTAAAC 58.375 37.037 0.00 0.00 35.16 2.01
3823 4226 7.779798 CCAAATTAGAATGGAGGGATGTCTAAA 59.220 37.037 0.00 0.00 39.12 1.85
3824 4227 7.128728 TCCAAATTAGAATGGAGGGATGTCTAA 59.871 37.037 0.00 0.00 40.74 2.10
3825 4228 6.619437 TCCAAATTAGAATGGAGGGATGTCTA 59.381 38.462 0.00 0.00 40.74 2.59
3826 4229 5.433051 TCCAAATTAGAATGGAGGGATGTCT 59.567 40.000 0.00 0.00 40.74 3.41
3834 4237 5.945784 TGTCCAGTTCCAAATTAGAATGGAG 59.054 40.000 15.15 1.22 45.94 3.86
3838 4241 5.892348 AGGTGTCCAGTTCCAAATTAGAAT 58.108 37.500 0.00 0.00 0.00 2.40
3854 4257 2.879026 GTTTCAGGTCTTCAAGGTGTCC 59.121 50.000 0.00 0.00 0.00 4.02
3876 4279 5.131067 AGTGTACATCTATCGAGCCTGTAA 58.869 41.667 0.00 0.00 0.00 2.41
3885 4289 8.838365 ACTACTAAGGAAAGTGTACATCTATCG 58.162 37.037 0.00 0.00 0.00 2.92
3893 4297 7.405769 CGCTACTACTACTAAGGAAAGTGTAC 58.594 42.308 0.00 0.00 0.00 2.90
3916 4320 1.680668 TGCAAAATAACGAAGTGCGC 58.319 45.000 0.00 0.00 45.00 6.09
3918 4322 8.979817 TTTAAAAATGCAAAATAACGAAGTGC 57.020 26.923 0.00 0.00 45.00 4.40
3921 4325 9.516091 GCTCTTTAAAAATGCAAAATAACGAAG 57.484 29.630 0.00 0.00 0.00 3.79
3922 4326 8.491950 GGCTCTTTAAAAATGCAAAATAACGAA 58.508 29.630 0.00 0.00 0.00 3.85
3927 4331 9.855021 GACTAGGCTCTTTAAAAATGCAAAATA 57.145 29.630 0.00 0.00 0.00 1.40
3928 4332 7.819415 GGACTAGGCTCTTTAAAAATGCAAAAT 59.181 33.333 0.00 0.00 0.00 1.82
3929 4333 7.151976 GGACTAGGCTCTTTAAAAATGCAAAA 58.848 34.615 0.00 0.00 0.00 2.44
3932 4336 5.321102 TGGACTAGGCTCTTTAAAAATGCA 58.679 37.500 0.00 0.00 0.00 3.96
3951 4355 3.431486 CCACTAGCTTCAGGAATCTGGAC 60.431 52.174 0.00 0.00 41.23 4.02
3952 4356 2.768527 CCACTAGCTTCAGGAATCTGGA 59.231 50.000 0.00 0.00 41.23 3.86
3953 4357 2.503356 ACCACTAGCTTCAGGAATCTGG 59.497 50.000 0.00 0.00 41.23 3.86
3954 4358 3.902881 ACCACTAGCTTCAGGAATCTG 57.097 47.619 0.00 0.00 42.21 2.90
3955 4359 3.707102 GGTACCACTAGCTTCAGGAATCT 59.293 47.826 7.15 0.00 0.00 2.40
3956 4360 4.061357 GGTACCACTAGCTTCAGGAATC 57.939 50.000 7.15 0.00 0.00 2.52
4104 4508 8.792633 CCTTGTTCTCATACATAACCTGAAAAA 58.207 33.333 0.00 0.00 0.00 1.94
4120 4524 2.270434 ATAGCCTCCCCTTGTTCTCA 57.730 50.000 0.00 0.00 0.00 3.27
4162 4566 6.017026 TCACGACATTCTCGAATAGCTCTATT 60.017 38.462 0.00 2.03 46.14 1.73
4180 4584 2.726850 CTTCAGCGACCGTCACGACA 62.727 60.000 0.00 0.00 0.00 4.35
4233 4637 2.761208 AGATCGGGATCGTCACTTTTCT 59.239 45.455 3.19 0.00 42.48 2.52
4234 4638 3.117046 GAGATCGGGATCGTCACTTTTC 58.883 50.000 3.19 0.00 42.48 2.29
4258 4662 2.898729 ATCCTAGCTCATTGTCCACG 57.101 50.000 0.00 0.00 0.00 4.94
4364 4772 2.159114 TGAAGCAGGCAAAACAGGTTTC 60.159 45.455 0.00 0.00 31.45 2.78
4379 4787 3.523606 ACAACACAAGCAAATGAAGCA 57.476 38.095 0.00 0.00 0.00 3.91
4380 4788 4.803088 TGTAACAACACAAGCAAATGAAGC 59.197 37.500 0.00 0.00 0.00 3.86
4471 4880 0.599991 CGCCGCCATTATCTACAGCA 60.600 55.000 0.00 0.00 0.00 4.41
4529 4938 9.216117 AGATATAACAAAACTATAATGCGGTCC 57.784 33.333 0.00 0.00 0.00 4.46
4572 4990 5.448654 CAACATTTCTCCCATTCCTCCATA 58.551 41.667 0.00 0.00 0.00 2.74
4752 5174 6.015519 TCTGAATTTTTGGGATCACATCGTTT 60.016 34.615 0.00 0.00 0.00 3.60
4769 5191 9.835389 TTCAAATTTGTTGGAATCTCTGAATTT 57.165 25.926 17.47 0.00 0.00 1.82
4826 5248 4.569943 TGATTCAACAAGAGTCTGCTACC 58.430 43.478 0.00 0.00 34.34 3.18
4842 5265 8.165239 ACAGTATTTGTTAGCTTGTTGATTCA 57.835 30.769 0.00 0.00 36.31 2.57
4913 5336 3.577649 TCTTTGTAACTCTCTGCCTCG 57.422 47.619 0.00 0.00 0.00 4.63
4939 5362 2.997986 CAGCCAAAAGATGTTCCATTGC 59.002 45.455 0.00 0.00 0.00 3.56
4950 5373 5.592282 TCTGTTGATTTACACAGCCAAAAGA 59.408 36.000 0.00 0.00 30.97 2.52
4955 5382 3.191162 GCATCTGTTGATTTACACAGCCA 59.809 43.478 0.00 0.00 32.16 4.75
5000 5442 4.296621 TGGATATTCTCATCATGGGCTG 57.703 45.455 0.00 0.00 0.00 4.85
5001 5443 5.262009 CAATGGATATTCTCATCATGGGCT 58.738 41.667 0.00 0.00 0.00 5.19
5002 5444 4.142227 GCAATGGATATTCTCATCATGGGC 60.142 45.833 0.00 0.00 0.00 5.36
5003 5445 5.014202 TGCAATGGATATTCTCATCATGGG 58.986 41.667 0.00 0.00 0.00 4.00
5004 5446 6.584185 TTGCAATGGATATTCTCATCATGG 57.416 37.500 0.00 0.00 0.00 3.66
5013 5455 4.443315 CCCCCAAGTTTGCAATGGATATTC 60.443 45.833 17.40 0.00 36.27 1.75
5037 5479 4.221041 GTCCTACTGACACTTAGGCTCTTT 59.779 45.833 0.00 0.00 43.85 2.52
5054 5497 4.727507 TCTCTGCTTGATGAAGTCCTAC 57.272 45.455 0.00 0.00 0.00 3.18
5057 5500 4.438472 GCATTTCTCTGCTTGATGAAGTCC 60.438 45.833 0.00 0.00 39.12 3.85
5066 5509 3.345414 AGAAGAGGCATTTCTCTGCTTG 58.655 45.455 0.00 0.00 45.16 4.01
5072 5515 5.115480 CCACTAGAAGAAGAGGCATTTCTC 58.885 45.833 0.00 0.00 33.92 2.87
5130 5820 3.652869 TGATCTCCTTTGTTCTGGGACTT 59.347 43.478 0.00 0.00 0.00 3.01
5150 5841 6.376864 TCAAATTCCAACACTGAAGAAACTGA 59.623 34.615 0.00 0.00 0.00 3.41
5187 5878 3.555966 CTCCAAGTTCTGGGACTGTTTT 58.444 45.455 0.00 0.00 46.44 2.43
5188 5879 2.158608 CCTCCAAGTTCTGGGACTGTTT 60.159 50.000 0.00 0.00 46.44 2.83
5189 5880 1.421646 CCTCCAAGTTCTGGGACTGTT 59.578 52.381 0.00 0.00 46.44 3.16
5191 5882 1.352083 TCCTCCAAGTTCTGGGACTG 58.648 55.000 0.00 0.00 46.44 3.51
5192 5883 1.981495 CTTCCTCCAAGTTCTGGGACT 59.019 52.381 0.00 0.00 46.44 3.85
5193 5884 1.978580 TCTTCCTCCAAGTTCTGGGAC 59.021 52.381 0.00 0.00 46.44 4.46
5194 5885 2.415983 TCTTCCTCCAAGTTCTGGGA 57.584 50.000 0.00 0.00 46.44 4.37
5195 5886 4.844349 TTATCTTCCTCCAAGTTCTGGG 57.156 45.455 0.00 0.00 46.44 4.45
5196 5887 7.148000 GGAAAATTATCTTCCTCCAAGTTCTGG 60.148 40.741 0.85 0.00 39.49 3.86
5197 5888 7.766283 GGAAAATTATCTTCCTCCAAGTTCTG 58.234 38.462 0.85 0.00 39.49 3.02
5198 5889 7.946381 GGAAAATTATCTTCCTCCAAGTTCT 57.054 36.000 0.85 0.00 39.49 3.01
5214 5905 4.526650 GGAACCTGCTCCAAAGGAAAATTA 59.473 41.667 0.00 0.00 38.27 1.40
5243 5935 3.511699 TGCTGCTGTATGTTCGAGTTAG 58.488 45.455 0.00 0.00 0.00 2.34
5252 5944 1.542915 CTTTTGGCTGCTGCTGTATGT 59.457 47.619 15.64 0.00 39.59 2.29
5268 5960 8.932791 CAATGCTTAGATGCAAAATCTTCTTTT 58.067 29.630 0.00 0.00 46.61 2.27
5282 7672 6.183360 TGGAAATGTGCTACAATGCTTAGATG 60.183 38.462 0.00 0.00 0.00 2.90
5287 7677 4.870123 TTGGAAATGTGCTACAATGCTT 57.130 36.364 0.00 0.00 0.00 3.91
5301 7691 8.596293 ACAAGTGGATTCACAATATTTGGAAAT 58.404 29.630 6.96 0.00 45.91 2.17
5303 7693 7.537596 ACAAGTGGATTCACAATATTTGGAA 57.462 32.000 6.96 2.06 45.91 3.53
5309 7699 7.362056 GCAACTGTACAAGTGGATTCACAATAT 60.362 37.037 6.96 0.00 45.91 1.28
5383 7804 2.409378 GCATCAAATTCCAACAACAGCG 59.591 45.455 0.00 0.00 0.00 5.18
5385 7806 5.559417 GCTTTGCATCAAATTCCAACAACAG 60.559 40.000 0.00 0.00 32.70 3.16
5412 7836 0.514691 GCAGTTCCAAGAGCTCAACG 59.485 55.000 17.77 8.83 0.00 4.10
5414 7838 1.417517 TCAGCAGTTCCAAGAGCTCAA 59.582 47.619 17.77 0.00 34.61 3.02
5417 7841 2.434428 CATTCAGCAGTTCCAAGAGCT 58.566 47.619 0.00 0.00 37.95 4.09
5443 7868 0.894835 TTCGCATGCCTCTGTCTACA 59.105 50.000 13.15 0.00 0.00 2.74
5459 7884 4.260538 GCCAAACTGCATAGATCTCTTTCG 60.261 45.833 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.