Multiple sequence alignment - TraesCS3A01G506200

Loading Multiple Alignment...

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 TraesCS3A01G506200 chr3A 100.000 5353 0 0 1 5353 727989073 727994425 0.000000e+00 9886.0
1 TraesCS3A01G506200 chr3D 93.648 3999 165 40 706 4670 598009886 598013829 0.000000e+00 5895.0
2 TraesCS3A01G506200 chr3D 88.409 509 34 2 4845 5353 598013822 598014305 1.660000e-164 590.0
3 TraesCS3A01G506200 chr3D 85.855 304 38 5 414 716 598009306 598009605 8.650000e-83 318.0
4 TraesCS3A01G506200 chr3D 83.402 241 28 6 163 395 268520190 268520426 4.200000e-51 213.0
5 TraesCS3A01G506200 chr3D 82.510 263 25 9 163 413 31402636 31402383 1.510000e-50 211.0
6 TraesCS3A01G506200 chr3D 86.047 129 12 4 1 129 598009191 598009313 3.360000e-27 134.0
7 TraesCS3A01G506200 chr3D 89.286 56 5 1 21 76 410510693 410510639 9.620000e-08 69.4
8 TraesCS3A01G506200 chr3D 97.059 34 1 0 380 413 9731301 9731268 2.080000e-04 58.4
9 TraesCS3A01G506200 chr3B 92.851 3539 193 25 1855 5351 804669105 804672625 0.000000e+00 5079.0
10 TraesCS3A01G506200 chr3B 92.581 620 33 9 1248 1862 804666985 804667596 0.000000e+00 878.0
11 TraesCS3A01G506200 chr3B 94.545 495 18 5 670 1156 804666287 804666780 0.000000e+00 756.0
12 TraesCS3A01G506200 chr3B 82.456 114 15 3 21 129 396725439 396725552 1.590000e-15 95.3
13 TraesCS3A01G506200 chr5B 86.447 273 18 11 130 395 79084210 79083950 1.140000e-71 281.0
14 TraesCS3A01G506200 chr6A 85.547 256 25 8 163 410 609114209 609114460 1.910000e-64 257.0
15 TraesCS3A01G506200 chr2D 88.018 217 19 3 202 413 375159188 375158974 3.200000e-62 250.0
16 TraesCS3A01G506200 chr2D 84.956 226 21 9 163 379 314505132 314505353 3.250000e-52 217.0
17 TraesCS3A01G506200 chr5A 83.630 281 26 13 128 395 9214764 9215037 4.140000e-61 246.0
18 TraesCS3A01G506200 chr5A 94.595 37 2 0 380 416 10481794 10481758 2.080000e-04 58.4
19 TraesCS3A01G506200 chr5A 100.000 30 0 0 3653 3682 469053581 469053552 7.490000e-04 56.5
20 TraesCS3A01G506200 chr2B 81.818 308 29 12 126 409 677041509 677041205 3.220000e-57 233.0
21 TraesCS3A01G506200 chr2B 83.951 243 25 7 165 395 556433777 556433537 2.510000e-53 220.0
22 TraesCS3A01G506200 chr2B 78.451 297 28 15 125 395 199702498 199702212 1.540000e-35 161.0
23 TraesCS3A01G506200 chr2B 83.621 116 12 5 21 130 688373924 688373810 9.490000e-18 102.0
24 TraesCS3A01G506200 chr2B 100.000 31 0 0 385 415 673109251 673109221 2.080000e-04 58.4
25 TraesCS3A01G506200 chr2B 100.000 30 0 0 1463 1492 109972796 109972767 7.490000e-04 56.5
26 TraesCS3A01G506200 chr1D 88.660 194 15 3 202 395 3959550 3959736 4.170000e-56 230.0
27 TraesCS3A01G506200 chr1D 87.719 57 7 0 21 77 261894187 261894131 3.460000e-07 67.6
28 TraesCS3A01G506200 chr1D 90.476 42 3 1 385 425 44998224 44998183 3.000000e-03 54.7
29 TraesCS3A01G506200 chr1A 78.648 281 46 13 415 688 450098764 450099037 1.980000e-39 174.0
30 TraesCS3A01G506200 chr2A 77.660 282 49 10 415 684 762648263 762647984 5.550000e-35 159.0
31 TraesCS3A01G506200 chr5D 86.885 122 13 3 4477 4596 384630576 384630696 3.360000e-27 134.0
32 TraesCS3A01G506200 chr5D 100.000 34 0 0 382 415 70204107 70204074 4.480000e-06 63.9
33 TraesCS3A01G506200 chr1B 81.208 149 20 8 540 684 471766836 471766980 4.380000e-21 113.0
34 TraesCS3A01G506200 chr7B 82.243 107 17 1 4531 4635 379416950 379417056 2.050000e-14 91.6
35 TraesCS3A01G506200 chr7B 91.228 57 4 1 21 77 570252772 570252827 5.750000e-10 76.8
36 TraesCS3A01G506200 chr7B 100.000 33 0 0 381 413 549604423 549604391 1.610000e-05 62.1
37 TraesCS3A01G506200 chr4D 80.000 110 17 4 21 130 418775854 418775958 5.750000e-10 76.8
38 TraesCS3A01G506200 chr4D 89.474 57 6 0 21 77 488961882 488961938 7.440000e-09 73.1
39 TraesCS3A01G506200 chr4B 77.236 123 23 3 22 144 515069640 515069523 3.460000e-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 TraesCS3A01G506200 chr3A 727989073 727994425 5352 False 9886.000000 9886 100.000000 1 5353 1 chr3A.!!$F1 5352
1 TraesCS3A01G506200 chr3D 598009191 598014305 5114 False 1734.250000 5895 88.489750 1 5353 4 chr3D.!!$F2 5352
2 TraesCS3A01G506200 chr3B 804666287 804672625 6338 False 2237.666667 5079 93.325667 670 5351 3 chr3B.!!$F2 4681

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
545 546 0.036164 TGCCGCACTGGTCAAATAGT 59.964 50.000 0.00 0.0 41.21 2.12 F
2012 3943 0.317479 CGAGGGACTTCAAGTCGGTT 59.683 55.000 11.52 0.0 45.96 4.44 F
2435 4366 1.074248 CTGGTACCCGGTGGCTTTT 59.926 57.895 10.07 0.0 33.59 2.27 F
2962 4901 0.120377 TACACCCACCATCCCTTCCT 59.880 55.000 0.00 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2536 4468 0.179076 CACCTGAGAGCACACACACA 60.179 55.0 0.00 0.00 0.00 3.72 R
2943 4882 0.120377 AGGAAGGGATGGTGGGTGTA 59.880 55.0 0.00 0.00 0.00 2.90 R
4071 6027 0.901827 TGTGCATACGGGTCATCTGT 59.098 50.0 0.00 0.00 38.72 3.41 R
4703 6661 0.036858 GACCTCAAAGGCTCGAGCTT 60.037 55.0 34.46 26.82 39.63 3.74 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
34 35 3.230976 AGTAAAAGTTTTGGCTCTGGGG 58.769 45.455 11.18 0.00 0.00 4.96
138 139 6.870769 TGTTAGTCTAACAAGTATACCTGGC 58.129 40.000 20.73 0.00 44.95 4.85
139 140 6.127253 TGTTAGTCTAACAAGTATACCTGGCC 60.127 42.308 20.73 0.00 44.95 5.36
140 141 4.359105 AGTCTAACAAGTATACCTGGCCA 58.641 43.478 4.71 4.71 0.00 5.36
141 142 4.781087 AGTCTAACAAGTATACCTGGCCAA 59.219 41.667 7.01 0.00 0.00 4.52
142 143 5.249852 AGTCTAACAAGTATACCTGGCCAAA 59.750 40.000 7.01 0.00 0.00 3.28
143 144 5.353400 GTCTAACAAGTATACCTGGCCAAAC 59.647 44.000 7.01 0.00 0.00 2.93
144 145 3.081710 ACAAGTATACCTGGCCAAACC 57.918 47.619 7.01 0.00 39.84 3.27
145 146 2.647802 ACAAGTATACCTGGCCAAACCT 59.352 45.455 7.01 0.00 40.22 3.50
146 147 3.279434 CAAGTATACCTGGCCAAACCTC 58.721 50.000 7.01 0.00 40.22 3.85
147 148 1.485066 AGTATACCTGGCCAAACCTCG 59.515 52.381 7.01 0.00 40.22 4.63
148 149 0.834612 TATACCTGGCCAAACCTCGG 59.165 55.000 7.01 5.79 40.22 4.63
149 150 1.921869 ATACCTGGCCAAACCTCGGG 61.922 60.000 7.01 4.92 40.22 5.14
193 194 4.554036 GCCTAGCCAAGCCCGAGG 62.554 72.222 0.00 0.00 0.00 4.63
232 233 2.102578 CCATCAGGCCTGGTTTTTAGG 58.897 52.381 32.23 18.53 38.39 2.69
238 239 2.868253 CCTGGTTTTTAGGCCCGAG 58.132 57.895 0.00 0.00 0.00 4.63
239 240 1.313091 CCTGGTTTTTAGGCCCGAGC 61.313 60.000 0.00 0.00 38.76 5.03
257 258 3.283684 CAGGCCCGAACACGCAAA 61.284 61.111 0.00 0.00 0.00 3.68
258 259 2.517402 AGGCCCGAACACGCAAAA 60.517 55.556 0.00 0.00 0.00 2.44
259 260 2.050442 GGCCCGAACACGCAAAAG 60.050 61.111 0.00 0.00 0.00 2.27
260 261 2.729491 GCCCGAACACGCAAAAGC 60.729 61.111 0.00 0.00 0.00 3.51
261 262 2.050442 CCCGAACACGCAAAAGCC 60.050 61.111 0.00 0.00 0.00 4.35
262 263 2.050442 CCGAACACGCAAAAGCCC 60.050 61.111 0.00 0.00 0.00 5.19
263 264 2.426752 CGAACACGCAAAAGCCCG 60.427 61.111 0.00 0.00 0.00 6.13
264 265 2.887889 CGAACACGCAAAAGCCCGA 61.888 57.895 0.00 0.00 0.00 5.14
265 266 1.370051 GAACACGCAAAAGCCCGAC 60.370 57.895 0.00 0.00 0.00 4.79
266 267 3.175976 AACACGCAAAAGCCCGACG 62.176 57.895 0.00 0.00 0.00 5.12
267 268 4.383602 CACGCAAAAGCCCGACGG 62.384 66.667 6.99 6.99 0.00 4.79
299 300 3.661648 GCCAGGCCCCTTCAGGAA 61.662 66.667 0.00 0.00 38.24 3.36
300 301 3.180282 CCAGGCCCCTTCAGGAAA 58.820 61.111 0.00 0.00 38.24 3.13
301 302 1.699752 CCAGGCCCCTTCAGGAAAT 59.300 57.895 0.00 0.00 38.24 2.17
302 303 0.396278 CCAGGCCCCTTCAGGAAATC 60.396 60.000 0.00 0.00 38.24 2.17
303 304 0.749454 CAGGCCCCTTCAGGAAATCG 60.749 60.000 0.00 0.00 38.24 3.34
304 305 2.121538 GGCCCCTTCAGGAAATCGC 61.122 63.158 0.00 0.00 38.24 4.58
305 306 1.378514 GCCCCTTCAGGAAATCGCA 60.379 57.895 0.00 0.00 38.24 5.10
306 307 0.965363 GCCCCTTCAGGAAATCGCAA 60.965 55.000 0.00 0.00 38.24 4.85
307 308 1.544724 CCCCTTCAGGAAATCGCAAA 58.455 50.000 0.00 0.00 38.24 3.68
308 309 2.102578 CCCCTTCAGGAAATCGCAAAT 58.897 47.619 0.00 0.00 38.24 2.32
309 310 3.287222 CCCCTTCAGGAAATCGCAAATA 58.713 45.455 0.00 0.00 38.24 1.40
310 311 3.891366 CCCCTTCAGGAAATCGCAAATAT 59.109 43.478 0.00 0.00 38.24 1.28
311 312 4.261741 CCCCTTCAGGAAATCGCAAATATG 60.262 45.833 0.00 0.00 38.24 1.78
312 313 4.580167 CCCTTCAGGAAATCGCAAATATGA 59.420 41.667 0.00 0.00 38.24 2.15
313 314 5.506317 CCCTTCAGGAAATCGCAAATATGAC 60.506 44.000 0.00 0.00 38.24 3.06
314 315 4.794248 TCAGGAAATCGCAAATATGACG 57.206 40.909 0.00 0.00 0.00 4.35
315 316 3.559655 TCAGGAAATCGCAAATATGACGG 59.440 43.478 0.00 0.00 0.00 4.79
316 317 2.878406 AGGAAATCGCAAATATGACGGG 59.122 45.455 0.00 0.00 0.00 5.28
317 318 2.616842 GGAAATCGCAAATATGACGGGT 59.383 45.455 0.00 0.00 0.00 5.28
318 319 3.303791 GGAAATCGCAAATATGACGGGTC 60.304 47.826 0.00 0.00 0.00 4.46
319 320 1.878953 ATCGCAAATATGACGGGTCC 58.121 50.000 0.00 0.00 0.00 4.46
320 321 0.528901 TCGCAAATATGACGGGTCCG 60.529 55.000 7.97 7.97 46.03 4.79
321 322 1.495584 CGCAAATATGACGGGTCCGG 61.496 60.000 14.25 0.00 44.69 5.14
322 323 1.164041 GCAAATATGACGGGTCCGGG 61.164 60.000 14.25 0.00 44.69 5.73
323 324 1.147600 AAATATGACGGGTCCGGGC 59.852 57.895 14.25 0.00 44.69 6.13
324 325 2.333701 AAATATGACGGGTCCGGGCC 62.334 60.000 19.72 19.72 44.69 5.80
325 326 3.768833 ATATGACGGGTCCGGGCCT 62.769 63.158 27.44 5.55 44.69 5.19
353 354 2.498167 CCATCGGGCTCAAAATCTAGG 58.502 52.381 0.00 0.00 0.00 3.02
354 355 1.876156 CATCGGGCTCAAAATCTAGGC 59.124 52.381 0.00 0.00 37.55 3.93
357 358 2.707902 GGCTCAAAATCTAGGCCCG 58.292 57.895 0.00 0.00 37.12 6.13
358 359 0.180406 GGCTCAAAATCTAGGCCCGA 59.820 55.000 0.00 0.00 37.12 5.14
359 360 1.587547 GCTCAAAATCTAGGCCCGAG 58.412 55.000 0.00 0.00 0.00 4.63
360 361 1.587547 CTCAAAATCTAGGCCCGAGC 58.412 55.000 0.00 0.00 38.76 5.03
406 407 4.374584 CCGGGTTTCCCATGGCCA 62.375 66.667 8.56 8.56 45.83 5.36
407 408 2.755469 CGGGTTTCCCATGGCCAG 60.755 66.667 13.05 3.10 45.83 4.85
408 409 2.364186 GGGTTTCCCATGGCCAGG 60.364 66.667 13.05 12.17 44.65 4.45
409 410 2.445155 GGTTTCCCATGGCCAGGT 59.555 61.111 17.55 0.00 0.00 4.00
410 411 1.694856 GGTTTCCCATGGCCAGGTA 59.305 57.895 17.55 0.90 0.00 3.08
411 412 0.261696 GGTTTCCCATGGCCAGGTAT 59.738 55.000 17.55 0.00 0.00 2.73
412 413 1.497286 GGTTTCCCATGGCCAGGTATA 59.503 52.381 17.55 0.00 0.00 1.47
413 414 2.583143 GTTTCCCATGGCCAGGTATAC 58.417 52.381 17.55 5.80 0.00 1.47
414 415 2.174854 GTTTCCCATGGCCAGGTATACT 59.825 50.000 17.55 0.00 0.00 2.12
415 416 3.354233 TTCCCATGGCCAGGTATACTA 57.646 47.619 17.55 0.00 0.00 1.82
416 417 3.354233 TCCCATGGCCAGGTATACTAA 57.646 47.619 17.55 0.00 0.00 2.24
417 418 2.976882 TCCCATGGCCAGGTATACTAAC 59.023 50.000 17.55 0.00 0.00 2.34
418 419 2.708861 CCCATGGCCAGGTATACTAACA 59.291 50.000 17.55 0.00 0.00 2.41
421 422 4.141482 CCATGGCCAGGTATACTAACAAGT 60.141 45.833 17.55 0.00 0.00 3.16
425 426 4.323257 GGCCAGGTATACTAACAAGTGTGT 60.323 45.833 0.00 0.00 40.75 3.72
442 443 8.031864 ACAAGTGTGTTTGACAATTTTCATGTA 58.968 29.630 0.00 0.00 39.87 2.29
444 445 8.994429 AGTGTGTTTGACAATTTTCATGTAAA 57.006 26.923 0.00 0.00 35.91 2.01
445 446 9.429359 AGTGTGTTTGACAATTTTCATGTAAAA 57.571 25.926 1.36 3.97 41.21 1.52
454 455 7.317390 ACAATTTTCATGTAAAACGGGATACC 58.683 34.615 1.36 0.00 45.11 2.73
475 476 3.564511 CGATGCTTCGTTGGTGAAAAAT 58.435 40.909 13.46 0.00 40.53 1.82
501 502 8.816640 ACAAAATTAAGTGTAGCATTTGAAGG 57.183 30.769 0.00 0.00 32.29 3.46
512 513 8.466798 GTGTAGCATTTGAAGGTAATATTTGGT 58.533 33.333 0.00 0.00 0.00 3.67
520 521 9.451002 TTTGAAGGTAATATTTGGTGTTCGATA 57.549 29.630 0.00 0.00 0.00 2.92
528 529 7.985634 ATATTTGGTGTTCGATATGTTTTGC 57.014 32.000 0.00 0.00 0.00 3.68
534 535 1.732941 TCGATATGTTTTGCCGCACT 58.267 45.000 0.00 0.00 0.00 4.40
545 546 0.036164 TGCCGCACTGGTCAAATAGT 59.964 50.000 0.00 0.00 41.21 2.12
549 550 3.189702 GCCGCACTGGTCAAATAGTTTAA 59.810 43.478 0.00 0.00 41.21 1.52
556 557 7.438160 GCACTGGTCAAATAGTTTAAGCTTTTT 59.562 33.333 3.20 0.00 0.00 1.94
559 560 8.865590 TGGTCAAATAGTTTAAGCTTTTTCAC 57.134 30.769 3.20 0.00 0.00 3.18
583 584 7.706179 CACTAAATAATTGCAGGTACCATTTGG 59.294 37.037 15.94 12.94 42.17 3.28
597 598 4.122143 CCATTTGGGTGCGACAATAAAT 57.878 40.909 0.00 0.00 0.00 1.40
604 605 5.919755 TGGGTGCGACAATAAATACATCTA 58.080 37.500 0.00 0.00 0.00 1.98
609 610 9.730420 GGTGCGACAATAAATACATCTAATTTT 57.270 29.630 0.00 0.00 0.00 1.82
653 655 3.810310 AAAACATTTTTGACGGGCAGA 57.190 38.095 0.00 0.00 0.00 4.26
991 1287 4.081972 CACATCTTCTTCCTTCTCCGAGAA 60.082 45.833 10.44 10.44 32.50 2.87
1020 1316 0.989747 TAGGAATTTCCCCGGACCCC 60.990 60.000 11.92 0.00 37.19 4.95
1082 1378 1.004560 AGCGTCCATGACCACAGTG 60.005 57.895 0.00 0.00 0.00 3.66
1160 1456 3.601443 CGAAAGGTCAGTTCTCTCCAT 57.399 47.619 0.00 0.00 0.00 3.41
1161 1457 3.257393 CGAAAGGTCAGTTCTCTCCATG 58.743 50.000 0.00 0.00 0.00 3.66
1162 1458 3.056536 CGAAAGGTCAGTTCTCTCCATGA 60.057 47.826 0.00 0.00 0.00 3.07
1175 1554 5.368145 TCTCTCCATGAACAAATTATCCCG 58.632 41.667 0.00 0.00 0.00 5.14
1219 1598 8.292444 TGAATTTCTAGTGTATCCCCAAATTG 57.708 34.615 0.00 0.00 0.00 2.32
1249 1628 2.358737 CTGGTCGAACTGCACCCC 60.359 66.667 0.33 0.00 0.00 4.95
1250 1629 3.164977 TGGTCGAACTGCACCCCA 61.165 61.111 0.33 0.00 0.00 4.96
1253 1632 3.948719 TCGAACTGCACCCCACCC 61.949 66.667 0.00 0.00 0.00 4.61
1254 1633 4.263572 CGAACTGCACCCCACCCA 62.264 66.667 0.00 0.00 0.00 4.51
1284 1694 5.934625 GTGAACTGAGTAACTCATGATGGTT 59.065 40.000 0.00 0.20 39.92 3.67
1285 1695 6.091441 GTGAACTGAGTAACTCATGATGGTTC 59.909 42.308 3.78 1.45 39.92 3.62
1289 1699 6.212388 ACTGAGTAACTCATGATGGTTCTCTT 59.788 38.462 17.74 9.59 39.92 2.85
1295 1705 6.566197 ACTCATGATGGTTCTCTTTTTGTC 57.434 37.500 0.00 0.00 0.00 3.18
1322 1732 2.431683 GTGCAGGGAGTTGGCAGA 59.568 61.111 0.00 0.00 38.38 4.26
1328 1738 0.475906 AGGGAGTTGGCAGATATGGC 59.524 55.000 6.99 6.99 0.00 4.40
1361 1771 2.507944 GCGGTGCTCAGGGATGAT 59.492 61.111 0.00 0.00 0.00 2.45
1707 2118 4.532521 GGTACTGATCAGGGTAAGGCATAT 59.467 45.833 26.08 3.63 0.00 1.78
1709 2120 6.384305 GGTACTGATCAGGGTAAGGCATATAT 59.616 42.308 26.08 3.00 0.00 0.86
1840 2251 7.443879 TGCACTTACTGAATTTCACAATGAGTA 59.556 33.333 0.00 0.00 0.00 2.59
1849 2260 7.936847 TGAATTTCACAATGAGTACTACTGGTT 59.063 33.333 0.00 0.00 0.00 3.67
2009 3940 0.809385 TAGCGAGGGACTTCAAGTCG 59.191 55.000 11.52 1.71 45.96 4.18
2012 3943 0.317479 CGAGGGACTTCAAGTCGGTT 59.683 55.000 11.52 0.00 45.96 4.44
2077 4008 3.872240 GCAAAGGCTCACAACCAGGTATA 60.872 47.826 0.00 0.00 36.96 1.47
2091 4022 4.939439 ACCAGGTATATTTGTTGTCGGAAC 59.061 41.667 0.00 0.00 0.00 3.62
2092 4023 5.183228 CCAGGTATATTTGTTGTCGGAACT 58.817 41.667 0.00 0.00 0.00 3.01
2093 4024 5.293569 CCAGGTATATTTGTTGTCGGAACTC 59.706 44.000 0.00 0.00 0.00 3.01
2094 4025 5.005394 CAGGTATATTTGTTGTCGGAACTCG 59.995 44.000 0.00 0.00 40.90 4.18
2095 4026 4.269363 GGTATATTTGTTGTCGGAACTCGG 59.731 45.833 0.00 0.00 39.77 4.63
2096 4027 2.536761 ATTTGTTGTCGGAACTCGGA 57.463 45.000 0.00 0.00 39.77 4.55
2100 4031 1.409790 TGTTGTCGGAACTCGGAAGAA 59.590 47.619 0.00 0.00 41.32 2.52
2101 4032 2.036733 TGTTGTCGGAACTCGGAAGAAT 59.963 45.455 0.00 0.00 41.32 2.40
2102 4033 2.649331 TGTCGGAACTCGGAAGAATC 57.351 50.000 0.00 0.00 41.32 2.52
2103 4034 1.203994 TGTCGGAACTCGGAAGAATCC 59.796 52.381 0.00 0.00 41.32 3.01
2104 4035 1.477295 GTCGGAACTCGGAAGAATCCT 59.523 52.381 0.00 0.00 44.17 3.24
2105 4036 1.476891 TCGGAACTCGGAAGAATCCTG 59.523 52.381 0.00 0.00 44.17 3.86
2106 4037 1.476891 CGGAACTCGGAAGAATCCTGA 59.523 52.381 0.00 0.00 44.17 3.86
2107 4038 2.101582 CGGAACTCGGAAGAATCCTGAT 59.898 50.000 0.00 0.00 44.17 2.90
2122 4053 6.995091 AGAATCCTGATAAAGACCTTGCATAC 59.005 38.462 0.00 0.00 0.00 2.39
2123 4054 5.036117 TCCTGATAAAGACCTTGCATACC 57.964 43.478 0.00 0.00 0.00 2.73
2207 4138 1.806461 CGGCCCTCGATAAGCTAGCA 61.806 60.000 18.83 0.00 42.43 3.49
2337 4268 2.273912 ACTTCCTCCACGGTCCGAC 61.274 63.158 20.51 0.00 0.00 4.79
2387 4318 1.815003 CTCAACATTTCTGGCCCTGTC 59.185 52.381 0.00 0.00 0.00 3.51
2435 4366 1.074248 CTGGTACCCGGTGGCTTTT 59.926 57.895 10.07 0.00 33.59 2.27
2447 4378 1.338020 GTGGCTTTTTCCAGTGACCTG 59.662 52.381 0.00 0.00 36.67 4.00
2493 4424 5.990120 AAATGCCTGTCTCAAAGCTAATT 57.010 34.783 0.00 0.00 0.00 1.40
2508 4440 4.770795 AGCTAATTGATAGTTTGCGGTCT 58.229 39.130 0.00 0.00 33.55 3.85
2763 4702 7.607607 TCTTATGCTCATTAGTGTTGTGACATT 59.392 33.333 0.00 0.00 38.23 2.71
2793 4732 8.102800 TGATGATGTCCAAGTAATATTGCATC 57.897 34.615 6.31 0.00 33.66 3.91
2962 4901 0.120377 TACACCCACCATCCCTTCCT 59.880 55.000 0.00 0.00 0.00 3.36
3019 4958 5.503927 AGGTAAAGAACATCATGATGCTGT 58.496 37.500 31.17 18.06 42.39 4.40
3134 5073 1.676014 CCGGTGGAACATGGACTTCTC 60.676 57.143 0.00 0.00 44.52 2.87
3155 5094 6.123651 TCTCTTGGACAATCTACTAGACCTC 58.876 44.000 0.00 0.00 0.00 3.85
3191 5130 3.004752 ACTCATACATCCACCTTTGCC 57.995 47.619 0.00 0.00 0.00 4.52
3228 5167 9.614792 GTGTTCCAAGGTATTTCTATACATCTT 57.385 33.333 0.00 0.00 38.71 2.40
3247 5186 5.593679 TCTTATGGCACCAAGTAGTAGAC 57.406 43.478 9.71 0.00 0.00 2.59
3260 5199 3.957497 AGTAGTAGACCTGGCTGATGAAG 59.043 47.826 0.00 0.00 0.00 3.02
3266 5205 1.425066 ACCTGGCTGATGAAGGAACAA 59.575 47.619 0.00 0.00 34.97 2.83
3271 5210 5.138125 TGGCTGATGAAGGAACAATTTTC 57.862 39.130 0.00 0.00 0.00 2.29
3296 5236 9.768215 TCTATCCATGGTCATATTATGTCTGTA 57.232 33.333 12.58 0.00 0.00 2.74
3313 5253 5.065859 TGTCTGTACAAACCAACATGTTGAG 59.934 40.000 34.76 26.24 36.26 3.02
3314 5254 5.065988 GTCTGTACAAACCAACATGTTGAGT 59.934 40.000 34.76 26.81 42.93 3.41
3665 5605 1.255667 GGCTACACTCCCTCCGTTCA 61.256 60.000 0.00 0.00 0.00 3.18
3803 5759 6.371548 GTCTAACTGTTCTGACAATGGCAATA 59.628 38.462 16.49 0.00 34.85 1.90
3816 5772 6.866480 ACAATGGCAATATTTCACGATCTTT 58.134 32.000 0.00 0.00 0.00 2.52
4035 5991 5.247110 ACATGACATCACCTGTAGTCTCTTT 59.753 40.000 0.00 0.00 38.54 2.52
4036 5992 5.392767 TGACATCACCTGTAGTCTCTTTC 57.607 43.478 0.00 0.00 38.54 2.62
4345 6302 7.661127 TGTTACTGTCAAAGCGTACATAATT 57.339 32.000 0.00 0.00 0.00 1.40
4565 6523 4.717279 AACCAGCAAACTTTAGTCCCTA 57.283 40.909 0.00 0.00 0.00 3.53
4607 6565 0.541063 TAGTCCCTCGTGCCACTTCA 60.541 55.000 0.00 0.00 0.00 3.02
4658 6616 1.702401 TGGCTTGAACTATGTGGGACA 59.298 47.619 0.00 0.00 0.00 4.02
4684 6642 3.554934 TGTCTGTGGCAGAAACTCAAAT 58.445 40.909 0.00 0.00 42.46 2.32
4687 6645 4.072131 TCTGTGGCAGAAACTCAAATACC 58.928 43.478 0.00 0.00 37.57 2.73
4689 6647 2.161609 GTGGCAGAAACTCAAATACCGG 59.838 50.000 0.00 0.00 0.00 5.28
4690 6648 2.224670 TGGCAGAAACTCAAATACCGGT 60.225 45.455 13.98 13.98 0.00 5.28
4691 6649 3.008157 TGGCAGAAACTCAAATACCGGTA 59.992 43.478 18.46 18.46 0.00 4.02
4692 6650 3.373130 GGCAGAAACTCAAATACCGGTAC 59.627 47.826 18.55 0.13 0.00 3.34
4693 6651 3.373130 GCAGAAACTCAAATACCGGTACC 59.627 47.826 18.55 0.16 0.00 3.34
4694 6652 4.828829 CAGAAACTCAAATACCGGTACCT 58.171 43.478 18.55 4.07 0.00 3.08
4695 6653 5.625197 GCAGAAACTCAAATACCGGTACCTA 60.625 44.000 18.55 0.00 0.00 3.08
4696 6654 6.400568 CAGAAACTCAAATACCGGTACCTAA 58.599 40.000 18.55 0.00 0.00 2.69
4698 6656 5.349061 AACTCAAATACCGGTACCTAAGG 57.651 43.478 18.55 6.55 0.00 2.69
4699 6657 4.356436 ACTCAAATACCGGTACCTAAGGT 58.644 43.478 18.55 12.53 41.73 3.50
4700 6658 4.403752 ACTCAAATACCGGTACCTAAGGTC 59.596 45.833 18.55 0.00 39.31 3.85
4701 6659 3.706086 TCAAATACCGGTACCTAAGGTCC 59.294 47.826 18.55 0.00 39.31 4.46
4702 6660 3.695357 AATACCGGTACCTAAGGTCCT 57.305 47.619 18.55 0.00 39.31 3.85
4703 6661 4.814224 AATACCGGTACCTAAGGTCCTA 57.186 45.455 18.55 0.00 39.31 2.94
4706 6666 1.685517 CCGGTACCTAAGGTCCTAAGC 59.314 57.143 10.90 0.00 37.09 3.09
4716 6676 0.537653 GGTCCTAAGCTCGAGCCTTT 59.462 55.000 32.94 23.38 43.38 3.11
4727 6687 1.002366 CGAGCCTTTGAGGTCATTCG 58.998 55.000 0.00 0.00 37.80 3.34
4743 6703 4.970003 GTCATTCGGTGCACTATATTTTGC 59.030 41.667 17.98 2.06 39.33 3.68
4744 6704 3.666883 TTCGGTGCACTATATTTTGCG 57.333 42.857 17.98 8.39 41.96 4.85
4746 6706 2.350192 TCGGTGCACTATATTTTGCGTG 59.650 45.455 17.98 0.00 41.96 5.34
4747 6707 2.538737 CGGTGCACTATATTTTGCGTGG 60.539 50.000 17.98 0.00 41.96 4.94
4748 6708 2.450160 GTGCACTATATTTTGCGTGGC 58.550 47.619 10.32 0.00 41.96 5.01
4754 6723 3.877508 ACTATATTTTGCGTGGCTCCTTC 59.122 43.478 0.00 0.00 0.00 3.46
4769 6738 0.390860 CCTTCCGCCACTGATAGGAG 59.609 60.000 0.00 0.00 33.89 3.69
4775 6744 1.411651 GCCACTGATAGGAGGGTCCC 61.412 65.000 0.00 0.00 37.19 4.46
4784 6753 0.903454 AGGAGGGTCCCACGTAGTTG 60.903 60.000 11.55 0.00 34.44 3.16
4795 6764 3.000727 CCACGTAGTTGGAGTCAAATCC 58.999 50.000 0.00 0.00 41.61 3.01
4808 6777 4.265073 AGTCAAATCCACTCCATGTTAGC 58.735 43.478 0.00 0.00 0.00 3.09
4809 6778 4.009675 GTCAAATCCACTCCATGTTAGCA 58.990 43.478 0.00 0.00 0.00 3.49
4821 6790 1.600023 TGTTAGCAAGAAACCACCCG 58.400 50.000 0.00 0.00 0.00 5.28
4847 6816 1.439679 CACGAGGGGCTAAACTTGTC 58.560 55.000 0.00 0.00 0.00 3.18
4873 6842 7.317390 GTGTTTTGAAAGTTAAGGGAGTGAAA 58.683 34.615 0.00 0.00 0.00 2.69
4891 6867 8.141268 GGAGTGAAATTTGATGTTTTGGAGTTA 58.859 33.333 0.00 0.00 0.00 2.24
5154 7153 9.689976 CTCAACCAAATAACATATTGTCAAACA 57.310 29.630 0.00 0.00 0.00 2.83
5175 7174 5.624159 ACAATTCATGTTGAGAGAAGTCCA 58.376 37.500 3.26 0.00 40.06 4.02
5176 7175 5.471456 ACAATTCATGTTGAGAGAAGTCCAC 59.529 40.000 3.26 0.00 40.06 4.02
5210 7209 2.311463 CAGATCCGTCCTCTACATGGT 58.689 52.381 0.00 0.00 0.00 3.55
5219 7218 2.234661 TCCTCTACATGGTGTTCTGCTG 59.765 50.000 0.00 0.00 0.00 4.41
5317 7316 2.636647 TGTGTCCTCATGCTTTGTCA 57.363 45.000 0.00 0.00 0.00 3.58
5320 7319 4.650734 TGTGTCCTCATGCTTTGTCATTA 58.349 39.130 0.00 0.00 0.00 1.90
5323 7322 3.063997 GTCCTCATGCTTTGTCATTACGG 59.936 47.826 0.00 0.00 0.00 4.02
5339 7338 3.044305 GGCAACGTTCGCTCTGCT 61.044 61.111 17.89 0.00 35.13 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 7.648112 CCAGAGCCAAAACTTTTACTACTTTTC 59.352 37.037 0.00 0.00 0.00 2.29
12 13 4.105057 TCCCCAGAGCCAAAACTTTTACTA 59.895 41.667 0.00 0.00 0.00 1.82
17 18 2.001076 CTCCCCAGAGCCAAAACTTT 57.999 50.000 0.00 0.00 32.13 2.66
34 35 5.474578 TGTTCATCAGGGAGTATATGCTC 57.525 43.478 12.04 12.04 34.89 4.26
93 94 7.894376 AACATGAACAGCCAAATAAAATCAG 57.106 32.000 0.00 0.00 0.00 2.90
95 96 8.986477 ACTAACATGAACAGCCAAATAAAATC 57.014 30.769 0.00 0.00 0.00 2.17
97 98 8.177119 AGACTAACATGAACAGCCAAATAAAA 57.823 30.769 0.00 0.00 0.00 1.52
127 128 1.485066 CGAGGTTTGGCCAGGTATACT 59.515 52.381 5.11 0.00 40.61 2.12
128 129 1.474498 CCGAGGTTTGGCCAGGTATAC 60.474 57.143 5.11 0.40 40.61 1.47
129 130 0.834612 CCGAGGTTTGGCCAGGTATA 59.165 55.000 5.11 0.00 40.61 1.47
130 131 1.607612 CCGAGGTTTGGCCAGGTAT 59.392 57.895 5.11 0.00 40.61 2.73
131 132 2.598787 CCCGAGGTTTGGCCAGGTA 61.599 63.158 5.11 0.00 40.61 3.08
132 133 3.966543 CCCGAGGTTTGGCCAGGT 61.967 66.667 5.11 0.00 40.61 4.00
177 178 4.554036 GCCTCGGGCTTGGCTAGG 62.554 72.222 7.58 10.20 46.69 3.02
212 213 2.102578 CCTAAAAACCAGGCCTGATGG 58.897 52.381 34.91 21.25 43.87 3.51
220 221 1.313091 GCTCGGGCCTAAAAACCAGG 61.313 60.000 0.84 0.00 36.16 4.45
221 222 2.180674 GCTCGGGCCTAAAAACCAG 58.819 57.895 0.84 0.00 0.00 4.00
222 223 4.408378 GCTCGGGCCTAAAAACCA 57.592 55.556 0.84 0.00 0.00 3.67
240 241 2.731587 CTTTTGCGTGTTCGGGCCTG 62.732 60.000 4.71 4.71 37.56 4.85
241 242 2.517402 TTTTGCGTGTTCGGGCCT 60.517 55.556 0.84 0.00 37.56 5.19
242 243 2.050442 CTTTTGCGTGTTCGGGCC 60.050 61.111 0.00 0.00 37.56 5.80
243 244 2.729491 GCTTTTGCGTGTTCGGGC 60.729 61.111 0.00 0.00 37.56 6.13
282 283 2.520657 ATTTCCTGAAGGGGCCTGGC 62.521 60.000 11.05 11.05 35.41 4.85
283 284 0.396278 GATTTCCTGAAGGGGCCTGG 60.396 60.000 0.84 0.00 35.41 4.45
284 285 0.749454 CGATTTCCTGAAGGGGCCTG 60.749 60.000 0.84 0.00 35.41 4.85
285 286 1.609783 CGATTTCCTGAAGGGGCCT 59.390 57.895 0.84 0.00 35.41 5.19
286 287 2.121538 GCGATTTCCTGAAGGGGCC 61.122 63.158 0.00 0.00 35.41 5.80
287 288 0.965363 TTGCGATTTCCTGAAGGGGC 60.965 55.000 0.00 0.00 35.41 5.80
288 289 1.544724 TTTGCGATTTCCTGAAGGGG 58.455 50.000 0.00 0.00 35.41 4.79
289 290 4.580167 TCATATTTGCGATTTCCTGAAGGG 59.420 41.667 0.00 0.00 35.41 3.95
290 291 5.514279 GTCATATTTGCGATTTCCTGAAGG 58.486 41.667 0.00 0.00 0.00 3.46
291 292 5.200454 CGTCATATTTGCGATTTCCTGAAG 58.800 41.667 0.00 0.00 0.00 3.02
292 293 4.035091 CCGTCATATTTGCGATTTCCTGAA 59.965 41.667 0.00 0.00 0.00 3.02
293 294 3.559655 CCGTCATATTTGCGATTTCCTGA 59.440 43.478 0.00 0.00 0.00 3.86
294 295 3.303990 CCCGTCATATTTGCGATTTCCTG 60.304 47.826 0.00 0.00 0.00 3.86
295 296 2.878406 CCCGTCATATTTGCGATTTCCT 59.122 45.455 0.00 0.00 0.00 3.36
296 297 2.616842 ACCCGTCATATTTGCGATTTCC 59.383 45.455 0.00 0.00 0.00 3.13
297 298 3.303791 GGACCCGTCATATTTGCGATTTC 60.304 47.826 0.00 0.00 0.00 2.17
298 299 2.616842 GGACCCGTCATATTTGCGATTT 59.383 45.455 0.00 0.00 0.00 2.17
299 300 2.218603 GGACCCGTCATATTTGCGATT 58.781 47.619 0.00 0.00 0.00 3.34
300 301 1.872237 CGGACCCGTCATATTTGCGAT 60.872 52.381 0.00 0.00 34.35 4.58
301 302 0.528901 CGGACCCGTCATATTTGCGA 60.529 55.000 0.00 0.00 34.35 5.10
302 303 1.495584 CCGGACCCGTCATATTTGCG 61.496 60.000 0.00 0.00 37.81 4.85
303 304 1.164041 CCCGGACCCGTCATATTTGC 61.164 60.000 0.73 0.00 37.81 3.68
304 305 1.164041 GCCCGGACCCGTCATATTTG 61.164 60.000 0.73 0.00 37.81 2.32
305 306 1.147600 GCCCGGACCCGTCATATTT 59.852 57.895 0.73 0.00 37.81 1.40
306 307 2.814835 GGCCCGGACCCGTCATATT 61.815 63.158 0.73 0.00 37.81 1.28
307 308 3.239253 GGCCCGGACCCGTCATAT 61.239 66.667 0.73 0.00 37.81 1.78
308 309 4.468769 AGGCCCGGACCCGTCATA 62.469 66.667 1.77 0.00 37.81 2.15
333 334 2.498167 CCTAGATTTTGAGCCCGATGG 58.502 52.381 0.00 0.00 0.00 3.51
334 335 1.876156 GCCTAGATTTTGAGCCCGATG 59.124 52.381 0.00 0.00 0.00 3.84
335 336 1.202818 GGCCTAGATTTTGAGCCCGAT 60.203 52.381 0.00 0.00 37.66 4.18
336 337 0.180406 GGCCTAGATTTTGAGCCCGA 59.820 55.000 0.00 0.00 37.66 5.14
337 338 2.707902 GGCCTAGATTTTGAGCCCG 58.292 57.895 0.00 0.00 37.66 6.13
339 340 0.180406 TCGGGCCTAGATTTTGAGCC 59.820 55.000 0.84 0.00 43.09 4.70
340 341 1.587547 CTCGGGCCTAGATTTTGAGC 58.412 55.000 0.84 0.00 0.00 4.26
341 342 1.587547 GCTCGGGCCTAGATTTTGAG 58.412 55.000 9.63 2.79 0.00 3.02
342 343 3.780624 GCTCGGGCCTAGATTTTGA 57.219 52.632 9.63 0.00 0.00 2.69
393 394 2.174854 AGTATACCTGGCCATGGGAAAC 59.825 50.000 17.65 13.54 0.00 2.78
394 395 2.498441 AGTATACCTGGCCATGGGAAA 58.502 47.619 17.65 5.77 0.00 3.13
395 396 2.206322 AGTATACCTGGCCATGGGAA 57.794 50.000 17.65 9.02 0.00 3.97
396 397 2.976882 GTTAGTATACCTGGCCATGGGA 59.023 50.000 17.65 12.89 0.00 4.37
397 398 2.708861 TGTTAGTATACCTGGCCATGGG 59.291 50.000 20.97 16.10 0.00 4.00
398 399 4.141482 ACTTGTTAGTATACCTGGCCATGG 60.141 45.833 5.51 13.05 31.21 3.66
399 400 4.816385 CACTTGTTAGTATACCTGGCCATG 59.184 45.833 5.51 6.06 31.96 3.66
400 401 4.473559 ACACTTGTTAGTATACCTGGCCAT 59.526 41.667 5.51 0.00 31.96 4.40
401 402 3.841845 ACACTTGTTAGTATACCTGGCCA 59.158 43.478 4.71 4.71 31.96 5.36
402 403 4.189231 CACACTTGTTAGTATACCTGGCC 58.811 47.826 0.00 0.00 31.96 5.36
403 404 4.828829 ACACACTTGTTAGTATACCTGGC 58.171 43.478 0.00 0.00 31.96 4.85
404 405 6.932400 TCAAACACACTTGTTAGTATACCTGG 59.068 38.462 0.00 0.00 45.69 4.45
405 406 7.439955 TGTCAAACACACTTGTTAGTATACCTG 59.560 37.037 0.00 0.00 45.69 4.00
406 407 7.502696 TGTCAAACACACTTGTTAGTATACCT 58.497 34.615 0.00 0.00 45.69 3.08
407 408 7.718272 TGTCAAACACACTTGTTAGTATACC 57.282 36.000 0.00 0.00 45.69 2.73
411 412 9.562583 GAAAATTGTCAAACACACTTGTTAGTA 57.437 29.630 0.00 0.00 45.69 1.82
412 413 8.085296 TGAAAATTGTCAAACACACTTGTTAGT 58.915 29.630 0.00 0.00 45.69 2.24
413 414 8.459521 TGAAAATTGTCAAACACACTTGTTAG 57.540 30.769 0.00 0.00 45.69 2.34
414 415 8.867935 CATGAAAATTGTCAAACACACTTGTTA 58.132 29.630 1.55 0.00 45.69 2.41
416 417 6.873076 ACATGAAAATTGTCAAACACACTTGT 59.127 30.769 1.55 0.00 37.67 3.16
417 418 7.293402 ACATGAAAATTGTCAAACACACTTG 57.707 32.000 1.55 0.00 33.41 3.16
418 419 8.994429 TTACATGAAAATTGTCAAACACACTT 57.006 26.923 1.55 0.00 33.41 3.16
421 422 8.376203 CGTTTTACATGAAAATTGTCAAACACA 58.624 29.630 1.55 0.00 39.45 3.72
425 426 7.265673 TCCCGTTTTACATGAAAATTGTCAAA 58.734 30.769 1.55 0.00 39.22 2.69
455 456 5.457140 TGTATTTTTCACCAACGAAGCATC 58.543 37.500 0.00 0.00 0.00 3.91
456 457 5.446143 TGTATTTTTCACCAACGAAGCAT 57.554 34.783 0.00 0.00 0.00 3.79
461 462 9.804758 ACTTAATTTTGTATTTTTCACCAACGA 57.195 25.926 0.00 0.00 0.00 3.85
462 463 9.842444 CACTTAATTTTGTATTTTTCACCAACG 57.158 29.630 0.00 0.00 0.00 4.10
475 476 9.906660 CCTTCAAATGCTACACTTAATTTTGTA 57.093 29.630 0.00 0.00 0.00 2.41
497 498 9.052759 ACATATCGAACACCAAATATTACCTTC 57.947 33.333 0.00 0.00 0.00 3.46
498 499 8.974060 ACATATCGAACACCAAATATTACCTT 57.026 30.769 0.00 0.00 0.00 3.50
505 506 6.326375 GGCAAAACATATCGAACACCAAATA 58.674 36.000 0.00 0.00 0.00 1.40
512 513 1.807142 TGCGGCAAAACATATCGAACA 59.193 42.857 0.00 0.00 0.00 3.18
520 521 1.106351 TGACCAGTGCGGCAAAACAT 61.106 50.000 3.23 0.00 39.03 2.71
527 528 1.165270 AACTATTTGACCAGTGCGGC 58.835 50.000 0.00 0.00 39.03 6.53
528 529 4.671766 GCTTAAACTATTTGACCAGTGCGG 60.672 45.833 0.00 0.00 42.50 5.69
534 535 8.691797 AGTGAAAAAGCTTAAACTATTTGACCA 58.308 29.630 0.00 0.00 0.00 4.02
549 550 7.670364 ACCTGCAATTATTTAGTGAAAAAGCT 58.330 30.769 0.00 0.00 0.00 3.74
556 557 8.465999 CAAATGGTACCTGCAATTATTTAGTGA 58.534 33.333 14.36 0.00 0.00 3.41
559 560 7.209475 CCCAAATGGTACCTGCAATTATTTAG 58.791 38.462 14.36 2.18 0.00 1.85
583 584 9.730420 AAAATTAGATGTATTTATTGTCGCACC 57.270 29.630 0.00 0.00 0.00 5.01
665 667 3.514645 CAAAAATCCAATCGGCTCTTGG 58.485 45.455 8.24 8.24 43.77 3.61
673 675 6.743575 AGACTTCTACCAAAAATCCAATCG 57.256 37.500 0.00 0.00 0.00 3.34
733 1027 4.273318 GGACAGGAAATTATCAGCAAGGT 58.727 43.478 0.00 0.00 0.00 3.50
737 1031 2.421388 CCGGGACAGGAAATTATCAGCA 60.421 50.000 0.00 0.00 0.00 4.41
991 1287 5.013183 CCGGGGAAATTCCTATATCTCTGTT 59.987 44.000 12.28 0.00 36.57 3.16
1027 1323 1.077429 GCAGCGGGAAAAGAGGGAT 60.077 57.895 0.00 0.00 0.00 3.85
1156 1452 5.949354 AGTTTCGGGATAATTTGTTCATGGA 59.051 36.000 0.00 0.00 0.00 3.41
1157 1453 6.207691 AGTTTCGGGATAATTTGTTCATGG 57.792 37.500 0.00 0.00 0.00 3.66
1159 1455 7.703058 AGAAGTTTCGGGATAATTTGTTCAT 57.297 32.000 0.00 0.00 0.00 2.57
1160 1456 7.229707 TGAAGAAGTTTCGGGATAATTTGTTCA 59.770 33.333 0.00 0.00 34.47 3.18
1161 1457 7.590279 TGAAGAAGTTTCGGGATAATTTGTTC 58.410 34.615 0.00 0.00 30.38 3.18
1162 1458 7.447238 TCTGAAGAAGTTTCGGGATAATTTGTT 59.553 33.333 0.00 0.00 0.00 2.83
1237 1616 4.263572 TGGGTGGGGTGCAGTTCG 62.264 66.667 0.00 0.00 0.00 3.95
1250 1629 0.401738 CTCAGTTCACCATGGTGGGT 59.598 55.000 38.12 23.03 43.37 4.51
1253 1632 3.997021 GAGTTACTCAGTTCACCATGGTG 59.003 47.826 35.00 35.00 46.64 4.17
1254 1633 3.646162 TGAGTTACTCAGTTCACCATGGT 59.354 43.478 13.00 13.00 35.39 3.55
1270 1680 7.095229 CGACAAAAAGAGAACCATCATGAGTTA 60.095 37.037 0.09 0.00 0.00 2.24
1284 1694 4.094294 CACCACAGTTTCGACAAAAAGAGA 59.906 41.667 0.00 0.00 0.00 3.10
1285 1695 4.342772 CACCACAGTTTCGACAAAAAGAG 58.657 43.478 0.00 0.00 0.00 2.85
1289 1699 1.813178 TGCACCACAGTTTCGACAAAA 59.187 42.857 0.00 0.00 0.00 2.44
1295 1705 1.227823 TCCCTGCACCACAGTTTCG 60.228 57.895 0.00 0.00 45.68 3.46
1322 1732 3.740115 GTACACCTTGATTCCGCCATAT 58.260 45.455 0.00 0.00 0.00 1.78
1328 1738 1.418342 CCGCGTACACCTTGATTCCG 61.418 60.000 4.92 0.00 0.00 4.30
1361 1771 1.005097 TCCTTCAGGTAGTCGGCACTA 59.995 52.381 0.00 0.00 33.62 2.74
1427 1837 0.824759 CCTTCTCGATCGGAACCCTT 59.175 55.000 16.41 0.00 0.00 3.95
1771 2182 9.877178 TGAACTTACTACTACAGTACTACCTAC 57.123 37.037 0.00 0.00 39.52 3.18
1798 2209 5.474578 AAGTGCAGACTGAGACATTTCTA 57.525 39.130 6.65 0.00 30.61 2.10
1811 2222 5.673337 TGTGAAATTCAGTAAGTGCAGAC 57.327 39.130 0.00 0.00 0.00 3.51
2012 3943 1.064825 GGTCTTTCCTCAGGTTCCCA 58.935 55.000 0.00 0.00 0.00 4.37
2033 3964 1.075050 AGTTCCTCCTGTAGACCGTCA 59.925 52.381 0.40 0.00 0.00 4.35
2039 3970 2.024176 TTGCCAGTTCCTCCTGTAGA 57.976 50.000 0.00 0.00 0.00 2.59
2077 4008 2.536761 TCCGAGTTCCGACAACAAAT 57.463 45.000 0.00 0.00 41.76 2.32
2094 4025 5.298026 GCAAGGTCTTTATCAGGATTCTTCC 59.702 44.000 0.00 0.00 42.96 3.46
2095 4026 5.882557 TGCAAGGTCTTTATCAGGATTCTTC 59.117 40.000 0.00 0.00 0.00 2.87
2096 4027 5.819991 TGCAAGGTCTTTATCAGGATTCTT 58.180 37.500 0.00 0.00 0.00 2.52
2100 4031 5.370880 AGGTATGCAAGGTCTTTATCAGGAT 59.629 40.000 0.00 0.00 0.00 3.24
2101 4032 4.721776 AGGTATGCAAGGTCTTTATCAGGA 59.278 41.667 0.00 0.00 0.00 3.86
2102 4033 4.818546 CAGGTATGCAAGGTCTTTATCAGG 59.181 45.833 0.00 0.00 0.00 3.86
2103 4034 5.431765 ACAGGTATGCAAGGTCTTTATCAG 58.568 41.667 0.00 0.00 0.00 2.90
2104 4035 5.435686 ACAGGTATGCAAGGTCTTTATCA 57.564 39.130 0.00 0.00 0.00 2.15
2105 4036 6.428159 CCATACAGGTATGCAAGGTCTTTATC 59.572 42.308 12.82 0.00 41.10 1.75
2106 4037 6.101150 TCCATACAGGTATGCAAGGTCTTTAT 59.899 38.462 12.82 0.00 41.10 1.40
2107 4038 5.427157 TCCATACAGGTATGCAAGGTCTTTA 59.573 40.000 12.82 0.00 41.10 1.85
2122 4053 3.703001 AACAGTGAGGTTCCATACAGG 57.297 47.619 0.00 0.00 39.47 4.00
2123 4054 5.639506 CAGTTAACAGTGAGGTTCCATACAG 59.360 44.000 8.61 0.00 32.29 2.74
2207 4138 0.762418 TGACCACCGTCTCCATTTGT 59.238 50.000 0.00 0.00 39.94 2.83
2360 4291 2.416747 CCAGAAATGTTGAGACTGCGA 58.583 47.619 0.00 0.00 0.00 5.10
2387 4318 2.163010 CAGATTGGCACTGTAAGGCTTG 59.837 50.000 10.69 0.00 39.30 4.01
2435 4366 2.303022 GTCATCCTTCAGGTCACTGGAA 59.697 50.000 0.00 0.00 44.99 3.53
2447 4378 3.873952 GCTCTACCATTGTGTCATCCTTC 59.126 47.826 0.00 0.00 0.00 3.46
2493 4424 6.459670 TGTATCTAAGACCGCAAACTATCA 57.540 37.500 0.00 0.00 0.00 2.15
2536 4468 0.179076 CACCTGAGAGCACACACACA 60.179 55.000 0.00 0.00 0.00 3.72
2537 4469 1.502163 GCACCTGAGAGCACACACAC 61.502 60.000 0.00 0.00 0.00 3.82
2645 4577 2.290514 TGAACCAAGATCAAGAGGGCAG 60.291 50.000 0.00 0.00 0.00 4.85
2648 4580 3.008375 TCACTGAACCAAGATCAAGAGGG 59.992 47.826 0.00 0.00 0.00 4.30
2789 4728 5.065731 CCTGAAGGTTGTTCATAGAAGATGC 59.934 44.000 0.00 0.00 0.00 3.91
2790 4729 5.587844 CCCTGAAGGTTGTTCATAGAAGATG 59.412 44.000 0.00 0.00 0.00 2.90
2806 4745 1.139058 CGAATACTCCCACCCTGAAGG 59.861 57.143 0.00 0.00 43.78 3.46
2940 4879 0.919289 AAGGGATGGTGGGTGTAGGG 60.919 60.000 0.00 0.00 0.00 3.53
2943 4882 0.120377 AGGAAGGGATGGTGGGTGTA 59.880 55.000 0.00 0.00 0.00 2.90
3134 5073 4.498345 GCGAGGTCTAGTAGATTGTCCAAG 60.498 50.000 2.51 0.08 0.00 3.61
3155 5094 1.017387 GAGTAAAAGGGGCATGAGCG 58.983 55.000 0.00 0.00 43.41 5.03
3191 5130 4.404691 GGAACACTCCAGCCCTTG 57.595 61.111 0.00 0.00 41.96 3.61
3228 5167 3.704566 CAGGTCTACTACTTGGTGCCATA 59.295 47.826 0.00 0.00 31.69 2.74
3247 5186 2.205022 TTGTTCCTTCATCAGCCAGG 57.795 50.000 0.00 0.00 0.00 4.45
3260 5199 6.773976 TGACCATGGATAGAAAATTGTTCC 57.226 37.500 21.47 0.00 0.00 3.62
3271 5210 9.809096 GTACAGACATAATATGACCATGGATAG 57.191 37.037 21.47 0.00 0.00 2.08
3313 5253 8.905702 CACAAAGCTGAGAATAATAACACAAAC 58.094 33.333 0.00 0.00 0.00 2.93
3314 5254 8.845227 TCACAAAGCTGAGAATAATAACACAAA 58.155 29.630 0.00 0.00 0.00 2.83
3803 5759 4.074970 AGACCTGCAAAAGATCGTGAAAT 58.925 39.130 0.00 0.00 0.00 2.17
3816 5772 3.265221 AGATCCTCATTCAAGACCTGCAA 59.735 43.478 0.00 0.00 0.00 4.08
4035 5991 3.329386 CAAAGAAATGGCACGAGAGAGA 58.671 45.455 0.00 0.00 0.00 3.10
4036 5992 2.159599 GCAAAGAAATGGCACGAGAGAG 60.160 50.000 0.00 0.00 0.00 3.20
4071 6027 0.901827 TGTGCATACGGGTCATCTGT 59.098 50.000 0.00 0.00 38.72 3.41
4345 6302 1.477700 GGAGCATGCTTTTGCCATACA 59.522 47.619 23.61 0.00 46.87 2.29
4490 6448 7.663905 TCGAAAGAGTTGAGGGATGAAAAATAA 59.336 33.333 0.00 0.00 34.84 1.40
4525 6483 3.253432 GGTTTGGAGTTGAGTGACCATTC 59.747 47.826 0.00 0.00 32.31 2.67
4607 6565 1.898574 CGGCAGCAAGAAACCACCT 60.899 57.895 0.00 0.00 0.00 4.00
4667 6625 2.811431 CGGTATTTGAGTTTCTGCCACA 59.189 45.455 0.00 0.00 0.00 4.17
4684 6642 3.688414 GCTTAGGACCTTAGGTACCGGTA 60.688 52.174 11.16 11.16 37.20 4.02
4687 6645 2.622470 GAGCTTAGGACCTTAGGTACCG 59.378 54.545 10.53 0.30 37.20 4.02
4689 6647 3.549794 TCGAGCTTAGGACCTTAGGTAC 58.450 50.000 12.00 5.25 35.25 3.34
4690 6648 3.818180 CTCGAGCTTAGGACCTTAGGTA 58.182 50.000 12.00 0.00 35.25 3.08
4691 6649 2.657143 CTCGAGCTTAGGACCTTAGGT 58.343 52.381 11.86 11.86 39.44 3.08
4692 6650 1.338655 GCTCGAGCTTAGGACCTTAGG 59.661 57.143 29.88 0.00 38.21 2.69
4693 6651 1.338655 GGCTCGAGCTTAGGACCTTAG 59.661 57.143 34.46 0.00 41.70 2.18
4694 6652 1.063867 AGGCTCGAGCTTAGGACCTTA 60.064 52.381 34.46 0.00 41.70 2.69
4695 6653 0.324830 AGGCTCGAGCTTAGGACCTT 60.325 55.000 34.46 8.41 41.70 3.50
4696 6654 0.324830 AAGGCTCGAGCTTAGGACCT 60.325 55.000 34.46 19.40 41.70 3.85
4698 6656 1.204941 TCAAAGGCTCGAGCTTAGGAC 59.795 52.381 34.46 18.16 41.70 3.85
4699 6657 1.478510 CTCAAAGGCTCGAGCTTAGGA 59.521 52.381 34.46 25.13 41.70 2.94
4700 6658 1.472376 CCTCAAAGGCTCGAGCTTAGG 60.472 57.143 34.46 26.13 41.70 2.69
4701 6659 1.205893 ACCTCAAAGGCTCGAGCTTAG 59.794 52.381 34.46 23.21 39.63 2.18
4702 6660 1.204941 GACCTCAAAGGCTCGAGCTTA 59.795 52.381 34.46 13.56 39.63 3.09
4703 6661 0.036858 GACCTCAAAGGCTCGAGCTT 60.037 55.000 34.46 26.82 39.63 3.74
4706 6666 2.275318 GAATGACCTCAAAGGCTCGAG 58.725 52.381 8.45 8.45 39.63 4.04
4716 6676 1.262417 TAGTGCACCGAATGACCTCA 58.738 50.000 14.63 0.00 0.00 3.86
4727 6687 2.794631 GCCACGCAAAATATAGTGCACC 60.795 50.000 14.63 0.00 40.94 5.01
4747 6707 0.249657 CTATCAGTGGCGGAAGGAGC 60.250 60.000 0.00 0.00 0.00 4.70
4748 6708 0.390860 CCTATCAGTGGCGGAAGGAG 59.609 60.000 0.00 0.00 0.00 3.69
4754 6723 1.749334 GACCCTCCTATCAGTGGCGG 61.749 65.000 0.00 0.00 0.00 6.13
4769 6738 1.190178 ACTCCAACTACGTGGGACCC 61.190 60.000 2.45 2.45 39.34 4.46
4775 6744 3.432252 GTGGATTTGACTCCAACTACGTG 59.568 47.826 0.00 0.00 46.66 4.49
4788 6757 4.299586 TGCTAACATGGAGTGGATTTGA 57.700 40.909 0.00 0.00 0.00 2.69
4793 6762 4.072131 GTTTCTTGCTAACATGGAGTGGA 58.928 43.478 0.00 0.00 0.00 4.02
4795 6764 3.820467 TGGTTTCTTGCTAACATGGAGTG 59.180 43.478 0.00 0.00 0.00 3.51
4808 6777 1.303317 CCCCTCGGGTGGTTTCTTG 60.303 63.158 0.55 0.00 38.25 3.02
4809 6778 2.535331 CCCCCTCGGGTGGTTTCTT 61.535 63.158 0.55 0.00 45.50 2.52
4838 6807 9.332301 CTTAACTTTCAAAACACGACAAGTTTA 57.668 29.630 0.00 0.00 38.17 2.01
4847 6816 5.065474 TCACTCCCTTAACTTTCAAAACACG 59.935 40.000 0.00 0.00 0.00 4.49
4873 6842 7.454380 TGATCCCTTAACTCCAAAACATCAAAT 59.546 33.333 0.00 0.00 0.00 2.32
5009 6987 6.627087 TTCTTCCATCACAGAAGGATTACT 57.373 37.500 1.03 0.00 40.94 2.24
5154 7153 5.874093 AGTGGACTTCTCTCAACATGAATT 58.126 37.500 0.00 0.00 0.00 2.17
5155 7154 5.495926 AGTGGACTTCTCTCAACATGAAT 57.504 39.130 0.00 0.00 0.00 2.57
5156 7155 4.963318 AGTGGACTTCTCTCAACATGAA 57.037 40.909 0.00 0.00 0.00 2.57
5157 7156 4.963318 AAGTGGACTTCTCTCAACATGA 57.037 40.909 0.00 0.00 0.00 3.07
5158 7157 7.388776 TCATTAAAGTGGACTTCTCTCAACATG 59.611 37.037 0.00 0.00 34.61 3.21
5159 7158 7.453393 TCATTAAAGTGGACTTCTCTCAACAT 58.547 34.615 0.00 0.00 34.61 2.71
5160 7159 6.826668 TCATTAAAGTGGACTTCTCTCAACA 58.173 36.000 0.00 0.00 34.61 3.33
5161 7160 7.572168 GCTTCATTAAAGTGGACTTCTCTCAAC 60.572 40.741 0.00 0.00 37.31 3.18
5162 7161 6.428159 GCTTCATTAAAGTGGACTTCTCTCAA 59.572 38.462 0.00 0.00 37.31 3.02
5163 7162 5.934625 GCTTCATTAAAGTGGACTTCTCTCA 59.065 40.000 0.00 0.00 37.31 3.27
5164 7163 6.169800 AGCTTCATTAAAGTGGACTTCTCTC 58.830 40.000 0.00 0.00 37.31 3.20
5165 7164 6.120507 AGCTTCATTAAAGTGGACTTCTCT 57.879 37.500 0.00 0.00 37.31 3.10
5166 7165 5.352846 GGAGCTTCATTAAAGTGGACTTCTC 59.647 44.000 0.00 0.00 37.31 2.87
5167 7166 5.221925 TGGAGCTTCATTAAAGTGGACTTCT 60.222 40.000 0.00 0.00 37.31 2.85
5168 7167 5.003804 TGGAGCTTCATTAAAGTGGACTTC 58.996 41.667 0.00 0.00 37.31 3.01
5169 7168 4.985538 TGGAGCTTCATTAAAGTGGACTT 58.014 39.130 0.00 0.00 37.31 3.01
5170 7169 4.287067 TCTGGAGCTTCATTAAAGTGGACT 59.713 41.667 0.00 0.00 37.31 3.85
5171 7170 4.579869 TCTGGAGCTTCATTAAAGTGGAC 58.420 43.478 0.00 0.00 37.31 4.02
5172 7171 4.908601 TCTGGAGCTTCATTAAAGTGGA 57.091 40.909 0.00 0.00 37.31 4.02
5173 7172 4.578105 GGATCTGGAGCTTCATTAAAGTGG 59.422 45.833 0.00 0.00 37.31 4.00
5174 7173 4.272018 CGGATCTGGAGCTTCATTAAAGTG 59.728 45.833 0.00 0.00 37.31 3.16
5175 7174 4.080863 ACGGATCTGGAGCTTCATTAAAGT 60.081 41.667 6.47 0.00 37.31 2.66
5176 7175 4.446371 ACGGATCTGGAGCTTCATTAAAG 58.554 43.478 6.47 0.00 38.08 1.85
5210 7209 3.169908 TCACCTACCATACAGCAGAACA 58.830 45.455 0.00 0.00 0.00 3.18
5219 7218 5.296780 CACACAAATCCATCACCTACCATAC 59.703 44.000 0.00 0.00 0.00 2.39
5280 7279 1.895131 ACAATCCACCACAAAGGATGC 59.105 47.619 0.00 0.00 43.67 3.91
5308 7307 1.069568 CGTTGCCGTAATGACAAAGCA 60.070 47.619 0.00 0.00 0.00 3.91
5323 7322 2.171940 CAGCAGAGCGAACGTTGC 59.828 61.111 5.00 10.14 36.83 4.17


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

AutoCloner maintained by Alex Coulton.