Multiple sequence alignment - TraesCS6A01G135200

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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 TraesCS6A01G135200 chr6A 100.000 5258 0 0 1 5258 107115321 107120578 0.000000e+00 9710.0
1 TraesCS6A01G135200 chr6D 94.489 3738 153 17 1409 5111 89006828 89010547 0.000000e+00 5712.0
2 TraesCS6A01G135200 chr6D 88.980 735 50 18 662 1377 89006031 89006753 0.000000e+00 880.0
3 TraesCS6A01G135200 chr6D 84.167 360 19 12 1 325 89005468 89005824 1.100000e-81 315.0
4 TraesCS6A01G135200 chr6D 83.003 353 13 17 332 670 89005690 89006009 5.190000e-70 276.0
5 TraesCS6A01G135200 chr6D 99.324 148 1 0 5111 5258 89010787 89010934 8.680000e-68 268.0
6 TraesCS6A01G135200 chr6B 93.370 3801 182 26 1404 5178 169321176 169324932 0.000000e+00 5559.0
7 TraesCS6A01G135200 chr6B 87.945 1236 93 27 4055 5253 169395925 169397141 0.000000e+00 1406.0
8 TraesCS6A01G135200 chr6B 85.550 1128 70 45 327 1386 169320012 169321114 0.000000e+00 1094.0
9 TraesCS6A01G135200 chr6B 81.538 325 17 21 1 299 169319810 169320117 1.470000e-55 228.0
10 TraesCS6A01G135200 chr2A 90.164 61 4 2 4643 4701 706284778 706284718 1.570000e-10 78.7
11 TraesCS6A01G135200 chr2B 89.474 57 5 1 4646 4701 678568385 678568329 2.630000e-08 71.3


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 TraesCS6A01G135200 chr6A 107115321 107120578 5257 False 9710.000000 9710 100.000000 1 5258 1 chr6A.!!$F1 5257
1 TraesCS6A01G135200 chr6D 89005468 89010934 5466 False 1490.200000 5712 89.992600 1 5258 5 chr6D.!!$F1 5257
2 TraesCS6A01G135200 chr6B 169319810 169324932 5122 False 2293.666667 5559 86.819333 1 5178 3 chr6B.!!$F2 5177
3 TraesCS6A01G135200 chr6B 169395925 169397141 1216 False 1406.000000 1406 87.945000 4055 5253 1 chr6B.!!$F1 1198

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
399 435 0.034337 TCCCCAGTCAACGCAGTAAC 59.966 55.0 0.0 0.0 45.00 2.50 F
400 436 0.034896 CCCCAGTCAACGCAGTAACT 59.965 55.0 0.0 0.0 45.00 2.24 F
1861 2012 0.174617 CCTCTTTCTCTGACGGAGCC 59.825 60.0 6.4 0.0 41.60 4.70 F
2093 2244 0.036022 AGAGCAAGGTCTCTGTTGGC 59.964 55.0 0.0 0.0 41.57 4.52 F
3600 3754 0.111446 TCAAGGGTGCCGATGGAAAA 59.889 50.0 0.0 0.0 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1823 1974 0.034896 GAAACCGAGCTTCACCTCCA 59.965 55.000 0.0 0.00 0.00 3.86 R
2093 2244 0.039617 GATGGTCATCTCGAGGCTCG 60.040 60.000 30.1 30.10 42.10 5.03 R
3702 3856 0.248539 GGAGAGACCCGTTCGAATCG 60.249 60.000 0.0 7.14 0.00 3.34 R
3852 4006 0.376852 TTGTGTTCAGCAACTCACGC 59.623 50.000 0.0 0.00 36.08 5.34 R
4797 5004 2.482721 TCCTTTTTGGAGCGTCGATTTC 59.517 45.455 0.0 0.00 40.56 2.17 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
41 45 4.436998 CCGTGACCCTCTGCCGAC 62.437 72.222 0.00 0.00 0.00 4.79
42 46 4.778415 CGTGACCCTCTGCCGACG 62.778 72.222 0.00 0.00 0.00 5.12
72 76 2.443390 GGTCCGGCAGCCCTAGTA 60.443 66.667 5.63 0.00 0.00 1.82
73 77 2.499827 GGTCCGGCAGCCCTAGTAG 61.500 68.421 5.63 0.00 0.00 2.57
74 78 2.838225 TCCGGCAGCCCTAGTAGC 60.838 66.667 5.63 0.00 0.00 3.58
75 79 3.930012 CCGGCAGCCCTAGTAGCC 61.930 72.222 5.63 0.00 43.61 3.93
77 81 3.930012 GGCAGCCCTAGTAGCCCG 61.930 72.222 0.00 0.00 41.25 6.13
78 82 3.930012 GCAGCCCTAGTAGCCCGG 61.930 72.222 0.00 0.00 0.00 5.73
80 84 2.123382 AGCCCTAGTAGCCCGGAC 60.123 66.667 0.73 0.00 0.00 4.79
279 315 3.120442 ACGCAGTAACTATTTTTCACCGC 60.120 43.478 0.00 0.00 41.94 5.68
289 325 0.882927 TTTTCACCGCTTGGTCTCCG 60.883 55.000 0.00 0.00 45.05 4.63
293 329 4.760047 CCGCTTGGTCTCCGGTGG 62.760 72.222 0.00 0.00 37.36 4.61
306 342 4.329545 GGTGGCAGCAAGGGTCGA 62.330 66.667 12.58 0.00 0.00 4.20
307 343 3.050275 GTGGCAGCAAGGGTCGAC 61.050 66.667 7.13 7.13 0.00 4.20
308 344 4.329545 TGGCAGCAAGGGTCGACC 62.330 66.667 27.04 27.04 40.67 4.79
320 356 3.108343 TCGACCTCGAGCGGAATC 58.892 61.111 6.99 0.00 44.22 2.52
321 357 1.451567 TCGACCTCGAGCGGAATCT 60.452 57.895 6.99 0.00 44.22 2.40
322 358 1.298713 CGACCTCGAGCGGAATCTG 60.299 63.158 6.99 0.00 43.02 2.90
323 359 1.715862 CGACCTCGAGCGGAATCTGA 61.716 60.000 6.99 0.00 43.02 3.27
324 360 0.456221 GACCTCGAGCGGAATCTGAA 59.544 55.000 6.99 0.00 0.00 3.02
325 361 0.457851 ACCTCGAGCGGAATCTGAAG 59.542 55.000 6.99 0.00 0.00 3.02
326 362 0.249238 CCTCGAGCGGAATCTGAAGG 60.249 60.000 6.99 0.00 0.00 3.46
327 363 0.457851 CTCGAGCGGAATCTGAAGGT 59.542 55.000 0.00 0.00 0.00 3.50
328 364 0.456221 TCGAGCGGAATCTGAAGGTC 59.544 55.000 0.00 0.00 0.00 3.85
329 365 0.528684 CGAGCGGAATCTGAAGGTCC 60.529 60.000 0.00 0.00 0.00 4.46
330 366 0.537188 GAGCGGAATCTGAAGGTCCA 59.463 55.000 0.00 0.00 0.00 4.02
331 367 1.139853 GAGCGGAATCTGAAGGTCCAT 59.860 52.381 0.00 0.00 0.00 3.41
332 368 1.139853 AGCGGAATCTGAAGGTCCATC 59.860 52.381 0.00 0.00 0.00 3.51
333 369 1.858091 CGGAATCTGAAGGTCCATCG 58.142 55.000 0.00 0.00 0.00 3.84
334 370 1.587547 GGAATCTGAAGGTCCATCGC 58.412 55.000 0.00 0.00 0.00 4.58
335 371 1.587547 GAATCTGAAGGTCCATCGCC 58.412 55.000 0.00 0.00 0.00 5.54
336 372 0.179073 AATCTGAAGGTCCATCGCCG 60.179 55.000 0.00 0.00 0.00 6.46
337 373 2.650813 ATCTGAAGGTCCATCGCCGC 62.651 60.000 0.00 0.00 0.00 6.53
338 374 4.467084 TGAAGGTCCATCGCCGCC 62.467 66.667 0.00 0.00 0.00 6.13
359 395 2.564975 GGCGAGAAACGACGGAGA 59.435 61.111 0.00 0.00 45.77 3.71
360 396 1.080974 GGCGAGAAACGACGGAGAA 60.081 57.895 0.00 0.00 45.77 2.87
361 397 1.071567 GGCGAGAAACGACGGAGAAG 61.072 60.000 0.00 0.00 45.77 2.85
362 398 1.071567 GCGAGAAACGACGGAGAAGG 61.072 60.000 0.00 0.00 45.77 3.46
363 399 0.240411 CGAGAAACGACGGAGAAGGT 59.760 55.000 0.00 0.00 45.77 3.50
364 400 1.728502 CGAGAAACGACGGAGAAGGTC 60.729 57.143 0.00 0.00 45.77 3.85
365 401 0.602060 AGAAACGACGGAGAAGGTCC 59.398 55.000 0.00 0.00 42.85 4.46
377 413 4.657013 GGAGAAGGTCCATTCCATTATCC 58.343 47.826 0.00 0.00 46.10 2.59
378 414 4.507512 GGAGAAGGTCCATTCCATTATCCC 60.508 50.000 0.00 0.00 46.10 3.85
379 415 3.399305 AGAAGGTCCATTCCATTATCCCC 59.601 47.826 0.00 0.00 0.00 4.81
380 416 3.095299 AGGTCCATTCCATTATCCCCT 57.905 47.619 0.00 0.00 0.00 4.79
381 417 2.989571 AGGTCCATTCCATTATCCCCTC 59.010 50.000 0.00 0.00 0.00 4.30
382 418 2.041755 GGTCCATTCCATTATCCCCTCC 59.958 54.545 0.00 0.00 0.00 4.30
383 419 2.041755 GTCCATTCCATTATCCCCTCCC 59.958 54.545 0.00 0.00 0.00 4.30
384 420 1.359130 CCATTCCATTATCCCCTCCCC 59.641 57.143 0.00 0.00 0.00 4.81
385 421 2.072973 CATTCCATTATCCCCTCCCCA 58.927 52.381 0.00 0.00 0.00 4.96
386 422 1.833187 TTCCATTATCCCCTCCCCAG 58.167 55.000 0.00 0.00 0.00 4.45
387 423 0.653397 TCCATTATCCCCTCCCCAGT 59.347 55.000 0.00 0.00 0.00 4.00
388 424 1.068121 CCATTATCCCCTCCCCAGTC 58.932 60.000 0.00 0.00 0.00 3.51
389 425 1.698928 CCATTATCCCCTCCCCAGTCA 60.699 57.143 0.00 0.00 0.00 3.41
390 426 2.135189 CATTATCCCCTCCCCAGTCAA 58.865 52.381 0.00 0.00 0.00 3.18
391 427 1.591768 TTATCCCCTCCCCAGTCAAC 58.408 55.000 0.00 0.00 0.00 3.18
392 428 0.689745 TATCCCCTCCCCAGTCAACG 60.690 60.000 0.00 0.00 0.00 4.10
393 429 4.410400 CCCCTCCCCAGTCAACGC 62.410 72.222 0.00 0.00 0.00 4.84
394 430 3.636231 CCCTCCCCAGTCAACGCA 61.636 66.667 0.00 0.00 0.00 5.24
395 431 2.046892 CCTCCCCAGTCAACGCAG 60.047 66.667 0.00 0.00 0.00 5.18
397 433 1.541310 CCTCCCCAGTCAACGCAGTA 61.541 60.000 0.00 0.00 45.00 2.74
398 434 0.320374 CTCCCCAGTCAACGCAGTAA 59.680 55.000 0.00 0.00 45.00 2.24
399 435 0.034337 TCCCCAGTCAACGCAGTAAC 59.966 55.000 0.00 0.00 45.00 2.50
400 436 0.034896 CCCCAGTCAACGCAGTAACT 59.965 55.000 0.00 0.00 45.00 2.24
401 437 1.274167 CCCCAGTCAACGCAGTAACTA 59.726 52.381 0.00 0.00 45.00 2.24
402 438 2.607187 CCCAGTCAACGCAGTAACTAG 58.393 52.381 0.00 0.00 45.00 2.57
403 439 2.029290 CCCAGTCAACGCAGTAACTAGT 60.029 50.000 0.00 0.00 45.00 2.57
404 440 3.554337 CCCAGTCAACGCAGTAACTAGTT 60.554 47.826 13.68 13.68 45.00 2.24
405 441 4.056050 CCAGTCAACGCAGTAACTAGTTT 58.944 43.478 14.49 0.00 45.00 2.66
406 442 4.510340 CCAGTCAACGCAGTAACTAGTTTT 59.490 41.667 14.49 0.00 45.00 2.43
407 443 5.333111 CCAGTCAACGCAGTAACTAGTTTTC 60.333 44.000 14.49 7.82 45.00 2.29
408 444 5.233476 CAGTCAACGCAGTAACTAGTTTTCA 59.767 40.000 14.49 0.00 45.00 2.69
416 452 4.062991 AGTAACTAGTTTTCACCGCTTGG 58.937 43.478 14.49 0.00 39.35 3.61
495 531 1.469703 CTGAATCCAAATCTGCGCACA 59.530 47.619 5.66 0.00 0.00 4.57
578 622 2.351544 CCGCCTTTCGTACTATAGGAGC 60.352 54.545 7.90 0.00 36.19 4.70
581 625 3.318557 GCCTTTCGTACTATAGGAGCAGT 59.681 47.826 7.90 0.00 0.00 4.40
582 626 4.202131 GCCTTTCGTACTATAGGAGCAGTT 60.202 45.833 7.90 0.00 0.00 3.16
583 627 5.681695 GCCTTTCGTACTATAGGAGCAGTTT 60.682 44.000 7.90 0.00 0.00 2.66
584 628 5.978322 CCTTTCGTACTATAGGAGCAGTTTC 59.022 44.000 4.43 0.00 0.00 2.78
585 629 6.183360 CCTTTCGTACTATAGGAGCAGTTTCT 60.183 42.308 4.43 0.00 0.00 2.52
586 630 6.770746 TTCGTACTATAGGAGCAGTTTCTT 57.229 37.500 4.43 0.00 0.00 2.52
608 652 3.971245 TTCTCTTCTCCTCTTCCTTGC 57.029 47.619 0.00 0.00 0.00 4.01
682 756 1.153469 CGGCTCTTCTTCCTGCTCC 60.153 63.158 0.00 0.00 0.00 4.70
731 805 4.082026 CCTTCCAAATTCCAAGCAGTAAGG 60.082 45.833 0.00 0.00 0.00 2.69
736 810 5.870978 CCAAATTCCAAGCAGTAAGGAAATG 59.129 40.000 0.00 0.00 43.96 2.32
782 856 1.433837 AACAACGAACGCCACAGGAC 61.434 55.000 0.00 0.00 0.00 3.85
802 876 0.537653 GCTGACTCCCCTACCACTTC 59.462 60.000 0.00 0.00 0.00 3.01
803 877 1.897647 GCTGACTCCCCTACCACTTCT 60.898 57.143 0.00 0.00 0.00 2.85
804 878 2.623502 GCTGACTCCCCTACCACTTCTA 60.624 54.545 0.00 0.00 0.00 2.10
828 902 7.454899 ACTACCAGAATCATCTGCTAGTGCG 62.455 48.000 11.22 0.00 46.29 5.34
829 903 2.133553 CAGAATCATCTGCTAGTGCGG 58.866 52.381 0.00 0.00 46.11 5.69
853 933 2.178521 CGACACCGGGAGTCTTCG 59.821 66.667 21.98 10.08 33.89 3.79
922 1022 6.353323 CAAGATATAGCGATCCTCCTCTCTA 58.647 44.000 0.00 0.00 0.00 2.43
924 1024 7.865530 AGATATAGCGATCCTCCTCTCTATA 57.134 40.000 0.00 0.00 32.73 1.31
926 1026 8.890472 AGATATAGCGATCCTCCTCTCTATATT 58.110 37.037 5.53 0.00 36.76 1.28
927 1027 8.862325 ATATAGCGATCCTCCTCTCTATATTG 57.138 38.462 0.00 0.00 34.66 1.90
928 1028 3.699038 AGCGATCCTCCTCTCTATATTGC 59.301 47.826 0.00 0.00 0.00 3.56
929 1029 3.699038 GCGATCCTCCTCTCTATATTGCT 59.301 47.826 0.00 0.00 0.00 3.91
930 1030 4.439974 GCGATCCTCCTCTCTATATTGCTG 60.440 50.000 0.00 0.00 0.00 4.41
954 1056 3.144120 CTGAGGCGAGACCCATCGG 62.144 68.421 0.00 0.00 42.94 4.18
992 1094 2.107953 GACGGGCATCTGAGAGGC 59.892 66.667 11.11 11.11 38.72 4.70
1149 1251 0.967887 CCTCTGCTCCTCCGTCTTCA 60.968 60.000 0.00 0.00 0.00 3.02
1158 1260 1.067495 CCTCCGTCTTCACTGGTTCTC 60.067 57.143 0.00 0.00 0.00 2.87
1176 1278 0.959553 TCGATGGGGATCTCGTAAGC 59.040 55.000 2.51 0.00 36.33 3.09
1209 1311 3.759581 TGTAGGATAGGGACGGATGTAC 58.240 50.000 0.00 0.00 0.00 2.90
1280 1383 3.695060 TGAGTACGAGTCCCTTTCATCTC 59.305 47.826 0.00 0.00 0.00 2.75
1281 1384 3.025262 AGTACGAGTCCCTTTCATCTCC 58.975 50.000 0.00 0.00 0.00 3.71
1284 1387 2.907042 ACGAGTCCCTTTCATCTCCTTT 59.093 45.455 0.00 0.00 0.00 3.11
1285 1388 4.094476 ACGAGTCCCTTTCATCTCCTTTA 58.906 43.478 0.00 0.00 0.00 1.85
1286 1389 4.530946 ACGAGTCCCTTTCATCTCCTTTAA 59.469 41.667 0.00 0.00 0.00 1.52
1290 1393 7.361286 CGAGTCCCTTTCATCTCCTTTAAAAAG 60.361 40.741 0.00 0.00 35.79 2.27
1319 1425 5.335191 CCTCTGTTGTTTACTCATGGAAAGC 60.335 44.000 0.00 0.00 0.00 3.51
1393 1514 5.091261 ACCTTTAGTCCATTAGCAGTCAG 57.909 43.478 0.00 0.00 0.00 3.51
1396 1517 9.942131 GACCTTTAGTCCATTAGCAGTCAGCAT 62.942 44.444 0.00 0.00 42.33 3.79
1439 1590 9.953565 TTACAAGTAATCCTTACTGTTTGCTAT 57.046 29.630 0.57 0.00 45.33 2.97
1475 1626 8.874156 AGCATCATATAATCCTCACTGTTTAGA 58.126 33.333 0.00 0.00 0.00 2.10
1509 1660 3.979911 TGGATGCAGGTGGACAAAATAT 58.020 40.909 0.00 0.00 0.00 1.28
1562 1713 2.760650 GGAGGAAATTTTAGGCACTGGG 59.239 50.000 0.00 0.00 41.52 4.45
1580 1731 1.810151 GGGCAGACGTTTGCTTATGAA 59.190 47.619 27.59 0.00 43.57 2.57
1589 1740 3.058293 CGTTTGCTTATGAAGAACTGCCA 60.058 43.478 0.00 0.00 0.00 4.92
1631 1782 3.452474 ACTGAAGACGATGCTGCTTATC 58.548 45.455 0.00 0.00 0.00 1.75
1673 1824 4.058817 CACCTGACAAGTCTTCTGTTACC 58.941 47.826 1.53 0.00 0.00 2.85
1676 1827 4.263068 CCTGACAAGTCTTCTGTTACCCAT 60.263 45.833 1.53 0.00 0.00 4.00
1698 1849 4.623002 TGACTGTATCCGCGCAAATTATA 58.377 39.130 8.75 0.00 0.00 0.98
1749 1900 2.114616 ACTATCTTGAGGACCAGCAGG 58.885 52.381 0.00 0.00 42.21 4.85
1837 1988 1.515020 CCTCTGGAGGTGAAGCTCG 59.485 63.158 8.39 0.00 43.61 5.03
1861 2012 0.174617 CCTCTTTCTCTGACGGAGCC 59.825 60.000 6.40 0.00 41.60 4.70
1862 2013 0.179150 CTCTTTCTCTGACGGAGCCG 60.179 60.000 7.48 7.48 41.60 5.52
1979 2130 1.486310 TCACCTTCGGATAAGCAGCAT 59.514 47.619 0.00 0.00 0.00 3.79
2006 2157 8.324163 ACTACATAAAATTGGTCTTGACTGTC 57.676 34.615 0.00 0.00 0.00 3.51
2090 2241 3.209410 CAACAAGAGCAAGGTCTCTGTT 58.791 45.455 16.56 16.56 42.25 3.16
2093 2244 0.036022 AGAGCAAGGTCTCTGTTGGC 59.964 55.000 0.00 0.00 41.57 4.52
2121 2272 3.382865 TCGAGATGACCATCCTCTTCTTG 59.617 47.826 6.40 0.00 38.58 3.02
2194 2345 3.665745 ATGTTGGATTGTTCTTGGTGC 57.334 42.857 0.00 0.00 0.00 5.01
2230 2381 1.205657 GCATCAATTTCATGCAGGCG 58.794 50.000 12.44 0.00 45.19 5.52
2354 2505 5.175673 GCTGTTTTAAAACCTCAACTGATGC 59.824 40.000 24.55 11.19 38.11 3.91
2628 2782 1.523758 CTCCAAGACCCAAACTTCGG 58.476 55.000 0.00 0.00 0.00 4.30
3003 3157 5.730550 TGAAGGTAGCTGTTCGTTCATAAT 58.269 37.500 14.62 0.00 34.86 1.28
3033 3187 4.397420 TGTTGATTGGTCATGTAGCTTGT 58.603 39.130 0.00 0.00 33.56 3.16
3142 3296 7.977293 GGAAATGAACTTCCTAGACTACTTCTC 59.023 40.741 0.00 0.00 41.56 2.87
3148 3302 5.188359 ACTTCCTAGACTACTTCTCGAGACT 59.812 44.000 16.36 10.37 35.55 3.24
3168 3322 7.009999 CGAGACTATCTTGAGAATGAAACCAAG 59.990 40.741 0.00 0.00 29.08 3.61
3283 3437 4.979388 CTTTTGCTTACAAGAGGATCAGC 58.021 43.478 0.00 0.00 37.04 4.26
3600 3754 0.111446 TCAAGGGTGCCGATGGAAAA 59.889 50.000 0.00 0.00 0.00 2.29
3639 3793 4.137116 TGTTGTCCAGGAGATTATTCGG 57.863 45.455 0.00 0.00 0.00 4.30
3702 3856 0.246910 GGACTCAACCTTCCGGAGAC 59.753 60.000 3.34 0.00 33.00 3.36
3714 3868 4.396854 GGAGACGATTCGAACGGG 57.603 61.111 13.95 7.50 34.93 5.28
3718 3872 0.450983 AGACGATTCGAACGGGTCTC 59.549 55.000 13.95 9.61 32.86 3.36
3807 3961 3.699038 TGGTTAATGCCAAGAACATAGCC 59.301 43.478 0.00 0.00 35.25 3.93
3810 3964 1.439353 ATGCCAAGAACATAGCCGCG 61.439 55.000 0.00 0.00 0.00 6.46
3852 4006 1.376543 CCAGTGTATTGCAGCTCAGG 58.623 55.000 0.00 0.00 0.00 3.86
3896 4050 3.685139 GTTCCTGAACTCTGACATGGA 57.315 47.619 0.00 0.00 38.25 3.41
3934 4088 2.125512 GATTCCACCGCTCGCTGT 60.126 61.111 0.00 0.00 0.00 4.40
3945 4099 1.000233 GCTCGCTGTCACGTTTCGTA 61.000 55.000 0.00 0.00 38.32 3.43
4043 4197 3.548014 CGGTATTTCCATGGAAACGATGC 60.548 47.826 36.31 24.92 45.34 3.91
4072 4226 2.603560 GACGGATTTAGCCTCTTTGTCG 59.396 50.000 0.00 0.00 0.00 4.35
4182 4336 1.604604 GCAGTTGTAACCCAGCTTCA 58.395 50.000 0.00 0.00 31.42 3.02
4218 4372 2.291741 GGAGAAACAGTTTCCTGCAGTG 59.708 50.000 20.47 6.33 42.81 3.66
4344 4503 5.065218 CCCATTTGCAGAGACATTACTGTAC 59.935 44.000 0.00 0.00 35.14 2.90
4367 4526 5.106197 ACACATACAAATGCCACATACACAG 60.106 40.000 0.00 0.00 36.50 3.66
4372 4531 0.394762 ATGCCACATACACAGGGCTG 60.395 55.000 0.00 0.00 46.53 4.85
4373 4532 1.299648 GCCACATACACAGGGCTGA 59.700 57.895 0.00 0.00 43.09 4.26
4374 4533 0.322456 GCCACATACACAGGGCTGAA 60.322 55.000 0.00 0.00 43.09 3.02
4375 4534 1.453155 CCACATACACAGGGCTGAAC 58.547 55.000 0.00 0.00 0.00 3.18
4376 4535 1.003580 CCACATACACAGGGCTGAACT 59.996 52.381 0.00 0.00 0.00 3.01
4377 4536 2.079158 CACATACACAGGGCTGAACTG 58.921 52.381 0.00 0.00 41.64 3.16
4390 4554 4.380867 GGGCTGAACTGAATACATGTTTGG 60.381 45.833 2.30 0.00 0.00 3.28
4400 4564 6.422333 TGAATACATGTTTGGAGAGGCATTA 58.578 36.000 2.30 0.00 0.00 1.90
4473 4641 4.870221 TCTGATGAAATTCATGCACTCG 57.130 40.909 13.82 1.26 37.20 4.18
4765 4972 6.183360 ACCTGCATGTAAATATTTGTGATGGG 60.183 38.462 11.05 9.22 0.00 4.00
4775 4982 7.901283 AATATTTGTGATGGGATGACATTCA 57.099 32.000 0.00 0.00 0.00 2.57
4880 5087 8.141268 TCCATGATTGTCATTTCATCATGATTG 58.859 33.333 19.96 1.86 46.81 2.67
4975 5182 4.092091 CGGTTTTACTGTTCATCTGAGCTC 59.908 45.833 6.82 6.82 0.00 4.09
4976 5183 4.997395 GGTTTTACTGTTCATCTGAGCTCA 59.003 41.667 17.19 17.19 0.00 4.26
4977 5184 5.645497 GGTTTTACTGTTCATCTGAGCTCAT 59.355 40.000 18.63 0.00 0.00 2.90
4978 5185 6.183360 GGTTTTACTGTTCATCTGAGCTCATC 60.183 42.308 18.63 4.76 0.00 2.92
4979 5186 5.929058 TTACTGTTCATCTGAGCTCATCT 57.071 39.130 18.63 4.47 0.00 2.90
4980 5187 4.126208 ACTGTTCATCTGAGCTCATCTG 57.874 45.455 18.63 16.99 0.00 2.90
4981 5188 3.768215 ACTGTTCATCTGAGCTCATCTGA 59.232 43.478 18.63 18.98 39.84 3.27
4982 5189 4.142116 ACTGTTCATCTGAGCTCATCTGAG 60.142 45.833 18.63 12.83 44.75 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 79 1.675641 CAAGAAAGCCCTGGTCCGG 60.676 63.158 0.00 0.00 0.00 5.14
77 81 0.322906 CTCCAAGAAAGCCCTGGTCC 60.323 60.000 0.00 0.00 0.00 4.46
78 82 0.402121 ACTCCAAGAAAGCCCTGGTC 59.598 55.000 0.00 0.00 0.00 4.02
80 84 0.322906 GGACTCCAAGAAAGCCCTGG 60.323 60.000 0.00 0.00 0.00 4.45
87 100 1.420138 GACCCACTGGACTCCAAGAAA 59.580 52.381 0.00 0.00 30.80 2.52
174 191 4.451150 GATGGACTCCGCCGTGCA 62.451 66.667 0.00 0.00 39.57 4.57
231 262 2.445654 GGGCTGGGGAGGAGAGAG 60.446 72.222 0.00 0.00 0.00 3.20
279 315 2.046892 CTGCCACCGGAGACCAAG 60.047 66.667 9.46 0.00 0.00 3.61
289 325 4.329545 TCGACCCTTGCTGCCACC 62.330 66.667 0.00 0.00 0.00 4.61
293 329 2.435059 GAGGTCGACCCTTGCTGC 60.435 66.667 30.82 8.14 46.51 5.25
304 340 1.298713 CAGATTCCGCTCGAGGTCG 60.299 63.158 15.58 10.04 41.45 4.79
305 341 0.456221 TTCAGATTCCGCTCGAGGTC 59.544 55.000 15.58 0.00 0.00 3.85
306 342 0.457851 CTTCAGATTCCGCTCGAGGT 59.542 55.000 15.58 0.00 0.00 3.85
307 343 0.249238 CCTTCAGATTCCGCTCGAGG 60.249 60.000 15.58 4.19 0.00 4.63
308 344 0.457851 ACCTTCAGATTCCGCTCGAG 59.542 55.000 8.45 8.45 0.00 4.04
309 345 0.456221 GACCTTCAGATTCCGCTCGA 59.544 55.000 0.00 0.00 0.00 4.04
310 346 0.528684 GGACCTTCAGATTCCGCTCG 60.529 60.000 0.00 0.00 0.00 5.03
311 347 0.537188 TGGACCTTCAGATTCCGCTC 59.463 55.000 0.00 0.00 31.38 5.03
312 348 1.139853 GATGGACCTTCAGATTCCGCT 59.860 52.381 2.51 0.00 31.38 5.52
313 349 1.587547 GATGGACCTTCAGATTCCGC 58.412 55.000 2.51 0.00 31.38 5.54
314 350 1.858091 CGATGGACCTTCAGATTCCG 58.142 55.000 8.04 0.00 31.38 4.30
315 351 1.587547 GCGATGGACCTTCAGATTCC 58.412 55.000 8.04 0.00 0.00 3.01
316 352 1.587547 GGCGATGGACCTTCAGATTC 58.412 55.000 8.04 0.00 0.00 2.52
317 353 0.179073 CGGCGATGGACCTTCAGATT 60.179 55.000 0.00 0.00 0.00 2.40
318 354 1.443407 CGGCGATGGACCTTCAGAT 59.557 57.895 0.00 0.00 0.00 2.90
319 355 2.892640 CGGCGATGGACCTTCAGA 59.107 61.111 0.00 0.00 0.00 3.27
320 356 2.892425 GCGGCGATGGACCTTCAG 60.892 66.667 12.98 2.42 0.00 3.02
321 357 4.467084 GGCGGCGATGGACCTTCA 62.467 66.667 12.98 0.00 0.00 3.02
337 373 3.170585 GTCGTTTCTCGCCGTCGG 61.171 66.667 6.99 6.99 39.67 4.79
338 374 3.521220 CGTCGTTTCTCGCCGTCG 61.521 66.667 0.00 0.00 36.18 5.12
339 375 3.170585 CCGTCGTTTCTCGCCGTC 61.171 66.667 0.00 0.00 39.28 4.79
340 376 3.606065 CTCCGTCGTTTCTCGCCGT 62.606 63.158 0.00 0.00 39.28 5.68
341 377 2.791396 TTCTCCGTCGTTTCTCGCCG 62.791 60.000 0.00 0.00 40.61 6.46
342 378 1.071567 CTTCTCCGTCGTTTCTCGCC 61.072 60.000 0.00 0.00 39.67 5.54
343 379 1.071567 CCTTCTCCGTCGTTTCTCGC 61.072 60.000 0.00 0.00 39.67 5.03
344 380 0.240411 ACCTTCTCCGTCGTTTCTCG 59.760 55.000 0.00 0.00 41.41 4.04
345 381 1.402588 GGACCTTCTCCGTCGTTTCTC 60.403 57.143 0.00 0.00 0.00 2.87
346 382 0.602060 GGACCTTCTCCGTCGTTTCT 59.398 55.000 0.00 0.00 0.00 2.52
347 383 0.316204 TGGACCTTCTCCGTCGTTTC 59.684 55.000 0.00 0.00 43.03 2.78
348 384 0.974383 ATGGACCTTCTCCGTCGTTT 59.026 50.000 0.00 0.00 43.03 3.60
349 385 0.974383 AATGGACCTTCTCCGTCGTT 59.026 50.000 0.00 0.00 43.03 3.85
350 386 0.531200 GAATGGACCTTCTCCGTCGT 59.469 55.000 0.00 0.00 43.03 4.34
351 387 0.179108 GGAATGGACCTTCTCCGTCG 60.179 60.000 0.00 0.00 43.03 5.12
352 388 0.902531 TGGAATGGACCTTCTCCGTC 59.097 55.000 0.00 0.00 43.03 4.79
353 389 1.584724 ATGGAATGGACCTTCTCCGT 58.415 50.000 0.00 0.00 43.03 4.69
354 390 2.717639 AATGGAATGGACCTTCTCCG 57.282 50.000 0.00 0.00 43.03 4.63
355 391 4.507512 GGGATAATGGAATGGACCTTCTCC 60.508 50.000 0.00 0.00 39.97 3.71
356 392 4.507512 GGGGATAATGGAATGGACCTTCTC 60.508 50.000 0.00 0.00 0.00 2.87
357 393 3.399305 GGGGATAATGGAATGGACCTTCT 59.601 47.826 0.00 0.00 0.00 2.85
358 394 3.399305 AGGGGATAATGGAATGGACCTTC 59.601 47.826 0.00 0.00 0.00 3.46
359 395 3.399305 GAGGGGATAATGGAATGGACCTT 59.601 47.826 0.00 0.00 0.00 3.50
360 396 2.989571 GAGGGGATAATGGAATGGACCT 59.010 50.000 0.00 0.00 0.00 3.85
361 397 2.041755 GGAGGGGATAATGGAATGGACC 59.958 54.545 0.00 0.00 0.00 4.46
362 398 2.041755 GGGAGGGGATAATGGAATGGAC 59.958 54.545 0.00 0.00 0.00 4.02
363 399 2.358258 GGGAGGGGATAATGGAATGGA 58.642 52.381 0.00 0.00 0.00 3.41
364 400 1.359130 GGGGAGGGGATAATGGAATGG 59.641 57.143 0.00 0.00 0.00 3.16
365 401 2.042162 CTGGGGAGGGGATAATGGAATG 59.958 54.545 0.00 0.00 0.00 2.67
366 402 2.362208 CTGGGGAGGGGATAATGGAAT 58.638 52.381 0.00 0.00 0.00 3.01
367 403 1.012049 ACTGGGGAGGGGATAATGGAA 59.988 52.381 0.00 0.00 0.00 3.53
368 404 0.653397 ACTGGGGAGGGGATAATGGA 59.347 55.000 0.00 0.00 0.00 3.41
369 405 1.068121 GACTGGGGAGGGGATAATGG 58.932 60.000 0.00 0.00 0.00 3.16
370 406 1.819753 TGACTGGGGAGGGGATAATG 58.180 55.000 0.00 0.00 0.00 1.90
371 407 2.136026 GTTGACTGGGGAGGGGATAAT 58.864 52.381 0.00 0.00 0.00 1.28
372 408 1.591768 GTTGACTGGGGAGGGGATAA 58.408 55.000 0.00 0.00 0.00 1.75
373 409 0.689745 CGTTGACTGGGGAGGGGATA 60.690 60.000 0.00 0.00 0.00 2.59
374 410 1.995626 CGTTGACTGGGGAGGGGAT 60.996 63.158 0.00 0.00 0.00 3.85
375 411 2.606519 CGTTGACTGGGGAGGGGA 60.607 66.667 0.00 0.00 0.00 4.81
376 412 4.410400 GCGTTGACTGGGGAGGGG 62.410 72.222 0.00 0.00 0.00 4.79
377 413 3.612247 CTGCGTTGACTGGGGAGGG 62.612 68.421 0.00 0.00 0.00 4.30
378 414 1.541310 TACTGCGTTGACTGGGGAGG 61.541 60.000 0.00 0.00 0.00 4.30
379 415 0.320374 TTACTGCGTTGACTGGGGAG 59.680 55.000 0.00 0.00 0.00 4.30
380 416 0.034337 GTTACTGCGTTGACTGGGGA 59.966 55.000 0.00 0.00 0.00 4.81
381 417 0.034896 AGTTACTGCGTTGACTGGGG 59.965 55.000 0.00 0.00 0.00 4.96
382 418 2.029290 ACTAGTTACTGCGTTGACTGGG 60.029 50.000 0.00 6.12 0.00 4.45
383 419 3.299340 ACTAGTTACTGCGTTGACTGG 57.701 47.619 0.00 0.00 0.00 4.00
384 420 5.233476 TGAAAACTAGTTACTGCGTTGACTG 59.767 40.000 8.92 0.00 0.00 3.51
385 421 5.233689 GTGAAAACTAGTTACTGCGTTGACT 59.766 40.000 8.92 0.00 0.00 3.41
386 422 5.429615 GTGAAAACTAGTTACTGCGTTGAC 58.570 41.667 8.92 0.00 0.00 3.18
387 423 4.508861 GGTGAAAACTAGTTACTGCGTTGA 59.491 41.667 8.92 0.00 0.00 3.18
388 424 4.607557 CGGTGAAAACTAGTTACTGCGTTG 60.608 45.833 8.92 0.00 0.00 4.10
389 425 3.492011 CGGTGAAAACTAGTTACTGCGTT 59.508 43.478 8.92 0.00 0.00 4.84
390 426 3.054878 CGGTGAAAACTAGTTACTGCGT 58.945 45.455 8.92 0.00 0.00 5.24
391 427 2.159881 GCGGTGAAAACTAGTTACTGCG 60.160 50.000 19.82 11.22 34.42 5.18
392 428 3.064931 AGCGGTGAAAACTAGTTACTGC 58.935 45.455 24.22 24.22 42.42 4.40
393 429 4.084013 CCAAGCGGTGAAAACTAGTTACTG 60.084 45.833 8.92 9.78 0.00 2.74
394 430 4.062991 CCAAGCGGTGAAAACTAGTTACT 58.937 43.478 8.92 0.00 0.00 2.24
395 431 3.811497 ACCAAGCGGTGAAAACTAGTTAC 59.189 43.478 8.92 3.41 46.79 2.50
396 432 4.075963 ACCAAGCGGTGAAAACTAGTTA 57.924 40.909 8.92 0.00 46.79 2.24
397 433 2.927028 ACCAAGCGGTGAAAACTAGTT 58.073 42.857 1.12 1.12 46.79 2.24
398 434 2.632987 ACCAAGCGGTGAAAACTAGT 57.367 45.000 0.00 0.00 46.79 2.57
416 452 3.941657 GACTGCTGCCACGGGAGAC 62.942 68.421 9.03 0.68 35.50 3.36
449 485 2.193532 TCGAGCTCGATCCTTTGCT 58.806 52.632 33.84 0.00 44.22 3.91
471 507 3.444742 TGCGCAGATTTGGATTCAGATTT 59.555 39.130 5.66 0.00 0.00 2.17
495 531 4.521062 GCTCGCTCGTGCCCTCAT 62.521 66.667 3.52 0.00 35.36 2.90
578 622 7.041440 GGAAGAGGAGAAGAGAAAAAGAAACTG 60.041 40.741 0.00 0.00 0.00 3.16
581 625 7.142995 AGGAAGAGGAGAAGAGAAAAAGAAA 57.857 36.000 0.00 0.00 0.00 2.52
582 626 6.755542 AGGAAGAGGAGAAGAGAAAAAGAA 57.244 37.500 0.00 0.00 0.00 2.52
583 627 6.529220 CAAGGAAGAGGAGAAGAGAAAAAGA 58.471 40.000 0.00 0.00 0.00 2.52
584 628 5.181056 GCAAGGAAGAGGAGAAGAGAAAAAG 59.819 44.000 0.00 0.00 0.00 2.27
585 629 5.066593 GCAAGGAAGAGGAGAAGAGAAAAA 58.933 41.667 0.00 0.00 0.00 1.94
586 630 4.505742 GGCAAGGAAGAGGAGAAGAGAAAA 60.506 45.833 0.00 0.00 0.00 2.29
608 652 3.206211 GAGAGGATCGAGCGCCTGG 62.206 68.421 2.29 0.00 42.67 4.45
736 810 1.097547 CAAGACGTGGATGGATGCCC 61.098 60.000 0.00 0.00 0.00 5.36
782 856 1.258445 AAGTGGTAGGGGAGTCAGCG 61.258 60.000 0.00 0.00 0.00 5.18
853 933 1.654023 GCCGTTGGTTATGGAGCACC 61.654 60.000 0.00 0.00 35.04 5.01
922 1022 1.476471 GCCTCAGTGGAGCAGCAATAT 60.476 52.381 0.00 0.00 39.96 1.28
924 1024 1.378250 GCCTCAGTGGAGCAGCAAT 60.378 57.895 0.00 0.00 39.96 3.56
926 1026 4.383861 CGCCTCAGTGGAGCAGCA 62.384 66.667 0.00 0.00 39.96 4.41
927 1027 4.074526 TCGCCTCAGTGGAGCAGC 62.075 66.667 6.19 0.00 39.96 5.25
928 1028 2.183811 CTCGCCTCAGTGGAGCAG 59.816 66.667 6.19 0.34 39.96 4.24
929 1029 2.283173 TCTCGCCTCAGTGGAGCA 60.283 61.111 6.19 0.00 39.96 4.26
930 1030 2.183046 GTCTCGCCTCAGTGGAGC 59.817 66.667 0.00 0.00 39.96 4.70
954 1056 2.171003 CTCCCAAAACCCACCATCTTC 58.829 52.381 0.00 0.00 0.00 2.87
1044 1146 4.452733 CTCGAGGGCCCGACCAAC 62.453 72.222 18.44 4.14 42.05 3.77
1056 1158 1.150536 CTCTCCTCCCCCTCTCGAG 59.849 68.421 5.93 5.93 0.00 4.04
1113 1215 1.557371 GAGGTTGAGGAAGAAGAGGGG 59.443 57.143 0.00 0.00 0.00 4.79
1125 1227 1.254284 ACGGAGGAGCAGAGGTTGAG 61.254 60.000 0.00 0.00 0.00 3.02
1128 1230 0.543174 AAGACGGAGGAGCAGAGGTT 60.543 55.000 0.00 0.00 0.00 3.50
1149 1251 1.123928 GATCCCCATCGAGAACCAGT 58.876 55.000 0.00 0.00 0.00 4.00
1158 1260 0.673985 TGCTTACGAGATCCCCATCG 59.326 55.000 0.00 0.94 44.36 3.84
1176 1278 5.835819 TCCCTATCCTACAAGAATGAGAGTG 59.164 44.000 0.00 0.00 0.00 3.51
1209 1311 9.490379 AAAGAAATCCACAACTAACTGTACTAG 57.510 33.333 0.00 0.00 0.00 2.57
1280 1383 5.535030 ACAACAGAGGCCTACTTTTTAAAGG 59.465 40.000 4.42 0.00 40.31 3.11
1281 1384 6.635030 ACAACAGAGGCCTACTTTTTAAAG 57.365 37.500 4.42 0.80 41.73 1.85
1284 1387 7.284820 AGTAAACAACAGAGGCCTACTTTTTA 58.715 34.615 4.42 2.43 0.00 1.52
1285 1388 6.127101 AGTAAACAACAGAGGCCTACTTTTT 58.873 36.000 4.42 3.47 0.00 1.94
1286 1389 5.691896 AGTAAACAACAGAGGCCTACTTTT 58.308 37.500 4.42 1.20 0.00 2.27
1290 1393 4.267349 TGAGTAAACAACAGAGGCCTAC 57.733 45.455 4.42 0.00 0.00 3.18
1352 1458 0.901827 TCCAGAAACAGCCTGCGATA 59.098 50.000 0.00 0.00 0.00 2.92
1356 1462 0.538287 AAGGTCCAGAAACAGCCTGC 60.538 55.000 0.00 0.00 0.00 4.85
1381 1502 9.571810 TTTAATTGTAAATGCTGACTGCTAATG 57.428 29.630 5.87 0.00 43.37 1.90
1475 1626 3.386726 CCTGCATCCATCCATGAAACATT 59.613 43.478 0.00 0.00 0.00 2.71
1509 1660 6.714810 ACTATGTCTTGTAAGCAAATTGACCA 59.285 34.615 0.00 0.00 33.73 4.02
1562 1713 4.083802 AGTTCTTCATAAGCAAACGTCTGC 60.084 41.667 5.51 5.51 42.97 4.26
1580 1731 2.165998 GAAGAATGGCTTGGCAGTTCT 58.834 47.619 2.88 8.85 36.83 3.01
1589 1740 3.243359 TCACCCTTTGAAGAATGGCTT 57.757 42.857 0.00 0.00 40.25 4.35
1631 1782 0.391793 GAAGAAGGGCCAGGAGTTCG 60.392 60.000 6.18 0.00 0.00 3.95
1634 1785 1.151810 TGGAAGAAGGGCCAGGAGT 60.152 57.895 6.18 0.00 0.00 3.85
1673 1824 0.809636 TTGCGCGGATACAGTCATGG 60.810 55.000 8.83 0.00 0.00 3.66
1676 1827 1.732941 AATTTGCGCGGATACAGTCA 58.267 45.000 8.83 0.00 0.00 3.41
1698 1849 0.038599 TGTGACATGCCCAAGCTGAT 59.961 50.000 0.00 0.00 40.80 2.90
1749 1900 4.537936 AGAAGTTTGAACGAAGCAAGAC 57.462 40.909 0.00 0.00 0.00 3.01
1823 1974 0.034896 GAAACCGAGCTTCACCTCCA 59.965 55.000 0.00 0.00 0.00 3.86
1837 1988 2.299297 TCCGTCAGAGAAAGAGGAAACC 59.701 50.000 0.00 0.00 0.00 3.27
1861 2012 0.808755 GTTGGGAGGTGTAAATGGCG 59.191 55.000 0.00 0.00 0.00 5.69
1862 2013 2.092323 GAGTTGGGAGGTGTAAATGGC 58.908 52.381 0.00 0.00 0.00 4.40
1979 2130 9.787435 ACAGTCAAGACCAATTTTATGTAGTTA 57.213 29.630 0.00 0.00 0.00 2.24
2090 2241 2.440247 TCATCTCGAGGCTCGCCA 60.440 61.111 31.01 19.72 40.21 5.69
2093 2244 0.039617 GATGGTCATCTCGAGGCTCG 60.040 60.000 30.10 30.10 42.10 5.03
2121 2272 1.135972 CGTGTTAGCCAACTGCATGTC 60.136 52.381 0.00 0.00 44.83 3.06
2157 2308 3.073274 ACATAGGTTGACAAGAAGGGC 57.927 47.619 0.00 0.00 0.00 5.19
2230 2381 1.772063 GCACGGATATTGGGTGACGC 61.772 60.000 6.07 0.00 33.58 5.19
2239 2390 2.037772 GACTGGAGGATGCACGGATATT 59.962 50.000 0.00 0.00 28.70 1.28
2240 2391 1.620819 GACTGGAGGATGCACGGATAT 59.379 52.381 0.00 0.00 28.70 1.63
2299 2450 3.746949 GACTCATGCTGCCTCCGGG 62.747 68.421 0.00 0.00 0.00 5.73
2354 2505 3.777925 CTTGCGCGGGAGTTGACG 61.778 66.667 8.83 0.00 0.00 4.35
2628 2782 6.272822 AGAACTTTGTTCCAATAGAATGGC 57.727 37.500 6.80 0.00 40.46 4.40
2869 3023 0.617413 CATGCTGAGGTGAAGGGTCT 59.383 55.000 0.00 0.00 0.00 3.85
3003 3157 8.673711 GCTACATGACCAATCAACAATAGTTTA 58.326 33.333 0.00 0.00 38.69 2.01
3044 3198 3.118884 GCAGGAACATGCATCTTTTCCAT 60.119 43.478 23.83 12.31 45.77 3.41
3142 3296 6.333416 TGGTTTCATTCTCAAGATAGTCTCG 58.667 40.000 0.00 0.00 0.00 4.04
3148 3302 8.102676 TCATCACTTGGTTTCATTCTCAAGATA 58.897 33.333 8.62 0.00 38.96 1.98
3168 3322 2.235898 AGTTTCAGCTCCTCCTCATCAC 59.764 50.000 0.00 0.00 0.00 3.06
3283 3437 2.676839 AGATGACATGAAAAGCAGAGCG 59.323 45.455 0.00 0.00 0.00 5.03
3600 3754 6.207691 ACAACAAAGTGAAGCAATGTAGTT 57.792 33.333 0.00 0.00 0.00 2.24
3639 3793 3.562779 TTCGCGGACACCTTCGGAC 62.563 63.158 6.13 0.00 0.00 4.79
3696 3850 1.585521 CCCGTTCGAATCGTCTCCG 60.586 63.158 0.00 0.00 0.00 4.63
3702 3856 0.248539 GGAGAGACCCGTTCGAATCG 60.249 60.000 0.00 7.14 0.00 3.34
3714 3868 1.478510 TCGCCATCTTCTTGGAGAGAC 59.521 52.381 0.00 0.00 40.17 3.36
3718 3872 2.428890 AGTACTCGCCATCTTCTTGGAG 59.571 50.000 0.00 0.00 39.25 3.86
3810 3964 3.002451 CAGACAAAGCATCAGCATCTAGC 59.998 47.826 0.00 0.00 45.49 3.42
3852 4006 0.376852 TTGTGTTCAGCAACTCACGC 59.623 50.000 0.00 0.00 36.08 5.34
3896 4050 8.091449 GGAATCCACTATTCTCATCTATCGTTT 58.909 37.037 0.00 0.00 43.14 3.60
3934 4088 2.729360 CTGCATGTTCTACGAAACGTGA 59.271 45.455 19.19 0.62 45.08 4.35
3945 4099 3.262660 TGGTCTCATTCTCTGCATGTTCT 59.737 43.478 0.00 0.00 0.00 3.01
4043 4197 3.458189 AGGCTAAATCCGTCATCTTTCG 58.542 45.455 0.00 0.00 0.00 3.46
4182 4336 4.105697 TGTTTCTCCTGGGGATTTAACTGT 59.894 41.667 10.19 0.00 0.00 3.55
4218 4372 5.519566 CGAGCTATCTAAATGATCATCCAGC 59.480 44.000 9.06 10.92 36.65 4.85
4344 4503 5.307926 TGTGTATGTGGCATTTGTATGTG 57.692 39.130 0.00 0.00 34.12 3.21
4367 4526 4.380867 CCAAACATGTATTCAGTTCAGCCC 60.381 45.833 0.00 0.00 0.00 5.19
4372 4531 5.163713 GCCTCTCCAAACATGTATTCAGTTC 60.164 44.000 0.00 0.00 0.00 3.01
4373 4532 4.702131 GCCTCTCCAAACATGTATTCAGTT 59.298 41.667 0.00 0.00 0.00 3.16
4374 4533 4.263462 TGCCTCTCCAAACATGTATTCAGT 60.263 41.667 0.00 0.00 0.00 3.41
4375 4534 4.264253 TGCCTCTCCAAACATGTATTCAG 58.736 43.478 0.00 0.00 0.00 3.02
4376 4535 4.299586 TGCCTCTCCAAACATGTATTCA 57.700 40.909 0.00 0.00 0.00 2.57
4377 4536 5.841957 AATGCCTCTCCAAACATGTATTC 57.158 39.130 0.00 0.00 0.00 1.75
4390 4554 5.064452 GCATGCATATACAGTAATGCCTCTC 59.936 44.000 14.21 7.37 46.34 3.20
4400 4564 4.756642 GTGTATGTGGCATGCATATACAGT 59.243 41.667 27.08 15.76 39.29 3.55
4473 4641 7.291567 CAAGAACGGATCTCAAGTTAGAAAAC 58.708 38.462 0.00 0.00 37.42 2.43
4719 4925 6.426633 CAGGTAAACACACATTGATGTCTGTA 59.573 38.462 5.62 0.00 38.65 2.74
4765 4972 9.859427 TTAATCCAAACTTTCATGAATGTCATC 57.141 29.630 22.89 0.00 34.28 2.92
4797 5004 2.482721 TCCTTTTTGGAGCGTCGATTTC 59.517 45.455 0.00 0.00 40.56 2.17
4861 5068 7.441458 TGCAAAACAATCATGATGAAATGACAA 59.559 29.630 9.46 0.00 39.32 3.18
4880 5087 2.548875 TGTTTCACCTGCATGCAAAAC 58.451 42.857 27.34 27.34 0.00 2.43
4938 5145 8.623310 ACAGTAAAACCGTGTGAAATAAAAAG 57.377 30.769 0.00 0.00 0.00 2.27
4939 5146 8.983307 AACAGTAAAACCGTGTGAAATAAAAA 57.017 26.923 0.00 0.00 0.00 1.94
5009 5216 7.218228 TGAGTACCGAAATAGTGACAACTTA 57.782 36.000 0.00 0.00 37.88 2.24
5025 5232 4.750098 GTCCATGGTGAATTATGAGTACCG 59.250 45.833 12.58 0.00 34.16 4.02


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

AutoCloner maintained by Alex Coulton.