Multiple sequence alignment - TraesCS1A01G218200

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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 TraesCS1A01G218200 chr1A 100.000 5649 0 0 1 5649 386719119 386724767 0.000000e+00 10432.0
1 TraesCS1A01G218200 chr1D 93.347 4840 176 63 669 5428 307459562 307464335 0.000000e+00 7020.0
2 TraesCS1A01G218200 chr1D 85.500 600 61 15 1 599 307458848 307459422 2.250000e-168 603.0
3 TraesCS1A01G218200 chr1D 94.949 99 5 0 5550 5648 307464815 307464913 7.580000e-34 156.0
4 TraesCS1A01G218200 chr1D 96.970 66 1 1 592 656 307459451 307459516 5.980000e-20 110.0
5 TraesCS1A01G218200 chr1B 93.191 4641 192 49 933 5497 416125759 416130351 0.000000e+00 6706.0
6 TraesCS1A01G218200 chr1B 84.674 659 83 11 1 656 416124844 416125487 4.770000e-180 641.0
7 TraesCS1A01G218200 chr1B 91.630 227 8 3 669 889 416125533 416125754 2.560000e-78 303.0
8 TraesCS1A01G218200 chr1B 87.013 154 8 9 5496 5648 416130389 416130531 4.530000e-36 163.0
9 TraesCS1A01G218200 chr1B 75.986 279 51 12 257 528 489267150 489267419 4.590000e-26 130.0
10 TraesCS1A01G218200 chr1B 94.444 36 2 0 487 522 678064180 678064215 7.910000e-04 56.5
11 TraesCS1A01G218200 chr6B 84.203 671 46 25 4782 5420 529654228 529654870 1.050000e-166 597.0
12 TraesCS1A01G218200 chr2A 74.733 281 54 11 260 535 159074239 159073971 5.980000e-20 110.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G218200 chr1A 386719119 386724767 5648 False 10432.00 10432 100.0000 1 5649 1 chr1A.!!$F1 5648
1 TraesCS1A01G218200 chr1D 307458848 307464913 6065 False 1972.25 7020 92.6915 1 5648 4 chr1D.!!$F1 5647
2 TraesCS1A01G218200 chr1B 416124844 416130531 5687 False 1953.25 6706 89.1270 1 5648 4 chr1B.!!$F3 5647
3 TraesCS1A01G218200 chr6B 529654228 529654870 642 False 597.00 597 84.2030 4782 5420 1 chr6B.!!$F1 638

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
426 428 0.037590 TTGACCGGGTTCAATCAGGG 59.962 55.0 6.32 0.0 30.29 4.45 F
715 789 0.105408 TATACGGAAAAGAGGCCCGC 59.895 55.0 0.00 0.0 46.54 6.13 F
947 1027 0.257616 AAGACGGAGAGAGAGGGAGG 59.742 60.0 0.00 0.0 0.00 4.30 F
1662 1761 0.319641 ACGACCGCCTCAAAGAAGAC 60.320 55.0 0.00 0.0 0.00 3.01 F
2122 2221 1.732941 TCGCCATTACACGAATTGCT 58.267 45.0 0.00 0.0 34.69 3.91 F
3326 3441 1.353076 GCATTGCCTTTTGCTGCTAC 58.647 50.0 0.00 0.0 37.95 3.58 F
4108 4227 0.035439 AAGTGGACAGCATTACCCCG 60.035 55.0 0.00 0.0 0.00 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1649 1748 1.341606 CTCGTCGTCTTCTTTGAGGC 58.658 55.000 0.0 0.0 0.00 4.70 R
1686 1785 1.378124 CCGTCTCCTCCTCGTCTTCC 61.378 65.000 0.0 0.0 0.00 3.46 R
2656 2766 1.462616 TGATGGCCGAAAACATCAGG 58.537 50.000 0.0 0.0 46.05 3.86 R
2807 2917 1.929836 GCTCTCTTCATGGTGTAAGCG 59.070 52.381 0.0 0.0 36.92 4.68 R
3667 3786 1.667830 TAGTGGCAGCTTGTGACGC 60.668 57.895 0.0 0.0 46.23 5.19 R
4522 4641 0.037326 TGTTGAGCGTCATGGACCTC 60.037 55.000 0.0 0.0 33.59 3.85 R
5330 5538 0.035915 GGAGCCCCAGAAGTCAAGAC 60.036 60.000 0.0 0.0 0.00 3.01 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
93 94 1.053424 TCCGTTTAGGGCTTGTGTCT 58.947 50.000 0.00 0.00 41.52 3.41
132 133 1.070758 GATGGCGGCTTCCTGAAGATA 59.929 52.381 11.43 0.00 40.79 1.98
186 187 2.165641 ACGGTTCGTCTAGCATCATCAA 59.834 45.455 0.00 0.00 33.69 2.57
197 198 1.792993 GCATCATCAAAGAGCGTGTGC 60.793 52.381 0.00 0.00 43.24 4.57
200 201 1.150827 CATCAAAGAGCGTGTGCAGA 58.849 50.000 0.00 0.00 46.23 4.26
209 210 0.588252 GCGTGTGCAGATGTGTCTTT 59.412 50.000 4.83 0.00 42.15 2.52
224 225 0.606096 TCTTTGGCGGATCTCGTGAA 59.394 50.000 5.66 0.00 41.72 3.18
246 247 2.459060 TCGGTTGGCGTTTATCTTCA 57.541 45.000 0.00 0.00 0.00 3.02
272 273 5.221441 TGGATACACTTGGATATGGTCTTCG 60.221 44.000 0.00 0.00 46.17 3.79
278 279 3.159353 TGGATATGGTCTTCGTTCGTG 57.841 47.619 0.00 0.00 0.00 4.35
284 285 0.661187 GGTCTTCGTTCGTGTGCGTA 60.661 55.000 0.00 0.00 39.49 4.42
285 286 0.701303 GTCTTCGTTCGTGTGCGTAG 59.299 55.000 0.00 0.00 39.49 3.51
290 291 1.210545 CGTTCGTGTGCGTAGGTGTT 61.211 55.000 0.00 0.00 39.49 3.32
291 292 0.932399 GTTCGTGTGCGTAGGTGTTT 59.068 50.000 0.00 0.00 39.49 2.83
357 359 3.541632 AGGTTGTTGTTCTGGTGTACTG 58.458 45.455 0.00 0.00 0.00 2.74
383 385 4.792068 TGGGACCTTACCATGATGATTTC 58.208 43.478 0.00 0.00 31.83 2.17
391 393 4.743057 ACCATGATGATTTCTCGACTGA 57.257 40.909 0.00 0.00 0.00 3.41
410 412 6.229936 ACTGACTACTACAACAAGGTTTGA 57.770 37.500 0.00 0.00 0.00 2.69
415 417 1.877443 CTACAACAAGGTTTGACCGGG 59.123 52.381 6.32 0.00 44.90 5.73
419 421 0.256464 ACAAGGTTTGACCGGGTTCA 59.744 50.000 6.32 0.00 44.90 3.18
422 424 1.905637 AGGTTTGACCGGGTTCAATC 58.094 50.000 6.32 6.86 44.90 2.67
426 428 0.037590 TTGACCGGGTTCAATCAGGG 59.962 55.000 6.32 0.00 30.29 4.45
427 429 1.077716 GACCGGGTTCAATCAGGGG 60.078 63.158 6.32 0.00 0.00 4.79
428 430 2.275418 CCGGGTTCAATCAGGGGG 59.725 66.667 0.00 0.00 0.00 5.40
429 431 2.612493 CCGGGTTCAATCAGGGGGT 61.612 63.158 0.00 0.00 0.00 4.95
430 432 1.378514 CGGGTTCAATCAGGGGGTG 60.379 63.158 0.00 0.00 0.00 4.61
431 433 1.000359 GGGTTCAATCAGGGGGTGG 60.000 63.158 0.00 0.00 0.00 4.61
432 434 1.000359 GGTTCAATCAGGGGGTGGG 60.000 63.158 0.00 0.00 0.00 4.61
433 435 1.000359 GTTCAATCAGGGGGTGGGG 60.000 63.158 0.00 0.00 0.00 4.96
434 436 2.245379 TTCAATCAGGGGGTGGGGG 61.245 63.158 0.00 0.00 0.00 5.40
435 437 2.616893 CAATCAGGGGGTGGGGGA 60.617 66.667 0.00 0.00 0.00 4.81
490 492 8.554528 ACTCGATCTAGTAAATTTAATCGTCGA 58.445 33.333 20.92 20.10 37.74 4.20
504 506 1.136891 TCGTCGATAGGTGGTCTACGA 59.863 52.381 0.00 0.00 40.14 3.43
506 508 2.547211 CGTCGATAGGTGGTCTACGAAT 59.453 50.000 0.00 0.00 37.06 3.34
513 515 4.180377 AGGTGGTCTACGAATCTGGATA 57.820 45.455 0.00 0.00 0.00 2.59
517 519 6.434652 AGGTGGTCTACGAATCTGGATATAAG 59.565 42.308 0.00 0.00 0.00 1.73
623 664 4.931002 AGAAATGACATGGAAATTTTGGCG 59.069 37.500 0.00 0.00 0.00 5.69
715 789 0.105408 TATACGGAAAAGAGGCCCGC 59.895 55.000 0.00 0.00 46.54 6.13
738 818 9.548208 CCGCTAAAGAAGAAGAAGAAAATAAAG 57.452 33.333 0.00 0.00 0.00 1.85
762 842 3.824414 AGGAGCAACGGAAATTAAACG 57.176 42.857 0.00 0.00 0.00 3.60
811 891 3.626924 ACGCACCCACCTCACTCC 61.627 66.667 0.00 0.00 0.00 3.85
814 894 2.203998 CACCCACCTCACTCCCCT 60.204 66.667 0.00 0.00 0.00 4.79
897 977 1.912731 AGGAAGAGGAAGAAGAAGCCC 59.087 52.381 0.00 0.00 0.00 5.19
898 978 1.630878 GGAAGAGGAAGAAGAAGCCCA 59.369 52.381 0.00 0.00 0.00 5.36
899 979 2.040412 GGAAGAGGAAGAAGAAGCCCAA 59.960 50.000 0.00 0.00 0.00 4.12
900 980 3.342719 GAAGAGGAAGAAGAAGCCCAAG 58.657 50.000 0.00 0.00 0.00 3.61
943 1023 2.399856 CGGAAGACGGAGAGAGAGG 58.600 63.158 0.00 0.00 39.42 3.69
947 1027 0.257616 AAGACGGAGAGAGAGGGAGG 59.742 60.000 0.00 0.00 0.00 4.30
949 1029 2.197324 CGGAGAGAGAGGGAGGGG 59.803 72.222 0.00 0.00 0.00 4.79
950 1030 2.387772 CGGAGAGAGAGGGAGGGGA 61.388 68.421 0.00 0.00 0.00 4.81
951 1031 1.541672 GGAGAGAGAGGGAGGGGAG 59.458 68.421 0.00 0.00 0.00 4.30
1662 1761 0.319641 ACGACCGCCTCAAAGAAGAC 60.320 55.000 0.00 0.00 0.00 3.01
2122 2221 1.732941 TCGCCATTACACGAATTGCT 58.267 45.000 0.00 0.00 34.69 3.91
2161 2261 7.440523 TCTCTCAAGTGCTTTAGGATTTTTC 57.559 36.000 0.00 0.00 0.00 2.29
2176 2276 9.691362 TTAGGATTTTTCTAACAAAGATGCAAC 57.309 29.630 0.00 0.00 33.05 4.17
2226 2326 5.521372 GCTTTAGCATTTTGGCTTAATCTGG 59.479 40.000 0.00 0.00 42.71 3.86
2515 2615 2.991190 GAGTGCATTGCTCAAATTGGTG 59.009 45.455 10.49 0.00 33.45 4.17
2521 2621 2.798976 TGCTCAAATTGGTGTTGCTC 57.201 45.000 0.00 0.00 0.00 4.26
2574 2683 5.748630 TGCTATGACTGTTAGTTATGCTTCG 59.251 40.000 0.00 0.00 0.00 3.79
2648 2758 2.029649 TGACCCAACTACGTTGCTAGAC 60.030 50.000 0.00 0.00 41.62 2.59
2656 2766 6.359087 CCAACTACGTTGCTAGACGATATTAC 59.641 42.308 10.62 0.00 45.47 1.89
2670 2780 4.510340 ACGATATTACCTGATGTTTTCGGC 59.490 41.667 0.00 0.00 0.00 5.54
2698 2808 4.881920 ACAAATTCCAAATTCTTCCACCG 58.118 39.130 0.00 0.00 0.00 4.94
2769 2879 4.300803 AGTTGTGCGTCGTCTGTATTTAA 58.699 39.130 0.00 0.00 0.00 1.52
2770 2880 4.927425 AGTTGTGCGTCGTCTGTATTTAAT 59.073 37.500 0.00 0.00 0.00 1.40
2771 2881 6.094719 AGTTGTGCGTCGTCTGTATTTAATA 58.905 36.000 0.00 0.00 0.00 0.98
2791 2901 3.541242 AACCCATGGTCAAGGATGAAA 57.459 42.857 11.73 0.00 37.30 2.69
2801 2911 5.415701 TGGTCAAGGATGAAATGAAACTAGC 59.584 40.000 0.00 0.00 37.30 3.42
2802 2912 5.649831 GGTCAAGGATGAAATGAAACTAGCT 59.350 40.000 0.00 0.00 37.30 3.32
2803 2913 6.823689 GGTCAAGGATGAAATGAAACTAGCTA 59.176 38.462 0.00 0.00 37.30 3.32
2804 2914 7.336931 GGTCAAGGATGAAATGAAACTAGCTAA 59.663 37.037 0.00 0.00 37.30 3.09
2805 2915 8.730680 GTCAAGGATGAAATGAAACTAGCTAAA 58.269 33.333 0.00 0.00 37.30 1.85
2806 2916 9.295825 TCAAGGATGAAATGAAACTAGCTAAAA 57.704 29.630 0.00 0.00 30.99 1.52
2807 2917 9.346725 CAAGGATGAAATGAAACTAGCTAAAAC 57.653 33.333 0.00 0.00 0.00 2.43
2808 2918 7.752695 AGGATGAAATGAAACTAGCTAAAACG 58.247 34.615 0.00 0.00 0.00 3.60
2809 2919 6.469275 GGATGAAATGAAACTAGCTAAAACGC 59.531 38.462 0.00 0.00 0.00 4.84
2810 2920 6.554334 TGAAATGAAACTAGCTAAAACGCT 57.446 33.333 0.00 0.00 43.83 5.07
2811 2921 6.966021 TGAAATGAAACTAGCTAAAACGCTT 58.034 32.000 0.00 0.00 41.30 4.68
2812 2922 8.090250 TGAAATGAAACTAGCTAAAACGCTTA 57.910 30.769 0.00 0.00 41.30 3.09
2844 2954 4.610945 GAGAGCTCTATCTCTTTGTGCTC 58.389 47.826 18.25 0.00 43.05 4.26
2872 2982 7.056635 AGGATTCTGGTAGGTACAAATGAATG 58.943 38.462 0.00 0.00 0.00 2.67
2970 3085 7.169982 GGTGTCTTGATACAATGTATAGCAGTC 59.830 40.741 5.81 2.09 0.00 3.51
3297 3412 3.130280 TGCTGAGCATGAGAAAGTTCA 57.870 42.857 1.40 0.00 31.71 3.18
3326 3441 1.353076 GCATTGCCTTTTGCTGCTAC 58.647 50.000 0.00 0.00 37.95 3.58
3327 3442 2.000429 CATTGCCTTTTGCTGCTACC 58.000 50.000 0.00 0.00 42.00 3.18
3353 3468 7.431084 CGAAACCACTACAACATTTATATTGGC 59.569 37.037 0.00 0.00 0.00 4.52
3368 3483 9.826574 ATTTATATTGGCTAAGTTTAGTGACGA 57.173 29.630 0.00 0.00 33.32 4.20
3381 3496 6.423001 AGTTTAGTGACGACAAATAGTGTTCC 59.577 38.462 0.00 0.00 41.96 3.62
3420 3535 7.340487 AGTTTGGGATAGAATGTGATTCCTTTC 59.660 37.037 0.00 0.00 40.13 2.62
3443 3558 4.228912 AGTTATTGCACTGCACTTGTTC 57.771 40.909 2.26 0.00 38.71 3.18
3445 3560 2.787601 ATTGCACTGCACTTGTTCTG 57.212 45.000 2.26 0.00 38.71 3.02
3537 3656 2.479566 TTGAACTTCTGCAGGCTAGG 57.520 50.000 15.13 0.00 0.00 3.02
3544 3663 2.039462 TGCAGGCTAGGGAGAGCA 59.961 61.111 0.00 0.00 44.76 4.26
3667 3786 1.726248 TGCAATCACTGATCGTTGTCG 59.274 47.619 0.00 0.00 38.55 4.35
3871 3990 1.297689 GCTGAGCATGTGGAGGTCA 59.702 57.895 0.00 0.00 40.79 4.02
3910 4029 4.742417 AGACACAGAATGAGATCGTTCAG 58.258 43.478 15.30 10.57 42.71 3.02
3970 4089 1.079750 GTCCGACCTTCACAGGCTC 60.080 63.158 0.00 0.00 45.56 4.70
4078 4197 0.393402 TGTATGGCTGGCTGAAGCTG 60.393 55.000 2.00 0.00 43.06 4.24
4108 4227 0.035439 AAGTGGACAGCATTACCCCG 60.035 55.000 0.00 0.00 0.00 5.73
4175 4294 2.029844 GACGAGTGGAAGCAGGCAC 61.030 63.158 0.00 0.00 0.00 5.01
4375 4494 0.100146 CGTACTCGTTGGTAGGCCTC 59.900 60.000 9.68 0.00 35.27 4.70
4522 4641 1.669115 CAAGGCTGTGGAGGTGACG 60.669 63.158 0.00 0.00 0.00 4.35
4534 4653 1.153823 GGTGACGAGGTCCATGACG 60.154 63.158 0.00 0.00 32.65 4.35
4537 4656 1.226717 GACGAGGTCCATGACGCTC 60.227 63.158 0.00 0.07 32.65 5.03
4558 4677 0.773644 ACAACATCCAGACTGGCCTT 59.226 50.000 17.33 4.59 37.47 4.35
4660 4787 0.613572 TGCGGTAGGATGTCAGACCA 60.614 55.000 0.00 0.00 31.89 4.02
4692 4819 4.963318 TCATTTTGGTGTGTCTCTCTCT 57.037 40.909 0.00 0.00 0.00 3.10
4693 4820 4.635223 TCATTTTGGTGTGTCTCTCTCTG 58.365 43.478 0.00 0.00 0.00 3.35
4694 4821 3.475566 TTTTGGTGTGTCTCTCTCTGG 57.524 47.619 0.00 0.00 0.00 3.86
4695 4822 0.681733 TTGGTGTGTCTCTCTCTGGC 59.318 55.000 0.00 0.00 0.00 4.85
4777 4920 1.557832 CTTAGGGATGAAACGTGGGGA 59.442 52.381 0.00 0.00 0.00 4.81
4778 4921 1.200519 TAGGGATGAAACGTGGGGAG 58.799 55.000 0.00 0.00 0.00 4.30
4779 4922 0.546747 AGGGATGAAACGTGGGGAGA 60.547 55.000 0.00 0.00 0.00 3.71
4780 4923 0.326927 GGGATGAAACGTGGGGAGAA 59.673 55.000 0.00 0.00 0.00 2.87
4813 4956 3.289128 GGCTGGTTTTGCCTTGTTC 57.711 52.632 0.00 0.00 46.38 3.18
4814 4957 0.597377 GGCTGGTTTTGCCTTGTTCG 60.597 55.000 0.00 0.00 46.38 3.95
4825 4968 1.904287 CCTTGTTCGTTGGGGATTGA 58.096 50.000 0.00 0.00 0.00 2.57
4826 4969 2.446435 CCTTGTTCGTTGGGGATTGAT 58.554 47.619 0.00 0.00 0.00 2.57
4866 5010 0.323269 TGATTTTGCCCAGGATCGCA 60.323 50.000 0.00 0.00 0.00 5.10
4875 5019 0.319727 CCAGGATCGCAGCTCATCTC 60.320 60.000 0.00 0.00 0.00 2.75
4996 5151 1.351017 TCCCCTCTCGCAAACTTGAAT 59.649 47.619 0.00 0.00 0.00 2.57
5012 5167 7.934855 AACTTGAATTCTATGCTCATGTCTT 57.065 32.000 7.05 0.00 29.90 3.01
5013 5168 7.551035 ACTTGAATTCTATGCTCATGTCTTC 57.449 36.000 7.05 0.00 0.00 2.87
5027 5208 4.952957 TCATGTCTTCAGCTAAGCTCTACT 59.047 41.667 0.00 0.00 36.40 2.57
5033 5214 6.018180 GTCTTCAGCTAAGCTCTACTCTCTAC 60.018 46.154 0.00 0.00 36.40 2.59
5053 5241 2.945668 ACTGTTTGAAGTGGTTCAGAGC 59.054 45.455 0.00 0.00 43.66 4.09
5059 5247 1.265365 GAAGTGGTTCAGAGCTGTTGC 59.735 52.381 0.00 0.00 34.36 4.17
5060 5248 0.536006 AGTGGTTCAGAGCTGTTGCC 60.536 55.000 0.00 0.00 40.80 4.52
5061 5249 0.536006 GTGGTTCAGAGCTGTTGCCT 60.536 55.000 0.00 0.00 40.80 4.75
5062 5250 0.535780 TGGTTCAGAGCTGTTGCCTG 60.536 55.000 0.00 0.00 40.80 4.85
5063 5251 0.536006 GGTTCAGAGCTGTTGCCTGT 60.536 55.000 0.00 0.00 40.80 4.00
5064 5252 1.312815 GTTCAGAGCTGTTGCCTGTT 58.687 50.000 0.00 0.00 40.80 3.16
5065 5253 1.002033 GTTCAGAGCTGTTGCCTGTTG 60.002 52.381 0.00 0.00 40.80 3.33
5066 5254 0.535780 TCAGAGCTGTTGCCTGTTGG 60.536 55.000 0.00 0.00 40.80 3.77
5119 5316 0.388520 GATGCTGTGTTTTTCCCGGC 60.389 55.000 0.00 0.00 0.00 6.13
5184 5382 1.142748 CCTGGATGCAGGACGTCTC 59.857 63.158 28.19 4.26 45.00 3.36
5234 5439 1.680555 CCACCGCAGTTAATTGCCCTA 60.681 52.381 16.34 0.00 41.01 3.53
5315 5523 1.091771 CCATACGCTCTGTGCAAGGG 61.092 60.000 2.42 0.00 43.06 3.95
5324 5532 2.234661 CTCTGTGCAAGGGATACTGTCA 59.765 50.000 0.00 0.00 0.00 3.58
5333 5541 4.054359 AGGGATACTGTCACTTGAGTCT 57.946 45.455 0.00 0.00 37.24 3.24
5335 5543 4.221703 AGGGATACTGTCACTTGAGTCTTG 59.778 45.833 0.00 0.00 37.24 3.02
5336 5544 4.220821 GGGATACTGTCACTTGAGTCTTGA 59.779 45.833 0.00 0.00 0.00 3.02
5337 5545 5.164954 GGATACTGTCACTTGAGTCTTGAC 58.835 45.833 11.17 11.17 40.14 3.18
5338 5546 5.047660 GGATACTGTCACTTGAGTCTTGACT 60.048 44.000 16.24 2.59 40.34 3.41
5339 5547 4.744795 ACTGTCACTTGAGTCTTGACTT 57.255 40.909 16.24 5.78 40.34 3.01
5340 5548 4.688021 ACTGTCACTTGAGTCTTGACTTC 58.312 43.478 16.24 0.09 40.34 3.01
5341 5549 4.404073 ACTGTCACTTGAGTCTTGACTTCT 59.596 41.667 16.24 2.53 40.34 2.85
5342 5550 4.686972 TGTCACTTGAGTCTTGACTTCTG 58.313 43.478 16.24 1.56 40.34 3.02
5350 5558 0.178891 TCTTGACTTCTGGGGCTCCT 60.179 55.000 3.07 0.00 0.00 3.69
5354 5562 1.116308 GACTTCTGGGGCTCCTAGTC 58.884 60.000 3.07 10.68 33.29 2.59
5382 5590 3.641986 GCGACGCACCGTTTGGAA 61.642 61.111 16.42 0.00 41.37 3.53
5383 5591 2.247267 CGACGCACCGTTTGGAAC 59.753 61.111 0.00 0.00 41.37 3.62
5405 5617 5.721232 ACTTCCGACAACAGGAACTAATAG 58.279 41.667 0.00 0.00 42.33 1.73
5423 5635 0.748729 AGGCCGTTTCACCGTGAAAA 60.749 50.000 24.74 9.49 46.53 2.29
5432 5655 2.302260 TCACCGTGAAAATTCCAAGCA 58.698 42.857 0.00 0.00 0.00 3.91
5437 5660 4.082787 ACCGTGAAAATTCCAAGCATGTAG 60.083 41.667 0.00 0.00 0.00 2.74
5439 5662 4.853196 CGTGAAAATTCCAAGCATGTAGTG 59.147 41.667 0.00 0.00 0.00 2.74
5440 5663 5.163513 GTGAAAATTCCAAGCATGTAGTGG 58.836 41.667 0.00 0.00 0.00 4.00
5441 5664 4.220382 TGAAAATTCCAAGCATGTAGTGGG 59.780 41.667 10.39 0.00 32.95 4.61
5450 6024 5.012046 CCAAGCATGTAGTGGGAGTATGATA 59.988 44.000 0.00 0.00 0.00 2.15
5457 6031 4.166246 AGTGGGAGTATGATACTGACGA 57.834 45.455 10.29 0.00 39.59 4.20
5473 6047 2.483877 TGACGATTTCACCATGAAGCAC 59.516 45.455 0.00 0.00 37.70 4.40
5518 6131 2.125552 CGGCCTGCGATTCTGTGA 60.126 61.111 0.00 0.00 0.00 3.58
5526 6139 1.086634 GCGATTCTGTGAGTGGGAGC 61.087 60.000 0.00 0.00 0.00 4.70
5531 6144 0.827925 TCTGTGAGTGGGAGCGAAGT 60.828 55.000 0.00 0.00 0.00 3.01
5532 6145 0.668706 CTGTGAGTGGGAGCGAAGTG 60.669 60.000 0.00 0.00 0.00 3.16
5534 6147 1.533033 TGAGTGGGAGCGAAGTGGA 60.533 57.895 0.00 0.00 0.00 4.02
5535 6148 1.216710 GAGTGGGAGCGAAGTGGAG 59.783 63.158 0.00 0.00 0.00 3.86
5536 6149 1.534235 AGTGGGAGCGAAGTGGAGT 60.534 57.895 0.00 0.00 0.00 3.85
5537 6150 1.374758 GTGGGAGCGAAGTGGAGTG 60.375 63.158 0.00 0.00 0.00 3.51
5538 6151 1.837051 TGGGAGCGAAGTGGAGTGT 60.837 57.895 0.00 0.00 0.00 3.55
5539 6152 1.374758 GGGAGCGAAGTGGAGTGTG 60.375 63.158 0.00 0.00 0.00 3.82
5540 6153 1.374758 GGAGCGAAGTGGAGTGTGG 60.375 63.158 0.00 0.00 0.00 4.17
5541 6154 1.367840 GAGCGAAGTGGAGTGTGGT 59.632 57.895 0.00 0.00 0.00 4.16
5542 6155 0.946221 GAGCGAAGTGGAGTGTGGTG 60.946 60.000 0.00 0.00 0.00 4.17
5543 6156 1.227556 GCGAAGTGGAGTGTGGTGT 60.228 57.895 0.00 0.00 0.00 4.16
5544 6157 0.032952 GCGAAGTGGAGTGTGGTGTA 59.967 55.000 0.00 0.00 0.00 2.90
5545 6158 1.935300 GCGAAGTGGAGTGTGGTGTAG 60.935 57.143 0.00 0.00 0.00 2.74
5612 6226 2.040544 CACGGCAAGGCTACAAGGG 61.041 63.158 0.00 0.00 0.00 3.95
5630 6244 3.098958 CGCACGTTGGCATGCAAC 61.099 61.111 21.36 19.09 42.17 4.17
5648 6262 0.033366 ACGCAATGCAACCTTTTCCC 59.967 50.000 5.91 0.00 0.00 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 4.039245 TCACCTTCCTCAGTTAGACACAAG 59.961 45.833 0.00 0.00 0.00 3.16
93 94 3.254093 TCACCTCACCTTCCTCAGTTA 57.746 47.619 0.00 0.00 0.00 2.24
132 133 0.392336 GGCGAGGAGAGCATCATTCT 59.608 55.000 0.00 0.00 37.82 2.40
186 187 0.250038 ACACATCTGCACACGCTCTT 60.250 50.000 0.00 0.00 39.64 2.85
197 198 1.667724 GATCCGCCAAAGACACATCTG 59.332 52.381 0.00 0.00 34.48 2.90
200 201 1.740380 CGAGATCCGCCAAAGACACAT 60.740 52.381 0.00 0.00 0.00 3.21
209 210 1.651987 GAATTTCACGAGATCCGCCA 58.348 50.000 0.00 0.00 43.32 5.69
224 225 3.754323 TGAAGATAAACGCCAACCGAATT 59.246 39.130 0.00 0.00 41.02 2.17
246 247 6.770286 AGACCATATCCAAGTGTATCCATT 57.230 37.500 0.00 0.00 0.00 3.16
255 256 3.194968 ACGAACGAAGACCATATCCAAGT 59.805 43.478 0.14 0.00 0.00 3.16
263 264 1.282248 CGCACACGAACGAAGACCAT 61.282 55.000 0.14 0.00 43.93 3.55
272 273 0.932399 AAACACCTACGCACACGAAC 59.068 50.000 0.00 0.00 43.93 3.95
290 291 3.037549 ACAAGGATCCAACCTGCAAAAA 58.962 40.909 15.82 0.00 40.49 1.94
291 292 2.364970 CACAAGGATCCAACCTGCAAAA 59.635 45.455 15.82 0.00 40.49 2.44
324 326 2.226330 CAACAACCTCCACCGATGAAA 58.774 47.619 0.00 0.00 0.00 2.69
371 373 4.691175 AGTCAGTCGAGAAATCATCATGG 58.309 43.478 0.00 0.00 0.00 3.66
374 376 6.598064 TGTAGTAGTCAGTCGAGAAATCATCA 59.402 38.462 0.00 0.00 0.00 3.07
377 379 6.206048 TGTTGTAGTAGTCAGTCGAGAAATCA 59.794 38.462 0.00 0.00 0.00 2.57
383 385 4.215827 ACCTTGTTGTAGTAGTCAGTCGAG 59.784 45.833 0.00 0.00 0.00 4.04
391 393 4.374399 CGGTCAAACCTTGTTGTAGTAGT 58.626 43.478 0.00 0.00 35.66 2.73
410 412 2.612493 CCCCCTGATTGAACCCGGT 61.612 63.158 0.00 0.00 0.00 5.28
415 417 1.000359 CCCCACCCCCTGATTGAAC 60.000 63.158 0.00 0.00 0.00 3.18
419 421 2.287194 CTCCCCCACCCCCTGATT 60.287 66.667 0.00 0.00 0.00 2.57
430 432 4.880426 TCATCGCCCCTCTCCCCC 62.880 72.222 0.00 0.00 0.00 5.40
431 433 3.551407 GTCATCGCCCCTCTCCCC 61.551 72.222 0.00 0.00 0.00 4.81
432 434 3.917760 CGTCATCGCCCCTCTCCC 61.918 72.222 0.00 0.00 0.00 4.30
433 435 3.917760 CCGTCATCGCCCCTCTCC 61.918 72.222 0.00 0.00 35.54 3.71
434 436 4.593864 GCCGTCATCGCCCCTCTC 62.594 72.222 0.00 0.00 35.54 3.20
454 456 2.747989 ACTAGATCGAGTTGAAGACGCA 59.252 45.455 2.18 0.00 0.00 5.24
456 458 7.972623 AATTTACTAGATCGAGTTGAAGACG 57.027 36.000 13.99 0.00 0.00 4.18
483 485 2.141517 CGTAGACCACCTATCGACGAT 58.858 52.381 15.74 15.74 44.77 3.73
490 492 4.180377 TCCAGATTCGTAGACCACCTAT 57.820 45.455 0.00 0.00 34.32 2.57
506 508 9.802039 ACACCAAAAGTAAAACTTATATCCAGA 57.198 29.630 0.00 0.00 37.47 3.86
513 515 8.528044 TGGAGAACACCAAAAGTAAAACTTAT 57.472 30.769 0.00 0.00 35.28 1.73
517 519 9.406828 GAATATGGAGAACACCAAAAGTAAAAC 57.593 33.333 0.00 0.00 43.47 2.43
526 529 5.414789 TTCGAGAATATGGAGAACACCAA 57.585 39.130 0.00 0.00 43.47 3.67
738 818 5.116528 CGTTTAATTTCCGTTGCTCCTTTTC 59.883 40.000 0.00 0.00 0.00 2.29
743 823 3.425758 CCTCGTTTAATTTCCGTTGCTCC 60.426 47.826 0.00 0.00 0.00 4.70
782 862 4.389576 GTGCGTGCGCCTTCCTTG 62.390 66.667 14.16 0.00 41.09 3.61
811 891 2.028930 GGAGTGTGTACTTGAGTGAGGG 60.029 54.545 0.00 0.00 37.25 4.30
814 894 2.552743 CGAGGAGTGTGTACTTGAGTGA 59.447 50.000 0.00 0.00 37.25 3.41
872 952 4.622933 GCTTCTTCTTCCTCTTCCTCTTCC 60.623 50.000 0.00 0.00 0.00 3.46
897 977 2.697654 CTTCTCTCTCCACTTGGCTTG 58.302 52.381 0.00 0.00 34.44 4.01
898 978 1.003003 GCTTCTCTCTCCACTTGGCTT 59.997 52.381 0.00 0.00 34.44 4.35
899 979 0.612744 GCTTCTCTCTCCACTTGGCT 59.387 55.000 0.00 0.00 34.44 4.75
900 980 0.739112 CGCTTCTCTCTCCACTTGGC 60.739 60.000 0.00 0.00 34.44 4.52
926 1006 0.256464 TCCCTCTCTCTCCGTCTTCC 59.744 60.000 0.00 0.00 0.00 3.46
962 1052 4.598894 CCCGCGCAGATCTCCCTG 62.599 72.222 8.75 0.00 37.23 4.45
988 1078 4.598894 CCCCATCGCTGCCTCTCG 62.599 72.222 0.00 0.00 0.00 4.04
1179 1269 3.062466 TGGGAGACGGTGAGCGAG 61.062 66.667 12.27 0.00 0.00 5.03
1649 1748 1.341606 CTCGTCGTCTTCTTTGAGGC 58.658 55.000 0.00 0.00 0.00 4.70
1678 1777 2.190578 CTCGTCTTCCCCATGGCC 59.809 66.667 6.09 0.00 0.00 5.36
1686 1785 1.378124 CCGTCTCCTCCTCGTCTTCC 61.378 65.000 0.00 0.00 0.00 3.46
2122 2221 3.657610 TGAGAGAATAGCATTCTGGGGA 58.342 45.455 13.78 0.00 0.00 4.81
2161 2261 4.787598 AGAAAGCGTTGCATCTTTGTTAG 58.212 39.130 12.06 0.00 33.14 2.34
2176 2276 3.126729 CCATTTGGGCAAGAAAGCG 57.873 52.632 0.00 0.00 34.64 4.68
2226 2326 1.801178 CGTCTCTGCCAAAGGAGAAAC 59.199 52.381 0.00 0.00 39.81 2.78
2270 2370 3.106407 GTCGACGCCAGTGCTGAC 61.106 66.667 0.00 0.00 34.43 3.51
2498 2598 2.096119 GCAACACCAATTTGAGCAATGC 60.096 45.455 0.00 0.00 0.00 3.56
2515 2615 7.083858 TGACAATTTTTATACAGCAGAGCAAC 58.916 34.615 0.00 0.00 0.00 4.17
2574 2683 2.159881 GCGTGTTCCATCGACAACTAAC 60.160 50.000 0.00 0.00 0.00 2.34
2648 2758 4.084013 GGCCGAAAACATCAGGTAATATCG 60.084 45.833 0.00 0.00 0.00 2.92
2656 2766 1.462616 TGATGGCCGAAAACATCAGG 58.537 50.000 0.00 0.00 46.05 3.86
2670 2780 6.935771 TGGAAGAATTTGGAATTTGTTGATGG 59.064 34.615 0.00 0.00 0.00 3.51
2749 2859 6.183360 GGTTATTAAATACAGACGACGCACAA 60.183 38.462 0.00 0.00 0.00 3.33
2769 2879 4.879295 TTCATCCTTGACCATGGGTTAT 57.121 40.909 18.09 0.00 35.25 1.89
2770 2880 4.666412 TTTCATCCTTGACCATGGGTTA 57.334 40.909 18.09 0.00 35.25 2.85
2771 2881 3.541242 TTTCATCCTTGACCATGGGTT 57.459 42.857 18.09 0.00 35.25 4.11
2801 2911 5.637810 TCTCTTCATGGTGTAAGCGTTTTAG 59.362 40.000 0.00 0.00 36.92 1.85
2802 2912 5.543714 TCTCTTCATGGTGTAAGCGTTTTA 58.456 37.500 0.00 0.00 36.92 1.52
2803 2913 4.385825 TCTCTTCATGGTGTAAGCGTTTT 58.614 39.130 0.00 0.00 36.92 2.43
2804 2914 3.997021 CTCTCTTCATGGTGTAAGCGTTT 59.003 43.478 0.00 0.00 36.92 3.60
2805 2915 3.589988 CTCTCTTCATGGTGTAAGCGTT 58.410 45.455 0.00 0.00 36.92 4.84
2806 2916 2.675317 GCTCTCTTCATGGTGTAAGCGT 60.675 50.000 0.00 0.00 36.92 5.07
2807 2917 1.929836 GCTCTCTTCATGGTGTAAGCG 59.070 52.381 0.00 0.00 36.92 4.68
2808 2918 3.118811 AGAGCTCTCTTCATGGTGTAAGC 60.119 47.826 11.45 0.00 36.31 3.09
2809 2919 4.734398 AGAGCTCTCTTCATGGTGTAAG 57.266 45.455 11.45 0.00 36.31 2.34
2810 2920 6.132658 AGATAGAGCTCTCTTCATGGTGTAA 58.867 40.000 22.17 0.00 40.93 2.41
2811 2921 5.700183 AGATAGAGCTCTCTTCATGGTGTA 58.300 41.667 22.17 0.00 40.93 2.90
2812 2922 4.545678 AGATAGAGCTCTCTTCATGGTGT 58.454 43.478 22.17 0.00 40.93 4.16
2838 2948 3.706594 CCTACCAGAATCCTAAGAGCACA 59.293 47.826 0.00 0.00 0.00 4.57
2840 2950 3.995636 ACCTACCAGAATCCTAAGAGCA 58.004 45.455 0.00 0.00 0.00 4.26
2844 2954 7.792032 TCATTTGTACCTACCAGAATCCTAAG 58.208 38.462 0.00 0.00 0.00 2.18
2922 3032 5.181748 CCAACTTCAAATCTAGAGAGGTGG 58.818 45.833 10.58 10.58 0.00 4.61
2970 3085 3.070015 ACAATTGCTGAACAAAAGGGAGG 59.930 43.478 5.05 0.00 42.86 4.30
3113 3228 5.486526 GTTAGGAGATCTAATGGCATGGAG 58.513 45.833 0.00 1.63 39.82 3.86
3115 3230 4.042062 TGGTTAGGAGATCTAATGGCATGG 59.958 45.833 0.00 0.00 39.82 3.66
3286 3401 2.239654 CCCCAGCCTATGAACTTTCTCA 59.760 50.000 0.00 0.00 0.00 3.27
3297 3412 2.199535 GGCAATGCCCCAGCCTAT 59.800 61.111 14.47 0.00 44.06 2.57
3326 3441 7.913297 CCAATATAAATGTTGTAGTGGTTTCGG 59.087 37.037 3.84 0.00 37.60 4.30
3327 3442 7.431084 GCCAATATAAATGTTGTAGTGGTTTCG 59.569 37.037 11.27 0.00 42.25 3.46
3353 3468 8.516811 ACACTATTTGTCGTCACTAAACTTAG 57.483 34.615 0.00 0.00 29.79 2.18
3368 3483 5.897250 AGGAAACCAAAGGAACACTATTTGT 59.103 36.000 0.00 0.00 41.74 2.83
3381 3496 6.946009 TCTATCCCAAACTAAGGAAACCAAAG 59.054 38.462 0.00 0.00 35.30 2.77
3420 3535 3.968649 ACAAGTGCAGTGCAATAACTTG 58.031 40.909 30.03 30.03 41.47 3.16
3537 3656 5.061853 TCATGCTCAATCTTAATGCTCTCC 58.938 41.667 0.00 0.00 0.00 3.71
3544 3663 7.055378 AGCTTCTTCTCATGCTCAATCTTAAT 58.945 34.615 0.00 0.00 0.00 1.40
3667 3786 1.667830 TAGTGGCAGCTTGTGACGC 60.668 57.895 0.00 0.00 46.23 5.19
3819 3938 8.909708 TGTCAAAATTCAGAAACAGTTAAGTG 57.090 30.769 8.81 8.81 0.00 3.16
3871 3990 4.038763 TGTGTCTCGTGGAAGTAGTTCATT 59.961 41.667 12.31 0.00 33.93 2.57
4297 4416 2.093711 GGTCTTCTTCTCCAGCTCCTTC 60.094 54.545 0.00 0.00 0.00 3.46
4522 4641 0.037326 TGTTGAGCGTCATGGACCTC 60.037 55.000 0.00 0.00 33.59 3.85
4534 4653 1.808945 CCAGTCTGGATGTTGTTGAGC 59.191 52.381 14.26 0.00 40.96 4.26
4537 4656 0.883833 GGCCAGTCTGGATGTTGTTG 59.116 55.000 23.77 0.00 40.96 3.33
4558 4677 2.308722 GGCCTGGAACATCCCTGGA 61.309 63.158 9.61 0.00 45.16 3.86
4660 4787 5.302568 ACACACCAAAATGATGTTCTGATGT 59.697 36.000 0.00 0.00 0.00 3.06
4692 4819 1.072266 ACATACCACCCAAAGAGCCA 58.928 50.000 0.00 0.00 0.00 4.75
4693 4820 1.818674 CAACATACCACCCAAAGAGCC 59.181 52.381 0.00 0.00 0.00 4.70
4694 4821 2.790433 TCAACATACCACCCAAAGAGC 58.210 47.619 0.00 0.00 0.00 4.09
4695 4822 4.848357 AGATCAACATACCACCCAAAGAG 58.152 43.478 0.00 0.00 0.00 2.85
4777 4920 1.284313 CCAGGGAAGCCTTCTCTTCT 58.716 55.000 3.47 0.00 38.82 2.85
4778 4921 0.393673 GCCAGGGAAGCCTTCTCTTC 60.394 60.000 3.47 0.00 38.82 2.87
4779 4922 0.844221 AGCCAGGGAAGCCTTCTCTT 60.844 55.000 3.47 0.00 38.82 2.85
4780 4923 1.229788 AGCCAGGGAAGCCTTCTCT 60.230 57.895 0.00 0.00 42.52 3.10
4810 4953 6.391227 AAATGATATCAATCCCCAACGAAC 57.609 37.500 9.99 0.00 0.00 3.95
4811 4954 6.183360 CCAAAATGATATCAATCCCCAACGAA 60.183 38.462 9.99 0.00 0.00 3.85
4813 4956 5.068987 ACCAAAATGATATCAATCCCCAACG 59.931 40.000 9.99 0.00 0.00 4.10
4814 4957 6.484364 ACCAAAATGATATCAATCCCCAAC 57.516 37.500 9.99 0.00 0.00 3.77
4866 5010 1.009429 AGGGAGGAAAGGAGATGAGCT 59.991 52.381 0.00 0.00 0.00 4.09
4960 5104 2.504175 AGGGGAGAGCAAGCGTAAAATA 59.496 45.455 0.00 0.00 0.00 1.40
4961 5105 1.282157 AGGGGAGAGCAAGCGTAAAAT 59.718 47.619 0.00 0.00 0.00 1.82
4962 5106 0.690762 AGGGGAGAGCAAGCGTAAAA 59.309 50.000 0.00 0.00 0.00 1.52
4977 5121 1.826385 ATTCAAGTTTGCGAGAGGGG 58.174 50.000 0.00 0.00 0.00 4.79
4996 5151 4.750021 AGCTGAAGACATGAGCATAGAA 57.250 40.909 0.00 0.00 0.00 2.10
5012 5167 5.104693 ACAGTAGAGAGTAGAGCTTAGCTGA 60.105 44.000 13.01 0.00 39.88 4.26
5013 5168 5.123227 ACAGTAGAGAGTAGAGCTTAGCTG 58.877 45.833 13.01 0.00 39.88 4.24
5027 5208 5.362717 TCTGAACCACTTCAAACAGTAGAGA 59.637 40.000 0.00 0.00 35.92 3.10
5033 5214 3.003068 CAGCTCTGAACCACTTCAAACAG 59.997 47.826 0.00 0.00 35.92 3.16
5053 5241 1.604593 CCTCCCCAACAGGCAACAG 60.605 63.158 0.00 0.00 41.41 3.16
5059 5247 1.002857 AATCCTTCCTCCCCAACAGG 58.997 55.000 0.00 0.00 0.00 4.00
5060 5248 1.064389 GGAATCCTTCCTCCCCAACAG 60.064 57.143 0.00 0.00 46.57 3.16
5061 5249 0.999712 GGAATCCTTCCTCCCCAACA 59.000 55.000 0.00 0.00 46.57 3.33
5062 5250 3.905331 GGAATCCTTCCTCCCCAAC 57.095 57.895 0.00 0.00 46.57 3.77
5083 5273 1.471684 CATCTGCTTTCACTTCAGGCC 59.528 52.381 0.00 0.00 0.00 5.19
5184 5382 1.666888 GGGCAGCAGAAAATCAACGTG 60.667 52.381 0.00 0.00 0.00 4.49
5196 5395 2.361610 ACCGAAATGGGGCAGCAG 60.362 61.111 0.00 0.00 44.64 4.24
5234 5439 0.538977 ACAATGGAAGCAGCAGCAGT 60.539 50.000 3.17 0.00 45.49 4.40
5315 5523 6.019779 AGTCAAGACTCAAGTGACAGTATC 57.980 41.667 7.56 0.00 43.34 2.24
5324 5532 2.370189 CCCCAGAAGTCAAGACTCAAGT 59.630 50.000 2.78 0.00 41.58 3.16
5330 5538 0.035915 GGAGCCCCAGAAGTCAAGAC 60.036 60.000 0.00 0.00 0.00 3.01
5332 5540 1.484240 CTAGGAGCCCCAGAAGTCAAG 59.516 57.143 0.00 0.00 33.88 3.02
5333 5541 1.203313 ACTAGGAGCCCCAGAAGTCAA 60.203 52.381 0.00 0.00 33.88 3.18
5335 5543 1.116308 GACTAGGAGCCCCAGAAGTC 58.884 60.000 0.00 0.00 34.27 3.01
5336 5544 0.325765 GGACTAGGAGCCCCAGAAGT 60.326 60.000 0.00 0.00 33.88 3.01
5337 5545 0.325671 TGGACTAGGAGCCCCAGAAG 60.326 60.000 0.00 0.00 33.88 2.85
5338 5546 0.325671 CTGGACTAGGAGCCCCAGAA 60.326 60.000 0.00 0.00 46.84 3.02
5339 5547 1.311403 CTGGACTAGGAGCCCCAGA 59.689 63.158 0.00 0.00 46.84 3.86
5340 5548 2.439104 GCTGGACTAGGAGCCCCAG 61.439 68.421 0.00 0.00 46.67 4.45
5341 5549 2.365635 GCTGGACTAGGAGCCCCA 60.366 66.667 0.00 0.00 33.88 4.96
5382 5590 4.618920 ATTAGTTCCTGTTGTCGGAAGT 57.381 40.909 4.72 4.72 44.31 3.01
5383 5591 5.109903 CCTATTAGTTCCTGTTGTCGGAAG 58.890 45.833 0.00 0.00 40.97 3.46
5405 5617 0.312729 ATTTTCACGGTGAAACGGCC 59.687 50.000 30.14 0.00 45.03 6.13
5423 5635 2.578021 ACTCCCACTACATGCTTGGAAT 59.422 45.455 8.99 0.00 31.39 3.01
5432 5655 5.473846 CGTCAGTATCATACTCCCACTACAT 59.526 44.000 0.00 0.00 36.76 2.29
5437 5660 5.455056 AATCGTCAGTATCATACTCCCAC 57.545 43.478 0.00 0.00 36.76 4.61
5439 5662 5.921408 GTGAAATCGTCAGTATCATACTCCC 59.079 44.000 0.00 0.00 36.74 4.30
5440 5663 5.921408 GGTGAAATCGTCAGTATCATACTCC 59.079 44.000 0.00 0.00 36.74 3.85
5441 5664 6.504398 TGGTGAAATCGTCAGTATCATACTC 58.496 40.000 0.00 0.00 36.74 2.59
5450 6024 2.744202 GCTTCATGGTGAAATCGTCAGT 59.256 45.455 0.00 0.00 35.73 3.41
5457 6031 1.547372 GGCAGTGCTTCATGGTGAAAT 59.453 47.619 16.11 0.00 35.73 2.17
5510 6123 0.976641 TTCGCTCCCACTCACAGAAT 59.023 50.000 0.00 0.00 0.00 2.40
5518 6131 1.534235 ACTCCACTTCGCTCCCACT 60.534 57.895 0.00 0.00 0.00 4.00
5526 6139 1.611977 TCTACACCACACTCCACTTCG 59.388 52.381 0.00 0.00 0.00 3.79
5531 6144 1.532604 CGGCTCTACACCACACTCCA 61.533 60.000 0.00 0.00 0.00 3.86
5532 6145 1.215647 CGGCTCTACACCACACTCC 59.784 63.158 0.00 0.00 0.00 3.85
5534 6147 1.754380 TTGCGGCTCTACACCACACT 61.754 55.000 0.00 0.00 0.00 3.55
5535 6148 1.291877 CTTGCGGCTCTACACCACAC 61.292 60.000 0.00 0.00 0.00 3.82
5536 6149 1.005037 CTTGCGGCTCTACACCACA 60.005 57.895 0.00 0.00 0.00 4.17
5537 6150 1.741770 CCTTGCGGCTCTACACCAC 60.742 63.158 0.00 0.00 0.00 4.16
5538 6151 2.662596 CCTTGCGGCTCTACACCA 59.337 61.111 0.00 0.00 0.00 4.17
5630 6244 2.826277 GGGAAAAGGTTGCATTGCG 58.174 52.632 3.84 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.