Multiple sequence alignment - TraesCS6A01G037300

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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 TraesCS6A01G037300 chr6A 100.000 5206 0 0 1 5206 18460147 18465352 0.000000e+00 9614
1 TraesCS6A01G037300 chr6A 81.029 3342 579 48 938 4252 603091661 603094974 0.000000e+00 2608
2 TraesCS6A01G037300 chr6A 80.866 3350 586 48 927 4252 603081514 603084832 0.000000e+00 2584
3 TraesCS6A01G037300 chr6A 83.705 2062 285 43 2212 4252 603101909 603103940 0.000000e+00 1899
4 TraesCS6A01G037300 chr6A 94.012 167 10 0 4478 4644 51753065 51753231 2.410000e-63 254
5 TraesCS6A01G037300 chr6D 95.871 4456 150 10 25 4478 17499336 17503759 0.000000e+00 7179
6 TraesCS6A01G037300 chr6D 81.035 3343 592 38 927 4252 456424398 456427715 0.000000e+00 2623
7 TraesCS6A01G037300 chr6D 79.787 3290 605 43 983 4251 456408499 456411749 0.000000e+00 2337
8 TraesCS6A01G037300 chr6D 94.321 405 14 3 4642 5043 17503758 17504156 3.450000e-171 612
9 TraesCS6A01G037300 chr6D 95.604 91 4 0 5116 5206 17504158 17504248 4.200000e-31 147
10 TraesCS6A01G037300 chr6B 92.794 3719 246 19 768 4479 30889498 30893201 0.000000e+00 5363
11 TraesCS6A01G037300 chr6B 92.690 3721 247 20 768 4478 31690629 31686924 0.000000e+00 5341
12 TraesCS6A01G037300 chr6B 94.025 569 26 4 4642 5206 31686925 31686361 0.000000e+00 856
13 TraesCS6A01G037300 chr6B 93.849 569 27 4 4642 5206 30893198 30893762 0.000000e+00 850
14 TraesCS6A01G037300 chr6B 80.275 218 31 11 359 574 30888816 30889023 2.510000e-33 154
15 TraesCS6A01G037300 chr7A 81.999 2561 415 31 1673 4202 725447751 725445206 0.000000e+00 2134
16 TraesCS6A01G037300 chr7A 98.182 165 3 0 4480 4644 23350883 23351047 6.600000e-74 289
17 TraesCS6A01G037300 chr7D 82.614 2341 367 25 1890 4202 629393877 629391549 0.000000e+00 2032
18 TraesCS6A01G037300 chr3B 78.413 3238 604 60 997 4186 26652845 26649655 0.000000e+00 2019
19 TraesCS6A01G037300 chr3B 78.166 3238 611 62 997 4186 14983249 14986438 0.000000e+00 1975
20 TraesCS6A01G037300 chr1A 77.795 3184 639 50 1061 4201 530163234 530160076 0.000000e+00 1901
21 TraesCS6A01G037300 chr1A 98.182 165 3 0 4480 4644 570159118 570158954 6.600000e-74 289
22 TraesCS6A01G037300 chr1A 87.826 115 14 0 574 688 106228181 106228067 9.090000e-28 135
23 TraesCS6A01G037300 chr4A 97.024 168 5 0 4477 4644 613568866 613568699 3.070000e-72 283
24 TraesCS6A01G037300 chr4A 92.771 166 12 0 4479 4644 393525635 393525470 1.870000e-59 241
25 TraesCS6A01G037300 chr3A 94.706 170 8 1 4475 4644 652496325 652496493 4.000000e-66 263
26 TraesCS6A01G037300 chr3A 94.118 170 10 0 4475 4644 652291351 652291520 5.170000e-65 259
27 TraesCS6A01G037300 chr2A 95.152 165 7 1 4480 4644 715425080 715425243 5.170000e-65 259
28 TraesCS6A01G037300 chr2A 92.727 165 12 0 4480 4644 765962509 765962673 6.740000e-59 239
29 TraesCS6A01G037300 chr2A 88.596 114 12 1 580 692 170470491 170470378 2.530000e-28 137
30 TraesCS6A01G037300 chr2B 88.525 122 13 1 572 692 216462916 216462795 4.200000e-31 147
31 TraesCS6A01G037300 chr5B 88.073 109 13 0 580 688 55371038 55370930 4.230000e-26 130
32 TraesCS6A01G037300 chr5B 87.156 109 14 0 572 680 70795548 70795656 1.970000e-24 124
33 TraesCS6A01G037300 chr1D 87.963 108 13 0 574 681 128529105 128529212 1.520000e-25 128
34 TraesCS6A01G037300 chr1B 87.156 109 14 0 580 688 160325318 160325210 1.970000e-24 124
35 TraesCS6A01G037300 chr2D 85.345 116 16 1 574 689 619562449 619562335 9.160000e-23 119
36 TraesCS6A01G037300 chr7B 85.586 111 15 1 571 681 153749785 153749676 1.180000e-21 115


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 TraesCS6A01G037300 chr6A 18460147 18465352 5205 False 9614.000000 9614 100.000000 1 5206 1 chr6A.!!$F1 5205
1 TraesCS6A01G037300 chr6A 603091661 603094974 3313 False 2608.000000 2608 81.029000 938 4252 1 chr6A.!!$F4 3314
2 TraesCS6A01G037300 chr6A 603081514 603084832 3318 False 2584.000000 2584 80.866000 927 4252 1 chr6A.!!$F3 3325
3 TraesCS6A01G037300 chr6A 603101909 603103940 2031 False 1899.000000 1899 83.705000 2212 4252 1 chr6A.!!$F5 2040
4 TraesCS6A01G037300 chr6D 17499336 17504248 4912 False 2646.000000 7179 95.265333 25 5206 3 chr6D.!!$F3 5181
5 TraesCS6A01G037300 chr6D 456424398 456427715 3317 False 2623.000000 2623 81.035000 927 4252 1 chr6D.!!$F2 3325
6 TraesCS6A01G037300 chr6D 456408499 456411749 3250 False 2337.000000 2337 79.787000 983 4251 1 chr6D.!!$F1 3268
7 TraesCS6A01G037300 chr6B 31686361 31690629 4268 True 3098.500000 5341 93.357500 768 5206 2 chr6B.!!$R1 4438
8 TraesCS6A01G037300 chr6B 30888816 30893762 4946 False 2122.333333 5363 88.972667 359 5206 3 chr6B.!!$F1 4847
9 TraesCS6A01G037300 chr7A 725445206 725447751 2545 True 2134.000000 2134 81.999000 1673 4202 1 chr7A.!!$R1 2529
10 TraesCS6A01G037300 chr7D 629391549 629393877 2328 True 2032.000000 2032 82.614000 1890 4202 1 chr7D.!!$R1 2312
11 TraesCS6A01G037300 chr3B 26649655 26652845 3190 True 2019.000000 2019 78.413000 997 4186 1 chr3B.!!$R1 3189
12 TraesCS6A01G037300 chr3B 14983249 14986438 3189 False 1975.000000 1975 78.166000 997 4186 1 chr3B.!!$F1 3189
13 TraesCS6A01G037300 chr1A 530160076 530163234 3158 True 1901.000000 1901 77.795000 1061 4201 1 chr1A.!!$R2 3140

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
240 241 0.176680 CGCAATGCCTCCTCTGTAGT 59.823 55.0 0.00 0.0 0.00 2.73 F
1035 1351 0.030101 TGCTGCTTTTGTTGCCGTAC 59.970 50.0 0.00 0.0 0.00 3.67 F
1793 2130 0.394899 CACCTCCCAAATCTCAGGGC 60.395 60.0 0.00 0.0 45.07 5.19 F
2742 3079 2.776536 AGAATTCAGACTCATGGGAGGG 59.223 50.0 8.44 0.0 45.81 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1581 1918 0.041312 CGAGTTGGTTTGCGGTGAAG 60.041 55.000 0.00 0.0 0.00 3.02 R
2854 3191 0.321653 ACACCCTGCGATGGAACTTC 60.322 55.000 0.00 0.0 0.00 3.01 R
2957 3294 2.557924 GTGTGTTCCATTGATTCTGGCA 59.442 45.455 0.00 0.0 33.56 4.92 R
4520 4951 0.037590 ATTTAGCGGCAACACCCTCA 59.962 50.000 1.45 0.0 33.26 3.86 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
19 20 1.386533 CCACCATGATGCTGTCTTCC 58.613 55.000 0.00 0.00 0.00 3.46
20 21 1.064906 CCACCATGATGCTGTCTTCCT 60.065 52.381 0.00 0.00 0.00 3.36
21 22 2.619849 CCACCATGATGCTGTCTTCCTT 60.620 50.000 0.00 0.00 0.00 3.36
22 23 3.087031 CACCATGATGCTGTCTTCCTTT 58.913 45.455 0.00 0.00 0.00 3.11
23 24 4.264253 CACCATGATGCTGTCTTCCTTTA 58.736 43.478 0.00 0.00 0.00 1.85
24 25 4.095483 CACCATGATGCTGTCTTCCTTTAC 59.905 45.833 0.00 0.00 0.00 2.01
25 26 4.018960 ACCATGATGCTGTCTTCCTTTACT 60.019 41.667 0.00 0.00 0.00 2.24
26 27 4.946157 CCATGATGCTGTCTTCCTTTACTT 59.054 41.667 0.00 0.00 0.00 2.24
27 28 5.065731 CCATGATGCTGTCTTCCTTTACTTC 59.934 44.000 0.00 0.00 0.00 3.01
28 29 4.579869 TGATGCTGTCTTCCTTTACTTCC 58.420 43.478 0.00 0.00 0.00 3.46
29 30 4.287067 TGATGCTGTCTTCCTTTACTTCCT 59.713 41.667 0.00 0.00 0.00 3.36
30 31 4.706842 TGCTGTCTTCCTTTACTTCCTT 57.293 40.909 0.00 0.00 0.00 3.36
31 32 4.389374 TGCTGTCTTCCTTTACTTCCTTG 58.611 43.478 0.00 0.00 0.00 3.61
34 35 4.134563 TGTCTTCCTTTACTTCCTTGCAC 58.865 43.478 0.00 0.00 0.00 4.57
45 46 2.978156 TCCTTGCACCATCTTTTCCT 57.022 45.000 0.00 0.00 0.00 3.36
58 59 2.669744 TTTTCCTGCATGCCCCCACA 62.670 55.000 16.68 0.00 0.00 4.17
68 69 4.596585 CCCCCACACCCACACACC 62.597 72.222 0.00 0.00 0.00 4.16
71 72 4.596585 CCACACCCACACACCCCC 62.597 72.222 0.00 0.00 0.00 5.40
72 73 3.498071 CACACCCACACACCCCCT 61.498 66.667 0.00 0.00 0.00 4.79
73 74 3.498071 ACACCCACACACCCCCTG 61.498 66.667 0.00 0.00 0.00 4.45
120 121 3.362399 CTCCTGCAGCGACACCGAT 62.362 63.158 8.66 0.00 38.22 4.18
195 196 1.344393 ACCTACCAGCTGATCCCATGA 60.344 52.381 17.39 0.00 0.00 3.07
240 241 0.176680 CGCAATGCCTCCTCTGTAGT 59.823 55.000 0.00 0.00 0.00 2.73
247 248 1.402984 GCCTCCTCTGTAGTTCACACG 60.403 57.143 0.00 0.00 32.33 4.49
249 250 2.351835 CCTCCTCTGTAGTTCACACGTG 60.352 54.545 15.48 15.48 32.33 4.49
311 312 3.517100 CCATCCTCTCTTCAGAAACCAGA 59.483 47.826 0.00 0.00 0.00 3.86
348 349 1.771255 AGGTATGTGATCCAAGCCTCC 59.229 52.381 0.00 0.00 28.67 4.30
415 416 2.065512 CATAGCGTGTGCACAGTTACA 58.934 47.619 22.40 5.11 46.23 2.41
616 671 5.044428 GCTGATGCTCAAATGGATGTATC 57.956 43.478 0.00 0.00 36.03 2.24
617 672 4.760715 GCTGATGCTCAAATGGATGTATCT 59.239 41.667 0.00 0.00 36.03 1.98
618 673 5.936372 GCTGATGCTCAAATGGATGTATCTA 59.064 40.000 0.00 0.00 36.03 1.98
619 674 6.429078 GCTGATGCTCAAATGGATGTATCTAA 59.571 38.462 0.00 0.00 36.03 2.10
620 675 7.572724 GCTGATGCTCAAATGGATGTATCTAAC 60.573 40.741 0.00 0.00 36.03 2.34
621 676 7.281841 TGATGCTCAAATGGATGTATCTAACA 58.718 34.615 0.00 0.00 43.86 2.41
622 677 6.925610 TGCTCAAATGGATGTATCTAACAC 57.074 37.500 0.00 0.00 42.09 3.32
623 678 6.653020 TGCTCAAATGGATGTATCTAACACT 58.347 36.000 0.00 0.00 42.09 3.55
624 679 6.539826 TGCTCAAATGGATGTATCTAACACTG 59.460 38.462 0.00 0.00 42.09 3.66
625 680 6.763135 GCTCAAATGGATGTATCTAACACTGA 59.237 38.462 0.00 0.00 42.09 3.41
626 681 7.443575 GCTCAAATGGATGTATCTAACACTGAT 59.556 37.037 0.00 0.00 42.09 2.90
627 682 9.987272 CTCAAATGGATGTATCTAACACTGATA 57.013 33.333 0.00 0.00 42.09 2.15
632 687 8.631480 TGGATGTATCTAACACTGATATACGT 57.369 34.615 0.00 0.00 42.09 3.57
633 688 8.727910 TGGATGTATCTAACACTGATATACGTC 58.272 37.037 0.00 0.00 42.09 4.34
634 689 8.948145 GGATGTATCTAACACTGATATACGTCT 58.052 37.037 0.00 0.00 42.09 4.18
712 794 9.688592 AAAAGAAAAAGATCACATAGAAGCAAG 57.311 29.630 0.00 0.00 0.00 4.01
713 795 6.850555 AGAAAAAGATCACATAGAAGCAAGC 58.149 36.000 0.00 0.00 0.00 4.01
714 796 6.432162 AGAAAAAGATCACATAGAAGCAAGCA 59.568 34.615 0.00 0.00 0.00 3.91
734 816 6.360370 AGCACAAGGTCTGACTTTATTAGA 57.640 37.500 7.85 0.00 0.00 2.10
795 1105 1.806496 TCCGGATGTTCTGGGATGAT 58.194 50.000 0.00 0.00 43.23 2.45
1035 1351 0.030101 TGCTGCTTTTGTTGCCGTAC 59.970 50.000 0.00 0.00 0.00 3.67
1036 1352 0.030101 GCTGCTTTTGTTGCCGTACA 59.970 50.000 0.00 0.00 0.00 2.90
1218 1549 4.278956 CACAGGGTTACGGTGCTC 57.721 61.111 0.00 0.00 38.40 4.26
1383 1714 8.653338 CATCTTAATTTTTCCAGCAATTCACTG 58.347 33.333 0.00 0.00 34.82 3.66
1510 1847 5.263599 TGCCAAATCTGAAGACCATACAAT 58.736 37.500 0.00 0.00 0.00 2.71
1581 1918 1.264020 TCAGCACTGCAAACAATCGAC 59.736 47.619 3.30 0.00 0.00 4.20
1718 2055 5.541484 TCTTTAACCTTTCCTCTCTAACCGT 59.459 40.000 0.00 0.00 0.00 4.83
1790 2127 2.619074 GGGTTCACCTCCCAAATCTCAG 60.619 54.545 0.00 0.00 44.05 3.35
1793 2130 0.394899 CACCTCCCAAATCTCAGGGC 60.395 60.000 0.00 0.00 45.07 5.19
1845 2182 4.406003 GGATACCTTCCAGCTTCTCTTGTA 59.594 45.833 0.00 0.00 44.74 2.41
1902 2239 3.452990 TCAATGGCTTCACCGGTAGATTA 59.547 43.478 6.87 0.00 43.94 1.75
2035 2372 3.670203 CGCCTTCGTGTATTAAAGCTTG 58.330 45.455 0.00 0.00 0.00 4.01
2158 2495 7.838079 ATACCATTTGGCATAAGCAATCTTA 57.162 32.000 0.00 0.00 44.61 2.10
2263 2600 8.236585 ACAAGCCTTGTTTATGCATGATAATA 57.763 30.769 10.16 0.00 42.22 0.98
2474 2811 4.307432 CTGTCGAACACACTAGATTTGGT 58.693 43.478 0.00 0.00 0.00 3.67
2598 2935 5.779529 ATGAACTCAGCAATTGTCAAAGT 57.220 34.783 7.40 3.51 0.00 2.66
2739 3076 4.080695 CCTCAAGAATTCAGACTCATGGGA 60.081 45.833 8.44 0.00 0.00 4.37
2742 3079 2.776536 AGAATTCAGACTCATGGGAGGG 59.223 50.000 8.44 0.00 45.81 4.30
2854 3191 3.499918 GTCCTTCAATAATCTGGATGGCG 59.500 47.826 0.00 0.00 0.00 5.69
2957 3294 0.042431 TTACATTTGCCCCCATGCCT 59.958 50.000 0.00 0.00 0.00 4.75
3095 3441 6.490040 AGAAAGAAATCAAAAGATCGGTCCAA 59.510 34.615 0.00 0.00 0.00 3.53
3285 3631 4.320057 GCTGTGAAGGTGTTTGATCTTCAG 60.320 45.833 5.39 0.00 44.82 3.02
3630 3987 5.575606 TCTTCTTAACGAGGATTTAGTTGCG 59.424 40.000 0.00 0.00 0.00 4.85
3771 4132 9.860898 AGCTCAAATTTTCTAACATTACATTCC 57.139 29.630 0.00 0.00 0.00 3.01
3772 4133 9.638239 GCTCAAATTTTCTAACATTACATTCCA 57.362 29.630 0.00 0.00 0.00 3.53
4001 4400 5.528690 GCTAATGCAGATTGTTGATCCAGTA 59.471 40.000 0.00 0.00 39.41 2.74
4115 4541 0.099259 TTGCGCTATCATGCAGCAAC 59.901 50.000 9.73 9.77 42.46 4.17
4475 4906 2.688958 GCTTCCGAGCCTACTCTCTAAA 59.311 50.000 0.00 0.00 43.29 1.85
4476 4907 3.130693 GCTTCCGAGCCTACTCTCTAAAA 59.869 47.826 0.00 0.00 43.29 1.52
4477 4908 4.381718 GCTTCCGAGCCTACTCTCTAAAAA 60.382 45.833 0.00 0.00 43.29 1.94
4478 4909 4.985538 TCCGAGCCTACTCTCTAAAAAG 57.014 45.455 0.00 0.00 41.09 2.27
4479 4910 3.130693 TCCGAGCCTACTCTCTAAAAAGC 59.869 47.826 0.00 0.00 41.09 3.51
4480 4911 3.119101 CCGAGCCTACTCTCTAAAAAGCA 60.119 47.826 0.00 0.00 41.09 3.91
4481 4912 4.442192 CCGAGCCTACTCTCTAAAAAGCAT 60.442 45.833 0.00 0.00 41.09 3.79
4482 4913 5.221263 CCGAGCCTACTCTCTAAAAAGCATA 60.221 44.000 0.00 0.00 41.09 3.14
4483 4914 5.918011 CGAGCCTACTCTCTAAAAAGCATAG 59.082 44.000 0.00 0.00 41.09 2.23
4484 4915 6.460399 CGAGCCTACTCTCTAAAAAGCATAGT 60.460 42.308 0.00 0.00 41.09 2.12
4485 4916 7.189079 AGCCTACTCTCTAAAAAGCATAGTT 57.811 36.000 0.00 0.00 0.00 2.24
4486 4917 7.625469 AGCCTACTCTCTAAAAAGCATAGTTT 58.375 34.615 0.00 0.00 0.00 2.66
4487 4918 8.103935 AGCCTACTCTCTAAAAAGCATAGTTTT 58.896 33.333 0.00 0.00 33.00 2.43
4488 4919 9.379791 GCCTACTCTCTAAAAAGCATAGTTTTA 57.620 33.333 0.00 0.00 30.95 1.52
4496 4927 9.997482 TCTAAAAAGCATAGTTTTAAATAGCCG 57.003 29.630 0.00 0.00 31.77 5.52
4497 4928 9.233232 CTAAAAAGCATAGTTTTAAATAGCCGG 57.767 33.333 0.00 0.00 31.77 6.13
4498 4929 4.830826 AGCATAGTTTTAAATAGCCGGC 57.169 40.909 21.89 21.89 0.00 6.13
4499 4930 4.461198 AGCATAGTTTTAAATAGCCGGCT 58.539 39.130 34.85 34.85 0.00 5.52
4500 4931 5.617252 AGCATAGTTTTAAATAGCCGGCTA 58.383 37.500 36.88 36.88 0.00 3.93
4501 4932 6.238648 AGCATAGTTTTAAATAGCCGGCTAT 58.761 36.000 37.79 37.79 40.63 2.97
4502 4933 7.391620 AGCATAGTTTTAAATAGCCGGCTATA 58.608 34.615 41.53 28.18 38.20 1.31
4503 4934 7.549488 AGCATAGTTTTAAATAGCCGGCTATAG 59.451 37.037 41.53 23.03 38.20 1.31
4504 4935 7.676572 GCATAGTTTTAAATAGCCGGCTATAGC 60.677 40.741 41.53 29.09 38.20 2.97
4518 4949 4.945645 TAGCCCCGCTATAGCTGT 57.054 55.556 21.98 3.34 40.44 4.40
4519 4950 3.143010 TAGCCCCGCTATAGCTGTT 57.857 52.632 21.98 10.87 40.44 3.16
4520 4951 1.420430 TAGCCCCGCTATAGCTGTTT 58.580 50.000 21.98 6.95 40.44 2.83
4521 4952 0.179045 AGCCCCGCTATAGCTGTTTG 60.179 55.000 21.98 6.39 36.99 2.93
4522 4953 0.179056 GCCCCGCTATAGCTGTTTGA 60.179 55.000 21.98 0.00 39.32 2.69
4523 4954 1.871080 CCCCGCTATAGCTGTTTGAG 58.129 55.000 21.98 4.97 39.32 3.02
4524 4955 1.541233 CCCCGCTATAGCTGTTTGAGG 60.541 57.143 21.98 13.33 39.32 3.86
4525 4956 1.541233 CCCGCTATAGCTGTTTGAGGG 60.541 57.143 21.98 18.02 39.32 4.30
4526 4957 1.139058 CCGCTATAGCTGTTTGAGGGT 59.861 52.381 21.98 0.00 39.32 4.34
4527 4958 2.205074 CGCTATAGCTGTTTGAGGGTG 58.795 52.381 21.98 0.00 39.32 4.61
4528 4959 2.418746 CGCTATAGCTGTTTGAGGGTGT 60.419 50.000 21.98 0.00 39.32 4.16
4529 4960 3.610911 GCTATAGCTGTTTGAGGGTGTT 58.389 45.455 17.75 0.00 38.21 3.32
4530 4961 3.375299 GCTATAGCTGTTTGAGGGTGTTG 59.625 47.826 17.75 0.00 38.21 3.33
4531 4962 1.604604 TAGCTGTTTGAGGGTGTTGC 58.395 50.000 0.00 0.00 0.00 4.17
4532 4963 1.109323 AGCTGTTTGAGGGTGTTGCC 61.109 55.000 0.00 0.00 0.00 4.52
4533 4964 1.654220 CTGTTTGAGGGTGTTGCCG 59.346 57.895 0.00 0.00 38.44 5.69
4534 4965 2.335011 GTTTGAGGGTGTTGCCGC 59.665 61.111 0.00 0.00 38.44 6.53
4535 4966 2.193536 GTTTGAGGGTGTTGCCGCT 61.194 57.895 0.00 0.00 38.44 5.52
4536 4967 0.887387 GTTTGAGGGTGTTGCCGCTA 60.887 55.000 0.00 0.00 38.44 4.26
4537 4968 0.179015 TTTGAGGGTGTTGCCGCTAA 60.179 50.000 0.00 0.00 38.44 3.09
4538 4969 0.179015 TTGAGGGTGTTGCCGCTAAA 60.179 50.000 0.00 0.00 38.44 1.85
4539 4970 0.037590 TGAGGGTGTTGCCGCTAAAT 59.962 50.000 0.00 0.00 38.44 1.40
4540 4971 0.451783 GAGGGTGTTGCCGCTAAATG 59.548 55.000 0.00 0.00 38.44 2.32
4541 4972 0.037590 AGGGTGTTGCCGCTAAATGA 59.962 50.000 0.00 0.00 38.44 2.57
4542 4973 1.102978 GGGTGTTGCCGCTAAATGAT 58.897 50.000 0.00 0.00 38.44 2.45
4543 4974 1.476488 GGGTGTTGCCGCTAAATGATT 59.524 47.619 0.00 0.00 38.44 2.57
4544 4975 2.094234 GGGTGTTGCCGCTAAATGATTT 60.094 45.455 0.00 0.00 38.44 2.17
4545 4976 3.179048 GGTGTTGCCGCTAAATGATTTC 58.821 45.455 0.00 0.00 0.00 2.17
4546 4977 3.366883 GGTGTTGCCGCTAAATGATTTCA 60.367 43.478 0.00 0.00 0.00 2.69
4547 4978 4.423732 GTGTTGCCGCTAAATGATTTCAT 58.576 39.130 0.00 0.00 38.41 2.57
4548 4979 4.266029 GTGTTGCCGCTAAATGATTTCATG 59.734 41.667 0.00 0.00 36.56 3.07
4549 4980 4.082300 TGTTGCCGCTAAATGATTTCATGT 60.082 37.500 0.00 0.00 36.56 3.21
4550 4981 5.124617 TGTTGCCGCTAAATGATTTCATGTA 59.875 36.000 0.00 0.00 36.56 2.29
4551 4982 5.168526 TGCCGCTAAATGATTTCATGTAC 57.831 39.130 0.00 0.00 36.56 2.90
4552 4983 4.637977 TGCCGCTAAATGATTTCATGTACA 59.362 37.500 0.00 0.00 36.56 2.90
4553 4984 5.124617 TGCCGCTAAATGATTTCATGTACAA 59.875 36.000 0.00 0.00 36.56 2.41
4554 4985 6.183360 TGCCGCTAAATGATTTCATGTACAAT 60.183 34.615 0.00 0.00 36.56 2.71
4555 4986 6.697019 GCCGCTAAATGATTTCATGTACAATT 59.303 34.615 0.00 0.00 36.56 2.32
4556 4987 7.222611 GCCGCTAAATGATTTCATGTACAATTT 59.777 33.333 0.00 2.18 36.56 1.82
4557 4988 8.533965 CCGCTAAATGATTTCATGTACAATTTG 58.466 33.333 0.00 0.00 36.56 2.32
4558 4989 8.051909 CGCTAAATGATTTCATGTACAATTTGC 58.948 33.333 0.00 5.70 36.56 3.68
4559 4990 8.330302 GCTAAATGATTTCATGTACAATTTGCC 58.670 33.333 0.00 0.00 36.56 4.52
4560 4991 9.368674 CTAAATGATTTCATGTACAATTTGCCA 57.631 29.630 0.00 0.00 36.56 4.92
4561 4992 7.599630 AATGATTTCATGTACAATTTGCCAC 57.400 32.000 0.00 0.00 36.56 5.01
4562 4993 6.343716 TGATTTCATGTACAATTTGCCACT 57.656 33.333 0.00 0.00 0.00 4.00
4563 4994 7.459795 TGATTTCATGTACAATTTGCCACTA 57.540 32.000 0.00 0.00 0.00 2.74
4564 4995 8.065473 TGATTTCATGTACAATTTGCCACTAT 57.935 30.769 0.00 0.00 0.00 2.12
4565 4996 9.183368 TGATTTCATGTACAATTTGCCACTATA 57.817 29.630 0.00 0.00 0.00 1.31
4566 4997 9.669353 GATTTCATGTACAATTTGCCACTATAG 57.331 33.333 0.00 0.00 0.00 1.31
4567 4998 6.618287 TCATGTACAATTTGCCACTATAGC 57.382 37.500 0.00 0.00 0.00 2.97
4568 4999 6.356556 TCATGTACAATTTGCCACTATAGCT 58.643 36.000 0.00 0.00 0.00 3.32
4569 5000 6.483307 TCATGTACAATTTGCCACTATAGCTC 59.517 38.462 0.00 0.00 0.00 4.09
4570 5001 5.123227 TGTACAATTTGCCACTATAGCTCC 58.877 41.667 0.00 0.00 0.00 4.70
4571 5002 3.206150 ACAATTTGCCACTATAGCTCCG 58.794 45.455 0.00 0.00 0.00 4.63
4572 5003 1.884235 ATTTGCCACTATAGCTCCGC 58.116 50.000 0.00 0.00 0.00 5.54
4573 5004 0.830648 TTTGCCACTATAGCTCCGCT 59.169 50.000 0.00 0.00 43.41 5.52
4574 5005 1.699730 TTGCCACTATAGCTCCGCTA 58.300 50.000 0.00 0.00 45.55 4.26
4585 5016 3.655615 AGCTCCGCTATAGCCTACTAT 57.344 47.619 19.00 0.00 41.02 2.12
4586 5017 4.774660 AGCTCCGCTATAGCCTACTATA 57.225 45.455 19.00 0.00 41.02 1.31
4594 5025 3.767309 ATAGCCTACTATAGCCCAGCT 57.233 47.619 0.00 6.07 43.41 4.24
4595 5026 4.883021 ATAGCCTACTATAGCCCAGCTA 57.117 45.455 13.54 13.54 45.55 3.32
4614 5045 5.405331 GCTATAGCTGTTTTTAAGGGTCG 57.595 43.478 17.75 0.00 38.21 4.79
4615 5046 4.260661 GCTATAGCTGTTTTTAAGGGTCGC 60.261 45.833 17.75 0.00 38.21 5.19
4616 5047 1.244816 AGCTGTTTTTAAGGGTCGCC 58.755 50.000 0.00 0.00 0.00 5.54
4617 5048 0.109919 GCTGTTTTTAAGGGTCGCCG 60.110 55.000 0.00 0.00 0.00 6.46
4618 5049 0.109919 CTGTTTTTAAGGGTCGCCGC 60.110 55.000 0.00 0.00 0.00 6.53
4619 5050 0.535553 TGTTTTTAAGGGTCGCCGCT 60.536 50.000 0.00 0.00 34.93 5.52
4620 5051 1.270732 TGTTTTTAAGGGTCGCCGCTA 60.271 47.619 0.00 0.00 32.78 4.26
4621 5052 1.805943 GTTTTTAAGGGTCGCCGCTAA 59.194 47.619 0.00 0.00 32.78 3.09
4622 5053 2.181954 TTTTAAGGGTCGCCGCTAAA 57.818 45.000 0.00 0.00 32.78 1.85
4623 5054 2.406596 TTTAAGGGTCGCCGCTAAAT 57.593 45.000 0.00 0.00 32.78 1.40
4624 5055 1.658994 TTAAGGGTCGCCGCTAAATG 58.341 50.000 0.00 0.00 32.78 2.32
4625 5056 0.812412 TAAGGGTCGCCGCTAAATGC 60.812 55.000 0.00 0.00 38.57 3.56
4626 5057 3.583086 GGGTCGCCGCTAAATGCC 61.583 66.667 0.00 0.00 38.78 4.40
4627 5058 2.822255 GGTCGCCGCTAAATGCCA 60.822 61.111 0.00 0.00 38.78 4.92
4628 5059 2.186826 GGTCGCCGCTAAATGCCAT 61.187 57.895 0.00 0.00 38.78 4.40
4629 5060 0.882927 GGTCGCCGCTAAATGCCATA 60.883 55.000 0.00 0.00 38.78 2.74
4630 5061 0.512952 GTCGCCGCTAAATGCCATAG 59.487 55.000 0.00 0.00 38.78 2.23
4631 5062 1.207593 CGCCGCTAAATGCCATAGC 59.792 57.895 3.20 3.20 41.85 2.97
4632 5063 1.581447 GCCGCTAAATGCCATAGCC 59.419 57.895 6.85 0.00 42.18 3.93
4633 5064 1.866853 GCCGCTAAATGCCATAGCCC 61.867 60.000 6.85 0.00 42.18 5.19
4634 5065 1.577328 CCGCTAAATGCCATAGCCCG 61.577 60.000 6.85 0.00 42.18 6.13
4635 5066 1.581447 GCTAAATGCCATAGCCCGC 59.419 57.895 2.08 0.00 39.87 6.13
4636 5067 0.890996 GCTAAATGCCATAGCCCGCT 60.891 55.000 0.00 0.00 39.87 5.52
4637 5068 1.610624 GCTAAATGCCATAGCCCGCTA 60.611 52.381 0.00 0.00 39.87 4.26
4638 5069 2.941415 GCTAAATGCCATAGCCCGCTAT 60.941 50.000 3.31 3.31 39.87 2.97
4639 5070 2.292828 AAATGCCATAGCCCGCTATT 57.707 45.000 6.48 0.00 37.16 1.73
4640 5071 2.292828 AATGCCATAGCCCGCTATTT 57.707 45.000 6.48 0.00 37.16 1.40
4983 5418 2.221169 TCACAACACCATCTCAAGTGC 58.779 47.619 0.00 0.00 37.51 4.40
5043 5478 2.557920 AGGCACTTCAGACTTCAAGG 57.442 50.000 0.00 0.00 27.25 3.61
5153 5590 2.169978 GGGGCTAATGTAACTTCTCCGT 59.830 50.000 0.00 0.00 0.00 4.69
5168 5605 1.180456 TCCGTACAAGTTCCGAGGCA 61.180 55.000 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.446442 AAAGGAAGACAGCATCATGGT 57.554 42.857 0.00 0.00 0.00 3.55
5 6 5.045286 AGGAAGTAAAGGAAGACAGCATCAT 60.045 40.000 0.00 0.00 0.00 2.45
6 7 4.287067 AGGAAGTAAAGGAAGACAGCATCA 59.713 41.667 0.00 0.00 0.00 3.07
7 8 4.837972 AGGAAGTAAAGGAAGACAGCATC 58.162 43.478 0.00 0.00 0.00 3.91
8 9 4.917906 AGGAAGTAAAGGAAGACAGCAT 57.082 40.909 0.00 0.00 0.00 3.79
9 10 4.389374 CAAGGAAGTAAAGGAAGACAGCA 58.611 43.478 0.00 0.00 0.00 4.41
10 11 3.189495 GCAAGGAAGTAAAGGAAGACAGC 59.811 47.826 0.00 0.00 0.00 4.40
11 12 4.214332 GTGCAAGGAAGTAAAGGAAGACAG 59.786 45.833 0.00 0.00 0.00 3.51
12 13 4.134563 GTGCAAGGAAGTAAAGGAAGACA 58.865 43.478 0.00 0.00 0.00 3.41
13 14 3.502595 GGTGCAAGGAAGTAAAGGAAGAC 59.497 47.826 0.00 0.00 0.00 3.01
14 15 3.137544 TGGTGCAAGGAAGTAAAGGAAGA 59.862 43.478 0.00 0.00 0.00 2.87
15 16 3.486383 TGGTGCAAGGAAGTAAAGGAAG 58.514 45.455 0.00 0.00 0.00 3.46
16 17 3.586470 TGGTGCAAGGAAGTAAAGGAA 57.414 42.857 0.00 0.00 0.00 3.36
17 18 3.330701 AGATGGTGCAAGGAAGTAAAGGA 59.669 43.478 0.00 0.00 0.00 3.36
18 19 3.690460 AGATGGTGCAAGGAAGTAAAGG 58.310 45.455 0.00 0.00 0.00 3.11
19 20 5.712152 AAAGATGGTGCAAGGAAGTAAAG 57.288 39.130 0.00 0.00 0.00 1.85
20 21 5.010617 GGAAAAGATGGTGCAAGGAAGTAAA 59.989 40.000 0.00 0.00 0.00 2.01
21 22 4.522789 GGAAAAGATGGTGCAAGGAAGTAA 59.477 41.667 0.00 0.00 0.00 2.24
22 23 4.079253 GGAAAAGATGGTGCAAGGAAGTA 58.921 43.478 0.00 0.00 0.00 2.24
23 24 2.893489 GGAAAAGATGGTGCAAGGAAGT 59.107 45.455 0.00 0.00 0.00 3.01
24 25 3.057033 CAGGAAAAGATGGTGCAAGGAAG 60.057 47.826 0.00 0.00 0.00 3.46
25 26 2.892852 CAGGAAAAGATGGTGCAAGGAA 59.107 45.455 0.00 0.00 0.00 3.36
26 27 2.517959 CAGGAAAAGATGGTGCAAGGA 58.482 47.619 0.00 0.00 0.00 3.36
27 28 1.067354 GCAGGAAAAGATGGTGCAAGG 60.067 52.381 0.00 0.00 34.18 3.61
28 29 1.614903 TGCAGGAAAAGATGGTGCAAG 59.385 47.619 0.00 0.00 41.05 4.01
29 30 1.702182 TGCAGGAAAAGATGGTGCAA 58.298 45.000 0.00 0.00 41.05 4.08
30 31 3.435846 TGCAGGAAAAGATGGTGCA 57.564 47.368 0.00 0.00 41.72 4.57
31 32 1.738030 GCATGCAGGAAAAGATGGTGC 60.738 52.381 14.21 0.00 34.62 5.01
34 35 0.462789 GGGCATGCAGGAAAAGATGG 59.537 55.000 21.36 0.00 0.00 3.51
68 69 3.058160 CAACGGCAAGAGCAGGGG 61.058 66.667 0.00 0.00 44.61 4.79
95 96 2.507992 CGCTGCAGGAGACGGAAG 60.508 66.667 17.12 0.00 33.70 3.46
120 121 5.503002 GGACTTATTACAACTTTGGGGCTA 58.497 41.667 0.00 0.00 0.00 3.93
195 196 7.292713 TCATATGCTCCATGTAATTGCAATT 57.707 32.000 26.72 26.72 37.20 2.32
291 292 4.323409 GCTTCTGGTTTCTGAAGAGAGGAT 60.323 45.833 14.30 0.00 45.80 3.24
311 312 3.508845 ACCTTGTGTTGTATCCTGCTT 57.491 42.857 0.00 0.00 0.00 3.91
348 349 6.798959 GCACAAATACAAAAGAGCAACTCTAG 59.201 38.462 0.00 0.00 40.28 2.43
415 416 3.305335 GGATTGCGGAACATGTGTTTTCT 60.305 43.478 0.00 0.00 38.56 2.52
599 654 6.539826 CAGTGTTAGATACATCCATTTGAGCA 59.460 38.462 0.00 0.00 39.39 4.26
618 673 8.948145 GGATGTATCTAGACGTATATCAGTGTT 58.052 37.037 10.50 0.00 0.00 3.32
619 674 7.278203 CGGATGTATCTAGACGTATATCAGTGT 59.722 40.741 10.50 0.00 0.00 3.55
620 675 7.278203 ACGGATGTATCTAGACGTATATCAGTG 59.722 40.741 12.02 5.55 30.34 3.66
621 676 7.329499 ACGGATGTATCTAGACGTATATCAGT 58.671 38.462 10.50 9.67 32.30 3.41
622 677 7.773864 ACGGATGTATCTAGACGTATATCAG 57.226 40.000 10.50 9.21 32.30 2.90
623 678 8.448615 CAAACGGATGTATCTAGACGTATATCA 58.551 37.037 10.50 0.00 33.85 2.15
624 679 8.663025 TCAAACGGATGTATCTAGACGTATATC 58.337 37.037 0.00 0.00 33.85 1.63
625 680 8.557592 TCAAACGGATGTATCTAGACGTATAT 57.442 34.615 0.00 0.00 33.85 0.86
626 681 7.360691 GCTCAAACGGATGTATCTAGACGTATA 60.361 40.741 0.00 0.00 33.85 1.47
627 682 6.568081 GCTCAAACGGATGTATCTAGACGTAT 60.568 42.308 0.00 0.00 33.85 3.06
628 683 5.277683 GCTCAAACGGATGTATCTAGACGTA 60.278 44.000 0.00 0.00 33.85 3.57
629 684 4.497674 GCTCAAACGGATGTATCTAGACGT 60.498 45.833 0.00 0.00 35.95 4.34
630 685 3.975670 GCTCAAACGGATGTATCTAGACG 59.024 47.826 0.00 0.00 0.00 4.18
631 686 3.975670 CGCTCAAACGGATGTATCTAGAC 59.024 47.826 0.00 0.00 0.00 2.59
632 687 3.630769 ACGCTCAAACGGATGTATCTAGA 59.369 43.478 0.00 0.00 37.37 2.43
633 688 3.966154 ACGCTCAAACGGATGTATCTAG 58.034 45.455 0.00 0.00 37.37 2.43
634 689 3.379057 TGACGCTCAAACGGATGTATCTA 59.621 43.478 0.00 0.00 37.37 1.98
635 690 2.165641 TGACGCTCAAACGGATGTATCT 59.834 45.455 0.00 0.00 37.37 1.98
711 793 6.360370 TCTAATAAAGTCAGACCTTGTGCT 57.640 37.500 0.00 0.00 0.00 4.40
712 794 7.435068 TTTCTAATAAAGTCAGACCTTGTGC 57.565 36.000 0.00 0.00 0.00 4.57
713 795 9.831737 CATTTTCTAATAAAGTCAGACCTTGTG 57.168 33.333 0.00 0.00 0.00 3.33
714 796 9.793259 TCATTTTCTAATAAAGTCAGACCTTGT 57.207 29.630 0.00 0.00 0.00 3.16
734 816 5.010617 ACCCTCGTGCTTAAACATTCATTTT 59.989 36.000 0.00 0.00 0.00 1.82
1035 1351 0.250038 CCCATGCCGACTGGAGTATG 60.250 60.000 0.00 0.00 37.49 2.39
1036 1352 2.044806 GCCCATGCCGACTGGAGTAT 62.045 60.000 0.00 0.00 37.49 2.12
1134 1456 1.200020 GTAGTTGTGTTCCATGCAGCC 59.800 52.381 0.00 0.00 0.00 4.85
1198 1529 4.278956 CACCGTAACCCTGTGCTC 57.721 61.111 0.00 0.00 0.00 4.26
1236 1567 2.156098 GGTGTTATTGTTCCGGCAAGA 58.844 47.619 0.00 0.00 0.00 3.02
1327 1658 4.268405 CCGAAATAAACAGCCAATTGATGC 59.732 41.667 7.12 2.46 0.00 3.91
1383 1714 3.133362 TGTCCGGGTTTACATCACTATCC 59.867 47.826 0.00 0.00 0.00 2.59
1510 1847 5.308497 TCCCAGTGAAGTTGTTCCTATACAA 59.692 40.000 0.00 0.00 35.75 2.41
1581 1918 0.041312 CGAGTTGGTTTGCGGTGAAG 60.041 55.000 0.00 0.00 0.00 3.02
1772 2109 1.635487 CCCTGAGATTTGGGAGGTGAA 59.365 52.381 0.00 0.00 46.15 3.18
1793 2130 0.625849 ATTGGTGCCAAGGAGTAGGG 59.374 55.000 9.65 0.00 39.47 3.53
1974 2311 1.625818 GTCATGAACTCCCAGTCCTGT 59.374 52.381 0.00 0.00 0.00 4.00
2035 2372 2.019156 GCCACCTAGCATGTTTCCCTC 61.019 57.143 0.00 0.00 0.00 4.30
2263 2600 3.524095 TGGAATGAACCCTGTCAACAT 57.476 42.857 0.00 0.00 0.00 2.71
2598 2935 3.949113 GGTCCAACAAGAGTGTTACCAAA 59.051 43.478 6.65 0.00 46.47 3.28
2724 3061 2.575921 TCCCTCCCATGAGTCTGAAT 57.424 50.000 0.00 0.00 36.86 2.57
2728 3065 2.575921 TGAATCCCTCCCATGAGTCT 57.424 50.000 0.00 0.00 36.86 3.24
2854 3191 0.321653 ACACCCTGCGATGGAACTTC 60.322 55.000 0.00 0.00 0.00 3.01
2957 3294 2.557924 GTGTGTTCCATTGATTCTGGCA 59.442 45.455 0.00 0.00 33.56 4.92
3095 3441 4.132122 AGTTGAAATCCTCCCATGGTTT 57.868 40.909 11.73 3.82 0.00 3.27
3630 3987 2.700773 GCCGAAGTCCCCAATGTGC 61.701 63.158 0.00 0.00 0.00 4.57
3771 4132 5.593183 TGCATGCAAAAATGTATGTTGTG 57.407 34.783 20.30 0.00 34.95 3.33
3772 4133 6.615264 TTTGCATGCAAAAATGTATGTTGT 57.385 29.167 36.92 0.00 42.16 3.32
4001 4400 4.985538 TGGCTTCTTCAATGGAAAGTAGT 58.014 39.130 0.00 0.00 31.35 2.73
4115 4541 0.325933 TCCTCTCTGTTGGTGCATGG 59.674 55.000 0.00 0.00 0.00 3.66
4475 4906 5.359860 AGCCGGCTATTTAAAACTATGCTTT 59.640 36.000 31.86 0.00 0.00 3.51
4476 4907 4.887655 AGCCGGCTATTTAAAACTATGCTT 59.112 37.500 31.86 0.00 0.00 3.91
4477 4908 4.461198 AGCCGGCTATTTAAAACTATGCT 58.539 39.130 31.86 0.00 0.00 3.79
4478 4909 4.830826 AGCCGGCTATTTAAAACTATGC 57.169 40.909 31.86 0.00 0.00 3.14
4479 4910 7.685594 GCTATAGCCGGCTATTTAAAACTATG 58.314 38.462 44.65 24.19 39.65 2.23
4480 4911 7.845066 GCTATAGCCGGCTATTTAAAACTAT 57.155 36.000 44.65 26.21 39.65 2.12
4501 4932 1.070134 CAAACAGCTATAGCGGGGCTA 59.930 52.381 25.55 0.00 45.55 3.93
4508 4939 3.268023 ACACCCTCAAACAGCTATAGC 57.732 47.619 17.33 17.33 42.49 2.97
4509 4940 3.375299 GCAACACCCTCAAACAGCTATAG 59.625 47.826 0.00 0.00 0.00 1.31
4510 4941 3.343617 GCAACACCCTCAAACAGCTATA 58.656 45.455 0.00 0.00 0.00 1.31
4511 4942 2.162681 GCAACACCCTCAAACAGCTAT 58.837 47.619 0.00 0.00 0.00 2.97
4512 4943 1.604604 GCAACACCCTCAAACAGCTA 58.395 50.000 0.00 0.00 0.00 3.32
4513 4944 1.109323 GGCAACACCCTCAAACAGCT 61.109 55.000 0.00 0.00 0.00 4.24
4514 4945 1.363807 GGCAACACCCTCAAACAGC 59.636 57.895 0.00 0.00 0.00 4.40
4515 4946 1.654220 CGGCAACACCCTCAAACAG 59.346 57.895 0.00 0.00 33.26 3.16
4516 4947 2.485795 GCGGCAACACCCTCAAACA 61.486 57.895 0.00 0.00 33.26 2.83
4517 4948 0.887387 TAGCGGCAACACCCTCAAAC 60.887 55.000 1.45 0.00 33.26 2.93
4518 4949 0.179015 TTAGCGGCAACACCCTCAAA 60.179 50.000 1.45 0.00 33.26 2.69
4519 4950 0.179015 TTTAGCGGCAACACCCTCAA 60.179 50.000 1.45 0.00 33.26 3.02
4520 4951 0.037590 ATTTAGCGGCAACACCCTCA 59.962 50.000 1.45 0.00 33.26 3.86
4521 4952 0.451783 CATTTAGCGGCAACACCCTC 59.548 55.000 1.45 0.00 33.26 4.30
4522 4953 0.037590 TCATTTAGCGGCAACACCCT 59.962 50.000 1.45 0.00 33.26 4.34
4523 4954 1.102978 ATCATTTAGCGGCAACACCC 58.897 50.000 1.45 0.00 33.26 4.61
4524 4955 2.939460 AATCATTTAGCGGCAACACC 57.061 45.000 1.45 0.00 0.00 4.16
4525 4956 3.832276 TGAAATCATTTAGCGGCAACAC 58.168 40.909 1.45 0.00 0.00 3.32
4526 4957 4.082300 ACATGAAATCATTTAGCGGCAACA 60.082 37.500 0.00 0.00 33.61 3.33
4527 4958 4.423732 ACATGAAATCATTTAGCGGCAAC 58.576 39.130 0.00 0.00 33.61 4.17
4528 4959 4.717233 ACATGAAATCATTTAGCGGCAA 57.283 36.364 0.00 0.00 33.61 4.52
4529 4960 4.637977 TGTACATGAAATCATTTAGCGGCA 59.362 37.500 0.00 0.00 33.61 5.69
4530 4961 5.168526 TGTACATGAAATCATTTAGCGGC 57.831 39.130 0.00 0.00 33.61 6.53
4531 4962 8.533965 CAAATTGTACATGAAATCATTTAGCGG 58.466 33.333 0.00 0.00 33.61 5.52
4532 4963 8.051909 GCAAATTGTACATGAAATCATTTAGCG 58.948 33.333 0.00 0.00 33.61 4.26
4533 4964 8.330302 GGCAAATTGTACATGAAATCATTTAGC 58.670 33.333 0.00 4.99 33.61 3.09
4534 4965 9.368674 TGGCAAATTGTACATGAAATCATTTAG 57.631 29.630 0.00 0.00 33.61 1.85
4535 4966 9.149225 GTGGCAAATTGTACATGAAATCATTTA 57.851 29.630 0.00 0.00 33.61 1.40
4536 4967 7.879160 AGTGGCAAATTGTACATGAAATCATTT 59.121 29.630 0.00 0.00 33.61 2.32
4537 4968 7.388437 AGTGGCAAATTGTACATGAAATCATT 58.612 30.769 0.00 0.00 33.61 2.57
4538 4969 6.938507 AGTGGCAAATTGTACATGAAATCAT 58.061 32.000 0.00 0.00 36.96 2.45
4539 4970 6.343716 AGTGGCAAATTGTACATGAAATCA 57.656 33.333 0.00 0.00 0.00 2.57
4540 4971 9.669353 CTATAGTGGCAAATTGTACATGAAATC 57.331 33.333 0.00 0.00 0.00 2.17
4541 4972 8.137437 GCTATAGTGGCAAATTGTACATGAAAT 58.863 33.333 0.00 0.00 0.00 2.17
4542 4973 7.339212 AGCTATAGTGGCAAATTGTACATGAAA 59.661 33.333 0.00 0.00 0.00 2.69
4543 4974 6.828273 AGCTATAGTGGCAAATTGTACATGAA 59.172 34.615 0.00 0.00 0.00 2.57
4544 4975 6.356556 AGCTATAGTGGCAAATTGTACATGA 58.643 36.000 0.00 0.00 0.00 3.07
4545 4976 6.293626 GGAGCTATAGTGGCAAATTGTACATG 60.294 42.308 0.00 0.00 0.00 3.21
4546 4977 5.765182 GGAGCTATAGTGGCAAATTGTACAT 59.235 40.000 0.00 0.00 0.00 2.29
4547 4978 5.123227 GGAGCTATAGTGGCAAATTGTACA 58.877 41.667 0.84 0.00 0.00 2.90
4548 4979 4.211374 CGGAGCTATAGTGGCAAATTGTAC 59.789 45.833 0.84 0.00 0.00 2.90
4549 4980 4.377021 CGGAGCTATAGTGGCAAATTGTA 58.623 43.478 0.84 0.00 0.00 2.41
4550 4981 3.206150 CGGAGCTATAGTGGCAAATTGT 58.794 45.455 0.84 0.00 0.00 2.71
4551 4982 3.885484 CGGAGCTATAGTGGCAAATTG 57.115 47.619 0.84 0.00 0.00 2.32
4592 5023 4.260661 GCGACCCTTAAAAACAGCTATAGC 60.261 45.833 17.33 17.33 42.49 2.97
4593 5024 4.272748 GGCGACCCTTAAAAACAGCTATAG 59.727 45.833 0.00 0.00 0.00 1.31
4594 5025 4.193865 GGCGACCCTTAAAAACAGCTATA 58.806 43.478 0.00 0.00 0.00 1.31
4595 5026 3.014623 GGCGACCCTTAAAAACAGCTAT 58.985 45.455 0.00 0.00 0.00 2.97
4596 5027 2.429478 GGCGACCCTTAAAAACAGCTA 58.571 47.619 0.00 0.00 0.00 3.32
4597 5028 1.244816 GGCGACCCTTAAAAACAGCT 58.755 50.000 0.00 0.00 0.00 4.24
4598 5029 0.109919 CGGCGACCCTTAAAAACAGC 60.110 55.000 0.00 0.00 0.00 4.40
4599 5030 0.109919 GCGGCGACCCTTAAAAACAG 60.110 55.000 12.98 0.00 0.00 3.16
4600 5031 0.535553 AGCGGCGACCCTTAAAAACA 60.536 50.000 12.98 0.00 0.00 2.83
4601 5032 1.441738 TAGCGGCGACCCTTAAAAAC 58.558 50.000 12.98 0.00 0.00 2.43
4602 5033 2.181954 TTAGCGGCGACCCTTAAAAA 57.818 45.000 12.98 0.00 0.00 1.94
4603 5034 2.181954 TTTAGCGGCGACCCTTAAAA 57.818 45.000 12.98 0.00 0.00 1.52
4604 5035 2.011222 CATTTAGCGGCGACCCTTAAA 58.989 47.619 12.98 7.21 0.00 1.52
4605 5036 1.658994 CATTTAGCGGCGACCCTTAA 58.341 50.000 12.98 0.00 0.00 1.85
4606 5037 0.812412 GCATTTAGCGGCGACCCTTA 60.812 55.000 12.98 0.00 0.00 2.69
4607 5038 2.112815 GCATTTAGCGGCGACCCTT 61.113 57.895 12.98 0.00 0.00 3.95
4608 5039 2.513897 GCATTTAGCGGCGACCCT 60.514 61.111 12.98 0.00 0.00 4.34
4617 5048 0.890996 AGCGGGCTATGGCATTTAGC 60.891 55.000 12.79 12.79 41.08 3.09
4618 5049 2.472695 TAGCGGGCTATGGCATTTAG 57.527 50.000 4.78 0.00 40.87 1.85
4619 5050 3.433306 AATAGCGGGCTATGGCATTTA 57.567 42.857 13.53 0.00 39.03 1.40
4620 5051 2.292828 AATAGCGGGCTATGGCATTT 57.707 45.000 13.53 0.00 39.03 2.32
4621 5052 2.292828 AAATAGCGGGCTATGGCATT 57.707 45.000 13.53 2.26 39.03 3.56
4622 5053 3.433306 TTAAATAGCGGGCTATGGCAT 57.567 42.857 13.53 4.88 39.03 4.40
4623 5054 2.940994 TTAAATAGCGGGCTATGGCA 57.059 45.000 13.53 0.00 39.03 4.92
4624 5055 3.408634 TCTTTAAATAGCGGGCTATGGC 58.591 45.455 13.53 0.00 39.03 4.40
4625 5056 4.642429 ACTCTTTAAATAGCGGGCTATGG 58.358 43.478 13.53 3.62 39.03 2.74
4626 5057 5.527582 ACAACTCTTTAAATAGCGGGCTATG 59.472 40.000 13.53 1.90 39.03 2.23
4627 5058 5.527582 CACAACTCTTTAAATAGCGGGCTAT 59.472 40.000 7.36 7.36 40.63 2.97
4628 5059 4.873827 CACAACTCTTTAAATAGCGGGCTA 59.126 41.667 2.42 2.42 0.00 3.93
4629 5060 3.689649 CACAACTCTTTAAATAGCGGGCT 59.310 43.478 0.00 0.00 0.00 5.19
4630 5061 3.439129 ACACAACTCTTTAAATAGCGGGC 59.561 43.478 0.74 0.00 0.00 6.13
4631 5062 6.730960 TTACACAACTCTTTAAATAGCGGG 57.269 37.500 0.74 0.00 0.00 6.13
4632 5063 7.696453 CCATTTACACAACTCTTTAAATAGCGG 59.304 37.037 0.74 0.00 0.00 5.52
4633 5064 8.447833 TCCATTTACACAACTCTTTAAATAGCG 58.552 33.333 0.74 0.00 0.00 4.26
4637 5068 8.088365 GCCTTCCATTTACACAACTCTTTAAAT 58.912 33.333 0.00 0.00 0.00 1.40
4638 5069 7.430441 GCCTTCCATTTACACAACTCTTTAAA 58.570 34.615 0.00 0.00 0.00 1.52
4639 5070 6.293735 CGCCTTCCATTTACACAACTCTTTAA 60.294 38.462 0.00 0.00 0.00 1.52
4640 5071 5.180492 CGCCTTCCATTTACACAACTCTTTA 59.820 40.000 0.00 0.00 0.00 1.85
4878 5310 6.430007 AGAAGATATGCATATTGAATCCCCC 58.570 40.000 20.00 4.62 0.00 5.40
4983 5418 1.746615 CCGGACCAGACTGGCATTG 60.747 63.158 21.95 8.84 42.67 2.82
5043 5478 1.173913 GTGCATGTGGGGTTCCTAAC 58.826 55.000 0.00 0.00 0.00 2.34
5098 5535 6.768861 ACGTTGGAAAATAATCCCGAATATGA 59.231 34.615 0.00 0.00 38.82 2.15
5153 5590 3.270027 CATGAATGCCTCGGAACTTGTA 58.730 45.455 0.00 0.00 0.00 2.41
5168 5605 3.711863 AGGGTGTTGCATAACCATGAAT 58.288 40.909 17.48 0.00 38.27 2.57


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

AutoCloner maintained by Alex Coulton.