Multiple sequence alignment - TraesCS2B01G447400

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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 TraesCS2B01G447400 chr2B 100.000 5125 0 0 787 5911 640334477 640339601 0.000000e+00 9465.0
1 TraesCS2B01G447400 chr2B 100.000 2095 0 0 6132 8226 640339822 640341916 0.000000e+00 3869.0
2 TraesCS2B01G447400 chr2B 100.000 332 0 0 1 332 640333691 640334022 1.520000e-171 614.0
3 TraesCS2B01G447400 chr2B 92.157 51 2 2 4251 4299 308719676 308719726 4.120000e-08 71.3
4 TraesCS2B01G447400 chr2D 97.495 3912 57 14 2013 5911 537502315 537506198 0.000000e+00 6643.0
5 TraesCS2B01G447400 chr2D 94.050 1563 55 7 6132 7672 537506228 537507774 0.000000e+00 2337.0
6 TraesCS2B01G447400 chr2D 93.484 1243 56 9 787 2011 537501116 537502351 0.000000e+00 1823.0
7 TraesCS2B01G447400 chr2D 86.957 276 26 7 62 332 537500812 537501082 1.340000e-77 302.0
8 TraesCS2B01G447400 chr2D 92.381 105 5 2 7920 8022 537510193 537510296 6.650000e-31 147.0
9 TraesCS2B01G447400 chr2D 96.970 66 2 0 4303 4368 30487678 30487613 2.430000e-20 111.0
10 TraesCS2B01G447400 chr2D 88.235 85 7 1 2233 2314 537502605 537502689 1.890000e-16 99.0
11 TraesCS2B01G447400 chr2D 96.154 52 2 0 7729 7780 537507939 537507990 1.470000e-12 86.1
12 TraesCS2B01G447400 chr2D 92.157 51 2 2 4251 4299 268894282 268894332 4.120000e-08 71.3
13 TraesCS2B01G447400 chr2A 96.982 2220 48 7 2092 4299 680078523 680080735 0.000000e+00 3711.0
14 TraesCS2B01G447400 chr2A 98.664 1572 18 2 4303 5871 680080794 680082365 0.000000e+00 2784.0
15 TraesCS2B01G447400 chr2A 94.882 1563 55 10 6132 7672 680082488 680084047 0.000000e+00 2420.0
16 TraesCS2B01G447400 chr2A 87.855 1268 88 27 787 2011 680077251 680078495 0.000000e+00 1428.0
17 TraesCS2B01G447400 chr2A 91.443 409 28 4 7675 8078 680084172 680084578 9.330000e-154 555.0
18 TraesCS2B01G447400 chr2A 90.323 124 10 2 8094 8217 680085059 680085180 2.380000e-35 161.0
19 TraesCS2B01G447400 chr2A 88.235 85 7 1 2233 2314 680078748 680078832 1.890000e-16 99.0
20 TraesCS2B01G447400 chr7B 80.984 894 114 30 1157 2012 150928742 150929617 0.000000e+00 658.0
21 TraesCS2B01G447400 chr7B 80.403 893 119 33 1157 2012 439679764 439678891 5.420000e-176 628.0
22 TraesCS2B01G447400 chr7B 92.105 76 4 2 4303 4378 78066907 78066834 1.130000e-18 106.0
23 TraesCS2B01G447400 chr7B 93.151 73 3 2 4303 4373 536117647 536117575 1.130000e-18 106.0
24 TraesCS2B01G447400 chr7B 100.000 33 0 0 2013 2045 150929581 150929613 2.480000e-05 62.1
25 TraesCS2B01G447400 chr7B 97.222 36 1 0 2013 2048 439678927 439678892 2.480000e-05 62.1
26 TraesCS2B01G447400 chr7D 80.670 895 115 33 1157 2012 182511976 182512851 6.960000e-180 641.0
27 TraesCS2B01G447400 chr7D 100.000 33 0 0 2013 2045 182512815 182512847 2.480000e-05 62.1
28 TraesCS2B01G447400 chr3D 80.543 884 106 33 1157 2012 598301349 598300504 3.260000e-173 619.0
29 TraesCS2B01G447400 chr3D 97.222 36 1 0 2013 2048 598300540 598300505 2.480000e-05 62.1
30 TraesCS2B01G447400 chr1A 84.472 483 50 15 1553 2012 534953168 534952688 3.500000e-123 453.0
31 TraesCS2B01G447400 chr1A 83.707 491 47 18 1553 2012 504260827 504260339 4.560000e-117 433.0
32 TraesCS2B01G447400 chr1A 77.572 593 52 22 936 1502 534954763 534954226 4.860000e-72 283.0
33 TraesCS2B01G447400 chr1A 77.066 593 55 22 936 1502 504262421 504261884 4.890000e-67 267.0
34 TraesCS2B01G447400 chr1A 97.727 44 0 1 4256 4299 202099443 202099401 3.180000e-09 75.0
35 TraesCS2B01G447400 chr6D 83.898 472 65 8 1550 2012 454447255 454447724 2.730000e-119 440.0
36 TraesCS2B01G447400 chr6D 85.441 261 32 1 4939 5199 58460485 58460231 4.890000e-67 267.0
37 TraesCS2B01G447400 chr3A 83.673 490 51 16 1550 2012 503847135 503847622 1.270000e-117 435.0
38 TraesCS2B01G447400 chr3A 77.441 594 53 23 936 1503 503845543 503846081 6.290000e-71 279.0
39 TraesCS2B01G447400 chr3A 80.980 347 45 12 1157 1502 728414646 728414320 1.060000e-63 255.0
40 TraesCS2B01G447400 chr3A 95.833 48 0 2 4254 4299 256240012 256240059 8.850000e-10 76.8
41 TraesCS2B01G447400 chr3A 92.000 50 4 0 4250 4299 291804382 291804431 4.120000e-08 71.3
42 TraesCS2B01G447400 chr6B 82.540 315 42 6 4940 5253 131930725 131930423 1.760000e-66 265.0
43 TraesCS2B01G447400 chr6A 79.693 261 34 8 4939 5199 73681009 73680768 3.950000e-38 171.0
44 TraesCS2B01G447400 chr5B 90.678 118 11 0 1169 1286 356196475 356196592 3.070000e-34 158.0
45 TraesCS2B01G447400 chr5B 92.105 76 4 2 4303 4378 419853003 419853076 1.130000e-18 106.0
46 TraesCS2B01G447400 chr1D 94.366 71 2 2 4303 4371 60409667 60409597 3.140000e-19 108.0
47 TraesCS2B01G447400 chr4A 92.208 77 2 4 4303 4378 420020433 420020360 1.130000e-18 106.0
48 TraesCS2B01G447400 chr7A 92.000 75 5 1 4307 4381 733338474 733338547 4.060000e-18 104.0
49 TraesCS2B01G447400 chr1B 86.458 96 5 7 4303 4394 510207371 510207462 1.890000e-16 99.0
50 TraesCS2B01G447400 chr3B 95.833 48 0 2 4254 4299 352239651 352239698 8.850000e-10 76.8
51 TraesCS2B01G447400 chr5A 93.878 49 2 1 4251 4299 363848603 363848650 1.150000e-08 73.1


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 TraesCS2B01G447400 chr2B 640333691 640341916 8225 False 4649.333333 9465 100.000000 1 8226 3 chr2B.!!$F2 8225
1 TraesCS2B01G447400 chr2D 537500812 537510296 9484 False 1633.871429 6643 92.679429 62 8022 7 chr2D.!!$F2 7960
2 TraesCS2B01G447400 chr2A 680077251 680085180 7929 False 1594.000000 3711 92.626286 787 8217 7 chr2A.!!$F1 7430
3 TraesCS2B01G447400 chr7B 150928742 150929617 875 False 360.050000 658 90.492000 1157 2045 2 chr7B.!!$F1 888
4 TraesCS2B01G447400 chr7B 439678891 439679764 873 True 345.050000 628 88.812500 1157 2048 2 chr7B.!!$R3 891
5 TraesCS2B01G447400 chr7D 182511976 182512851 875 False 351.550000 641 90.335000 1157 2045 2 chr7D.!!$F1 888
6 TraesCS2B01G447400 chr3D 598300504 598301349 845 True 340.550000 619 88.882500 1157 2048 2 chr3D.!!$R1 891
7 TraesCS2B01G447400 chr1A 534952688 534954763 2075 True 368.000000 453 81.022000 936 2012 2 chr1A.!!$R3 1076
8 TraesCS2B01G447400 chr1A 504260339 504262421 2082 True 350.000000 433 80.386500 936 2012 2 chr1A.!!$R2 1076
9 TraesCS2B01G447400 chr3A 503845543 503847622 2079 False 357.000000 435 80.557000 936 2012 2 chr3A.!!$F3 1076

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
34 35 0.041535 TTACAAGCGGGGTCCTCCTA 59.958 55.000 0.00 0.00 35.33 2.94 F
35 36 0.263765 TACAAGCGGGGTCCTCCTAT 59.736 55.000 0.00 0.00 35.33 2.57 F
36 37 0.263765 ACAAGCGGGGTCCTCCTATA 59.736 55.000 0.00 0.00 35.33 1.31 F
857 866 0.321671 TTTTGACGCTCTCCCCTCTG 59.678 55.000 0.00 0.00 0.00 3.35 F
1365 1447 0.609406 GCCTGTTTTCCCTCCTGGTC 60.609 60.000 0.00 0.00 34.77 4.02 F
1435 1517 0.815213 CGCCCGTGGAATGATGTCAT 60.815 55.000 0.00 0.00 38.41 3.06 F
1838 2948 1.202533 TGCTACTAATCTTGCCGGAGC 60.203 52.381 5.05 0.57 40.48 4.70 F
1924 3053 1.466186 AGAAACCCCTTCCAGCCCT 60.466 57.895 0.00 0.00 34.21 5.19 F
2044 3173 2.108250 ACCTTGTCCAATGCAAGTACCT 59.892 45.455 0.00 0.00 41.08 3.08 F
4301 5444 1.464997 CGGTAAAGCTGTTGCCTTCTC 59.535 52.381 11.70 0.00 40.80 2.87 F
5167 6368 0.475906 ACTGGTTTCTGCTGGCTTCT 59.524 50.000 0.00 0.00 0.00 2.85 F
6375 7597 1.152546 AGGCTTGCTCCGGGTTTTT 60.153 52.632 0.00 0.00 0.00 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1364 1446 0.234625 GCACACGCAATCAAACGAGA 59.765 50.000 0.00 0.0 38.36 4.04 R
1922 3051 0.250553 TCGCTTTAACCACCCACAGG 60.251 55.000 0.00 0.0 40.04 4.00 R
1924 3053 0.759959 TCTCGCTTTAACCACCCACA 59.240 50.000 0.00 0.0 0.00 4.17 R
2556 3687 0.396435 ACTGTCTCCAATGCGGTTGA 59.604 50.000 3.45 0.0 40.37 3.18 R
2995 4126 1.879380 TGTCCTGCCAAAATCGAACTG 59.121 47.619 0.00 0.0 0.00 3.16 R
3397 4529 0.820226 TGACATCCTCTTCTCAGGCG 59.180 55.000 0.00 0.0 32.91 5.52 R
3694 4828 6.656945 GCAGACAGCACTATTCAATGATAAG 58.343 40.000 0.00 0.0 44.79 1.73 R
4220 5363 4.624336 TTGTCTCAAAGTTAAAGCGCAA 57.376 36.364 11.47 0.0 0.00 4.85 R
4552 5753 8.524870 AACATCATCTGCATAAAGTTCAAAAC 57.475 30.769 0.00 0.0 0.00 2.43 R
6632 7855 2.582728 AGCAAGCTCTCAGAATCTCG 57.417 50.000 0.00 0.0 0.00 4.04 R
6892 8115 0.386113 GAGGGGCATCGAGTGAGTAC 59.614 60.000 0.00 0.0 0.00 2.73 R
8088 11505 0.393537 CAGGACAATGACTCCCAGCC 60.394 60.000 0.00 0.0 0.00 4.85 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 2.067414 TTATCACGCGTGCACTTACA 57.933 45.000 33.63 15.71 0.00 2.41
20 21 2.067414 TATCACGCGTGCACTTACAA 57.933 45.000 33.63 14.92 0.00 2.41
21 22 0.790207 ATCACGCGTGCACTTACAAG 59.210 50.000 33.63 6.98 0.00 3.16
22 23 1.438710 CACGCGTGCACTTACAAGC 60.439 57.895 28.16 8.68 40.98 4.01
24 25 2.173382 GCGTGCACTTACAAGCGG 59.827 61.111 16.19 0.00 35.41 5.52
25 26 2.860293 CGTGCACTTACAAGCGGG 59.140 61.111 16.19 0.00 0.00 6.13
26 27 2.677003 CGTGCACTTACAAGCGGGG 61.677 63.158 16.19 0.00 0.00 5.73
27 28 1.599797 GTGCACTTACAAGCGGGGT 60.600 57.895 10.32 0.00 0.00 4.95
28 29 1.302192 TGCACTTACAAGCGGGGTC 60.302 57.895 0.00 0.00 0.00 4.46
29 30 2.038837 GCACTTACAAGCGGGGTCC 61.039 63.158 0.00 0.00 0.00 4.46
30 31 1.677552 CACTTACAAGCGGGGTCCT 59.322 57.895 0.00 0.00 0.00 3.85
31 32 0.391263 CACTTACAAGCGGGGTCCTC 60.391 60.000 0.00 0.00 0.00 3.71
32 33 1.221021 CTTACAAGCGGGGTCCTCC 59.779 63.158 0.00 0.00 0.00 4.30
33 34 1.229400 TTACAAGCGGGGTCCTCCT 60.229 57.895 0.00 0.00 35.33 3.69
34 35 0.041535 TTACAAGCGGGGTCCTCCTA 59.958 55.000 0.00 0.00 35.33 2.94
35 36 0.263765 TACAAGCGGGGTCCTCCTAT 59.736 55.000 0.00 0.00 35.33 2.57
36 37 0.263765 ACAAGCGGGGTCCTCCTATA 59.736 55.000 0.00 0.00 35.33 1.31
37 38 1.343681 ACAAGCGGGGTCCTCCTATAA 60.344 52.381 0.00 0.00 35.33 0.98
38 39 1.766496 CAAGCGGGGTCCTCCTATAAA 59.234 52.381 0.00 0.00 35.33 1.40
39 40 2.171870 CAAGCGGGGTCCTCCTATAAAA 59.828 50.000 0.00 0.00 35.33 1.52
40 41 2.484602 AGCGGGGTCCTCCTATAAAAA 58.515 47.619 0.00 0.00 35.33 1.94
41 42 3.053826 AGCGGGGTCCTCCTATAAAAAT 58.946 45.455 0.00 0.00 35.33 1.82
42 43 3.072622 AGCGGGGTCCTCCTATAAAAATC 59.927 47.826 0.00 0.00 35.33 2.17
43 44 3.181448 GCGGGGTCCTCCTATAAAAATCA 60.181 47.826 0.00 0.00 35.33 2.57
44 45 4.687769 GCGGGGTCCTCCTATAAAAATCAA 60.688 45.833 0.00 0.00 35.33 2.57
45 46 5.442391 CGGGGTCCTCCTATAAAAATCAAA 58.558 41.667 0.00 0.00 35.33 2.69
46 47 6.068670 CGGGGTCCTCCTATAAAAATCAAAT 58.931 40.000 0.00 0.00 35.33 2.32
47 48 6.206829 CGGGGTCCTCCTATAAAAATCAAATC 59.793 42.308 0.00 0.00 35.33 2.17
48 49 7.066781 GGGGTCCTCCTATAAAAATCAAATCA 58.933 38.462 0.00 0.00 35.33 2.57
49 50 7.563556 GGGGTCCTCCTATAAAAATCAAATCAA 59.436 37.037 0.00 0.00 35.33 2.57
50 51 8.414003 GGGTCCTCCTATAAAAATCAAATCAAC 58.586 37.037 0.00 0.00 0.00 3.18
51 52 8.966868 GGTCCTCCTATAAAAATCAAATCAACA 58.033 33.333 0.00 0.00 0.00 3.33
60 61 9.787532 ATAAAAATCAAATCAACATACCTGACG 57.212 29.630 0.00 0.00 0.00 4.35
83 84 2.837591 TGGATTAGACCTAGCTGCAACA 59.162 45.455 1.02 0.00 0.00 3.33
94 95 2.154462 AGCTGCAACAGATTACACCAC 58.846 47.619 1.02 0.00 32.44 4.16
96 97 2.095567 GCTGCAACAGATTACACCACTG 60.096 50.000 0.00 0.00 37.62 3.66
99 100 4.905429 TGCAACAGATTACACCACTGTAT 58.095 39.130 0.00 0.00 42.81 2.29
101 102 8.052005 CTGCAACAGATTACACCACTGTATGG 62.052 46.154 0.00 0.00 43.77 2.74
123 124 5.530171 TGGCGTTTTGTACAACAAACCTATA 59.470 36.000 8.07 0.00 46.53 1.31
126 127 6.575942 GCGTTTTGTACAACAAACCTATAGTG 59.424 38.462 8.07 0.00 46.53 2.74
127 128 7.632721 CGTTTTGTACAACAAACCTATAGTGT 58.367 34.615 8.07 0.00 46.53 3.55
128 129 8.763356 CGTTTTGTACAACAAACCTATAGTGTA 58.237 33.333 8.07 0.00 46.53 2.90
145 150 9.832445 CTATAGTGTAAAACCATCACCAATAGT 57.168 33.333 0.00 0.00 31.46 2.12
149 154 7.120726 AGTGTAAAACCATCACCAATAGTTAGC 59.879 37.037 0.00 0.00 33.21 3.09
165 170 5.366829 AGTTAGCGGTTTGTGTAATTTCC 57.633 39.130 0.00 0.00 0.00 3.13
167 172 5.180680 AGTTAGCGGTTTGTGTAATTTCCTC 59.819 40.000 0.00 0.00 0.00 3.71
169 174 4.142038 AGCGGTTTGTGTAATTTCCTCTT 58.858 39.130 0.00 0.00 0.00 2.85
203 209 2.612212 GCTTATGTAACCATGTGTCCCG 59.388 50.000 0.00 0.00 32.29 5.14
293 302 7.421530 AAAAATCATCGACGAAAAGAGAGAA 57.578 32.000 0.00 0.00 0.00 2.87
294 303 7.421530 AAAATCATCGACGAAAAGAGAGAAA 57.578 32.000 0.00 0.00 0.00 2.52
295 304 6.639671 AATCATCGACGAAAAGAGAGAAAG 57.360 37.500 0.00 0.00 0.00 2.62
296 305 5.372547 TCATCGACGAAAAGAGAGAAAGA 57.627 39.130 0.00 0.00 0.00 2.52
297 306 5.769367 TCATCGACGAAAAGAGAGAAAGAA 58.231 37.500 0.00 0.00 0.00 2.52
302 311 5.915758 CGACGAAAAGAGAGAAAGAAAGAGA 59.084 40.000 0.00 0.00 0.00 3.10
304 313 6.220201 ACGAAAAGAGAGAAAGAAAGAGAGG 58.780 40.000 0.00 0.00 0.00 3.69
851 860 2.033194 CCCGGTTTTGACGCTCTCC 61.033 63.158 0.00 0.00 0.00 3.71
857 866 0.321671 TTTTGACGCTCTCCCCTCTG 59.678 55.000 0.00 0.00 0.00 3.35
890 902 2.186903 CCCGAACATCCCACCTCG 59.813 66.667 0.00 0.00 0.00 4.63
926 938 2.820197 GGAACGGAGCCAATTTTCTTCT 59.180 45.455 0.00 0.00 0.00 2.85
948 960 2.203070 CTCCGGATTTCCCTGCCG 60.203 66.667 3.57 0.00 44.42 5.69
1363 1445 0.610232 CTGCCTGTTTTCCCTCCTGG 60.610 60.000 0.00 0.00 0.00 4.45
1364 1446 1.360393 TGCCTGTTTTCCCTCCTGGT 61.360 55.000 0.00 0.00 34.77 4.00
1365 1447 0.609406 GCCTGTTTTCCCTCCTGGTC 60.609 60.000 0.00 0.00 34.77 4.02
1410 1492 4.994201 TTCGACGCGCGCTGTTCT 62.994 61.111 32.58 9.39 40.61 3.01
1435 1517 0.815213 CGCCCGTGGAATGATGTCAT 60.815 55.000 0.00 0.00 38.41 3.06
1497 1584 3.810579 GCGTTTGCCATTGGATTGA 57.189 47.368 6.95 0.00 33.98 2.57
1506 1593 5.486735 TGCCATTGGATTGAAGAAACAAT 57.513 34.783 6.95 0.00 42.19 2.71
1658 2765 2.275812 GTGATTACGTGCGCGCAC 60.276 61.111 45.38 45.38 42.83 5.34
1838 2948 1.202533 TGCTACTAATCTTGCCGGAGC 60.203 52.381 5.05 0.57 40.48 4.70
1908 3037 7.392953 TCCATAAAAGTGTATGTTCAATGCAGA 59.607 33.333 0.00 0.00 30.72 4.26
1913 3042 4.218417 AGTGTATGTTCAATGCAGAAACCC 59.782 41.667 0.00 0.00 0.00 4.11
1922 3051 1.979155 GCAGAAACCCCTTCCAGCC 60.979 63.158 0.00 0.00 34.21 4.85
1924 3053 1.466186 AGAAACCCCTTCCAGCCCT 60.466 57.895 0.00 0.00 34.21 5.19
2011 3140 4.469657 TGTCCAATGCAAGTACCTCTTTT 58.530 39.130 0.00 0.00 33.63 2.27
2014 3143 6.547880 TGTCCAATGCAAGTACCTCTTTTTAA 59.452 34.615 0.00 0.00 33.63 1.52
2015 3144 7.232534 TGTCCAATGCAAGTACCTCTTTTTAAT 59.767 33.333 0.00 0.00 33.63 1.40
2017 3146 9.303116 TCCAATGCAAGTACCTCTTTTTAATTA 57.697 29.630 0.00 0.00 33.63 1.40
2018 3147 9.921637 CCAATGCAAGTACCTCTTTTTAATTAA 57.078 29.630 0.00 0.00 33.63 1.40
2037 3166 7.716799 AATTAAAGATACCTTGTCCAATGCA 57.283 32.000 0.00 0.00 31.91 3.96
2038 3167 7.716799 ATTAAAGATACCTTGTCCAATGCAA 57.283 32.000 0.00 0.00 31.91 4.08
2039 3168 5.649782 AAAGATACCTTGTCCAATGCAAG 57.350 39.130 0.00 0.00 42.00 4.01
2040 3169 4.307032 AGATACCTTGTCCAATGCAAGT 57.693 40.909 0.00 0.00 41.08 3.16
2041 3170 5.435686 AGATACCTTGTCCAATGCAAGTA 57.564 39.130 0.00 0.00 41.08 2.24
2042 3171 5.186198 AGATACCTTGTCCAATGCAAGTAC 58.814 41.667 0.00 0.00 41.08 2.73
2043 3172 2.514803 ACCTTGTCCAATGCAAGTACC 58.485 47.619 0.00 0.00 41.08 3.34
2044 3173 2.108250 ACCTTGTCCAATGCAAGTACCT 59.892 45.455 0.00 0.00 41.08 3.08
2045 3174 2.749621 CCTTGTCCAATGCAAGTACCTC 59.250 50.000 0.00 0.00 41.08 3.85
2046 3175 3.560025 CCTTGTCCAATGCAAGTACCTCT 60.560 47.826 0.00 0.00 41.08 3.69
2047 3176 3.788227 TGTCCAATGCAAGTACCTCTT 57.212 42.857 0.00 0.00 36.75 2.85
2048 3177 4.901197 TGTCCAATGCAAGTACCTCTTA 57.099 40.909 0.00 0.00 34.66 2.10
2049 3178 4.575885 TGTCCAATGCAAGTACCTCTTAC 58.424 43.478 0.00 0.00 34.66 2.34
2050 3179 3.939592 GTCCAATGCAAGTACCTCTTACC 59.060 47.826 0.00 0.00 34.66 2.85
2051 3180 3.844211 TCCAATGCAAGTACCTCTTACCT 59.156 43.478 0.00 0.00 34.66 3.08
2052 3181 4.288626 TCCAATGCAAGTACCTCTTACCTT 59.711 41.667 0.00 0.00 34.66 3.50
2053 3182 4.396166 CCAATGCAAGTACCTCTTACCTTG 59.604 45.833 0.00 0.00 34.66 3.61
2054 3183 4.910458 ATGCAAGTACCTCTTACCTTGT 57.090 40.909 0.00 0.00 34.66 3.16
2055 3184 4.267349 TGCAAGTACCTCTTACCTTGTC 57.733 45.455 0.00 0.00 34.66 3.18
2056 3185 3.901844 TGCAAGTACCTCTTACCTTGTCT 59.098 43.478 0.00 0.00 34.66 3.41
2057 3186 5.081728 TGCAAGTACCTCTTACCTTGTCTA 58.918 41.667 0.00 0.00 34.66 2.59
2058 3187 5.541101 TGCAAGTACCTCTTACCTTGTCTAA 59.459 40.000 0.00 0.00 34.66 2.10
2059 3188 6.212791 TGCAAGTACCTCTTACCTTGTCTAAT 59.787 38.462 0.00 0.00 34.66 1.73
2060 3189 6.535508 GCAAGTACCTCTTACCTTGTCTAATG 59.464 42.308 0.00 0.00 34.66 1.90
2061 3190 6.223351 AGTACCTCTTACCTTGTCTAATGC 57.777 41.667 0.00 0.00 0.00 3.56
2062 3191 5.720041 AGTACCTCTTACCTTGTCTAATGCA 59.280 40.000 0.00 0.00 0.00 3.96
2063 3192 5.499004 ACCTCTTACCTTGTCTAATGCAA 57.501 39.130 0.00 0.00 0.00 4.08
2064 3193 5.491982 ACCTCTTACCTTGTCTAATGCAAG 58.508 41.667 0.00 0.00 42.00 4.01
2065 3194 5.013183 ACCTCTTACCTTGTCTAATGCAAGT 59.987 40.000 0.00 0.00 41.08 3.16
2066 3195 6.212791 ACCTCTTACCTTGTCTAATGCAAGTA 59.787 38.462 0.00 0.00 41.08 2.24
2067 3196 6.535508 CCTCTTACCTTGTCTAATGCAAGTAC 59.464 42.308 0.00 0.00 41.08 2.73
2068 3197 6.403878 TCTTACCTTGTCTAATGCAAGTACC 58.596 40.000 0.00 0.00 41.08 3.34
2069 3198 4.910458 ACCTTGTCTAATGCAAGTACCT 57.090 40.909 0.00 0.00 41.08 3.08
2070 3199 4.833390 ACCTTGTCTAATGCAAGTACCTC 58.167 43.478 0.00 0.00 41.08 3.85
2071 3200 4.532521 ACCTTGTCTAATGCAAGTACCTCT 59.467 41.667 0.00 0.00 41.08 3.69
2072 3201 5.013183 ACCTTGTCTAATGCAAGTACCTCTT 59.987 40.000 0.00 0.00 41.08 2.85
2073 3202 6.212791 ACCTTGTCTAATGCAAGTACCTCTTA 59.787 38.462 0.00 0.00 41.08 2.10
2074 3203 6.535508 CCTTGTCTAATGCAAGTACCTCTTAC 59.464 42.308 0.00 0.00 41.08 2.34
2075 3204 5.974108 TGTCTAATGCAAGTACCTCTTACC 58.026 41.667 0.00 0.00 34.66 2.85
2076 3205 5.720041 TGTCTAATGCAAGTACCTCTTACCT 59.280 40.000 0.00 0.00 34.66 3.08
2077 3206 6.212791 TGTCTAATGCAAGTACCTCTTACCTT 59.787 38.462 0.00 0.00 34.66 3.50
2078 3207 6.535508 GTCTAATGCAAGTACCTCTTACCTTG 59.464 42.308 0.00 0.00 34.66 3.61
2079 3208 4.910458 ATGCAAGTACCTCTTACCTTGT 57.090 40.909 0.00 0.00 34.66 3.16
2080 3209 4.267349 TGCAAGTACCTCTTACCTTGTC 57.733 45.455 0.00 0.00 34.66 3.18
2081 3210 3.007614 TGCAAGTACCTCTTACCTTGTCC 59.992 47.826 0.00 0.00 34.66 4.02
2082 3211 3.007614 GCAAGTACCTCTTACCTTGTCCA 59.992 47.826 0.00 0.00 34.66 4.02
2083 3212 4.504340 GCAAGTACCTCTTACCTTGTCCAA 60.504 45.833 0.00 0.00 34.66 3.53
2084 3213 5.803470 GCAAGTACCTCTTACCTTGTCCAAT 60.803 44.000 0.00 0.00 34.66 3.16
2085 3214 5.422214 AGTACCTCTTACCTTGTCCAATG 57.578 43.478 0.00 0.00 0.00 2.82
2086 3215 3.073274 ACCTCTTACCTTGTCCAATGC 57.927 47.619 0.00 0.00 0.00 3.56
2087 3216 2.375174 ACCTCTTACCTTGTCCAATGCA 59.625 45.455 0.00 0.00 0.00 3.96
2088 3217 3.181434 ACCTCTTACCTTGTCCAATGCAA 60.181 43.478 0.00 0.00 0.00 4.08
2089 3218 3.441572 CCTCTTACCTTGTCCAATGCAAG 59.558 47.826 0.00 0.00 42.00 4.01
2090 3219 4.074970 CTCTTACCTTGTCCAATGCAAGT 58.925 43.478 0.00 0.00 41.08 3.16
2126 3255 4.462483 TCCAATGCAAAAGTCCAATCCTAC 59.538 41.667 0.00 0.00 0.00 3.18
2199 3328 6.948309 ACAAATCTGCCCAACTATAAACTTCT 59.052 34.615 0.00 0.00 0.00 2.85
2354 3485 9.353999 GTCACATTATCCCTTGTTTCAAATTAC 57.646 33.333 0.00 0.00 0.00 1.89
2438 3569 7.362142 GCAAAGTTCCCTAGTAAAAAGGATGAG 60.362 40.741 0.00 0.00 36.08 2.90
2510 3641 4.348168 CCTAATATTACCACCCTGCTGTCT 59.652 45.833 0.00 0.00 0.00 3.41
2770 3901 9.320295 TCAAAAGAAATGTATATTTTCCCAGGT 57.680 29.630 0.00 0.00 36.66 4.00
2987 4118 6.194508 CGCATGGTTCAGTTATTTCATTTACG 59.805 38.462 0.00 0.00 0.00 3.18
2995 4126 5.283717 CAGTTATTTCATTTACGTGTGCAGC 59.716 40.000 0.00 0.00 0.00 5.25
3000 4131 2.223144 TCATTTACGTGTGCAGCAGTTC 59.777 45.455 0.00 0.00 0.00 3.01
3397 4529 2.858745 TCCAAACCAAGTACAAGCTCC 58.141 47.619 0.00 0.00 0.00 4.70
3694 4828 7.696872 GCGGACTATTTTCTCCACTAATTTTTC 59.303 37.037 0.00 0.00 0.00 2.29
3887 5021 7.039853 TGGTGATGATTTCAATTGCACTTCTTA 60.040 33.333 0.00 0.00 35.70 2.10
4220 5363 2.319136 TCCGTTGTGTACTTTGCTGT 57.681 45.000 0.00 0.00 0.00 4.40
4300 5443 1.523758 CGGTAAAGCTGTTGCCTTCT 58.476 50.000 11.70 0.00 40.80 2.85
4301 5444 1.464997 CGGTAAAGCTGTTGCCTTCTC 59.535 52.381 11.70 0.00 40.80 2.87
4676 5877 8.023021 TCTGCTTAATGTATCCACTACTCATT 57.977 34.615 0.00 0.00 34.02 2.57
4793 5994 1.544691 AGCTGCTTTCCTCATTGCAAG 59.455 47.619 4.94 0.00 34.90 4.01
5167 6368 0.475906 ACTGGTTTCTGCTGGCTTCT 59.524 50.000 0.00 0.00 0.00 2.85
5305 6506 5.604758 ATGCTTCAGTATTCTGCACTCTA 57.395 39.130 0.00 0.00 41.10 2.43
5597 6798 5.741040 GTGAACTCAAACAGAAGCTTTCAAG 59.259 40.000 0.00 0.00 0.00 3.02
5857 7058 3.059884 CGCTGTATTGCCAGGTATGTAG 58.940 50.000 0.00 0.00 32.92 2.74
5877 7078 6.127793 TGTAGATGGACTCTAGTTTAGGTCC 58.872 44.000 12.80 12.80 42.03 4.46
5892 7093 6.443849 AGTTTAGGTCCATCTGAATTACAGGA 59.556 38.462 0.00 0.00 45.76 3.86
6154 7355 4.910458 AGGTCTTAGCACTACCAAATGT 57.090 40.909 0.00 0.00 35.64 2.71
6188 7389 2.161410 CGATTTTCTCCATTCGTGCCAA 59.839 45.455 0.00 0.00 0.00 4.52
6243 7444 4.024670 CCAGTTAGTGGTCCTACTAGCTT 58.975 47.826 12.15 0.00 41.06 3.74
6244 7445 5.198965 CCAGTTAGTGGTCCTACTAGCTTA 58.801 45.833 12.15 0.00 41.06 3.09
6277 7478 7.861629 AGGTTCCATATTATGTTCAACTCTCA 58.138 34.615 3.10 0.00 0.00 3.27
6290 7491 3.745975 TCAACTCTCATACAACCGCAAAG 59.254 43.478 0.00 0.00 0.00 2.77
6299 7521 6.148948 TCATACAACCGCAAAGAAAATGAAG 58.851 36.000 0.00 0.00 0.00 3.02
6369 7591 2.463589 TTACCACAGGCTTGCTCCGG 62.464 60.000 0.00 0.00 0.00 5.14
6372 7594 3.570212 ACAGGCTTGCTCCGGGTT 61.570 61.111 0.00 0.00 0.00 4.11
6373 7595 2.282462 CAGGCTTGCTCCGGGTTT 60.282 61.111 0.00 0.00 0.00 3.27
6374 7596 1.903404 CAGGCTTGCTCCGGGTTTT 60.903 57.895 0.00 0.00 0.00 2.43
6375 7597 1.152546 AGGCTTGCTCCGGGTTTTT 60.153 52.632 0.00 0.00 0.00 1.94
6436 7658 7.033185 CACTAATACATTTGTTACCAAAGGGC 58.967 38.462 2.47 0.00 44.47 5.19
6443 7665 2.303175 TGTTACCAAAGGGCTTGACAC 58.697 47.619 0.00 0.00 37.17 3.67
6448 7671 2.092103 ACCAAAGGGCTTGACACACTTA 60.092 45.455 0.00 0.00 37.17 2.24
6458 7681 4.084900 GCTTGACACACTTATTTTGCTTGC 60.085 41.667 0.00 0.00 0.00 4.01
6467 7690 7.325821 CACACTTATTTTGCTTGCGAGAATTAA 59.674 33.333 4.70 0.00 0.00 1.40
6567 7790 4.758688 TCTTCATGTACATTGACGAGCAT 58.241 39.130 5.37 0.00 0.00 3.79
6632 7855 3.758554 ACCATCAAGTATGAACTGTTGGC 59.241 43.478 0.00 0.00 39.49 4.52
6677 7900 9.658799 TTCAGTCTATGGAATCAACTCTAAAAG 57.341 33.333 0.00 0.00 0.00 2.27
6715 7938 4.380531 ACTTGATAATGCACAGATACGGG 58.619 43.478 0.00 0.00 0.00 5.28
6892 8115 2.431260 GCACCAAACGGCAGCATG 60.431 61.111 0.00 0.00 40.87 4.06
6982 8205 0.107945 GCTCAACGCCTCAAGATCCT 60.108 55.000 0.00 0.00 0.00 3.24
6983 8206 1.649664 CTCAACGCCTCAAGATCCTG 58.350 55.000 0.00 0.00 0.00 3.86
6984 8207 0.250234 TCAACGCCTCAAGATCCTGG 59.750 55.000 0.00 0.00 0.00 4.45
7030 8253 2.011947 CTGGAGCTCGCATTCATCAAA 58.988 47.619 7.83 0.00 0.00 2.69
7096 8319 1.072331 GTCAAAGCCAGGAAGGACTCA 59.928 52.381 0.00 0.00 41.22 3.41
7328 8551 3.665745 AGGAACAACAATGGTGATTGC 57.334 42.857 4.82 1.12 42.54 3.56
7392 8615 0.335019 TGGCTAGGACAGTAGGAGCA 59.665 55.000 0.00 0.00 34.76 4.26
7416 8639 6.706270 CACATGTCTCCTGTAAGTTTTGTACT 59.294 38.462 0.00 0.00 39.32 2.73
7579 8802 2.863137 GAGTGCTAGCTGAAAAGGATCG 59.137 50.000 17.23 0.00 0.00 3.69
7638 8861 2.125391 GCCATCGAGCAGTGCTGA 60.125 61.111 25.35 19.72 39.88 4.26
7660 8883 7.467947 GCTGATGCTTTATCCTTACCTTTTCTC 60.468 40.741 0.00 0.00 34.77 2.87
7672 8895 6.314896 CCTTACCTTTTCTCATCTGCACTTAG 59.685 42.308 0.00 0.00 0.00 2.18
7673 8896 4.006319 ACCTTTTCTCATCTGCACTTAGC 58.994 43.478 0.00 0.00 45.96 3.09
7711 9056 4.880886 TCTGCGACAATTAATGTGGATG 57.119 40.909 0.00 0.00 44.12 3.51
7722 9067 1.807814 ATGTGGATGGGAGGGAGTAC 58.192 55.000 0.00 0.00 0.00 2.73
7734 9079 5.065914 GGGAGGGAGTACGTTTTAGTTTTT 58.934 41.667 0.00 0.00 0.00 1.94
7808 9184 1.339055 CGATGGTGTCATCCTTGTGGT 60.339 52.381 0.00 0.00 45.20 4.16
7957 11370 2.205074 CATACGGCTGAAGGTGTCATC 58.795 52.381 0.00 0.00 35.07 2.92
8038 11455 1.337728 GGGTGTGCAAGCCCAAAATAC 60.338 52.381 18.92 0.00 44.23 1.89
8039 11456 1.668628 GGTGTGCAAGCCCAAAATACG 60.669 52.381 0.00 0.00 0.00 3.06
8053 11470 6.707161 GCCCAAAATACGGACTACATATAACA 59.293 38.462 0.00 0.00 0.00 2.41
8078 11495 2.089201 CCAAATTTCTACCCGGTGTCC 58.911 52.381 0.00 0.00 0.00 4.02
8079 11496 2.553466 CCAAATTTCTACCCGGTGTCCA 60.553 50.000 0.00 0.00 0.00 4.02
8080 11497 2.747446 CAAATTTCTACCCGGTGTCCAG 59.253 50.000 0.00 0.00 0.00 3.86
8081 11498 1.652947 ATTTCTACCCGGTGTCCAGT 58.347 50.000 0.00 0.00 0.00 4.00
8083 11500 0.178955 TTCTACCCGGTGTCCAGTCA 60.179 55.000 0.00 0.00 0.00 3.41
8084 11501 0.896940 TCTACCCGGTGTCCAGTCAC 60.897 60.000 0.00 0.00 37.57 3.67
8085 11502 1.152504 TACCCGGTGTCCAGTCACA 60.153 57.895 0.00 0.00 39.76 3.58
8086 11503 1.466025 TACCCGGTGTCCAGTCACAC 61.466 60.000 0.00 0.00 45.20 3.82
8090 11507 2.665185 GTGTCCAGTCACACCGGC 60.665 66.667 0.00 0.00 40.84 6.13
8091 11508 2.842462 TGTCCAGTCACACCGGCT 60.842 61.111 0.00 0.00 0.00 5.52
8092 11509 2.357517 GTCCAGTCACACCGGCTG 60.358 66.667 0.00 0.00 0.00 4.85
8101 11983 2.224159 ACACCGGCTGGGAGTCATT 61.224 57.895 18.00 0.00 34.07 2.57
8103 11985 2.224159 ACCGGCTGGGAGTCATTGT 61.224 57.895 18.00 0.00 40.75 2.71
8111 11993 1.375908 GGAGTCATTGTCCTGCGCA 60.376 57.895 10.98 10.98 0.00 6.09
8119 12001 2.815647 GTCCTGCGCAGTAGCCAC 60.816 66.667 33.75 18.30 39.50 5.01
8161 12043 1.801178 CCGAAGAACCACTTTGAGAGC 59.199 52.381 0.00 0.00 41.25 4.09
8167 12049 1.388547 ACCACTTTGAGAGCGCAAAA 58.611 45.000 11.47 3.73 37.32 2.44
8174 12056 0.889186 TGAGAGCGCAAAAGGTTCCC 60.889 55.000 11.47 0.00 0.00 3.97
8223 12105 8.894768 ATTGGTACAGTTTATAAGAGCATCTC 57.105 34.615 0.00 0.00 44.46 2.75
8224 12106 7.272978 TTGGTACAGTTTATAAGAGCATCTCC 58.727 38.462 0.00 0.00 44.46 3.71
8225 12107 7.093068 TTGGTACAGTTTATAAGAGCATCTCCA 60.093 37.037 0.00 0.00 44.46 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.067414 TGTAAGTGCACGCGTGATAA 57.933 45.000 41.19 23.02 0.00 1.75
1 2 1.989864 CTTGTAAGTGCACGCGTGATA 59.010 47.619 41.19 26.01 0.00 2.15
2 3 0.790207 CTTGTAAGTGCACGCGTGAT 59.210 50.000 41.19 24.50 0.00 3.06
3 4 1.827315 GCTTGTAAGTGCACGCGTGA 61.827 55.000 41.19 23.48 0.00 4.35
4 5 1.438710 GCTTGTAAGTGCACGCGTG 60.439 57.895 34.01 34.01 0.00 5.34
5 6 2.935955 GCTTGTAAGTGCACGCGT 59.064 55.556 5.58 5.58 0.00 6.01
7 8 2.173382 CCGCTTGTAAGTGCACGC 59.827 61.111 12.01 6.64 35.25 5.34
8 9 2.677003 CCCCGCTTGTAAGTGCACG 61.677 63.158 12.01 0.00 35.25 5.34
9 10 1.574702 GACCCCGCTTGTAAGTGCAC 61.575 60.000 9.40 9.40 35.25 4.57
10 11 1.302192 GACCCCGCTTGTAAGTGCA 60.302 57.895 0.00 0.00 35.25 4.57
11 12 2.038837 GGACCCCGCTTGTAAGTGC 61.039 63.158 0.00 0.00 35.25 4.40
12 13 0.391263 GAGGACCCCGCTTGTAAGTG 60.391 60.000 0.00 0.00 36.32 3.16
13 14 1.551019 GGAGGACCCCGCTTGTAAGT 61.551 60.000 0.00 0.00 0.00 2.24
14 15 1.221021 GGAGGACCCCGCTTGTAAG 59.779 63.158 0.00 0.00 0.00 2.34
15 16 0.041535 TAGGAGGACCCCGCTTGTAA 59.958 55.000 0.00 0.00 36.73 2.41
16 17 0.263765 ATAGGAGGACCCCGCTTGTA 59.736 55.000 0.00 0.00 36.73 2.41
17 18 0.263765 TATAGGAGGACCCCGCTTGT 59.736 55.000 0.00 0.00 36.73 3.16
18 19 1.420430 TTATAGGAGGACCCCGCTTG 58.580 55.000 0.00 0.00 36.73 4.01
19 20 2.185663 TTTATAGGAGGACCCCGCTT 57.814 50.000 0.00 0.00 36.73 4.68
20 21 2.185663 TTTTATAGGAGGACCCCGCT 57.814 50.000 0.00 0.00 36.73 5.52
21 22 3.181448 TGATTTTTATAGGAGGACCCCGC 60.181 47.826 0.00 0.00 36.73 6.13
22 23 4.699925 TGATTTTTATAGGAGGACCCCG 57.300 45.455 0.00 0.00 36.73 5.73
23 24 7.066781 TGATTTGATTTTTATAGGAGGACCCC 58.933 38.462 0.00 0.00 36.73 4.95
24 25 8.414003 GTTGATTTGATTTTTATAGGAGGACCC 58.586 37.037 0.00 0.00 36.73 4.46
25 26 8.966868 TGTTGATTTGATTTTTATAGGAGGACC 58.033 33.333 0.00 0.00 0.00 4.46
34 35 9.787532 CGTCAGGTATGTTGATTTGATTTTTAT 57.212 29.630 0.00 0.00 0.00 1.40
35 36 8.788806 ACGTCAGGTATGTTGATTTGATTTTTA 58.211 29.630 0.00 0.00 0.00 1.52
36 37 7.657336 ACGTCAGGTATGTTGATTTGATTTTT 58.343 30.769 0.00 0.00 0.00 1.94
37 38 7.214467 ACGTCAGGTATGTTGATTTGATTTT 57.786 32.000 0.00 0.00 0.00 1.82
38 39 6.817765 ACGTCAGGTATGTTGATTTGATTT 57.182 33.333 0.00 0.00 0.00 2.17
39 40 6.817765 AACGTCAGGTATGTTGATTTGATT 57.182 33.333 0.00 0.00 35.93 2.57
48 49 5.416947 GTCTAATCCAACGTCAGGTATGTT 58.583 41.667 6.86 2.45 37.84 2.71
49 50 4.142004 GGTCTAATCCAACGTCAGGTATGT 60.142 45.833 6.86 0.00 0.00 2.29
50 51 4.099573 AGGTCTAATCCAACGTCAGGTATG 59.900 45.833 6.86 0.00 0.00 2.39
51 52 4.287552 AGGTCTAATCCAACGTCAGGTAT 58.712 43.478 6.86 1.08 0.00 2.73
52 53 3.705051 AGGTCTAATCCAACGTCAGGTA 58.295 45.455 6.86 0.00 0.00 3.08
53 54 2.537143 AGGTCTAATCCAACGTCAGGT 58.463 47.619 6.86 0.00 0.00 4.00
54 55 3.491104 GCTAGGTCTAATCCAACGTCAGG 60.491 52.174 0.00 0.00 0.00 3.86
55 56 3.381908 AGCTAGGTCTAATCCAACGTCAG 59.618 47.826 0.00 0.00 0.00 3.51
56 57 3.130516 CAGCTAGGTCTAATCCAACGTCA 59.869 47.826 0.00 0.00 0.00 4.35
57 58 3.707793 CAGCTAGGTCTAATCCAACGTC 58.292 50.000 0.00 0.00 0.00 4.34
58 59 2.159085 GCAGCTAGGTCTAATCCAACGT 60.159 50.000 0.00 0.00 0.00 3.99
59 60 2.159099 TGCAGCTAGGTCTAATCCAACG 60.159 50.000 0.00 0.00 0.00 4.10
60 61 3.543680 TGCAGCTAGGTCTAATCCAAC 57.456 47.619 0.00 0.00 0.00 3.77
94 95 4.475763 TGTTGTACAAAACGCCATACAG 57.524 40.909 10.51 0.00 32.47 2.74
123 124 7.120726 GCTAACTATTGGTGATGGTTTTACACT 59.879 37.037 0.00 0.00 39.74 3.55
126 127 6.457799 CCGCTAACTATTGGTGATGGTTTTAC 60.458 42.308 0.00 0.00 39.74 2.01
127 128 5.587043 CCGCTAACTATTGGTGATGGTTTTA 59.413 40.000 0.00 0.00 39.74 1.52
128 129 4.398044 CCGCTAACTATTGGTGATGGTTTT 59.602 41.667 0.00 0.00 39.74 2.43
132 137 3.194005 ACCGCTAACTATTGGTGATGG 57.806 47.619 0.00 0.00 32.33 3.51
145 150 5.310451 AGAGGAAATTACACAAACCGCTAA 58.690 37.500 0.00 0.00 0.00 3.09
149 154 4.517453 TCCAAGAGGAAATTACACAAACCG 59.483 41.667 0.00 0.00 42.23 4.44
167 172 9.788960 GGTTACATAAGCTAAATTCTTTCCAAG 57.211 33.333 0.00 0.00 0.00 3.61
169 174 8.871629 TGGTTACATAAGCTAAATTCTTTCCA 57.128 30.769 0.00 0.00 34.93 3.53
183 188 4.131649 TCGGGACACATGGTTACATAAG 57.868 45.455 0.00 0.00 34.99 1.73
203 209 2.365582 ACCGCATTTAGGGTCATGTTC 58.634 47.619 0.00 0.00 0.00 3.18
249 258 9.852091 GATTTTTAGATTCTCACTGAAAGCATT 57.148 29.630 0.00 0.00 38.29 3.56
250 259 9.017509 TGATTTTTAGATTCTCACTGAAAGCAT 57.982 29.630 0.00 0.00 38.29 3.79
251 260 8.394971 TGATTTTTAGATTCTCACTGAAAGCA 57.605 30.769 0.00 0.00 38.29 3.91
252 261 9.500864 GATGATTTTTAGATTCTCACTGAAAGC 57.499 33.333 0.00 0.00 38.29 3.51
259 268 7.451281 TCGTCGATGATTTTTAGATTCTCAC 57.549 36.000 2.39 0.00 0.00 3.51
261 270 9.414834 CTTTTCGTCGATGATTTTTAGATTCTC 57.585 33.333 8.43 0.00 0.00 2.87
293 302 3.779738 CAATCTCCCTCCCTCTCTTTCTT 59.220 47.826 0.00 0.00 0.00 2.52
294 303 3.383223 CAATCTCCCTCCCTCTCTTTCT 58.617 50.000 0.00 0.00 0.00 2.52
295 304 2.437651 CCAATCTCCCTCCCTCTCTTTC 59.562 54.545 0.00 0.00 0.00 2.62
296 305 2.046447 TCCAATCTCCCTCCCTCTCTTT 59.954 50.000 0.00 0.00 0.00 2.52
297 306 1.653918 TCCAATCTCCCTCCCTCTCTT 59.346 52.381 0.00 0.00 0.00 2.85
302 311 1.415716 CCAGATCCAATCTCCCTCCCT 60.416 57.143 0.00 0.00 37.58 4.20
304 313 1.696884 GACCAGATCCAATCTCCCTCC 59.303 57.143 0.00 0.00 37.58 4.30
831 840 0.601841 GAGAGCGTCAAAACCGGGAA 60.602 55.000 6.32 0.00 0.00 3.97
851 860 0.181350 GTAGTGGAATGGGCAGAGGG 59.819 60.000 0.00 0.00 0.00 4.30
857 866 2.516225 GGGCGTAGTGGAATGGGC 60.516 66.667 0.00 0.00 0.00 5.36
1340 1415 2.283894 GGGAAAACAGGCAGGGGG 60.284 66.667 0.00 0.00 0.00 5.40
1341 1416 1.304464 GAGGGAAAACAGGCAGGGG 60.304 63.158 0.00 0.00 0.00 4.79
1342 1417 1.304464 GGAGGGAAAACAGGCAGGG 60.304 63.158 0.00 0.00 0.00 4.45
1343 1418 0.610232 CAGGAGGGAAAACAGGCAGG 60.610 60.000 0.00 0.00 0.00 4.85
1344 1419 0.610232 CCAGGAGGGAAAACAGGCAG 60.610 60.000 0.00 0.00 40.01 4.85
1345 1420 1.360393 ACCAGGAGGGAAAACAGGCA 61.360 55.000 0.00 0.00 41.15 4.75
1363 1445 1.937359 CACACGCAATCAAACGAGAC 58.063 50.000 0.00 0.00 0.00 3.36
1364 1446 0.234625 GCACACGCAATCAAACGAGA 59.765 50.000 0.00 0.00 38.36 4.04
1365 1447 1.054348 CGCACACGCAATCAAACGAG 61.054 55.000 0.00 0.00 38.40 4.18
1453 1535 2.724349 CTAATCAAAATCGGCAGCAGC 58.276 47.619 0.00 0.00 41.10 5.25
1497 1584 7.148755 GCAACGATCTGCAAATTATTGTTTCTT 60.149 33.333 2.23 0.00 42.17 2.52
1506 1593 2.351418 CCGAGCAACGATCTGCAAATTA 59.649 45.455 9.38 0.00 45.18 1.40
1576 2671 3.502211 ACGAAACATGGATGAAGGAACAC 59.498 43.478 0.00 0.00 0.00 3.32
1612 2707 0.456221 CGCGTCCTGATTACCAGTCT 59.544 55.000 0.00 0.00 41.33 3.24
1658 2765 6.345723 GCACAAGAAAATGGTCACAAATAACG 60.346 38.462 0.00 0.00 0.00 3.18
1838 2948 2.173519 ACAGATGGAGGCAAACATTGG 58.826 47.619 0.00 0.00 0.00 3.16
1908 3037 2.091283 ACAGGGCTGGAAGGGGTTT 61.091 57.895 0.00 0.00 34.19 3.27
1922 3051 0.250553 TCGCTTTAACCACCCACAGG 60.251 55.000 0.00 0.00 40.04 4.00
1924 3053 0.759959 TCTCGCTTTAACCACCCACA 59.240 50.000 0.00 0.00 0.00 4.17
2011 3140 9.249053 TGCATTGGACAAGGTATCTTTAATTAA 57.751 29.630 0.00 0.00 0.00 1.40
2014 3143 7.716799 TTGCATTGGACAAGGTATCTTTAAT 57.283 32.000 0.00 0.00 0.00 1.40
2015 3144 7.156876 CTTGCATTGGACAAGGTATCTTTAA 57.843 36.000 0.00 0.00 40.68 1.52
2017 3146 5.649782 CTTGCATTGGACAAGGTATCTTT 57.350 39.130 0.00 0.00 40.68 2.52
2026 3155 3.788227 AGAGGTACTTGCATTGGACAA 57.212 42.857 5.18 0.00 41.55 3.18
2028 3157 3.939592 GGTAAGAGGTACTTGCATTGGAC 59.060 47.826 0.00 0.00 41.55 4.02
2029 3158 3.844211 AGGTAAGAGGTACTTGCATTGGA 59.156 43.478 0.00 0.00 41.55 3.53
2030 3159 4.222124 AGGTAAGAGGTACTTGCATTGG 57.778 45.455 0.00 0.00 41.55 3.16
2033 3162 4.532521 AGACAAGGTAAGAGGTACTTGCAT 59.467 41.667 0.00 0.00 41.55 3.96
2034 3163 3.901844 AGACAAGGTAAGAGGTACTTGCA 59.098 43.478 0.00 0.00 41.55 4.08
2035 3164 4.538746 AGACAAGGTAAGAGGTACTTGC 57.461 45.455 0.00 0.00 41.55 4.01
2036 3165 6.535508 GCATTAGACAAGGTAAGAGGTACTTG 59.464 42.308 0.00 0.00 41.55 3.16
2037 3166 6.212791 TGCATTAGACAAGGTAAGAGGTACTT 59.787 38.462 0.00 0.00 41.55 2.24
2038 3167 7.579723 CTTGCATTAGACAAGGTAAGAGGTACT 60.580 40.741 0.00 0.00 39.56 2.73
2039 3168 5.974108 TGCATTAGACAAGGTAAGAGGTAC 58.026 41.667 0.00 0.00 0.00 3.34
2040 3169 6.614694 TTGCATTAGACAAGGTAAGAGGTA 57.385 37.500 0.00 0.00 0.00 3.08
2041 3170 5.491982 CTTGCATTAGACAAGGTAAGAGGT 58.508 41.667 0.00 0.00 39.56 3.85
2051 3180 6.212791 AGGTAAGAGGTACTTGCATTAGACAA 59.787 38.462 0.00 0.00 41.55 3.18
2052 3181 5.720041 AGGTAAGAGGTACTTGCATTAGACA 59.280 40.000 0.00 0.00 41.55 3.41
2053 3182 6.223351 AGGTAAGAGGTACTTGCATTAGAC 57.777 41.667 0.00 0.00 41.55 2.59
2054 3183 6.212791 ACAAGGTAAGAGGTACTTGCATTAGA 59.787 38.462 0.00 0.00 41.54 2.10
2055 3184 6.407202 ACAAGGTAAGAGGTACTTGCATTAG 58.593 40.000 0.00 0.00 41.54 1.73
2056 3185 6.368779 ACAAGGTAAGAGGTACTTGCATTA 57.631 37.500 0.00 0.00 41.54 1.90
2057 3186 5.242795 ACAAGGTAAGAGGTACTTGCATT 57.757 39.130 0.00 0.00 43.45 3.56
2058 3187 4.323562 GGACAAGGTAAGAGGTACTTGCAT 60.324 45.833 0.00 0.00 41.55 3.96
2059 3188 3.007614 GGACAAGGTAAGAGGTACTTGCA 59.992 47.826 0.00 0.00 41.55 4.08
2060 3189 3.007614 TGGACAAGGTAAGAGGTACTTGC 59.992 47.826 0.00 0.00 41.55 4.01
2061 3190 4.884668 TGGACAAGGTAAGAGGTACTTG 57.115 45.455 0.00 0.00 41.55 3.16
2062 3191 5.803470 GCATTGGACAAGGTAAGAGGTACTT 60.803 44.000 0.00 0.00 41.55 2.24
2063 3192 9.845396 CTTGCATTGGACAAGGTAAGAGGTACT 62.845 44.444 18.24 0.00 43.86 2.73
2064 3193 3.939592 GCATTGGACAAGGTAAGAGGTAC 59.060 47.826 0.00 0.00 0.00 3.34
2065 3194 3.585289 TGCATTGGACAAGGTAAGAGGTA 59.415 43.478 0.00 0.00 0.00 3.08
2066 3195 2.375174 TGCATTGGACAAGGTAAGAGGT 59.625 45.455 0.00 0.00 0.00 3.85
2067 3196 3.071874 TGCATTGGACAAGGTAAGAGG 57.928 47.619 0.00 0.00 0.00 3.69
2068 3197 4.691860 CTTGCATTGGACAAGGTAAGAG 57.308 45.455 18.24 0.00 43.86 2.85
2076 3205 3.222173 ACAGGTACTTGCATTGGACAA 57.778 42.857 4.65 0.00 34.60 3.18
2077 3206 2.949177 ACAGGTACTTGCATTGGACA 57.051 45.000 4.65 0.00 34.60 4.02
2078 3207 3.933332 GACTACAGGTACTTGCATTGGAC 59.067 47.826 4.65 0.00 34.60 4.02
2079 3208 3.838317 AGACTACAGGTACTTGCATTGGA 59.162 43.478 4.65 0.00 34.60 3.53
2080 3209 4.081420 AGAGACTACAGGTACTTGCATTGG 60.081 45.833 4.65 0.00 34.60 3.16
2081 3210 5.078411 AGAGACTACAGGTACTTGCATTG 57.922 43.478 4.65 0.00 34.60 2.82
2082 3211 4.160626 GGAGAGACTACAGGTACTTGCATT 59.839 45.833 4.65 0.00 34.60 3.56
2083 3212 3.702045 GGAGAGACTACAGGTACTTGCAT 59.298 47.826 4.65 0.00 34.60 3.96
2084 3213 3.090037 GGAGAGACTACAGGTACTTGCA 58.910 50.000 4.65 0.00 34.60 4.08
2085 3214 3.090037 TGGAGAGACTACAGGTACTTGC 58.910 50.000 4.65 0.00 34.60 4.01
2086 3215 5.655488 CATTGGAGAGACTACAGGTACTTG 58.345 45.833 2.98 2.98 34.60 3.16
2087 3216 4.160626 GCATTGGAGAGACTACAGGTACTT 59.839 45.833 0.00 0.00 34.60 2.24
2088 3217 3.702045 GCATTGGAGAGACTACAGGTACT 59.298 47.826 0.00 0.00 43.88 2.73
2089 3218 3.447586 TGCATTGGAGAGACTACAGGTAC 59.552 47.826 0.00 0.00 0.00 3.34
2090 3219 3.708451 TGCATTGGAGAGACTACAGGTA 58.292 45.455 0.00 0.00 0.00 3.08
2199 3328 6.206438 TGAATTGGAATCTCGTTTTCATGTCA 59.794 34.615 0.00 0.00 0.00 3.58
2310 3439 2.158740 TGACTCTCCGAGGTCTGATAGG 60.159 54.545 14.41 0.00 33.35 2.57
2373 3504 9.855021 GTAGCTTGTCACCAAAATATTATGTTT 57.145 29.630 0.00 0.00 0.00 2.83
2438 3569 3.253188 TGGCATCACTAAGCACTTTGAAC 59.747 43.478 0.00 0.00 0.00 3.18
2556 3687 0.396435 ACTGTCTCCAATGCGGTTGA 59.604 50.000 3.45 0.00 40.37 3.18
2770 3901 8.493607 TCATCTCATAATTAAACACATCTCCCA 58.506 33.333 0.00 0.00 0.00 4.37
2987 4118 2.046313 CAAAATCGAACTGCTGCACAC 58.954 47.619 0.00 0.00 0.00 3.82
2995 4126 1.879380 TGTCCTGCCAAAATCGAACTG 59.121 47.619 0.00 0.00 0.00 3.16
3000 4131 4.396166 AGAAATACTGTCCTGCCAAAATCG 59.604 41.667 0.00 0.00 0.00 3.34
3264 4395 8.911018 AGCCTGTAACATATCCCTGTATAATA 57.089 34.615 0.00 0.00 0.00 0.98
3397 4529 0.820226 TGACATCCTCTTCTCAGGCG 59.180 55.000 0.00 0.00 32.91 5.52
3694 4828 6.656945 GCAGACAGCACTATTCAATGATAAG 58.343 40.000 0.00 0.00 44.79 1.73
4220 5363 4.624336 TTGTCTCAAAGTTAAAGCGCAA 57.376 36.364 11.47 0.00 0.00 4.85
4552 5753 8.524870 AACATCATCTGCATAAAGTTCAAAAC 57.475 30.769 0.00 0.00 0.00 2.43
4793 5994 4.631813 AGATATGTTCAGGTGTCTTTTCGC 59.368 41.667 0.00 0.00 0.00 4.70
5167 6368 4.151883 AGAGCAGAATAAAGCCCAAACAA 58.848 39.130 0.00 0.00 0.00 2.83
5597 6798 4.819088 GCCCCAGTTTTCTCATTAGATCTC 59.181 45.833 0.00 0.00 0.00 2.75
5877 7078 6.808008 ACAACAGTTCCTGTAATTCAGATG 57.192 37.500 0.00 0.00 44.62 2.90
6137 7338 5.099042 ACCCTACATTTGGTAGTGCTAAG 57.901 43.478 0.00 0.00 46.68 2.18
6154 7355 5.163248 TGGAGAAAATCGCATTCATACCCTA 60.163 40.000 0.00 0.00 0.00 3.53
6188 7389 8.691661 ATATTTTCAGTAGTAATGGGCGAAAT 57.308 30.769 0.00 3.51 0.00 2.17
6244 7445 9.707957 TGAACATAATATGGAACCTACCATTTT 57.292 29.630 5.16 7.01 47.00 1.82
6267 7468 3.394674 TGCGGTTGTATGAGAGTTGAA 57.605 42.857 0.00 0.00 0.00 2.69
6277 7478 6.084326 ACTTCATTTTCTTTGCGGTTGTAT 57.916 33.333 0.00 0.00 0.00 2.29
6290 7491 9.206870 TGATTTGGCATTTCTTACTTCATTTTC 57.793 29.630 0.00 0.00 0.00 2.29
6299 7521 8.131731 GGACTATTCTGATTTGGCATTTCTTAC 58.868 37.037 0.00 0.00 0.00 2.34
6375 7597 9.722184 TCATGGATCAAAGCAAATCAAATTTAA 57.278 25.926 0.00 0.00 0.00 1.52
6376 7598 9.893634 ATCATGGATCAAAGCAAATCAAATTTA 57.106 25.926 0.00 0.00 0.00 1.40
6380 7602 9.893634 AATAATCATGGATCAAAGCAAATCAAA 57.106 25.926 0.00 0.00 0.00 2.69
6432 7654 3.005791 GCAAAATAAGTGTGTCAAGCCCT 59.994 43.478 0.00 0.00 0.00 5.19
6436 7658 4.146961 CGCAAGCAAAATAAGTGTGTCAAG 59.853 41.667 0.00 0.00 0.00 3.02
6443 7665 7.795431 TTAATTCTCGCAAGCAAAATAAGTG 57.205 32.000 0.00 0.00 37.18 3.16
6471 7694 6.038936 ACAGTACTTTTTGCGTTCTACCAATT 59.961 34.615 0.00 0.00 0.00 2.32
6472 7695 5.529800 ACAGTACTTTTTGCGTTCTACCAAT 59.470 36.000 0.00 0.00 0.00 3.16
6474 7697 4.271533 CACAGTACTTTTTGCGTTCTACCA 59.728 41.667 0.00 0.00 0.00 3.25
6615 7838 3.325870 TCTCGCCAACAGTTCATACTTG 58.674 45.455 0.00 0.00 30.26 3.16
6622 7845 2.670414 CTCAGAATCTCGCCAACAGTTC 59.330 50.000 0.00 0.00 0.00 3.01
6632 7855 2.582728 AGCAAGCTCTCAGAATCTCG 57.417 50.000 0.00 0.00 0.00 4.04
6715 7938 4.574828 TGCTCCTGTTTCTTGTCTTTGTAC 59.425 41.667 0.00 0.00 0.00 2.90
6890 8113 0.753262 GGGGCATCGAGTGAGTACAT 59.247 55.000 0.00 0.00 0.00 2.29
6892 8115 0.386113 GAGGGGCATCGAGTGAGTAC 59.614 60.000 0.00 0.00 0.00 2.73
6982 8205 3.482436 GTTCTGTGTGTAATCCAACCCA 58.518 45.455 0.00 0.00 0.00 4.51
6983 8206 2.817844 GGTTCTGTGTGTAATCCAACCC 59.182 50.000 0.00 0.00 0.00 4.11
6984 8207 3.751518 AGGTTCTGTGTGTAATCCAACC 58.248 45.455 0.00 0.00 33.37 3.77
7030 8253 0.539051 CTCCAGATTCCTTCGCCTGT 59.461 55.000 0.00 0.00 0.00 4.00
7096 8319 8.868522 TTATGATCAACTTCTTGAAGAACCAT 57.131 30.769 16.21 12.55 39.90 3.55
7259 8482 6.294473 ACTGGATAAGTAGATTGCCATGAAG 58.706 40.000 0.00 0.00 37.36 3.02
7328 8551 1.818674 AGTTAAGCATTTGCCTTCCGG 59.181 47.619 0.00 0.00 43.38 5.14
7392 8615 6.706270 CAGTACAAAACTTACAGGAGACATGT 59.294 38.462 0.00 0.00 35.76 3.21
7510 8733 0.994995 CACAGAATCGAAGGAGCACG 59.005 55.000 0.00 0.00 0.00 5.34
7620 8843 1.969200 ATCAGCACTGCTCGATGGCT 61.969 55.000 0.00 0.00 36.40 4.75
7638 8861 8.277918 AGATGAGAAAAGGTAAGGATAAAGCAT 58.722 33.333 0.00 0.00 0.00 3.79
7673 8896 6.560205 GTCGCAGATTTAGTGCAACTTTGTG 61.560 44.000 0.00 0.00 43.68 3.33
7674 8897 4.554723 GTCGCAGATTTAGTGCAACTTTGT 60.555 41.667 0.00 0.00 43.68 2.83
7675 8898 3.908382 GTCGCAGATTTAGTGCAACTTTG 59.092 43.478 0.00 0.00 43.68 2.77
7676 8899 3.563808 TGTCGCAGATTTAGTGCAACTTT 59.436 39.130 0.00 0.00 43.68 2.66
7679 8902 3.536158 TTGTCGCAGATTTAGTGCAAC 57.464 42.857 0.00 0.00 41.26 4.17
7683 9028 6.688385 CCACATTAATTGTCGCAGATTTAGTG 59.312 38.462 0.00 0.00 40.67 2.74
7711 9056 3.969287 AACTAAAACGTACTCCCTCCC 57.031 47.619 0.00 0.00 0.00 4.30
7734 9079 8.898761 ACACACTCATCACTAATTTAAAACACA 58.101 29.630 0.00 0.00 0.00 3.72
7876 9255 1.532437 CAGCGATTCTGCTCAACACAA 59.468 47.619 0.00 0.00 45.23 3.33
7905 9284 1.306997 CCCTACCTTCTCCCAGCCA 60.307 63.158 0.00 0.00 0.00 4.75
7906 9285 2.073101 CCCCTACCTTCTCCCAGCC 61.073 68.421 0.00 0.00 0.00 4.85
7908 9287 0.914417 TTGCCCCTACCTTCTCCCAG 60.914 60.000 0.00 0.00 0.00 4.45
7957 11370 0.809241 GGAAGAGACATGCAGCGAGG 60.809 60.000 0.00 0.00 0.00 4.63
8024 11441 1.173913 AGTCCGTATTTTGGGCTTGC 58.826 50.000 0.00 0.00 38.62 4.01
8038 11455 9.849166 AATTTGGTTTTTGTTATATGTAGTCCG 57.151 29.630 0.00 0.00 0.00 4.79
8053 11470 4.406326 ACACCGGGTAGAAATTTGGTTTTT 59.594 37.500 6.32 0.00 0.00 1.94
8078 11495 3.596066 CTCCCAGCCGGTGTGACTG 62.596 68.421 1.90 0.42 0.00 3.51
8079 11496 3.314331 CTCCCAGCCGGTGTGACT 61.314 66.667 1.90 0.00 0.00 3.41
8080 11497 3.591254 GACTCCCAGCCGGTGTGAC 62.591 68.421 1.90 0.00 38.49 3.67
8081 11498 3.311110 GACTCCCAGCCGGTGTGA 61.311 66.667 1.90 0.00 38.49 3.58
8083 11500 2.224159 AATGACTCCCAGCCGGTGT 61.224 57.895 1.90 0.00 41.14 4.16
8084 11501 1.746615 CAATGACTCCCAGCCGGTG 60.747 63.158 1.90 0.00 0.00 4.94
8085 11502 2.185310 GACAATGACTCCCAGCCGGT 62.185 60.000 1.90 0.00 0.00 5.28
8086 11503 1.450312 GACAATGACTCCCAGCCGG 60.450 63.158 0.00 0.00 0.00 6.13
8087 11504 1.450312 GGACAATGACTCCCAGCCG 60.450 63.158 0.00 0.00 0.00 5.52
8088 11505 0.393537 CAGGACAATGACTCCCAGCC 60.394 60.000 0.00 0.00 0.00 4.85
8089 11506 1.028868 GCAGGACAATGACTCCCAGC 61.029 60.000 0.00 0.00 0.00 4.85
8090 11507 0.742281 CGCAGGACAATGACTCCCAG 60.742 60.000 0.00 0.00 0.00 4.45
8091 11508 1.296392 CGCAGGACAATGACTCCCA 59.704 57.895 0.00 0.00 0.00 4.37
8092 11509 2.109126 GCGCAGGACAATGACTCCC 61.109 63.158 0.30 0.00 0.00 4.30
8101 11983 3.310307 TGGCTACTGCGCAGGACA 61.310 61.111 38.27 27.80 40.82 4.02
8103 11985 4.082523 GGTGGCTACTGCGCAGGA 62.083 66.667 38.27 31.72 40.82 3.86
8111 11993 0.916358 ATGCTTCAGGGGTGGCTACT 60.916 55.000 0.00 0.00 0.00 2.57
8141 12023 1.801178 GCTCTCAAAGTGGTTCTTCGG 59.199 52.381 0.00 0.00 35.02 4.30
8151 12033 1.680338 ACCTTTTGCGCTCTCAAAGT 58.320 45.000 9.73 0.00 37.27 2.66
8167 12049 6.011628 TCTTCTTATGGAAATTCTGGGAACCT 60.012 38.462 0.00 0.00 41.04 3.50


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

AutoCloner maintained by Alex Coulton.