Multiple sequence alignment - TraesCS2A01G206300

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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 TraesCS2A01G206300 chr2A 100.000 6646 0 0 1 6646 185272304 185278949 0.000000e+00 12273.0
1 TraesCS2A01G206300 chr2A 93.548 248 14 1 1 246 408796247 408796000 1.050000e-97 368.0
2 TraesCS2A01G206300 chr2A 93.548 248 14 1 1 246 408798025 408797778 1.050000e-97 368.0
3 TraesCS2A01G206300 chr2A 75.367 341 73 6 240 570 26932777 26933116 3.210000e-33 154.0
4 TraesCS2A01G206300 chr2A 88.660 97 8 3 2011 2107 605185401 605185308 1.510000e-21 115.0
5 TraesCS2A01G206300 chr2D 93.729 3508 178 21 626 4114 165480600 165477116 0.000000e+00 5221.0
6 TraesCS2A01G206300 chr2D 90.923 2578 122 35 4115 6643 165477055 165474541 0.000000e+00 3362.0
7 TraesCS2A01G206300 chr2B 93.508 2326 96 17 1801 4114 232269320 232271602 0.000000e+00 3408.0
8 TraesCS2A01G206300 chr2B 90.405 2616 108 52 4115 6646 232271663 232274219 0.000000e+00 3308.0
9 TraesCS2A01G206300 chr2B 87.839 1587 136 28 249 1809 232265803 232267358 0.000000e+00 1808.0
10 TraesCS2A01G206300 chr6B 81.804 621 106 7 2879 3496 470792545 470793161 1.280000e-141 514.0
11 TraesCS2A01G206300 chr6B 79.055 487 90 7 4603 5079 470793927 470794411 2.310000e-84 324.0
12 TraesCS2A01G206300 chr6B 76.399 411 67 26 965 1361 470786013 470786407 1.890000e-45 195.0
13 TraesCS2A01G206300 chr6B 83.333 108 12 5 1883 1986 396550969 396550864 1.970000e-15 95.3
14 TraesCS2A01G206300 chr6A 81.613 620 109 5 2879 3496 440539257 440538641 5.950000e-140 508.0
15 TraesCS2A01G206300 chr6A 80.342 468 80 6 4622 5079 440536596 440536131 1.770000e-90 344.0
16 TraesCS2A01G206300 chr6D 81.481 621 108 7 2879 3496 306054187 306053571 2.770000e-138 503.0
17 TraesCS2A01G206300 chr6D 92.913 254 16 1 1 252 379081136 379080883 1.050000e-97 368.0
18 TraesCS2A01G206300 chr6D 79.487 468 78 8 4622 5079 306052805 306052346 3.870000e-82 316.0
19 TraesCS2A01G206300 chr6D 90.217 92 6 1 2011 2102 105560548 105560460 4.210000e-22 117.0
20 TraesCS2A01G206300 chr5D 93.952 248 13 1 1 246 291700384 291700137 2.260000e-99 374.0
21 TraesCS2A01G206300 chr5D 92.248 258 17 2 1 255 72714942 72715199 4.900000e-96 363.0
22 TraesCS2A01G206300 chr5D 89.157 83 8 1 1884 1965 116723585 116723503 1.180000e-17 102.0
23 TraesCS2A01G206300 chr7D 93.548 248 14 1 1 246 267998673 267998920 1.050000e-97 368.0
24 TraesCS2A01G206300 chr7D 93.548 248 14 1 1 246 267999133 267999380 1.050000e-97 368.0
25 TraesCS2A01G206300 chr7D 92.045 88 4 1 2011 2098 601057626 601057710 3.260000e-23 121.0
26 TraesCS2A01G206300 chr7D 87.629 97 8 4 2002 2098 518644002 518643910 7.050000e-20 110.0
27 TraesCS2A01G206300 chr4D 93.548 248 14 1 1 246 112874411 112874164 1.050000e-97 368.0
28 TraesCS2A01G206300 chr4D 89.157 83 8 1 1884 1965 455739630 455739548 1.180000e-17 102.0
29 TraesCS2A01G206300 chr1D 92.913 254 16 1 1 252 128012502 128012249 1.050000e-97 368.0
30 TraesCS2A01G206300 chr3A 74.640 347 76 8 261 597 584020179 584019835 6.950000e-30 143.0
31 TraesCS2A01G206300 chr3A 85.000 100 8 7 1880 1974 472485418 472485515 1.970000e-15 95.3
32 TraesCS2A01G206300 chr1A 92.045 88 4 3 2011 2098 30338676 30338592 3.260000e-23 121.0
33 TraesCS2A01G206300 chr1A 84.259 108 11 6 1884 1986 218226988 218226882 4.240000e-17 100.0
34 TraesCS2A01G206300 chr7B 89.474 95 5 2 2011 2105 505750360 505750271 1.510000e-21 115.0
35 TraesCS2A01G206300 chr4B 90.805 87 2 2 2012 2098 180544742 180544662 1.960000e-20 111.0
36 TraesCS2A01G206300 chr5B 87.368 95 11 1 1880 1973 631468832 631468926 2.530000e-19 108.0
37 TraesCS2A01G206300 chr3D 89.157 83 8 1 1884 1965 454890583 454890501 1.180000e-17 102.0
38 TraesCS2A01G206300 chr5A 76.608 171 36 4 254 422 43265036 43264868 2.550000e-14 91.6


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G206300 chr2A 185272304 185278949 6645 False 12273.000000 12273 100.0000 1 6646 1 chr2A.!!$F2 6645
1 TraesCS2A01G206300 chr2A 408796000 408798025 2025 True 368.000000 368 93.5480 1 246 2 chr2A.!!$R2 245
2 TraesCS2A01G206300 chr2D 165474541 165480600 6059 True 4291.500000 5221 92.3260 626 6643 2 chr2D.!!$R1 6017
3 TraesCS2A01G206300 chr2B 232265803 232274219 8416 False 2841.333333 3408 90.5840 249 6646 3 chr2B.!!$F1 6397
4 TraesCS2A01G206300 chr6B 470792545 470794411 1866 False 419.000000 514 80.4295 2879 5079 2 chr6B.!!$F2 2200
5 TraesCS2A01G206300 chr6A 440536131 440539257 3126 True 426.000000 508 80.9775 2879 5079 2 chr6A.!!$R1 2200
6 TraesCS2A01G206300 chr6D 306052346 306054187 1841 True 409.500000 503 80.4840 2879 5079 2 chr6D.!!$R3 2200
7 TraesCS2A01G206300 chr7D 267998673 267999380 707 False 368.000000 368 93.5480 1 246 2 chr7D.!!$F2 245

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
246 2027 0.606604 AGGTGTGTCCGAAGCGTTAT 59.393 50.000 0.00 0.0 41.99 1.89 F
1541 3342 0.031857 TCCTGCGGTGTTGCAATTTG 59.968 50.000 0.59 0.0 45.74 2.32 F
2329 6119 0.764271 TGTGAGACTGCCATGGTGAA 59.236 50.000 14.67 0.0 0.00 3.18 F
2330 6120 1.352017 TGTGAGACTGCCATGGTGAAT 59.648 47.619 14.67 0.0 0.00 2.57 F
3648 7456 1.602311 ACAGGAGCTTGCAGAAACAG 58.398 50.000 0.00 0.0 0.00 3.16 F
4121 8009 1.002134 ACCGCATCCTGTTTCTGGG 60.002 57.895 0.00 0.0 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1554 3356 0.756294 TCCACGGAGCTTTTCACTCA 59.244 50.0 0.00 0.00 35.79 3.41 R
2867 6668 1.412079 AGCTCAGGTCATCAGCTAGG 58.588 55.0 0.00 0.00 41.84 3.02 R
3716 7524 0.723414 ATGCACGCGAAGTTCATGAG 59.277 50.0 15.93 0.00 35.44 2.90 R
3720 7528 2.073117 TAGAATGCACGCGAAGTTCA 57.927 45.0 15.93 2.82 0.00 3.18 R
4870 10300 0.035881 ACATCCTGTGCTGTGGTGAG 59.964 55.0 0.00 0.00 0.00 3.51 R
5865 11341 0.027586 GCACGGTACCGCATTTCATC 59.972 55.0 33.62 10.12 44.19 2.92 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
70 71 1.373570 GAAGCCCATTCGGACAGAAG 58.626 55.000 0.00 0.00 42.92 2.85
108 109 4.256920 GCTCAGCTTGGAGTAATTTCAGA 58.743 43.478 3.27 0.00 37.24 3.27
110 111 5.391416 GCTCAGCTTGGAGTAATTTCAGAAC 60.391 44.000 3.27 0.00 37.24 3.01
158 1939 1.227409 TGCGCGAGTGAGGACAAAA 60.227 52.632 12.10 0.00 0.00 2.44
170 1951 3.181482 TGAGGACAAAATGCGCAGAAAAA 60.181 39.130 18.32 0.00 0.00 1.94
225 2006 2.044555 CAGGAGTAGCGACCACCGA 61.045 63.158 0.00 0.00 41.76 4.69
227 2008 2.338015 GGAGTAGCGACCACCGACA 61.338 63.158 0.00 0.00 41.76 4.35
246 2027 0.606604 AGGTGTGTCCGAAGCGTTAT 59.393 50.000 0.00 0.00 41.99 1.89
247 2028 1.820519 AGGTGTGTCCGAAGCGTTATA 59.179 47.619 0.00 0.00 41.99 0.98
258 2039 1.683943 AGCGTTATAGAGGGCGTGTA 58.316 50.000 0.00 0.00 0.00 2.90
259 2040 2.026641 AGCGTTATAGAGGGCGTGTAA 58.973 47.619 0.00 0.00 0.00 2.41
270 2051 1.589803 GGCGTGTAAAGGTGTGTCTT 58.410 50.000 0.00 0.00 0.00 3.01
296 2077 0.750546 ATCTCGTGGGATTCGGTCGA 60.751 55.000 0.00 0.00 0.00 4.20
304 2085 1.677820 GGGATTCGGTCGATGTTGGTT 60.678 52.381 0.00 0.00 0.00 3.67
308 2089 1.141645 TCGGTCGATGTTGGTTTTCG 58.858 50.000 0.00 0.00 0.00 3.46
318 2099 3.283751 TGTTGGTTTTCGGTGAATCTGT 58.716 40.909 0.00 0.00 0.00 3.41
321 2102 4.561735 TGGTTTTCGGTGAATCTGTTTC 57.438 40.909 0.00 0.00 34.72 2.78
322 2103 4.204012 TGGTTTTCGGTGAATCTGTTTCT 58.796 39.130 0.70 0.00 35.23 2.52
325 2106 6.488683 TGGTTTTCGGTGAATCTGTTTCTATT 59.511 34.615 0.70 0.00 35.23 1.73
344 2125 6.697395 TCTATTTGGTCTTCGTTCATCTTCA 58.303 36.000 0.00 0.00 0.00 3.02
350 2131 6.227522 TGGTCTTCGTTCATCTTCATTTGTA 58.772 36.000 0.00 0.00 0.00 2.41
354 2135 8.230486 GTCTTCGTTCATCTTCATTTGTATGTT 58.770 33.333 0.00 0.00 33.34 2.71
368 2149 9.173021 TCATTTGTATGTTTATTGGTTCGATCT 57.827 29.630 0.00 0.00 33.34 2.75
372 2153 9.834628 TTGTATGTTTATTGGTTCGATCTTTTC 57.165 29.630 0.00 0.00 0.00 2.29
417 2198 2.472695 TGGTTGCTTCTCTAATGCGT 57.527 45.000 0.00 0.00 0.00 5.24
432 2220 2.046285 GCGTTGGTGGCCTTAGCAT 61.046 57.895 3.32 0.00 42.56 3.79
437 2225 1.526917 GGTGGCCTTAGCATGCGAT 60.527 57.895 13.01 0.00 42.56 4.58
440 2228 1.024271 TGGCCTTAGCATGCGATTTC 58.976 50.000 13.01 2.91 42.56 2.17
441 2229 1.312815 GGCCTTAGCATGCGATTTCT 58.687 50.000 13.01 0.00 42.56 2.52
442 2230 1.678101 GGCCTTAGCATGCGATTTCTT 59.322 47.619 13.01 0.00 42.56 2.52
452 2240 4.272018 GCATGCGATTTCTTGACTGTCTAT 59.728 41.667 0.00 0.00 0.00 1.98
455 2243 7.307632 GCATGCGATTTCTTGACTGTCTATTAT 60.308 37.037 0.00 0.00 0.00 1.28
502 2290 4.451150 GAGGCGATGACGGTGGCA 62.451 66.667 0.00 0.00 40.15 4.92
514 2302 3.432186 GTGGCACGCCTTCAACTT 58.568 55.556 9.92 0.00 36.94 2.66
517 2305 2.721231 GCACGCCTTCAACTTGCA 59.279 55.556 0.00 0.00 33.24 4.08
520 2308 1.817941 ACGCCTTCAACTTGCACGT 60.818 52.632 0.00 0.00 0.00 4.49
524 2312 0.732571 CCTTCAACTTGCACGTGTGT 59.267 50.000 18.38 10.98 0.00 3.72
530 2318 3.188667 TCAACTTGCACGTGTGTTTGTAA 59.811 39.130 18.38 0.00 0.00 2.41
539 2327 3.803231 ACGTGTGTTTGTAATCGTTGCTA 59.197 39.130 0.00 0.00 0.00 3.49
553 2341 1.122632 TTGCTAGGTGGTCCACGGAA 61.123 55.000 15.93 7.05 34.83 4.30
554 2342 1.079336 GCTAGGTGGTCCACGGAAC 60.079 63.158 15.93 1.90 34.83 3.62
558 2346 2.668550 GTGGTCCACGGAACTGGC 60.669 66.667 6.18 0.00 32.08 4.85
559 2347 2.847234 TGGTCCACGGAACTGGCT 60.847 61.111 2.19 0.00 32.08 4.75
560 2348 2.358737 GGTCCACGGAACTGGCTG 60.359 66.667 0.00 0.00 0.00 4.85
561 2349 2.426023 GTCCACGGAACTGGCTGT 59.574 61.111 0.00 0.00 0.00 4.40
562 2350 1.669440 GTCCACGGAACTGGCTGTA 59.331 57.895 0.00 0.00 0.00 2.74
576 2364 9.923143 GGAACTGGCTGTAATTTTTATTAGTTT 57.077 29.630 0.00 0.00 0.00 2.66
722 2513 4.100653 TGTTTGTTTGGCTGATTGATCCAA 59.899 37.500 0.00 0.00 38.03 3.53
723 2514 5.221682 TGTTTGTTTGGCTGATTGATCCAAT 60.222 36.000 0.00 0.00 39.36 3.16
736 2528 2.309755 TGATCCAATTGAGGCCTGACTT 59.690 45.455 12.00 0.00 0.00 3.01
754 2546 6.866770 CCTGACTTTCGTAGTAGATGAAAACA 59.133 38.462 0.00 0.00 41.49 2.83
759 2551 8.524487 ACTTTCGTAGTAGATGAAAACATCTCT 58.476 33.333 14.60 13.43 41.49 3.10
762 2554 9.706691 TTCGTAGTAGATGAAAACATCTCTTTT 57.293 29.630 14.60 0.00 41.65 2.27
772 2564 7.999679 TGAAAACATCTCTTTTCACTGAATGT 58.000 30.769 3.52 0.00 42.55 2.71
777 2569 3.494626 TCTCTTTTCACTGAATGTGCGTC 59.505 43.478 0.00 0.00 45.81 5.19
780 2572 1.565156 TTCACTGAATGTGCGTCGCC 61.565 55.000 15.88 6.76 45.81 5.54
790 2582 0.717224 GTGCGTCGCCGAAAATTCTA 59.283 50.000 15.88 0.00 35.63 2.10
800 2592 8.580431 CGTCGCCGAAAATTCTAAAATAAATTT 58.420 29.630 0.00 0.00 36.81 1.82
853 2645 4.215908 CTGGTGGACTAAGGATAGCACTA 58.784 47.826 0.00 0.00 31.96 2.74
875 2667 4.715534 TCCTCTTAACCATCCAACACAA 57.284 40.909 0.00 0.00 0.00 3.33
886 2678 4.502962 CATCCAACACAAGTTTGGTTTGT 58.497 39.130 1.21 0.00 39.23 2.83
922 2714 6.662865 TGTTATGTGATCAACAAATGGGTT 57.337 33.333 0.00 0.00 43.61 4.11
1150 2945 3.931907 TCCATCCTCCGATGTGATTTT 57.068 42.857 0.00 0.00 43.87 1.82
1420 3215 2.287915 CGGTGGCATAGCAGTGATTTAC 59.712 50.000 0.00 0.00 0.00 2.01
1457 3258 5.807520 GCTCTCTTGATGTAAAGTTCGATGA 59.192 40.000 0.00 0.00 0.00 2.92
1473 3274 6.093495 AGTTCGATGACAACAAAGTTGAGAAA 59.907 34.615 15.99 0.24 0.00 2.52
1535 3336 0.387239 GTCAATTCCTGCGGTGTTGC 60.387 55.000 0.00 0.00 0.00 4.17
1541 3342 0.031857 TCCTGCGGTGTTGCAATTTG 59.968 50.000 0.59 0.00 45.74 2.32
1598 3401 3.181476 ACCAAAATGTCAGTCCTTGCAAC 60.181 43.478 0.00 0.00 0.00 4.17
1841 5618 7.595819 AAAAGGTACACAATCTCATTTGGAA 57.404 32.000 0.00 0.00 0.00 3.53
1844 5621 7.595819 AGGTACACAATCTCATTTGGAAAAA 57.404 32.000 0.00 0.00 0.00 1.94
1924 5701 2.298163 AGGAGCACTGCCTTTTCATTTG 59.702 45.455 0.00 0.00 29.44 2.32
2029 5806 9.096823 TGACTATTACTCCCTCTGTAAAGAAAA 57.903 33.333 0.00 0.00 34.20 2.29
2128 5905 1.140312 ATATCTTCCGTGGCATGGGT 58.860 50.000 25.01 11.57 0.00 4.51
2159 5936 1.446792 CATGTCGCGTTGGAGAGCT 60.447 57.895 5.77 0.00 0.00 4.09
2165 5942 1.513158 GCGTTGGAGAGCTAGAGCA 59.487 57.895 4.01 0.00 45.16 4.26
2290 6067 1.076485 CCTCCTTCAGGCCATTGGG 60.076 63.158 5.01 1.48 34.56 4.12
2325 6115 1.100510 CCAATGTGAGACTGCCATGG 58.899 55.000 7.63 7.63 0.00 3.66
2328 6118 0.986527 ATGTGAGACTGCCATGGTGA 59.013 50.000 14.67 0.00 0.00 4.02
2329 6119 0.764271 TGTGAGACTGCCATGGTGAA 59.236 50.000 14.67 0.00 0.00 3.18
2330 6120 1.352017 TGTGAGACTGCCATGGTGAAT 59.648 47.619 14.67 0.00 0.00 2.57
2331 6121 2.571202 TGTGAGACTGCCATGGTGAATA 59.429 45.455 14.67 0.00 0.00 1.75
2332 6122 3.201290 GTGAGACTGCCATGGTGAATAG 58.799 50.000 14.67 7.03 0.00 1.73
2333 6123 3.106827 TGAGACTGCCATGGTGAATAGA 58.893 45.455 14.67 0.00 0.00 1.98
2334 6124 3.519107 TGAGACTGCCATGGTGAATAGAA 59.481 43.478 14.67 0.00 0.00 2.10
2335 6125 4.125703 GAGACTGCCATGGTGAATAGAAG 58.874 47.826 14.67 1.51 0.00 2.85
2336 6126 3.521126 AGACTGCCATGGTGAATAGAAGT 59.479 43.478 14.67 4.62 0.00 3.01
2337 6127 3.614092 ACTGCCATGGTGAATAGAAGTG 58.386 45.455 14.67 0.00 0.00 3.16
2338 6128 3.009473 ACTGCCATGGTGAATAGAAGTGT 59.991 43.478 14.67 0.00 0.00 3.55
2339 6129 4.012374 CTGCCATGGTGAATAGAAGTGTT 58.988 43.478 14.67 0.00 0.00 3.32
2340 6130 3.758023 TGCCATGGTGAATAGAAGTGTTG 59.242 43.478 14.67 0.00 0.00 3.33
2383 6173 5.693769 TTCTCTCCCGTCCAATCTTTAAT 57.306 39.130 0.00 0.00 0.00 1.40
2468 6258 2.621407 CCCCAGACATAGTTGGCATTGT 60.621 50.000 0.00 0.00 30.96 2.71
2550 6340 9.856488 GACATCACTCAGTTTAGTATGTCTAAA 57.144 33.333 0.00 0.00 43.65 1.85
2633 6430 2.892374 TGAGAGGTACATGCATTCACG 58.108 47.619 0.00 0.00 0.00 4.35
2679 6479 8.718734 GTGTATCTCTTCGTTTAGGTTCAAATT 58.281 33.333 0.00 0.00 0.00 1.82
2690 6490 2.368548 AGGTTCAAATTGGCAAAGACCC 59.631 45.455 3.01 5.13 0.00 4.46
2773 6573 3.006752 CCCAAAGGTTTCAGCAGCAATAA 59.993 43.478 0.00 0.00 0.00 1.40
2807 6608 3.425404 CCAAACGTTGACTTTGTGAGTG 58.575 45.455 0.00 0.00 39.19 3.51
2867 6668 3.653344 TGCCTAGCATGTCATCGATTAC 58.347 45.455 2.68 2.68 31.71 1.89
2912 6714 7.160726 ACATTTTGCTGGTTAATTTGTATGCT 58.839 30.769 0.00 0.00 0.00 3.79
3390 7198 8.193438 TCATTAATCGCATATCAGGATCTGTAG 58.807 37.037 0.00 0.00 32.61 2.74
3540 7348 1.603456 TTGCTTGAATGAACGGCAGA 58.397 45.000 0.00 0.00 34.37 4.26
3632 7440 7.968405 GGTGCCAAAACTATTTAATCTGTACAG 59.032 37.037 17.17 17.17 0.00 2.74
3648 7456 1.602311 ACAGGAGCTTGCAGAAACAG 58.398 50.000 0.00 0.00 0.00 3.16
3716 7524 3.364549 TCCATCCCATTGTTCATTGTCC 58.635 45.455 0.00 0.00 0.00 4.02
3720 7528 4.320546 TCCCATTGTTCATTGTCCTCAT 57.679 40.909 0.00 0.00 0.00 2.90
3730 7538 1.428448 TTGTCCTCATGAACTTCGCG 58.572 50.000 0.00 0.00 0.00 5.87
3746 7554 1.136110 TCGCGTGCATTCTATCTTGGA 59.864 47.619 5.77 0.00 0.00 3.53
3793 7601 7.804843 TTCTACTACTCCTCTACTTGCATAC 57.195 40.000 0.00 0.00 0.00 2.39
3809 7617 4.318332 TGCATACATTCTACCAGCTATGC 58.682 43.478 4.24 4.24 37.86 3.14
3837 7645 1.628340 ACCCAATGGAGTCATTCGACA 59.372 47.619 0.00 0.00 41.29 4.35
3888 7696 2.297701 GTCACAAAGCTGACAGGGAAA 58.702 47.619 4.26 0.00 40.40 3.13
3967 7775 5.157781 TGTATTCCGCACAAATTTAGCAAC 58.842 37.500 13.28 5.51 0.00 4.17
4064 7874 1.847968 CCTCTCTTGGTGGGGTGGT 60.848 63.158 0.00 0.00 0.00 4.16
4121 8009 1.002134 ACCGCATCCTGTTTCTGGG 60.002 57.895 0.00 0.00 0.00 4.45
4134 8791 3.505680 TGTTTCTGGGCATTATGTGTGTC 59.494 43.478 0.00 0.00 0.00 3.67
4154 8811 5.235616 GTGTCGGACACTATTTTCTCAAACA 59.764 40.000 29.09 0.00 45.27 2.83
4322 9732 7.658982 ACATTATGAGATTCATAGCACGTTGAT 59.341 33.333 0.00 0.00 40.13 2.57
4427 9839 4.109766 GGCGTAAAGTTTTCTTGCAGTTT 58.890 39.130 0.00 0.00 40.37 2.66
4453 9865 6.707440 TTTAATGAAGCACTGTCCTTTTGA 57.293 33.333 0.00 0.00 0.00 2.69
4550 9962 6.971602 TGTAAATACCATTTTTGTTCGCTCA 58.028 32.000 0.00 0.00 0.00 4.26
4551 9963 6.858993 TGTAAATACCATTTTTGTTCGCTCAC 59.141 34.615 0.00 0.00 0.00 3.51
4554 9966 3.482436 ACCATTTTTGTTCGCTCACCTA 58.518 40.909 0.00 0.00 0.00 3.08
4569 9981 2.168521 TCACCTATGGTAGCTGTTCAGC 59.831 50.000 15.88 15.88 32.11 4.26
4870 10300 0.463474 GTCTCCTGAGATTGGCCAGC 60.463 60.000 5.11 1.90 39.97 4.85
5080 10510 2.545106 GGCAGGTTTGTTGCATTTTCTG 59.455 45.455 0.00 0.00 43.28 3.02
5144 10580 8.330466 AGTGACTATCTTAGACTAATCATCGG 57.670 38.462 0.00 0.00 0.00 4.18
5262 10698 2.494059 ACACTCAAATCAAGGTGTCCG 58.506 47.619 0.00 0.00 38.32 4.79
5297 10749 1.339610 CAATGGTTCCAACTTGCGGAA 59.660 47.619 0.00 0.00 40.26 4.30
5322 10774 4.382291 TGTTTACACATACGCTGACCTTT 58.618 39.130 0.00 0.00 0.00 3.11
5389 10841 1.737355 TTTGTGTGCAGGAAGCTGGC 61.737 55.000 0.00 0.00 45.94 4.85
5439 10891 5.239306 TGTTAAGCCAGAACTCAGTCAAATG 59.761 40.000 0.00 0.00 0.00 2.32
5484 10936 7.994334 TCACCGGCATTAGTATTATAACCTTTT 59.006 33.333 0.00 0.00 0.00 2.27
5564 11029 1.936547 CTAACAGGGCGCAGAATTCTC 59.063 52.381 10.83 0.02 0.00 2.87
5601 11066 1.013596 TCTTGTGACAAACGGTGCTG 58.986 50.000 0.00 0.00 0.00 4.41
5678 11146 1.311859 CAGCTTCAAACAGGAGCACA 58.688 50.000 0.00 0.00 0.00 4.57
5748 11222 0.103937 GGTCTCGCATTCAGAGAGGG 59.896 60.000 0.00 0.00 44.41 4.30
5749 11223 0.103937 GTCTCGCATTCAGAGAGGGG 59.896 60.000 0.00 0.00 44.41 4.79
5750 11224 0.033109 TCTCGCATTCAGAGAGGGGA 60.033 55.000 0.00 0.00 43.50 4.81
5751 11225 0.826715 CTCGCATTCAGAGAGGGGAA 59.173 55.000 0.00 0.00 40.11 3.97
5752 11226 1.208052 CTCGCATTCAGAGAGGGGAAA 59.792 52.381 0.00 0.00 40.11 3.13
5779 11253 6.515272 ACGCATCCTTGTTCAGAATATTTT 57.485 33.333 0.00 0.00 0.00 1.82
5897 11373 1.519455 CCGTGCTCGATGTTCCCTC 60.519 63.158 10.21 0.00 39.71 4.30
5914 11390 2.608261 CCCTCGAGTCGGCATCTAAATC 60.608 54.545 13.54 0.00 0.00 2.17
5923 11399 1.876156 GGCATCTAAATCGCCTTCAGG 59.124 52.381 0.00 0.00 42.78 3.86
5973 11450 3.263425 TCTGAACCTGTTGGATAACCCTC 59.737 47.826 0.00 0.00 35.92 4.30
5979 11456 3.274288 CTGTTGGATAACCCTCAGAAGC 58.726 50.000 5.14 0.00 38.70 3.86
6154 11642 1.704641 AAAAGACACCCCCAAAGCTC 58.295 50.000 0.00 0.00 0.00 4.09
6206 11696 0.825425 TGCAAAATCGGCACCTTCCA 60.825 50.000 0.00 0.00 36.11 3.53
6214 11704 0.451783 CGGCACCTTCCAAGCATAAC 59.548 55.000 0.00 0.00 0.00 1.89
6216 11706 0.451783 GCACCTTCCAAGCATAACCG 59.548 55.000 0.00 0.00 0.00 4.44
6217 11707 1.948611 GCACCTTCCAAGCATAACCGA 60.949 52.381 0.00 0.00 0.00 4.69
6218 11708 2.643551 CACCTTCCAAGCATAACCGAT 58.356 47.619 0.00 0.00 0.00 4.18
6219 11709 3.016736 CACCTTCCAAGCATAACCGATT 58.983 45.455 0.00 0.00 0.00 3.34
6222 11712 4.082245 ACCTTCCAAGCATAACCGATTTTG 60.082 41.667 0.00 0.00 0.00 2.44
6223 11713 3.502191 TCCAAGCATAACCGATTTTGC 57.498 42.857 0.00 0.00 41.54 3.68
6224 11714 2.822561 TCCAAGCATAACCGATTTTGCA 59.177 40.909 7.72 0.00 43.09 4.08
6225 11715 3.256879 TCCAAGCATAACCGATTTTGCAA 59.743 39.130 7.72 0.00 43.09 4.08
6226 11716 3.993081 CCAAGCATAACCGATTTTGCAAA 59.007 39.130 8.05 8.05 43.09 3.68
6227 11717 4.450419 CCAAGCATAACCGATTTTGCAAAA 59.550 37.500 25.76 25.76 43.09 2.44
6228 11718 5.122082 CCAAGCATAACCGATTTTGCAAAAT 59.878 36.000 32.11 32.11 43.09 1.82
6229 11719 6.242829 CAAGCATAACCGATTTTGCAAAATC 58.757 36.000 38.01 38.01 46.72 2.17
6236 11726 2.687370 GATTTTGCAAAATCGGCACCT 58.313 42.857 36.25 17.24 43.17 4.00
6237 11727 2.611225 TTTTGCAAAATCGGCACCTT 57.389 40.000 20.46 0.00 41.75 3.50
6238 11728 2.147436 TTTGCAAAATCGGCACCTTC 57.853 45.000 10.02 0.00 41.75 3.46
6239 11729 0.316841 TTGCAAAATCGGCACCTTCC 59.683 50.000 0.00 0.00 41.75 3.46
6240 11730 0.825425 TGCAAAATCGGCACCTTCCA 60.825 50.000 0.00 0.00 36.11 3.53
6255 11745 0.904394 TTCCAAGCCCAGCAAATCCC 60.904 55.000 0.00 0.00 0.00 3.85
6257 11747 2.362889 AAGCCCAGCAAATCCCCG 60.363 61.111 0.00 0.00 0.00 5.73
6269 11759 1.186917 AATCCCCGTCACGTACACCA 61.187 55.000 0.00 0.00 0.00 4.17
6272 11762 2.260434 CCGTCACGTACACCAGGG 59.740 66.667 0.00 0.00 0.00 4.45
6276 11766 2.126071 CACGTACACCAGGGCGAG 60.126 66.667 0.00 0.00 0.00 5.03
6294 11784 0.959372 AGCTTTACTGCTGCAGCCAG 60.959 55.000 34.64 29.81 42.33 4.85
6404 11895 6.234177 ACATTATATCTTCTTGCTGTAGCCC 58.766 40.000 0.80 0.00 41.18 5.19
6424 11915 0.322816 ATGCTGACTTTGATGGGCGT 60.323 50.000 0.00 0.00 0.00 5.68
6425 11916 0.323302 TGCTGACTTTGATGGGCGTA 59.677 50.000 0.00 0.00 0.00 4.42
6426 11917 1.271108 TGCTGACTTTGATGGGCGTAA 60.271 47.619 0.00 0.00 0.00 3.18
6427 11918 2.017049 GCTGACTTTGATGGGCGTAAT 58.983 47.619 0.00 0.00 0.00 1.89
6458 11951 4.397417 AGGCTACTGATCAGATGTTTTTGC 59.603 41.667 29.27 16.41 0.00 3.68
6459 11952 4.439289 GGCTACTGATCAGATGTTTTTGCC 60.439 45.833 29.27 20.92 0.00 4.52
6464 11957 2.798976 TCAGATGTTTTTGCCTGCAC 57.201 45.000 0.00 0.00 0.00 4.57
6465 11958 1.001487 TCAGATGTTTTTGCCTGCACG 60.001 47.619 0.00 0.00 0.00 5.34
6477 11970 1.057822 CTGCACGAAGTCGCGATTG 59.942 57.895 14.06 3.26 41.61 2.67
6478 11971 2.276058 GCACGAAGTCGCGATTGC 60.276 61.111 14.06 5.59 41.61 3.56
6566 12065 0.250513 GTCGAAGGCATCAAGAGGGT 59.749 55.000 0.00 0.00 0.00 4.34
6567 12066 0.984230 TCGAAGGCATCAAGAGGGTT 59.016 50.000 0.00 0.00 0.00 4.11
6568 12067 2.093658 GTCGAAGGCATCAAGAGGGTTA 60.094 50.000 0.00 0.00 0.00 2.85
6569 12068 2.569853 TCGAAGGCATCAAGAGGGTTAA 59.430 45.455 0.00 0.00 0.00 2.01
6570 12069 2.678336 CGAAGGCATCAAGAGGGTTAAC 59.322 50.000 0.00 0.00 0.00 2.01
6572 12071 3.356529 AGGCATCAAGAGGGTTAACTG 57.643 47.619 5.42 0.00 0.00 3.16
6573 12072 2.025887 AGGCATCAAGAGGGTTAACTGG 60.026 50.000 5.42 0.00 0.00 4.00
6575 12074 3.372025 GGCATCAAGAGGGTTAACTGGAT 60.372 47.826 5.42 0.00 0.00 3.41
6576 12075 4.141482 GGCATCAAGAGGGTTAACTGGATA 60.141 45.833 5.42 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 1.871039 TGAGCACGCTTAACTTTGGAC 59.129 47.619 0.00 0.00 0.00 4.02
170 1951 3.136626 GGCCCCACAGATCAATACTAGTT 59.863 47.826 0.00 0.00 0.00 2.24
225 2006 2.029073 CGCTTCGGACACACCTGT 59.971 61.111 0.00 0.00 36.31 4.00
227 2008 0.606604 ATAACGCTTCGGACACACCT 59.393 50.000 0.00 0.00 36.31 4.00
238 2019 0.822164 ACACGCCCTCTATAACGCTT 59.178 50.000 0.00 0.00 0.00 4.68
239 2020 1.683943 TACACGCCCTCTATAACGCT 58.316 50.000 0.00 0.00 0.00 5.07
246 2027 1.274167 CACACCTTTACACGCCCTCTA 59.726 52.381 0.00 0.00 0.00 2.43
247 2028 0.034896 CACACCTTTACACGCCCTCT 59.965 55.000 0.00 0.00 0.00 3.69
258 2039 0.748450 TCCGACGAAGACACACCTTT 59.252 50.000 0.00 0.00 0.00 3.11
259 2040 0.966920 ATCCGACGAAGACACACCTT 59.033 50.000 0.00 0.00 0.00 3.50
270 2051 0.750546 AATCCCACGAGATCCGACGA 60.751 55.000 10.05 3.59 41.76 4.20
296 2077 3.888930 ACAGATTCACCGAAAACCAACAT 59.111 39.130 0.00 0.00 0.00 2.71
304 2085 6.488683 ACCAAATAGAAACAGATTCACCGAAA 59.511 34.615 0.00 0.00 40.72 3.46
308 2089 7.454260 AAGACCAAATAGAAACAGATTCACC 57.546 36.000 0.00 0.00 40.72 4.02
318 2099 7.659799 TGAAGATGAACGAAGACCAAATAGAAA 59.340 33.333 0.00 0.00 0.00 2.52
321 2102 6.968131 TGAAGATGAACGAAGACCAAATAG 57.032 37.500 0.00 0.00 0.00 1.73
322 2103 7.921786 AATGAAGATGAACGAAGACCAAATA 57.078 32.000 0.00 0.00 0.00 1.40
325 2106 5.530915 ACAAATGAAGATGAACGAAGACCAA 59.469 36.000 0.00 0.00 0.00 3.67
393 2174 3.375299 GCATTAGAGAAGCAACCATCGTT 59.625 43.478 0.00 0.00 0.00 3.85
411 2192 1.595093 GCTAAGGCCACCAACGCATT 61.595 55.000 5.01 0.00 34.19 3.56
417 2198 2.045708 CGCATGCTAAGGCCACCAA 61.046 57.895 17.13 0.00 37.74 3.67
432 2220 9.031360 GTTATAATAGACAGTCAAGAAATCGCA 57.969 33.333 2.66 0.00 0.00 5.10
477 2265 1.676014 CCGTCATCGCCTCTCCTTTTT 60.676 52.381 0.00 0.00 35.54 1.94
478 2266 0.108138 CCGTCATCGCCTCTCCTTTT 60.108 55.000 0.00 0.00 35.54 2.27
479 2267 1.258445 ACCGTCATCGCCTCTCCTTT 61.258 55.000 0.00 0.00 35.54 3.11
481 2269 2.043852 ACCGTCATCGCCTCTCCT 60.044 61.111 0.00 0.00 35.54 3.69
502 2290 1.817941 ACGTGCAAGTTGAAGGCGT 60.818 52.632 7.16 7.73 0.00 5.68
510 2298 3.833545 TTACAAACACACGTGCAAGTT 57.166 38.095 17.22 15.10 0.00 2.66
511 2299 3.545228 CGATTACAAACACACGTGCAAGT 60.545 43.478 17.22 9.36 0.00 3.16
514 2302 1.934525 ACGATTACAAACACACGTGCA 59.065 42.857 17.22 0.00 32.93 4.57
517 2305 2.610374 AGCAACGATTACAAACACACGT 59.390 40.909 0.00 0.00 35.56 4.49
520 2308 4.212425 CACCTAGCAACGATTACAAACACA 59.788 41.667 0.00 0.00 0.00 3.72
524 2312 3.998341 GACCACCTAGCAACGATTACAAA 59.002 43.478 0.00 0.00 0.00 2.83
530 2318 0.249398 GTGGACCACCTAGCAACGAT 59.751 55.000 14.16 0.00 37.04 3.73
539 2327 2.516888 CCAGTTCCGTGGACCACCT 61.517 63.158 19.11 7.16 40.44 4.00
576 2364 7.939782 ACAATTGACAGTACAAATGACATCAA 58.060 30.769 13.59 0.00 35.18 2.57
577 2365 7.228308 TGACAATTGACAGTACAAATGACATCA 59.772 33.333 13.59 0.00 33.36 3.07
579 2367 7.509141 TGACAATTGACAGTACAAATGACAT 57.491 32.000 13.59 0.00 33.36 3.06
647 2435 3.688272 CAAGTGTGTGAGCTTTGTTCAG 58.312 45.455 0.00 0.00 0.00 3.02
648 2436 2.159393 GCAAGTGTGTGAGCTTTGTTCA 60.159 45.455 0.00 0.00 0.00 3.18
814 2606 6.661805 GTCCACCAGGGTTCAAAATCTTAATA 59.338 38.462 0.00 0.00 38.11 0.98
816 2608 4.830600 GTCCACCAGGGTTCAAAATCTTAA 59.169 41.667 0.00 0.00 38.11 1.85
825 2617 1.132657 TCCTTAGTCCACCAGGGTTCA 60.133 52.381 0.00 0.00 38.11 3.18
830 2622 2.103263 GTGCTATCCTTAGTCCACCAGG 59.897 54.545 0.00 0.00 0.00 4.45
853 2645 4.927267 TGTGTTGGATGGTTAAGAGGAT 57.073 40.909 0.00 0.00 0.00 3.24
957 2752 1.068250 GAGCAGGACGGCTGATACC 59.932 63.158 0.00 0.00 45.99 2.73
1240 3035 3.221222 AAGGGGAGATCGCTTCCG 58.779 61.111 0.00 0.00 43.99 4.30
1244 3039 1.458588 GAGGGAAGGGGAGATCGCT 60.459 63.158 0.00 0.00 41.01 4.93
1420 3215 5.392767 TCAAGAGAGCTACTTTACAGTGG 57.607 43.478 3.33 0.00 34.06 4.00
1554 3356 0.756294 TCCACGGAGCTTTTCACTCA 59.244 50.000 0.00 0.00 35.79 3.41
1579 3381 3.701040 ACAGTTGCAAGGACTGACATTTT 59.299 39.130 21.00 0.00 45.72 1.82
1583 3385 3.070878 TCATACAGTTGCAAGGACTGACA 59.929 43.478 21.00 10.22 45.72 3.58
1598 3401 8.430828 CAATATGTCTCGTGCTTTATCATACAG 58.569 37.037 0.00 0.00 0.00 2.74
1844 5621 9.787435 TTGTTGTTCTACTCTGTATGGTTAAAT 57.213 29.630 0.00 0.00 0.00 1.40
1924 5701 6.161381 TGTACATAAACCTTCTTCTTCGTCC 58.839 40.000 0.00 0.00 0.00 4.79
1965 5742 3.232720 GGTTTCCACCAAGTTCCCTTA 57.767 47.619 0.00 0.00 43.61 2.69
1978 5755 4.349636 TCTGTTCCTGTCTTATGGTTTCCA 59.650 41.667 0.00 0.00 38.19 3.53
2070 5847 8.858094 ACTCCCTCCGTAAAGAAATACTATAAG 58.142 37.037 0.00 0.00 0.00 1.73
2074 5851 6.547510 GGTACTCCCTCCGTAAAGAAATACTA 59.452 42.308 0.00 0.00 0.00 1.82
2075 5852 5.362143 GGTACTCCCTCCGTAAAGAAATACT 59.638 44.000 0.00 0.00 0.00 2.12
2076 5853 5.362143 AGGTACTCCCTCCGTAAAGAAATAC 59.638 44.000 0.00 0.00 40.71 1.89
2105 5882 2.575532 CATGCCACGGAAGATATTGGT 58.424 47.619 0.00 0.00 0.00 3.67
2112 5889 2.350895 CACCCATGCCACGGAAGA 59.649 61.111 0.00 0.00 0.00 2.87
2128 5905 2.916703 ACATGGCTTTTGGGCGCA 60.917 55.556 10.83 0.00 44.11 6.09
2159 5936 3.084039 CCATTTTGAGGTTGCTGCTCTA 58.916 45.455 0.00 0.00 0.00 2.43
2165 5942 2.242043 CTCACCCATTTTGAGGTTGCT 58.758 47.619 0.00 0.00 37.44 3.91
2208 5985 5.242838 GGAACATATGGAAGAAACACAACCA 59.757 40.000 7.80 0.00 35.09 3.67
2262 6039 0.318441 CTGAAGGAGGTCAAGCGACA 59.682 55.000 0.00 0.00 44.54 4.35
2290 6067 0.830648 TTGGTGGGACGAGATGATCC 59.169 55.000 0.00 0.00 0.00 3.36
2325 6115 3.000727 CGGACCCAACACTTCTATTCAC 58.999 50.000 0.00 0.00 0.00 3.18
2328 6118 1.339727 GGCGGACCCAACACTTCTATT 60.340 52.381 0.00 0.00 0.00 1.73
2329 6119 0.252197 GGCGGACCCAACACTTCTAT 59.748 55.000 0.00 0.00 0.00 1.98
2330 6120 1.675219 GGCGGACCCAACACTTCTA 59.325 57.895 0.00 0.00 0.00 2.10
2331 6121 2.430367 GGCGGACCCAACACTTCT 59.570 61.111 0.00 0.00 0.00 2.85
2332 6122 3.047877 CGGCGGACCCAACACTTC 61.048 66.667 0.00 0.00 0.00 3.01
2337 6127 3.767630 ATATGGCGGCGGACCCAAC 62.768 63.158 9.78 0.00 34.25 3.77
2338 6128 3.469863 GATATGGCGGCGGACCCAA 62.470 63.158 9.78 0.00 34.25 4.12
2339 6129 3.936203 GATATGGCGGCGGACCCA 61.936 66.667 9.78 8.29 35.21 4.51
2340 6130 4.699522 GGATATGGCGGCGGACCC 62.700 72.222 9.78 1.24 0.00 4.46
2383 6173 4.007644 CAGCGGTCTGGAGCCACA 62.008 66.667 0.00 0.00 36.68 4.17
2468 6258 3.148412 CATTTGATGGCCGTATGATCCA 58.852 45.455 0.00 0.00 0.00 3.41
2556 6346 8.704849 TTCAGGTATATATGTTGGAATTTGGG 57.295 34.615 0.00 0.00 0.00 4.12
2616 6413 2.309528 TCCGTGAATGCATGTACCTC 57.690 50.000 0.00 0.00 0.00 3.85
2633 6430 6.272822 ACACAAGAAATAATTCTGGCTTCC 57.727 37.500 0.00 0.00 45.19 3.46
2679 6479 1.799933 ACCAAAATGGGTCTTTGCCA 58.200 45.000 0.87 0.00 43.37 4.92
2703 6503 4.693566 TCTCAGTAACCGCAATAAAACTGG 59.306 41.667 0.00 0.00 36.01 4.00
2711 6511 2.028112 TGCTCTTCTCAGTAACCGCAAT 60.028 45.455 0.00 0.00 0.00 3.56
2773 6573 2.371306 ACGTTTGGGTTTAGTGCAGTT 58.629 42.857 0.00 0.00 0.00 3.16
2807 6608 4.096833 TCACCATTAAATGATGCACTGAGC 59.903 41.667 0.00 0.00 45.96 4.26
2867 6668 1.412079 AGCTCAGGTCATCAGCTAGG 58.588 55.000 0.00 0.00 41.84 3.02
3076 6878 3.317149 CAGGGTAAATGTGGCATCAGATG 59.683 47.826 5.98 5.98 0.00 2.90
3390 7198 5.227908 TGATAACTCAGTGGAACGAACTTC 58.772 41.667 0.00 0.00 45.86 3.01
3540 7348 9.579932 CTCCCATAAAATAATTAGGAAGAGCTT 57.420 33.333 0.00 0.00 0.00 3.74
3632 7440 0.886563 ATGCTGTTTCTGCAAGCTCC 59.113 50.000 8.68 0.00 41.24 4.70
3648 7456 3.429925 GCTCAGCCAGCCTAATGC 58.570 61.111 0.00 0.00 43.17 3.56
3716 7524 0.723414 ATGCACGCGAAGTTCATGAG 59.277 50.000 15.93 0.00 35.44 2.90
3720 7528 2.073117 TAGAATGCACGCGAAGTTCA 57.927 45.000 15.93 2.82 0.00 3.18
3730 7538 5.529060 CCCTTAAGTCCAAGATAGAATGCAC 59.471 44.000 0.97 0.00 0.00 4.57
3746 7554 4.985538 TCTTGCAGAATCAACCCTTAAGT 58.014 39.130 0.97 0.00 0.00 2.24
3793 7601 7.118390 GGTTAGTTATGCATAGCTGGTAGAATG 59.882 40.741 27.60 0.00 0.00 2.67
3809 7617 6.017934 CGAATGACTCCATTGGGTTAGTTATG 60.018 42.308 2.09 0.00 42.66 1.90
3837 7645 9.378551 GAAAGGTACAATTTTCAAAAGAAAGGT 57.621 29.630 10.20 0.00 34.31 3.50
3888 7696 4.497291 TTGTGGACTCTTACAACTTGGT 57.503 40.909 0.00 0.00 32.30 3.67
3967 7775 3.813443 ACTATGCCTGTTATGCTCCTTG 58.187 45.455 0.00 0.00 0.00 3.61
4064 7874 9.109393 GTGATAAGCCTTATAATGAACACAGAA 57.891 33.333 0.00 0.00 0.00 3.02
4134 8791 5.007234 TGTGTGTTTGAGAAAATAGTGTCCG 59.993 40.000 0.00 0.00 0.00 4.79
4322 9732 6.040278 TGTGGAAAATCATCAAGCTACAAACA 59.960 34.615 0.00 0.00 0.00 2.83
4404 9814 2.286772 ACTGCAAGAAAACTTTACGCCG 60.287 45.455 0.00 0.00 37.43 6.46
4453 9865 9.777297 ACTTGGTATTATCAAAGTTTGCAAATT 57.223 25.926 16.21 8.48 0.00 1.82
4488 9900 7.934120 GCCAAACTAAGTATTCAGACATCCTAT 59.066 37.037 0.00 0.00 0.00 2.57
4616 10028 4.960938 TGTAGTGACCATGATCTATTGCC 58.039 43.478 0.00 0.00 0.00 4.52
4870 10300 0.035881 ACATCCTGTGCTGTGGTGAG 59.964 55.000 0.00 0.00 0.00 3.51
5136 10572 4.965814 AGCATTATCACTCACCGATGATT 58.034 39.130 0.00 0.00 36.87 2.57
5144 10580 4.186926 TCAGCAAGAGCATTATCACTCAC 58.813 43.478 0.00 0.00 45.49 3.51
5234 10670 1.890876 TGATTTGAGTGTTCACCCGG 58.109 50.000 0.00 0.00 31.71 5.73
5262 10698 3.667360 ACCATTGGAATTTCAAGCAAGC 58.333 40.909 10.37 0.00 0.00 4.01
5297 10749 5.914033 AGGTCAGCGTATGTGTAAACATAT 58.086 37.500 8.99 0.00 35.37 1.78
5322 10774 3.788227 ATGCAAACAGTGGGAGTAGAA 57.212 42.857 0.00 0.00 0.00 2.10
5564 11029 0.391263 GAACACCGCCTGAAGGGTAG 60.391 60.000 0.00 0.00 33.95 3.18
5612 11077 2.683362 TGCTGATATCAGTTCGACGAGT 59.317 45.455 28.92 0.00 45.45 4.18
5627 11092 3.313526 GCATCTATTCGTGGTTTGCTGAT 59.686 43.478 0.00 0.00 0.00 2.90
5637 11102 5.630061 TGTGAAACATTGCATCTATTCGTG 58.370 37.500 0.00 0.00 45.67 4.35
5752 11226 4.647424 TTCTGAACAAGGATGCGTTTTT 57.353 36.364 0.00 0.00 0.00 1.94
5779 11253 5.048782 GGAACTGTGCTGTTTGATTCATGTA 60.049 40.000 0.00 0.00 0.00 2.29
5792 11268 1.972872 AGTCAAAGGGAACTGTGCTG 58.027 50.000 0.00 0.00 45.96 4.41
5864 11340 1.364721 CACGGTACCGCATTTCATCA 58.635 50.000 33.62 0.00 44.19 3.07
5865 11341 0.027586 GCACGGTACCGCATTTCATC 59.972 55.000 33.62 10.12 44.19 2.92
5866 11342 0.392461 AGCACGGTACCGCATTTCAT 60.392 50.000 33.62 10.05 44.19 2.57
5897 11373 0.778815 GCGATTTAGATGCCGACTCG 59.221 55.000 0.00 0.00 0.00 4.18
5914 11390 2.482142 GGACTGTAGAATCCTGAAGGCG 60.482 54.545 0.00 0.00 34.44 5.52
5923 11399 3.055094 TGAAGGCCAAGGACTGTAGAATC 60.055 47.826 5.01 0.00 31.22 2.52
5973 11450 1.067142 ACCATGCAATGCAAGCTTCTG 60.067 47.619 13.45 4.48 44.97 3.02
5979 11456 1.529622 CGTACGACCATGCAATGCAAG 60.530 52.381 13.45 7.95 44.97 4.01
6058 11535 1.757118 TCCGAGATTTCGCTTCTCCAT 59.243 47.619 0.00 0.00 45.38 3.41
6195 11683 0.451783 GTTATGCTTGGAAGGTGCCG 59.548 55.000 0.00 0.00 0.00 5.69
6206 11696 6.407475 GATTTTGCAAAATCGGTTATGCTT 57.593 33.333 36.25 15.49 43.17 3.91
6216 11706 2.687370 AGGTGCCGATTTTGCAAAATC 58.313 42.857 38.01 38.01 46.72 2.17
6217 11707 2.837532 AGGTGCCGATTTTGCAAAAT 57.162 40.000 32.11 32.11 41.06 1.82
6218 11708 2.478831 GAAGGTGCCGATTTTGCAAAA 58.521 42.857 25.76 25.76 41.06 2.44
6219 11709 1.270041 GGAAGGTGCCGATTTTGCAAA 60.270 47.619 8.05 8.05 41.06 3.68
6222 11712 0.316841 TTGGAAGGTGCCGATTTTGC 59.683 50.000 0.00 0.00 0.00 3.68
6223 11713 1.669795 GCTTGGAAGGTGCCGATTTTG 60.670 52.381 0.00 0.00 0.00 2.44
6224 11714 0.603065 GCTTGGAAGGTGCCGATTTT 59.397 50.000 0.00 0.00 0.00 1.82
6225 11715 1.250840 GGCTTGGAAGGTGCCGATTT 61.251 55.000 0.00 0.00 37.11 2.17
6226 11716 1.678970 GGCTTGGAAGGTGCCGATT 60.679 57.895 0.00 0.00 37.11 3.34
6227 11717 2.044946 GGCTTGGAAGGTGCCGAT 60.045 61.111 0.00 0.00 37.11 4.18
6228 11718 4.344865 GGGCTTGGAAGGTGCCGA 62.345 66.667 0.00 0.00 46.97 5.54
6229 11719 4.659172 TGGGCTTGGAAGGTGCCG 62.659 66.667 0.00 0.00 46.97 5.69
6230 11720 2.677875 CTGGGCTTGGAAGGTGCC 60.678 66.667 0.00 0.00 45.42 5.01
6231 11721 3.376918 GCTGGGCTTGGAAGGTGC 61.377 66.667 0.00 0.00 0.00 5.01
6232 11722 1.114722 TTTGCTGGGCTTGGAAGGTG 61.115 55.000 0.00 0.00 0.00 4.00
6233 11723 0.178924 ATTTGCTGGGCTTGGAAGGT 60.179 50.000 0.00 0.00 0.00 3.50
6234 11724 0.533951 GATTTGCTGGGCTTGGAAGG 59.466 55.000 0.00 0.00 0.00 3.46
6235 11725 0.533951 GGATTTGCTGGGCTTGGAAG 59.466 55.000 0.00 0.00 0.00 3.46
6236 11726 0.904394 GGGATTTGCTGGGCTTGGAA 60.904 55.000 0.00 0.00 0.00 3.53
6237 11727 1.305213 GGGATTTGCTGGGCTTGGA 60.305 57.895 0.00 0.00 0.00 3.53
6238 11728 2.361567 GGGGATTTGCTGGGCTTGG 61.362 63.158 0.00 0.00 0.00 3.61
6239 11729 2.713967 CGGGGATTTGCTGGGCTTG 61.714 63.158 0.00 0.00 0.00 4.01
6240 11730 2.362889 CGGGGATTTGCTGGGCTT 60.363 61.111 0.00 0.00 0.00 4.35
6255 11745 2.260434 CCCTGGTGTACGTGACGG 59.740 66.667 10.66 0.00 0.00 4.79
6257 11747 2.431942 CGCCCTGGTGTACGTGAC 60.432 66.667 0.00 0.00 0.00 3.67
6269 11759 1.078848 CAGCAGTAAAGCTCGCCCT 60.079 57.895 0.00 0.00 44.54 5.19
6272 11762 1.423056 CTGCAGCAGTAAAGCTCGC 59.577 57.895 14.90 0.00 44.54 5.03
6276 11766 1.505353 CTGGCTGCAGCAGTAAAGC 59.495 57.895 37.63 20.06 44.36 3.51
6294 11784 2.733593 GTGTCCAGACCGTCGTGC 60.734 66.667 0.00 0.00 0.00 5.34
6295 11785 1.371758 CAGTGTCCAGACCGTCGTG 60.372 63.158 0.00 0.00 0.00 4.35
6404 11895 0.099968 CGCCCATCAAAGTCAGCATG 59.900 55.000 0.00 0.00 37.54 4.06
6425 11916 9.941325 CATCTGATCAGTAGCCTTTCTTATATT 57.059 33.333 21.92 0.00 0.00 1.28
6426 11917 9.099071 ACATCTGATCAGTAGCCTTTCTTATAT 57.901 33.333 21.92 0.53 0.00 0.86
6427 11918 8.484214 ACATCTGATCAGTAGCCTTTCTTATA 57.516 34.615 21.92 0.00 0.00 0.98
6464 11957 1.870458 TACGGCAATCGCGACTTCG 60.870 57.895 12.93 15.79 43.89 3.79
6465 11958 1.629504 GTACGGCAATCGCGACTTC 59.370 57.895 12.93 0.00 43.89 3.01
6478 11971 2.373269 CTATTCTGAAGACGCGTACGG 58.627 52.381 13.97 12.32 46.04 4.02
6566 12065 4.640201 GGCAGCATTTCAGTATCCAGTTAA 59.360 41.667 0.00 0.00 0.00 2.01
6567 12066 4.080356 AGGCAGCATTTCAGTATCCAGTTA 60.080 41.667 0.00 0.00 0.00 2.24
6568 12067 3.019564 GGCAGCATTTCAGTATCCAGTT 58.980 45.455 0.00 0.00 0.00 3.16
6569 12068 2.240667 AGGCAGCATTTCAGTATCCAGT 59.759 45.455 0.00 0.00 0.00 4.00
6570 12069 2.617308 CAGGCAGCATTTCAGTATCCAG 59.383 50.000 0.00 0.00 0.00 3.86
6572 12071 2.615912 GACAGGCAGCATTTCAGTATCC 59.384 50.000 0.00 0.00 0.00 2.59
6573 12072 2.286294 CGACAGGCAGCATTTCAGTATC 59.714 50.000 0.00 0.00 0.00 2.24
6575 12074 1.725641 CGACAGGCAGCATTTCAGTA 58.274 50.000 0.00 0.00 0.00 2.74
6576 12075 1.580845 GCGACAGGCAGCATTTCAGT 61.581 55.000 0.00 0.00 42.87 3.41


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

AutoCloner maintained by Alex Coulton.