Multiple sequence alignment - TraesCS5D01G529700

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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 TraesCS5D01G529700 chr5D 100.000 4140 0 0 1 4140 546088108 546083969 0.000000e+00 7646.0
1 TraesCS5D01G529700 chr5D 81.982 222 20 16 1995 2198 546085880 546085661 1.980000e-38 171.0
2 TraesCS5D01G529700 chr5D 81.982 222 20 16 2229 2448 546086114 546085911 1.980000e-38 171.0
3 TraesCS5D01G529700 chr5B 90.381 3618 166 80 598 4140 689376959 689373449 0.000000e+00 4586.0
4 TraesCS5D01G529700 chr5B 84.259 324 37 11 3820 4140 527840309 527840621 1.870000e-78 303.0
5 TraesCS5D01G529700 chr5B 86.829 205 20 5 2245 2448 689375603 689375405 5.390000e-54 222.0
6 TraesCS5D01G529700 chr4A 92.322 2188 121 22 810 2959 623315104 623317282 0.000000e+00 3066.0
7 TraesCS5D01G529700 chr4A 93.621 1066 59 7 3077 4140 623317342 623318400 0.000000e+00 1583.0
8 TraesCS5D01G529700 chr4A 81.933 476 79 7 81 551 623314246 623314719 3.000000e-106 396.0
9 TraesCS5D01G529700 chr4A 84.375 320 38 9 3822 4140 655565367 655565675 1.870000e-78 303.0
10 TraesCS5D01G529700 chr4A 81.982 222 22 9 2229 2448 623316309 623316514 5.500000e-39 172.0
11 TraesCS5D01G529700 chr4A 80.717 223 24 13 1995 2198 623316550 623316772 5.540000e-34 156.0
12 TraesCS5D01G529700 chr4A 97.436 39 1 0 600 638 623314950 623314988 2.670000e-07 67.6
13 TraesCS5D01G529700 chr2B 86.268 619 62 12 2013 2612 22843838 22844452 0.000000e+00 651.0
14 TraesCS5D01G529700 chr2B 86.107 619 63 12 2013 2612 22904036 22904650 0.000000e+00 645.0
15 TraesCS5D01G529700 chr2B 85.093 322 36 9 3820 4140 35130036 35129726 6.680000e-83 318.0
16 TraesCS5D01G529700 chr2B 74.304 467 69 39 2245 2684 22904034 22904476 2.580000e-32 150.0
17 TraesCS5D01G529700 chr2B 74.187 461 68 33 2245 2678 22843836 22844272 1.200000e-30 145.0
18 TraesCS5D01G529700 chr2B 92.157 51 4 0 2050 2100 22844372 22844422 5.740000e-09 73.1
19 TraesCS5D01G529700 chr2B 92.157 51 4 0 2050 2100 22904570 22904620 5.740000e-09 73.1
20 TraesCS5D01G529700 chr4B 84.314 306 37 8 3835 4140 90861134 90860840 5.240000e-74 289.0
21 TraesCS5D01G529700 chr3D 81.690 213 31 7 3859 4070 592170591 592170796 1.980000e-38 171.0
22 TraesCS5D01G529700 chr3D 81.690 213 31 7 3859 4070 592238821 592239026 1.980000e-38 171.0
23 TraesCS5D01G529700 chr3D 80.751 213 33 7 3859 4070 592319107 592319312 4.280000e-35 159.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G529700 chr5D 546083969 546088108 4139 True 2662.666667 7646 87.988000 1 4140 3 chr5D.!!$R1 4139
1 TraesCS5D01G529700 chr5B 689373449 689376959 3510 True 2404.000000 4586 88.605000 598 4140 2 chr5B.!!$R1 3542
2 TraesCS5D01G529700 chr4A 623314246 623318400 4154 False 906.766667 3066 88.001833 81 4140 6 chr4A.!!$F2 4059
3 TraesCS5D01G529700 chr2B 22843836 22844452 616 False 289.700000 651 84.204000 2013 2678 3 chr2B.!!$F1 665
4 TraesCS5D01G529700 chr2B 22904034 22904650 616 False 289.366667 645 84.189333 2013 2684 3 chr2B.!!$F2 671

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
74 75 0.039165 CTCCTTTTGCCGCCTTTGTC 60.039 55.000 0.00 0.00 0.00 3.18 F
93 94 0.039256 CTGTGCCATTGGTTTCACCG 60.039 55.000 4.26 0.00 42.58 4.94 F
898 1108 0.103026 CTCGCTCAATCACCATCCGA 59.897 55.000 0.00 0.00 0.00 4.55 F
1968 2203 0.236711 TCAAGAAGGACGACGACGAC 59.763 55.000 15.32 7.84 42.66 4.34 F
2403 2666 1.209504 TGAATTACAGCCCTCTTCCGG 59.790 52.381 0.00 0.00 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1938 2173 0.895530 CCTTCTTGAGGCGAGTGGTA 59.104 55.000 0.00 0.00 39.09 3.25 R
2041 2291 1.294780 CTGGTCCAGCTGGTCTGAC 59.705 63.158 31.58 21.67 45.72 3.51 R
2755 3033 0.671472 CTGAACCAGAGCATGACGCA 60.671 55.000 0.00 0.00 46.13 5.24 R
2944 3227 0.966920 AGTAGAACAGGTGTCACGGG 59.033 55.000 0.00 0.00 0.00 5.28 R
3884 4198 1.073199 CGGTTGGCAAGAGAAGGGT 59.927 57.895 0.00 0.00 0.00 4.34 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
34 35 9.612620 AAATCTCTATGTTCTTTAAAACAAGCG 57.387 29.630 0.00 0.00 42.10 4.68
35 36 7.956420 TCTCTATGTTCTTTAAAACAAGCGA 57.044 32.000 0.00 0.00 42.10 4.93
36 37 7.793902 TCTCTATGTTCTTTAAAACAAGCGAC 58.206 34.615 0.00 0.00 42.10 5.19
37 38 7.439955 TCTCTATGTTCTTTAAAACAAGCGACA 59.560 33.333 0.00 0.00 42.10 4.35
38 39 7.349711 TCTATGTTCTTTAAAACAAGCGACAC 58.650 34.615 0.00 0.00 42.10 3.67
39 40 5.298197 TGTTCTTTAAAACAAGCGACACA 57.702 34.783 0.00 0.00 36.25 3.72
40 41 5.090083 TGTTCTTTAAAACAAGCGACACAC 58.910 37.500 0.00 0.00 36.25 3.82
41 42 4.948608 TCTTTAAAACAAGCGACACACA 57.051 36.364 0.00 0.00 0.00 3.72
42 43 5.493133 TCTTTAAAACAAGCGACACACAT 57.507 34.783 0.00 0.00 0.00 3.21
43 44 5.507077 TCTTTAAAACAAGCGACACACATC 58.493 37.500 0.00 0.00 0.00 3.06
44 45 5.295787 TCTTTAAAACAAGCGACACACATCT 59.704 36.000 0.00 0.00 0.00 2.90
45 46 6.480651 TCTTTAAAACAAGCGACACACATCTA 59.519 34.615 0.00 0.00 0.00 1.98
46 47 4.732285 AAAACAAGCGACACACATCTAG 57.268 40.909 0.00 0.00 0.00 2.43
47 48 1.714794 ACAAGCGACACACATCTAGC 58.285 50.000 0.00 0.00 0.00 3.42
48 49 1.273606 ACAAGCGACACACATCTAGCT 59.726 47.619 0.00 0.00 36.40 3.32
49 50 2.492088 ACAAGCGACACACATCTAGCTA 59.508 45.455 0.00 0.00 34.24 3.32
50 51 3.111838 CAAGCGACACACATCTAGCTAG 58.888 50.000 15.01 15.01 34.24 3.42
51 52 2.370349 AGCGACACACATCTAGCTAGT 58.630 47.619 20.10 5.41 32.73 2.57
52 53 2.755655 AGCGACACACATCTAGCTAGTT 59.244 45.455 20.10 9.59 32.73 2.24
53 54 3.109619 GCGACACACATCTAGCTAGTTC 58.890 50.000 20.10 6.13 0.00 3.01
54 55 3.427638 GCGACACACATCTAGCTAGTTCA 60.428 47.826 20.10 1.66 0.00 3.18
55 56 4.099120 CGACACACATCTAGCTAGTTCAC 58.901 47.826 20.10 4.98 0.00 3.18
56 57 4.142578 CGACACACATCTAGCTAGTTCACT 60.143 45.833 20.10 0.00 0.00 3.41
57 58 5.317733 ACACACATCTAGCTAGTTCACTC 57.682 43.478 20.10 0.00 0.00 3.51
58 59 4.158764 ACACACATCTAGCTAGTTCACTCC 59.841 45.833 20.10 0.00 0.00 3.85
59 60 4.400884 CACACATCTAGCTAGTTCACTCCT 59.599 45.833 20.10 0.00 0.00 3.69
60 61 5.020132 ACACATCTAGCTAGTTCACTCCTT 58.980 41.667 20.10 0.00 0.00 3.36
61 62 5.482175 ACACATCTAGCTAGTTCACTCCTTT 59.518 40.000 20.10 0.00 0.00 3.11
62 63 6.014156 ACACATCTAGCTAGTTCACTCCTTTT 60.014 38.462 20.10 0.00 0.00 2.27
63 64 6.312426 CACATCTAGCTAGTTCACTCCTTTTG 59.688 42.308 20.10 0.00 0.00 2.44
64 65 4.822026 TCTAGCTAGTTCACTCCTTTTGC 58.178 43.478 20.10 0.00 0.00 3.68
65 66 2.784347 AGCTAGTTCACTCCTTTTGCC 58.216 47.619 0.00 0.00 0.00 4.52
66 67 1.464997 GCTAGTTCACTCCTTTTGCCG 59.535 52.381 0.00 0.00 0.00 5.69
67 68 1.464997 CTAGTTCACTCCTTTTGCCGC 59.535 52.381 0.00 0.00 0.00 6.53
68 69 1.172812 AGTTCACTCCTTTTGCCGCC 61.173 55.000 0.00 0.00 0.00 6.13
69 70 1.150536 TTCACTCCTTTTGCCGCCT 59.849 52.632 0.00 0.00 0.00 5.52
70 71 0.467290 TTCACTCCTTTTGCCGCCTT 60.467 50.000 0.00 0.00 0.00 4.35
71 72 0.467290 TCACTCCTTTTGCCGCCTTT 60.467 50.000 0.00 0.00 0.00 3.11
72 73 0.318955 CACTCCTTTTGCCGCCTTTG 60.319 55.000 0.00 0.00 0.00 2.77
73 74 0.755327 ACTCCTTTTGCCGCCTTTGT 60.755 50.000 0.00 0.00 0.00 2.83
74 75 0.039165 CTCCTTTTGCCGCCTTTGTC 60.039 55.000 0.00 0.00 0.00 3.18
75 76 0.467290 TCCTTTTGCCGCCTTTGTCT 60.467 50.000 0.00 0.00 0.00 3.41
76 77 0.318955 CCTTTTGCCGCCTTTGTCTG 60.319 55.000 0.00 0.00 0.00 3.51
77 78 0.385390 CTTTTGCCGCCTTTGTCTGT 59.615 50.000 0.00 0.00 0.00 3.41
78 79 0.102120 TTTTGCCGCCTTTGTCTGTG 59.898 50.000 0.00 0.00 0.00 3.66
79 80 2.348605 TTTGCCGCCTTTGTCTGTGC 62.349 55.000 0.00 0.00 0.00 4.57
83 84 1.526575 CCGCCTTTGTCTGTGCCATT 61.527 55.000 0.00 0.00 0.00 3.16
90 91 2.064434 TGTCTGTGCCATTGGTTTCA 57.936 45.000 4.26 1.07 0.00 2.69
93 94 0.039256 CTGTGCCATTGGTTTCACCG 60.039 55.000 4.26 0.00 42.58 4.94
95 96 0.240945 GTGCCATTGGTTTCACCGAG 59.759 55.000 4.26 0.00 42.58 4.63
96 97 0.179004 TGCCATTGGTTTCACCGAGT 60.179 50.000 4.26 0.00 42.58 4.18
109 110 1.069022 CACCGAGTGCCTGTTTCAATG 60.069 52.381 0.00 0.00 0.00 2.82
112 113 2.146342 CGAGTGCCTGTTTCAATGACT 58.854 47.619 0.00 0.00 0.00 3.41
118 119 4.276926 GTGCCTGTTTCAATGACTCTCTTT 59.723 41.667 0.00 0.00 0.00 2.52
121 122 5.009010 GCCTGTTTCAATGACTCTCTTTTCA 59.991 40.000 0.00 0.00 0.00 2.69
126 127 7.173907 TGTTTCAATGACTCTCTTTTCATCCTC 59.826 37.037 0.00 0.00 30.96 3.71
156 157 5.435686 ACCACATTGTTGCCTATCTTCTA 57.564 39.130 0.00 0.00 0.00 2.10
157 158 5.186198 ACCACATTGTTGCCTATCTTCTAC 58.814 41.667 0.00 0.00 0.00 2.59
161 162 7.417911 CCACATTGTTGCCTATCTTCTACTAGA 60.418 40.741 0.00 0.00 0.00 2.43
167 168 8.350722 TGTTGCCTATCTTCTACTAGATTTACG 58.649 37.037 0.00 0.00 36.34 3.18
193 194 6.844097 GAGAATTATCTCCCGACTATCCTT 57.156 41.667 0.00 0.00 45.35 3.36
199 200 7.850935 TTATCTCCCGACTATCCTTAATTGT 57.149 36.000 0.00 0.00 0.00 2.71
213 214 8.625786 ATCCTTAATTGTTACTAACCAAACGT 57.374 30.769 0.00 0.00 0.00 3.99
240 241 4.713824 ATCAAACAACCTCATGATGCAG 57.286 40.909 0.00 0.00 31.60 4.41
244 245 3.988976 ACAACCTCATGATGCAGTACT 57.011 42.857 0.00 0.00 0.00 2.73
246 247 5.016051 ACAACCTCATGATGCAGTACTAG 57.984 43.478 0.00 0.00 0.00 2.57
250 251 4.056740 CCTCATGATGCAGTACTAGCAAG 58.943 47.826 19.25 13.18 46.27 4.01
252 253 3.118665 TCATGATGCAGTACTAGCAAGCA 60.119 43.478 19.25 18.91 46.27 3.91
256 257 4.095334 TGATGCAGTACTAGCAAGCAAATG 59.905 41.667 19.25 0.00 46.27 2.32
259 260 4.154737 TGCAGTACTAGCAAGCAAATGAAG 59.845 41.667 14.89 0.00 39.39 3.02
267 268 3.558418 AGCAAGCAAATGAAGTGCAAAAG 59.442 39.130 0.00 0.00 44.74 2.27
268 269 3.303526 GCAAGCAAATGAAGTGCAAAAGG 60.304 43.478 0.00 0.00 44.74 3.11
318 320 1.369625 CTCTACCGGACCACATTTGC 58.630 55.000 9.46 0.00 0.00 3.68
321 323 2.091541 CTACCGGACCACATTTGCAAT 58.908 47.619 9.46 0.00 0.00 3.56
335 337 1.350071 TGCAATGAGGCCAAAATGGT 58.650 45.000 5.01 0.00 40.46 3.55
337 339 2.078392 GCAATGAGGCCAAAATGGTTG 58.922 47.619 5.01 1.07 40.46 3.77
353 355 1.589803 GTTGTAGGCAACCAAGTCGT 58.410 50.000 0.00 0.00 46.81 4.34
355 357 0.753867 TGTAGGCAACCAAGTCGTCA 59.246 50.000 0.00 0.00 37.17 4.35
360 364 1.467342 GGCAACCAAGTCGTCATTACC 59.533 52.381 0.00 0.00 0.00 2.85
361 365 2.423577 GCAACCAAGTCGTCATTACCT 58.576 47.619 0.00 0.00 0.00 3.08
371 375 3.126514 GTCGTCATTACCTTCTGTCGAGA 59.873 47.826 0.00 0.00 34.55 4.04
381 385 3.119173 CCTTCTGTCGAGATCTCAAAGCT 60.119 47.826 22.31 0.00 0.00 3.74
383 387 2.425312 TCTGTCGAGATCTCAAAGCTCC 59.575 50.000 22.31 2.57 0.00 4.70
386 390 1.402259 TCGAGATCTCAAAGCTCCGAC 59.598 52.381 22.31 0.00 0.00 4.79
397 401 1.520342 GCTCCGACCTTGCTAGCAG 60.520 63.158 18.45 10.04 33.38 4.24
398 402 1.520342 CTCCGACCTTGCTAGCAGC 60.520 63.158 18.45 8.06 42.82 5.25
404 408 0.911769 ACCTTGCTAGCAGCCATGTA 59.088 50.000 18.45 0.00 41.51 2.29
407 411 2.636830 CTTGCTAGCAGCCATGTAGTT 58.363 47.619 18.45 0.00 41.51 2.24
413 417 1.021390 GCAGCCATGTAGTTCGTGCT 61.021 55.000 0.00 0.00 0.00 4.40
414 418 0.723414 CAGCCATGTAGTTCGTGCTG 59.277 55.000 2.61 2.61 34.07 4.41
419 423 2.621338 CATGTAGTTCGTGCTGGACAT 58.379 47.619 0.00 0.00 0.00 3.06
438 442 3.569701 ACATCCCAAACACAGTGATCAAC 59.430 43.478 7.81 0.00 0.00 3.18
439 443 3.576078 TCCCAAACACAGTGATCAACT 57.424 42.857 7.81 0.00 40.93 3.16
447 451 2.286826 AGTGATCAACTGCGGCCTA 58.713 52.632 0.00 0.00 37.88 3.93
460 465 0.533755 CGGCCTATTCAGCAAGAGGG 60.534 60.000 0.00 0.00 40.87 4.30
468 473 0.547471 TCAGCAAGAGGGGGATGACA 60.547 55.000 0.00 0.00 0.00 3.58
469 474 0.107312 CAGCAAGAGGGGGATGACAG 60.107 60.000 0.00 0.00 0.00 3.51
473 478 0.119155 AAGAGGGGGATGACAGGACA 59.881 55.000 0.00 0.00 0.00 4.02
476 481 0.995024 AGGGGGATGACAGGACAAAG 59.005 55.000 0.00 0.00 0.00 2.77
488 493 3.648067 ACAGGACAAAGGATGAGAAGACA 59.352 43.478 0.00 0.00 0.00 3.41
489 494 4.252073 CAGGACAAAGGATGAGAAGACAG 58.748 47.826 0.00 0.00 0.00 3.51
492 497 4.020662 GGACAAAGGATGAGAAGACAGAGT 60.021 45.833 0.00 0.00 0.00 3.24
496 501 3.096092 AGGATGAGAAGACAGAGTCCAC 58.904 50.000 0.00 0.00 32.18 4.02
501 506 2.490115 GAGAAGACAGAGTCCACGTCAT 59.510 50.000 7.47 0.00 32.18 3.06
509 514 0.104304 AGTCCACGTCATAATCCCGC 59.896 55.000 0.00 0.00 0.00 6.13
536 541 1.645710 GAGTCTCCTTTCCCACCTCA 58.354 55.000 0.00 0.00 0.00 3.86
552 557 2.568696 CTCATACGAGGTCACACCAG 57.431 55.000 0.00 0.00 41.95 4.00
553 558 2.092323 CTCATACGAGGTCACACCAGA 58.908 52.381 0.00 0.00 41.95 3.86
554 559 1.816835 TCATACGAGGTCACACCAGAC 59.183 52.381 0.00 0.00 41.95 3.51
561 566 2.133195 GTCACACCAGACCACCTCA 58.867 57.895 0.00 0.00 32.36 3.86
562 567 0.687354 GTCACACCAGACCACCTCAT 59.313 55.000 0.00 0.00 32.36 2.90
563 568 1.899814 GTCACACCAGACCACCTCATA 59.100 52.381 0.00 0.00 32.36 2.15
564 569 1.899814 TCACACCAGACCACCTCATAC 59.100 52.381 0.00 0.00 0.00 2.39
566 571 0.175760 CACCAGACCACCTCATACGG 59.824 60.000 0.00 0.00 0.00 4.02
567 572 0.976073 ACCAGACCACCTCATACGGG 60.976 60.000 0.00 0.00 0.00 5.28
568 573 1.144057 CAGACCACCTCATACGGGC 59.856 63.158 0.00 0.00 0.00 6.13
570 575 1.144057 GACCACCTCATACGGGCTG 59.856 63.158 0.00 0.00 0.00 4.85
571 576 1.305802 ACCACCTCATACGGGCTGA 60.306 57.895 0.00 0.00 0.00 4.26
572 577 1.144057 CCACCTCATACGGGCTGAC 59.856 63.158 0.00 0.00 0.00 3.51
574 579 1.001760 ACCTCATACGGGCTGACCT 59.998 57.895 0.00 0.00 36.97 3.85
576 581 1.342674 ACCTCATACGGGCTGACCTAA 60.343 52.381 0.00 0.00 36.97 2.69
577 582 1.971357 CCTCATACGGGCTGACCTAAT 59.029 52.381 0.00 0.00 36.97 1.73
578 583 2.368875 CCTCATACGGGCTGACCTAATT 59.631 50.000 0.00 0.00 36.97 1.40
579 584 3.555168 CCTCATACGGGCTGACCTAATTC 60.555 52.174 0.00 0.00 36.97 2.17
580 585 3.305720 TCATACGGGCTGACCTAATTCT 58.694 45.455 0.00 0.00 36.97 2.40
581 586 4.476297 TCATACGGGCTGACCTAATTCTA 58.524 43.478 0.00 0.00 36.97 2.10
582 587 4.897076 TCATACGGGCTGACCTAATTCTAA 59.103 41.667 0.00 0.00 36.97 2.10
583 588 5.364446 TCATACGGGCTGACCTAATTCTAAA 59.636 40.000 0.00 0.00 36.97 1.85
584 589 4.772886 ACGGGCTGACCTAATTCTAAAT 57.227 40.909 0.00 0.00 36.97 1.40
585 590 5.112129 ACGGGCTGACCTAATTCTAAATT 57.888 39.130 0.00 0.00 36.97 1.82
587 592 5.949952 ACGGGCTGACCTAATTCTAAATTTT 59.050 36.000 0.00 0.00 36.97 1.82
588 593 7.114095 ACGGGCTGACCTAATTCTAAATTTTA 58.886 34.615 0.00 0.00 36.97 1.52
589 594 7.282450 ACGGGCTGACCTAATTCTAAATTTTAG 59.718 37.037 9.48 9.48 36.97 1.85
590 595 7.497909 CGGGCTGACCTAATTCTAAATTTTAGA 59.502 37.037 13.62 13.62 36.97 2.10
592 597 9.174166 GGCTGACCTAATTCTAAATTTTAGACA 57.826 33.333 16.59 9.71 0.00 3.41
661 847 2.163509 GGCTTTGACTCCTTCCTTTCC 58.836 52.381 0.00 0.00 0.00 3.13
664 850 3.504134 GCTTTGACTCCTTCCTTTCCTTC 59.496 47.826 0.00 0.00 0.00 3.46
701 909 2.125350 GAGCTGAGGTGGAAGCGG 60.125 66.667 0.00 0.00 44.34 5.52
702 910 4.400961 AGCTGAGGTGGAAGCGGC 62.401 66.667 0.00 0.00 44.34 6.53
735 944 4.008933 GTCCCTGCACGTGCTCCT 62.009 66.667 37.59 0.00 42.66 3.69
736 945 3.695606 TCCCTGCACGTGCTCCTC 61.696 66.667 37.59 12.49 42.66 3.71
739 948 4.731612 CTGCACGTGCTCCTCGCT 62.732 66.667 37.59 0.00 42.66 4.93
740 949 4.299547 TGCACGTGCTCCTCGCTT 62.300 61.111 37.59 0.00 42.66 4.68
741 950 3.482783 GCACGTGCTCCTCGCTTC 61.483 66.667 32.55 0.00 40.11 3.86
742 951 3.175240 CACGTGCTCCTCGCTTCG 61.175 66.667 0.82 0.00 40.11 3.79
771 980 4.702081 GCTCCACTCGTCACGCGT 62.702 66.667 5.58 5.58 42.13 6.01
772 981 2.502080 CTCCACTCGTCACGCGTC 60.502 66.667 9.86 0.00 42.13 5.19
773 982 3.948086 CTCCACTCGTCACGCGTCC 62.948 68.421 9.86 1.15 42.13 4.79
776 985 4.380628 ACTCGTCACGCGTCCGTC 62.381 66.667 22.46 5.86 46.39 4.79
881 1091 1.075151 CCTCCCTCCCCAGGTACTC 60.075 68.421 0.00 0.00 38.30 2.59
882 1092 1.455959 CTCCCTCCCCAGGTACTCG 60.456 68.421 0.00 0.00 38.30 4.18
884 1094 2.042843 CCTCCCCAGGTACTCGCT 60.043 66.667 0.00 0.00 34.60 4.93
887 1097 0.970937 CTCCCCAGGTACTCGCTCAA 60.971 60.000 0.00 0.00 34.60 3.02
889 1099 0.105039 CCCCAGGTACTCGCTCAATC 59.895 60.000 0.00 0.00 34.60 2.67
890 1100 0.824109 CCCAGGTACTCGCTCAATCA 59.176 55.000 0.00 0.00 34.60 2.57
896 1106 2.474816 GTACTCGCTCAATCACCATCC 58.525 52.381 0.00 0.00 0.00 3.51
897 1107 0.179100 ACTCGCTCAATCACCATCCG 60.179 55.000 0.00 0.00 0.00 4.18
898 1108 0.103026 CTCGCTCAATCACCATCCGA 59.897 55.000 0.00 0.00 0.00 4.55
903 1113 2.138320 CTCAATCACCATCCGAATCCG 58.862 52.381 0.00 0.00 0.00 4.18
912 1122 2.009774 CATCCGAATCCGCTCTTGTTT 58.990 47.619 0.00 0.00 0.00 2.83
921 1131 4.685169 TCCGCTCTTGTTTGATTTGATC 57.315 40.909 0.00 0.00 0.00 2.92
935 1153 6.083487 TGATTTGATCCCAAAGAATCCTCT 57.917 37.500 0.00 0.00 44.53 3.69
939 1157 2.403252 TCCCAAAGAATCCTCTTCGC 57.597 50.000 0.00 0.00 41.23 4.70
1008 1240 2.741985 TTGCCAGCCATGTCGTCG 60.742 61.111 0.00 0.00 0.00 5.12
1073 1305 3.482783 GAGCAGCAAGGACGACGC 61.483 66.667 0.00 0.00 0.00 5.19
1106 1338 2.831526 AGAAGAAGCAGGAGGAGAAGAC 59.168 50.000 0.00 0.00 0.00 3.01
1461 1696 3.900892 CGGAGCACCTACGCGGAT 61.901 66.667 12.47 0.00 36.85 4.18
1512 1747 1.035932 TCCGGGTCATCTTCCTCGTC 61.036 60.000 0.00 0.00 0.00 4.20
1518 1753 0.725686 TCATCTTCCTCGTCGACGTC 59.274 55.000 34.40 5.18 40.80 4.34
1683 1918 2.135664 ACAAGAACGACTTCGACCTG 57.864 50.000 5.47 2.33 43.02 4.00
1686 1921 1.737008 GAACGACTTCGACCTGGGC 60.737 63.158 5.47 0.00 43.02 5.36
1968 2203 0.236711 TCAAGAAGGACGACGACGAC 59.763 55.000 15.32 7.84 42.66 4.34
1971 2206 1.225691 GAAGGACGACGACGACGAG 60.226 63.158 25.15 9.88 42.66 4.18
2018 2257 4.806330 CATCTGCTGCTCTGTTTTCATTT 58.194 39.130 0.00 0.00 0.00 2.32
2041 2291 2.621338 TCCTCTGCATCTTGCTTAACG 58.379 47.619 0.75 0.00 45.31 3.18
2157 2410 2.969628 CTGAATTACAGCCCTCTCGT 57.030 50.000 0.00 0.00 39.86 4.18
2307 2567 4.461081 CCATCATACTAGCTAGACCAGGTC 59.539 50.000 27.45 12.25 36.15 3.85
2359 2619 8.596293 ACAATGGAAGAAATTGATATGGTGTTT 58.404 29.630 3.32 0.00 38.21 2.83
2382 2645 3.069158 ACCTATTATTAGAGCGCAACGGT 59.931 43.478 11.47 1.56 41.33 4.83
2403 2666 1.209504 TGAATTACAGCCCTCTTCCGG 59.790 52.381 0.00 0.00 0.00 5.14
2404 2667 1.209747 GAATTACAGCCCTCTTCCGGT 59.790 52.381 0.00 0.00 0.00 5.28
2627 2902 1.327764 GTAGGCGTGCAATAGCTGAAC 59.672 52.381 0.00 0.00 42.74 3.18
2641 2916 2.969262 AGCTGAACTATAGCCCTCTTCC 59.031 50.000 0.00 0.00 42.07 3.46
2655 2930 4.881850 GCCCTCTTCCGAATTTTTCTGATA 59.118 41.667 0.00 0.00 0.00 2.15
2755 3033 3.089573 GCTTCTCAGCTTGTTTTGCTT 57.910 42.857 0.00 0.00 43.51 3.91
2798 3076 8.535592 CAGTTGAAACTCGCTAGTAGAAATATG 58.464 37.037 0.00 0.00 37.08 1.78
2944 3227 5.119898 CGCCATATCAGATCTGAGCTAAAAC 59.880 44.000 28.26 14.11 43.61 2.43
3014 3297 6.481976 TCAAGAACAGATGAAAGAAAAGCGTA 59.518 34.615 0.00 0.00 0.00 4.42
3204 3487 3.177997 GAGGATCCAGCTGAACTCTTC 57.822 52.381 17.39 10.48 31.74 2.87
3205 3488 1.836802 AGGATCCAGCTGAACTCTTCC 59.163 52.381 17.39 11.25 0.00 3.46
3254 3537 0.744874 ATCATCCGAACATCGTCCGT 59.255 50.000 0.00 0.00 38.40 4.69
3314 3597 5.491982 ACTCATCCAGTGTGTATTCTTTCC 58.508 41.667 0.00 0.00 33.06 3.13
3334 3617 3.064271 TCCGTGTTAACTTTGTCAAGTGC 59.936 43.478 7.22 0.00 42.89 4.40
3381 3664 1.788229 CCCCTTTCTTGTTTGTGGGT 58.212 50.000 0.00 0.00 33.13 4.51
3700 3984 3.236047 ACCTACATTTTGTGGTTTCCCC 58.764 45.455 0.00 0.00 31.09 4.81
3703 3989 2.325484 ACATTTTGTGGTTTCCCCCTC 58.675 47.619 0.00 0.00 0.00 4.30
3751 4038 4.340381 CAGATTTTCCTTCCCATGACATCC 59.660 45.833 0.00 0.00 0.00 3.51
3907 4221 2.154462 CTTCTCTTGCCAACCGATGTT 58.846 47.619 0.00 0.00 34.14 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 9.612620 CGCTTGTTTTAAAGAACATAGAGATTT 57.387 29.630 0.00 0.00 39.12 2.17
9 10 8.999431 TCGCTTGTTTTAAAGAACATAGAGATT 58.001 29.630 0.00 0.00 39.12 2.40
10 11 8.443937 GTCGCTTGTTTTAAAGAACATAGAGAT 58.556 33.333 9.49 0.00 39.12 2.75
11 12 7.439955 TGTCGCTTGTTTTAAAGAACATAGAGA 59.560 33.333 0.00 1.18 39.12 3.10
12 13 7.530861 GTGTCGCTTGTTTTAAAGAACATAGAG 59.469 37.037 0.00 0.00 39.12 2.43
13 14 7.011576 TGTGTCGCTTGTTTTAAAGAACATAGA 59.988 33.333 0.00 0.00 39.12 1.98
14 15 7.111593 GTGTGTCGCTTGTTTTAAAGAACATAG 59.888 37.037 0.00 0.00 39.12 2.23
15 16 6.908284 GTGTGTCGCTTGTTTTAAAGAACATA 59.092 34.615 0.00 0.00 39.12 2.29
16 17 5.741982 GTGTGTCGCTTGTTTTAAAGAACAT 59.258 36.000 0.00 0.00 39.12 2.71
17 18 5.090083 GTGTGTCGCTTGTTTTAAAGAACA 58.910 37.500 0.00 0.00 37.73 3.18
18 19 5.090083 TGTGTGTCGCTTGTTTTAAAGAAC 58.910 37.500 0.00 0.00 0.00 3.01
19 20 5.298197 TGTGTGTCGCTTGTTTTAAAGAA 57.702 34.783 0.00 0.00 0.00 2.52
20 21 4.948608 TGTGTGTCGCTTGTTTTAAAGA 57.051 36.364 0.00 0.00 0.00 2.52
21 22 5.510671 AGATGTGTGTCGCTTGTTTTAAAG 58.489 37.500 0.00 0.00 0.00 1.85
22 23 5.493133 AGATGTGTGTCGCTTGTTTTAAA 57.507 34.783 0.00 0.00 0.00 1.52
23 24 5.333798 GCTAGATGTGTGTCGCTTGTTTTAA 60.334 40.000 0.00 0.00 0.00 1.52
24 25 4.151689 GCTAGATGTGTGTCGCTTGTTTTA 59.848 41.667 0.00 0.00 0.00 1.52
25 26 3.058914 GCTAGATGTGTGTCGCTTGTTTT 60.059 43.478 0.00 0.00 0.00 2.43
26 27 2.480419 GCTAGATGTGTGTCGCTTGTTT 59.520 45.455 0.00 0.00 0.00 2.83
27 28 2.069273 GCTAGATGTGTGTCGCTTGTT 58.931 47.619 0.00 0.00 0.00 2.83
28 29 1.273606 AGCTAGATGTGTGTCGCTTGT 59.726 47.619 0.00 0.00 0.00 3.16
29 30 2.001812 AGCTAGATGTGTGTCGCTTG 57.998 50.000 0.00 0.00 0.00 4.01
30 31 2.755655 ACTAGCTAGATGTGTGTCGCTT 59.244 45.455 27.45 0.00 0.00 4.68
31 32 2.370349 ACTAGCTAGATGTGTGTCGCT 58.630 47.619 27.45 0.00 0.00 4.93
32 33 2.853731 ACTAGCTAGATGTGTGTCGC 57.146 50.000 27.45 0.00 0.00 5.19
33 34 4.099120 GTGAACTAGCTAGATGTGTGTCG 58.901 47.826 27.45 0.00 0.00 4.35
34 35 5.317733 AGTGAACTAGCTAGATGTGTGTC 57.682 43.478 27.45 11.69 0.00 3.67
35 36 4.158764 GGAGTGAACTAGCTAGATGTGTGT 59.841 45.833 27.45 0.27 0.00 3.72
36 37 4.400884 AGGAGTGAACTAGCTAGATGTGTG 59.599 45.833 27.45 0.00 0.00 3.82
37 38 4.605183 AGGAGTGAACTAGCTAGATGTGT 58.395 43.478 27.45 8.43 0.00 3.72
38 39 5.590530 AAGGAGTGAACTAGCTAGATGTG 57.409 43.478 27.45 1.17 0.00 3.21
39 40 6.402222 CAAAAGGAGTGAACTAGCTAGATGT 58.598 40.000 27.45 11.53 0.00 3.06
40 41 5.293079 GCAAAAGGAGTGAACTAGCTAGATG 59.707 44.000 27.45 1.98 0.00 2.90
41 42 5.423886 GCAAAAGGAGTGAACTAGCTAGAT 58.576 41.667 27.45 16.06 0.00 1.98
42 43 4.322801 GGCAAAAGGAGTGAACTAGCTAGA 60.323 45.833 27.45 1.72 0.00 2.43
43 44 3.935828 GGCAAAAGGAGTGAACTAGCTAG 59.064 47.826 19.44 19.44 0.00 3.42
44 45 3.616560 CGGCAAAAGGAGTGAACTAGCTA 60.617 47.826 0.00 0.00 0.00 3.32
45 46 2.784347 GGCAAAAGGAGTGAACTAGCT 58.216 47.619 0.00 0.00 0.00 3.32
46 47 1.464997 CGGCAAAAGGAGTGAACTAGC 59.535 52.381 0.00 0.00 0.00 3.42
47 48 1.464997 GCGGCAAAAGGAGTGAACTAG 59.535 52.381 0.00 0.00 0.00 2.57
48 49 1.519408 GCGGCAAAAGGAGTGAACTA 58.481 50.000 0.00 0.00 0.00 2.24
49 50 1.172812 GGCGGCAAAAGGAGTGAACT 61.173 55.000 3.07 0.00 0.00 3.01
50 51 1.172812 AGGCGGCAAAAGGAGTGAAC 61.173 55.000 13.08 0.00 0.00 3.18
51 52 0.467290 AAGGCGGCAAAAGGAGTGAA 60.467 50.000 13.08 0.00 0.00 3.18
52 53 0.467290 AAAGGCGGCAAAAGGAGTGA 60.467 50.000 13.08 0.00 0.00 3.41
53 54 0.318955 CAAAGGCGGCAAAAGGAGTG 60.319 55.000 13.08 0.00 0.00 3.51
54 55 0.755327 ACAAAGGCGGCAAAAGGAGT 60.755 50.000 13.08 0.00 0.00 3.85
55 56 0.039165 GACAAAGGCGGCAAAAGGAG 60.039 55.000 13.08 0.00 0.00 3.69
56 57 0.467290 AGACAAAGGCGGCAAAAGGA 60.467 50.000 13.08 0.00 0.00 3.36
57 58 0.318955 CAGACAAAGGCGGCAAAAGG 60.319 55.000 13.08 0.00 0.00 3.11
58 59 0.385390 ACAGACAAAGGCGGCAAAAG 59.615 50.000 13.08 0.00 0.00 2.27
59 60 0.102120 CACAGACAAAGGCGGCAAAA 59.898 50.000 13.08 0.00 0.00 2.44
60 61 1.732917 CACAGACAAAGGCGGCAAA 59.267 52.632 13.08 0.00 0.00 3.68
61 62 2.844451 GCACAGACAAAGGCGGCAA 61.844 57.895 13.08 0.00 0.00 4.52
62 63 3.286751 GCACAGACAAAGGCGGCA 61.287 61.111 13.08 0.00 0.00 5.69
63 64 4.043200 GGCACAGACAAAGGCGGC 62.043 66.667 0.00 0.00 0.00 6.53
64 65 2.594303 TGGCACAGACAAAGGCGG 60.594 61.111 0.00 0.00 0.00 6.13
90 91 1.202758 TCATTGAAACAGGCACTCGGT 60.203 47.619 0.00 0.00 34.60 4.69
93 94 3.406764 AGAGTCATTGAAACAGGCACTC 58.593 45.455 0.00 0.00 34.60 3.51
95 96 3.406764 AGAGAGTCATTGAAACAGGCAC 58.593 45.455 0.00 0.00 0.00 5.01
96 97 3.777106 AGAGAGTCATTGAAACAGGCA 57.223 42.857 0.00 0.00 0.00 4.75
109 110 5.186797 TGGAAGAGAGGATGAAAAGAGAGTC 59.813 44.000 0.00 0.00 0.00 3.36
112 113 5.280215 GGTTGGAAGAGAGGATGAAAAGAGA 60.280 44.000 0.00 0.00 0.00 3.10
118 119 2.978978 TGTGGTTGGAAGAGAGGATGAA 59.021 45.455 0.00 0.00 0.00 2.57
121 122 3.331889 ACAATGTGGTTGGAAGAGAGGAT 59.668 43.478 0.00 0.00 42.28 3.24
126 127 2.288395 GGCAACAATGTGGTTGGAAGAG 60.288 50.000 7.99 0.00 46.36 2.85
161 162 7.447853 AGTCGGGAGATAATTCTCTACGTAAAT 59.552 37.037 13.44 0.00 46.46 1.40
165 166 4.716794 AGTCGGGAGATAATTCTCTACGT 58.283 43.478 13.44 0.00 46.46 3.57
167 168 7.114095 AGGATAGTCGGGAGATAATTCTCTAC 58.886 42.308 3.26 0.00 46.46 2.59
173 174 8.881262 ACAATTAAGGATAGTCGGGAGATAATT 58.119 33.333 0.00 0.00 43.27 1.40
174 175 8.437274 ACAATTAAGGATAGTCGGGAGATAAT 57.563 34.615 0.00 0.00 43.27 1.28
176 177 7.850935 AACAATTAAGGATAGTCGGGAGATA 57.149 36.000 0.00 0.00 43.27 1.98
182 183 8.199449 TGGTTAGTAACAATTAAGGATAGTCGG 58.801 37.037 14.81 0.00 0.00 4.79
183 184 9.590451 TTGGTTAGTAACAATTAAGGATAGTCG 57.410 33.333 14.81 0.00 0.00 4.18
188 189 8.625786 ACGTTTGGTTAGTAACAATTAAGGAT 57.374 30.769 14.81 0.00 0.00 3.24
193 194 8.380743 ACATGACGTTTGGTTAGTAACAATTA 57.619 30.769 14.81 0.00 0.00 1.40
199 200 8.497554 GTTTGATACATGACGTTTGGTTAGTAA 58.502 33.333 0.00 0.00 0.00 2.24
212 213 6.741992 TCATGAGGTTGTTTGATACATGAC 57.258 37.500 0.00 0.00 38.02 3.06
213 214 6.183360 GCATCATGAGGTTGTTTGATACATGA 60.183 38.462 9.42 0.00 43.74 3.07
240 241 4.083324 TGCACTTCATTTGCTTGCTAGTAC 60.083 41.667 0.00 0.00 40.86 2.73
244 245 4.319139 TTTGCACTTCATTTGCTTGCTA 57.681 36.364 0.00 0.00 40.86 3.49
246 247 3.303526 CCTTTTGCACTTCATTTGCTTGC 60.304 43.478 0.00 0.00 40.86 4.01
250 251 2.545106 CCACCTTTTGCACTTCATTTGC 59.455 45.455 0.00 0.00 40.63 3.68
252 253 2.771372 ACCCACCTTTTGCACTTCATTT 59.229 40.909 0.00 0.00 0.00 2.32
256 257 4.380550 GCTATAACCCACCTTTTGCACTTC 60.381 45.833 0.00 0.00 0.00 3.01
259 260 2.165641 GGCTATAACCCACCTTTTGCAC 59.834 50.000 0.00 0.00 0.00 4.57
267 268 4.596212 AGGTAATACTGGCTATAACCCACC 59.404 45.833 0.00 0.00 0.00 4.61
268 269 5.306160 TGAGGTAATACTGGCTATAACCCAC 59.694 44.000 0.00 0.00 0.00 4.61
283 285 4.471548 GGTAGAGCCTGACTGAGGTAATA 58.528 47.826 0.00 0.00 44.97 0.98
298 300 1.369625 CAAATGTGGTCCGGTAGAGC 58.630 55.000 0.00 0.00 43.62 4.09
304 306 0.887247 TCATTGCAAATGTGGTCCGG 59.113 50.000 1.71 0.00 0.00 5.14
305 307 1.135315 CCTCATTGCAAATGTGGTCCG 60.135 52.381 1.71 0.00 0.00 4.79
318 320 3.405823 ACAACCATTTTGGCCTCATTG 57.594 42.857 3.32 1.71 42.67 2.82
321 323 2.524306 CCTACAACCATTTTGGCCTCA 58.476 47.619 3.32 0.00 42.67 3.86
335 337 1.139256 TGACGACTTGGTTGCCTACAA 59.861 47.619 0.00 0.00 0.00 2.41
337 339 2.094762 ATGACGACTTGGTTGCCTAC 57.905 50.000 0.00 0.00 0.00 3.18
349 351 3.126514 TCTCGACAGAAGGTAATGACGAC 59.873 47.826 0.00 0.00 38.35 4.34
350 352 3.340928 TCTCGACAGAAGGTAATGACGA 58.659 45.455 0.00 0.00 40.30 4.20
351 353 3.759527 TCTCGACAGAAGGTAATGACG 57.240 47.619 0.00 0.00 36.24 4.35
352 354 5.066634 TGAGATCTCGACAGAAGGTAATGAC 59.933 44.000 17.76 0.00 30.24 3.06
353 355 5.193679 TGAGATCTCGACAGAAGGTAATGA 58.806 41.667 17.76 0.00 30.24 2.57
355 357 6.531503 TTTGAGATCTCGACAGAAGGTAAT 57.468 37.500 17.76 0.00 30.24 1.89
360 364 4.104776 GAGCTTTGAGATCTCGACAGAAG 58.895 47.826 17.76 15.24 30.24 2.85
361 365 3.119316 GGAGCTTTGAGATCTCGACAGAA 60.119 47.826 17.76 3.37 30.02 3.02
371 375 1.677217 GCAAGGTCGGAGCTTTGAGAT 60.677 52.381 19.06 0.00 32.99 2.75
381 385 2.579201 GCTGCTAGCAAGGTCGGA 59.421 61.111 19.86 0.00 41.89 4.55
383 387 1.153289 ATGGCTGCTAGCAAGGTCG 60.153 57.895 19.86 7.74 44.75 4.79
386 390 1.134280 ACTACATGGCTGCTAGCAAGG 60.134 52.381 19.86 9.33 44.75 3.61
397 401 0.391130 TCCAGCACGAACTACATGGC 60.391 55.000 0.00 0.00 0.00 4.40
398 402 1.337728 TGTCCAGCACGAACTACATGG 60.338 52.381 0.00 0.00 0.00 3.66
404 408 1.296715 GGGATGTCCAGCACGAACT 59.703 57.895 0.86 0.00 37.91 3.01
413 417 1.492599 TCACTGTGTTTGGGATGTCCA 59.507 47.619 7.79 0.00 45.43 4.02
414 418 2.270352 TCACTGTGTTTGGGATGTCC 57.730 50.000 7.79 0.00 0.00 4.02
419 423 3.576078 AGTTGATCACTGTGTTTGGGA 57.424 42.857 7.79 0.00 32.83 4.37
438 442 0.462581 TCTTGCTGAATAGGCCGCAG 60.463 55.000 11.89 11.89 33.48 5.18
439 443 0.462581 CTCTTGCTGAATAGGCCGCA 60.463 55.000 0.00 0.00 0.00 5.69
441 445 0.533755 CCCTCTTGCTGAATAGGCCG 60.534 60.000 0.00 0.00 0.00 6.13
447 451 1.213926 GTCATCCCCCTCTTGCTGAAT 59.786 52.381 0.00 0.00 0.00 2.57
460 465 2.239654 TCATCCTTTGTCCTGTCATCCC 59.760 50.000 0.00 0.00 0.00 3.85
468 473 4.163427 TCTGTCTTCTCATCCTTTGTCCT 58.837 43.478 0.00 0.00 0.00 3.85
469 474 4.020662 ACTCTGTCTTCTCATCCTTTGTCC 60.021 45.833 0.00 0.00 0.00 4.02
473 478 4.020662 GTGGACTCTGTCTTCTCATCCTTT 60.021 45.833 0.00 0.00 32.47 3.11
476 481 2.159310 CGTGGACTCTGTCTTCTCATCC 60.159 54.545 0.00 0.00 32.47 3.51
488 493 1.681793 CGGGATTATGACGTGGACTCT 59.318 52.381 0.00 0.00 0.00 3.24
489 494 1.868519 GCGGGATTATGACGTGGACTC 60.869 57.143 0.00 0.00 0.00 3.36
492 497 1.046472 AGGCGGGATTATGACGTGGA 61.046 55.000 0.00 0.00 0.00 4.02
496 501 1.372997 CGGAGGCGGGATTATGACG 60.373 63.158 0.00 0.00 0.00 4.35
516 521 0.533032 GAGGTGGGAAAGGAGACTCG 59.467 60.000 0.00 0.00 42.68 4.18
522 527 2.108168 CTCGTATGAGGTGGGAAAGGA 58.892 52.381 3.83 0.00 38.65 3.36
547 552 0.175760 CCGTATGAGGTGGTCTGGTG 59.824 60.000 0.00 0.00 0.00 4.17
548 553 0.976073 CCCGTATGAGGTGGTCTGGT 60.976 60.000 0.00 0.00 0.00 4.00
551 556 1.001760 AGCCCGTATGAGGTGGTCT 59.998 57.895 0.00 0.00 0.00 3.85
552 557 1.144057 CAGCCCGTATGAGGTGGTC 59.856 63.158 0.00 0.00 0.00 4.02
553 558 1.305802 TCAGCCCGTATGAGGTGGT 60.306 57.895 0.00 0.00 32.40 4.16
554 559 1.144057 GTCAGCCCGTATGAGGTGG 59.856 63.158 0.00 0.00 32.40 4.61
556 561 0.260816 TAGGTCAGCCCGTATGAGGT 59.739 55.000 0.00 0.00 38.74 3.85
557 562 1.410004 TTAGGTCAGCCCGTATGAGG 58.590 55.000 0.00 0.00 38.74 3.86
560 565 3.753294 AGAATTAGGTCAGCCCGTATG 57.247 47.619 0.00 0.00 38.74 2.39
561 566 5.881923 TTTAGAATTAGGTCAGCCCGTAT 57.118 39.130 0.00 0.00 38.74 3.06
562 567 5.881923 ATTTAGAATTAGGTCAGCCCGTA 57.118 39.130 0.00 0.00 38.74 4.02
563 568 4.772886 ATTTAGAATTAGGTCAGCCCGT 57.227 40.909 0.00 0.00 38.74 5.28
564 569 6.451064 AAAATTTAGAATTAGGTCAGCCCG 57.549 37.500 0.00 0.00 38.74 6.13
566 571 9.174166 TGTCTAAAATTTAGAATTAGGTCAGCC 57.826 33.333 16.12 1.79 0.00 4.85
581 586 8.367911 GGGAGGACTCAAATTTGTCTAAAATTT 58.632 33.333 17.47 3.55 39.60 1.82
582 587 7.039011 GGGGAGGACTCAAATTTGTCTAAAATT 60.039 37.037 17.47 0.00 34.01 1.82
583 588 6.437477 GGGGAGGACTCAAATTTGTCTAAAAT 59.563 38.462 17.47 0.24 34.01 1.82
584 589 5.773176 GGGGAGGACTCAAATTTGTCTAAAA 59.227 40.000 17.47 0.00 34.01 1.52
585 590 5.074515 AGGGGAGGACTCAAATTTGTCTAAA 59.925 40.000 17.47 0.00 34.01 1.85
587 592 4.175962 AGGGGAGGACTCAAATTTGTCTA 58.824 43.478 17.47 0.00 34.01 2.59
588 593 2.989571 AGGGGAGGACTCAAATTTGTCT 59.010 45.455 17.47 10.87 34.01 3.41
589 594 3.441500 AGGGGAGGACTCAAATTTGTC 57.558 47.619 17.47 8.91 0.00 3.18
590 595 3.117131 ACAAGGGGAGGACTCAAATTTGT 60.117 43.478 17.47 0.00 0.00 2.83
592 597 3.500471 GGACAAGGGGAGGACTCAAATTT 60.500 47.826 1.32 0.00 0.00 1.82
595 600 1.064825 GGACAAGGGGAGGACTCAAA 58.935 55.000 1.32 0.00 0.00 2.69
661 847 2.434359 GTCGGTCGCCAAGGGAAG 60.434 66.667 0.00 0.00 0.00 3.46
664 850 4.760047 CTGGTCGGTCGCCAAGGG 62.760 72.222 7.62 0.00 35.32 3.95
704 912 4.717313 GGACGGGGTTGGGCTGTC 62.717 72.222 0.00 0.00 0.00 3.51
718 927 3.941657 GAGGAGCACGTGCAGGGAC 62.942 68.421 39.21 23.69 45.16 4.46
738 947 4.832608 GCGGTAGTGGGGGCGAAG 62.833 72.222 0.00 0.00 0.00 3.79
743 952 3.782443 GTGGAGCGGTAGTGGGGG 61.782 72.222 0.00 0.00 0.00 5.40
744 953 2.683933 AGTGGAGCGGTAGTGGGG 60.684 66.667 0.00 0.00 0.00 4.96
770 979 2.987547 TGGAGTGGACGGACGGAC 60.988 66.667 0.00 0.00 0.00 4.79
771 980 2.675423 CTGGAGTGGACGGACGGA 60.675 66.667 0.00 0.00 0.00 4.69
772 981 4.436998 GCTGGAGTGGACGGACGG 62.437 72.222 0.00 0.00 0.00 4.79
773 982 3.374402 AGCTGGAGTGGACGGACG 61.374 66.667 0.00 0.00 0.00 4.79
774 983 2.262915 CAGCTGGAGTGGACGGAC 59.737 66.667 5.57 0.00 0.00 4.79
775 984 3.695606 GCAGCTGGAGTGGACGGA 61.696 66.667 17.12 0.00 0.00 4.69
776 985 4.767255 GGCAGCTGGAGTGGACGG 62.767 72.222 17.12 0.00 0.00 4.79
778 987 4.767255 CCGGCAGCTGGAGTGGAC 62.767 72.222 16.28 0.00 29.82 4.02
800 1009 4.446413 GTGTCGCGGTAGTGGGGG 62.446 72.222 6.13 0.00 0.00 5.40
801 1010 4.789075 CGTGTCGCGGTAGTGGGG 62.789 72.222 6.13 0.00 36.85 4.96
881 1091 1.528586 GATTCGGATGGTGATTGAGCG 59.471 52.381 0.00 0.00 0.00 5.03
882 1092 1.876156 GGATTCGGATGGTGATTGAGC 59.124 52.381 0.00 0.00 0.00 4.26
884 1094 1.810031 GCGGATTCGGATGGTGATTGA 60.810 52.381 0.00 0.00 36.79 2.57
887 1097 0.034059 GAGCGGATTCGGATGGTGAT 59.966 55.000 0.00 0.00 36.79 3.06
889 1099 0.179073 AAGAGCGGATTCGGATGGTG 60.179 55.000 0.00 0.00 36.79 4.17
890 1100 0.179073 CAAGAGCGGATTCGGATGGT 60.179 55.000 0.00 0.00 36.79 3.55
896 1106 3.747099 AATCAAACAAGAGCGGATTCG 57.253 42.857 0.00 0.00 39.81 3.34
897 1107 5.046910 TCAAATCAAACAAGAGCGGATTC 57.953 39.130 0.00 0.00 0.00 2.52
898 1108 5.393461 GGATCAAATCAAACAAGAGCGGATT 60.393 40.000 0.00 0.00 0.00 3.01
903 1113 4.789012 TGGGATCAAATCAAACAAGAGC 57.211 40.909 0.00 0.00 0.00 4.09
912 1122 6.083487 AGAGGATTCTTTGGGATCAAATCA 57.917 37.500 0.00 0.00 41.45 2.57
921 1131 2.113860 TGCGAAGAGGATTCTTTGGG 57.886 50.000 6.65 0.00 43.63 4.12
935 1153 2.237143 AGATGGAAAGTGGAGATGCGAA 59.763 45.455 0.00 0.00 0.00 4.70
939 1157 5.293319 AGATGAGATGGAAAGTGGAGATG 57.707 43.478 0.00 0.00 0.00 2.90
1008 1240 1.957695 GTTGGGGTTGTCCGACGAC 60.958 63.158 10.12 10.12 39.66 4.34
1073 1305 1.071605 CTTCTTCTTCTTGTCGGCGG 58.928 55.000 7.21 0.00 0.00 6.13
1106 1338 2.837291 CGCCCTCCTCCTCCTCTG 60.837 72.222 0.00 0.00 0.00 3.35
1461 1696 1.053835 TGATGCTCCCGGGCTTGATA 61.054 55.000 18.49 0.00 0.00 2.15
1635 1870 3.717294 AGGTGGATGGTGGCCGTC 61.717 66.667 0.00 0.00 38.72 4.79
1683 1918 4.666253 TGCAGCAGGTTGAGGCCC 62.666 66.667 0.00 0.00 0.00 5.80
1686 1921 1.016130 CGTACTGCAGCAGGTTGAGG 61.016 60.000 26.38 10.15 35.51 3.86
1824 2059 1.153489 CATGTCCCAGACGGCAGAG 60.153 63.158 0.00 0.00 34.95 3.35
1938 2173 0.895530 CCTTCTTGAGGCGAGTGGTA 59.104 55.000 0.00 0.00 39.09 3.25
1968 2203 6.868864 ACGAAATGAAATGATATACCTCCTCG 59.131 38.462 0.00 0.00 0.00 4.63
1971 2206 7.602644 TGCTACGAAATGAAATGATATACCTCC 59.397 37.037 0.00 0.00 0.00 4.30
2039 2278 2.574955 GGTCCAGCTGGTCTGACGT 61.575 63.158 31.58 0.00 45.72 4.34
2041 2291 1.294780 CTGGTCCAGCTGGTCTGAC 59.705 63.158 31.58 21.67 45.72 3.51
2123 2376 8.158169 CTGTAATTCAGCTATTGCATTCCTAA 57.842 34.615 1.12 0.00 42.74 2.69
2174 2429 7.148689 GGGTTGTGTACTATTTTTAGTGTCGAG 60.149 40.741 0.00 0.00 0.00 4.04
2180 2435 7.994334 TCTGTTGGGTTGTGTACTATTTTTAGT 59.006 33.333 0.00 0.00 0.00 2.24
2359 2619 4.279169 ACCGTTGCGCTCTAATAATAGGTA 59.721 41.667 9.73 0.00 0.00 3.08
2361 2621 3.650139 ACCGTTGCGCTCTAATAATAGG 58.350 45.455 9.73 4.05 0.00 2.57
2374 2637 1.602191 GCTGTAATTCAACCGTTGCG 58.398 50.000 6.37 0.00 0.00 4.85
2382 2645 2.355716 CCGGAAGAGGGCTGTAATTCAA 60.356 50.000 0.00 0.00 0.00 2.69
2627 2902 6.203723 CAGAAAAATTCGGAAGAGGGCTATAG 59.796 42.308 0.00 0.00 43.69 1.31
2641 2916 5.502544 GCCGAACCTCTATCAGAAAAATTCG 60.503 44.000 0.00 0.00 36.93 3.34
2655 2930 2.109425 ATTTTTAGCGCCGAACCTCT 57.891 45.000 2.29 0.00 0.00 3.69
2755 3033 0.671472 CTGAACCAGAGCATGACGCA 60.671 55.000 0.00 0.00 46.13 5.24
2920 3203 4.446994 TTAGCTCAGATCTGATATGGCG 57.553 45.455 25.30 13.65 39.13 5.69
2944 3227 0.966920 AGTAGAACAGGTGTCACGGG 59.033 55.000 0.00 0.00 0.00 5.28
3014 3297 4.165950 TCACAAATGCCCAGGTCTATATGT 59.834 41.667 0.00 0.00 0.00 2.29
3204 3487 6.426646 ACAAAGATACCATAAGCTAGAGGG 57.573 41.667 0.00 0.00 0.00 4.30
3205 3488 7.500992 TCAACAAAGATACCATAAGCTAGAGG 58.499 38.462 0.00 0.00 0.00 3.69
3254 3537 4.336993 ACTGAGCACCGAAACATAAAAACA 59.663 37.500 0.00 0.00 0.00 2.83
3314 3597 4.009798 TGCACTTGACAAAGTTAACACG 57.990 40.909 8.61 0.00 44.47 4.49
3334 3617 7.452880 TGGAATTTATTCTCAGGTCTGTTTG 57.547 36.000 2.77 0.00 37.00 2.93
3662 3946 2.609747 AGGTTCCTTAGCTGTCTGACA 58.390 47.619 10.50 10.50 32.15 3.58
3700 3984 2.191128 AGGCAAGCAGTTTGTAGAGG 57.809 50.000 0.00 0.00 39.08 3.69
3703 3989 2.683968 TCGTAGGCAAGCAGTTTGTAG 58.316 47.619 0.00 0.00 39.08 2.74
3751 4038 2.432456 TGAGTAAGCACGCTGGCG 60.432 61.111 13.56 13.56 46.03 5.69
3797 4084 3.233980 AGAGGTGCCGACTGTGCA 61.234 61.111 0.00 0.00 36.12 4.57
3884 4198 1.073199 CGGTTGGCAAGAGAAGGGT 59.927 57.895 0.00 0.00 0.00 4.34
3945 4260 2.287608 GGAAAAAGAAGTGACCGCCAAG 60.288 50.000 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.