Multiple sequence alignment - TraesCS5D01G319600

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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 TraesCS5D01G319600 chr5D 100.000 4491 0 0 1 4491 412315313 412310823 0.000000e+00 8294
1 TraesCS5D01G319600 chr5B 91.104 3406 178 59 665 4016 496270095 496266761 0.000000e+00 4495
2 TraesCS5D01G319600 chr5B 90.096 313 23 6 4092 4398 496266767 496266457 2.520000e-107 399
3 TraesCS5D01G319600 chr5B 90.114 263 22 1 1 263 496272321 496272063 5.560000e-89 339
4 TraesCS5D01G319600 chr5B 78.804 552 79 23 1 526 496273470 496272931 2.000000e-88 337
5 TraesCS5D01G319600 chr5B 78.009 432 63 19 156 561 496273992 496273567 4.490000e-60 243
6 TraesCS5D01G319600 chr5B 89.855 138 11 3 4355 4491 496266449 496266314 1.660000e-39 174
7 TraesCS5D01G319600 chr5A 89.535 1548 95 31 1424 2925 524054107 524052581 0.000000e+00 1899
8 TraesCS5D01G319600 chr5A 92.785 596 33 7 2927 3515 524052484 524051892 0.000000e+00 854
9 TraesCS5D01G319600 chr5A 83.526 692 63 22 638 1311 524054828 524054170 2.310000e-167 599
10 TraesCS5D01G319600 chr5A 96.296 216 4 2 4280 4491 524050972 524050757 7.150000e-93 351
11 TraesCS5D01G319600 chr5A 90.210 143 10 1 4148 4286 524051292 524051150 2.760000e-42 183
12 TraesCS5D01G319600 chr5A 98.611 72 1 0 3957 4028 19818229 19818300 1.310000e-25 128
13 TraesCS5D01G319600 chr5A 98.611 72 1 0 3957 4028 667828827 667828756 1.310000e-25 128
14 TraesCS5D01G319600 chr5A 97.059 68 1 1 3534 3600 422040424 422040357 3.670000e-21 113
15 TraesCS5D01G319600 chr5A 95.652 69 2 1 3535 3603 381757768 381757701 4.750000e-20 110
16 TraesCS5D01G319600 chr5A 95.522 67 3 0 3534 3600 447544502 447544568 1.710000e-19 108
17 TraesCS5D01G319600 chr7A 78.824 1530 239 52 1487 2979 2696109 2694628 0.000000e+00 952
18 TraesCS5D01G319600 chr7A 84.234 222 29 6 3030 3249 2694544 2694327 1.270000e-50 211
19 TraesCS5D01G319600 chr7A 97.222 72 2 0 3957 4028 4909923 4909994 6.100000e-24 122
20 TraesCS5D01G319600 chr4D 97.222 72 2 0 3957 4028 123499115 123499186 6.100000e-24 122
21 TraesCS5D01G319600 chr4D 94.118 68 4 0 3534 3601 282196923 282196990 2.210000e-18 104
22 TraesCS5D01G319600 chr4A 97.222 72 2 0 3957 4028 67506789 67506718 6.100000e-24 122
23 TraesCS5D01G319600 chr3A 97.222 72 2 0 3957 4028 51893428 51893499 6.100000e-24 122
24 TraesCS5D01G319600 chr3A 95.588 68 2 1 3535 3601 621834406 621834339 1.710000e-19 108
25 TraesCS5D01G319600 chr2A 98.529 68 1 0 3959 4026 444299137 444299204 2.190000e-23 121
26 TraesCS5D01G319600 chr2A 91.954 87 6 1 2558 2644 566597909 566597824 2.190000e-23 121
27 TraesCS5D01G319600 chr7D 97.143 70 2 0 3957 4026 307191093 307191162 7.890000e-23 119
28 TraesCS5D01G319600 chr6A 94.444 72 4 0 3534 3605 614533977 614534048 1.320000e-20 111
29 TraesCS5D01G319600 chr7B 95.522 67 1 2 3535 3600 296330826 296330891 6.140000e-19 106
30 TraesCS5D01G319600 chr3B 93.056 72 3 2 3533 3603 636452111 636452041 2.210000e-18 104


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 TraesCS5D01G319600 chr5D 412310823 412315313 4490 True 8294.000000 8294 100.000000 1 4491 1 chr5D.!!$R1 4490
1 TraesCS5D01G319600 chr5B 496266314 496273992 7678 True 997.833333 4495 86.330333 1 4491 6 chr5B.!!$R1 4490
2 TraesCS5D01G319600 chr5A 524050757 524054828 4071 True 777.200000 1899 90.470400 638 4491 5 chr5A.!!$R4 3853
3 TraesCS5D01G319600 chr7A 2694327 2696109 1782 True 581.500000 952 81.529000 1487 3249 2 chr7A.!!$R1 1762

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
138 1810 0.027455 CATGTGCGACACGTGTGTTT 59.973 50.0 28.82 0.00 45.05 2.83 F
139 1811 0.027455 ATGTGCGACACGTGTGTTTG 59.973 50.0 28.82 13.79 45.05 2.93 F
589 3903 0.109532 TCGGGCATTCAAGTTCACCA 59.890 50.0 0.00 0.00 0.00 4.17 F
2103 5526 0.316204 ATGCAGCTCAGGTTTGTTGC 59.684 50.0 0.00 0.00 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1150 4481 0.036765 TTCACCCAACGATTCTCGGG 60.037 55.0 1.29 0.0 45.59 5.14 R
1204 4537 0.123266 AGGGGAGGAAAGGGATGGAA 59.877 55.0 0.00 0.0 0.00 3.53 R
2173 5596 0.479589 TTCTGGGACCCCCTCCAAAT 60.480 55.0 8.45 0.0 45.70 2.32 R
4021 7603 0.107214 ATGCCCAATTGTCCGTCGAT 60.107 50.0 4.43 0.0 0.00 3.59 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
26 1698 1.745087 ACATAAATGCTCACCCAAGCG 59.255 47.619 0.00 0.00 45.54 4.68
42 1714 1.776662 AGCGTTGCTCCTATGGTAGA 58.223 50.000 0.00 0.00 30.62 2.59
44 1716 1.538419 GCGTTGCTCCTATGGTAGACC 60.538 57.143 0.00 0.00 0.00 3.85
117 1789 2.766651 TGGCCGTGGGACCTATCC 60.767 66.667 0.00 0.00 45.42 2.59
137 1809 1.641140 CATGTGCGACACGTGTGTT 59.359 52.632 28.82 0.00 45.05 3.32
138 1810 0.027455 CATGTGCGACACGTGTGTTT 59.973 50.000 28.82 0.00 45.05 2.83
139 1811 0.027455 ATGTGCGACACGTGTGTTTG 59.973 50.000 28.82 13.79 45.05 2.93
140 1812 1.932564 GTGCGACACGTGTGTTTGC 60.933 57.895 28.82 22.79 45.05 3.68
141 1813 2.351888 GCGACACGTGTGTTTGCC 60.352 61.111 28.82 9.48 45.05 4.52
142 1814 2.053465 CGACACGTGTGTTTGCCG 60.053 61.111 28.82 18.18 45.05 5.69
143 1815 2.326550 GACACGTGTGTTTGCCGG 59.673 61.111 28.82 0.00 45.05 6.13
144 1816 2.437002 ACACGTGTGTTTGCCGGT 60.437 55.556 22.71 0.00 41.83 5.28
145 1817 2.024022 CACGTGTGTTTGCCGGTG 59.976 61.111 7.58 0.00 0.00 4.94
146 1818 3.883180 ACGTGTGTTTGCCGGTGC 61.883 61.111 1.90 0.00 38.26 5.01
147 1819 4.954680 CGTGTGTTTGCCGGTGCG 62.955 66.667 1.90 0.00 41.78 5.34
188 1860 0.456995 GCACCTGCTCTAGACGTCAC 60.457 60.000 19.50 2.01 38.21 3.67
202 1874 0.653323 CGTCACTGTTGGCGTTTTCG 60.653 55.000 0.00 0.00 46.09 3.46
212 1884 1.501337 GGCGTTTTCGGACTCGGTTT 61.501 55.000 0.00 0.00 44.29 3.27
236 1908 2.355412 CCGGAGTGGGTTTTACTTAGGG 60.355 54.545 0.00 0.00 0.00 3.53
263 1935 0.622136 TCACAAGGATCTGCATGCCT 59.378 50.000 16.68 0.68 0.00 4.75
271 3160 0.183014 ATCTGCATGCCTCCTTCTGG 59.817 55.000 16.68 0.00 0.00 3.86
310 3614 2.024414 GGGAAGGGGAATGAAATCACG 58.976 52.381 0.00 0.00 0.00 4.35
313 3617 3.954258 GGAAGGGGAATGAAATCACGATT 59.046 43.478 0.00 0.00 0.00 3.34
350 3656 7.334921 CGTATACTAACTTGGTTTTTGGGATGA 59.665 37.037 0.56 0.00 0.00 2.92
352 3658 3.726291 AACTTGGTTTTTGGGATGACG 57.274 42.857 0.00 0.00 0.00 4.35
378 3686 2.648426 GTGTAAGCTCGGCGTATACTC 58.352 52.381 6.85 3.99 33.65 2.59
379 3687 2.290093 GTGTAAGCTCGGCGTATACTCT 59.710 50.000 6.85 0.00 33.65 3.24
381 3689 1.676746 AAGCTCGGCGTATACTCTGA 58.323 50.000 6.85 4.38 0.00 3.27
382 3690 1.676746 AGCTCGGCGTATACTCTGAA 58.323 50.000 6.85 0.00 0.00 3.02
422 3735 5.901552 ACAACAACTCTGTTACCCATTTTG 58.098 37.500 0.00 0.00 44.15 2.44
431 3744 3.754323 TGTTACCCATTTTGACCGTGATC 59.246 43.478 0.00 0.00 0.00 2.92
451 3765 4.191033 TCGTCACACGGTGGTTATTATT 57.809 40.909 13.48 0.00 42.81 1.40
463 3777 5.411361 GGTGGTTATTATTGCTATCGATGCA 59.589 40.000 8.54 12.87 38.80 3.96
493 3807 7.372918 CGACGACTCTACTATAACTGCTTTTAC 59.627 40.741 0.00 0.00 0.00 2.01
510 3824 5.119125 GCTTTTACAACTTGCAACCATGATC 59.881 40.000 0.00 0.00 0.00 2.92
525 3839 7.549839 CAACCATGATCACAACCAAAAGATAT 58.450 34.615 0.00 0.00 0.00 1.63
528 3842 8.686334 ACCATGATCACAACCAAAAGATATTAC 58.314 33.333 0.00 0.00 0.00 1.89
530 3844 9.941664 CATGATCACAACCAAAAGATATTACTC 57.058 33.333 0.00 0.00 0.00 2.59
531 3845 8.196802 TGATCACAACCAAAAGATATTACTCG 57.803 34.615 0.00 0.00 0.00 4.18
532 3846 8.038351 TGATCACAACCAAAAGATATTACTCGA 58.962 33.333 0.00 0.00 0.00 4.04
533 3847 8.786826 ATCACAACCAAAAGATATTACTCGAA 57.213 30.769 0.00 0.00 0.00 3.71
534 3848 8.610248 TCACAACCAAAAGATATTACTCGAAA 57.390 30.769 0.00 0.00 0.00 3.46
535 3849 8.717821 TCACAACCAAAAGATATTACTCGAAAG 58.282 33.333 0.00 0.00 0.00 2.62
536 3850 7.962918 CACAACCAAAAGATATTACTCGAAAGG 59.037 37.037 0.00 0.00 0.00 3.11
537 3851 7.881232 ACAACCAAAAGATATTACTCGAAAGGA 59.119 33.333 0.00 0.00 0.00 3.36
538 3852 8.726988 CAACCAAAAGATATTACTCGAAAGGAA 58.273 33.333 0.00 0.00 0.00 3.36
539 3853 8.857694 ACCAAAAGATATTACTCGAAAGGAAA 57.142 30.769 0.00 0.00 0.00 3.13
540 3854 9.292195 ACCAAAAGATATTACTCGAAAGGAAAA 57.708 29.630 0.00 0.00 0.00 2.29
541 3855 9.556030 CCAAAAGATATTACTCGAAAGGAAAAC 57.444 33.333 0.00 0.00 0.00 2.43
549 3863 5.358298 ACTCGAAAGGAAAACATAAGTGC 57.642 39.130 0.00 0.00 0.00 4.40
550 3864 5.063880 ACTCGAAAGGAAAACATAAGTGCT 58.936 37.500 0.00 0.00 0.00 4.40
551 3865 5.179555 ACTCGAAAGGAAAACATAAGTGCTC 59.820 40.000 0.00 0.00 0.00 4.26
552 3866 5.060506 TCGAAAGGAAAACATAAGTGCTCA 58.939 37.500 0.00 0.00 0.00 4.26
553 3867 5.049680 TCGAAAGGAAAACATAAGTGCTCAC 60.050 40.000 0.00 0.00 0.00 3.51
554 3868 4.749245 AAGGAAAACATAAGTGCTCACG 57.251 40.909 0.00 0.00 36.20 4.35
555 3869 2.484264 AGGAAAACATAAGTGCTCACGC 59.516 45.455 0.00 0.00 36.20 5.34
556 3870 2.225491 GGAAAACATAAGTGCTCACGCA 59.775 45.455 0.00 0.00 45.60 5.24
564 3878 3.345808 TGCTCACGCAAGCGAACC 61.346 61.111 22.30 6.81 44.62 3.62
565 3879 3.345808 GCTCACGCAAGCGAACCA 61.346 61.111 22.30 0.67 42.83 3.67
566 3880 2.680913 GCTCACGCAAGCGAACCAT 61.681 57.895 22.30 0.00 42.83 3.55
567 3881 1.133253 CTCACGCAAGCGAACCATG 59.867 57.895 22.30 8.52 42.83 3.66
568 3882 2.176546 CACGCAAGCGAACCATGG 59.823 61.111 22.30 11.19 42.83 3.66
569 3883 3.737172 ACGCAAGCGAACCATGGC 61.737 61.111 22.30 0.00 42.83 4.40
570 3884 3.434319 CGCAAGCGAACCATGGCT 61.434 61.111 13.04 0.00 43.05 4.75
571 3885 2.486966 GCAAGCGAACCATGGCTC 59.513 61.111 13.04 8.66 40.00 4.70
572 3886 2.787249 CAAGCGAACCATGGCTCG 59.213 61.111 29.01 29.01 40.00 5.03
573 3887 2.436646 AAGCGAACCATGGCTCGG 60.437 61.111 32.42 17.90 40.00 4.63
574 3888 3.976701 AAGCGAACCATGGCTCGGG 62.977 63.158 32.42 11.85 40.00 5.14
576 3890 4.776322 CGAACCATGGCTCGGGCA 62.776 66.667 26.43 6.05 43.52 5.36
578 3892 1.754234 GAACCATGGCTCGGGCATT 60.754 57.895 13.04 0.00 46.61 3.56
579 3893 1.728490 GAACCATGGCTCGGGCATTC 61.728 60.000 13.04 1.32 46.61 2.67
580 3894 2.124193 CCATGGCTCGGGCATTCA 60.124 61.111 10.74 0.00 46.61 2.57
581 3895 1.753848 CCATGGCTCGGGCATTCAA 60.754 57.895 10.74 0.00 46.61 2.69
582 3896 1.731433 CCATGGCTCGGGCATTCAAG 61.731 60.000 10.74 0.00 46.61 3.02
583 3897 1.033746 CATGGCTCGGGCATTCAAGT 61.034 55.000 10.74 0.00 46.61 3.16
584 3898 0.323725 ATGGCTCGGGCATTCAAGTT 60.324 50.000 10.74 0.00 46.61 2.66
585 3899 0.960364 TGGCTCGGGCATTCAAGTTC 60.960 55.000 10.74 0.00 40.87 3.01
586 3900 0.960364 GGCTCGGGCATTCAAGTTCA 60.960 55.000 10.74 0.00 40.87 3.18
587 3901 0.169009 GCTCGGGCATTCAAGTTCAC 59.831 55.000 0.00 0.00 38.54 3.18
588 3902 0.804989 CTCGGGCATTCAAGTTCACC 59.195 55.000 0.00 0.00 0.00 4.02
589 3903 0.109532 TCGGGCATTCAAGTTCACCA 59.890 50.000 0.00 0.00 0.00 4.17
590 3904 0.523072 CGGGCATTCAAGTTCACCAG 59.477 55.000 0.00 0.00 0.00 4.00
591 3905 1.881925 CGGGCATTCAAGTTCACCAGA 60.882 52.381 0.00 0.00 0.00 3.86
592 3906 1.815003 GGGCATTCAAGTTCACCAGAG 59.185 52.381 0.00 0.00 0.00 3.35
595 3909 3.128242 GGCATTCAAGTTCACCAGAGATG 59.872 47.826 0.00 0.00 0.00 2.90
603 3917 6.385176 TCAAGTTCACCAGAGATGATCCTATT 59.615 38.462 0.00 0.00 0.00 1.73
604 3918 6.418057 AGTTCACCAGAGATGATCCTATTC 57.582 41.667 0.00 0.00 0.00 1.75
607 3921 3.262915 CACCAGAGATGATCCTATTCCCC 59.737 52.174 0.00 0.00 0.00 4.81
611 3925 2.164624 GAGATGATCCTATTCCCCGACG 59.835 54.545 0.00 0.00 0.00 5.12
617 3931 1.135024 TCCTATTCCCCGACGAAAACG 60.135 52.381 0.00 0.00 0.00 3.60
709 4023 9.908152 TGGATATGACATTGTAATCTTACTACG 57.092 33.333 0.00 0.00 34.77 3.51
738 4052 3.932710 TCTATCTGTGCCACGTCATTTTC 59.067 43.478 0.00 0.00 0.00 2.29
834 4149 1.456923 GAAAAGATTGCGTTGCCAAGC 59.543 47.619 0.00 0.00 0.00 4.01
859 4174 1.215423 AGCAAGGGACACAAAGGAAGT 59.785 47.619 0.00 0.00 0.00 3.01
861 4176 3.074538 AGCAAGGGACACAAAGGAAGTAT 59.925 43.478 0.00 0.00 0.00 2.12
908 4223 3.712016 AAAGAAGAGAAGAGAAGGGGC 57.288 47.619 0.00 0.00 0.00 5.80
909 4224 2.334006 AGAAGAGAAGAGAAGGGGCA 57.666 50.000 0.00 0.00 0.00 5.36
942 4271 5.308237 AGGTAGTCTCCATCACTTTGACTTT 59.692 40.000 0.00 0.00 38.67 2.66
945 4274 3.503748 GTCTCCATCACTTTGACTTTGGG 59.496 47.826 0.00 0.00 27.88 4.12
946 4275 3.394274 TCTCCATCACTTTGACTTTGGGA 59.606 43.478 0.00 0.00 27.88 4.37
947 4276 3.754965 TCCATCACTTTGACTTTGGGAG 58.245 45.455 0.00 0.00 27.88 4.30
948 4277 2.229784 CCATCACTTTGACTTTGGGAGC 59.770 50.000 0.00 0.00 0.00 4.70
950 4279 2.575532 TCACTTTGACTTTGGGAGCAG 58.424 47.619 0.00 0.00 0.00 4.24
1031 4360 1.194781 GCTGAGTGGGACAGGGAAGA 61.195 60.000 0.00 0.00 41.80 2.87
1032 4361 0.901124 CTGAGTGGGACAGGGAAGAG 59.099 60.000 0.00 0.00 41.80 2.85
1086 4417 1.704070 GCCGTCACTCTCTGTTCTTC 58.296 55.000 0.00 0.00 0.00 2.87
1088 4419 1.613925 CCGTCACTCTCTGTTCTTCCA 59.386 52.381 0.00 0.00 0.00 3.53
1091 4422 3.648009 GTCACTCTCTGTTCTTCCACTG 58.352 50.000 0.00 0.00 0.00 3.66
1100 4431 0.537188 TTCTTCCACTGATCTCCGGC 59.463 55.000 0.00 0.00 0.00 6.13
1136 4467 5.047660 GCAAGGTACAGATATTCCTCGATCT 60.048 44.000 0.00 0.00 32.48 2.75
1139 4470 5.010933 GGTACAGATATTCCTCGATCTCCA 58.989 45.833 0.00 0.00 29.73 3.86
1142 4473 5.328565 ACAGATATTCCTCGATCTCCATCA 58.671 41.667 0.00 0.00 29.73 3.07
1144 4475 5.418524 CAGATATTCCTCGATCTCCATCAGT 59.581 44.000 0.00 0.00 29.73 3.41
1149 4480 2.544694 CCTCGATCTCCATCAGTTTCCG 60.545 54.545 0.00 0.00 0.00 4.30
1150 4481 1.202417 TCGATCTCCATCAGTTTCCGC 60.202 52.381 0.00 0.00 0.00 5.54
1175 4506 3.670625 AGAATCGTTGGGTGAATTTCGA 58.329 40.909 0.00 0.00 0.00 3.71
1254 4587 1.823250 GCCCAAGATTGCCCGGATATT 60.823 52.381 0.73 0.00 0.00 1.28
1257 4590 3.490348 CCAAGATTGCCCGGATATTCTT 58.510 45.455 0.73 6.15 0.00 2.52
1269 4603 4.392940 CGGATATTCTTTGGATTCTGCCT 58.607 43.478 0.00 0.00 0.00 4.75
1272 4606 5.457342 GGATATTCTTTGGATTCTGCCTCCT 60.457 44.000 0.00 0.00 33.69 3.69
1276 4610 4.082125 TCTTTGGATTCTGCCTCCTTTTC 58.918 43.478 0.00 0.00 33.69 2.29
1299 4633 1.066908 CTTTTTGTTCTTGGAGCGGCA 59.933 47.619 1.45 0.00 0.00 5.69
1302 4636 1.243342 TTGTTCTTGGAGCGGCATGG 61.243 55.000 1.45 0.00 0.00 3.66
1306 4640 1.890979 CTTGGAGCGGCATGGCTAG 60.891 63.158 18.09 3.61 44.93 3.42
1325 4659 2.089980 AGCATGCCATCAGTTCAGAAC 58.910 47.619 15.66 5.00 0.00 3.01
1342 4676 4.593206 TCAGAACTGAGCCGGGAAATATAT 59.407 41.667 2.18 0.00 34.14 0.86
1344 4678 5.409826 CAGAACTGAGCCGGGAAATATATTC 59.590 44.000 2.18 0.00 0.00 1.75
1346 4680 6.497259 AGAACTGAGCCGGGAAATATATTCTA 59.503 38.462 2.18 0.00 0.00 2.10
1354 4688 5.050091 CCGGGAAATATATTCTATGCGATGC 60.050 44.000 0.00 0.00 0.00 3.91
1394 4728 3.334272 AAAATAGTGCTTATTCGGCGC 57.666 42.857 0.00 0.00 40.08 6.53
1484 4833 6.876257 AGAAAAGTCCTGACTGCTATGTTTAG 59.124 38.462 0.00 0.00 41.58 1.85
1579 4950 7.878127 TGAAATTTGGTTCTTAGTCAGTCTAGG 59.122 37.037 0.00 0.00 0.00 3.02
1762 5144 4.704833 GCTGCAGGGGAGCGTCAA 62.705 66.667 17.12 0.00 37.31 3.18
1933 5330 2.109229 ATATAGTGCCACTGCTCCCT 57.891 50.000 7.83 0.00 38.71 4.20
2010 5414 1.991430 CTCACGCGTGCTACATGTC 59.009 57.895 33.63 0.00 0.00 3.06
2017 5421 1.737838 CGTGCTACATGTCCATGGTT 58.262 50.000 12.58 0.00 42.91 3.67
2103 5526 0.316204 ATGCAGCTCAGGTTTGTTGC 59.684 50.000 0.00 0.00 0.00 4.17
2111 5534 3.430790 GCTCAGGTTTGTTGCTTCCTTTT 60.431 43.478 0.00 0.00 0.00 2.27
2173 5596 4.501229 GGATTCCAAATGTGTGCACTGAAA 60.501 41.667 19.41 0.00 0.00 2.69
2178 5605 4.024725 CCAAATGTGTGCACTGAAATTTGG 60.025 41.667 29.76 29.76 40.98 3.28
2206 5634 4.823989 GGTCCCAGAATCATAAGTTGATGG 59.176 45.833 0.00 0.00 44.51 3.51
2314 5743 2.836479 ACGTTCTTTGACGGTTTTGG 57.164 45.000 2.39 0.00 46.77 3.28
2405 5845 9.458374 CAAAAGGTTTAAGGTTGTGTTATACTG 57.542 33.333 0.00 0.00 0.00 2.74
2407 5847 6.300703 AGGTTTAAGGTTGTGTTATACTGCA 58.699 36.000 0.00 0.00 0.00 4.41
2408 5848 6.946009 AGGTTTAAGGTTGTGTTATACTGCAT 59.054 34.615 0.00 0.00 0.00 3.96
2409 5849 7.450323 AGGTTTAAGGTTGTGTTATACTGCATT 59.550 33.333 0.00 0.00 0.00 3.56
2413 5853 6.267496 AGGTTGTGTTATACTGCATTTTCC 57.733 37.500 0.00 0.00 0.00 3.13
2414 5854 5.185056 AGGTTGTGTTATACTGCATTTTCCC 59.815 40.000 0.00 0.00 0.00 3.97
2415 5855 5.407502 GTTGTGTTATACTGCATTTTCCCC 58.592 41.667 0.00 0.00 0.00 4.81
2416 5856 4.667573 TGTGTTATACTGCATTTTCCCCA 58.332 39.130 0.00 0.00 0.00 4.96
2417 5857 5.268387 TGTGTTATACTGCATTTTCCCCAT 58.732 37.500 0.00 0.00 0.00 4.00
2418 5858 5.126869 TGTGTTATACTGCATTTTCCCCATG 59.873 40.000 0.00 0.00 0.00 3.66
2419 5859 4.648762 TGTTATACTGCATTTTCCCCATGG 59.351 41.667 4.14 4.14 0.00 3.66
2431 5873 5.736951 TTTCCCCATGGTTTTGACATTAG 57.263 39.130 11.73 0.00 0.00 1.73
2441 5883 7.475771 TGGTTTTGACATTAGAAACAATTGC 57.524 32.000 5.05 0.00 35.53 3.56
2452 5894 9.079833 CATTAGAAACAATTGCACATAAAGAGG 57.920 33.333 5.05 0.00 0.00 3.69
2470 5912 5.596836 AGAGGCACACTTTGATTTTTGAA 57.403 34.783 0.00 0.00 0.00 2.69
2498 5941 8.579006 TCTTGTAGCACATGAAAATCTCATTTT 58.421 29.630 0.00 0.00 42.46 1.82
2511 5954 9.429600 GAAAATCTCATTTTTGAGCAACTTTTG 57.570 29.630 0.00 0.00 42.15 2.44
2585 6028 7.015682 GTAGGAACTCAATCCAGAGGATTATCA 59.984 40.741 10.70 0.00 45.01 2.15
2680 6123 7.484007 CGATGAGTACGTGACAGTTAGTTTTAT 59.516 37.037 0.00 0.00 0.00 1.40
2710 6155 7.969536 ATCGATCATCATTTTGTAACCCTAG 57.030 36.000 0.00 0.00 0.00 3.02
2870 6315 9.797556 GATTAACAAGGTAAAACTCAGTTTTGT 57.202 29.630 23.38 11.60 44.09 2.83
3166 6741 3.001939 GGTATTCGGTTAACTTGCGATGG 59.998 47.826 5.42 0.00 0.00 3.51
3178 6755 1.614996 TGCGATGGTTGTGGATGTTT 58.385 45.000 0.00 0.00 0.00 2.83
3274 6852 5.310451 TGGTCTACCGTGCTTTAAGAAAAT 58.690 37.500 0.00 0.00 39.43 1.82
3299 6877 6.709281 TGTATTTTGGATCATGCCATGTTTT 58.291 32.000 4.31 0.00 37.86 2.43
3367 6945 2.685522 CGGGCAGTGGGTTATATGGTTT 60.686 50.000 0.00 0.00 0.00 3.27
3383 6961 4.392921 TGGTTTGCAATTTTCCGAGAAA 57.607 36.364 0.00 0.00 0.00 2.52
3390 6968 3.798548 GCAATTTTCCGAGAAAGCAACCA 60.799 43.478 0.00 0.00 0.00 3.67
3559 7139 7.486407 ACTCCCTCCGTAAAGAAATAAAGTA 57.514 36.000 0.00 0.00 0.00 2.24
3566 7146 9.804758 CTCCGTAAAGAAATAAAGTAGTGATCT 57.195 33.333 0.00 0.00 0.00 2.75
3723 7305 6.100004 ACTTCGTTTGTGGTCTATGATACAG 58.900 40.000 0.00 0.00 0.00 2.74
3730 7312 4.095932 TGTGGTCTATGATACAGTGACGAC 59.904 45.833 0.00 0.00 37.06 4.34
3738 7320 3.119137 TGATACAGTGACGACCATGAAGG 60.119 47.826 0.00 0.00 45.67 3.46
3741 7323 1.056660 AGTGACGACCATGAAGGGTT 58.943 50.000 0.00 0.00 42.53 4.11
3799 7381 2.297597 CGGGCCACAAAATTCTAACCAA 59.702 45.455 4.39 0.00 0.00 3.67
3850 7432 1.747355 CCTCACAACCATCTCAATGCC 59.253 52.381 0.00 0.00 0.00 4.40
3932 7514 2.198827 TCATGTGAGCCCAAAATCGT 57.801 45.000 0.00 0.00 0.00 3.73
3943 7525 4.396166 AGCCCAAAATCGTCAACAATCTAG 59.604 41.667 0.00 0.00 0.00 2.43
3969 7551 6.870439 CGATGTTCACTATGATCACATGGTAT 59.130 38.462 0.00 0.00 44.27 2.73
4013 7595 0.532573 CTCTACTGCGCCAGGAAGAA 59.467 55.000 4.18 0.00 35.51 2.52
4014 7596 0.973632 TCTACTGCGCCAGGAAGAAA 59.026 50.000 4.18 0.00 35.51 2.52
4015 7597 1.346395 TCTACTGCGCCAGGAAGAAAA 59.654 47.619 4.18 0.00 35.51 2.29
4016 7598 1.734465 CTACTGCGCCAGGAAGAAAAG 59.266 52.381 4.18 0.00 35.51 2.27
4017 7599 1.211190 CTGCGCCAGGAAGAAAAGC 59.789 57.895 4.18 0.00 0.00 3.51
4018 7600 1.228245 TGCGCCAGGAAGAAAAGCT 60.228 52.632 4.18 0.00 0.00 3.74
4019 7601 1.211190 GCGCCAGGAAGAAAAGCTG 59.789 57.895 0.00 0.00 0.00 4.24
4020 7602 1.878775 CGCCAGGAAGAAAAGCTGG 59.121 57.895 0.00 0.00 38.17 4.85
4021 7603 0.606401 CGCCAGGAAGAAAAGCTGGA 60.606 55.000 0.00 0.00 37.37 3.86
4022 7604 1.844687 GCCAGGAAGAAAAGCTGGAT 58.155 50.000 0.00 0.00 37.37 3.41
4023 7605 1.747924 GCCAGGAAGAAAAGCTGGATC 59.252 52.381 0.00 0.00 37.37 3.36
4024 7606 2.012673 CCAGGAAGAAAAGCTGGATCG 58.987 52.381 0.00 0.00 37.37 3.69
4025 7607 2.355108 CCAGGAAGAAAAGCTGGATCGA 60.355 50.000 0.00 0.00 37.37 3.59
4026 7608 2.675348 CAGGAAGAAAAGCTGGATCGAC 59.325 50.000 0.00 0.00 0.00 4.20
4027 7609 1.661112 GGAAGAAAAGCTGGATCGACG 59.339 52.381 0.00 0.00 0.00 5.12
4028 7610 1.661112 GAAGAAAAGCTGGATCGACGG 59.339 52.381 0.00 0.00 0.00 4.79
4029 7611 0.895530 AGAAAAGCTGGATCGACGGA 59.104 50.000 0.00 0.00 0.00 4.69
4030 7612 1.000145 GAAAAGCTGGATCGACGGAC 59.000 55.000 0.00 0.00 0.00 4.79
4042 7624 1.809207 GACGGACAATTGGGCATGG 59.191 57.895 10.83 0.00 0.00 3.66
4045 7627 0.173255 CGGACAATTGGGCATGGTTC 59.827 55.000 10.83 0.00 0.00 3.62
4047 7629 1.901833 GGACAATTGGGCATGGTTCTT 59.098 47.619 10.83 0.00 0.00 2.52
4049 7631 3.588955 GACAATTGGGCATGGTTCTTTC 58.411 45.455 10.83 0.00 0.00 2.62
4051 7633 3.007182 ACAATTGGGCATGGTTCTTTCAG 59.993 43.478 10.83 0.00 0.00 3.02
4059 7641 3.817647 GCATGGTTCTTTCAGTCAGAAGT 59.182 43.478 0.00 0.00 37.57 3.01
4063 7645 6.479972 TGGTTCTTTCAGTCAGAAGTTAGA 57.520 37.500 0.00 0.00 37.57 2.10
4073 7655 5.636965 CAGTCAGAAGTTAGACAATGACCTG 59.363 44.000 9.76 0.00 38.20 4.00
4112 7694 5.066375 TCCAGATGAAACTGAAACACACTTG 59.934 40.000 0.00 0.00 39.94 3.16
4133 7715 7.711339 CACTTGTACCAATCTAGAATAGGAACC 59.289 40.741 13.54 0.00 39.78 3.62
4135 7717 6.449956 TGTACCAATCTAGAATAGGAACCCT 58.550 40.000 13.54 0.00 39.78 4.34
4137 7719 6.502074 ACCAATCTAGAATAGGAACCCTTC 57.498 41.667 13.54 0.00 39.78 3.46
4141 7728 8.151596 CCAATCTAGAATAGGAACCCTTCTAAC 58.848 40.741 0.00 0.00 39.78 2.34
4172 7852 6.882140 TCAGTTAGTTCTTTTGTCCAACAAGA 59.118 34.615 0.00 0.00 39.53 3.02
4173 7853 7.556275 TCAGTTAGTTCTTTTGTCCAACAAGAT 59.444 33.333 0.00 0.00 39.53 2.40
4174 7854 8.836413 CAGTTAGTTCTTTTGTCCAACAAGATA 58.164 33.333 0.00 0.00 39.53 1.98
4180 7861 6.970484 TCTTTTGTCCAACAAGATAAGCTTC 58.030 36.000 0.00 0.00 39.53 3.86
4286 8155 2.348411 AGGCTGCACACCCATATTAC 57.652 50.000 0.50 0.00 0.00 1.89
4348 8217 3.742433 TGGTTGCTTAAACAATGGTGG 57.258 42.857 0.00 0.00 40.86 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.418057 TTGGGTGAGCATTTATGTTTTTCT 57.582 33.333 0.00 0.00 0.00 2.52
1 2 5.120674 GCTTGGGTGAGCATTTATGTTTTTC 59.879 40.000 0.00 0.00 42.25 2.29
2 3 4.996758 GCTTGGGTGAGCATTTATGTTTTT 59.003 37.500 0.00 0.00 42.25 1.94
3 4 4.568956 GCTTGGGTGAGCATTTATGTTTT 58.431 39.130 0.00 0.00 42.25 2.43
4 5 3.367292 CGCTTGGGTGAGCATTTATGTTT 60.367 43.478 0.00 0.00 42.83 2.83
12 1684 2.629656 GCAACGCTTGGGTGAGCAT 61.630 57.895 9.43 0.00 42.83 3.79
47 1719 1.087771 GTGGGTACACGCTATGGTGC 61.088 60.000 0.12 0.00 41.65 5.01
188 1860 0.234884 GAGTCCGAAAACGCCAACAG 59.765 55.000 0.00 0.00 0.00 3.16
212 1884 4.020307 CCTAAGTAAAACCCACTCCGGTTA 60.020 45.833 0.00 0.00 45.63 2.85
323 3627 6.767456 TCCCAAAAACCAAGTTAGTATACGA 58.233 36.000 0.00 0.00 0.00 3.43
324 3628 7.334921 TCATCCCAAAAACCAAGTTAGTATACG 59.665 37.037 0.00 0.00 0.00 3.06
325 3629 8.456471 GTCATCCCAAAAACCAAGTTAGTATAC 58.544 37.037 0.00 0.00 0.00 1.47
326 3630 7.334921 CGTCATCCCAAAAACCAAGTTAGTATA 59.665 37.037 0.00 0.00 0.00 1.47
327 3631 6.150474 CGTCATCCCAAAAACCAAGTTAGTAT 59.850 38.462 0.00 0.00 0.00 2.12
350 3656 1.516386 CGAGCTTACACGGATGCGT 60.516 57.895 6.39 6.39 0.00 5.24
357 3663 1.003116 AGTATACGCCGAGCTTACACG 60.003 52.381 0.00 0.00 0.00 4.49
395 3703 2.224113 GGGTAACAGAGTTGTTGTCGGA 60.224 50.000 3.33 0.00 46.63 4.55
403 3711 4.320202 CGGTCAAAATGGGTAACAGAGTTG 60.320 45.833 0.00 0.00 39.74 3.16
431 3744 3.484557 GCAATAATAACCACCGTGTGACG 60.485 47.826 5.71 0.00 42.11 4.35
451 3765 2.031508 TCGTCGTATTGCATCGATAGCA 60.032 45.455 15.52 15.52 40.85 3.49
463 3777 6.705381 AGCAGTTATAGTAGAGTCGTCGTATT 59.295 38.462 0.00 0.00 0.00 1.89
467 3781 5.406767 AAGCAGTTATAGTAGAGTCGTCG 57.593 43.478 0.00 0.00 0.00 5.12
493 3807 3.646611 TGTGATCATGGTTGCAAGTTG 57.353 42.857 0.00 0.00 0.00 3.16
499 3813 3.383620 TTTGGTTGTGATCATGGTTGC 57.616 42.857 0.00 0.00 0.00 4.17
510 3824 7.962918 CCTTTCGAGTAATATCTTTTGGTTGTG 59.037 37.037 0.00 0.00 0.00 3.33
525 3839 6.708949 AGCACTTATGTTTTCCTTTCGAGTAA 59.291 34.615 0.00 0.00 0.00 2.24
528 3842 5.179368 TGAGCACTTATGTTTTCCTTTCGAG 59.821 40.000 0.00 0.00 0.00 4.04
530 3844 5.147162 GTGAGCACTTATGTTTTCCTTTCG 58.853 41.667 0.00 0.00 0.00 3.46
531 3845 5.147162 CGTGAGCACTTATGTTTTCCTTTC 58.853 41.667 0.00 0.00 0.00 2.62
532 3846 5.108385 CGTGAGCACTTATGTTTTCCTTT 57.892 39.130 0.00 0.00 0.00 3.11
533 3847 4.749245 CGTGAGCACTTATGTTTTCCTT 57.251 40.909 0.00 0.00 0.00 3.36
549 3863 1.133253 CATGGTTCGCTTGCGTGAG 59.867 57.895 14.70 0.00 0.00 3.51
550 3864 2.324330 CCATGGTTCGCTTGCGTGA 61.324 57.895 14.70 2.62 0.00 4.35
551 3865 2.176546 CCATGGTTCGCTTGCGTG 59.823 61.111 14.70 5.36 0.00 5.34
552 3866 3.737172 GCCATGGTTCGCTTGCGT 61.737 61.111 14.67 0.00 0.00 5.24
553 3867 3.386867 GAGCCATGGTTCGCTTGCG 62.387 63.158 13.27 8.87 34.84 4.85
554 3868 2.486966 GAGCCATGGTTCGCTTGC 59.513 61.111 13.27 0.00 34.84 4.01
555 3869 2.753966 CCGAGCCATGGTTCGCTTG 61.754 63.158 37.01 23.77 45.19 4.01
556 3870 2.436646 CCGAGCCATGGTTCGCTT 60.437 61.111 37.01 7.93 45.19 4.68
557 3871 4.473520 CCCGAGCCATGGTTCGCT 62.474 66.667 37.01 18.56 45.19 4.93
559 3873 4.776322 TGCCCGAGCCATGGTTCG 62.776 66.667 35.88 35.88 45.90 3.95
560 3874 1.728490 GAATGCCCGAGCCATGGTTC 61.728 60.000 18.11 18.11 38.69 3.62
561 3875 1.754234 GAATGCCCGAGCCATGGTT 60.754 57.895 14.67 7.37 38.69 3.67
562 3876 2.124151 GAATGCCCGAGCCATGGT 60.124 61.111 14.67 0.00 38.69 3.55
563 3877 1.731433 CTTGAATGCCCGAGCCATGG 61.731 60.000 7.63 7.63 38.69 3.66
564 3878 1.033746 ACTTGAATGCCCGAGCCATG 61.034 55.000 0.00 0.00 38.69 3.66
565 3879 0.323725 AACTTGAATGCCCGAGCCAT 60.324 50.000 0.00 0.00 38.69 4.40
566 3880 0.960364 GAACTTGAATGCCCGAGCCA 60.960 55.000 0.00 0.00 38.69 4.75
567 3881 0.960364 TGAACTTGAATGCCCGAGCC 60.960 55.000 0.00 0.00 38.69 4.70
568 3882 0.169009 GTGAACTTGAATGCCCGAGC 59.831 55.000 0.00 0.00 40.48 5.03
569 3883 0.804989 GGTGAACTTGAATGCCCGAG 59.195 55.000 0.00 0.00 0.00 4.63
570 3884 0.109532 TGGTGAACTTGAATGCCCGA 59.890 50.000 0.00 0.00 0.00 5.14
571 3885 0.523072 CTGGTGAACTTGAATGCCCG 59.477 55.000 0.00 0.00 0.00 6.13
572 3886 1.815003 CTCTGGTGAACTTGAATGCCC 59.185 52.381 0.00 0.00 0.00 5.36
573 3887 2.783135 TCTCTGGTGAACTTGAATGCC 58.217 47.619 0.00 0.00 0.00 4.40
574 3888 4.005650 TCATCTCTGGTGAACTTGAATGC 58.994 43.478 0.00 0.00 0.00 3.56
575 3889 5.296283 GGATCATCTCTGGTGAACTTGAATG 59.704 44.000 0.00 0.00 0.00 2.67
576 3890 5.191323 AGGATCATCTCTGGTGAACTTGAAT 59.809 40.000 0.00 0.00 0.00 2.57
577 3891 4.533707 AGGATCATCTCTGGTGAACTTGAA 59.466 41.667 0.00 0.00 0.00 2.69
578 3892 4.099633 AGGATCATCTCTGGTGAACTTGA 58.900 43.478 0.00 0.00 0.00 3.02
579 3893 4.484537 AGGATCATCTCTGGTGAACTTG 57.515 45.455 0.00 0.00 0.00 3.16
580 3894 6.183361 GGAATAGGATCATCTCTGGTGAACTT 60.183 42.308 0.00 0.00 0.00 2.66
581 3895 5.306678 GGAATAGGATCATCTCTGGTGAACT 59.693 44.000 0.00 0.00 0.00 3.01
582 3896 5.512232 GGGAATAGGATCATCTCTGGTGAAC 60.512 48.000 0.00 0.00 0.00 3.18
583 3897 4.594920 GGGAATAGGATCATCTCTGGTGAA 59.405 45.833 0.00 0.00 0.00 3.18
584 3898 4.163427 GGGAATAGGATCATCTCTGGTGA 58.837 47.826 0.00 0.00 0.00 4.02
585 3899 3.262915 GGGGAATAGGATCATCTCTGGTG 59.737 52.174 0.00 0.00 0.00 4.17
586 3900 3.525862 GGGGAATAGGATCATCTCTGGT 58.474 50.000 0.00 0.00 0.00 4.00
587 3901 2.499289 CGGGGAATAGGATCATCTCTGG 59.501 54.545 0.00 0.00 0.00 3.86
588 3902 3.194542 GTCGGGGAATAGGATCATCTCTG 59.805 52.174 0.00 0.00 0.00 3.35
589 3903 3.436243 GTCGGGGAATAGGATCATCTCT 58.564 50.000 0.00 0.00 0.00 3.10
590 3904 2.164624 CGTCGGGGAATAGGATCATCTC 59.835 54.545 0.00 0.00 0.00 2.75
591 3905 2.171840 CGTCGGGGAATAGGATCATCT 58.828 52.381 0.00 0.00 0.00 2.90
592 3906 2.168496 TCGTCGGGGAATAGGATCATC 58.832 52.381 0.00 0.00 0.00 2.92
595 3909 3.129109 GTTTTCGTCGGGGAATAGGATC 58.871 50.000 0.00 0.00 0.00 3.36
603 3917 0.179062 TTTTCCGTTTTCGTCGGGGA 60.179 50.000 4.58 0.00 46.82 4.81
604 3918 0.236449 CTTTTCCGTTTTCGTCGGGG 59.764 55.000 4.58 0.00 46.82 5.73
653 3967 7.816995 GGATTATGTATGGTTGTTTCTGCAAAA 59.183 33.333 0.00 0.00 0.00 2.44
654 3968 7.039434 TGGATTATGTATGGTTGTTTCTGCAAA 60.039 33.333 0.00 0.00 0.00 3.68
656 3970 5.948758 TGGATTATGTATGGTTGTTTCTGCA 59.051 36.000 0.00 0.00 0.00 4.41
658 3972 7.864108 TCTGGATTATGTATGGTTGTTTCTG 57.136 36.000 0.00 0.00 0.00 3.02
662 3976 6.910191 TCCATCTGGATTATGTATGGTTGTT 58.090 36.000 0.00 0.00 39.78 2.83
663 3977 6.514012 TCCATCTGGATTATGTATGGTTGT 57.486 37.500 0.00 0.00 39.78 3.32
706 4020 5.505159 CGTGGCACAGATAGAATAGAACGTA 60.505 44.000 19.09 0.00 41.80 3.57
707 4021 4.683832 GTGGCACAGATAGAATAGAACGT 58.316 43.478 13.86 0.00 41.80 3.99
708 4022 3.731216 CGTGGCACAGATAGAATAGAACG 59.269 47.826 19.09 0.00 41.80 3.95
709 4023 4.683832 ACGTGGCACAGATAGAATAGAAC 58.316 43.478 19.09 0.00 41.80 3.01
711 4025 3.951680 TGACGTGGCACAGATAGAATAGA 59.048 43.478 19.09 0.00 41.80 1.98
712 4026 4.307443 TGACGTGGCACAGATAGAATAG 57.693 45.455 19.09 0.00 41.80 1.73
713 4027 4.937201 ATGACGTGGCACAGATAGAATA 57.063 40.909 19.09 0.00 41.80 1.75
714 4028 3.827008 ATGACGTGGCACAGATAGAAT 57.173 42.857 19.09 0.00 41.80 2.40
715 4029 3.610040 AATGACGTGGCACAGATAGAA 57.390 42.857 19.09 0.00 41.80 2.10
716 4030 3.610040 AAATGACGTGGCACAGATAGA 57.390 42.857 19.09 0.00 41.80 1.98
834 4149 1.610522 CTTTGTGTCCCTTGCTCTTGG 59.389 52.381 0.00 0.00 0.00 3.61
859 4174 6.014755 TGGTTTGTCTTGATTTGCATTCCATA 60.015 34.615 0.00 0.00 0.00 2.74
861 4176 4.100653 TGGTTTGTCTTGATTTGCATTCCA 59.899 37.500 0.00 0.00 0.00 3.53
890 4205 2.334006 TGCCCCTTCTCTTCTCTTCT 57.666 50.000 0.00 0.00 0.00 2.85
908 4223 3.833732 TGGAGACTACCTACTGGCTATG 58.166 50.000 0.00 0.00 36.63 2.23
909 4224 4.106502 TGATGGAGACTACCTACTGGCTAT 59.893 45.833 0.00 0.00 36.63 2.97
979 4308 2.244651 GCTATTGTGCTACGGGCGG 61.245 63.158 0.00 0.00 45.43 6.13
1018 4347 2.124996 CCCCTCTTCCCTGTCCCA 59.875 66.667 0.00 0.00 0.00 4.37
1086 4417 2.635229 CTTCCGCCGGAGATCAGTGG 62.635 65.000 5.05 0.00 31.21 4.00
1088 4419 3.082579 GCTTCCGCCGGAGATCAGT 62.083 63.158 5.05 0.00 31.21 3.41
1110 4441 3.555168 CGAGGAATATCTGTACCTTGCCC 60.555 52.174 0.00 0.00 32.53 5.36
1121 4452 5.579047 ACTGATGGAGATCGAGGAATATCT 58.421 41.667 0.00 0.00 0.00 1.98
1122 4453 5.913137 ACTGATGGAGATCGAGGAATATC 57.087 43.478 0.00 0.00 0.00 1.63
1136 4467 2.238847 CTCGGGCGGAAACTGATGGA 62.239 60.000 0.00 0.00 0.00 3.41
1139 4470 0.541863 ATTCTCGGGCGGAAACTGAT 59.458 50.000 0.00 0.00 0.00 2.90
1142 4473 1.153628 CGATTCTCGGGCGGAAACT 60.154 57.895 0.00 0.00 36.00 2.66
1144 4475 1.017177 CAACGATTCTCGGGCGGAAA 61.017 55.000 1.29 0.00 45.59 3.13
1149 4480 2.106683 CACCCAACGATTCTCGGGC 61.107 63.158 1.29 0.00 45.59 6.13
1150 4481 0.036765 TTCACCCAACGATTCTCGGG 60.037 55.000 1.29 0.00 45.59 5.14
1175 4506 1.639635 ATTGCCCCGGATCAAGAGCT 61.640 55.000 0.73 0.00 0.00 4.09
1204 4537 0.123266 AGGGGAGGAAAGGGATGGAA 59.877 55.000 0.00 0.00 0.00 3.53
1237 4570 4.261741 CCAAAGAATATCCGGGCAATCTTG 60.262 45.833 0.00 0.00 0.00 3.02
1254 4587 3.814504 AAAGGAGGCAGAATCCAAAGA 57.185 42.857 0.00 0.00 39.47 2.52
1257 4590 2.557452 GGGAAAAGGAGGCAGAATCCAA 60.557 50.000 0.00 0.00 39.47 3.53
1269 4603 4.163268 CCAAGAACAAAAAGGGGAAAAGGA 59.837 41.667 0.00 0.00 0.00 3.36
1272 4606 4.383661 GCTCCAAGAACAAAAAGGGGAAAA 60.384 41.667 0.00 0.00 0.00 2.29
1276 4610 1.000274 CGCTCCAAGAACAAAAAGGGG 60.000 52.381 0.00 0.00 0.00 4.79
1302 4636 1.602851 CTGAACTGATGGCATGCTAGC 59.397 52.381 18.92 15.88 0.00 3.42
1306 4640 2.089980 AGTTCTGAACTGATGGCATGC 58.910 47.619 21.47 9.90 41.01 4.06
1318 4652 0.762418 TTTCCCGGCTCAGTTCTGAA 59.238 50.000 0.00 0.00 0.00 3.02
1325 4659 5.525378 GCATAGAATATATTTCCCGGCTCAG 59.475 44.000 0.00 0.00 0.00 3.35
1342 4676 2.438021 ACCCCTTTAGCATCGCATAGAA 59.562 45.455 0.00 0.00 0.00 2.10
1344 4678 2.417719 GACCCCTTTAGCATCGCATAG 58.582 52.381 0.00 0.00 0.00 2.23
1346 4680 0.532862 CGACCCCTTTAGCATCGCAT 60.533 55.000 0.00 0.00 0.00 4.73
1354 4688 9.209175 CTATTTTATCAATCTCGACCCCTTTAG 57.791 37.037 0.00 0.00 0.00 1.85
1471 4820 6.607004 AGTTGTACTCCTAAACATAGCAGT 57.393 37.500 0.00 0.00 0.00 4.40
1517 4870 5.189180 GCTCTGGAGGAAGTACAAAATCAT 58.811 41.667 0.00 0.00 0.00 2.45
1579 4950 6.293462 GCCGTGTATTATTCCTCTTTCCATTC 60.293 42.308 0.00 0.00 0.00 2.67
1762 5144 0.964358 GAGCTGCCATTGCTGAACCT 60.964 55.000 0.00 0.00 41.30 3.50
2010 5414 4.892433 TGCCTAAAAACAATGAACCATGG 58.108 39.130 11.19 11.19 0.00 3.66
2017 5421 2.621055 ACACGCTGCCTAAAAACAATGA 59.379 40.909 0.00 0.00 0.00 2.57
2103 5526 3.555586 CCCAATGAGCCAACAAAAGGAAG 60.556 47.826 0.00 0.00 0.00 3.46
2111 5534 2.025131 TGATGATCCCAATGAGCCAACA 60.025 45.455 0.00 0.00 0.00 3.33
2173 5596 0.479589 TTCTGGGACCCCCTCCAAAT 60.480 55.000 8.45 0.00 45.70 2.32
2178 5605 2.118403 TATGATTCTGGGACCCCCTC 57.882 55.000 8.45 0.00 45.70 4.30
2194 5622 7.966753 GCATATACAGATTGCCATCAACTTATG 59.033 37.037 0.01 4.19 34.60 1.90
2206 5634 2.227388 GCCACCTGCATATACAGATTGC 59.773 50.000 4.39 0.00 40.25 3.56
2231 5659 1.335810 TCCGGGTCGACATTATCTTCG 59.664 52.381 18.91 7.24 36.55 3.79
2314 5743 6.811170 TGTGTTCAGAAAATTGTTTGTTCTCC 59.189 34.615 0.00 0.00 29.10 3.71
2405 5845 3.073678 GTCAAAACCATGGGGAAAATGC 58.926 45.455 18.09 0.00 38.05 3.56
2407 5847 5.581350 AATGTCAAAACCATGGGGAAAAT 57.419 34.783 18.09 3.22 38.05 1.82
2408 5848 5.841237 TCTAATGTCAAAACCATGGGGAAAA 59.159 36.000 18.09 0.00 38.05 2.29
2409 5849 5.398236 TCTAATGTCAAAACCATGGGGAAA 58.602 37.500 18.09 3.50 38.05 3.13
2413 5853 6.095432 TGTTTCTAATGTCAAAACCATGGG 57.905 37.500 18.09 0.00 33.06 4.00
2414 5854 8.497554 CAATTGTTTCTAATGTCAAAACCATGG 58.502 33.333 11.19 11.19 33.06 3.66
2415 5855 8.011106 GCAATTGTTTCTAATGTCAAAACCATG 58.989 33.333 7.40 0.00 33.06 3.66
2416 5856 7.714377 TGCAATTGTTTCTAATGTCAAAACCAT 59.286 29.630 7.40 0.00 33.06 3.55
2417 5857 7.010923 GTGCAATTGTTTCTAATGTCAAAACCA 59.989 33.333 7.40 0.00 33.06 3.67
2418 5858 7.010923 TGTGCAATTGTTTCTAATGTCAAAACC 59.989 33.333 7.40 0.00 33.06 3.27
2419 5859 7.904094 TGTGCAATTGTTTCTAATGTCAAAAC 58.096 30.769 7.40 0.00 34.30 2.43
2431 5873 5.119125 GTGCCTCTTTATGTGCAATTGTTTC 59.881 40.000 7.40 0.00 35.16 2.78
2441 5883 5.633830 ATCAAAGTGTGCCTCTTTATGTG 57.366 39.130 3.11 0.00 34.35 3.21
2452 5894 7.687445 ACAAGATTTCAAAAATCAAAGTGTGC 58.313 30.769 13.29 0.00 0.00 4.57
2465 5907 9.195411 GATTTTCATGTGCTACAAGATTTCAAA 57.805 29.630 0.00 0.00 0.00 2.69
2466 5908 8.579006 AGATTTTCATGTGCTACAAGATTTCAA 58.421 29.630 0.00 0.00 0.00 2.69
2467 5909 8.114331 AGATTTTCATGTGCTACAAGATTTCA 57.886 30.769 0.00 0.00 0.00 2.69
2470 5912 7.692460 TGAGATTTTCATGTGCTACAAGATT 57.308 32.000 0.00 0.00 0.00 2.40
2498 5941 9.474920 CCAAAATAATAGTCAAAAGTTGCTCAA 57.525 29.630 0.00 0.00 0.00 3.02
2511 5954 8.263940 TGCTACAGAACACCAAAATAATAGTC 57.736 34.615 0.00 0.00 0.00 2.59
2529 5972 3.062639 CCGATTGCTTGTAGTTGCTACAG 59.937 47.826 8.69 5.61 45.83 2.74
2585 6028 5.649265 TCCAGGTAGCTTATCAGATCATCT 58.351 41.667 0.00 0.00 0.00 2.90
2591 6034 2.091055 AGGCTCCAGGTAGCTTATCAGA 60.091 50.000 0.00 0.00 42.37 3.27
2680 6123 8.397906 GGTTACAAAATGATGATCGATTCAGAA 58.602 33.333 0.00 0.00 37.89 3.02
2710 6155 7.277981 GGGTATCACACGATAATATGTTCATCC 59.722 40.741 0.00 0.00 35.87 3.51
3026 6599 6.764379 TGTACACCAAGATATCAGACAACAA 58.236 36.000 5.32 0.00 0.00 2.83
3166 6741 1.335872 CGAGGCCAAAACATCCACAAC 60.336 52.381 5.01 0.00 0.00 3.32
3192 6769 7.002276 AGCAAGATTGTCCATTATCATGATGA 58.998 34.615 18.72 10.78 31.07 2.92
3274 6852 5.936187 ACATGGCATGATCCAAAATACAA 57.064 34.783 32.74 0.00 39.96 2.41
3299 6877 5.163077 TGACAAAACTAAGTTGGGGGACATA 60.163 40.000 0.00 0.00 0.00 2.29
3367 6945 3.380142 GTTGCTTTCTCGGAAAATTGCA 58.620 40.909 7.31 7.31 0.00 4.08
3383 6961 1.602888 CTGCTCCTGCTTGGTTGCT 60.603 57.895 13.57 0.00 40.48 3.91
3390 6968 4.467795 TCATCTACTTAACTGCTCCTGCTT 59.532 41.667 0.00 0.00 40.48 3.91
3508 7088 9.227777 ACGCTCCAAAGTATAAAAAGAAAGTAT 57.772 29.630 0.00 0.00 0.00 2.12
3510 7090 7.506328 ACGCTCCAAAGTATAAAAAGAAAGT 57.494 32.000 0.00 0.00 0.00 2.66
3511 7091 8.718734 AGTACGCTCCAAAGTATAAAAAGAAAG 58.281 33.333 0.00 0.00 0.00 2.62
3512 7092 8.611654 AGTACGCTCCAAAGTATAAAAAGAAA 57.388 30.769 0.00 0.00 0.00 2.52
3513 7093 8.248117 GAGTACGCTCCAAAGTATAAAAAGAA 57.752 34.615 0.00 0.00 35.76 2.52
3514 7094 7.823149 GAGTACGCTCCAAAGTATAAAAAGA 57.177 36.000 0.00 0.00 35.76 2.52
3531 7111 1.098050 TCTTTACGGAGGGAGTACGC 58.902 55.000 0.00 0.00 0.00 4.42
3533 7113 7.326454 ACTTTATTTCTTTACGGAGGGAGTAC 58.674 38.462 0.00 0.00 0.00 2.73
3566 7146 9.241317 CTCCGTAAAGAAATATAAGAGCGTTTA 57.759 33.333 0.00 0.00 0.00 2.01
3643 7223 9.689976 TTCATTCGGTTATAATTTTGCATATGG 57.310 29.630 4.56 0.00 0.00 2.74
3661 7242 6.420604 ACTTTGCAAAAACATAGTTCATTCGG 59.579 34.615 13.84 0.00 28.93 4.30
3723 7305 2.754946 TAACCCTTCATGGTCGTCAC 57.245 50.000 0.00 0.00 37.76 3.67
3777 7359 2.164338 GGTTAGAATTTTGTGGCCCGA 58.836 47.619 0.00 0.00 0.00 5.14
3874 7456 8.676401 CCTTTTGTTCTTCCAAAACATTTCAAT 58.324 29.630 0.00 0.00 38.90 2.57
3875 7457 7.880195 TCCTTTTGTTCTTCCAAAACATTTCAA 59.120 29.630 0.00 0.00 38.90 2.69
3876 7458 7.390027 TCCTTTTGTTCTTCCAAAACATTTCA 58.610 30.769 0.00 0.00 38.90 2.69
3882 7464 7.010183 GCTAAGTTCCTTTTGTTCTTCCAAAAC 59.990 37.037 0.00 0.00 38.90 2.43
3885 7467 5.654650 TGCTAAGTTCCTTTTGTTCTTCCAA 59.345 36.000 0.00 0.00 0.00 3.53
3915 7497 2.198827 TGACGATTTTGGGCTCACAT 57.801 45.000 0.00 0.00 0.00 3.21
3932 7514 4.820897 AGTGAACATCGCTAGATTGTTGA 58.179 39.130 9.30 0.53 35.10 3.18
3943 7525 4.084171 CCATGTGATCATAGTGAACATCGC 60.084 45.833 0.00 0.00 31.86 4.58
3969 7551 1.480954 GTCCATTGGGCGTAGAGAGAA 59.519 52.381 2.09 0.00 0.00 2.87
4013 7595 0.320374 TTGTCCGTCGATCCAGCTTT 59.680 50.000 0.00 0.00 0.00 3.51
4014 7596 0.537188 ATTGTCCGTCGATCCAGCTT 59.463 50.000 0.00 0.00 0.00 3.74
4015 7597 0.537188 AATTGTCCGTCGATCCAGCT 59.463 50.000 0.00 0.00 0.00 4.24
4016 7598 0.652592 CAATTGTCCGTCGATCCAGC 59.347 55.000 0.00 0.00 0.00 4.85
4017 7599 1.290203 CCAATTGTCCGTCGATCCAG 58.710 55.000 4.43 0.00 0.00 3.86
4018 7600 0.107897 CCCAATTGTCCGTCGATCCA 60.108 55.000 4.43 0.00 0.00 3.41
4019 7601 1.436983 GCCCAATTGTCCGTCGATCC 61.437 60.000 4.43 0.00 0.00 3.36
4020 7602 0.742990 TGCCCAATTGTCCGTCGATC 60.743 55.000 4.43 0.00 0.00 3.69
4021 7603 0.107214 ATGCCCAATTGTCCGTCGAT 60.107 50.000 4.43 0.00 0.00 3.59
4022 7604 1.024046 CATGCCCAATTGTCCGTCGA 61.024 55.000 4.43 0.00 0.00 4.20
4023 7605 1.429021 CATGCCCAATTGTCCGTCG 59.571 57.895 4.43 0.00 0.00 5.12
4024 7606 0.965363 ACCATGCCCAATTGTCCGTC 60.965 55.000 4.43 0.00 0.00 4.79
4025 7607 0.541764 AACCATGCCCAATTGTCCGT 60.542 50.000 4.43 0.00 0.00 4.69
4026 7608 0.173255 GAACCATGCCCAATTGTCCG 59.827 55.000 4.43 0.00 0.00 4.79
4027 7609 1.560505 AGAACCATGCCCAATTGTCC 58.439 50.000 4.43 0.00 0.00 4.02
4028 7610 3.006752 TGAAAGAACCATGCCCAATTGTC 59.993 43.478 4.43 0.00 0.00 3.18
4029 7611 2.971330 TGAAAGAACCATGCCCAATTGT 59.029 40.909 4.43 0.00 0.00 2.71
4030 7612 3.007182 ACTGAAAGAACCATGCCCAATTG 59.993 43.478 0.00 0.00 37.43 2.32
4042 7624 7.772332 TTGTCTAACTTCTGACTGAAAGAAC 57.228 36.000 0.00 0.00 37.43 3.01
4045 7627 7.095439 GGTCATTGTCTAACTTCTGACTGAAAG 60.095 40.741 0.00 0.00 42.29 2.62
4047 7629 6.042093 AGGTCATTGTCTAACTTCTGACTGAA 59.958 38.462 0.00 0.00 34.77 3.02
4049 7631 5.636965 CAGGTCATTGTCTAACTTCTGACTG 59.363 44.000 0.00 0.00 34.77 3.51
4051 7633 5.542779 ACAGGTCATTGTCTAACTTCTGAC 58.457 41.667 0.00 0.00 33.86 3.51
4059 7641 8.856153 TGCTAATAAAACAGGTCATTGTCTAA 57.144 30.769 0.00 0.00 0.00 2.10
4063 7645 6.515272 CCTGCTAATAAAACAGGTCATTGT 57.485 37.500 0.00 0.00 44.91 2.71
4073 7655 7.391148 TTCATCTGGAACCTGCTAATAAAAC 57.609 36.000 0.00 0.00 0.00 2.43
4088 7670 4.780815 AGTGTGTTTCAGTTTCATCTGGA 58.219 39.130 0.00 0.00 36.25 3.86
4090 7672 5.883661 ACAAGTGTGTTTCAGTTTCATCTG 58.116 37.500 0.00 0.00 37.58 2.90
4112 7694 6.997942 AGGGTTCCTATTCTAGATTGGTAC 57.002 41.667 0.00 0.81 28.47 3.34
4172 7852 4.226427 TCCAGATTGCACTGAAGCTTAT 57.774 40.909 0.00 0.00 39.94 1.73
4173 7853 3.701205 TCCAGATTGCACTGAAGCTTA 57.299 42.857 0.00 0.00 39.94 3.09
4174 7854 2.574006 TCCAGATTGCACTGAAGCTT 57.426 45.000 0.00 0.00 39.94 3.74
4180 7861 1.941294 GCAGAGATCCAGATTGCACTG 59.059 52.381 0.00 0.00 37.61 3.66
4286 8155 5.013495 TGCTAATTCCAGGATCCAAGGATAG 59.987 44.000 22.35 20.86 34.60 2.08
4348 8217 2.683968 TCAGTACCATTTGCAGTCGAC 58.316 47.619 7.70 7.70 0.00 4.20


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

AutoCloner maintained by Alex Coulton.