Multiple sequence alignment - TraesCS5D01G242400

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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 TraesCS5D01G242400 chr5D 100.000 4377 0 0 686 5062 350989362 350984986 0.000000e+00 8083.0
1 TraesCS5D01G242400 chr5D 84.239 920 97 23 1795 2672 116660655 116659742 0.000000e+00 852.0
2 TraesCS5D01G242400 chr5D 100.000 328 0 0 1 328 350990047 350989720 1.560000e-169 606.0
3 TraesCS5D01G242400 chr5D 81.984 383 38 14 994 1347 116661812 116661432 3.830000e-76 296.0
4 TraesCS5D01G242400 chr5A 92.045 3306 180 33 1400 4642 451457881 451454596 0.000000e+00 4571.0
5 TraesCS5D01G242400 chr5A 87.059 765 44 20 687 1401 451458900 451458141 0.000000e+00 813.0
6 TraesCS5D01G242400 chr5A 92.163 319 23 2 4744 5062 451447810 451447494 2.780000e-122 449.0
7 TraesCS5D01G242400 chr5A 82.102 352 27 11 1 323 451459331 451458987 8.350000e-68 268.0
8 TraesCS5D01G242400 chr5A 88.506 87 10 0 4632 4718 451453425 451453339 6.930000e-19 106.0
9 TraesCS5D01G242400 chr5A 96.296 54 2 0 4689 4742 451453337 451453284 6.980000e-14 89.8
10 TraesCS5D01G242400 chr5B 90.498 2189 114 37 687 2799 411802998 411800828 0.000000e+00 2804.0
11 TraesCS5D01G242400 chr5B 93.298 1880 79 9 2801 4652 411800785 411798925 0.000000e+00 2730.0
12 TraesCS5D01G242400 chr5B 97.573 206 3 2 4858 5062 411790656 411790452 8.060000e-93 351.0
13 TraesCS5D01G242400 chr5B 98.425 127 2 0 4744 4870 411797387 411797261 1.830000e-54 224.0
14 TraesCS5D01G242400 chr7D 82.254 1792 208 58 963 2672 446192672 446194435 0.000000e+00 1447.0
15 TraesCS5D01G242400 chr7D 83.963 979 109 25 1737 2672 215268839 215267866 0.000000e+00 894.0
16 TraesCS5D01G242400 chr4B 81.762 1771 209 58 994 2674 377159727 377157981 0.000000e+00 1376.0
17 TraesCS5D01G242400 chr4B 82.222 630 64 16 1664 2274 193973910 193973310 2.720000e-137 499.0
18 TraesCS5D01G242400 chr4B 84.783 368 39 7 1921 2274 609108957 609108593 2.240000e-93 353.0
19 TraesCS5D01G242400 chr4D 83.726 934 104 23 1781 2672 82858499 82859426 0.000000e+00 839.0
20 TraesCS5D01G242400 chr4D 81.633 392 41 14 982 1344 82857344 82857733 3.830000e-76 296.0
21 TraesCS5D01G242400 chr4D 88.398 181 19 2 994 1174 65392163 65391985 3.070000e-52 217.0
22 TraesCS5D01G242400 chr2A 87.669 592 49 8 1935 2506 526300843 526301430 0.000000e+00 667.0
23 TraesCS5D01G242400 chr6B 82.268 626 74 15 1664 2271 297532274 297532880 1.630000e-139 507.0
24 TraesCS5D01G242400 chr6B 82.667 150 24 2 2182 2330 64266779 64266631 1.140000e-26 132.0
25 TraesCS5D01G242400 chr6B 94.828 58 3 0 2391 2448 45830111 45830054 1.940000e-14 91.6
26 TraesCS5D01G242400 chr2D 81.978 627 64 18 1664 2271 624266622 624267218 2.120000e-133 486.0


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 TraesCS5D01G242400 chr5D 350984986 350990047 5061 True 4344.500000 8083 100.000000 1 5062 2 chr5D.!!$R2 5061
1 TraesCS5D01G242400 chr5D 116659742 116661812 2070 True 574.000000 852 83.111500 994 2672 2 chr5D.!!$R1 1678
2 TraesCS5D01G242400 chr5A 451453284 451459331 6047 True 1169.560000 4571 89.201600 1 4742 5 chr5A.!!$R2 4741
3 TraesCS5D01G242400 chr5B 411797261 411802998 5737 True 1919.333333 2804 94.073667 687 4870 3 chr5B.!!$R2 4183
4 TraesCS5D01G242400 chr7D 446192672 446194435 1763 False 1447.000000 1447 82.254000 963 2672 1 chr7D.!!$F1 1709
5 TraesCS5D01G242400 chr7D 215267866 215268839 973 True 894.000000 894 83.963000 1737 2672 1 chr7D.!!$R1 935
6 TraesCS5D01G242400 chr4B 377157981 377159727 1746 True 1376.000000 1376 81.762000 994 2674 1 chr4B.!!$R2 1680
7 TraesCS5D01G242400 chr4B 193973310 193973910 600 True 499.000000 499 82.222000 1664 2274 1 chr4B.!!$R1 610
8 TraesCS5D01G242400 chr4D 82857344 82859426 2082 False 567.500000 839 82.679500 982 2672 2 chr4D.!!$F1 1690
9 TraesCS5D01G242400 chr2A 526300843 526301430 587 False 667.000000 667 87.669000 1935 2506 1 chr2A.!!$F1 571
10 TraesCS5D01G242400 chr6B 297532274 297532880 606 False 507.000000 507 82.268000 1664 2271 1 chr6B.!!$F1 607
11 TraesCS5D01G242400 chr2D 624266622 624267218 596 False 486.000000 486 81.978000 1664 2271 1 chr2D.!!$F1 607

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
286 316 0.109532 TTGGCTCCATGTTCAACGGA 59.890 50.000 0.00 0.0 0.00 4.69 F
795 837 0.183971 TTCTTTTCTGAACCCGGCCA 59.816 50.000 2.24 0.0 0.00 5.36 F
796 838 0.404040 TCTTTTCTGAACCCGGCCAT 59.596 50.000 2.24 0.0 0.00 4.40 F
941 997 0.545309 TTCCCCAGACCAGACCAGAG 60.545 60.000 0.00 0.0 0.00 3.35 F
2107 3058 1.144913 TCTCCCTTGTTTTGGTCTGGG 59.855 52.381 0.00 0.0 36.14 4.45 F
3686 4737 0.608130 ATGACTAGCAACTGACGCCA 59.392 50.000 0.00 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2169 3124 0.181114 TAGCTGCACACCATCATCCC 59.819 55.000 1.02 0.0 0.00 3.85 R
2489 3472 2.204237 CCGATCATGAAGCGAATGACA 58.796 47.619 19.19 0.0 36.89 3.58 R
2720 3717 6.925165 TGAAATCTGTCTTTTGGAATTTGAGC 59.075 34.615 0.00 0.0 0.00 4.26 R
2881 3931 2.768253 AGCATCTTCCACGTCAATCA 57.232 45.000 0.00 0.0 0.00 2.57 R
4040 5093 0.106335 AGAATGAGGCGCTCCAGATG 59.894 55.000 7.64 0.0 33.74 2.90 R
4950 8728 0.111639 GGGTAAGGTGGTTGGCAAGA 59.888 55.000 0.00 0.0 0.00 3.02 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
39 41 3.119708 ACTTTCTGGAGCATCGATTTTGC 60.120 43.478 0.00 0.00 40.45 3.68
71 73 5.056480 CCACGACTTCCATGAATGCTATTA 58.944 41.667 0.00 0.00 0.00 0.98
79 81 9.404848 ACTTCCATGAATGCTATTATATGATGG 57.595 33.333 0.00 0.00 0.00 3.51
81 83 9.978336 TTCCATGAATGCTATTATATGATGGAA 57.022 29.630 0.00 0.00 42.43 3.53
117 119 4.797868 TGAAAACATCTGACAAAGTTTGCG 59.202 37.500 15.59 4.84 33.23 4.85
126 128 3.362237 TGACAAAGTTTGCGACAAAAACG 59.638 39.130 15.59 0.00 41.41 3.60
127 129 3.310246 ACAAAGTTTGCGACAAAAACGT 58.690 36.364 15.59 0.00 41.41 3.99
179 209 3.054361 AGCTCAATTAATCCACGTCCCTT 60.054 43.478 0.00 0.00 0.00 3.95
195 225 4.595986 GTCCCTTCTAGGCAAAAATACCA 58.404 43.478 0.00 0.00 32.73 3.25
209 239 9.699703 GGCAAAAATACCACAAGTTCTAAATTA 57.300 29.630 0.00 0.00 0.00 1.40
218 248 9.832445 ACCACAAGTTCTAAATTATGTATCGAT 57.168 29.630 2.16 2.16 0.00 3.59
285 315 1.176527 ATTGGCTCCATGTTCAACGG 58.823 50.000 0.00 0.00 0.00 4.44
286 316 0.109532 TTGGCTCCATGTTCAACGGA 59.890 50.000 0.00 0.00 0.00 4.69
760 791 4.641645 CCCGTTCACAGCCCTGCA 62.642 66.667 0.00 0.00 0.00 4.41
770 801 1.228245 AGCCCTGCATTGTGAACGT 60.228 52.632 0.00 0.00 0.00 3.99
789 831 5.358298 ACGTAGCATTTCTTTTCTGAACC 57.642 39.130 0.00 0.00 0.00 3.62
791 833 3.923017 AGCATTTCTTTTCTGAACCCG 57.077 42.857 0.00 0.00 0.00 5.28
793 835 2.926586 GCATTTCTTTTCTGAACCCGGC 60.927 50.000 0.00 0.00 0.00 6.13
795 837 0.183971 TTCTTTTCTGAACCCGGCCA 59.816 50.000 2.24 0.00 0.00 5.36
796 838 0.404040 TCTTTTCTGAACCCGGCCAT 59.596 50.000 2.24 0.00 0.00 4.40
798 840 0.965439 TTTTCTGAACCCGGCCATTG 59.035 50.000 2.24 0.00 0.00 2.82
824 875 7.706100 AGATTAAACTAGTCTTCTTCTCCGT 57.294 36.000 0.00 0.00 0.00 4.69
940 996 0.836400 GTTCCCCAGACCAGACCAGA 60.836 60.000 0.00 0.00 0.00 3.86
941 997 0.545309 TTCCCCAGACCAGACCAGAG 60.545 60.000 0.00 0.00 0.00 3.35
960 1016 2.111043 CCCAGGCGACACACAGTT 59.889 61.111 0.00 0.00 0.00 3.16
973 1039 3.004524 ACACACAGTTACGGAGAGAGTTC 59.995 47.826 0.00 0.00 0.00 3.01
975 1041 2.483106 CACAGTTACGGAGAGAGTTCGA 59.517 50.000 0.00 0.00 0.00 3.71
1332 1464 2.383527 GGAGCTGCAGGTCGTTTCG 61.384 63.158 32.99 0.00 43.03 3.46
1443 1838 9.203421 GCTTGGTTGCATTTTAAAAAGTACTAT 57.797 29.630 4.44 0.00 0.00 2.12
1508 1913 1.243902 ACGCTGTAAACACCCATTGG 58.756 50.000 0.00 0.00 37.80 3.16
1633 2043 7.054491 AGAAATAGTTGCAAGTGAAAATGGT 57.946 32.000 17.21 0.00 0.00 3.55
1634 2044 7.147976 AGAAATAGTTGCAAGTGAAAATGGTC 58.852 34.615 17.21 4.33 0.00 4.02
1793 2715 3.618594 CAGTACGTTGACATGAATCCTGG 59.381 47.826 0.00 0.00 0.00 4.45
1813 2735 7.632861 TCCTGGAAAATGATCTGAATCTGTTA 58.367 34.615 0.00 0.00 32.75 2.41
1819 2742 9.448294 GAAAATGATCTGAATCTGTTAGCATTC 57.552 33.333 0.00 0.00 32.75 2.67
1845 2773 6.484288 TGCATTATCTATTGGGGGACTAATG 58.516 40.000 0.00 0.00 42.08 1.90
2064 2994 2.173356 CCTGGATGCCTCAAGGTTCATA 59.827 50.000 4.27 0.00 37.77 2.15
2065 2995 3.209410 CTGGATGCCTCAAGGTTCATAC 58.791 50.000 0.00 0.00 37.57 2.39
2066 2996 2.575735 TGGATGCCTCAAGGTTCATACA 59.424 45.455 0.00 0.00 37.57 2.29
2069 2999 4.037208 GGATGCCTCAAGGTTCATACATTG 59.963 45.833 0.00 0.00 45.02 2.82
2070 3000 2.754552 TGCCTCAAGGTTCATACATTGC 59.245 45.455 0.00 0.00 43.73 3.56
2071 3001 2.754552 GCCTCAAGGTTCATACATTGCA 59.245 45.455 0.00 0.00 43.73 4.08
2102 3053 3.891366 CTGATTGTCTCCCTTGTTTTGGT 59.109 43.478 0.00 0.00 0.00 3.67
2105 3056 2.930950 TGTCTCCCTTGTTTTGGTCTG 58.069 47.619 0.00 0.00 0.00 3.51
2107 3058 1.144913 TCTCCCTTGTTTTGGTCTGGG 59.855 52.381 0.00 0.00 36.14 4.45
2121 3072 3.216944 CTGGGTGTTGCTTGCTGGC 62.217 63.158 0.00 0.00 0.00 4.85
2132 3083 1.603931 GCTTGCTGGCTTTCTTGTTCC 60.604 52.381 0.00 0.00 0.00 3.62
2169 3124 6.741992 TGCAGAGGTGTATTTAATCAACTG 57.258 37.500 0.00 0.00 31.32 3.16
2353 3325 2.862541 AGCTCATACAGTTTGTTGCCA 58.137 42.857 7.62 0.00 0.00 4.92
2355 3327 2.813754 GCTCATACAGTTTGTTGCCAGA 59.186 45.455 0.00 0.00 0.00 3.86
2486 3469 5.079998 AGAAATTGGAAGAGGAAAAGGGT 57.920 39.130 0.00 0.00 0.00 4.34
2489 3472 3.680777 TTGGAAGAGGAAAAGGGTGTT 57.319 42.857 0.00 0.00 0.00 3.32
2752 3749 6.356556 TCCAAAAGACAGATTTCACTCAAGA 58.643 36.000 0.00 0.00 0.00 3.02
2757 3754 8.455903 AAAGACAGATTTCACTCAAGATTCAA 57.544 30.769 0.00 0.00 0.00 2.69
2852 3902 6.996282 AGTAACCTGTGTTTATGCTTTACAGT 59.004 34.615 0.00 0.00 37.61 3.55
2881 3931 2.129555 AACAGCGCCCTTGATCAGGT 62.130 55.000 2.29 0.00 42.02 4.00
2885 3935 0.749454 GCGCCCTTGATCAGGTGATT 60.749 55.000 16.55 0.00 42.02 2.57
3018 4068 9.431887 CCAAATCTTCTTGACATCATTGATTTT 57.568 29.630 0.00 0.00 32.69 1.82
3290 4341 9.847224 TCCCAATAATATTGAAGAGAACTAACC 57.153 33.333 14.10 0.00 0.00 2.85
3393 4444 1.718280 AGTCTGGACCGGTTCTTTCT 58.282 50.000 15.59 6.45 0.00 2.52
3436 4487 9.465985 GAAAACACTATCTAGCTATTACAGTCC 57.534 37.037 0.00 0.00 0.00 3.85
3514 4565 2.550978 AGTTCGAAATACCATGAGCCG 58.449 47.619 0.00 0.00 0.00 5.52
3630 4681 9.814899 CATCTCAGTCAACAAGTAAGATTAGAT 57.185 33.333 0.00 0.00 0.00 1.98
3686 4737 0.608130 ATGACTAGCAACTGACGCCA 59.392 50.000 0.00 0.00 0.00 5.69
3699 4750 2.710698 CGCCACCGTGTTTTCGTT 59.289 55.556 0.00 0.00 0.00 3.85
3750 4801 0.635731 CGAACGAAGATGTGTCGCTC 59.364 55.000 0.00 0.00 42.27 5.03
3793 4844 1.805945 GTGGAGCACATCGACGACC 60.806 63.158 0.00 0.00 34.08 4.79
3813 4864 1.672356 GGACATGTGCTGCGGAACT 60.672 57.895 10.51 0.00 0.00 3.01
3858 4909 7.992608 TCAGTTGTTATTATCTACACCATGCAT 59.007 33.333 0.00 0.00 0.00 3.96
3859 4910 8.071967 CAGTTGTTATTATCTACACCATGCATG 58.928 37.037 20.19 20.19 0.00 4.06
4040 5093 2.586357 GGCGAAGGAGACGATGCC 60.586 66.667 0.00 0.00 38.09 4.40
4066 5119 1.139734 GCGCCTCATTCTGACGAGA 59.860 57.895 0.00 0.00 0.00 4.04
4089 5142 8.006298 AGATCCTAACAAGTATTCAGAGTCAG 57.994 38.462 0.00 0.00 0.00 3.51
4120 5173 3.190953 GTCCGGGTATAGATGTAGACAGC 59.809 52.174 0.00 0.00 0.00 4.40
4128 5181 2.027385 AGATGTAGACAGCGCAGATCA 58.973 47.619 11.47 0.96 37.34 2.92
4129 5182 2.627221 AGATGTAGACAGCGCAGATCAT 59.373 45.455 11.47 6.35 37.34 2.45
4130 5183 3.823304 AGATGTAGACAGCGCAGATCATA 59.177 43.478 11.47 0.00 37.34 2.15
4131 5184 4.462132 AGATGTAGACAGCGCAGATCATAT 59.538 41.667 11.47 0.91 37.34 1.78
4170 5227 1.177401 CCGAGTGTGAGATCAGACCA 58.823 55.000 6.51 0.00 40.59 4.02
4208 5265 3.181491 GGAGACGACAAGAGAAGAGATGG 60.181 52.174 0.00 0.00 0.00 3.51
4212 5269 2.928757 CGACAAGAGAAGAGATGGCTTG 59.071 50.000 0.00 0.00 41.15 4.01
4280 5338 4.477975 CGGACGGACGCACCTCTC 62.478 72.222 6.88 0.00 36.31 3.20
4284 5342 0.733223 GACGGACGCACCTCTCTTTC 60.733 60.000 0.00 0.00 36.31 2.62
4285 5343 1.179814 ACGGACGCACCTCTCTTTCT 61.180 55.000 0.00 0.00 36.31 2.52
4286 5344 0.038159 CGGACGCACCTCTCTTTCTT 60.038 55.000 0.00 0.00 36.31 2.52
4449 5534 4.202010 GCAGTTGGAAGTTGAACAAAGCTA 60.202 41.667 0.00 0.00 0.00 3.32
4470 5555 6.663523 AGCTAGGCTTTGTGTATAACCAAAAT 59.336 34.615 0.00 0.00 33.89 1.82
4483 5568 8.832521 TGTATAACCAAAATATCATCGTTGTCC 58.167 33.333 0.00 0.00 0.00 4.02
4484 5569 5.576447 AACCAAAATATCATCGTTGTCCC 57.424 39.130 0.00 0.00 0.00 4.46
4508 5593 4.209703 CGCCGTCTTTTGTCTTTTGTACTA 59.790 41.667 0.00 0.00 0.00 1.82
4642 6911 5.221382 ACCTATGGATCAGATGCAAAAATGC 60.221 40.000 8.90 0.00 33.18 3.56
4652 6921 2.674954 TGCAAAAATGCCATTCACTCG 58.325 42.857 0.00 0.00 0.00 4.18
4654 6923 1.650153 CAAAAATGCCATTCACTCGCG 59.350 47.619 0.00 0.00 0.00 5.87
4660 6929 2.006772 CCATTCACTCGCGGTAAGC 58.993 57.895 6.13 0.00 43.95 3.09
4680 6949 7.950496 GGTAAGCATACGTTGAAATTCGATATC 59.050 37.037 0.00 0.00 32.51 1.63
4683 6952 6.146184 AGCATACGTTGAAATTCGATATCCAG 59.854 38.462 0.00 0.00 0.00 3.86
4722 7022 3.557185 ACCGAAACAACCTAAAACGTCTC 59.443 43.478 0.00 0.00 0.00 3.36
4742 7042 7.148672 ACGTCTCTCCGTTACACGATAATATAG 60.149 40.741 0.00 0.00 46.05 1.31
4787 8565 1.066143 CGGTGCATCTCCAAACTAGGT 60.066 52.381 0.00 0.00 0.00 3.08
4803 8581 7.363431 CAAACTAGGTGTCTTTCCAAAATCTC 58.637 38.462 0.00 0.00 0.00 2.75
4870 8648 6.877611 TTCAACCTTAACTCTCATCAAACC 57.122 37.500 0.00 0.00 0.00 3.27
4871 8649 6.187727 TCAACCTTAACTCTCATCAAACCT 57.812 37.500 0.00 0.00 0.00 3.50
4872 8650 6.601332 TCAACCTTAACTCTCATCAAACCTT 58.399 36.000 0.00 0.00 0.00 3.50
4873 8651 7.060421 TCAACCTTAACTCTCATCAAACCTTT 58.940 34.615 0.00 0.00 0.00 3.11
4874 8652 7.228706 TCAACCTTAACTCTCATCAAACCTTTC 59.771 37.037 0.00 0.00 0.00 2.62
4875 8653 6.842676 ACCTTAACTCTCATCAAACCTTTCT 58.157 36.000 0.00 0.00 0.00 2.52
4876 8654 7.974504 ACCTTAACTCTCATCAAACCTTTCTA 58.025 34.615 0.00 0.00 0.00 2.10
4877 8655 8.097662 ACCTTAACTCTCATCAAACCTTTCTAG 58.902 37.037 0.00 0.00 0.00 2.43
4878 8656 8.314751 CCTTAACTCTCATCAAACCTTTCTAGA 58.685 37.037 0.00 0.00 0.00 2.43
4879 8657 9.712305 CTTAACTCTCATCAAACCTTTCTAGAA 57.288 33.333 0.00 0.00 0.00 2.10
4880 8658 7.971183 AACTCTCATCAAACCTTTCTAGAAC 57.029 36.000 4.18 0.00 0.00 3.01
4881 8659 6.159988 ACTCTCATCAAACCTTTCTAGAACG 58.840 40.000 4.18 2.97 0.00 3.95
4882 8660 6.015350 ACTCTCATCAAACCTTTCTAGAACGA 60.015 38.462 10.40 0.00 0.00 3.85
4883 8661 6.755206 TCTCATCAAACCTTTCTAGAACGAA 58.245 36.000 10.40 0.00 0.00 3.85
4884 8662 6.868864 TCTCATCAAACCTTTCTAGAACGAAG 59.131 38.462 10.40 3.34 0.00 3.79
4885 8663 6.755206 TCATCAAACCTTTCTAGAACGAAGA 58.245 36.000 10.40 2.89 0.00 2.87
4886 8664 7.214381 TCATCAAACCTTTCTAGAACGAAGAA 58.786 34.615 10.40 0.00 0.00 2.52
4887 8665 7.878127 TCATCAAACCTTTCTAGAACGAAGAAT 59.122 33.333 10.40 0.00 33.17 2.40
4888 8666 8.507249 CATCAAACCTTTCTAGAACGAAGAATT 58.493 33.333 10.40 0.00 33.17 2.17
4889 8667 8.084590 TCAAACCTTTCTAGAACGAAGAATTC 57.915 34.615 10.40 0.00 43.09 2.17
4911 8689 2.680577 GCATCTTTGCTGAAACTTGGG 58.319 47.619 0.00 0.00 45.77 4.12
4912 8690 2.297033 GCATCTTTGCTGAAACTTGGGA 59.703 45.455 0.00 0.00 45.77 4.37
4913 8691 3.858503 GCATCTTTGCTGAAACTTGGGAC 60.859 47.826 0.00 0.00 45.77 4.46
4914 8692 3.011566 TCTTTGCTGAAACTTGGGACA 57.988 42.857 0.00 0.00 0.00 4.02
4915 8693 3.565307 TCTTTGCTGAAACTTGGGACAT 58.435 40.909 0.00 0.00 39.30 3.06
4916 8694 3.318839 TCTTTGCTGAAACTTGGGACATG 59.681 43.478 0.00 0.00 39.30 3.21
4917 8695 1.619654 TGCTGAAACTTGGGACATGG 58.380 50.000 0.00 0.00 39.30 3.66
4918 8696 1.133513 TGCTGAAACTTGGGACATGGT 60.134 47.619 0.00 0.00 39.30 3.55
4919 8697 1.541588 GCTGAAACTTGGGACATGGTC 59.458 52.381 0.00 0.00 39.30 4.02
4920 8698 2.815589 GCTGAAACTTGGGACATGGTCT 60.816 50.000 0.00 0.00 39.30 3.85
4921 8699 3.490348 CTGAAACTTGGGACATGGTCTT 58.510 45.455 0.00 0.00 39.30 3.01
4922 8700 3.221771 TGAAACTTGGGACATGGTCTTG 58.778 45.455 0.00 0.00 39.30 3.02
4923 8701 2.292828 AACTTGGGACATGGTCTTGG 57.707 50.000 0.00 0.00 39.30 3.61
4924 8702 0.405585 ACTTGGGACATGGTCTTGGG 59.594 55.000 0.00 0.00 39.30 4.12
4925 8703 0.967380 CTTGGGACATGGTCTTGGGC 60.967 60.000 0.00 0.00 39.30 5.36
4926 8704 2.043953 GGGACATGGTCTTGGGCC 60.044 66.667 0.00 0.00 32.47 5.80
4927 8705 2.438434 GGACATGGTCTTGGGCCG 60.438 66.667 0.00 0.00 32.47 6.13
4928 8706 2.668632 GACATGGTCTTGGGCCGA 59.331 61.111 0.00 0.00 0.00 5.54
4929 8707 1.002624 GACATGGTCTTGGGCCGAA 60.003 57.895 0.00 0.00 0.00 4.30
4930 8708 0.394352 GACATGGTCTTGGGCCGAAT 60.394 55.000 0.00 0.00 0.00 3.34
4931 8709 0.680921 ACATGGTCTTGGGCCGAATG 60.681 55.000 0.00 0.00 0.00 2.67
4932 8710 0.680921 CATGGTCTTGGGCCGAATGT 60.681 55.000 0.00 0.00 0.00 2.71
4933 8711 0.916086 ATGGTCTTGGGCCGAATGTA 59.084 50.000 0.00 0.00 0.00 2.29
4934 8712 0.916086 TGGTCTTGGGCCGAATGTAT 59.084 50.000 0.00 0.00 0.00 2.29
4935 8713 1.283613 TGGTCTTGGGCCGAATGTATT 59.716 47.619 0.00 0.00 0.00 1.89
4936 8714 2.291282 TGGTCTTGGGCCGAATGTATTT 60.291 45.455 0.00 0.00 0.00 1.40
4937 8715 2.099098 GGTCTTGGGCCGAATGTATTTG 59.901 50.000 0.00 0.00 0.00 2.32
4938 8716 2.752903 GTCTTGGGCCGAATGTATTTGT 59.247 45.455 0.00 0.00 0.00 2.83
4939 8717 3.192633 GTCTTGGGCCGAATGTATTTGTT 59.807 43.478 0.00 0.00 0.00 2.83
4940 8718 3.829601 TCTTGGGCCGAATGTATTTGTTT 59.170 39.130 0.00 0.00 0.00 2.83
4941 8719 4.282195 TCTTGGGCCGAATGTATTTGTTTT 59.718 37.500 0.00 0.00 0.00 2.43
4942 8720 3.919216 TGGGCCGAATGTATTTGTTTTG 58.081 40.909 0.00 0.00 0.00 2.44
4943 8721 2.670905 GGGCCGAATGTATTTGTTTTGC 59.329 45.455 0.00 0.00 0.00 3.68
4944 8722 2.344142 GGCCGAATGTATTTGTTTTGCG 59.656 45.455 0.00 0.00 0.00 4.85
4945 8723 2.344142 GCCGAATGTATTTGTTTTGCGG 59.656 45.455 0.00 0.00 39.23 5.69
4946 8724 2.344142 CCGAATGTATTTGTTTTGCGGC 59.656 45.455 0.00 0.00 0.00 6.53
4947 8725 2.983136 CGAATGTATTTGTTTTGCGGCA 59.017 40.909 0.00 0.00 0.00 5.69
4948 8726 3.426859 CGAATGTATTTGTTTTGCGGCAA 59.573 39.130 12.11 12.11 0.00 4.52
4949 8727 4.662891 CGAATGTATTTGTTTTGCGGCAAC 60.663 41.667 16.15 6.37 0.00 4.17
4950 8728 3.444703 TGTATTTGTTTTGCGGCAACT 57.555 38.095 16.15 0.00 0.00 3.16
4951 8729 3.376540 TGTATTTGTTTTGCGGCAACTC 58.623 40.909 16.15 11.64 0.00 3.01
4952 8730 2.888834 ATTTGTTTTGCGGCAACTCT 57.111 40.000 16.15 0.00 0.00 3.24
4953 8731 2.663826 TTTGTTTTGCGGCAACTCTT 57.336 40.000 16.15 0.00 0.00 2.85
4954 8732 1.919918 TTGTTTTGCGGCAACTCTTG 58.080 45.000 16.15 0.00 0.00 3.02
4964 8742 3.116091 CAACTCTTGCCAACCACCT 57.884 52.632 0.00 0.00 0.00 4.00
4965 8743 1.402787 CAACTCTTGCCAACCACCTT 58.597 50.000 0.00 0.00 0.00 3.50
4966 8744 2.582052 CAACTCTTGCCAACCACCTTA 58.418 47.619 0.00 0.00 0.00 2.69
4967 8745 2.271944 ACTCTTGCCAACCACCTTAC 57.728 50.000 0.00 0.00 0.00 2.34
4968 8746 1.202891 ACTCTTGCCAACCACCTTACC 60.203 52.381 0.00 0.00 0.00 2.85
4969 8747 0.111639 TCTTGCCAACCACCTTACCC 59.888 55.000 0.00 0.00 0.00 3.69
4970 8748 1.228306 TTGCCAACCACCTTACCCG 60.228 57.895 0.00 0.00 0.00 5.28
4971 8749 2.360726 GCCAACCACCTTACCCGG 60.361 66.667 0.00 0.00 0.00 5.73
4972 8750 2.360726 CCAACCACCTTACCCGGC 60.361 66.667 0.00 0.00 0.00 6.13
4973 8751 2.432563 CAACCACCTTACCCGGCA 59.567 61.111 0.00 0.00 0.00 5.69
4974 8752 1.228306 CAACCACCTTACCCGGCAA 60.228 57.895 0.00 0.00 0.00 4.52
4975 8753 1.074248 AACCACCTTACCCGGCAAG 59.926 57.895 0.00 0.84 0.00 4.01
4976 8754 2.750237 CCACCTTACCCGGCAAGC 60.750 66.667 0.00 0.00 0.00 4.01
4977 8755 2.033448 CACCTTACCCGGCAAGCA 59.967 61.111 0.00 0.00 0.00 3.91
4978 8756 1.602323 CACCTTACCCGGCAAGCAA 60.602 57.895 0.00 0.00 0.00 3.91
4979 8757 1.602605 ACCTTACCCGGCAAGCAAC 60.603 57.895 0.00 0.00 0.00 4.17
4980 8758 1.303317 CCTTACCCGGCAAGCAACT 60.303 57.895 0.00 0.00 0.00 3.16
4981 8759 0.893727 CCTTACCCGGCAAGCAACTT 60.894 55.000 0.00 0.00 0.00 2.66
4982 8760 0.240945 CTTACCCGGCAAGCAACTTG 59.759 55.000 0.00 2.95 43.57 3.16
4983 8761 0.179015 TTACCCGGCAAGCAACTTGA 60.179 50.000 11.38 0.00 43.42 3.02
4984 8762 0.179015 TACCCGGCAAGCAACTTGAA 60.179 50.000 11.38 0.00 43.42 2.69
4985 8763 1.007387 CCCGGCAAGCAACTTGAAC 60.007 57.895 11.38 2.55 43.42 3.18
4986 8764 1.370414 CCGGCAAGCAACTTGAACG 60.370 57.895 11.38 12.98 43.42 3.95
4987 8765 1.646540 CGGCAAGCAACTTGAACGA 59.353 52.632 11.38 0.00 43.42 3.85
4988 8766 0.657368 CGGCAAGCAACTTGAACGAC 60.657 55.000 11.38 0.00 43.42 4.34
4989 8767 0.317854 GGCAAGCAACTTGAACGACC 60.318 55.000 11.38 0.00 43.42 4.79
4990 8768 0.380378 GCAAGCAACTTGAACGACCA 59.620 50.000 11.38 0.00 43.42 4.02
4991 8769 1.001378 GCAAGCAACTTGAACGACCAT 60.001 47.619 11.38 0.00 43.42 3.55
4992 8770 2.543653 GCAAGCAACTTGAACGACCATT 60.544 45.455 11.38 0.00 43.42 3.16
4993 8771 3.705604 CAAGCAACTTGAACGACCATTT 58.294 40.909 0.97 0.00 43.42 2.32
4994 8772 4.111916 CAAGCAACTTGAACGACCATTTT 58.888 39.130 0.97 0.00 43.42 1.82
4995 8773 3.964909 AGCAACTTGAACGACCATTTTC 58.035 40.909 0.00 0.00 0.00 2.29
4996 8774 3.632145 AGCAACTTGAACGACCATTTTCT 59.368 39.130 0.00 0.00 0.00 2.52
4997 8775 4.819630 AGCAACTTGAACGACCATTTTCTA 59.180 37.500 0.00 0.00 0.00 2.10
4998 8776 5.049405 AGCAACTTGAACGACCATTTTCTAG 60.049 40.000 0.00 0.00 32.75 2.43
4999 8777 5.147162 CAACTTGAACGACCATTTTCTAGC 58.853 41.667 0.00 0.00 30.49 3.42
5000 8778 4.385825 ACTTGAACGACCATTTTCTAGCA 58.614 39.130 0.00 0.00 30.49 3.49
5001 8779 4.819630 ACTTGAACGACCATTTTCTAGCAA 59.180 37.500 0.00 0.00 30.49 3.91
5002 8780 5.049405 ACTTGAACGACCATTTTCTAGCAAG 60.049 40.000 0.00 0.00 36.15 4.01
5003 8781 3.188460 TGAACGACCATTTTCTAGCAAGC 59.812 43.478 0.00 0.00 0.00 4.01
5004 8782 2.778299 ACGACCATTTTCTAGCAAGCA 58.222 42.857 0.00 0.00 0.00 3.91
5005 8783 3.347216 ACGACCATTTTCTAGCAAGCAT 58.653 40.909 0.00 0.00 0.00 3.79
5006 8784 3.758554 ACGACCATTTTCTAGCAAGCATT 59.241 39.130 0.00 0.00 0.00 3.56
5007 8785 4.218417 ACGACCATTTTCTAGCAAGCATTT 59.782 37.500 0.00 0.00 0.00 2.32
5008 8786 4.560035 CGACCATTTTCTAGCAAGCATTTG 59.440 41.667 0.00 0.00 37.36 2.32
5009 8787 5.473039 GACCATTTTCTAGCAAGCATTTGT 58.527 37.500 0.00 0.00 36.65 2.83
5010 8788 5.473039 ACCATTTTCTAGCAAGCATTTGTC 58.527 37.500 0.00 0.00 36.65 3.18
5011 8789 4.866486 CCATTTTCTAGCAAGCATTTGTCC 59.134 41.667 0.00 0.00 36.65 4.02
5012 8790 5.337009 CCATTTTCTAGCAAGCATTTGTCCT 60.337 40.000 0.00 0.00 36.65 3.85
5013 8791 5.789643 TTTTCTAGCAAGCATTTGTCCTT 57.210 34.783 0.00 0.00 36.65 3.36
5014 8792 4.771590 TTCTAGCAAGCATTTGTCCTTG 57.228 40.909 0.00 0.00 40.97 3.61
5015 8793 4.019792 TCTAGCAAGCATTTGTCCTTGA 57.980 40.909 4.70 0.00 40.59 3.02
5016 8794 4.592942 TCTAGCAAGCATTTGTCCTTGAT 58.407 39.130 4.70 0.87 40.59 2.57
5017 8795 5.012239 TCTAGCAAGCATTTGTCCTTGATT 58.988 37.500 4.70 0.00 40.59 2.57
5018 8796 4.612264 AGCAAGCATTTGTCCTTGATTT 57.388 36.364 4.70 0.00 40.59 2.17
5019 8797 4.563061 AGCAAGCATTTGTCCTTGATTTC 58.437 39.130 4.70 0.00 40.59 2.17
5020 8798 4.039488 AGCAAGCATTTGTCCTTGATTTCA 59.961 37.500 4.70 0.00 40.59 2.69
5021 8799 4.751098 GCAAGCATTTGTCCTTGATTTCAA 59.249 37.500 4.70 0.00 40.59 2.69
5022 8800 5.107220 GCAAGCATTTGTCCTTGATTTCAAG 60.107 40.000 12.40 12.40 42.85 3.02
5035 8813 5.512942 TGATTTCAAGGTACTCAATCCCA 57.487 39.130 0.00 0.00 38.49 4.37
5036 8814 5.500234 TGATTTCAAGGTACTCAATCCCAG 58.500 41.667 0.00 0.00 38.49 4.45
5037 8815 4.301072 TTTCAAGGTACTCAATCCCAGG 57.699 45.455 0.00 0.00 38.49 4.45
5038 8816 2.915869 TCAAGGTACTCAATCCCAGGT 58.084 47.619 0.00 0.00 38.49 4.00
5039 8817 3.256704 TCAAGGTACTCAATCCCAGGTT 58.743 45.455 0.00 0.00 38.49 3.50
5040 8818 4.431378 TCAAGGTACTCAATCCCAGGTTA 58.569 43.478 0.00 0.00 38.49 2.85
5041 8819 4.224370 TCAAGGTACTCAATCCCAGGTTAC 59.776 45.833 0.00 0.00 38.49 2.50
5042 8820 3.113043 AGGTACTCAATCCCAGGTTACC 58.887 50.000 0.00 0.00 0.00 2.85
5043 8821 2.172082 GGTACTCAATCCCAGGTTACCC 59.828 54.545 0.00 0.00 0.00 3.69
5044 8822 2.361085 ACTCAATCCCAGGTTACCCT 57.639 50.000 0.00 0.00 44.02 4.34
5045 8823 2.644151 ACTCAATCCCAGGTTACCCTT 58.356 47.619 0.00 0.00 39.89 3.95
5046 8824 2.308866 ACTCAATCCCAGGTTACCCTTG 59.691 50.000 0.00 0.00 39.89 3.61
5047 8825 2.576191 CTCAATCCCAGGTTACCCTTGA 59.424 50.000 0.00 0.00 39.89 3.02
5048 8826 3.197983 TCAATCCCAGGTTACCCTTGAT 58.802 45.455 0.00 0.00 39.89 2.57
5049 8827 3.202151 TCAATCCCAGGTTACCCTTGATC 59.798 47.826 0.00 0.00 39.89 2.92
5050 8828 2.661176 TCCCAGGTTACCCTTGATCT 57.339 50.000 0.00 0.00 39.89 2.75
5051 8829 2.929301 TCCCAGGTTACCCTTGATCTT 58.071 47.619 0.00 0.00 39.89 2.40
5052 8830 3.265489 TCCCAGGTTACCCTTGATCTTT 58.735 45.455 0.00 0.00 39.89 2.52
5053 8831 3.265995 TCCCAGGTTACCCTTGATCTTTC 59.734 47.826 0.00 0.00 39.89 2.62
5054 8832 3.010138 CCCAGGTTACCCTTGATCTTTCA 59.990 47.826 0.00 0.00 39.89 2.69
5055 8833 4.265073 CCAGGTTACCCTTGATCTTTCAG 58.735 47.826 0.00 0.00 39.89 3.02
5056 8834 3.691609 CAGGTTACCCTTGATCTTTCAGC 59.308 47.826 0.00 0.00 39.89 4.26
5057 8835 3.017442 GGTTACCCTTGATCTTTCAGCC 58.983 50.000 0.00 0.00 32.27 4.85
5058 8836 3.308473 GGTTACCCTTGATCTTTCAGCCT 60.308 47.826 0.00 0.00 32.27 4.58
5059 8837 4.080526 GGTTACCCTTGATCTTTCAGCCTA 60.081 45.833 0.00 0.00 32.27 3.93
5060 8838 3.636153 ACCCTTGATCTTTCAGCCTAC 57.364 47.619 0.00 0.00 32.27 3.18
5061 8839 2.912956 ACCCTTGATCTTTCAGCCTACA 59.087 45.455 0.00 0.00 32.27 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 41 0.040067 GGAAGTCGTGGCAAAGCAAG 60.040 55.000 0.00 0.00 0.00 4.01
42 44 0.109597 CATGGAAGTCGTGGCAAAGC 60.110 55.000 0.00 0.00 0.00 3.51
94 96 4.797868 CGCAAACTTTGTCAGATGTTTTCA 59.202 37.500 3.48 0.00 31.30 2.69
103 105 4.488573 CGTTTTTGTCGCAAACTTTGTCAG 60.489 41.667 3.48 0.00 32.79 3.51
106 108 3.310246 ACGTTTTTGTCGCAAACTTTGT 58.690 36.364 3.48 0.80 32.79 2.83
139 148 2.413837 GCTCGAGCTCCAAAACTTGTA 58.586 47.619 29.88 0.00 38.21 2.41
163 172 3.071167 GCCTAGAAGGGACGTGGATTAAT 59.929 47.826 0.00 0.00 35.37 1.40
171 180 2.943036 TTTTTGCCTAGAAGGGACGT 57.057 45.000 0.00 0.00 34.53 4.34
179 209 6.303839 AGAACTTGTGGTATTTTTGCCTAGA 58.696 36.000 0.00 0.00 0.00 2.43
209 239 7.487822 AGAAATCCATGTCCTATCGATACAT 57.512 36.000 0.00 3.68 34.22 2.29
258 288 4.344679 TGAACATGGAGCCAATTTTGTCTT 59.655 37.500 0.00 0.00 0.00 3.01
260 290 4.255833 TGAACATGGAGCCAATTTTGTC 57.744 40.909 0.00 0.00 0.00 3.18
262 292 3.429543 CGTTGAACATGGAGCCAATTTTG 59.570 43.478 0.00 0.00 0.00 2.44
268 298 0.327924 ATCCGTTGAACATGGAGCCA 59.672 50.000 0.00 0.00 44.45 4.75
297 327 8.942338 AAACAAAATACTTTTCCTTGTTCTCC 57.058 30.769 0.00 0.00 28.17 3.71
298 328 9.031360 GGAAACAAAATACTTTTCCTTGTTCTC 57.969 33.333 5.29 0.00 43.39 2.87
698 728 1.048601 TCTCAGGGACAGTGACAACC 58.951 55.000 0.00 0.00 0.00 3.77
757 788 3.501828 AGAAATGCTACGTTCACAATGCA 59.498 39.130 0.00 0.00 34.88 3.96
760 791 6.857964 CAGAAAAGAAATGCTACGTTCACAAT 59.142 34.615 0.00 0.00 0.00 2.71
770 801 3.756434 CCGGGTTCAGAAAAGAAATGCTA 59.244 43.478 0.00 0.00 0.00 3.49
789 831 4.881850 ACTAGTTTAATCTTCAATGGCCGG 59.118 41.667 0.00 0.00 0.00 6.13
791 833 7.631717 AAGACTAGTTTAATCTTCAATGGCC 57.368 36.000 0.00 0.00 0.00 5.36
798 840 8.245491 ACGGAGAAGAAGACTAGTTTAATCTTC 58.755 37.037 21.23 21.23 45.77 2.87
824 875 0.481128 GGGGGAGGGAAACACAAAGA 59.519 55.000 0.00 0.00 0.00 2.52
955 1011 2.775890 TCGAACTCTCTCCGTAACTGT 58.224 47.619 0.00 0.00 0.00 3.55
960 1016 2.414481 CGTTCTTCGAACTCTCTCCGTA 59.586 50.000 0.00 0.00 42.86 4.02
973 1039 1.738099 CAGCCACCTCCGTTCTTCG 60.738 63.158 0.00 0.00 39.52 3.79
975 1041 2.750350 CCAGCCACCTCCGTTCTT 59.250 61.111 0.00 0.00 0.00 2.52
1112 1178 2.445654 GGGAGAGGAGAGGGGCTG 60.446 72.222 0.00 0.00 0.00 4.85
1443 1838 8.948631 TGATGCCAAAGTTTACAAACATTTAA 57.051 26.923 7.53 0.00 41.30 1.52
1486 1890 3.049206 CAATGGGTGTTTACAGCGTTTG 58.951 45.455 6.04 8.11 44.67 2.93
1508 1913 1.132588 GATGCTGCCGATCGAAGTAC 58.867 55.000 18.66 2.37 0.00 2.73
1666 2081 5.104109 TCAGAGAATTACATACCAAAGGGGG 60.104 44.000 0.00 0.00 42.91 5.40
1793 2715 9.448294 GAATGCTAACAGATTCAGATCATTTTC 57.552 33.333 0.00 0.00 34.60 2.29
1819 2742 4.990526 AGTCCCCCAATAGATAATGCAAG 58.009 43.478 0.00 0.00 0.00 4.01
1845 2773 8.050778 TCTACACACAAAAATGATATGTTCCC 57.949 34.615 0.00 0.00 0.00 3.97
2064 2994 4.221262 ACAATCAGGTAGCATTTGCAATGT 59.779 37.500 0.00 0.00 45.16 2.71
2065 2995 4.751060 ACAATCAGGTAGCATTTGCAATG 58.249 39.130 0.00 2.13 45.16 2.82
2066 2996 4.708421 AGACAATCAGGTAGCATTTGCAAT 59.292 37.500 0.00 0.00 45.16 3.56
2069 2999 3.065925 GGAGACAATCAGGTAGCATTTGC 59.934 47.826 0.00 0.00 42.49 3.68
2070 3000 3.629398 GGGAGACAATCAGGTAGCATTTG 59.371 47.826 0.00 0.00 0.00 2.32
2071 3001 3.525199 AGGGAGACAATCAGGTAGCATTT 59.475 43.478 0.00 0.00 0.00 2.32
2102 3053 1.529010 CCAGCAAGCAACACCCAGA 60.529 57.895 0.00 0.00 0.00 3.86
2105 3056 2.031674 AAAGCCAGCAAGCAACACCC 62.032 55.000 0.55 0.00 34.23 4.61
2107 3058 0.386838 AGAAAGCCAGCAAGCAACAC 59.613 50.000 0.55 0.00 34.23 3.32
2121 3072 6.453092 TCGGTTCTAACTAGGAACAAGAAAG 58.547 40.000 11.08 3.88 43.20 2.62
2132 3083 3.381908 ACCTCTGCATCGGTTCTAACTAG 59.618 47.826 1.44 0.00 0.00 2.57
2169 3124 0.181114 TAGCTGCACACCATCATCCC 59.819 55.000 1.02 0.00 0.00 3.85
2353 3325 6.571537 GCTCAACTCTTAGCAGAAAGTACTCT 60.572 42.308 0.00 0.00 38.63 3.24
2355 3327 5.245075 AGCTCAACTCTTAGCAGAAAGTACT 59.755 40.000 0.00 0.00 41.32 2.73
2486 3469 3.062504 CGATCATGAAGCGAATGACAACA 59.937 43.478 14.08 0.00 36.89 3.33
2489 3472 2.204237 CCGATCATGAAGCGAATGACA 58.796 47.619 19.19 0.00 36.89 3.58
2720 3717 6.925165 TGAAATCTGTCTTTTGGAATTTGAGC 59.075 34.615 0.00 0.00 0.00 4.26
2881 3931 2.768253 AGCATCTTCCACGTCAATCA 57.232 45.000 0.00 0.00 0.00 2.57
2885 3935 3.885724 TGAATAGCATCTTCCACGTCA 57.114 42.857 0.00 0.00 0.00 4.35
3018 4068 3.006940 GTGTTGAACTGTTGACACCTCA 58.993 45.455 18.71 0.05 37.11 3.86
3278 4329 9.574516 AAAATACATCACTTGGTTAGTTCTCTT 57.425 29.630 0.00 0.00 33.85 2.85
3283 4334 9.344772 TGTACAAAATACATCACTTGGTTAGTT 57.655 29.630 0.00 0.00 33.85 2.24
3284 4335 8.911918 TGTACAAAATACATCACTTGGTTAGT 57.088 30.769 0.00 0.00 37.68 2.24
3285 4336 8.450964 CCTGTACAAAATACATCACTTGGTTAG 58.549 37.037 0.00 0.00 0.00 2.34
3286 4337 8.158132 TCCTGTACAAAATACATCACTTGGTTA 58.842 33.333 0.00 0.00 0.00 2.85
3290 4341 7.485913 GCATTCCTGTACAAAATACATCACTTG 59.514 37.037 0.00 0.00 0.00 3.16
3393 4444 6.657541 AGTGTTTTCAGAAGGTTTACTTGTCA 59.342 34.615 0.00 0.00 40.21 3.58
3436 4487 8.668510 AAAATAGTAGGATGCACTGATACTTG 57.331 34.615 7.71 0.00 0.00 3.16
3514 4565 1.893801 TCTCCGAACTTCCAGAACTCC 59.106 52.381 0.00 0.00 0.00 3.85
3630 4681 7.823799 TGTTGTCTGAATGAGCATTATCTGTTA 59.176 33.333 0.00 0.00 0.00 2.41
3686 4737 2.545106 GGTGATACAACGAAAACACGGT 59.455 45.455 0.00 0.00 37.61 4.83
3699 4750 1.230149 AAGGGGGCTGGGTGATACA 60.230 57.895 0.00 0.00 0.00 2.29
3750 4801 1.889105 CCCGATGAACCATGCTCCG 60.889 63.158 0.00 0.00 0.00 4.63
3793 4844 4.758251 TCCGCAGCACATGTCCCG 62.758 66.667 0.00 0.00 0.00 5.14
3813 4864 1.420138 GAAAGGAACTGACCTGGTGGA 59.580 52.381 2.82 0.00 40.86 4.02
3858 4909 2.373169 AGTGCCAAATCTTCAGAGACCA 59.627 45.455 0.00 0.00 33.99 4.02
3859 4910 3.064900 AGTGCCAAATCTTCAGAGACC 57.935 47.619 0.00 0.00 33.99 3.85
3953 5006 1.006571 GCACCTCCAGTCGAACGAA 60.007 57.895 0.00 0.00 0.00 3.85
4037 5090 4.166888 GAGGCGCTCCAGATGGCA 62.167 66.667 7.64 0.00 34.44 4.92
4040 5093 0.106335 AGAATGAGGCGCTCCAGATG 59.894 55.000 7.64 0.00 33.74 2.90
4066 5119 6.897966 TCCTGACTCTGAATACTTGTTAGGAT 59.102 38.462 0.00 0.00 38.12 3.24
4089 5142 1.962100 CTATACCCGGACAGAACCTCC 59.038 57.143 0.73 0.00 0.00 4.30
4170 5227 0.250727 CTCCCACCCAATCGTGTTGT 60.251 55.000 3.40 0.00 31.47 3.32
4208 5265 6.997239 TCATCATCAGATAATATGCCAAGC 57.003 37.500 0.00 0.00 31.88 4.01
4212 5269 9.952188 CATTCATTCATCATCAGATAATATGCC 57.048 33.333 0.00 0.00 31.88 4.40
4284 5342 9.723447 GGTACAAAAGAGAAAGAGAAAGAAAAG 57.277 33.333 0.00 0.00 0.00 2.27
4285 5343 9.462606 AGGTACAAAAGAGAAAGAGAAAGAAAA 57.537 29.630 0.00 0.00 0.00 2.29
4286 5344 9.462606 AAGGTACAAAAGAGAAAGAGAAAGAAA 57.537 29.630 0.00 0.00 0.00 2.52
4309 5367 7.227873 TGACTATCACCTCTATCTCTACAAGG 58.772 42.308 0.00 0.00 0.00 3.61
4411 5490 3.952323 CCAACTGCTTCAAGGATGATCAT 59.048 43.478 8.25 8.25 34.96 2.45
4449 5534 8.588290 TGATATTTTGGTTATACACAAAGCCT 57.412 30.769 0.00 0.00 37.80 4.58
4470 5555 1.444250 GGCGGGGACAACGATGATA 59.556 57.895 0.00 0.00 0.00 2.15
4483 5568 0.666374 AAAAGACAAAAGACGGCGGG 59.334 50.000 13.24 0.00 0.00 6.13
4484 5569 1.064952 ACAAAAGACAAAAGACGGCGG 59.935 47.619 13.24 0.00 0.00 6.13
4508 5593 1.045407 TCCTTAACTCTGGCACACGT 58.955 50.000 0.00 0.00 0.00 4.49
4580 5668 2.167487 AGAAAGCCGGCAGAAAACAAAA 59.833 40.909 31.54 0.00 0.00 2.44
4642 6911 0.739462 TGCTTACCGCGAGTGAATGG 60.739 55.000 8.23 0.00 43.27 3.16
4652 6921 3.668596 ATTTCAACGTATGCTTACCGC 57.331 42.857 4.31 0.00 39.77 5.68
4654 6923 5.459110 TCGAATTTCAACGTATGCTTACC 57.541 39.130 4.31 0.00 0.00 2.85
4660 6929 7.283633 CACTGGATATCGAATTTCAACGTATG 58.716 38.462 0.00 0.00 0.00 2.39
4664 6933 4.024893 CCCACTGGATATCGAATTTCAACG 60.025 45.833 0.00 0.00 0.00 4.10
4674 6943 1.541233 GGTCAAGCCCACTGGATATCG 60.541 57.143 0.00 0.00 0.00 2.92
4742 7042 1.141858 CCCTCCAATACCTGAGCCTTC 59.858 57.143 0.00 0.00 0.00 3.46
4787 8565 4.878971 TCAACACGAGATTTTGGAAAGACA 59.121 37.500 0.00 0.00 0.00 3.41
4803 8581 1.199097 GTGGGCAATAACCTCAACACG 59.801 52.381 0.00 0.00 0.00 4.49
4870 8648 6.712241 TGCTGAATTCTTCGTTCTAGAAAG 57.288 37.500 6.78 9.57 35.43 2.62
4871 8649 7.099764 AGATGCTGAATTCTTCGTTCTAGAAA 58.900 34.615 6.78 0.00 35.43 2.52
4872 8650 6.634805 AGATGCTGAATTCTTCGTTCTAGAA 58.365 36.000 7.05 0.00 36.18 2.10
4873 8651 6.214191 AGATGCTGAATTCTTCGTTCTAGA 57.786 37.500 7.05 0.00 0.00 2.43
4874 8652 6.900568 AAGATGCTGAATTCTTCGTTCTAG 57.099 37.500 7.05 0.00 0.00 2.43
4875 8653 7.065216 CAAAGATGCTGAATTCTTCGTTCTA 57.935 36.000 7.05 0.00 31.09 2.10
4876 8654 5.936054 CAAAGATGCTGAATTCTTCGTTCT 58.064 37.500 7.05 0.50 31.09 3.01
4892 8670 3.318839 TGTCCCAAGTTTCAGCAAAGATG 59.681 43.478 0.00 0.00 0.00 2.90
4893 8671 3.565307 TGTCCCAAGTTTCAGCAAAGAT 58.435 40.909 0.00 0.00 0.00 2.40
4894 8672 3.011566 TGTCCCAAGTTTCAGCAAAGA 57.988 42.857 0.00 0.00 0.00 2.52
4895 8673 3.553508 CCATGTCCCAAGTTTCAGCAAAG 60.554 47.826 0.00 0.00 0.00 2.77
4896 8674 2.364970 CCATGTCCCAAGTTTCAGCAAA 59.635 45.455 0.00 0.00 0.00 3.68
4897 8675 1.962807 CCATGTCCCAAGTTTCAGCAA 59.037 47.619 0.00 0.00 0.00 3.91
4898 8676 1.133513 ACCATGTCCCAAGTTTCAGCA 60.134 47.619 0.00 0.00 0.00 4.41
4899 8677 1.541588 GACCATGTCCCAAGTTTCAGC 59.458 52.381 0.00 0.00 0.00 4.26
4900 8678 3.146104 AGACCATGTCCCAAGTTTCAG 57.854 47.619 0.00 0.00 32.18 3.02
4901 8679 3.221771 CAAGACCATGTCCCAAGTTTCA 58.778 45.455 0.00 0.00 32.18 2.69
4902 8680 2.558359 CCAAGACCATGTCCCAAGTTTC 59.442 50.000 0.00 0.00 32.18 2.78
4903 8681 2.597455 CCAAGACCATGTCCCAAGTTT 58.403 47.619 0.00 0.00 32.18 2.66
4904 8682 1.203050 CCCAAGACCATGTCCCAAGTT 60.203 52.381 0.00 0.00 32.18 2.66
4905 8683 0.405585 CCCAAGACCATGTCCCAAGT 59.594 55.000 0.00 0.00 32.18 3.16
4906 8684 0.967380 GCCCAAGACCATGTCCCAAG 60.967 60.000 0.00 0.00 32.18 3.61
4907 8685 1.076549 GCCCAAGACCATGTCCCAA 59.923 57.895 0.00 0.00 32.18 4.12
4908 8686 2.763215 GCCCAAGACCATGTCCCA 59.237 61.111 0.00 0.00 32.18 4.37
4909 8687 2.043953 GGCCCAAGACCATGTCCC 60.044 66.667 0.00 0.00 32.18 4.46
4910 8688 2.438434 CGGCCCAAGACCATGTCC 60.438 66.667 0.00 0.00 32.18 4.02
4911 8689 0.394352 ATTCGGCCCAAGACCATGTC 60.394 55.000 0.00 0.00 0.00 3.06
4912 8690 0.680921 CATTCGGCCCAAGACCATGT 60.681 55.000 0.00 0.00 0.00 3.21
4913 8691 0.680921 ACATTCGGCCCAAGACCATG 60.681 55.000 0.00 0.00 0.00 3.66
4914 8692 0.916086 TACATTCGGCCCAAGACCAT 59.084 50.000 0.00 0.00 0.00 3.55
4915 8693 0.916086 ATACATTCGGCCCAAGACCA 59.084 50.000 0.00 0.00 0.00 4.02
4916 8694 2.052782 AATACATTCGGCCCAAGACC 57.947 50.000 0.00 0.00 0.00 3.85
4917 8695 2.752903 ACAAATACATTCGGCCCAAGAC 59.247 45.455 0.00 0.00 0.00 3.01
4918 8696 3.080300 ACAAATACATTCGGCCCAAGA 57.920 42.857 0.00 0.00 0.00 3.02
4919 8697 3.866883 AACAAATACATTCGGCCCAAG 57.133 42.857 0.00 0.00 0.00 3.61
4920 8698 4.310769 CAAAACAAATACATTCGGCCCAA 58.689 39.130 0.00 0.00 0.00 4.12
4921 8699 3.862642 GCAAAACAAATACATTCGGCCCA 60.863 43.478 0.00 0.00 0.00 5.36
4922 8700 2.670905 GCAAAACAAATACATTCGGCCC 59.329 45.455 0.00 0.00 0.00 5.80
4923 8701 2.344142 CGCAAAACAAATACATTCGGCC 59.656 45.455 0.00 0.00 0.00 6.13
4924 8702 2.344142 CCGCAAAACAAATACATTCGGC 59.656 45.455 0.00 0.00 0.00 5.54
4925 8703 2.344142 GCCGCAAAACAAATACATTCGG 59.656 45.455 0.00 0.00 37.60 4.30
4926 8704 2.983136 TGCCGCAAAACAAATACATTCG 59.017 40.909 0.00 0.00 0.00 3.34
4927 8705 4.447389 AGTTGCCGCAAAACAAATACATTC 59.553 37.500 7.54 0.00 0.00 2.67
4928 8706 4.376146 AGTTGCCGCAAAACAAATACATT 58.624 34.783 7.54 0.00 0.00 2.71
4929 8707 3.987220 GAGTTGCCGCAAAACAAATACAT 59.013 39.130 7.54 0.00 0.00 2.29
4930 8708 3.067461 AGAGTTGCCGCAAAACAAATACA 59.933 39.130 7.54 0.00 0.00 2.29
4931 8709 3.638484 AGAGTTGCCGCAAAACAAATAC 58.362 40.909 7.54 0.00 0.00 1.89
4932 8710 4.047822 CAAGAGTTGCCGCAAAACAAATA 58.952 39.130 7.54 0.00 0.00 1.40
4933 8711 2.865551 CAAGAGTTGCCGCAAAACAAAT 59.134 40.909 7.54 0.00 0.00 2.32
4934 8712 2.266554 CAAGAGTTGCCGCAAAACAAA 58.733 42.857 7.54 0.00 0.00 2.83
4935 8713 1.919918 CAAGAGTTGCCGCAAAACAA 58.080 45.000 7.54 0.00 0.00 2.83
4936 8714 3.639162 CAAGAGTTGCCGCAAAACA 57.361 47.368 7.54 0.00 0.00 2.83
4946 8724 1.402787 AAGGTGGTTGGCAAGAGTTG 58.597 50.000 0.00 0.00 0.00 3.16
4947 8725 2.583143 GTAAGGTGGTTGGCAAGAGTT 58.417 47.619 0.00 0.00 0.00 3.01
4948 8726 1.202891 GGTAAGGTGGTTGGCAAGAGT 60.203 52.381 0.00 0.00 0.00 3.24
4949 8727 1.534729 GGTAAGGTGGTTGGCAAGAG 58.465 55.000 0.00 0.00 0.00 2.85
4950 8728 0.111639 GGGTAAGGTGGTTGGCAAGA 59.888 55.000 0.00 0.00 0.00 3.02
4951 8729 1.241315 CGGGTAAGGTGGTTGGCAAG 61.241 60.000 0.00 0.00 0.00 4.01
4952 8730 1.228306 CGGGTAAGGTGGTTGGCAA 60.228 57.895 0.00 0.00 0.00 4.52
4953 8731 2.432563 CGGGTAAGGTGGTTGGCA 59.567 61.111 0.00 0.00 0.00 4.92
4954 8732 2.360726 CCGGGTAAGGTGGTTGGC 60.361 66.667 0.00 0.00 0.00 4.52
4955 8733 2.360726 GCCGGGTAAGGTGGTTGG 60.361 66.667 2.18 0.00 0.00 3.77
4956 8734 1.228306 TTGCCGGGTAAGGTGGTTG 60.228 57.895 2.18 0.00 0.00 3.77
4957 8735 1.074248 CTTGCCGGGTAAGGTGGTT 59.926 57.895 16.20 0.00 0.00 3.67
4958 8736 2.754375 CTTGCCGGGTAAGGTGGT 59.246 61.111 16.20 0.00 0.00 4.16
4959 8737 2.750237 GCTTGCCGGGTAAGGTGG 60.750 66.667 23.61 2.55 0.00 4.61
4960 8738 1.602323 TTGCTTGCCGGGTAAGGTG 60.602 57.895 23.61 2.90 0.00 4.00
4961 8739 1.602605 GTTGCTTGCCGGGTAAGGT 60.603 57.895 23.61 0.00 0.00 3.50
4962 8740 0.893727 AAGTTGCTTGCCGGGTAAGG 60.894 55.000 23.61 8.16 0.00 2.69
4963 8741 0.240945 CAAGTTGCTTGCCGGGTAAG 59.759 55.000 19.19 19.19 34.63 2.34
4964 8742 0.179015 TCAAGTTGCTTGCCGGGTAA 60.179 50.000 2.18 0.00 40.84 2.85
4965 8743 0.179015 TTCAAGTTGCTTGCCGGGTA 60.179 50.000 2.18 0.00 40.84 3.69
4966 8744 1.454847 TTCAAGTTGCTTGCCGGGT 60.455 52.632 2.18 0.00 40.84 5.28
4967 8745 1.007387 GTTCAAGTTGCTTGCCGGG 60.007 57.895 2.18 0.00 40.84 5.73
4968 8746 1.370414 CGTTCAAGTTGCTTGCCGG 60.370 57.895 0.00 0.00 40.84 6.13
4969 8747 0.657368 GTCGTTCAAGTTGCTTGCCG 60.657 55.000 0.00 8.59 40.84 5.69
4970 8748 0.317854 GGTCGTTCAAGTTGCTTGCC 60.318 55.000 0.00 0.00 40.84 4.52
4971 8749 0.380378 TGGTCGTTCAAGTTGCTTGC 59.620 50.000 0.00 0.00 40.84 4.01
4972 8750 3.354089 AATGGTCGTTCAAGTTGCTTG 57.646 42.857 0.00 2.71 42.25 4.01
4973 8751 4.097892 AGAAAATGGTCGTTCAAGTTGCTT 59.902 37.500 0.00 0.00 0.00 3.91
4974 8752 3.632145 AGAAAATGGTCGTTCAAGTTGCT 59.368 39.130 0.00 0.00 0.00 3.91
4975 8753 3.964909 AGAAAATGGTCGTTCAAGTTGC 58.035 40.909 0.00 0.00 0.00 4.17
4976 8754 5.147162 GCTAGAAAATGGTCGTTCAAGTTG 58.853 41.667 0.00 0.00 0.00 3.16
4977 8755 4.819630 TGCTAGAAAATGGTCGTTCAAGTT 59.180 37.500 0.00 0.00 0.00 2.66
4978 8756 4.385825 TGCTAGAAAATGGTCGTTCAAGT 58.614 39.130 0.00 0.00 0.00 3.16
4979 8757 5.356882 TTGCTAGAAAATGGTCGTTCAAG 57.643 39.130 0.00 0.00 0.00 3.02
4980 8758 4.320202 GCTTGCTAGAAAATGGTCGTTCAA 60.320 41.667 0.00 0.00 0.00 2.69
4981 8759 3.188460 GCTTGCTAGAAAATGGTCGTTCA 59.812 43.478 0.00 0.00 0.00 3.18
4982 8760 3.188460 TGCTTGCTAGAAAATGGTCGTTC 59.812 43.478 0.00 0.00 0.00 3.95
4983 8761 3.146066 TGCTTGCTAGAAAATGGTCGTT 58.854 40.909 0.00 0.00 0.00 3.85
4984 8762 2.778299 TGCTTGCTAGAAAATGGTCGT 58.222 42.857 0.00 0.00 0.00 4.34
4985 8763 4.361451 AATGCTTGCTAGAAAATGGTCG 57.639 40.909 0.00 0.00 0.00 4.79
4986 8764 5.473039 ACAAATGCTTGCTAGAAAATGGTC 58.527 37.500 0.00 0.00 35.84 4.02
4987 8765 5.473039 GACAAATGCTTGCTAGAAAATGGT 58.527 37.500 0.00 0.00 35.84 3.55
4988 8766 4.866486 GGACAAATGCTTGCTAGAAAATGG 59.134 41.667 0.00 0.00 35.84 3.16
4989 8767 5.717119 AGGACAAATGCTTGCTAGAAAATG 58.283 37.500 0.00 0.00 35.84 2.32
4990 8768 5.990120 AGGACAAATGCTTGCTAGAAAAT 57.010 34.783 0.00 0.00 35.84 1.82
4991 8769 5.531634 CAAGGACAAATGCTTGCTAGAAAA 58.468 37.500 0.00 0.00 45.79 2.29
4992 8770 5.125100 CAAGGACAAATGCTTGCTAGAAA 57.875 39.130 0.00 0.00 45.79 2.52
4993 8771 4.771590 CAAGGACAAATGCTTGCTAGAA 57.228 40.909 0.00 0.00 45.79 2.10
5012 8790 5.886609 TGGGATTGAGTACCTTGAAATCAA 58.113 37.500 0.00 0.00 34.64 2.57
5013 8791 5.500234 CTGGGATTGAGTACCTTGAAATCA 58.500 41.667 0.00 0.00 0.00 2.57
5014 8792 4.884164 CCTGGGATTGAGTACCTTGAAATC 59.116 45.833 0.00 0.00 0.00 2.17
5015 8793 4.292306 ACCTGGGATTGAGTACCTTGAAAT 59.708 41.667 0.00 0.00 0.00 2.17
5016 8794 3.655777 ACCTGGGATTGAGTACCTTGAAA 59.344 43.478 0.00 0.00 0.00 2.69
5017 8795 3.256704 ACCTGGGATTGAGTACCTTGAA 58.743 45.455 0.00 0.00 0.00 2.69
5018 8796 2.915869 ACCTGGGATTGAGTACCTTGA 58.084 47.619 0.00 0.00 0.00 3.02
5019 8797 3.721087 AACCTGGGATTGAGTACCTTG 57.279 47.619 0.00 0.00 0.00 3.61
5020 8798 3.522343 GGTAACCTGGGATTGAGTACCTT 59.478 47.826 0.00 0.00 0.00 3.50
5021 8799 3.113043 GGTAACCTGGGATTGAGTACCT 58.887 50.000 0.00 0.00 0.00 3.08
5022 8800 3.555527 GGTAACCTGGGATTGAGTACC 57.444 52.381 0.00 0.00 0.00 3.34
5037 8815 3.956744 AGGCTGAAAGATCAAGGGTAAC 58.043 45.455 0.00 0.00 34.49 2.50
5038 8816 4.534500 TGTAGGCTGAAAGATCAAGGGTAA 59.466 41.667 0.00 0.00 34.49 2.85
5039 8817 4.101114 TGTAGGCTGAAAGATCAAGGGTA 58.899 43.478 0.00 0.00 34.49 3.69
5040 8818 2.912956 TGTAGGCTGAAAGATCAAGGGT 59.087 45.455 0.00 0.00 34.49 4.34
5041 8819 3.634397 TGTAGGCTGAAAGATCAAGGG 57.366 47.619 0.00 0.00 34.49 3.95


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

AutoCloner maintained by Alex Coulton.