Multiple sequence alignment - TraesCS5B01G572200

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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 TraesCS5B01G572200 chr5B 100.000 2377 0 0 1 2377 712891260 712888884 0.000000e+00 4390
1 TraesCS5B01G572200 chr5B 100.000 570 0 0 2717 3286 712888544 712887975 0.000000e+00 1053
2 TraesCS5B01G572200 chr5B 84.236 628 54 23 3 589 610510356 610509733 1.320000e-158 569
3 TraesCS5B01G572200 chr5B 99.138 232 2 0 358 589 712895846 712895615 5.070000e-113 418
4 TraesCS5B01G572200 chr5B 98.707 232 3 0 358 589 508149511 508149280 2.360000e-111 412
5 TraesCS5B01G572200 chr5B 97.585 207 5 0 383 589 508147149 508146943 4.030000e-94 355
6 TraesCS5B01G572200 chr5D 94.167 1303 50 8 865 2146 562431955 562430658 0.000000e+00 1962
7 TraesCS5B01G572200 chr5D 93.478 1288 57 13 843 2108 562488463 562487181 0.000000e+00 1888
8 TraesCS5B01G572200 chr5D 93.473 1287 59 11 843 2108 562531308 562530026 0.000000e+00 1888
9 TraesCS5B01G572200 chr5D 85.215 1231 135 20 900 2108 561804277 561803072 0.000000e+00 1221
10 TraesCS5B01G572200 chr5D 94.975 199 6 1 2179 2377 562430406 562430212 3.180000e-80 309
11 TraesCS5B01G572200 chr5D 92.517 147 0 5 683 820 562488706 562488562 2.000000e-47 200
12 TraesCS5B01G572200 chr5D 92.517 147 0 5 683 820 562531551 562531407 2.000000e-47 200
13 TraesCS5B01G572200 chr5D 86.614 127 7 3 2717 2834 562430208 562430083 7.400000e-27 132
14 TraesCS5B01G572200 chr5D 98.333 60 1 0 589 648 562488857 562488798 4.480000e-19 106
15 TraesCS5B01G572200 chr5D 96.667 60 2 0 589 648 562531702 562531643 2.090000e-17 100
16 TraesCS5B01G572200 chr7B 92.993 1313 68 12 818 2108 128300 129610 0.000000e+00 1893
17 TraesCS5B01G572200 chr7B 92.952 1277 68 6 879 2134 222251 223526 0.000000e+00 1840
18 TraesCS5B01G572200 chr7B 82.586 1516 178 40 906 2372 1020437 1021915 0.000000e+00 1258
19 TraesCS5B01G572200 chr7B 82.237 1520 182 44 906 2372 1154063 1155547 0.000000e+00 1230
20 TraesCS5B01G572200 chr7B 85.835 1186 128 17 980 2135 229022 230197 0.000000e+00 1223
21 TraesCS5B01G572200 chr7B 87.013 616 48 14 3 590 632707769 632708380 0.000000e+00 665
22 TraesCS5B01G572200 chr7B 86.111 612 48 26 1 589 709883587 709884184 2.780000e-175 625
23 TraesCS5B01G572200 chr7B 93.868 212 7 2 2168 2377 223850 224057 6.840000e-82 315
24 TraesCS5B01G572200 chr7B 96.581 117 2 2 704 820 128087 128201 3.350000e-45 193
25 TraesCS5B01G572200 chr1D 90.610 607 37 13 3 590 3243834 3244439 0.000000e+00 787
26 TraesCS5B01G572200 chr1D 85.595 597 61 21 6 590 408770721 408770138 1.300000e-168 603
27 TraesCS5B01G572200 chr1D 90.256 195 7 3 396 589 3239388 3239571 9.110000e-61 244
28 TraesCS5B01G572200 chr6B 91.720 471 31 6 1 465 47194603 47195071 0.000000e+00 647
29 TraesCS5B01G572200 chr6B 88.934 244 20 6 183 419 475610422 475610179 8.920000e-76 294
30 TraesCS5B01G572200 chr6B 90.769 195 12 4 396 589 47152390 47152579 4.210000e-64 255
31 TraesCS5B01G572200 chr6B 82.039 206 19 11 394 589 125460981 125460784 3.390000e-35 159
32 TraesCS5B01G572200 chr1B 85.806 620 52 16 3 590 641109668 641110283 2.780000e-175 625
33 TraesCS5B01G572200 chr1B 89.815 216 22 0 3071 3286 444335879 444335664 8.980000e-71 278
34 TraesCS5B01G572200 chr4B 85.299 619 55 16 3 589 222613973 222614587 1.010000e-169 606
35 TraesCS5B01G572200 chr4B 83.824 612 51 26 3 589 651748701 651749289 3.730000e-149 538
36 TraesCS5B01G572200 chr3D 84.211 608 69 18 3 589 6349738 6349137 1.710000e-157 566
37 TraesCS5B01G572200 chr3B 92.166 217 16 1 3070 3286 194813853 194814068 4.120000e-79 305
38 TraesCS5B01G572200 chr3B 91.429 105 9 0 2962 3066 194813036 194813140 9.500000e-31 145
39 TraesCS5B01G572200 chr3B 95.506 89 4 0 2848 2936 194812752 194812664 3.420000e-30 143
40 TraesCS5B01G572200 chr3A 88.889 216 24 0 3071 3286 397103137 397103352 1.940000e-67 267


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 TraesCS5B01G572200 chr5B 712887975 712891260 3285 True 2721.500000 4390 100.000000 1 3286 2 chr5B.!!$R4 3285
1 TraesCS5B01G572200 chr5B 610509733 610510356 623 True 569.000000 569 84.236000 3 589 1 chr5B.!!$R1 586
2 TraesCS5B01G572200 chr5B 508146943 508149511 2568 True 383.500000 412 98.146000 358 589 2 chr5B.!!$R3 231
3 TraesCS5B01G572200 chr5D 561803072 561804277 1205 True 1221.000000 1221 85.215000 900 2108 1 chr5D.!!$R1 1208
4 TraesCS5B01G572200 chr5D 562430083 562431955 1872 True 801.000000 1962 91.918667 865 2834 3 chr5D.!!$R2 1969
5 TraesCS5B01G572200 chr5D 562487181 562488857 1676 True 731.333333 1888 94.776000 589 2108 3 chr5D.!!$R3 1519
6 TraesCS5B01G572200 chr5D 562530026 562531702 1676 True 729.333333 1888 94.219000 589 2108 3 chr5D.!!$R4 1519
7 TraesCS5B01G572200 chr7B 1020437 1021915 1478 False 1258.000000 1258 82.586000 906 2372 1 chr7B.!!$F2 1466
8 TraesCS5B01G572200 chr7B 1154063 1155547 1484 False 1230.000000 1230 82.237000 906 2372 1 chr7B.!!$F3 1466
9 TraesCS5B01G572200 chr7B 229022 230197 1175 False 1223.000000 1223 85.835000 980 2135 1 chr7B.!!$F1 1155
10 TraesCS5B01G572200 chr7B 222251 224057 1806 False 1077.500000 1840 93.410000 879 2377 2 chr7B.!!$F7 1498
11 TraesCS5B01G572200 chr7B 128087 129610 1523 False 1043.000000 1893 94.787000 704 2108 2 chr7B.!!$F6 1404
12 TraesCS5B01G572200 chr7B 632707769 632708380 611 False 665.000000 665 87.013000 3 590 1 chr7B.!!$F4 587
13 TraesCS5B01G572200 chr7B 709883587 709884184 597 False 625.000000 625 86.111000 1 589 1 chr7B.!!$F5 588
14 TraesCS5B01G572200 chr1D 3243834 3244439 605 False 787.000000 787 90.610000 3 590 1 chr1D.!!$F2 587
15 TraesCS5B01G572200 chr1D 408770138 408770721 583 True 603.000000 603 85.595000 6 590 1 chr1D.!!$R1 584
16 TraesCS5B01G572200 chr1B 641109668 641110283 615 False 625.000000 625 85.806000 3 590 1 chr1B.!!$F1 587
17 TraesCS5B01G572200 chr4B 222613973 222614587 614 False 606.000000 606 85.299000 3 589 1 chr4B.!!$F1 586
18 TraesCS5B01G572200 chr4B 651748701 651749289 588 False 538.000000 538 83.824000 3 589 1 chr4B.!!$F2 586
19 TraesCS5B01G572200 chr3D 6349137 6349738 601 True 566.000000 566 84.211000 3 589 1 chr3D.!!$R1 586
20 TraesCS5B01G572200 chr3B 194813036 194814068 1032 False 225.000000 305 91.797500 2962 3286 2 chr3B.!!$F1 324

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
528 2959 0.034059 GCATATACCAGGCTCGCACT 59.966 55.000 0.0 0.0 0.0 4.40 F
672 3177 0.250338 AACTCTCGGTGGACTTTGCC 60.250 55.000 0.0 0.0 0.0 4.52 F
679 3184 0.678048 GGTGGACTTTGCCCTGCTAG 60.678 60.000 0.0 0.0 0.0 3.42 F
680 3185 1.002134 TGGACTTTGCCCTGCTAGC 60.002 57.895 8.1 8.1 0.0 3.42 F
2149 4821 1.003972 GGTTGATGTGTGTGTGTGTCG 60.004 52.381 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1349 3975 0.400213 TTGTTGGAGCCAAGGTCGAT 59.600 50.000 1.41 0.0 36.52 3.59 R
2166 4838 1.002544 CGAGGAGTTCAAAAGGAGGCT 59.997 52.381 0.00 0.0 0.00 4.58 R
2232 5196 3.242446 GCTTGGATAGTAGCAGCGAAAAC 60.242 47.826 0.00 0.0 37.35 2.43 R
2252 5216 3.693807 ACATCATGTCATCAACCTTGCT 58.306 40.909 0.00 0.0 0.00 3.91 R
3010 5983 0.396974 AGGCACCTCCAAAACAGCAA 60.397 50.000 0.00 0.0 37.29 3.91 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 27 0.871057 GTCAAGCACAGAGGCAGAAC 59.129 55.000 0.00 0.00 35.83 3.01
94 95 7.441157 CAGTCTATGTTGAAAGAACTTGGTGTA 59.559 37.037 0.00 0.00 0.00 2.90
135 136 3.389656 TGTCTATGGTGTGACAACCTTGA 59.610 43.478 0.00 0.00 39.82 3.02
528 2959 0.034059 GCATATACCAGGCTCGCACT 59.966 55.000 0.00 0.00 0.00 4.40
640 3072 7.210873 AGCCTAAATCTATCTCAGTTAAACGG 58.789 38.462 0.00 0.00 0.00 4.44
651 3156 2.779471 CAGTTAAACGGAAAACACGTGC 59.221 45.455 17.22 0.00 44.83 5.34
666 3171 0.456312 CGTGCTAACTCTCGGTGGAC 60.456 60.000 0.00 0.00 0.00 4.02
667 3172 0.889306 GTGCTAACTCTCGGTGGACT 59.111 55.000 0.00 0.00 0.00 3.85
668 3173 1.272769 GTGCTAACTCTCGGTGGACTT 59.727 52.381 0.00 0.00 0.00 3.01
669 3174 1.968493 TGCTAACTCTCGGTGGACTTT 59.032 47.619 0.00 0.00 0.00 2.66
670 3175 2.288825 TGCTAACTCTCGGTGGACTTTG 60.289 50.000 0.00 0.00 0.00 2.77
671 3176 2.338500 CTAACTCTCGGTGGACTTTGC 58.662 52.381 0.00 0.00 0.00 3.68
672 3177 0.250338 AACTCTCGGTGGACTTTGCC 60.250 55.000 0.00 0.00 0.00 4.52
673 3178 1.376037 CTCTCGGTGGACTTTGCCC 60.376 63.158 0.00 0.00 0.00 5.36
674 3179 1.831652 CTCTCGGTGGACTTTGCCCT 61.832 60.000 0.00 0.00 0.00 5.19
675 3180 1.672356 CTCGGTGGACTTTGCCCTG 60.672 63.158 0.00 0.00 0.00 4.45
676 3181 3.365265 CGGTGGACTTTGCCCTGC 61.365 66.667 0.00 0.00 0.00 4.85
677 3182 2.116125 GGTGGACTTTGCCCTGCT 59.884 61.111 0.00 0.00 0.00 4.24
678 3183 1.378762 GGTGGACTTTGCCCTGCTA 59.621 57.895 0.00 0.00 0.00 3.49
679 3184 0.678048 GGTGGACTTTGCCCTGCTAG 60.678 60.000 0.00 0.00 0.00 3.42
680 3185 1.002134 TGGACTTTGCCCTGCTAGC 60.002 57.895 8.10 8.10 0.00 3.42
681 3186 1.301293 GGACTTTGCCCTGCTAGCT 59.699 57.895 17.23 0.00 0.00 3.32
710 3224 5.862924 TGTTCGAGAAGAAACATTCATCC 57.137 39.130 0.00 0.00 41.10 3.51
775 3289 7.148474 ACGCGTTTGAACAAGTTGATATAAGAT 60.148 33.333 5.58 0.00 0.00 2.40
820 3334 3.643792 AGTCGGCCAGCTTAAGATAAGAT 59.356 43.478 6.67 0.00 0.00 2.40
821 3335 3.991121 GTCGGCCAGCTTAAGATAAGATC 59.009 47.826 6.67 0.00 0.00 2.75
822 3336 3.898123 TCGGCCAGCTTAAGATAAGATCT 59.102 43.478 6.67 0.00 42.61 2.75
824 3338 4.688413 CGGCCAGCTTAAGATAAGATCTTC 59.312 45.833 12.24 0.00 46.17 2.87
826 3340 6.058183 GGCCAGCTTAAGATAAGATCTTCAA 58.942 40.000 12.24 0.00 46.17 2.69
827 3341 6.204495 GGCCAGCTTAAGATAAGATCTTCAAG 59.796 42.308 12.24 9.64 46.17 3.02
829 3343 6.765036 CCAGCTTAAGATAAGATCTTCAAGCA 59.235 38.462 24.81 8.64 46.17 3.91
830 3344 7.444792 CCAGCTTAAGATAAGATCTTCAAGCAT 59.555 37.037 24.81 12.05 46.17 3.79
832 3346 7.384660 AGCTTAAGATAAGATCTTCAAGCATCG 59.615 37.037 24.81 10.12 46.17 3.84
835 3349 9.599866 TTAAGATAAGATCTTCAAGCATCGAAA 57.400 29.630 12.24 6.26 46.17 3.46
837 3351 8.140677 AGATAAGATCTTCAAGCATCGAAAAG 57.859 34.615 12.24 0.00 35.76 2.27
838 3352 7.984050 AGATAAGATCTTCAAGCATCGAAAAGA 59.016 33.333 12.24 0.00 35.76 2.52
841 3355 7.206981 AGATCTTCAAGCATCGAAAAGAAAA 57.793 32.000 0.00 0.00 30.43 2.29
920 3538 2.537401 GCGGGCACTTACTTGTAGTAG 58.463 52.381 0.00 0.00 31.47 2.57
921 3539 2.094338 GCGGGCACTTACTTGTAGTAGT 60.094 50.000 0.00 0.00 31.47 2.73
922 3540 3.129287 GCGGGCACTTACTTGTAGTAGTA 59.871 47.826 0.00 0.00 31.47 1.82
977 3599 2.629051 GCACACCCTATAAGACACCAC 58.371 52.381 0.00 0.00 0.00 4.16
1010 3632 3.377172 AGCAGTTTGTACAACACCAAGAC 59.623 43.478 8.07 1.87 0.00 3.01
1349 3975 3.939837 CTTGCGCGGCTTGAGGAGA 62.940 63.158 8.83 0.00 0.00 3.71
1372 3998 1.609072 GACCTTGGCTCCAACAACTTC 59.391 52.381 0.00 0.00 0.00 3.01
1546 4172 3.330720 AAGGGCAGGGTTCCGGAG 61.331 66.667 3.34 0.00 0.00 4.63
1597 4223 2.028748 GCTTGATTTGTCTGGCAACCAT 60.029 45.455 0.00 0.00 36.72 3.55
1600 4226 5.782047 CTTGATTTGTCTGGCAACCATTTA 58.218 37.500 0.00 0.00 36.72 1.40
1824 4450 2.092753 ACGAGCTCCCAAATGTCATCAT 60.093 45.455 8.47 0.00 35.59 2.45
1831 4457 3.785325 TCCCAAATGTCATCATAGGGACA 59.215 43.478 13.56 0.00 45.35 4.02
2050 4722 7.069085 AGCTACAATAACGTATCTGGGAGTAAA 59.931 37.037 0.00 0.00 0.00 2.01
2103 4775 7.959152 TGTATCTGGGAGGAACCATATTGTATA 59.041 37.037 0.00 0.00 40.36 1.47
2142 4814 2.260844 ACAGGAGGTTGATGTGTGTG 57.739 50.000 0.00 0.00 0.00 3.82
2146 4818 1.603802 GGAGGTTGATGTGTGTGTGTG 59.396 52.381 0.00 0.00 0.00 3.82
2148 4820 2.287915 GAGGTTGATGTGTGTGTGTGTC 59.712 50.000 0.00 0.00 0.00 3.67
2149 4821 1.003972 GGTTGATGTGTGTGTGTGTCG 60.004 52.381 0.00 0.00 0.00 4.35
2152 4824 1.407258 TGATGTGTGTGTGTGTCGAGA 59.593 47.619 0.00 0.00 0.00 4.04
2153 4825 2.035832 TGATGTGTGTGTGTGTCGAGAT 59.964 45.455 0.00 0.00 0.00 2.75
2154 4826 1.851658 TGTGTGTGTGTGTCGAGATG 58.148 50.000 0.00 0.00 0.00 2.90
2155 4827 1.407258 TGTGTGTGTGTGTCGAGATGA 59.593 47.619 0.00 0.00 0.00 2.92
2156 4828 2.054363 GTGTGTGTGTGTCGAGATGAG 58.946 52.381 0.00 0.00 0.00 2.90
2159 4831 2.919859 GTGTGTGTGTCGAGATGAGATG 59.080 50.000 0.00 0.00 0.00 2.90
2160 4832 2.819608 TGTGTGTGTCGAGATGAGATGA 59.180 45.455 0.00 0.00 0.00 2.92
2161 4833 3.445096 TGTGTGTGTCGAGATGAGATGAT 59.555 43.478 0.00 0.00 0.00 2.45
2162 4834 3.795639 GTGTGTGTCGAGATGAGATGATG 59.204 47.826 0.00 0.00 0.00 3.07
2163 4835 3.445096 TGTGTGTCGAGATGAGATGATGT 59.555 43.478 0.00 0.00 0.00 3.06
2164 4836 4.082026 TGTGTGTCGAGATGAGATGATGTT 60.082 41.667 0.00 0.00 0.00 2.71
2165 4837 4.267214 GTGTGTCGAGATGAGATGATGTTG 59.733 45.833 0.00 0.00 0.00 3.33
2166 4838 4.158394 TGTGTCGAGATGAGATGATGTTGA 59.842 41.667 0.00 0.00 0.00 3.18
2232 5196 5.413833 AGATGATGTTGAGCCTTTTGTAGTG 59.586 40.000 0.00 0.00 0.00 2.74
2250 5214 3.522553 AGTGTTTTCGCTGCTACTATCC 58.477 45.455 0.00 0.00 39.39 2.59
2251 5215 3.056107 AGTGTTTTCGCTGCTACTATCCA 60.056 43.478 0.00 0.00 39.39 3.41
2252 5216 3.682858 GTGTTTTCGCTGCTACTATCCAA 59.317 43.478 0.00 0.00 0.00 3.53
2253 5217 3.932710 TGTTTTCGCTGCTACTATCCAAG 59.067 43.478 0.00 0.00 0.00 3.61
2782 5746 4.704057 TGGTACATCTTTATGCATGCACAA 59.296 37.500 25.37 16.54 36.50 3.33
2786 5750 3.574284 TCTTTATGCATGCACAACACC 57.426 42.857 25.37 0.00 0.00 4.16
2787 5751 2.230992 TCTTTATGCATGCACAACACCC 59.769 45.455 25.37 0.00 0.00 4.61
2788 5752 1.625511 TTATGCATGCACAACACCCA 58.374 45.000 25.37 0.00 0.00 4.51
2789 5753 0.887247 TATGCATGCACAACACCCAC 59.113 50.000 25.37 0.00 0.00 4.61
2790 5754 1.114119 ATGCATGCACAACACCCACA 61.114 50.000 25.37 0.00 0.00 4.17
2808 5781 5.968167 ACCCACAATTATACTCCTTGAGGTA 59.032 40.000 0.00 0.00 33.35 3.08
2809 5782 6.619852 ACCCACAATTATACTCCTTGAGGTAT 59.380 38.462 0.00 0.00 33.35 2.73
2810 5783 7.128883 ACCCACAATTATACTCCTTGAGGTATT 59.871 37.037 0.00 0.00 33.35 1.89
2821 5794 3.411446 CTTGAGGTATTGTGGCAACTCA 58.589 45.455 0.00 0.00 38.54 3.41
2844 5817 4.322385 GCAACGCCCACCACGAAC 62.322 66.667 0.00 0.00 0.00 3.95
2845 5818 2.897846 CAACGCCCACCACGAACA 60.898 61.111 0.00 0.00 0.00 3.18
2846 5819 2.898343 AACGCCCACCACGAACAC 60.898 61.111 0.00 0.00 0.00 3.32
2851 5824 4.619227 CCACCACGAACACGCCCT 62.619 66.667 0.00 0.00 0.00 5.19
2852 5825 3.345808 CACCACGAACACGCCCTG 61.346 66.667 0.00 0.00 0.00 4.45
2866 5839 4.514577 CCTGCGGTAGGTGGCGAG 62.515 72.222 3.69 0.00 42.00 5.03
2871 5844 3.537874 GGTAGGTGGCGAGCGGAT 61.538 66.667 0.00 0.00 0.00 4.18
2872 5845 2.198287 GGTAGGTGGCGAGCGGATA 61.198 63.158 0.00 0.00 0.00 2.59
2873 5846 1.286260 GTAGGTGGCGAGCGGATAG 59.714 63.158 0.00 0.00 0.00 2.08
2874 5847 1.901948 TAGGTGGCGAGCGGATAGG 60.902 63.158 0.00 0.00 0.00 2.57
2875 5848 4.971125 GGTGGCGAGCGGATAGGC 62.971 72.222 0.00 0.00 0.00 3.93
2876 5849 4.221422 GTGGCGAGCGGATAGGCA 62.221 66.667 0.00 0.00 36.73 4.75
2877 5850 4.221422 TGGCGAGCGGATAGGCAC 62.221 66.667 0.00 0.00 34.10 5.01
2878 5851 4.971125 GGCGAGCGGATAGGCACC 62.971 72.222 0.00 0.00 34.64 5.01
2879 5852 4.221422 GCGAGCGGATAGGCACCA 62.221 66.667 0.00 0.00 34.64 4.17
2880 5853 2.499205 CGAGCGGATAGGCACCAA 59.501 61.111 0.00 0.00 34.64 3.67
2881 5854 1.592669 CGAGCGGATAGGCACCAAG 60.593 63.158 0.00 0.00 34.64 3.61
2882 5855 1.889573 GAGCGGATAGGCACCAAGC 60.890 63.158 0.00 0.00 44.65 4.01
2883 5856 2.190578 GCGGATAGGCACCAAGCT 59.809 61.111 0.00 0.00 44.79 3.74
2884 5857 1.889573 GCGGATAGGCACCAAGCTC 60.890 63.158 0.00 0.00 44.79 4.09
2885 5858 1.592669 CGGATAGGCACCAAGCTCG 60.593 63.158 0.00 0.00 44.79 5.03
2886 5859 1.889573 GGATAGGCACCAAGCTCGC 60.890 63.158 0.00 0.00 44.79 5.03
2887 5860 1.153369 GATAGGCACCAAGCTCGCA 60.153 57.895 0.00 0.00 44.79 5.10
2888 5861 1.153289 ATAGGCACCAAGCTCGCAG 60.153 57.895 0.00 0.00 44.79 5.18
2889 5862 3.958147 TAGGCACCAAGCTCGCAGC 62.958 63.158 0.00 0.47 44.79 5.25
2899 5872 4.426112 CTCGCAGCTGTCTCCGCA 62.426 66.667 16.64 0.28 0.00 5.69
2900 5873 4.724602 TCGCAGCTGTCTCCGCAC 62.725 66.667 16.64 0.00 0.00 5.34
2902 5875 4.385405 GCAGCTGTCTCCGCACCT 62.385 66.667 16.64 0.00 0.00 4.00
2903 5876 2.345244 CAGCTGTCTCCGCACCTT 59.655 61.111 5.25 0.00 0.00 3.50
2904 5877 2.031516 CAGCTGTCTCCGCACCTTG 61.032 63.158 5.25 0.00 0.00 3.61
2905 5878 2.743928 GCTGTCTCCGCACCTTGG 60.744 66.667 0.00 0.00 0.00 3.61
2906 5879 2.743928 CTGTCTCCGCACCTTGGC 60.744 66.667 0.00 0.00 0.00 4.52
2907 5880 4.329545 TGTCTCCGCACCTTGGCC 62.330 66.667 0.00 0.00 0.00 5.36
2911 5884 4.572571 TCCGCACCTTGGCCGTTT 62.573 61.111 0.00 0.00 0.00 3.60
2912 5885 2.670251 CCGCACCTTGGCCGTTTA 60.670 61.111 0.00 0.00 0.00 2.01
2913 5886 2.262303 CCGCACCTTGGCCGTTTAA 61.262 57.895 0.00 0.00 0.00 1.52
2914 5887 1.655329 CGCACCTTGGCCGTTTAAA 59.345 52.632 0.00 0.00 0.00 1.52
2915 5888 0.662077 CGCACCTTGGCCGTTTAAAC 60.662 55.000 8.35 8.35 0.00 2.01
2916 5889 0.386113 GCACCTTGGCCGTTTAAACA 59.614 50.000 18.07 0.00 0.00 2.83
2917 5890 1.601914 GCACCTTGGCCGTTTAAACAG 60.602 52.381 18.07 8.14 0.00 3.16
2918 5891 1.679153 CACCTTGGCCGTTTAAACAGT 59.321 47.619 18.07 1.31 0.00 3.55
2919 5892 1.679153 ACCTTGGCCGTTTAAACAGTG 59.321 47.619 18.07 7.08 0.00 3.66
2920 5893 1.000717 CCTTGGCCGTTTAAACAGTGG 60.001 52.381 18.07 11.90 0.00 4.00
2921 5894 0.386113 TTGGCCGTTTAAACAGTGGC 59.614 50.000 21.08 21.08 44.98 5.01
2922 5895 4.957266 GCCGTTTAAACAGTGGCC 57.043 55.556 19.43 0.00 39.83 5.36
2923 5896 2.034607 GCCGTTTAAACAGTGGCCA 58.965 52.632 19.43 0.00 39.83 5.36
2924 5897 0.318360 GCCGTTTAAACAGTGGCCAC 60.318 55.000 29.22 29.22 39.83 5.01
2925 5898 0.040781 CCGTTTAAACAGTGGCCACG 60.041 55.000 29.68 24.87 36.20 4.94
2926 5899 0.938713 CGTTTAAACAGTGGCCACGA 59.061 50.000 29.68 11.45 36.20 4.35
2927 5900 1.533731 CGTTTAAACAGTGGCCACGAT 59.466 47.619 29.68 19.14 36.20 3.73
2928 5901 2.412325 CGTTTAAACAGTGGCCACGATC 60.412 50.000 29.68 6.60 36.20 3.69
2929 5902 2.812011 GTTTAAACAGTGGCCACGATCT 59.188 45.455 29.68 17.90 36.20 2.75
2930 5903 2.380084 TAAACAGTGGCCACGATCTC 57.620 50.000 29.68 5.33 36.20 2.75
2931 5904 0.687354 AAACAGTGGCCACGATCTCT 59.313 50.000 29.68 8.90 36.20 3.10
2932 5905 0.036952 AACAGTGGCCACGATCTCTG 60.037 55.000 29.68 22.54 36.20 3.35
2933 5906 1.188219 ACAGTGGCCACGATCTCTGT 61.188 55.000 29.68 23.20 36.20 3.41
2934 5907 0.459237 CAGTGGCCACGATCTCTGTC 60.459 60.000 29.68 2.00 36.20 3.51
2935 5908 0.613292 AGTGGCCACGATCTCTGTCT 60.613 55.000 29.68 5.62 36.20 3.41
2936 5909 0.179124 GTGGCCACGATCTCTGTCTC 60.179 60.000 22.49 0.00 0.00 3.36
2937 5910 1.323271 TGGCCACGATCTCTGTCTCC 61.323 60.000 0.00 0.00 0.00 3.71
2938 5911 1.439644 GCCACGATCTCTGTCTCCC 59.560 63.158 0.00 0.00 0.00 4.30
2939 5912 2.022240 GCCACGATCTCTGTCTCCCC 62.022 65.000 0.00 0.00 0.00 4.81
2940 5913 1.729470 CCACGATCTCTGTCTCCCCG 61.729 65.000 0.00 0.00 0.00 5.73
2941 5914 2.122167 ACGATCTCTGTCTCCCCGC 61.122 63.158 0.00 0.00 0.00 6.13
2942 5915 2.851071 CGATCTCTGTCTCCCCGCC 61.851 68.421 0.00 0.00 0.00 6.13
2943 5916 1.456705 GATCTCTGTCTCCCCGCCT 60.457 63.158 0.00 0.00 0.00 5.52
2944 5917 1.002274 ATCTCTGTCTCCCCGCCTT 59.998 57.895 0.00 0.00 0.00 4.35
2945 5918 0.618968 ATCTCTGTCTCCCCGCCTTT 60.619 55.000 0.00 0.00 0.00 3.11
2946 5919 1.078848 CTCTGTCTCCCCGCCTTTG 60.079 63.158 0.00 0.00 0.00 2.77
2947 5920 2.747855 CTGTCTCCCCGCCTTTGC 60.748 66.667 0.00 0.00 0.00 3.68
2948 5921 4.344865 TGTCTCCCCGCCTTTGCC 62.345 66.667 0.00 0.00 0.00 4.52
2949 5922 4.344865 GTCTCCCCGCCTTTGCCA 62.345 66.667 0.00 0.00 0.00 4.92
2950 5923 3.338250 TCTCCCCGCCTTTGCCAT 61.338 61.111 0.00 0.00 0.00 4.40
2951 5924 2.362889 CTCCCCGCCTTTGCCATT 60.363 61.111 0.00 0.00 0.00 3.16
2952 5925 1.984026 CTCCCCGCCTTTGCCATTT 60.984 57.895 0.00 0.00 0.00 2.32
2953 5926 2.229690 CTCCCCGCCTTTGCCATTTG 62.230 60.000 0.00 0.00 0.00 2.32
2954 5927 2.282039 CCCCGCCTTTGCCATTTGA 61.282 57.895 0.00 0.00 0.00 2.69
2955 5928 1.670590 CCCGCCTTTGCCATTTGAA 59.329 52.632 0.00 0.00 0.00 2.69
2956 5929 0.034616 CCCGCCTTTGCCATTTGAAA 59.965 50.000 0.00 0.00 0.00 2.69
2957 5930 1.542108 CCCGCCTTTGCCATTTGAAAA 60.542 47.619 0.00 0.00 0.00 2.29
2958 5931 2.425539 CCGCCTTTGCCATTTGAAAAT 58.574 42.857 0.00 0.00 0.00 1.82
2959 5932 2.813172 CCGCCTTTGCCATTTGAAAATT 59.187 40.909 0.00 0.00 0.00 1.82
2960 5933 3.365164 CCGCCTTTGCCATTTGAAAATTG 60.365 43.478 0.00 0.00 0.00 2.32
2973 5946 2.380571 AAAATTGGCCACCGTCCCCT 62.381 55.000 3.88 0.00 0.00 4.79
3010 5983 1.729267 AACCTGGACATTGGGCCACT 61.729 55.000 5.23 0.00 0.00 4.00
3016 5989 1.152483 ACATTGGGCCACTTGCTGT 60.152 52.632 5.23 2.14 40.92 4.40
3017 5990 0.760189 ACATTGGGCCACTTGCTGTT 60.760 50.000 5.23 0.00 40.92 3.16
3022 5995 1.398958 GGGCCACTTGCTGTTTTGGA 61.399 55.000 4.39 0.00 40.92 3.53
3025 5998 1.402787 CCACTTGCTGTTTTGGAGGT 58.597 50.000 0.00 0.00 0.00 3.85
3059 6032 4.719369 AGCGTGGCGTTCGAGGAC 62.719 66.667 0.00 0.00 0.00 3.85
3066 6039 3.048602 CGTTCGAGGACCCAGTGT 58.951 61.111 0.00 0.00 0.00 3.55
3067 6040 1.366366 CGTTCGAGGACCCAGTGTT 59.634 57.895 0.00 0.00 0.00 3.32
3080 6762 1.528309 AGTGTTGGCAAACCCCTCG 60.528 57.895 0.00 0.00 35.25 4.63
3095 6777 0.951040 CCTCGGTGACTTGCTGGAAC 60.951 60.000 0.00 0.00 0.00 3.62
3102 6784 0.507358 GACTTGCTGGAACGTTCGAC 59.493 55.000 21.34 13.46 0.00 4.20
3119 6801 2.098298 CGCTTGAACAATCCGGCG 59.902 61.111 0.00 0.00 38.47 6.46
3138 6820 1.461127 CGAAAAGAAGAGCGGTGAAGG 59.539 52.381 0.00 0.00 0.00 3.46
3170 6852 4.317671 TTCGGTTAAGCCTAGCATAGTC 57.682 45.455 0.00 0.00 36.82 2.59
3209 6891 4.773323 ACTTGCCTTTGTAGATGCTTTC 57.227 40.909 0.00 0.00 0.00 2.62
3236 6918 2.268076 GCAATGTTGTGGCCCGTCT 61.268 57.895 0.00 0.00 0.00 4.18
3242 6924 0.893727 GTTGTGGCCCGTCTTTGGAT 60.894 55.000 0.00 0.00 0.00 3.41
3243 6925 0.893270 TTGTGGCCCGTCTTTGGATG 60.893 55.000 0.00 0.00 0.00 3.51
3244 6926 2.046285 GTGGCCCGTCTTTGGATGG 61.046 63.158 0.00 0.00 45.68 3.51
3245 6927 3.140814 GGCCCGTCTTTGGATGGC 61.141 66.667 0.00 0.00 44.97 4.40
3260 6942 3.203716 GGATGGCTTTTCCTACTTACCG 58.796 50.000 0.00 0.00 35.26 4.02
3264 6946 1.648504 CTTTTCCTACTTACCGGCGG 58.351 55.000 27.06 27.06 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 95 0.469144 ATGGAGCCGGTGTGGTTTTT 60.469 50.000 1.90 0.00 41.21 1.94
135 136 5.656416 GGATTAGCAGAGAGATAGGTAGCAT 59.344 44.000 0.00 0.00 0.00 3.79
490 585 2.629137 TGCGTACAGGAGTTTGTTAGGA 59.371 45.455 0.00 0.00 32.56 2.94
528 2959 4.142708 CGTGTTGCATGTTATAAAGGCAGA 60.143 41.667 0.00 0.00 35.68 4.26
640 3072 2.155155 CCGAGAGTTAGCACGTGTTTTC 59.845 50.000 18.38 9.86 0.00 2.29
651 3156 2.338500 GCAAAGTCCACCGAGAGTTAG 58.662 52.381 0.00 0.00 0.00 2.34
666 3171 1.831580 AAAGAGCTAGCAGGGCAAAG 58.168 50.000 18.83 0.00 0.00 2.77
667 3172 2.292828 AAAAGAGCTAGCAGGGCAAA 57.707 45.000 18.83 0.00 0.00 3.68
668 3173 2.292828 AAAAAGAGCTAGCAGGGCAA 57.707 45.000 18.83 0.00 0.00 4.52
710 3224 9.507280 AATTGAAATTATTAATGTGCGACAGAG 57.493 29.630 0.00 0.00 0.00 3.35
775 3289 8.177119 ACTACTGATGCAAGGATTTTGTTTTA 57.823 30.769 0.00 0.00 0.00 1.52
779 3293 4.393062 CGACTACTGATGCAAGGATTTTGT 59.607 41.667 0.00 0.00 0.00 2.83
780 3294 4.201851 CCGACTACTGATGCAAGGATTTTG 60.202 45.833 0.00 0.00 0.00 2.44
781 3295 3.941483 CCGACTACTGATGCAAGGATTTT 59.059 43.478 0.00 0.00 0.00 1.82
820 3334 7.026631 TCTTTTTCTTTTCGATGCTTGAAGA 57.973 32.000 0.00 0.00 0.00 2.87
821 3335 7.806960 AGATCTTTTTCTTTTCGATGCTTGAAG 59.193 33.333 0.00 0.00 0.00 3.02
822 3336 7.651808 AGATCTTTTTCTTTTCGATGCTTGAA 58.348 30.769 0.00 0.00 0.00 2.69
823 3337 7.206981 AGATCTTTTTCTTTTCGATGCTTGA 57.793 32.000 0.00 0.00 0.00 3.02
824 3338 7.592533 TGAAGATCTTTTTCTTTTCGATGCTTG 59.407 33.333 9.87 0.00 36.10 4.01
826 3340 7.206981 TGAAGATCTTTTTCTTTTCGATGCT 57.793 32.000 9.87 0.00 36.10 3.79
827 3341 7.410193 GCTTGAAGATCTTTTTCTTTTCGATGC 60.410 37.037 9.87 0.00 36.10 3.91
829 3343 7.651808 TGCTTGAAGATCTTTTTCTTTTCGAT 58.348 30.769 9.87 0.00 36.10 3.59
830 3344 7.026631 TGCTTGAAGATCTTTTTCTTTTCGA 57.973 32.000 9.87 0.00 36.10 3.71
832 3346 7.805071 TCGATGCTTGAAGATCTTTTTCTTTTC 59.195 33.333 9.87 1.93 36.10 2.29
835 3349 6.808008 TCGATGCTTGAAGATCTTTTTCTT 57.192 33.333 9.87 0.00 38.65 2.52
837 3351 7.858052 TTTTCGATGCTTGAAGATCTTTTTC 57.142 32.000 9.87 0.00 0.00 2.29
977 3599 3.340814 ACAAACTGCTAGGGTGATGAG 57.659 47.619 0.00 0.00 0.00 2.90
1010 3632 1.467734 GAGTGATTGGCAAGTGCTCTG 59.532 52.381 5.96 0.00 41.70 3.35
1228 3854 0.179020 CACAGCTCACACCTTCCCAA 60.179 55.000 0.00 0.00 0.00 4.12
1349 3975 0.400213 TTGTTGGAGCCAAGGTCGAT 59.600 50.000 1.41 0.00 36.52 3.59
1372 3998 3.009033 TGAGTACCCCTGAGATGTTTTGG 59.991 47.826 0.00 0.00 0.00 3.28
1546 4172 3.988379 TTCTTGCATTGAGACAACCAC 57.012 42.857 0.00 0.00 0.00 4.16
1831 4457 5.221244 GCTCCCAGATGTTACAAAGTTGTTT 60.221 40.000 1.35 0.00 42.35 2.83
2050 4722 6.909550 TTGTTGCTCCCAAATACTACATTT 57.090 33.333 0.00 0.00 31.68 2.32
2103 4775 5.261216 CTGTTATAACCTTGTTGTCCCCAT 58.739 41.667 13.01 0.00 0.00 4.00
2142 4814 4.039151 ACATCATCTCATCTCGACACAC 57.961 45.455 0.00 0.00 0.00 3.82
2146 4818 3.735240 GCTCAACATCATCTCATCTCGAC 59.265 47.826 0.00 0.00 0.00 4.20
2148 4820 3.058450 GGCTCAACATCATCTCATCTCG 58.942 50.000 0.00 0.00 0.00 4.04
2149 4821 4.309099 GAGGCTCAACATCATCTCATCTC 58.691 47.826 10.25 0.00 0.00 2.75
2152 4824 3.047115 AGGAGGCTCAACATCATCTCAT 58.953 45.455 17.69 0.00 0.00 2.90
2153 4825 2.475155 AGGAGGCTCAACATCATCTCA 58.525 47.619 17.69 0.00 0.00 3.27
2154 4826 3.557228 AAGGAGGCTCAACATCATCTC 57.443 47.619 17.69 0.00 0.00 2.75
2155 4827 4.015084 CAAAAGGAGGCTCAACATCATCT 58.985 43.478 17.69 0.00 0.00 2.90
2156 4828 4.012374 TCAAAAGGAGGCTCAACATCATC 58.988 43.478 17.69 0.00 0.00 2.92
2159 4831 3.823304 AGTTCAAAAGGAGGCTCAACATC 59.177 43.478 17.69 0.00 0.00 3.06
2160 4832 3.823304 GAGTTCAAAAGGAGGCTCAACAT 59.177 43.478 17.69 0.00 32.78 2.71
2161 4833 3.214328 GAGTTCAAAAGGAGGCTCAACA 58.786 45.455 17.69 0.00 32.78 3.33
2162 4834 2.554462 GGAGTTCAAAAGGAGGCTCAAC 59.446 50.000 17.69 10.67 33.61 3.18
2163 4835 2.443255 AGGAGTTCAAAAGGAGGCTCAA 59.557 45.455 17.69 0.00 33.61 3.02
2164 4836 2.039084 GAGGAGTTCAAAAGGAGGCTCA 59.961 50.000 17.69 0.00 33.61 4.26
2165 4837 2.705730 GAGGAGTTCAAAAGGAGGCTC 58.294 52.381 5.78 5.78 0.00 4.70
2166 4838 1.002544 CGAGGAGTTCAAAAGGAGGCT 59.997 52.381 0.00 0.00 0.00 4.58
2232 5196 3.242446 GCTTGGATAGTAGCAGCGAAAAC 60.242 47.826 0.00 0.00 37.35 2.43
2250 5214 4.082408 ACATCATGTCATCAACCTTGCTTG 60.082 41.667 0.00 0.00 0.00 4.01
2251 5215 4.084287 ACATCATGTCATCAACCTTGCTT 58.916 39.130 0.00 0.00 0.00 3.91
2252 5216 3.693807 ACATCATGTCATCAACCTTGCT 58.306 40.909 0.00 0.00 0.00 3.91
2253 5217 4.418392 GAACATCATGTCATCAACCTTGC 58.582 43.478 0.00 0.00 0.00 4.01
2730 5694 5.880054 AGATACACAATACAACTTGGCAC 57.120 39.130 0.00 0.00 0.00 5.01
2782 5746 5.339200 CCTCAAGGAGTATAATTGTGGGTGT 60.339 44.000 0.00 0.00 35.13 4.16
2786 5750 7.993183 ACAATACCTCAAGGAGTATAATTGTGG 59.007 37.037 2.30 4.25 41.25 4.17
2787 5751 8.830580 CACAATACCTCAAGGAGTATAATTGTG 58.169 37.037 2.30 16.60 38.94 3.33
2788 5752 7.993183 CCACAATACCTCAAGGAGTATAATTGT 59.007 37.037 2.30 6.09 38.94 2.71
2789 5753 7.041098 GCCACAATACCTCAAGGAGTATAATTG 60.041 40.741 2.30 5.57 38.94 2.32
2790 5754 6.998673 GCCACAATACCTCAAGGAGTATAATT 59.001 38.462 2.30 0.00 38.94 1.40
2810 5783 0.754587 TGCCATTGTGAGTTGCCACA 60.755 50.000 0.00 0.00 44.45 4.17
2834 5807 4.619227 AGGGCGTGTTCGTGGTGG 62.619 66.667 0.00 0.00 39.49 4.61
2835 5808 3.345808 CAGGGCGTGTTCGTGGTG 61.346 66.667 0.00 0.00 39.49 4.17
2854 5827 2.143594 CTATCCGCTCGCCACCTACC 62.144 65.000 0.00 0.00 0.00 3.18
2855 5828 1.286260 CTATCCGCTCGCCACCTAC 59.714 63.158 0.00 0.00 0.00 3.18
2856 5829 1.901948 CCTATCCGCTCGCCACCTA 60.902 63.158 0.00 0.00 0.00 3.08
2857 5830 3.227276 CCTATCCGCTCGCCACCT 61.227 66.667 0.00 0.00 0.00 4.00
2858 5831 4.971125 GCCTATCCGCTCGCCACC 62.971 72.222 0.00 0.00 0.00 4.61
2859 5832 4.221422 TGCCTATCCGCTCGCCAC 62.221 66.667 0.00 0.00 0.00 5.01
2860 5833 4.221422 GTGCCTATCCGCTCGCCA 62.221 66.667 0.00 0.00 0.00 5.69
2861 5834 4.971125 GGTGCCTATCCGCTCGCC 62.971 72.222 0.00 0.00 0.00 5.54
2862 5835 3.733344 TTGGTGCCTATCCGCTCGC 62.733 63.158 0.00 0.00 0.00 5.03
2863 5836 1.592669 CTTGGTGCCTATCCGCTCG 60.593 63.158 0.00 0.00 0.00 5.03
2864 5837 1.889573 GCTTGGTGCCTATCCGCTC 60.890 63.158 0.00 0.00 35.15 5.03
2865 5838 2.190578 GCTTGGTGCCTATCCGCT 59.809 61.111 0.00 0.00 35.15 5.52
2866 5839 1.889573 GAGCTTGGTGCCTATCCGC 60.890 63.158 0.00 0.00 44.23 5.54
2867 5840 1.592669 CGAGCTTGGTGCCTATCCG 60.593 63.158 0.00 0.00 44.23 4.18
2868 5841 1.889573 GCGAGCTTGGTGCCTATCC 60.890 63.158 2.37 0.00 44.23 2.59
2869 5842 1.153369 TGCGAGCTTGGTGCCTATC 60.153 57.895 2.37 0.00 44.23 2.08
2870 5843 1.153289 CTGCGAGCTTGGTGCCTAT 60.153 57.895 2.37 0.00 44.23 2.57
2871 5844 2.265739 CTGCGAGCTTGGTGCCTA 59.734 61.111 2.37 0.00 44.23 3.93
2885 5858 4.385405 AGGTGCGGAGACAGCTGC 62.385 66.667 15.27 6.85 46.17 5.25
2888 5861 2.743928 CCAAGGTGCGGAGACAGC 60.744 66.667 0.00 0.00 38.33 4.40
2889 5862 2.743928 GCCAAGGTGCGGAGACAG 60.744 66.667 0.00 0.00 0.00 3.51
2890 5863 4.329545 GGCCAAGGTGCGGAGACA 62.330 66.667 0.00 0.00 0.00 3.41
2894 5867 2.677765 TTAAACGGCCAAGGTGCGGA 62.678 55.000 2.24 0.00 35.71 5.54
2895 5868 1.797211 TTTAAACGGCCAAGGTGCGG 61.797 55.000 2.24 0.00 37.56 5.69
2896 5869 0.662077 GTTTAAACGGCCAAGGTGCG 60.662 55.000 2.24 0.00 0.00 5.34
2897 5870 0.386113 TGTTTAAACGGCCAAGGTGC 59.614 50.000 13.45 0.00 0.00 5.01
2898 5871 1.679153 ACTGTTTAAACGGCCAAGGTG 59.321 47.619 24.08 4.46 38.89 4.00
2899 5872 1.679153 CACTGTTTAAACGGCCAAGGT 59.321 47.619 24.08 3.74 38.89 3.50
2900 5873 1.000717 CCACTGTTTAAACGGCCAAGG 60.001 52.381 24.08 17.13 38.89 3.61
2901 5874 1.601914 GCCACTGTTTAAACGGCCAAG 60.602 52.381 24.08 12.86 38.89 3.61
2902 5875 0.386113 GCCACTGTTTAAACGGCCAA 59.614 50.000 24.08 1.41 38.89 4.52
2903 5876 2.034607 GCCACTGTTTAAACGGCCA 58.965 52.632 24.08 1.84 38.89 5.36
2904 5877 4.957266 GCCACTGTTTAAACGGCC 57.043 55.556 24.08 11.14 38.89 6.13
2905 5878 0.318360 GTGGCCACTGTTTAAACGGC 60.318 55.000 29.12 22.43 42.21 5.68
2906 5879 0.040781 CGTGGCCACTGTTTAAACGG 60.041 55.000 32.28 22.85 41.10 4.44
2907 5880 0.938713 TCGTGGCCACTGTTTAAACG 59.061 50.000 32.28 16.67 0.00 3.60
2908 5881 2.812011 AGATCGTGGCCACTGTTTAAAC 59.188 45.455 32.28 11.54 0.00 2.01
2909 5882 3.071479 GAGATCGTGGCCACTGTTTAAA 58.929 45.455 32.28 10.76 0.00 1.52
2910 5883 2.301870 AGAGATCGTGGCCACTGTTTAA 59.698 45.455 32.28 11.70 0.00 1.52
2911 5884 1.899814 AGAGATCGTGGCCACTGTTTA 59.100 47.619 32.28 13.44 0.00 2.01
2912 5885 0.687354 AGAGATCGTGGCCACTGTTT 59.313 50.000 32.28 16.24 0.00 2.83
2913 5886 0.036952 CAGAGATCGTGGCCACTGTT 60.037 55.000 32.28 19.99 0.00 3.16
2914 5887 1.188219 ACAGAGATCGTGGCCACTGT 61.188 55.000 32.28 24.58 34.46 3.55
2915 5888 0.459237 GACAGAGATCGTGGCCACTG 60.459 60.000 32.28 23.92 0.00 3.66
2916 5889 0.613292 AGACAGAGATCGTGGCCACT 60.613 55.000 32.28 16.25 0.00 4.00
2917 5890 0.179124 GAGACAGAGATCGTGGCCAC 60.179 60.000 26.78 26.78 0.00 5.01
2918 5891 1.323271 GGAGACAGAGATCGTGGCCA 61.323 60.000 0.00 0.00 0.00 5.36
2919 5892 1.439644 GGAGACAGAGATCGTGGCC 59.560 63.158 0.00 0.00 0.00 5.36
2920 5893 1.439644 GGGAGACAGAGATCGTGGC 59.560 63.158 3.52 0.00 0.00 5.01
2921 5894 1.729470 CGGGGAGACAGAGATCGTGG 61.729 65.000 3.52 0.00 0.00 4.94
2922 5895 1.730487 CGGGGAGACAGAGATCGTG 59.270 63.158 0.00 0.00 0.00 4.35
2923 5896 2.122167 GCGGGGAGACAGAGATCGT 61.122 63.158 0.00 0.00 0.00 3.73
2924 5897 2.725008 GCGGGGAGACAGAGATCG 59.275 66.667 0.00 0.00 0.00 3.69
2925 5898 1.045911 AAGGCGGGGAGACAGAGATC 61.046 60.000 0.00 0.00 0.00 2.75
2926 5899 0.618968 AAAGGCGGGGAGACAGAGAT 60.619 55.000 0.00 0.00 0.00 2.75
2927 5900 1.229209 AAAGGCGGGGAGACAGAGA 60.229 57.895 0.00 0.00 0.00 3.10
2928 5901 1.078848 CAAAGGCGGGGAGACAGAG 60.079 63.158 0.00 0.00 0.00 3.35
2929 5902 3.068881 CAAAGGCGGGGAGACAGA 58.931 61.111 0.00 0.00 0.00 3.41
2930 5903 2.747855 GCAAAGGCGGGGAGACAG 60.748 66.667 0.00 0.00 0.00 3.51
2931 5904 4.344865 GGCAAAGGCGGGGAGACA 62.345 66.667 0.00 0.00 42.47 3.41
2932 5905 3.645268 ATGGCAAAGGCGGGGAGAC 62.645 63.158 0.00 0.00 42.47 3.36
2933 5906 2.439553 AAATGGCAAAGGCGGGGAGA 62.440 55.000 0.00 0.00 42.47 3.71
2934 5907 1.984026 AAATGGCAAAGGCGGGGAG 60.984 57.895 0.00 0.00 42.47 4.30
2935 5908 2.119391 AAATGGCAAAGGCGGGGA 59.881 55.556 0.00 0.00 42.47 4.81
2936 5909 1.825281 TTCAAATGGCAAAGGCGGGG 61.825 55.000 0.00 0.00 42.47 5.73
2937 5910 0.034616 TTTCAAATGGCAAAGGCGGG 59.965 50.000 0.00 0.00 42.47 6.13
2938 5911 1.876322 TTTTCAAATGGCAAAGGCGG 58.124 45.000 0.00 0.00 42.47 6.13
2939 5912 3.365164 CCAATTTTCAAATGGCAAAGGCG 60.365 43.478 0.00 0.00 42.47 5.52
2940 5913 3.612241 GCCAATTTTCAAATGGCAAAGGC 60.612 43.478 9.52 0.00 39.84 4.35
2941 5914 3.057386 GGCCAATTTTCAAATGGCAAAGG 60.057 43.478 15.24 0.00 40.84 3.11
2942 5915 3.568853 TGGCCAATTTTCAAATGGCAAAG 59.431 39.130 15.24 0.00 40.84 2.77
2943 5916 3.317430 GTGGCCAATTTTCAAATGGCAAA 59.683 39.130 7.24 2.02 40.84 3.68
2944 5917 2.883386 GTGGCCAATTTTCAAATGGCAA 59.117 40.909 7.24 2.61 40.84 4.52
2945 5918 2.502295 GTGGCCAATTTTCAAATGGCA 58.498 42.857 7.24 7.10 40.84 4.92
2946 5919 1.811965 GGTGGCCAATTTTCAAATGGC 59.188 47.619 7.24 6.23 39.60 4.40
2947 5920 2.075338 CGGTGGCCAATTTTCAAATGG 58.925 47.619 7.24 0.00 0.00 3.16
2948 5921 2.736192 GACGGTGGCCAATTTTCAAATG 59.264 45.455 7.24 0.00 0.00 2.32
2949 5922 2.289382 GGACGGTGGCCAATTTTCAAAT 60.289 45.455 7.24 0.00 0.00 2.32
2950 5923 1.069358 GGACGGTGGCCAATTTTCAAA 59.931 47.619 7.24 0.00 0.00 2.69
2951 5924 0.676736 GGACGGTGGCCAATTTTCAA 59.323 50.000 7.24 0.00 0.00 2.69
2952 5925 1.182385 GGGACGGTGGCCAATTTTCA 61.182 55.000 7.24 0.00 0.00 2.69
2953 5926 1.589630 GGGACGGTGGCCAATTTTC 59.410 57.895 7.24 1.03 0.00 2.29
2954 5927 1.911269 GGGGACGGTGGCCAATTTT 60.911 57.895 7.24 0.00 0.00 1.82
2955 5928 2.283604 GGGGACGGTGGCCAATTT 60.284 61.111 7.24 0.00 0.00 1.82
2956 5929 3.264845 AGGGGACGGTGGCCAATT 61.265 61.111 7.24 0.00 0.00 2.32
2957 5930 3.728373 GAGGGGACGGTGGCCAAT 61.728 66.667 7.24 0.00 0.00 3.16
2958 5931 4.974438 AGAGGGGACGGTGGCCAA 62.974 66.667 7.24 0.00 0.00 4.52
2959 5932 4.974438 AAGAGGGGACGGTGGCCA 62.974 66.667 0.00 0.00 0.00 5.36
2960 5933 4.097361 GAAGAGGGGACGGTGGCC 62.097 72.222 0.00 0.00 0.00 5.36
2966 5939 1.515020 CTGAGCAGAAGAGGGGACG 59.485 63.158 0.00 0.00 0.00 4.79
2973 5946 1.625818 GTTTCCCTCCTGAGCAGAAGA 59.374 52.381 0.00 0.00 0.00 2.87
3010 5983 0.396974 AGGCACCTCCAAAACAGCAA 60.397 50.000 0.00 0.00 37.29 3.91
3016 5989 0.538057 CAGAGCAGGCACCTCCAAAA 60.538 55.000 0.00 0.00 37.29 2.44
3017 5990 1.073722 CAGAGCAGGCACCTCCAAA 59.926 57.895 0.00 0.00 37.29 3.28
3045 6018 3.934391 CTGGGTCCTCGAACGCCAC 62.934 68.421 2.28 0.00 0.00 5.01
3059 6032 2.506957 GGGGTTTGCCAACACTGGG 61.507 63.158 2.58 0.00 43.74 4.45
3080 6762 0.586802 GAACGTTCCAGCAAGTCACC 59.413 55.000 17.68 0.00 0.00 4.02
3095 6777 1.461888 GGATTGTTCAAGCGTCGAACG 60.462 52.381 0.00 0.00 44.63 3.95
3102 6784 1.906994 TTCGCCGGATTGTTCAAGCG 61.907 55.000 5.05 9.48 42.77 4.68
3106 6788 1.885560 TCTTTTCGCCGGATTGTTCA 58.114 45.000 5.05 0.00 0.00 3.18
3119 6801 2.739379 CTCCTTCACCGCTCTTCTTTTC 59.261 50.000 0.00 0.00 0.00 2.29
3138 6820 6.738832 AGGCTTAACCGAATCTAAAAACTC 57.261 37.500 0.00 0.00 46.52 3.01
3170 6852 4.107622 CAAGTTTGGTCTCTTGCAAACAG 58.892 43.478 0.00 0.00 39.27 3.16
3194 6876 6.749118 GCAATAACAGGAAAGCATCTACAAAG 59.251 38.462 0.00 0.00 0.00 2.77
3195 6877 6.208402 TGCAATAACAGGAAAGCATCTACAAA 59.792 34.615 0.00 0.00 0.00 2.83
3209 6891 2.995258 GCCACAACATTGCAATAACAGG 59.005 45.455 12.53 11.49 0.00 4.00
3236 6918 5.014202 GGTAAGTAGGAAAAGCCATCCAAA 58.986 41.667 3.20 0.00 39.55 3.28
3242 6924 1.339342 GCCGGTAAGTAGGAAAAGCCA 60.339 52.381 1.90 0.00 40.02 4.75
3243 6925 1.376543 GCCGGTAAGTAGGAAAAGCC 58.623 55.000 1.90 0.00 0.00 4.35
3244 6926 1.004595 CGCCGGTAAGTAGGAAAAGC 58.995 55.000 1.90 0.00 0.00 3.51
3245 6927 1.205417 TCCGCCGGTAAGTAGGAAAAG 59.795 52.381 1.63 0.00 0.00 2.27
3260 6942 3.213402 CCTCTCGTCTCCTCCGCC 61.213 72.222 0.00 0.00 0.00 6.13
3264 6946 2.351706 ATACCACCTCTCGTCTCCTC 57.648 55.000 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.