Multiple sequence alignment - TraesCS3B01G268300

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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 TraesCS3B01G268300 chr3B 100.000 6454 0 0 1 6454 431577922 431584375 0.000000e+00 11919.0
1 TraesCS3B01G268300 chr3A 94.128 2231 62 18 1596 3793 450009655 450011849 0.000000e+00 3330.0
2 TraesCS3B01G268300 chr3A 96.287 1670 40 8 4169 5822 450011856 450013519 0.000000e+00 2721.0
3 TraesCS3B01G268300 chr3A 94.737 760 20 10 785 1532 450008906 450009657 0.000000e+00 1164.0
4 TraesCS3B01G268300 chr3A 96.574 467 15 1 5985 6451 450013517 450013982 0.000000e+00 773.0
5 TraesCS3B01G268300 chr3A 91.873 283 23 0 127 409 450007372 450007654 4.690000e-106 396.0
6 TraesCS3B01G268300 chr3A 88.344 163 6 5 570 719 450007715 450007877 3.970000e-42 183.0
7 TraesCS3B01G268300 chr3A 97.895 95 2 0 12 106 450007285 450007379 1.440000e-36 165.0
8 TraesCS3B01G268300 chr3A 90.000 60 6 0 2267 2326 568001360 568001301 1.930000e-10 78.7
9 TraesCS3B01G268300 chr3A 88.235 51 4 2 2380 2430 128148999 128148951 6.990000e-05 60.2
10 TraesCS3B01G268300 chr3D 92.175 2198 110 20 2415 4576 332628633 332630804 0.000000e+00 3049.0
11 TraesCS3B01G268300 chr3D 92.087 2022 100 21 12 1987 332626115 332628122 0.000000e+00 2793.0
12 TraesCS3B01G268300 chr3D 96.036 1009 29 8 4580 5584 332631109 332632110 0.000000e+00 1631.0
13 TraesCS3B01G268300 chr3D 90.084 474 31 8 5985 6451 332632773 332633237 9.260000e-168 601.0
14 TraesCS3B01G268300 chr3D 95.390 282 11 1 1987 2268 332628353 332628632 1.280000e-121 448.0
15 TraesCS3B01G268300 chr3D 95.882 170 5 1 5820 5989 556140978 556141145 2.290000e-69 274.0
16 TraesCS3B01G268300 chr3D 92.105 152 7 3 2267 2413 368346006 368346157 6.560000e-50 209.0
17 TraesCS3B01G268300 chr3D 87.640 89 4 5 5527 5609 254362235 254362322 5.330000e-16 97.1
18 TraesCS3B01G268300 chr2B 89.272 261 26 2 6134 6394 520204306 520204564 6.240000e-85 326.0
19 TraesCS3B01G268300 chr2B 85.938 256 33 3 6140 6394 791843865 791844118 2.970000e-68 270.0
20 TraesCS3B01G268300 chr2B 84.279 229 35 1 6166 6394 398011875 398012102 8.420000e-54 222.0
21 TraesCS3B01G268300 chr2B 78.755 273 48 10 4510 4778 215940747 215940481 2.390000e-39 174.0
22 TraesCS3B01G268300 chr7B 88.281 256 28 2 6140 6394 263721358 263721104 8.130000e-79 305.0
23 TraesCS3B01G268300 chr7B 83.913 230 34 3 6166 6394 281024831 281025058 3.920000e-52 217.0
24 TraesCS3B01G268300 chr4D 87.843 255 30 1 6140 6394 271271361 271271108 1.360000e-76 298.0
25 TraesCS3B01G268300 chr7A 94.054 185 5 5 5808 5990 156116015 156115835 6.370000e-70 276.0
26 TraesCS3B01G268300 chr7A 95.808 167 5 1 5820 5986 547092339 547092503 1.070000e-67 268.0
27 TraesCS3B01G268300 chr7A 87.978 183 8 6 2251 2421 187107863 187107683 3.050000e-48 204.0
28 TraesCS3B01G268300 chr7A 90.541 74 5 2 5527 5598 26656615 26656688 5.330000e-16 97.1
29 TraesCS3B01G268300 chr7D 94.886 176 7 1 5811 5986 312574119 312574292 2.290000e-69 274.0
30 TraesCS3B01G268300 chr7D 95.322 171 5 2 5820 5989 363148833 363149001 1.070000e-67 268.0
31 TraesCS3B01G268300 chr7D 92.647 136 8 2 2251 2386 183790248 183790381 1.840000e-45 195.0
32 TraesCS3B01G268300 chr7D 95.000 40 2 0 2380 2419 591456768 591456729 5.400000e-06 63.9
33 TraesCS3B01G268300 chr6A 95.266 169 6 1 5819 5987 458217875 458217709 3.840000e-67 267.0
34 TraesCS3B01G268300 chr5D 95.266 169 6 1 5820 5988 42949560 42949726 3.840000e-67 267.0
35 TraesCS3B01G268300 chr5D 92.021 188 8 5 5820 6005 48983479 48983297 2.310000e-64 257.0
36 TraesCS3B01G268300 chr6D 91.979 187 8 5 5820 6004 318765119 318764938 8.300000e-64 255.0
37 TraesCS3B01G268300 chr6D 95.238 126 6 0 2264 2389 438321898 438321773 3.950000e-47 200.0
38 TraesCS3B01G268300 chr4B 85.217 230 31 3 6166 6394 434166066 434165839 3.890000e-57 233.0
39 TraesCS3B01G268300 chr4B 89.333 150 16 0 2267 2416 447764966 447764817 8.540000e-44 189.0
40 TraesCS3B01G268300 chr5A 91.946 149 10 2 2266 2413 521663063 521662916 2.360000e-49 207.0
41 TraesCS3B01G268300 chr2D 92.754 138 6 4 2251 2386 428554864 428554999 5.110000e-46 196.0
42 TraesCS3B01G268300 chr2D 89.404 151 14 1 2267 2417 317588389 317588537 8.540000e-44 189.0
43 TraesCS3B01G268300 chr4A 84.348 115 18 0 2267 2381 16983030 16983144 5.290000e-21 113.0
44 TraesCS3B01G268300 chrUn 87.356 87 7 3 5527 5609 416910955 416910869 5.330000e-16 97.1
45 TraesCS3B01G268300 chrUn 89.189 74 6 2 5527 5598 286166397 286166470 2.480000e-14 91.6
46 TraesCS3B01G268300 chrUn 86.207 87 8 3 5527 5609 389704419 389704333 2.480000e-14 91.6
47 TraesCS3B01G268300 chr5B 87.356 87 7 3 5527 5609 39572074 39571988 5.330000e-16 97.1
48 TraesCS3B01G268300 chr1A 89.189 74 6 2 5527 5598 404150294 404150367 2.480000e-14 91.6


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G268300 chr3B 431577922 431584375 6453 False 11919.000000 11919 100.000000 1 6454 1 chr3B.!!$F1 6453
1 TraesCS3B01G268300 chr3A 450007285 450013982 6697 False 1247.428571 3330 94.262571 12 6451 7 chr3A.!!$F1 6439
2 TraesCS3B01G268300 chr3D 332626115 332633237 7122 False 1704.400000 3049 93.154400 12 6451 5 chr3D.!!$F4 6439

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
904 1883 1.115467 ATCTACTCCTGAAGGCACGG 58.885 55.000 0.00 0.0 34.44 4.94 F
1325 2314 1.734707 CGAGGCTTACGGTTCATTCGT 60.735 52.381 0.00 0.0 43.64 3.85 F
3070 4313 0.316522 GATGCTCTAGCTCGCCATGA 59.683 55.000 3.26 0.0 42.66 3.07 F
3972 5231 0.179070 GGGTGGCGATCTCTTCCTTC 60.179 60.000 0.00 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2902 4145 0.038892 TCTGCTGTTACGACCCGTTC 60.039 55.000 0.00 0.0 41.54 3.95 R
3184 4427 1.001378 GCTTCAATGCACTTGAACGGT 60.001 47.619 15.74 0.0 46.45 4.83 R
4085 5344 0.530744 CGTTCCATCCCTCTTCGTCA 59.469 55.000 0.00 0.0 0.00 4.35 R
5970 8127 0.178970 TATGTACTCCCTCCGCTCCC 60.179 60.000 0.00 0.0 0.00 4.30 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
83 84 9.702494 CAGAAAAGAGAAAATTGCTAAATTCCT 57.298 29.630 0.00 0.00 34.84 3.36
106 107 5.381184 TTGTTAGCATTTCCATAGGCCTA 57.619 39.130 16.60 16.60 0.00 3.93
127 128 9.672673 GGCCTAATTCATAGTGTTGTGATATAT 57.327 33.333 0.00 0.00 0.00 0.86
171 172 5.488645 TCAAACTTTTGAAGTAACGGGTC 57.511 39.130 1.81 0.00 43.62 4.46
264 265 7.230849 TCCGTATCTGTTTACCTAGTTTTCA 57.769 36.000 0.00 0.00 0.00 2.69
296 297 4.487948 CCATGTGTGTGGTCATTCATTTC 58.512 43.478 0.00 0.00 34.46 2.17
310 311 7.315142 GTCATTCATTTCTGTAGGCAAATTCA 58.685 34.615 0.00 0.00 0.00 2.57
394 395 4.380761 CCAAATCAGACATGGCGATCAAAA 60.381 41.667 6.39 0.00 0.00 2.44
404 405 5.163301 ACATGGCGATCAAAACCTAGACTAT 60.163 40.000 0.00 0.00 0.00 2.12
411 412 6.512903 CGATCAAAACCTAGACTATGAGCGTA 60.513 42.308 10.88 0.00 40.54 4.42
418 419 5.651139 ACCTAGACTATGAGCGTACTTTTGA 59.349 40.000 0.00 0.00 0.00 2.69
423 424 2.080286 TGAGCGTACTTTTGAGAGGC 57.920 50.000 0.00 0.00 0.00 4.70
474 475 5.948162 AGCTCATGGACAAAACTACATGAAT 59.052 36.000 0.00 0.00 46.17 2.57
516 517 7.092137 TCTTTGATTTCCTGTATGATTGCAG 57.908 36.000 0.00 0.00 35.54 4.41
523 524 3.143728 CCTGTATGATTGCAGCATAGCA 58.856 45.455 10.53 0.00 43.99 3.49
541 542 1.451028 AAGCTGCGGATCCTTGCTC 60.451 57.895 18.76 9.00 33.10 4.26
601 602 4.449068 GTGTATCCGCTGGACATAAAGATG 59.551 45.833 0.00 0.00 39.16 2.90
670 682 3.001939 GCCGGATCGTTAATACCACTTTG 59.998 47.826 5.05 0.00 0.00 2.77
807 1785 6.204688 CGCATATTAATACCACCACTTGACAT 59.795 38.462 0.00 0.00 0.00 3.06
904 1883 1.115467 ATCTACTCCTGAAGGCACGG 58.885 55.000 0.00 0.00 34.44 4.94
1065 2044 4.946160 TGTGGTAAATCCTCCATCCTTT 57.054 40.909 0.00 0.00 36.09 3.11
1286 2275 7.012989 CGAGGTTTAGGGATTAGGGTTTTAATG 59.987 40.741 0.00 0.00 0.00 1.90
1325 2314 1.734707 CGAGGCTTACGGTTCATTCGT 60.735 52.381 0.00 0.00 43.64 3.85
1503 2492 7.473366 CCTATGTAGGATATCGTATGTGTGAC 58.527 42.308 8.30 0.00 46.63 3.67
1777 2767 6.542370 ACTGGGTCATGTTAATACAATGCTAC 59.458 38.462 0.00 0.00 37.91 3.58
1937 2927 6.423001 GCATGTTGATTTCTCTTCAGCTTTTT 59.577 34.615 0.00 0.00 0.00 1.94
2074 3302 5.039920 TGACTGCCTATTCATACAATGCT 57.960 39.130 0.00 0.00 0.00 3.79
2075 3303 5.439721 TGACTGCCTATTCATACAATGCTT 58.560 37.500 0.00 0.00 0.00 3.91
2076 3304 5.297527 TGACTGCCTATTCATACAATGCTTG 59.702 40.000 0.00 0.00 0.00 4.01
2112 3341 6.267070 GCAGTATGTACCTTCTGTAGAAGAC 58.733 44.000 20.30 12.90 46.01 3.01
2127 3356 4.189639 AGAAGACACGGTTCTTGGTATC 57.810 45.455 5.58 0.00 35.90 2.24
2221 3450 9.208022 TCTTATGATCGCTTTTATAACCATCTG 57.792 33.333 0.00 0.00 0.00 2.90
2455 3698 4.024387 GCATTCGCGAATTTTACCATAGGA 60.024 41.667 30.71 0.00 0.00 2.94
2618 3861 4.929819 TTTGGCCTTTTTACCAGTTCTC 57.070 40.909 3.32 0.00 37.24 2.87
2779 4022 6.934083 GCCATCAAAGAAGGAACCATTTTTAA 59.066 34.615 0.00 0.00 0.00 1.52
2902 4145 2.872557 CTGCACCATGGCAACGAG 59.127 61.111 13.04 0.00 44.40 4.18
2934 4177 3.996150 ACAGCAGAAAACCATCAGTTG 57.004 42.857 0.00 0.00 39.19 3.16
2936 4179 4.460263 ACAGCAGAAAACCATCAGTTGTA 58.540 39.130 0.00 0.00 39.19 2.41
2956 4199 2.902705 TAAGTTCCACTGACGTGCTT 57.097 45.000 0.00 0.00 39.86 3.91
3070 4313 0.316522 GATGCTCTAGCTCGCCATGA 59.683 55.000 3.26 0.00 42.66 3.07
3077 4320 0.613260 TAGCTCGCCATGACCTTTGT 59.387 50.000 0.00 0.00 0.00 2.83
3182 4425 3.134127 GGTCATGGCTGCGGGTTC 61.134 66.667 0.00 0.00 0.00 3.62
3183 4426 2.359850 GTCATGGCTGCGGGTTCA 60.360 61.111 0.00 0.00 0.00 3.18
3184 4427 1.971167 GTCATGGCTGCGGGTTCAA 60.971 57.895 0.00 0.00 0.00 2.69
3185 4428 1.971167 TCATGGCTGCGGGTTCAAC 60.971 57.895 0.00 0.00 0.00 3.18
3186 4429 2.676471 ATGGCTGCGGGTTCAACC 60.676 61.111 0.00 0.00 37.60 3.77
3341 4584 7.986889 ACCCTATTGAAATGCAATATCCAAAAC 59.013 33.333 0.00 0.00 45.68 2.43
3453 4702 7.095102 CGAACATATGGACATGCTTATGAATCA 60.095 37.037 7.80 0.00 0.00 2.57
3516 4769 2.558359 GTTGAAGTATGCTGCCAAGGTT 59.442 45.455 0.00 0.00 0.00 3.50
3531 4784 2.143876 AGGTTCAAAGTGCTGTGGTT 57.856 45.000 0.00 0.00 0.00 3.67
3701 4959 1.594836 GTTCCGTTGTGGCCACGTA 60.595 57.895 30.07 18.31 37.80 3.57
3706 4964 1.957186 GTTGTGGCCACGTAGCGAA 60.957 57.895 30.07 15.31 0.00 4.70
3788 5046 2.629017 AAAATGATGGCAGGGAAGGT 57.371 45.000 0.00 0.00 0.00 3.50
3793 5051 2.202236 GATGGCAGGGAAGGTGCTGA 62.202 60.000 0.00 0.00 40.97 4.26
3796 5054 1.676967 GCAGGGAAGGTGCTGAAGG 60.677 63.158 0.00 0.00 37.96 3.46
3798 5056 2.361737 GGGAAGGTGCTGAAGGCC 60.362 66.667 0.00 0.00 40.92 5.19
3799 5057 2.759795 GGAAGGTGCTGAAGGCCT 59.240 61.111 0.00 0.00 40.92 5.19
3832 5090 1.228521 TTGGTGCCATGGTGACCAG 60.229 57.895 27.13 0.00 40.81 4.00
3835 5093 2.042831 GTGCCATGGTGACCAGAGC 61.043 63.158 18.67 18.67 36.75 4.09
3859 5117 4.329545 TCAAGGTCCAGCCGGCAC 62.330 66.667 31.54 18.58 43.70 5.01
3900 5158 1.079819 CACGACATGGCGAGTTCCT 60.080 57.895 31.27 0.00 34.83 3.36
3902 5160 1.079819 CGACATGGCGAGTTCCTGT 60.080 57.895 18.41 0.00 0.00 4.00
3907 5165 1.903877 ATGGCGAGTTCCTGTGGGAG 61.904 60.000 0.00 0.00 43.29 4.30
3929 5188 5.880341 AGGCGATACTTTGTTTAATTGCTC 58.120 37.500 0.00 0.00 0.00 4.26
3943 5202 8.461222 TGTTTAATTGCTCGAATCAAATCTGAT 58.539 29.630 4.21 0.00 44.54 2.90
3972 5231 0.179070 GGGTGGCGATCTCTTCCTTC 60.179 60.000 0.00 0.00 0.00 3.46
3974 5233 0.537188 GTGGCGATCTCTTCCTTCCA 59.463 55.000 0.00 0.00 0.00 3.53
3986 5245 3.055530 TCTTCCTTCCAAGAGAGATGTGC 60.056 47.826 0.00 0.00 0.00 4.57
4007 5266 4.009675 GCTTCCAACTGGTGATCATAACA 58.990 43.478 0.00 0.00 36.34 2.41
4010 5269 5.434182 TCCAACTGGTGATCATAACATGA 57.566 39.130 0.00 0.00 39.00 3.07
4013 5272 3.813443 ACTGGTGATCATAACATGAGGC 58.187 45.455 0.00 0.00 43.53 4.70
4018 5277 4.371786 GTGATCATAACATGAGGCGAAGA 58.628 43.478 0.00 0.00 43.53 2.87
4025 5284 4.756084 AACATGAGGCGAAGAAAAAGAG 57.244 40.909 0.00 0.00 0.00 2.85
4039 5298 8.345565 CGAAGAAAAAGAGGAGAAAATGAAAGA 58.654 33.333 0.00 0.00 0.00 2.52
4118 5377 1.770061 TGGAACGGGGAACACTAAGTT 59.230 47.619 0.00 0.00 44.93 2.66
4120 5379 2.810274 GGAACGGGGAACACTAAGTTTC 59.190 50.000 0.00 0.00 41.51 2.78
4124 5383 5.294734 ACGGGGAACACTAAGTTTCTTTA 57.705 39.130 0.00 0.00 41.51 1.85
4125 5384 5.303165 ACGGGGAACACTAAGTTTCTTTAG 58.697 41.667 0.00 0.00 41.51 1.85
4126 5385 5.070847 ACGGGGAACACTAAGTTTCTTTAGA 59.929 40.000 0.21 0.00 41.51 2.10
4127 5386 5.407691 CGGGGAACACTAAGTTTCTTTAGAC 59.592 44.000 0.21 0.00 41.51 2.59
4128 5387 6.293698 GGGGAACACTAAGTTTCTTTAGACA 58.706 40.000 0.21 0.00 41.51 3.41
4388 5662 5.804692 TCGAAAAGTGTTGAGCTGTTTTA 57.195 34.783 0.00 0.00 0.00 1.52
4389 5663 6.184580 TCGAAAAGTGTTGAGCTGTTTTAA 57.815 33.333 0.00 0.00 0.00 1.52
4448 5724 5.063204 TCACTTGTTTGTTGATTCCGATCT 58.937 37.500 0.00 0.00 33.28 2.75
4490 5772 2.091102 TAGCCGCCCCGTTATGTAGC 62.091 60.000 0.00 0.00 0.00 3.58
4551 5833 9.691362 GTTGTAACAATTTGTCAAATACTGGAT 57.309 29.630 11.18 4.19 0.00 3.41
4576 5858 5.011431 GCGGGTGTTATACTTAAGTAGGGAT 59.989 44.000 19.58 7.54 33.52 3.85
4919 6505 2.687700 TTGTGCCAAACTGTTGCATT 57.312 40.000 8.52 0.00 33.01 3.56
5267 6853 8.980143 ATCGTGTTTTTCTTTCTCTTTTGAAA 57.020 26.923 0.00 0.00 35.07 2.69
5313 6899 9.874205 ATGTTGTGCTTGTTAATTGCTTATATT 57.126 25.926 0.00 0.00 0.00 1.28
5502 7088 0.910566 TATAACGTGGGGTGGCACCT 60.911 55.000 33.87 17.13 38.64 4.00
5590 7176 7.338449 ACCATCATAGTGTTAAAAACGCCTTAT 59.662 33.333 0.00 0.00 42.76 1.73
5623 7211 9.845214 ATAGAGGGAGTAATATATGACCAGTTT 57.155 33.333 0.00 0.00 0.00 2.66
5659 7247 2.161030 TGCATTGCACTGTGCTGAATA 58.839 42.857 30.43 9.89 45.31 1.75
5714 7302 3.853307 GCATTTGTCAACAGTGCACCTAC 60.853 47.826 14.63 5.50 38.41 3.18
5715 7303 1.577468 TTGTCAACAGTGCACCTACG 58.423 50.000 14.63 2.17 0.00 3.51
5720 7308 1.460743 CAACAGTGCACCTACGTCATG 59.539 52.381 14.63 4.99 0.00 3.07
5747 7335 4.012374 CTGCATAAGGTGAACAACAGGAT 58.988 43.478 0.00 0.00 0.00 3.24
5819 7976 3.315470 TGAGTCGCGAATACATAGCTTCT 59.685 43.478 12.06 0.00 0.00 2.85
5820 7977 4.514066 TGAGTCGCGAATACATAGCTTCTA 59.486 41.667 12.06 0.00 0.00 2.10
5821 7978 4.785417 AGTCGCGAATACATAGCTTCTAC 58.215 43.478 12.06 0.00 0.00 2.59
5822 7979 4.515944 AGTCGCGAATACATAGCTTCTACT 59.484 41.667 12.06 0.00 0.00 2.57
5823 7980 5.008811 AGTCGCGAATACATAGCTTCTACTT 59.991 40.000 12.06 0.00 0.00 2.24
5824 7981 5.340138 GTCGCGAATACATAGCTTCTACTTC 59.660 44.000 12.06 0.00 0.00 3.01
5825 7982 4.617645 CGCGAATACATAGCTTCTACTTCC 59.382 45.833 0.00 0.00 0.00 3.46
5826 7983 5.563085 CGCGAATACATAGCTTCTACTTCCT 60.563 44.000 0.00 0.00 0.00 3.36
5827 7984 5.859648 GCGAATACATAGCTTCTACTTCCTC 59.140 44.000 0.00 0.00 0.00 3.71
5828 7985 6.383415 CGAATACATAGCTTCTACTTCCTCC 58.617 44.000 0.00 0.00 0.00 4.30
5829 7986 5.968528 ATACATAGCTTCTACTTCCTCCG 57.031 43.478 0.00 0.00 0.00 4.63
5830 7987 3.633418 ACATAGCTTCTACTTCCTCCGT 58.367 45.455 0.00 0.00 0.00 4.69
5831 7988 4.024670 ACATAGCTTCTACTTCCTCCGTT 58.975 43.478 0.00 0.00 0.00 4.44
5832 7989 4.098196 ACATAGCTTCTACTTCCTCCGTTC 59.902 45.833 0.00 0.00 0.00 3.95
5833 7990 1.826096 AGCTTCTACTTCCTCCGTTCC 59.174 52.381 0.00 0.00 0.00 3.62
5834 7991 1.826096 GCTTCTACTTCCTCCGTTCCT 59.174 52.381 0.00 0.00 0.00 3.36
5835 7992 3.022406 GCTTCTACTTCCTCCGTTCCTA 58.978 50.000 0.00 0.00 0.00 2.94
5836 7993 3.446516 GCTTCTACTTCCTCCGTTCCTAA 59.553 47.826 0.00 0.00 0.00 2.69
5837 7994 4.081807 GCTTCTACTTCCTCCGTTCCTAAA 60.082 45.833 0.00 0.00 0.00 1.85
5838 7995 5.395435 GCTTCTACTTCCTCCGTTCCTAAAT 60.395 44.000 0.00 0.00 0.00 1.40
5839 7996 6.183360 GCTTCTACTTCCTCCGTTCCTAAATA 60.183 42.308 0.00 0.00 0.00 1.40
5840 7997 7.471679 GCTTCTACTTCCTCCGTTCCTAAATAT 60.472 40.741 0.00 0.00 0.00 1.28
5841 7998 9.075678 CTTCTACTTCCTCCGTTCCTAAATATA 57.924 37.037 0.00 0.00 0.00 0.86
5842 7999 9.425248 TTCTACTTCCTCCGTTCCTAAATATAA 57.575 33.333 0.00 0.00 0.00 0.98
5843 8000 9.075678 TCTACTTCCTCCGTTCCTAAATATAAG 57.924 37.037 0.00 0.00 0.00 1.73
5844 8001 7.672122 ACTTCCTCCGTTCCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
5845 8002 7.724287 ACTTCCTCCGTTCCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
5846 8003 7.564292 ACTTCCTCCGTTCCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
5847 8004 7.909485 TCCTCCGTTCCTAAATATAAGTCTT 57.091 36.000 0.00 0.00 0.00 3.01
5848 8005 8.315220 TCCTCCGTTCCTAAATATAAGTCTTT 57.685 34.615 0.00 0.00 0.00 2.52
5849 8006 8.765517 TCCTCCGTTCCTAAATATAAGTCTTTT 58.234 33.333 0.00 0.00 0.00 2.27
5850 8007 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
5867 8024 9.750125 AAGTCTTTTTAGACATTTCAAATGGAC 57.250 29.630 14.70 8.92 41.02 4.02
5868 8025 9.136323 AGTCTTTTTAGACATTTCAAATGGACT 57.864 29.630 14.70 14.18 41.02 3.85
5878 8035 8.964420 ACATTTCAAATGGACTACAAAATACG 57.036 30.769 14.70 0.00 0.00 3.06
5879 8036 8.026607 ACATTTCAAATGGACTACAAAATACGG 58.973 33.333 14.70 0.00 0.00 4.02
5880 8037 7.747155 TTTCAAATGGACTACAAAATACGGA 57.253 32.000 0.00 0.00 0.00 4.69
5881 8038 7.931578 TTCAAATGGACTACAAAATACGGAT 57.068 32.000 0.00 0.00 0.00 4.18
5882 8039 7.315247 TCAAATGGACTACAAAATACGGATG 57.685 36.000 0.00 0.00 0.00 3.51
5883 8040 6.882140 TCAAATGGACTACAAAATACGGATGT 59.118 34.615 0.00 0.00 0.00 3.06
5884 8041 8.041919 TCAAATGGACTACAAAATACGGATGTA 58.958 33.333 0.00 0.00 34.45 2.29
5885 8042 8.836413 CAAATGGACTACAAAATACGGATGTAT 58.164 33.333 0.00 0.00 43.14 2.29
5886 8043 7.962964 ATGGACTACAAAATACGGATGTATG 57.037 36.000 0.00 0.00 40.42 2.39
5887 8044 6.880484 TGGACTACAAAATACGGATGTATGT 58.120 36.000 0.00 0.00 40.42 2.29
5888 8045 8.009622 TGGACTACAAAATACGGATGTATGTA 57.990 34.615 0.00 0.00 40.42 2.29
5889 8046 8.139350 TGGACTACAAAATACGGATGTATGTAG 58.861 37.037 18.90 18.90 42.27 2.74
5890 8047 8.355169 GGACTACAAAATACGGATGTATGTAGA 58.645 37.037 23.91 0.92 40.69 2.59
5891 8048 9.178427 GACTACAAAATACGGATGTATGTAGAC 57.822 37.037 23.91 17.69 40.69 2.59
5892 8049 8.689061 ACTACAAAATACGGATGTATGTAGACA 58.311 33.333 23.91 0.00 40.69 3.41
5893 8050 9.692749 CTACAAAATACGGATGTATGTAGACAT 57.307 33.333 16.93 0.08 40.69 3.06
5924 8081 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
5925 8082 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
5926 8083 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
5927 8084 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
5928 8085 3.438087 AGATTCACTCATTTTGCTCCGTG 59.562 43.478 0.00 0.00 0.00 4.94
5929 8086 2.254546 TCACTCATTTTGCTCCGTGT 57.745 45.000 0.00 0.00 0.00 4.49
5930 8087 1.872952 TCACTCATTTTGCTCCGTGTG 59.127 47.619 0.00 0.00 0.00 3.82
5931 8088 1.603802 CACTCATTTTGCTCCGTGTGT 59.396 47.619 0.00 0.00 0.00 3.72
5932 8089 2.805671 CACTCATTTTGCTCCGTGTGTA 59.194 45.455 0.00 0.00 0.00 2.90
5933 8090 3.067106 ACTCATTTTGCTCCGTGTGTAG 58.933 45.455 0.00 0.00 0.00 2.74
5934 8091 3.067106 CTCATTTTGCTCCGTGTGTAGT 58.933 45.455 0.00 0.00 0.00 2.73
5935 8092 3.064207 TCATTTTGCTCCGTGTGTAGTC 58.936 45.455 0.00 0.00 0.00 2.59
5936 8093 2.605837 TTTTGCTCCGTGTGTAGTCA 57.394 45.000 0.00 0.00 0.00 3.41
5937 8094 1.860676 TTTGCTCCGTGTGTAGTCAC 58.139 50.000 0.00 0.00 44.08 3.67
5938 8095 1.037493 TTGCTCCGTGTGTAGTCACT 58.963 50.000 0.00 0.00 44.14 3.41
5939 8096 1.037493 TGCTCCGTGTGTAGTCACTT 58.963 50.000 0.00 0.00 44.14 3.16
5940 8097 1.269569 TGCTCCGTGTGTAGTCACTTG 60.270 52.381 0.00 0.00 44.14 3.16
5941 8098 1.269621 GCTCCGTGTGTAGTCACTTGT 60.270 52.381 0.00 0.00 44.14 3.16
5942 8099 2.802057 GCTCCGTGTGTAGTCACTTGTT 60.802 50.000 0.00 0.00 44.14 2.83
5943 8100 2.794910 CTCCGTGTGTAGTCACTTGTTG 59.205 50.000 0.00 0.00 44.14 3.33
5944 8101 1.864711 CCGTGTGTAGTCACTTGTTGG 59.135 52.381 0.00 0.00 44.14 3.77
5945 8102 2.482316 CCGTGTGTAGTCACTTGTTGGA 60.482 50.000 0.00 0.00 44.14 3.53
5946 8103 3.191669 CGTGTGTAGTCACTTGTTGGAA 58.808 45.455 0.00 0.00 44.14 3.53
5947 8104 3.807622 CGTGTGTAGTCACTTGTTGGAAT 59.192 43.478 0.00 0.00 44.14 3.01
5948 8105 4.084537 CGTGTGTAGTCACTTGTTGGAATC 60.085 45.833 0.00 0.00 44.14 2.52
5949 8106 5.057149 GTGTGTAGTCACTTGTTGGAATCT 58.943 41.667 0.00 0.00 44.14 2.40
5950 8107 5.177696 GTGTGTAGTCACTTGTTGGAATCTC 59.822 44.000 0.00 0.00 44.14 2.75
5951 8108 5.070446 TGTGTAGTCACTTGTTGGAATCTCT 59.930 40.000 0.00 0.00 44.14 3.10
5952 8109 6.266786 TGTGTAGTCACTTGTTGGAATCTCTA 59.733 38.462 0.00 0.00 44.14 2.43
5953 8110 7.152645 GTGTAGTCACTTGTTGGAATCTCTAA 58.847 38.462 0.00 0.00 40.98 2.10
5954 8111 7.656137 GTGTAGTCACTTGTTGGAATCTCTAAA 59.344 37.037 0.00 0.00 40.98 1.85
5955 8112 8.208224 TGTAGTCACTTGTTGGAATCTCTAAAA 58.792 33.333 0.00 0.00 0.00 1.52
5956 8113 9.052759 GTAGTCACTTGTTGGAATCTCTAAAAA 57.947 33.333 0.00 0.00 0.00 1.94
5957 8114 8.159344 AGTCACTTGTTGGAATCTCTAAAAAG 57.841 34.615 2.17 2.17 37.94 2.27
5958 8115 7.993183 AGTCACTTGTTGGAATCTCTAAAAAGA 59.007 33.333 9.03 0.00 35.06 2.52
5959 8116 8.070769 GTCACTTGTTGGAATCTCTAAAAAGAC 58.929 37.037 9.03 0.00 35.06 3.01
5960 8117 7.993183 TCACTTGTTGGAATCTCTAAAAAGACT 59.007 33.333 9.03 0.00 35.06 3.24
5961 8118 8.624776 CACTTGTTGGAATCTCTAAAAAGACTT 58.375 33.333 9.03 0.00 35.06 3.01
5962 8119 9.847224 ACTTGTTGGAATCTCTAAAAAGACTTA 57.153 29.630 9.03 0.00 35.06 2.24
5975 8132 9.174166 TCTAAAAAGACTTATACATTTGGGAGC 57.826 33.333 0.00 0.00 0.00 4.70
5976 8133 6.436843 AAAAGACTTATACATTTGGGAGCG 57.563 37.500 0.00 0.00 0.00 5.03
5977 8134 4.073293 AGACTTATACATTTGGGAGCGG 57.927 45.455 0.00 0.00 0.00 5.52
5978 8135 3.709653 AGACTTATACATTTGGGAGCGGA 59.290 43.478 0.00 0.00 0.00 5.54
5979 8136 4.058817 GACTTATACATTTGGGAGCGGAG 58.941 47.826 0.00 0.00 0.00 4.63
5980 8137 3.181454 ACTTATACATTTGGGAGCGGAGG 60.181 47.826 0.00 0.00 0.00 4.30
5981 8138 0.474184 ATACATTTGGGAGCGGAGGG 59.526 55.000 0.00 0.00 0.00 4.30
5982 8139 0.619255 TACATTTGGGAGCGGAGGGA 60.619 55.000 0.00 0.00 0.00 4.20
5983 8140 1.153086 CATTTGGGAGCGGAGGGAG 60.153 63.158 0.00 0.00 0.00 4.30
6113 8272 6.074088 CCGAGACATAACTATTGCTTCATCAC 60.074 42.308 0.00 0.00 0.00 3.06
6286 8449 5.623264 TCTGAATTATTGTTTGTCAAACGCG 59.377 36.000 20.63 3.53 44.28 6.01
6322 8485 4.521146 CAACTGGAAAGATGGCTAGTCAT 58.479 43.478 10.24 10.24 0.00 3.06
6337 8500 5.409826 GGCTAGTCATTATCATGCACCTTAC 59.590 44.000 0.00 0.00 0.00 2.34
6437 8600 2.918968 GCAACCGGTTGATTGGTAAACG 60.919 50.000 43.76 18.50 42.93 3.60
6451 8614 3.995705 TGGTAAACGTTCTAAATCACCGG 59.004 43.478 0.00 0.00 0.00 5.28
6452 8615 3.371898 GGTAAACGTTCTAAATCACCGGG 59.628 47.826 6.32 0.00 0.00 5.73
6453 8616 2.845363 AACGTTCTAAATCACCGGGT 57.155 45.000 6.32 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.171630 AGTCTTGGTATGTAGGAGTAGTTTG 57.828 40.000 0.00 0.00 0.00 2.93
1 2 7.793948 AAGTCTTGGTATGTAGGAGTAGTTT 57.206 36.000 0.00 0.00 0.00 2.66
2 3 7.793948 AAAGTCTTGGTATGTAGGAGTAGTT 57.206 36.000 0.00 0.00 0.00 2.24
3 4 7.341512 GGTAAAGTCTTGGTATGTAGGAGTAGT 59.658 40.741 0.00 0.00 0.00 2.73
4 5 7.201893 GGGTAAAGTCTTGGTATGTAGGAGTAG 60.202 44.444 0.00 0.00 0.00 2.57
5 6 6.608808 GGGTAAAGTCTTGGTATGTAGGAGTA 59.391 42.308 0.00 0.00 0.00 2.59
6 7 5.424573 GGGTAAAGTCTTGGTATGTAGGAGT 59.575 44.000 0.00 0.00 0.00 3.85
7 8 5.424252 TGGGTAAAGTCTTGGTATGTAGGAG 59.576 44.000 0.00 0.00 0.00 3.69
8 9 5.343715 TGGGTAAAGTCTTGGTATGTAGGA 58.656 41.667 0.00 0.00 0.00 2.94
9 10 5.424252 TCTGGGTAAAGTCTTGGTATGTAGG 59.576 44.000 0.00 0.00 0.00 3.18
10 11 6.540438 TCTGGGTAAAGTCTTGGTATGTAG 57.460 41.667 0.00 0.00 0.00 2.74
83 84 4.609301 AGGCCTATGGAAATGCTAACAAA 58.391 39.130 1.29 0.00 0.00 2.83
106 107 8.796475 GGCCAATATATCACAACACTATGAATT 58.204 33.333 0.00 0.00 0.00 2.17
152 153 3.795877 TCGACCCGTTACTTCAAAAGTT 58.204 40.909 0.00 0.00 42.81 2.66
167 168 1.808411 TTGAACTCATGCTTCGACCC 58.192 50.000 0.00 0.00 0.00 4.46
171 172 5.575957 AGCATTTATTGAACTCATGCTTCG 58.424 37.500 0.00 0.00 40.49 3.79
207 208 7.987458 GGAGATGACCATGACAATTTACTTAGA 59.013 37.037 0.00 0.00 0.00 2.10
264 265 0.700564 ACACACATGGGCCAGAAGAT 59.299 50.000 13.78 0.00 0.00 2.40
296 297 9.807649 AATAAAGCTTTATGAATTTGCCTACAG 57.192 29.630 27.99 0.00 33.85 2.74
387 388 5.593010 ACGCTCATAGTCTAGGTTTTGATC 58.407 41.667 0.00 0.00 0.00 2.92
394 395 5.651139 TCAAAAGTACGCTCATAGTCTAGGT 59.349 40.000 0.00 0.00 0.00 3.08
404 405 1.618837 AGCCTCTCAAAAGTACGCTCA 59.381 47.619 0.00 0.00 0.00 4.26
411 412 1.419387 AGCTCACAGCCTCTCAAAAGT 59.581 47.619 0.00 0.00 43.77 2.66
418 419 2.645838 TTTTGAAGCTCACAGCCTCT 57.354 45.000 0.00 0.00 43.77 3.69
423 424 8.356533 ACAAACATTAATTTTGAAGCTCACAG 57.643 30.769 20.36 0.00 37.39 3.66
474 475 5.647658 TCAAAGAACACTCTTCAGCTTTCAA 59.352 36.000 0.00 0.00 41.23 2.69
516 517 1.573436 GATCCGCAGCTTGCTATGC 59.427 57.895 0.00 0.00 42.25 3.14
523 524 1.451028 GAGCAAGGATCCGCAGCTT 60.451 57.895 23.37 11.76 35.36 3.74
601 602 2.399356 GCACTAGCCCTTGCGGAAC 61.399 63.158 0.00 0.00 44.33 3.62
706 718 9.868277 TCTCAAAAAGTGCTAAAAATCTCAAAA 57.132 25.926 0.00 0.00 0.00 2.44
772 1730 7.201750 GGTGGTATTAATATGCGGTCTCAAAAA 60.202 37.037 0.00 0.00 0.00 1.94
781 1739 5.049680 GTCAAGTGGTGGTATTAATATGCGG 60.050 44.000 0.00 0.00 0.00 5.69
782 1740 5.525745 TGTCAAGTGGTGGTATTAATATGCG 59.474 40.000 0.00 0.00 0.00 4.73
784 1742 7.719193 TCCATGTCAAGTGGTGGTATTAATATG 59.281 37.037 0.00 0.00 37.96 1.78
785 1743 7.811282 TCCATGTCAAGTGGTGGTATTAATAT 58.189 34.615 0.00 0.00 37.96 1.28
787 1745 6.073447 TCCATGTCAAGTGGTGGTATTAAT 57.927 37.500 0.00 0.00 37.96 1.40
807 1785 1.774217 AACTGTGAGGCCCCTTCCA 60.774 57.895 0.00 0.00 0.00 3.53
850 1829 2.047655 TCGAAAACGATGGCGCCT 60.048 55.556 29.70 13.55 42.48 5.52
904 1883 2.041115 GCTTCTTCCTTCCGGTGCC 61.041 63.158 0.00 0.00 0.00 5.01
1065 2044 2.909006 GAGATGCTGGGATATCCAAGGA 59.091 50.000 25.03 23.41 46.51 3.36
1095 2074 1.097232 TTAGTCGAAATCCGCGGAGA 58.903 50.000 33.87 21.88 38.37 3.71
1257 2246 3.043418 CCCTAATCCCTAAACCTCGGAA 58.957 50.000 0.00 0.00 0.00 4.30
1286 2275 1.546923 CGTTACCCAAAATGAACCCCC 59.453 52.381 0.00 0.00 0.00 5.40
1325 2314 4.113815 CAATCCTGCGAGCCCCCA 62.114 66.667 0.00 0.00 0.00 4.96
1497 2486 6.545504 TTCAAGCAGAGATAAAAGTCACAC 57.454 37.500 0.00 0.00 0.00 3.82
1503 2492 6.798959 CGGTTTCTTTCAAGCAGAGATAAAAG 59.201 38.462 0.00 0.00 0.00 2.27
1555 2545 6.966534 ACCTGTTCAAGAATTTCACATTCT 57.033 33.333 0.00 0.00 39.82 2.40
1573 2563 7.338710 ACAATATACAAAGTGAGCATACCTGT 58.661 34.615 0.00 0.00 0.00 4.00
1624 2614 9.066892 AGCATGAAGTGTGAGAAAAATTAGTTA 57.933 29.630 0.00 0.00 0.00 2.24
1754 2744 5.525745 CGTAGCATTGTATTAACATGACCCA 59.474 40.000 0.00 0.00 34.97 4.51
1777 2767 0.167470 CATCAGTGCTGGAAGTTGCG 59.833 55.000 0.00 0.00 35.30 4.85
2028 3256 4.191544 TGAAACAGAACACAAGGAGACTG 58.808 43.478 0.00 0.00 42.68 3.51
2112 3341 3.498927 ACTACGATACCAAGAACCGTG 57.501 47.619 0.00 0.00 35.05 4.94
2127 3356 2.828877 TCTGGTTTGGTGTCAACTACG 58.171 47.619 0.00 0.00 31.78 3.51
2221 3450 8.547173 AGGGAGGATGTCATCAGATTTATAATC 58.453 37.037 14.72 0.00 0.00 1.75
2389 3632 6.041751 ACACTCCCTCCGTTCCTAAATATAAG 59.958 42.308 0.00 0.00 0.00 1.73
2392 3635 4.296056 ACACTCCCTCCGTTCCTAAATAT 58.704 43.478 0.00 0.00 0.00 1.28
2455 3698 3.350219 AATTATGCTTCTGGTCACCGT 57.650 42.857 0.00 0.00 0.00 4.83
2505 3748 6.754193 TCCATAAGAACACATCATACGCATA 58.246 36.000 0.00 0.00 0.00 3.14
2618 3861 4.651778 TCCTTGTACCACCTTCAAATGAG 58.348 43.478 0.00 0.00 0.00 2.90
2739 3982 5.920193 TTGATGGCCAATAAAGGAAGAAG 57.080 39.130 10.96 0.00 0.00 2.85
2744 3987 4.711355 CCTTCTTTGATGGCCAATAAAGGA 59.289 41.667 29.70 24.86 42.99 3.36
2779 4022 5.365619 CACGGGCATTTTCCTAGTAACTAT 58.634 41.667 0.00 0.00 0.00 2.12
2902 4145 0.038892 TCTGCTGTTACGACCCGTTC 60.039 55.000 0.00 0.00 41.54 3.95
2956 4199 1.205655 CGAAGGAAGATGAGGAGCACA 59.794 52.381 0.00 0.00 0.00 4.57
3070 4313 1.963515 GAATGGCCAACTGACAAAGGT 59.036 47.619 10.96 0.00 0.00 3.50
3077 4320 3.430862 GCGCGAATGGCCAACTGA 61.431 61.111 10.96 0.00 38.94 3.41
3180 4423 2.685388 TCAATGCACTTGAACGGTTGAA 59.315 40.909 0.00 0.00 40.92 2.69
3181 4424 2.293170 TCAATGCACTTGAACGGTTGA 58.707 42.857 0.00 0.29 40.92 3.18
3182 4425 2.772568 TCAATGCACTTGAACGGTTG 57.227 45.000 0.00 0.00 40.92 3.77
3183 4426 2.543653 GCTTCAATGCACTTGAACGGTT 60.544 45.455 15.74 0.00 46.45 4.44
3184 4427 1.001378 GCTTCAATGCACTTGAACGGT 60.001 47.619 15.74 0.00 46.45 4.83
3185 4428 1.001487 TGCTTCAATGCACTTGAACGG 60.001 47.619 15.74 10.84 46.45 4.44
3186 4429 2.404265 TGCTTCAATGCACTTGAACG 57.596 45.000 15.74 13.48 46.45 3.95
3187 4430 6.956299 ATAAATGCTTCAATGCACTTGAAC 57.044 33.333 15.74 13.61 46.45 3.18
3223 4466 2.204029 TGTTTAGACCCCGGGCCT 60.204 61.111 17.73 16.93 0.00 5.19
3453 4702 0.620556 AGGACAATGCACGGAAGGAT 59.379 50.000 0.00 0.00 0.00 3.24
3516 4769 1.064758 ACTGGAACCACAGCACTTTGA 60.065 47.619 0.00 0.00 42.21 2.69
3552 4805 2.358125 CGATGGGCGTGTTCCACA 60.358 61.111 0.00 0.00 37.08 4.17
3670 4926 1.204146 ACGGAACCTGCAGGATATGT 58.796 50.000 39.19 25.87 38.94 2.29
3673 4929 0.981183 ACAACGGAACCTGCAGGATA 59.019 50.000 39.19 0.00 38.94 2.59
3678 4934 2.904866 GCCACAACGGAACCTGCA 60.905 61.111 0.00 0.00 36.56 4.41
3701 4959 0.532417 GATCTGCATGGAGCTTCGCT 60.532 55.000 9.76 0.00 45.94 4.93
3706 4964 0.104487 CACGAGATCTGCATGGAGCT 59.896 55.000 9.76 0.00 45.94 4.09
3832 5090 2.035442 GGACCTTGACTTGCCGCTC 61.035 63.158 0.00 0.00 0.00 5.03
3835 5093 2.328099 GCTGGACCTTGACTTGCCG 61.328 63.158 0.00 0.00 0.00 5.69
3884 5142 1.079819 ACAGGAACTCGCCATGTCG 60.080 57.895 0.00 0.00 34.60 4.35
3900 5158 0.981183 ACAAAGTATCGCCTCCCACA 59.019 50.000 0.00 0.00 0.00 4.17
3902 5160 2.871096 AAACAAAGTATCGCCTCCCA 57.129 45.000 0.00 0.00 0.00 4.37
3907 5165 4.728608 CGAGCAATTAAACAAAGTATCGCC 59.271 41.667 0.00 0.00 0.00 5.54
3929 5188 2.146342 CCCCCGATCAGATTTGATTCG 58.854 52.381 0.00 5.81 44.01 3.34
3972 5231 2.746362 GTTGGAAGCACATCTCTCTTGG 59.254 50.000 0.00 0.00 0.00 3.61
3974 5233 3.558746 CCAGTTGGAAGCACATCTCTCTT 60.559 47.826 0.00 0.00 37.39 2.85
3986 5245 5.882000 TCATGTTATGATCACCAGTTGGAAG 59.118 40.000 4.92 0.00 34.98 3.46
4007 5266 3.261897 TCTCCTCTTTTTCTTCGCCTCAT 59.738 43.478 0.00 0.00 0.00 2.90
4010 5269 3.771577 TTCTCCTCTTTTTCTTCGCCT 57.228 42.857 0.00 0.00 0.00 5.52
4013 5272 8.345565 TCTTTCATTTTCTCCTCTTTTTCTTCG 58.654 33.333 0.00 0.00 0.00 3.79
4018 5277 9.413734 TCTTCTCTTTCATTTTCTCCTCTTTTT 57.586 29.630 0.00 0.00 0.00 1.94
4025 5284 8.791327 AAGATCTCTTCTCTTTCATTTTCTCC 57.209 34.615 0.00 0.00 31.78 3.71
4039 5298 6.658391 CCAAATGAACAGGAAAGATCTCTTCT 59.342 38.462 0.00 0.00 34.61 2.85
4085 5344 0.530744 CGTTCCATCCCTCTTCGTCA 59.469 55.000 0.00 0.00 0.00 4.35
4098 5357 1.426751 ACTTAGTGTTCCCCGTTCCA 58.573 50.000 0.00 0.00 0.00 3.53
4118 5377 7.792364 TGGTAAATCTCTCCTGTCTAAAGAA 57.208 36.000 0.00 0.00 0.00 2.52
4150 5410 9.791801 AAAATAATTAAAGTTCAATGGCCAACT 57.208 25.926 10.96 5.56 34.16 3.16
4361 5635 5.273944 ACAGCTCAACACTTTTCGAAATTC 58.726 37.500 12.12 0.00 0.00 2.17
4388 5662 9.804758 AAAAATGACAAAAATGCATCACAAATT 57.195 22.222 0.00 0.00 0.00 1.82
4416 5692 5.415221 TCAACAAACAAGTGAAATTGACCC 58.585 37.500 0.00 0.00 34.20 4.46
4448 5724 4.594123 TTCAATGTAACGACTGAGGACA 57.406 40.909 0.00 0.00 0.00 4.02
4551 5833 4.099881 CCCTACTTAAGTATAACACCCGCA 59.900 45.833 15.57 0.00 0.00 5.69
4919 6505 6.065374 TGGATAGCAGTACAAGGAAACAAAA 58.935 36.000 0.00 0.00 0.00 2.44
5267 6853 9.723601 ACAACATGCATTAATAATTTCCAAGTT 57.276 25.926 0.00 0.00 0.00 2.66
5313 6899 6.685541 TCACCTACAGGACATAAATAGGGTA 58.314 40.000 1.29 0.00 37.35 3.69
5502 7088 6.605471 ACCAGTACACACTAATGAGAATGA 57.395 37.500 0.00 0.00 32.21 2.57
5578 7164 8.630037 CCCTCTATCAAAATATAAGGCGTTTTT 58.370 33.333 0.00 0.00 0.00 1.94
5623 7211 4.756135 GCAATGCATTTTCCAAGGAGAAAA 59.244 37.500 9.83 2.27 46.63 2.29
5659 7247 4.280174 AGTGAGAACTGCAGCAATCAAAAT 59.720 37.500 15.27 2.55 0.00 1.82
5803 7391 5.774630 AGGAAGTAGAAGCTATGTATTCGC 58.225 41.667 0.00 0.00 0.00 4.70
5819 7976 8.773033 ACTTATATTTAGGAACGGAGGAAGTA 57.227 34.615 0.00 0.00 0.00 2.24
5820 7977 7.564292 AGACTTATATTTAGGAACGGAGGAAGT 59.436 37.037 0.00 0.00 0.00 3.01
5821 7978 7.953752 AGACTTATATTTAGGAACGGAGGAAG 58.046 38.462 0.00 0.00 0.00 3.46
5822 7979 7.909485 AGACTTATATTTAGGAACGGAGGAA 57.091 36.000 0.00 0.00 0.00 3.36
5823 7980 7.909485 AAGACTTATATTTAGGAACGGAGGA 57.091 36.000 0.00 0.00 0.00 3.71
5824 7981 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
5841 7998 9.750125 GTCCATTTGAAATGTCTAAAAAGACTT 57.250 29.630 15.93 0.00 39.41 3.01
5842 7999 9.136323 AGTCCATTTGAAATGTCTAAAAAGACT 57.864 29.630 15.93 14.21 39.41 3.24
5852 8009 9.061610 CGTATTTTGTAGTCCATTTGAAATGTC 57.938 33.333 15.93 9.10 0.00 3.06
5853 8010 8.026607 CCGTATTTTGTAGTCCATTTGAAATGT 58.973 33.333 15.93 1.43 0.00 2.71
5854 8011 8.240682 TCCGTATTTTGTAGTCCATTTGAAATG 58.759 33.333 10.84 10.84 0.00 2.32
5855 8012 8.343168 TCCGTATTTTGTAGTCCATTTGAAAT 57.657 30.769 0.00 0.00 0.00 2.17
5856 8013 7.747155 TCCGTATTTTGTAGTCCATTTGAAA 57.253 32.000 0.00 0.00 0.00 2.69
5857 8014 7.392113 ACATCCGTATTTTGTAGTCCATTTGAA 59.608 33.333 0.00 0.00 0.00 2.69
5858 8015 6.882140 ACATCCGTATTTTGTAGTCCATTTGA 59.118 34.615 0.00 0.00 0.00 2.69
5859 8016 7.083875 ACATCCGTATTTTGTAGTCCATTTG 57.916 36.000 0.00 0.00 0.00 2.32
5860 8017 8.836413 CATACATCCGTATTTTGTAGTCCATTT 58.164 33.333 0.00 0.00 36.11 2.32
5861 8018 7.990886 ACATACATCCGTATTTTGTAGTCCATT 59.009 33.333 0.00 0.00 36.11 3.16
5862 8019 7.506114 ACATACATCCGTATTTTGTAGTCCAT 58.494 34.615 0.00 0.00 36.11 3.41
5863 8020 6.880484 ACATACATCCGTATTTTGTAGTCCA 58.120 36.000 0.00 0.00 36.11 4.02
5864 8021 8.355169 TCTACATACATCCGTATTTTGTAGTCC 58.645 37.037 0.00 0.00 38.60 3.85
5865 8022 9.178427 GTCTACATACATCCGTATTTTGTAGTC 57.822 37.037 0.00 0.00 38.60 2.59
5866 8023 8.689061 TGTCTACATACATCCGTATTTTGTAGT 58.311 33.333 0.00 0.00 38.60 2.73
5867 8024 9.692749 ATGTCTACATACATCCGTATTTTGTAG 57.307 33.333 0.00 0.00 38.71 2.74
5902 8059 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
5903 8060 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
5904 8061 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
5905 8062 4.631377 CACGGAGCAAAATGAGTGAATCTA 59.369 41.667 0.00 0.00 0.00 1.98
5906 8063 3.438087 CACGGAGCAAAATGAGTGAATCT 59.562 43.478 0.00 0.00 0.00 2.40
5907 8064 3.189287 ACACGGAGCAAAATGAGTGAATC 59.811 43.478 0.19 0.00 34.16 2.52
5908 8065 3.058016 CACACGGAGCAAAATGAGTGAAT 60.058 43.478 0.19 0.00 34.16 2.57
5909 8066 2.290367 CACACGGAGCAAAATGAGTGAA 59.710 45.455 0.19 0.00 34.16 3.18
5910 8067 1.872952 CACACGGAGCAAAATGAGTGA 59.127 47.619 0.19 0.00 34.16 3.41
5911 8068 1.603802 ACACACGGAGCAAAATGAGTG 59.396 47.619 0.00 0.00 35.89 3.51
5912 8069 1.967319 ACACACGGAGCAAAATGAGT 58.033 45.000 0.00 0.00 0.00 3.41
5913 8070 3.067106 ACTACACACGGAGCAAAATGAG 58.933 45.455 0.00 0.00 0.00 2.90
5914 8071 3.064207 GACTACACACGGAGCAAAATGA 58.936 45.455 0.00 0.00 0.00 2.57
5915 8072 2.805671 TGACTACACACGGAGCAAAATG 59.194 45.455 0.00 0.00 0.00 2.32
5916 8073 2.806244 GTGACTACACACGGAGCAAAAT 59.194 45.455 0.00 0.00 45.32 1.82
5917 8074 2.206750 GTGACTACACACGGAGCAAAA 58.793 47.619 0.00 0.00 45.32 2.44
5918 8075 1.860676 GTGACTACACACGGAGCAAA 58.139 50.000 0.00 0.00 45.32 3.68
5919 8076 3.580904 GTGACTACACACGGAGCAA 57.419 52.632 0.00 0.00 45.32 3.91
5928 8085 5.542779 AGAGATTCCAACAAGTGACTACAC 58.457 41.667 0.00 0.00 46.24 2.90
5929 8086 5.808366 AGAGATTCCAACAAGTGACTACA 57.192 39.130 0.00 0.00 0.00 2.74
5930 8087 8.603242 TTTTAGAGATTCCAACAAGTGACTAC 57.397 34.615 0.00 0.00 0.00 2.73
5931 8088 9.273016 CTTTTTAGAGATTCCAACAAGTGACTA 57.727 33.333 0.00 0.00 0.00 2.59
5932 8089 7.993183 TCTTTTTAGAGATTCCAACAAGTGACT 59.007 33.333 0.00 0.00 0.00 3.41
5933 8090 8.070769 GTCTTTTTAGAGATTCCAACAAGTGAC 58.929 37.037 0.00 0.00 0.00 3.67
5934 8091 7.993183 AGTCTTTTTAGAGATTCCAACAAGTGA 59.007 33.333 0.00 0.00 0.00 3.41
5935 8092 8.159344 AGTCTTTTTAGAGATTCCAACAAGTG 57.841 34.615 0.00 0.00 0.00 3.16
5936 8093 8.753497 AAGTCTTTTTAGAGATTCCAACAAGT 57.247 30.769 0.00 0.00 0.00 3.16
5949 8106 9.174166 GCTCCCAAATGTATAAGTCTTTTTAGA 57.826 33.333 0.00 0.00 0.00 2.10
5950 8107 8.122952 CGCTCCCAAATGTATAAGTCTTTTTAG 58.877 37.037 0.00 0.00 0.00 1.85
5951 8108 7.066525 CCGCTCCCAAATGTATAAGTCTTTTTA 59.933 37.037 0.00 0.00 0.00 1.52
5952 8109 6.127730 CCGCTCCCAAATGTATAAGTCTTTTT 60.128 38.462 0.00 0.00 0.00 1.94
5953 8110 5.357032 CCGCTCCCAAATGTATAAGTCTTTT 59.643 40.000 0.00 0.00 0.00 2.27
5954 8111 4.881850 CCGCTCCCAAATGTATAAGTCTTT 59.118 41.667 0.00 0.00 0.00 2.52
5955 8112 4.163458 TCCGCTCCCAAATGTATAAGTCTT 59.837 41.667 0.00 0.00 0.00 3.01
5956 8113 3.709653 TCCGCTCCCAAATGTATAAGTCT 59.290 43.478 0.00 0.00 0.00 3.24
5957 8114 4.058817 CTCCGCTCCCAAATGTATAAGTC 58.941 47.826 0.00 0.00 0.00 3.01
5958 8115 3.181454 CCTCCGCTCCCAAATGTATAAGT 60.181 47.826 0.00 0.00 0.00 2.24
5959 8116 3.403038 CCTCCGCTCCCAAATGTATAAG 58.597 50.000 0.00 0.00 0.00 1.73
5960 8117 2.105821 CCCTCCGCTCCCAAATGTATAA 59.894 50.000 0.00 0.00 0.00 0.98
5961 8118 1.697432 CCCTCCGCTCCCAAATGTATA 59.303 52.381 0.00 0.00 0.00 1.47
5962 8119 0.474184 CCCTCCGCTCCCAAATGTAT 59.526 55.000 0.00 0.00 0.00 2.29
5963 8120 0.619255 TCCCTCCGCTCCCAAATGTA 60.619 55.000 0.00 0.00 0.00 2.29
5964 8121 1.915078 CTCCCTCCGCTCCCAAATGT 61.915 60.000 0.00 0.00 0.00 2.71
5965 8122 1.153086 CTCCCTCCGCTCCCAAATG 60.153 63.158 0.00 0.00 0.00 2.32
5966 8123 0.326238 TACTCCCTCCGCTCCCAAAT 60.326 55.000 0.00 0.00 0.00 2.32
5967 8124 1.079621 TACTCCCTCCGCTCCCAAA 59.920 57.895 0.00 0.00 0.00 3.28
5968 8125 1.684734 GTACTCCCTCCGCTCCCAA 60.685 63.158 0.00 0.00 0.00 4.12
5969 8126 2.043248 GTACTCCCTCCGCTCCCA 60.043 66.667 0.00 0.00 0.00 4.37
5970 8127 0.178970 TATGTACTCCCTCCGCTCCC 60.179 60.000 0.00 0.00 0.00 4.30
5971 8128 1.546476 CATATGTACTCCCTCCGCTCC 59.454 57.143 0.00 0.00 0.00 4.70
5972 8129 1.546476 CCATATGTACTCCCTCCGCTC 59.454 57.143 1.24 0.00 0.00 5.03
5973 8130 1.133136 ACCATATGTACTCCCTCCGCT 60.133 52.381 1.24 0.00 0.00 5.52
5974 8131 1.272769 GACCATATGTACTCCCTCCGC 59.727 57.143 1.24 0.00 0.00 5.54
5975 8132 2.558795 CTGACCATATGTACTCCCTCCG 59.441 54.545 1.24 0.00 0.00 4.63
5976 8133 2.300437 GCTGACCATATGTACTCCCTCC 59.700 54.545 1.24 0.00 0.00 4.30
5977 8134 2.965831 TGCTGACCATATGTACTCCCTC 59.034 50.000 1.24 0.00 0.00 4.30
5978 8135 2.968574 CTGCTGACCATATGTACTCCCT 59.031 50.000 1.24 0.00 0.00 4.20
5979 8136 2.548920 GCTGCTGACCATATGTACTCCC 60.549 54.545 1.24 0.00 0.00 4.30
5980 8137 2.103094 TGCTGCTGACCATATGTACTCC 59.897 50.000 0.00 0.00 0.00 3.85
5981 8138 3.459232 TGCTGCTGACCATATGTACTC 57.541 47.619 0.00 0.00 0.00 2.59
5982 8139 3.736720 CATGCTGCTGACCATATGTACT 58.263 45.455 0.00 0.00 0.00 2.73
5983 8140 2.225019 GCATGCTGCTGACCATATGTAC 59.775 50.000 11.37 0.00 40.96 2.90
6113 8272 6.638873 GTGGAATAGATTATGATATCGCTCCG 59.361 42.308 0.00 0.00 30.45 4.63
6304 8467 6.499106 TGATAATGACTAGCCATCTTTCCA 57.501 37.500 0.00 0.00 0.00 3.53
6337 8500 4.566488 GCCATCCCATCTACTATTCCTTGG 60.566 50.000 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.