Multiple sequence alignment - TraesCS3B01G013000

Loading Multiple Alignment...

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 TraesCS3B01G013000 chr3B 100.000 5829 0 0 1 5829 5894990 5889162 0.000000e+00 10765.0
1 TraesCS3B01G013000 chr3B 80.916 131 15 9 5456 5580 75710117 75709991 1.730000e-15 95.3
2 TraesCS3B01G013000 chr3D 91.808 2246 103 22 278 2481 697641 695435 0.000000e+00 3053.0
3 TraesCS3B01G013000 chr3D 89.016 1575 78 37 3134 4638 619612 618063 0.000000e+00 1862.0
4 TraesCS3B01G013000 chr3D 88.056 1080 59 26 3618 4638 693879 692811 0.000000e+00 1216.0
5 TraesCS3B01G013000 chr3D 87.776 679 35 9 2703 3357 694534 693880 0.000000e+00 750.0
6 TraesCS3B01G013000 chr3D 87.952 332 24 7 4965 5289 692599 692277 1.530000e-100 377.0
7 TraesCS3B01G013000 chr3D 96.682 211 6 1 2480 2690 695331 695122 3.340000e-92 350.0
8 TraesCS3B01G013000 chr3D 93.506 231 12 3 4667 4896 618064 617836 2.010000e-89 340.0
9 TraesCS3B01G013000 chr3D 92.704 233 12 3 4667 4896 692812 692582 1.210000e-86 331.0
10 TraesCS3B01G013000 chr3D 83.415 205 33 1 1 204 697976 697772 7.710000e-44 189.0
11 TraesCS3B01G013000 chr3D 79.167 144 18 9 5454 5595 476044383 476044516 8.050000e-14 89.8
12 TraesCS3B01G013000 chr3A 89.931 1440 72 18 1291 2690 8935345 8936751 0.000000e+00 1788.0
13 TraesCS3B01G013000 chr3A 88.090 1377 101 36 3312 4638 8938058 8939421 0.000000e+00 1576.0
14 TraesCS3B01G013000 chr3A 90.917 1112 68 16 212 1302 8933643 8934742 0.000000e+00 1463.0
15 TraesCS3B01G013000 chr3A 86.612 732 45 18 2703 3404 8937480 8938188 0.000000e+00 760.0
16 TraesCS3B01G013000 chr3A 81.735 761 68 31 5093 5828 8939722 8940436 2.360000e-158 569.0
17 TraesCS3B01G013000 chr3A 92.609 230 16 1 4667 4896 8939420 8939648 4.350000e-86 329.0
18 TraesCS3B01G013000 chr3A 98.718 78 0 1 4897 4974 437863630 437863554 2.830000e-28 137.0
19 TraesCS3B01G013000 chr3A 95.238 42 2 0 3137 3178 484106813 484106772 3.770000e-07 67.6
20 TraesCS3B01G013000 chr1A 85.488 441 42 6 4034 4474 67690727 67690309 1.930000e-119 440.0
21 TraesCS3B01G013000 chr1A 85.434 357 39 10 2328 2678 67692610 67692261 5.550000e-95 359.0
22 TraesCS3B01G013000 chr1A 83.140 344 57 1 2703 3045 67691433 67691090 4.390000e-81 313.0
23 TraesCS3B01G013000 chr1A 95.181 83 0 4 4897 4979 91423502 91423424 1.700000e-25 128.0
24 TraesCS3B01G013000 chr6B 85.515 359 37 7 3177 3521 31518006 31517649 1.540000e-95 361.0
25 TraesCS3B01G013000 chr6B 80.952 126 18 6 5442 5566 101708001 101707881 1.730000e-15 95.3
26 TraesCS3B01G013000 chr6B 76.630 184 22 17 5455 5627 282978604 282978777 1.350000e-11 82.4
27 TraesCS3B01G013000 chr1D 84.594 357 41 10 2328 2678 69108687 69108339 5.590000e-90 342.0
28 TraesCS3B01G013000 chr1D 81.977 344 59 3 2703 3045 69107510 69107169 7.390000e-74 289.0
29 TraesCS3B01G013000 chr1D 92.442 172 12 1 4303 4474 69106506 69106336 1.620000e-60 244.0
30 TraesCS3B01G013000 chr1D 74.020 408 62 26 4515 4896 69105723 69105334 6.130000e-25 126.0
31 TraesCS3B01G013000 chr1D 80.992 121 13 6 1562 1675 69109521 69109404 2.890000e-13 87.9
32 TraesCS3B01G013000 chr1B 82.267 344 58 3 2703 3045 110619299 110618958 1.590000e-75 294.0
33 TraesCS3B01G013000 chr1B 80.822 365 44 15 2328 2668 110620469 110620107 4.480000e-66 263.0
34 TraesCS3B01G013000 chr1B 92.442 172 12 1 4303 4474 110618296 110618126 1.620000e-60 244.0
35 TraesCS3B01G013000 chr1B 74.103 390 60 23 4515 4878 110617540 110617166 7.930000e-24 122.0
36 TraesCS3B01G013000 chr5A 77.833 406 61 20 5340 5736 68401064 68400679 2.110000e-54 224.0
37 TraesCS3B01G013000 chr5D 77.694 399 44 27 5453 5829 96425143 96425518 9.900000e-48 202.0
38 TraesCS3B01G013000 chr7B 98.701 77 0 1 4897 4972 255064633 255064709 1.020000e-27 135.0
39 TraesCS3B01G013000 chr7B 97.468 79 0 2 4897 4975 642366577 642366653 3.660000e-27 134.0
40 TraesCS3B01G013000 chr7B 78.488 172 21 15 5446 5604 735521182 735521350 1.340000e-16 99.0
41 TraesCS3B01G013000 chr7B 80.952 126 17 7 5454 5576 336664346 336664467 6.220000e-15 93.5
42 TraesCS3B01G013000 chr7B 83.505 97 13 2 5446 5541 735539164 735539258 2.890000e-13 87.9
43 TraesCS3B01G013000 chr4B 96.341 82 1 2 4897 4977 516506051 516505971 3.660000e-27 134.0
44 TraesCS3B01G013000 chr4B 95.238 84 3 1 4897 4979 106034205 106034122 1.320000e-26 132.0
45 TraesCS3B01G013000 chr4A 98.684 76 0 1 4897 4972 626975378 626975452 3.660000e-27 134.0
46 TraesCS3B01G013000 chr7A 95.238 84 3 1 4897 4980 71013201 71013283 1.320000e-26 132.0
47 TraesCS3B01G013000 chr2A 95.181 83 2 2 4897 4979 530355000 530354920 4.740000e-26 130.0
48 TraesCS3B01G013000 chr4D 94.231 52 2 1 3185 3235 75049119 75049170 1.740000e-10 78.7


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 TraesCS3B01G013000 chr3B 5889162 5894990 5828 True 10765.000000 10765 100.000000 1 5829 1 chr3B.!!$R1 5828
1 TraesCS3B01G013000 chr3D 617836 619612 1776 True 1101.000000 1862 91.261000 3134 4896 2 chr3D.!!$R1 1762
2 TraesCS3B01G013000 chr3D 692277 697976 5699 True 895.142857 3053 89.770429 1 5289 7 chr3D.!!$R2 5288
3 TraesCS3B01G013000 chr3A 8933643 8940436 6793 False 1080.833333 1788 88.315667 212 5828 6 chr3A.!!$F1 5616
4 TraesCS3B01G013000 chr1A 67690309 67692610 2301 True 370.666667 440 84.687333 2328 4474 3 chr1A.!!$R2 2146
5 TraesCS3B01G013000 chr1D 69105334 69109521 4187 True 217.780000 342 82.805000 1562 4896 5 chr1D.!!$R1 3334
6 TraesCS3B01G013000 chr1B 110617166 110620469 3303 True 230.750000 294 82.408500 2328 4878 4 chr1B.!!$R1 2550

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
966 1063 0.179156 GGACGCATGCTGTGATTTGG 60.179 55.0 17.13 0.0 0.00 3.28 F
1339 2052 0.604578 GTGCGACAAGTAGGGGTGTA 59.395 55.0 0.00 0.0 0.00 2.90 F
2103 2858 0.032515 TGCCCTCCTCGGATCTAACA 60.033 55.0 0.00 0.0 33.16 2.41 F
3239 5192 1.094785 CACCCACGGATGATTTGGTC 58.905 55.0 0.00 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2007 2760 0.108585 GGTATCCGCACATGACCCAT 59.891 55.0 0.0 0.0 0.0 4.00 R
2278 3176 0.811281 GGACAACAACAGCATAGCCC 59.189 55.0 0.0 0.0 0.0 5.19 R
3400 5385 0.606401 CCTGTTCGTCATGCCCTTGT 60.606 55.0 0.0 0.0 0.0 3.16 R
4831 7575 0.041312 CAAGTGTGCAGCGTTACCAC 60.041 55.0 0.0 0.0 0.0 4.16 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
33 34 3.209410 CATGCTACTCCCTCCAATTCAC 58.791 50.000 0.00 0.00 0.00 3.18
40 41 5.104259 ACTCCCTCCAATTCACATTACTC 57.896 43.478 0.00 0.00 0.00 2.59
44 45 3.551890 CCTCCAATTCACATTACTCGTCG 59.448 47.826 0.00 0.00 0.00 5.12
46 47 2.030457 CCAATTCACATTACTCGTCGCC 59.970 50.000 0.00 0.00 0.00 5.54
49 50 0.604073 TCACATTACTCGTCGCCCAA 59.396 50.000 0.00 0.00 0.00 4.12
62 63 0.937304 CGCCCAAACGGATGTATCTG 59.063 55.000 0.00 0.00 39.11 2.90
65 66 2.561569 CCCAAACGGATGTATCTGGAC 58.438 52.381 5.74 0.00 37.50 4.02
66 67 2.201732 CCAAACGGATGTATCTGGACG 58.798 52.381 5.74 0.00 37.50 4.79
73 74 5.287226 ACGGATGTATCTGGACGTATTTTC 58.713 41.667 5.74 0.00 37.50 2.29
88 89 6.736123 ACGTATTTTCGTGCTAGATACATCT 58.264 36.000 0.00 0.00 42.56 2.90
93 95 8.668510 ATTTTCGTGCTAGATACATCTGATTT 57.331 30.769 1.88 0.00 37.76 2.17
99 101 4.624882 GCTAGATACATCTGATTTGAGCGG 59.375 45.833 1.88 0.00 37.76 5.52
102 104 1.376543 ACATCTGATTTGAGCGGCAG 58.623 50.000 1.45 0.00 0.00 4.85
108 110 2.016318 TGATTTGAGCGGCAGGTAATG 58.984 47.619 1.45 0.00 0.00 1.90
111 113 0.323302 TTGAGCGGCAGGTAATGTGA 59.677 50.000 1.45 0.00 0.00 3.58
125 127 3.821421 AATGTGAATCGGAGGGAGTAC 57.179 47.619 0.00 0.00 0.00 2.73
166 168 7.152645 AGTGTTCTGCTTTTCGATTTACTAGA 58.847 34.615 0.00 0.00 0.00 2.43
175 177 8.883168 GCTTTTCGATTTACTAGAAAATATGCG 58.117 33.333 0.00 0.00 41.26 4.73
176 178 8.762149 TTTTCGATTTACTAGAAAATATGCGC 57.238 30.769 0.00 0.00 38.47 6.09
178 180 4.776532 CGATTTACTAGAAAATATGCGCGC 59.223 41.667 27.26 27.26 0.00 6.86
179 181 5.388475 CGATTTACTAGAAAATATGCGCGCT 60.388 40.000 33.29 19.73 0.00 5.92
187 189 2.365444 AATATGCGCGCTCGTTGCAG 62.365 55.000 33.29 0.00 42.65 4.41
195 197 2.671070 CTCGTTGCAGTGGGGGAT 59.329 61.111 0.00 0.00 0.00 3.85
198 200 0.693622 TCGTTGCAGTGGGGGATAAA 59.306 50.000 0.00 0.00 0.00 1.40
204 206 1.818674 GCAGTGGGGGATAAACAACAG 59.181 52.381 0.00 0.00 0.00 3.16
206 208 3.496331 CAGTGGGGGATAAACAACAGTT 58.504 45.455 0.00 0.00 0.00 3.16
207 209 3.895041 CAGTGGGGGATAAACAACAGTTT 59.105 43.478 0.00 0.00 38.83 2.66
208 210 4.343814 CAGTGGGGGATAAACAACAGTTTT 59.656 41.667 0.00 0.00 36.83 2.43
209 211 5.536916 CAGTGGGGGATAAACAACAGTTTTA 59.463 40.000 0.00 0.00 36.83 1.52
210 212 6.210584 CAGTGGGGGATAAACAACAGTTTTAT 59.789 38.462 0.00 0.00 36.83 1.40
211 213 6.210584 AGTGGGGGATAAACAACAGTTTTATG 59.789 38.462 0.00 0.00 36.83 1.90
213 215 5.717654 GGGGGATAAACAACAGTTTTATGGA 59.282 40.000 0.00 0.00 36.83 3.41
235 312 6.667414 TGGAATACATGCCTTTAAAATGACCT 59.333 34.615 5.56 0.00 0.00 3.85
236 313 6.980397 GGAATACATGCCTTTAAAATGACCTG 59.020 38.462 5.56 0.00 0.00 4.00
247 324 2.789409 AATGACCTGTAACAGAGGCC 57.211 50.000 0.00 0.00 33.39 5.19
336 422 7.330208 GCAGTTTCAATGCTTTTGACATCTAAT 59.670 33.333 2.65 0.00 40.59 1.73
338 424 9.199982 AGTTTCAATGCTTTTGACATCTAATTG 57.800 29.630 2.65 0.00 0.00 2.32
442 533 2.935849 CAACACCAAACCTTCCAAAAGC 59.064 45.455 0.00 0.00 0.00 3.51
448 539 3.243873 CCAAACCTTCCAAAAGCCTTCTC 60.244 47.826 0.00 0.00 0.00 2.87
475 566 3.411446 TGTGTGTCAAAGCTATTCCCAG 58.589 45.455 0.00 0.00 0.00 4.45
585 676 3.076621 TGGAAGAAGCAATGCACAGTAG 58.923 45.455 8.35 0.00 0.00 2.57
666 757 6.663093 TGGTGATGCAACTTAAAAGGACATAT 59.337 34.615 0.00 0.00 0.00 1.78
667 758 6.974622 GGTGATGCAACTTAAAAGGACATATG 59.025 38.462 0.00 0.00 0.00 1.78
675 766 9.113876 CAACTTAAAAGGACATATGAAAACGAC 57.886 33.333 10.38 0.00 0.00 4.34
686 777 8.445275 ACATATGAAAACGACAAGGCAATATA 57.555 30.769 10.38 0.00 0.00 0.86
704 795 7.761249 GGCAATATAACAAGAGTGCAGATTTTT 59.239 33.333 0.00 0.00 33.66 1.94
734 826 5.426689 AAACAGTTAGCCATGAGATCAGA 57.573 39.130 0.00 0.00 0.00 3.27
811 904 7.545615 GCCTTTCAACTGAGGGTATTTTAATTG 59.454 37.037 0.00 0.00 33.52 2.32
906 1002 5.220854 GCATTTACTAGTGGTAAGCATGGTG 60.221 44.000 5.39 3.19 40.87 4.17
966 1063 0.179156 GGACGCATGCTGTGATTTGG 60.179 55.000 17.13 0.00 0.00 3.28
1060 1157 7.456725 TCCATTTAAAATTGGAGATTTTGCCA 58.543 30.769 6.46 0.00 37.10 4.92
1254 1352 7.247019 GCCACTCAATCTAAACATTTCTCTTC 58.753 38.462 0.00 0.00 0.00 2.87
1339 2052 0.604578 GTGCGACAAGTAGGGGTGTA 59.395 55.000 0.00 0.00 0.00 2.90
1350 2063 2.056223 GGGGTGTACGCTAGCCTCA 61.056 63.158 9.66 3.06 36.02 3.86
1392 2105 3.632145 GGCGGGAATAATGACAAGTGAAT 59.368 43.478 0.00 0.00 0.00 2.57
1393 2106 4.097892 GGCGGGAATAATGACAAGTGAATT 59.902 41.667 0.00 0.00 0.00 2.17
1394 2107 5.394115 GGCGGGAATAATGACAAGTGAATTT 60.394 40.000 0.00 0.00 0.00 1.82
1395 2108 5.743872 GCGGGAATAATGACAAGTGAATTTC 59.256 40.000 0.00 0.00 0.00 2.17
1396 2109 6.404734 GCGGGAATAATGACAAGTGAATTTCT 60.405 38.462 0.00 0.00 0.00 2.52
1397 2110 7.201696 GCGGGAATAATGACAAGTGAATTTCTA 60.202 37.037 0.00 0.00 0.00 2.10
1398 2111 8.673711 CGGGAATAATGACAAGTGAATTTCTAA 58.326 33.333 0.00 0.00 0.00 2.10
1441 2154 9.695526 TCTTGTTGTAAGATTTGATCAAAATGG 57.304 29.630 23.91 5.49 38.64 3.16
1444 2157 7.384660 TGTTGTAAGATTTGATCAAAATGGCAC 59.615 33.333 23.91 17.08 38.64 5.01
1497 2210 7.575414 AGGATATCACTAGTATATGCTTCGG 57.425 40.000 14.70 0.00 35.25 4.30
1750 2498 5.297569 AGAGGAAACATGGCCTATACTTC 57.702 43.478 3.32 0.35 33.84 3.01
1818 2566 4.530946 ACCTTCGACCTTGAATCTTTAGGA 59.469 41.667 0.00 0.00 33.21 2.94
1824 2572 5.331876 ACCTTGAATCTTTAGGAGTCTCG 57.668 43.478 0.00 0.00 39.49 4.04
1825 2573 4.773149 ACCTTGAATCTTTAGGAGTCTCGT 59.227 41.667 0.00 0.00 39.49 4.18
1878 2626 7.630242 TCTATCTAGGAATTGTTTGGCTTTG 57.370 36.000 0.00 0.00 0.00 2.77
1879 2627 7.402054 TCTATCTAGGAATTGTTTGGCTTTGA 58.598 34.615 0.00 0.00 0.00 2.69
1893 2646 5.116069 TGGCTTTGAACTTTATTTCGTCC 57.884 39.130 0.00 0.00 0.00 4.79
1971 2724 1.971357 CTCTACACACACCCTGGTTCT 59.029 52.381 0.00 0.00 0.00 3.01
1981 2734 1.971357 ACCCTGGTTCTGAGTACAGTG 59.029 52.381 0.00 0.00 43.81 3.66
2007 2760 2.121506 ACTTCCTCCCAAGGGGCA 60.122 61.111 5.08 0.00 43.94 5.36
2016 2769 1.759299 CCAAGGGGCATGGGTCATG 60.759 63.158 3.72 3.72 43.91 3.07
2055 2810 4.081862 CGTGGAACCTCCTTAGTATTGACA 60.082 45.833 0.00 0.00 37.46 3.58
2064 2819 4.078805 TCCTTAGTATTGACAGCTCCCCTA 60.079 45.833 0.00 0.00 0.00 3.53
2095 2850 1.342819 CTTATCTTCTGCCCTCCTCGG 59.657 57.143 0.00 0.00 0.00 4.63
2103 2858 0.032515 TGCCCTCCTCGGATCTAACA 60.033 55.000 0.00 0.00 33.16 2.41
2118 2873 8.479689 TCGGATCTAACATGTTAACCTTCATTA 58.520 33.333 18.55 0.00 0.00 1.90
2202 2958 8.928733 AGAAAATCATAATGAAATGCACACAAC 58.071 29.630 0.00 0.00 0.00 3.32
2238 2996 6.917533 AGCATTTGGTAAGAATTGAACTCTG 58.082 36.000 0.00 0.00 0.00 3.35
2276 3174 3.721087 ACAAAGGGCTATGCTACACTT 57.279 42.857 0.00 0.00 0.00 3.16
2278 3176 3.758554 ACAAAGGGCTATGCTACACTTTG 59.241 43.478 14.40 14.40 46.04 2.77
2283 3181 2.158813 GGCTATGCTACACTTTGGGCTA 60.159 50.000 0.00 0.00 0.00 3.93
2288 3186 1.672881 GCTACACTTTGGGCTATGCTG 59.327 52.381 0.00 0.00 0.00 4.41
2316 3214 7.039011 TGTTGTCCACAAGTCTATGAACTAGAT 60.039 37.037 0.00 0.00 33.88 1.98
2384 3332 4.083802 AGACGATGAAGCTTTTTCTTTCCG 60.084 41.667 0.00 0.00 0.00 4.30
2395 3343 5.973565 GCTTTTTCTTTCCGATACATCATGG 59.026 40.000 0.00 0.00 0.00 3.66
2463 3431 4.670896 TCGCTTGACCATAATCTCATGA 57.329 40.909 0.00 0.00 0.00 3.07
2493 3568 8.774586 ACAAATATAACACTTCTGTTCACTCAC 58.225 33.333 0.00 0.00 41.15 3.51
2583 3658 2.286872 GTCACAGAATCTGGGCATCTG 58.713 52.381 15.38 2.69 44.77 2.90
2680 3756 8.447053 TCTTTTGCACATAACCTTTTGTTTTTC 58.553 29.630 0.00 0.00 38.42 2.29
2731 4663 9.063615 ACCAAGATTATAACTGTTCGTTTTCTT 57.936 29.630 0.00 0.00 37.05 2.52
2745 4677 6.880822 TCGTTTTCTTTACACCTCATATCG 57.119 37.500 0.00 0.00 0.00 2.92
2754 4686 3.638860 ACACCTCATATCGTTACTCCCA 58.361 45.455 0.00 0.00 0.00 4.37
2892 4825 1.134098 CAGTGGTATAGGGGGCAACAG 60.134 57.143 0.00 0.00 39.74 3.16
2908 4841 3.068165 GCAACAGGTTCCTAAGCACTTTT 59.932 43.478 0.00 0.00 0.00 2.27
3023 4956 7.750903 GCAGATTATTGAGTTGACCAGTAAAAC 59.249 37.037 0.00 0.00 0.00 2.43
3132 5085 7.191551 TGACCGAGTCTGTAGAAAAATATACG 58.808 38.462 5.77 0.00 33.15 3.06
3175 5128 3.436359 CCAATAGCATTTTGGTTTGGCAC 59.564 43.478 0.00 0.00 39.05 5.01
3186 5139 2.627699 TGGTTTGGCACTCTCAAATTCC 59.372 45.455 0.00 0.00 36.64 3.01
3239 5192 1.094785 CACCCACGGATGATTTGGTC 58.905 55.000 0.00 0.00 0.00 4.02
3418 5403 1.069022 CAACAAGGGCATGACGAACAG 60.069 52.381 0.00 0.00 0.00 3.16
3475 5462 8.600449 ATCGATTCAAATAGATGAAAGAGGTC 57.400 34.615 0.00 0.00 42.22 3.85
3476 5463 7.555965 TCGATTCAAATAGATGAAAGAGGTCA 58.444 34.615 0.00 0.00 42.22 4.02
3534 5521 2.352805 CTCCTGCACTTGGGGGAC 59.647 66.667 0.00 0.00 0.00 4.46
3549 5536 3.414700 GACGGCTGCGGTTGAGTG 61.415 66.667 14.21 0.00 0.00 3.51
3577 5564 2.655364 CGGCGACTCCATACAGCG 60.655 66.667 0.00 0.00 34.01 5.18
3583 5570 2.238847 GACTCCATACAGCGGTGGCA 62.239 60.000 20.20 6.60 43.41 4.92
3612 5599 2.690510 AGGAGGCTTCCCAGCTCC 60.691 66.667 11.97 2.83 46.44 4.70
3765 5764 4.806342 GTAATTCACGAAATATGGCGGT 57.194 40.909 0.00 0.00 0.00 5.68
3792 5791 2.915659 TCCGAGCGTGTCCCTGTT 60.916 61.111 0.00 0.00 0.00 3.16
3842 5862 5.556915 CTTTGTAGTCTGGTGGTCCAATTA 58.443 41.667 0.00 0.00 43.81 1.40
3906 5927 4.928661 AGATGACACGCACTGATAAAAC 57.071 40.909 0.00 0.00 0.00 2.43
4013 6098 5.653507 TCATGCTGATTATTGGTTTTCTGC 58.346 37.500 0.00 0.00 34.71 4.26
4044 6129 7.492669 ACCAACATTATCAGAGACAATAACTCG 59.507 37.037 0.00 0.00 39.12 4.18
4048 6133 7.712639 ACATTATCAGAGACAATAACTCGCATT 59.287 33.333 0.00 0.00 39.12 3.56
4115 6200 1.244019 GGGTGAAGGCGAGCAATGTT 61.244 55.000 0.00 0.00 0.00 2.71
4120 6205 0.890542 AAGGCGAGCAATGTTCTGCA 60.891 50.000 13.26 0.00 45.18 4.41
4174 6259 2.952310 GTCCATCATTAAAGGCTGGACC 59.048 50.000 16.70 0.00 46.57 4.46
4197 6282 1.337541 ACCTCTTTCGGCGGTAAGTTC 60.338 52.381 7.21 0.00 0.00 3.01
4199 6284 0.037046 TCTTTCGGCGGTAAGTTCCC 60.037 55.000 7.21 0.00 0.00 3.97
4281 6389 3.248024 AGGTGATCCTTGACCAGTTGTA 58.752 45.455 3.04 0.00 42.12 2.41
4284 6417 4.246458 GTGATCCTTGACCAGTTGTAGAC 58.754 47.826 0.00 0.00 0.00 2.59
4285 6418 3.901222 TGATCCTTGACCAGTTGTAGACA 59.099 43.478 0.00 0.00 0.00 3.41
4286 6419 4.532126 TGATCCTTGACCAGTTGTAGACAT 59.468 41.667 0.00 0.00 0.00 3.06
4287 6420 4.537135 TCCTTGACCAGTTGTAGACATC 57.463 45.455 0.00 0.00 0.00 3.06
4288 6421 4.160329 TCCTTGACCAGTTGTAGACATCT 58.840 43.478 0.00 0.00 0.00 2.90
4333 6477 7.177041 ACCTTATATTCCGCAGTTTAAACCAAA 59.823 33.333 14.72 3.34 0.00 3.28
4438 6583 4.712829 TGGTTCATCCTAAATCTGGTACGA 59.287 41.667 0.00 0.00 37.07 3.43
4600 7317 3.424829 CCATCAAAACACATTCGTCGGAG 60.425 47.826 0.00 0.00 0.00 4.63
4618 7335 6.566187 CGTCGGAGAGAAACATCGTATCTAAT 60.566 42.308 0.00 0.00 36.95 1.73
4619 7336 7.359849 CGTCGGAGAGAAACATCGTATCTAATA 60.360 40.741 0.00 0.00 36.95 0.98
4620 7337 8.288208 GTCGGAGAGAAACATCGTATCTAATAA 58.712 37.037 0.00 0.00 36.95 1.40
4663 7380 2.940994 TCCTGACATCCACGGAAAAA 57.059 45.000 0.00 0.00 0.00 1.94
4664 7381 2.778299 TCCTGACATCCACGGAAAAAG 58.222 47.619 0.00 0.00 0.00 2.27
4665 7382 1.200020 CCTGACATCCACGGAAAAAGC 59.800 52.381 0.00 0.00 0.00 3.51
4695 7412 2.026356 CACACATATCACCAGACCCCAA 60.026 50.000 0.00 0.00 0.00 4.12
4761 7499 4.681978 GCCTGCCACCGTCGAACT 62.682 66.667 0.00 0.00 0.00 3.01
4831 7575 3.436015 CAGCAGAACAACAGAGATGAAGG 59.564 47.826 0.00 0.00 0.00 3.46
4883 7630 3.252554 GGGGGTTTATGGGCATTATGA 57.747 47.619 0.00 0.00 0.00 2.15
4906 7653 8.162878 TGAGATATACTTAGTAAAGTGGTCGG 57.837 38.462 0.00 0.00 45.63 4.79
4907 7654 7.994911 TGAGATATACTTAGTAAAGTGGTCGGA 59.005 37.037 0.00 0.00 45.63 4.55
4908 7655 8.164058 AGATATACTTAGTAAAGTGGTCGGAC 57.836 38.462 0.00 0.00 45.63 4.79
4909 7656 3.949842 ACTTAGTAAAGTGGTCGGACC 57.050 47.619 20.36 20.36 44.40 4.46
4910 7657 2.564504 ACTTAGTAAAGTGGTCGGACCC 59.435 50.000 23.81 14.91 44.40 4.46
4911 7658 2.610438 TAGTAAAGTGGTCGGACCCT 57.390 50.000 23.81 16.82 37.50 4.34
4912 7659 1.725803 AGTAAAGTGGTCGGACCCTT 58.274 50.000 23.81 21.08 37.50 3.95
4913 7660 1.622312 AGTAAAGTGGTCGGACCCTTC 59.378 52.381 23.81 13.97 37.50 3.46
4914 7661 0.978907 TAAAGTGGTCGGACCCTTCC 59.021 55.000 23.81 9.51 37.50 3.46
4915 7662 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
4916 7663 2.606826 GTGGTCGGACCCTTCCCT 60.607 66.667 23.81 0.00 38.99 4.20
4917 7664 2.606519 TGGTCGGACCCTTCCCTG 60.607 66.667 23.81 0.00 38.99 4.45
4918 7665 3.400054 GGTCGGACCCTTCCCTGG 61.400 72.222 16.55 0.00 38.99 4.45
4919 7666 2.284405 GTCGGACCCTTCCCTGGA 60.284 66.667 0.00 0.00 38.99 3.86
4920 7667 2.284405 TCGGACCCTTCCCTGGAC 60.284 66.667 0.00 0.00 38.99 4.02
4921 7668 3.400054 CGGACCCTTCCCTGGACC 61.400 72.222 0.00 0.00 38.99 4.46
4922 7669 3.015753 GGACCCTTCCCTGGACCC 61.016 72.222 0.00 0.00 35.57 4.46
4923 7670 2.125225 GACCCTTCCCTGGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
4924 7671 2.204151 ACCCTTCCCTGGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
4925 7672 3.732849 CCCTTCCCTGGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
4926 7673 4.101448 CCTTCCCTGGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
4927 7674 4.785453 CTTCCCTGGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
4952 7699 3.558674 GAGCTACATGCACCAGGTT 57.441 52.632 0.00 0.00 45.94 3.50
4953 7700 1.089920 GAGCTACATGCACCAGGTTG 58.910 55.000 0.00 0.00 45.94 3.77
4954 7701 0.962356 AGCTACATGCACCAGGTTGC 60.962 55.000 8.03 8.03 44.17 4.17
4955 7702 1.937546 GCTACATGCACCAGGTTGCC 61.938 60.000 10.46 0.00 39.88 4.52
4956 7703 1.304052 TACATGCACCAGGTTGCCC 60.304 57.895 10.46 0.00 42.25 5.36
4957 7704 1.788518 TACATGCACCAGGTTGCCCT 61.789 55.000 10.46 0.00 42.25 5.19
4958 7705 1.909781 CATGCACCAGGTTGCCCTT 60.910 57.895 10.46 0.00 42.25 3.95
4959 7706 1.152269 ATGCACCAGGTTGCCCTTT 60.152 52.632 10.46 0.00 42.25 3.11
4960 7707 0.763986 ATGCACCAGGTTGCCCTTTT 60.764 50.000 10.46 0.00 42.25 2.27
4961 7708 0.980231 TGCACCAGGTTGCCCTTTTT 60.980 50.000 10.46 0.00 42.25 1.94
5011 7758 4.442375 ACCACATCAGCTCTATATACGC 57.558 45.455 0.00 0.00 0.00 4.42
5073 7820 1.546548 GGCAGCAGAGGGAGACTTTTT 60.547 52.381 0.00 0.00 0.00 1.94
5083 7830 3.636764 AGGGAGACTTTTTGCGACATTTT 59.363 39.130 0.00 0.00 0.00 1.82
5134 7883 2.755929 GCTGTTACTCGGCAGAAGG 58.244 57.895 0.00 0.00 46.78 3.46
5200 7950 3.864983 TTCTGAACCTCCGGGGCCT 62.865 63.158 0.84 0.00 39.10 5.19
5211 7961 1.227674 CGGGGCCTAATCAGACTGC 60.228 63.158 0.84 0.00 0.00 4.40
5231 7981 0.893727 ACAAAAGCTAAGGCCCGTGG 60.894 55.000 0.00 0.00 39.73 4.94
5234 7984 2.764637 AAAGCTAAGGCCCGTGGTGG 62.765 60.000 0.00 0.00 39.73 4.61
5241 7991 2.114411 GCCCGTGGTGGAAAAGGA 59.886 61.111 0.00 0.00 42.00 3.36
5242 7992 1.529713 GCCCGTGGTGGAAAAGGAA 60.530 57.895 0.00 0.00 42.00 3.36
5305 8059 7.692291 CACAAGTATTAAACGAGCAAATGGTAG 59.308 37.037 0.00 0.00 0.00 3.18
5309 8063 8.204836 AGTATTAAACGAGCAAATGGTAGAGAT 58.795 33.333 0.00 0.00 0.00 2.75
5312 8066 3.798202 ACGAGCAAATGGTAGAGATTCC 58.202 45.455 0.00 0.00 0.00 3.01
5331 8085 4.150897 TCCTGGAATTTCCTATTGGACG 57.849 45.455 16.25 0.00 43.06 4.79
5332 8086 2.618709 CCTGGAATTTCCTATTGGACGC 59.381 50.000 16.25 0.00 43.06 5.19
5334 8088 3.885297 CTGGAATTTCCTATTGGACGCAT 59.115 43.478 16.25 0.00 43.06 4.73
5335 8089 3.631686 TGGAATTTCCTATTGGACGCATG 59.368 43.478 16.25 0.00 43.06 4.06
5336 8090 3.632145 GGAATTTCCTATTGGACGCATGT 59.368 43.478 8.25 0.00 43.06 3.21
5337 8091 4.097892 GGAATTTCCTATTGGACGCATGTT 59.902 41.667 8.25 0.00 43.06 2.71
5338 8092 4.637483 ATTTCCTATTGGACGCATGTTG 57.363 40.909 0.00 0.00 43.06 3.33
5339 8093 2.779755 TCCTATTGGACGCATGTTGT 57.220 45.000 0.00 0.00 37.46 3.32
5340 8094 2.355197 TCCTATTGGACGCATGTTGTG 58.645 47.619 0.00 0.00 37.46 3.33
5344 8098 1.098869 TTGGACGCATGTTGTGTTGT 58.901 45.000 0.00 0.00 41.77 3.32
5355 8109 2.161410 TGTTGTGTTGTGTCAAGCTGTC 59.839 45.455 0.00 0.00 0.00 3.51
5362 8116 1.684450 TGTGTCAAGCTGTCGAGGTTA 59.316 47.619 0.00 0.00 37.85 2.85
5363 8117 2.059541 GTGTCAAGCTGTCGAGGTTAC 58.940 52.381 0.00 0.00 37.85 2.50
5375 8129 1.003718 AGGTTACGCACAGGCTTCC 60.004 57.895 0.00 0.00 38.10 3.46
5376 8130 2.038837 GGTTACGCACAGGCTTCCC 61.039 63.158 0.00 0.00 38.10 3.97
5377 8131 2.047655 TTACGCACAGGCTTCCCG 60.048 61.111 0.00 0.00 38.10 5.14
5378 8132 2.575893 TTACGCACAGGCTTCCCGA 61.576 57.895 4.71 0.00 38.10 5.14
5379 8133 2.501223 TTACGCACAGGCTTCCCGAG 62.501 60.000 4.71 0.00 38.10 4.63
5398 8152 3.044305 GAGCGCGTGATATGGGCC 61.044 66.667 8.43 0.00 43.20 5.80
5427 8181 2.224450 TGATGATGATTGCTGCGATCCT 60.224 45.455 23.55 15.87 0.00 3.24
5434 8188 1.327303 TTGCTGCGATCCTGGTTTTT 58.673 45.000 0.00 0.00 0.00 1.94
5444 8198 3.390175 TCCTGGTTTTTGGAACCTTCA 57.610 42.857 9.15 0.00 40.88 3.02
5450 8204 1.770294 TTTTGGAACCTTCAAGCCGT 58.230 45.000 0.00 0.00 0.00 5.68
5543 8297 9.483916 TTTTCGTTTTCCTTCTTTTTCTTTTCT 57.516 25.926 0.00 0.00 0.00 2.52
5544 8298 8.683550 TTCGTTTTCCTTCTTTTTCTTTTCTC 57.316 30.769 0.00 0.00 0.00 2.87
5546 8300 8.182227 TCGTTTTCCTTCTTTTTCTTTTCTCTC 58.818 33.333 0.00 0.00 0.00 3.20
5547 8301 7.432545 CGTTTTCCTTCTTTTTCTTTTCTCTCC 59.567 37.037 0.00 0.00 0.00 3.71
5548 8302 8.470805 GTTTTCCTTCTTTTTCTTTTCTCTCCT 58.529 33.333 0.00 0.00 0.00 3.69
5549 8303 8.595362 TTTCCTTCTTTTTCTTTTCTCTCCTT 57.405 30.769 0.00 0.00 0.00 3.36
5634 8405 9.913451 TTAATTTTGCATTTTCTTTCTTCAACG 57.087 25.926 0.00 0.00 0.00 4.10
5635 8406 6.959671 TTTTGCATTTTCTTTCTTCAACGT 57.040 29.167 0.00 0.00 0.00 3.99
5759 8538 9.997482 GTTCTGAGTACTAAAACAATCACAAAA 57.003 29.630 0.00 0.00 0.00 2.44
5827 8607 5.346181 TTTTCCGGAGTTCCAAAAATGTT 57.654 34.783 3.34 0.00 35.14 2.71
5828 8608 4.577834 TTCCGGAGTTCCAAAAATGTTC 57.422 40.909 3.34 0.00 35.14 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 5.045213 TGAATTGGAGGGAGTAGCATGTTTA 60.045 40.000 0.00 0.00 0.00 2.01
11 12 2.846206 TGAATTGGAGGGAGTAGCATGT 59.154 45.455 0.00 0.00 0.00 3.21
12 13 3.209410 GTGAATTGGAGGGAGTAGCATG 58.791 50.000 0.00 0.00 0.00 4.06
17 18 5.163447 CGAGTAATGTGAATTGGAGGGAGTA 60.163 44.000 0.00 0.00 0.00 2.59
33 34 0.368907 CGTTTGGGCGACGAGTAATG 59.631 55.000 0.00 0.00 42.82 1.90
40 41 0.808453 ATACATCCGTTTGGGCGACG 60.808 55.000 0.00 0.00 40.05 5.12
44 45 1.134220 TCCAGATACATCCGTTTGGGC 60.134 52.381 0.00 0.00 35.24 5.36
46 47 2.201732 CGTCCAGATACATCCGTTTGG 58.798 52.381 0.00 0.00 0.00 3.28
49 50 4.931661 AATACGTCCAGATACATCCGTT 57.068 40.909 0.00 0.00 0.00 4.44
62 63 5.276270 TGTATCTAGCACGAAAATACGTCC 58.724 41.667 0.00 0.00 44.76 4.79
65 66 6.856426 TCAGATGTATCTAGCACGAAAATACG 59.144 38.462 0.00 0.00 34.85 3.06
66 67 8.749841 ATCAGATGTATCTAGCACGAAAATAC 57.250 34.615 0.00 0.00 34.85 1.89
73 74 5.118357 GCTCAAATCAGATGTATCTAGCACG 59.882 44.000 7.03 0.00 34.85 5.34
78 79 4.039124 TGCCGCTCAAATCAGATGTATCTA 59.961 41.667 0.00 0.00 34.85 1.98
79 80 3.181462 TGCCGCTCAAATCAGATGTATCT 60.181 43.478 0.00 0.00 37.72 1.98
81 82 3.136763 CTGCCGCTCAAATCAGATGTAT 58.863 45.455 0.00 0.00 0.00 2.29
82 83 2.554142 CTGCCGCTCAAATCAGATGTA 58.446 47.619 0.00 0.00 0.00 2.29
88 89 2.016318 CATTACCTGCCGCTCAAATCA 58.984 47.619 0.00 0.00 0.00 2.57
93 95 0.323302 TTCACATTACCTGCCGCTCA 59.677 50.000 0.00 0.00 0.00 4.26
99 101 2.213499 CCTCCGATTCACATTACCTGC 58.787 52.381 0.00 0.00 0.00 4.85
102 104 2.434702 ACTCCCTCCGATTCACATTACC 59.565 50.000 0.00 0.00 0.00 2.85
108 110 1.481871 TGGTACTCCCTCCGATTCAC 58.518 55.000 0.00 0.00 0.00 3.18
111 113 3.431766 CGATTTTGGTACTCCCTCCGATT 60.432 47.826 0.00 0.00 0.00 3.34
125 127 7.224753 AGCAGAACACTATACATACGATTTTGG 59.775 37.037 0.00 0.00 0.00 3.28
166 168 0.861450 GCAACGAGCGCGCATATTTT 60.861 50.000 35.10 11.72 42.48 1.82
178 180 0.251916 TTATCCCCCACTGCAACGAG 59.748 55.000 0.00 0.00 0.00 4.18
179 181 0.693622 TTTATCCCCCACTGCAACGA 59.306 50.000 0.00 0.00 0.00 3.85
187 189 4.948341 AAAACTGTTGTTTATCCCCCAC 57.052 40.909 0.00 0.00 44.70 4.61
195 197 9.632807 GCATGTATTCCATAAAACTGTTGTTTA 57.367 29.630 0.00 0.00 44.70 2.01
198 200 6.437162 AGGCATGTATTCCATAAAACTGTTGT 59.563 34.615 0.00 0.00 30.71 3.32
208 210 8.637986 GGTCATTTTAAAGGCATGTATTCCATA 58.362 33.333 0.00 0.00 30.71 2.74
209 211 7.345392 AGGTCATTTTAAAGGCATGTATTCCAT 59.655 33.333 0.00 0.00 0.00 3.41
210 212 6.667414 AGGTCATTTTAAAGGCATGTATTCCA 59.333 34.615 0.00 0.00 0.00 3.53
211 213 6.980397 CAGGTCATTTTAAAGGCATGTATTCC 59.020 38.462 0.00 0.00 0.00 3.01
213 215 7.480760 ACAGGTCATTTTAAAGGCATGTATT 57.519 32.000 0.00 0.00 0.00 1.89
220 297 6.349363 CCTCTGTTACAGGTCATTTTAAAGGC 60.349 42.308 12.79 0.00 31.51 4.35
235 312 6.252599 AGATTATTCATGGCCTCTGTTACA 57.747 37.500 3.32 0.00 0.00 2.41
236 313 6.767902 TGAAGATTATTCATGGCCTCTGTTAC 59.232 38.462 3.32 0.00 0.00 2.50
292 369 6.461110 AACTGCTCCCTATGATGAAATTTG 57.539 37.500 0.00 0.00 0.00 2.32
394 482 8.717821 GCTAATGTTAGTTTCATTATGCCGATA 58.282 33.333 2.11 0.00 37.22 2.92
396 484 6.017440 GGCTAATGTTAGTTTCATTATGCCGA 60.017 38.462 15.58 0.00 39.30 5.54
397 485 6.142817 GGCTAATGTTAGTTTCATTATGCCG 58.857 40.000 15.58 0.00 39.30 5.69
398 486 7.038154 TGGCTAATGTTAGTTTCATTATGCC 57.962 36.000 19.49 19.49 42.97 4.40
399 487 7.973388 TGTTGGCTAATGTTAGTTTCATTATGC 59.027 33.333 2.11 0.00 37.22 3.14
400 488 9.289303 GTGTTGGCTAATGTTAGTTTCATTATG 57.711 33.333 2.11 0.00 37.22 1.90
401 489 8.466798 GGTGTTGGCTAATGTTAGTTTCATTAT 58.533 33.333 2.11 0.00 37.22 1.28
410 498 4.522789 AGGTTTGGTGTTGGCTAATGTTAG 59.477 41.667 0.00 0.00 0.00 2.34
442 533 5.755813 CTTTGACACACAAGATTGAGAAGG 58.244 41.667 0.00 0.00 39.77 3.46
448 539 6.088824 GGAATAGCTTTGACACACAAGATTG 58.911 40.000 0.00 0.00 39.77 2.67
488 579 3.379057 TGCATGTGGATGTGCTTATTGAG 59.621 43.478 0.00 0.00 41.78 3.02
585 676 6.885952 TGATGCCAGTTATCTAGAGTCTAC 57.114 41.667 0.00 0.00 0.00 2.59
666 757 6.561737 TGTTATATTGCCTTGTCGTTTTCA 57.438 33.333 0.00 0.00 0.00 2.69
667 758 7.302524 TCTTGTTATATTGCCTTGTCGTTTTC 58.697 34.615 0.00 0.00 0.00 2.29
675 766 5.355071 TCTGCACTCTTGTTATATTGCCTTG 59.645 40.000 0.00 0.00 0.00 3.61
686 777 4.685924 CACCAAAAATCTGCACTCTTGTT 58.314 39.130 0.00 0.00 0.00 2.83
704 795 3.147553 TGGCTAACTGTTTATGCACCA 57.852 42.857 0.00 0.00 0.00 4.17
1060 1157 3.243975 CCTTCATCAAAGCACTTTGCCTT 60.244 43.478 16.53 3.47 46.52 4.35
1254 1352 6.061231 TGACATGAGTATACTAGAAGTGCG 57.939 41.667 5.09 0.00 0.00 5.34
1339 2052 0.977395 ACCTTTTCTGAGGCTAGCGT 59.023 50.000 10.22 10.22 40.65 5.07
1350 2063 4.273318 GCCCATGTAGAATGACCTTTTCT 58.727 43.478 0.00 0.00 37.25 2.52
1421 2134 7.092079 CAGTGCCATTTTGATCAAATCTTACA 58.908 34.615 21.10 12.96 32.24 2.41
1438 2151 0.549950 CCCTCTCAATCCAGTGCCAT 59.450 55.000 0.00 0.00 0.00 4.40
1441 2154 0.460987 CGACCCTCTCAATCCAGTGC 60.461 60.000 0.00 0.00 0.00 4.40
1444 2157 1.769026 TCTCGACCCTCTCAATCCAG 58.231 55.000 0.00 0.00 0.00 3.86
1497 2210 7.606839 AGACTTAAAGAGCACCAAATAGTTACC 59.393 37.037 0.00 0.00 0.00 2.85
1614 2336 9.561069 TCAACAAGGCTCTTATATAAATCCTTC 57.439 33.333 14.71 0.00 30.75 3.46
1750 2498 3.614159 CATAATCAATGGCCTGTCGTG 57.386 47.619 3.32 0.00 31.38 4.35
1818 2566 5.470047 ACACCAATAAAGAAGACGAGACT 57.530 39.130 0.00 0.00 0.00 3.24
1824 2572 5.948992 AGCTGAACACCAATAAAGAAGAC 57.051 39.130 0.00 0.00 0.00 3.01
1825 2573 6.299141 AGAAGCTGAACACCAATAAAGAAGA 58.701 36.000 0.00 0.00 0.00 2.87
1878 2626 4.153655 GTGACCCAGGACGAAATAAAGTTC 59.846 45.833 0.00 0.00 0.00 3.01
1879 2627 4.070009 GTGACCCAGGACGAAATAAAGTT 58.930 43.478 0.00 0.00 0.00 2.66
1981 2734 1.375326 GGGAGGAAGTGTGGTGGAC 59.625 63.158 0.00 0.00 0.00 4.02
2007 2760 0.108585 GGTATCCGCACATGACCCAT 59.891 55.000 0.00 0.00 0.00 4.00
2016 2769 2.279517 CGGCAGAGGTATCCGCAC 60.280 66.667 0.00 0.00 36.53 5.34
2031 2784 3.449737 TCAATACTAAGGAGGTTCCACGG 59.550 47.826 0.00 0.00 39.61 4.94
2055 2810 0.266152 AGTAGTGCCATAGGGGAGCT 59.734 55.000 0.00 0.00 40.01 4.09
2064 2819 4.202305 GGCAGAAGATAAGAGTAGTGCCAT 60.202 45.833 5.16 0.00 46.93 4.40
2136 2891 4.017499 ACCTATGGGTTGTGAGCCTTAATT 60.017 41.667 0.00 0.00 44.73 1.40
2137 2892 3.527665 ACCTATGGGTTGTGAGCCTTAAT 59.472 43.478 0.00 0.00 44.73 1.40
2238 2996 9.961265 GCCCTTTGTATTATAAAACTAATGACC 57.039 33.333 0.00 0.00 0.00 4.02
2276 3174 1.885887 GACAACAACAGCATAGCCCAA 59.114 47.619 0.00 0.00 0.00 4.12
2278 3176 0.811281 GGACAACAACAGCATAGCCC 59.189 55.000 0.00 0.00 0.00 5.19
2283 3181 2.358898 GACTTGTGGACAACAACAGCAT 59.641 45.455 0.00 0.00 43.96 3.79
2288 3186 5.527582 AGTTCATAGACTTGTGGACAACAAC 59.472 40.000 0.00 0.00 43.96 3.32
2316 3214 9.403583 CTAGCACCCAAGGTTTAATCTAATTTA 57.596 33.333 0.00 0.00 31.02 1.40
2384 3332 6.042638 AGTGCCATACTACCATGATGTATC 57.957 41.667 0.00 0.00 38.04 2.24
2421 3369 9.764363 AAGCGATCAGACTGATGTTATTATTAA 57.236 29.630 22.64 0.00 37.20 1.40
2484 3557 4.080687 ACCCTACTGTAGAGTGAGTGAAC 58.919 47.826 16.22 0.00 33.21 3.18
2493 3568 6.980416 AAAGCCTTATACCCTACTGTAGAG 57.020 41.667 16.22 5.57 0.00 2.43
2698 3774 9.961265 CGAACAGTTATAATCTTGGTCAGTATA 57.039 33.333 11.01 0.00 0.00 1.47
2699 3775 8.475639 ACGAACAGTTATAATCTTGGTCAGTAT 58.524 33.333 11.01 0.00 0.00 2.12
2700 3776 7.833786 ACGAACAGTTATAATCTTGGTCAGTA 58.166 34.615 11.01 0.00 0.00 2.74
2723 4655 6.642683 ACGATATGAGGTGTAAAGAAAACG 57.357 37.500 0.00 0.00 0.00 3.60
2731 4663 5.202765 TGGGAGTAACGATATGAGGTGTAA 58.797 41.667 0.00 0.00 0.00 2.41
2745 4677 1.204704 GCAAAGGGCATTGGGAGTAAC 59.795 52.381 4.71 0.00 43.97 2.50
2892 4825 5.763088 CTCTTTGAAAAGTGCTTAGGAACC 58.237 41.667 2.88 0.00 37.31 3.62
2908 4841 1.824852 TGCTATCACCTCGCTCTTTGA 59.175 47.619 0.00 0.00 0.00 2.69
3023 4956 6.072673 GGAGTAAATGTTTACCTCAACCACAG 60.073 42.308 11.03 0.00 43.03 3.66
3132 5085 2.290093 GGAGCTAGCATTGCAGATGTTC 59.710 50.000 18.83 0.29 0.00 3.18
3164 5117 3.069443 GGAATTTGAGAGTGCCAAACCAA 59.931 43.478 0.00 0.00 36.48 3.67
3175 5128 2.089980 CTGGTGCTGGGAATTTGAGAG 58.910 52.381 0.00 0.00 0.00 3.20
3186 5139 2.833913 AACCTGGACCTGGTGCTGG 61.834 63.158 32.68 32.68 45.37 4.85
3239 5192 5.183713 TGATTGGTGCTTCATGTTAAGGAAG 59.816 40.000 6.96 6.96 45.06 3.46
3362 5347 1.453762 GCTTCCCCATGCTGCTCATC 61.454 60.000 0.00 0.00 31.79 2.92
3400 5385 0.606401 CCTGTTCGTCATGCCCTTGT 60.606 55.000 0.00 0.00 0.00 3.16
3418 5403 3.756727 GCTGCTGCTTGCTTCCCC 61.757 66.667 8.53 0.00 43.37 4.81
3468 5455 2.303311 GAGCAGGTAACCTTGACCTCTT 59.697 50.000 0.00 0.00 44.33 2.85
3475 5462 2.859992 GCTGGAGCAGGTAACCTTG 58.140 57.895 0.00 0.00 41.59 3.61
3601 5588 0.613012 CAAAAGGGGGAGCTGGGAAG 60.613 60.000 0.00 0.00 0.00 3.46
3762 5761 1.368493 CTCGGACACGCGTATACCG 60.368 63.158 30.63 30.63 44.09 4.02
3765 5764 2.325511 CGCTCGGACACGCGTATA 59.674 61.111 13.44 0.00 44.01 1.47
3906 5927 5.396484 AGCATGAAAGTTCATTTGATGTCG 58.604 37.500 3.75 0.00 45.13 4.35
4013 6098 7.864108 TTGTCTCTGATAATGTTGGTTATGG 57.136 36.000 0.00 0.00 0.00 2.74
4044 6129 5.467735 AGAAAAATGTCAAGCAGGAAAATGC 59.532 36.000 0.00 0.00 46.88 3.56
4048 6133 6.239008 CCTGTAGAAAAATGTCAAGCAGGAAA 60.239 38.462 0.00 0.00 42.38 3.13
4115 6200 3.885297 CTCAGGTCCTTTTTCTTTGCAGA 59.115 43.478 0.00 0.00 0.00 4.26
4120 6205 2.177888 AGGCCTCAGGTCCTTTTTCTTT 59.822 45.455 0.00 0.00 0.00 2.52
4174 6259 0.171007 TTACCGCCGAAAGAGGTACG 59.829 55.000 0.00 0.00 41.44 3.67
4197 6282 4.019231 AGAAGCTAGAACCTAAACCTTGGG 60.019 45.833 0.00 0.00 37.31 4.12
4199 6284 8.794335 ATTTAGAAGCTAGAACCTAAACCTTG 57.206 34.615 10.83 0.00 34.96 3.61
4438 6583 7.781693 AGCCATATATTTCCACAAAAGATCAGT 59.218 33.333 0.00 0.00 31.45 3.41
4618 7335 5.360591 GTGCTCCTCTTATTGCTTAGCTTA 58.639 41.667 5.60 0.00 0.00 3.09
4619 7336 4.195416 GTGCTCCTCTTATTGCTTAGCTT 58.805 43.478 5.60 0.00 0.00 3.74
4620 7337 3.432890 GGTGCTCCTCTTATTGCTTAGCT 60.433 47.826 5.60 0.00 0.00 3.32
4631 7348 0.908198 GTCAGGATGGTGCTCCTCTT 59.092 55.000 6.34 0.00 44.04 2.85
4636 7353 0.543277 TGGATGTCAGGATGGTGCTC 59.457 55.000 0.00 0.00 36.16 4.26
4637 7354 0.254178 GTGGATGTCAGGATGGTGCT 59.746 55.000 0.00 0.00 36.16 4.40
4638 7355 1.091771 CGTGGATGTCAGGATGGTGC 61.092 60.000 0.00 0.00 36.16 5.01
4649 7366 1.468520 CATCGCTTTTTCCGTGGATGT 59.531 47.619 0.00 0.00 0.00 3.06
4651 7368 1.094785 CCATCGCTTTTTCCGTGGAT 58.905 50.000 0.00 0.00 32.46 3.41
4663 7380 0.104855 ATATGTGTGTCGCCATCGCT 59.895 50.000 0.00 0.00 35.26 4.93
4664 7381 0.508641 GATATGTGTGTCGCCATCGC 59.491 55.000 0.00 0.00 35.26 4.58
4665 7382 1.522676 GTGATATGTGTGTCGCCATCG 59.477 52.381 0.00 0.00 0.00 3.84
4685 7402 2.186903 CCGTCGATTGGGGTCTGG 59.813 66.667 0.00 0.00 0.00 3.86
4831 7575 0.041312 CAAGTGTGCAGCGTTACCAC 60.041 55.000 0.00 0.00 0.00 4.16
4883 7630 7.230309 GGTCCGACCACTTTACTAAGTATATCT 59.770 40.741 13.05 0.00 42.67 1.98
4896 7643 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
4898 7645 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
4899 7646 2.606826 AGGGAAGGGTCCGACCAC 60.607 66.667 19.43 8.70 46.04 4.16
4900 7647 2.606519 CAGGGAAGGGTCCGACCA 60.607 66.667 19.43 0.00 46.04 4.02
4901 7648 3.400054 CCAGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
4902 7649 2.284405 TCCAGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
4903 7650 2.284405 GTCCAGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
4904 7651 3.400054 GGTCCAGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
4905 7652 3.015753 GGGTCCAGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
4906 7653 2.125225 AGGGTCCAGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
4907 7654 2.204151 CAGGGTCCAGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
4908 7655 3.732849 GCAGGGTCCAGGGAAGGG 61.733 72.222 0.00 0.00 0.00 3.95
4909 7656 4.101448 CGCAGGGTCCAGGGAAGG 62.101 72.222 0.00 0.00 0.00 3.46
4910 7657 4.785453 GCGCAGGGTCCAGGGAAG 62.785 72.222 0.30 0.00 0.00 3.46
4922 7669 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
4925 7672 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
4926 7673 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
4927 7674 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
4928 7675 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
4934 7681 1.089920 CAACCTGGTGCATGTAGCTC 58.910 55.000 14.15 0.00 45.94 4.09
4935 7682 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.000 14.15 0.00 44.29 3.32
4936 7683 1.508088 GCAACCTGGTGCATGTAGC 59.492 57.895 6.00 6.00 44.29 3.58
4937 7684 2.183409 GGCAACCTGGTGCATGTAG 58.817 57.895 18.44 0.00 46.81 2.74
4938 7685 4.413928 GGCAACCTGGTGCATGTA 57.586 55.556 18.44 0.00 46.81 2.29
4974 7721 9.011095 GCTGATGTGGTATATACTCACTAAGTA 57.989 37.037 23.42 11.68 44.49 2.24
4975 7722 7.726291 AGCTGATGTGGTATATACTCACTAAGT 59.274 37.037 23.42 13.54 42.33 2.24
4976 7723 8.116651 AGCTGATGTGGTATATACTCACTAAG 57.883 38.462 23.42 19.54 32.36 2.18
4977 7724 7.945109 AGAGCTGATGTGGTATATACTCACTAA 59.055 37.037 23.42 12.63 32.36 2.24
4978 7725 7.462590 AGAGCTGATGTGGTATATACTCACTA 58.537 38.462 23.42 15.55 32.36 2.74
4979 7726 6.310941 AGAGCTGATGTGGTATATACTCACT 58.689 40.000 23.42 14.57 32.36 3.41
4980 7727 6.582677 AGAGCTGATGTGGTATATACTCAC 57.417 41.667 19.50 19.50 0.00 3.51
5011 7758 0.940126 CAGAGATCGGCCATTTTCGG 59.060 55.000 2.24 0.00 0.00 4.30
5027 7774 1.295792 GCCGATTCCGCAAATACAGA 58.704 50.000 0.00 0.00 0.00 3.41
5083 7830 3.772387 TCATGGCCCAAATACTCACAAA 58.228 40.909 0.00 0.00 0.00 2.83
5086 7833 2.887152 GGATCATGGCCCAAATACTCAC 59.113 50.000 0.00 0.00 0.00 3.51
5134 7883 0.600782 CAACCAGCCCATGTTTGCAC 60.601 55.000 0.00 0.00 0.00 4.57
5139 7888 2.627699 CAAGTAACAACCAGCCCATGTT 59.372 45.455 0.00 0.00 40.22 2.71
5142 7891 1.427368 TCCAAGTAACAACCAGCCCAT 59.573 47.619 0.00 0.00 0.00 4.00
5144 7893 1.202891 AGTCCAAGTAACAACCAGCCC 60.203 52.381 0.00 0.00 0.00 5.19
5197 7947 3.671702 GCTTTTGTGCAGTCTGATTAGGC 60.672 47.826 3.32 0.00 0.00 3.93
5200 7950 5.412594 CCTTAGCTTTTGTGCAGTCTGATTA 59.587 40.000 3.32 0.00 34.99 1.75
5211 7961 0.240945 CACGGGCCTTAGCTTTTGTG 59.759 55.000 0.84 0.00 39.73 3.33
5305 8059 6.605119 TCCAATAGGAAATTCCAGGAATCTC 58.395 40.000 15.53 11.07 42.23 2.75
5331 8085 1.854126 GCTTGACACAACACAACATGC 59.146 47.619 0.00 0.00 0.00 4.06
5332 8086 3.110358 CAGCTTGACACAACACAACATG 58.890 45.455 0.00 0.00 0.00 3.21
5334 8088 2.158559 ACAGCTTGACACAACACAACA 58.841 42.857 0.00 0.00 0.00 3.33
5335 8089 2.785679 GACAGCTTGACACAACACAAC 58.214 47.619 0.00 0.00 0.00 3.32
5336 8090 1.396648 CGACAGCTTGACACAACACAA 59.603 47.619 0.00 0.00 0.00 3.33
5337 8091 1.006086 CGACAGCTTGACACAACACA 58.994 50.000 0.00 0.00 0.00 3.72
5338 8092 1.258982 CTCGACAGCTTGACACAACAC 59.741 52.381 0.00 0.00 0.00 3.32
5339 8093 1.570813 CTCGACAGCTTGACACAACA 58.429 50.000 0.00 0.00 0.00 3.33
5340 8094 0.861837 CCTCGACAGCTTGACACAAC 59.138 55.000 0.00 0.00 0.00 3.32
5344 8098 1.335597 CGTAACCTCGACAGCTTGACA 60.336 52.381 0.00 0.00 0.00 3.58
5355 8109 1.352156 GAAGCCTGTGCGTAACCTCG 61.352 60.000 0.00 0.00 44.33 4.63
5362 8116 4.379243 CTCGGGAAGCCTGTGCGT 62.379 66.667 0.00 0.00 44.33 5.24
5375 8129 3.881092 ATATCACGCGCTCGCTCGG 62.881 63.158 5.73 0.00 39.84 4.63
5376 8130 2.427575 ATATCACGCGCTCGCTCG 60.428 61.111 5.73 3.87 39.84 5.03
5377 8131 2.368105 CCATATCACGCGCTCGCTC 61.368 63.158 5.73 0.00 39.84 5.03
5378 8132 2.355126 CCATATCACGCGCTCGCT 60.355 61.111 5.73 0.00 39.84 4.93
5379 8133 3.406361 CCCATATCACGCGCTCGC 61.406 66.667 5.73 3.90 39.84 5.03
5380 8134 3.406361 GCCCATATCACGCGCTCG 61.406 66.667 5.73 0.00 42.43 5.03
5381 8135 3.044305 GGCCCATATCACGCGCTC 61.044 66.667 5.73 0.00 0.00 5.03
5382 8136 4.969196 CGGCCCATATCACGCGCT 62.969 66.667 5.73 0.00 0.00 5.92
5398 8152 1.336517 GCAATCATCATCAATGGGCCG 60.337 52.381 0.00 0.00 35.94 6.13
5403 8157 3.619233 TCGCAGCAATCATCATCAATG 57.381 42.857 0.00 0.00 36.65 2.82
5404 8158 3.190744 GGATCGCAGCAATCATCATCAAT 59.809 43.478 0.00 0.00 0.00 2.57
5407 8161 2.159824 CAGGATCGCAGCAATCATCATC 59.840 50.000 0.00 0.00 0.00 2.92
5408 8162 2.152016 CAGGATCGCAGCAATCATCAT 58.848 47.619 0.00 0.00 0.00 2.45
5409 8163 1.589803 CAGGATCGCAGCAATCATCA 58.410 50.000 0.00 0.00 0.00 3.07
5410 8164 0.873054 CCAGGATCGCAGCAATCATC 59.127 55.000 0.00 0.00 0.00 2.92
5427 8181 2.169561 GGCTTGAAGGTTCCAAAAACCA 59.830 45.455 9.45 0.00 42.69 3.67
5434 8188 1.770294 AAAACGGCTTGAAGGTTCCA 58.230 45.000 0.00 0.00 0.00 3.53
5536 8290 7.561356 ACAGAAAATGGAAAAGGAGAGAAAAGA 59.439 33.333 0.00 0.00 0.00 2.52
5538 8292 7.660030 ACAGAAAATGGAAAAGGAGAGAAAA 57.340 32.000 0.00 0.00 0.00 2.29
5542 8296 9.987272 AAATAAACAGAAAATGGAAAAGGAGAG 57.013 29.630 0.00 0.00 0.00 3.20
5609 8380 9.092876 ACGTTGAAGAAAGAAAATGCAAAATTA 57.907 25.926 0.00 0.00 0.00 1.40
5610 8381 7.973601 ACGTTGAAGAAAGAAAATGCAAAATT 58.026 26.923 0.00 0.00 0.00 1.82
5611 8382 7.538303 ACGTTGAAGAAAGAAAATGCAAAAT 57.462 28.000 0.00 0.00 0.00 1.82
5612 8383 6.959671 ACGTTGAAGAAAGAAAATGCAAAA 57.040 29.167 0.00 0.00 0.00 2.44
5613 8384 6.811170 AGAACGTTGAAGAAAGAAAATGCAAA 59.189 30.769 5.00 0.00 0.00 3.68
5614 8385 6.329496 AGAACGTTGAAGAAAGAAAATGCAA 58.671 32.000 5.00 0.00 0.00 4.08
5615 8386 5.890334 AGAACGTTGAAGAAAGAAAATGCA 58.110 33.333 5.00 0.00 0.00 3.96
5616 8387 6.812481 AAGAACGTTGAAGAAAGAAAATGC 57.188 33.333 5.00 0.00 0.00 3.56
5651 8422 9.794685 ACCAAATTTTAAAACGCAATGATTTTT 57.205 22.222 1.97 0.61 30.80 1.94
5656 8427 7.539712 TGAACCAAATTTTAAAACGCAATGA 57.460 28.000 1.97 0.00 0.00 2.57
5732 8503 8.725405 TTGTGATTGTTTTAGTACTCAGAACA 57.275 30.769 0.00 6.59 0.00 3.18
5733 8504 9.997482 TTTTGTGATTGTTTTAGTACTCAGAAC 57.003 29.630 0.00 3.89 0.00 3.01
5775 8554 8.669243 GGGACATTTGTAACAATTTTTGAAACA 58.331 29.630 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.