Multiple sequence alignment - TraesCS2A01G330900

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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 TraesCS2A01G330900 chr2A 100.000 7900 0 0 1656 9555 563765562 563773461 0.000000e+00 14589.0
1 TraesCS2A01G330900 chr2A 100.000 1242 0 0 1 1242 563763907 563765148 0.000000e+00 2294.0
2 TraesCS2A01G330900 chr2A 91.645 383 20 6 8103 8475 553267846 553267466 3.950000e-143 520.0
3 TraesCS2A01G330900 chr2A 83.256 215 34 2 9036 9250 632301305 632301517 7.570000e-46 196.0
4 TraesCS2A01G330900 chr2A 100.000 41 0 0 9010 9050 563772875 563772915 1.030000e-09 76.8
5 TraesCS2A01G330900 chr2A 100.000 41 0 0 8969 9009 563772916 563772956 1.030000e-09 76.8
6 TraesCS2A01G330900 chr2D 97.863 7253 113 16 1656 8892 424860139 424852913 0.000000e+00 12497.0
7 TraesCS2A01G330900 chr2D 93.681 633 18 6 619 1242 424860907 424860288 0.000000e+00 928.0
8 TraesCS2A01G330900 chr2D 91.139 553 41 3 9010 9555 424834054 424833503 0.000000e+00 743.0
9 TraesCS2A01G330900 chr2D 91.864 381 17 8 8103 8472 433874745 433875122 3.950000e-143 520.0
10 TraesCS2A01G330900 chr2D 77.904 353 49 12 318 652 160659094 160659435 9.790000e-45 193.0
11 TraesCS2A01G330900 chr2D 76.667 270 56 7 467 730 367240985 367241253 1.000000e-29 143.0
12 TraesCS2A01G330900 chr2D 84.375 128 17 3 9374 9499 121421623 121421497 1.300000e-23 122.0
13 TraesCS2A01G330900 chr2B 97.215 7253 159 21 1656 8900 500195786 500188569 0.000000e+00 12235.0
14 TraesCS2A01G330900 chr2B 88.118 1153 89 23 105 1242 500197052 500195933 0.000000e+00 1327.0
15 TraesCS2A01G330900 chr2B 91.384 383 18 7 8103 8472 512924047 512924427 2.380000e-140 510.0
16 TraesCS2A01G330900 chr2B 83.154 558 79 11 9010 9555 500188492 500187938 6.660000e-136 496.0
17 TraesCS2A01G330900 chr2B 86.066 122 14 2 9374 9493 212407358 212407478 2.800000e-25 128.0
18 TraesCS2A01G330900 chr2B 85.366 123 15 2 9373 9493 268356559 268356680 3.620000e-24 124.0
19 TraesCS2A01G330900 chr2B 83.099 71 11 1 8939 9009 37352984 37353053 8.010000e-06 63.9
20 TraesCS2A01G330900 chr5D 76.063 447 77 17 9010 9429 551614831 551615274 1.260000e-48 206.0
21 TraesCS2A01G330900 chr5D 93.069 101 6 1 1 100 222784503 222784603 7.730000e-31 147.0
22 TraesCS2A01G330900 chr4A 78.983 295 55 3 9010 9298 616615511 616615218 2.720000e-45 195.0
23 TraesCS2A01G330900 chr4A 75.266 376 61 14 304 659 549426987 549427350 5.980000e-32 150.0
24 TraesCS2A01G330900 chr4A 84.146 82 10 2 105 184 252642274 252642194 1.030000e-09 76.8
25 TraesCS2A01G330900 chr3D 76.456 395 63 13 304 679 352701287 352701670 4.560000e-43 187.0
26 TraesCS2A01G330900 chr3D 78.909 275 42 9 383 652 285575361 285575098 1.280000e-38 172.0
27 TraesCS2A01G330900 chr3D 92.453 106 7 1 1 105 583583026 583583131 5.980000e-32 150.0
28 TraesCS2A01G330900 chr3D 91.509 106 7 2 1 105 267925976 267926080 2.780000e-30 145.0
29 TraesCS2A01G330900 chr3D 90.000 110 8 3 1 107 418869926 418869817 1.290000e-28 139.0
30 TraesCS2A01G330900 chr3D 82.716 81 12 2 104 183 418869779 418869700 4.790000e-08 71.3
31 TraesCS2A01G330900 chr5B 87.662 154 18 1 9402 9555 581421492 581421340 2.740000e-40 178.0
32 TraesCS2A01G330900 chr5B 86.420 81 9 2 105 184 297798253 297798332 4.750000e-13 87.9
33 TraesCS2A01G330900 chr1D 76.178 382 61 16 331 694 75641278 75640909 3.550000e-39 174.0
34 TraesCS2A01G330900 chr1D 80.874 183 32 3 9039 9220 139138553 139138373 3.600000e-29 141.0
35 TraesCS2A01G330900 chr1D 85.246 122 15 2 9374 9493 231158640 231158760 1.300000e-23 122.0
36 TraesCS2A01G330900 chr1D 81.481 81 14 1 104 184 250330675 250330596 2.230000e-06 65.8
37 TraesCS2A01G330900 chr7D 76.923 351 52 14 320 652 443298267 443297928 1.280000e-38 172.0
38 TraesCS2A01G330900 chr7D 76.554 354 54 10 304 638 129323852 129323509 5.940000e-37 167.0
39 TraesCS2A01G330900 chr7D 90.741 108 7 3 1 105 467510069 467510176 3.600000e-29 141.0
40 TraesCS2A01G330900 chr7D 90.566 106 9 1 1 105 630496852 630496747 1.290000e-28 139.0
41 TraesCS2A01G330900 chr5A 74.249 466 84 22 9034 9468 415566584 415566124 7.680000e-36 163.0
42 TraesCS2A01G330900 chr5A 90.909 66 5 1 8944 9009 509720641 509720577 4.750000e-13 87.9
43 TraesCS2A01G330900 chr4B 82.888 187 27 4 470 652 290338822 290338637 7.680000e-36 163.0
44 TraesCS2A01G330900 chr4B 75.449 334 55 9 301 618 374312077 374312399 4.650000e-28 137.0
45 TraesCS2A01G330900 chr7B 77.104 297 55 7 9010 9298 586068215 586068506 9.930000e-35 159.0
46 TraesCS2A01G330900 chr7B 92.157 102 7 1 1 101 9017927 9017826 1.000000e-29 143.0
47 TraesCS2A01G330900 chr1A 80.275 218 36 6 467 679 470689876 470690091 3.570000e-34 158.0
48 TraesCS2A01G330900 chr1A 85.246 122 15 3 9374 9493 357644322 357644442 1.300000e-23 122.0
49 TraesCS2A01G330900 chr1A 85.246 122 15 3 9374 9493 396717033 396717153 1.300000e-23 122.0
50 TraesCS2A01G330900 chr1A 84.146 82 12 1 105 185 481211804 481211885 2.860000e-10 78.7
51 TraesCS2A01G330900 chr1A 82.927 82 12 2 104 184 320407223 320407143 1.330000e-08 73.1
52 TraesCS2A01G330900 chr3B 75.127 394 66 13 304 678 558001837 558001457 1.280000e-33 156.0
53 TraesCS2A01G330900 chr3B 93.396 106 6 1 1 105 780826212 780826317 1.280000e-33 156.0
54 TraesCS2A01G330900 chr3B 92.453 106 7 1 1 105 780837626 780837731 5.980000e-32 150.0
55 TraesCS2A01G330900 chr1B 75.200 375 64 11 318 674 386065942 386065579 5.980000e-32 150.0
56 TraesCS2A01G330900 chr1B 84.375 128 17 3 9374 9499 461161540 461161414 1.300000e-23 122.0
57 TraesCS2A01G330900 chr3A 74.169 391 69 12 302 671 247844392 247844771 6.020000e-27 134.0
58 TraesCS2A01G330900 chr3A 75.301 332 55 16 304 618 300666144 300665823 6.020000e-27 134.0
59 TraesCS2A01G330900 chr3A 83.544 79 13 0 105 183 532312217 532312295 3.700000e-09 75.0
60 TraesCS2A01G330900 chr6B 75.000 336 55 19 304 621 218438314 218437990 2.800000e-25 128.0
61 TraesCS2A01G330900 chr7A 80.000 160 28 2 9073 9232 17890124 17889969 2.180000e-21 115.0
62 TraesCS2A01G330900 chr7A 95.000 40 2 0 8939 8978 108831887 108831848 8.010000e-06 63.9
63 TraesCS2A01G330900 chr4D 84.146 82 10 2 105 184 268085257 268085337 1.030000e-09 76.8


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 TraesCS2A01G330900 chr2A 563763907 563773461 9554 False 4259.15 14589 100.000000 1 9555 4 chr2A.!!$F2 9554
1 TraesCS2A01G330900 chr2D 424852913 424860907 7994 True 6712.50 12497 95.772000 619 8892 2 chr2D.!!$R3 8273
2 TraesCS2A01G330900 chr2D 424833503 424834054 551 True 743.00 743 91.139000 9010 9555 1 chr2D.!!$R2 545
3 TraesCS2A01G330900 chr2B 500187938 500197052 9114 True 4686.00 12235 89.495667 105 9555 3 chr2B.!!$R1 9450

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
254 256 0.469917 CCACCTGTTCTCTGTGGTGT 59.530 55.000 9.67 0.00 46.02 4.16 F
467 476 0.899720 TATCCACTTCCGTGACACCC 59.100 55.000 0.00 0.00 43.97 4.61 F
786 795 1.107945 GGCCGGCCTATATCTCTCTC 58.892 60.000 38.76 6.46 0.00 3.20 F
2399 2415 0.550147 ATGAGGTAGTTGGGGGCAGT 60.550 55.000 0.00 0.00 0.00 4.40 F
3280 3305 1.882623 GACACCCCTTCTTGAAGCTTG 59.117 52.381 2.10 0.00 0.00 4.01 F
3618 3643 1.202348 GCCACTTTCTGGTATGTTGCC 59.798 52.381 0.00 0.00 42.99 4.52 F
4584 4611 1.065600 GCACCAAAGCAAGTTCGCA 59.934 52.632 0.00 0.00 0.00 5.10 F
4774 4801 2.872245 TCCTGTTTGCAAAGTCTTCTCG 59.128 45.455 13.26 0.00 0.00 4.04 F
5852 5879 1.588082 GCAATGGGTGTGCTCCAAG 59.412 57.895 0.00 0.00 39.00 3.61 F
7085 7115 1.006832 CAGGCCAATCGACCGTAAAG 58.993 55.000 5.01 0.00 0.00 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1745 1760 1.202818 AGCAGGAACCAGACCAAGAAC 60.203 52.381 0.00 0.0 0.00 3.01 R
2366 2382 0.395311 CCTCATCAGGCACCTGCAAT 60.395 55.000 12.03 0.0 43.31 3.56 R
2676 2696 0.893727 AACCCCAAGCTGCTAAACCG 60.894 55.000 0.90 0.0 0.00 4.44 R
3618 3643 1.009903 CACACCGCACATGCAAATGG 61.010 55.000 4.49 0.0 42.21 3.16 R
4584 4611 1.536943 GGGTCGAGCAACCTCTGTCT 61.537 60.000 17.59 0.0 39.42 3.41 R
4991 5018 1.748493 GCAAACCACCTTGTTCACAGA 59.252 47.619 0.00 0.0 0.00 3.41 R
5852 5879 2.282701 TGTTAGTGATACCCGAACGC 57.717 50.000 0.00 0.0 0.00 4.84 R
6299 6326 3.300388 AGACACTGTCCTCTTTGAGTCA 58.700 45.455 5.51 0.0 32.18 3.41 R
7469 7499 0.754217 ACATAGGACTAGGCGGCGAA 60.754 55.000 12.98 0.0 0.00 4.70 R
8938 8980 1.016130 CGGGCAGCATTAGATAGCGG 61.016 60.000 0.00 0.0 35.48 5.52 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
24 25 5.297569 AGAATAAGTCCTCTTACCCATGC 57.702 43.478 0.00 0.00 38.71 4.06
25 26 4.103311 AGAATAAGTCCTCTTACCCATGCC 59.897 45.833 0.00 0.00 38.71 4.40
26 27 1.972588 AAGTCCTCTTACCCATGCCT 58.027 50.000 0.00 0.00 31.46 4.75
27 28 2.868964 AGTCCTCTTACCCATGCCTA 57.131 50.000 0.00 0.00 0.00 3.93
28 29 3.352611 AGTCCTCTTACCCATGCCTAT 57.647 47.619 0.00 0.00 0.00 2.57
29 30 3.669949 AGTCCTCTTACCCATGCCTATT 58.330 45.455 0.00 0.00 0.00 1.73
30 31 4.047883 AGTCCTCTTACCCATGCCTATTT 58.952 43.478 0.00 0.00 0.00 1.40
31 32 4.478686 AGTCCTCTTACCCATGCCTATTTT 59.521 41.667 0.00 0.00 0.00 1.82
32 33 5.044105 AGTCCTCTTACCCATGCCTATTTTT 60.044 40.000 0.00 0.00 0.00 1.94
33 34 6.159751 AGTCCTCTTACCCATGCCTATTTTTA 59.840 38.462 0.00 0.00 0.00 1.52
34 35 7.004691 GTCCTCTTACCCATGCCTATTTTTAT 58.995 38.462 0.00 0.00 0.00 1.40
35 36 7.505923 GTCCTCTTACCCATGCCTATTTTTATT 59.494 37.037 0.00 0.00 0.00 1.40
36 37 8.729047 TCCTCTTACCCATGCCTATTTTTATTA 58.271 33.333 0.00 0.00 0.00 0.98
37 38 9.533831 CCTCTTACCCATGCCTATTTTTATTAT 57.466 33.333 0.00 0.00 0.00 1.28
43 44 9.654919 ACCCATGCCTATTTTTATTATAAGTGT 57.345 29.630 0.00 0.00 0.00 3.55
62 63 7.865706 AAGTGTTCTTAGTGTCAACTTGATT 57.134 32.000 0.00 0.00 37.88 2.57
63 64 7.865706 AGTGTTCTTAGTGTCAACTTGATTT 57.134 32.000 0.00 0.00 37.88 2.17
64 65 8.281212 AGTGTTCTTAGTGTCAACTTGATTTT 57.719 30.769 0.00 0.00 37.88 1.82
65 66 8.184192 AGTGTTCTTAGTGTCAACTTGATTTTG 58.816 33.333 0.00 0.00 37.88 2.44
66 67 8.181573 GTGTTCTTAGTGTCAACTTGATTTTGA 58.818 33.333 0.00 0.00 37.88 2.69
67 68 8.902806 TGTTCTTAGTGTCAACTTGATTTTGAT 58.097 29.630 0.00 0.00 37.88 2.57
68 69 9.387123 GTTCTTAGTGTCAACTTGATTTTGATC 57.613 33.333 0.00 0.00 37.88 2.92
69 70 7.796838 TCTTAGTGTCAACTTGATTTTGATCG 58.203 34.615 0.00 0.00 37.88 3.69
70 71 5.362556 AGTGTCAACTTGATTTTGATCGG 57.637 39.130 0.00 0.00 35.47 4.18
71 72 4.821805 AGTGTCAACTTGATTTTGATCGGT 59.178 37.500 0.00 0.00 35.47 4.69
72 73 5.049405 AGTGTCAACTTGATTTTGATCGGTC 60.049 40.000 0.00 0.00 35.47 4.79
73 74 4.819088 TGTCAACTTGATTTTGATCGGTCA 59.181 37.500 0.00 0.00 35.47 4.02
74 75 5.298026 TGTCAACTTGATTTTGATCGGTCAA 59.702 36.000 7.11 7.11 42.41 3.18
82 83 2.559698 TTGATCGGTCAAAAGCTGGA 57.440 45.000 9.09 0.00 41.22 3.86
83 84 2.559698 TGATCGGTCAAAAGCTGGAA 57.440 45.000 0.00 0.00 0.00 3.53
84 85 3.071874 TGATCGGTCAAAAGCTGGAAT 57.928 42.857 0.00 0.00 0.00 3.01
85 86 3.420893 TGATCGGTCAAAAGCTGGAATT 58.579 40.909 0.00 0.00 0.00 2.17
86 87 4.584874 TGATCGGTCAAAAGCTGGAATTA 58.415 39.130 0.00 0.00 0.00 1.40
87 88 5.007034 TGATCGGTCAAAAGCTGGAATTAA 58.993 37.500 0.00 0.00 0.00 1.40
88 89 5.652014 TGATCGGTCAAAAGCTGGAATTAAT 59.348 36.000 0.00 0.00 0.00 1.40
89 90 5.975693 TCGGTCAAAAGCTGGAATTAATT 57.024 34.783 0.00 0.00 0.00 1.40
90 91 5.949735 TCGGTCAAAAGCTGGAATTAATTC 58.050 37.500 18.22 18.22 36.08 2.17
91 92 5.710099 TCGGTCAAAAGCTGGAATTAATTCT 59.290 36.000 23.85 5.18 37.00 2.40
92 93 6.030228 CGGTCAAAAGCTGGAATTAATTCTC 58.970 40.000 23.85 15.81 37.00 2.87
93 94 6.127897 CGGTCAAAAGCTGGAATTAATTCTCT 60.128 38.462 23.85 16.35 37.00 3.10
94 95 7.254137 GGTCAAAAGCTGGAATTAATTCTCTC 58.746 38.462 23.85 14.19 37.00 3.20
95 96 6.963805 GTCAAAAGCTGGAATTAATTCTCTCG 59.036 38.462 23.85 12.75 37.00 4.04
96 97 5.491635 AAAGCTGGAATTAATTCTCTCGC 57.508 39.130 23.85 19.54 37.00 5.03
97 98 4.142609 AGCTGGAATTAATTCTCTCGCA 57.857 40.909 23.85 13.79 37.00 5.10
98 99 4.517285 AGCTGGAATTAATTCTCTCGCAA 58.483 39.130 23.85 4.84 37.00 4.85
99 100 4.943705 AGCTGGAATTAATTCTCTCGCAAA 59.056 37.500 23.85 3.73 37.00 3.68
100 101 5.415701 AGCTGGAATTAATTCTCTCGCAAAA 59.584 36.000 23.85 2.91 37.00 2.44
101 102 6.096001 AGCTGGAATTAATTCTCTCGCAAAAT 59.904 34.615 23.85 6.66 37.00 1.82
102 103 6.416161 GCTGGAATTAATTCTCTCGCAAAATC 59.584 38.462 23.85 6.87 37.00 2.17
103 104 7.630242 TGGAATTAATTCTCTCGCAAAATCT 57.370 32.000 23.85 0.00 37.00 2.40
107 108 8.606727 AATTAATTCTCTCGCAAAATCTTTCG 57.393 30.769 0.00 0.00 0.00 3.46
111 112 6.575083 TTCTCTCGCAAAATCTTTCGATAG 57.425 37.500 0.00 0.00 0.00 2.08
117 118 4.033358 CGCAAAATCTTTCGATAGCTCAGT 59.967 41.667 0.00 0.00 0.00 3.41
124 125 3.340337 TTCGATAGCTCAGTGTCATCG 57.660 47.619 6.47 6.47 39.77 3.84
128 129 3.573598 GATAGCTCAGTGTCATCGATGG 58.426 50.000 24.61 8.80 0.00 3.51
162 164 7.277981 GCGAGAATCATTTCTACTTCTTTACCA 59.722 37.037 0.00 0.00 42.34 3.25
195 197 5.135552 AGGGACTAATCAATCCACCATGGA 61.136 45.833 21.47 0.00 45.93 3.41
208 210 1.300963 CATGGACCCACACTCCCTG 59.699 63.158 0.00 0.00 0.00 4.45
211 213 2.750350 GACCCACACTCCCTGGTG 59.250 66.667 0.00 0.00 42.34 4.17
218 220 2.448542 ACTCCCTGGTGGTGTGCT 60.449 61.111 0.00 0.00 39.36 4.40
228 230 0.546598 GTGGTGTGCTTAGGCCCTAT 59.453 55.000 0.00 0.00 37.74 2.57
252 254 1.451936 GCCACCTGTTCTCTGTGGT 59.548 57.895 9.42 0.00 37.50 4.16
254 256 0.469917 CCACCTGTTCTCTGTGGTGT 59.530 55.000 9.67 0.00 46.02 4.16
269 271 0.980231 GGTGTCCATGAGGCTCCTCT 60.980 60.000 12.86 0.00 43.12 3.69
271 273 2.111384 GTGTCCATGAGGCTCCTCTTA 58.889 52.381 12.86 0.00 43.12 2.10
272 274 2.501723 GTGTCCATGAGGCTCCTCTTAA 59.498 50.000 12.86 0.00 43.12 1.85
273 275 2.768527 TGTCCATGAGGCTCCTCTTAAG 59.231 50.000 12.86 0.00 43.12 1.85
276 278 4.835615 GTCCATGAGGCTCCTCTTAAGATA 59.164 45.833 12.86 0.00 43.12 1.98
279 281 6.212388 TCCATGAGGCTCCTCTTAAGATATTC 59.788 42.308 12.86 0.04 43.12 1.75
305 307 7.450124 TTGGTTATAAAATCACGCTTACCAA 57.550 32.000 0.00 0.00 39.91 3.67
343 347 7.663664 GTGATAATACACGTTTGTCACAGTAG 58.336 38.462 18.04 0.00 41.84 2.57
348 352 3.181469 ACACGTTTGTCACAGTAGGTCAT 60.181 43.478 0.00 0.00 0.00 3.06
349 353 3.184379 CACGTTTGTCACAGTAGGTCATG 59.816 47.826 0.00 0.00 0.00 3.07
357 361 4.065088 TCACAGTAGGTCATGTTTTCTGC 58.935 43.478 0.00 0.00 0.00 4.26
366 375 5.124457 AGGTCATGTTTTCTGCATGTACATC 59.876 40.000 5.07 2.00 42.94 3.06
367 376 5.124457 GGTCATGTTTTCTGCATGTACATCT 59.876 40.000 5.07 0.00 42.94 2.90
383 392 9.986833 CATGTACATCTGTTTCGATTTTATGAA 57.013 29.630 5.07 0.00 0.00 2.57
414 423 1.756375 CTGTGCTATCGCGGAAGTGC 61.756 60.000 6.13 4.89 42.50 4.40
416 425 1.084370 GTGCTATCGCGGAAGTGCTT 61.084 55.000 6.13 0.00 42.50 3.91
427 436 3.126858 GCGGAAGTGCTTCATGACAATAA 59.873 43.478 13.16 0.00 41.20 1.40
430 439 5.504665 CGGAAGTGCTTCATGACAATAATCC 60.505 44.000 13.16 0.00 41.20 3.01
439 448 9.970395 GCTTCATGACAATAATCCATTTATCAA 57.030 29.630 0.00 0.00 29.96 2.57
443 452 9.172820 CATGACAATAATCCATTTATCAACACG 57.827 33.333 0.00 0.00 29.96 4.49
459 468 2.955614 ACACGAAAGTATCCACTTCCG 58.044 47.619 0.00 0.00 46.75 4.30
464 473 3.613193 CGAAAGTATCCACTTCCGTGACA 60.613 47.826 0.00 0.00 44.41 3.58
465 474 3.314541 AAGTATCCACTTCCGTGACAC 57.685 47.619 0.00 0.00 41.25 3.67
467 476 0.899720 TATCCACTTCCGTGACACCC 59.100 55.000 0.00 0.00 43.97 4.61
474 483 1.465200 TTCCGTGACACCCGTGATGA 61.465 55.000 0.96 0.00 0.00 2.92
532 541 2.027073 CGACACATGACACCCACCG 61.027 63.158 0.00 0.00 0.00 4.94
558 567 1.202290 GGTCGCCGTTAAGTTATCGGA 60.202 52.381 28.47 11.71 46.05 4.55
568 577 2.413310 AGTTATCGGATGCGGGTTTT 57.587 45.000 6.82 0.00 0.00 2.43
569 578 3.547054 AGTTATCGGATGCGGGTTTTA 57.453 42.857 6.82 0.00 0.00 1.52
570 579 4.081322 AGTTATCGGATGCGGGTTTTAT 57.919 40.909 6.82 0.00 0.00 1.40
597 606 2.750237 CTGTTAACAGCCCCGGCC 60.750 66.667 22.03 0.00 43.17 6.13
598 607 3.253838 TGTTAACAGCCCCGGCCT 61.254 61.111 3.59 0.00 43.17 5.19
614 623 2.224079 CGGCCTATGATGATTTTCCACG 59.776 50.000 0.00 0.00 0.00 4.94
616 625 3.003689 GGCCTATGATGATTTTCCACGTG 59.996 47.826 9.08 9.08 0.00 4.49
617 626 3.627577 GCCTATGATGATTTTCCACGTGT 59.372 43.478 15.65 0.00 0.00 4.49
619 628 4.875536 CCTATGATGATTTTCCACGTGTCA 59.124 41.667 15.65 11.46 0.00 3.58
621 630 5.902613 ATGATGATTTTCCACGTGTCAAT 57.097 34.783 15.65 9.15 0.00 2.57
622 631 5.703978 TGATGATTTTCCACGTGTCAATT 57.296 34.783 15.65 3.13 0.00 2.32
623 632 6.083098 TGATGATTTTCCACGTGTCAATTT 57.917 33.333 15.65 0.00 0.00 1.82
624 633 6.148948 TGATGATTTTCCACGTGTCAATTTC 58.851 36.000 15.65 6.54 0.00 2.17
625 634 5.766150 TGATTTTCCACGTGTCAATTTCT 57.234 34.783 15.65 0.00 0.00 2.52
626 635 6.142818 TGATTTTCCACGTGTCAATTTCTT 57.857 33.333 15.65 0.00 0.00 2.52
627 636 7.265647 TGATTTTCCACGTGTCAATTTCTTA 57.734 32.000 15.65 0.00 0.00 2.10
628 637 7.881142 TGATTTTCCACGTGTCAATTTCTTAT 58.119 30.769 15.65 0.00 0.00 1.73
629 638 8.356657 TGATTTTCCACGTGTCAATTTCTTATT 58.643 29.630 15.65 0.00 0.00 1.40
630 639 8.742554 ATTTTCCACGTGTCAATTTCTTATTC 57.257 30.769 15.65 0.00 0.00 1.75
631 640 5.873179 TCCACGTGTCAATTTCTTATTCC 57.127 39.130 15.65 0.00 0.00 3.01
632 641 4.698304 TCCACGTGTCAATTTCTTATTCCC 59.302 41.667 15.65 0.00 0.00 3.97
633 642 4.457603 CCACGTGTCAATTTCTTATTCCCA 59.542 41.667 15.65 0.00 0.00 4.37
634 643 5.048364 CCACGTGTCAATTTCTTATTCCCAA 60.048 40.000 15.65 0.00 0.00 4.12
660 669 1.301953 ATGTCAGCTCTGCGTTGCA 60.302 52.632 0.00 0.00 36.92 4.08
683 692 4.401022 ACATGTGTCACCATTCAACAGAT 58.599 39.130 0.00 0.00 0.00 2.90
703 712 6.150307 ACAGATGATACACGCCAATTAAACAA 59.850 34.615 0.00 0.00 0.00 2.83
714 723 3.919804 CCAATTAAACAATGGCACGTGAG 59.080 43.478 22.23 5.30 0.00 3.51
748 757 5.221087 CCGTGGTTCTTTACTTAAAAAGCCA 60.221 40.000 0.00 0.00 36.58 4.75
786 795 1.107945 GGCCGGCCTATATCTCTCTC 58.892 60.000 38.76 6.46 0.00 3.20
787 796 1.341581 GGCCGGCCTATATCTCTCTCT 60.342 57.143 38.76 0.00 0.00 3.10
808 817 1.943340 GGAGCTGCAGTTATTAGTGGC 59.057 52.381 16.64 0.00 0.00 5.01
849 864 1.144936 GAGAACCAGATGCCTCCGG 59.855 63.158 0.00 0.00 0.00 5.14
1176 1191 4.280494 CGCCGGGTGGATCTACCG 62.280 72.222 20.77 16.89 46.79 4.02
1715 1730 8.761575 TTAAGCTATTTTTCCTTTGATGCTTG 57.238 30.769 0.00 0.00 38.45 4.01
1718 1733 6.015180 AGCTATTTTTCCTTTGATGCTTGTGA 60.015 34.615 0.00 0.00 0.00 3.58
1745 1760 5.350640 GTCTTAATTAACCACACGGAGAAGG 59.649 44.000 0.00 0.00 35.59 3.46
1847 1862 4.752604 GCTAGGCTAGTGCTCCTTTATTTC 59.247 45.833 21.92 0.00 39.59 2.17
1967 1982 1.842562 GTTAAACTACCCCTCCCTCCC 59.157 57.143 0.00 0.00 0.00 4.30
2143 2159 5.945784 CCCACTAATCCACTTCTTGATTTGA 59.054 40.000 0.00 0.00 33.46 2.69
2189 2205 7.060383 AGACTCTACTGATATTTCATGTGGG 57.940 40.000 0.00 0.00 0.00 4.61
2192 2208 7.633789 ACTCTACTGATATTTCATGTGGGTTT 58.366 34.615 0.00 0.00 0.00 3.27
2193 2209 8.109634 ACTCTACTGATATTTCATGTGGGTTTT 58.890 33.333 0.00 0.00 0.00 2.43
2277 2293 1.419387 CAATCACTCCTCCATCTCCCC 59.581 57.143 0.00 0.00 0.00 4.81
2361 2377 3.312736 ACATGGGTCTTGGTTTCTGTT 57.687 42.857 0.00 0.00 0.00 3.16
2362 2378 3.642141 ACATGGGTCTTGGTTTCTGTTT 58.358 40.909 0.00 0.00 0.00 2.83
2363 2379 3.384467 ACATGGGTCTTGGTTTCTGTTTG 59.616 43.478 0.00 0.00 0.00 2.93
2364 2380 1.754226 TGGGTCTTGGTTTCTGTTTGC 59.246 47.619 0.00 0.00 0.00 3.68
2365 2381 1.754226 GGGTCTTGGTTTCTGTTTGCA 59.246 47.619 0.00 0.00 0.00 4.08
2366 2382 2.167487 GGGTCTTGGTTTCTGTTTGCAA 59.833 45.455 0.00 0.00 0.00 4.08
2399 2415 0.550147 ATGAGGTAGTTGGGGGCAGT 60.550 55.000 0.00 0.00 0.00 4.40
2644 2664 4.846168 AAGGTGAGAAATAAGAGGGACC 57.154 45.455 0.00 0.00 0.00 4.46
2731 2751 2.270352 TGGTGGATTTGCGTCTTTCT 57.730 45.000 0.00 0.00 0.00 2.52
3038 3059 5.755849 TCCTTATTGATGTTTTCCTCTCCC 58.244 41.667 0.00 0.00 0.00 4.30
3082 3103 4.042311 TCCAGTTGACCATTACTTAAGCCA 59.958 41.667 1.29 0.00 0.00 4.75
3092 3113 8.823220 ACCATTACTTAAGCCATTTGAATACT 57.177 30.769 1.29 0.00 0.00 2.12
3093 3114 9.914834 ACCATTACTTAAGCCATTTGAATACTA 57.085 29.630 1.29 0.00 0.00 1.82
3267 3292 2.429610 TGAGAGCGTAATAAGACACCCC 59.570 50.000 0.00 0.00 0.00 4.95
3280 3305 1.882623 GACACCCCTTCTTGAAGCTTG 59.117 52.381 2.10 0.00 0.00 4.01
3368 3393 2.387445 CGGCGGACATGCGAAAAGA 61.387 57.895 0.00 0.00 35.06 2.52
3618 3643 1.202348 GCCACTTTCTGGTATGTTGCC 59.798 52.381 0.00 0.00 42.99 4.52
3839 3866 3.767673 TCTGTCAGGCTCCGTATAGTTTT 59.232 43.478 0.00 0.00 0.00 2.43
3911 3938 3.470645 AGAGCTTCAGTGTTTACGGTT 57.529 42.857 0.00 0.00 0.00 4.44
4151 4178 7.603963 TGCTAATGCGTCTGTTTTTATCTTA 57.396 32.000 0.00 0.00 43.34 2.10
4584 4611 1.065600 GCACCAAAGCAAGTTCGCA 59.934 52.632 0.00 0.00 0.00 5.10
4774 4801 2.872245 TCCTGTTTGCAAAGTCTTCTCG 59.128 45.455 13.26 0.00 0.00 4.04
4991 5018 2.874701 GCTATCGATTTGTCTGTGCCAT 59.125 45.455 1.71 0.00 0.00 4.40
5675 5702 6.127310 TGTTAGCTTCCTCTCCAGTCTATTTC 60.127 42.308 0.00 0.00 0.00 2.17
5776 5803 4.597032 CTCTGAGGAGGAGCCGAT 57.403 61.111 0.00 0.00 43.43 4.18
5852 5879 1.588082 GCAATGGGTGTGCTCCAAG 59.412 57.895 0.00 0.00 39.00 3.61
6064 6091 8.467598 AGTCAATGAAAATGATGATCAGGAAAG 58.532 33.333 0.09 0.00 0.00 2.62
6067 6094 5.582953 TGAAAATGATGATCAGGAAAGGGT 58.417 37.500 0.09 0.00 0.00 4.34
6080 6107 5.536161 TCAGGAAAGGGTTTCTTCAAGATTG 59.464 40.000 0.00 0.00 39.59 2.67
6185 6212 7.504924 TCTTGCGAAGAGAAAAATTAAGGAA 57.495 32.000 0.00 0.00 32.71 3.36
6297 6324 7.331026 TGTTTCCATTAGAGGTCTGAGTAATG 58.669 38.462 0.00 0.00 34.15 1.90
6298 6325 7.180229 TGTTTCCATTAGAGGTCTGAGTAATGA 59.820 37.037 0.00 0.00 35.68 2.57
6299 6326 7.921041 TTCCATTAGAGGTCTGAGTAATGAT 57.079 36.000 0.00 0.00 35.68 2.45
6341 6368 9.538508 GTGTCTACTTCTAAGGTGTTAAGAAAA 57.461 33.333 0.00 0.00 0.00 2.29
6601 6628 6.260870 TGTGACACAACAAACAACAAGTAT 57.739 33.333 5.62 0.00 0.00 2.12
6783 6810 1.740025 GCTCCACTAAGCAATCCACAC 59.260 52.381 0.00 0.00 42.05 3.82
6784 6811 2.875672 GCTCCACTAAGCAATCCACACA 60.876 50.000 0.00 0.00 42.05 3.72
6785 6812 3.614092 CTCCACTAAGCAATCCACACAT 58.386 45.455 0.00 0.00 0.00 3.21
7085 7115 1.006832 CAGGCCAATCGACCGTAAAG 58.993 55.000 5.01 0.00 0.00 1.85
7151 7181 1.519719 GAAGTCGATGCCTCCAGCT 59.480 57.895 0.00 0.00 44.23 4.24
7256 7286 4.090761 TGAAAGTTCAACAGCCAGATCT 57.909 40.909 0.00 0.00 33.55 2.75
7449 7479 3.132824 TGCGACAGATTGTATCAGACCAT 59.867 43.478 0.00 0.00 0.00 3.55
7450 7480 4.122776 GCGACAGATTGTATCAGACCATT 58.877 43.478 0.00 0.00 0.00 3.16
7469 7499 4.159135 CCATTATTGCAAACTCAGCTTCCT 59.841 41.667 1.71 0.00 0.00 3.36
7478 7508 4.767255 CAGCTTCCTTCGCCGCCT 62.767 66.667 0.00 0.00 0.00 5.52
7955 7985 1.756538 CCATTTTACTGCCATCCACCC 59.243 52.381 0.00 0.00 0.00 4.61
8462 8493 8.319143 TCTTTCTTTTTGGTACTTATCTTCCG 57.681 34.615 0.00 0.00 0.00 4.30
8472 8503 0.753262 TTATCTTCCGCTCTGCTCCC 59.247 55.000 0.00 0.00 0.00 4.30
8529 8560 5.252969 CAACTGCAGTATATGTTGCCAAT 57.747 39.130 22.01 0.00 39.54 3.16
8731 8766 3.064207 TCGACCATTGTTGCTAACTGAC 58.936 45.455 0.00 0.00 0.00 3.51
8765 8807 4.640771 TTGCTATCTGAAACTTGGGAGT 57.359 40.909 0.00 0.00 37.87 3.85
8782 8824 0.673437 AGTTGTTTGGCAATCCACCG 59.327 50.000 0.00 0.00 43.33 4.94
8831 8873 1.899814 ACCTATTTGCTCACTCCACGA 59.100 47.619 0.00 0.00 0.00 4.35
8904 8946 2.122768 CTCTGAAGAGGCCCTTATGGT 58.877 52.381 0.00 0.00 38.48 3.55
8905 8947 3.309296 CTCTGAAGAGGCCCTTATGGTA 58.691 50.000 0.00 0.00 38.48 3.25
8906 8948 3.309296 TCTGAAGAGGCCCTTATGGTAG 58.691 50.000 0.00 0.00 34.68 3.18
8907 8949 3.052109 TCTGAAGAGGCCCTTATGGTAGA 60.052 47.826 0.00 0.68 34.68 2.59
8908 8950 3.039011 TGAAGAGGCCCTTATGGTAGAC 58.961 50.000 0.00 0.00 34.68 2.59
8909 8951 3.310193 GAAGAGGCCCTTATGGTAGACT 58.690 50.000 0.00 0.00 34.68 3.24
8910 8952 2.965562 AGAGGCCCTTATGGTAGACTC 58.034 52.381 0.00 0.04 36.04 3.36
8911 8953 2.520549 AGAGGCCCTTATGGTAGACTCT 59.479 50.000 0.00 4.09 36.04 3.24
8912 8954 2.630580 GAGGCCCTTATGGTAGACTCTG 59.369 54.545 0.00 0.00 36.04 3.35
8913 8955 2.247635 AGGCCCTTATGGTAGACTCTGA 59.752 50.000 0.00 0.00 36.04 3.27
8914 8956 3.039011 GGCCCTTATGGTAGACTCTGAA 58.961 50.000 0.00 0.00 36.04 3.02
8915 8957 3.070302 GGCCCTTATGGTAGACTCTGAAG 59.930 52.174 0.00 0.00 36.04 3.02
8916 8958 3.961408 GCCCTTATGGTAGACTCTGAAGA 59.039 47.826 0.00 0.00 36.04 2.87
8917 8959 4.038642 GCCCTTATGGTAGACTCTGAAGAG 59.961 50.000 5.77 5.77 41.44 2.85
8918 8960 4.586841 CCCTTATGGTAGACTCTGAAGAGG 59.413 50.000 11.87 0.00 46.13 3.69
8926 8968 3.467374 GACTCTGAAGAGGCCCTTATG 57.533 52.381 11.87 0.00 44.42 1.90
8927 8969 2.103941 GACTCTGAAGAGGCCCTTATGG 59.896 54.545 11.87 0.00 44.42 2.74
8928 8970 2.122768 CTCTGAAGAGGCCCTTATGGT 58.877 52.381 0.00 0.00 38.48 3.55
8946 8988 2.108425 TGGTATCTCCAGACCGCTATCT 59.892 50.000 0.00 0.00 41.93 1.98
8949 8991 4.951094 GGTATCTCCAGACCGCTATCTAAT 59.049 45.833 0.00 0.00 35.97 1.73
8950 8992 5.163602 GGTATCTCCAGACCGCTATCTAATG 60.164 48.000 0.00 0.00 35.97 1.90
8952 8994 2.560542 CTCCAGACCGCTATCTAATGCT 59.439 50.000 0.00 0.00 0.00 3.79
8954 8996 2.064762 CAGACCGCTATCTAATGCTGC 58.935 52.381 0.00 0.00 0.00 5.25
8970 9012 2.954989 TGCTGCCCGCATATATTTCAAA 59.045 40.909 0.00 0.00 45.47 2.69
8971 9013 3.243367 TGCTGCCCGCATATATTTCAAAC 60.243 43.478 0.00 0.00 45.47 2.93
8972 9014 3.243367 GCTGCCCGCATATATTTCAAACA 60.243 43.478 0.00 0.00 38.92 2.83
8973 9015 4.290155 CTGCCCGCATATATTTCAAACAC 58.710 43.478 0.00 0.00 0.00 3.32
8974 9016 3.951037 TGCCCGCATATATTTCAAACACT 59.049 39.130 0.00 0.00 0.00 3.55
8975 9017 4.400884 TGCCCGCATATATTTCAAACACTT 59.599 37.500 0.00 0.00 0.00 3.16
8977 9019 5.810074 GCCCGCATATATTTCAAACACTTTT 59.190 36.000 0.00 0.00 0.00 2.27
8978 9020 6.312672 GCCCGCATATATTTCAAACACTTTTT 59.687 34.615 0.00 0.00 0.00 1.94
9132 9174 7.907214 AATATCTAAAACTCTTTGCACGTCT 57.093 32.000 0.00 0.00 0.00 4.18
9239 9281 1.153745 GGCAACTCGCTCGTCAGAT 60.154 57.895 0.00 0.00 41.91 2.90
9244 9286 0.179187 ACTCGCTCGTCAGATTGTCG 60.179 55.000 0.00 0.00 0.00 4.35
9253 9310 2.096013 CGTCAGATTGTCGTGAGCTCTA 59.904 50.000 16.19 0.00 0.00 2.43
9254 9311 3.242903 CGTCAGATTGTCGTGAGCTCTAT 60.243 47.826 16.19 0.00 0.00 1.98
9255 9312 4.024809 CGTCAGATTGTCGTGAGCTCTATA 60.025 45.833 16.19 0.00 0.00 1.31
9256 9313 5.334491 CGTCAGATTGTCGTGAGCTCTATAT 60.334 44.000 16.19 0.00 0.00 0.86
9257 9314 6.442952 GTCAGATTGTCGTGAGCTCTATATT 58.557 40.000 16.19 0.00 0.00 1.28
9258 9315 6.580791 GTCAGATTGTCGTGAGCTCTATATTC 59.419 42.308 16.19 3.71 0.00 1.75
9259 9316 6.488344 TCAGATTGTCGTGAGCTCTATATTCT 59.512 38.462 16.19 5.90 0.00 2.40
9260 9317 7.013750 TCAGATTGTCGTGAGCTCTATATTCTT 59.986 37.037 16.19 0.00 0.00 2.52
9261 9318 7.651304 CAGATTGTCGTGAGCTCTATATTCTTT 59.349 37.037 16.19 0.00 0.00 2.52
9265 9322 6.096987 TGTCGTGAGCTCTATATTCTTTCCTT 59.903 38.462 16.19 0.00 0.00 3.36
9298 9355 3.333189 CCGGATGCGTCGCTCATG 61.333 66.667 19.50 5.98 0.00 3.07
9299 9356 3.993234 CGGATGCGTCGCTCATGC 61.993 66.667 19.50 8.82 37.56 4.06
9300 9357 2.587194 GGATGCGTCGCTCATGCT 60.587 61.111 19.50 0.00 37.96 3.79
9301 9358 2.176273 GGATGCGTCGCTCATGCTT 61.176 57.895 19.50 0.00 37.96 3.91
9303 9360 2.370824 GATGCGTCGCTCATGCTTGG 62.371 60.000 19.50 0.00 37.96 3.61
9305 9362 2.434884 CGTCGCTCATGCTTGGGT 60.435 61.111 0.92 0.00 36.97 4.51
9388 9464 1.669115 CAGGGCAAGACACCGACTG 60.669 63.158 0.00 0.00 0.00 3.51
9391 9467 0.249398 GGGCAAGACACCGACTGTAT 59.751 55.000 0.00 0.00 31.03 2.29
9469 9545 4.035792 CGTGTTCTACTTCTCCTCGATGAT 59.964 45.833 0.00 0.00 0.00 2.45
9548 9624 0.948623 CAAGGACATGTTGACGGCGA 60.949 55.000 16.62 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.183361 GGCATGGGTAAGAGGACTTATTCTTA 60.183 42.308 0.00 0.00 40.15 2.10
3 4 4.103311 AGGCATGGGTAAGAGGACTTATTC 59.897 45.833 0.00 0.00 40.15 1.75
4 5 4.047883 AGGCATGGGTAAGAGGACTTATT 58.952 43.478 0.00 0.00 40.15 1.40
7 8 1.972588 AGGCATGGGTAAGAGGACTT 58.027 50.000 0.00 0.00 39.81 3.01
8 9 2.868964 TAGGCATGGGTAAGAGGACT 57.131 50.000 0.00 0.00 0.00 3.85
9 10 4.439253 AAATAGGCATGGGTAAGAGGAC 57.561 45.455 0.00 0.00 0.00 3.85
10 11 5.466127 AAAAATAGGCATGGGTAAGAGGA 57.534 39.130 0.00 0.00 0.00 3.71
11 12 7.839680 AATAAAAATAGGCATGGGTAAGAGG 57.160 36.000 0.00 0.00 0.00 3.69
17 18 9.654919 ACACTTATAATAAAAATAGGCATGGGT 57.345 29.630 0.00 0.00 0.00 4.51
36 37 9.561069 AATCAAGTTGACACTAAGAACACTTAT 57.439 29.630 7.96 0.00 30.68 1.73
37 38 8.958119 AATCAAGTTGACACTAAGAACACTTA 57.042 30.769 7.96 0.00 30.68 2.24
38 39 7.865706 AATCAAGTTGACACTAAGAACACTT 57.134 32.000 7.96 0.00 30.68 3.16
39 40 7.865706 AAATCAAGTTGACACTAAGAACACT 57.134 32.000 7.96 0.00 30.68 3.55
40 41 8.181573 TCAAAATCAAGTTGACACTAAGAACAC 58.818 33.333 7.96 0.00 30.68 3.32
41 42 8.275015 TCAAAATCAAGTTGACACTAAGAACA 57.725 30.769 7.96 0.00 30.68 3.18
42 43 9.387123 GATCAAAATCAAGTTGACACTAAGAAC 57.613 33.333 7.96 0.00 37.80 3.01
43 44 8.282592 CGATCAAAATCAAGTTGACACTAAGAA 58.717 33.333 7.96 0.00 37.80 2.52
44 45 7.095229 CCGATCAAAATCAAGTTGACACTAAGA 60.095 37.037 7.96 2.65 37.80 2.10
45 46 7.017645 CCGATCAAAATCAAGTTGACACTAAG 58.982 38.462 7.96 0.00 37.80 2.18
46 47 6.485313 ACCGATCAAAATCAAGTTGACACTAA 59.515 34.615 7.96 0.00 37.80 2.24
47 48 5.995282 ACCGATCAAAATCAAGTTGACACTA 59.005 36.000 7.96 0.00 37.80 2.74
48 49 4.821805 ACCGATCAAAATCAAGTTGACACT 59.178 37.500 7.96 0.00 37.80 3.55
49 50 5.108385 ACCGATCAAAATCAAGTTGACAC 57.892 39.130 7.96 0.00 37.80 3.67
50 51 4.819088 TGACCGATCAAAATCAAGTTGACA 59.181 37.500 7.96 0.00 37.80 3.58
51 52 5.356882 TGACCGATCAAAATCAAGTTGAC 57.643 39.130 7.96 0.00 37.80 3.18
63 64 2.559698 TCCAGCTTTTGACCGATCAA 57.440 45.000 0.00 0.00 43.28 2.57
64 65 2.559698 TTCCAGCTTTTGACCGATCA 57.440 45.000 0.00 0.00 0.00 2.92
65 66 5.560966 TTAATTCCAGCTTTTGACCGATC 57.439 39.130 0.00 0.00 0.00 3.69
66 67 6.378280 AGAATTAATTCCAGCTTTTGACCGAT 59.622 34.615 21.86 0.00 37.51 4.18
67 68 5.710099 AGAATTAATTCCAGCTTTTGACCGA 59.290 36.000 21.86 0.00 37.51 4.69
68 69 5.954335 AGAATTAATTCCAGCTTTTGACCG 58.046 37.500 21.86 0.00 37.51 4.79
69 70 7.163001 AGAGAATTAATTCCAGCTTTTGACC 57.837 36.000 21.86 0.00 37.51 4.02
70 71 6.963805 CGAGAGAATTAATTCCAGCTTTTGAC 59.036 38.462 21.86 6.70 37.51 3.18
71 72 6.403636 GCGAGAGAATTAATTCCAGCTTTTGA 60.404 38.462 21.86 0.00 37.51 2.69
72 73 5.741040 GCGAGAGAATTAATTCCAGCTTTTG 59.259 40.000 21.86 12.55 37.51 2.44
73 74 5.415701 TGCGAGAGAATTAATTCCAGCTTTT 59.584 36.000 21.86 4.31 37.51 2.27
74 75 4.943705 TGCGAGAGAATTAATTCCAGCTTT 59.056 37.500 21.86 4.99 37.51 3.51
75 76 4.517285 TGCGAGAGAATTAATTCCAGCTT 58.483 39.130 21.86 5.68 37.51 3.74
76 77 4.142609 TGCGAGAGAATTAATTCCAGCT 57.857 40.909 21.86 16.90 37.51 4.24
77 78 4.882671 TTGCGAGAGAATTAATTCCAGC 57.117 40.909 21.86 20.31 37.51 4.85
78 79 7.701445 AGATTTTGCGAGAGAATTAATTCCAG 58.299 34.615 21.86 12.94 37.51 3.86
79 80 7.630242 AGATTTTGCGAGAGAATTAATTCCA 57.370 32.000 21.86 11.25 37.51 3.53
80 81 8.917415 AAAGATTTTGCGAGAGAATTAATTCC 57.083 30.769 21.86 14.34 37.51 3.01
81 82 8.728630 CGAAAGATTTTGCGAGAGAATTAATTC 58.271 33.333 18.70 18.70 37.55 2.17
82 83 8.450964 TCGAAAGATTTTGCGAGAGAATTAATT 58.549 29.630 0.00 0.00 39.42 1.40
83 84 7.974675 TCGAAAGATTTTGCGAGAGAATTAAT 58.025 30.769 0.00 0.00 39.42 1.40
84 85 7.359262 TCGAAAGATTTTGCGAGAGAATTAA 57.641 32.000 0.00 0.00 39.42 1.40
85 86 6.961359 TCGAAAGATTTTGCGAGAGAATTA 57.039 33.333 0.00 0.00 39.42 1.40
86 87 5.862924 TCGAAAGATTTTGCGAGAGAATT 57.137 34.783 0.00 0.00 39.42 2.17
101 102 6.653987 TCGATGACACTGAGCTATCGAAAGA 61.654 44.000 11.91 0.00 44.33 2.52
102 103 3.728221 CGATGACACTGAGCTATCGAAAG 59.272 47.826 6.92 0.00 42.16 2.62
103 104 3.377172 TCGATGACACTGAGCTATCGAAA 59.623 43.478 11.91 0.00 44.33 3.46
107 108 3.254411 TCCATCGATGACACTGAGCTATC 59.746 47.826 26.86 0.00 0.00 2.08
111 112 2.299993 TTCCATCGATGACACTGAGC 57.700 50.000 26.86 0.00 0.00 4.26
137 138 8.703604 TGGTAAAGAAGTAGAAATGATTCTCG 57.296 34.615 0.00 0.00 44.75 4.04
138 139 9.877178 TCTGGTAAAGAAGTAGAAATGATTCTC 57.123 33.333 0.00 0.00 38.28 2.87
151 153 6.500751 TCCCTTTAGTGATCTGGTAAAGAAGT 59.499 38.462 16.97 0.00 38.79 3.01
162 164 7.348274 TGGATTGATTAGTCCCTTTAGTGATCT 59.652 37.037 0.00 0.00 33.45 2.75
170 172 4.946160 TGGTGGATTGATTAGTCCCTTT 57.054 40.909 0.00 0.00 33.45 3.11
195 197 2.854032 CCACCAGGGAGTGTGGGT 60.854 66.667 0.70 0.00 46.67 4.51
198 200 3.240491 ACACCACCAGGGAGTGTG 58.760 61.111 14.39 7.07 42.89 3.82
208 210 2.361230 GGGCCTAAGCACACCACC 60.361 66.667 0.84 0.00 44.19 4.61
234 236 4.386413 CCACAGAGAACAGGTGGC 57.614 61.111 0.00 0.00 44.84 5.01
242 244 1.625315 CCTCATGGACACCACAGAGAA 59.375 52.381 17.64 0.00 39.72 2.87
243 245 1.269958 CCTCATGGACACCACAGAGA 58.730 55.000 17.64 4.62 39.72 3.10
245 247 0.837691 AGCCTCATGGACACCACAGA 60.838 55.000 0.00 0.00 35.80 3.41
246 248 0.392193 GAGCCTCATGGACACCACAG 60.392 60.000 0.00 0.00 35.80 3.66
252 254 2.550277 TAAGAGGAGCCTCATGGACA 57.450 50.000 18.16 0.00 44.99 4.02
254 256 3.404869 TCTTAAGAGGAGCCTCATGGA 57.595 47.619 18.16 8.01 44.99 3.41
276 278 9.783256 GTAAGCGTGATTTTATAACCAAAGAAT 57.217 29.630 0.00 0.00 0.00 2.40
279 281 7.531716 TGGTAAGCGTGATTTTATAACCAAAG 58.468 34.615 0.00 0.00 31.83 2.77
321 325 6.694447 ACCTACTGTGACAAACGTGTATTAT 58.306 36.000 0.00 0.00 38.41 1.28
324 328 4.038282 TGACCTACTGTGACAAACGTGTAT 59.962 41.667 0.00 0.00 38.41 2.29
325 329 3.380954 TGACCTACTGTGACAAACGTGTA 59.619 43.478 0.00 0.00 38.41 2.90
343 347 4.764679 TGTACATGCAGAAAACATGACC 57.235 40.909 10.49 1.67 46.33 4.02
348 352 6.389830 AAACAGATGTACATGCAGAAAACA 57.610 33.333 14.43 0.00 0.00 2.83
349 353 5.565259 CGAAACAGATGTACATGCAGAAAAC 59.435 40.000 14.43 0.00 0.00 2.43
357 361 9.986833 TTCATAAAATCGAAACAGATGTACATG 57.013 29.630 14.43 3.72 0.00 3.21
402 411 0.108186 TCATGAAGCACTTCCGCGAT 60.108 50.000 8.23 0.00 38.77 4.58
427 436 7.773224 TGGATACTTTCGTGTTGATAAATGGAT 59.227 33.333 0.00 0.00 37.61 3.41
430 439 7.974675 AGTGGATACTTTCGTGTTGATAAATG 58.025 34.615 0.00 0.00 31.66 2.32
459 468 4.034048 GTCATTTATCATCACGGGTGTCAC 59.966 45.833 0.00 0.00 0.00 3.67
461 470 3.245284 CGTCATTTATCATCACGGGTGTC 59.755 47.826 0.00 0.00 0.00 3.67
464 473 3.194861 CACGTCATTTATCATCACGGGT 58.805 45.455 0.00 0.00 34.75 5.28
465 474 3.194861 ACACGTCATTTATCATCACGGG 58.805 45.455 0.00 0.00 39.79 5.28
491 500 5.555818 CGGTTACTCTTGACGAAAACACTTC 60.556 44.000 0.00 0.00 0.00 3.01
543 552 1.790623 CCGCATCCGATAACTTAACGG 59.209 52.381 10.49 10.49 46.71 4.44
558 567 4.224370 AGGTATCGGATATAAAACCCGCAT 59.776 41.667 0.29 0.00 42.70 4.73
568 577 5.186409 GGGCTGTTAACAGGTATCGGATATA 59.814 44.000 31.42 0.00 43.94 0.86
569 578 4.020485 GGGCTGTTAACAGGTATCGGATAT 60.020 45.833 31.42 0.00 43.94 1.63
570 579 3.322828 GGGCTGTTAACAGGTATCGGATA 59.677 47.826 31.42 0.00 43.94 2.59
597 606 6.421377 TTGACACGTGGAAAATCATCATAG 57.579 37.500 21.57 0.00 0.00 2.23
598 607 7.389803 AATTGACACGTGGAAAATCATCATA 57.610 32.000 21.57 0.00 0.00 2.15
614 623 7.090808 GGTCTTTGGGAATAAGAAATTGACAC 58.909 38.462 0.00 0.00 33.71 3.67
616 625 7.090808 GTGGTCTTTGGGAATAAGAAATTGAC 58.909 38.462 0.00 0.00 33.71 3.18
617 626 6.780031 TGTGGTCTTTGGGAATAAGAAATTGA 59.220 34.615 0.00 0.00 33.71 2.57
619 628 7.235399 ACATGTGGTCTTTGGGAATAAGAAATT 59.765 33.333 0.00 0.00 33.71 1.82
621 630 6.074648 ACATGTGGTCTTTGGGAATAAGAAA 58.925 36.000 0.00 0.00 33.71 2.52
622 631 5.640147 ACATGTGGTCTTTGGGAATAAGAA 58.360 37.500 0.00 0.00 33.71 2.52
623 632 5.253330 GACATGTGGTCTTTGGGAATAAGA 58.747 41.667 1.15 0.00 43.46 2.10
624 633 5.567138 GACATGTGGTCTTTGGGAATAAG 57.433 43.478 1.15 0.00 43.46 1.73
660 669 8.661145 ATCATCTGTTGAATGGTGACACATGTT 61.661 37.037 8.08 0.00 38.88 2.71
683 692 5.645624 CCATTGTTTAATTGGCGTGTATCA 58.354 37.500 0.00 0.00 0.00 2.15
703 712 4.002506 TGCCGTCTCACGTGCCAT 62.003 61.111 11.67 0.00 40.58 4.40
748 757 0.321653 CCGCTAACTTTGACTGGGCT 60.322 55.000 0.00 0.00 0.00 5.19
786 795 3.201290 CCACTAATAACTGCAGCTCCAG 58.799 50.000 15.27 2.15 38.78 3.86
787 796 2.680805 GCCACTAATAACTGCAGCTCCA 60.681 50.000 15.27 0.00 0.00 3.86
849 864 2.978010 CACCAACCACTCGCACCC 60.978 66.667 0.00 0.00 0.00 4.61
1672 1687 1.760192 AAGATCCAGCATGAACAGCC 58.240 50.000 0.00 0.00 39.69 4.85
1715 1730 5.163794 CCGTGTGGTTAATTAAGACCATCAC 60.164 44.000 19.41 19.41 46.74 3.06
1718 1733 5.046159 TCTCCGTGTGGTTAATTAAGACCAT 60.046 40.000 11.34 0.00 46.74 3.55
1745 1760 1.202818 AGCAGGAACCAGACCAAGAAC 60.203 52.381 0.00 0.00 0.00 3.01
1847 1862 4.511838 TTTTTCTTCGGCCTGGGG 57.488 55.556 0.00 0.00 0.00 4.96
2143 2159 1.756561 GCACAAGTGGGTTGGTGGT 60.757 57.895 2.00 0.00 40.90 4.16
2277 2293 7.953158 ATCTATCGTGTCATTTTATGTGGAG 57.047 36.000 0.00 0.00 0.00 3.86
2363 2379 0.459585 CATCAGGCACCTGCAATTGC 60.460 55.000 23.69 23.69 43.31 3.56
2364 2380 1.134367 CTCATCAGGCACCTGCAATTG 59.866 52.381 12.03 0.00 43.31 2.32
2365 2381 1.471119 CTCATCAGGCACCTGCAATT 58.529 50.000 12.03 0.00 43.31 2.32
2366 2382 0.395311 CCTCATCAGGCACCTGCAAT 60.395 55.000 12.03 0.00 43.31 3.56
2571 2587 1.303561 GCAGGATCTTGGTGTGCCA 60.304 57.895 6.99 0.00 44.38 4.92
2676 2696 0.893727 AACCCCAAGCTGCTAAACCG 60.894 55.000 0.90 0.00 0.00 4.44
2731 2751 1.520564 GTGCGGTGCGTATGGATCA 60.521 57.895 0.00 0.00 0.00 2.92
2959 2980 9.892130 AACATCACTAAGTAGGGAAAAAGATAG 57.108 33.333 0.00 0.00 39.54 2.08
3013 3034 6.663523 GGGAGAGGAAAACATCAATAAGGAAA 59.336 38.462 0.00 0.00 0.00 3.13
3032 3053 5.133221 TGTCAAAAGGAAGAAAAGGGAGAG 58.867 41.667 0.00 0.00 0.00 3.20
3038 3059 7.229506 ACTGGACTATGTCAAAAGGAAGAAAAG 59.770 37.037 0.07 0.00 33.68 2.27
3095 3116 7.985184 CCAGTAAACCATATATGCCACGTATAT 59.015 37.037 7.24 0.00 0.00 0.86
3235 3260 1.299541 ACGCTCTCAAAATATGCCCG 58.700 50.000 0.00 0.00 0.00 6.13
3267 3292 5.517770 CACTTTCCAAACAAGCTTCAAGAAG 59.482 40.000 0.00 5.46 41.24 2.85
3280 3305 1.111277 AGCACCCACACTTTCCAAAC 58.889 50.000 0.00 0.00 0.00 2.93
3618 3643 1.009903 CACACCGCACATGCAAATGG 61.010 55.000 4.49 0.00 42.21 3.16
3641 3666 1.016653 GCGAGGAGACTGCAACCTTC 61.017 60.000 0.00 0.00 44.43 3.46
3689 3714 2.499289 TGTTCCTTTGTGGCATGTTTGT 59.501 40.909 0.00 0.00 35.26 2.83
3911 3938 3.394606 AGCCACACCTTCCTCTTTAGAAA 59.605 43.478 0.00 0.00 0.00 2.52
4038 4065 9.920133 TGTTCAAATGATTCGGATTTAAATTGA 57.080 25.926 1.43 1.31 0.00 2.57
4151 4178 7.066284 CCTCGAATCAAAAACATAATCTCTGGT 59.934 37.037 0.00 0.00 0.00 4.00
4584 4611 1.536943 GGGTCGAGCAACCTCTGTCT 61.537 60.000 17.59 0.00 39.42 3.41
4774 4801 6.817765 TTCAAAGTGGTATTTGATGGAGAC 57.182 37.500 3.00 0.00 45.83 3.36
4991 5018 1.748493 GCAAACCACCTTGTTCACAGA 59.252 47.619 0.00 0.00 0.00 3.41
5773 5800 3.873361 AGGTTTCTGTGTATGCATGATCG 59.127 43.478 10.16 0.00 0.00 3.69
5776 5803 5.046663 TCAGTAGGTTTCTGTGTATGCATGA 60.047 40.000 10.16 0.00 34.86 3.07
5852 5879 2.282701 TGTTAGTGATACCCGAACGC 57.717 50.000 0.00 0.00 0.00 4.84
6064 6091 6.207417 TGATCTGAACAATCTTGAAGAAACCC 59.793 38.462 0.00 0.00 0.00 4.11
6067 6094 9.903682 GAATTGATCTGAACAATCTTGAAGAAA 57.096 29.630 12.69 0.00 37.04 2.52
6080 6107 4.530875 ACCATCTGGGAATTGATCTGAAC 58.469 43.478 0.54 0.00 41.15 3.18
6245 6272 4.646492 AGACAAGGTTCAGAGCATTTTGTT 59.354 37.500 0.00 0.00 0.00 2.83
6297 6324 4.021544 AGACACTGTCCTCTTTGAGTCATC 60.022 45.833 5.51 0.00 32.18 2.92
6298 6325 3.900601 AGACACTGTCCTCTTTGAGTCAT 59.099 43.478 5.51 0.00 32.18 3.06
6299 6326 3.300388 AGACACTGTCCTCTTTGAGTCA 58.700 45.455 5.51 0.00 32.18 3.41
6341 6368 3.880490 GAGTCCTCGATACAGATCTGTGT 59.120 47.826 33.76 28.81 44.63 3.72
6601 6628 4.776435 TCACCTTCAGAATCCATATGCA 57.224 40.909 0.00 0.00 0.00 3.96
6783 6810 7.532571 ACAATGTTTGACACATGAGTATGATG 58.467 34.615 0.00 0.00 46.23 3.07
6784 6811 7.692460 ACAATGTTTGACACATGAGTATGAT 57.308 32.000 0.00 0.00 46.23 2.45
6785 6812 7.509141 AACAATGTTTGACACATGAGTATGA 57.491 32.000 0.00 0.00 46.23 2.15
7085 7115 4.134563 TGCTCTTTTCAAGTGTCCTAACC 58.865 43.478 0.00 0.00 0.00 2.85
7151 7181 2.972713 AGCCAACTGTTCACCTTCTCTA 59.027 45.455 0.00 0.00 0.00 2.43
7256 7286 6.509418 ACTTGTTTTCTAGCAAAAGTGTCA 57.491 33.333 0.00 0.00 0.00 3.58
7449 7479 4.083324 CGAAGGAAGCTGAGTTTGCAATAA 60.083 41.667 0.00 0.00 0.00 1.40
7450 7480 3.436704 CGAAGGAAGCTGAGTTTGCAATA 59.563 43.478 0.00 0.00 0.00 1.90
7469 7499 0.754217 ACATAGGACTAGGCGGCGAA 60.754 55.000 12.98 0.00 0.00 4.70
7478 7508 4.895889 CCCATCAGTCTCAACATAGGACTA 59.104 45.833 0.00 0.00 38.12 2.59
8213 8244 4.089361 TGAGAGTCAGGCATCTTAAGACA 58.911 43.478 7.48 0.00 0.00 3.41
8425 8456 7.323420 ACCAAAAAGAAAGAAGAGGAAAACTG 58.677 34.615 0.00 0.00 0.00 3.16
8472 8503 3.649277 CTGGCGACGAACCTCCCAG 62.649 68.421 0.00 0.17 37.35 4.45
8478 8509 1.278637 CACAAACTGGCGACGAACC 59.721 57.895 0.00 0.00 0.00 3.62
8782 8824 2.713708 AGATCCTTAATTCTGGGGAGCC 59.286 50.000 0.00 0.00 35.15 4.70
8831 8873 2.901839 AGGTGGAGCTGCAATTCAAAAT 59.098 40.909 10.44 0.00 0.00 1.82
8856 8898 3.706373 CCACCACTCCACTCCCGG 61.706 72.222 0.00 0.00 0.00 5.73
8900 8942 2.393646 GGCCTCTTCAGAGTCTACCAT 58.606 52.381 0.00 0.00 40.48 3.55
8901 8943 1.619977 GGGCCTCTTCAGAGTCTACCA 60.620 57.143 0.84 0.00 40.48 3.25
8904 8946 2.930109 AAGGGCCTCTTCAGAGTCTA 57.070 50.000 6.46 0.00 40.48 2.59
8905 8947 2.930109 TAAGGGCCTCTTCAGAGTCT 57.070 50.000 6.46 0.00 40.48 3.24
8906 8948 2.103941 CCATAAGGGCCTCTTCAGAGTC 59.896 54.545 6.46 0.00 40.48 3.36
8907 8949 2.122768 CCATAAGGGCCTCTTCAGAGT 58.877 52.381 6.46 0.00 40.48 3.24
8908 8950 2.122768 ACCATAAGGGCCTCTTCAGAG 58.877 52.381 6.46 0.00 42.05 3.35
8909 8951 2.270434 ACCATAAGGGCCTCTTCAGA 57.730 50.000 6.46 0.00 42.05 3.27
8910 8952 3.906846 AGATACCATAAGGGCCTCTTCAG 59.093 47.826 6.46 0.00 42.05 3.02
8911 8953 3.904339 GAGATACCATAAGGGCCTCTTCA 59.096 47.826 6.46 0.00 42.05 3.02
8912 8954 3.262151 GGAGATACCATAAGGGCCTCTTC 59.738 52.174 6.46 0.00 42.05 2.87
8913 8955 3.252351 GGAGATACCATAAGGGCCTCTT 58.748 50.000 6.46 7.24 42.05 2.85
8914 8956 2.182312 TGGAGATACCATAAGGGCCTCT 59.818 50.000 6.46 0.00 44.64 3.69
8915 8957 2.621070 TGGAGATACCATAAGGGCCTC 58.379 52.381 6.46 0.00 44.64 4.70
8916 8958 2.815357 TGGAGATACCATAAGGGCCT 57.185 50.000 0.00 0.00 44.64 5.19
8926 8968 2.797786 AGATAGCGGTCTGGAGATACC 58.202 52.381 0.00 0.00 39.54 2.73
8927 8969 5.677598 GCATTAGATAGCGGTCTGGAGATAC 60.678 48.000 0.00 0.00 0.00 2.24
8928 8970 4.399618 GCATTAGATAGCGGTCTGGAGATA 59.600 45.833 0.00 0.00 0.00 1.98
8938 8980 1.016130 CGGGCAGCATTAGATAGCGG 61.016 60.000 0.00 0.00 35.48 5.52
8939 8981 2.449548 CGGGCAGCATTAGATAGCG 58.550 57.895 0.00 0.00 35.48 4.26
8952 8994 3.951037 AGTGTTTGAAATATATGCGGGCA 59.049 39.130 0.00 0.00 0.00 5.36
8954 8996 7.826260 AAAAAGTGTTTGAAATATATGCGGG 57.174 32.000 0.00 0.00 0.00 6.13
9052 9094 4.685628 TCGTCCCGTTTATATAAAATCCGC 59.314 41.667 9.48 0.00 0.00 5.54
9132 9174 2.410322 AATGAAGCTCCACACGGCCA 62.410 55.000 2.24 0.00 0.00 5.36
9167 9209 4.020839 GGCCGGCCTTAGACTAATGTATTA 60.021 45.833 38.76 0.00 0.00 0.98
9169 9211 2.302157 GGCCGGCCTTAGACTAATGTAT 59.698 50.000 38.76 0.00 0.00 2.29
9174 9216 3.085119 GCGGCCGGCCTTAGACTAA 62.085 63.158 41.01 0.00 34.80 2.24
9239 9281 6.096987 AGGAAAGAATATAGAGCTCACGACAA 59.903 38.462 17.77 0.00 0.00 3.18
9244 9286 9.418045 GATACAAGGAAAGAATATAGAGCTCAC 57.582 37.037 17.77 0.00 0.00 3.51
9253 9310 6.521527 AGGGCAGATACAAGGAAAGAATAT 57.478 37.500 0.00 0.00 0.00 1.28
9254 9311 5.975988 AGGGCAGATACAAGGAAAGAATA 57.024 39.130 0.00 0.00 0.00 1.75
9255 9312 4.870021 AGGGCAGATACAAGGAAAGAAT 57.130 40.909 0.00 0.00 0.00 2.40
9256 9313 5.191722 ACATAGGGCAGATACAAGGAAAGAA 59.808 40.000 0.00 0.00 0.00 2.52
9257 9314 4.721776 ACATAGGGCAGATACAAGGAAAGA 59.278 41.667 0.00 0.00 0.00 2.52
9258 9315 5.041191 ACATAGGGCAGATACAAGGAAAG 57.959 43.478 0.00 0.00 0.00 2.62
9259 9316 4.141482 GGACATAGGGCAGATACAAGGAAA 60.141 45.833 0.00 0.00 0.00 3.13
9260 9317 3.391296 GGACATAGGGCAGATACAAGGAA 59.609 47.826 0.00 0.00 0.00 3.36
9261 9318 2.972713 GGACATAGGGCAGATACAAGGA 59.027 50.000 0.00 0.00 0.00 3.36
9265 9322 1.133294 TCCGGACATAGGGCAGATACA 60.133 52.381 0.00 0.00 0.00 2.29
9298 9355 1.678970 AATCGCCTCCAACCCAAGC 60.679 57.895 0.00 0.00 0.00 4.01
9299 9356 1.315257 CCAATCGCCTCCAACCCAAG 61.315 60.000 0.00 0.00 0.00 3.61
9300 9357 1.304052 CCAATCGCCTCCAACCCAA 60.304 57.895 0.00 0.00 0.00 4.12
9301 9358 2.354729 CCAATCGCCTCCAACCCA 59.645 61.111 0.00 0.00 0.00 4.51
9303 9360 2.440247 CCCCAATCGCCTCCAACC 60.440 66.667 0.00 0.00 0.00 3.77
9305 9362 2.493273 GAACCCCCAATCGCCTCCAA 62.493 60.000 0.00 0.00 0.00 3.53
9388 9464 2.461110 CGAGGCAACACCCGCATAC 61.461 63.158 0.00 0.00 40.58 2.39


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

AutoCloner maintained by Alex Coulton.