Multiple sequence alignment - TraesCS3A01G164600

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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 TraesCS3A01G164600 chr3A 100.000 7502 0 0 1 7502 169851836 169844335 0.000000e+00 13854.0
1 TraesCS3A01G164600 chr3A 93.635 927 51 8 3068 3991 711469589 711470510 0.000000e+00 1378.0
2 TraesCS3A01G164600 chr3A 87.288 118 11 2 3077 3192 618458824 618458709 1.700000e-26 132.0
3 TraesCS3A01G164600 chr3A 94.444 54 2 1 6782 6835 169845022 169844970 1.730000e-11 82.4
4 TraesCS3A01G164600 chr3A 94.444 54 2 1 6815 6867 169845055 169845002 1.730000e-11 82.4
5 TraesCS3A01G164600 chr3A 90.323 62 4 2 6921 6981 528595092 528595152 6.240000e-11 80.5
6 TraesCS3A01G164600 chr3A 93.750 48 1 2 7451 7497 483273335 483273289 3.760000e-08 71.3
7 TraesCS3A01G164600 chr3D 98.036 2851 43 5 3984 6831 158081637 158084477 0.000000e+00 4942.0
8 TraesCS3A01G164600 chr3D 95.246 2503 67 28 598 3076 158079171 158081645 0.000000e+00 3916.0
9 TraesCS3A01G164600 chr3D 85.111 450 18 12 6815 7264 158084429 158084829 1.510000e-111 414.0
10 TraesCS3A01G164600 chr3D 84.135 208 22 3 3076 3273 233179288 233179494 2.760000e-44 191.0
11 TraesCS3A01G164600 chr3B 96.258 2325 76 5 4510 6831 235863593 235865909 0.000000e+00 3801.0
12 TraesCS3A01G164600 chr3B 96.640 744 16 5 938 1680 235861086 235861821 0.000000e+00 1227.0
13 TraesCS3A01G164600 chr3B 96.636 654 21 1 2424 3076 235862487 235863140 0.000000e+00 1085.0
14 TraesCS3A01G164600 chr3B 94.718 549 18 4 1682 2223 235861886 235862430 0.000000e+00 843.0
15 TraesCS3A01G164600 chr3B 84.848 561 43 18 1 555 235860042 235860566 1.850000e-145 527.0
16 TraesCS3A01G164600 chr3B 92.120 368 21 7 578 942 235860555 235860917 5.190000e-141 512.0
17 TraesCS3A01G164600 chr3B 92.945 326 17 3 6815 7139 235865859 235866179 3.170000e-128 470.0
18 TraesCS3A01G164600 chr3B 96.903 226 7 0 3984 4209 235863132 235863357 5.490000e-101 379.0
19 TraesCS3A01G164600 chr3B 85.484 310 22 10 7200 7502 235866181 235866474 1.220000e-77 302.0
20 TraesCS3A01G164600 chr3B 84.021 194 19 6 3077 3260 807220074 807219883 7.740000e-40 176.0
21 TraesCS3A01G164600 chr3B 87.786 131 10 5 3061 3189 242677719 242677593 1.690000e-31 148.0
22 TraesCS3A01G164600 chr3B 100.000 30 0 0 528 557 793079919 793079890 1.000000e-03 56.5
23 TraesCS3A01G164600 chr7A 85.461 901 66 26 3136 3983 425837414 425838302 0.000000e+00 878.0
24 TraesCS3A01G164600 chr7A 97.101 207 6 0 4303 4509 437406791 437406997 4.310000e-92 350.0
25 TraesCS3A01G164600 chr5A 85.261 631 75 10 3359 3986 151373706 151373091 1.060000e-177 634.0
26 TraesCS3A01G164600 chr5A 96.875 32 1 0 15 46 270185887 270185856 4.000000e-03 54.7
27 TraesCS3A01G164600 chr6A 97.073 205 6 0 4305 4509 581809260 581809464 5.570000e-91 346.0
28 TraesCS3A01G164600 chr6A 91.018 167 15 0 2261 2427 108947700 108947866 7.570000e-55 226.0
29 TraesCS3A01G164600 chr6A 81.818 231 28 7 3077 3294 24778072 24778301 1.660000e-41 182.0
30 TraesCS3A01G164600 chr6A 77.419 186 34 8 3801 3983 58148126 58148306 3.700000e-18 104.0
31 TraesCS3A01G164600 chr2B 96.635 208 7 0 4305 4512 227857822 227858029 5.570000e-91 346.0
32 TraesCS3A01G164600 chr2B 91.716 169 13 1 2263 2430 50021478 50021646 4.530000e-57 233.0
33 TraesCS3A01G164600 chr2B 89.189 185 17 3 2263 2446 562222482 562222664 2.110000e-55 228.0
34 TraesCS3A01G164600 chr2B 87.766 188 21 2 2264 2451 76912138 76912323 1.270000e-52 219.0
35 TraesCS3A01G164600 chr1D 96.635 208 7 0 4305 4512 204435068 204434861 5.570000e-91 346.0
36 TraesCS3A01G164600 chr1D 77.326 172 26 8 3082 3242 442049668 442049499 1.040000e-13 89.8
37 TraesCS3A01G164600 chr6D 96.154 208 8 0 4305 4512 309809256 309809049 2.590000e-89 340.0
38 TraesCS3A01G164600 chr6D 94.884 215 10 1 4298 4512 28681309 28681522 1.210000e-87 335.0
39 TraesCS3A01G164600 chr6D 91.463 164 14 0 2264 2427 90112399 90112236 7.570000e-55 226.0
40 TraesCS3A01G164600 chr7D 95.673 208 9 0 4305 4512 208130811 208131018 1.210000e-87 335.0
41 TraesCS3A01G164600 chr7D 100.000 28 0 0 6922 6949 416626535 416626562 1.400000e-02 52.8
42 TraesCS3A01G164600 chr7B 95.192 208 9 1 4305 4512 136967745 136967539 2.020000e-85 327.0
43 TraesCS3A01G164600 chr1B 95.181 166 7 1 2260 2425 314565535 314565699 2.080000e-65 261.0
44 TraesCS3A01G164600 chr2A 91.228 171 12 3 2263 2432 696850716 696850884 5.850000e-56 230.0
45 TraesCS3A01G164600 chr2A 75.431 232 43 11 13 236 637233352 637233577 4.790000e-17 100.0
46 TraesCS3A01G164600 chr4A 88.827 179 17 3 2256 2433 97530161 97529985 4.560000e-52 217.0
47 TraesCS3A01G164600 chr4A 83.843 229 26 5 3077 3294 280382946 280383174 2.740000e-49 207.0
48 TraesCS3A01G164600 chr4A 90.678 118 11 0 3073 3190 280384134 280384017 2.800000e-34 158.0
49 TraesCS3A01G164600 chr4A 89.394 66 7 0 249 314 583871642 583871577 4.820000e-12 84.2
50 TraesCS3A01G164600 chr4A 91.667 60 4 1 6915 6974 67170267 67170209 1.730000e-11 82.4
51 TraesCS3A01G164600 chr4A 84.706 85 8 3 6919 7003 478196 478275 6.240000e-11 80.5
52 TraesCS3A01G164600 chr4A 81.443 97 17 1 6922 7017 5917272 5917368 2.240000e-10 78.7
53 TraesCS3A01G164600 chr4A 90.000 50 3 2 6922 6970 38358589 38358541 6.280000e-06 63.9
54 TraesCS3A01G164600 chr5B 79.828 233 33 8 3073 3294 134907243 134907472 2.800000e-34 158.0
55 TraesCS3A01G164600 chr4B 82.209 163 24 5 3825 3985 604703446 604703605 1.310000e-27 135.0
56 TraesCS3A01G164600 chr4D 78.182 220 41 6 164 379 108833069 108832853 4.720000e-27 134.0
57 TraesCS3A01G164600 chr4D 84.043 94 15 0 163 256 482513751 482513844 2.880000e-14 91.6
58 TraesCS3A01G164600 chr2D 78.977 176 27 3 3077 3242 637561949 637562124 2.210000e-20 111.0
59 TraesCS3A01G164600 chr6B 92.453 53 3 1 6922 6974 665702256 665702307 2.900000e-09 75.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G164600 chr3A 169844335 169851836 7501 True 13854.000000 13854 100.000000 1 7502 1 chr3A.!!$R1 7501
1 TraesCS3A01G164600 chr3A 711469589 711470510 921 False 1378.000000 1378 93.635000 3068 3991 1 chr3A.!!$F2 923
2 TraesCS3A01G164600 chr3D 158079171 158084829 5658 False 3090.666667 4942 92.797667 598 7264 3 chr3D.!!$F2 6666
3 TraesCS3A01G164600 chr3B 235860042 235866474 6432 False 1016.222222 3801 92.950222 1 7502 9 chr3B.!!$F1 7501
4 TraesCS3A01G164600 chr7A 425837414 425838302 888 False 878.000000 878 85.461000 3136 3983 1 chr7A.!!$F1 847
5 TraesCS3A01G164600 chr5A 151373091 151373706 615 True 634.000000 634 85.261000 3359 3986 1 chr5A.!!$R1 627

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
88 89 0.653636 TTCGTCTTCGGTTTGTGTGC 59.346 50.000 0.00 0.00 37.69 4.57 F
1187 1388 0.394565 GTCAGCACCACCTCTCAAGT 59.605 55.000 0.00 0.00 0.00 3.16 F
1190 1391 0.536006 AGCACCACCTCTCAAGTTGC 60.536 55.000 0.00 0.00 0.00 4.17 F
1741 2007 1.068588 AGCTTCGTGCAACACTAGACA 59.931 47.619 0.00 0.00 45.94 3.41 F
3130 3436 0.105504 GCTCCCCTATTTGGCCCAAT 60.106 55.000 7.31 7.31 0.00 3.16 F
4290 4766 1.078143 GCCTAGGCAAGAGGGTGTG 60.078 63.158 29.33 0.00 41.49 3.82 F
4474 4950 2.547855 GGCAACCATCCAAACAAAGACC 60.548 50.000 0.00 0.00 0.00 3.85 F
5815 6294 0.991146 TGCTCAGCATTGGTCCCTTA 59.009 50.000 0.00 0.00 31.71 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1382 1585 0.614134 ACCAGTAGTCCCCGGTCTTC 60.614 60.000 0.00 0.00 0.00 2.87 R
1988 2254 3.265737 TGGAGAGTAATGGGCTAGCAAAA 59.734 43.478 18.24 0.87 0.00 2.44 R
3114 3420 3.653164 ACTTTATTGGGCCAAATAGGGG 58.347 45.455 24.97 13.39 38.09 4.79 R
3722 4083 0.880718 GCCGTGGAGCTATAACAGGC 60.881 60.000 10.60 10.60 36.32 4.85 R
4675 5153 1.133025 CACCGAAAATGGAGACCATGC 59.867 52.381 3.97 0.00 44.40 4.06 R
5703 6182 0.036294 GTACCCCCTGCTCTGTTGAC 60.036 60.000 0.00 0.00 0.00 3.18 R
6386 6865 0.679505 TCCACACCCTTCTCTCAACG 59.320 55.000 0.00 0.00 0.00 4.10 R
6864 7346 0.108138 GGTTGGACATAGCGCACTCT 60.108 55.000 11.47 0.00 0.00 3.24 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
46 47 1.790755 TCGATCGGTGTTGGTCTTTG 58.209 50.000 16.41 0.00 0.00 2.77
49 50 1.535462 GATCGGTGTTGGTCTTTGGTG 59.465 52.381 0.00 0.00 0.00 4.17
60 61 2.305927 GGTCTTTGGTGGATCTCCTTGA 59.694 50.000 8.45 2.99 36.82 3.02
67 68 4.425772 TGGTGGATCTCCTTGAAGTCTTA 58.574 43.478 8.45 0.00 36.82 2.10
78 79 4.617645 CCTTGAAGTCTTAGTTCGTCTTCG 59.382 45.833 0.00 0.00 37.78 3.79
79 80 4.156664 TGAAGTCTTAGTTCGTCTTCGG 57.843 45.455 0.00 0.00 37.78 4.30
80 81 3.567164 TGAAGTCTTAGTTCGTCTTCGGT 59.433 43.478 0.00 0.00 37.78 4.69
81 82 4.037208 TGAAGTCTTAGTTCGTCTTCGGTT 59.963 41.667 0.00 0.00 37.78 4.44
82 83 4.581077 AGTCTTAGTTCGTCTTCGGTTT 57.419 40.909 0.00 0.00 37.69 3.27
83 84 4.296690 AGTCTTAGTTCGTCTTCGGTTTG 58.703 43.478 0.00 0.00 37.69 2.93
84 85 4.047142 GTCTTAGTTCGTCTTCGGTTTGT 58.953 43.478 0.00 0.00 37.69 2.83
85 86 4.046462 TCTTAGTTCGTCTTCGGTTTGTG 58.954 43.478 0.00 0.00 37.69 3.33
86 87 2.304751 AGTTCGTCTTCGGTTTGTGT 57.695 45.000 0.00 0.00 37.69 3.72
87 88 1.931172 AGTTCGTCTTCGGTTTGTGTG 59.069 47.619 0.00 0.00 37.69 3.82
88 89 0.653636 TTCGTCTTCGGTTTGTGTGC 59.346 50.000 0.00 0.00 37.69 4.57
89 90 1.155424 TCGTCTTCGGTTTGTGTGCC 61.155 55.000 0.00 0.00 37.69 5.01
90 91 1.157870 CGTCTTCGGTTTGTGTGCCT 61.158 55.000 0.00 0.00 0.00 4.75
91 92 1.870580 CGTCTTCGGTTTGTGTGCCTA 60.871 52.381 0.00 0.00 0.00 3.93
92 93 1.529865 GTCTTCGGTTTGTGTGCCTAC 59.470 52.381 0.00 0.00 0.00 3.18
93 94 1.414919 TCTTCGGTTTGTGTGCCTACT 59.585 47.619 0.00 0.00 0.00 2.57
94 95 2.158871 TCTTCGGTTTGTGTGCCTACTT 60.159 45.455 0.00 0.00 0.00 2.24
95 96 1.588674 TCGGTTTGTGTGCCTACTTG 58.411 50.000 0.00 0.00 0.00 3.16
96 97 1.134340 TCGGTTTGTGTGCCTACTTGT 60.134 47.619 0.00 0.00 0.00 3.16
97 98 1.673920 CGGTTTGTGTGCCTACTTGTT 59.326 47.619 0.00 0.00 0.00 2.83
98 99 2.540769 CGGTTTGTGTGCCTACTTGTTG 60.541 50.000 0.00 0.00 0.00 3.33
99 100 2.223711 GGTTTGTGTGCCTACTTGTTGG 60.224 50.000 0.00 0.00 0.00 3.77
100 101 2.685897 GTTTGTGTGCCTACTTGTTGGA 59.314 45.455 5.48 0.00 0.00 3.53
107 108 3.826729 GTGCCTACTTGTTGGATCCTTTT 59.173 43.478 14.23 0.00 0.00 2.27
111 112 6.723977 TGCCTACTTGTTGGATCCTTTTAATT 59.276 34.615 14.23 0.72 0.00 1.40
113 114 7.545615 GCCTACTTGTTGGATCCTTTTAATTTG 59.454 37.037 14.23 0.00 0.00 2.32
133 134 1.363744 CACTTCTCTTCATGGGCGAC 58.636 55.000 0.00 0.00 0.00 5.19
134 135 0.976641 ACTTCTCTTCATGGGCGACA 59.023 50.000 0.00 0.00 0.00 4.35
135 136 1.347707 ACTTCTCTTCATGGGCGACAA 59.652 47.619 0.00 0.00 0.00 3.18
139 140 0.955428 TCTTCATGGGCGACAACTGC 60.955 55.000 0.00 0.00 0.00 4.40
146 147 2.675056 GGCGACAACTGCTGCTCTG 61.675 63.158 0.00 0.00 0.00 3.35
154 155 1.449246 CTGCTGCTCTGGTGTAGGC 60.449 63.158 0.00 0.00 0.00 3.93
177 178 2.658422 GGGGCCTTAACACGACGA 59.342 61.111 0.84 0.00 0.00 4.20
179 180 1.739196 GGGCCTTAACACGACGACC 60.739 63.158 0.84 0.00 0.00 4.79
190 191 2.606272 ACACGACGACCTTTCAACTTTC 59.394 45.455 0.00 0.00 0.00 2.62
211 212 5.957842 TCTATTACAACAAGTTTGGCCAG 57.042 39.130 5.11 0.00 0.00 4.85
237 238 2.764128 GAGGGAGGGGCGATGACA 60.764 66.667 0.00 0.00 0.00 3.58
238 239 2.765807 AGGGAGGGGCGATGACAG 60.766 66.667 0.00 0.00 0.00 3.51
251 252 1.059692 GATGACAGCGACACACATTCG 59.940 52.381 0.00 0.00 39.56 3.34
260 261 0.667487 ACACACATTCGGCTCACTCG 60.667 55.000 0.00 0.00 0.00 4.18
280 281 2.539142 CGAGTGCTTATAGTCGTCGCTT 60.539 50.000 0.00 0.00 38.39 4.68
287 288 1.992170 ATAGTCGTCGCTTGGTTGTC 58.008 50.000 0.00 0.00 0.00 3.18
297 298 1.406341 GCTTGGTTGTCTACGGGCATA 60.406 52.381 0.00 0.00 0.00 3.14
305 306 6.439375 TGGTTGTCTACGGGCATAGATATAAT 59.561 38.462 1.58 0.00 33.78 1.28
352 353 3.959478 GCCATGGCATGATGAACAG 57.041 52.632 32.08 10.86 41.49 3.16
356 357 2.225727 CCATGGCATGATGAACAGATCG 59.774 50.000 28.43 3.38 0.00 3.69
360 361 3.624410 TGGCATGATGAACAGATCGAAAG 59.376 43.478 0.00 0.00 0.00 2.62
365 367 5.034554 TGATGAACAGATCGAAAGTTTGC 57.965 39.130 0.00 0.00 0.00 3.68
379 381 8.467402 TCGAAAGTTTGCTCACAAAATAAAAA 57.533 26.923 0.00 0.00 46.94 1.94
555 562 7.971183 TTGGTACGATATTAATTGCATGCTA 57.029 32.000 20.33 12.49 0.00 3.49
556 563 7.971183 TGGTACGATATTAATTGCATGCTAA 57.029 32.000 20.33 11.86 0.00 3.09
557 564 8.560355 TGGTACGATATTAATTGCATGCTAAT 57.440 30.769 20.33 16.15 0.00 1.73
558 565 9.008965 TGGTACGATATTAATTGCATGCTAATT 57.991 29.630 20.33 21.85 0.00 1.40
559 566 9.840427 GGTACGATATTAATTGCATGCTAATTT 57.160 29.630 23.65 13.85 0.00 1.82
640 648 7.624360 TTGACATAGTTTATGCCGAGATTTT 57.376 32.000 0.00 0.00 39.79 1.82
750 771 6.660949 ACAAGGGAAAGATCCTAATCAGTTTG 59.339 38.462 0.00 0.00 45.77 2.93
766 787 5.144100 TCAGTTTGGCTATTTCAAGGGAAA 58.856 37.500 0.00 0.00 46.36 3.13
902 929 4.845307 CCCCTCCCCTCCCCTTCC 62.845 77.778 0.00 0.00 0.00 3.46
903 930 4.845307 CCCTCCCCTCCCCTTCCC 62.845 77.778 0.00 0.00 0.00 3.97
904 931 3.711782 CCTCCCCTCCCCTTCCCT 61.712 72.222 0.00 0.00 0.00 4.20
905 932 2.040359 CTCCCCTCCCCTTCCCTC 60.040 72.222 0.00 0.00 0.00 4.30
906 933 3.707189 TCCCCTCCCCTTCCCTCC 61.707 72.222 0.00 0.00 0.00 4.30
908 935 4.416601 CCCTCCCCTTCCCTCCGT 62.417 72.222 0.00 0.00 0.00 4.69
1181 1382 1.302832 CCAAGGTCAGCACCACCTC 60.303 63.158 2.01 0.00 44.03 3.85
1182 1383 1.757306 CAAGGTCAGCACCACCTCT 59.243 57.895 2.01 0.00 44.03 3.69
1184 1385 0.764369 AAGGTCAGCACCACCTCTCA 60.764 55.000 2.01 0.00 44.03 3.27
1187 1388 0.394565 GTCAGCACCACCTCTCAAGT 59.605 55.000 0.00 0.00 0.00 3.16
1188 1389 1.131638 TCAGCACCACCTCTCAAGTT 58.868 50.000 0.00 0.00 0.00 2.66
1189 1390 1.202687 TCAGCACCACCTCTCAAGTTG 60.203 52.381 0.00 0.00 0.00 3.16
1190 1391 0.536006 AGCACCACCTCTCAAGTTGC 60.536 55.000 0.00 0.00 0.00 4.17
1192 1393 1.270839 GCACCACCTCTCAAGTTGCTA 60.271 52.381 0.00 0.00 0.00 3.49
1193 1394 2.417719 CACCACCTCTCAAGTTGCTAC 58.582 52.381 0.00 0.00 0.00 3.58
1194 1395 2.047061 ACCACCTCTCAAGTTGCTACA 58.953 47.619 0.13 0.00 0.00 2.74
1195 1396 2.639839 ACCACCTCTCAAGTTGCTACAT 59.360 45.455 0.13 0.00 0.00 2.29
1196 1397 3.265791 CCACCTCTCAAGTTGCTACATC 58.734 50.000 0.13 0.00 0.00 3.06
1197 1398 3.306989 CCACCTCTCAAGTTGCTACATCA 60.307 47.826 0.13 0.00 0.00 3.07
1198 1399 4.318332 CACCTCTCAAGTTGCTACATCAA 58.682 43.478 0.13 0.00 0.00 2.57
1206 1407 7.391275 TCTCAAGTTGCTACATCAATTTCATCA 59.609 33.333 0.13 0.00 0.00 3.07
1394 1597 3.082055 GAGGGGAAGACCGGGGAC 61.082 72.222 6.32 0.00 41.60 4.46
1463 1666 1.213296 ACAGGATGGTAAGGGCGATT 58.787 50.000 0.00 0.00 43.62 3.34
1739 2005 3.868757 ATAGCTTCGTGCAACACTAGA 57.131 42.857 0.00 0.00 45.94 2.43
1741 2007 1.068588 AGCTTCGTGCAACACTAGACA 59.931 47.619 0.00 0.00 45.94 3.41
1742 2008 2.069273 GCTTCGTGCAACACTAGACAT 58.931 47.619 0.00 0.00 42.31 3.06
1813 2079 5.063564 GCAGTGCTCAATACCAGTTACTAAC 59.936 44.000 8.18 0.00 0.00 2.34
2213 2502 9.522804 TGAACAAACAATGGTTAAATAGTTCAC 57.477 29.630 9.01 0.00 35.82 3.18
2236 2541 4.503741 AGATTTGTGTGCGCAAATTAGT 57.496 36.364 14.00 0.00 45.68 2.24
2270 2575 1.204704 TGCAGTTCACATCTACTCCCG 59.795 52.381 0.00 0.00 0.00 5.14
2290 2595 3.992427 CCGCCGTTCCTAAATATAAGTCC 59.008 47.826 0.00 0.00 0.00 3.85
2358 2663 8.865001 GTGAATCTACACTCTAAAACATGTCTC 58.135 37.037 0.00 0.00 37.73 3.36
2359 2664 8.807118 TGAATCTACACTCTAAAACATGTCTCT 58.193 33.333 0.00 0.00 0.00 3.10
2389 2694 9.261180 CATCCGTATGTAGTCTGTATTGAAATT 57.739 33.333 0.00 0.00 0.00 1.82
2514 2819 7.073265 GCATAATGATTTAATGTTTGGCATGC 58.927 34.615 9.90 9.90 37.96 4.06
2817 3122 2.552315 ACCCGATGTGCAAGTTTTGTAG 59.448 45.455 0.00 0.00 0.00 2.74
3068 3374 9.635404 AGTTATACTAAAGTCAGAGTGCTATCT 57.365 33.333 0.00 0.00 0.00 1.98
3114 3420 4.893608 TGGCCCTTTCTTAAATTTTGCTC 58.106 39.130 0.00 0.00 0.00 4.26
3126 3432 1.567357 TTTTGCTCCCCTATTTGGCC 58.433 50.000 0.00 0.00 0.00 5.36
3130 3436 0.105504 GCTCCCCTATTTGGCCCAAT 60.106 55.000 7.31 7.31 0.00 3.16
3134 3440 3.897505 CTCCCCTATTTGGCCCAATAAAG 59.102 47.826 10.30 5.31 0.00 1.85
3142 3448 7.931407 CCTATTTGGCCCAATAAAGTTTATTCC 59.069 37.037 16.34 14.90 0.00 3.01
3176 3482 7.560368 TGACACCAAATGTTAAATTTGTTCCT 58.440 30.769 7.05 0.00 43.56 3.36
3210 3516 1.276989 TGACTACTTTGGCCCCTAACG 59.723 52.381 0.00 0.00 0.00 3.18
3273 3579 5.334879 GGCTGAGAAAAAGAGCGTTCATTTA 60.335 40.000 2.91 0.00 33.26 1.40
3421 3761 5.770162 AGGATTTGTACTGCAGTAGCTTTTT 59.230 36.000 26.70 9.87 42.74 1.94
3640 4001 6.477688 GCCGTGTTTATATTTGCAGTACTAGA 59.522 38.462 0.00 0.00 0.00 2.43
3761 4122 1.688197 CAATGTCTTGGCTGGGTTGTT 59.312 47.619 0.00 0.00 0.00 2.83
3788 4149 2.079925 GGCTGAAGAAATGAACGCTCT 58.920 47.619 0.00 0.00 0.00 4.09
3894 4255 7.721842 TGAAAGTGTCACATAGGGAACAAATTA 59.278 33.333 5.62 0.00 0.00 1.40
3977 4338 3.821748 AGAAAGGGCCGAATAAGGAATC 58.178 45.455 0.00 0.00 0.00 2.52
4164 4525 8.248253 ACATTTTACCCATTTTTAATCTCCGAC 58.752 33.333 0.00 0.00 0.00 4.79
4290 4766 1.078143 GCCTAGGCAAGAGGGTGTG 60.078 63.158 29.33 0.00 41.49 3.82
4474 4950 2.547855 GGCAACCATCCAAACAAAGACC 60.548 50.000 0.00 0.00 0.00 3.85
4615 5091 3.492383 CAGTTAAGCGAGACCATAGCATG 59.508 47.826 0.00 0.00 30.80 4.06
5007 5485 4.040047 TCATATTCCCTGGACATGTCACT 58.960 43.478 26.47 3.43 0.00 3.41
5255 5734 5.760131 AGCTGATCTATTTTACTTTGCCCT 58.240 37.500 0.00 0.00 0.00 5.19
5383 5862 3.144506 ACCTTGCTGTCTGTTCAGAATG 58.855 45.455 3.99 2.28 37.61 2.67
5815 6294 0.991146 TGCTCAGCATTGGTCCCTTA 59.009 50.000 0.00 0.00 31.71 2.69
6102 6581 5.028375 GGCGTTATCAATGCTTCAAAGTAC 58.972 41.667 3.35 0.00 42.98 2.73
6320 6799 2.264124 CTGCTGCTGCACAGGATTT 58.736 52.632 14.93 0.00 46.69 2.17
6509 6988 1.271217 GGCGAAGAAGTAAACTGGGGT 60.271 52.381 0.00 0.00 0.00 4.95
6580 7060 1.459592 CCGATTCGTGTCTGGTTTGTC 59.540 52.381 5.20 0.00 0.00 3.18
6600 7080 1.467713 CGAGGTGACTAAGAAGACCGC 60.468 57.143 0.00 0.00 44.43 5.68
6633 7113 3.194005 TGGTTCGCTTCTGTTTCTCTT 57.806 42.857 0.00 0.00 0.00 2.85
6733 7215 9.555727 GGATGGTAACTATCAAAGCTATTGTAA 57.444 33.333 0.00 0.00 37.61 2.41
6764 7246 6.313519 TGTCTCTGGCAGGATTAGTATTTT 57.686 37.500 15.73 0.00 0.00 1.82
6890 7372 3.386726 TGCGCTATGTCCAACCTAATACT 59.613 43.478 9.73 0.00 0.00 2.12
6892 7374 4.922103 GCGCTATGTCCAACCTAATACTAC 59.078 45.833 0.00 0.00 0.00 2.73
6893 7375 5.508489 GCGCTATGTCCAACCTAATACTACA 60.508 44.000 0.00 0.00 0.00 2.74
6894 7376 6.509656 CGCTATGTCCAACCTAATACTACAA 58.490 40.000 0.00 0.00 0.00 2.41
6895 7377 6.982141 CGCTATGTCCAACCTAATACTACAAA 59.018 38.462 0.00 0.00 0.00 2.83
6896 7378 7.169308 CGCTATGTCCAACCTAATACTACAAAG 59.831 40.741 0.00 0.00 0.00 2.77
6897 7379 7.985752 GCTATGTCCAACCTAATACTACAAAGT 59.014 37.037 0.00 0.00 39.91 2.66
6900 7382 8.192743 TGTCCAACCTAATACTACAAAGTACA 57.807 34.615 0.00 0.00 40.98 2.90
6901 7383 8.090214 TGTCCAACCTAATACTACAAAGTACAC 58.910 37.037 0.00 0.00 40.98 2.90
6902 7384 7.547019 GTCCAACCTAATACTACAAAGTACACC 59.453 40.741 0.00 0.00 40.98 4.16
6903 7385 6.820152 CCAACCTAATACTACAAAGTACACCC 59.180 42.308 0.00 0.00 40.98 4.61
6904 7386 7.310858 CCAACCTAATACTACAAAGTACACCCT 60.311 40.741 0.00 0.00 40.98 4.34
6905 7387 7.415592 ACCTAATACTACAAAGTACACCCTC 57.584 40.000 0.00 0.00 40.98 4.30
6906 7388 7.187676 ACCTAATACTACAAAGTACACCCTCT 58.812 38.462 0.00 0.00 40.98 3.69
6907 7389 7.123847 ACCTAATACTACAAAGTACACCCTCTG 59.876 40.741 0.00 0.00 40.98 3.35
6908 7390 6.930068 AATACTACAAAGTACACCCTCTGT 57.070 37.500 0.00 0.00 40.98 3.41
6909 7391 6.930068 ATACTACAAAGTACACCCTCTGTT 57.070 37.500 0.00 0.00 40.98 3.16
6910 7392 5.211174 ACTACAAAGTACACCCTCTGTTC 57.789 43.478 0.00 0.00 32.84 3.18
6911 7393 3.487120 ACAAAGTACACCCTCTGTTCC 57.513 47.619 0.00 0.00 33.91 3.62
6912 7394 3.046374 ACAAAGTACACCCTCTGTTCCT 58.954 45.455 0.00 0.00 33.91 3.36
6913 7395 4.228824 ACAAAGTACACCCTCTGTTCCTA 58.771 43.478 0.00 0.00 33.91 2.94
6914 7396 4.657039 ACAAAGTACACCCTCTGTTCCTAA 59.343 41.667 0.00 0.00 33.91 2.69
6915 7397 4.886496 AAGTACACCCTCTGTTCCTAAC 57.114 45.455 0.00 0.00 33.91 2.34
6916 7398 3.853207 AGTACACCCTCTGTTCCTAACA 58.147 45.455 0.00 0.00 39.52 2.41
6950 7456 6.014840 CCCTCTGATCCAAATTAATTGATGGG 60.015 42.308 15.75 11.00 41.85 4.00
7110 7616 0.248621 GTGCAGGTATGAATTGCCGC 60.249 55.000 0.00 0.00 37.03 6.53
7149 7655 3.521605 CGAGATGCGTGGGGTAGA 58.478 61.111 0.00 0.00 34.64 2.59
7150 7656 1.360551 CGAGATGCGTGGGGTAGAG 59.639 63.158 0.00 0.00 34.64 2.43
7151 7657 1.742768 GAGATGCGTGGGGTAGAGG 59.257 63.158 0.00 0.00 0.00 3.69
7152 7658 0.755698 GAGATGCGTGGGGTAGAGGA 60.756 60.000 0.00 0.00 0.00 3.71
7153 7659 0.325296 AGATGCGTGGGGTAGAGGAA 60.325 55.000 0.00 0.00 0.00 3.36
7154 7660 0.105039 GATGCGTGGGGTAGAGGAAG 59.895 60.000 0.00 0.00 0.00 3.46
7155 7661 1.338136 ATGCGTGGGGTAGAGGAAGG 61.338 60.000 0.00 0.00 0.00 3.46
7156 7662 1.684734 GCGTGGGGTAGAGGAAGGA 60.685 63.158 0.00 0.00 0.00 3.36
7157 7663 1.677637 GCGTGGGGTAGAGGAAGGAG 61.678 65.000 0.00 0.00 0.00 3.69
7158 7664 0.033405 CGTGGGGTAGAGGAAGGAGA 60.033 60.000 0.00 0.00 0.00 3.71
7159 7665 1.618888 CGTGGGGTAGAGGAAGGAGAA 60.619 57.143 0.00 0.00 0.00 2.87
7160 7666 2.547990 GTGGGGTAGAGGAAGGAGAAA 58.452 52.381 0.00 0.00 0.00 2.52
7161 7667 2.910977 GTGGGGTAGAGGAAGGAGAAAA 59.089 50.000 0.00 0.00 0.00 2.29
7162 7668 3.055021 GTGGGGTAGAGGAAGGAGAAAAG 60.055 52.174 0.00 0.00 0.00 2.27
7163 7669 2.506231 GGGGTAGAGGAAGGAGAAAAGG 59.494 54.545 0.00 0.00 0.00 3.11
7164 7670 3.182976 GGGTAGAGGAAGGAGAAAAGGT 58.817 50.000 0.00 0.00 0.00 3.50
7165 7671 4.359996 GGGTAGAGGAAGGAGAAAAGGTA 58.640 47.826 0.00 0.00 0.00 3.08
7166 7672 4.406326 GGGTAGAGGAAGGAGAAAAGGTAG 59.594 50.000 0.00 0.00 0.00 3.18
7167 7673 4.406326 GGTAGAGGAAGGAGAAAAGGTAGG 59.594 50.000 0.00 0.00 0.00 3.18
7168 7674 4.421574 AGAGGAAGGAGAAAAGGTAGGA 57.578 45.455 0.00 0.00 0.00 2.94
7169 7675 4.764491 AGAGGAAGGAGAAAAGGTAGGAA 58.236 43.478 0.00 0.00 0.00 3.36
7170 7676 4.780554 AGAGGAAGGAGAAAAGGTAGGAAG 59.219 45.833 0.00 0.00 0.00 3.46
7171 7677 3.264706 AGGAAGGAGAAAAGGTAGGAAGC 59.735 47.826 0.00 0.00 0.00 3.86
7174 7680 3.108376 AGGAGAAAAGGTAGGAAGCGAT 58.892 45.455 0.00 0.00 0.00 4.58
7198 7704 9.994432 GATGAAGAACATAAAATCAATCGAACT 57.006 29.630 0.00 0.00 39.56 3.01
7241 7747 0.693049 ACTTGCCTCTACCCCAAGTG 59.307 55.000 4.64 0.00 45.22 3.16
7298 7804 9.535170 CCTCATCTTAGTATTAGAGGACCAATA 57.465 37.037 0.00 0.00 44.12 1.90
7306 7812 8.964476 AGTATTAGAGGACCAATACAACATTG 57.036 34.615 13.07 0.00 39.19 2.82
7307 7813 8.768397 AGTATTAGAGGACCAATACAACATTGA 58.232 33.333 13.07 0.00 39.19 2.57
7308 7814 9.391006 GTATTAGAGGACCAATACAACATTGAA 57.609 33.333 7.86 0.00 37.50 2.69
7309 7815 8.877864 ATTAGAGGACCAATACAACATTGAAA 57.122 30.769 0.00 0.00 0.00 2.69
7310 7816 8.698973 TTAGAGGACCAATACAACATTGAAAA 57.301 30.769 0.00 0.00 0.00 2.29
7311 7817 7.219484 AGAGGACCAATACAACATTGAAAAG 57.781 36.000 0.00 0.00 0.00 2.27
7312 7818 6.777580 AGAGGACCAATACAACATTGAAAAGT 59.222 34.615 0.00 0.00 0.00 2.66
7313 7819 7.287696 AGAGGACCAATACAACATTGAAAAGTT 59.712 33.333 0.00 0.00 0.00 2.66
7314 7820 7.433680 AGGACCAATACAACATTGAAAAGTTC 58.566 34.615 0.00 0.00 0.00 3.01
7315 7821 7.069331 AGGACCAATACAACATTGAAAAGTTCA 59.931 33.333 0.00 0.00 38.04 3.18
7316 7822 7.382218 GGACCAATACAACATTGAAAAGTTCAG 59.618 37.037 0.00 0.00 41.38 3.02
7317 7823 7.209475 ACCAATACAACATTGAAAAGTTCAGG 58.791 34.615 0.00 0.00 41.38 3.86
7318 7824 7.069331 ACCAATACAACATTGAAAAGTTCAGGA 59.931 33.333 0.00 0.00 41.38 3.86
7349 7855 6.679327 ACACCGAGAAATATTTTAGCCTTC 57.321 37.500 1.43 0.00 0.00 3.46
7351 7857 6.093633 ACACCGAGAAATATTTTAGCCTTCAC 59.906 38.462 1.43 0.00 0.00 3.18
7352 7858 5.589050 ACCGAGAAATATTTTAGCCTTCACC 59.411 40.000 1.43 0.00 0.00 4.02
7353 7859 5.588648 CCGAGAAATATTTTAGCCTTCACCA 59.411 40.000 1.43 0.00 0.00 4.17
7354 7860 6.458342 CCGAGAAATATTTTAGCCTTCACCAC 60.458 42.308 1.43 0.00 0.00 4.16
7355 7861 6.436843 AGAAATATTTTAGCCTTCACCACG 57.563 37.500 1.43 0.00 0.00 4.94
7357 7863 5.560966 AATATTTTAGCCTTCACCACGTG 57.439 39.130 9.08 9.08 34.45 4.49
7358 7864 2.623878 TTTTAGCCTTCACCACGTGA 57.376 45.000 19.30 0.00 41.09 4.35
7359 7865 2.851263 TTTAGCCTTCACCACGTGAT 57.149 45.000 19.30 0.00 42.40 3.06
7361 7867 1.557099 TAGCCTTCACCACGTGATCT 58.443 50.000 19.30 0.00 42.40 2.75
7362 7868 0.247736 AGCCTTCACCACGTGATCTC 59.752 55.000 19.30 0.00 42.40 2.75
7363 7869 0.037326 GCCTTCACCACGTGATCTCA 60.037 55.000 19.30 0.00 42.40 3.27
7377 7888 3.063180 GTGATCTCAGAAGCGGTGAAATG 59.937 47.826 0.00 0.00 0.00 2.32
7398 7909 2.738314 GCAATGCTGATTTTTCCACCAC 59.262 45.455 0.00 0.00 0.00 4.16
7408 7919 2.922740 TTTCCACCACTTAAGCGACT 57.077 45.000 1.29 0.00 0.00 4.18
7409 7920 2.450609 TTCCACCACTTAAGCGACTC 57.549 50.000 1.29 0.00 0.00 3.36
7413 7924 1.045407 ACCACTTAAGCGACTCACCA 58.955 50.000 1.29 0.00 0.00 4.17
7418 7929 2.162338 TTAAGCGACTCACCACCCCG 62.162 60.000 0.00 0.00 0.00 5.73
7460 7972 2.738314 GCTTTGAATTGCAACATGACCC 59.262 45.455 0.00 0.00 35.91 4.46
7461 7973 3.803021 GCTTTGAATTGCAACATGACCCA 60.803 43.478 0.00 0.00 35.91 4.51
7462 7974 4.378774 CTTTGAATTGCAACATGACCCAA 58.621 39.130 0.00 0.00 35.91 4.12
7463 7975 3.663995 TGAATTGCAACATGACCCAAG 57.336 42.857 0.00 0.00 0.00 3.61
7464 7976 2.964464 TGAATTGCAACATGACCCAAGT 59.036 40.909 0.00 0.00 0.00 3.16
7471 7983 3.119708 GCAACATGACCCAAGTCTGAATC 60.120 47.826 0.00 0.00 43.91 2.52
7485 7997 5.174395 AGTCTGAATCACAACTATGAGTGC 58.826 41.667 0.00 0.00 35.76 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.785679 GAATCTCGCAAAATCCGTTGG 58.214 47.619 0.00 0.00 0.00 3.77
17 18 1.277326 CACCGATCGAATCTCGCAAA 58.723 50.000 18.66 0.00 40.21 3.68
46 47 3.990959 AAGACTTCAAGGAGATCCACC 57.009 47.619 0.92 0.00 38.89 4.61
49 50 5.105675 ACGAACTAAGACTTCAAGGAGATCC 60.106 44.000 0.00 0.00 0.00 3.36
60 61 4.581077 AACCGAAGACGAACTAAGACTT 57.419 40.909 0.00 0.00 42.66 3.01
67 68 1.931172 CACACAAACCGAAGACGAACT 59.069 47.619 0.00 0.00 42.66 3.01
78 79 2.223711 CCAACAAGTAGGCACACAAACC 60.224 50.000 0.00 0.00 0.00 3.27
79 80 2.685897 TCCAACAAGTAGGCACACAAAC 59.314 45.455 0.00 0.00 0.00 2.93
80 81 3.006112 TCCAACAAGTAGGCACACAAA 57.994 42.857 0.00 0.00 0.00 2.83
81 82 2.719531 TCCAACAAGTAGGCACACAA 57.280 45.000 0.00 0.00 0.00 3.33
82 83 2.552155 GGATCCAACAAGTAGGCACACA 60.552 50.000 6.95 0.00 0.00 3.72
83 84 2.084546 GGATCCAACAAGTAGGCACAC 58.915 52.381 6.95 0.00 0.00 3.82
84 85 1.985159 AGGATCCAACAAGTAGGCACA 59.015 47.619 15.82 0.00 0.00 4.57
85 86 2.789409 AGGATCCAACAAGTAGGCAC 57.211 50.000 15.82 0.00 0.00 5.01
86 87 3.806949 AAAGGATCCAACAAGTAGGCA 57.193 42.857 15.82 0.00 0.00 4.75
87 88 6.775594 ATTAAAAGGATCCAACAAGTAGGC 57.224 37.500 15.82 0.00 0.00 3.93
88 89 7.545615 GCAAATTAAAAGGATCCAACAAGTAGG 59.454 37.037 15.82 0.00 0.00 3.18
89 90 8.087750 TGCAAATTAAAAGGATCCAACAAGTAG 58.912 33.333 15.82 0.00 0.00 2.57
90 91 7.870445 GTGCAAATTAAAAGGATCCAACAAGTA 59.130 33.333 15.82 0.00 0.00 2.24
91 92 6.705825 GTGCAAATTAAAAGGATCCAACAAGT 59.294 34.615 15.82 0.00 0.00 3.16
92 93 6.930722 AGTGCAAATTAAAAGGATCCAACAAG 59.069 34.615 15.82 0.00 0.00 3.16
93 94 6.825610 AGTGCAAATTAAAAGGATCCAACAA 58.174 32.000 15.82 2.48 0.00 2.83
94 95 6.418057 AGTGCAAATTAAAAGGATCCAACA 57.582 33.333 15.82 0.00 0.00 3.33
95 96 7.154656 AGAAGTGCAAATTAAAAGGATCCAAC 58.845 34.615 15.82 0.00 0.00 3.77
96 97 7.233348 AGAGAAGTGCAAATTAAAAGGATCCAA 59.767 33.333 15.82 0.00 0.00 3.53
97 98 6.721208 AGAGAAGTGCAAATTAAAAGGATCCA 59.279 34.615 15.82 0.00 0.00 3.41
98 99 7.163001 AGAGAAGTGCAAATTAAAAGGATCC 57.837 36.000 2.48 2.48 0.00 3.36
99 100 8.299570 TGAAGAGAAGTGCAAATTAAAAGGATC 58.700 33.333 0.00 0.00 0.00 3.36
100 101 8.181904 TGAAGAGAAGTGCAAATTAAAAGGAT 57.818 30.769 0.00 0.00 0.00 3.24
107 108 4.158394 GCCCATGAAGAGAAGTGCAAATTA 59.842 41.667 0.00 0.00 0.00 1.40
111 112 1.538047 GCCCATGAAGAGAAGTGCAA 58.462 50.000 0.00 0.00 0.00 4.08
113 114 0.391661 TCGCCCATGAAGAGAAGTGC 60.392 55.000 0.00 0.00 0.00 4.40
133 134 1.436600 CTACACCAGAGCAGCAGTTG 58.563 55.000 0.00 0.00 0.00 3.16
134 135 0.322975 CCTACACCAGAGCAGCAGTT 59.677 55.000 0.00 0.00 0.00 3.16
135 136 1.978473 CCTACACCAGAGCAGCAGT 59.022 57.895 0.00 0.00 0.00 4.40
139 140 2.586792 GGGCCTACACCAGAGCAG 59.413 66.667 0.84 0.00 0.00 4.24
160 161 1.739196 GTCGTCGTGTTAAGGCCCC 60.739 63.158 0.00 0.00 0.00 5.80
167 168 3.441496 AGTTGAAAGGTCGTCGTGTTA 57.559 42.857 0.00 0.00 0.00 2.41
177 178 9.185680 ACTTGTTGTAATAGAAAGTTGAAAGGT 57.814 29.630 0.00 0.00 0.00 3.50
190 191 4.618227 GCCTGGCCAAACTTGTTGTAATAG 60.618 45.833 7.01 0.00 0.00 1.73
211 212 2.812619 CCCCTCCCTCATCGAAGCC 61.813 68.421 0.00 0.00 0.00 4.35
237 238 1.738099 GAGCCGAATGTGTGTCGCT 60.738 57.895 0.00 0.00 37.18 4.93
238 239 2.027073 TGAGCCGAATGTGTGTCGC 61.027 57.895 0.00 0.00 37.18 5.19
260 261 2.759538 AGCGACGACTATAAGCACTC 57.240 50.000 0.00 0.00 0.00 3.51
280 281 1.855295 TCTATGCCCGTAGACAACCA 58.145 50.000 0.00 0.00 0.00 3.67
335 336 2.225727 CGATCTGTTCATCATGCCATGG 59.774 50.000 7.63 7.63 0.00 3.66
352 353 7.851822 TTATTTTGTGAGCAAACTTTCGATC 57.148 32.000 0.00 0.00 43.47 3.69
422 427 8.925700 CGTGCATTACATGTATGTATTCACTAT 58.074 33.333 6.36 0.00 42.32 2.12
423 428 7.923878 ACGTGCATTACATGTATGTATTCACTA 59.076 33.333 6.36 0.00 46.90 2.74
424 429 6.761242 ACGTGCATTACATGTATGTATTCACT 59.239 34.615 6.36 0.00 46.90 3.41
570 577 9.597170 TCAATTTTAGCATGCAATTATTTAGCA 57.403 25.926 21.98 0.00 43.14 3.49
581 588 9.970395 CCTATATTTCTTCAATTTTAGCATGCA 57.030 29.630 21.98 2.77 0.00 3.96
582 589 9.971922 ACCTATATTTCTTCAATTTTAGCATGC 57.028 29.630 10.51 10.51 0.00 4.06
617 624 7.624360 AAAAATCTCGGCATAAACTATGTCA 57.376 32.000 0.00 0.00 40.73 3.58
640 648 9.575868 AAAGATACCGAGAGAGACATATCTAAA 57.424 33.333 0.00 0.00 34.34 1.85
717 738 6.893020 AGGATCTTTCCCTTGTGTACTTAT 57.107 37.500 0.00 0.00 43.76 1.73
721 742 6.650120 TGATTAGGATCTTTCCCTTGTGTAC 58.350 40.000 0.00 0.00 43.76 2.90
724 745 5.749462 ACTGATTAGGATCTTTCCCTTGTG 58.251 41.667 0.00 0.00 43.76 3.33
725 746 6.394345 AACTGATTAGGATCTTTCCCTTGT 57.606 37.500 0.00 0.00 43.76 3.16
766 787 3.634448 TGTGTGTTGTTTCGATTGGGATT 59.366 39.130 0.00 0.00 0.00 3.01
771 792 4.035017 GGAAGTGTGTGTTGTTTCGATTG 58.965 43.478 0.00 0.00 0.00 2.67
906 933 3.431725 GAGAAGCGGGGGCAAACG 61.432 66.667 0.00 0.00 0.00 3.60
907 934 3.062466 GGAGAAGCGGGGGCAAAC 61.062 66.667 0.00 0.00 0.00 2.93
908 935 3.140073 TTGGAGAAGCGGGGGCAAA 62.140 57.895 0.00 0.00 0.00 3.68
1181 1382 7.532571 TGATGAAATTGATGTAGCAACTTGAG 58.467 34.615 0.00 0.00 0.00 3.02
1182 1383 7.451501 TGATGAAATTGATGTAGCAACTTGA 57.548 32.000 0.00 0.00 0.00 3.02
1184 1385 6.327934 GCTGATGAAATTGATGTAGCAACTT 58.672 36.000 0.00 0.00 0.00 2.66
1187 1388 4.731483 GCGCTGATGAAATTGATGTAGCAA 60.731 41.667 0.00 0.00 0.00 3.91
1188 1389 3.242837 GCGCTGATGAAATTGATGTAGCA 60.243 43.478 0.00 0.00 0.00 3.49
1189 1390 3.003068 AGCGCTGATGAAATTGATGTAGC 59.997 43.478 10.39 0.00 0.00 3.58
1190 1391 4.808077 AGCGCTGATGAAATTGATGTAG 57.192 40.909 10.39 0.00 0.00 2.74
1192 1393 4.445452 AAAGCGCTGATGAAATTGATGT 57.555 36.364 12.58 0.00 0.00 3.06
1193 1394 4.266976 GGAAAAGCGCTGATGAAATTGATG 59.733 41.667 12.58 0.00 0.00 3.07
1194 1395 4.427312 GGAAAAGCGCTGATGAAATTGAT 58.573 39.130 12.58 0.00 0.00 2.57
1195 1396 3.367292 GGGAAAAGCGCTGATGAAATTGA 60.367 43.478 12.58 0.00 0.00 2.57
1196 1397 2.925563 GGGAAAAGCGCTGATGAAATTG 59.074 45.455 12.58 0.00 0.00 2.32
1197 1398 2.094026 GGGGAAAAGCGCTGATGAAATT 60.094 45.455 12.58 0.00 0.00 1.82
1198 1399 1.478105 GGGGAAAAGCGCTGATGAAAT 59.522 47.619 12.58 0.00 0.00 2.17
1267 1469 3.424433 GCGGAATTCGAAATTTGAGACGT 60.424 43.478 0.00 0.00 42.43 4.34
1382 1585 0.614134 ACCAGTAGTCCCCGGTCTTC 60.614 60.000 0.00 0.00 0.00 2.87
1394 1597 0.968901 TGGCCTCGTGGTACCAGTAG 60.969 60.000 16.93 15.21 35.27 2.57
1496 1699 1.708551 CCCTTCTTCCCCTTGTTACCA 59.291 52.381 0.00 0.00 0.00 3.25
1499 1702 1.354368 CTGCCCTTCTTCCCCTTGTTA 59.646 52.381 0.00 0.00 0.00 2.41
1691 1957 1.200716 ACCAGCAAGCATTTCATCACG 59.799 47.619 0.00 0.00 0.00 4.35
1739 2005 3.064207 CGCCGCACCAAGTTATATATGT 58.936 45.455 0.00 0.00 0.00 2.29
1741 2007 3.064207 CACGCCGCACCAAGTTATATAT 58.936 45.455 0.00 0.00 0.00 0.86
1742 2008 2.475818 CACGCCGCACCAAGTTATATA 58.524 47.619 0.00 0.00 0.00 0.86
1988 2254 3.265737 TGGAGAGTAATGGGCTAGCAAAA 59.734 43.478 18.24 0.87 0.00 2.44
2067 2333 9.547753 TTGCTATGGTCTAAATGAGAGAATTAC 57.452 33.333 0.00 0.00 33.72 1.89
2213 2502 4.681025 ACTAATTTGCGCACACAAATCTTG 59.319 37.500 11.12 3.96 46.80 3.02
2227 2532 7.975616 TGCAAGAGAATGGAAATACTAATTTGC 59.024 33.333 0.00 0.00 42.13 3.68
2236 2541 6.003326 TGTGAACTGCAAGAGAATGGAAATA 58.997 36.000 0.00 0.00 37.43 1.40
2270 2575 6.522946 AGAAGGACTTATATTTAGGAACGGC 58.477 40.000 0.00 0.00 0.00 5.68
2290 2595 9.126151 TGTAGTCTGTATTGGAATCTCTAGAAG 57.874 37.037 0.00 0.00 0.00 2.85
2358 2663 9.989869 CAATACAGACTACATACGGATGTATAG 57.010 37.037 20.64 14.36 45.42 1.31
2359 2664 9.729281 TCAATACAGACTACATACGGATGTATA 57.271 33.333 20.64 10.32 45.42 1.47
2360 2665 8.631480 TCAATACAGACTACATACGGATGTAT 57.369 34.615 20.64 11.04 45.42 2.29
2514 2819 8.822652 AAAAAGAAATCAGTAGGAATTTGCAG 57.177 30.769 0.00 0.00 0.00 4.41
2667 2972 7.944729 ATAAATACCTGCTCAAGACAACAAT 57.055 32.000 0.00 0.00 0.00 2.71
3070 3376 8.043113 GGCCAAATAAGGAATTCTCTCAAAATT 58.957 33.333 5.23 0.00 0.00 1.82
3071 3377 7.365028 GGGCCAAATAAGGAATTCTCTCAAAAT 60.365 37.037 4.39 0.00 0.00 1.82
3072 3378 6.070824 GGGCCAAATAAGGAATTCTCTCAAAA 60.071 38.462 4.39 0.00 0.00 2.44
3073 3379 5.422012 GGGCCAAATAAGGAATTCTCTCAAA 59.578 40.000 4.39 0.00 0.00 2.69
3074 3380 4.956075 GGGCCAAATAAGGAATTCTCTCAA 59.044 41.667 4.39 0.00 0.00 3.02
3075 3381 4.230502 AGGGCCAAATAAGGAATTCTCTCA 59.769 41.667 6.18 0.00 0.00 3.27
3094 3400 4.253685 GGGAGCAAAATTTAAGAAAGGGC 58.746 43.478 0.00 0.00 0.00 5.19
3095 3401 4.532126 AGGGGAGCAAAATTTAAGAAAGGG 59.468 41.667 0.00 0.00 0.00 3.95
3114 3420 3.653164 ACTTTATTGGGCCAAATAGGGG 58.347 45.455 24.97 13.39 38.09 4.79
3130 3436 9.457436 GTGTCAAATAGGGAGGAATAAACTTTA 57.543 33.333 0.00 0.00 0.00 1.85
3134 3440 6.184789 TGGTGTCAAATAGGGAGGAATAAAC 58.815 40.000 0.00 0.00 0.00 2.01
3176 3482 6.929049 CCAAAGTAGTCAGAAGTGTCACATAA 59.071 38.462 5.62 0.00 0.00 1.90
3210 3516 5.586643 GGGTAGAATGGTCTTTTCATGTCTC 59.413 44.000 0.00 0.00 35.12 3.36
3273 3579 4.949856 ACCAATAAATCGGCTCAGTGAAAT 59.050 37.500 0.00 0.00 0.00 2.17
3640 4001 2.061773 CTCGCGTGAAGATGACAAGTT 58.938 47.619 5.77 0.00 0.00 2.66
3717 4078 4.439057 CGTGGAGCTATAACAGGCTTTAA 58.561 43.478 0.00 0.00 39.05 1.52
3718 4079 3.181469 CCGTGGAGCTATAACAGGCTTTA 60.181 47.826 0.00 0.00 39.05 1.85
3722 4083 0.880718 GCCGTGGAGCTATAACAGGC 60.881 60.000 10.60 10.60 36.32 4.85
3761 4122 0.677731 CATTTCTTCAGCCTGGCGGA 60.678 55.000 17.72 17.72 0.00 5.54
3977 4338 5.745227 TGACTGCCTAAAATTAAGGAGAGG 58.255 41.667 10.30 0.00 36.08 3.69
4393 4869 8.855110 TCTAGTTCATTTTTCTTGCCAATGTTA 58.145 29.630 0.00 0.00 31.08 2.41
4615 5091 5.407407 TCCAGTTGGAAGAGATAGACAAC 57.593 43.478 0.00 0.00 42.18 3.32
4675 5153 1.133025 CACCGAAAATGGAGACCATGC 59.867 52.381 3.97 0.00 44.40 4.06
5007 5485 9.929180 GATAACCAGTTATCATGCACTAATCTA 57.071 33.333 20.54 0.00 46.51 1.98
5255 5734 3.213506 CTGGTTGGTGTCTGTCAATGAA 58.786 45.455 0.00 0.00 0.00 2.57
5341 5820 4.082245 GGTATTGTCAACAGAACCATTGGG 60.082 45.833 7.78 0.00 41.29 4.12
5383 5862 0.600782 CGGCCCATATTTGCAATGCC 60.601 55.000 1.53 5.34 0.00 4.40
5409 5888 2.590821 ACAGCAGCAACTTGATTTCCT 58.409 42.857 0.00 0.00 0.00 3.36
5617 6096 1.301716 GTGAGCTCCGACTGGCAAA 60.302 57.895 12.15 0.00 34.14 3.68
5703 6182 0.036294 GTACCCCCTGCTCTGTTGAC 60.036 60.000 0.00 0.00 0.00 3.18
5815 6294 7.675619 ACCAGAAGGGATCAAATCAGTATTTTT 59.324 33.333 0.00 0.00 41.15 1.94
6102 6581 6.620678 ACCAAATTGTTCGACATATGAAAGG 58.379 36.000 10.38 0.00 0.00 3.11
6320 6799 5.394663 GCACTCAGGAGCTTATCTTCTAACA 60.395 44.000 0.00 0.00 0.00 2.41
6386 6865 0.679505 TCCACACCCTTCTCTCAACG 59.320 55.000 0.00 0.00 0.00 4.10
6509 6988 3.964031 AGGTGGCAAAACATCCAGTAAAA 59.036 39.130 0.00 0.00 32.15 1.52
6580 7060 1.467713 GCGGTCTTCTTAGTCACCTCG 60.468 57.143 0.00 0.00 0.00 4.63
6596 7076 3.271055 ACCAAATAATTACTCCGCGGT 57.729 42.857 27.15 9.68 0.00 5.68
6600 7080 5.293569 AGAAGCGAACCAAATAATTACTCCG 59.706 40.000 0.00 0.00 0.00 4.63
6633 7113 4.866508 ACTCGACATAAGGTTCAGACAA 57.133 40.909 0.00 0.00 0.00 3.18
6733 7215 1.489649 CCTGCCAGAGACATCCTGAAT 59.510 52.381 0.00 0.00 33.65 2.57
6858 7340 2.481969 GGACATAGCGCACTCTGATGAA 60.482 50.000 11.47 0.00 0.00 2.57
6861 7343 1.114627 TGGACATAGCGCACTCTGAT 58.885 50.000 11.47 0.00 0.00 2.90
6862 7344 0.894835 TTGGACATAGCGCACTCTGA 59.105 50.000 11.47 0.00 0.00 3.27
6863 7345 1.002366 GTTGGACATAGCGCACTCTG 58.998 55.000 11.47 3.36 0.00 3.35
6864 7346 0.108138 GGTTGGACATAGCGCACTCT 60.108 55.000 11.47 0.00 0.00 3.24
6865 7347 0.108138 AGGTTGGACATAGCGCACTC 60.108 55.000 11.47 0.00 0.00 3.51
6890 7372 4.228824 AGGAACAGAGGGTGTACTTTGTA 58.771 43.478 0.00 0.00 39.03 2.41
6892 7374 3.771577 AGGAACAGAGGGTGTACTTTG 57.228 47.619 0.00 0.00 39.03 2.77
6893 7375 4.657039 TGTTAGGAACAGAGGGTGTACTTT 59.343 41.667 0.00 0.00 39.03 2.66
6894 7376 4.228824 TGTTAGGAACAGAGGGTGTACTT 58.771 43.478 0.00 0.00 39.03 2.24
6895 7377 3.853207 TGTTAGGAACAGAGGGTGTACT 58.147 45.455 0.00 0.00 39.03 2.73
6919 7401 4.779993 AATTTGGATCAGAGGGAGTACC 57.220 45.455 0.00 0.00 40.67 3.34
6924 7406 6.779049 CCATCAATTAATTTGGATCAGAGGGA 59.221 38.462 11.95 0.00 35.92 4.20
7017 7523 8.033038 TCGTTACTGCTGATTACTGAAAAGTAT 58.967 33.333 0.00 0.00 0.00 2.12
7023 7529 5.534407 TGTTCGTTACTGCTGATTACTGAA 58.466 37.500 0.00 0.00 0.00 3.02
7094 7600 1.229428 ATCGCGGCAATTCATACCTG 58.771 50.000 6.13 0.00 0.00 4.00
7110 7616 1.268032 GCGGAGGCATTGTGTTTATCG 60.268 52.381 0.00 0.00 39.62 2.92
7149 7655 3.264706 GCTTCCTACCTTTTCTCCTTCCT 59.735 47.826 0.00 0.00 0.00 3.36
7150 7656 3.611970 GCTTCCTACCTTTTCTCCTTCC 58.388 50.000 0.00 0.00 0.00 3.46
7151 7657 3.056035 TCGCTTCCTACCTTTTCTCCTTC 60.056 47.826 0.00 0.00 0.00 3.46
7152 7658 2.904434 TCGCTTCCTACCTTTTCTCCTT 59.096 45.455 0.00 0.00 0.00 3.36
7153 7659 2.537143 TCGCTTCCTACCTTTTCTCCT 58.463 47.619 0.00 0.00 0.00 3.69
7154 7660 3.118738 TCATCGCTTCCTACCTTTTCTCC 60.119 47.826 0.00 0.00 0.00 3.71
7155 7661 4.124851 TCATCGCTTCCTACCTTTTCTC 57.875 45.455 0.00 0.00 0.00 2.87
7156 7662 4.223032 TCTTCATCGCTTCCTACCTTTTCT 59.777 41.667 0.00 0.00 0.00 2.52
7157 7663 4.504858 TCTTCATCGCTTCCTACCTTTTC 58.495 43.478 0.00 0.00 0.00 2.29
7158 7664 4.553330 TCTTCATCGCTTCCTACCTTTT 57.447 40.909 0.00 0.00 0.00 2.27
7159 7665 4.254492 GTTCTTCATCGCTTCCTACCTTT 58.746 43.478 0.00 0.00 0.00 3.11
7160 7666 3.260884 TGTTCTTCATCGCTTCCTACCTT 59.739 43.478 0.00 0.00 0.00 3.50
7161 7667 2.832129 TGTTCTTCATCGCTTCCTACCT 59.168 45.455 0.00 0.00 0.00 3.08
7162 7668 3.247006 TGTTCTTCATCGCTTCCTACC 57.753 47.619 0.00 0.00 0.00 3.18
7163 7669 6.903883 TTTATGTTCTTCATCGCTTCCTAC 57.096 37.500 0.00 0.00 37.91 3.18
7164 7670 7.768582 TGATTTTATGTTCTTCATCGCTTCCTA 59.231 33.333 0.00 0.00 37.91 2.94
7165 7671 6.599244 TGATTTTATGTTCTTCATCGCTTCCT 59.401 34.615 0.00 0.00 37.91 3.36
7166 7672 6.785191 TGATTTTATGTTCTTCATCGCTTCC 58.215 36.000 0.00 0.00 37.91 3.46
7167 7673 8.847444 ATTGATTTTATGTTCTTCATCGCTTC 57.153 30.769 0.00 0.00 37.91 3.86
7168 7674 7.641411 CGATTGATTTTATGTTCTTCATCGCTT 59.359 33.333 0.00 0.00 37.91 4.68
7169 7675 7.011389 TCGATTGATTTTATGTTCTTCATCGCT 59.989 33.333 0.00 0.00 37.91 4.93
7170 7676 7.125755 TCGATTGATTTTATGTTCTTCATCGC 58.874 34.615 0.00 0.00 37.91 4.58
7171 7677 8.937932 GTTCGATTGATTTTATGTTCTTCATCG 58.062 33.333 0.00 0.00 37.91 3.84
7174 7680 8.998377 TCAGTTCGATTGATTTTATGTTCTTCA 58.002 29.630 0.00 0.00 0.00 3.02
7214 7720 4.140782 TGGGGTAGAGGCAAGTCATAGATA 60.141 45.833 0.00 0.00 0.00 1.98
7241 7747 6.079424 AGAGTACAAGTGTGAGAGAAAGAC 57.921 41.667 0.00 0.00 0.00 3.01
7293 7799 7.432869 TCCTGAACTTTTCAATGTTGTATTGG 58.567 34.615 0.00 0.00 39.58 3.16
7327 7833 6.458342 GGTGAAGGCTAAAATATTTCTCGGTG 60.458 42.308 0.10 0.00 0.00 4.94
7330 7836 6.487103 GTGGTGAAGGCTAAAATATTTCTCG 58.513 40.000 0.10 0.00 0.00 4.04
7331 7837 6.093633 ACGTGGTGAAGGCTAAAATATTTCTC 59.906 38.462 0.10 0.00 0.00 2.87
7349 7855 1.354040 GCTTCTGAGATCACGTGGTG 58.646 55.000 17.00 0.00 34.45 4.17
7351 7857 0.803768 CCGCTTCTGAGATCACGTGG 60.804 60.000 17.00 0.00 0.00 4.94
7352 7858 0.109086 ACCGCTTCTGAGATCACGTG 60.109 55.000 9.94 9.94 0.00 4.49
7353 7859 0.109086 CACCGCTTCTGAGATCACGT 60.109 55.000 0.00 0.00 0.00 4.49
7354 7860 0.171231 TCACCGCTTCTGAGATCACG 59.829 55.000 0.00 0.00 0.00 4.35
7355 7861 2.370281 TTCACCGCTTCTGAGATCAC 57.630 50.000 0.00 0.00 0.00 3.06
7357 7863 2.031437 GCATTTCACCGCTTCTGAGATC 59.969 50.000 0.00 0.00 0.00 2.75
7358 7864 2.012673 GCATTTCACCGCTTCTGAGAT 58.987 47.619 0.00 0.00 0.00 2.75
7359 7865 1.270785 TGCATTTCACCGCTTCTGAGA 60.271 47.619 0.00 0.00 0.00 3.27
7361 7867 1.603456 TTGCATTTCACCGCTTCTGA 58.397 45.000 0.00 0.00 0.00 3.27
7362 7868 2.256174 CATTGCATTTCACCGCTTCTG 58.744 47.619 0.00 0.00 0.00 3.02
7363 7869 1.403249 GCATTGCATTTCACCGCTTCT 60.403 47.619 3.15 0.00 0.00 2.85
7377 7888 2.738314 GTGGTGGAAAAATCAGCATTGC 59.262 45.455 0.00 0.00 43.18 3.56
7398 7909 0.391263 GGGGTGGTGAGTCGCTTAAG 60.391 60.000 3.25 0.00 0.00 1.85
7408 7919 2.184194 TAATCTCCCCGGGGTGGTGA 62.184 60.000 38.73 28.97 35.15 4.02
7409 7920 1.276140 TTAATCTCCCCGGGGTGGTG 61.276 60.000 38.73 25.17 35.15 4.17
7413 7924 1.730851 GAGATTAATCTCCCCGGGGT 58.269 55.000 38.73 22.63 45.88 4.95
7438 7950 3.391965 GGTCATGTTGCAATTCAAAGCA 58.608 40.909 0.59 0.00 39.32 3.91
7439 7951 2.738314 GGGTCATGTTGCAATTCAAAGC 59.262 45.455 0.59 0.00 36.26 3.51
7443 7955 2.964464 ACTTGGGTCATGTTGCAATTCA 59.036 40.909 0.59 0.00 0.00 2.57
7460 7972 6.401903 GCACTCATAGTTGTGATTCAGACTTG 60.402 42.308 7.66 6.83 36.38 3.16
7461 7973 5.641209 GCACTCATAGTTGTGATTCAGACTT 59.359 40.000 7.66 0.00 36.38 3.01
7462 7974 5.046735 AGCACTCATAGTTGTGATTCAGACT 60.047 40.000 7.53 7.53 36.38 3.24
7463 7975 5.063186 CAGCACTCATAGTTGTGATTCAGAC 59.937 44.000 0.00 0.00 36.38 3.51
7464 7976 5.047092 TCAGCACTCATAGTTGTGATTCAGA 60.047 40.000 0.00 0.00 36.38 3.27
7471 7983 2.353889 GGCATCAGCACTCATAGTTGTG 59.646 50.000 0.00 0.00 44.61 3.33


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

AutoCloner maintained by Alex Coulton.